Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D02
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: 67659327
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 461372 characters in sequence are not A, C, G, or T
File 68 of 216
Found at i:20368424 original size:16 final size:17
Alignment explanation
Indices: 20368403--20368445 Score: 52
Period size: 16 Copynumber: 2.5 Consensus size: 17
20368393 TCTTTATGAT
20368403 TTATATATTTAT-TACC
1 TTATATATTTATGTACC
* *
20368419 TTATATATATATGTACG
1 TTATATATTTATGTACC
20368436 TATATATATT
1 T-TATATATT
20368446 ATACTTTCTA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
16 11 0.50
17 4 0.18
18 7 0.32
ACGTcount: A:0.35, C:0.07, G:0.05, T:0.53
Consensus pattern (17 bp):
TTATATATTTATGTACC
Found at i:20368462 original size:20 final size:20
Alignment explanation
Indices: 20368439--20368489 Score: 68
Period size: 20 Copynumber: 2.6 Consensus size: 20
20368429 ATGTACGTAT
*
20368439 ATATATTATACTTTCTATAC
1 ATATATTATAATTTCTATAC
* *
20368459 ATATTTTATAATTTCTATAT
1 ATATATTATAATTTCTATAC
20368479 ATATA-TATAAT
1 ATATATTATAAT
20368490 CATTATCTTT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
19 6 0.22
20 21 0.78
ACGTcount: A:0.39, C:0.08, G:0.00, T:0.53
Consensus pattern (20 bp):
ATATATTATAATTTCTATAC
Found at i:20368465 original size:102 final size:101
Alignment explanation
Indices: 20368343--20368586 Score: 400
Period size: 102 Copynumber: 2.4 Consensus size: 101
20368333 TATATGTACG
*
20368343 TATACTTTCTATACATATTTTATAATTTCTATATATATATATAATCATTATCTTTATGATTTATA
1 TATACTTTCTATACATATTTTATAATTTCTATATATATATATAATCATTATCTTTATGATCTATA
* *
20368408 TATTTATTACCTTATATATATATGTACGTATATA-TAT
66 TATTTATTAAC-T-TATACATATGTACGTATATAGTAT
20368445 TATACTTTCTATACATATTTTATAATTTCTATATATATATATAATCATTATCTTTATGATCTATA
1 TATACTTTCTATACATATTTTATAATTTCTATATATATATATAATCATTATCTTTATGATCTATA
20368510 TATTTATTAACTTATACATATGTACGTATATATGTAT
66 TATTTATTAACTTATACATATGTACGTATATA-GTAT
* * *
20368547 TATACTTTCTATCCACATTTTATAATTTCTATATGTATAT
1 TATACTTTCTATACATATTTTATAATTTCTATATATATAT
20368587 TTTATTTATT
Statistics
Matches: 134, Mismatches: 6, Indels: 4
0.93 0.04 0.03
Matches are distributed among these distances:
100 19 0.14
101 1 0.01
102 114 0.85
ACGTcount: A:0.34, C:0.10, G:0.03, T:0.52
Consensus pattern (101 bp):
TATACTTTCTATACATATTTTATAATTTCTATATATATATATAATCATTATCTTTATGATCTATA
TATTTATTAACTTATACATATGTACGTATATAGTAT
Found at i:20368479 original size:54 final size:49
Alignment explanation
Indices: 20368343--20368587 Score: 169
Period size: 54 Copynumber: 4.8 Consensus size: 49
20368333 TATATGTACG
20368343 TATACTTTCTATACATATTTTATAATTTCTATATATATA-TATAATCAT
1 TATACTTTCTATACATATTTTATAATTTCTATATATATATTATAATCAT
* ** * ** *
20368391 TAT-CTTTATGATTTATATATTTATTACCT-TATATATATATGTACGTATATATAT
1 TATACTTTCT-ATACATAT-TTTATAATTTCTATATATATAT-TA--TA-AT-CAT
20368445 TATACTTTCTATACATATTTTATAATTTCTATATATATA-TATAATCAT
1 TATACTTTCTATACATATTTTATAATTTCTATATATATATTATAATCAT
* * * * * * *
20368493 TAT-CTTTATGAT-CTATATATTTATTAACTTATACATATGTACGTATATATGTAT
1 TATACTTTCT-ATAC-ATAT-TTTA-TAATTTCTATATATATA-TTATA-AT-CAT
* * *
20368547 TATACTTTCTATCCACATTTTATAATTTCTATATGTATATT
1 TATACTTTCTATACATATTTTATAATTTCTATATATATATT
20368588 TTATTTATTC
Statistics
Matches: 149, Mismatches: 28, Indels: 37
0.70 0.13 0.17
Matches are distributed among these distances:
47 11 0.07
48 30 0.20
49 13 0.09
50 17 0.11
51 1 0.01
52 20 0.13
53 15 0.10
54 31 0.21
55 11 0.07
ACGTcount: A:0.34, C:0.10, G:0.03, T:0.52
Consensus pattern (49 bp):
TATACTTTCTATACATATTTTATAATTTCTATATATATATTATAATCAT
Found at i:20368582 original size:50 final size:49
Alignment explanation
Indices: 20368426--20368583 Score: 155
Period size: 48 Copynumber: 3.2 Consensus size: 49
20368416 ACCTTATATA
*
20368426 TATATGTACGTATATA-TATTATACTTTCTATACATATTTTATAATTTC
1 TATATGTACGTATATATTATTATACTTTCTATCCATATTTTATAATTTC
* * * *
20368474 TATATATA--TATATAATCATTAT-CTTTATGATCTATATATTTATTAACTTATAC
1 TATATGTACGTATAT-ATTATTATACTTTCT-ATCCATAT-TTTA-TAA-TT-T-C
*
20368527 -ATATGTACGTATATATGTATTATACTTTCTATCCACATTTTATAATTTC
1 TATATGTACGTATATAT-TATTATACTTTCTATCCATATTTTATAATTTC
20368576 TATATGTA
1 TATATGTA
20368584 TATTTTATTT
Statistics
Matches: 87, Mismatches: 10, Indels: 24
0.72 0.08 0.20
Matches are distributed among these distances:
46 5 0.06
47 6 0.07
48 18 0.21
49 5 0.06
50 11 0.13
51 4 0.05
52 10 0.11
53 7 0.08
54 16 0.18
55 5 0.06
ACGTcount: A:0.34, C:0.11, G:0.04, T:0.51
Consensus pattern (49 bp):
TATATGTACGTATATATTATTATACTTTCTATCCATATTTTATAATTTC
Found at i:20373332 original size:29 final size:29
Alignment explanation
Indices: 20373300--20373369 Score: 104
Period size: 29 Copynumber: 2.4 Consensus size: 29
20373290 GAACAAACCA
* *
20373300 AAACAAAATAGAGTAGAACAACACATTTC
1 AAACAAAATAGAGCAGAACAACACAATTC
* *
20373329 AAACAGAACAGAGCAGAACAACACAATTC
1 AAACAAAATAGAGCAGAACAACACAATTC
20373358 AAACAAAATAGA
1 AAACAAAATAGA
20373370 ACCGAATAAA
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 35 1.00
ACGTcount: A:0.59, C:0.19, G:0.11, T:0.11
Consensus pattern (29 bp):
AAACAAAATAGAGCAGAACAACACAATTC
Found at i:20373396 original size:20 final size:20
Alignment explanation
Indices: 20373367--20373409 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 20
20373357 CAAACAAAAT
*
20373367 AGAACCGAATA-AAGCAGAGC
1 AGAACAGAATAGAA-CAGAGC
20373387 AGAACAGAATAGAACAGAGC
1 AGAACAGAATAGAACAGAGC
20373407 AGA
1 AGA
20373410 GCAATGCTGA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 19 0.90
21 2 0.10
ACGTcount: A:0.53, C:0.16, G:0.26, T:0.05
Consensus pattern (20 bp):
AGAACAGAATAGAACAGAGC
Found at i:20373407 original size:25 final size:25
Alignment explanation
Indices: 20373379--20373429 Score: 68
Period size: 25 Copynumber: 2.0 Consensus size: 25
20373369 AACCGAATAA
20373379 AGCAGAGCAGA-ACAGAATAGAACAG
1 AGCAGAGCA-ATACAGAATAGAACAG
* *
20373404 AGCAGAGCAATGCTGAATAGAACAG
1 AGCAGAGCAATACAGAATAGAACAG
20373429 A
1 A
20373430 ACAGGATAGA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 1 0.04
25 22 0.96
ACGTcount: A:0.49, C:0.16, G:0.27, T:0.08
Consensus pattern (25 bp):
AGCAGAGCAATACAGAATAGAACAG
Found at i:20385445 original size:19 final size:20
Alignment explanation
Indices: 20385421--20385506 Score: 75
Period size: 20 Copynumber: 4.2 Consensus size: 20
20385411 TACAGAGTAC
* *
20385421 GCCACAAAGG-TAATATAAT
1 GCCACAAAGGCTAACAAAAT
*
20385440 GCCACAATGGCTAACAAAAT
1 GCCACAAAGGCTAACAAAAT
*
20385460 GTCACAAAGGCCTAATCAAAAT
1 GCCACAAAGG-CTAA-CAAAAT
* *
20385482 ACGCCATAAAGACTAACAAAAT
1 --GCCACAAAGGCTAACAAAAT
20385504 GCC
1 GCC
20385507 CCCAAGCACC
Statistics
Matches: 54, Mismatches: 8, Indels: 9
0.76 0.11 0.13
Matches are distributed among these distances:
19 9 0.17
20 18 0.33
21 4 0.07
22 12 0.22
23 4 0.07
24 7 0.13
ACGTcount: A:0.47, C:0.23, G:0.14, T:0.16
Consensus pattern (20 bp):
GCCACAAAGGCTAACAAAAT
Found at i:20395803 original size:18 final size:18
Alignment explanation
Indices: 20395780--20395814 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
20395770 TAGGCTAACT
20395780 AAGTATATTGAAACTCTC
1 AAGTATATTGAAACTCTC
20395798 AAGTATATTGAAACTCT
1 AAGTATATTGAAACTCT
20395815 AATTAATGTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.40, C:0.14, G:0.11, T:0.34
Consensus pattern (18 bp):
AAGTATATTGAAACTCTC
Found at i:20400060 original size:9 final size:9
Alignment explanation
Indices: 20399982--20400119 Score: 59
Period size: 10 Copynumber: 14.7 Consensus size: 9
20399972 GACATGTGGC
*
20399982 AAAAATGAT
1 AAAAATTAT
20399991 AAAAA--AT
1 AAAAATTAT
*
20399998 AAAAATCAAT
1 AAAAAT-TAT
* *
20400008 AAAATTTGT
1 AAAAATTAT
20400017 AAAAATTATT
1 AAAAATTA-T
**
20400027 AAATTTTAAT
1 AAAAATT-AT
*
20400037 AAAAATTAGAA
1 AAAAATT--AT
20400048 AAAAATTAT
1 AAAAATTAT
20400057 AAAAA-TAGT
1 AAAAATTA-T
20400066 AAAAAATTATT
1 -AAAAATTA-T
**
20400077 AAATTTTAT
1 AAAAATTAT
*
20400086 AAAAATCAT
1 AAAAATTAT
20400095 -AAAATATAT
1 AAAAAT-TAT
*
20400104 AGAAATGTAT
1 AAAAAT-TAT
20400114 AAAAAT
1 AAAAAT
20400120 ATAGAAAAGA
Statistics
Matches: 96, Mismatches: 22, Indels: 21
0.69 0.16 0.15
Matches are distributed among these distances:
7 7 0.07
8 7 0.07
9 28 0.29
10 42 0.44
11 12 0.12
ACGTcount: A:0.63, C:0.01, G:0.04, T:0.31
Consensus pattern (9 bp):
AAAAATTAT
Found at i:20400079 original size:20 final size:20
Alignment explanation
Indices: 20400035--20400075 Score: 66
Period size: 19 Copynumber: 2.1 Consensus size: 20
20400025 TTAAATTTTA
20400035 ATAAAAATTAGAAAAAAATT
1 ATAAAAATTAGAAAAAAATT
*
20400055 ATAAAAA-TAGTAAAAAATT
1 ATAAAAATTAGAAAAAAATT
20400074 AT
1 AT
20400076 TAAATTTTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
19 13 0.65
20 7 0.35
ACGTcount: A:0.68, C:0.00, G:0.05, T:0.27
Consensus pattern (20 bp):
ATAAAAATTAGAAAAAAATT
Found at i:20400114 original size:10 final size:10
Alignment explanation
Indices: 20400048--20400139 Score: 59
Period size: 10 Copynumber: 9.4 Consensus size: 10
20400038 AAAATTAGAA
20400048 AAAAAT-TAT
1 AAAAATATAT
20400057 AAAAATAGTA-
1 AAAAATA-TAT
20400067 AAAAAT-TAT
1 AAAAATATAT
* * *
20400076 TAAATTTTAT
1 AAAAATATAT
*
20400086 AAAAAT-CAT
1 AAAAATATAT
20400095 -AAAATATAT
1 AAAAATATAT
* *
20400104 AGAAATGTAT
1 AAAAATATAT
*
20400114 AAAAATATAGA
1 AAAAATATA-T
20400125 AAAGAATATAT
1 AAA-AATATAT
20400136 AAAA
1 AAAA
20400140 TTTTATAAAG
Statistics
Matches: 63, Mismatches: 12, Indels: 15
0.70 0.13 0.17
Matches are distributed among these distances:
8 7 0.11
9 14 0.22
10 28 0.44
11 8 0.13
12 6 0.10
ACGTcount: A:0.64, C:0.01, G:0.05, T:0.29
Consensus pattern (10 bp):
AAAAATATAT
Found at i:20400134 original size:20 final size:18
Alignment explanation
Indices: 20400093--20400128 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
20400083 TATAAAAATC
*
20400093 ATAAAATATATAGAAATGT
1 ATAAAA-ATATAGAAAAGT
20400112 ATAAAAATATAGAAAAG
1 ATAAAAATATAGAAAAG
20400129 AATATATAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 10 0.62
19 6 0.38
ACGTcount: A:0.64, C:0.00, G:0.11, T:0.25
Consensus pattern (18 bp):
ATAAAAATATAGAAAAGT
Found at i:20400210 original size:21 final size:21
Alignment explanation
Indices: 20400151--20400211 Score: 70
Period size: 20 Copynumber: 3.0 Consensus size: 21
20400141 TTTATAAAGT
* * *
20400151 CGTAAGAAAATGATAAAAAAA
1 CGTAAAAAAATTATAAAAATA
* *
20400172 TGTAAAAAAAATAT-AAAATA
1 CGTAAAAAAATTATAAAAATA
20400192 CGTAAAAAAATTATAAAAAT
1 CGTAAAAAAATTATAAAAAT
20400212 TATCATACCA
Statistics
Matches: 32, Mismatches: 7, Indels: 2
0.78 0.17 0.05
Matches are distributed among these distances:
20 17 0.53
21 15 0.47
ACGTcount: A:0.67, C:0.03, G:0.08, T:0.21
Consensus pattern (21 bp):
CGTAAAAAAATTATAAAAATA
Found at i:20400435 original size:20 final size:20
Alignment explanation
Indices: 20400412--20400453 Score: 50
