Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D13
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: 60343961
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 596159 characters in sequence are not A, C, G, or T
File 11 of 204
Found at i:3507788 original size:233 final size:238
Alignment explanation
Indices: 3507219--3507831 Score: 751
Period size: 233 Copynumber: 2.6 Consensus size: 238
3507209 TTATTATCCC
* ** * ** * *
3507219 TAGCAAATTTAAAGTGAATATTAGTTCTTGAATATCCAAAATGGCTTGAACTAGCAATGGCCGAC
1 TAGCAAATTCAAAGTGAATATTAGCCCTCGAATATCCAAAATGGCTTGAACTAATAATGACCCAC
* * * * *
3507284 CTAAAAATCCTAGACTCAAACTACTTGAGCCCAAAA-AACTCGAACACAAAATTAATTCAAACCC
66 TTAAAAATCCTAGACTCAAACCACTTGAACCCAAAACAACTCGAACACAAAATTGATCCAAACCC
* * *
3507348 TTCTCCAAGTAGTGCAGATTTGAATATTTGCAAATATCTAACTTGCTTTTTAGGATTCAGATATT
131 TTCTCCAAGTAGTGCAGATTCGAATATTTGCAAATATCTAACTTGCTTTTGAAGATTCAGATATT
* *
3507413 GTAGATTCGAATGATATTTAAATTCGGATTTTCTAATTACTATTCT
196 G-AGATTCG-A-GATATTTAAATTCGAATTTTCTAATTACCATTCT
* ** *
3507459 TAGTAAATTCAAAGTGAATATTAGTTCTCGTATATCCAAAATGGCTTGAACTAATAATGACCCAC
1 TAGCAAATTCAAAGTGAATATTAGCCCTCGAATATCCAAAATGGCTTGAACTAATAATGACCCAC
* *
3507524 TTAAAAATCCTTGACTCAAACCACATGAACCCAAAACAACTCGAACACAAAATTGATCCAAACCC
66 TTAAAAATCCTAGACTCAAACCACTTGAACCCAAAACAACTCGAACACAAAATTGATCCAAACCC
* * *
3507589 TTCTTCAAGTAGTGTAGATTCGAATATTTGCAAATATCTAACTTGCCTTTTGAAGATT-GGATAT
131 TTCTCCAAGTAGTGCAGATTCGAATATTTGCAAATATCTAACTTG-CTTTTGAAGATTCAGATAT
*
3507653 TG-GA-T-G-G-TATTTAAATTTGAATATTT-TAATTACCATT-T
195 TGAGATTCGAGATATTTAAATTCGAAT-TTTCTAATTACCATTCT
* ** * * *
3507691 CTAGCATATTTGAAGT-AGATATTAGCCCTCGAATATCCAAAATGGCTTGAATTAATAGTGTCCC
1 -TAGCAAATTCAAAGTGA-ATATTAGCCCTCGAATATCCAAAATGGCTTGAACTAATAATGACCC
* * * *
3507755 ACTTAAAAATTCAAGACTCAAGCCACTTGAACCCAAAACAACTTGAACACAAAATTGATCCAAAC
64 ACTTAAAAATCCTAGACTCAAACCACTTGAACCCAAAACAACTCGAACACAAAATTGATCCAAAC
3507820 CCTTCTCCAAGT
129 CCTTCTCCAAGT
3507832 TTGCATTTGT
Statistics
Matches: 327, Mismatches: 41, Indels: 17
0.85 0.11 0.04
Matches are distributed among these distances:
232 2 0.01
233 144 0.44
234 4 0.01
237 1 0.00
238 1 0.00
239 2 0.01
240 88 0.27
241 75 0.23
242 10 0.03
ACGTcount: A:0.37, C:0.19, G:0.13, T:0.31
Consensus pattern (238 bp):
TAGCAAATTCAAAGTGAATATTAGCCCTCGAATATCCAAAATGGCTTGAACTAATAATGACCCAC
TTAAAAATCCTAGACTCAAACCACTTGAACCCAAAACAACTCGAACACAAAATTGATCCAAACCC
TTCTCCAAGTAGTGCAGATTCGAATATTTGCAAATATCTAACTTGCTTTTGAAGATTCAGATATT
GAGATTCGAGATATTTAAATTCGAATTTTCTAATTACCATTCT
Found at i:3512673 original size:37 final size:37
Alignment explanation
Indices: 3512621--3512712 Score: 121
Period size: 37 Copynumber: 2.5 Consensus size: 37
3512611 ACATCATCAC
** **
3512621 TTTCATAGATGATTGTATTTGGAAGACATTGAGCTAT
1 TTTCATAGATGATTGTATTCAGAAGACAAGGAGCTAT
* * *
3512658 TTTCATAGATCATTGTAGTCAGAAGACAAGGATCTAT
1 TTTCATAGATGATTGTATTCAGAAGACAAGGAGCTAT
3512695 TTTCATAGATGATTGTAT
1 TTTCATAGATGATTGTAT
3512713 CAACCCTAAT
Statistics
Matches: 46, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
37 46 1.00
ACGTcount: A:0.32, C:0.10, G:0.20, T:0.39
Consensus pattern (37 bp):
TTTCATAGATGATTGTATTCAGAAGACAAGGAGCTAT
Found at i:3516910 original size:15 final size:15
Alignment explanation
Indices: 3516890--3516921 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
3516880 AACATCTCTA
3516890 TTAAAAAATTGTGGG
1 TTAAAAAATTGTGGG
3516905 TTAAAAAATTGTGGG
1 TTAAAAAATTGTGGG
3516920 TT
1 TT
3516922 TAGGTTGCTT
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:0.38, C:0.00, G:0.25, T:0.38
Consensus pattern (15 bp):
TTAAAAAATTGTGGG
Found at i:3517454 original size:19 final size:18
Alignment explanation
Indices: 3517430--3517474 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 18
3517420 TTATATTTAA
* *
3517430 AAAAAATATTAATTACTAT
1 AAAAAATATT-AGTACGAT
3517449 AAAAAATTATTAGTACGAT
1 AAAAAA-TATTAGTACGAT
3517468 AAAAAAT
1 AAAAAAT
3517475 CTAAACAAGT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
18 1 0.04
19 18 0.78
20 4 0.17
ACGTcount: A:0.60, C:0.04, G:0.04, T:0.31
Consensus pattern (18 bp):
AAAAAATATTAGTACGAT
Found at i:3518004 original size:18 final size:20
Alignment explanation
Indices: 3517965--3518009 Score: 60
Period size: 18 Copynumber: 2.4 Consensus size: 20
3517955 AAAATTTATA
3517965 ATATT-TTTTTATAAATAAAT
1 ATATTATTTTTATAAAT-AAT
3517985 ATATTATTTTTAT-AAT-AT
1 ATATTATTTTTATAAATAAT
3518003 ATATTAT
1 ATATTAT
3518010 GGACTCGTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
18 9 0.38
20 8 0.33
21 7 0.29
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (20 bp):
ATATTATTTTTATAAATAAT
Found at i:3521416 original size:6 final size:6
Alignment explanation
Indices: 3521368--3521396 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
3521358 GCCGGTTTTT
3521368 AATTAA AATTAA AATTAA AATTAA AATTA
1 AATTAA AATTAA AATTAA AATTAA AATTA
3521397 TTTTTTAATA
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:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (6 bp):
AATTAA
Found at i:3521428 original size:16 final size:16
Alignment explanation
Indices: 3521409--3521450 Score: 75
Period size: 16 Copynumber: 2.6 Consensus size: 16
3521399 TTTTAATAAA
3521409 ATTAAAATTAATTGTT
1 ATTAAAATTAATTGTT
3521425 ATTAAAATTAATTGTT
1 ATTAAAATTAATTGTT
*
3521441 AGTAAAATTA
1 ATTAAAATTA
3521451 TCAAATTATT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.07, T:0.45
Consensus pattern (16 bp):
ATTAAAATTAATTGTT
Found at i:3521450 original size:22 final size:22
Alignment explanation
Indices: 3521383--3521435 Score: 79
Period size: 22 Copynumber: 2.4 Consensus size: 22
3521373 AAATTAAAAT
* *
3521383 TAAAATTAAAATTATTTTTTAA
1 TAAAATTAAAATTAATTGTTAA
*
3521405 TAAAATTAAAATTAATTGTTAT
1 TAAAATTAAAATTAATTGTTAA
3521427 TAAAATTAA
1 TAAAATTAA
3521436 TTGTTAGTAA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (22 bp):
TAAAATTAAAATTAATTGTTAA
Found at i:3521509 original size:66 final size:67
Alignment explanation
Indices: 3521439--3521581 Score: 261
Period size: 68 Copynumber: 2.1 Consensus size: 67
3521429 AAATTAATTG
3521439 TTAGTAAAATTATCAAATTATTAATTG-TTAATTGTATTAATTGTTGTAATAAAATCTAACATTT
1 TTAGTAAAATTATCAAATTATTAATTGATTAATTGTATTAATTGTTGTAATAAAATCTAACATTT
3521503 GA
66 GA
*
3521505 TTAGTAAATTTATCAAATTATTAATTGTATTAATTGTATTAATTGTTGTAATAAAATCTAACATT
1 TTAGTAAAATTATCAAATTATTAATTG-ATTAATTGTATTAATTGTTGTAATAAAATCTAACATT
3521570 TGA
65 TGA
3521573 TTAGTAAAA
1 TTAGTAAAA
3521582 CAAACTTGAT
Statistics
Matches: 73, Mismatches: 2, Indels: 2
0.95 0.03 0.03
Matches are distributed among these distances:
66 26 0.36
68 47 0.64
ACGTcount: A:0.41, C:0.04, G:0.09, T:0.45
Consensus pattern (67 bp):
TTAGTAAAATTATCAAATTATTAATTGATTAATTGTATTAATTGTTGTAATAAAATCTAACATTT
GA
Found at i:3521556 original size:9 final size:9
Alignment explanation
Indices: 3521523--3521550 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
3521513 TTTATCAAAT
3521523 TATTAATTG
1 TATTAATTG
3521532 TATTAATTG
1 TATTAATTG
3521541 TATTAATTG
1 TATTAATTG
3521550 T
1 T
3521551 TGTAATAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.32, C:0.00, G:0.11, T:0.57
Consensus pattern (9 bp):
TATTAATTG
Found at i:3521687 original size:25 final size:26
Alignment explanation
Indices: 3521647--3521696 Score: 68
Period size: 25 Copynumber: 2.0 Consensus size: 26
3521637 AAATAAACTT
*
3521647 AAAATAAAAAACTA-TT-ATATTTTA
1 AAAATAAAAAAATATTTAATATTTTA
3521671 AAAATAAAAAAAATATTTAATATTTT
1 AAAAT-AAAAAAATATTTAATATTTT
3521697 TCGGGCCGGG
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
24 5 0.23
25 8 0.36
26 2 0.09
27 7 0.32
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (26 bp):
AAAATAAAAAAATATTTAATATTTTA
Found at i:3521974 original size:18 final size:18
Alignment explanation
Indices: 3521950--3522002 Score: 63
Period size: 18 Copynumber: 2.9 Consensus size: 18
3521940 TTAAAAAAGC
3521950 ATAAAAAT-TATTAAATA
1 ATAAAAATATATTAAATA
*
3521967 TATAAAAAATATATTTAATA
1 -AT-AAAAATATATTAAATA
*
3521987 ATAAAAATATAATAAA
1 ATAAAAATATATTAAA
3522003 ATTCTATAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
18 14 0.47
19 8 0.27
20 8 0.27
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (18 bp):
ATAAAAATATATTAAATA
Found at i:3527694 original size:24 final size:25
Alignment explanation
Indices: 3527667--3527714 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 25
3527657 AAAGGAAAGT
3527667 TTAAAGAACATAAAA-GAAAAAAAA
1 TTAAAGAACATAAAACGAAAAAAAA
** *
3527691 TTAAATTACTTAAAACGAAAAAAA
1 TTAAAGAACATAAAACGAAAAAAA
3527715 TATGGGGATC
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
24 12 0.60
25 8 0.40
ACGTcount: A:0.69, C:0.06, G:0.06, T:0.19
Consensus pattern (25 bp):
TTAAAGAACATAAAACGAAAAAAAA
Found at i:3531080 original size:42 final size:42
Alignment explanation
Indices: 3531009--3531192 Score: 188
Period size: 42 Copynumber: 4.3 Consensus size: 42
3530999 AAGACGAATA
* * * * *
3531009 AATTATACTGGCATGCGTAGTGCATCATCGAATAAACCAAAGC
1 AATTATACTAGCACGC-AAGTGCATCATCGGATATACCAAAGC
* * * *
3531052 AATTATGCTAGCACGTAAGTGCATCATCGGATGTACCAAAGA
1 AATTATACTAGCACGCAAGTGCATCATCGGATATACCAAAGC
* * * *
3531094 AAATATATTTGCACGCAAGTGCATCATCGGATATACCGAAGC
1 AATTATACTAGCACGCAAGTGCATCATCGGATATACCAAAGC
* * * *
3531136 AACTATACTAGCACACACAATGCATCATCCGATATACCAAAGC
1 AATTATACTAGCACGCA-AGTGCATCATCGGATATACCAAAGC
*
3531179 AATTATACTGGCAC
1 AATTATACTAGCAC
3531193 ACACGGTGCA
Statistics
Matches: 114, Mismatches: 26, Indels: 2
0.80 0.18 0.01
Matches are distributed among these distances:
42 68 0.60
43 46 0.40
ACGTcount: A:0.38, C:0.23, G:0.17, T:0.23
Consensus pattern (42 bp):
AATTATACTAGCACGCAAGTGCATCATCGGATATACCAAAGC
Found at i:3531212 original size:41 final size:43
Alignment explanation
Indices: 3531113--3531207 Score: 118
Period size: 43 Copynumber: 2.2 Consensus size: 43
3531103 TGCACGCAAG
* * *
3531113 TGCATCATCGGATATACCGAAGCAACTATACTAGCACACACAA
1 TGCAACATCCGATATACCAAAGCAACTATACTAGCACACACAA
* * * **
3531156 TGCATCATCCGATATACCAAAGCAATTATACTGGCACACACGG
1 TGCAACATCCGATATACCAAAGCAACTATACTAGCACACACAA
3531199 TGCAACATC
1 TGCAACATC
3531208 ATATATATCG
Statistics
Matches: 45, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
43 45 1.00
ACGTcount: A:0.37, C:0.28, G:0.15, T:0.20
Consensus pattern (43 bp):
TGCAACATCCGATATACCAAAGCAACTATACTAGCACACACAA
Found at i:3531655 original size:35 final size:35
Alignment explanation
Indices: 3531609--3531678 Score: 131
Period size: 35 Copynumber: 2.0 Consensus size: 35
3531599 CGGGTCAATG
3531609 TTAGCCACGAATAATCACAAAACATATAGTACTAT
1 TTAGCCACGAATAATCACAAAACATATAGTACTAT
*
3531644 TTAGCCACGAATAATCGCAAAACATATAGTACTAT
1 TTAGCCACGAATAATCACAAAACATATAGTACTAT
3531679 CGCTTTCCAA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 34 1.00
ACGTcount: A:0.44, C:0.20, G:0.10, T:0.26
Consensus pattern (35 bp):
TTAGCCACGAATAATCACAAAACATATAGTACTAT
Found at i:3532243 original size:22 final size:21
Alignment explanation
Indices: 3532200--3532243 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 21
3532190 TTGTTTTATT
* **
3532200 TTATACCTTTTATAATTTTAA
1 TTATACCTTTAATAATAATAA
3532221 TTATAACCTTTAATAATAATAA
1 TTAT-ACCTTTAATAATAATAA
3532243 T
1 T
3532244 AAAACAAAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
21 4 0.21
22 15 0.79
ACGTcount: A:0.41, C:0.09, G:0.00, T:0.50
Consensus pattern (21 bp):
TTATACCTTTAATAATAATAA
Found at i:3532754 original size:13 final size:13
Alignment explanation
