Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold5184.1
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: 30403
ACGTcount: A:0.25, C:0.12, G:0.13, T:0.25
Warning! 7487 characters in sequence are not A, C, G, or T
Found at i:5483 original size:6 final size:6
Alignment explanation
Indices: 5472--5519 Score: 51
Period size: 6 Copynumber: 8.0 Consensus size: 6
5462 TATGCAGTCA
* * * * *
5472 TCAAAT TCAAAT TCGAAT TCAGAT CCAAAT CCAAAT TCAAAT CCAAAT
1 TCAAAT TCAAAT TCAAAT TCAAAT TCAAAT TCAAAT TCAAAT TCAAAT
5520 CCAGATCCAC
Statistics
Matches: 35, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
6 35 1.00
ACGTcount: A:0.46, C:0.23, G:0.04, T:0.27
Consensus pattern (6 bp):
TCAAAT
Found at i:5508 original size:18 final size:18
Alignment explanation
Indices: 5472--5549 Score: 75
Period size: 18 Copynumber: 4.3 Consensus size: 18
5462 TATGCAGTCA
* * *
5472 TCAAATTCAAATTCGAAT
1 TCAAATCCAAATCCAAAT
*
5490 TCAGATCCAAATCCAAAT
1 TCAAATCCAAATCCAAAT
*
5508 TCAAATCCAAATCCAGAT
1 TCAAATCCAAATCCAAAT
* * *
5526 CCACATCCACATCCAAAAT
1 TCAAATCCAAATCC-AAAT
5545 TCAAA
1 TCAAA
5550 AGTCATATCC
Statistics
Matches: 47, Mismatches: 12, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
18 41 0.87
19 6 0.13
ACGTcount: A:0.45, C:0.28, G:0.04, T:0.23
Consensus pattern (18 bp):
TCAAATCCAAATCCAAAT
Found at i:5514 original size:12 final size:12
Alignment explanation
Indices: 5472--5549 Score: 57
Period size: 12 Copynumber: 6.4 Consensus size: 12
5462 TATGCAGTCA
*
5472 TCAAATTCAAAT
1 TCAAATCCAAAT
* * *
5484 TCGAATTCAGAT
1 TCAAATCCAAAT
*
5496 CCAAATCCAAAT
1 TCAAATCCAAAT
5508 TCAAATCCAAAT
1 TCAAATCCAAAT
* * *
5520 CCAGATCCACAT
1 TCAAATCCAAAT
* *
5532 CCACATCCAAAAT
1 TCAAATCC-AAAT
5545 TCAAA
1 TCAAA
5550 AGTCATATCC
Statistics
Matches: 51, Mismatches: 14, Indels: 1
0.77 0.21 0.02
Matches are distributed among these distances:
12 45 0.88
13 6 0.12
ACGTcount: A:0.45, C:0.28, G:0.04, T:0.23
Consensus pattern (12 bp):
TCAAATCCAAAT
Found at i:5520 original size:6 final size:6
Alignment explanation
Indices: 5494--5542 Score: 62
Period size: 6 Copynumber: 8.2 Consensus size: 6
5484 TCGAATTCAG
* * * *
5494 ATCCAA ATCCAA ATTCAA ATCCAA ATCCAG ATCCAC ATCCAC ATCCAA
1 ATCCAA ATCCAA ATCCAA ATCCAA ATCCAA ATCCAA ATCCAA ATCCAA
5542 A
1 A
5543 ATTCAAAAGT
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
6 38 1.00
ACGTcount: A:0.45, C:0.35, G:0.02, T:0.18
Consensus pattern (6 bp):
ATCCAA
Found at i:5722 original size:43 final size:42
Alignment explanation
Indices: 5675--5757 Score: 148
Period size: 43 Copynumber: 2.0 Consensus size: 42
5665 ATATTTTTAT
5675 TTATGTTTTAGTAGTTTATTAAAATAAGGGAAACTATTTTCCC
1 TTATGTTTTAGTAGTTTATTAAAATAAGGG-AACTATTTTCCC
*
5718 TTATGTTTTAGTAGTTTATTAGAATAAGGGAACTATTTTC
1 TTATGTTTTAGTAGTTTATTAAAATAAGGGAACTATTTTC
5758 TGAATTAGGA
Statistics
Matches: 39, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
42 10 0.26
43 29 0.74
ACGTcount: A:0.31, C:0.07, G:0.16, T:0.46
Consensus pattern (42 bp):
TTATGTTTTAGTAGTTTATTAAAATAAGGGAACTATTTTCCC
Found at i:6397 original size:16 final size:16
Alignment explanation
Indices: 6376--6406 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
6366 ACCCTAAAAA
6376 AATAAAAAAAATCAAG
1 AATAAAAAAAATCAAG
*
6392 AATAAAGAAAATCAA
1 AATAAAAAAAATCAA
6407 TCAAAAAAAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.74, C:0.06, G:0.06, T:0.13
Consensus pattern (16 bp):
AATAAAAAAAATCAAG
Found at i:7824 original size:84 final size:83
Alignment explanation
Indices: 7710--8097 Score: 410
Period size: 84 Copynumber: 4.6 Consensus size: 83
7700 TGGAGTAGGC
*
7710 TAAAAAGTTCAAATTCTGTTTCCTCGAGATGGTAGTGGAGCAGACTGAAGATTAAAGTCTTCCTG
1 TAAAAAGTTCAGATTCTG-TTCCTCGAGATGGTAGTGGAGCAGACTGAAGATTAAAGTCTTCCTG
