Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold215
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: 2124891
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
File 2 of 16
Found at i:210064 original size:13 final size:13
Alignment explanation
Indices: 210046--210071 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
210036 TACAGCAAGT
210046 ATGTATCGATACA
1 ATGTATCGATACA
210059 ATGTATCGATACA
1 ATGTATCGATACA
210072 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:212320 original size:21 final size:21
Alignment explanation
Indices: 212287--212331 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
212277 TTGCAAGTTG
*
212287 AAATAAAGAAGTTGGCTAATGA
1 AAATAAAGAAGTTAGCTAA-GA
*
212309 AAATAATG-AGTTAGCTAAGA
1 AAATAAAGAAGTTAGCTAAGA
212329 AAA
1 AAA
212332 ATGAAAACTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 9 0.43
22 7 0.33
ACGTcount: A:0.53, C:0.04, G:0.20, T:0.22
Consensus pattern (21 bp):
AAATAAAGAAGTTAGCTAAGA
Found at i:213243 original size:15 final size:15
Alignment explanation
Indices: 213223--213253 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
213213 ATTTTGTTTG
*
213223 GAGCTTCTTCATTTT
1 GAGCTTCCTCATTTT
213238 GAGCTTCCTCATTTT
1 GAGCTTCCTCATTTT
213253 G
1 G
213254 GACATTTTTA
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:0.13, C:0.23, G:0.16, T:0.48
Consensus pattern (15 bp):
GAGCTTCCTCATTTT
Found at i:215084 original size:21 final size:21
Alignment explanation
Indices: 215055--215099 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
215045 AAGTTTTTAT
*
215055 TTTTCTTAGCTAAC-TCATTA
1 TTTTCTTAGCCAACTTCATTA
*
215075 TTTTCATTAGCCAACTTCTTTA
1 TTTTC-TTAGCCAACTTCATTA
215097 TTT
1 TTT
215100 CAACTTACAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 8 0.38
22 8 0.38
ACGTcount: A:0.22, C:0.20, G:0.04, T:0.53
Consensus pattern (21 bp):
TTTTCTTAGCCAACTTCATTA
Found at i:217325 original size:20 final size:20
Alignment explanation
Indices: 217300--217351 Score: 88
Period size: 19 Copynumber: 2.6 Consensus size: 20
217290 TACAAGCCAA
*
217300 TGTATCGATACAATTTTTTG
1 TGTATCGATACAATATTTTG
217320 TGTATCGATAC-ATATTTTG
1 TGTATCGATACAATATTTTG
217339 TGTATCGATACAA
1 TGTATCGATACAA
217352 GTTTGGCTAC
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 18 0.60
20 12 0.40
ACGTcount: A:0.29, C:0.12, G:0.15, T:0.44
Consensus pattern (20 bp):
TGTATCGATACAATATTTTG
Found at i:218260 original size:21 final size:22
Alignment explanation
Indices: 218219--218273 Score: 69
Period size: 21 Copynumber: 2.5 Consensus size: 22
218209 TGTCATTTTA
*
218219 TTATTTTATGTTTATATTGTTAT
1 TTATTTTAT-TTCATATTGTTAT
218242 TTATTTTATTTCA-ATTGTTAT
1 TTATTTTATTTCATATTGTTAT
218263 TGTA-TTTATTT
1 T-TATTTTATTT
218274 TATGCTTACA
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
21 16 0.53
22 5 0.17
23 9 0.30
ACGTcount: A:0.22, C:0.02, G:0.07, T:0.69
Consensus pattern (22 bp):
TTATTTTATTTCATATTGTTAT
Found at i:218299 original size:49 final size:48
Alignment explanation
Indices: 218198--218301 Score: 111
Period size: 48 Copynumber: 2.1 Consensus size: 48
218188 TTTATTTTAC
* * * * * *
218198 TTTATTTCCATTGTCATTTTATTATTTTATGTTTATATTGTTATTTAT
1 TTTATTTCAATTGTCATTGTATTATTTTATGCTTACATTGATATTCAT
* *
218246 TTTATTTCAATTGTTATTGTATTTATTTTATGCTTACATT-ATGTTCAT
1 TTTATTTCAATTGTCATTGTA-TTATTTTATGCTTACATTGATATTCAT
218294 GTTTATTT
1 -TTTATTT
218302 TTTTCTTATT
Statistics
Matches: 46, Mismatches: 8, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
48 23 0.50
49 23 0.50
ACGTcount: A:0.21, C:0.07, G:0.08, T:0.64
Consensus pattern (48 bp):
TTTATTTCAATTGTCATTGTATTATTTTATGCTTACATTGATATTCAT
Found at i:220079 original size:51 final size:51
Alignment explanation
Indices: 219982--220119 Score: 179
Period size: 51 Copynumber: 2.7 Consensus size: 51
219972 TCCAGAAGGA
* *
219982 AAATATATCGATACATTTTTATTGTATCGATACATTCTGGGTTTTTGACCC
1 AAATATATCGATACATTTTCATTGTATCGATACATTCTAGGTTTTTGACCC
* * *
220033 AAATGTATCGATACATTATACATTGTATCGATACATTTTAGG-TTTTGACCC
1 AAATATATCGATACATT-TTCATTGTATCGATACATTCTAGGTTTTTGACCC
* * *
220084 AAATATTTTGATACATTCTTCAATGTATCGATACAT
1 AAATATATCGATACATT-TTCATTGTATCGATACAT
220120 GCAGACCATT
Statistics
Matches: 75, Mismatches: 11, Indels: 2
0.85 0.12 0.02
Matches are distributed among these distances:
51 55 0.73
52 20 0.27
ACGTcount: A:0.31, C:0.15, G:0.12, T:0.41
Consensus pattern (51 bp):
AAATATATCGATACATTTTCATTGTATCGATACATTCTAGGTTTTTGACCC
Found at i:222523 original size:78 final size:79
Alignment explanation
Indices: 222329--222721 Score: 330
Period size: 79 Copynumber: 5.0 Consensus size: 79
222319 AAATTTCTCC
* * * * * * *
222329 TTCCAAAAGCATTGAATTTTTCACCATTGGAGATACTCCAACCCCATCATTTTCGAA-GGGATAC
1 TTCCAAAA-TATTAAATTTTTCACC-TCGGGGATACTCCAACCCCACCA-TCTCTAAGGGGATAC
* * ** * *
222393 TCTAATCATATTTTTAC
63 TCCAACCCCATTTTAAT
* * * * * *
222410 TTCCAAAATATTAAATTTCTCATCTCAGGGATACTCCGACCCCACCATCACTGAGGGGATACTCC
1 TTCCAAAATATTAAATTTTTCACCTCGGGGATACTCCAACCCCACCATCTCTAAGGGGATACTCC
222475 AACCCCATTTT-AT
66 AACCCCATTTTAAT
* *** *
222488 TTCCAAAATATT-AATTTTTCACCATCGGGGATACTCCAACCTCGTTATTTCTAAGGGGATACTC
1 TTCCAAAATATTAAATTTTTCACC-TCGGGGATACTCCAACCCCACCATCTCTAAGGGGATACTC
*
222552 TAACCCCATTTTGAAT
65 CAACCCCATTTT-AAT
* * * * * *
222568 TT-CAAAATATTAAATTTTTCATCTTGAGGATGCTCCAACCCCACCATCTCTAAGGGGATATTCT
1 TTCCAAAATATTAAATTTTTCACCTCGGGGATACTCCAACCCCACCATCTCTAAGGGGATACTCC
*
222632 AACCCCATTTTCAT
66 AACCCCATTTTAAT
* * * * **
222646 TTACAAAATATT-GATTTTTCACCATCGGGGATACTCCAACCCCATCATTTCTGAA-GAAATACT
1 TTCCAAAATATTAAATTTTTCACC-TCGGGGATACTCCAACCCCACCATCTCT-AAGGGGATACT
*
222709 CCAACCCTATTTT
64 CCAACCCCATTTT
222722 TGATTATGAA
Statistics
Matches: 251, Mismatches: 53, Indels: 18
0.78 0.16 0.06
Matches are distributed among these distances:
77 9 0.04
78 71 0.28
79 135 0.54
80 28 0.11
81 8 0.03
ACGTcount: A:0.30, C:0.26, G:0.11, T:0.33
Consensus pattern (79 bp):
TTCCAAAATATTAAATTTTTCACCTCGGGGATACTCCAACCCCACCATCTCTAAGGGGATACTCC
AACCCCATTTTAAT
Found at i:222636 original size:157 final size:158
Alignment explanation
Indices: 222329--222695 Score: 470
Period size: 157 Copynumber: 2.3 Consensus size: 158
222319 AAATTTCTCC
* * *
222329 TTCCAAAAGCATTGAATTTTTCACCATTGGAGATACTCCAACCCCATCATTTTCGAAGGGATACT
1 TTCCAAAA-TATT-AATTTTTCACCATCGGGGATACTCCAACCCCATCATTTTCGAAGGGATACT
* * * * *
222394 CTAATCATATTTTTACTTCCAAAATATTAAATTTCTCATCTCAGGGATACTCCGACCCCACCATC
64 CTAACCACATTTTGAATTCCAAAATATTAAATTTCTCATCTCAGGGATACTCCAACCCCACCATC
*
222459 ACTGAGGGGATACTCCAACCCCATTTT-AT
129 ACTAAGGGGATACTCCAACCCCATTTTCAT
* * * *
222488 TTCCAAAATATTAATTTTTCACCATCGGGGATACTCCAACCTCGTTA-TTTCTAAGGGGATACTC
1 TTCCAAAATATTAATTTTTCACCATCGGGGATACTCCAACCCCATCATTTTCGAA-GGGATACTC
* * * * *
222552 TAACCCCATTTTGAATTTCAAAATATTAAATTTTTCATCT-TGAGGATGCTCCAACCCCACCATC
65 TAACCACATTTTGAATTCCAAAATATTAAATTTCTCATCTCAG-GGATACTCCAACCCCACCATC
* * *
222616 TCTAAGGGGATATTCTAACCCCATTTTCAT
129 ACTAAGGGGATACTCCAACCCCATTTTCAT
* *
222646 TTACAAAATATTGATTTTTCACCATCGGGGATACTCCAACCCCATCATTT
1 TTCCAAAATATTAATTTTTCACCATCGGGGATACTCCAACCCCATCATTT
222696 CTGAAGAAAT
Statistics
Matches: 178, Mismatches: 26, Indels: 8
0.84 0.12 0.04
Matches are distributed among these distances:
156 7 0.04
157 114 0.64
158 47 0.26
159 10 0.06
ACGTcount: A:0.30, C:0.26, G:0.11, T:0.33
Consensus pattern (158 bp):
TTCCAAAATATTAATTTTTCACCATCGGGGATACTCCAACCCCATCATTTTCGAAGGGATACTCT
AACCACATTTTGAATTCCAAAATATTAAATTTCTCATCTCAGGGATACTCCAACCCCACCATCAC
TAAGGGGATACTCCAACCCCATTTTCAT
Found at i:224600 original size:11 final size:10
Alignment explanation
Indices: 224589--224672 Score: 50
Period size: 9 Copynumber: 8.3 Consensus size: 10
224579 AAATCAAAAT
224589 AAAAAAGCAA
1 AAAAAAGCAA
*
224599 TAAAAAAGTAA
1 -AAAAAAGCAA
**
224610 AAAAATTC-A
1 AAAAAAGCAA
224619 AAAAAA-CAA
1 AAAAAAGCAA
*
224628 AAAAAATCAA
1 AAAAAAGCAA
*
224638 TCAAAAAGTCAAA
1 -AAAAAAG-C-AA
224651 AAAAGAAG-AA
1 AAAA-AAGCAA
224661 AAAAAAG-AA
1 AAAAAAGCAA
224670 AAA
1 AAA
224673 GGGTTCGGAT
Statistics
Matches: 59, Mismatches: 8, Indels: 14
0.73 0.10 0.17
Matches are distributed among these distances:
8 1 0.02
9 21 0.36
10 14 0.24
11 14 0.24
12 4 0.07
13 5 0.08
ACGTcount: A:0.77, C:0.07, G:0.07, T:0.08
Consensus pattern (10 bp):
AAAAAAGCAA
Found at i:224621 original size:18 final size:18
Alignment explanation
Indices: 224574--224637 Score: 60
Period size: 18 Copynumber: 3.7 Consensus size: 18
224564 AAATCAAATG
*
224574 AAAAAAAATCAAAATAA-
1 AAAAAAAATCAAAAAAAC
** **
224591 AAAAGCAAT-AAAAAAGT
1 AAAAAAAATCAAAAAAAC
*
224608 AAAAAAATTCAAAAAAAC
1 AAAAAAAATCAAAAAAAC
224626 AAAAAAAATCAA
1 AAAAAAAATCAA
224638 TCAAAAAGTC
Statistics
Matches: 35, Mismatches: 10, Indels: 3
0.73 0.21 0.06
Matches are distributed among these distances:
16 5 0.14
17 13 0.37
18 17 0.49
ACGTcount: A:0.78, C:0.08, G:0.03, T:0.11
Consensus pattern (18 bp):
AAAAAAAATCAAAAAAAC
Found at i:224663 original size:39 final size:37
Alignment explanation
Indices: 224584--224673 Score: 92
Period size: 39 Copynumber: 2.3 Consensus size: 37
224574 AAAAAAAATC
*
224584 AAAATAAAAAAGCAATAAAAAAGTAAAAAAATTCAAAA
1 AAAAAAAAAAAGCAATAAAAAAGTAAAAAAA-TCAAAA
* * *
224622 AAACAAAAAAAATCAATCAAAAAGTCAAAAAAA-GAAGAA
1 AAA-AAAAAAAAGCAATAAAAAAGT-AAAAAAATCAA-AA
224661 AAAAAAGAAAAAG
1 AAAAAA-AAAAAG
224674 GGTTCGGATG
Statistics
Matches: 43, Mismatches: 5, Indels: 7
0.78 0.09 0.13
Matches are distributed among these distances:
38 8 0.19
39 28 0.65
40 7 0.16
ACGTcount: A:0.77, C:0.07, G:0.08, T:0.09
Consensus pattern (37 bp):
AAAAAAAAAAAGCAATAAAAAAGTAAAAAAATCAAAA
Found at i:225909 original size:29 final size:29
Alignment explanation
Indices: 225784--226012 Score: 158
Period size: 29 Copynumber: 7.8 Consensus size: 29
225774 ACTTCTCAGT
* *
225784 GTCCACAACTCTGTGGTACCCTTT-TCAAA
1 GTCCACAACTCCGTGGCACCCTTTCT-AAA
** * *
225813 GTGTACAACTCCTGTGGCACCCTTCCCAAA
1 GTCCACAACTCC-GTGGCACCCTTTCTAAA
* * * * *
225843 GTCCATAACTCTGTGTCACTCTTT-TCGAA
1 GTCCACAACTCCGTGGCACCCTTTCT-AAA
* * * * *
225872 GTTCTCAACTCCGTGGAACCTTTTTTAAA
1 GTCCACAACTCCGTGGCACCCTTTCTAAA
* * *
225901 GTACACAACTTCGTAGCACCCTTTCTAAA
1 GTCCACAACTCCGTGGCACCCTTTCTAAA
* * *
225930 GTCCATAACTCCGTGGCACCCTTCCCAAA
1 GTCCACAACTCCGTGGCACCCTTTCTAAA
**
225959 GTCCACAACTCTATGGCACCTTCTTT-TAAA
1 GTCCACAACTCCGTGGCACC--CTTTCTAAA
* *
225989 GTCCACAACTCCATGGCACTCTTT
1 GTCCACAACTCCGTGGCACCCTTT
226013 TCAAAAGCCC
Statistics
Matches: 150, Mismatches: 44, Indels: 13
0.72 0.21 0.06
Matches are distributed among these distances:
28 4 0.03
29 100 0.67
30 43 0.29
31 3 0.02
ACGTcount: A:0.24, C:0.32, G:0.13, T:0.30
