Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr13
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: 55873576
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.32
Warning! 1239791 characters in sequence are not A, C, G, or T
File 35 of 182
Found at i:11420488 original size:30 final size:30
Alignment explanation
Indices: 11420453--11420526 Score: 98
Period size: 30 Copynumber: 2.5 Consensus size: 30
11420443 AGTTTTTCCC
11420453 AGCTCGATTT-AGCTCACA-TGAGCTTAATTT
1 AGCTCG-TTTGAGCTCA-ATTGAGCTTAATTT
* *
11420483 AGCTCGTTTGAGCTCAATTTAGCTTACTTT
1 AGCTCGTTTGAGCTCAATTGAGCTTAATTT
11420513 AGCTCGTTTGAGCT
1 AGCTCGTTTGAGCT
11420527 TGGCTTAAGT
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
29 4 0.10
30 36 0.90
ACGTcount: A:0.22, C:0.20, G:0.19, T:0.39
Consensus pattern (30 bp):
AGCTCGTTTGAGCTCAATTGAGCTTAATTT
Found at i:11420516 original size:20 final size:20
Alignment explanation
Indices: 11420453--11420517 Score: 53
Period size: 20 Copynumber: 3.2 Consensus size: 20
11420443 AGTTTTTCCC
* * * *
11420453 AGCTCGATTTAGCTCACATG
1 AGCTCAATTTAGCTTACTTT
*
11420473 AGCTTAATTTAGC-T-CGTTT
1 AGCTCAATTTAGCTTAC-TTT
11420492 GAGCTCAATTTAGCTTACTTT
1 -AGCTCAATTTAGCTTACTTT
11420513 AGCTC
1 AGCTC
11420518 GTTTGAGCTT
Statistics
Matches: 35, Mismatches: 6, Indels: 8
0.71 0.12 0.16
Matches are distributed among these distances:
18 1 0.03
19 1 0.03
20 28 0.80
21 4 0.11
22 1 0.03
ACGTcount: A:0.23, C:0.22, G:0.17, T:0.38
Consensus pattern (20 bp):
AGCTCAATTTAGCTTACTTT
Found at i:11425895 original size:42 final size:42
Alignment explanation
Indices: 11425841--11426042 Score: 255
Period size: 42 Copynumber: 4.8 Consensus size: 42
11425831 TCATATACAG
11425841 TGCAATGAAAAGTAAATGGACCTCCACACCTAGGCCTTTAAA
1 TGCAATGAAAAGTAAATGGACCTCCACACCTAGGCCTTTAAA
* *
11425883 TTCAATGAAAAGTAAATGGACCTCCACACCT-GAGCCTCTAAA
1 TGCAATGAAAAGTAAATGGACCTCCACACCTAG-GCCTTTAAA
* * * **
11425925 TGCAAGGATAAGTAAATAGATGTCCACACCTAGGCCTTTAAA
1 TGCAATGAAAAGTAAATGGACCTCCACACCTAGGCCTTTAAA
* * *
11425967 TGCAATGAAAAATAAATGGGCCTCCACATCTAGG-CTATTAAA
1 TGCAATGAAAAGTAAATGGACCTCCACACCTAGGCCT-TTAAA
* * *
11426009 TACAATGAAAAGTGAATGGACCTCCACATCTAGG
1 TGCAATGAAAAGTAAATGGACCTCCACACCTAGG
11426043 TCGTATTAAA
Statistics
Matches: 136, Mismatches: 21, Indels: 6
0.83 0.13 0.04
Matches are distributed among these distances:
41 3 0.02
42 132 0.97
43 1 0.01
ACGTcount: A:0.39, C:0.22, G:0.17, T:0.22
Consensus pattern (42 bp):
TGCAATGAAAAGTAAATGGACCTCCACACCTAGGCCTTTAAA
Found at i:11426647 original size:41 final size:41
Alignment explanation
Indices: 11426586--11426751 Score: 181
Period size: 41 Copynumber: 4.0 Consensus size: 41
11426576 AGAATAATGA
* *
11426586 TGAATTGCACATACGCGCCCCTATTTGTA-TTTCGGTACCCC
1 TGAATTGCACATACGTGCCCCTATTTGTACTTT-GATACCCC
* *
11426627 TAAATTGCACATACGTGCCCCTATTTGTACTTTGATACACC
1 TGAATTGCACATACGTGCCCCTATTTGTACTTTGATACCCC
* * * * **
11426668 TGAATTACTCATACATGCCCCTGTTTGTACTTTGATACCTT
1 TGAATTGCACATACGTGCCCCTATTTGTACTTTGATACCCC
* ** * *
11426709 TGAATTGCACAGACGTGCCTGTGTTTGTACTTCGATACCCC
1 TGAATTGCACATACGTGCCCCTATTTGTACTTTGATACCCC
11426750 TG
1 TG
11426752 GATGTATTTT
Statistics
Matches: 103, Mismatches: 21, Indels: 2
0.82 0.17 0.02
Matches are distributed among these distances:
41 100 0.97
42 3 0.03
ACGTcount: A:0.22, C:0.27, G:0.16, T:0.35
Consensus pattern (41 bp):
TGAATTGCACATACGTGCCCCTATTTGTACTTTGATACCCC
Found at i:11429554 original size:18 final size:20
Alignment explanation
Indices: 11429509--11429556 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 20
11429499 TGATTGTAAA
11429509 ATTATAAAAAATAAAGAATAT
1 ATTA-AAAAAATAAAGAATAT
**
11429530 ACAAAAAAAATAAA-AA-AT
1 ATTAAAAAAATAAAGAATAT
11429548 ATTAAAAAA
1 ATTAAAAAA
11429557 TATTATATGG
Statistics
Matches: 23, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
18 9 0.39
19 2 0.09
20 10 0.43
21 2 0.09
ACGTcount: A:0.75, C:0.02, G:0.02, T:0.21
Consensus pattern (20 bp):
ATTAAAAAAATAAAGAATAT
Found at i:11437139 original size:22 final size:20
Alignment explanation
Indices: 11437111--11437162 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 20
11437101 TTCCATGTGG
11437111 TATCGATACCACTTAAGGAAAA
1 TATCGATACC-CTTAA-GAAAA
* * *
11437133 TATCGATTCCCTTGAGACAA
1 TATCGATACCCTTAAGAAAA
11437153 TATCGATACC
1 TATCGATACC
11437163 TACATAACAG
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
20 13 0.50
21 4 0.15
22 9 0.35
ACGTcount: A:0.37, C:0.23, G:0.13, T:0.27
Consensus pattern (20 bp):
TATCGATACCCTTAAGAAAA
Found at i:11452223 original size:13 final size:13
Alignment explanation
Indices: 11452205--11452229 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
11452195 CTGTGATAAA
11452205 ACATGAAAATATC
1 ACATGAAAATATC
11452218 ACATGAAAATAT
1 ACATGAAAATAT
11452230 GTAGGTGTAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.56, C:0.12, G:0.08, T:0.24
Consensus pattern (13 bp):
ACATGAAAATATC
Found at i:11452312 original size:37 final size:37
Alignment explanation
Indices: 11452270--11452342 Score: 121
Period size: 37 Copynumber: 2.0 Consensus size: 37
11452260 TTGCTATAGA
11452270 AATTTGGAAAACCATTTT-TAAAAGATCATTTTTGAGG
1 AATTTGGAAAACC-TTTTCTAAAAGATCATTTTTGAGG
*
11452307 AATTTGGAAAATCTTTTCTAAAAGATCATTTTTGAG
1 AATTTGGAAAACCTTTTCTAAAAGATCATTTTTGAG
11452343 TTTTGCGTTT
Statistics
Matches: 34, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
36 4 0.12
37 30 0.88
ACGTcount: A:0.37, C:0.08, G:0.15, T:0.40
Consensus pattern (37 bp):
AATTTGGAAAACCTTTTCTAAAAGATCATTTTTGAGG
Found at i:11457272 original size:79 final size:81
Alignment explanation
Indices: 11457136--11457320 Score: 229
Period size: 79 Copynumber: 2.3 Consensus size: 81
11457126 TTGAATGATG
*
11457136 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATT
11457200 TGTGCGAGA-TACTA-A
66 TGTGCGA-ATTACTATA
* * * **
11457215 TTCCGGGCTAAG-CCCGAAGGCATTTGTGC-GAGTTACTAAATCCGGGTTAAG-TCCCGAAGGCA
1 -TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGAT-CCGAAGGCA
11457277 TTTGTGCGAATTACTATA
64 TTTGTGCGAATTACTATA
* *
11457295 ACCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
11457321 AACGAGGAGC
Statistics
Matches: 92, Mismatches: 8, Indels: 10
0.84 0.07 0.09
Matches are distributed among these distances:
78 2 0.02
79 57 0.62
80 33 0.36
ACGTcount: A:0.25, C:0.23, G:0.27, T:0.25
Consensus pattern (81 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATT
TGTGCGAATTACTATA
Found at i:11457334 original size:40 final size:39
Alignment explanation
Indices: 11457137--11457320 Score: 189
Period size: 40 Copynumber: 4.6 Consensus size: 39
11457127 TGAATGATGT
* * *
11457137 CCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGT-ACTATAA
* *
11457177 CCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTA-ATT
1 CCGGGCTAAG-TCCCGAAGGCATTTGTGCGAG-TACTATA-A
11457217 CCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTA-AA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAG-TACTATAA
* *
11457255 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAATTACTATAA
1 -CCGGGCTAAGTCCCGAAGGCATTTGTGCG-AGTACTATAA
*
11457296 CCGGGCTATGTCCCGAAGGCATTTG
1 CCGGGCTAAGTCCCGAAGGCATTTG
11457321 AACGAGGAGC
Statistics
Matches: 125, Mismatches: 10, Indels: 18
0.82 0.07 0.12
Matches are distributed among these distances:
39 35 0.28
40 78 0.62
41 12 0.10
ACGTcount: A:0.25, C:0.23, G:0.27, T:0.25
Consensus pattern (39 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTACTATAA
Found at i:11457342 original size:79 final size:79
Alignment explanation
Indices: 11457137--11457353 Score: 194
Period size: 79 Copynumber: 2.7 Consensus size: 79
11457127 TGAATGATGT
** * * * **
11457137 CCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCCGGACTAAGAT-CCGAAGGCATT
1 CCGGGCTAAG-CCCGAAGGCATTTGAAC-GAGTGACTAAATCCGGGTTAA-ATCCCGAAGGCATT
*
11457200 TGTGCGAGATACTAATT
63 TGTGCGAGATACTAATA
** * *
11457217 CCGGGCTAAGCCCGAAGGCATTTGTGCGAGTTACTAAATCCGGGTTAAGTCCCGAAGGCATTTGT
1 CCGGGCTAAGCCCGAAGGCATTTGAACGAGTGACTAAATCCGGGTTAAATCCCGAAGGCATTTGT
11457282 GCGA-ATTACT-ATAA
66 GCGAGA-TACTAAT-A
* * *
11457296 CCGGGCTATGTCCCGAAGGCATTTGAACGAG-GAGCTATATCC-GGTTAAATTCCGAAGG
1 CCGGGCTAAG-CCCGAAGGCATTTGAACGAGTGA-CTAAATCCGGGTTAAATCCCGAAGG
11457354 TACGTGATTT
Statistics
Matches: 116, Mismatches: 15, Indels: 13
0.81 0.10 0.09
Matches are distributed among these distances:
78 4 0.03
79 70 0.60
80 42 0.36
ACGTcount: A:0.26, C:0.22, G:0.27, T:0.24
Consensus pattern (79 bp):
CCGGGCTAAGCCCGAAGGCATTTGAACGAGTGACTAAATCCGGGTTAAATCCCGAAGGCATTTGT
GCGAGATACTAATA
Found at i:11457548 original size:47 final size:47
Alignment explanation
Indices: 11457479--11457572 Score: 188
Period size: 47 Copynumber: 2.0 Consensus size: 47
11457469 AGTATTCGCT
11457479 CAGTTGATAAACGAGCTACCGGCCTTTGGCTGAGTTGATCTTTTGTG
1 CAGTTGATAAACGAGCTACCGGCCTTTGGCTGAGTTGATCTTTTGTG
11457526 CAGTTGATAAACGAGCTACCGGCCTTTGGCTGAGTTGATCTTTTGTG
1 CAGTTGATAAACGAGCTACCGGCCTTTGGCTGAGTTGATCTTTTGTG
11457573 TATGTACATA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
47 47 1.00
ACGTcount: A:0.19, C:0.19, G:0.28, T:0.34
Consensus pattern (47 bp):
CAGTTGATAAACGAGCTACCGGCCTTTGGCTGAGTTGATCTTTTGTG
Found at i:11468791 original size:11 final size:11
Alignment explanation
Indices: 11468777--11468806 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
11468767 TTTATTCATT
11468777 TTTTAATTTTG
1 TTTTAATTTTG
11468788 TTTTAATTTTG
1 TTTTAATTTTG
*
11468799 TTTAAATT
1 TTTTAATT
11468807 ACAAAATAGC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.23, C:0.00, G:0.07, T:0.70
Consensus pattern (11 bp):
TTTTAATTTTG
Found at i:11478684 original size:69 final size:69
Alignment explanation
Indices: 11478573--11478708 Score: 263
Period size: 69 Copynumber: 2.0 Consensus size: 69
11478563 AGACTATATC
*
11478573 GCCCTACCACCACTACAAAACCTGCTGAAAATCCTACAGCCACTGTTATTCCTGTTTTGGAACCT
1 GCCCTACCACAACTACAAAACCTGCTGAAAATCCTACAGCCACTGTTATTCCTGTTTTGGAACCT
11478638 GTCA
66 GTCA
11478642 GCCCTACCACAACTACAAAACCTGCTGAAAATCCTACAGCCACTGTTATTCCTGTTTTGGAACCT
1 GCCCTACCACAACTACAAAACCTGCTGAAAATCCTACAGCCACTGTTATTCCTGTTTTGGAACCT
11478707 GT
66 GT
11478709 TTTTCCTATC
Statistics
Matches: 66, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
69 66 1.00
ACGTcount: A:0.28, C:0.32, G:0.13, T:0.26
Consensus pattern (69 bp):
GCCCTACCACAACTACAAAACCTGCTGAAAATCCTACAGCCACTGTTATTCCTGTTTTGGAACCT
GTCA
Found at i:11481806 original size:45 final size:45
