Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold159
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: 552906
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 499 characters in sequence are not A, C, G, or T
File 4 of 4
Found at i:422056 original size:21 final size:21
Alignment explanation
Indices: 422032--422105 Score: 121
Period size: 21 Copynumber: 3.5 Consensus size: 21
422022 TATACGAGAT
*
422032 GTATCGATGCATGTACTATTG
1 GTATCGATACATGTACTATTG
*
422053 GTATCGATACATGTATTATTG
1 GTATCGATACATGTACTATTG
*
422074 GTATCGATACACGTACTATTG
1 GTATCGATACATGTACTATTG
422095 GTATCGATACA
1 GTATCGATACA
422106 CAAGGTTGAC
Statistics
Matches: 49, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 49 1.00
ACGTcount: A:0.28, C:0.15, G:0.20, T:0.36
Consensus pattern (21 bp):
GTATCGATACATGTACTATTG
Found at i:423524 original size:13 final size:13
Alignment explanation
Indices: 423506--423531 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
423496 CAATTTTTTG
423506 TGTATCGATACAT
1 TGTATCGATACAT
423519 TGTATCGATACAT
1 TGTATCGATACAT
423532 ACTTGCTGTA
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):
TGTATCGATACAT
Found at i:423617 original size:20 final size:20
Alignment explanation
Indices: 423592--423664 Score: 92
Period size: 20 Copynumber: 3.6 Consensus size: 20
423582 ATCTTTTTTT
423592 ATGTATCGATACATTGCAAC
1 ATGTATCGATACATTGCAAC
*****
423612 ATGTATCGATACATCTTTTTT
1 ATGTATCGATACAT-TGCAAC
423633 ATGTATCGATACATTGCAAC
1 ATGTATCGATACATTGCAAC
423653 ATGTATCGATAC
1 ATGTATCGATAC
423665 TTTGAATTGT
Statistics
Matches: 42, Mismatches: 10, Indels: 2
0.78 0.19 0.04
Matches are distributed among these distances:
20 27 0.64
21 15 0.36
ACGTcount: A:0.32, C:0.18, G:0.14, T:0.37
Consensus pattern (20 bp):
ATGTATCGATACATTGCAAC
Found at i:423643 original size:41 final size:42
Alignment explanation
Indices: 423570--423664 Score: 183
Period size: 41 Copynumber: 2.3 Consensus size: 42
423560 CTGCCAAGAA
423570 ATGTATCGATACATCTTTTTTTATGTATCGATACATTGCAAC
1 ATGTATCGATACATCTTTTTTTATGTATCGATACATTGCAAC
423612 ATGTATCGATACATC-TTTTTTATGTATCGATACATTGCAAC
1 ATGTATCGATACATCTTTTTTTATGTATCGATACATTGCAAC
423653 ATGTATCGATAC
1 ATGTATCGATAC
423665 TTTGAATTGT
Statistics
Matches: 53, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
41 38 0.72
42 15 0.28
ACGTcount: A:0.29, C:0.17, G:0.13, T:0.41
Consensus pattern (42 bp):
ATGTATCGATACATCTTTTTTTATGTATCGATACATTGCAAC
Found at i:426120 original size:13 final size:13
Alignment explanation
Indices: 426102--426140 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
426092 ATAATCACCC
*
426102 TGTATCGATACAG
1 TGTATCGATACAA
426115 TGTATCGATACAA
1 TGTATCGATACAA
426128 TGTATCGATACAA
1 TGTATCGATACAA
426141 AGAAAAATGT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.36, C:0.15, G:0.18, T:0.31
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:426151 original size:20 final size:20
Alignment explanation
Indices: 426126--426204 Score: 70
Period size: 20 Copynumber: 3.7 Consensus size: 20
426116 GTATCGATAC
426126 AATGTATCGATACAAAGAAA
1 AATGTATCGATACAAAGAAA
*
426146 AATGTATCGATACATAGAATTTCCA
1 AATGTATCGATACAAAGAA-----A
*
426171 GATGTATCGATACACAA-AAA
1 AATGTATCGATACA-AAGAAA
*
426191 CATGTATCGATACA
1 AATGTATCGATACA
426205 TTTTGGACAT
Statistics
Matches: 49, Mismatches: 4, Indels: 12
0.75 0.06 0.18
Matches are distributed among these distances:
20 32 0.65
25 16 0.33
26 1 0.02
ACGTcount: A:0.46, C:0.15, G:0.14, T:0.25
Consensus pattern (20 bp):
AATGTATCGATACAAAGAAA
Found at i:428248 original size:15 final size:15
Alignment explanation
Indices: 428212--428249 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
428202 TACATCAATT
* *
428212 TCATTTGGAGCTTCT
1 TCATTTTGAGCTTCC
428227 TCATTTTGAGCTTCC
1 TCATTTTGAGCTTCC
428242 TCATTTTG
1 TCATTTTG
428250 GACATCTTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.13, C:0.21, G:0.16, T:0.50
Consensus pattern (15 bp):
TCATTTTGAGCTTCC
Found at i:432329 original size:13 final size:13
Alignment explanation
Indices: 432311--432336 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
432301 CAATTTTTTG
432311 TGTATCGATACAT
1 TGTATCGATACAT
432324 TGTATCGATACAT
1 TGTATCGATACAT
432337 ACTTGCTGTA
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):
TGTATCGATACAT
Found at i:432422 original size:20 final size:20
Alignment explanation
Indices: 432397--432469 Score: 92
Period size: 20 Copynumber: 3.6 Consensus size: 20
432387 ATCTTTTTTT
432397 ATGTATCGATACATTGCAAC
1 ATGTATCGATACATTGCAAC
*****
432417 ATGTATCGATACATCTTTTTT
1 ATGTATCGATACAT-TGCAAC
432438 ATGTATCGATACATTGCAAC
1 ATGTATCGATACATTGCAAC
432458 ATGTATCGATAC
1 ATGTATCGATAC
432470 TTTGAATTGT
Statistics
Matches: 42, Mismatches: 10, Indels: 2
0.78 0.19 0.04
Matches are distributed among these distances:
20 27 0.64
21 15 0.36
ACGTcount: A:0.32, C:0.18, G:0.14, T:0.37
Consensus pattern (20 bp):
ATGTATCGATACATTGCAAC
Found at i:432448 original size:41 final size:42
Alignment explanation
Indices: 432375--432469 Score: 183
Period size: 41 Copynumber: 2.3 Consensus size: 42
432365 CTGCCAAGAA
432375 ATGTATCGATACATCTTTTTTTATGTATCGATACATTGCAAC
1 ATGTATCGATACATCTTTTTTTATGTATCGATACATTGCAAC
432417 ATGTATCGATACATC-TTTTTTATGTATCGATACATTGCAAC
1 ATGTATCGATACATCTTTTTTTATGTATCGATACATTGCAAC
432458 ATGTATCGATAC
1 ATGTATCGATAC
432470 TTTGAATTGT
Statistics
Matches: 53, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
41 38 0.72
42 15 0.28
ACGTcount: A:0.29, C:0.17, G:0.13, T:0.41
Consensus pattern (42 bp):
ATGTATCGATACATCTTTTTTTATGTATCGATACATTGCAAC
Found at i:432823 original size:34 final size:34
Alignment explanation
Indices: 432764--432873 Score: 127
Period size: 34 Copynumber: 3.3 Consensus size: 34
432754 CCTAACACTT
*
432764 TGAAAAGA-TAGGAA-AAGGTTCTATCTTAGCCCG
1 TGAAAAGATTAGGAAGAA-GTTCTATCTTAGCCAG
*
432797 TGAAAAGATTGGGAAGAAGTTCTATCTTAGCCAG
1 TGAAAAGATTAGGAAGAAGTTCTATCTTAGCCAG
** **
432831 TGAAAAGACAAGG-AGAAAGTTCTATCTTAGCTTG
1 TGAAAAGATTAGGAAG-AAGTTCTATCTTAGCCAG
432865 TGAAAAGAT
1 TGAAAAGAT
432874 AAGGTTGTAA
Statistics
Matches: 66, Mismatches: 8, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
33 10 0.15
34 54 0.82
35 2 0.03
ACGTcount: A:0.38, C:0.12, G:0.25, T:0.25
Consensus pattern (34 bp):
TGAAAAGATTAGGAAGAAGTTCTATCTTAGCCAG
Found at i:435459 original size:20 final size:21
Alignment explanation
Indices: 435434--435473 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
435424 GATTGATTTT
435434 ATGTTTGGT-GTTAATTATTG
1 ATGTTTGGTGGTTAATTATTG
*
435454 ATGTTTTGTGGTTAATTATT
1 ATGTTTGGTGGTTAATTATT
435474 CTTAATTTGA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 8 0.44
21 10 0.56
ACGTcount: A:0.20, C:0.00, G:0.23, T:0.57
Consensus pattern (21 bp):
ATGTTTGGTGGTTAATTATTG
Found at i:437280 original size:21 final size:20
Alignment explanation
Indices: 437254--437305 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 20
437244 TATCGATACG
437254 TTGTATCGATACAT-AATTAAA
1 TTGTATCGATACATCAA--AAA
* *
437275 TTGTATCGACACATCAAGAA
1 TTGTATCGATACATCAAAAA
437295 TTGTATCGATA
1 TTGTATCGATA
437306 TATTTGGCTC
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
20 12 0.44
21 13 0.48
22 2 0.07
ACGTcount: A:0.38, C:0.13, G:0.13, T:0.35
Consensus pattern (20 bp):
TTGTATCGATACATCAAAAA
Found at i:437794 original size:33 final size:34
Alignment explanation
Indices: 437736--437828 Score: 100
Period size: 34 Copynumber: 2.7 Consensus size: 34
437726 GATTGAGAGG
* * *
437736 TTCTATCTTAACCTTTGAAAAAGATA-GGAAAAAA
1 TTCTATATTAGCCTGTG-AAAAGATAGGGAAAAAA
*
437770 GTTTTA-ATTAGCCTGTGAAAAGATAGGGAAAAAA
1 -TTCTATATTAGCCTGTGAAAAGATAGGGAAAAAA
* *
437804 TTCTATCTTAGCTTGTGAAAAGATA
1 TTCTATATTAGCCTGTGAAAAGATA
437829 AAGAGAAGGT
Statistics
Matches: 49, Mismatches: 7, Indels: 5
0.80 0.11 0.08
Matches are distributed among these distances:
33 12 0.24
34 33 0.67
35 4 0.08
ACGTcount: A:0.42, C:0.10, G:0.17, T:0.31
Consensus pattern (34 bp):
TTCTATATTAGCCTGTGAAAAGATAGGGAAAAAA
Found at i:437842 original size:34 final size:36
Alignment explanation
Indices: 437777--437870 Score: 84
Period size: 34 Copynumber: 2.6 Consensus size: 36
437767 AAAGTTTTAA
* **
437777 TTAGCCTGTGAAAAGATAGGGAAAAAATTCTA-T-C
1 TTAGCTTGTGAAAAGATAAAGAAAAAATTCTATTAC
* **
437811 TTAGCTTGTGAAAAGATAAAGAGAAGGTTCTATTTTAAC
1 TTAGCTTGTGAAAAGATAAAGAAAAAATTCTA--TT-AC
*
437850 TTAACTTGTGAAAAGATAAAG
1 TTAGCTTGTGAAAAGATAAAG
437871 TTGTAAGGTT
Statistics
Matches: 48, Mismatches: 7, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
34 26 0.54
37 1 0.02
39 21 0.44
ACGTcount: A:0.41, C:0.09, G:0.20, T:0.30
Consensus pattern (36 bp):
TTAGCTTGTGAAAAGATAAAGAAAAAATTCTATTAC
Found at i:438317 original size:13 final size:14
Alignment explanation
Indices: 438298--438331 Score: 54
Period size: 13 Copynumber: 2.6 Consensus size: 14
438288 TAAAAATCAT
438298 AAATTTTAAAATTC
1 AAATTTTAAAATTC
438312 -AATTTT-AAATTC
1 AAATTTTAAAATTC