Indices: 3532747--3532771 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3532737 TTATTCTTGC
3532747 AATTTATTTTGTA
1 AATTTATTTTGTA
3532760 AATTTATTTTGT
1 AATTTATTTTGT
3532772 GTTTCCTTAT
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:0.28, C:0.00, G:0.08, T:0.64
Consensus pattern (13 bp):
AATTTATTTTGTA
Found at i:3534858 original size:41 final size:41
Alignment explanation
Indices: 3534752--3535046 Score: 227
Period size: 41 Copynumber: 7.0 Consensus size: 41
3534742 TAACCGTTAC
* * ** *
3534752 ACGGTGGAATCAACACTTAGCAACCACCTCATGTTCAAAGGAT
1 ACGG-GGAATCAACACATAGCAACCACCTTATAATC-AATGAT
* * * *
3534795 CCCGGTGGAATCAGCACTTAGCAACCACCTTATAATCAATTAT
1 -ACGG-GGAATCAACACATAGCAACCACCTTATAATCAATGAT
* *
3534838 ACGGGGAATCAACACATAGCAACC-CCTTTCACAATCAAGGAT
1 ACGGGGAATCAACACATAGCAACCACC-TT-ATAATCAATGAT
** *
3534880 ACGGTGGAATCAACATTTAGCAACCACCTTATAATCAATAAT
1 ACGG-GGAATCAACACATAGCAACCACCTTATAATCAATGAT
* * * *
3534922 ACGGGGAATCAGCACATTGCAACC-CCTTTCACAATCAAGGAT
1 ACGGGGAATCAACACATAGCAACCACC-TT-ATAATCAATGAT
* * * * *
3534964 ACGGTAGAATTAGCACTTAGCAAACACCTTATAATCAATGAT
1 ACGG-GGAATCAACACATAGCAACCACCTTATAATCAATGAT
* * * *
3535006 ACAGAGAATCAACACATAGCAACC-CCTATTTGATCAATGAT
1 ACGGGGAATCAACACATAGCAACCACCT-TATAATCAATGAT
3535047 TTAGGGAATC
Statistics
Matches: 203, Mismatches: 39, Indels: 21
0.77 0.15 0.08
Matches are distributed among these distances:
40 7 0.03
41 65 0.32
42 55 0.27
43 41 0.20
44 35 0.17
ACGTcount: A:0.37, C:0.25, G:0.15, T:0.22
Consensus pattern (41 bp):
ACGGGGAATCAACACATAGCAACCACCTTATAATCAATGAT
Found at i:3534909 original size:84 final size:84
Alignment explanation
Indices: 3534797--3535032 Score: 373
Period size: 84 Copynumber: 2.8 Consensus size: 84
3534787 CAAAGGATCC
*
3534797 CGGTGGAATCAGCACTTAGCAACCACCTTATAATCAATTATACGGGGAATCAACACATAGCAACC
1 CGGTGGAATCAGCACTTAGCAACCACCTTATAATCAATAATACGGGGAATCAACACATAGCAACC
3534862 CCTTTCACAATCAAGGATA
66 CCTTTCACAATCAAGGATA
* * * *
3534881 CGGTGGAATCAACATTTAGCAACCACCTTATAATCAATAATACGGGGAATCAGCACATTGCAACC
1 CGGTGGAATCAGCACTTAGCAACCACCTTATAATCAATAATACGGGGAATCAACACATAGCAACC
3534946 CCTTTCACAATCAAGGATA
66 CCTTTCACAATCAAGGATA
* * * * * *
3534965 CGGTAGAATTAGCACTTAGCAAACACCTTATAATCAATGATACAGAGAATCAACACATAGCAACC
1 CGGTGGAATCAGCACTTAGCAACCACCTTATAATCAATAATACGGGGAATCAACACATAGCAACC
3535030 CCT
66 CCT
3535033 ATTTGATCAA
Statistics
Matches: 137, Mismatches: 15, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
84 137 1.00
ACGTcount: A:0.38, C:0.25, G:0.15, T:0.22
Consensus pattern (84 bp):
CGGTGGAATCAGCACTTAGCAACCACCTTATAATCAATAATACGGGGAATCAACACATAGCAACC
CCTTTCACAATCAAGGATA
Found at i:3538698 original size:25 final size:25
Alignment explanation
Indices: 3538662--3538717 Score: 85
Period size: 25 Copynumber: 2.2 Consensus size: 25
3538652 TGGCTCTCAT
*
3538662 GAGCTTCCCGTTAAATGGTTCTTAC
1 GAGCTTCCCGTTAAATAGTTCTTAC
* *
3538687 GAGCTTCTCGTTAAATAGTTCTTGC
1 GAGCTTCCCGTTAAATAGTTCTTAC
3538712 GAGCTT
1 GAGCTT
3538718 TAGAGCATCC
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.20, C:0.21, G:0.21, T:0.38
Consensus pattern (25 bp):
GAGCTTCCCGTTAAATAGTTCTTAC
Found at i:3540781 original size:33 final size:32
Alignment explanation
Indices: 3540744--3540825 Score: 123
Period size: 33 Copynumber: 2.6 Consensus size: 32
3540734 ATTTGTTATG
3540744 AAAATGAACATGTTATATGGAAATATGATAAGA
1 AAAATGAACATGTTATATGGAAATATGATAA-A
*
3540777 AAAATGTACATGTTATATGGAAATATGATAAA
1 AAAATGAACATGTTATATGGAAATATGATAAA
*
3540809 AAAA-GAATATG-TATATG
1 AAAATGAACATGTTATATG
3540826 AAAGTTATTA
Statistics
Matches: 46, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
30 6 0.13
31 5 0.11
32 5 0.11
33 30 0.65
ACGTcount: A:0.51, C:0.02, G:0.17, T:0.29
Consensus pattern (32 bp):
AAAATGAACATGTTATATGGAAATATGATAAA
Found at i:3544144 original size:37 final size:36
Alignment explanation
Indices: 3544094--3544217 Score: 133
Period size: 36 Copynumber: 3.4 Consensus size: 36
3544084 ATCTTTTGGC
3544094 GATATAAAATGTAAGAGGTGTGAAACCATTCATTGAT
1 GATATAAAATGTAAGAGGTGT-AAACCATTCATTGAT
* * *** **
3544131 GATATAAAATGTAAGAAGTGCAAATTGTTTGTTGAT
1 GATATAAAATGTAAGAGGTGTAAACCATTCATTGAT
* * *
3544167 GATATAAAATGGAA-AGAGTGTAAACCACTCATTGGT
1 GATATAAAATGTAAGAG-GTGTAAACCATTCATTGAT
3544203 GATATAAAATGTAAG
1 GATATAAAATGTAAG
3544218 CAACACATAT
Statistics
Matches: 67, Mismatches: 18, Indels: 4
0.75 0.20 0.04
Matches are distributed among these distances:
35 1 0.01
36 47 0.70
37 19 0.28
ACGTcount: A:0.42, C:0.06, G:0.22, T:0.30
Consensus pattern (36 bp):
GATATAAAATGTAAGAGGTGTAAACCATTCATTGAT
Found at i:3544171 original size:73 final size:72
Alignment explanation
Indices: 3544059--3544217 Score: 196
Period size: 73 Copynumber: 2.2 Consensus size: 72
3544049 CGTTGGTACT
* * * *
3544059 ATATAAAATGTAAGAAATGCATACTATCTTTTGGCGATATAAAAT-GTAAGAGGTGTGAAACCAT
1 ATATAAAATGTAAGAAATGCAAACTATCTTTTGACGATATAAAATGGAAAGA-GTGT-AAACCAC
3544123 TCATTGATG
64 TCATTGATG
* * * *
3544132 ATATAAAATGTAAGAAGTGCAAATTGT-TTGTTGATGATATAAAATGGAAAGAGTGTAAACCACT
1 ATATAAAATGTAAGAAATGCAAACTATCTT-TTGACGATATAAAATGGAAAGAGTGTAAACCACT
*
3544196 CATTGGTG
65 CATTGATG
3544204 ATATAAAATGTAAG
1 ATATAAAATGTAAG
3544218 CAACACATAT
Statistics
Matches: 75, Mismatches: 9, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
72 30 0.40
73 40 0.53
74 5 0.07
ACGTcount: A:0.42, C:0.08, G:0.20, T:0.31
Consensus pattern (72 bp):
ATATAAAATGTAAGAAATGCAAACTATCTTTTGACGATATAAAATGGAAAGAGTGTAAACCACTC
ATTGATG
Found at i:3544230 original size:72 final size:73
Alignment explanation
Indices: 3544094--3544230 Score: 181
Period size: 72 Copynumber: 1.9 Consensus size: 73
3544084 ATCTTTTGGC
* * **
3544094 GATATAAAATGTAAGAGGTGTGAAACCATTCATTGATGATATAAAATGTAAGAAGTGCAAATTGT
1 GATATAAAATGAAAGAGGTGTGAAACCACTCATTGATGATATAAAATGTAAGAAGCACAAATTGT
3544159 TTGTTGAT
66 TTGTTGAT
* *
3544167 GATATAAAATGGAAAGA-GTGT-AAACCACTCATTGGTGATATAAAATGTAAGCAA-CACATATT
1 GATATAAAAT-GAAAGAGGTGTGAAACCACTCATTGATGATATAAAATGTAAG-AAGCACAAATT
3544229 GT
64 GT
3544231 CCATTAGAAT
Statistics
Matches: 56, Mismatches: 6, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
72 35 0.62
73 16 0.29
74 5 0.09
ACGTcount: A:0.42, C:0.08, G:0.20, T:0.30
Consensus pattern (73 bp):
GATATAAAATGAAAGAGGTGTGAAACCACTCATTGATGATATAAAATGTAAGAAGCACAAATTGT
TTGTTGAT
Found at i:3544870 original size:47 final size:48
Alignment explanation
Indices: 3544684--3544902 Score: 126
Period size: 49 Copynumber: 4.5 Consensus size: 48
3544674 AAATCGATAA
* * * * * * * *
3544684 ATAATAAAGTGACTCTGCTCCCAGATGCATGGAGGAGCCTTACGGAAAG
1 ATAATAAAATGACACTGCTCCCAAACGCTTGGGGGAGGCTTA-AGAAAG
* * * * * *
3544733 -TAATAAAGTTACCCTGCT-CCAAGACACATGAGGGGAGGCTTACGAAAAG
1 ATAATAAAATGACACTGCTCCCAA-ACGCTTG-GGGGAGGCTTAAG-AAAG
* * * * *
3544782 A-AATAAAATGGCCCTACTCCCAGATG-TATAGGGGGAGGCTTAAGAAAG
1 ATAATAAAATGACACTGCTCCCAAACGCT-T-GGGGGAGGCTTAAGAAAG
*
3544830 ATAATAAAAT-A-ACTGCTCCCAAACGCTTGGGGGTAGGCTTATGAAAG
1 ATAATAAAATGACACTGCTCCCAAACGCTTGGGGG-AGGCTTAAGAAAG
* * *
3544877 GTAATAAGATGACTCTGCTCCCAAAC
1 ATAATAAAATGACACTGCTCCCAAAC
3544903 ACATGAGAGA
Statistics
Matches: 132, Mismatches: 26, Indels: 24
0.73 0.14 0.13
Matches are distributed among these distances:
46 5 0.04
47 34 0.26
48 29 0.22
49 60 0.45
50 4 0.03
ACGTcount: A:0.36, C:0.20, G:0.24, T:0.21
Consensus pattern (48 bp):
ATAATAAAATGACACTGCTCCCAAACGCTTGGGGGAGGCTTAAGAAAG
Found at i:3544898 original size:96 final size:96
Alignment explanation
Indices: 3544685--3544899 Score: 206
Period size: 96 Copynumber: 2.2 Consensus size: 96
3544675 AATCGATAAA
* * *
3544685 TAATAAAGTGACTCTGCTCCCAGATGCATGGAGGAGCCTTACGGAAAGTAATAAAGTTACCCTGC
1 TAATAAA-TGACTCTGCTCCCAGATGCATGGAGGAGCCTTACAGAAAGTAATAAAGATACACTGC
3544750 TCCAAGACACATGAGGGGAGGCTTACGAAAAG
65 TCCAAGACACATGAGGGGAGGCTTACGAAAAG
* * * * * * *
3544782 AAATAAAATGGCCCTACTCCCAGATGTATAGGGGGAGGCTTA-AGAAAGATAATAAA-ATA-ACT
1 TAAT-AAATGACTCTGCTCCCAGATGCAT-GGAGGAGCCTTACAGAAAG-TAATAAAGATACACT
* * * *
3544844 GCTCCCAA-ACGCTTG-GGGGTAGGCTTATGAAAGG
63 GCT-CCAAGACACATGAGGGG-AGGCTTACGAAAAG
3544878 TAATAAGATGACTCTGCTCCCA
1 TAATAA-ATGACTCTGCTCCCA
3544900 AACACATGAG
Statistics
Matches: 94, Mismatches: 18, Indels: 13
0.75 0.14 0.10
Matches are distributed among these distances:
95 6 0.06
96 37 0.39
97 31 0.33
98 20 0.21
ACGTcount: A:0.35, C:0.20, G:0.25, T:0.21
Consensus pattern (96 bp):
TAATAAATGACTCTGCTCCCAGATGCATGGAGGAGCCTTACAGAAAGTAATAAAGATACACTGCT
CCAAGACACATGAGGGGAGGCTTACGAAAAG
Found at i:3546502 original size:45 final size:45
Alignment explanation
Indices: 3546447--3546549 Score: 179
Period size: 45 Copynumber: 2.3 Consensus size: 45
3546437 CTGATACATA
* *
3546447 TTCATGCAATTCACAAGTCTTAATAATTCAATACTTCATTTTCAT
1 TTCATTCAATTCACAAGTCTTAATAATTCAATACTTCATTTCCAT
*
3546492 TTCATTCAATTCACAAGTCTTAATAATTCAATGCTTCATTTCCAT
1 TTCATTCAATTCACAAGTCTTAATAATTCAATACTTCATTTCCAT
3546537 TTCATTCAATTCA
1 TTCATTCAATTCA
3546550 TAAATTTCTC
Statistics
Matches: 55, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
45 55 1.00
ACGTcount: A:0.32, C:0.21, G:0.04, T:0.43
Consensus pattern (45 bp):
TTCATTCAATTCACAAGTCTTAATAATTCAATACTTCATTTCCAT
Found at i:3548347 original size:76 final size:76
Alignment explanation
Indices: 3548260--3548412 Score: 306
Period size: 76 Copynumber: 2.0 Consensus size: 76
3548250 TTTTCAGCAT
3548260 GTTCATCCATGGCAAAATTTCCATACCTTGATAACTTTTCAAATAAATCCTCAAAATAGAGAGAA
1 GTTCATCCATGGCAAAATTTCCATACCTTGATAACTTTTCAAATAAATCCTCAAAATAGAGAGAA
3548325 CATTTTATCTC
66 CATTTTATCTC
3548336 GTTCATCCATGGCAAAATTTCCATACCTTGATAACTTTTCAAATAAATCCTCAAAATAGAGAGAA
1 GTTCATCCATGGCAAAATTTCCATACCTTGATAACTTTTCAAATAAATCCTCAAAATAGAGAGAA
3548401 CATTTTATCTC
66 CATTTTATCTC
3548412 G
1 G
3548413 ATATCAAAAA
Statistics
Matches: 77, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
76 77 1.00
ACGTcount: A:0.37, C:0.21, G:0.10, T:0.33
Consensus pattern (76 bp):
GTTCATCCATGGCAAAATTTCCATACCTTGATAACTTTTCAAATAAATCCTCAAAATAGAGAGAA
CATTTTATCTC
Found at i:3549180 original size:15 final size:15
Alignment explanation
Indices: 3549160--3549190 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
3549150 AATAAAAACA
3549160 ATAGAGAAGAGTAGT
1 ATAGAGAAGAGTAGT
3549175 ATAGAGAAGAGTAGT
1 ATAGAGAAGAGTAGT
3549190 A
1 A
3549191 GACACCCTAT
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:0.48, C:0.00, G:0.32, T:0.19
Consensus pattern (15 bp):
ATAGAGAAGAGTAGT
Found at i:3550677 original size:30 final size:30
Alignment explanation
Indices: 3550643--3550700 Score: 82
Period size: 30 Copynumber: 1.9 Consensus size: 30
3550633 TTCTCGAAAT
3550643 CCACACAGG-TCAACCACACGACCATGTGAC
1 CCACACAGGCT-AACCACACGACCATGTGAC
* *
3550673 CCACACAGGCTAACCACATGGCCATGTG
1 CCACACAGGCTAACCACACGACCATGTG
3550701 GATATTGGAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
30 24 0.96
31 1 0.04
ACGTcount: A:0.31, C:0.38, G:0.19, T:0.12
Consensus pattern (30 bp):
CCACACAGGCTAACCACACGACCATGTGAC
Found at i:3553228 original size:7 final size:7
Alignment explanation
Indices: 3553212--3553248 Score: 56
Period size: 7 Copynumber: 5.3 Consensus size: 7
3553202 CTTTTTTTTT
*
3553212 AAGTAAA
1 AAGTTAA
*
3553219 AAGTTGA
1 AAGTTAA
3553226 AAGTTAA
1 AAGTTAA
3553233 AAGTTAA
1 AAGTTAA
3553240 AAGTTAA
1 AAGTTAA
3553247 AA
1 AA
3553249 TAGGTTTTAA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
7 27 1.00
ACGTcount: A:0.59, C:0.00, G:0.16, T:0.24
Consensus pattern (7 bp):
AAGTTAA
Found at i:3558914 original size:4 final size:4
Alignment explanation