Alignment explanation
Indices: 11481722--11481808 Score: 113
Period size: 45 Copynumber: 1.9 Consensus size: 45
11481712 AACCTTAATT
* * *
11481722 CTATTAACCCTCTAGTAGGGTATTTCTCCTAAAAGTCTTACTGTC
1 CTATTAACCCTCTAGTAGGGTATTTATACTAAAACTCTTACTGTC
* *
11481767 CTATTAACCTTCTAGT-GGAGTATTTATACTAGAACTCTTACT
1 CTATTAACCCTCTAGTAGG-GTATTTATACTAAAACTCTTACT
11481809 ATTAACAATA
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
44 2 0.06
45 34 0.94
ACGTcount: A:0.26, C:0.22, G:0.13, T:0.39
Consensus pattern (45 bp):
CTATTAACCCTCTAGTAGGGTATTTATACTAAAACTCTTACTGTC
Found at i:11489137 original size:9 final size:9
Alignment explanation
Indices: 11489123--11489148 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
11489113 TTTTAATGTG
11489123 AAAATAAAA
1 AAAATAAAA
11489132 AAAATAAAA
1 AAAATAAAA
11489141 AAAATAAA
1 AAAATAAA
11489149 GAACACACAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (9 bp):
AAAATAAAA
Found at i:11493562 original size:5 final size:5
Alignment explanation
Indices: 11493552--11493595 Score: 51
Period size: 5 Copynumber: 9.6 Consensus size: 5
11493542 CCAATTTGTG
*
11493552 AAAAT AAAAT AAAAT AAAA- AATA- AAAAT -AAA- AAAAT AAAAT AAA
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAA
11493596 GAACACACAA
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
4 12 0.35
5 22 0.65
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (5 bp):
AAAAT
Found at i:11493580 original size:13 final size:13
Alignment explanation
Indices: 11493557--11493595 Score: 55
Period size: 13 Copynumber: 3.1 Consensus size: 13
11493547 TTGTGAAAAT
11493557 AAAAT-AAAATAA
1 AAAATAAAAATAA
11493569 AAAATAAAAATAA
1 AAAATAAAAATAA
11493582 AAAA-ATAAAATAA
1 AAAATA-AAAATAA
11493595 A
1 A
11493596 GAACACACAA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
12 6 0.24
13 19 0.76
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (13 bp):
AAAATAAAAATAA
Found at i:11495320 original size:46 final size:45
Alignment explanation
Indices: 11495214--11495436 Score: 158
Period size: 46 Copynumber: 4.9 Consensus size: 45
11495204 ATAATGAATC
* * * * * * * *
11495214 ATAGTGCTTGGTTACCCATCAGGGTTAAACCTAAACGAATCGGATG
1 ATAGTGCATGGTCACCCATTAGGGTTGAACCTACACAAAT-AGATA
* * * *
11495260 ATAATGCCTAGTCACCCATTAGGGTTGAACTTACACAAATCAGATA
1 ATAGTGCATGGTCACCCATTAGGGTTGAACCTACACAAAT-AGATA
* * * * * *
11495306 ATAGTGAATGGTCACTCGTCAGGGTTGAACCTACACGAATAATATA
1 ATAGTGCATGGTCACCCATTAGGGTTGAACCTACACAAAT-AGATA
* * * * * * *
11495352 ATAATGCCTAGTCACTCGTTAGGGTTAAACCTACACGAATAGGATA
1 ATAGTGCATGGTCACCCATTAGGGTTGAACCTACACAAATA-GATA
* * *
11495398 ATAGTGCTTGGTTACCCATTAAGGTTGAACCTACACAAA
1 ATAGTGCATGGTCACCCATTAGGGTTGAACCTACACAAA
11495437 AAATAGCCTA
Statistics
Matches: 138, Mismatches: 38, Indels: 2
0.78 0.21 0.01
Matches are distributed among these distances:
45 1 0.01
46 137 0.99
ACGTcount: A:0.34, C:0.20, G:0.20, T:0.26
Consensus pattern (45 bp):
ATAGTGCATGGTCACCCATTAGGGTTGAACCTACACAAATAGATA
Found at i:11495424 original size:92 final size:93
Alignment explanation
Indices: 11495179--11495433 Score: 280
Period size: 92 Copynumber: 2.8 Consensus size: 93
11495169 GCGTTTGGTT
* * * * *
11495179 ACTCGTTTGGGTTAAACCTATACGAATAATGAATCATAGTGCTTGGTTACCCATCAGGGTTAAAC
1 ACTCGTTAGGGTTAAACCTACACGAATAA-GGATAATAGTGCTTGGTTACCCATCAGGGTTGAAC
* ** *
11495244 CTAAACGAATCGGATGATAATGCCTAGTC
65 CTACACGAATAAGATAATAATGCCTAGTC
* * * * * * ** * * *
11495273 ACCCATTAGGGTTGAACTTACACAAATCA-GATAATAGTGAATGGTCACTCGTCAGGGTTGAACC
1 ACTCGTTAGGGTTAAACCTACACGAATAAGGATAATAGTGCTTGGTTACCCATCAGGGTTGAACC
*
11495337 TACACGAATAATATAATAATGCCTAGTC
66 TACACGAATAAGATAATAATGCCTAGTC
* *
11495365 ACTCGTTAGGGTTAAACCTACACGAAT-AGGATAATAGTGCTTGGTTACCCATTAAGGTTGAACC
1 ACTCGTTAGGGTTAAACCTACACGAATAAGGATAATAGTGCTTGGTTACCCATCAGGGTTGAACC
11495429 TACAC
66 TACAC
11495434 AAAAAATAGC
Statistics
Matches: 127, Mismatches: 33, Indels: 4
0.77 0.20 0.02
Matches are distributed among these distances:
91 1 0.01
92 105 0.83
94 21 0.17
ACGTcount: A:0.33, C:0.20, G:0.20, T:0.27
Consensus pattern (93 bp):
ACTCGTTAGGGTTAAACCTACACGAATAAGGATAATAGTGCTTGGTTACCCATCAGGGTTGAACC
TACACGAATAAGATAATAATGCCTAGTC
Found at i:11499927 original size:46 final size:45
Alignment explanation
Indices: 11499871--11500046 Score: 176
Period size: 46 Copynumber: 3.8 Consensus size: 45
11499861 ATTTTGGGCA
11499871 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-G
* *** * *
11499917 TCTGAACTCGTTGAGTTGAGTCCGAGTTCGAGAGATGTAACTAG-GCA-
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-ACTTATG-GA-T-GCGAAG
* * * *
11499964 TCCGAGCTCATTGAGTTGAGTCCGATTTCACTTATGGATGCAAACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-G
* *
11500010 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
11500047 GCGGGTTACA
Statistics
Matches: 104, Mismatches: 19, Indels: 14
0.76 0.14 0.10
Matches are distributed among these distances:
43 1 0.01
44 2 0.02
45 1 0.01
46 66 0.63
47 29 0.28
48 1 0.01
49 3 0.03
50 1 0.01
ACGTcount: A:0.22, C:0.20, G:0.28, T:0.30
Consensus pattern (45 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAAG
Found at i:11500026 original size:93 final size:93
Alignment explanation
Indices: 11499867--11500038 Score: 272
Period size: 93 Copynumber: 1.8 Consensus size: 93
11499857 AGGAATTTTG
* * * * *
11499867 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCTGAACTCGTTGAG
1 GGCATCCGAACTCATTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACGCCCGAACTCGTTGAG
11499932 TTGAGTCCGAGTTCGAGAGATGTAACTA
66 TTGAGTCCGAGTTCGAGAGATGTAACTA
* * *
11499960 GGCATCCGAGCTCATTGAGTTGAGTCCGATTTCACTTATGGATGCAAACGCCCGAGCTCGTTGAG
1 GGCATCCGAACTCATTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACGCCCGAACTCGTTGAG
11500025 TTGAGTCCGAGTTC
66 TTGAGTCCGAGTTC
11500039 ACTTATGGGC
Statistics
Matches: 71, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
93 71 1.00
ACGTcount: A:0.22, C:0.21, G:0.28, T:0.28
Consensus pattern (93 bp):
GGCATCCGAACTCATTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACGCCCGAACTCGTTGAG
TTGAGTCCGAGTTCGAGAGATGTAACTA
Found at i:11507838 original size:40 final size:40
Alignment explanation
Indices: 11507789--11507969 Score: 235
Period size: 40 Copynumber: 4.5 Consensus size: 40
11507779 CTCATACAAT
11507789 GCCTTCGGGACTTAACCCGGAATTAGTATCTCGCACAAAG
1 GCCTTCGGGACTTAACCCGGAATTAGTATCTCGCACAAAG
11507829 GCCTTCGGGACTTAACCCGGAATTAGTATCTCGCACAAAG
1 GCCTTCGGGACTTAACCCGGAATTAGTATCTCGCACAAAG
* * *
11507869 GCCTTCGGGGCTTAACCCGGAATTTGTATCTCGCACAAAT
1 GCCTTCGGGACTTAACCCGGAATTAGTATCTCGCACAAAG
** *
11507909 GCCTTC-GGATCTTAGTCCGG-ATATAGTCA-CTTAGCACAAA-
1 GCCTTCGGGA-CTTAACCCGGAAT-TAGT-ATC-TCGCACAAAG
*
11507949 GCCTTCGGGACTTAGCCCGGA
1 GCCTTCGGGACTTAACCCGGA
11507970 CAGCATTCAA
Statistics
Matches: 126, Mismatches: 9, Indels: 11
0.86 0.06 0.08
Matches are distributed among these distances:
39 4 0.03
40 110 0.87
41 12 0.10
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.24
Consensus pattern (40 bp):
GCCTTCGGGACTTAACCCGGAATTAGTATCTCGCACAAAG
Found at i:11507929 original size:80 final size:80
Alignment explanation
Indices: 11507750--11507969 Score: 243
Period size: 80 Copynumber: 2.8 Consensus size: 80
11507740 TCGTTCAAGT
* * * * * * *
11507750 GCCTTCGGGACATAGCCCGGTTATAGTAACTCA-TACAATGCCTTCGGGACTTAACCCGGAATTA
1 GCCTTCGGGACTTAACCCGGATATAGTCACTTAGCACAAAGCCTTCGGGACTTAACCCGGAATTA
11507814 GTATCTCGCACAAAG
66 GTATCTCGCACAAAG
* *
11507829 GCCTTCGGGACTTAACCCGGA-ATTAGT-A-TCTCGCACAAAGGCCTTCGGGGCTTAACCCGGAA
1 GCCTTCGGGACTTAACCCGGATA-TAGTCACT-TAGCACAAA-GCCTTCGGGACTTAACCCGGAA
* *
11507891 TTTGTATCTCGCACAAAT
63 TTAGTATCTCGCACAAAG
** *
11507909 GCCTTC-GGATCTTAGTCCGGATATAGTCACTTAGCACAAAGCCTTCGGGACTTAGCCCGGA
1 GCCTTCGGGA-CTTAACCCGGATATAGTCACTTAGCACAAAGCCTTCGGGACTTAACCCGGA
11507970 CAGCATTCAA
Statistics
Matches: 118, Mismatches: 15, Indels: 15
0.80 0.10 0.10
Matches are distributed among these distances:
77 1 0.01
78 2 0.02
79 29 0.25
80 75 0.64
81 10 0.08
82 1 0.01
ACGTcount: A:0.25, C:0.27, G:0.23, T:0.25
Consensus pattern (80 bp):
GCCTTCGGGACTTAACCCGGATATAGTCACTTAGCACAAAGCCTTCGGGACTTAACCCGGAATTA
GTATCTCGCACAAAG
Found at i:11512775 original size:158 final size:158
Alignment explanation
Indices: 11512487--11512803 Score: 634
Period size: 158 Copynumber: 2.0 Consensus size: 158
11512477 CCCTAAAACA
11512487 AAAGGATCTATATAATCTCGTTTTTCTTTGTTTGAGTCTAGCAGCCTCCAAAGAAAAATAACTCT
1 AAAGGATCTATATAATCTCGTTTTTCTTTGTTTGAGTCTAGCAGCCTCCAAAGAAAAATAACTCT
11512552 CAAAACTGTTTTGGGGATTCCTTCCGTTCGTAGTCAACTGGGTGGATTACGTAGAGGCCGGAATC
66 CAAAACTGTTTTGGGGATTCCTTCCGTTCGTAGTCAACTGGGTGGATTACGTAGAGGCCGGAATC
11512617 ACGATAGATTGCGGTTTGGTTCGACAGC
131 ACGATAGATTGCGGTTTGGTTCGACAGC
11512645 AAAGGATCTATATAATCTCGTTTTTCTTTGTTTGAGTCTAGCAGCCTCCAAAGAAAAATAACTCT
1 AAAGGATCTATATAATCTCGTTTTTCTTTGTTTGAGTCTAGCAGCCTCCAAAGAAAAATAACTCT
11512710 CAAAACTGTTTTGGGGATTCCTTCCGTTCGTAGTCAACTGGGTGGATTACGTAGAGGCCGGAATC
66 CAAAACTGTTTTGGGGATTCCTTCCGTTCGTAGTCAACTGGGTGGATTACGTAGAGGCCGGAATC
11512775 ACGATAGATTGCGGTTTGGTTCGACAGC
131 ACGATAGATTGCGGTTTGGTTCGACAGC
11512803 A
1 A
11512804 GATCAGACTA
Statistics
Matches: 159, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
158 159 1.00
ACGTcount: A:0.26, C:0.19, G:0.23, T:0.32
Consensus pattern (158 bp):
AAAGGATCTATATAATCTCGTTTTTCTTTGTTTGAGTCTAGCAGCCTCCAAAGAAAAATAACTCT
CAAAACTGTTTTGGGGATTCCTTCCGTTCGTAGTCAACTGGGTGGATTACGTAGAGGCCGGAATC
ACGATAGATTGCGGTTTGGTTCGACAGC
Found at i:11513467 original size:18 final size:17
Alignment explanation
Indices: 11513446--11513522 Score: 77
Period size: 18 Copynumber: 4.5 Consensus size: 17
11513436 TTTTCTCTCA
11513446 CTTTTTCGATTTCTTTTT
1 CTTTTTC-ATTTCTTTTT
*
11513464 CTTTTGCAATTTCTTTTT
1 CTTTTTC-ATTTCTTTTT
11513482 CTTTTTCATTTTCTTTTT
1 CTTTTTCA-TTTCTTTTT
* **
11513500 -GTTTTC-TTTCAATTT
1 CTTTTTCATTTCTTTTT
11513515 CTTTTTCA
1 CTTTTTCA
11513523 ATCTCTTTCT
Statistics
Matches: 49, Mismatches: 7, Indels: 7
0.78 0.11 0.11
Matches are distributed among these distances:
15 7 0.14
16 5 0.10
17 6 0.12
18 31 0.63
ACGTcount: A:0.09, C:0.17, G:0.04, T:0.70
Consensus pattern (17 bp):
CTTTTTCATTTCTTTTT
Found at i:11513504 original size:11 final size:12
Alignment explanation
Indices: 11513415--11513522 Score: 66
Period size: 12 Copynumber: 9.1 Consensus size: 12
11513405 TTCCTTTCCA
11513415 ATTTTCTTTTCTTC
1 ATTTTC-TTT-TTC
11513429 ATTTTCTTTTTC
1 ATTTTCTTTTTC
**
11513441 -TCTCACTTTTTC
1 AT-TTTCTTTTTC
11513453 GA-TTTCTTTTTC
