Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold108
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: 2128633
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 114048 characters in sequence are not A, C, G, or T
File 2 of 6
Found at i:367376 original size:153 final size:152
Alignment explanation
Indices: 367098--367442 Score: 446
Period size: 153 Copynumber: 2.3 Consensus size: 152
367088 TATCGATGAA
* * *
367098 CACGTGTGTAGTACTGTGTGAAGGCTACTACGTGTATCGGTAAATAATGGTCACGTGTGTAGTAC
1 CACGTGTGTAGTACTGTGTGAAGGCTACTACGTGTATCGATAAATAATGGCCACATGTGTAGTAC
** * *
367163 TGTGTGAAGGCTACTACGTGTATCGATAAATAATGGTCACATGTGTAGTACTAAGTGAAGGCTAC
66 TAAGTGAAGGCTACTACGTGTACCGATAAATAATGATCACATGTGTAGTACTAAGTGAAGGCTAC
* * * * *
367228 TATGTGTACCG-AGAAGCTTTGGT
131 TACGTGAACAGTA-AAAC-TTGAT
* *
367251 CACGTGTGTAGTACTGTGTGAAGGCTACTATGTGTATCGATAAATGATGGCCACATGTGTAGTA-
1 CACGTGTGTAGTACTGTGTGAAGGCTACTACGTGTATCGATAAATAATGGCCACATGTGTAGTAC
* * * *
367315 TAAAGTGAAGGCTACTATGTGTACCGA-AAAGCT-TTGATCACGTGTGTAGTACTATGTGAAGGC
66 T-AAGTGAAGGCTACTACGTGTACCGATAAA--TAATGATCACATGTGTAGTACTAAGTGAAGGC
367378 TACTACGTGAACAGTAAAACTTGAT
128 TACTACGTGAACAGTAAAACTTGAT
*
367403 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGTATCGA
1 CACGTGTGTAGTACTGTGTGAAGGCTACTACGTGTATCGA
367443 ATGATTAAAG
Statistics
Matches: 168, Mismatches: 20, Indels: 9
0.85 0.10 0.05
Matches are distributed among these distances:
152 46 0.27
153 120 0.71
154 2 0.01
ACGTcount: A:0.28, C:0.15, G:0.27, T:0.30
Consensus pattern (152 bp):
CACGTGTGTAGTACTGTGTGAAGGCTACTACGTGTATCGATAAATAATGGCCACATGTGTAGTAC
TAAGTGAAGGCTACTACGTGTACCGATAAATAATGATCACATGTGTAGTACTAAGTGAAGGCTAC
TACGTGAACAGTAAAACTTGAT
Found at i:371056 original size:42 final size:43
Alignment explanation
Indices: 370900--371180 Score: 243
Period size: 42 Copynumber: 6.6 Consensus size: 43
370890 GTTTTTGTAC
* * ** *
370900 AAAAGCGCCGCTAAAGACCATGTTCTGTAGCGATG-TTTG-TAA
1 AAAAACGCCGCTAAAGACCATGTTCTTTAGCGGCGCTTAGAT-A
** * * * **
370942 AAAAAGCGCCGCTAAAGATTATGATCTCTAGCGGCGTTTTTATA
1 AAAAA-CGCCGCTAAAGACCATGTTCTTTAGCGGCGCTTAGATA
* * * * * * *
370986 CAAAGCGCTGTTAAAGAACATGCTCTTTAGCGACGCTTA-ATA
1 AAAAACGCCGCTAAAGACCATGTTCTTTAGCGGCGCTTAGATA
** * *
371028 AAAAACGCAACTAGAGATCATGTTCTTTAGCGGCGCTT--ATGA
1 AAAAACGCCGCTAAAGACCATGTTCTTTAGCGGCGCTTAGAT-A
* * * *
371070 AAAAACACCGCTAAAGAACATGTTATTCAGCGGCGCTTAGA-A
1 AAAAACGCCGCTAAAGACCATGTTCTTTAGCGGCGCTTAGATA
371112 AAAAACGCCGCTAAAGACCATGTTCTTTAGCGGCGCTTAGAT-
1 AAAAACGCCGCTAAAGACCATGTTCTTTAGCGGCGCTTAGATA
371154 AAAAACGCCGCTAAAGACCATGTTCTT
1 AAAAACGCCGCTAAAGACCATGTTCTT
371181 CAGTGACGTT
Statistics
Matches: 193, Mismatches: 39, Indels: 14
0.78 0.16 0.06
Matches are distributed among these distances:
41 2 0.01
42 133 0.69
43 49 0.25
44 8 0.04
45 1 0.01
ACGTcount: A:0.34, C:0.21, G:0.20, T:0.25
Consensus pattern (43 bp):
AAAAACGCCGCTAAAGACCATGTTCTTTAGCGGCGCTTAGATA
Found at i:371205 original size:42 final size:42
Alignment explanation
Indices: 371159--371277 Score: 157
Period size: 42 Copynumber: 2.8 Consensus size: 42
371149 TAGATAAAAA
* *
371159 CGCCGCTAAAGACCATGTTCTTCAGTGACGTTTTTCTCTAAG
1 CGCCGCTAAAGAACATGTTCTTCAGCGACGTTTTTCTCTAAG
* * * *
371201 CGCCGCCAAAAAACATGTTCTTTAGCGGCGTTTTTCTCTAAG
1 CGCCGCTAAAGAACATGTTCTTCAGCGACGTTTTTCTCTAAG
* * *
371243 CGCCGCTAAAGAACATGATCTTTAACGACGTTTTT
1 CGCCGCTAAAGAACATGTTCTTCAGCGACGTTTTT
371278 GGTTGTAAAC
Statistics
Matches: 66, Mismatches: 11, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
42 66 1.00
ACGTcount: A:0.24, C:0.25, G:0.18, T:0.32
Consensus pattern (42 bp):
CGCCGCTAAAGAACATGTTCTTCAGCGACGTTTTTCTCTAAG
Found at i:371205 original size:84 final size:84
Alignment explanation
Indices: 370997--371230 Score: 211
Period size: 84 Copynumber: 2.8 Consensus size: 84
370987 AAAGCGCTGT
* * * ** * * * *
370997 TAAAGAACATGCTCTTTAGCGACGCTTA-ATAAAAAACGCAACTAGAGATCATGTTCTTTAGCGG
1 TAAAGAACATGTTATTCAGCGACGCTTAGA-AAAAAACGCCGCCAAAAAACATGTTCTTTAGCGG
371061 CGCTTATGAAAAAACACCGC
65 CGCTTATGAAAAAACACCGC
* * * *
371081 TAAAGAACATGTTATTCAGCGGCGCTTAGAAAAAAACGCCGCTAAAGACCATGTTCTTTAGCGGC
1 TAAAGAACATGTTATTCAGCGACGCTTAGAAAAAAACGCCGCCAAAAAACATGTTCTTTAGCGGC
*
371146 GCTTA-GATAAAAACGCCGC
66 GCTTATGA-AAAAACACCGC
* * * * ****** *
371165 TAAAGACCATGTTCTTCAGTGACGTTTTTCTCTAAGCGCCGCCAAAAAACATGTTCTTTAGCGGC
1 TAAAGAACATGTTATTCAGCGACGCTTAGAAAAAAACGCCGCCAAAAAACATGTTCTTTAGCGGC
371230 G
66 G
371231 TTTTTCTCTA
Statistics
Matches: 124, Mismatches: 24, Indels: 4
0.82 0.16 0.03
Matches are distributed among these distances:
83 2 0.02
84 121 0.98
85 1 0.01
ACGTcount: A:0.33, C:0.23, G:0.20, T:0.25
Consensus pattern (84 bp):
TAAAGAACATGTTATTCAGCGACGCTTAGAAAAAAACGCCGCCAAAAAACATGTTCTTTAGCGGC
GCTTATGAAAAAACACCGC
Found at i:372392 original size:296 final size:296
Alignment explanation
Indices: 371832--372411 Score: 713
Period size: 296 Copynumber: 2.0 Consensus size: 296
371822 AAGCAATAGC
* * * *
371832 GGCGATTGTACAAGAAACGCCGCAAAAGTGACTTAAAATTTTGGTTGAACGACGCCGTTTCTGTC
1 GGCGATTGTACAAGAAACGCCGCAAAAGTGACTTAAAATTTTGGCTAAACGACGCCGTCTCTGTA
371897 CACGATTTTTAACTTAGCATTTTCTCTATATTAACAAAACGACACCGTTTATATTAATTTTTCGT
66 CACGATTTTTAACTTAGCATTTTCTCTATATTAACAAAACGACACCGTTTATATTAATTTTTCGT
* * * * *
371962 GGCGTTTGTTCAAGAAATGCCGCAAAAGTGACTTCAAATATTGGCTAAACGTTGACGTCTAACTT
131 GGCGTTTGTTCAACAAACGCCGCAAAAGTGACATAAAATATTGCCTAAACGTT-ACGTCTAACTT
* *
372027 AAGCAAATTAATTTTTAGTGGCGCTTTAAAGGAAAACGCCAGAAATGTGCATTAAATCTTAACAA
195 AAGCAAATTAATTTTTACTGGCGCTTTAAAGGAAAACGCCAGAAATGTGCATTAAAGCTTAACAA
372092 AACGGCGCCGTTTCAGATTAGAACCTTCATTCTTTGT
260 AACGGCGCCGTTTCAGATTAGAACCTTCATTCTTTGT
* * * * * * * *
372129 GGCGTTTGTTCAATAAACGCCGCGAAAGTGTCTTTAAATTTTTGCTAAACGGCGCCGTCTCTGTA
1 GGCGATTGTACAAGAAACGCCGCAAAAGTGACTTAAAATTTTGGCTAAACGACGCCGTCTCTGTA
* * *** *** *
372194 TACG-CTTTTATACTTAGCATTTTCTCTATATTAATTCAACGGTGCCGTTTCTATTAATTTTT-G
66 CACGATTTTTA-ACTTAGCATTTTCTCTATATTAACAAAACGACACCGTTTATATTAATTTTTCG
* * * *
372257 TGGCGTTT-TTACACCAAACGCCGCAAAAGTGACATAAAATATTGCCTAAATGGCTT-CGTTTAG
130 TGGCGTTTGTT-CAACAAACGCCGCAAAAGTGACATAAAATATTGCCTAAA-CG-TTACGTCTAA
* *
372320 CTTAAGCAAATTAATTTTTACTGGCG-TTTAATCA-GAAAACTCCAGAAATGTGCATTACAGCTT
192 CTTAAGCAAATTAATTTTTACTGGCGCTTTAA--AGGAAAACGCCAGAAATGTGCATTAAAGCTT
* * **
372383 AATAAAACGGCGCTGTTTTGGATTAGAAC
255 AACAAAACGGCGCCGTTTCAGATTAGAAC
372412 TTTAAATTTT
Statistics
Matches: 239, Mismatches: 38, Indels: 13
0.82 0.13 0.04
Matches are distributed among these distances:
295 7 0.03
296 128 0.54
297 102 0.43
298 2 0.01
ACGTcount: A:0.30, C:0.19, G:0.18, T:0.33
Consensus pattern (296 bp):
GGCGATTGTACAAGAAACGCCGCAAAAGTGACTTAAAATTTTGGCTAAACGACGCCGTCTCTGTA
CACGATTTTTAACTTAGCATTTTCTCTATATTAACAAAACGACACCGTTTATATTAATTTTTCGT
GGCGTTTGTTCAACAAACGCCGCAAAAGTGACATAAAATATTGCCTAAACGTTACGTCTAACTTA
AGCAAATTAATTTTTACTGGCGCTTTAAAGGAAAACGCCAGAAATGTGCATTAAAGCTTAACAAA
ACGGCGCCGTTTCAGATTAGAACCTTCATTCTTTGT
Found at i:373517 original size:13 final size:13
Alignment explanation
Indices: 373499--373559 Score: 60
Period size: 13 Copynumber: 4.9 Consensus size: 13
373489 CGTTGCCTAC
373499 ATAACTTACATAG
1 ATAACTTACATAG
373512 ATAACTTAC----
1 ATAACTTACATAG
373521 ATAACTTACATAG
1 ATAACTTACATAG
*
373534 ATAACTTA-ATTTAC
1 ATAACTTACA--TAG
373548 ATAACTTACATA
1 ATAACTTACATA
373560 ACTTACATAA
Statistics
Matches: 40, Mismatches: 1, Indels: 14
0.73 0.02 0.25
Matches are distributed among these distances:
9 9 0.22
12 1 0.03
13 19 0.47
14 10 0.25
15 1 0.03
ACGTcount: A:0.46, C:0.16, G:0.03, T:0.34
Consensus pattern (13 bp):
ATAACTTACATAG
Found at i:373697 original size:117 final size:117
Alignment explanation
Indices: 373516--374415 Score: 1748
Period size: 117 Copynumber: 7.7 Consensus size: 117
373506 ACATAGATAA
* * *
373516 CTTACATAACTTACATAGA-TAACTTAATTTACATAACTTACATAACTTACATAAATTAAATAAC
1 CTTACATAACTTACATAAATTAA-GTAACTTACATAACTTACATAACTTACATAAATTAAATAAC
373580 TTACATAACTTACATAAATTAAGTAACTTACATAACTTACAAAAATTAAATAT
65 TTACATAACTTACATAAATTAAGTAACTTACATAACTTACAAAAATTAAATAT
373633 CTTACATAACTTACATAAATTAAGTAACTTACATAACTTACATAACTTACATAAATTAAATAACT
1 CTTACATAACTTACATAAATTAAGTAACTTACATAACTTACATAACTTACATAAATTAAATAACT
373698 TACATAACTTACATAAATTAAGTAACTTACATAACTTACAAAAATTAAATAT
66 TACATAACTTACATAAATTAAGTAACTTACATAACTTACAAAAATTAAATAT
373750 CTTACATAACTTACATAAATTAAGTAACTTACATAACTTACATAACTTACATAAATTAAATAACT
1 CTTACATAACTTACATAAATTAAGTAACTTACATAACTTACATAACTTACATAAATTAAATAACT
373815 TACATAACTTACATAAATTAAGTAACTTACATAACTTACAAAAATTAAATAT
66 TACATAACTTACATAAATTAAGTAACTTACATAACTTACAAAAATTAAATAT
373867 CTTACATAACTTACATAAATTAAGTAACTTACATAACTTACATAACTTACATAAATTAAATAACT
1 CTTACATAACTTACATAAATTAAGTAACTTACATAACTTACATAACTTACATAAATTAAATAACT
373932 TACATAACTTACATAAATTAAGTAACTTACATAACTTACAAAAATTAAATAT
66 TACATAACTTACATAAATTAAGTAACTTACATAACTTACAAAAATTAAATAT
373984 CTTACATAACTTACATAAATTAAGTAACTTACATAACTTACATAACTTACATAAATTAAATAACT
1 CTTACATAACTTACATAAATTAAGTAACTTACATAACTTACATAACTTACATAAATTAAATAACT
374049 TACATAACTTACATAAATTAAGTAACTTACATAACTTACAAAAATTAAATAT
66 TACATAACTTACATAAATTAAGTAACTTACATAACTTACAAAAATTAAATAT
374101 CTTACATAACTTACATAAATTAAGTAACTTACATAACTTACATAACTTACATAAATTAAATAACT
1 CTTACATAACTTACATAAATTAAGTAACTTACATAACTTACATAACTTACATAAATTAAATAACT
374166 TACATAACTTACATAAATTAAGTAACTTACATAACTTACAAAAATTAAATAT
66 TACATAACTTACATAAATTAAGTAACTTACATAACTTACAAAAATTAAATAT
374218 CTTACATAACTTACATAAATTAAGTAACTTACATAACTTACATAACTTACATAAATTAAATAACT
1 CTTACATAACTTACATAAATTAAGTAACTTACATAACTTACATAACTTACATAAATTAAATAACT
374283 TACATAACTTACATAAATTAAGTAACTTACATAACTTACAAAAATTAAATAT
66 TACATAACTTACATAAATTAAGTAACTTACATAACTTACAAAAATTAAATAT
374335 CTTACATAACTTACATAAATTAAGTAACTTACATAACTTACATAACTTACATAAATTAAATAACT
1 CTTACATAACTTACATAAATTAAGTAACTTACATAACTTACATAACTTACATAAATTAAATAACT
*
374400 TACATAACTTAAATAA
66 TACATAACTTACATAA
374416 CTTACATAAT
Statistics
Matches: 778, Mismatches: 4, Indels: 2
0.99 0.01 0.00
Matches are distributed among these distances:
117 775 1.00
118 3 0.00
ACGTcount: A:0.49, C:0.15, G:0.02, T:0.33
Consensus pattern (117 bp):
CTTACATAACTTACATAAATTAAGTAACTTACATAACTTACATAACTTACATAAATTAAATAACT
TACATAACTTACATAAATTAAGTAACTTACATAACTTACAAAAATTAAATAT
Found at i:374289 original size:27 final size:27
Alignment explanation
Indices: 373496--374449 Score: 1043
Period size: 27 Copynumber: 33.3 Consensus size: 27
373486 ATACGTTGCC
*
373496 TACATAACTTACATAGATAACTTACATAACT
1 TACATAACTTACAT--A-AA-TTAAATAACT
** * * * *
373527 TACATAGATAACTTAATTTACATAACT
1 TACATAACTTACATAAATTAAATAACT
373554 TACATAACTTACATAAATTAAATAACT
1 TACATAACTTACATAAATTAAATAACT
*
373581 TACATAACTTACATAAATTAAGTAACT
1 TACATAACTTACATAAATTAAATAACT
* *
373608 TACATAACTTACAAAAATTAAATATCT
1 TACATAACTTACATAAATTAAATAACT
373635 TACATAACTTACATAAATTAAGTAACTTACATAACT
1 TACATAACTTACATAAA-T---T-A---A-ATAACT
373671 TACATAACTTACATAAATTAAATAACT
1 TACATAACTTACATAAATTAAATAACT
*
373698 TACATAACTTACATAAATTAAGTAACT
1 TACATAACTTACATAAATTAAATAACT
* *
373725 TACATAACTTACAAAAATTAAATATCT
1 TACATAACTTACATAAATTAAATAACT
373752 TACATAACTTACATAAATTAAGTAACTTACATAACT
1 TACATAACTTACATAAA-T---T-A---A-ATAACT
373788 TACATAACTTACATAAATTAAATAACT
1 TACATAACTTACATAAATTAAATAACT
*
373815 TACATAACTTACATAAATTAAGTAACT
1 TACATAACTTACATAAATTAAATAACT
* *
373842 TACATAACTTACAAAAATTAAATATCT
1 TACATAACTTACATAAATTAAATAACT
373869 TACATAACTTACATAAATTAAGTAACTTACATAACT
1 TACATAACTTACATAAA-T---T-A---A-ATAACT
373905 TACATAACTTACATAAATTAAATAACT
1 TACATAACTTACATAAATTAAATAACT
*
373932 TACATAACTTACATAAATTAAGTAACT
1 TACATAACTTACATAAATTAAATAACT
* *
373959 TACATAACTTACAAAAATTAAATATCT
1 TACATAACTTACATAAATTAAATAACT
373986 TACATAACTTACATAAATTAAGTAACTTACATAACT
1 TACATAACTTACATAAA-T---T-A---A-ATAACT
374022 TACATAACTTACATAAATTAAATAACT
1 TACATAACTTACATAAATTAAATAACT
*
374049 TACATAACTTACATAAATTAAGTAACT
1 TACATAACTTACATAAATTAAATAACT
* *
374076 TACATAACTTACAAAAATTAAATATCT
1 TACATAACTTACATAAATTAAATAACT
374103 TACATAACTTACATAAATTAAGTAACTTACATAACT
1 TACATAACTTACATAAA-T---T-A---A-ATAACT
374139 TACATAACTTACATAAATTAAATAACT
1 TACATAACTTACATAAATTAAATAACT
*
374166 TACATAACTTACATAAATTAAGTAACT
1 TACATAACTTACATAAATTAAATAACT
* *
374193 TACATAACTTACAAAAATTAAATATCT