Indices: 3558905--3558969 Score: 94
Period size: 4 Copynumber: 16.2 Consensus size: 4
3558895 GTGCCCCCGT
* * * *
3558905 TACA TACA TACA TACA TTCA TTCA TACA TACC TACA TACA TACG TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
3558953 TACA TACA TACA TACA T
1 TACA TACA TACA TACA T
3558970 GCTACTCAAT
Statistics
Matches: 55, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
4 55 1.00
ACGTcount: A:0.43, C:0.26, G:0.02, T:0.29
Consensus pattern (4 bp):
TACA
Found at i:3561364 original size:17 final size:18
Alignment explanation
Indices: 3561342--3561382 Score: 68
Period size: 17 Copynumber: 2.4 Consensus size: 18
3561332 CTTTTCTTTC
3561342 TTTCTTTTC-TTTTTCTT
1 TTTCTTTTCGTTTTTCTT
3561359 TTTC-TTTCGTTTTTCTT
1 TTTCTTTTCGTTTTTCTT
3561376 TTTCTTT
1 TTTCTTT
3561383 CCGCTTTCAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
16 4 0.18
17 16 0.73
18 2 0.09
ACGTcount: A:0.00, C:0.17, G:0.02, T:0.80
Consensus pattern (18 bp):
TTTCTTTTCGTTTTTCTT
Found at i:3561373 original size:7 final size:6
Alignment explanation
Indices: 3561333--3561382 Score: 52
Period size: 6 Copynumber: 8.3 Consensus size: 6
3561323 ATTATCCCTC
3561333 TTTTCT TTCTT-T CTTTTCT TTTTCT TTTTC- -TTTCGT TTTTCT TTTTCT
1 TTTTCT TT-TTCT -TTTTCT TTTTCT TTTTCT TTTTC-T TTTTCT TTTTCT
3561381 TT
1 TT
3561383 CCGCTTTCAA
Statistics
Matches: 38, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
4 4 0.11
6 25 0.66
7 9 0.24
ACGTcount: A:0.00, C:0.18, G:0.02, T:0.80
Consensus pattern (6 bp):
TTTTCT
Found at i:3561383 original size:17 final size:16
Alignment explanation
Indices: 3561338--3561383 Score: 67
Period size: 17 Copynumber: 2.9 Consensus size: 16
3561328 CCCTCTTTTC
*
3561338 TTTCTTTCT-TTTCTT
1 TTTCTTTTTCTTTCTT
3561353 TTTCTTTTTCTTTCGTT
1 TTTCTTTTTCTTTC-TT
3561370 TTTCTTTTTCTTTC
1 TTTCTTTTTCTTTC
3561384 CGCTTTCAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
15 8 0.29
16 4 0.14
17 16 0.57
ACGTcount: A:0.00, C:0.20, G:0.02, T:0.78
Consensus pattern (16 bp):
TTTCTTTTTCTTTCTT
Found at i:3565814 original size:3 final size:3
Alignment explanation
Indices: 3565801--3565836 Score: 63
Period size: 3 Copynumber: 12.0 Consensus size: 3
3565791 CCTCCTAAAC
*
3565801 TCA TTA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA
1 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA
3565837 ATTTTACCAA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.33, C:0.31, G:0.00, T:0.36
Consensus pattern (3 bp):
TCA
Found at i:3569030 original size:26 final size:27
Alignment explanation
Indices: 3569001--3569051 Score: 77
Period size: 27 Copynumber: 1.9 Consensus size: 27
3568991 ATGTTGTAAT
3569001 ATATAATATTA-AAAAATAAAAGAAGA
1 ATATAATATTATAAAAATAAAAGAAGA
* *
3569027 ATATCATATTATAAAATTAAAAGAA
1 ATATAATATTATAAAAATAAAAGAA
3569052 AGGATTGGCA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 10 0.45
27 12 0.55
ACGTcount: A:0.65, C:0.02, G:0.06, T:0.27
Consensus pattern (27 bp):
ATATAATATTATAAAAATAAAAGAAGA
Found at i:3569623 original size:19 final size:20
Alignment explanation
Indices: 3569601--3569638 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
3569591 TTTAGTCCCT
*
3569601 AATTTAATATTT-AATCATA
1 AATTTAAAATTTAAATCATA
3569620 AATTTAAAATTTAAATCAT
1 AATTTAAAATTTAAATCAT
3569639 CTCAACTTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 11 0.65
20 6 0.35
ACGTcount: A:0.50, C:0.05, G:0.00, T:0.45
Consensus pattern (20 bp):
AATTTAAAATTTAAATCATA
Found at i:3572951 original size:12 final size:11
Alignment explanation
Indices: 3572914--3572953 Score: 55
Period size: 11 Copynumber: 3.6 Consensus size: 11
3572904 TTCACACATT
3572914 ATTTCT-TCAA
1 ATTTCTCTCAA
*
3572924 TTTTCTCTCAA
1 ATTTCTCTCAA
3572935 ATTTCTCTCTAA
1 ATTTCTCTC-AA
3572947 ATTTCTC
1 ATTTCTC
3572954 GAAGCACTCT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
10 5 0.19
11 12 0.46
12 9 0.35
ACGTcount: A:0.23, C:0.25, G:0.00, T:0.53
Consensus pattern (11 bp):
ATTTCTCTCAA
Found at i:3573131 original size:24 final size:24
Alignment explanation
Indices: 3573077--3573134 Score: 66
Period size: 24 Copynumber: 2.4 Consensus size: 24
3573067 TAATTTTTCA
*
3573077 ATATTATTTTAATTTTTTTAATTT
1 ATATAATTTTAATTTTTTTAATTT
*
3573101 ATGTAATTTTAATTAATTTTT-ATTT
1 ATATAATTTTAATT--TTTTTAATTT
3573126 -TATAATTTT
1 ATATAATTTT
3573135 TTATAACAGT
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
24 20 0.69
25 4 0.14
26 5 0.17
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (24 bp):
ATATAATTTTAATTTTTTTAATTT
Found at i:3574633 original size:18 final size:18
Alignment explanation
Indices: 3574606--3574641 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
3574596 TGCTAGGTGC
3574606 GTATCCTAACCCTTATAT
1 GTATCCTAACCCTTATAT
*
3574624 GTATCTTAACCCTTATAT
1 GTATCCTAACCCTTATAT
3574642 ATTTCCTTTT
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:0.28, C:0.25, G:0.06, T:0.42
Consensus pattern (18 bp):
GTATCCTAACCCTTATAT
Found at i:3574912 original size:21 final size:21
Alignment explanation
Indices: 3574888--3574928 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
3574878 CCAACACCAA
**
3574888 CAACCACAACCTTCACCGGAG
1 CAACCACAACCCCCACCGGAG
*
3574909 CAACCATAACCCCCACCGGA
1 CAACCACAACCCCCACCGGA
3574929 AGCTGAATCA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.34, C:0.46, G:0.12, T:0.07
Consensus pattern (21 bp):
CAACCACAACCCCCACCGGAG
Found at i:3578413 original size:126 final size:126
Alignment explanation
Indices: 3578185--3578453 Score: 321
Period size: 126 Copynumber: 2.1 Consensus size: 126
3578175 GGCCAAACAG
* * * * *
3578185 GAACTACTGTA-AAAAAAGAGCGTCTACGTGGGAGCATTTTTCAATAATTTTGCTGACTGTGTAT
1 GAACTACTGTAGAAAAAAGAGCGTCCACGTAGAAGCATTTTTCAATAATTTTGCTGACAGTGCAT
3578249 CCTGCTTAAAGCGTTTTTGACACAATTTGTTCAAAACCGTCTTCTCAAAATTATTTTTTTAA
66 CCTGCTTAAAGCGTTTTTGACACAATTTGTTCAAAACCGTCTTCTCAAAATTA-TTTTTTAA
* *
3578311 GAACTACTGTAGAAAAAA-AGTGTCCACGTAGAAGC-TTTTTTAAGTAATTTTGCTGACAGTGCA
1 GAACTACTGTAGAAAAAAGAGCGTCCACGTAGAAGCATTTTTCAA-TAATTTTGCTGACAGTGCA
* ** * ** * * *
3578374 TCCTGCTTGAATTGTTTTTTACATTATCTT-TTCAGAACCGTTTTCTCAAAATTATTTTTTCA
65 TCCTGCTTAAAGCGTTTTTGACACAAT-TTGTTCAAAACCGTCTTCTCAAAATTATTTTTTAA
*
3578436 GAAACTATTGTAGAAAAA
1 G-AACTACTGTAGAAAAA
3578454 CAAACAAAAG
Statistics
Matches: 122, Mismatches: 17, Indels: 8
0.83 0.12 0.05
Matches are distributed among these distances:
125 15 0.12
126 99 0.81
127 8 0.07
ACGTcount: A:0.31, C:0.16, G:0.15, T:0.38
Consensus pattern (126 bp):
GAACTACTGTAGAAAAAAGAGCGTCCACGTAGAAGCATTTTTCAATAATTTTGCTGACAGTGCAT
CCTGCTTAAAGCGTTTTTGACACAATTTGTTCAAAACCGTCTTCTCAAAATTATTTTTTAA
Found at i:3578634 original size:15 final size:15
Alignment explanation
Indices: 3578610--3578641 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
3578600 AACCTACCAA
*
3578610 AAACCTAAAAACCCT
1 AAACCAAAAAACCCT
3578625 AAACCAAAAAACCCT
1 AAACCAAAAAACCCT
3578640 AA
1 AA
3578642 GGACTAAACA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.59, C:0.31, G:0.00, T:0.09
Consensus pattern (15 bp):
AAACCAAAAAACCCT
Found at i:3586939 original size:9 final size:9
Alignment explanation
Indices: 3586911--3586983 Score: 58
Period size: 9 Copynumber: 7.4 Consensus size: 9
3586901 CACGTGGTAT
3586911 AAAATTATA
1 AAAATTATA
3586920 AAAATCATATA
1 AAAAT--TATA
3586931 AAAATTATA
1 AAAATTATA
3586940 CAAGAATTATA
1 -AA-AATTATA
*
3586951 AAAATGA-A
1 AAAATTATA
*
3586959 TAAAATTAGAA
1 -AAAATTA-TA
3586970 AAAATATATA
1 AAAAT-TATA
3586980 AAAA
1 AAAA
3586984 ATCTATTTTT
Statistics
Matches: 53, Mismatches: 3, Indels: 15
0.75 0.04 0.21
Matches are distributed among these distances:
8 1 0.02
9 19 0.36
10 14 0.26
11 19 0.36
ACGTcount: A:0.67, C:0.03, G:0.04, T:0.26
Consensus pattern (9 bp):
AAAATTATA
Found at i:3592840 original size:374 final size:374
Alignment explanation
Indices: 3592151--3592882 Score: 1455
Period size: 374 Copynumber: 2.0 Consensus size: 374
3592141 CTAATCTTGT
3592151 GTAGTAGTCTTTGAAATGTTGAAGTTGGCAATGCCTTAGTAAAAACATATGCTAAATTATCACTA
1 GTAGTAGTCTTTGAAATGTTGAAGTTGGCAATGCCTTAGTAAAAACATATGCTAAATTATCACTA
3592216 GAATGAATTTGTTGAACATTTATATCACCTCTTTTCTCAAGATCATGGGTGAAGAATAATTTTGG
66 GAATGAATTTGTTGAACATTTATATCACCTCTTTTCTCAAGATCATGGGTGAAGAATAATTTTGG
3592281 CGAAATATGTTTCGTTCTATCACCTTTGATGTAACCACTCTTCAATTGAGCCATACATGTTGCAT
131 CGAAATATGTTTCGTTCTATCACCTTTGATGTAACCACTCTTCAATTGAGCCATACATGTTGCAT
3592346 TATCTTCATATAAGATAGTTGGCATCTTTTCCTATAAAGGCAAATTACATATCTTCTGGATATGT
196 TATCTTCATATAAGATAGTTGGCATCTTTTCCTATAAAGGCAAATTACATATCTTCTGGATATGT
3592411 TGGGTCAATAACCTTAGTCAAACACACTCTCGACTTGCCTCATTCATTGCAATTATTTCTAAATG
261 TGGGTCAATAACCTTAGTCAAACACACTCTCGACTTGCCTCATTCATTGCAATTATTTCTAAATG
3592476 ATTTGAAGAAGCAACAGCTAATGTTTGCTTTGTCAAACGTCATGATATG
326 ATTTGAAGAAGCAACAGCTAATGTTTGCTTTGTCAAACGTCATGATATG
3592525 GTAGTAGTCTTTGAAATGTTGAAGTTGGCAATGCCTTAGTAAAAACATATGCTAAATTATCACTA
1 GTAGTAGTCTTTGAAATGTTGAAGTTGGCAATGCCTTAGTAAAAACATATGCTAAATTATCACTA
3592590 GAATGAATTTGTTGAACATTTATATCACCTCTTTTCTCAAGATCATGGGTGAAGAATAATTTTGG
66 GAATGAATTTGTTGAACATTTATATCACCTCTTTTCTCAAGATCATGGGTGAAGAATAATTTTGG
*
3592655 CGAAATATGTTTCGTTCTATCACCTTTGATGTAACCACTCTTCAATTGAGCTATACATGTTGCAT
131 CGAAATATGTTTCGTTCTATCACCTTTGATGTAACCACTCTTCAATTGAGCCATACATGTTGCAT
3592720 TATCTTCATATAAGATAGTTGGCATCTTTTCCTATAAAGGCAAATTACATATCTTCTGGATATGT
196 TATCTTCATATAAGATAGTTGGCATCTTTTCCTATAAAGGCAAATTACATATCTTCTGGATATGT
3592785 TGGGTCAATAACCTTAGTCAAACACACTCTCGACTTGCCTCATTCATTGCAATTATTTCTAAATG
261 TGGGTCAATAACCTTAGTCAAACACACTCTCGACTTGCCTCATTCATTGCAATTATTTCTAAATG
3592850 ATTTGAAGAAGCAACAGCTAATGTTTGCTTTGT
326 ATTTGAAGAAGCAACAGCTAATGTTTGCTTTGT
3592883 ATCTACATAT
Statistics
Matches: 357, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
374 357 1.00
ACGTcount: A:0.31, C:0.17, G:0.16, T:0.36
Consensus pattern (374 bp):
GTAGTAGTCTTTGAAATGTTGAAGTTGGCAATGCCTTAGTAAAAACATATGCTAAATTATCACTA
GAATGAATTTGTTGAACATTTATATCACCTCTTTTCTCAAGATCATGGGTGAAGAATAATTTTGG
CGAAATATGTTTCGTTCTATCACCTTTGATGTAACCACTCTTCAATTGAGCCATACATGTTGCAT
TATCTTCATATAAGATAGTTGGCATCTTTTCCTATAAAGGCAAATTACATATCTTCTGGATATGT
TGGGTCAATAACCTTAGTCAAACACACTCTCGACTTGCCTCATTCATTGCAATTATTTCTAAATG
ATTTGAAGAAGCAACAGCTAATGTTTGCTTTGTCAAACGTCATGATATG
Found at i:3595931 original size:20 final size:20
Alignment explanation
Indices: 3595908--3595959 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 20
3595898 TAATTTTTAT
*
3595908 TAAAAATCATATAAAAAGTA
1 TAAAAATCATACAAAAAGTA
* * *
3595928 TAAAAATTATACAAGAATTA
1 TAAAAATCATACAAAAAGTA
3595948 TAAAAATGCATA
1 TAAAAAT-CATA
3595960 AATTAGAAAA
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
20 23 0.88
21 3 0.12
ACGTcount: A:0.62, C:0.06, G:0.06, T:0.27
Consensus pattern (20 bp):
TAAAAATCATACAAAAAGTA
Found at i:3602992 original size:9 final size:9
Alignment explanation
Indices: 3602978--3603015 Score: 58
Period size: 9 Copynumber: 4.0 Consensus size: 9
3602968 TTAAAAATCA
3602978 TATAAAAAT
1 TATAAAAAT
3602987 TATAAAAAT
1 TATAAAAAT
3602996 TATACAAGAAT
1 TATA-AA-AAT
3603007 TATAAAAAT
1 TATAAAAAT
3603016 GCATAAATTA
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
9 16 0.59
10 4 0.15
11 7 0.26
ACGTcount: A:0.63, C:0.03, G:0.03, T:0.32
Consensus pattern (9 bp):
TATAAAAAT
Found at i:3602994 original size:20 final size:20
Alignment explanation
Indices: 3602969--3603020 Score: 68
Period size: 20 Copynumber: 2.5 Consensus size: 20
3602959 TAATTTTTAT
*
3602969 TAAAAATCATATAAAAATTA
1 TAAAAATCATACAAAAATTA
* *
3602989 TAAAAATTATACAAGAATTA
