Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D05
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: 64368997
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1610000 characters in sequence are not A, C, G, or T
File 80 of 208
Found at i:28369723 original size:132 final size:132
Alignment explanation
Indices: 28369486--28369833 Score: 457
Period size: 132 Copynumber: 2.6 Consensus size: 132
28369476 TGGAGTACAT
*
28369486 TAATTCTACTTCCCTGGACAACGGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGTAG
1 TAATTCTACTTCCCTGGACAACAGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGTAG
* * *
28369551 TAGTGGAGCAGATCGAGGATGGCAGATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCC
66 TAGTGGAGTAGATCGAAGATGGCAGATTTTACCTCACTGTGGTTACAGTGGAGTACATTGAAGCC
28369616 AA
131 AA
* *
28369618 TAATTCTACTTCCCTGGGCAACAGAGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGTAG
1 TAATTCTACTTCCCTGGACAACAGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGTAG
** * *
28369683 TAGTGGAGTAGATCGAAGATGGTGGATTTTACCTCACTGTGGTTATAGTGGAGTACATTGAAGCT
66 TAGTGGAGTAGATCGAAGATGGCAGATTTTACCTCACTGTGGTTACAGTGGAGTACATTGAAGCC
*
28369748 AG
131 AA
** * * * * * *
28369750 TAAACCTA-TCTCCCTAGTCAGCAGTGGAATAGGTTGAAGATTGTAAG-TCTTATCTCCCTGCAG
1 TAATTCTACT-TCCCTGGACAACAGTGGAATAGATTGAAGATT-TCAGATCTTATCTCCCT-AAG
* * *
28369813 TTGCAGTGGAGTGGATCGAAG
63 TAGTAGTGGAGTAGATCGAAG
28369834 CACTAGTTCC
Statistics
Matches: 190, Mismatches: 23, Indels: 5
0.87 0.11 0.02
Matches are distributed among these distances:
131 1 0.01
132 166 0.87
133 23 0.12
ACGTcount: A:0.28, C:0.18, G:0.25, T:0.30
Consensus pattern (132 bp):
TAATTCTACTTCCCTGGACAACAGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGTAG
TAGTGGAGTAGATCGAAGATGGCAGATTTTACCTCACTGTGGTTACAGTGGAGTACATTGAAGCC
AA
Found at i:28371455 original size:37 final size:38
Alignment explanation
Indices: 28371369--28371456 Score: 94
Period size: 37 Copynumber: 2.3 Consensus size: 38
28371359 TTTTTTCATA
28371369 TTTATA-TATATACATATATTTTTTTAATGTAGATATTAT
1 TTTATATTATATAC--ATATTTTTTTAATGTAGATATTAT
* * *
28371408 TTTACA-TATATACATATTTTTTTAATG-A-ATGTTCT
1 TTTATATTATATACATATTTTTTTAATGTAGATATTAT
28371443 TTTATATTTATATA
1 TTTATA-TTATATA
28371457 TATACGTATG
Statistics
Matches: 43, Mismatches: 4, Indels: 6
0.81 0.08 0.11
Matches are distributed among these distances:
35 10 0.23
36 1 0.02
37 20 0.47
39 12 0.28
ACGTcount: A:0.34, C:0.05, G:0.05, T:0.57
Consensus pattern (38 bp):
TTTATATTATATACATATTTTTTTAATGTAGATATTAT
Found at i:28374192 original size:16 final size:18
Alignment explanation
Indices: 28374153--28374186 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
28374143 TAAATTTATA
28374153 ATATTT-TATATTATGTT
1 ATATTTATATATTATGTT
*
28374170 ATTTTTATATATTATGT
1 ATATTTATATATTATGT
28374187 AATTTAAAAC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.29, C:0.00, G:0.06, T:0.65
Consensus pattern (18 bp):
ATATTTATATATTATGTT
Found at i:28374300 original size:26 final size:27
Alignment explanation
Indices: 28374271--28374330 Score: 70
Period size: 27 Copynumber: 2.2 Consensus size: 27
28374261 TAAGATGACT
*
28374271 ATATAAAAATT-TTCAATAAATAAAA-A
1 ATATAAAAATTATTAAAT-AATAAAATA
*
28374297 ATATATAAAATTATTAAATATTAAAATA
1 ATATA-AAAATTATTAAATAATAAAATA
28374325 ATATAA
1 ATATAA
28374331 TATAGATATT
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
26 5 0.17
27 13 0.45
28 11 0.38
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (27 bp):
ATATAAAAATTATTAAATAATAAAATA
Found at i:28374316 original size:28 final size:28
Alignment explanation
Indices: 28374270--28374329 Score: 70
Period size: 28 Copynumber: 2.1 Consensus size: 28
28374260 TTAAGATGAC
*
28374270 TATATAAAAATTTTCAATAAATAAAA-AA
1 TATATAAAAATTTTAAAT-AATAAAATAA
*
28374298 TATAT-AAAATTATTAAATATTAAAATAA
1 TATATAAAAATT-TTAAATAATAAAATAA
28374326 TATA
1 TATA
28374330 ATATAGATAT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
27 12 0.43
28 16 0.57
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.37
Consensus pattern (28 bp):
TATATAAAAATTTTAAATAATAAAATAA
Found at i:28377249 original size:31 final size:33
Alignment explanation
Indices: 28377191--28377251 Score: 90
Period size: 33 Copynumber: 1.9 Consensus size: 33
28377181 ATTTTTTTAA
28377191 ATTTACATATTATTATGAATTTTTAAAATTGAT
1 ATTTACATATTATTATGAATTTTTAAAATTGAT
* *
28377224 ATTTATATATTTTTA-GAA-TTTTAAAATT
1 ATTTACATATTATTATGAATTTTTAAAATT
28377252 TTATTCTTAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
31 10 0.38
32 3 0.12
33 13 0.50
ACGTcount: A:0.39, C:0.02, G:0.05, T:0.54
Consensus pattern (33 bp):
ATTTACATATTATTATGAATTTTTAAAATTGAT
Found at i:28380511 original size:33 final size:32
Alignment explanation
Indices: 28380439--28380515 Score: 82
Period size: 33 Copynumber: 2.3 Consensus size: 32
28380429 TAAATACATG
* * **
28380439 TGTAAGACCATAGTTGGGCTATGACATTCCGA
1 TGTAAGACCATAATTGGGCTATGACATACAAA
* *
28380471 TGATAAGACCATAATTGGGTTATGGCACTACAAA
1 TG-TAAGACCATAATTGGGCTATGACA-TACAAA
28380505 TGTAAGACCAT
1 TGTAAGACCAT
28380516 GGCAATGCAT
Statistics
Matches: 37, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
32 2 0.05
33 30 0.81
34 5 0.14
ACGTcount: A:0.34, C:0.17, G:0.22, T:0.27
Consensus pattern (32 bp):
TGTAAGACCATAATTGGGCTATGACATACAAA
Found at i:28387784 original size:105 final size:105
Alignment explanation
Indices: 28387589--28387785 Score: 243
Period size: 105 Copynumber: 1.9 Consensus size: 105
28387579 AATGTTTAAA
* * * * *
28387589 TGTAAGACTATAGCTGGGCTATGACATTTTAATGAAAATACTATAACTGGGTTATGACACCTTAA
1 TGTAAGACCATAGCTGGGCTATGACATTCTAATGAAAAGACCATAACTGGGTTATGACACCTCAA
** *
28387654 ACGTAAAACCATGGTTGGACGATGGCAGTATAAATACATG
66 ACGTAAAACCATGGCAGGACCATGGCAGTATAAATACATG
* * * *
28387694 TGTAAGACCATAGGTGGGCTATGACATTCTGATGATAAGACCATAACTGGGTTATGGCA-CTACA
1 TGTAAGACCATAGCTGGGCTATGACATTCTAATGAAAAGACCATAACTGGGTTATGACACCT-CA
* * *
28387758 AATGTAAGACCATGGCAGGGCCATGGCA
65 AACGTAAAACCATGGCAGGACCATGGCA
28387786 ATGCATGTGT
Statistics
Matches: 76, Mismatches: 15, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
104 2 0.03
105 74 0.97
ACGTcount: A:0.34, C:0.16, G:0.24, T:0.26
Consensus pattern (105 bp):
TGTAAGACCATAGCTGGGCTATGACATTCTAATGAAAAGACCATAACTGGGTTATGACACCTCAA
ACGTAAAACCATGGCAGGACCATGGCAGTATAAATACATG
Found at i:28394157 original size:20 final size:21
Alignment explanation
Indices: 28394124--28394162 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
28394114 ATTTTACATG
*
28394124 AAAATGATTAAAAATTTATCA
1 AAAATGATTAAAAAGTTATCA
*
28394145 AAAAT-ATTTAAAAGTTAT
1 AAAATGATTAAAAAGTTAT
28394163 AGTTATTATT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 11 0.69
21 5 0.31
ACGTcount: A:0.56, C:0.03, G:0.05, T:0.36
Consensus pattern (21 bp):
AAAATGATTAAAAAGTTATCA
Found at i:28421835 original size:50 final size:50
Alignment explanation
Indices: 28421781--28421909 Score: 179
Period size: 50 Copynumber: 2.6 Consensus size: 50
28421771 TAAAGCCTAT
*
28421781 GGGCTTAGCACTTGGTGCCTAGGTATGTTTTTAGAGGGATGTTAG-CTTAC
1 GGGCTTAGCACTTGGTGCCTAGGCATGTTTTTAGAGGGATGTTAGTC-TAC
* *
28421831 GGGCTTGGCACTTGGTGCCTAGGCGTGTTTTTAGAGGGATGTTAGTCTAC
1 GGGCTTAGCACTTGGTGCCTAGGCATGTTTTTAGAGGGATGTTAGTCTAC
* * * *
28421881 AGGCTAAGCACTTGGTGCCCAAGCATGTT
1 GGGCTTAGCACTTGGTGCCTAGGCATGTT
28421910 CTTGGTTAGA
Statistics
Matches: 69, Mismatches: 9, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
50 68 0.99
51 1 0.01
ACGTcount: A:0.18, C:0.17, G:0.33, T:0.33
Consensus pattern (50 bp):
GGGCTTAGCACTTGGTGCCTAGGCATGTTTTTAGAGGGATGTTAGTCTAC
Found at i:28427003 original size:89 final size:88
Alignment explanation
Indices: 28426910--28427079 Score: 227
Period size: 89 Copynumber: 1.9 Consensus size: 88
28426900 AAAACTGTCT
* *
28426910 TTTTTTTTTTCACTCAATTGAATACTTGAA-TTTTCAAAATACATACAAAAAG-TCCTTAGACTT
1 TTTTTTTTTTCACTCAATTGAATACTTGAACTTTT-AAAATACATA-AAAAAGATCCTCA-AATT
28426973 CTTAAAAAAAACAATTAAGTTACTGC
63 CTTAAAAAAAACAATTAAGTTACTGC
* * * * *
28426999 TTTTTTTTTTCATTCAATTGGATACTTGAACTTTTAAAATGCATAAAATAGATCCTCAAATTTTT
1 TTTTTTTTTTCACTCAATTGAATACTTGAACTTTTAAAATACATAAAAAAGATCCTCAAATTCTT
*
28427064 CAAAAAAACAATTAAG
66 AAAAAAAACAATTAAG
28427080 CCCCCGCTAT
Statistics
Matches: 71, Mismatches: 8, Indels: 5
0.85 0.10 0.06
Matches are distributed among these distances:
88 25 0.35
89 42 0.59
90 4 0.06
ACGTcount: A:0.39, C:0.14, G:0.07, T:0.39
Consensus pattern (88 bp):
TTTTTTTTTTCACTCAATTGAATACTTGAACTTTTAAAATACATAAAAAAGATCCTCAAATTCTT
AAAAAAAACAATTAAGTTACTGC
Found at i:28427475 original size:23 final size:22
Alignment explanation
Indices: 28427438--28427492 Score: 58
Period size: 22 Copynumber: 2.4 Consensus size: 22
28427428 GCTTTATAAA
28427438 ATTTTTATATTTCTATGTATTTT-AT
1 ATTTTT-T-TTTCTA-GT-TTTTAAT
28427463 ATTTTTTTTTCTAGTTTTTAAT
1 ATTTTTTTTTCTAGTTTTTAAT
*
28427485 AATTTTTT
1 ATTTTTTT
28427493 AATATTTAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
21 4 0.14
22 11 0.39
23 6 0.21
24 1 0.04
25 6 0.21
ACGTcount: A:0.22, C:0.04, G:0.04, T:0.71
Consensus pattern (22 bp):
ATTTTTTTTTCTAGTTTTTAAT
Found at i:28427946 original size:11 final size:11
Alignment explanation
Indices: 28427930--28427959 Score: 51
Period size: 11 Copynumber: 2.6 Consensus size: 11
28427920 TTTGTTTTTT
28427930 TATTTTTAAAA
1 TATTTTTAAAA
28427941 TATTTTTAAAA
1 TATTTTTAAAA
28427952 TACTTTTT
1 TA-TTTTT
28427960 TATATTTTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 13 0.72
12 5 0.28
ACGTcount: A:0.37, C:0.03, G:0.00, T:0.60
Consensus pattern (11 bp):
TATTTTTAAAA
Found at i:28427995 original size:26 final size:27
Alignment explanation
Indices: 28427941--28427997 Score: 71
Period size: 27 Copynumber: 2.1 Consensus size: 27
28427931 ATTTTTAAAA
** *
28427941 TATTTTTAAAATACTTTTTTATATTTT
1 TATTTTTAAAATAAATTTTTATATGTT
*
28427968 TATTTTTAAAATAAATTTTTA-GTGTT
1 TATTTTTAAAATAAATTTTTATATGTT
28427994 TATT
1 TATT
28427998 AAAAAAATAG
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
26 7 0.27
27 19 0.73
ACGTcount: A:0.32, C:0.02, G:0.04, T:0.63
Consensus pattern (27 bp):
TATTTTTAAAATAAATTTTTATATGTT
Found at i:28438625 original size:320 final size:320
Alignment explanation
Indices: 28438043--28438674 Score: 1255
Period size: 320 Copynumber: 2.0 Consensus size: 320
28438033 CTGCAGTATG
28438043 ATATTGTTGTTGTAAGGTTATATTGTTGCTCTGGCTCATTATATTATCACCTTTATAAAACTAGA
1 ATATTGTTGTTGTAAGGTTATATTGTTGCTCTGGCTCATTATATTATCACCTTTATAAAACTAGA
28438108 GCATTTGTTTTTCGCAATAAATTAACTAATTTTGCTTCTCATGTTCCCAGTGGCTAATATTCTCT
66 GCATTTGTTTTTCGCAATAAATTAACTAATTTTGCTTCTCATGTTCCCAGTGGCTAATATTCTCT
28438173 TGTGGAAGCAGTGAAGTGTTTCTTTTGGCATTATCATCATTGCTACTATTGATTGGCTCATATTT
131 TGTGGAAGCAGTGAAGTGTTTCTTTTGGCATTATCATCATTGCTACTATTGATTGGCTCATATTT
28438238 GAGAAATCTGGATTACTATTGTTACCTATTTGTTCAGATGTTTTGCTGGTATTAATTGTGCTATT
196 GAGAAATCTGGATTACTATTGTTACCTATTTGTTCAGATGTTTTGCTGGTATTAATTGTGCTATT
28438303 GTTCATTTATGCCAACCATGCTGCTTATGGAAATAGGTATGACTAATATTGCTTCTCATT
261 GTTCATTTATGCCAACCATGCTGCTTATGGAAATAGGTATGACTAATATTGCTTCTCATT
28438363 ATATTGTTGTTGTAAGGTTATATTGTTGCTCTGGCTCATTATATTATCACCTTTATAAAACTAGA
1 ATATTGTTGTTGTAAGGTTATATTGTTGCTCTGGCTCATTATATTATCACCTTTATAAAACTAGA
28438428 GCATTTGTTTTTCGCAATAAATTAACTAATTTTGCTTCTCATGTTCCCAGTGGCTAATATTCTCT