Consensus pattern (29 bp):
GTCCACAACTCCGTGGCACCCTTTCTAAA
Found at i:225968 original size:87 final size:88
Alignment explanation
Indices: 225784--226000 Score: 229
Period size: 87 Copynumber: 2.5 Consensus size: 88
225774 ACTTCTCAGT
* * * ** *
225784 GTCCACAACTCTGTGGTACCCTTTTCAAAGTGTACAACTCCTGTGGCACCCTTCCCAAAGTCCAT
1 GTCCACAACTCTGTGGAACCTTTTTTAAAGTACACAACTCCTGTAGCACCCTTCCCAAAGTCCAT
* * * ** *
225849 AACTCTGTGTCACTCTTTTCGAA
66 AACTCCGTGGCACCCTTCCCAAA
* * * * * *
225872 GTTCTCAACTCCGTGGAACCTTTTTTAAAGTACACAACTTC-GTAGCACCCTTTCTAAAGTCCAT
1 GTCCACAACTCTGTGGAACCTTTTTTAAAGTACACAACTCCTGTAGCACCCTTCCCAAAGTCCAT
225936 AACTCCGTGGCACCCTTCCCAAA
66 AACTCCGTGGCACCCTTCCCAAA
* * *
225959 GTCCACAACTCTATGGCACCTTCTTTTAAAGTCCACAACTCC
1 GTCCACAACTCTGTGGAACCTT-TTTTAAAGTACACAACTCC
226001 ATGGCACTCT
Statistics
Matches: 103, Mismatches: 25, Indels: 2
0.79 0.19 0.02
Matches are distributed among these distances:
87 54 0.52
88 49 0.48
ACGTcount: A:0.25, C:0.33, G:0.13, T:0.29
Consensus pattern (88 bp):
GTCCACAACTCTGTGGAACCTTTTTTAAAGTACACAACTCCTGTAGCACCCTTCCCAAAGTCCAT
AACTCCGTGGCACCCTTCCCAAA
Found at i:226006 original size:59 final size:58
Alignment explanation
Indices: 225784--226007 Score: 195
Period size: 58 Copynumber: 3.8 Consensus size: 58
225774 ACTTCTCAGT
* * **
225784 GTCCACAACTCTGTGGTACCCTTTTCAAAGTGTACAACTCCTGTGGCACCCTTCCCAAA
1 GTCCACAACTCTATGGCACCCTTTTCAAAGTCCACAACTCC-GTGGCACCCTTCCCAAA
* * * * * * * * * ***
225843 GTCCATAACTCTGTGTCACTCTTTTCGAAGTTCTCAACTCCGTGGAACCTTTTTTAAA
1 GTCCACAACTCTATGGCACCCTTTTCAAAGTCCACAACTCCGTGGCACCCTTCCCAAA
* *
225901 GTACACAACTTCGTA--GCACCC-TTTCTAAAGTCCATAACTCCGTGGCACCCTTCCCAAA
1 GTCCACAAC-TC-TATGGCACCCTTTTC-AAAGTCCACAACTCCGTGGCACCCTTCCCAAA
*
225959 GTCCACAACTCTATGGCACCTTCTTTT-AAAGTCCACAACTCCATGGCAC
1 GTCCACAACTCTATGGCACC--CTTTTCAAAGTCCACAACTCCGTGGCAC
226008 TCTTTTCAAA
Statistics
Matches: 127, Mismatches: 30, Indels: 16
0.73 0.17 0.09
Matches are distributed among these distances:
56 2 0.02
57 6 0.05
58 59 0.46
59 55 0.43
60 2 0.02
61 3 0.02
ACGTcount: A:0.25, C:0.33, G:0.13, T:0.29
Consensus pattern (58 bp):
GTCCACAACTCTATGGCACCCTTTTCAAAGTCCACAACTCCGTGGCACCCTTCCCAAA
Found at i:226046 original size:33 final size:33
Alignment explanation
Indices: 226009--226135 Score: 152
Period size: 33 Copynumber: 3.9 Consensus size: 33
225999 CCATGGCACT
*
226009 CTTTTCAAAAGCCCATACAAGTTGGTGGCAACC
1 CTTTTCAAAAGCCCACACAAGTTGGTGGCAACC
* * *
226042 CTTTTCAAAAGCTCACATAGGTTGGTGGCAACC
1 CTTTTCAAAAGCCCACACAAGTTGGTGGCAACC
* * *
226075 C-TTTC-AAAGCCTACATAAGTTGGTGGC-ATC
1 CTTTTCAAAAGCCCACACAAGTTGGTGGCAACC
*
226105 CTTTCTCAAAAGCCTACACAAGTTGGTGGCA
1 CTTT-TCAAAAGCCCACACAAGTTGGTGGCA
226136 TTTTTTCTCA
Statistics
Matches: 81, Mismatches: 9, Indels: 7
0.84 0.09 0.07
Matches are distributed among these distances:
30 3 0.04
31 21 0.26
32 6 0.07
33 51 0.63
ACGTcount: A:0.28, C:0.25, G:0.20, T:0.27
Consensus pattern (33 bp):
CTTTTCAAAAGCCCACACAAGTTGGTGGCAACC
Found at i:226510 original size:52 final size:52
Alignment explanation
Indices: 226422--226533 Score: 161
Period size: 52 Copynumber: 2.2 Consensus size: 52
226412 AAACCCGCAT
* * *
226422 ATTGACACCTTTATCATCTTCAAGTCTAATGTCGCTAACCTTGAATTAGCAC
1 ATTGACACCCTTATCATCTTCAAGTCCAATGTCGCTAACCTTGAATAAGCAC
* * * *
226474 ATTGGCACCCTTATCATCTTTAAGTCCAATGTCGCTAGCCTTGAATAAGCAT
1 ATTGACACCCTTATCATCTTCAAGTCCAATGTCGCTAACCTTGAATAAGCAC
226526 ATTGACAC
1 ATTGACAC
226534 TTGCCAAAAC
Statistics
Matches: 52, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
52 52 1.00
ACGTcount: A:0.29, C:0.25, G:0.13, T:0.33
Consensus pattern (52 bp):
ATTGACACCCTTATCATCTTCAAGTCCAATGTCGCTAACCTTGAATAAGCAC
Found at i:226594 original size:111 final size:110
Alignment explanation
Indices: 226449--226946 Score: 404
Period size: 111 Copynumber: 4.6 Consensus size: 110
226439 CTTCAAGTCT
** * * * *
226449 AATGTCGCTAACCTTGAATTAGCACATTGGCACCCTTATCATCTTTAAGTCCAATGTCGCTAGCC
1 AATGTCGCTGGCCTTGAATCAGCACATTAGCACCCTTATCATCTTTAAATCCAATGTCACTAGCC
*
226514 TTGAATAAGCATATTGACACTTGCCAAAACCGTCTTTCCAAAACC
66 TTGAATAAGCATATTGACACTTGCCAAAACCTTCTTTCCAAAACC
** *
226559 TAATGTCAATGGCCTTGAATCAGCATATTAGCACCCTTATCATC-TT---T--AA-GTC-C-A-C
1 -AATGTCGCTGGCCTTGAATCAGCACATTAGCACCCTTATCATCTTTAAATCCAATGTCACTAGC
* * * *
226614 CTTGAATCAGCATATTAACACTTGCCAAAACCTTCTTTCTAAAGTCC
65 CTTGAATAAGCATATTGACACTTGCCAAAACCTTCTTTCCAAA-ACC
* * ** * * * * *
226661 AATGTTGCTGGCCTAGAATCAGCACATTAGGGCCCTTATTATCTTAAAATTCAATGTCATTGGCC
1 AATGTCGCTGGCCTTGAATCAGCACATTAGCACCCTTATCATCTTTAAATCCAATGTCACTAGCC
* * * * * *
226726 TTGAATCAGCACATTGACACTTGCTAAACCCTTTTTTCCAAAGCCC
66 TTGAATAAGCATATTGACACTTGCCAAAACCTTCTTTCCAAA-ACC
* * ** *
226772 AATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTTATCATCTTTAAATCTGATGTCACTGGCC
1 AATGTCGCTGGCCTTGAATCAGCACATTAGCACCCTTATCATCTTTAAATCCAATGTCACTAGCC
* * * * * *
226837 TTGAATAAGCACATT-AGCACCTT-----TATCATATTT--AAACCC
66 TTGAATAAGCATATTGA-CA-CTTGCCAAAACCTTCTTTCCAAAACC
* * * * *
226876 AATGTCGCTGGCCTTAAATCAGCACATT-GACACCCTTATCATCTCTAAGTCCAGTGTCACAAGC
1 AATGTCGCTGGCCTTGAATCAGCACATTAG-CACCCTTATCATCTTTAAATCCAATGTCACTAGC
226940 CTTGAAT
65 CTTGAAT
226947 CTGCACATTA
Statistics
Matches: 316, Mismatches: 57, Indels: 35
0.77 0.14 0.09
Matches are distributed among these distances:
101 75 0.24
102 4 0.01
103 2 0.01
104 66 0.21
105 6 0.02
107 8 0.03
108 3 0.01
110 3 0.01
111 146 0.46
112 3 0.01
ACGTcount: A:0.29, C:0.26, G:0.14, T:0.31
Consensus pattern (110 bp):
AATGTCGCTGGCCTTGAATCAGCACATTAGCACCCTTATCATCTTTAAATCCAATGTCACTAGCC
TTGAATAAGCATATTGACACTTGCCAAAACCTTCTTTCCAAAACC
Found at i:226836 original size:52 final size:51
Alignment explanation
Indices: 226771--226960 Score: 202
Period size: 52 Copynumber: 3.7 Consensus size: 51
226761 TTCCAAAGCC
* *
226771 CAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTTATCATCTTTAAAT
1 CAATGTCACTGGCCTTGAATCAGCACATTAGCACCTTTATCATCTTTAAAT
* * * *
226822 CTGATGTCACTGGCCTTGAATAAGCACATTAGCACCTTTATCATATTTAAACC
1 C-AATGTCACTGGCCTTGAATCAGCACATTAGCACCTTTATCATCTTTAAA-T
* * * * *
226875 CAATGTCGCTGGCCTTAAATCAGCACATT-GACACCCTTATCATCTCTAAGT
1 CAATGTCACTGGCCTTGAATCAGCACATTAG-CACCTTTATCATCTTTAAAT
* ** *
226926 CCAGTGTCACAAGCCTTGAATCTGCACATTAGCAC
1 -CAATGTCACTGGCCTTGAATCAGCACATTAGCAC
226961 ATTCGTCAAG
Statistics
Matches: 113, Mismatches: 21, Indels: 9
0.79 0.15 0.06
Matches are distributed among these distances:
51 2 0.02
52 109 0.96
53 2 0.02
ACGTcount: A:0.28, C:0.27, G:0.15, T:0.30
Consensus pattern (51 bp):
CAATGTCACTGGCCTTGAATCAGCACATTAGCACCTTTATCATCTTTAAAT
Found at i:226915 original size:104 final size:104
Alignment explanation
Indices: 226769--226960 Score: 278
Period size: 104 Copynumber: 1.8 Consensus size: 104
226759 TTTTCCAAAG
* * * * * *
226769 CCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTTATCATCTTTAAAT-CTGATGTCACT
1 CCCAATGTCGCTGGCCTTAAATCAGCACATTGACACCCTTATCATCTCTAAATCCAG-TGTCACA
*
226833 GGCCTTGAATAAGCACATTAGCACCTTTATCATATTTAAA
65 AGCCTTGAATAAGCACATTAGCACCTTTATCATATTTAAA
*
226873 CCCAATGTCGCTGGCCTTAAATCAGCACATTGACACCCTTATCATCTCTAAGTCCAGTGTCACAA
1 CCCAATGTCGCTGGCCTTAAATCAGCACATTGACACCCTTATCATCTCTAAATCCAGTGTCACAA
**
226938 GCCTTGAATCTGCACATTAGCAC
66 GCCTTGAATAAGCACATTAGCAC
226961 ATTCGTCAAG
Statistics
Matches: 77, Mismatches: 10, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
104 75 0.97
105 2 0.03
ACGTcount: A:0.28, C:0.28, G:0.15, T:0.30
Consensus pattern (104 bp):
CCCAATGTCGCTGGCCTTAAATCAGCACATTGACACCCTTATCATCTCTAAATCCAGTGTCACAA
GCCTTGAATAAGCACATTAGCACCTTTATCATATTTAAA
Found at i:227745 original size:53 final size:51
Alignment explanation
Indices: 227620--227793 Score: 188
Period size: 53 Copynumber: 3.4 Consensus size: 51
227610 TCTAAAAAGA
* * * * * * *
227620 AAATGTATCGATATATTTTTTATTATATTGATACATTCTA-GATTTGATCC
1 AAATGTATCGATACATTATTCATTATATCGATAAATTCTAGGTTTTGACCC
* * * * * *
227670 AAATGTAGCGATACATTTTTCATTATATCGATACATTTTGGGTTTTTGACACT
1 AAATGTATCGATACATTATTCATTATATCGATAAATTCTAGG-TTTTGAC-CC
*
227723 AAATGTATCGATACGTTATTCATTATATCGATAAATTCTAGGTTTTGACCC
1 AAATGTATCGATACATTATTCATTATATCGATAAATTCTAGGTTTTGACCC
*
227774 AAATGTATCGATACAATATT
1 AAATGTATCGATACATTATT
227794 TAATGTATCG
Statistics
Matches: 103, Mismatches: 18, Indels: 5
0.82 0.14 0.04
Matches are distributed among these distances:
50 34 0.33
51 20 0.19
52 12 0.12
53 37 0.36
ACGTcount: A:0.32, C:0.13, G:0.13, T:0.43
Consensus pattern (51 bp):
AAATGTATCGATACATTATTCATTATATCGATAAATTCTAGGTTTTGACCC
Found at i:228469 original size:33 final size:33
Alignment explanation
Indices: 228425--228492 Score: 127
Period size: 33 Copynumber: 2.1 Consensus size: 33
228415 TTTTTACAAT
228425 TTGTATAGATACATTGTTCATTGTATCGATACA
1 TTGTATAGATACATTGTTCATTGTATCGATACA
*
228458 TTGTATCGATACATTGTTCATTGTATCGATACA
1 TTGTATAGATACATTGTTCATTGTATCGATACA
228491 TT
1 TT
228493 CTGGGTTTAC
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.28, C:0.13, G:0.15, T:0.44
Consensus pattern (33 bp):
TTGTATAGATACATTGTTCATTGTATCGATACA
Found at i:228479 original size:20 final size:20
Alignment explanation
Indices: 228425--228492 Score: 78
Period size: 20 Copynumber: 3.8 Consensus size: 20
228415 TTTTTACAAT
*
228425 TTGTATAGATACATTGTTCA
1 TTGTATCGATACATTGTTCA
228445 TTGTATCGAT--A-----CA
1 TTGTATCGATACATTGTTCA
228458 TTGTATCGATACATTGTTCA
1 TTGTATCGATACATTGTTCA
228478 TTGTATCGATACATT
1 TTGTATCGATACATT
228493 CTGGGTTTAC
Statistics
Matches: 40, Mismatches: 1, Indels: 14
0.73 0.02 0.25
Matches are distributed among these distances:
13 12 0.30
15 1 0.03
18 1 0.03
20 26 0.65
ACGTcount: A:0.28, C:0.13, G:0.15, T:0.44
Consensus pattern (20 bp):
TTGTATCGATACATTGTTCA
Found at i:228492 original size:13 final size:13
Alignment explanation
Indices: 228443--228474 Score: 64
Period size: 13 Copynumber: 2.5 Consensus size: 13
228433 ATACATTGTT
228443 CATTGTATCGATA
1 CATTGTATCGATA
228456 CATTGTATCGATA
1 CATTGTATCGATA
228469 CATTGT
1 CATTGT
228475 TCATTGTATC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.28, C:0.16, G:0.16, T:0.41
Consensus pattern (13 bp):
CATTGTATCGATA
Found at i:231079 original size:80 final size:78
Alignment explanation
Indices: 230816--231086 Score: 283
Period size: 79 Copynumber: 3.4 Consensus size: 78
230806 TTTTCATCTC
** * *
230816 GGGGATACTCCAACCCTGGTTTTATTTCTAAAACATTAATTTTTCATAATCGGGGATACTCCAAT
1 GGGGATACTCCAACCCTGACTTTATTTCCAAAACATTAATTTTTCACAATCGGGGATACTCCAA-
230881 CCCGTTATTTTCGA
65 CCCGTTATTTTCGA
* * * * * **
230895 GGGGATACTCCAACCC-CAGCTTTATTTCTAAAATATTTATTTCTCACAATCAAGGATACTCCAA
1 GGGGATACTCCAACCCTGA-CTTTATTTCCAAAACATTAATTTTTCACAATCGGGGATACTCCAA