1 -ATTTTCTTTTTC
**
11513465 -TTTTGCAATTTC
1 ATTTT-CTTTTTC
*
11513477 TTTTTCTTTTTC
1 ATTTTCTTTTTC
11513489 ATTTTCTTTTT-
1 ATTTTCTTTTTC
*
11513500 GTTTTC--TTTC
1 ATTTTCTTTTTC
*
11513510 AATTTCTTTTTC
1 ATTTTCTTTTTC
11513522 A
1 A
11513523 ATCTCTTTCT
Statistics
Matches: 73, Mismatches: 12, Indels: 20
0.70 0.11 0.19
Matches are distributed among these distances:
9 3 0.04
10 4 0.05
11 9 0.12
12 44 0.60
13 7 0.10
14 6 0.08
ACGTcount: A:0.09, C:0.19, G:0.03, T:0.69
Consensus pattern (12 bp):
ATTTTCTTTTTC
Found at i:11513521 original size:6 final size:6
Alignment explanation
Indices: 11513416--11513508 Score: 62
Period size: 6 Copynumber: 15.3 Consensus size: 6
11513406 TCCTTTCCAA
* * ** * *
11513416 TTTTCTT TTCTTCA TTTTCT TTTTCT CTCACT TTTTCG ATTTCT TTTTCT
1 TTTTC-T TT-TTCT TTTTCT TTTTCT TTTTCT TTTTCT TTTTCT TTTTCT
* * * * *
11513466 TTTGCA ATTTCT TTTTCT TTTTCA TTTTCT TTTT-G TTTTCT TT
1 TTTTCT TTTTCT TTTTCT TTTTCT TTTTCT TTTTCT TTTTCT TT
11513509 CAATTTCTTT
Statistics
Matches: 62, Mismatches: 22, Indels: 5
0.70 0.25 0.06
Matches are distributed among these distances:
5 4 0.06
6 51 0.82
7 4 0.06
8 3 0.05
ACGTcount: A:0.06, C:0.18, G:0.03, T:0.72
Consensus pattern (6 bp):
TTTTCT
Found at i:11516154 original size:20 final size:20
Alignment explanation
Indices: 11516129--11516167 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
11516119 GGGTTGAGGT
*
11516129 TGAGCTGAATTGAACTCGAA
1 TGAGCTAAATTGAACTCGAA
*
11516149 TGAGCTAAATTGAGCTCGA
1 TGAGCTAAATTGAACTCGA
11516168 GTGTGCTGGA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.33, C:0.15, G:0.26, T:0.26
Consensus pattern (20 bp):
TGAGCTAAATTGAACTCGAA
Found at i:11519873 original size:39 final size:40
Alignment explanation
Indices: 11519778--11520039 Score: 337
Period size: 39 Copynumber: 6.7 Consensus size: 40
11519768 TTGAATGATG
*
11519778 TCCGGGCTAAGTCCCGAAGGC--TTGTGCTA-AGTGAC-AAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGA-T-ACTAAT
*
11519816 ATCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTAAT
1 -TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGATACTAAT
11519857 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
11519896 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
* *
11519935 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
*
11519974 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGA-ATTACT-AT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGA-TACTAAT
* *
11520013 AACCGGGCTATGTCCCGAAGGCATTTG
1 -TCCGGGCTAAGTCCCGAAGGCATTTG
11520040 AACGAGGAGC
Statistics
Matches: 203, Mismatches: 11, Indels: 17
0.88 0.05 0.07
Matches are distributed among these distances:
39 132 0.65
40 59 0.29
41 11 0.05
42 1 0.00
ACGTcount: A:0.26, C:0.23, G:0.27, T:0.24
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
Found at i:11536375 original size:29 final size:28
Alignment explanation
Indices: 11536328--11536398 Score: 97
Period size: 29 Copynumber: 2.5 Consensus size: 28
11536318 GATCATCAAC
*
11536328 TATGAAAAGGGATTACTTCGGCTATTGAA
1 TATGAAAAGGGA-TACTTCGGCTATCGAA
*
11536357 TATGAAAAGGGATAGCTTCGGCTATCGAT
1 TATGAAAAGGGATA-CTTCGGCTATCGAA
*
11536386 TATAAAAAGGGAT
1 TATGAAAAGGGAT
11536399 GGTGACAACA
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
28 2 0.05
29 36 0.95
ACGTcount: A:0.37, C:0.10, G:0.25, T:0.28
Consensus pattern (28 bp):
TATGAAAAGGGATACTTCGGCTATCGAA
Found at i:11547836 original size:12 final size:12
Alignment explanation
Indices: 11547819--11547844 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
11547809 AACATCACCA
11547819 AAATAAATGTCC
1 AAATAAATGTCC
11547831 AAATAAATGTCC
1 AAATAAATGTCC
11547843 AA
1 AA
11547845 TGTCCATTAC
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:0.54, C:0.15, G:0.08, T:0.23
Consensus pattern (12 bp):
AAATAAATGTCC
Found at i:11548521 original size:34 final size:34
Alignment explanation
Indices: 11548483--11548552 Score: 140
Period size: 34 Copynumber: 2.1 Consensus size: 34
11548473 CAACTATGTC
11548483 CAATGGATCCACCATGCAATGTTGCCAATATAAT
1 CAATGGATCCACCATGCAATGTTGCCAATATAAT
11548517 CAATGGATCCACCATGCAATGTTGCCAATATAAT
1 CAATGGATCCACCATGCAATGTTGCCAATATAAT
11548551 CA
1 CA
11548553 TACATACAAG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 36 1.00
ACGTcount: A:0.36, C:0.24, G:0.14, T:0.26
Consensus pattern (34 bp):
CAATGGATCCACCATGCAATGTTGCCAATATAAT
Found at i:11553294 original size:16 final size:16
Alignment explanation
Indices: 11553273--11553324 Score: 86
Period size: 16 Copynumber: 3.2 Consensus size: 16
11553263 TTTGGTTCGC
11553273 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
11553289 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
* *
11553305 TGTAATGGAATAGAGG
1 TGTATTGGATTAGAGG
11553321 TGTA
1 TGTA
11553325 ATAGCAAATC
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 34 1.00
ACGTcount: A:0.29, C:0.00, G:0.37, T:0.35
Consensus pattern (16 bp):
TGTATTGGATTAGAGG
Found at i:11553372 original size:45 final size:44
Alignment explanation
Indices: 11553305--11553399 Score: 127
Period size: 44 Copynumber: 2.1 Consensus size: 44
11553295 GGATTAGAGG
**
11553305 TGTAATGGAATAGAGGTGTAATAGCAAATCAACTGTTTGGTTGAA
1 TGTAATGGAATAGAGGCATAATAG-AAATCAACTGTTTGGTTGAA
* ***
11553350 TGTAATGGAATAGAGGCATAATAGTAATCCTGTGTTTGGTTGAA
1 TGTAATGGAATAGAGGCATAATAGAAATCAACTGTTTGGTTGAA
11553394 TGTAAT
1 TGTAAT
11553400 AGAGGTGTAA
Statistics
Matches: 44, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
44 22 0.50
45 22 0.50
ACGTcount: A:0.34, C:0.06, G:0.26, T:0.34
Consensus pattern (44 bp):
TGTAATGGAATAGAGGCATAATAGAAATCAACTGTTTGGTTGAA
Found at i:11553581 original size:18 final size:17
Alignment explanation
Indices: 11553560--11553594 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
11553550 TTATTATTAA
*
11553560 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
11553578 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
11553595 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:11553731 original size:155 final size:157
Alignment explanation
Indices: 11553447--11553761 Score: 553
Period size: 155 Copynumber: 2.0 Consensus size: 157
11553437 TAGAATACCC
*
11553447 TTAGCATAAATTTGTTTTGGTAAATGATTATTGTTATTGTTATTTAAATTTTAATAAGATTATTA
1 TTAGCAGAAATTTGTTTTGGTAAATGATTATTGTTATTGTTATTTAAATTTTAATAAGATTATTA
* * * *
11553512 TTATCAATAATAAATAATTTAATTATATTTAAACATAATTATTATTAAATATATTTTAATTAAAA
66 ATATCAATAATAAATAAGTTAATCATATTTAAACATAATTATTATTAAATATATTATAATTAAAA
*
11553577 TATATAATTTAATAAAATTCTTAATAA
131 TATATAATTTAATAAAATTCTTAAGAA
*
11553604 TTAGCAGAAATTTGTTTTGGTAAATTA-T-TTGTTATTGTTATTTAAATTTTAATAAGATTATTA
1 TTAGCAGAAATTTGTTTTGGTAAATGATTATTGTTATTGTTATTTAAATTTTAATAAGATTATTA
11553667 ATATCAATAATAAATAAGTTAATCATATTTAAACATAATTATTATTAAATATATTATAATTAAAA
66 ATATCAATAATAAATAAGTTAATCATATTTAAACATAATTATTATTAAATATATTATAATTAAAA
11553732 TATATAATTTAATAAAATTCTTAAGAA
131 TATATAATTTAATAAAATTCTTAAGAA
11553759 TTA
1 TTA
11553762 ATATTCTTAT
Statistics
Matches: 151, Mismatches: 7, Indels: 2
0.94 0.04 0.01
Matches are distributed among these distances:
155 125 0.83
156 1 0.01
157 25 0.17
ACGTcount: A:0.44, C:0.03, G:0.06, T:0.47
Consensus pattern (157 bp):
TTAGCAGAAATTTGTTTTGGTAAATGATTATTGTTATTGTTATTTAAATTTTAATAAGATTATTA
ATATCAATAATAAATAAGTTAATCATATTTAAACATAATTATTATTAAATATATTATAATTAAAA
TATATAATTTAATAAAATTCTTAAGAA
Found at i:11553732 original size:16 final size:16
Alignment explanation
Indices: 11553695--11553736 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
11553685 TTAATCATAT
*
11553695 TTAAACATA-ATTATTA
1 TTAAA-ATATATTATAA
11553711 TT-AAATATATTATAA
1 TTAAAATATATTATAA
11553726 TTAAAATATAT
1 TTAAAATATAT
11553737 AATTTAATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 3 0.13
15 10 0.43
16 10 0.43
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (16 bp):
TTAAAATATATTATAA
Found at i:11553743 original size:14 final size:15
Alignment explanation
Indices: 11553704--11553745 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
11553694 TTTAAACATA
*
11553704 ATTATTATTAAATAT
1 ATTATAATTAAATAT
11553719 ATTATAATTAAA-AT
1 ATTATAATTAAATAT
*
11553733 A-TATAATTTAATA
1 ATTATAATTAAATA
11553746 AAATTCTTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 9 0.38
14 4 0.17
15 11 0.46
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
ATTATAATTAAATAT
Found at i:11553863 original size:14 final size:15
Alignment explanation
Indices: 11553814--11553865 Score: 56
Period size: 15 Copynumber: 3.6 Consensus size: 15
11553804 ATAAAATATA
11553814 AATTAACATA-ATTAT
1 AATTAA-ATATATTAT
*
11553829 TATTAAATATATTAT
1 AATTAAATATATTAT
11553844 AATTAAA-ATA-TAT
1 AATTAAATATATTAT
*
11553857 AATTTAATA
1 AATTAAATA
11553866 AAATTCTTAA
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
13 9 0.28
14 7 0.22
15 16 0.50
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (15 bp):
AATTAAATATATTAT
Found at i:11556411 original size:40 final size:40
Alignment explanation
Indices: 11556320--11556489 Score: 207
Period size: 40 Copynumber: 4.3 Consensus size: 40
11556310 TCCTCGTTCA
* * * * *
11556320 AATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACAC-
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* * *
11556359 CATGCCTTCGGGACGTAACCCGGATTTAACAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
*
11556399 AATGCCTTCGGGACTTAACCCGGCTTTAATAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* * * *
11556439 AATGCCCTCGGGACTTAACCCGGATTTAGTATCTCGCACA
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
*
11556479 AAGGCCTTCGG
1 AATGCCTTCGG
11556490 ATCTTAGTCC
Statistics
Matches: 112, Mismatches: 18, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
39 32 0.29
40 80 0.71
ACGTcount: A:0.25, C:0.30, G:0.22, T:0.24
Consensus pattern (40 bp):
AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
Found at i:11560924 original size:10 final size:10
Alignment explanation
Indices: 11560908--11560965 Score: 64
Period size: 10 Copynumber: 5.7 Consensus size: 10
11560898 CAACTCCGAC
11560908 CAGCTCAATT
1 CAGCTCAATT
* *
11560918 GAGCTCATTT
1 CAGCTCAATT
11560928 CAGCTCAA-T
1 CAGCTCAATT
11560937 CGAGCTCAATT
1 C-AGCTCAATT
*
11560948 TAGCTACAATT
1 CAGCT-CAATT
11560959 CAGCTCA
1 CAGCTCA
11560966 TTTATTTTAT
Statistics
Matches: 39, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
9 2 0.05
10 27 0.69
11 10 0.26
ACGTcount: A:0.29, C:0.28, G:0.14, T:0.29
