Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold234
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: 616507
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32
File 4 of 5
Found at i:440775 original size:165 final size:165
Alignment explanation
Indices: 440603--441274 Score: 496
Period size: 165 Copynumber: 4.1 Consensus size: 165
440593 CTTTTAATTC
* * * * * * *
440603 TAAAATTCTTTAAATATTATCATTTAA-TCACCATAAAATTAGTTTTGAAAAATTCTTTTTATTT
1 TAAAATTCATCAAATATTATTATTTAATTCA-TATAAAATTAGTTTTCAAAAATTC-ATTCATTT
* *
440667 T-ATGA-CTTGATAATTTCTT-TTGAAATTTCTCCTATTTTCAAAATAC-AGAGTTTTCTACTTC
64 TCATGAGCTTGATAATTTCTTCTTAAAATTT-T-CTATTTTCAAAATACGA-AGTTTTCTACTCC
* * **
440728 ATAAGTTTTTTTGGGAGGATTTTTATT-GATCTAAAATTTT
126 ATAAATGTTTTCAGGAGGATTTTTATTAG-TCTAAAATTTT
* * *
440768 TAAAATTCATCAAATATTATTATTTAATTCATATTAAATCAGGTTTCAAAAATTCATTCATTTTC
1 TAAAATTCATCAAATATTATTATTTAATTCATATAAAATTAGTTTTCAAAAATTCATTCATTTTC
* ** * * *
440833 ATGAGTTTTTTAATTTTTTCTTAAAATTTTTTATTTTCAAAATACGAAGTTTTCTACTCCGTAAA
66 ATGAGCTTGATAATTTCTTCTTAAAATTTTCTATTTTCAAAATACGAAGTTTTCTACTCCATAAA
* * **
440898 TGTTTTCAGGAGGATTTTTCTTAGTTTTTAATTTT
131 TGTTTTCAGGAGGATTTTTATTAGTCTAAAATTTT
* * *
440933 TAAAATTCATCAAATATTATTACTTAATTCATATCAAATTAGTTTTTAAAAATTCATTCATTTTC
1 TAAAATTCATCAAATATTATTATTTAATTCATATAAAATTAGTTTTCAAAAATTCATTCATTTTC
* ** * * * * * *
440998 ATAAG-TTTTTCATTTTTTTCTTAAAATTTCCTA-TTTCTGAAATAC-AGAGTTTTCTACCCCGT
66 ATGAGCTTGAT-AATTTCTTCTTAAAATTTTCTATTTTC-AAAATACGA-AGTTTTCTACTCCAT
* * * * * * **
441060 AAAT-ATGTC-GAAGGATTTTTTTTTGGTTTTTAATTTT
128 AAATGTTTTCAGGAGGA-TTTTTATTAGTCTAAAATTTT
* * * * *
441097 TAAAATTCATCAAATA-TATTTATTTTATTCATATTAAATAATTTTTCAAAAAAATTCATTTATT
1 TAAAATTCATCAAATATTA-TTATTTAATTCATATAAAATTAGTTTTC--AAAAATTCATTCATT
* * * *
441161 TTCATGAG-TT-TTGAATTT-TTCTTTGAAATTTCTCTATTTTTGAAAA-ATCG-AGTTTTCTAT
63 TTCATGAGCTTGAT-AATTTCTTC-TTAAAATTT-TCTA-TTTTCAAAATA-CGAAGTTTTCTAC
* * * * * * * *
441221 TCCATAGATGTTCTCTGGGGGATTTTTCTCAATTTAAAATTTT
123 TCCATAAATGTTTTCAGGAGGATTTTTATTAGTCTAAAATTTT
441264 TAAAATTCATC
1 TAAAATTCATC
441275 TAACATTTTC
Statistics
Matches: 416, Mismatches: 70, Indels: 40
0.79 0.13 0.08
Matches are distributed among these distances:
163 7 0.02
164 80 0.19
165 223 0.54
166 58 0.14
167 41 0.10
168 7 0.02
ACGTcount: A:0.32, C:0.11, G:0.08, T:0.49
Consensus pattern (165 bp):
TAAAATTCATCAAATATTATTATTTAATTCATATAAAATTAGTTTTCAAAAATTCATTCATTTTC
ATGAGCTTGATAATTTCTTCTTAAAATTTTCTATTTTCAAAATACGAAGTTTTCTACTCCATAAA
TGTTTTCAGGAGGATTTTTATTAGTCTAAAATTTT
Found at i:441130 original size:164 final size:163
Alignment explanation
Indices: 440762--441219 Score: 550
Period size: 165 Copynumber: 2.8 Consensus size: 163
440752 ATTGATCTAA
* * *
440762 AATTTTTAAAATTCATCAAATATTATTATTTAATTCATATTAAATCAGGTTTCAAAAATTCATTC
1 AATTTTTAAAATTCATCAAATATTATTATTTAATTCATATTAAATTAGTTTTTAAAAATTCATTC
** * *
440827 ATTTTCATGAGTTTTTTAA-TTTTTTCTTAAAATTTTTTATTTTCAAAATACGAAGTTTTCTACT
66 ATTTTCATGAG-TTTTTAATTTTTTTCTTAAAATTTCCTATTTT-GAAATACG-AGTTTTCTACC
* * *
440891 CCGTAAATGTTTTCAGGAGGATTTTTCTTAGTTTTT
128 CCGTAAATGATGTCAGAAGGATTTTTCTTAGTTTTT
* *
440927 AATTTTTAAAATTCATCAAATATTATTACTTAATTCATATCAAATTAGTTTTTAAAAATTCATTC
1 AATTTTTAAAATTCATCAAATATTATTATTTAATTCATATTAAATTAGTTTTTAAAAATTCATTC
* *
440992 ATTTTCATAAGTTTTTCATTTTTTTCTTAAAATTTCCTATTTCTGAAATACAGAGTTTTCTACCC
66 ATTTTCATGAGTTTTTAATTTTTTTCTTAAAATTTCCTATTT-TGAAATAC-GAGTTTTCTACCC
* *
441057 CGTAAAT-ATGTC-GAAGGATTTTTTTTTGGTTTTT
129 CGTAAATGATGTCAGAAGGA-TTTTTCTTAGTTTTT
* *
441091 AATTTTTAAAATTCATCAAATA-TATTTATTTTATTCATATTAAA-TAATTTTTCAAAAAAATTC
1 AATTTTTAAAATTCATCAAATATTA-TTATTTAATTCATATTAAATTAGTTTTT---AAAAATTC
* * * * *
441154 ATTTATTTTCATGAGTTTTGAATTTTTCT-TTGAAATTTCTCTATTTTTGAAAAATCGAGTTTTC
62 ATTCATTTTCATGAGTTTTTAATTTTTTTCTTAAAATTTC-CTA-TTTTGAAATA-CGAGTTTTC
441218 TA
124 TA
441220 TTCCATAGAT
Statistics
Matches: 255, Mismatches: 27, Indels: 21
0.84 0.09 0.07
Matches are distributed among these distances:
163 14 0.05
164 60 0.24
165 124 0.49
166 53 0.21
167 4 0.02
ACGTcount: A:0.32, C:0.10, G:0.07, T:0.50
Consensus pattern (163 bp):
AATTTTTAAAATTCATCAAATATTATTATTTAATTCATATTAAATTAGTTTTTAAAAATTCATTC
ATTTTCATGAGTTTTTAATTTTTTTCTTAAAATTTCCTATTTTGAAATACGAGTTTTCTACCCCG
TAAATGATGTCAGAAGGATTTTTCTTAGTTTTT
Found at i:441817 original size:14 final size:14
Alignment explanation
Indices: 441798--441824 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
441788 GCAAGTGAGG
441798 AAAAAAAAGAGAAA
1 AAAAAAAAGAGAAA
441812 AAAAAAAAGAGAA
1 AAAAAAAAGAGAA
441825 GAAGAAAGAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (14 bp):
AAAAAAAAGAGAAA
Found at i:442715 original size:16 final size:15
Alignment explanation
Indices: 442696--442725 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
442686 AATGTAAAAT
442696 TAAATAAATTAAATAA
1 TAAATAAA-TAAATAA
442712 TAAATAAATAAATA
1 TAAATAAATAAATA
442726 TTCTTATCAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (15 bp):
TAAATAAATAAATAA
Found at i:447053 original size:20 final size:19
Alignment explanation
Indices: 447026--447080 Score: 83
Period size: 20 Copynumber: 2.8 Consensus size: 19
447016 TCAAAAACTT
*
447026 AGAATGTATCGATACAATG
1 AGAATGTATCGATACAATA
447045 AGAAATGTATCGATACAATA
1 AG-AATGTATCGATACAATA
*
447065 AGTATGTATCGATACA
1 AGAATGTATCGATACA
447081 TTTACTTATA
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
19 15 0.45
20 18 0.55
ACGTcount: A:0.44, C:0.11, G:0.18, T:0.27
Consensus pattern (19 bp):
AGAATGTATCGATACAATA
Found at i:447174 original size:21 final size:20
Alignment explanation
Indices: 447125--447178 Score: 72
Period size: 20 Copynumber: 2.6 Consensus size: 20
447115 TGTAGGGTGG
447125 TTTTGTATCGATACATTCAC
1 TTTTGTATCGATACATTCAC
** *
447145 TCATGTATCGATACATTTAC
1 TTTTGTATCGATACATTCAC
447165 TGTTTGTATCGATA
1 T-TTTGTATCGATA
447179 TAATTTGTTG
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
20 18 0.64
21 10 0.36
ACGTcount: A:0.26, C:0.17, G:0.13, T:0.44
Consensus pattern (20 bp):
TTTTGTATCGATACATTCAC
Found at i:449707 original size:18 final size:19
Alignment explanation
Indices: 449669--449710 Score: 68
Period size: 19 Copynumber: 2.3 Consensus size: 19
449659 GTATGAGAGA
449669 GAAAATAAGATTTTAAAAG
1 GAAAATAAGATTTTAAAAG
*
449688 GAAAATAAGGTTTT-AAAG
1 GAAAATAAGATTTTAAAAG
449706 GAAAA
1 GAAAA
449711 GAAAATAAAG
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
18 9 0.41
19 13 0.59
ACGTcount: A:0.57, C:0.00, G:0.19, T:0.24
Consensus pattern (19 bp):
GAAAATAAGATTTTAAAAG
Found at i:449715 original size:23 final size:24
Alignment explanation
Indices: 449683--449728 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 24
449673 ATAAGATTTT
* *
449683 AAAAGGAAAATAAGGTTTTAAAGG
1 AAAAGGAAAATAAAGTTTCAAAGG
449707 AAAA-GAAAATAAAGTTTCAAAG
1 AAAAGGAAAATAAAGTTTCAAAG
449729 CTTTAAAATA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 16 0.80
24 4 0.20
ACGTcount: A:0.59, C:0.02, G:0.20, T:0.20
Consensus pattern (24 bp):
AAAAGGAAAATAAAGTTTCAAAGG
Found at i:453817 original size:166 final size:165
Alignment explanation
Indices: 453364--453942 Score: 494
Period size: 165 Copynumber: 3.5 Consensus size: 165
453354 TTTAAACATC
* * ** ***
453364 AAAATTCTTCAAATATTATTATTTAATTCT-CATCAAATCAGTTTCAAAAAATTTCTTTTATTTT
1 AAAATTCATCAAATATTATTATTTAATT-TACATTAAATCAGTTTTGAAAAA-TTAAATTATTTT
* * * * * * * **
453428 -TTGCGTTATTAATTTTCTT--TTGGAATTCCTCCTATTTTC-AAATTAC-GATTTTTCTTTTCC
64 CATGAGTT-TTGATTTT-TTCCTTGAAATT-CTCCTATTTTCGAAA-AACAAAATTTTCTACTCC
* * * *
453488 GTAAATTTTTTTGGGAGGA-TTTTCATAAGTTTAAAATTTTT
125 ATAAATGTTTTTAGGAGGATTTTTC-TCAGTTTAAAATTTTT
* ** * * * * * * *
453529 AAAATTCATCAAATATTATTATTTAATTCATGTTGAATCAGTTTTCAAGAATTCACTCATCTTCA
1 AAAATTCATCAAATATTATTATTTAATTTACATTAAATCAGTTTTGAAAAATTAAATTATTTTCA
* * ** * *
453594 TGAGTTTTTGATTTTTTCCTTGAAATTCTCCTATTTTTGAAATACGGAGTTTTCTACTCCGTAAA
66 TGAG-TTTTGATTTTTTCCTTGAAATTCTCCTATTTTCGAAAAACAAAATTTTCTACTCCATAAA
** **
453659 TGTTTTTGAGG-GAGATTTTTCTTGGTTTTTAATTTTT
130 TGTTTTT-AGGAG-GATTTTTCTCAGTTTAAAATTTTT
* * * *
453696 AAAATTCATCAAATATTATCATTTGATTTACATTAAATTAGTTTTGAAAAATTAATTTATTTTCA
1 AAAATTCATCAAATATTATTATTTAATTTACATTAAATCAGTTTTGAAAAATTAAATTATTTTCA
* *
453761 TGAGTTTTGATTTTTT-CTTCGAAATTTTTCTATTTTCGAAAAACAAAATTTTCTACTCCATAAA
66 TGAGTTTTGATTTTTTCCTT-GAAATTCTCCTATTTTCGAAAAACAAAATTTTCTACTCCATAAA
453825 TGTTTTTAGGAGGATTTTTCTCAGTTTAAAATTTTT
130 TGTTTTTAGGAGGATTTTTCTCAGTTTAAAATTTTT
* * * * * *
453861 AAAATTTATCTAATATTGTTATTAAATTTCCATTAAATCAGCTTTGAAAAATTTAAATTA-TTTC
1 AAAATTCATCAAATATTATTATTTAATTTACATTAAATCAGTTTTGAAAAA-TTAAATTATTTTC
*
453925 ATGAATTTTGAATTTTTT
65 ATGAGTTTTG-ATTTTTT
453943 TGTATATATT
Statistics
Matches: 337, Mismatches: 63, Indels: 27
0.79 0.15 0.06
Matches are distributed among these distances:
164 10 0.03
165 145 0.43
166 105 0.31
167 72 0.21
168 5 0.01
ACGTcount: A:0.31, C:0.11, G:0.09, T:0.49
Consensus pattern (165 bp):
AAAATTCATCAAATATTATTATTTAATTTACATTAAATCAGTTTTGAAAAATTAAATTATTTTCA
TGAGTTTTGATTTTTTCCTTGAAATTCTCCTATTTTCGAAAAACAAAATTTTCTACTCCATAAAT
GTTTTTAGGAGGATTTTTCTCAGTTTAAAATTTTT
Found at i:454337 original size:17 final size:17
Alignment explanation
Indices: 454295--454330 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
454285 AAATGTGGTG
*
454295 AAAGGAAAT-AAAATGA
1 AAAGAAAATGAAAATGA
454311 AAAGAAAATGAAAATGA
1 AAAGAAAATGAAAATGA
454328 AAA
1 AAA
454331 AGCAATGGCA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 8 0.44
17 10 0.56
ACGTcount: A:0.72, C:0.00, G:0.17, T:0.11
Consensus pattern (17 bp):
AAAGAAAATGAAAATGA
Found at i:454452 original size:21 final size:21
Alignment explanation
Indices: 454426--454489 Score: 67
Period size: 21 Copynumber: 3.0 Consensus size: 21
454416 AGCTTCAGCT
* *
454426 AGAAAAAGAGAAAAAAAGGAA
1 AGAAAAAGAAAAAAAAAGAAA
*
454447 AGAAAAA-AATAAAGAAAGAAA
1 AGAAAAAGAA-AAAAAAAGAAA
* *
454468 AGAAAGAGAAAAAAAAACAAA
1 AGAAAAAGAAAAAAAAAGAAA
454489 A
1 A
454490 ACTAAGAAAA
Statistics
Matches: 35, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
20 1 0.03
21 32 0.91
22 2 0.06
ACGTcount: A:0.80, C:0.02, G:0.17, T:0.02
Consensus pattern (21 bp):
AGAAAAAGAAAAAAAAAGAAA
Found at i:454454 original size:12 final size:12
Alignment explanation
Indices: 454434--454490 Score: 62
Period size: 13 Copynumber: 4.6 Consensus size: 12
454424 CTAGAAAAAG
454434 AGAAAAAAAGGAA
1 AGAAAAAAA-GAA
*
454447 AGAAAAAAATAA
1 AGAAAAAAAGAA
454459 AGAAAGAAAAGAA
1 AGAAA-AAAAGAA
454472 AGAGAAAAAA-AA
1 AGA-AAAAAAGAA
*
454484 ACAAAAA
1 AGAAAAA
454491 CTAAGAAAAT
Statistics
Matches: 39, Mismatches: 3, Indels: 6
0.81 0.06 0.12
Matches are distributed among these distances:
11 4 0.10
12 11 0.28
13 22 0.56
14 2 0.05
ACGTcount: A:0.81, C:0.02, G:0.16, T:0.02
Consensus pattern (12 bp):
AGAAAAAAAGAA
Found at i:454454 original size:15 final size:16
Alignment explanation
Indices: 454430--454468 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
454420 TCAGCTAGAA
* *
454430 AAAGAGAAAAA-AAGG
1 AAAGAAAAAAATAAAG
454445 AAAGAAAAAAATAAAG
1 AAAGAAAAAAATAAAG
454461 AAAGAAAA
1 AAAGAAAA
454469 GAAAGAGAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 10 0.48
16 11 0.52
ACGTcount: A:0.79, C:0.00, G:0.18, T:0.03
Consensus pattern (16 bp):
AAAGAAAAAAATAAAG
Found at i:454463 original size:16 final size:15
Alignment explanation
Indices: 454430--454489 Score: 59
Period size: 15 Copynumber: 3.9 Consensus size: 15
454420 TCAGCTAGAA
* *
454430 AAAGAGAAAAAAAGG
1 AAAGAAAAAAAAAAG
454445 AAAGAAAAAAATAAAG
1 AAAGAAAAAAA-AAAG
* *
454461 AAAGAAAAGAAAGAG
1 AAAGAAAAAAAAAAG
454476 AAA-AAAAAACAAAA
1 AAAGAAAAAA-AAAA
454490 ACTAAGAAAA
Statistics
Matches: 37, Mismatches: 6, Indels: 4
0.79 0.13 0.09
Matches are distributed among these distances:
14 5 0.14
15 19 0.51
16 13 0.35
ACGTcount: A:0.80, C:0.02, G:0.17, T:0.02
Consensus pattern (15 bp):
AAAGAAAAAAAAAAG
Found at i:454463 original size:25 final size:24
Alignment explanation
Indices: 454428--454490 Score: 74
Period size: 25 Copynumber: 2.5 Consensus size: 24
454418 CTTCAGCTAG
*
454428 AAAAAGAGAAAAAAAGGAAAGA-AA
1 AAAAAAAGAAAAAAA-GAAAGAGAA
454452 AAAATAAAGAAAGAAAAGAAAGAGAA
1 AAAA-AAAGAAA-AAAAGAAAGAGAA
*
454478 AAAAAAACAAAAA
1 AAAAAAAGAAAAA
454491 CTAAGAAAAT
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
24 6 0.18
25 18 0.53
26 10 0.29
ACGTcount: A:0.81, C:0.02, G:0.16, T:0.02
Consensus pattern (24 bp):
AAAAAAAGAAAAAAAGAAAGAGAA
Found at i:454468 original size:27 final size:27
Alignment explanation
Indices: 454430--454482 Score: 65
Period size: 27 Copynumber: 2.0 Consensus size: 27
454420 TCAGCTAGAA
*
454430 AAAGAGAAAAAAAGGAA-AGAAAAAAAT
1 AAAGAG-AAAAAAGAAAGAGAAAAAAAT
454457 AAAGA-AAGAAAAGAAAGAGAAAAAAA
1 AAAGAGAA-AAAAGAAAGAGAAAAAAA
454483 AACAAAAACT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
25 2 0.09
26 7 0.30
27 14 0.61
ACGTcount: A:0.79, C:0.00, G:0.19, T:0.02
Consensus pattern (27 bp):
AAAGAGAAAAAAGAAAGAGAAAAAAAT
Found at i:455866 original size:3 final size:3
Alignment explanation
Indices: 455860--455898 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
455850 TCTATCCTAC
