Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168270.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_5, whole genome shotgun sequence
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: 27802247
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 124000 characters in sequence are not A, C, G, or T
File 97 of 147
Found at i:17849079 original size:71 final size:70
Alignment explanation
Indices: 17848934--17849106 Score: 192
Period size: 71 Copynumber: 2.4 Consensus size: 70
17848924 TCGACTGTTG
* * *
17848934 GTGTTGTCCCAGTCATTTTTACTTTTTGACTTGCAGTGTTGTTCTAATCATATTTATTTTCTTGA
1 GTGTTGTCCCAGTCATTTTT-TTTTTTGACCTGCAGCGTTGTTCTAATCATATTTATTTTCTTGA
17848999 CCTACA
65 CCTACA
**
17849005 GTGTTGTCCCAGTCATTTTTGTTTTTTGACCTG-ATGCGTTGTTCTGGTCATATTTATTTT-TTC
1 GTGTTGTCCCAGTCATTTTT-TTTTTTGACCTGCA-GCGTTGTTCTAATCATATTTATTTTCTT-
*
17849068 GACC-ATTA
63 GACCTA-CA
* *
17849076 GTGTTATCCTAGTCATCTTTTTTTTTT-ACCT
1 GTGTTGTCCCAGTCAT-TTTTTTTTTTGACCT
17849107 ATAGTATTAT
Statistics
Matches: 89, Mismatches: 9, Indels: 9
0.83 0.08 0.08
Matches are distributed among these distances:
70 8 0.09
71 77 0.87
72 4 0.04
ACGTcount: A:0.16, C:0.18, G:0.15, T:0.51
Consensus pattern (70 bp):
GTGTTGTCCCAGTCATTTTTTTTTTTGACCTGCAGCGTTGTTCTAATCATATTTATTTTCTTGAC
CTACA
Found at i:17849091 original size:36 final size:35
Alignment explanation
Indices: 17848981--17849172 Score: 106
Period size: 36 Copynumber: 5.4 Consensus size: 35
17848971 GTTGTTCTAA
* * *
17848981 TCATATTTATTTTCTTGACC-TACAGTGTTGTCCCAG
1 TCATATTTATTTT-TTGACCAT-TAGTGTTATCCTAG
* * * * * * *
17849017 TCATTTTTGTTTTTTGACC-TGATGCGTTGTTCTGG
1 TCATATTTATTTTTTGACCATTA-GTGTTATCCTAG
17849052 TCATATTTATTTTTTCGACCATTAGTGTTATCCTAG
1 TCATATTTATTTTTT-GACCATTAGTGTTATCCTAG
* * * *
17849088 TCATCTTT-TTTTTTTACC-TATAGTATTATCCCAG
1 TCATATTTATTTTTTGACCAT-TAGTGTTATCCTAG
* * * * *
17849122 TCATCTTTGATTTCTTGATCATTGGTGTTGTCCTAG
1 TCATATTT-ATTTTTTGACCATTAGTGTTATCCTAG
*
17849158 TTA-ACTTTATTTTTT
1 TCATA-TTTATTTTTT
17849173 TAACCTACAG
Statistics
Matches: 120, Mismatches: 28, Indels: 17
0.73 0.17 0.10
Matches are distributed among these distances:
33 1 0.01
34 24 0.20
35 40 0.33
36 52 0.43
37 3 0.03
ACGTcount: A:0.17, C:0.17, G:0.14, T:0.52
Consensus pattern (35 bp):
TCATATTTATTTTTTGACCATTAGTGTTATCCTAG
Found at i:17849201 original size:72 final size:69
Alignment explanation
Indices: 17849051--17849210 Score: 158
Period size: 70 Copynumber: 2.3 Consensus size: 69
17849041 CGTTGTTCTG
* * * * *
17849051 GTCATATTTATTTTTTCGACCATTAGTGTTATCCTAGTCATCTTTTTTTTTTACCTATAGTATTA
1 GTCATCTTTATTTCTT-GATCATTAGTGTTATCCTAGTCAACTTTTTTTTTTACCTACAGTATTA
17849116 TCCCA
65 TCCCA