438324 AAATTTTA
1 AAATTTTA
438332 GTTTTGAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 4
0.82 0.00 0.18
Matches are distributed among these distances:
12 6 0.33
13 12 0.67
ACGTcount: A:0.47, C:0.06, G:0.00, T:0.47
Consensus pattern (14 bp):
AAATTTTAAAATTC
Found at i:441223 original size:69 final size:69
Alignment explanation
Indices: 441144--441283 Score: 244
Period size: 69 Copynumber: 2.0 Consensus size: 69
441134 CTAACACTAA
*
441144 AACATGGTAAAGAGAAAGATTTGTCTTCTTTTAAAGAAAAAATTGCAGTCTATCTAATGAATTGA
1 AACATGGTAAAGAGAAAGATTTGTCTCCTTTTAAAGAAAAAATTGCAGTCTATCTAATGAATTGA
441209 TAAT
66 TAAT
* * *
441213 AACATTGTAAAGAGAAAGTTTTGTCTCCTTTTAAAGAAAAAATTGCAGTCTGTCTAATGAATTGA
1 AACATGGTAAAGAGAAAGATTTGTCTCCTTTTAAAGAAAAAATTGCAGTCTATCTAATGAATTGA
441278 TAAT
66 TAAT
441282 AA
1 AA
441284 AAAAGTTTTC
Statistics
Matches: 67, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
69 67 1.00
ACGTcount: A:0.41, C:0.09, G:0.16, T:0.34
Consensus pattern (69 bp):
AACATGGTAAAGAGAAAGATTTGTCTCCTTTTAAAGAAAAAATTGCAGTCTATCTAATGAATTGA
TAAT
Found at i:441630 original size:56 final size:56
Alignment explanation
Indices: 441564--441679 Score: 205
Period size: 56 Copynumber: 2.1 Consensus size: 56
441554 AACCCATTAA
*
441564 AACAAAGAGGGATTACCAAACTGACAATATTAATCAACATACATGGAAAAGTGAAG
1 AACAAAGAGGGATTACCAAACTGACAATATTAATCAACATACACGGAAAAGTGAAG
**
441620 AACAAAGAGGGATTTTCAAACTGACAATATTAATCAACATACACGGAAAAGTGAAG
1 AACAAAGAGGGATTACCAAACTGACAATATTAATCAACATACACGGAAAAGTGAAG
441676 AACA
1 AACA
441680 GATGATACTG
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
56 57 1.00
ACGTcount: A:0.50, C:0.15, G:0.17, T:0.18
Consensus pattern (56 bp):
AACAAAGAGGGATTACCAAACTGACAATATTAATCAACATACACGGAAAAGTGAAG
Found at i:442486 original size:24 final size:24
Alignment explanation
Indices: 442445--442500 Score: 71
Period size: 24 Copynumber: 2.4 Consensus size: 24
442435 ATATAAAAAT
*
442445 AATATAA-TAAAATGATATATTTA
1 AATATAATTAAAATAATATATTTA
* *
442468 AATATAATTAATATAATATTTTTA
1 AATATAATTAAAATAATATATTTA
442492 AA-ATAATTA
1 AATATAATTA
442501 TTTATGTATA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
23 14 0.48
24 15 0.52
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (24 bp):
AATATAATTAAAATAATATATTTA
Found at i:444292 original size:19 final size:19
Alignment explanation
Indices: 444255--444292 Score: 51
Period size: 20 Copynumber: 2.0 Consensus size: 19
444245 TATTATAATT
*
444255 ATTTTAATATTTTGATTTA
1 ATTTTAATATATTGATTTA
444274 ATTTGTAATATATTG-TTTA
1 ATTT-TAATATATTGATTTA
444293 GTAATTAAGG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 8 0.47
20 9 0.53
ACGTcount: A:0.32, C:0.00, G:0.08, T:0.61
Consensus pattern (19 bp):
ATTTTAATATATTGATTTA
Found at i:444549 original size:21 final size:21
Alignment explanation
Indices: 444525--444566 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
444515 TTATAGTTTT
444525 TATCCTTTCATTAGAAAAGAC
1 TATCCTTTCATTAGAAAAGAC
*
444546 TATCCTTTCATTAGAAGAGAC
1 TATCCTTTCATTAGAAAAGAC
444567 CATCGAAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.36, C:0.19, G:0.12, T:0.33
Consensus pattern (21 bp):
TATCCTTTCATTAGAAAAGAC
Found at i:445819 original size:52 final size:52
Alignment explanation
Indices: 445741--445864 Score: 230
Period size: 52 Copynumber: 2.4 Consensus size: 52
445731 CATGCTTACT
* *
445741 ATGTATTGATACATTATTCATTGTATTGATATATTCTGGATTTTTGACCCAA
1 ATGTATCGATACATTCTTCATTGTATTGATATATTCTGGATTTTTGACCCAA
445793 ATGTATCGATACATTCTTCATTGTATTGATATATTCTGGATTTTTGACCCAA
1 ATGTATCGATACATTCTTCATTGTATTGATATATTCTGGATTTTTGACCCAA
445845 ATGTATCGATACATTCTTCA
1 ATGTATCGATACATTCTTCA
445865 ACGTATCTAT
Statistics
Matches: 70, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
52 70 1.00
ACGTcount: A:0.28, C:0.15, G:0.13, T:0.44
Consensus pattern (52 bp):
ATGTATCGATACATTCTTCATTGTATTGATATATTCTGGATTTTTGACCCAA
Found at i:448306 original size:95 final size:97
Alignment explanation
Indices: 448134--448315 Score: 262
Period size: 95 Copynumber: 1.9 Consensus size: 97
448124 AGAACAGGGT
* ** * * * *
448134 TGGAGTATCCCTGATGATGATAATTTAAGCAAAAACAAAACTTAAATCTTGATGAGTTTAAAGAT
1 TGGAGTATACCTGATGACAACAATTTAAGCAAAAACAAAACTTAAATCTTGATGACTTTAAAAAC
448199 GGGGTTAGAGTA-TCTCCTCAGAAGATTGGAGC
66 GGGGTTAGAGTATTC-CCTCAGAAGATTGGAGC
*
448231 TGGAGTATACCTGATGACAACAATTTAAGC-AAAA-AAGACTTAAATCTTGATGACTTTAAAAAC
1 TGGAGTATACCTGATGACAACAATTTAAGCAAAAACAAAACTTAAATCTTGATGACTTTAAAAAC
448294 GGGGTTAGAGTATTCCCTCAGA
66 GGGGTTAGAGTATTCCCTCAGA
448316 TGATAGGATT
Statistics
Matches: 76, Mismatches: 8, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
95 44 0.58
96 6 0.08
97 26 0.34
ACGTcount: A:0.37, C:0.14, G:0.21, T:0.28
Consensus pattern (97 bp):
TGGAGTATACCTGATGACAACAATTTAAGCAAAAACAAAACTTAAATCTTGATGACTTTAAAAAC
GGGGTTAGAGTATTCCCTCAGAAGATTGGAGC
Found at i:449804 original size:34 final size:32
Alignment explanation
Indices: 449741--449805 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 32
449731 TAGCCAAACT
*
449741 TGTATCGATACACAAAATATGTATAGATACAA
1 TGTATCGATACACAAAAAATGTATAGATACAA
*
449773 TGTATCGATACACAAAAAAATTGTATCGATACA
1 TGTATCGATACAC-AAAAAA-TGTATAGATACA
449806 TTGGCTTGTA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
32 13 0.45
33 5 0.17
34 11 0.38
ACGTcount: A:0.46, C:0.14, G:0.12, T:0.28
Consensus pattern (32 bp):
TGTATCGATACACAAAAAATGTATAGATACAA
Found at i:453872 original size:15 final size:15
Alignment explanation
Indices: 453852--453882 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
453842 TAAAAATATC
*
453852 CAAAATGAGGAAGCT
1 CAAAATGAAGAAGCT
453867 CAAAATGAAGAAGCT
1 CAAAATGAAGAAGCT
453882 C
1 C
453883 CAAACGAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.48, C:0.16, G:0.23, T:0.13
Consensus pattern (15 bp):
CAAAATGAAGAAGCT
Found at i:455983 original size:13 final size:13
Alignment explanation
Indices: 455965--456028 Score: 101
Period size: 13 Copynumber: 4.9 Consensus size: 13
455955 CATTTTTCTT
*
455965 TGTATCGATATAA
1 TGTATCGATACAA
*
455978 TGTATCGATACAC
1 TGTATCGATACAA
455991 TGTATCGATACAA
1 TGTATCGATACAA
*
456004 TGTATCGATACAC
1 TGTATCGATACAA
456017 TGTATCGATACA
1 TGTATCGATACA
456029 GAGGGATTAT
Statistics
Matches: 47, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
13 47 1.00
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:456005 original size:26 final size:26
Alignment explanation
Indices: 455965--456028 Score: 119
Period size: 26 Copynumber: 2.5 Consensus size: 26
455955 CATTTTTCTT
*
455965 TGTATCGATATAATGTATCGATACAC
1 TGTATCGATACAATGTATCGATACAC
455991 TGTATCGATACAATGTATCGATACAC
1 TGTATCGATACAATGTATCGATACAC
456017 TGTATCGATACA
1 TGTATCGATACA
456029 GAGGGATTAT
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 37 1.00
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Consensus pattern (26 bp):
TGTATCGATACAATGTATCGATACAC
Found at i:456183 original size:20 final size:20
Alignment explanation
Indices: 456140--456185 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 20
456130 AAATCTTTTG
456140 CAAAATACTTGTTTTTCACTT
1 CAAAATACTTGTTTTTCAC-T
*
456161 CAAATTACTTCGTTTTTCA-T
1 CAAAATACTT-GTTTTTCACT
456181 CAAAA
1 CAAAA
456186 CCAGCATCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
20 5 0.23
21 9 0.41
22 8 0.36
ACGTcount: A:0.33, C:0.20, G:0.04, T:0.43
Consensus pattern (20 bp):
CAAAATACTTGTTTTTCACT
Found at i:457884 original size:20 final size:20
Alignment explanation
Indices: 457839--457885 Score: 87
Period size: 19 Copynumber: 2.4 Consensus size: 20
457829 CTTGATTAAG
457839 GGGGAGATTTATTAATAAAA
1 GGGGAGATTTATTAATAAAA
457859 -GGGAGATTTATTAATAAAA
1 GGGGAGATTTATTAATAAAA
457878 GGGGAGAT
1 GGGGAGAT
457886 AAAGGGGAGA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
19 19 0.73
20 7 0.27
ACGTcount: A:0.43, C:0.00, G:0.30, T:0.28
Consensus pattern (20 bp):
GGGGAGATTTATTAATAAAA
Found at i:458586 original size:32 final size:31
Alignment explanation
Indices: 458545--458606 Score: 106
Period size: 32 Copynumber: 2.0 Consensus size: 31
458535 TAGCCAAACT
*
458545 TGTATCGATACACAAAATATGTATTGATACAA
1 TGTATCGATACACAAAAT-TGTATCGATACAA
458577 TGTATCGATACACAAAATTGTATCGATACA
1 TGTATCGATACACAAAATTGTATCGATACA
458607 TTGGCTTGTA
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
31 11 0.38
32 18 0.62
ACGTcount: A:0.42, C:0.15, G:0.13, T:0.31
Consensus pattern (31 bp):
TGTATCGATACACAAAATTGTATCGATACAA
Found at i:458600 original size:18 final size:18
Alignment explanation
Indices: 458539--458606 Score: 74
Period size: 18 Copynumber: 4.0 Consensus size: 18
458529 TGGCAGTAGC
*
458539 CAAACTTGTATCGATACA
1 CAAAATTGTATCGATACA
*
458557 CAAAATATGTATTGAT--A
1 CAAAAT-TGTATCGATACA
458574 C--AA-TGTATCGATACA
1 CAAAATTGTATCGATACA
458589 CAAAATTGTATCGATACA
1 CAAAATTGTATCGATACA
458607 TTGGCTTGTA
Statistics
Matches: 41, Mismatches: 3, Indels: 12
0.73 0.05 0.21
Matches are distributed among these distances:
13 8 0.20
15 4 0.10
17 4 0.10
18 17 0.41
19 8 0.20