455860 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
455899 AGATTTTTTT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:457532 original size:17 final size:17
Alignment explanation
Indices: 457507--457539 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
457497 TAAGAAACCA
*
457507 AAGTTTGCATAAAAATT
1 AAGTATGCATAAAAATT
457524 AAGTATGCATAAAAAT
1 AAGTATGCATAAAAAT
457540 CCTAAATACA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.52, C:0.06, G:0.12, T:0.30
Consensus pattern (17 bp):
AAGTATGCATAAAAATT
Found at i:459750 original size:24 final size:24
Alignment explanation
Indices: 459705--459750 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
459695 AAAATTAAAA
**
459705 TTTTTATATTTAAATATTATTTAT
1 TTTTTATATTTAAATAAAATTTAT
*
459729 TTTTTATATTTTAATAAAATTT
1 TTTTTATATTTAAATAAAATTT
459751 CAATTAAATT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (24 bp):
TTTTTATATTTAAATAAAATTTAT
Found at i:460084 original size:17 final size:17
Alignment explanation
Indices: 460032--460099 Score: 70
Period size: 17 Copynumber: 4.2 Consensus size: 17
460022 CTTGAAACTT
*
460032 AAATAATTTAAAT-TTA
1 AAATAATTCAAATCTTA
* *
460048 AAATAACTCGAATC--A
1 AAATAATTCAAATCTTA
460063 AAATAATTCAAATCTTA
1 AAATAATTCAAATCTTA
* *
460080 AAATAATCCAAATATTA
1 AAATAATTCAAATCTTA
460097 AAA
1 AAA
460100 ACTTAAATTT
Statistics
Matches: 42, Mismatches: 7, Indels: 5
0.78 0.13 0.09
Matches are distributed among these distances:
15 13 0.31
16 10 0.24
17 19 0.45
ACGTcount: A:0.57, C:0.10, G:0.01, T:0.31
Consensus pattern (17 bp):
AAATAATTCAAATCTTA
Found at i:460087 original size:26 final size:25
Alignment explanation
Indices: 460058--460106 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
460048 AAATAACTCG
* *
460058 AATCAAAATAATTCAAATCTTAAAAT
1 AATCAAAAT-ATTAAAAACTTAAAAT
*
460084 AATCCAAATATTAAAAACTTAAA
1 AATCAAAATATTAAAAACTTAAA
460107 TTTACTTATC
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
25 12 0.60
26 8 0.40
ACGTcount: A:0.59, C:0.12, G:0.00, T:0.29
Consensus pattern (25 bp):
AATCAAAATATTAAAAACTTAAAAT
Found at i:469163 original size:3 final size:3
Alignment explanation
Indices: 469155--469188 Score: 59
Period size: 3 Copynumber: 11.3 Consensus size: 3
469145 ATTAAGTGCA
*
469155 TAT TAT TAT TAT TGT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
469189 TTGCACCAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.29, C:0.00, G:0.03, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:471771 original size:2 final size:2
Alignment explanation
Indices: 471764--471789 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
471754 TGACCAATCC
471764 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
471790 TTATGATGAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:479642 original size:19 final size:19
Alignment explanation
Indices: 479618--479659 Score: 66
Period size: 19 Copynumber: 2.2 Consensus size: 19
479608 ATGCATTTTG
479618 ATGAACATGCAAGAAAATA
1 ATGAACATGCAAGAAAATA
* *
479637 ATGAACATGCAATAAAATG
1 ATGAACATGCAAGAAAATA
479656 ATGA
1 ATGA
479660 GTGATATTCA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.55, C:0.10, G:0.17, T:0.19
Consensus pattern (19 bp):
ATGAACATGCAAGAAAATA
Found at i:480990 original size:20 final size:21
Alignment explanation
Indices: 480954--481004 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 21
480944 CGATAGGGTC
* *
480954 TATCGATATATTTACTT-ATA
1 TATCGATACATTAACTTGATA
* *
480974 TATCGATACATTAACTTGTTG
1 TATCGATACATTAACTTGATA
480995 TATCGATACA
1 TATCGATACA
481005 AATTGTAAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
20 15 0.58
21 11 0.42
ACGTcount: A:0.33, C:0.14, G:0.10, T:0.43
Consensus pattern (21 bp):
TATCGATACATTAACTTGATA
Found at i:482700 original size:16 final size:16
Alignment explanation
Indices: 482679--482725 Score: 60
Period size: 16 Copynumber: 2.9 Consensus size: 16
482669 GCAGGTGTAA
482679 AATTAATTAATTTTTT
1 AATTAATTAATTTTTT
482695 AATTAATTAATTATTTT
1 AATTAATTAATT-TTTT
* *
482712 ATTTTATT-ATTTTT
1 AATTAATTAATTTTT
482726 ATTTTTATAT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
15 3 0.11
16 15 0.54
17 10 0.36
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (16 bp):
AATTAATTAATTTTTT
Found at i:486977 original size:107 final size:107
Alignment explanation
Indices: 486856--487051 Score: 270
Period size: 107 Copynumber: 1.8 Consensus size: 107
486846 ACGGGTTGGA
* * * *
486856 GTATCCCTTCGAAAACAACGGGGTTGGAGTAT-CCCTAATGGTGAGAAATCAATATTTTGGAAAT
1 GTATCCCTTCGAAAACAACAGGGTTGGAGTATCCCCT-ATAGTGAAAAATCAATATTTTAGAAAT
*
486920 AAAAATAGGGTTGGAGTATCCCCTCAGAATTGACGGGGTTTGT
65 AAAAACAGGGTTGGAGTATCCCCTCAGAATTGACGGGGTTTGT
* * *
486963 GTATCCCCTT-GAAAATAACAGGGTTGGAGTATCCCCTATAGTGAAAAATCGATGTTTTAGAAAT
1 GTAT-CCCTTCGAAAACAACAGGGTTGGAGTATCCCCTATAGTGAAAAATCAATATTTTAGAAAT
* *
487027 AAAACCGGGGTTGGAGTATCCCCTC
65 AAAAACAGGGTTGGAGTATCCCCTC
487052 GAAAATAATG
Statistics
Matches: 77, Mismatches: 10, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
107 68 0.88
108 9 0.12
ACGTcount: A:0.31, C:0.17, G:0.24, T:0.28
Consensus pattern (107 bp):
GTATCCCTTCGAAAACAACAGGGTTGGAGTATCCCCTATAGTGAAAAATCAATATTTTAGAAATA
AAAACAGGGTTGGAGTATCCCCTCAGAATTGACGGGGTTTGT
Found at i:487075 original size:107 final size:108
Alignment explanation
Indices: 486848--487076 Score: 268
Period size: 107 Copynumber: 2.1 Consensus size: 108
486838 AGATAAAAAC
* * *
486848 GGGTTGGAGTAT-CCCTTCGAAAACAACGGGGTTGGAGTATCCCTAATGGTGAGAAATCAATATT
1 GGGTTGGAGTATCCCCTTCGAAAACAACAGGGTTGGAGTATCCCTAATAGTGAAAAATCAATATT
* * * *
486912 TTGGAAATAAAAATAGGGTTGGAGTATCCCCTCAGAATTGACG
66 TTAGAAATAAAAACAGGGTTGGAGTATCCCCTCAGAAATAACG
* * * * *
486955 GGGTTTGTGTATCCCCTT-GAAAATAACAGGGTTGGAGTATCCCCT-ATAGTGAAAAATCGATGT
1 GGGTTGGAGTATCCCCTTCGAAAACAACAGGGTTGGAGTAT-CCCTAATAGTGAAAAATCAATAT
* * *
487018 TTTAGAAATAAAACCGGGGTTGGAGTATCCCCTC-GAAAATAATG
65 TTTAGAAATAAAAACAGGGTTGGAGTATCCCCTCAG-AAATAACG
*
487062 GGGTTGGAATATCCC
1 GGGTTGGAGTATCCC
487077 GATGGTGGAA
Statistics
Matches: 101, Mismatches: 18, Indels: 6
0.81 0.14 0.05
Matches are distributed among these distances:
106 1 0.01
107 91 0.90
108 9 0.09
ACGTcount: A:0.31, C:0.16, G:0.26, T:0.27
Consensus pattern (108 bp):
GGGTTGGAGTATCCCCTTCGAAAACAACAGGGTTGGAGTATCCCTAATAGTGAAAAATCAATATT
TTAGAAATAAAAACAGGGTTGGAGTATCCCCTCAGAAATAACG
Found at i:487130 original size:78 final size:79
Alignment explanation
Indices: 486953--487266 Score: 355
Period size: 79 Copynumber: 4.0 Consensus size: 79
486943 TCAGAATTGA
* * * * * *
486953 CGGGGTTTGTGTATCCCCTTGAAAATAACAGGGTTGGAGTATCCCCTATAGTGAAAAATCGATGT
1 CGGGGTTAGAGTATCCCCTCGAAAATAACAGGGTTGGAGTATCCTCGATAGTGAAAAATCGGTGT
*
487018 TTTAGAAATAAAAC
66 TTTAGAAATAAAAT
* ** * * *
487032 CGGGGTTGGAGTATCCCCTCGAAAATAATGGGGTTGGAATATCC-CGATGGTGGAAAATCGGTGT
1 CGGGGTTAGAGTATCCCCTCGAAAATAACAGGGTTGGAGTATCCTCGATAGTGAAAAATCGGTGT
*
487096 TTAAGAAATAAAAT
66 TTTAGAAATAAAAT
* * * * * * *
487110 CGGGGTTAGAATATCTCCTCGAAAATAATAGGGTTGGAGTATCCTTGATGGTGAAAAATTGGTAT
1 CGGGGTTAGAGTATCCCCTCGAAAATAACAGGGTTGGAGTATCCTCGATAGTGAAAAATCGGTGT
487175 TTTAGAAATAAAAT
66 TTTAGAAATAAAAT
* * * *
487189 TGGGGTTAGAGTATCTCTTCGAAAATAAC-GGTGTTGGAGTATCCTCGATAGTGGAAAAATC-GA
1 CGGGGTTAGAGTATCCCCTCGAAAATAACAGG-GTTGGAGTATCCTCGATAGT-GAAAAATCGGT
*
487252 GTTTTAGGAATAAAA
64 GTTTTAGAAATAAAA
487267 CATCAGTGAA
Statistics
Matches: 200, Mismatches: 32, Indels: 6
0.84 0.13 0.03
Matches are distributed among these distances:
78 69 0.34
79 124 0.62
80 7 0.04
ACGTcount: A:0.33, C:0.12, G:0.26, T:0.29
Consensus pattern (79 bp):
CGGGGTTAGAGTATCCCCTCGAAAATAACAGGGTTGGAGTATCCTCGATAGTGAAAAATCGGTGT
TTTAGAAATAAAAT
Found at i:492161 original size:89 final size:89
Alignment explanation
Indices: 492045--492739 Score: 951
Period size: 89 Copynumber: 7.8 Consensus size: 89
492035 TCTGTCGTAT
* * * * * * *
492045 CATTAGTCAAATATTTTCCGTCGTGTCAGAAGGAATATGATATCCACATGCATCTATCACATCTT
1 CATTAGTCAAATATTTTCTGTCATGTCAGAAAGAATCTGATACCCGCATGCATCTGTCACATCTT
* * *
492110 TTGGGTTCCAAAAAATTTATTAGT
66 TCGGGTTCCAAGAAATTTATTAGG
* * *
492134 CATTAGTCAAATATTTTCTGTCATGTCAGAAAGAATCTAATACCCGCATGCATTTATCACATCTT
1 CATTAGTCAAATATTTTCTGTCATGTCAGAAAGAATCTGATACCCGCATGCATCTGTCACATCTT
*
492199 TCGGGTTCCAAGAAATTTGTTAGG
66 TCGGGTTCCAAGAAATTTATTAGG
* * *
492223 CATTAGTCAAATATTTTCTGCCATGTTAGAAAGAATCTGATACCCGTATGCATCTGTCACATCTT
1 CATTAGTCAAATATTTTCTGTCATGTCAGAAAGAATCTGATACCCGCATGCATCTGTCACATCTT
* * *
492288 TTGGGTTCTAAGAAATTTATTAGT
66 TCGGGTTCCAAGAAATTTATTAGG
* *
492312 CATTAGTCAAATATTTTCTGTCGTGTTAGAAAGAATCTGATACCCGCATGCATCTGTCACATCTT
1 CATTAGTCAAATATTTTCTGTCATGTCAGAAAGAATCTGATACCCGCATGCATCTGTCACATCTT
*
492377 TCGGGTTCCAAAAAATTTATTAGG
66 TCGGGTTCCAAGAAATTTATTAGG
* * * * *
492401 CATTAGTCAAATATTTTTTGCCATGTCAGAAAGAATCTCATACCGGCATGTATCTGTCACATCTT
1 CATTAGTCAAATATTTTCTGTCATGTCAGAAAGAATCTGATACCCGCATGCATCTGTCACATCTT
* *
492466 TCGAGTTCCAAGAAATTAATTAGG
66 TCGGGTTCCAAGAAATTTATTAGG
* * * *
492490 CATTAGTCAAATATTTTCTGTCGTGTCAGAAAGAATCTAATACCCGCATGTATCTATCACATCTT
1 CATTAGTCAAATATTTTCTGTCATGTCAGAAAGAATCTGATACCCGCATGCATCTGTCACATCTT
* *
492555 TCGAGTTCTAAGAAATTTATTAGG
66 TCGGGTTCCAAGAAATTTATTAGG
* * * *
492579 CATTAGTCAAATATTTTCTATCGTGTCA-AAAGGAATATGATACTCGCATGCATCTGTCACATCT
1 CATTAGTCAAATATTTTCTGTCATGTCAGAAA-GAATCTGATACCCGCATGCATCTGTCACATCT
* *
492643 TTCGAGTTCTAAGAAATTTATTAGG
65 TTCGGGTTCCAAGAAATTTATTAGG
* * * *
492668 AATTAGTCAAATATTTTCTATCATGTCAGAAAGAATCTGATACCTGCATGCATCTGTTACATCTT
1 CATTAGTCAAATATTTTCTGTCATGTCAGAAAGAATCTGATACCCGCATGCATCTGTCACATCTT
*
492733 TTGGGTT
66 TCGGGTT
492740 AGTCAAATAT
Statistics
Matches: 543, Mismatches: 61, Indels: 4
0.89 0.10 0.01
Matches are distributed among these distances:
88 3 0.01
89 537 0.99
90 3 0.01
ACGTcount: A:0.31, C:0.18, G:0.16, T:0.36
Consensus pattern (89 bp):
CATTAGTCAAATATTTTCTGTCATGTCAGAAAGAATCTGATACCCGCATGCATCTGTCACATCTT
TCGGGTTCCAAGAAATTTATTAGG
Found at i:492779 original size:68 final size:68
Alignment explanation
Indices: 492670--492807 Score: 222
Period size: 68 Copynumber: 2.0 Consensus size: 68
492660 TTATTAGGAA
* *
492670 TTAGTCAAATATTTTCTATCATGTCAGAAAGAATCTGATACCTGCATGCATCTGTTACATCTTTT
1 TTAGTCAAATATTTTCTATCATGTCAGAAAGAATCTGATACCCGCATGCATCTGTCACATCTTTT
492735 GGG
66 GGG
* * * *
492738 TTAGTCAAATATTTTTTGTCGTGTCAGAAAGAATCTGATACCCGCATGCATCTGTCATATCTTTT
1 TTAGTCAAATATTTTCTATCATGTCAGAAAGAATCTGATACCCGCATGCATCTGTCACATCTTTT
492803 GGG
66 GGG
492806 TT
1 TT
492808 TCAAGAAATT
Statistics
Matches: 64, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
68 64 1.00
ACGTcount: A:0.26, C:0.17, G:0.17, T:0.39
Consensus pattern (68 bp):
TTAGTCAAATATTTTCTATCATGTCAGAAAGAATCTGATACCCGCATGCATCTGTCACATCTTTT
GGG
Found at i:492875 original size:157 final size:157
Alignment explanation
Indices: 492581--492896 Score: 431
Period size: 157 Copynumber: 2.0 Consensus size: 157
492571 TTATTAGGCA
*
492581 TTAGTCAAATATTTTCTATCGTGTCAAAAGGAATATGATACTCGCATGCATCTGTCACATCTTTC
1 TTAGTCAAATATTTTCTATCGTGTCAAAAGGAATATGATACCCGCATGCATCTGTCACATCTTTC
492646 GAGTTCTAAGAAATTTATTAGGAATTAGTCAAATATTTTCTATCATGTCAGAAAGAATCTGATAC
66 GAGTTCTAAGAAATTTATTAGGAATTAGTCAAATATTTTCTATCATGTCAGAAAGAATCTGATAC
** * *
492711 CTGCATGCATCTGTTACATCTTTTGGG
131 CCACATGCATCTATCACATCTTTTGGG
* * * *
492738 TTAGTCAAATATTTTTTGTCGTGTCAGAAA-GAATCTGATACCCGCATGCATCTGTCATATCTTT
1 TTAGTCAAATATTTTCTATCGTGTCA-AAAGGAATATGATACCCGCATGCATCTGTCACATCTTT
* * * * * *
492802 TGGGTT-TCAAGAAATTTATTAGGCATTAGTCAAATATTTTCTGTCGTGTCCA-TAAGAATCTGA
65 CGAGTTCT-AAGAAATTTATTAGGAATTAGTCAAATATTTTCTATCATGT-CAGAAAGAATCTGA
* *
492865 TTCCCACATGCATTTATCACATCTTTTGGG
128 TACCCACATGCATCTATCACATCTTTTGGG
492895 TT
1 TT
492897 CTAAGAAATT
Statistics
Matches: 139, Mismatches: 17, Indels: 6
0.86 0.10 0.04
Matches are distributed among these distances:
156 1 0.01
157 133 0.96
158 5 0.04
ACGTcount: A:0.28, C:0.17, G:0.16, T:0.38
Consensus pattern (157 bp):
TTAGTCAAATATTTTCTATCGTGTCAAAAGGAATATGATACCCGCATGCATCTGTCACATCTTTC
GAGTTCTAAGAAATTTATTAGGAATTAGTCAAATATTTTCTATCATGTCAGAAAGAATCTGATAC
CCACATGCATCTATCACATCTTTTGGG
Found at i:492889 original size:89 final size:89
Alignment explanation
Indices: 492738--493163 Score: 615
Period size: 89 Copynumber: 4.8 Consensus size: 89
492728 ATCTTTTGGG
* * *
492738 TTAGTCAAATATTTTTTGTCGTGTCAGAAAGAATCTGATACCCGCATGCATCTGTCATATCTTTT
1 TTAGTCAAATATTTTCTGTCGTGTCAGAAAGAATCTGATACCCGCATGCATCTGTCACATCTTTC
492803 GGGTT-TCAAGAAATTTATTAGGCA
66 GGGTTCT-AAGAAATTTATTAGGCA
* * * * *
492827 TTAGTCAAATATTTTCTGTCGTGTCCA-TAAGAATCTGATTCCCACATGCATTTATCACATCTTT
1 TTAGTCAAATATTTTCTGTCGTGT-CAGAAAGAATCTGATACCCGCATGCATCTGTCACATCTTT
*
492891 TGGGTTCTAAGAAATTTATTAGGCA
65 CGGGTTCTAAGAAATTTATTAGGCA
*
492916 TTAGTAAAATATTTTCTGTCGTGTCAGAAAGAATCTGATACCCGCATGCATCTGTCACATCTTTC
1 TTAGTCAAATATTTTCTGTCGTGTCAGAAAGAATCTGATACCCGCATGCATCTGTCACATCTTTC
*
492981 AGGTTCTAAGAAATTTATTAGGCA
66 GGGTTCTAAGAAATTTATTAGGCA
* * * *
493005 TTAGTCAAATATTTTCTATCGTGTCA-AAAGGAATATGATACTCGCATGCATCTGTCATATCTTT
1 TTAGTCAAATATTTTCTGTCGTGTCAGAAA-GAATCTGATACCCGCATGCATCTGTCACATCTTT
*
493069 CGAGTTCTAAGAAATTTATTAGGCA
65 CGGGTTCTAAGAAATTTATTAGGCA
* * * * *
