Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold29
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: 5511024
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 57772 characters in sequence are not A, C, G, or T
File 3 of 34
Found at i:416323 original size:3 final size:3
Alignment explanation
Indices: 416317--416342 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
416307 TCAAGTACGC
416317 ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA AT
416343 TGGTGACTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
ATA
Found at i:428272 original size:12 final size:12
Alignment explanation
Indices: 428255--428279 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
428245 GCAACCTGCT
428255 TCTCCACTTTAG
1 TCTCCACTTTAG
428267 TCTCCACTTTAG
1 TCTCCACTTTAG
428279 T
1 T
428280 TTTCTGATGG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.16, C:0.32, G:0.08, T:0.44
Consensus pattern (12 bp):
TCTCCACTTTAG
Found at i:430398 original size:15 final size:15
Alignment explanation
Indices: 430365--430408 Score: 54
Period size: 15 Copynumber: 2.9 Consensus size: 15
430355 TGCTGATAGC
*
430365 GATAGAATAGAAAAG
1 GATAGAGTAGAAAAG
430380 GATAGAGTAG-AAAG
1 GATAGAGTAGAAAAG
*
430394 AGATAGTGTAGAAAA
1 -GATAGAGTAGAAAA
430409 AGAAGAGAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
14 4 0.16
15 18 0.72
16 3 0.12
ACGTcount: A:0.55, C:0.00, G:0.30, T:0.16
Consensus pattern (15 bp):
GATAGAGTAGAAAAG
Found at i:441247 original size:2 final size:2
Alignment explanation
Indices: 441242--441272 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
441232 TCTTTCTCTC
441242 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
441273 CTGAATCTTG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:449625 original size:18 final size:18
Alignment explanation
Indices: 449602--449638 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
449592 GACGTAATTC
449602 AGCTTTATTAGTATTAAT
1 AGCTTTATTAGTATTAAT
*
449620 AGCTTTATTGGTATTAAT
1 AGCTTTATTAGTATTAAT
449638 A
1 A
449639 TAAATAAGTG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.32, C:0.05, G:0.14, T:0.49
Consensus pattern (18 bp):
AGCTTTATTAGTATTAAT
Found at i:452159 original size:89 final size:89
Alignment explanation
Indices: 452040--452217 Score: 257
Period size: 89 Copynumber: 2.0 Consensus size: 89
452030 AAAAAGCATG
* * ** *
452040 ATCATTTCATGGAATTTTGAAAAGAGCTTTTCATAATATTTATCTTTATCCTTCTAGTTAAGTTG
1 ATCATTTCATGGAATTTTGAAAAGAACTTTTCATAATATATATCAGTAGCCTTCTAGTTAAGTTG
*
452105 AATTTGGTGGTGGCAGCATCACAT
66 AATTTGGTGGTAGCAGCATCACAT
* * * *
452129 ATCATTTCTTGTAATTTTGAAAAGAACTTTTCATGATATATATCAGTAGCTTTCTAGTTAAGTTG
1 ATCATTTCATGGAATTTTGAAAAGAACTTTTCATAATATATATCAGTAGCCTTCTAGTTAAGTTG
*
452194 AATTTGGTGGTAGTAGCATCACAT
66 AATTTGGTGGTAGCAGCATCACAT
452218 GCAGTTAAGA
Statistics
Matches: 78, Mismatches: 11, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
89 78 1.00
ACGTcount: A:0.29, C:0.12, G:0.17, T:0.42
Consensus pattern (89 bp):
ATCATTTCATGGAATTTTGAAAAGAACTTTTCATAATATATATCAGTAGCCTTCTAGTTAAGTTG
AATTTGGTGGTAGCAGCATCACAT
Found at i:455242 original size:20 final size:20
Alignment explanation
Indices: 455219--455272 Score: 108
Period size: 20 Copynumber: 2.7 Consensus size: 20
455209 ACATGTTGCA
455219 ATGTATCGATACATGAAAAG
1 ATGTATCGATACATGAAAAG
455239 ATGTATCGATACATGAAAAG
1 ATGTATCGATACATGAAAAG
455259 ATGTATCGATACAT
1 ATGTATCGATACAT
455273 TTCTTGGCAG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.43, C:0.11, G:0.19, T:0.28
Consensus pattern (20 bp):
ATGTATCGATACATGAAAAG
Found at i:455329 original size:13 final size:13
Alignment explanation
Indices: 455311--455336 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
455301 TACAGCAAGT
455311 ATGTATCGATACA
1 ATGTATCGATACA
455324 ATGTATCGATACA
1 ATGTATCGATACA
455337 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:457587 original size:21 final size:21
Alignment explanation
Indices: 457554--457598 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
457544 TTGCAAGTTG
*
457554 AAATAAAGAAGTTGGCTAATGA
1 AAATAAAGAAGTTAGCTAA-GA
*
457576 AAATAATG-AGTTAGCTAAGA
1 AAATAAAGAAGTTAGCTAAGA
457596 AAA
1 AAA
457599 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:459422 original size:15 final size:15
Alignment explanation
Indices: 459402--459432 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
459392 TAAAAATGTC
*
459402 CAAAATGAGGAAGCT
1 CAAAATGAAGAAGCT
459417 CAAAATGAAGAAGCT
1 CAAAATGAAGAAGCT
459432 C
1 C
459433 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:461507 original size:20 final size:20
Alignment explanation
Indices: 461439--461517 Score: 70
Period size: 20 Copynumber: 3.8 Consensus size: 20
461429 AATGTCCAAA
*
461439 ATGTATCGATA-ATGTTTCT
1 ATGTATCGATACATTTTTCT
* *
461458 GTGTATCGATACATCTGGAAATTCT
1 ATGTATCGATACAT-T----TTTCT
461483 ATGTATCGATACATTTTTCT
1 ATGTATCGATACATTTTTCT
*
461503 TTGTATCGATACATT
1 ATGTATCGATACATT
461518 ATATCGATAC
Statistics
Matches: 48, Mismatches: 6, Indels: 11
0.74 0.09 0.17
Matches are distributed among these distances:
19 10 0.21
20 20 0.42
24 1 0.02
25 17 0.35
ACGTcount: A:0.27, C:0.14, G:0.15, T:0.44
Consensus pattern (20 bp):
ATGTATCGATACATTTTTCT
Found at i:461524 original size:13 final size:13
Alignment explanation
Indices: 461506--461541 Score: 54
Period size: 13 Copynumber: 2.8 Consensus size: 13
461496 TTTTTCTTTG
*
461506 TATCGATACATTA
1 TATCGATACACTA
*
461519 TATCGATACACTG
1 TATCGATACACTA
461532 TATCGATACA
1 TATCGATACA
461542 GGGTGATTAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.36, C:0.19, G:0.11, T:0.33
Consensus pattern (13 bp):
TATCGATACACTA
Found at i:461686 original size:21 final size:21
Alignment explanation
Indices: 461662--461708 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
461652 AAATCTTTTG
461662 CAAAAT-ACTT-GTTTTTCACTT
1 CAAAATAACTTCGTTTTTCA--T
461683 C-AAATAACTTCGTTTTTCAT
1 CAAAATAACTTCGTTTTTCAT
461703 CAAAAT
1 CAAAAT
461709 CAGCATCAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
20 6 0.26
21 9 0.39
22 8 0.35
ACGTcount: A:0.34, C:0.19, G:0.04, T:0.43
Consensus pattern (21 bp):
CAAAATAACTTCGTTTTTCAT
Found at i:461705 original size:20 final size:19
Alignment explanation
Indices: 461664--461706 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 19
461654 ATCTTTTGCA
461664 AAATACTTGTTTTTCACTTC
1 AAATACTTGTTTTTCAC-TC
461684 AAATAACTTCGTTTTTCA-TC
1 AAAT-ACTT-GTTTTTCACTC
461704 AAA
1 AAA
461707 ATCAGCATCA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
20 9 0.43
21 4 0.19
22 8 0.38
ACGTcount: A:0.33, C:0.19, G:0.05, T:0.44
Consensus pattern (19 bp):
AAATACTTGTTTTTCACTC
Found at i:464085 original size:13 final size:13
Alignment explanation
Indices: 464067--464092 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
464057 TACAGCAAGT
464067 ATGTATCGATACA
1 ATGTATCGATACA
464080 ATGTATCGATACA
1 ATGTATCGATACA
464093 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:465436 original size:19 final size:20
Alignment explanation
Indices: 465412--465464 Score: 90
Period size: 19 Copynumber: 2.7 Consensus size: 20
465402 GTCAATACAA
465412 TGTATCGATACATGCTC-AT
1 TGTATCGATACATGCTCAAT
*
465431 TGTATCGATACATACTCAAT
1 TGTATCGATACATGCTCAAT
465451 TGTATCGATACATG
1 TGTATCGATACATG
465465 AAACTGGCAG
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 16 0.52
20 15 0.48
ACGTcount: A:0.30, C:0.19, G:0.15, T:0.36
Consensus pattern (20 bp):
TGTATCGATACATGCTCAAT
Found at i:465588 original size:20 final size:21
Alignment explanation
Indices: 465563--465615 Score: 65
Period size: 20 Copynumber: 2.6 Consensus size: 21
465553 ATTAATACAT
*
465563 TGTATCGATACATG-ACCA-AA
1 TGTATCGATACATGTA-AAGAA
*
465583 TGTATCGATACTTGTAAAGAA
1 TGTATCGATACATGTAAAGAA
465604 TGTATCGATACA
1 TGTATCGATACA
465616 GGTCATTGGC
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
20 14 0.50
21 14 0.50
ACGTcount: A:0.38, C:0.15, G:0.17, T:0.30
Consensus pattern (21 bp):
TGTATCGATACATGTAAAGAA
Found at i:465681 original size:19 final size:19
Alignment explanation
Indices: 465657--465719 Score: 84
Period size: 19 Copynumber: 3.6 Consensus size: 19
465647 CTTAACTGTT
465657 TGTATCGATACACACAAGA
1 TGTATCGATACACACAAGA
465676 TGTATCGAT----AC-A-A
1 TGTATCGATACACACAAGA
465689 TGTATCGATACACACAAGA
1 TGTATCGATACACACAAGA
465708 TGTATCGATACA
1 TGTATCGATACA
465720 ATGTATCGAT
Statistics
Matches: 38, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
13 10 0.26
14 1 0.03
15 2 0.05
17 2 0.05
18 1 0.03
19 22 0.58
ACGTcount: A:0.40, C:0.19, G:0.16, T:0.25
Consensus pattern (19 bp):
TGTATCGATACACACAAGA
Found at i:465693 original size:13 final size:13
Alignment explanation
Indices: 465675--465732 Score: 62
Period size: 13 Copynumber: 4.0 Consensus size: 13
465665 TACACACAAG
465675 ATGTATCGATACA
1 ATGTATCGATACA
465688 ATGTATCGATACACACAA
1 ATGTATCGAT----AC-A
465706 GATGTATCGATACA
1 -ATGTATCGATACA
465720 ATGTATCGATACA
1 ATGTATCGATACA
465733 TCCCAAATTG
Statistics
Matches: 39, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
13 23 0.59
14 1 0.03
15 2 0.05
17 2 0.05
18 1 0.03
19 10 0.26
ACGTcount: A:0.40, C:0.17, G:0.16, T:0.28
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:465698 original size:32 final size:32
Alignment explanation
Indices: 465657--465752 Score: 158
Period size: 32 Copynumber: 3.0 Consensus size: 32
465647 CTTAACTGTT
465657 TGTATCGATACACACAAGATGTATCGATACAA
1 TGTATCGATACACACAAGATGTATCGATACAA
465689 TGTATCGATACACACAAGATGTATCGATACAA
1 TGTATCGATACACACAAGATGTATCGATACAA
*
465721 TGTATCGATACATCCCAA-ATTGTATCGATACA
1 TGTATCGATACA-CACAAGA-TGTATCGATACA
465753 TTGGCTTGTA
Statistics
Matches: 61, Mismatches: 1, Indels: 3
0.94 0.02 0.05
Matches are distributed among these distances:
32 45 0.74
33 16 0.26
ACGTcount: A:0.39, C:0.20, G:0.15, T:0.27
Consensus pattern (32 bp):
TGTATCGATACACACAAGATGTATCGATACAA
Found at i:471240 original size:19 final size:20
Alignment explanation
Indices: 471216--471268 Score: 72
Period size: 19 Copynumber: 2.7 Consensus size: 20
471206 ATCGATATAA
471216 TGTATCGATACATGCTC-AT
1 TGTATCGATACATGCTCAAT
***
471235 TGTATCGATACACATTCAAT
