Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D07
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: 58101237
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1550000 characters in sequence are not A, C, G, or T
File 83 of 199
Found at i:23384802 original size:59 final size:61
Alignment explanation
Indices: 23384732--23384848 Score: 166
Period size: 62 Copynumber: 1.9 Consensus size: 61
23384722 ATCATTTTAC
* * *
23384732 TATTAAATTAATATAATA-TATAT-CAAGAGAAATATTAGATTAAATTTAATATTAAATCT
1 TATTAAATTAATAGAATATTATATACAAGAGAAATATTAAATTAAATTTAAGATTAAATCT
* *
23384791 TATTAAATTAATAGAATATTTATCTACAAGATAAATATTAAATTAAATTTAAGATTAA
1 TATTAAATTAATAGAATA-TTATATACAAGAGAAATATTAAATTAAATTTAAGATTAA
23384849 GATAATCACT
Statistics
Matches: 50, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
59 17 0.34
61 4 0.08
62 29 0.58
ACGTcount: A:0.51, C:0.03, G:0.05, T:0.40
Consensus pattern (61 bp):
TATTAAATTAATAGAATATTATATACAAGAGAAATATTAAATTAAATTTAAGATTAAATCT
Found at i:23386725 original size:21 final size:21
Alignment explanation
Indices: 23386701--23386741 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
23386691 TAATCAATTT
23386701 TAAAT-TTTTATGATGTAAAAA
1 TAAATATTTTAT-ATGTAAAAA
*
23386722 TAAATATTTTATATTTAAAA
1 TAAATATTTTATATGTAAAA
23386742 TAGTAAAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 12 0.67
22 6 0.33
ACGTcount: A:0.49, C:0.00, G:0.05, T:0.46
Consensus pattern (21 bp):
TAAATATTTTATATGTAAAAA
Found at i:23390173 original size:14 final size:14
Alignment explanation
Indices: 23390154--23390207 Score: 56
Period size: 16 Copynumber: 3.8 Consensus size: 14
23390144 CCCCAAGCCC
23390154 TATTTTTATTTATT
1 TATTTTTATTTATT
*
23390168 TATTTTTTTATTTATA
1 TA--TTTTTATTTATT
*
23390184 CATTTTTATTT-TT
1 TATTTTTATTTATT
*
23390197 AATTTTTATTT
1 TATTTTTATTT
23390208 TCTAGATTTA
Statistics
Matches: 34, Mismatches: 4, Indels: 5
0.79 0.09 0.12
Matches are distributed among these distances:
13 11 0.32
14 11 0.32
16 12 0.35
ACGTcount: A:0.22, C:0.02, G:0.00, T:0.76
Consensus pattern (14 bp):
TATTTTTATTTATT
Found at i:23390189 original size:13 final size:13
Alignment explanation
Indices: 23390162--23390207 Score: 58
Period size: 14 Copynumber: 3.5 Consensus size: 13
23390152 CCTATTTTTA
*
23390162 TTTATTTAT-TTT
1 TTTATTTATAATT
23390174 TTTATTTATACATT
1 TTTATTTATA-ATT
*
23390188 TTTATTTTTAATT
1 TTTATTTATAATT
23390201 TTTATTT
1 TTTATTT
23390208 TCTAGATTTA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
12 9 0.30
13 10 0.33
14 11 0.37
ACGTcount: A:0.22, C:0.02, G:0.00, T:0.76
Consensus pattern (13 bp):
TTTATTTATAATT
Found at i:23390194 original size:36 final size:35
Alignment explanation
Indices: 23390154--23390240 Score: 97
Period size: 36 Copynumber: 2.5 Consensus size: 35
23390144 CCCCAAGCCC
**
23390154 TATTTTTATTTATTTATTTT-TTTATTTATACATTTT
1 TATTTTTATTT-TTTATTTTCTAGATTTATACA-TTT
* *
23390190 TATTTTTAATTTTTATTTTCTAGATTTATATATTT
1 TATTTTTATTTTTTATTTTCTAGATTTATACATTT
23390225 TA-TTTTATTTTATTAT
1 TATTTTTATTTT-TTAT
23390241 GCATTTTTTG
Statistics
Matches: 44, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
34 8 0.18
35 17 0.39
36 19 0.43
ACGTcount: A:0.24, C:0.02, G:0.01, T:0.72
Consensus pattern (35 bp):
TATTTTTATTTTTTATTTTCTAGATTTATACATTT
Found at i:23390216 original size:28 final size:27
Alignment explanation
Indices: 23390155--23390237 Score: 78
Period size: 28 Copynumber: 2.9 Consensus size: 27
23390145 CCCAAGCCCT
*
23390155 ATTTTTATTTATTTATTTTTTTATTTATAC
1 ATTTTTA-TT-TTTATTTTTAT-TTTATAC
* *
23390185 ATTTTTATTTTTAATTTTTATTTTCTAG
1 ATTTTTATTTTT-ATTTTTATTTTATAC
*
23390213 ATTTATATATTTTA-TTTTATTTTAT
1 ATTTTTAT-TTTTATTTTTATTTTAT
23390238 TATGCATTTT
Statistics
Matches: 46, Mismatches: 5, Indels: 7
0.79 0.09 0.12
Matches are distributed among these distances:
27 10 0.22
28 16 0.35
29 13 0.28
30 7 0.15
ACGTcount: A:0.24, C:0.02, G:0.01, T:0.72
Consensus pattern (27 bp):
ATTTTTATTTTTATTTTTATTTTATAC
Found at i:23409500 original size:17 final size:17
Alignment explanation
Indices: 23409415--23409499 Score: 91
Period size: 17 Copynumber: 5.1 Consensus size: 17
23409405 TACAATGTAG
* *
23409415 TATT-AATGAATTATTA
1 TATTGAATGAACTGTTA
23409431 TATTGAATGAACTGTTA
1 TATTGAATGAACTGTTA
* * *
23409448 TATTGTACGAATTGTTA
1 TATTGAATGAACTGTTA
*
23409465 TATGGAATGAACTGTTA
1 TATTGAATGAACTGTTA
* *
23409482 TTTTGCATGAACTGTTA
1 TATTGAATGAACTGTTA
23409499 T
1 T
23409500 TCGAATATTT
Statistics
Matches: 56, Mismatches: 12, Indels: 1
0.81 0.17 0.01
Matches are distributed among these distances:
16 4 0.07
17 52 0.93
ACGTcount: A:0.33, C:0.06, G:0.16, T:0.45
Consensus pattern (17 bp):
TATTGAATGAACTGTTA
Found at i:23410562 original size:15 final size:15
Alignment explanation
Indices: 23410542--23410575 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
23410532 ATATTTAAAC
*
23410542 AAATAAAAATAATGA
1 AAATAAAAACAATGA
*
23410557 AAATAAAAACAATTA
1 AAATAAAAACAATGA
23410572 AAAT
1 AAAT
23410576 TAACACACTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.74, C:0.03, G:0.03, T:0.21
Consensus pattern (15 bp):
AAATAAAAACAATGA
Found at i:23428873 original size:102 final size:99
Alignment explanation
Indices: 23428541--23428875 Score: 311
Period size: 97 Copynumber: 3.4 Consensus size: 99
23428531 TTTTGGTGCC
* * * * * * **
23428541 GCCTTTTCATGTGAAGGCACCAAAACCTGTAATAAAA-AATTTCTTAATGCCAACACCAAATGTC
1 GCCTCTTCATGTGGAGGCACCAAAATCAGTAA-AAAATAACTCCTTGGTGCCAACACCAAATG-C
* *
23428605 GTGGCACCAATAATTTCTTTTTACTTTTTCGGTGTT
64 GCGGCACCAATAATTTTTTTTTACTTTTTCGGTGTT
* * * *
23428641 ACCTCTTAATGTGGAGGCACCAAAATCAGT--AAAATAACTCCTTGGAGCCAACTCCAAATATG-
1 GCCTCTTCATGTGGAGGCACCAAAATCAGTAAAAAATAACTCCTTGGTGCCAACACC-AA-ATGC
* * *
23428703 GCGACACCAATAA-TTTTTTTAAATTTTTCGGTGTT
64 GCGGCACCAATAATTTTTTTTTACTTTTTCGGTGTT
* * * * *
23428738 GCCTCTTCATGTGGAGGCACCCAAATCAATAAAAAATTATTTCTCTGGTGCCAACACCAAATGCG
1 GCCTCTTCATGTGGAGGCACCAAAATCAGTAAAAAATAACTCCT-TGGTGCCAACACCAAATGCG
* * **
23428803 ACGGCACCAATAATTTTTTTTTTACTTTCTGGGTGCC
65 -CGGCACCAATAA-TTTTTTTTTACTTTTTCGGTGTT
* * *
23428840 GCCTCTTCATGTAGAGGCACTAAAATTAGTAAAAAA
1 GCCTCTTCATGTGGAGGCACCAAAATCAGTAAAAAA
23428876 ATTTATTTTC
Statistics
Matches: 187, Mismatches: 38, Indels: 18
0.77 0.16 0.07
Matches are distributed among these distances:
97 49 0.26
98 28 0.15
99 14 0.07
100 49 0.26
102 47 0.25
ACGTcount: A:0.31, C:0.21, G:0.16, T:0.32
Consensus pattern (99 bp):
GCCTCTTCATGTGGAGGCACCAAAATCAGTAAAAAATAACTCCTTGGTGCCAACACCAAATGCGC
GGCACCAATAATTTTTTTTTACTTTTTCGGTGTT
Found at i:23433553 original size:22 final size:22
Alignment explanation
Indices: 23433514--23433598 Score: 82
Period size: 22 Copynumber: 3.7 Consensus size: 22
23433504 CACATTTCTC
23433514 TTTCTATT-TTTTATTTCTATTCA
1 TTTCT-TTCTTTT-TTTCTATTCA
* * * *
23433537 TTTCTCTCTCTTTTTCTAATAA
1 TTTCTTTCTTTTTTTCTATTCA
23433559 TTTCTTTTTCTTTTCTTTCTATTCA
1 TTTC--TTTCTTTT-TTTCTATTCA
23433584 TTTCTTTCTTTTTTT
1 TTTCTTTCTTTTTTT
23433599 AATTCTTTTA
Statistics
Matches: 50, Mismatches: 8, Indels: 9
0.75 0.12 0.13
Matches are distributed among these distances:
22 16 0.32
23 16 0.32
24 6 0.12
25 12 0.24
ACGTcount: A:0.12, C:0.18, G:0.00, T:0.71
Consensus pattern (22 bp):
TTTCTTTCTTTTTTTCTATTCA
Found at i:23433563 original size:45 final size:45
Alignment explanation
Indices: 23433514--23433601 Score: 117
Period size: 47 Copynumber: 2.0 Consensus size: 45
23433504 CACATTTCTC
23433514 TTTC-TATT-TTTTATTTCTATTCATTTCTCTCTCTTTTTCTAATAA
1 TTTCTTATTCTTTTATTTCTATTCATTTCT-T-TCTTTTTCTAATAA
* * *
23433559 TTTCTTTTTCTTTTCTTTCTATTCATTTCTTTCTTTTTTTAAT
1 TTTCTTATTCTTTTATTTCTATTCATTTCTTTCTTTTTCTAAT
23433602 TCTTTTAATA
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
45 15 0.39
46 4 0.11
47 19 0.50
ACGTcount: A:0.14, C:0.17, G:0.00, T:0.69
Consensus pattern (45 bp):
TTTCTTATTCTTTTATTTCTATTCATTTCTTTCTTTTTCTAATAA
Found at i:23433644 original size:7 final size:7
Alignment explanation
Indices: 23433632--23433656 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
23433622 CTTTTATTCA
23433632 TTTCATT
1 TTTCATT
23433639 TTTCATT
1 TTTCATT
23433646 TTTCATT
1 TTTCATT
23433653 TTTC
1 TTTC
23433657 TTATCATCTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.12, C:0.16, G:0.00, T:0.72
Consensus pattern (7 bp):
TTTCATT
Found at i:23436174 original size:18 final size:18
Alignment explanation
Indices: 23436151--23436188 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
23436141 ATCAACTCTT
23436151 TGCCTTAACCTCTACCTC
1 TGCCTTAACCTCTACCTC
* *
23436169 TGCCTTGACCTCTAGCTC
1 TGCCTTAACCTCTACCTC
23436187 TG
1 TG
23436189 TCTCAACCTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.13, C:0.39, G:0.13, T:0.34
Consensus pattern (18 bp):
TGCCTTAACCTCTACCTC
Found at i:23442379 original size:24 final size:24
Alignment explanation
Indices: 23442351--23442402 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
23442341 TTAGTAGGTC
* *
23442351 AAATAAACTATGCTAATAAATGCT
1 AAATAAACTATACTAATAAATACT
* *
23442375 AAATATATTATACTAATAAATACT
1 AAATAAACTATACTAATAAATACT
23442399 AAAT
1 AAAT
23442403 CTTTTAAAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.54, C:0.10, G:0.04, T:0.33
Consensus pattern (24 bp):
AAATAAACTATACTAATAAATACT
Found at i:23444220 original size:24 final size:24
Alignment explanation
Indices: 23444175--23444221 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 24
23444165 ATAAAAACTA
* *
23444175 AACCCTGAAAACCCAAAAACAAAG
1 AACCCTCAAAACACAAAAACAAAG
* *
23444199 AACCCTCAAAACATAAACACAAA
1 AACCCTCAAAACACAAAAACAAA
23444222 ATTCTCTAAA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.60, C:0.30, G:0.04, T:0.06
Consensus pattern (24 bp):
AACCCTCAAAACACAAAAACAAAG
Found at i:23446569 original size:94 final size:94
Alignment explanation
Indices: 23446408--23446598 Score: 355
Period size: 94 Copynumber: 2.0 Consensus size: 94
23446398 AATTAAAAAA
*
23446408 TTTCCAAAAATATATTTAAGATGTGTTTGGGTAAGGAATTTATAGGAGGGGTTTCAATTGTATCA
1 TTTCCAAAAATATACTTAAGATGTGTTTGGGTAAGGAATTTATAGGAGGGGTTTCAATTGTATCA
23446473 AGGTTTTTAAAATTCTAAAAATGAATTTG
66 AGGTTTTTAAAATTCTAAAAATGAATTTG
* *
23446502 TTTCCCAAAATATACTTAAGATGTGTTTGGGTAAGGAATTTATAGGAGGGGTTTCATTTGTATCA
1 TTTCCAAAAATATACTTAAGATGTGTTTGGGTAAGGAATTTATAGGAGGGGTTTCAATTGTATCA
23446567 AGGTTTTTAAAATTCTAAAAATGAATTTG
66 AGGTTTTTAAAATTCTAAAAATGAATTTG
23446596 TTT
1 TTT
23446599 GTTTGGGTAA
Statistics
Matches: 94, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
94 94 1.00
ACGTcount: A:0.34, C:0.06, G:0.20, T:0.40
Consensus pattern (94 bp):
TTTCCAAAAATATACTTAAGATGTGTTTGGGTAAGGAATTTATAGGAGGGGTTTCAATTGTATCA
AGGTTTTTAAAATTCTAAAAATGAATTTG
