Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: chr9
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: 38630433
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 2298367 characters in sequence are not A, C, G, or T
File 22 of 97
Found at i:9600570 original size:30 final size:30
Alignment explanation
Indices: 9600530--9600599 Score: 131
Period size: 30 Copynumber: 2.3 Consensus size: 30
9600520 TAAATCGTAT
*
9600530 ATCTTAATATGTTAACCATATTAGATCATA
1 ATCTTCATATGTTAACCATATTAGATCATA
9600560 ATCTTCATATGTTAACCATATTAGATCATA
1 ATCTTCATATGTTAACCATATTAGATCATA
9600590 ATCTTCATAT
1 ATCTTCATAT
9600600 TGCCTTGACT
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
30 39 1.00
ACGTcount: A:0.37, C:0.16, G:0.06, T:0.41
Consensus pattern (30 bp):
ATCTTCATATGTTAACCATATTAGATCATA
Found at i:9616652 original size:6 final size:6
Alignment explanation
Indices: 9616641--9616669 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
9616631 AGACTACAGA
9616641 AGGTGG AGGTGG AGGTGG AGGTGG AGGTG
1 AGGTGG AGGTGG AGGTGG AGGTGG AGGTG
9616670 CCCGACAAGT
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:0.17, C:0.00, G:0.66, T:0.17
Consensus pattern (6 bp):
AGGTGG
Found at i:9617386 original size:23 final size:22
Alignment explanation
Indices: 9617360--9617403 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 22
9617350 AAATTTATAA
9617360 AAATATAAAAAATAATAAAATTT
1 AAATATAAAAAATAA-AAAATTT
* *
9617383 AAATTTAAATAATAAAAAATT
1 AAATATAAAAAATAAAAAATT
9617404 CAATATTAAC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 6 0.32
23 13 0.68
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (22 bp):
AAATATAAAAAATAAAAAATTT
Found at i:9617722 original size:12 final size:13
Alignment explanation
Indices: 9617699--9617735 Score: 51
Period size: 12 Copynumber: 3.0 Consensus size: 13
9617689 TTTTTTATAA
*
9617699 ATTAATATAATAT
1 ATTAAAATAATAT
9617712 A-TAAAATAATAT
1 ATTAAAATAATAT
9617724 ATTAAAA-AATAT
1 ATTAAAATAATAT
9617736 TACAAATTAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
12 16 0.73
13 6 0.27
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (13 bp):
ATTAAAATAATAT
Found at i:9617779 original size:18 final size:19
Alignment explanation
Indices: 9617751--9617801 Score: 61
Period size: 18 Copynumber: 2.7 Consensus size: 19
9617741 ATTAATTAAT
*
9617751 AATTATAATTTTATGA-ATG
1 AATT-TAATTTTATAATATG
9617770 AATTTAA-TTTATAATATG
1 AATTTAATTTTATAATATG
9617788 AATTTATATTTTAT
1 AATTTA-ATTTTAT
9617802 TACATAAAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
17 6 0.21
18 12 0.43
19 5 0.18
20 5 0.18
ACGTcount: A:0.41, C:0.00, G:0.06, T:0.53
Consensus pattern (19 bp):
AATTTAATTTTATAATATG
Found at i:9619765 original size:26 final size:26
Alignment explanation
Indices: 9619740--9619987 Score: 113
Period size: 26 Copynumber: 10.3 Consensus size: 26
9619730 TTGGATATTA
*
9619740 CGTGACTAATTTTTGATAAGGCATTA
1 CGTGACTAATTTTTGATAAGGCATTG
* * *
9619766 CG-CACTAGTTTCTGATAAGGCATTG
1 CGTGACTAATTTTTGATAAGGCATTG
* * *
9619791 CATGACT-A--GTTAATAA-GCATTG
1 CGTGACTAATTTTTGATAAGGCATTG
* * *
9619813 CGTGACTGA-CTTTG----GGTATTG
1 CGTGACTAATTTTTGATAAGGCATTG
* * * *
9619834 CGTGACTAGTTTCTAATAAGACATTG
1 CGTGACTAATTTTTGATAAGGCATTG
* * *
9619860 CGTGACTAGTTTCTGATAAGGCATTA
1 CGTGACTAATTTTTGATAAGGCATTG
* * * *
9619886 CGTGATTAGTTTCTGATAAGGTATTG
1 CGTGACTAATTTTTGATAAGGCATTG
* *
9619912 CATGACT-A--GTTGAT-AGGCATTG
1 CGTGACTAATTTTTGATAAGGCATTG
*
9619934 CGTGACT--TATTTG-TAAGGCATTG
1 CGTGACTAATTTTTGATAAGGCATTG
* * *
9619957 CATGACT-A-GTTTG-TAAGGCATTA
1 CGTGACTAATTTTTGATAAGGCATTG
9619980 CGTGACTA
1 CGTGACTA
9619988 GTTCGTAAGG
Statistics
Matches: 169, Mismatches: 39, Indels: 30
0.71 0.16 0.13
Matches are distributed among these distances:
21 12 0.07
22 28 0.17
23 46 0.27
24 2 0.01
25 20 0.12
26 61 0.36
ACGTcount: A:0.27, C:0.14, G:0.24, T:0.35
Consensus pattern (26 bp):
CGTGACTAATTTTTGATAAGGCATTG
Found at i:9619898 original size:52 final size:49
Alignment explanation
Indices: 9619834--9619990 Score: 173
Period size: 52 Copynumber: 3.2 Consensus size: 49
9619824 TTGGGTATTG
* *
9619834 CGTGACTAGTTTCTAATAAGACATTGCGTGACTAGTTTCTGATAAGGCATTA
1 CGTGACTAGTTTCT-ATAAGGCATTGCATGACTAG-TT-TGATAAGGCATTA
* * *
9619886 CGTGATTAGTTTCTGATAAGGTATTGCATGACTAG-TTGAT-AGGCATTG
1 CGTGACTAGTTTCT-ATAAGGCATTGCATGACTAGTTTGATAAGGCATTA
*
9619934 CGTGACT--TATT-TGTAAGGCATTGCATGACTAGTTTG-TAAGGCATTA
1 CGTGACTAGT-TTCTATAAGGCATTGCATGACTAGTTTGATAAGGCATTA
9619980 CGTGACTAGTT
1 CGTGACTAGTT
9619991 CGTAAGGTAT
Statistics
Matches: 90, Mismatches: 10, Indels: 15
0.78 0.09 0.13
Matches are distributed among these distances:
45 19 0.21
46 19 0.21
47 3 0.03
48 14 0.16
49 4 0.04
50 1 0.01
52 30 0.33
ACGTcount: A:0.26, C:0.13, G:0.24, T:0.36
Consensus pattern (49 bp):
CGTGACTAGTTTCTATAAGGCATTGCATGACTAGTTTGATAAGGCATTA
Found at i:9619918 original size:95 final size:92
Alignment explanation
Indices: 9619710--9619896 Score: 221
Period size: 94 Copynumber: 2.0 Consensus size: 92
9619700 GATTAGTTTT
* * * *
9619710 TAAGCATTGCGTGATTGACTTTGGATATTACGTGACTAATTTTTGATAAGGCATTACGCACTAGT
1 TAAGCATTGC--GACTGACTTTGGATATTACGTGACTAATTTCTAATAAGACATTACGCACTAGT
*
9619775 TTCTGATAAGGCATTGCATGACTAGTTAA
64 TTCTGATAAGGCATTACATGACTAGTTAA
* * * * *
9619804 TAAGCATTGCGTGACTGACTTTGGGTATTGCGTGACTAGTTTCTAATAAGACATTGCGTGACTAG
1 TAAGCATTGC--GACTGACTTTGGATATTACGTGACTAATTTCTAATAAGACATTACG-CACTAG
* *
9619869 TTTCTGATAAGGCATTACGTGATTAGTT
63 TTTCTGATAAGGCATTACATGACTAGTT
9619897 TCTGATAAGG
Statistics
Matches: 80, Mismatches: 12, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
94 50 0.62
95 30 0.38
ACGTcount: A:0.27, C:0.14, G:0.23, T:0.36
Consensus pattern (92 bp):
TAAGCATTGCGACTGACTTTGGATATTACGTGACTAATTTCTAATAAGACATTACGCACTAGTTT
CTGATAAGGCATTACATGACTAGTTAA
Found at i:9619956 original size:23 final size:23
Alignment explanation
Indices: 9619781--9620009 Score: 157
Period size: 23 Copynumber: 9.7 Consensus size: 23
9619771 TAGTTTCTGA
* **
9619781 TAAGGCATTGCATGACTAGTTAA
1 TAAGGCATTGCGTGACTAGTTTG
*
9619804 TAA-GCATTGCGTGACTGACTTTG
1 TAAGGCATTGCGTGACT-AGTTTG
* *
9619827 ---GGTATTGCGTGACTAGTTTCTAA
1 TAAGGCATTGCGTGACTAG-TT-T-G
*
9619850 TAAGACATTGCGTGACTAGTTTCTG
1 TAAGGCATTGCGTGACTAG-TT-TG
* *
9619875 ATAAGGCATTACGTGATTAGTTTCTG
1 -TAAGGCATTGCGTGACTAG-TT-TG
* *
9619901 ATAAGGTATTGCATGACTAG-TTG
1 -TAAGGCATTGCGTGACTAGTTTG
9619924 -ATAGGCATTGCGTGACTTA-TTTG
1 TA-AGGCATTGCGTGAC-TAGTTTG
*
9619947 TAAGGCATTGCATGACTAGTTTG
1 TAAGGCATTGCGTGACTAGTTTG
* *
9619970 TAAGGCATTACGTGACTAGTTCG
1 TAAGGCATTGCGTGACTAGTTTG
* *
9619993 TAAGGTATTGTGTGACT
1 TAAGGCATTGCGTGACT
9620010 TAGGCATTGC
Statistics
Matches: 166, Mismatches: 26, Indels: 28
0.75 0.12 0.13
Matches are distributed among these distances:
20 1 0.01
21 15 0.09
22 27 0.16
23 64 0.39
24 2 0.01
26 57 0.34
ACGTcount: A:0.26, C:0.13, G:0.25, T:0.36
Consensus pattern (23 bp):
TAAGGCATTGCGTGACTAGTTTG
Found at i:9620054 original size:22 final size:22
Alignment explanation
Indices: 9620021--9620077 Score: 64
Period size: 22 Copynumber: 2.6 Consensus size: 22
9620011 AGGCATTGCT
*
9620021 TAAAAA-TCAGTCATGCAATGTA-
1 TAAAAACT-AGTCATACAATG-AC
*
9620043 TAAAAACTAGTCATATAATGAC
1 TAAAAACTAGTCATACAATGAC
9620065 TAAAAACTAGTCA
1 TAAAAACTAGTCA
9620078 CACGGTGATT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
21 1 0.03
22 29 0.94
23 1 0.03
ACGTcount: A:0.49, C:0.14, G:0.11, T:0.26
Consensus pattern (22 bp):
TAAAAACTAGTCATACAATGAC
Found at i:9625068 original size:3 final size:3
Alignment explanation
Indices: 9625062--9625102 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
9625052 TCTCATCATC
9625062 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
9625103 TATCATTTTC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:9633235 original size:23 final size:23
Alignment explanation
Indices: 9633209--9633252 Score: 88
Period size: 23 Copynumber: 1.9 Consensus size: 23
9633199 AAGTCCATAA
9633209 GAATAATTACACCTTTTGATTGG
1 GAATAATTACACCTTTTGATTGG
9633232 GAATAATTACACCTTTTGATT
1 GAATAATTACACCTTTTGATT
9633253 AATTAAGAGG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.32, C:0.14, G:0.14, T:0.41
Consensus pattern (23 bp):
GAATAATTACACCTTTTGATTGG
Found at i:9636473 original size:92 final size:92
Alignment explanation
Indices: 9636277--9636462 Score: 311
Period size: 92 Copynumber: 2.0 Consensus size: 92
9636267 ATATATATGT
* *
9636277 ATGGACTAGGAACGGTAGGCAAGCAAATTTGCCAAGGAATAAATGAACATTGAATATTCAAAGAA
1 ATGGACTAGGAAAGGTAGGCAAGCAAATTTGCCAAGGAATAAATGAACATTGAATACTCAAAGAA
* *
9636342 CTAAAGATCATGAGCGGCAAAAAGAGA
66 CTAAAGATCATGAGCAGCAAAAAGAAA
* *
9636369 ATGGACTAGGAAAGGTAGGGAAGCAAATTTGCCTAGGAATAAATGAACATTGAATACTCAAA-AA
1 ATGGACTAGGAAAGGTAGGCAAGCAAATTTGCCAAGGAATAAATGAACATTGAATACTCAAAGAA
9636433 CTAAAGATCATGAGCAGCAAAAAGAAA
66 CTAAAGATCATGAGCAGCAAAAAGAAA
9636460 ATG
1 ATG
9636463 TGGTTAGGAA
Statistics
Matches: 88, Mismatches: 6, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
91 30 0.34
92 58 0.66
ACGTcount: A:0.47, C:0.12, G:0.23, T:0.18
Consensus pattern (92 bp):
ATGGACTAGGAAAGGTAGGCAAGCAAATTTGCCAAGGAATAAATGAACATTGAATACTCAAAGAA
CTAAAGATCATGAGCAGCAAAAAGAAA
Found at i:9637991 original size:16 final size:16
Alignment explanation
Indices: 9637970--9638020 Score: 52
Period size: 16 Copynumber: 3.1 Consensus size: 16
9637960 ACTAATATAC
9637970 TAATATAGTATTTTGT
1 TAATATAGTATTTTGT
9637986 TAATATA-TAATTTTTGAT
1 TAATATAGT-A-TTTTG-T
*
9638004 TAAT-TAGTATATTGT
1 TAATATAGTATTTTGT
9638019 TA
1 TA
9638021 TTGGCTAATT
Statistics
Matches: 30, Mismatches: 1, Indels: 9
0.75 0.03 0.22
Matches are distributed among these distances:
15 4 0.13
16 12 0.40
17 8 0.27
18 6 0.20
ACGTcount: A:0.35, C:0.00, G:0.10, T:0.55
Consensus pattern (16 bp):
TAATATAGTATTTTGT
Found at i:9640066 original size:3 final size:3
Alignment explanation
Indices: 9640058--9640083 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
9640048 AACATGCGTT
9640058 ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA AT
9640084 GTATATTTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
ATA
Found at i:9641102 original size:5 final size:5
Alignment explanation
Indices: 9641086--9641115 Score: 51
Period size: 5 Copynumber: 5.8 Consensus size: 5
9641076 TCTTTCTTCT
9641086 TATAC ATATAC TATAC TATAC TATAC TATA
1 TATAC -TATAC TATAC TATAC TATAC TATA
9641116 TTTTTGCTGA
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 19 0.79
6 5 0.21
ACGTcount: A:0.43, C:0.17, G:0.00, T:0.40
Consensus pattern (5 bp):
TATAC
Found at i:9644842 original size:18 final size:19
Alignment explanation
Indices: 9644819--9644895 Score: 76
Period size: 18 Copynumber: 4.4 Consensus size: 19
9644809 ATTATATTTA
9644819 ATTACTAATATAAGTTA-T
1 ATTACTAATATAAGTTACT
9644837 ATTACT-ATATAA--TACT
1 ATTACTAATATAAGTTACT
* * *
9644853 AATATTAATATAAATTACT
1 ATTACTAATATAAGTTACT
*
9644872 -TTAATAATATAAGTTA-T
1 ATTACTAATATAAGTTACT
9644889 ATTACTA
1 ATTACTA
9644896 TAGTATACTA
Statistics
Matches: 48, Mismatches: 6, Indels: 10
0.75 0.09 0.16
Matches are distributed among these distances:
15 2 0.04
16 5 0.10
17 13 0.27
18 24 0.50
19 4 0.08
ACGTcount: A:0.47, C:0.06, G:0.03, T:0.44
Consensus pattern (19 bp):
ATTACTAATATAAGTTACT
Found at i:9647292 original size:67 final size:64
Alignment explanation
Indices: 9647205--9647336 Score: 237
Period size: 67 Copynumber: 2.0 Consensus size: 64
9647195 AATCACCTGG
9647205 TGACACATGTCAAGTTTTAATATTTTTATAATTGCCTTTATAAATTCAACACAAACTCTCTCAT
1 TGACACATGTCAAGTTTTAATATTTTTATAATTGCCTTTATAAATTCAACACAAACTCTCTCAT
9647269 NTGACACATGTACTAAGTTTTAATATTTTTATAATTGCCTTTATAAATTCAACACAAACTCTCTC
1 -TGACACATGT-C-AAGTTTTAATATTTTTATAATTGCCTTTATAAATTCAACACAAACTCTCTC
9647334 AT
63 AT
9647336 T
1 T
9647337 TCATTCTTCA
Statistics
Matches: 65, Mismatches: 0, Indels: 3
0.96 0.00 0.04
Matches are distributed among these distances:
65 10 0.15
66 2 0.03
67 53 0.82
ACGTcount: A:0.34, C:0.18, G:0.06, T:0.41
Consensus pattern (64 bp):
TGACACATGTCAAGTTTTAATATTTTTATAATTGCCTTTATAAATTCAACACAAACTCTCTCAT