493094 TTAGTCAAATATTTTCTATCATGTCAGAAATAATCTGATACCTGCATGCATCTGTTACATCTTTC
1 TTAGTCAAATATTTTCTGTCGTGTCAGAAAGAATCTGATACCCGCATGCATCTGTCACATCTTTC
493159 GGGTT
66 GGGTT
493164 AGTCAAATAT
Statistics
Matches: 302, Mismatches: 30, Indels: 10
0.88 0.09 0.03
Matches are distributed among these distances:
88 5 0.02
89 291 0.96
90 6 0.02
ACGTcount: A:0.29, C:0.17, G:0.16, T:0.38
Consensus pattern (89 bp):
TTAGTCAAATATTTTCTGTCGTGTCAGAAAGAATCTGATACCCGCATGCATCTGTCACATCTTTC
GGGTTCTAAGAAATTTATTAGGCA
Found at i:492928 original size:246 final size:246
Alignment explanation
Indices: 492492--493492 Score: 827
Period size: 246 Copynumber: 4.0 Consensus size: 246
492482 TAATTAGGCA
*
492492 TTAGTCAAATATTTTCTGTCGTGTCAGAAAGAATCTAATACCCGCATGTATCTATCACATCTTTC
1 TTAGTCAAATATTTTCTGTCGTGTCAGAAAGAATCTAATACCCGCATGCATCTATCACATCTTTC
492557 GAGTTCTAAGAAATTTATTAGGCATTAGTCAAATATTTTCTATCGTGTCAAAAGGAATATGATAC
66 GAGTTCTAAGAAATTTATTAGGCATTAGTCAAATATTTTCTATCGTGTCAAAAGGAATATGATAC
* * * *
492622 TCGCATGCATCTGTCACATCTTTCGAGTTCTAAGAAATTTATTAGGAATTAGTCAAATATTTTCT
131 CCACATGCATCTATCACATCTTTCGAGTTCTAAGAAATTTATTAGGAATTAGTAAAATATTTTCT
* *
492687 ATCATGTCAGAAAGAATCTGATACCTGCATGCATCTGTTACATCTTTTGGG
196 ATCATGTCAGAAAGAATCTGATACCCGCATGCATCTGTCACATCTTTTGGG
* * * * *
492738 TTAGTCAAATATTTTTTGTCGTGTCAGAAAGAATCTGATACCCGCATGCATCTGTCATATCTTTT
1 TTAGTCAAATATTTTCTGTCGTGTCAGAAAGAATCTAATACCCGCATGCATCTATCACATCTTTC
* * * *
492803 GGGTT-TCAAGAAATTTATTAGGCATTAGTCAAATATTTTCTGTCGTGTCCATAA-GAATCTGAT
66 GAGTTCT-AAGAAATTTATTAGGCATTAGTCAAATATTTTCTATCGTGT-CAAAAGGAATATGAT
* * * * *
492866 TCCCACATGCATTTATCACATCTTTTGGGTTCTAAGAAATTTATTAGGCATTAGTAAAATATTTT
129 ACCCACATGCATCTATCACATCTTTCGAGTTCTAAGAAATTTATTAGGAATTAGTAAAATATTTT
* *
492931 CTGTCGTGTCAGAAAGAATCTGATACCCGCATGCATCTGTCACATCTTTCAGGTTCTAAGAAATT
194 CTATCATGTCAGAAAGAATCTGATACCCGCATGCATCTGTCACATC--T----TT-T--G-----
492996 TATTAGG
245 -----GG
* * * * * *
493003 CATTAGTCAAATATTTTCTATCGTGTCA-AAAGGAATATGATACTCGCATGCATCTGTCATATCT
1 --TTAGTCAAATATTTTCTGTCGTGTCAGAAA-GAATCTAATACCCGCATGCATCTATCACATCT
* * *
493067 TTCGAGTTCTAAGAAATTTATTAGGCATTAGTCAAATATTTTCTATCATGTCAGAAA-TAATCTG
63 TTCGAGTTCTAAGAAATTTATTAGGCATTAGTCAAATATTTTCTATCGTGTCA-AAAGGAATATG
** * * *
493131 ATACCTGCATGCATCTGTTACATC--T----TTC---G----------GG--TTAGTCAAATATT
127 ATACCCACATGCATCTATCACATCTTTCGAGTTCTAAGAAATTTATTAGGAATTAGTAAAATATT
* * *
493175 TTCTGTCGTGTCAGAAAGAATCTGATACCCGCATGCATCTGTCATATCTTTTGGGTTCCAAGAAA
192 TTCTATCATGTCAGAAAGAATCTGATACCCGCATGCATCTGTCACATCTTTT--G------G---
493240 TTTATTAAG
246 --------G
* * * * *
493249 TATTAGTCAAATATTTTCTGTCGTGTCCA-TAAGAATCTGATTCCCACATGCATTTATCACATCT
1 --TTAGTCAAATATTTTCTGTCGTGT-CAGAAAGAATCTAATACCCGCATGCATCTATCACATCT
* * * * *
493313 TTTGGGTTCTAAGAAATTTATTAGGCATTAGTAAAATATTTTCTGTCGTGTCAGAAA-GAATCTG
63 TTCGAGTTCTAAGAAATTTATTAGGCATTAGTCAAATATTTTCTATCGTGTCA-AAAGGAATATG
* * * *
493377 ATACCCGCATGCATCTGTCACATCTTTC-AGGTTCTAAGAAATTTATTAGGCATTAGTCAAATAT
127 ATACCCACATGCATCTATCACATCTTTCGA-GTTCTAAGAAATTTATTAGGAATTAGTAAAATAT
* * * *
493441 TTTCTATCGTGTCA-AAAGGAATATGATACTCGCATGCATCTCTCACATCTTT
191 TTTCTATCATGTCAGAAA-GAATCTGATACCCGCATGCATCTGTCACATCTTT
493493 CGAGTTCTAA
Statistics
Matches: 626, Mismatches: 69, Indels: 99
0.79 0.09 0.12
Matches are distributed among these distances:
235 4 0.01
239 2 0.00
240 2 0.00
244 1 0.00
245 1 0.00
246 398 0.64
247 8 0.01
248 4 0.01
252 5 0.01
253 1 0.00
255 2 0.00
258 1 0.00
261 3 0.00
265 5 0.01
266 8 0.01
267 180 0.29
268 1 0.00
ACGTcount: A:0.30, C:0.17, G:0.16, T:0.37
Consensus pattern (246 bp):
TTAGTCAAATATTTTCTGTCGTGTCAGAAAGAATCTAATACCCGCATGCATCTATCACATCTTTC
GAGTTCTAAGAAATTTATTAGGCATTAGTCAAATATTTTCTATCGTGTCAAAAGGAATATGATAC
CCACATGCATCTATCACATCTTTCGAGTTCTAAGAAATTTATTAGGAATTAGTAAAATATTTTCT
ATCATGTCAGAAAGAATCTGATACCCGCATGCATCTGTCACATCTTTTGGG
Found at i:493102 original size:424 final size:424
Alignment explanation
Indices: 492314--493582 Score: 2164
Period size: 424 Copynumber: 3.0 Consensus size: 424
492304 TTATTAGTCA
* * *
492314 TTAGTCAAATATTTTCTGTCGTGTTAGAAAGAATCTGATACCCGCATGCATCTGTCACATCTTTC
1 TTAGTCAAATATTTTCTGTCGTGTCAGAAAGAATCTGATACCCGCATGCATCTGTCATATCTTTT
* * * * * * *
492379 GGGTTCCAAAAAATTTATTAGGCATTAGTCAAATATTTTTTGCCATGT-CAGAAAGAATCTCATA
66 GGGTTCCAAGAAATTTATTAGGCATTAGTCAAATATTTTCTGTCGTGTCCA-TAAGAATCTGATT
** * * * * * * * *
492443 CCGGCATGTATCTGTCACATCTTTCGAGTTCCAAGAAATTAATTAGGCATTAGTCAAATATTTTC
130 CCCACATGCATTTATCACATCTTTTGGGTTCTAAGAAATTTATTAGGCATTAGTAAAATATTTTC
* * *
492508 TGTCGTGTCAGAAAGAATCTAATACCCGCATGTATCTATCACATCTTTC-GAGTTCTAAGAAATT
195 TGTCGTGTCAGAAAGAATCTGATACCCGCATGCATCTGTCACATCTTTCAG-GTTCTAAGAAATT
492572 TATTAGGCATTAGTCAAATATTTTCTATCGTGTCAAAAGGAATATGATACTCGCATGCATCTGTC
259 TATTAGGCATTAGTCAAATATTTTCTATCGTGTCAAAAGGAATATGATACTCGCATGCATCTGTC
*
492637 ACATCTTTCGAGTTCTAAGAAATTTATTAGGAATTAGTCAAATATTTTCTATCATGTCAGAAAGA
324 ACATCTTTCGAGTTCTAAGAAATTTATTAGGCATTAGTCAAATATTTTCTATCATGTCAGAAAGA
*
492702 ATCTGATACCTGCATGCATCTGTTACATCTTTTGGG
389 ATCTGATACCTGCATGCATCTGTTACATCTTTCGGG
*
492738 TTAGTCAAATATTTTTTGTCGTGTCAGAAAGAATCTGATACCCGCATGCATCTGTCATATCTTTT
1 TTAGTCAAATATTTTCTGTCGTGTCAGAAAGAATCTGATACCCGCATGCATCTGTCATATCTTTT
*
492803 GGGTTTCAAGAAATTTATTAGGCATTAGTCAAATATTTTCTGTCGTGTCCATAAGAATCTGATTC
66 GGGTTCCAAGAAATTTATTAGGCATTAGTCAAATATTTTCTGTCGTGTCCATAAGAATCTGATTC
492868 CCACATGCATTTATCACATCTTTTGGGTTCTAAGAAATTTATTAGGCATTAGTAAAATATTTTCT
131 CCACATGCATTTATCACATCTTTTGGGTTCTAAGAAATTTATTAGGCATTAGTAAAATATTTTCT
492933 GTCGTGTCAGAAAGAATCTGATACCCGCATGCATCTGTCACATCTTTCAGGTTCTAAGAAATTTA
196 GTCGTGTCAGAAAGAATCTGATACCCGCATGCATCTGTCACATCTTTCAGGTTCTAAGAAATTTA
*
492998 TTAGGCATTAGTCAAATATTTTCTATCGTGTCAAAAGGAATATGATACTCGCATGCATCTGTCAT
261 TTAGGCATTAGTCAAATATTTTCTATCGTGTCAAAAGGAATATGATACTCGCATGCATCTGTCAC
*
493063 ATCTTTCGAGTTCTAAGAAATTTATTAGGCATTAGTCAAATATTTTCTATCATGTCAGAAATAAT
326 ATCTTTCGAGTTCTAAGAAATTTATTAGGCATTAGTCAAATATTTTCTATCATGTCAGAAAGAAT
493128 CTGATACCTGCATGCATCTGTTACATCTTTCGGG
391 CTGATACCTGCATGCATCTGTTACATCTTTCGGG
493162 TTAGTCAAATATTTTCTGTCGTGTCAGAAAGAATCTGATACCCGCATGCATCTGTCATATCTTTT
1 TTAGTCAAATATTTTCTGTCGTGTCAGAAAGAATCTGATACCCGCATGCATCTGTCATATCTTTT
* *
493227 GGGTTCCAAGAAATTTATTAAGTATTAGTCAAATATTTTCTGTCGTGTCCATAAGAATCTGATTC
66 GGGTTCCAAGAAATTTATTAGGCATTAGTCAAATATTTTCTGTCGTGTCCATAAGAATCTGATTC
493292 CCACATGCATTTATCACATCTTTTGGGTTCTAAGAAATTTATTAGGCATTAGTAAAATATTTTCT
131 CCACATGCATTTATCACATCTTTTGGGTTCTAAGAAATTTATTAGGCATTAGTAAAATATTTTCT
493357 GTCGTGTCAGAAAGAATCTGATACCCGCATGCATCTGTCACATCTTTCAGGTTCTAAGAAATTTA
196 GTCGTGTCAGAAAGAATCTGATACCCGCATGCATCTGTCACATCTTTCAGGTTCTAAGAAATTTA
*
493422 TTAGGCATTAGTCAAATATTTTCTATCGTGTCAAAAGGAATATGATACTCGCATGCATCTCTCAC
261 TTAGGCATTAGTCAAATATTTTCTATCGTGTCAAAAGGAATATGATACTCGCATGCATCTGTCAC
* *
493487 ATCTTTCGAGTTCTAAGAAATTTATTAGGCATTAGTCAAATATTTTATATCGTGTCAGAAAGAAT
326 ATCTTTCGAGTTCTAAGAAATTTATTAGGCATTAGTCAAATATTTTCTATCATGTCAGAAAGAAT
* * * *
493552 CTAATACCCGCATGCATCTGTCATATCTTTC
391 CTGATACCTGCATGCATCTGTTACATCTTTC
493583 AGATTCCAAG
Statistics
Matches: 801, Mismatches: 42, Indels: 4
0.95 0.05 0.00
Matches are distributed among these distances:
424 798 1.00
425 3 0.00
ACGTcount: A:0.30, C:0.18, G:0.16, T:0.37
Consensus pattern (424 bp):
TTAGTCAAATATTTTCTGTCGTGTCAGAAAGAATCTGATACCCGCATGCATCTGTCATATCTTTT
GGGTTCCAAGAAATTTATTAGGCATTAGTCAAATATTTTCTGTCGTGTCCATAAGAATCTGATTC
CCACATGCATTTATCACATCTTTTGGGTTCTAAGAAATTTATTAGGCATTAGTAAAATATTTTCT
GTCGTGTCAGAAAGAATCTGATACCCGCATGCATCTGTCACATCTTTCAGGTTCTAAGAAATTTA
TTAGGCATTAGTCAAATATTTTCTATCGTGTCAAAAGGAATATGATACTCGCATGCATCTGTCAC
ATCTTTCGAGTTCTAAGAAATTTATTAGGCATTAGTCAAATATTTTCTATCATGTCAGAAAGAAT
CTGATACCTGCATGCATCTGTTACATCTTTCGGG
Found at i:493168 original size:335 final size:333
Alignment explanation
Indices: 492491--493496 Score: 1164
Period size: 335 Copynumber: 3.0 Consensus size: 333
492481 TTAATTAGGC
* *
492491 ATTAGTCAAATATTTTCTGTCGTGTCAGAAAGAATCTAATACCCGCATGTATCTATCACATCTTT
1 ATTAGTCAAATATTTTCTGTCGTGTCAGAAAGAATCTGATACCCGCATGCATCTATCACATCTTT
* * * *
492556 CGAGTTCTAAGAAATTTATTAGGCATTAGTCAAATATTTTCTATCGTGTCAAAAGGAATATGATA
66 TGGGTTCTAAGAAATTTATTAGGCATTAGTCAAATATTTTCTGTCGTGTCAAAA-GAATCTGATA
* *
492621 CTCGCATGCATCTGTCACATCTTTCGAGTTCTAAGAAATTTATTAGGAATTAGTCAAATATTTTC
130 CCCGCATGCATCTGTCACATCTTTCG-GTTCTAAGAAATTTATTAGGCATTAGTCAAATATTTTC
*
492686 TATCATGTCAGAAAGAATCTGATACCTGCATGCATCTGT--TA-----CA--TC--------TT-
194 TATCGTGTCAGAAAGAATCTGATACC-GCATGCATCTGTCATATCTTTCAGTTCTAAGAAATTTA
* * * *
492733 TT-GG-GTTAGTCAAATATTTTTTGTCGTGTCAGAAAGAATCTGATACCCGCATGCATCTGTCAT
258 TTAGGCATTAGTCAAATATTTTCTATCGTGTCAGAAAGAATCTGATACCTGCATGCATCTGT--T
* *
492796 ATCTTTTGGGTTTCAAGAAATTTATTAGG
321 A-C--AT--CTTTC--G---------AGG
* * * *
492825 CATTAGTCAAATATTTTCTGTCGTGTCCA-TAAGAATCTGATTCCCACATGCATTTATCACATCT
1 -ATTAGTCAAATATTTTCTGTCGTGT-CAGAAAGAATCTGATACCCGCATGCATCTATCACATCT
*
492889 TTTGGGTTCTAAGAAATTTATTAGGCATTAGTAAAATATTTTCTGTCGTGTCAGAAAGAATCTGA
64 TTTGGGTTCTAAGAAATTTATTAGGCATTAGTCAAATATTTTCTGTCGTGTCA-AAAGAATCTGA
492954 TACCCGCATGCATCTGTCACATCTTTCAGGTTCTAAGAAATTTATTAGGCATTAGTCAAATATTT
128 TACCCGCATGCATCTGTCACATCTTTC-GGTTCTAAGAAATTTATTAGGCATTAGTCAAATATTT
*
493019 TCTATCGTGTCA-AAAGGAATATGATACTCGCATGCATCTGTCATATCTTTCGAGTTCTAAGAAA
192 TCTATCGTGTCAGAAA-GAATCTGATAC-CGCATGCATCTGTCATATCTTTC-AGTTCTAAGAAA
* *
493083 TTTATTAGGCATTAGTCAAATATTTTCTATCATGTCAGAAATAATCTGATACCTGCATGCATCTG
254 TTTATTAGGCATTAGTCAAATATTTTCTATCGTGTCAGAAAGAATCTGATACCTGCATGCATCTG
493148 TTACATCTTTCG-GG
319 TTACATCTTTCGAGG
* *
493162 -TTAGTCAAATATTTTCTGTCGTGTCAGAAAGAATCTGATACCCGCATGCATCTGTCATATCTTT
1 ATTAGTCAAATATTTTCTGTCGTGTCAGAAAGAATCTGATACCCGCATGCATCTATCACATCTTT
* * * * *
493226 TGGGTTCCAAGAAATTTATTAAGTATTAGTCAAATATTTTCTGTCGTGTCCATAAGAATCTGATT
66 TGGGTTCTAAGAAATTTATTAGGCATTAGTCAAATATTTTCTGTCGTGT-CAAAAGAATCTGATA
* * * * *
493291 CCCACATGCATTTATCACATCTTTTGGGTTCTAAGAAATTTATTAGGCATTAGTAAAATATTTTC
130 CCCGCATGCATCTGTCACATC-TTTCGGTTCTAAGAAATTTATTAGGCATTAGTCAAATATTTTC
* *
493356 TGTCGTGTCAGAAAGAATCTGATACCCGCATGCATCTGTCACATCTTTCAGGTTCTAAGAAATTT
194 TATCGTGTCAGAAAGAATCTGATA-CCGCATGCATCTGTCATATCTTTCA-GTTCTAAGAAATTT
* *
493421 ATTAGGCATTAGTCAAATATTTTCTATCGTGTCA-AAAGGAATATGATA-CTCGCATGCATCTCT
257 ATTAGGCATTAGTCAAATATTTTCTATCGTGTCAGAAA-GAATCTGATACCT-GCATGCATCTGT
*
493484 CACATCTTTCGAG
320 TACATCTTTCGAG
493497 TTCTAAGAAA
Statistics
Matches: 588, Mismatches: 48, Indels: 69
0.83 0.07 0.10
Matches are distributed among these distances:
334 11 0.02
335 487 0.83
336 17 0.03
337 4 0.01
342 1 0.00
343 1 0.00
345 2 0.00
347 1 0.00
349 4 0.01
351 1 0.00
353 3 0.01
354 4 0.01
355 2 0.00
356 50 0.09
ACGTcount: A:0.30, C:0.17, G:0.16, T:0.37
Consensus pattern (333 bp):
ATTAGTCAAATATTTTCTGTCGTGTCAGAAAGAATCTGATACCCGCATGCATCTATCACATCTTT
TGGGTTCTAAGAAATTTATTAGGCATTAGTCAAATATTTTCTGTCGTGTCAAAAGAATCTGATAC
CCGCATGCATCTGTCACATCTTTCGGTTCTAAGAAATTTATTAGGCATTAGTCAAATATTTTCTA
TCGTGTCAGAAAGAATCTGATACCGCATGCATCTGTCATATCTTTCAGTTCTAAGAAATTTATTA
GGCATTAGTCAAATATTTTCTATCGTGTCAGAAAGAATCTGATACCTGCATGCATCTGTTACATC
TTTCGAGG
Found at i:493203 original size:68 final size:68
Alignment explanation
Indices: 493094--493231 Score: 213
Period size: 68 Copynumber: 2.0 Consensus size: 68
493084 TTATTAGGCA
* * *
493094 TTAGTCAAATATTTTCTATCATGTCAGAAATAATCTGATACCTGCATGCATCTGTTACATCTTTC
1 TTAGTCAAATATTTTCTATCATGTCAGAAAGAATCTGATACCCGCATGCATCTGTCACATCTTTC
493159 GGG
66 GGG
* * * *
493162 TTAGTCAAATATTTTCTGTCGTGTCAGAAAGAATCTGATACCCGCATGCATCTGTCATATCTTTT
1 TTAGTCAAATATTTTCTATCATGTCAGAAAGAATCTGATACCCGCATGCATCTGTCACATCTTTC
493227 GGG
66 GGG
493230 TT
1 TT
493232 CCAAGAAATT
Statistics
Matches: 63, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
68 63 1.00
ACGTcount: A:0.26, C:0.19, G:0.17, T:0.38
Consensus pattern (68 bp):
TTAGTCAAATATTTTCTATCATGTCAGAAAGAATCTGATACCCGCATGCATCTGTCACATCTTTC
GGG
Found at i:493299 original size:157 final size:157
Alignment explanation
Indices: 493005--493320 Score: 429
Period size: 157 Copynumber: 2.0 Consensus size: 157
492995 TTATTAGGCA
*
493005 TTAGTCAAATATTTTCTATCGTGTCAAAAGGAATATGATACTCGCATGCATCTGTCATATCTTTC
1 TTAGTCAAATATTTTCTATCGTGTCAAAAGGAATATGATACCCGCATGCATCTGTCATATCTTTC
* * *
493070 GAGTTCTAAGAAATTTATTAGGCATTAGTCAAATATTTTCTATCATGTCAGAAATAATCTGATAC
66 GAGTTCCAAGAAATTTATTAAGCATTAGTCAAATATTTTCTATCATGTCAGAAAGAATCTGATAC
** * *
493135 CTGCATGCATCTGTTACATCTTTCGGG
131 CCACATGCATCTATCACATCTTTCGGG
* *
493162 TTAGTCAAATATTTTCTGTCGTGTCAGAAA-GAATCTGATACCCGCATGCATCTGTCATATCTTT
1 TTAGTCAAATATTTTCTATCGTGTCA-AAAGGAATATGATACCCGCATGCATCTGTCATATCTTT
* * * * * *
493226 TGGGTTCCAAGAAATTTATTAAGTATTAGTCAAATATTTTCTGTCGTGTCCA-TAAGAATCTGAT
65 CGAGTTCCAAGAAATTTATTAAGCATTAGTCAAATATTTTCTATCATGT-CAGAAAGAATCTGAT
* * *
493290 TCCCACATGCATTTATCACATCTTTTGGG
129 ACCCACATGCATCTATCACATCTTTCGGG
493319 TT
1 TT
493321 CTAAGAAATT
Statistics
Matches: 138, Mismatches: 19, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
157 133 0.96
158 5 0.04
ACGTcount: A:0.28, C:0.18, G:0.16, T:0.38
Consensus pattern (157 bp):
TTAGTCAAATATTTTCTATCGTGTCAAAAGGAATATGATACCCGCATGCATCTGTCATATCTTTC
GAGTTCCAAGAAATTTATTAAGCATTAGTCAAATATTTTCTATCATGTCAGAAAGAATCTGATAC
CCACATGCATCTATCACATCTTTCGGG