1 TGTATCGATACATGCTCAAT
471255 TGTATCGATACATG
1 TGTATCGATACATG
471269 AAACTGGCAA
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
19 14 0.50
20 14 0.50
ACGTcount: A:0.30, C:0.19, G:0.15, T:0.36
Consensus pattern (20 bp):
TGTATCGATACATGCTCAAT
Found at i:480143 original size:19 final size:20
Alignment explanation
Indices: 480115--480167 Score: 72
Period size: 19 Copynumber: 2.7 Consensus size: 20
480105 ATTGATATAA
480115 TGTATCGATACATGCTC-AT
1 TGTATCGATACATGCTCAAT
* **
480134 TGTTTCGATACACACTCAAT
1 TGTATCGATACATGCTCAAT
480154 TGTATCGATACATG
1 TGTATCGATACATG
480168 AAACTGGCAG
Statistics
Matches: 27, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
19 14 0.52
20 13 0.48
ACGTcount: A:0.28, C:0.21, G:0.15, T:0.36
Consensus pattern (20 bp):
TGTATCGATACATGCTCAAT
Found at i:480234 original size:13 final size:13
Alignment explanation
Indices: 480212--480241 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
480202 GATACATTGG
480212 ACATTATATCGAT
1 ACATTATATCGAT
*
480225 ACATTGTATCGAT
1 ACATTATATCGAT
480238 ACAT
1 ACAT
480242 GAAGAATTGT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.37, C:0.17, G:0.10, T:0.37
Consensus pattern (13 bp):
ACATTATATCGAT
Found at i:482242 original size:15 final size:15
Alignment explanation
Indices: 482210--482243 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
482200 ACCCCAATTC
*
482210 AAAAAAAATTAACGA
1 AAAAAAAATTAACCA
*
482225 AAAAAAAATTATCCA
1 AAAAAAAATTAACCA
482240 AAAA
1 AAAA
482244 TATATACATA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.74, C:0.09, G:0.03, T:0.15
Consensus pattern (15 bp):
AAAAAAAATTAACCA
Found at i:483249 original size:13 final size:13
Alignment explanation
Indices: 483231--483258 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
483221 ATTATGAAAT
483231 ATCTTGTTAGTTC
1 ATCTTGTTAGTTC
483244 ATCTTGTTAGTTC
1 ATCTTGTTAGTTC
483257 AT
1 AT
483259 TAGCTTTAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.18, C:0.14, G:0.14, T:0.54
Consensus pattern (13 bp):
ATCTTGTTAGTTC
Found at i:483680 original size:20 final size:20
Alignment explanation
Indices: 483655--483704 Score: 73
Period size: 20 Copynumber: 2.5 Consensus size: 20
483645 CGATACAATA
**
483655 TATCGATACATGACTAAATG
1 TATCGATACATGAAAAAATG
*
483675 TATCGATACTTGAAAAAATG
1 TATCGATACATGAAAAAATG
483695 TATCGATACA
1 TATCGATACA
483705 AGTCATTAGC
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.42, C:0.14, G:0.14, T:0.30
Consensus pattern (20 bp):
TATCGATACATGAAAAAATG
Found at i:483761 original size:19 final size:19
Alignment explanation
Indices: 483737--483787 Score: 59
Period size: 19 Copynumber: 2.6 Consensus size: 19
483727 TAGCTAAACT
*
483737 TGTATCGATACACACAT-TA
1 TGTATCGATACAC-CATAAA
*
483756 TGTATCAATACACCATAAAA
1 TGTATCGATACACCAT-AAA
483776 TGTATCGATACA
1 TGTATCGATACA
483788 TTGGCTTGTA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
18 3 0.11
19 12 0.44
20 12 0.44
ACGTcount: A:0.41, C:0.20, G:0.10, T:0.29
Consensus pattern (19 bp):
TGTATCGATACACCATAAA
Found at i:494196 original size:29 final size:29
Alignment explanation
Indices: 494127--494198 Score: 78
Period size: 29 Copynumber: 2.5 Consensus size: 29
494117 AATTATTAAA
494127 TTAAATATATATTT-TTATTAATAATTACT
1 TTAAATAT-TATTTATTATTAATAATTACT
* *
494156 ATAACAT-TTATTTATTATTAA-AATTATT
1 TTAA-ATATTATTTATTATTAATAATTACT
494184 TTAAATATCTATTTA
1 TTAAATAT-TATTTA
494199 AAATTTATTA
Statistics
Matches: 36, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
27 2 0.06
28 15 0.42
29 17 0.47
30 2 0.06
ACGTcount: A:0.42, C:0.04, G:0.00, T:0.54
Consensus pattern (29 bp):
TTAAATATTATTTATTATTAATAATTACT
Found at i:494295 original size:21 final size:22
Alignment explanation
Indices: 494253--494296 Score: 56
Period size: 21 Copynumber: 2.0 Consensus size: 22
494243 CAAAGACCAA
*
494253 ATTTATTTAATTTTTGGTTTGG
1 ATTTATTTAATTTTTGGATTGG
494275 ATTT-TTTAACTTTTT-GATTGG
1 ATTTATTTAA-TTTTTGGATTGG
494296 A
1 A
494297 AGAGCATTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
21 11 0.55
22 9 0.45
ACGTcount: A:0.20, C:0.02, G:0.16, T:0.61
Consensus pattern (22 bp):
ATTTATTTAATTTTTGGATTGG
Found at i:497082 original size:21 final size:21
Alignment explanation
Indices: 497049--497093 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
497039 TTGCAAGTTG
*
497049 AAATAAAGAAGTTGGCTAATGA
1 AAATAAAGAAGTTAGCTAA-GA
*
497071 AAATAATG-AGTTAGCTAAGA
1 AAATAAAGAAGTTAGCTAAGA
497091 AAA
1 AAA
497094 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:498917 original size:15 final size:15
Alignment explanation
Indices: 498897--498927 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
498887 TAAAAATGTC
*
498897 CAAAATGAGGAAGCT
1 CAAAATGAAGAAGCT
498912 CAAAATGAAGAAGCT
1 CAAAATGAAGAAGCT
498927 C
1 C
498928 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:501012 original size:13 final size:13
Alignment explanation
Indices: 500994--501032 Score: 78
Period size: 13 Copynumber: 3.0 Consensus size: 13
500984 CATTTTTTCT
500994 TTGTATCGATACA
1 TTGTATCGATACA
501007 TTGTATCGATACA
1 TTGTATCGATACA
501020 TTGTATCGATACA
1 TTGTATCGATACA
501033 GGGTGATTAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 26 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:501177 original size:21 final size:20
Alignment explanation
Indices: 501153--501199 Score: 51
Period size: 21 Copynumber: 2.3 Consensus size: 20
501143 AAATCTTTTG
*
501153 CAAAATACTT-GTTTTTCACTT
1 CAAAATACTTCATTTTTCA--T
*
501174 CAAATTACTTCATTTTTCAT
1 CAAAATACTTCATTTTTCAT
501194 CAAAAT
1 CAAAAT
501200 CAGCATCAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
20 6 0.27
21 9 0.41
22 7 0.32
ACGTcount: A:0.34, C:0.19, G:0.02, T:0.45
Consensus pattern (20 bp):
CAAAATACTTCATTTTTCAT
Found at i:505157 original size:26 final size:27
Alignment explanation
Indices: 505112--505182 Score: 67
Period size: 27 Copynumber: 2.7 Consensus size: 27
505102 TAGTGCACAT
505112 AAGTTTTTT-TTTACTT-TTTTGTTCAA-
1 AAGTTTTTTATTT--TTATTTTGTTCAAC
* *
505138 TAGTTTTTTATTTTTATTTTTTTCAAC
1 AAGTTTTTTATTTTTATTTTGTTCAAC
* *
505165 AATTTTTTTGTTTTTATT
1 AAGTTTTTTATTTTTATT
505183 AGCTTTTATA
Statistics
Matches: 37, Mismatches: 5, Indels: 5
0.79 0.11 0.11
Matches are distributed among these distances:
25 2 0.05
26 17 0.46
27 18 0.49
ACGTcount: A:0.18, C:0.06, G:0.06, T:0.70
Consensus pattern (27 bp):
AAGTTTTTTATTTTTATTTTGTTCAAC
Found at i:506661 original size:13 final size:13
Alignment explanation
Indices: 506643--506667 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
506633 ACGTAAGTGT
506643 TGTATCGATACAA
1 TGTATCGATACAA
506656 TGTATCGATACA
1 TGTATCGATACA
506668 TAAGTGTTGT
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:506700 original size:31 final size:32
Alignment explanation
Indices: 506624--506725 Score: 161
Period size: 32 Copynumber: 3.2 Consensus size: 32
506614 AATAAGTAAC
*
506624 TGTATCGATACGTAAGTGTTGTATCGATACAA
1 TGTATCGATACATAAGTGTTGTATCGATACAA
506656 TGTATCGATACATAAGTGTTGTATCGATACAA
1 TGTATCGATACATAAGTGTTGTATCGATACAA
* * *
506688 T-TTTTGATACATAAGTTTTGTATCGATACAA
1 TGTATCGATACATAAGTGTTGTATCGATACAA
506719 TGTATCG
1 TGTATCG
506726 CTACGAAGCT
Statistics
Matches: 63, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
31 28 0.44
32 35 0.56
ACGTcount: A:0.31, C:0.12, G:0.19, T:0.38
Consensus pattern (32 bp):
TGTATCGATACATAAGTGTTGTATCGATACAA
Found at i:506717 original size:19 final size:19
Alignment explanation
Indices: 506600--506717 Score: 73
Period size: 19 Copynumber: 6.7 Consensus size: 19
506590 AATTCAACAA
506600 TTTGTATCGATACAAATAAGT
1 TTTGTATCGATAC--ATAAGT
** *
506621 AACTGTATCGATACGTAAGT
1 -TTTGTATCGATACATAAGT
*
506641 GTTGTATCGATAC--AA--
1 TTTGTATCGATACATAAGT
506656 --TGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
*
506673 GTTGTATCGATAC--AA--
1 TTTGTATCGATACATAAGT
506688 TTT-T-T-GATACATAAGT
1 TTTGTATCGATACATAAGT
506704 TTTGTATCGATACA
1 TTTGTATCGATACA
506718 ATGTATCGCT
Statistics
Matches: 77, Mismatches: 6, Indels: 29
0.69 0.05 0.26
Matches are distributed among these distances:
12 5 0.06
13 12 0.16
14 3 0.04
15 4 0.05
16 3 0.04
17 5 0.06
18 1 0.01
19 28 0.36
20 5 0.06
22 11 0.14
ACGTcount: A:0.34, C:0.12, G:0.17, T:0.37
Consensus pattern (19 bp):
TTTGTATCGATACATAAGT
Found at i:506788 original size:13 final size:13
Alignment explanation
Indices: 506770--506797 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
506760 ATTACTCAAA
506770 TGTATCGATACAT
1 TGTATCGATACAT
506783 TGTATCGATACAT
1 TGTATCGATACAT
506796 TG
1 TG
506798 ACCTTTGTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.29, C:0.14, G:0.18, T:0.39
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:510046 original size:30 final size:30
Alignment explanation
Indices: 510010--510115 Score: 97
Period size: 30 Copynumber: 3.5 Consensus size: 30
510000 GTATTGATAT
*
510010 AATGTATCGCTACAAAGCTACTACCAAGGA
1 AATGTATCGATACAAAGCTACTACCAAGGA
* ** *** *
510040 AATGTATCGATACATAAGTGTTGTATTGA-TA
1 AATGTATCGATACA-AAG-CTACTACCAAGGA
*
510071 TAATGTATCGCTACAAAGCTACTACCAAGGA
1 -AATGTATCGATACAAAGCTACTACCAAGGA
510102 AATGTATCGATACA
1 AATGTATCGATACA
510116 TTATTCAATG
Statistics
Matches: 55, Mismatches: 17, Indels: 8
0.69 0.21 0.10
Matches are distributed among these distances:
30 30 0.55
31 8 0.15
32 17 0.31
ACGTcount: A:0.39, C:0.17, G:0.17, T:0.27
Consensus pattern (30 bp):
AATGTATCGATACAAAGCTACTACCAAGGA
Found at i:510074 original size:62 final size:62
Alignment explanation
Indices: 509977--510116 Score: 280
Period size: 62 Copynumber: 2.3 Consensus size: 62
509967 TACAAACAGT
509977 AAATGTATCGATACATAAGTGTTGTATTGATATAATGTATCGCTACAAAGCTACTACCAAGG
1 AAATGTATCGATACATAAGTGTTGTATTGATATAATGTATCGCTACAAAGCTACTACCAAGG
510039 AAATGTATCGATACATAAGTGTTGTATTGATATAATGTATCGCTACAAAGCTACTACCAAGG
1 AAATGTATCGATACATAAGTGTTGTATTGATATAATGTATCGCTACAAAGCTACTACCAAGG
510101 AAATGTATCGATACAT
1 AAATGTATCGATACAT
510117 TATTCAATGT
Statistics
Matches: 78, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
62 78 1.00
ACGTcount: A:0.38, C:0.14, G:0.17, T:0.31
Consensus pattern (62 bp):
AAATGTATCGATACATAAGTGTTGTATTGATATAATGTATCGCTACAAAGCTACTACCAAGG