Found at i:9660281 original size:105 final size:104
Alignment explanation
Indices: 9660096--9660327 Score: 333
Period size: 105 Copynumber: 2.2 Consensus size: 104
9660086 TAACCATGCA
* * *
9660096 TGTGCACGATGTGGGCGTTGCACATGCCTGTGATGACGAGGTGCGGGAGTGTGAATAATGATATT
1 TGTGCGCGATGTGGGGGTTGCACATGCCTGTGATGACGAGGTGCAGGAGTGTGAATAATGATATT
* * *
9660161 GCCTGTGCGCGATGTGGGGGTGCACGTGATGGCGTTAGC
66 GCCTGTGCGCGATGTGAGGGTGCACATGATGGCATTAGC
* *
9660200 TTGTGCGCGATGTGGGGGTTGCACATGCC-GATGATGACGGGGTGCAGGAGTGTGAATGATGATA
1 -TGTGCGCGATGTGGGGGTTGCACATGCCTG-TGATGACGAGGTGCAGGAGTGTGAATAATGATA
*
9660264 TTGCCTGTGCGCTATGTGAGGGTGCACATGATGGCATTAGC
64 TTGCCTGTGCGCGATGTGAGGGTGCACATGATGGCATTAGC
* *
9660305 TGTGTGCGATGTAGGGG-TGCACA
1 TGTGCGCGATGTGGGGGTTGCACA
9660328 CGATGGTATT
Statistics
Matches: 115, Mismatches: 11, Indels: 4
0.88 0.08 0.03
Matches are distributed among these distances:
103 6 0.05
104 16 0.14
105 93 0.81
ACGTcount: A:0.18, C:0.16, G:0.40, T:0.26
Consensus pattern (104 bp):
TGTGCGCGATGTGGGGGTTGCACATGCCTGTGATGACGAGGTGCAGGAGTGTGAATAATGATATT
GCCTGTGCGCGATGTGAGGGTGCACATGATGGCATTAGC
Found at i:9660308 original size:36 final size:36
Alignment explanation
Indices: 9660268--9660368 Score: 141
Period size: 36 Copynumber: 2.8 Consensus size: 36
9660258 ATGATATTGC
* *
9660268 CTGTGCGCTATGTGAGGGTGCACATGATGGCATTAG
1 CTGTGCGCGATGTGAGGGTGCACACGATGGCATTAG
* *
9660304 CTGTGTGCGATGT-AGGGGTGCACACGATGGTATTAG
1 CTGTGCGCGATGTGA-GGGTGCACACGATGGCATTAG
*
9660340 CTGTGCACGATGTGAGGGTGCACACGATG
1 CTGTGCGCGATGTGAGGGTGCACACGATG
9660369 ACTCCAACTA
Statistics
Matches: 57, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
35 1 0.02
36 55 0.96
37 1 0.02
ACGTcount: A:0.20, C:0.17, G:0.38, T:0.26
Consensus pattern (36 bp):
CTGTGCGCGATGTGAGGGTGCACACGATGGCATTAG
Found at i:9662546 original size:2 final size:2
Alignment explanation
Indices: 9662541--9662586 Score: 76
Period size: 2 Copynumber: 23.0 Consensus size: 2
9662531 GTGTGTGTGT
9662541 GA GA GA GA GA GA GA GA GA GA GA GA GA GA -A GA GA TGA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA -GA GA GA GA
9662583 GA GA
1 GA GA
9662587 ATGTGCTCTA
Statistics
Matches: 42, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
1 1 0.02
2 39 0.93
3 2 0.05
ACGTcount: A:0.50, C:0.00, G:0.48, T:0.02
Consensus pattern (2 bp):
GA
Found at i:9663165 original size:2 final size:2
Alignment explanation
Indices: 9663158--9663208 Score: 72
Period size: 2 Copynumber: 26.5 Consensus size: 2
9663148 AGATGGCTTA
9663158 AT AT AT AT AT AT AT AT AT AT AT AT AGT A- AT AT AT AT -T AT A-
1 AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT
9663198 AT AT AT AT AT A
1 AT AT AT AT AT A
9663209 ATTGAATAAG
Statistics
Matches: 45, Mismatches: 0, Indels: 8
0.85 0.00 0.15
Matches are distributed among these distances:
1 3 0.07
2 40 0.89
3 2 0.04
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (2 bp):
AT
Found at i:9663489 original size:2 final size:2
Alignment explanation
Indices: 9663482--9663537 Score: 82
Period size: 2 Copynumber: 29.0 Consensus size: 2
9663472 CATGCTTGTT
9663482 GA GA GA GA GA GA GA GA GA GA TGA -A GA -A GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA -GA GA GA GA GA GA GA GA GA GA GA
9663523 GA GA -A GA GA GA GA GA
1 GA GA GA GA GA GA GA GA
9663538 AATGTGCTCT
Statistics
Matches: 50, Mismatches: 0, Indels: 8
0.86 0.00 0.14
Matches are distributed among these distances:
1 3 0.06
2 45 0.90
3 2 0.04
ACGTcount: A:0.52, C:0.00, G:0.46, T:0.02
Consensus pattern (2 bp):
GA
Found at i:9663513 original size:19 final size:19
Alignment explanation
Indices: 9663482--9663537 Score: 89
Period size: 19 Copynumber: 3.0 Consensus size: 19
9663472 CATGCTTGTT
9663482 GAGAGAG-AGAGAGAGAGA
1 GAGAGAGAAGAGAGAGAGA
9663500 GATGA-AGAAGAGAGAGAGA
1 GA-GAGAGAAGAGAGAGAGA
9663519 GAGAGAGAAGAGAGAGAGA
1 GAGAGAGAAGAGAGAGAGA
9663538 AATGTGCTCT
Statistics
Matches: 35, Mismatches: 0, Indels: 5
0.88 0.00 0.12
Matches are distributed among these distances:
18 6 0.17
19 29 0.83
ACGTcount: A:0.52, C:0.00, G:0.46, T:0.02
Consensus pattern (19 bp):
GAGAGAGAAGAGAGAGAGA
Found at i:9663581 original size:952 final size:949
Alignment explanation
Indices: 9662541--9664421 Score: 3569
Period size: 952 Copynumber: 2.0 Consensus size: 949
9662531 GTGTGTGTGT
*
9662541 GAGAGAGAGAGAGAGAGAGAGAGAGAGAAGAGATGAGAGAGAGAGAATGTGCTCTACGACTTCAA
1 GAGAGAGAGAGAGAGAGAGAGAGAGAGAAGAGAAGAGAGAGAGAGAATGTGCTCTACGACTTCAA
9662606 ATTTATACAAAGGGCAGATTTATGTGATTGCCGGAGGTGTGTCAACATAGTATTGCACATTCTGA
66 ATTTATACAAAGGGCAGATTTATGTGATTGCCGGAGGTGTGTCAACATAGTATTGCACATTCTGA
9662671 AATGTTAATGCTGAGGGATCAAAAGGTAATACCATCCTCCCTGTGATAGAGACAAAGCAAACGAG
131 AATGTTAATGCTGAGGGATCAAAAGGTAATACCATCCTCCCTGTGATAGAGACAAAGCAAACGAG
9662736 AATATGGTTCAAATGAGCTTTTAAAAAGCAGTGATATTGGTTTGGTTAAGCTTACAATGGTAAAG
196 AATATGGTTCAAATGAGCTTTTAAAAAGCAGTGATATTGGTTTGGTTAAGCTTACAATGGTAAAG
9662801 GTCAAGAAGAGAAAATATTGGACAGTGGCTAATATTTGCTCCATAGCAACACCAATGGATTCTTT
261 GTCAAGAAGAGAAAATATTGGACAGTGGCTAATATTTGCTCCATAGCAACACCAATGGATTCTTT
9662866 TGGCTGCCCATTCAAATCTTATATAACCAACAACCAATGCACAGACATCTTATCACACACAAGTC
326 TGGCTGCCCATTCAAATCTTATATAACCAACAACCAATGCACAGACATCTTATCACACACAAGTC
9662931 CTTTATTCTTCAATTTACCTTTTCCTGTTTTTCTACAATTTTTTTCAACATCTCGAGTTTTAGAC
391 CTTTATTCTTCAATTTACCTTTTCCTGTTTTTCTACAATTTTTTTCAACATCTCGAGTTTTAGAC
9662996 TAGTTAAGAGGTAACATATACAATTGATAAAAGGTCTGAACT-A-ATAATAATAATAATAATAAA
456 TAGTTAAGAGGTAACATATACAATTGATAAAAGGTCTGAACTAATATAATAATAATAATAATAAA
*
9663059 TACATATATGCCTGGACTAGGAAAGGTAGAGGAAAAAAGAGACCGCATATGGTTGGGAAAATCTT
521 TACATATATGCCTGGACTAGGAAAGGTAGAGAAAAAAAGAGACCGCATATGGTTGGGAAAATCTT
9663124 CACCTAGTTGTTTTGATTTAGGTTAGATGGCTTAATATATATATA--TATATATATATATAGTA-
586 CACCTAGTTGTTTTGATTTAGGTTAGATGGCTTAATATATATATACTTATATATATATATA-TAT
9663186 ATAT-ATATTATAATATATATATAATTGAATAAGTAAAGTTTTCTCTAAACTACTCTAGTCAGTT
650 ATATAATA-TATAATATATATATAA-TG-AT-AGTAAAGTTTTCTCTAAACTACTCTAGTCAGTT
9663250 TTTGTGAAGCTCTATATTGAATAACATTATTCAAATATTAATGTTCTATGAGCTATTCATTTATC
711 TTTGTGAAGCTCTATATTGAATAACATTATTCAAATATTAATGTTCTATGAGCTATTCATTTATC
9663315 AATAAATTATTCAACTGATTTTATATTGCCTATTAACCAAAATTTGCATTATAATCTGACTTTTA
776 AATAAATTATTCAACTGATTTTATATTGCCTATTAACCAAAATTTGCATTATAATCTGACTTTTA
9663380 TCGTGTCACAATTGTAATATTATGATGACACATATCTATGTATTGGGGATTCCATCCATTGGCAA
841 TCGTGTCACAATTGTAATATTATGATGACACATATCTATGTATTGGGGATTCCATCCATTGGCAA
9663445 CAAATTAAGTAAAATTTTAGAAANTTGCATGCTTGTTGAGAGAGA
906 CAAATTAAGTAAAATTTTAGAAA-TTGCATGCTTGTTGAGAGAGA
9663490 GAGAGAGAGAGATGAAGAAGAGAGAGAGAGAGAGAGAAGAGAGAGAGA-AATGTGCTCTACGACT
1 GAGAGAGAGAGA-G-AG-AGAGAGAGAGAGA-AGAGAAGAGAGAGAGAGAATGTGCTCTACGACT
9663554 TCAAATTTATACAAAGGGCAGATTTATGTGATTGCCGGAGGTGTGTCAACATAGTATTGCACATT
62 TCAAATTTATACAAAGGGCAGATTTATGTGATTGCCGGAGGTGTGTCAACATAGTATTGCACATT
*
9663619 CTGAAATTTTAATGCTGAGGGATCAAAAGGTAATACCATCCTCCCTGTGATAGAGACAAAGCAAA
127 CTGAAATGTTAATGCTGAGGGATCAAAAGGTAATACCATCCTCCCTGTGATAGAGACAAAGCAAA
9663684 CGAGAATATGGTTCAAATGAGCTTTTAAAAAGCAGTGATATTGGTTTGGTTAAGCTTACAATGGT
192 CGAGAATATGGTTCAAATGAGCTTTTAAAAAGCAGTGATATTGGTTTGGTTAAGCTTACAATGGT
9663749 AAAGGTCAAGAAGAGAAAATATTGGACAGTGGCTAATATTTGCTCCATAGCAACACCAATGGATT
257 AAAGGTCAAGAAGAGAAAATATTGGACAGTGGCTAATATTTGCTCCATAGCAACACCAATGGATT
9663814 CTTTTGGCTGCCCATTCAAATCTTATATAACCAACAACCAATGCACAGACATCTTATCACACACA
322 CTTTTGGCTGCCCATTCAAATCTTATATAACCAACAACCAATGCACAGACATCTTATCACACACA
9663879 AGTCCTTTATTCTTCAATTTACCTTTTCCTGTTTTTCTACAATTTTTTTCAACATCTCGAGTTTT
387 AGTCCTTTATTCTTCAATTTACCTTTTCCTGTTTTTCTACAATTTTTTTCAACATCTCGAGTTTT
9663944 AGACTAGTTAAGAGGTAACATATACAATTGATAAAAGGTCTGAACTAATATAATAATAATAATAA
452 AGACTAGTTAAGAGGTAACATATACAATTGATAAAAGGTCTGAACTAATATAATAATAATAATAA
*
9664009 TAAGTACATATATGCCTGGACTAGGAAAGGTAGAGAAAAAAAGAGACCGCATATGGTTGGGAAAA
517 TAAATACATATATGCCTGGACTAGGAAAGGTAGAGAAAAAAAGAGACCGCATATGGTTGGGAAAA
9664074 TCTTCACCTAGTTGTTTTGATTTAGGTTAGATGGCTTAATATATATATAGCTTATATATATATAT
582 TCTTCACCTAGTTGTTTTGATTTAGGTTAGATGGCTTAATATATATATA-CTTATATATATATAT
*
9664139 ATATATATAATATATATTATATATATAATGATAGTAAAGTTTTCTCTAAACTACTCTAGTCAGTT
646 ATATATATAATATATAATATATATATAATGATAGTAAAGTTTTCTCTAAACTACTCTAGTCAGTT
9664204 TTTGTGAAGCTCTATATTGAATAACATTATTCAAATATTAATGTTCTATGAGCTATTCATTTATC
711 TTTGTGAAGCTCTATATTGAATAACATTATTCAAATATTAATGTTCTATGAGCTATTCATTTATC
9664269 AATAAATTATTCAACTGATTTTATATTGCCTATTAACCAAAATTTGCATTATAATCTGACTTTTA
776 AATAAATTATTCAACTGATTTTATATTGCCTATTAACCAAAATTTGCATTATAATCTGACTTTTA
9664334 TCGTGTCACAATTGTAATATTATGATGACACATATCTATGTATTGGGGATTCCATCCATTGGCAA
841 TCGTGTCACAATTGTAATATTATGATGACACATATCTATGTATTGGGGATTCCATCCATTGGCAA
9664399 CAAATTAAGTAAAATTTTAGAAA
906 CAAATTAAGTAAAATTTTAGAAA
9664422 GAGCTTAAAA
Statistics
Matches: 916, Mismatches: 5, Indels: 17
0.98 0.01 0.02
Matches are distributed among these distances:
949 12 0.01
950 1 0.00
951 2 0.00
952 464 0.51
953 16 0.02
954 379 0.41
955 2 0.00
956 4 0.00
957 33 0.04
958 3 0.00
ACGTcount: A:0.36, C:0.14, G:0.17, T:0.33
Consensus pattern (949 bp):
GAGAGAGAGAGAGAGAGAGAGAGAGAGAAGAGAAGAGAGAGAGAGAATGTGCTCTACGACTTCAA
ATTTATACAAAGGGCAGATTTATGTGATTGCCGGAGGTGTGTCAACATAGTATTGCACATTCTGA
AATGTTAATGCTGAGGGATCAAAAGGTAATACCATCCTCCCTGTGATAGAGACAAAGCAAACGAG
AATATGGTTCAAATGAGCTTTTAAAAAGCAGTGATATTGGTTTGGTTAAGCTTACAATGGTAAAG
GTCAAGAAGAGAAAATATTGGACAGTGGCTAATATTTGCTCCATAGCAACACCAATGGATTCTTT
TGGCTGCCCATTCAAATCTTATATAACCAACAACCAATGCACAGACATCTTATCACACACAAGTC
CTTTATTCTTCAATTTACCTTTTCCTGTTTTTCTACAATTTTTTTCAACATCTCGAGTTTTAGAC
TAGTTAAGAGGTAACATATACAATTGATAAAAGGTCTGAACTAATATAATAATAATAATAATAAA
TACATATATGCCTGGACTAGGAAAGGTAGAGAAAAAAAGAGACCGCATATGGTTGGGAAAATCTT
CACCTAGTTGTTTTGATTTAGGTTAGATGGCTTAATATATATATACTTATATATATATATATATA
TATAATATATAATATATATATAATGATAGTAAAGTTTTCTCTAAACTACTCTAGTCAGTTTTTGT
GAAGCTCTATATTGAATAACATTATTCAAATATTAATGTTCTATGAGCTATTCATTTATCAATAA
ATTATTCAACTGATTTTATATTGCCTATTAACCAAAATTTGCATTATAATCTGACTTTTATCGTG
TCACAATTGTAATATTATGATGACACATATCTATGTATTGGGGATTCCATCCATTGGCAACAAAT
TAAGTAAAATTTTAGAAATTGCATGCTTGTTGAGAGAGA
Found at i:9664119 original size:2 final size:2
Alignment explanation
Indices: 9664112--9664165 Score: 69
Period size: 2 Copynumber: 28.5 Consensus size: 2
9664102 AGATGGCTTA
* *
9664112 AT AT AT AT AT AG CT -T AT AT AT AT AT AT AT AT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
9664152 AT AT -T AT AT AT AT A
1 AT AT AT AT AT AT AT A
9664166 ATGATAGTAA
Statistics
Matches: 46, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
1 3 0.07
2 43 0.93
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (2 bp):
AT
Found at i:9664482 original size:50 final size:50
Alignment explanation
Indices: 9664385--9664483 Score: 155
Period size: 50 Copynumber: 2.0 Consensus size: 50
9664375 ATTGGGGATT
**
9664385 CCATCCATTGGCAACAAATTAAGTAAAATTTTAGAAAGAGCTTAAAAAGC
1 CCATCCATTGGCAACAAATTAAGTAAAATTTTAGAAAGAGCAAAAAAAGC
*
9664435 CCATGCATTGGCAACAAATT-AGTAAAATTTTAGAAAGCAGCAAAAAAAG
1 CCATCCATTGGCAACAAATTAAGTAAAATTTTAGAAAG-AGCAAAAAAAG
9664484 AAAAAGCATG
Statistics
Matches: 45, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
49 17 0.38
50 28 0.62
ACGTcount: A:0.47, C:0.15, G:0.15, T:0.22
Consensus pattern (50 bp):
CCATCCATTGGCAACAAATTAAGTAAAATTTTAGAAAGAGCAAAAAAAGC
Found at i:9668626 original size:15 final size:16
Alignment explanation
Indices: 9668606--9668638 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
9668596 ATTTTTTTAT
9668606 TTTAAAATATT-AATA
1 TTTAAAATATTAAATA
*
9668621 TTTAAATTATTAAATA
1 TTTAAAATATTAAATA
9668637 TT
1 TT
9668639 ATTAAAACTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 10 0.62
16 6 0.38
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (16 bp):
TTTAAAATATTAAATA
Found at i:9673466 original size:26 final size:26
Alignment explanation
Indices: 9673416--9673479 Score: 85
Period size: 26 Copynumber: 2.5 Consensus size: 26
9673406 CAAGAAAAGC
* *
9673416 AAATCCAAGCAAGGGTAAGACGAAGT
1 AAATCCAAACAAGGGTAAGACGAAGA
*
9673442 AAATCCAAACAAGGGTAA-AGGGAAGA
1 AAATCCAAACAAGGGTAAGA-CGAAGA
9673468 AAATCCAAACAA
1 AAATCCAAACAA
9673480 AGTTTAGCCT
