Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A05
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: 100714657
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 3970000 characters in sequence are not A, C, G, or T
File 10 of 318
Found at i:3420066 original size:11 final size:11
Alignment explanation
Indices: 3420043--3420076 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
3420033 ATGTTTAATC
*
3420043 ATCAAAAATAA
1 ATCAAAAACAA
*
3420054 ATCAAGAACAA
1 ATCAAAAACAA
3420065 ATCAAAAACAA
1 ATCAAAAACAA
3420076 A
1 A
3420077 ACTAAATGCG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.71, C:0.15, G:0.03, T:0.12
Consensus pattern (11 bp):
ATCAAAAACAA
Found at i:3421677 original size:121 final size:120
Alignment explanation
Indices: 3421462--3421740 Score: 420
Period size: 121 Copynumber: 2.3 Consensus size: 120
3421452 CATCCATTGT
* * *
3421462 ATTAGGAGAAAACAATTAATAAAGTAATAGTTATATTAAATGTTAGAGTAAAGGCATTGGAAAAT
1 ATTAGGAGAAAACAATTAATAAAGTAATAGTTATATTAAATGTTAAAGTAAAGACAATGGAAAAT
*
3421527 CAACATTGAAATAAGTAGTTATAATTATTGTCAACTGTTTCCATAAATTAAATTCA
66 CAACATTGAAATAAGTAGTTATAATTATTGTCAACTGTTCCCATAAATTAAATT-A
* * *
3421583 TTTAGGAGAAAACAATTAATAAAGTAATAGTTATATTAAATGTTAAAGTAAAGATAATGGACAAT
1 ATTAGGAGAAAACAATTAATAAAGTAATAGTTATATTAAATGTTAAAGTAAAGACAATGGAAAAT
* * *
3421648 TAACATTGAAATTAA-TAGTTATAATTATTGTCAACTGTTCCCCTAAATTCAATTA
66 CAACATTGAAA-TAAGTAGTTATAATTATTGTCAACTGTTCCCATAAATTAAATTA
*
3421703 ATTAGGAGAAAACAATTAATAAA-TTATA-TTATATTAAA
1 ATTAGGAGAAAACAATTAATAAAGTAATAGTTATATTAAA
3421741 ATTAGATTTA
Statistics
Matches: 145, Mismatches: 12, Indels: 5
0.90 0.07 0.03
Matches are distributed among these distances:
118 10 0.07
119 4 0.03
120 23 0.16
121 105 0.72
122 3 0.02
ACGTcount: A:0.47, C:0.07, G:0.12, T:0.34
Consensus pattern (120 bp):
ATTAGGAGAAAACAATTAATAAAGTAATAGTTATATTAAATGTTAAAGTAAAGACAATGGAAAAT
CAACATTGAAATAAGTAGTTATAATTATTGTCAACTGTTCCCATAAATTAAATTA
Found at i:3424319 original size:52 final size:48
Alignment explanation
Indices: 3424300--3424502 Score: 256
Period size: 46 Copynumber: 4.3 Consensus size: 48
3424290 TGACAAGTGG
* * *
3424300 AAAGTGATAAGTAATAGCTTCGGCTATACTTATCTGATCAAGTGAC--
1 AAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGTGACAA
*
3424346 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAAGTGA
1 AAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGTGAC-A---A
* *
3424398 AAAGTGATAAGTGATAGCTTCAGCTATACTTATCTGATCAAGAGAC--
1 AAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGTGACAA
* *
3424444 AAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAAGAGAC--
1 AAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGTGACAA
3424490 AAAGTGATAAGTG
1 AAAGTGATAAGTG
3424503 GCTACACTTA
Statistics
Matches: 144, Mismatches: 7, Indels: 12
0.88 0.04 0.07
Matches are distributed among these distances:
46 101 0.70
52 43 0.30
ACGTcount: A:0.36, C:0.14, G:0.21, T:0.28
Consensus pattern (48 bp):
AAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGTGACAA
Found at i:3424354 original size:98 final size:98
Alignment explanation
Indices: 3424234--3424502 Score: 448
Period size: 98 Copynumber: 2.7 Consensus size: 98
3424224 TTTGAGTACT
*
3424234 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGACAAGTG
1 TCTGATCAAGTGACAAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAAGTGACAAGTG
* *
3424299 GAAAGTGATAAGTAATAGCTTCGGCTATACTTA
66 AAAAGTGATAAGTAATAGCTTCAGCTATACTTA
**
3424332 TCTGATCAAGTGACAAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAAGTG
1 TCTGATCAAGTGACAAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAAGTGACAAGTG
*
3424397 AAAAGTGATAAGTGATAGCTTCAGCTATACTTA
66 AAAAGTGATAAGTAATAGCTTCAGCTATACTTA
* *
3424430 TCTGATCAAGAGACAAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAAGAGACAAAGT
1 TCTGATCAAGTGACAAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAAGTGAC-AAGT
*
3424495 GATAAGTG
65 GAAAAGTG
3424503 GCTACACTTA
Statistics
Matches: 159, Mismatches: 11, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
98 148 0.93
99 11 0.07
ACGTcount: A:0.35, C:0.14, G:0.22, T:0.28
Consensus pattern (98 bp):
TCTGATCAAGTGACAAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAAGTGACAAGTG
AAAAGTGATAAGTAATAGCTTCAGCTATACTTA
Found at i:3424510 original size:37 final size:37
Alignment explanation
Indices: 3424466--3424611 Score: 242
Period size: 37 Copynumber: 4.0 Consensus size: 37
3424456 GATAGCTTTA
*
3424466 GCTACACTTATCTGATCAAGAGACAAAGTGATAAGTG
1 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
3424503 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
1 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
*
3424540 GCTACACTTATCTGATCAAGAAACAAAGTGATAGGTG
1 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
**
3424577 GCTACACTTATCTGATC-AGGGAC-AAGTGATAAGTG
1 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
3424612 ATCATACGTA
Statistics
Matches: 104, Mismatches: 5, Indels: 2
0.94 0.05 0.02
Matches are distributed among these distances:
35 11 0.11
36 4 0.04
37 89 0.86
ACGTcount: A:0.37, C:0.16, G:0.22, T:0.25
Consensus pattern (37 bp):
GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
Found at i:3447235 original size:22 final size:22
Alignment explanation
Indices: 3447205--3447247 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
3447195 TAAAATGCTT
3447205 AAATAATAATT-TAATATAATTA
1 AAATAATAATTATAAT-TAATTA
*
3447227 AAATCATAATTATAATTAATT
1 AAATAATAATTATAATTAATT
3447248 CTCTAAATCC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 15 0.79
23 4 0.21
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (22 bp):
AAATAATAATTATAATTAATTA
Found at i:3455084 original size:18 final size:19
Alignment explanation
Indices: 3455058--3455095 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 19
3455048 TTTAAAAATA
* *
3455058 TAAATTTTAGAAA-TATTT
1 TAAAATTTACAAATTATTT
3455076 TAAAATTTACAAATTATTT
1 TAAAATTTACAAATTATTT
3455095 T
1 T
3455096 GTAGTTCTTG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 11 0.65
19 6 0.35
ACGTcount: A:0.45, C:0.03, G:0.03, T:0.50
Consensus pattern (19 bp):
TAAAATTTACAAATTATTT
Found at i:3460355 original size:37 final size:37
Alignment explanation
Indices: 3460305--3460379 Score: 150
Period size: 37 Copynumber: 2.0 Consensus size: 37
3460295 AAACATGACT
3460305 AAGATTACATCCTAATCATTCTTGAAAATACTTCTTC
1 AAGATTACATCCTAATCATTCTTGAAAATACTTCTTC
3460342 AAGATTACATCCTAATCATTCTTGAAAATACTTCTTC
1 AAGATTACATCCTAATCATTCTTGAAAATACTTCTTC
3460379 A
1 A
3460380 TTATCCTAAC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.36, C:0.21, G:0.05, T:0.37
Consensus pattern (37 bp):
AAGATTACATCCTAATCATTCTTGAAAATACTTCTTC
Found at i:3467029 original size:29 final size:29
Alignment explanation
Indices: 3466987--3467044 Score: 107
Period size: 29 Copynumber: 2.0 Consensus size: 29
3466977 TCATGTTGTT
*
3466987 GCAAAGAGTTCAAAATCTTATTAAGAGTC
1 GCAAAGAGTTCAAAATCTTATAAAGAGTC
3467016 GCAAAGAGTTCAAAATCTTATAAAGAGTC
1 GCAAAGAGTTCAAAATCTTATAAAGAGTC
3467045 ACAAGTGAGT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.43, C:0.14, G:0.17, T:0.26
Consensus pattern (29 bp):
GCAAAGAGTTCAAAATCTTATAAAGAGTC
Found at i:3479750 original size:3 final size:3
Alignment explanation
Indices: 3479742--3479780 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
3479732 TGAGCCGAAG
3479742 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
3479781 AGATCACAAT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:3485562 original size:20 final size:20
Alignment explanation
Indices: 3485524--3485564 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
3485514 TTATCTGATA
*
3485524 AATTTATATTTTAGGAAATT
1 AATTTATATTTTAGAAAATT
3485544 AATTTAATATTTTA-AAAATT
1 AATTT-ATATTTTAGAAAATT
3485564 A
1 A
3485565 TAAATATATA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 11 0.58
21 8 0.42
ACGTcount: A:0.46, C:0.00, G:0.05, T:0.49
Consensus pattern (20 bp):
AATTTATATTTTAGAAAATT
Found at i:3488962 original size:15 final size:15
Alignment explanation
Indices: 3488942--3488973 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
3488932 AGCAATCTTG
3488942 TTCCAGTGTACCTGT
1 TTCCAGTGTACCTGT
3488957 TTCCAGTGTACCTGT
1 TTCCAGTGTACCTGT
3488972 TT
1 TT
3488974 AAGCAATGCC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.12, C:0.25, G:0.19, T:0.44
Consensus pattern (15 bp):
TTCCAGTGTACCTGT
Found at i:3519281 original size:43 final size:44
Alignment explanation
Indices: 3519213--3519341 Score: 158
Period size: 46 Copynumber: 2.9 Consensus size: 44
3519203 CTTTTATTCA
* *
3519213 TTCACCGGCATT-TTGCCTGCTAGGCTCG-AGGCCTG-ATATCAT-
1 TTCACCGGCATTATAGCCTGCTAGGCTCGAAGGCCCGAATA-C-TG
3519255 TTCACCGGCATTATAGCCTGCTAGGCTCGAAAGGCCCGAATACTG
1 TTCACCGGCATTATAGCCTGCTAGGCTCG-AAGGCCCGAATACTG
* *
3519300 TCTCACCGGCATAATAGCCTGCTAGGCTCAAAGGCCCGAATA
1 T-TCACCGGCATTATAGCCTGCTAGGCTCGAAGGCCCGAATA
3519342 TAATACCAGC
Statistics
Matches: 77, Mismatches: 4, Indels: 9
0.86 0.04 0.10
Matches are distributed among these distances:
42 12 0.16
43 15 0.19
44 1 0.01
45 20 0.26
46 29 0.38
ACGTcount: A:0.23, C:0.29, G:0.23, T:0.24
Consensus pattern (44 bp):
TTCACCGGCATTATAGCCTGCTAGGCTCGAAGGCCCGAATACTG
Found at i:3519390 original size:38 final size:38
Alignment explanation
Indices: 3519334--3519496 Score: 227
Period size: 38 Copynumber: 4.2 Consensus size: 38
3519324 GGCTCAAAGG
* * * * *
3519334 CCCGAATATAATACCAGCACTAGGCCTACTGGATTTAA
1 CCCGGATATAATACCAGCACGAAGCCTGCGGGATTTAA
3519372 CCCGGATATAATACCAGCACGAAGCCTGCGGGATTTAA
1 CCCGGATATAATACCAGCACGAAGCCTGCGGGATTTAA
*
3519410 CCCGGATATATTACCAGCACGAAGCCTGCGGGATTTAA
1 CCCGGATATAATACCAGCACGAAGCCTGCGGGATTTAA
* * *
3519448 CCCGGTTATATTACCAGCACGAAGCCCGCGGGATTTTAA
1 CCCGGATATAATACCAGCACGAAGCCTGCGGGA-TTTAA
3519487 GCCCGGATAT
1 -CCCGGATAT
3519497 CATATTTCGA
Statistics
Matches: 114, Mismatches: 9, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
38 101 0.89
39 5 0.04
40 8 0.07
ACGTcount: A:0.29, C:0.27, G:0.22, T:0.21
Consensus pattern (38 bp):