1 TACATAACTTACATAAATTAAATAACT
374220 TACATAACTTACATAAATTAAGTAACTTACATAACT
1 TACATAACTTACATAAA-T---T-A---A-ATAACT
374256 TACATAACTTACATAAATTAAATAACT
1 TACATAACTTACATAAATTAAATAACT
*
374283 TACATAACTTACATAAATTAAGTAACT
1 TACATAACTTACATAAATTAAATAACT
* *
374310 TACATAACTTACAAAAATTAAATATCT
1 TACATAACTTACATAAATTAAATAACT
*
374337 TACATAACTTACATAAATTAAGTAACT
1 TACATAACTTACATAAATTAAATAACT
* * *
374364 TACATAACTTACATAACTTACATAAAT
1 TACATAACTTACATAAATTAAATAACT
* *
374391 TAAATAACTTACATAACTTAAATAACT
1 TACATAACTTACATAAATTAAATAACT
*
374418 TACATAA--TACAT-AA-TACATAACT
1 TACATAACTTACATAAATTAAATAACT
374441 TACATAACT
1 TACATAACT
374450 CATTTATGGT
Statistics
Matches: 803, Mismatches: 64, Indels: 118
0.82 0.06 0.12
Matches are distributed among these distances:
23 15 0.02
24 1 0.00
25 5 0.01
27 590 0.73
28 13 0.02
29 1 0.00
31 22 0.03
32 12 0.01
35 12 0.01
36 132 0.16
ACGTcount: A:0.49, C:0.16, G:0.02, T:0.33
Consensus pattern (27 bp):
TACATAACTTACATAAATTAAATAACT
Found at i:379741 original size:21 final size:21
Alignment explanation
Indices: 379715--379786 Score: 117
Period size: 21 Copynumber: 3.4 Consensus size: 21
379705 CTACAACTTA
* *
379715 AAGCAGAGGCGGCAGCGAGGG
1 AAGCAGAGGCTGCAGCGAGAG
379736 AAGCAGAGGCTGCAGCGAGAG
1 AAGCAGAGGCTGCAGCGAGAG
*
379757 AAGTAGAGGCTGCAGCGAGAG
1 AAGCAGAGGCTGCAGCGAGAG
379778 AAGCAGAGG
1 AAGCAGAGG
379787 TTCAAAAGAA
Statistics
Matches: 47, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 47 1.00
ACGTcount: A:0.33, C:0.17, G:0.46, T:0.04
Consensus pattern (21 bp):
AAGCAGAGGCTGCAGCGAGAG
Found at i:380280 original size:42 final size:42
Alignment explanation
Indices: 380217--380425 Score: 301
Period size: 42 Copynumber: 5.0 Consensus size: 42
380207 TTTGTGAAGA
* * *
380217 AAGCGCCGCTAAAGAACATGATCTATAGCGGCGTTTTTTACC
1 AAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTTCT
* * *
380259 AAGCGCCGCTAAAGAATATGATTTTTAGCGGCGTTTTTGTCT
1 AAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTTCT
* *
380301 AAGCGCCTCTAAAGAACATGATCTTTAGCGGCGTCTTTTTTTT
1 AAGCGCCGCTAAAGAACATGATCTTTAGCGGCGT-TTTTTTCT
* *
380344 AAGCGCCGCTAAAGAACATGACCTTTAGCGGTGTTTTTTTCT
1 AAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTTCT
* *
380386 AAGCGCCACTAAAGAACATGACCTTTAGCGGCGTTTTTTT
1 AAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTT
380426 TCTGTAAACG
Statistics
Matches: 149, Mismatches: 17, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
42 112 0.75
43 37 0.25
ACGTcount: A:0.25, C:0.21, G:0.21, T:0.33
Consensus pattern (42 bp):
AAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTTCT
Found at i:380348 original size:85 final size:84
Alignment explanation
Indices: 380217--380427 Score: 305
Period size: 85 Copynumber: 2.5 Consensus size: 84
380207 TTTGTGAAGA
* * ** * **
380217 AAGCGCCGCTAAAGAACATGATCTATAGCGGCGTTTTTTACCAAGCGCCGCTAAAGAATATGATT
1 AAGCGCCACTAAAGAACATGATCTTTAGCGGCGTTTTTTTTCAAGCGCCGCTAAAGAACATGACC
380282 TTTAGCGGCGTTTTTGTCT
66 TTTAGCGGCGTTTTTGTCT
* *
380301 AAGCGCCTCTAAAGAACATGATCTTTAGCGGCGTCTTTTTTTTAAGCGCCGCTAAAGAACATGAC
1 AAGCGCCACTAAAGAACATGATCTTTAGCGGCGT-TTTTTTTCAAGCGCCGCTAAAGAACATGAC
* *
380366 CTTTAGCGGTGTTTTTTTCT
65 CTTTAGCGGCGTTTTTGTCT
*
380386 AAGCGCCACTAAAGAACATGACCTTTAGCGGCGTTTTTTTTC
1 AAGCGCCACTAAAGAACATGATCTTTAGCGGCGTTTTTTTTC
380428 TGTAAACGCT
Statistics
Matches: 113, Mismatches: 13, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
84 39 0.35
85 74 0.65
ACGTcount: A:0.25, C:0.21, G:0.21, T:0.33
Consensus pattern (84 bp):
AAGCGCCACTAAAGAACATGATCTTTAGCGGCGTTTTTTTTCAAGCGCCGCTAAAGAACATGACC
TTTAGCGGCGTTTTTGTCT
Found at i:391334 original size:10 final size:9
Alignment explanation
Indices: 391306--391363 Score: 55
Period size: 9 Copynumber: 6.2 Consensus size: 9
391296 AATAACTTTT
391306 AAATTTTAA
1 AAATTTTAA
391315 AAATTTTAA
1 AAATTTTAA
391324 AAATTTCTAAA
1 AAATTT-T-AA
*
391335 AAATATATAA
1 AAAT-TTTAA
**
391345 AAAGGTT-A
1 AAATTTTAA
391353 AAATTTTAA
1 AAATTTTAA
391362 AA
1 AA
391364 TTATTCTAAA
Statistics
Matches: 39, Mismatches: 6, Indels: 8
0.74 0.11 0.15
Matches are distributed among these distances:
8 6 0.15
9 19 0.49
10 6 0.15
11 7 0.18
12 1 0.03
ACGTcount: A:0.59, C:0.02, G:0.03, T:0.36
Consensus pattern (9 bp):
AAATTTTAA
Found at i:400889 original size:27 final size:27
Alignment explanation
Indices: 400859--400927 Score: 74
Period size: 27 Copynumber: 2.6 Consensus size: 27
400849 AGTTGATAAA
400859 AATTAATATATAAATTAT-AAATTATAT
1 AATTAATATATAAATTATCAAATTAT-T
400886 AATT-ATATATTAAAGTTTATCAAATTATT
1 AATTAATATA-TAAA--TTATCAAATTATT
400915 AA-TAATAT-TAAAT
1 AATTAATATATAAAT
400928 ATATTTATTC
Statistics
Matches: 37, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
25 1 0.03
26 5 0.14
27 12 0.32
28 1 0.03
29 11 0.30
30 7 0.19
ACGTcount: A:0.52, C:0.01, G:0.01, T:0.45
Consensus pattern (27 bp):
AATTAATATATAAATTATCAAATTATT
Found at i:400891 original size:15 final size:16
Alignment explanation
Indices: 400865--400897 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
400855 TAAAAATTAA
400865 TATATAAATTATAAAT
1 TATATAAATTATAAAT
*
400881 TATAT-AATTATATAT
1 TATATAAATTATAAAT
400896 TA
1 TA
400898 AAGTTTATCA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (16 bp):
TATATAAATTATAAAT
Found at i:407786 original size:6 final size:6
Alignment explanation
Indices: 407775--407826 Score: 97
Period size: 6 Copynumber: 8.8 Consensus size: 6
407765 AGGTTTCCAA
407775 AAATGG AAATGG AAATGG AAATGG AAATGG AAATGG AAATGG AAAT-G
1 AAATGG AAATGG AAATGG AAATGG AAATGG AAATGG AAATGG AAATGG
407822 AAATG
1 AAATG
407827 TGTAACACCC
Statistics
Matches: 45, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
5 5 0.11
6 40 0.89
ACGTcount: A:0.52, C:0.00, G:0.31, T:0.17
Consensus pattern (6 bp):
AAATGG
Found at i:409918 original size:18 final size:18
Alignment explanation
Indices: 409897--409931 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
409887 TTTTATGTTT
409897 TGTT-TATTGTTTAATAAA
1 TGTTATATT-TTTAATAAA
409915 TGTTATATTTTTAATAA
1 TGTTATATTTTTAATAA
409932 TATAATATAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 12 0.75
19 4 0.25
ACGTcount: A:0.34, C:0.00, G:0.09, T:0.57
Consensus pattern (18 bp):
TGTTATATTTTTAATAAA
Found at i:410067 original size:3 final size:3
Alignment explanation
Indices: 410054--410087 Score: 61
Period size: 3 Copynumber: 11.7 Consensus size: 3
410044 TATTTATTTG
410054 ATA AT- ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
410088 TTAATAACAT
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.07
3 28 0.93
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
ATA
Found at i:410865 original size:28 final size:28
Alignment explanation
Indices: 410825--410909 Score: 107
Period size: 28 Copynumber: 3.0 Consensus size: 28
410815 CAGTATAAGT
*
410825 ACAGTGTGGGCCTTAGCCCATTACAGTA
1 ACAGTGTGGGCCTTAGCCCAATACAGTA
* * *
410853 ACAGTGTGAGCCTTAACCCAATACTGTA
1 ACAGTGTGGGCCTTAGCCCAATACAGTA
* * *
410881 ACAATATGGGCATTAGCCCAATACAGTA
1 ACAGTGTGGGCCTTAGCCCAATACAGTA
410909 A
1 A
410910 TTAGTTCAAT
Statistics
Matches: 47, Mismatches: 10, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
28 47 1.00
ACGTcount: A:0.33, C:0.24, G:0.20, T:0.24
Consensus pattern (28 bp):
ACAGTGTGGGCCTTAGCCCAATACAGTA
Found at i:411044 original size:26 final size:25
Alignment explanation
Indices: 411014--411093 Score: 97
Period size: 26 Copynumber: 3.1 Consensus size: 25
411004 GCCAAGACAC
* *
411014 CAATATCGCAGCAACGCTGCTAGTAA
1 CAATAACGCAGCAA-GCTGCCAGTAA
*
411040 TAATAACGCAGCAGAGCTGCCAGTAA
1 CAATAACGCAGCA-AGCTGCCAGTAA
*
411066 CAATAACGCAACAAAGCTGCCAGTAA
1 CAATAACGCAGC-AAGCTGCCAGTAA
411092 CA
1 CA
411094 TTATATGTGG
Statistics
Matches: 47, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
26 45 0.96
27 2 0.04
ACGTcount: A:0.40, C:0.26, G:0.19, T:0.15
Consensus pattern (25 bp):
CAATAACGCAGCAAGCTGCCAGTAA
Found at i:411334 original size:27 final size:27
Alignment explanation
Indices: 411275--411534 Score: 315
Period size: 27 Copynumber: 9.6 Consensus size: 27
411265 TTCATCTCCT
** * *
411275 AGGGTATAACGGTCATTTTACCCCTTTG
1 AGGGTATTTCGGTAATTTTA-CCCTTCG
* *
411303 AGGGTATTTCGGTCATTTTACCCTTTG
1 AGGGTATTTCGGTAATTTTACCCTTCG
* *
411330 AGGGTATTTTGGTAATTTTACCCTTCA
1 AGGGTATTTCGGTAATTTTACCCTTCG
**
411357 AGGGTATTTTAGTAATTTTACCCTTCG
1 AGGGTATTTCGGTAATTTTACCCTTCG
*
411384 AGGGTATTTCGATAATTTTACCCTTCG
1 AGGGTATTTCGGTAATTTTACCCTTCG
** *
411411 AGGGTATTTCAATAATTTTACCCTT-T
1 AGGGTATTTCGGTAATTTTACCCTTCG
* *
411437 AGGGTTATTTCGGTAATTTTACCTTTTG
1 AGGG-TATTTCGGTAATTTTACCCTTCG
**
411465 AGGGTATTTTAGTAATTTTACCCTTCG
1 AGGGTATTTCGGTAATTTTACCCTTCG
*
411492 AGGGTATTTCGATAATTTTACCCTTCG
1 AGGGTATTTCGGTAATTTTACCCTTCG
*
411519 AGGGTATTTCAGTAAT
1 AGGGTATTTCGGTAAT
411535 CTTGGGTCCA
Statistics
Matches: 204, Mismatches: 26, Indels: 5
0.87 0.11 0.02
Matches are distributed among these distances:
26 4 0.02
27 178 0.87
28 22 0.11
ACGTcount: A:0.22, C:0.16, G:0.19, T:0.43
Consensus pattern (27 bp):
AGGGTATTTCGGTAATTTTACCCTTCG
Found at i:437824 original size:18 final size:19
Alignment explanation
Indices: 437803--437841 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
437793 CTTAAGTATG
437803 TATTAGTAATT-AACTAAT
1 TATTAGTAATTAAACTAAT
**
437821 TATTCTTAATTAAACTAAT
1 TATTAGTAATTAAACTAAT
437840 TA
1 TA
437842 AATTCTTAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 9 0.50
19 9 0.50
ACGTcount: A:0.44, C:0.08, G:0.03, T:0.46
Consensus pattern (19 bp):
TATTAGTAATTAAACTAAT
Found at i:437848 original size:21 final size:18
Alignment explanation
Indices: 437809--437852 Score: 61
Period size: 21 Copynumber: 2.3 Consensus size: 18
437799 TATGTATTAG
437809 TAATTAACTAATTATTCT
1 TAATTAACTAATTATTCT
437827 TAATTAAACTAATTAAATTCT
1 TAATT-AACTAATT--ATTCT
437848 TAATT
1 TAATT
437853 GTTTTATATT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 5 0.22
19 8 0.35
21 10 0.43
ACGTcount: A:0.43, C:0.09, G:0.00, T:0.48
Consensus pattern (18 bp):
TAATTAACTAATTATTCT
Found at i:451651 original size:13 final size:13
Alignment explanation
Indices: 451628--451669 Score: 57
Period size: 13 Copynumber: 3.2 Consensus size: 13
451618 GTTAGGGGTA
*
451628 TCGCAAAATCACC
1 TCGCAATATCACC
*
451641 TCGCGATATCACC
1 TCGCAATATCACC
*
451654 TCGCAATCTCACC
1 TCGCAATATCACC
451667 TCG
1 TCG
451670 TTGTACCACC
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.26, C:0.40, G:0.12, T:0.21
Consensus pattern (13 bp):
TCGCAATATCACC
Found at i:451700 original size:25 final size:25
Alignment explanation
Indices: 451672--451750 Score: 88
Period size: 25 Copynumber: 3.1 Consensus size: 25
451662 TCACCTCGTT
451672 GTACCACCTCGCAACACACCTCACA
1 GTACCACCTCGCAACACACCTCACA
* *
451697 GTACCACCTCACAACACACCTCTC-
1 GTACCACCTCGCAACACACCTCACA
* * *
451721 GCAACCACCTCGTAATACCACCTCACA
1 G-TACCACCTCGCAACA-CACCTCACA
451748 GTA
1 GTA
451751 TCACTTAGCG
Statistics
Matches: 43, Mismatches: 8, Indels: 5
0.77 0.14 0.09
Matches are distributed among these distances:
24 1 0.02
25 33 0.77
26 8 0.19
27 1 0.02
ACGTcount: A:0.32, C:0.46, G:0.08, T:0.15
Consensus pattern (25 bp):
GTACCACCTCGCAACACACCTCACA
Found at i:458616 original size:271 final size:271
Alignment explanation
Indices: 458133--458924 Score: 1325
Period size: 271 Copynumber: 2.9 Consensus size: 271
458123 AATCACTTTA
* * *
458133 ATATTAAATTAATATAATATTTATCTGTAGGATAAATATTTAATTTAATTTAATATTAAATCTAT
1 ATATTAAATTAATAGAATATTTATCTATAAGATAAATATTTAATTTAATTTAATATTAAATCTAT
458198 TAAAATTTTTTGGGATAGTTAATTTGAAATCAAATTATCTGGTAGAGTCCCAATAGGAGTGTGAT
66 TAAAATTTTTTGGGATAGTTAATTTGAAATCAAATTATCTGGTAGAGTCCCAATAGGAGTGTGAT
458263 TCCTCCATTGCTCAACAGTCGAAGAACCACCCACAGGCCACTGGAATGTCACCGTTGGCACCGTC
131 TCCTCCATTGCTCAACAGTCGAAGAACCACCCACAGGCCACTGGAATGTCACCGTTGGCACCGTC
458328 GTGCTCGGTGGTGCCATCACAGGTGCGAGACCCTCATGGCACCCCAAGCCTAATTAGATTATATT
196 GTGCTCGGTGGTGCCATCACAGGTGCGAGACCCTCATGGCACCCCAAGCCTAATTAGATTATATT
458393 TAATATTAAAT
261 TAATATTAAAT
458404 ATATTAAATTAATAGAATATTTATCTATAAGATAAATATTTAATTTAATTTAATATTAAATCTAT
1 ATATTAAATTAATAGAATATTTATCTATAAGATAAATATTTAATTTAATTTAATATTAAATCTAT