*
7775 ATATGACAGGGAAGCAAAT
65 AAATGACAGGGAAGCAAAT
** * * * * *
7794 TGGAAAGTTTAGATTCTATCTCCTCGAGATGGTAGT-GAGGTAGACTGAAGATTGAGGTCTTCCT
1 TAAAAAGTTCAGATTCTGT-TCCTCGAGATGGTAGTGGA-GCAGACTGAAGATTAAAGTCTTCCT
* *
7858 GAAATAGTA-A-GGAAGTAGAT
64 GAAAT-G-ACAGGGAAGCAAAT
* *
7878 TAAAAAGTTCAGATTATGTTCCCTCGAGATGGTAGTGGAGCAGACTGAAGGTTAAAGTCTTCCTG
1 TAAAAAGTTCAGATTCTGTT-CCTCGAGATGGTAGTGGAGCAGACTGAAGATTAAAGTCTTCCTG
* *
7943 ATATGACAGAGAAGCAAAT
65 AAATGACAGGGAAGCAAAT
* * *
7962 TAGAAAGTTCAGATTCTGTCTCCTCGAGAT-GTAGT-GAGGCAGATTGAAGATTGAAGTCTTCCT
1 TAAAAAGTTCAGATTCTGT-TCCTCGAGATGGTAGTGGA-GCAGACTGAAGATTAAAGTCTTCCT
* * *
8025 GAAAT-AGCAAGGAAGCAGAC
64 GAAATGA-CAGGGAAGCAAAT
* * * * *
8045 TAAAAATTTTAGATCCTGTTCCCTCGATATGGTAGTGGAGCACACTGAAGATT
1 TAAAAAGTTCAGATTCTGTT-CCTCGAGATGGTAGTGGAGCAGACTGAAGATT
8098 GCAGAATAAA
Statistics
Matches: 249, Mismatches: 41, Indels: 28
0.78 0.13 0.09
Matches are distributed among these distances:
82 5 0.02
83 69 0.28
84 167 0.67
85 7 0.03
86 1 0.00
ACGTcount: A:0.33, C:0.14, G:0.25, T:0.28
Consensus pattern (83 bp):
TAAAAAGTTCAGATTCTGTTCCTCGAGATGGTAGTGGAGCAGACTGAAGATTAAAGTCTTCCTGA
AATGACAGGGAAGCAAAT
Found at i:7988 original size:168 final size:167
Alignment explanation
Indices: 7709--8097 Score: 598
Period size: 168 Copynumber: 2.3 Consensus size: 167
7699 GTGGAGTAGG
* *
7709 CTAAAAAGTTCAAATTCTGTTTCCTCGAGATGGTAGTGGAGCAGACTGAAGATTAAAGTCTTCCT
1 CTAAAAAGTTCAGATTCTGTTCCCTCGAGATGGTAGTGGAGCAGACTGAAGATTAAAGTCTTCCT
* * * *
7774 GATATGACAGGGAAGCAAATTGGAAAGTTTAGATTCTATCTCCTCGAGATGGTAGTGAGGTAGAC
66 GATATGACAGAGAAGCAAATTAGAAAGTTCAGATTCTATCTCCTCGAGAT-GTAGTGAGGCAGAC
* * *
7839 TGAAGATTGAGGTCTTCCTGAAATAGTAAGGAAGTAGA
130 TGAAGATTGAAGTCTTCCTGAAATAGCAAGGAAGCAGA
* * *
7877 TTAAAAAGTTCAGATTATGTTCCCTCGAGATGGTAGTGGAGCAGACTGAAGGTTAAAGTCTTCCT
1 CTAAAAAGTTCAGATTCTGTTCCCTCGAGATGGTAGTGGAGCAGACTGAAGATTAAAGTCTTCCT
* *
7942 GATATGACAGAGAAGCAAATTAGAAAGTTCAGATTCTGTCTCCTCGAGATGTAGTGAGGCAGATT
66 GATATGACAGAGAAGCAAATTAGAAAGTTCAGATTCTATCTCCTCGAGATGTAGTGAGGCAGACT
8007 GAAGATTGAAGTCTTCCTGAAATAGCAAGGAAGCAGA
131 GAAGATTGAAGTCTTCCTGAAATAGCAAGGAAGCAGA
* * * * *
8044 CTAAAAATTTTAGATCCTGTTCCCTCGATATGGTAGTGGAGCACACTGAAGATT
1 CTAAAAAGTTCAGATTCTGTTCCCTCGAGATGGTAGTGGAGCAGACTGAAGATT
8098 GCAGAATAAA
Statistics
Matches: 199, Mismatches: 22, Indels: 1
0.90 0.10 0.00
Matches are distributed among these distances:
167 93 0.47
168 106 0.53
ACGTcount: A:0.33, C:0.14, G:0.25, T:0.28
Consensus pattern (167 bp):
CTAAAAAGTTCAGATTCTGTTCCCTCGAGATGGTAGTGGAGCAGACTGAAGATTAAAGTCTTCCT
GATATGACAGAGAAGCAAATTAGAAAGTTCAGATTCTATCTCCTCGAGATGTAGTGAGGCAGACT
GAAGATTGAAGTCTTCCTGAAATAGCAAGGAAGCAGA
Found at i:8136 original size:59 final size:59
Alignment explanation
Indices: 8039--8157 Score: 152
Period size: 59 Copynumber: 2.0 Consensus size: 59
8029 TAGCAAGGAA
* * * * *
8039 GCAGACTAAAAATTTTAGATCCTGTTCCCTCGATATGGTAGTG-GAGCACACTGAAGATT
1 GCAGAATAAAAAGTTCAGATCCTGTTCCCTCGAGATGGTAGTGAG-GCAAACTGAAGATT
*
8098 GCAGAATAAAAAGTTCAGATTCTG-TCTCCTCGAGATGGTAGTGAGGCAAACTGAAGATT
1 GCAGAATAAAAAGTTCAGATCCTGTTC-CCTCGAGATGGTAGTGAGGCAAACTGAAGATT
8157 G
1 G
8158 AAGTCTTCCT
Statistics
Matches: 52, Mismatches: 6, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
58 2 0.04
59 49 0.94
60 1 0.02
ACGTcount: A:0.32, C:0.17, G:0.24, T:0.27
Consensus pattern (59 bp):
GCAGAATAAAAAGTTCAGATCCTGTTCCCTCGAGATGGTAGTGAGGCAAACTGAAGATT
Found at i:8222 original size:143 final size:142
Alignment explanation
Indices: 7965--8241 Score: 371
Period size: 143 Copynumber: 1.9 Consensus size: 142
7955 AGCAAATTAG
* *
7965 AAAGTTCAGATTCTGTCTCCTCGAGATGTAGTGAGGCAGATTGAAGATTGAAGTCTTCCTGAAAT
1 AAAGTTCAGATTCTGTCTCCTCGAGATGTAGTGAGGCAAACTGAAGATTGAAGTCTTCCTGAAAT