Found at i:513459 original size:13 final size:13
Alignment explanation
Indices: 513441--513465 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
513431 AATTTTTTGG
513441 GTATCGATACATT
1 GTATCGATACATT
513454 GTATCGATACAT
1 GTATCGATACAT
513466 ACTTTGTGTA
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):
GTATCGATACATT
Found at i:513482 original size:32 final size:33
Alignment explanation
Indices: 513420--513483 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 33
513410 TACAAGCCAA
**
513420 TGTATCGATACAATTTTTTGGGTATCGATACAT
1 TGTATCGATACAATACTTTGGGTATCGATACAT
*
513453 TGTATCGATAC-ATACTTTGTGTATCGATACA
1 TGTATCGATACAATACTTTGGGTATCGATACA
513484 AGTTTGGCTA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 17 0.61
33 11 0.39
ACGTcount: A:0.28, C:0.14, G:0.17, T:0.41
Consensus pattern (33 bp):
TGTATCGATACAATACTTTGGGTATCGATACAT
Found at i:517419 original size:52 final size:52
Alignment explanation
Indices: 517341--517489 Score: 264
Period size: 52 Copynumber: 2.9 Consensus size: 52
517331 CGAAATATGA
517341 AAATTTGCCTGCATGTATCGATACATTGAATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTGAATAGTGTATCGATACATCTGGGC
517393 AAATTTGCCTGCATGTATCGATACATTGAATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTGAATAGTGTATCGATACATCTGGGC
**
517445 AAATTTGCCTGCATGTATCGATACAAAG-ATCAGTGTATCGATACA
1 AAATTTGCCTGCATGTATCGATACATTGAAT-AGTGTATCGATACA
517490 ATGTATCGAT
Statistics
Matches: 94, Mismatches: 2, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
51 2 0.02
52 92 0.98
ACGTcount: A:0.31, C:0.17, G:0.20, T:0.32
Consensus pattern (52 bp):
AAATTTGCCTGCATGTATCGATACATTGAATAGTGTATCGATACATCTGGGC
Found at i:517496 original size:13 final size:13
Alignment explanation
Indices: 517478--517502 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
517468 CAAAGATCAG
517478 TGTATCGATACAA
1 TGTATCGATACAA
517491 TGTATCGATACA
1 TGTATCGATACA
517503 TTTAAGTGAT
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:517580 original size:33 final size:33
Alignment explanation
Indices: 517543--517609 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
517533 AGTAGCTTGA
517543 ATTGTATCGATACAAAAAAATATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
* ***
517576 ATTGTATCGATACAACACTTTATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
517609 A
1 A
517610 AATCGTTGAA
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:0.40, C:0.15, G:0.12, T:0.33
Consensus pattern (33 bp):
ATTGTATCGATACAAAAAAATATGTATCGATAC
Found at i:517583 original size:13 final size:13
Alignment explanation
Indices: 517565--517589 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
517555 CAAAAAAATA
517565 TGTATCGATACAT
1 TGTATCGATACAT
517578 TGTATCGATACA
1 TGTATCGATACA
517590 ACACTTTATG
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:518493 original size:52 final size:54
Alignment explanation
Indices: 518361--518514 Score: 168
Period size: 52 Copynumber: 2.9 Consensus size: 54
518351 GAAAAGTGAT
* * * * **
518361 AAAGATGCCAATATGTTGATTCACGGCCAACGATATTGGGCTTAAAAATGAGAAA
1 AAAGATGCCAATATGCTGATTCAAGGCCAGCTATATTGAACTTAAAAATGAG-AA
* * * *
518416 AAAGATGTCAATGTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATG-G-A
1 AAAGATGCCAATATGCTGATTCAAGGCCAGCTATATTGAACTTAAAAATGAGAA
* **
518468 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGGCTTAAAA
1 AAAGATGCCAATATGCTGATTCAAGGCCAGCTATATTGAACTTAAAA
518515 GGAGACGCCA
Statistics
Matches: 82, Mismatches: 17, Indels: 3
0.80 0.17 0.03
Matches are distributed among these distances:
52 41 0.50
54 1 0.01
55 40 0.49
ACGTcount: A:0.37, C:0.16, G:0.23, T:0.25
Consensus pattern (54 bp):
AAAGATGCCAATATGCTGATTCAAGGCCAGCTATATTGAACTTAAAAATGAGAA
Found at i:518590 original size:28 final size:28
Alignment explanation
Indices: 518533--518631 Score: 110
Period size: 28 Copynumber: 3.5 Consensus size: 28
518523 CACCAACTTG
** *
518533 TGTGGGCTTTTGAGAGGTTTGCA-TCAACT
1 TGTGGGCTTTTGA-AGGTTACCACT-GACT
* * *
518562 TGTGTGCTTTTGAAGGTTGCTACTGACT
1 TGTGGGCTTTTGAAGGTTACCACTGACT
*
518590 TGTGGGCTTTTAAAGGTTACCACTGACT
1 TGTGGGCTTTTGAAGGTTACCACTGACT
518618 TGTGGGCTTTTGAA
1 TGTGGGCTTTTGAA
518632 AAGGGTGCCA
Statistics
Matches: 59, Mismatches: 10, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
28 46 0.78
29 13 0.22
ACGTcount: A:0.17, C:0.14, G:0.29, T:0.39
Consensus pattern (28 bp):
TGTGGGCTTTTGAAGGTTACCACTGACT
Found at i:518717 original size:35 final size:34
Alignment explanation
Indices: 518630--518720 Score: 103
Period size: 35 Copynumber: 2.6 Consensus size: 34
518620 TGGGCTTTTG
* * *
518630 AAAAGGGTGCCACTA-ATTTGTGGGCTTAAAAAGA
1 AAAAGAGTGCCAC-AGAGTTGTGAGCTTAAAAAGA
* *
518664 AAAAGAGTGCTATAGAGTTGTGAGCTTACAAAAGA
1 AAAAGAGTGCCACAGAGTTGTGAGCTTA-AAAAGA
*
518699 AAAAGAGTGCCACGGAGTTGTG
1 AAAAGAGTGCCACAGAGTTGTG
518721 GACTTTGGAA
Statistics
Matches: 47, Mismatches: 8, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
33 1 0.02
34 21 0.45
35 25 0.53
ACGTcount: A:0.38, C:0.11, G:0.29, T:0.22
Consensus pattern (34 bp):
AAAAGAGTGCCACAGAGTTGTGAGCTTAAAAAGA
Found at i:518748 original size:29 final size:29
Alignment explanation
Indices: 518699--519112 Score: 325
Period size: 29 Copynumber: 13.9 Consensus size: 29
518689 TTACAAAAGA
* * *
518699 AAAAGAGTGCCACGGAGTTGTGGACTTTGG
1 AAAAGA-TGCCACTGACTTGTGGGCTTTGG
* *
518729 AAAAGATGCCACCGACTTGTGGGCTTCGG
1 AAAAGATGCCACTGACTTGTGGGCTTTGG
* *
518758 AAAAGGGTGCCACTGATTTGTGGGCTTT-G
1 AAAA-GATGCCACTGACTTGTGGGCTTTGG
* * *
518787 -AAGGTTGCCACTGACTTGTGGGCTTTTGAA
1 AAAAGATGCCACTGACTTGTGGGC-TTTG-G
* *
518817 AAAAAATGCCACTGACTTGTGGGCTTTGA
1 AAAAGATGCCACTGACTTGTGGGCTTTGG
*
518846 AAAAGATGCCACTGACTTGTGGGCTTT-T
1 AAAAGATGCCACTGACTTGTGGGCTTTGG
* * *
518874 AAAGGTTGCCACTGACTTGTGGGCTTTTG
1 AAAAGATGCCACTGACTTGTGGGCTTTGG
* * * * *
518903 AAAAGGGTGCCACTAACTTATGGGCTTAAAAAGA
1 AAAA-GATGCCACTGACTTGTGGGCTT----TGG
* * *
518937 AAAAGAGTGCCACGGAGTTGTGGACTTTGG
1 AAAAGA-TGCCACTGACTTGTGGGCTTTGG
* *
518967 AAAAGATGCCACCGACTTGTGGGCTTCGG
1 AAAAGATGCCACTGACTTGTGGGCTTTGG
* * *
518996 AAAAGGGTGCCACTGATTTGTAGGCTTT-G
1 AAAA-GATGCCACTGACTTGTGGGCTTTGG
* * *
519025 -AAGGTTGCCACTGACTTGTGGGCTTTTGAAAA
1 AAAAGATGCCACTGACTTGTGGGC-TTTG---G
* * *
519057 AAAAAATGTCACTGACTTGTGGGCTTTGA
1 AAAAGATGCCACTGACTTGTGGGCTTTGG
* *
519086 AAAATATGCCACTGACTTGTGGACTTT
1 AAAAGATGCCACTGACTTGTGGGCTTT
519113 TGAAGGGTGA
Statistics
Matches: 309, Mismatches: 56, Indels: 39
0.76 0.14 0.10
Matches are distributed among these distances:
27 35 0.11
28 35 0.11
29 103 0.33
30 73 0.24
31 20 0.06
32 4 0.01
33 20 0.06
34 19 0.06
ACGTcount: A:0.26, C:0.17, G:0.29, T:0.28
Consensus pattern (29 bp):
AAAAGATGCCACTGACTTGTGGGCTTTGG
Found at i:518957 original size:238 final size:242
Alignment explanation
Indices: 518583--519121 Score: 811
Period size: 238 Copynumber: 2.2 Consensus size: 242
518573 GAAGGTTGCT
* * * * *
518583 ACTGACTTGTGGGCTTT-TAAAGGTTACCACTGACTTGTGGGCTTTTGAAAAGGGTGCCACTAAT
1 ACTGACTTGTGGGCTTTGAAAAAGATGCCACTGACTTGTGGGCTTTT--AAAGGGTGCCACTAAC
* * *
518647 TTGTGGGCTTAAAAAGAAAAAGAGTGCTATAGAGTTGTGAGCTTACAAAAGAAAAAGAGTGCCAC
64 TTGTGGGCTT--AAAGAAAAAGAGTGCCATAGACTTATGAGCTTACAAAAGAAAAAGAGTGCCAC
518712 GGAGTTGTGGACTTTGGAAAAGATGCCACCGACTTGTGGGCTTCGGAAAAGGGTGCCACTGATTT
127 GGAGTTGTGGACTTTGGAAAAGATGCCACCGACTTGTGGGCTTCGGAAAAGGGTGCCACTGATTT
*
518777 GTGGGCTTTGAAGGTTGCCACTGACTTGTGGGCTTTTG-AAAAAAAATGCC
192 GTAGGCTTTGAAGGTTGCCACTGACTTGTGGGCTTTTGAAAAAAAAATGCC
* *
518827 ACTGACTTGTGGGCTTTGAAAAAGATGCCACTGACTTGTGGGCTTTTAAAGGTTGCCACTGACTT
1 ACTGACTTGTGGGCTTTGAAAAAGATGCCACTGACTTGTGGGCTTTTAAAGGGTGCCACTAACTT
** * *
518892 GTGGGCTT-TTG-AAAAGGGTGCCACTA-ACTTATGGGCTTA-AAAAGAAAAAGAGTGCCACGGA
66 GTGGGCTTAAAGAAAAAGAGTGCCA-TAGACTTATGAGCTTACAAAAGAAAAAGAGTGCCACGGA
518953 GTTGTGGACTTTGGAAAAGATGCCACCGACTTGTGGGCTTCGGAAAAGGGTGCCACTGATTTGTA
130 GTTGTGGACTTTGGAAAAGATGCCACCGACTTGTGGGCTTCGGAAAAGGGTGCCACTGATTTGTA
*
519018 GGCTTTGAAGGTTGCCACTGACTTGTGGGCTTTTGAAAAAAAAAATGTC
195 GGCTTTGAAGGTTGCCACTGACTTGTGGGCTTTTG-AAAAAAAAATGCC
* * *
519067 ACTGACTTGTGGGCTTTGAAAAATATGCCACTGACTTGTGGACTTTTGAAGGGTG
1 ACTGACTTGTGGGCTTTGAAAAAGATGCCACTGACTTGTGGGCTTTTAAAGGGTG
519122 AGGAATGTCT
Statistics
Matches: 271, Mismatches: 20, Indels: 12
0.89 0.07 0.04
Matches are distributed among these distances:
238 121 0.45
239 20 0.07
240 65 0.24
243 23 0.08
244 17 0.06
245 25 0.09
ACGTcount: A:0.27, C:0.16, G:0.29, T:0.28
Consensus pattern (242 bp):
ACTGACTTGTGGGCTTTGAAAAAGATGCCACTGACTTGTGGGCTTTTAAAGGGTGCCACTAACTT
GTGGGCTTAAAGAAAAAGAGTGCCATAGACTTATGAGCTTACAAAAGAAAAAGAGTGCCACGGAG
TTGTGGACTTTGGAAAAGATGCCACCGACTTGTGGGCTTCGGAAAAGGGTGCCACTGATTTGTAG
GCTTTGAAGGTTGCCACTGACTTGTGGGCTTTTGAAAAAAAAATGCC
Found at i:520498 original size:1 final size:1
Alignment explanation
Indices: 520492--520585 Score: 98
Period size: 1 Copynumber: 94.0 Consensus size: 1
520482 TCCGGACCCC
* * * * * * * *
520492 TTTTTTTTTGTTTTTTTTGTTTTTTTTTGTTGTTTTTTTTTGTTTTTGTTTTTTTTTGTTTTGTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
* *
520557 TTTTTTTTTTTTTGTTTTGTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTT
520586 GTGGAGGACG
Statistics
Matches: 73, Mismatches: 20, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
1 73 1.00
ACGTcount: A:0.00, C:0.00, G:0.11, T:0.89
Consensus pattern (1 bp):
T
Found at i:520507 original size:10 final size:10
Alignment explanation
Indices: 520492--520585 Score: 122
Period size: 10 Copynumber: 9.5 Consensus size: 10
520482 TCCGGACCCC
520492 TTTTTTTTTG
1 TTTTTTTTTG
520502 -TTTTTTTTG
1 TTTTTTTTTG
520511 TTTTTTTTTG
1 TTTTTTTTTG
*
520521 TTGTTTTTT-
1 TTTTTTTTTG
*
520530 TTTGTTTTTG
1 TTTTTTTTTG
520540 TTTTTTTTTG
1 TTTTTTTTTG
*
520550 TTTTGTTTTTT
1 TTTT-TTTTTG
520561 TTTTTTTTTG
1 TTTTTTTTTG
520571 TTTTGTTTTT-
1 TTTT-TTTTTG
520581 TTTTT
1 TTTTT
520586 GTGGAGGACG
Statistics
Matches: 74, Mismatches: 6, Indels: 9
0.83 0.07 0.10
Matches are distributed among these distances:
9 17 0.23
10 43 0.58
11 14 0.19
ACGTcount: A:0.00, C:0.00, G:0.11, T:0.89
Consensus pattern (10 bp):
TTTTTTTTTG
Found at i:520514 original size:16 final size:15
Alignment explanation