Found at i:493313 original size:89 final size:89
Alignment explanation
Indices: 493162--493641 Score: 626
Period size: 89 Copynumber: 5.4 Consensus size: 89
493152 ATCTTTCGGG
* *
493162 TTAGTCAAATATTTTCTGTCGTGTCAGAAAGAATCTGATACCCGCATGCATCTGTCATATCTTTT
1 TTAGTCAAATATTTTCTGTCGTGTCAGAAAGAATCTGATACCCGCATGCATCTGTCACATCTTTC
* * *
493227 GGGTTCCAAGAAATTTATTAAGTA
66 GGGTTCTAAGAAATTTATTAGGCA
* * * * *
493251 TTAGTCAAATATTTTCTGTCGTGTCCA-TAAGAATCTGATTCCCACATGCATTTATCACATCTTT
1 TTAGTCAAATATTTTCTGTCGTGT-CAGAAAGAATCTGATACCCGCATGCATCTGTCACATCTTT
*
493315 TGGGTTCTAAGAAATTTATTAGGCA
65 CGGGTTCTAAGAAATTTATTAGGCA
*
493340 TTAGTAAAATATTTTCTGTCGTGTCAGAAAGAATCTGATACCCGCATGCATCTGTCACATCTTTC
1 TTAGTCAAATATTTTCTGTCGTGTCAGAAAGAATCTGATACCCGCATGCATCTGTCACATCTTTC
*
493405 AGGTTCTAAGAAATTTATTAGGCA
66 GGGTTCTAAGAAATTTATTAGGCA
* * * *
493429 TTAGTCAAATATTTTCTATCGTGTCA-AAAGGAATATGATACTCGCATGCATCTCTCACATCTTT
1 TTAGTCAAATATTTTCTGTCGTGTCAGAAA-GAATCTGATACCCGCATGCATCTGTCACATCTTT
*
493493 CGAGTTCTAAGAAATTTATTAGGCA
65 CGGGTTCTAAGAAATTTATTAGGCA
* * * *
493518 TTAGTCAAATATTTTATATCGTGTCAGAAAGAATCTAATACCCGCATGCATCTGTCATATCTTTC
1 TTAGTCAAATATTTTCTGTCGTGTCAGAAAGAATCTGATACCCGCATGCATCTGTCACATCTTTC
* * * * *
493583 AGATTCCAAGAATTTTAATTTA--TA
66 GGGTTCTAAGAAATTT-A-TTAGGCA
* * *
493607 TTAGCCAAATATTTTCTGTCGTATCAAAAAGAATC
1 TTAGTCAAATATTTTCTGTCGTGTCAGAAAGAATC
493642 CGATCTAATA
Statistics
Matches: 344, Mismatches: 41, Indels: 12
0.87 0.10 0.03
Matches are distributed among these distances:
88 5 0.01
89 330 0.96
90 6 0.02
91 3 0.01
ACGTcount: A:0.31, C:0.17, G:0.15, T:0.37
Consensus pattern (89 bp):
TTAGTCAAATATTTTCTGTCGTGTCAGAAAGAATCTGATACCCGCATGCATCTGTCACATCTTTC
GGGTTCTAAGAAATTTATTAGGCA
Found at i:493717 original size:2 final size:2
Alignment explanation
Indices: 493712--493823 Score: 81
Period size: 2 Copynumber: 63.0 Consensus size: 2
493702 AAAAAATTAT
* *
493712 TA TA TA T- TT TA TA TA TA TA T- TA TA TA -A TA T- TA TA T- TG
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * *
493749 TA T- TA T- TA TA TA T- TA CA TA TC TA T- TA TA TA TA TT TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
493787 T- TA -A TA TA TA T- TA TA TA T- TA TA TA T- TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
493824 AAACATATAA
Statistics
Matches: 88, Mismatches: 8, Indels: 28
0.71 0.06 0.23
Matches are distributed among these distances:
1 14 0.16
2 74 0.84
ACGTcount: A:0.42, C:0.02, G:0.01, T:0.55
Consensus pattern (2 bp):
TA
Found at i:493795 original size:14 final size:14
Alignment explanation
Indices: 493770--493818 Score: 53
Period size: 15 Copynumber: 3.2 Consensus size: 14
493760 ATTACATATC
493770 TATTATATATATTTA
1 TATTA-ATATATTTA
493785 TATTAATATATATTA
1 TATTAATATAT-TTA
*
493800 TATATTATATATTATA
1 TAT-TAATATATT-TA
493816 TAT
1 TAT
493819 ATATAAAACA
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
14 6 0.20
15 12 0.40
16 12 0.40
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (14 bp):
TATTAATATATTTA
Found at i:493822 original size:41 final size:41
Alignment explanation
Indices: 493707--493822 Score: 143
Period size: 41 Copynumber: 2.9 Consensus size: 41
493697 TTTTCAAAAA
* *
493707 ATTATTATATATTTTATA-TATATATTATATA-ATA-TTAT
1 ATTAATATATATTATATATTATATATTATATATATATTTAT
* *
493745 ATT-GTAT-TATTATATATTACATATCTATTATATATATTTAT
1 ATTAATATATATTATATATTATATAT-TA-TATATATATTTAT
493786 ATTAATATATATTATATATTATATATTATATATATAT
1 ATTAATATATATTATATATTATATATTATATATATAT
493823 AAAACATATA
Statistics
Matches: 66, Mismatches: 5, Indels: 11
0.80 0.06 0.13
Matches are distributed among these distances:
36 8 0.12
37 9 0.14
38 5 0.08
39 4 0.06
40 3 0.05
41 16 0.24
42 5 0.08
43 16 0.24
ACGTcount: A:0.41, C:0.02, G:0.01, T:0.56
Consensus pattern (41 bp):
ATTAATATATATTATATATTATATATTATATATATATTTAT
Found at i:495142 original size:3 final size:3
Alignment explanation
Indices: 495134--495172 Score: 69
Period size: 3 Copynumber: 13.0 Consensus size: 3
495124 ATACAATATT
*
495134 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AAA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
495173 TGGATTTTAA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
ATA
Found at i:500779 original size:20 final size:19
Alignment explanation
Indices: 500736--500812 Score: 84
Period size: 20 Copynumber: 3.9 Consensus size: 19
500726 TTTTACCCAG
*
500736 ATGTATCGATACATTGA-AA
1 ATGTATCGATACATT-ATGA
500755 ATGTATCGATACATGTATGA
1 ATGTATCGATACAT-TATGA
* *
500775 ATGTATCGATACATTTTTCA
1 ATGTATCGATACA-TTATGA
*
500795 ATGTATCAATACATTATG
1 ATGTATCGATACATTATG
500813 TTTTTTTACC
Statistics
Matches: 49, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
19 18 0.37
20 30 0.61
21 1 0.02
ACGTcount: A:0.36, C:0.12, G:0.14, T:0.38
Consensus pattern (19 bp):
ATGTATCGATACATTATGA
Found at i:500889 original size:51 final size:51
Alignment explanation
Indices: 500774--500890 Score: 164
Period size: 50 Copynumber: 2.3 Consensus size: 51
500764 TACATGTATG
**** *
500774 AATGTATCGATACATTTTTCAATGTATCAATACATTATGTTTTTTTACCCA
1 AATGTATCGATACATTGAAAAATGTATCAATACATTATATTTTTTTACCCA
* *
500825 AA-GTATCGATACATTGAAAAATGTATCGATACATTCTATTTTTTTACCCA
1 AATGTATCGATACATTGAAAAATGTATCAATACATTATATTTTTTTACCCA
500875 AATGTATCGATACATT
1 AATGTATCGATACATT
500891 TTTCAATGTA
Statistics
Matches: 58, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
50 43 0.74
51 15 0.26
ACGTcount: A:0.34, C:0.15, G:0.09, T:0.41
Consensus pattern (51 bp):
AATGTATCGATACATTGAAAAATGTATCAATACATTATATTTTTTTACCCA
Found at i:501322 original size:20 final size:20
Alignment explanation
Indices: 501297--501371 Score: 96
Period size: 20 Copynumber: 3.8 Consensus size: 20
501287 TTTTACCTAG
501297 ATGTATCGATACATTTTTCA
1 ATGTATCGATACATTTTTCA
* * *
501317 ATGTATCGATACATGTATGA
1 ATGTATCGATACATTTTTCA
* *
501337 ATGTATCAATACATTCTTCA
1 ATGTATCGATACATTTTTCA
*
501357 ATGGATCGATACATT
1 ATGTATCGATACATT
501372 CTGTCTTTTT
Statistics
Matches: 45, Mismatches: 10, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 45 1.00
ACGTcount: A:0.33, C:0.15, G:0.13, T:0.39
Consensus pattern (20 bp):
ATGTATCGATACATTTTTCA
Found at i:502343 original size:20 final size:21
Alignment explanation
Indices: 502306--502344 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
502296 AGCCTTTGAC
**
502306 CATGCATTTTTTTTTATGTTT
1 CATGCATTTTTTAATATGTTT
502327 CATGCA-TTTTTAATATGT
1 CATGCATTTTTTAATATGT
502345 CCAGCATCTC
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 10 0.62
21 6 0.38
ACGTcount: A:0.21, C:0.10, G:0.10, T:0.59
Consensus pattern (21 bp):
CATGCATTTTTTAATATGTTT
Found at i:507082 original size:9 final size:9
Alignment explanation
Indices: 507070--507111 Score: 52
Period size: 9 Copynumber: 4.8 Consensus size: 9
507060 GGATATTTAT
507070 TTTATTTCA
1 TTTATTTCA
507079 TTTATTTCA
1 TTTATTTCA
507088 TTTATTT-A
1 TTTATTTCA
*
507096 -TTATTGTTA
1 TTTATT-TCA
507105 TTTATTT
1 TTTATTT
507112 AAAAAGGTAA
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
7 5 0.17
8 2 0.07
9 18 0.60
10 5 0.17
ACGTcount: A:0.21, C:0.05, G:0.02, T:0.71
Consensus pattern (9 bp):
TTTATTTCA
Found at i:508208 original size:167 final size:166
Alignment explanation
Indices: 507996--508350 Score: 429
Period size: 167 Copynumber: 2.1 Consensus size: 166
507986 AAGGGTTTAA
* * * ** *
507996 AATTTTT-AAATTCTTTAAATATTAAAATTTAATTCATACTAAATTAGTTTTCAGAAATTCATTC
1 AATTTTTAAAATTCATTAAATACTAAAATTTAATTCACACTAAATTAGTTAGCAAAAATTCA--C
*
508060 A-TTATCATGAG-TTTTTGAATTTTTTCCTTGAAA-TTCCCT-TACTTTTGAAATATGGAG-TTT
64 AGTTATCATGAGCTTTTT--ATTTTTTCCTTGAAATTTCCCTGT--TTTCGAAATATGGAGTTTT
* *
508120 TCTACTCTGTAAATGTTTT-TGGAAGGATTTTTCTTGGTTTTT
125 TCTACTCTGTAAATATTTTCGGGAA-GATTTTTCTTGGTTTTT
** *
508162 AATTTTTAAAATTCATTAAATACTATTATTTAA-TCACCATTAAATTAGTTAGCAAAAATTCACA
1 AATTTTTAAAATTCATTAAATACTAAAATTTAATTCA-CACTAAATTAGTTAGCAAAAATTCACA
* * *
508226 TGTTTTCATGAGCTTTTTATTTTTTCCTTGAAATTTTCCTGTTTTCGAAATATGGAGTTTTTTTA
65 -GTTATCATGAGCTTTTTATTTTTTCCTTGAAATTTCCCTGTTTTCGAAATATGGAGTTTTTCTA
508291 CTCTGTAAATATTTTCGGGAAGATTTTTCTTGGTTTTT
129 CTCTGTAAATATTTTCGGGAAGATTTTTCTTGGTTTTT
*
508329 AATTTTTAAAATTCATCAAATA
1 AATTTTTAAAATTCATTAAATA
508351 TCATCATTTA
Statistics
Matches: 164, Mismatches: 16, Indels: 17
0.83 0.08 0.09
Matches are distributed among these distances:
165 2 0.01
166 39 0.24
167 113 0.69
168 10 0.06
ACGTcount: A:0.30, C:0.11, G:0.10, T:0.49
Consensus pattern (166 bp):
AATTTTTAAAATTCATTAAATACTAAAATTTAATTCACACTAAATTAGTTAGCAAAAATTCACAG
TTATCATGAGCTTTTTATTTTTTCCTTGAAATTTCCCTGTTTTCGAAATATGGAGTTTTTCTACT
CTGTAAATATTTTCGGGAAGATTTTTCTTGGTTTTT
Found at i:510299 original size:43 final size:43
Alignment explanation
Indices: 510224--510391 Score: 192
Period size: 43 Copynumber: 3.7 Consensus size: 43
510214 TTAAGGTAGG
*
510224 TAAAGGTGCCAATATGCTGATTCAAGGCCAGTGATATTGGACT
1 TAAATGTGCCAATATGCTGATTCAAGGCCAGTGATATTGGACT
* * *
510267 TAAATGTGCTAATGTGCTGATTCAAGGCCAGTGACATTGGACT
1 TAAATGTGCCAATATGCTGATTCAAGGCCAGTGATATTGGACT
*
510310 TAAAGATGACAAAGACGCCAATATGCTGATTCAAGGCCAGTGATATTGGACT
1 T-AA-AT------G-TGCCAATATGCTGATTCAAGGCCAGTGATATTGGACT
* *
510362 TAAAAGTGCCAATGTGCTGATTCAAGGCCA
1 TAAATGTGCCAATATGCTGATTCAAGGCCA
510392 ACGAAATTGG
Statistics
Matches: 105, Mismatches: 11, Indels: 18
0.78 0.08 0.13
Matches are distributed among these distances:
43 62 0.59
44 3 0.03
45 2 0.02
50 1 0.01
51 3 0.03
52 34 0.32
ACGTcount: A:0.32, C:0.17, G:0.24, T:0.26
Consensus pattern (43 bp):
TAAATGTGCCAATATGCTGATTCAAGGCCAGTGATATTGGACT
Found at i:510401 original size:95 final size:95
Alignment explanation
Indices: 510231--510406 Score: 298
Period size: 95 Copynumber: 1.9 Consensus size: 95
510221 AGGTAAAGGT
* *
510231 GCCAATATGCTGATTCAAGGCCAGTGATATTGGACTTAAATGTGCTAATGTGCTGATTCAAGGCC
1 GCCAATATGCTGATTCAAGGCCAGTGATATTGGACTTAAAAGTGCCAATGTGCTGATTCAAGGCC
** *
510296 AGTGACATTGGACTTAAAGATGACAAAGAC
66 AACGAAATTGGACTTAAAGATGACAAAGAC
510326 GCCAATATGCTGATTCAAGGCCAGTGATATTGGACTTAAAAGTGCCAATGTGCTGATTCAAGGCC
1 GCCAATATGCTGATTCAAGGCCAGTGATATTGGACTTAAAAGTGCCAATGTGCTGATTCAAGGCC
*
510391 AACGAAATTGGGCTTA
66 AACGAAATTGGACTTA
510407 GAAGGGTTGC
Statistics
Matches: 75, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
95 75 1.00
ACGTcount: A:0.32, C:0.18, G:0.24, T:0.26
Consensus pattern (95 bp):
GCCAATATGCTGATTCAAGGCCAGTGATATTGGACTTAAAAGTGCCAATGTGCTGATTCAAGGCC
AACGAAATTGGACTTAAAGATGACAAAGAC
Found at i:510514 original size:33 final size:32
Alignment explanation
Indices: 510471--510897 Score: 293
Period size: 34 Copynumber: 12.8 Consensus size: 32
510461 GTGGGCTTTG
* ** *
510471 AAAAGAAAAAGGTGCCATGGAGTTGTGGGCTT
1 AAAAGGAAAAGGTGCCACAGAGTTGTGGACTT
* *
510503 AAAAAGGAAAAGCTGCCAC-GAAGATGTGGACTT
1 -AAAAGGAAAAGGTGCCACAG-AGTTGTGGACTT
**
510536 AAAAGGAAAAAGGGTGCCATTGAGTTGTGGA-TT
1 AAAAGG-AAAA-GGTGCCACAGAGTTGTGGACTT
*
510569 -----TAAAAGGTGCCACAGAGTTGTGGACTT
1 AAAAGGAAAAGGTGCCACAGAGTTGTGGACTT
*
510596 AAAAGGAAAAAGGGTGCCACGGAGTTGT-GACTT
1 AAAAGG-AAAA-GGTGCCACAGAGTTGTGGACTT
* *
510629 AAAAGGAAAAAAAAATGTGCCACGGAGTTGTGGACTT
1 AAAAGG-----AAAAGGTGCCACAGAGTTGTGGACTT
510666 AAAAGGAAAAGGGGTGCCAC-GAAGTTGTGGACTT
1 AAAAGGAAAA--GGTGCCACAG-AGTTGTGGACTT
510700 AAAAGGAAAAGGTGCCACTA-AGTTGTAGG-CTTT
1 AAAAGGAAAAGGTGCCAC-AGAGTTGT-GGAC-TT
** * * *
510733 GAAAAAAAAAAGTTGCCGCAGAGTTGTGGGCTTT
1 -AAAAGGAAAAGGTGCCACAGAGTTGTGGAC-TT
* *
510767 GAAAAGAAAAAGGTGTCACAGAGTTGT-GAGCTTT
1 -AAAAGGAAAAGGTGCCACAGAGTTGTGGA-C-TT
* * * *
510801 GAAAAGAAAAAACGTGCCACAGAGTTATAGACTT
1 -AAAAG-GAAAAGGTGCCACAGAGTTGTGGACTT
*
510835 AAAAGGAAAAAAAGGATGCCATAGAGTTGTGGACTT
1 AAAAGG---AAAAGG-TGCCACAGAGTTGTGGACTT
*
510871 AAAAGGAAAAGGTACCACAGAGTTGTG
1 AAAAGGAAAAGGTGCCACAGAGTTGTG
510898 AGATTTGGGA
Statistics
Matches: 326, Mismatches: 34, Indels: 69
0.76 0.08 0.16
Matches are distributed among these distances:
26 17 0.05
27 6 0.02
32 39 0.12
33 66 0.20
34 117 0.36
35 25 0.08
36 40 0.12
37 16 0.05
ACGTcount: A:0.39, C:0.11, G:0.30, T:0.20
Consensus pattern (32 bp):
AAAAGGAAAAGGTGCCACAGAGTTGTGGACTT
Found at i:510580 original size:26 final size:26
Alignment explanation
Indices: 510543--510601 Score: 82
Period size: 26 Copynumber: 2.2 Consensus size: 26
510533 CTTAAAAGGA
** *
510543 AAAAGGGTGCCATTGAGTTGTGGATTT
1 AAAA-GGTGCCACAGAGTTGTGGACTT
510570 AAAAGGTGCCACAGAGTTGTGGACTT
1 AAAAGGTGCCACAGAGTTGTGGACTT
510596 AAAAGG
1 AAAAGG
510602 AAAAAGGGTG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
26 25 0.86
27 4 0.14
ACGTcount: A:0.32, C:0.10, G:0.32, T:0.25
Consensus pattern (26 bp):
AAAAGGTGCCACAGAGTTGTGGACTT
Found at i:510591 original size:60 final size:59
Alignment explanation
Indices: 510510--510634 Score: 180
Period size: 60 Copynumber: 2.1 Consensus size: 59
510500 CTTAAAAAGG
* ** *
510510 AAAAGCTGCCACGAAGATGTGGACTTAAAAGGAAAAAGGGTGCCATTGAGTTGTGGATTT
1 AAAAGGTGCCACGAAGATGTGGACTTAAAAGGAAAAAGGGTGCCACGGAGTTGT-GACTT
*
510570 AAAAGGTGCCAC-AGAGTTGTGGACTTAAAAGGAAAAAGGGTGCCACGGAGTTGTGACTT
1 AAAAGGTGCCACGA-AGATGTGGACTTAAAAGGAAAAAGGGTGCCACGGAGTTGTGACTT
510629 AAAAGG
1 AAAAGG
510635 AAAAAAAAAT
Statistics
Matches: 59, Mismatches: 5, Indels: 3
0.88 0.07 0.04