Period size: 20 Copynumber: 2.1 Consensus size: 20
20400402 TTTTTTATGA
20400412 TTTTCATGA-AATTTTACAAT
1 TTTTCAT-ATAATTTTACAAT
* *
20400432 TTTTTATATATTTTTACAAT
1 TTTTCATATAATTTTACAAT
20400452 TT
1 TT
20400454 ATATATATTC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
19 1 0.05
20 18 0.95
ACGTcount: A:0.31, C:0.07, G:0.02, T:0.60
Consensus pattern (20 bp):
TTTTCATATAATTTTACAAT
Found at i:20400444 original size:19 final size:18
Alignment explanation
Indices: 20400422--20400462 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 18
20400412 TTTTCATGAA
*
20400422 ATTTTACAATTTTTTATAT
1 ATTTTACAA-TTTATATAT
20400441 ATTTTTACAATTTATATAT
1 A-TTTTACAATTTATATAT
20400460 ATT
1 ATT
20400463 CTAATTTTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
18 2 0.10
19 10 0.50
20 8 0.40
ACGTcount: A:0.34, C:0.05, G:0.00, T:0.61
Consensus pattern (18 bp):
ATTTTACAATTTATATAT
Found at i:20400510 original size:9 final size:9
Alignment explanation
Indices: 20400397--20400543 Score: 60
Period size: 9 Copynumber: 15.1 Consensus size: 9
20400387 TGATGCATTC
20400397 TATAATTTTT
1 TATAA-TTTT
*
20400407 TATGATTTT
1 TATAATTTT
* *
20400416 CATGAAATTT
1 TAT-AATTTT
*
20400426 TACAATTTTT
1 TATAA-TTTT
20400436 TATATATTTT
1 TATA-ATTTT
* *
20400446 TACAATTTA
1 TATAATTTT
20400455 TATATATTCTAAT
1 TATA-ATT-T--T
*
20400468 TTTAATTTT
1 TATAATTTT
*
20400477 TTTATATTTT
1 TATA-ATTTT
*
20400487 TAATAAGTTT
1 T-ATAATTTT
*
20400497 AATAATTTT
1 TATAATTTT
*
20400506 TATAACTTT
1 TATAATTTT
* *
20400515 TATTGATTAT
1 TA-TAATTTT
**
20400525 TATTTTTTT
1 TATAATTTT
20400534 TATAATTTT
1 TATAATTTT
20400543 T
1 T
20400544 GTCACACGTG
Statistics
Matches: 100, Mismatches: 27, Indels: 21
0.68 0.18 0.14
Matches are distributed among these distances:
9 48 0.48
10 41 0.41
11 5 0.05
12 3 0.03
13 3 0.03
ACGTcount: A:0.31, C:0.03, G:0.03, T:0.63
Consensus pattern (9 bp):
TATAATTTT
Found at i:20402242 original size:96 final size:96
Alignment explanation
Indices: 20401868--20402222 Score: 577
Period size: 96 Copynumber: 3.7 Consensus size: 96
20401858 GCCTTATCCT
* * * *
20401868 ACAATGGAACCCCACTACTGTTCTCTTAATGAAGTGTCCTATGAATACACGGAAGATTCTGAGAC
1 ACAAAGGAACCTCAGTATTGTTCTCTTAATGAAGTGTCCTATGAATACACGGAAGATTCTGAGAC
20401933 CAGGCTTGACGTGGGGCTTTCTGGTTGTGAA
66 CAGGCTTGACGTGGGGCTTTCTGGTTGTGAA
*
20401964 ACAAAGGAACCTCAGTATTGTTCTCTTAATGAAGTGTCCTATGAATACACGGAAGATTCTGAAAC
1 ACAAAGGAACCTCAGTATTGTTCTCTTAATGAAGTGTCCTATGAATACACGGAAGATTCTGAGAC
*
20402029 CAGGCTTGACATGGGGCTTTCTGGTTGTGAA
66 CAGGCTTGACGTGGGGCTTTCTGGTTGTGAA
*
20402060 ACAAAGGAACCTCAGTATTGTTCTCTTAATGAAGTGTCCTATGAATACATGGAAGATTCTGAGAC
1 ACAAAGGAACCTCAGTATTGTTCTCTTAATGAAGTGTCCTATGAATACACGGAAGATTCTGAGAC
*
20402125 CAGGCTTGACGTGGGGCTTTCTGG-CGCTGAA
66 CAGGCTTGACGTGGGGCTTTCTGGTTG-TGAA
* * * * *
20402156 ACAAAGGAACCTCAGTATTGTTGTCTTAATGAAGTGTCCTATGAATATAGGGAAAATTTTGAGAC
1 ACAAAGGAACCTCAGTATTGTTCTCTTAATGAAGTGTCCTATGAATACACGGAAGATTCTGAGAC
20402221 CA
66 CA
20402223 AGTTTGATGT
Statistics
Matches: 243, Mismatches: 15, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
95 1 0.00
96 242 1.00
ACGTcount: A:0.29, C:0.18, G:0.24, T:0.29
Consensus pattern (96 bp):
ACAAAGGAACCTCAGTATTGTTCTCTTAATGAAGTGTCCTATGAATACACGGAAGATTCTGAGAC
CAGGCTTGACGTGGGGCTTTCTGGTTGTGAA
Found at i:20408776 original size:124 final size:124
Alignment explanation
Indices: 20408556--20408905 Score: 585
Period size: 124 Copynumber: 2.8 Consensus size: 124
20408546 TTATTTCGAG
* *
20408556 TTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTACTAGGATGCTATTTGAGAAGAAATTGTG
1 TTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTACCAGGATGCTATTTGAAAAGAAATTGTG
20408621 AAATCGCGCCCTCGTGGACGCGATTTTGCTACAGTAGGTCATGTAAGAAATAATTTTTT
66 AAATCGCGCCCTCGTGGACGCGATTTTGCTACAGTAGGTCATGTAAGAAATAATTTTTT
20408680 TTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTACCAGGATGCTATTTGAAAAGAAATTGTG
1 TTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTACCAGGATGCTATTTGAAAAGAAATTGTG
* * * *
20408745 AAATCGTGCCTTCGTGGACGCGATTTTGCTACAGTTGGTTATGTAAGAAATAATTTTTT
66 AAATCGCGCCCTCGTGGACGCGATTTTGCTACAGTAGGTCATGTAAGAAATAATTTTTT
* * *
20408804 TTGACGTTTCTGAGCAAATAATATAAAATCGCTTATACCAGGATGTTATTT-AAGAAGAAATTGT
1 TTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTACCAGGATGCTATTTGAA-AAGAAATTGT
* *
20408868 GAAATCGCGCCCTCATGGACGCGATTTTGCTATAGTAG
65 GAAATCGCGCCCTCGTGGACGCGATTTTGCTACAGTAG
20408906 CAAGTTTGGG
Statistics
Matches: 211, Mismatches: 14, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
123 2 0.01
124 209 0.99
ACGTcount: A:0.31, C:0.15, G:0.21, T:0.33
Consensus pattern (124 bp):
TTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTACCAGGATGCTATTTGAAAAGAAATTGTG
AAATCGCGCCCTCGTGGACGCGATTTTGCTACAGTAGGTCATGTAAGAAATAATTTTTT
Found at i:20410983 original size:17 final size:17
Alignment explanation
Indices: 20410961--20410999 Score: 78
Period size: 17 Copynumber: 2.3 Consensus size: 17
20410951 ACCAACATGG
20410961 GTATTTAGTCTATAACT
1 GTATTTAGTCTATAACT
20410978 GTATTTAGTCTATAACT
1 GTATTTAGTCTATAACT
20410995 GTATT
1 GTATT
20411000 ATTATCTCGT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.28, C:0.10, G:0.13, T:0.49
Consensus pattern (17 bp):
GTATTTAGTCTATAACT
Found at i:20428293 original size:15 final size:15
Alignment explanation
Indices: 20428273--20428331 Score: 66
Period size: 15 Copynumber: 3.8 Consensus size: 15
20428263 AAAATATTTG
20428273 AAATATTTTAATATA
1 AAATATTTTAATATA
*
20428288 AAATA-TTTAATTTCA
1 AAATATTTTAATAT-A
*
20428303 AAATATAATTTAAAATA
1 AAATAT--TTTAATATA
20428320 AAATATTTTAAT
1 AAATATTTTAAT
20428332 TAATTTAATA
Statistics
Matches: 36, Mismatches: 4, Indels: 8
0.75 0.08 0.17
Matches are distributed among these distances:
14 7 0.19
15 16 0.44
17 7 0.19
18 6 0.17
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (15 bp):
AAATATTTTAATATA
Found at i:20428357 original size:24 final size:24
Alignment explanation
Indices: 20428308--20428358 Score: 68
Period size: 24 Copynumber: 2.1 Consensus size: 24
20428298 TTTCAAAATA
*
20428308 TAATTTAAAATAAAATATTTTAAT
1 TAATTTAAAATAAAATATTATAAT
*
20428332 TAATTTAATATAAAATAATTAT-AT
1 TAATTTAAAATAAAAT-ATTATAAT
20428356 TAA
1 TAA
20428359 CAATATTATT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
24 20 0.83
25 4 0.17
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (24 bp):
TAATTTAAAATAAAATATTATAAT
Found at i:20428402 original size:16 final size:16
Alignment explanation
Indices: 20428378--20428453 Score: 55
Period size: 16 Copynumber: 4.6 Consensus size: 16
20428368 TAAATTATAT
20428378 ATTATTATTTTTATTAA
1 ATTA-TATTTTTATTAA
* *
20428395 ATTATATTTAATAATTAT
1 ATTATATTT--TTATTAA
* * * *
20428413 ATTAAAATATGATTAA
1 ATTATATTTTTATTAA
*
20428429 ATTATTTTTTTATTAA
1 ATTATATTTTTATTAA
20428445 ATTAT-TTTT
1 ATTATATTTT
20428454 AATAATAATC
Statistics
Matches: 45, Mismatches: 12, Indels: 6
0.71 0.19 0.10
Matches are distributed among these distances:
15 4 0.09
16 26 0.58
17 4 0.09
18 11 0.24
ACGTcount: A:0.39, C:0.00, G:0.01, T:0.59
Consensus pattern (16 bp):
ATTATATTTTTATTAA
Found at i:20428420 original size:24 final size:23
Alignment explanation
Indices: 20428348--20428459 Score: 75
Period size: 24 Copynumber: 4.7 Consensus size: 23
20428338 AATATAAAAT
*
20428348 AATTATA-TTAACAA-TATTATTA
1 AATTATATTTAATAATTA-TATTA
* * *
20428370 AATTATATATTATTATTTTTATTA
1 AATTATAT-TTAATAATTATATTA
20428394 AATTATATTTAATAATTATATTA
1 AATTATATTTAATAATTATATTA
* * * *
20428417 AAATATGATTAAATTATTTTTTTATTA
1 AATTAT-ATTTAA-TA--ATTATATTA
*
20428444 AATTATTTTTAATAAT
1 AATTATATTTAATAAT
20428460 AATCCTATTA
Statistics
Matches: 68, Mismatches: 15, Indels: 13
0.71 0.16 0.14
Matches are distributed among these distances:
22 7 0.10
23 18 0.26
24 22 0.32
25 5 0.07
26 4 0.06
27 12 0.18
ACGTcount: A:0.44, C:0.01, G:0.01, T:0.54
Consensus pattern (23 bp):
AATTATATTTAATAATTATATTA
Found at i:20428636 original size:44 final size:46
Alignment explanation
Indices: 20428568--20428656 Score: 112
Period size: 44 Copynumber: 2.0 Consensus size: 46
20428558 TTACAACATC
* *
20428568 ATTCTATTCAACCAAACACATGAA-TACT-ACTACAATTCTATTCT
1 ATTCCATTCAACCAAACACATGAATTACTAACTACAACTCTATTCT
* *
20428612 ATTCCATTCAACTAAACA-ATTGAATTACTAATTACAACTCTATTC
1 ATTCCATTCAACCAAACACA-TGAATTACTAACTACAACTCTATTC
20428657 CATTATAGCT
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
43 1 0.03
44 20 0.53
45 4 0.11
46 13 0.34
ACGTcount: A:0.39, C:0.24, G:0.02, T:0.35
Consensus pattern (46 bp):
ATTCCATTCAACCAAACACATGAATTACTAACTACAACTCTATTCT
Found at i:20432550 original size:71 final size:71
Alignment explanation
Indices: 20432434--20432591 Score: 226
Period size: 71 Copynumber: 2.2 Consensus size: 71
20432424 AAAAGAAAGA
* * * * * * *
20432434 GTATCGTGATATCAACACCTTGGAATTGCGATACCTTTAATAGTATTGAAGAATGGAGACATCTT
1 GTATCGCGATATCCACACCTTGGAATCGCGATACCTCTAACAGTATTGAAGAATGGAGACACCCT
*
20432499 TCAGTG
66 TCAATG
* *
20432505 GTATCGCGATATCCACACCTTGGAATCGTGATACCTCTAACAGTATTGAAGAATGGGGACACCCT
1 GTATCGCGATATCCACACCTTGGAATCGCGATACCTCTAACAGTATTGAAGAATGGAGACACCCT
20432570 TCAATG
66 TCAATG
20432576 GTATCGCGATATCCAC
1 GTATCGCGATATCCAC
20432592 CTTTCCAAAA
Statistics
Matches: 77, Mismatches: 10, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
71 77 1.00
ACGTcount: A:0.30, C:0.21, G:0.21, T:0.28
Consensus pattern (71 bp):
GTATCGCGATATCCACACCTTGGAATCGCGATACCTCTAACAGTATTGAAGAATGGAGACACCCT
TCAATG
Found at i:20432681 original size:22 final size:22
Alignment explanation
Indices: 20432628--20432682 Score: 56
Period size: 22 Copynumber: 2.5 Consensus size: 22
20432618 CACTGCCTAA
*
20432628 GGTATCGTGATATCCTCTTATG
1 GGTATCGCGATATCCTCTTATG
*** * *
20432650 AAAATTGCGATATCTTCTTATG
1 GGTATCGCGATATCCTCTTATG
20432672 GGTATCGCGAT
1 GGTATCGCGAT
20432683 GTAATAGCCC
Statistics
Matches: 23, Mismatches: 10, Indels: 0
0.70 0.30 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.24, C:0.16, G:0.22, T:0.38
Consensus pattern (22 bp):
GGTATCGCGATATCCTCTTATG
Found at i:20435325 original size:13 final size:13
Alignment explanation
Indices: 20435307--20435331 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
20435297 TAACTTATAT
20435307 GTGTGAAAATTTC
1 GTGTGAAAATTTC
20435320 GTGTGAAAATTT
1 GTGTGAAAATTT
20435332 TATCATTTTT
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:0.04, G:0.24, T:0.40
Consensus pattern (13 bp):
GTGTGAAAATTTC
Found at i:20447261 original size:26 final size:25
Alignment explanation
Indices: 20447232--20447289 Score: 80
Period size: 28 Copynumber: 2.2 Consensus size: 25
20447222 TTCATCTGAA
20447232 AATATGAGGCACACTCCACAAATTGT
1 AATAT-AGGCACACTCCACAAATTGT
20447258 AATAACATAGGCACACTCCACAAATTGT
1 AAT---ATAGGCACACTCCACAAATTGT
20447286 AATA
1 AATA
20447290 ACATACTTAT
Statistics
Matches: 29, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