CCCGGATATAATACCAGCACGAAGCCTGCGGGATTTAA
Found at i:3522322 original size:33 final size:33
Alignment explanation
Indices: 3522279--3522345 Score: 125
Period size: 33 Copynumber: 2.0 Consensus size: 33
3522269 GCCACTACAA
*
3522279 ATTAGTCTATAGCATTTTCAGAAATTTTCACAT
1 ATTAGCCTATAGCATTTTCAGAAATTTTCACAT
3522312 ATTAGCCTATAGCATTTTCAGAAATTTTCACAT
1 ATTAGCCTATAGCATTTTCAGAAATTTTCACAT
3522345 A
1 A
3522346 AGTCTTATTT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.34, C:0.16, G:0.09, T:0.40
Consensus pattern (33 bp):
ATTAGCCTATAGCATTTTCAGAAATTTTCACAT
Found at i:3525001 original size:46 final size:44
Alignment explanation
Indices: 3524903--3525017 Score: 137
Period size: 46 Copynumber: 2.6 Consensus size: 44
3524893 TCGGCATTTC
* *
3524903 GCCTGCTAGGCTCG--AGGCCTGATATAATTTCACCAGCATTATA
1 GCCTGCTAGGCTCGAAAGGCCCGA-ATAATTTCACCAGCATAATA
*
3524946 GCCTGCTAGGCTCGAAAGGCCCGAATAATGTCTCACCGGCATAATA
1 GCCTGCTAGGCTCGAAAGGCCCGAATAAT-T-TCACCAGCATAATA
* *
3524992 GCCTACTAGGCTC-AAAGGCCCAAATA
1 GCCTGCTAGGCTCGAAAGGCCCGAATA
3525018 TAATACCAGC
Statistics
Matches: 63, Mismatches: 5, Indels: 6
0.85 0.07 0.08
Matches are distributed among these distances:
43 14 0.22
44 5 0.08
45 20 0.32
46 24 0.38
ACGTcount: A:0.29, C:0.28, G:0.22, T:0.22
Consensus pattern (44 bp):
GCCTGCTAGGCTCGAAAGGCCCGAATAATTTCACCAGCATAATA
Found at i:3525059 original size:38 final size:38
Alignment explanation
Indices: 3525015--3525134 Score: 168
Period size: 38 Copynumber: 3.1 Consensus size: 38
3525005 AAAGGCCCAA
* * * *
3525015 ATATAATACCAGCACTAGGCCTACTGGATTTAACCCGG
1 ATATAATACCAGCACGAAGCCTGCGGGATTTAACCCGG
3525053 ATATAATACCAGCACGAAGCCTGCGGGATTTAACCCGG
1 ATATAATACCAGCACGAAGCCTGCGGGATTTAACCCGG
* *
3525091 TTATATTACCAGCACGAAGCCTGCGGGATTTTAAGCCCGG
1 ATATAATACCAGCACGAAGCCTGCGGGA-TTTAA-CCCGG
3525131 ATAT
1 ATAT
3525135 CATATTTCGA
Statistics
Matches: 73, Mismatches: 7, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
38 60 0.82
39 5 0.07
40 8 0.11
ACGTcount: A:0.30, C:0.25, G:0.22, T:0.23
Consensus pattern (38 bp):
ATATAATACCAGCACGAAGCCTGCGGGATTTAACCCGG
Found at i:3528215 original size:16 final size:16
Alignment explanation
Indices: 3528147--3528215 Score: 52
Period size: 16 Copynumber: 4.1 Consensus size: 16
3528137 CACATTTTTT
3528147 ATTTTTTATTT-TCAAA
1 ATTTTTTATTTAT-AAA
* *
3528163 ATTTTTTATTTTTAATTT
1 ATTTTTTATTTATAA--A
*
3528181 ATCTTTTTAATTA-ATAA
1 AT-TTTTTATTTATA-AA
3528198 ATTTTTTATTTATAAA
1 ATTTTTTATTTATAAA
3528214 AT
1 AT
3528216 AAAATAATTA
Statistics
Matches: 42, Mismatches: 5, Indels: 12
0.71 0.08 0.20
Matches are distributed among these distances:
16 26 0.62
17 4 0.10
18 3 0.07
19 9 0.21
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.64
Consensus pattern (16 bp):
ATTTTTTATTTATAAA
Found at i:3528260 original size:16 final size:16
Alignment explanation
Indices: 3528215--3528260 Score: 51
Period size: 16 Copynumber: 2.9 Consensus size: 16
3528205 ATTTATAAAA
*
3528215 TAAA-ATAATTATT-G
1 TAAATATAATTTTTAG
*
3528229 TAAATATTATTTTTTAG
1 TAAATA-TAATTTTTAG
3528246 TAAATATAATTTTTA
1 TAAATATAATTTTTA
3528261 TACGTGTAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
14 4 0.15
15 1 0.04
16 14 0.54
17 7 0.27
ACGTcount: A:0.43, C:0.00, G:0.04, T:0.52
Consensus pattern (16 bp):
TAAATATAATTTTTAG
Found at i:3530832 original size:17 final size:17
Alignment explanation
Indices: 3530810--3530844 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
3530800 TTTGCATGTC
3530810 ATTTAATGATTAAATTA
1 ATTTAATGATTAAATTA
3530827 ATTTAATGATTAAATTA
1 ATTTAATGATTAAATTA
3530844 A
1 A
3530845 CGGTTTCAAT
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:0.49, C:0.00, G:0.06, T:0.46
Consensus pattern (17 bp):
ATTTAATGATTAAATTA
Found at i:3534830 original size:72 final size:72
Alignment explanation
Indices: 3534708--3534851 Score: 184
Period size: 72 Copynumber: 2.0 Consensus size: 72
3534698 TGATTTGAAT
* * * * * *
3534708 GATTTACTATTTTGTTGTCTGTAATACTTCGTAACCCTGTTCTGATGACGGATACGGGTTAG-GG
1 GATTGACTATTCTGTTGTCTGTAATACTCCGTAACCCTGTTCAGACGACGGATACGAGTTAGAGG
3534772 TGTTACA
66 TGTTACA
*
3534779 GATTGACTATTCTGTTGTCTTGTAATACTCCGTAACCTTGTTCCAG-CGACGGATACGAGTTAGA
1 GATTGACTATTCTGTTGTC-TGTAATACTCCGTAACCCTGTT-CAGACGACGGATACGAGTTAGA
*
3534843 TGTGTTACA
64 GGTGTTACA
3534852 TATAAATAAT
Statistics
Matches: 62, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
71 17 0.27
72 35 0.56
73 10 0.16
ACGTcount: A:0.22, C:0.17, G:0.23, T:0.38
Consensus pattern (72 bp):
GATTGACTATTCTGTTGTCTGTAATACTCCGTAACCCTGTTCAGACGACGGATACGAGTTAGAGG
TGTTACA
Found at i:3539229 original size:19 final size:19
Alignment explanation
Indices: 3539205--3539243 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
3539195 GCTTTTTTTC
3539205 TTGGGTTATATAGTTATGT
1 TTGGGTTATATAGTTATGT
3539224 TTGGGTTATATAGTTATGT
1 TTGGGTTATATAGTTATGT
3539243 T
1 T
3539244 AAAAGGGTGA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.21, C:0.00, G:0.26, T:0.54
Consensus pattern (19 bp):
TTGGGTTATATAGTTATGT
Found at i:3540854 original size:2 final size:2
Alignment explanation
Indices: 3540847--3540871 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
3540837 TACACGTCAA
3540847 TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC T
3540872 ATATATATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:3548839 original size:2 final size:2
Alignment explanation
Indices: 3548832--3548857 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
3548822 TTTACCAATA
3548832 TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC
3548858 CCTCCCCCCC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:3570500 original size:21 final size:21
Alignment explanation
Indices: 3570476--3570540 Score: 64
Period size: 21 Copynumber: 3.1 Consensus size: 21
3570466 AATTTAGTCT
3570476 ATTTACTTTTTAAATTTTAAA
1 ATTTACTTTTTAAATTTTAAA
* *
3570497 ATTTAC-TATTAACATTGTTAAG
1 ATTTACTTTTTAA-ATT-TTAAA
*
3570519 A-TTA-TTTTTAAATTTTTAA
1 ATTTACTTTTTAAATTTTAAA
3570538 ATT
1 ATT
3570541 ATTTTAATTA
Statistics
Matches: 35, Mismatches: 5, Indels: 9
0.71 0.10 0.18
Matches are distributed among these distances:
19 4 0.11
20 9 0.26
21 17 0.49
22 5 0.14
ACGTcount: A:0.37, C:0.05, G:0.03, T:0.55
Consensus pattern (21 bp):
ATTTACTTTTTAAATTTTAAA
Found at i:3575045 original size:14 final size:14
Alignment explanation
Indices: 3575028--3575054 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
3575018 ATTAAATTAT
3575028 AATGTTACAATTTA
1 AATGTTACAATTTA
3575042 AATGTTACAATTT
1 AATGTTACAATTT
3575055 GCTCAAAGTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.41, C:0.07, G:0.07, T:0.44
Consensus pattern (14 bp):
AATGTTACAATTTA
Found at i:3588319 original size:16 final size:16
Alignment explanation
Indices: 3588300--3588354 Score: 51
Period size: 16 Copynumber: 3.5 Consensus size: 16
3588290 AATAAAAACG
3588300 ATCTAAAACTAAAATA
1 ATCTAAAACTAAAATA
*
3588316 ATCT-AAACTCAAATTA
1 ATCTAAAACT-AAAATA
* *
3588332 AT-TTAAACAAAAATA
1 ATCTAAAACTAAAATA
*
3588347 ATCCAAAA
1 ATCTAAAA
3588355 ATTTTAAAAC
Statistics
Matches: 31, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
15 13 0.42
16 18 0.58
ACGTcount: A:0.60, C:0.15, G:0.00, T:0.25
Consensus pattern (16 bp):
ATCTAAAACTAAAATA
Found at i:3588727 original size:3 final size:3
Alignment explanation
Indices: 3588713--3588744 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
3588703 ATAAAACCCG
*
3588713 TTC TTT TTC TTC TTC TTC TTC TTC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
3588745 ATTGTTCTTG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (3 bp):
TTC
Found at i:3595629 original size:39 final size:38
Alignment explanation
Indices: 3595585--3595694 Score: 170
Period size: 39 Copynumber: 2.9 Consensus size: 38
3595575 TGAAGTATAT
3595585 AAGTGCTAAATGGAAGCCCGAAGGCTAACTGAAGCACAC
1 AAGTGCTAAATGGAAGCCCGAAGGCTAACTGAAGC-CAC
* * *
3595624 AAGTGCTAAACGGAATCCTGAAGGCTAACTGAAG-CAC
1 AAGTGCTAAATGGAAGCCCGAAGGCTAACTGAAGCCAC
3595661 -AGTGCTAAATGGAAGCCCGAAGGCTAACTGAAGC
1 AAGTGCTAAATGGAAGCCCGAAGGCTAACTGAAGC
3595695 TCATCAGAGC
Statistics
Matches: 64, Mismatches: 6, Indels: 4
0.86 0.08 0.05
Matches are distributed among these distances:
36 30 0.47
37 3 0.05
39 31 0.48
ACGTcount: A:0.37, C:0.22, G:0.26, T:0.15
Consensus pattern (38 bp):
AAGTGCTAAATGGAAGCCCGAAGGCTAACTGAAGCCAC
Found at i:3595683 original size:36 final size:37
Alignment explanation
Indices: 3595585--3595694 Score: 168
Period size: 36 Copynumber: 2.9 Consensus size: 37
3595575 TGAAGTATAT
3595585 AAGTGCTAAATGGAAGCCCGAAGGCTAACTGAAGCACAC
1 AAGTGCTAAATGGAAGCCCGAAGGCTAACTGAAG--CAC
* * *
3595624 AAGTGCTAAACGGAATCCTGAAGGCTAACTGAAGCAC
1 AAGTGCTAAATGGAAGCCCGAAGGCTAACTGAAGCAC
3595661 -AGTGCTAAATGGAAGCCCGAAGGCTAACTGAAGC
1 AAGTGCTAAATGGAAGCCCGAAGGCTAACTGAAGC
3595695 TCATCAGAGC
Statistics
Matches: 65, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
36 31 0.48
37 3 0.05
39 31 0.48
ACGTcount: A:0.37, C:0.22, G:0.26, T:0.15
Consensus pattern (37 bp):
AAGTGCTAAATGGAAGCCCGAAGGCTAACTGAAGCAC
Found at i:3598841 original size:46 final size:46
Alignment explanation
Indices: 3598789--3598964 Score: 198
Period size: 46 Copynumber: 3.8 Consensus size: 46
3598779 TGGTTGAGCA
3598789 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * * * *
3598835 TTCGAACTCGTTGAGTTGAGGCCGAGTTC-GTGA--GATG-TAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T--G
*
3598880 CATCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * *
3598928 CCCGAGCTTGTTGAGTTGAGTCCGAGTTCACTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
3598965 GCGGGTTACA
Statistics
Matches: 108, Mismatches: 13, Indels: 18
0.78 0.09 0.13
Matches are distributed among these distances:
42 2 0.02
43 5 0.05
45 3 0.03
46 62 0.57
47 26 0.24
48 3 0.03
50 5 0.05
51 2 0.02
ACGTcount: A:0.20, C:0.19, G:0.30, T:0.30
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
Found at i:3598945 original size:93 final size:93
Alignment explanation
Indices: 3598786--3598956 Score: 288