Indices: 520492--520587 Score: 122
Period size: 16 Copynumber: 6.1 Consensus size: 15
520482 TCCGGACCCC
520492 TTTTTTTTTGTTTTT-
1 TTTTTTTTT-TTTTTG
520507 TTTGTTTTTTTTTGTTG
1 TTT-TTTTTTTTT-TTG
520524 TTTTTTTTTGTTTTTG
1 TTTTTTTTT-TTTTTG
*
520540 TTTTTTTTTGTTTTG
1 TTTTTTTTTTTTTTG
520555 TTTTTTTTTTTTTTTG
1 -TTTTTTTTTTTTTTG
520571 TTTTGTTTTTTTTTTG
1 TTTT-TTTTTTTTTTG
520587 T
1 T
520588 GGAGGACGCC
Statistics
Matches: 73, Mismatches: 2, Indels: 11
0.85 0.02 0.13
Matches are distributed among these distances:
15 15 0.21
16 52 0.71
17 6 0.08
ACGTcount: A:0.00, C:0.00, G:0.11, T:0.89
Consensus pattern (15 bp):
TTTTTTTTTTTTTTG
Found at i:520516 original size:21 final size:20
Alignment explanation
Indices: 520492--520585 Score: 125
Period size: 21 Copynumber: 4.5 Consensus size: 20
520482 TCCGGACCCC
*
520492 TTTTTTTTTGTTTTTTTTGTT
1 TTTTTTTTTTTTTTTTTTG-T
520513 TTTTTTTGTTGTTTTTTTTTGT
1 TTTTTTT-TT-TTTTTTTTTGT
*
520535 TTTTGTTTTTTTTTGTTTTGT
1 TTTT-TTTTTTTTTTTTTTGT
520556 TTTTTTTTTTTTTTGTTTTGT
1 TTTTTTTTTTTTTT-TTTTGT
520577 TTTTTTTTT
1 TTTTTTTTT
520586 GTGGAGGACG
Statistics
Matches: 66, Mismatches: 3, Indels: 8
0.86 0.04 0.10
Matches are distributed among these distances:
20 9 0.14
21 36 0.55
22 9 0.14
23 12 0.18
ACGTcount: A:0.00, C:0.00, G:0.11, T:0.89
Consensus pattern (20 bp):
TTTTTTTTTTTTTTTTTTGT
Found at i:534503 original size:52 final size:51
Alignment explanation
Indices: 534425--534573 Score: 226
Period size: 52 Copynumber: 2.9 Consensus size: 51
534415 CGAAATATGA
534425 AAATTTGCCTGCATGTATCGATACATTGAATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTG-ATAGTGTATCGATACATCTGGGC
* * *
534477 AAATTTGCCTGCATGGATCGATACATTTTATAATGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACA-TTGATAGTGTATCGATACATCTGGGC
**
534529 AAATTTGCCTGCATGTATCGATACAAAGATCAGTGTATCGATACA
1 AAATTTGCCTGCATGTATCGATACATTGAT-AGTGTATCGATACA
534574 ATGTATCGAT
Statistics
Matches: 87, Mismatches: 8, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
51 2 0.02
52 83 0.95
53 2 0.02
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.32
Consensus pattern (51 bp):
AAATTTGCCTGCATGTATCGATACATTGATAGTGTATCGATACATCTGGGC
Found at i:534580 original size:13 final size:13
Alignment explanation
Indices: 534562--534586 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
534552 CAAAGATCAG
534562 TGTATCGATACAA
1 TGTATCGATACAA
534575 TGTATCGATACA
1 TGTATCGATACA
534587 TTTAAGTGAT
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:534664 original size:33 final size:33
Alignment explanation
Indices: 534627--534693 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
534617 AGTAGCTTGA
534627 ATTGTATCGATACAAAAAAATATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
* ***
534660 ATTGTATCGATACAACACTTTATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
534693 A
1 A
534694 AATCGTTGAA
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:0.40, C:0.15, G:0.12, T:0.33
Consensus pattern (33 bp):
ATTGTATCGATACAAAAAAATATGTATCGATAC
Found at i:534667 original size:13 final size:13
Alignment explanation
Indices: 534649--534673 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
534639 CAAAAAAATA
534649 TGTATCGATACAT
1 TGTATCGATACAT
534662 TGTATCGATACA
1 TGTATCGATACA
534674 ACACTTTATG
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:536239 original size:21 final size:20
Alignment explanation
Indices: 536210--536252 Score: 50
Period size: 20 Copynumber: 2.1 Consensus size: 20
536200 GACTAGTGTG
* *
536210 GGGACTGCCCGGTTGTGACCT
1 GGGACTG-CCGGTCGCGACCT
*
536231 GGGAGTGCCGGTCGCGACCT
1 GGGACTGCCGGTCGCGACCT
536251 GG
1 GG
536253 TGGTGCTGCC
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
20 13 0.68
21 6 0.32
ACGTcount: A:0.09, C:0.28, G:0.44, T:0.19
Consensus pattern (20 bp):
GGGACTGCCGGTCGCGACCT
Found at i:536702 original size:13 final size:13
Alignment explanation
Indices: 536684--536721 Score: 58
Period size: 13 Copynumber: 2.9 Consensus size: 13
536674 ATAATCCCCC
536684 TGTATCGATACAG
1 TGTATCGATACAG
*
536697 TGTATCGATACAT
1 TGTATCGATACAG
*
536710 TATATCGATACA
1 TGTATCGATACA
536722 AAGAAAAATG
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:542885 original size:20 final size:20
Alignment explanation
Indices: 542860--542924 Score: 81
Period size: 20 Copynumber: 3.6 Consensus size: 20
542850 TACAAGCCAA
542860 TGTATCGATACAATTTTTTG
1 TGTATCGATACAATTTTTTG
542880 TGTATCGATAC-A-----T-
1 TGTATCGATACAATTTTTTG
542893 TGTATCGATACAATTTTTTG
1 TGTATCGATACAATTTTTTG
542913 TGTATCGATACA
1 TGTATCGATACA
542925 TTGTATCGAT
Statistics
Matches: 38, Mismatches: 0, Indels: 14
0.73 0.00 0.27
Matches are distributed among these distances:
13 11 0.29
14 2 0.05
19 2 0.05
20 23 0.61
ACGTcount: A:0.28, C:0.12, G:0.15, T:0.45
Consensus pattern (20 bp):
TGTATCGATACAATTTTTTG
Found at i:542898 original size:13 final size:13
Alignment explanation
Indices: 542880--542938 Score: 55
Period size: 13 Copynumber: 4.0 Consensus size: 13
542870 CAATTTTTTG
542880 TGTATCGATACAT
1 TGTATCGATACAT
542893 TGTATCGATACAATTTTTT
1 TGTATCGATAC-A-----T
542912 GTGTATCGATACAT
1 -TGTATCGATACAT
542926 TGTATCGATACAT
1 TGTATCGATACAT
542939 ACTTTGTGTA
Statistics
Matches: 39, Mismatches: 0, Indels: 14
0.74 0.00 0.26
Matches are distributed among these distances:
13 24 0.62
14 2 0.05
19 2 0.05
20 11 0.28
ACGTcount: A:0.29, C:0.14, G:0.15, T:0.42
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:542902 original size:33 final size:33
Alignment explanation
Indices: 542860--542956 Score: 169
Period size: 33 Copynumber: 3.0 Consensus size: 33
542850 TACAAGCCAA
542860 TGTATCGATACAATTTTTTGTGTATCGATACAT
1 TGTATCGATACAATTTTTTGTGTATCGATACAT
542893 TGTATCGATACAATTTTTTGTGTATCGATACAT
1 TGTATCGATACAATTTTTTGTGTATCGATACAT
**
542926 TGTATCGATAC-ATACTTTGTGTATCGATACA
1 TGTATCGATACAATTTTTTGTGTATCGATACA
542957 AGTTTGGCTA
Statistics
Matches: 62, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
32 18 0.29
33 44 0.71
ACGTcount: A:0.28, C:0.13, G:0.15, T:0.43
Consensus pattern (33 bp):
TGTATCGATACAATTTTTTGTGTATCGATACAT
Found at i:545482 original size:36 final size:36
Alignment explanation
Indices: 545432--545500 Score: 129
Period size: 36 Copynumber: 1.9 Consensus size: 36
545422 AAATCTAGGT
545432 CATAATCATATTGGTCATCACTGTCATCAAATTCAG
1 CATAATCATATTGGTCATCACTGTCATCAAATTCAG
*
545468 CATAATCATCTTGGTCATCACTGTCATCAAATT
1 CATAATCATATTGGTCATCACTGTCATCAAATT
545501 TAGTATACTT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 32 1.00
ACGTcount: A:0.32, C:0.23, G:0.10, T:0.35
Consensus pattern (36 bp):
CATAATCATATTGGTCATCACTGTCATCAAATTCAG
Found at i:546448 original size:20 final size:20
Alignment explanation
Indices: 546423--546472 Score: 91
Period size: 20 Copynumber: 2.5 Consensus size: 20
546413 CCCTAAAAAT
546423 TATCGATACAAGCCCAGAAG
1 TATCGATACAAGCCCAGAAG
*
546443 TATCGATACAAGCCTAGAAG
1 TATCGATACAAGCCCAGAAG
546463 TATCGATACA
1 TATCGATACA
546473 TATTGCTTTG
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.40, C:0.22, G:0.18, T:0.20
Consensus pattern (20 bp):
TATCGATACAAGCCCAGAAG
Found at i:547660 original size:45 final size:44
Alignment explanation
Indices: 547610--547697 Score: 104
Period size: 45 Copynumber: 2.0 Consensus size: 44
547600 TAATGAACTA
*
547610 GGGTATTTATAATGGAGTAAAAAAAAATTTGATACCTCATGCATG
1 GGGTATTTATAATCGAGTAAAAAAAAATTTGATA-CTCATGCATG
* * * * * *
547655 GGGTATTTTTTATCGTGTTAAAAAGAATTTGATACTTATGCAT
1 GGGTATTTATAATCGAGTAAAAAAAAATTTGATACTCATGCAT
547698 CTGTCACATT
Statistics
Matches: 36, Mismatches: 7, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
44 8 0.22
45 28 0.78
ACGTcount: A:0.35, C:0.08, G:0.19, T:0.38
Consensus pattern (44 bp):
GGGTATTTATAATCGAGTAAAAAAAAATTTGATACTCATGCATG
Found at i:548589 original size:16 final size:16
Alignment explanation
Indices: 548560--548593 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
548550 TATCACTGAC
* *
548560 TTTTACTTTTAAATTT
1 TTTTAATTTAAAATTT
548576 TTTTAATTTAAAATTT
1 TTTTAATTTAAAATTT
548592 TT
1 TT
548594 ATTTTATTAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.29, C:0.03, G:0.00, T:0.68
Consensus pattern (16 bp):
TTTTAATTTAAAATTT
Found at i:548678 original size:32 final size:32
Alignment explanation
Indices: 548636--548746 Score: 86
Period size: 32 Copynumber: 3.4 Consensus size: 32
548626 TTTTTAATAA
*
548636 ATTTTTTTAAATTTAATTAATTTTTAATTTTT
1 ATTTTATTAAATTTAATTAATTTTTAATTTTT
** * *
548668 ATTTTATTAAAATTTAA-TAATTAAT-ATGTTG
1 ATTTTATT-AAATTTAATTAATTTTTAATTTTT
* *
548699 ATTTTAATATAAATTT-TTTAATTTAATTAAATTTT
1 ATTTT-AT-TAAATTTAATTAATTT--TTAATTTTT
548734 ATTTT-TTAAATTT
1 ATTTTATTAAATTT
548747 TCATAGTAAA
Statistics
Matches: 61, Mismatches: 11, Indels: 14
0.71 0.13 0.16
Matches are distributed among these distances:
31 9 0.15
32 33 0.54
33 10 0.16
34 1 0.02
35 8 0.13
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (32 bp):
ATTTTATTAAATTTAATTAATTTTTAATTTTT
Found at i:548724 original size:73 final size:73
Alignment explanation
Indices: 548566--548741 Score: 230
Period size: 74 Copynumber: 2.4 Consensus size: 73
548556 TGACTTTTAC
** ** *
548566 TTTTAAATTTTTTTAATTTAAAATTTTTATTTTATTAAAAATAATAATTAATATTTTGATTTTTT
1 TTTTAAATTTAATTAATTTTTAATTTTTATTTTATTAAAAATAATAATTAATATGTTGA-TTTTT
*
548631 AATAAATTT
65 AATAAAATT
*
548640 TTTTAAATTTAATTAATTTTTAATTTTTATTTTATTAAAATTTAATAATTAATATGTTGA-TTTT
1 TTTTAAATTTAATTAATTTTTAATTTTTATTTTATTAAAA-ATAATAATTAATATGTTGATTTTT
548704 AATATAAATT
65 AATA-AAATT
* *
548714 TTTT-AATTTAATTAAATTTTATTTTTTA
1 TTTTAAATTTAATTAATTTTTAATTTTTA
548742 AATTTTCATA
Statistics
Matches: 91, Mismatches: 9, Indels: 5
0.87 0.09 0.05
Matches are distributed among these distances:
73 30 0.33
74 44 0.48
75 17 0.19
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (73 bp):
TTTTAAATTTAATTAATTTTTAATTTTTATTTTATTAAAAATAATAATTAATATGTTGATTTTTA
ATAAAATT
Found at i:548741 original size:18 final size:19
Alignment explanation
Indices: 548699--548742 Score: 56
Period size: 18 Copynumber: 2.4 Consensus size: 19
548689 TAATATGTTG
548699 ATTTTAATATAAATTTTTT
1 ATTTTAATATAAATTTTTT
*
548718 AATTTAAT-TAAATTTTATT
1 ATTTTAATATAAATTTT-TT