Found at i:23462623 original size:14 final size:15
Alignment explanation
Indices: 23462604--23462632 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
23462594 TCACGAAACT
23462604 TTCACACAT-ATAAA
1 TTCACACATAATAAA
23462618 TTCACACATAATAAA
1 TTCACACATAATAAA
23462633 CACAGAAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.52, C:0.21, G:0.00, T:0.28
Consensus pattern (15 bp):
TTCACACATAATAAA
Found at i:23462731 original size:3 final size:3
Alignment explanation
Indices: 23462723--23462781 Score: 118
Period size: 3 Copynumber: 19.7 Consensus size: 3
23462713 GGCTGTTACA
23462723 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
23462771 CTT CTT CTT CT
1 CTT CTT CTT CT
23462782 CGTCTCTGAT
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 56 1.00
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (3 bp):
CTT
Found at i:23465541 original size:7 final size:7
Alignment explanation
Indices: 23465529--23465554 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
23465519 CATATGATAG
23465529 AATTATT
1 AATTATT
23465536 AATTATT
1 AATTATT
23465543 AATTATT
1 AATTATT
23465550 AATTA
1 AATTA
23465555 AATAATTTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (7 bp):
AATTATT
Found at i:23466079 original size:18 final size:18
Alignment explanation
Indices: 23466056--23466090 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
23466046 TCAAGTCTTT
* *
23466056 TATTTTGATTTTCTTATG
1 TATTTTAATTTTATTATG
23466074 TATTTTAATTTTATTAT
1 TATTTTAATTTTATTAT
23466091 CCACCTCCAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.23, C:0.03, G:0.06, T:0.69
Consensus pattern (18 bp):
TATTTTAATTTTATTATG
Found at i:23470187 original size:21 final size:21
Alignment explanation
Indices: 23470163--23470203 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
23470153 TAAAAGAGTC
23470163 TATTTATAGGCTAAATTCATT
1 TATTTATAGGCTAAATTCATT
*
23470184 TATTTATAGGTTAAATTCAT
1 TATTTATAGGCTAAATTCAT
23470204 ATGTCAAATA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.34, C:0.07, G:0.10, T:0.49
Consensus pattern (21 bp):
TATTTATAGGCTAAATTCATT
Found at i:23471263 original size:21 final size:21
Alignment explanation
Indices: 23471218--23471265 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
23471208 AAACTTCCTC
23471218 TCTT-CTTTTTTTTCTTCGTT
1 TCTTCCTTTTTTTTCTTCGTT
*
23471238 T-TTCCTTTTTCTTTCTT-TTT
1 TCTTCCTTTTT-TTTCTTCGTT
23471258 TCTTCCTT
1 TCTTCCTT
23471266 CCCTTTTTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
19 2 0.08
20 10 0.42
21 12 0.50
ACGTcount: A:0.00, C:0.23, G:0.02, T:0.75
Consensus pattern (21 bp):
TCTTCCTTTTTTTTCTTCGTT
Found at i:23480025 original size:90 final size:91
Alignment explanation
Indices: 23479852--23480027 Score: 214
Period size: 91 Copynumber: 1.9 Consensus size: 91
23479842 ATGCACCAAG
* * ** *
23479852 CAGCTCTCAAAATACATGCACAATTGGGTGCATGTTCTTCATTAAATTAGCTTCATTGAATCTGG
1 CAGCTCTCAAAATACATGCACAATCGGGTGCATGCTCCACATTAAATTAGCTTCAATGAATCTGG
23479917 AAAATTCATGAATGTCCAGCTGCAAT
66 AAAATTCATGAATGTCCAGCTGCAAT
** * *
23479943 CAGCTCTCAATGTATATGCACAATCGGGTGCATGCTCCACATT-TATTAGCTTCAATGAAT-TGG
1 CAGCTCTCAAAATACATGCACAATCGGGTGCATGCTCCACATTAAATTAGCTTCAATGAATCTGG
* *
23480006 -CATTGTGCATGAATGTCCAGCT
66 AAAAT-T-CATGAATGTCCAGCT
23480028 ACATGCATTA
Statistics
Matches: 72, Mismatches: 11, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
88 2 0.03
89 4 0.06
90 30 0.42
91 36 0.50
ACGTcount: A:0.29, C:0.21, G:0.18, T:0.32
Consensus pattern (91 bp):
CAGCTCTCAAAATACATGCACAATCGGGTGCATGCTCCACATTAAATTAGCTTCAATGAATCTGG
AAAATTCATGAATGTCCAGCTGCAAT
Found at i:23481164 original size:36 final size:36
Alignment explanation
Indices: 23481060--23481196 Score: 163
Period size: 37 Copynumber: 3.7 Consensus size: 36
23481050 CCTTAGATGT
23481060 GTCTATCCCAACCTTTTTTAAAGGTTGCCTTAGACAG
1 GTCTATCCCAACC-TTTTTAAAGGTTGCCTTAGACAG
23481097 GTCTATCCTC-ACACTTTTTAAAGGTTGCCTTAGACAAG
1 GTCTATCC-CAAC-CTTTTTAAAGGTTGCCTTAGAC-AG
* *
23481135 GTCTATCCCAACCATTTT-AAGGTTGCCTTAGA-TG
1 GTCTATCCCAACCTTTTTAAAGGTTGCCTTAGACAG
* *
23481169 GATTTATCCCAACCTTTTTTAAATGTTG
1 G-TCTATCCCAACC-TTTTTAAAGGTTG
23481197 GCATTGACTA
Statistics
Matches: 88, Mismatches: 5, Indels: 14
0.82 0.05 0.13
Matches are distributed among these distances:
34 2 0.02
35 11 0.12
36 18 0.20
37 43 0.49
38 14 0.16
ACGTcount: A:0.25, C:0.23, G:0.15, T:0.37
Consensus pattern (36 bp):
GTCTATCCCAACCTTTTTAAAGGTTGCCTTAGACAG
Found at i:23483607 original size:39 final size:41
Alignment explanation
Indices: 23483564--23483653 Score: 130
Period size: 39 Copynumber: 2.2 Consensus size: 41
23483554 TCAATTTATA
* * * *
23483564 TTTAATATAATAAAATATTTATTATA-TT-TATTTGTGTTT
1 TTTAATATAATAAAACATTTATTATACTTAGAGTAGTGTTT
23483603 TTTAATATAATAAAACATTTATTATACTTAGAGTAGTGTTT
1 TTTAATATAATAAAACATTTATTATACTTAGAGTAGTGTTT
23483644 TTTAATATAA
1 TTTAATATAA
23483654 ATATTTTTAG
Statistics
Matches: 45, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
39 25 0.56
40 2 0.04
41 18 0.40
ACGTcount: A:0.39, C:0.02, G:0.07, T:0.52
Consensus pattern (41 bp):
TTTAATATAATAAAACATTTATTATACTTAGAGTAGTGTTT
Found at i:23488574 original size:19 final size:21
Alignment explanation
Indices: 23488536--23488574 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 21
23488526 CCTTTTTTAA
*
23488536 AATCGTAAATAAGTAAAAAAT
1 AATCGTAAATAAGAAAAAAAT
23488557 AATCG-AAA-AAGAAAAAAA
1 AATCGTAAATAAGAAAAAAA
23488575 CAGTAAACCA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 9 0.53
20 3 0.18
21 5 0.29
ACGTcount: A:0.69, C:0.05, G:0.10, T:0.15
Consensus pattern (21 bp):
AATCGTAAATAAGAAAAAAAT
Found at i:23488775 original size:25 final size:22
Alignment explanation
Indices: 23488747--23488804 Score: 73
Period size: 21 Copynumber: 2.5 Consensus size: 22
23488737 AAATTAAATC
23488747 TCTAAGATTACAAAATCATATCATA
1 TCTAAGATTAC--AAT-ATATCATA
*
23488772 TCTAAGATTGC-ATATATCATA
1 TCTAAGATTACAATATATCATA
23488793 TCTAAGATTACA
1 TCTAAGATTACA
23488805 TATCCTCGAA
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
21 18 0.60
22 2 0.07
25 10 0.33
ACGTcount: A:0.43, C:0.16, G:0.07, T:0.34
Consensus pattern (22 bp):
TCTAAGATTACAATATATCATA
Found at i:23488789 original size:21 final size:21
Alignment explanation
Indices: 23488764--23488807 Score: 79
Period size: 21 Copynumber: 2.1 Consensus size: 21
23488754 TTACAAAATC
*
23488764 ATATCATATCTAAGATTGCAT
1 ATATCATATCTAAGATTACAT
23488785 ATATCATATCTAAGATTACAT
1 ATATCATATCTAAGATTACAT
23488806 AT
1 AT
23488808 CCTCGAAGAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.41, C:0.14, G:0.07, T:0.39
Consensus pattern (21 bp):
ATATCATATCTAAGATTACAT
Found at i:23489306 original size:20 final size:20
Alignment explanation
Indices: 23489281--23489336 Score: 69
Period size: 20 Copynumber: 2.8 Consensus size: 20
23489271 TTCTAACGTG
23489281 TATTAAAATTTAG-AATTAAA
1 TATTAAAATTT-GTAATTAAA
23489301 TATTAAAATTTGTAATTAAA
1 TATTAAAATTTGTAATTAAA
* * *
23489321 TTTTAAGATTTCTAAT
1 TATTAAAATTTGTAAT
23489337 GTAGTACCAC
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
19 1 0.03
20 31 0.97
ACGTcount: A:0.46, C:0.02, G:0.05, T:0.46
Consensus pattern (20 bp):
TATTAAAATTTGTAATTAAA
Found at i:23489537 original size:20 final size:19
Alignment explanation
Indices: 23489506--23489580 Score: 82
Period size: 20 Copynumber: 3.8 Consensus size: 19
23489496 TTTTTTACGG
23489506 ATACTAAAATTTCTAACTAA
1 ATAC-AAAATTTCTAACTAA
*
23489526 ATACAAATATTTC-AGA-TGA
1 ATACAAA-ATTTCTA-ACTAA
23489545 ATACCAAAATTTCTAACTAA
1 ATA-CAAAATTTCTAACTAA
23489565 ATACATAAATTTCTAA
1 ATACA-AAATTTCTAA
23489581 TGGATGCCAA
Statistics
Matches: 47, Mismatches: 2, Indels: 12
0.77 0.03 0.20
Matches are distributed among these distances:
19 17 0.36
20 30 0.64
ACGTcount: A:0.49, C:0.15, G:0.03, T:0.33
Consensus pattern (19 bp):
ATACAAAATTTCTAACTAA
Found at i:23489616 original size:25 final size:25
Alignment explanation
Indices: 23489571--23489618 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
23489561 CTAAATACAT
* **
23489571 AAATTTCTAATGGATGCCAAAATCA
1 AAATTTATAATGGATAACAAAATCA
23489596 AAATTTATAATGGATAACAAAAT
1 AAATTTATAATGGATAACAAAAT
23489619 TATATAGAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.50, C:0.10, G:0.10, T:0.29
Consensus pattern (25 bp):
AAATTTATAATGGATAACAAAATCA
Found at i:23491922 original size:14 final size:15
Alignment explanation
Indices: 23491905--23491938 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
23491895 GAGTAAGGTA
23491905 AAATA-TTAAAAAAT
1 AAATATTTAAAAAAT
23491919 AAATATTTAAAAAAT
1 AAATATTTAAAAAAT
*
23491934 TAATA
1 AAATA
23491939 ATAGTTGAGT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 5 0.28
15 13 0.72
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (15 bp):
AAATATTTAAAAAAT
Found at i:23492874 original size:3 final size:3
Alignment explanation
Indices: 23492852--23492889 Score: 51
Period size: 3 Copynumber: 12.7 Consensus size: 3
23492842 CACTTCACCT
*
23492852 GAA GGA GAA GAAA GAA -AA GAA GAA GAA GAA GAA GAA GA
1 GAA GAA GAA G-AA GAA GAA GAA GAA GAA GAA GAA GAA GA
23492890 GGGCAGTGAC
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
2 2 0.06
3 26 0.84
4 3 0.10
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:23492928 original size:20 final size:20
Alignment explanation
Indices: 23492905--23492961 Score: 55
Period size: 20 Copynumber: 2.8 Consensus size: 20
23492895 GTGACGGAAA
23492905 AAAGAAA-AGAAAAAAGAGAG
1 AAAGAAAGAGAAAAAAG-GAG
* *
23492925 AAAGAGAATAG-AGAAAGGAG
1 AAAGA-AAGAGAAAAAAGGAG
23492945 AAAGAAAGAGAAGAAAA
1 AAAGAAAGAGAA-AAAA
23492962 AAAATAGAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 7
0.75 0.08 0.17
Matches are distributed among these distances:
19 4 0.13
20 14 0.47
21 10 0.33
22 2 0.07
ACGTcount: A:0.70, C:0.00, G:0.28, T:0.02
Consensus pattern (20 bp):
AAAGAAAGAGAAAAAAGGAG
Found at i:23492970 original size:24 final size:24
Alignment explanation
Indices: 23492906--23492971 Score: 60
Period size: 24 Copynumber: 2.7 Consensus size: 24
23492896 TGACGGAAAA
*
23492906 AAGAAAAGAAAAAAGAGAGAAAGAG
1 AAGAAAA-AAAAAAGAAAGAAAGAG
* * * **
23492931 AATAGAGAAAGGAGAAAGAAAGAG
1 AAGAAAAAAAAAAGAAAGAAAGAG
*
23492955 AAGAAAAAAAATAGAAA
1 AAGAAAAAAAAAAGAAA
23492972 AAATAAGGTA
Statistics
Matches: 30, Mismatches: 11, Indels: 1
0.71 0.26 0.02
Matches are distributed among these distances:
24 26 0.87
25 4 0.13
ACGTcount: A:0.71, C:0.00, G:0.26, T:0.03
Consensus pattern (24 bp):
AAGAAAAAAAAAAGAAAGAAAGAG
Found at i:23493316 original size:37 final size:38
Alignment explanation
Indices: 23493268--23493362 Score: 122
Period size: 38 Copynumber: 2.5 Consensus size: 38