* * * * *
8030 AGCAAGGAAGCAGACTAAAAATTTTAGATCCTGTTCCCTCGATATGGTAGTG-GAGCACACTGAA
66 AGCAAGGAAGCAAACTAAAAAGTTCAGATCCTATTCCCTCGAGATGGTAGTGAG-GCACACTGAA
8094 GATTGCAGAATAA
130 GATTGCAGAATAA
*
8107 AAAGTTCAGATTCTGTCTCCTCGAGATGGTAGTGAGGCAAACTGAAGATTGAAGTCTTCCTGATA
1 AAAGTTCAGATTCTGTCTCCTCGAGAT-GTAGTGAGGCAAACTGAAGATTGAAGTCTTCCTGAAA
* * * * * *
8172 T-GACAGGGAAGTAAATTGAAAAGTTCAGATTCTA-TCTCCTCGAGATGGTAGTGAGGCAGACTG
65 TAG-CAAGGAAGCAAACTAAAAAGTTCAGATCCTATTC-CCTCGAGATGGTAGTGAGGCACACTG
8235 AAGATTG
128 AAGATTG
8242 AAGTCTTCCT
Statistics
Matches: 117, Mismatches: 14, Indels: 7
0.85 0.10 0.05
Matches are distributed among these distances:
142 30 0.26
143 86 0.74
144 1 0.01
ACGTcount: A:0.32, C:0.16, G:0.25, T:0.27
Consensus pattern (142 bp):
AAAGTTCAGATTCTGTCTCCTCGAGATGTAGTGAGGCAAACTGAAGATTGAAGTCTTCCTGAAAT
AGCAAGGAAGCAAACTAAAAAGTTCAGATCCTATTCCCTCGAGATGGTAGTGAGGCACACTGAAG
ATTGCAGAATAA
Found at i:8247 original size:84 final size:84
Alignment explanation
Indices: 8104--8325 Score: 306
Period size: 84 Copynumber: 2.6 Consensus size: 84
8094 GATTGCAGAA
*
8104 TAAAAAGTTCAGATTCTGTCTCCTCGAGATGGTAGTGAGGCAAACTGAAGATTGAAGTCTTCCTG
1 TAAAAAGTTCAGATTCTGTCTCCTCGAGATGGTAGTGAGGCAGACTGAAGATTGAAGTCTTCCTG
* * *
8169 ATAT-GACAGGGAAGTAAAT
66 AAATAG-CAAGGAAGCAAAT
* *
8188 TGAAAAGTTCAGATTCTATCTCCTCGAGATGGTAGTGAGGCAGACTGAAGATTGAAGTCTTCCTG
1 TAAAAAGTTCAGATTCTGTCTCCTCGAGATGGTAGTGAGGCAGACTGAAGATTGAAGTCTTCCTG
*
8253 AAATAGCAAGGAAGCAGAT
66 AAATAGCAAGGAAGCAAAT
* * *
8272 TAAAAATTTCAGATTTTGT-TCTCTCGAGATGGTAGTG-GAGCAGTCTGAAGATTG
1 TAAAAAGTTCAGATTCTGTCTC-CTCGAGATGGTAGTGAG-GCAGACTGAAGATTG
8326 CAGAGTGAAA
Statistics
Matches: 123, Mismatches: 12, Indels: 6
0.87 0.09 0.04
Matches are distributed among these distances:
83 3 0.02
84 119 0.97
85 1 0.01
ACGTcount: A:0.32, C:0.14, G:0.26, T:0.28
Consensus pattern (84 bp):
TAAAAAGTTCAGATTCTGTCTCCTCGAGATGGTAGTGAGGCAGACTGAAGATTGAAGTCTTCCTG
AAATAGCAAGGAAGCAAAT
Found at i:8326 original size:227 final size:225
Alignment explanation
Indices: 7878--8480 Score: 831
Period size: 227 Copynumber: 2.7 Consensus size: 225
7868 GGAAGTAGAT
* *
7878 TAAAAAGTTCAGATTATGT-TCCCTCGAGATGGTAGTG-GAGCAGACTGAAGGTTAAAGTCTTCC
1 TAAAAAGTTCAGATTCTGTCT-CCTCGAGATGGTAGTGAG-GCAGACTGAAGATT-AAGTCTTCC
*
7941 TGATATGACAGAGAAGCAAATTAGAAAGTTCAGATTCTGTCTCCTCGAGAT-GTAGTGAGGCAGA
63 TGATATGACAGGGAAGCAAATTA-AAAGTTCAGATTCTGTCTCCTCGAGATGGTAGTGAGGCAGA
* *
8005 TTGAAGATTGAAGTCTTCCTGAAATAGCAAGGAAGCAGACTAAAAATTTTAGATCCTGTTCCCTC
127 CTGAAGATTGAAGTCTTCCTGAAATAGCAAGGAAGCAGACTAAAAATTTCAGATCCTGTTCCCTC
*
8070 GATATGGTAGTGGAGCACACTGAAGATTGCAGAA
192 GAGATGGTAGTGGAGCACACTGAAGATTGCAGAA
*
8104 TAAAAAGTTCAGATTCTGTCTCCTCGAGATGGTAGTGAGGCAAACTGAAGATTGAAGTCTTCCTG
1 TAAAAAGTTCAGATTCTGTCTCCTCGAGATGGTAGTGAGGCAGACTGAAGATT-AAGTCTTCCTG
* *
8169 ATATGACAGGGAAGTAAATTGAAAAGTTCAGATTCTATCTCCTCGAGATGGTAGTGAGGCAGACT
65 ATATGACAGGGAAGCAAATT-AAAAGTTCAGATTCTGTCTCCTCGAGATGGTAGTGAGGCAGACT
* ** *
8234 GAAGATTGAAGTCTTCCTGAAATAGCAAGGAAGCAGATTAAAAATTTCAGATTTTGTTCTCTCGA
129 GAAGATTGAAGTCTTCCTGAAATAGCAAGGAAGCAGACTAAAAATTTCAGATCCTGTTCCCTCGA
** *
8299 GATGGTAGTGGAGCAGTCTGAAGATTGCAGAG
194 GATGGTAGTGGAGCACACTGAAGATTGCAGAA
* * * *
8331 TGAAAAGTTCAGATTCTTTCTCCTCAAGATGGTAGTGAGGCAGACTGAAGATTAAGGTATTCCTG
1 TAAAAAGTTCAGATTCTGTCTCCTCGAGATGGTAGTGAGGCAGACTGAAGATTAA-GTCTTCCTG
* * * * * *
8396 AAAT-AGCAAGGAAGCAGATTAAAAAATTCAGATTCTGT-TCTCTCGATATGGTAGTG-GAGCGG
65 ATATGA-CAGGGAAGCAAATT-AAAAGTTCAGATTCTGTCTC-CTCGAGATGGTAGTGAG-GCAG
8458 ACTGAAGATTGAAGTCTTCCTGA
126 ACTGAAGATTGAAGTCTTCCTGA
8481 TATGATAGGG
Statistics
Matches: 338, Mismatches: 31, Indels: 15
0.88 0.08 0.04
Matches are distributed among these distances:
226 107 0.32
227 231 0.68
ACGTcount: A:0.33, C:0.15, G:0.25, T:0.28