66 GCATTTGTTTTTCGCAATAAATTAACTAATTTTGCTTCTCATGTTCCCAGTGGCTAATATTCTCT
28438493 TGTGGAAGCAGTGAAGTGTTTCTTTTGGCATTATCATCATTGCTACTATTGATTGGCTCATATTT
131 TGTGGAAGCAGTGAAGTGTTTCTTTTGGCATTATCATCATTGCTACTATTGATTGGCTCATATTT
28438558 GAGAAATCTGGATTACTATTGTTACCTATTTGTTCAGATGTTTTGCTGGTATTAATTGTGCTATT
196 GAGAAATCTGGATTACTATTGTTACCTATTTGTTCAGATGTTTTGCTGGTATTAATTGTGCTATT
*
28438623 GTTCATTTATGCCAACTATGCTGCTTATGGAAATAGGTATGACTAATATTGC
261 GTTCATTTATGCCAACCATGCTGCTTATGGAAATAGGTATGACTAATATTGC
28438675 CTCTTTATGT
Statistics
Matches: 311, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
320 311 1.00
ACGTcount: A:0.25, C:0.15, G:0.17, T:0.43
Consensus pattern (320 bp):
ATATTGTTGTTGTAAGGTTATATTGTTGCTCTGGCTCATTATATTATCACCTTTATAAAACTAGA
GCATTTGTTTTTCGCAATAAATTAACTAATTTTGCTTCTCATGTTCCCAGTGGCTAATATTCTCT
TGTGGAAGCAGTGAAGTGTTTCTTTTGGCATTATCATCATTGCTACTATTGATTGGCTCATATTT
GAGAAATCTGGATTACTATTGTTACCTATTTGTTCAGATGTTTTGCTGGTATTAATTGTGCTATT
GTTCATTTATGCCAACCATGCTGCTTATGGAAATAGGTATGACTAATATTGCTTCTCATT
Found at i:28439364 original size:8 final size:9
Alignment explanation
Indices: 28439345--28439388 Score: 51
Period size: 8 Copynumber: 5.3 Consensus size: 9
28439335 CGTACAAATT
28439345 AGAAAGAA-
1 AGAAAGAAG
28439353 AGAAA-AAG
1 AGAAAGAAG
28439361 AGAAAGAA-
1 AGAAAGAAG
*
28439369 AGAAAG-GG
1 AGAAAGAAG
28439377 AGAAAGAAG
1 AGAAAGAAG
28439386 AGA
1 AGA
28439389 CGCACGACCA
Statistics
Matches: 30, Mismatches: 2, Indels: 7
0.77 0.05 0.18
Matches are distributed among these distances:
7 2 0.07
8 22 0.73
9 6 0.20
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (9 bp):
AGAAAGAAG
Found at i:28439366 original size:16 final size:16
Alignment explanation
Indices: 28439345--28439384 Score: 62
Period size: 16 Copynumber: 2.5 Consensus size: 16
28439335 CGTACAAATT
28439345 AGAAAGAAAGAAAAAG
1 AGAAAGAAAGAAAAAG
**
28439361 AGAAAGAAAGAAAGGG
1 AGAAAGAAAGAAAAAG
28439377 AGAAAGAA
1 AGAAAGAA
28439385 GAGACGCACG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (16 bp):
AGAAAGAAAGAAAAAG
Found at i:28449557 original size:27 final size:24
Alignment explanation
Indices: 28449519--28449651 Score: 96
Period size: 27 Copynumber: 5.4 Consensus size: 24
28449509 GAGATGAAGG
28449519 CTTGATTGAAAACTTAATGATTAAAAA
1 CTTGA-TGAAAACTTAATGA--AAAAA
* *
28449546 CTTGATGGAAAACTTTATGAAAAGA
1 CTTGAT-GAAAACTTAATGAAAAAA
*
28449571 CTTGATGAAAAGCTTAA--AAAGAA
1 CTTGATGAAAA-CTTAATGAAAAAA
*
28449594 CTTGATGCAAACTT-A--AAAAAA
1 CTTGATGAAAACTTAATGAAAAAA
* *
28449615 CTTGATAAAAGAACTTGATGAAAAACA
1 CTTGAT-GAA-AACTTAATGAAAAA-A
*
28449642 CTTGAAGAAA
1 CTTGATGAAA
28449652 GAAAACACTT
Statistics
Matches: 87, Mismatches: 11, Indels: 18
0.75 0.09 0.16
Matches are distributed among these distances:
21 12 0.14
22 4 0.05
23 19 0.22
24 6 0.07
25 15 0.17
26 8 0.09
27 23 0.26
ACGTcount: A:0.50, C:0.10, G:0.15, T:0.26
Consensus pattern (24 bp):
CTTGATGAAAACTTAATGAAAAAA
Found at i:28449608 original size:22 final size:23
Alignment explanation
Indices: 28449565--28449625 Score: 85
Period size: 22 Copynumber: 2.8 Consensus size: 23
28449555 AAACTTTATG
28449565 AAAAG-ACTTGATGAAAAGCTTA
1 AAAAGAACTTGATGAAAAGCTTA
*
28449587 AAAAGAACTTGATGCAAA-CTTA
1 AAAAGAACTTGATGAAAAGCTTA
28449609 AAAA-AACTTGAT-AAAAG
1 AAAAGAACTTGATGAAAAG
28449626 AACTTGATGA
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
20 3 0.09
21 8 0.23
22 13 0.37
23 11 0.31
ACGTcount: A:0.54, C:0.10, G:0.15, T:0.21
Consensus pattern (23 bp):
AAAAGAACTTGATGAAAAGCTTA
Found at i:28449644 original size:14 final size:13
Alignment explanation
Indices: 28449527--28449651 Score: 65
Period size: 12 Copynumber: 10.1 Consensus size: 13
28449517 GGCTTGATTG
*
28449527 AAAACTTAATGATTA
1 AAAACTTGATGA--A
*
28449542 AAAACTTGATG-G
1 AAAACTTGATGAA
*
28449554 AAAACTTTATGAA
1 AAAACTTGATGAA
*
28449567 AAGACTTGATG-A
1 AAAACTTGATGAA
*
28449579 AAAGCTT-A--AA
1 AAAACTTGATGAA
28449589 AAGAACTTGATG--
1 AA-AACTTGATGAA
*
28449601 CAAACTT-A--AA
1 AAAACTTGATGAA
28449611 AAAACTTGAT-AA
1 AAAACTTGATGAA
28449623 AAGAACTTGATGAA
1 AA-AACTTGATGAA
*
28449637 AAACACTTGAAGAA
1 AAA-ACTTGATGAA
28449651 A
1 A
28449652 GAAAACACTT
Statistics
Matches: 85, Mismatches: 12, Indels: 27
0.69 0.10 0.22
Matches are distributed among these distances:
10 10 0.12
11 11 0.13
12 22 0.26
13 18 0.21
14 14 0.16
15 10 0.12
ACGTcount: A:0.52, C:0.10, G:0.14, T:0.24
Consensus pattern (13 bp):
AAAACTTGATGAA
Found at i:28452740 original size:21 final size:23
Alignment explanation
Indices: 28452716--28452767 Score: 65
Period size: 22 Copynumber: 2.4 Consensus size: 23
28452706 TGTAGTTTTC
28452716 TAGGTGAAAAG-CT-GGATGTGA
1 TAGGTGAAAAGACTAGGATGTGA
* *
28452737 TAGGTG-AAAGATTAGGATTTGA
1 TAGGTGAAAAGACTAGGATGTGA
28452759 TAGGTGAAA
1 TAGGTGAAA
28452768 GGTTGATGGG
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
20 4 0.15
21 7 0.27
22 13 0.50
23 2 0.08
ACGTcount: A:0.37, C:0.02, G:0.35, T:0.27
Consensus pattern (23 bp):
TAGGTGAAAAGACTAGGATGTGA
Found at i:28458885 original size:29 final size:29
Alignment explanation
Indices: 28458843--28458902 Score: 120
Period size: 29 Copynumber: 2.1 Consensus size: 29
28458833 CTGGTCATGA
28458843 AGATGATTTAGACAATTATAAGTGTTGCC
1 AGATGATTTAGACAATTATAAGTGTTGCC
28458872 AGATGATTTAGACAATTATAAGTGTTGCC
1 AGATGATTTAGACAATTATAAGTGTTGCC
28458901 AG
1 AG
28458903 TCCCCGGCAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.35, C:0.10, G:0.22, T:0.33
Consensus pattern (29 bp):
AGATGATTTAGACAATTATAAGTGTTGCC
Found at i:28460017 original size:27 final size:24
Alignment explanation
Indices: 28459979--28460111 Score: 96
Period size: 27 Copynumber: 5.4 Consensus size: 24
28459969 GAGATGAAAG
28459979 CTTGATTGAAAACTTAATGATTAAAAA
1 CTTGA-TGAAAACTTAATGA--AAAAA
* *
28460006 CTTGATGGAAAACTTTATGAAAAGA
1 CTTGAT-GAAAACTTAATGAAAAAA
*
28460031 CTTGATGAAAAGCTTAA--AAAGAA
1 CTTGATGAAAA-CTTAATGAAAAAA
*
28460054 CTTGATGCAAACTT-A--AAAAAA
1 CTTGATGAAAACTTAATGAAAAAA
* *
28460075 CTTGATAAAAGAACTTGATGAAAAACA
1 CTTGAT-GAA-AACTTAATGAAAAA-A
*
28460102 CTTGAAGAAA
1 CTTGATGAAA
28460112 GAAAACACTT
Statistics
Matches: 87, Mismatches: 11, Indels: 18
0.75 0.09 0.16
Matches are distributed among these distances:
21 12 0.14
22 4 0.05
23 19 0.22
24 6 0.07
25 15 0.17
26 8 0.09
27 23 0.26
ACGTcount: A:0.50, C:0.10, G:0.15, T:0.26
Consensus pattern (24 bp):
CTTGATGAAAACTTAATGAAAAAA
Found at i:28460068 original size:22 final size:23
Alignment explanation
Indices: 28460025--28460085 Score: 85
Period size: 22 Copynumber: 2.8 Consensus size: 23
28460015 AAACTTTATG
28460025 AAAAG-ACTTGATGAAAAGCTTA
1 AAAAGAACTTGATGAAAAGCTTA
*
28460047 AAAAGAACTTGATGCAAA-CTTA
1 AAAAGAACTTGATGAAAAGCTTA
28460069 AAAA-AACTTGAT-AAAAG
1 AAAAGAACTTGATGAAAAG
28460086 AACTTGATGA
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
20 3 0.09
21 8 0.23
22 13 0.37
23 11 0.31
ACGTcount: A:0.54, C:0.10, G:0.15, T:0.21
Consensus pattern (23 bp):
AAAAGAACTTGATGAAAAGCTTA
Found at i:28460104 original size:14 final size:13
Alignment explanation
Indices: 28459987--28460111 Score: 65
Period size: 12 Copynumber: 10.1 Consensus size: 13
28459977 AGCTTGATTG
*
28459987 AAAACTTAATGATTA
1 AAAACTTGATGA--A
*
28460002 AAAACTTGATG-G
1 AAAACTTGATGAA
*
28460014 AAAACTTTATGAA
1 AAAACTTGATGAA
*
28460027 AAGACTTGATG-A
1 AAAACTTGATGAA
*
28460039 AAAGCTT-A--AA
1 AAAACTTGATGAA
28460049 AAGAACTTGATG--
1 AA-AACTTGATGAA
*
28460061 CAAACTT-A--AA
1 AAAACTTGATGAA
28460071 AAAACTTGAT-AA
1 AAAACTTGATGAA
28460083 AAGAACTTGATGAA
1 AA-AACTTGATGAA
*
28460097 AAACACTTGAAGAA
1 AAA-ACTTGATGAA
28460111 A
1 A
28460112 GAAAACACTT
Statistics
Matches: 85, Mismatches: 12, Indels: 27
0.69 0.10 0.22
Matches are distributed among these distances:
10 10 0.12
11 11 0.13
12 22 0.26
13 18 0.21
14 14 0.16
15 10 0.12
ACGTcount: A:0.52, C:0.10, G:0.14, T:0.24
Consensus pattern (13 bp):
AAAACTTGATGAA
Found at i:28460564 original size:21 final size:20
Alignment explanation
Indices: 28460509--28460564 Score: 53
Period size: 21 Copynumber: 2.8 Consensus size: 20
28460499 AAGAATTCAC
*
28460509 ATCAATCTTTAATTAGTTTA
1 ATCAATCATTAATTAGTTTA
*
28460529 ATCAAGTTATT-ATTA-TACTTA
1 ATCAA-TCATTAATTAGT--TTA
28460550 ATCAATCATTAATTA
1 ATCAATCATTAATTA
28460565 AACAAAAGTG
Statistics
Matches: 29, Mismatches: 3, Indels: 7
0.74 0.08 0.18
Matches are distributed among these distances:
19 1 0.03
20 13 0.45
21 15 0.52
ACGTcount: A:0.39, C:0.11, G:0.04, T:0.46
Consensus pattern (20 bp):
ATCAATCATTAATTAGTTTA
Found at i:28467723 original size:305 final size:305
Alignment explanation
Indices: 28467130--28467735 Score: 1128
Period size: 304 Copynumber: 2.0 Consensus size: 305
28467120 ATATTAAAAA
28467130 AAAAATTGGAGGGGAGAGGATTTGGGATAGATGGGAGGTGAGATTGGAAGGGAATAAAAGTTTTA
1 AAAAATTGGAGGGGAGAGGATTTGGGATAGATGGGAGGTGAGATTGGAAGGGAATAAAAGTTTTA
*
28467195 GGGGAAAAGTGGGATGGAGTAAAAATTTTGGGGGAAAATAAAAGGTTTTGAGGGTTTTTGGGAGT
66 GGGGAAAAGTGGGATGGAGTAAAAATTTTGGGGGAAAATAAAAGGTTTTGAGGGTTTTTAGGAGT
*
28467260 AAAATTTTGAGAAAAAATAAATGGGAGAGTAAAATTTTGGTGGGAAATGGATTTTGGGTAGGTTG
131 AAAATTTTGAGAAAAAATAAATGGGAGAGTAAAATTTTGGTGGGAAATGGATTTTGGGTAGATTG
*
28467325 GGGGGGTTGGGGGAGGGGAGTAAAAGTTTTGGGGGGAAAGTGGGAAGGAGTAAAAGTTTTAAGGG
196 GGGGGATTGGGGGAGGGGAGTAAAAGTTTTGGGGGGAAAGTGGGAAGGAGTAAAAGTTTTAAGGG
28467390 AAAAGTAAAAAGGTTTGGGAGTTTGGGGTAAAAATGTAAAAATGT
261 AAAAGTAAAAAGGTTTGGGAGTTTGGGGTAAAAATGTAAAAATGT
28467435 AAAAATTGGAGGGG-GAGGATTTGGGATAGATGGGAGGTGAGATTGGAAGGGAATAAAAGTTTTA
1 AAAAATTGGAGGGGAGAGGATTTGGGATAGATGGGAGGTGAGATTGGAAGGGAATAAAAGTTTTA
28467499 GGGGAAAAGTGGGATGGAGTAAAAATTTTGGGGGAAAATAAAAGGTTTTGAGGGTTTTTAGGAGT
66 GGGGAAAAGTGGGATGGAGTAAAAATTTTGGGGGAAAATAAAAGGTTTTGAGGGTTTTTAGGAGT
28467564 AAAA-TTTGAG-AAAAATAAATGGGAGAGTAAAATTTTGGTGGGAAATGGATTTTGGGTAGATTG
131 AAAATTTTGAGAAAAAATAAATGGGAGAGTAAAATTTTGGTGGGAAATGGATTTTGGGTAGATTG
*
28467627 GGGGGATTGGGAGGGGAGGGGAGTAAAAGTTTTGGGGGGAAAGTGGGAAGGAGTAAAAGTTTTGA
196 GGGGGATT--G-GGGGAGGGGAGTAAAAGTTTTGGGGGGAAAGTGGGAAGGAGTAAAAGTTTTAA
28467692 GGGAAAAGTAAAAAGGTTTGGGAGTTTGGGGTAAAAATGTAAAA
258 GGGAAAAGTAAAAAGGTTTGGGAGTTTGGGGTAAAAATGTAAAA
28467736 TATTATAGTT
Statistics
Matches: 294, Mismatches: 4, Indels: 6
0.97 0.01 0.02
Matches are distributed among these distances:
302 59 0.20
303 6 0.02
304 119 0.40
305 110 0.37
ACGTcount: A:0.36, C:0.00, G:0.39, T:0.25
Consensus pattern (305 bp):
AAAAATTGGAGGGGAGAGGATTTGGGATAGATGGGAGGTGAGATTGGAAGGGAATAAAAGTTTTA
GGGGAAAAGTGGGATGGAGTAAAAATTTTGGGGGAAAATAAAAGGTTTTGAGGGTTTTTAGGAGT
AAAATTTTGAGAAAAAATAAATGGGAGAGTAAAATTTTGGTGGGAAATGGATTTTGGGTAGATTG
GGGGGATTGGGGGAGGGGAGTAAAAGTTTTGGGGGGAAAGTGGGAAGGAGTAAAAGTTTTAAGGG
AAAAGTAAAAAGGTTTGGGAGTTTGGGGTAAAAATGTAAAAATGT
Found at i:28467763 original size:9 final size:9
Alignment explanation
Indices: 28467749--28467785 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
28467739 TATAGTTTGA
28467749 TATTCGAAT
1 TATTCGAAT
28467758 TATTCGAAT
1 TATTCGAAT
*
28467767 TATTCGAGT
1 TATTCGAAT
28467776 TATTCGAAT
1 TATTCGAAT
28467785 T
1 T
28467786 CGAAAACTCA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.30, C:0.11, G:0.14, T:0.46
Consensus pattern (9 bp):
TATTCGAAT
Found at i:28472170 original size:26 final size:23