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
25 1 0.03
26 33 0.97
ACGTcount: A:0.53, C:0.16, G:0.22, T:0.09
Consensus pattern (26 bp):
AAATCCAAACAAGGGTAAGACGAAGA
Found at i:9676625 original size:2 final size:2
Alignment explanation
Indices: 9676618--9676647 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
9676608 CATGTTGTTT
9676618 TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
9676648 TTACAAGTAT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:9677388 original size:37 final size:39
Alignment explanation
Indices: 9677308--9677391 Score: 111
Period size: 37 Copynumber: 2.2 Consensus size: 39
9677298 TCACATATCA
* * *
9677308 ATGACTTCTCTCCCTCTCTTTTTTCTTTTTGTCAGTTTG
1 ATGACTTCTCTCCCTCTCTTTTTTCTTTTCGTCAGATCG
*
9677347 -TGACTTCTCTCCCTTTC-TTTTTCTTTTCGTC-GATCG
1 ATGACTTCTCTCCCTCTCTTTTTTCTTTTCGTCAGATCG
9677383 ATGACTTCT
1 ATGACTTCT
9677392 TTTTATTCCA
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
36 3 0.08
37 21 0.52
38 16 0.40
ACGTcount: A:0.08, C:0.27, G:0.11, T:0.54
Consensus pattern (39 bp):
ATGACTTCTCTCCCTCTCTTTTTTCTTTTCGTCAGATCG
Found at i:9679678 original size:30 final size:30
Alignment explanation
Indices: 9679642--9679716 Score: 132
Period size: 30 Copynumber: 2.5 Consensus size: 30
9679632 GGATGCATTT
9679642 TCGCTGCAGCGAGAATGACACTGTAGCTTC
1 TCGCTGCAGCGAGAATGACACTGTAGCTTC
* *
9679672 TCGCTGCAGCAAGAATGACACTGTAGTTTC
1 TCGCTGCAGCGAGAATGACACTGTAGCTTC
9679702 TCGCTGCAGCGAGAA
1 TCGCTGCAGCGAGAA
9679717 ACTTTCTATT
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 42 1.00
ACGTcount: A:0.25, C:0.25, G:0.27, T:0.23
Consensus pattern (30 bp):
TCGCTGCAGCGAGAATGACACTGTAGCTTC
Found at i:9680654 original size:8 final size:8
Alignment explanation
Indices: 9680641--9680721 Score: 51
Period size: 8 Copynumber: 10.1 Consensus size: 8
9680631 CTCTTCTTTC
9680641 TTTTTTAT
1 TTTTTTAT
9680649 TTTTTTA-
1 TTTTTTAT
*
9680656 ATTTTTAT
1 TTTTTTAT
***
9680664 TAGATTAT
1 TTTTTTAT
*
9680672 TTTTTTAA
1 TTTTTTAT
9680680 TTTTTTA-
1 TTTTTTAT
*
9680687 -TTTATAT
1 TTTTTTAT
9680694 TTTTATATAT
1 TTTT-T-TAT
9680704 ATTTTTTAT
1 -TTTTTTAT
*
9680713 ATTTTTAT
1 TTTTTTAT
9680721 T
1 T
9680722 GAATGGGTGT
Statistics
Matches: 54, Mismatches: 13, Indels: 12
0.68 0.16 0.15
Matches are distributed among these distances:
6 5 0.09
7 6 0.11
8 32 0.59
9 3 0.06
10 4 0.07
11 4 0.07
ACGTcount: A:0.23, C:0.00, G:0.01, T:0.75
Consensus pattern (8 bp):
TTTTTTAT
Found at i:9680697 original size:13 final size:13
Alignment explanation
Indices: 9680657--9680712 Score: 57
Period size: 12 Copynumber: 4.5 Consensus size: 13
9680647 ATTTTTTTAA
*
9680657 TTTTTA-TTAGAT
1 TTTTTATTTATAT
9680669 TATTTT-TTTA-AT
1 T-TTTTATTTATAT
9680681 TTTTTATTTATA-
1 TTTTTATTTATAT
*
9680693 TTTTTATATATAT
1 TTTTTATTTATAT
9680706 TTTTTAT
1 TTTTTAT
9680713 ATTTTTATTG
Statistics
Matches: 38, Mismatches: 1, Indels: 9
0.79 0.02 0.19
Matches are distributed among these distances:
11 4 0.11
12 19 0.50
13 15 0.39
ACGTcount: A:0.25, C:0.00, G:0.02, T:0.73
Consensus pattern (13 bp):
TTTTTATTTATAT
Found at i:9680697 original size:23 final size:25
Alignment explanation
Indices: 9680645--9680712 Score: 79
Period size: 25 Copynumber: 2.8 Consensus size: 25
9680635 TCTTTCTTTT
9680645 TTATTTTTTTAA-TTTTTA-TTAGA
1 TTATTTTTTTAATTTTTTATTTAGA
*
9680668 TTATTTTTTTAATTTTTTATTTATA
1 TTATTTTTTTAATTTTTTATTTAGA
* *
9680693 TT-TTTATATATATTTTTTAT
1 TTATTTTTTTA-ATTTTTTAT
9680713 ATTTTTATTG
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
23 12 0.31
24 12 0.31
25 15 0.38
ACGTcount: A:0.25, C:0.00, G:0.01, T:0.74
Consensus pattern (25 bp):
TTATTTTTTTAATTTTTTATTTAGA
Found at i:9680998 original size:59 final size:59
Alignment explanation
Indices: 9680932--9681348 Score: 460
Period size: 59 Copynumber: 6.9 Consensus size: 59
9680922 AATTCGATTA
* * *
9680932 AAATTCCTAAACTTAATCTAGGCTTAACCTATCTCACAACAGGTTTGATTTAAAAATTC
1 AAATTCCTAAACTTAATTTAGGCTTGACCTATCTCACAACAGGTTCGATTTAAAAATTC
* ** *
9680991 AAATTCCTAAACTTATTTTAGGCTCAACCTATCTCACAATAGGTTCGATTTAAAAAAAATTC
1 AAATTCCTAAACTTAATTTAGGCTTGACCTATCTCACAACAGGTTCGATTT---AAAAATTC
* * * * *
9681053 AAATTCCTAAATTTAATTTAGGTTTGACCAATCTCAAAATAGGTTCGATTTAAAAATTC
1 AAATTCCTAAACTTAATTTAGGCTTGACCTATCTCACAACAGGTTCGATTTAAAAATTC
* *
9681112 AAATTCCTAAACTTAATTTAGCCTCGACCTATCTCACAACAGGTTCGATTTAAAAATTC
1 AAATTCCTAAACTTAATTTAGGCTTGACCTATCTCACAACAGGTTCGATTTAAAAATTC
* * * *
9681171 AAATTCCTAAACTTAATTTAGG-TTCAACCTATCTCACAACAAGTTCAATTTAAAAAAATTGA
1 AAATTCCTAAACTTAATTTAGGCTT-GACCTATCTCACAACAGGTTCGATTT--AAAAATT-C
* * * * *
9681233 AAACTCCTAGAGTTAATTTAGGCTCGACCTATCTCACAACAGGTTCGATTTAAAATAAATTAA
1 AAATTCCTAAACTTAATTTAGGCTTGACCTATCTCACAACAGGTTCGATTT--AA-AAATT-C
** * * *
9681296 AAATTTTTAGACTTAATCTAGG-TTCGACCTATCTCAAAACAGGTTCGATTTAA
1 AAATTCCTAAACTTAATTTAGGCTT-GACCTATCTCACAACAGGTTCGATTTAA
9681349 TTCACGAGGC
Statistics
Matches: 308, Mismatches: 40, Indels: 18
0.84 0.11 0.05
Matches are distributed among these distances:
58 1 0.00
59 150 0.49
61 9 0.03
62 99 0.32
63 49 0.16
ACGTcount: A:0.38, C:0.19, G:0.10, T:0.34
Consensus pattern (59 bp):
AAATTCCTAAACTTAATTTAGGCTTGACCTATCTCACAACAGGTTCGATTTAAAAATTC
Found at i:9681097 original size:121 final size:121
Alignment explanation
Indices: 9680932--9681348 Score: 527
Period size: 121 Copynumber: 3.4 Consensus size: 121
9680922 AATTCGATTA
* *
9680932 AAATTCCTAAACTTAATCTAGGCTT-AACCTATCTCACAACAGGTTTGATTTAAAAATTCAAATT
1 AAATTCCTAAACTTAATCTAGG-TTCAACCTATCTCAAAACAGGTTCGATTTAAAAATTCAAATT
* * *
9680996 CCTAAACTTATTTTAGGCTCAACCTATCTCACAATAGGTTCGATTTAAAAAAAATTC
65 CCTAAACTTAATTTAGGCTCGACCTATCTCACAACAGGTTCGATTTAAAAAAAATTC
* * ** * *
9681053 AAATTCCTAAATTTAATTTAGGTTTGACCAATCTCAAAATAGGTTCGATTTAAAAATTCAAATTC
1 AAATTCCTAAACTTAATCTAGGTTCAACCTATCTCAAAACAGGTTCGATTTAAAAATTCAAATTC
*
9681118 CTAAACTTAATTTAGCCTCGACCTATCTCACAACAGGTTCGATTT---AAAAATTC
66 CTAAACTTAATTTAGGCTCGACCTATCTCACAACAGGTTCGATTTAAAAAAAATTC
* * * * *
9681171 AAATTCCTAAACTTAATTTAGGTTCAACCTATCTCACAACAAGTTCAATTTAAAAAAATTGAAAA
1 AAATTCCTAAACTTAATCTAGGTTCAACCTATCTCAAAACAGGTTCGATTT--AAAAATT-CAAA
* * * * *
9681236 CTCCTAGAGTTAATTTAGGCTCGACCTATCTCACAACAGGTTCGATTTAAAATAAATTAA
63 TTCCTAAACTTAATTTAGGCTCGACCTATCTCACAACAGGTTCGATTTAAAAAAAATT-C
** * *
9681296 AAATTTTTAGACTTAATCTAGGTTCGACCTATCTCAAAACAGGTTCGATTTAA
1 AAATTCCTAAACTTAATCTAGGTTCAACCTATCTCAAAACAGGTTCGATTTAA
9681349 TTCACGAGGC
Statistics
Matches: 254, Mismatches: 34, Indels: 14
0.84 0.11 0.05
Matches are distributed among these distances:
118 51 0.20
120 9 0.04
121 143 0.56
123 2 0.01
124 6 0.02
125 43 0.17
ACGTcount: A:0.38, C:0.19, G:0.10, T:0.34
Consensus pattern (121 bp):
AAATTCCTAAACTTAATCTAGGTTCAACCTATCTCAAAACAGGTTCGATTTAAAAATTCAAATTC
CTAAACTTAATTTAGGCTCGACCTATCTCACAACAGGTTCGATTTAAAAAAAATTC
Found at i:9681144 original size:180 final size:183
Alignment explanation
Indices: 9680931--9681348 Score: 565
Period size: 180 Copynumber: 2.3 Consensus size: 183
9680921 AAATTCGATT
** *
9680931 AAAATTCCTAAACTTAATCTAGGCTTAACCTATCTCACAACAGGTTTGATTTAAAAATTCAAATT
1 AAAATTCCTAAACTTAATCTAGGCTCGACCTATCTCACAACAGGTTCGATTTAAAAATTCAAATT
* * * * * *
9680996 CCTAAACTTATTTTAGGCTCAACCTATCTCACAATAGGTTCGATTTAAAAAAAATT-CAAATTCC
66 CCTAAACTTAATTTAGGCTCAACCTATCTCACAACAAGTTCAATTT-AAAAAAATTGAAAACTCC
* * * *
9681060 TAAATTTAATTTAGGTTTGACCAATCTCAAAATAGGTTCGATTT-AA-AAATT-
130 TAAAGTTAATTTAGGCTCGACCAATCTCAAAACAGGTTCGATTTAAATAAATTA
* * *
9681111 CAAATTCCTAAACTTAATTTAGCCTCGACCTATCTCACAACAGGTTCGATTTAAAAATTCAAATT
1 AAAATTCCTAAACTTAATCTAGGCTCGACCTATCTCACAACAGGTTCGATTTAAAAATTCAAATT
*
9681176 CCTAAACTTAATTTAGGTTCAACCTATCTCACAACAAGTTCAATTTAAAAAAATTGAAAACTCCT
66 CCTAAACTTAATTTAGGCTCAACCTATCTCACAACAAGTTCAATTTAAAAAAATTGAAAACTCCT
* * *
9681241 AGAGTTAATTTAGGCTCGACCTATCTCACAACAGGTTCGATTTAAAATAAATTA
131 AAAGTTAATTTAGGCTCGACCAATCTCAAAACAGGTTCGATTT-AAATAAATTA
** * * *
9681295 AAAATTTTTAGACTTAATCTAGGTTCGACCTATCTCAAAACAGGTTCGATTTAA
1 AAAATTCCTAAACTTAATCTAGGCTCGACCTATCTCACAACAGGTTCGATTTAA
9681349 TTCACGAGGC
Statistics
Matches: 205, Mismatches: 28, Indels: 6
0.86 0.12 0.03
Matches are distributed among these distances:
179 9 0.04
180 143 0.70
182 2 0.01
183 5 0.02
184 46 0.22
ACGTcount: A:0.38, C:0.19, G:0.10, T:0.33
Consensus pattern (183 bp):
AAAATTCCTAAACTTAATCTAGGCTCGACCTATCTCACAACAGGTTCGATTTAAAAATTCAAATT
CCTAAACTTAATTTAGGCTCAACCTATCTCACAACAAGTTCAATTTAAAAAAATTGAAAACTCCT
AAAGTTAATTTAGGCTCGACCAATCTCAAAACAGGTTCGATTTAAATAAATTA
Found at i:9687936 original size:49 final size:49
Alignment explanation
Indices: 9687864--9687974 Score: 177
Period size: 49 Copynumber: 2.3 Consensus size: 49
9687854 CATTCATTGT
* *
9687864 CATAGTCGGGTCATCATCATCATCGGCTTATGCGCACTCCCTACTCGCA
1 CATAGCCGGGTCATCATCATCATCGGCTTATACGCACTCCCTACTCGCA
* * *
9687913 CATAGCCGAGTCATCATCATCATCGGCTTATACGCACTTCTTACTCGCA
1 CATAGCCGGGTCATCATCATCATCGGCTTATACGCACTCCCTACTCGCA
9687962 CATAGCCGGGTCA
1 CATAGCCGGGTCA
9687975 ATATTATCAC
Statistics
Matches: 56, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
49 56 1.00
ACGTcount: A:0.23, C:0.33, G:0.18, T:0.26
Consensus pattern (49 bp):
CATAGCCGGGTCATCATCATCATCGGCTTATACGCACTCCCTACTCGCA
Found at i:9690271 original size:12 final size:12
Alignment explanation
Indices: 9690254--9690278 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
9690244 CTTTGAATGG
9690254 CCTTAGGCATAC
1 CCTTAGGCATAC
9690266 CCTTAGGCATAC
1 CCTTAGGCATAC
9690278 C
1 C
9690279 AAGCTCAATA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.36, G:0.16, T:0.24
Consensus pattern (12 bp):
CCTTAGGCATAC
Found at i:9694668 original size:49 final size:49
Alignment explanation
Indices: 9694611--9694730 Score: 170
Period size: 49 Copynumber: 2.4 Consensus size: 49
9694601 CATTCATCGT
9694611 CATAGCCGGGTCATAATTATCATCGGCTTATGCGCAATCCCTACTCGCA
1 CATAGCCGGGTCATAATTATCATCGGCTTATGCGCAATCCCTACTCGCA
* * * * *
9694660 CATAGCCGGGTTATCATCATCATCGGCTTATGCGCACTCCCTACTCGTA
1 CATAGCCGGGTCATAATTATCATCGGCTTATGCGCAATCCCTACTCGCA
*
9694709 CATAGCCGAGTCA-ATATTATCA
1 CATAGCCGGGTCATA-ATTATCA
9694731 CACAACATTA
Statistics
Matches: 61, Mismatches: 9, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
49 61 1.00
ACGTcount: A:0.25, C:0.30, G:0.17, T:0.28
Consensus pattern (49 bp):
CATAGCCGGGTCATAATTATCATCGGCTTATGCGCAATCCCTACTCGCA
Found at i:9700417 original size:19 final size:19
Alignment explanation
Indices: 9700395--9700432 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
9700385 TGCAAGTTAT
* *
9700395 TTTCTTTTTTTATTTTTTA
1 TTTCATTTTATATTTTTTA
9700414 TTTCATTTTATATTTTTTA
1 TTTCATTTTATATTTTTTA
9700433 AACAATTATT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.16, C:0.05, G:0.00, T:0.79
Consensus pattern (19 bp):
TTTCATTTTATATTTTTTA
Found at i:9700833 original size:16 final size:15
Alignment explanation
Indices: 9700811--9700843 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 15
9700801 AAACTCTGCA
9700811 TTTTTATTATTATTT
1 TTTTTATTATTATTT
9700826 TNTTTTATTATTATTT
1 T-TTTTATTATTATTT
9700842 TT
1 TT
9700844 ATTTTGTATT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 2 0.12
16 15 0.88
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.79
Consensus pattern (15 bp):
TTTTTATTATTATTT
Found at i:9701334 original size:38 final size:38
Alignment explanation
Indices: 9701284--9701360 Score: 109
Period size: 38 Copynumber: 2.0 Consensus size: 38
9701274 CTCTCTCTCT
*
9701284 TCTCCCTATCTTTTTCCTTTTTGTCCATCGGTGACTTC
1 TCTCCCTATCTTTTTCCTTTTCGTCCATCGGTGACTTC
* ***
9701322 TCTCCCTCTCTTTTTCCTTTTCGTTGGTCGGTGACTTC
1 TCTCCCTATCTTTTTCCTTTTCGTCCATCGGTGACTTC
9701360 T
1 T
9701361 TTCTATTCCC
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
38 34 1.00
ACGTcount: A:0.05, C:0.31, G:0.13, T:0.51
Consensus pattern (38 bp):
TCTCCCTATCTTTTTCCTTTTCGTCCATCGGTGACTTC
Found at i:9701501 original size:18 final size:19
Alignment explanation
Indices: 9701480--9701535 Score: 60
Period size: 20 Copynumber: 2.9 Consensus size: 19
9701470 TAAAACACTA
*
9701480 ATTTTTTTTTG-TTTATTT
1 ATTTGTTTTTGCTTTATTT
9701498 ATTTGTTTTTGCTTTATTT