Consensus pattern (225 bp):
TAAAAAGTTCAGATTCTGTCTCCTCGAGATGGTAGTGAGGCAGACTGAAGATTAAGTCTTCCTGA
TATGACAGGGAAGCAAATTAAAAGTTCAGATTCTGTCTCCTCGAGATGGTAGTGAGGCAGACTGA
AGATTGAAGTCTTCCTGAAATAGCAAGGAAGCAGACTAAAAATTTCAGATCCTGTTCCCTCGAGA
TGGTAGTGGAGCACACTGAAGATTGCAGAA
Found at i:8376 original size:143 final size:143
Alignment explanation
Indices: 8188--8468 Score: 474
Period size: 143 Copynumber: 2.0 Consensus size: 143
8178 GGAAGTAAAT
* *
8188 TGAAAAGTTCAGATTCTATCTCCTCGAGATGGTAGTGAGGCAGACTGAAGATTGAA-GTCTTCCT
1 TGAAAAGTTCAGATTCTATCTCCTCAAGATGGTAGTGAGGCAGACTGAAGATT-AAGGTATTCCT
* * *
8252 GAAATAGCAAGGAAGCAGATTAAAAATTTCAGATTTTGTTCTCTCGAGATGGTAGTGGAGCAGTC
65 GAAATAGCAAGGAAGCAGATTAAAAAATTCAGATTCTGTTCTCTCGAGATGGTAGTGGAGCAGAC
8317 TGAAGATTGCAGAG
130 TGAAGATTGCAGAG
*
8331 TGAAAAGTTCAGATTCTTTCTCCTCAAGATGGTAGTGAGGCAGACTGAAGATTAAGGTATTCCTG
1 TGAAAAGTTCAGATTCTATCTCCTCAAGATGGTAGTGAGGCAGACTGAAGATTAAGGTATTCCTG
* *
8396 AAATAGCAAGGAAGCAGATTAAAAAATTCAGATTCTGTTCTCTCGATATGGTAGTGGAGCGGACT
66 AAATAGCAAGGAAGCAGATTAAAAAATTCAGATTCTGTTCTCTCGAGATGGTAGTGGAGCAGACT
8461 GAAGATTG
131 GAAGATTG
8469 AAGTCTTCCT
Statistics
Matches: 129, Mismatches: 8, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
142 2 0.02
143 127 0.98
ACGTcount: A:0.32, C:0.14, G:0.26, T:0.28
Consensus pattern (143 bp):
TGAAAAGTTCAGATTCTATCTCCTCAAGATGGTAGTGAGGCAGACTGAAGATTAAGGTATTCCTG
AAATAGCAAGGAAGCAGATTAAAAAATTCAGATTCTGTTCTCTCGAGATGGTAGTGGAGCAGACT
GAAGATTGCAGAG
Found at i:8466 original size:84 final size:84
Alignment explanation
Indices: 8325--8636 Score: 307
Period size: 84 Copynumber: 3.7 Consensus size: 84
8315 TCTGAAGATT
* *
8325 GCAGAGTGAAAAGTTCAGATTCT-TTCTCCTCAAGATGGTAGTGAGGCAGACTGAAGATT-AAGG
1 GCAGATTGAAAAGTTCAGATTCTGTTCT-CTCGAGATGGTAGTGAGGCAGACTGAAGATTGAA-G
*
8388 TATTCCTGAAATAGCAAGGAA
64 TCTTCCTGAAATAGCAAGGAA
* * * *
8409 GCAGATTAAAAAATTCAGATTCTGTTCTCTCGATATGGTAGTG-GAGCGGACTGAAGATTGAAGT
1 GCAGATTGAAAAGTTCAGATTCTGTTCTCTCGAGATGGTAGTGAG-GCAGACTGAAGATTGAAGT
*
8473 CTTCCTGATAT-G-ATAGGGAA
65 CTTCCTGAAATAGCA-A-GGAA
* * * * * * *
8493 GTAAATTGGAAAGTTCAAATTCTG-TCTTATTGAGATGGTAGTGAGGCAGACAGAAGATTGAAGT
1 GCAGATTGAAAAGTTCAGATTCTGTTC-TCTCGAGATGGTAGTGAGGCAGACTGAAGATTGAAGT
8557 CTTCCTGAAATAGCAAGGAA
65 CTTCCTGAAATAGCAAGGAA
* * * * * *
8577 GCAGATTGAAAATTTTAGATTTTGTTCCCTTGAAATGGTAGTG-GAGCA-ATCTGAAGATTG
1 GCAGATTGAAAAGTTCAGATTCTGTTCTCTCGAGATGGTAGTGAG-GCAGA-CTGAAGATTG
8637 CAGAGTGAAA
Statistics
Matches: 185, Mismatches: 31, Indels: 24
0.77 0.13 0.10
Matches are distributed among these distances:
82 1 0.01
83 7 0.04
84 165 0.89
85 11 0.06
86 1 0.01
ACGTcount: A:0.33, C:0.12, G:0.26, T:0.29
Consensus pattern (84 bp):
GCAGATTGAAAAGTTCAGATTCTGTTCTCTCGAGATGGTAGTGAGGCAGACTGAAGATTGAAGTC
TTCCTGAAATAGCAAGGAA
Found at i:8497 original size:311 final size:311
Alignment explanation
Indices: 8098--8787 Score: 1037
Period size: 311 Copynumber: 2.2 Consensus size: 311
8088 ACTGAAGATT
*
8098 GCAGAATAAAAAGTTCAGATTCTGTCTCCTCGAGATGGTAGTGAGGCAAACTGAAGATTGAAGTC
1 GCAGATTAAAAAGTTCAGATTCTGTCTCCTCGAGATGGTAGTGAGGCAAACTGAAGATTGAAGTC
* *
8163 TTCCTGATATGACAGGGAAGTAAATTGAAAAGTTCAGATTCTATCTCCTCGAGATGGTAGTGAGG
66 TTCCTGATATGACAGGGAAGTAAATTGAAAAGTTCAAATTCTATCTCATCGAGATGGTAGTGAGG
*
8228 CAGACTGAAGATTGAAGTCTTCCTGAAATAGCAAGGAAGCAGATTAAAAATTTCAGATTTTGTTC
131 CAGACAGAAGATTGAAGTCTTCCTGAAATAGCAAGGAAGCAGATTAAAAATTTCAGATTTTGTTC
* * * * *
8293 TCTCGAGATGGTAGTGGAGCAGTCTGAAGATTGCAGAGTGAAAAGTTCAGATTCTTTCTCCTCAA
196 CCTCGAAATGGTAGTGGAGCAATCTGAAGATTGCAGAGTGAAAAGTTCAGATTCTGTCTCCCCAA
*
8358 GATGGTAGTGAGGCAGACTGAAGATT-AAGGTATTCCTGAAAT-AGCAAGGAA
261 GATGGTAGTGAGGCAAACTGAAGATTGAA-GTATTCCTGAAATGA-CAAGGAA
* * **
8409 GCAGATTAAAAAATTCAGATTCTGT-TCTCTCGATATGGTAGTG-GAGCGGACTGAAGATTGAAG