Alignment explanation
Indices: 28472121--28472170 Score: 55
Period size: 23 Copynumber: 2.0 Consensus size: 23
28472111 CTCCAAAAAA
* *
28472121 AAAAAAAGAATCTGAATTCCATG
1 AAAAAAAGAATCTGAAATCAATG
28472144 AAAAAAAGAATCTAGAACATCTAATG
1 AAAAAAAGAATCT-GAA-ATC-AATG
28472170 A
1 A
28472171 CCTAGCAAAG
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
23 13 0.59
24 3 0.14
25 2 0.09
26 4 0.18
ACGTcount: A:0.56, C:0.12, G:0.12, T:0.20
Consensus pattern (23 bp):
AAAAAAAGAATCTGAAATCAATG
Found at i:28484671 original size:4 final size:4
Alignment explanation
Indices: 28484662--28484814 Score: 79
Period size: 4 Copynumber: 38.0 Consensus size: 4
28484652 GAAGGAGAGG
* * * *
28484662 GAAA GAAA GAAA GAAA GAAA GAAA GAAA GAAA GGAAG GAAG GAAG GAAG
1 GAAA GAAA GAAA GAAA GAAA GAAA GAAA GAAA -GAAA GAAA GAAA GAAA
* * * * *
28484711 GAGAG GAGAG GAAA GAAGA AAAA GAAG GAAA GAAAA GGAAA G-GA GAAGA
1 GA-AA GA-AA GAAA GAA-A GAAA GAAA GAAA G-AAA -GAAA GAAA GAA-A
28484760 GAAA -AAA -AAA GAAA G-AA G-AA GAAGA GGAAA G-AA GAAA GAAA -AAA
1 GAAA GAAA GAAA GAAA GAAA GAAA GAA-A -GAAA GAAA GAAA GAAA GAAA
*
28484804 -AAG GAAA GAAA
1 GAAA GAAA GAAA
28484815 AGGAAAGGAG
Statistics
Matches: 126, Mismatches: 10, Indels: 26
0.78 0.06 0.16
Matches are distributed among these distances:
3 22 0.17
4 73 0.58
5 27 0.21
6 4 0.03
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (4 bp):
GAAA
Found at i:28484725 original size:39 final size:37
Alignment explanation
Indices: 28484682--28484843 Score: 121
Period size: 37 Copynumber: 4.5 Consensus size: 37
28484672 AAGAAAGAAA
* * *
28484682 GAAAGAA-AGAAAGGAAGGAAGGAAGGAAGGAGAGGAGAG
1 GAAAGAAGA-AAAAGAAGGAAAGAA--AAGGAAAGGAGAG
28484721 GAAAGAAGAAAAAGAAGGAAAGAAAAGGAAAGGAGA-
1 GAAAGAAGAAAAAGAAGGAAAGAAAAGGAAAGGAGAG
* *
28484757 -AGAGAA-AAAAA-AA-GAAAGAAGAA-GAAGAGGA-AA
1 GAAAGAAGAAAAAGAAGGAAAGAA-AAGGAA-AGGAGAG
*
28484790 G-AAGAAAGAAAAAAAAGGAAAGAAAAGGAAAGGAGAAG
1 GAAAG-AAGAAAAAGAAGGAAAGAAAAGGAAAGGAG-AG
28484828 AGAAA-AA-AAAAAGAAG
1 -GAAAGAAGAAAAAGAAG
28484844 AGGGAAGGAA
Statistics
Matches: 102, Mismatches: 7, Indels: 30
0.73 0.05 0.22
Matches are distributed among these distances:
32 11 0.11
33 10 0.10
34 7 0.07
35 10 0.10
36 8 0.08
37 29 0.28
38 3 0.03
39 21 0.21
40 3 0.03
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (37 bp):
GAAAGAAGAAAAAGAAGGAAAGAAAAGGAAAGGAGAG
Found at i:28484741 original size:10 final size:10
Alignment explanation
Indices: 28484722--28484834 Score: 53
Period size: 10 Copynumber: 11.3 Consensus size: 10
28484712 AGAGGAGAGG
28484722 AAAGAA-GAA
1 AAAGAAGGAA
28484731 AAAGAAGGAA
1 AAAGAAGGAA
28484741 AGAA-AAGGAA
1 A-AAGAAGGAA
*
28484751 AGGAGAAGAGAA
1 A-AAGAAG-GAA
28484763 AAA-AA--AA
1 AAAGAAGGAA
28484770 GAAAGAA-GAA
1 -AAAGAAGGAA
*
28484780 GAAG-AGGAA
1 AAAGAAGGAA
*
28484789 AGAAGAAAGAA
1 A-AAGAAGGAA
*
28484800 AAAAAAGGAA
1 AAAGAAGGAA
28484810 AGAA-AAGGAA
1 A-AAGAAGGAA
*
28484820 AGGAGAAGAGAA
1 A-AAGAAG-GAA
28484832 AAA
1 AAA
28484835 AAAAAGAAGA
Statistics
Matches: 82, Mismatches: 9, Indels: 24
0.71 0.08 0.21
Matches are distributed among these distances:
7 2 0.02
8 4 0.05
9 14 0.17
10 37 0.45
11 17 0.21
12 8 0.10
ACGTcount: A:0.71, C:0.00, G:0.29, T:0.00
Consensus pattern (10 bp):
AAAGAAGGAA
Found at i:28484749 original size:27 final size:26
Alignment explanation
Indices: 28484661--28484826 Score: 97
Period size: 24 Copynumber: 6.8 Consensus size: 26
28484651 AGAAGGAGAG
*
28484661 GGAAAG-AAA-GAAAGAAAGAAAGAAA
1 GGAAAGAAAAGGAAAG-AAGAAAAAAA
* * **
28484686 -GAAAG-AAAGGAAGGAAGGAAGGAA
1 GGAAAGAAAAGGAAAGAAGAAAAAAA
* * *
28484710 GGAGAGGAGAGGAAAGAAGAAAAAGAA
1 GGAAAGAAAAGGAAAGAAGAAAAA-AA
* * *
28484737 GGAAAGAAAAGGAAAGGAGAAGAGAA
1 GGAAAGAAAAGGAAAGAAGAAAAAAA
* *
28484763 --AAA-AAAA-GAAAGAAGAAGAAGA
1 GGAAAGAAAAGGAAAGAAGAAAAAAA
28484785 GGAAAG--AA-GAAAG-A-AAAAAAA
1 GGAAAGAAAAGGAAAGAAGAAAAAAA
*
28484806 GGAAAGAAAAGGAAAGGAGAA
1 GGAAAGAAAAGGAAAGAAGAA
28484827 GAGAAAAAAA
Statistics
Matches: 109, Mismatches: 20, Indels: 23
0.72 0.13 0.15
Matches are distributed among these distances:
21 11 0.10
22 13 0.12
23 13 0.12
24 27 0.25
25 9 0.08
26 16 0.15
27 20 0.18
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (26 bp):
GGAAAGAAAAGGAAAGAAGAAAAAAA
Found at i:28484765 original size:32 final size:33
Alignment explanation
Indices: 28484714--28484837 Score: 148
Period size: 32 Copynumber: 3.7 Consensus size: 33
28484704 AAGGAAGGAG
* *
28484714 AGGAGAGGA-AAGAAGAAAAAGAAGGAAAGAAA
1 AGGAAAGGAGAAGAAGAAAAAAAAGGAAAGAAA
*
28484746 AGGAAAGGAGAAG-AGAAAAAAAAAGAAAGAAGA
1 AGGAAAGGAGAAGAAGAAAAAAAAGGAAAGAA-A
28484779 A-GAAGAGGAAAGAAGAAAGAAAAAAAAGGAAAGAAA
1 AGGAA-AGG--AGAAG-AAGAAAAAAAAGGAAAGAAA
28484815 AGGAAAGGAGAAG-AGAAAAAAAA
1 AGGAAAGGAGAAGAAGAAAAAAAA
28484838 AAGAAGAGGG
Statistics
Matches: 80, Mismatches: 4, Indels: 16
0.80 0.04 0.16
Matches are distributed among these distances:
32 37 0.46
33 8 0.10
34 5 0.06
35 5 0.06
36 5 0.06
37 20 0.25
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (33 bp):
AGGAAAGGAGAAGAAGAAAAAAAAGGAAAGAAA
Found at i:28484857 original size:69 final size:71
Alignment explanation
Indices: 28484707--28484878 Score: 219
Period size: 69 Copynumber: 2.5 Consensus size: 71
28484697 AGGAAGGAAG
* * * *
28484707 GAAGGAGAGG-AGAGGAAAGAAGAAAAAGAAGGAAAGAAAAGGAAAGGAGAAGAGAAAAAAAAAG
1 GAAGAAGAGGAAGAGAAAAAAAGAAAAAAAAGGAAAGAAAAGGAAAGGAGAAGAGAAAAAAAAAG
28484771 AAAGAA
66 AAAGAA
*
28484777 GAAGAAGAGGAA-AG-AAGAAAGAAAAAAAAGGAAAGAAAAGGAAAGGAGAAGAGAAAAAAAAA-
1 GAAGAAGAGGAAGAGAAAAAAAGAAAAAAAAGGAAAGAAAAGGAAAGGAGAAGAGAAAAAAAAAG
*
28484839 AGAAGAGG
66 A-AAGA-A
* *
28484847 GAAGGA-AGGAAGGGAAAAAAAGAAAAAAAAGG
1 GAAGAAGAGGAAGAGAAAAAAAGAAAAAAAAGG
28484879 TAATTTTTAT
Statistics
Matches: 89, Mismatches: 8, Indels: 9
0.84 0.08 0.08
Matches are distributed among these distances:
68 1 0.01
69 54 0.61
70 17 0.19
71 17 0.19
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (71 bp):
GAAGAAGAGGAAGAGAAAAAAAGAAAAAAAAGGAAAGAAAAGGAAAGGAGAAGAGAAAAAAAAAG
AAAGAA
Found at i:28484864 original size:31 final size:31
Alignment explanation
Indices: 28484778--28484871 Score: 86
Period size: 31 Copynumber: 3.1 Consensus size: 31
28484768 AAGAAAGAAG
* ** *
28484778 AAGAAGA-GGAAAGAAGAAAGAAAAAAAAGGA
1 AAGAAGAGGGAAGGAAG-AAGGGAAAAAAAGA
* * *
28484809 AAGAAAAGGAAAGG-AGAAGAGAAAAAAA-A
1 AAGAAGAGGGAAGGAAGAAGGGAAAAAAAGA
28484838 AAGAAGAGGGAAGGAAGGAAGGGAAAAAAAGA
1 AAGAAGAGGGAAGGAA-GAAGGGAAAAAAAGA
28484870 AA
1 AA
28484872 AAAAAGGTAA
Statistics
Matches: 51, Mismatches: 8, Indels: 7
0.77 0.12 0.11
Matches are distributed among these distances:
29 13 0.25
30 11 0.22
31 20 0.39
32 7 0.14
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (31 bp):
AAGAAGAGGGAAGGAAGAAGGGAAAAAAAGA
Found at i:28488480 original size:9 final size:9
Alignment explanation
Indices: 28488466--28488505 Score: 71
Period size: 9 Copynumber: 4.4 Consensus size: 9
28488456 GTTAAACGAA
28488466 TCGAGTTAT
1 TCGAGTTAT
*
28488475 TCGAGTTAA
1 TCGAGTTAT
28488484 TCGAGTTAT
1 TCGAGTTAT
28488493 TCGAGTTAT
1 TCGAGTTAT
28488502 TCGA
1 TCGA
28488506 ATCAACTCGA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
9 29 1.00
ACGTcount: A:0.25, C:0.12, G:0.23, T:0.40
Consensus pattern (9 bp):
TCGAGTTAT
Found at i:28495854 original size:27 final size:27
Alignment explanation
Indices: 28495770--28495845 Score: 143
Period size: 27 Copynumber: 2.8 Consensus size: 27
28495760 CCAATCAGTA
*
28495770 TGGCACCATTGGTGCCACCAATGGCTT
1 TGGCACCATTGGTGCCGCCAATGGCTT
28495797 TGGCACCATTGGTGCCGCCAATGGCTT
1 TGGCACCATTGGTGCCGCCAATGGCTT
28495824 TGGCACCATTGGTGCCGCCAAT
1 TGGCACCATTGGTGCCGCCAAT
28495846 CACCTTGGCT
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
27 48 1.00
ACGTcount: A:0.17, C:0.30, G:0.28, T:0.25
Consensus pattern (27 bp):
TGGCACCATTGGTGCCGCCAATGGCTT
Found at i:28495946 original size:26 final size:27
Alignment explanation
Indices: 28495914--28495969 Score: 96
Period size: 27 Copynumber: 2.1 Consensus size: 27
28495904 TTTTTTTTGT
28495914 ATATTTTGGTAAAT-AAAAAAATTATA
1 ATATTTTGGTAAATAAAAAAAATTATA
*
28495940 ATATTTTGTTAAATAAAAAAAATTATA
1 ATATTTTGGTAAATAAAAAAAATTATA
28495967 ATA
1 ATA
28495970 ATTTAGTTAT
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
26 13 0.46
27 15 0.54
ACGTcount: A:0.55, C:0.00, G:0.05, T:0.39
Consensus pattern (27 bp):
ATATTTTGGTAAATAAAAAAAATTATA
Found at i:28495966 original size:27 final size:26
Alignment explanation
Indices: 28495914--28495978 Score: 94
Period size: 27 Copynumber: 2.4 Consensus size: 26
28495904 TTTTTTTTGT
*
28495914 ATATTTTGGTAAATAAAAAAATTATA
1 ATATTTTGTTAAATAAAAAAATTATA
28495940 ATATTTTGTTAAATAAAAAAAATTATA
1 ATATTTTGTTAAAT-AAAAAAATTATA
*
28495967 ATAATTTAGTTA
1 AT-ATTTTGTTA
28495979 TTTTTTATTT
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
26 13 0.37
27 14 0.40
28 8 0.23
ACGTcount: A:0.52, C:0.00, G:0.06, T:0.42
Consensus pattern (26 bp):
ATATTTTGTTAAATAAAAAAATTATA
Found at i:28497269 original size:7 final size:7
Alignment explanation
Indices: 28497257--28497282 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
28497247 TACAATATAG
28497257 GAATTCA
1 GAATTCA
28497264 GAATTCA
1 GAATTCA
28497271 GAATTCA
1 GAATTCA
28497278 GAATT
1 GAATT
28497283 TTCACTACTC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.42, C:0.12, G:0.15, T:0.31
Consensus pattern (7 bp):
GAATTCA
Found at i:28499678 original size:44 final size:45
Alignment explanation
Indices: 28499589--28499678 Score: 114
Period size: 44 Copynumber: 2.0 Consensus size: 45
28499579 GATGTAATTG
*
28499589 AATAGAGCTGTAATAAGTAATTTAATTGTTTGATTGAATGGAATGA
1 AATAGAGCTGTAATAAGTAATTT-ATTGTTTGATTGAATGAAATGA
*
28499635 AATAGAGCTGTAATAA-T-ATTCT-TGTGTTTGGTTGAATGAAATGA
1 AATAGAGCTGTAATAAGTAATT-TAT-TGTTTGATTGAATGAAATGA
28499679 TGTTGTAATA
Statistics
Matches: 40, Mismatches: 2, Indels: 6
0.83 0.04 0.12
Matches are distributed among these distances:
43 1 0.03
44 21 0.52
45 2 0.05
46 16 0.40
ACGTcount: A:0.37, C:0.03, G:0.22, T:0.38
Consensus pattern (45 bp):
AATAGAGCTGTAATAAGTAATTTATTGTTTGATTGAATGAAATGA
Found at i:28520873 original size:10 final size:10
Alignment explanation
Indices: 28520858--28520891 Score: 50
Period size: 10 Copynumber: 3.3 Consensus size: 10
28520848 TTATAACTAT
28520858 TTAAATAATA
1 TTAAATAATA
*
28520868 TTAAATTTATA
1 TTAAA-TAATA
28520879 TTAAATAATA
1 TTAAATAATA
28520889 TTA
1 TTA
28520892 TTTAAATAGT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
10 12 0.57
11 9 0.43
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (10 bp):
TTAAATAATA
Found at i:28527779 original size:20 final size:20
Alignment explanation
Indices: 28527754--28527791 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
28527744 TTTCAATATT
28527754 GAACACCAAAACTAAATTGG
1 GAACACCAAAACTAAATTGG
*
28527774 GAACACCAAAAGTAAATT
1 GAACACCAAAACTAAATT
28527792 AAAACTACGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.53, C:0.18, G:0.13, T:0.16
Consensus pattern (20 bp):
GAACACCAAAACTAAATTGG
Found at i:28527969 original size:15 final size:15
Alignment explanation
Indices: 28527949--28527978 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
28527939 ACTTAATAGT
28527949 ATACACACTTGAGAA
1 ATACACACTTGAGAA