548737 -TTTTAA
1 ATTTTAA
548743 ATTTTCATAG
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
18 13 0.59
19 9 0.41
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (19 bp):
ATTTTAATATAAATTTTTT
Found at i:548873 original size:14 final size:14
Alignment explanation
Indices: 548854--548887 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
548844 AATTATACGT
548854 AAAAAATATATTTC
1 AAAAAATATATTTC
* *
548868 AAAAAATATTTTTT
1 AAAAAATATATTTC
548882 AAAAAA
1 AAAAAA
548888 CTTAATATAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.35
Consensus pattern (14 bp):
AAAAAATATATTTC
Found at i:551691 original size:21 final size:18
Alignment explanation
Indices: 551654--551706 Score: 54
Period size: 21 Copynumber: 2.8 Consensus size: 18
551644 TGTTGACGCA
551654 TTAATTAATTTAATATTT
1 TTAATTAATTTAATATTT
551672 TTAATGTAAGTTTAGATATTT
1 TTAAT-TAA-TTTA-ATATTT
*
551693 TATTATT-ATTTAAT
1 T-TAATTAATTTAAT
551707 TACACACAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 8
0.77 0.03 0.21
Matches are distributed among these distances:
18 7 0.23
19 7 0.23
20 5 0.17
21 8 0.27
22 3 0.10
ACGTcount: A:0.36, C:0.00, G:0.06, T:0.58
Consensus pattern (18 bp):
TTAATTAATTTAATATTT
Found at i:551721 original size:3 final size:3
Alignment explanation
Indices: 551715--551758 Score: 88
Period size: 3 Copynumber: 14.7 Consensus size: 3
551705 ATTACACACA
551715 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
551759 CAAGTTTAAT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:551845 original size:16 final size:16
Alignment explanation
Indices: 551819--551858 Score: 55
Period size: 16 Copynumber: 2.6 Consensus size: 16
551809 AAATTTAAAT
*
551819 ATAAA-AATAAAATTA
1 ATAAATAATAAAATCA
551834 ATAAATAATAAAATCA
1 ATAAATAATAAAATCA
*
551850 ATAATTAAT
1 ATAAATAAT
551859 TATTTAAATT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 5 0.23
16 17 0.77
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.30
Consensus pattern (16 bp):
ATAAATAATAAAATCA
Found at i:551911 original size:25 final size:22
Alignment explanation
Indices: 551883--551934 Score: 59
Period size: 22 Copynumber: 2.2 Consensus size: 22
551873 TATTTTTATC
551883 TAAATTATATAAAATTTACTTTTAA
1 TAAATTAT-T-AAATTT-CTTTTAA
* *
551908 TAAATTCTTAAATTTTTTTTAA
1 TAAATTATTAAATTTCTTTTAA
551930 TAAAT
1 TAAAT
551935 ATACTTTTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
22 11 0.44
23 6 0.24
24 1 0.04
25 7 0.28
ACGTcount: A:0.44, C:0.04, G:0.00, T:0.52
Consensus pattern (22 bp):
TAAATTATTAAATTTCTTTTAA
Found at i:553934 original size:43 final size:44
Alignment explanation
Indices: 553846--553934 Score: 110
Period size: 43 Copynumber: 2.0 Consensus size: 44
553836 ATTTAACGGG
* *
553846 AATAAAATAAAATAAAAGTATATATTACATAATTTGATTGATTA
1 AATAAAATAAAATAAAAATATATATTACATAATTTAATTGATTA
* * *
553890 AATAAAAT-AAATAAAAA-ATATTATTATATTATTTAATTGGTTA
1 AATAAAATAAAATAAAAATATA-TATTACATAATTTAATTGATTA
553933 AA
1 AA
553935 ATTATATTAA
Statistics
Matches: 39, Mismatches: 5, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
42 3 0.08
43 28 0.72
44 8 0.21
ACGTcount: A:0.55, C:0.01, G:0.06, T:0.38
Consensus pattern (44 bp):
AATAAAATAAAATAAAAATATATATTACATAATTTAATTGATTA
Found at i:558122 original size:37 final size:39
Alignment explanation
Indices: 558079--558186 Score: 140
Period size: 37 Copynumber: 2.9 Consensus size: 39
558069 TCACTGATTT
* *
558079 TAAGAATCACAGATATTTTTT-CGAA-TCTTAGATTTTC
1 TAAGAATCACAGATATTTTTTAAGAATTATTAGATTTTC
558116 TAAGAATCAC-GA-ATTTTTTAAGAATTATTAGATTTTC
1 TAAGAATCACAGATATTTTTTAAGAATTATTAGATTTTC
*
558153 TAAGAATCACAG--ATTTTTTAAAAATTA-TAGATTT
1 TAAGAATCACAGATATTTTTTAAGAATTATTAGATTT
558187 CTGTAATCAT
Statistics
Matches: 65, Mismatches: 3, Indels: 7
0.87 0.04 0.09
Matches are distributed among these distances:
35 7 0.11
36 12 0.18
37 45 0.69
38 1 0.02
ACGTcount: A:0.38, C:0.09, G:0.10, T:0.43
Consensus pattern (39 bp):
TAAGAATCACAGATATTTTTTAAGAATTATTAGATTTTC
Found at i:558131 original size:18 final size:19
Alignment explanation
Indices: 558108--558169 Score: 74
Period size: 18 Copynumber: 3.4 Consensus size: 19
558098 TTCGAATCTT
558108 AGATTTTCTAAGAATCACG
1 AGATTTTCTAAGAATCACG
* * **
558127 A-ATTTTTTAAGAATTATT
1 AGATTTTCTAAGAATCACG
558145 AGATTTTCTAAGAATCAC-
1 AGATTTTCTAAGAATCACG
558163 AGATTTT
1 AGATTTT
558170 TTAAAAATTA
Statistics
Matches: 35, Mismatches: 7, Indels: 3
0.78 0.16 0.07
Matches are distributed among these distances:
18 21 0.60
19 14 0.40
ACGTcount: A:0.37, C:0.10, G:0.11, T:0.42
Consensus pattern (19 bp):
AGATTTTCTAAGAATCACG
Found at i:558150 original size:19 final size:18
Alignment explanation
Indices: 558110--558204 Score: 72
Period size: 18 Copynumber: 5.3 Consensus size: 18
558100 CGAATCTTAG
*
558110 ATTTTCTAAGAATCA-CG
1 ATTTTCTAAGAATCATAG
* *
558127 AATTTTTTAAGAATTATTAG
1 -ATTTTCTAAGAATCA-TAG
*
558147 ATTTTCTAAGAATCACAG
1 ATTTTCTAAGAATCATAG
* * *
558165 ATTTTTTAAAAATTATAG
1 ATTTTCTAAGAATCATAG
558183 A-TTTCT--GTAATCATAG
1 ATTTTCTAAG-AATCATAG
558199 ATTTTC
1 ATTTTC
558205 AACCCTAATA
Statistics
Matches: 60, Mismatches: 13, Indels: 9
0.73 0.16 0.11
Matches are distributed among these distances:
16 8 0.13
17 8 0.13
18 30 0.50
19 13 0.22
20 1 0.02
ACGTcount: A:0.37, C:0.09, G:0.09, T:0.44
Consensus pattern (18 bp):
ATTTTCTAAGAATCATAG
Found at i:558184 original size:18 final size:18
Alignment explanation
Indices: 558128--558186 Score: 73
Period size: 18 Copynumber: 3.2 Consensus size: 18
558118 AGAATCACGA
558128 ATTTTTTAAGAATTATTAG
1 ATTTTTTAAGAATTA-TAG
* * *
558147 ATTTTCTAAGAATCACAG
1 ATTTTTTAAGAATTATAG
*
558165 ATTTTTTAAAAATTATAG
1 ATTTTTTAAGAATTATAG
558183 ATTT
1 ATTT
558187 CTGTAATCAT
Statistics
Matches: 33, Mismatches: 7, Indels: 1
0.80 0.17 0.02
Matches are distributed among these distances:
18 20 0.61
19 13 0.39
ACGTcount: A:0.39, C:0.05, G:0.08, T:0.47
Consensus pattern (18 bp):
ATTTTTTAAGAATTATAG
Found at i:558201 original size:34 final size:36
Alignment explanation
Indices: 558106--558203 Score: 114
Period size: 37 Copynumber: 2.7 Consensus size: 36
558096 TTTTCGAATC
*
558106 TTAGATTTTCTAAGAATCAC-GAATTTTTTAAGAATTA
1 TTAGATTTTCT-AGAATCACAG-ATTTTTTAAAAATTA
558143 TTAGATTTTCTAAGAATCACAGATTTTTTAAAAATTA
1 TTAGATTTTCT-AGAATCACAGATTTTTTAAAAATTA
*
558180 -TAGA-TTTCT-GTAATCATAGATTTT
1 TTAGATTTTCTAG-AATCACAGATTTT
558204 CAACCCTAAT
Statistics
Matches: 57, Mismatches: 2, Indels: 7
0.86 0.03 0.11
Matches are distributed among these distances:
33 1 0.02
34 12 0.21
35 5 0.09
36 4 0.07
37 34 0.60
38 1 0.02
ACGTcount: A:0.37, C:0.08, G:0.10, T:0.45
Consensus pattern (36 bp):
TTAGATTTTCTAGAATCACAGATTTTTTAAAAATTA
Found at i:561021 original size:19 final size:18
Alignment explanation
Indices: 560968--561022 Score: 51
Period size: 16 Copynumber: 3.1 Consensus size: 18
560958 GGATCAGCAT
*
560968 AAATCATAGAATTT--AG
1 AAATCATAGATTTTAAAG
* *
560984 GAATCATAGATTTTCAAG
1 AAATCATAGATTTTAAAG
*
561002 AAATCTTAGATTTTTAAAG
1 AAATCATAGA-TTTTAAAG
561021 AA
1 AA
561023 TAACAGATTT
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
16 12 0.39
18 10 0.32
19 9 0.29
ACGTcount: A:0.45, C:0.07, G:0.13, T:0.35
Consensus pattern (18 bp):
AAATCATAGATTTTAAAG
Found at i:561299 original size:19 final size:18
Alignment explanation
Indices: 561254--561301 Score: 60
Period size: 18 Copynumber: 2.6 Consensus size: 18
561244 GCCAAGTACG
*
561254 ATTGTTTACTAATTCCTA
1 ATTGTTTATTAATTCCTA
* *
561272 ATGGTTTATTAATTTCTCA
1 ATTGTTTATTAATTCCT-A
561291 ATTGTTTATTA
1 ATTGTTTATTA
561302 GTTTGTTCAC
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
18 14 0.56
19 11 0.44
ACGTcount: A:0.27, C:0.10, G:0.08, T:0.54
Consensus pattern (18 bp):
ATTGTTTATTAATTCCTA
Found at i:563365 original size:81 final size:80
Alignment explanation
Indices: 563178--563390 Score: 220
Period size: 81 Copynumber: 2.7 Consensus size: 80
563168 GGAAGTTAAA
* * * *
563178 ATGGGGCTGGAGTAT-CTTCGATGGTAAAAAATT-GATATTTTGAAAGTAAAAATGGAGTTGGAC
1 ATGGGGTTGGAGTATCCTT-GATGGTGAAAAATTCGATATTTTGGAAGTAAAAACGGAGTTGGAC
* *
563241 TATTCCTTCGAAAATG
65 TATCCCTTCAAAAATG
* ** * * * *
563257 ATAGGGTT-GATGTATCC-CCATTAGTGAAAATTTCGATGCTTTTGGAAGTAAAAACGGGGTTGG
1 ATGGGGTTGGA-GTATCCTTGA-TGGTGAAAAATTCGAT-ATTTTGGAAGTAAAAACGGAGTTGG
*
563320 AGTATCCCTTCAAAAATG
63 ACTATCCCTTCAAAAATG
563338 ATGGGGTTGGAGTATCCTTGATGGTGAAAAATTCGATATTTTTGGAAG-AAAAA
1 ATGGGGTTGGAGTATCCTTGATGGTGAAAAATTCGATA-TTTTGGAAGTAAAAA
563391 TTTTAAAAAT
Statistics
Matches: 106, Mismatches: 20, Indels: 15
0.75 0.14 0.11
Matches are distributed among these distances:
78 3 0.03
79 19 0.18
80 9 0.08
81 72 0.68
82 3 0.03
ACGTcount: A:0.33, C:0.10, G:0.26, T:0.31
Consensus pattern (80 bp):
ATGGGGTTGGAGTATCCTTGATGGTGAAAAATTCGATATTTTGGAAGTAAAAACGGAGTTGGACT
ATCCCTTCAAAAATG
Found at i:564981 original size:52 final size:51
Alignment explanation
Indices: 564867--565005 Score: 176
Period size: 51 Copynumber: 2.7 Consensus size: 51
564857 AATGGTCTGC
* * *
564867 ATGTATGGATACATTGAAGAATGTATCGATACA-TTTAGGTCAAAACCCAAA
1 ATGTATCGATACAATGAA-AATGTATCGATACATTTTAGGTAAAAACCCAAA
*
564918 ATGTATCGATACAATGAATAATGTATCGATA-ATTTTGGGTTAAAAACCCAAA
1 ATGTATCGATACAATGAA-AATGTATCGATACATTTTAGG-TAAAAACCCAAA
*
564970 ATGTATTGATACAAT-AGAAATGTATCGATACATTTT
1 ATGTATCGATACAATGA-AAATGTATCGATACATTTT
565006 CCTTCCAAAA
Statistics
Matches: 78, Mismatches: 6, Indels: 7
0.86 0.07 0.08
Matches are distributed among these distances:
50 1 0.01
51 46 0.59
52 31 0.40
ACGTcount: A:0.41, C:0.12, G:0.16, T:0.32
Consensus pattern (51 bp):
ATGTATCGATACAATGAAAATGTATCGATACATTTTAGGTAAAAACCCAAA
Found at i:567039 original size:20 final size:20
Alignment explanation
Indices: 567011--567061 Score: 84
Period size: 20 Copynumber: 2.5 Consensus size: 20
567001 ATAGTAAATA
567011 TATCAATACATAAGTGAATG
1 TATCAATACATAAGTGAATG
*
567031 TATCCATACATAAGTGAATG
1 TATCAATACATAAGTGAATG
*
567051 TATTAATACAT
1 TATCAATACAT
567062 GCCTAAAATG
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.43, C:0.12, G:0.12, T:0.33
Consensus pattern (20 bp):
TATCAATACATAAGTGAATG
Found at i:570275 original size:52 final size:51
Alignment explanation