* * *
230959 CCCCATTATTTTGGC
65 -CCCGTTATTTTCGA
* * * **
230974 GGGGATACTCTAACCCCGACCTTATTTCCAAAAGCATCGATTTTTCACAATCGGGGATACTCCAA
1 GGGGATACTCCAACCCTGACTTTATTTCCAAAA-CATTAATTTTTCACAATCGGGGATACTCCAA
**
231039 CCCTGTTGCTTTCGA
65 CCC-GTTATTTTCGA
* *
231054 GGGGATACTCCAACCCTGATTTTATTTTCAAAA
1 GGGGATACTCCAACCCTGACTTTATTTCCAAAA
231087 TGTCAATTTT
Statistics
Matches: 155, Mismatches: 33, Indels: 7
0.79 0.17 0.04
Matches are distributed among these distances:
79 95 0.61
80 60 0.39
ACGTcount: A:0.27, C:0.25, G:0.15, T:0.33
Consensus pattern (78 bp):
GGGGATACTCCAACCCTGACTTTATTTCCAAAACATTAATTTTTCACAATCGGGGATACTCCAAC
CCGTTATTTTCGA
Found at i:243455 original size:1 final size:1
Alignment explanation
Indices: 243451--243505 Score: 56
Period size: 1 Copynumber: 55.0 Consensus size: 1
243441 ACATTTTTTT
* * * * * *
243451 AAAAAAAAGAACAAAAAAAACAAAAAAAAATAAAAAAAATAAAAAAAGAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
243506 GAGAGAAAAG
Statistics
Matches: 42, Mismatches: 12, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
1 42 1.00
ACGTcount: A:0.89, C:0.04, G:0.04, T:0.04
Consensus pattern (1 bp):
A
Found at i:243477 original size:19 final size:19
Alignment explanation
Indices: 243452--243505 Score: 74
Period size: 19 Copynumber: 2.8 Consensus size: 19
243442 CATTTTTTTA
*
243452 AAAAAAAGAACAAAAAAAAC
1 AAAAAAAGAA-AAAAAAAAT
243472 AAAAAAA-AATAAAAAAAAT
1 AAAAAAAGAA-AAAAAAAAT
243491 AAAAAAAGAAAAAAA
1 AAAAAAAGAAAAAAA
243506 GAGAGAAAAG
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
19 22 0.71
20 9 0.29
ACGTcount: A:0.89, C:0.04, G:0.04, T:0.04
Consensus pattern (19 bp):
AAAAAAAGAAAAAAAAAAT
Found at i:244733 original size:61 final size:61
Alignment explanation
Indices: 244615--245105 Score: 556
Period size: 61 Copynumber: 8.1 Consensus size: 61
244605 GAGCAGGATG
* * *
244615 CCTTTCAAAGCCCACACAAGCTAGGTGGCACTTTTCTAGTCCTCAAAGAGCTA-GACACCTTTC
1 CCTTTTAAAGCCCACACAAG-TTGGTGGCAC-TTTCTAGTCCTCAAAGAGC-AGGACACCTTTT
* *
244678 CCTTTTAAAGCCCACACAAGTTGGTGGCACCTTCTAGTCCTCAAAGAGTAGGACACCTTTT
1 CCTTTTAAAGCCCACACAAGTTGGTGGCACTTTCTAGTCCTCAAAGAGCAGGACACCTTTT
* * * *
244739 ACTTTTAAAGCCCACACAAGTTGGTGGCA-TTTCCCAATCCTCAAAGAGCAGG--A-C---G
1 CCTTTTAAAGCCCACACAAGTTGGTGGCACTTT-CTAGTCCTCAAAGAGCAGGACACCTTTT
* * * * * * *
244794 CCTTTTAAAGCCTACAAAAGTTGGTGGCATTTTTTTAGTCCTCAAAGAGCACGACGCTTTTT
1 CCTTTTAAAGCCCACACAAGTTGGTGGCA-CTTTCTAGTCCTCAAAGAGCAGGACACCTTTT
* * *
244856 CCTTTTAAAGCCCACACAAGTCGGTGGCACCTTCTAGTCCTCAAAGAGCAGAACACCTTTTT
1 CCTTTTAAAGCCCACACAAGTTGGTGGCACTTTCTAGTCCTCAAAGAGCAGGACACC-TTTT
* * *
244918 CCTTTTAAAGCCCACACAAGTTGGTGGCACTTTCCAGTCCTCAAAGAGCAAGACGCCTTTT
1 CCTTTTAAAGCCCACACAAGTTGGTGGCACTTTCTAGTCCTCAAAGAGCAGGACACCTTTT
* * * *
244979 CCTTTTAAAGCCCACACAAGCTGGTGGCACCTT-TAGTCCTTACAA-AGCAGGA-AGCTTTCT
1 CCTTTTAAAGCCCACACAAGTTGGTGGCACTTTCTAGTCCTCA-AAGAGCAGGACACCTTT-T
* * *
245039 CCTTTTAAAGCTCACACAAGTTGGTGGCACGTTTC-AGTCCTCAAAGAGTAGGACGCCTTTT
1 CCTTTTAAAGCCCACACAAGTTGGTGGCAC-TTTCTAGTCCTCAAAGAGCAGGACACCTTTT
245100 CCTTTT
1 CCTTTT
245106 CTCCTTTGCC
Statistics
Matches: 360, Mismatches: 51, Indels: 36
0.81 0.11 0.08
Matches are distributed among these distances:
55 26 0.07
56 15 0.04
57 3 0.01
58 1 0.00
59 5 0.01
60 47 0.13
61 150 0.42
62 94 0.26
63 19 0.05
ACGTcount: A:0.26, C:0.28, G:0.18, T:0.28
Consensus pattern (61 bp):
CCTTTTAAAGCCCACACAAGTTGGTGGCACTTTCTAGTCCTCAAAGAGCAGGACACCTTTT
Found at i:244854 original size:55 final size:55
Alignment explanation
Indices: 244740--244978 Score: 160
Period size: 62 Copynumber: 4.1 Consensus size: 55
244730 ACACCTTTTA
* *
244740 CTTTTAAAGCCCACACAAGTTGGTGGCATTTCCCAATCCTCAAAGAGCAGGACGC
1 CTTTTAAAGCCCACAAAAGTTGGTGGCATTTCCCAATCCTCAAAGAGCACGACGC
* *** *
244795 CTTTTAAAGCCTACAAAAGTTGGTGGCATTTTTTTAGTCCTCAAAGAGCACGACGCTTTTTC
1 CTTTTAAAGCCCACAAAAGTTGGTGGCA-TTTCCCAATCCTCAAAGAGCACGACG------C
* * * * * *
244857 CTTTTAAAGCCCACACAAGTCGGTGGCACCTT-CTAGTCCTCAAAGAGCA-GAACACCTTTTTC
1 CTTTTAAAGCCCACAAAAGTTGGTGGCA-TTTCCCAATCCTCAAAGAGCACG---A-C----GC
* * *
244919 CTTTTAAAGCCCACACAAGTTGGTGGCACTTT-CCAGTCCTCAAAGAGCAAGACGC
1 CTTTTAAAGCCCACAAAAGTTGGTGGCA-TTTCCCAATCCTCAAAGAGCACGACGC
244974 CTTTT
1 CTTTT
244979 CCTTTTAAAG
Statistics
Matches: 150, Mismatches: 18, Indels: 32
0.75 0.09 0.16
Matches are distributed among these distances:
55 32 0.21
56 21 0.14
59 1 0.01
60 2 0.01
61 16 0.11
62 75 0.50
63 2 0.01
64 1 0.01
ACGTcount: A:0.27, C:0.27, G:0.18, T:0.28
Consensus pattern (55 bp):
CTTTTAAAGCCCACAAAAGTTGGTGGCATTTCCCAATCCTCAAAGAGCACGACGC
Found at i:244961 original size:179 final size:176
Alignment explanation
Indices: 244595--245105 Score: 634
Period size: 178 Copynumber: 2.8 Consensus size: 176
244585 TTCACCCTTT
* * * *
244595 AGTCCTCAAAGAGCAGGATGCCTTTCAAAGCCCACACAAGCTAGGTGGCACTTTTCTAGTCCTCA
1 AGTCCTCAAAGAGCAGGACGCCTTTTAAAGCCCACACAAG-TTGGTGGCA-TTTTTTAGTCCTCA
* * *
244660 AAGAGCTAGACACCTTTCCCTTTTAAAGCCCACACAAGTTGGTGGCACCTTCTAGTCCTCAAAGA
64 AAGAGC-AGACGCTTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACCTTCTAGTCCTCAAAGA
*
244725 GTAGGACACCTTTTACTTTTAAAGCCCACACAAGTTGGTGGCATTTCCC
128 GTAGGACACCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCATTTCCC
* * *
244774 AATCCTCAAAGAGCAGGACGCCTTTTAAAGCCTACAAAAGTTGGTGGCATTTTTTTAGTCCTCAA
1 AGTCCTCAAAGAGCAGGACGCCTTTTAAAGCCCACACAAGTTGGTGGCA-TTTTTTAGTCCTCAA
*
244839 AGAGCACGACGCTTTTTCCTTTTAAAGCCCACACAAGTCGGTGGCACCTTCTAGTCCTCAAAGAG
65 AGAGCA-GACGCTTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACCTTCTAGTCCTCAAAGAG
* *
244904 CAGAACACCTTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACTTT-CC
129 TAGGACACC-TTTTCCTTTTAAAGCCCACACAAGTTGGTGGCA-TTTCCC
* * **
244953 AGTCCTCAAAGAGCAAGACGCCTTTTCCTTTTAAAGCCCACACAAGCTGGTGGCA-CCTTTAGTC
1 AGTCCTCAAAGAGCAGGACG------CCTTTTAAAGCCCACACAAGTTGGTGGCATTTTTTAGTC
* * * * *
245017 CTTACAA-AGCAGGAAGCTTTCTCCTTTTAAAGCTCACACAAGTTGGTGGCACGTT-TCAGTCCT
60 CTCA-AAGAGCA-GACGCTTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACCTTCT-AGTCCT
*
245080 CAAAGAGTAGGACGCCTTTTCCTTTT
122 CAAAGAGTAGGACACCTTTTCCTTTT
245106 CTCCTTTGCC
Statistics
Matches: 289, Mismatches: 32, Indels: 19
0.85 0.09 0.06
Matches are distributed among these distances:
177 1 0.00
178 88 0.30
179 87 0.30
180 3 0.01
182 11 0.04
183 71 0.25
184 2 0.01
185 26 0.09
ACGTcount: A:0.27, C:0.27, G:0.18, T:0.27
Consensus pattern (176 bp):
AGTCCTCAAAGAGCAGGACGCCTTTTAAAGCCCACACAAGTTGGTGGCATTTTTTAGTCCTCAAA
GAGCAGACGCTTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACCTTCTAGTCCTCAAAGAGTA
GGACACCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCATTTCCC
Found at i:245308 original size:41 final size:40
Alignment explanation
Indices: 245199--245329 Score: 131
Period size: 41 Copynumber: 3.2 Consensus size: 40
245189 CCTTCTAGTT
*
245199 CTCAAAGAGCAGGATACATTTTATTCTCCTTTTTCCTTTGTC
1 CTCAAAGAGCA-GATACATATTATT-TCCTTTTTCCTTTGTC
* *
245241 CTCAAAAAGCA-ATACACATTTAATTTCCTTTTTCCTTTGTC
1 CTCAAAGAGCAGATACATA-TT-ATTTCCTTTTTCCTTTGTC
* * * *
245282 TTCAAAGGGCATGATGCATATTATTTCCTTTTTTCCTTAGTC
1 CTCAAAGAGCA-GATACATATTATTTCC-TTTTTCCTTTGTC
245324 C-CAAAG
1 CTCAAAG
245330 GAGTAGGACC
Statistics
Matches: 74, Mismatches: 10, Indels: 11
0.78 0.11 0.12
Matches are distributed among these distances:
40 5 0.07
41 37 0.50
42 27 0.36
43 5 0.07
ACGTcount: A:0.25, C:0.23, G:0.11, T:0.41
Consensus pattern (40 bp):
CTCAAAGAGCAGATACATATTATTTCCTTTTTCCTTTGTC
Found at i:245947 original size:13 final size:13
Alignment explanation
Indices: 245931--245960 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
245921 TTACATTGTT
245931 CATTGTATCGATA
1 CATTGTATCGATA
245944 CATTGTATCGATA
1 CATTGTATCGATA
245957 CATT
1 CATT
245961 CTGGGTTTAC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.30, C:0.17, G:0.13, T:0.40
Consensus pattern (13 bp):
CATTGTATCGATA
Found at i:245949 original size:20 final size:20
Alignment explanation
Indices: 245893--245949 Score: 87
Period size: 20 Copynumber: 2.9 Consensus size: 20
245883 TTTTTACAAT
*
245893 TTGTATCGATACATTGCTCA
1 TTGTATCGATACATTGTTCA
* *
245913 TTGTATTGTTACATTGTTCA
1 TTGTATCGATACATTGTTCA
245933 TTGTATCGATACATTGT
1 TTGTATCGATACATTGT
245950 ATCGATACAT
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.23, C:0.14, G:0.16, T:0.47
Consensus pattern (20 bp):
TTGTATCGATACATTGTTCA
Found at i:248524 original size:80 final size:78
Alignment explanation
Indices: 248280--248593 Score: 294
Period size: 79 Copynumber: 4.0 Consensus size: 78
248270 TTTCATCTTA
* * * * * *
248280 GGGATACTCTAACCTCAGGTTTTATTTTCAAAACATCAATTTTTCATAATTAGGGATACTCCAAT
1 GGGATACTCCAACC-CCGGCTTTATTTTCAAAACATCGATTTTTCATAATCAGGGATACTCCAAC
248345 CCCGTTATTTCTGAG
65 CCCGTTATTTC-GAG
** * * * *
248360 GGGATACTCCAACTTCGGCTTTATTTAT-AAAATATTGATTTCTCACAATC-GAGGATACTCCAA
1 GGGATACTCCAACCCCGGCTTTATTT-TCAAAACATCGATTTTTCATAATCAG-GGATACTCCAA
*
248423 CCCCGTTATTTTG-G
64 CCCCGTTATTTCGAG
* * * * *
248437 CGAGGATACTCCAACCCCGGCCTTATTTCCAAAAGCGTCGATTTTTCATAATCGGGGATATTCCA
1 -G-GGATACTCCAACCCCGGCTTTATTTTCAAAA-CATCGATTTTTCATAATCAGGGATACTCCA
* *
248502 ACCCCGTTGCTTTCAAG
63 ACCCCGTT-ATTTCGAG
* ** *
248519 GGGATACTCCAACCCTGATTTTATTTTCAAAACGTCGA-TTTTCTATAATCAGGGATACTCCAAC
1 GGGATACTCCAACCCCGGCTTTATTTTCAAAACATCGATTTTTC-ATAATCAGGGATACTCCAAC
*
248583 CCTGTTATTTC
65 CCCGTTATTTC
248594 CGAAGGGGTA
Statistics
Matches: 189, Mismatches: 35, Indels: 22
0.77 0.14 0.09
Matches are distributed among these distances:
77 1 0.01
78 12 0.06
79 101 0.53
80 69 0.37
81 5 0.03
82 1 0.01
ACGTcount: A:0.27, C:0.24, G:0.15, T:0.34
Consensus pattern (78 bp):
GGGATACTCCAACCCCGGCTTTATTTTCAAAACATCGATTTTTCATAATCAGGGATACTCCAACC
CCGTTATTTCGAG
Found at i:255177 original size:20 final size:20
Alignment explanation
Indices: 255152--255245 Score: 120
Period size: 20 Copynumber: 4.7 Consensus size: 20
255142 TTTACCCAGA
*
255152 TGTATCGATACATT-TTGCAT
1 TGTATCGATACATTGCT-CAT
255172 TGTATCGATACATTGCTCAT
1 TGTATCGATACATTGCTCAT
*
255192 TGTATCAATACATTGCTCAT
1 TGTATCGATACATTGCTCAT
* *
255212 TGTATCGATACATT-TTACAA
1 TGTATCGATACATTGCT-CAT
255232 TGTATCGATACATT
1 TGTATCGATACATT
255246 CAGGCATTTT
Statistics
Matches: 67, Mismatches: 5, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
19 1 0.01
20 65 0.97
21 1 0.01
ACGTcount: A:0.29, C:0.17, G:0.13, T:0.41
Consensus pattern (20 bp):
TGTATCGATACATTGCTCAT
Found at i:257676 original size:51 final size:51
Alignment explanation
Indices: 257566--257684 Score: 134
Period size: 51 Copynumber: 2.4 Consensus size: 51
257556 AATTTTTCTT
* * * *
257566 AATC-GGGATACTCCAACTCCGATTTTATTTCTAAAGCATCGATTTACCGC