28527964 ATACACACTTGAGAA
1 ATACACACTTGAGAA
28527979 GGGAAAAGTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.47, C:0.20, G:0.13, T:0.20
Consensus pattern (15 bp):
ATACACACTTGAGAA
Found at i:28540473 original size:13 final size:13
Alignment explanation
Indices: 28540455--28540490 Score: 72
Period size: 13 Copynumber: 2.8 Consensus size: 13
28540445 ATTATGCGAA
28540455 ATTGAAATAAGTT
1 ATTGAAATAAGTT
28540468 ATTGAAATAAGTT
1 ATTGAAATAAGTT
28540481 ATTGAAATAA
1 ATTGAAATAA
28540491 TGTCTTAACT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.50, C:0.00, G:0.14, T:0.36
Consensus pattern (13 bp):
ATTGAAATAAGTT
Found at i:28550831 original size:16 final size:16
Alignment explanation
Indices: 28550800--28550847 Score: 51
Period size: 16 Copynumber: 2.8 Consensus size: 16
28550790 AATATTATGA
*
28550800 AAAAGAAAAGGGGAAG
1 AAAAGAAAAGAGGAAG
*
28550816 AAAAGAAAAGATGAAG
1 AAAAGAAAAGAGGAAG
28550832 ATATAGAGAAAAGAGG
1 A-A-A-AGAAAAGAGG
28550848 GAGGAATTCT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
16 15 0.58
17 1 0.04
18 1 0.04
19 9 0.35
ACGTcount: A:0.62, C:0.00, G:0.31, T:0.06
Consensus pattern (16 bp):
AAAAGAAAAGAGGAAG
Found at i:28553926 original size:33 final size:31
Alignment explanation
Indices: 28553868--28553928 Score: 95
Period size: 33 Copynumber: 1.9 Consensus size: 31
28553858 TAATTAAATA
*
28553868 ATAAAATAACTAAAATGTACTAAAATAACTT
1 ATAAAATAACTAAAATCTACTAAAATAACTT
28553899 ATAAAATAAACTAAAATCCTACTAAAATAA
1 ATAAAAT-AACTAAAAT-CTACTAAAATAA
28553929 TAGACAAATA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
31 7 0.26
32 9 0.33
33 11 0.41
ACGTcount: A:0.61, C:0.11, G:0.02, T:0.26
Consensus pattern (31 bp):
ATAAAATAACTAAAATCTACTAAAATAACTT
Found at i:28553938 original size:32 final size:31
Alignment explanation
Indices: 28553870--28553939 Score: 81
Period size: 32 Copynumber: 2.2 Consensus size: 31
28553860 ATTAAATAAT
* *
28553870 AAAAT-AACTAAAATGTACTAAAATAACTTAT
1 AAAATAAACTAAAATCTACTAAAATAAC-TAG
28553901 AAAATAAACTAAAATCCTACTAAAATAA-TAG
1 AAAATAAACTAAAAT-CTACTAAAATAACTAG
28553932 ACAAATAA
1 A-AAATAA
28553940 CTCTAAGATT
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
31 8 0.24
32 15 0.44
33 11 0.32
ACGTcount: A:0.61, C:0.11, G:0.03, T:0.24
Consensus pattern (31 bp):
AAAATAAACTAAAATCTACTAAAATAACTAG
Found at i:28556351 original size:49 final size:49
Alignment explanation
Indices: 28556306--28556403 Score: 121
Period size: 49 Copynumber: 2.0 Consensus size: 49
28556296 GTGAGCCATG
*
28556306 TAACGGGAAGCTT-ATAAGAGTTAT-AATCGGGAAGTT-CAAACGAGCCAA
1 TAACGGGAAGCTTCA-AAGAGCTATAAATCGGGAAGTTCCAAA-GAGCCAA
* * *
28556354 TATCGGGAAGCTTCAGAGAGCTATAAATTGGGAAGTTCCAAAGAGCCAA
1 TAACGGGAAGCTTCAAAGAGCTATAAATCGGGAAGTTCCAAAGAGCCAA
28556403 T
1 T
28556404 TATCGAAAAG
Statistics
Matches: 43, Mismatches: 4, Indels: 5
0.83 0.08 0.10
Matches are distributed among these distances:
48 19 0.44
49 20 0.47
50 4 0.09
ACGTcount: A:0.38, C:0.15, G:0.26, T:0.21
Consensus pattern (49 bp):
TAACGGGAAGCTTCAAAGAGCTATAAATCGGGAAGTTCCAAAGAGCCAA
Found at i:28556358 original size:24 final size:23
Alignment explanation
Indices: 28556331--28556408 Score: 75
Period size: 25 Copynumber: 3.2 Consensus size: 23
28556321 AAGAGTTATA
28556331 ATCGGGAAGTTCAAACGAGCCAAT
1 ATCGGGAAGTTCAAA-GAGCCAAT
* * *
28556355 ATCGGGAAGCTTCAGAGAGCTATAA
1 ATCGGGAAG-TTCAAAGAGCCA-AT
*
28556380 ATTGGGAAGTTCCAAAGAGCCAATT
1 ATCGGGAAGTT-CAAAGAGCCAA-T
28556405 ATCG
1 ATCG
28556409 AAAAGCTCCG
Statistics
Matches: 42, Mismatches: 8, Indels: 7
0.74 0.14 0.12
Matches are distributed among these distances:
24 17 0.40
25 25 0.60
ACGTcount: A:0.36, C:0.18, G:0.26, T:0.21
Consensus pattern (23 bp):
ATCGGGAAGTTCAAAGAGCCAAT
Found at i:28556435 original size:49 final size:49
Alignment explanation
Indices: 28556334--28556437 Score: 122
Period size: 50 Copynumber: 2.1 Consensus size: 49
28556324 AGTTATAATC
** * * *
28556334 GGGAAGTTCAAACGAGCCAATATCGGGAAGCTTCAGAGAGCTATAAATT
1 GGGAAGTTCAAACGAGCCAATATCGAAAAGCTCCAGAGAACCATAAATT
*
28556383 GGGAAGTTCCAAA-GAGCCAATTATCGAAAAGCTCCGGAGAACCATAAA-T
1 GGGAAGTT-CAAACGAGCCAA-TATCGAAAAGCTCCAGAGAACCATAAATT
28556432 GGGAAG
1 GGGAAG
28556438 CTCGCAAGAA
Statistics
Matches: 47, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
49 22 0.47
50 25 0.53
ACGTcount: A:0.38, C:0.17, G:0.27, T:0.17
Consensus pattern (49 bp):
GGGAAGTTCAAACGAGCCAATATCGAAAAGCTCCAGAGAACCATAAATT
Found at i:28561107 original size:91 final size:90
Alignment explanation
Indices: 28560933--28561113 Score: 213
Period size: 91 Copynumber: 2.0 Consensus size: 90
28560923 AGTGTTGTAG
* * * * **
28560933 GTTAATACGGTGTCAGTAGTTTTGAATGCACAGCGGGTTTGCATATAAAAGCTGTCAGTAAAAGT
1 GTTAATACGCTGTCAGTAGTTGTGAATGCACAACGAGTTTGCATATAAAAGCTACCAG-AAAAGT
*
28560998 TGTAGGTAAACCACCAATGTTTGCAT
65 TGGAGGTAAACCACCAATGTTTGCAT
* * *
28561024 GTTAATACGCTTTTAGTAGGTTGTGAATGCACAACGAGTTTGCATATAAAAGCTACCA-ATAAGT
1 GTTAATACGCTGTCAGTA-GTTGTGAATGCACAACGAGTTTGCATATAAAAGCTACCAGAAAAG-
*
28561088 TTGCGA-GTAAACCATCAATGTTTGCA
64 TTG-GAGGTAAACCACCAATGTTTGCA
28561114 GATAAATTGT
Statistics
Matches: 76, Mismatches: 11, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
90 4 0.05
91 37 0.49
92 35 0.46
ACGTcount: A:0.32, C:0.15, G:0.22, T:0.31
Consensus pattern (90 bp):
GTTAATACGCTGTCAGTAGTTGTGAATGCACAACGAGTTTGCATATAAAAGCTACCAGAAAAGTT
GGAGGTAAACCACCAATGTTTGCAT
Found at i:28562615 original size:34 final size:34
Alignment explanation
Indices: 28562577--28562645 Score: 104
Period size: 34 Copynumber: 2.0 Consensus size: 34
28562567 CAAGCATGTC
28562577 ATTTGCAACTAAATC-AATATGTTATAAGCATAAT
1 ATTTGCAACTAAATCGAAT-TGTTATAAGCATAAT
* *
28562611 ATTTGCCACTGAATCGAATTGTTATAAGCATAAT
1 ATTTGCAACTAAATCGAATTGTTATAAGCATAAT
28562645 A
1 A
28562646 ATTACTACCG
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
34 29 0.91
35 3 0.09
ACGTcount: A:0.41, C:0.13, G:0.12, T:0.35
Consensus pattern (34 bp):
ATTTGCAACTAAATCGAATTGTTATAAGCATAAT
Found at i:28562884 original size:44 final size:45
Alignment explanation
Indices: 28562822--28562907 Score: 111
Period size: 44 Copynumber: 1.9 Consensus size: 45
28562812 CTACACCGTT
* * * * *
28562822 TGAGTGGTTTATCCACACTGTAC-AGTAGCTTTTATTTGCAACAA
1 TGAGTGGTTTAACCACACTATACTAGCAGCTTTAATATGCAACAA
*
28562866 TGAGTGGTTTAACTACACTATACTAGCAGCTTTAATATGCAA
1 TGAGTGGTTTAACCACACTATACTAGCAGCTTTAATATGCAA
28562908 ACATGTTGTG
Statistics
Matches: 35, Mismatches: 6, Indels: 1
0.83 0.14 0.02
Matches are distributed among these distances:
44 20 0.57
45 15 0.43
ACGTcount: A:0.30, C:0.17, G:0.17, T:0.35
Consensus pattern (45 bp):
TGAGTGGTTTAACCACACTATACTAGCAGCTTTAATATGCAACAA
Found at i:28563036 original size:21 final size:21
Alignment explanation
Indices: 28563010--28563052 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
28563000 GGTTTATCCG
28563010 CAATGAATGGTCCATCCACAA
1 CAATGAATGGTCCATCCACAA
* **
28563031 CAATGAGTGGTTTATCCACAA
1 CAATGAATGGTCCATCCACAA
28563052 C
1 C
28563053 GTTGTGTAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.35, C:0.26, G:0.16, T:0.23
Consensus pattern (21 bp):
CAATGAATGGTCCATCCACAA
Found at i:28565291 original size:20 final size:20
Alignment explanation
Indices: 28565266--28565304 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
28565256 CAGACTGAGT
*
28565266 TTATTCTGTTTACTGTCTGA
1 TTATTCTGTGTACTGTCTGA
28565286 TTATTCTGTGTACTGTCTG
1 TTATTCTGTGTACTGTCTG
28565305 TTTGTTTGCA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.13, C:0.15, G:0.18, T:0.54
Consensus pattern (20 bp):
TTATTCTGTGTACTGTCTGA
Found at i:28578684 original size:5 final size:5
Alignment explanation
Indices: 28578674--28578700 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
28578664 AGCTTAGTAT
28578674 TTTTC TTTTC TTTTC TTTTC TTTTC TT
1 TTTTC TTTTC TTTTC TTTTC TTTTC TT
28578701 GTTAACATCG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (5 bp):
TTTTC
Found at i:28581260 original size:114 final size:113
Alignment explanation
Indices: 28580900--28581477 Score: 466
Period size: 113 Copynumber: 5.1 Consensus size: 113
28580890 CCTGAAGAAC
* * *
28580900 TAGTGGCGTTTCTAAAAAAACGCCGTAAAAGAACATAATTAGTGGCGTTTA-TTGTAAGCACCGC
1 TAGTGGCGTTT-TTAAAAAACGCCGTAAAAGAACATAATTAGTGGCGTTTATTTGGAAGCGCCGC
* *
28580964 AAAATACCTTAACCAAAACGCAGCG-TTGGTTCAATTGTATATTAGA-AT
65 AAAATACCTTAACCAAAACGCAGCGTTTGGTTCAA-GGTAGATTAGATAT
* * * * * *****
28581012 TCGTGGTGTTTTTTATAAAAACACCGCT-AAAGAATAGT-ATTAGCGGCGTTTAACAAAAAGCGC
1 TAGTGGCG-TTTTTA-AAAAACGCCG-TAAAAGAACA-TAATTAGTGGCGTTTATTTGGAAGCGC
* ** * ** **
28581075 CGC-AAATATCTTAAGGAAAACGCACCGTTTTATCTTGAGGTAGATTA-ATAT
62 CGCAAAATACCTTAACCAAAACGCAGCGTTTGGT-TCAAGGTAGATTAGATAT
*
28581126 TAGTGGCGTTTTTAAAAAAACGCCGTAAAAGAACATAATTAGTGGCGTTTATTTGGATGCGCCGC
1 TAGTGGCGTTTTT-AAAAAACGCCGTAAAAGAACATAATTAGTGGCGTTTATTTGGAAGCGCCGC
* * *
28581191 AAAATACCTTAACCAAAACGCAGCGTTTGGTTCAATTGTATATTAGACAT
65 AAAATACCTTAACCAAAACGCAGCGTTTGGTTCAA-GGTAGATTAGATAT
* * * * * * *
28581241 T-GTGGCGTTTTCTATAAAACGCCGCAGAAGAATAGT-ATTCGCGGCG-TT-TTCGGTAAAGCGC
1 TAGTGGCGTTTT-TAAAAAACGCCGTAAAAGAACA-TAATTAGTGGCGTTTATTTGG--AAGCGC
* ** * **
28581302 CGC-AAATATCTTAATGAAAACGCA-CTGTTTCGTCTTGAGGTAGATTAG-TAT
62 CGCAAAATACCTTAACCAAAACGCAGC-GTTTGGT-TCAAGGTAGATTAGATAT
* ** *
28581353 TAGTGGCGTTTTTAGAAAAACACCGTAAAAGAACATAATTAGTGGCGTTTATTTTTATGCGCCGC
1 TAGTGGCGTTTTTA-AAAAACGCCGTAAAAGAACATAATTAGTGGCGTTTATTTGGAAGCGCCGC
** * *
28581418 AAAATACCTTAACCAAAACGCAGCGTTTGGTTTTGAGGTATATAAGA-AT
65 AAAATACCTTAACCAAAACGCAGCGTTTGG-TTCAAGGTAGATTAGATAT
28581467 TAGTGGCGTTT
1 TAGTGGCGTTT
28581478 ACGATAAAAC
Statistics
Matches: 360, Mismatches: 77, Indels: 56
0.73 0.16 0.11
Matches are distributed among these distances:
112 21 0.06
113 172 0.48
114 155 0.43
115 12 0.03
ACGTcount: A:0.33, C:0.16, G:0.21, T:0.30
Consensus pattern (113 bp):
TAGTGGCGTTTTTAAAAAACGCCGTAAAAGAACATAATTAGTGGCGTTTATTTGGAAGCGCCGCA
AAATACCTTAACCAAAACGCAGCGTTTGGTTCAAGGTAGATTAGATAT
Found at i:28581301 original size:227 final size:226
Alignment explanation
Indices: 28580900--28581495 Score: 869
Period size: 227 Copynumber: 2.6 Consensus size: 226
28580890 CCTGAAGAAC
* * *
28580900 TAGTGGCGTTTCTAAAAAAACGCCGTAAAAGAACATAATTAGTGGCGTTTA-TTGTAAGCACCGC
1 TAGTGGCGTTTTTAAAAAAACGCCGTAAAAGAACATAATTAGTGGCGTTTATTTGTATGCGCCGC
* * *
28580964 AAAATACCTTAACCAAAACGCAGCG-TTGGTTCAATTGTATATTAGAATTCGTGGTGTTTTTTAT
66 AAAATACCTTAACCAAAACGCAGCGTTTGGTTCAATTGTATATTAGAATTAGTGGCGTTTTCTAT
*
28581028 AAAAACACCGCTAAAGAATAGTATTAGCGGCGTTTAACAAAAAGCGCCGCAAATATCTTAAGGAA
131 -AAAACGCCGC-AAAGAATAGTATTAGCGGCGTTTAACAAAAAGCGCCGCAAATATCTTAAGGAA
*
28581093 AACGCACCGTTTTATCTTGAGGTAGATTAATAT
194 AACGCACCGTTTCATCTTGAGGTAGATTAATAT
*
28581126 TAGTGGCGTTTTTAAAAAAACGCCGTAAAAGAACATAATTAGTGGCGTTTATTTGGATGCGCCGC
1 TAGTGGCGTTTTTAAAAAAACGCCGTAAAAGAACATAATTAGTGGCGTTTATTTGTATGCGCCGC
28581191 AAAATACCTTAACCAAAACGCAGCGTTTGGTTCAATTGTATATTAGACATT-GTGGCGTTTTCTA
66 AAAATACCTTAACCAAAACGCAGCGTTTGGTTCAATTGTATATTAGA-ATTAGTGGCGTTTTCTA
* * ** *
28581255 TAAAACGCCGCAGAAGAATAGTATTCGCGGCGTTT-TCGGTAAAGCGCCGCAAATATCTTAATGA
130 TAAAACGCCGCA-AAGAATAGTATTAGCGGCGTTTAAC-AAAAAGCGCCGCAAATATCTTAAGGA
* * *
28581319 AAACGCACTGTTTCGTCTTGAGGTAGATTAGTAT