458469 TAAAATTTTTTGGGATAGTTAATTTGAAATCAAATTATCTGGTAGAGTCCCAATAGGAGTGTGAT
66 TAAAATTTTTTGGGATAGTTAATTTGAAATCAAATTATCTGGTAGAGTCCCAATAGGAGTGTGAT
458534 TCCTCCATTGCTCAACAGTCGAAGAACCACCCACAGGCCACTGGAATGTCACCGTTGGCACCGTC
131 TCCTCCATTGCTCAACAGTCGAAGAACCACCCACAGGCCACTGGAATGTCACCGTTGGCACCGTC
458599 GTGCTCGGTGGTGCCATCACAGGTGCGAGACCCTCATGGCACCCCAAGCCTAATTAGATTATATT
196 GTGCTCGGTGGTGCCATCACAGGTGCGAGACCCTCATGGCACCCCAAGCCTAATTAGATTATATT
458664 TAATATTAAAT
261 TAATATTAAAT
458675 ATATTAAATTAATAGAATATTTATCTATAAGATAAATATTTAATTTAATTTAATATTAAATCTAT
1 ATATTAAATTAATAGAATATTTATCTATAAGATAAATATTTAATTTAATTTAATATTAAATCTAT
* * * * *
458740 TAAAATAATATTATTTTTGGAATAATTAATTTTAAATCAAATTATCCGGTAGAGTCCCAGTAGGA
66 T---A-AA-A-T-TTTTTGGGATAGTTAATTTGAAATCAAATTATCTGGTAGAGTCCCAATAGGA
* * * * * * * *
458805 ATGTGATTCATCAATTACTCAACGGCCGAAGAACCACCCACCA-GCCACCGGAATGTCACCGTCG
124 GTGTGATTCCTCCATTGCTCAACAGTCGAAGAACCACCCA-CAGGCCACTGGAATGTCACCGTTG
* * **
458869 GCACCGTCGTGCTCGGCGGTGCCATCACAGGTGCAAGACCCTCACAGCACCCCAAG
188 GCACCGTCGTGCTCGGTGGTGCCATCACAGGTGCGAGACCCTCATGGCACCCCAAG
458925 TCGATTCAAT
Statistics
Matches: 493, Mismatches: 20, Indels: 9
0.94 0.04 0.02
Matches are distributed among these distances:
271 334 0.68
274 1 0.00
275 2 0.00
276 1 0.00
277 1 0.00
278 152 0.31
279 2 0.00
ACGTcount: A:0.34, C:0.19, G:0.16, T:0.31
Consensus pattern (271 bp):
ATATTAAATTAATAGAATATTTATCTATAAGATAAATATTTAATTTAATTTAATATTAAATCTAT
TAAAATTTTTTGGGATAGTTAATTTGAAATCAAATTATCTGGTAGAGTCCCAATAGGAGTGTGAT
TCCTCCATTGCTCAACAGTCGAAGAACCACCCACAGGCCACTGGAATGTCACCGTTGGCACCGTC
GTGCTCGGTGGTGCCATCACAGGTGCGAGACCCTCATGGCACCCCAAGCCTAATTAGATTATATT
TAATATTAAAT
Found at i:461725 original size:26 final size:26
Alignment explanation
Indices: 461130--461723 Score: 577
Period size: 26 Copynumber: 22.9 Consensus size: 26
461120 ACATACATTA
* *
461130 TAATAACAACTCACATACATGCAAGG
1 TAATAACAGCTCGCATACATGCAAGG
*
461156 TAATAACAGCTCGCATACATGTAAGG
1 TAATAACAGCTCGCATACATGCAAGG
* * *
461182 TAATAACAACTCGCACACATG-ATTGG
1 TAATAACAGCTCGCATACATGCA-AGG
* * **
461208 TAATAAAATCTCATATACATGCAAGG
1 TAATAACAGCTCGCATACATGCAAGG
* ** * * *
461234 TAATAAAAATTTGCACACATGCATGG
1 TAATAACAGCTCGCATACATGCAAGG
* * * * * *
461260 TAATAATAGTTCACACACATGTATGG
1 TAATAACAGCTCGCATACATGCAAGG
** * *
461286 TAATAACAGCTCATACACATACAAGG
1 TAATAACAGCTCGCATACATGCAAGG
* *
461312 TAATAACAGCTCGCACACATGCATGG
1 TAATAACAGCTCGCATACATGCAAGG
* * * *
461338 GAATAATAGCTCACATTCATGCAAGG
1 TAATAACAGCTCGCATACATGCAAGG
*
461364 TAATAACAACTCGCATACATGCAAGG
1 TAATAACAGCTCGCATACATGCAAGG
* * *
461390 TAATAACAGCTCAC-GACATGCATGG
1 TAATAACAGCTCGCATACATGCAAGG
* * *
461415 TAATAATAGCAT-ACATTCATGCAAGG
1 TAATAACAGC-TCGCATACATGCAAGG
* * *
461441 TAATAATAGCTTGCACACATGCAAGG
1 TAATAACAGCTCGCATACATGCAAGG
* * *
461467 TAATAACAACTCAG-ACACATGCATGG
1 TAATAACAGCTC-GCATACATGCAAGG
461493 TAATAACAGCTCGCATACATGCAAGG
1 TAATAACAGCTCGCATACATGCAAGG
461519 TAATAACAGCTCGCATACATGCAAGG
1 TAATAACAGCTCGCATACATGCAAGG
*
461545 TAATAACAGCTCGTATACATGCAAGG
1 TAATAACAGCTCGCATACATGCAAGG
461571 TAATAACAGCTCGCATACATGCAAGG
1 TAATAACAGCTCGCATACATGCAAGG
** *
461597 TAATAACAG-TCCGCACGCATGCATGG
1 TAATAACAGCT-CGCATACATGCAAGG
* *
461623 TAATAACAGCTCACATACATGCGAGG
1 TAATAACAGCTCGCATACATGCAAGG
* * *
461649 TAATAACAGCTCACACACATGCATGG
1 TAATAACAGCTCGCATACATGCAAGG
** * * * *
461675 TAATAACAAATCACAAACATGCATGT
1 TAATAACAGCTCGCATACATGCAAGG
461701 TAATAACAGCTCGCATACATGCA
1 TAATAACAGCTCGCATACATGCA
461724 TGGCATGGTA
Statistics
Matches: 475, Mismatches: 84, Indels: 18
0.82 0.15 0.03
Matches are distributed among these distances:
25 24 0.05
26 448 0.94
27 3 0.01
ACGTcount: A:0.40, C:0.22, G:0.16, T:0.22
Consensus pattern (26 bp):
TAATAACAGCTCGCATACATGCAAGG
Found at i:461773 original size:26 final size:26
Alignment explanation
Indices: 461112--461775 Score: 559
Period size: 26 Copynumber: 25.4 Consensus size: 26
461102 TACTTTCAAT
* ***
461112 GCTCGCACACATACATTATAATAACA
1 GCTCGCACACATGCAAGGTAATAACA
* * *
461138 ACTCACATACATGCAAGGTAATAACA
1 GCTCGCACACATGCAAGGTAATAACA
* *
461164 GCTCGCATACATGTAAGGTAATAACA
1 GCTCGCACACATGCAAGGTAATAACA
* * *
461190 ACTCGCACACATG-ATTGGTAATAAAA
1 GCTCGCACACATGCA-AGGTAATAACA
* ** * *
461216 TCTCATATACATGCAAGGTAATAAAA
1 GCTCGCACACATGCAAGGTAATAACA
** * * *
461242 ATTTGCACACATGCATGGTAATAATA
1 GCTCGCACACATGCAAGGTAATAACA
* * * *
461268 GTTCACACACATGTATGGTAATAACA
1 GCTCGCACACATGCAAGGTAATAACA
** *
461294 GCTCATACACATACAAGGTAATAACA
1 GCTCGCACACATGCAAGGTAATAACA
* * *
461320 GCTCGCACACATGCATGGGAATAATA
1 GCTCGCACACATGCAAGGTAATAACA
* **
461346 GCTCACATTCATGCAAGGTAATAACA
1 GCTCGCACACATGCAAGGTAATAACA
* *
461372 ACTCGCATACATGCAAGGTAATAACA
1 GCTCGCACACATGCAAGGTAATAACA
* *
461398 GCT--CACGACATGCATGGTAATAATA
1 GCTCGCAC-ACATGCAAGGTAATAACA
* ** *
461423 GCAT-ACATTCATGCAAGGTAATAATA
1 GC-TCGCACACATGCAAGGTAATAACA
*
461449 GCTTGCACACATGCAAGGTAATAACA
1 GCTCGCACACATGCAAGGTAATAACA
* *
461475 ACTCAG-ACACATGCATGGTAATAACA
1 GCTC-GCACACATGCAAGGTAATAACA
*
461501 GCTCGCATACATGCAAGGTAATAACA
1 GCTCGCACACATGCAAGGTAATAACA
*
461527 GCTCGCATACATGCAAGGTAATAACA
1 GCTCGCACACATGCAAGGTAATAACA
* *
461553 GCTCGTATACATGCAAGGTAATAACA
1 GCTCGCACACATGCAAGGTAATAACA
*
461579 GCTCGCATACATGCAAGGTAATAACA
1 GCTCGCACACATGCAAGGTAATAACA
* *
461605 G-TCCGCACGCATGCATGGTAATAACA
1 GCT-CGCACACATGCAAGGTAATAACA
* * *
461631 GCTCACATACATGCGAGGTAATAACA
1 GCTCGCACACATGCAAGGTAATAACA
* *
461657 GCTCACACACATGCATGGTAATAACA
1 GCTCGCACACATGCAAGGTAATAACA
** * * * *
461683 AATCACAAACATGCATGTTAATAACA
1 GCTCGCACACATGCAAGGTAATAACA
*
461709 GCTCGCATACATGCATGGCATGGTAAT-ACTA
1 GCTCGC--ACA--CAT-GCAAGGTAATAAC-A
* * *
461740 GTTGGCACACATGCATGGTAATAACA
1 GCTCGCACACATGCAAGGTAATAACA
*
461766 GCTAGCACAC
1 GCTCGCACAC
461776 CTTCCTCTTT
Statistics
Matches: 526, Mismatches: 95, Indels: 34
0.80 0.15 0.05
Matches are distributed among these distances:
24 2 0.00
25 22 0.04
26 468 0.89
27 10 0.02
28 2 0.00
29 3 0.01
30 5 0.01
31 14 0.03
ACGTcount: A:0.39, C:0.22, G:0.17, T:0.22
Consensus pattern (26 bp):
GCTCGCACACATGCAAGGTAATAACA
Found at i:465165 original size:28 final size:27
Alignment explanation
Indices: 465134--465207 Score: 78
Period size: 28 Copynumber: 2.7 Consensus size: 27
465124 ACTTACGCCG
465134 TGTTTACTATCCCGATAGACTTACCTCA
1 TGTTTACTATCCCGATAGACTTA-CTCA
* * *
465162 TGTTTATTATCTC-AGTGGACTTACTCA
1 TGTTTACTATCCCGA-TAGACTTACTCA
* *
465189 TATTTACTGTCCCGATAGA
1 TGTTTACTATCCCGATAGA
465208 TTATCTCTAT
Statistics
Matches: 36, Mismatches: 8, Indels: 5
0.73 0.16 0.10
Matches are distributed among these distances:
27 17 0.47
28 19 0.53
ACGTcount: A:0.24, C:0.23, G:0.14, T:0.39
Consensus pattern (27 bp):
TGTTTACTATCCCGATAGACTTACTCA
Found at i:465233 original size:33 final size:33
Alignment explanation
Indices: 465191--465279 Score: 108
Period size: 33 Copynumber: 2.7 Consensus size: 33
465181 CTTACTCATA
* * *
465191 TTTACTGTCCC-GATAGATTATCTCTATTTTATG
1 TTTACTGTCCCAG-TAGACTATCTATATTCTATG
* *
465224 TTTACTGTCCCAGTAGACTATCTATGTTCTGTG
1 TTTACTGTCCCAGTAGACTATCTATATTCTATG
*
465257 TTTACTGTCCCAGCAGACTATCT
1 TTTACTGTCCCAGTAGACTATCT
465280 CTGTGGATGC
Statistics
Matches: 49, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
33 48 0.98
34 1 0.02
ACGTcount: A:0.20, C:0.22, G:0.15, T:0.43
Consensus pattern (33 bp):
TTTACTGTCCCAGTAGACTATCTATATTCTATG
Found at i:473953 original size:2 final size:2
Alignment explanation
Indices: 473948--473977 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
473938 ACACACACTC
473948 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
473978 TATTGTAGGA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:474407 original size:40 final size:40
Alignment explanation
Indices: 474318--474436 Score: 100
Period size: 40 Copynumber: 2.9 Consensus size: 40
474308 TATTTTCCGC
* * * **
474318 GAAATCGCGTCCACGTCAGCACGATGT-CAAGGTACGTGTCAG
1 GAAATCGCGTCCACGTCAGCGCGATTTGC--TG-ACGTGGAAG
*
474360 GACATCGCGTCCACGTCAGCGCGATTTGCTGACGTGGAAG
1 GAAATCGCGTCCACGTCAGCGCGATTTGCTGACGTGGAAG
* *
474400 GAAATCGCG-CCCCCT-AGGACGCGATTTGCTGACGTGG
1 GAAATCGCGTCCACGTCA-G-CGCGATTTGCTGACGTGG
474437 CATGAACAGT
Statistics
Matches: 65, Mismatches: 9, Indels: 8
0.79 0.11 0.10
Matches are distributed among these distances:
38 1 0.02
39 5 0.08
40 33 0.51
41 1 0.02
42 24 0.37
43 1 0.02
ACGTcount: A:0.22, C:0.28, G:0.31, T:0.19
Consensus pattern (40 bp):
GAAATCGCGTCCACGTCAGCGCGATTTGCTGACGTGGAAG
Found at i:475296 original size:30 final size:29
Alignment explanation
Indices: 475229--475296 Score: 84
Period size: 29 Copynumber: 2.3 Consensus size: 29
475219 CGATTTCGCG
475229 AAAAAT-GGCCCATTCCGGTAAATAATTA
1 AAAAATCGGCCCATTCCGGTAAATAATTA
* * **
475257 AAAAGTCGGCCCATTTCGGTAAATTTTGTA
1 AAAAATCGGCCCATTCCGGTAAATAAT-TA
475287 AAAAATCGGC
1 AAAAATCGGC
475297 TTTTTTTGGT
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
28 5 0.15
29 17 0.52
30 11 0.33
ACGTcount: A:0.38, C:0.18, G:0.18, T:0.26
Consensus pattern (29 bp):
AAAAATCGGCCCATTCCGGTAAATAATTA
Found at i:477046 original size:19 final size:19
Alignment explanation
Indices: 477022--477074 Score: 97
Period size: 19 Copynumber: 2.8 Consensus size: 19
477012 AATCATATCT
477022 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
*
477041 TCTAAGATTACATATCATA
1 TCTAAGATTGCATATCATA
477060 TCTAAGATTGCATAT
1 TCTAAGATTGCATAT
477075 TCTTGAAGAT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 32 1.00
ACGTcount: A:0.38, C:0.15, G:0.09, T:0.38
Consensus pattern (19 bp):
TCTAAGATTGCATATCATA
Found at i:480165 original size:70 final size:67
Alignment explanation
Indices: 480050--480177 Score: 193
Period size: 70 Copynumber: 1.9 Consensus size: 67
480040 TAAACAATAC
* **
480050 AATGGTTTTGCCTTTTAACTTAATGAGTAAACATTTATCAAAACGACATAGTTTTGCCCTTTAAC
1 AATGGTTTTGACTTTTAACTTAAAAAGTAAACATTTATCAAAACGACATAGTTTTGCCCTTTAAC
480115 TT
66 TT
*
480117 AATGGTTTTGACTTTTAACTTTAGAAAAGGTAAACATTTATCAAAACGACTTAGTTTTGCC
1 AATGGTTTTGACTTTTAAC-TTA-AAAA-GTAAACATTTATCAAAACGACATAGTTTTGCC
480178 TTTTCTTATT
Statistics
Matches: 54, Mismatches: 4, Indels: 3
0.89 0.07 0.05
Matches are distributed among these distances:
67 18 0.33
68 3 0.06
69 2 0.04
70 31 0.57
ACGTcount: A:0.33, C:0.15, G:0.13, T:0.39
Consensus pattern (67 bp):
AATGGTTTTGACTTTTAACTTAAAAAGTAAACATTTATCAAAACGACATAGTTTTGCCCTTTAAC
TT
Found at i:483383 original size:8 final size:8
Alignment explanation
Indices: 483370--483396 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
483360 ACCATTTTTT
483370 AAAAAAGA
1 AAAAAAGA
483378 AAAAAAGA
1 AAAAAAGA
483386 AAAAAAGA
1 AAAAAAGA
483394 AAA
1 AAA
483397 CGGGAGTCGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.89, C:0.00, G:0.11, T:0.00
Consensus pattern (8 bp):
AAAAAAGA
Found at i:486877 original size:28 final size:28
Alignment explanation
Indices: 486837--486905 Score: 93
Period size: 28 Copynumber: 2.5 Consensus size: 28
486827 AAATGAGATT
* *
486837 AGCACTAAGTGTGCGAGTTTAATTGTAA
1 AGCACTAAGTGTGCGAGATTAATTATAA
* *
486865 AGCACTAAGTGTGCGAGATTGATTATTA
1 AGCACTAAGTGTGCGAGATTAATTATAA
*
486893 AGCACTAATTGTG
1 AGCACTAAGTGTG
486906 TGAACTTATT
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 36 1.00
ACGTcount: A:0.32, C:0.12, G:0.25, T:0.32
Consensus pattern (28 bp):
AGCACTAAGTGTGCGAGATTAATTATAA
Found at i:487993 original size:23 final size:23
Alignment explanation
Indices: 487960--488541 Score: 361
Period size: 23 Copynumber: 24.7 Consensus size: 23
487950 AGATACTTAA
* * *
487960 ATGCTGCCCAAATTGTTATATAT
1 ATGCTGTCCAATTTGTTGTATAT
* * *
487983 ATGCTGTCCAAATTTTGGTGTAAAA
1 ATGCTGTCC-AA-TTTGTTGTATAT
* * * *
488008 ATGCTGTTCAATTTGGTATATAA
1 ATGCTGTCCAATTTGTTGTATAT
*
488031 ATGCTGCCCAATTTGTTGTATAT
1 ATGCTGTCCAATTTGTTGTATAT
* * * *
488054 ATGCTGTCCGATTTTTGGTGTAAAA
1 ATGCTGTCC-A-ATTTGTTGTATAT
* *
488079 ATGTTG-CTCAATTTGTTGTATTT
1 ATGCTGTC-CAATTTGTTGTATAT
* *
488102 ATGCTGCCCAAATTGTTGTATAT
1 ATGCTGTCCAATTTGTTGTATAT
* * *
488125 ATGCTGTCCAATTTTGATGTAAAA
1 ATGCTGTCCAA-TTTGTTGTATAT
* * *
488149 ATGTTG-CTCAATTTGGTATATAT
1 ATGCTGTC-CAATTTGTTGTATAT
* * *
488172 ATGTTGCCCAATTTGTTTTATAT
1 ATGCTGTCCAATTTGTTGTATAT
* * * *
488195 ACGCTGTCCAATTTTTGGTGTAAAA
1 ATGCTGTCCAA--TTTGTTGTATAT