23493258 TTTTACATTA
* *
23493268 TATTATTGTTAGTTATTATTTTTAG-AATAACTCTAAT
1 TATTATTGTTAGTTATTATTTTTAGAAAAAACTATAAT
*
23493305 TATTATTGTTAG-TATTATTTTTAGTAAAAAACTATTAT
1 TATTATTGTTAGTTATTATTTTTAG-AAAAAACTATAAT
23493343 TATTATTGTGTTAGTTATTA
1 TATTA-T-TGTTAGTTATTA
23493363 GGATTAGTGG
Statistics
Matches: 50, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
36 12 0.24
37 12 0.24
38 14 0.28
39 1 0.02
40 6 0.12
41 5 0.10
ACGTcount: A:0.33, C:0.03, G:0.09, T:0.55
Consensus pattern (38 bp):
TATTATTGTTAGTTATTATTTTTAGAAAAAACTATAAT
Found at i:23496896 original size:159 final size:159
Alignment explanation
Indices: 23496335--23497392 Score: 1775
Period size: 159 Copynumber: 6.6 Consensus size: 159
23496325 ACTTCAAAAC
* * *
23496335 AAATTTAGTAAAAAACCCTTAGTTTGGCCATTTGTTCGTATTTTTCTTTTTTCCCAGATTTTATT
1 AAATTTAGTAAAAAACCCTTATTTTGGCCCTTTGTTCGTATTTTTCTTTTTTCCCGGATTTTATT
*
23496400 ACTTTCAAAAAATATACTATTTTCGTATTTTATTATTTTATAATATTTTAGTACATAATGTTTGA
66 ACTTTCAAAAAATATACTATTTTCGTATTTTATTATTTTATATTATTTTAGTACATAATGTTTGA
23496465 AATGTATTAATTTAGTGTGTTTTTTTATAT
131 AATGTATTAATTTAGTGTG-TTTTTTATAT
*
23496495 AAATTTAGTAAAAAACCCTTATTTTGGCCCTTTGTTTGTATTTTTCTTTTTTCCCGGATTTTATT
1 AAATTTAGTAAAAAACCCTTATTTTGGCCCTTTGTTCGTATTTTTCTTTTTTCCCGGATTTTATT
* * *
23496560 ACTTTTAAAAAATATATTATTTTTGTATTTTATTATTTTATATTATTTTAGTACATAATGTTTGA
66 ACTTTCAAAAAATATACTATTTTCGTATTTTATTATTTTATATTATTTTAGTACATAATGTTTGA
*
23496625 AATGTATTAATTTAGTATGTTTTTTTTATAT
131 AATGTATTAATTTAG--TGTGTTTTTTATAT
* *
23496656 AAATTTAGTAAAAAAACCCTTATTTTGGCCCTTTGTTCGTATTTTTCTTTTTTCCCGTATCTTAT
1 AAATTTAGT-AAAAAACCCTTATTTTGGCCCTTTGTTCGTATTTTTCTTTTTTCCCGGATTTTAT
*
23496721 TACTTTCAAAAAATATACTATTTTCGTATTTTATTATTTTATATTATTTTAGTACATAATATTTG
65 TACTTTCAAAAAATATACTATTTTCGTATTTTATTATTTTATATTATTTTAGTACATAATGTTTG
*
23496786 AAATGTATTAATTTAGTGTGCTTTTTATAT
130 AAATGTATTAATTTAGTGTGTTTTTTATAT
* * *
23496816 AAATTTAGTAAAAAACCCTTATTTTGGCCCTTTGTTCGTAGTTCTCTTTTTTCTCGGATTTTATT
1 AAATTTAGTAAAAAACCCTTATTTTGGCCCTTTGTTCGTATTTTTCTTTTTTCCCGGATTTTATT
*
23496881 ACTTTCAAAAAATATACTATTTTCGTATTTTATTATTTTATATTATTTTACTACATAATGTTTGA
66 ACTTTCAAAAAATATACTATTTTCGTATTTTATTATTTTATATTATTTTAGTACATAATGTTTGA
23496946 AATGTATTAATTTAGTGTG-TTTTTATAT
131 AATGTATTAATTTAGTGTGTTTTTTATAT
*
23496974 AAATTTAGTAAAAAACTCTTATTTTGGCCCTTTGTTCGTATTTTTCTTTTTTCCCGGATTTTATT
1 AAATTTAGTAAAAAACCCTTATTTTGGCCCTTTGTTCGTATTTTTCTTTTTTCCCGGATTTTATT
*
23497039 ACTTTCAAAAAATATACTATTTTCGTATTTTATTATTTTATATTATTTTAGTACATTATGTTTGA
66 ACTTTCAAAAAATATACTATTTTCGTATTTTATTATTTTATATTATTTTAGTACATAATGTTTGA
23497104 AATGTATTAATTTAGTGTGTTTTTTATAT
131 AATGTATTAATTTAGTGTGTTTTTTATAT
* *
23497133 AAATTTAGTAAAAAACCCTTATTTTGGCCCTTTGTTCGTATTTTTCTTTTTTCCCGTATCTTATT
1 AAATTTAGTAAAAAACCCTTATTTTGGCCCTTTGTTCGTATTTTTCTTTTTTCCCGGATTTTATT
*
23497198 ACTTTCAAAAAATATACTATTTTCGTATTTTATTATTTTATATTATTTTAGTACATAATATTTGA
66 ACTTTCAAAAAATATACTATTTTCGTATTTTATTATTTTATATTATTTTAGTACATAATGTTTGA
23497263 AATGTATTAATTTAGTGTGTTTTTTATAT
131 AATGTATTAATTTAGTGTGTTTTTTATAT
* * *
23497292 AAATTTAGTAAAAAAATCCTTATTTTGGCCATTTGTTCGTATTTTTCTTATTTT--CGAATTTTA
1 AAATTTAGT-AAAAAACCCTTATTTTGGCCCTTTGTTCGTATTTTTCTT-TTTTCCCGGATTTTA
** *
23497355 TTACTTTCAGTAAATATACTATTTTTGT-TTTT-TTATTT
64 TTACTTTCAAAAAATATACTATTTTCGTATTTTATTATTT
23497393 CTTTTCGTAT
Statistics
Matches: 849, Mismatches: 43, Indels: 15
0.94 0.05 0.02
Matches are distributed among these distances:
157 6 0.01
158 156 0.18
159 337 0.40
160 195 0.23
161 23 0.03
162 132 0.16
ACGTcount: A:0.28, C:0.10, G:0.09, T:0.53
Consensus pattern (159 bp):
AAATTTAGTAAAAAACCCTTATTTTGGCCCTTTGTTCGTATTTTTCTTTTTTCCCGGATTTTATT
ACTTTCAAAAAATATACTATTTTCGTATTTTATTATTTTATATTATTTTAGTACATAATGTTTGA
AATGTATTAATTTAGTGTGTTTTTTATAT
Found at i:23497135 original size:317 final size:317
Alignment explanation
Indices: 23496335--23497392 Score: 1764
Period size: 317 Copynumber: 3.3 Consensus size: 317
23496325 ACTTCAAAAC
* *
23496335 AAATTTAGTAAAAAACCCTTAGTTTGGCCATTTGTTCGTATTTTTCTTTTTTCCCAGATTTTATT
1 AAATTTAGTAAAAAACCCTTATTTTGGCCATTTGTTCGTATTTTTCTTTTTTCCCGGATTTTATT
*
23496400 ACTTTCAAAAAATATACTATTTTCGTATTTTATTATTTTATAATATTTTAGTACATAATGTTTGA
66 ACTTTCAAAAAATATACTATTTTCGTATTTTATTATTTTATATTATTTTAGTACATAATGTTTGA
23496465 AATGTATTAATTTAGTGTGTTTTTTTATATAAATTTAGTAAAAAACCCTTATTTTGGCCCTTTGT
131 AATGTATTAATTTAGTGTG-TTTTTTATATAAATTTAGTAAAAAACCCTTATTTTGGCCCTTTGT
* * * *
23496530 TTGTATTTTTCTTTTTTCCCGGATTTTATTACTTTTAAAAAATATATTATTTTTGTATTTTATTA
195 TCGTATTTTTCTTTTTTCCCGGATTTTATTACTTTCAAAAAATATACTATTTTCGTATTTTATTA
*
23496595 TTTTATATTATTTTAGTACATAATGTTTGAAATGTATTAATTTAGTATGTTTTTTTTATAT
260 TTTTATATTATTTTAGTACATAATGTTTGAAATGTATTAATTTAG--TG-TGTTTTTATAT
* * *
23496656 AAATTTAGTAAAAAAACCCTTATTTTGGCCCTTTGTTCGTATTTTTCTTTTTTCCCGTATCTTAT
1 AAATTTAGT-AAAAAACCCTTATTTTGGCCATTTGTTCGTATTTTTCTTTTTTCCCGGATTTTAT
*
23496721 TACTTTCAAAAAATATACTATTTTCGTATTTTATTATTTTATATTATTTTAGTACATAATATTTG
65 TACTTTCAAAAAATATACTATTTTCGTATTTTATTATTTTATATTATTTTAGTACATAATGTTTG
*
23496786 AAATGTATTAATTTAGTGTGCTTTTTATATAAATTTAGTAAAAAACCCTTATTTTGGCCCTTTGT
130 AAATGTATTAATTTAGTGTGTTTTTTATATAAATTTAGTAAAAAACCCTTATTTTGGCCCTTTGT
* * *
23496851 TCGTAGTTCTCTTTTTTCTCGGATTTTATTACTTTCAAAAAATATACTATTTTCGTATTTTATTA
195 TCGTATTTTTCTTTTTTCCCGGATTTTATTACTTTCAAAAAATATACTATTTTCGTATTTTATTA
*
23496916 TTTTATATTATTTTACTACATAATGTTTGAAATGTATTAATTTAGTGTGTTTTTATAT
260 TTTTATATTATTTTAGTACATAATGTTTGAAATGTATTAATTTAGTGTGTTTTTATAT
* *
23496974 AAATTTAGTAAAAAACTCTTATTTTGGCCCTTTGTTCGTATTTTTCTTTTTTCCCGGATTTTATT
1 AAATTTAGTAAAAAACCCTTATTTTGGCCATTTGTTCGTATTTTTCTTTTTTCCCGGATTTTATT
*
23497039 ACTTTCAAAAAATATACTATTTTCGTATTTTATTATTTTATATTATTTTAGTACATTATGTTTGA
66 ACTTTCAAAAAATATACTATTTTCGTATTTTATTATTTTATATTATTTTAGTACATAATGTTTGA
23497104 AATGTATTAATTTAGTGTGTTTTTTATATAAATTTAGTAAAAAACCCTTATTTTGGCCCTTTGTT
131 AATGTATTAATTTAGTGTGTTTTTTATATAAATTTAGTAAAAAACCCTTATTTTGGCCCTTTGTT
* *
23497169 CGTATTTTTCTTTTTTCCCGTATCTTATTACTTTCAAAAAATATACTATTTTCGTATTTTATTAT
196 CGTATTTTTCTTTTTTCCCGGATTTTATTACTTTCAAAAAATATACTATTTTCGTATTTTATTAT
*
23497234 TTTATATTATTTTAGTACATAATATTTGAAATGTATTAATTTAGTGTGTTTTTTATAT
261 TTTATATTATTTTAGTACATAATGTTTGAAATGTATTAATTTAGTGTG-TTTTTATAT
* *
23497292 AAATTTAGTAAAAAAATCCTTATTTTGGCCATTTGTTCGTATTTTTCTTATTTT--CGAATTTTA
1 AAATTTAGT-AAAAAACCCTTATTTTGGCCATTTGTTCGTATTTTTCTT-TTTTCCCGGATTTTA
** *
23497355 TTACTTTCAGTAAATATACTATTTTTGT-TTTT-TTATTT
64 TTACTTTCAAAAAATATACTATTTTCGTATTTTATTATTT
23497393 CTTTTCGTAT
Statistics
Matches: 696, Mismatches: 37, Indels: 13
0.93 0.05 0.02
Matches are distributed among these distances:
316 6 0.01
317 290 0.42
318 70 0.10
319 38 0.05
320 4 0.01
321 155 0.22
322 133 0.19
ACGTcount: A:0.28, C:0.10, G:0.09, T:0.53
Consensus pattern (317 bp):
AAATTTAGTAAAAAACCCTTATTTTGGCCATTTGTTCGTATTTTTCTTTTTTCCCGGATTTTATT
ACTTTCAAAAAATATACTATTTTCGTATTTTATTATTTTATATTATTTTAGTACATAATGTTTGA
AATGTATTAATTTAGTGTGTTTTTTATATAAATTTAGTAAAAAACCCTTATTTTGGCCCTTTGTT
CGTATTTTTCTTTTTTCCCGGATTTTATTACTTTCAAAAAATATACTATTTTCGTATTTTATTAT
TTTATATTATTTTAGTACATAATGTTTGAAATGTATTAATTTAGTGTGTTTTTATAT
Found at i:23497796 original size:27 final size:27
Alignment explanation
Indices: 23497748--23497810 Score: 81
Period size: 27 Copynumber: 2.3 Consensus size: 27
23497738 TTATAATGGG
* ** * *
23497748 TGGTGCCGCCTGTGGTAGTGGCACCTT
1 TGGTGCCGCCTCTGCCACTGGCACCTC
23497775 TGGTGCCGCCTCTGCCACTGGCACCTC
1 TGGTGCCGCCTCTGCCACTGGCACCTC
23497802 TGGTGCCGC
1 TGGTGCCGC
23497811 TTGTGGCAGG
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 31 1.00
ACGTcount: A:0.06, C:0.35, G:0.33, T:0.25
Consensus pattern (27 bp):
TGGTGCCGCCTCTGCCACTGGCACCTC
Found at i:23498259 original size:29 final size:29
Alignment explanation
Indices: 23498199--23498261 Score: 76
Period size: 29 Copynumber: 2.2 Consensus size: 29
23498189 TAAAGGTTTA
**
23498199 TTTTAGTAAATTTTAAAAAAATGGTCTAT
1 TTTTAGTAAATTTTAAAAAAATGACCTAT
23498228 TTTTA-TAATATTTTAAAAAAATTGACCT-T
1 TTTTAGTAA-ATTTTAAAAAAA-TGACCTAT
23498257 TTTTA
1 TTTTA
23498262 AAAACTTAGT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
28 3 0.10
29 23 0.77
30 4 0.13
ACGTcount: A:0.40, C:0.05, G:0.06, T:0.49
Consensus pattern (29 bp):
TTTTAGTAAATTTTAAAAAAATGACCTAT
Found at i:23499728 original size:3 final size:3
Alignment explanation
Indices: 23499720--23499756 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
23499710 TAATCTAATA
23499720 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT T
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT T
23499757 GTGTTTTATT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TCT
Found at i:23503618 original size:13 final size:13
Alignment explanation
Indices: 23503600--23503624 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
23503590 TATGTTACTA
23503600 AATTATAATATTT
1 AATTATAATATTT
23503613 AATTATAATATT
1 AATTATAATATT
23503625 AAAATTTTCT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (13 bp):
AATTATAATATTT
Found at i:23503729 original size:10 final size:10
Alignment explanation
Indices: 23503716--23503791 Score: 54
Period size: 10 Copynumber: 7.8 Consensus size: 10
23503706 AAAAAAATAT
23503716 TATTAAATTA
1 TATTAAATTA
*
23503726 TATTTAA-TA
1 TATTAAATTA
23503735 -A-T-AATTA
1 TATTAAATTA
*
23503742 TATTAAAATA
1 TATTAAATTA
23503752 TGATTAAATTA
1 T-ATTAAATTA
*
23503763 T-TTATTATTTA
1 TATTA--AATTA
23503774 TATTAAATTA
1 TATTAAATTA
*
23503784 AATTAAAT
1 TATTAAAT
23503792 AATAATCTTA
Statistics
Matches: 52, Mismatches: 6, Indels: 16
0.70 0.08 0.22
Matches are distributed among these distances:
6 2 0.04
7 3 0.06
8 2 0.04
9 6 0.12
10 22 0.42
11 14 0.27
12 3 0.06
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.50
Consensus pattern (10 bp):
TATTAAATTA
Found at i:23503745 original size:26 final size:26
Alignment explanation
Indices: 23503716--23503806 Score: 76
Period size: 26 Copynumber: 3.3 Consensus size: 26
23503706 AAAAAAATAT
*
23503716 TATTAAATTATATTTAATAATAATTA
1 TATTAAATTATATTAAATAATAATTA
* *
23503742 TATTAAAATATGATTAAATTATTTATTATTTA
1 TATTAAATTAT-ATTAAA-TA---A-TAATTA
*
23503774 TATTAAATTAAATTAAATAATAATCT-
1 TATTAAATTATATTAAATAATAAT-TA
23503800 TATTAAA
1 TATTAAA
23503807 ATTTAATAAC
Statistics
Matches: 52, Mismatches: 6, Indels: 14
0.72 0.08 0.19
Matches are distributed among these distances:
26 20 0.38
27 7 0.13
28 2 0.04
30 2 0.04
31 7 0.13
32 14 0.27
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.48
Consensus pattern (26 bp):
TATTAAATTATATTAAATAATAATTA
Found at i:23503784 original size:37 final size:37
Alignment explanation
Indices: 23503709--23503785 Score: 93
Period size: 37 Copynumber: 2.1 Consensus size: 37