Indices: 570197--570315 Score: 177
Period size: 52 Copynumber: 2.3 Consensus size: 51
570187 CCCGAAATAT
* *
570197 GAAAAGTTGCTTGCATGTATCGATACA-TTTAATAGTGTATCGATACATCTGG
1 GAAAA-TTGCCTGCATGTATCGATACATTTTAA-AATGTATCGATACATCTGG
570249 GAAAATTTGCCTGCATGTATCGATACATTTTAAAATGTATCGATACATCTGG
1 GAAAA-TTGCCTGCATGTATCGATACATTTTAAAATGTATCGATACATCTGG
*
570301 GCAAATTGCCTGCAT
1 GAAAATTGCCTGCAT
570316 AGGTCGAATC
Statistics
Matches: 62, Mismatches: 4, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
51 10 0.16
52 47 0.76
53 5 0.08
ACGTcount: A:0.31, C:0.16, G:0.19, T:0.34
Consensus pattern (51 bp):
GAAAATTGCCTGCATGTATCGATACATTTTAAAATGTATCGATACATCTGG
Found at i:571132 original size:49 final size:49
Alignment explanation
Indices: 571015--571680 Score: 838
Period size: 49 Copynumber: 13.7 Consensus size: 49
571005 AAAAGGATGT
* *
571015 CAATGTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGAAAAGGTGC
1 CAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAT-G--AAGGTGC
* *
571067 CGATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGC
1 CAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
* * *
571116 CAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATAAAGGTGC
1 CAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
* * *
571165 CAATATGCTGATTCAAGGCCAGCTATA-TGGACTTAATGGTGCAA-GTGC
1 CAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATG-AAGGTGC
* * *
571213 CAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATAAAGGTGC
1 CAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
* * *
571262 CAATATGCTGATTCAAGGCCAGCTATATTGGACTTAATGGTGAAGGTGC
1 CAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
* * * *
571311 CAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATGATGATGC
1 CAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
* *
571360 CAATATGCTGATTCAAGGCCAGCGATATTGGACTT----A--AAGGTGC
1 CAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
* *
571403 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGATGC
1 CAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
* *
571452 CAATATGCTGATTCAAGGCCAGCGATATTGGACTT----A--AAGGTGC
1 CAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
* *
571495 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGG
1 CAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
* * *
571544 CAATATGCTGATTCAAGGCCAGCTATATTGGACTTAATGGTGAAGGTGC
1 CAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
* * *
571593 CAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATGGAAAATGTGC
1 CAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAT-G--AAGGTGC
* * *
571645 CGATATGCTGATTCAAGGCCAGCTATATTGGGCTTA
1 CAATATGCTGATTCAAGGCCAGCTACATTGGACTTA
571681 GAAGGGTTGC
Statistics
Matches: 528, Mismatches: 68, Indels: 36
0.84 0.11 0.06
Matches are distributed among these distances:
43 75 0.14
45 2 0.00
47 2 0.00
48 41 0.08
49 332 0.63
50 1 0.00
51 1 0.00
52 74 0.14
ACGTcount: A:0.31, C:0.18, G:0.26, T:0.25
Consensus pattern (49 bp):
CAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
Found at i:571361 original size:98 final size:98
Alignment explanation
Indices: 571015--571680 Score: 1009
Period size: 98 Copynumber: 6.9 Consensus size: 98
571005 AAAAGGATGT
* * *
571015 CAATGTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGAAAAGGTGCCGATATGCTGATT
1 CAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGAT-G--AAGGTGCCAATATGCTGATT
* *
571080 CAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGC
63 CAAGGCCAGCTATATTGGACTTAATGGTGAAGGTGC
*
571116 CAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATAAAGGTGCCAATATGCTGATTCAA
1 CAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATATGCTGATTCAA
571181 GGCCAGCTATA-TGGACTTAATGGTGCAA-GTGC
66 GGCCAGCTATATTGGACTTAATGGTG-AAGGTGC
*
571213 CAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATAAAGGTGCCAATATGCTGATTCAA
1 CAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATATGCTGATTCAA
571278 GGCCAGCTATATTGGACTTAATGGTGAAGGTGC
66 GGCCAGCTATATTGGACTTAATGGTGAAGGTGC
* *
571311 CAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATGATGATGCCAATATGCTGATTCAA
1 CAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATATGCTGATTCAA
*
571376 GGCCAGCGATATTGGACTT-A-----AAGGTGC
66 GGCCAGCTATATTGGACTTAATGGTGAAGGTGC
* *
571403 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGATGCCAATATGCTGATTCAA
1 CAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATATGCTGATTCAA
*
571468 GGCCAGCGATATTGGACTT-A-----AAGGTGC
66 GGCCAGCTATATTGGACTTAATGGTGAAGGTGC
* *
571495 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGGCAATATGCTGATTCAA
1 CAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATATGCTGATTCAA
571560 GGCCAGCTATATTGGACTTAATGGTGAAGGTGC
66 GGCCAGCTATATTGGACTTAATGGTGAAGGTGC
* *
571593 CAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATGGAAAATGTGCCGATATGCTGATT
1 CAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGAT-G--AAGGTGCCAATATGCTGATT
*
571658 CAAGGCCAGCTATATTGGGCTTA
63 CAAGGCCAGCTATATTGGACTTA
571681 GAAGGGTTGC
Statistics
Matches: 533, Mismatches: 20, Indels: 24
0.92 0.03 0.04
Matches are distributed among these distances:
92 178 0.33
93 1 0.00
97 95 0.18
98 180 0.34
99 1 0.00
101 78 0.15
ACGTcount: A:0.31, C:0.18, G:0.26, T:0.25
Consensus pattern (98 bp):
CAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATATGCTGATTCAA
GGCCAGCTATATTGGACTTAATGGTGAAGGTGC
Found at i:571692 original size:98 final size:93
Alignment explanation
Indices: 571006--571685 Score: 904
Period size: 92 Copynumber: 7.1 Consensus size: 93
570996 AGATGATGAA
* * * *
571006 AAAGGATGTCAATGTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGAAAAGGTGCCGAT
1 AAAGG-TGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGAT-G-AAAGGTGCCAAT
571071 ATGCTGATTCAAGGCCAGCTATATTGGACTT
63 ATGCTGATTCAAGGCCAGCTATATTGGACTT
571102 AAAGATGAAGGTGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGAT-AAAGGTGCC
1 ----A--AAGGTGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATGAAAGGTGCC
571166 AATATGCTGATTCAAGGCCAGCTATA-TGGACTT
60 AATATGCTGATTCAAGGCCAGCTATATTGGACTT
*
571199 AATGGTGCAAGTGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGAT-AAAGGTGCC
1 AA------AGGTGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATGAAAGGTGCC
571263 AATATGCTGATTCAAGGCCAGCTATATTGGACTT
60 AATATGCTGATTCAAGGCCAGCTATATTGGACTT
* *
571297 AATGGTGAAGGTGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATG-ATGATGCC
1 -A-----AAGGTGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATGAAAGGTGCC
*
571361 AATATGCTGATTCAAGGCCAGCGATATTGGACTT
60 AATATGCTGATTCAAGGCCAGCTATATTGGACTT
* *
571395 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATG-AAGATGCCAATATG
1 AAAGGTGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATGAAAGGTGCCAATATG
*
571459 CTGATTCAAGGCCAGCGATATTGGACTT
66 CTGATTCAAGGCCAGCTATATTGGACTT
* *
571487 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATG-AAGGTGGCAATATG
1 AAAGGTGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATGAAAGGTGCCAATATG
571551 CTGATTCAAGGCCAGCTATATTGGACTT
66 CTGATTCAAGGCCAGCTATATTGGACTT
*
571579 AATGGTGAAGGTGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATGGAAAATGTG
1 -A-----AAGGTGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGAT-G-AAAGGTG
* *
571644 CCGATATGCTGATTCAAGGCCAGCTATATTGGGCTT
58 CCAATATGCTGATTCAAGGCCAGCTATATTGGACTT
571680 AGAAGG
1 A-AAGG
571686 GTTGCCACCG
Statistics
Matches: 536, Mismatches: 19, Indels: 54
0.88 0.03 0.09
Matches are distributed among these distances:
91 1 0.00
92 178 0.33
93 2 0.00
96 5 0.01
97 89 0.17
98 173 0.32
99 2 0.00
100 2 0.00
101 79 0.15
102 4 0.01
104 1 0.00
ACGTcount: A:0.31, C:0.17, G:0.26, T:0.25
Consensus pattern (93 bp):
AAAGGTGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATGAAAGGTGCCAATATG
CTGATTCAAGGCCAGCTATATTGGACTT
Found at i:571724 original size:33 final size:35
Alignment explanation
Indices: 571680--571749 Score: 126
Period size: 33 Copynumber: 2.1 Consensus size: 35
571670 TATTGGGCTT
571680 AGAAGGGTTGCCACCGACTTGTGTGGGCTTT-GGA
1 AGAAGGGTTGCCACCGACTTGTGTGGGCTTTAGGA
571714 AGAA-GGTTGCCACCGACTTGTGTGGGCTTTAGGA
1 AGAAGGGTTGCCACCGACTTGTGTGGGCTTTAGGA
571748 AG
1 AG
571750 GGAGAAAGAT
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
33 26 0.74
34 9 0.26
ACGTcount: A:0.20, C:0.17, G:0.37, T:0.26
Consensus pattern (35 bp):
AGAAGGGTTGCCACCGACTTGTGTGGGCTTTAGGA
Found at i:571809 original size:71 final size:70
Alignment explanation
Indices: 571734--572319 Score: 476
Period size: 71 Copynumber: 8.6 Consensus size: 70
571724 CACCGACTTG
* * *
571734 TGTGGGCTTTAGGAAGGGAGAAAGATGCCACGGAGTTGTGGAC-TT-AAAAGGGAAAAAGAGTGC
1 TGTGGGCTTTA--AAAGGAAAAAG-TGCCACGGAGTTGTGGGCTTTAAAAAGGGAAAAAGAGTGC
571797 CACGGAGT
63 CACGGAGT
* *
571805 TGTGGGGCTTTAAAAGAAAAAAGTGCCACGGAGTTGTGGGCTTTGAAAAGGGAAAAAGAGTGCCA
1 TGT-GGGCTTTAAAAGGAAAAAGTGCCACGGAGTTGTGGGCTTTAAAAAGGGAAAAAGAGTGCCA
571870 CGGAGT
65 CGGAGT
*
571876 TGTGGGCTTTAAACA-GAAAAAGGTGCCACGGAGTTGTGGGCTTTAAAAAGGGAAAGAGAGTGCC
1 TGTGGGCTTTAAA-AGGAAAAA-GTGCCACGGAGTTGTGGGCTTTAAAAAGGGAAAAAGAGTGCC
**
571940 ACAAAGT
64 ACGGAGT
* *** * *** * ***** ** * *
571947 TGTAGG-TGCCACA-G-AGTTGTG----GG-CTT-T--AAAAGAAAAAGGTGCCACAGAGT--T-
1 TGTGGGCTTTAAAAGGAAAAAGTGCCACGGAGTTGTGGGCTTTAAAAAGG-GAAAAAGAGTGCCA
571998 ------
65 CGGAGT
*
571998 -GTGGGC-TTAGAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAAAAAGGGAAAAAGAGTGCC
1 TGTGGGCTTTAAAAGG-AAAA-AGTGCCACGGAGTTGTGGGCTTTAAAAAGGGAAAAAGAGTGCC
572061 ACGGAGT
64 ACGGAGT
* *
572068 TGTGGGCTTTAAAAAGAAAAAGATGCCACGGAGTTGTGGGCTTTGAAAAGGGAAAAAGAGTGCCA
1 TGTGGGCTTTAAAAGGAAAAAG-TGCCACGGAGTTGTGGGCTTTAAAAAGGGAAAAAGAGTGCCA
*
572133 CAGAGT
65 CGGAGT
* * *
572139 TGTGGGCTTTAAAAAGAAAAAGAGTGCCACAGAGTTGTGGGCTTTAAAAA--GAAAAAGTGTGCC
1 TGTGGGCTTT-AAAAGGAAAA-AGTGCCACGGAGTTGTGGGCTTTAAAAAGGGAAAAAGAGTGCC
*
572202 ACAGAGT
64 ACGGAGT
* *
572209 TGTGGGCTTTAAAA-GAAAAAGGTGCCACGGAGTTGTGAGCTTTGAAAAGGGAAAAAGAGTGCCA
1 TGTGGGCTTTAAAAGGAAAAA-GTGCCACGGAGTTGTGGGCTTTAAAAAGGGAAAAAGAGTGCCA
572273 CGGAGT
65 CGGAGT
* * * * *
572279 TGTGGGCTTT-GAA-GAAAAAATGCCACTGAGTCGTGGACTTT
1 TGTGGGCTTTAAAAGGAAAAAGTGCCACGGAGTTGTGGGCTTT
