Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000515.1 Hibiscus syriacus cultivar Beakdansim tig00000982_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: 59636
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.34
Found at i:9322 original size:21 final size:20
Alignment explanation
Indices: 9297--9335 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
9287 CATCAAGGTC
*
9297 TTTGTTGAAGCCATGAAATCT
1 TTTGTCGAAGCCAT-AAATCT
*
9318 TTTGTCGAGGCCATAAAT
1 TTTGTCGAAGCCATAAAT
9336 TCCTGCAATG
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 4 0.25
21 12 0.75
ACGTcount: A:0.28, C:0.15, G:0.21, T:0.36
Consensus pattern (20 bp):
TTTGTCGAAGCCATAAATCT
Found at i:23585 original size:54 final size:51
Alignment explanation
Indices: 23433--23637 Score: 213
Period size: 54 Copynumber: 3.9 Consensus size: 51
23423 ATTAAGAAAT
* * *
23433 CTTG-GCAGAAGCCACAGAAAAGGATGAATGTGTTGTCAAACGCTTTATGAA
1 CTTGAGCAGAAGCCACAGAAAAGGATGAATGTGTTGTCAAATGTTTTA-CAA
* *
23484 CGTCTGAGCAAAAACCACA-AGAAAGGATGAATGTGTTGTCAAATGTTTTACAAA
1 C-T-TGAGCAGAAGCCACAGA-AAAGGATGAATGTGTTGTCAAATGTTTTAC-AA
* *
23538 CATATGAGCAGAAGCCACAGAAAAGGATGAATGTGTTGTCAAGTGTTTTACAT
1 C-T-TGAGCAGAAGCCACAGAAAAGGATGAATGTGTTGTCAAATGTTTTACAA
* *
23591 CTCGA-CAGATA-CCACATGAAAA-GATGAATGTATTGTCAAATGTTTTA
1 CTTGAGCAGA-AGCCACA-GAAAAGGATGAATGTGTTGTCAAATGTTTTA
23638 TGAACCAGTG
Statistics
Matches: 132, Mismatches: 14, Indels: 17
0.81 0.09 0.10
Matches are distributed among these distances:
50 32 0.24
51 9 0.07
52 2 0.02
53 5 0.04
54 83 0.63
55 1 0.01
ACGTcount: A:0.38, C:0.15, G:0.22, T:0.26
Consensus pattern (51 bp):
CTTGAGCAGAAGCCACAGAAAAGGATGAATGTGTTGTCAAATGTTTTACAA
Found at i:24036 original size:22 final size:22
Alignment explanation
Indices: 24007--24061 Score: 92
Period size: 22 Copynumber: 2.5 Consensus size: 22
23997 ATCTACACTC
*
24007 TTCAAAGATGATAGATTCTCTT
1 TTCAAAGATGACAGATTCTCTT
*
24029 TTTAAAGATGACAGATTCTCTT
1 TTCAAAGATGACAGATTCTCTT
24051 TTCAAAGATGA
1 TTCAAAGATGA
24062 AAACTTTATG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.35, C:0.13, G:0.15, T:0.38
Consensus pattern (22 bp):
TTCAAAGATGACAGATTCTCTT
Found at i:24658 original size:113 final size:113
Alignment explanation
Indices: 24460--25529 Score: 1987
Period size: 113 Copynumber: 9.5 Consensus size: 113
24450 TAGCAAAGAT
* * *
24460 TCAAATCCATCATATGATGGATCCGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGA
1 TCAAATCCATCATCTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACACATCTGA
24525 AGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGC
66 AGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGC
*
24573 TCAAATCCATCATCTGATGGATCAGCTTTTCCAGAAAAAGTTTATAATGAGAAGAACACATCTGA
1 TCAAATCCATCATCTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACACATCTGA
*
24638 AGAAGGAAGAATAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGC
66 AGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGC
*
24686 TCAAATCCATCATCTGATGGATCAGCTTTTCCAAAAAAAGTTCATAATGAGAAGAACACATCTGA
1 TCAAATCCATCATCTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACACATCTGA
24751 AGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGC
66 AGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGC
*
24799 TCAAATCCATCATCTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGA
1 TCAAATCCATCATCTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACACATCTGA
24864 AGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGC
66 AGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGC
24912 TCAAATCCATCATCTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACACATCTGA
1 TCAAATCCATCATCTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACACATCTGA
*
24977 AGAAGGAAGAAGAGATTCATAATGAGAAGAATTTGTTCAACCTTTTGC
66 AGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGC
* *
25025 TCAAATCCATCATCTGATGGATCAGCTCTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGA
1 TCAAATCCATCATCTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACACATCTGA
25090 AGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGC
66 AGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGC
25138 TCAAATCCATCATCTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACACATCTGA
1 TCAAATCCATCATCTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACACATCTGA
*
25203 AGAAGGAATAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGC
66 AGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGC
** *
25251 TCAAATCCATCATCTGATAAATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGA
1 TCAAATCCATCATCTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACACATCTGA
25316 AGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGC
66 AGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGC
25364 TCAAATCCATCATCTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACACATCTGA
1 TCAAATCCATCATCTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACACATCTGA
25429 AGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGC
66 AGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGC
** *
25477 TCAAATCCATCATCTGATAAATCAGCTTTTCCAGAGAAAGTTCATAATGAGAA
1 TCAAATCCATCATCTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAA
25530 TAATTTATTC
Statistics
Matches: 929, Mismatches: 28, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
113 929 1.00
ACGTcount: A:0.40, C:0.16, G:0.17, T:0.27
Consensus pattern (113 bp):
TCAAATCCATCATCTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACACATCTGA
AGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGC
Found at i:25550 original size:186 final size:185
Alignment explanation
Indices: 25326--25661 Score: 566
Period size: 186 Copynumber: 1.8 Consensus size: 185
25316 AGAAGGAAGA
* *
25326 AGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGCTCAAATCCATCA-TCTGATGGATCAGC
1 AGAAATTCATAATGAGAAGAATTTATTCAACCTTTTGCTCAAATACATCACT-TGATGGATCAGC
25390 TTTTCCAGAAAAAGTTCATAATGAGAAGAACACATCTGAAGAAGGAAGAAGAAATTCATAATGAG
65 TTTTCCAGAAAAAGTTCATAATGAGAAGAACACATCTGAAGAAGGAAGAAGAAATTCATAATGAG
25455 AAGAATTTGTTCAACCTTTTGCTCAAATCCATCATCTGATAAATCAGCTTTTCCAG
130 AAGAATTTGTTCAACCTTTTGCTCAAATCCATCATCTGATAAATCAGCTTTTCCAG
* * *
25511 AGAAAGTTCATAATGAGAATAATTTATTCAATCTTTTGCTCAAATACATCACTTGATGGATCCGC
1 AGAAA-TTCATAATGAGAAGAATTTATTCAACCTTTTGCTCAAATACATCACTTGATGGATCAGC
* * *
25576 TTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAG
65 TTTTCCAGAAAAAGTTCATAATGAGAAGAACACATCTGAAGAAGGAAGAAGAAATTCATAATGAG
*
25641 AAGAATTTGTTCAACTTTTTG
130 AAGAATTTGTTCAACCTTTTG
25662 TTTGAATTCA
Statistics
Matches: 140, Mismatches: 9, Indels: 3
0.92 0.06 0.02
Matches are distributed among these distances:
185 5 0.04
186 134 0.96
187 1 0.01
ACGTcount: A:0.38, C:0.15, G:0.17, T:0.30
Consensus pattern (185 bp):
AGAAATTCATAATGAGAAGAATTTATTCAACCTTTTGCTCAAATACATCACTTGATGGATCAGCT
TTTCCAGAAAAAGTTCATAATGAGAAGAACACATCTGAAGAAGGAAGAAGAAATTCATAATGAGA
AGAATTTGTTCAACCTTTTGCTCAAATCCATCATCTGATAAATCAGCTTTTCCAG
Found at i:25578 original size:73 final size:73
Alignment explanation
Indices: 25439--25605 Score: 248
Period size: 73 Copynumber: 2.3 Consensus size: 73
25429 AGAAGGAAGA
* *
25439 AGAAA-TTCATAATGAGAAGAATTTGTTCAACCTTTTGCTCAAATCCATCATCTGATAAATCAGC
1 AGAAAGTTCATAATGAGAAGAATTTATTCAACCTTTTGCTCAAATACATCATCTGATAAATCAGC
25503 TTTTCCAG
66 TTTTCCAG
* * ** *
25511 AGAAAGTTCATAATGAGAATAATTTATTCAATCTTTTGCTCAAATACATCA-CTTGATGGATCCG
1 AGAAAGTTCATAATGAGAAGAATTTATTCAACCTTTTGCTCAAATACATCATC-TGATAAATCAG
25575 CTTTTCCAG
65 CTTTTCCAG
25584 AGAAAGTTCATAATGAGAAGAA
1 AGAAAGTTCATAATGAGAAGAA
25606 CTCATCTGAA
Statistics
Matches: 85, Mismatches: 8, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
72 6 0.07
73 79 0.93
ACGTcount: A:0.37, C:0.17, G:0.14, T:0.32
Consensus pattern (73 bp):
AGAAAGTTCATAATGAGAAGAATTTATTCAACCTTTTGCTCAAATACATCATCTGATAAATCAGC
TTTTCCAG
Found at i:25597 original size:299 final size:301
Alignment explanation
Indices: 25213--25834 Score: 957
Period size: 299 Copynumber: 2.1 Consensus size: 301
25203 AGAAGGAATA
* *
25213 AGAAA-TTCATAATGAGAAGAATTTGTTCAACCTTTTGCTCAAATCCATCATCTGATAAATCAGC
1 AGAAAGTTCATAATGAGAAGAATTTATTCAACCTTTTGCTCAAATACATCATCTGATAAATCAGC
25277 TTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAG
66 TTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAG
* * *
25342 AAGAATTTGTTCAACCTTTTGCTCAAATCCATCATCTGATGGATCAGCTTTTCCAGAAAAAGTTC
131 AAGAATTTGTTCAACCTTTTGCTCAAATCCATCATCTGATGGATCAACATTCCCAGAAAAAGTTC
*
25407 ATAATGAGAAGAA-C-ACATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAAC
196 ACAATGAGAAGAACCGACATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAAC
*
25470 CTTTTGCTCAAATCCATCA-TCTGATAAATCAGCTTTTCCAG
261 CTTTTGATCAAATCCATCACT-TGATAAATCAGCTTTTCCAG
* * ** *