23503699 GAATAATAAA
* *
23503709 AAAATATTATTAAATTATATTTAATAATAATTATATT
1 AAAATATGATTAAATTATATTTAATAATAATTAAATT
* * *
23503746 AAAATATGATTAAATTATTTATTATTTAT-ATTAAATT
1 AAAATATGATTAAATTATAT-TTAATAATAATTAAATT
23503783 AAA
1 AAA
23503786 TTAAATAATA
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
37 28 0.82
38 6 0.18
ACGTcount: A:0.51, C:0.00, G:0.01, T:0.48
Consensus pattern (37 bp):
AAAATATGATTAAATTATATTTAATAATAATTAAATT
Found at i:23505128 original size:16 final size:16
Alignment explanation
Indices: 23505107--23505175 Score: 120
Period size: 16 Copynumber: 4.3 Consensus size: 16
23505097 TTGGTTTGCT
23505107 GTAATGGAATAGAGGC
1 GTAATGGAATAGAGGC
*
23505123 GTAATGGAATAGAGCC
1 GTAATGGAATAGAGGC
*
23505139 GTAATGGAATAGATGC
1 GTAATGGAATAGAGGC
23505155 GTAATGGAATAGAGGC
1 GTAATGGAATAGAGGC
23505171 GTAAT
1 GTAAT
23505176 AGGTAATTCT
Statistics
Matches: 49, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 49 1.00
ACGTcount: A:0.38, C:0.07, G:0.33, T:0.22
Consensus pattern (16 bp):
GTAATGGAATAGAGGC
Found at i:23505244 original size:44 final size:46
Alignment explanation
Indices: 23505157--23505249 Score: 154
Period size: 44 Copynumber: 2.1 Consensus size: 46
23505147 ATAGATGCGT
23505157 AATGGAATAGAGGCGTAATAGGTAATTCTTATATTTGGTTGAATGG
1 AATGGAATAGAGGCGTAATAGGTAATTCTTATATTTGGTTGAATGG
* *
23505203 AATGGAATAGAGGCGTAAT-GGT-ATTCTTGTGTTTGGTTGAATGG
1 AATGGAATAGAGGCGTAATAGGTAATTCTTATATTTGGTTGAATGG
23505247 AAT
1 AAT
23505250 AGAGGTGTAA
Statistics
Matches: 45, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
44 23 0.51
45 3 0.07
46 19 0.42
ACGTcount: A:0.30, C:0.04, G:0.30, T:0.35
Consensus pattern (46 bp):
AATGGAATAGAGGCGTAATAGGTAATTCTTATATTTGGTTGAATGG
Found at i:23505245 original size:39 final size:44
Alignment explanation
Indices: 23505157--23505262 Score: 132
Period size: 39 Copynumber: 2.5 Consensus size: 44
23505147 ATAGATGCGT
23505157 AATGGAATAGAGGCGTAATAGGTAATTCTTATATTTGGTTGAATGG
1 AATGGAATAGAGGCGTAATAGGTAATTCTTATATTTGGTT--ATGG
* *
23505203 AATGGAATAGAGGCGTAAT-GGT-ATTCTTGTGTTTGG-T-T-G
1 AATGGAATAGAGGCGTAATAGGTAATTCTTATATTTGGTTATGG
*
23505242 AATGGAATAGAGGTGTAATAG
1 AATGGAATAGAGGCGTAATAG
23505263 CATAAGTAAA
Statistics
Matches: 56, Mismatches: 3, Indels: 8
0.84 0.04 0.12
Matches are distributed among these distances:
39 19 0.34
40 2 0.04
43 1 0.02
44 12 0.21
45 3 0.05
46 19 0.34
ACGTcount: A:0.31, C:0.04, G:0.31, T:0.34
Consensus pattern (44 bp):
AATGGAATAGAGGCGTAATAGGTAATTCTTATATTTGGTTATGG
Found at i:23505461 original size:18 final size:17
Alignment explanation
Indices: 23505409--23505461 Score: 79
Period size: 18 Copynumber: 3.0 Consensus size: 17
23505399 TTTTTATTAA
23505409 ATATAATTTAATAAAAAT
1 ATATAATTTAAT-AAAAT
23505427 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
*
23505444 ATATGAATTTACTAAAAT
1 ATAT-AATTTAATAAAAT
23505462 CATAATATAT
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
17 9 0.27
18 24 0.73
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.40
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:23505518 original size:26 final size:26
Alignment explanation
Indices: 23505500--23505700 Score: 163
Period size: 26 Copynumber: 7.1 Consensus size: 26
23505490 TTAAAAGTCT
23505500 TATTATTAAATATAATTTAATAAAAA
1 TATTATTAAATATAATTTAATAAAAA
23505526 TATTATTAAATATAATTTAATAAAAA
1 TATTATTAAATATAATTTAATAAAAA
** * *
23505552 TATATAATTTGATAAAATTCTAGTATTAAAA
1 TAT-T-ATTAAATATAATT-TA--ATAAAAA
*
23505583 TATTATT--ATATGAATTTACTAAAATCA
1 TATTATTAAATAT-AATTTAATAAAA--A
* *
23505610 TAATATATAATACTATAAATTATAATTTAAAA
1 TATTAT-TAA-A-TAT-AATT-TAA-TAAAAA
23505642 TAATTATTATTAAATATAATTTAATAAAAA
1 ----TATTATTAAATATAATTTAATAAAAA
23505672 TATTATTAAATATAATTTAATAAAAA
1 TATTATTAAATATAATTTAATAAAAA
23505698 TAT
1 TAT
23505701 ATAATTTGAT
Statistics
Matches: 143, Mismatches: 13, Indels: 38
0.74 0.07 0.20
Matches are distributed among these distances:
25 4 0.03
26 58 0.41
27 12 0.08
28 15 0.10
29 5 0.03
30 6 0.04
31 13 0.09
32 12 0.08
33 5 0.03
34 5 0.03
35 3 0.02
36 5 0.03
ACGTcount: A:0.54, C:0.02, G:0.01, T:0.43
Consensus pattern (26 bp):
TATTATTAAATATAATTTAATAAAAA
Found at i:23505528 original size:16 final size:15
Alignment explanation
Indices: 23505507--23505569 Score: 53
Period size: 18 Copynumber: 4.3 Consensus size: 15
23505497 TCTTATTATT
23505507 AAATATAATTTAATA
1 AAATATAATTTAATA
*
23505522 AAA-AT-A-TT-ATT
1 AAATATAATTTAATA
23505533 AAATATAATTTAATAAA
1 AAATATAATTTAAT--A
*
23505550 AATATATAATTTGATA
1 AA-ATATAATTTAATA
23505566 AAAT
1 AAAT
23505570 TCTAGTATTA
Statistics
Matches: 38, Mismatches: 3, Indels: 14
0.69 0.05 0.25
Matches are distributed among these distances:
11 5 0.13
12 4 0.11
13 2 0.05
14 4 0.11
15 7 0.18
16 3 0.08
17 2 0.05
18 11 0.29
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.40
Consensus pattern (15 bp):
AAATATAATTTAATA
Found at i:23505627 original size:146 final size:146
Alignment explanation
Indices: 23505443--23505809 Score: 675
Period size: 146 Copynumber: 2.5 Consensus size: 146
23505433 TTTAATAAAA
* *
23505443 TATATGAATTTACTAAAATCATAATATATAATACTATAAAATATATTTTAAAAGT-CTTATTATT
1 TATATGAATTTACTAAAATCATAATATATAATACTATAAAATATAATTTAAAA-TAATTATTATT
*
23505507 AAATATAATTTAATAAAAATATTATTAAATATAATTTAATAAAAATATATAATTTGATAAAATTC
65 AAATATAATTTAATAAAAATATTATTAAATATAATTTAATAAAAATATATAATTTGATAAAATTA
23505572 TAGTATTAAAATATTAT
130 TAGTATTAAAATATTAT
*
23505589 TATATGAATTTACTAAAATCATAATATATAATACTATAAATTATAATTTAAAATAATTATTATTA
1 TATATGAATTTACTAAAATCATAATATATAATACTATAAAATATAATTTAAAATAATTATTATTA
23505654 AATATAATTTAATAAAAATATTATTAAATATAATTTAATAAAAATATATAATTTGATAAAATTAT
66 AATATAATTTAATAAAAATATTATTAAATATAATTTAATAAAAATATATAATTTGATAAAATTAT
23505719 AGTATTAAAATATTAT
131 AGTATTAAAATATTAT
23505735 TATATGAATTTACTAAAATCATAATATATAATACTAT-AAATATAATTTAAAATAATTATTATTA
1 TATATGAATTTACTAAAATCATAATATATAATACTATAAAATATAATTTAAAATAATTATTATTA
23505799 AATATAATTTA
66 AATATAATTTA
23505810 TAATCTATTT
Statistics
Matches: 215, Mismatches: 5, Indels: 3
0.96 0.02 0.01
Matches are distributed among these distances:
145 38 0.18
146 177 0.82
ACGTcount: A:0.52, C:0.03, G:0.02, T:0.43
Consensus pattern (146 bp):
TATATGAATTTACTAAAATCATAATATATAATACTATAAAATATAATTTAAAATAATTATTATTA
AATATAATTTAATAAAAATATTATTAAATATAATTTAATAAAAATATATAATTTGATAAAATTAT
AGTATTAAAATATTAT
Found at i:23505643 original size:22 final size:21
Alignment explanation
Indices: 23505599--23505643 Score: 54
Period size: 22 Copynumber: 2.1 Consensus size: 21
23505589 TATATGAATT
*
23505599 TACTAAAATCATAATATATAA
1 TACTAAAATCATAATATAAAA
* *
23505620 TACTATAAATTATAATTTAAAA
1 TACTA-AAATCATAATATAAAA
23505642 TA
1 TA
23505644 ATTATTATTA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
21 5 0.25
22 15 0.75
ACGTcount: A:0.56, C:0.07, G:0.00, T:0.38
Consensus pattern (21 bp):
TACTAAAATCATAATATAAAA
Found at i:23505648 original size:16 final size:17
Alignment explanation
Indices: 23505627--23505666 Score: 50
Period size: 16 Copynumber: 2.5 Consensus size: 17
23505617 TAATACTATA
23505627 AATTATAATTTAAA-AT
1 AATTATAATTTAAATAT
*
23505643 AATTATTA-TTAAATAT
1 AATTATAATTTAAATAT
23505659 AATT-TAAT
1 AATTATAAT
23505667 AAAAATATTA
Statistics
Matches: 20, Mismatches: 2, Indels: 4
0.77 0.08 0.15
Matches are distributed among these distances:
15 7 0.35
16 13 0.65
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (17 bp):
AATTATAATTTAAATAT
Found at i:23505672 original size:16 final size:15
Alignment explanation
Indices: 23505653--23505715 Score: 53
Period size: 18 Copynumber: 4.3 Consensus size: 15
23505643 AATTATTATT
23505653 AAATATAATTTAATA
1 AAATATAATTTAATA
*
23505668 AAA-AT-A-TT-ATT
1 AAATATAATTTAATA
23505679 AAATATAATTTAATAAA
1 AAATATAATTTAAT--A
*
23505696 AATATATAATTTGATA
1 AA-ATATAATTTAATA
23505712 AAAT
1 AAAT
23505716 TATAGTATTA
Statistics
Matches: 38, Mismatches: 3, Indels: 14
0.69 0.05 0.25
Matches are distributed among these distances:
11 5 0.13
12 4 0.11
13 2 0.05
14 4 0.11
15 7 0.18
16 3 0.08
17 2 0.05
18 11 0.29
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.40
Consensus pattern (15 bp):
AAATATAATTTAATA
Found at i:23505702 original size:18 final size:18
Alignment explanation
Indices: 23505681--23505719 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
23505671 ATATTATTAA
23505681 ATATAATTTAATAAAAAT
1 ATATAATTTAATAAAAAT
* *
23505699 ATATAATTTGATAAAATT
1 ATATAATTTAATAAAAAT
23505717 ATA
1 ATA
23505720 GTATTAAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.41
Consensus pattern (18 bp):
ATATAATTTAATAAAAAT
Found at i:23505788 original size:21 final size:21
Alignment explanation
Indices: 23505745--23505788 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
23505735 TATATGAATT
*
23505745 TACTAAAATCATAATATATAA
1 TACTAAAATCATAATATAAAA
*
23505766 TACTATAAAT-ATAATTTAAAA
1 TACTA-AAATCATAATATAAAA
23505787 TA
1 TA
23505789 ATTATTATTA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 16 0.80
22 4 0.20
ACGTcount: A:0.57, C:0.07, G:0.00, T:0.36
Consensus pattern (21 bp):
TACTAAAATCATAATATAAAA
Found at i:23509124 original size:2 final size:2
Alignment explanation
Indices: 23509117--23509141 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
23509107 TATTAAAATA
23509117 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
23509142 ACAAAAGAGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:23509733 original size:24 final size:27
Alignment explanation
Indices: 23509682--23509734 Score: 67
Period size: 27 Copynumber: 2.1 Consensus size: 27
23509672 TATATGTAAT
*
23509682 ATTATTAAAATAATATTTTTTATTTTA
1 ATTATTAAAATAATATTTTTTATATTA
*
23509709 ATTATTTAAA-AATA-TTTTTA-ATTA
1 ATTATTAAAATAATATTTTTTATATTA
23509733 AT
1 AT
23509735 GCGGTGTATA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
24 5 0.21
25 6 0.25
26 4 0.17
27 9 0.38
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (27 bp):
ATTATTAAAATAATATTTTTTATATTA
Found at i:23512345 original size:13 final size:13
Alignment explanation
Indices: 23512327--23512353 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
23512317 AGCTTTTAAG
23512327 CAATGGTAATATC
1 CAATGGTAATATC
23512340 CAATGGTAATATC
1 CAATGGTAATATC
23512353 C
1 C
23512354 TTAAACAACA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.37, C:0.19, G:0.15, T:0.30
Consensus pattern (13 bp):
CAATGGTAATATC
Found at i:23517900 original size:8 final size:8
Alignment explanation
Indices: 23517887--23517919 Score: 50
Period size: 8 Copynumber: 4.2 Consensus size: 8
23517877 AAGAAAACGC
23517887 AAGAAAAT
1 AAGAAAAT
23517895 AAGAAAAT
1 AAGAAAAT
23517903 AA-AAAAT
1 AAGAAAAT
*
23517910 AAAAAAAT