Consensus pattern (10 bp):
CAGCTCAATT
Found at i:11560931 original size:20 final size:20
Alignment explanation
Indices: 11560908--11560968 Score: 79
Period size: 20 Copynumber: 3.0 Consensus size: 20
11560898 CAACTCCGAC
11560908 CAGCTCAATTGAGCTCATTT
1 CAGCTCAATTGAGCTCATTT
*
11560928 CAGCTCAATCGAGCTCAATTT
1 CAGCTCAATTGAGCTC-ATTT
*
11560949 -AGCTACAATTCAGCTCATTT
1 CAGCT-CAATTGAGCTCATTT
11560969 ATTTTATTGG
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
20 23 0.64
21 13 0.36
ACGTcount: A:0.28, C:0.26, G:0.13, T:0.33
Consensus pattern (20 bp):
CAGCTCAATTGAGCTCATTT
Found at i:11567632 original size:16 final size:17
Alignment explanation
Indices: 11567611--11567648 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 17
11567601 TATCAAGTTG
11567611 AAAAAAAAA-TTCGTGA
1 AAAAAAAAATTTCGTGA
11567627 AAAAAAAAATTTTCGTGA
1 AAAAAAAAA-TTTCGTGA
11567645 AAAA
1 AAAA
11567649 GAAGAAGCTA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
16 9 0.45
18 11 0.55
ACGTcount: A:0.63, C:0.05, G:0.11, T:0.21
Consensus pattern (17 bp):
AAAAAAAAATTTCGTGA
Found at i:11574101 original size:165 final size:165
Alignment explanation
Indices: 11573829--11574352 Score: 1048
Period size: 165 Copynumber: 3.2 Consensus size: 165
11573819 CCTCATATGG
11573829 TGATGTGATCCGGCTCGGTTGATTGAGTCGATTCACTTGATTGCCCGATCGTCGACGAGGAATAG
1 TGATGTGATCCGGCTCGGTTGATTGAGTCGATTCACTTGATTGCCCGATCGTCGACGAGGAATAG
11573894 TTGAGTTATCGGAAATAGGATGAAATAAGGCTAAAGATGCGGAAGCTTTCAAATGGTTTTAAAGG
66 TTGAGTTATCGGAAATAGGATGAAATAAGGCTAAAGATGCGGAAGCTTTCAAATGGTTTTAAAGG
11573959 TTGGCTAAGGTGATGGTAAATTTATAAGGGTAGTA
131 TTGGCTAAGGTGATGGTAAATTTATAAGGGTAGTA
11573994 TGATGTGATCCGGCTCGGTTGATTGAGTCGATTCACTTGATTGCCCGATCGTCGACGAGGAATAG
1 TGATGTGATCCGGCTCGGTTGATTGAGTCGATTCACTTGATTGCCCGATCGTCGACGAGGAATAG
11574059 TTGAGTTATCGGAAATAGGATGAAATAAGGCTAAAGATGCGGAAGCTTTCAAATGGTTTTAAAGG
66 TTGAGTTATCGGAAATAGGATGAAATAAGGCTAAAGATGCGGAAGCTTTCAAATGGTTTTAAAGG
11574124 TTGGCTAAGGTGATGGTAAATTTATAAGGGTAGTA
131 TTGGCTAAGGTGATGGTAAATTTATAAGGGTAGTA
11574159 TGATGTGATCCGGCTCGGTTGATTGAGTCGATTCACTTGATTGCCCGATCGTCGACGAGGAATAG
1 TGATGTGATCCGGCTCGGTTGATTGAGTCGATTCACTTGATTGCCCGATCGTCGACGAGGAATAG
11574224 TTGAGTTATCGGAAATAGGATGAAATAAGGCTAAAGATGCGGAAGCTTTCAAATGGTTTTAAAGG
66 TTGAGTTATCGGAAATAGGATGAAATAAGGCTAAAGATGCGGAAGCTTTCAAATGGTTTTAAAGG
11574289 TTGGCTAAGGTGATGGTAAATTTATAAGGGTAGTA
131 TTGGCTAAGGTGATGGTAAATTTATAAGGGTAGTA
11574324 TGATGTGATCCGGCTCGGTTGATTGAGTC
1 TGATGTGATCCGGCTCGGTTGATTGAGTC
11574353 NNNNNNNNNN
Statistics
Matches: 359, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
165 359 1.00
ACGTcount: A:0.28, C:0.12, G:0.30, T:0.30
Consensus pattern (165 bp):
TGATGTGATCCGGCTCGGTTGATTGAGTCGATTCACTTGATTGCCCGATCGTCGACGAGGAATAG
TTGAGTTATCGGAAATAGGATGAAATAAGGCTAAAGATGCGGAAGCTTTCAAATGGTTTTAAAGG
TTGGCTAAGGTGATGGTAAATTTATAAGGGTAGTA
Found at i:11574670 original size:18 final size:18
Alignment explanation
Indices: 11574649--11574700 Score: 61
Period size: 18 Copynumber: 2.9 Consensus size: 18
11574639 CTCTCTTTCT
11574649 TTTTCAATCTCATTTTGC
1 TTTTCAATCTCATTTTGC
* *
11574667 TTTTCACTCTC-TTTTGT
1 TTTTCAATCTCATTTTGC
*
11574684 TTTTGAAATCTCATTTT
1 TTTT-CAATCTCATTTT
11574701 CATATTTTTC
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
17 9 0.32
18 15 0.54
19 4 0.14
ACGTcount: A:0.15, C:0.19, G:0.06, T:0.60
Consensus pattern (18 bp):
TTTTCAATCTCATTTTGC
Found at i:11574714 original size:6 final size:6
Alignment explanation
Indices: 11574705--11574796 Score: 76
Period size: 6 Copynumber: 14.8 Consensus size: 6
11574695 CATTTTCATA
* * * **
11574705 TTTTTC TTTTTC AATTTTC TTTTCTTC ATTTTC TTTTTC TCTCAC TTTTTC
1 TTTTTC TTTTTC -TTTTTC -TTT-TTC TTTTTC TTTTTC TTTTTC TTTTTC
* * **
11574756 GTTTTC TTTTTC GTTTTC TTTTTC TTTTTC ACTTTC TTTTT
1 TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC TTTTT
11574797 TGAATTCATT
Statistics
Matches: 65, Mismatches: 19, Indels: 4
0.74 0.22 0.05
Matches are distributed among these distances:
6 53 0.82
7 9 0.14
8 3 0.05
ACGTcount: A:0.05, C:0.20, G:0.02, T:0.73
Consensus pattern (6 bp):
TTTTTC
Found at i:11575774 original size:21 final size:20
Alignment explanation
Indices: 11575750--11575788 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
11575740 TCCACGAATT
11575750 TTTTTCTTTTACTTTTTTTTA
1 TTTTTCTTTTA-TTTTTTTTA
*
11575771 TTTTTTTTTTATTTTTTT
1 TTTTTCTTTTATTTTTTT
11575789 AAATTTTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.08, C:0.05, G:0.00, T:0.87
Consensus pattern (20 bp):
TTTTTCTTTTATTTTTTTTA
Found at i:11575775 original size:10 final size:10
Alignment explanation
Indices: 11575750--11575798 Score: 53
Period size: 10 Copynumber: 4.7 Consensus size: 10
11575740 TCCACGAATT
11575750 TTTTTCTTTTA
1 TTTTT-TTTTA
*
11575761 CTTTTTTTTA
1 TTTTTTTTTA
11575771 TTTTTTTTTTA
1 -TTTTTTTTTA
**
11575782 TTTTTTTAAA
1 TTTTTTTTTA
11575792 TTTTTTT
1 TTTTTTT
11575799 AATCACTTAC
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
10 20 0.61
11 13 0.39
ACGTcount: A:0.12, C:0.04, G:0.00, T:0.84
Consensus pattern (10 bp):
TTTTTTTTTA
Found at i:11575776 original size:11 final size:11
Alignment explanation
Indices: 11575749--11575788 Score: 55
Period size: 11 Copynumber: 3.6 Consensus size: 11
11575739 ATCCACGAAT
11575749 TTTTTTCTTTTA
1 TTTTTT-TTTTA
*
11575761 -CTTTTTTTTA
1 TTTTTTTTTTA
11575771 TTTTTTTTTTA
1 TTTTTTTTTTA
11575782 TTTTTTT
1 TTTTTTT
11575789 AAATTTTTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
10 5 0.20
11 20 0.80
ACGTcount: A:0.07, C:0.05, G:0.00, T:0.88
Consensus pattern (11 bp):
TTTTTTTTTTA
Found at i:11575794 original size:21 final size:21
Alignment explanation
Indices: 11575749--11575798 Score: 66
Period size: 20 Copynumber: 2.4 Consensus size: 21
11575739 ATCCACGAAT
*
11575749 TTTTTTCTTTTACTTTTTTTTA
1 TTTTTT-TTTTACTTTTTTTAA
11575771 TTTTTTTTTTA-TTTTTTTAA
1 TTTTTTTTTTACTTTTTTTAA
*
11575791 ATTTTTTT
1 TTTTTTTT
11575799 AATCACTTAC
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
20 15 0.58
21 5 0.19
22 6 0.23
ACGTcount: A:0.12, C:0.04, G:0.00, T:0.84
Consensus pattern (21 bp):
TTTTTTTTTTACTTTTTTTAA
Found at i:11577351 original size:20 final size:21
Alignment explanation
Indices: 11577326--11577364 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
11577316 TCAAACAAGC
11577326 AAATGAGCTCAA-TGAGCTGG
1 AAATGAGCTCAATTGAGCTGG
*
11577346 AAATGAGCTGAATTGAGCT
1 AAATGAGCTCAATTGAGCT
11577365 CAACGAGCTG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.36, C:0.13, G:0.28, T:0.23
Consensus pattern (21 bp):
AAATGAGCTCAATTGAGCTGG
Found at i:11583112 original size:54 final size:54
Alignment explanation
Indices: 11583030--11583137 Score: 207
Period size: 54 Copynumber: 2.0 Consensus size: 54
11583020 TTGGGACCTT
*
11583030 AATCTATTTTCCATGCTTTATAATATTTCTTTTAACCACTGCACTCTTTCCTCA
1 AATCTATTTTCCATGCTTTATAATATTTCTTTTAACCACTGAACTCTTTCCTCA
11583084 AATCTATTTTCCATGCTTTATAATATTTCTTTTAACCACTGAACTCTTTCCTCA
1 AATCTATTTTCCATGCTTTATAATATTTCTTTTAACCACTGAACTCTTTCCTCA
11583138 CTCTTGAAAC
Statistics
Matches: 53, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
54 53 1.00
ACGTcount: A:0.25, C:0.25, G:0.04, T:0.46
Consensus pattern (54 bp):
AATCTATTTTCCATGCTTTATAATATTTCTTTTAACCACTGAACTCTTTCCTCA
Found at i:11583172 original size:14 final size:14
Alignment explanation
Indices: 11583149--11583185 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
11583139 TCTTGAAACA
*
11583149 ATTTTGAAATATTT
1 ATTTTAAAATATTT
11583163 ATTTTAAAATATTT
1 ATTTTAAAATATTT
11583177 ATTTTAAAA
1 ATTTTAAAA
11583186 CAGGTGAGTC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.54
Consensus pattern (14 bp):
ATTTTAAAATATTT
Found at i:11587045 original size:22 final size:22
Alignment explanation
Indices: 11587017--11587080 Score: 83
Period size: 22 Copynumber: 2.9 Consensus size: 22
11587007 CCTTTTTGAA
11587017 CCATTACCATTTCGTACCAAAT
1 CCATTACCATTTCGTACCAAAT
* ** *
11587039 CCATTACCATTTTGTGTCACAT
1 CCATTACCATTTCGTACCAAAT
*
11587061 CCTTTACCATTTCGTACCAA
1 CCATTACCATTTCGTACCAA
11587081 TTCCCAAATA
Statistics
Matches: 33, Mismatches: 9, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
22 33 1.00
ACGTcount: A:0.27, C:0.31, G:0.06, T:0.36
Consensus pattern (22 bp):
CCATTACCATTTCGTACCAAAT
Found at i:11591551 original size:13 final size:12
Alignment explanation
Indices: 11591533--11591564 Score: 55
Period size: 13 Copynumber: 2.6 Consensus size: 12
11591523 TAGTTTCTTC
11591533 AAAAAAAATTCGA
1 AAAAAAAATTC-A
11591546 AAAAAAAATTCA
1 AAAAAAAATTCA
11591558 AAAAAAA
1 AAAAAAA
11591565 TTGGTTTCCT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 8 0.42
13 11 0.58
ACGTcount: A:0.78, C:0.06, G:0.03, T:0.12
Consensus pattern (12 bp):
AAAAAAAATTCA
Found at i:11591565 original size:11 final size:11
Alignment explanation
Indices: 11591530--11591566 Score: 56
Period size: 11 Copynumber: 3.2 Consensus size: 11
11591520 TAGTAGTTTC
11591530 TTCAAAAAAAA
1 TTCAAAAAAAA
11591541 TTCGAAAAAAAAA
1 TTC--AAAAAAAA
11591554 TTCAAAAAAAA
1 TTCAAAAAAAA
11591565 TT
1 TT
11591567 GGTTTCCTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
11 13 0.54
13 11 0.46
ACGTcount: A:0.68, C:0.08, G:0.03, T:0.22
Consensus pattern (11 bp):
TTCAAAAAAAA
Found at i:11596127 original size:19 final size:18
Alignment explanation
Indices: 11596091--11596130 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
11596081 TTTCCACTCG
*
11596091 TTTCTTTTTCAACTTCTC
1 TTTCTTTTTCAACATCTC
*
11596109 TTTCTTTTTCCACAATCTC
1 TTTCTTTTTCAAC-ATCTC
11596128 TTT
1 TTT
11596131 GTTTGTTGAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 12 0.63
19 7 0.37
ACGTcount: A:0.12, C:0.28, G:0.00, T:0.60
Consensus pattern (18 bp):
TTTCTTTTTCAACATCTC
Found at i:11597208 original size:14 final size:14
Alignment explanation
Indices: 11597189--11597237 Score: 91
Period size: 14 Copynumber: 3.6 Consensus size: 14
11597179 ACTAGCTCTC
11597189 TTTTTTTTTCACAA
1 TTTTTTTTTCACAA
11597203 TTTTTTTTTCACAA
1 TTTTTTTTTCACAA
11597217 TTTTTTTTTCA-AA
1 TTTTTTTTTCACAA
11597230 TTTTTTTT
1 TTTTTTTT
11597238 ACAACTTGAT
Statistics
Matches: 35, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
13 10 0.29
14 25 0.71
ACGTcount: A:0.18, C:0.10, G:0.00, T:0.71
Consensus pattern (14 bp):
TTTTTTTTTCACAA
Found at i:11597297 original size:12 final size:12
Alignment explanation
Indices: 11597280--11597324 Score: 63
Period size: 12 Copynumber: 3.7 Consensus size: 12