Period size: 93 Copynumber: 1.8 Consensus size: 93
3598776 GGATGGTTGA
**
3598786 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTTCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGCCCGAACTCGTTGAGT
3598851 TGAGGCCGAGTTCGTGAGATGTAACTAG
66 TGAGGCCGAGTTCGTGAGATGTAACTAG
* * *
3598879 GCATCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGCCCGAGCTTGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGCCCGAACTCGTTGAGT
*
3598944 TGAGTCCGAGTTC
66 TGAGGCCGAGTTC
3598957 ACTTATGGGC
Statistics
Matches: 72, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
93 72 1.00
ACGTcount: A:0.20, C:0.20, G:0.30, T:0.29
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGCCCGAACTCGTTGAGT
TGAGGCCGAGTTCGTGAGATGTAACTAG
Found at i:3602147 original size:46 final size:46
Alignment explanation
Indices: 3602080--3602254 Score: 196
Period size: 46 Copynumber: 3.8 Consensus size: 46
3602070 TGTAACCCGC
3602080 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCCTTCTCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCCTTCTCAT
*
3602126 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCAGATGCCTAGT-TACAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTC-G-GGCCT--TCT-CAT
* * * ** * *
3602176 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGAACATTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCCTTCTCAT
*
3602219 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGG
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGG
3602255 ATGCTCAATC
Statistics
Matches: 109, Mismatches: 11, Indels: 18
0.79 0.08 0.13
Matches are distributed among these distances:
43 4 0.04
44 1 0.01
45 4 0.04
46 62 0.57
47 26 0.24
48 6 0.06
49 2 0.02
50 4 0.04
ACGTcount: A:0.30, C:0.30, G:0.19, T:0.21
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCCTTCTCAT
Found at i:3602200 original size:93 final size:93
Alignment explanation
Indices: 3602088--3602258 Score: 279
Period size: 93 Copynumber: 1.8 Consensus size: 93
3602078 GCCCATAAGT
** * *
3602088 GAACTCGGACTCAACTCAACGAGCTCGGGCCTTCTCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGAACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
3602153 CGAGCTCAGATGCCTAGTTACATCTCAC
66 CGAGCTCAGATGCCTAGTTACATCTCAC
*
3602181 GAACTCGGACTCAACTCAACGAGTTCGAACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGAACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
* *
3602246 CGAGTTCGGATGC
66 CGAGCTCAGATGC
3602259 TCAATCATCC
Statistics
Matches: 71, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
93 71 1.00
ACGTcount: A:0.29, C:0.30, G:0.19, T:0.21
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACGAGCTCGAACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
CGAGCTCAGATGCCTAGTTACATCTCAC
Found at i:3607697 original size:59 final size:59
Alignment explanation
Indices: 3607620--3607731 Score: 154
Period size: 59 Copynumber: 1.9 Consensus size: 59
3607610 TTTTTATCAC
*
3607620 CTAATTATGAAAAGTTACAAAAT-AGTCACCCAAATATTAATAAATTTATTTTTAGGTCA
1 CTAATTATAAAAAGTTACAAAATGA-TCACCCAAATATTAATAAATTTATTTTTAGGTCA
* ** * *
3607679 CTAATTATAAAAAGTTACAAGATGATCACTTAACTATTAGTAAATTTATTTTT
1 CTAATTATAAAAAGTTACAAAATGATCACCCAAATATTAATAAATTTATTTTT
3607732 TAATCCCTCA
Statistics
Matches: 46, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
59 45 0.98
60 1 0.02
ACGTcount: A:0.43, C:0.11, G:0.08, T:0.38
Consensus pattern (59 bp):
CTAATTATAAAAAGTTACAAAATGATCACCCAAATATTAATAAATTTATTTTTAGGTCA
Found at i:3623003 original size:39 final size:39
Alignment explanation
Indices: 3622960--3623038 Score: 149
Period size: 39 Copynumber: 2.0 Consensus size: 39
3622950 AAAAAAAGAA
3622960 AGAAAAAAGGAGGAGCGGTTTCTACGTTAAAAGCTAAAC
1 AGAAAAAAGGAGGAGCGGTTTCTACGTTAAAAGCTAAAC
*
3622999 AGAAAAAAGGGGGAGCGGTTTCTACGTTAAAAGCTAAAC
1 AGAAAAAAGGAGGAGCGGTTTCTACGTTAAAAGCTAAAC
3623038 A
1 A
3623039 TCTTTTCTTT
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
39 39 1.00
ACGTcount: A:0.43, C:0.13, G:0.27, T:0.18
Consensus pattern (39 bp):
AGAAAAAAGGAGGAGCGGTTTCTACGTTAAAAGCTAAAC
Found at i:3633799 original size:28 final size:28
Alignment explanation
Indices: 3633759--3633822 Score: 110
Period size: 28 Copynumber: 2.3 Consensus size: 28
3633749 TTTAATTAAG
*
3633759 AATTTTTTATACCTGATATATTTTTTAC
1 AATTTTTTATACCTGATATAATTTTTAC
*
3633787 AATTTTTTATACCTGTTATAATTTTTAC
1 AATTTTTTATACCTGATATAATTTTTAC
3633815 AATTTTTT
1 AATTTTTT
3633823 TAAAATTCAT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
28 34 1.00
ACGTcount: A:0.28, C:0.09, G:0.03, T:0.59
Consensus pattern (28 bp):
AATTTTTTATACCTGATATAATTTTTAC
Found at i:3651549 original size:45 final size:46
Alignment explanation
Indices: 3651496--3651639 Score: 143
Period size: 46 Copynumber: 3.2 Consensus size: 46
3651486 TCTTATTCAC
* *
3651496 GGTCTTATTTATTTT-TGACATGATGCCATAGTGTCTTTCAACTAT
1 GGTCTTATTTATTTTCTGACATGATGCCATAGTATCTTTCAACCAT
* * * *
3651541 GGTTTTATTTATTTTCTGTCATGTTGCCATGGTATCTTTCAACCAT
1 GGTCTTATTTATTTTCTGACATGATGCCATAGTATCTTTCAACCAT
* * * *
3651587 GGTCTTGTTTA-TTTCAT-ATCACGTTGTCAT-GTTATCTTTCAACCAT
1 GGTCTTATTTATTTTC-TGA-CATGATGCCATAG-TATCTTTCAACCAT
3651633 GGTCTTA
1 GGTCTTA
3651640 CACATTTCAT
Statistics
Matches: 83, Mismatches: 12, Indels: 7
0.81 0.12 0.07
Matches are distributed among these distances:
45 19 0.23
46 64 0.77
ACGTcount: A:0.19, C:0.17, G:0.15, T:0.48
Consensus pattern (46 bp):
GGTCTTATTTATTTTCTGACATGATGCCATAGTATCTTTCAACCAT
Found at i:3651579 original size:46 final size:46
Alignment explanation
Indices: 3651563--3651791 Score: 296
Period size: 46 Copynumber: 5.0 Consensus size: 46
3651553 TTTCTGTCAT
**** *
3651563 GTTGCCATGGTATCTTTCAACCATGGTCTTGTTTATTTCATATCAC
1 GTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAG
* * *
3651609 GTTGTCATGTTATCTTTCAACCATGGTCTTACACATTTCATATTAG
1 GTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAG
** * * *
3651655 GTTGTTATGGTATCTTTCAACTATGGTTTTACACATTTTATATCAG
1 GTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAG
* *
3651701 GTTGCTATGATATCTTTCAACCATGGTCTTACACATTTCATATCAG
1 GTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAG
* * *
3651747 ATTGCCATGGTATCTTTCAATCATGGTCTTACACATTTTATATCA
1 GTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCA
3651792 AAGAGCACAC
Statistics
Matches: 159, Mismatches: 24, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
46 159 1.00
ACGTcount: A:0.24, C:0.19, G:0.14, T:0.43
Consensus pattern (46 bp):
GTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAG
Found at i:3651777 original size:138 final size:138
Alignment explanation
Indices: 3651529--3651789 Score: 362
Period size: 138 Copynumber: 1.9 Consensus size: 138
3651519 TGCCATAGTG
*** * * * * *
3651529 TCTTTCAACTATGGTTTTATTTATTTTCTGTCATGTTGCCATGGTATCTTTCAACCATGGTCTTG
1 TCTTTCAACTATGGTTTTACACATTTTATATCAGGTTGCCATGATATCTTTCAACCATGGTCTTA
*** * *
3651594 TTTATTTCATATCACGTTGTCATGTTATCTTTCAACCATGGTCTTACACATTTCATATTAGGTTG
66 CACATTTCATATCACGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATTAGGTTG
3651659 TTATGGTA
131 TTATGGTA
*
3651667 TCTTTCAACTATGGTTTTACACATTTTATATCAGGTTGCTATGATATCTTTCAACCATGGTCTTA
1 TCTTTCAACTATGGTTTTACACATTTTATATCAGGTTGCCATGATATCTTTCAACCATGGTCTTA
* *
3651732 CACATTTCATATCA-GATTGCCATGGTATCTTTCAATCATGGTCTTACACATTTTATAT
66 CACATTTCATATCACG-TTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATAT
3651790 CAAAGAGCAC
Statistics
Matches: 106, Mismatches: 16, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
137 1 0.01
138 105 0.99
ACGTcount: A:0.23, C:0.18, G:0.13, T:0.46
Consensus pattern (138 bp):
TCTTTCAACTATGGTTTTACACATTTTATATCAGGTTGCCATGATATCTTTCAACCATGGTCTTA
CACATTTCATATCACGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATTAGGTTG
TTATGGTA
Found at i:3653895 original size:11 final size:11
Alignment explanation
Indices: 3653875--3653909 Score: 61
Period size: 11 Copynumber: 3.2 Consensus size: 11
3653865 AATAATTAAC
3653875 AATAAAATAAT
1 AATAAAATAAT
*
3653886 AATGAAATAAT
1 AATAAAATAAT
3653897 AATAAAATAAT
1 AATAAAATAAT
3653908 AA
1 AA
3653910 AATAACTCAT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
11 22 1.00
ACGTcount: A:0.71, C:0.00, G:0.03, T:0.26
Consensus pattern (11 bp):
AATAAAATAAT
Found at i:3653943 original size:20 final size:20
Alignment explanation
Indices: 3653877--3653952 Score: 59
Period size: 20 Copynumber: 3.8 Consensus size: 20
3653867 TAATTAACAA
*
3653877 TAAAATAATA-ATGAAATAAT
1 TAAAATAATATAT-AACTAAT
* *
3653897 AATAAAATAATAAAATAACTCAT
1 --TAAAATAAT-ATATAACTAAT
*
3653920 TAAAATAATATATATCTAAT
1 TAAAATAATATATAACTAAT
3653940 T-AAATAAT-TATAA
1 TAAAATAATATATAA
3653953 AATATCATCA
Statistics
Matches: 46, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
18 4 0.09
19 7 0.15
20 9 0.20
21 9 0.20
22 9 0.20
23 6 0.13
24 2 0.04
ACGTcount: A:0.62, C:0.04, G:0.01, T:0.33
Consensus pattern (20 bp):
TAAAATAATATATAACTAAT
Found at i:3654601 original size:35 final size:35
Alignment explanation
Indices: 3654555--3654625 Score: 142
Period size: 35 Copynumber: 2.0 Consensus size: 35
3654545 CCACAACAAG
3654555 GTTTGATATCAAAAGACCTAATATCCCACTTTCCT
1 GTTTGATATCAAAAGACCTAATATCCCACTTTCCT
3654590 GTTTGATATCAAAAGACCTAATATCCCACTTTCCT
1 GTTTGATATCAAAAGACCTAATATCCCACTTTCCT
3654625 G
1 G
3654626 ACTCTTTTCT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.31, C:0.25, G:0.10, T:0.34
Consensus pattern (35 bp):
GTTTGATATCAAAAGACCTAATATCCCACTTTCCT
Found at i:3655338 original size:31 final size:31
Alignment explanation
Indices: 3655303--3655362 Score: 86
Period size: 31 Copynumber: 1.9 Consensus size: 31
3655293 GAAAATCCTA
*
3655303 AAGCTCAAG-CTTCAATATGAGAATAATTGTC
1 AAGCTCAAGTC-TCAATATGAGAACAATTGTC
*
3655334 AAGCTTAAGTCTCAATATGAGAACAATTG
1 AAGCTCAAGTCTCAATATGAGAACAATTG
3655363 CCAATTTTTG
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
31 25 0.96
32 1 0.04
ACGTcount: A:0.40, C:0.15, G:0.17, T:0.28
Consensus pattern (31 bp):
AAGCTCAAGTCTCAATATGAGAACAATTGTC
Found at i:3657960 original size:24 final size:24
Alignment explanation