1 AATCAGGGATACTCCAACTCCGATTTTATTTCTAAAACACCAATTTACCAC
* **
257616 AATCAGGGATACTCCAACTCTGATTTTATTT-TCAAAACACCAATTTTTCAC
1 AATCAGGGATACTCCAACTCCGATTTTATTTCT-AAAACACCAATTTACCAC
**
257667 AATTGGGGATACTCCAAC
1 AATCAGGGATACTCCAAC
257685 CCCGTTATTC
Statistics
Matches: 58, Mismatches: 9, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
50 5 0.09
51 53 0.91
ACGTcount: A:0.31, C:0.24, G:0.13, T:0.32
Consensus pattern (51 bp):
AATCAGGGATACTCCAACTCCGATTTTATTTCTAAAACACCAATTTACCAC
Found at i:257701 original size:27 final size:28
Alignment explanation
Indices: 257671--257743 Score: 121
Period size: 28 Copynumber: 2.6 Consensus size: 28
257661 TTTCACAATT
257671 GGGGATACTCCAACCCCGTTA-TTCCAA
1 GGGGATACTCCAACCCCGTTATTTCCAA
* *
257698 GGGGATACTCCAACCCCGTTATTTTCGA
1 GGGGATACTCCAACCCCGTTATTTCCAA
257726 GGGGATACTCCAACCCCG
1 GGGGATACTCCAACCCCG
257744 GCTTTATATC
Statistics
Matches: 43, Mismatches: 2, Indels: 1
0.93 0.04 0.02
Matches are distributed among these distances:
27 21 0.49
28 22 0.51
ACGTcount: A:0.23, C:0.33, G:0.22, T:0.22
Consensus pattern (28 bp):
GGGGATACTCCAACCCCGTTATTTCCAA
Found at i:257877 original size:109 final size:107
Alignment explanation
Indices: 257621--257895 Score: 260
Period size: 109 Copynumber: 2.6 Consensus size: 107
257611 ACCGCAATCA
* *
257621 GGGATACTCCAA-CTCTGATTTTATTT-TCAAAACACCAA--TTTTTCACAATTGGGGATACTCC
1 GGGATACTCCAACCT-TGATTTTATTTCT-AAAACATCAATTTTTTTCACAATCGGGGATACTCC
* * *
257682 AACCCCGTTATTCCAAGGGGATACTCCAACCCCGTTATTTTCGAG
64 AACCCCGTTATTCCAA-GAGATACTCCAACCCCGTTATTTCCAAG
** ** * * ** *
257727 GGGATACTCCAACCCCGGCTTTATATCTAAAATATTGATTTTTTTCATAATCGAGGG-TACTCCA
1 GGGATACTCCAACCTTGATTTTATTTCTAAAACATCAATTTTTTTCACAATCG-GGGATACTCCA
* *
257791 ACCCCGTTATGTCATCAA-AGATACTCTAACCCTGTTATTTCCAAG
65 ACCCCGTTAT-TC--CAAGAGATACTCCAACCCCGTTATTTCCAAG
* * *
257836 GGGATACTCCAACCTTAATTTTATTTCTAAAACATCAA--TTTTCCATAATCGGGGATACTC
1 GGGATACTCCAACCTTGATTTTATTTCTAAAACATCAATTTTTTTCACAATCGGGGATACTC
257896 TAACTCCGAT
Statistics
Matches: 134, Mismatches: 26, Indels: 17
0.76 0.15 0.10
Matches are distributed among these distances:
106 28 0.21
107 19 0.14
108 28 0.21
109 56 0.42
111 3 0.02
ACGTcount: A:0.29, C:0.25, G:0.14, T:0.33
Consensus pattern (107 bp):
GGGATACTCCAACCTTGATTTTATTTCTAAAACATCAATTTTTTTCACAATCGGGGATACTCCAA
CCCCGTTATTCCAAGAGATACTCCAACCCCGTTATTTCCAAG
Found at i:257895 original size:51 final size:52
Alignment explanation
Indices: 257835--257951 Score: 166
Period size: 51 Copynumber: 2.3 Consensus size: 52
257825 TTATTTCCAA
* * *
257835 GGGGATACTCCAACCT-TAATTTTATTTCTAAAACATCAATTTTCCATAATC
1 GGGGATACTCCAACCTCCAATTTTATTTCCAAAACATCAATTTTCCACAATC
* * *
257886 GGGGATACTCTAA-CTCCGATTTTATTTCCAAAACATCAATTTTTCACAATC
1 GGGGATACTCCAACCTCCAATTTTATTTCCAAAACATCAATTTTCCACAATC
257937 GGGGATACTCCAACC
1 GGGGATACTCCAACC
257952 CCATTATTTC
Statistics
Matches: 57, Mismatches: 7, Indels: 3
0.85 0.10 0.04
Matches are distributed among these distances:
50 2 0.04
51 54 0.95
52 1 0.02
ACGTcount: A:0.32, C:0.24, G:0.11, T:0.33
Consensus pattern (52 bp):
GGGGATACTCCAACCTCCAATTTTATTTCCAAAACATCAATTTTCCACAATC
Found at i:259430 original size:19 final size:19
Alignment explanation
Indices: 259369--259433 Score: 55
Period size: 19 Copynumber: 3.4 Consensus size: 19
259359 AGTAATTTAA
**
259369 ATAAATTATATTATCTATTG
1 ATAAATTATA-TAGATATTG
*
259389 ATAAA-TATA-AGA-ATTA
1 ATAAATTATATAGATATTG
259405 ATTTAAATTATATAGATATTG
1 A--TAAATTATATAGATATTG
259426 ATAAATTA
1 ATAAATTA
259434 ATTATTATAT
Statistics
Matches: 36, Mismatches: 4, Indels: 11
0.71 0.08 0.22
Matches are distributed among these distances:
16 4 0.11
17 1 0.03
18 4 0.11
19 15 0.42
20 8 0.22
21 4 0.11
ACGTcount: A:0.49, C:0.02, G:0.06, T:0.43
Consensus pattern (19 bp):
ATAAATTATATAGATATTG
Found at i:265276 original size:16 final size:16
Alignment explanation
Indices: 265255--265287 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
265245 AATAAAAGTA
*
265255 TGAATTAAAATGAACT
1 TGAATTAAAACGAACT
265271 TGAATTAAAACGAACT
1 TGAATTAAAACGAACT
265287 T
1 T
265288 TTTATCAATA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.48, C:0.09, G:0.12, T:0.30
Consensus pattern (16 bp):
TGAATTAAAACGAACT
Found at i:270144 original size:27 final size:27
Alignment explanation
Indices: 270114--270186 Score: 101
Period size: 27 Copynumber: 2.7 Consensus size: 27
270104 AAAAACCACC
*
270114 CTTTGTGTTTATCAAAAATGGTGATTA
1 CTTTGTGTTTGTCAAAAATGGTGATTA
* * *
270141 CTTTGTATTTGTCAAAAATGGTGGTTC
1 CTTTGTGTTTGTCAAAAATGGTGATTA
*
270168 CTTTTTGTTTGTCAAAAAT
1 CTTTGTGTTTGTCAAAAAT
270187 TATGGCTTAT
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
27 40 1.00
ACGTcount: A:0.26, C:0.10, G:0.18, T:0.47
Consensus pattern (27 bp):
CTTTGTGTTTGTCAAAAATGGTGATTA
Found at i:270206 original size:24 final size:25
Alignment explanation
Indices: 270172--270227 Score: 73
Period size: 24 Copynumber: 2.3 Consensus size: 25
270162 TGGTTCCTTT
*
270172 TTGTTTGTCAAAAATT-ATGGCTT-A
1 TTGTTTATC-AAAATTGATGGCTTAA
270196 TTGTTTATCAAAATTGATGGCTTAA
1 TTGTTTATCAAAATTGATGGCTTAA
270221 TT-TTTAT
1 TTGTTTAT
270228 TGCAAAATGG
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
23 6 0.21
24 20 0.69
25 3 0.10
ACGTcount: A:0.29, C:0.07, G:0.14, T:0.50
Consensus pattern (25 bp):
TTGTTTATCAAAATTGATGGCTTAA
Found at i:274759 original size:27 final size:27
Alignment explanation
Indices: 274681--274759 Score: 86
Period size: 27 Copynumber: 2.9 Consensus size: 27
274671 CAAAAATCAA
* *
274681 CCTTTGTGTTTGTCAAAACTTATGGTT
1 CCTTTGTGTTTGTCAAAAATTGTGGTT
* * * * *
274708 ACTTTGTATTGGTAAAAAATGGTGGTT
1 CCTTTGTGTTTGTCAAAAATTGTGGTT
*
274735 CCTTTTTGTTTGTCAAAAATTGTGG
1 CCTTTGTGTTTGTCAAAAATTGTGG
274760 CTTGTTATTT
Statistics
Matches: 39, Mismatches: 13, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
27 39 1.00
ACGTcount: A:0.23, C:0.10, G:0.22, T:0.46
Consensus pattern (27 bp):
CCTTTGTGTTTGTCAAAAATTGTGGTT
Found at i:276601 original size:20 final size:21
Alignment explanation
Indices: 276564--276602 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
276554 TAGATTTATA
* *
276564 TATTTTTATATATGTTATAAT
1 TATTTTTATAAATATTATAAT
276585 TATTTTT-TAAATATTATA
1 TATTTTTATAAATATTATA
276603 TATTTAAATA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 9 0.56
21 7 0.44
ACGTcount: A:0.36, C:0.00, G:0.03, T:0.62
Consensus pattern (21 bp):
TATTTTTATAAATATTATAAT
Found at i:276644 original size:17 final size:19
Alignment explanation
Indices: 276610--276656 Score: 53
Period size: 19 Copynumber: 2.5 Consensus size: 19
276600 ATATATTTAA
*
276610 ATAAATTTTAATAAGTAA-T
1 ATAAATTTTGAT-AGTAATT
276629 ATAAATTTTGAT-GTAATT
1 ATAAATTTTGATAGTAATT
*
276647 ATAATTTTTG
1 ATAAATTTTG
276657 TCATATTTAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
17 4 0.16
18 10 0.40
19 11 0.44
ACGTcount: A:0.43, C:0.00, G:0.09, T:0.49
Consensus pattern (19 bp):
ATAAATTTTGATAGTAATT
Found at i:276972 original size:57 final size:57
Alignment explanation
Indices: 276904--277013 Score: 184
Period size: 57 Copynumber: 1.9 Consensus size: 57
276894 GTTATTATTA
* **
276904 TTTTGTGTTTGATGACAGATAGGAGAGAGGACTCTTTGGGTTTCTATAATTCCTTGT
1 TTTTGTATTTGATGACAGATAGGAGAGAGGACTCTTTCAGTTTCTATAATTCCTTGT
*
276961 TTTTGTATTTGATGACAGATAGGTGAGAGGACTCTTTCAGTTTCTATAATTCC
1 TTTTGTATTTGATGACAGATAGGAGAGAGGACTCTTTCAGTTTCTATAATTCC
277014 GTCCCAAAGC
Statistics
Matches: 49, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
57 49 1.00
ACGTcount: A:0.23, C:0.12, G:0.24, T:0.42
Consensus pattern (57 bp):
TTTTGTATTTGATGACAGATAGGAGAGAGGACTCTTTCAGTTTCTATAATTCCTTGT
Found at i:282519 original size:22 final size:22
Alignment explanation
Indices: 282491--282534 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
282481 ATGAATTAAC
282491 TGTTAAAACTGAACCAGAAAAA
1 TGTTAAAACTGAACCAGAAAAA
*
282513 TGTTAAAACTGAACCAGGAAAA
1 TGTTAAAACTGAACCAGAAAAA
282535 CCTTTATTTC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.52, C:0.14, G:0.16, T:0.18
Consensus pattern (22 bp):
TGTTAAAACTGAACCAGAAAAA
Found at i:287245 original size:22 final size:23
Alignment explanation
Indices: 287217--287262 Score: 67
Period size: 22 Copynumber: 2.0 Consensus size: 23
287207 ATCTGATGCC
* *
287217 ATGTTAAAATTGAA-TAAGAAAA
1 ATGTTAAAACTGAACCAAGAAAA
287239 ATGTTAAAACTGAACCAAGAAAA
1 ATGTTAAAACTGAACCAAGAAAA
287262 A
1 A
287263 CTTTATTTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 13 0.62
23 8 0.38
ACGTcount: A:0.59, C:0.07, G:0.13, T:0.22
Consensus pattern (23 bp):
ATGTTAAAACTGAACCAAGAAAA
Found at i:289254 original size:41 final size:41
Alignment explanation
Indices: 289197--289274 Score: 122
Period size: 41 Copynumber: 1.9 Consensus size: 41
289187 AACCCATCTA
*
289197 CAACCAATAATTGACTTACCAA-GAAGGAGTTTCACATTCTC
1 CAACCAATAATTGACTTACCAACAAAGG-GTTTCACATTCTC
*
289238 CAACCAATAATTGACTTTCCAACAAAGGGTTTCACAT
1 CAACCAATAATTGACTTACCAACAAAGGGTTTCACAT
289275 GTTCCCAAGA
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
41 30 0.88
42 4 0.12
ACGTcount: A:0.37, C:0.24, G:0.12, T:0.27
Consensus pattern (41 bp):
CAACCAATAATTGACTTACCAACAAAGGGTTTCACATTCTC
Found at i:293287 original size:22 final size:22
Alignment explanation
Indices: 293261--293308 Score: 96
Period size: 22 Copynumber: 2.2 Consensus size: 22
293251 CTTAATTTTT
293261 TTTATAATCCAACAAATTTCAG
1 TTTATAATCCAACAAATTTCAG
293283 TTTATAATCCAACAAATTTCAG
1 TTTATAATCCAACAAATTTCAG
293305 TTTA
1 TTTA
293309 CTTAATTTGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.40, C:0.17, G:0.04, T:0.40
Consensus pattern (22 bp):
TTTATAATCCAACAAATTTCAG
Found at i:295820 original size:2 final size:2
Alignment explanation
Indices: 295807--295836 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
295797 ATTAGACATT
*
295807 AG AG AG AC AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
295837 CTCCATGGAG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.03, G:0.47, T:0.00
Consensus pattern (2 bp):
AG
Found at i:296303 original size:2 final size:2
Alignment explanation
Indices: 296296--296325 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
296286 TCTTCCCTCC
296296 CT 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
296326 TGTTGTTACG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:297507 original size:2 final size:2
Alignment explanation
Indices: 297502--297531 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
297492 TTGTATATGC
297502 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
297532 TAAATTATAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:303346 original size:42 final size:38