1 TAAAAATCATACAAAAATTA
3603009 TAAAAATGCATA
1 TAAAAAT-CATA
3603021 AATTAGAAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
20 24 0.89
21 3 0.11
ACGTcount: A:0.62, C:0.06, G:0.04, T:0.29
Consensus pattern (20 bp):
TAAAAATCATACAAAAATTA
Found at i:3603666 original size:6 final size:6
Alignment explanation
Indices: 3603655--3603679 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
3603645 CTACACTGGT
3603655 TGGGGC TGGGGC TGGGGC TGGGGC T
1 TGGGGC TGGGGC TGGGGC TGGGGC T
3603680 CCTCGAAGTC
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:0.16, G:0.64, T:0.20
Consensus pattern (6 bp):
TGGGGC
Found at i:3611109 original size:15 final size:15
Alignment explanation
Indices: 3611084--3611116 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
3611074 TACCCAATTA
3611084 CAACACCCAATA-CC
1 CAACACCCAATAGCC
3611098 CAACAGCCCAATAGCC
1 CAACA-CCCAATAGCC
3611114 CAA
1 CAA
3611117 AATCATCAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 5 0.29
15 7 0.41
16 5 0.29
ACGTcount: A:0.42, C:0.45, G:0.06, T:0.06
Consensus pattern (15 bp):
CAACACCCAATAGCC
Found at i:3623549 original size:1 final size:1
Alignment explanation
Indices: 3623543--3623579 Score: 74
Period size: 1 Copynumber: 37.0 Consensus size: 1
3623533 TTTGCTTCCT
3623543 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
3623580 GGGACTTTGG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 36 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:3624987 original size:86 final size:88
Alignment explanation
Indices: 3624785--3625039 Score: 304
Period size: 86 Copynumber: 2.9 Consensus size: 88
3624775 CAGATCAATG
* * *
3624785 AAGACAAAGGATCTTGCCTTTCTGCATTGACAGCGAAGCAGATCGAAGACACAAA-CCTTGCCTC
1 AAGACAAAAGATCTTGCCTTCCTGCATTAACAGCGAAGCAGATCGAA-ACACAAAGCCTTGCCTC
** * * * *
3624849 TTTCGGTTG-TGATAGAGCTGGTTG
65 CATCGGTTGCAG-TGGAGCTAGTTA
* * *
3624873 AAGACAAAAGATCTTGCCTTCTTACATTAACAGCGAAGCAGATCGAAA-ACAAAGCCTTGCATCC
1 AAGACAAAAGATCTTGCCTTCCTGCATTAACAGCGAAGCAGATCGAAACACAAAGCCTTGCCTCC
*
3624937 ATCGATTGCAGTGGAGCTAGTTA
66 ATCGGTTGCAGTGGAGCTAGTTA
** *
3624960 AAGA-AGTAGATCTTGCCTTCCTGCATTAACAGCGAAGCAGATC-AAAGACAAAGCCTTGCCTCC
1 AAGACAAAAGATCTTGCCTTCCTGCATTAACAGCGAAGCAGATCGAAACACAAAGCCTTGCCTCC
*
3625023 ATCGGTTGCATTGGAGC
66 ATCGGTTGCAGTGGAGC
3625040 AGATTGAAGC
Statistics
Matches: 144, Mismatches: 20, Indels: 8
0.84 0.12 0.05
Matches are distributed among these distances:
85 3 0.02
86 70 0.49
87 28 0.19
88 43 0.30
ACGTcount: A:0.31, C:0.23, G:0.22, T:0.24
Consensus pattern (88 bp):
AAGACAAAAGATCTTGCCTTCCTGCATTAACAGCGAAGCAGATCGAAACACAAAGCCTTGCCTCC
ATCGGTTGCAGTGGAGCTAGTTA
Found at i:3625057 original size:86 final size:84
Alignment explanation
Indices: 3624794--3625093 Score: 291
Period size: 86 Copynumber: 3.5 Consensus size: 84
3624784 GAAGACAAAG
* * * * **
3624794 GATCTTGCCTTTCTGCATTGACAGCGAAGCAGATCGAAGACACAAACCTTGCCTCTTTCGGTTGT
1 GATCTTGCCTTCCTGCATTAACAGCGAAGCAGATCAAAGACA-AAGCCTTGCCTCCATCGGTTG-
* * * *
3624859 GATAGAGCTGGTTGAAGACAAAA
64 CATGGAGC-AGTTGAAG-CAAGA
* * * *
3624882 GATCTTGCCTTCTTACATTAACAGCGAAGCAGATCGAAA-ACAAAGCCTTGCATCCATCGATTGC
1 GATCTTGCCTTCCTGCATTAACAGCGAAGCAGATC-AAAGACAAAGCCTTGCCTCCATCGGTTGC
*
3624946 AGTGGAGCTAGTTAAAG-AAGTA
65 A-TGGAGC-AGTTGAAGCAAG-A
3624968 GATCTTGCCTTCCTGCATTAACAGCGAAGCAGATCAAAGACAAAGCCTTGCCTCCATCGGTTGCA
1 GATCTTGCCTTCCTGCATTAACAGCGAAGCAGATCAAAGACAAAGCCTTGCCTCCATCGGTTGCA
*
3625033 TTGGAGCAGATTGAAGCCAGA
66 -TGGAGCAG-TTGAAGCAAGA
** * * *
3625054 GATCTTATCTCCCTGAGATT-ACAGCGGAGCAGATCAAAGA
1 GATCTTGCCTTCCTG-CATTAACAGCGAAGCAGATCAAAGA
3625094 TAGTAATCCT
Statistics
Matches: 178, Mismatches: 27, Indels: 16
0.81 0.12 0.07
Matches are distributed among these distances:
85 7 0.04
86 102 0.57
87 33 0.19
88 34 0.19
89 2 0.01
ACGTcount: A:0.31, C:0.23, G:0.23, T:0.24
Consensus pattern (84 bp):
GATCTTGCCTTCCTGCATTAACAGCGAAGCAGATCAAAGACAAAGCCTTGCCTCCATCGGTTGCA
TGGAGCAGTTGAAGCAAGA
Found at i:3625107 original size:44 final size:43
Alignment explanation
Indices: 3625055--3625512 Score: 257
Period size: 44 Copynumber: 10.6 Consensus size: 43
3625045 GAAGCCAGAG
*
3625055 ATCTTATCTCCCTGAGATTACAGCGGAGCAGATCAAAGATAGTA
1 ATCTTATCTCCCTGAGATTACAGTGGAGCAGATCAAAGATAG-A
* * * * *
3625099 ATCCTATCTCCTTGAGATTACAATGGAGCGGATTAAAG---G-
1 ATCTTATCTCCCTGAGATTACAGTGGAGCAGATCAAAGATAGA
* * * *
3625138 ATCTTATCTCTCTGA-AGTTACAGTAGAGAAGATC--ACATCAG-
1 ATCTTATCTCCCTGAGA-TTACAGTGGAGCAGATCAAAGAT-AGA
* * *
3625179 GTCTTATCTCCCTGAGATTACAGTGGAACAGACCAAAGAATTTCAG-
1 ATCTTATCTCCCTGAGATTACAGTGGAGCAGATCAAAG-A--T-AGA
* * * *
3625225 ATCTTATCTCCCTGAGGTTACAGCGGAGCAGATCGAAGATATA
1 ATCTTATCTCCCTGAGATTACAGTGGAGCAGATCAAAGATAGA
* * * *
3625268 ATCCTATCTCCCTGA-AGTTACAGTGGAGCGGATTAAA-ATAAAGG
1 ATCTTATCTCCCTGAGA-TTACAGTGGAGCAGATCAAAGAT--AGA
* * *
3625312 ATCTTATCTCTCTGA-AGTTACAGTAGAGTAGATC---GCATCAG-
1 ATCTTATCTCCCTGAGA-TTACAGTGGAGCAGATCAAAG-AT-AGA
* * * * * * *
3625353 GTCTTATCTCTCTGAGGTTACAGTGGAGTAGACCGAAGAATTGCA
1 ATCTTATCTCCCTGAGATTACAGTGGAGCAGATCAAAG-ATAG-A
* ** **
3625398 GATCTTATCTCCCTGAGGTTACAGTGGAGCAGATTGAAGCCAGA
1 -ATCTTATCTCCCTGAGATTACAGTGGAGCAGATCAAAGATAGA
* * * **
3625442 GATCTTATCTCCCTGAGATTACAGCGGAGCAGATCGAAGACACT
1 -ATCTTATCTCCCTGAGATTACAGTGGAGCAGATCAAAGATAGA
*
3625486 ATCCTATCTCCCTGA-AGTTACAGTGGA
1 ATCTTATCTCCCTGAGA-TTACAGTGGA
3625513 ATGGATTAAA
Statistics
Matches: 323, Mismatches: 66, Indels: 51
0.73 0.15 0.12
Matches are distributed among these distances:
37 1 0.00
38 1 0.00
39 24 0.07
41 57 0.18
42 7 0.02
43 58 0.18
44 104 0.32
45 2 0.01
46 69 0.21
ACGTcount: A:0.31, C:0.21, G:0.22, T:0.27
Consensus pattern (43 bp):
ATCTTATCTCCCTGAGATTACAGTGGAGCAGATCAAAGATAGA
Found at i:3625247 original size:46 final size:46
Alignment explanation
Indices: 3625175--3625481 Score: 219
Period size: 46 Copynumber: 6.9 Consensus size: 46
3625165 GAAGATCACA
* * * *
3625175 TCAGGTCTTATCTCCCTGAGATTACAGTGGAACAGACCAAAGAATT
1 TCAGATCTTATCTCCCTGAGGTTACAGTGGAGCAGACCGAAGAATT
* * *
3625221 TCAGATCTTATCTCCCTGAGGTTACAGCGGAGCAGATCGAAG-ATA
1 TCAGATCTTATCTCCCTGAGGTTACAGTGGAGCAGACCGAAGAATT
* * * **
3625266 T-A-ATCCTATCTCCCTGAAGTTACAGTGGAGCGGA-TTAA-AA-T
1 TCAGATCTTATCTCCCTGAGGTTACAGTGGAGCAGACCGAAGAATT
** * * * * * *
3625307 AAAGGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATC---GCA--
1 TCA-GATCTTATCTCCCTGAGGTTACAGTGGAGCAGACCGAAGAATT
* * *
3625349 TCAGGTCTTATCTCTCTGAGGTTACAGTGGAGTAGACCGAAGAATT
1 TCAGATCTTATCTCCCTGAGGTTACAGTGGAGCAGACCGAAGAATT
* ** *
3625395 GCAGATCTTATCTCCCTGAGGTTACAGTGGAGCAGATTGAAGCCA--
1 TCAGATCTTATCTCCCTGAGGTTACAGTGGAGCAGACCGAAG-AATT
* * * *
3625440 -GAGATCTTATCTCCCTGAGATTACAGCGGAGCAGATCGAAGA
1 TCAGATCTTATCTCCCTGAGGTTACAGTGGAGCAGACCGAAGA
3625482 CACTATCCTA
Statistics
Matches: 208, Mismatches: 41, Indels: 27
0.75 0.15 0.10
Matches are distributed among these distances:
41 31 0.15
42 5 0.02
43 29 0.14
44 67 0.32
45 3 0.01
46 72 0.35
47 1 0.00
ACGTcount: A:0.30, C:0.20, G:0.23, T:0.26
Consensus pattern (46 bp):
TCAGATCTTATCTCCCTGAGGTTACAGTGGAGCAGACCGAAGAATT
Found at i:3625353 original size:174 final size:169
Alignment explanation
Indices: 3625053--3625471 Score: 588
Period size: 174 Copynumber: 2.4 Consensus size: 169
3625043 TTGAAGCCAG
* * *
3625053 AGATCTTATCTCCCTGAGATTACAGCGGAGCAGATCAAAGATAGTAATCCTATCTCCTTGAGATT
1 AGATCTTATCTCCCTGAGGTTACAGCGGAGCAGATCGAAGATA-TAATCCTATCTCCCTGAGATT
*
3625118 ACAATGGAGCGGATTAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGAAGATCACATCAGGTCT
65 ACAGTGGAGCGGATTAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGAAGATCACATCAGGTCT
*
3625183 TATCTCCCTGAGATTACAGTGGAACAGACCAAAGAATTTC
130 TATCTCCCTGAGATTACAGTGGAACAGACCAAAGAATTGC
3625223 AGATCTTATCTCCCTGAGGTTACAGCGGAGCAGATCGAAGATATAATCCTATCTCCCTGA-AGTT
1 AGATCTTATCTCCCTGAGGTTACAGCGGAGCAGATCGAAGATATAATCCTATCTCCCTGAGA-TT
* *
3625287 ACAGTGGAGCGGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCGCATCA
65 ACAGTGGAGCGGA-T----TAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGAAGATCACATCA
* * ** *
3625352 GGTCTTATCTCTCTGAGGTTACAGTGGAGTAGACCGAAGAATTGC
125 GGTCTTATCTCCCTGAGATTACAGTGGAACAGACCAAAGAATTGC
* * ** * *
3625397 AGATCTTATCTCCCTGAGGTTACAGTGGAGCAGATTGAAGCCAGAGATCTTATCTCCCTGAGATT
1 AGATCTTATCTCCCTGAGGTTACAGCGGAGCAGATCGAAGATATA-ATCCTATCTCCCTGAGATT
*
3625462 ACAGCGGAGC
65 ACAGTGGAGC
3625472 AGATCGAAGA
Statistics
Matches: 222, Mismatches: 19, Indels: 11
0.88 0.08 0.04
Matches are distributed among these distances:
168 1 0.00
169 30 0.14
170 42 0.19
174 123 0.55
175 25 0.11
176 1 0.00
ACGTcount: A:0.31, C:0.20, G:0.22, T:0.27
Consensus pattern (169 bp):
AGATCTTATCTCCCTGAGGTTACAGCGGAGCAGATCGAAGATATAATCCTATCTCCCTGAGATTA
CAGTGGAGCGGATTAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGAAGATCACATCAGGTCTT
ATCTCCCTGAGATTACAGTGGAACAGACCAAAGAATTGC
Found at i:3625402 original size:87 final size:87
Alignment explanation
Indices: 3625137--3625509 Score: 321
Period size: 87 Copynumber: 4.3 Consensus size: 87
3625127 CGGATTAAAG
* * *
3625137 GATCTTATCTCTCTGAAGTTACAGTAGAGAAGATCACATCAGGTCTTATCTCCCTGAGATTACAG
1 GATCTTATCTCCCTGAAGTTACAGTAGAGCAGATCGCATCAGGTCTTATCTCCCTGAGATTACAG
* * *
3625202 TGGAACAGACCAAAGAATTTCA
66 TGGAGCAGACCGAAGAATTACA
* ** * ** *
3625224 GATCTTATCTCCCTGAGGTTACAGCGGAGCAGATCGAAGAT-ATAATCCTATCTCCCTGA-AGTT
1 GATCTTATCTCCCTGAAGTTACAGTAGAGCAGATCG--CATCA-GGTCTTATCTCCCTGAGA-TT
* ** *
3625287 ACAGTGGAGCGGA-TTAA-AA-TAAA
62 ACAGTGGAGCAGACCGAAGAATTACA
* * * *
3625310 GGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCGCATCAGGTCTTATCTCTCTGAGGTTACA
1 -GATCTTATCTCCCTGAAGTTACAGTAGAGCAGATCGCATCAGGTCTTATCTCCCTGAGATTACA
* *
3625375 GTGGAGTAGACCGAAGAATTGCA
65 GTGGAGCAGACCGAAGAATTACA
* * * * *
3625398 GATCTTATCTCCCTGAGGTTACAGTGGAGCAGATTGAAGCCAGAGATCTTATCTCCCTGAGATTA
1 GATCTTATCTCCCTGAAGTTACAGTAGAGCAGATCGCA-TCAG-G-TCTTATCTCCCTGAGATTA
* * *
3625463 CAGCGGAGCAGATCGAAG-A-CAC-
63 CAGTGGAGCAGACCGAAGAATTACA
* *
3625485 TATCCTATCTCCCTGAAGTTACAGT
1 GATCTTATCTCCCTGAAGTTACAGT
3625510 GGAATGGATT
Statistics
Matches: 223, Mismatches: 50, Indels: 26
0.75 0.17 0.09
Matches are distributed among these distances:
85 27 0.12
86 5 0.02
87 119 0.53
88 10 0.04
89 30 0.13
90 32 0.14
ACGTcount: A:0.30, C:0.21, G:0.22, T:0.27
Consensus pattern (87 bp):
GATCTTATCTCCCTGAAGTTACAGTAGAGCAGATCGCATCAGGTCTTATCTCCCTGAGATTACAG
TGGAGCAGACCGAAGAATTACA
Found at i:3625446 original size:131 final size:128
Alignment explanation
Indices: 3625221--3625465 Score: 298
Period size: 131 Copynumber: 1.9 Consensus size: 128
3625211 CCAAAGAATT
*
3625221 TCAGATCTTATCTCCCTGAGGTTACAGCGGAGCAGATCGAAGATATAATCCTATCTCCCTGAAGT
1 TCAGATCTTATCTCCCTGAGGTTACAGCGGAGCAGACCGAAGATATAATCCTATCTCCCTGAAGT
* * *
3625286 TACAGTGGAGCGGATTAAAATAAAGGATCTTATCTCTCTGA-AGTTACAGTAGAGTAGATCGCA
66 TACAGTGGAGCAGATTAAAACAAAGGATCTTATCTCCCTGAGA-TTACAGTAGAGTAGATCGCA
* * * * *
3625349 TCAGGTCTTATCTCTCTGAGGTTACAGTGGAGTAGACCGAAGA-ATTGCAGATCTTATCTCCCTG
1 TCAGATCTTATCTCCCTGAGGTTACAGCGGAGCAGACCGAAGATA-T--A-ATCCTATCTCCCTG
* * * *
3625413 AGGTTACAGTGGAGCAGATTGAAGC-CAGAGATCTTATCTCCCTGAGATTACAG
62 AAGTTACAGTGGAGCAGATTAAAACAAAG-GATCTTATCTCCCTGAGATTACAG
3625466 CGGAGCAGAT
Statistics
Matches: 98, Mismatches: 13, Indels: 9
0.82 0.11 0.08
Matches are distributed among these distances:
127 1 0.01
128 39 0.40
130 3 0.03
131 54 0.55
132 1 0.01
ACGTcount: A:0.29, C:0.20, G:0.23, T:0.28
Consensus pattern (128 bp):
TCAGATCTTATCTCCCTGAGGTTACAGCGGAGCAGACCGAAGATATAATCCTATCTCCCTGAAGT