11597270 GGAAACTAGT
11597280 TTTTTTTTCGAA
1 TTTTTTTTCGAA
*
11597292 TTTTTTTTTGAA
1 TTTTTTTTCGAA
*
11597304 TTTTTTTTTCGAG
1 -TTTTTTTTCGAA
11597317 TTTTTTTT
1 TTTTTTTT
11597325 TCGAGAAACT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
12 19 0.66
13 10 0.34
ACGTcount: A:0.11, C:0.04, G:0.09, T:0.76
Consensus pattern (12 bp):
TTTTTTTTCGAA
Found at i:11597297 original size:13 final size:13
Alignment explanation
Indices: 11597279--11597328 Score: 84
Period size: 13 Copynumber: 3.9 Consensus size: 13
11597269 TGGAAACTAG
11597279 TTTTTTTTTCGAA
1 TTTTTTTTTCGAA
11597292 TTTTTTTTT-GAA
1 TTTTTTTTTCGAA
*
11597304 TTTTTTTTTCGAG
1 TTTTTTTTTCGAA
11597317 TTTTTTTTTCGA
1 TTTTTTTTTCGA
11597329 GAAACTACTA
Statistics
Matches: 35, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
12 12 0.34
13 23 0.66
ACGTcount: A:0.12, C:0.06, G:0.10, T:0.72
Consensus pattern (13 bp):
TTTTTTTTTCGAA
Found at i:11597696 original size:46 final size:46
Alignment explanation
Indices: 11597643--11597736 Score: 163
Period size: 46 Copynumber: 2.0 Consensus size: 46
11597633 CAAAGAAAAG
*
11597643 ACCTCGACCCACTATCAA-GAATGATAGGAACCTTGGTATATGATGA
1 ACCTCGACCCACTATCAATG-ATGATAAGAACCTTGGTATATGATGA
11597689 ACCTCGACCCACTATCAATGATGATAAGAACCTTGGTATATGATGA
1 ACCTCGACCCACTATCAATGATGATAAGAACCTTGGTATATGATGA
11597735 AC
1 AC
11597737 GCCACACTAT
Statistics
Matches: 46, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
46 45 0.98
47 1 0.02
ACGTcount: A:0.35, C:0.22, G:0.18, T:0.24
Consensus pattern (46 bp):
ACCTCGACCCACTATCAATGATGATAAGAACCTTGGTATATGATGA
Found at i:11606470 original size:18 final size:18
Alignment explanation
Indices: 11606446--11606775 Score: 106
Period size: 19 Copynumber: 17.6 Consensus size: 18
11606436 ACAAAATAAC
11606446 AATTTTTGAAAACAC-AA
1 AATTTTTGAAAACACGAA
11606463 AGATTTTTG-AAACACGAA
1 A-ATTTTTGAAAACACGAA
11606481 AATTTTTTGAAAACACGAAAACACAA
1 AA-TTTTTGAAAACACG-------AA
* **
11606507 AATATTTT--TAACACGGG
1 AAT-TTTTGAAAACACGAA
11606524 AATTTTTGAAAACACGACA
1 AATTTTTGAAAACACGA-A
** ***
11606543 GTTTTTTTTTAACACGAA
1 AATTTTTGAAAACACGAA
11606561 AATTTTTTGAAAACACAGAA
1 AA-TTTTTGAAAACAC-GAA
* * *
11606581 ATTTTTTGAAAACAAGGA
1 AATTTTTGAAAACACGAA
* * * *
11606599 AATTTTAG-ATACATGAG
1 AATTTTTGAAAACACGAA
11606616 AATTCTTTG---ACACGAA
1 AATT-TTTGAAAACACGAA
* * *
11606632 AAATTTTGAAAACATGAG
1 AATTTTTGAAAACACGAA
** *
11606650 AA-TTCCGAAAACATG--
1 AATTTTTGAAAACACGAA
* *
11606665 AATTTTTTAAAACATGAA
1 AATTTTTGAAAACACGAA
* *
11606683 ATTTTTTAAAAAACACGAGA
1 AATTTTT-GAAAACACGA-A
*
11606703 ATTTTTTGAAAACACGAAA
1 AATTTTTGAAAACACG-AA
**
11606722 ACATGAAAATTTTGAAAACACAGGT
1 A-AT-----TTTTGAAAACAC-GAA
11606747 AATTTTTGAAAACACGAA
1 AATTTTTGAAAACACGAA
*
11606765 AATTTCTGAAA
1 AATTTTTGAAA
11606776 GACGGGAGTT
Statistics
Matches: 233, Mismatches: 46, Indels: 67
0.67 0.13 0.19
Matches are distributed among these distances:
15 6 0.03
16 22 0.09
17 31 0.13
18 58 0.25
19 71 0.30
20 14 0.06
24 8 0.03
25 14 0.06
26 9 0.04
ACGTcount: A:0.46, C:0.11, G:0.12, T:0.31
Consensus pattern (18 bp):
AATTTTTGAAAACACGAA
Found at i:11606475 original size:17 final size:17
Alignment explanation
Indices: 11606446--11606501 Score: 69
Period size: 18 Copynumber: 3.1 Consensus size: 17
11606436 ACAAAATAAC
11606446 AATTTTTGAAAACAC-AA
1 AATTTTTG-AAACACGAA
11606463 AGATTTTTGAAACACGAA
1 A-ATTTTTGAAACACGAA
11606481 AATTTTTTGAAAACACGAA
1 AA-TTTTTG-AAACACGAA
11606500 AA
1 AA
11606502 CACAAAATAT
Statistics
Matches: 35, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
17 8 0.23
18 16 0.46
19 11 0.31
ACGTcount: A:0.50, C:0.11, G:0.11, T:0.29
Consensus pattern (17 bp):
AATTTTTGAAACACGAA
Found at i:11606503 original size:44 final size:42
Alignment explanation
Indices: 11606453--11606540 Score: 115
Period size: 42 Copynumber: 2.0 Consensus size: 42
11606443 AACAATTTTT
11606453 GAAAACACAAAGAT-TTTTGAAACACGAAAATTTTTTGAAAACAC
1 GAAAACACAAA-ATATTTT-AAACACGAAAA-TTTTTGAAAACAC
* **
11606497 GAAAACACAAAATATTTTTAACACGGGAATTTTTGAAAACAC
1 GAAAACACAAAATATTTTAAACACGAAAATTTTTGAAAACAC
11606539 GA
1 GA
11606541 CAGTTTTTTT
Statistics
Matches: 40, Mismatches: 3, Indels: 4
0.85 0.06 0.09
Matches are distributed among these distances:
42 15 0.38
43 10 0.25
44 15 0.38
ACGTcount: A:0.49, C:0.14, G:0.12, T:0.25
Consensus pattern (42 bp):
GAAAACACAAAATATTTTAAACACGAAAATTTTTGAAAACAC
Found at i:11606586 original size:37 final size:36
Alignment explanation
Indices: 11606497--11606587 Score: 98
Period size: 37 Copynumber: 2.5 Consensus size: 36
11606487 TTGAAAACAC
* **
11606497 GAAAACACA-AAA-TATTTTTAACACGGGAATTTTT
1 GAAAACACAGAAATTTTTTTTAACACGAAAATTTTT
*
11606531 GAAAACAC-GACAGTTTTTTTTTAACACGAAAATTTTTT
1 GAAAACACAGA-A-ATTTTTTTTAACACGAAAA-TTTTT
11606569 GAAAACACAGAAATTTTTT
1 GAAAACACAGAAATTTTTT
11606588 GAAAACAAGG
Statistics
Matches: 46, Mismatches: 5, Indels: 9
0.77 0.08 0.15
Matches are distributed among these distances:
34 9 0.20
35 1 0.02
37 20 0.43
38 14 0.30
39 2 0.04
ACGTcount: A:0.42, C:0.12, G:0.11, T:0.35
Consensus pattern (36 bp):
GAAAACACAGAAATTTTTTTTAACACGAAAATTTTT
Found at i:11606653 original size:17 final size:16
Alignment explanation
Indices: 11606632--11606687 Score: 67
Period size: 16 Copynumber: 3.4 Consensus size: 16
11606622 TTGACACGAA
11606632 AAATTTTGAAAACATG
1 AAATTTTGAAAACATG
**
11606648 AGAATTCCGAAAACATG
1 A-AATTTTGAAAACATG
* *
11606665 AATTTTTTAAAACATG
1 AAATTTTGAAAACATG
11606681 AAATTTT
1 AAATTTT
11606688 TTAAAAAACA
Statistics
Matches: 32, Mismatches: 7, Indels: 2
0.78 0.17 0.05
Matches are distributed among these distances:
16 18 0.56
17 14 0.44
ACGTcount: A:0.46, C:0.09, G:0.11, T:0.34
Consensus pattern (16 bp):
AAATTTTGAAAACATG
Found at i:11606723 original size:27 final size:25
Alignment explanation
Indices: 11606692--11606742 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
11606682 AATTTTTTAA
*
11606692 AAAACACGAGAATTTTTTGAAAACACG
1 AAAACACGA-AA-ATTTTGAAAACACG
*
11606719 AAAACATGAAAATTTTGAAAACAC
1 AAAACACGAAAATTTTGAAAACAC
11606743 AGGTAATTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
25 12 0.55
26 2 0.09
27 8 0.36
ACGTcount: A:0.53, C:0.14, G:0.12, T:0.22
Consensus pattern (25 bp):
AAAACACGAAAATTTTGAAAACACG
Found at i:11606753 original size:44 final size:46
Alignment explanation
Indices: 11606673--11606766 Score: 131
Period size: 46 Copynumber: 2.1 Consensus size: 46
11606663 TGAATTTTTT
* *
11606673 AAAACATGAAATTTTTTAAAAAACACGAGAATTTTTTGAAAACACG
1 AAAACATGAAAATTTTGAAAAAACACGAGAATTTTTTGAAAACACG
*
11606719 AAAACATGAAAATTTTGAAAACACA-G-GTAA-TTTTTGAAAACACG
1 AAAACATGAAAATTTTGAAAAAACACGAG-AATTTTTTGAAAACACG
11606763 AAAA
1 AAAA
11606767 TTTCTGAAAG
Statistics
Matches: 44, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
44 19 0.43
45 3 0.07
46 22 0.50
ACGTcount: A:0.52, C:0.11, G:0.12, T:0.26
Consensus pattern (46 bp):
AAAACATGAAAATTTTGAAAAAACACGAGAATTTTTTGAAAACACG
Found at i:11606858 original size:24 final size:23
Alignment explanation
Indices: 11606799--11606890 Score: 113
Period size: 23 Copynumber: 4.2 Consensus size: 23
11606789 TTGTTTTTTG
11606799 TTTT-ATTTTAAAACACGAAAAT
1 TTTTCATTTTAAAACACGAAAAT
*
11606821 TTTTCATTTGAAAACACGAAAAT
1 TTTTCATTTTAAAACACGAAAAT
*
11606844 TTGTTCATTTTAAAACGCG--AAT
1 TT-TTCATTTTAAAACACGAAAAT
*
11606866 TTTT--TTTTAAAACACGAAAAC
1 TTTTCATTTTAAAACACGAAAAT
11606887 TTTT
1 TTTT
11606891 GAAAACGCGA
Statistics
Matches: 61, Mismatches: 5, Indels: 9
0.81 0.07 0.12
Matches are distributed among these distances:
19 11 0.18
21 8 0.13
22 9 0.15
23 19 0.31
24 14 0.23
ACGTcount: A:0.39, C:0.12, G:0.08, T:0.41
Consensus pattern (23 bp):
TTTTCATTTTAAAACACGAAAAT
Found at i:11606890 original size:19 final size:18
Alignment explanation
Indices: 11606869--11606903 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
11606859 CGCGAATTTT
*
11606869 TTTTTAAAACACGAAAAC
1 TTTTGAAAACACGAAAAC
*
11606887 TTTTGAAAACGCGAAAA
1 TTTTGAAAACACGAAAA
11606904 GTCGAAAATT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.49, C:0.14, G:0.11, T:0.26
Consensus pattern (18 bp):
TTTTGAAAACACGAAAAC
Found at i:11608218 original size:30 final size:30
Alignment explanation
Indices: 11608178--11608279 Score: 107
Period size: 30 Copynumber: 3.4 Consensus size: 30
11608168 ATTTAGGATT
* * *
11608178 AAAATGAAATTTAATGAAATTTTAGGGGTC
1 AAAATGAAATTTAAAGAAAGTTTAAGGGTC
* *
11608208 TAAGTGAAATTTAAAGAAAGTTTAAGGGTC
1 AAAATGAAATTTAAAGAAAGTTTAAGGGTC
* **
11608238 AAAATGAAATTT-AGGAAAAGTTTGGGGGTC
1 AAAATGAAATTTAAAG-AAAGTTTAAGGGTC
*
11608268 AAAATGCAATTT
1 AAAATGAAATTT
11608280 TTATTTTTTA
Statistics
Matches: 60, Mismatches: 11, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
29 2 0.03
30 58 0.97
ACGTcount: A:0.43, C:0.04, G:0.23, T:0.30
Consensus pattern (30 bp):
AAAATGAAATTTAAAGAAAGTTTAAGGGTC
Found at i:11608363 original size:60 final size:60
Alignment explanation
Indices: 11608291--11608405 Score: 230
Period size: 60 Copynumber: 1.9 Consensus size: 60
11608281 TATTTTTTAA
11608291 TTTTTTTTTGAAATTTTGAAAATTAAACACAAATTCTAGTCGGACAAAAATTTAGAAATT
1 TTTTTTTTTGAAATTTTGAAAATTAAACACAAATTCTAGTCGGACAAAAATTTAGAAATT
11608351 TTTTTTTTTGAAATTTTGAAAATTAAACACAAATTCTAGTCGGACAAAAATTTAG
1 TTTTTTTTTGAAATTTTGAAAATTAAACACAAATTCTAGTCGGACAAAAATTTAG
11608406 TGCTTACATT
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
60 55 1.00
ACGTcount: A:0.41, C:0.09, G:0.10, T:0.40
Consensus pattern (60 bp):
TTTTTTTTTGAAATTTTGAAAATTAAACACAAATTCTAGTCGGACAAAAATTTAGAAATT
Found at i:11609735 original size:22 final size:20
Alignment explanation
Indices: 11609694--11609735 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
11609684 TTGTATTTTT
*
11609694 AATAATTTTTATTTTTTAAA
1 AATAATTTTTATATTTTAAA
11609714 AATAATTTTATAATATTTTAAA
1 AATAATTTT-T-ATATTTTAAA
11609736 TTTTTTAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 9 0.47
21 1 0.05
22 9 0.47
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (20 bp):
AATAATTTTTATATTTTAAA
Found at i:11609739 original size:17 final size:16
Alignment explanation
Indices: 11609717--11609751 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 16
11609707 TTTTAAAAAT
11609717 AATTTTATAATATTTTA
1 AATTTTATAA-ATTTTA
*
11609734 AATTTTTTAAATTTTA
1 AATTTTATAAATTTTA
11609750 AA
1 AA
11609752 AAATTNNNNN
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 8 0.47
17 9 0.53
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (16 bp):