25 1 0.03
26 3 0.10
28 23 0.79
29 2 0.07
ACGTcount: A:0.43, C:0.22, G:0.12, T:0.22
Consensus pattern (25 bp):
AATATAGGCACACTCCACAAATTGT
Found at i:20447269 original size:28 final size:28
Alignment explanation
Indices: 20447238--20447294 Score: 114
Period size: 28 Copynumber: 2.0 Consensus size: 28
20447228 TGAAAATATG
20447238 AGGCACACTCCACAAATTGTAATAACAT
1 AGGCACACTCCACAAATTGTAATAACAT
20447266 AGGCACACTCCACAAATTGTAATAACAT
1 AGGCACACTCCACAAATTGTAATAACAT
20447294 A
1 A
20447295 CTTATTTACC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.44, C:0.25, G:0.11, T:0.21
Consensus pattern (28 bp):
AGGCACACTCCACAAATTGTAATAACAT
Found at i:20448526 original size:15 final size:15
Alignment explanation
Indices: 20448508--20448538 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
20448498 AGTTTTTAAG
20448508 TCTATTCAATTTAGT
1 TCTATTCAATTTAGT
20448523 TCTATTCAATTTAGT
1 TCTATTCAATTTAGT
20448538 T
1 T
20448539 TAATTTTGCA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.26, C:0.13, G:0.06, T:0.55
Consensus pattern (15 bp):
TCTATTCAATTTAGT
Found at i:20450075 original size:26 final size:25
Alignment explanation
Indices: 20450046--20450117 Score: 108
Period size: 26 Copynumber: 2.8 Consensus size: 25
20450036 AACACGTCAG
20450046 AAAAGGAAGCCATTGTGGCATAATAT
1 AAAAGGAAGCC-TTGTGGCATAATAT
20450072 AAAAGGAAGCCTTTGTGGCATAATAT
1 AAAAGGAAGCC-TTGTGGCATAATAT
*
20450098 AAAAGAAAGCCTCTGTGGCA
1 AAAAGGAAGCCT-TGTGGCA
20450118 AAACTCGAAA
Statistics
Matches: 43, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
25 1 0.02
26 42 0.98
ACGTcount: A:0.40, C:0.14, G:0.24, T:0.22
Consensus pattern (25 bp):
AAAAGGAAGCCTTGTGGCATAATAT
Found at i:20450143 original size:28 final size:28
Alignment explanation
Indices: 20450053--20450171 Score: 70
Period size: 26 Copynumber: 4.4 Consensus size: 28
20450043 CAGAAAAGGA
* * * *
20450053 AGCCATTGTGGCATAATATAAAAGG-A-
1 AGCCCTTGTGGCAAAACATGAAAGGAAT
* * * *
20450079 AGCCTTTGTGGCATAATAT-AAAAGAA-
1 AGCCCTTGTGGCAAAACATGAAAGGAAT
20450105 AG-CCTCTGTGGCAAAAC-TCGAAAGGAAT
1 AGCCCT-TGTGGCAAAACAT-GAAAGGAAT
** * *
20450133 AGCCCTTGTGGTGAACCATGAAAGGAGT
1 AGCCCTTGTGGCAAAACATGAAAGGAAT
20450161 AGCCCTTGTGG
1 AGCCCTTGTGG
20450172 AAACCCATTT
Statistics
Matches: 76, Mismatches: 10, Indels: 12
0.78 0.10 0.12
Matches are distributed among these distances:
25 7 0.09
26 30 0.39
27 6 0.08
28 29 0.38
29 4 0.05
ACGTcount: A:0.34, C:0.17, G:0.26, T:0.23
Consensus pattern (28 bp):
AGCCCTTGTGGCAAAACATGAAAGGAAT
Found at i:20450179 original size:28 final size:28
Alignment explanation
Indices: 20450124--20450176 Score: 81
Period size: 28 Copynumber: 1.9 Consensus size: 28
20450114 GGCAAAACTC
*
20450124 GAAAGGAATAGCCCTTGTGGTGAACCAT
1 GAAAGGAATAGCCCTTGTGGTAAACCAT
*
20450152 GAAAGGAGTAGCCCTTGTGG-AAACC
1 GAAAGGAATAGCCCTTGTGGTAAACC
20450177 CATTTGAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
27 4 0.17
28 19 0.83
ACGTcount: A:0.32, C:0.19, G:0.30, T:0.19
Consensus pattern (28 bp):
GAAAGGAATAGCCCTTGTGGTAAACCAT
Found at i:20452729 original size:3 final size:3
Alignment explanation
Indices: 20452721--20452754 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
20452711 AAAGTACAGA
20452721 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
20452755 GGTGATAAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:20453394 original size:19 final size:18
Alignment explanation
Indices: 20453370--20453416 Score: 60
Period size: 19 Copynumber: 2.6 Consensus size: 18
20453360 GAATAAAAGA
20453370 AAAAGAAAACAAAGAATCG
1 AAAAGAAAACAAAG-ATCG
*
20453389 AAAAGAAAAAAAAGATCG
1 AAAAGAAAACAAAGATCG
*
20453407 AGAA-AAAACA
1 AAAAGAAAACA
20453417 GAAAATAAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
17 5 0.20
18 7 0.28
19 13 0.52
ACGTcount: A:0.72, C:0.09, G:0.15, T:0.04
Consensus pattern (18 bp):
AAAAGAAAACAAAGATCG
Found at i:20457980 original size:43 final size:43
Alignment explanation
Indices: 20457910--20458051 Score: 153
Period size: 43 Copynumber: 3.3 Consensus size: 43
20457900 TTTTTCAAAT
* *
20457910 AAACGCCGCTATAGATCAT-TACTTTTAGCGGCGCTTTTAT-ATC
1 AAACGCCGCTAAAGATCATGTTC-TTTAGCGGCGCTTTTATCA-C
*
20457953 AAACGCCGCTAAAGGTCATGTTCTTTAGCGGCGCTTTTATCAC
1 AAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTTTATCAC
* * * * * *
20457996 AAACACCACTAAAGAACATGATCTTTAGCGGCGCTTTTTTCAT
1 AAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTTTATCAC
* *
20458039 AAACACCACTAAA
1 AAACGCCGCTAAA
20458052 AGTATCGTTC
Statistics
Matches: 87, Mismatches: 10, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
43 84 0.97
44 3 0.03
ACGTcount: A:0.30, C:0.25, G:0.15, T:0.30
Consensus pattern (43 bp):
AAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTTTATCAC
Found at i:20458064 original size:43 final size:42
Alignment explanation
Indices: 20457933--20458065 Score: 151
Period size: 43 Copynumber: 3.1 Consensus size: 42
20457923 GATCATTACT
* * *
20457933 TTTAGCGGCGCTTTTAT-ATCAAACGCCGCTAAAGGTCATGTTC
1 TTTAGCGGCGCTTTTATCAT-AAACACCACTAAAAGT-ATGTTC
* ** *
20457976 TTTAGCGGCGCTTTTATCACAAACACCACTAAAGAACATGATC
1 TTTAGCGGCGCTTTTATCATAAACACCACTAAA-AGTATGTTC
*
20458019 TTTAGCGGCGCTTTTTTCATAAACACCACTAAAAGTATCGTTC
1 TTTAGCGGCGCTTTTATCATAAACACCACTAAAAGTAT-GTTC
20458062 TTTA
1 TTTA
20458066 ATGGCGTTTT
Statistics
Matches: 75, Mismatches: 12, Indels: 6
0.81 0.13 0.06
Matches are distributed among these distances:
42 3 0.04
43 71 0.95
44 1 0.01
ACGTcount: A:0.29, C:0.23, G:0.16, T:0.32
Consensus pattern (42 bp):
TTTAGCGGCGCTTTTATCATAAACACCACTAAAAGTATGTTC
Found at i:20458398 original size:21 final size:21
Alignment explanation
Indices: 20458374--20458423 Score: 91
Period size: 21 Copynumber: 2.4 Consensus size: 21
20458364 TTCTGTTCTG
*
20458374 CTCTGCTTCCCTCGCTGCTGC
1 CTCTGCTTCCCTCGCTACTGC
20458395 CTCTGCTTCCCTCGCTACTGC
1 CTCTGCTTCCCTCGCTACTGC
20458416 CTCTGCTT
1 CTCTGCTT
20458424 TAAGTTGTAG
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.02, C:0.46, G:0.16, T:0.36
Consensus pattern (21 bp):
CTCTGCTTCCCTCGCTACTGC
Found at i:20463800 original size:9 final size:9
Alignment explanation
Indices: 20463786--20464173 Score: 131
Period size: 9 Copynumber: 42.0 Consensus size: 9
20463776 TAAGTATAAT
20463786 TAAGTTATG
1 TAAGTTATG
20463795 TAAGTTATG
1 TAAGTTATG
* * *
20463804 ATATGATATA
1 -TAAGTTATG
*
20463814 T-ATTTATG
1 TAAGTTATG
20463822 TAAGTTA--
1 TAAGTTATG
20463829 TAAG-TATG
1 TAAGTTATG
20463837 ATTAAGTTATG
1 --TAAGTTATG
20463848 TAAGTTATG
1 TAAGTTATG
* *
20463857 TGAGTTACG
1 TAAGTTATG
20463866 TAAGTTATG
1 TAAGTTATG
* *
20463875 ATATGATATATATA
1 -TA--A-GT-TATG
20463889 TAAGTTAT-
1 TAAGTTATG
20463897 TAAGTTATG
1 TAAGTTATG
*
20463906 TAAGATATG
1 TAAGTTATG
*
20463915 TGAGTTATG
1 TAAGTTATG
* *
20463924 ATATGATATATA
1 -TAAG-T-TATG
* *
20463936 TAAGTAATT
1 TAAGTTATG
20463945 TAAGAATTTTATG
1 TAAG----TTATG
*
20463958 TATG-TATG
1 TAAGTTATG
*
20463966 TGAGTTATG
1 TAAGTTATG
20463975 TAAGTTATG
1 TAAGTTATG
* * *
20463984 ATATGATATA
1 -TAAGTTATG
*
20463994 T-ATTTATG
1 TAAGTTATG
20464002 T-A-TTATG
1 TAAGTTATG
*
20464009 TAAATTATG
1 TAAGTTATG
20464018 TAAGTTATG
1 TAAGTTATG
* *
20464027 TATTTGTTTTG
1 TA--AGTTATG
20464038 TAAGTTATGG
1 TAAGTTAT-G
* *
20464048 TATGATATATA
1 TAAG-T-TATG
*
20464059 TAAATTAT-
1 TAAGTTATG
20464067 TAAGTTATG
1 TAAGTTATG
*
20464076 TGAGTTATG
1 TAAGTTATG
* *
20464085 ATATGATATATA
1 -TAAG-T-TATG
20464097 TAAGTTAT-
1 TAAGTTATG
20464105 TAAGTTATG
1 TAAGTTATG
*
20464114 TATG-TATG
1 TAAGTTATG
*
20464122 TGAGTTATG
1 TAAGTTATG
20464131 TAAGTTATG
1 TAAGTTATG
* * *
20464140 ATATGATATA
1 -TAAGTTATG
*
20464150 T-ATTTATG
1 TAAGTTATG
20464158 T-A-TTATG
1 TAAGTTATG
20464165 TAAGTTATG
1 TAAGTTATG
20464174 GTATGATATA
Statistics
Matches: 278, Mismatches: 63, Indels: 76
0.67 0.15 0.18
Matches are distributed among these distances:
6 2 0.01
7 16 0.06
8 51 0.18
9 128 0.46
10 36 0.13
11 23 0.08
12 10 0.04
13 9 0.03
14 3 0.01
ACGTcount: A:0.35, C:0.00, G:0.18, T:0.46
Consensus pattern (9 bp):
TAAGTTATG
Found at i:20463853 original size:26 final size:26
Alignment explanation
Indices: 20463775--20463855 Score: 110
Period size: 26 Copynumber: 3.1 Consensus size: 26
20463765 GGGTTTAAGG
*
20463775 ATAAGTATAATTAAGTTATGTAAGTT
1 ATAAGTATGATTAAGTTATGTAAGTT
* *
20463801 ATGA-TATGATATATATTTATGTAAGTT
1 ATAAGTATGAT-TA-AGTTATGTAAGTT
20463828 ATAAGTATGATTAAGTTATGTAAGTT
1 ATAAGTATGATTAAGTTATGTAAGTT
20463854 AT
1 AT
20463856 GTGAGTTACG
Statistics
Matches: 47, Mismatches: 5, Indels: 6
0.81 0.09 0.10
Matches are distributed among these distances:
25 5 0.11
26 19 0.40
27 17 0.36
28 6 0.13
ACGTcount: A:0.40, C:0.00, G:0.16, T:0.44
Consensus pattern (26 bp):
ATAAGTATGATTAAGTTATGTAAGTT
Found at i:20463874 original size:53 final size:55
Alignment explanation
Indices: 20463775--20464027 Score: 138
Period size: 53 Copynumber: 4.5 Consensus size: 55
20463765 GGGTTTAAGG
* *
20463775 ATAAGTATAATTAAGTTATGTAAGTTATGAT-ATGATATATATTTATG-TAAG-T-T
1 ATAAGTATAATTAAGTTATGTAAGTTATG-TGA-GTTATATAGTTATGATAAGATAT
* *
20463828 ATAAGTATGATTAAGTTATGTAAGTTATGTGAGTTACGTA-AGTTATGATATGATAT
1 ATAAGTATAATTAAGTTATGTAAGTTATGTGAGTTA--TATAGTTATGATAAGATAT
* * *
20463884 ATATA-TAAGTTATTAAGTTATGTAAGATATGTGAG-T-TAT-GATATGAT---ATAT
1 ATA-AGT-A-TAATTAAGTTATGTAAGTTATGTGAGTTATATAGTTATGATAAGATAT
* * * *
20463935 ATAAGTA-ATTTAAGAATTTTATGTATG-TATGTGAGTTATGTAAGTTATGATATGATAT
1 ATAAGTATAATTAAG----TTATGTAAGTTATGTGAGTTATAT-AGTTATGATAAGATAT
* *
20463993 ATATTTATGTATTATGTAAATTATGTAAGTTATGT
1 ATA---A-GTATAAT-TAAGTTATGTAAGTTATGT
20464028 ATTTGTTTTG
Statistics
Matches: 155, Mismatches: 16, Indels: 50
0.70 0.07 0.23
Matches are distributed among these distances:
48 5 0.03
50 2 0.01
51 16 0.10
52 13 0.08
53 37 0.24
54 14 0.09
55 8 0.05
56 5 0.03
57 3 0.02
58 31 0.20
60 8 0.05
61 6 0.04
62 3 0.02
63 1 0.01
64 3 0.02
ACGTcount: A:0.37, C:0.00, G:0.18, T:0.45
Consensus pattern (55 bp):
ATAAGTATAATTAAGTTATGTAAGTTATGTGAGTTATATAGTTATGATAAGATAT
Found at i:20463909 original size:58 final size:58
Alignment explanation
Indices: 20463827--20464202 Score: 238
Period size: 58 Copynumber: 6.3 Consensus size: 58
20463817 TTATGTAAGT
*
20463827 TATAAGTATGATTAAGTTATGTAAGTTATGTGAGTTACGTAAGTTATGATATGATATATA
1 TATAAGT-T-ATTAAGTTATGTAAGTTATGTGAGTTATGTAAGTTATGATATGATATATA
*
20463887 TATAAGTTATTAAGTTATGTAAGATATGTGAGTTATG--A--TATGATAT-ATATA-A
1 TATAAGTTATTAAGTTATGTAAGTTATGTGAGTTATGTAAGTTATGATATGATATATA
* * ** * *
20463939 -GTAATTTAAGAATTTTATGTATG-TATGTGAGTTATGTAAGTTATGATATGATATATA
1 TATAAGTTATTAA-GTTATGTAAGTTATGTGAGTTATGTAAGTTATGATATGATATATA
* * * * *
20463996 TTTATGTATTATGTAAATTATGTAAGTTATGT-ATTTGTTTTGTAAGTTATGGTATGATATATA
1 TATAAG--TTAT-TAAGTTATGTAAGTTATGTGA---GTTATGTAAGTTATGATATGATATATA
* * * *
20464059 TA-AA-TTATTAAGTTATGTGAGTTATGAT-ATGATATATATAAGTTATTAAGTTATG-TATGTA