1 AAGAAAAT
23517918 AA
1 AA
23517920 AACCAAGTTG
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
7 7 0.29
8 17 0.71
ACGTcount: A:0.82, C:0.00, G:0.06, T:0.12
Consensus pattern (8 bp):
AAGAAAAT
Found at i:23517910 original size:15 final size:15
Alignment explanation
Indices: 23517890--23517921 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
23517880 AAAACGCAAG
*
23517890 AAAATAAGAAAATAA
1 AAAATAAAAAAATAA
23517905 AAAATAAAAAAATAA
1 AAAATAAAAAAATAA
23517920 AA
1 AA
23517922 CCAAGTTGAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.84, C:0.00, G:0.03, T:0.12
Consensus pattern (15 bp):
AAAATAAAAAAATAA
Found at i:23522702 original size:26 final size:24
Alignment explanation
Indices: 23522647--23522713 Score: 64
Period size: 24 Copynumber: 2.8 Consensus size: 24
23522637 TTTCAATATG
*
23522647 TTTTATTAATTTTATAATTTATTA
1 TTTTATTAATTTTATAAATTATTA
* * *
23522671 TATTATTAGATTTTTTAAAATTATTT
1 TTTTATTA-ATTTTAT-AAATTATTA
*
23522697 TTTTA-TAAATTTATAAA
1 TTTTATTAATTTTATAAA
23522714 AATAATATTT
Statistics
Matches: 34, Mismatches: 7, Indels: 5
0.74 0.15 0.11
Matches are distributed among these distances:
23 3 0.09
24 12 0.35
25 8 0.24
26 11 0.32
ACGTcount: A:0.37, C:0.00, G:0.01, T:0.61
Consensus pattern (24 bp):
TTTTATTAATTTTATAAATTATTA
Found at i:23522767 original size:20 final size:20
Alignment explanation
Indices: 23522714--23522773 Score: 70
Period size: 19 Copynumber: 3.0 Consensus size: 20
23522704 AATTTATAAA
*
23522714 AATAATATTTA-AAATATTT
1 AATAATTTTTATAAATATTT
*
23522733 AATAATTTTTGTAAATATTT
1 AATAATTTTTATAAATATTT
23522753 -ATAATTTTTCATAAATTATTT
1 AATAATTTTT-ATAAA-TATTT
23522774 GATTTTTTAT
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
19 18 0.51
20 12 0.34
21 5 0.14
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.53
Consensus pattern (20 bp):
AATAATTTTTATAAATATTT
Found at i:23532962 original size:43 final size:43
Alignment explanation
Indices: 23532911--23533026 Score: 119
Period size: 43 Copynumber: 2.7 Consensus size: 43
23532901 ATGTGTTTTT
* *
23532911 CATGTAAGACCACATCAGGGACATTGGCATCGACT-TGTGTTTA
1 CATGTAAGACCACGTCAGGGACATTGGCATCGA-TATGTGATTA
* ** ** *
23532954 CGTGTAAGACCTTGTTTGGGACAGTGGCATCGATATGTGATTA
1 CATGTAAGACCACGTCAGGGACATTGGCATCGATATGTGATTA
*
23532997 CATGTAAGACCACGTCTA-GGACGTTGGCAT
1 CATGTAAGACCACGTC-AGGGACATTGGCAT
23533027 TGTATGAGCT
Statistics
Matches: 56, Mismatches: 15, Indels: 4
0.75 0.20 0.05
Matches are distributed among these distances:
42 1 0.02
43 55 0.98
ACGTcount: A:0.26, C:0.19, G:0.27, T:0.28
Consensus pattern (43 bp):
CATGTAAGACCACGTCAGGGACATTGGCATCGATATGTGATTA
Found at i:23546196 original size:21 final size:22
Alignment explanation
Indices: 23546171--23546215 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 22
23546161 TATTTAACCC
*
23546171 AAAATTAATTGGATTAT-AATT
1 AAAATTAATTAGATTATAAATT
*
23546192 AAAATTAATTATATTATAAATT
1 AAAATTAATTAGATTATAAATT
23546214 AA
1 AA
23546216 TATTCATAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 15 0.71
22 6 0.29
ACGTcount: A:0.53, C:0.00, G:0.04, T:0.42
Consensus pattern (22 bp):
AAAATTAATTAGATTATAAATT
Found at i:23546204 original size:16 final size:16
Alignment explanation
Indices: 23546183--23546216 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
23546173 AATTAATTGG
23546183 ATTATAATTA-AAATTA
1 ATTAT-ATTATAAATTA
23546199 ATTATATTATAAATTA
1 ATTATATTATAAATTA
23546215 AT
1 AT
23546217 ATTCATAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 4 0.24
16 13 0.76
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (16 bp):
ATTATATTATAAATTA
Found at i:23549064 original size:15 final size:16
Alignment explanation
Indices: 23549040--23549072 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
23549030 TTTTTAAATT
23549040 AAAAATTTAAGTACTG
1 AAAAATTTAAGTACTG
*
23549056 AAAAA-TTAAGTATTG
1 AAAAATTTAAGTACTG
23549071 AA
1 AA
23549073 TTTATATTAG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 11 0.69
16 5 0.31
ACGTcount: A:0.55, C:0.03, G:0.12, T:0.30
Consensus pattern (16 bp):
AAAAATTTAAGTACTG
Found at i:23549283 original size:26 final size:25
Alignment explanation
Indices: 23549245--23549312 Score: 64
Period size: 27 Copynumber: 2.6 Consensus size: 25
23549235 AAGTATATTA
* *
23549245 ATTTGAATATTTTTTAAAATATAATTT
1 ATTT-AAT-TTTTTTAAAATAAAATTG
*
23549272 ATTTCAATTTTTAATAAAATAAAATTG
1 ATTT-AATTTTT-TTAAAATAAAATTG
*
23549299 AGTTAATTTTTTTA
1 ATTTAATTTTTTTA
23549313 CATTAAGTGA
Statistics
Matches: 34, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
25 2 0.06
26 11 0.32
27 21 0.62
ACGTcount: A:0.41, C:0.01, G:0.04, T:0.53
Consensus pattern (25 bp):
ATTTAATTTTTTTAAAATAAAATTG
Found at i:23558270 original size:31 final size:31
Alignment explanation
Indices: 23558234--23558292 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
23558224 ACATGGACAT
*
23558234 TGAACTATTCGAA-AGTTTTCATTTAAGTCAC
1 TGAACTACTC-AATAGTTTTCATTTAAGTCAC
*
23558265 TGAACTACTCAATAGTTTTTATTTAAGT
1 TGAACTACTCAATAGTTTTCATTTAAGT
23558293 TACCAAGCTA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
30 2 0.08
31 23 0.92
ACGTcount: A:0.32, C:0.14, G:0.12, T:0.42
Consensus pattern (31 bp):
TGAACTACTCAATAGTTTTCATTTAAGTCAC
Found at i:23559867 original size:21 final size:21
Alignment explanation
Indices: 23559820--23559902 Score: 85
Period size: 21 Copynumber: 4.0 Consensus size: 21
23559810 CTTTCCGTTT
* * *
23559820 AGCTCTTTCGAGCTTCAGTTT
1 AGCTCTTACGAGCTTCTGTTC
23559841 AGCTCTTACGAGCTTCTGTTC
1 AGCTCTTACGAGCTTCTGTTC
* * *
23559862 AACTCTTATGAGTTTCTGTTC
1 AGCTCTTACGAGCTTCTGTTC
* **
23559883 GGCTCTTTTGAGCTTCTGTT
1 AGCTCTTACGAGCTTCTGTT
23559903 GTAGTATCTA
Statistics
Matches: 52, Mismatches: 10, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 52 1.00
ACGTcount: A:0.13, C:0.23, G:0.19, T:0.45
Consensus pattern (21 bp):
AGCTCTTACGAGCTTCTGTTC
Found at i:23563930 original size:34 final size:34
Alignment explanation
Indices: 23563891--23563962 Score: 90
Period size: 34 Copynumber: 2.1 Consensus size: 34
23563881 ATATATAAAG
*
23563891 TATAAAGTATAAAATATATAAGTACGTACATATA
1 TATAAAGTAAAAAATATATAAGTACGTACATATA
* * * **
23563925 TATAAATTAAAAAATATGTAAGTATGTGTATATA
1 TATAAAGTAAAAAATATATAAGTACGTACATATA
23563959 TATA
1 TATA
23563963 TATAAAACAA
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
34 32 1.00
ACGTcount: A:0.51, C:0.03, G:0.10, T:0.36
Consensus pattern (34 bp):
TATAAAGTAAAAAATATATAAGTACGTACATATA
Found at i:23565881 original size:44 final size:44
Alignment explanation
Indices: 23565650--23566439 Score: 611
Period size: 44 Copynumber: 18.2 Consensus size: 44
23565640 GTTTTTTCTG
* * * * *
23565650 TCTGCTCCGCTACTGCTTAGGGAGATAAGA-CT--TG-ATGCGA
1 TCTGCTCCACTACTGCTTAGGGAGATAGGATCTACCGTCTTCGA
* * ** **
23565690 TCTGCTCCACTACTGCTTAAGGAGATAAGATCTATGGT-TTTAA
1 TCTGCTCCACTACTGCTTAGGGAGATAGGATCTACCGTCTTCGA
* * ****
23565733 TCCGCTCTACTGTAACT--TTAGGGAGATAGGAT-TGGTTTCTTCTG-
1 TCTGCTCCAC--T-ACTGCTTAGGGAGATAGGATCTACCGTCTTC-GA
* * * *
23565777 TCTGCTCCACTACTGCTTAGGGAGATAAGA-CT--TG-ATGCGA
1 TCTGCTCCACTACTGCTTAGGGAGATAGGATCTACCGTCTTCGA
* **
23565817 TCTGCTCCACTACTGCTTAGGGAGATAAGATCTACAATCTTCGA
1 TCTGCTCCACTACTGCTTAGGGAGATAGGATCTACCGTCTTCGA
* *** * **
23565861 CCTGCTCCACTACTGCTTAGGGAGATAGGA-CTGGTGGCTTAAA
1 TCTGCTCCACTACTGCTTAGGGAGATAGGATCTACCGTCTTCGA
* * * *
23565904 TCTGCTTCACTACTGCTTAGGAAGATAAGAT-TCGCCGTCTT-GAA
1 TCTGCTCCACTACTGCTTAGGGAGATAGGATCT-ACCGTCTTCG-A
* *
23565948 TCTGCTCCACTACTGCTTAGGGAGATAGGATCTACCATCTTTGA
1 TCTGCTCCACTACTGCTTAGGGAGATAGGATCTACCGTCTTCGA
*
23565992 TCTGCTCCACTACTGCTTAGGGAGATAGGATCTACCATCTTCGA
1 TCTGCTCCACTACTGCTTAGGGAGATAGGATCTACCGTCTTCGA
* ** * **
23566036 CCTGCTCCACTACTGCTTAGGGAGATAGGA-CTAGTGGCTTAAA
1 TCTGCTCCACTACTGCTTAGGGAGATAGGATCTACCGTCTTCGA
* * *
23566079 TCTGCTTCACTACTGCTTAGGAAGATAAGAT-TCACCGTCTTCGA
1 TCTGCTCCACTACTGCTTAGGGAGATAGGATCT-ACCGTCTTCGA
* * *
23566123 TCTGCTCCACTACTGCTTAGAGAGATAGGATCTACCATCTTTGA
1 TCTGCTCCACTACTGCTTAGGGAGATAGGATCTACCGTCTTCGA
*** * **
23566167 TCTGCTCCACTACTGCTTAGGGAGATAGGA-CTGGTGGCTTAAA
1 TCTGCTCCACTACTGCTTAGGGAGATAGGATCTACCGTCTTCGA
* *
23566210 TCTGCTTCACTACTGCTTAGGAAGAT-GAGAT-TCACCGTCTTCGA
1 TCTGCTCCACTACTGCTTAGGGAGATAG-GATCT-ACCGTCTTCGA
** *
23566254 TCTGCTCCACTACTGCTTAGGGAGATAGGATCTACTATCTTTGA
1 TCTGCTCCACTACTGCTTAGGGAGATAGGATCTACCGTCTTCGA
* *** * **
23566298 CCTGCTCCACTACTGCTTAGGGAGATAGGA-CTGGTGGCTTAAA
1 TCTGCTCCACTACTGCTTAGGGAGATAGGATCTACCGTCTTCGA
* * * * *
23566341 TCTGCTTCACTACTACTTAGGAAGAT-GAGAT-TCGCCGTCTTTGA
1 TCTGCTCCACTACTGCTTAGGGAGATAG-GATCT-ACCGTCTTCGA
* * * *
23566385 TCTGCTCCACTACTGCTTAAGGAGATAGGATCTAACATCTTTGA
1 TCTGCTCCACTACTGCTTAGGGAGATAGGATCTACCGTCTTCGA
*
23566429 CCTGCTCCACT
1 TCTGCTCCACT
23566440 GCAACCGATG
Statistics
Matches: 599, Mismatches: 116, Indels: 66
0.77 0.15 0.08
Matches are distributed among these distances:
39 1 0.00
40 60 0.10
41 8 0.01
42 3 0.01
43 159 0.27
44 357 0.60
45 8 0.01
46 3 0.01
ACGTcount: A:0.24, C:0.24, G:0.22, T:0.31
Consensus pattern (44 bp):
TCTGCTCCACTACTGCTTAGGGAGATAGGATCTACCGTCTTCGA
Found at i:23565988 original size:131 final size:131
Alignment explanation
Indices: 23565778--23566439 Score: 847
Period size: 131 Copynumber: 5.1 Consensus size: 131
23565768 TTTCTTCTGT
* * * * *
23565778 CTGCTCCACTACTGCTTAGGGAGATAAGACTTGAT-GC---GATCTGCTCCACTACTGCTTAGGG
1 CTGCTCCACTACTGCTTAGGGAGATAGGAC-TGGTGGCTTAAATCTGCTTCACTACTGCTTAGGA
* ** * ***** *
23565839 AGATAAGA-TCTACAATCTTCGACCTGCTCCACTACTGCTTAGGGAGATAGGA-CTGGTGGCTTA
65 AGATAGGATTC-ACCGTCTTCGATCTGCTCCACTACTGCTTAGGGAGATAGGATCTACCATCTTT
* *
23565902 AAT
129 GAC
* * * * ** * * * *
23565905 CTGCTTCACTACTGCTTAGGAAGATAAGATTCGCCGTCTTGAATCTGCTCCACTACTGCTTAGGG
1 CTGCTCCACTACTGCTTAGGGAGATAGGACT-GGTGGCTTAAATCTGCTTCACTACTGCTTAGGA
* * *
23565970 AGATAGGA-TCTACCATCTTTGATCTGCTCCACTACTGCTTAGGGAGATAGGATCTACCATCTTC
65 AGATAGGATTC-ACCGTCTTCGATCTGCTCCACTACTGCTTAGGGAGATAGGATCTACCATCTTT
23566034 GAC
129 GAC
*
23566037 CTGCTCCACTACTGCTTAGGGAGATAGGACTAGTGGCTTAAATCTGCTTCACTACTGCTTAGGAA
1 CTGCTCCACTACTGCTTAGGGAGATAGGACTGGTGGCTTAAATCTGCTTCACTACTGCTTAGGAA
* *
23566102 GATAAGATTCACCGTCTTCGATCTGCTCCACTACTGCTTAGAGAGATAGGATCTACCATCTTTGA
66 GATAGGATTCACCGTCTTCGATCTGCTCCACTACTGCTTAGGGAGATAGGATCTACCATCTTTGA
*
23566167 T
131 C
23566168 CTGCTCCACTACTGCTTAGGGAGATAGGACTGGTGGCTTAAATCTGCTTCACTACTGCTTAGGAA
1 CTGCTCCACTACTGCTTAGGGAGATAGGACTGGTGGCTTAAATCTGCTTCACTACTGCTTAGGAA
*
23566233 GAT-GAGATTCACCGTCTTCGATCTGCTCCACTACTGCTTAGGGAGATAGGATCTACTATCTTTG
66 GATAG-GATTCACCGTCTTCGATCTGCTCCACTACTGCTTAGGGAGATAGGATCTACCATCTTTG
23566297 AC
130 AC
*
23566299 CTGCTCCACTACTGCTTAGGGAGATAGGACTGGTGGCTTAAATCTGCTTCACTACTACTTAGGAA