TACAGTGGAGCAGATTAAAACAAAGGATCTTATCTCCCTGAGATTACAGTAGAGTAGATCGCA
Found at i:3625997 original size:15 final size:15
Alignment explanation
Indices: 3625972--3626004 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
3625962 TACCCAATTA
3625972 CAACACCCAATA-CC
1 CAACACCCAATAGCC
3625986 CAACAGCCCAATAGCC
1 CAACA-CCCAATAGCC
3626002 CAA
1 CAA
3626005 AATCATCAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 5 0.29
15 7 0.41
16 5 0.29
ACGTcount: A:0.42, C:0.45, G:0.06, T:0.06
Consensus pattern (15 bp):
CAACACCCAATAGCC
Found at i:3626915 original size:15 final size:16
Alignment explanation
Indices: 3626895--3626928 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
3626885 CCTCCGCAGT
3626895 TTTAAT-TATTTTTAA
1 TTTAATCTATTTTTAA
*
3626910 TTTAATCTTTTTTTAA
1 TTTAATCTATTTTTAA
3626926 TTT
1 TTT
3626929 TTGCAAATTG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 6 0.35
16 11 0.65
ACGTcount: A:0.26, C:0.03, G:0.00, T:0.71
Consensus pattern (16 bp):
TTTAATCTATTTTTAA
Found at i:3629213 original size:15 final size:15
Alignment explanation
Indices: 3629194--3629228 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
3629184 TTTAAAGTTT
3629194 ATTTATTTCTTAATA
1 ATTTATTTCTTAATA
* *
3629209 TTTTATTTTTTAATA
1 ATTTATTTCTTAATA
3629224 ATTTA
1 ATTTA
3629229 AAATATGTTT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.31, C:0.03, G:0.00, T:0.66
Consensus pattern (15 bp):
ATTTATTTCTTAATA
Found at i:3629811 original size:16 final size:16
Alignment explanation
Indices: 3629787--3629817 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
3629777 TAGGATTAGA
*
3629787 ATGATTGAATTTATGG
1 ATGAATGAATTTATGG
3629803 ATGAATGAATTTATG
1 ATGAATGAATTTATG
3629818 ATCTTAATTA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.35, C:0.00, G:0.23, T:0.42
Consensus pattern (16 bp):
ATGAATGAATTTATGG
Found at i:3635611 original size:17 final size:16
Alignment explanation
Indices: 3635572--3635615 Score: 52
Period size: 16 Copynumber: 2.6 Consensus size: 16
3635562 AAATGACTTC
*
3635572 AACTCAAAATAACCTGA
1 AACT-AAAATTACCTGA
*
3635589 AACTAAAATTACCTTA
1 AACTAAAATTACCTGA
3635605 AACCTAAAATT
1 AA-CTAAAATT
3635616 TAATATTAGC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
16 12 0.50
17 12 0.50
ACGTcount: A:0.52, C:0.20, G:0.02, T:0.25
Consensus pattern (16 bp):
AACTAAAATTACCTGA
Found at i:3639386 original size:22 final size:23
Alignment explanation
Indices: 3639356--3639398 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
3639346 TCTAGGGACA
*
3639356 AAATGAAATTTTA-ATATTTAAT
1 AAATGAAATTTAACATATTTAAT
*
3639378 AAATTAAATTTAACATATTTA
1 AAATGAAATTTAACATATTTA
3639399 GCATTTTACT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 11 0.61
23 7 0.39
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.44
Consensus pattern (23 bp):
AAATGAAATTTAACATATTTAAT
Found at i:3645368 original size:16 final size:17
Alignment explanation
Indices: 3645347--3645411 Score: 64
Period size: 17 Copynumber: 4.0 Consensus size: 17
3645337 AAAAGTATAT
3645347 GTTTTCTAT-CATTCTA
1 GTTTTCTATCCATTCTA
* *
3645363 GTTTTCTATCCCTTCAA
1 GTTTTCTATCCATTCTA
* *
3645380 TTTTTC-AT-CTTTCTA
1 GTTTTCTATCCATTCTA
*
3645395 GTTTTCTTTCCATTCTA
1 GTTTTCTATCCATTCTA
3645412 CCTAGCAAAG
Statistics
Matches: 38, Mismatches: 8, Indels: 5
0.75 0.16 0.10
Matches are distributed among these distances:
15 10 0.26
16 12 0.32
17 16 0.42
ACGTcount: A:0.15, C:0.23, G:0.05, T:0.57
Consensus pattern (17 bp):
GTTTTCTATCCATTCTA
Found at i:3645995 original size:18 final size:18
Alignment explanation
Indices: 3645960--3645999 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
3645950 TTTAATATCA
* *
3645960 ATTTTATTATTTCGTAAT
1 ATTTTATTAGTTAGTAAT
*
3645978 ATTTTATTAGTTATTAAT
1 ATTTTATTAGTTAGTAAT
3645996 ATTT
1 ATTT
3646000 AGCCTCTACA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.30, C:0.03, G:0.05, T:0.62
Consensus pattern (18 bp):
ATTTTATTAGTTAGTAAT
Found at i:3649701 original size:12 final size:12
Alignment explanation
Indices: 3649684--3649710 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
3649674 CATAAGTGAC
3649684 TAAAATGTAACT
1 TAAAATGTAACT
3649696 TAAAATGTAACT
1 TAAAATGTAACT
3649708 TAA
1 TAA
3649711 GGTAAACAAA
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:0.52, C:0.07, G:0.07, T:0.33
Consensus pattern (12 bp):
TAAAATGTAACT
Found at i:3659205 original size:2 final size:2
Alignment explanation
Indices: 3659198--3659222 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
3659188 AAGTGAAAAT
3659198 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
3659223 CACCCCTATT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3670463 original size:29 final size:29
Alignment explanation
Indices: 3670408--3670464 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 29
3670398 TTTATATTGG
*
3670408 ATAAATATAATTATTTATATATGCAATAT
1 ATAAATATAATGATTTATATATGCAATAT
3670437 ATAAATATAAAATGATTT-TATAT-CAATA
1 ATAAATAT--AATGATTTATATATGCAATA
3670465 ATTGTGTTGA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
29 13 0.52
30 5 0.20
31 7 0.28
ACGTcount: A:0.51, C:0.04, G:0.04, T:0.42
Consensus pattern (29 bp):
ATAAATATAATGATTTATATATGCAATAT
Found at i:3671821 original size:14 final size:15
Alignment explanation
Indices: 3671802--3671844 Score: 54
Period size: 14 Copynumber: 2.9 Consensus size: 15
3671792 TAAAATTTTA
3671802 ATAAA-TAAAAATAT
1 ATAAATTAAAAATAT
*
3671816 ATAAATTATTAAATAT
1 ATAAATTA-AAAATAT
3671832 -TAAATTAAAAATA
1 ATAAATTAAAAATA
3671845 ATATGGGCAG
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
14 10 0.40
15 9 0.36
16 6 0.24
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (15 bp):
ATAAATTAAAAATAT
Found at i:3677518 original size:25 final size:25
Alignment explanation
Indices: 3677490--3677539 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
3677480 CAGTTAAAAA
* *
3677490 GATTAAAGCCACATCGGTGAATCTT
1 GATTAAAGCCACAACAGTGAATCTT
*
3677515 GATTAAAGCTACAACAGTGAATCTT
1 GATTAAAGCCACAACAGTGAATCTT
3677540 ACGCCCCAAG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.36, C:0.18, G:0.18, T:0.28
Consensus pattern (25 bp):
GATTAAAGCCACAACAGTGAATCTT
Found at i:3678036 original size:25 final size:25
Alignment explanation
Indices: 3677990--3678039 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
3677980 CAGTTAAAAA
* * *
3677990 GATTAAAGCCACATCGGTGAATCTT
1 GATTAAAGCCACAACAGCGAATCTT
*
3678015 GATTAAAGCTACAACAGCGAATCTT
1 GATTAAAGCCACAACAGCGAATCTT
3678040 ACGCCCCAAG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.36, C:0.20, G:0.18, T:0.26
Consensus pattern (25 bp):
GATTAAAGCCACAACAGCGAATCTT
Found at i:3678139 original size:125 final size:125
Alignment explanation
Indices: 3677461--3678127 Score: 1199
Period size: 125 Copynumber: 5.3 Consensus size: 125
3677451 ACATCAAATT
3677461 TCTTGTTTCTCCGACATTGCAGTTAAAAAGATTAAAGCCACATCGGTGAATCTTGATTAAAGCTA
1 TCTTGTTTCTCCGACATTGCAGTTAAAAAGATTAAAGCCACATCGGTGAATCTTGATTAAAGCTA
* * *
3677526 CAACAGTGAATCTTACGCCCCAAGCAATGCAATGGAATAGATTAAAGCCAAATTGGTGAA
66 CAACAGCGAATCTTACGCCCCAAGCGATGCAGTGGAATAGATTAAAGCCAAATTGGTGAA
*
3677586 TCTTGTTTCTCCGACATTGCAGTTAAAAAGATTAAAGCCATATCGGTGAATCTTGATTAAAGCTA
1 TCTTGTTTCTCCGACATTGCAGTTAAAAAGATTAAAGCCACATCGGTGAATCTTGATTAAAGCTA
* * *
3677651 CAACAGCGAATCTTACGCCCTAAGCGATGCAGTGGAATACATTAAAGCTAAATTGGTGAA
66 CAACAGCGAATCTTACGCCCCAAGCGATGCAGTGGAATAGATTAAAGCCAAATTGGTGAA
3677711 TCTTGTTTCTCCGACATTGCAGTTAAAAAGATTAAAGCCACATCGGTGAATCTTGATTAAAGCTA
1 TCTTGTTTCTCCGACATTGCAGTTAAAAAGATTAAAGCCACATCGGTGAATCTTGATTAAAGCTA
* *
3677776 CAACAACGAATCTTACGCCCCAAGCAATGCAGTGGAATAGATTAAAGCCAAATTGGTGAA
66 CAACAGCGAATCTTACGCCCCAAGCGATGCAGTGGAATAGATTAAAGCCAAATTGGTGAA
* *
3677836 TCTTGTTTCTCCGACATTGCATTTAAAAAGATTAAAGCCACATTGGTGAATCTTGATTAAAGCTA
1 TCTTGTTTCTCCGACATTGCAGTTAAAAAGATTAAAGCCACATCGGTGAATCTTGATTAAAGCTA
*
3677901 CAACAGTGAATCTTACGCCCCAAGCGATGCAGTGGAATAGATTAAAGCCAAATTGGTGAA
66 CAACAGCGAATCTTACGCCCCAAGCGATGCAGTGGAATAGATTAAAGCCAAATTGGTGAA
3677961 TCTTGTTTCTCCGACATTGCAGTTAAAAAGATTAAAGCCACATCGGTGAATCTTGATTAAAGCTA
1 TCTTGTTTCTCCGACATTGCAGTTAAAAAGATTAAAGCCACATCGGTGAATCTTGATTAAAGCTA
* * *
3678026 CAACAGCGAATCTTACGCCCCAAGCGATGCAGTGGAACAAATTAAAACCAAATTGGTGAA
66 CAACAGCGAATCTTACGCCCCAAGCGATGCAGTGGAATAGATTAAAGCCAAATTGGTGAA
3678086 TCTTGTTTCTCCGACATTGCAGTTAAAAAGATTAAAGCCACA
1 TCTTGTTTCTCCGACATTGCAGTTAAAAAGATTAAAGCCACA
3678128 ATGACGAATC
Statistics
Matches: 518, Mismatches: 24, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
125 518 1.00
ACGTcount: A:0.35, C:0.19, G:0.18, T:0.27
Consensus pattern (125 bp):
TCTTGTTTCTCCGACATTGCAGTTAAAAAGATTAAAGCCACATCGGTGAATCTTGATTAAAGCTA
CAACAGCGAATCTTACGCCCCAAGCGATGCAGTGGAATAGATTAAAGCCAAATTGGTGAA
Found at i:3680900 original size:25 final size:25
Alignment explanation
Indices: 3680854--3680903 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
3680844 CAGTTAAAAA
* * *
3680854 GATTAAAGCCACATCGGTGAATCTT
1 GATTAAAGCCACAACAGCGAATCTT
*
3680879 GATTAAAGCTACAACAGCGAATCTT
1 GATTAAAGCCACAACAGCGAATCTT
3680904 ACGCCCCAAG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.36, C:0.20, G:0.18, T:0.26
Consensus pattern (25 bp):
GATTAAAGCCACAACAGCGAATCTT
Found at i:3681132 original size:25 final size:25
Alignment explanation
Indices: 3681104--3681153 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
3681094 CAGTTAAAAA
* *
3681104 GATTAAAGCCACATCGGTGAATCTT
1 GATTAAAGCCACAACAGTGAATCTT
*
3681129 GATTAAAGCTACAACAGTGAATCTT
1 GATTAAAGCCACAACAGTGAATCTT
3681154 ACGCCCCAAG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.36, C:0.18, G:0.18, T:0.28
Consensus pattern (25 bp):
GATTAAAGCCACAACAGTGAATCTT
Found at i:3681400 original size:25 final size:25
Alignment explanation
Indices: 3681354--3681403 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
3681344 CAGTTAAAAA
* * *
3681354 GATTAAAGCCACATCGGTGAATCTT
1 GATTAAAGCCACAACAGCGAATCTT
*
3681379 GATTAAAGCTACAACAGCGAATCTT
1 GATTAAAGCCACAACAGCGAATCTT
3681404 ACGCCCCAAG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.36, C:0.20, G:0.18, T:0.26
Consensus pattern (25 bp):
GATTAAAGCCACAACAGCGAATCTT
Found at i:3681503 original size:125 final size:125
Alignment explanation
Indices: 3680729--3681491 Score: 1355
Period size: 125 Copynumber: 6.1 Consensus size: 125
3680719 CAATTCAAAC
* * *
3680729 GATTAAAGCCACCTCGGTGAATCTTGATTAAAGCTACAACAGCAAATCTTACGCCCCAAGCGATA
1 GATTAAAGCCACATCGGTGAATCTTGATTAAAGCTACAACAGCGAATCTTACGCCCCAAGCGATG
3680794 CAGTGGAATAGATTAAAGCCAAATTGGTGAATCTTGTTTCTCCGACATTGCAGTTAAAAA
66 CAGTGGAATAGATTAAAGCCAAATTGGTGAATCTTGTTTCTCCGACATTGCAGTTAAAAA
*
3680854 GATTAAAGCCACATCGGTGAATCTTGATTAAAGCTACAACAGCGAATCTTACGCCCCAAGCAATG
1 GATTAAAGCCACATCGGTGAATCTTGATTAAAGCTACAACAGCGAATCTTACGCCCCAAGCGATG
**
3680919 CAGTGGAATAGATTAAAGCCAAATTGGTGAATCTTGTTTCTCTAACATTGCAGTTAAAAA
66 CAGTGGAATAGATTAAAGCCAAATTGGTGAATCTTGTTTCTCCGACATTGCAGTTAAAAA
* * *
3680979 GATTAAAGCCACATTGGTGAATCTTGATTAAAACTACAACAGTGAATCTTACGCCCCAAGCGATG
1 GATTAAAGCCACATCGGTGAATCTTGATTAAAGCTACAACAGCGAATCTTACGCCCCAAGCGATG
3681044 CAGTGGAATAGATTAAAGCCAAATTGGTGAATCTTGTTTCTCCGACATTGCAGTTAAAAA
66 CAGTGGAATAGATTAAAGCCAAATTGGTGAATCTTGTTTCTCCGACATTGCAGTTAAAAA
* *
3681104 GATTAAAGCCACATCGGTGAATCTTGATTAAAGCTACAACAGTGAATCTTACGCCCCAAGCAATG
1 GATTAAAGCCACATCGGTGAATCTTGATTAAAGCTACAACAGCGAATCTTACGCCCCAAGCGATG
*
3681169 CAGTGGAATAGATTAAAGCCAAATTGGTGAATCTTGTTTCTCTGACATTGCAGTTAAAAA
66 CAGTGGAATAGATTAAAGCCAAATTGGTGAATCTTGTTTCTCCGACATTGCAGTTAAAAA
* * *