AATTTTATAAATTTTA
Found at i:11610545 original size:18 final size:18
Alignment explanation
Indices: 11610473--11610889 Score: 193
Period size: 17 Copynumber: 23.2 Consensus size: 18
11610463 NNNNNNTTTT
*
11610473 TTTTTGAAAACAAGAAAA
1 TTTTTGAAAACATGAAAA
* * * *
11610491 -TTTTCAAAATACGAGAA
1 TTTTTGAAAACATGAAAA
* *
11610508 TTTTTGAAAACAGGGGAAA
1 TTTTTGAAAACA-TGAAAA
11610527 TTTTTGAAAACATGAAAA
1 TTTTTGAAAACATGAAAA
*
11610545 TTTTTG-AAACACT-AGAA
1 TTTTTGAAAACA-TGAAAA
* *
11610562 -TTTTGAAAACACGAAGA
1 TTTTTGAAAACATGAAAA
* *
11610579 TTTTT-TAAACATGAGAA
1 TTTTTGAAAACATGAAAA
* * *
11610596 TTTTTGAAAACACGAGGAT
1 TTTTTGAAAACATGA-AAA
*
11610615 TTTTTGAAATACA--AACA
1 TTTTTGAAA-ACATGAAAA
*
11610632 TTTTAG-AAACATGAAAA
1 TTTTTGAAAACATGAAAA
*
11610649 TTTTT-AAAACATGACAATT
1 TTTTTGAAAACATGA-AA-A
11610668 TTTTTGAAACACGA-GAAATTTA
1 TTTTTGAAA-AC-ATGAAA---A
* *
11610690 TTTTTTAAAACATAAAAA
1 TTTTTGAAAACATGAAAA
* * *
11610708 ATTTT-AAAACACGAGAA
1 TTTTTGAAAACATGAAAA
* *
11610725 TTTGTG-AAAC-TCGAGAA
1 TTTTTGAAAACAT-GAAAA
* * *
11610742 TTGTTGAAAAAAATAAAAA
1 TTTTTG-AAAACATGAAAA
* * *
11610761 ATTTTGAAAATACG-AAA
1 TTTTTGAAAACATGAAAA
** *
11610778 TTTTTTTAAACACGAAAA
1 TTTTTGAAAACATGAAAA
* * *
11610796 TTTTAG-AAATATGGAAA
1 TTTTTGAAAACATGAAAA
*
11610813 TTTTTAGAAAACACGAAAA
1 TTTTT-GAAAACATGAAAA
*
11610832 ATTTTGAAAA-AT-AAAA
1 TTTTTGAAAACATGAAAA
* *
11610848 TTTTTTGAAAACACGAGAA
1 -TTTTTGAAAACATGAAAA
*
11610867 TTTTTGAAAACACGAAAAA
1 TTTTTGAAAACATG-AAAA
11610886 TTTT
1 TTTT
11610890 CTGATTTTTC
Statistics
Matches: 299, Mismatches: 68, Indels: 63
0.70 0.16 0.15
Matches are distributed among these distances:
15 3 0.01
16 11 0.04
17 121 0.40
18 72 0.24
19 63 0.21
20 10 0.03
21 9 0.03
22 10 0.03
ACGTcount: A:0.47, C:0.08, G:0.12, T:0.32
Consensus pattern (18 bp):
TTTTTGAAAACATGAAAA
Found at i:11610829 original size:36 final size:34
Alignment explanation
Indices: 11610758--11610876 Score: 116
Period size: 35 Copynumber: 3.4 Consensus size: 34
11610748 AAAAAAATAA
**
11610758 AAAATTTTG-AAAATACGAAATTTTT-TTAAACACG
1 AAAATTTTGAAAAATA--AAATTTTTAGAAAACACG
* *
11610792 AAAATTTTAGAAATATGGAAATTTTTAGAAAACACG
1 AAAATTTT-GAAAAAT-AAAATTTTTAGAAAACACG
*
11610828 AAAAATTTTGAAAAATAAAATTTTTTGAAAACACG
1 -AAAATTTTGAAAAATAAAATTTTTAGAAAACACG
*
11610863 AGAATTTTTGAAAA
1 A-AAATTTTGAAAA
11610877 CACGAAAAAT
Statistics
Matches: 71, Mismatches: 8, Indels: 11
0.79 0.09 0.12
Matches are distributed among these distances:
34 9 0.13
35 37 0.52
36 17 0.24
37 8 0.11
ACGTcount: A:0.50, C:0.06, G:0.11, T:0.33
Consensus pattern (34 bp):
AAAATTTTGAAAAATAAAATTTTTAGAAAACACG
Found at i:11610849 original size:35 final size:34
Alignment explanation
Indices: 11610524--11610876 Score: 121
Period size: 36 Copynumber: 9.9 Consensus size: 34
11610514 AAAACAGGGG
* * *
11610524 AAATTTTTGAAAACATGAAAATTTTTGAAACACTA
1 AAATTTTTGAAAACACGAAAAATTTTGAAA-AATA
* * * * *
11610559 GAA-TTTTGAAAACACGAAGATTTTTTAAACATGA
1 AAATTTTTGAAAACACGAAAAATTTTGAAAAAT-A
* * ** * *
11610593 GAATTTTTGAAAACACGAGGATTTTTTGAAATACA
1 AAATTTTTGAAAACACGA-AAAATTTTGAAAAATA
* * *
11610628 AACATTTTAG-AAACATG-AAAATTTTTAAAACATGA
1 AA-ATTTTTGAAAACACGAAAAATTTTGAAAA-AT-A
* *
11610663 CAATTTTTTTG-AAACACGAGAAATTTATTTTTTAAAACATAA
1 -AA-ATTTTTGAAAACACGA-AAA---A-TTTTGAAAA-AT-A
* * *
11610705 AAAATTTT-AAAACACG-AGAATTTGTG-AAACTCGA
1 AAATTTTTGAAAACACGAAAAATTT-TGAAAAAT--A
* * * **
11610739 GAATTGTTGAAAAAAATAAAAAATTTTG-AAAATA
1 AAATTTTTG-AAAACACGAAAAATTTTGAAAAATA
** * *
11610773 CGAAATTTTTTTAAACACG-AAAATTTTAGAAATATGG
1 --AAATTTTTGAAAACACGAAAAATTTT-GAAAAAT-A
11610810 AAATTTTTAGAAAACACGAAAAATTTTGAAAAATA
1 AAATTTTT-GAAAACACGAAAAATTTTGAAAAATA
* *
11610845 AAATTTTTTGAAAACACGAGAATTTTTGAAAA
1 AAA-TTTTTGAAAACACGAAAAATTTTGAAAA
11610877 CACGAAAAAT
Statistics
Matches: 236, Mismatches: 55, Indels: 54
0.68 0.16 0.16
Matches are distributed among these distances:
33 10 0.04
34 49 0.21
35 64 0.27
36 67 0.28
37 14 0.06
38 5 0.02
40 11 0.05
41 3 0.01
42 13 0.06
ACGTcount: A:0.48, C:0.08, G:0.12, T:0.33
Consensus pattern (34 bp):
AAATTTTTGAAAACACGAAAAATTTTGAAAAATA
Found at i:11611034 original size:21 final size:22
Alignment explanation
Indices: 11610994--11611036 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
11610984 CGTTACCTTA
*
11610994 TTTTTGAAAACATGAGAAATTT
1 TTTTTGAAAACACGAGAAATTT
*
11611016 TTTTTGAAGACACGA-AAATTT
1 TTTTTGAAAACACGAGAAATTT
11611037 CGAAACGCGA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 6 0.32
22 13 0.68
ACGTcount: A:0.40, C:0.07, G:0.14, T:0.40
Consensus pattern (22 bp):
TTTTTGAAAACACGAGAAATTT
Found at i:11611230 original size:6 final size:5
Alignment explanation
Indices: 11611203--11611265 Score: 54
Period size: 5 Copynumber: 12.0 Consensus size: 5
11611193 TAAAAGTATT
* * *
11611203 TAAAA TAAAA TAAAA TAAAA TAAAAA TAAAAA TTAAAT TAAAT TAAAT
1 TAAAA TAAAA TAAAA TAAAA T-AAAA T-AAAA -TAAAA TAAAA TAAAA
* *
11611251 TAAAT TAAAT TAAAA
1 TAAAA TAAAA TAAAA
11611266 ATATAAATGC
Statistics
Matches: 54, Mismatches: 2, Indels: 4
0.90 0.03 0.07
Matches are distributed among these distances:
5 40 0.74
6 13 0.24
7 1 0.02
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (5 bp):
TAAAA
Found at i:11611240 original size:22 final size:22
Alignment explanation
Indices: 11611204--11611254 Score: 59
Period size: 22 Copynumber: 2.4 Consensus size: 22
11611194 AAAAGTATTT
11611204 AAAAT-AAAATAAAATAAAATA
1 AAAATAAAAATAAAATAAAATA
* * *
11611225 AAAATAAAAATTAAATTAAATT
1 AAAATAAAAATAAAATAAAATA
*
11611247 AAATTAAA
1 AAAATAAA
11611255 TTAAATTAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
21 5 0.20
22 20 0.80
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (22 bp):
AAAATAAAAATAAAATAAAATA
Found at i:11611454 original size:17 final size:16
Alignment explanation
Indices: 11611416--11611457 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 16
11611406 TGAACCCCTT
11611416 TTTTTCTTGTTTTTTC
1 TTTTTCTTGTTTTTTC
11611432 TCTTTTCTT-TTTTTCTCC
1 T-TTTTCTTGTTTTT-T-C
11611450 TTTTTCTT
1 TTTTTCTT
11611458 CCTTTTTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
16 6 0.26
17 15 0.65
18 2 0.09
ACGTcount: A:0.00, C:0.19, G:0.02, T:0.79
Consensus pattern (16 bp):
TTTTTCTTGTTTTTTC
Found at i:11611753 original size:3 final size:3
Alignment explanation
Indices: 11611747--11611805 Score: 73
Period size: 3 Copynumber: 18.0 Consensus size: 3
11611737 TTTCTTTTTT
11611747 TTC TTC TTTC TTC TTC TCTC TTTC TTTC TTC TTC TTC TTC TTCC TTC
1 TTC TTC -TTC TTC TTC T-TC -TTC -TTC TTC TTC TTC TTC TT-C TTC
11611794 TTC TTC TTC TTC
1 TTC TTC TTC TTC
11611806 AAAATCGAGC
Statistics
Matches: 52, Mismatches: 0, Indels: 8
0.87 0.00 0.13
Matches are distributed among these distances:
3 37 0.71
4 14 0.27
5 1 0.02
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (3 bp):
TTC
Found at i:11611758 original size:16 final size:16
Alignment explanation
Indices: 11611737--11611804 Score: 91
Period size: 16 Copynumber: 4.1 Consensus size: 16
11611727 TTAAATTTTT
* *
11611737 TTTCTTTTTTTTCTTC
1 TTTCTTCTTCTTCTTC
11611753 TTTCTTCTTCTCTCTTTC
1 TTTCTTCTTCT-TC-TTC
11611771 TTTCTTCTTCTTCTTC
1 TTTCTTCTTCTTCTTC
*
11611787 TTCCTTCTTCTTCTTC
1 TTTCTTCTTCTTCTTC
11611803 TT
1 TT
11611805 CAAAATCGAG
Statistics
Matches: 47, Mismatches: 3, Indels: 4
0.87 0.06 0.07
Matches are distributed among these distances:
16 29 0.62
17 4 0.09
18 14 0.30
ACGTcount: A:0.00, C:0.29, G:0.00, T:0.71
Consensus pattern (16 bp):
TTTCTTCTTCTTCTTC
Found at i:11611785 original size:34 final size:33
Alignment explanation
Indices: 11611737--11611801 Score: 94
Period size: 34 Copynumber: 1.9 Consensus size: 33
11611727 TTAAATTTTT
* * *
11611737 TTTCTTTTTTTTCTTCTTTCTTCTTCTCTCTTTC
1 TTTCTTCTTCTTCTTCTTCCTTCTTCT-TCTTTC
11611771 TTTCTTCTTCTTCTTCTTCCTTCTTCTTCTT
1 TTTCTTCTTCTTCTTCTTCCTTCTTCTTCTT
11611802 CTTCAAAATC
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
33 4 0.14
34 24 0.86
ACGTcount: A:0.00, C:0.29, G:0.00, T:0.71
Consensus pattern (33 bp):
TTTCTTCTTCTTCTTCTTCCTTCTTCTTCTTTC
Found at i:11612197 original size:29 final size:29
Alignment explanation
Indices: 11612164--11612280 Score: 103
Period size: 30 Copynumber: 3.9 Consensus size: 29
11612154 TGTAATTTTT
*
11612164 AGAAAATTTAGGATTAAAATGAAATTTAA
1 AGAAAATTTAGGGTTAAAATGAAATTTAA
* *
11612193 TGAAAGTTTAGGGGTCT-AAATGAAATTTAA
1 AGAAAATTTA-GGGT-TAAAATGAAATTTAA
* *
11612223 AGAAAGTTTAAGGGTCAAAATGAAATTT-A
1 AGAAAATTT-AGGGTTAAAATGAAATTTAA
* * *
11612252 GGAAAAGTTTAGGGGTCAAAATGCAATTT
1 AGAAAA-TTTA-GGGTTAAAATGAAATTT
11612281 TTATTTTTTA
Statistics
Matches: 74, Mismatches: 8, Indels: 11
0.80 0.09 0.12
Matches are distributed among these distances:
29 14 0.19
30 58 0.78
31 2 0.03
ACGTcount: A:0.45, C:0.03, G:0.21, T:0.30
Consensus pattern (29 bp):
AGAAAATTTAGGGTTAAAATGAAATTTAA
Found at i:11612216 original size:30 final size:30
Alignment explanation
Indices: 11612179--11612280 Score: 143
Period size: 30 Copynumber: 3.4 Consensus size: 30
11612169 ATTTAGGATT
*
11612179 AAAATGAAATTTAATGAAAGTTTAGGGGTC
1 AAAATGAAATTTAAAGAAAGTTTAGGGGTC
* *
11612209 TAAATGAAATTTAAAGAAAGTTTAAGGGTC
1 AAAATGAAATTTAAAGAAAGTTTAGGGGTC
*
11612239 AAAATGAAATTT-AGGAAAAGTTTAGGGGTC
1 AAAATGAAATTTAAAG-AAAGTTTAGGGGTC
*
11612269 AAAATGCAATTT
1 AAAATGAAATTT
11612281 TTATTTTTTA
Statistics
Matches: 64, Mismatches: 7, Indels: 2
0.88 0.10 0.03
Matches are distributed among these distances:
29 2 0.03
30 62 0.97
ACGTcount: A:0.45, C:0.04, G:0.22, T:0.29
Consensus pattern (30 bp):
AAAATGAAATTTAAAGAAAGTTTAGGGGTC
Found at i:11612259 original size:60 final size:59
Alignment explanation
Indices: 11612145--11612280 Score: 159
Period size: 60 Copynumber: 2.3 Consensus size: 59
11612135 CAAAACTTCT
* ** * *
11612145 GGGG-CTAAATGTAATTTTTAGAAAATTTAGGATTAAAATGAAATTTAATGAAAGTTTA
1 GGGGTCTAAATGAAATTTAAAGAAAATTTAGGATCAAAATGAAATTTAAGGAAAGTTTA
* *
11612203 GGGGTCTAAATGAAATTTAAAGAAAGTTTAAGGGTCAAAATGAAATTT-AGGAAAAGTTTA
1 GGGGTCTAAATGAAATTTAAAGAAAATTT-AGGATCAAAATGAAATTTAAGG-AAAGTTTA
* *
11612263 GGGGTCAAAATGCAATTT
1 GGGGTCTAAATGAAATTT
11612281 TTATTTTTTA
Statistics
Matches: 66, Mismatches: 9, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
58 4 0.06
59 22 0.33
60 40 0.61
ACGTcount: A:0.43, C:0.04, G:0.22, T:0.32
Consensus pattern (59 bp):
GGGGTCTAAATGAAATTTAAAGAAAATTTAGGATCAAAATGAAATTTAAGGAAAGTTTA
Found at i:11613586 original size:26 final size:26