1 CTGCTCCACTACTGCTTAGGGAGATAGGACTGGTGGCTTAAATCTGCTTCACTACTGCTTAGGAA
* * * *
23566364 GAT-GAGATTCGCCGTCTTTGATCTGCTCCACTACTGCTTAAGGAGATAGGATCTAACATCTTTG
66 GATAG-GATTCACCGTCTTCGATCTGCTCCACTACTGCTTAGGGAGATAGGATCTACCATCTTTG
23566428 AC
130 AC
23566430 CTGCTCCACT
1 CTGCTCCACT
23566440 GCAACCGATG
Statistics
Matches: 480, Mismatches: 47, Indels: 12
0.89 0.09 0.02
Matches are distributed among these distances:
126 1 0.00
127 28 0.06
128 1 0.00
131 415 0.86
132 35 0.07
ACGTcount: A:0.24, C:0.24, G:0.22, T:0.30
Consensus pattern (131 bp):
CTGCTCCACTACTGCTTAGGGAGATAGGACTGGTGGCTTAAATCTGCTTCACTACTGCTTAGGAA
GATAGGATTCACCGTCTTCGATCTGCTCCACTACTGCTTAGGGAGATAGGATCTACCATCTTTGA
C
Found at i:23566043 original size:175 final size:175
Alignment explanation
Indices: 23565777--23566327 Score: 715
Period size: 175 Copynumber: 3.2 Consensus size: 175
23565767 GTTTCTTCTG
* **
23565777 TCTGCTCCACTACTGCTTAGGGAGATAAGA-CT-TGATGC---GATCTGCTCCACTACTGCTTAG
1 TCTGCTCCACTACTGCTTAGGGAGATAGGATCTACCAT-CTTTGATCTGCTCCACTACTGCTTAG
* *
23565837 GGAGATAAGATCTACAATCTTCGACCTGCTCCACTACTGCTTAGGGAGATAGGACTGGTGGCTTA
65 GGAGATAGGATCTACAATCTTCGACCTGCTCCACTACTGCTTAGGGAGATAGGACTAGTGGCTTA
*
23565902 AATCTGCTTCACTACTGCTTAGGAAGATAAGATTCGCCGTCTT-GAA
130 AATCTGCTTCACTACTGCTTAGGAAGATAAGATTCACCGTCTTCG-A
23565948 TCTGCTCCACTACTGCTTAGGGAGATAGGATCTACCATCTTTGATCTGCTCCACTACTGCTTAGG
1 TCTGCTCCACTACTGCTTAGGGAGATAGGATCTACCATCTTTGATCTGCTCCACTACTGCTTAGG
*
23566013 GAGATAGGATCTACCATCTTCGACCTGCTCCACTACTGCTTAGGGAGATAGGACTAGTGGCTTAA
66 GAGATAGGATCTACAATCTTCGACCTGCTCCACTACTGCTTAGGGAGATAGGACTAGTGGCTTAA
23566078 ATCTGCTTCACTACTGCTTAGGAAGATAAGATTCACCGTCTTCGA
131 ATCTGCTTCACTACTGCTTAGGAAGATAAGATTCACCGTCTTCGA
*
23566123 TCTGCTCCACTACTGCTTAGAGAGATAGGATCTACCATCTTTGATCTGCTCCACTACTGCTTAGG
1 TCTGCTCCACTACTGCTTAGGGAGATAGGATCTACCATCTTTGATCTGCTCCACTACTGCTTAGG
***** ** * * * * ** *
23566188 GAGATAGGA-CTGGTGGCTTAAATCTGCTTCACTACTGCTTAGGAAGAT-GAGATTCACCGTCTT
66 GAGATAGGATCTACAATCTTCGACCTGCTCCACTACTGCTTAGGGAGATAG-GACT-AGTGGCTT
** * * * ** *
23566251 CGATCTGCTCCACTACTGCTTAGGGAGATAGGA-TCTACTATCTTTGA
129 AAATCTGCTTCACTACTGCTTAGGAAGATAAGATTC-ACCGTCTTCGA
*
23566298 CCTGCTCCACTACTGCTTAGGGAGATAGGA
1 TCTGCTCCACTACTGCTTAGGGAGATAGGA
23566328 CTGGTGGCTT
Statistics
Matches: 339, Mismatches: 32, Indels: 14
0.88 0.08 0.04
Matches are distributed among these distances:
171 29 0.09
172 3 0.01
173 3 0.01
174 34 0.10
175 269 0.79
176 1 0.00
ACGTcount: A:0.24, C:0.24, G:0.22, T:0.30
Consensus pattern (175 bp):
TCTGCTCCACTACTGCTTAGGGAGATAGGATCTACCATCTTTGATCTGCTCCACTACTGCTTAGG
GAGATAGGATCTACAATCTTCGACCTGCTCCACTACTGCTTAGGGAGATAGGACTAGTGGCTTAA
ATCTGCTTCACTACTGCTTAGGAAGATAAGATTCACCGTCTTCGA
Found at i:23566439 original size:175 final size:176
Alignment explanation
Indices: 23565650--23566418 Score: 663
Period size: 175 Copynumber: 4.4 Consensus size: 176
23565640 GTTTTTTCTG
* * ** *
23565650 TCTGCTCCGCTACTGCTTAGGGAGATAAGA-CT-TGA--TGCGATCTGCTCCACTACTGCTTAAG
1 TCTGCTCCACTACTGCTTAGGGAGATAGGATCTACCATCTTCGATCTGCTCCACTACTGCTTAAG
* * * * * * ****
23565711 GAGATAAGATCTATG-GT-TTTAATCCGCTCTACTGTAACT--TTAGGGAGATAGGATT-GGTTT
66 GAGATAGGATCTA-GCGTCTTAAATCTGCTCCAC--T-ACTGCTTAGGAAGATAAGATTCACCGT
* **
23565771 CTTCTG-TCTGCTCCACTACTGCTTAGGGAGATAAGA-CT-TGATGC---GA
127 CTT-TGATCTGCTCCACTACTGCTTAGGGAGATAGGATCTACCA-GCTTTGA
* * * *
23565817 TCTGCTCCACTACTGCTTAGGGAGATAAGATCTACAATCTTCGACCTGCTCCACTACTGCTTAGG
1 TCTGCTCCACTACTGCTTAGGGAGATAGGATCTACCATCTTCGATCTGCTCCACTACTGCTTAAG
* * * * *
23565882 GAGATAGGA-CTGGTGGCTTAAATCTGCTTCACTACTGCTTAGGAAGATAAGATTCGCCGTC-TT
66 GAGATAGGATCTAGCGTCTTAAATCTGCTCCACTACTGCTTAGGAAGATAAGATTCACCGTCTTT
*
23565945 GAATCTGCTCCACTACTGCTTAGGGAGATAGGATCTACCATCTTTGA
131 G-ATCTGCTCCACTACTGCTTAGGGAGATAGGATCTACCAGCTTTGA
* *
23565992 TCTGCTCCACTACTGCTTAGGGAGATAGGATCTACCATCTTCGACCTGCTCCACTACTGCTTAGG
1 TCTGCTCCACTACTGCTTAGGGAGATAGGATCTACCATCTTCGATCTGCTCCACTACTGCTTAAG
* * * *
23566057 GAGATAGGA-CTAGTGGCTTAAATCTGCTTCACTACTGCTTAGGAAGATAAGATTCACCGTCTTC
66 GAGATAGGATCTAGCGTCTTAAATCTGCTCCACTACTGCTTAGGAAGATAAGATTCACCGTCTTT
* *
23566121 GATCTGCTCCACTACTGCTTAGAGAGATAGGATCTACCATCTTTGA
131 GATCTGCTCCACTACTGCTTAGGGAGATAGGATCTACCAGCTTTGA
***** ** *
23566167 TCTGCTCCACTACTGCTTAGGGAGATAGGA-CTGGTGGCTTAAATCTGCTTCACTACTGCTT-AG
1 TCTGCTCCACTACTGCTTAGGGAGATAGGATCTACCATCTTCGATCTGCTCCACTACTGCTTAAG
* ** * * **
23566230 GAAGAT-GAGAT-TCACCGTCTTCGATCTGCTCCACTACTGCTTAGGGAGATAGGA-TCTACTAT
66 G-AGATAG-GATCT-AGCGTCTTAAATCTGCTCCACTACTGCTTAGGAAGATAAGATTC-ACCGT
* **** **
23566292 CTTTGACCTGCTCCACTACTGCTTAGGGAGATAGGA-CTGGTGGCTTAAA
127 CTTTGATCTGCTCCACTACTGCTTAGGGAGATAGGATCTACCAGCTTTGA
* * * * * *
23566341 TCTGCTTCACTACTACTTAGGAAGAT-GAGAT-TCGCCGTCTTTGATCTGCTCCACTACTGCTTA
1 TCTGCTCCACTACTGCTTAGGGAGATAG-GATCT-ACCATCTTCGATCTGCTCCACTACTGCTTA
23566404 AGGAGATAGGATCTA
64 AGGAGATAGGATCTA
23566419 ACATCTTTGA
Statistics
Matches: 507, Mismatches: 67, Indels: 48
0.82 0.11 0.08
Matches are distributed among these distances:
167 29 0.06
168 5 0.01
169 5 0.01
170 18 0.04
171 74 0.15
172 3 0.01
173 5 0.01
174 63 0.12
175 298 0.59
176 7 0.01
ACGTcount: A:0.24, C:0.23, G:0.22, T:0.31
Consensus pattern (176 bp):
TCTGCTCCACTACTGCTTAGGGAGATAGGATCTACCATCTTCGATCTGCTCCACTACTGCTTAAG
GAGATAGGATCTAGCGTCTTAAATCTGCTCCACTACTGCTTAGGAAGATAAGATTCACCGTCTTT
GATCTGCTCCACTACTGCTTAGGGAGATAGGATCTACCAGCTTTGA
Found at i:23576757 original size:34 final size:34
Alignment explanation
Indices: 23576719--23576790 Score: 90
Period size: 34 Copynumber: 2.1 Consensus size: 34
23576709 ATATATAAAG
*
23576719 TATAAAGTATAAAATATATAAGTACGTACATATA
1 TATAAAGTAAAAAATATATAAGTACGTACATATA
* * * **
23576753 TATAAATTAAAAAATATGTAAGTATGTGTATATA
1 TATAAAGTAAAAAATATATAAGTACGTACATATA
23576787 TATA
1 TATA
23576791 TAACAAGATT
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
34 32 1.00
ACGTcount: A:0.51, C:0.03, G:0.10, T:0.36
Consensus pattern (34 bp):
TATAAAGTAAAAAATATATAAGTACGTACATATA
Found at i:23583629 original size:22 final size:22
Alignment explanation
Indices: 23583603--23583648 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
23583593 AAGCTACCCC
*
23583603 TTTTATTTTATTT-TATTTTATT
1 TTTTATATTATTTAT-TTTTATT
23583625 TTTTATATTATTTATTTTTATT
1 TTTTATATTATTTATTTTTATT
23583647 TT
1 TT
23583649 CCTAATTTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 21 0.95
23 1 0.05
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (22 bp):
TTTTATATTATTTATTTTTATT
Found at i:23583638 original size:16 final size:17
Alignment explanation
Indices: 23583608--23583643 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
23583598 ACCCCTTTTA
*
23583608 TTTTATTTTATTTTATT
1 TTTTATATTATTTTATT
23583625 TTTTATATTA-TTTATT
1 TTTTATATTATTTTATT
23583641 TTT
1 TTT
23583644 ATTTTCCTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 9 0.50
17 9 0.50
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (17 bp):
TTTTATATTATTTTATT
Found at i:23583660 original size:22 final size:22
Alignment explanation
Indices: 23583613--23583669 Score: 64
Period size: 22 Copynumber: 2.6 Consensus size: 22
23583603 TTTTATTTTA
*
23583613 TTTTA-TTTTATTTTTTATATT
1 TTTTATTTTTATTTTCTATATT
*
23583634 ATTTATTTTTATTTTCCTA-ATT
1 TTTTATTTTTATTTT-CTATATT
23583656 TTTTATTTATTATT
1 TTTTATTT-TTATT
23583670 CTAATACTTA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
21 4 0.13
22 19 0.63
23 7 0.23
ACGTcount: A:0.21, C:0.04, G:0.00, T:0.75
Consensus pattern (22 bp):
TTTTATTTTTATTTTCTATATT
Found at i:23583710 original size:17 final size:18
Alignment explanation
Indices: 23583690--23583723 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
23583680 GATTTTAAAT
23583690 TTATTTTAATT-TTTCTA
1 TTATTTTAATTATTTCTA
*
23583707 TTATTTTTATTATTTCT
1 TTATTTTAATTATTTCT
23583724 TTTTTACTAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.21, C:0.06, G:0.00, T:0.74
Consensus pattern (18 bp):
TTATTTTAATTATTTCTA
Found at i:23583856 original size:27 final size:25
Alignment explanation
Indices: 23583821--23583872 Score: 68
Period size: 25 Copynumber: 2.0 Consensus size: 25
23583811 TTTTAGTTGC
* *
23583821 TTTATTTATTTATTTTCTTAAACTTAT
1 TTTAATTA-TTATTTT-TTAAAATTAT
23583848 TTTAATTATTATTTTTTAAAATTAT
1 TTTAATTATTATTTTTTAAAATTAT
23583873 ATTTTATGGT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
25 9 0.39
26 7 0.30
27 7 0.30
ACGTcount: A:0.31, C:0.04, G:0.00, T:0.65
Consensus pattern (25 bp):
TTTAATTATTATTTTTTAAAATTAT
Found at i:23586509 original size:19 final size:19
Alignment explanation
Indices: 23586485--23586523 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
23586475 GTCTCATGCC
23586485 ACAAT-CTATAAAAATTATT
1 ACAATCCTA-AAAAATTATT
*
23586504 ACAATCCTAGAAAATTATT
1 ACAATCCTAAAAAATTATT
23586523 A
1 A
23586524 AAATAAAGTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 15 0.83
20 3 0.17
ACGTcount: A:0.51, C:0.13, G:0.03, T:0.33
Consensus pattern (19 bp):
ACAATCCTAAAAAATTATT
Found at i:23586951 original size:60 final size:59
Alignment explanation
Indices: 23586858--23587051 Score: 192
Period size: 60 Copynumber: 3.2 Consensus size: 59
23586848 GCACATCAAT
* ** * * *
23586858 TTGTGGACAAGCCACCAGTATTTTAGGTAAACTGCCA-AAATTGCAAACAAGCTGCCAGTA
1 TTGTGGACAAGCCACCAGTAATGCAGATAAACTGCCAGAAAGTG--AACAAGCTACCAGTA
* * * *
23586918 TTGTGGACAAGCCACCAGTAATGCATATAAACTGCTAGTAAAGTGGACTAGCTACCAGTA
1 TTGTGGACAAGCCACCAGTAATGCAGATAAACTGCCAG-AAAGTGAACAAGCTACCAGTA
* * * * *
23586978 ATGTGAACAAGCCACCAGTAATGCAGATAAACTGCTAGTAATGTGAACTAGCTACCAGTA
1 TTGTGGACAAGCCACCAGTAATGCAGATAAACTGCCAG-AAAGTGAACAAGCTACCAGTA
* *
23587038 ATGTGAACAAGCCA
1 TTGTGGACAAGCCA
23587052 TCAAAATTGC
Statistics
Matches: 117, Mismatches: 15, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
60 112 0.96
62 5 0.04
ACGTcount: A:0.37, C:0.21, G:0.21, T:0.22
Consensus pattern (59 bp):
TTGTGGACAAGCCACCAGTAATGCAGATAAACTGCCAGAAAGTGAACAAGCTACCAGTA
Found at i:23586977 original size:20 final size:20
Alignment explanation
Indices: 23586954--23586998 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
23586944 ATAAACTGCT
* * *
23586954 AGTAAAGTGGACTAGCTACC
1 AGTAAAGTGAACAAGCCACC
*
23586974 AGTAATGTGAACAAGCCACC
1 AGTAAAGTGAACAAGCCACC
23586994 AGTAA
1 AGTAA
23586999 TGCAGATAAA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.40, C:0.20, G:0.22, T:0.18
Consensus pattern (20 bp):
AGTAAAGTGAACAAGCCACC
Found at i:23586999 original size:20 final size:20
Alignment explanation
Indices: 23586971--23587051 Score: 76
Period size: 20 Copynumber: 4.0 Consensus size: 20
23586961 TGGACTAGCT
23586971 ACCAGTAATGTGAACAAGCC
1 ACCAGTAATGTGAACAAGCC
* *
23586991 ACCAGTAATGCAGATA-AA-CT
