Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008280.1 Hibiscus syriacus cultivar Beakdansim tig00110940_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 3557051
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 17
Found at i:520048 original size:448 final size:445
Alignment explanation
Indices: 519226--520106 Score: 1500
Period size: 448 Copynumber: 2.0 Consensus size: 445
519216 GAAAATACCC
* *
519226 GACCCGACCCGAAAGAATATATAATATTACCTTATATATTTAGGAATAATTACAATAATACCCCT
1 GACCCGACCCGAAAGAATATATAATATTACCATATATAATTAGGAATAATTACAATAATACCCCT
519291 CTATATATAATTTTTTTCAATTAAGTCATTGTTTTTATTGAATAAAAATATTTTTTTATTATTTC
66 CTATATATAA----TTTCAATTAAGTCATTGTTTTTATTGAATAAAAATATTTTTTTATTATTTC
* *
519356 GGGTCGGGTCGGGTGAAACTTTATTTTGGTTGGGTCGGGTCAGGTCTCGGGTGGAGGTTCCCTTG
127 GGGTCGGGTCGGGTGAAACATTATTTTGGTCGGGTCGGGTCAGGTCTCGGGTGGAGGTTCCCTTG
* * * *
519421 TTCTCGGGTCGGGTGGACCAAAAACCCTACCCATGACCATCCCTAATTGGGATGATTTTAACTTA
192 TTCTCGGGTCAGGTGGACCAAAAACCCGACCCATGACCATCCCTAATTGGGACGATTTAAACTTA
519486 TAATGTTTATTAGTATGATTTTTATAATTTATTGAAATGAATAATCAATCAATAAAATAAAAATT
257 TAATGTTTATTAGTATGATTTTTATAATTTATTGAAATGAATAATCAATCAATAAAATAAAAATT
*
519551 TAATATTTTTTAAATTTTATAATATATTGCTACATGTAAGTTATAAAACAAATTAAAATTAAGCA
322 TAATATTTTTTAAATTTTATAATATATTGCTACATGTAAGTTATAAAACAAACTAAAATTAAGCA
519616 AAAAAATAAGAAAGACAATTATGTCATTTTACATTACTGAAATAAAAAATACCCGACCA
387 AAAAAATAAGAAAGACAATTATGTCATTTTACATTACTGAAATAAAAAATACCCGACCA
519675 GACCCGACCCGAAAGAATATATAATATTACCATATATAATTAGGAATAATTACAATAATACCCCT
1 GACCCGACCCGAAAGAATATATAATATTACCATATATAATTAGGAATAATTACAATAATACCCCT
*
519740 GTATATAT-A-TTCAATTAAGTCATTGTTTTTATTGAATAAAAATAATTTTTTTATTATTTCGGG
66 CTATATATAATTTCAATTAAGTCATTGTTTTTATTGAATAAAAAT-ATTTTTTTATTATTTCGGG
519803 TCGGGTCGGGTGAAACATTATTTTGGTCGGGTCGGGTC-GGTCTCGGGTGGAGGTTCCCTTGTTC
130 TCGGGTCGGGTGAAACATTATTTTGGTCGGGTCGGGTCAGGTCTCGGGTGGAGGTTCCCTTGTTC
519867 TTGGGTCGGGTCAGGTGGACCAAAAACCCGACCCAT-AGCCATCCCTAATTGGGACGATTTAAAC
195 -----TCGGGTCAGGTGGACCAAAAACCCGACCCATGA-CCATCCCTAATTGGGACGATTTAAAC
* *
519931 TTATGATGTTTATTAGTATGATTTTTATAATTTATTGAAATGAATAATCAATCAATAAAATGAAA
254 TTATAATGTTTATTAGTATGATTTTTATAATTTATTGAAATGAATAATCAATCAATAAAATAAAA
519996 ATTTAATATTTTTTAAATTTTATAATATATTGCTACATGTAAGTTATAAAACAAACTAAAATTAA
319 ATTTAATATTTTTTAAATTTTATAATATATTGCTACATGTAAGTTATAAAACAAACTAAAATTAA
* * *
520061 GCAAAAAAATAAGAAGGGCAATTTTGTCATTTTACATTACTGAAAT
384 GCAAAAAAATAAGAAAGACAATTATGTCATTTTACATTACTGAAAT
520107 CAAATTCATC
Statistics
Matches: 410, Mismatches: 15, Indels: 15
0.93 0.03 0.03
Matches are distributed among these distances:
443 60 0.15
444 55 0.13
447 1 0.00
448 224 0.55
449 70 0.17
ACGTcount: A:0.36, C:0.13, G:0.15, T:0.36
Consensus pattern (445 bp):
GACCCGACCCGAAAGAATATATAATATTACCATATATAATTAGGAATAATTACAATAATACCCCT
CTATATATAATTTCAATTAAGTCATTGTTTTTATTGAATAAAAATATTTTTTTATTATTTCGGGT
CGGGTCGGGTGAAACATTATTTTGGTCGGGTCGGGTCAGGTCTCGGGTGGAGGTTCCCTTGTTCT
CGGGTCAGGTGGACCAAAAACCCGACCCATGACCATCCCTAATTGGGACGATTTAAACTTATAAT
GTTTATTAGTATGATTTTTATAATTTATTGAAATGAATAATCAATCAATAAAATAAAAATTTAAT
ATTTTTTAAATTTTATAATATATTGCTACATGTAAGTTATAAAACAAACTAAAATTAAGCAAAAA
AATAAGAAAGACAATTATGTCATTTTACATTACTGAAATAAAAAATACCCGACCA
Found at i:520209 original size:16 final size:18
Alignment explanation
Indices: 520188--520235 Score: 73
Period size: 18 Copynumber: 2.8 Consensus size: 18
520178 AAACAGGTTT
*
520188 CAGATTCCAATTCC-T-A
1 CAGATTTCAATTCCTTCA
520204 CAGATTTCAATTCCTTCA
1 CAGATTTCAATTCCTTCA
520222 CAGATTTCAATTCC
1 CAGATTTCAATTCC
520236 CTCAAAACAT
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
16 13 0.45
17 1 0.03
18 15 0.52
ACGTcount: A:0.29, C:0.29, G:0.06, T:0.35
Consensus pattern (18 bp):
CAGATTTCAATTCCTTCA
Found at i:528727 original size:30 final size:30
Alignment explanation
Indices: 528693--528788 Score: 147
Period size: 30 Copynumber: 3.2 Consensus size: 30
528683 AAGAATATTG
528693 ATGTATTATTTATTACTTTAGATACGTGAC
1 ATGTATTATTTATTACTTTAGATACGTGAC
528723 ATGTATTATTTATTACTTTAGATACGTGAC
1 ATGTATTATTTATTACTTTAGATACGTGAC
* * * * *
528753 ATGTACTATATATCACTTTAGACACGTGAT
1 ATGTATTATTTATTACTTTAGATACGTGAC
528783 ATGTAT
1 ATGTAT
528789 CACATCATCA
Statistics
Matches: 60, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 60 1.00
ACGTcount: A:0.31, C:0.11, G:0.14, T:0.44
Consensus pattern (30 bp):
ATGTATTATTTATTACTTTAGATACGTGAC
Found at i:528836 original size:61 final size:58
Alignment explanation
Indices: 528764--528910 Score: 188
Period size: 61 Copynumber: 2.5 Consensus size: 58
528754 TGTACTATAT
* *
528764 ATCACTTTAGACACGTGATATGTATCACATCATCACTTATGTACATGTGACATATTTCAC-A
1 ATCACTTTAGACATGTGATATGTATCACATCATCA-TT-T-TACA-CTGACATATTTCACAA
* * *
528825 ATCACTTTAGACATGTGATATGTATCATATCGTCATTTTAGACTGACATATTTCACATA
1 ATCACTTTAGACATGTGATATGTATCACATCATCATTTTACACTGACATATTTCACA-A
*
528884 ATCACTTTAAACATGTGATATGTATCA
1 ATCACTTTAGACATGTGATATGTATCA
528911 TTTCGTCATT
Statistics
Matches: 78, Mismatches: 6, Indels: 6
0.87 0.07 0.07
Matches are distributed among these distances:
57 13 0.17
58 3 0.04
59 28 0.36
60 2 0.03
61 32 0.41
ACGTcount: A:0.33, C:0.18, G:0.12, T:0.37
Consensus pattern (58 bp):
ATCACTTTAGACATGTGATATGTATCACATCATCATTTTACACTGACATATTTCACAA
Found at i:528898 original size:59 final size:57
Alignment explanation
Indices: 528764--528926 Score: 209
Period size: 59 Copynumber: 2.8 Consensus size: 57
528754 TGTACTATAT
* * * * *
528764 ATCACTTTAGACACGTGATATGTATCACATCATCACTTATGTACATGTGACATATTTCACA
1 ATCACTTTAGACATGTGATATGTATCATATCGTCA-TT-T-TAGA-CTGACATATTTCACA
528825 ATCACTTTAGACATGTGATATGTATCATATCGTCATTTTAGACTGACATATTTCACATA
1 ATCACTTTAGACATGTGATATGTATCATATCGTCATTTTAGACTGACATATTTCAC--A
* *
528884 ATCACTTTAAACATGTGATATGTATCATTTCGTCATTTTAGAC
1 ATCACTTTAGACATGTGATATGTATCATATCGTCATTTTAGAC
528927 ACATGACGTG
Statistics
Matches: 93, Mismatches: 7, Indels: 6
0.88 0.07 0.06
Matches are distributed among these distances:
57 13 0.14
58 3 0.03
59 43 0.46
60 2 0.02
61 32 0.34
ACGTcount: A:0.32, C:0.18, G:0.12, T:0.38
Consensus pattern (57 bp):
ATCACTTTAGACATGTGATATGTATCATATCGTCATTTTAGACTGACATATTTCACA
Found at i:531528 original size:6 final size:6
Alignment explanation
Indices: 531517--531546 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
531507 AATTAGCCAC
531517 CAACAG CAACAG CAACAG CAACAG CAACAG
1 CAACAG CAACAG CAACAG CAACAG CAACAG
531547 TCTAAATTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.50, C:0.33, G:0.17, T:0.00
Consensus pattern (6 bp):
CAACAG
Found at i:541851 original size:28 final size:29
Alignment explanation
Indices: 541800--541858 Score: 111
Period size: 28 Copynumber: 2.1 Consensus size: 29
541790 ATTTTATTTC
541800 AAACAATAGCATTATATTGGCATTAACAG
1 AAACAATAGCATTATATTGGCATTAACAG
541829 AAACAATAGCA-TATATTGGCATTAACAG
1 AAACAATAGCATTATATTGGCATTAACAG
541857 AA
1 AA
541859 GCTTTACTGA
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
28 19 0.63
29 11 0.37
ACGTcount: A:0.47, C:0.14, G:0.14, T:0.25
Consensus pattern (29 bp):
AAACAATAGCATTATATTGGCATTAACAG
Found at i:553352 original size:21 final size:20
Alignment explanation
Indices: 553266--553422 Score: 93
Period size: 20 Copynumber: 7.8 Consensus size: 20
553256 AAATGACCAA
**
553266 CAAAATCGCAACGCGA-AAT
1 CAAAATCGCAACGCGATTTT
* ***
553285 AAAAATCGCAACGCGATCCC
1 CAAAATCGCAACGCGATTTT
* ** *
553305 CAGAATCGCAAATC-AGTTTC
1 CAAAATCGCAACGCGA-TTTT
553325 CAAAATCGCAACGCGATTCTT
1 CAAAATCGCAACGCGATT-TT
* * **
553346 GAAAATCGCAATGCGATAGT
1 CAAAATCGCAACGCGATTTT
* **
553366 CAAATTCGCATTGCGATTTT
1 CAAAATCGCAACGCGATTTT
* *
553386 CCAAAATCGCAACGCGAATAT
1 -CAAAATCGCAACGCGATTTT
*
553407 GAAAATCGCAACGCGA
1 CAAAATCGCAACGCGA
553423 ACACATAAAT
Statistics
Matches: 104, Mismatches: 29, Indels: 9
0.73 0.20 0.06
Matches are distributed among these distances:
19 16 0.15
20 56 0.54
21 32 0.31
ACGTcount: A:0.38, C:0.25, G:0.17, T:0.19
Consensus pattern (20 bp):
CAAAATCGCAACGCGATTTT
Found at i:553375 original size:41 final size:41
Alignment explanation
Indices: 553266--553422 Score: 126
Period size: 41 Copynumber: 3.9 Consensus size: 41
553256 AAATGACCAA
* **
553266 CAAAATCGCAACGCGAA-ATAAAAATCGCAACGCGA-TCCC
1 CAAAATCGCAACGCGAATATCAAAATCGCAACGCGATTTTC
* ** * *
553305 CAGAATCGCAAATC-AGTTTCCAAAATCGCAACGCGATTCTT-
1 CAAAATCGCAACGCGAATAT-CAAAATCGCAACGCGATT-TTC
* * * **
553346 GAAAATCGCAATGCG-ATAGTCAAATTCGCATTGCGATTTTC
1 CAAAATCGCAACGCGAATA-TCAAAATCGCAACGCGATTTTC
*
553387 CAAAATCGCAACGCGAATATGAAAATCGCAACGCGA
1 CAAAATCGCAACGCGAATATCAAAATCGCAACGCGA
553423 ACACATAAAT
Statistics
Matches: 87, Mismatches: 23, Indels: 14
0.70 0.19 0.11
Matches are distributed among these distances:
38 1 0.01
39 12 0.14
40 17 0.20
41 53 0.61
42 4 0.05
ACGTcount: A:0.38, C:0.25, G:0.17, T:0.19
Consensus pattern (41 bp):
CAAAATCGCAACGCGAATATCAAAATCGCAACGCGATTTTC
Found at i:553482 original size:20 final size:20
Alignment explanation
Indices: 553389--553598 Score: 174
Period size: 20 Copynumber: 10.5 Consensus size: 20
553379 CGATTTTCCA
* ** *
553389 AAATCGCAACGCGAATATGA
1 AAATCGCAACGCGTATCCGT
* *
553409 AAATCGCAACGCG-AACACAT
1 AAATCGCAACGCGTATC-CGT
*
553429 AAATCGCAACGTGTATCCGT
1 AAATCGCAACGCGTATCCGT
**
553449 AAATCGCAACGCGTATGGGT
1 AAATCGCAACGCGTATCCGT
*
553469 AAATCGCAACGCGTTTCCGT
1 AAATCGCAACGCGTATCCGT
* *
553489 ATATCGCACCGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
553509 AAATCGCAACG-ATAATCCGT
1 AAATCGCAACGCGT-ATCCGT
* * *
553529 AAATCGCAACGAGAATCTGT
1 AAATCGCAACGCGTATCCGT
* *
553549 AAATCGCAACG-ATAATCCAT
1 AAATCGCAACGCGT-ATCCGT
* * *
553569 AAATCGCAACGAGAATCTGT
1 AAATCGCAACGCGTATCCGT
*
553589 AAATCACAAC
1 AAATCGCAAC
553599 ACTGAAATTT
Statistics
Matches: 152, Mismatches: 32, Indels: 12
0.78 0.16 0.06
Matches are distributed among these distances:
19 2 0.01
20 148 0.97
21 2 0.01
ACGTcount: A:0.37, C:0.25, G:0.18, T:0.20
Consensus pattern (20 bp):
AAATCGCAACGCGTATCCGT
Found at i:554320 original size:24 final size:24
Alignment explanation
Indices: 554281--554327 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
554271 AAATTTGGTC
554281 TTGGTCAATATCCGGACTTTGATA
1 TTGGTCAATATCCGGACTTTGATA
*
554305 TTGGTCAATA-CACGGATTTTGAT
1 TTGGTCAATATC-CGGACTTTGAT
554328 GATGTTTCAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.26, C:0.15, G:0.21, T:0.38
Consensus pattern (24 bp):
TTGGTCAATATCCGGACTTTGATA
Found at i:554519 original size:12 final size:12
Alignment explanation
Indices: 554502--554526 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
554492 ATATAATCCT
554502 GAAGAAGAAAAA
1 GAAGAAGAAAAA
554514 GAAGAAGAAAAA
1 GAAGAAGAAAAA
554526 G
1 G
554527 TCCCTGAAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:556823 original size:19 final size:19
Alignment explanation
Indices: 556801--556931 Score: 156
Period size: 19 Copynumber: 7.4 Consensus size: 19