Indices: 3657916--3657975 Score: 61
Period size: 24 Copynumber: 2.5 Consensus size: 24
3657906 GATGTGAATT
3657916 TAATGAAAATAATTTACTAAATAAA-
1 TAAT-AAAATAATTTACTAAA-AAAG
*
3657941 TAATAAAATATATTT-TTAAAAAAG
1 TAATAAAATA-ATTTACTAAAAAAG
*
3657965 TACTAAAATAA
1 TAATAAAATAA
3657976 AATAATATTT
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
23 4 0.13
24 19 0.61
25 8 0.26
ACGTcount: A:0.60, C:0.03, G:0.03, T:0.33
Consensus pattern (24 bp):
TAATAAAATAATTTACTAAAAAAG
Found at i:3660985 original size:60 final size:60
Alignment explanation
Indices: 3660921--3661039 Score: 168
Period size: 60 Copynumber: 2.0 Consensus size: 60
3660911 GCTGGCAGAG
*
3660921 ATAATGGAGCT-GGAGCTGGAGCTGGAGCCGCTGCAGCTAGTGGTTTTGGAGCTGGTGGAA
1 ATAAT-GAGCTCGGAGCTGGAGCTGGAGCCGCTGCAGCTAGTGGTTTTGGAGATGGTGGAA
*** * *
3660981 ATAATGCTTTCGGAGCTGGAGCTGGAGCCGCTGGAGCTGGTGGTTTTGGAGATGGTGGA
1 ATAATGAGCTCGGAGCTGGAGCTGGAGCCGCTGCAGCTAGTGGTTTTGGAGATGGTGGA
3661040 GATGATGGTT
Statistics
Matches: 52, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
59 2 0.04
60 50 0.96
ACGTcount: A:0.18, C:0.14, G:0.42, T:0.25
Consensus pattern (60 bp):
ATAATGAGCTCGGAGCTGGAGCTGGAGCCGCTGCAGCTAGTGGTTTTGGAGATGGTGGAA
Found at i:3665043 original size:19 final size:19
Alignment explanation
Indices: 3664994--3665044 Score: 50
Period size: 20 Copynumber: 2.7 Consensus size: 19
3664984 ATATATAAAA
* *
3664994 TATAAATTTTAA-ATACTT
1 TATAAAATTTAATATAATT
* *
3665012 TTTAAACTATTAATATAATT
1 TATAAAAT-TTAATATAATT
3665032 TATAAAATTTAAT
1 TATAAAATTTAAT
3665045 TTAAAATATT
Statistics
Matches: 26, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
18 6 0.23
19 9 0.35
20 11 0.42
ACGTcount: A:0.47, C:0.04, G:0.00, T:0.49
Consensus pattern (19 bp):
TATAAAATTTAATATAATT
Found at i:3665866 original size:18 final size:18
Alignment explanation
Indices: 3665843--3665880 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
3665833 TTAAAATTAT
3665843 TTTTTTACATTT-TTATAA
1 TTTTTTA-ATTTCTTATAA
*
3665861 TTTTTTATTTTCTTATAA
1 TTTTTTAATTTCTTATAA
3665879 TT
1 TT
3665881 AAGATGAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 3 0.17
18 15 0.83
ACGTcount: A:0.24, C:0.05, G:0.00, T:0.71
Consensus pattern (18 bp):
TTTTTTAATTTCTTATAA
Found at i:3667665 original size:33 final size:33
Alignment explanation
Indices: 3667628--3667690 Score: 81
Period size: 33 Copynumber: 1.9 Consensus size: 33
3667618 ATGTGCATGA
* *
3667628 TTGAATCAAAATTAAAGTTTCATATATATATAT
1 TTGAACCAAAATCAAAGTTTCATATATATATAT
* * *
3667661 TTGAACCACAATCAAAGTTTTATGTATATA
1 TTGAACCAAAATCAAAGTTTCATATATATA
3667691 ATTATACCAT
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
33 25 1.00
ACGTcount: A:0.43, C:0.10, G:0.08, T:0.40
Consensus pattern (33 bp):
TTGAACCAAAATCAAAGTTTCATATATATATAT
Found at i:3685931 original size:40 final size:40
Alignment explanation
Indices: 3685875--3685960 Score: 163
Period size: 40 Copynumber: 2.1 Consensus size: 40
3685865 ATAGTCAGAG
*
3685875 AAAGATTCTCATAGCAGATTATTCTAAAACAGGATAAAGA
1 AAAGATTCTCACAGCAGATTATTCTAAAACAGGATAAAGA
3685915 AAAGATTCTCACAGCAGATTATTCTAAAACAGGATAAAGA
1 AAAGATTCTCACAGCAGATTATTCTAAAACAGGATAAAGA
3685955 AAAGAT
1 AAAGAT
3685961 ATTATGTAGA
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
40 45 1.00
ACGTcount: A:0.49, C:0.13, G:0.15, T:0.23
Consensus pattern (40 bp):
AAAGATTCTCACAGCAGATTATTCTAAAACAGGATAAAGA
Found at i:3697643 original size:19 final size:18
Alignment explanation
Indices: 3697601--3697699 Score: 53
Period size: 19 Copynumber: 5.2 Consensus size: 18
3697591 TAAAGAGATC
*
3697601 ATTTAATATCTATATTTGAT
1 ATTTAATAT-TA-ATTTAAT
3697621 -TTTAATATTCAATTTAAT
1 ATTTAATATT-AATTTAAT
*
3697639 ATTTAA-ATT-TTTTATATT
1 ATTTAATATTAATTTA-A-T
* *
3697657 AATTTAATAATTAAACTTGA-
1 -ATTTAAT-ATT-AATTTAAT
3697677 ATTTAATATTTAATTTAAT
1 ATTTAATA-TTAATTTAAT
3697696 ATTT
1 ATTT
3697700 GAATCAAACA
Statistics
Matches: 61, Mismatches: 7, Indels: 23
0.67 0.08 0.25
Matches are distributed among these distances:
16 4 0.07
17 1 0.02
18 17 0.28
19 33 0.54
21 3 0.05
22 1 0.02
23 2 0.03
ACGTcount: A:0.39, C:0.03, G:0.02, T:0.56
Consensus pattern (18 bp):
ATTTAATATTAATTTAAT
Found at i:3699526 original size:214 final size:215
Alignment explanation
Indices: 3699151--3699582 Score: 742
Period size: 213 Copynumber: 2.0 Consensus size: 215
3699141 AATTGTTAGG
3699151 ATTTTGTTGAATTCTAAATCTCATAGTTCTTTTGAGGGCTTCTAGTTCTAGTTATGTTTTCCTTT
1 ATTTTGTTGAATTCTAAATCTCATAGTTCTTTTGAGGGCTTCTAGTTCTAGTTATGTTTTCCTTT
*
3699216 GGTATATAGCTTCTTCCATAGCACTTGAAGATGTTCGATTCTTCTTGTATTCTACAATATTTATA
66 GGTATATAGCTTCTTCCATAGCACTTGAAGATGTTCGATTCTTCTTGGATTCTACAATATTTATA
* * *
3699281 GCTGGACAAACTTAAAAAGAGAAGAGG-AAAAAAAGAGAGCAATCAATCTATGGTTGTTGTTACC
131 GCGGGACAAACTTAAAAAGAAAAGAGGAAAAAAAAAAGAGCAATCAATCTATGGTTGTTGTTACC
3699345 GCATGACGATGTATCTAACC
196 GCATGACGATGTATCTAACC
3699365 ATTTTGTTGAATTCTAAATCTCATAGTTCTTTTGAGGGCTTCTAGTTCTAGTTATGTTTTCCTTT
1 ATTTTGTTGAATTCTAAATCTCATAGTTCTTTTGAGGGCTTCTAGTTCTAGTTATGTTTTCCTTT
* * *
3699430 GGTATA-ATCTTTTTCCATAGCACTTGAAGATGTTCTATTCTTCTTGGATTCTACAATATTTATA
66 GGTATATAGCTTCTTCCATAGCACTTGAAGATGTTCGATTCTTCTTGGATTCTACAATATTTATA
* *
3699494 GCGGGACAAATTTAAAAAGAAAAGAGGGAAAAAAAAAAAGAGCAATCAATTTATGGTTGTTGTTA
131 GCGGGACAAACTTAAAAAGAAAAGA-GG-AAAAAAAAAAGAGCAATCAATCTATGGTTGTTGTTA
*
3699559 CTGCATGACGATGTATCTAACC
194 CCGCATGACGATGTATCTAACC
3699581 AT
1 AT
3699583 ATAACGAACA
Statistics
Matches: 205, Mismatches: 10, Indels: 4
0.94 0.05 0.02
Matches are distributed among these distances:
213 76 0.37
214 73 0.36
216 56 0.27
ACGTcount: A:0.30, C:0.14, G:0.17, T:0.38
Consensus pattern (215 bp):
ATTTTGTTGAATTCTAAATCTCATAGTTCTTTTGAGGGCTTCTAGTTCTAGTTATGTTTTCCTTT
GGTATATAGCTTCTTCCATAGCACTTGAAGATGTTCGATTCTTCTTGGATTCTACAATATTTATA
GCGGGACAAACTTAAAAAGAAAAGAGGAAAAAAAAAAGAGCAATCAATCTATGGTTGTTGTTACC
GCATGACGATGTATCTAACC
Found at i:3714579 original size:22 final size:21
Alignment explanation
Indices: 3714554--3714596 Score: 50
Period size: 22 Copynumber: 2.0 Consensus size: 21
3714544 TAAATAAAAT
3714554 TTTAAAATAATTTAATAATTAA
1 TTTAAAATAATTTAA-AATTAA
* **
3714576 TTTATAATTTTTTAAAATTAA
1 TTTAAAATAATTTAAAATTAA
3714597 GTTATTAAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
21 6 0.33
22 12 0.67
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (21 bp):
TTTAAAATAATTTAAAATTAA
Found at i:3714619 original size:16 final size:14
Alignment explanation
Indices: 3714580--3714622 Score: 50
Period size: 14 Copynumber: 2.9 Consensus size: 14
3714570 AATTAATTTA
*
3714580 TAATTTTTTAAAAT
1 TAATTTATTAAAAT
*
3714594 TAAGTTATTAAAAT
1 TAATTTATTAAAAT
3714608 GTAAATTTATTAAAA
1 -T-AATTTATTAAAA
3714623 AAATTAATAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
14 12 0.50
15 1 0.04
16 11 0.46
ACGTcount: A:0.49, C:0.00, G:0.05, T:0.47
Consensus pattern (14 bp):
TAATTTATTAAAAT
Found at i:3723641 original size:22 final size:21
Alignment explanation
Indices: 3723611--3723655 Score: 72
Period size: 22 Copynumber: 2.1 Consensus size: 21
3723601 ACACCAAAAC
*
3723611 AGGCTTTTAGCGGCGCTGTTTT
1 AGGCCTTTAGCGGCGCT-TTTT
3723633 AGGCCTTTAGCGGCGCTTTTT
1 AGGCCTTTAGCGGCGCTTTTT
3723654 AG
1 AG
3723656 CGCCGCTAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 6 0.27
22 16 0.73
ACGTcount: A:0.11, C:0.20, G:0.31, T:0.38
Consensus pattern (21 bp):
AGGCCTTTAGCGGCGCTTTTT
Found at i:3723727 original size:43 final size:43
Alignment explanation
Indices: 3723680--3723925 Score: 314
Period size: 43 Copynumber: 5.7 Consensus size: 43
3723670 GCGTCGCTAA
* * *
3723680 CTTTAGCGGCGCTTTTCCCACAAACGCCGCTAAAAACCAGGAC
1 CTTTAGCGGCGCTTTTCCCACAAACGCCGCTATAGATCAGGAC
*
3723723 CTTTAGCGGCGCTTTTCCCACAAACGCCGCTATAGATCAGAAC
1 CTTTAGCGGCGCTTTTCCCACAAACGCCGCTATAGATCAGGAC
* *
3723766 CTTTAGCGACACTTTTCCCACAAACGCCGCTATAGATCAGGAC
1 CTTTAGCGGCGCTTTTCCCACAAACGCCGCTATAGATCAGGAC
* * *
3723809 CTTTAGCGGCACTTTT-ACACAAACGCCGCTATAGATCAAGAC
1 CTTTAGCGGCGCTTTTCCCACAAACGCCGCTATAGATCAGGAC
*** * *
3723851 CTTTAGCGGCGCTTTTTTTATAAACGCCGCTATAGATCATGAC
1 CTTTAGCGGCGCTTTTCCCACAAACGCCGCTATAGATCAGGAC
* * * **
3723894 TTTTAGCGACGTTTTTTTCACAAACGCCGCTA
1 CTTTAGCGGCGCTTTTCCCACAAACGCCGCTA
3723926 AAAGTGCCAT
Statistics
Matches: 182, Mismatches: 20, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
42 39 0.21
43 143 0.79
ACGTcount: A:0.26, C:0.30, G:0.17, T:0.26
Consensus pattern (43 bp):
CTTTAGCGGCGCTTTTCCCACAAACGCCGCTATAGATCAGGAC
Found at i:3723865 original size:128 final size:129
Alignment explanation
Indices: 3723680--3723925 Score: 334
Period size: 128 Copynumber: 1.9 Consensus size: 129
3723670 GCGTCGCTAA
* * *
3723680 CTTTAGCGGCGCTTTTCCCACAAACGCCGCTAAAAACCAGGACCTTTAGCGGCGCTTTTCCCACA
1 CTTTAGCGGCACTTTTCACACAAACGCCGCTAAAAACCAAGACCTTTAGCGGCGCTTTTCCCACA
3723745 AACGCCGCTATAGATCA-GAACCTTTAGCGACACTTTTCCCACAAACGCCGCTATAGATCAGGAC
66 AACGCCGCTATAGATCATG-ACCTTTAGCGACACTTTTCCCACAAACGCCGCTATAGATCAGGAC
* * * *** *
3723809 CTTTAGCGGCACTTTT-ACACAAACGCCGCTATAGATCAAGACCTTTAGCGGCGCTTTTTTTATA
1 CTTTAGCGGCACTTTTCACACAAACGCCGCTAAAAACCAAGACCTTTAGCGGCGCTTTTCCCACA
* ** **
3723873 AACGCCGCTATAGATCATGACTTTTAGCGACGTTTTTTTCACAAACGCCGCTA
66 AACGCCGCTATAGATCATGACCTTTAGCGACACTTTTCCCACAAACGCCGCTA
3723926 AAAGTGCCAT
Statistics
Matches: 101, Mismatches: 15, Indels: 3
0.85 0.13 0.03
Matches are distributed among these distances:
128 85 0.84
129 16 0.16
ACGTcount: A:0.26, C:0.30, G:0.17, T:0.26
Consensus pattern (129 bp):
CTTTAGCGGCACTTTTCACACAAACGCCGCTAAAAACCAAGACCTTTAGCGGCGCTTTTCCCACA
AACGCCGCTATAGATCATGACCTTTAGCGACACTTTTCCCACAAACGCCGCTATAGATCAGGAC
Found at i:3728504 original size:21 final size:21
Alignment explanation
Indices: 3728480--3728520 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
3728470 AACCCTAAAT
3728480 CCCTAACTCTTAACCCCTAAC
1 CCCTAACTCTTAACCCCTAAC
*
3728501 CCCTAACTCTTAATCCCTAA
1 CCCTAACTCTTAACCCCTAA
3728521 ACCTTAAATC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.29, C:0.44, G:0.00, T:0.27
Consensus pattern (21 bp):
CCCTAACTCTTAACCCCTAAC
Found at i:3728757 original size:23 final size:24