1 ACCAGTAATG-TGA-ACAAGCC
* * * *
23587011 GCTAGTAATGTGAACTAGCT
1 ACCAGTAATGTGAACAAGCC
23587031 ACCAGTAATGTGAACAAGCC
1 ACCAGTAATGTGAACAAGCC
23587051 A
1 A
23587052 TCAAAATTGC
Statistics
Matches: 47, Mismatches: 10, Indels: 8
0.72 0.15 0.12
Matches are distributed among these distances:
18 1 0.02
19 3 0.06
20 38 0.81
21 4 0.09
22 1 0.02
ACGTcount: A:0.40, C:0.21, G:0.20, T:0.20
Consensus pattern (20 bp):
ACCAGTAATGTGAACAAGCC
Found at i:23587063 original size:60 final size:60
Alignment explanation
Indices: 23586907--23587077 Score: 236
Period size: 60 Copynumber: 2.9 Consensus size: 60
23586897 ATTGCAAACA
* * * * *
23586907 AGCTGCCAGTATTGTGGACAAGCCACCAGTAATGCATATAAACTGCTAGTAAAGTGGACT
1 AGCTACCAGTAATGTGAACAAGCCACCAGTAATGCAGATAAACTGCTAGTAAAGTGAACT
*
23586967 AGCTACCAGTAATGTGAACAAGCCACCAGTAATGCAGATAAACTGCTAGTAATGTGAACT
1 AGCTACCAGTAATGTGAACAAGCCACCAGTAATGCAGATAAACTGCTAGTAAAGTGAACT
* * * *
23587027 AGCTACCAGTAATGTGAACAAGCCATCA-AAATTGCAGACAAGCTGCTAGTA
1 AGCTACCAGTAATGTGAACAAGCCACCAGTAA-TGCAGATAAACTGCTAGTA
23587078 CTTCATTCGT
Statistics
Matches: 100, Mismatches: 10, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
59 2 0.02
60 98 0.98
ACGTcount: A:0.37, C:0.20, G:0.21, T:0.22
Consensus pattern (60 bp):
AGCTACCAGTAATGTGAACAAGCCACCAGTAATGCAGATAAACTGCTAGTAAAGTGAACT
Found at i:23592342 original size:37 final size:39
Alignment explanation
Indices: 23592283--23592357 Score: 100
Period size: 37 Copynumber: 2.0 Consensus size: 39
23592273 CATGTTAACA
* *
23592283 TTTAATTGATTTTTAAAATTTAAAAA-TATTTTTTATAT
1 TTTAATTGAATTTTAAAATTTAAAAACAATTTTTTATAT
**
23592321 TTTAA-TGAATTTTAATTTTTAAAAACAATTTTTTATA
1 TTTAATTGAATTTTAAAATTTAAAAACAATTTTTTATA
23592358 ATTGTTTTTT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
37 17 0.53
38 15 0.47
ACGTcount: A:0.40, C:0.01, G:0.03, T:0.56
Consensus pattern (39 bp):
TTTAATTGAATTTTAAAATTTAAAAACAATTTTTTATAT
Found at i:23596768 original size:21 final size:21
Alignment explanation
Indices: 23596742--23596782 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
23596732 AGACGAGCAA
* *
23596742 TACTCCACAGCAGGTGGAGTG
1 TACTCCAAAACAGGTGGAGTG
23596763 TACTCCAAAACAGGTGGAGT
1 TACTCCAAAACAGGTGGAGT
23596783 TTGAGCAGAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.29, C:0.22, G:0.29, T:0.20
Consensus pattern (21 bp):
TACTCCAAAACAGGTGGAGTG
Found at i:23600207 original size:18 final size:18
Alignment explanation
Indices: 23600168--23600209 Score: 50
Period size: 17 Copynumber: 2.3 Consensus size: 18
23600158 ATTTCGAATT
*
23600168 TTTTATAATTATTAAGTA
1 TTTTATAATTATTAAGGA
*
23600186 TTTTA-AATTATTTAGGA
1 TTTTATAATTATTAAGGA
23600203 GTTTTAT
1 -TTTTAT
23600210 GTTAACAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 3
0.80 0.08 0.12
Matches are distributed among these distances:
17 10 0.50
18 10 0.50
ACGTcount: A:0.33, C:0.00, G:0.10, T:0.57
Consensus pattern (18 bp):
TTTTATAATTATTAAGGA
Found at i:23607520 original size:25 final size:25
Alignment explanation
Indices: 23607492--23607543 Score: 63
Period size: 28 Copynumber: 2.0 Consensus size: 25
23607482 TTTAGATCTT
23607492 TGTTC-TT-TTATTTTGTTCATTTTTA
1 TGTTCATTCTTATTTTGTT--TTTTTA
23607517 TGTTCATTTCTTATTTTGTTTTTTTA
1 TGTTCA-TTCTTATTTTGTTTTTTTA
23607543 T
1 T
23607544 AGAACTATTT
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
25 5 0.21
26 7 0.29
27 2 0.08
28 10 0.42
ACGTcount: A:0.12, C:0.08, G:0.08, T:0.73
Consensus pattern (25 bp):
TGTTCATTCTTATTTTGTTTTTTTA
Found at i:23620963 original size:100 final size:100
Alignment explanation
Indices: 23620790--23620990 Score: 249
Period size: 100 Copynumber: 2.0 Consensus size: 100
23620780 TACCCCTGAG
* * * * * *
23620790 GTTGCAATTTAAAAGATTAAAGCCACAATAGCAGATTTTACTTTCCTGACTGTGTAGTGGAATAG
1 GTTGCAATTAAAAAGATTAAAGCCACAATAGCAGATCTTACTTTCCTGACGGTGCAGTAGAACAG
** *
23620855 ATTGAAGCTACAACAGCGGATCTTGCTTCCCCGAC
66 ATTGAAGCTACAACAGCAAATCTTACTTCCCCGAC
* * * ** * *
23620890 GTTGCAGTTAAAAAGATTGAAGCCACAATGGTGGATCTTACTTTCTTGGCGGTGCAGTAGAACAG
1 GTTGCAATTAAAAAGATTAAAGCCACAATAGCAGATCTTACTTTCCTGACGGTGCAGTAGAACAG
*
23620955 ATTGAAGCTACAACAGCAAATCTTACTTCCCTGAC
66 ATTGAAGCTACAACAGCAAATCTTACTTCCCCGAC
23620990 G
1 G
23620991 AACCTTATTT
Statistics
Matches: 84, Mismatches: 17, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
100 84 1.00
ACGTcount: A:0.31, C:0.20, G:0.21, T:0.28
Consensus pattern (100 bp):
GTTGCAATTAAAAAGATTAAAGCCACAATAGCAGATCTTACTTTCCTGACGGTGCAGTAGAACAG
ATTGAAGCTACAACAGCAAATCTTACTTCCCCGAC
Found at i:23623267 original size:70 final size:70
Alignment explanation
Indices: 23623149--23623279 Score: 210
Period size: 70 Copynumber: 1.9 Consensus size: 70
23623139 TCTTTTCAAA
*
23623149 CTCACGTTTTAAACGACCCCGGGAATTAAGAAGAAATCATGTCCTAACTTACTGGGCATGATCCT
1 CTCAAGTTTTAAACGACCCCGGGAATTAAGAAGAAATCATGTCCTAACTTACTGGGCATGATCCT
23623214 TTTTT
66 TTTTT
* * *
23623219 CTCAAGTTTTAAACGATCTCGGGAATTAAGAA-AAGATCGTGTCCTAACTTACTGGGCATGA
1 CTCAAGTTTTAAACGACCCCGGGAATTAAGAAGAA-ATCATGTCCTAACTTACTGGGCATGA
23623280 CCCCTTTTCT
Statistics
Matches: 56, Mismatches: 4, Indels: 2
0.90 0.06 0.03
Matches are distributed among these distances:
69 2 0.04
70 54 0.96
ACGTcount: A:0.31, C:0.21, G:0.19, T:0.30
Consensus pattern (70 bp):
CTCAAGTTTTAAACGACCCCGGGAATTAAGAAGAAATCATGTCCTAACTTACTGGGCATGATCCT
TTTTT
Found at i:23624448 original size:11 final size:10
Alignment explanation
Indices: 23624403--23624462 Score: 54
Period size: 9 Copynumber: 6.1 Consensus size: 10
23624393 TGATTTAGAA
23624403 TATTAAAAA-
1 TATTAAAAAT
23624412 TATTAAAAA-
1 TATTAAAAAT
**
23624421 TGGTAAAGAAT
1 TATTAAA-AAT
23624432 TATTAAAAAT
1 TATTAAAAAT
23624442 TATTTAAAAAT
1 TA-TTAAAAAT
*
23624453 T-CTAAAAAT
1 TATTAAAAAT
23624462 T
1 T
23624463 CTAAATTCTA
Statistics
Matches: 43, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
9 22 0.51
10 7 0.16
11 14 0.33
ACGTcount: A:0.57, C:0.02, G:0.05, T:0.37
Consensus pattern (10 bp):
TATTAAAAAT
Found at i:23626106 original size:25 final size:25
Alignment explanation
Indices: 23626011--23626094 Score: 78
Period size: 25 Copynumber: 3.2 Consensus size: 25
23626001 AATGGTAAGA
* * *
23626011 TACTTTGATGTTTATAATGATGAAT
1 TACTTTGATTTTTGTAATGAGGAAT
** *
23626036 TACTTTGATTCTTCTACGTTTTTAGGAAT
1 TACTTTGATT-TT-T--GTAATGAGGAAT
23626065 TACTTTGATTTTTGTAATGAGGAAT
1 TACTTTGATTTTTGTAATGAGGAAT
23626090 TACTT
1 TACTT
23626095 GTTTAGTTGT
Statistics
Matches: 46, Mismatches: 9, Indels: 8
0.73 0.14 0.13
Matches are distributed among these distances:
25 23 0.50
26 2 0.04
27 2 0.04
28 2 0.04
29 17 0.37
ACGTcount: A:0.26, C:0.08, G:0.15, T:0.50
Consensus pattern (25 bp):
TACTTTGATTTTTGTAATGAGGAAT
Found at i:23627441 original size:55 final size:57
Alignment explanation
Indices: 23627320--23627467 Score: 198
Period size: 55 Copynumber: 2.6 Consensus size: 57
23627310 ATTATGATTT
23627320 TTATT-AATTCATATTTTAATAATAATTATATTAAAAATGTTATTAAATTATATATTATA
1 TTATTAAATT-ATA-TTTAATAATAATTATATTAAAAATG-TATTAAATTATATATTATA
* *
23627379 TTATTAAATTATATTTAATAATAATTATGTTAAAATATG-ATTAAATTATTTA-T-TA
1 TTATTAAATTATATTTAATAATAATTATATTAAAA-ATGTATTAAATTATATATTATA
*
23627434 TTATTAAATTATATTTAATAATAACT-TATTAAAA
1 TTATTAAATTATATTTAATAATAATTATATTAAAA
23627468 TTTAATAATA
Statistics
Matches: 83, Mismatches: 4, Indels: 9
0.86 0.04 0.09
Matches are distributed among these distances:
54 7 0.08
55 27 0.33
56 1 0.01
57 12 0.14
58 21 0.25
59 11 0.13
60 4 0.05
ACGTcount: A:0.47, C:0.01, G:0.02, T:0.50
Consensus pattern (57 bp):
TTATTAAATTATATTTAATAATAATTATATTAAAAATGTATTAAATTATATATTATA
Found at i:23627450 original size:20 final size:19
Alignment explanation
Indices: 23627359--23627450 Score: 77
Period size: 20 Copynumber: 4.9 Consensus size: 19
23627349 ATTAAAAATG
23627359 TTATTAAATTATATATTATA
1 TTATTAAATTATAT-TTATA
23627379 TTATTAAATTATATTTA-A
1 TTATTAAATTATATTTATA
* * *
23627397 -TAAT-AATTATGTTAAAATA
1 TTATTAAATTATATT--TATA
*
23627416 TGATTAAA-T-TATTTATTA
1 TTATTAAATTATATTTA-TA
23627434 TTATTAAATTATATTTA
1 TTATTAAATTATATTTA
23627451 ATAATAACTT
Statistics
Matches: 56, Mismatches: 8, Indels: 16
0.70 0.10 0.20
Matches are distributed among these distances:
16 8 0.14
17 4 0.07
18 11 0.20
19 8 0.14
20 23 0.41
21 2 0.04
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (19 bp):
TTATTAAATTATATTTATA
Found at i:23633456 original size:31 final size:32
Alignment explanation
Indices: 23633408--23633480 Score: 107
Period size: 31 Copynumber: 2.4 Consensus size: 32
23633398 AAATAAACAC
* *
23633408 TAAAAA-AATTTAGAAAATTAAAAAAGTATTT
1 TAAAAATATTTTAGAAAATAAAAAAAGTATTT
23633439 TAAAAATATTTTA-AAAATAAAAAAAGTATTT
1 TAAAAATATTTTAGAAAATAAAAAAAGTATTT
23633470 T-AAAATATTTT
1 TAAAAATATTTT
23633481 TTTAAAAAAA
Statistics
Matches: 39, Mismatches: 2, Indels: 3
0.89 0.05 0.07
Matches are distributed among these distances:
30 10 0.26
31 24 0.62
32 5 0.13
ACGTcount: A:0.59, C:0.00, G:0.04, T:0.37
Consensus pattern (32 bp):
TAAAAATATTTTAGAAAATAAAAAAAGTATTT
Found at i:23636856 original size:16 final size:17
Alignment explanation
Indices: 23636837--23636870 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
23636827 GAATAATTTT
*
23636837 ATTTTTAT-TAATTTAA
1 ATTTTTATAAAATTTAA
23636853 ATTTTTATAAAATTTAA
1 ATTTTTATAAAATTTAA
23636870 A
1 A
23636871 AAGTATCTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 8 0.50
17 8 0.50
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (17 bp):
ATTTTTATAAAATTTAA
Found at i:23638301 original size:32 final size:32
Alignment explanation
Indices: 23638223--23638327 Score: 86
Period size: 32 Copynumber: 3.2 Consensus size: 32
23638213 TGGTTCTGTG
* ** * * *
23638223 AAATAATAACAAATATCAAAATTTCATGTTGTG
1 AAATGATAACAAATATC-AACGTTAATTTTGTA
*
23638256 AAATCATAACAAAT-TACAACGTTAATTTTGTA
1 AAATGATAACAAATAT-CAACGTTAATTTTGTA
* * * *
23638288 AAATGATAACAAATATCAACTTTCATTTTCTT
1 AAATGATAACAAATATCAACGTTAATTTTGTA
23638320 AAATGATA
1 AAATGATA
23638328 CAACGTTAAT
Statistics
Matches: 59, Mismatches: 11, Indels: 5
0.79 0.15 0.07
Matches are distributed among these distances:
32 44 0.75
33 15 0.25
ACGTcount: A:0.47, C:0.11, G:0.07, T:0.35
Consensus pattern (32 bp):
AAATGATAACAAATATCAACGTTAATTTTGTA
Found at i:23640932 original size:42 final size:42
Alignment explanation
Indices: 23640817--23640938 Score: 147
Period size: 42 Copynumber: 2.9 Consensus size: 42
23640807 GTTTCTGTTT
* * *
23640817 AACCCTAATGGGTTTCCT-TTCAGCTCTTTTAAGCTTCAGTTT
1 AACCCTAATGGGTTT-CTGTTCAGCTCTTATATGCTTCAGTTC
* *
23640859 AACCCTTATGGGTTTCTGTTCAGCTCTTATATGCTTCCGTTC
1 AACCCTAATGGGTTTCTGTTCAGCTCTTATATGCTTCAGTTC
* * *
23640901 AACCCTCATGGGTTTCTGTTTAGCACTTATATGTCTTC