556791 CGGAAATTAC
*
556801 AATCGCAACGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
556820 AATCCCAA--C---ATGAA
1 AATCGCAATGCGAAATGAA
556834 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
556853 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
556867 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
556886 AATCGCAATACGAAATGAA
1 AATCGCAATGCGAAATGAA
556905 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
556924 AATCGCAA
1 AATCGCAA
556932 CGAGAGAATC
Statistics
Matches: 96, Mismatches: 6, Indels: 20
0.79 0.05 0.16
Matches are distributed among these distances:
14 22 0.23
15 1 0.01
16 3 0.03
17 3 0.03
18 1 0.01
19 66 0.69
ACGTcount: A:0.48, C:0.19, G:0.19, T:0.14
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:556847 original size:33 final size:33
Alignment explanation
Indices: 556801--556953 Score: 191
Period size: 33 Copynumber: 4.5 Consensus size: 33
556791 CGGAAATTAC
*
556801 AATCGCAACGCGAAATGAAAATCCCAAC-ATGAA
1 AATCGCAATGCGAAATGAAAATCCCAACGA-GAA
* *
556834 AATCGCAATGCGAAATGAAAATCGCAACGAGAG
1 AATCGCAATGCGAAATGAAAATCCCAACGAGAA
*
556867 AATCGCAATGCGAAATGAAAATCGCAATACGAAATGAA
1 AATCGCAATGCGAAATGAAAATC-CCA-ACG--A-GAA
* *
556905 AATCGCAATGCGAAATGAAAATCGCAACGAGAG
1 AATCGCAATGCGAAATGAAAATCCCAACGAGAA
556938 AATCGCAATGCGAAAT
1 AATCGCAATGCGAAAT
556954 AAACGCATTG
Statistics
Matches: 105, Mismatches: 9, Indels: 12
0.83 0.07 0.10
Matches are distributed among these distances:
33 69 0.66
34 3 0.03
35 3 0.03
36 3 0.03
37 2 0.02
38 25 0.24
ACGTcount: A:0.47, C:0.19, G:0.20, T:0.14
Consensus pattern (33 bp):
AATCGCAATGCGAAATGAAAATCCCAACGAGAA
Found at i:556921 original size:71 final size:66
Alignment explanation
Indices: 556801--556953 Score: 243
Period size: 71 Copynumber: 2.2 Consensus size: 66
556791 CGGAAATTAC
* *
556801 AATCGCAACGCGAAATGAAAATCCCAACATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGA
1 AATCGCAATGCGAAATGAAAATCCAAACATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGA
556866 G
66 G
556867 AATCGCAATGCGAAATGAAAATCGCAATACGAAATGAAAATCGCAATGCGAAATGAAAATCGCAA
1 AATCGCAATGCGAAATGAAAATC-CAA-AC---ATGAAAATCGCAATGCGAAATGAAAATCGCAA
556932 CGAGAG
61 CGAGAG
556938 AATCGCAATGCGAAAT
1 AATCGCAATGCGAAAT
556954 AAACGCATTG
Statistics
Matches: 80, Mismatches: 2, Indels: 5
0.92 0.02 0.06
Matches are distributed among these distances:
66 22 0.28
67 2 0.03
68 2 0.03
71 54 0.68
ACGTcount: A:0.47, C:0.19, G:0.20, T:0.14
Consensus pattern (66 bp):
AATCGCAATGCGAAATGAAAATCCAAACATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGA
G
Found at i:557069 original size:52 final size:53
Alignment explanation
Indices: 556957--557072 Score: 216
Period size: 53 Copynumber: 2.2 Consensus size: 53
556947 GCGAAATAAA
*
556957 CGCATTGCGGTTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATTT
1 CGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATTT
557010 CGCATTGCGATTCTCTCGTTGCGATTTTCATTT-CGCATTGCGATTTTCATTT
1 CGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATTT
557062 CGCATTGCGAT
1 CGCATTGCGAT
557073 AGTCATTTTT
Statistics
Matches: 62, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
52 30 0.48
53 32 0.52
ACGTcount: A:0.13, C:0.24, G:0.19, T:0.44
Consensus pattern (53 bp):
CGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATTT
Found at i:557080 original size:19 final size:19
Alignment explanation
Indices: 556975--557072 Score: 143
Period size: 19 Copynumber: 5.4 Consensus size: 19
556965 GGTTCTCTCG
556975 TTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTT-CGCA
556995 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
557014 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
557028 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
557047 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
557066 TTGCGAT
1 TTGCGAT
557073 AGTCATTTTT
Statistics
Matches: 71, Mismatches: 2, Indels: 11
0.85 0.02 0.13
Matches are distributed among these distances:
14 6 0.08
16 7 0.10
17 7 0.10
19 36 0.51
20 15 0.21
ACGTcount: A:0.14, C:0.22, G:0.17, T:0.46
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:557198 original size:14 final size:14
Alignment explanation
Indices: 557179--557215 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
557169 CATCAATTAC
557179 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
557193 ACAAATCATCTTTT
1 ACAAATCAACTTTT
557207 ACAAATCAA
1 ACAAATCAA
557216 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:559209 original size:14 final size:14
Alignment explanation
Indices: 559190--559246 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
559180 GCGAAATGAA
*
559190 AATCGCAACGACAG
1 AATCGCAACGAAAG
559204 AATCGCAATGCGAAATG
1 AATCGCAA--CGAAA-G
559221 AAAATCGCAACGAAAG
1 --AATCGCAACGAAAG
559237 AATCGCAACG
1 AATCGCAACG
559247 CGAAATGAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 18 0.49
16 5 0.14
17 6 0.16
19 8 0.22
ACGTcount: A:0.46, C:0.23, G:0.21, T:0.11
Consensus pattern (14 bp):
AATCGCAACGAAAG
Found at i:559217 original size:33 final size:33
Alignment explanation
Indices: 559171--559263 Score: 168
Period size: 33 Copynumber: 2.8 Consensus size: 33
559161 GCGAAGCCAA
*
559171 AATCGCAACGCGAAATGAAAATCGCAACGACAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
*
559204 AATCGCAATGCGAAATGAAAATCGCAACGAAAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
559237 AATCGCAACGCGAAATGAAAATCGCAA
1 AATCGCAACGCGAAATGAAAATCGCAA
559264 TGCGATTTTG
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 57 1.00
ACGTcount: A:0.47, C:0.22, G:0.20, T:0.11
Consensus pattern (33 bp):
AATCGCAACGCGAAATGAAAATCGCAACGAAAG
Found at i:559228 original size:19 final size:19
Alignment explanation
Indices: 559134--559268 Score: 119
Period size: 19 Copynumber: 7.6 Consensus size: 19
559124 TAGTTTACTT
* *
559134 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAA-TGAAAA
***
559154 TCGCAACGCGAAGCCAAAA
1 TCGCAACGCGAAATGAAAA
559173 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
559192 TCGCAA--CGACA-G--AA
1 TCGCAACGCGAAATGAAAA
*
559206 TCGCAATGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
559225 TCGCAA--CGAAA-G--AA
1 TCGCAACGCGAAATGAAAA
559239 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
559258 TCGCAATGCGA
1 TCGCAACGCGA
559269 TTTTGGTTTC
Statistics
Matches: 95, Mismatches: 10, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 16 0.17
16 11 0.12
17 11 0.12
19 46 0.48
20 11 0.12
ACGTcount: A:0.45, C:0.24, G:0.20, T:0.11
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:559286 original size:19 final size:19
Alignment explanation
Indices: 559264--559391 Score: 116
Period size: 19 Copynumber: 7.3 Consensus size: 19
559254 AAAATCGCAA
559264 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
559283 TGCGATCTT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
559297 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
559316 TGCGATTCT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
**
559330 TGCGATTTTCATTTCGCGT
1 TGCGATTTTGGTTTCGCGT
559349 TGCGA-TTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
* *
559367 TGCGATTTTAAGTTTCGTGT
1 TGCGATTTT-GGTTTCGCGT
559387 TGCGA
1 TGCGA
559392 AAGTAAACTA
Statistics
Matches: 88, Mismatches: 9, Indels: 23
0.73 0.08 0.19
Matches are distributed among these distances:
14 22 0.25
15 1 0.01
16 2 0.02
17 2 0.02
18 18 0.20
19 30 0.34
20 13 0.15
ACGTcount: A:0.09, C:0.17, G:0.29, T:0.45
Consensus pattern (19 bp):
TGCGATTTTGGTTTCGCGT
Found at i:559306 original size:33 final size:33
Alignment explanation
Indices: 559264--559355 Score: 150
Period size: 33 Copynumber: 2.8 Consensus size: 33
559254 AAAATCGCAA
559264 TGCGATTTTGGTTTCGCGTTGCGA-TCTTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTC-TGTCGT
559297 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
**
559330 TGCGATTTTCATTTCGCGTTGCGATT
1 TGCGATTTTGGTTTCGCGTTGCGATT
559356 TGGTTTCGCG
Statistics
Matches: 56, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
33 54 0.96
34 2 0.04
ACGTcount: A:0.08, C:0.18, G:0.28, T:0.46
Consensus pattern (33 bp):
TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
Found at i:559727 original size:92 final size:93
Alignment explanation
Indices: 559439--559812 Score: 718
Period size: 92 Copynumber: 4.1 Consensus size: 93
559429 ATGGATTGCA
559439 TTAC-TTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
559503 TAGCAGAATTGGCAGCAACCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
559531 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
559596 TAGCAGAATTGGCAGCAACCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
559624 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTA-TTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
559688 TAGCAGAATTGGCAGCAACCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
559716 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTT-AAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
*
559780 TAGCAGAATTGGCAGCAACCGAATAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
559808 TTACT
1 TTACT
559813 AAGCAATCTA
Statistics
Matches: 279, Mismatches: 1, Indels: 4
0.98 0.00 0.01
Matches are distributed among these distances:
92 142 0.51
93 137 0.49
ACGTcount: A:0.46, C:0.19, G:0.13, T:0.22
Consensus pattern (93 bp):
TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
TAGCAGAATTGGCAGCAACCGAACAAAT
Found at i:559756 original size:185 final size:185
Alignment explanation
Indices: 559439--559812 Score: 716
Period size: 185 Copynumber: 2.0 Consensus size: 185
559429 ATGGATTGCA
559439 TTAC-TTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
559503 TAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACT
66 TAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACT
559568 ATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAACAAAT
131 ATTTCACAGTGTT-AAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAACAAAT
559624 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTA-TTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
559688 TAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACT
66 TAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACT
*
559753 ATTTCACAGTGTTAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAATAAAT
131 ATTTCACAGTGTTAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAACAAAT
559808 TTACT
1 TTACT
559813 AAGCAATCTA
Statistics
Matches: 187, Mismatches: 1, Indels: 3
0.98 0.01 0.02
Matches are distributed among these distances:
184 46 0.25
185 108 0.58
186 33 0.18
ACGTcount: A:0.46, C:0.19, G:0.13, T:0.22
Consensus pattern (185 bp):
TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
TAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACT
ATTTCACAGTGTTAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAACAAAT
Found at i:561532 original size:14 final size:14
Alignment explanation
Indices: 561513--561569 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
561503 TTGAAATGAA
561513 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
561527 AATCGCAACGCGAAATGAC
1 AATCGCAA--CG--A-GAG
561546 AATCGCAACGAGAG
1 AATCGCAACGAGAG
561560 AATCGCAACG
1 AATCGCAACG
561570 CGAAATGAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.28
ACGTcount: A:0.42, C:0.25, G:0.25, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:561550 original size:33 final size:33
Alignment explanation
Indices: 561505--561588 Score: 159
Period size: 33 Copynumber: 2.5 Consensus size: 33
561495 TCTTTTGGTT
561505 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
*
561538 GAAATGACAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
561571 GAAATGAAAATCGCAACG
1 GAAATGAAAATCGCAACG
561589 CGAAATGAAA
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 49 1.00
ACGTcount: A:0.45, C:0.21, G:0.24, T:0.10
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:561551 original size:19 final size:19
Alignment explanation
Indices: 561527--561610 Score: 106
Period size: 19 Copynumber: 4.7 Consensus size: 19
561517 GCAACGAGAG
*
561527 AATCGCAACGCGAAATGAC
1 AATCGCAACGCGAAATGAA
*
561546 AATCGCAA--CG--A-GAG
1 AATCGCAACGCGAAATGAA
561560 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAA
561579 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAA
*
561598 AATCGCAATGCGA
1 AATCGCAACGCGA
561611 TTTTGGTTTC
Statistics
Matches: 57, Mismatches: 3, Indels: 10
0.81 0.04 0.14
Matches are distributed among these distances:
14 10 0.18
15 1 0.02
16 2 0.04
17 2 0.04
18 1 0.02
19 41 0.72
ACGTcount: A:0.44, C:0.23, G:0.23, T:0.11
Consensus pattern (19 bp):
AATCGCAACGCGAAATGAA
Found at i:561641 original size:14 final size:14
Alignment explanation
Indices: 561622--561678 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
561612 TTTGGTTTCG
561622 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
561636 CGTTGCGATTTTCATAT
1 CGTTGCGA--TTC-TCT
561653 CGCTTTGCGATTCTCT
1 CG--TTGCGATTCTCT
561669 CGTTGCGATT
1 CGTTGCGATT
561679 TTCATTTCTC
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 16 0.44
16 7 0.19
17 7 0.19
19 6 0.17
ACGTcount: A:0.11, C:0.25, G:0.21, T:0.44
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:561661 original size:33 final size:33
Alignment explanation
Indices: 561619--561683 Score: 121
Period size: 33 Copynumber: 2.0 Consensus size: 33
561609 GATTTTGGTT
561619 TCGCGTTGCGATTCTCTCGTTGCGATTTTCATA
1 TCGCGTTGCGATTCTCTCGTTGCGATTTTCATA
*
561652 TCGCTTTGCGATTCTCTCGTTGCGATTTTCAT
1 TCGCGTTGCGATTCTCTCGTTGCGATTTTCAT
561684 TTCTCTCGTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.11, C:0.25, G:0.20, T:0.45
Consensus pattern (33 bp):
TCGCGTTGCGATTCTCTCGTTGCGATTTTCATA
Found at i:561719 original size:41 final size:41
Alignment explanation
Indices: 561662--561739 Score: 147
Period size: 41 Copynumber: 1.9 Consensus size: 41
561652 TCGCTTTGCG
*
561662 ATTCTCTCGTTGCGATTTTCATTTCTCTCGTTGCGACAGTC
1 ATTCTCTCGTTGCGATTTTCATTTATCTCGTTGCGACAGTC
561703 ATTCTCTCGTTGCGATTTTCATTTATCTCGTTGCGAC
1 ATTCTCTCGTTGCGATTTTCATTTATCTCGTTGCGAC
561740 TCTTCTGCAA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
41 36 1.00
ACGTcount: A:0.13, C:0.26, G:0.17, T:0.45
Consensus pattern (41 bp):
ATTCTCTCGTTGCGATTTTCATTTATCTCGTTGCGACAGTC
Found at i:561724 original size:20 final size:21
Alignment explanation
Indices: 561663--561738 Score: 109
Period size: 21 Copynumber: 3.7 Consensus size: 21
561653 CGCTTTGCGA
561663 TTCTCTCGTTGCGATTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
***
561684 TTCTCTCGTTGCGACAGTCA-
1 TTCTCTCGTTGCGATTTTCAT
561704 TTCTCTCGTTGCGATTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
*
561725 TTATCTCGTTGCGA
1 TTCTCTCGTTGCGA
561739 CTCTTCTGCA
Statistics
Matches: 47, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
20 17 0.36
21 30 0.64
ACGTcount: A:0.12, C:0.25, G:0.17, T:0.46
Consensus pattern (21 bp):
TTCTCTCGTTGCGATTTTCAT
Found at i:561860 original size:33 final size:33
Alignment explanation
Indices: 561818--561888 Score: 124
Period size: 33 Copynumber: 2.2 Consensus size: 33
561808 AATACTAACT
561818 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
1 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
* *
561851 TGAAAATCGCAACGAGAGAATCGTAACGCGAAA
1 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
561884 TGAAA
1 TGAAA
561889 TCTAAGTGAA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.48, C:0.17, G:0.24, T:0.11
Consensus pattern (33 bp):
TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
Found at i:562122 original size:22 final size:22
Alignment explanation
Indices: 562070--562124 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
562060 TGGTTGTGAG
**
562070 GGATTTCGCCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
**
562092 GGAAATCTTCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
562114 GGATTTCTTCG
1 GGATTTCTTCG
562125 CCGTAGAGAG
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.20, C:0.16, G:0.40, T:0.24
Consensus pattern (22 bp):
GGATTTCTTCGGAGATGGGGAC
Found at i:562297 original size:20 final size:20
Alignment explanation
Indices: 562272--562465 Score: 203
Period size: 20 Copynumber: 9.7 Consensus size: 20
562262 CTTTAAATAT
562272 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
562292 CGCGTTGCGATTTTATGTATTA
1 CGCGTTGCGA-TTTACGGA-TA
* *
562314 -TCGTTGCGATTTACCGATA
1 CGCGTTGCGATTTACGGATA
*
562333 CGCGTTGCGATATACGGATA
1 CGCGTTGCGATTTACGGATA
* **
562353 CGCATTGCGATTTACCCATA
1 CGCGTTGCGATTTACGGATA
562373 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
562393 CACGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* * *
562413 CGCATTGCGATTTATGTG-TT
1 CGCGTTGCGATTTACG-GATA
* ** *
562433 CGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATA
562453 CGCGTTGCGATTT
1 CGCGTTGCGATTT
562466 TCAAGAATCG
Statistics
Matches: 143, Mismatches: 26, Indels: 10
0.80 0.15 0.06
Matches are distributed among these distances:
19 2 0.01
20 124 0.87
21 15 0.10
22 2 0.01
ACGTcount: A:0.20, C:0.20, G:0.25, T:0.36
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:562439 original size:40 final size:40
Alignment explanation
Indices: 562271--562486 Score: 209
Period size: 40 Copynumber: 5.3 Consensus size: 40
562261 GCTTTAAATA
* * *
562271 TCGCGTTGCGATTTACGGATACGCGTTGCGATTTTATGTAT
1 TCGCGTTGCGATTTACCGATACGCGTTGCGA-TTTACGGAT
** *
562312 TATCGTTGCGATTTACCGATACGCGTTGCGATATACGGAT
1 TCGCGTTGCGATTTACCGATACGCGTTGCGATTTACGGAT
* * *
562352 ACGCATTGCGATTTACCCATACGCGTTGCGATTTACGGAT
1 TCGCGTTGCGATTTACCGATACGCGTTGCGATTTACGGAT
* * * * *
562392 ACACGTTGCGATTTACGGATACGCATTGCGATTTATGTG-T
1 TCGCGTTGCGATTTACCGATACGCGTTGCGATTTACG-GAT
* ** * * * *
562432 TCGCGTTGCGATTTTCATATTCGCGTTGCGATTTTCAAGAA
1 TCGCGTTGCGATTTACCGATACGCGTTGCGATTTAC-GGAT
562473 TCGCGTTGCGATTT
1 TCGCGTTGCGATTT
562487 TGGAAACTGA
Statistics
Matches: 143, Mismatches: 29, Indels: 6
0.80 0.16 0.03
Matches are distributed among these distances:
40 100 0.70
41 43 0.30
ACGTcount: A:0.20, C:0.20, G:0.25, T:0.36
Consensus pattern (40 bp):
TCGCGTTGCGATTTACCGATACGCGTTGCGATTTACGGAT
Found at i:562459 original size:60 final size:60
Alignment explanation
Indices: 562272--562465 Score: 244
Period size: 60 Copynumber: 3.2 Consensus size: 60
562262 CTTTAAATAT
* ** *
562272 CGCGTTGCGATTTACGGATACGCGTTGCGATTTTATGTATTATCGTTGCGATTTACCGATA
1 CGCGTTGCGATTTACGGATACGCATTGCGA-TTTATGTATTCGCGTTGCGATTTACAGATA
* *** * *
562333 CGCGTTGCGATATACGGATACGCATTGCGATTTACCCATACGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCATTGCGATTTATGTATTCGCGTTGCGATTTACAGATA
* * * * *
562393 CACGTTGCGATTTACGGATACGCATTGCGATTTATGTGTTCGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATACGCATTGCGATTTATGTATTCGCGTTGCGATTTACAGATA
562453 CGCGTTGCGATTT
1 CGCGTTGCGATTT
562466 TCAAGAATCG
Statistics
Matches: 112, Mismatches: 21, Indels: 1
0.84 0.16 0.01
Matches are distributed among these distances:
60 84 0.75
61 28 0.25
ACGTcount: A:0.20, C:0.20, G:0.25, T:0.36
Consensus pattern (60 bp):
CGCGTTGCGATTTACGGATACGCATTGCGATTTATGTATTCGCGTTGCGATTTACAGATA
Found at i:562466 original size:20 final size:21
Alignment explanation
Indices: 562431--562487 Score: 89
Period size: 20 Copynumber: 2.8 Consensus size: 21
562421 GATTTATGTG
*
562431 TTCGCGTTGCGATTTTC-ATA
1 TTCGCGTTGCGATTTTCAAGA
562451 TTCGCGTTGCGATTTTCAAGA
1 TTCGCGTTGCGATTTTCAAGA
*
562472 ATCGCGTTGCGATTTT
1 TTCGCGTTGCGATTTT
562488 GGAAACTGAT
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
20 17 0.50
21 17 0.50
ACGTcount: A:0.16, C:0.19, G:0.23, T:0.42
Consensus pattern (21 bp):
TTCGCGTTGCGATTTTCAAGA
Found at i:562478 original size:21 final size:20
Alignment explanation
Indices: 562432--562487 Score: 85
Period size: 21 Copynumber: 2.8 Consensus size: 20
562422 ATTTATGTGT
* *
562432 TCGCGTTGCGATTTTCATAT
1 TCGCGTTGCGATTTTCAGAA
562452 TCGCGTTGCGATTTTCAAGAA
1 TCGCGTTGCGATTTTC-AGAA
562473 TCGCGTTGCGATTTT
1 TCGCGTTGCGATTTT
562488 GGAAACTGAT
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
20 16 0.48
21 17 0.52
ACGTcount: A:0.16, C:0.20, G:0.23, T:0.41
Consensus pattern (20 bp):
TCGCGTTGCGATTTTCAGAA
Found at i:575428 original size:14 final size:14
Alignment explanation
Indices: 575409--575436 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
575399 TAACAGACTT
575409 GTCTGTTTTCTACA
1 GTCTGTTTTCTACA
575423 GTCTGTTTTCTACA
1 GTCTGTTTTCTACA
575437 TGGTATCAGG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.14, C:0.21, G:0.14, T:0.50
Consensus pattern (14 bp):
GTCTGTTTTCTACA
Found at i:577258 original size:51 final size:51
Alignment explanation
Indices: 577199--577299 Score: 184
Period size: 51 Copynumber: 2.0 Consensus size: 51
577189 TCAGGGGGAG
* *
577199 AGTTACAAGGAATTTCAGCCTGTTCAAACCGATATTTCTTTACAGCCTATT
1 AGTTACAAGGAATTTCAACCTGTTCAAACCGATATTTCTTTACAACCTATT
577250 AGTTACAAGGAATTTCAACCTGTTCAAACCGATATTTCTTTACAACCTAT
1 AGTTACAAGGAATTTCAACCTGTTCAAACCGATATTTCTTTACAACCTAT
577300 CCTTTCCTTA
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
51 48 1.00
ACGTcount: A:0.32, C:0.22, G:0.12, T:0.35
Consensus pattern (51 bp):
AGTTACAAGGAATTTCAACCTGTTCAAACCGATATTTCTTTACAACCTATT
Found at i:578140 original size:51 final size:51
Alignment explanation
Indices: 578081--578181 Score: 184
Period size: 51 Copynumber: 2.0 Consensus size: 51
578071 TTCAGGGGAG
* *
578081 AGTTACAAGGAATTTCAGCCTGTTCAAACCGATATTTCTTTACAGCCTATT
1 AGTTACAAGGAATTTCAACCTGTTCAAACCGATATTTCTTTACAACCTATT
578132 AGTTACAAGGAATTTCAACCTGTTCAAACCGATATTTCTTTACAACCTAT
1 AGTTACAAGGAATTTCAACCTGTTCAAACCGATATTTCTTTACAACCTAT
578182 CCTTTCCTTA
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