* * * *
17849121 GTCATCTTTGATTTCTTGATCATTGGTGTTGTCCTAGTTAACTTTATTTTTTTAACCTACAGTGT
1 GTCATCTTT-ATTTCTTGATCATTAGTGTTATCCTAGTCAACTTT-TTTTTTT-ACCTACAGTAT
* **
17849186 TGTTTCA
63 TATCCCA
* *
17849193 GTTATCTTTATTTTTTGA
1 GTCATCTTTATTTCTTGA
17849211 CTTGCGATGT
Statistics
Matches: 73, Mismatches: 14, Indels: 5
0.79 0.15 0.05
Matches are distributed among these distances:
70 31 0.42
71 21 0.29
72 21 0.29
ACGTcount: A:0.19, C:0.16, G:0.12, T:0.53
Consensus pattern (69 bp):
GTCATCTTTATTTCTTGATCATTAGTGTTATCCTAGTCAACTTTTTTTTTTACCTACAGTATTAT
CCCA
Found at i:17849263 original size:32 final size:34
Alignment explanation
Indices: 17849196--17849264 Score: 97
Period size: 35 Copynumber: 2.1 Consensus size: 34
17849186 TGTTTCAGTT
*
17849196 ATCTTTATTTTTTGACTTGCGATGTTATCTCGATC
1 ATCTTTACTTTTTGACTT-CGATGTTATCTCGATC
*
17849231 ATCTTTACTTTTTGACTT-G-TGTTATCTTGATC
1 ATCTTTACTTTTTGACTTCGATGTTATCTCGATC
17849263 AT
1 AT
17849265 ATTCGTTTTC
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
32 14 0.44
33 1 0.03
35 17 0.53
ACGTcount: A:0.17, C:0.16, G:0.13, T:0.54
Consensus pattern (34 bp):
ATCTTTACTTTTTGACTTCGATGTTATCTCGATC
Found at i:17849608 original size:6 final size:6
Alignment explanation
Indices: 17849599--17849732 Score: 110
Period size: 6 Copynumber: 21.0 Consensus size: 6
17849589 TTTTTCAAAT
* *
17849599 CAAAAA CAAAAA -AAAGA CAAAAA CAAAAA CAAAAA CAAAGAA AACAAAA
1 CAAAAA CAAAAA CAAAAA CAAAAA CAAAAA CAAAAA CAAA-AA CA-AAAA
* * * *
17849648 CAATAAA TAAAAA TAAAAAA CAAAAA CAAAAA CATACAAA CAAAAT CAAAAT
1 CAA-AAA CAAAAA -CAAAAA CAAAAA CAAAAA CA-A-AAA CAAAAA CAAAAA
17849700 CAAAACAA CAAGAAA CAAAAA -ACAAAA CAAAAA
1 C-AAA-AA CAA-AAA CAAAAA CA-AAAA CAAAAA
17849733 GGAAAAAGAA
Statistics
Matches: 107, Mismatches: 9, Indels: 24
0.76 0.06 0.17
Matches are distributed among these distances:
5 5 0.05
6 63 0.59
7 29 0.27
8 10 0.09
ACGTcount: A:0.78, C:0.15, G:0.02, T:0.04
Consensus pattern (6 bp):
CAAAAA
Found at i:17849672 original size:40 final size:38
Alignment explanation
Indices: 17849601--17849746 Score: 62
Period size: 40 Copynumber: 3.9 Consensus size: 38
17849591 TTTCAAATCA
* * *
17849601 AAAAC-AAAAAA-AAGACAAAAACAAAAA-CAAAAACA
1 AAAACAAAAAAACAAAACAAAAATAAAAATAAAAAACA
* * * *
17849636 AAGAA-AACAAAACAATA-AATAA-AAATA-AAA-AACA
1 AA-AACAAAAAAACAAAACAAAAATAAAAATAAAAAACA
*
17849670 AAAACAAAAACATAC-AAAC-AAAATCAAAATCAAAACAACA
1 AAAACAAAAA-A-ACAAAACAAAAATAAAAAT-AAAA-AACA
* *
17849710 AGAAAC-AAAAAACAAAACAAAAAGGAAAAAGAAAAAA
1 A-AAACAAAAAAACAAAACAAAAA-TAAAAATAAAAAA
17849747 GGAAATAGGG
Statistics
Matches: 82, Mismatches: 13, Indels: 28
0.67 0.11 0.23
Matches are distributed among these distances:
33 2 0.02
34 10 0.12
35 14 0.17
36 16 0.20
37 3 0.04
38 5 0.06
39 7 0.09
40 17 0.21
41 8 0.10
ACGTcount: A:0.79, C:0.13, G:0.04, T:0.04
Consensus pattern (38 bp):
AAAACAAAAAAACAAAACAAAAATAAAAATAAAAAACA
Found at i:17849738 original size:12 final size:12
Alignment explanation
Indices: 17849600--17849732 Score: 85
Period size: 13 Copynumber: 10.3 Consensus size: 12
17849590 TTTTCAAATC
17849600 AAAAACAAAA-A
1 AAAAACAAAACA
*
17849611 AAAGACAAAA-A
1 AAAAACAAAACA
17849622 CAAAAACAAAAACAA
1 -AAAAAC-AAAAC-A
17849637 AGAAAACAAAACA
1 A-AAAACAAAACA
*
17849650 ATAAATA-AAAATA
1 A-AAA-ACAAAACA
17849663 AAAAACAAAAACA
1 AAAAAC-AAAACA
*
17849676 AAAACATACAAAC-
1 AAAA-ACA-AAACA
*
17849689 AAAATCAAAATCA
1 AAAAACAAAA-CA
17849702 AAACAACAAGAAACA
1 AAA-AAC-A-AAACA
17849717 AAAAACAAAACA
1 AAAAACAAAACA
17849729 AAAA
1 AAAA
17849733 GGAAAAAGAA
Statistics
Matches: 98, Mismatches: 9, Indels: 29
0.72 0.07 0.21
Matches are distributed among these distances:
11 14 0.14
12 19 0.19
13 33 0.34
14 17 0.17
15 12 0.12
16 3 0.03
ACGTcount: A:0.79, C:0.14, G:0.02, T:0.05
Consensus pattern (12 bp):
AAAAACAAAACA
Found at i:17850996 original size:144 final size:145
Alignment explanation
Indices: 17850731--17850997 Score: 376
Period size: 144 Copynumber: 1.8 Consensus size: 145
17850721 AAAATATCCC
** * * **
17850731 TTTCATAATTTGGCCTTCTTGAGCTTGAATTTTCATAAAACTTTTTAGATCTTAATTTTTTAATA
1 TTTCATAATTTGGCCTTCTCAAGCTCGAATTTTCATAAAACTTTTTAGATCCTAATTTCATAATA
* * * **
17850796 TTTTATGATTTTTGGTGTATTTGAAATCACAGTAATACCCCTGAGAGGTGTGAATTACAAAAATA
66 TTTAATGATTTTTGGTGCATTTAAAATCACAACAATACCCCTGAGAGGTGTGAATTACAAAAATA
17850861 TCCCTTTAAAGATAT
131 TCCCTTTAAAGATAT
* *
17850876 TTTCATAATTTGGCCTTCTCAAGCTCGGATTTTCATAAAAC-TTTTAGATCCTAATTTCATCATA
1 TTTCATAATTTGGCCTTCTCAAGCTCGAATTTTCATAAAACTTTTTAGATCCTAATTTCATAATA
* *
17850940 TTTAATGATTTTTGGTGCATTTAAAATCACAACAGTATCCCTG-GAGGTGTGAAATTAC
66 TTTAATGATTTTTGGTGCATTTAAAATCACAACAATACCCCTGAGAGGTGTG-AATTAC
17850998 GAAGTCTGAA
Statistics
Matches: 106, Mismatches: 15, Indels: 3
0.85 0.12 0.02
Matches are distributed among these distances:
143 8 0.08
144 61 0.58
145 37 0.35
ACGTcount: A:0.30, C:0.15, G:0.13, T:0.42
Consensus pattern (145 bp):
TTTCATAATTTGGCCTTCTCAAGCTCGAATTTTCATAAAACTTTTTAGATCCTAATTTCATAATA
TTTAATGATTTTTGGTGCATTTAAAATCACAACAATACCCCTGAGAGGTGTGAATTACAAAAATA
TCCCTTTAAAGATAT
Found at i:17852591 original size:3 final size:3
Alignment explanation
Indices: 17852583--17852616 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
17852573 TGTCATAAAC
17852583 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
17852617 TTGGATGCAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:17854282 original size:25 final size:25