*
488220 ATGCTGAT-CAATTTGTTGTATTT
1 ATGCTG-TCCAATTTGTTGTATAT
* *
488243 ATGCTGCCCAAATTGTTGTATAT
1 ATGCTGTCCAATTTGTTGTATAT
* * *
488266 ATGCTGTCCAATTTTGATGTAAAA
1 ATGCTGTCCAA-TTTGTTGTATAT
* * *
488290 ATGCT-ACTCAATTTGGTATATAT
1 ATGCTGTC-CAATTTGTTGTATAT
*
488313 ATGCTGCCCAATTTGTTGTATAT
1 ATGCTGTCCAATTTGTTGTATAT
* * *
488336 ATGCTGTCCAAATTTTGGTGTAAAA
1 ATGCTGTCC-AA-TTTGTTGTATAT
* *
488361 ATGCTG-CTCAATTTGTGGTATTT
1 ATGCTGTC-CAATTTGTTGTATAT
* *
488384 ATGCTGCCCAAATTGTTGTATAT
1 ATGCTGTCCAATTTGTTGTATAT
* * *
488407 ATGCTTTCCAATTT-TAATGTAAAA
1 ATGCTGTCCAATTTGT--TGTATAT
* *
488431 ATGCTG-CTCAATTTGGTATATAT
1 ATGCTGTC-CAATTTGTTGTATAT
* *
488454 ATGCTGCCCAATTTGTTTTATAT
1 ATGCTGTCCAATTTGTTGTATAT
* * *
488477 ATGCTGTCCAATTTTTGGTGTAAAA
1 ATGCTGTCCAA--TTTGTTGTATAT
*
488502 ATGCTG-CTCAATTTATTGTATAT
1 ATGCTGTC-CAATTTGTTGTATAT
* *
488525 ATGCTGCCCAAATTGTT
1 ATGCTGTCCAATTTGTT
488542 ACAGGGTAGA
Statistics
Matches: 427, Mismatches: 103, Indels: 58
0.73 0.18 0.10
Matches are distributed among these distances:
22 1 0.00
23 279 0.65
24 67 0.16
25 79 0.19
26 1 0.00
ACGTcount: A:0.27, C:0.14, G:0.17, T:0.43
Consensus pattern (23 bp):
ATGCTGTCCAATTTGTTGTATAT
Found at i:488041 original size:71 final size:71
Alignment explanation
Indices: 487960--488541 Score: 814
Period size: 71 Copynumber: 8.2 Consensus size: 71
487950 AGATACTTAA
* *
487960 ATGCTGCCCAAATTGTTATATATATGCTGTCCAAATTTTGGTGTAAAAATGCTGTTCAATTTGGT
1 ATGCTGCCCAAATTGTTGTATATATGCTGTCCAAATTTTGGTGTAAAAATGCTGCTCAATTTGGT
*
488025 ATATAA
66 ATATAT
* * * * *
488031 ATGCTGCCCAATTTGTTGTATATATGCTGTCCGATTTTTGGTGTAAAAATGTTGCTCAATTTGTT
1 ATGCTGCCCAAATTGTTGTATATATGCTGTCCAAATTTTGGTGTAAAAATGCTGCTCAATTTGGT
* *
488096 GTATTT
66 ATATAT
* *
488102 ATGCTGCCCAAATTGTTGTATATATGCTGTCC-AATTTTGATGTAAAAATGTTGCTCAATTTGGT
1 ATGCTGCCCAAATTGTTGTATATATGCTGTCCAAATTTTGGTGTAAAAATGCTGCTCAATTTGGT
488166 ATATAT
66 ATATAT
* * * * * * *
488172 ATGTTGCCCAATTTGTTTTATATACGCTGTCCAATTTTTGGTGTAAAAATGCTGATCAATTTGTT
1 ATGCTGCCCAAATTGTTGTATATATGCTGTCCAAATTTTGGTGTAAAAATGCTGCTCAATTTGGT
* *
488237 GTATTT
66 ATATAT
* *
488243 ATGCTGCCCAAATTGTTGTATATATGCTGTCC-AATTTTGATGTAAAAATGCTACTCAATTTGGT
1 ATGCTGCCCAAATTGTTGTATATATGCTGTCCAAATTTTGGTGTAAAAATGCTGCTCAATTTGGT
488307 ATATAT
66 ATATAT
*
488313 ATGCTGCCCAATTTGTTGTATATATGCTGTCCAAATTTTGGTGTAAAAATGCTGCTCAATTTGTG
1 ATGCTGCCCAAATTGTTGTATATATGCTGTCCAAATTTTGGTGTAAAAATGCTGCTCAA-TT-TG
488378 GTAT-T-T
64 GTATATAT
* **
488384 ATGCTGCCCAAATTGTTGTATATATGCTTTCC-AATTTTAATGTAAAAATGCTGCTCAATTTGGT
1 ATGCTGCCCAAATTGTTGTATATATGCTGTCCAAATTTTGGTGTAAAAATGCTGCTCAATTTGGT
488448 ATATAT
66 ATATAT
* * * **
488454 ATGCTGCCCAATTTGTTTTATATATGCTGTCCAATTTTTGGTGTAAAAATGCTGCTCAATTTATT
1 ATGCTGCCCAAATTGTTGTATATATGCTGTCCAAATTTTGGTGTAAAAATGCTGCTCAATTTGGT
*
488519 GTATAT
66 ATATAT
488525 ATGCTGCCCAAATTGTT
1 ATGCTGCCCAAATTGTT
488542 ACAGGGTAGA
Statistics
Matches: 449, Mismatches: 55, Indels: 14
0.87 0.11 0.03
Matches are distributed among these distances:
68 6 0.01
69 3 0.01
70 177 0.39
71 254 0.57
72 3 0.01
73 6 0.01
ACGTcount: A:0.27, C:0.14, G:0.17, T:0.43
Consensus pattern (71 bp):
ATGCTGCCCAAATTGTTGTATATATGCTGTCCAAATTTTGGTGTAAAAATGCTGCTCAATTTGGT
ATATAT
Found at i:488166 original size:141 final size:141
Alignment explanation
Indices: 487960--488541 Score: 984
Period size: 141 Copynumber: 4.1 Consensus size: 141
487950 AGATACTTAA
* * *
487960 ATGCTGCCCAAATTGTTATATATATGCTGTCCAAATTTTGGTGTAAAAATGCTGTTCAATTTGGT
1 ATGCTGCCCAAATTGTTGTATATATGCTGTCC-AATTTTGATGTAAAAATGCTGCTCAATTTGGT
* * *
488025 ATATAAATGCTGCCCAATTTGTTGTATATATGCTGTCCGATTTTTGGTGTAAAAATGTTGCTCAA
65 ATATATATGCTGCCCAATTTGTTGTATATATGCTGTCCAATTTTTGGTGTAAAAATGCTGCTCAA
488090 TTTGTTGTATTT
130 TTTGTTGTATTT
*
488102 ATGCTGCCCAAATTGTTGTATATATGCTGTCCAATTTTGATGTAAAAATGTTGCTCAATTTGGTA
1 ATGCTGCCCAAATTGTTGTATATATGCTGTCCAATTTTGATGTAAAAATGCTGCTCAATTTGGTA
* * * *
488167 TATATATGTTGCCCAATTTGTTTTATATACGCTGTCCAATTTTTGGTGTAAAAATGCTGATCAAT
66 TATATATGCTGCCCAATTTGTTGTATATATGCTGTCCAATTTTTGGTGTAAAAATGCTGCTCAAT
488232 TTGTTGTATTT
131 TTGTTGTATTT
*
488243 ATGCTGCCCAAATTGTTGTATATATGCTGTCCAATTTTGATGTAAAAATGCTACTCAATTTGGTA
1 ATGCTGCCCAAATTGTTGTATATATGCTGTCCAATTTTGATGTAAAAATGCTGCTCAATTTGGTA
*
488308 TATATATGCTGCCCAATTTGTTGTATATATGCTGTCCAAATTTTGGTGTAAAAATGCTGCTCAAT
66 TATATATGCTGCCCAATTTGTTGTATATATGCTGTCCAATTTTTGGTGTAAAAATGCTGCTCAAT
*
488373 TTGTGGTATTT
131 TTGTTGTATTT
* *
488384 ATGCTGCCCAAATTGTTGTATATATGCTTTCCAATTTTAATGTAAAAATGCTGCTCAATTTGGTA
1 ATGCTGCCCAAATTGTTGTATATATGCTGTCCAATTTTGATGTAAAAATGCTGCTCAATTTGGTA
*
488449 TATATATGCTGCCCAATTTGTTTTATATATGCTGTCCAATTTTTGGTGTAAAAATGCTGCTCAAT
66 TATATATGCTGCCCAATTTGTTGTATATATGCTGTCCAATTTTTGGTGTAAAAATGCTGCTCAAT
* *
488514 TTATTGTATAT
131 TTGTTGTATTT
488525 ATGCTGCCCAAATTGTT
1 ATGCTGCCCAAATTGTT
488542 ACAGGGTAGA
Statistics
Matches: 413, Mismatches: 27, Indels: 1
0.94 0.06 0.00
Matches are distributed among these distances:
141 382 0.92
142 31 0.08
ACGTcount: A:0.27, C:0.14, G:0.17, T:0.43
Consensus pattern (141 bp):
ATGCTGCCCAAATTGTTGTATATATGCTGTCCAATTTTGATGTAAAAATGCTGCTCAATTTGGTA
TATATATGCTGCCCAATTTGTTGTATATATGCTGTCCAATTTTTGGTGTAAAAATGCTGCTCAAT
TTGTTGTATTT
Found at i:496709 original size:4 final size:4
Alignment explanation
Indices: 496696--496729 Score: 61
Period size: 4 Copynumber: 8.8 Consensus size: 4
496686 AACATTTTCA
496696 AAAT -AAT AAAT AAAT AAAT AAAT AAAT AAAT AAA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAA
496730 ATATTTTACG
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 3 0.10
4 26 0.90
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (4 bp):
AAAT
Found at i:505106 original size:17 final size:17
Alignment explanation
Indices: 505084--505117 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
505074 TGGTAGTAAA
*
505084 GGTGGTGAGGGTTAGGG
1 GGTGGTGAGGGTAAGGG
505101 GGTGGTGAGGGTAAGGG
1 GGTGGTGAGGGTAAGGG
505118 TCAGGGAGAG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.15, C:0.00, G:0.65, T:0.21
Consensus pattern (17 bp):
GGTGGTGAGGGTAAGGG
Found at i:505164 original size:68 final size:69
Alignment explanation
Indices: 505001--505164 Score: 192
Period size: 68 Copynumber: 2.4 Consensus size: 69
504991 AGGTGGCGAG
* * * * *
505001 GTTGTTGGCAGTAAATGTAGTG-GGGGTGAGGGTGGTGAGGTGGTAAGGGTGAGGGAGAGGGTGG
1 GTTGCTGGCAGTAAAGGTAGTGAGGGTTGAGGGTGGTGAGGTGGTAAGGGTCAGGGAGAGGATGG
505065 TAAA
66 TAAA
* * * *
505069 GTTGTTGGTAGTAAAGGTGGTGAGGGTTAGGGGGTGGTGA-G-GGTAAGGGTCAGGGAGAGGATG
1 GTTGCTGGCAGTAAAGGTAGTGAGGGTT-GAGGGTGGTGAGGTGGTAAGGGTCAGGGAGAGGATG
*
505132 GT-GA
65 GTAAA
505136 GTTTGCTGGCAGTAAAGGTAGTGAGGGTT
1 G-TTGCTGGCAGTAAAGGTAGTGAGGGTT
505165 CGGGTTCGGG
Statistics
Matches: 82, Mismatches: 11, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
67 2 0.02
68 65 0.79
69 5 0.06
70 10 0.12
ACGTcount: A:0.21, C:0.02, G:0.51, T:0.25
Consensus pattern (69 bp):
GTTGCTGGCAGTAAAGGTAGTGAGGGTTGAGGGTGGTGAGGTGGTAAGGGTCAGGGAGAGGATGG
TAAA
Found at i:505269 original size:54 final size:54
Alignment explanation
Indices: 505197--505319 Score: 165
Period size: 54 Copynumber: 2.3 Consensus size: 54
505187 TAAAGGTTTA
* * * *
505197 GGTAGGGAGGGTGATGATGTTGCTGTCAGCGAAGGTGGTGAGAGTGATAGAGGC
1 GGTAAGGAGGGGGTTGATGTTGCTGTCAACGAAGGTGGTGAGAGTGATAGAGGC
* * * *
505251 GGTGAGGAGGGGGTTGATGTTGCTGTCAATGAAGGTGGTGAGAGTGATGGAGGT
1 GGTAAGGAGGGGGTTGATGTTGCTGTCAACGAAGGTGGTGAGAGTGATAGAGGC
*
505305 GGTAAGGAAGGGGTT
1 GGTAAGGAGGGGGTT
505320 AGGGAAGTGG
Statistics
Matches: 59, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
54 59 1.00
ACGTcount: A:0.22, C:0.05, G:0.50, T:0.24
Consensus pattern (54 bp):
GGTAAGGAGGGGGTTGATGTTGCTGTCAACGAAGGTGGTGAGAGTGATAGAGGC
Found at i:506967 original size:18 final size:18
Alignment explanation
Indices: 506944--506986 Score: 52
Period size: 17 Copynumber: 2.4 Consensus size: 18
506934 TAATTACGGG
*
506944 TTTTAAATGATTTTTTAA
1 TTTTAAATGATTTCTTAA
*
506962 TTTT-AATTATTTCTTAA
1 TTTTAAATGATTTCTTAA
*
506979 GTTTAAAT
1 TTTTAAAT
506987 TCATTTGTTG
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
17 14 0.67
18 7 0.33
ACGTcount: A:0.33, C:0.02, G:0.05, T:0.60
Consensus pattern (18 bp):
TTTTAAATGATTTCTTAA
Found at i:509855 original size:14 final size:14
Alignment explanation
Indices: 509810--509857 Score: 51
Period size: 14 Copynumber: 3.3 Consensus size: 14
509800 AAAAATTAAA
*
509810 AATTATAAAAAATT
1 AATTTTAAAAAATT
* *
509824 TATTTTAAATAATTTT
1 AATTTTAAA-AA-ATT
509840 AATTTTAAAAAATT
1 AATTTTAAAAAATT
509854 AATT
1 AATT
509858 AATTGCTAAT
Statistics
Matches: 27, Mismatches: 5, Indels: 4
0.75 0.14 0.11
Matches are distributed among these distances:
14 13 0.48
15 4 0.15
16 10 0.37
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (14 bp):
AATTTTAAAAAATT
Found at i:510411 original size:19 final size:18
Alignment explanation
Indices: 510366--510398 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
510356 AACATTAATT
510366 TCAT-TATA-TATTTTTA
1 TCATATATACTATTTTTA
510382 TCATATATACTATTTTT
1 TCATATATACTATTTTT
510399 TTGATATAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 4 0.27
17 4 0.27
18 7 0.47
ACGTcount: A:0.30, C:0.09, G:0.00, T:0.61
Consensus pattern (18 bp):
TCATATATACTATTTTTA
Found at i:514737 original size:24 final size:23
Alignment explanation
Indices: 514695--514745 Score: 66
Period size: 24 Copynumber: 2.2 Consensus size: 23
514685 AATCAAAGTC
* *
514695 AAATATATTATGCTAATAAATGCT
1 AAATATATTATACTAAT-AATACT
*
514719 AAATATATTATACTCATAATACT
1 AAATATATTATACTAATAATACT
514742 AAAT
1 AAAT
514746 CTTTTAGAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
23 9 0.38
24 15 0.62
ACGTcount: A:0.49, C:0.10, G:0.04, T:0.37
Consensus pattern (23 bp):
AAATATATTATACTAATAATACT
Found at i:525992 original size:14 final size:15
Alignment explanation
Indices: 525973--526019 Score: 60
Period size: 14 Copynumber: 3.1 Consensus size: 15
525963 TATTTTTCAA
525973 TCATCCCTCATCCT-
1 TCATCCCTCATCCTC
*
525987 TCATCCTTCATCCTTC
1 TCATCCCTCATCC-TC
*
526003 TCATCTCTCATCCTC
1 TCATCCCTCATCCTC
526018 TC
1 TC
526020 TCTCAACTCT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
14 12 0.43
15 5 0.18
16 11 0.39
ACGTcount: A:0.13, C:0.47, G:0.00, T:0.40
Consensus pattern (15 bp):
TCATCCCTCATCCTC
Found at i:534077 original size:24 final size:24
Alignment explanation
Indices: 534040--534091 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
534030 TTTCTAGAAG
* * *
534040 ATTTAGTATTTATTAGTATAATAT
1 ATTTAGAATATATTAGCATAATAT
*
534064 ATTTAGAATATATTAGCATAATTT
1 ATTTAGAATATATTAGCATAATAT
534088 ATTT
1 ATTT
534092 GACCTACGAA
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:0.38, C:0.02, G:0.08, T:0.52
Consensus pattern (24 bp):
ATTTAGAATATATTAGCATAATAT
Found at i:537833 original size:16 final size:18
Alignment explanation
Indices: 537812--537849 Score: 53
Period size: 16 Copynumber: 2.2 Consensus size: 18
537802 TAGGGGGAGA
537812 GAATAAAA-AATTGG-AT
1 GAATAAAATAATTGGAAT
*
537828 GAATAAAATATTTGGAAT
1 GAATAAAATAATTGGAAT
537846 GAAT
1 GAAT
537850 TATCATTATC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 8 0.42
17 5 0.26
18 6 0.32
ACGTcount: A:0.53, C:0.00, G:0.18, T:0.29
Consensus pattern (18 bp):
GAATAAAATAATTGGAAT
Found at i:542012 original size:9 final size:9
Alignment explanation
Indices: 542000--542024 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
541990 TTAAATTCGA
542000 TTAATTTGG
1 TTAATTTGG
542009 TTAATTTGG
1 TTAATTTGG
542018 TTAATTT
1 TTAATTT
542025 TTTATATGGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.24, C:0.00, G:0.16, T:0.60
Consensus pattern (9 bp):
TTAATTTGG
Found at i:544122 original size:30 final size:29
Alignment explanation
Indices: 544081--544145 Score: 80
Period size: 29 Copynumber: 2.2 Consensus size: 29
544071 TCTGCCATAG
*
544081 AGGCA-TTCCTTTAATAGAGATC-GCCATGA
1 AGGCATTTCCTTTAATA-A-ATCTACCATGA
*
544110 AGGCATTTCCTTTCATAAATCTACCATGA
1 AGGCATTTCCTTTAATAAATCTACCATGA
544139 AGGCATT
1 AGGCATT
544146 CTTTTTCATT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
28 3 0.09
29 19 0.59
30 10 0.31
ACGTcount: A:0.31, C:0.22, G:0.17, T:0.31
Consensus pattern (29 bp):