Alignment explanation
Indices: 3728718--3728771 Score: 76
Period size: 22 Copynumber: 2.3 Consensus size: 24
3728708 TATATGAAAT
*
3728718 TATTTAATATATAAATTAAAAAAA
1 TATTTAATAAATAAATTAAAAAAA
3728742 TATTTAA-AAATAAATT-AAAAAA
1 TATTTAATAAATAAATTAAAAAAA
*
3728764 TAATTAAT
1 TATTTAAT
3728772 CTAAACCCAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
22 12 0.44
23 8 0.30
24 7 0.26
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (24 bp):
TATTTAATAAATAAATTAAAAAAA
Found at i:3728836 original size:22 final size:22
Alignment explanation
Indices: 3728801--3728863 Score: 83
Period size: 22 Copynumber: 2.9 Consensus size: 22
3728791 TTGACCCATG
* *
3728801 AACTCATAAACCCTAAATCCCT
1 AACTCATAACCCCTAAACCCCT
*
3728823 AACTCTTAACCCCTAAACCCCT
1 AACTCATAACCCCTAAACCCCT
3728845 AAC-CACTAACCCCTAAACC
1 AACTCA-TAACCCCTAAACC
3728864 TTAAATCTCA
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
21 1 0.03
22 35 0.97
ACGTcount: A:0.38, C:0.43, G:0.00, T:0.19
Consensus pattern (22 bp):
AACTCATAACCCCTAAACCCCT
Found at i:3728912 original size:15 final size:15
Alignment explanation
Indices: 3728876--3728916 Score: 59
Period size: 14 Copynumber: 2.9 Consensus size: 15
3728866 AAATCTCAAC
3728876 CCTTAAA-CCATAAT
1 CCTTAAATCCATAAT
*
3728890 CCCT-AATCCATAAT
1 CCTTAAATCCATAAT
3728904 CCTTAAATCCATA
1 CCTTAAATCCATA
3728917 CTCCATAAAC
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
13 2 0.09
14 13 0.57
15 8 0.35
ACGTcount: A:0.39, C:0.32, G:0.00, T:0.29
Consensus pattern (15 bp):
CCTTAAATCCATAAT
Found at i:3728925 original size:15 final size:15
Alignment explanation
Indices: 3728879--3728925 Score: 53
Period size: 15 Copynumber: 3.3 Consensus size: 15
3728869 TCTCAACCCT
*
3728879 TAAA-CCATAATCCC
1 TAAATCCATAATCCA
*
3728893 T-AATCCATAATCCT
1 TAAATCCATAATCCA
*
3728907 TAAATCCATACTCCA
1 TAAATCCATAATCCA
3728922 TAAA
1 TAAA
3728926 CCTTAAAACA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
13 2 0.07
14 11 0.39
15 15 0.54
ACGTcount: A:0.43, C:0.30, G:0.00, T:0.28
Consensus pattern (15 bp):
TAAATCCATAATCCA
Found at i:3729207 original size:41 final size:40
Alignment explanation
Indices: 3729150--3729265 Score: 162
Period size: 41 Copynumber: 2.9 Consensus size: 40
3729140 TAAAATGTTT
*
3729150 TTAGCGGTGCTTTTCCAAAAACGCCGCTAAAGCCCTTA-CCA
1 TTAGCGGCGCTTTTCCAAAAACGCCGCTAAAGCCC--AGCCA
*
3729191 TTAGCGGCGCTTTTCCAAAAACGCCGCTAAAGACCCAGGCA
1 TTAGCGGCGCTTTTCCAAAAACGCCGCTAAAG-CCCAGCCA
**
3729232 TTAGCGGCGCTTTTTGAAAAACGCCGCTAAAGCC
1 TTAGCGGCGCTTTTCCAAAAACGCCGCTAAAGCC
3729266 ACGAAATGTT
Statistics
Matches: 69, Mismatches: 4, Indels: 5
0.88 0.05 0.06
Matches are distributed among these distances:
40 3 0.04
41 63 0.91
42 3 0.04
ACGTcount: A:0.28, C:0.30, G:0.21, T:0.22
Consensus pattern (40 bp):
TTAGCGGCGCTTTTCCAAAAACGCCGCTAAAGCCCAGCCA
Found at i:3729345 original size:39 final size:39
Alignment explanation
Indices: 3729301--3729379 Score: 131
Period size: 39 Copynumber: 2.0 Consensus size: 39
3729291 TGGGCTAAGG
* *
3729301 TTTTTTGCGGCGTTTTTTTGAAAAACGCCACTAATGCTCA
1 TTTTTAGCGGCATTTTTTT-AAAAACGCCACTAATGCTCA
3729341 TTTTTAGCGGCATTTTTTTAAAAACGCCACTAATGCTCA
1 TTTTTAGCGGCATTTTTTTAAAAACGCCACTAATGCTCA
3729380 ATCTTTAGTG
Statistics
Matches: 37, Mismatches: 2, Indels: 1
0.93 0.05 0.03
Matches are distributed among these distances:
39 20 0.54
40 17 0.46
ACGTcount: A:0.25, C:0.20, G:0.15, T:0.39
Consensus pattern (39 bp):
TTTTTAGCGGCATTTTTTTAAAAACGCCACTAATGCTCA
Found at i:3729351 original size:40 final size:40
Alignment explanation
Indices: 3729301--3729438 Score: 136
Period size: 40 Copynumber: 3.5 Consensus size: 40
3729291 TGGGCTAAGG
*
3729301 TTTTTTGCGGCGTTTTTTTGAAAAACGCCACTAATGCTCA
1 TTTTTAGCGGCGTTTTTTTGAAAAACGCCACTAATGCTCA
*
3729341 TTTTTAGCGGCATTTTTTT-AAAAACGCCACTAATGCTCAA
1 TTTTTAGCGGCGTTTTTTTGAAAAACGCCACTAATGCTC-A
* * * *** * * *
3729381 TCTTTAGTGGCGATTTCCAG-AAAGCGCCGCTAATGCTTAA
1 TTTTTAGCGGCGTTTTTTTGAAAAACGCCACTAATGC-TCA
*
3729421 TTTTTACCGGCGTTTTTT
1 TTTTTAGCGGCGTTTTTT
3729439 GTCCAAACGC
Statistics
Matches: 77, Mismatches: 18, Indels: 6
0.76 0.18 0.06
Matches are distributed among these distances:
39 19 0.25
40 57 0.74
41 1 0.01
ACGTcount: A:0.23, C:0.20, G:0.17, T:0.39
Consensus pattern (40 bp):
TTTTTAGCGGCGTTTTTTTGAAAAACGCCACTAATGCTCA
Found at i:3731760 original size:42 final size:42
Alignment explanation
Indices: 3731667--3731760 Score: 136
Period size: 42 Copynumber: 2.2 Consensus size: 42
3731657 GAGGCATTCA
*
3731667 ACATGAAGAGCCTGTTAAGATAAAATGCTCAAATCTTAACAG
1 ACATGAAGAGCCTGTTAAGATAAAATGCTCAAATCTAAACAG
*
3731709 ACATAAAGAGCCTGTTAAGATAAAATGCTCAAATGC-AAACAG
1 ACATGAAGAGCCTGTTAAGATAAAATGCTCAAAT-CTAAACAG
* *
3731751 GCCTGAAGAG
1 ACATGAAGAG
3731761 GTAATTTTCC
Statistics
Matches: 46, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
42 45 0.98
43 1 0.02
ACGTcount: A:0.44, C:0.17, G:0.19, T:0.20
Consensus pattern (42 bp):
ACATGAAGAGCCTGTTAAGATAAAATGCTCAAATCTAAACAG
Found at i:3735212 original size:20 final size:18
Alignment explanation
Indices: 3735187--3735223 Score: 56
Period size: 20 Copynumber: 1.9 Consensus size: 18
3735177 ATATTATTTG
3735187 AATTTTTATGATTTTGTTTA
1 AATTTTTAT--TTTTGTTTA
3735207 AATTTTTATTTTTGTTT
1 AATTTTTATTTTTGTTT
3735224 TGTTAAATGC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 8 0.47
20 9 0.53
ACGTcount: A:0.22, C:0.00, G:0.08, T:0.70
Consensus pattern (18 bp):
AATTTTTATTTTTGTTTA
Found at i:3736818 original size:23 final size:23
Alignment explanation
Indices: 3736786--3736886 Score: 79
Period size: 21 Copynumber: 4.4 Consensus size: 23
3736776 TTAACAAGTC
*
3736786 AATAACTTAAATAAAATATTTTA
1 AATAATTTAAATAAAATATTTTA
3736809 AATAATTTAATTATGAAAAT-TTTTA
1 AATAATTTAA--AT-AAAATATTTTA
*
3736834 AATAATTT-AAT-AAATTTTTTA
1 AATAATTTAAATAAAATATTTTA
* *
3736855 AATGA-TTAAA-AATAA-ATTTATT
1 AATAATTTAAATAA-AATATTT-TA
3736877 AATAATTTAA
1 AATAATTTAA
3736887 TGATATTAGG
Statistics
Matches: 64, Mismatches: 5, Indels: 18
0.74 0.06 0.21
Matches are distributed among these distances:
20 6 0.09
21 15 0.23
22 9 0.14
23 13 0.20
24 1 0.02
25 15 0.23
26 5 0.08
ACGTcount: A:0.52, C:0.01, G:0.02, T:0.45
Consensus pattern (23 bp):
AATAATTTAAATAAAATATTTTA
Found at i:3747968 original size:21 final size:22
Alignment explanation
Indices: 3747944--3747984 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
3747934 ATATTTGAAA
3747944 TTTATTAAAA-AT-TAGAAAAAT
1 TTTA-TAAAATATATAGAAAAAT
3747965 TTTATAAAATATATAGAAAA
1 TTTATAAAATATATAGAAAA
3747985 TTATAAATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 5 0.28
21 6 0.33
22 7 0.39
ACGTcount: A:0.59, C:0.00, G:0.05, T:0.37
Consensus pattern (22 bp):
TTTATAAAATATATAGAAAAAT
Found at i:3747989 original size:10 final size:9
Alignment explanation
Indices: 3747949--3748034 Score: 57
Period size: 10 Copynumber: 8.9 Consensus size: 9
3747939 TGAAATTTAT
3747949 TAAAAATTA
1 TAAAAATTA
* *
3747958 GAAAAATTT
1 TAAAAATTA
3747967 TATAAAATATA
1 TA-AAAAT-TA
3747978 TAGAAAATTA
1 TA-AAAATTA
*
3747988 TAAATAAATA
1 TAAA-AATTA
*
3747998 TAAATAAATA
1 TAAA-AATTA
*
3748008 T-AAAATTCT
1 TAAAAATT-A
3748017 TAAAAAATTA
1 T-AAAAATTA
3748027 TAAAAATT
1 TAAAAATT
3748035 TATAGTACCA
Statistics
Matches: 62, Mismatches: 9, Indels: 12
0.75 0.11 0.14
Matches are distributed among these distances:
8 3 0.05
9 20 0.32
10 25 0.40
11 14 0.23
ACGTcount: A:0.63, C:0.01, G:0.02, T:0.34
Consensus pattern (9 bp):
TAAAAATTA
Found at i:3748024 original size:28 final size:29
Alignment explanation
Indices: 3747966--3748030 Score: 71
Period size: 28 Copynumber: 2.2 Consensus size: 29
3747956 TAGAAAAATT
*
3747966 TTATAAAATATATAGAAAATTATAAATAAA
1 TTAT-AAATAAATAGAAAATTATAAATAAA
* *
3747996 -TATAAATAAATATAAAATTCTTAAA-AAA
1 TTATAAATAAATAGAAAATT-ATAAATAAA
3748024 TTATAAA
1 TTATAAA
3748031 AATTTATAGT
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
28 17 0.57
29 13 0.43
ACGTcount: A:0.63, C:0.02, G:0.02, T:0.34
Consensus pattern (29 bp):
TTATAAATAAATAGAAAATTATAAATAAA
Found at i:3757996 original size:6 final size:6
Alignment explanation
Indices: 3757987--3758011 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
3757977 ATGGCAGCAA
3757987 CTGAAG CTGAAG CTGAAG CTGAAG C
1 CTGAAG CTGAAG CTGAAG CTGAAG C
3758012 AGAGCAGAGC
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:0.32, C:0.20, G:0.32, T:0.16
Consensus pattern (6 bp):
CTGAAG
Found at i:3784206 original size:21 final size:22
Alignment explanation
Indices: 3784180--3784226 Score: 78
Period size: 21 Copynumber: 2.2 Consensus size: 22
3784170 CTCTGCTCAA
*
3784180 ACTCCACCTGCTGCGGAGTAC-
1 ACTCCACCTGCTGCGAAGTACT
3784201 ACTCCACCTGCTGCGAAGTACT
1 ACTCCACCTGCTGCGAAGTACT
3784223 ACTC
1 ACTC
3784227 ACTCCTTCTG
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 20 0.83
22 4 0.17
ACGTcount: A:0.21, C:0.38, G:0.19, T:0.21
Consensus pattern (22 bp):
ACTCCACCTGCTGCGAAGTACT
Found at i:3806818 original size:33 final size:33
Alignment explanation
Indices: 3806781--3806916 Score: 167
Period size: 33 Copynumber: 4.3 Consensus size: 33
3806771 GTCTGCTTTA
*
3806781 TGTTTCTCTATTTTCTGTTTCTGTACCGTGTTT
1 TGTTTCTCTATTTTCTGTTTCTGTACCATGTTT
*
3806814 TGTTTCTTTATTTTCTGTTTCTGTACCATGTTT
1 TGTTTCTCTATTTTCTGTTTCTGTACCATGTTT
* * *
3806847 TGTTCCTCTATTTTCTGTAGT-GGT----T-TTT
1 TGTTTCTCTATTTTCTGT-TTCTGTACCATGTTT
3806875 TGTTTCTCTATTTTCTGTTTCTGTACCATGTTT
1 TGTTTCTCTATTTTCTGTTTCTGTACCATGTTT
*
3806908 TGTTCCTCT
1 TGTTTCTCT
3806917 TGCCATTTTT
Statistics
Matches: 86, Mismatches: 10, Indels: 14
0.78 0.09 0.13
Matches are distributed among these distances:
27 1 0.01
28 22 0.26
29 1 0.01
32 1 0.01
33 60 0.70
34 1 0.01
ACGTcount: A:0.07, C:0.18, G:0.14, T:0.61
Consensus pattern (33 bp):
TGTTTCTCTATTTTCTGTTTCTGTACCATGTTT
Found at i:3806819 original size:18 final size:17
Alignment explanation
Indices: 3806796--3806850 Score: 53
Period size: 18 Copynumber: 3.2 Consensus size: 17
3806786 CTCTATTTTC
3806796 TGTTTCTGTACCGTGTTT
1 TGTTTCTGTACC-TGTTT
*