Alignment explanation
Indices: 11613550--11613633 Score: 150
Period size: 26 Copynumber: 3.2 Consensus size: 26
11613540 TGATACAAAT
11613550 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATAGGTTAGGTAAATGTTCCA
11613576 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATAGGTTAGGTAAATGTTCCA
* *
11613602 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATAGGTTAGGTAAATGTTCCA
11613628 TGATAA
1 TGATAA
11613634 GAATTTCATG
Statistics
Matches: 56, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 56 1.00
ACGTcount: A:0.35, C:0.06, G:0.24, T:0.36
Consensus pattern (26 bp):
TGATAATAGGTTAGGTAAATGTTCCA
Found at i:11615666 original size:137 final size:137
Alignment explanation
Indices: 11615420--11615706 Score: 520
Period size: 137 Copynumber: 2.1 Consensus size: 137
11615410 GAGTAGTCTC
*
11615420 CCCAAACGGGCTTGCATATGTTTACTGATGTTGCATGTATTTTGAAATGGGCCTATGGGCCATAC
1 CCCAAATGGGCTTGCATATGTTTACTGATGTTGCATGTATTTTGAAATGGGCCTATGGGCCATAC
* *
11615485 TGTTATCTGAATAAGAGGCTAAGGCCTAGTTTATTGTAATCTGAAAATGGCTCTGGCCCAGTACC
66 TGTTATCTGAATAAGAGGCTAAGGCCTAGTTTATTGTAATCTGAAAAGGGCTCTGGCCCAATACC
11615550 ACTGTTA
131 ACTGTTA
11615557 CCCAAATGGGCTTGCATATGTTTACTGATGTTGCATGTATTTTGAAATGGGCCTATGGGCCATAC
1 CCCAAATGGGCTTGCATATGTTTACTGATGTTGCATGTATTTTGAAATGGGCCTATGGGCCATAC
*
11615622 TGTTATCTGAATAAGGGGCTAAGGCCTAGTTTATTGTAATCTGAAAAGGGCTCTGGCCCAATACC
66 TGTTATCTGAATAAGAGGCTAAGGCCTAGTTTATTGTAATCTGAAAAGGGCTCTGGCCCAATACC
11615687 ACTGTTA
131 ACTGTTA
**
11615694 CCTGAATGGGCTT
1 CCCAAATGGGCTT
11615707 AGGCCCAATG
Statistics
Matches: 144, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
137 144 1.00
ACGTcount: A:0.25, C:0.19, G:0.24, T:0.32
Consensus pattern (137 bp):
CCCAAATGGGCTTGCATATGTTTACTGATGTTGCATGTATTTTGAAATGGGCCTATGGGCCATAC
TGTTATCTGAATAAGAGGCTAAGGCCTAGTTTATTGTAATCTGAAAAGGGCTCTGGCCCAATACC
ACTGTTA
Found at i:11617887 original size:16 final size:16
Alignment explanation
Indices: 11617866--11617898 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
11617856 TAAAAGATTA
11617866 AAAGTAA-ATAATACAC
1 AAAGTAATAT-ATACAC
11617882 AAAGTAATATATACAC
1 AAAGTAATATATACAC
11617898 A
1 A
11617899 GGAAAAGCTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 14 0.88
17 2 0.12
ACGTcount: A:0.61, C:0.12, G:0.06, T:0.21
Consensus pattern (16 bp):
AAAGTAATATATACAC
Found at i:11619138 original size:15 final size:16
Alignment explanation
Indices: 11619120--11619149 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
11619110 GGTTTTGGGC
11619120 TGTTGGG-TTTTTAGA
1 TGTTGGGCTTTTTAGA
11619135 TGTTGGGCTTTTTAG
1 TGTTGGGCTTTTTAG
11619150 CCCGGACAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.10, C:0.03, G:0.33, T:0.53
Consensus pattern (16 bp):
TGTTGGGCTTTTTAGA
Found at i:11619978 original size:205 final size:205
Alignment explanation
Indices: 11619521--11620272 Score: 1182
Period size: 205 Copynumber: 3.7 Consensus size: 205
11619511 AAATCTGCTT
* * * * *
11619521 CTTCGATTTGTTCCCTGACAATACAGAGATGCCAAATCATCTTAGATTTGCTTTACCATAAGCAC
1 CTTCGACTTGTTCTCTGACAATACAGAGATGCCAAATCATCTTAGACTTGCTTTAGCGTAAGCAC
* * *
11619586 GTGAAAGCCAAATCAGCTATGTCTTCGATTTGCTCATTGTAAGCACAAGGATGCCAAATCATCTT
66 GCGAAAACCAAATCAGCTATGTCTTCGATTTGCTCATTGTAAGCACAAGGATGCCAAACCATCTT
* * * *
11619651 GGATCTTGCTTCAGTATAAACATCTGAAGGCCAGATCTGCTATGTATCTACTCTCCGTCAAAATG
131 GGATC-TACTTCAGTGTAAACATCTGAAGGCTAGATCTGCTATGTATCTGCTCTCCGTCAAAATG
11619716 GAGATGCCAGA
195 GAGATGCCAGA
*
11619727 CTTCGATTTGTTCTCTGACAATACAGAGATGCCAAATCATCTTAGACTTGCTTTAGCGTAAGCAC
1 CTTCGACTTGTTCTCTGACAATACAGAGATGCCAAATCATCTTAGACTTGCTTTAGCGTAAGCAC
* * *
11619792 GCGAAAACCAAATCAGCTATGTCTTCGATTTGCTCCTTGTAAGCACAATGATGTCAAACCATCTT
66 GCGAAAACCAAATCAGCTATGTCTTCGATTTGCTCATTGTAAGCACAAGGATGCCAAACCATCTT
** * * *
11619857 GGATCTACTTCAGTGTAAACATCTGAAGTTTGGATCTGCTATGTGTCTGCCCTCCGTCAAAATGG
131 GGATCTACTTCAGTGTAAACATCTGAAGGCTAGATCTGCTATGTATCTGCTCTCCGTCAAAATGG
* *
11619922 AGATTCCAGG
196 AGATGCCAGA
11619932 CTTCGACTTGTTCTCTGACAATACAGAGATGCCAAATCATCTTAGACTTGCTTTAGCGTAAGCAC
1 CTTCGACTTGTTCTCTGACAATACAGAGATGCCAAATCATCTTAGACTTGCTTTAGCGTAAGCAC
* *
11619997 GCGAAAACCAAATCAGCTATGTCTTCGATTTGCTCCTTGTAAGCACAAGGATGCCAAATCATCTT
66 GCGAAAACCAAATCAGCTATGTCTTCGATTTGCTCATTGTAAGCACAAGGATGCCAAACCATCTT
* * * *
11620062 AGATCTACTTCAGTG-AAATCATCTGAAGGCTAGATCTTCTATGTATCTGCTCTCCATCGAAATG
131 GGATCTACTTCAGTGTAAA-CATCTGAAGGCTAGATCTGCTATGTATCTGCTCTCCGTCAAAATG
*
11620126 GAGATGCTAGA
195 GAGATGCCAGA
* *
11620137 CTTCGACTTGTTATCTGACAATACAGAGTTGCCAAATCATCTTAGACTTGCTTTAGCGTAAGCAC
1 CTTCGACTTGTTCTCTGACAATACAGAGATGCCAAATCATCTTAGACTTGCTTTAGCGTAAGCAC
*
11620202 GCGAAAACCAAATCAGCTATGTCTTCGATTTGCTCATTGTAAGCACAAGGATGCCAAACCATTTT
66 GCGAAAACCAAATCAGCTATGTCTTCGATTTGCTCATTGTAAGCACAAGGATGCCAAACCATCTT
11620267 GGATCT
131 GGATCT
11620273 GCTTTAGCCA
Statistics
Matches: 502, Mismatches: 43, Indels: 3
0.92 0.08 0.01
Matches are distributed among these distances:
204 3 0.01
205 374 0.75
206 125 0.25
ACGTcount: A:0.29, C:0.23, G:0.18, T:0.30
Consensus pattern (205 bp):
CTTCGACTTGTTCTCTGACAATACAGAGATGCCAAATCATCTTAGACTTGCTTTAGCGTAAGCAC
GCGAAAACCAAATCAGCTATGTCTTCGATTTGCTCATTGTAAGCACAAGGATGCCAAACCATCTT
GGATCTACTTCAGTGTAAACATCTGAAGGCTAGATCTGCTATGTATCTGCTCTCCGTCAAAATGG
AGATGCCAGA
Found at i:11628702 original size:16 final size:16
Alignment explanation
Indices: 11628681--11628713 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
11628671 TAAAAGATTA
11628681 AAAGTAAT-TAATACAC
1 AAAGTAATAT-ATACAC
11628697 AAAGTAATATATACAC
1 AAAGTAATATATACAC
11628713 A
1 A
11628714 GGAAAAGCTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 15 0.94
17 1 0.06
ACGTcount: A:0.58, C:0.12, G:0.06, T:0.24
Consensus pattern (16 bp):
AAAGTAATATATACAC
Found at i:11629940 original size:15 final size:16
Alignment explanation
Indices: 11629922--11629951 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
11629912 GGTTTTGGGC
11629922 TGTTGGG-TTTTTAGA
1 TGTTGGGCTTTTTAGA
11629937 TGTTGGGCTTTTTAG
1 TGTTGGGCTTTTTAG
11629952 CCCGGGCAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.10, C:0.03, G:0.33, T:0.53
Consensus pattern (16 bp):
TGTTGGGCTTTTTAGA
Found at i:11630897 original size:10 final size:10
Alignment explanation
Indices: 11630882--11630914 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
11630872 AGGTTACCAT
11630882 ATTTTATTTC
1 ATTTTATTTC
*
11630892 ATTTTATTTT
1 ATTTTATTTC
11630902 ATTTT-TTTC
1 ATTTTATTTC
11630911 ATTT
1 ATTT
11630915 ACAAATCTGT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
9 7 0.33
10 14 0.67
ACGTcount: A:0.18, C:0.06, G:0.00, T:0.76
Consensus pattern (10 bp):
ATTTTATTTC
Found at i:11631639 original size:3 final size:3
Alignment explanation
Indices: 11631623--11631692 Score: 54
Period size: 3 Copynumber: 23.7 Consensus size: 3
11631613 TATTTATTCC
* ** * *
11631623 TAT TAT T-T TA- TAT TAT TGT CGT TAT TAA TAT ATAC TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT -TAT TAT TAT TAT
* *
11631667 CAT TAA TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TA
11631693 CTAATATCAC
Statistics
Matches: 52, Mismatches: 12, Indels: 6
0.74 0.17 0.09
Matches are distributed among these distances:
2 4 0.08
3 46 0.88
4 2 0.04
ACGTcount: A:0.34, C:0.04, G:0.03, T:0.59
Consensus pattern (3 bp):
TAT
Found at i:11631767 original size:26 final size:26
Alignment explanation
Indices: 11631730--11631820 Score: 71
Period size: 26 Copynumber: 3.5 Consensus size: 26
11631720 AGCAAATCAC
*
11631730 TATCATC-GTTTTTTATTACTATTAT
1 TATCATCATTTTTTTATTACTATTAT
*
11631755 TATCATCATTTTTTTATCTAATA-TAT
1 TATCATCATTTTTTTAT-TACTATTAT
* * *
11631781 TATTAACCTTTTATTATTATTACTATTAT
1 TA-TCATCATTT-TT-TTATTACTATTAT
*
11631810 TATTAT-ATTTT
1 TATCATCATTTT
11631821 CTTTTTATTT
Statistics
Matches: 51, Mismatches: 9, Indels: 11
0.72 0.13 0.15
Matches are distributed among these distances:
25 7 0.14
26 14 0.27
27 13 0.25
28 8 0.16
29 9 0.18
ACGTcount: A:0.29, C:0.10, G:0.01, T:0.60
Consensus pattern (26 bp):
TATCATCATTTTTTTATTACTATTAT
Found at i:11632008 original size:3 final size:3
Alignment explanation
Indices: 11631996--11632196 Score: 122
Period size: 3 Copynumber: 67.3 Consensus size: 3
11631986 ATTATTTGTG
* * ** *
11631996 TTA TTG TTA TTA TTA CTTT TTA TTA TTA CCA TTA TTA TTA CTA TTA
1 TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* * * *
11632042 TTT TTA CTT- TTA TTA CTA TTA CTA -TA TTA TTA TTA TTA TTT TCTA
1 TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA
* ** * * * * * *
11632087 TTA CTA TCG TTA TTA TTA ATA CTA ATA TTA ATA TTC TTA TTA TTA CTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* * ** *
11632135 TTA TTA TTA TCA TTA GTA TTA TTA TT- TT- TTA CCA CTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* *
11632181 TCA ATA TTA TTA TTA T
1 TTA TTA TTA TTA TTA T
11632197 CGTTTTCATT
Statistics
Matches: 147, Mismatches: 45, Indels: 12
0.72 0.22 0.06
Matches are distributed among these distances:
2 8 0.05
3 133 0.90
4 6 0.04
ACGTcount: A:0.31, C:0.09, G:0.01, T:0.59
Consensus pattern (3 bp):
TTA
Found at i:11632207 original size:18 final size:18
Alignment explanation
Indices: 11632186--11632220 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
11632176 TATTATCAAT
*
11632186 ATTATTATTATCGTTTTC
1 ATTATCATTATCGTTTTC
*
11632204 ATTATCATTGTCGTTTT
1 ATTATCATTATCGTTTT
11632221 TATTTTTCCA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.20, C:0.11, G:0.09, T:0.60
Consensus pattern (18 bp):
ATTATCATTATCGTTTTC
Found at i:11633905 original size:25 final size:25
Alignment explanation
Indices: 11633871--11633919 Score: 89
Period size: 25 Copynumber: 2.0 Consensus size: 25
11633861 GCGGTGAAGG
*
11633871 TATAAATTGGGAGAAAATGTTTAAT
1 TATAAATTGGAAGAAAATGTTTAAT
11633896 TATAAATTGGAAGAAAATGTTTAA
1 TATAAATTGGAAGAAAATGTTTAA
11633920 AGCTTGGTGG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.47, C:0.00, G:0.18, T:0.35
Consensus pattern (25 bp):
TATAAATTGGAAGAAAATGTTTAAT
Found at i:11635311 original size:30 final size:28
Alignment explanation
Indices: 11635277--11635336 Score: 84
Period size: 29 Copynumber: 2.1 Consensus size: 28
11635267 CATTTAATTC
11635277 ATTTCTAAACTATTAAAAATAATTTTTATA
1 ATTTCT-AACTATTAAAAATAA-TTTTATA
* *
11635307 ATTTCTAATTTTTAAAAATAATTTTATA
1 ATTTCTAACTATTAAAAATAATTTTATA
11635335 AT
1 AT
11635337 ATTTTAAAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
28 9 0.32
29 13 0.46
30 6 0.21