1 TATAAGTTATTAAGTTATGTAAGTTATG-TGA-G-T-TATGTAAGTTA-T--GATATGATATATA
* * * * * *
20464120 TGTGAGTTATGTAAGTTATGATATGATATATATTTATGTATTATGTAAGTTATGGTATGATATAT
1 TATAAGTTAT-TAAGTTATG-TAAG-T-TAT-GTGA-G--TTATGTAAGTTATGATATGATATAT
20464185 A
58 A
20464186 TATAAGTTATTAAGTTA
1 TATAAGTTATTAAGTTA
20464203 AGATCCAAAG
Statistics
Matches: 250, Mismatches: 35, Indels: 57
0.73 0.10 0.17
Matches are distributed among these distances:
51 21 0.08
52 9 0.04
53 6 0.02
54 8 0.03
55 8 0.03
56 6 0.02
57 3 0.01
58 46 0.18
59 16 0.06
60 20 0.08
61 13 0.05
62 7 0.03
63 30 0.12
64 9 0.04
65 14 0.06
66 14 0.06
67 5 0.02
68 13 0.05
69 2 0.01
ACGTcount: A:0.36, C:0.00, G:0.18, T:0.46
Consensus pattern (58 bp):
TATAAGTTATTAAGTTATGTAAGTTATGTGAGTTATGTAAGTTATGATATGATATATA
Found at i:20463921 original size:49 final size:50
Alignment explanation
Indices: 20463839--20463937 Score: 155
Period size: 49 Copynumber: 2.0 Consensus size: 50
20463829 TAAGTATGAT
* *
20463839 TAAGTTATGTAAGTTATGTGAGTTACGTAAGTTATGATATGATATATATA
1 TAAGTTATGTAAGTTATGTAAGATACGTAAGTTATGATATGATATATATA
* *
20463889 TAAGTTAT-TAAGTTATGTAAGATATGTGAGTTATGATATGATATATATA
1 TAAGTTATGTAAGTTATGTAAGATACGTAAGTTATGATATGATATATATA
20463938 AGTAATTTAA
Statistics
Matches: 45, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
49 37 0.82
50 8 0.18
ACGTcount: A:0.37, C:0.01, G:0.19, T:0.42
Consensus pattern (50 bp):
TAAGTTATGTAAGTTATGTAAGATACGTAAGTTATGATATGATATATATA
Found at i:20463962 original size:47 final size:48
Alignment explanation
Indices: 20463839--20464130 Score: 134
Period size: 49 Copynumber: 5.7 Consensus size: 48
20463829 TAAGTATGAT
* * * * *
20463839 TAAGTTATGTAAGTTATGTGAGTTACGTAAGTTATGATATGATATATATA
1 TAAGTAAT-TAAGTTATGTAAGATATGTGAGTTATGATATGA-ATATATA
*
20463889 TAAGTTATTAAGTTATGTAAGATATGTGAGTTATGATATG-ATATATA
1 TAAGTAATTAAGTTATGTAAGATATGTGAGTTATGATATGAATATATA
*
20463936 TAAGTAATTTAAGAATTTTATGTATG-TATGTGAGTTATGTAAGTTATGATATGATATA
1 TAAGTAA-TTAAG----TTATGTAAGATATGTGAGTTATG--A--TATGA-AT-ATATA
* * * * *
20463994 TATTTATGTATTATGTAAATTATGTAAGTTATGT-A-TT-TGTTTTGTAAGT-TATGG
1 TA---A-GTA--AT-TAAGTTATGTAAGATATGTGAGTTATGATATG-AA-TATAT-A
* * *
20464048 TATGATATATATAAATTAT-TAAGTTATGTGAGTTATGATATG-ATATATA
1 TAAG-TA-AT-TAAGTTATGTAAGATATGTGAGTTATGATATGAATATATA
* *
20464097 TAAGTTATTAAGTTATGTATG-TATGTGAGTTATG
1 TAAGTAATTAAGTTATGTAAGATATGTGAGTTATG
20464131 TAAGTTATGA
Statistics
Matches: 193, Mismatches: 20, Indels: 62
0.70 0.07 0.23
Matches are distributed among these distances:
46 20 0.10
47 18 0.09
48 6 0.03
49 42 0.22
50 25 0.13
51 17 0.09
52 13 0.07
53 4 0.02
54 6 0.03
55 6 0.03
57 2 0.01
58 9 0.05
59 2 0.01
60 9 0.05
61 6 0.03
62 3 0.02
63 1 0.01
64 4 0.02
ACGTcount: A:0.35, C:0.00, G:0.19, T:0.46
Consensus pattern (48 bp):
TAAGTAATTAAGTTATGTAAGATATGTGAGTTATGATATGAATATATA
Found at i:20463969 original size:51 final size:49
Alignment explanation
Indices: 20463839--20463974 Score: 139
Period size: 49 Copynumber: 2.7 Consensus size: 49
20463829 TAAGTATGAT
* * * * *
20463839 TAAGTTATGTAAGTTATGTGAGTTACGTAAGTTATGATATGATATATATA
1 TAAGTTAAG-AAGTTATGTAAGATATGTGAGTTATGATATGATATATATA
**
20463889 TAAGTTATTAAGTTATGTAAGATATGTGAGTTATGATATGATATATATAA
1 TAAGTTAAGAAGTTATGTAAGATATGTGAGTTATGATATGATATATAT-A
* * *
20463939 GTAATTTAAGAATTTTATGTATG-TATGTGAGTTATG
1 -TAAGTTAAGAA-GTTATGTAAGATATGTGAGTTATG
20463975 TAAGTTATGA
Statistics
Matches: 73, Mismatches: 10, Indels: 5
0.83 0.11 0.06
Matches are distributed among these distances:
49 35 0.48
50 9 0.12
51 21 0.29
52 8 0.11
ACGTcount: A:0.36, C:0.01, G:0.20, T:0.43
Consensus pattern (49 bp):
TAAGTTAAGAAGTTATGTAAGATATGTGAGTTATGATATGATATATATA
Found at i:20464082 original size:38 final size:38
Alignment explanation
Indices: 20464040--20464114 Score: 132
Period size: 38 Copynumber: 2.0 Consensus size: 38
20464030 TTGTTTTGTA
*
20464040 AGTTATGGTATGATATATATAAATTATTAAGTTATGTG
1 AGTTATGATATGATATATATAAATTATTAAGTTATGTG
*
20464078 AGTTATGATATGATATATATAAGTTATTAAGTTATGT
1 AGTTATGATATGATATATATAAATTATTAAGTTATGT
20464115 ATGTATGTGA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
38 35 1.00
ACGTcount: A:0.37, C:0.00, G:0.17, T:0.45
Consensus pattern (38 bp):
AGTTATGATATGATATATATAAATTATTAAGTTATGTG
Found at i:20464249 original size:9 final size:9
Alignment explanation
Indices: 20464235--20464320 Score: 75
Period size: 9 Copynumber: 9.3 Consensus size: 9
20464225 TCTTTAAAGG
*
20464235 TATGTAAAT
1 TATGTAAGT
20464244 TATGTAAGT
1 TATGTAAGT
*
20464253 TATGATATGAT
1 TATG-TAAG-T
20464264 TAT-TAAGT
1 TATGTAAGT
20464272 TATGTAAGT
1 TATGTAAGT
*
20464281 TATGTGAGT
1 TATGTAAGT
*
20464290 TAATGTAAAT
1 T-ATGTAAGT
*
20464300 TATATAAGT
1 TATGTAAGT
* *
20464309 TACGTAAAT
1 TATGTAAGT
20464318 TAT
1 TAT
20464321 ATATTCATTT
Statistics
Matches: 61, Mismatches: 12, Indels: 8
0.75 0.15 0.10
Matches are distributed among these distances:
8 4 0.07
9 43 0.70
10 10 0.16
11 4 0.07
ACGTcount: A:0.38, C:0.01, G:0.16, T:0.44
Consensus pattern (9 bp):
TATGTAAGT
Found at i:20464276 original size:37 final size:37
Alignment explanation
Indices: 20464235--20464320 Score: 104
Period size: 37 Copynumber: 2.3 Consensus size: 37
20464225 TCTTTAAAGG
*
20464235 TATGTAAATTATGTAAGTT-ATGATATGATTAT-TAAGT
1 TATGTAAATTATGTAAGTTAATG-TA-AATTATATAAGT
* *
20464272 TATGTAAGTTATGTGAGTTAATGTAAATTATATAAGT
1 TATGTAAATTATGTAAGTTAATGTAAATTATATAAGT
*
20464309 TACGTAAATTAT
1 TATGTAAATTAT
20464321 ATATTCATTT
Statistics
Matches: 42, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
36 5 0.12
37 34 0.81
38 3 0.07
ACGTcount: A:0.38, C:0.01, G:0.16, T:0.44
Consensus pattern (37 bp):
TATGTAAATTATGTAAGTTAATGTAAATTATATAAGT
Found at i:20464302 original size:28 final size:29
Alignment explanation
Indices: 20464235--20464310 Score: 88
Period size: 28 Copynumber: 2.7 Consensus size: 29
20464225 TCTTTAAAGG
20464235 TATGTAAATTATGTAAGTTATGATATGAT
1 TATGTAAATTATGTAAGTTATGATATGAT
*
20464264 TAT-TAAGTTATGTAAGTTATG---TGAGT
1 TATGTAAATTATGTAAGTTATGATATGA-T
*
20464290 TAATGTAAATTATATAAGTTA
1 T-ATGTAAATTATGTAAGTTA
20464311 CGTAAATTAT
Statistics
Matches: 41, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
25 3 0.07
26 2 0.05
27 2 0.05
28 31 0.76
29 3 0.07
ACGTcount: A:0.38, C:0.00, G:0.17, T:0.45
Consensus pattern (29 bp):
TATGTAAATTATGTAAGTTATGATATGAT
Found at i:20464461 original size:20 final size:20
Alignment explanation
Indices: 20464436--20464476 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
20464426 TTGAGTAAAC
20464436 TCAATTTTGCTTTCCTTGTA
1 TCAATTTTGCTTTCCTTGTA
20464456 TCAATTTTGCTTTCCTTGTA
1 TCAATTTTGCTTTCCTTGTA
20464476 T
1 T
20464477 TAGTGGGGGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.15, C:0.20, G:0.10, T:0.56
Consensus pattern (20 bp):
TCAATTTTGCTTTCCTTGTA
Found at i:20464661 original size:75 final size:74
Alignment explanation
Indices: 20464532--20464725 Score: 295
Period size: 75 Copynumber: 2.6 Consensus size: 74
20464522 CAAAATAAGT
*
20464532 AAAATATA-TAAAATT-AAAAAAA-AAGACATTGAGTTGGCATTACAAGATACAATTAATTTGTC
1 AAAATA-AGTAAAATTAAAAAAAATAAGACTTTGAGTTGGCATTACAAGATACAATTAATTTGTC
*
20464594 TATATTTATC
65 TATATTGATC
* * * *
20464604 AAAATAAGTTAAATTAAAAAAAAATAAGCCTTTGAGTTGGCATTACAATATATAATTAATTTGTC
1 AAAATAAGTAAAATT-AAAAAAAATAAGACTTTGAGTTGGCATTACAAGATACAATTAATTTGTC
20464669 TATATTGATC
65 TATATTGATC
20464679 AAAATAAGTAAAATTAAAAAAAATAAGACTTTGAGTTGGCATTACAA
1 AAAATAAGTAAAATTAAAAAAAATAAGACTTTGAGTTGGCATTACAA
20464726 AATAAATATA
Statistics
Matches: 110, Mismatches: 8, Indels: 6
0.89 0.06 0.05
Matches are distributed among these distances:
71 1 0.01
72 12 0.11
74 38 0.35
75 59 0.54
ACGTcount: A:0.49, C:0.08, G:0.11, T:0.32
Consensus pattern (74 bp):
AAAATAAGTAAAATTAAAAAAAATAAGACTTTGAGTTGGCATTACAAGATACAATTAATTTGTCT
ATATTGATC
Found at i:20464955 original size:66 final size:65
Alignment explanation
Indices: 20464858--20465008 Score: 203
Period size: 66 Copynumber: 2.3 Consensus size: 65
20464848 TATAAAATCG
* ** * * * *
20464858 ATAATTTATTAAATTACATAAAAAATTGATAATTTATTGACATAAAATCAAATAAACTAATCAAA
1 ATAATTTATTCAATTA-ATCGATAATCGATAATTTATTCACATAAAACCAAATAAACTAATCAAA
20464923 C
65 C
* *
20464924 ATAATTTATTCAATTTAATCGATAATCGATAATTTATTCACATTAAACCGAATAAACTAATCAAA
1 ATAATTTATTCAA-TTAATCGATAATCGATAATTTATTCACATAAAACCAAATAAACTAATCAAA
20464989 C
65 C
20464990 ATAATTTATTCAATTAATC
1 ATAATTTATTCAATTAATC
20465009 AAATATATAA
Statistics
Matches: 75, Mismatches: 9, Indels: 3
0.86 0.10 0.03
Matches are distributed among these distances:
65 6 0.08
66 66 0.88
67 3 0.04
ACGTcount: A:0.49, C:0.12, G:0.03, T:0.36
Consensus pattern (65 bp):
ATAATTTATTCAATTAATCGATAATCGATAATTTATTCACATAAAACCAAATAAACTAATCAAAC
Found at i:20467496 original size:29 final size:28
Alignment explanation
Indices: 20467454--20467553 Score: 98
Period size: 29 Copynumber: 3.5 Consensus size: 28
20467444 CTAATTAATC
*
20467454 TAAATCTTAAACCCCTAACCCCTATCCCT
1 TAAACCTTAAA-CCCTAACCCCTATCCCT
20467483 TAAACCTTAAACCCTAAGCCCCTAAAT-CC-
1 TAAACCTTAAACCCTAA-CCCCT--ATCCCT
* *
20467512 TAAACCTTAAACCTTAAACCCC-AACCCT
1 TAAACCTTAAACCCT-AACCCCTATCCCT
*
20467540 TAAACCCTAAACCC
1 TAAACCTTAAACCC
20467554 ATAATCCATA
Statistics
Matches: 60, Mismatches: 5, Indels: 13
0.77 0.06 0.17
Matches are distributed among these distances:
26 1 0.02
27 2 0.03
28 18 0.30
29 33 0.55
30 4 0.07
31 2 0.03
ACGTcount: A:0.37, C:0.40, G:0.01, T:0.22
Consensus pattern (28 bp):
TAAACCTTAAACCCTAACCCCTATCCCT
Found at i:20467522 original size:7 final size:7
Alignment explanation
Indices: 20467480--20467658 Score: 78
Period size: 7 Copynumber: 25.1 Consensus size: 7
20467470 AACCCCTATC
20467480 CCTTAAA
1 CCTTAAA
20467487 CCTTAAA
1 CCTTAAA
* *
20467494 CCCTAAGC
1 CCTTAA-A
*
20467502 CCCTAAA
1 CCTTAAA
20467509 TCC-TAAA
1 -CCTTAAA
20467516 CCTTAAA
1 CCTTAAA
20467523 CCTTAAA
1 CCTTAAA
** *
20467530 CCCCAAC
1 CCTTAAA
20467537 CCTTAAA
1 CCTTAAA
*
20467544 CCCTAAA
1 CCTTAAA
* *
20467551 CCCATAAT
1 -CCTTAAA
*
20467559 CCATAAA
1 CCTTAAA
20467566 CCTTAAA
1 CCTTAAA
*
20467573 --ATAGTAA
1 CCTTA--AA
*
20467580 CTCCTAAA
1 C-CTTAAA
20467588 CCTTAAA
1 CCTTAAA
*
20467595 CCATAAA
1 CCTTAAA
* *
20467602 CCATAAT
1 CCTTAAA
*
20467609 CCCTAAA
1 CCTTAAA
*
20467616 TCTTAAA
1 CCTTAAA
20467623 CCTTAAAA
1 CCTT-AAA
20467631 CC-TAAA
1 CCTTAAA
* *
20467637 CCATATA
1 CCTTAAA
*
20467644 CCCTAAA
1 CCTTAAA
*
20467651 CCATAAA
1 CCTTAAA
20467658 C
1 C
20467659 TCTAAACTAT
Statistics
Matches: 133, Mismatches: 28, Indels: 22
0.73 0.15 0.12
Matches are distributed among these distances:
5 2 0.02
6 7 0.05
7 101 0.76
8 21 0.16
10 2 0.02
ACGTcount: A:0.44, C:0.33, G:0.01, T:0.22
Consensus pattern (7 bp):
CCTTAAA
Found at i:20467529 original size:14 final size:14
Alignment explanation
Indices: 20467480--20467665 Score: 90