ACGTcount: A:0.43, C:0.16, G:0.12, T:0.29
Consensus pattern (18 bp):
CAAAATTGTATCGATACA
Found at i:459519 original size:89 final size:89
Alignment explanation
Indices: 459398--459577 Score: 306
Period size: 89 Copynumber: 2.0 Consensus size: 89
459388 ATCGATTGAG
*
459398 GCTAACATACTTAACTTGGGACTTTTTTGAAAAATTAGTCTTTAAAAGCAAACAAGCATACACTT
1 GCTAAAATACTTAACTTGGGACTTTTTTGAAAAATTAGTCTTTAAAAGCAAACAAGCATACACTT
459463 TAACAAGGAAAACATGATGAACAT
66 TAACAAGGAAAACATGATGAACAT
* * *
459487 GCTAAAATGCTTAACTTGGGGCTTTTTTGAAAAATTAGTCTTTAAAAGCAAACAAGCATGCACTT
1 GCTAAAATACTTAACTTGGGACTTTTTTGAAAAATTAGTCTTTAAAAGCAAACAAGCATACACTT
* *
459552 TGATAAGGAAAACATGATGAACAT
66 TAACAAGGAAAACATGATGAACAT
459576 GC
1 GC
459578 AAGAAAATGA
Statistics
Matches: 85, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
89 85 1.00
ACGTcount: A:0.41, C:0.15, G:0.16, T:0.28
Consensus pattern (89 bp):
GCTAAAATACTTAACTTGGGACTTTTTTGAAAAATTAGTCTTTAAAAGCAAACAAGCATACACTT
TAACAAGGAAAACATGATGAACAT
Found at i:465032 original size:5 final size:5
Alignment explanation
Indices: 465014--465072 Score: 57
Period size: 5 Copynumber: 11.2 Consensus size: 5
465004 CATGGAAGTG
* *
465014 ATTTT ATTTCT ATTTT ATTTC ATTTTT ACATTTT ATTTA ATTTT ATTTT
1 ATTTT ATTT-T ATTTT ATTTT A-TTTT --ATTTT ATTTT ATTTT ATTTT
465063 A-TTT ATTTT A
1 ATTTT ATTTT A
465073 AAATATATAA
Statistics
Matches: 45, Mismatches: 4, Indels: 10
0.76 0.07 0.17
Matches are distributed among these distances:
4 4 0.09
5 28 0.62
6 8 0.18
7 4 0.09
8 1 0.02
ACGTcount: A:0.24, C:0.05, G:0.00, T:0.71
Consensus pattern (5 bp):
ATTTT
Found at i:465069 original size:9 final size:10
Alignment explanation
Indices: 465014--465072 Score: 57
Period size: 11 Copynumber: 5.6 Consensus size: 10
465004 CATGGAAGTG
465014 ATTTTATTTCT
1 ATTTTATTT-T
*
465025 ATTTTATTTC
1 ATTTTATTTT
465035 ATTTTTACATTTT
1 A-TTTT--ATTTT
*
465048 ATTTAATTTT
1 ATTTTATTTT
465058 ATTTTA-TTT
1 ATTTTATTTT
465067 ATTTTA
1 ATTTTA
465073 AAATATATAA
Statistics
Matches: 41, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
9 9 0.22
10 11 0.27
11 13 0.32
12 3 0.07
13 5 0.12
ACGTcount: A:0.24, C:0.05, G:0.00, T:0.71
Consensus pattern (10 bp):
ATTTTATTTT
Found at i:472896 original size:13 final size:13
Alignment explanation
Indices: 472878--472903 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
472868 TACAGCAAGT
472878 ATGTATCGATACA
1 ATGTATCGATACA
472891 ATGTATCGATACA
1 ATGTATCGATACA
472904 CAAAAAATTG
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:475163 original size:21 final size:21
Alignment explanation
Indices: 475130--475174 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
475120 TTGCAAGTTG
*
475130 AAATAAAGAAGTTGGCTAATGA
1 AAATAAAGAAGTTAGCTAA-GA
*
475152 AAATAATG-AGTTAGCTAAGA
1 AAATAAAGAAGTTAGCTAAGA
475172 AAA
1 AAA
475175 ATGAAAACTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 9 0.43
22 7 0.33
ACGTcount: A:0.53, C:0.04, G:0.20, T:0.22
Consensus pattern (21 bp):
AAATAAAGAAGTTAGCTAAGA
Found at i:476998 original size:15 final size:15
Alignment explanation
Indices: 476978--477016 Score: 60
Period size: 15 Copynumber: 2.6 Consensus size: 15
476968 TAAAAATGTC
*
476978 CAAAATGAGGAAGCT
1 CAAAATGAAGAAGCT
476993 CAAAATGAAGAAGCT
1 CAAAATGAAGAAGCT
*
477008 CCAAATGAA
1 CAAAATGAA
477017 ATTGATGAAC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.51, C:0.15, G:0.21, T:0.13
Consensus pattern (15 bp):
CAAAATGAAGAAGCT
Found at i:479095 original size:13 final size:13
Alignment explanation
Indices: 479077--479115 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
479067 ACATTTTTCT
*
479077 TTGTATTGATACA
1 TTGTATCGATACA
479090 TTGTATCGATACA
1 TTGTATCGATACA
479103 TTGTATCGATACA
1 TTGTATCGATACA
479116 GGGTGATTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.31, C:0.13, G:0.15, T:0.41
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:484718 original size:21 final size:21
Alignment explanation
Indices: 484694--484734 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
484684 TCTAAGTAAA
484694 ATACGTATT-GTATCAATACAT
1 ATAC-TATTAGTATCAATACAT
*
484715 ATACTATTAGTATTAATACA
1 ATACTATTAGTATCAATACA
484735 CAAGGTTGAC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.41, C:0.12, G:0.07, T:0.39
Consensus pattern (21 bp):
ATACTATTAGTATCAATACAT
Found at i:484799 original size:20 final size:21
Alignment explanation
Indices: 484767--484826 Score: 79
Period size: 20 Copynumber: 3.0 Consensus size: 21
484757 GGTCAAAACC
* *
484767 TTGAAAAGTATCGATACACAT
1 TTGAATAGTATCGATACACAA
484788 TTGAAT-GTATCGATACA-AA
1 TTGAATAGTATCGATACACAA
*
484807 TTGCATAGTATCGATACACA
1 TTGAATAGTATCGATACACA
484827 CAAATATGTA
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
19 6 0.18
20 22 0.65
21 6 0.18
ACGTcount: A:0.40, C:0.15, G:0.15, T:0.30
Consensus pattern (21 bp):
TTGAATAGTATCGATACACAA
Found at i:484905 original size:53 final size:53
Alignment explanation
Indices: 484814--484950 Score: 238
Period size: 53 Copynumber: 2.6 Consensus size: 53
484804 AAATTGCATA
*
484814 GTATCGATACACACAAATATGTATCGATATAGGACATTGGCAGTAGCCAAATTT
1 GTATCGATACACAC-AATATGTATCGATACAGGACATTGGCAGTAGCCAAATTT
*
484868 GTATCGATACACACAATATGTATCGATACAGGTCATTGGCAGTAGCCAAATTT
1 GTATCGATACACACAATATGTATCGATACAGGACATTGGCAGTAGCCAAATTT
*
484921 GTATCGATACACAAAATATGTATCGATACA
1 GTATCGATACACACAATATGTATCGATACA
484951 TTGGAAGTAG
Statistics
Matches: 80, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
53 66 0.82
54 14 0.17
ACGTcount: A:0.37, C:0.18, G:0.18, T:0.28
Consensus pattern (53 bp):
GTATCGATACACACAATATGTATCGATACAGGACATTGGCAGTAGCCAAATTT
Found at i:485026 original size:21 final size:22
Alignment explanation
Indices: 484996--485047 Score: 97
Period size: 21 Copynumber: 2.4 Consensus size: 22
484986 ACTATTCATA
484996 ACTGTTCATGTATCGATACATC
1 ACTGTTCATGTATCGATACATC
485018 ACT-TTCATGTATCGATACATC
1 ACTGTTCATGTATCGATACATC
485039 ACTGTTCAT
1 ACTGTTCAT
485048 AGGTCACTGT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
21 21 0.72
22 8 0.28
ACGTcount: A:0.27, C:0.23, G:0.12, T:0.38
Consensus pattern (22 bp):
ACTGTTCATGTATCGATACATC
Found at i:485155 original size:13 final size:13
Alignment explanation
Indices: 485137--485162 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
485127 ACATATTTGT
485137 GTGTATCGATACA
1 GTGTATCGATACA
485150 GTGTATCGATACA
1 GTGTATCGATACA
485163 TCATAAATAG
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:0.23, T:0.31
Consensus pattern (13 bp):
GTGTATCGATACA
Found at i:488386 original size:20 final size:20
Alignment explanation
Indices: 488333--488389 Score: 80
Period size: 20 Copynumber: 2.9 Consensus size: 20
488323 GTTGGGCATA
* *
488333 ATGTATCGATACAATTCTTC
1 ATGTATCGATACATTTCTCC
488353 ATGTATCGATACATTATC-CC
1 ATGTATCGATACATT-TCTCC
488373 ATGTATCGATACATTTC
1 ATGTATCGATACATTTC
488390 ACTTAAGGTA
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
19 2 0.06
20 30 0.88
21 2 0.06
ACGTcount: A:0.30, C:0.21, G:0.11, T:0.39
Consensus pattern (20 bp):
ATGTATCGATACATTTCTCC
Found at i:488440 original size:20 final size:19
Alignment explanation
Indices: 488414--488467 Score: 63
Period size: 19 Copynumber: 2.8 Consensus size: 19
488404 CTACTACTTT
* *
488414 CATGTATCGATACTATTGAG
1 CATGTATCGATAC-AATGAA
* *
488434 TATGTATCAATACAATGAA
1 CATGTATCGATACAATGAA
488453 CATGTATCGATACAA
1 CATGTATCGATACAA
488468 AGCATAATGT
Statistics
Matches: 28, Mismatches: 6, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
19 17 0.61
20 11 0.39
ACGTcount: A:0.39, C:0.15, G:0.15, T:0.31
Consensus pattern (19 bp):
CATGTATCGATACAATGAA
Found at i:489523 original size:36 final size:35
Alignment explanation
Indices: 489440--489537 Score: 125
Period size: 36 Copynumber: 2.9 Consensus size: 35
489430 CCTTACAACA
*
489440 CTATC-TTTCAAA-GCTAAGATAGAA--AC-CTCC
1 CTATCTTTTCAAAGGCTAAGATAGAACCTCTCTCC
**
489470 CTATCTTTTCACGGGCTAAGATAGAACCTCTCTCC
1 CTATCTTTTCAAAGGCTAAGATAGAACCTCTCTCC
489505 CTATCTTTTTCAAAGGCTAAGATAGAACCTCTC
1 CTATC-TTTTCAAAGGCTAAGATAGAACCTCTC
489538 AATCACTTAG
Statistics
Matches: 57, Mismatches: 5, Indels: 6
0.84 0.07 0.09
Matches are distributed among these distances:
30 5 0.09
31 5 0.09
32 12 0.21
34 1 0.02
35 9 0.16
36 25 0.44
ACGTcount: A:0.30, C:0.28, G:0.12, T:0.31
Consensus pattern (35 bp):
CTATCTTTTCAAAGGCTAAGATAGAACCTCTCTCC
Found at i:490012 original size:22 final size:22
Alignment explanation
Indices: 489986--490079 Score: 109
Period size: 22 Copynumber: 4.3 Consensus size: 22
489976 TACTATTCAT
*
489986 ATGTATAGATACATGAACAGCG
1 ATGTATAGATACATGAACAGTG
*
490008 ATGTATCGATACATGAACAGTG
1 ATGTATAGATACATGAACAGTG
*
490030 ATGTATCA-ATACATCAACAGTG
1 ATGTAT-AGATACATGAACAGTG
* * * *
490052 ATGTATTGATACATCAATAGTA
1 ATGTATAGATACATGAACAGTG
490074 ATGTAT
1 ATGTAT
490080 CAATTAAAAG
Statistics
Matches: 63, Mismatches: 7, Indels: 4
0.85 0.09 0.05
Matches are distributed among these distances:
22 63 1.00