1 ATTTGTTTTTGCTTTATTT
* * *
9701517 TTATTGATTTTGATTTATT
1 AT-TTGTTTTTGCTTTATT
9701536 GTTTTTATTG
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
18 10 0.31
19 8 0.25
20 14 0.44
ACGTcount: A:0.14, C:0.02, G:0.09, T:0.75
Consensus pattern (19 bp):
ATTTGTTTTTGCTTTATTT
Found at i:9701506 original size:19 final size:18
Alignment explanation
Indices: 9701482--9701516 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
9701472 AAACACTAAT
9701482 TTTTTTTTG-TTTATTTA
1 TTTTTTTTGCTTTATTTA
9701499 TTTGTTTTTGCTTTATTT
1 TTT-TTTTTGCTTTATTT
9701517 TTATTGATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 3 0.19
18 6 0.38
19 7 0.44
ACGTcount: A:0.09, C:0.03, G:0.09, T:0.80
Consensus pattern (18 bp):
TTTTTTTTGCTTTATTTA
Found at i:9707881 original size:50 final size:50
Alignment explanation
Indices: 9707784--9707882 Score: 146
Period size: 50 Copynumber: 2.0 Consensus size: 50
9707774 ATTGGGGATT
* **
9707784 CCATCCATTGGCAACAAATTAAGTAAAATTTTAGAGAGAGCTTAAAAAGC
1 CCATCCATTGGCAACAAATTAAGTAAAATTTTAGAAAGAGCAAAAAAAGC
*
9707834 CCATGCATTGGCAACAAATT-AGTAAAATTTTAGAAAGCAGCAAAAAAAG
1 CCATCCATTGGCAACAAATTAAGTAAAATTTTAGAAAG-AGCAAAAAAAG
9707883 AAAAAGCTTG
Statistics
Matches: 44, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
49 16 0.36
50 28 0.64
ACGTcount: A:0.46, C:0.15, G:0.16, T:0.22
Consensus pattern (50 bp):
CCATCCATTGGCAACAAATTAAGTAAAATTTTAGAAAGAGCAAAAAAAGC
Found at i:9712657 original size:7 final size:7
Alignment explanation
Indices: 9712615--9712676 Score: 52
Period size: 7 Copynumber: 8.3 Consensus size: 7
9712605 NNNNNTATGC
9712615 TTTTATT
1 TTTTATT
*
9712622 TTTTTTT
1 TTTTATT
9712629 TTTTATT
1 TTTTATT
* *
9712636 CTATTACTA
1 -TTTTA-TT
9712645 TTTTATT
1 TTTTATT
9712652 TTTTATTAT
1 TTTTA-T-T
9712661 TTTTATT
1 TTTTATT
*
9712668 TTCTATT
1 TTTTATT
9712675 TT
1 TT
9712677 CTTTAAAATG
Statistics
Matches: 44, Mismatches: 7, Indels: 8
0.75 0.12 0.14
Matches are distributed among these distances:
7 27 0.61
8 10 0.23
9 7 0.16
ACGTcount: A:0.16, C:0.05, G:0.00, T:0.79
Consensus pattern (7 bp):
TTTTATT
Found at i:9712674 original size:23 final size:21
Alignment explanation
Indices: 9712615--9712681 Score: 64
Period size: 22 Copynumber: 3.0 Consensus size: 21
9712605 NNNNNTATGC
9712615 TTTTATTTTT-TTTTTTTTAT
1 TTTTATTTTTATTTTTTTTAT
9712635 TCTATTACTATTTTATTTTTTATTAT
1 T-T-TTA-T-TTTTATTTTTT-TTAT
*
9712661 TTTTATTTTCTATTTTCTTTA
1 TTTTATTTT-TATTTTTTTTA
9712682 AAATGAGCAT
Statistics
Matches: 39, Mismatches: 1, Indels: 12
0.75 0.02 0.23
Matches are distributed among these distances:
20 1 0.03
21 1 0.03
22 9 0.23
23 9 0.23
24 7 0.18
25 7 0.18
26 5 0.13
ACGTcount: A:0.16, C:0.06, G:0.00, T:0.78
Consensus pattern (21 bp):
TTTTATTTTTATTTTTTTTAT
Found at i:9712681 original size:16 final size:16
Alignment explanation
Indices: 9712615--9712674 Score: 56
Period size: 16 Copynumber: 3.9 Consensus size: 16
9712605 NNNNNTATGC
9712615 TTTTATTTT-T-TT-T
1 TTTTATTTTCTATTAT
*
9712628 TTTT-TATTCTATTACT
1 TTTTATTTTCTATTA-T
*
9712644 ATTTTATTTTTTATTAT
1 -TTTTATTTTCTATTAT
9712661 TTTTATTTTCTATT
1 TTTTATTTTCTATT
9712675 TTCTTTAAAA
Statistics
Matches: 37, Mismatches: 4, Indels: 9
0.74 0.08 0.18
Matches are distributed among these distances:
12 3 0.08
13 5 0.14
14 2 0.05
16 14 0.38
17 5 0.14
18 8 0.22
ACGTcount: A:0.17, C:0.05, G:0.00, T:0.78
Consensus pattern (16 bp):
TTTTATTTTCTATTAT
Found at i:9713213 original size:37 final size:38
Alignment explanation
Indices: 9713103--9713216 Score: 158
Period size: 38 Copynumber: 3.0 Consensus size: 38
9713093 CTCTCTCTCT
** *
9713103 TCTCCCTCTCTTTTTCCTTTTCACCGATCAATGACTTC
1 TCTCCCTCTCTTTTTCCTTTTCGTCGATCGATGACTTC
* *
9713141 TCTCCCTCTTTTTTTCCTTTTCGTCGATCGGTGACTTC
1 TCTCCCTCTCTTTTTCCTTTTCGTCGATCGATGACTTC
* *
9713179 TCTGCCTCTCTTTTT-CTTTTCGTCGGTCGATGACTTC
1 TCTCCCTCTCTTTTTCCTTTTCGTCGATCGATGACTTC
9713216 T
1 T
9713217 TTTTATTCCA
Statistics
Matches: 67, Mismatches: 9, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
37 21 0.31
38 46 0.69
ACGTcount: A:0.08, C:0.32, G:0.11, T:0.48
Consensus pattern (38 bp):
TCTCCCTCTCTTTTTCCTTTTCGTCGATCGATGACTTC
Found at i:9713451 original size:17 final size:18
Alignment explanation
Indices: 9713426--9713464 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 18
9713416 AAAACACTAA
*
9713426 TTTTCTTTTTTG-TTTGT
1 TTTTCTTTTTTGCTCTGT
*
9713443 TTTTTTTTTTTGCTCTGT
1 TTTTCTTTTTTGCTCTGT
9713461 TTTT
1 TTTT
9713465 ATTGATTTTG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 11 0.58
18 8 0.42
ACGTcount: A:0.00, C:0.08, G:0.10, T:0.82
Consensus pattern (18 bp):
TTTTCTTTTTTGCTCTGT
Found at i:9713874 original size:9 final size:9
Alignment explanation
Indices: 9713860--9713937 Score: 50
Period size: 9 Copynumber: 8.3 Consensus size: 9
9713850 CTCTTCTTTC
9713860 TTTTTTATT
1 TTTTTTATT
9713869 TTTTTTATT
1 TTTTTTATT
* *
9713878 TTTATTAGAT
1 TTTTTTA-TT
*
9713888 TTATTT-TT
1 TTTTTTATT
*
9713896 TTTATTATT
1 TTTTTTATT
* *
9713905 ATTTATATT
1 TTTTTTATT
9713914 TTTATATATATT
1 TTT-T-T-TATT
*
9713926 TTTTATATT
1 TTTTTTATT
9713935 TTT
1 TTT
9713938 ATTGAATGGG
Statistics
Matches: 51, Mismatches: 13, Indels: 10
0.69 0.18 0.14
Matches are distributed among these distances:
8 5 0.10
9 32 0.63
10 6 0.12
11 1 0.02
12 7 0.14
ACGTcount: A:0.22, C:0.00, G:0.01, T:0.77
Consensus pattern (9 bp):
TTTTTTATT
Found at i:9713899 original size:18 final size:20
Alignment explanation
Indices: 9713876--9713937 Score: 65
Period size: 21 Copynumber: 3.1 Consensus size: 20
9713866 ATTTTTTTTA
9713876 TTTTTATTA-GATTTAT-TT
1 TTTTTATTATGATTTATATT
*
9713894 TTTTTATTATTATTTATATT
1 TTTTTATTATGATTTATATT
* **
9713914 TTTATATATATTTTTTATATT
1 TTTTTAT-TATGATTTATATT
9713935 TTT
1 TTT
9713938 ATTGAATGGG
Statistics
Matches: 38, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
18 9 0.24
19 6 0.16
20 8 0.21
21 15 0.39
ACGTcount: A:0.24, C:0.00, G:0.02, T:0.74
Consensus pattern (20 bp):
TTTTTATTATGATTTATATT
Found at i:9713913 original size:21 final size:21
Alignment explanation
Indices: 9713865--9713937 Score: 67
Period size: 24 Copynumber: 3.3 Consensus size: 21
9713855 CTTTCTTTTT
* *
9713865 TATTTTTTTTATTTTTATTAGATT
1 TATTTTTTTTATTATTATT---TA
9713889 TATTTTTTTTATTATTATTTA
1 TATTTTTTTTATTATTATTTA
* *
9713910 TA-TTTTTATATATATTTTTTA
1 TATTTTTTTTAT-TATTATTTA
9713931 TATTTTT
1 TATTTTT
9713938 ATTGAATGGG
Statistics
Matches: 43, Mismatches: 4, Indels: 6
0.81 0.08 0.11
Matches are distributed among these distances:
20 8 0.19
21 13 0.30
22 4 0.09
24 18 0.42
ACGTcount: A:0.23, C:0.00, G:0.01, T:0.75
Consensus pattern (21 bp):
TATTTTTTTTATTATTATTTA
Found at i:9713940 original size:33 final size:33
Alignment explanation
Indices: 9713860--9713940 Score: 94
Period size: 33 Copynumber: 2.5 Consensus size: 33
9713850 CTCTTCTTTC
* *
9713860 TTTTTTATTTTT-TTTATTTTTATTAGATTTATT
1 TTTTTTATTTTTATTTATATTTATTAGATATA-T
* *
9713893 TTTTTTATTATTATTTATATTT-TTATATATAT
1 TTTTTTATTTTTATTTATATTTATTAGATATAT
9713925 TTTTTATATTTTTATT
1 TTTTT-TATTTTTATT
9713941 GAATGGGTGT
Statistics
Matches: 41, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
32 6 0.15
33 27 0.66
34 8 0.20
ACGTcount: A:0.22, C:0.00, G:0.01, T:0.77
Consensus pattern (33 bp):
TTTTTTATTTTTATTTATATTTATTAGATATAT
Found at i:9714217 original size:59 final size:59
Alignment explanation
Indices: 9714151--9714559 Score: 461
Period size: 59 Copynumber: 6.9 Consensus size: 59
9714141 AATTCGATTA
* * * *
9714151 AAATTCCTAAATTTAATCTAGGTTCGACCTATCTCACAACAGGTTTGATTTAAAAATTC
1 AAATTCCTAAACTTAATTTAGGCTCGACCTATCTCACAACAGGTTCGATTTAAAAATTC
* *
9714210 AAATTCCTAAACTTATTTTAGGCTCAACCTATCTCACAACAGGTTCGATTTAAAAAAAAATTC
1 AAATTCCTAAACTTAATTTAGGCTCGACCTATCTCACAACAGGTTCGATTT----AAAAATTC
* * * * *
9714273 AAATTCCTAAATTTAATTTAGGTTTGACCTATCTCATAATAGGTTCGATTTAAAAATTC
1 AAATTCCTAAACTTAATTTAGGCTCGACCTATCTCACAACAGGTTCGATTTAAAAATTC
* * *
9714332 AAATTCCTAAACTTAATTTAGCCTCGACCTATCTCACAACAGATTTGATTTAAAAATTC
1 AAATTCCTAAACTTAATTTAGGCTCGACCTATCTCACAACAGGTTCGATTTAAAAATTC
* * ** * *
9714391 AAATTTCTAAACTTAATTTAGGTTTAACCTATCTCACAACAAGTTCAATTT-AAAA---
1 AAATTCCTAAACTTAATTTAGGCTCGACCTATCTCACAACAGGTTCGATTTAAAAATTC
* * *
9714446 AAATT--GAAACTTAATTTAGGCTCGACCTATCTCACAACAAGTTCGATTTAAAATAAATTGA
1 AAATTCCTAAACTTAATTTAGGCTCGACCTATCTCACAACAGGTTCGATTT--AA-AAATT-C
* * * *
9714507 AAATTCCTAGACTTAATCTAGGCTCGACCTATCTTAAAACAGGTTCGATTTAA
1 AAATTCCTAAACTTAATTTAGGCTCGACCTATCTCACAACAGGTTCGATTTAA
9714560 TTCACGAGGC
Statistics
Matches: 295, Mismatches: 41, Indels: 26
0.81 0.11 0.07
Matches are distributed among these distances:
53 39 0.13
55 5 0.02
56 1 0.00
57 3 0.01
58 4 0.01
59 146 0.49
61 7 0.02
63 90 0.31
ACGTcount: A:0.38, C:0.18, G:0.09, T:0.34
Consensus pattern (59 bp):
AAATTCCTAAACTTAATTTAGGCTCGACCTATCTCACAACAGGTTCGATTTAAAAATTC
Found at i:9714287 original size:122 final size:121
Alignment explanation
Indices: 9714151--9714559 Score: 503
Period size: 122 Copynumber: 3.4 Consensus size: 121
9714141 AATTCGATTA
* *
9714151 AAATTCCTAAATTTAATCTAGGTTCGACCTATCTCACAACAGGTTTGATTTAAAAATTCAAATTC
1 AAATTCCTAAACTTAATCTAGGTTCGACCTATCTCACAACAGGTTCGATTTAAAAATTCAAATTC
* *
9714216 CTAAACTTATTTTAGGCTCAACCTATCTCACAACAGGTTCGATTTAAAAAAAAATTC
66 CTAAACTTAATTTAGGCTCGACCTATCTCACAACAGGTTCGATTT-AAAAAAAATTC
* * * * *
9714273 AAATTCCTAAATTTAATTTAGGTTTGACCTATCTCATAATAGGTTCGATTTAAAAATTCAAATTC
1 AAATTCCTAAACTTAATCTAGGTTCGACCTATCTCACAACAGGTTCGATTTAAAAATTCAAATTC
* * *
9714338 CTAAACTTAATTTAGCCTCGACCTATCTCACAACAGATTTGATTT---AAAAATTC
66 CTAAACTTAATTTAGGCTCGACCTATCTCACAACAGGTTCGATTTAAAAAAAATTC
* * ** * *
9714391 AAATTTCTAAACTTAATTTAGGTTTAACCTATCTCACAACAAGTTCAATTT-AAAA---AAATT-
1 AAATTCCTAAACTTAATCTAGGTTCGACCTATCTCACAACAGGTTCGATTTAAAAATTCAAATTC
* * * *
9714451 -GAAACTTAATTTAGGCTCGACCTATCTCACAACAAGTTCGATTTAAAATAAATTGA
66 CTAAACTTAATTTAGGCTCGACCTATCTCACAACAGGTTCGATTTAAAAAAAATT-C
* * * *
9714507 AAATTCCTAGACTTAATCTAGGCTCGACCTATCTTAAAACAGGTTCGATTTAA
1 AAATTCCTAAACTTAATCTAGGTTCGACCTATCTCACAACAGGTTCGATTTAA
9714560 TTCACGAGGC
Statistics
Matches: 248, Mismatches: 34, Indels: 15
0.84 0.11 0.05
Matches are distributed among these distances:
112 39 0.16
114 5 0.02
115 6 0.02
116 41 0.17
117 5 0.02
118 52 0.21
122 100 0.40
ACGTcount: A:0.38, C:0.18, G:0.09, T:0.34
Consensus pattern (121 bp):
AAATTCCTAAACTTAATCTAGGTTCGACCTATCTCACAACAGGTTCGATTTAAAAATTCAAATTC
CTAAACTTAATTTAGGCTCGACCTATCTCACAACAGGTTCGATTTAAAAAAAATTC
Found at i:9727956 original size:49 final size:49
Alignment explanation
Indices: 9727894--9728013 Score: 152
Period size: 49 Copynumber: 2.4 Consensus size: 49
9727884 CATTCATCGT
* * * *
9727894 CATAACCGGGTCATAATTATCATCGATTTATGCGCACTCCCTACTTGCA
1 CATAGCCGGGTCATAATTATCATCGACTTATGCACACTCCCTACTCGCA
* * *
9727943 CATAGCCGGGTCATCATCATCATCGGCTTATGCACACTCCCTACTCGCA
1 CATAGCCGGGTCATAATTATCATCGACTTATGCACACTCCCTACTCGCA
*
9727992 CATAGCCGAGTCA-ATATTATCA
1 CATAGCCGGGTCATA-ATTATCA
9728014 CACAACATTA
Statistics
Matches: 60, Mismatches: 10, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
49 60 1.00
ACGTcount: A:0.27, C:0.31, G:0.15, T:0.28
Consensus pattern (49 bp):
CATAGCCGGGTCATAATTATCATCGACTTATGCACACTCCCTACTCGCA
Found at i:9730723 original size:25 final size:25
Alignment explanation
Indices: 9730694--9730743 Score: 82
Period size: 25 Copynumber: 2.0 Consensus size: 25
9730684 TTTCCCAATC
9730694 ACGTTCTATTTTTCGAATTTTCTTT
1 ACGTTCTATTTTTCGAATTTTCTTT
* *
9730719 ACGTTTTATTTTTTGAATTTTCTTT
1 ACGTTCTATTTTTCGAATTTTCTTT
9730744 CTTTGTTTGG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.16, C:0.12, G:0.08, T:0.64
Consensus pattern (25 bp):
ACGTTCTATTTTTCGAATTTTCTTT
Found at i:9733959 original size:27 final size:27
Alignment explanation
Indices: 9733924--9733982 Score: 86
Period size: 27 Copynumber: 2.2 Consensus size: 27
9733914 TTTCTTATAA
9733924 TTTTT-TTATATTTGTATCATG-TATT
1 TTTTTATTATATTTGTATCATGTTATT
*
9733949 TTTTTANTTATATTTGTATCATGTTGTT
1 TTTTTA-TTATATTTGTATCATGTTATT
9733977 TTTTTA
1 TTTTTA
9733983 AAATATATAT
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