25511 AGAAAGTTCATAATGAGAATAATTTATTCAATCTTTTGCTCAAATACATCA-CTTGATGGATCCG
1 AGAAAGTTCATAATGAGAAGAATTTATTCAACCTTTTGCTCAAATACATCATC-TGATAAATCAG
* *
25575 CTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGA
65 CTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGA
* * ** * * ** *
25640 GAAGAATTTGTTCAACTTTTTGTTTGAATTCATCATTTGATGGATCAACATTCCCAGGTAGAGTT
130 GAAGAATTTGTTCAACCTTTTGCTCAAATCCATCATCTGATGGATCAACATTCCCAGAAAAAGTT
* *
25705 CACAATGAGAAGAACTCGTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCA
195 CACAATGAGAAGAAC-CGACATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCA
25770 ACCTTTTGATCAAATCCATCACTTGATAAATCAGCTTTTCCAG
259 ACCTTTTGATCAAATCCATCACTTGATAAATCAGCTTTTCCAG
25813 AGAAAGTTCATAATGAGAAGAA
1 AGAAAGTTCATAATGAGAAGAA
25835 CTCATCTGAA
Statistics
Matches: 292, Mismatches: 26, Indels: 8
0.90 0.08 0.02
Matches are distributed among these distances:
298 6 0.02
299 178 0.61
301 1 0.00
302 106 0.36
303 1 0.00
ACGTcount: A:0.38, C:0.16, G:0.17, T:0.29
Consensus pattern (301 bp):
AGAAAGTTCATAATGAGAAGAATTTATTCAACCTTTTGCTCAAATACATCATCTGATAAATCAGC
TTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAG
AAGAATTTGTTCAACCTTTTGCTCAAATCCATCATCTGATGGATCAACATTCCCAGAAAAAGTTC
ACAATGAGAAGAACCGACATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAAC
CTTTTGATCAAATCCATCACTTGATAAATCAGCTTTTCCAG
Found at i:25714 original size:186 final size:186
Alignment explanation
Indices: 25326--25718 Score: 558
Period size: 186 Copynumber: 2.1 Consensus size: 186
25316 AGAAGGAAGA
* *
25326 AGAAA-TTCATAATGAGAAGAATTTGTTCAACCTTTTGCTCAAATCCATCATCTGATGGATCAGC
1 AGAAAGTTCATAATGAGAAGAATTTATTCAACCTTTTGCTCAAATACATCATCTGATGGATCAGC
25390 TTTTCCAGAAAAAGTTCATAATGAGAAGAACACATCTGAAGAAGGAAGAAGAAATTCATAATGAG
66 TTTTCCAGAAAAAGTTCATAATGAGAAGAACACATCTGAAGAAGGAAGAAGAAATTCATAATGAG
* * *
25455 AAGAATTTGTTCAACCTTTTGCTCAAATCCATCATCTGATAAATCAGCTTTTCCAG
131 AAGAATTTGTTCAACCTTTTGCTCAAATCCATCATCTGATAAATCAACATTCCCAG
* * *
25511 AGAAAGTTCATAATGAGAATAATTTATTCAATCTTTTGCTCAAATACATCA-CTTGATGGATCCG
1 AGAAAGTTCATAATGAGAAGAATTTATTCAACCTTTTGCTCAAATACATCATC-TGATGGATCAG
* * *
25575 CTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGA
65 CTTTTCCAGAAAAAGTTCATAATGAGAAGAACACATCTGAAGAAGGAAGAAGAAATTCATAATGA
* * ** * * **
25640 GAAGAATTTGTTCAACTTTTTGTTTGAATTCATCATTTGATGGATCAACATTCCCAG
130 GAAGAATTTGTTCAACCTTTTGCTCAAATCCATCATCTGATAAATCAACATTCCCAG
* *
25697 -GTAGAGTTCACAATGAGAAGAA
1 AG-AAAGTTCATAATGAGAAGAA
25719 CTCGTCATCT
Statistics
Matches: 183, Mismatches: 22, Indels: 5
0.87 0.10 0.02
Matches are distributed among these distances:
185 7 0.04
186 176 0.96
ACGTcount: A:0.37, C:0.16, G:0.17, T:0.30
Consensus pattern (186 bp):
AGAAAGTTCATAATGAGAAGAATTTATTCAACCTTTTGCTCAAATACATCATCTGATGGATCAGC
TTTTCCAGAAAAAGTTCATAATGAGAAGAACACATCTGAAGAAGGAAGAAGAAATTCATAATGAG
AAGAATTTGTTCAACCTTTTGCTCAAATCCATCATCTGATAAATCAACATTCCCAG
Found at i:25769 original size:116 final size:113
Alignment explanation
Indices: 25514--25870 Score: 465
Period size: 116 Copynumber: 3.2 Consensus size: 113
25504 TTTCCAGAGA
* * * *
25514 AAGTTCATAATGAGAATAATTTATTCAA-TCTTTTGCTCAAATACATCACTTGATGGATCCGCTT
1 AAGTTCATAATGAGAAGAATTTGTTCAACT-TTTTGATCAAATACATCACTTGATGGATCAGCTT
25578 TTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAG
65 TTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAG
* ** * * * *
25627 AAGTTCATAATGAGAAGAATTTGTTCAACTTTTTGTTTGAATTCATCATTTGATGGATCAACATT
1 AAGTTCATAATGAGAAGAATTTGTTCAACTTTTTGATCAAATACATCACTTGATGGATCAGCTTT
* * *
25692 CCCAG-GTAGAGTTCACAATGAGAAGAACTCGTCATCTGAAGAAGGAAGAAG
66 TCCAGAG-AAAGTTCATAATGAGAAGAA--C-TCATCTGAAGAAGGAAGAAG
* * **
25743 AAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGATCAAATCCATCACTTGATAAATCAGCTTT
1 AAGTTCATAATGAGAAGAATTTGTTCAACTTTTTGATCAAATACATCACTTGATGGATCAGCTTT
25808 TCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAA-G-A-AA-
66 TCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAG
25852 AAGTTCATAATGAGAAGAA
1 AAGTTCATAATGAGAAGAA
25871 CTAATCTGAA
Statistics
Matches: 212, Mismatches: 26, Indels: 16
0.83 0.10 0.06
Matches are distributed among these distances:
109 19 0.09
110 2 0.01
111 1 0.00
112 2 0.01
113 87 0.41
114 2 0.01
115 1 0.00
116 97 0.46
117 1 0.00
ACGTcount: A:0.39, C:0.14, G:0.18, T:0.29
Consensus pattern (113 bp):
AAGTTCATAATGAGAAGAATTTGTTCAACTTTTTGATCAAATACATCACTTGATGGATCAGCTTT
TCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAG
Found at i:25858 original size:36 final size:36
Alignment explanation
Indices: 25815--25905 Score: 137
Period size: 36 Copynumber: 2.5 Consensus size: 36
25805 TTTTCCAGAG
* *
25815 AAAGTTCATAATGAGAAGAACTCATCTGAAGAAGAA
1 AAAGTTCATAATGAGAAGAACTAATCTGAAAAAGAA
25851 AAAGTTCATAATGAGAAGAACTAATCTGAAAAAGAA
1 AAAGTTCATAATGAGAAGAACTAATCTGAAAAAGAA
* * *
25887 GAAGTTCACAATGAAAAGA
1 AAAGTTCATAATGAGAAGA
25906 GCTTGTTCAA
Statistics
Matches: 50, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 50 1.00
ACGTcount: A:0.53, C:0.10, G:0.19, T:0.19
Consensus pattern (36 bp):
AAAGTTCATAATGAGAAGAACTAATCTGAAAAAGAA
Found at i:26164 original size:3 final size:3
Alignment explanation
Indices: 26156--26247 Score: 132
Period size: 3 Copynumber: 31.0 Consensus size: 3
26146 ATTAATTTAT
* * *
26156 TTA TTA TTA TTA TAA TTA TAA TTA TTA TTA TTA TTA TTA TAA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* *
26204 TAA ATA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
26248 AATATATATA
Statistics
Matches: 78, Mismatches: 10, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
2 2 0.03
3 76 0.97
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (3 bp):
TTA
Found at i:28304 original size:21 final size:21
Alignment explanation
Indices: 28280--28359 Score: 62
Period size: 21 Copynumber: 3.9 Consensus size: 21
28270 TTAAAATTTC
28280 ATATATTTA-AT-TTAATTTTTT
1 ATATATTTACATATT-A-TTTTT
*
28301 ATATATATACATATTATTTTT
1 ATATATTTACATATTATTTTT
* *
28322 ATAGTATTTATATA-TATTATT
1 ATA-TATTTACATATTATTTTT
*
28343 A-ATA-TTACATTTTATTT
1 ATATATTTACATATTATTT
28360 GCAAGTATTT
Statistics
Matches: 48, Mismatches: 7, Indels: 10
0.74 0.11 0.15
Matches are distributed among these distances:
18 5 0.10
19 6 0.12
20 1 0.02
21 23 0.48
22 11 0.23
23 2 0.04
ACGTcount: A:0.36, C:0.03, G:0.01, T:0.60
Consensus pattern (21 bp):
ATATATTTACATATTATTTTT
Found at i:28338 original size:24 final size:22
Alignment explanation
Indices: 28294--28342 Score: 62
Period size: 24 Copynumber: 2.1 Consensus size: 22
28284 ATTTAATTTA
28294 ATTTTTTATATATATACATATT
1 ATTTTTTATATATATACATATT
* *
28316 ATTTTTATAGTATTTATATATATT
1 ATTTTT-TA-TATATATACATATT
28340 ATT
1 ATT
28343 AATATTACAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
22 6 0.26
23 2 0.09
24 15 0.65
ACGTcount: A:0.35, C:0.02, G:0.02, T:0.61
Consensus pattern (22 bp):
ATTTTTTATATATATACATATT
Found at i:29998 original size:14 final size:14
Alignment explanation
Indices: 29966--30013 Score: 51
Period size: 14 Copynumber: 3.4 Consensus size: 14
29956 ATTTTAAAAA
* *
29966 ATTTACATATTTAA
1 ATTTGCATATTTAC
29980 ATTTGCATATTTAC
1 ATTTGCATATTTAC
* *
29994 ATTTGGCATCTTTGC
1 ATTT-GCATATTTAC
30009 ATTTG
1 ATTTG
30014 TATTTTTATG
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
14 17 0.59
15 12 0.41
ACGTcount: A:0.27, C:0.12, G:0.10, T:0.50
Consensus pattern (14 bp):
ATTTGCATATTTAC
Found at i:30011 original size:15 final size:15
Alignment explanation
Indices: 29971--30013 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
29961 AAAAAATTTA
*
29971 CATATTTAAATTT-G
1 CATATTTACATTTGG
29985 CATATTTACATTTGG
1 CATATTTACATTTGG
* *
30000 CATCTTTGCATTTG
1 CATATTTACATTTG
30014 TATTTTTATG
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
14 12 0.48
15 13 0.52
ACGTcount: A:0.26, C:0.14, G:0.12, T:0.49
Consensus pattern (15 bp):
CATATTTACATTTGG
Found at i:32848 original size:2 final size:2
Alignment explanation
Indices: 32841--32868 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
32831 TTATCCTTTA
32841 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
32869 CCTTTGTTGT
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:35731 original size:114 final size:114
Alignment explanation
Indices: 35447--35787 Score: 574
Period size: 114 Copynumber: 3.0 Consensus size: 114
35437 AAGTGCCATG
35447 TGCTCATAGTAGAAATAAGAAGACTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATC
1 TGCTCATAGTAGAAATAAGAAGACTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATC
* *
35512 TGGTTTGGTATAAACCCCAAAAACCAATCATTGGATTTTAAAGATGAATT
66 TGGTTTGGTATGAACCCC-AAAACCAATCATTGGATTTAAAAGATGAATT
35562 TGCTCATAGTAGAAATAAGAAGACTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATC
1 TGCTCATAGTAGAAATAAGAAGACTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATC
35627 TGGTTTGGTATGAACCCCAAAACCAATCATTGGATTTAAAAGATGAATT
66 TGGTTTGGTATGAACCCCAAAACCAATCATTGGATTTAAAAGATGAATT
* *
35676 TGCTCATAGTAGAAATAAGGAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATC
1 TGCTCATAGTAGAAATAAGAAGACTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATC
* * * * * * *
35741 TGATTCGGTAGGAACCCCAGAACCGATCATTGGAATTGAAAGATGAA
66 TGGTTTGGTATGAACCCCAAAACCAATCATTGGATTTAAAAGATGAA
35788 CTGCATGATC
Statistics
Matches: 215, Mismatches: 11, Indels: 1
0.95 0.05 0.00
Matches are distributed among these distances:
114 133 0.62
115 82 0.38
ACGTcount: A:0.33, C:0.16, G:0.20, T:0.31
Consensus pattern (114 bp):
TGCTCATAGTAGAAATAAGAAGACTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATC
TGGTTTGGTATGAACCCCAAAACCAATCATTGGATTTAAAAGATGAATT
Found at i:38058 original size:50 final size:53
Alignment explanation
Indices: 37878--38078 Score: 230
Period size: 54 Copynumber: 3.8 Consensus size: 53
37868 AGAAATCTTG
* * * ** *
37878 GCAGAAGCCACAGAAAAGGATGAATGTGTTGTCAAACGCTTTATGAACGTCTGA
1 GCAGAAACCACA-AAAAGGATGAATGTGTTGTCAAATGTTTTACAAACATCTGA
*
37932 GCAAAAACCACAAGAAAGGATGAATGTGTTGTCAAATGTTTTACAAACATCTGA
1 GCAGAAACCACAA-AAAGGATGAATGTGTTGTCAAATGTTTTACAAACATCTGA
* * *
37986 GCAGAAGCCACAGAAAAGGATGAATGTGTTGTCAAGTGTTTTAC-ATC-TC-GA
1 GCAGAAACCACA-AAAAGGATGAATGTGTTGTCAAATGTTTTACAAACATCTGA
* *
38037 -CAGAAACCACATAAAAAGATGAATGTATTGTCAAATGTTTTA
1 GCAGAAACCACA-AAAAGGATGAATGTGTTGTCAAATGTTTTA
38079 TGAACCAGTG
Statistics
Matches: 129, Mismatches: 16, Indels: 8
0.84 0.10 0.05
Matches are distributed among these distances:
50 37 0.29
51 2 0.02
52 2 0.02
53 3 0.02
54 84 0.65
55 1 0.01
ACGTcount: A:0.39, C:0.15, G:0.21, T:0.25
Consensus pattern (53 bp):
GCAGAAACCACAAAAAGGATGAATGTGTTGTCAAATGTTTTACAAACATCTGA
Found at i:38479 original size:22 final size:22
Alignment explanation
Indices: 38450--38504 Score: 92
Period size: 22 Copynumber: 2.5 Consensus size: 22
38440 ATCTACACTC
*
38450 TTCAAAGATGATAGATTCTCTT
1 TTCAAAGATGACAGATTCTCTT
*
38472 TTTAAAGATGACAGATTCTCTT
1 TTCAAAGATGACAGATTCTCTT
38494 TTCAAAGATGA
1 TTCAAAGATGA
38505 AAACTTTATG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.35, C:0.13, G:0.15, T:0.38
Consensus pattern (22 bp):
TTCAAAGATGACAGATTCTCTT
Found at i:39102 original size:113 final size:113
Alignment explanation
Indices: 38904--40425 Score: 2873
Period size: 113 Copynumber: 13.5 Consensus size: 113
38894 TAGCAAAGAT
* * *
38904 TCAAATCCATCATATGATGGATCCGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGA
1 TCAAATCCATCATCTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACACATCTGA
38969 AGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGC
66 AGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGC
39017 TCAAATCCATCATCTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACACATCTGA
1 TCAAATCCATCATCTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACACATCTGA
39082 AGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGC
66 AGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGC
39130 TCAAATCCATCATCTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACACATCTGA
1 TCAAATCCATCATCTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACACATCTGA
*
39195 AGAATGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGC
66 AGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGC
*
39243 TCAAATCCATCATCTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGA
1 TCAAATCCATCATCTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACACATCTGA
39308 AGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGC
66 AGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGC
39356 TCAAATCCATCATCTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACACATCTGA
1 TCAAATCCATCATCTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACACATCTGA
39421 AGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGC
66 AGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGC
* *
39469 TCAAATCCATCATCTGATGGATCAACTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGA
1 TCAAATCCATCATCTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACACATCTGA
39534 AGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGC
66 AGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGC
39582 TCAAATCCATCATCTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACACATCTGA
1 TCAAATCCATCATCTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACACATCTGA
*
39647 AGAAGGAAGAAGAAATTCCTAATGAGAAGAATTTGTTCAACCTTTTGC
66 AGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGC
*
39695 TCAAATCCATCATCTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGA
1 TCAAATCCATCATCTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACACATCTGA
39760 AGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGC
66 AGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGC
39808 TCAAATCCATCATCTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACACATCTGA
1 TCAAATCCATCATCTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACACATCTGA
*
39873 AGAAGGAAGAAGAAATTCCTAATGAGAAGAATTTGTTCAACCTTTTGC
66 AGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGC
*
39921 TCAAATCCATCATCTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGA
1 TCAAATCCATCATCTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACACATCTGA
39986 AGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGC
66 AGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGC
40034 TCAAATCCATCATCTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACACATCTGA
1 TCAAATCCATCATCTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACACATCTGA
*
40099 AGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCATTTGC
66 AGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGC
** *
40147 TCAAATCCATCATCTGATAAATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGA
1 TCAAATCCATCATCTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACACATCTGA
*
40212 AGACGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGC
66 AGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGC
40260 TCAAATCCATCATCTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACACATCTGA
1 TCAAATCCATCATCTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACACATCTGA
40325 AGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGC
66 AGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGC
** *
40373 TCAAATCCATCATCTGATAAATCAGCTTTTCCAGAGAAAGTTCATAATGAGAA
1 TCAAATCCATCATCTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAA
40426 TAATTTATTC
Statistics
Matches: 1377, Mismatches: 32, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
113 1377 1.00
ACGTcount: A:0.39, C:0.16, G:0.17, T:0.27
Consensus pattern (113 bp):
TCAAATCCATCATCTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACACATCTGA
AGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGC
Found at i:40446 original size:186 final size:185
Alignment explanation
Indices: 40222--40557 Score: 566
Period size: 186 Copynumber: 1.8 Consensus size: 185
40212 AGACGGAAGA
* *
40222 AGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGCTCAAATCCATCA-TCTGATGGATCAGC
1 AGAAATTCATAATGAGAAGAATTTATTCAACCTTTTGCTCAAATACATCACT-TGATGGATCAGC
40286 TTTTCCAGAAAAAGTTCATAATGAGAAGAACACATCTGAAGAAGGAAGAAGAAATTCATAATGAG
65 TTTTCCAGAAAAAGTTCATAATGAGAAGAACACATCTGAAGAAGGAAGAAGAAATTCATAATGAG
40351 AAGAATTTGTTCAACCTTTTGCTCAAATCCATCATCTGATAAATCAGCTTTTCCAG
130 AAGAATTTGTTCAACCTTTTGCTCAAATCCATCATCTGATAAATCAGCTTTTCCAG
* * *
40407 AGAAAGTTCATAATGAGAATAATTTATTCAATCTTTTGCTCAAATACATCACTTGATGGATCCGC
1 AGAAA-TTCATAATGAGAAGAATTTATTCAACCTTTTGCTCAAATACATCACTTGATGGATCAGC
* * *
40472 TTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAG
65 TTTTCCAGAAAAAGTTCATAATGAGAAGAACACATCTGAAGAAGGAAGAAGAAATTCATAATGAG
*
40537 AAGAATTTGTTCAACTTTTTG
130 AAGAATTTGTTCAACCTTTTG
40558 TTTGAATTCA
Statistics
Matches: 140, Mismatches: 9, Indels: 3
0.92 0.06 0.02
Matches are distributed among these distances:
185 5 0.04
186 134 0.96
187 1 0.01
ACGTcount: A:0.38, C:0.15, G:0.17, T:0.30
Consensus pattern (185 bp):
AGAAATTCATAATGAGAAGAATTTATTCAACCTTTTGCTCAAATACATCACTTGATGGATCAGCT
TTTCCAGAAAAAGTTCATAATGAGAAGAACACATCTGAAGAAGGAAGAAGAAATTCATAATGAGA
AGAATTTGTTCAACCTTTTGCTCAAATCCATCATCTGATAAATCAGCTTTTCCAG
Found at i:40474 original size:73 final size:73
Alignment explanation
Indices: 40335--40501 Score: 248
Period size: 73 Copynumber: 2.3 Consensus size: 73
40325 AGAAGGAAGA
* *
40335 AGAAA-TTCATAATGAGAAGAATTTGTTCAACCTTTTGCTCAAATCCATCATCTGATAAATCAGC
1 AGAAAGTTCATAATGAGAAGAATTTATTCAACCTTTTGCTCAAATACATCATCTGATAAATCAGC
40399 TTTTCCAG
66 TTTTCCAG
* * ** *
40407 AGAAAGTTCATAATGAGAATAATTTATTCAATCTTTTGCTCAAATACATCA-CTTGATGGATCCG
1 AGAAAGTTCATAATGAGAAGAATTTATTCAACCTTTTGCTCAAATACATCATC-TGATAAATCAG