Alignment explanation
Indices: 17854235--17854287 Score: 72
Period size: 25 Copynumber: 2.1 Consensus size: 25
17854225 ACCTTAAACG
* *
17854235 TGTTTATTCCACATGATTATTTTCT
1 TGTTCATTCCACATGACTATTTTCT
17854260 TGTTCATTCCACATGACCT-TTTTCT
1 TGTTCATTCCACATGA-CTATTTTCT
17854285 TGT
1 TGT
17854288 AATGACTTTC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 24 0.96
26 1 0.04
ACGTcount: A:0.17, C:0.21, G:0.09, T:0.53
Consensus pattern (25 bp):
TGTTCATTCCACATGACTATTTTCT
Found at i:17855867 original size:32 final size:32
Alignment explanation
Indices: 17855831--17855933 Score: 104
Period size: 32 Copynumber: 3.3 Consensus size: 32
17855821 CCAAATTATT
*
17855831 TGGCACCAATGAAGTCTTAAGCCTAATTTAGC
1 TGGCACCAATGAAGTTTTAAGCCTAATTTAGC
* * *
17855863 TGGCA-C--TAAAGTTTTAAGCCCAAATTAGC
1 TGGCACCAATGAAGTTTTAAGCCTAATTTAGC
** * *
17855892 TGGTGCCAATGAAGTTTTAAGCCTAATTAAGT
1 TGGCACCAATGAAGTTTTAAGCCTAATTTAGC
*
17855924 TGGCATCAAT
1 TGGCACCAAT
17855934 CACAATTTAT
Statistics
Matches: 54, Mismatches: 14, Indels: 6
0.73 0.19 0.08
Matches are distributed among these distances:
29 22 0.41
30 1 0.02
31 1 0.02
32 30 0.56
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.30
Consensus pattern (32 bp):
TGGCACCAATGAAGTTTTAAGCCTAATTTAGC
Found at i:17855879 original size:29 final size:29
Alignment explanation
Indices: 17855837--17855928 Score: 85
Period size: 29 Copynumber: 3.1 Consensus size: 29
17855827 TATTTGGCAC
* *
17855837 CAATGAAGTCTTAAGCCTAATTTAGCTGG
1 CAATAAAGTTTTAAGCCTAATTTAGCTGG
* * *
17855866 CACTAAAGTTTTAAGCCCAAATTAGCTGGTG
1 CAATAAAGTTTTAAGCCTAATTTAGCT-G-G
* * *
17855897 CCAATGAAGTTTTAAGCCTAATTAAGTTGG
1 -CAATAAAGTTTTAAGCCTAATTTAGCTGG
17855927 CA
1 CA
17855929 TCAATCACAA
Statistics
Matches: 49, Mismatches: 11, Indels: 6
0.74 0.17 0.09
Matches are distributed among these distances:
29 24 0.49
30 2 0.04
31 2 0.04
32 21 0.43
ACGTcount: A:0.33, C:0.17, G:0.20, T:0.30
Consensus pattern (29 bp):
CAATAAAGTTTTAAGCCTAATTTAGCTGG
Found at i:17855912 original size:61 final size:61
Alignment explanation
Indices: 17855809--17855928 Score: 159
Period size: 61 Copynumber: 2.0 Consensus size: 61
17855799 ATTCTCATAA
** *
17855809 AAAGATTTAAACCCAAATTATTTGGCACCAATGAAGTCTTAAGCCTAATTTAGCTGGCACT
1 AAAGATTTAAACCCAAATTAGCTGGCACCAATGAAGTCTTAAGCCTAATTAAGCTGGCACT
* * ** * *
17855870 AAAGTTTTAAGCCCAAATTAGCTGGTGCCAATGAAGTTTTAAGCCTAATTAAGTTGGCA
1 AAAGATTTAAACCCAAATTAGCTGGCACCAATGAAGTCTTAAGCCTAATTAAGCTGGCA
17855929 TCAATCACAA
Statistics
Matches: 50, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
61 50 1.00
ACGTcount: A:0.35, C:0.17, G:0.17, T:0.30
Consensus pattern (61 bp):