25 5 0.17
27 16 0.53
28 9 0.30
ACGTcount: A:0.19, C:0.03, G:0.08, T:0.68
Consensus pattern (27 bp):
TTTTTATTATATTTGTATCATGTTATT
Found at i:9733989 original size:29 final size:27
Alignment explanation
Indices: 9733930--9733990 Score: 77
Period size: 27 Copynumber: 2.2 Consensus size: 27
9733920 ATAATTTTTT
**
9733930 TATATTTGTATCATGTATTTTTTTANT
1 TATATTTGTATCATGTATTTTTTTAAA
*
9733957 TATATTTGTATCATGTTGTTTTTTTAAAA
1 TATATTTGTATCATG-TATTTTTTT-AAA
9733986 TATAT
1 TATAT
9733991 ATTACATTTA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
27 15 0.52
28 8 0.28
29 6 0.21
ACGTcount: A:0.26, C:0.03, G:0.08, T:0.61
Consensus pattern (27 bp):
TATATTTGTATCATGTATTTTTTTAAA
Found at i:9734175 original size:3 final size:3
Alignment explanation
Indices: 9734167--9734200 Score: 52
Period size: 3 Copynumber: 11.7 Consensus size: 3
9734157 CTCTGCATTT
*
9734167 TTA TTA TTA TT- TTA TTA TTA TTA CTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
9734201 TTTTATTTTG
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
2 2 0.07
3 26 0.93
ACGTcount: A:0.29, C:0.03, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:9734722 original size:38 final size:38
Alignment explanation
Indices: 9734649--9734725 Score: 102
Period size: 38 Copynumber: 2.0 Consensus size: 38
9734639 TTCTCTCTCT
* * * *
9734649 TCTCCCTCTCTTTTTCCTTTTTGTCGATTGGTGACTTC
1 TCTCCCTCTCTTTTTCCTTTTCGTAGATCGATGACTTC
9734687 TCTCCCTCTCTTTTTCCTTTTCGTTAG-TCGATGACTTC
1 TCTCCCTCTCTTTTTCCTTTTCG-TAGATCGATGACTTC
9734725 T
1 T
9734726 TTCTATTCCC
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
38 32 0.94
39 2 0.06
ACGTcount: A:0.06, C:0.30, G:0.12, T:0.52
Consensus pattern (38 bp):
TCTCCCTCTCTTTTTCCTTTTCGTAGATCGATGACTTC
Found at i:9735290 original size:9 final size:9
Alignment explanation
Indices: 9735278--9735318 Score: 64
Period size: 10 Copynumber: 4.3 Consensus size: 9
9735268 CTTTTCTTTC
9735278 TTTTTTATT
1 TTTTTTATT
9735287 TTTTTTATT
1 TTTTTTATT
9735296 TTTATTTATT
1 TTT-TTTATT
9735306 TTTTTATATT
1 TTTTT-TATT
9735316 TTT
1 TTT
9735319 ATTGAATGGG
Statistics
Matches: 30, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
9 14 0.47
10 16 0.53
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (9 bp):
TTTTTTATT
Found at i:9735291 original size:8 final size:8
Alignment explanation
Indices: 9735278--9735321 Score: 52
Period size: 9 Copynumber: 5.1 Consensus size: 8
9735268 CTTTTCTTTC
9735278 TTTTTTATT
1 TTTTTTA-T
9735287 TTTTTTATT
1 TTTTTTA-T
9735296 TTTATTTAT
1 TTT-TTTAT
9735305 TTTTTTAT
1 TTTTTTAT
*
9735313 ATTTTTAT
1 TTTTTTAT
9735321 T
1 T
9735322 GAATGGGTGT
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
8 12 0.38
9 16 0.50
10 4 0.12
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (8 bp):
TTTTTTAT
Found at i:9735303 original size:19 final size:20
Alignment explanation
Indices: 9735281--9735321 Score: 75
Period size: 19 Copynumber: 2.1 Consensus size: 20
9735271 TTCTTTCTTT
9735281 TTTATTTTTTT-TATTTTTA
1 TTTATTTTTTTATATTTTTA
9735300 TTTATTTTTTTATATTTTTA
1 TTTATTTTTTTATATTTTTA
9735320 TT
1 TT
9735322 GAATGGGTGT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 11 0.52
20 10 0.48
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (20 bp):
TTTATTTTTTTATATTTTTA
Found at i:9737947 original size:5 final size:5
Alignment explanation
Indices: 9737933--9737994 Score: 74
Period size: 5 Copynumber: 12.4 Consensus size: 5
9737923 TTCCTTGTTA
* *
9737933 TTTTC TTTTC CTTTC TTTTC TTTTC TTTTTT TTTTC TTTTC TTTTC -TTTC
1 TTTTC TTTTC TTTTC TTTTC TTTTC -TTTTC TTTTC TTTTC TTTTC TTTTC
9737983 -TTTC TTTCTC TT
1 TTTTC TTT-TC TT
9737995 CCATCGTCTA
Statistics
Matches: 50, Mismatches: 4, Indels: 5
0.85 0.07 0.08
Matches are distributed among these distances:
4 8 0.16
5 34 0.68
6 8 0.16
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (5 bp):
TTTTC
Found at i:9737968 original size:21 final size:22
Alignment explanation
Indices: 9737934--9737991 Score: 82
Period size: 21 Copynumber: 2.6 Consensus size: 22
9737924 TCCTTGTTAT
9737934 TTTCTTTTCCTTTCTTTTCTTTTC
1 TTTC-TTT-CTTTCTTTTCTTTTC
*
9737958 TTT-TTTTTTTCTTTTCTTTTC
1 TTTCTTTCTTTCTTTTCTTTTC
9737979 TTTCTTTCTTTCT
1 TTTCTTTCTTTCT
9737992 CTTCCATCGT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
21 17 0.55
22 11 0.35
24 3 0.10
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (22 bp):
TTTCTTTCTTTCTTTTCTTTTC
Found at i:9738331 original size:34 final size:34
Alignment explanation
Indices: 9738303--9738385 Score: 121
Period size: 34 Copynumber: 2.4 Consensus size: 34
9738293 GCACTTTTTG
**
9738303 GCCTCCAAAATCAGCAGAAAAATGGCACTTTCCA
1 GCCTCCAAAATCAGCAGAAAAACAGCACTTTCCA
* * *
9738337 ACCTCCAAAACCAGCAGAAAAACAGCTCTTTCCA
1 GCCTCCAAAATCAGCAGAAAAACAGCACTTTCCA
9738371 GCCTCCAAAATCAGC
1 GCCTCCAAAATCAGC
9738386 CCTTAAATGG
Statistics
Matches: 42, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
34 42 1.00
ACGTcount: A:0.39, C:0.34, G:0.12, T:0.16
Consensus pattern (34 bp):
GCCTCCAAAATCAGCAGAAAAACAGCACTTTCCA
Found at i:9748441 original size:60 final size:59
Alignment explanation
Indices: 9748367--9748503 Score: 170
Period size: 59 Copynumber: 2.3 Consensus size: 59
9748357 TTGATGCTCA
* * *
9748367 AGGCTTCAAGTCCCCTTTTACCTACTCGTGGGACTTCCC-ACACCACCAAATATAAAATCG
1 AGGCTTCAGGTCCCCTTTTACATACTCGT-GGA-TGCCCTACACCACCAAATATAAAATCG
* * *
9748427 AGGCTTCAGGTCCCCTTTTACATACTCGTGGATGCCCTACACGATCAAATATAAAATTG
1 AGGCTTCAGGTCCCCTTTTACATACTCGTGGATGCCCTACACCACCAAATATAAAATCG
*
9748486 -GGCTTTAGGTCTCCCTTT
1 AGGCTTCAGGTC-CCCTTT
9748504 AAAATCAAAT
Statistics
Matches: 68, Mismatches: 7, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
58 14 0.21
59 27 0.40
60 27 0.40
ACGTcount: A:0.26, C:0.29, G:0.16, T:0.29
Consensus pattern (59 bp):
AGGCTTCAGGTCCCCTTTTACATACTCGTGGATGCCCTACACCACCAAATATAAAATCG
Found at i:9748884 original size:2 final size:2
Alignment explanation
Indices: 9748877--9748901 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
9748867 AAACATGTAT
9748877 AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC A
9748902 ACAATATAGG
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:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:9749175 original size:14 final size:13
Alignment explanation
Indices: 9749152--9749181 Score: 51
Period size: 14 Copynumber: 2.2 Consensus size: 13
9749142 AAGTTTCTAG
9749152 CAAGCTTTTAAAT
1 CAAGCTTTTAAAT
9749165 CAAGTCTTTTAAAT
1 CAAG-CTTTTAAAT
9749179 CAA
1 CAA
9749182 ATCAAATTGT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 4 0.25
14 12 0.75
ACGTcount: A:0.40, C:0.17, G:0.07, T:0.37
Consensus pattern (13 bp):
CAAGCTTTTAAAT
Found at i:9755855 original size:79 final size:78
Alignment explanation
Indices: 9755718--9755887 Score: 232
Period size: 79 Copynumber: 2.2 Consensus size: 78
9755708 GGATGTTGTT
* * * * * *
9755718 AGCATGGCATGTAACATGTCGAGACAACATGGGCATGGTGTGTGACAACTCTAGGGATTTCCCTG
1 AGCATGGCATGTAACATATCAAGACAAAATGGGCACGGTGTGTGACAACTCTAAGGATTT-CCTA
9755783 AGTACATGAATATA
65 AGTACATGAATATA
* * *
9755797 AGCATGGCATGTAACATATTAAGACAAAATGGGCGCGGTGTGTGACAACTTTAAGGATTTCCTAA
1 AGCATGGCATGTAACATATCAAGACAAAATGGGCACGGTGTGTGACAACTCTAAGGATTTCCTAA
*
9755862 GTGCATGAATATA
66 GTACATGAATATA
*
9755875 GGCATGGCATGTA
1 AGCATGGCATGTA
9755888 GCATCATTTA
Statistics
Matches: 80, Mismatches: 11, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
78 28 0.35
79 52 0.65
ACGTcount: A:0.32, C:0.16, G:0.26, T:0.26
Consensus pattern (78 bp):
AGCATGGCATGTAACATATCAAGACAAAATGGGCACGGTGTGTGACAACTCTAAGGATTTCCTAA
GTACATGAATATA
Found at i:9755972 original size:30 final size:30
Alignment explanation
Indices: 9755908--9756451 Score: 250
Period size: 30 Copynumber: 18.5 Consensus size: 30
9755898 TGAATTTCAA
* * *
9755908 CATGGCGTGTGGCAACTTA-GATTGTTAAG
1 CATGGCGTGTAGCAACTTAGGATTTTTAGG
9755937 CATGGCGTGTAGCAACTTAGGATTTTTAGG
1 CATGGCGTGTAGCAACTTAGGATTTTTAGG
* * * *
9755967 CATGGCATGTACCATCTTAGGAATTTTAGG
1 CATGGCGTGTAGCAACTTAGGATTTTTAGG
* * **
9755997 CATGGCATGTACCAACTTA-G-TCATTAGG
1 CATGGCGTGTAGCAACTTAGGATTTTTAGG
* ** * *
9756025 CATGGCTTGTAGCAACCAAGAATTTATAGG
1 CATGGCGTGTAGCAACTTAGGATTTTTAGG
* *
9756055 TATGGCGTGTAGCAACTAAGGATTTTTAGG
1 CATGGCGTGTAGCAACTTAGGATTTTTAGG
* * * * * *
9756085 CTTGACGTGTAACAGCCTAGGAATTTTAGG
1 CATGGCGTGTAGCAACTTAGGATTTTTAGG
** * * *
9756115 CATGATGTGTAGCATCTTAGGAATTTTAAG
1 CATGGCGTGTAGCAACTTAGGATTTTTAGG
* * * *
9756145 CATAGCATGTAACAACTTA-G-TTATTAGG
1 CATGGCGTGTAGCAACTTAGGATTTTTAGG
* * * *
9756173 CATGGTGTGTAGCAACTAAGAATTTGTAGG
1 CATGGCGTGTAGCAACTTAGGATTTTTAGG
* ** * ** *
9756203 TATGATGTTTAGCAACCAAAGATTTTTAGG
1 CATGGCGTGTAGCAACTTAGGATTTTTAGG
* * * * * * *
9756233 CTTGGTGTGTAGTAGCCTAAGAATTTTAGG
1 CATGGCGTGTAGCAACTTAGGATTTTTAGG
*** * *
9756263 CATGAAATGTAGCATCTTAGGAATTTTAGG
1 CATGGCGTGTAGCAACTTAGGATTTTTAGG
* * ** * ** *
9756293 CAAGGTGTGTAATAGCTTA-G-TCATTAAG
1 CATGGCGTGTAGCAACTTAGGATTTTTAGG
* **
9756321 CATGGCGTGTAACAACTTA-G-TCATTAGG
1 CATGGCGTGTAGCAACTTAGGATTTTTAGG
* * *
9756349 CATGGCATGTAGCAA-TTGAGAATTTTTAGA
1 CATGGCGTGTAGCAACTT-AGGATTTTTAGG
* ** **
9756379 CATGGCATAAAGCAACCAAGGA-TTTTAGG
1 CATGGCGTGTAGCAACTTAGGATTTTTAGG
* * ** * *
9756408 TACGATGTGTAACAACTTA-G-TTATTAGG
1 CATGGCGTGTAGCAACTTAGGATTTTTAGG
*
9756436 CATGGCGTGTAACAAC
1 CATGGCGTGTAGCAAC
9756452 ATTTAACTTG
Statistics
Matches: 384, Mismatches: 121, Indels: 21
0.73 0.23 0.04
Matches are distributed among these distances:
27 2 0.01
28 99 0.26
29 36 0.09
30 247 0.64
ACGTcount: A:0.30, C:0.14, G:0.25, T:0.31
Consensus pattern (30 bp):
CATGGCGTGTAGCAACTTAGGATTTTTAGG
Found at i:9756036 original size:88 final size:89
Alignment explanation
Indices: 9755871--9756085 Score: 218
Period size: 88 Copynumber: 2.4 Consensus size: 89
9755861 AGTGCATGAA
* * * * ** **
9755871 TATAGGCATGGCATGTAGCATCATTTATGAATTTCA-ACATGGCGTGTGGCAACTTAGATTGTTA
1 TATAGGCATGGCATGTAGCATC--TTAGGAATTTTAGGCATGGCATGTACCAACTTAGATCATTA
** *
9755935 AGCATGGCGTGTAGCAACTTAGGATT
64 AGCATGGCGTGTAGCAACCAAGAATT
* * *
9755961 TTTAGGCATGGCATGTACCATCTTAGGAATTTTAGGCATGGCATGTACCAACTTAG-TCATTAGG
1 TATAGGCATGGCATGTAGCATCTTAGGAATTTTAGGCATGGCATGTACCAACTTAGATCATTAAG
*
9756025 CATGGCTTGTAGCAACCAAGAATT
66 CATGGCGTGTAGCAACCAAGAATT
* * * * *
9756049 TATAGGTATGGCGTGTAGCAACTAAGGATTTTTAGGC
1 TATAGGCATGGCATGTAGCATCTTAGGAATTTTAGGC
9756086 TTGACGTGTA
Statistics
Matches: 102, Mismatches: 22, Indels: 4
0.80 0.17 0.03
Matches are distributed among these distances:
88 65 0.64
89 17 0.17
90 20 0.20
ACGTcount: A:0.28, C:0.15, G:0.25, T:0.32
Consensus pattern (89 bp):
TATAGGCATGGCATGTAGCATCTTAGGAATTTTAGGCATGGCATGTACCAACTTAGATCATTAAG
CATGGCGTGTAGCAACCAAGAATT
Found at i:9756141 original size:148 final size:147
Alignment explanation
Indices: 9755909--9756336 Score: 498
Period size: 148 Copynumber: 2.9 Consensus size: 147
9755899 GAATTTCAAC
* * * * * * * * **
9755909 ATGGCGTGTGGCAACTTAGATTGTTAAGCATGGCGTGTAGCAACTTAGGATTTTTAGGCATGGCA
1 ATGGCGTGTAGCAACTAAGATTTTTAGGCTTGGCGTGTAGCAGCCTAGGAATTTTAGGCATGAAA
* *
9755974 TGTACCATCTTAGGAATTTTAGGCATGGCATGTACCAACTTAGTCATTAGGCATGGCTTGTAGCA
66 TGTAGCATCTTAGGAATTTTAGGCATGGCATGTAACAACTTAGTCATTAGGCATGGCTTGTAGCA
9756039 ACCAAGAATTTATAGGT
131 ACCAAGAATTTATAGGT
* * *
9756056 ATGGCGTGTAGCAACTAAGGATTTTTAGGCTTGACGTGTAACAGCCTAGGAATTTTAGGCATGAT
1 ATGGCGTGTAGCAACTAA-GATTTTTAGGCTTGGCGTGTAGCAGCCTAGGAATTTTAGGCATGAA
* * * *
9756121 GTGTAGCATCTTAGGAATTTTAAGCATAGCATGTAACAACTTAGTTATTAGGCATGG-TGTGTAG
65 ATGTAGCATCTTAGGAATTTTAGGCATGGCATGTAACAACTTAGTCATTAGGCATGGCT-TGTAG
* *
9756185 CAACTAAGAATTTGTAGGT
129 CAACCAAGAATTTATAGGT
** * * * * *
9756204 ATGATGTTTAGCAACCAAAGATTTTTAGGCTTGGTGTGTAGTAGCCTAAGAATTTTAGGCATGAA
1 ATGGCGTGTAGCAA-CTAAGATTTTTAGGCTTGGCGTGTAGCAGCCTAGGAATTTTAGGCATGAA
* ** * * * * *
9756269 ATGTAGCATCTTAGGAATTTTAGGCAAGGTGTGTAATAGCTTAGTCATTAAGCATGGCGTGTAAC
65 ATGTAGCATCTTAGGAATTTTAGGCATGGCATGTAACAACTTAGTCATTAGGCATGGCTTGTAGC
9756334 AAC
130 AAC
9756337 TTAGTCATTA
Statistics
Matches: 235, Mismatches: 42, Indels: 7
0.83 0.15 0.02
Matches are distributed among these distances:
147 17 0.07
148 215 0.91
149 3 0.01
ACGTcount: A:0.29, C:0.13, G:0.25, T:0.32
Consensus pattern (147 bp):
ATGGCGTGTAGCAACTAAGATTTTTAGGCTTGGCGTGTAGCAGCCTAGGAATTTTAGGCATGAAA
TGTAGCATCTTAGGAATTTTAGGCATGGCATGTAACAACTTAGTCATTAGGCATGGCTTGTAGCA
ACCAAGAATTTATAGGT
Found at i:9756339 original size:28 final size:28
Alignment explanation
Indices: 9756299--9756359 Score: 86
Period size: 28 Copynumber: 2.2 Consensus size: 28
9756289 TAGGCAAGGT
* *
9756299 GTGTAATAGCTTAGTCATTAAGCATGGC
1 GTGTAACAACTTAGTCATTAAGCATGGC
*
9756327 GTGTAACAACTTAGTCATTAGGCATGGC
1 GTGTAACAACTTAGTCATTAAGCATGGC
*
9756355 ATGTA
1 GTGTA
9756360 GCAATTGAGA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.30, C:0.15, G:0.25, T:0.31
Consensus pattern (28 bp):
GTGTAACAACTTAGTCATTAAGCATGGC
Found at i:9756503 original size:31 final size:31
Alignment explanation
Indices: 9756437--9756508 Score: 85
Period size: 31 Copynumber: 2.3 Consensus size: 31
9756427 GTTATTAGGC
* *
9756437 ATGGCGTGTAACAACATTTAACTTGTTTTGC
1 ATGGCATGTAACAACATTTAACTTGTTTTGA
*
9756468 ATGGCATGTAACAACA-TTAA-TTTTTTTGTAA
1 ATGGCATGTAACAACATTTAACTTGTTTTG--A
9756499 ATGGCATGTA
1 ATGGCATGTA
9756509 GCTTCTCTAA
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
29 7 0.19
30 4 0.11
31 25 0.69
ACGTcount: A:0.31, C:0.12, G:0.18, T:0.39
Consensus pattern (31 bp):
ATGGCATGTAACAACATTTAACTTGTTTTGA
Found at i:9759609 original size:21 final size:20
Alignment explanation
Indices: 9759584--9759641 Score: 57
Period size: 18 Copynumber: 2.9 Consensus size: 20
9759574 GGATGATGTT
9759584 AGTGGTGGTGATGACGATGAC
1 AGTGGTGG-GATGACGATGAC
* *
9759605 GGTGGT-GGA-GACGATGAT
1 AGTGGTGGGATGACGATGAC
*
9759623 AGTGGTGGCGATGAGGATG
1 AGTGGTGG-GATGACGATG
9759642 TGGAGCAAGC
Statistics
Matches: 30, Mismatches: 4, Indels: 6
0.75 0.10 0.15
Matches are distributed among these distances:
18 13 0.43
19 3 0.10
20 3 0.10
21 11 0.37
ACGTcount: A:0.22, C:0.07, G:0.48, T:0.22
Consensus pattern (20 bp):
AGTGGTGGGATGACGATGAC
Found at i:9760303 original size:32 final size:33
Alignment explanation
Indices: 9760267--9760339 Score: 103
Period size: 33 Copynumber: 2.2 Consensus size: 33
9760257 CGTCCTGTGT
* *
9760267 AAGTGCCATGAAGG-CCTAACCATTGATCATTC
1 AAGTGCAACGAAGGCCCTAACCATTGATCATTC
* *
9760299 AAGTGCAACGTAGGCCCTAACCATTGATCGTTC
1 AAGTGCAACGAAGGCCCTAACCATTGATCATTC
9760332 AAGTGCAA
1 AAGTGCAA
9760340 TTATGAAAAT
Statistics
Matches: 36, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
32 11 0.31
33 25 0.69
ACGTcount: A:0.32, C:0.25, G:0.21, T:0.23
Consensus pattern (33 bp):
AAGTGCAACGAAGGCCCTAACCATTGATCATTC
Found at i:9764034 original size:29 final size:29
Alignment explanation
Indices: 9764001--9764056 Score: 94
Period size: 29 Copynumber: 1.9 Consensus size: 29
9763991 AAATATTTGT
9764001 AATATCCATAGTAGCTAAACAAGATATAC
1 AATATCCATAGTAGCTAAACAAGATATAC
**
9764030 AATATCCATAGTAGCTAAGTAAGATAT
1 AATATCCATAGTAGCTAAACAAGATAT
9764057 CTTGAATATA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.46, C:0.14, G:0.12, T:0.27
Consensus pattern (29 bp):
AATATCCATAGTAGCTAAACAAGATATAC
Found at i:9764104 original size:26 final size:26
Alignment explanation
Indices: 9764074--9764126 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
9764064 ATATATAATA
9764074 ACTAGCACATAATATTCAACAAAACC
1 ACTAGCACATAATATTCAACAAAACC
9764100 ACTAGCACATAATATTCAACAAAACC
1 ACTAGCACATAATATTCAACAAAACC
9764126 A
1 A
9764127 TAACTAAGCA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.51, C:0.26, G:0.04, T:0.19
Consensus pattern (26 bp):
ACTAGCACATAATATTCAACAAAACC
Found at i:9765224 original size:19 final size:19
Alignment explanation
Indices: 9765183--9765225 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 19
9765173 TGAGAAAAGA
** *
9765183 TAATTCTAAAGCTTGATGT
1 TAATTCTAAAGCTAAATGC
*
9765202 TAATTTTAAAGCTAAATGC
1 TAATTCTAAAGCTAAATGC
9765221 TAATT
1 TAATT
9765226 GAAAAAACTT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.37, C:0.09, G:0.12, T:0.42
Consensus pattern (19 bp):
TAATTCTAAAGCTAAATGC
Found at i:9770280 original size:31 final size:29
Alignment explanation
Indices: 9770211--9770267 Score: 105
Period size: 29 Copynumber: 2.0 Consensus size: 29
9770201 AAATAGTTAT
*
9770211 AATATCCACAGTAGCTAAGCAAGATATAC
1 AATATCCATAGTAGCTAAGCAAGATATAC
9770240 AATATCCATAGTAGCTAAGCAAGATATA
1 AATATCCATAGTAGCTAAGCAAGATATA
9770268 TTGAATATCC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.46, C:0.18, G:0.14, T:0.23
Consensus pattern (29 bp):
AATATCCATAGTAGCTAAGCAAGATATAC
Found at i:9772164 original size:2 final size:2
Alignment explanation
Indices: 9772152--9772181 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
9772142 ACCATATACC
*
9772152 AT AT AT GT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
9772182 CAATCATCAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:9772275 original size:42 final size:42
Alignment explanation
Indices: 9772222--9772384 Score: 173
Period size: 42 Copynumber: 3.9 Consensus size: 42
9772212 CATCTCATAT
* * * * * *
9772222 GCAACGGCTTATGCGTACTCCCACTCGCATATAGCGGGGTTA
1 GCAACAGCTTATGTGCACTCCCACTCGCACATAGCCGGGTCA
* * *
9772264 GCAATAGCTTATGTGCACTCCCACTCACACATAACCGGGTCA
1 GCAACAGCTTATGTGCACTCCCACTCGCACATAGCCGGGTCA
* * **
9772306 GCAACGGCTTATGTGCACTCCTACTCGCACATAGTTGGGTCA
1 GCAACAGCTTATGTGCACTCCCACTCGCACATAGCCGGGTCA
* ***
9772348 GCAACGGCTTATGTGCACTTTTACTCGCACATAGCCG
1 GCAACAGCTTATGTGCACTCCCACTCGCACATAGCCG
9772385 AGTCCACATC
Statistics
Matches: 101, Mismatches: 20, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
42 101 1.00
ACGTcount: A:0.23, C:0.30, G:0.22, T:0.25
Consensus pattern (42 bp):
GCAACAGCTTATGTGCACTCCCACTCGCACATAGCCGGGTCA
Found at i:9776426 original size:31 final size:31
Alignment explanation
Indices: 9776391--9776484 Score: 98
Period size: 31 Copynumber: 3.0 Consensus size: 31
9776381 TTCTGACATG
* *
9776391 CCATGCATATCAAATCAAACATTGTGACACA
1 CCATGCATATCAAGTCAAATATTGTGACACA
* * * * **
9776422 CCATGTATAACAAGTAAAATATTCTGACATG
1 CCATGCATATCAAGTCAAATATTGTGACACA
* *
9776453 CCATGCATATCAAGTCTAATATTGTCACACA
1 CCATGCATATCAAGTCAAATATTGTGACACA
9776484 C
1 C
9776485 TAAGGCTGAT
Statistics
Matches: 47, Mismatches: 16, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
31 47 1.00
ACGTcount: A:0.39, C:0.23, G:0.11, T:0.27
Consensus pattern (31 bp):
CCATGCATATCAAGTCAAATATTGTGACACA
Found at i:9777276 original size:156 final size:155
Alignment explanation
Indices: 9776838--9777284 Score: 546
Period size: 152 Copynumber: 2.9 Consensus size: 155
9776828 CAATTAGGTC
* * *
9776838 AACTGCAATAACATATATAACTGTGTTATTCAATAATCATATATGAAATTGTTGAACATTAACTG
1 AACTGCAATTACATATATAACTGTGTTATTCAATAATCATGTATGGAATTGTTGAACATTAACTG
* * * * * *
9776903 TTACAACTTTAATATCCTAACTGACGGCTCGTTAGCAGTCTGCGGTGGAGCCAAATCGATCAGTG
66 TTACAACTTTAATATCCTTACTG-CGGCTCGTTAGCTGTATGCGGTGGAGCCAGACCGATCGGTG
* * * * * *
9776968 CTTAAGAACTTGTCGTCGCTTTTGTA
130 CTTAAGGACCTATCATCACTTTCGTA
*
9776994 AACTGCAATTACATATATAAC--TG-T-TTCAATAATCATGTATGGAATTGTTGAACATTAACCG
1 AACTGCAATTACATATATAACTGTGTTATTCAATAATCATGTATGGAATTGTTGAACATTAACTG
* * * **
9777055 TTACAACTTTAATATCCTTACTG-GTGACTTGTTAG-TAGTTTGTGGTGGAGCTGGACCGATCGG
66 TTACAACTTTAATATCCTTACTGCG-G-CTCGTTAGCT-GTATGCGGTGGAGCCAGACCGATCGG
* *
9777118 TGCTTAAGGACCTATCATTACTTTCGTT
128 TGCTTAAGGACCTATCATCACTTTCGTA
*
9777146 AACTGTAATTACATATATAACTGTGTTATTCAATAATCATGTATGGAATTGTTGAACATTAACTG
1 AACTGCAATTACATATATAACTGTGTTATTCAATAATCATGTATGGAATTGTTGAACATTAACTG
* * * *
9777211 TTACAACTTTAATATCTTTATTAGCGGCTCATTAGCTGTATGCGGTGGAGCCAGACCGATTGGTG
66 TTACAACTTTAATATCCTTACT-GCGGCTCGTTAGCTGTATGCGGTGGAGCCAGACCGATCGGTG
*
9777276 CTTGAGGAC
130 CTTAAGGAC
9777285 TTGTCGTCGT
Statistics
Matches: 247, Mismatches: 34, Indels: 20
0.82 0.11 0.07
Matches are distributed among these distances:
150 1 0.00
151 1 0.00
152 122 0.49
153 1 0.00
154 4 0.02
155 1 0.00
156 113 0.46
157 3 0.01
158 1 0.00
ACGTcount: A:0.30, C:0.17, G:0.19, T:0.35
Consensus pattern (155 bp):
AACTGCAATTACATATATAACTGTGTTATTCAATAATCATGTATGGAATTGTTGAACATTAACTG
TTACAACTTTAATATCCTTACTGCGGCTCGTTAGCTGTATGCGGTGGAGCCAGACCGATCGGTGC
TTAAGGACCTATCATCACTTTCGTA
Found at i:9777306 original size:156 final size:155
Alignment explanation
Indices: 9776838--9777329 Score: 582
Period size: 156 Copynumber: 3.2 Consensus size: 155
9776828 CAATTAGGTC
* *
9776838 AACTGCAATAACATATATAACTGTGTTATTCAATAATCATATATGAAATTGTTGAACATTAACTG
1 AACTGCAATAACATATATAACTGTGTTATTCAATAATCATGTATGGAATTGTTGAACATTAACTG
* * * * * *
9776903 TTACAACTTTAATATCCTAACTGACGGCTCGTTAGCAGTCTGCGGTGGAGCCAAATCGATCAGTG
66 TTACAACTTTAATATCCTTACTG-CGGCTCGTTAGCTGTATGCGGTGGAGCCAGACCGATCGGTG
*
9776968 CTTAAGAACTTGTCGTCGCTTTTGTA
130 CTTAAGGACTTGTCGTCGCTTTTGTA
* *
9776994 AACTGCAATTACATATATAAC--TG-T-TTCAATAATCATGTATGGAATTGTTGAACATTAACCG
1 AACTGCAATAACATATATAACTGTGTTATTCAATAATCATGTATGGAATTGTTGAACATTAACTG
* * * **
9777055 TTACAACTTTAATATCCTTACTG-GTGACTTGTTAG-TAGTTTGTGGTGGAGCTGGACCGATCGG
66 TTACAACTTTAATATCCTTACTGCG-G-CTCGTTAGCT-GTATGCGGTGGAGCCAGACCGATCGG
* * * ** * *
9777118 TGCTTAAGGACCTATCATTACTTTCGTT
128 TGCTTAAGGACTTGTCGTCGCTTTTGTA
* *
9777146 AACTGTAATTACATATATAACTGTGTTATTCAATAATCATGTATGGAATTGTTGAACATTAACTG
1 AACTGCAATAACATATATAACTGTGTTATTCAATAATCATGTATGGAATTGTTGAACATTAACTG
* * * *
9777211 TTACAACTTTAATATCTTTATTAGCGGCTCATTAGCTGTATGCGGTGGAGCCAGACCGATTGGTG
66 TTACAACTTTAATATCCTTACT-GCGGCTCGTTAGCTGTATGCGGTGGAGCCAGACCGATCGGTG
* *
9777276 CTTGAGGACTTGTCGTCGTTTTTGTA
130 CTTAAGGACTTGTCGTCGCTTTTGTA
* * * *
9777302 AACTGTAATAACAGAAATTACTGTGTTA
1 AACTGCAATAACATATATAACTGTGTTA
9777330 CTCGATAAGC
Statistics
Matches: 280, Mismatches: 46, Indels: 20
0.81 0.13 0.06
Matches are distributed among these distances:
150 1 0.00
151 1 0.00
152 122 0.44
153 1 0.00
154 4 0.01
155 1 0.00
156 146 0.52
157 3 0.01
158 1 0.00
ACGTcount: A:0.29, C:0.16, G:0.19, T:0.36
Consensus pattern (155 bp):
AACTGCAATAACATATATAACTGTGTTATTCAATAATCATGTATGGAATTGTTGAACATTAACTG
TTACAACTTTAATATCCTTACTGCGGCTCGTTAGCTGTATGCGGTGGAGCCAGACCGATCGGTGC
TTAAGGACTTGTCGTCGCTTTTGTA
Found at i:9779012 original size:31 final size:31
Alignment explanation
Indices: 9778974--9779045 Score: 126
Period size: 31 Copynumber: 2.3 Consensus size: 31
9778964 AATAAGGAAT
*
9778974 AAATGTTGTGACACGCCATGCATAGCAAGCA
1 AAATGTTGTGACACGCCATGCATAACAAGCA
*
9779005 AAATGTTGTGACACGCCATGCATAACAAGTA
1 AAATGTTGTGACACGCCATGCATAACAAGCA
9779036 AAATGTTGTG
1 AAATGTTGTG
9779046 TAAAATGTTG
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
31 39 1.00
ACGTcount: A:0.36, C:0.18, G:0.22, T:0.24
Consensus pattern (31 bp):
AAATGTTGTGACACGCCATGCATAACAAGCA
Found at i:9779044 original size:62 final size:62
Alignment explanation
Indices: 9778974--9779261 Score: 281
Period size: 62 Copynumber: 4.5 Consensus size: 62
9778964 AATAAGGAAT
*
9778974 AAATGTTGTGACACGCCATGCATAGCAAGCAAAATGTTGTGACACGCCATGCATAACAAGTAAAA
1 AAATGTTGTGACACGCCATGCATATCAAGCAAAATGTTGTGACACGCCATGCATAAC------AA
9779039 TGTTGTGTA
60 ------GTA
* * *
9779048 AAATGTTGTGACACACCATGCATATCAAGTAAAATGTTGTGACACGCCATGCATAACAAGTT
1 AAATGTTGTGACACGCCATGCATATCAAGCAAAATGTTGTGACACGCCATGCATAACAAGTA
* * ** * *
9779110 AAATCTTGTGACACGCCATGCATAACAAGTTAAATCTTGTGACACGCCATGCATATCAAGTA
1 AAATGTTGTGACACGCCATGCATATCAAGCAAAATGTTGTGACACGCCATGCATAACAAGTA
* * * * * * *
9779172 AAATGCTATCACAGGCCATGCATATCAA-CTAAAATGTTGTCACACGCTATGCATATCAAGTA
1 AAATGTTGTGACACGCCATGCATATCAAGC-AAAATGTTGTGACACGCCATGCATAACAAGTA
* *
9779234 AAATGTTGTCACACGCTATGCATATCAA
1 AAATGTTGTGACACGCCATGCATATCAA
9779262 ATCGAATCAT
Statistics
Matches: 187, Mismatches: 26, Indels: 14
0.82 0.11 0.06
Matches are distributed among these distances:
62 131 0.70
68 2 0.01
74 54 0.29
ACGTcount: A:0.36, C:0.20, G:0.17, T:0.26
Consensus pattern (62 bp):
AAATGTTGTGACACGCCATGCATATCAAGCAAAATGTTGTGACACGCCATGCATAACAAGTA
Found at i:9779050 original size:12 final size:12
Alignment explanation
Indices: 9779033--9779057 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
9779023 TGCATAACAA
9779033 GTAAAATGTTGT
1 GTAAAATGTTGT