Matches are distributed among these distances:
59 11 0.19
60 48 0.81
ACGTcount: A:0.36, C:0.12, G:0.31, T:0.21
Consensus pattern (59 bp):
AAAAGGTGCCACGAAGATGTGGACTTAAAAGGAAAAAGGGTGCCACGGAGTTGTGACTT
Found at i:510663 original size:70 final size:71
Alignment explanation
Indices: 510570--510880 Score: 248
Period size: 70 Copynumber: 4.5 Consensus size: 71
510560 TTGTGGATTT
*
510570 AAAAGGTGCCACAGAGTTGTGGACTTAAAAGGAAAAAGGGTGCCACGGAGTTGT-GACTTAAAAG
1 AAAAGGTGCCACAGAGTTGTGGACTTAAAAGGAAAAAGGGTGCCACGAAGTTGTGGACTTAAAAG
510634 GAAAAA
66 GAAAAA
* * *
510640 AAAATGTGCCACGGAGTTGTGGACTTAAAAGGAAAAGGGGTGCCACGAAGTTGTGGACTTAAAAG
1 AAAAGGTGCCACAGAGTTGTGGACTTAAAAGGAAAAAGGGTGCCACGAAGTTGTGGACTTAAAAG
510705 G-----
66 GAAAAA
* * * *
510706 AAAAGGTGCCACTA-AGTTGTAGG-CTTTGAAAA--AAAAAAGTTGCCGC-AGAGTTGTGGGCTT
1 AAAAGGTGCCAC-AGAGTTGT-GGAC-TT-AAAAGGAAAAAGGGTGCCACGA-AGTTGTGGACTT
*
510766 ----TGAAAAGA
61 AAAAGGAAAA-A
* ** * *
510774 AAAAGGTGTCACAGAGTTGT-GAGCTTTGAAAA-GAAAAAACGTGCCAC-AGAGTTATAGACTTA
1 AAAAGGTGCCACAGAGTTGTGGA-C-TT-AAAAGGAAAAAGGGTGCCACGA-AGTTGTGGACTTA
510836 AAAGG--AAA
62 AAAGGAAAAA
*
510844 AAAAGGATGCCATAGAGTTGTGGACTTAAAAGGAAAA
1 AAAAGG-TGCCACAGAGTTGTGGACTTAAAAGGAAAA
510881 GGTACCACAG
Statistics
Matches: 196, Mismatches: 22, Indels: 46
0.74 0.08 0.17
Matches are distributed among these distances:
62 1 0.01
65 1 0.01
66 40 0.20
67 5 0.03
68 30 0.15
69 26 0.13
70 64 0.33
71 26 0.13
72 2 0.01
73 1 0.01
ACGTcount: A:0.40, C:0.11, G:0.29, T:0.20
Consensus pattern (71 bp):
AAAAGGTGCCACAGAGTTGTGGACTTAAAAGGAAAAAGGGTGCCACGAAGTTGTGGACTTAAAAG
GAAAAA
Found at i:510899 original size:103 final size:100
Alignment explanation
Indices: 510471--510897 Score: 337
Period size: 102 Copynumber: 4.3 Consensus size: 100
510461 GTGGGCTTTG
* ** * * * * *
510471 AAAAGAAAAAGGTGCCATGGAGTTGTGGGCTTAAAA-AGGAAAAGCTGCCAC-GAAGATGTGGAC
1 AAAAGGAAAAGGTGCCACAGAGTTGTGGACTTAAAAGA-AAAAAGGTGCCACAG-AGTTGTAGAC
* * **
510534 TTAAAAGG-AAAAAGGGTGCCATTGAGTTGTGGA-TT
64 TTAAAAGGAAAAAAAGATGCCACAGAGTTGTGGACTT
* * *
510569 -----TAAAAGGTGCCACAGAGTTGTGGACTTAAAAGGAAAAAGGGTGCCACGGAGTTGT-GACT
1 AAAAGGAAAAGGTGCCACAGAGTTGTGGACTTAAAA-GAAAAAAGGTGCCACAGAGTTGTAGACT
* *
510628 TAAAAGGAAAAAAAAATGTGCCACGGAGTTGTGGACTT
65 TAAAAGGAAAAAAAGA--TGCCACAGAGTTGTGGACTT
*
510666 AAAAGGAAAAGGGGTGCCAC-GAAGTTGTGGACTTAAAAG-GAAAAGGTGCCACTA-AGTTGTAG
1 AAAAGGAAAA--GGTGCCACAG-AGTTGTGGACTTAAAAGAAAAAAGGTGCCAC-AGAGTTGTAG
* * * * *
510728 GCTTTGAAA--AAAAAAAGTTGCCGCAGAGTTGTGGGCTTT
62 AC-TTAAAAGGAAAAAAAGATGCCACAGAGTTGTGGAC-TT
* * * *
510767 GAAAAGAAAAAGGTGTCACAGAGTTGT-GAGCTTTGAAAAGAAAAAACGTGCCACAGAGTTATAG
1 -AAAAGGAAAAGGTGCCACAGAGTTGTGGA-C-TT-AAAAGAAAAAAGGTGCCACAGAGTTGTAG
*
510831 ACTTAAAAGGAAAAAAAGGATGCCATAGAGTTGTGGACTT
62 ACTTAAAAGGAAAAAAA-GATGCCACAGAGTTGTGGACTT
*
510871 AAAAGGAAAAGGTACCACAGAGTTGTG
1 AAAAGGAAAAGGTGCCACAGAGTTGTG
510898 AGATTTGGGA
Statistics
Matches: 261, Mismatches: 38, Indels: 54
0.74 0.11 0.15
Matches are distributed among these distances:
93 38 0.15
94 20 0.08
95 2 0.01
96 15 0.06
97 2 0.01
99 2 0.01
100 29 0.11
101 5 0.02
102 48 0.18
103 46 0.18
104 38 0.15
105 16 0.06
ACGTcount: A:0.39, C:0.11, G:0.30, T:0.20
Consensus pattern (100 bp):
AAAAGGAAAAGGTGCCACAGAGTTGTGGACTTAAAAGAAAAAAGGTGCCACAGAGTTGTAGACTT
AAAAGGAAAAAAAGATGCCACAGAGTTGTGGACTT
Found at i:510944 original size:171 final size:169
Alignment explanation
Indices: 510570--510944 Score: 359
Period size: 171 Copynumber: 2.2 Consensus size: 169
510560 TTGTGGATTT
* ** * * **
510570 AAAAGGTGCCACAGAGTTGTGGACTT--AAAAGGAAAAAGGGTGCCACGGAGTTGTGA-CTTAAA
1 AAAAGATGCCACAGAGTCATGGACTTGGAAAA-GAAAAA-GGTGTCACAGAGTTGTGAGCTTTGA
* * * * * * * *
510632 AGGAAAAAAAAATGTGCCACGGAGTTGTGGACTTAAAAGGAAAAGGGGTGCCACGAAGTTGTGGA
64 A--AAGAAAAAACGTGCCACAGAGTTATAGACTTAAAAGGAAAAAGGATGCCAAGAAGTTGTGGA
* *
510697 CTTAAAAGGAAAAGGTGCCACTAAGTTGTAGGCTTTGAAAAAA
127 CTTAAAAGGAAAAGGTACCACTAAGTTGTAGGATTTGAAAAAA
* * ** * *
510740 AAAAGTTGCCGCAGAGTTGTGGGCTTTGAAAAGAAAAAGGTGTCACAGAGTTGTGAGCTTTGAAA
1 AAAAGATGCCACAGAGTCATGGACTTGGAAAAGAAAAAGGTGTCACAGAGTTGTGAGCTTTGAAA
510805 AGAAAAAACGTGCCACAGAGTTATAGACTTAAAAGGAAAAAAAGGATGCCATAG-AGTTGTGGAC
66 AGAAAAAACGTGCCACAGAGTTATAGACTTAAAAGG--AAAAAGGATGCCA-AGAAGTTGTGGAC
** *
510869 TTAAAAGGAAAAGGTACCAC-AGAGTTGT-GAGATTTGGGAGAA
128 TTAAAAGGAAAAGGTACCACTA-AGTTGTAG-GATTTGAAAAAA
* *
510911 AAAGGATGCTACTA-AGTCATGGACTTGGAAAAGA
1 AAAAGATGCCAC-AGAGTCATGGACTTGGAAAAGA
510945 TTACCCTCTT
Statistics
Matches: 168, Mismatches: 28, Indels: 17
0.79 0.13 0.08
Matches are distributed among these distances:
169 32 0.19
170 41 0.24
171 89 0.53
172 6 0.04
ACGTcount: A:0.39, C:0.11, G:0.29, T:0.20
Consensus pattern (169 bp):
AAAAGATGCCACAGAGTCATGGACTTGGAAAAGAAAAAGGTGTCACAGAGTTGTGAGCTTTGAAA
AGAAAAAACGTGCCACAGAGTTATAGACTTAAAAGGAAAAAGGATGCCAAGAAGTTGTGGACTTA
AAAGGAAAAGGTACCACTAAGTTGTAGGATTTGAAAAAA
Found at i:512272 original size:28 final size:28
Alignment explanation
Indices: 512191--512272 Score: 96
Period size: 28 Copynumber: 2.9 Consensus size: 28
512181 TTTTGGAGAT
*
512191 AATAACGAGGTTGGAGTGTTCCCTCG--GA
1 AATAACGAGGTTGGAGT-AT-CCTCGATGA
* * *
512219 AGTAACGGGGTTGGAGTATCCCCGATGA
1 AATAACGAGGTTGGAGTATCCTCGATGA
512247 AATAACGAGGTTGGAGTATCCTCGAT
1 AATAACGAGGTTGGAGTATCCTCGAT
512273 TGTGAAAAAT
Statistics
Matches: 45, Mismatches: 7, Indels: 4
0.80 0.12 0.07
Matches are distributed among these distances:
26 4 0.09
27 1 0.02
28 40 0.89
ACGTcount: A:0.27, C:0.17, G:0.32, T:0.24
Consensus pattern (28 bp):
AATAACGAGGTTGGAGTATCCTCGATGA
Found at i:512413 original size:51 final size:51
Alignment explanation
Indices: 512255--512423 Score: 196
Period size: 51 Copynumber: 3.3 Consensus size: 51
512245 GAAATAACGA
* * *
512255 GGTTGGAGTATCCTCGATTGTGAAAAATTGGTA-TTTGGAAATAAAATCGG
1 GGTTGGAGTATCCCCGATTATGAAAAATTGGTATTTTGAAAATAAAATCGG
** * * * * *
512305 AATTGGAGTATCCCCGATTAAAGGAGAAATTGGTGTTGTGAAAATAAAACCGG
1 GGTTGGAGTATCCCCGATT--ATGAAAAATTGGTATTTTGAAAATAAAATCGG
* * *
512358 GGTTGGAGTATCCCCGATTATGAAAAATCGATATTTTGAAAATAAAGTCGG
1 GGTTGGAGTATCCCCGATTATGAAAAATTGGTATTTTGAAAATAAAATCGG
512409 GGTTGGAGTATCCCC
1 GGTTGGAGTATCCCC
512424 TCAGAAATAA
Statistics
Matches: 96, Mismatches: 20, Indels: 5
0.79 0.17 0.04
Matches are distributed among these distances:
50 16 0.17
51 39 0.41
52 10 0.10
53 31 0.32
ACGTcount: A:0.33, C:0.12, G:0.27, T:0.28
Consensus pattern (51 bp):
GGTTGGAGTATCCCCGATTATGAAAAATTGGTATTTTGAAAATAAAATCGG
Found at i:512469 original size:27 final size:28
Alignment explanation
Indices: 512406--512481 Score: 102
Period size: 27 Copynumber: 2.8 Consensus size: 28
512396 AAAATAAAGT
*
512406 CGGGGTTGGAGTATCCCCTCA-GAAATAA
1 CGGGGTTGGAGTATCCCC-GATGAAATAA
*
512434 CGGGGTTGGAGTATCCCCGATG-ATTAA
1 CGGGGTTGGAGTATCCCCGATGAAATAA
*
512461 CGGGGTTGGAGTGTCCCCGAT
1 CGGGGTTGGAGTATCCCCGAT
512482 TGTGAAGAAA
Statistics
Matches: 44, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
27 25 0.57
28 19 0.43
ACGTcount: A:0.21, C:0.21, G:0.34, T:0.24
Consensus pattern (28 bp):
CGGGGTTGGAGTATCCCCGATGAAATAA
Found at i:512532 original size:54 final size:51
Alignment explanation
Indices: 512465--512595 Score: 140
Period size: 51 Copynumber: 2.5 Consensus size: 51
512455 GATTAACGGG
* **
512465 GTTGGAGTGTCCCCGATTGTGAAGAAATTGGTGTTTTTTGGAAA-TAAAATCGGA
1 GTTGGAGTATCCCCGATTGTG-AGAAATTAATG--TTTT-GAAAGTAAAATCGGA
*
512519 GTTGGAGTATCCCCGATTAT-AGAAAATTAATGTTTTGAAAGTAAAATCGGA
1 GTTGGAGTATCCCCGATTGTGAG-AAATTAATGTTTTGAAAGTAAAATCGGA
* *
512570 GTTGGAATATCCTCGATTGTGGAGAA
1 GTTGGAGTATCCCCGATTGT-GAGAA
512596 TTGAGCAACT
Statistics
Matches: 66, Mismatches: 7, Indels: 10
0.80 0.08 0.12
Matches are distributed among these distances:
50 4 0.06
51 31 0.47
52 4 0.06
53 9 0.14
54 18 0.27
ACGTcount: A:0.31, C:0.10, G:0.27, T:0.32
Consensus pattern (51 bp):
GTTGGAGTATCCCCGATTGTGAGAAATTAATGTTTTGAAAGTAAAATCGGA
Found at i:514963 original size:13 final size:13
Alignment explanation
Indices: 514945--514970 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
514935 ACAAAGATCC
514945 ATGTATCGATACA
1 ATGTATCGATACA
514958 ATGTATCGATACA
1 ATGTATCGATACA
514971 CAGAAAAATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:514966 original size:33 final size:33
Alignment explanation
Indices: 514924--514990 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
514914 AAAATTTCCA
***
514924 AATGTATCGATACAAAGATCCATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
*
514957 AATGTATCGATACACAGAAAAATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
514990 A
1 A
514991 TTTCCTTGGC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.43, C:0.16, G:0.15, T:0.25
Consensus pattern (33 bp):
AATGTATCGATACAAAGAAAAATGTATCGATAC
Found at i:515034 original size:19 final size:18
Alignment explanation
Indices: 515010--515077 Score: 83
Period size: 19 Copynumber: 3.9 Consensus size: 18
515000 CAGTAGCTAA
515010 TTATGTATCGATACAATAC
1 TTATGTATCGATACAA-AC
515029 TTATGTATCGATAC--A-
1 TTATGTATCGATACAAAC
515044 -T-TGTATCGATACAAAAC
1 TTATGTATCGATAC-AAAC
515061 TTATGTATCGATACAAA
1 TTATGTATCGATACAAA
515078 TTGTTGAATT
Statistics
Matches: 43, Mismatches: 0, Indels: 13
0.77 0.00 0.23
Matches are distributed among these distances:
13 11 0.26
14 1 0.02
16 2 0.05
18 4 0.09
19 25 0.58
ACGTcount: A:0.38, C:0.15, G:0.12, T:0.35
Consensus pattern (18 bp):
TTATGTATCGATACAAAC
Found at i:515050 original size:13 final size:13
Alignment explanation
Indices: 515032--515056 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
515022 ACAATACTTA
515032 TGTATCGATACAT
1 TGTATCGATACAT
515045 TGTATCGATACA
1 TGTATCGATACA
515057 AAACTTATGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:515054 original size:32 final size:32
Alignment explanation
Indices: 515013--515075 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
515003 TAGCTAATTA
*
515013 TGTATCGATACAATACTTATGTATCGATACAT
1 TGTATCGATACAAAACTTATGTATCGATACAT
515045 TGTATCGATACAAAACTTATGTATCGATACA
1 TGTATCGATACAAAACTTATGTATCGATACA
515076 AATTGTTGAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.37, C:0.16, G:0.13, T:0.35
Consensus pattern (32 bp):
TGTATCGATACAAAACTTATGTATCGATACAT
Found at i:515157 original size:21 final size:21
Alignment explanation
Indices: 515133--515189 Score: 105
Period size: 21 Copynumber: 2.7 Consensus size: 21
515123 CATTTGTAGG
515133 ATGTATCGATACATTCCACAA
1 ATGTATCGATACATTCCACAA
*
515154 ATGTATCGATACATTCTACAA
1 ATGTATCGATACATTCCACAA
515175 ATGTATCGATACATT
1 ATGTATCGATACATT
515190 TAAATTTTTT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.37, C:0.19, G:0.11, T:0.33
Consensus pattern (21 bp):
ATGTATCGATACATTCCACAA
Found at i:515218 original size:14 final size:14
Alignment explanation
Indices: 515201--515228 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
515191 AAATTTTTTT
515201 TTTTTTTTTTTCAA
1 TTTTTTTTTTTCAA
515215 TTTTTTTTTTTCAA
1 TTTTTTTTTTTCAA
515229 ACACTTTATC
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:0.07, G:0.00, T:0.79
Consensus pattern (14 bp):
TTTTTTTTTTTCAA
Found at i:519491 original size:151 final size:147
Alignment explanation
Indices: 519314--519592 Score: 348
Period size: 148 Copynumber: 1.9 Consensus size: 147
519304 TGGGATATCC
* * * *
519314 TTAAAACCTACCATCGACATAGAAGTGCTTGGAGATCCTAGAGGACTTAGAAAAGATAAAAACAT
1 TTAAAACCTACCATCGACATAAAAGTGCCTGGAGATCCTAAAAGA-TT--AAAA-ATAAAAA-AT
* *
519379 G-CCTACTCCTAATTCATACCTTCGGCGTAGAAGCGAAC-CTAGCAG-TGTTATAGGACTAGGTT
61 GACCTACTCCTAATTCATACCTTCGGCATAGAAACGAACTC-AGCAGCT-TTATAGGACTAGGTT
519441 TTGGAGAAAATGTTAAAATGTTTT
124 TTGGAGAAAATGTTAAAATGTTTT
* * * * *
519465 TTAAGACCTACCATCGACATAAAAGTGCCTGGTGATCCTAAAATATTAAAAATTAAAAGTGAACC
1 TTAAAACCTACCATCGACATAAAAGTGCCTGGAGATCCTAAAAGATTAAAAATAAAAAATG-ACC
* *
519530 TACTCTTAATTCATACCTTCGGCATAGAAACGAACTCAGTAGCTTTATAGGACTAGGTTTTGG
65 TACTCCTAATTCATACCTTCGGCATAGAAACGAACTCAGCAGCTTTATAGGACTAGGTTTTGG
519593 GGGAATGCTA
Statistics
Matches: 111, Mismatches: 13, Indels: 11
0.82 0.10 0.08
Matches are distributed among these distances:
146 2 0.02
147 6 0.05
148 61 0.55
149 2 0.02
150 2 0.02
151 38 0.34
ACGTcount: A:0.35, C:0.18, G:0.19, T:0.28
Consensus pattern (147 bp):
TTAAAACCTACCATCGACATAAAAGTGCCTGGAGATCCTAAAAGATTAAAAATAAAAAATGACCT
ACTCCTAATTCATACCTTCGGCATAGAAACGAACTCAGCAGCTTTATAGGACTAGGTTTTGGAGA
AAATGTTAAAATGTTTT
Found at i:521948 original size:164 final size:159
Alignment explanation
Indices: 521675--522199 Score: 450
Period size: 164 Copynumber: 3.2 Consensus size: 159
521665 TAAATTGAAT
* ** * * *
521675 TTTTCAAAACTAATTTA-ATAAGAATCT-AATGACAATATTAGATGAATTATAAAAAATTT-AAA
1 TTTTCAAAACTAATTTACAT--G-ATTTAAATGATGATATTTGATGAA-TATTAAAATTTTGAAA
* * * * *
521737 TCGAGAAAAATCCCCCTGAAAATATTTATGAAATGGAAAACTTGGTTTTTCAAAAACAAGAGAAT
62 T-GAGAAAAATCCTCCTGAAAACATTTATGGAATAGAAAATTTGGTTTTTCAAAAACAAGA-AAT
521802 TTCGAGGAAAAAATGAAAAACTTATGAAAATAAATAAAA
125 TTC-AGGAAAAAAT-AAAAACTTATG-AAATAAA-AAAA
*
521841 TTTTCAAAACTAATTTACTATGATTTAAATGATGATATTTGATGAATATTAAAATTTTGAACTGA
1 TTTTCAAAACTAATTTAC-ATGATTTAAATGATGATATTTGATGAATATTAAAATTTTGAAATGA
* *
521906 -AAAAATCCTCCTGAAAACATTTATGGAATAGAAAATTTGGTTTTTCAAAAATAGGAAAATTTCA