40471 CTTTTCCAG
65 CTTTTCCAG
40480 AGAAAGTTCATAATGAGAAGAA
1 AGAAAGTTCATAATGAGAAGAA
40502 CTCATCTGAA
Statistics
Matches: 85, Mismatches: 8, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
72 6 0.07
73 79 0.93
ACGTcount: A:0.37, C:0.17, G:0.14, T:0.32
Consensus pattern (73 bp):
AGAAAGTTCATAATGAGAAGAATTTATTCAACCTTTTGCTCAAATACATCATCTGATAAATCAGC
TTTTCCAG
Found at i:40499 original size:299 final size:301
Alignment explanation
Indices: 40109--40730 Score: 932
Period size: 299 Copynumber: 2.1 Consensus size: 301
40099 AGAAGGAAGA
* *
40109 AGAAA-TTCATAATGAGAAGAATTTGTTCAACCATTTGCTCAAATCCATCATCTGATAAATCAGC
1 AGAAAGTTCATAATGAGAAGAATTTATTCAACCATTTGCTCAAATACATCATCTGATAAATCAGC
*
40173 TTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGAAGACGGAAGAAGAAATTCATAATGAG
66 TTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAG
* *
40238 AAGAATTTGTTCAACCTTTTGCTCAAATCCATCATCTGATGGATCAGCT-TTTCCAGAAAAAGTT
131 AAGAATTTGTTCAACCTTTTGCTCAAATCCATCATCTGATGGATCA-ATATTCCCAGAAAAAGTT
*
40302 CATAATGAGAAGAA-C-ACATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAA
195 CACAATGAGAAGAACCGACATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAA
40365 CCTTTTGCTCAAATCCATCA-TCTGATAAATCAGCTTTTCCAG
260 CCTTTTGCTCAAATCCATCACT-TGATAAATCAGCTTTTCCAG
* * * ** *
40407 AGAAAGTTCATAATGAGAATAATTTATTCAATCTTTTGCTCAAATACATCA-CTTGATGGATCCG
1 AGAAAGTTCATAATGAGAAGAATTTATTCAACCATTTGCTCAAATACATCATC-TGATAAATCAG
* *
40471 CTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGA
65 CTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGA
* * ** * * ** *
40536 GAAGAATTTGTTCAACTTTTTGTTTGAATTCATCATTTGATGGATCAATATTCCCAGGTAGAGTT
130 GAAGAATTTGTTCAACCTTTTGCTCAAATCCATCATCTGATGGATCAATATTCCCAGAAAAAGTT
* *
40601 CACAATGAGAAGAACTCGTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCA
195 CACAATGAGAAGAAC-CGACATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCA
*
40666 ACCTTTTGTTCAAATCCATCACTTGATAAATCAGCTTTTCCAG
259 ACCTTTTGCTCAAATCCATCACTTGATAAATCAGCTTTTCCAG
40709 AGAAAGTTCATAATGAGAAGAA
1 AGAAAGTTCATAATGAGAAGAA
40731 CTCATCTGAA
Statistics
Matches: 290, Mismatches: 27, Indels: 10
0.89 0.08 0.03
Matches are distributed among these distances:
298 7 0.02
299 175 0.60
301 1 0.00
302 106 0.37
303 1 0.00
ACGTcount: A:0.38, C:0.16, G:0.17, T:0.29
Consensus pattern (301 bp):
AGAAAGTTCATAATGAGAAGAATTTATTCAACCATTTGCTCAAATACATCATCTGATAAATCAGC
TTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAG
AAGAATTTGTTCAACCTTTTGCTCAAATCCATCATCTGATGGATCAATATTCCCAGAAAAAGTTC
ACAATGAGAAGAACCGACATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAAC
CTTTTGCTCAAATCCATCACTTGATAAATCAGCTTTTCCAG
Found at i:40610 original size:186 final size:186
Alignment explanation
Indices: 40222--40614 Score: 551
Period size: 186 Copynumber: 2.1 Consensus size: 186
40212 AGACGGAAGA
* *
40222 AGAAA-TTCATAATGAGAAGAATTTGTTCAACCTTTTGCTCAAATCCATCATCTGATGGATCAGC
1 AGAAAGTTCATAATGAGAAGAATTTATTCAACCTTTTGCTCAAATACATCATCTGATGGATCAGC
40286 TTTTCCAGAAAAAGTTCATAATGAGAAGAACACATCTGAAGAAGGAAGAAGAAATTCATAATGAG
66 TTTTCCAGAAAAAGTTCATAATGAGAAGAACACATCTGAAGAAGGAAGAAGAAATTCATAATGAG
* *
40351 AAGAATTTGTTCAACCTTTTGCTCAAATCCATCATCTGATAAATCAGCTTTTCCAG
131 AAGAATTTGTTCAACCTTTTGCTCAAATCCATCATCTGATAAATCAGATTTCCCAG
* * *
40407 AGAAAGTTCATAATGAGAATAATTTATTCAATCTTTTGCTCAAATACATCA-CTTGATGGATCCG
1 AGAAAGTTCATAATGAGAAGAATTTATTCAACCTTTTGCTCAAATACATCATC-TGATGGATCAG
* * *
40471 CTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGA
65 CTTTTCCAGAAAAAGTTCATAATGAGAAGAACACATCTGAAGAAGGAAGAAGAAATTCATAATGA
* * ** * * **
40536 GAAGAATTTGTTCAACTTTTTGTTTGAATTCATCATTTGATGGATCA-ATATTCCCAG
130 GAAGAATTTGTTCAACCTTTTGCTCAAATCCATCATCTGATAAATCAGAT-TTCCCAG
* *
40593 -GTAGAGTTCACAATGAGAAGAA
1 AG-AAAGTTCATAATGAGAAGAA
40615 CTCGTCATCT
Statistics
Matches: 183, Mismatches: 21, Indels: 7
0.87 0.10 0.03
Matches are distributed among these distances:
185 8 0.04
186 175 0.96
ACGTcount: A:0.37, C:0.15, G:0.17, T:0.30
Consensus pattern (186 bp):
AGAAAGTTCATAATGAGAAGAATTTATTCAACCTTTTGCTCAAATACATCATCTGATGGATCAGC
TTTTCCAGAAAAAGTTCATAATGAGAAGAACACATCTGAAGAAGGAAGAAGAAATTCATAATGAG
AAGAATTTGTTCAACCTTTTGCTCAAATCCATCATCTGATAAATCAGATTTCCCAG
Found at i:40665 original size:116 final size:112
Alignment explanation
Indices: 40410--40766 Score: 456
Period size: 116 Copynumber: 3.2 Consensus size: 112