3806814 TGTTTCTTTA--T-TTT
1 TGTTTCTGTACCTGTTT
3806828 CTGTTTCTGTACCATGTTT
1 -TGTTTCTGTACC-TGTTT
3806847 TGTT
1 TGTT
3806851 CCTCTATTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 10
0.71 0.05 0.24
Matches are distributed among these distances:
14 3 0.10
15 10 0.33
18 14 0.47
19 3 0.10
ACGTcount: A:0.07, C:0.15, G:0.16, T:0.62
Consensus pattern (17 bp):
TGTTTCTGTACCTGTTT
Found at i:3806862 original size:27 final size:28
Alignment explanation
Indices: 3806831--3806892 Score: 72
Period size: 28 Copynumber: 2.2 Consensus size: 28
3806821 TTATTTTCTG
3806831 TTTCTGTA-CCATGTTTTGTTCCTCTAT
1 TTTCTGTAGCCATGTTTTGTTCCTCTAT
*** * *
3806858 TTTCTGTAGTGGTTTTTTGTTTCTCTAT
1 TTTCTGTAGCCATGTTTTGTTCCTCTAT
3806886 TTTCTGT
1 TTTCTGT
3806893 TTCTGTACCA
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
27 8 0.28
28 21 0.72
ACGTcount: A:0.08, C:0.16, G:0.15, T:0.61
Consensus pattern (28 bp):
TTTCTGTAGCCATGTTTTGTTCCTCTAT
Found at i:3808010 original size:21 final size:22
Alignment explanation
Indices: 3807984--3808039 Score: 87
Period size: 21 Copynumber: 2.6 Consensus size: 22
3807974 AGTTTCCCCC
3807984 GTTTGCAGTGGCTATACAA-TT
1 GTTTGCAGTGGCTATACAATTT
*
3808005 GTTTGCAGTGGCTATATAATTT
1 GTTTGCAGTGGCTATACAATTT
*
3808027 ATTTGCAGTGGCT
1 GTTTGCAGTGGCT
3808040 CCATCTGCTT
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
21 18 0.56
22 14 0.44
ACGTcount: A:0.21, C:0.12, G:0.25, T:0.41
Consensus pattern (22 bp):
GTTTGCAGTGGCTATACAATTT
Found at i:3811497 original size:11 final size:11
Alignment explanation
Indices: 3811481--3811507 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
3811471 TAGAAATTAG
3811481 TTTGTGAAACT
1 TTTGTGAAACT
3811492 TTTGTGAAACT
1 TTTGTGAAACT
3811503 TTTGT
1 TTTGT
3811508 ATTGATTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.22, C:0.07, G:0.19, T:0.52
Consensus pattern (11 bp):
TTTGTGAAACT
Found at i:3813037 original size:93 final size:92
Alignment explanation
Indices: 3812905--3813099 Score: 286
Period size: 93 Copynumber: 2.1 Consensus size: 92
3812895 TTGATTTTAG
* *
3812905 TAAATTCATATAAGAACATTTTATTATTAAGAATTTTATGAAATTATATATCACTA-TATAATTA
1 TAAATTCATATAAGAAAATTTTATTATCAAGAATTTTATGAAATTATATATCACTATTA-AATTA
* *
3812969 TATTTAAT-ATTAATTATTTTAAATTGTA
65 TATGTAATAATT-ATTATTTTAAATTATA
* *
3812997 TAAATTCATATAAGAAAATTTTTATTATCAAGAATTTTATGAAATTATATATTATTATTAAATTA
1 TAAATTCATATAAGAAAA-TTTTATTATCAAGAATTTTATGAAATTATATATCACTATTAAATTA
3813062 TATGTAATAATTATTATTTTAAATTATA
65 TATGTAATAATTATTATTTTAAATTATA
*
3813090 CAAATTCATA
1 TAAATTCATA
3813100 AACTATAATC
Statistics
Matches: 93, Mismatches: 7, Indels: 5
0.89 0.07 0.05
Matches are distributed among these distances:
92 17 0.18
93 71 0.76
94 5 0.05
ACGTcount: A:0.45, C:0.04, G:0.04, T:0.47
Consensus pattern (92 bp):
TAAATTCATATAAGAAAATTTTATTATCAAGAATTTTATGAAATTATATATCACTATTAAATTAT
ATGTAATAATTATTATTTTAAATTATA
Found at i:3813157 original size:17 final size:17
Alignment explanation
Indices: 3813132--3813165 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
3813122 ATAATTTTAA
*
3813132 ATTTTATTAAATCATAT
1 ATTTAATTAAATCATAT
3813149 ATTTAATTAAATCATAT
1 ATTTAATTAAATCATAT
3813166 TTAATATTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.44, C:0.06, G:0.00, T:0.50
Consensus pattern (17 bp):
ATTTAATTAAATCATAT
Found at i:3813167 original size:15 final size:16
Alignment explanation
Indices: 3813132--3813170 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 16
3813122 ATAATTTTAA
*
3813132 ATTTTATTAAATCATAT
1 ATTTAATTAAATCA-AT
3813149 ATTTAATTAAATC-AT
1 ATTTAATTAAATCAAT
3813164 ATTTAAT
1 ATTTAAT
3813171 ATTAATTATT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 9 0.43
17 12 0.57
ACGTcount: A:0.44, C:0.05, G:0.00, T:0.51
Consensus pattern (16 bp):
ATTTAATTAAATCAAT
Found at i:3813174 original size:17 final size:18
Alignment explanation
Indices: 3813136--3813175 Score: 57
Period size: 17 Copynumber: 2.3 Consensus size: 18
3813126 TTTTAAATTT
*
3813136 TATTAAATCATATATTTA
1 TATTAAATCATATATTAA
3813154 -ATTAAATCATAT-TTAA
1 TATTAAATCATATATTAA
3813170 TATTAA
1 TATTAA
3813176 TTATTTGAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
16 3 0.15
17 17 0.85
ACGTcount: A:0.47, C:0.05, G:0.00, T:0.47
Consensus pattern (18 bp):
TATTAAATCATATATTAA
Found at i:3813290 original size:15 final size:15
Alignment explanation
Indices: 3813255--3813389 Score: 70
Period size: 15 Copynumber: 8.9 Consensus size: 15
3813245 TTAAGAATTT
*
3813255 TATTAAATTAT-ATA
1 TATTTAATTATAATA
3813269 T-TTTAATTATAATA
1 TATTTAATTATAATA
*
3813283 TATTTAATAATAAT-
1 TATTTAATTATAATA
3813297 TATGTTAATT-T-ATA
1 TAT-TTAATTATAATA
* *
3813311 T-TTTACAGTATCATA
1 TATTTA-ATTATAATA
*
3813326 TATTATGATTTGAGTAAATTCA
1 TATT-T-AATT-A-T-AA-T-A
*
3813348 TATTAAATTAT-ATA
1 TATTTAATTATAATA
3813362 T-TTTAATTATAATA
1 TATTTAATTATAATA
*
3813376 TATTTAATAATAAT
1 TATTTAATTATAAT
3813390 TATGTTTAAA
Statistics
Matches: 93, Mismatches: 11, Indels: 33
0.68 0.08 0.24
Matches are distributed among these distances:
12 3 0.03
13 21 0.23
14 17 0.18
15 32 0.34
16 3 0.03
17 2 0.02
18 3 0.03
19 2 0.02
20 4 0.04
21 1 0.01
22 5 0.05
ACGTcount: A:0.43, C:0.02, G:0.04, T:0.51
Consensus pattern (15 bp):
TATTTAATTATAATA
Found at i:3813297 original size:120 final size:119
Alignment explanation
Indices: 3813131--3813349 Score: 345
Period size: 120 Copynumber: 1.8 Consensus size: 119
3813121 AATAATTTTA
* *
3813131 AATTTTATTAAATCATATATTTAATTAAATCATATTTAATATTAATTAT-TTGAAATTT-TCTTT
1 AATTTTATTAAATCATATATTTAATTAAATCATATTTAATAATAATTATGTT--AATTTATATTT
*
3813194 TATAGTATCATATATTATGATTTGAGTAAATTCATAGAAGAATTTTATTTATTAAG
64 TACAGTATCATATATTATGATTTGAGTAAATTCATAGAAGAATTTTATTTATTAAG
*
3813250 AATTTTATTAAATTATATATTTTAATTATAAT-ATATTTAATAATAATTATGTTAATTTATATTT
1 AATTTTATTAAATCATATA-TTTAATTA-AATCATATTTAATAATAATTATGTTAATTTATATTT
3813314 TACAGTATCATATATTATGATTTGAGTAAATTCATA
64 TACAGTATCATATATTATGATTTGAGTAAATTCATA
3813350 TTAAATTATA
Statistics
Matches: 92, Mismatches: 4, Indels: 7
0.89 0.04 0.07
Matches are distributed among these distances:
119 23 0.25
120 64 0.70
121 5 0.05
ACGTcount: A:0.40, C:0.04, G:0.06, T:0.50
Consensus pattern (119 bp):
AATTTTATTAAATCATATATTTAATTAAATCATATTTAATAATAATTATGTTAATTTATATTTTA
CAGTATCATATATTATGATTTGAGTAAATTCATAGAAGAATTTTATTTATTAAG
Found at i:3813378 original size:16 final size:16
Alignment explanation
Indices: 3813357--3813398 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
3813347 ATATTAAATT
*
3813357 ATATATTTTAATTATA
1 ATATATTTTAATAATA
3813373 ATATA-TTTAATAATA
1 ATATATTTTAATAATA
3813388 AT-TATGTTTAA
1 ATATAT-TTTAA
3813399 ATATGATTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 2 0.09
15 11 0.48
16 10 0.43
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (16 bp):
ATATATTTTAATAATA
Found at i:3813506 original size:154 final size:156
Alignment explanation
Indices: 3813348--3813645 Score: 537
Period size: 154 Copynumber: 1.9 Consensus size: 156
3813338 AGTAAATTCA
*
3813348 TATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTTAAATATGATTAAATTA
1 TATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTTAAATATGATTAAATTA
3813413 TTTATTATTGAT-AT-TAATCTTATTAAAATTTAAATAACAATAACAATAATAATTTACCAAAAC
66 TTTATTATTGATAATATAATCTTATTAAAATTTAAATAACAATAACAATAATAATTTACCAAAAC
3813476 AAATTTATGCTAATTATTAAGAATTT
131 AAATTTATGCTAATTATTAAGAATTT
3813502 TATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTTAAATATGATTAAATTA
1 TATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTTAAATATGATTAAATTA
* *
3813567 TTTATTATTGATAATAATAATCTTATTAAAATTTAAATAACAATAACAATAATCATTTATCAAAA
66 TTTATTATTGATAAT-ATAATCTTATTAAAATTTAAATAACAATAACAATAATAATTTACCAAAA
*
3813632 CAAATTTCTGCTAA
130 CAAATTTATGCTAA
3813646 GGGTATTCTA
Statistics
Matches: 137, Mismatches: 4, Indels: 3
0.95 0.03 0.02
Matches are distributed among these distances:
154 76 0.55
155 2 0.01
157 59 0.43
ACGTcount: A:0.47, C:0.05, G:0.03, T:0.45
Consensus pattern (156 bp):
TATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTTAAATATGATTAAATTA
TTTATTATTGATAATATAATCTTATTAAAATTTAAATAACAATAACAATAATAATTTACCAAAAC
AAATTTATGCTAATTATTAAGAATTT
Found at i:3813526 original size:18 final size:17
Alignment explanation
Indices: 3813498--3813532 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
3813488 ATTATTAAGA
*
3813498 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
3813515 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
3813533 TTAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:3813786 original size:16 final size:16
Alignment explanation
Indices: 3813765--3813803 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
3813755 TTGATTTGCT
*
3813765 ATTACACAGCTTTTCC
1 ATTACACAGCTATTCC
**
3813781 ATTACACCTCTATTCC
1 ATTACACAGCTATTCC
3813797 ATTACAC
1 ATTACAC
3813804 CTCTAATCCA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.28, C:0.33, G:0.03, T:0.36
Consensus pattern (16 bp):
ATTACACAGCTATTCC
Found at i:3813804 original size:16 final size:16
Alignment explanation
Indices: 3813778--3813834 Score: 87
Period size: 16 Copynumber: 3.6 Consensus size: 16
3813768 ACACAGCTTT
* *
3813778 TCCATTACACCTCTAT
1 TCCAATACACCTCTAA
*
3813794 TCCATTACACCTCTAA
1 TCCAATACACCTCTAA
3813810 TCCAATACACCTCTAA
1 TCCAATACACCTCTAA
3813826 TCCAATACA
1 TCCAATACA
3813835 GCGAACCAAA
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 39 1.00
ACGTcount: A:0.33, C:0.37, G:0.00, T:0.30
Consensus pattern (16 bp):
TCCAATACACCTCTAA
Found at i:3813986 original size:21 final size:21
Alignment explanation
Indices: 3813957--3813996 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
3813947 TAGAAAAAGC
*
3813957 AGGAGAGAAAGAAACGAAACA
1 AGGAAAGAAAGAAACGAAACA
*
3813978 AGGAAAGAAAGAAAGGAAA
1 AGGAAAGAAAGAAACGAAA
3813997 GAAAAAGAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.65, C:0.05, G:0.30, T:0.00
Consensus pattern (21 bp):
AGGAAAGAAAGAAACGAAACA
Found at i:3814024 original size:16 final size:14
Alignment explanation
Indices: 3813963--3814015 Score: 54