Alignment explanation
Indices: 303275--303369 Score: 115
Period size: 42 Copynumber: 2.4 Consensus size: 38
303265 ATGTGAATTT
303275 TTTAAAAA-A-TAAAAATATTATAATTAAAATTTTTGAA
1 TTTAAAAATATTAAAAATATTATAATTAAAATTTTT-AA
*
303312 TATTAAAATTATATTAAAAATA-TATATTTCAAAATTTTTAA
1 T-TTAAAA--ATATTAAAAATATTATAATT-AAAATTTTTAA
303353 TTTAAAAATATTAAAAA
1 TTTAAAAATATTAAAAA
303370 AAAAAAGATG
Statistics
Matches: 51, Mismatches: 1, Indels: 11
0.81 0.02 0.17
Matches are distributed among these distances:
37 1 0.02
38 16 0.31
40 7 0.14
41 10 0.20
42 17 0.33
ACGTcount: A:0.56, C:0.01, G:0.01, T:0.42
Consensus pattern (38 bp):
TTTAAAAATATTAAAAATATTATAATTAAAATTTTTAA
Found at i:303502 original size:16 final size:15
Alignment explanation
Indices: 303479--303554 Score: 65
Period size: 13 Copynumber: 5.4 Consensus size: 15
303469 GTATAAAATT
303479 TTTAATTAAATAAAA
1 TTTAATTAAATAAAA
303494 TTATAATT-AATAAAA
1 TT-TAATTAAATAAAA
* *
303509 TTTATTTAAAT-ATA
1 TTTAATTAAATAAAA
*
303523 TTTTA-TAAAT-AAA
1 TTTAATTAAATAAAA
*
303536 TTTAA--AATTAAAA
1 TTTAATTAAATAAAA
303549 TTTAAT
1 TTTAAT
303555 CATATAAAAA
Statistics
Matches: 50, Mismatches: 7, Indels: 9
0.76 0.11 0.14
Matches are distributed among these distances:
12 3 0.06
13 19 0.38
14 9 0.18
15 14 0.28
16 5 0.10
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (15 bp):
TTTAATTAAATAAAA
Found at i:303507 original size:15 final size:16
Alignment explanation
Indices: 303471--303520 Score: 59
Period size: 15 Copynumber: 3.2 Consensus size: 16
303461 CCCGCCTCGT
*
303471 ATAAAATTTTTAATTAA
1 ATAAAA-TTATAATTAA
303488 ATAAAATTATAATT-A
1 ATAAAATTATAATTAA
*
303503 ATAAAATT-TATTTAA
1 ATAAAATTATAATTAA
303518 ATA
1 ATA
303521 TATTTTATAA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
14 4 0.13
15 13 0.43
16 7 0.23
17 6 0.20
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (16 bp):
ATAAAATTATAATTAA
Found at i:303598 original size:17 final size:17
Alignment explanation
Indices: 303572--303605 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
303562 AAAATTTATA
*
303572 TAAAATATAAAATAAAT
1 TAAAACATAAAATAAAT
*
303589 TAAAACATAATATAAAT
1 TAAAACATAAAATAAAT
303606 ATAATATTAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.29
Consensus pattern (17 bp):
TAAAACATAAAATAAAT
Found at i:303614 original size:24 final size:24
Alignment explanation
Indices: 303575--303636 Score: 76
Period size: 24 Copynumber: 2.7 Consensus size: 24
303565 ATTTATATAA
*
303575 AATATAAA-ATAA-ATTAAAACAT
1 AATATAAATATAATATTAAAAAAT
303597 AATATAAATATAATATTAAAAAAT
1 AATATAAATATAATATTAAAAAAT
*
303621 AATGA-AAATAAAATAT
1 AAT-ATAAATATAATAT
303637 GACTTAAAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
22 8 0.23
23 4 0.11
24 22 0.63
25 1 0.03
ACGTcount: A:0.68, C:0.02, G:0.02, T:0.29
Consensus pattern (24 bp):
AATATAAATATAATATTAAAAAAT
Found at i:303721 original size:18 final size:18
Alignment explanation
Indices: 303676--303727 Score: 60
Period size: 18 Copynumber: 3.1 Consensus size: 18
303666 ATACATAAAC
303676 ATATAAATATTTATATAA
1 ATATAAATATTTATATAA
303694 A-AT-AA-A-TTAT-TAA
1 ATATAAATATTTATATAA
303707 TATATAAATATTTATATAA
1 -ATATAAATATTTATATAA
303726 AT
1 AT
303728 TTAAGATAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 12
0.70 0.00 0.30
Matches are distributed among these distances:
13 3 0.11
14 5 0.18
15 3 0.11
16 4 0.14
17 3 0.11
18 7 0.25
19 3 0.11
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (18 bp):
ATATAAATATTTATATAA
Found at i:304311 original size:10 final size:10
Alignment explanation
Indices: 304296--304358 Score: 53
Period size: 10 Copynumber: 6.5 Consensus size: 10
304286 GAATACACGT
304296 ATATATAAAA
1 ATATATAAAA
304306 ATATATATAAA
1 ATATATA-AAA
304317 ATA-A-AATAA
1 ATATATAA-AA
* *
304326 AT-TATTAAT
1 ATATATAAAA
304335 ATATA-AAAA
1 ATATATAAAA
*
304344 ATATACAAAA
1 ATATATAAAA
304354 ATATA
1 ATATA
304359 ATATTTTAAA
Statistics
Matches: 43, Mismatches: 4, Indels: 12
0.73 0.07 0.20
Matches are distributed among these distances:
8 1 0.02
9 16 0.37
10 20 0.47
11 6 0.14
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.32
Consensus pattern (10 bp):
ATATATAAAA
Found at i:304342 original size:37 final size:34
Alignment explanation
Indices: 304296--304382 Score: 99
Period size: 37 Copynumber: 2.5 Consensus size: 34
304286 GAATACACGT
304296 ATATATAAAAATATATATAAAATAAAATAA-ATTATTA
1 ATATATAAAAA-ATATA-AAAA-AAAATAATATT-TTA
* *
304333 ATATATAAAAAATATACAAAAATATAATATTTTA
1 ATATATAAAAAATATAAAAAAAAATAATATTTTA
304367 A-ATATAAAAAA-ATAAA
1 ATATATAAAAAATATAAA
304383 TACCAACATA
Statistics
Matches: 46, Mismatches: 3, Indels: 7
0.82 0.05 0.12
Matches are distributed among these distances:
32 4 0.09
33 10 0.22
34 10 0.22
35 6 0.13
36 5 0.11
37 11 0.24
ACGTcount: A:0.67, C:0.01, G:0.00, T:0.32
Consensus pattern (34 bp):
ATATATAAAAAATATAAAAAAAAATAATATTTTA
Found at i:304413 original size:9 final size:8
Alignment explanation
Indices: 304397--304447 Score: 57
Period size: 8 Copynumber: 5.9 Consensus size: 8
304387 AACATATAAT
304397 TTTTTTTC
1 TTTTTTTC
304405 TTTTCTTTC
1 TTTT-TTTC
*
304414 TTTTTTTA
1 TTTTTTTC
304422 TTTTTTTC
1 TTTTTTTC
304430 TCCTTTCTTTC
1 T--TTT-TTTC
304441 TTTTTTT
1 TTTTTTT
304448 TTCAACGAAA
Statistics
Matches: 37, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
8 18 0.49
9 11 0.30
10 3 0.08
11 5 0.14
ACGTcount: A:0.02, C:0.16, G:0.00, T:0.82
Consensus pattern (8 bp):
TTTTTTTC
Found at i:304426 original size:23 final size:24
Alignment explanation
Indices: 304396--304450 Score: 71
Period size: 23 Copynumber: 2.4 Consensus size: 24
304386 CAACATATAA
*
304396 TTTTTTTTCTT-TTCTTTCTTT-T
1 TTTTTTTTCTTCTCCTTTCTTTCT
304418 TTTATTTTT-TTCTCCTTTCTTTCT
1 TTT-TTTTTCTTCTCCTTTCTTTCT
304442 TTTTTTTTC
1 TTTTTTTTC
304451 AACGAAATAA
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
22 5 0.18
23 19 0.68
24 4 0.14
ACGTcount: A:0.02, C:0.16, G:0.00, T:0.82
Consensus pattern (24 bp):
TTTTTTTTCTTCTCCTTTCTTTCT
Found at i:304436 original size:27 final size:26
Alignment explanation
Indices: 304395--304447 Score: 88
Period size: 27 Copynumber: 2.0 Consensus size: 26
304385 CCAACATATA
*
304395 ATTTTTTTTCTTTTCTTTCTTTTTTT
1 ATTTTTTTTCCTTTCTTTCTTTTTTT
304421 ATTTTTTTCTCCTTTCTTTCTTTTTTT
1 ATTTTTTT-TCCTTTCTTTCTTTTTTT
304448 TTCAACGAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
26 8 0.32
27 17 0.68
ACGTcount: A:0.04, C:0.15, G:0.00, T:0.81
Consensus pattern (26 bp):
ATTTTTTTTCCTTTCTTTCTTTTTTT
Found at i:304851 original size:14 final size:13
Alignment explanation
Indices: 304832--304872 Score: 55
Period size: 13 Copynumber: 3.1 Consensus size: 13
304822 TACGGATAGA
304832 TTTCTTTTCCTTTT
1 TTTCTTTT-CTTTT
*
304846 TTTCTTTTGTTTT
1 TTTCTTTTCTTTT
*
304859 TTTTTTTTCTTTT
1 TTTCTTTTCTTTT
304872 T
1 T
304873 GGGTTTAAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
13 16 0.67
14 8 0.33
ACGTcount: A:0.00, C:0.12, G:0.02, T:0.85
Consensus pattern (13 bp):
TTTCTTTTCTTTT
Found at i:305175 original size:16 final size:18
Alignment explanation
Indices: 305142--305202 Score: 65
Period size: 17 Copynumber: 3.4 Consensus size: 18
305132 TCAAAATTTT
305142 AATTTTTATATATTTTTT-G
1 AATTTTT-T-TATTTTTTAG
305161 AAATTTTTTTATTTTTTAG
1 -AATTTTTTTATTTTTTAG
*
305180 AA-TTTTTTA-TTTTTAT
1 AATTTTTTTATTTTTTAG
305196 AATTTTT
1 AATTTTT
305203 GTTTTATGAT
Statistics
Matches: 38, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
16 8 0.21
17 11 0.29
18 10 0.26
19 2 0.05
20 7 0.18
ACGTcount: A:0.26, C:0.00, G:0.03, T:0.70
Consensus pattern (18 bp):
AATTTTTTTATTTTTTAG
Found at i:305207 original size:15 final size:16
Alignment explanation
Indices: 305165--305202 Score: 58
Period size: 16 Copynumber: 2.3 Consensus size: 16
305155 TTTTTGAAAT
305165 TTTTTTATTTTTTAGAA
1 TTTTTTA-TTTTTAGAA
*
305182 TTTTTTATTTTTATAA
1 TTTTTTATTTTTAGAA
305198 TTTTT
1 TTTTT
305203 GTTTTATGAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
16 13 0.65
17 7 0.35
ACGTcount: A:0.21, C:0.00, G:0.03, T:0.76
Consensus pattern (16 bp):
TTTTTTATTTTTAGAA
Found at i:306209 original size:13 final size:13
Alignment explanation
Indices: 306193--306244 Score: 51
Period size: 13 Copynumber: 4.3 Consensus size: 13
306183 AAATTAGCTT
306193 AATAAATATTTAA
1 AATAAATATTTAA
306206 AAT--ATATTT--
1 AATAAATATTTAA
*
306215 AATAAA-ATTTATT
1 AATAAATATTTA-A
306228 AATAAATATTTAA
1 AATAAATATTTAA
306241 AATA
1 AATA
306245 TATTTAGTAA
Statistics
Matches: 32, Mismatches: 1, Indels: 12
0.71 0.02 0.27
Matches are distributed among these distances:
9 3 0.09
10 4 0.12
11 7 0.22
13 13 0.41
14 5 0.16
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (13 bp):
AATAAATATTTAA
Found at i:306212 original size:11 final size:12
Alignment explanation
Indices: 306191--306250 Score: 65
Period size: 11 Copynumber: 5.2 Consensus size: 12
306181 TCAAATTAGC
306191 TTAATAA-ATAT
1 TTAATAATATAT
306202 TTAA-AATATAT
1 TTAATAATATAT
* *
306213 TTAATAAAATTT
1 TTAATAATATAT
306225 ATTAATAA-ATAT
1 -TTAATAATATAT
306237 TTAA-AATATAT
1 TTAATAATATAT
306248 TTA
1 TTA
306251 GTAAAACATA
Statistics
Matches: 42, Mismatches: 3, Indels: 8
0.79 0.06 0.15
Matches are distributed among these distances:
10 4 0.10
11 23 0.55
12 8 0.19
13 7 0.17
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (12 bp):
TTAATAATATAT
Found at i:310464 original size:19 final size:19
Alignment explanation
Indices: 310440--310504 Score: 70
Period size: 21 Copynumber: 3.6 Consensus size: 19
310430 TAGCCAAACT
310440 TGTATCGATACACAAAATA
1 TGTATCGATACACAAAATA
310459 TGTATCGAT--AC---A-A
1 TGTATCGATACACAAAATA
310472 TGTATCGATACACAAAAAATA
1 TGTATCGATACAC--AAAATA
310493 TGTATCGATACA
1 TGTATCGATACA
310505 TTGGCTTGTA
Statistics
Matches: 38, Mismatches: 0, Indels: 14
0.73 0.00 0.27
Matches are distributed among these distances:
13 10 0.26
14 1 0.03
15 2 0.05
17 2 0.05
19 9 0.24
20 1 0.03
21 13 0.34
ACGTcount: A:0.45, C:0.15, G:0.12, T:0.28
Consensus pattern (19 bp):
TGTATCGATACACAAAATA
Found at i:310476 original size:13 final size:13
Alignment explanation
Indices: 310458--310483 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
310448 TACACAAAAT
310458 ATGTATCGATACA
1 ATGTATCGATACA
310471 ATGTATCGATACA
1 ATGTATCGATACA
310484 CAAAAAATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:310481 original size:32 final size:33
Alignment explanation
Indices: 310440--310504 Score: 114
Period size: 34 Copynumber: 2.0 Consensus size: 33
310430 TAGCCAAACT
310440 TGTATCGATACAC-AAAATATGTATCGATACAA
1 TGTATCGATACACAAAAATATGTATCGATACAA