AGGCATTTCCTTTAATAAATCTACCATGA
Found at i:544651 original size:53 final size:53
Alignment explanation
Indices: 544565--544677 Score: 163
Period size: 53 Copynumber: 2.1 Consensus size: 53
544555 CTTGAATTTC
* * *
544565 CCCATATGATGCCATAACCCACTAGTTATGGTCTTACATGATATGATATTATT
1 CCCATATGATGCCATAACCCACCAATTACGGTCTTACATGATATGATATTATT
* * * *
544618 TCCATATGATGCCATAACCCACCAATTACGGTCTTATATGATATGGTATTCTT
1 CCCATATGATGCCATAACCCACCAATTACGGTCTTACATGATATGATATTATT
544671 CCCATAT
1 CCCATAT
544678 AACCCATCAA
Statistics
Matches: 52, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
53 52 1.00
ACGTcount: A:0.29, C:0.23, G:0.12, T:0.35
Consensus pattern (53 bp):
CCCATATGATGCCATAACCCACCAATTACGGTCTTACATGATATGATATTATT
Found at i:547381 original size:19 final size:20
Alignment explanation
Indices: 547359--547423 Score: 69
Period size: 20 Copynumber: 3.3 Consensus size: 20
547349 TTACTGGTGA
547359 CTTGTC-ACATTACTGGCAG
1 CTTGTCTACATTACTGGCAG
*
547378 CTTGTCTGCATTACTGGCAG
1 CTTGTCTACATTACTGGCAG
* * * * *
547398 TTTATCTGCATTACTTGTAG
1 CTTGTCTACATTACTGGCAG
547418 CTTGTC
1 CTTGTC
547424 CACAAATTGG
Statistics
Matches: 38, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
19 6 0.16
20 32 0.84
ACGTcount: A:0.17, C:0.23, G:0.20, T:0.40
Consensus pattern (20 bp):
CTTGTCTACATTACTGGCAG
Found at i:547391 original size:20 final size:20
Alignment explanation
Indices: 547366--547423 Score: 80
Period size: 20 Copynumber: 2.9 Consensus size: 20
547356 TGACTTGTCA
547366 CATTACTGGCAGCTTGTCTG
1 CATTACTGGCAGCTTGTCTG
* *
547386 CATTACTGGCAGTTTATCTG
1 CATTACTGGCAGCTTGTCTG
* *
547406 CATTACTTGTAGCTTGTC
1 CATTACTGGCAGCTTGTC
547424 CACAAATTGG
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.17, C:0.22, G:0.21, T:0.40
Consensus pattern (20 bp):
CATTACTGGCAGCTTGTCTG
Found at i:549867 original size:79 final size:78
Alignment explanation
Indices: 549722--549879 Score: 307
Period size: 79 Copynumber: 2.0 Consensus size: 78
549712 TGCGCTAAGT
549722 GAGAATTAAAATTATTTTTTGCTTTAGTTTCATTTTTTATTATTAAAAAAAATCTGATTGGTCTT
1 GAGAATTAAAATTATTTTTTGCTTTAGTTTCATTTTTTATTATTAAAAAAAATCTGATTGGTCTT
549787 TTGTTAAAAGTAA
66 TTGTTAAAAGTAA
549800 GAGAATTAAAATTATTTTTTGCTTTAGTTTCATTTTTTTATTATTAAAAAAAATCTGATTGGTCT
1 GAGAATTAAAATTATTTTTTGCTTTAGTTTCA-TTTTTTATTATTAAAAAAAATCTGATTGGTCT
549865 TTTGTTAAAAGTAA
65 TTTGTTAAAAGTAA
549879 G
1 G
549880 TTTTAATTAT
Statistics
Matches: 79, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
78 32 0.41
79 47 0.59
ACGTcount: A:0.34, C:0.05, G:0.12, T:0.49
Consensus pattern (78 bp):
GAGAATTAAAATTATTTTTTGCTTTAGTTTCATTTTTTATTATTAAAAAAAATCTGATTGGTCTT
TTGTTAAAAGTAA
Found at i:550458 original size:19 final size:19
Alignment explanation
Indices: 550434--550480 Score: 94
Period size: 19 Copynumber: 2.5 Consensus size: 19
550424 AATTTTTCCT
550434 GTCACACGGCCCGGAGTGG
1 GTCACACGGCCCGGAGTGG
550453 GTCACACGGCCCGGAGTGG
1 GTCACACGGCCCGGAGTGG
550472 GTCACACGG
1 GTCACACGG
550481 GTTGGCCACA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.17, C:0.32, G:0.40, T:0.11
Consensus pattern (19 bp):
GTCACACGGCCCGGAGTGG
Found at i:554164 original size:22 final size:22
Alignment explanation
Indices: 554111--554154 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
554101 ACAATTTTAA
554111 TAAA-TAAAAAAATACTAAATAT
1 TAAATTAAAAAAATA-TAAATAT
*
554133 TAAATTAAAATAATATAAATAT
1 TAAATTAAAAAAATATAAATAT
554155 ATATTTAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 11 0.55
23 9 0.45
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (22 bp):
TAAATTAAAAAAATATAAATAT
Found at i:562370 original size:20 final size:21
Alignment explanation
Indices: 562342--562381 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
562332 GTAATTTGTC
*
562342 AAATAAAAGATAAATTAGTTA
1 AAATAAAAGACAAATTAGTTA
562363 AAAT-AAAGACAAATTAGTT
1 AAATAAAAGACAAATTAGTT
562382 GTCATTTGTG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 14 0.78
21 4 0.22
ACGTcount: A:0.60, C:0.03, G:0.10, T:0.28
Consensus pattern (21 bp):
AAATAAAAGACAAATTAGTTA
Found at i:563320 original size:44 final size:43
Alignment explanation
Indices: 563255--563371 Score: 141
Period size: 44 Copynumber: 2.7 Consensus size: 43
563245 TATATGTTAT
563255 CATGTAAGACCAC-GTCTGGGACGTTGGCATCGACT-TGTGACTTA
1 CATGTAAGACC-CTGTCTGGGACGTTGGCATCGA-TATGTGA-TTA
* *
563299 CGTGTAAGACCCTGTCTGGGACAG-TGGTATCGATATGTGATTA
1 CATGTAAGACCCTGTCTGGGAC-GTTGGCATCGATATGTGATTA
* *
563342 CATATAAGACCATGTCTGGGACGTTGGCAT
1 CATGTAAGACCCTGTCTGGGACGTTGGCAT
563372 TGTACGAAAT
Statistics
Matches: 63, Mismatches: 6, Indels: 9
0.81 0.08 0.12
Matches are distributed among these distances:
42 1 0.02
43 29 0.46
44 32 0.51
45 1 0.02
ACGTcount: A:0.24, C:0.20, G:0.28, T:0.28
Consensus pattern (43 bp):
CATGTAAGACCCTGTCTGGGACGTTGGCATCGATATGTGATTA
Found at i:569029 original size:27 final size:28
Alignment explanation
Indices: 568993--569045 Score: 74
Period size: 27 Copynumber: 1.9 Consensus size: 28
568983 CGAAAAATAT
568993 ATAATAATTAT-AAAATAATTAAATTTCA
1 ATAATAATTATGAAAAT-ATTAAATTTCA
*
569021 ATAA-AATTATGAAAATTTTAAATTT
1 ATAATAATTATGAAAATATTAAATTT
569046 TAAATAGTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
27 14 0.61
28 9 0.39
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.42
Consensus pattern (28 bp):
ATAATAATTATGAAAATATTAAATTTCA
Found at i:569051 original size:28 final size:28
Alignment explanation
Indices: 568993--569051 Score: 68
Period size: 28 Copynumber: 2.1 Consensus size: 28
568983 CGAAAAATAT
*
568993 ATAATAATTATAAAATAATTAAATTTCA
1 ATAATAATTATAAAATAATTAAATTTAA
*
569021 ATAA-AATTATGAAAAT-TTTAAATTTTAA
1 ATAATAATTAT-AAAATAATTAAA-TTTAA
569049 ATA
1 ATA
569052 GTTTTATATC
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
27 11 0.41
28 16 0.59
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.41
Consensus pattern (28 bp):
ATAATAATTATAAAATAATTAAATTTAA
Found at i:577916 original size:7 final size:7
Alignment explanation
Indices: 577904--577955 Score: 63
Period size: 7 Copynumber: 7.3 Consensus size: 7
577894 GTTCAGATTT
577904 AATAAAA
1 AATAAAA
577911 AATAAAAAA
1 AAT--AAAA
577920 AATCAAAA
1 AAT-AAAA
577928 AAT-AAA
1 AATAAAA
577934 AATAAAA
1 AATAAAA
577941 AAT-AAA
1 AATAAAA
577947 AATAAAA
1 AATAAAA
577954 AA
1 AA
577956 ATCAATAAAA
Statistics
Matches: 40, Mismatches: 1, Indels: 8
0.82 0.02 0.16
Matches are distributed among these distances:
6 12 0.30
7 14 0.35
8 7 0.17
9 7 0.17
ACGTcount: A:0.85, C:0.02, G:0.00, T:0.13
Consensus pattern (7 bp):
AATAAAA
Found at i:577940 original size:13 final size:13
Alignment explanation
Indices: 577917--577978 Score: 74
Period size: 13 Copynumber: 4.8 Consensus size: 13
577907 AAAAAATAAA
577917 AAAAATCAAAAAAT
1 AAAAAT-AAAAAAT
577931 AAAAATAAAAAAT
1 AAAAATAAAAAAT
577944 AAAAATAAAAAA-
1 AAAAATAAAAAAT
**
577956 ATCAAT-AAAAAT
1 AAAAATAAAAAAT
*
577968 CAAAATAAAAA
1 AAAAATAAAAA
577979 CATGAGAATG
Statistics
Matches: 41, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
11 5 0.12
12 7 0.17
13 23 0.56
14 6 0.15
ACGTcount: A:0.81, C:0.05, G:0.00, T:0.15
Consensus pattern (13 bp):
AAAAATAAAAAAT
Found at i:577940 original size:30 final size:30
Alignment explanation
Indices: 577904--577978 Score: 93
Period size: 30 Copynumber: 2.5 Consensus size: 30
577894 GTTCAGATTT
577904 AATAAAAAATAAAAA-AAATCAAAA-AATAAA
1 AATAAAAAATAAAAATAAA--AAAACAATAAA
577934 AATAAAAAATAAAAATAAAAAAATCAATAAA
1 AATAAAAAATAAAAATAAAAAAA-CAATAAA
*
577965 AAT-CAAAATAAAAA
1 AATAAAAAATAAAAA
577979 CATGAGAATG
Statistics
Matches: 41, Mismatches: 1, Indels: 6
0.85 0.02 0.12
Matches are distributed among these distances:
29 4 0.10
30 25 0.61
31 12 0.29
ACGTcount: A:0.81, C:0.04, G:0.00, T:0.15
Consensus pattern (30 bp):
AATAAAAAATAAAAATAAAAAAACAATAAA
Found at i:577955 original size:37 final size:37
Alignment explanation
Indices: 577908--577978 Score: 110
Period size: 37 Copynumber: 1.9 Consensus size: 37
577898 AGATTTAATA
577908 AAAAATAAAAAAAATC-A-AAAAATAAAAATAAAAAAT
1 AAAAAT-AAAAAAATCAATAAAAATAAAAATAAAAAAT
*
577944 AAAAATAAAAAAATCAATAAAAATCAAAATAAAAA
1 AAAAATAAAAAAATCAATAAAAATAAAAATAAAAA
577979 CATGAGAATG
Statistics
Matches: 32, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
35 9 0.28
36 7 0.22
37 16 0.50
ACGTcount: A:0.82, C:0.04, G:0.00, T:0.14
Consensus pattern (37 bp):
AAAAATAAAAAAATCAATAAAAATAAAAATAAAAAAT
Found at i:577972 original size:7 final size:6
Alignment explanation
Indices: 577908--577978 Score: 67
Period size: 6 Copynumber: 11.8 Consensus size: 6
577898 AGATTTAATA
*
577908 AAAAAT AAAAA- AAATCA- AAAAAT AAAAAT AAAAAAT AAAAAT AAAAA-
1 AAAAAT AAAAAT AAA-AAT AAAAAT AAAAAT -AAAAAT AAAAAT AAAAAT
* *
577955 AATCAAT AAAAAT CAAAAT AAAAA
1 AA-AAAT AAAAAT AAAAAT AAAAA
577979 CATGAGAATG
Statistics
Matches: 54, Mismatches: 6, Indels: 10
0.77 0.09 0.14
Matches are distributed among these distances:
5 6 0.11
6 40 0.74
7 8 0.15
ACGTcount: A:0.82, C:0.04, G:0.00, T:0.14
Consensus pattern (6 bp):
AAAAAT
Found at i:578009 original size:12 final size:12
Alignment explanation
Indices: 577992--578026 Score: 61
Period size: 12 Copynumber: 2.9 Consensus size: 12
577982 GAGAATGATA
577992 AAAAGGAAAAAG
1 AAAAGGAAAAAG
578004 AAAAGGAAAAAG
1 AAAAGGAAAAAG
*
578016 AAAAAGAAAAA
1 AAAAGGAAAAA
578027 AAGAAAAAAG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (12 bp):
AAAAGGAAAAAG
Found at i:578036 original size:7 final size:6
Alignment explanation
Indices: 577991--578026 Score: 54
Period size: 6 Copynumber: 5.8 Consensus size: 6
577981 TGAGAATGAT
*
577991 AAAAAGG AAAAAG AAAAGG AAAAAG AAAAAG AAAAA
1 AAAAA-G AAAAAG AAAAAG AAAAAG AAAAAG AAAAA
578027 AAGAAAAAAG
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
6 22 0.81
7 5 0.19
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (6 bp):
AAAAAG
Found at i:580301 original size:44 final size:44
Alignment explanation
Indices: 580242--580705 Score: 569
Period size: 44 Copynumber: 10.5 Consensus size: 44
580232 ATCACAAAGC
* *
580242 CCTATCTCCCTGACCAGCAGTGGAATAGGTTGAAGATTGTAAGC
1 CCTATCTCCCTGAACAGCAGTGGAATAGGTTGAAGATTGTAAGT
* * *
580286 CCTATCTCCCTGACCAGTAGTGGAATAGGCTGAAGATTGTAAGT
1 CCTATCTCCCTGAACAGCAGTGGAATAGGTTGAAGATTGTAAGT
* * * *
580330 CCTAGCTCCCTGAACAGCAATGGAATAGGTCGAAGATTGTAAGC
1 CCTATCTCCCTGAACAGCAGTGGAATAGGTTGAAGATTGTAAGT
** * **
580374 CCTATCTCCCTGCCCAGCAGTGGAATAGGCTGAAGATCATAAGT
1 CCTATCTCCCTGAACAGCAGTGGAATAGGTTGAAGATTGTAAGT
* *
580418 CCTAGCTCCCTGAACAGCAGTGGAATAGGTCGAAGATTGTAAGT
1 CCTATCTCCCTGAACAGCAGTGGAATAGGTTGAAGATTGTAAGT
* * * * *
580462 CCTAGCTCCCTGAATAACAGTGGAATAGGTCGAAGATGGTAAG-
1 CCTATCTCCCTGAACAGCAGTGGAATAGGTTGAAGATTGTAAGT
* *
580505 CTCTTTCTCCCT-AACCAGTAGTGGAATAGGTTGAAGATTGTAAGT
1 C-CTATCTCCCTGAA-CAGCAGTGGAATAGGTTGAAGATTGTAAGT
* *
580550 CCTTTCTCCCT-AACCAGCAGTGGAATAGGTTGAAGATTGCAAGT
1 CCTATCTCCCTGAA-CAGCAGTGGAATAGGTTGAAGATTGTAAGT
* * *
580594 CCTATCTCCCTGAACAACAGTGGAATAGGTGGAAGATTGTATGT
1 CCTATCTCCCTGAACAGCAGTGGAATAGGTTGAAGATTGTAAGT
*
580638 CCTATCTCCCTGAACAGCAGTGGAATAGGTTAAAGATTGT-AGAT
1 CCTATCTCCCTGAACAGCAGTGGAATAGGTTGAAGATTGTAAG-T
* *
580682 CCTGTCTCCCT-AAGCAGTAGTGGA
1 CCTATCTCCCTGAA-CAGCAGTGGA
580706 GCAGATCGAA
Statistics
Matches: 365, Mismatches: 49, Indels: 12
0.86 0.12 0.03
Matches are distributed among these distances:
43 6 0.02
44 356 0.98
45 3 0.01
ACGTcount: A:0.29, C:0.21, G:0.25, T:0.25
Consensus pattern (44 bp):
CCTATCTCCCTGAACAGCAGTGGAATAGGTTGAAGATTGTAAGT
Found at i:580475 original size:132 final size:132
Alignment explanation
Indices: 580238--580705 Score: 629
Period size: 132 Copynumber: 3.5 Consensus size: 132
580228 TGAAATCACA
* *
580238 AAGCCCTATCTCCCTGACCAGCAGTGGAATAGGTTGAAGATTGTAAGCCCTATCTCCCTGACCAG
1 AAGCCCTATCTCCCTGACCAGCAGTGGAATAGGTTGAAGATTGTAAGTCCTATCTCCCTGAACAG
* * *
580303 TAGTGGAATAGG-CTGAAGATTGTAAGTCCTAGCTCCCTGAACAGCAATGGAATAGGTCGAAGAT
66 CAGTGGAATAGGTC-GAAGATTGTAAGTCCTAGCTCCCTGAACAACAGTGGAATAGGTCGAAGAT
580367 TGT
130 TGT
* * ** *
580370 AAGCCCTATCTCCCTGCCCAGCAGTGGAATAGGCTGAAGATCATAAGTCCTAGCTCCCTGAACAG
1 AAGCCCTATCTCCCTGACCAGCAGTGGAATAGGTTGAAGATTGTAAGTCCTATCTCCCTGAACAG
* *