40400 TTTCCAGAGA
* * * *
40410 AAGTTCATAATGAGAATAATTTATTCAA-TCTTTTGCTCAAATACATCACTTGATGGATCCGCTT
1 AAGTTCATAATGAGAAGAATTTGTTCAACT-TTTTGTTCAAATACATCACTTGATGGAT-CACTT
40474 TTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAG
64 TTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAG
** * * *
40523 AAGTTCATAATGAGAAGAATTTGTTCAACTTTTTGTTTGAATTCATCATTTGATGGATCAATATT
1 AAGTTCATAATGAGAAGAATTTGTTCAACTTTTTGTTCAAATACATCACTTGATGGATCACT-TT
* * *
40588 CCCAG-GTAGAGTTCACAATGAGAAGAACTCGTCATCTGAAGAAGGAAGAAG
65 TCCAGAG-AAAGTTCATAATGAGAAGAA--C-TCATCTGAAGAAGGAAGAAG
* * **
40639 AAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGTTCAAATCCATCACTTGATAAATCAGCTTT
1 AAGTTCATAATGAGAAGAATTTGTTCAACTTTTTGTTCAAATACATCACTTGATGGATCA-CTTT
40704 TCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAA-G-A-AA-
65 TCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAG
40748 AAGTTCATAATGAGAAGAA
1 AAGTTCATAATGAGAAGAA
40767 CTAATCTGAA
Statistics
Matches: 213, Mismatches: 23, Indels: 20
0.83 0.09 0.08
Matches are distributed among these distances:
109 19 0.09
110 2 0.01
111 1 0.00
112 4 0.02
113 85 0.40
114 2 0.01
115 1 0.00
116 97 0.46
117 2 0.01
ACGTcount: A:0.38, C:0.14, G:0.18, T:0.29
Consensus pattern (112 bp):
AAGTTCATAATGAGAAGAATTTGTTCAACTTTTTGTTCAAATACATCACTTGATGGATCACTTTT
CCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAG
Found at i:40754 original size:36 final size:36
Alignment explanation
Indices: 40711--40801 Score: 137
Period size: 36 Copynumber: 2.5 Consensus size: 36
40701 TTTTCCAGAG
* *
40711 AAAGTTCATAATGAGAAGAACTCATCTGAAGAAGAA
1 AAAGTTCATAATGAGAAGAACTAATCTGAAAAAGAA
40747 AAAGTTCATAATGAGAAGAACTAATCTGAAAAAGAA
1 AAAGTTCATAATGAGAAGAACTAATCTGAAAAAGAA
* * *
40783 GAAGTTCACAATGAAAAGA
1 AAAGTTCATAATGAGAAGA
40802 GCTTGTTCAG
Statistics
Matches: 50, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 50 1.00
ACGTcount: A:0.53, C:0.10, G:0.19, T:0.19
Consensus pattern (36 bp):
AAAGTTCATAATGAGAAGAACTAATCTGAAAAAGAA
Found at i:41059 original size:3 final size:3
Alignment explanation
Indices: 41051--41130 Score: 115
Period size: 3 Copynumber: 26.7 Consensus size: 3
41041 ATTAATTTAT
* *
41051 TTA TTA TTA TTA TAA TTA TTA TTA TTA TTA TTA TTA TTA TAA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* * *
41099 TAA ATG TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
41131 TATATTAAAT
Statistics
Matches: 67, Mismatches: 10, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
3 67 1.00
ACGTcount: A:0.36, C:0.00, G:0.01, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:44605 original size:19 final size:19
Alignment explanation
Indices: 44581--44644 Score: 119
Period size: 19 Copynumber: 3.4 Consensus size: 19
44571 AAAAATAGTT
44581 AATATCACAGTTTACTATA
1 AATATCACAGTTTACTATA
44600 AATATCACAGTTTACTATA
1 AATATCACAGTTTACTATA
44619 AATATCACAGTTTACTATA
1 AATATCACAGTTTACTATA
*
44638 AAAATCA
1 AATATCA
44645 AGAATATTTA
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
19 44 1.00
ACGTcount: A:0.45, C:0.16, G:0.05, T:0.34
Consensus pattern (19 bp):
AATATCACAGTTTACTATA
Found at i:48004 original size:21 final size:21
Alignment explanation
Indices: 47980--48023 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
47970 CATCACCAAT
*
47980 CATCGTGGACTGTCACATTAA
1 CATCGTGGACTGTCACATCAA
*
48001 CATCGTGGATTGTCACATCAA
1 CATCGTGGACTGTCACATCAA
48022 CA
1 CA
48024 GTATGAAGTA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.30, C:0.25, G:0.18, T:0.27
Consensus pattern (21 bp):
CATCGTGGACTGTCACATCAA
Found at i:49831 original size:15 final size:15
Alignment explanation
Indices: 49791--49833 Score: 61
Period size: 15 Copynumber: 2.9 Consensus size: 15
49781 CTATTTAATA
49791 AAAAATTAAAATTTT
1 AAAAATTAAAATTTT
*
49806 -AAATTTCAAAATTTT
1 AAAAATT-AAAATTTT
49821 AAAAATTAAAATT
1 AAAAATTAAAATT
49834 AAAATATACG
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
14 5 0.21
15 14 0.58
16 5 0.21
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (15 bp):
AAAAATTAAAATTTT
Found at i:52182 original size:2 final size:2
Alignment explanation
Indices: 52175--52202 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
52165 ATTTTTGAAC
52175 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
52203 ATTGGCCTTT
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):
TA
Done.