572320 GAGACAAAAT
Statistics
Matches: 412, Mismatches: 67, Indels: 75
0.74 0.12 0.14
Matches are distributed among these distances:
50 5 0.01
51 1 0.00
53 1 0.00
54 3 0.01
58 2 0.00
59 9 0.02
60 8 0.02
61 8 0.02
62 9 0.02
63 2 0.00
67 4 0.01
68 46 0.11
69 31 0.08
70 86 0.21
71 149 0.36
72 46 0.11
73 2 0.00
ACGTcount: A:0.34, C:0.12, G:0.33, T:0.20
Consensus pattern (70 bp):
TGTGGGCTTTAAAAGGAAAAAGTGCCACGGAGTTGTGGGCTTTAAAAAGGGAAAAAGAGTGCCAC
GGAGT
Found at i:571876 original size:37 final size:36
Alignment explanation
Indices: 571734--572288 Score: 595
Period size: 35 Copynumber: 15.3 Consensus size: 36
571724 CACCGACTTG
* *
571734 TGTGGGCTTTAGGAAGGGAGAAAGA-TGCCACGGAGT
1 TGTGGGCTTTA-AAAGGGAAAAAGAGTGCCACGGAGT
*
571770 TGTGGAC-TTAAAAGGGAAAAAGAGTGCCACGGAGT
1 TGTGGGCTTTAAAAGGGAAAAAGAGTGCCACGGAGT
571805 TGTGGGGCTTTAAAA--GAAAAA-AGTGCCACGGAGT
1 TGT-GGGCTTTAAAAGGGAAAAAGAGTGCCACGGAGT
571839 TGTGGGCTTTGAAAAGGGAAAAAGAGTGCCACGGAGT
1 TGTGGGCTTT-AAAAGGGAAAAAGAGTGCCACGGAGT
571876 TGTGGGCTTTAAACA--GAAAAAG-GTGCCACGGAGT
1 TGTGGGCTTTAAA-AGGGAAAAAGAGTGCCACGGAGT
* **
571910 TGTGGGCTTTAAAAAGGGAAAGAGAGTGCCACAAAGT
1 TGTGGGCTTT-AAAAGGGAAAAAGAGTGCCACGGAGT
*** ** * *
571947 TGTAGGTGCCACAGAGTTGTGGGCTTTAAAAGAAAAAGGTGCCACAGAGT
1 TGT-GG-GCTTTA-A---AAGGG------AA-AAAGA-GTGCCACGGAGT
*
571997 TGTGGGC-TTAGAA-GGAAAAAGAGTGCCACGGAGT
1 TGTGGGCTTTAAAAGGGAAAAAGAGTGCCACGGAGT
572031 TGTGGGCTTTAAAAAGGGAAAAAGAGTGCCACGGAGT
1 TGTGGGCTTT-AAAAGGGAAAAAGAGTGCCACGGAGT
*
572068 TGTGGGCTTTAAAA-AGAAAAAGA-TGCCACGGAGT
1 TGTGGGCTTTAAAAGGGAAAAAGAGTGCCACGGAGT
*
572102 TGTGGGCTTTGAAAAGGGAAAAAGAGTGCCACAGAGT
1 TGTGGGCTTT-AAAAGGGAAAAAGAGTGCCACGGAGT
* *
572139 TGTGGGCTTTAAAA-AGAAAAAGAGTGCCACAGAGT
1 TGTGGGCTTTAAAAGGGAAAAAGAGTGCCACGGAGT
* * *
572174 TGTGGGCTTTAAAA-AGAAAAAGTGTGCCACAGAGT
1 TGTGGGCTTTAAAAGGGAAAAAGAGTGCCACGGAGT
572209 TGTGGGCTTTAAAA--GAAAAAG-GTGCCACGGAGT
1 TGTGGGCTTTAAAAGGGAAAAAGAGTGCCACGGAGT
*
572242 TGTGAGCTTTGAAAAGGGAAAAAGAGTGCCACGGAGT
1 TGTGGGCTTT-AAAAGGGAAAAAGAGTGCCACGGAGT
572279 TGTGGGCTTT
1 TGTGGGCTTT
572289 GAAGAAAAAA
Statistics
Matches: 452, Mismatches: 31, Indels: 71
0.82 0.06 0.13
Matches are distributed among these distances:
33 27 0.06
34 104 0.23
35 119 0.26
36 52 0.12
37 115 0.25
38 3 0.01
39 3 0.01
42 5 0.01
47 1 0.00
48 4 0.01
49 5 0.01
50 14 0.03
ACGTcount: A:0.34, C:0.12, G:0.34, T:0.20
Consensus pattern (36 bp):
TGTGGGCTTTAAAAGGGAAAAAGAGTGCCACGGAGT
Found at i:572045 original size:121 final size:124
Alignment explanation
Indices: 571827--572062 Score: 374
Period size: 121 Copynumber: 1.9 Consensus size: 124
571817 AAAGAAAAAA
* *
571827 GTGCCACGGAGTTGTGGGCTTTGAAAAGGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAAACAG
1 GTGCCACAGAGTTGTGGGCTTTGAAAA-GGAAAAAGAGTGCCACAGAGTTGTGGGCTTTAAACAG
*
571892 AAAAAGGTGCCACGGAGTTGTGGGCTTTAAAAAGGGAAAGAGAGTGCCACAAAGTTGTAG
65 AAAAAGGTGCCACGGAGTTGTGGGCTTTAAAAAGGGAAAAAGAGTGCCACAAAGTTGTAG
*
571952 GTGCCACAGAGTTGTGGGCTTT-AAAA-GAAAAAG-GTGCCACAGAGTTGTGGGC-TTAGAA-GG
1 GTGCCACAGAGTTGTGGGCTTTGAAAAGGAAAAAGAGTGCCACAGAGTTGTGGGCTTTA-AACAG
572012 AAAAAGAGTGCCACGGAGTTGTGGGCTTTAAAAAGGGAAAAAGAGTGCCAC
65 AAAAAG-GTGCCACGGAGTTGTGGGCTTTAAAAAGGGAAAAAGAGTGCCAC
572063 GGAGTTGTGG
Statistics
Matches: 105, Mismatches: 4, Indels: 8
0.90 0.03 0.07
Matches are distributed among these distances:
120 10 0.10
121 63 0.60
122 7 0.07
124 4 0.04
125 21 0.20
ACGTcount: A:0.33, C:0.13, G:0.34, T:0.19
Consensus pattern (124 bp):
GTGCCACAGAGTTGTGGGCTTTGAAAAGGAAAAAGAGTGCCACAGAGTTGTGGGCTTTAAACAGA
AAAAGGTGCCACGGAGTTGTGGGCTTTAAAAAGGGAAAAAGAGTGCCACAAAGTTGTAG
Found at i:572414 original size:31 final size:31
Alignment explanation
Indices: 572268--572422 Score: 199
Period size: 31 Copynumber: 5.0 Consensus size: 31
572258 GGAAAAAGAG
* * * *
572268 TGCCACGGAGTTGTGGGCTTTGAAGAA-AAAA
1 TGCCACTGAGTCGTGGGCTTTG-AGAAGAGAT
* *
572299 TGCCACTGAGTCGTGGACTTTGAGACA-A-AA
1 TGCCACTGAGTCGTGGGCTTTGAGA-AGAGAT
* *
572329 TGCCACTGAGTCATGGACTTTGAGAAGAGAT
1 TGCCACTGAGTCGTGGGCTTTGAGAAGAGAT
572360 TGCCACTGAGTCGTGGGCTTTGAGAAGAGAT
1 TGCCACTGAGTCGTGGGCTTTGAGAAGAGAT
572391 TGCCACTGAGTCGTGGGCTTTGAGAAGAGAT
1 TGCCACTGAGTCGTGGGCTTTGAGAAGAGAT
572422 T
1 T
572423 TGAAGAATTG
Statistics
Matches: 114, Mismatches: 7, Indels: 6
0.90 0.06 0.05
Matches are distributed among these distances:
29 1 0.01
30 30 0.26
31 83 0.73
ACGTcount: A:0.27, C:0.16, G:0.32, T:0.25
Consensus pattern (31 bp):
TGCCACTGAGTCGTGGGCTTTGAGAAGAGAT
Found at i:580719 original size:52 final size:51
Alignment explanation
Indices: 580641--580770 Score: 199
Period size: 52 Copynumber: 2.5 Consensus size: 51
580631 CCCGAAATAT
* *
580641 GAAAAGTTGCTTGCATGTATCGATACA-TTTAATAGTGTATCGATACATCTGG
1 GAAAA-TTGCCTGCATGTATCGATACATTTTAA-AATGTATCGATACATCTGG
580693 GAAAATTTGCCTGCATGTATCGATACATTTTAAAATGTATCGATACATCTGG
1 GAAAA-TTGCCTGCATGTATCGATACATTTTAAAATGTATCGATACATCTGG
*
580745 GCAAATTGCCTGCATGTATCGATACA
1 GAAAATTGCCTGCATGTATCGATACA
580771 AAGATCAGTG
Statistics
Matches: 73, Mismatches: 4, Indels: 3
0.91 0.05 0.04
Matches are distributed among these distances:
51 21 0.29
52 47 0.64
53 5 0.07
ACGTcount: A:0.32, C:0.16, G:0.19, T:0.33
Consensus pattern (51 bp):
GAAAATTGCCTGCATGTATCGATACATTTTAAAATGTATCGATACATCTGG
Found at i:580783 original size:51 final size:50
Alignment explanation
Indices: 580641--580790 Score: 171
Period size: 52 Copynumber: 2.9 Consensus size: 50
580631 CCCGAAATAT
* * *
580641 GAAAAGTTGCTTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGG
1 GAAAATTTGCCTGCATGTATCGATACA--AAATAGTGTATCGATACATCTGG
580693 GAAAATTTGCCTGCATGTATCGATACATTTTAAA-A-TGTATCGATACATCTGG
1 GAAAATTTGCCTGCATGTATCGATACA----AAATAGTGTATCGATACATCTGG
*
580745 GCAAA-TTGCCTGCATGTATCGATACAAAGATCAGTGTATCGATACA
1 GAAAATTTGCCTGCATGTATCGATACAAA-AT-AGTGTATCGATACA
580791 ATGTATCGAT
Statistics
Matches: 88, Mismatches: 4, Indels: 13
0.84 0.04 0.12
Matches are distributed among these distances:
47 2 0.02
48 1 0.01
50 1 0.01
51 33 0.38
52 46 0.52
53 1 0.01
54 4 0.05
ACGTcount: A:0.33, C:0.16, G:0.19, T:0.32
Consensus pattern (50 bp):
GAAAATTTGCCTGCATGTATCGATACAAAATAGTGTATCGATACATCTGG
Found at i:580797 original size:13 final size:13
Alignment explanation
Indices: 580779--580803 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
580769 CAAAGATCAG
580779 TGTATCGATACAA
1 TGTATCGATACAA
580792 TGTATCGATACA
1 TGTATCGATACA
580804 TTTGAGTAAT
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:580883 original size:13 final size:13
Alignment explanation
Indices: 580865--580889 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
580855 ACAAAAAATA
580865 TGTATCGATACAT
1 TGTATCGATACAT
580878 TGTATCGATACA
1 TGTATCGATACA
580890 ACATTTTATG
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:580885 original size:32 final size:33
Alignment explanation
Indices: 580844--580909 Score: 98
Period size: 32 Copynumber: 2.0 Consensus size: 33
580834 AGTAGCTTAA
580844 ATTGTATCGATACAA-AAAATATGTATCGATAC
1 ATTGTATCGATACAACAAAATATGTATCGATAC
***
580876 ATTGTATCGATACAACATTTTATGTATCGATAC
1 ATTGTATCGATACAACAAAATATGTATCGATAC
580909 A
1 A
580910 AATCGTTGAA
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 15 0.50
33 15 0.50
ACGTcount: A:0.39, C:0.14, G:0.12, T:0.35
Consensus pattern (33 bp):
ATTGTATCGATACAACAAAATATGTATCGATAC
Found at i:583933 original size:78 final size:76
Alignment explanation
Indices: 583741--583942 Score: 192
Period size: 78 Copynumber: 2.6 Consensus size: 76
583731 ATTTTATCTC
* ** * *
583741 AGGGATACTCTAACCCCATTTTTATTTAAAAAATATTAAAATTTTAATCTCGGGGATACTTCAAC
1 AGGGATACTCCAACCCCATTTTTATTTTCAAAATATT-AAATTTT-TTCCCGGGGATACTTCAAC
*
583806 ACCATCAATTTCG
64 ACCATCAATTTCA
* * *
583819 AGGGAATATTTCAACCCCCTTTTT-TTTTCCAAAATATTAAATTTTTTCACCGCGGGATA-TTCC
1 AGGG-ATACTCCAACCCCATTTTTATTTT-CAAAATATTAAATTTTTTC-CCG-GGGATACTT-C
* * * *
583882 AACCCCGTTATTTTCA
61 AACACCATCAATTTCA
* *
583898 AGGGATACTCCAACCCCGTTTTTATTTTCAAAATATTAAAATTTT
1 AGGGATACTCCAACCCCATTTTTATTTTCAAAATATTAAATTTTT
583943 CATCTTGAGG
Statistics
Matches: 101, Mismatches: 17, Indels: 12
0.78 0.13 0.09
Matches are distributed among these distances:
77 2 0.02
78 50 0.50
79 49 0.49
ACGTcount: A:0.32, C:0.21, G:0.10, T:0.38
Consensus pattern (76 bp):
AGGGATACTCCAACCCCATTTTTATTTTCAAAATATTAAATTTTTTCCCGGGGATACTTCAACAC
CATCAATTTCA
Found at i:583955 original size:78 final size:77
Alignment explanation
Indices: 583741--584013 Score: 226
Period size: 79 Copynumber: 3.5 Consensus size: 77
583731 ATTTTATCTC
* ** *
583741 AGGGATACTCTAACCCCATTTTTATTTAAAAAATATTAAAATTTTAATCTCGGGGATACTT-CAA
1 AGGGATACTCCAACCCCATTTTTATTTTCAAAATATTAAAATTTTCATCTC-GGGATA-TTCCAA
* * * * *
583805 CACCATCAATTTCG
64 CCCCGTTATTTTCA
* * * * * *
583819 AGGGAATATTTCAACCCCCTTTTT-TTTTCCAAAATATTAAATTTTTTCACCGCGGGATATTCCA
1 AGGG-ATACTCCAACCCCATTTTTATTTT-CAAAATATTAAA-ATTTTCATCTCGGGATATTCCA
583883 ACCCCGTTATTTTCA
63 ACCCCGTTATTTTCA
* * * *
583898 AGGGATACTCCAACCCCGTTTTTATTTTCAAAATATTAAAATTTTCATCTTGAGGATACTCTAAC
1 AGGGATACTCCAACCCCATTTTTATTTTCAAAATATTAAAATTTTCATCTCG-GGATATTCCAAC
* **
583963 CTCGTTATTTAAA
65 CCCGTTATTTTCA
* ** *
583976 AGGGGATGCTTTAACCCCCATTTTTATTTTTAAAATAT
1 A-GGGATACTCCAA-CCCCATTTTTATTTTCAAAATAT
584014 CAATTTTTCA
Statistics
Matches: 155, Mismatches: 32, Indels: 14
0.77 0.16 0.07
Matches are distributed among these distances:
77 8 0.05
78 58 0.37
79 61 0.39
80 28 0.18
ACGTcount: A:0.31, C:0.20, G:0.11, T:0.38
Consensus pattern (77 bp):
AGGGATACTCCAACCCCATTTTTATTTTCAAAATATTAAAATTTTCATCTCGGGATATTCCAACC
CCGTTATTTTCA
Found at i:584912 original size:13 final size:13
Alignment explanation
Indices: 584894--584919 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
584884 TACAGCAAGC
584894 ATGTATCGATACA
1 ATGTATCGATACA
584907 ATGTATCGATACA
1 ATGTATCGATACA
584920 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:587170 original size:21 final size:21
Alignment explanation
Indices: 587137--587181 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
587127 TTGCAAGTTG
*
587137 AAATAAAGAAGTTGGCTAATGA
1 AAATAAAGAAGTTAGCTAA-GA
*
587159 AAATAATG-AGTTAGCTAAGA
1 AAATAAAGAAGTTAGCTAAGA
587179 AAA
1 AAA