9779045 GTAAAATGTTGT
1 GTAAAATGTTGT
9779057 G
1 G
9779058 ACACACCATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.32, C:0.00, G:0.28, T:0.40
Consensus pattern (12 bp):
GTAAAATGTTGT
Found at i:9779067 original size:43 final size:43
Alignment explanation
Indices: 9779004--9779088 Score: 152
Period size: 43 Copynumber: 2.0 Consensus size: 43
9778994 CATAGCAAGC
*
9779004 AAAATGTTGTGACACGCCATGCATAACAAGTAAAATGTTGTGT
1 AAAATGTTGTGACACACCATGCATAACAAGTAAAATGTTGTGT
*
9779047 AAAATGTTGTGACACACCATGCATATCAAGTAAAATGTTGTG
1 AAAATGTTGTGACACACCATGCATAACAAGTAAAATGTTGTG
9779089 ACACGCCATG
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
43 40 1.00
ACGTcount: A:0.38, C:0.14, G:0.20, T:0.28
Consensus pattern (43 bp):
AAAATGTTGTGACACACCATGCATAACAAGTAAAATGTTGTGT
Found at i:9779083 original size:31 final size:31
Alignment explanation
Indices: 9779045--9779261 Score: 290
Period size: 31 Copynumber: 7.0 Consensus size: 31
9779035 AAAATGTTGT
*
9779045 GTAAAATGTTGTGACACACCATGCATATCAA
1 GTAAAATGTTGTGACACGCCATGCATATCAA
*
9779076 GTAAAATGTTGTGACACGCCATGCATAACAA
1 GTAAAATGTTGTGACACGCCATGCATATCAA
* * *
9779107 GTTAAATCTTGTGACACGCCATGCATAACAA
1 GTAAAATGTTGTGACACGCCATGCATATCAA
* *
9779138 GTTAAATCTTGTGACACGCCATGCATATCAA
1 GTAAAATGTTGTGACACGCCATGCATATCAA
* * * *
9779169 GTAAAATGCTATCACAGGCCATGCATATCAA
1 GTAAAATGTTGTGACACGCCATGCATATCAA
* * *
9779200 CTAAAATGTTGTCACACGCTATGCATATCAA
1 GTAAAATGTTGTGACACGCCATGCATATCAA
* *
9779231 GTAAAATGTTGTCACACGCTATGCATATCAA
1 GTAAAATGTTGTGACACGCCATGCATATCAA
9779262 ATCGAATCAT
Statistics
Matches: 169, Mismatches: 17, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 169 1.00
ACGTcount: A:0.36, C:0.21, G:0.16, T:0.26
Consensus pattern (31 bp):
GTAAAATGTTGTGACACGCCATGCATATCAA
Found at i:9779095 original size:74 final size:74
Alignment explanation
Indices: 9778974--9779119 Score: 247
Period size: 74 Copynumber: 2.0 Consensus size: 74
9778964 AATAAGGAAT
*
9778974 AAATGTTGTGACACGCCATGCATAGCAAGCAAAATGTTGTGACACGCCATGCATAACAAGTAAAA
1 AAATGTTGTGACACACCATGCATAGCAAGCAAAATGTTGTGACACGCCATGCATAACAAGTAAAA
*
9779039 TGTTGTGTA
66 TCTTGTGTA
* * *
9779048 AAATGTTGTGACACACCATGCATATCAAGTAAAATGTTGTGACACGCCATGCATAACAAGTTAAA
1 AAATGTTGTGACACACCATGCATAGCAAGCAAAATGTTGTGACACGCCATGCATAACAAGTAAAA
9779113 TCTTGTG
66 TCTTGTG
9779120 ACACGCCATG
Statistics
Matches: 67, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
74 67 1.00
ACGTcount: A:0.36, C:0.18, G:0.20, T:0.26
Consensus pattern (74 bp):
AAATGTTGTGACACACCATGCATAGCAAGCAAAATGTTGTGACACGCCATGCATAACAAGTAAAA
TCTTGTGTA
Found at i:9779932 original size:47 final size:46
Alignment explanation
Indices: 9779869--9780257 Score: 323
Period size: 47 Copynumber: 8.3 Consensus size: 46
9779859 GACCATGGCA
* *
9779869 TGTCACCAACTCTGAACTCTGGCATGTCACAGCTTTCCTCCATGGTG
1 TGTCACCAACTCT-AACTCTGGCATGTCACAGATTCCCTCCATGGTG
* * * *
9779916 TGTCACCAACTTTGAACTCTGACATGTCACAGATTCCCTCTATGGAG
1 TGTCACCAACTCT-AACTCTGGCATGTCACAGATTCCCTCCATGGTG
* ** * * ** * *
9779963 TCTCATGAACTCTGAACGCTAGTGTGTCACAAATTCCCTCCATGCTG
1 TGTCACCAACTCT-AACTCTGGCATGTCACAGATTCCCTCCATGGTG
* *
9780010 TGTCACCAACTCTTAATTTTGGCATGTCACAGATTCCCTCCATGGTG
1 TGTCACCAACTC-TAACTCTGGCATGTCACAGATTCCCTCCATGGTG
* * * * * **
9780057 TCTCACCAACTCTAAATGCTGACGTGTCACAGATTCCCACCATGGCA
1 TGTCACCAACTCTAACT-CTGGCATGTCACAGATTCCCTCCATGGTG
* ** *
9780104 TGTCACCAACTCTTAACTCCGGTGTGTCACAGATTCCCTCCATGGCG
1 TGTCACCAACTC-TAACTCTGGCATGTCACAGATTCCCTCCATGGTG
* * * * * *
9780151 TCTCACCAACTCTAAATGTTGACTTGTCACAGATTCCCACCATGGTG
1 TGTCACCAACTCTAACT-CTGGCATGTCACAGATTCCCTCCATGGTG
* * * *
9780198 TGTCACCAACTTTTAACTCTAGG-GTGCCACAGATTCCTTCCATGGCT-
1 TGTCACCAAC-TCTAACTCT-GGCATGTCACAGATTCCCTCCATGG-TG
*
9780245 TCTCACCAACTCT
1 TGTCACCAACTCT
9780258 TACCCAATTT
Statistics
Matches: 270, Mismatches: 65, Indels: 15
0.77 0.19 0.04
Matches are distributed among these distances:
46 10 0.04
47 248 0.92
48 12 0.04
ACGTcount: A:0.23, C:0.31, G:0.16, T:0.30
Consensus pattern (46 bp):
TGTCACCAACTCTAACTCTGGCATGTCACAGATTCCCTCCATGGTG
Found at i:9780036 original size:94 final size:94
Alignment explanation
Indices: 9779893--9780257 Score: 380
Period size: 94 Copynumber: 3.9 Consensus size: 94
9779883 AACTCTGGCA
* * * * * *
9779893 TGTCACAGCTTTCCTCCATGGTGTGTCACCAACT-TTGAACTCTGACATGTCACAGATTCCCTCT
1 TGTCACAGATTCCCACCATGCTGTGTCACCAACTCTT-AACTCTGGCATGTCACAGATTCCCTCC
** * *
9779957 ATGGAGTCTCATGAACTCTGAACGCTAGTG
65 ATGGAGTCTCACCAACTCTAAATGCTAGTG
* * * *
9779987 TGTCACAAATTCCCTCCATGCTGTGTCACCAACTCTTAATTTTGGCATGTCACAGATTCCCTCCA
1 TGTCACAGATTCCCACCATGCTGTGTCACCAACTCTTAACTCTGGCATGTCACAGATTCCCTCCA
* *
9780052 TGGTGTCTCACCAACTCTAAATGCT-GACG
66 TGGAGTCTCACCAACTCTAAATGCTAG-TG
* * **
9780081 TGTCACAGATTCCCACCATGGC-ATGTCACCAACTCTTAACTCCGGTGTGTCACAGATTCCCTCC
1 TGTCACAGATTCCCACCAT-GCTGTGTCACCAACTCTTAACTCTGGCATGTCACAGATTCCCTCC
* * *
9780145 ATGGCGTCTCACCAACTCTAAATGTTGACT-
65 ATGGAGTCTCACCAACTCTAAATGCT-AGTG
* * * * *
9780175 TGTCACAGATTCCCACCATGGTGTGTCACCAACTTTTAACTCTAGG-GTGCCACAGATTCCTTCC
1 TGTCACAGATTCCCACCATGCTGTGTCACCAACTCTTAACTCT-GGCATGTCACAGATTCCCTCC
**
9780239 ATGGCTTCTCACCAACTCT
65 ATGGAGTCTCACCAACTCT
9780258 TACCCAATTT
Statistics
Matches: 231, Mismatches: 33, Indels: 14
0.83 0.12 0.05
Matches are distributed among these distances:
93 2 0.01
94 223 0.97
95 6 0.03
ACGTcount: A:0.23, C:0.31, G:0.16, T:0.30
Consensus pattern (94 bp):
TGTCACAGATTCCCACCATGCTGTGTCACCAACTCTTAACTCTGGCATGTCACAGATTCCCTCCA
TGGAGTCTCACCAACTCTAAATGCTAGTG
Found at i:9780229 original size:141 final size:141
Alignment explanation
Indices: 9779891--9780259 Score: 431
Period size: 141 Copynumber: 2.6 Consensus size: 141
9779881 TGAACTCTGG
* * * *
9779891 CATGTCACAGCTTTCCTCCATGGTGTGTCACCAACTTTGAACTCTGACATGTCACAGATTCCCTC
1 CATGTCACAGATTCCCTCCATGGTGTGTCACCAACTTTTAACTCTGACGTGTCACAGATTCCCTC
* ** * * *
9779956 TATGG-AGTCTCATGAACTCTGAACGCTAGTGTGTCACAAATTCCCTCCATGCTGTGTCACCAAC
66 CATGGCA-TCTCACCAACTCTTAACGCCAGTGTGTCACAAATTCCCTCCATGCTGTCTCACCAAC
* * *
9780020 TCTTAATTTTGG
130 TCTAAATGTTGA
* * * *
9780032 CATGTCACAGATTCCCTCCATGGTGTCTCACCAAC-TCTAAATGCTGACGTGTCACAGATTCCCA
1 CATGTCACAGATTCCCTCCATGGTGTGTCACCAACTTTTAACT-CTGACGTGTCACAGATTCCCT
* * * *
9780096 CCATGGCATGTCACCAACTCTTAACTCCGGTGTGTCACAGATTCCCTCCATGGC-GTCTCACCAA
65 CCATGGCATCTCACCAACTCTTAACGCCAGTGTGTCACAAATTCCCTCCAT-GCTGTCTCACCAA
9780160 CTCTAAATGTTGA
129 CTCTAAATGTTGA
* * * * *
9780173 CTTGTCACAGATTCCCACCATGGTGTGTCACCAACTTTTAACTCT-AGGGTGCCACAGATTCCTT
1 CATGTCACAGATTCCCTCCATGGTGTGTCACCAACTTTTAACTCTGA-CGTGTCACAGATTCCCT
*
9780237 CCATGGCTTCTCACCAACTCTTA
65 CCATGGCATCTCACCAACTCTTA
9780260 CCCAATTTAA
Statistics
Matches: 191, Mismatches: 32, Indels: 10
0.82 0.14 0.04
Matches are distributed among these distances:
140 5 0.03
141 178 0.93
142 8 0.04
ACGTcount: A:0.23, C:0.31, G:0.16, T:0.30
Consensus pattern (141 bp):
CATGTCACAGATTCCCTCCATGGTGTGTCACCAACTTTTAACTCTGACGTGTCACAGATTCCCTC
CATGGCATCTCACCAACTCTTAACGCCAGTGTGTCACAAATTCCCTCCATGCTGTCTCACCAACT
CTAAATGTTGA
Found at i:9781658 original size:21 final size:21
Alignment explanation
Indices: 9781621--9781666 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 21
9781611 AATAAATTAA
9781621 AAAATTTTAAAGTTTTAAAAGT
1 AAAATTTTAAAG-TTTAAAAGT
*
9781643 AAAATTTATAAA-TTTAAGAGT
1 AAAATTT-TAAAGTTTAAAAGT
9781664 AAA
1 AAA
9781667 TTTGGTTCTT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
21 11 0.50
22 7 0.32
23 4 0.18
ACGTcount: A:0.54, C:0.00, G:0.09, T:0.37
Consensus pattern (21 bp):
AAAATTTTAAAGTTTAAAAGT
Found at i:9790575 original size:33 final size:33
Alignment explanation
Indices: 9790533--9790597 Score: 103
Period size: 33 Copynumber: 2.0 Consensus size: 33
9790523 AGTTTGGTCT
***
9790533 TTTGATATTTGTTTTGGCTTTGGTGTTTAGACC
1 TTTGATATTTGTTTCAACTTTGGTGTTTAGACC
9790566 TTTGATATTTGTTTCAACTTTGGTGTTTAGAC
1 TTTGATATTTGTTTCAACTTTGGTGTTTAGAC
9790598 TTGATTTATT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.15, C:0.09, G:0.22, T:0.54
Consensus pattern (33 bp):
TTTGATATTTGTTTCAACTTTGGTGTTTAGACC
Found at i:9792857 original size:31 final size:31
Alignment explanation
Indices: 9792780--9792858 Score: 95
Period size: 31 Copynumber: 2.5 Consensus size: 31
9792770 CACATCAAAA
* *
9792780 GGATTAAATTGAATAAAAATGTAGAGTACAT
1 GGATTAAATTGAATAAAAATATAAAGTACAT
* * * * *
9792811 AGACTGAATTCAATAAAATTATAAAGTACAT
1 GGATTAAATTGAATAAAAATATAAAGTACAT
9792842 GGATTAAATTGAATAAA
1 GGATTAAATTGAATAAA
9792859 TATCTATCAT
Statistics
Matches: 37, Mismatches: 11, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
31 37 1.00
ACGTcount: A:0.51, C:0.05, G:0.15, T:0.29
Consensus pattern (31 bp):
GGATTAAATTGAATAAAAATATAAAGTACAT
Found at i:9794292 original size:31 final size:31
Alignment explanation
Indices: 9794219--9794301 Score: 105
Period size: 31 Copynumber: 2.7 Consensus size: 31
9794209 ATGATAGATC
* **
9794219 TTTGTTCAATTTAGTCCATATACTCTATAAT
1 TTTGTTCAATTTAATCTTTATACTCTATAAT
* *
9794250 TTTACTT-AATTTAATCTTTGTACTCTATAAT
1 TTT-GTTCAATTTAATCTTTATACTCTATAAT
9794281 TTTGTTCAATTTAATCTTTAT
1 TTTGTTCAATTTAATCTTTAT
9794302 GACGTGATAC
Statistics
Matches: 43, Mismatches: 7, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
30 2 0.05
31 39 0.91
32 2 0.05
ACGTcount: A:0.28, C:0.13, G:0.05, T:0.54
Consensus pattern (31 bp):
TTTGTTCAATTTAATCTTTATACTCTATAAT
Found at i:9802982 original size:19 final size:19
Alignment explanation
Indices: 9802960--9802996 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
9802950 ATTCAATTAA
9802960 AACTTTAAAATTAAAAAAC
1 AACTTTAAAATTAAAAAAC
* *
9802979 AACTTTTAATTTAAAAAA
1 AACTTTAAAATTAAAAAA
9802997 TTAAAAAAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.59, C:0.08, G:0.00, T:0.32
Consensus pattern (19 bp):
AACTTTAAAATTAAAAAAC
Found at i:9807553 original size:79 final size:79
Alignment explanation
Indices: 9807422--9807586 Score: 253
Period size: 79 Copynumber: 2.1 Consensus size: 79
9807412 TTAAAGGAGG
* * * *
9807422 GAGAAAAAAGGGTGAAAGCAGTGCTGCGCACCAGATTCGGAGACATTGGAGATTTGGCCGATGAA
1 GAGAAGAAAGGGTGAAAGCAGTGCCGCGCACCAGATTCGGAGACATTGGAGATCTGGCCGACGAA
9807487 AAGGTGGCTTTAGA
66 AAGGTGGCTTTAGA
*
9807501 GAGAAGAAAGGGTGAAAGCAGTGCCGCGCACCAGA-TCTGGCA-ACGTTGGAGATCTGGCCGACG
1 GAGAAGAAAGGGTGAAAGCAGTGCCGCGCACCAGATTC-GG-AGACATTGGAGATCTGGCCGACG
9807564 AAAAGGTGGCTTTAGA
64 AAAAGGTGGCTTTAGA
9807580 GAGAAGA
1 GAGAAGA
9807587 GAGAAGAGGA
Statistics
Matches: 79, Mismatches: 5, Indels: 4
0.90 0.06 0.05
Matches are distributed among these distances:
78 2 0.03
79 76 0.96
80 1 0.01
ACGTcount: A:0.33, C:0.16, G:0.35, T:0.16
Consensus pattern (79 bp):
GAGAAGAAAGGGTGAAAGCAGTGCCGCGCACCAGATTCGGAGACATTGGAGATCTGGCCGACGAA
AAGGTGGCTTTAGA
Found at i:9807644 original size:14 final size:13
Alignment explanation
Indices: 9807619--9807667 Score: 62
Period size: 14 Copynumber: 3.5 Consensus size: 13
9807609 GCCAGCAGGG
9807619 AGAAAGGAGAAAAA
1 AGAAA-GAGAAAAA
9807633 GAGAAAGAGAAAGAA
1 -AGAAAGAGAAA-AA
*
9807648 AGAAAGAGGAAAA
1 AGAAAGAGAAAAA
9807661 AGAAAGA
1 AGAAAGA
9807668 AGAAGCCAGC
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
13 9 0.28
14 16 0.50
15 7 0.22
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (13 bp):
AGAAAGAGAAAAA
Found at i:9807644 original size:21 final size:23
Alignment explanation
Indices: 9807618--9807672 Score: 64
Period size: 21 Copynumber: 2.6 Consensus size: 23
9807608 CGCCAGCAGG
9807618 GAGAAAGGAGAA-AAAGA-GAAA
1 GAGAAAGGAGAAGAAAGAGGAAA
9807639 GAGAAA-GA-AAGAAAGAGGAAA
1 GAGAAAGGAGAAGAAAGAGGAAA
* *
9807660 AAGAAAGAAGAAG
1 GAGAAAGGAGAAG
9807673 CCAGCGAGGA
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
19 2 0.07
20 7 0.25
21 15 0.54
22 1 0.04
23 3 0.11
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (23 bp):
GAGAAAGGAGAAGAAAGAGGAAA
Found at i:9807712 original size:9 final size:8
Alignment explanation
Indices: 9807618--9807713 Score: 50
Period size: 7 Copynumber: 12.8 Consensus size: 8
9807608 CGCCAGCAGG
9807618 GAGAAAG-
1 GAGAAAGA
*
9807625 GAGAAAAA
1 GAGAAAGA
9807633 GAG-AA-A
1 GAGAAAGA
9807639 GAGAAAGA