Period size: 14 Copynumber: 13.1 Consensus size: 14
20467470 AACCCCTATC
*
20467480 CCTTAAACCTTAAA
1 CCTTAAACCCTAAA
* *
20467494 CCCTAAGCCCCTAAA
1 CCTTAA-ACCCTAAA
*
20467509 TCC-TAAACCTTAAA
1 -CCTTAAACCCTAAA
* *
20467523 CCTTAAACCCCAAC
1 CCTTAAACCCTAAA
20467537 CCTTAAACCCTAAA
1 CCTTAAACCCTAAA
* * *
20467551 CCCATAATCCATAAA
1 -CCTTAAACCCTAAA
*
20467566 CCTTAAA--ATAGTAA
1 CCTTAAACCCTA--AA
* *
20467580 CTCCTAAACCTTAAA
1 C-CTTAAACCCTAAA
* * *
20467595 CCATAAACCATAAT
1 CCTTAAACCCTAAA
* * *
20467609 CCCTAAATCTTAAA
1 CCTTAAACCCTAAA
*
20467623 CCTTAAAACCTAAA
1 CCTTAAACCCTAAA
* *
20467637 CCATATACCCTAAA
1 CCTTAAACCCTAAA
* *
20467651 CCATAAACTCTAAA
1 CCTTAAACCCTAAA
20467665 C
1 C
20467666 TATAATAATA
Statistics
Matches: 131, Mismatches: 32, Indels: 18
0.72 0.18 0.10
Matches are distributed among these distances:
12 3 0.02
13 2 0.02
14 94 0.72
15 28 0.21
16 2 0.02
17 2 0.02
ACGTcount: A:0.44, C:0.33, G:0.01, T:0.23
Consensus pattern (14 bp):
CCTTAAACCCTAAA
Found at i:20467572 original size:22 final size:21
Alignment explanation
Indices: 20467519--20467607 Score: 72
Period size: 22 Copynumber: 4.1 Consensus size: 21
20467509 TCCTAAACCT
** * *
20467519 TAAACCTTAAACCCCAACCCT
1 TAAACCTTAAACCATAATCCA
*
20467540 TAAACCCTAAACCCATAATCCA
1 TAAACCTTAAA-CCATAATCCA
**
20467562 TAAACCTTAAAATAGTAACTCC-
1 TAAACCTTAAACCA-TAA-TCCA
*
20467584 TAAACCTTAAACCATAAACCA
1 TAAACCTTAAACCATAATCCA
20467605 TAA
1 TAA
20467608 TCCCTAAATC
Statistics
Matches: 53, Mismatches: 11, Indels: 8
0.74 0.15 0.11
Matches are distributed among these distances:
20 2 0.04
21 17 0.32
22 31 0.58
23 3 0.06
ACGTcount: A:0.46, C:0.31, G:0.01, T:0.21
Consensus pattern (21 bp):
TAAACCTTAAACCATAATCCA
Found at i:20467658 original size:35 final size:35
Alignment explanation
Indices: 20467480--20467658 Score: 100
Period size: 36 Copynumber: 5.0 Consensus size: 35
20467470 AACCCCTATC
* * *
20467480 CCTTAAACCTTAAACCCTAAGCCCCTAAATCC-TAAA
1 CCTTAAACCATAAACCATAA-TCCCTAAA-CCATAAA
* ** *
20467516 CCTTAAACCTTAAACCCCAA-CCCTTAAACCCTAAA
1 CCTTAAACCATAAACCATAATCCC-TAAACCATAAA
* * * ** *
20467551 CCCATAATCCATAAACCTTAA--AATAGTAACTCCTAAA
1 -CCTTAAACCATAAACCATAATCCCTA--AAC-CATAAA
* *
20467588 CCTTAAACCATAAACCATAATCCCTAAATCTTAAA
1 CCTTAAACCATAAACCATAATCCCTAAACCATAAA
20467623 CCTTAAAACC-TAAACCAT-ATACCCTAAACCATAAA
1 CCTT-AAACCATAAACCATAAT-CCCTAAACCATAAA
20467658 C
1 C
20467659 TCTAAACTAT
Statistics
Matches: 116, Mismatches: 17, Indels: 21
0.75 0.11 0.14
Matches are distributed among these distances:
34 9 0.08
35 38 0.33
36 61 0.53
37 6 0.05
38 2 0.02
ACGTcount: A:0.44, C:0.33, G:0.01, T:0.22
Consensus pattern (35 bp):
CCTTAAACCATAAACCATAATCCCTAAACCATAAA
Found at i:20468141 original size:111 final size:113
Alignment explanation
Indices: 20467963--20468263 Score: 464
Period size: 114 Copynumber: 2.7 Consensus size: 113
20467953 GTTTTTAATT
* * * *
20467963 TTTTTTGCGGCGTTTTTCAAA-AGCGTCGCTAATGCTCGACATATAGCGACATTTTTCAAAAAAG
1 TTTTTTGCGGCGTTTTTCAAAGAGCGCCGCTAATGCTCGACCTATAGCGGCATTTTTC-AACAAG
*
20468027 CGCCGCTAATGCCACTAAAGCTCAACAT-AAA-ACGGCGTTGTGCTTAA
65 CGCCGCTAATGCCACTAAAGCTCAACATAAAACACGGCATTGTGCTTAA
* * *
20468074 TTTTTTGCGGCGTGTTTCAAAGAGCGCCACTAATGCTCGACCTATAGCGGCGTTTTTCAACAAGC
1 TTTTTTGCGGCGTTTTTCAAAGAGCGCCGCTAATGCTCGACCTATAGCGGCATTTTTCAACAAGC
*
20468139 GCCGCTAATTCCACTAAAGCTCAACATAAAACGACGGCATTGTGCTTAA
66 GCCGCTAATGCCACTAAAGCTCAACATAAAAC-ACGGCATTGTGCTTAA
* *
20468188 ATTTTTGCGGCGTTTTTCAAAGAGCGCCGCTAATGCTCGACCTATAGTGGCATTTTTCAACAAGC
1 TTTTTTGCGGCGTTTTTCAAAGAGCGCCGCTAATGCTCGACCTATAGCGGCATTTTTCAACAAGC
20468253 GCCGCTAATGC
66 GCCGCTAATGC
20468264 ACGACATATT
Statistics
Matches: 171, Mismatches: 15, Indels: 5
0.90 0.08 0.03
Matches are distributed among these distances:
111 52 0.30
112 34 0.20
114 85 0.50
ACGTcount: A:0.27, C:0.24, G:0.20, T:0.29
Consensus pattern (113 bp):
TTTTTTGCGGCGTTTTTCAAAGAGCGCCGCTAATGCTCGACCTATAGCGGCATTTTTCAACAAGC
GCCGCTAATGCCACTAAAGCTCAACATAAAACACGGCATTGTGCTTAA
Found at i:20468255 original size:40 final size:40
Alignment explanation
Indices: 20468194--20468301 Score: 128
Period size: 40 Copynumber: 2.7 Consensus size: 40
20468184 TTAAATTTTT
* * *
20468194 GCGGCGTTTTTCAA-AGAGCGCCGCTAATGCTCGACCTATA
1 GCGGCATTTTTCAACA-AGCGCCGCTAATGCACGACATATA
* *
20468234 GTGGCATTTTTCAACAAGCGCCGCTAATGCACGACATATT
1 GCGGCATTTTTCAACAAGCGCCGCTAATGCACGACATATA
* * *
20468274 GCGGCGTTTTTCAACTATCGCCGCTAAT
1 GCGGCATTTTTCAACAAGCGCCGCTAAT
20468302 TCCCAATATA
Statistics
Matches: 58, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
40 57 0.98
41 1 0.02
ACGTcount: A:0.23, C:0.27, G:0.22, T:0.28
Consensus pattern (40 bp):
GCGGCATTTTTCAACAAGCGCCGCTAATGCACGACATATA
Found at i:20468415 original size:10 final size:10
Alignment explanation
Indices: 20468397--20468430 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
20468387 AAGTCATTAA
*
20468397 AATCCTAATT
1 AATCTTAATT
20468407 AATCTTAATT
1 AATCTTAATT
*
20468417 AAACTTAATT
1 AATCTTAATT
20468427 AATC
1 AATC
20468431 ATCTATGAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.44, C:0.15, G:0.00, T:0.41
Consensus pattern (10 bp):
AATCTTAATT
Found at i:20474549 original size:19 final size:19
Alignment explanation
Indices: 20474517--20474554 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
20474507 TATATACATT
20474517 TTTAGTTTTCAAA-TAAAA
1 TTTAGTTTTCAAATTAAAA
*
20474535 TTTAGTTTTTTAAATTAAAA
1 TTTAG-TTTTCAAATTAAAA
20474555 AATTAGAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 5 0.29
19 7 0.41
20 5 0.29
ACGTcount: A:0.42, C:0.03, G:0.05, T:0.50
Consensus pattern (19 bp):
TTTAGTTTTCAAATTAAAA
Found at i:20475273 original size:12 final size:12
Alignment explanation
Indices: 20475256--20475282 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
20475246 ATAGACTTCC
20475256 ATTGACTAAAAT
1 ATTGACTAAAAT
20475268 ATTGACTAAAAT
1 ATTGACTAAAAT
20475280 ATT
1 ATT
20475283 AATTTTTTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.48, C:0.07, G:0.07, T:0.37
Consensus pattern (12 bp):
ATTGACTAAAAT
Found at i:20479794 original size:43 final size:43
Alignment explanation
Indices: 20479733--20479820 Score: 176
Period size: 43 Copynumber: 2.0 Consensus size: 43
20479723 CAGTAACAAA
20479733 CAAAGGCGCGAGTGATATATTGATATCCATTTGGTATGCAGTT
1 CAAAGGCGCGAGTGATATATTGATATCCATTTGGTATGCAGTT
20479776 CAAAGGCGCGAGTGATATATTGATATCCATTTGGTATGCAGTT
1 CAAAGGCGCGAGTGATATATTGATATCCATTTGGTATGCAGTT
20479819 CA
1 CA
20479821 GCGAGTGAAC
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 45 1.00
ACGTcount: A:0.28, C:0.15, G:0.25, T:0.32
Consensus pattern (43 bp):
CAAAGGCGCGAGTGATATATTGATATCCATTTGGTATGCAGTT
Found at i:20482584 original size:74 final size:74
Alignment explanation
Indices: 20482494--20482640 Score: 260
Period size: 74 Copynumber: 2.0 Consensus size: 74
20482484 TCTTCCTATC
20482494 AATAGATCACACGGTAGAGTTATTTATACAAATTTAAATATATAAATTTCATTTATTGTTATTCT
1 AATAGATCACACGGTAGAGTTATTTATACAAATTTAAATATATAAATTTCATTTATTGTTATTCT
20482559 ACTTAAAGG
66 ACTTAAAGG
* *
20482568 AATAGA-CGACACGGTAGAGTTATTTATACAAATTTGAATATATAAGTTTCATTTATTGTTATTC
1 AATAGATC-ACACGGTAGAGTTATTTATACAAATTTAAATATATAAATTTCATTTATTGTTATTC
20482632 TACTTAAAG
65 TACTTAAAG
20482641 TAGTAAAAAT
Statistics
Matches: 70, Mismatches: 2, Indels: 2
0.95 0.03 0.03
Matches are distributed among these distances:
73 1 0.01
74 69 0.99
ACGTcount: A:0.38, C:0.10, G:0.12, T:0.40
Consensus pattern (74 bp):
AATAGATCACACGGTAGAGTTATTTATACAAATTTAAATATATAAATTTCATTTATTGTTATTCT
ACTTAAAGG
Found at i:20483978 original size:13 final size:14
Alignment explanation
Indices: 20483955--20483983 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
20483945 AAGATACACC
20483955 AAGATAATAAAAAA
1 AAGATAATAAAAAA
20483969 AAGA-AATAAAAAA
1 AAGATAATAAAAAA
20483982 AA
1 AA
20483984 TCAATATGTC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.73
14 4 0.27
ACGTcount: A:0.83, C:0.00, G:0.07, T:0.10
Consensus pattern (14 bp):
AAGATAATAAAAAA
Found at i:20484049 original size:11 final size:11
Alignment explanation
Indices: 20484033--20484064 Score: 64
Period size: 11 Copynumber: 2.9 Consensus size: 11
20484023 ATACACGAAT
20484033 TCAAAATAGAC
1 TCAAAATAGAC
20484044 TCAAAATAGAC
1 TCAAAATAGAC
20484055 TCAAAATAGA
1 TCAAAATAGA
20484065 ATTAAAATAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.56, C:0.16, G:0.09, T:0.19
Consensus pattern (11 bp):
TCAAAATAGAC
Found at i:20484071 original size:11 final size:11
Alignment explanation
Indices: 20484033--20484073 Score: 55
Period size: 11 Copynumber: 3.7 Consensus size: 11
20484023 ATACACGAAT
*
20484033 TCAAAATAGAC
1 TCAAAATAGAA
*
20484044 TCAAAATAGAC
1 TCAAAATAGAA
20484055 TCAAAATAGAA
1 TCAAAATAGAA
*
20484066 TTAAAATA
1 TCAAAATA
20484074 ACCATTGAGT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
11 28 1.00
ACGTcount: A:0.59, C:0.12, G:0.07, T:0.22
Consensus pattern (11 bp):
TCAAAATAGAA
Found at i:20485480 original size:15 final size:15
Alignment explanation
Indices: 20485460--20485490 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
20485450 GATCCCCAAT
20485460 ACTTCAATCTGCCCC
1 ACTTCAATCTGCCCC
*
20485475 ACTTCAGTCTGCCCC
1 ACTTCAATCTGCCCC
20485490 A
1 A
20485491 TTGCAATTTT
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:0.19, C:0.45, G:0.10, T:0.26
Consensus pattern (15 bp):
ACTTCAATCTGCCCC
Found at i:20485851 original size:217 final size:217
Alignment explanation
Indices: 20485476--20485988 Score: 792
Period size: 217 Copynumber: 2.4 Consensus size: 217
20485466 ATCTGCCCCA
* * *
20485476 CTTCAGTCTGCCCCATTGCAATTTTAGGAGGATAAGATCTGCTTTCTCAGTCTGCTCCGCTGTAA
1 CTTCAGTCTGCCCCATTGCAACTTTAGGAGGATAAAACCTGCTTTCTCAGTCTGCTCCGCTGTAA
* *
20485541 CTTCAGGGAGATAAGACTAGATACGATTTGCTCTCTGCAACTTCAAAGAGATAAGATCTGTCATT
66 CTTCAAGGAGATAAGACTAGATACGATCTGCTCTCTGCAACTTCAAAGAGATAAGATCTGTCATT
* *
20485606 TTAATCCGCTTCATTGCAACTTCAGGGAGATAGGATTATTGGCTTTAATCTGCTCCACTGCAACT
131 TTAATCCACTTCACTGCAACTTCAGGGAGATAGGATTATTGGCTTTAATCTGCTCCACTGCAACT
20485671 TCAGGGAGATAAGATTCACCAT
196 TCAGGGAGATAAGATTCACCAT
* *
20485693 CTTCAGTCTGCCCCACTGCAACTTTAGGAGGATAAAACCTGCTTTCTCAGTCTGCTCCGTTGTAA
1 CTTCAGTCTGCCCCATTGCAACTTTAGGAGGATAAAACCTGCTTTCTCAGTCTGCTCCGCTGTAA
* *
20485758 CTTCAATGAGATAAGACTAGATACGATCTGCTCTCTGCAACTTCAGAGAGATAAGATCTGTCATT
66 CTTCAAGGAGATAAGACTAGATACGATCTGCTCTCTGCAACTTCAAAGAGATAAGATCTGTCATT
** *
20485823 TTAATCCACTTTGCTGTAACTTCAGGGAGATAGGATTATTGGCTTTAATCTGCTCCACTGCAACT
131 TTAATCCACTTCACTGCAACTTCAGGGAGATAGGATTATTGGCTTTAATCTGCTCCACTGCAACT
*
20485888 TCAGGGAGATAAGATTCGCCAT
196 TCAGGGAGATAAGATTCACCAT
* * * * * * * * *
20485910 CTTCAGTCTGCCCCATTGCAACTTCAGGGGGATAAGACTTGCTATCTTCAATCCGCTCCACTATA
1 CTTCAGTCTGCCCCATTGCAACTTTAGGAGGATAAAACCTGCTTTC-TCAGTCTGCTCCGCTGTA
*
20485975 ACTTCAGGGAGATA
65 ACTTCAAGGAGATA
20485989 GAATTTGTGA
Statistics