51 48 1.00
ACGTcount: A:0.32, C:0.22, G:0.12, T:0.35
Consensus pattern (51 bp):
AGTTACAAGGAATTTCAACCTGTTCAAACCGATATTTCTTTACAACCTATT
Found at i:580424 original size:14 final size:14
Alignment explanation
Indices: 580405--580432 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
580395 TAACAGACTT
580405 GTCTGTTTTCTACA
1 GTCTGTTTTCTACA
580419 GTCTGTTTTCTACA
1 GTCTGTTTTCTACA
580433 CTAATAACAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.14, C:0.21, G:0.14, T:0.50
Consensus pattern (14 bp):
GTCTGTTTTCTACA
Found at i:588387 original size:150 final size:150
Alignment explanation
Indices: 588114--588407 Score: 462
Period size: 150 Copynumber: 2.0 Consensus size: 150
588104 TTCCTCGCCA
* * *
588114 TCATCATTCTTATCATTACCTTCTTTCTTTTCCTCGGTTTTATCCTTGAAAAGTTTCCGGAAAAA
1 TCATCATTCTTATCATTACCGTCTTTATTTTCCTCGGATTTATCCTTGAAAAGTTTCCGGAAAAA
* * * *
588179 ACCCTCCTTTTCATCATATTCACCTGATTTTGAAGTTTTTTCAGCAGAATTCACCATATGTACAT
66 ACCCTCCTTTTCATCATATTCACCGGATTTTGAAGCTTTTTCAGCAGAACTCACCATATGCACAT
*
588244 CATCAGTTCTATCAGCTACG
131 CATCAATTCTATCAGCTACG
*
588264 TCATCATTCTTATCATTCCCGTCTTTATTTTCCTCGGATTTATCCTTGAAAAGTTTCCGGAAAAA
1 TCATCATTCTTATCATTACCGTCTTTATTTTCCTCGGATTTATCCTTGAAAAGTTTCCGGAAAAA
* * ** *
588329 ACCCTCCTTTTCATCATCTTCACCGGATTTTGAAGCTTTTTCTGCAGTGCTCATCATATGCACAT
66 ACCCTCCTTTTCATCATATTCACCGGATTTTGAAGCTTTTTCAGCAGAACTCACCATATGCACAT
588394 CATCAATTCTATCA
131 CATCAATTCTATCA
588408 TTTACATCTT
Statistics
Matches: 130, Mismatches: 14, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
150 130 1.00
ACGTcount: A:0.24, C:0.26, G:0.10, T:0.40
Consensus pattern (150 bp):
TCATCATTCTTATCATTACCGTCTTTATTTTCCTCGGATTTATCCTTGAAAAGTTTCCGGAAAAA
ACCCTCCTTTTCATCATATTCACCGGATTTTGAAGCTTTTTCAGCAGAACTCACCATATGCACAT
CATCAATTCTATCAGCTACG
Found at i:589857 original size:15 final size:15
Alignment explanation
Indices: 589837--589866 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
589827 GAATACAAAA
589837 TTCTGAATTTAGTGC
1 TTCTGAATTTAGTGC
589852 TTCTGAATTTAGTGC
1 TTCTGAATTTAGTGC
589867 GAGGAAGAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.20, C:0.13, G:0.20, T:0.47
Consensus pattern (15 bp):
TTCTGAATTTAGTGC
Found at i:590327 original size:22 final size:20
Alignment explanation
Indices: 590301--590354 Score: 60
Period size: 19 Copynumber: 2.8 Consensus size: 20
590291 TTAAAAGAAA
590301 TAAAAATATAATTATAATAATT
1 TAAAAAT-TAATTAT-ATAATT
590323 T-AAAATT-ATTAT-TAATT
1 TAAAAATTAATTATATAATT
*
590340 TAAAAAGTAATTATA
1 TAAAAATTAATTATA
590355 CTATCAAAGT
Statistics
Matches: 28, Mismatches: 1, Indels: 8
0.76 0.03 0.22
Matches are distributed among these distances:
17 6 0.21
18 5 0.18
19 10 0.36
20 1 0.04
21 5 0.18
22 1 0.04
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.43
Consensus pattern (20 bp):
TAAAAATTAATTATATAATT
Found at i:590331 original size:16 final size:17
Alignment explanation
Indices: 590310--590344 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
590300 ATAAAAATAT
590310 AATTA-TAATAATTTAA
1 AATTATTAATAATTTAA
*
590326 AATTATTATTAATTTAA
1 AATTATTAATAATTTAA
590343 AA
1 AA
590345 AGTAATTATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 5 0.29
17 12 0.71
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
AATTATTAATAATTTAA
Found at i:590485 original size:23 final size:23
Alignment explanation
Indices: 590455--590503 Score: 98
Period size: 23 Copynumber: 2.1 Consensus size: 23
590445 GCAGTTTGTG
590455 TACAAATGGTTTAGAGTAAATTA
1 TACAAATGGTTTAGAGTAAATTA
590478 TACAAATGGTTTAGAGTAAATTA
1 TACAAATGGTTTAGAGTAAATTA
590501 TAC
1 TAC
590504 TGATTCCCCA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.43, C:0.06, G:0.16, T:0.35
Consensus pattern (23 bp):
TACAAATGGTTTAGAGTAAATTA
Found at i:595937 original size:13 final size:13
Alignment explanation
Indices: 595919--595944 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
595909 AAGAAAATCC
595919 GTCTTTTAATTTT
1 GTCTTTTAATTTT
595932 GTCTTTTAATTTT
1 GTCTTTTAATTTT
595945 TAGAGGAAGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.15, C:0.08, G:0.08, T:0.69
Consensus pattern (13 bp):
GTCTTTTAATTTT
Found at i:601031 original size:17 final size:17
Alignment explanation
Indices: 600967--601033 Score: 55
Period size: 17 Copynumber: 3.8 Consensus size: 17
600957 ACTGGAGAAT
*
600967 TTTTTTCTAATATAAA-A
1 TTTTTT-TAAAATAAATA
* * *
600984 TGTTTTTAAAATTATTA
1 TTTTTTTAAAATAAATA
601001 TTTTTTTAAAAAAATAAATA
1 TTTTTTT---AAAATAAATA
601021 TTTTTTTAAAATA
1 TTTTTTTAAAATA
601034 TATCAACATG
Statistics
Matches: 39, Mismatches: 7, Indels: 8
0.72 0.13 0.15
Matches are distributed among these distances:
16 6 0.15
17 18 0.46
20 15 0.38
ACGTcount: A:0.43, C:0.01, G:0.01, T:0.54
Consensus pattern (17 bp):
TTTTTTTAAAATAAATA
Found at i:602525 original size:2 final size:2
Alignment explanation
Indices: 602520--602549 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
602510 TATATATATA
*
602520 TG TG TG TG TG TG TG TG CG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
602550 ATCCTTATAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.00, C:0.03, G:0.50, T:0.47
Consensus pattern (2 bp):
TG
Found at i:602774 original size:16 final size:16
Alignment explanation
Indices: 602753--602786 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
602743 GTGTTATATC
602753 TTTTTAATGAGTGAAT
1 TTTTTAATGAGTGAAT
* *
602769 TTTTTAATTAGTGTAT
1 TTTTTAATGAGTGAAT
602785 TT
1 TT
602787 AAATATTATA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.26, C:0.00, G:0.15, T:0.59
Consensus pattern (16 bp):
TTTTTAATGAGTGAAT
Found at i:605262 original size:18 final size:19
Alignment explanation
Indices: 605221--605262 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 19
605211 CTCTAAATCA
*
605221 TTTTCAAAATTTCATTTGG
1 TTTTCAAAATATCATTTGG
* *
605240 CTTTCAAAATAT-ATTTTG
1 TTTTCAAAATATCATTTGG
605258 TTTTC
1 TTTTC
605263 TAAAGAAAAT
Statistics
Matches: 19, Mismatches: 4, Indels: 1
0.79 0.17 0.04
Matches are distributed among these distances:
18 9 0.47
19 10 0.53
ACGTcount: A:0.26, C:0.12, G:0.07, T:0.55
Consensus pattern (19 bp):
TTTTCAAAATATCATTTGG
Found at i:606396 original size:483 final size:492
Alignment explanation
Indices: 605730--606706 Score: 1800
Period size: 494 Copynumber: 2.0 Consensus size: 492
605720 AGCTTCTTCT
605730 AGGATCGTCTCAAAGTGGTTAAACCTTCTTAACGAGTTAGGCTCTGATACCAATGTTGGGATTTT
1 AGGATCGTCTCAAAGTGGTTAAACCTTCTTAACGAGTTAGGCTCTGATACCAATGTTGGGATTTT
605795 CTGAAGCTCGAATCGACAACCGGAACGGTTTGCAAAGAGGGTCGAAACGGTTTTGTGTTTAGGGA
66 CTGAAGCTCGAATCGACAACCGGAACGGTTTGCAAAGAGGGTCGAAACGGTTTTGTGTTTAGGGA
605860 GTAAGGAGAGATGAAAGATAGAGAATTGCACATCGATTTATAGTGGTTCGACTTTCTCAACC-AA
131 GTAAGGAGAGATGAAAGATAGAGAATTGCACATCGATTTATAGTGGTTCGACTTTCTCAACCAAA
605924 -TC-A-GTTCCAACTACCTTAGCTCCTCA-CAAGGATTTTCTAACAATTTCACTAATTTGTTA-T
196 GTCTACG-TCC-ACTACCTTAGCTCCTCACCAAGGATTTTCTAACAATTTCACTAATTTGTTATT
605984 TC-TTGAGGATAAAGAGTAACCTTACAAAACCCTCAAGAA-TATA-CCCAAATTC-TGAG-ACA-
259 TCTTTGAGGATAAAGAGTAACCTTACAAAACCCTCAAGAATTATACCCCAAATTCTTGAGAACAC
606043 ACTCTCCCAAAGAGAATAATACAAATTTTGCAAACTTACAAGAAAATCCTCACAAGGCAAGATGT
324 ACTCTCCCAAAGAGAATAATACAAATTTTGCAAACTTACAAGAAAATCCTCACAAGGCAAGATGT
606108 TTGCACAATTATAGAACAAAGAAAGAACACTCAAGAATAATTCAATTGAGCACAATAAGTGTTAT
389 TTGCACAATTATAGAACAAAGAAAGAACACTCAAGAATAATTCAATTGAGCACAATAAGTGTTAT
606173 TGAAAGTAAAAATGAATATTAAATGAAGTAGGCTTGAAA
454 TGAAAGTAAAAATGAATATTAAATGAAGTAGGCTTGAAA
606212 AGGATCGTCTCAAAGTGGTTAAACCTTCTTAACGAGTTAGGCTCTGATACCAATTGTTGGGATTT
1 AGGATCGTCTCAAAGTGGTTAAACCTTCTTAACGAGTTAGGCTCTGATACCAA-TGTTGGGATTT
606277 TCTGAAGCTCGAATCGACAACCGGAACGGTTTGCAAAGAGGGGTCGAAACGGTTTTGTGTTTAGG
65 TCTGAAGCTCGAATCGACAACCGGAACGGTTTGCAAAGA-GGGTCGAAACGGTTTTGTGTTTAGG
*
606342 GAGTAAGGAGA-TTGAAAGATAGAGAATTGCACATCGATTTATAGTGGTTCGACTTTCTCAACCA
129 GAGTAAGGAGAGATGAAAGATAGAGAATTGCACATCGATTTATAGTGGTTCGACTTTCTCAACCA
606406 AAGTCTACGTCCACTACCTTAGCTCCTCACCAAGGATTTTCTAACAATTTCACTAATTTGTTATT
194 AAGTCTACGTCCACTACCTTAGCTCCTCACCAAGGATTTTCTAACAATTTCACTAATTTGTTATT
606471 TCTTTTGAGGATAAAGAGTAACCTTACAAAACCCTCAAGAATTATACCCCAAATTCTTGAGAACA
259 TC-TTTGAGGATAAAGAGTAACCTTACAAAACCCTCAAGAATTATACCCCAAATTCTTGAGAACA
*
606536 CTCTCTCCCAAAGAGAATAATACAAATTTTGCAAACTTACAAGAAAATCCTCACAAGGCAAGATG
323 CACTCTCCCAAAGAGAATAATACAAATTTTGCAAACTTACAAGAAAATCCTCACAAGGCAAGATG
606601 TTTGCACAATTATAGAACAAAGAAAGAACACTCAAGAATAATTCAATTGAGCACAATAAGTGTTA
388 TTTGCACAATTATAGAACAAAGAAAGAACACTCAAGAATAATTCAATTGAGCACAATAAGTGTTA
606666 TTGAAAGTAAAAATGAATATTAAATGAAGTAGGCTTGAAA
453 TTGAAAGTAAAAATGAATATTAAATGAAGTAGGCTTGAAA
606706 A
1 A
606707 TGCTCAAACT
Statistics
Matches: 478, Mismatches: 2, Indels: 18
0.96 0.00 0.04
Matches are distributed among these distances:
482 53 0.11
483 101 0.21
484 38 0.08
485 19 0.04
486 37 0.08
487 4 0.01
489 37 0.08
490 4 0.01
491 9 0.02
492 4 0.01
493 3 0.01
494 169 0.35
ACGTcount: A:0.37, C:0.17, G:0.18, T:0.27
Consensus pattern (492 bp):
AGGATCGTCTCAAAGTGGTTAAACCTTCTTAACGAGTTAGGCTCTGATACCAATGTTGGGATTTT
CTGAAGCTCGAATCGACAACCGGAACGGTTTGCAAAGAGGGTCGAAACGGTTTTGTGTTTAGGGA
GTAAGGAGAGATGAAAGATAGAGAATTGCACATCGATTTATAGTGGTTCGACTTTCTCAACCAAA
GTCTACGTCCACTACCTTAGCTCCTCACCAAGGATTTTCTAACAATTTCACTAATTTGTTATTTC
TTTGAGGATAAAGAGTAACCTTACAAAACCCTCAAGAATTATACCCCAAATTCTTGAGAACACAC
TCTCCCAAAGAGAATAATACAAATTTTGCAAACTTACAAGAAAATCCTCACAAGGCAAGATGTTT
GCACAATTATAGAACAAAGAAAGAACACTCAAGAATAATTCAATTGAGCACAATAAGTGTTATTG
AAAGTAAAAATGAATATTAAATGAAGTAGGCTTGAAA
Found at i:618084 original size:31 final size:31
Alignment explanation
Indices: 618046--618142 Score: 158
Period size: 31 Copynumber: 3.1 Consensus size: 31
618036 GTATAGTAAT
* *
618046 GGTCACTGAACTTTTCTTAAGTTTTTATTTA
1 GGTCACTGAACTTTTCTTAAGCTTTCATTTA
618077 GGTCACTGAACTTTTCTTAAGCTTTCATTTA
1 GGTCACTGAACTTTTCTTAAGCTTTCATTTA
* *
618108 GGTCACTAAACTTTTCTCAAGCTTTCATTTA
1 GGTCACTGAACTTTTCTTAAGCTTTCATTTA
618139 GGTC
1 GGTC
618143 CTCCAACTTT
Statistics
Matches: 62, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 62 1.00
ACGTcount: A:0.23, C:0.19, G:0.13, T:0.45
Consensus pattern (31 bp):
GGTCACTGAACTTTTCTTAAGCTTTCATTTA
Found at i:618970 original size:64 final size:63
Alignment explanation
Indices: 618882--619044 Score: 211
Period size: 64 Copynumber: 2.5 Consensus size: 63
618872 TCCTTAACAT
* * * * *
618882 GTGCATCGATGCACTAACTATGCATCGATACACAAATCATATTCGATG-TTTCTATTTTTAATGG
1 GTGCATCGATACACTACCTGTGCATCGATACACAAATCACATTCGATGTTTTC-A-TTTTAAGGG
* *
618946 GTGCATCGATACACTTCCTGTGCATCGATACACAAATTACATTCGATGTTTTCATTTTAAGGG
1 GTGCATCGATACACTACCTGTGCATCGATACACAAATCACATTCGATGTTTTCATTTTAAGGG
*
619009 GTGCATCGATGCACACTCCCTGTGCATCGATACACA
1 GTGCATCGAT--ACACTACCTGTGCATCGATACACA
619045 CTGAATAATT
Statistics
Matches: 88, Mismatches: 8, Indels: 5
0.87 0.08 0.05
Matches are distributed among these distances:
63 18 0.20
64 43 0.49
65 27 0.31
ACGTcount: A:0.28, C:0.23, G:0.17, T:0.33
Consensus pattern (63 bp):
GTGCATCGATACACTACCTGTGCATCGATACACAAATCACATTCGATGTTTTCATTTTAAGGG
Found at i:622800 original size:14 final size:14
Alignment explanation
Indices: 622778--622816 Score: 60
Period size: 14 Copynumber: 2.8 Consensus size: 14
622768 TCCATATTAG
*
622778 TATTCTAATTGATA
1 TATTATAATTGATA
*
622792 TATTTTAATTGATA
1 TATTATAATTGATA
622806 TATTATAATTG
1 TATTATAATTG
622817 CTCACTCCTT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.36, C:0.03, G:0.08, T:0.54
Consensus pattern (14 bp):
TATTATAATTGATA
Found at i:623071 original size:65 final size:65
Alignment explanation
Indices: 622910--623072 Score: 206
Period size: 64 Copynumber: 2.5 Consensus size: 65
622900 TCCTTAACAT
* * * *
622910 GTGCATCGATGA-ACTAACTATGCATCGATACACAAATCACATTCGATGTTTCTATTTTTAATGG
1 GTGCATCGATGACACTACCTATGCATCGATACATAAATCACATTCGATGTTTCTAATTTTAAGGG
* * * * *
622974 GTACATCGAT-ACACTTCATGTGCATCGATACATAAATTACATTCGATGTTT-TAATTTTAAGGG
1 GTGCATCGATGACACTACCTATGCATCGATACATAAATCACATTCGATGTTTCTAATTTTAAGGG
*
623037 GTGCATCGATGCACACTCCCTATGCATCGATACATA
1 GTGCATCGATG-ACACTACCTATGCATCGATACATA
623073 CTGAATAATT
Statistics
Matches: 83, Mismatches: 13, Indels: 5
0.82 0.13 0.05
Matches are distributed among these distances:
63 20 0.24
64 42 0.51
65 21 0.25
ACGTcount: A:0.31, C:0.20, G:0.16, T:0.33
Consensus pattern (65 bp):
GTGCATCGATGACACTACCTATGCATCGATACATAAATCACATTCGATGTTTCTAATTTTAAGGG
Found at i:624008 original size:22 final size:20
Alignment explanation
Indices: 623961--624034 Score: 89
Period size: 22 Copynumber: 3.6 Consensus size: 20
623951 TTCAGTATTT
623961 GTCCCGAAGGACCACT-ATA
1 GTCCCGAAGGACCACTGATA
623980 -TCCCGAAGGACCACTAGATA
1 GTCCCGAAGGACCACT-GATA
624000 CGTCCCGAAGGACCACTGGATA
1 -GTCCCGAAGGACCACT-GATA
*
624022 TATCCCGAAGGAC
1 -GTCCCGAAGGAC
624035 TAATATACCC
Statistics
Matches: 48, Mismatches: 3, Indels: 5
0.86 0.05 0.09
Matches are distributed among these distances:
18 15 0.31
20 3 0.06
22 30 0.62
ACGTcount: A:0.31, C:0.31, G:0.23, T:0.15
Consensus pattern (20 bp):
GTCCCGAAGGACCACTGATA
Found at i:628516 original size:35 final size:35
Alignment explanation
Indices: 628442--628516 Score: 105
Period size: 35 Copynumber: 2.1 Consensus size: 35
628432 AAAATACTTC
*
628442 AATTTAAGGTTTAGAATATAATTAAAGTATTTTGA
1 AATTTAAGGTTTAGAATATAATTAAAGTACTTTGA
* * * *
628477 AATTTAGGGTTTAGAATGTAATTAAAGTGCTTTGG
1 AATTTAAGGTTTAGAATATAATTAAAGTACTTTGA
628512 AATTT
1 AATTT
628517 TGAACATGAA
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.37, C:0.01, G:0.19, T:0.43
Consensus pattern (35 bp):
AATTTAAGGTTTAGAATATAATTAAAGTACTTTGA
Found at i:633010 original size:3 final size:3
Alignment explanation
Indices: 633002--633031 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
632992 AGTAGAGTAG
633002 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
633032 GGAAGTCTTC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:633533 original size:27 final size:25
Alignment explanation
Indices: 633503--633590 Score: 60
Period size: 27 Copynumber: 3.5 Consensus size: 25
633493 AAGGATGAAC
633503 CTGATTCTGATGAGAATGACAAGAAAT
1 CTGATTCTGATGAGAATG--AAGAAAT
*
633530 CTGA---AGA-GAGCAATG-AGAAAT
1 CTGATTCTGATGAG-AATGAAGAAAT
* * *
633551 CTGAATCTGATGGGAATGATGATAAAT
1 CTGATTCTGATGAGAATGA--AGAAAT
633578 CTGATTCTGATGA
1 CTGATTCTGATGA
633591 TGGTGAAAAG
Statistics
Matches: 47, Mismatches: 6, Indels: 16
0.68 0.09 0.23
Matches are distributed among these distances:
21 10 0.21
23 3 0.06
24 12 0.26
25 2 0.04
27 20 0.43
ACGTcount: A:0.39, C:0.10, G:0.25, T:0.26
Consensus pattern (25 bp):
CTGATTCTGATGAGAATGAAGAAAT
Found at i:639715 original size:78 final size:78
Alignment explanation
Indices: 639586--639733 Score: 208
Period size: 78 Copynumber: 1.9 Consensus size: 78
639576 TTTGGCAGCA
* * *
639586 ACCTTCTTATGAACCTTCATCTGTAGCAGGAACTCCAGCAGATCAAAACCATCAACCTAGACAGC
1 ACCTTCTTATGAACCTGCATCTCTAGCAGGAACTCCAGCAGATCAAAACCATCAACCCAGACAGC
639651 AAGCCTCGTTTAT
66 AAGCCTCGTTTAT
* * ** *
639664 ACCTTCTTATGCACCTGCATCTCTAGCAGGAACTTCAGTC-GATCGGAACCATCACCCCAGACAG
1 ACCTTCTTATGAACCTGCATCTCTAGCAGGAACTCCAG-CAGATCAAAACCATCAACCCAGACAG
639728 CAAGCC
65 CAAGCC
639734 CCATCTATAC
Statistics
Matches: 61, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
78 60 0.98
79 1 0.02
ACGTcount: A:0.30, C:0.32, G:0.16, T:0.22
Consensus pattern (78 bp):
ACCTTCTTATGAACCTGCATCTCTAGCAGGAACTCCAGCAGATCAAAACCATCAACCCAGACAGC
AAGCCTCGTTTAT
Found at i:646319 original size:259 final size:260
Alignment explanation
Indices: 645629--646393 Score: 1316
Period size: 260 Copynumber: 2.9 Consensus size: 260
645619 GGCCCTCGAA
* * *
645629 TTCCTCGTCTCCTTTACTTTCTATTGATGCCGCCTTTCTCGGTTCCTCAGGTTTTCCCCTTTCCC
1 TTCCTCGTCTCCTTTTCTTTCTATTGATGCCGCCTTTCTCGGTTCCTCAGGTTTGCCCCTTTCCA
* ** *
645694 TCTCGTTTTCATTAAGATTTGTCTGGTTTTAGATAATTATACTTGTTTATTCTTCTTTTTAATCT
66 TTTCGTTTTCATTAAGATCCGTCTGGTTTTAGATAATTATACTCGTTTATTCTTCTTTTTAATCT
645759 TAAATCTTGCTTTCCTTTTCATTTCTCGGATTTTGTTGGAAGTGTGAATGTTTTTAGTACTCAAC
131 TAAATCTTGCTTTCCTTTTCATTTCTCGGATTTTGTTGGAAGTGTGAATGTTTTTAGTACTCAAC
*
645824 TATGTTGTTACTTAGCTCTAAAATGTTTTTGAATGTGTATTAAATCTGGGTTCCTCAGGTTTGCT
196 TATGTTGTTACTTAGCTCTAAAATGTTTTTGAATGTGTATTAAATCTGGGTTCCTCAAGTTTGCT
* * *
645889 TTCCTCGTCTCCTTTTCTTTCTATTGTTGCCGCCTTTCTTGGTTCCTCAGGTTTGCCCTTTTCCA
1 TTCCTCGTCTCCTTTTCTTTCTATTGATGCCGCCTTTCTCGGTTCCTCAGGTTTGCCCCTTTCCA
* *
645954 TTTCGTTTTCATTAAGATCCGTCTGGTTTTAGATATTTATACTCGTTTATTCTTCTTTCTAATCT
66 TTTCGTTTTCATTAAGATCCGTCTGGTTTTAGATAATTATACTCGTTTATTCTTCTTTTTAATCT
* *
646019 TAAATCTTGCTTTCCTTTTCATTTCTCGAATTTTTTTGGAAGTGTGAATGTTTTTAGTACTCAAC
131 TAAATCTTGCTTTCCTTTTCATTTCTCGGATTTTGTTGGAAGTGTGAATGTTTTTAGTACTCAAC
*
646084 TATGTTGTTACTTAGCTCTAAAATGTTTTTGAATGTGTATTAAATTTGGGTTCCTCAAGTTTGCT
196 TATGTTGTTACTTAGCTCTAAAATGTTTTTGAATGTGTATTAAATCTGGGTTCCTCAAGTTTGCT
* *
646149 TTCCTCGTCTCATTTTCTTTCTATTG-TGCCACCTTTCTCGGTTCCTCAGGTTTGCCCCTTTCCA
1 TTCCTCGTCTCCTTTTCTTTCTATTGATGCCGCCTTTCTCGGTTCCTCAGGTTTGCCCCTTTCCA
* * * *
646213 TTTCGTTTTCATTAAGATCCGTCTAGTTTTAGATACTTGTACTCGTTTTTTCTTCTTTTTAATCT
66 TTTCGTTTTCATTAAGATCCGTCTGGTTTTAGATAATTATACTCGTTTATTCTTCTTTTTAATCT
646278 TAAATCTTGCTTTCCTTTTCATTTCTCGGATTTTGTTGGAAGTGTGAATGTTTTTAGTACTCAAC
131 TAAATCTTGCTTTCCTTTTCATTTCTCGGATTTTGTTGGAAGTGTGAATGTTTTTAGTACTCAAC
*
646343 TATGCTGTTACTTAGCTCTAAAATGTTTTTGAATGTGTATTAAATCTGGGT
196 TATGTTGTTACTTAGCTCTAAAATGTTTTTGAATGTGTATTAAATCTGGGT
646394 ATTGACTATT
Statistics
Matches: 476, Mismatches: 29, Indels: 1
0.94 0.06 0.00
Matches are distributed among these distances:
259 207 0.43
260 269 0.57
ACGTcount: A:0.17, C:0.19, G:0.15, T:0.49
Consensus pattern (260 bp):
TTCCTCGTCTCCTTTTCTTTCTATTGATGCCGCCTTTCTCGGTTCCTCAGGTTTGCCCCTTTCCA
TTTCGTTTTCATTAAGATCCGTCTGGTTTTAGATAATTATACTCGTTTATTCTTCTTTTTAATCT
TAAATCTTGCTTTCCTTTTCATTTCTCGGATTTTGTTGGAAGTGTGAATGTTTTTAGTACTCAAC
TATGTTGTTACTTAGCTCTAAAATGTTTTTGAATGTGTATTAAATCTGGGTTCCTCAAGTTTGCT
Found at i:647380 original size:23 final size:23
Alignment explanation
Indices: 647354--647421 Score: 93
Period size: 23 Copynumber: 3.0 Consensus size: 23
647344 TTTTGTAGAT
*
647354 TCAAATTCGAGTTTGAATCGAGC
1 TCAAATTCGAGCTTGAATCGAGC
*
647377 TCAAAATCGAGCTTGAATCGAGC
1 TCAAATTCGAGCTTGAATCGAGC
*
647400 TCAAAATT-GAGCTTCAATCGAG
1 TC-AAATTCGAGCTTGAATCGAG
647422 TTCCTGAAAT
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
23 36 0.90
24 4 0.10
ACGTcount: A:0.34, C:0.19, G:0.21, T:0.26
Consensus pattern (23 bp):
TCAAATTCGAGCTTGAATCGAGC
Found at i:647386 original size:12 final size:12
Alignment explanation
Indices: 647369--647412 Score: 54
Period size: 12 Copynumber: 3.8 Consensus size: 12
647359 TTCGAGTTTG
647369 AATCGAGCTCAA
1 AATCGAGCTCAA
**
647381 AATCGAGCT-TG
1 AATCGAGCTCAA
647392 AATCGAGCTCAA
1 AATCGAGCTCAA
*
647404 AATTGAGCT
1 AATCGAGCT
647413 TCAATCGAGT
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
11 9 0.35
12 17 0.65
ACGTcount: A:0.36, C:0.20, G:0.20, T:0.23
Consensus pattern (12 bp):
AATCGAGCTCAA
Found at i:651525 original size:21 final size:20
Alignment explanation
Indices: 651498--651596 Score: 81
Period size: 21 Copynumber: 4.8 Consensus size: 20
651488 AATCAGTTTC
651498 CAAAATCGCAACGCGATTCTT
1 CAAAATCGCAACGCGATT-TT
* * * *
651519 GAAAATCGCAATGCGATAGTA
1 CAAAATCGCAACGCGAT-TTT
* **
651540 CAAATTCGCATTGCGATTTT
1 CAAAATCGCAACGCGATTTT
* *
651560 CCAAAATCGCAACGCGAATAT
1 -CAAAATCGCAACGCGATTTT
*
651581 GAAAATCGCAACGCGA
1 CAAAATCGCAACGCGA
651597 ACACATAAAT
Statistics
Matches: 61, Mismatches: 15, Indels: 5
0.75 0.19 0.06
Matches are distributed among these distances:
20 16 0.26
21 45 0.74
ACGTcount: A:0.37, C:0.23, G:0.18, T:0.21
Consensus pattern (20 bp):
CAAAATCGCAACGCGATTTT
Found at i:651625 original size:20 final size:20
Alignment explanation
Indices: 651563--651756 Score: 221
Period size: 20 Copynumber: 9.7 Consensus size: 20
651553 CGATTTTCCA
* ** *
651563 AAATCGCAACGCGAATATGA
1 AAATCGCAACGCGTATCCGT
* *
651583 AAATCGCAACGCG-AACACAT
1 AAATCGCAACGCGTATC-CGT
651603 AAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
651623 AAATCGCAACGTGTATCCGT
1 AAATCGCAACGCGTATCCGT
**
651643 AAATCGCAACGCGTATGGGT
1 AAATCGCAACGCGTATCCGT
*
651663 AAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
651683 ATATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
* * *
651703 AAATCGCAACG-ATAATACAT
1 AAATCGCAACGCGT-ATCCGT
651723 AAAATCGCAACGCGTATCCGT
1 -AAATCGCAACGCGTATCCGT
651744 AAATCGCAACGCG
1 AAATCGCAACGCG
651757 ATATTTAAAG
Statistics
Matches: 146, Mismatches: 23, Indels: 10
0.82 0.13 0.06
Matches are distributed among these distances:
19 2 0.01
20 126 0.86
21 17 0.12
22 1 0.01
ACGTcount: A:0.36, C:0.26, G:0.20, T:0.19
Consensus pattern (20 bp):
AAATCGCAACGCGTATCCGT
Found at i:651647 original size:60 final size:60
Alignment explanation
Indices: 651563--651756 Score: 253
Period size: 60 Copynumber: 3.2 Consensus size: 60
651553 CGATTTTCCA
* ** * *
651563 AAATCGCAACGCGAATATGAAAATCGCAACGCGAACACATAAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGT
* * *** *
651623 AAATCGCAACGTGTATCCGTAAATCGCAACGCGTATGGGTAAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGT
* **
651683 ATATCGCAACGCGTATCCGTAAATCGCAACGATAATACATAAAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACAT-AAATCGCAACGCGTATCCGT
651744 AAATCGCAACGCG
1 AAATCGCAACGCG
651757 ATATTTAAAG
Statistics
Matches: 112, Mismatches: 21, Indels: 1
0.84 0.16 0.01
Matches are distributed among these distances:
60 81 0.72
61 31 0.28
ACGTcount: A:0.36, C:0.26, G:0.20, T:0.19
Consensus pattern (60 bp):
AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGT
Found at i:652177 original size:33 final size:33
Alignment explanation
Indices: 652138--652208 Score: 99