587182 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:589005 original size:15 final size:15
Alignment explanation
Indices: 588985--589015 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
588975 TAAAAATGTC
*
588985 CAAAATGAGGAAGCT
1 CAAAATGAAGAAGCT
589000 CAAAATGAAGAAGCT
1 CAAAATGAAGAAGCT
589015 C
1 C
589016 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:591285 original size:20 final size:20
Alignment explanation
Indices: 591242--591287 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 20
591232 AAATCTTTTG
591242 CAAAATACTTGTTTTTCACTT
1 CAAAATACTTGTTTTTCAC-T
*
591263 CAAATTACTTCGTTTTTCA-T
1 CAAAATACTT-GTTTTTCACT
591283 CAAAA
1 CAAAA
591288 CCAGCATTAA
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:593683 original size:13 final size:13
Alignment explanation
Indices: 593665--593690 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
593655 TACAGCAAGC
593665 ATGTATCGATACA
1 ATGTATCGATACA
593678 ATGTATCGATACA
1 ATGTATCGATACA
593691 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:595234 original size:21 final size:21
Alignment explanation
Indices: 595200--595262 Score: 54
Period size: 21 Copynumber: 3.0 Consensus size: 21
595190 ATTTTAATTC
* *
595200 ATCACTACAGTAATCAATTTA
1 ATCACTATAATAATCAATTTA
* * * * *
595221 ATTACTATATTAATTAATCTC
1 ATCACTATAATAATCAATTTA
*
595242 ATCGCTATAATAATCAATTTA
1 ATCACTATAATAATCAATTTA
595263 GTTGCTATTG
Statistics
Matches: 30, Mismatches: 12, Indels: 0
0.71 0.29 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.41, C:0.16, G:0.03, T:0.40
Consensus pattern (21 bp):
ATCACTATAATAATCAATTTA
Found at i:595269 original size:21 final size:20
Alignment explanation
Indices: 595210--595270 Score: 50
Period size: 21 Copynumber: 2.9 Consensus size: 20
595200 ATCACTACAG
* *
595210 TAATCAATTTAATTACTATAT
1 TAATCAATTT-ATTGCTATAA
* * *
595231 TAATTAATCTCATCGCTATAA
1 TAATCAAT-TTATTGCTATAA
595252 TAATCAATTTAGTTGCTAT
1 TAATCAATTTA-TTGCTAT
595271 TGTAGAAACT
Statistics
Matches: 30, Mismatches: 8, Indels: 4
0.71 0.19 0.10
Matches are distributed among these distances:
20 2 0.07
21 27 0.90
22 1 0.03
ACGTcount: A:0.38, C:0.13, G:0.05, T:0.44
Consensus pattern (20 bp):
TAATCAATTTATTGCTATAA
Found at i:596192 original size:19 final size:20
Alignment explanation
Indices: 596170--596216 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 20
596160 ATCTTTCCTT
*
596170 AACA-ATTTTCAACTTTAAA
1 AACACATTTTCAACTTCAAA
*
596189 AACACA-CTTCAACTTCAAA
1 AACACATTTTCAACTTCAAA
596208 AACACATTT
1 AACACATTT
596217 CTACACTTAG
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
19 21 0.91
20 2 0.09
ACGTcount: A:0.47, C:0.23, G:0.00, T:0.30
Consensus pattern (20 bp):
AACACATTTTCAACTTCAAA
Found at i:599607 original size:71 final size:69
Alignment explanation
Indices: 599474--599624 Score: 194
Period size: 71 Copynumber: 2.2 Consensus size: 69
599464 TACCTAGATA
* *
599474 TATCGATACATTTATCAATTATCGATACACTCTATCTTTTACCCAGATGTATCAATACATTTTTC
1 TATCGATACATGTATCAATTATAGATACACTCTATCTTTTACCCAGATGTATCAATACATTTTTC
599539 AATG
66 AATG
* * * * * * * *
599543 TATCGATACATGTATGATTGTATAGATACATTCTGTCTTTTTATCCAGATTTATCGATATATTTT
1 TATCGATACATGTATCAAT-TATAGATACACTCTATC-TTTTACCCAGATGTATCAATACATTTT
599608 TCAATG
64 TCAATG
599614 TATCGATACAT
1 TATCGATACAT
599625 CTAGTTAAAA
Statistics
Matches: 70, Mismatches: 10, Indels: 2
0.85 0.12 0.02
Matches are distributed among these distances:
69 16 0.23
70 14 0.20
71 40 0.57
ACGTcount: A:0.30, C:0.17, G:0.10, T:0.43
Consensus pattern (69 bp):
TATCGATACATGTATCAATTATAGATACACTCTATCTTTTACCCAGATGTATCAATACATTTTTC
AATG
Found at i:611176 original size:13 final size:12
Alignment explanation
Indices: 611151--611183 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
611141 CTTTTGTACC
611151 AAAAAA-AATAA
1 AAAAAACAATAA
611162 AAAAAACAATAA
1 AAAAAACAATAA
611174 AAACAAACAA
1 AAA-AAACAA
611184 ACAAAAAAGA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 6 0.30
12 8 0.40
13 6 0.30
ACGTcount: A:0.85, C:0.09, G:0.00, T:0.06
Consensus pattern (12 bp):
AAAAAACAATAA
Found at i:612499 original size:28 final size:28
Alignment explanation
Indices: 612467--612830 Score: 340
Period size: 28 Copynumber: 12.6 Consensus size: 28
612457 CAATACGATG
* *
612467 CTTTTCAAAGCCCACAAGTTAGTGGCAT
1 CTTTTCAAAGCCCACAAGTCAGTGGCAC
*
612495 CTTTTCAAAGCCAACAAGTCAGTGGCATC
1 CTTTTCAAAGCCCACAAGTCAGTGGCA-C
*
612524 C-TTTCAAAGCCCACAAGTCAGTGGAATC
1 CTTTTCAAAGCCCACAAGTCAGTGGCA-C
* * *
612552 CTTCTCAAAGCCCACAAGTTAGTAGCATC
1 CTTTTCAAAGCCCACAAGTCAGTGGCA-C
* *
612581 CATGTCAAAGCCCACAAGTCAGTGGCATC
1 CTTTTCAAAGCCCACAAGTCAGTGGCA-C
*
612610 C-TTTCAAAGCCCACACAAGTCGGTGGCAAC
1 CTTTTCAAAG-CC-CACAAGTCAGTGGC-AC
*
612640 CTCTCTCAAAGCCCACAAGTCAGTGGCAC
1 CT-TTTCAAAGCCCACAAGTCAGTGGCAC
*
612669 CCTTTCAAAGCCCACATAAGTCAGTGGCAAC
1 CTTTTCAAAGCCCAC--AAGTCAGTGGC-AC
* * *
612700 CTCTCTCAAAGTCCACAAGTTAGTGGCAAC
1 CT-TTTCAAAGCCCACAAGTCAGTGGC-AC
* * *
612730 C-ATTCAAAGCTCACAAGTTAGTGGCAC
1 CTTTTCAAAGCCCACAAGTCAGTGGCAC
* * *
612757 CCTTTCGAAGCCCACAAATCAGTGGCACC
1 CTTTTCAAAGCCCACAAGTCAGTGGCA-C
**
612786 CTTTT-AAAGCCCACAAGTTGGTGGCAAC
1 CTTTTCAAAGCCCACAAGTCAGTGGC-AC
*
612814 CTTCTCTAAAGCCCACA
1 CTTTTC-AAAGCCCACA
612831 CAAGTTGGTG
Statistics
Matches: 282, Mismatches: 38, Indels: 30
0.81 0.11 0.09
Matches are distributed among these distances:
27 3 0.01
28 131 0.46
29 61 0.22
30 63 0.22
31 6 0.02
32 18 0.06
ACGTcount: A:0.30, C:0.31, G:0.17, T:0.21
Consensus pattern (28 bp):
CTTTTCAAAGCCCACAAGTCAGTGGCAC
Found at i:612663 original size:60 final size:59
Alignment explanation
Indices: 612471--612830 Score: 389
Period size: 60 Copynumber: 6.2 Consensus size: 59
612461 ACGATGCTTT
* * *
612471 TCAAAGCCCACAAGTTAGTGGCATCTTTTCAAAGCCA-ACAAGTCAGTGGCATCCT-T-
1 TCAAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCCACACAAGTCAGTGGCAACCTCTC
* * * * * *
612527 TCAAAGCCCACAAGTCAGTGGAATCCTTCTCAAAGCC-CACAAGTTAGTAGCATCC-ATG
1 TCAAAGCCCACAAGTCAGTGGCATCCTT-TCAAAGCCACACAAGTCAGTGGCAACCTCTC
*
612585 TCAAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCCCACACAAGTCGGTGGCAACCTCTC
1 TCAAAGCCCACAAGTCAGTGGCATCCTTTCAAAG-CCACACAAGTCAGTGGCAACCTCTC
* *
612645 TCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACATAAGTCAGTGGCAACCTCTC
1 TCAAAGCCCACAAGTCAGTGGCATCCTTTCAAAG-CCACACAAGTCAGTGGCAACCTCTC
* * * * * * *
612705 TCAAAGTCCACAAGTTAGTGGCAACCATTCAAAG-CTCACAAGTTAGTGGC-ACC-CTT
1 TCAAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCCACACAAGTCAGTGGCAACCTCTC
* * * * **
612761 TCGAAGCCCACAAATCAGTGGCACCCTTTTAAAGCC-CACAAGTTGGTGGCAACCT-TC
1 TCAAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCCACACAAGTCAGTGGCAACCTCTC
612818 TCTAAAGCCCACA
1 TC-AAAGCCCACA
612831 CAAGTTGGTG
Statistics
Matches: 260, Mismatches: 33, Indels: 20
0.83 0.11 0.06
Matches are distributed among these distances:
56 67 0.26
57 40 0.15
58 51 0.20
59 14 0.05
60 88 0.34
ACGTcount: A:0.31, C:0.31, G:0.17, T:0.21
Consensus pattern (59 bp):
TCAAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCCACACAAGTCAGTGGCAACCTCTC
Found at i:613898 original size:20 final size:20
Alignment explanation
Indices: 613821--613898 Score: 86
Period size: 20 Copynumber: 3.9 Consensus size: 20
613811 TTTTTACCAA
** *
613821 AATGTATCGATGTATTTTTC
1 AATGTATCGATACATTCTTC
* *
613841 AATGTATCGATACATGT-ATG
1 AATGTATCGATACAT-TCTTC
*
613861 AATGTGTCGATACATTCTTC
1 AATGTATCGATACATTCTTC
613881 AATGTATCGATACATTCT
1 AATGTATCGATACATTCT
613899 ATCTTTTTAC
Statistics
Matches: 48, Mismatches: 8, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
19 1 0.02
20 46 0.96
21 1 0.02
ACGTcount: A:0.29, C:0.14, G:0.15, T:0.41
Consensus pattern (20 bp):
AATGTATCGATACATTCTTC
Found at i:617191 original size:52 final size:52
Alignment explanation
Indices: 617058--617198 Score: 230
Period size: 52 Copynumber: 2.7 Consensus size: 52
617048 TGAAAAGTTA
617058 CTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAATTTGC
1 CTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAATTTGC
* *
617110 CTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAATTTGC
1 CTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAATTTGC
**
617162 CTGCATGTATCGATACA-AAAATCAGTGTATCGATACA
1 CTGCATGTATCGATACATTTAAT-AGTGTATCGATACA
617199 ATGTATCGAT
Statistics
Matches: 82, Mismatches: 6, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
51 2 0.02
52 80 0.98
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33
Consensus pattern (52 bp):
CTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAATTTGC
Found at i:617205 original size:13 final size:13
Alignment explanation
Indices: 617187--617211 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
617177 CAAAAATCAG
617187 TGTATCGATACAA
1 TGTATCGATACAA
617200 TGTATCGATACA
1 TGTATCGATACA
617212 TGTGAGTAAT
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:617296 original size:13 final size:13
Alignment explanation
Indices: 617278--617302 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
617268 TACAAAAAAA
617278 TGTATCGATACAT
1 TGTATCGATACAT
617291 TGTATCGATACA
1 TGTATCGATACA
617303 ACATTTTATG
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:618338 original size:49 final size:49
Alignment explanation
Indices: 618192--618349 Score: 147
Period size: 49 Copynumber: 3.1 Consensus size: 49
618182 AAAAGTGATA
* * * * *
618192 AAGATGCCAATATGTTGATTCATGGCCAACGATATTGGGCCTAAAGATGAG
1 AAGATGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGAT--G
* ** * * *
618243 AAAAAGGATGTCAACGTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATG
1 ---AA-GATGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATG
618296 AAGATGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAA-ATG
1 AAGATGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATG
*
618344 ATGATG
1 AAGATG
618350 AGAAAAGTGA
Statistics
Matches: 85, Mismatches: 18, Indels: 8
0.77 0.16 0.07
Matches are distributed among these distances:
48 8 0.09
49 37 0.44
50 2 0.02
53 1 0.01
54 2 0.02
55 35 0.41
ACGTcount: A:0.35, C:0.16, G:0.24, T:0.25
Consensus pattern (49 bp):
AAGATGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATG
Done.