3681229 GATTAAAGCCACATTGGTGAATCTTGATTAAAACTACAACAGTGAATCTTACGCCCCAAGCGATG
1 GATTAAAGCCACATCGGTGAATCTTGATTAAAGCTACAACAGCGAATCTTACGCCCCAAGCGATG
*
3681294 CAGTGGAATAGATTAAAGCCAAATTGGTGAATCTTGTTTCTCTGACATTGCAGTTAAAAA
66 CAGTGGAATAGATTAAAGCCAAATTGGTGAATCTTGTTTCTCCGACATTGCAGTTAAAAA
3681354 GATTAAAGCCACATCGGTGAATCTTGATTAAAGCTACAACAGCGAATCTTACGCCCCAAGCGATG
1 GATTAAAGCCACATCGGTGAATCTTGATTAAAGCTACAACAGCGAATCTTACGCCCCAAGCGATG
* **
3681419 CAGTGGAACAGATTAAAATCAAATTGGTGAATCTTGTTTCTCCGACATTGCAGTTAAAAA
66 CAGTGGAATAGATTAAAGCCAAATTGGTGAATCTTGTTTCTCCGACATTGCAGTTAAAAA
3681479 GATTAAAGCCACA
1 GATTAAAGCCACA
3681492 ATGACGAATC
Statistics
Matches: 612, Mismatches: 26, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
125 612 1.00
ACGTcount: A:0.36, C:0.19, G:0.19, T:0.26
Consensus pattern (125 bp):
GATTAAAGCCACATCGGTGAATCTTGATTAAAGCTACAACAGCGAATCTTACGCCCCAAGCGATG
CAGTGGAATAGATTAAAGCCAAATTGGTGAATCTTGTTTCTCCGACATTGCAGTTAAAAA
Found at i:3684025 original size:30 final size:30
Alignment explanation
Indices: 3683979--3684102 Score: 203
Period size: 30 Copynumber: 4.1 Consensus size: 30
3683969 TTTTATTATG
*
3683979 CCAATATCTCGATACCCATATCTTTGACTTT
1 CCAATAT-TTGATACCCATATCTTTGACTTT
3684010 CCAATATTTGATACCCATATCTTTGACTTT
1 CCAATATTTGATACCCATATCTTTGACTTT
3684040 CCAATATTTGATACCCATATCTTTGACTTT
1 CCAATATTTGATACCCATATCTTTGACTTT
* * *
3684070 CTATTATTTGATACCCATATCTTTGATTTT
1 CCAATATTTGATACCCATATCTTTGACTTT
3684100 CCA
1 CCA
3684103 TAAATATGGA
Statistics
Matches: 88, Mismatches: 5, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
30 81 0.92
31 7 0.08
ACGTcount: A:0.26, C:0.24, G:0.06, T:0.44
Consensus pattern (30 bp):
CCAATATTTGATACCCATATCTTTGACTTT
Found at i:3684034 original size:15 final size:15
Alignment explanation
Indices: 3683989--3684096 Score: 78
Period size: 15 Copynumber: 7.2 Consensus size: 15
3683979 CCAATATCTC
3683989 GATACCCATATCTTT
1 GATACCCATATCTTT
** *
3684004 GACTTTCCA-ATATTT
1 GA-TACCCATATCTTT
3684019 GATACCCATATCTTT
1 GATACCCATATCTTT
** *
3684034 GACTTTCCA-ATATTT
1 GA-TACCCATATCTTT
3684049 GATACCCATATCTTT
1 GATACCCATATCTTT
** * *
3684064 GACTTTCTAT-TATTT
1 GA-TACCCATATCTTT
3684079 GATACCCATATCTTT
1 GATACCCATATCTTT
3684094 GAT
1 GAT
3684097 TTTCCATAAA
Statistics
Matches: 67, Mismatches: 20, Indels: 12
0.68 0.20 0.12
Matches are distributed among these distances:
14 12 0.18
15 43 0.64
16 12 0.18
ACGTcount: A:0.26, C:0.22, G:0.07, T:0.44
Consensus pattern (15 bp):
GATACCCATATCTTT
Found at i:3687923 original size:30 final size:30
Alignment explanation
Indices: 3687877--3688000 Score: 203
Period size: 30 Copynumber: 4.1 Consensus size: 30
3687867 TTTTATTATG
*
3687877 CCAATATCTCGATACCCATATCTTTGACTTT
1 CCAATAT-TTGATACCCATATCTTTGACTTT
3687908 CCAATATTTGATACCCATATCTTTGACTTT
1 CCAATATTTGATACCCATATCTTTGACTTT
3687938 CCAATATTTGATACCCATATCTTTGACTTT
1 CCAATATTTGATACCCATATCTTTGACTTT
* * *
3687968 CTATTATTTGATACCCATATCTTTGATTTT
1 CCAATATTTGATACCCATATCTTTGACTTT
3687998 CCA
1 CCA
3688001 TAAATATGGA
Statistics
Matches: 88, Mismatches: 5, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
30 81 0.92
31 7 0.08
ACGTcount: A:0.26, C:0.24, G:0.06, T:0.44
Consensus pattern (30 bp):
CCAATATTTGATACCCATATCTTTGACTTT
Found at i:3687932 original size:15 final size:15
Alignment explanation
Indices: 3687887--3687994 Score: 78
Period size: 15 Copynumber: 7.2 Consensus size: 15
3687877 CCAATATCTC
3687887 GATACCCATATCTTT
1 GATACCCATATCTTT
** *
3687902 GACTTTCCA-ATATTT
1 GA-TACCCATATCTTT
3687917 GATACCCATATCTTT
1 GATACCCATATCTTT
** *
3687932 GACTTTCCA-ATATTT
1 GA-TACCCATATCTTT
3687947 GATACCCATATCTTT
1 GATACCCATATCTTT
** * *
3687962 GACTTTCTAT-TATTT
1 GA-TACCCATATCTTT
3687977 GATACCCATATCTTT
1 GATACCCATATCTTT
3687992 GAT
1 GAT
3687995 TTTCCATAAA
Statistics
Matches: 67, Mismatches: 20, Indels: 12
0.68 0.20 0.12
Matches are distributed among these distances:
14 12 0.18
15 43 0.64
16 12 0.18
ACGTcount: A:0.26, C:0.22, G:0.07, T:0.44
Consensus pattern (15 bp):
GATACCCATATCTTT
Found at i:3688456 original size:110 final size:105
Alignment explanation
Indices: 3688258--3688541 Score: 386
Period size: 110 Copynumber: 2.7 Consensus size: 105
3688248 TCAAAAAAGG
* *
3688258 AAAATATTTCAAAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACATGCCCTAAGGTGTT
1 AAAA-ATTTCAAAATAAGGCAATGTTTTGCGTTTGGAAATTTGAGAAAACATGCCCTAAGGTGCT
* * *
3688323 GGGTGTCGATTTTTCTCGTTCAACCAAATGGCTTAATATCCTTC
65 GGGTGTCGATTTTTCTCATTCAACCAAATAGCTAAATA-CC--C
3688367 TTAAAAATTTCAAAATAAGGCAATGTTTTGCGTTTGGAAATTTGAGAAAACATGCCCTAAGGTGC
1 --AAAAATTTCAAAATAAGGCAATGTTTTGCGTTTGGAAATTTGAGAAAACATGCCCTAAGGTGC
3688432 TGGGTGTCGATTTTTCTCATTCAACCAAATAGCTAAATACCC
64 TGGGTGTCGATTTTTCTCATTCAACCAAATAGCTAAATACCC
* *
3688474 -----CTTC-AAA-AAGGCAATGTTTTGCGTTTGGAAATTTGAG-GAACATGCCCTAAGGTGCTG
1 AAAAATTTCAAAATAAGGCAATGTTTTGCGTTTGGAAATTTGAGAAAACATGCCCTAAGGTGCTG
*
3688531 GGTTTCGATTT
66 GGTGTCGATTT
3688542 CTCGTTTATC
Statistics
Matches: 165, Mismatches: 8, Indels: 14
0.88 0.04 0.07
Matches are distributed among these distances:
97 29 0.18
98 30 0.18
99 3 0.02
100 3 0.02
107 1 0.01
109 2 0.01
110 93 0.56
111 4 0.02
ACGTcount: A:0.30, C:0.16, G:0.20, T:0.33
Consensus pattern (105 bp):
AAAAATTTCAAAATAAGGCAATGTTTTGCGTTTGGAAATTTGAGAAAACATGCCCTAAGGTGCTG
GGTGTCGATTTTTCTCATTCAACCAAATAGCTAAATACCC
Found at i:3694091 original size:116 final size:116
Alignment explanation
Indices: 3693887--3694104 Score: 409
Period size: 116 Copynumber: 1.9 Consensus size: 116
3693877 TGATAAATTG
3693887 TATTAAGTCAAAAAATTGTATTAATGGATAGTAAAATTATCAAATTATATAAAATTATTAATTGT
1 TATTAAGTCAAAAAATTGTATTAATGGATAGTAAAATTATCAAATTATATAAAATTATTAATTGT
3693952 TAGTACCAGTCAAAACATTTTTCCAAATCTAACATTATGTGAATGTAAAAT
66 TAGTACCAGTCAAAACATTTTTCCAAATCTAACATTATGTGAATGTAAAAT
* * *
3694003 TATTAAGTCAAAAAATTGTATTAATGGTTAGTAAAATTATCAAATTATGTAAAATTATTATTTGT
1 TATTAAGTCAAAAAATTGTATTAATGGATAGTAAAATTATCAAATTATATAAAATTATTAATTGT
3694068 TAGTACCAGTCAAAACATTTTTCCAAATCTAACATTA
66 TAGTACCAGTCAAAACATTTTTCCAAATCTAACATTA
3694105 CGTTAAGGTT
Statistics
Matches: 99, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
116 99 1.00
ACGTcount: A:0.44, C:0.09, G:0.09, T:0.38
Consensus pattern (116 bp):
TATTAAGTCAAAAAATTGTATTAATGGATAGTAAAATTATCAAATTATATAAAATTATTAATTGT
TAGTACCAGTCAAAACATTTTTCCAAATCTAACATTATGTGAATGTAAAAT
Found at i:3694145 original size:23 final size:23
Alignment explanation
Indices: 3694113--3694845 Score: 555
Period size: 23 Copynumber: 29.7 Consensus size: 23
3694103 TACGTTAAGG
3694113 TTAGGATTAGGGTTTTTAATTAAA
1 TTAGG-TTAGGGTTTTTAATTAAA
*
3694137 TTAAGTTAGGGTTTTTAATTAATTTA
1 TTAGGTTAGGGTTTTTAATTAA---A
3694163 GGTTAAGGTTAGGGTTTTTAAGTT-AA
1 --TT-AGGTTAGGGTTTTTAA-TTAAA
**
3694189 -GGGGTTAGGGTTTTTAATTAAA
1 TTAGGTTAGGGTTTTTAATTAAA
3694211 TTAGGTTAGGGTTTTTAATTAAA
1 TTAGGTTAGGGTTTTTAATTAAA
3694234 TTAGGTTAGGGTTTTTAATTAAA
1 TTAGGTTAGGGTTTTTAATTAAA
3694257 TTAGGTTAGGGGGGTTTTTAATTAAA
1 TTAGGTTA---GGGTTTTTAATTAAA
3694283 TTAGGTTAGGGTTTTTAATTAAATTA
1 TTAGGTTAGGGTTTTTAATT-AA--A
3694309 GGTTAGGGTTTAGGGTTTTTAATTAAA
1 --TTA-GG-TTAGGGTTTTTAATTAAA
*
3694336 TTAGGTTAGAGTTTTTAATTAAA
1 TTAGGTTAGGGTTTTTAATTAAA
3694359 TTAGGTTAGGGTTTTTAATT-AA
1 TTAGGTTAGGGTTTTTAATTAAA
* *
3694381 --GGGTTTAGAGTTTTTAATTAAATTA
1 TTAGG-TTAGGGTTTTTAATT-AA--A
3694406 GTTTATGGTTAGGGTTTTTAATTAAA
1 --TTA-GGTTAGGGTTTTTAATTAAA
* *
3694432 TTAGGTTAAGGTTAGGGTTT--TTAAG
1 TTAGGTTAGGGTT----TTTAATTAAA
3694457 TTAAGGGTTTAGGGTTTTTAATTAAA
1 TT-A-GG-TTAGGGTTTTTAATTAAA
3694483 TTAGGTTAGGGTTTTTAATTAAA
1 TTAGGTTAGGGTTTTTAATTAAA
3694506 TTAGGTTAGGGTTAGGGTTT--TT-AA
1 TTAGGTTAGGGTT----TTTAATTAAA
3694530 TTAAGGGTTTAGGGTTTTTAATTAAA
1 TT-A-GG-TTAGGGTTTTTAATTAAA
* *
3694556 TTAGGTTAAGGTTAGGGTTT--TTAAG
1 TTAGGTTAGGGTT----TTTAATTAAA
* *
3694581 TTAAGGGTTTATGGTTTTAAATTAAA
1 TT-A-GG-TTAGGGTTTTTAATTAAA
3694607 TTAGGTTAGGGTTTTTAATTAATTTA
1 TTAGGTTAGGGTTTTTAATTAA---A
3694633 GGTTAGGGTTAGGGTTTTTAATT-AA
1 --TTA-GGTTAGGGTTTTTAATTAAA
3694658 -T-GGTTTAGGGTTTTTAATTAAA
1 TTAGG-TTAGGGTTTTTAATTAAA
* *
3694680 TTAGGTTAGGATTTTCAATTAAA
1 TTAGGTTAGGGTTTTTAATTAAA
*
3694703 TTAGGTTAGGGTTTTAAATTAAA
1 TTAGGTTAGGGTTTTTAATTAAA
* *
3694726 TTAGGTTAAGGTTAGGGTTT--TTAAGT
1 TTAGGTTAGGGTT----TTTAATTAA-A
*
3694752 TTAGGGTTTAAGGTTTTTAATTAAATTA
1 TTA-GG-TTAGGGTTTTTAATT-AA--A
3694780 GGTTAGGGTTAGGGTTTTTAATTAAA
1 --TTA-GGTTAGGGTTTTTAATTAAA
****
3694806 TTAGGTTAGGGTTTAGGGTTAAA
1 TTAGGTTAGGGTTTTTAATTAAA
3694829 TTAGGTTAGGGTTTTTA
1 TTAGGTTAGGGTTTTTA
3694846 TTACATCAAA
Statistics
Matches: 589, Mismatches: 40, Indels: 161
0.75 0.05 0.20
Matches are distributed among these distances:
20 4 0.01
21 31 0.05
22 22 0.04
23 262 0.44
24 34 0.06
25 29 0.05
26 54 0.09
27 28 0.05
28 35 0.06
29 65 0.11
30 25 0.04
ACGTcount: A:0.29, C:0.00, G:0.25, T:0.47
Consensus pattern (23 bp):
TTAGGTTAGGGTTTTTAATTAAA
Found at i:3694497 original size:147 final size:147
Alignment explanation
Indices: 3694110--3694845 Score: 612
Period size: 147 Copynumber: 4.9 Consensus size: 147
3694100 CATTACGTTA
* * **** *
3694110 AGGTTAGGATTAGGGTTTTTAATTAAATTAAGTTAGGGTTTTTAATTAATTTAGGTTAA-GG-TT
1 AGGTTAGG-TTAGGGTTTTTAATTAAATTAGGTTAAGG-TTAGGGTT--TTTAAGTTAAGGGTTT
**
3694173 AGGGTTTTTAAGTT-AA-GGGGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTTTTAATTAAATT
62 AGGGTTTTTAA-TTAAATTAGGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTTTTAATTAAA-T
3694236 AGGTTAGGGTTTTTAATTAAATT
125 AGGTTAGGGTTTTTAATTAAATT
* * **** * *
3694259 AGGTTAGG--GGGGTTTTTAATTAAATTAGGTTAGGGTTTTTAATTAAATTAGGTT-AGGGTTTA
1 AGGTTAGGTTAGGGTTTTTAATTAAATTAGGTTAAGG-TTAGGGTT--TTTAAGTTAAGGGTTTA
* *
3694321 GGGTTTTTAATTAAATTAGGTTAGAGTTTTTAATTAAATTAGGTTAGGGTTTTTAATT-AA-GGG
63 GGGTTTTTAATTAAATTAGGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTTTTAATTAAATAGG
*
3694384 TTTAGAGTTTTTAATTAAATT
128 -TTAGGGTTTTTAATTAAATT
*
3694405 AGTTTATGGTTAGGGTTTTTAATTAAATTAGGTTAAGGTTAGGGTTTTTAAGTTAAGGGTTTAGG
1 AGGTTA-GGTTAGGGTTTTTAATTAAATTAGGTTAAGGTTAGGGTTTTTAAGTTAAGGGTTTAGG
3694470 GTTTTTAATTAAATTAGGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTAGGGTTTTTAATT-AA
65 GTTTTTAATTAAATTAGGTTAGGGTTTTTAATT-AA--A--TTA-GGTTAGGGTTTTTAATTAAA
*
3694534 -GGGTTTAGGGTTTTTAATTAAATT
124 TAGG-TTAGGGTTTTTAATTAAATT
* * * *
3694558 AGGTTAAGGTTAGGGTTTTTAAGTT--A--AGG----GTTTATGG-TTTTAAATTAAATTAGG-T
1 AGGTT-AGGTTAGGGTTTTTAA-TTAAATTAGGTTAAGGTTAGGGTTTTTAAGTT-AA--GGGTT
3694613 TAGGGTTTTTAATTAATTTAGGTTAGGGTTAGGGTTTTTAATT-AA-T-GGTTTAGGGTTTTTAA
61 TAGGGTTTTTAATTAA---A--TTA-GGTTAGGGTTTTTAATTAAATTAGG-TTAGGGTTTTTAA
* *
3694675 TTAAATTAGGTTAGGATTTTCAATT-AA--
119 TTAAA-TAGGTTAGGGTTTTTAATTAAATT
* * *
3694702 A--TTAGGTTAGGGTTTTAAATTAAATTAGGTTAAGGTTAGGGTTTTTAAGTTTAGGGTTTAAGG
1 AGGTTAGGTTAGGGTTTTTAATTAAATTAGGTTAAGGTTAGGGTTTTTAAGTTAAGGGTTTAGGG
****
3694765 TTTTTAATTAAATTAGGTTAGGGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTTAGGGTTAAAT
66 TTTTTAATT-AA--A--TTA-GGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTTTTAATTAAA-
3694830 TAGGTTAGGGTTTTTA
124 TAGGTTAGGGTTTTTA
3694846 TTACATCAAA
Statistics
Matches: 503, Mismatches: 40, Indels: 88
0.80 0.06 0.14
Matches are distributed among these distances:
140 2 0.00
141 15 0.03
142 3 0.01
144 6 0.01
145 26 0.05
146 92 0.18
147 131 0.26
148 60 0.12
149 72 0.14
150 7 0.01
151 1 0.00
152 7 0.01
153 78 0.16
154 3 0.01
ACGTcount: A:0.29, C:0.00, G:0.25, T:0.46
Consensus pattern (147 bp):
AGGTTAGGTTAGGGTTTTTAATTAAATTAGGTTAAGGTTAGGGTTTTTAAGTTAAGGGTTTAGGG
TTTTTAATTAAATTAGGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTTTTAATTAAATAGGTTA
GGGTTTTTAATTAAATT
Found at i:3694519 original size:74 final size:74
Alignment explanation
Indices: 3694113--3694825 Score: 511
Period size: 74 Copynumber: 9.6 Consensus size: 74
3694103 TACGTTAAGG
* **** *
3694113 TTAGGATTAGGGTTTTTAATTAAATTAAGTTAGGGTTTTTAATTAATTTAGGTTAA-GG-TTAGG
1 TTAGG-TTAGGGTTTTTAATTAAATTAGGTTAGGG-TTAGGGTT--TTTAAGTTAAGGGTTTAGG
3694176 GTTTTTAAGTT-AA
62 GTTTTTAA-TTAAA
** *
3694189 -GGGGTTAGGGTTTTTAATTAAATTAGGTTAGGGTT----TTTAATTAAATT-A-GG-TTAGGGT
1 TTAGGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTAGGGTTT--TTAAGTTAAGGGTTTAGGGT
3694246 TTTTAATTAAA
64 TTTTAATTAAA
**** * *
3694257 TTAGGTTAGGGGGGTTTTTAATTAAATTAGGTTAGGGTTTTTAATTAAATTAGGTT-AGGGTTTA
1 TTAGGTTA---GGGTTTTTAATTAAATTAGGTTAGGG-TTAGGGTT--TTTAAGTTAAGGGTTTA
3694321 GGGTTTTTAATTAAA
60 GGGTTTTTAATTAAA
* *
3694336 TTAGGTTAGAGTTTTTAATT-AA--A--TTA-GGTTAGGGTTTTTAA-TTAAGGGTTTAGAGTTT
1 TTAGGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTAGGGTTTTTAAGTTAAGGGTTTAGGGTTT
3694394 TTAATTAAATTA
66 TTAATT-AA--A
*
3694406 GTTTATGGTTAGGGTTTTTAATTAAATTAGGTTAAGGTTAGGGTTTTTAAGTTAAGGGTTTAGGG
1 --TTA-GGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTAGGGTTTTTAAGTTAAGGGTTTAGGG
3694471 TTTTTAATTAAA
63 TTTTTAATTAAA
3694483 TTAGGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTAGGGTTTTTAA-TTAAGGGTTTAGGGTTT
1 TTAGGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTAGGGTTTTTAAGTTAAGGGTTTAGGGTTT
3694547 TTAATTAAA
66 TTAATTAAA
* **** * * * * *
3694556 TTAGGTTAAGG-TTAGGGTT--TTTAAGTTAAGGGTTTATGG-TTTTAAATTAAATTAGG-TTAG
1 TTAGGTTAGGGTTTTTAATTAAATTAGGTT-AGGG-TTAGGGTTTTTAAGTT-AA--GGGTTTAG
*
3694616 GGTTTTTAATTAAT
61 GGTTTTTAATTAAA
* * *
3694630 TTAGGTTAGGGTTAGGGTTT--TT-AATTA--AT-GGTTTAGGGTTTTTAA-TTAAATTAGG-TT
1 TTAGGTTAGGGTT----TTTAATTAAATTAGGTTAGGGTTAGGGTTTTTAAGTT-AA--GGGTTT
* *
3694687 AGGATTTTCAATTAAA
59 AGGGTTTTTAATTAAA
* * * *
3694703 TTAGGTTAGGGTTTTAAATTAAATTAGGTTAAGGTTAGGGTTTTTAAGTTTAGGGTTTAAGGTTT
1 TTAGGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTAGGGTTTTTAAGTTAAGGGTTTAGGGTTT
3694768 TTAATTAAATTA
66 TTAATT-AA--A
3694780 GGTTAGGGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTTAGGGTT
1 --TTA-GGTTAGGGTTTTTAATTAAATTAGGTTAGGG-TTAGGGTT
3694826 AAATTAGGTT
Statistics
Matches: 527, Mismatches: 52, Indels: 111
0.76 0.08 0.16
Matches are distributed among these distances:
66 2 0.00
67 25 0.05
68 20 0.04
69 18 0.03
70 9 0.02
71 15 0.03
72 45 0.09
73 104 0.20
74 121 0.23
75 27 0.05
76 15 0.03
77 12 0.02
78 8 0.02
79 47 0.09
80 51 0.10
81 8 0.02
ACGTcount: A:0.28, C:0.00, G:0.25, T:0.47
Consensus pattern (74 bp):
TTAGGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTAGGGTTTTTAAGTTAAGGGTTTAGGGTTT
TTAATTAAA
Found at i:3694542 original size:124 final size:123
Alignment explanation
Indices: 3694191--3694738 Score: 651
Period size: 124 Copynumber: 4.4 Consensus size: 123
3694181 TAAGTTAAGG
3694191 GGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTTTTAATTAA
1 GGTTAGGGTTTTTAATTAAA-TAGGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTTTTAATTAA
*
3694256 ATTAGGTTAGGG---GGGTTTTTAATTAAATTAGGTTAGGGTTTTTAATTAAATTAGGTTAG
65 ATTAGGTTAGGGTTAGGGTTTTTAATT-AA-T-GGTTAGGGTTTTTAATTAAATTAGGTTAA
*
3694315 GGTTTAGGGTTTTTAATTAAATTAGGTTAGAGTTTTTAATTAAATTAGGTTAGGGTTTTTAATT-
1 GG-TTAGGGTTTTTAATTAAA-TAGGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTTTTAATTA
* * **** * * *
3694379 AA--GGGTTTAGAGTTTTTAATTAAATTAGTTTATGGTTAGGGTTTTTAATTAAATTAGGTTAA
64 AATTAGG-TTAG-GGTTAGGGTT--TTTAATTAATGGTTAGGGTTTTTAATTAAATTAGGTTAA
*
3694441 GGTTAGGGTTTTTAAGTT-AA-GGGTTTAGGGTTTTTAATTAAATTAGGTTAGGGTTTTTAATTA
1 GGTTAGGGTTTTTAA-TTAAATAGG-TTAGGGTTTTTAATTAAATTAGGTTAGGGTTTTTAATTA
*
3694504 AATTAGGTTAGGGTTAGGGTTTTTAATTAAGGGTTTAGGGTTTTTAATTAAATTAGGTTAA
64 AATTAGGTTAGGGTTAGGGTTTTTAATTAATGG-TTAGGGTTTTTAATTAAATTAGGTTAA
* * *
3694565 GGTTAGGGTTTTTAAGTT-AA-GGGTTTATGGTTTTAAATTAAATTAGGTTAGGGTTTTTAATTA
1 GGTTAGGGTTTTTAA-TTAAATAGG-TTAGGGTTTTTAATTAAATTAGGTTAGGGTTTTTAATTA
*
3694628 ATTTAGGTTAGGGTTAGGGTTTTTAATTAATGGTTTAGGGTTTTTAATTAAATTAGGTT-A
64 AATTAGGTTAGGGTTAGGGTTTTTAATTAATGG-TTAGGGTTTTTAATTAAATTAGGTTAA
* * *
3694688 GG--A---TTTTCAATTAAATTAGGTTAGGGTTTTAAATTAAATTAGGTTAAGGTT
1 GGTTAGGGTTTTTAATTAAA-TAGGTTAGGGTTTTTAATTAAATTAGGTTAGGGTT
3694739 AGGGTTTTTA
Statistics
Matches: 377, Mismatches: 30, Indels: 39
0.85 0.07 0.09
Matches are distributed among these distances:
117 2 0.01
118 8 0.02
119 29 0.08
120 2 0.01
121 1 0.00
122 2 0.01
123 17 0.05
124 187 0.50
125 82 0.22
126 36 0.10
127 5 0.01
128 1 0.00
129 5 0.01
ACGTcount: A:0.29, C:0.00, G:0.24, T:0.47
Consensus pattern (123 bp):
GGTTAGGGTTTTTAATTAAATAGGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTTTTAATTAAA
TTAGGTTAGGGTTAGGGTTTTTAATTAATGGTTAGGGTTTTTAATTAAATTAGGTTAA
Found at i:3694749 original size:15 final size:15
Alignment explanation
Indices: 3694731--3694760 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
3694721 TTAAATTAGG
3694731 TTAAGGTTAGGGTTT
1 TTAAGGTTAGGGTTT
*
3694746 TTAAGTTTAGGGTTT
1 TTAAGGTTAGGGTTT
3694761 AAGGTTTTTA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.20, C:0.00, G:0.30, T:0.50
Consensus pattern (15 bp):
TTAAGGTTAGGGTTT
Found at i:3694767 original size:51 final size:49
Alignment explanation
Indices: 3694602--3694802 Score: 218
Period size: 51 Copynumber: 4.1 Consensus size: 49
3694592 TGGTTTTAAA
* * *
3694602 TTAAATTAGG-TTAGGGTTTTTAATTAATTTAGGTTAGGGTTAGGGTTT
1 TTAATTTAGGTTTAGGGTTTTTAATTAAATTAGGTTAAGGTTAGGGTTT
* *
3694650 TTAATTAATGGTTTAGGGTTTTTAATTAAATTAGGTT-AGGATT----TTCAA
1 TTAATTTA-GGTTTAGGGTTTTTAATTAAATTAGGTTAAGG-TTAGGGTT--T
* *
3694698 TTAAATTAGG-TTAGGGTTTTAAATTAAATTAGGTTAAGGTTAGGGTTT
1 TTAATTTAGGTTTAGGGTTTTTAATTAAATTAGGTTAAGGTTAGGGTTT
* *
3694746 TTAAGTTTAGGGTTTAAGGTTTTTAATTAAATTAGGTTAGGGTTAGGGTTT
1 TTAA-TTTA-GGTTTAGGGTTTTTAATTAAATTAGGTTAAGGTTAGGGTTT
3694797 TTAATT
1 TTAATT
3694803 AAATTAGGTT
Statistics
Matches: 127, Mismatches: 13, Indels: 24
0.77 0.08 0.15
Matches are distributed among these distances:
46 28 0.22
47 5 0.04
48 16 0.13
49 7 0.06
50 32 0.25
51 39 0.31
ACGTcount: A:0.28, C:0.00, G:0.24, T:0.47
Consensus pattern (49 bp):
TTAATTTAGGTTTAGGGTTTTTAATTAAATTAGGTTAAGGTTAGGGTTT
Found at i:3694870 original size:26 final size:25
Alignment explanation
Indices: 3694841--3694934 Score: 170
Period size: 25 Copynumber: 3.7 Consensus size: 25
3694831 AGGTTAGGGT
3694841 TTTTATTACATCAAATAAACTTCTA
1 TTTTATTACATCAAATAAACTTCTA
*
3694866 TTTTTATTACATTAAATAAACTTCTA
1 -TTTTATTACATCAAATAAACTTCTA
3694892 TTTTATTACATCAAATAAACTTCTA
1 TTTTATTACATCAAATAAACTTCTA
3694917 TTTTATTACATCAAATAA
1 TTTTATTACATCAAATAA
3694935 TATCAAAATA
Statistics
Matches: 66, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
25 42 0.64
26 24 0.36
ACGTcount: A:0.40, C:0.14, G:0.00, T:0.46
Consensus pattern (25 bp):
TTTTATTACATCAAATAAACTTCTA
Found at i:3694976 original size:43 final size:45
Alignment explanation
Indices: 3694902--3694987 Score: 140
Period size: 43 Copynumber: 2.0 Consensus size: 45
3694892 TTTTATTACA
*
3694902 TCAAATAAACTTCTATTTTATTACATCAAATAATATCAAAATAAC
1 TCAAATAAACTTCTATTTTATTACATAAAATAATATCAAAATAAC
*
3694947 TCAAA-AAATTTCTATTTT-TTACATAAAATAATATCAAAATA
1 TCAAATAAACTTCTATTTTATTACATAAAATAATATCAAAATA
3694988 TTCAAAATAT
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
43 22 0.56
44 12 0.31
45 5 0.13
ACGTcount: A:0.50, C:0.13, G:0.00, T:0.37
Consensus pattern (45 bp):
TCAAATAAACTTCTATTTTATTACATAAAATAATATCAAAATAAC
Found at i:3695443 original size:18 final size:18
Alignment explanation
Indices: 3695409--3695443 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
3695399 CGAAAAAGGA
**
3695409 TACATATAAGGGTTAGGG
1 TACATATAAGGCCTAGGG
3695427 TACATATAAGGCCTAGG
1 TACATATAAGGCCTAGG
3695444 AAACGCACCT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.34, C:0.11, G:0.29, T:0.26
Consensus pattern (18 bp):
TACATATAAGGCCTAGGG
Found at i:3696091 original size:7 final size:7
Alignment explanation
Indices: 3696079--3696103 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
3696069 TTATATGCAT
3696079 AATACTA
1 AATACTA
3696086 AATACTA
1 AATACTA
3696093 AATACTA
1 AATACTA
3696100 AATA
1 AATA
3696104 TCAATCGAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.60, C:0.12, G:0.00, T:0.28
Consensus pattern (7 bp):
AATACTA
Found at i:3697092 original size:25 final size:25
Alignment explanation
Indices: 3697042--3697108 Score: 70
Period size: 25 Copynumber: 2.8 Consensus size: 25
3697032 CTTTTATAAC
*
3697042 AAATAATAAATTAATAATTATCTAA
1 AAATAATAAATTAAAAATTATCTAA
*
3697067 AAATACATAAA-TAAAAATT-TCT-T
1 AAATA-ATAAATTAAAAATTATCTAA
*
3697090 AAATAAT-ATTTAAAAATTA
1 AAATAATAAATTAAAAATTA
3697109 AATTTAACAC
Statistics
Matches: 36, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
21 1 0.03
22 10 0.28
23 5 0.14
24 3 0.08
25 12 0.33
26 5 0.14
ACGTcount: A:0.60, C:0.04, G:0.00, T:0.36
Consensus pattern (25 bp):
AAATAATAAATTAAAAATTATCTAA
Found at i:3697353 original size:22 final size:22
Alignment explanation
Indices: 3697283--3697356 Score: 98
Period size: 22 Copynumber: 3.4 Consensus size: 22
3697273 AAATATGGAT
*
3697283 TTGAGAGAATTTTGGAAGGAAA
1 TTGAGAGAAATTTGGAAGGAAA
3697305 TTGAGAGAAATTTGGAAGGAAA
1 TTGAGAGAAATTTGGAAGGAAA
*
3697327 TTGAGAGGAA-TT-GAGAGGAAA
1 TTGAGAGAAATTTGGA-AGGAAA
3697348 TATGAGAGA
1 T-TGAGAGA
3697357 GGATTTGTTT
Statistics
Matches: 47, Mismatches: 3, Indels: 4
0.87 0.06 0.07
Matches are distributed among these distances:
20 2 0.04
21 9 0.19
22 36 0.77
ACGTcount: A:0.43, C:0.00, G:0.34, T:0.23
Consensus pattern (22 bp):
TTGAGAGAAATTTGGAAGGAAA
Found at i:3697355 original size:12 final size:11
Alignment explanation
Indices: 3697299--3697355 Score: 66
Period size: 10 Copynumber: 5.2 Consensus size: 11
3697289 GAATTTTGGA
3697299 AGGAAATTGAG
1 AGGAAATTGAG
3697310 A-GAAATTTG-G
1 AGGAAA-TTGAG
3697320 AAGGAAATTGAG
1 -AGGAAATTGAG
3697332 AGG-AATTGAG
1 AGGAAATTGAG
3697342 AGGAAATATGAG
1 AGGAAAT-TGAG
3697354 AG
1 AG
3697356 AGGATTTGTT
Statistics
Matches: 40, Mismatches: 0, Indels: 11
0.78 0.00 0.22
Matches are distributed among these distances:
10 15 0.38
11 14 0.35
12 11 0.28
ACGTcount: A:0.46, C:0.00, G:0.35, T:0.19
Consensus pattern (11 bp):
AGGAAATTGAG
Found at i:3697669 original size:18 final size:19
Alignment explanation
Indices: 3697646--3697690 Score: 67
Period size: 18 Copynumber: 2.5 Consensus size: 19
3697636 GTTCAAGGTG
3697646 TAATTAATTTAAATTT-TT
1 TAATTAATTTAAATTTATT
3697664 TAATTAA-TTAAATTTATT
1 TAATTAATTTAAATTTATT
*
3697682 TAATGAATT
1 TAATTAATT
3697691 ATTTAATTAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
17 8 0.33
18 15 0.62
19 1 0.04
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (19 bp):
TAATTAATTTAAATTTATT
Found at i:3701744 original size:13 final size:13
Alignment explanation
Indices: 3701726--3701750 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3701716 TCAAACTTTT
3701726 TATTTTTAATATA
1 TATTTTTAATATA
3701739 TATTTTTAATAT
1 TATTTTTAATAT
3701751 TTTATATATT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (13 bp):
TATTTTTAATATA
Found at i:3702380 original size:15 final size:15
Alignment explanation
Indices: 3702349--3702389 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
3702339 TATGACACAA
3702349 TTATAATATAAAATTT
1 TTATAA-ATAAAATTT
*
3702365 TTATAAATATAATTT
1 TTATAAATAAAATTT