65 GAAAAATCCTCCTGAAAACATTTATGGAATAGAAAATTTGGTTTTTCAAAAACAAG-AAATTTC-
* *
521970 AGAAAAAAATAAAAAACTCATG-------AAAA
128 AGGAAAAAAT-AAAAACTTATGAAATAAAAAAA
* *
521996 -TTTCAAAACTGATTTACAGTGATTTAAATGATGATATTTGATGAATATTTAAAATTTTGAATTG
1 TTTTCAAAACTAATTTACA-TGATTTAAATGATGATATTTGATGAATA-TTAAAATTTTGAAATG
* ** * * * *
522060 AGAAAAACCCTTCCCCAATAACATTTATGGAATAAAAAACTCT-ATATTTTGAAAATACAA-AAA
64 AGAAAAATCC-TCCTGAA-AACATTTATGGAATAGAAAA-TTTGGT-TTTTCAAAA-ACAAGAAA
* *
522123 TTTCAAGAAAAAATAAAAAATTCATGAAATAAAAGAAAA
124 TTTCAGGAAAAAATAAAAACTT-ATGAAAT-AAA-AAAA
* * * *
522162 TTTTCAAAATTGATTTA-GTGAATTAAATGATGATATTT
1 TTTTCAAAACTAATTTACATGATTTAAATGATGATATTT
522200 AAAGAATTTT
Statistics
Matches: 299, Mismatches: 36, Indels: 49
0.78 0.09 0.13
Matches are distributed among these distances:
153 1 0.00
154 44 0.15
155 20 0.07
156 13 0.04
157 16 0.05
158 27 0.09
159 10 0.03
160 2 0.01
164 73 0.24
165 35 0.12
166 41 0.14
167 15 0.05
168 2 0.01
ACGTcount: A:0.49, C:0.09, G:0.11, T:0.32
Consensus pattern (159 bp):
TTTTCAAAACTAATTTACATGATTTAAATGATGATATTTGATGAATATTAAAATTTTGAAATGAG
AAAAATCCTCCTGAAAACATTTATGGAATAGAAAATTTGGTTTTTCAAAAACAAGAAATTTCAGG
AAAAAATAAAAACTTATGAAATAAAAAAA
Found at i:522019 original size:154 final size:158
Alignment explanation
Indices: 521837--522151 Score: 430
Period size: 154 Copynumber: 2.0 Consensus size: 158
521827 GAAAATAAAT
521837 AAAATTTTCAAAACTAATTTACTATGATTTAAATGATGATATTTGATGAATA-TTAAAATTTTGA
1 AAAATTTTCAAAACTAATTTACTATGATTTAAATGATGATATTTGATGAATATTTAAAATTTTGA
* ** * * * **
521901 ACTGA-AAAAATCC-TCCTGAA-AACATTTATGGAATAGAAAA-TTTGGT-TTTTCAAAAATAGG
66 ACTGAGAAAAACCCTTCCCCAATAACATTTATGGAATAAAAAACTCT-ATATTTT-AAAAATACA
521961 AAAATTTCAAGAAAAAAATAAAAAACTCATG
129 AAAATTTCAAG-AAAAAATAAAAAACTCATG
*
521992 AAAA-TTTCAAAACTGATTTAC-AGTGATTTAAATGATGATATTTGATGAATATTTAAAATTTTG
1 AAAATTTTCAAAACTAATTTACTA-TGATTTAAATGATGATATTTGATGAATATTTAAAATTTTG
* *
522055 AATTGAGAAAAACCCTTCCCCAATAACATTTATGGAATAAAAAACTCTATATTTTGAAAATACAA
65 AACTGAGAAAAACCCTTCCCCAATAACATTTATGGAATAAAAAACTCTATATTTTAAAAATACAA
*
522120 AAATTTCAAGAAAAAATAAAAAATTCATG
130 AAATTTCAAGAAAAAATAAAAAACTCATG
522149 AAA
1 AAA
522152 TAAAAGAAAA
Statistics
Matches: 141, Mismatches: 12, Indels: 12
0.85 0.07 0.07
Matches are distributed among these distances:
153 1 0.01
154 44 0.31
155 20 0.14
156 7 0.05
157 26 0.18
158 37 0.26
159 6 0.04
ACGTcount: A:0.48, C:0.09, G:0.10, T:0.32
Consensus pattern (158 bp):
AAAATTTTCAAAACTAATTTACTATGATTTAAATGATGATATTTGATGAATATTTAAAATTTTGA
ACTGAGAAAAACCCTTCCCCAATAACATTTATGGAATAAAAAACTCTATATTTTAAAAATACAAA
AATTTCAAGAAAAAATAAAAAACTCATG
Found at i:522140 original size:19 final size:19
Alignment explanation
Indices: 522118--522164 Score: 51
Period size: 19 Copynumber: 2.4 Consensus size: 19
522108 TTGAAAATAC
522118 AAAAATTTCAAGAAA-AAA
1 AAAAATTTCAAGAAATAAA
* *
522136 TAAAAAATTCATGAAATAAA
1 -AAAAATTTCAAGAAATAAA
522156 AGAAAATTT
1 A-AAAATTT
522165 TCAAAATTGA
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
19 14 0.61
20 9 0.39
ACGTcount: A:0.66, C:0.04, G:0.06, T:0.23
Consensus pattern (19 bp):
AAAAATTTCAAGAAATAAA
Found at i:525794 original size:149 final size:150
Alignment explanation
Indices: 525544--525813 Score: 357
Period size: 149 Copynumber: 1.8 Consensus size: 150
525534 ATATCCTAGA
* * * * * **
525544 GGACTTGGAAAAGATAAAAACAAACCCATTCATAATTCACACCTTTGGCGTAGAAGCGGACTCGA
1 GGACTTGAAAAAGATAAAAACAAACCCACTCATAATTAACACCTTTGACATAGAAGCAAACTCGA
** * *
525609 TAGTTTTATAAGGCTAGGTTTTGGGGAAAATGCTAAAATATCTCTAAGGTTTACCAACGACTTAG
66 TAGTTTTATAAGGCTAGGTTTCAGGGAAAATACTAAAATATCCCTAAGGTTTACCAACGACTTAG
525674 AAGTGCCCGATGATCGTAAG
131 AAGTGCCCGATGATCGTAAG
* * *
525694 GGACTTGAAAAAGATAAAAACAAA-CCACTCCTAATTAATA-CTTTCGACATAGAAGCAAACTGG
1 GGACTTGAAAAAGATAAAAACAAACCCACTCATAATTAACACCTTT-GACATAGAAGCAAACTCG
* *
525757 GTAGTTTT-TTAGGACTAGGTTTCAGGGAAAATACTAAAATATCCCTAAGGTTTACCA
65 ATAGTTTTATAAGG-CTAGGTTTCAGGGAAAATACTAAAATATCCCTAAGGTTTACCA
525814 TTGCCTTAAA
Statistics
Matches: 102, Mismatches: 16, Indels: 5
0.83 0.13 0.04
Matches are distributed among these distances:
148 8 0.08
149 71 0.70
150 23 0.23
ACGTcount: A:0.37, C:0.17, G:0.20, T:0.26
Consensus pattern (150 bp):
GGACTTGAAAAAGATAAAAACAAACCCACTCATAATTAACACCTTTGACATAGAAGCAAACTCGA
TAGTTTTATAAGGCTAGGTTTCAGGGAAAATACTAAAATATCCCTAAGGTTTACCAACGACTTAG
AAGTGCCCGATGATCGTAAG
Found at i:527297 original size:10 final size:10
Alignment explanation
Indices: 527278--527306 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
527268 TAGTTGGAAA
527278 AAAT-AAATT
1 AAATAAAATT
527287 AAATAAAATT
1 AAATAAAATT
527297 AAATAAAATT
1 AAATAAAATT
527307 TTTAAAAATC
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 4 0.21
10 15 0.79
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (10 bp):
AAATAAAATT
Found at i:527717 original size:166 final size:163
Alignment explanation
Indices: 527398--527753 Score: 391
Period size: 166 Copynumber: 2.1 Consensus size: 163
527388 GATCAGAAGT
* * *
527398 TGAAATAAATTGAGTTTTTAAAAATGATTTAATGTGAATTTAATGATAATAATAGATGAATTTTA
1 TGAAATAAA-TGAATTTTTAAAAATAATTTAATGTGAATTTAATGACAATAATAGATGAATTTTA
* * * * *
527463 AAAATTTTAAATCAAGAAAAGTCCCTTCGAAAATATTTAGGAATAGAAAACTTAGTTTTTTAGAA
65 AAAATTTTAAACCAAGAAAAGACCC-TCGAAAATATTTAGGAAGAGAAAACTTAGTATTTCAGAA
* *
527528 ATAGGAGAATTTTAGAGAAAAAAATGAAAAAATTA
129 ATAGGAGAATTTAAGAGAAAAAAATGAAAAAATCA
* *
527563 TGAAAATAAATGAATTTTTCAAAAATAATTTAATTTGAATTTAATGACAATATTAGATGAATTTT
1 TG-AAATAAATGAATTTTT-AAAAATAATTTAATGTGAATTTAATGACAATAATAGATGAATTTT
* * *
527628 AAAAATTTTGAACCGAGAAAA-ACACC-CGAAAATATTTACGGAAGAGCAAACTCT-GTATTTCA
64 AAAAATTTTAAACCAAGAAAAGAC-CCTCGAAAATATTTA-GGAAGAGAAAACT-TAGTATTTCA
* *
527690 -AAATCATGTAG-ATTTCAAG-GAAAAAAAATGAAAAACTCA
126 GAAAT-A-GGAGAATTT-AAGAG-AAAAAAATGAAAAAATCA
* *
527729 TGAAATAAAAGGAATTTTGAAAAAT
1 TGAAAT-AAATGAATTTTTAAAAAT
527754 TGATTTGATG
Statistics
Matches: 162, Mismatches: 19, Indels: 20
0.81 0.09 0.10
Matches are distributed among these distances:
164 16 0.10
165 44 0.27
166 102 0.63
ACGTcount: A:0.49, C:0.06, G:0.13, T:0.31
Consensus pattern (163 bp):
TGAAATAAATGAATTTTTAAAAATAATTTAATGTGAATTTAATGACAATAATAGATGAATTTTAA
AAATTTTAAACCAAGAAAAGACCCTCGAAAATATTTAGGAAGAGAAAACTTAGTATTTCAGAAAT
AGGAGAATTTAAGAGAAAAAAATGAAAAAATCA
Found at i:536524 original size:13 final size:13
Alignment explanation
Indices: 536506--536543 Score: 58
Period size: 13 Copynumber: 2.9 Consensus size: 13
536496 CAGCATTCTC
*
536506 TGTATCGATACAT
1 TGTATCGATACAG
536519 TGTATCGATACAG
1 TGTATCGATACAG
*
536532 TGTATCAATACA
1 TGTATCGATACA
536544 AGGGGTTTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Consensus pattern (13 bp):
TGTATCGATACAG
Found at i:537016 original size:20 final size:21
Alignment explanation
Indices: 536981--537032 Score: 70
Period size: 21 Copynumber: 2.4 Consensus size: 21
536971 CCCCTAGGCA
*
536981 GCACCCACCGGGTCGCAA-CTG
1 GCACCC-CCAGGTCGCAACCTG
537002 GCACCCCCAGGTCGCAACCTG
1 GCACCCCCAGGTCGCAACCTG
537023 GCAGCCCCCA
1 GCA-CCCCCA
537033 CACTAGCAGC
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
20 10 0.36
21 12 0.43
22 6 0.21
ACGTcount: A:0.19, C:0.48, G:0.25, T:0.08
Consensus pattern (21 bp):
GCACCCCCAGGTCGCAACCTG
Found at i:538478 original size:21 final size:22
Alignment explanation
Indices: 538438--538482 Score: 74
Period size: 22 Copynumber: 2.0 Consensus size: 22
538428 CGAAATTGTT
538438 AAATTATTTTATTAAGGGGGAG
1 AAATTATTTTATTAAGGGGGAG
538460 AAATT-TTTTGATTAAGGGGGAG
1 AAATTATTTT-ATTAAGGGGGAG
538482 A
1 A
538483 GAAAAGAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
21 4 0.18
22 18 0.82
ACGTcount: A:0.36, C:0.00, G:0.29, T:0.36
Consensus pattern (22 bp):
AAATTATTTTATTAAGGGGGAG
Found at i:539206 original size:20 final size:21
Alignment explanation
Indices: 539181--539235 Score: 76
Period size: 20 Copynumber: 2.7 Consensus size: 21
539171 GTATTGATAC
**
539181 AATGTATCGATACATGACCA-
1 AATGTATCGATACATGAAAAG
*
539201 AATGTATCGATACTTGAAAAG
1 AATGTATCGATACATGAAAAG
539222 AATGTATCGATACA
1 AATGTATCGATACA
539236 GGTCATTGGT
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
20 17 0.57
21 13 0.43
ACGTcount: A:0.42, C:0.15, G:0.16, T:0.27
Consensus pattern (21 bp):
AATGTATCGATACATGAAAAG
Found at i:539305 original size:27 final size:27
Alignment explanation
Indices: 539267--539350 Score: 100
Period size: 27 Copynumber: 3.0 Consensus size: 27
539257 GTAGCCAAAT
*
539267 TGTATCGATACACAATATGTATCGATA
1 TGTATCGATACACAAAATGTATCGATA
539294 TGTATCGATACATCACAAAT-TATCGATA
1 TGTATCGATACA-CA-AAATGTATCGATA
539322 T-TATCGATACATCACAAAATGTATCGATA
1 TGTATCGAT--A-CACAAAATGTATCGATA
539351 CATTGGCTTG
Statistics
Matches: 50, Mismatches: 1, Indels: 10
0.82 0.02 0.16
Matches are distributed among these distances:
27 19 0.38
28 15 0.30
29 14 0.28
30 2 0.04
ACGTcount: A:0.39, C:0.17, G:0.12, T:0.32
Consensus pattern (27 bp):
TGTATCGATACACAAAATGTATCGATA
Found at i:542319 original size:20 final size:22
Alignment explanation
Indices: 542274--542321 Score: 57
Period size: 20 Copynumber: 2.3 Consensus size: 22
542264 TATGGATATG
542274 TATAT-ATAATAAAATCAAAAT
1 TATATCATAATAAAATCAAAAT
* *
542295 CATATCATAA-AAAA-CAACAT
1 TATATCATAATAAAATCAAAAT
542315 TATATCA
1 TATATCA
542322 ACAAGCAACA
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
20 11 0.48
21 8 0.35
22 4 0.17
ACGTcount: A:0.58, C:0.12, G:0.00, T:0.29
Consensus pattern (22 bp):
TATATCATAATAAAATCAAAAT
Found at i:545202 original size:69 final size:70
Alignment explanation
Indices: 545111--545773 Score: 418
Period size: 69 Copynumber: 9.4 Consensus size: 70
545101 GGTGGCATCT
* *
545111 TTTTATCC-TTTTAGTCTTCAAAGAGCAAGATGTTTTTTCTTTTCAAAACCCACACAAGTTGGTG
1 TTTTATCCTTTTTAGTCCTCAAAGAGCAAGATGTTTTTTCTTTTCAAAGCCCACACAAGTTGGTG
545175 AGACC
66 AGACC
* *
545180 TTTTA-CCTTTTTAGTCCTCAAAGAGCAGGATG-CTTTT-TTTT-AAAGCCCACACAAGTTGGTG
1 TTTTATCCTTTTTAGTCCTCAAAGAGCAAGATGTTTTTTCTTTTCAAAGCCCACACAAGTTGGTG
*
545241 -GCATC
66 AG-ACC
* * * *
545246 TTTTA-CCTTTTTAGTCTTCAAAGAGCAGGACGTTTTTTCTCTT-AAAGCCCACACAAGTTGGTG
1 TTTTATCCTTTTTAGTCCTCAAAGAGCAAGATGTTTTTTCTTTTCAAAGCCCACACAAGTTGGT-
*
545309 GCATACC
65 G-AGACC
* * * ** * * * * *
545316 TTTTTATCC-TTTTAGTCCTTAAAGAGCCGGACAT-TTTTTTCTTTTTGAAGCGCGCGCAAGCTA
1 -TTTTATCCTTTTTAGTCCTCAAAGAG-C-AAGATGTTTTTTCTTTTCAAAGCCCACACAAGTTG
545379 GTG-GCACCC
63 GTGAG-A-CC
* ** * *
545388 ATTTTATACTTTTTTCTCCTCAAAGAGTAAGATACTTTTCCTTTTTCTTTTTCAAAGCCCACACA
1 -TTTTATCCTTTTTAGTCCTCAAAGAGCAAG--A--TGT--TTTTTC-TTTTCAAAGCCCACACA
* * * *
545453 AGCTAGTGACATCT
58 AGTTGGTGAGA-CC
* * *
545467 TTTTATCC-TTTTAGTCTTTCAAAGAACAAGATG-CTTTT-TTTTCAAAGCCCACACAAGTTGGT
1 TTTTATCCTTTTTAGTC-CTCAAAGAGCAAGATGTTTTTTCTTTTCAAAGCCCACACAAGTTGGT
*
545529 GACACC
65 GAGACC
* * ** * *
545535 -TTTA-CCTTTTTAGTCTTTAAAGAGCAAGACACTTTTTT-TTTCCAAAGCCCACATAAGTTGGT
1 TTTTATCCTTTTTAGTCCTCAAAGAGCAAGA-TGTTTTTTCTTTTCAAAGCCCACACAAGTTGGT
*
545597 G-GCATC
65 GAG-ACC
* ** * * *
545603 TTTTA-CCTTTTTAGTCCTCAAAGAGCAGGACATTTTTTCTCTT-AAAGCTCACACAAGTTAGTG
1 TTTTATCCTTTTTAGTCCTCAAAGAGCAAGATGTTTTTTCTTTTCAAAGCCCACACAAGTTGGT-
*
545666 GCACACC
65 G-AGACC
* * ** * * *
545673 TTTTTATCC-TTTTAGTCCTTAAAGAGGAAGATGCACTTTTCTTTTTAAAGCCCACACAAGCTAG
1 -TTTTATCCTTTTTAGTCCTCAAAGAGCAAGATG-TTTTTTCTTTTCAAAGCCCACACAAGTTGG
545737 TG-GCACCC
64 TGAG-A-CC
*
545745 GTTTTATACATTTTTA-TCCTCAAAGAGCA
1 -TTTTAT-CCTTTTTAGTCCTCAAAGAGCA
545774 TGACACTTTT
Statistics
Matches: 464, Mismatches: 88, Indels: 80
0.73 0.14 0.13
Matches are distributed among these distances:
65 1 0.00
66 65 0.14
67 20 0.04
68 80 0.17
69 83 0.18
70 4 0.01
71 51 0.11
72 42 0.09
73 58 0.12
74 6 0.01
75 1 0.00
76 2 0.00
77 6 0.01
78 23 0.05
79 22 0.05
ACGTcount: A:0.26, C:0.22, G:0.15, T:0.37
Consensus pattern (70 bp):
TTTTATCCTTTTTAGTCCTCAAAGAGCAAGATGTTTTTTCTTTTCAAAGCCCACACAAGTTGGTG
AGACC
Found at i:545735 original size:357 final size:355
Alignment explanation
Indices: 545055--545827 Score: 1097
Period size: 357 Copynumber: 2.2 Consensus size: 355
545045 TTTAGTCATT
* * * * ** *
545055 AAGAGCAAGACGCTTTTCCTTTTTCTTTTT-AATGACCACATAAATTGGTGGCATCTTTTTATCC
1 AAGAGCAAGACACTTTTCCTTTTTCTTTTTCAAAGCCCACACAAGCTAGTGGCATCTTTTTATCC
* * *
545119 TTTTAGTCTTCAAAGAGCAAGATGTTTTTTCTTTTCAAAACCCACACAAGTTGGTGAGACCTTTT
66 TTTTAGTCTTCAAAGAACAAGATGTCTTTTCTTTTCAAAACCCACACAAGTTGGTGACACCTTTT
* **
545184 ACCTTTTTAGTCCTCAAAGAGCAGGATGCTTTTTTTTAAAGCCCACACAAGTTGGTGGCATCTTT
131 ACCTTTTTAGTCCTCAAAGAGCAAGACACTTTTTTTTAAAGCCCACACAAGTTGGTGGCATCTTT
* * * *
545249 TACCTTTTTAGTCTTCAAAGAGCAGGACGTTTTTTCTCTTAAAGCCCACACAAGTTGGTGGCATA
196 TACCTTTTTAGTCCTCAAAGAGCAGGACATTTTTTCTCTTAAAGCCCACACAAGTTAGTGGCACA
* ** * * * *
545314 CCTTTTTATCCTTTTAGTCCTTAAAGAGCCGGACATTTTTTTCTTTTTGAAGCGCGCGCAAGCTA
261 CCTTTTTATCCTTTTAGTCCTTAAAGAG-CGAACATACTTTTCTTTTTAAAGCCCACACAAGCTA
* *
545379 GTGGCACCCATTTTATACTTTTTTCTCCTCA
325 GTGGCACCCATTTTATACATTTTTATCCTCA
* * *
545410 AAGAGTAAGATACTTTTCCTTTTTCTTTTTCAAAGCCCACACAAGCTAGTGACATCTTTTTATCC
1 AAGAGCAAGACACTTTTCCTTTTTCTTTTTCAAAGCCCACACAAGCTAGTGGCATCTTTTTATCC
*
545475 TTTTAGTCTTTCAAAGAACAAGATG-CTTTT-TTTTCAAAGCCCACACAAGTTGGTGACACC-TT
66 TTTTAGTC-TTCAAAGAACAAGATGTCTTTTCTTTTCAAAACCCACACAAGTTGGTGACACCTTT