Matches: 267, Mismatches: 28, Indels: 1
0.90 0.09 0.00
Matches are distributed among these distances:
217 242 0.91
218 25 0.09
ACGTcount: A:0.27, C:0.23, G:0.19, T:0.31
Consensus pattern (217 bp):
CTTCAGTCTGCCCCATTGCAACTTTAGGAGGATAAAACCTGCTTTCTCAGTCTGCTCCGCTGTAA
CTTCAAGGAGATAAGACTAGATACGATCTGCTCTCTGCAACTTCAAAGAGATAAGATCTGTCATT
TTAATCCACTTCACTGCAACTTCAGGGAGATAGGATTATTGGCTTTAATCTGCTCCACTGCAACT
TCAGGGAGATAAGATTCACCAT
Found at i:20485935 original size:45 final size:45
Alignment explanation
Indices: 20485526--20485988 Score: 182
Period size: 44 Copynumber: 10.6 Consensus size: 45
20485516 GCTTTCTCAG
* * * * *
20485526 TCTGCTCCGCTGTAACTTCAGGGAGATAAGACTAG--A--TACGA
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGACTTGCCATCTTCAA
* * ** * *
20485567 TTTGCT-CTCTGCAACTTCAAAGAGATAAGA-TCTGTCAT-TTTAA
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGACT-TGCCATCTTCAA
* * * * * *
20485610 TCCGCTTCATTGCAACTTCAGGGAGATAGGATTATTGGC-T-TT-AA
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGA--CTTGCCATCTTCAA
* *
20485654 TCTGCTCCACTGCAACTTCAGGGAGATAAGA-TTCACCATCTTCAG
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGACTT-GCCATCTTCAA
* * * * ** *
20485699 TCTGCCCCACTGCAACTTTA-GGAGGATAAAACCTGCTTTC-TCAG
1 TCTGCTCCACTGCAACTTCAGGGA-GATAAGACTTGCCATCTTCAA
** * ** * * *
20485743 TCTGCTCCGTTGTAACTTCAATGAGATAAGACTAG--A--TACGA
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGACTTGCCATCTTCAA
* * * *
20485784 TCTGCT-CTCTGCAACTTCAGAGAGATAAGA-TCTGTCAT-TTTAA
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGACT-TGCCATCTTCAA
** *** * * * *
20485827 TCCACTTTGCTGTAACTTCAGGGAGATAGGATTATTGGC-T-TT-AA
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGA--CTTGCCATCTTCAA
*
20485871 TCTGCTCCACTGCAACTTCAGGGAGATAAGA-TTCGCCATCTTCAG
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGACTT-GCCATCTTCAA
* * * *
20485916 TCTGCCCCATTGCAACTTCAGGGGGATAAGACTTGCTATCTTCAA
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGACTTGCCATCTTCAA
* **
20485961 TCCGCTCCACTATAACTTCAGGGAGATA
1 TCTGCTCCACTGCAACTTCAGGGAGATA
20485989 GAATTTGTGA
Statistics
Matches: 312, Mismatches: 81, Indels: 54
0.70 0.18 0.12
Matches are distributed among these distances:
39 2 0.01
40 41 0.13
41 16 0.05
42 5 0.02
43 14 0.04
44 127 0.41
45 96 0.31
46 9 0.03
47 2 0.01
ACGTcount: A:0.27, C:0.23, G:0.19, T:0.30
Consensus pattern (45 bp):
TCTGCTCCACTGCAACTTCAGGGAGATAAGACTTGCCATCTTCAA
Found at i:20494388 original size:3 final size:3
Alignment explanation
Indices: 20494380--20494440 Score: 50
Period size: 3 Copynumber: 20.3 Consensus size: 3
20494370 AACTAATACA
* * * * * * *
20494380 AAT AAT AAT ACT AAT AAT TAT AGT AAC ATT AAT AAT AAT AAT AAC AAC
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
*
20494428 AAT AAT AAA AAT A
1 AAT AAT AAT AAT A
20494441 GTTAAGTAAT
Statistics
Matches: 44, Mismatches: 14, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
3 44 1.00
ACGTcount: A:0.62, C:0.07, G:0.02, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:20494412 original size:18 final size:18
Alignment explanation
Indices: 20494380--20494440 Score: 59
Period size: 18 Copynumber: 3.4 Consensus size: 18
20494370 AACTAATACA
* *
20494380 AATAATAATACTAATAAT
1 AATAATAACATTAATAAT
* *
20494398 TATAGTAACATTAATAAT
1 AATAATAACATTAATAAT
**
20494416 AATAATAACAACAATAAT
1 AATAATAACATTAATAAT
*
20494434 AAAAATA
1 AATAATA
20494441 GTTAAGTAAT
Statistics
Matches: 34, Mismatches: 9, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
18 34 1.00
ACGTcount: A:0.62, C:0.07, G:0.02, T:0.30
Consensus pattern (18 bp):
AATAATAACATTAATAAT
Found at i:20498065 original size:32 final size:32
Alignment explanation
Indices: 20498024--20498087 Score: 119
Period size: 32 Copynumber: 2.0 Consensus size: 32
20498014 AGCCTCTTGG
*
20498024 AATTTTCTTTCCCACCTATTGGCTTTGCTTCT
1 AATTTTCTTTCCCACCTATCGGCTTTGCTTCT
20498056 AATTTTCTTTCCCACCTATCGGCTTTGCTTCT
1 AATTTTCTTTCCCACCTATCGGCTTTGCTTCT
20498088 TTCTTCTTAG
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.12, C:0.30, G:0.09, T:0.48
Consensus pattern (32 bp):
AATTTTCTTTCCCACCTATCGGCTTTGCTTCT
Found at i:20501530 original size:36 final size:34
Alignment explanation
Indices: 20501494--20501564 Score: 110
Period size: 36 Copynumber: 2.1 Consensus size: 34
20501484 TGTATATAAG
20501494 TAAG-TTTTTTT-AAAAAGAAATAAATTACATAT
1 TAAGTTTTTTTTAAAAAAGAAATAAATTACATAT
20501526 TAAGTTTTTTTTAAAAAAAAGAAATAAATTACATAT
1 TAAGTTTTTTTT--AAAAAAGAAATAAATTACATAT
20501562 TAA
1 TAA
20501565 TAAAATTGGT
Statistics
Matches: 35, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
32 4 0.11
33 7 0.20
36 24 0.69
ACGTcount: A:0.52, C:0.03, G:0.06, T:0.39
Consensus pattern (34 bp):
TAAGTTTTTTTTAAAAAAGAAATAAATTACATAT
Found at i:20506342 original size:40 final size:41
Alignment explanation
Indices: 20506280--20506375 Score: 117
Period size: 39 Copynumber: 2.4 Consensus size: 41
20506270 CGATTTAACT
* * *
20506280 GATGAGACACTGG-GAATTAATTTACTACTTCAGATTTATTC
1 GATGAGACACTGGTGAATCAATTTAATACTTC-GAATTATTC
20506321 GATGAGACACTGGTG-A-CAATTTAATACTTCGAATTATTC
1 GATGAGACACTGGTGAATCAATTTAATACTTCGAATTATTC
*
20506360 GATGAGGCACTAGGTG
1 GATGAGACACT-GGTG
20506376 CCAAACTGGT
Statistics
Matches: 49, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
39 18 0.37
40 16 0.33
41 14 0.29
42 1 0.02
ACGTcount: A:0.31, C:0.15, G:0.22, T:0.32
Consensus pattern (41 bp):
GATGAGACACTGGTGAATCAATTTAATACTTCGAATTATTC
Found at i:20506759 original size:17 final size:18
Alignment explanation
Indices: 20506729--20506763 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
20506719 AAATGTTGTT
20506729 TTAAATATTCAATTGTGC
1 TTAAATATTCAATTGTGC
*
20506747 TTAAA-ATTTAATTGTGC
1 TTAAATATTCAATTGTGC
20506764 CTATTATACT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 11 0.69
18 5 0.31
ACGTcount: A:0.34, C:0.09, G:0.11, T:0.46
Consensus pattern (18 bp):
TTAAATATTCAATTGTGC
Found at i:20512086 original size:17 final size:18
Alignment explanation
Indices: 20512054--20512088 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
20512044 AAATGTGGTT
20512054 TTAAATATTCAATTGTGC
1 TTAAATATTCAATTGTGC
*
20512072 TTAAA-ATTTAATTGTGC
1 TTAAATATTCAATTGTGC
20512089 CTATTATATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 11 0.69
18 5 0.31
ACGTcount: A:0.34, C:0.09, G:0.11, T:0.46
Consensus pattern (18 bp):
TTAAATATTCAATTGTGC
Found at i:20513177 original size:17 final size:18
Alignment explanation
Indices: 20513149--20513183 Score: 63
Period size: 17 Copynumber: 2.0 Consensus size: 18
20513139 AAATGTGGTT
20513149 TTAAATATTTAATTGTGC
1 TTAAATATTTAATTGTGC
20513167 TTAAA-ATTTAATTGTGC
1 TTAAATATTTAATTGTGC
20513184 CTATTAAATT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 12 0.71
18 5 0.29
ACGTcount: A:0.34, C:0.06, G:0.11, T:0.49
Consensus pattern (18 bp):
TTAAATATTTAATTGTGC
Found at i:20526068 original size:17 final size:18
Alignment explanation
Indices: 20526038--20526072 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
20526028 AAATGTTGTT
20526038 TTAAATATTCAATTGTGC
1 TTAAATATTCAATTGTGC
*
20526056 TTAAA-ATTTAATTGTGC
1 TTAAATATTCAATTGTGC
20526073 CTATTATATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 11 0.69
18 5 0.31
ACGTcount: A:0.34, C:0.09, G:0.11, T:0.46
Consensus pattern (18 bp):
TTAAATATTCAATTGTGC
Found at i:20529537 original size:14 final size:15
Alignment explanation
Indices: 20529514--20529554 Score: 50
Period size: 14 Copynumber: 2.8 Consensus size: 15
20529504 TCAACCTTTA
20529514 TTTTAATTTTAT-AT
1 TTTTAATTTTATCAT
*
20529528 TTTTAGTTTTATCA-
1 TTTTAATTTTATCAT
20529542 TTTTAATGTTTAT
1 TTTTAAT-TTTAT
20529555 GAAGATATAT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
14 17 0.74
15 6 0.26
ACGTcount: A:0.24, C:0.02, G:0.05, T:0.68
Consensus pattern (15 bp):
TTTTAATTTTATCAT
Found at i:20529742 original size:35 final size:35
Alignment explanation
Indices: 20529610--20529742 Score: 131
Period size: 35 Copynumber: 3.8 Consensus size: 35
20529600 TTTAAATGAG
* * * * *
20529610 TATATCCCAATCTTTTTAAGGTTGCCTTAAATATA
1 TATATCCCAACCTTTTTAAGGTTGTCTTAGACAAA
* * * * *
20529645 TTTATCCCAACCTTTTTGAGGTTGCCTTAGACTAG
1 TATATCCCAACCTTTTTAAGGTTGTCTTAGACAAA
* *
20529680 TATATCTCAACCTTTTTAGGGTTGTCTTAGACAAA
1 TATATCCCAACCTTTTTAAGGTTGTCTTAGACAAA
* * *
20529715 TCTATCCCAACCTTTTTAAAGTCGTCTT
1 TATATCCCAACCTTTTTAAGGTTGTCTT
20529743 TGACTTGGGC
Statistics
Matches: 78, Mismatches: 20, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
35 78 1.00
ACGTcount: A:0.26, C:0.21, G:0.12, T:0.41
Consensus pattern (35 bp):
TATATCCCAACCTTTTTAAGGTTGTCTTAGACAAA
Found at i:20531843 original size:6 final size:6
Alignment explanation
Indices: 20531832--20531860 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
20531822 TAATAAAACA
20531832 AATGGG AATGGG AATGGG AATGGG AATGG
1 AATGGG AATGGG AATGGG AATGGG AATGG
20531861 TAGTGGTTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.34, C:0.00, G:0.48, T:0.17
Consensus pattern (6 bp):
AATGGG
Found at i:20534246 original size:9 final size:9
Alignment explanation
Indices: 20534232--20534260 Score: 58
Period size: 9 Copynumber: 3.2 Consensus size: 9
20534222 AGCGATATAT
20534232 ATATATTAG
1 ATATATTAG
20534241 ATATATTAG
1 ATATATTAG
20534250 ATATATTAG
1 ATATATTAG
20534259 AT
1 AT
20534261 TAGCACACAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.45, C:0.00, G:0.10, T:0.45
Consensus pattern (9 bp):
ATATATTAG
Found at i:20534442 original size:29 final size:30
Alignment explanation
Indices: 20534376--20534442 Score: 86
Period size: 29 Copynumber: 2.3 Consensus size: 30
20534366 ATATATATTT
*
20534376 TTAT-ATTTTTATAATTTTTAAAGGTTAAA
1 TTATAATTTTTATAATTTTTAAAGGTCAAA
* *
20534405 TTA-ATTTTTTATCATTTTTAAA-GTCAAA
1 TTATAATTTTTATAATTTTTAAAGGTCAAA
20534433 TTATAATTTT
1 TTATAATTTT
20534443 AGCGTTAATA
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
28 8 0.25
29 24 0.75
ACGTcount: A:0.36, C:0.03, G:0.04, T:0.57
Consensus pattern (30 bp):
TTATAATTTTTATAATTTTTAAAGGTCAAA
Found at i:20538875 original size:5 final size:5
Alignment explanation
Indices: 20538865--20538916 Score: 104
Period size: 5 Copynumber: 10.4 Consensus size: 5
20538855 TAAATTTTAT
20538865 ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA
1 ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA
20538915 AT
1 AT
20538917 CAATGAATAA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 47 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (5 bp):
ATATA
Found at i:20540225 original size:34 final size:34
Alignment explanation
Indices: 20540187--20540252 Score: 105
Period size: 34 Copynumber: 1.9 Consensus size: 34
20540177 CTACGGTGCC
20540187 TTGGTGTGGTGTAATTATCGCTCTATTAAGCCTT
1 TTGGTGTGGTGTAATTATCGCTCTATTAAGCCTT
* * *
20540221 TTGGTGTGGTGTAGTTATCGCTTTATTGAGCC