ACGTcount: A:0.39, C:0.13, G:0.18, T:0.30
Consensus pattern (22 bp):
ATGTATAGATACATGAACAGTG
Found at i:490043 original size:44 final size:44
Alignment explanation
Indices: 489986--490083 Score: 126
Period size: 44 Copynumber: 2.2 Consensus size: 44
489976 TACTATTCAT
* * *
489986 ATGTAT-AGATACATGAACAGCGATGTATCGATACATGAACAGTG
1 ATGTATCA-ATACATCAACAGCGATGTATCGATACATCAACAGTA
* * *
490030 ATGTATCAATACATCAACAGTGATGTATTGATACATCAATAGTA
1 ATGTATCAATACATCAACAGCGATGTATCGATACATCAACAGTA
490074 ATGTATCAAT
1 ATGTATCAAT
490084 TAAAAGTGTT
Statistics
Matches: 47, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
44 46 0.98
45 1 0.02
ACGTcount: A:0.40, C:0.13, G:0.17, T:0.30
Consensus pattern (44 bp):
ATGTATCAATACATCAACAGCGATGTATCGATACATCAACAGTA
Found at i:490195 original size:33 final size:32
Alignment explanation
Indices: 490134--490198 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 32
490124 GCAATTCATG
*
490134 ATGTATCGATATAATAAACATGTATTGATACA
1 ATGTATCGATATAACAAACATGTATTGATACA
490166 ATGTATCGATACTAAGCAAA-ATGTATTGATACA
1 ATGTATCGATA-TAA-CAAACATGTATTGATACA
490199 TCTGGGTGAA
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
32 11 0.37
33 16 0.53
34 3 0.10
ACGTcount: A:0.43, C:0.11, G:0.14, T:0.32
Consensus pattern (32 bp):
ATGTATCGATATAACAAACATGTATTGATACA
Found at i:494918 original size:35 final size:31
Alignment explanation
Indices: 494829--494919 Score: 94
Period size: 35 Copynumber: 2.8 Consensus size: 31
494819 CCTTATAACA
494829 CTATC-TTTCAAGGCTAAGATAGAAACCTCC
1 CTATCTTTTCAAGGCTAAGATAGAAACCTCC
* * * *
494859 CTATCTTTTTAGGGTCTAAAATAGAATCTCTCTCC
1 CTATCTTTTCAAGG-CTAAGATAGAA--AC-CTCC
494894 CTATCTTTTCAAAGGCTAAGATAGAA
1 CTATCTTTTC-AAGGCTAAGATAGAA
494920 CCTTTCAATC
Statistics
Matches: 48, Mismatches: 7, Indels: 7
0.77 0.11 0.11
Matches are distributed among these distances:
30 5 0.10
31 6 0.12
32 10 0.21
34 1 0.02
35 23 0.48
36 3 0.06
ACGTcount: A:0.32, C:0.22, G:0.13, T:0.33
Consensus pattern (31 bp):
CTATCTTTTCAAGGCTAAGATAGAAACCTCC
Found at i:495480 original size:19 final size:19
Alignment explanation
Indices: 495436--495503 Score: 82
Period size: 19 Copynumber: 3.5 Consensus size: 19
495426 TACCAGTTTT
* **
495436 ATGTATCAATACAATTCATG
1 ATGTATCAATACAA-TAAAC
* *
495456 ATGTATCGATACAATGAAC
1 ATGTATCAATACAATAAAC
495475 ATGTATCAATACAATAAAC
1 ATGTATCAATACAATAAAC
495494 ATGTATCAAT
1 ATGTATCAAT
495504 TGTAGACACT
Statistics
Matches: 42, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
19 29 0.69
20 13 0.31
ACGTcount: A:0.44, C:0.15, G:0.10, T:0.31
Consensus pattern (19 bp):
ATGTATCAATACAATAAAC
Found at i:495844 original size:13 final size:13
Alignment explanation
Indices: 495826--495850 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
495816 CATAAAGTGT
495826 TGTATCGATACAA
1 TGTATCGATACAA
495839 TGTATCGATACA
1 TGTATCGATACA
495851 TGTTTTTTTG
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:495931 original size:13 final size:13
Alignment explanation
Indices: 495913--495937 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
495903 ATCACTTAAA
495913 TGTATCGATACAT
1 TGTATCGATACAT
495926 TGTATCGATACA
1 TGTATCGATACA
495938 CTGATCTTTG
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:496074 original size:52 final size:52
Alignment explanation
Indices: 495946--496066 Score: 224
Period size: 52 Copynumber: 2.3 Consensus size: 52
495936 CACTGATCTT
*
495946 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACATTATAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
*
495998 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATTAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
496050 TGTATCGATACATGCAG
1 TGTATCGATACATGCAG
496067 ATAAATTTTC
Statistics
Matches: 67, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
52 67 1.00
ACGTcount: A:0.35, C:0.18, G:0.18, T:0.29
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
Found at i:504419 original size:30 final size:31
Alignment explanation
Indices: 504316--504464 Score: 180
Period size: 31 Copynumber: 4.8 Consensus size: 31
504306 TCAAATCTCT
*
504316 TCTCAAAGTCCACGACTCAGTGGCAATCTCTG
1 TCTCAAAGTCCACGACTCAGTGGC-ATCTTTG
504348 -CTCAAAGTCCACGACTCAGTGGCATCTTT-
1 TCTCAAAGTCCACGACTCAGTGGCATCTTTG
*
504377 TCCTTTAAAGTCCACGACTCAGTGGCAT-TTTG
1 T-C-TCAAAGTCCACGACTCAGTGGCATCTTTG
*
504409 TCTCAAAGTCCACGACTCAGTGGCAT-TTTT
1 TCTCAAAGTCCACGACTCAGTGGCATCTTTG
* * *
504439 TCTTCAAAGCCCACAACTCTGTGGCA
1 TC-TCAAAGTCCACGACTCAGTGGCA
504465 CACTTTTTCT
Statistics
Matches: 105, Mismatches: 7, Indels: 11
0.85 0.06 0.09
Matches are distributed among these distances:
30 33 0.31
31 48 0.46
32 24 0.23
ACGTcount: A:0.24, C:0.30, G:0.17, T:0.29
Consensus pattern (31 bp):
TCTCAAAGTCCACGACTCAGTGGCATCTTTG
Found at i:504588 original size:34 final size:34
Alignment explanation
Indices: 504418--505011 Score: 759
Period size: 33 Copynumber: 17.6 Consensus size: 34
504408 GTCTCAAAGT
* * *
504418 CCACGACTCAGTGGCA-T-TTTTT-CTTCAAAGC
1 CCACAACTCCGTGGCACTCTTTTTCCTTCTAAGC
* * * *
504449 CCACAACTCTGTGGCACACTTTTTCTTTTTAAAGC
1 CCACAACTCCGTGGCACTCTTTTTCCTTCT-AAGC
* * *
504484 CCACAACTCTGTGGCCCTCTTTTTCCCTTTTCAAAGC
1 CCACAACTCCGTGGCACTCTTTTT-CC--TTCTAAGC
504521 CCACAACTCCGTGGCAC-C-TTTTCCTT-TAAAGC
1 CCACAACTCCGTGGCACTCTTTTTCCTTCT-AAGC
* *
504553 CCACAACTCCGTGGCAC-CTTCTTCTTTTCTAAGC
1 CCACAACTCCGTGGCACTCTTTTTC-CTTCTAAGC
*
504587 CCACAACTACGTGGCACTC-TTTTCCTTCTAAGC
1 CCACAACTCCGTGGCACTCTTTTTCCTTCTAAGC
*
504620 CCACAACTACGTGGCACT-TTTTTCCTTCTAAGC
1 CCACAACTCCGTGGCACTCTTTTTCCTTCTAAGC
* *
504653 CCACATCTACGTGGCACTC-TTTTCCTTCTAAGC
1 CCACAACTCCGTGGCACTCTTTTTCCTTCTAAGC
504686 CCACAACTCCGTGGCACTCTTTTTCCTTCTAAGC
1 CCACAACTCCGTGGCACTCTTTTTCCTTCTAAGC
* *
504720 CTACAACTACGTGGCACTC-TTTTCCTTCTAAGC
1 CCACAACTCCGTGGCACTCTTTTTCCTTCTAAGC
*
504753 CCACAACTACGTGGCACT-TTTTTCCTTCTAAGC
1 CCACAACTCCGTGGCACTCTTTTTCCTTCTAAGC
*
504786 CCACAACTACGTGGCACTC-TTTTCCTTCTAAGC
1 CCACAACTCCGTGGCACTCTTTTTCCTTCTAAGC
504819 CCACAACTCCGTGGCACTCTTTTTCCTTCTAAGC
1 CCACAACTCCGTGGCACTCTTTTTCCTTCTAAGC
504853 CCACAACTCCGTGGCACTCTTTTTCCTTCTAAGC
1 CCACAACTCCGTGGCACTCTTTTTCCTTCTAAGC
*
504887 CCACAACTTCGTGGCACTCTTTTTCCTTCTAAGC
1 CCACAACTCCGTGGCACTCTTTTTCCTTCTAAGC
*
504921 CCACAACTCCGTGGCACTCTTTTTTCCCTTTTAAAGC
1 CCACAACTCCGTGGCACTC-TTTTT-CCTTCT-AAGC
* * * *
504958 CCACAACTCCGTGGCACT-TTGTTCTTTTTAAGT
1 CCACAACTCCGTGGCACTCTTTTTCCTTCTAAGC
*
504991 CCACAACTTCGTGGCA-TCTTT
1 CCACAACTCCGTGGCACTCTTT
505012 CACCCTTTCT
Statistics
Matches: 507, Mismatches: 34, Indels: 42
0.87 0.06 0.07
Matches are distributed among these distances:
31 14 0.03
32 25 0.05
33 212 0.42
34 165 0.33
35 41 0.08
36 7 0.01
37 41 0.08
38 2 0.00
ACGTcount: A:0.20, C:0.35, G:0.12, T:0.33
Consensus pattern (34 bp):
CCACAACTCCGTGGCACTCTTTTTCCTTCTAAGC
Found at i:504690 original size:133 final size:135
Alignment explanation
Indices: 504413--505011 Score: 785
Period size: 133 Copynumber: 4.5 Consensus size: 135
504403 ATTTTGTCTC
* * * * *
504413 AAAGTCCACGACTCAGTGGCA-T-TTTTT-CTTCAAAGCCCACAACT-CTGTGGCACACTTTTTC
1 AAAGCCCACAACTCCGTGGCACTCTTTTTCCTTCTAAGCCCACAACTAC-GTGGCACTC-TTTTC
* * * * *
504474 TTTTTAAAGCCCACAACT-CTGTGGCCCTCTTTTTCCCTTTTCAAAGCCCACAACTCCGTGGCAC
64 CTTCT-AAGCCCACAACTAC-GTGGCACTCTTTTT-CC--TTCTAAGCCCACAACTACGTGGCAC
504538 -CTTTTCCTT-T
124 TCTTTTCCTTCT
* *
504548 AAAGCCCACAACTCCGTGGCAC-CTTCTTCTTTTCTAAGCCCACAACTACGTGGCACTCTTTTCC
1 AAAGCCCACAACTCCGTGGCACTCTTTTTC-CTTCTAAGCCCACAACTACGTGGCACTCTTTTCC
*
504612 TTCTAAGCCCACAACTACGTGGCACT-TTTTTCCTTCTAAGCCCACATCTACGTGGCACTCTTTT
65 TTCTAAGCCCACAACTACGTGGCACTCTTTTTCCTTCTAAGCCCACAACTACGTGGCACTCTTTT
504676 CCTTCT
130 CCTTCT
*
504682 -AAGCCCACAACTCCGTGGCACTCTTTTTCCTTCTAAGCCTACAACTACGTGGCACTCTTTTCCT
1 AAAGCCCACAACTCCGTGGCACTCTTTTTCCTTCTAAGCCCACAACTACGTGGCACTCTTTTCCT
504746 TCTAAGCCCACAACTACGTGGCACT-TTTTTCCTTCTAAGCCCACAACTACGTGGCACTCTTTTC
66 TCTAAGCCCACAACTACGTGGCACTCTTTTTCCTTCTAAGCCCACAACTACGTGGCACTCTTTTC
504810 CTTCT
131 CTTCT
*
504815 -AAGCCCACAACTCCGTGGCACTCTTTTTCCTTCTAAGCCCACAACTCCGTGGCACTCTTTTTCC
1 AAAGCCCACAACTCCGTGGCACTCTTTTTCCTTCTAAGCCCACAACTACGTGGCACTC-TTTTCC
* *
504879 TTCTAAGCCCACAACTTCGTGGCACTCTTTTTCCTTCTAAGCCCACAACTCCGTGGCACTCTTTT
65 TTCTAAGCCCACAACTACGTGGCACTCTTTTTCCTTCTAAGCCCACAACTACGTGGCACTC--TT
*
504944 TTCCCTTTT
128 TT-CCTTCT
* * * * *
504953 AAAGCCCACAACTCCGTGGCACT-TTGTTCTTTTTAAGTCCACAACTTCGTGGCA-TCTTT
1 AAAGCCCACAACTCCGTGGCACTCTTTTTCCTTCTAAGCCCACAACTACGTGGCACTCTTT
505012 CACCCTTTCT
Statistics
Matches: 422, Mismatches: 27, Indels: 29
0.88 0.06 0.06
Matches are distributed among these distances:
132 22 0.05
133 186 0.44
134 40 0.09
135 56 0.13
136 26 0.06
137 15 0.04
138 54 0.13
139 23 0.05
ACGTcount: A:0.20, C:0.35, G:0.12, T:0.33
Consensus pattern (135 bp):
AAAGCCCACAACTCCGTGGCACTCTTTTTCCTTCTAAGCCCACAACTACGTGGCACTCTTTTCCT
TCTAAGCCCACAACTACGTGGCACTCTTTTTCCTTCTAAGCCCACAACTACGTGGCACTCTTTTC
CTTCT
Found at i:505056 original size:33 final size:33
Alignment explanation