Period size: 33 Copynumber: 2.2 Consensus size: 33
652128 TTCACTTAGA
*
652138 TTTCATTTCGCGTTACGATTCTGTCGTTGC-GAT
1 TTTCATTTCGCGTTACGATTCTCTCGTT-CTGAT
* *
652171 TTTCATTTCGCGTTGCTATTCTCTCGTTCTGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTCTGAT
652204 TTTCA
1 TTTCA
652209 AGTTAGTATT
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
32 1 0.03
33 33 0.97
ACGTcount: A:0.11, C:0.23, G:0.17, T:0.49
Consensus pattern (33 bp):
TTTCATTTCGCGTTACGATTCTCTCGTTCTGAT
Found at i:652314 original size:21 final size:20
Alignment explanation
Indices: 652288--652393 Score: 91
Period size: 21 Copynumber: 5.5 Consensus size: 20
652278 TGCAGAAGAG
652288 TCGCAACGAGATAAATGAAAA
1 TCGCAACGAGA-AAATGAAAA
* ***
652309 TCGCAACGAGAGAATGACTG
1 TCGCAACGAGAAAATGAAAA
652329 TCGCAACGAGAGAAATGAAAA
1 TCGCAACGAGA-AAATGAAAA
*
652350 GCGCAACGAG---A-G--AA
1 TCGCAACGAGAAAATGAAAA
*
652364 TCGCAACGCG-AAATGAAAA
1 TCGCAACGAGAAAATGAAAA
652383 TCGCAACGAGA
1 TCGCAACGAGA
652394 GAATCGCAAC
Statistics
Matches: 66, Mismatches: 12, Indels: 15
0.71 0.13 0.16
Matches are distributed among these distances:
14 10 0.15
16 2 0.03
17 2 0.03
19 11 0.17
20 16 0.24
21 25 0.38
ACGTcount: A:0.45, C:0.19, G:0.25, T:0.10
Consensus pattern (20 bp):
TCGCAACGAGAAAATGAAAA
Found at i:652332 original size:20 final size:21
Alignment explanation
Indices: 652286--652364 Score: 92
Period size: 21 Copynumber: 3.8 Consensus size: 21
652276 TTTGCAGAAG
*
652286 AGTCGCAACGAGATAAATGAAA
1 AGTCGCAACGAGA-GAATGAAA
*
652308 A-TCGCAACGAGAGAATG-AC
1 AGTCGCAACGAGAGAATGAAA
*
652327 TGTCGCAACGAGAGAAATGAAA
1 AGTCGCAACGAGAG-AATGAAA
652349 AG-CGCAACGAGAGAAT
1 AGTCGCAACGAGAGAAT
652365 CGCAACGCGA
Statistics
Matches: 49, Mismatches: 5, Indels: 8
0.79 0.08 0.13
Matches are distributed among these distances:
19 1 0.02
20 19 0.39
21 26 0.53
22 3 0.06
ACGTcount: A:0.46, C:0.16, G:0.27, T:0.11
Consensus pattern (21 bp):
AGTCGCAACGAGAGAATGAAA
Found at i:652345 original size:41 final size:38
Alignment explanation
Indices: 652281--652397 Score: 136
Period size: 41 Copynumber: 3.1 Consensus size: 38
652271 TTCAATTTGC
* *
652281 AGAAGAGTCGCAACGAGATAAATGAAAATCGCAACGAG
1 AGAATAGTCGCAACGAGAGAAATGAAAATCGCAACGAG
*
652319 AGAATGACTGTCGCAACGAGAGAAATGAAAAGCGCAACGAG
1 AGAAT-A--GTCGCAACGAGAGAAATGAAAATCGCAACGAG
*
652360 AG-A-A-TCGCAAC--GCGAAATGAAAATCGCAACGAG
1 AGAATAGTCGCAACGAGAGAAATGAAAATCGCAACGAG
652393 AGAAT
1 AGAAT
652398 CGCAACGCGA
Statistics
Matches: 69, Mismatches: 5, Indels: 13
0.79 0.06 0.15
Matches are distributed among these distances:
33 22 0.32
34 1 0.01
35 7 0.10
38 5 0.07
39 1 0.01
40 1 0.01
41 32 0.46
ACGTcount: A:0.46, C:0.17, G:0.26, T:0.10
Consensus pattern (38 bp):
AGAATAGTCGCAACGAGAGAAATGAAAATCGCAACGAG
Found at i:652370 original size:14 final size:14
Alignment explanation
Indices: 652351--652404 Score: 54
Period size: 14 Copynumber: 3.5 Consensus size: 14
652341 AAATGAAAAG
652351 CGCAACGAGAGAAT
1 CGCAACGAGAGAAT
*
652365 CGCAACGCGAAATGAAAAT
1 CGCAA--CG--A-GAGAAT
652384 CGCAACGAGAGAAT
1 CGCAACGAGAGAAT
652398 CGCAACG
1 CGCAACG
652405 CGAAACCAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 10
0.73 0.04 0.22
Matches are distributed among these distances:
14 17 0.52
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.30
ACGTcount: A:0.43, C:0.24, G:0.26, T:0.07
Consensus pattern (14 bp):
CGCAACGAGAGAAT
Found at i:652380 original size:33 final size:33
Alignment explanation
Indices: 652340--652409 Score: 131
Period size: 33 Copynumber: 2.1 Consensus size: 33
652330 CGCAACGAGA
652340 GAAATGAAAAGCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAAGCGCAACGAGAGAATCGCAACGC
*
652373 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAAGCGCAACGAGAGAATCGCAACGC
652406 GAAA
1 GAAA
652410 CCAAAATCGC
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.47, C:0.20, G:0.26, T:0.07
Consensus pattern (33 bp):
GAAATGAAAAGCGCAACGAGAGAATCGCAACGC
Found at i:652416 original size:33 final size:33
Alignment explanation
Indices: 652346--652420 Score: 123
Period size: 33 Copynumber: 2.3 Consensus size: 33
652336 GAGAGAAATG
* **
652346 AAAAGCGCAACGAGAGAATCGCAACGCGAAATG
1 AAAATCGCAACGAGAGAATCGCAACGCGAAACC
652379 AAAATCGCAACGAGAGAATCGCAACGCGAAACC
1 AAAATCGCAACGAGAGAATCGCAACGCGAAACC
652412 AAAATCGCA
1 AAAATCGCA
652421 TTGCGATTTT
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 39 1.00
ACGTcount: A:0.47, C:0.24, G:0.23, T:0.07
Consensus pattern (33 bp):
AAAATCGCAACGAGAGAATCGCAACGCGAAACC
Found at i:652438 original size:19 final size:19
Alignment explanation
Indices: 652416--652513 Score: 81
Period size: 19 Copynumber: 5.7 Consensus size: 19
652406 GAAACCAAAA
*
652416 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
652435 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
652449 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
652468 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* * *
652482 TCTCGTTGCGATTGTCATA
1 TCGCGTTGCGATTTTCATT
652501 TCGCGTTGCGATT
1 TCGCGTTGCGATT
652514 CTCTCGTTGC
Statistics
Matches: 63, Mismatches: 6, Indels: 20
0.71 0.07 0.22
Matches are distributed among these distances:
14 20 0.32
16 5 0.08
17 6 0.10
19 32 0.51
ACGTcount: A:0.11, C:0.23, G:0.22, T:0.43
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:652457 original size:14 final size:14
Alignment explanation
Indices: 652438--652527 Score: 72
Period size: 14 Copynumber: 5.7 Consensus size: 14
652428 TTTCATTTCG
652438 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
652452 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
652471 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
652485 CGTTGCGATTGTCATATCG
1 CGTTGCGA-T-TC---TCT
652504 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
652518 CGTTGCGATT
1 CGTTGCGATT
652528 TTCATTTCAA
Statistics
Matches: 62, Mismatches: 4, Indels: 20
0.72 0.05 0.23
Matches are distributed among these distances:
14 30 0.48
15 1 0.02
16 5 0.08
17 5 0.08
18 1 0.02
19 20 0.32
ACGTcount: A:0.10, C:0.24, G:0.23, T:0.42
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:652463 original size:33 final size:33
Alignment explanation
Indices: 652421--652535 Score: 212
Period size: 33 Copynumber: 3.5 Consensus size: 33
652411 CAAAATCGCA
652421 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
652454 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
* *
652487 TTGCGATTGTCATATCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
652520 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
652536 AACCAAAAGA
Statistics
Matches: 78, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 78 1.00
ACGTcount: A:0.10, C:0.23, G:0.21, T:0.45
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
Found at i:654392 original size:93 final size:93
Alignment explanation
Indices: 654233--654799 Score: 1107
Period size: 93 Copynumber: 6.1 Consensus size: 93
654223 TAGATTGCTT
*
654233 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
654298 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
654326 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
654391 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
654419 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
654484 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
654512 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
654577 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
*
654605 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTATAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
654670 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
*
654698 AGTAAATTTGTTCGGTTGTTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
654763 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
654791 AGTAAATTT
1 AGTAAATTT
654800 ATCCATTCAA
Statistics
Matches: 470, Mismatches: 4, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
93 470 1.00
ACGTcount: A:0.22, C:0.13, G:0.19, T:0.46
Consensus pattern (93 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:654883 original size:19 final size:19
Alignment explanation
Indices: 654843--654971 Score: 125
Period size: 19 Copynumber: 7.3 Consensus size: 19
654833 TAGTTTACTT
* *
654843 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAAC-CAAAA
654863 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
**
654882 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAACCAAAA
*
654901 TCGCAA--CG--A-CAGAA
1 TCGCAACGCGAAACCAAAA
654915 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
*
654934 TCGCAA--CG--A-CAAGA
1 TCGCAACGCGAAACCAAAA
654948 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
654967 TCGCA
1 TCGCA
654972 TTGCGATTTT
Statistics
Matches: 90, Mismatches: 9, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 19 0.21
15 2 0.02
16 4 0.04
17 4 0.04
18 2 0.02
19 46 0.51
20 13 0.14
ACGTcount: A:0.46, C:0.29, G:0.17, T:0.09
Consensus pattern (19 bp):
TCGCAACGCGAAACCAAAA
Found at i:654922 original size:33 final size:32
Alignment explanation
Indices: 654879--654971 Score: 150
Period size: 33 Copynumber: 2.8 Consensus size: 32
654869 CGCGAAACCA
**
654879 AAATCGCAACGCGAAATGAAAATCGCAACGAC
1 AAATCGCAACGCGAAACCAAAATCGCAACGAC
654911 AGAATCGCAACGCGAAACCAAAATCGCAACGAC
1 A-AATCGCAACGCGAAACCAAAATCGCAACGAC
654944 AAGATCGCAACGCGAAACCAAAATCGCA
1 AA-ATCGCAACGCGAAACCAAAATCGCA
654972 TTGCGATTTT
Statistics
Matches: 57, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
32 2 0.04
33 55 0.96
ACGTcount: A:0.46, C:0.28, G:0.18, T:0.08
Consensus pattern (32 bp):
AAATCGCAACGCGAAACCAAAATCGCAACGAC
Found at i:654969 original size:52 final size:52
Alignment explanation
Indices: 654843--654971 Score: 140
Period size: 52 Copynumber: 2.5 Consensus size: 52
654833 TAGTTTACTT
**
654843 TCGCAACACGAAACTTAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
1 TCGCAACACGAAACACAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
* * *
654895 T-G-AAAATCGCAACGACAGAATCGCAACGCGAAACCAAAATCGCAACGAC-AAGA
1 TCGCAACA-CGAAAC-ACAAAATCGCAACGCGAAACCAAAATCGCAACG-CGAA-A
*
654948 TCGCAACGCGAAAC-CAAAATCGCA
1 TCGCAACACGAAACACAAAATCGCA
654972 TTGCGATTTT
Statistics
Matches: 62, Mismatches: 9, Indels: 12
0.75 0.11 0.14
Matches are distributed among these distances:
50 3 0.05
51 6 0.10
52 42 0.68
53 3 0.05
54 6 0.10
55 2 0.03
ACGTcount: A:0.46, C:0.29, G:0.17, T:0.09
Consensus pattern (52 bp):
TCGCAACACGAAACACAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
Found at i:654989 original size:19 final size:19
Alignment explanation
Indices: 654967--655101 Score: 128
Period size: 19 Copynumber: 7.6 Consensus size: 19
654957 GAAACCAAAA
*
654967 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
654986 TCGCGTTGCGA--TTC-TT
1 TCGCGTTGCGATTTTCATT
655002 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