580435 CAGTGGAATAGGTCGAAGATTGTAAGTCCTAGCTCCCTGAATAACAGTGGAATAGGTCGAAGATG
66 CAGTGGAATAGGTCGAAGATTGTAAGTCCTAGCTCCCTGAACAACAGTGGAATAGGTCGAAGATT
580500 GT
131 GT
* * * * *
580502 AAGCTCTTTCTCCCTAACCAGTAGTGGAATAGGTTGAAGATTGTAAGTCCTTTCTCCCT-AACCA
1 AAGCCCTATCTCCCTGACCAGCAGTGGAATAGGTTGAAGATTGTAAGTCCTATCTCCCTGAA-CA
* * * *
580566 GCAGTGGAATAGGTTGAAGATTGCAAGTCCTATCTCCCTGAACAACAGTGGAATAGGTGGAAGAT
65 GCAGTGGAATAGGTCGAAGATTGTAAGTCCTAGCTCCCTGAACAACAGTGGAATAGGTCGAAGAT
580631 TGT
130 TGT
* * * * *
580634 ATGTCCTATCTCCCTGAACAGCAGTGGAATAGGTTAAAGATTGT-AGATCCTGTCTCCCT-AAGC
1 AAGCCCTATCTCCCTGACCAGCAGTGGAATAGGTTGAAGATTGTAAG-TCCTATCTCCCTGAA-C
*
580697 AGTAGTGGA
64 AGCAGTGGA
580706 GCAGATCGAA
Statistics
Matches: 294, Mismatches: 39, Indels: 6
0.87 0.12 0.02
Matches are distributed among these distances:
131 4 0.01
132 289 0.98
133 1 0.00
ACGTcount: A:0.29, C:0.21, G:0.25, T:0.25
Consensus pattern (132 bp):
AAGCCCTATCTCCCTGACCAGCAGTGGAATAGGTTGAAGATTGTAAGTCCTATCTCCCTGAACAG
CAGTGGAATAGGTCGAAGATTGTAAGTCCTAGCTCCCTGAACAACAGTGGAATAGGTCGAAGATT
GT
Found at i:592194 original size:9 final size:8
Alignment explanation
Indices: 592175--592208 Score: 50
Period size: 9 Copynumber: 4.0 Consensus size: 8
592165 TTACTTATTA
592175 ATTTTTTT
1 ATTTTTTT
592183 ATTTTCTTT
1 ATTTT-TTT
592192 ATTCTTTTT
1 ATT-TTTTT
592201 ATTTTTTT
1 ATTTTTTT
592209 GTGATTTTCT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
8 10 0.42
9 12 0.50
10 2 0.08
ACGTcount: A:0.12, C:0.06, G:0.00, T:0.82
Consensus pattern (8 bp):
ATTTTTTT
Found at i:593535 original size:20 final size:20
Alignment explanation
Indices: 593512--593566 Score: 110
Period size: 20 Copynumber: 2.8 Consensus size: 20
593502 GTAGTAATTT
593512 AGTAAATAAAAGAAATTTTA
1 AGTAAATAAAAGAAATTTTA
593532 AGTAAATAAAAGAAATTTTA
1 AGTAAATAAAAGAAATTTTA
593552 AGTAAATAAAAGAAA
1 AGTAAATAAAAGAAA
593567 AAAGAAAGAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 35 1.00
ACGTcount: A:0.64, C:0.00, G:0.11, T:0.25
Consensus pattern (20 bp):
AGTAAATAAAAGAAATTTTA
Found at i:594951 original size:206 final size:207
Alignment explanation
Indices: 594591--595005 Score: 661
Period size: 206 Copynumber: 2.0 Consensus size: 207
594581 CATTCCCGAG
* * * * *
594591 TATCCAATGTAATCCTAGATGGTTCAGCAGGTACGCAAAGGTTAATTGTCAAGGCATGTATAAAA
1 TATCAAATGTAATCCTAGATGGTTCAACAGGCAAGCAAAGGTTAATTGGCAAGGCATGTATAAAA
* *
594656 TTGAATAATGGTTCATGATCCTATGAAATGGTTAATGAGTTACATGATGTGCATATGAAATGTAC
66 TTGAATAATGGTTCATGATCCTATGAAATGGTTAATGAGTTAAATGATGTGCATATGAAATCTAC
* * * *
594721 TTATTATATAATTGAACTCATATGTATCATGTATGAATTTACTAACTTGTGAGTTTGATGGTTCT
131 GTATGATATAATTGAACTCATATGTATCATGTATGAACTTACTAACTTGTGAGTTTGATGGTGCT
594786 TGTATAAGATTT
196 TGTATAAGATTT
* *
594798 TATCAAATGTAATCCTAGATGGTTCAACGGGCAAGCAAAGGTTAA-TGGCAAGGCATGTATACAA
1 TATCAAATGTAATCCTAGATGGTTCAACAGGCAAGCAAAGGTTAATTGGCAAGGCATGTATAAAA
* * **
594862 TTGAATAATTGTTCATGATCCTATGAAATGGTTTATGAGTTAAATGATGTTTATATGAAATCTAC
66 TTGAATAATGGTTCATGATCCTATGAAATGGTTAATGAGTTAAATGATGTGCATATGAAATCTAC
594927 GTATGATATAATTGAACTCATATGTATCATGTATGAACTTACTAACTTGTGAGTTTGATGGTGCT
131 GTATGATATAATTGAACTCATATGTATCATGTATGAACTTACTAACTTGTGAGTTTGATGGTGCT
*
594992 TGTATAGGATTT
196 TGTATAAGATTT
595004 TA
1 TA
595006 CTATGCTTAT
Statistics
Matches: 190, Mismatches: 18, Indels: 1
0.91 0.09 0.00
Matches are distributed among these distances:
206 150 0.79
207 40 0.21
ACGTcount: A:0.33, C:0.11, G:0.20, T:0.37
Consensus pattern (207 bp):
TATCAAATGTAATCCTAGATGGTTCAACAGGCAAGCAAAGGTTAATTGGCAAGGCATGTATAAAA
TTGAATAATGGTTCATGATCCTATGAAATGGTTAATGAGTTAAATGATGTGCATATGAAATCTAC
GTATGATATAATTGAACTCATATGTATCATGTATGAACTTACTAACTTGTGAGTTTGATGGTGCT
TGTATAAGATTT
Found at i:598703 original size:16 final size:16
Alignment explanation
Indices: 598682--598713 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
598672 AACTTGGGTA
598682 ATCGATCCACGATAAC
1 ATCGATCCACGATAAC
598698 ATCGATCCACGATAAC
1 ATCGATCCACGATAAC
598714 CCAGACAGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.38, C:0.31, G:0.12, T:0.19
Consensus pattern (16 bp):
ATCGATCCACGATAAC
Found at i:607002 original size:41 final size:41
Alignment explanation
Indices: 606945--607029 Score: 170
Period size: 41 Copynumber: 2.1 Consensus size: 41
606935 AATTCGTAAA
606945 GTATGTGAAATTGAATAATATTGACTGATACCAACACAATG
1 GTATGTGAAATTGAATAATATTGACTGATACCAACACAATG
606986 GTATGTGAAATTGAATAATATTGACTGATACCAACACAATG
1 GTATGTGAAATTGAATAATATTGACTGATACCAACACAATG
607027 GTA
1 GTA
607030 ATTTGAAAGA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 44 1.00
ACGTcount: A:0.41, C:0.12, G:0.18, T:0.29
Consensus pattern (41 bp):
GTATGTGAAATTGAATAATATTGACTGATACCAACACAATG
Found at i:607330 original size:24 final size:23
Alignment explanation
Indices: 607283--607333 Score: 66
Period size: 23 Copynumber: 2.2 Consensus size: 23
607273 TCAATTTATC
*
607283 GCATTTTTACTAGCAACTTGTTT
1 GCATTTTTACTAGCAAATTGTTT
* *
607306 GCATTTTTACTGGCAGAATTTTTT
1 GCATTTTTACTAGCA-AATTGTTT
607330 GCAT
1 GCAT
607334 GTTGTTATCG
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
23 14 0.58
24 10 0.42
ACGTcount: A:0.22, C:0.16, G:0.16, T:0.47
Consensus pattern (23 bp):
GCATTTTTACTAGCAAATTGTTT
Found at i:607875 original size:31 final size:33
Alignment explanation
Indices: 607822--607887 Score: 84
Period size: 31 Copynumber: 2.1 Consensus size: 33
607812 ATAAGTATTA
*
607822 TTAAATATTTATTGGTTTTGGCTT-GTAA-TTT
1 TTAAATATTTATTGGTTATGGCTTGGTAACTTT
*
607853 TTAATTATTT-TTGGTCTATGGCTTGGTAACTTT
1 TTAAATATTTATTGGT-TATGGCTTGGTAACTTT
607886 TT
1 TT
607888 TTTCGGGGAT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
30 5 0.17
31 16 0.53
32 4 0.13
33 5 0.17
ACGTcount: A:0.20, C:0.06, G:0.17, T:0.58
Consensus pattern (33 bp):
TTAAATATTTATTGGTTATGGCTTGGTAACTTT
Found at i:613578 original size:19 final size:20
Alignment explanation
Indices: 613556--613593 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
613546 TTACAGTAGT
613556 AATTT-AGTAAATAAAAGAA
1 AATTTAAGTAAATAAAAGAA
613575 AATTTAAGTAAATAAAAGA
1 AATTTAAGTAAATAAAAGA
613594 CAAAAGAAAG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 5 0.28
20 13 0.72
ACGTcount: A:0.63, C:0.00, G:0.11, T:0.26
Consensus pattern (20 bp):
AATTTAAGTAAATAAAAGAA
Found at i:615049 original size:40 final size:40
Alignment explanation
Indices: 614994--615256 Score: 287
Period size: 40 Copynumber: 6.6 Consensus size: 40
614984 GAATAAAATT
* * * * *
614994 CCCCTAAAAGCACATATGTTCCCCTTTTTGTACTCCGGTA
1 CCCCTGAATGCACATACGTGCCCCTTTTTGTACTTCGGTA
* * **
615034 CCCCTGAATGTACATACGTGCCCCTGTTTGTACTTTAGTA
1 CCCCTGAATGCACATACGTGCCCCTTTTTGTACTTCGGTA
* * *
615074 CACCTGAATGCACATATGTGCCCCTGTTTT-TACTTTGGTA
1 CCCCTGAATGCACATACGTGCCCCT-TTTTGTACTTCGGTA
* * *
615114 ACCCTGAATGCACATACGTGCCCCTGTTTGTACGTCGGTA
1 CCCCTGAATGCACATACGTGCCCCTTTTTGTACTTCGGTA
* * *
615154 CCCCTGAATGCACATACATG-CCCTTGTTTATACTTTGGTA
1 CCCCTGAATGCACATACGTGCCCCTT-TTTGTACTTCGGTA
* * *
615194 TCCCTGAATGCACATGCGTGCCCCTATTTGTACTTCGGTA
1 CCCCTGAATGCACATACGTGCCCCTTTTTGTACTTCGGTA
* *
615234 CCACTGAATGCACATGCGTGCCC
1 CCCCTGAATGCACATACGTGCCC
615257 TTGTTCTGCA
Statistics
Matches: 185, Mismatches: 34, Indels: 8
0.81 0.15 0.04
Matches are distributed among these distances:
39 7 0.04
40 171 0.92
41 7 0.04
ACGTcount: A:0.21, C:0.30, G:0.18, T:0.32
Consensus pattern (40 bp):
CCCCTGAATGCACATACGTGCCCCTTTTTGTACTTCGGTA
Found at i:615057 original size:20 final size:20
Alignment explanation
Indices: 615034--615176 Score: 56
Period size: 20 Copynumber: 7.2 Consensus size: 20
615024 TACTCCGGTA
615034 CCCCTGAATGTACATACGTG
1 CCCCTGAATGTACATACGTG
** * *
615054 CCCCTGTTTGTACTTTA-GTA
1 CCCCTGAATGTAC-ATACGTG
* * *
615074 CACCTGAATGCACATATGTG
1 CCCCTGAATGTACATACGTG
** * * ** *
615094 CCCCTGTTTTTACTTTGGTA
1 CCCCTGAATGTACATACGTG
* *
615114 ACCCTGAATGCACATACGTG
1 CCCCTGAATGTACATACGTG
** * *
615134 CCCCTGTTTGTACGT-CGGTA
1 CCCCTGAATGTACATAC-GTG
* *
615154 CCCCTGAATGCACATACATG
1 CCCCTGAATGTACATACGTG
615174 CCC
1 CCC
615177 TTGTTTATAC
Statistics
Matches: 79, Mismatches: 40, Indels: 8
0.62 0.31 0.06
Matches are distributed among these distances:
19 3 0.04
20 73 0.92
21 3 0.04
ACGTcount: A:0.21, C:0.30, G:0.18, T:0.31
Consensus pattern (20 bp):
CCCCTGAATGTACATACGTG
Found at i:615216 original size:120 final size:120
Alignment explanation
Indices: 615003--615261 Score: 335
Period size: 120 Copynumber: 2.2 Consensus size: 120
614993 TCCCCTAAAA
* * * * * *
615003 GCACATATGTTCCCCTTTTTGTACTCCGGTACCCCTGAATGTACATACGTGCCCCTGTTTGTACT
1 GCACATACGTGCCCCTGTTTGTACTCCGGTACCCCTGAATGCACATACATGCCCCTGTTTATACT
* * * *
615068 TTAGTACACCTGAATGCACATATGTGCCCCTGTTTTTACTTTGGTAACC-CTGAAT
66 TTAGTACACCTGAATGCACATACGTGCCCCTATTTGTACTTCGGT-ACCACTGAAT
*
615123 GCACATACGTGCCCCTGTTTGTACGT-CGGTACCCCTGAATGCACATACATGCCCTTGTTTATAC
1 GCACATACGTGCCCCTGTTTGTAC-TCCGGTACCCCTGAATGCACATACATGCCCCTGTTTATAC
* *
615187 TTTGGTATC-CCTGAATGCACATGCGTGCCCCTATTTGTACTTCGGTACCACTGAAT
65 TTTAGTA-CACCTGAATGCACATACGTGCCCCTATTTGTACTTCGGTACCACTGAAT
* *
615243 GCACATGCGTGCCCTTGTT
1 GCACATACGTGCCCCTGTT
615262 CTGCATCTAC
Statistics
Matches: 121, Mismatches: 15, Indels: 6
0.85 0.11 0.04
Matches are distributed among these distances:
119 3 0.02
120 116 0.96
121 2 0.02
ACGTcount: A:0.19, C:0.29, G:0.19, T:0.34
Consensus pattern (120 bp):
GCACATACGTGCCCCTGTTTGTACTCCGGTACCCCTGAATGCACATACATGCCCCTGTTTATACT
TTAGTACACCTGAATGCACATACGTGCCCCTATTTGTACTTCGGTACCACTGAAT
Found at i:615256 original size:80 final size:80
Alignment explanation
Indices: 615030--615261 Score: 322
Period size: 80 Copynumber: 2.9 Consensus size: 80
615020 TTTGTACTCC
* * ** *
615030 GGTACCCCTGAATGTACATACGTGCCCCTGTTTGTACTTTAGTA-CACCTGAATGCACATATGTG
1 GGTAACCCTGAATGCACATACGTGCCCCTGTTTGTACTTCGGTACCA-CTGAATGCACATACGTG
* *
615094 CCCCTGTTTTTACTTT
65 CCCTTGTTTATACTTT
* * *
615110 GGTAACCCTGAATGCACATACGTGCCCCTGTTTGTACGTCGGTACCCCTGAATGCACATACATGC
1 GGTAACCCTGAATGCACATACGTGCCCCTGTTTGTACTTCGGTACCACTGAATGCACATACGTGC
615175 CCTTGTTTATACTTT
66 CCTTGTTTATACTTT
* * * *
615190 GGTATCCCTGAATGCACATGCGTGCCCCTATTTGTACTTCGGTACCACTGAATGCACATGCGTGC
1 GGTAACCCTGAATGCACATACGTGCCCCTGTTTGTACTTCGGTACCACTGAATGCACATACGTGC
615255 CCTTGTT
66 CCTTGTT
615262 CTGCATCTAC
Statistics
Matches: 134, Mismatches: 17, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
80 133 0.99
81 1 0.01
ACGTcount: A:0.20, C:0.28, G:0.19, T:0.33
Consensus pattern (80 bp):
GGTAACCCTGAATGCACATACGTGCCCCTGTTTGTACTTCGGTACCACTGAATGCACATACGTGC
CCTTGTTTATACTTT
Found at i:616661 original size:23 final size:24
Alignment explanation
Indices: 616635--616696 Score: 83
Period size: 23 Copynumber: 2.6 Consensus size: 24
616625 ACCTAGATTT
616635 AGTCAAAGTAATTCTCAAG-AAAA
1 AGTCAAAGTAATTCTCAAGAAAAA
*
616658 AGTC-AAGCTAATTTTCAAGAAAAA
1 AGTCAAAG-TAATTCTCAAGAAAAA
*
616682 AGTCAAAATAATTCT
1 AGTCAAAGTAATTCT
616697 TGATTATTTA
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
22 3 0.09
23 14 0.42
24 14 0.42
25 2 0.06
ACGTcount: A:0.50, C:0.13, G:0.11, T:0.26
Consensus pattern (24 bp):
AGTCAAAGTAATTCTCAAGAAAAA
Found at i:617582 original size:19 final size:20
Alignment explanation
Indices: 617558--617595 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
617548 TTAAAGTAGT
617558 AATTT-AGTAAATAAAAGAA
1 AATTTAAGTAAATAAAAGAA
617577 AATTTAAGTAAATAAAAGA
1 AATTTAAGTAAATAAAAGA
617596 CAAAAGAAAG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 5 0.28
20 13 0.72
ACGTcount: A:0.63, C:0.00, G:0.11, T:0.26
Consensus pattern (20 bp):
AATTTAAGTAAATAAAAGAA
Found at i:632135 original size:17 final size:17
Alignment explanation
Indices: 632113--632149 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 17
632103 GAGGTTTGTG
632113 AAGTATGCCAGCTAGGT
1 AAGTATGCCAGCTAGGT
*
632130 AAGTATGCTAGCTAGGT
1 AAGTATGCCAGCTAGGT
632147 AAG
1 AAG
632150 CAAGCCAGGA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.32, C:0.14, G:0.30, T:0.24
Consensus pattern (17 bp):
AAGTATGCCAGCTAGGT
Found at i:647258 original size:28 final size:28
Alignment explanation
Indices: 647198--647265 Score: 73
Period size: 28 Copynumber: 2.4 Consensus size: 28
647188 GGTTGTTGGA
** *
647198 CTGGCCTGCTGTGCTGCTGGGTTGGGTG