193 AAACGCACCGTTTCATCTTGAGGTAGATTAATAT
* * *
28581353 TAGTGGCGTTTTTAGAAAAACACCGTAAAAGAACATAATTAGTGGCGTTTATTTTTATGCGCCGC
1 TAGTGGCGTTTTTAAAAAAACGCCGTAAAAGAACATAATTAGTGGCGTTTATTTGTATGCGCCGC
** * * * *
28581418 AAAATACCTTAACCAAAACGCAGCGTTTGGTTTTGA-GGTATATAAGAATTAGTGGCGTTTACGA
66 AAAATACCTTAACCAAAACGCAGCGTTTGG-TTCAATTGTATATTAGAATTAGTGGCGTTTTCTA
28581482 TAAAACGCCGCAAA
130 TAAAACGCCGCAAA
28581496 CATCTTAACG
Statistics
Matches: 337, Mismatches: 26, Indels: 14
0.89 0.07 0.04
Matches are distributed among these distances:
226 57 0.17
227 241 0.72
228 36 0.11
229 3 0.01
ACGTcount: A:0.34, C:0.17, G:0.21, T:0.29
Consensus pattern (226 bp):
TAGTGGCGTTTTTAAAAAAACGCCGTAAAAGAACATAATTAGTGGCGTTTATTTGTATGCGCCGC
AAAATACCTTAACCAAAACGCAGCGTTTGGTTCAATTGTATATTAGAATTAGTGGCGTTTTCTAT
AAAACGCCGCAAAGAATAGTATTAGCGGCGTTTAACAAAAAGCGCCGCAAATATCTTAAGGAAAA
CGCACCGTTTCATCTTGAGGTAGATTAATAT
Found at i:28581527 original size:188 final size:188
Alignment explanation
Indices: 28581283--28581677 Score: 630
Period size: 188 Copynumber: 2.1 Consensus size: 188
28581273 TAGTATTCGC
* * * * *
28581283 GGCGTTTTCGGTAAAGCGCCGCAAATATCTTAATGAAAACGCACTGTTTCGTCTTGAGGTAGATT
1 GGCGTTTACGGTAAAACGCCGCAAACATCTTAACGAAAACGCACCGTTTCGTCTTGAGGTAGATT
* ** *
28581348 AGTATTAGTGGCG-TTTTTAGAAAAACACCGTAAAAGAACATAATTAGTGGCGTTTATTTTTATG
66 AATATTAGTGGCGTTTTTTA-AAAAACACCGTAAAAGAACATAATTAGTGGCGTTTATTTGGAAG
28581412 CGCCGCAAAATACCTTAACCAAAACGCAGCGTTTGGTTTTGAGGTATATAAGAATTAGT
130 CGCCGCAAAATACCTTAACCAAAACGCAGCGTTTGGTTTTGAGGTATATAAGAATTAGT
* *
28581471 GGCGTTTACGATAAAACGCCGCAAACATCTTAACGAAAACGCACCGTTTGGTCTTGAGGTAGATT
1 GGCGTTTACGGTAAAACGCCGCAAACATCTTAACGAAAACGCACCGTTTCGTCTTGAGGTAGATT
28581536 AATATTAGTGGCGTTTTTTAAAAAACACCGTAAAAGAACATAATTAGTGGCGTTTATTTGGAAGC
66 AATATTAGTGGCGTTTTTTAAAAAACACCGTAAAAGAACATAATTAGTGGCGTTTATTTGGAAGC
* * * *
28581601 GCCGCAAAATGCCTTAACCAAAACGCAGTGTTTGGTTTTGATGTATATTAGAATTAGT
131 GCCGCAAAATACCTTAACCAAAACGCAGCGTTTGGTTTTGAGGTATATAAGAATTAGT
*
28581659 GGCGTTTATGGTAAAACGC
1 GGCGTTTACGGTAAAACGC
28581678 TGCTAAAGAA
Statistics
Matches: 189, Mismatches: 17, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
188 183 0.97
189 6 0.03
ACGTcount: A:0.32, C:0.16, G:0.22, T:0.30
Consensus pattern (188 bp):
GGCGTTTACGGTAAAACGCCGCAAACATCTTAACGAAAACGCACCGTTTCGTCTTGAGGTAGATT
AATATTAGTGGCGTTTTTTAAAAAACACCGTAAAAGAACATAATTAGTGGCGTTTATTTGGAAGC
GCCGCAAAATACCTTAACCAAAACGCAGCGTTTGGTTTTGAGGTATATAAGAATTAGT
Found at i:28581528 original size:74 final size:74
Alignment explanation
Indices: 28581412--28581551 Score: 194
Period size: 74 Copynumber: 1.9 Consensus size: 74
28581402 TATTTTTATG
* * *
28581412 CGCCGCAAAATACCTTAACCAAAACGCAGCGTTTGGTTTTGAGGTATA-TAAGAATTAGTGGCGT
1 CGCCGCAAAATA-CTTAACCAAAACGCACCGTTTGGTCTTGAGGTAGATTAA-AATTAGTGGCGT
28581476 TTACGATAAAA
64 TTACGATAAAA
* *
28581487 CGCCGCAAACAT-CTTAACGAAAACGCACCGTTTGGTCTTGAGGTAGATTAATATTAGTGGCGTT
1 CGCCGCAAA-ATACTTAACCAAAACGCACCGTTTGGTCTTGAGGTAGATTAAAATTAGTGGCGTT
28581551 T
65 T
28581552 TTTAAAAAAC
Statistics
Matches: 58, Mismatches: 5, Indels: 5
0.85 0.07 0.07
Matches are distributed among these distances:
74 44 0.76
75 12 0.21
76 2 0.03
ACGTcount: A:0.31, C:0.19, G:0.22, T:0.28
Consensus pattern (74 bp):
CGCCGCAAAATACTTAACCAAAACGCACCGTTTGGTCTTGAGGTAGATTAAAATTAGTGGCGTTT
ACGATAAAA
Found at i:28582102 original size:7 final size:7
Alignment explanation
Indices: 28582092--28582142 Score: 79
Period size: 7 Copynumber: 7.6 Consensus size: 7
28582082 AGTTTACAGA
28582092 TTAGGGG
1 TTAGGGG
28582099 TTAGGGG
1 TTAGGGG
28582106 TTAGGGG
1 TTAGGGG
*
28582113 TTATGGG
1 TTAGGGG
28582120 TTAGGGG
1 TTAGGGG
28582127 TTA--GG
1 TTAGGGG
28582132 TTAGGGG
1 TTAGGGG
28582139 TTAG
1 TTAG
28582143 ATGTTAAGAG
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
5 5 0.12
7 35 0.88
ACGTcount: A:0.16, C:0.00, G:0.51, T:0.33
Consensus pattern (7 bp):
TTAGGGG
Found at i:28582156 original size:33 final size:33
Alignment explanation
Indices: 28582097--28582164 Score: 91
Period size: 33 Copynumber: 2.1 Consensus size: 33
28582087 ACAGATTAGG
* * *
28582097 GGTTAGGGGTTAGGGGTTATGGGTTAGGGGTTA
1 GGTTAGGGGTTAGAGGTTAAGAGTTAGGGGTTA
* *
28582130 GGTTAGGGGTTAGATGTTAAGAGTTAGGGTTTA
1 GGTTAGGGGTTAGAGGTTAAGAGTTAGGGGTTA
28582163 GG
1 GG
28582165 ATTTATAAAA
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.19, C:0.00, G:0.47, T:0.34
Consensus pattern (33 bp):
GGTTAGGGGTTAGAGGTTAAGAGTTAGGGGTTA
Found at i:28582256 original size:7 final size:7
Alignment explanation
Indices: 28582244--28582323 Score: 63
Period size: 7 Copynumber: 11.4 Consensus size: 7
28582234 ATAAGTTTTG
28582244 GGGGTTA
1 GGGGTTA
28582251 GGGGTTA
1 GGGGTTA
* * *
28582258 GAGATCA
1 GGGGTTA
*
28582265 TGGGTTAA
1 GGGGTT-A
*
28582273 GGGTTTA
1 GGGGTTA
28582280 -GGGTTA
1 GGGGTTA
*
28582286 AGGGTTA
1 GGGGTTA
*
28582293 AGGGTTA
1 GGGGTTA
*
28582300 AGGGTTA
1 GGGGTTA
28582307 GGGGTTA
1 GGGGTTA
*
28582314 CGGGTTA
1 GGGGTTA
28582321 GGG
1 GGG
28582324 ATTGGGTTAT
Statistics
Matches: 58, Mismatches: 13, Indels: 4
0.77 0.17 0.05
Matches are distributed among these distances:
6 5 0.09
7 48 0.83
8 5 0.09
ACGTcount: A:0.21, C:0.03, G:0.47, T:0.29
Consensus pattern (7 bp):
GGGGTTA
Found at i:28582283 original size:14 final size:13
Alignment explanation
Indices: 28582266--28582323 Score: 80
Period size: 14 Copynumber: 4.2 Consensus size: 13
28582256 TAGAGATCAT
28582266 GGGTTAAGGGTTTA
1 GGGTTAAGGG-TTA
28582280 GGGTTAAGGGTTAA
1 GGGTTAAGGGTT-A
28582294 GGGTTAAGGGTTA
1 GGGTTAAGGGTTA
*
28582307 GGGGTTACGGGTTA
1 -GGGTTAAGGGTTA
28582321 GGG
1 GGG
28582324 ATTGGGTTAT
Statistics
Matches: 41, Mismatches: 1, Indels: 5
0.87 0.02 0.11
Matches are distributed among these distances:
13 6 0.15
14 35 0.85
ACGTcount: A:0.21, C:0.02, G:0.48, T:0.29
Consensus pattern (13 bp):
GGGTTAAGGGTTA
Found at i:28582290 original size:21 final size:21
Alignment explanation
Indices: 28582266--28582323 Score: 82
Period size: 21 Copynumber: 2.8 Consensus size: 21
28582256 TAGAGATCAT
28582266 GGGTTAAGGGTTTAGGGTTAA
1 GGGTTAAGGGTTTAGGGTTAA
* *
28582287 GGGTTAAGGGTTAAGGGTTAG
1 GGGTTAAGGGTTTAGGGTTAA
*
28582308 GGGTTACGGG-TTAGGG
1 GGGTTAAGGGTTTAGGG
28582324 ATTGGGTTAT
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
20 5 0.15
21 28 0.85
ACGTcount: A:0.21, C:0.02, G:0.48, T:0.29
Consensus pattern (21 bp):
GGGTTAAGGGTTTAGGGTTAA
Found at i:28582481 original size:95 final size:96
Alignment explanation
Indices: 28582294--28582478 Score: 212
Period size: 95 Copynumber: 1.9 Consensus size: 96
28582284 TAAGGGTTAA
* * * * *
28582294 GGGTTAAGGGTTAGGGGTTACGGGTTAGGGATTGGGTTATGGTTTAAGGTTTAGATTAATTAGTG
1 GGGTTAAGGGTTAGGGGTTACGGGTTAGGGATCGGGTTAGGGATTAAGATTTAGATTAATTAGTC
* * * * *
28582359 TTTTTTATTTTATATTTTAAATAAAGTTTAG
66 TTATTTAATTAACATATTAAATAAAGTTTAG
* * * *
28582390 GGGTTAGGGGTTA-GGGTTATGGGTT-TGGAGTCGGGTTAGGGATTAAGATTTGGATTAATTAGT
1 GGGTTAAGGGTTAGGGGTTACGGGTTAGGGA-TCGGGTTAGGGATTAAGATTTAGATTAATTAGT
28582453 ACTTATTTAATTAACATATTAAATAA
65 -CTTATTTAATTAACATATTAAATAA
28582479 GTTCTTTATA
Statistics
Matches: 73, Mismatches: 14, Indels: 4
0.80 0.15 0.04
Matches are distributed among these distances:
94 3 0.04
95 39 0.53
96 31 0.42
ACGTcount: A:0.27, C:0.02, G:0.29, T:0.42
Consensus pattern (96 bp):
GGGTTAAGGGTTAGGGGTTACGGGTTAGGGATCGGGTTAGGGATTAAGATTTAGATTAATTAGTC
TTATTTAATTAACATATTAAATAAAGTTTAG
Found at i:28582568 original size:14 final size:14
Alignment explanation
Indices: 28582549--28582575 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
28582539 GATATGCAAT
28582549 ATATAATAATTTGA
1 ATATAATAATTTGA
28582563 ATATAATAATTTG
1 ATATAATAATTTG
28582576 GAATTGTAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.48, C:0.00, G:0.07, T:0.44
Consensus pattern (14 bp):
ATATAATAATTTGA
Found at i:28582614 original size:19 final size:19
Alignment explanation
Indices: 28582577--28582617 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
28582567 AATAATTTGG
**
28582577 AATTGTAAAAATTGTAAAA
1 AATTGTAAAAATTACAAAA
*
28582596 AATTGTCAAAATTACAAAA
1 AATTGTAAAAATTACAAAA
28582615 AAT
1 AAT
28582618 AAAATGAAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.59, C:0.05, G:0.07, T:0.29
Consensus pattern (19 bp):
AATTGTAAAAATTACAAAA
Found at i:28582632 original size:18 final size:17
Alignment explanation
Indices: 28582611--28582668 Score: 98
Period size: 17 Copynumber: 3.4 Consensus size: 17
28582601 TCAAAATTAC
*
28582611 AAAAAATAAAATGAAAAT
1 AAAAAATAAAAAG-AAAT
28582629 AAAAAATAAAAAGAAAT
1 AAAAAATAAAAAGAAAT
28582646 AAAAAATAAAAAGAAAT
1 AAAAAATAAAAAGAAAT
28582663 AAAAAA
1 AAAAAA
28582669 ACTAAAATTT
Statistics
Matches: 39, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
17 27 0.69
18 12 0.31
ACGTcount: A:0.83, C:0.00, G:0.05, T:0.12
Consensus pattern (17 bp):
AAAAAATAAAAAGAAAT
Found at i:28582647 original size:10 final size:10
Alignment explanation
Indices: 28582614--28582667 Score: 55
Period size: 10 Copynumber: 5.9 Consensus size: 10
28582604 AAATTACAAA
*
28582614 AAATAAAATG
1 AAATAAAAAG
*
28582624 AAA-ATAAA-
1 AAATAAAAAG
28582632 AAATAAAAAG
1 AAATAAAAAG
28582642 AAAT--AAA-
1 AAATAAAAAG
28582649 AAATAAAAAG
1 AAATAAAAAG
28582659 AAATAAAAA
1 AAATAAAAA
28582668 AACTAAAATT
Statistics
Matches: 36, Mismatches: 3, Indels: 10
0.73 0.06 0.20
Matches are distributed among these distances:
7 4 0.11
8 6 0.17
9 10 0.28
10 16 0.44
ACGTcount: A:0.81, C:0.00, G:0.06, T:0.13
Consensus pattern (10 bp):
AAATAAAAAG
Found at i:28582669 original size:18 final size:18
Alignment explanation
Indices: 28582611--28582675 Score: 89
Period size: 18 Copynumber: 3.6 Consensus size: 18
28582601 TCAAAATTAC
*
28582611 AAAAAATAAAATGAAA-A
1 AAAAAATAAAAAGAAATA
28582628 TAAAAAATAAAAAGAAAT-
1 -AAAAAATAAAAAGAAATA
28582646 AAAAAATAAAAAGAAATA
1 AAAAAATAAAAAGAAATA
28582664 AAAAAACTAAAA
1 AAAAAA-TAAAA
28582676 TTTTTATTTT
Statistics
Matches: 43, Mismatches: 1, Indels: 5
0.88 0.02 0.10
Matches are distributed among these distances:
17 17 0.40
18 21 0.49
19 5 0.12
ACGTcount: A:0.82, C:0.02, G:0.05, T:0.12
Consensus pattern (18 bp):
AAAAAATAAAAAGAAATA
Found at i:28582715 original size:47 final size:47
Alignment explanation
Indices: 28582664--28582755 Score: 112
Period size: 47 Copynumber: 2.0 Consensus size: 47
28582654 AAAAGAAATA
** *
28582664 AAAAAACTAAAATTTTTATTTTTACCTAATTTTTATAAATATTACTT
1 AAAAAACTAAAATTGATAATTTTACCTAATTTTTATAAATATTACTT
* * * * *
28582711 AAAAAATTGAGATTGATAATTTTATCTAATTTTTTTAAATATTAC
1 AAAAAACTAAAATTGATAATTTTACCTAATTTTTATAAATATTAC
28582756 CGAAATTAAC
Statistics
Matches: 37, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
47 37 1.00
ACGTcount: A:0.42, C:0.07, G:0.03, T:0.48
Consensus pattern (47 bp):
AAAAAACTAAAATTGATAATTTTACCTAATTTTTATAAATATTACTT
Found at i:28583496 original size:198 final size:197
Alignment explanation
Indices: 28583143--28583553 Score: 644
Period size: 198 Copynumber: 2.1 Consensus size: 197
28583133 AGCGTTTATG
**
28583143 TATAAACGCCGCAATTTTAAGAAATTGTTTACGAAAACGGCTCCGTTTTCTTATTTATCTTTAGT
1 TATAAACGCCGCAA-AGTAAGAAATTGTTTACGAAAACGGCTCCGTTTTCTTATTTATCTTTAGT
* * *
28583208 GGCGCTTTTAGTACACGCCGCAAAATTATTTTAATTTTTATGGAGACGATGCCGTTTTGTCTAAA