* *
655019 TCGCATTGCGA--TTC-TG
1 TCGCGTTGCGATTTTCATT
655035 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
**
655052 TCGCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTCATT
*
655071 TCGCGTTGCGATTTTAAGTT
1 TCGCGTTGCGATTTTCA-TT
*
655091 TCGTGTTGCGA
1 TCGCGTTGCGA
655102 AAGTAAACTA
Statistics
Matches: 95, Mismatches: 10, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 15 0.16
16 11 0.12
17 11 0.12
19 46 0.48
20 12 0.13
ACGTcount: A:0.11, C:0.19, G:0.24, T:0.46
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:655008 original size:14 final size:14
Alignment explanation
Indices: 654989--655045 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
654979 TTTCATTTCG
654989 CGTTGCGATTCTTT
1 CGTTGCGATTCTTT
655003 CGTTGCGATTTTCATTT
1 CGTTGCGA--TTC-TTT
*
655020 CGCATTGCGATTCTGT
1 CG--TTGCGATTCTTT
655036 CGTTGCGATT
1 CGTTGCGATT
655046 TTCATTTCGC
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 16 0.43
16 7 0.19
17 8 0.22
19 6 0.16
ACGTcount: A:0.11, C:0.21, G:0.23, T:0.46
Consensus pattern (14 bp):
CGTTGCGATTCTTT
Found at i:655014 original size:33 final size:33
Alignment explanation
Indices: 654972--655064 Score: 168
Period size: 33 Copynumber: 2.8 Consensus size: 33
654962 CAAAATCGCA
*
654972 TTGCGATTTTCATTTCGCGTTGCGATTCTTTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
*
655005 TTGCGATTTTCATTTCGCATTGCGATTCTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
655038 TTGCGATTTTCATTTCGCGTTGCGATT
1 TTGCGATTTTCATTTCGCGTTGCGATT
655065 TTGGTTTCGC
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 57 1.00
ACGTcount: A:0.11, C:0.20, G:0.22, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
Found at i:657045 original size:14 final size:14
Alignment explanation
Indices: 657026--657061 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
657016 ATTGTTTAAT
657026 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
657040 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
657054 TGATTTGT
1 TGATTTGT
657062 GTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.22, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:657192 original size:19 final size:19
Alignment explanation
Indices: 657168--657265 Score: 134
Period size: 19 Copynumber: 5.4 Consensus size: 19
657158 AAAATTGACT
657168 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
657187 ATCGCAATGCGAAATAAAA
1 ATCGCAATGCGAAATGAAA
*
657206 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
657220 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
657239 ATCGCAATGCGGAAATGAAA
1 ATCGCAATGC-GAAATGAAA
657259 ATCGCAA
1 ATCGCAA
657266 CGAGAGAATC
Statistics
Matches: 69, Mismatches: 4, Indels: 11
0.82 0.05 0.13
Matches are distributed among these distances:
14 9 0.13
15 1 0.01
16 2 0.03
17 2 0.03
18 1 0.01
19 38 0.55
20 16 0.23
ACGTcount: A:0.47, C:0.17, G:0.21, T:0.14
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:657297 original size:53 final size:53
Alignment explanation
Indices: 657168--657284 Score: 218
Period size: 53 Copynumber: 2.2 Consensus size: 53
657158 AAAATTGACT
657168 ATCGCAATGCGAAATGAAAATCGCAATGC-GAAATAAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATAAAAATCGCAACGAGAGA
*
657220 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATAAAAATCGCAACGAGAGA
657273 ATCGCAATGCGA
1 ATCGCAATGCGA
657285 TTTTCATTTC
Statistics
Matches: 63, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
52 29 0.46
53 34 0.54
ACGTcount: A:0.45, C:0.18, G:0.23, T:0.14
Consensus pattern (53 bp):
ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATAAAAATCGCAACGAGAGA
Found at i:659619 original size:12 final size:12
Alignment explanation
Indices: 659602--659626 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
659592 TCTTCGGGGA
659602 CTTTTTCTTCTT
1 CTTTTTCTTCTT
659614 CTTTTTCTTCTT
1 CTTTTTCTTCTT
659626 C
1 C
659627 AGGATTATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:659835 original size:24 final size:24
Alignment explanation
Indices: 659801--659847 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
659791 CTGAAACATC
659801 ATCAAAATCCGTG-TATTGACCAAT
1 ATCAAAATCCG-GATATTGACCAAT
*
659825 ATCAAAGTCCGGATATTGACCAA
1 ATCAAAATCCGGATATTGACCAA
659848 GACCAAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.38, C:0.21, G:0.15, T:0.26
Consensus pattern (24 bp):
ATCAAAATCCGGATATTGACCAAT
Found at i:660558 original size:20 final size:20
Alignment explanation
Indices: 660530--660779 Score: 268
Period size: 20 Copynumber: 12.5 Consensus size: 20
660520 AAATTTCAGT
* * *
660530 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGC
**
660550 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCGC
* *
660570 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGC
**
660590 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCGC
* *
660610 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGC
*
660630 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
* *
660650 GTTGCGATATACGGATACGC
1 GTTGCGATTTACGGATTCGC
* ** *
660670 ATTGCGATTTACCCATACGC
1 GTTGCGATTTACGGATTCGC
*
660690 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
*
660710 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
*
660730 GTTGCGATTTATGTG-TTCGC
1 GTTGCGATTTACG-GATTCGC
* **
660750 GTTGCGATTTTCATATTCGC
1 GTTGCGATTTACGGATTCGC
660770 GTTGCGATTT
1 GTTGCGATTT
660780 TGGAAAATCG
Statistics
Matches: 202, Mismatches: 26, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
20 201 1.00
21 1 0.00
ACGTcount: A:0.19, C:0.19, G:0.25, T:0.37
Consensus pattern (20 bp):
GTTGCGATTTACGGATTCGC
Found at i:660796 original size:21 final size:21
Alignment explanation
Indices: 660766--660848 Score: 78
Period size: 21 Copynumber: 4.0 Consensus size: 21
660756 ATTTTCATAT
*
660766 TCGCGTTGCGATTTTGGAAAA
1 TCGCATTGCGATTTTGGAAAA
* * * **
660787 TCGCAATGCGAATTTGTACTA
1 TCGCATTGCGATTTTGGAAAA
*
660808 TCGCATTGCGATTTT-CAAGAA
1 TCGCATTGCGATTTTGGAA-AA
*
660829 TCGCGTTGCGATTTTGGAAA
1 TCGCATTGCGATTTTGGAAA
660849 CTGATTTGCG
Statistics
Matches: 47, Mismatches: 13, Indels: 4
0.73 0.20 0.06
Matches are distributed among these distances:
20 1 0.02
21 44 0.94
22 2 0.04
ACGTcount: A:0.25, C:0.17, G:0.24, T:0.34
Consensus pattern (21 bp):
TCGCATTGCGATTTTGGAAAA
Found at i:660839 original size:42 final size:43
Alignment explanation
Indices: 660746--660844 Score: 100
Period size: 42 Copynumber: 2.4 Consensus size: 43
660736 ATTTATGTGT
* *
660746 TCGCGTTGCG-ATTT-TCATATTCGCGTTGCGATTTTGGAAAA
1 TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTTTGCAAAA
**
660787 TCGCAATGCGAATTTGT-ACTA-TCGCATTGCGATTTT-CAAGAA
1 TCGCGTTGCGAATTTGTCA-TATTCGCATTGCGATTTTGCAA-AA
*
660829 TCGCGTTGCGATTTTG
1 TCGCGTTGCGAATTTG
660845 GAAACTGATT
Statistics
Matches: 47, Mismatches: 7, Indels: 7
0.77 0.11 0.11
Matches are distributed among these distances:
41 10 0.21
42 34 0.72
43 3 0.06
ACGTcount: A:0.21, C:0.18, G:0.23, T:0.37
Consensus pattern (43 bp):
TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTTTGCAAAA
Found at i:666204 original size:66 final size:66
Alignment explanation
Indices: 666127--666254 Score: 229
Period size: 66 Copynumber: 1.9 Consensus size: 66
666117 TACAGAAGTA
* * *
666127 CACAACATAATTTCGAATTTCATTTTAATATTTGATTAAATAAATATTTTAGTTTTTATTTTAGT
1 CACAACATAATTTCAAATATCATTTTAATACTTGATTAAATAAATATTTTAGTTTTTATTTTAGT
666192 G
66 G
666193 CACAACATAATTTCAAATATCATTTTAATACTTGATTAAATAAATATTTTAGTTTTTATTTT
1 CACAACATAATTTCAAATATCATTTTAATACTTGATTAAATAAATATTTTAGTTTTTATTTT
666255 CTAAAGTACT
Statistics
Matches: 59, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
66 59 1.00
ACGTcount: A:0.37, C:0.09, G:0.05, T:0.49
Consensus pattern (66 bp):
CACAACATAATTTCAAATATCATTTTAATACTTGATTAAATAAATATTTTAGTTTTTATTTTAGT
G
Found at i:668978 original size:13 final size:14
Alignment explanation
Indices: 668960--668992 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
668950 TTCGATTAAA
*
668960 AATTTTATTT-TTT
1 AATTTTATTTGATT
668973 AATTTTATTTGATT
1 AATTTTATTTGATT
668987 AATTTT
1 AATTTT
668993 TTTACTCAAG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 10 0.56
14 8 0.44
ACGTcount: A:0.27, C:0.00, G:0.03, T:0.70
Consensus pattern (14 bp):
AATTTTATTTGATT
Found at i:672701 original size:19 final size:20
Alignment explanation
Indices: 672662--672701 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
672652 TAAGTGTTAA
* *
672662 TGAATTTTAAGATTTTATAT
1 TGAAATTTAAGATTATATAT
672682 TGAAATTTAA-ATTATATAT
1 TGAAATTTAAGATTATATAT
672701 T
1 T
672702 CGATTAAATT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 9 0.50
20 9 0.50
ACGTcount: A:0.40, C:0.00, G:0.07, T:0.53
Consensus pattern (20 bp):
TGAAATTTAAGATTATATAT
Found at i:672987 original size:21 final size:21
Alignment explanation
Indices: 672935--672994 Score: 77
Period size: 22 Copynumber: 2.8 Consensus size: 21
672925 TAACAGAATG
672935 CTCAGATGGTATCGATACCCC
1 CTCAGATGGTATCGATACCCC
*
672956 CATGCA-ATGGTACCGATACCCC
1 C-T-CAGATGGTATCGATACCCC
*
672978 CTCAGGTGGTATCGATA
1 CTCAGATGGTATCGATA
672995 GCCTCAGGCA
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
20 2 0.06
21 12 0.36
22 17 0.52
23 2 0.06
ACGTcount: A:0.25, C:0.30, G:0.22, T:0.23
Consensus pattern (21 bp):
CTCAGATGGTATCGATACCCC
Found at i:676977 original size:79 final size:79
Alignment explanation
Indices: 676846--677003 Score: 298
Period size: 79 Copynumber: 2.0 Consensus size: 79
676836 GCTTCAATGA
676846 ATTCAAACTTTATCAAATAAATGTTAAAAGTACATTTTAAAATAGTTTTATAAAAGAAGAAGTGT
1 ATTCAAACTTTATCAAATAAATGTTAAAAGTACATTTTAAAATAGTTTTATAAAAGAAGAAGTGT
676911 ATGTGGAACAACCT
66 ATGTGGAACAACCT
* *
676925 ATTCAAACTTTATCAAATGAATGTTAAAAGTACATTTTAAAATGGTTTTATAAAAGAAGAAGTGT
1 ATTCAAACTTTATCAAATAAATGTTAAAAGTACATTTTAAAATAGTTTTATAAAAGAAGAAGTGT
676990 ATGTGGAACAACCT
66 ATGTGGAACAACCT
677004 CCAGGTTTTG
Statistics
Matches: 77, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
79 77 1.00
ACGTcount: A:0.44, C:0.09, G:0.14, T:0.33
Consensus pattern (79 bp):
ATTCAAACTTTATCAAATAAATGTTAAAAGTACATTTTAAAATAGTTTTATAAAAGAAGAAGTGT
ATGTGGAACAACCT
Found at i:677991 original size:15 final size:15
Alignment explanation
Indices: 677971--678000 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
677961 TAGAACTAAG
*
677971 CATATTAAAATTAGA
1 CATATTAAAAATAGA
677986 CATATTAAAAATAGA
1 CATATTAAAAATAGA
678001 GAAAGCAAGA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.57, C:0.07, G:0.07, T:0.30
Consensus pattern (15 bp):
CATATTAAAAATAGA
Found at i:680100 original size:48 final size:48
Alignment explanation
Indices: 680029--680124 Score: 192
Period size: 48 Copynumber: 2.0 Consensus size: 48
680019 GTTGATAAGG
680029 GAGGCATTGGATCAGGCAAGCATTTTAACAATTTCTTCTCCAACTTTT
1 GAGGCATTGGATCAGGCAAGCATTTTAACAATTTCTTCTCCAACTTTT