Period size: 16 Copynumber: 3.5 Consensus size: 14
3813953 AAGCAGGAGA
3813963 GAAAGAAACGAAACAAG
1 GAAAGAAA-G-AA-AAG
3813980 GAAAGAAAG-AAAG
1 GAAAGAAAGAAAAG
3813993 GAAAGAAAAAGAAAAG
1 GAAAG--AAAGAAAAG
3814009 GAAAGAA
1 GAAAGAA
3814016 GGAGAAAAGA
Statistics
Matches: 33, Mismatches: 0, Indels: 9
0.79 0.00 0.21
Matches are distributed among these distances:
13 8 0.24
14 3 0.09
15 4 0.12
16 10 0.30
17 8 0.24
ACGTcount: A:0.70, C:0.04, G:0.26, T:0.00
Consensus pattern (14 bp):
GAAAGAAAGAAAAG
Found at i:3821643 original size:41 final size:41
Alignment explanation
Indices: 3821586--3821824 Score: 340
Period size: 41 Copynumber: 5.8 Consensus size: 41
3821576 GAATGTAATA
3821586 CAGACTTTAAGTCTAGCAGGCTTAATGCCGGTGATACATTT
1 CAGACTTTAAGTCTAGCAGGCTTAATGCCGGTGATACATTT
*
3821627 CAGACTTTAAGTCTAGCAAGCTTAATGCCGGTGATACATTT
1 CAGACTTTAAGTCTAGCAGGCTTAATGCCGGTGATACATTT
3821668 CAGACTTTAAGTCTAGCAGGCTTAATGCCGGTGATACATTT
1 CAGACTTTAAGTCTAGCAGGCTTAATGCCGGTGATACATTT
* *
3821709 CAGACTATATGTCTAGCAGGCTTAATGCCGGTGATACATTT
1 CAGACTTTAAGTCTAGCAGGCTTAATGCCGGTGATACATTT
* * *
3821750 CAGACTATATGTCTAGCAGGC-TAAGTGCCGGTG-TAC-TGAAT
1 CAGACTTTAAGTCTAGCAGGCTTAA-TGCCGGTGATACAT--TT
* * **
3821791 CAGGCTTTAAGCCTAGCAGGCAAAATGCCGGTGA
1 CAGACTTTAAGTCTAGCAGGCTTAATGCCGGTGA
3821825 ATCTGTTTAA
Statistics
Matches: 183, Mismatches: 10, Indels: 9
0.91 0.05 0.04
Matches are distributed among these distances:
39 1 0.01
40 6 0.03
41 174 0.95
42 2 0.01
ACGTcount: A:0.28, C:0.20, G:0.23, T:0.29
Consensus pattern (41 bp):
CAGACTTTAAGTCTAGCAGGCTTAATGCCGGTGATACATTT
Found at i:3828783 original size:41 final size:41
Alignment explanation
Indices: 3828726--3829084 Score: 571
Period size: 41 Copynumber: 8.8 Consensus size: 41
3828716 TGTAATACAA
3828726 ACTTTAAGTCTAGCAGGCTTAATGCCGGTGATACATTTCAG
1 ACTTTAAGTCTAGCAGGCTTAATGCCGGTGATACATTTCAG
3828767 ACTTTAAGTCTAGCAGGCTTAATGCCGGTGATACATTTCAG
1 ACTTTAAGTCTAGCAGGCTTAATGCCGGTGATACATTTCAG
3828808 ACTTTAAGTCTAGCAGGCTTAATGCCGGTGATACATTTCAG
1 ACTTTAAGTCTAGCAGGCTTAATGCCGGTGATACATTTCAG
* *
3828849 ACTATATGTCTAGCAGGCTTAATGCCGGTGATACATTTCAG
1 ACTTTAAGTCTAGCAGGCTTAATGCCGGTGATACATTTCAG
3828890 ACTTTAAGTCTAGCAGGCTTAATGCCGGTGATACATTTCAG
1 ACTTTAAGTCTAGCAGGCTTAATGCCGGTGATACATTTCAG
3828931 ACTTTAAGTCTAGCAGGCTTAATGCCGGTGATACATTTCAG
1 ACTTTAAGTCTAGCAGGCTTAATGCCGGTGATACATTTCAG
* *
3828972 ACTATATGTCTAGCAGGCTTAATGCCGGTGATACATTTCAG
1 ACTTTAAGTCTAGCAGGCTTAATGCCGGTGATACATTTCAG
* * *
3829013 ACTATATGTCTAGCAGGC-TAAGTGCCGGTG-TAC-TGAATCAG
1 ACTTTAAGTCTAGCAGGCTTAA-TGCCGGTGATACAT--TTCAG
* * **
3829054 GCTTTAAGCCTAGCAGGCAAAATGCCGGTGA
1 ACTTTAAGTCTAGCAGGCTTAATGCCGGTGA
3829085 ATCTGTTTAA
Statistics
Matches: 301, Mismatches: 12, Indels: 9
0.93 0.04 0.03
Matches are distributed among these distances:
39 1 0.00
40 6 0.02
41 292 0.97
42 2 0.01
ACGTcount: A:0.27, C:0.20, G:0.23, T:0.30
Consensus pattern (41 bp):
ACTTTAAGTCTAGCAGGCTTAATGCCGGTGATACATTTCAG
Found at i:3834048 original size:5 final size:5
Alignment explanation
Indices: 3834047--3834077 Score: 53
Period size: 5 Copynumber: 6.2 Consensus size: 5
3834037 TAATATATTA
*
3834047 TATAT TATAT TATAT TATAT TATAT AATAT T
1 TATAT TATAT TATAT TATAT TATAT TATAT T
3834078 GTATGTCTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (5 bp):
TATAT
Found at i:3837943 original size:150 final size:150
Alignment explanation
Indices: 3837672--3837953 Score: 555
Period size: 150 Copynumber: 1.9 Consensus size: 150
3837662 AATTCATATT
3837672 TTTAAACCGAATATACTGTGAATAATCATAAAAATAATTATTCCATTGAAACGTTCATTATTATA
1 TTTAAACCGAATATACTGTGAATAATCATAAAAATAATTATTCCATTGAAACGTTCATTATTATA
*
3837737 AACTATACCATACAAATAGACGAAAAATTAAAATATAATCCAATAAACACTACAGGAAAATGGGG
66 AACTATACCATACAAATAGACGAAAAATTAAAATATAATCCAATAAACACTACAGGAAAATAGGG
3837802 CTATTGCTCTGTTTTTAGCG
131 CTATTGCTCTGTTTTTAGCG
3837822 TTTAAACCGAATATACTGTGAATAATCATAAAAATAATTATTCCATTGAAACGTTCATTATTATA
1 TTTAAACCGAATATACTGTGAATAATCATAAAAATAATTATTCCATTGAAACGTTCATTATTATA
3837887 AACTATACCATACAAATAGACGAAAAATTAAAATATAATCCAATAAACACTACAGGAAAATAGGG
66 AACTATACCATACAAATAGACGAAAAATTAAAATATAATCCAATAAACACTACAGGAAAATAGGG
3837952 CT
131 CT
3837954 TTAGCGGCGT
Statistics
Matches: 131, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
150 131 1.00
ACGTcount: A:0.46, C:0.15, G:0.10, T:0.29
Consensus pattern (150 bp):
TTTAAACCGAATATACTGTGAATAATCATAAAAATAATTATTCCATTGAAACGTTCATTATTATA
AACTATACCATACAAATAGACGAAAAATTAAAATATAATCCAATAAACACTACAGGAAAATAGGG
CTATTGCTCTGTTTTTAGCG
Found at i:3838017 original size:18 final size:18
Alignment explanation
Indices: 3837994--3838029 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
3837984 AAATGTCGCT
3837994 AAAAACGCCACTAAAAAC
1 AAAAACGCCACTAAAAAC
*
3838012 AAAAACGCCGCTAAAAAC
1 AAAAACGCCACTAAAAAC
3838030 CAGAGCAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.58, C:0.28, G:0.08, T:0.06
Consensus pattern (18 bp):
AAAAACGCCACTAAAAAC
Found at i:3838058 original size:41 final size:41
Alignment explanation
Indices: 3838013--3838312 Score: 433
Period size: 41 Copynumber: 7.4 Consensus size: 41
3838003 ACTAAAAACA
* * *
3838013 AAAACGCCGCTAAAAACCAGAGCAATAGCGGCGCTTTTGGT
1 AAAACGCCGCTAAAAACCAGAGCATTAGCGGCGCTTTCGAT
3838054 AAAACGCCGCTAAAAACCAGAGCATTAGCGGCGCTTTCGAT
1 AAAACGCCGCTAAAAACCAGAGCATTAGCGGCGCTTTCGAT
* *
3838095 AAAACGCCGCTAAAAATCAGAGCATTAGC-GCACTTTCGAT
1 AAAACGCCGCTAAAAACCAGAGCATTAGCGGCGCTTTCGAT
* * * *
3838135 AAAACGCCGCTAAAAACTAGAGCATTAGCGGCGTTTTTGGT
1 AAAACGCCGCTAAAAACCAGAGCATTAGCGGCGCTTTCGAT
*
3838176 AAAACGCCGCTAAAAATCAGAGCATTAGCGGCGCTTTCGAT
1 AAAACGCCGCTAAAAACCAGAGCATTAGCGGCGCTTTCGAT
* * * * *
3838217 AAAACGCCTCTAGAAACCATAGAATTAGCGGCGCTTCCGAT
1 AAAACGCCGCTAAAAACCAGAGCATTAGCGGCGCTTTCGAT
* *
3838258 -AAACGCCACTAAAAACCAGAGCATTAGCGGCGCTTTCGGT
1 AAAACGCCGCTAAAAACCAGAGCATTAGCGGCGCTTTCGAT
3838298 AAAACGCCGCTAAAA
1 AAAACGCCGCTAAAA
3838313 GTCATATACT
Statistics
Matches: 228, Mismatches: 29, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
40 71 0.31
41 157 0.69
ACGTcount: A:0.35, C:0.25, G:0.21, T:0.19
Consensus pattern (41 bp):
AAAACGCCGCTAAAAACCAGAGCATTAGCGGCGCTTTCGAT
Found at i:3838162 original size:81 final size:82
Alignment explanation
Indices: 3838013--3838312 Score: 433
Period size: 81 Copynumber: 3.7 Consensus size: 82
3838003 ACTAAAAACA
* * *
3838013 AAAACGCCGCTAAAAACCAGAGCAATAGCGGCGCTTTTGGTAAAACGCCGCTAAAAACCAGAGCA
1 AAAACGCCGCTAAAAACCAGAGCATTAGCGGCGCTTTCGATAAAACGCCGCTAAAAACCAGAGCA
3838078 TTAGCGGCGCTTTCGAT
66 TTAGCGGCGCTTTCGAT
* * *
3838095 AAAACGCCGCTAAAAATCAGAGCATTAGC-GCACTTTCGATAAAACGCCGCTAAAAACTAGAGCA
1 AAAACGCCGCTAAAAACCAGAGCATTAGCGGCGCTTTCGATAAAACGCCGCTAAAAACCAGAGCA
* * *
3838159 TTAGCGGCGTTTTTGGT
66 TTAGCGGCGCTTTCGAT
* * * * *
3838176 AAAACGCCGCTAAAAATCAGAGCATTAGCGGCGCTTTCGATAAAACGCCTCTAGAAACCATAGAA
1 AAAACGCCGCTAAAAACCAGAGCATTAGCGGCGCTTTCGATAAAACGCCGCTAAAAACCAGAGCA
*
3838241 TTAGCGGCGCTTCCGAT
66 TTAGCGGCGCTTTCGAT
* *
3838258 -AAACGCCACTAAAAACCAGAGCATTAGCGGCGCTTTCGGTAAAACGCCGCTAAAA
1 AAAACGCCGCTAAAAACCAGAGCATTAGCGGCGCTTTCGATAAAACGCCGCTAAAA
3838313 GTCATATACT
Statistics
Matches: 193, Mismatches: 24, Indels: 3
0.88 0.11 0.01
Matches are distributed among these distances:
81 124 0.64
82 69 0.36
ACGTcount: A:0.35, C:0.25, G:0.21, T:0.19
Consensus pattern (82 bp):
AAAACGCCGCTAAAAACCAGAGCATTAGCGGCGCTTTCGATAAAACGCCGCTAAAAACCAGAGCA
TTAGCGGCGCTTTCGAT
Found at i:3838173 original size:122 final size:123
Alignment explanation
Indices: 3838013--3838312 Score: 469
Period size: 122 Copynumber: 2.5 Consensus size: 123
3838003 ACTAAAAACA
*
3838013 AAAACGCCGCTAAAAACCAGAGCAATAGCGGCGCTTTTGGTAAAACGCCGCTAAAAACCAGAGCA
1 AAAACGCCGCTAAAAACCAGAGCATTAGCGGCGCTTTTGGTAAAACGCCGCTAAAAACCAGAGCA
* * *
3838078 TTAGCGGCGCTTTCGATAAAACGCCGCTAAAAATCAGAGCATTAGC-GCACTTTCGAT
66 TTAGCGGCGCTTTCGATAAAACGCCGCTAAAAACCAGAGAATTAGCGGCACTTCCGAT
* * *
3838135 AAAACGCCGCTAAAAACTAGAGCATTAGCGGCGTTTTTGGTAAAACGCCGCTAAAAATCAGAGCA
1 AAAACGCCGCTAAAAACCAGAGCATTAGCGGCGCTTTTGGTAAAACGCCGCTAAAAACCAGAGCA
* * * *
3838200 TTAGCGGCGCTTTCGATAAAACGCCTCTAGAAACCATAGAATTAGCGGCGCTTCCGAT
66 TTAGCGGCGCTTTCGATAAAACGCCGCTAAAAACCAGAGAATTAGCGGCACTTCCGAT
* *
3838258 -AAACGCCACTAAAAACCAGAGCATTAGCGGCGCTTTCGGTAAAACGCCGCTAAAA
1 AAAACGCCGCTAAAAACCAGAGCATTAGCGGCGCTTTTGGTAAAACGCCGCTAAAA
3838313 GTCATATACT
Statistics
Matches: 162, Mismatches: 15, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
122 153 0.94
123 9 0.06
ACGTcount: A:0.35, C:0.25, G:0.21, T:0.19
Consensus pattern (123 bp):
AAAACGCCGCTAAAAACCAGAGCATTAGCGGCGCTTTTGGTAAAACGCCGCTAAAAACCAGAGCA
TTAGCGGCGCTTTCGATAAAACGCCGCTAAAAACCAGAGAATTAGCGGCACTTCCGAT
Found at i:3850173 original size:26 final size:26
Alignment explanation
Indices: 3850137--3850188 Score: 95
Period size: 26 Copynumber: 2.0 Consensus size: 26
3850127 AATAAACTCT
*
3850137 CAGAGCTAGCTAAAATTTATGGTTTA
1 CAGAGCTAGCTAAAATGTATGGTTTA
3850163 CAGAGCTAGCTAAAATGTATGGTTTA
1 CAGAGCTAGCTAAAATGTATGGTTTA
3850189 AAAACTAGTA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.35, C:0.12, G:0.21, T:0.33
Consensus pattern (26 bp):
CAGAGCTAGCTAAAATGTATGGTTTA
Found at i:3853815 original size:24 final size:24
Alignment explanation
Indices: 3853782--3853830 Score: 89
Period size: 24 Copynumber: 2.0 Consensus size: 24
3853772 TAACAGTTCA
*
3853782 GTTTAGTGTAAAGACTTCTAACTC
1 GTTTACTGTAAAGACTTCTAACTC
3853806 GTTTACTGTAAAGACTTCTAACTC
1 GTTTACTGTAAAGACTTCTAACTC
3853830 G
1 G
3853831 AAGAGTGATC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.29, C:0.18, G:0.16, T:0.37
Consensus pattern (24 bp):
GTTTACTGTAAAGACTTCTAACTC
Found at i:3858197 original size:13 final size:13
Alignment explanation
Indices: 3858179--3858207 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
3858169 AATACCCAGA
3858179 AAGCGTACAAAGG
1 AAGCGTACAAAGG
3858192 AAGCGTACAAAGG
1 AAGCGTACAAAGG
3858205 AAG
1 AAG
3858208 AACCAGGAGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.48, C:0.14, G:0.31, T:0.07
Consensus pattern (13 bp):
AAGCGTACAAAGG
Found at i:3863856 original size:56 final size:57