310472 TGTATCGATACACAAAAAATATGTATCGATACA
1 TGTATCGATACAC-AAAAATATGTATCGATACA
310505 TTGGCTTGTA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
32 13 0.42
34 18 0.58
ACGTcount: A:0.45, C:0.15, G:0.12, T:0.28
Consensus pattern (33 bp):
TGTATCGATACACAAAAATATGTATCGATACAA
Found at i:314568 original size:15 final size:15
Alignment explanation
Indices: 314548--314578 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
314538 TAAAAATGTC
*
314548 CAAAATGAGGAAGCT
1 CAAAATGAAGAAGCT
314563 CAAAATGAAGAAGCT
1 CAAAATGAAGAAGCT
314578 C
1 C
314579 CAAACGAAAT
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:0.48, C:0.16, G:0.23, T:0.13
Consensus pattern (15 bp):
CAAAATGAAGAAGCT
Found at i:316658 original size:13 final size:13
Alignment explanation
Indices: 316640--316690 Score: 93
Period size: 13 Copynumber: 3.9 Consensus size: 13
316630 GGAAATTCAA
316640 TGTATCGATACAC
1 TGTATCGATACAC
*
316653 TGTATCGATACAA
1 TGTATCGATACAC
316666 TGTATCGATACAC
1 TGTATCGATACAC
316679 TGTATCGATACA
1 TGTATCGATACA
316691 GGGGGATTAT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 36 1.00
ACGTcount: A:0.33, C:0.20, G:0.16, T:0.31
Consensus pattern (13 bp):
TGTATCGATACAC
Found at i:316673 original size:26 final size:26
Alignment explanation
Indices: 316637--316690 Score: 108
Period size: 26 Copynumber: 2.1 Consensus size: 26
316627 TCTGGAAATT
316637 CAATGTATCGATACACTGTATCGATA
1 CAATGTATCGATACACTGTATCGATA
316663 CAATGTATCGATACACTGTATCGATA
1 CAATGTATCGATACACTGTATCGATA
316689 CA
1 CA
316691 GGGGGATTAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.35, C:0.20, G:0.15, T:0.30
Consensus pattern (26 bp):
CAATGTATCGATACACTGTATCGATA
Found at i:316845 original size:20 final size:20
Alignment explanation
Indices: 316802--316847 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 20
316792 AAATCTTTTG
316802 CAAAATACTTGTTTTTCACTT
1 CAAAATACTTGTTTTTCAC-T
*
316823 CAAATTACTTCGTTTTTCA-T
1 CAAAATACTT-GTTTTTCACT
316843 CAAAA
1 CAAAA
316848 CCAGCATCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
20 5 0.23
21 9 0.41
22 8 0.36
ACGTcount: A:0.33, C:0.20, G:0.04, T:0.43
Consensus pattern (20 bp):
CAAAATACTTGTTTTTCACT
Found at i:319257 original size:13 final size:13
Alignment explanation
Indices: 319239--319264 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
319229 TACACAAAAT
319239 ATGTATCGATACA
1 ATGTATCGATACA
319252 ATGTATCGATACA
1 ATGTATCGATACA
319265 CAAAAAATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:319262 original size:32 final size:33
Alignment explanation
Indices: 319221--319285 Score: 105
Period size: 34 Copynumber: 2.0 Consensus size: 33
319211 TAGCCAAACT
*
319221 TGTATCGATACAC-AAAATATGTATCGATACAA
1 TGTATCGATACACAAAAATATGTATCAATACAA
319253 TGTATCGATACACAAAAAATATGTATCAATACA
1 TGTATCGATACAC-AAAAATATGTATCAATACA
319286 TTGGCTTGTA
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
32 13 0.43
34 17 0.57
ACGTcount: A:0.46, C:0.15, G:0.11, T:0.28
Consensus pattern (33 bp):
TGTATCGATACACAAAAATATGTATCAATACAA
Found at i:325781 original size:20 final size:20
Alignment explanation
Indices: 325721--325771 Score: 84
Period size: 20 Copynumber: 2.5 Consensus size: 20
325711 GTCAACTAAA
* *
325721 TGTATCGATAAAAATAGTGT
1 TGTATCGATACAAATAGTAT
325741 TGTATCGATACAAATAGTAT
1 TGTATCGATACAAATAGTAT
325761 TGTATCGATAC
1 TGTATCGATAC
325772 TTCTAGTATT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.37, C:0.10, G:0.18, T:0.35
Consensus pattern (20 bp):
TGTATCGATACAAATAGTAT
Found at i:326561 original size:13 final size:13
Alignment explanation
Indices: 326543--326572 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
326533 GATACATCAG
*
326543 ACATTGTATCGAT
1 ACATTGTATCAAT
326556 ACATTGTATCAAT
1 ACATTGTATCAAT
326569 ACAT
1 ACAT
326573 AGTAAAAAGT
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:0.37, C:0.17, G:0.10, T:0.37
Consensus pattern (13 bp):
ACATTGTATCAAT
Found at i:328456 original size:19 final size:19
Alignment explanation
Indices: 328432--328470 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
328422 AATTTGGAGA
*
328432 AAATGAAGATGGCACTATT
1 AAATGAAAATGGCACTATT
328451 AAATGAAAATGGCACTATT
1 AAATGAAAATGGCACTATT
328470 A
1 A
328471 GCATTTTTGT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.46, C:0.10, G:0.18, T:0.26
Consensus pattern (19 bp):
AAATGAAAATGGCACTATT
Found at i:329153 original size:13 final size:13
Alignment explanation
Indices: 329135--329159 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
329125 CATAAAGTGT
329135 TGTATCGATACAA
1 TGTATCGATACAA
329148 TGTATCGATACA
1 TGTATCGATACA
329160 TAAGTGTTGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:329170 original size:32 final size:32
Alignment explanation
Indices: 329115--329215 Score: 166
Period size: 32 Copynumber: 3.1 Consensus size: 32
329105 TTCAACGATT
329115 TGTATCGATACATAAAGTGTTGTATCGATACAA
1 TGTATCGATACAT-AAGTGTTGTATCGATACAA
*
329148 TGTATCGATACATAAGTGTTGTATCGAAACAA
1 TGTATCGATACATAAGTGTTGTATCGATACAA
* *
329180 TGGATCGATACATAAGTTTTGTATCGATACAA
1 TGTATCGATACATAAGTGTTGTATCGATACAA
329212 TGTA
1 TGTA
329216 AGCTACTACC
Statistics
Matches: 63, Mismatches: 5, Indels: 1
0.91 0.07 0.01
Matches are distributed among these distances:
32 50 0.79
33 13 0.21
ACGTcount: A:0.36, C:0.12, G:0.19, T:0.34
Consensus pattern (32 bp):
TGTATCGATACATAAGTGTTGTATCGATACAA
Found at i:329172 original size:19 final size:19
Alignment explanation
Indices: 329114--329210 Score: 83
Period size: 19 Copynumber: 5.7 Consensus size: 19
329104 TTTCAACGAT
329114 TTGTATCGATACATAAAGTG
1 TTGTATCGATACAT-AAGTG
329134 TTGTATCGATAC--AA---
1 TTGTATCGATACATAAGTG
329148 -TGTATCGATACATAAGTG
1 TTGTATCGATACATAAGTG
*
329166 TTGTATCGA-A-ACAA-TG
1 TTGTATCGATACATAAGTG
*
329182 --G-ATCGATACATAAGTT
1 TTGTATCGATACATAAGTG
329198 TTGTATCGATACA
1 TTGTATCGATACA
329211 ATGTAAGCTA
Statistics
Matches: 62, Mismatches: 3, Indels: 25
0.69 0.03 0.28
Matches are distributed among these distances:
13 16 0.26
14 2 0.03
15 5 0.08
16 3 0.05
17 5 0.08
18 2 0.03
19 17 0.27
20 12 0.19
ACGTcount: A:0.35, C:0.12, G:0.19, T:0.34
Consensus pattern (19 bp):
TTGTATCGATACATAAGTG
Found at i:329271 original size:13 final size:13
Alignment explanation
Indices: 329253--329277 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
329243 ATTACTCAAA
329253 TGTATCGATACAT
1 TGTATCGATACAT
329266 TGTATCGATACA
1 TGTATCGATACA
329278 CTGATCTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:329331 original size:52 final size:52
Alignment explanation
Indices: 329286--329414 Score: 231
Period size: 52 Copynumber: 2.5 Consensus size: 52
329276 CACTGATCTT
* *
329286 TGTATCGATACATGCTGGCAAATTTGCCCAGATGTATCGACACACTATAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
*
329338 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATGAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
329390 TGTATCGATACATGCAGGCAAATTT
1 TGTATCGATACATGCAGGCAAATTT
329415 TCATATTTTG
Statistics
Matches: 74, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 74 1.00
ACGTcount: A:0.34, C:0.19, G:0.19, T:0.28
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
Found at i:343279 original size:20 final size:18
Alignment explanation
Indices: 343255--343349 Score: 83
Period size: 20 Copynumber: 5.3 Consensus size: 18
343245 TGTCCTCCAT
*
343255 AAAAAAAAACCAAATAAAC
1 AAAAAAAAAACAAA-AAAC
343274 AGAAAAAAAAACAAAAAAC
1 A-AAAAAAAAACAAAAAAC
343293 ---AAAAAAAC-AAAAA-
1 AAAAAAAAAACAAAAAAC
* *
343306 AAAAATAAAGCAAAAAAC
1 AAAAAAAAAACAAAAAAC
343324 AAAAACAAAAACAACAACAAC
1 AAAAA-AAAAACAA-AA-AAC
343345 AAAAA
1 AAAAA
343350 GGGTCCGGAT
Statistics
Matches: 62, Mismatches: 5, Indels: 16
0.75 0.06 0.19
Matches are distributed among these distances:
14 5 0.08
15 8 0.13
16 6 0.10
17 5 0.08
18 5 0.08
19 11 0.18
20 14 0.23
21 8 0.13
ACGTcount: A:0.82, C:0.14, G:0.02, T:0.02
Consensus pattern (18 bp):
AAAAAAAAAACAAAAAAC
Found at i:343291 original size:12 final size:12
Alignment explanation
Indices: 343270--343337 Score: 64
Period size: 12 Copynumber: 5.5 Consensus size: 12
343260 AAAACCAAAT
*
343270 AAACAGAAAAAA
1 AAACAAAAAAAA
343282 AAACAAAAAACAA
1 AAACAAAAAA-AA
*
343295 AAAAACAAAAAAA
1 AAACA-AAAAAAA
* **
343308 AAATAAAGCAAA
1 AAACAAAAAAAA
*
343320 AAACAAAAACAA
1 AAACAAAAAAAA
343332 AAACAA
1 AAACAA
343338 CAACAACAAA
Statistics
Matches: 45, Mismatches: 9, Indels: 4
0.78 0.16 0.07
Matches are distributed among these distances:
12 28 0.62
13 12 0.27
14 5 0.11
ACGTcount: A:0.84, C:0.12, G:0.03, T:0.01
Consensus pattern (12 bp):
AAACAAAAAAAA
Found at i:343298 original size:15 final size:15
Alignment explanation
Indices: 343278--343349 Score: 80
Period size: 15 Copynumber: 4.9 Consensus size: 15
343268 ATAAACAGAA
343278 AAAAAAACAAAAAAC
1 AAAAAAACAAAAAAC
343293 AAAAAAACAAAAAA-
1 AAAAAAACAAAAAAC
343307 AAAATAAAGCAAAAAAC
1 AAAA-AAA-CAAAAAAC
343324 --AAAAAC-AAAAAC
1 AAAAAAACAAAAAAC
*
343336 AACAACAACAAAAA
1 AA-AAAAACAAAAA
343350 GGGTCCGGAT
Statistics
Matches: 49, Mismatches: 1, Indels: 13
0.78 0.02 0.21
Matches are distributed among these distances:
12 6 0.12
13 1 0.02
14 7 0.14
15 24 0.49
16 11 0.22
ACGTcount: A:0.83, C:0.14, G:0.01, T:0.01
Consensus pattern (15 bp):
AAAAAAACAAAAAAC
Found at i:343346 original size:6 final size:6
Alignment explanation
Indices: 343270--343343 Score: 57
Period size: 6 Copynumber: 12.0 Consensus size: 6
343260 AAAACCAAAT
343270 AAACAGA AAA-AA AAACAAA AAACAA AAA-AA CAAA-AA AAA-AA TAAAGCAAA
1 AAACA-A AAACAA AAAC-AA AAACAA AAACAA -AAACAA AAACAA -AAA-C-AA
*
343320 AAACAA AAACAA AAACAA CAACAA
1 AAACAA AAACAA AAACAA AAACAA
343344 CAAAAAGGGT
Statistics
Matches: 59, Mismatches: 1, Indels: 15
0.79 0.01 0.20
Matches are distributed among these distances:
5 11 0.19
6 33 0.56
7 10 0.17
8 3 0.05
9 2 0.03
ACGTcount: A:0.82, C:0.14, G:0.03, T:0.01
Consensus pattern (6 bp):
AAACAA
Found at i:344862 original size:29 final size:29
Alignment explanation
Indices: 344821--345171 Score: 571
Period size: 29 Copynumber: 12.0 Consensus size: 29
344811 GGCACCTTTT
344821 TCTTTT-CAAAGCCCACAAGTCAGTGGCA
1 TCTTTTCCAAAGCCCACAAGTCAGTGGCA
344849 TCTTTTCCAAAGCCCACAAGTCAGTGGCA
1 TCTTTTCCAAAGCCCACAAGTCAGTGGCA
344878 TCTTTTCCAAAGCCCACAAGTCAGTGGCA
1 TCTTTTCCAAAGCCCACAAGTCAGTGGCA
*
344907 CCCTTTTCCAAAGCCCACAAGTCAGTGGCA
1 -TCTTTTCCAAAGCCCACAAGTCAGTGGCA
344937 TCTTTTCCAAAGCCCACAAGTCAGTGGCA
1 TCTTTTCCAAAGCCCACAAGTCAGTGGCA
344966 TCTTTTCCAAAGCCCACAAGTCAGTGGCA
1 TCTTTTCCAAAGCCCACAAGTCAGTGGCA
* *
344995 CCCTTTTCCAAAGCCCACAAGTCAGTGGTA