1 GCAGATTAAAAAGTTCAGATTCTGTCTC-CTCGAGATGGTAGTGAG-GCAAACTGAAGATTGAAG
* * * * *
8472 TCTTCCTGATATGATAGGGAAGTAAATTGGAAAGTTCAAATTCTGTCTTATTGAGATGGTAGTGA
64 TCTTCCTGATATGACAGGGAAGTAAATTGAAAAGTTCAAATTCTATCTCATCGAGATGGTAGTGA
* *
8537 GGCAGACAGAAGATTGAAGTCTTCCTGAAATAGCAAGGAAGCAGATTGAAAATTTTAGATTTTGT
129 GGCAGACAGAAGATTGAAGTCTTCCTGAAATAGCAAGGAAGCAGATTAAAAATTTCAGATTTTGT
*
8602 TCCCTTGAAATGGTAGTGGAGCAATCTGAAGATTGCAGAGTGAAAAGTTCAGATTCTGTCTCCCC
194 TCCCTCGAAATGGTAGTGGAGCAATCTGAAGATTGCAGAGTGAAAAGTTCAGATTCTGTCTCCCC
* * * * *
8667 GAGATGTTAGTGAGGCAAACTGAAGATTGAAGTCTTCCTGATATGACAGGGAA
259 AAGATGGTAGTGAGGCAAACTGAAGATTGAAGTATTCCTGAAATGACAAGGAA
* ** *
8720 GCAAATTGGAAAGTTCAGATTCTGTCTCCTCGAGATGGTAGTGAGGCAAACTGCAGATTGAAGTC
1 GCAGATTAAAAAGTTCAGATTCTGTCTCCTCGAGATGGTAGTGAGGCAAACTGAAGATTGAAGTC
8785 TTC
66 TTC
8788 TTGAAATAGA
Statistics
Matches: 338, Mismatches: 35, Indels: 12
0.88 0.09 0.03
Matches are distributed among these distances:
310 3 0.01
311 329 0.97
312 6 0.02
ACGTcount: A:0.32, C:0.14, G:0.26, T:0.28
Consensus pattern (311 bp):
GCAGATTAAAAAGTTCAGATTCTGTCTCCTCGAGATGGTAGTGAGGCAAACTGAAGATTGAAGTC
TTCCTGATATGACAGGGAAGTAAATTGAAAAGTTCAAATTCTATCTCATCGAGATGGTAGTGAGG
CAGACAGAAGATTGAAGTCTTCCTGAAATAGCAAGGAAGCAGATTAAAAATTTCAGATTTTGTTC
CCTCGAAATGGTAGTGGAGCAATCTGAAGATTGCAGAGTGAAAAGTTCAGATTCTGTCTCCCCAA
GATGGTAGTGAGGCAAACTGAAGATTGAAGTATTCCTGAAATGACAAGGAA
Found at i:8655 original size:227 final size:227
Alignment explanation
Indices: 8417--8851 Score: 624
Period size: 227 Copynumber: 1.9 Consensus size: 227
8407 AAGCAGATTA
* * **
8417 AAAAATTCAGATTCTGT-TCTCTCGATATGGTAGTG-GAGCGGACTGAAGATTGAAGTCTTCCTG
1 AAAAATTCAGATTCTGTCTC-CCCGAGATGGTAGTGAG-GCAAACTGAAGATTGAAGTCTTCCTG
* * * * *
8480 ATATGATAGGGAAGTAAATTGGAAAGTTCAAATTCTGTCTTATTGAGATGGTAGTGAGGCAGACA
64 ATATGACAGGGAAGCAAATTGGAAAGTTCAAATTCTGTCTCATCGAGATGGTAGTGAGGCAAACA
* * *
8545 GAAGATTGAAGTCTTCCTGAAATAGCAAGGAAGCAGATTGAAAATTTTAGATTTTGTTCCCTTGA
129 GAAGATTGAAGTCTTCCTGAAATAGAAAGGAAGCAGATTGAAAATTTCAGATTTTGTTCCCTCGA
8610 AATGGT-AGTGGAGCAATCTGAAGATTGCAGAGTG
194 AATGGTAAG-GGAGCAATCTGAAGATTGCAGAGTG
* *
8644 AAAAGTTCAGATTCTGTCTCCCCGAGATGTTAGTGAGGCAAACTGAAGATTGAAGTCTTCCTGAT
1 AAAAATTCAGATTCTGTCTCCCCGAGATGGTAGTGAGGCAAACTGAAGATTGAAGTCTTCCTGAT
* * * *
8709 ATGACAGGGAAGCAAATTGGAAAGTTCAGATTCTGTCTCCTCGAGATGGTAGTGAGGCAAACTGC
66 ATGACAGGGAAGCAAATTGGAAAGTTCAAATTCTGTCTCATCGAGATGGTAGTGAGGCAAACAGA
* * * *
8774 AGATTGAAGTCTTCTTGAAATAGAAAGGAAGCAGTTTGAAAATTTCAGCTTTTGTTCCCTCGAGA
131 AGATTGAAGTCTTCCTGAAATAGAAAGGAAGCAGATTGAAAATTTCAGATTTTGTTCCCTCGAAA
8839 TGGTAAGGGAGCA
196 TGGTAAGGGAGCA
8852 GATCGTAGAA
Statistics
Matches: 183, Mismatches: 22, Indels: 6
0.87 0.10 0.03
Matches are distributed among these distances:
227 178 0.97
228 5 0.03
ACGTcount: A:0.31, C:0.14, G:0.26, T:0.29
Consensus pattern (227 bp):
AAAAATTCAGATTCTGTCTCCCCGAGATGGTAGTGAGGCAAACTGAAGATTGAAGTCTTCCTGAT
ATGACAGGGAAGCAAATTGGAAAGTTCAAATTCTGTCTCATCGAGATGGTAGTGAGGCAAACAGA
AGATTGAAGTCTTCCTGAAATAGAAAGGAAGCAGATTGAAAATTTCAGATTTTGTTCCCTCGAAA
TGGTAAGGGAGCAATCTGAAGATTGCAGAGTG
Found at i:8656 original size:59 final size:59
Alignment explanation
Indices: 8577--8695 Score: 134
Period size: 59 Copynumber: 2.0 Consensus size: 59
8567 TAGCAAGGAA
* * * * * *
8577 GCAGATTGAAAATTTTAGATTTTGT-TCCCTTGAAATGGTAGTG-GAGCAATCTGAAGATT
1 GCAGAGTGAAAAGTTCAGATTCTGTCTCCC-CGAAATGGTAGTGAG-GCAAACTGAAGATT
* *
8636 GCAGAGTGAAAAGTTCAGATTCTGTCTCCCCGAGATGTTAGTGAGGCAAACTGAAGATT
1 GCAGAGTGAAAAGTTCAGATTCTGTCTCCCCGAAATGGTAGTGAGGCAAACTGAAGATT
8695 G
1 G
8696 AAGTCTTCCT
Statistics
Matches: 50, Mismatches: 8, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
59 45 0.90
60 5 0.10
ACGTcount: A:0.30, C:0.13, G:0.26, T:0.30
Consensus pattern (59 bp):