Alignment explanation
Indices: 3863770--3863883 Score: 212
Period size: 56 Copynumber: 2.0 Consensus size: 57
3863760 AAGTAATGCA
*
3863770 TTCAAAACTACTATCTTTAATTGGTATAA-TTTTTATGAAAAGTAGCAAGTTTCGCT
1 TTCAAAACTACTATCTTTAACTGGTATAATTTTTTATGAAAAGTAGCAAGTTTCGCT
3863826 TTCAAAACTACTATCTTTAACTGGTATAATTTTTTATGAAAAGTAGCAAGTTTCGCT
1 TTCAAAACTACTATCTTTAACTGGTATAATTTTTTATGAAAAGTAGCAAGTTTCGCT
3863883 T
1 T
3863884 CTAATGTATT
Statistics
Matches: 56, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
56 28 0.50
57 28 0.50
ACGTcount: A:0.33, C:0.13, G:0.12, T:0.41
Consensus pattern (57 bp):
TTCAAAACTACTATCTTTAACTGGTATAATTTTTTATGAAAAGTAGCAAGTTTCGCT
Found at i:3864779 original size:4 final size:4
Alignment explanation
Indices: 3864770--3864795 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
3864760 CTTTCTAGTT
3864770 TTTA TTTA TTTA TTTA TTTA TTTA TT
1 TTTA TTTA TTTA TTTA TTTA TTTA TT
3864796 ACTTAATCGA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (4 bp):
TTTA
Found at i:3866586 original size:9 final size:9
Alignment explanation
Indices: 3866569--3866600 Score: 55
Period size: 9 Copynumber: 3.4 Consensus size: 9
3866559 GCATCATCTT
3866569 CATCTTCCTC
1 CATC-TCCTC
3866579 CATCTCCTC
1 CATCTCCTC
3866588 CATCTCCTC
1 CATCTCCTC
3866597 CATC
1 CATC
3866601 ACATAATTAC
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
9 18 0.82
10 4 0.18
ACGTcount: A:0.12, C:0.53, G:0.00, T:0.34
Consensus pattern (9 bp):
CATCTCCTC
Found at i:3871861 original size:46 final size:46
Alignment explanation
Indices: 3871813--3872040 Score: 271
Period size: 46 Copynumber: 5.0 Consensus size: 46
3871803 GCTATCTGAT
* * * *
3871813 ATGAAATGTGTAATACCATGGTTGAAAGATACCATGGCAACCTGAT
1 ATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAACATGAC
*
3871859 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGAC
1 ATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAACATGAC
* *** * *
3871905 GA-GAAATGAATAAGACCATGGTTGAAAGATATGGTGGCAGCATAAC
1 -ATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAACATGAC
*
3871951 ATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACATGAC
1 ATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAACATGAC
* * * * *
3871997 A-GAAAAAGAGTAAGACCATAGTTGAAAGACACTATGGCATCATG
1 ATG-AAATGAGTAAGACCATGGTTGAAAGATACCATGGCAACATG
3872041 TCAAGGATAA
Statistics
Matches: 158, Mismatches: 21, Indels: 6
0.85 0.11 0.03
Matches are distributed among these distances:
45 2 0.01
46 155 0.98
47 1 0.01
ACGTcount: A:0.41, C:0.14, G:0.24, T:0.21
Consensus pattern (46 bp):
ATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAACATGAC
Found at i:3884049 original size:19 final size:21
Alignment explanation
Indices: 3884008--3884054 Score: 62
Period size: 20 Copynumber: 2.3 Consensus size: 21
3883998 TCTTATATAT
*
3884008 AAATAAAAGTCATAAATTT-A
1 AAATAAAAATCATAAATTTAA
*
3884028 AAATAAAAAT-ATATATTTAA
1 AAATAAAAATCATAAATTTAA
3884048 AAATAAA
1 AAATAAA
3884055 TAATGAAACA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 7 0.29
20 17 0.71
ACGTcount: A:0.66, C:0.02, G:0.02, T:0.30
Consensus pattern (21 bp):
AAATAAAAATCATAAATTTAA
Found at i:3888035 original size:39 final size:40
Alignment explanation
Indices: 3887992--3888103 Score: 113
Period size: 39 Copynumber: 2.8 Consensus size: 40
3887982 TCAGATAGTT
*
3887992 CGAAGTAATAGTTGACACCCAGTGTCTCATCG-GCCTAGC
1 CGAAGTAATAGTTGACACCCAGTGTCTCATCGAACCTAGC
** ** * *
3888031 CGAAGTAA-AGTTGGTACCCAGTACCTCATCGAATCTATC
1 CGAAGTAATAGTTGACACCCAGTGTCTCATCGAACCTAGC
*
3888070 CGAAGAAATA-TAGTGACACCCAGTGTCTCATCGA
1 CGAAGTAATAGT--TGACACCCAGTGTCTCATCGA
3888104 CTCGAGGTTG
Statistics
Matches: 57, Mismatches: 12, Indels: 6
0.76 0.16 0.08
Matches are distributed among these distances:
38 19 0.33
39 20 0.35
40 1 0.02
41 17 0.30
ACGTcount: A:0.30, C:0.26, G:0.21, T:0.23
Consensus pattern (40 bp):
CGAAGTAATAGTTGACACCCAGTGTCTCATCGAACCTAGC
Found at i:3889683 original size:5 final size:5
Alignment explanation
Indices: 3889665--3889700 Score: 63
Period size: 5 Copynumber: 7.0 Consensus size: 5
3889655 TTTCTTTTAT
3889665 ATATA ATAATA ATATA ATATA ATATA ATATA ATATA
1 ATATA AT-ATA ATATA ATATA ATATA ATATA ATATA
3889701 CTTAATTATT
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
5 25 0.83
6 5 0.17
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (5 bp):
ATATA
Found at i:3892346 original size:18 final size:17
Alignment explanation
Indices: 3892311--3892343 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
3892301 CTTTTTATTC
3892311 TTTTATTATTTCATTTA
1 TTTTATTATTTCATTTA
3892328 TTTTACTTATTT-ATTT
1 TTTTA-TTATTTCATTT
3892344 TATCATTTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.21, C:0.06, G:0.00, T:0.73
Consensus pattern (17 bp):
TTTTATTATTTCATTTA
Found at i:3896801 original size:39 final size:37
Alignment explanation
Indices: 3896734--3896826 Score: 98
Period size: 39 Copynumber: 2.5 Consensus size: 37
3896724 ACCAGAATGG
* *
3896734 CACCCAGTGCCTCATCGGATAGTTCGAAGCAATAGTTGA
1 CACCCAGTGCCTCATCGGAAAGTCCGAAG-AA-AGTTGA
* *
3896773 CACCCAGTGTCTCATCGGCAAAG-CCGAAGAAAGTTGG
1 CACCCAGTGCCTCATCGG-AAAGTCCGAAGAAAGTTGA
* *
3896810 TACCCAGTACCTCATCG
1 CACCCAGTGCCTCATCG
3896827 AATCTATCCG
Statistics
Matches: 46, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
37 19 0.41
38 2 0.04
39 22 0.48
40 3 0.07
ACGTcount: A:0.28, C:0.29, G:0.23, T:0.20
Consensus pattern (37 bp):
CACCCAGTGCCTCATCGGAAAGTCCGAAGAAAGTTGA
Found at i:3897187 original size:3 final size:3
Alignment explanation
Indices: 3897179--3897221 Score: 52
Period size: 3 Copynumber: 14.7 Consensus size: 3
3897169 TAATTCCCAC
* * *
3897179 TAA TAA TAA TAA TAA TAA TAC TAA TAA TAA -AT TAA TAC TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
3897222 TTATACTTAC
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
2 1 0.03
3 32 0.97
ACGTcount: A:0.60, C:0.05, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:3897947 original size:17 final size:16
Alignment explanation
Indices: 3897915--3897948 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
3897905 TTGGCTATTC
*
3897915 TGTTTCTTTCTTCTTT
1 TGTTTCTTTATTCTTT
3897931 TGTTTCTTTTATTCTTT
1 TGTTTC-TTTATTCTTT
3897948 T
1 T
3897949 ATTTTAACTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.03, C:0.15, G:0.06, T:0.76
Consensus pattern (16 bp):
TGTTTCTTTATTCTTT
Found at i:3897996 original size:14 final size:14
Alignment explanation
Indices: 3897937--3897987 Score: 50
Period size: 14 Copynumber: 3.6 Consensus size: 14
3897927 CTTTTGTTTC
*
3897937 TTTTA-TTCTTTTA
1 TTTTATTTCCTTTA
* *
3897950 TTTTAACTTACTTTA
1 TTTT-ATTTCCTTTA
*
3897965 CTTTATTTCCTTTA
1 TTTTATTTCCTTTA
3897979 TTTTATTTC
1 TTTTATTTC
3897988 TTTTGTTTTC
Statistics
Matches: 30, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
13 4 0.13
14 17 0.57
15 9 0.30
ACGTcount: A:0.18, C:0.14, G:0.00, T:0.69
Consensus pattern (14 bp):
TTTTATTTCCTTTA
Found at i:3898156 original size:14 final size:17
Alignment explanation
Indices: 3898137--3898173 Score: 53
Period size: 14 Copynumber: 2.4 Consensus size: 17
3898127 ATTTATTTCT
3898137 TAATATAA-T-ATTT-A
1 TAATATAATTAATTTAA
3898151 TAATATAATTAATTTAA
1 TAATATAATTAATTTAA
3898168 TAATAT
1 TAATAT
3898174 CCTTTATAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
14 8 0.40
15 1 0.05
16 4 0.20
17 7 0.35
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (17 bp):
TAATATAATTAATTTAA
Found at i:3904910 original size:25 final size:25
Alignment explanation
Indices: 3904882--3904940 Score: 73
Period size: 25 Copynumber: 2.4 Consensus size: 25
3904872 ATGGCTCTTA
* *
3904882 TGAGCTTGCCGATATACAGCTCGAT
1 TGAGCTTCCCGATATACAACTCGAT
* *
3904907 TGAGCTTCCCGTTATACAACTCGAA
1 TGAGCTTCCCGATATACAACTCGAT
*
3904932 AGAGCTTCC
1 TGAGCTTCC
3904941 TGTTTACATG
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
25 29 1.00
ACGTcount: A:0.25, C:0.27, G:0.20, T:0.27
Consensus pattern (25 bp):
TGAGCTTCCCGATATACAACTCGAT
Found at i:3912734 original size:21 final size:22
Alignment explanation
Indices: 3912708--3912754 Score: 78
Period size: 21 Copynumber: 2.2 Consensus size: 22
3912698 CTCTGCTCAA
*
3912708 ACTCCACCTGCTGCGGAGTAC-
1 ACTCCACCTGCTGCGAAGTACT
3912729 ACTCCACCTGCTGCGAAGTACT
1 ACTCCACCTGCTGCGAAGTACT
3912751 ACTC
1 ACTC
3912755 ACTCCTTCTG
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 20 0.83
22 4 0.17
ACGTcount: A:0.21, C:0.38, G:0.19, T:0.21
Consensus pattern (22 bp):
ACTCCACCTGCTGCGAAGTACT
Found at i:3920034 original size:38 final size:38
Alignment explanation
Indices: 3919987--3920060 Score: 130
Period size: 38 Copynumber: 1.9 Consensus size: 38
3919977 GTTATATAGA
* *
3919987 ATAAGAGTAGTACTTAAATAGACAGATCTAAACAATAT
1 ATAACAGTAGTACTTAAATAGACAAATCTAAACAATAT
3920025 ATAACAGTAGTACTTAAATAGACAAATCTAAACAAT
1 ATAACAGTAGTACTTAAATAGACAAATCTAAACAAT
3920061 CAAAAGATAT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
38 34 1.00
ACGTcount: A:0.51, C:0.12, G:0.11, T:0.26
Consensus pattern (38 bp):
ATAACAGTAGTACTTAAATAGACAAATCTAAACAATAT
Found at i:3923690 original size:25 final size:24
Alignment explanation
Indices: 3923645--3923692 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
3923635 CTTTATATTT
*
3923645 TTTTTACAAACTTAATATTTTTTA
1 TTTTTACAAAATTAATATTTTTTA
* *
3923669 TTTTTATAAAATTCAATTTTTTTT
1 TTTTTACAAAATT-AATATTTTTT
3923693 GCTAATTTGA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
24 11 0.55
25 9 0.45
ACGTcount: A:0.31, C:0.06, G:0.00, T:0.62
Consensus pattern (24 bp):
TTTTTACAAAATTAATATTTTTTA
Found at i:3924312 original size:8 final size:8
Alignment explanation
Indices: 3924299--3924335 Score: 74
Period size: 8 Copynumber: 4.6 Consensus size: 8
3924289 TTATGTTTAG
3924299 TATATTAT
1 TATATTAT
3924307 TATATTAT
1 TATATTAT
3924315 TATATTAT
1 TATATTAT
3924323 TATATTAT
1 TATATTAT
3924331 TATAT
1 TATAT
3924336 AATAAAGATA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 29 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (8 bp):
TATATTAT
Done.