Indices: 505015--505152 Score: 208
Period size: 33 Copynumber: 4.2 Consensus size: 33
505005 CATCTTTCAC
505015 CCTT-TCTAAAGCCCACACAAGTCGGTGGCAAA
1 CCTTCTCTAAAGCCCACACAAGTCGGTGGCAAA
*
505047 CCTTCTCTAAAGCCCACACAAGTCAGTGGCAAA
1 CCTTCTCTAAAGCCCACACAAGTCGGTGGCAAA
* *
505080 CCCTTCTCCAAAGCCCACACAAGTTGGTGGC-AA
1 -CCTTCTCTAAAGCCCACACAAGTCGGTGGCAAA
*
505113 CCATTCTCTAAAGCCCACACAAGTCGGTGGCAAC
1 CC-TTCTCTAAAGCCCACACAAGTCGGTGGCAAA
505147 CCTTCT
1 CCTTCT
505153 AAGCCCAATA
Statistics
Matches: 95, Mismatches: 7, Indels: 7
0.87 0.06 0.06
Matches are distributed among these distances:
32 6 0.06
33 59 0.62
34 30 0.32
ACGTcount: A:0.29, C:0.35, G:0.17, T:0.20
Consensus pattern (33 bp):
CCTTCTCTAAAGCCCACACAAGTCGGTGGCAAA
Found at i:505109 original size:67 final size:66
Alignment explanation
Indices: 505013--505152 Score: 221
Period size: 67 Copynumber: 2.1 Consensus size: 66
505003 GGCATCTTTC
*
505013 ACCCTT-TCTAAAGCCCACACAAGTCGGTGGCAAACC-TTCTCTAAAGCCCACACAAGTCAGTGG
1 ACCCTTCTCCAAAGCCCACACAAGTCGGTGGC-AACCATTCTCTAAAGCCCACACAAGTCAGTGG
505076 CAA
65 C-A
* *
505079 ACCCTTCTCCAAAGCCCACACAAGTTGGTGGCAACCATTCTCTAAAGCCCACACAAGTCGGTGGC
1 ACCCTTCTCCAAAGCCCACACAAGTCGGTGGCAACCATTCTCTAAAGCCCACACAAGTCAGTGGC
505144 A
66 A
505145 ACCCTTCT
1 ACCCTTCT
505153 AAGCCCAATA
Statistics
Matches: 69, Mismatches: 3, Indels: 4
0.91 0.04 0.05
Matches are distributed among these distances:
66 19 0.28
67 50 0.72
ACGTcount: A:0.29, C:0.35, G:0.16, T:0.19
Consensus pattern (66 bp):
ACCCTTCTCCAAAGCCCACACAAGTCGGTGGCAACCATTCTCTAAAGCCCACACAAGTCAGTGGC
A
Found at i:505210 original size:49 final size:49
Alignment explanation
Indices: 505152--506084 Score: 1258
Period size: 49 Copynumber: 19.7 Consensus size: 49
505142 GCAACCCTTC
* * * *
505152 TAAGCCCAATATAGCTGGCCCTGAATCAGCATATTGGCACCTTCATCTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTT
*
505201 TAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCA----C--CTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTT
* * *
505244 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTT
*
505293 TAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCA----C--CTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTT
* *
505336 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTT
*
505385 TAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCA----C--CTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTT
* * *
505428 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTT
*
505477 TAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCA----C--CTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTT
* * *
505520 TAAGTCCAATATAGCTGACCTTGAAATCAGCATATTGGCACCTTCATCTT
1 TAAGTCCAATGTAGCTGGCCTTG-AATCAGCACATTGGCACCTTCATCTT
*
505570 TAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCA----C--CTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTT
* * *
505613 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTT
*
505662 TAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCACCTTCATCTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTT
*
505711 TAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCACCTTCATCTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTT
*
505760 TAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCACCTTCATCTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTT
505809 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACC-TCATCTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTT
* *
505857 TAAGCCCAATGTAGCTGGCCTTGACTCAGCACATTGGCACCTTCATCTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTT
* *
505906 TAAGTCCAACGTAGCTGGCCTTGAATCAGCACATTGGCACC-TCACCTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTT
505954 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCA----C--CTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTT
* * *
505997 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATCGGCACCTTTTCCATCTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACC--TT-CATCTT
*
506049 TAAGTTCAATGTAGCTGGCCTTGAATCAGCACATTG
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTG
506085 ACATCCTTTT
Statistics
Matches: 785, Mismatches: 58, Indels: 79
0.85 0.06 0.09
Matches are distributed among these distances:
43 219 0.28
44 14 0.02
45 4 0.01
47 1 0.00
48 91 0.12
49 396 0.50
50 25 0.03
52 35 0.04
ACGTcount: A:0.25, C:0.27, G:0.18, T:0.30
Consensus pattern (49 bp):
TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTT
Found at i:505314 original size:92 final size:92
Alignment explanation
Indices: 505147--506093 Score: 1475
Period size: 92 Copynumber: 10.1 Consensus size: 92
505137 CGGTGGCAAC
* *
505147 CCTTCTAAGCCCAATATAGCTGGCCCTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATG
1 CCTT-TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATG
505212 TAGCTGGCCTTGACTCAGCACATTGGCA
65 TAGCTGGCCTTGACTCAGCACATTGGCA
*
505240 CCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGTCCAATGT
1 CCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGT
505305 AGCTGGCCTTGACTCAGCACATTGGCA
66 AGCTGGCCTTGACTCAGCACATTGGCA
505332 CCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGT
1 CCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGT
505397 AGCTGGCCTTGACTCAGCACATTGGCA
66 AGCTGGCCTTGACTCAGCACATTGGCA
*
505424 CCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGTCCAATGT
1 CCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGT
505489 AGCTGGCCTTGACTCAGCACATTGGCA
66 AGCTGGCCTTGACTCAGCACATTGGCA
*
505516 CCTTTAAGTCCAATATAGCTGACCTTGAAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATG
1 CCTTTAAGTCCAATATAGCTGGCCTTG-AATCAGCATATTGGCACCTTCATCTTTAAGTCCAATG
505581 TAGCTGGCCTTGACTCAGCACATTGGCA
65 TAGCTGGCCTTGACTCAGCACATTGGCA
*
505609 CCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGTCCAATGT
1 CCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGT
505674 AGCTGGCCTTGACTCAGCACATTGGCA
66 AGCTGGCCTTGACTCAGCACATTGGCA
* * *
505701 CCTTCATCTTTAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCACCTTCATCTTTAAGTC
1 ----C--CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTC
505766 CAATGTAGCTGGCCTTGACTCAGCACATTGGCA
60 CAATGTAGCTGGCCTTGACTCAGCACATTGGCA
* * *
505799 CCTTCATCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACC-TCATCTTTAAGCC
1 ----C--CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTC
505863 CAATGTAGCTGGCCTTGACTCAGCACATTGGCA
60 CAATGTAGCTGGCCTTGACTCAGCACATTGGCA
** * *
505896 CCTTCATCTTTAAGTCCAACGTAGCTGGCCTTGAATCAGCACATTGGCACC-TCACCTTTAAGTC
1 ----C--CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTC
*
505960 CAATGTAGCTGGCCTTGAATCAGCACATTGGCA
60 CAATGTAGCTGGCCTTGACTCAGCACATTGGCA
* *
505993 CCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATCGGCACCTTTTCCATCTTTAAGTTCAA
1 CCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACC--TT-CATCTTTAAGTCCAA
* *
506058 TGTAGCTGGCCTTGAATCAGCACATTGACA
63 TGTAGCTGGCCTTGACTCAGCACATTGGCA
506088 TCCTTT
1 -CCTTT
506094 TTCTCATCTT
Statistics
Matches: 816, Mismatches: 26, Indels: 21
0.95 0.03 0.02
Matches are distributed among these distances:
91 40 0.05
92 357 0.44
93 95 0.12
94 1 0.00
95 42 0.05
96 6 0.01
97 138 0.17
98 137 0.17
ACGTcount: A:0.25, C:0.27, G:0.18, T:0.30
Consensus pattern (92 bp):
CCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGT
AGCTGGCCTTGACTCAGCACATTGGCA
Found at i:506072 original size:52 final size:55
Alignment explanation
Indices: 505994--506114 Score: 167
Period size: 52 Copynumber: 2.3 Consensus size: 55
505984 ACATTGGCAC
* *
505994 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATCGGCA-CC-TTTTC-CAT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATCGACATCCTTTTTCTCAT
* * *
506046 CTTTAAGTTCAATGTAGCTGGCCTTGAATCAGCACATTGACATCCTTTTTCTCAT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATCGACATCCTTTTTCTCAT
*
506101 CTTTAAGCCCAATA
1 CTTTAAGTCCAATA
506115 GCGTTGGCCG
Statistics
Matches: 58, Mismatches: 8, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
52 37 0.64
53 2 0.03
54 5 0.09
55 14 0.24
ACGTcount: A:0.26, C:0.26, G:0.14, T:0.35
Consensus pattern (55 bp):
CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATCGACATCCTTTTTCTCAT
Found at i:506205 original size:67 final size:68
Alignment explanation
Indices: 506097--506223 Score: 175
Period size: 67 Copynumber: 1.9 Consensus size: 68
506087 ATCCTTTTTC
* * *
506097 TCATCTTTAAGCCCAATAGCGTTGGCCGTGAATCAACATATTGGCATCTTTATCA-CTTTTCTCA
1 TCATCTTTAAGCCCAATAGCGCTGGCCGTGAATCAACATATTGGCACCTTCATCATCTTTTCTCA
506161 TCT
66 TCT
* ** * *
506164 TCATCTTTAAGTCCAATATTGCTGGCCTTGAATCAGCATATTGGCACCTTCATCATCTTT
1 TCATCTTTAAGCCCAATAGCGCTGGCCGTGAATCAACATATTGGCACCTTCATCATCTTT
506224 AAAACCCAAT
Statistics
Matches: 51, Mismatches: 8, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
67 47 0.92
68 4 0.08
ACGTcount: A:0.24, C:0.25, G:0.13, T:0.38
Consensus pattern (68 bp):
TCATCTTTAAGCCCAATAGCGCTGGCCGTGAATCAACATATTGGCACCTTCATCATCTTTTCTCA