1 -TCTTTTCCAAAGCCCACAAGTCAGTGGCA
*
345025 TCTTTTCAAAAGCCCACAAGTCAGTGGCA
1 TCTTTTCCAAAGCCCACAAGTCAGTGGCA
345054 -CATTTTTCCAAAGCCCACAAGTCAGTGGCA
1 TC--TTTTCCAAAGCCCACAAGTCAGTGGCA
345084 TCTTTTCCAAAGCCCACAAGTCAGTGGCA
1 TCTTTTCCAAAGCCCACAAGTCAGTGGCA
* *
345113 CCCTTTTCCAAAGCCCACAAGTCAGTGGTA
1 -TCTTTTCCAAAGCCCACAAGTCAGTGGCA
* *
345143 TCTCTTCAAAAGCCCACAAGTCAGTGGCA
1 TCTTTTCCAAAGCCCACAAGTCAGTGGCA
345172 ACCTTCAAAA
Statistics
Matches: 302, Mismatches: 14, Indels: 13
0.92 0.04 0.04
Matches are distributed among these distances:
28 7 0.02
29 186 0.62
30 108 0.36
31 1 0.00
ACGTcount: A:0.28, C:0.31, G:0.17, T:0.23
Consensus pattern (29 bp):
TCTTTTCCAAAGCCCACAAGTCAGTGGCA
Found at i:344930 original size:59 final size:58
Alignment explanation
Indices: 344821--345171 Score: 571
Period size: 59 Copynumber: 6.0 Consensus size: 58
344811 GGCACCTTTT
344821 TCTTTT-CAAAGCCCACAAGTCAGTGGCATCTTTTCCAAAGCCCACAAGTCAGTGGCA
1 TCTTTTCCAAAGCCCACAAGTCAGTGGCATCTTTTCCAAAGCCCACAAGTCAGTGGCA
*
344878 TCTTTTCCAAAGCCCACAAGTCAGTGGCACCCTTTTCCAAAGCCCACAAGTCAGTGGCA
1 TCTTTTCCAAAGCCCACAAGTCAGTGGCA-TCTTTTCCAAAGCCCACAAGTCAGTGGCA
344937 TCTTTTCCAAAGCCCACAAGTCAGTGGCATCTTTTCCAAAGCCCACAAGTCAGTGGCA
1 TCTTTTCCAAAGCCCACAAGTCAGTGGCATCTTTTCCAAAGCCCACAAGTCAGTGGCA
* * *
344995 CCCTTTTCCAAAGCCCACAAGTCAGTGGTATCTTTTCAAAAGCCCACAAGTCAGTGGCA
1 -TCTTTTCCAAAGCCCACAAGTCAGTGGCATCTTTTCCAAAGCCCACAAGTCAGTGGCA
345054 -CATTTTTCCAAAGCCCACAAGTCAGTGGCATCTTTTCCAAAGCCCACAAGTCAGTGGCA
1 TC--TTTTCCAAAGCCCACAAGTCAGTGGCATCTTTTCCAAAGCCCACAAGTCAGTGGCA
* * * *
345113 CCCTTTTCCAAAGCCCACAAGTCAGTGGTATCTCTTCAAAAGCCCACAAGTCAGTGGCA
1 -TCTTTTCCAAAGCCCACAAGTCAGTGGCATCTTTTCCAAAGCCCACAAGTCAGTGGCA
345172 ACCTTCAAAA
Statistics
Matches: 277, Mismatches: 10, Indels: 12
0.93 0.03 0.04
Matches are distributed among these distances:
57 7 0.03
58 50 0.18
59 219 0.79
61 1 0.00
ACGTcount: A:0.28, C:0.31, G:0.17, T:0.23
Consensus pattern (58 bp):
TCTTTTCCAAAGCCCACAAGTCAGTGGCATCTTTTCCAAAGCCCACAAGTCAGTGGCA
Found at i:344948 original size:88 final size:88
Alignment explanation
Indices: 344822--345176 Score: 590
Period size: 88 Copynumber: 4.0 Consensus size: 88
344812 GCACCTTTTT
344822 CTTTT-CAAAGCCCACAAGTCAGTGGCATCTTTTCCAAAGCCCACAAGTCAGTGGCATCTTTTCC
1 CTTTTCCAAAGCCCACAAGTCAGTGGCATCTTTTCCAAAGCCCACAAGTCAGTGGCATCTTTTCC
344886 AAAGCCCACAAGTCAGTGGCACC
66 AAAGCCCACAAGTCAGTGGCACC
344909 CTTTTCCAAAGCCCACAAGTCAGTGGCATCTTTTCCAAAGCCCACAAGTCAGTGGCATCTTTTCC
1 CTTTTCCAAAGCCCACAAGTCAGTGGCATCTTTTCCAAAGCCCACAAGTCAGTGGCATCTTTTCC
344974 AAAGCCCACAAGTCAGTGGCACC
66 AAAGCCCACAAGTCAGTGGCACC
* *
344997 CTTTTCCAAAGCCCACAAGTCAGTGGTATCTTTTCAAAAGCCCACAAGTCAGTGGCA-CATTTTT
1 CTTTTCCAAAGCCCACAAGTCAGTGGCATCTTTTCCAAAGCCCACAAGTCAGTGGCATC--TTTT
*
345061 CCAAAGCCCACAAGTCAGTGGCA-T
64 CCAAAGCCCACAAGTCAGTGGCACC
* * *
345085 CTTTTCCAAAGCCCACAAGTCAGTGGCACCCTTTTCCAAAGCCCACAAGTCAGTGGTATCTCTTC
1 CTTTTCCAAAGCCCACAAGTCAGTGGCA-TCTTTTCCAAAGCCCACAAGTCAGTGGCATCTTTTC
* *
345150 AAAAGCCCACAAGTCAGTGGCAAC
65 CAAAGCCCACAAGTCAGTGGCACC
345174 CTT
1 CTT
345177 CAAAAGCACA
Statistics
Matches: 252, Mismatches: 10, Indels: 10
0.93 0.04 0.04
Matches are distributed among these distances:
87 6 0.02
88 189 0.75
89 56 0.22
90 1 0.00
ACGTcount: A:0.28, C:0.32, G:0.17, T:0.23
Consensus pattern (88 bp):
CTTTTCCAAAGCCCACAAGTCAGTGGCATCTTTTCCAAAGCCCACAAGTCAGTGGCATCTTTTCC
AAAGCCCACAAGTCAGTGGCACC
Found at i:345221 original size:31 final size:28
Alignment explanation
Indices: 345146--345227 Score: 96
Period size: 28 Copynumber: 2.9 Consensus size: 28
345136 AGTGGTATCT
**
345146 CTTCAAAAGCC-CACAAGTCAGTGGCAAC
1 CTTCAAAAGCCACACAAGTTGGT-GCAAC
345174 CTTCAAAAG-CACACAAGTTGGTGCAAC
1 CTTCAAAAGCCACACAAGTTGGTGCAAC
345201 CTTTTCAAAAGCCCACACAAGTTGGTG
1 C--TTCAAAAG-CCACACAAGTTGGTG
345228 GCATCTTCTT
Statistics
Matches: 47, Mismatches: 2, Indels: 7
0.84 0.04 0.12
Matches are distributed among these distances:
27 7 0.15
28 18 0.38
29 8 0.17
31 14 0.30
ACGTcount: A:0.34, C:0.28, G:0.18, T:0.20
Consensus pattern (28 bp):
CTTCAAAAGCCACACAAGTTGGTGCAAC
Found at i:345222 original size:59 final size:57
Alignment explanation
Indices: 344827--345217 Score: 505
Period size: 59 Copynumber: 6.7 Consensus size: 57
344817 TTTTTCTTTT
* *
344827 CAAAGCCCACAAGTCAGTGGCATCTTTTCCAAAGCCCACAAGTCAGTGGCATCTTTTC
1 CAAAGCCCACAAGTCAGTGGCATCTTTTCCAAAGCCCACAAGTCAGTGGCAAC-CTTC
* * *
344885 CAAAGCCCACAAGTCAGTGGCACCCTTTTCCAAAGCCCACAAGTCAGTGGCATCTTTTC
1 CAAAGCCCACAAGTCAGTGGCA-TCTTTTCCAAAGCCCACAAGTCAGTGGCAAC-CTTC
*
344944 CAAAGCCCACAAGTCAGTGGCATCTTTTCCAAAGCCCACAAGTCAGTGGCACCCTTTTC
1 CAAAGCCCACAAGTCAGTGGCATCTTTTCCAAAGCCCACAAGTCAGTGGCAACC--TTC
* * **
345003 CAAAGCCCACAAGTCAGTGGTATCTTTTCAAAAGCCCACAAGTCAGTGGCACATTTTTC
1 CAAAGCCCACAAGTCAGTGGCATCTTTTCCAAAGCCCACAAGTCAGTGGCA-A-CCTTC
*
345062 CAAAGCCCACAAGTCAGTGGCATCTTTTCCAAAGCCCACAAGTCAGTGGCACCCTTTTC
1 CAAAGCCCACAAGTCAGTGGCATCTTTTCCAAAGCCCACAAGTCAGTGGCAACC--TTC
* * *
345121 CAAAGCCCACAAGTCAGTGGTATCTCTTCAAAAGCCCACAAGTCAGTGGCAACCTTC
1 CAAAGCCCACAAGTCAGTGGCATCTTTTCCAAAGCCCACAAGTCAGTGGCAACCTTC
* * ** * *
345178 AAAAGCACACAAGTTGGT-GCAACCTTTTCAAAAGCCCACA
1 CAAAGCCCACAAGTCAGTGGC-ATCTTTTCCAAAGCCCACA
345218 CAAGTTGGTG
Statistics
Matches: 300, Mismatches: 25, Indels: 17
0.88 0.07 0.05
Matches are distributed among these distances:
56 1 0.00
57 34 0.11
58 51 0.17
59 214 0.71
ACGTcount: A:0.30, C:0.31, G:0.17, T:0.22
Consensus pattern (57 bp):
CAAAGCCCACAAGTCAGTGGCATCTTTTCCAAAGCCCACAAGTCAGTGGCAACCTTC
Found at i:345222 original size:88 final size:88
Alignment explanation
Indices: 344822--345217 Score: 552
Period size: 88 Copynumber: 4.5 Consensus size: 88
344812 GCACCTTTTT
* *
344822 CTTTTCAAAGCCCACAAGTCAGTGGC-ATCTTTTCCAAAGCCCACAAGTCAGTGGCATCTTTTCC
1 CTTTCCAAAGCCCACAAGTCAGTGGCAACCTTTTCCAAAGCCCACAAGTCAGTGGCATCTTTTCC
344886 AAAGCCCACAAGTCAGTGGCACC
66 AAAGCCCACAAGTCAGTGGCACC
*
344909 CTTTTCCAAAGCCCACAAGTCAGTGGC-ATCTTTTCCAAAGCCCACAAGTCAGTGGCATCTTTTC
1 C-TTTCCAAAGCCCACAAGTCAGTGGCAACCTTTTCCAAAGCCCACAAGTCAGTGGCATCTTTTC
344973 CAAAGCCCACAAGTCAGTGGCACC
65 CAAAGCCCACAAGTCAGTGGCACC
* * *
344997 CTTTTCCAAAGCCCACAAGTCAGTGG-TATCTTTTCAAAAGCCCACAAGTCAGTGGCA-CATTTT
1 C-TTTCCAAAGCCCACAAGTCAGTGGCAACCTTTTCCAAAGCCCACAAGTCAGTGGCATC--TTT
*
345060 TCCAAAGCCCACAAGTCAGTGGCATC
63 TCCAAAGCCCACAAGTCAGTGGCACC
* * * * *
345086 TTTTCCAAAGCCCACAAGTCAGTGGCACCCTTTTCCAAAGCCCACAAGTCAGTGGTATCTCTTCA
1 CTTTCCAAAGCCCACAAGTCAGTGGCAACCTTTTCCAAAGCCCACAAGTCAGTGGCATCTTTTCC
*
345151 AAAGCCCACAAGTCAGTGGCAAC
66 AAAGCCCACAAGTCAGTGGCACC
* * ** *
345174 C-TTCAAAAGCACACAAGTTGGT-GCAACCTTTTCAAAAGCCCACA
1 CTTTCCAAAGCCCACAAGTCAGTGGCAACCTTTTCCAAAGCCCACA
345218 CAAGTTGGTG
Statistics
Matches: 284, Mismatches: 19, Indels: 13
0.90 0.06 0.04
Matches are distributed among these distances:
86 20 0.07
87 19 0.07
88 190 0.67
89 54 0.19
90 1 0.00
ACGTcount: A:0.29, C:0.31, G:0.17, T:0.23
Consensus pattern (88 bp):
CTTTCCAAAGCCCACAAGTCAGTGGCAACCTTTTCCAAAGCCCACAAGTCAGTGGCATCTTTTCC
AAAGCCCACAAGTCAGTGGCACC
Found at i:345291 original size:43 final size:43
Alignment explanation
Indices: 345239--345466 Score: 231
Period size: 43 Copynumber: 5.0 Consensus size: 43
345229 CATCTTCTTC
345239 TAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCACCTT
1 TAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCACCTT
* * *
345282 TAAGTCCAATATCGCTGGTCTTGAATTAGCATATTGGCACCTTCATCTT
1 TAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCA----C--CTT
** * * * *
345331 TAAAACCCAAATGTCGTTGGCCTTGAATAAACACATTGGCATTCTTCTT
1 T-AAGTCC-AATATCGCTGGCCTTGAATCAGCACATTGGCA--C--CTT
345380 CTAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCACCTT
1 -TAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCACCTT
* * *
345424 TAAGTCCAATATCGCTAGTCTTGAATCAGCATATTGGCACCTT
1 TAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCACCTT
345467 CATCATCTTT
Statistics
Matches: 155, Mismatches: 21, Indels: 18
0.80 0.11 0.09
Matches are distributed among these distances:
43 76 0.49
44 3 0.02
46 1 0.01
47 1 0.01
48 28 0.18
49 15 0.10
50 5 0.03
51 26 0.17
ACGTcount: A:0.27, C:0.25, G:0.17, T:0.32
Consensus pattern (43 bp):
TAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCACCTT
Found at i:353508 original size:49 final size:49
Alignment explanation
Indices: 353447--353618 Score: 197
Period size: 49 Copynumber: 3.5 Consensus size: 49
353437 CAAAAAATGA
* ** *
353447 CAATGTGCTGATTCATTGCCAGCGACGTTGATCTTAAAGATGATGGTGC
1 CAATATGCTGATTCAAGGCCAGCGACGTTGATCTTAAAGATGAAGGTGC
* *
353496 CAATATGCTGATTCAAAGCCAGCGATACCG--GA-CTTAAAGATGAAGATGC
1 CAATATGCTGATTCAAGGCCAGCG--A-CGTTGATCTTAAAGATGAAGGTGC
* * * *
353545 CAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGATGACGGTGC
1 CAATATGCTGATTCAAGGCCAGCGACGTTGATCTTAAAGATGAAGGTGC
*
353594 CACTATGCTGATTCAAGGCCAGCGA
1 CAATATGCTGATTCAAGGCCAGCGA
353619 TATTGAACTT
Statistics
Matches: 104, Mismatches: 13, Indels: 12
0.81 0.10 0.09
Matches are distributed among these distances:
46 1 0.01
47 1 0.01
48 1 0.01
49 96 0.92
50 2 0.02
51 1 0.01
52 2 0.02
ACGTcount: A:0.29, C:0.21, G:0.26, T:0.24
Consensus pattern (49 bp):
CAATATGCTGATTCAAGGCCAGCGACGTTGATCTTAAAGATGAAGGTGC
Found at i:353629 original size:98 final size:96
Alignment explanation
Indices: 353447--353642 Score: 275
Period size: 98 Copynumber: 2.0 Consensus size: 96
353437 CAAAAAATGA
** * *
353447 CAATGTGCTGATTCATTGCCAGCGACGTTGATCTTAAAGATGATGGTGCCAATATGCTGATTCAA
1 CAATGTGCTGATTCAAGGCCAGCGACATTGATCTTAAAGATGACGGTGCCAATATGCTGATTCAA
* *
353512 AGCCAGCGATACCGGACTTAAAGATGAAGATGC
66 AGCCAGCGATACCGAACTT--AGAAGAAGATGC
* *
353545 CAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGATGACGGTGCCACTATGCTGATTCAA
1 CAATGTGCTGATTCAAGGCCAGCGACATTGATCTTAAAGATGACGGTGCCAATATGCTGATTCAA
* **
353610 GGCCAGCGATATTGAACTTAGAAGAAGATGC
66 AGCCAGCGATACCGAACTTAGAAGAAGATGC
353641 CA
1 CA
353643 CCAACTTGTG
Statistics
Matches: 87, Mismatches: 11, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
96 13 0.15
98 74 0.85
ACGTcount: A:0.31, C:0.20, G:0.25, T:0.24
Consensus pattern (96 bp):
CAATGTGCTGATTCAAGGCCAGCGACATTGATCTTAAAGATGACGGTGCCAATATGCTGATTCAA
AGCCAGCGATACCGAACTTAGAAGAAGATGC
Found at i:353716 original size:31 final size:30
Alignment explanation
Indices: 353663--353775 Score: 108
Period size: 27 Copynumber: 3.9 Consensus size: 30
353653 TGGGCTTTTG
* *
353663 AAGGTTGCCATTGACTTGTGGGCTTTGGAAA
1 AAGGTTGCCACTGACTTATGGGCTTT-GAAA
* *
353694 AAGGGTGCCACTGATTTATGGGCTTTG---
1 AAGGTTGCCACTGACTTATGGGCTTTGAAA
*
353721 AATGTTGCCACTGACTTATGGGCTTTGAAA
1 AAGGTTGCCACTGACTTATGGGCTTTGAAA
* * * *
353751 AA-GATGCCACTAACTTGTGTGCTTT