680077 GAGGCATTGGATCAGGCAAGCATTTTAACAATTTCTTCTCCAACTTTT
1 GAGGCATTGGATCAGGCAAGCATTTTAACAATTTCTTCTCCAACTTTT
680125 TCAGTTCTAT
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
48 48 1.00
ACGTcount: A:0.27, C:0.21, G:0.17, T:0.35
Consensus pattern (48 bp):
GAGGCATTGGATCAGGCAAGCATTTTAACAATTTCTTCTCCAACTTTT
Found at i:690155 original size:70 final size:70
Alignment explanation
Indices: 690035--690177 Score: 250
Period size: 70 Copynumber: 2.0 Consensus size: 70
690025 TTGATCACAG
*
690035 TAAAAGCCATTACATGTACTAATCTGCAAAATAGATCATTTATTTCGTTATTATATAAATAAAAT
1 TAAAAGCCATTACATGTACTAATCTGCAAAATAGATCAATTATTTCGTTATTATATAAATAAAAT
690100 AAAAA
66 AAAAA
* * *
690105 TAAAAGCCATTACATGTACTAATCTGCAAAATAGATCAATTCTTTTGTTATTATGTAAATAAAAT
1 TAAAAGCCATTACATGTACTAATCTGCAAAATAGATCAATTATTTCGTTATTATATAAATAAAAT
690170 AAAAA
66 AAAAA
690175 TAA
1 TAA
690178 TGACTCTGAA
Statistics
Matches: 69, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
70 69 1.00
ACGTcount: A:0.47, C:0.11, G:0.08, T:0.34
Consensus pattern (70 bp):
TAAAAGCCATTACATGTACTAATCTGCAAAATAGATCAATTATTTCGTTATTATATAAATAAAAT
AAAAA
Found at i:693719 original size:20 final size:20
Alignment explanation
Indices: 693696--693737 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
693686 AATTAGCGTT
*
693696 GCGAAAATGAAATTCACAAC
1 GCGAAAATCAAATTCACAAC
* *
693716 GCGAAAGTCAAATTCGCAAC
1 GCGAAAATCAAATTCACAAC
693736 GC
1 GC
693738 AAATAGTTAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.43, C:0.24, G:0.19, T:0.14
Consensus pattern (20 bp):
GCGAAAATCAAATTCACAAC
Found at i:693770 original size:40 final size:40
Alignment explanation
Indices: 693726--693805 Score: 133
Period size: 40 Copynumber: 2.0 Consensus size: 40
693716 GCGAAAGTCA
*
693726 AATTCGCAACGCAAATAGTTAAATCGCAACGATAATATAT
1 AATTCGCAACGCAAATAGGTAAATCGCAACGATAATATAT
* *
693766 AATTCTCAACGCGAATAGGTAAATCGCAACGATAATATAT
1 AATTCGCAACGCAAATAGGTAAATCGCAACGATAATATAT
693806 GTAAATCGTA
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
40 37 1.00
ACGTcount: A:0.44, C:0.17, G:0.14, T:0.25
Consensus pattern (40 bp):
AATTCGCAACGCAAATAGGTAAATCGCAACGATAATATAT
Found at i:693802 original size:20 final size:20
Alignment explanation
Indices: 693729--693802 Score: 69
Period size: 20 Copynumber: 3.7 Consensus size: 20
693719 AAAGTCAAAT
*
693729 TCGCAACGCA-AATAGTTAAA
1 TCGCAACG-ATAATAGATAAA
* *
693749 TCGCAACGATAATATATAAT
1 TCGCAACGATAATAGATAAA
* ** *
693769 TCTCAACGCGAATAGGTAAA
1 TCGCAACGATAATAGATAAA
693789 TCGCAACGATAATA
1 TCGCAACGATAATA
693803 TATGTAAATC
Statistics
Matches: 41, Mismatches: 12, Indels: 2
0.75 0.22 0.04
Matches are distributed among these distances:
19 1 0.02
20 40 0.98
ACGTcount: A:0.43, C:0.19, G:0.15, T:0.23
Consensus pattern (20 bp):
TCGCAACGATAATAGATAAA
Found at i:693812 original size:22 final size:21
Alignment explanation
Indices: 693740--693818 Score: 72
Period size: 20 Copynumber: 3.8 Consensus size: 21
693730 CGCAACGCAA
693740 ATAGTTAAATCGCAACGATAAT
1 ATAG-TAAATCGCAACGATAAT
* * **
693762 ATA-TAATTCTCAACGCGAAT
1 ATAGTAAATCGCAACGATAAT
*
693782 A-GGTAAATCGCAACGATAAT
1 ATAGTAAATCGCAACGATAAT
*
693802 ATATGTAAATCGTAACG
1 ATA-GTAAATCGCAACG
693819 CGAATTCTCC
Statistics
Matches: 43, Mismatches: 11, Indels: 6
0.72 0.18 0.10
Matches are distributed among these distances:
20 28 0.65
22 15 0.35
ACGTcount: A:0.43, C:0.15, G:0.15, T:0.27
Consensus pattern (21 bp):
ATAGTAAATCGCAACGATAAT
Found at i:694004 original size:20 final size:20
Alignment explanation
Indices: 693938--694012 Score: 71
Period size: 20 Copynumber: 3.7 Consensus size: 20
693928 ATTTGGAAAA
693938 TCGCAACGCGAATTTCATTT
1 TCGCAACGCGAATTTCATTT
* ***
693958 TGGCAACGCG-ATTCTCCAAAA
1 TCGCAACGCGAATT-T-CATTT
*
693979 TCGCAACGCGAATTTCGTTT
1 TCGCAACGCGAATTTCATTT
*
693999 TCGCAACGCTAATT
1 TCGCAACGCGAATT
694013 ACCTATATCG
Statistics
Matches: 42, Mismatches: 10, Indels: 6
0.72 0.17 0.10
Matches are distributed among these distances:
19 3 0.07
20 24 0.57
21 12 0.29
22 3 0.07
ACGTcount: A:0.27, C:0.27, G:0.17, T:0.29
Consensus pattern (20 bp):
TCGCAACGCGAATTTCATTT
Found at i:694458 original size:14 final size:14
Alignment explanation
Indices: 694439--694467 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
694429 AAAATTAATT
694439 ATATTTTTTGAAAA
1 ATATTTTTTGAAAA
694453 ATATTTTTTGAAAA
1 ATATTTTTTGAAAA
694467 A
1 A
694468 CGTTTTACGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.45, C:0.00, G:0.07, T:0.48
Consensus pattern (14 bp):
ATATTTTTTGAAAA
Found at i:694646 original size:20 final size:20
Alignment explanation
Indices: 694594--694646 Score: 54
Period size: 20 Copynumber: 2.5 Consensus size: 20
694584 AACTTAATAT
694594 TATTATTTTTAAAATATTAAAA
1 TATTATTTTT--AATATTAAAA
* *
694616 TAATT-TATTTAGTATTAAAA
1 T-ATTATTTTTAATATTAAAA
694636 TATTATTTTTA
1 TATTATTTTTA
694647 TAATTTTATT
Statistics
Matches: 26, Mismatches: 3, Indels: 6
0.74 0.09 0.17
Matches are distributed among these distances:
19 3 0.12
20 15 0.58
22 5 0.19
23 3 0.12
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (20 bp):
TATTATTTTTAATATTAAAA
Found at i:694674 original size:31 final size:31
Alignment explanation
Indices: 694632--694700 Score: 83
Period size: 29 Copynumber: 2.3 Consensus size: 31
694622 ATTTAGTATT
*
694632 AAAATATT-AT-TTTTATAATTTTATT-AAT-
1 AAAATATTAATATTTT-TTATTTTATTAAATA
694660 AAAATATTAATATTTTTTATTTTATTGAAATA
1 AAAATATTAATATTTTTTATTTTATT-AAATA
694692 AAAATATTA
1 AAAATATTA
694701 TAAATTATAT
Statistics
Matches: 35, Mismatches: 1, Indels: 6
0.83 0.02 0.14
Matches are distributed among these distances:
28 8 0.23
29 11 0.31
30 4 0.11
31 3 0.09
32 9 0.26
ACGTcount: A:0.46, C:0.00, G:0.01, T:0.52
Consensus pattern (31 bp):
AAAATATTAATATTTTTTATTTTATTAAATA
Found at i:694791 original size:23 final size:23
Alignment explanation
Indices: 694742--694792 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 23
694732 GTGTTATATT
**
694742 ATATTTTAAAAATATTAATTAGT
1 ATATTTTAAAAATATTAATTAAA
* * *
694765 ATATTTTAAATATCTTTATTAAA
1 ATATTTTAAAAATATTAATTAAA
694788 ATATT
1 ATATT
694793 ATTAGATTAT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.51
Consensus pattern (23 bp):
ATATTTTAAAAATATTAATTAAA
Found at i:694955 original size:23 final size:23
Alignment explanation
Indices: 694925--694975 Score: 68
Period size: 23 Copynumber: 2.2 Consensus size: 23
694915 TTAAAATAAA
694925 AATATAATAT-CTTATATTATTAT
1 AATATAAT-TGCTTATATTATTAT
* *
694948 AATATAATTGGTTATTTTATTAT
1 AATATAATTGCTTATATTATTAT
694971 AATAT
1 AATAT
694976 TGACAGGAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 1 0.04
23 24 0.96
ACGTcount: A:0.41, C:0.02, G:0.04, T:0.53
Consensus pattern (23 bp):
AATATAATTGCTTATATTATTAT
Found at i:697015 original size:3 final size:3
Alignment explanation
Indices: 697009--697045 Score: 67
Period size: 3 Copynumber: 12.7 Consensus size: 3
696999 TTTTCTTCTA
697009 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT -TT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
697046 AACTCATGAA
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.06
3 31 0.94
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
ATT
Found at i:697694 original size:17 final size:17
Alignment explanation
Indices: 697672--697722 Score: 52
Period size: 17 Copynumber: 3.0 Consensus size: 17
697662 TATTAATTAT
697672 TAATTTTTTATATTTTA
1 TAATTTTTTATATTTTA
*
697689 TAATTTTATA-ACTTTTA
1 TAATTTTTTATA-TTTTA
*
697706 T-ACTTTTTATAATTTTA
1 TAATTTTTTAT-ATTTTA
697723 AAAAATTTGT
Statistics
Matches: 28, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
16 7 0.25
17 20 0.71
18 1 0.04
ACGTcount: A:0.31, C:0.04, G:0.00, T:0.65
Consensus pattern (17 bp):
TAATTTTTTATATTTTA
Found at i:697704 original size:9 final size:8
Alignment explanation
Indices: 697677--697722 Score: 58
Period size: 8 Copynumber: 5.6 Consensus size: 8
697667 ATTATTAATT
697677 TTTTAT-A
1 TTTTATAA
697684 TTTTATAA
1 TTTTATAA
697692 TTTTATAA
1 TTTTATAA
*
697700 CTTTTATACT
1 -TTTTATA-A
697710 TTTTATAA
1 TTTTATAA
697718 TTTTA
1 TTTTA
697723 AAAAATTTGT
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
7 6 0.18
8 14 0.41
9 14 0.41
ACGTcount: A:0.30, C:0.04, G:0.00, T:0.65
Consensus pattern (8 bp):
TTTTATAA
Found at i:717796 original size:37 final size:36
Alignment explanation
Indices: 717721--717796 Score: 100
Period size: 36 Copynumber: 2.1 Consensus size: 36
717711 TTTTTATATT
*
717721 TTTAATTTTGTAAAAAAATTATATAAATATTATGAA
1 TTTAATTTTGTAAAAAAATTATATAAATATTATCAA
* *
717757 TTTAATTTTTTAAAGAAAA-TATATAAATATTTTACAA
1 TTTAATTTTGTAAA-AAAATTATATAAATATTAT-CAA
717794 TTT
1 TTT
717797 GTAATATTAT
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
36 26 0.74
37 9 0.26
ACGTcount: A:0.47, C:0.01, G:0.04, T:0.47
Consensus pattern (36 bp):
TTTAATTTTGTAAAAAAATTATATAAATATTATCAA
Found at i:725030 original size:30 final size:31
Alignment explanation
Indices: 724996--725056 Score: 97
Period size: 31 Copynumber: 2.0 Consensus size: 31
724986 AAACTTTGAA
* *
724996 TAAATTTAATT-AAGTCCAAAAATCATTTTG
1 TAAATTCAATTCAAGTCCAAAAACCATTTTG
725026 TAAATTCAATTCAAGTCCAAAAACCATTTTG
1 TAAATTCAATTCAAGTCCAAAAACCATTTTG
725057 CCTTAAATTG
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
30 10 0.36
31 18 0.64
ACGTcount: A:0.43, C:0.15, G:0.07, T:0.36
Consensus pattern (31 bp):
TAAATTCAATTCAAGTCCAAAAACCATTTTG
Found at i:727782 original size:20 final size:20
Alignment explanation
Indices: 727757--727803 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
727747 TTGGTACATG
*
727757 GATGCACAGCAGGATGCATC
1 GATGCACAACAGGATGCATC
* *
727777 GATGCACAATAGGATGTATC
1 GATGCACAACAGGATGCATC
727797 GATGCAC
1 GATGCAC
727804 TAAGTGCATT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.32, C:0.21, G:0.28, T:0.19
Consensus pattern (20 bp):
GATGCACAACAGGATGCATC
Found at i:728015 original size:30 final size:31
Alignment explanation
Indices: 727981--728041 Score: 115
Period size: 31 Copynumber: 2.0 Consensus size: 31
727971 AAACTTTGAA
727981 TAAATTCAATT-AAGTCCAAAAACCATTTTG
1 TAAATTCAATTCAAGTCCAAAAACCATTTTG
728011 TAAATTCAATTCAAGTCCAAAAACCATTTTG
1 TAAATTCAATTCAAGTCCAAAAACCATTTTG
728042 CCTTAAATTG
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
30 11 0.37
31 19 0.63
ACGTcount: A:0.43, C:0.18, G:0.07, T:0.33
Consensus pattern (31 bp):
TAAATTCAATTCAAGTCCAAAAACCATTTTG
Found at i:729930 original size:12 final size:13
Alignment explanation
Indices: 729905--729933 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
729895 TCAATATTGT
729905 TTTAAAAGAATAG
1 TTTAAAAGAATAG
729918 TTTAAAA-AATAG
1 TTTAAAAGAATAG
729930 TTTA
1 TTTA
729934 TTTAAAAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 9 0.56
13 7 0.44
ACGTcount: A:0.52, C:0.00, G:0.10, T:0.38
Consensus pattern (13 bp):
TTTAAAAGAATAG
Done.