*
3702380 TGATAAATAA
1 TTATAAATAA
3702390 CACTATTAGT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
15 16 0.73
16 6 0.27
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.46
Consensus pattern (15 bp):
TTATAAATAAAATTT
Found at i:3705292 original size:29 final size:30
Alignment explanation
Indices: 3705239--3705312 Score: 132
Period size: 29 Copynumber: 2.5 Consensus size: 30
3705229 CAAATAATTT
3705239 TAAAATTATTAAAATTATTTTTTTGAAATA
1 TAAAATTATTAAAATTATTTTTTTGAAATA
3705269 TAAAATTATT-AAATTATTTTTTTGAAATA
1 TAAAATTATTAAAATTATTTTTTTGAAATA
*
3705298 TAAAATTATCAAAAT
1 TAAAATTATTAAAAT
3705313 AGATCGTTGT
Statistics
Matches: 42, Mismatches: 1, Indels: 2
0.93 0.02 0.04
Matches are distributed among these distances:
29 28 0.67
30 14 0.33
ACGTcount: A:0.49, C:0.01, G:0.03, T:0.47
Consensus pattern (30 bp):
TAAAATTATTAAAATTATTTTTTTGAAATA
Found at i:3705854 original size:15 final size:15
Alignment explanation
Indices: 3705829--3705880 Score: 56
Period size: 14 Copynumber: 3.5 Consensus size: 15
3705819 AGCAATCCCC
3705829 AAAACCTCTAAAATCA
1 AAAACC-CTAAAATCA
3705845 AAAACCCT-AAA-CA
1 AAAACCCTAAAATCA
*
3705858 AAAATCCCCAAAATC-
1 AAAA-CCCTAAAATCA
3705873 AAAACCCT
1 AAAACCCT
3705881 TACCCAAAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 8
0.76 0.05 0.20
Matches are distributed among these distances:
13 6 0.19
14 9 0.29
15 9 0.29
16 7 0.23
ACGTcount: A:0.56, C:0.31, G:0.00, T:0.13
Consensus pattern (15 bp):
AAAACCCTAAAATCA
Found at i:3705876 original size:28 final size:29
Alignment explanation
Indices: 3705838--3705897 Score: 86
Period size: 28 Copynumber: 2.1 Consensus size: 29
3705828 CAAAACCTCT
3705838 AAAATCAAAAACCCTAAACAAAAATCCCC
1 AAAATCAAAAACCCTAAACAAAAATCCCC
* * *
3705867 AAAATC-AAAACCCTTACCCAAAATCCCC
1 AAAATCAAAAACCCTAAACAAAAATCCCC
3705895 AAA
1 AAA
3705898 TTTGACAAAC
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
28 22 0.79
29 6 0.21
ACGTcount: A:0.55, C:0.33, G:0.00, T:0.12
Consensus pattern (29 bp):
AAAATCAAAAACCCTAAACAAAAATCCCC
Found at i:3726952 original size:33 final size:30
Alignment explanation
Indices: 3726910--3726972 Score: 72
Period size: 30 Copynumber: 2.0 Consensus size: 30
3726900 TTGATATATA
*
3726910 AATTTTAATTTAGAATCATATATATATAATTTT
1 AATTATAA-TTAGAAT-ATATATAT-TAATTTT
* *
3726943 AATTATAATTCGAATGTATATATTAATTTT
1 AATTATAATTAGAATATATATATTAATTTT
3726973 TATTTTTATT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
30 7 0.26
31 7 0.26
32 6 0.22
33 7 0.26
ACGTcount: A:0.41, C:0.03, G:0.05, T:0.51
Consensus pattern (30 bp):
AATTATAATTAGAATATATATATTAATTTT
Found at i:3728809 original size:17 final size:17
Alignment explanation
Indices: 3728787--3728826 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
3728777 TAATTAACTA
3728787 ATTTTTTAAATAAA-AAT
1 ATTTTTTAAA-AAATAAT
*
3728804 ATTTTTTAAAAAATTAT
1 ATTTTTTAAAAAATAAT
3728821 ATTTTT
1 ATTTTT
3728827 AATTTTTAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 3 0.14
17 18 0.86
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (17 bp):
ATTTTTTAAAAAATAAT
Found at i:3728832 original size:23 final size:24
Alignment explanation
Indices: 3728806--3728857 Score: 70
Period size: 23 Copynumber: 2.2 Consensus size: 24
3728796 ATAAAAATAT
*
3728806 TTTTTAAAAAATTAT-ATTTTTAA
1 TTTTTAAAAAATTATAATTTTAAA
* *
3728829 TTTTTAAACAATTTTAATTTTAAA
1 TTTTTAAAAAATTATAATTTTAAA
3728853 TTTTT
1 TTTTT
3728858 TATACTTTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
23 13 0.52
24 12 0.48
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (24 bp):
TTTTTAAAAAATTATAATTTTAAA
Found at i:3728889 original size:17 final size:17
Alignment explanation
Indices: 3728823--3728891 Score: 52
Period size: 17 Copynumber: 4.1 Consensus size: 17
3728813 AAAATTATAT
* *
3728823 TTTTAATTTTTAAACAA
1 TTTTAAATTTTAAAAAA
**
3728840 TTTT-AATTTT-AAATT
1 TTTTAAATTTTAAAAAA
* **
3728855 TTTTATACTTTTTGAAAA
1 TTTTA-AATTTTAAAAAA
3728873 TTTTAAATTTTAAAAAA
1 TTTTAAATTTTAAAAAA
3728890 TT
1 TT
3728892 AATTAATTGC
Statistics
Matches: 38, Mismatches: 11, Indels: 6
0.69 0.20 0.11
Matches are distributed among these distances:
15 6 0.16
16 5 0.13
17 20 0.53
18 7 0.18
ACGTcount: A:0.39, C:0.03, G:0.01, T:0.57
Consensus pattern (17 bp):
TTTTAAATTTTAAAAAA
Found at i:3734250 original size:15 final size:15
Alignment explanation
Indices: 3734230--3734290 Score: 54
Period size: 15 Copynumber: 4.1 Consensus size: 15
3734220 GGATTTATTA
*
3734230 ACTCGACTCGATTTG
1 ACTCGATTCGATTTG
*
3734245 ACTCGAAATT--TTTTG
1 ACTCG--ATTCGATTTG
*
3734260 ACTCGATTCGATTCG
1 ACTCGATTCGATTTG
*
3734275 ATTCGATTCGATTTG
1 ACTCGATTCGATTTG
3734290 A
1 A
3734291 AAAAATTCAA
Statistics
Matches: 36, Mismatches: 6, Indels: 8
0.72 0.12 0.16
Matches are distributed among these distances:
13 3 0.08
15 31 0.86
17 2 0.06
ACGTcount: A:0.23, C:0.20, G:0.18, T:0.39
Consensus pattern (15 bp):
ACTCGATTCGATTTG
Found at i:3734272 original size:5 final size:5
Alignment explanation
Indices: 3734262--3734287 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
3734252 ATTTTTTGAC
3734262 TCGAT TCGAT TCGAT TCGAT TCGAT T
1 TCGAT TCGAT TCGAT TCGAT TCGAT T
3734288 TGAAAAAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.19, C:0.19, G:0.19, T:0.42
Consensus pattern (5 bp):
TCGAT
Found at i:3736241 original size:16 final size:15
Alignment explanation
Indices: 3736220--3736267 Score: 69
Period size: 16 Copynumber: 3.1 Consensus size: 15
3736210 GATGGGAATA
3736220 ATAAAATATATAAAAT
1 ATAAAATAT-TAAAAT
3736236 ATAAAATATTAAAAT
1 ATAAAATATTAAAAT
*
3736251 ATCAAAATATTAGAAT
1 AT-AAAATATTAAAAT
3736267 A
1 A
3736268 ATAATAATTA
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
15 8 0.27
16 22 0.73
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.31
Consensus pattern (15 bp):
ATAAAATATTAAAAT
Found at i:3736250 original size:8 final size:8
Alignment explanation
Indices: 3736216--3736267 Score: 61
Period size: 8 Copynumber: 6.5 Consensus size: 8
3736206 CAATGATGGG
*
3736216 AATAATAA
1 AATATTAA
3736224 AATATATAA
1 AATAT-TAA
3736233 AATA-TAA
1 AATATTAA
3736240 AATATTAA
1 AATATTAA
*
3736248 AATATCAA
1 AATATTAA
*
3736256 AATATTAG
1 AATATTAA
3736264 AATA
1 AATA
3736268 ATAATAATTA
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
7 7 0.18
8 24 0.63
9 7 0.18
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.31
Consensus pattern (8 bp):
AATATTAA
Found at i:3736267 original size:24 final size:24
Alignment explanation
Indices: 3736215--3736271 Score: 71
Period size: 24 Copynumber: 2.4 Consensus size: 24
3736205 ACAATGATGG
*
3736215 GAATAATAAAATATATAAAATATA
1 GAATAATAAAATATACAAAATATA
* *
3736239 AAATATTAAAATAT-CAAAATATTA
1 GAATAATAAAATATACAAAATA-TA
3736263 GAATAATAA
1 GAATAATAA
3736272 TAATTAATAT
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
23 6 0.22
24 21 0.78
ACGTcount: A:0.65, C:0.02, G:0.04, T:0.30
Consensus pattern (24 bp):
GAATAATAAAATATACAAAATATA
Found at i:3736429 original size:20 final size:20
Alignment explanation
Indices: 3736379--3736433 Score: 60
Period size: 19 Copynumber: 2.9 Consensus size: 20
3736369 ATACTACATC
3736379 AATATGTACAT-ATATAAAA
1 AATATGTACATAATATAAAA
** * *
3736398 AATAAAT-GATAATATTAAA
1 AATATGTACATAATATAAAA
3736417 AATATGTACATAATATA
1 AATATGTACATAATATA
3736434 GTGTTAAAAA
Statistics
Matches: 26, Mismatches: 8, Indels: 3
0.70 0.22 0.08
Matches are distributed among these distances:
18 2 0.08
19 17 0.65
20 7 0.27
ACGTcount: A:0.58, C:0.04, G:0.05, T:0.33
Consensus pattern (20 bp):
AATATGTACATAATATAAAA
Found at i:3736440 original size:25 final size:25
Alignment explanation
Indices: 3736412--3736460 Score: 80
Period size: 25 Copynumber: 2.0 Consensus size: 25
3736402 AATGATAATA
**
3736412 TTAAAAATATGTACATAATATAGTG
1 TTAAAAATACATACATAATATAGTG
3736437 TTAAAAATACATACATAATATAGT
1 TTAAAAATACATACATAATATAGT
3736461 TAAGATATAT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.51, C:0.06, G:0.08, T:0.35
Consensus pattern (25 bp):
TTAAAAATACATACATAATATAGTG
Found at i:3736529 original size:16 final size:17
Alignment explanation
Indices: 3736493--3736533 Score: 52
Period size: 16 Copynumber: 2.6 Consensus size: 17
3736483 TGTAGAAAAA
*
3736493 ATATAT-ATATATAAAT
1 ATATATAATATATAAAG
3736509 A-ATATAATAT-TAAAG
1 ATATATAATATATAAAG
3736524 ATATATAATA
1 ATATATAATA
3736534 AAATAGTATA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
15 9 0.41
16 13 0.59
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (17 bp):
ATATATAATATATAAAG
Found at i:3736551 original size:24 final size:24
Alignment explanation
Indices: 3736497--3736631 Score: 71
Period size: 24 Copynumber: 5.5 Consensus size: 24
3736487 GAAAAAATAT
* *
3736497 ATATATATAAATAATATAATATTAA
1 ATATATAT-AATAAAATAATATAAA
* *
3736522 AGATATATAATAAAATAGTATAAA
1 ATATATATAATAAAATAATATAAA
* *
3736546 ATATATATATACGTAATATAAATTTAAA
1 ATATATATA-A--TAAAAT-AATATAAA
** * * *
3736574 ATATACCTAATATATTAA-A-AGA
1 ATATATATAATAAAATAATATAAA
* *
3736596 ATATATATAATATAATATTA-AGAA
1 ATATATATAATAAAATAATATA-AA
3736620 ATATA-ATAATAA
1 ATATATATAATAA
3736632 CAAAAAAAGA
Statistics
Matches: 83, Mismatches: 21, Indels: 14
0.70 0.18 0.12
Matches are distributed among these distances:
22 16 0.19
23 8 0.10
24 29 0.35
25 11 0.13
27 6 0.07
28 13 0.16
ACGTcount: A:0.59, C:0.02, G:0.04, T:0.36
Consensus pattern (24 bp):
ATATATATAATAAAATAATATAAA
Found at i:3736623 original size:22 final size:22
Alignment explanation
Indices: 3736559--3736630 Score: 60
Period size: 22 Copynumber: 3.2 Consensus size: 22
3736549 TATATATACG
*
3736559 TAATATAA-ATTTA-AAATATA
1 TAATATAATATTAAGAAATATA
* *
3736579 CCTAATATATTA-AAAGAATATATA
1 --TAATATAATATTAAGAA-ATATA
3736603 TAATATAATATTAAGAAATATAA
1 TAATATAATATTAAGAAATAT-A
3736626 TAATA
1 TAATA
3736631 ACAAAAAAAG
Statistics
Matches: 40, Mismatches: 5, Indels: 9
0.74 0.09 0.17
Matches are distributed among these distances:
22 21 0.52
23 14 0.35
24 5 0.12
ACGTcount: A:0.58, C:0.03, G:0.03, T:0.36
Consensus pattern (22 bp):
TAATATAATATTAAGAAATATA
Found at i:3737187 original size:30 final size:30
Alignment explanation
Indices: 3737109--3737241 Score: 162
Period size: 30 Copynumber: 4.4 Consensus size: 30
3737099 TAGGTACAAG
* *
3737109 TGGTGGTGGAGCAA-GTGTGGTTAGTGGAGT
1 TGGTGGTGGA-AAAGGTGTGGCTAGTGGAGT
* ** * *
3737139 AGGTAATGGAGCAA-GTGTGGCTAGTGGATT
1 TGGTGGTGGA-AAAGGTGTGGCTAGTGGAGT
3737169 TGGTGGTGGAAAAGGTGTGGCTAGTGGAGT
1 TGGTGGTGGAAAAGGTGTGGCTAGTGGAGT
*
3737199 TGGTGGTGGAAAAGGAGTGGCTAGTGGAGT
1 TGGTGGTGGAAAAGGTGTGGCTAGTGGAGT
3737229 TGGTGGTGGAAAA
1 TGGTGGTGGAAAA
3737242 AGCTAAGATT
Statistics
Matches: 91, Mismatches: 11, Indels: 2
0.88 0.11 0.02
Matches are distributed among these distances:
29 2 0.02
30 89 0.98
ACGTcount: A:0.23, C:0.04, G:0.47, T:0.26
Consensus pattern (30 bp):
TGGTGGTGGAAAAGGTGTGGCTAGTGGAGT
Found at i:3738150 original size:13 final size:14
Alignment explanation
Indices: 3738102--3738164 Score: 74
Period size: 14 Copynumber: 4.5 Consensus size: 14
3738092 GAGTTGATTT
* *
3738102 TTGAAAAATATAAA
1 TTGAAAAACAGAAA
3738116 TTGGAAAAACAGAAA
1 TT-GAAAAACAGAAA
*
3738131 TTGAAAAGCAGAAA
1 TTGAAAAACAGAAA
*
3738145 TT-AAAAACAGAAT
1 TTGAAAAACAGAAA
3738158 TTGAAAA
1 TTGAAAA
3738165 GACCTCAGCG
Statistics
Matches: 42, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
13 11 0.26
14 19 0.45
15 12 0.29
ACGTcount: A:0.60, C:0.05, G:0.14, T:0.21
Consensus pattern (14 bp):
TTGAAAAACAGAAA
Done.