1 CTGGCCTGCTGTGCTGCTGGGTCAGGCG
* * *
647226 TTGGCCTGTTGTGCTGCTTGGTCAGGCG
1 CTGGCCTGCTGTGCTGCTGGGTCAGGCG
*
647254 CTGGCCTACTGT
1 CTGGCCTGCTGT
647266 TTGTTAGGCT
Statistics
Matches: 31, Mismatches: 9, Indels: 0
0.77 0.22 0.00
Matches are distributed among these distances:
28 31 1.00
ACGTcount: A:0.03, C:0.24, G:0.40, T:0.34
Consensus pattern (28 bp):
CTGGCCTGCTGTGCTGCTGGGTCAGGCG
Found at i:647448 original size:7 final size:7
Alignment explanation
Indices: 647436--647492 Score: 62
Period size: 7 Copynumber: 7.9 Consensus size: 7
647426 TTATATATTT
647436 TTTTTTC
1 TTTTTTC
647443 TTTTTTC
1 TTTTTTC
647450 TTTCTTTC
1 TTT-TTTC
647458 TTTTTTC
1 TTTTTTC
647465 TTTCTTT-
1 TTT-TTTC
* *
647472 TTTCTTA
1 TTTTTTC
647479 TTTTTTC
1 TTTTTTC
647486 TTATTTT
1 TT-TTTT
647493 TTCCTCCTTC
Statistics
Matches: 43, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
6 2 0.05
7 27 0.63
8 14 0.33
ACGTcount: A:0.04, C:0.14, G:0.00, T:0.82
Consensus pattern (7 bp):
TTTTTTC
Found at i:647448 original size:10 final size:10
Alignment explanation
Indices: 647433--647495 Score: 81
Period size: 11 Copynumber: 6.0 Consensus size: 10
647423 CATTTATATA
647433 TTTTTTTTTC
1 TTTTTTTTTC
647443 TTTTTTCTTTC
1 TTTTTT-TTTC
647454 TTTCTTTTTTC
1 TTT-TTTTTTC
647465 TTTCTTTTTTC
1 TTT-TTTTTTC
*
647476 TTATTTTTTC
1 TTTTTTTTTC
*
647486 TTATTTTTTC
1 TTTTTTTTTC
647496 CTCCTTCTTC
Statistics
Matches: 50, Mismatches: 1, Indels: 4
0.91 0.02 0.07
Matches are distributed among these distances:
10 23 0.46
11 24 0.48
12 3 0.06
ACGTcount: A:0.03, C:0.14, G:0.00, T:0.83
Consensus pattern (10 bp):
TTTTTTTTTC
Found at i:647453 original size:4 final size:4
Alignment explanation
Indices: 647439--647477 Score: 57
Period size: 4 Copynumber: 10.5 Consensus size: 4
647429 TATATTTTTT
647439 TTTC TTT- TTTC TTTC TTTC TTT- TTTC TTTC TTT- TTTC TT
1 TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TT
647478 ATTTTTTCTT
Statistics
Matches: 32, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
3 9 0.28
4 23 0.72
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (4 bp):
TTTC
Found at i:647453 original size:11 final size:11
Alignment explanation
Indices: 647436--647514 Score: 74
Period size: 11 Copynumber: 7.0 Consensus size: 11
647426 TTATATATTT
647436 TTTTTTCTTT-
1 TTTTTTCTTTC
647446 TTTCTTTCTTTC
1 TTT-TTTCTTTC
647458 TTTTTTCTTTC
1 TTTTTTCTTTC
*
647469 TTTTTTC-TTA
1 TTTTTTCTTTC
647479 TTTTTTCTTAT-
1 TTTTTTCTT-TC
*
647490 TTTTTCCTCCTTC
1 TTTTT--TCTTTC
647503 TTCTTTTCTTTC
1 TT-TTTTCTTTC
647515 CCTCTTCTTC
Statistics
Matches: 58, Mismatches: 3, Indels: 14
0.77 0.04 0.19
Matches are distributed among these distances:
10 12 0.21
11 28 0.48
12 10 0.17
13 5 0.09
14 3 0.05
ACGTcount: A:0.03, C:0.20, G:0.00, T:0.77
Consensus pattern (11 bp):
TTTTTTCTTTC
Found at i:647523 original size:46 final size:46
Alignment explanation
Indices: 647431--647523 Score: 107
Period size: 46 Copynumber: 2.0 Consensus size: 46
647421 ATCATTTATA
* * * * ** *
647431 TATTTTTTTTTCTTTTTTCTTTCTTTCTTTTTTCTTTCTTTTTTCT
1 TATTTTTTCTTATTTTTTCTCTCCTTCTTTTTTCTTTCCCTCTTCT
647477 TATTTTTTCTTATTTTTTC-CTCCTTCTTCTTTTCTTTCCCTCTTCT
1 TATTTTTTCTTATTTTTTCTCTCCTTCTT-TTTTCTTTCCCTCTTCT
647523 T
1 T
647524 CTTAAAACCC
Statistics
Matches: 39, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
45 7 0.18
46 32 0.82
ACGTcount: A:0.03, C:0.22, G:0.00, T:0.75
Consensus pattern (46 bp):
TATTTTTTCTTATTTTTTCTCTCCTTCTTTTTTCTTTCCCTCTTCT
Found at i:648033 original size:30 final size:28
Alignment explanation
Indices: 647997--648137 Score: 155
Period size: 30 Copynumber: 4.9 Consensus size: 28
647987 AAAGGTTACA
*
647997 AAAATTTTAGGG-CTAAAGTGTAATTTTAAG
1 AAAAGTTTAGGGTC-AAA-TGTAATTTT-AG
*
648027 AAAA-TTTAGGGTTAAATGTAATTTTAG
1 AAAAGTTTAGGGTCAAATGTAATTTTAG
*
648054 GAAAGTTTAGGGGTCAAAGTGTAATTTTAG
1 AAAAGTTTA-GGGTCAAA-TGTAATTTTAG
648084 AAAAGTTTAGTGGTCAAATGTAATTTTA-
1 AAAAGTTTAG-GGTCAAATGTAATTTTAG
*
648112 AAAAG-TTAGGGTCAAAATGTATTTTT
1 AAAAGTTTAGGGTC-AAATGTAATTTT
648138 TATTTTTTAT
Statistics
Matches: 100, Mismatches: 5, Indels: 15
0.83 0.04 0.12
Matches are distributed among these distances:
26 4 0.04
27 20 0.20
28 18 0.18
29 28 0.28
30 30 0.30
ACGTcount: A:0.38, C:0.03, G:0.21, T:0.38
Consensus pattern (28 bp):
AAAAGTTTAGGGTCAAATGTAATTTTAG
Found at i:648042 original size:29 final size:27
Alignment explanation
Indices: 647997--648137 Score: 142
Period size: 29 Copynumber: 4.9 Consensus size: 27
647987 AAAGGTTACA
647997 AAAATTTTAGGG-CTAAAGTGTAATTTTAAG
1 AAAA-TTTAGGGTC-AAA-TGTAATTTT-AG
*
648027 AAAATTTAGGGTTAAATGTAATTTTAGG
1 AAAATTTAGGGTCAAATGTAATTTTA-G
*
648055 AAAGTTTAGGGGTCAAAGTGTAATTTTAG
1 AAAATTTA-GGGTCAAA-TGTAATTTTAG
648084 AAAAGTTTAGTGGTCAAATGTAATTTTA-
1 AAAA-TTTAG-GGTCAAATGTAATTTTAG
* *
648112 AAAAGTTAGGGTCAAAATGTATTTTT
1 AAAATTTAGGGTC-AAATGTAATTTT
648138 TATTTTTTAT
Statistics
Matches: 98, Mismatches: 6, Indels: 17
0.81 0.05 0.14
Matches are distributed among these distances:
26 4 0.04
27 16 0.16
28 21 0.21
29 32 0.33
30 25 0.26
ACGTcount: A:0.38, C:0.03, G:0.21, T:0.38
Consensus pattern (27 bp):
AAAATTTAGGGTCAAATGTAATTTTAG
Found at i:648093 original size:58 final size:58
Alignment explanation
Indices: 647996--648137 Score: 177
Period size: 58 Copynumber: 2.5 Consensus size: 58
647986 AAAAGGTTAC
* * *
647996 AAAAATTTTAGGGCT-AAAGTGTAATTTTAAGAAAATTTAG-GGTTAAATGTAATTTT
1 AAAAAGTTTAGGGGTCAAAGTGTAATTTTAAGAAAATTTAGTGGTCAAATGTAATTTT
*
648052 AGGAAAGTTTAGGGGTCAAAGTGTAATTTT-AGAAAAGTTTAGTGGTCAAATGTAATTTT
1 A-AAAAGTTTAGGGGTCAAAGTGTAATTTTAAGAAAA-TTTAGTGGTCAAATGTAATTTT
* *
648111 AAAAAG-TTA-GGGTCAAAATGTATTTTT
1 AAAAAGTTTAGGGGTCAAAGTGTAATTTT
648138 TATTTTTTAT
Statistics
Matches: 75, Mismatches: 7, Indels: 8
0.83 0.08 0.09
Matches are distributed among these distances:
56 17 0.23
57 20 0.27
58 22 0.29
59 16 0.21
ACGTcount: A:0.39, C:0.03, G:0.21, T:0.37
Consensus pattern (58 bp):
AAAAAGTTTAGGGGTCAAAGTGTAATTTTAAGAAAATTTAGTGGTCAAATGTAATTTT
Found at i:648170 original size:16 final size:15
Alignment explanation
Indices: 648144--648174 Score: 53
Period size: 16 Copynumber: 2.0 Consensus size: 15
648134 TTTTTATTTT
648144 TTATTTTTAAAATTA
1 TTATTTTTAAAATTA
648159 TTATTATTTAAAATTA
1 TTATT-TTTAAAATTA
648175 ATAAAATAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 5 0.33
16 10 0.67
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (15 bp):
TTATTTTTAAAATTA
Found at i:648731 original size:147 final size:149
Alignment explanation
Indices: 648416--648958 Score: 668
Period size: 147 Copynumber: 3.6 Consensus size: 149
648406 TATTTTTTTG
* * * * * * *
648416 AAAAATAGAAATCGAAAATAGCTCGGCGCGTGATCTGAAGCTCAACTCACCTCTCGGATTATGAG
1 AAAAATAGAAATTGAAAATACCTCAGTG-TTGACCTGAGGCTCAACTCACCTCTCGGATTATGAG
* * * *
648481 TTGATCTTTGAAAAACAGAAATTG-AAAATACCCCAGCGTGAGATCCAAGGCTCAACTCACCTCT
65 TTGATTTTTGAAAAACAGAAATTGAAAAATACCTCAGCGTGAGACCCGAGGCTCAACTCACCTCT
* **
648545 CGGATTATCAGTTGATATTTT
130 CGGATTATGAGTTGAT-TTAA
* *
648566 AAAAATAGAAATTGAAAATACCTCAGTGTATGACCTGAGGCTCAGCTCACTTCTCGGATTATGAG
1 AAAAATAGAAATTGAAAATACCTCAGTGT-TGACCTGAGGCTCAACTCACCTCTCGGATTATGAG
** *
648631 TTGA-TTTTGAAAAA-A-AAATT-AAAAATACCTCAATGTGCGACCCGAGGCTCAACTCACCTCT
65 TTGATTTTTGAAAAACAGAAATTGAAAAATACCTCAGCGTGAGACCCGAGGCTCAACTCACCTCT
648692 CGGATTATGAGTTGATTTAA
130 CGGATTATGAGTTGATTTAA
* * *
648712 AAAAATAGAGATTGAAAAATACCTCGACGTG-TGACCTAAGGCTCAACTCACCTCTCGGATTATC
1 AAAAATAGAAATTG-AAAATACCTC-A-GTGTTGACCTGAGGCTCAACTCACCTCTCGGATTATG
* * *
648776 AGTTGATTTTTGAAAAACAGAAATTGAAAAATACCTCGGCGTGTGACTCGAGGCTCAACTCACCT
63 AGTTGATTTTTGAAAAACAGAAATTGAAAAATACCTCAGCGTGAGACCCGAGGCTCAACTCACCT
* *
648841 CTTGGATTATGAGTTGATCTTTGA
128 CTCGGATTATGAGTTGA--TTTAA
* * *
648865 AAAAATAGAAAGTGAAAATACCTCAGCG-TGCAACCCGAGGCTCAACTCACCTCTCGGATTATGA
1 AAAAATAGAAATTGAAAATACCTCAGTGTTG--ACCTGAGGCTCAACTCACCTCTCGGATTATGA
*
648929 GTTGATTTTTGAAAAACATAAATTGAAAAA
64 GTTGATTTTTGAAAAACAGAAATTGAAAAA
648959 AAGAAATAAT
Statistics
Matches: 342, Mismatches: 38, Indels: 24
0.85 0.09 0.06
Matches are distributed among these distances:
146 15 0.04
147 99 0.29
148 12 0.04
149 13 0.04
150 68 0.20
151 51 0.15
152 68 0.20
153 16 0.05
ACGTcount: A:0.35, C:0.20, G:0.18, T:0.27
Consensus pattern (149 bp):
AAAAATAGAAATTGAAAATACCTCAGTGTTGACCTGAGGCTCAACTCACCTCTCGGATTATGAGT
TGATTTTTGAAAAACAGAAATTGAAAAATACCTCAGCGTGAGACCCGAGGCTCAACTCACCTCTC
GGATTATGAGTTGATTTAA
Found at i:648830 original size:76 final size:75
Alignment explanation
Indices: 648410--648957 Score: 630
Period size: 75 Copynumber: 7.3 Consensus size: 75
648400 TATATTTATT
* * * * *
648410 TTTTTGAAAAATAGAAATCGAAAATAGCTCGGCGCGTGA-TCTGAAGCTCAACTCACCTCTCGGA
1 TTTTTGAAAAATAGAAATTGAAAATACCTCAGCGTGTGACTC-GAGGCTCAACTCACCTCTCGGA
648474 TTATGAGTTGA
65 TTATGAGTTGA
* * * * *
648485 TCTTTGAAAAACAGAAATTGAAAATACCCCAGCGTGAGA-TCCAAGGCTCAACTCACCTCTCGGA
1 TTTTTGAAAAATAGAAATTGAAAATACCTCAGCGTGTGACT-CGAGGCTCAACTCACCTCTCGGA
*
648549 TTATCAGTTGA
65 TTATGAGTTGA
* * * *
648560 TATTTT-AAAAATAGAAATTGAAAATACCTCAGTGTATGAC-CTGAGGCTCAGCTCACTTCTCGG
1 T-TTTTGAAAAATAGAAATTGAAAATACCTCAGCGTGTGACTC-GAGGCTCAACTCACCTCTCGG
648623 ATTATGAGTTGA
64 ATTATGAGTTGA
* ** * *
648635 -TTTTGAAAAA-A-AAATTAAAAATACCTCAATGTGCGACCCGAGGCTCAACTCACCTCTCGGAT
1 TTTTTGAAAAATAGAAATTGAAAATACCTCAGCGTGTGACTCGAGGCTCAACTCACCTCTCGGAT
648697 TATGAGTTGA
66 TATGAGTTGA
** * *
648707 -TTTAAAAAAATAGAGATTGAAAAATACCTC-GACGTGTGAC-CTAAGGCTCAACTCACCTCTCG
1 TTTTTGAAAAATAGAAATTG-AAAATACCTCAG-CGTGTGACTC-GAGGCTCAACTCACCTCTCG
*
648769 GATTATCAGTTGA
63 GATTATGAGTTGA
* * *
648782 TTTTTGAAAAACAGAAATTGAAAAATACCTCGGCGTGTGACTCGAGGCTCAACTCACCTCTTGGA
1 TTTTTGAAAAATAGAAATTG-AAAATACCTCAGCGTGTGACTCGAGGCTCAACTCACCTCTCGGA
648847 TTATGAGTTGA
65 TTATGAGTTGA
* * ** *
648858 TCTTTGAAAAAATAGAAAGTGAAAATACCTCAGCGTGCAACCCGAGGCTCAACTCACCTCTCGGA
1 TTTTTG-AAAAATAGAAATTGAAAATACCTCAGCGTGTGACTCGAGGCTCAACTCACCTCTCGGA
648923 TTATGAGTTGA
65 TTATGAGTTGA
* *
648934 TTTTTGAAAAACATAAATTGAAAA
1 TTTTTGAAAAATAGAAATTGAAAA
648958 AAAGAAATAA
Statistics
Matches: 403, Mismatches: 55, Indels: 30
0.83 0.11 0.06
Matches are distributed among these distances:
72 61 0.15
73 7 0.02
74 11 0.03
75 182 0.45
76 128 0.32
77 14 0.03
ACGTcount: A:0.35, C:0.19, G:0.18, T:0.27
Consensus pattern (75 bp):
TTTTTGAAAAATAGAAATTGAAAATACCTCAGCGTGTGACTCGAGGCTCAACTCACCTCTCGGAT
TATGAGTTGA
Found at i:660938 original size:7 final size:7
Alignment explanation
Indices: 660928--661019 Score: 66
Period size: 7 Copynumber: 13.3 Consensus size: 7
660918 TATTTTTAAA
660928 TTTTTCT
1 TTTTTCT
*
660935 TTTTTAT
1 TTTTTCT
*
660942 TCTTTCT
1 TTTTTCT
*
660949 TTATTC-
1 TTTTTCT
660955 --TTTCT
1 TTTTTCT
*
660960 TTTTCCT
1 TTTTTCT
*
660967 TCCTTT-T
1 T-TTTTCT
*
660974 TTCTTCT
1 TTTTTCT
660981 TTTTTCCT
1 TTTTT-CT
660989 TTTTTCT
1 TTTTTCT
660996 TTTTTCT
1 TTTTTCT
*
661003 TCTTTCT
1 TTTTTCT
661010 TCTTTTCT
1 T-TTTTCT
661018 TT
1 TT
661020 CCCTTTTCTT
Statistics
Matches: 64, Mismatches: 14, Indels: 14
0.70 0.15 0.15
Matches are distributed among these distances:
4 3 0.05
6 2 0.03
7 44 0.69
8 15 0.23
ACGTcount: A:0.02, C:0.21, G:0.00, T:0.77
Consensus pattern (7 bp):
TTTTTCT
Found at i:660973 original size:36 final size:36
Alignment explanation
Indices: 660933--661004 Score: 92
Period size: 36 Copynumber: 2.0 Consensus size: 36
660923 TTAAATTTTT
660933 CTTTTTTATTCTTTCTTT-ATTCTTTCTTTTTCCTTC
1 CTTTTTTATTCTTT-TTTCATTCTTTCTTTTTCCTTC
* * * *
660969 CTTTTTTCTTCTTTTTTCCTTTTTTCTTTTTTCTTC
1 CTTTTTTATTCTTTTTTCATTCTTTCTTTTTCCTTC
661005 TTTCTTCTTT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
35 3 0.10
36 28 0.90
ACGTcount: A:0.03, C:0.22, G:0.00, T:0.75
Consensus pattern (36 bp):
CTTTTTTATTCTTTTTTCATTCTTTCTTTTTCCTTC
Found at i:660977 original size:22 final size:22
Alignment explanation
Indices: 660928--661020 Score: 83
Period size: 22 Copynumber: 4.5 Consensus size: 22
660918 TATTTTTAAA
*
660928 TTTTTCTTT-TTTATTCTTTCT
1 TTTTTCTTTCTTTATTCTTCCT
*
660949 TTATTCTTTCTTT-TTCCTTCCT
1 TTTTTCTTTCTTTATT-CTTCCT
660971 TTTTTC-TTC-TT-TT-TTCCT
1 TTTTTCTTTCTTTATTCTTCCT
* *
660989 TTTTTCTTT-TTTCTTCTTTCT
1 TTTTTCTTTCTTTATTCTTCCT