1 TTGGTGTGGTGTAATTATCGCTCTATTAAGCC
20540253 ATTGGATGTG
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
34 29 1.00
ACGTcount: A:0.15, C:0.14, G:0.27, T:0.44
Consensus pattern (34 bp):
TTGGTGTGGTGTAATTATCGCTCTATTAAGCCTT
Found at i:20540263 original size:34 final size:34
Alignment explanation
Indices: 20540187--20540264 Score: 104
Period size: 34 Copynumber: 2.3 Consensus size: 34
20540177 CTACGGTGCC
*
20540187 TTGGTGTGGTGTAATTATCGCTCTATTAAGCCTT
1 TTGGTGTGGTGTAATTATCGCTCTATTAAGCCTA
* * *
20540221 TTGGTGTGGTGTAGTTATCGCTTTATTGAGCC-A
1 TTGGTGTGGTGTAATTATCGCTCTATTAAGCCTA
20540254 TTGGATGTGGT
1 TTGG-TGTGGT
20540265 CTATTGAGCT
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
33 4 0.10
34 35 0.90
ACGTcount: A:0.15, C:0.12, G:0.29, T:0.44
Consensus pattern (34 bp):
TTGGTGTGGTGTAATTATCGCTCTATTAAGCCTA
Found at i:20549671 original size:6 final size:6
Alignment explanation
Indices: 20549660--20549687 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
20549650 TTTTCATTAC
20549660 CAGTAT CAGTAT CAGTAT CAGTAT CAGT
1 CAGTAT CAGTAT CAGTAT CAGTAT CAGT
20549688 TTAGGCCTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Consensus pattern (6 bp):
CAGTAT
Found at i:20554773 original size:20 final size:21
Alignment explanation
Indices: 20554738--20554779 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
20554728 CCCCTTCAGT
* *
20554738 TTAAAAATTTTCATATTTTTC
1 TTAAAAATTCTCATATGTTTC
20554759 TTAAAAATTCT-ATATGTTTC
1 TTAAAAATTCTCATATGTTTC
20554779 T
1 T
20554780 GATTTAGTCC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 9 0.47
21 10 0.53
ACGTcount: A:0.33, C:0.10, G:0.02, T:0.55
Consensus pattern (21 bp):
TTAAAAATTCTCATATGTTTC
Found at i:20561425 original size:34 final size:34
Alignment explanation
Indices: 20561383--20561451 Score: 138
Period size: 34 Copynumber: 2.0 Consensus size: 34
20561373 ACATGGCTAT
20561383 ACACACTTTGATCATCAACCACTCATACATTTCC
1 ACACACTTTGATCATCAACCACTCATACATTTCC
20561417 ACACACTTTGATCATCAACCACTCATACATTTCC
1 ACACACTTTGATCATCAACCACTCATACATTTCC
20561451 A
1 A
20561452 TACTTCCATG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.33, C:0.35, G:0.03, T:0.29
Consensus pattern (34 bp):
ACACACTTTGATCATCAACCACTCATACATTTCC
Found at i:20565027 original size:26 final size:26
Alignment explanation
Indices: 20564951--20565019 Score: 102
Period size: 26 Copynumber: 2.7 Consensus size: 26
20564941 CCCAACAAAA
*
20564951 TTTTGACAATTTTACCCATGGTAAAG
1 TTTTGACGATTTTACCCATGGTAAAG
* * *
20564977 TTTTGATGATTTTACACGTGGTAAAG
1 TTTTGACGATTTTACCCATGGTAAAG
20565003 TTTTGACGATTTTACCC
1 TTTTGACGATTTTACCC
20565020 TTAGTAAAAT
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
26 37 1.00
ACGTcount: A:0.26, C:0.14, G:0.17, T:0.42
Consensus pattern (26 bp):
TTTTGACGATTTTACCCATGGTAAAG
Found at i:20574169 original size:15 final size:13
Alignment explanation
Indices: 20574138--20574163 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
20574128 CTACAGGGGG
20574138 CACATGGCCATGT
1 CACATGGCCATGT
20574151 CACATGGCCATGT
1 CACATGGCCATGT
20574164 GTCACAGAAG
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:0.23, C:0.31, G:0.23, T:0.23
Consensus pattern (13 bp):
CACATGGCCATGT
Found at i:20579590 original size:19 final size:20
Alignment explanation
Indices: 20579560--20579607 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 20
20579550 TTGCTGTTAT
*
20579560 TATTTCTTTATTTTTGTTTA
1 TATTTCTTTATTTTGGTTTA
*
20579580 TATTT-TTTATTTTGGTTTT
1 TATTTCTTTATTTTGGTTTA
*
20579599 TTTTTCTTT
1 TATTTCTTT
20579608 CAGTCATTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
19 16 0.67
20 8 0.33
ACGTcount: A:0.10, C:0.04, G:0.06, T:0.79
Consensus pattern (20 bp):
TATTTCTTTATTTTGGTTTA
Found at i:20579840 original size:3 final size:3
Alignment explanation
Indices: 20579832--20579879 Score: 53
Period size: 3 Copynumber: 16.0 Consensus size: 3
20579822 ACTGTTTCTC
* * *
20579832 ATT ATT ATT ATT ATT ATT ATT ATC ATT TTT GTT ATTT ATT -TT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A-TT ATT ATT ATT
20579877 ATT
1 ATT
20579880 TATTTCATTT
Statistics
Matches: 38, Mismatches: 5, Indels: 4
0.81 0.11 0.09
Matches are distributed among these distances:
2 2 0.05
3 33 0.87
4 3 0.08
ACGTcount: A:0.27, C:0.02, G:0.02, T:0.69
Consensus pattern (3 bp):
ATT
Found at i:20585456 original size:46 final size:46
Alignment explanation
Indices: 20585385--20585653 Score: 206
Period size: 49 Copynumber: 5.8 Consensus size: 46
20585375 CATATCAAAC
* * *
20585385 CTTATCTCCCTAAAGTTGCAGTGGAACAGGTTAAAAATAAAACAAT
1 CTTATCTCCCTGAAGTTGCAGTGGAACAGATTAAAAACAAAACAAT
* * * *
20585431 CTTATCTCCCTGAAGTTGCAATGGAACAGATTGAAGACAAGCTACATAT
1 CTTATCTCCCTGAAGTTGCAGTGGAACAGATTAAAAACAA--AACA-AT
**
20585480 CTTATCTCCCTGAAGTTGCAGT-GAAGCAGATTAAAGCCACAAAC---
1 CTTATCTCCCTGAAGTTGCAGTGGAA-CAGATTAAAAACA-AAACAAT
* * * * *
20585524 CTTATCTCCCTGAAATTGCAGTGGAATAGGTTAAAAATAAACCAAT
1 CTTATCTCCCTGAAGTTGCAGTGGAACAGATTAAAAACAAAACAAT
* * * * ** * *
20585570 CTTCTCTCCCTGAAGTTGTAGTGGAGCAAATTGAAGATGGGCTACA-AAT
1 CTTATCTCCCTGAAGTTGCAGTGGAACAGATT-AA-A--AACAAAACAAT
* *
20585619 CTTATCTCCCTGAAGTTACAGTGGAGCAGATTAAA
1 CTTATCTCCCTGAAGTTGCAGTGGAACAGATTAAA
20585654 GCCACAAACC
Statistics
Matches: 175, Mismatches: 35, Indels: 25
0.74 0.15 0.11
Matches are distributed among these distances:
43 3 0.02
44 29 0.17
45 3 0.02
46 59 0.34
47 3 0.02
48 11 0.06
49 65 0.37
50 2 0.01
ACGTcount: A:0.35, C:0.20, G:0.19, T:0.27
Consensus pattern (46 bp):
CTTATCTCCCTGAAGTTGCAGTGGAACAGATTAAAAACAAAACAAT
Found at i:20585493 original size:49 final size:48
Alignment explanation
Indices: 20585385--20585653 Score: 225
Period size: 46 Copynumber: 5.7 Consensus size: 48
20585375 CATATCAAAC
* * *
20585385 CTTATCTCCCTAAAGTTGCAGTGGAACAGGTTAAAAATAA--AACAAT
1 CTTATCTCCCTGAAGTTGCAGTGGAACAGATTAAAAATAAGCTACAAT
* * * *
20585431 CTTATCTCCCTGAAGTTGCAATGGAACAGATTGAAGACAAGCTACATAT
1 CTTATCTCCCTGAAGTTGCAGTGGAACAGATTAAAAATAAGCTACA-AT
* *
20585480 CTTATCTCCCTGAAGTTGCAGT-GAAGCAGATT----A-AAGCCACAAAC
1 CTTATCTCCCTGAAGTTGCAGTGGAA-CAGATTAAAAATAAGCTAC-AAT
* * * *
20585524 CTTATCTCCCTGAAATTGCAGTGGAATAGGTTAAAAATAAAC--CAAT
1 CTTATCTCCCTGAAGTTGCAGTGGAACAGATTAAAAATAAGCTACAAT
* * * * * * **
20585570 CTTCTCTCCCTGAAGTTGTAGTGGAGCAAATTGAAGATGGGCTACAAAT
1 CTTATCTCCCTGAAGTTGCAGTGGAACAGATTAAAAATAAGCTAC-AAT
* *
20585619 CTTATCTCCCTGAAGTTACAGTGGAGCAGATTAAA
1 CTTATCTCCCTGAAGTTGCAGTGGAACAGATTAAA
20585654 GCCACAAACC
Statistics
Matches: 177, Mismatches: 32, Indels: 25
0.76 0.14 0.11
Matches are distributed among these distances:
44 32 0.18
45 5 0.03
46 66 0.37
47 1 0.01
48 8 0.05
49 65 0.37
ACGTcount: A:0.35, C:0.20, G:0.19, T:0.27
Consensus pattern (48 bp):
CTTATCTCCCTGAAGTTGCAGTGGAACAGATTAAAAATAAGCTACAAT
Found at i:20585543 original size:44 final size:45
Alignment explanation
Indices: 20585380--20585786 Score: 195
Period size: 44 Copynumber: 8.9 Consensus size: 45
20585370 CAGATCATAT
* * ***
20585380 CAAACCTTATCTCCCTAAAGTTGCAGTGGAA-CAGGTTAAAAATAA
1 CAAACCTTATCTCCCTGAAGTTGCAGT-GAAGCAGATTAAAAGCCA
* * * *
20585425 AACAATCTTATCTCCCTGAAGTTGCAATGGAA-CAGATTGAAGACAAGCTA
1 CA-AACCTTATCTCCCTGAAGTTGCAGT-GAAGCAGATT--A-A-AAGCCA
* *
20585475 CATATCTTATCTCCCTGAAGTTGCAGTGAAGCAGATT-AAAGCCA
1 CAAACCTTATCTCCCTGAAGTTGCAGTGAAGCAGATTAAAAGCCA
* * * ***
20585519 CAAACCTTATCTCCCTGAAATTGCAGTGGAA-TAGGTTAAAAATAAA
1 CAAACCTTATCTCCCTGAAGTTGCAGT-GAAGCAGATT-AAAAGCCA
* * * * * * * *
20585565 CCAATCTTCTCTCCCTGAAGTTGTAGTGGAGCAAATTGAAGATGGGCTA
1 CAAACCTTATCTCCCTGAAGTTGCAGTGAAGCAGATT-AA-A--AGCCA
* * *
20585614 CAAATCTTATCTCCCTGAAGTTACAGTGGAGCAGATT-AAAGCCA
1 CAAACCTTATCTCCCTGAAGTTGCAGTGAAGCAGATTAAAAGCCA
* * * * * **
20585658 CAAACCTTATCTCCTTGAAGTTACA-TTAGAGCAGGTT-GAAGATA
1 CAAACCTTATCTCCCTGAAGTTGCAGTGA-AGCAGATTAAAAGCCA
* * * * * *
20585702 CCAATCTTATCTCCCT-ACAGTTTCAGTGGAGCATATT-AAAGCTA
1 CAAACCTTATCTCCCTGA-AGTTGCAGTGAAGCAGATTAAAAGCCA
* * * *
20585746 CTAA-TTCTATCTCCTTGAAGTTGCAGTGCAGCAGATTAAAA
1 CAAACCT-TATCTCCCTGAAGTTGCAGTGAAGCAGATTAAAA
20585787 CGATGAATCC
Statistics
Matches: 278, Mismatches: 65, Indels: 38
0.73 0.17 0.10
Matches are distributed among these distances:
43 3 0.01
44 127 0.46
45 12 0.04
46 63 0.23
47 2 0.01
48 4 0.01
49 63 0.23
50 4 0.01
ACGTcount: A:0.34, C:0.21, G:0.18, T:0.28
Consensus pattern (45 bp):
CAAACCTTATCTCCCTGAAGTTGCAGTGAAGCAGATTAAAAGCCA
Found at i:20585549 original size:139 final size:139
Alignment explanation
Indices: 20585380--20585785 Score: 488
Period size: 139 Copynumber: 3.0 Consensus size: 139
20585370 CAGATCATAT
*
20585380 CAAACCTTATCTCCCT-AAAGTTGCAGTGGAACAGGTTAAAAATAAAACAATCTTATCTCCCTGA
1 CAAACCTTATCTCCCTGAAA-TTGCAGTGGAACAGGTTAAAAATAAACCAATCTTATCTCCCTGA
* * *
20585444 AGTTGCAATGGAACAGATTGAAGACAAGCTACATATCTTATCTCCCTGAAGTTGCAGTGAAGCAG
65 AGTTGCAGTGGAGCAAATTGAAGACAAGCTACATATCTTATCTCCCTGAAGTTGCAGTGAAGCAG
20585509 ATTAAAGCCA
130 ATTAAAGCCA
* *
20585519 CAAACCTTATCTCCCTGAAATTGCAGTGGAATAGGTTAAAAATAAACCAATCTTCTCTCCCTGAA
1 CAAACCTTATCTCCCTGAAATTGCAGTGGAACAGGTTAAAAATAAACCAATCTTATCTCCCTGAA
* *** * * *
20585584 GTTGTAGTGGAGCAAATTGAAGATGGGCTACAAATCTTATCTCCCTGAAGTTACAGTGGAGCAGA
66 GTTGCAGTGGAGCAAATTGAAGACAAGCTACATATCTTATCTCCCTGAAGTTGCAGTGAAGCAGA
20585649 TTAAAGCCA
131 TTAAAGCCA
* * * * * * * *
20585658 CAAACCTTATCTCCTTGAAGTTACATTAGAGCAGGTTGAAGAT--ACCAATCTTATCTCCCT-AC
1 CAAACCTTATCTCCCTGAAATTGCAGTGGAACAGGTTAAAAATAAACCAATCTTATCTCCCTGA-
* * * * * *
20585720 AGTTTCAGTGGAGCATATTAAAG-CTA-CTA-AT-TC-TATCTCCTTGAAGTTGCAGTGCAGCAG
65 AGTTGCAGTGGAGCAAATTGAAGACAAGCTACATATCTTATCTCCCTGAAGTTGCAGTGAAGCAG
20585780 ATTAAA
130 ATTAAA
20585786 ACGATGAATC
Statistics
Matches: 231, Mismatches: 34, Indels: 11
0.84 0.12 0.04
Matches are distributed among these distances:
132 30 0.13
133 2 0.01
134 1 0.00
135 3 0.01
136 1 0.00
137 35 0.15
139 156 0.68
140 3 0.01
ACGTcount: A:0.34, C:0.21, G:0.18, T:0.28
Consensus pattern (139 bp):
CAAACCTTATCTCCCTGAAATTGCAGTGGAACAGGTTAAAAATAAACCAATCTTATCTCCCTGAA
GTTGCAGTGGAGCAAATTGAAGACAAGCTACATATCTTATCTCCCTGAAGTTGCAGTGAAGCAGA
TTAAAGCCA
Found at i:20602042 original size:6 final size:6
Alignment explanation
Indices: 20602031--20602055 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
20602021 AATTTTCTGA
20602031 CTCTCC CTCTCC CTCTCC CTCTCC C
1 CTCTCC CTCTCC CTCTCC CTCTCC C
20602056 GCTACATCTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.00, C:0.68, G:0.00, T:0.32
Consensus pattern (6 bp):
CTCTCC
Found at i:20608053 original size:13 final size:14
Alignment explanation
Indices: 20608022--20608053 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
20608012 TAGCCATTTT
20608022 TATTTTTCTTTTAA
1 TATTTTTCTTTTAA
20608036 TATTTTTCTTTTAA
1 TATTTTTCTTTTAA
20608050 -ATTT
1 TATTT
20608054 AATTTAATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 4 0.22