GCAGAGTGAAAAGTTCAGATTCTGTCTCCCCGAAATGGTAGTGAGGCAAACTGAAGATT
Found at i:8804 original size:84 final size:84
Alignment explanation
Indices: 8642--8843 Score: 264
Period size: 84 Copynumber: 2.4 Consensus size: 84
8632 GATTGCAGAG
* *
8642 TGAAAAGTTCAGATTCTGTCTCCCCGAGATGTTAGTGAGGCAAACTGAAGATTGAAGTCTTCCTG
1 TGAAAAGTTCAGATTCTGTCTCCTCGAGATGGTAGTGAGGCAAACTGAAGATTGAAGTCTTCCTG
* *
8707 ATATGACAGGGAAGCAAAT
66 AAATGACAAGGAAGCAAAT
* * *
8726 TGGAAAGTTCAGATTCTGTCTCCTCGAGATGGTAGTGAGGCAAACTGCAGATTGAAGTCTTCTTG
1 TGAAAAGTTCAGATTCTGTCTCCTCGAGATGGTAGTGAGGCAAACTGAAGATTGAAGTCTTCCTG
**
8791 AAATAGA-AAGGAAGCAGTT
66 AAAT-GACAAGGAAGCAAAT
* * *
8810 TGAAAATTTCAGCTTTTGT-TCCCTCGAGATGGTA
1 TGAAAAGTTCAGATTCTGTCT-CCTCGAGATGGTA
8844 AGGGAGCAGA
Statistics
Matches: 103, Mismatches: 13, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
83 1 0.01
84 100 0.97
85 2 0.02
ACGTcount: A:0.30, C:0.16, G:0.25, T:0.29
Consensus pattern (84 bp):
TGAAAAGTTCAGATTCTGTCTCCTCGAGATGGTAGTGAGGCAAACTGAAGATTGAAGTCTTCCTG
AAATGACAAGGAAGCAAAT
Found at i:8992 original size:87 final size:88
Alignment explanation
Indices: 8845--9083 Score: 270
Period size: 89 Copynumber: 2.7 Consensus size: 88
8835 GAGATGGTAA
* * * ** *
8845 GGGAGCAGATCGTAGAAAGCAGATTTGACAATCC-CCATATTGGTGGGGAGCAGATCGAAGATAG
1 GGGAGCAGATCGAAGATAGCAGATTTGAC--GCCTCTGTATTGAT-GGGAGCAGATCGAAGATAG
*
8909 TAGATTTGGCATCTCTATATTA-AC-
63 CAGATTTGGCATCTCTATATTAGACG
* * *
8933 GGGAGCATATCGAAGATAGCAGATTTGGCGTCTCTGTATTGATGGAGAGCAGATCGAAGATAGCA
1 GGGAGCAGATCGAAGATAGCAGATTTGACGCCTCTGTATTGATGG-GAGCAGATCGAAGATAGCA
*
8998 GATTTGGCATCTCTGTATTAGACG
65 GATTTGGCATCTCTATATTAGACG
* * *
9022 GGGAGCAGATCGAAGATAGTAGATTTGATGCCTCTGTATTGGCA-GGGAGCAGATCAAAGATA
1 GGGAGCAGATCGAAGATAGCAGATTTGACGCCTCTGTATT-G-ATGGGAGCAGATCGAAGATA
9084 TCAGCATGAC
Statistics
Matches: 128, Mismatches: 17, Indels: 11
0.82 0.11 0.07
Matches are distributed among these distances:
86 3 0.02
87 44 0.34
88 27 0.21
89 50 0.39
90 3 0.02
91 1 0.01
ACGTcount: A:0.31, C:0.15, G:0.30, T:0.25
Consensus pattern (88 bp):
GGGAGCAGATCGAAGATAGCAGATTTGACGCCTCTGTATTGATGGGAGCAGATCGAAGATAGCAG
ATTTGGCATCTCTATATTAGACG
Found at i:8994 original size:44 final size:43
Alignment explanation
Indices: 8845--9083 Score: 239
Period size: 44 Copynumber: 5.4 Consensus size: 43
8835 GAGATGGTAA
* * * * ** **
8845 GGGAGCAGATCGTAGAAAGCAGATTTGACAATCCCCATATTGGTG
1 GGGAGCAGATCGAAGATAGCAGATTTGGC-ATCTCTGTATT-GAC
* * *
8890 GGGAGCAGATCGAAGATAGTAGATTTGGCATCTCTATATTAAC
1 GGGAGCAGATCGAAGATAGCAGATTTGGCATCTCTGTATTGAC
* * *
8933 GGGAGCATATCGAAGATAGCAGATTTGGCGTCTCTGTATTGAT
1 GGGAGCAGATCGAAGATAGCAGATTTGGCATCTCTGTATTGAC
8976 GGAGAGCAGATCGAAGATAGCAGATTTGGCATCTCTGTATTAGAC
1 GG-GAGCAGATCGAAGATAGCAGATTTGGCATCTCTGTATT-GAC
* *
9021 GGGGAGCAGATCGAAGATAGTAGATTT-G-ATGCCTCTGTATTGGC
1 -GGGAGCAGATCGAAGATAGCAGATTTGGCAT--CTCTGTATTGAC
*
9065 AGGGAGCAGATCAAAGATA
1 -GGGAGCAGATCGAAGATA
9084 TCAGCATGAC
Statistics
Matches: 167, Mismatches: 22, Indels: 11
0.83 0.11 0.05
Matches are distributed among these distances:
43 41 0.25
44 65 0.39
45 59 0.35
46 2 0.01
ACGTcount: A:0.31, C:0.15, G:0.30, T:0.25
Consensus pattern (43 bp):
GGGAGCAGATCGAAGATAGCAGATTTGGCATCTCTGTATTGAC
Found at i:10558 original size:3 final size:3
Alignment explanation
Indices: 10550--10885 Score: 134
Period size: 3 Copynumber: 115.3 Consensus size: 3
10540 GCATTATTTC
* * *
10550 TAT TAT TAT TAT TAT TAC TAT TAT TA- TAC T-T TAT TAT TAT T-G TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* * * * * *
10595 T-T TAA TAT CA- TAT CTAT TAT TAT TCT TAT TAA TA- TGT TAT TAG
1 TAT TAT TAT TAT TAT -TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* * * * *
10638 TAT TTT CTAT TAT TAT TGT TAT TAT TA- TAT TAT TTT TCT TA- TGT