661010 TCTTTTCTTTC
1 T-TTTTCTTTC
661021 CCTTTTCTTC
Statistics
Matches: 60, Mismatches: 4, Indels: 14
0.77 0.05 0.18
Matches are distributed among these distances:
18 11 0.18
19 4 0.07
20 6 0.10
21 18 0.30
22 21 0.35
ACGTcount: A:0.02, C:0.22, G:0.00, T:0.76
Consensus pattern (22 bp):
TTTTTCTTTCTTTATTCTTCCT
Found at i:660978 original size:18 final size:17
Alignment explanation
Indices: 660955--661015 Score: 70
Period size: 18 Copynumber: 3.5 Consensus size: 17
660945 TTCTTTATTC
660955 TTTCTTTTTCCTTCCTTT
1 TTTCTTTTT-CTTCCTTT
*
660973 TTTCTTCTTTTTTCCTTT
1 TTTCTT-TTTCTTCCTTT
660991 TTTCTTTTTTCTT-CTTT
1 TTTC-TTTTTCTTCCTTT
*
661008 CTTCTTTT
1 TTTCTTTT
661016 CTTTCCCTTT
Statistics
Matches: 38, Mismatches: 3, Indels: 6
0.81 0.06 0.13
Matches are distributed among these distances:
16 4 0.11
17 7 0.18
18 22 0.58
19 5 0.13
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (17 bp):
TTTCTTTTTCTTCCTTT
Found at i:660990 original size:29 final size:26
Alignment explanation
Indices: 660930--661032 Score: 92
Period size: 25 Copynumber: 4.1 Consensus size: 26
660920 TTTTTAAATT
* *
660930 TTTCTT-TTTTATT-CTTTCTTTATTC
1 TTTCTTCTTTTCTTCCTTT-TTTCTTC
*
660955 TTTCTT-TTTCCTTCCTTTTTTCTTC
1 TTTCTTCTTTTCTTCCTTTTTTCTTC
*
660980 TTTTTTCCTTTT-TT-CTTTTTTCTTC
1 TTTCTT-CTTTTCTTCCTTTTTTCTTC
*
661005 TTTCTTCTTTTCTTTCC-CTTTTCTTC
1 TTTCTTCTTTTC-TTCCTTTTTTCTTC
661031 TT
1 TT
661033 AAAACCCTAG
Statistics
Matches: 65, Mismatches: 7, Indels: 11
0.78 0.08 0.13
Matches are distributed among these distances:
24 5 0.08
25 38 0.58
26 18 0.28
27 4 0.06
ACGTcount: A:0.02, C:0.23, G:0.00, T:0.75
Consensus pattern (26 bp):
TTTCTTCTTTTCTTCCTTTTTTCTTC
Found at i:660997 original size:15 final size:15
Alignment explanation
Indices: 660972--661016 Score: 56
Period size: 15 Copynumber: 2.9 Consensus size: 15
660962 TTCCTTCCTT
660972 TTTTCTTCTTTTTTCC
1 TTTT-TTCTTTTTTCC
660988 TTTTTTCTTTTTT-C
1 TTTTTTCTTTTTTCC
*
661002 TTCTTTCTTCTTTTC
1 TTTTTTCTT-TTTTC
661017 TTTCCCTTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
14 9 0.35
15 13 0.50
16 4 0.15
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (15 bp):
TTTTTTCTTTTTTCC
Found at i:661519 original size:30 final size:29
Alignment explanation
Indices: 661458--661616 Score: 189
Period size: 30 Copynumber: 5.4 Consensus size: 29
661448 ATTTTGGGGC
* *
661458 AAAAGTGTAATTTTAGGTAAACTT-GGGGTT
1 AAAA-TGTAATTTTAAG-AAAGTTAGGGGTT
* *
661488 AAAATGTAATTTTAGGAAAGTTTAAGGGTT
1 AAAATGTAATTTTAAGAAAG-TTAGGGGTT
*
661518 AAAAGGTAATTTTAAGAAAGTTTAGGGGTT
1 AAAATGTAATTTTAAGAAAG-TTAGGGGTT
661548 AAAATGTAATTTTAA-AAAGTTA-GGGTT
1 AAAATGTAATTTTAAGAAAGTTAGGGGTT
* *
661575 AAAATGTAATTTTAAAAAAGTTAGGGAGTC
1 AAAATGTAATTTTAAGAAAGTTAGGG-GTT
661605 AAAATGTAATTT
1 AAAATGTAATTT
661617 ATATTTTTTG
Statistics
Matches: 117, Mismatches: 7, Indels: 10
0.87 0.05 0.07
Matches are distributed among these distances:
27 20 0.17
28 13 0.11
29 20 0.17
30 64 0.55
ACGTcount: A:0.42, C:0.01, G:0.22, T:0.35
Consensus pattern (29 bp):
AAAATGTAATTTTAAGAAAGTTAGGGGTT
Found at i:661589 original size:57 final size:59
Alignment explanation
Indices: 661482--661616 Score: 195
Period size: 57 Copynumber: 2.3 Consensus size: 59
661472 AGGTAAACTT
* *
661482 GGGGTTAAAATGTAATTTTAGGAAAGTTTAAGGGTTAAAAGGTAATTTTAAGAAAGTTTA
1 GGGGTTAAAATGTAATTTTAGAAAAGTTTAAGGGTTAAAAGGTAATTTTAAAAAAG-TTA
*
661542 GGGGTTAAAATGTAATTTTA-AAAAG-TT-AGGGTTAAAATGTAATTTTAAAAAAGTTA
1 GGGGTTAAAATGTAATTTTAGAAAAGTTTAAGGGTTAAAAGGTAATTTTAAAAAAGTTA
*
661598 GGGAGTCAAAATGTAATTT
1 GGG-GTTAAAATGTAATTT
661617 ATATTTTTTG
Statistics
Matches: 70, Mismatches: 4, Indels: 5
0.89 0.05 0.06
Matches are distributed among these distances:
56 6 0.09
57 38 0.54
58 2 0.03
59 4 0.06
60 20 0.29
ACGTcount: A:0.41, C:0.01, G:0.23, T:0.35
Consensus pattern (59 bp):
GGGGTTAAAATGTAATTTTAGAAAAGTTTAAGGGTTAAAAGGTAATTTTAAAAAAGTTA
Found at i:661664 original size:26 final size:26
Alignment explanation
Indices: 661614--661666 Score: 65
Period size: 26 Copynumber: 2.0 Consensus size: 26
661604 CAAAATGTAA
*
661614 TTTATATTTTTTGTATTTTTCAAAAT
1 TTTATATTTTTTGTATATTTCAAAAT
661640 TTTATTATTATTTTGT-TATTT-AAAAT
1 TTTA-TATT-TTTTGTATATTTCAAAAT
661666 T
1 T
661667 AATAAAATAT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
26 10 0.42
27 8 0.33
28 6 0.25
ACGTcount: A:0.28, C:0.02, G:0.04, T:0.66
Consensus pattern (26 bp):
TTTATATTTTTTGTATATTTCAAAAT
Found at i:665767 original size:20 final size:20
Alignment explanation
Indices: 665730--665770 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
665720 TTAAAAAACA
* **
665730 TATAATTATTCATTTAATAT
1 TATAACTATTCAAATAATAT
665750 TATAACTATTCAAATAATAT
1 TATAACTATTCAAATAATAT
665770 T
1 T
665771 GTTTAAACAG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.44, C:0.07, G:0.00, T:0.49
Consensus pattern (20 bp):
TATAACTATTCAAATAATAT
Found at i:666885 original size:6 final size:6
Alignment explanation
Indices: 666874--666903 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
666864 GATGGTTTGA
*
666874 GCATGG GCATGG GCATGG GCATGG TCATGG
1 GCATGG GCATGG GCATGG GCATGG GCATGG
666904 AAGTTTCTTA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.17, C:0.17, G:0.47, T:0.20
Consensus pattern (6 bp):
GCATGG
Found at i:678070 original size:25 final size:24
Alignment explanation
Indices: 678042--678097 Score: 69
Period size: 25 Copynumber: 2.2 Consensus size: 24
678032 ATATTACTTA
678042 ATATAAATGTATGTTATAA-TAAATT
1 ATATAAATGTATG-TA-AATTAAATT
*
678067 ATATAAAATGTATGTAAATTATATT
1 ATAT-AAATGTATGTAAATTAAATT
678092 ATATAA
1 ATATAA
678098 TAATTGTTAT
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
24 4 0.14
25 15 0.54
26 9 0.32
ACGTcount: A:0.50, C:0.00, G:0.07, T:0.43
Consensus pattern (24 bp):
ATATAAATGTATGTAAATTAAATT
Found at i:680746 original size:100 final size:100
Alignment explanation
Indices: 680551--680749 Score: 220
Period size: 100 Copynumber: 2.0 Consensus size: 100
680541 AGTTTAGTAA
* * ** * * *
680551 TGGGGTAAGATGAAGCTACAACCTCTAATCTTGTATCCTTAAAGATGCAGTGGACAGGATCAAAA
1 TGGGGCAAGATGAAGCTACAACCTCAAATCTCATATCCCTAAAGATGAACTGGACAGGATCAAAA
* * *
680616 CTATAGTAGCAAATCTCATCTCCATGAAGATGCAT
66 CTACAATAGCAAATCTCATCTCCATAAAGATGCAT
** ** *
680651 TGGGGCAAGATGAAGCTACAACCTCAAATCTCATATCCCTAAAGATGAACTGGATTGGATTGAAG
1 TGGGGCAAGATGAAGCTACAACCTCAAATCTCATATCCCTAAAGATGAACTGGACAGGATCAAAA
* * *
680716 CTACAATAGCAGATTTTATCTCTC-TAAAGATGCA
66 CTACAATAGCAAATCTCATCTC-CATAAAGATGCA
680750 GCGGAGTAAG
Statistics
Matches: 80, Mismatches: 18, Indels: 2
0.80 0.18 0.02
Matches are distributed among these distances:
100 79 0.99
101 1 0.01
ACGTcount: A:0.35, C:0.19, G:0.20, T:0.26
Consensus pattern (100 bp):
TGGGGCAAGATGAAGCTACAACCTCAAATCTCATATCCCTAAAGATGAACTGGACAGGATCAAAA
CTACAATAGCAAATCTCATCTCCATAAAGATGCAT
Found at i:681270 original size:21 final size:24
Alignment explanation
Indices: 681230--681274 Score: 69
Period size: 21 Copynumber: 2.0 Consensus size: 24
681220 TTTTCCGCCC
681230 CAAATAAAACAACAAATTAACAAA
1 CAAATAAAACAACAAATTAACAAA
681254 CAAAT-AAA-AAC-AATTAACAAA
1 CAAATAAAACAACAAATTAACAAA
681275 AGTCCATTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
21 10 0.48
22 3 0.14
23 3 0.14
24 5 0.24
ACGTcount: A:0.71, C:0.16, G:0.00, T:0.13
Consensus pattern (24 bp):
CAAATAAAACAACAAATTAACAAA
Found at i:700781 original size:10 final size:10
Alignment explanation
Indices: 700760--700797 Score: 51
Period size: 10 Copynumber: 3.7 Consensus size: 10
700750 TGTATTACAG
700760 CACATATTAAT
1 CACAT-TTAAT
700771 CACATTTAAT
1 CACATTTAAT
700781 CAC-TTTAAGT
1 CACATTTAA-T
700791 CACATTT
1 CACATTT
700798 TACGATAGTT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
9 5 0.20
10 12 0.48
11 8 0.32
ACGTcount: A:0.37, C:0.21, G:0.03, T:0.39
Consensus pattern (10 bp):
CACATTTAAT
Found at i:718067 original size:25 final size:25
Alignment explanation
Indices: 718034--718082 Score: 89
Period size: 25 Copynumber: 2.0 Consensus size: 25
718024 TTAATGTCCT
*
718034 TATTTATAGCTCATGTGAGCAATTA
1 TATTCATAGCTCATGTGAGCAATTA
718059 TATTCATAGCTCATGTGAGCAATT
1 TATTCATAGCTCATGTGAGCAATT
718083 TTAGTCTTGT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.31, C:0.14, G:0.16, T:0.39
Consensus pattern (25 bp):
TATTCATAGCTCATGTGAGCAATTA
Found at i:719084 original size:19 final size:19
Alignment explanation
Indices: 719036--719084 Score: 53
Period size: 20 Copynumber: 2.5 Consensus size: 19
719026 TTATAAACAA
*
719036 AAAAATCAAAATAACTTAC
1 AAAATTCAAAATAACTTAC
* **
719055 AAAACTTCAAAATAATTTTT
1 AAAA-TTCAAAATAACTTAC
719075 AAAATTCAAA
1 AAAATTCAAA
719085 TATTTATAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
19 10 0.40
20 15 0.60
ACGTcount: A:0.59, C:0.12, G:0.00, T:0.29
Consensus pattern (19 bp):
AAAATTCAAAATAACTTAC
Found at i:719864 original size:163 final size:163
Alignment explanation
Indices: 719656--719956 Score: 476
Period size: 163 Copynumber: 1.8 Consensus size: 163
719646 TTGATGCGAA
* * * *
719656 TAAATGTTGATTTTGGAAATTGTTGAAAAGATTCTACAAATGAAATGTTTATTTTGGGAAGTGTA
1 TAAATGTTGATTTTGGAAAATGATGAAAAGAGTCTACAAATGAAATGTTCATTTTGGGAAGTGTA
* * *
719721 TATGATATGTATATTAGGTTGAATTGTATATGTGTGGCTATTGGAGTATACATGTGTTTGAACCG
66 TATGATATGTACATTAGGTTGAATTGTATATCTGTGGCTATTGGAGTATACAAGTGTTTGAACCG
719786 AGAATATGGTTGCTTTTGGGATGCCTTATATTT
131 AGAATATGGTTGCTTTTGGGATGCCTTATATTT
* * * *
719819 TAAATGTTGATTTTTGAAAATGATGAAAATAGTCTATATATGAAATGTTCATTTTGGGAAGTGTA
1 TAAATGTTGATTTTGGAAAATGATGAAAAGAGTCTACAAATGAAATGTTCATTTTGGGAAGTGTA
* * *
719884 TATGATATGTACATTAGGTTGAATTGTTTATCTGTGGCTATTGGAGTATGCAAGTGTTTGAACTG
66 TATGATATGTACATTAGGTTGAATTGTATATCTGTGGCTATTGGAGTATACAAGTGTTTGAACCG
719949 AGAATATG
131 AGAATATG
719957 TTTGAAGTAT
Statistics
Matches: 124, Mismatches: 14, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
163 124 1.00
ACGTcount: A:0.30, C:0.05, G:0.24, T:0.41
Consensus pattern (163 bp):
TAAATGTTGATTTTGGAAAATGATGAAAAGAGTCTACAAATGAAATGTTCATTTTGGGAAGTGTA
TATGATATGTACATTAGGTTGAATTGTATATCTGTGGCTATTGGAGTATACAAGTGTTTGAACCG
AGAATATGGTTGCTTTTGGGATGCCTTATATTT
Found at i:722064 original size:9 final size:9
Alignment explanation
Indices: 722050--722086 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
722040 TATAGTTTGA
722050 TATTCGAAT
1 TATTCGAAT
722059 TATTCGAAT
1 TATTCGAAT
*
722068 TATTCGAGT
1 TATTCGAAT
722077 TATTCGAAT
1 TATTCGAAT
722086 T
1 T
722087 TGAAAACTCA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.30, C:0.11, G:0.14, T:0.46
Consensus pattern (9 bp):
TATTCGAAT
Found at i:723941 original size:58 final size:57
Alignment explanation
Indices: 723892--724002 Score: 168
Period size: 57 Copynumber: 1.9 Consensus size: 57
723882 TCTTTTTGAT
* * *
723892 TTTGGAGAAAACTACTATTCATTTCTAAATGATTCCATTTCTCCATTTTCATTTTCAG
1 TTTGGAGAAAACCA-TAATCATTTCCAAATGATTCCATTTCTCCATTTTCATTTTCAG
* *
723950 TTTGGAGAAAACCATAATCATTTCCAAATGTTTCTATTTCTCCATTTTCATTT
1 TTTGGAGAAAACCATAATCATTTCCAAATGATTCCATTTCTCCATTTTCATTT
724003 CATTTTCATT
Statistics
Matches: 48, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
57 35 0.73
58 13 0.27
ACGTcount: A:0.28, C:0.19, G:0.08, T:0.45
Consensus pattern (57 bp):
TTTGGAGAAAACCATAATCATTTCCAAATGATTCCATTTCTCCATTTTCATTTTCAG
Found at i:724005 original size:5 final size:5
Alignment explanation
Indices: 723995--724028 Score: 59
Period size: 5 Copynumber: 6.6 Consensus size: 5
723985 ATTTCTCCAT
723995 TTTCA TTTCA TTTTCA TTTCA TTTCA TTTCA TTT
1 TTTCA TTTCA -TTTCA TTTCA TTTCA TTTCA TTT
724029 TGGTAATTAT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
5 23 0.82
6 5 0.18
ACGTcount: A:0.18, C:0.18, G:0.00, T:0.65
Consensus pattern (5 bp):
TTTCA
Found at i:724008 original size:11 final size:11
Alignment explanation
Indices: 723992--724029 Score: 69
Period size: 11 Copynumber: 3.5 Consensus size: 11
723982 TCTATTTCTC
723992 CATTTTCATTT
1 CATTTTCATTT
724003 CATTTTCATTT
1 CATTTTCATTT
724014 CA-TTTCATTT
1 CATTTTCATTT
724024 CATTTT
1 CATTTT
724030 GGTAATTATT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
10 10 0.38
11 16 0.62
ACGTcount: A:0.18, C:0.18, G:0.00, T:0.63
Consensus pattern (11 bp):
CATTTTCATTT
Done.