* * *
545537 TACCTTTTTAGTCTTTAAAGAGCAAGACACTTTTTTTTTCCAAAGCCCACATAAGTTGGTGGCAT
130 TACCTTTTTAGTCCTCAAAGAGCAAGACAC-TTTTTTTT--AAAGCCCACACAAGTTGGTGGCAT
*
545602 CTTTTACCTTTTTAGTCCTCAAAGAGCAGGACATTTTTTCTCTTAAAGCTCACACAAGTTAGTGG
192 CTTTTACCTTTTTAGTCCTCAAAGAGCAGGACATTTTTTCTCTTAAAGCCCACACAAGTTAGTGG
*
545667 CACACCTTTTTATCCTTTTAGTCCTTAAAGAG-GAAGATGCACTTTTCTTTTTAAAGCCCACACA
257 CACACCTTTTTATCCTTTTAGTCCTTAAAGAGCGAACAT--ACTTTTCTTTTTAAAGCCCACACA
*
545731 AGCTAGTGGCACCCGTTTTATACATTTTTATCCTCA
320 AGCTAGTGGCACCCATTTTATACATTTTTATCCTCA
* * *
545767 AAGAGCATGACACTTTTTCTTTTTCTTTTTCAAAGCCCACACAAGCTAGTGGCACCTTTTT
1 AAGAGCAAGACACTTTTCCTTTTTCTTTTTCAAAGCCCACACAAGCTAGTGGCATCTTTTT
545828 TTTTTCTTTT
Statistics
Matches: 369, Mismatches: 42, Indels: 12
0.87 0.10 0.03
Matches are distributed among these distances:
354 27 0.07
355 67 0.18
356 39 0.11
357 236 0.64
ACGTcount: A:0.25, C:0.22, G:0.15, T:0.38
Consensus pattern (355 bp):
AAGAGCAAGACACTTTTCCTTTTTCTTTTTCAAAGCCCACACAAGCTAGTGGCATCTTTTTATCC
TTTTAGTCTTCAAAGAACAAGATGTCTTTTCTTTTCAAAACCCACACAAGTTGGTGACACCTTTT
ACCTTTTTAGTCCTCAAAGAGCAAGACACTTTTTTTTAAAGCCCACACAAGTTGGTGGCATCTTT
TACCTTTTTAGTCCTCAAAGAGCAGGACATTTTTTCTCTTAAAGCCCACACAAGTTAGTGGCACA
CCTTTTTATCCTTTTAGTCCTTAAAGAGCGAACATACTTTTCTTTTTAAAGCCCACACAAGCTAG
TGGCACCCATTTTATACATTTTTATCCTCA
Found at i:545868 original size:43 final size:43
Alignment explanation
Indices: 545779--545864 Score: 111
Period size: 42 Copynumber: 2.0 Consensus size: 43
545769 GAGCATGACA
* *
545779 CTTTTTCTTTTTCTTTTTCAAAGCCCACACAAGCTAGTGGCAC
1 CTTTTTCTTTTTCTTTTTCAAAACCCACACAAGCTAGTAGCAC
* * * *
545822 CTTTTT-TTTTTCTTTTTCAAAACCTATACAAGTTGGTAGCAC
1 CTTTTTCTTTTTCTTTTTCAAAACCCACACAAGCTAGTAGCAC
545864 C
1 C
545865 CTTTACCTTT
Statistics
Matches: 37, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
42 31 0.84
43 6 0.16
ACGTcount: A:0.22, C:0.24, G:0.10, T:0.43
Consensus pattern (43 bp):
CTTTTTCTTTTTCTTTTTCAAAACCCACACAAGCTAGTAGCAC
Found at i:545889 original size:118 final size:118
Alignment explanation
Indices: 545709--546087 Score: 462
Period size: 118 Copynumber: 3.2 Consensus size: 118
545699 GAAGATGCAC
* * * * *
545709 TTTTCTTTTT-AAAGCCCACACAAGCTAGTGGCACCCGTTTTATACATTTTTA-TCCTCAAAGAG
1 TTTTCTTTTTCAAAACCCACACAAGTTGGTAGCACCC---TT-TACCTTTTTAGTCCTCAAAGAG
*
545772 CATGACACTTTTTCTTTTTCTTTTTCAAAGCCCACACAAGCTAGTGGCACCTTTT-TT
62 CATGAC-CTTTTTCTTTTTCTTTTTCAAAGCCCACACAAGCTGGTGGCACCTTTTCTT
* * *
545829 TTTTCTTTTTCAAAACCTATACAAGTTGGTAGCACCCTTTACCTTTTTAGTCCTCAAAGAGCAAG
1 TTTTCTTTTTCAAAACCCACACAAGTTGGTAGCACCCTTTACCTTTTTAGTCCTCAAAGAGCATG
* * *
545894 AGGCTTTTCCTTTTTC-TTTTCAAAG-CCAAACAAGCTGGTGGCACCTTTTTCTT
66 A-CCTTTTTCTTTTTCTTTTTCAAAGCCCACACAAGCTGGTGGCACC-TTTTCTT
* * * *
545947 TTTTGTTTTTCAAAGCCCACAGAAGTTGGTGGCACCCTTTACCTTTTTAGTCCTCAAAGAGCATG
1 TTTTCTTTTTCAAAACCCACACAAGTTGGTAGCACCCTTTACCTTTTTAGTCCTCAAAGAGCATG
* * *
546012 ACGTTTTTCTTTTTTCTTTTTCAAAGCCCACACAAGTTGGTGGCAACCTTTTCCT
66 ACCTTTTTC-TTTTTCTTTTTCAAAGCCCACACAAGCTGGTGGC-ACCTTTTCTT
*
546067 TTTTCTTTTTCAAAGCCCACA
1 TTTTCTTTTTCAAAACCCACA
546088 TAAATTGGAG
Statistics
Matches: 224, Mismatches: 26, Indels: 18
0.84 0.10 0.07
Matches are distributed among these distances:
116 18 0.08
117 27 0.12
118 96 0.43
119 9 0.04
120 51 0.23
121 23 0.10
ACGTcount: A:0.23, C:0.25, G:0.13, T:0.39
Consensus pattern (118 bp):
TTTTCTTTTTCAAAACCCACACAAGTTGGTAGCACCCTTTACCTTTTTAGTCCTCAAAGAGCATG
ACCTTTTTCTTTTTCTTTTTCAAAGCCCACACAAGCTGGTGGCACCTTTTCTT
Found at i:545994 original size:44 final size:42
Alignment explanation
Indices: 545897--545994 Score: 115
Period size: 44 Copynumber: 2.3 Consensus size: 42
545887 GAGCAAGAGG
545897 CTTTTCCTTTTTCTTTTCAAAGCCAAACAAGCTGGTGGCACC
1 CTTTTCCTTTTTCTTTTCAAAGCCAAACAAGCTGGTGGCACC
* * * * * *
545939 TTTTTCTTTTTTGTTTTTCAAAGCCCACAGAAGTTGGTGGCACC
1 CTTTTCCTTTTT-CTTTTCAAAG-CCAAACAAGCTGGTGGCACC
*
545983 CTTTACCTTTTT
1 CTTTTCCTTTTT
545995 AGTCCTCAAA
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
42 10 0.22
43 9 0.20
44 26 0.58
ACGTcount: A:0.18, C:0.24, G:0.14, T:0.43
Consensus pattern (42 bp):
CTTTTCCTTTTTCTTTTCAAAGCCAAACAAGCTGGTGGCACC
Found at i:553468 original size:38 final size:39
Alignment explanation
Indices: 553420--553498 Score: 142
Period size: 38 Copynumber: 2.1 Consensus size: 39
553410 ATGAGGATGA
553420 TAAAAGGGAGGTTAAAATAGGAACCATAATTAATCAATC
1 TAAAAGGGAGGTTAAAATAGGAACCATAATTAATCAATC
*
553459 TAAAA-GGAGGTTAAAATAGGAACCATAATTAATTAATC
1 TAAAAGGGAGGTTAAAATAGGAACCATAATTAATCAATC
553497 TA
1 TA
553499 CTTGACAGGA
Statistics
Matches: 39, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
38 34 0.87
39 5 0.13
ACGTcount: A:0.49, C:0.09, G:0.16, T:0.25
Consensus pattern (39 bp):
TAAAAGGGAGGTTAAAATAGGAACCATAATTAATCAATC
Found at i:558222 original size:44 final size:44
Alignment explanation
Indices: 558182--558298 Score: 128
Period size: 44 Copynumber: 2.7 Consensus size: 44
558172 TCATTTTCTC
558182 CTGACATATGGTTACCACCCTAGTCAAATTTTTCTTATTTTGAT
1 CTGACATATGGTTACCACCCTAGTCAAATTTTTCTTATTTTGAT
* * * * * * *
558226 TTGACGTGTGGTTACCACCTTAGTCAGATTTTTCTCATTCTGAT
1 CTGACATATGGTTACCACCCTAGTCAAATTTTTCTTATTTTGAT
* * *
558270 TTGACATCTAGTTACCACCCT-GATCAAAT
1 CTGACATATGGTTACCACCCTAG-TCAAAT
558299 CCACTTTTTT
Statistics
Matches: 60, Mismatches: 12, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
43 1 0.02
44 59 0.98
ACGTcount: A:0.24, C:0.22, G:0.14, T:0.40
Consensus pattern (44 bp):
CTGACATATGGTTACCACCCTAGTCAAATTTTTCTTATTTTGAT
Found at i:558520 original size:42 final size:42
Alignment explanation
Indices: 558454--559022 Score: 377
Period size: 42 Copynumber: 13.5 Consensus size: 42
558444 TCCTACCTTC
* * * * *
558454 AGTCTGCCTATCAGTTTTGACCTTGGAGATTGCCTCATCTCA
1 AGTCTGCCTGTCGGCTTTGACCTTGGAGATTACCTCACCTCA
* * ** *
558496 AGTTTGCCTGTCGGCTTTAACCTTGGAGACTT-TTTTACCTTC-
1 AGTCTGCCTGTCGGCTTTGACCTTGGAGA-TTACCTCACC-TCA
* * * * * * ** *
558538 AGTCTGCCTATCGGTTTTGACCTAGCAGACTGCCTCAAATTA
1 AGTCTGCCTGTCGGCTTTGACCTTGGAGATTACCTCACCTCA
* ** ** * *
558580 AGTCTGCTTGTTAGCTTTGACCTTGGAGACTT-TTTTACC-CTT
1 AGTCTGCCTGTCGGCTTTGACCTTGGAGA-TTACCTCACCTC-A
* *
558622 AGTCTGCCTATCGGCTTTGACCTTGGAGACTACCTCACCTCA
1 AGTCTGCCTGTCGGCTTTGACCTTGGAGATTACCTCACCTCA
* ** * * * *
558664 AGTCTACCTGTTAGATTTGACCCTAGAGACTTTCCT-ACCTTC-
1 AGTCTGCCTGTCGGCTTTGACCTTGGAGA-TTACCTCACC-TCA
558706 AGTCTGCCTGTCGGCTTTGACCTTGGAGATTACCTCACCTCA
1 AGTCTGCCTGTCGGCTTTGACCTTGGAGATTACCTCACCTCA
** * * *
558748 AGTCTGTTTGTCGGCTTTAACCTTGGAGACTT-TCTTACCCTC-
1 AGTCTGCCTGTCGGCTTTGACCTTGGAGA-TTACCTCA-CCTCA
* * * * *
558790 AGTCTGCCTATCGACTTTGACCTTGGAGACTGCCTCATCTCA
1 AGTCTGCCTGTCGGCTTTGACCTTGGAGATTACCTCACCTCA
* * *
558832 AGTCTACCTGTCGGCTTTGACCCTGGAGACTTTCCT-ACCATC-
1 AGTCTGCCTGTCGGCTTTGACCTTGGAGA-TTACCTCACC-TCA
* * * *
558874 AGTCTGCCTGTCGACTTTGACCTTGGAGACTACCTCATCTTA
1 AGTCTGCCTGTCGGCTTTGACCTTGGAGATTACCTCACCTCA
* * * * *
558916 AGTCTGCCTGTCGACTTTGACCCTGGAGACTATCTCATCTCA
1 AGTCTGCCTGTCGGCTTTGACCTTGGAGATTACCTCACCTCA
* * * * *
558958 AATCTGCTTGTCGGCTTTGACCCTGGAGACTT-CCTTACCCTAA
1 AGTCTGCCTGTCGGCTTTGACCTTGGAGA-TTACCTCA-CCTCA
* *
559001 AGTCTGCCTATCAGCTTTGACC
1 AGTCTGCCTGTCGGCTTTGACC
559023 CTAGAGACTT
Statistics
Matches: 400, Mismatches: 105, Indels: 43
0.73 0.19 0.08
Matches are distributed among these distances:
41 19 0.05
42 335 0.84
43 46 0.12
ACGTcount: A:0.18, C:0.29, G:0.19, T:0.34
Consensus pattern (42 bp):
AGTCTGCCTGTCGGCTTTGACCTTGGAGATTACCTCACCTCA
Found at i:558597 original size:84 final size:84
Alignment explanation
Indices: 558442--559041 Score: 603
Period size: 84 Copynumber: 7.1 Consensus size: 84
558432 CCATTTGAAT
* * * * * *
558442 TTTCCTACCTTCAGTCTGCCTATCAGTTTTGACCTTGGAGATTGCCTCATCTCAAGTTTGCCTGT
1 TTTCTTACCTTCAGTCTGCCTATCGGCTTTGACCTTGGAGACTACCTCATCTCAAGTCTGCCTGT
*
558507 CGGCTTTAACCTTGGAGAC
66 CGGCTTTGACCTTGGAGAC
* * * * * ** * *
558526 TTTTTTACCTTCAGTCTGCCTATCGGTTTTGACCTAGCAGACTGCCTCAAATTAAGTCTGCTTGT
1 TTTCTTACCTTCAGTCTGCCTATCGGCTTTGACCTTGGAGACTACCTCATCTCAAGTCTGCCTGT
**
558591 TAGCTTTGACCTTGGAGAC
66 CGGCTTTGACCTTGGAGAC
* * *
558610 TTTTTTACCCTT-AGTCTGCCTATCGGCTTTGACCTTGGAGACTACCTCACCTCAAGTCTACCTG
1 TTTCTTA-CCTTCAGTCTGCCTATCGGCTTTGACCTTGGAGACTACCTCATCTCAAGTCTGCCTG
** * * *
558674 TTAGATTTGACCCTAGAGAC
65 TCGGCTTTGACCTTGGAGAC
* * * * **
558694 TTTCCTACCTTCAGTCTGCCTGTCGGCTTTGACCTTGGAGATTACCTCACCTCAAGTCTGTTTGT
1 TTTCTTACCTTCAGTCTGCCTATCGGCTTTGACCTTGGAGACTACCTCATCTCAAGTCTGCCTGT
*
558759 CGGCTTTAACCTTGGAGAC
66 CGGCTTTGACCTTGGAGAC
* * * *
558778 TTTCTTACCCTCAGTCTGCCTATCGACTTTGACCTTGGAGACTGCCTCATCTCAAGTCTACCTGT
1 TTTCTTACCTTCAGTCTGCCTATCGGCTTTGACCTTGGAGACTACCTCATCTCAAGTCTGCCTGT
*
558843 CGGCTTTGACCCTGGAGAC
66 CGGCTTTGACCTTGGAGAC
* * * * *
558862 TTTCCTACCATCAGTCTGCCTGTCGACTTTGACCTTGGAGACTACCTCATCTTAAGTCTGCCTGT
1 TTTCTTACCTTCAGTCTGCCTATCGGCTTTGACCTTGGAGACTACCTCATCTCAAGTCTGCCTGT
* *
558927 CGACTTTGACCCTGGAGAC
66 CGGCTTTGACCTTGGAGAC
* * * * * * * * * * *
558946 TATCTCATC-TCAAATCTGCTTGTCGGCTTTGACCCTGGAGACTTCCTTACCCTAAAGTCTGCCT
1 TTTCTTACCTTC-AGTCTGCCTATCGGCTTTGACCTTGGAGACTACCTCA-TCTCAAGTCTGCCT
* * * *
559010 ATCAGCTTTGACCCTAGAGAC
64 GTCGGCTTTGACCTTGGAGAC
559031 TTT-TTCACCTT
1 TTTCTT-ACCTT
559042 TTATCTGCCC
Statistics
Matches: 433, Mismatches: 77, Indels: 10
0.83 0.15 0.02
Matches are distributed among these distances:
83 6 0.01
84 389 0.90
85 37 0.09
86 1 0.00
ACGTcount: A:0.18, C:0.29, G:0.18, T:0.35
Consensus pattern (84 bp):
TTTCTTACCTTCAGTCTGCCTATCGGCTTTGACCTTGGAGACTACCTCATCTCAAGTCTGCCTGT
CGGCTTTGACCTTGGAGAC
Found at i:559765 original size:62 final size:61
Alignment explanation
Indices: 559668--559843 Score: 288
Period size: 57 Copynumber: 2.9 Consensus size: 61
559658 CCGAATTTGG
559668 TGGATTTCATGTTTAATTTGCTGCCACCTAAGCTTTCTAGGTGTCACTGCATTGCATTGCAT
1 TGGATTTCATGTTTAATTTGCTGCCACCTAAGCTTTCTAGGTGTCA-TGCATTGCATTGCAT
* *
559730 TGGATTTCGTGTTTAATTTGTTGCCACCTAAGCTTTCTAGGTGTCA--C--TGCATTGCAT
1 TGGATTTCATGTTTAATTTGCTGCCACCTAAGCTTTCTAGGTGTCATGCATTGCATTGCAT
559787 TGGATTTCATGTTTAATTTGCTGCCACCTAAGCTTTCTAGGTGTCATTGCATTGCAT
1 TGGATTTCATGTTTAATTTGCTGCCACCTAAGCTTTCTAGGTGTCA-TGCATTGCAT
559844 GCTTTCATTT
Statistics
Matches: 105, Mismatches: 4, Indels: 10
0.88 0.03 0.08
Matches are distributed among these distances:
57 54 0.51
59 1 0.01
60 1 0.01
62 49 0.47
ACGTcount: A:0.19, C:0.20, G:0.20, T:0.41
Consensus pattern (61 bp):
TGGATTTCATGTTTAATTTGCTGCCACCTAAGCTTTCTAGGTGTCATGCATTGCATTGCAT
Found at i:560470 original size:37 final size:34
Alignment explanation
Indices: 560384--560470 Score: 79
Period size: 34 Copynumber: 2.4 Consensus size: 34
560374 AACAGGGGGG
*
560384 AGGAGGAAAAAAAGAGAAAGAAAAAACCAAAAATT
1 AGGAGGAAAAAAA-AGAAAGAAAAAACCAAAAATC
* *
560419 A-CAGCAAAACAAAAGCAAA-AAAAAACAACACAAAATC
1 AGGAGGAAAA-AAAAG-AAAGAAAAAAC--CA-AAAATC
560456 AGGAGGAAAAAAAAG
1 AGGAGGAAAAAAAAG
560471 GAAATTATAG
Statistics
Matches: 41, Mismatches: 5, Indels: 10
0.73 0.09 0.18
Matches are distributed among these distances:
34 15 0.37
35 7 0.17
36 2 0.05
37 11 0.27
38 6 0.15
ACGTcount: A:0.69, C:0.11, G:0.16, T:0.03
Consensus pattern (34 bp):
AGGAGGAAAAAAAAGAAAGAAAAAACCAAAAATC
Found at i:560857 original size:22 final size:22
Alignment explanation
Indices: 560809--560860 Score: 68
Period size: 22 Copynumber: 2.4 Consensus size: 22
560799 CACCTGCAAG
* *
560809 CAAGCAAACACCAACAAAACAG
1 CAAGCAAGCACCAACAAAACAA
* *
560831 TAAGCAAGCACCAGCAAAACAA
1 CAAGCAAGCACCAACAAAACAA
560853 CAAGCAAG
1 CAAGCAAG
560861 GAAGACAATT
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.56, C:0.29, G:0.13, T:0.02
Consensus pattern (22 bp):
CAAGCAAGCACCAACAAAACAA
Found at i:562378 original size:20 final size:20
Alignment explanation
Indices: 562353--562416 Score: 79
Period size: 20 Copynumber: 3.5 Consensus size: 20
562343 CTAAGTGAAA
562353 TGTATCGATACATGGGACAT
1 TGTATCGATACATGGGACAT
562373 TGTATCGATAC----G---T
1 TGTATCGATACATGGGACAT
562386 TGTATCGATACATGGGACAT
1 TGTATCGATACATGGGACAT
562406 TGTATCGATAC
1 TGTATCGATAC
562417 GTTGTATCGA
Statistics
Matches: 37, Mismatches: 0, Indels: 14
0.73 0.00 0.27
Matches are distributed among these distances:
13 12 0.32
16 1 0.03
17 1 0.03
20 23 0.62
ACGTcount: A:0.28, C:0.16, G:0.23, T:0.33
Consensus pattern (20 bp):
TGTATCGATACATGGGACAT
Found at i:562390 original size:13 final size:13
Alignment explanation
Indices: 562372--562429 Score: 53
Period size: 13 Copynumber: 3.9 Consensus size: 13
562362 ACATGGGACA
562372 TTGTATCGATACG
1 TTGTATCGATACG
562385 TTGTATCGATACATGGG
1 TTGTATCGATAC----G
562402 ACATTGTATCGATACG
1 ---TTGTATCGATACG
562418 TTGTATCGATAC
1 TTGTATCGATAC
562430 ACGATAAAAA
Statistics
Matches: 38, Mismatches: 0, Indels: 14
0.73 0.00 0.27
Matches are distributed among these distances:
13 24 0.63
16 1 0.03
17 1 0.03
20 12 0.32
ACGTcount: A:0.26, C:0.16, G:0.22, T:0.36
Consensus pattern (13 bp):
TTGTATCGATACG
Found at i:562395 original size:33 final size:33
Alignment explanation
Indices: 562353--562430 Score: 156
Period size: 33 Copynumber: 2.4 Consensus size: 33
562343 CTAAGTGAAA
562353 TGTATCGATACATGGGACATTGTATCGATACGT
1 TGTATCGATACATGGGACATTGTATCGATACGT
562386 TGTATCGATACATGGGACATTGTATCGATACGT