65 GGCGCTTTTAGTAAACGCCGCAAAAATATTTTAATTTTTATGGAGACGATGCCGTTTTCTCTAAA
* * ** * *
28583273 ACGCCATGAGTTTTAGTTTACTAATCGGGGAACGACAGCGTTTGATCATATTACTAGTGGCGCTA
130 ACGCAATGACTTAGAGTTAACTAATCGGGAAACGACAGCGTTTGATCATATTACTAGTGGCGCTA
28583338 GTA
195 GTA
* *
28583341 TATAAACGCCGCAAAGTACAGAAATTGTTTAGGAAAACGGCTTCGTTTTCTTATTTA-CTTTTAG
1 TATAAACGCCGCAAAGTA-AGAAATTGTTTACGAAAACGGCTCCGTTTTCTTATTTATC-TTTAG
*
28583405 TGGCGCTTTTAGTAAACGCCGCAAAAATGTTTTAATTTTTATGGAGACGATGCCGTTTTCTCTAA
64 TGGCGCTTTTAGTAAACGCCGCAAAAATATTTTAATTTTTATGGAGACGATGCCGTTTTCTCTAA
*
28583470 AACGCAATTACTTAGAGTTAACTAATCGGGAAACGACAGCGTTTGATCATATTACTAGTGGCGCT
129 AACGCAATGACTTAGAGTTAACTAATCGGGAAACGACAGCGTTTGATCATATTACTAGTGGCGCT
*
28583535 GGTA
194 AGTA
28583539 TATAAACGCCGCAAA
1 TATAAACGCCGCAAA
28583554 TGGGTTAATT
Statistics
Matches: 195, Mismatches: 16, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
197 3 0.02
198 192 0.98
ACGTcount: A:0.29, C:0.17, G:0.20, T:0.34
Consensus pattern (197 bp):
TATAAACGCCGCAAAGTAAGAAATTGTTTACGAAAACGGCTCCGTTTTCTTATTTATCTTTAGTG
GCGCTTTTAGTAAACGCCGCAAAAATATTTTAATTTTTATGGAGACGATGCCGTTTTCTCTAAAA
CGCAATGACTTAGAGTTAACTAATCGGGAAACGACAGCGTTTGATCATATTACTAGTGGCGCTAG
TA
Found at i:28583882 original size:16 final size:16
Alignment explanation
Indices: 28583860--28583928 Score: 120
Period size: 16 Copynumber: 4.2 Consensus size: 16
28583850 TTTGGTTCGC
28583860 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
*
28583876 CGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
28583892 TGTATTGGGATTAGAGG
1 TGTATT-GGATTAGAGG
28583909 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
28583925 TGTA
1 TGTA
28583929 ATAGCTAATC
Statistics
Matches: 50, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
16 34 0.68
17 16 0.32
ACGTcount: A:0.25, C:0.01, G:0.38, T:0.36
Consensus pattern (16 bp):
TGTATTGGATTAGAGG
Found at i:28583906 original size:33 final size:32
Alignment explanation
Indices: 28583860--28583928 Score: 120
Period size: 33 Copynumber: 2.1 Consensus size: 32
28583850 TTTGGTTCGC
28583860 TGTATTGGATTAGAGGCGTATTGGATTAGAGG
1 TGTATTGGATTAGAGGCGTATTGGATTAGAGG
*
28583892 TGTATTGGGATTAGAGGTGTATTGGATTAGAGG
1 TGTATT-GGATTAGAGGCGTATTGGATTAGAGG
28583925 TGTA
1 TGTA
28583929 ATAGCTAATC
Statistics
Matches: 35, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
32 6 0.17
33 29 0.83
ACGTcount: A:0.25, C:0.01, G:0.38, T:0.36
Consensus pattern (32 bp):
TGTATTGGATTAGAGGCGTATTGGATTAGAGG
Found at i:28583993 original size:44 final size:45
Alignment explanation
Indices: 28583909--28583999 Score: 121
Period size: 45 Copynumber: 2.0 Consensus size: 45
28583899 GGATTAGAGG
* * *
28583909 TGTATTGGATTAGAGGTGTAATAGCTAATCCACTGTTTGGTTGAA
1 TGTAATGGAATAGAGGCGTAATAGCTAATCCACTGTTTGGTTGAA
***
28583954 TGTAATGGAATAGAGGCGTAATAG-TAATCTTGTGTTTGGTTGAA
1 TGTAATGGAATAGAGGCGTAATAGCTAATCCACTGTTTGGTTGAA
28583998 TG
1 TG
28584000 GAATAGAGGT
Statistics
Matches: 40, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
44 19 0.47
45 21 0.52
ACGTcount: A:0.27, C:0.07, G:0.29, T:0.37
Consensus pattern (45 bp):
TGTAATGGAATAGAGGCGTAATAGCTAATCCACTGTTTGGTTGAA
Found at i:28584185 original size:18 final size:17
Alignment explanation
Indices: 28584164--28584198 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
28584154 TTATTATTAA
*
28584164 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
28584182 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
28584199 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:28584360 original size:120 final size:120
Alignment explanation
Indices: 28584147--28584889 Score: 1414
Period size: 120 Copynumber: 6.2 Consensus size: 120
28584137 ATCATATTTA
28584147 AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
1 AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
28584212 TATTCTTATATTAATTTACTGAAATCATAATATATGATACTGTAAAATATAAATT
66 TATTCTTATATTAATTTACTGAAATCATAATATATGATACTGTAAAATATAAATT
*
28584267 AACATAATTATTATTAAATATATTTTAATTAAACTATATAATTTAATAAAATTCTTAATAATTAA
1 AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
*
28584332 TATTCTTATATTAATTTACTCAAATCATAATATATGATACTGTAAAATATAAATT
66 TATTCTTATATTAATTTACTGAAATCATAATATATGATACTGTAAAATATAAATT
*
28584387 AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATGAAATTCTTAATAATTAA
1 AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
28584452 TATTCTTATATTAATTTACTGAAATCATAATATATGATACTGTAAAATATAAATT
66 TATTCTTATATTAATTTACTGAAATCATAATATATGATACTGTAAAATATAAATT
*
28584507 AACATAATTATTATTAAATATATTTTAATTAAACTATATAATTTAATAAAATTCTTAATAATTAA
1 AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
28584572 TATTCTTATATTAATTTACTGAAATCATAATATATGATACTGTAAAATATAAATT
66 TATTCTTATATTAATTTACTGAAATCATAATATATGATACTGTAAAATATAAATT
*
28584627 AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATGAAATTCTTAATAATTAA
1 AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
28584692 TATTCTTATATTAATTTACTGAAATCATAATATATGATACTGTAAAATATAAATT
66 TATTCTTATATTAATTTACTGAAATCATAATATATGATACTGTAAAATATAAATT
* *
28584747 AACATAATTATTATTAAATATATTTTAATTAAACTATAAAATTTAATAAAATTCTTAATAATTAA
1 AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
*
28584812 TATTCTTATATTAATTTACTCAAATCATAATATATGATACTGTAAAATATAAATT
66 TATTCTTATATTAATTTACTGAAATCATAATATATGATACTGTAAAATATAAATT
28584867 AACATAATTATTATTAAATATAT
1 AACATAATTATTATTAAATATAT
28584890 AACTTGAAAA
Statistics
Matches: 610, Mismatches: 13, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
120 610 1.00
ACGTcount: A:0.48, C:0.06, G:0.02, T:0.44
Consensus pattern (120 bp):
AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
TATTCTTATATTAATTTACTGAAATCATAATATATGATACTGTAAAATATAAATT
Found at i:28587958 original size:33 final size:33
Alignment explanation
Indices: 28587919--28588028 Score: 127
Period size: 33 Copynumber: 3.3 Consensus size: 33
28587909 ATTATAAAGC
28587919 ATGTATAATTGACCTAAAATTAATTGTTGGTGT
1 ATGTATAATTGACCTAAAATTAATTGTTGGTGT
* *
28587952 ATGTATAATTGACCTAAAATTACTTGTTGGTTT
1 ATGTATAATTGACCTAAAATTAATTGTTGGTGT
* * *
28587985 AATGT-T-ATTGTCCCTAAAA-AACATTGCTGGTGT
1 -ATGTATAATTG-ACCTAAAATTA-ATTGTTGGTGT
28588018 ATGTATAATTG
1 ATGTATAATTG
28588029 TTGGTTTAAT
Statistics
Matches: 65, Mismatches: 7, Indels: 9
0.80 0.09 0.11
Matches are distributed among these distances:
32 9 0.14
33 48 0.74
34 8 0.12
ACGTcount: A:0.32, C:0.09, G:0.17, T:0.42
Consensus pattern (33 bp):
ATGTATAATTGACCTAAAATTAATTGTTGGTGT
Found at i:28588035 original size:51 final size:51
Alignment explanation
Indices: 28587975--28588128 Score: 283
Period size: 51 Copynumber: 3.0 Consensus size: 51
28587965 CTAAAATTAC
*
28587975 TTGTTGGTTTAATGTTATTGT-CCCTAAAAAACATTGCTGGTGTATGTATAA
1 TTGTTGGTTTAATGTTATT-TACCCTAAAAAACATTGTTGGTGTATGTATAA
28588026 TTGTTGGTTTAATGTTATTTACCCTAAAAAACATTGTTGGTGTATGTATAA
1 TTGTTGGTTTAATGTTATTTACCCTAAAAAACATTGTTGGTGTATGTATAA
28588077 TTGTTGGTTTAATGTTATTTACCCTAAAAAACATTGTTGGTGTATGTATAA
1 TTGTTGGTTTAATGTTATTTACCCTAAAAAACATTGTTGGTGTATGTATAA
28588128 T
1 T
28588129 CTTTTAATTT
Statistics
Matches: 101, Mismatches: 1, Indels: 2
0.97 0.01 0.02
Matches are distributed among these distances:
50 1 0.01
51 100 0.99
ACGTcount: A:0.29, C:0.08, G:0.18, T:0.45
Consensus pattern (51 bp):
TTGTTGGTTTAATGTTATTTACCCTAAAAAACATTGTTGGTGTATGTATAA
Found at i:28588306 original size:86 final size:86
Alignment explanation
Indices: 28588203--28588383 Score: 355
Period size: 86 Copynumber: 2.1 Consensus size: 86
28588193 TTCTCTCCAC
28588203 ATAA-AATTATATCAACATTAATACTTAACAAACAGGTTTCATGTTTATTATTAATTTCAAATTA
1 ATAATAATTATATCAACATTAATACTTAACAAACAGGTTTCATGTTTATTATTAATTTCAAATTA
28588267 TTAATATTAAAGATAAAAATT
66 TTAATATTAAAGATAAAAATT
28588288 ATAATAATTATATCAACATTAATACTTAACAAACAGGTTTCATGTTTATTATTAATTTCAAATTA
1 ATAATAATTATATCAACATTAATACTTAACAAACAGGTTTCATGTTTATTATTAATTTCAAATTA
28588353 TTAATATTAAAGATAAAAATT
66 TTAATATTAAAGATAAAAATT
28588374 ATAATAATTA
1 ATAATAATTA
28588384 CAATTATATT
Statistics
Matches: 95, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
85 4 0.04
86 91 0.96
ACGTcount: A:0.48, C:0.08, G:0.04, T:0.40
Consensus pattern (86 bp):
ATAATAATTATATCAACATTAATACTTAACAAACAGGTTTCATGTTTATTATTAATTTCAAATTA
TTAATATTAAAGATAAAAATT
Found at i:28592193 original size:10 final size:10
Alignment explanation
Indices: 28592178--28592212 Score: 70
Period size: 10 Copynumber: 3.5 Consensus size: 10
28592168 TCGAAAATTG
28592178 CAAAATTGTT
1 CAAAATTGTT
28592188 CAAAATTGTT
1 CAAAATTGTT
28592198 CAAAATTGTT
1 CAAAATTGTT
28592208 CAAAA
1 CAAAA
28592213 CCATGTCGAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 25 1.00
ACGTcount: A:0.46, C:0.11, G:0.09, T:0.34
Consensus pattern (10 bp):
CAAAATTGTT
Found at i:28592989 original size:18 final size:19
Alignment explanation
Indices: 28592966--28593009 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 19
28592956 CAGAAATTTC
*
28592966 TGTTTCTCTAGCA-TGTTA
1 TGTTTCTCTACCATTGTTA
* *
28592984 TGTTTCTGTACCATTTTTA
1 TGTTTCTCTACCATTGTTA
28593003 TGTTTCT
1 TGTTTCT
28593010 TTATTTTCTG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
18 11 0.50
19 11 0.50
ACGTcount: A:0.14, C:0.16, G:0.14, T:0.57
Consensus pattern (19 bp):
TGTTTCTCTACCATTGTTA
Found at i:28593025 original size:7 final size:7
Alignment explanation
Indices: 28593013--28593099 Score: 93
Period size: 7 Copynumber: 12.3 Consensus size: 7
28593003 TGTTTCTTTA
28593013 TTTTCTG
1 TTTTCTG
28593020 TTTTCTG
1 TTTTCTG
*
28593027 TTTTTTG
1 TTTTCTG
28593034 TTTTCTG
1 TTTTCTG
*
28593041 TTTTTTG
1 TTTTCTG
**
28593048 CATTCTG
1 TTTTCTG
*
28593055 TCTTCTG
1 TTTTCTG
*
28593062 TTTTCTA
1 TTTTCTG
*
28593069 TTTTTTG
1 TTTTCTG
28593076 TTTTCTG
1 TTTTCTG
*
28593083 TTTTGCTA
1 TTTT-CTG
28593091 TTTTCTG
1 TTTTCTG
28593098 TT
1 TT
28593100 GAATGAAGTG
Statistics
Matches: 64, Mismatches: 15, Indels: 2
0.79 0.19 0.02
Matches are distributed among these distances:
7 58 0.91
8 6 0.09
ACGTcount: A:0.03, C:0.13, G:0.13, T:0.71
Consensus pattern (7 bp):
TTTTCTG
Found at i:28593039 original size:21 final size:21
Alignment explanation
Indices: 28592998--28593086 Score: 97
Period size: 21 Copynumber: 4.2 Consensus size: 21
28592988 TCTGTACCAT
* *
28592998 TTTTATGTTTCTTTATTTTCTG
1 TTTTCTGTTT-TTTGTTTTCTG
28593020 TTTTCTGTTTTTTGTTTTCTG
1 TTTTCTGTTTTTTGTTTTCTG
* ** * *
28593041 TTTTTTGCATTCTGTCTTCTG
1 TTTTCTGTTTTTTGTTTTCTG
*
28593062 TTTTCTATTTTTTGTTTTCTG
1 TTTTCTGTTTTTTGTTTTCTG
28593083 TTTT
1 TTTT
28593087 GCTATTTTCT
Statistics
Matches: 54, Mismatches: 13, Indels: 1
0.79 0.19 0.01
Matches are distributed among these distances:
21 45 0.83
22 9 0.17
ACGTcount: A:0.04, C:0.11, G:0.11, T:0.73
Consensus pattern (21 bp):
TTTTCTGTTTTTTGTTTTCTG
Found at i:28593608 original size:100 final size:100
Alignment explanation
Indices: 28593501--28593865 Score: 685
Period size: 100 Copynumber: 3.6 Consensus size: 100
28593491 TAATATTAAA
**
28593501 AAATATATATATGTTAATATTTTTACAACATAATTTAACTTATTACTAATACATATATTGTTCGA
1 AAATATATATATGTTAATATTTTTACAATTTAATTTAACTTATTACTAATACATATATTGTTCGA
28593566 ATATAATTTTTTAAAATTTATATATTACATGACTT
66 ATATAATTTTTTAAAATTTATATATTACATGACTT
28593601 AAATATATATATGTTAATATTTTTACAATTTAATTTAACTTATTACTAATACATATATTGTTCGA
1 AAATATATATATGTTAATATTTTTACAATTTAATTTAACTTATTACTAATACATATATTGTTCGA