1 AACCCTAATGGGTTTCTGTTCAGCTCTTATATG-CTTC
23640939 TGAAAACGAT
Statistics
Matches: 70, Mismatches: 8, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
41 2 0.03
42 64 0.91
43 4 0.06
ACGTcount: A:0.17, C:0.25, G:0.16, T:0.43
Consensus pattern (42 bp):
AACCCTAATGGGTTTCTGTTCAGCTCTTATATGCTTCAGTTC
Found at i:23643181 original size:91 final size:92
Alignment explanation
Indices: 23642954--23643166 Score: 286
Period size: 92 Copynumber: 2.3 Consensus size: 92
23642944 TGAACACTCC
* * * *
23642954 AGTTTATGGATAAACCACAAGTATTTGCAGGTTAATACACTGCCAGTAGGTTGTGAATGCACAAC
1 AGTTTATGGATAAACCACCAGTATTTGCAGGTTAATAAACTGCCACTAGGTTGTAAATGCACAAC
23643019 ATGTTTGACAAATAAAAGTTGCCAGTA
66 ATGTTTGACAAATAAAAGTTGCCAGTA
* * *
23643046 AGTTTATGGATGAACCACCAGTGTTTGCAGGTTAATAAGCTGCCACTAGGTTGTAAATGCACAAC
1 AGTTTATGGATAAACCACCAGTATTTGCAGGTTAATAAACTGCCACTAGGTTGTAAATGCACAAC
* * * *
23643111 GTGTTTG-TAGATAAAAGCTT-CTAGTA
66 ATGTTTGACAAATAAAAG-TTGCCAGTA
* *
23643137 AGTTTGTGGATAAATCACCAGTATTTGCAG
1 AGTTTATGGATAAACCACCAGTATTTGCAG
23643167 ACTATTAAAT
Statistics
Matches: 105, Mismatches: 15, Indels: 3
0.85 0.12 0.02
Matches are distributed among these distances:
91 39 0.37
92 66 0.63
ACGTcount: A:0.33, C:0.15, G:0.22, T:0.30
Consensus pattern (92 bp):
AGTTTATGGATAAACCACCAGTATTTGCAGGTTAATAAACTGCCACTAGGTTGTAAATGCACAAC
ATGTTTGACAAATAAAAGTTGCCAGTA
Found at i:23643375 original size:38 final size:38
Alignment explanation
Indices: 23643244--23643376 Score: 135
Period size: 38 Copynumber: 3.5 Consensus size: 38
23643234 ATAGTACAAT
* **
23643244 ACAGAAACAGTGAA-CATGCTTAACATGTATTTGGTTCA
1 ACAGTAACAGT-AAGCATGCTTAACATGTATTCAGTTCA
* ** * *
23643282 ACACTAGTAGT-AGACATGCTTAACATGTATTCAATTTA
1 ACAGTAACAGTAAG-CATGCTTAACATGTATTCAGTTCA
* * *
23643320 ACAGCAACAGTAGGCATGTTTAACATGTATTCAGTTCA
1 ACAGTAACAGTAAGCATGCTTAACATGTATTCAGTTCA
23643358 ACAGTAACAGTAAGCATGC
1 ACAGTAACAGTAAGCATGC
23643377 AACCAGTAAC
Statistics
Matches: 73, Mismatches: 19, Indels: 6
0.74 0.19 0.06
Matches are distributed among these distances:
36 1 0.01
38 71 0.97
39 1 0.01
ACGTcount: A:0.37, C:0.17, G:0.17, T:0.29
Consensus pattern (38 bp):
ACAGTAACAGTAAGCATGCTTAACATGTATTCAGTTCA
Found at i:23645891 original size:13 final size:13
Alignment explanation
Indices: 23645875--23645899 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
23645865 AAATCTTAAA
23645875 ATTATTATTATTT
1 ATTATTATTATTT
23645888 ATTATTATTATT
1 ATTATTATTATT
23645900 ATTGCCATTA
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:0.00, G:0.00, T:0.68
Consensus pattern (13 bp):
ATTATTATTATTT
Found at i:23646190 original size:14 final size:13
Alignment explanation
Indices: 23646171--23646201 Score: 53
Period size: 14 Copynumber: 2.3 Consensus size: 13
23646161 TTCTCTTCCC
23646171 TTTTTCTTTTCTT
1 TTTTTCTTTTCTT
23646184 ATTTTTCTTTTCTT
1 -TTTTTCTTTTCTT
23646198 TTTT
1 TTTT
23646202 CTAGGCCTGC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 4 0.24
14 13 0.76
ACGTcount: A:0.03, C:0.13, G:0.00, T:0.84
Consensus pattern (13 bp):
TTTTTCTTTTCTT
Found at i:23651286 original size:7 final size:7
Alignment explanation
Indices: 23651263--23651287 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
23651253 TCAGTTGTCA
23651263 GTTAGTT
1 GTTAGTT
23651270 GTTAGTT
1 GTTAGTT
23651277 GTTAGTT
1 GTTAGTT
23651284 GTTA
1 GTTA
23651288 AGTCAGCAGT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.16, C:0.00, G:0.28, T:0.56
Consensus pattern (7 bp):
GTTAGTT
Found at i:23653922 original size:17 final size:16
Alignment explanation
Indices: 23653873--23653924 Score: 59
Period size: 18 Copynumber: 3.1 Consensus size: 16
23653863 ATGCAGGCCC
23653873 AGAAAAAGAAAAGAAA
1 AGAAAAAGAAAAGAAA
*
23653889 AGAAAAAGGGAAGAGAAA
1 AGAAAAA--GAAAAGAAA
*
23653907 GGAAAATAGAAAAGAAA
1 AGAAAA-AGAAAAGAAA
23653924 A
1 A
23653925 ATGAGGCATA
Statistics
Matches: 29, Mismatches: 4, Indels: 5
0.76 0.11 0.13
Matches are distributed among these distances:
16 7 0.24
17 8 0.28
18 13 0.45
19 1 0.03
ACGTcount: A:0.73, C:0.00, G:0.25, T:0.02
Consensus pattern (16 bp):
AGAAAAAGAAAAGAAA
Found at i:23654722 original size:20 final size:20
Alignment explanation
Indices: 23654697--23654745 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 20
23654687 TAATTATTTA
* *
23654697 GATAAAGTTTGTATTTCATT
1 GATAAAATTTCTATTTCATT
* *
23654717 GATAAAATTTCTGTTTCCTT
1 GATAAAATTTCTATTTCATT
23654737 GATAAAATT
1 GATAAAATT
23654746 CAACGATAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.33, C:0.08, G:0.12, T:0.47
Consensus pattern (20 bp):
GATAAAATTTCTATTTCATT
Found at i:23659566 original size:14 final size:14
Alignment explanation
Indices: 23659547--23659577 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
23659537 ATGATTGTTT
*
23659547 TAATCTAAATTTAC
1 TAATCTAAATTAAC
23659561 TAATCTAAATTAAC
1 TAATCTAAATTAAC
23659575 TAA
1 TAA
23659578 GAACGCGACA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.48, C:0.13, G:0.00, T:0.39
Consensus pattern (14 bp):
TAATCTAAATTAAC
Found at i:23660546 original size:22 final size:22
Alignment explanation
Indices: 23660517--23660584 Score: 91
Period size: 22 Copynumber: 3.1 Consensus size: 22
23660507 TGCACTGATG
23660517 AACAGAGAGCACTGAAGTGCTA
1 AACAGAGAGCACTGAAGTGCTA
* * * *
23660539 TACAGAGAGTACAGATGTGCTA
1 AACAGAGAGCACTGAAGTGCTA
*
23660561 AACAGAGAGCACTGACGTGCTA
1 AACAGAGAGCACTGAAGTGCTA
23660583 AA
1 AA
23660585 TATCAGAGAG
Statistics
Matches: 38, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 38 1.00
ACGTcount: A:0.40, C:0.18, G:0.26, T:0.16
Consensus pattern (22 bp):
AACAGAGAGCACTGAAGTGCTA
Found at i:23661721 original size:5 final size:5
Alignment explanation
Indices: 23661711--23661783 Score: 53
Period size: 5 Copynumber: 14.6 Consensus size: 5
23661701 TATATACATA
* * *
23661711 ATAAT ATAAT AAAAT ATTAT AATAAT ATAAT ATAAT A-ACAT ACTTAT
1 ATAAT ATAAT ATAAT ATAAT -ATAAT ATAAT ATAAT ATA-AT A-TAAT
* *
23661758 -TAAT TTAGT A-AAT ATAAT ATAAT ATA
1 ATAAT ATAAT ATAAT ATAAT ATAAT ATA
23661784 TATTTTAAAT
Statistics
Matches: 53, Mismatches: 9, Indels: 12
0.72 0.12 0.16
Matches are distributed among these distances:
4 7 0.13
5 40 0.75
6 6 0.11
ACGTcount: A:0.56, C:0.03, G:0.01, T:0.40
Consensus pattern (5 bp):
ATAAT
Found at i:23661731 original size:13 final size:13
Alignment explanation
Indices: 23661710--23661748 Score: 60
Period size: 13 Copynumber: 3.0 Consensus size: 13
23661700 ATATATACAT
23661710 AATAATATAATAA
1 AATAATATAATAA
*
23661723 AATATTATAATAA
1 AATAATATAATAA
*
23661736 TATAATATAATAA
1 AATAATATAATAA
23661749 CATACTTATT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (13 bp):
AATAATATAATAA
Found at i:23661732 original size:21 final size:21
Alignment explanation
Indices: 23661708--23661747 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
23661698 TTATATATAC
23661708 ATAATAATATAATAAAATATT
1 ATAATAATATAATAAAATATT
*
23661729 ATAATAATATAATATAATA
1 ATAATAATATAATAAAATA
23661748 ACATACTTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (21 bp):
ATAATAATATAATAAAATATT
Found at i:23663699 original size:9 final size:8
Alignment explanation
Indices: 23663683--23663707 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
23663673 TCAATATATA
23663683 TGTTTTTT
1 TGTTTTTT
23663691 TGTTTTTT
1 TGTTTTTT
23663699 TGTTTTTT
1 TGTTTTTT
23663707 T
1 T
23663708 ATTTGAGAGC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.00, C:0.00, G:0.12, T:0.88
Consensus pattern (8 bp):
TGTTTTTT
Found at i:23664699 original size:6 final size:6
Alignment explanation
Indices: 23664680--23664713 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
23664670 ATAAGTCTAA
* *
23664680 AAAAAT AACAAT AAACAT AAAAAT AAAAAT AAAA
1 AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT AAAA
23664714 CAAATGGACT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.79, C:0.06, G:0.00, T:0.15
Consensus pattern (6 bp):
AAAAAT
Found at i:23665697 original size:13 final size:13
Alignment explanation
Indices: 23665681--23665705 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
23665671 TAAAAATACA
23665681 TTTTAACTTGAAT
1 TTTTAACTTGAAT
23665694 TTTTAACTTGAA
1 TTTTAACTTGAA
23665706 AAAAATTGAA
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:0.08, G:0.08, T:0.52
Consensus pattern (13 bp):
TTTTAACTTGAAT
Found at i:23671975 original size:16 final size:16
Alignment explanation
Indices: 23671954--23671987 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
23671944 AAGAGGATAT
23671954 TTCTTGGGTAAGTGCA
1 TTCTTGGGTAAGTGCA
*
23671970 TTCTTGGGTAGGTGCA
1 TTCTTGGGTAAGTGCA
23671986 TT
1 TT
23671988 GTAGTCTCCT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.15, C:0.12, G:0.32, T:0.41
Consensus pattern (16 bp):
TTCTTGGGTAAGTGCA
Found at i:23673419 original size:5 final size:5
Alignment explanation
Indices: 23673409--23673434 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
23673399 GGTAAGTTCG
23673409 TAAAT TAAAT TAAAT TAAAT TAAAT T
1 TAAAT TAAAT TAAAT TAAAT TAAAT T
23673435 CTGTTTTGGT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (5 bp):
TAAAT
Found at i:23673659 original size:45 final size:45
Alignment explanation
Indices: 23673543--23673661 Score: 175
Period size: 45 Copynumber: 2.6 Consensus size: 45
23673533 TTCAAACATG
* * * *
23673543 TAAGACCATAATTGAAAGACACTATGACACTATACCATAGATGAA
1 TAAGACCATAGTTGAAAGACACTATGGCACTATACCAAAAATGAA
*
23673588 TAAGACCATAGTTGAAAGACACTATGGCACTATATCAAAAATGAA
1 TAAGACCATAGTTGAAAGACACTATGGCACTATACCAAAAATGAA
* *
23673633 TAAGTCCATAGTTGAAAGGCACTATGGCA
1 TAAGACCATAGTTGAAAGACACTATGGCA
23673662 TCATGTCAGA
Statistics
Matches: 67, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
45 67 1.00
ACGTcount: A:0.44, C:0.17, G:0.17, T:0.23
Consensus pattern (45 bp):
TAAGACCATAGTTGAAAGACACTATGGCACTATACCAAAAATGAA
Found at i:23673695 original size:45 final size:45
Alignment explanation
Indices: 23673543--23673684 Score: 169
Period size: 45 Copynumber: 3.2 Consensus size: 45
23673533 TTCAAACATG
* * * * * *
23673543 TAAGACCATAATTGAAAGACACTATGACACTATACCATAGATGAA
1 TAAGACCATAGTTGAAAGACACTATGGCACTATATCAAAAATAAA
*
23673588 TAAGACCATAGTTGAAAGACACTATGGCACTATATCAAAAATGAA
1 TAAGACCATAGTTGAAAGACACTATGGCACTATATCAAAAATAAA
* * * *
23673633 TAAGTCCATAGTTGAAAGGCACTATGGCA-TCATGTCAGAAATAAA
1 TAAGACCATAGTTGAAAGACACTATGGCACT-ATATCAAAAATAAA
23673678 TAAGACC
1 TAAGACC
23673685 GTGGCTGAAA
Statistics
Matches: 85, Mismatches: 11, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
44 1 0.01
45 84 0.99
ACGTcount: A:0.44, C:0.17, G:0.16, T:0.23
Consensus pattern (45 bp):
TAAGACCATAGTTGAAAGACACTATGGCACTATATCAAAAATAAA
Done.