TCT
Found at i:507052 original size:13 final size:13
Alignment explanation
Indices: 507034--507058 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
507024 CATAAAGTGT
507034 TGTATCGATACAA
1 TGTATCGATACAA
507047 TGTATCGATACA
1 TGTATCGATACA
507059 TGTTTTTTTG
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:507139 original size:13 final size:13
Alignment explanation
Indices: 507121--507145 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
507111 ATCACTTAAA
507121 TGTATCGATACAT
1 TGTATCGATACAT
507134 TGTATCGATACA
1 TGTATCGATACA
507146 CTGATCTTTG
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:507282 original size:52 final size:52
Alignment explanation
Indices: 507154--507274 Score: 224
Period size: 52 Copynumber: 2.3 Consensus size: 52
507144 CACTGATCTT
*
507154 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACATTATAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
*
507206 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATTAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
507258 TGTATCGATACATGCAG
1 TGTATCGATACATGCAG
507275 ATAAATTTTC
Statistics
Matches: 67, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
52 67 1.00
ACGTcount: A:0.35, C:0.18, G:0.18, T:0.29
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
Found at i:515629 original size:30 final size:31
Alignment explanation
Indices: 515526--515674 Score: 180
Period size: 31 Copynumber: 4.8 Consensus size: 31
515516 TCAAATCTCT
*
515526 TCTCAAAGTCCACGACTCAGTGGCAATCTCTG
1 TCTCAAAGTCCACGACTCAGTGGC-ATCTTTG
515558 -CTCAAAGTCCACGACTCAGTGGCATCTTT-
1 TCTCAAAGTCCACGACTCAGTGGCATCTTTG
*
515587 TCCTTTAAAGTCCACGACTCAGTGGCAT-TTTG
1 T-C-TCAAAGTCCACGACTCAGTGGCATCTTTG
*
515619 TCTCAAAGTCCACGACTCAGTGGCAT-TTTT
1 TCTCAAAGTCCACGACTCAGTGGCATCTTTG
* * *
515649 TCTTCAAAGCCCACAACTCTGTGGCA
1 TC-TCAAAGTCCACGACTCAGTGGCA
515675 CACTTTTTCT
Statistics
Matches: 105, Mismatches: 7, Indels: 11
0.85 0.06 0.09
Matches are distributed among these distances:
30 33 0.31
31 48 0.46
32 24 0.23
ACGTcount: A:0.24, C:0.30, G:0.17, T:0.29
Consensus pattern (31 bp):
TCTCAAAGTCCACGACTCAGTGGCATCTTTG
Found at i:515798 original size:34 final size:34
Alignment explanation
Indices: 515628--516221 Score: 759
Period size: 33 Copynumber: 17.6 Consensus size: 34
515618 GTCTCAAAGT
* * *
515628 CCACGACTCAGTGGCA-T-TTTTT-CTTCAAAGC
1 CCACAACTCCGTGGCACTCTTTTTCCTTCTAAGC
* * * *
515659 CCACAACTCTGTGGCACACTTTTTCTTTTTAAAGC
1 CCACAACTCCGTGGCACTCTTTTTCCTTCT-AAGC
* * *
515694 CCACAACTCTGTGGCCCTCTTTTTCCCTTTTCAAAGC
1 CCACAACTCCGTGGCACTCTTTTT-CC--TTCTAAGC
515731 CCACAACTCCGTGGCAC-C-TTTTCCTT-TAAAGC
1 CCACAACTCCGTGGCACTCTTTTTCCTTCT-AAGC
* *
515763 CCACAACTCCGTGGCAC-CTTCTTCTTTTCTAAGC
1 CCACAACTCCGTGGCACTCTTTTTC-CTTCTAAGC
*
515797 CCACAACTACGTGGCACTC-TTTTCCTTCTAAGC
1 CCACAACTCCGTGGCACTCTTTTTCCTTCTAAGC
*
515830 CCACAACTACGTGGCACT-TTTTTCCTTCTAAGC
1 CCACAACTCCGTGGCACTCTTTTTCCTTCTAAGC
* *
515863 CCACATCTACGTGGCACTC-TTTTCCTTCTAAGC
1 CCACAACTCCGTGGCACTCTTTTTCCTTCTAAGC
515896 CCACAACTCCGTGGCACTCTTTTTCCTTCTAAGC
1 CCACAACTCCGTGGCACTCTTTTTCCTTCTAAGC
* *
515930 CTACAACTACGTGGCACTC-TTTTCCTTCTAAGC
1 CCACAACTCCGTGGCACTCTTTTTCCTTCTAAGC
*
515963 CCACAACTACGTGGCACT-TTTTTCCTTCTAAGC
1 CCACAACTCCGTGGCACTCTTTTTCCTTCTAAGC
*
515996 CCACAACTACGTGGCACTC-TTTTCCTTCTAAGC
1 CCACAACTCCGTGGCACTCTTTTTCCTTCTAAGC
516029 CCACAACTCCGTGGCACTCTTTTTCCTTCTAAGC
1 CCACAACTCCGTGGCACTCTTTTTCCTTCTAAGC
516063 CCACAACTCCGTGGCACTCTTTTTCCTTCTAAGC
1 CCACAACTCCGTGGCACTCTTTTTCCTTCTAAGC
*
516097 CCACAACTTCGTGGCACTCTTTTTCCTTCTAAGC
1 CCACAACTCCGTGGCACTCTTTTTCCTTCTAAGC
*
516131 CCACAACTCCGTGGCACTCTTTTTTCCCTTTTAAAGC
1 CCACAACTCCGTGGCACTC-TTTTT-CCTTCT-AAGC
* * * *
516168 CCACAACTCCGTGGCACT-TTGTTCTTTTTAAGT
1 CCACAACTCCGTGGCACTCTTTTTCCTTCTAAGC
*
516201 CCACAACTTCGTGGCA-TCTTT
1 CCACAACTCCGTGGCACTCTTT
516222 CACCCTTTCT
Statistics
Matches: 507, Mismatches: 34, Indels: 42
0.87 0.06 0.07
Matches are distributed among these distances:
31 14 0.03
32 25 0.05
33 212 0.42
34 165 0.33
35 41 0.08
36 7 0.01
37 41 0.08
38 2 0.00
ACGTcount: A:0.20, C:0.35, G:0.12, T:0.33
Consensus pattern (34 bp):
CCACAACTCCGTGGCACTCTTTTTCCTTCTAAGC
Found at i:515900 original size:133 final size:135
Alignment explanation
Indices: 515623--516221 Score: 785
Period size: 133 Copynumber: 4.5 Consensus size: 135
515613 ATTTTGTCTC
* * * * *
515623 AAAGTCCACGACTCAGTGGCA-T-TTTTT-CTTCAAAGCCCACAACT-CTGTGGCACACTTTTTC
1 AAAGCCCACAACTCCGTGGCACTCTTTTTCCTTCTAAGCCCACAACTAC-GTGGCACTC-TTTTC
* * * * *
515684 TTTTTAAAGCCCACAACT-CTGTGGCCCTCTTTTTCCCTTTTCAAAGCCCACAACTCCGTGGCAC
64 CTTCT-AAGCCCACAACTAC-GTGGCACTCTTTTT-CC--TTCTAAGCCCACAACTACGTGGCAC
515748 -CTTTTCCTT-T
124 TCTTTTCCTTCT
* *
515758 AAAGCCCACAACTCCGTGGCAC-CTTCTTCTTTTCTAAGCCCACAACTACGTGGCACTCTTTTCC
1 AAAGCCCACAACTCCGTGGCACTCTTTTTC-CTTCTAAGCCCACAACTACGTGGCACTCTTTTCC
*
515822 TTCTAAGCCCACAACTACGTGGCACT-TTTTTCCTTCTAAGCCCACATCTACGTGGCACTCTTTT
65 TTCTAAGCCCACAACTACGTGGCACTCTTTTTCCTTCTAAGCCCACAACTACGTGGCACTCTTTT
515886 CCTTCT
130 CCTTCT
*
515892 -AAGCCCACAACTCCGTGGCACTCTTTTTCCTTCTAAGCCTACAACTACGTGGCACTCTTTTCCT
1 AAAGCCCACAACTCCGTGGCACTCTTTTTCCTTCTAAGCCCACAACTACGTGGCACTCTTTTCCT
515956 TCTAAGCCCACAACTACGTGGCACT-TTTTTCCTTCTAAGCCCACAACTACGTGGCACTCTTTTC
66 TCTAAGCCCACAACTACGTGGCACTCTTTTTCCTTCTAAGCCCACAACTACGTGGCACTCTTTTC
516020 CTTCT
131 CTTCT
*
516025 -AAGCCCACAACTCCGTGGCACTCTTTTTCCTTCTAAGCCCACAACTCCGTGGCACTCTTTTTCC
1 AAAGCCCACAACTCCGTGGCACTCTTTTTCCTTCTAAGCCCACAACTACGTGGCACTC-TTTTCC
* *
516089 TTCTAAGCCCACAACTTCGTGGCACTCTTTTTCCTTCTAAGCCCACAACTCCGTGGCACTCTTTT
65 TTCTAAGCCCACAACTACGTGGCACTCTTTTTCCTTCTAAGCCCACAACTACGTGGCACTC--TT
*
516154 TTCCCTTTT
128 TT-CCTTCT
* * * * *
516163 AAAGCCCACAACTCCGTGGCACT-TTGTTCTTTTTAAGTCCACAACTTCGTGGCA-TCTTT
1 AAAGCCCACAACTCCGTGGCACTCTTTTTCCTTCTAAGCCCACAACTACGTGGCACTCTTT
516222 CACCCTTTCT
Statistics
Matches: 422, Mismatches: 27, Indels: 29
0.88 0.06 0.06
Matches are distributed among these distances:
132 22 0.05
133 186 0.44
134 40 0.09
135 56 0.13
136 26 0.06
137 15 0.04
138 54 0.13
139 23 0.05
ACGTcount: A:0.20, C:0.35, G:0.12, T:0.33
Consensus pattern (135 bp):
AAAGCCCACAACTCCGTGGCACTCTTTTTCCTTCTAAGCCCACAACTACGTGGCACTCTTTTCCT
TCTAAGCCCACAACTACGTGGCACTCTTTTTCCTTCTAAGCCCACAACTACGTGGCACTCTTTTC
CTTCT
Found at i:516266 original size:33 final size:33
Alignment explanation
Indices: 516225--516362 Score: 208
Period size: 33 Copynumber: 4.2 Consensus size: 33
516215 CATCTTTCAC
516225 CCTT-TCTAAAGCCCACACAAGTCGGTGGCAAA
1 CCTTCTCTAAAGCCCACACAAGTCGGTGGCAAA
*
516257 CCTTCTCTAAAGCCCACACAAGTCAGTGGCAAA
1 CCTTCTCTAAAGCCCACACAAGTCGGTGGCAAA
* *
516290 CCCTTCTCCAAAGCCCACACAAGTTGGTGGC-AA
1 -CCTTCTCTAAAGCCCACACAAGTCGGTGGCAAA
*
516323 CCATTCTCTAAAGCCCACACAAGTCGGTGGCAAC
1 CC-TTCTCTAAAGCCCACACAAGTCGGTGGCAAA
516357 CCTTCT
1 CCTTCT
516363 AAGCCCAATA
Statistics
Matches: 95, Mismatches: 7, Indels: 7
0.87 0.06 0.06
Matches are distributed among these distances:
32 6 0.06
33 59 0.62
34 30 0.32
ACGTcount: A:0.29, C:0.35, G:0.17, T:0.20
Consensus pattern (33 bp):
CCTTCTCTAAAGCCCACACAAGTCGGTGGCAAA
Found at i:516319 original size:67 final size:66
Alignment explanation
Indices: 516223--516362 Score: 221
Period size: 67 Copynumber: 2.1 Consensus size: 66
516213 GGCATCTTTC
*
516223 ACCCTT-TCTAAAGCCCACACAAGTCGGTGGCAAACC-TTCTCTAAAGCCCACACAAGTCAGTGG
1 ACCCTTCTCCAAAGCCCACACAAGTCGGTGGC-AACCATTCTCTAAAGCCCACACAAGTCAGTGG
516286 CAA
65 C-A
* *
516289 ACCCTTCTCCAAAGCCCACACAAGTTGGTGGCAACCATTCTCTAAAGCCCACACAAGTCGGTGGC
1 ACCCTTCTCCAAAGCCCACACAAGTCGGTGGCAACCATTCTCTAAAGCCCACACAAGTCAGTGGC
516354 A
66 A
516355 ACCCTTCT
1 ACCCTTCT
516363 AAGCCCAATA
Statistics
Matches: 69, Mismatches: 3, Indels: 4
0.91 0.04 0.05
Matches are distributed among these distances:
66 19 0.28
67 50 0.72
ACGTcount: A:0.29, C:0.35, G:0.16, T:0.19
Consensus pattern (66 bp):
ACCCTTCTCCAAAGCCCACACAAGTCGGTGGCAACCATTCTCTAAAGCCCACACAAGTCAGTGGC
A
Found at i:516420 original size:49 final size:49
Alignment explanation
Indices: 516362--517293 Score: 1274
Period size: 49 Copynumber: 19.7 Consensus size: 49
516352 GCAACCCTTC
* * * *
516362 TAAGCCCAATATAGCTGGCCCTGAATCAGCATATTGGCACCTTCATCTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTT
*
516411 TAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCA----C--CTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTT
* * *
516454 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTT
*
516503 TAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCA----C--CTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTT
* *
516546 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTT
*
516595 TAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCA----C--CTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTT
* * *
516638 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTT
*
516687 TAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCA----C--CTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTT
* *
516730 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTT
*
516779 TAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCA----C--CTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTT
* * *
516822 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTT
*
516871 TAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCACCTTCATCTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTT
*
516920 TAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCACCTTCATCTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTT
*
516969 TAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCACCTTCATCTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTT
517018 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACC-TCATCTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTT
* *
517066 TAAGCCCAATGTAGCTGGCCTTGACTCAGCACATTGGCACCTTCATCTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTT
* *
517115 TAAGTCCAACGTAGCTGGCCTTGAATCAGCACATTGGCACC-TCACCTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTT
517163 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCA----C--CTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTT
* * *
517206 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATCGGCACCTTTTCCATCTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACC--TT-CATCTT
*
517258 TAAGTTCAATGTAGCTGGCCTTGAATCAGCACATTG
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTG
517294 ACATCCTTTT
Statistics
Matches: 787, Mismatches: 56, Indels: 77
0.86 0.06 0.08
Matches are distributed among these distances:
43 234 0.30
45 4 0.01
47 2 0.00
48 90 0.11
49 421 0.53
50 1 0.00
52 35 0.04
ACGTcount: A:0.25, C:0.27, G:0.18, T:0.30
Consensus pattern (49 bp):
TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTT
Found at i:516524 original size:92 final size:92
Alignment explanation
Indices: 516357--517302 Score: 1491
Period size: 92 Copynumber: 10.1 Consensus size: 92
516347 CGGTGGCAAC
* *
516357 CCTTCTAAGCCCAATATAGCTGGCCCTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATG
1 CCTT-TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATG
516422 TAGCTGGCCTTGACTCAGCACATTGGCA
65 TAGCTGGCCTTGACTCAGCACATTGGCA
*
516450 CCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGTCCAATGT
1 CCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGT
516515 AGCTGGCCTTGACTCAGCACATTGGCA
66 AGCTGGCCTTGACTCAGCACATTGGCA
516542 CCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGT
1 CCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGT
516607 AGCTGGCCTTGACTCAGCACATTGGCA
66 AGCTGGCCTTGACTCAGCACATTGGCA
*
516634 CCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGTCCAATGT
1 CCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGT
516699 AGCTGGCCTTGACTCAGCACATTGGCA
66 AGCTGGCCTTGACTCAGCACATTGGCA
516726 CCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGT
1 CCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGT
516791 AGCTGGCCTTGACTCAGCACATTGGCA
66 AGCTGGCCTTGACTCAGCACATTGGCA
*
516818 CCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGTCCAATGT
1 CCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGT
516883 AGCTGGCCTTGACTCAGCACATTGGCA
66 AGCTGGCCTTGACTCAGCACATTGGCA
* * *
516910 CCTTCATCTTTAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCACCTTCATCTTTAAGTC
1 ----C--CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTC
516975 CAATGTAGCTGGCCTTGACTCAGCACATTGGCA
60 CAATGTAGCTGGCCTTGACTCAGCACATTGGCA
* * *
517008 CCTTCATCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACC-TCATCTTTAAGCC
1 ----C--CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTC
517072 CAATGTAGCTGGCCTTGACTCAGCACATTGGCA
60 CAATGTAGCTGGCCTTGACTCAGCACATTGGCA
** * *
517105 CCTTCATCTTTAAGTCCAACGTAGCTGGCCTTGAATCAGCACATTGGCACC-TCACCTTTAAGTC
1 ----C--CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTC
*
517169 CAATGTAGCTGGCCTTGAATCAGCACATTGGCA
60 CAATGTAGCTGGCCTTGACTCAGCACATTGGCA
* *
517202 CCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATCGGCACCTTTTCCATCTTTAAGTTCAA
1 CCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACC--TT-CATCTTTAAGTCCAA
* *
517267 TGTAGCTGGCCTTGAATCAGCACATTGACA
63 TGTAGCTGGCCTTGACTCAGCACATTGGCA
517297 TCCTTT
1 -CCTTT
517303 TTCTCATCTT
Statistics
Matches: 818, Mismatches: 24, Indels: 19
0.95 0.03 0.02
Matches are distributed among these distances:
91 40 0.05
92 449 0.55
93 5 0.01
94 1 0.00
95 42 0.05
96 6 0.01
97 138 0.17
98 137 0.17
ACGTcount: A:0.25, C:0.27, G:0.18, T:0.30
Consensus pattern (92 bp):
CCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGT
AGCTGGCCTTGACTCAGCACATTGGCA
Found at i:517281 original size:52 final size:55
Alignment explanation
Indices: 517203--517323 Score: 167
Period size: 52 Copynumber: 2.3 Consensus size: 55
517193 ACATTGGCAC
* *
517203 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATCGGCA-CC-TTTTC-CAT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATCGACATCCTTTTTCTCAT
* * *
517255 CTTTAAGTTCAATGTAGCTGGCCTTGAATCAGCACATTGACATCCTTTTTCTCAT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATCGACATCCTTTTTCTCAT
*
517310 CTTTAAGCCCAATA
1 CTTTAAGTCCAATA
517324 GCGTTGGCCG
Statistics
Matches: 58, Mismatches: 8, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
52 37 0.64
53 2 0.03
54 5 0.09
55 14 0.24
ACGTcount: A:0.26, C:0.26, G:0.14, T:0.35
Consensus pattern (55 bp):
CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATCGACATCCTTTTTCTCAT
Found at i:517414 original size:67 final size:68
Alignment explanation
Indices: 517306--517432 Score: 175
Period size: 67 Copynumber: 1.9 Consensus size: 68
517296 ATCCTTTTTC
* * *
517306 TCATCTTTAAGCCCAATAGCGTTGGCCGTGAATCAACATATTGGCATCTTTATCA-CTTTTCTCA
1 TCATCTTTAAGCCCAATAGCGCTGGCCGTGAATCAACATATTGGCACCTTCATCATCTTTTCTCA
517370 TCT
66 TCT
* ** * *
517373 TCATCTTTAAGTCCAATATTGCTGGCCTTGAATCAGCATATTGGCACCTTCATCATCTTT
1 TCATCTTTAAGCCCAATAGCGCTGGCCGTGAATCAACATATTGGCACCTTCATCATCTTT
517433 AAAACCCAAT
Statistics
Matches: 51, Mismatches: 8, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
67 47 0.92
68 4 0.08
ACGTcount: A:0.24, C:0.25, G:0.13, T:0.38
Consensus pattern (68 bp):
TCATCTTTAAGCCCAATAGCGCTGGCCGTGAATCAACATATTGGCACCTTCATCATCTTTTCTCA
TCT
Found at i:518261 original size:13 final size:13
Alignment explanation
Indices: 518243--518267 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
518233 CATAAAGTGT
518243 TGTATCGATACAA
1 TGTATCGATACAA
518256 TGTATCGATACA
1 TGTATCGATACA
518268 TGTTTTTTTG
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:518348 original size:13 final size:13
Alignment explanation
Indices: 518330--518354 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
518320 ATCACTTAAA
518330 TGTATCGATACAT
1 TGTATCGATACAT
518343 TGTATCGATACA
1 TGTATCGATACA
518355 CTGATCTTTG
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:518491 original size:52 final size:52
Alignment explanation
Indices: 518363--518483 Score: 224
Period size: 52 Copynumber: 2.3 Consensus size: 52
518353 CACTGATCTT
*
518363 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACATTATAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
*
518415 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATTAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
518467 TGTATCGATACATGCAG
1 TGTATCGATACATGCAG
518484 ATAAATTTTC
Statistics
Matches: 67, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
52 67 1.00
ACGTcount: A:0.35, C:0.18, G:0.18, T:0.29
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
Found at i:525236 original size:21 final size:20
Alignment explanation
Indices: 525203--525241 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
525193 GAGGTGTTGG
525203 ACATACTAAAAATACATGAA
1 ACATACTAAAAATACATGAA
* *
525223 ACATAGCTTAAAATGCATG
1 ACATA-CTAAAAATACATG
525242 GACATGGGCT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 5 0.31
21 11 0.69
ACGTcount: A:0.51, C:0.15, G:0.10, T:0.23
Consensus pattern (20 bp):
ACATACTAAAAATACATGAA
Found at i:526452 original size:13 final size:13
Alignment explanation
Indices: 526436--526482 Score: 51
Period size: 13 Copynumber: 3.5 Consensus size: 13
526426 ACCTAAAACA
526436 CTTAAATCTATCC
1 CTTAAATCTATCC
* *
526449 CTTAAAT-TAAAACA
1 CTTAAATCT--ATCC
526463 CTTAAATCTATCC
1 CTTAAATCTATCC
526476 CTTAAAT
1 CTTAAAT
526483 TCGCTGCCCA
Statistics
Matches: 27, Mismatches: 4, Indels: 6
0.73 0.11 0.16
Matches are distributed among these distances:
12 1 0.04
13 16 0.59
14 9 0.33
15 1 0.04
ACGTcount: A:0.40, C:0.23, G:0.00, T:0.36
Consensus pattern (13 bp):
CTTAAATCTATCC
Found at i:526467 original size:27 final size:27
Alignment explanation
Indices: 526429--526483 Score: 110
Period size: 27 Copynumber: 2.0 Consensus size: 27
526419 AATCATCACC
526429 TAAAACACTTAAATCTATCCCTTAAAT
1 TAAAACACTTAAATCTATCCCTTAAAT
526456 TAAAACACTTAAATCTATCCCTTAAAT
1 TAAAACACTTAAATCTATCCCTTAAAT