* * *
28593666 ATATAATTTTTCAAAATTTATATGTTACATTACTT
66 ATATAATTTTTTAAAATTTATATATTACATGACTT
28593701 AAATATATATATGTTAATATTTTTACAATTTAATTTAACTTATTACTAATACATATATTGTTCGA
1 AAATATATATATGTTAATATTTTTACAATTTAATTTAACTTATTACTAATACATATATTGTTCGA
28593766 ATATAATTTTTTAAAATTTATATATTACATGACTT
66 ATATAATTTTTTAAAATTTATATATTACATGACTT
28593801 AAATATATATATGTTAATATTTTTACAATTTAATTTAACTTATTACTAATACATATATTGTTCGA
1 AAATATATATATGTTAATATTTTTACAATTTAATTTAACTTATTACTAATACATATATTGTTCGA
28593866 TATGTTCTGT
Statistics
Matches: 257, Mismatches: 8, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
100 257 1.00
ACGTcount: A:0.40, C:0.08, G:0.04, T:0.48
Consensus pattern (100 bp):
AAATATATATATGTTAATATTTTTACAATTTAATTTAACTTATTACTAATACATATATTGTTCGA
ATATAATTTTTTAAAATTTATATATTACATGACTT
Found at i:28593609 original size:52 final size:52
Alignment explanation
Indices: 28593553--28593815 Score: 231
Period size: 53 Copynumber: 5.2 Consensus size: 52
28593543 TTACTAATAC
*
28593553 ATATAT-TGTTCGAATATAATTTTTTAAAATTTATATATTACATGACTTAAAT
1 ATATATATGTTCGAATATAATTTTTTAAAATTTATAT-TTACATTACTTAAAT
*
28593605 ATATATATGTT---A-AT-A-TTTTTACAATTTA-ATTTA-ACTTA-TTACTAAT
1 ATATATATGTTCGAATATAATTTTTTAAAATTTATATTTACA-TTACTTA--AAT
* *
28593651 ACATATATTGTTCGAATATAATTTTTCAAAATTTATATGTTACATTACTTAAAT
1 ATATATA-TGTTCGAATATAATTTTTTAAAATTTATAT-TTACATTACTTAAAT
*
28593705 ATATATATGTT---A-AT-A-TTTTTACAATTTA-ATTTA-ACTTA-TTACTAAT
1 ATATATATGTTCGAATATAATTTTTTAAAATTTATATTTACA-TTACTTA--AAT
* *
28593751 ACATATATTGTTCGAATATAATTTTTTAAAATTTATATATTACATGACTTAAAT
1 ATATATA-TGTTCGAATATAATTTTTTAAAATTTATAT-TTACATTACTTAAAT
28593805 ATATATATGTT
1 ATATATATGTT
28593816 AATATTTTTA
Statistics
Matches: 170, Mismatches: 12, Indels: 57
0.71 0.05 0.24
Matches are distributed among these distances:
44 8 0.05
45 11 0.06
46 22 0.13
47 31 0.18
48 2 0.01
49 4 0.02
50 4 0.02
51 4 0.02
52 8 0.05
53 35 0.21
54 22 0.13
55 11 0.06
56 8 0.05
ACGTcount: A:0.40, C:0.07, G:0.05, T:0.49
Consensus pattern (52 bp):
ATATATATGTTCGAATATAATTTTTTAAAATTTATATTTACATTACTTAAAT
Found at i:28593624 original size:48 final size:46
Alignment explanation
Indices: 28593569--28593837 Score: 212
Period size: 47 Copynumber: 5.5 Consensus size: 46
28593559 TGTTCGAATA
*
28593569 TAAT-TTTTTAAAATTTATATATTACATGACTTAAATATATATATGT
1 TAATATTTTTAAAATTTATAT-TTACATTACTTAAATATATATATGT
* *
28593615 TAATATTTTTACAATTTA-ATTTA-ACTTA-TTACTAATACATATATTGT
1 TAATATTTTTAAAATTTATATTTACA-TTACTTA--AATATATATA-TGT
28593662 TCGAATATAATTTTTCAAAATTTATATGTTACATTACTTAAATATATATATGT
1 T---A-AT-ATTTTT-AAAATTTATAT-TTACATTACTTAAATATATATATGT
* *
28593715 TAATATTTTTACAATTTA-ATTTA-ACTTA-TTACTAATACATATATTGT
1 TAATATTTTTAAAATTTATATTTACA-TTACTTA--AATATATATA-TGT
*
28593762 TCGAATATAATTTTTTAAAATTTATATATTACATGACTTAAATATATATATGT
1 T---A-AT-A-TTTTTAAAATTTATAT-TTACATTACTTAAATATATATATGT
*
28593815 TAATATTTTTACAATTTA-ATTTA
1 TAATATTTTTAAAATTTATATTTA
28593838 ACTTATTACT
Statistics
Matches: 183, Mismatches: 11, Indels: 59
0.72 0.04 0.23
Matches are distributed among these distances:
44 8 0.04
45 14 0.08
46 28 0.15
47 39 0.21
48 7 0.04
49 4 0.02
50 4 0.02
51 4 0.02
52 7 0.04
53 27 0.15
54 22 0.12
55 11 0.06
56 8 0.04
ACGTcount: A:0.40, C:0.07, G:0.04, T:0.50
Consensus pattern (46 bp):
TAATATTTTTAAAATTTATATTTACATTACTTAAATATATATATGT
Found at i:28596596 original size:65 final size:65
Alignment explanation
Indices: 28596491--28596660 Score: 218
Period size: 66 Copynumber: 2.6 Consensus size: 65
28596481 GAGCAAATTA
* * * *
28596491 CACAACTTAAAGCGGAGGCAACATCGAGAGAAGCTGAGGTTC-A-AAAAGATATGAAGAACTCCA
1 CACAACTTAAAGCAGATGCAGCAGCGAGAGAAGCTGAGGTTCAACAAAAG-TATGAAGAACTCCA
28596554 G
65 G
*
28596555 CTACAACTGAAAGCAGATGCAGCAGCGAGAGAAGCTGAGGTTCAACAAAAGTATGAAGAACTCCA
1 C-ACAACTTAAAGCAGATGCAGCAGCGAGAGAAGCTGAGGTTCAACAAAAGTATGAAGAACTCCA
28596620 G
65 G
* * * *
28596621 CAGCAGCTTAAAGCAGATGCGGCAGCAAGAGAAGCAGAGG
1 CA-CAACTTAAAGCAGATGCAGCAGCGAGAGAAGCTGAGG
28596661 CGGCAGCGAG
Statistics
Matches: 92, Mismatches: 10, Indels: 6
0.85 0.09 0.06
Matches are distributed among these distances:
64 1 0.01
65 37 0.40
66 49 0.53
67 5 0.05
ACGTcount: A:0.41, C:0.19, G:0.28, T:0.12
Consensus pattern (65 bp):
CACAACTTAAAGCAGATGCAGCAGCGAGAGAAGCTGAGGTTCAACAAAAGTATGAAGAACTCCAG
Found at i:28596657 original size:21 final size:21
Alignment explanation
Indices: 28596631--28596703 Score: 74
Period size: 21 Copynumber: 3.5 Consensus size: 21
28596621 CAGCAGCTTA
*
28596631 AAGCAGATGCGGCAGCAAGAG
1 AAGCAGAGGCGGCAGCAAGAG
*
28596652 AAGCAGAGGCGGCAGCGAGAG
1 AAGCAGAGGCGGCAGCAAGAG
* * ** * *
28596673 AAGTACAGGCTACAGCGAGGG
1 AAGCAGAGGCGGCAGCAAGAG
28596694 AAGCAGAGGC
1 AAGCAGAGGC
28596704 TAAAGCGAGA
Statistics
Matches: 43, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 43 1.00
ACGTcount: A:0.36, C:0.19, G:0.41, T:0.04
Consensus pattern (21 bp):
AAGCAGAGGCGGCAGCAAGAG
Found at i:28596697 original size:42 final size:42
Alignment explanation
Indices: 28596651--28596743 Score: 132
Period size: 42 Copynumber: 2.2 Consensus size: 42
28596641 GGCAGCAAGA
**
28596651 GAAGCAGAGGCGGCAGCGAGAGAAGTACAGGCTACAGCGAGG
1 GAAGCAGAGGCGAAAGCGAGAGAAGTACAGGCTACAGCGAGG
* * * *
28596693 GAAGCAGAGGCTAAAGCGAGAGAAGTAGAGGCTGCAGTGAGG
1 GAAGCAGAGGCGAAAGCGAGAGAAGTACAGGCTACAGCGAGG
28596735 GAAGCAGAG
1 GAAGCAGAG
28596744 CAGCGTCAAA
Statistics
Matches: 45, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
42 45 1.00
ACGTcount: A:0.35, C:0.15, G:0.43, T:0.06
Consensus pattern (42 bp):
GAAGCAGAGGCGAAAGCGAGAGAAGTACAGGCTACAGCGAGG
Found at i:28596704 original size:21 final size:21
Alignment explanation
Indices: 28596643--28596743 Score: 103
Period size: 21 Copynumber: 4.8 Consensus size: 21
28596633 GCAGATGCGG
* **
28596643 CAGCAAGAGAAGCAGAGGCGG
1 CAGCGAGAGAAGCAGAGGCTA
* *
28596664 CAGCGAGAGAAGTACAGGCTA
1 CAGCGAGAGAAGCAGAGGCTA
*
28596685 CAGCGAGGGAAGCAGAGGCTA
1 CAGCGAGAGAAGCAGAGGCTA
* * *
28596706 AAGCGAGAGAAGTAGAGGCTG
1 CAGCGAGAGAAGCAGAGGCTA
* *
28596727 CAGTGAGGGAAGCAGAG
1 CAGCGAGAGAAGCAGAG
28596744 CAGCGTCAAA
Statistics
Matches: 64, Mismatches: 16, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
21 64 1.00
ACGTcount: A:0.37, C:0.16, G:0.42, T:0.06
Consensus pattern (21 bp):
CAGCGAGAGAAGCAGAGGCTA
Found at i:28596928 original size:10 final size:9
Alignment explanation
Indices: 28596906--28596959 Score: 51
Period size: 9 Copynumber: 6.2 Consensus size: 9
28596896 TAATACGATT
*
28596906 TTTATTTTA
1 TTTATTATA
28596915 TTTATTGATA
1 TTTATT-ATA
28596925 TTTATTATA
1 TTTATTATA
*
28596934 -TTATT-TG
1 TTTATTATA
*
28596941 TTTAATATA
1 TTTATTATA
28596950 TTTATT-TA
1 TTTATTATA
28596958 TT
1 TT
28596960 ACTTTTGGCT
Statistics
Matches: 37, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
7 1 0.03
8 13 0.35
9 15 0.41
10 8 0.22
ACGTcount: A:0.28, C:0.00, G:0.04, T:0.69
Consensus pattern (9 bp):
TTTATTATA
Found at i:28597224 original size:43 final size:43
Alignment explanation
Indices: 28597050--28597226 Score: 122
Period size: 43 Copynumber: 4.1 Consensus size: 43
28597040 ATCTGCCAAA
** * * *** *
28597050 TTTAGTGGCGTTTTTTAAAAAAACGCCACTAAAGGTGTTGGCC
1 TTTAGTGGCGTTTTTGGAAAAAACGCCGCTAAAGATCAGGGTC
** * *
28597093 TTTAGTGGCGTTTTTGGTCAAAGCGCCGCTATAGATCAGGGTC
1 TTTAGTGGCGTTTTTGGAAAAAACGCCGCTAAAGATCAGGGTC
* * ** * * * ** *
28597136 TATT-GCGGCGTTTTAGGGGAAAGCGCTGCTAAAGACCCTGATC
1 T-TTAGTGGCGTTTTTGGAAAAAACGCCGCTAAAGATCAGGGTC
* *
28597179 TTTAGTGGCGTTTTTGCAAAAAACGCCGCTAAAGATTAGGGTC
1 TTTAGTGGCGTTTTTGGAAAAAACGCCGCTAAAGATCAGGGTC
28597222 TTTAG
1 TTTAG
28597227 CGACGCTTCC
Statistics
Matches: 98, Mismatches: 34, Indels: 4
0.72 0.25 0.03
Matches are distributed among these distances:
42 2 0.02
43 94 0.96
44 2 0.02
ACGTcount: A:0.24, C:0.18, G:0.27, T:0.31
Consensus pattern (43 bp):
TTTAGTGGCGTTTTTGGAAAAAACGCCGCTAAAGATCAGGGTC
Found at i:28597387 original size:31 final size:31
Alignment explanation
Indices: 28597349--28597425 Score: 145
Period size: 31 Copynumber: 2.5 Consensus size: 31
28597339 CGGCGCTTTT
*
28597349 AAAAGCGCCGCTACAAGTATCTGCGGCGCTA
1 AAAAGCGCCGCTAAAAGTATCTGCGGCGCTA
28597380 AAAAGCGCCGCTAAAAGTATCTGCGGCGCTA
1 AAAAGCGCCGCTAAAAGTATCTGCGGCGCTA
28597411 AAAAGCGCCGCTAAA
1 AAAAGCGCCGCTAAA
28597426 GGCCTAAAAA
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
31 45 1.00
ACGTcount: A:0.34, C:0.27, G:0.25, T:0.14
Consensus pattern (31 bp):
AAAAGCGCCGCTAAAAGTATCTGCGGCGCTA
Found at i:28597393 original size:13 final size:13
Alignment explanation
Indices: 28597375--28597448 Score: 50
Period size: 13 Copynumber: 5.6 Consensus size: 13
28597365 GTATCTGCGG
28597375 CGCTAAAAAGCGC
1 CGCTAAAAAGCGC
*
28597388 CGCTAAAAGTATCTGCGG
1 CGCTAAAA--A---GCGC
28597406 CGCTAAAAAGCGC
1 CGCTAAAAAGCGC
28597419 CGCT--AAAG-G-
1 CGCTAAAAAGCGC
28597428 C-CTAAAAAAGCGC
1 CGCT-AAAAAGCGC
28597441 CGCTAAAA
1 CGCTAAAA
28597449 GCCTGTTTTG
Statistics
Matches: 48, Mismatches: 2, Indels: 22
0.67 0.03 0.31
Matches are distributed among these distances:
8 2 0.04
9 1 0.02
10 1 0.02
11 8 0.17
12 1 0.02
13 20 0.42
14 2 0.04
15 1 0.02
16 1 0.02
18 11 0.23
ACGTcount: A:0.38, C:0.27, G:0.23, T:0.12
Consensus pattern (13 bp):
CGCTAAAAAGCGC
Found at i:28597411 original size:18 final size:18
Alignment explanation
Indices: 28597357--28597413 Score: 61
Period size: 18 Copynumber: 3.4 Consensus size: 18
28597347 TTAAAAGCGC
*
28597357 CGCTACAAGTATCTGCGG
1 CGCTAAAAGTATCTGCGG
*
28597375 CGCTAAAA--A---GCGC
1 CGCTAAAAGTATCTGCGG
28597388 CGCTAAAAGTATCTGCGG
1 CGCTAAAAGTATCTGCGG
28597406 CGCTAAAA
1 CGCTAAAA
28597414 AGCGCCGCTA
Statistics
Matches: 31, Mismatches: 3, Indels: 10
0.70 0.07 0.23
Matches are distributed among these distances:
13 11 0.35
15 1 0.03
16 1 0.03
18 18 0.58
ACGTcount: A:0.32, C:0.26, G:0.25, T:0.18
Consensus pattern (18 bp):
CGCTAAAAGTATCTGCGG
Found at i:28597438 original size:22 final size:22
Alignment explanation
Indices: 28597410--28597452 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
28597400 CTGCGGCGCT
*
28597410 AAAAAGCGCCGCTAAAGGCCTA
1 AAAAAGCGCCGCTAAAAGCCTA
28597432 AAAAAGCGCCGCTAAAAGCCT
1 AAAAAGCGCCGCTAAAAGCCT
28597453 GTTTTGGTGT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.42, C:0.28, G:0.21, T:0.09
Consensus pattern (22 bp):
AAAAAGCGCCGCTAAAAGCCTA
Found at i:28597772 original size:11 final size:11
Alignment explanation
Indices: 28597756--28597789 Score: 52
Period size: 11 Copynumber: 3.1 Consensus size: 11
28597746 GTAATAATTT
28597756 ATAAATTTTTA
1 ATAAATTTTTA
28597767 ATAAATATTTT-
1 ATAAAT-TTTTA
28597778 ATAAATTTTTA
1 ATAAATTTTTA
28597789 A
1 A
28597790 ATTTTTATAA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
10 4 0.19
11 13 0.62
12 4 0.19
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (11 bp):
ATAAATTTTTA
Found at i:28597778 original size:22 final size:22
Alignment explanation
Indices: 28597748--28597789 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
28597738 TAATTTTTGT
28597748 AATAATTTATAAATTTTTAATA
1 AATAATTTATAAATTTTTAATA
*
28597770 AATATTTTATAAATTTTTAA
1 AATAATTTATAAATTTTTAA
28597790 ATTTTTATAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (22 bp):
AATAATTTATAAATTTTTAATA
Found at i:28598065 original size:31 final size:29