1 AAGGTTGCCACTGACTTATGGGCTTT
353776 TAAAGGGTGA
Statistics
Matches: 68, Mismatches: 11, Indels: 8
0.78 0.13 0.09
Matches are distributed among these distances:
27 24 0.35
29 19 0.28
30 3 0.04
31 22 0.32
ACGTcount: A:0.23, C:0.16, G:0.27, T:0.34
Consensus pattern (30 bp):
AAGGTTGCCACTGACTTATGGGCTTTGAAA
Found at i:353736 original size:58 final size:57
Alignment explanation
Indices: 353653--353761 Score: 157
Period size: 58 Copynumber: 1.9 Consensus size: 57
353643 CCAACTTGTG
* * *
353653 TGGGCTTTTGAAGGTTGCCATTGACTTGTGGGCTTTGGAAAAAGGGTGCCACTGATTTA
1 TGGGCTTTTGAAGGTTGCCACTGACTTATGGGCTTT-GAAAAA-GATGCCACTGATTTA
*
353712 TGGGC-TTTGAATGTTGCCACTGACTTATGGGCTTTGAAAAAGATGCCACT
1 TGGGCTTTTGAAGGTTGCCACTGACTTATGGGCTTTGAAAAAGATGCCACT
353762 AACTTGTGTG
Statistics
Matches: 46, Mismatches: 4, Indels: 3
0.87 0.08 0.06
Matches are distributed among these distances:
56 8 0.17
57 6 0.13
58 27 0.59
59 5 0.11
ACGTcount: A:0.22, C:0.16, G:0.29, T:0.33
Consensus pattern (57 bp):
TGGGCTTTTGAAGGTTGCCACTGACTTATGGGCTTTGAAAAAGATGCCACTGATTTA
Found at i:353739 original size:27 final size:27
Alignment explanation
Indices: 353653--353749 Score: 104
Period size: 27 Copynumber: 3.4 Consensus size: 27
353643 CCAACTTGTG
* *
353653 TGGGCTTTTGAAGGTTGCCATTGACTTG
1 TGGGC-TTTGAAGGTTGCCACTGACTTA
* *
353681 TGGGCTTTGGAAAAAGGGTGCCACTGATTTA
1 TGGGCTTT-G---AAGGTTGCCACTGACTTA
*
353712 TGGGCTTTGAATGTTGCCACTGACTTA
1 TGGGCTTTGAAGGTTGCCACTGACTTA
353739 TGGGCTTTGAA
1 TGGGCTTTGAA
353750 AAAGATGCCA
Statistics
Matches: 58, Mismatches: 7, Indels: 9
0.78 0.09 0.12
Matches are distributed among these distances:
27 29 0.50
28 6 0.10
30 1 0.02
31 22 0.38
ACGTcount: A:0.20, C:0.14, G:0.31, T:0.35
Consensus pattern (27 bp):
TGGGCTTTGAAGGTTGCCACTGACTTA
Found at i:355246 original size:18 final size:17
Alignment explanation
Indices: 355225--355282 Score: 57
Period size: 17 Copynumber: 3.4 Consensus size: 17
355215 TTTATTGTTG
355225 TTGTTTTTGTTATTTTTT
1 TTGTTTTTGTT-TTTTTT
*
355243 TTGTTTTCGTTTTTTGTT
1 TTGTTTTTGTTTTTT-TT
*
355261 TT-TTTCTT-CTTTTTTT
1 TTGTTT-TTGTTTTTTTT
355277 TTGTTT
1 TTGTTT
355283 ATTTGGTTGT
Statistics
Matches: 34, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
16 4 0.12
17 15 0.44
18 15 0.44
ACGTcount: A:0.02, C:0.05, G:0.10, T:0.83
Consensus pattern (17 bp):
TTGTTTTTGTTTTTTTT
Found at i:355246 original size:24 final size:23
Alignment explanation
Indices: 355213--355286 Score: 71
Period size: 24 Copynumber: 3.1 Consensus size: 23
355203 ATCCGGACCC
355213 TTTTTATTGTTGTTGTTTTTGTTA
1 TTTTTATTGTT-TTGTTTTTGTTA
*
355237 TTTTTTTTGTTTTCGTTTTTTGTT-
1 TTTTTATTGTTTT-G-TTTTTGTTA
* *
355261 TTTTTCTTCTTTT-TTTTTGTTTA
1 TTTTTATTGTTTTGTTTTTG-TTA
355284 TTT
1 TTT
355287 GGTTGTTTTT
Statistics
Matches: 43, Mismatches: 3, Indels: 9
0.78 0.05 0.16
Matches are distributed among these distances:
21 6 0.14
22 2 0.05
23 5 0.12
24 22 0.51
25 8 0.19
ACGTcount: A:0.04, C:0.04, G:0.11, T:0.81
Consensus pattern (23 bp):
TTTTTATTGTTTTGTTTTTGTTA
Found at i:355262 original size:21 final size:21
Alignment explanation
Indices: 355238--355287 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
355228 TTTTTGTTAT
355238 TTTTTTTGTT-TTCGTTTTTTG
1 TTTTTTTGTTCTT-GTTTTTTG
* *
355259 TTTTTTTCTTCTTTTTTTTTG
1 TTTTTTTGTTCTTGTTTTTTG
*
355280 TTTATTTG
1 TTTTTTTG
355288 GTTGTTTTTG
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
21 22 0.92
22 2 0.08
ACGTcount: A:0.02, C:0.06, G:0.10, T:0.82
Consensus pattern (21 bp):
TTTTTTTGTTCTTGTTTTTTG
Found at i:369252 original size:52 final size:52
Alignment explanation
Indices: 369104--369232 Score: 231
Period size: 52 Copynumber: 2.5 Consensus size: 52
369094 CGAAATATGA
* *
369104 AAATTTGCCTGCATGTATTGATACATTTCATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTAGGC
*
369156 AAATTTGCCTGCATGTATCGATACATTTTATAGTGTATCGATACATCTAGGC
1 AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTAGGC
369208 AAATTTGCCTGCATGTATCGATACA
1 AAATTTGCCTGCATGTATCGATACA
369233 AAGATCAGTG
Statistics
Matches: 74, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 74 1.00
ACGTcount: A:0.29, C:0.18, G:0.18, T:0.36
Consensus pattern (52 bp):
AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTAGGC
Found at i:369259 original size:13 final size:13
Alignment explanation
Indices: 369241--369265 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
369231 CAAAGATCAG
369241 TGTATCGATACAA
1 TGTATCGATACAA
369254 TGTATCGATACA
1 TGTATCGATACA
369266 TTTGAGTAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:369333 original size:19 final size:18
Alignment explanation
Indices: 369309--369406 Score: 72
Period size: 19 Copynumber: 5.8 Consensus size: 18
369299 TAGCTTACAT
369309 TGTATCGATACAAAACTTA
1 TGTATCGATAC-AAACTTA
*
369328 TGTATCAATAC--A--T-
1 TGTATCGATACAAACTTA
369341 TGTATCGATACAACACTTA
1 TGTATCGATACAA-ACTTA
369360 TGTATCGATAC--A--T-
1 TGTATCGATACAAACTTA
*
369373 TGTATCAATACAACACTTTA
1 TGTATCGATACAA-AC-TTA
369393 TGTATCGATACAAA
1 TGTATCGATACAAA
369407 TCGTTGAAAT
Statistics
Matches: 62, Mismatches: 4, Indels: 26
0.67 0.04 0.28
Matches are distributed among these distances:
13 20 0.32
14 2 0.03
16 4 0.06
18 1 0.02
19 23 0.37
20 12 0.19
ACGTcount: A:0.39, C:0.17, G:0.10, T:0.34
Consensus pattern (18 bp):
TGTATCGATACAAACTTA
Found at i:369345 original size:32 final size:32
Alignment explanation
Indices: 369304--369404 Score: 166
Period size: 32 Copynumber: 3.1 Consensus size: 32
369294 GGCAGTAGCT
* *
369304 TACATTGTATCGATACAAAACTTATGTATCAA
1 TACATTGTATCGATACAACACTTATGTATCGA
369336 TACATTGTATCGATACAACACTTATGTATCGA
1 TACATTGTATCGATACAACACTTATGTATCGA
*
369368 TACATTGTATCAATACAACACTTTATGTATCGA
1 TACATTGTATCGATACAACAC-TTATGTATCGA
369401 TACA
1 TACA
369405 AATCGTTGAA
Statistics
Matches: 65, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
32 50 0.77
33 15 0.23
ACGTcount: A:0.38, C:0.18, G:0.10, T:0.35
Consensus pattern (32 bp):
TACATTGTATCGATACAACACTTATGTATCGA
Found at i:371318 original size:13 final size:13
Alignment explanation
Indices: 371300--371324 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
371290 AATATTCCTT
371300 GTATCGATACATG
1 GTATCGATACATG
371313 GTATCGATACAT
1 GTATCGATACAT
371325 AGGTTACTAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.20, T:0.32
Consensus pattern (13 bp):
GTATCGATACATG
Found at i:373947 original size:13 final size:13
Alignment explanation
Indices: 373929--373959 Score: 62
Period size: 13 Copynumber: 2.4 Consensus size: 13
373919 CGATACATGG
373929 TACATTGTATCAA
1 TACATTGTATCAA
373942 TACATTGTATCAA
1 TACATTGTATCAA
373955 TACAT
1 TACAT
373960 GATAAATTGT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.39, C:0.16, G:0.06, T:0.39
Consensus pattern (13 bp):
TACATTGTATCAA
Found at i:373958 original size:33 final size:33
Alignment explanation
Indices: 373913--373981 Score: 102
Period size: 33 Copynumber: 2.1 Consensus size: 33
373903 CTACCACTGT
* * *
373913 TTGTATCGATACATGGTACATTGTATCAATACA
1 TTGTATCAATACATGATAAATTGTATCAATACA
*
373946 TTGTATCAATACATGATAAATTGTATCGATACA
1 TTGTATCAATACATGATAAATTGTATCAATACA
373979 TTG
1 TTG
373982 CTTCTAACGG
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.35, C:0.13, G:0.14, T:0.38
Consensus pattern (33 bp):
TTGTATCAATACATGATAAATTGTATCAATACA
Found at i:374983 original size:13 final size:13
Alignment explanation
Indices: 374965--374994 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
374955 ACAAGTCATC
*
374965 ATGTATCGATATA
1 ATGTATCGATACA
374978 ATGTATCGATACA
1 ATGTATCGATACA
374991 ATGT
1 ATGT
374995 GCCATGTATC
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:0.37, C:0.10, G:0.17, T:0.37
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:374985 original size:33 final size:33
Alignment explanation
Indices: 374943--375011 Score: 106
Period size: 33 Copynumber: 2.1 Consensus size: 33
374933 CCGTTAGAAG
374943 TAATGTATCGATACAA-GT-CATCATGTATCGATA
1 TAATGTATCGATACAATGTGC--CATGTATCGATA
374976 TAATGTATCGATACAATGTGCCATGTATCGATA
1 TAATGTATCGATACAATGTGCCATGTATCGATA
375009 TAA
1 TAA
375012 ACAATGGTAG
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
33 31 0.91
34 2 0.06
35 1 0.03
ACGTcount: A:0.36, C:0.14, G:0.16, T:0.33
Consensus pattern (33 bp):
TAATGTATCGATACAATGTGCCATGTATCGATA
Found at i:378155 original size:19 final size:19
Alignment explanation
Indices: 378127--378179 Score: 72
Period size: 19 Copynumber: 2.8 Consensus size: 19
378117 CGGTTTTGCT
* *
378127 TTGC-TTGCTGTTGGAGTG
1 TTGCTTTGCTGCTGGAATG
*
378145 TTGCTTTGCTGCTGAAATG
1 TTGCTTTGCTGCTGGAATG
378164 TTGCTTTGCTGCTGGA
1 TTGCTTTGCTGCTGGA
378180 TTGTGTTGGT
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
18 4 0.13
19 26 0.87
ACGTcount: A:0.09, C:0.15, G:0.32, T:0.43
Consensus pattern (19 bp):
TTGCTTTGCTGCTGGAATG
Found at i:379587 original size:25 final size:24
Alignment explanation
Indices: 379558--379608 Score: 75
Period size: 25 Copynumber: 2.1 Consensus size: 24
379548 AATTAATTAA
379558 TTATTACTATTTTATTCTTATATTT
1 TTATTACTATTTTATT-TTATATTT
* *
379583 TTATTATTATTTTATTTTTTATTT
1 TTATTACTATTTTATTTTATATTT
379607 TT
1 TT
379609 TTTGTTATTT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
24 9 0.38
25 15 0.62
ACGTcount: A:0.22, C:0.04, G:0.00, T:0.75
Consensus pattern (24 bp):
TTATTACTATTTTATTTTATATTT
Found at i:379589 original size:11 final size:10
Alignment explanation
Indices: 379565--379628 Score: 53
Period size: 11 Copynumber: 6.4 Consensus size: 10
379555 TAATTATTAC
*
379565 TATTTTATTCT
1 TATTTT-TTAT
379576 TATATTTTTAT
1 TAT-TTTTTAT
*
379587 TA-TTATT-T
1 TATTTTTTAT
379595 TATTTTTTAT
1 TATTTTTTAT
*
379605 T-TTTTTTGT
1 TATTTTTTAT
379614 TATTTTTTTAT
1 TA-TTTTTTAT
379625 TATT
1 TATT
379629 CATGTTAAAT
Statistics
Matches: 43, Mismatches: 5, Indels: 11
0.73 0.08 0.19
Matches are distributed among these distances:
8 3 0.07
9 16 0.37
10 4 0.09
11 17 0.40
12 3 0.07
ACGTcount: A:0.19, C:0.02, G:0.02, T:0.78
Consensus pattern (10 bp):
TATTTTTTAT
Found at i:379589 original size:17 final size:17
Alignment explanation
Indices: 379569--379628 Score: 50
Period size: 18 Copynumber: 3.5 Consensus size: 17
379559 TATTACTATT
*
379569 TTATTCTTATATTTTTA
1 TTATTATTATATTTTTA
*
379586 TTATTATTTTATTTTTTA
1 TTATTATTATA-TTTTTA
* * *
379604 TTTTTTTTGTTATTTTT-
1 TTATTATT-ATATTTTTA
379621 TTATTATT
1 TTATTATT
379629 CATGTTAAAT
Statistics
Matches: 35, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
17 15 0.43
18 17 0.49
19 3 0.09
ACGTcount: A:0.18, C:0.02, G:0.02, T:0.78
Consensus pattern (17 bp):
TTATTATTATATTTTTA
Done.