526483 T
1 T
526484 CGCTGCCCAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.44, C:0.22, G:0.00, T:0.35
Consensus pattern (27 bp):
TAAAACACTTAAATCTATCCCTTAAAT
Found at i:527670 original size:18 final size:18
Alignment explanation
Indices: 527644--527690 Score: 67
Period size: 18 Copynumber: 2.6 Consensus size: 18
527634 TATGATAATA
* *
527644 ATCCCAAGCACATTGATG
1 ATCCTAAGCACACTGATG
527662 ATCCTAAGCACACTGATG
1 ATCCTAAGCACACTGATG
*
527680 AGCCTAAGCAC
1 ATCCTAAGCAC
527691 CATGAAACGG
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.34, C:0.30, G:0.17, T:0.19
Consensus pattern (18 bp):
ATCCTAAGCACACTGATG
Found at i:529003 original size:20 final size:20
Alignment explanation
Indices: 528967--529007 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
528957 TGTAATCTTG
*
528967 AAACCCTAATTGGTATCGAT
1 AAACCCTAATTGATATCGAT
528987 AAACCTCTAATT-ATATCGAT
1 AAACC-CTAATTGATATCGAT
529007 A
1 A
529008 CAATTCAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 13 0.68
21 6 0.32
ACGTcount: A:0.39, C:0.20, G:0.10, T:0.32
Consensus pattern (20 bp):
AAACCCTAATTGATATCGAT
Found at i:532322 original size:13 final size:13
Alignment explanation
Indices: 532304--532329 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
532294 AATTTTTTTG
532304 TGTATCGATACAT
1 TGTATCGATACAT
532317 TGTATCGATACAT
1 TGTATCGATACAT
532330 ACTTGCTGTA
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):
TGTATCGATACAT
Found at i:532394 original size:21 final size:21
Alignment explanation
Indices: 532368--532443 Score: 100
Period size: 21 Copynumber: 3.7 Consensus size: 21
532358 CTGCCAAGAA
*
532368 ATGTATCGATACATCTTTTTT
1 ATGTATCGATACATCTTTTTC
****
532389 ATGTATCGATACAT-TGCAAC
1 ATGTATCGATACATCTTTTTC
532409 ATGTATCGATACATCTTTTTC
1 ATGTATCGATACATCTTTTTC
532430 ATGTATCGATACAT
1 ATGTATCGATACAT
532444 TGCAACATGT
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 15 0.33
21 30 0.67
ACGTcount: A:0.29, C:0.17, G:0.12, T:0.42
Consensus pattern (21 bp):
ATGTATCGATACATCTTTTTC
Found at i:532414 original size:20 final size:20
Alignment explanation
Indices: 532389--532461 Score: 101
Period size: 20 Copynumber: 3.6 Consensus size: 20
532379 CATCTTTTTT
532389 ATGTATCGATACATTGCAAC
1 ATGTATCGATACATTGCAAC
****
532409 ATGTATCGATACATCTTTTTC
1 ATGTATCGATACAT-TGCAAC
532430 ATGTATCGATACATTGCAAC
1 ATGTATCGATACATTGCAAC
532450 ATGTATCGATAC
1 ATGTATCGATAC
532462 TTTGAATTGT
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
20 28 0.64
21 16 0.36
ACGTcount: A:0.32, C:0.19, G:0.14, T:0.36
Consensus pattern (20 bp):
ATGTATCGATACATTGCAAC
Found at i:532425 original size:41 final size:41
Alignment explanation
Indices: 532368--532461 Score: 179
Period size: 41 Copynumber: 2.3 Consensus size: 41
532358 CTGCCAAGAA
*
532368 ATGTATCGATACATCTTTTTTATGTATCGATACATTGCAAC
1 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
532409 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
1 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
532450 ATGTATCGATAC
1 ATGTATCGATAC
532462 TTTGAATTGT
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.30, C:0.18, G:0.13, T:0.39
Consensus pattern (41 bp):
ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
Found at i:534922 original size:13 final size:13
Alignment explanation
Indices: 534904--534968 Score: 112
Period size: 13 Copynumber: 5.0 Consensus size: 13
534894 ATAATCACCC
*
534904 TGTATCGATACAG
1 TGTATCGATACAA
534917 TGTATCGATACAA
1 TGTATCGATACAA
*
534930 TGTATCGATACAG
1 TGTATCGATACAA
534943 TGTATCGATACAA
1 TGTATCGATACAA
534956 TGTATCGATACAA
1 TGTATCGATACAA
534969 AGAAAAATGT
Statistics
Matches: 49, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 49 1.00
ACGTcount: A:0.35, C:0.15, G:0.18, T:0.31
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:534933 original size:26 final size:26
Alignment explanation
Indices: 534904--534967 Score: 128
Period size: 26 Copynumber: 2.5 Consensus size: 26
534894 ATAATCACCC
534904 TGTATCGATACAGTGTATCGATACAA
1 TGTATCGATACAGTGTATCGATACAA
534930 TGTATCGATACAGTGTATCGATACAA
1 TGTATCGATACAGTGTATCGATACAA
534956 TGTATCGATACA
1 TGTATCGATACA
534968 AAGAAAAATG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 38 1.00
ACGTcount: A:0.34, C:0.16, G:0.19, T:0.31
Consensus pattern (26 bp):
TGTATCGATACAGTGTATCGATACAA
Found at i:534979 original size:20 final size:20
Alignment explanation
Indices: 534954--535032 Score: 70
Period size: 20 Copynumber: 3.7 Consensus size: 20
534944 GTATCGATAC
534954 AATGTATCGATACAAAGAAA
1 AATGTATCGATACAAAGAAA
*
534974 AATGTATCGATACATAGAATTTCCA
1 AATGTATCGATACAAAGAA-----A
*
534999 GATGTATCGATACACAA-AAA
1 AATGTATCGATACA-AAGAAA
*
535019 CATGTATCGATACA
1 AATGTATCGATACA
535033 TTTTGGACAT
Statistics
Matches: 49, Mismatches: 4, Indels: 12
0.75 0.06 0.18
Matches are distributed among these distances:
20 32 0.65
25 16 0.33
26 1 0.02
ACGTcount: A:0.46, C:0.15, G:0.14, T:0.25
Consensus pattern (20 bp):
AATGTATCGATACAAAGAAA
Found at i:537068 original size:15 final size:15
Alignment explanation
Indices: 537048--537078 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
537038 ATTTCGTTTG
*
537048 GAGCTTCTTCATTTT
1 GAGCTTCCTCATTTT
537063 GAGCTTCCTCATTTT
1 GAGCTTCCTCATTTT
537078 G
1 G
537079 GACATTTTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.23, G:0.16, T:0.48
Consensus pattern (15 bp):
GAGCTTCCTCATTTT
Found at i:538911 original size:21 final size:21
Alignment explanation
Indices: 538882--538926 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
538872 AAGTTTTCAT
*
538882 TTTTCTTAGCTAAC-TCATTA
1 TTTTCTTAGCCAACTTCATTA
*
538902 TTTTCATTAGCCAACTTCTTTA
1 TTTTC-TTAGCCAACTTCATTA
538924 TTT
1 TTT
538927 CAACTTGCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 8 0.38
22 8 0.38
ACGTcount: A:0.22, C:0.20, G:0.04, T:0.53
Consensus pattern (21 bp):
TTTTCTTAGCCAACTTCATTA
Found at i:541155 original size:13 final size:13
Alignment explanation
Indices: 541137--541162 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
541127 ATTTTTTTTG
541137 TGTATCGATACAT
1 TGTATCGATACAT
541150 TGTATCGATACAT
1 TGTATCGATACAT
541163 ACTTGCTGTA
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):
TGTATCGATACAT
Found at i:541227 original size:21 final size:21
Alignment explanation
Indices: 541201--541276 Score: 100
Period size: 21 Copynumber: 3.7 Consensus size: 21
541191 CTGCCAAGAA
*
541201 ATGTATCGATACATCTTTTTT
1 ATGTATCGATACATCTTTTTC
****
541222 ATGTATCGATACAT-TGCAAC
1 ATGTATCGATACATCTTTTTC
541242 ATGTATCGATACATCTTTTTC
1 ATGTATCGATACATCTTTTTC
541263 ATGTATCGATACAT
1 ATGTATCGATACAT
541277 TGCAACATGT
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 15 0.33
21 30 0.67
ACGTcount: A:0.29, C:0.17, G:0.12, T:0.42
Consensus pattern (21 bp):
ATGTATCGATACATCTTTTTC
Found at i:541247 original size:20 final size:20
Alignment explanation
Indices: 541222--541294 Score: 101
Period size: 20 Copynumber: 3.6 Consensus size: 20
541212 CATCTTTTTT
541222 ATGTATCGATACATTGCAAC
1 ATGTATCGATACATTGCAAC
****
541242 ATGTATCGATACATCTTTTTC
1 ATGTATCGATACAT-TGCAAC
541263 ATGTATCGATACATTGCAAC
1 ATGTATCGATACATTGCAAC
541283 ATGTATCGATAC
1 ATGTATCGATAC
541295 TTTGAATTGT
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
20 28 0.64
21 16 0.36
ACGTcount: A:0.32, C:0.19, G:0.14, T:0.36
Consensus pattern (20 bp):
ATGTATCGATACATTGCAAC
Found at i:541258 original size:41 final size:41
Alignment explanation
Indices: 541201--541294 Score: 179
Period size: 41 Copynumber: 2.3 Consensus size: 41
541191 CTGCCAAGAA
*
541201 ATGTATCGATACATCTTTTTTATGTATCGATACATTGCAAC
1 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
541242 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
1 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
541283 ATGTATCGATAC
1 ATGTATCGATAC
541295 TTTGAATTGT
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.30, C:0.18, G:0.13, T:0.39
Consensus pattern (41 bp):
ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
Found at i:549390 original size:14 final size:14
Alignment explanation
Indices: 549371--549405 Score: 70
Period size: 14 Copynumber: 2.5 Consensus size: 14
549361 AGAGAGATGT
549371 TTACATCTTTGTAA
1 TTACATCTTTGTAA
549385 TTACATCTTTGTAA
1 TTACATCTTTGTAA
549399 TTACATC
1 TTACATC
549406 CTTATTTACA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.29, C:0.17, G:0.06, T:0.49
Consensus pattern (14 bp):
TTACATCTTTGTAA
Found at i:550207 original size:27 final size:26
Alignment explanation
Indices: 550160--550211 Score: 77
Period size: 27 Copynumber: 2.0 Consensus size: 26
550150 ACTAAGAATG
* *
550160 CCATTTTTTCTCTCAATTTTGCCTTA
1 CCATTTTTCCTCACAATTTTGCCTTA
550186 CCATTTTCTCCTCACAATTTTGCCTT
1 CCATTTT-TCCTCACAATTTTGCCTT
550212 TGTTAATTTC
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 7 0.30
27 16 0.70
ACGTcount: A:0.15, C:0.31, G:0.04, T:0.50
Consensus pattern (26 bp):
CCATTTTTCCTCACAATTTTGCCTTA
Done.