ACGTcount: A:0.45, C:0.05, G:0.00, T:0.50
Consensus pattern (28 bp):
ATTTCTAACTATTAAAAATAATTTTATA
Found at i:11635349 original size:18 final size:17
Alignment explanation
Indices: 11635326--11635362 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 17
11635316 TTTTAAAAAT
11635326 AATTTTATAATATTTTAA
1 AATTTTATAA-ATTTTAA
*
11635344 AATTTTTTAAATTTTAA
1 AATTTTATAAATTTTAA
11635361 AA
1 AA
11635363 AATTAATTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 9 0.50
18 9 0.50
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
AATTTTATAAATTTTAA
Found at i:11642520 original size:21 final size:22
Alignment explanation
Indices: 11642494--11642548 Score: 96
Period size: 21 Copynumber: 2.6 Consensus size: 22
11642484 AACAGCGGTG
11642494 GCGGTGAGATTAGG-TACTGTA
1 GCGGTGAGATTAGGATACTGTA
11642515 GCGGTGAGATT-GGATACTGTA
1 GCGGTGAGATTAGGATACTGTA
11642536 GCGGTGAGATTAG
1 GCGGTGAGATTAG
11642549 AAACAGCGGT
Statistics
Matches: 32, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
20 2 0.06
21 29 0.91
22 1 0.03
ACGTcount: A:0.24, C:0.09, G:0.40, T:0.27
Consensus pattern (22 bp):
GCGGTGAGATTAGGATACTGTA
Found at i:11642684 original size:19 final size:18
Alignment explanation
Indices: 11642660--11642706 Score: 58
Period size: 19 Copynumber: 2.6 Consensus size: 18
11642650 AGAAGTTTTT
*
11642660 AAAATTATTTAACAATTA
1 AAAATTATTAAACAATTA
* *
11642678 CAAAATTAATAAATAATTA
1 -AAAATTATTAAACAATTA
11642697 AAAATTATTA
1 AAAATTATTA
11642707 CAATTATATT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
18 9 0.38
19 15 0.62
ACGTcount: A:0.60, C:0.04, G:0.00, T:0.36
Consensus pattern (18 bp):
AAAATTATTAAACAATTA
Found at i:11642908 original size:36 final size:34
Alignment explanation
Indices: 11642830--11642910 Score: 94
Period size: 36 Copynumber: 2.3 Consensus size: 34
11642820 TTAAATATAC
11642830 AATAAAATATTTTTAAATTATATTCATAATAAAAT
1 AATAAAATATTTTTAAATTATATT-ATAATAAAAT
*
11642865 -ATCAAAATATTTTTACAGATTATATT-TGAATCAAAT
1 AAT-AAAATATTTTTA-A-ATTATATTAT-AATAAAAT
11642901 AATAAAATAT
1 AATAAAATAT
11642911 AAATTAAATT
Statistics
Matches: 40, Mismatches: 1, Indels: 9
0.80 0.02 0.18
Matches are distributed among these distances:
34 2 0.05
35 13 0.32
36 15 0.38
37 10 0.25
ACGTcount: A:0.52, C:0.05, G:0.02, T:0.41
Consensus pattern (34 bp):
AATAAAATATTTTTAAATTATATTATAATAAAAT
Found at i:11646135 original size:28 final size:29
Alignment explanation
Indices: 11646084--11646157 Score: 82
Period size: 29 Copynumber: 2.6 Consensus size: 29
11646074 CAAAAAAAAC
* *
11646084 TATAAAGAATAATT-AAAATTAT-AAATTAT
1 TATAAA-ATTAATTAAAAATCATAAAATT-T
11646113 TAT-AAATTAATTAAAAATCATAAAATTT
1 TATAAAATTAATTAAAAATCATAAAATTT
*
11646141 TATAAAATAAATTAAAA
1 TATAAAATTAATTAAAA
11646158 CAAAGCTTTT
Statistics
Matches: 39, Mismatches: 3, Indels: 6
0.81 0.06 0.12
Matches are distributed among these distances:
27 6 0.15
28 13 0.33
29 20 0.51
ACGTcount: A:0.61, C:0.01, G:0.01, T:0.36
Consensus pattern (29 bp):
TATAAAATTAATTAAAAATCATAAAATTT
Found at i:11646394 original size:18 final size:18
Alignment explanation
Indices: 11646383--11646418 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
11646373 ATTTTATACG
11646383 TTTTAATAATTTCTAAAA
1 TTTTAATAATTTCTAAAA
*
11646401 TTTTAATAATTTATAAAA
1 TTTTAATAATTTCTAAAA
11646419 AAAACTTTAG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (18 bp):
TTTTAATAATTTCTAAAA
Found at i:11646475 original size:30 final size:30
Alignment explanation
Indices: 11646439--11646514 Score: 82
Period size: 29 Copynumber: 2.6 Consensus size: 30
11646429 AAAAAATCAT
*
11646439 TTTAATTATTTTATAATATTTTTTATAAAA
1 TTTAATTATTTTATAATATATTTTATAAAA
* * **
11646469 TTTAATTATTTGA-ATTATATTTTATAATT
1 TTTAATTATTTTATAATATATTTTATAAAA
* *
11646498 TTTTATTTTTTTATAAT
1 TTTAATTATTTTATAAT
11646515 TTCGAAATGA
Statistics
Matches: 36, Mismatches: 9, Indels: 2
0.77 0.19 0.04
Matches are distributed among these distances:
29 22 0.61
30 14 0.39
ACGTcount: A:0.34, C:0.00, G:0.01, T:0.64
Consensus pattern (30 bp):
TTTAATTATTTTATAATATATTTTATAAAA
Found at i:11647159 original size:17 final size:16
Alignment explanation
Indices: 11647137--11647186 Score: 55
Period size: 17 Copynumber: 3.0 Consensus size: 16
11647127 GCCACACCAA
*
11647137 AAAAAATTTAAAATTAT
1 AAAAAATTTAAAA-AAT
*
11647154 AAAAAATTCAAAAAAT
1 AAAAAATTTAAAAAAT
*
11647170 AAAAAGTTTATAAAAAT
1 AAAAAATTTA-AAAAAT
11647187 TCAAAAAATA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
16 10 0.36
17 18 0.64
ACGTcount: A:0.68, C:0.02, G:0.02, T:0.28
Consensus pattern (16 bp):
AAAAAATTTAAAAAAT
Found at i:11647166 original size:26 final size:27
Alignment explanation
Indices: 11647137--11647199 Score: 80
Period size: 26 Copynumber: 2.4 Consensus size: 27
11647127 GCCACACCAA
*
11647137 AAAAAATTTAAAA--TTATAAAAAATTC
1 AAAAAATTAAAAAGTTTAT-AAAAATTC
11647163 AAAAAA-TAAAAAGTTTATAAAAATTC
1 AAAAAATTAAAAAGTTTATAAAAATTC
11647189 AAAAAA-TAAAA
1 AAAAAATTAAAA
11647200 GAGTATGAAA
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
25 5 0.15
26 25 0.74
27 4 0.12
ACGTcount: A:0.70, C:0.03, G:0.02, T:0.25
Consensus pattern (27 bp):
AAAAAATTAAAAAGTTTATAAAAATTC
Found at i:11647296 original size:26 final size:26
Alignment explanation
Indices: 11647267--11647349 Score: 66
Period size: 26 Copynumber: 3.2 Consensus size: 26
11647257 TAATTTTTAA
11647267 TAAAAAATAGCAAGTCAACTATTTTT
1 TAAAAAATAGCAAGTCAACTATTTTT
* * * **
11647293 TAAAAATTTA--ATGGTTAA-T-TTTCAA
1 TAAAAA-ATAGCA-AGTCAACTATTT-TT
11647318 TAAAAAATAGCAAGTCAACTATTTTT
1 TAAAAAATAGCAAGTCAACTATTTTT
11647344 TAAAAA
1 TAAAAA
11647350 TTTAATGGTT
Statistics
Matches: 40, Mismatches: 10, Indels: 14
0.62 0.16 0.22
Matches are distributed among these distances:
24 5 0.12
25 12 0.30
26 18 0.45
27 5 0.12
ACGTcount: A:0.48, C:0.08, G:0.07, T:0.36
Consensus pattern (26 bp):
TAAAAAATAGCAAGTCAACTATTTTT
Found at i:11647372 original size:25 final size:25
Alignment explanation
Indices: 11647293--11647374 Score: 62
Period size: 25 Copynumber: 3.2 Consensus size: 25
11647283 AACTATTTTT
11647293 TAAAAATTTAATGGTTAATTTTCAA
1 TAAAAATTTAATGGTTAATTTTCAA
* * * **
11647318 TAAAAA-ATAGCA-AGTCAACTATTT-TT
1 TAAAAATTTA--ATGGTTAA-T-TTTCAA
11647344 TAAAAATTTAATGGTTAATTTTCAA
1 TAAAAATTTAATGGTTAATTTTCAA
11647369 TAAAAA
1 TAAAAA
11647375 ATAGCAAGTC
Statistics
Matches: 40, Mismatches: 10, Indels: 14
0.62 0.16 0.22
Matches are distributed among these distances:
24 5 0.12
25 18 0.45
26 12 0.30
27 5 0.12
ACGTcount: A:0.48, C:0.06, G:0.07, T:0.39
Consensus pattern (25 bp):
TAAAAATTTAATGGTTAATTTTCAA
Found at i:11647405 original size:51 final size:51
Alignment explanation
Indices: 11647240--11647394 Score: 292
Period size: 51 Copynumber: 3.0 Consensus size: 51
11647230 AGCTACCATG
* *
11647240 TTTAAAAATTTAATGATTAATTTTTAATAAAAAATAGCAAGTCAACTATTT
1 TTTAAAAATTTAATGGTTAATTTTCAATAAAAAATAGCAAGTCAACTATTT
11647291 TTTAAAAATTTAATGGTTAATTTTCAATAAAAAATAGCAAGTCAACTATTT
1 TTTAAAAATTTAATGGTTAATTTTCAATAAAAAATAGCAAGTCAACTATTT
11647342 TTTAAAAATTTAATGGTTAATTTTCAATAAAAAATAGCAAGTCAACTATTT
1 TTTAAAAATTTAATGGTTAATTTTCAATAAAAAATAGCAAGTCAACTATTT
11647393 TT
1 TT
11647395 GAAAGGTTTA
Statistics
Matches: 102, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
51 102 1.00
ACGTcount: A:0.45, C:0.07, G:0.07, T:0.41
Consensus pattern (51 bp):
TTTAAAAATTTAATGGTTAATTTTCAATAAAAAATAGCAAGTCAACTATTT
Found at i:11648415 original size:18 final size:18
Alignment explanation
Indices: 11648376--11648423 Score: 55
Period size: 19 Copynumber: 2.6 Consensus size: 18
11648366 ATTGTAATTA
11648376 TTTTATAATTTGAATGATT
1 TTTTATAATTT-AATGATT
11648395 TTTTATAATTTATTATG-TT
1 TTTTATAATTTA--ATGATT
11648414 TTTT-TAATTT
1 TTTTATAATTT
11648424 CGAAATGAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
18 7 0.26
19 17 0.63
20 3 0.11
ACGTcount: A:0.27, C:0.00, G:0.06, T:0.67
Consensus pattern (18 bp):
TTTTATAATTTAATGATT
Found at i:11650217 original size:15 final size:15
Alignment explanation
Indices: 11650197--11650225 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
11650187 CACTAGTTTT
11650197 GGCAAAGGGAGGATA
1 GGCAAAGGGAGGATA
11650212 GGCAAAGGGAGGAT
1 GGCAAAGGGAGGAT
11650226 CTCAAGGGCC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.38, C:0.07, G:0.48, T:0.07
Consensus pattern (15 bp):
GGCAAAGGGAGGATA
Found at i:11651106 original size:20 final size:21
Alignment explanation
Indices: 11651063--11651108 Score: 62
Period size: 20 Copynumber: 2.3 Consensus size: 21
11651053 ACTATTTTGT
11651063 TATGGG-CCAACTGTATTGAA
1 TATGGGCCCAACTGTATTGAA
*
11651083 -ATGGGCCCAACTGTGTT-AA
1 TATGGGCCCAACTGTATTGAA
11651102 TATGGGC
1 TATGGGC
11651109 AAGGCCCAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
19 7 0.30
20 16 0.70
ACGTcount: A:0.26, C:0.17, G:0.28, T:0.28
Consensus pattern (21 bp):
TATGGGCCCAACTGTATTGAA
Found at i:11660331 original size:25 final size:26
Alignment explanation
Indices: 11660298--11660348 Score: 68
Period size: 25 Copynumber: 2.0 Consensus size: 26
11660288 AACAAGTAAT
* *
11660298 TTAAAAATTATAA-AAAAATTAAAAA
1 TTAAAAATTAAAATAAAAAATAAAAA
*
11660323 TTAAGAATTAAAATAAAAAATAAAAA
1 TTAAAAATTAAAATAAAAAATAAAAA
11660349 AAGTATGAAG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
25 11 0.50
26 11 0.50
ACGTcount: A:0.73, C:0.00, G:0.02, T:0.25
Consensus pattern (26 bp):
TTAAAAATTAAAATAAAAAATAAAAA
Found at i:11666895 original size:53 final size:53
Alignment explanation
Indices: 11666838--11666943 Score: 194
Period size: 53 Copynumber: 2.0 Consensus size: 53
11666828 CTTTTTCACT
* *
11666838 TACATCATTTTACTTATATATATTTTAAAATTTGAGGTAGCCAATTTACTTAG
1 TACATCACTTTACTTATATATATTTTAAAATTTGAGGTAGCCAATTAACTTAG
11666891 TACATCACTTTACTTATATATATTTTAAAATTTGAGGTAGCCAATTAACTTAG
1 TACATCACTTTACTTATATATATTTTAAAATTTGAGGTAGCCAATTAACTTAG
11666944 GAATCTAACA
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
53 51 1.00
ACGTcount: A:0.35, C:0.12, G:0.09, T:0.43
Consensus pattern (53 bp):
TACATCACTTTACTTATATATATTTTAAAATTTGAGGTAGCCAATTAACTTAG
Found at i:11667965 original size:14 final size:14
Alignment explanation
Indices: 11667946--11667974 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
11667936 ATAACAATGG
11667946 TTTTTATCATGATT
1 TTTTTATCATGATT
11667960 TTTTTATCATGATT
1 TTTTTATCATGATT
11667974 T
1 T
11667975 GAAACAATTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.21, C:0.07, G:0.07, T:0.66
Consensus pattern (14 bp):
TTTTTATCATGATT
Done.