14 14 0.78
ACGTcount: A:0.22, C:0.06, G:0.00, T:0.72
Consensus pattern (14 bp):
TATTTTTCTTTTAA
Found at i:20611166 original size:22 final size:23
Alignment explanation
Indices: 20611123--20611180 Score: 66
Period size: 22 Copynumber: 2.6 Consensus size: 23
20611113 CTGAGTTGGT
*
20611123 AAACGGTAAGCTCTATCAAGCT-
1 AAACGGTAAGCTCCATCAAGCTA
* *
20611145 GAACGGTAAGCTCCGT-AGAGCTA
1 AAACGGTAAGCTCCATCA-AGCTA
20611168 AAACGGTAAGCTC
1 AAACGGTAAGCTC
20611181 ATAAGAGTTG
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
21 1 0.03
22 17 0.57
23 12 0.40
ACGTcount: A:0.34, C:0.22, G:0.24, T:0.19
Consensus pattern (23 bp):
AAACGGTAAGCTCCATCAAGCTA
Found at i:20611187 original size:23 final size:22
Alignment explanation
Indices: 20611122--20611212 Score: 78
Period size: 23 Copynumber: 4.0 Consensus size: 22
20611112 CCTGAGTTGG
*
20611122 TAAACGGTAAGCTCTATCA-AGC
1 TAAACGGTAAGCTC-ATAAGAGC
* *
20611144 TGAACGGTAAGCTCCGT-AGAGC
1 TAAACGGTAAGCT-CATAAGAGC
*
20611166 TAAAACGGTAAGCTCATAAGAGT
1 T-AAACGGTAAGCTCATAAGAGC
* *
20611189 TGAAACGATAAGCTCATACGAGC
1 T-AAACGGTAAGCTCATAAGAGC
20611212 T
1 T
20611213 GTGGTGAGTC
Statistics
Matches: 56, Mismatches: 9, Indels: 7
0.78 0.12 0.10
Matches are distributed among these distances:
21 1 0.02
22 19 0.34
23 36 0.64
ACGTcount: A:0.36, C:0.20, G:0.23, T:0.21
Consensus pattern (22 bp):
TAAACGGTAAGCTCATAAGAGC
Found at i:20613709 original size:17 final size:17
Alignment explanation
Indices: 20613675--20613708 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
20613665 GACCATGTTA
20613675 TAATTTCTTTGATATTT
1 TAATTTCTTTGATATTT
*
20613692 TAATTT-TTTTATATTT
1 TAATTTCTTTGATATTT
20613708 T
1 T
20613709 TCAAAAATTG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 10 0.62
17 6 0.38
ACGTcount: A:0.24, C:0.03, G:0.03, T:0.71
Consensus pattern (17 bp):
TAATTTCTTTGATATTT
Found at i:20616970 original size:89 final size:89
Alignment explanation
Indices: 20616786--20616980 Score: 207
Period size: 89 Copynumber: 2.2 Consensus size: 89
20616776 TGTTCCATTG
* * ** ** *
20616786 CAACATCAAGGCA-ATAAGAC-TGGTGTCTTCGATCTGCTTCTCTGCTGGTACAGGAAGACAAGA
1 CAAC-TCAAGG-AGATAAGACTTGCTATCTTCGATCTGCTTCGATGCCAGTACAGGAAAACAAGA
* ** *
20616849 TCTGCTATCTTTAGTCTTCACCGCTA
64 TCTACTATCTTTAACCTTCACCACTA
20616875 CAACTCAAGGAGATAAGACTTGCTATCTTCGATCTGCTTCGATGCCAGTACAGGAAAACAAGATC
1 CAACTCAAGGAGATAAGACTTGCTATCTTCGATCTGCTTCGATGCCAGTACAGGAAAACAAGATC
* *
20616940 TACTAT-TTTCAACCTTCTCCACTG
66 TACTATCTTT-AACCTTCACCACTA
* *
20616964 CTACTCAGGGAGATAAG
1 CAACTCAAGGAGATAAG
20616981 GCTTTATAGT
Statistics
Matches: 88, Mismatches: 15, Indels: 6
0.81 0.14 0.06
Matches are distributed among these distances:
87 1 0.01
88 16 0.18
89 71 0.81
ACGTcount: A:0.29, C:0.25, G:0.19, T:0.28
Consensus pattern (89 bp):
CAACTCAAGGAGATAAGACTTGCTATCTTCGATCTGCTTCGATGCCAGTACAGGAAAACAAGATC
TACTATCTTTAACCTTCACCACTA
Found at i:20624540 original size:3 final size:3
Alignment explanation
Indices: 20624532--20624569 Score: 51
Period size: 3 Copynumber: 12.3 Consensus size: 3
20624522 ATAAGGAAAC
20624532 AAT AAT AAT AA- AAT AAT AAT AAT AGATT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT A-A-T AAT AAT AAT A
20624570 TTAAACTGAA
Statistics
Matches: 32, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
2 2 0.06
3 26 0.81
4 2 0.06
5 2 0.06
ACGTcount: A:0.66, C:0.00, G:0.03, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:20624546 original size:11 final size:12
Alignment explanation
Indices: 20624532--20624569 Score: 51
Period size: 11 Copynumber: 3.1 Consensus size: 12
20624522 ATAAGGAAAC
20624532 AATAATAATAA-
1 AATAATAATAAT
20624543 AATAATAATAAT
1 AATAATAATAAT
20624555 AGATTAATAATAAT
1 A-A-TAATAATAAT
20624569 A
1 A
20624570 TTAAACTGAA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
11 11 0.46
12 1 0.04
13 1 0.04
14 11 0.46
ACGTcount: A:0.66, C:0.00, G:0.03, T:0.32
Consensus pattern (12 bp):
AATAATAATAAT
Found at i:20624549 original size:14 final size:14
Alignment explanation
Indices: 20624532--20624569 Score: 58
Period size: 14 Copynumber: 2.7 Consensus size: 14
20624522 ATAAGGAAAC
20624532 AATAATAATAAAAT
1 AATAATAATAAAAT
* *
20624546 AATAATAATAGATT
1 AATAATAATAAAAT
20624560 AATAATAATA
1 AATAATAATA
20624570 TTAAACTGAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.66, C:0.00, G:0.03, T:0.32
Consensus pattern (14 bp):
AATAATAATAAAAT
Found at i:20628394 original size:30 final size:30
Alignment explanation
Indices: 20628360--20628422 Score: 117
Period size: 30 Copynumber: 2.1 Consensus size: 30
20628350 ACATTTGAGG
*
20628360 TAGATTCTTAAGTATTATGTGACACAGGTT
1 TAGATTCTCAAGTATTATGTGACACAGGTT
20628390 TAGATTCTCAAGTATTATGTGACACAGGTT
1 TAGATTCTCAAGTATTATGTGACACAGGTT
20628420 TAG
1 TAG
20628423 CTCGAACTAG
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.30, C:0.11, G:0.21, T:0.38
Consensus pattern (30 bp):
TAGATTCTCAAGTATTATGTGACACAGGTT
Found at i:20630337 original size:21 final size:21
Alignment explanation
Indices: 20630312--20630351 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
20630302 AGAAAAGGGC
20630312 TTAATCGTGTAAA-ATGAAAAT
1 TTAATCGT-TAAATATGAAAAT
*
20630333 TTAATGGTTAAATATGAAA
1 TTAATCGTTAAATATGAAA
20630352 TTGCCTAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.47, C:0.03, G:0.15, T:0.35
Consensus pattern (21 bp):
TTAATCGTTAAATATGAAAAT
Found at i:20631467 original size:43 final size:43
Alignment explanation
Indices: 20631405--20631532 Score: 132
Period size: 43 Copynumber: 3.0 Consensus size: 43
20631395 CATAGGATCT
* *
20631405 TCGATATGTGTTTTTGTGTAAGACCACGTTTGGGACTTTGGCA
1 TCGATATGTGTTTTCGTGTAAGACCACGTTTGGGACATTGGCA
* * *
20631448 TCGATTTGTGTTTTCGTGTAAGACC-CTGTCTGGGACAGTGGCA
1 TCGATATGTGTTTTCGTGTAAGACCAC-GTTTGGGACATTGGCA
* * ** * * *
20631491 TCGATCTATGAATACATGTAAGACCACGTTTGGGACGTTGGC
1 TCGATATGTGTTTTCGTGTAAGACCACGTTTGGGACATTGGC
20631533 GTTGTACGAG
Statistics
Matches: 69, Mismatches: 14, Indels: 4
0.79 0.16 0.05
Matches are distributed among these distances:
42 1 0.01
43 67 0.97
44 1 0.01
ACGTcount: A:0.20, C:0.17, G:0.28, T:0.34
Consensus pattern (43 bp):
TCGATATGTGTTTTCGTGTAAGACCACGTTTGGGACATTGGCA
Found at i:20634191 original size:36 final size:36
Alignment explanation
Indices: 20634144--20634221 Score: 138
Period size: 36 Copynumber: 2.2 Consensus size: 36
20634134 TGTATTTTTT
*
20634144 ATATTGCTCTAAAATGAATTGAAACTTAATGGTTTG
1 ATATTGCTCTAAAATGAATTGAAACTTAATGGTATG
20634180 ATATTGCTCTAAAATGAATTGAAACTTAATGGTATG
1 ATATTGCTCTAAAATGAATTGAAACTTAATGGTATG
*
20634216 CTATTG
1 ATATTG
20634222 GAATGTTTGA
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
36 40 1.00
ACGTcount: A:0.36, C:0.09, G:0.17, T:0.38
Consensus pattern (36 bp):
ATATTGCTCTAAAATGAATTGAAACTTAATGGTATG
Found at i:20646067 original size:14 final size:14
Alignment explanation
Indices: 20646050--20646077 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
20646040 CTCACATTTC
20646050 TTTTCTTTTCTCCA
1 TTTTCTTTTCTCCA
20646064 TTTTCTTTTCTCCA
1 TTTTCTTTTCTCCA
20646078 GATTTCTGAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.07, C:0.29, G:0.00, T:0.64
Consensus pattern (14 bp):
TTTTCTTTTCTCCA
Found at i:20646152 original size:6 final size:6
Alignment explanation
Indices: 20646141--20646169 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
20646131 CTGTAAAATC
20646141 GATTTT GATTTT GATTTT GATTTT G-TTTT
1 GATTTT GATTTT GATTTT GATTTT GATTTT
20646170 ACTTTTGCTC
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 4 0.17
6 19 0.83
ACGTcount: A:0.14, C:0.00, G:0.17, T:0.69
Consensus pattern (6 bp):
GATTTT
Found at i:20647773 original size:17 final size:17
Alignment explanation
Indices: 20647753--20647787 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
20647743 ATATTAAGAA
20647753 TTTTATTAAATTATATT
1 TTTTATTAAATTATATT
20647770 TTTTATTAAATTATATT
1 TTTTATTAAATTATATT
20647787 T
1 T
20647788 AATAATAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (17 bp):
TTTTATTAAATTATATT
Found at i:20648575 original size:37 final size:38
Alignment explanation
Indices: 20648524--20648595 Score: 128
Period size: 37 Copynumber: 1.9 Consensus size: 38
20648514 AAAATTATCT
20648524 TTTTTTTTCTCTCTCATTTTATTTCCAAAGAGTTTTAG
1 TTTTTTTTCTCTCTCATTTTATTTCCAAAGAGTTTTAG
*
20648562 TTTTTTTT-TCTCTCATTTTATTTTCAAAGAGTTT
1 TTTTTTTTCTCTCTCATTTTATTTCCAAAGAGTTT
20648596 CCAAATATGC
Statistics
Matches: 33, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
37 25 0.76
38 8 0.24
ACGTcount: A:0.18, C:0.14, G:0.07, T:0.61
Consensus pattern (38 bp):
TTTTTTTTCTCTCTCATTTTATTTCCAAAGAGTTTTAG
Found at i:20648747 original size:26 final size:25
Alignment explanation
Indices: 20648700--20648757 Score: 64
Period size: 26 Copynumber: 2.3 Consensus size: 25
20648690 CGAAGAAATT
* *
20648700 TATTTGACTCAACTCAATTCGAATA
1 TATTTCACTCAACTCAATTCGAAAA
*
20648725 TCATTTCACTCAACTTGAA-TCGAAAA
1 T-ATTTCACTCAAC-TCAATTCGAAAA
20648751 TATTTCA
1 TATTTCA
20648758 AATCAAGTTA
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
25 7 0.25
26 18 0.64
27 3 0.11
ACGTcount: A:0.36, C:0.21, G:0.07, T:0.36
Consensus pattern (25 bp):
TATTTCACTCAACTCAATTCGAAAA
Found at i:20649646 original size:3 final size:3
Alignment explanation
Indices: 20649634--20649663 Score: 51
Period size: 3 Copynumber: 9.7 Consensus size: 3
20649624 GAAGGAAATA
20649634 TCT TCTT TCT TCT TCT TCT TCT TCT TCT TC
1 TCT TC-T TCT TCT TCT TCT TCT TCT TCT TC
20649664 ATCTCTATCA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 23 0.88
4 3 0.12
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
TCT
Found at i:20654331 original size:50 final size:50
Alignment explanation
Indices: 20654236--20654470 Score: 188
Period size: 50 Copynumber: 4.6 Consensus size: 50
20654226 AGATCACATC
* * * *
20654236 TAAGACCATGTCTGGGACATGACATTGGCATCATTGAGGTTATGAGAGGTCTCATG
1 TAAGACCATGTCTGGGACATGGCATTGGCA-C--CGA-G--ATGAAAGGTCCCATG
* * *
20654292 TAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATGAGAGGTCTCC-CG
1 TAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAAAGGTC-CCATG
* * * **
20654342 TAAGACCATGTCTGAGACATGGCATGGGCACCGATATGAAAACTCCCATG
1 TAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAAAGGTCCCATG
* * * * * * **
20654392 TAAGACCATATCTAGGATATGACATTGGCA--GTACAAGAAACATCCCATG
1 TAAGACCATGTCTGGGACATGGCATTGGCACCG-AGATGAAAGGTCCCATG
*
20654441 TAAGACCATGTCTGGGACATGGCTTTGGCA
1 TAAGACCATGTCTGGGACATGGCATTGGCA
20654471 TGTTATTATC
Statistics
Matches: 148, Mismatches: 28, Indels: 13
0.78 0.15 0.07
Matches are distributed among these distances:
48 1 0.01
49 40 0.27
50 74 0.50
51 1 0.01
52 1 0.01
53 2 0.01
55 1 0.01
56 28 0.19
ACGTcount: A:0.29, C:0.21, G:0.27, T:0.23
Consensus pattern (50 bp):
TAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAAAGGTCCCATG
Done.