1 TAT TAT -TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* * * * * * * * *
10682 TAT TAT TTT CTAT TCT TAT CAC CAT TAT TAA CA- TAT CAT TAT TAA
1 TAT TAT TAT -TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* * ** *
10727 TA- TAT T-T T-T TCAA TAT TTT TAT TAT TAT CGT TAT T-T CAT TAT
1 TAT TAT TAT TAT T-AT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* * *
10769 TAT ATCT TAC TAT TA- TATT TAT TAT TTT TAT T-T TAT T-T CTAT TAT
1 TAT -TAT TAT TAT TAT TA-T TAT TAT TAT TAT TAT TAT TAT -TAT TAT
* * *
10814 TAT T-T TCAT TAC TAT TAT TAT TAT TAT TAT TAT TTT TAT TAA TAT
1 TAT TAT T-AT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* *
10859 TAT GT-T T-T TAC TAT TAT AAT TAT TAT T
1 TAT -TAT TAT TAT TAT TAT TAT TAT TAT T
10886 TTTGCTACTA
Statistics
Matches: 242, Mismatches: 65, Indels: 52
0.67 0.18 0.14
Matches are distributed among these distances:
2 29 0.12
3 197 0.81
4 16 0.07
ACGTcount: A:0.29, C:0.07, G:0.02, T:0.62
Consensus pattern (3 bp):
TAT
Found at i:10575 original size:9 final size:9
Alignment explanation
Indices: 10542--10575 Score: 50
Period size: 9 Copynumber: 3.8 Consensus size: 9
10532 AATATTTTGC
*
10542 ATTATTTCT
1 ATTATTACT
*
10551 ATTATTATT
1 ATTATTACT
10560 ATTATTACT
1 ATTATTACT
10569 ATTATTA
1 ATTATTA
10576 TACTTTATTA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
9 22 1.00
ACGTcount: A:0.32, C:0.06, G:0.00, T:0.62
Consensus pattern (9 bp):
ATTATTACT
Found at i:10679 original size:17 final size:17
Alignment explanation
Indices: 10647--10695 Score: 55
Period size: 17 Copynumber: 2.8 Consensus size: 17
10637 GTATTTTCTA
*
10647 TTATTATTGTTATTAT-
1 TTATTATTTTTATTATG
*
10663 TATATTATTTTTCTTATG
1 T-TATTATTTTTATTATG
10681 TTATTATTTTCTATT
1 TTATTATTTT-TATT
10696 CTTATCACCA
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
16 1 0.04
17 22 0.81
18 4 0.15
ACGTcount: A:0.22, C:0.04, G:0.04, T:0.69
Consensus pattern (17 bp):
TTATTATTTTTATTATG
Found at i:10688 original size:20 final size:18
Alignment explanation
Indices: 10550--10671 Score: 58
Period size: 16 Copynumber: 6.7 Consensus size: 18
10540 GCATTATTTC
* *
10550 TATTATTATTATTATTAC
1 TATTATTATTATTGTTAT
*
10568 TATTATTA-TACT-TTAT
1 TATTATTATTATTGTTAT
* *
10584 TATTATT-GTATT-TTAA
1 TATTATTATTATTGTTAT
* *
10600 TATCATATCTATTATTATTCT
1 TAT--TAT-TATTATTGTTAT
*
10621 TATTAATATGTTATTAG-TAT
1 TATT-AT-TATTATT-GTTAT
*
10641 TTTCTATTATTATTGTTAT
1 TAT-TATTATTATTGTTAT
10660 TATTA-TATTATT
1 TATTATTATTATT
10672 TTTCTTATGT
Statistics
Matches: 80, Mismatches: 14, Indels: 21
0.70 0.12 0.18
Matches are distributed among these distances:
16 19 0.24
17 10 0.12
18 14 0.17
19 13 0.16
20 18 0.22
21 6 0.08
ACGTcount: A:0.30, C:0.05, G:0.03, T:0.61
Consensus pattern (18 bp):
TATTATTATTATTGTTAT
Found at i:10897 original size:21 final size:22
Alignment explanation
Indices: 10863--10905 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
10853 TAATATTATG
*
10863 TTTTTACTATTATAA-TTATTA
1 TTTTTACTACTATAATTTATTA
*
10884 TTTTTGCTACTATAATTTATTA
1 TTTTTACTACTATAATTTATTA
10906 CTTTATTTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 13 0.68
22 6 0.32
ACGTcount: A:0.30, C:0.07, G:0.02, T:0.60
Consensus pattern (22 bp):
TTTTTACTACTATAATTTATTA
Found at i:20917 original size:16 final size:16
Alignment explanation
Indices: 20898--20930 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
20888 GAATGGTCTC
*
20898 TGTTTCTTTTCTTCTT
1 TGTTTCTTTTATTCTT
20914 TGTTTCTTTTATTCTT
1 TGTTTCTTTTATTCTT
20930 T
1 T
20931 TACTTTATTT
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:0.03, C:0.15, G:0.06, T:0.76
Consensus pattern (16 bp):
TGTTTCTTTTATTCTT
Found at i:21710 original size:20 final size:18
Alignment explanation