Alignment explanation
Indices: 28597990--28598068 Score: 86
Period size: 29 Copynumber: 2.7 Consensus size: 29
28597980 TGTTTGGCTC
* *
28597990 ATGTTACATTTTAGTCACTTATGTTTGAA
1 ATGTAACATTTTAGTCACTTATGTTTCAA
* * *
28598019 ATGTTACGTTTTAGTCACTTATGTTATCACG
1 ATGTAACATTTTAGTCACTTATGTT-TCA-A
*
28598050 TTGTAACATTTTAGTCACT
1 ATGTAACATTTTAGTCACT
28598069 GAGCCGTTAG
Statistics
Matches: 42, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
29 24 0.57
30 2 0.05
31 16 0.38
ACGTcount: A:0.25, C:0.14, G:0.14, T:0.47
Consensus pattern (29 bp):
ATGTAACATTTTAGTCACTTATGTTTCAA
Found at i:28600880 original size:27 final size:28
Alignment explanation
Indices: 28600843--28600902 Score: 97
Period size: 28 Copynumber: 2.2 Consensus size: 28
28600833 CTATTTAGTA
28600843 ACAGT-ACAGTGT-GGCCTTAGCCCAAT
1 ACAGTAACAGTGTGGGCCTTAGCCCAAT
*
28600869 ACAGTAACAGTGTGGGCCTTAGCCCATT
1 ACAGTAACAGTGTGGGCCTTAGCCCAAT
28600897 ACAGTA
1 ACAGTA
28600903 TCAATACAGT
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
26 5 0.16
27 7 0.23
28 19 0.61
ACGTcount: A:0.28, C:0.25, G:0.23, T:0.23
Consensus pattern (28 bp):
ACAGTAACAGTGTGGGCCTTAGCCCAAT
Found at i:28601043 original size:26 final size:27
Alignment explanation
Indices: 28601014--28601083 Score: 90
Period size: 26 Copynumber: 2.7 Consensus size: 27
28601004 CACCAATATT
28601014 GCAGCAAAGCTGCCAGTAAT-AGTAAC
1 GCAGCAAAGCTGCCAGTAATCAGTAAC
* *
28601040 GCAGCAAAACTGCCAGT-ATCAGTATC
1 GCAGCAAAGCTGCCAGTAATCAGTAAC
* *
28601066 ACAGCAAAGCTGCTAGTA
1 GCAGCAAAGCTGCCAGTA
28601084 CAGTATACTT
Statistics
Matches: 37, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
25 2 0.05
26 35 0.95
ACGTcount: A:0.37, C:0.24, G:0.21, T:0.17
Consensus pattern (27 bp):
GCAGCAAAGCTGCCAGTAATCAGTAAC
Found at i:28602958 original size:15 final size:15
Alignment explanation
Indices: 28602938--28602972 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
28602928 ACAAGGTCAT
* *
28602938 CGATGATATTAATGA
1 CGATGACATGAATGA
28602953 CGATGACATGAATGA
1 CGATGACATGAATGA
28602968 CGATG
1 CGATG
28602973 GAAACATTAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.37, C:0.11, G:0.26, T:0.26
Consensus pattern (15 bp):
CGATGACATGAATGA
Found at i:28605173 original size:62 final size:62
Alignment explanation
Indices: 28605072--28605304 Score: 335
Period size: 62 Copynumber: 3.7 Consensus size: 62
28605062 CAATGTACCT
28605072 AATTTATATTACAAAGTTTGTTCCAAGTTTTAATGTTGTAATGTATTTAATTTATATAACAA
1 AATTTATATTACAAAGTTTGTTCCAAGTTTTAATGTTGTAATGTATTTAATTTATATAACAA
* *
28605134 AATTTATATTACAAAGTTTGTTCCAAGTTTTAATATTGTAATGTATTTAATTTATATTACAA
1 AATTTATATTACAAAGTTTGTTCCAAGTTTTAATGTTGTAATGTATTTAATTTATATAACAA
* **
28605196 AATTTATATTACAAAGTTTGTTCCAAGTTTTAATGTTGTAATGT-TGTAATGTTGCA-ATTAATT
1 AATTTATATTACAAAGTTTGTTCCAAGTTTTAATGTTGTAATGTATTTAAT-TT--ATA-TAACA
*
28605259 T
62 A
**
28605260 AATTTATGACCACAAAGTTTGTTCCAAGTTTTAATGTTGTAATGT
1 AATTTAT-ATTACAAAGTTTGTTCCAAGTTTTAATGTTGTAATGT
28605305 TATAATGCTA
Statistics
Matches: 156, Mismatches: 10, Indels: 7
0.90 0.06 0.04
Matches are distributed among these distances:
61 5 0.03
62 105 0.67
63 1 0.01
64 10 0.06
65 35 0.22
ACGTcount: A:0.34, C:0.07, G:0.12, T:0.47
Consensus pattern (62 bp):
AATTTATATTACAAAGTTTGTTCCAAGTTTTAATGTTGTAATGTATTTAATTTATATAACAA
Found at i:28605201 original size:14 final size:14
Alignment explanation
Indices: 28605182--28605210 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
28605172 TAATGTATTT
28605182 AATTTATATTACAA
1 AATTTATATTACAA
28605196 AATTTATATTACAA
1 AATTTATATTACAA
28605210 A
1 A
28605211 GTTTGTTCCA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.52, C:0.07, G:0.00, T:0.41
Consensus pattern (14 bp):
AATTTATATTACAA
Found at i:28605260 original size:73 final size:67
Alignment explanation
Indices: 28605206--28605363 Score: 243
Period size: 65 Copynumber: 2.4 Consensus size: 67
28605196 AATTTATATT
* * *
28605206 ACAAAGTTTGTTCCAAGTTTTAATGTTGTAATGTTGTAATGTTGCAATT-A-ATTTAATTTATGA
1 ACAAAGTTTGTTCCAAGTTTTAATGTTGTAATGTTATAATGCTACAATTAATATTTAATTTATGA
28605269 CC
66 CC
*
28605271 ACAAAGTTTGTTCCAAGTTTTAATGTTGTAATGTTATAATGCTACAATT-A-ATCTAATTTATGA
1 ACAAAGTTTGTTCCAAGTTTTAATGTTGTAATGTTATAATGCTACAATTAATATTTAATTTATGA
28605334 CC
66 CC
*
28605336 ACAAAGTTTGTTCTAAGTTTTAATGTTG
1 ACAAAGTTTGTTCCAAGTTTTAATGTTG
28605364 CAATTAATTT
Statistics
Matches: 88, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
65 88 1.00
ACGTcount: A:0.32, C:0.10, G:0.15, T:0.44
Consensus pattern (67 bp):
ACAAAGTTTGTTCCAAGTTTTAATGTTGTAATGTTATAATGCTACAATTAATATTTAATTTATGA
CC
Found at i:28605291 original size:65 final size:61
Alignment explanation
Indices: 28605072--28605386 Score: 307
Period size: 62 Copynumber: 5.0 Consensus size: 61
28605062 CAATGTACCT
** *
28605072 AATTTATATTACAAAGTTTGTTCCAAGTTTTAATGTTGTAATGTATTTAATTT-ATATAACAA
1 AATTTATACCACAAAGTTTGTTCCAAGTTTTAATGTTGTAATGTATTTAATTTAAT-TAA-TA
** *
28605134 AATTTATATTACAAAGTTTGTTCCAAGTTTTAATATTGTAATGTATTTAATTTATATTACA-A
1 AATTTATACCACAAAGTTTGTTCCAAGTTTTAATGTTGTAATGTATTTAATTTA-ATTA-ATA
** * *
28605196 AATTTATATTACAAAGTTTGTTCCAAGTTTTAATGTTGTAATGT-TGTAATGTTGCAATTAATTT
1 AATTTATACCACAAAGTTTGTTCCAAGTTTTAATGTTGTAATGTATTTAAT-TT--AATTAA-TA
* *
28605260 AATTTATGACCACAAAGTTTGTTCCAAGTTTTAATGTTGTAATGT-TATAATGCTACAATTAATC
1 AATTTAT-ACCACAAAGTTTGTTCCAAGTTTTAATGTTGTAATGTATTTAAT--T-TAATTAAT-
*
28605324 T
61 A
* * * *
28605325 AATTTATGACCACAAAGTTTGTTCTAAGTTTTAATGTTGCAAT-TAATTTAATTAAATAAATA
1 AATTTAT-ACCACAAAGTTTGTTCCAAGTTTTAATGTTGTAATGT-ATTTAATTTAATTAATA
28605387 CAAAGATTAT
Statistics
Matches: 224, Mismatches: 15, Indels: 28
0.84 0.06 0.10
Matches are distributed among these distances:
61 5 0.02
62 99 0.44
63 12 0.05
64 14 0.06
65 88 0.39
66 6 0.03
ACGTcount: A:0.36, C:0.08, G:0.11, T:0.45
Consensus pattern (61 bp):
AATTTATACCACAAAGTTTGTTCCAAGTTTTAATGTTGTAATGTATTTAATTTAATTAATA
Found at i:28608012 original size:26 final size:26
Alignment explanation
Indices: 28607983--28608039 Score: 62
Period size: 26 Copynumber: 2.2 Consensus size: 26
28607973 AATCCGAATT
28607983 AAATCAACAATAA-TAACAACAAAAA
1 AAATCAACAATAATTAACAACAAAAA
* * * *
28608008 CAAATTAACATTAATTTATAACAAAAA
1 -AAATCAACAATAATTAACAACAAAAA
28608035 AAATC
1 AAATC
28608040 TTTTCTTAAA
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
26 15 0.60
27 10 0.40
ACGTcount: A:0.65, C:0.14, G:0.00, T:0.21
Consensus pattern (26 bp):
AAATCAACAATAATTAACAACAAAAA
Found at i:28608167 original size:5 final size:5
Alignment explanation
Indices: 28608157--28608181 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
28608147 TTCTTTCTTT
28608157 TTCCC TTCCC TTCCC TTCCC TTCCC
1 TTCCC TTCCC TTCCC TTCCC TTCCC
28608182 GCCCTCTCCT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.00, C:0.60, G:0.00, T:0.40
Consensus pattern (5 bp):
TTCCC
Found at i:28609865 original size:21 final size:23
Alignment explanation
Indices: 28609841--28609912 Score: 60
Period size: 26 Copynumber: 3.1 Consensus size: 23
28609831 AATCTTAATT
* *
28609841 TATTTGTA-AAATTATTAAA-AA
1 TATTTGTATAAAATAATAAATAA
*
28609862 TATTTTTATAAAATAATAAATAA
1 TATTTGTATAAAATAATAAATAA
28609885 TATTTTAGTAATCAAAATAA-AAATAA
1 TA-TTT-GT-AT-AAAATAATAAATAA
28609911 TA
1 TA
28609913 AATATTATTT
Statistics
Matches: 41, Mismatches: 4, Indels: 7
0.79 0.08 0.13
Matches are distributed among these distances:
21 7 0.17
22 9 0.22
23 4 0.10
24 3 0.07
25 1 0.02
26 10 0.24
27 7 0.17
ACGTcount: A:0.56, C:0.01, G:0.03, T:0.40
Consensus pattern (23 bp):
TATTTGTATAAAATAATAAATAA
Found at i:28609874 original size:23 final size:23
Alignment explanation
Indices: 28609847--28609912 Score: 64
Period size: 23 Copynumber: 2.7 Consensus size: 23
28609837 AATTTATTTG
*
28609847 TAAAATTATTAAA-AATATTTTTA
1 TAAAA-TAATAAATAATATTTTTA
28609870 TAAAATAATAAATAATATTTTAGTAA
1 TAAAATAATAAATAATATTTT--T-A
28609896 TCAAAATAA-AAATAATA
1 T-AAAATAATAAATAATA
28609913 AATATTATTT
Statistics
Matches: 37, Mismatches: 1, Indels: 7
0.82 0.02 0.16
Matches are distributed among these distances:
22 6 0.16
23 13 0.35
25 1 0.03
26 10 0.27
27 7 0.19
ACGTcount: A:0.59, C:0.02, G:0.02, T:0.38
Consensus pattern (23 bp):
TAAAATAATAAATAATATTTTTA
Found at i:28610508 original size:14 final size:14
Alignment explanation
Indices: 28610477--28610507 Score: 55
Period size: 13 Copynumber: 2.3 Consensus size: 14
28610467 TAATTTGTTA
28610477 TTTTATATTAATTT
1 TTTTATATTAATTT
28610491 TTTTATA-TAATTT
1 TTTTATATTAATTT
28610504 TTTT
1 TTTT
28610508 TTCACCCACA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 10 0.59
14 7 0.41
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (14 bp):
TTTTATATTAATTT
Found at i:28615288 original size:11 final size:11
Alignment explanation
Indices: 28615261--28615293 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
28615251 TTTTTTTTTC
28615261 AAAATTA-AAA
1 AAAATTATAAA
*
28615271 GAAATTATAAA
1 AAAATTATAAA
28615282 AAAATTATAAA
1 AAAATTATAAA
28615293 A
1 A
28615294 GTATACGGAG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
10 6 0.30
11 14 0.70
ACGTcount: A:0.73, C:0.00, G:0.03, T:0.24
Consensus pattern (11 bp):
AAAATTATAAA
Found at i:28615969 original size:16 final size:16
Alignment explanation
Indices: 28615926--28615970 Score: 60
Period size: 16 Copynumber: 3.0 Consensus size: 16
28615916 GTAGCACATG
*
28615926 GTATCATAAACATACA
1 GTATCATAAATATACA
28615942 GTAT-AT--ATATACA
1 GTATCATAAATATACA
28615955 GTATCATAAATATACA
1 GTATCATAAATATACA
28615971 ATCGACTTAA
Statistics
Matches: 25, Mismatches: 1, Indels: 6
0.78 0.03 0.19
Matches are distributed among these distances:
13 10 0.40
14 2 0.08
15 2 0.08
16 11 0.44
ACGTcount: A:0.49, C:0.13, G:0.07, T:0.31
Consensus pattern (16 bp):
GTATCATAAATATACA
Found at i:28617320 original size:12 final size:12
Alignment explanation
Indices: 28617299--28617327 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
28617289 TATTTCAGAA
28617299 GATG-AAAACTT
1 GATGAAAAACTT
28617310 GATGAAAAACTT
1 GATGAAAAACTT
28617322 GATGAA
1 GATGAA
28617328 TGAATGAACA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 4 0.24
12 13 0.76
ACGTcount: A:0.48, C:0.07, G:0.21, T:0.24
Consensus pattern (12 bp):
GATGAAAAACTT
Found at i:28618833 original size:31 final size:31
Alignment explanation
Indices: 28618795--28618861 Score: 100
Period size: 31 Copynumber: 2.2 Consensus size: 31
28618785 TTTTTAAACT
28618795 AATTTGACCATCAACCTTTTA-AAACGAGTTG
1 AATTTGACCATCAACCTTTTAGAAA-GAGTTG
* *
28618826 AATTTGACTATTAACCTTTTAGAAAGAGTTG
1 AATTTGACCATCAACCTTTTAGAAAGAGTTG
28618857 AATTT
1 AATTT
28618862 TTTTTTTTAA
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
31 30 0.91
32 3 0.09
ACGTcount: A:0.36, C:0.13, G:0.13, T:0.37
Consensus pattern (31 bp):
AATTTGACCATCAACCTTTTAGAAAGAGTTG
Found at i:28620263 original size:16 final size:16
Alignment explanation
Indices: 28620242--28620275 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
28620232 TACTTAAAAG
28620242 TTAAAACTAATTGTTA
1 TTAAAACTAATTGTTA
*
28620258 TTAAAATTAATTGTTA
1 TTAAAACTAATTGTTA
28620274 TT
1 TT
28620276 GACTTTATAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.41, C:0.03, G:0.06, T:0.50
Consensus pattern (16 bp):
TTAAAACTAATTGTTA
Done.