1 TGTATCGATACATGGGACATTGTATCGATACGT
562419 TGTATCGATACA
1 TGTATCGATACA
562431 CGATAAAAAG
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 45 1.00
ACGTcount: A:0.28, C:0.15, G:0.23, T:0.33
Consensus pattern (33 bp):
TGTATCGATACATGGGACATTGTATCGATACGT
Found at i:562444 original size:33 final size:33
Alignment explanation
Indices: 562374--562454 Score: 99
Period size: 33 Copynumber: 2.5 Consensus size: 33
562364 ATGGGACATT
* * * **
562374 GTATCGATACGTTGTATCGATACATGGGACATT
1 GTATCGATACGTTGTATCGATACACGAGAAAAA
*
562407 GTATCGATACGTTGTATCGATACACGATAAAAA
1 GTATCGATACGTTGTATCGATACACGAGAAAAA
*
562440 GTATCGATACATTGT
1 GTATCGATACGTTGT
562455 GCCCAACGGC
Statistics
Matches: 41, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
33 41 1.00
ACGTcount: A:0.32, C:0.15, G:0.21, T:0.32
Consensus pattern (33 bp):
GTATCGATACGTTGTATCGATACACGAGAAAAA
Found at i:567174 original size:16 final size:16
Alignment explanation
Indices: 567150--567180 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
567140 AAAGGCATTC
*
567150 AAAATTTTTAATAGAA
1 AAAAGTTTTAATAGAA
567166 AAAAGTTTTAATAGA
1 AAAAGTTTTAATAGA
567181 GGAAATGTTG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.55, C:0.00, G:0.10, T:0.35
Consensus pattern (16 bp):
AAAAGTTTTAATAGAA
Found at i:571199 original size:19 final size:19
Alignment explanation
Indices: 571172--571227 Score: 76
Period size: 19 Copynumber: 2.9 Consensus size: 19
571162 TGTATTGATA
*
571172 CATTGTATCGATACATGTT
1 CATTGTATCGATACATGCT
* *
571191 CATTTTATCGATACATACT
1 CATTGTATCGATACATGCT
571210 CAATTGTATCGATACATG
1 C-ATTGTATCGATACATG
571228 AAACTAGCAG
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
19 17 0.55
20 14 0.45
ACGTcount: A:0.30, C:0.18, G:0.12, T:0.39
Consensus pattern (19 bp):
CATTGTATCGATACATGCT
Found at i:571294 original size:13 final size:13
Alignment explanation
Indices: 571276--571300 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
571266 CATGGGACAT
571276 TGTATCGATACAC
1 TGTATCGATACAC
571289 TGTATCGATACA
1 TGTATCGATACA
571301 TTGTGCCCAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.20, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAC
Found at i:574514 original size:23 final size:25
Alignment explanation
Indices: 574488--574542 Score: 60
Period size: 25 Copynumber: 2.2 Consensus size: 25
574478 TTGTAAATAT
574488 TTATTAT-TTAAAAATAA-AATTTA
1 TTATTATGTTAAAAATAATAATTTA
* * *
574511 TTATTTTTGTTAATATTAATAATTTA
1 TTA-TTATGTTAAAAATAATAATTTA
574537 TTATTA
1 TTATTA
574543 AAATATAAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
23 3 0.12
24 3 0.12
25 10 0.40
26 9 0.36
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (25 bp):
TTATTATGTTAAAAATAATAATTTA
Found at i:574571 original size:46 final size:46
Alignment explanation
Indices: 574486--574573 Score: 108
Period size: 46 Copynumber: 1.9 Consensus size: 46
574476 TTTTGTAAAT
* * **
574486 ATTTATTATTTAAAAATAAAATTTATTATTTTTGTTAATATTAATA
1 ATTTATTATTTAAAAATAAAATATATTATGTTTAATAATATTAATA
574532 ATTTATTA-TTAAAATATAAAA-ATATTTATGTTTAATAATATT
1 ATTTATTATTTAAAA-ATAAAATATA-TTATGTTTAATAATATT
574574 CAAGAAGTAT
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
45 8 0.22
46 28 0.78
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (46 bp):
ATTTATTATTTAAAAATAAAATATATTATGTTTAATAATATTAATA
Found at i:574648 original size:16 final size:15
Alignment explanation
Indices: 574600--574644 Score: 81
Period size: 15 Copynumber: 3.0 Consensus size: 15
574590 TTAAAATATC
574600 AAATACTTTTCATTT
1 AAATACTTTTCATTT
574615 AAATACTTTTCATTT
1 AAATACTTTTCATTT
*
574630 AAATACTTTTTATTT
1 AAATACTTTTCATTT
574645 TAAAAGTTTA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
15 29 1.00
ACGTcount: A:0.33, C:0.11, G:0.00, T:0.56
Consensus pattern (15 bp):
AAATACTTTTCATTT
Found at i:576125 original size:18 final size:19
Alignment explanation
Indices: 576104--576143 Score: 62
Period size: 21 Copynumber: 2.0 Consensus size: 19
576094 CAATATTTTG
576104 AAAATATTTATTATTTAAA
1 AAAATATTTATTATTTAAA
576123 AAATATAATTTATTATTTAAA
1 AAA-AT-ATTTATTATTTAAA
576144 TAATAAAATA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 3 0.16
20 2 0.11
21 14 0.74
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (19 bp):
AAAATATTTATTATTTAAA
Found at i:576135 original size:21 final size:21
Alignment explanation
Indices: 576109--576161 Score: 79
Period size: 21 Copynumber: 2.5 Consensus size: 21
576099 TTTTGAAAAT
*
576109 ATTTATTATTTAAAAAATATA
1 ATTTATTATTTAAAAAATAAA
*
576130 ATTTATTATTTAAATAATAAA
1 ATTTATTATTTAAAAAATAAA
*
576151 ATATATTATTT
1 ATTTATTATTT
576162 TTGTTAATAT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (21 bp):
ATTTATTATTTAAAAAATAAA
Found at i:577070 original size:21 final size:21
Alignment explanation
Indices: 577046--577085 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
577036 ATATATTCAC
577046 ATAAAATATTGATACATTTAT
1 ATAAAATATTGATACATTTAT
**
577067 ATAATGTATTGATACATTT
1 ATAAAATATTGATACATTT
577086 TCACTTGTAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.42, C:0.05, G:0.07, T:0.45
Consensus pattern (21 bp):
ATAAAATATTGATACATTTAT
Found at i:578629 original size:20 final size:20
Alignment explanation
Indices: 578600--578653 Score: 65
Period size: 20 Copynumber: 2.7 Consensus size: 20
578590 AAAACCCTTA
*
578600 AAAGTGTCGATACACAGTT-C
1 AAAGTATCGATACA-AGTTGC
*
578620 AAAGTATCGATACATGTTGC
1 AAAGTATCGATACAAGTTGC
*
578640 AATGTATCGATACA
1 AAAGTATCGATACA
578654 TGAAAAAGAT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
19 3 0.10
20 27 0.90
ACGTcount: A:0.37, C:0.17, G:0.19, T:0.28
Consensus pattern (20 bp):
AAAGTATCGATACAAGTTGC
Found at i:578750 original size:32 final size:34
Alignment explanation
Indices: 578707--578771 Score: 107
Period size: 34 Copynumber: 2.0 Consensus size: 34
578697 TAGCCAAACT
*
578707 TGTATCGATACAC-A-AAATATGTATCGATACAA
1 TGTATCAATACACAAGAAATATGTATCGATACAA
578739 TGTATCAATACACAAGAAATATGTATCGATACA
1 TGTATCAATACACAAGAAATATGTATCGATACA
578772 TTGGCTTGTA
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
32 12 0.40
33 1 0.03
34 17 0.57
ACGTcount: A:0.45, C:0.15, G:0.12, T:0.28
Consensus pattern (34 bp):
TGTATCAATACACAAGAAATATGTATCGATACAA
Found at i:580139 original size:21 final size:21
Alignment explanation
Indices: 580108--580164 Score: 78
Period size: 21 Copynumber: 2.7 Consensus size: 21
580098 ATATTTTTGA
580108 AAATATTTATTATTTAAAAAAT
1 AAAT-TTTATTATTTAAAAAAT
*
580130 AAATTTTATTATTTAAATAAT
1 AAATTTTATTATTTAAAAAAT
* *
580151 AAAATATATTATTT
1 AAATTTTATTATTT
580165 TTATTAATAT
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
21 28 0.88
22 4 0.12
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (21 bp):
AAATTTTATTATTTAAAAAAT
Found at i:580171 original size:26 final size:26
Alignment explanation
Indices: 580125--580190 Score: 64
Period size: 26 Copynumber: 2.5 Consensus size: 26
580115 TATTATTTAA
*
580125 AAAATAAATT-TTATTATTTAAATAAT
1 AAAATATATTATTATTATTT-AATAAT
* *
580151 AAAATATATTATTTTTA-TTAATATT
1 AAAATATATTATTATTATTTAATAAT
*
580176 AATAATTTATTATTA
1 AA-AATATATTATTA
580191 AAATATAAAA
Statistics
Matches: 33, Mismatches: 5, Indels: 4
0.79 0.12 0.10
Matches are distributed among these distances:
25 7 0.21
26 21 0.64
27 5 0.15
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (26 bp):
AAAATATATTATTATTATTTAATAAT
Found at i:580281 original size:16 final size:15
Alignment explanation
Indices: 580246--580277 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
580236 AATTAAAATA
580246 TTAAATACTTTTCAT
1 TTAAATACTTTTCAT
*
580261 TTAAATACTTTTTAT
1 TTAAATACTTTTCAT
580276 TT
1 TT
580278 TAAAATTTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.31, C:0.09, G:0.00, T:0.59
Consensus pattern (15 bp):
TTAAATACTTTTCAT
Found at i:581085 original size:13 final size:13
Alignment explanation
Indices: 581067--581093 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
581057 ACATTATGCT
581067 TTGTATCGATACA
1 TTGTATCGATACA
581080 TTGTATCGATACA
1 TTGTATCGATACA
581093 T
1 T
581094 GTTCATTGTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.41
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:581108 original size:32 final size:33
Alignment explanation
Indices: 581049--581112 Score: 96
Period size: 32 Copynumber: 2.0 Consensus size: 33
581039 ACACCTAGAA
*
581049 GTATCGATACATTATGCTTTGTATCGATACATT
1 GTATCGATACATTATGCATTGTATCGATACATT
581082 GTATCGATACATGT-T-CATTGTATCGATACAT
1 GTATCGATACAT-TATGCATTGTATCGATACAT
581113 GGACAATTGT
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
32 15 0.52
33 13 0.45
34 1 0.03
ACGTcount: A:0.28, C:0.16, G:0.16, T:0.41
Consensus pattern (33 bp):
GTATCGATACATTATGCATTGTATCGATACATT
Found at i:581123 original size:20 final size:19
Alignment explanation
Indices: 581077--581133 Score: 78
Period size: 19 Copynumber: 2.9 Consensus size: 19
581067 TTGTATCGAT
*
581077 ACATTGTATCGATACATGT
1 ACATTGTATCGATACATGG
*
581096 TCATTGTATCGATACATGG
1 ACATTGTATCGATACATGG
*
581115 ACAATTGTATCAATACATG
1 AC-ATTGTATCGATACATG
581134 AAACTGGCAG
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
19 18 0.55
20 15 0.45
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.35
Consensus pattern (19 bp):
ACATTGTATCGATACATGG
Found at i:581187 original size:20 final size:20
Alignment explanation
Indices: 581162--581215 Score: 83
Period size: 20 Copynumber: 2.7 Consensus size: 20
581152 CTACCACTGT
*
581162 TTGTATCGATACATGGT-ACA
1 TTGTATCGATACATGATGA-A
581182 TTGTATCGATACATGATGAA
1 TTGTATCGATACATGATGAA
581202 TTGTATCGATACAT
1 TTGTATCGATACAT
581216 TGCTTGTAAC
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
20 31 0.97
21 1 0.03
ACGTcount: A:0.31, C:0.13, G:0.19, T:0.37
Consensus pattern (20 bp):
TTGTATCGATACATGATGAA
Found at i:589996 original size:20 final size:20
Alignment explanation
Indices: 589950--590004 Score: 85
Period size: 19 Copynumber: 2.8 Consensus size: 20
589940 ATATTCATAC
**
589950 ATTGTATCGATACATGTTCA
1 ATTGTATCGATACATGGACA
589970 A-TGTATCGATACATGGACA
1 ATTGTATCGATACATGGACA
589989 ATTGTATCGATACATG
1 ATTGTATCGATACATG
590005 AAACTAGCAA
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
19 17 0.53
20 15 0.47
ACGTcount: A:0.33, C:0.15, G:0.18, T:0.35
Consensus pattern (20 bp):
ATTGTATCGATACATGGACA
Found at i:594371 original size:13 final size:13
Alignment explanation
Indices: 594353--594378 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
594343 AGGGTAGCTT
594353 TTGTATCGATACA
1 TTGTATCGATACA
594366 TTGTATCGATACA
1 TTGTATCGATACA
594379 ACACTTATGT
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:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:595131 original size:52 final size:52
Alignment explanation
Indices: 595037--595158 Score: 129
Period size: 52 Copynumber: 2.3 Consensus size: 52
595027 TGATAAAGGT
* * * * *
595037 GCCAATATGCTGATTCAAGACCAGTGATATTGGGCTTAAAGATGTAAAAG-AT
1 GCCAATGTGCTGATTCAAGACCAGTGACATTAGACTTAAAGATG-AAAAGAAA
* * ** * *
595089 GTCAATGTGCTGATTCACGGTCAGTGACATTAGACTTGAAGATGAGAAGAAA
1 GCCAATGTGCTGATTCAAGACCAGTGACATTAGACTTAAAGATGAAAAGAAA
595141 GCCAATGTGCTGATTCAA
1 GCCAATGTGCTGATTCAA
595159 AGCTAGCGAC
Statistics
Matches: 56, Mismatches: 13, Indels: 2
0.79 0.18 0.03
Matches are distributed among these distances:
51 4 0.07
52 52 0.93
ACGTcount: A:0.34, C:0.15, G:0.25, T:0.26
Consensus pattern (52 bp):
GCCAATGTGCTGATTCAAGACCAGTGACATTAGACTTAAAGATGAAAAGAAA
Found at i:595361 original size:70 final size:70
Alignment explanation
Indices: 595237--595371 Score: 225
Period size: 70 Copynumber: 1.9 Consensus size: 70
595227 CTTAAAGATG
* * * *
595237 AAGGTGCTAATATGCTGATTCAAGGCCAGCGATATTGGGCTTGTGCCAAGGTGCTGATTCAAGGC
1 AAGGTGCCAATATGCTAATTCAAGGCCAGCGATATTGGGCTTATACCAAGGTGCTGATTCAAGGC
595302 TAGCA
66 TAGCA
*
595307 AAGGTGCCAATATGCTAATTCAAGGCCAGCGATATTGGGCTTATACCAATGTGCTGATTCAAGGC
1 AAGGTGCCAATATGCTAATTCAAGGCCAGCGATATTGGGCTTATACCAAGGTGCTGATTCAAGGC
595372 CAGCGACGTT
Statistics
Matches: 60, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
70 60 1.00
ACGTcount: A:0.27, C:0.19, G:0.27, T:0.26
Consensus pattern (70 bp):
AAGGTGCCAATATGCTAATTCAAGGCCAGCGATATTGGGCTTATACCAAGGTGCTGATTCAAGGC
TAGCA
Found at i:595424 original size:49 final size:49
Alignment explanation
Indices: 595352--595529 Score: 233
Period size: 49 Copynumber: 3.8 Consensus size: 49
595342 TGGGCTTATA
* * *
595352 CCAATGTGCTGATTCAAGGCCAGCGACGTTGGTCTTAAAGGTGAAGGTG
1 CCAATGTGCTGATTCAAGGCCAGCAACATTGGACTTAAAGGTGAAGGTG
* *
595401 CCAATGTACTGATTCAAGGCCAGCAACATTGGACTCAAAGGTGAAGGTG
1 CCAATGTGCTGATTCAAGGCCAGCAACATTGGACTTAAAGGTGAAGGTG
*
595450 CCAATGTGTTGATTCAAGGCCAGCAACATTGGACTT--A----AAGGTG
1 CCAATGTGCTGATTCAAGGCCAGCAACATTGGACTTAAAGGTGAAGGTG
* * *
595493 CCAATATGTTGATTCAAGGCCAGCAATATTGGACTTA
1 CCAATGTGCTGATTCAAGGCCAGCAACATTGGACTTA
595530 GAAGAAGATG
Statistics
Matches: 118, Mismatches: 10, Indels: 7
0.87 0.07 0.05
Matches are distributed among these distances:
43 40 0.34
47 1 0.01
49 77 0.65
ACGTcount: A:0.30, C:0.19, G:0.26, T:0.25
Consensus pattern (49 bp):
CCAATGTGCTGATTCAAGGCCAGCAACATTGGACTTAAAGGTGAAGGTG
Done.