Indices: 21668--21718 Score: 52
Period size: 21 Copynumber: 2.7 Consensus size: 18
21658 ATATTCAAAA
21668 ATAAAATAAATTAAAATTC
1 ATAAAA-AAATTAAAATTC
21687 --AAAAAAATATACAAATTC
1 ATAAAAAAAT-TA-AAATTC
21705 ATAAAAAAAATTAA
1 AT-AAAAAAATTAA
21719 GTACACGTGG
Statistics
Matches: 27, Mismatches: 0, Indels: 10
0.73 0.00 0.27
Matches are distributed among these distances:
16 4 0.15
17 6 0.22
18 6 0.22
19 1 0.04
20 2 0.07
21 8 0.30
ACGTcount: A:0.69, C:0.06, G:0.00, T:0.25
Consensus pattern (18 bp):
ATAAAAAAATTAAAATTC
Found at i:26216 original size:25 final size:25
Alignment explanation
Indices: 26184--26297 Score: 81
Period size: 25 Copynumber: 4.5 Consensus size: 25
26174 CTAAAGATTC
*
26184 TTTA-TATTGTTTGTTTTAAAATGT
1 TTTATTATTATTTGTTTTAAAATGT
* ** *
26208 TTTATTATTATTTATTTTAAGTTTT
1 TTTATTATTATTTGTTTTAAAATGT
* *
26233 TTTATGTAGTATTTGTTTTAAACTGT
1 TTTAT-TATTATTTGTTTTAAAATGT
**
26259 TTTATCATATTATTCAT-TTTTAACTTGT
1 TTTAT--TATTATT--TGTTTTAAAATGT
26287 TTTA-TATTATT
1 TTTATTATTATT
26298 ATTCTAGATT
Statistics
Matches: 71, Mismatches: 14, Indels: 9
0.76 0.15 0.10
Matches are distributed among these distances:
24 4 0.06
25 27 0.38
26 20 0.28
27 6 0.08
28 13 0.18
29 1 0.01
ACGTcount: A:0.25, C:0.04, G:0.08, T:0.64
Consensus pattern (25 bp):
TTTATTATTATTTGTTTTAAAATGT
Found at i:26221 original size:49 final size:51
Alignment explanation
Indices: 26167--26272 Score: 117
Period size: 51 Copynumber: 2.1 Consensus size: 51
26157 TTCTCTATGA
* *
26167 TATTTATCTAAAGATTCTTTA-TATTGTTTGTTTTAAAATGTTTTAT-TAT
1 TATTTATCTAAAGATTCTTTAGTAGTATTTGTTTTAAAATGTTTTATATAT
* * * * *
26216 TATTTATTTTAAGTTTTTTTATGTAGTATTTGTTTTAAACTGTTTTATCATAT
1 TATTTATCTAAAGATTCTTTA-GTAGTATTTGTTTTAAAATGTTTTAT-ATAT
26269 TATT
1 TATT
26273 CATTTTTAAC
Statistics
Matches: 46, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
49 17 0.37
51 22 0.48
53 7 0.15
ACGTcount: A:0.26, C:0.04, G:0.08, T:0.61
Consensus pattern (51 bp):
TATTTATCTAAAGATTCTTTAGTAGTATTTGTTTTAAAATGTTTTATATAT
Found at i:26252 original size:26 final size:25
Alignment explanation
Indices: 26193--26263 Score: 79
Period size: 26 Copynumber: 2.8 Consensus size: 25
26183 CTTTATATTG
*
26193 TTTGTTTTAAAATGTTTTATTATTA
1 TTTGTTTTAAAATGTTTTATTAGTA
* ** *
26218 TTTATTTTAAGTTTTTTTATGTAGTA
1 TTTGTTTTAAAATGTTTTAT-TAGTA
*
26244 TTTGTTTTAAACTGTTTTAT
1 TTTGTTTTAAAATGTTTTAT
26264 CATATTATTC
Statistics
Matches: 36, Mismatches: 9, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
25 16 0.44
26 20 0.56
ACGTcount: A:0.24, C:0.01, G:0.10, T:0.65
Consensus pattern (25 bp):
TTTGTTTTAAAATGTTTTATTAGTA
Found at i:26280 original size:28 final size:28
Alignment explanation
Indices: 26210--26301 Score: 77
Period size: 27 Copynumber: 3.4 Consensus size: 28
26200 TAAAATGTTT
* *
26210 TATTATTATTTA-TTTTAAGTT-TTTT-
1 TATTATTATTCATTTTTAACTTGTTTTA
* ** *
26235 TATGTAGTATTTGTTTTAAAC-TGTTTTA
1 TAT-TATTATTCATTTTTAACTTGTTTTA
26263 TCA-TATTATTCATTTTTAACTTGTTTTA
1 T-ATTATTATTCATTTTTAACTTGTTTTA
26291 TATTATTATTC
1 TATTATTATTC
26302 TAGATTATTA
Statistics
Matches: 52, Mismatches: 8, Indels: 11
0.73 0.11 0.15
Matches are distributed among these distances:
25 3 0.06
26 8 0.15
27 23 0.44
28 17 0.33
29 1 0.02
ACGTcount: A:0.25, C:0.05, G:0.07, T:0.63
Consensus pattern (28 bp):
TATTATTATTCATTTTTAACTTGTTTTA
Found at i:26980 original size:17 final size:17
Alignment explanation
Indices: 26960--26993 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
26950 GGTTCGTCTT
26960 GATTTATCCAAGCATCC
1 GATTTATCCAAGCATCC
26977 GATTTATCCAAGCATCC
1 GATTTATCCAAGCATCC
26994 TTTTTTTTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.29, C:0.29, G:0.12, T:0.29
Consensus pattern (17 bp):
GATTTATCCAAGCATCC
Done.