1 GAGAAAGA
*
9807647 AAGAAAGA
1 GAGAAAGA
9807655 G-GAAA-A
1 GAGAAAGA
9807661 -AGAAAGA
1 GAGAAAGA
9807668 -AG-AAGCCA
1 GAGAAAG--A
* *
9807676 GCGAGGAGA
1 GAGA-AAGA
9807685 GAGAAAG-
1 GAGAAAGA
9807692 GA-AAAGA
1 GAGAAAGA
9807699 GAGAAAGA
1 GAGAAAGA
9807707 GAAGAAA
1 G-AGAAA
9807714 AAAAAAGAAA
Statistics
Matches: 69, Mismatches: 7, Indels: 24
0.69 0.07 0.24
Matches are distributed among these distances:
6 16 0.23
7 21 0.30
8 20 0.29
9 10 0.14
11 2 0.03
ACGTcount: A:0.62, C:0.03, G:0.34, T:0.00
Consensus pattern (8 bp):
GAGAAAGA
Found at i:9807722 original size:13 final size:13
Alignment explanation
Indices: 9807700--9807742 Score: 52
Period size: 13 Copynumber: 3.3 Consensus size: 13
9807690 AGGAAAAGAG
*
9807700 AGAAAGAGAAGAAA
1 AGAAAAAGAA-AAA
9807714 A-AAAAAGAAAAA
1 AGAAAAAGAAAAA
*
9807726 AGAAAAAGAAAGA
1 AGAAAAAGAAAAA
9807739 AGAA
1 AGAA
9807743 GCCGGCAGGG
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
12 4 0.15
13 21 0.81
14 1 0.04
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (13 bp):
AGAAAAAGAAAAA
Found at i:9807739 original size:71 final size:71
Alignment explanation
Indices: 9807619--9807808 Score: 210
Period size: 71 Copynumber: 2.7 Consensus size: 71
9807609 GCCAGCAGGG
* * * * *
9807619 AGAAAGGAGAAAAAGAGAAAGAGAAAGAAAGAAAGAGGAAAAAGAAAGAAGAAGCCAGC-GAGGA
1 AGAAAAGAGAGAAAGAG-AAGAAAAAGAAAGAAAAAAGAAAAAGAAAGAAGAAGCCAGCAG-GGA
9807683 GAGAGAAA
64 GAGAGAAA
* * *
9807691 GGAAAAGAGAGAAAGAGAAGAAAAAAAAAGAAAAAAGAAAAAGAAAGAAGAAGCCGGCAGGGAGA
1 AGAAAAGAGAGAAAGAGAAGAAAAAGAAAGAAAAAAGAAAAAGAAAGAAGAAGCCAGCAGGGAGA
9807756 GAGAAA
66 GAGAAA
* * *
9807762 AG-AAAGGGAG-AAG-GAA-AAAAGAGAGAGAAAGAAAGAAAAAAAAAGAA
1 AGAAAAGAGAGAAAGAGAAGAAAA-AGAAAGAAA-AAAGAAAAAGAAAGAA
9807809 AAAAGAAAAA
Statistics
Matches: 102, Mismatches: 13, Indels: 9
0.82 0.10 0.07
Matches are distributed among these distances:
67 4 0.04
68 10 0.10
69 18 0.18
70 7 0.07
71 48 0.47
72 15 0.15
ACGTcount: A:0.65, C:0.03, G:0.32, T:0.00
Consensus pattern (71 bp):
AGAAAAGAGAGAAAGAGAAGAAAAAGAAAGAAAAAAGAAAAAGAAAGAAGAAGCCAGCAGGGAGA
GAGAAA
Found at i:9807771 original size:17 final size:16
Alignment explanation
Indices: 9807749--9807796 Score: 50
Period size: 13 Copynumber: 3.1 Consensus size: 16
9807739 AGAAGCCGGC
9807749 AGGGAGAGAGAAAAGAA
1 AGGGAGAGAG-AAAGAA
9807766 AGGGAGA-AGGAAA-AA
1 AGGGAGAGA-GAAAGAA
9807781 A--GAGAGAGAAAGAA
1 AGGGAGAGAGAAAGAA
9807795 AG
1 AG
9807797 AAAAAAAAAG
Statistics
Matches: 27, Mismatches: 0, Indels: 10
0.73 0.00 0.27
Matches are distributed among these distances:
13 8 0.30
14 4 0.15
15 3 0.11
16 4 0.15
17 8 0.30
ACGTcount: A:0.60, C:0.00, G:0.40, T:0.00
Consensus pattern (16 bp):
AGGGAGAGAGAAAGAA
Found at i:9817231 original size:59 final size:59
Alignment explanation
Indices: 9817160--9817800 Score: 820
Period size: 59 Copynumber: 10.9 Consensus size: 59
9817150 CATTAAAGAA
*
9817160 TTAAATCGAACCTGTTGTGAGATAGGTCGAGCCTAGATTAAGTCTAAGAATTTCAATTT
1 TTAAATCGAACCTGTTGTGAGATAGGTCGAGCCTAGATTAAGTCTAGGAATTTCAATTT
* * **
9817219 TTAAATCTAACCTATTACGAGATAGGTCGAGCCTAGATTAAGTCTAGGAATTTCAATTT
1 TTAAATCGAACCTGTTGTGAGATAGGTCGAGCCTAGATTAAGTCTAGGAATTTCAATTT
* *
9817278 TTAAATCGAACCTGTTGTGAGATAGATCGAGCCTATATTAAGTCTAGGAATTTCAATTT
1 TTAAATCGAACCTGTTGTGAGATAGGTCGAGCCTAGATTAAGTCTAGGAATTTCAATTT
* * * * *
9817337 TTAAATCGAACCTGTTGTGAAATAAGTTGAACCTAGATTAAGTCTAGGAATTTTAATTT
1 TTAAATCGAACCTGTTGTGAGATAGGTCGAGCCTAGATTAAGTCTAGGAATTTCAATTT
*
9817396 TTAAATCGAACCTGTTGTGAGATAGGTCGAACCTAGATTAAG-CTAGGAATTTCAATTT
1 TTAAATCGAACCTGTTGTGAGATAGGTCGAGCCTAGATTAAGTCTAGGAATTTCAATTT
* * *
9817454 TTAAATCGAACCTGTTGTGAGATAGGTCGAGCCTAAATTAAGTTTAGAAATTTCAATTTTTT
1 TTAAATCGAACCTGTTGTGAGATAGGTCGAGCCTAGATTAAGTCTAGGAATTTCAA---TTT
*
9817516 TTAAATCGAACCTGTTGTGAGATAGGTCGAGCCTAAATTAAGTCTA-GAATTTCAA-TT
1 TTAAATCGAACCTGTTGTGAGATAGGTCGAGCCTAGATTAAGTCTAGGAATTTCAATTT
* * * * *
9817573 TTAAATTGAACCTGTTATGAGATAGGTCAAGCCTAAATTAAGTTTAGGAATTTCAATTTTGT
1 TTAAATCGAACCTGTTGTGAGATAGGTCGAGCCTAGATTAAGTCTAGGAATTTCAA--TT-T
*
9817635 TTAAATCGAACTTGTTGTGAGATAGGTCGAG-CTAAGATTAAGTCTAGG------AA-TT
1 TTAAATCGAACCTGTTGTGAGATAGGTCGAGCCT-AGATTAAGTCTAGGAATTTCAATTT
** * * * * * * *
9817687 TT-AATCGAATTTGTTCTAATATGGGTCAAGCCTAGATCAAGTCTAGAAATTTCAATTTTGT
1 TTAAATCGAACCTGTTGTGAGATAGGTCGAGCCTAGATTAAGTCTAGGAATTTCAA--TT-T
9817748 TTAAATCGAACCTGTTGTGAGATAGGTCGAGCCTAGATTAAGTCTAGGAATTT
1 TTAAATCGAACCTGTTGTGAGATAGGTCGAGCCTAGATTAAGTCTAGGAATTT
9817801 TAATCGAATT
Statistics
Matches: 505, Mismatches: 55, Indels: 41
0.84 0.09 0.07
Matches are distributed among these distances:
51 34 0.07
52 5 0.01
53 1 0.00
56 2 0.00
57 46 0.09
58 64 0.13
59 209 0.41
60 1 0.00
61 14 0.03
62 129 0.26
ACGTcount: A:0.33, C:0.12, G:0.19, T:0.35
Consensus pattern (59 bp):
TTAAATCGAACCTGTTGTGAGATAGGTCGAGCCTAGATTAAGTCTAGGAATTTCAATTT
Found at i:9817729 original size:51 final size:51
Alignment explanation
Indices: 9817669--9817853 Score: 163
Period size: 51 Copynumber: 3.4 Consensus size: 51
9817659 GGTCGAGCTA
*
9817669 AGATTAAGTCTAGGAATTTTAATCGAATTTGTTCTAATATGGGTCAAGCCT
1 AGATCAAGTCTAGGAATTTTAATCGAATTTGTTCTAATATGGGTCAAGCCT
* ** * * * * *
9817720 AGATCAAGTCTAGAAATTTCAATTTTGTTTAAATCGAACCTGTTGTGAGATAGGTCGAGCCT
1 AGATCAAGTCTAG------GAA---T-TTT-AATCGAATTTGTTCTAATATGGGTCAAGCCT
* *
9817782 AGATTAAGTCTAGGAATTTTAATCGAATTTGTTCTAATATGAGTCAAGCCT
1 AGATCAAGTCTAGGAATTTTAATCGAATTTGTTCTAATATGGGTCAAGCCT
*
9817833 AGATCAAGTCTAGAAATTTTA
1 AGATCAAGTCTAGGAATTTTA
9817854 TTTTTGTTTA
Statistics
Matches: 102, Mismatches: 21, Indels: 22
0.70 0.14 0.15
Matches are distributed among these distances:
51 54 0.53
52 3 0.03
53 1 0.01
56 2 0.02
57 2 0.02
60 1 0.01
61 3 0.03
62 36 0.35
ACGTcount: A:0.33, C:0.12, G:0.19, T:0.36
Consensus pattern (51 bp):
AGATCAAGTCTAGGAATTTTAATCGAATTTGTTCTAATATGGGTCAAGCCT
Found at i:9817764 original size:113 final size:114
Alignment explanation
Indices: 9817160--9817898 Score: 705
Period size: 113 Copynumber: 6.3 Consensus size: 114
9817150 CATTAAAGAA
*
9817160 TTAAATCGAACCTGTTGTGAGATAGGTCGAGCCTAGATTAAGTCTAAGAATTTCAATTTTTAAAT
1 TTAAATCGAACCTGTTGTGAGATAGGTCGAGCCTAGATTAAGTCT-AG-----GAA-TTTTAAAT
* * * * *
9817225 CTAACCTATTAC-GAGATAGGTCGAGCCTAGATTAAGTCTAGGAATTTCAA--TT-T
59 CGAACCTGTT-CTAAGATAGGTCAAGCCTAGATTAAGTCTAGAAATTTCAATTTTGT
* *
9817278 TTAAATCGAACCTGTTGTGAGATAGATCGAGCCTATATTAAGTCTAGGAATTTCAATTTTTAAAT
1 TTAAATCGAACCTGTTGTGAGATAGGTCGAGCCTAGATTAAGTCTAGG------AA-TTTTAAAT
* * * * *
9817343 CGAACCTGTTGTGAA-ATAAGTTGAA-CCTAGATTAAGTCTAGGAATTTTAA--TT-T
59 CGAACCTGTTCT-AAGAT-AGGTCAAGCCTAGATTAAGTCTAGAAATTTCAATTTTGT
*
9817396 TTAAATCGAACCTGTTGTGAGATAGGTCGAACCTAGATTAAG-CTAGGAATTTCAATTTTTAAAT
1 TTAAATCGAACCTGTTGTGAGATAGGTCGAGCCTAGATTAAGTCTAGG------AA-TTTTAAAT
* * * * * *
9817460 CGAACCTGTTGTGAGATAGGTCGAGCCTAAATTAAGTTTAGAAATTTCAATTTTTT
59 CGAACCTGTTCTAAGATAGGTCAAGCCTAGATTAAGTCTAGAAATTTCAATTTTGT
* * *
9817516 TTAAATCGAACCTGTTGTGAGATAGGTCGAGCCTAAATTAAGTCTAGAATTTCAATTTTAAATTG
1 TTAAATCGAACCTGTTGTGAGATAGGTCGAGCCTAGATTAAGTCTAG-----GAATTTTAAATCG
* * * * *
9817581 AACCTGTTATGAGATAGGTCAAGCCTAAATTAAGTTTAGGAATTTCAATTTTGT
61 AACCTGTTCTAAGATAGGTCAAGCCTAGATTAAGTCTAGAAATTTCAATTTTGT
* **
9817635 TTAAATCGAACTTGTTGTGAGATAGGTCGAG-CTAAGATTAAGTCTAGGAATTTT-AATCGAATT
1 TTAAATCGAACCTGTTGTGAGATAGGTCGAGCCT-AGATTAAGTCTAGGAATTTTAAATCGAACC
* * *
9817698 TGTTCTAATATGGGTCAAGCCTAGATCAAGTCTAGAAATTTCAATTTTGT
65 TGTTCTAAGATAGGTCAAGCCTAGATTAAGTCTAGAAATTTCAATTTTGT
**
9817748 TTAAATCGAACCTGTTGTGAGATAGGTCGAGCCTAGATTAAGTCTAGGAATTTT-AATCGAATTT
1 TTAAATCGAACCTGTTGTGAGATAGGTCGAGCCTAGATTAAGTCTAGGAATTTTAAATCGAACCT
* * * *
9817812 GTTCTAATAT-GAGTCAAGCCTAGATCAAGTCTAGAAATTTTATTTTTGT
66 GTTCTAAGATAG-GTCAAGCCTAGATTAAGTCTAGAAATTTCAATTTTGT
* * * *
9817861 TTAAATCGAACTTATTTTGAGATAAGTCGAGCCTAGAT
1 TTAAATCGAACCTGTTGTGAGATAGGTCGAGCCTAGAT
9817899 CCATTTGATT
Statistics
Matches: 547, Mismatches: 51, Indels: 51
0.84 0.08 0.08
Matches are distributed among these distances:
112 1 0.00
113 187 0.34
114 8 0.01
116 5 0.01
117 59 0.11
118 132 0.24
119 108 0.20
120 43 0.08
121 4 0.01
ACGTcount: A:0.33, C:0.12, G:0.19, T:0.36
Consensus pattern (114 bp):
TTAAATCGAACCTGTTGTGAGATAGGTCGAGCCTAGATTAAGTCTAGGAATTTTAAATCGAACCT
GTTCTAAGATAGGTCAAGCCTAGATTAAGTCTAGAAATTTCAATTTTGT
Found at i:9818034 original size:17 final size:17
Alignment explanation
Indices: 9818012--9818075 Score: 65
Period size: 17 Copynumber: 3.6 Consensus size: 17
9818002 CACCACAAAA
9818012 AAAATAAAAAATATAAT
1 AAAATAAAAAATATAAT
* *
9818029 AAAATAAAATATAAAAT
1 AAAATAAAAAATATAAT
** *
9818046 AAAATATTATATATAAT
1 AAAATAAAAAATATAAT
9818063 AATAATTAAAAAA
1 AA-AA-TAAAAAA
9818076 ATGAATGGCT
Statistics
Matches: 37, Mismatches: 8, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
17 31 0.84
18 2 0.05
19 4 0.11
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (17 bp):
AAAATAAAAAATATAAT
Found at i:9818042 original size:12 final size:12
Alignment explanation
Indices: 9818027--9818052 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
9818017 AAAAAATATA
9818027 ATAAAATAAAAT
1 ATAAAATAAAAT
9818039 ATAAAATAAAAT
1 ATAAAATAAAAT
9818051 AT
1 AT
9818053 TATATATAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (12 bp):
ATAAAATAAAAT
Found at i:9818657 original size:79 final size:79
Alignment explanation
Indices: 9818491--9818658 Score: 230
Period size: 79 Copynumber: 2.1 Consensus size: 79
9818481 TGCTTAAGGG
* * * * **
9818491 AGAGAGAAAAAAGGGTGAAAGCAGTGTCGCGCACCAGATCTGGCGACGTTGGAGATTTGGCCGGT
1 AGAGAGAAGAAAGGGTGAAAGCAGTGCCGCGCACCAGATCTGGCGACATTGGAGATCTGGCCGAC
9818556 AAAAAAATGGCTTT
66 AAAAAAATGGCTTT
*
9818570 AGAGAGAAGAAAGGGTGAAAGCAGTGCCGTGCACCAGAT-TCGGCGACATTGGAGATCTGGCCGA
1 AGAGAGAAGAAAGGGTGAAAGCAGTGCCGCGCACCAGATCT-GGCGACATTGGAGATCTGGCCGA
* **
9818634 CGAAAAGGTGGCTTT
65 CAAAAAAATGGCTTT
9818649 AGAGAGAAGA
1 AGAGAGAAGA
9818659 GAGAAGAGGA
Statistics
Matches: 78, Mismatches: 10, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
78 1 0.01
79 77 0.99
ACGTcount: A:0.33, C:0.15, G:0.35, T:0.17
Consensus pattern (79 bp):
AGAGAGAAGAAAGGGTGAAAGCAGTGCCGCGCACCAGATCTGGCGACATTGGAGATCTGGCCGAC
AAAAAAATGGCTTT
Found at i:9818736 original size:17 final size:19
Alignment explanation
Indices: 9818689--9818741 Score: 65
Period size: 17 Copynumber: 2.8 Consensus size: 19
9818679 ACGCTGGCAG
*
9818689 GGAGAAAGGAGAGAAAGAGAA
1 GGAGAAA-GAAAGAAAGAG-A
9818710 GGAGAAAGAAAGAAAGAG-
1 GGAGAAAGAAAGAAAGAGA
9818728 GGA-AAAGAAAGAAA
1 GGAGAAAGAAAGAAA
9818742 AAGCCAGCGG
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
17 11 0.35
18 3 0.10
20 10 0.32
21 7 0.23
ACGTcount: A:0.62, C:0.00, G:0.38, T:0.00
Consensus pattern (19 bp):
GGAGAAAGAAAGAAAGAGA
Found at i:9818760 original size:52 final size:52
Alignment explanation
Indices: 9818697--9818815 Score: 139
Period size: 52 Copynumber: 2.2 Consensus size: 52
9818687 AGGGAGAAAG
* *
9818697 GAGAGAAAGAGAAGGAGAAAGAAAGAAAGAGGGAAAAGAAAGAAAAAGCCAGCGGGGA
1 GAGAGAAAGAGAA-GA-AAA-AAA-AAA-A-GAAAAAGAAAGAAAAAGCCAGCAGGGA
* **
9818755 GAGAGAAAGAGAAGAAAAAAAAAAAGAAAAAGAAAGAAGAAGCTGGCAGGGA
1 GAGAGAAAGAGAAGAAAAAAAAAAAGAAAAAGAAAGAAAAAGCCAGCAGGGA
9818807 GAGAGAAAG
1 GAGAGAAAG
9818816 GAAATGGAGA
Statistics
Matches: 56, Mismatches: 5, Indels: 6
0.84 0.07 0.09
Matches are distributed among these distances:
52 31 0.55
53 1 0.02
54 3 0.05
55 3 0.05
56 3 0.05
57 2 0.04
58 13 0.23
ACGTcount: A:0.60, C:0.04, G:0.35, T:0.01
Consensus pattern (52 bp):
GAGAGAAAGAGAAGAAAAAAAAAAAGAAAAAGAAAGAAAAAGCCAGCAGGGA
Found at i:9818858 original size:26 final size:29
Alignment explanation
Indices: 9818805--9818862 Score: 77
Period size: 26 Copynumber: 2.1 Consensus size: 29
9818795 AGCTGGCAGG
*
9818805 GAGAGAGAAAGGAAATGGAGAAGGAAAAAA
1 GAGAGAGAAAGGAAA-GGAGAAGAAAAAAA
9818835 GAGAGAGAAA-GAAA-GA-AAGAAAAAAA
1 GAGAGAGAAAGGAAAGGAGAAGAAAAAAA
9818861 GA
1 GA
9818863 AAAAAGAAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
26 11 0.41
27 2 0.07
29 4 0.15
30 10 0.37
ACGTcount: A:0.66, C:0.00, G:0.33, T:0.02
Consensus pattern (29 bp):
GAGAGAGAAAGGAAAGGAGAAGAAAAAAA
Done.