AAAGATTTAAACCCAAATTAGCTGGCACCAATGAAGTCTTAAGCCTAATTAAGCTGGCACT
Found at i:17855969 original size:22 final size:22
Alignment explanation
Indices: 17855944--17856004 Score: 77
Period size: 22 Copynumber: 2.8 Consensus size: 22
17855934 CACAATTTAT
*
17855944 GCCTAGATTAGTTGGCACATAA
1 GCCTAGATTAGCTGGCACATAA
*
17855966 GCCTAGTTTAGCTGGCACATAA
1 GCCTAGATTAGCTGGCACATAA
* * *
17855988 ACCAAGTTTAGCTGGCA
1 GCCTAGATTAGCTGGCA
17856005 TGTAAGCTGA
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 35 1.00
ACGTcount: A:0.30, C:0.21, G:0.23, T:0.26
Consensus pattern (22 bp):
GCCTAGATTAGCTGGCACATAA
Found at i:17856161 original size:108 final size:108
Alignment explanation
Indices: 17855972--17856190 Score: 341
Period size: 108 Copynumber: 2.0 Consensus size: 108
17855962 ATAAGCCTAG
** * *
17855972 TTTAGCTGGCACATAAACCAAGTTTAGCTGGCATGTAAGCTGAATTAGCCAATAAAGTATACACC
1 TTTAGCTGGCACATAAACCAAGTTTAGCTAACATGTAAGCCGAATTAGCCAAAAAAGTATACACC
* *
17856037 TTTTATGCCTTTTAAGTGAAATCTTTTTACATCAACAAAAATA
66 TTTTATCCCTTTTAAGTGAAATCTTTTTAAATCAACAAAAATA
* *
17856080 TTTAGTTGGCACATAAACCAAGTTTAGCTAACATGTAAGCCGAATTAGCTAAAAAAGTATAC-CC
1 TTTAGCTGGCACATAAACCAAGTTTAGCTAACATGTAAGCCGAATTAGCCAAAAAAGTATACACC
*
17856144 ATTTTATCCCTTTTAAGTGAAATCTTTTTAAATCAACAGAAATA
66 -TTTTATCCCTTTTAAGTGAAATCTTTTTAAATCAACAAAAATA
17856188 TTT
1 TTT
17856191 GGGTGTAAAA
Statistics
Matches: 101, Mismatches: 9, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
107 2 0.02
108 99 0.98
ACGTcount: A:0.37, C:0.17, G:0.13, T:0.33
Consensus pattern (108 bp):
TTTAGCTGGCACATAAACCAAGTTTAGCTAACATGTAAGCCGAATTAGCCAAAAAAGTATACACC
TTTTATCCCTTTTAAGTGAAATCTTTTTAAATCAACAAAAATA
Found at i:17856407 original size:65 final size:64
Alignment explanation
Indices: 17856296--17856948 Score: 349
Period size: 65 Copynumber: 10.0 Consensus size: 64
17856286 AGTTTTAACT
* * * **
17856296 CTAGTGTAGTTGGCACTTAATGAAGATTTGAGCCTAGAGTAGCTGGCACCCAATGAAGATTTAAG
1 CTAGTTTAGTTGGCACCTAATGAA-ATTTAAGCCTAGTTTAGCTGGCACCCAATGAA-ATTTAAG
17856361 C
64 C
* * * *
17856362 CTAGTTTAGTTAGCACCTAATGAGATTTAAGCCTAGTTTAGCTGGCGCTCAAT-AAAGTTTTAAG
1 CTAGTTTAGTTGGCACCTAATGAAATTTAAGCCTAGTTTAGCTGGCACCCAATGAAA--TTTAAG
17856426 C
64 C
* ** * * * *
17856427 CCAAATTA-TCTGGAACC-AATGAAAATTTAAG-CTCAGTTT-GACTGGAATCCAATGAAATTTT
1 CTAGTTTAGT-TGGCACCTAATG-AAATTTAAGCCT-AGTTTAG-CTGGCACCCAATGAAATTTA
*
17856488 AGG
62 AGC
** * * * * * * *
17856491 CTCAAATTA-TCTAGCACC-AATGAAAATTTAAGCCCAATTTGGTTGACATCCAATGGAAATTTA
1 CT-AGTTTAGT-TGGCACCTAATG-AAATTTAAGCCTAGTTTAGCTGGCACCCAAT-GAAATTTA
17856554 AGC
62 AGC
* * * * * *
17856557 CCAGATTATTTGGCA-CTAAT-AAAGTTTTAAGCCTAGTTTAGCTAGCACCAAATGAAAAATTAA
1 CTAGTTTAGTTGGCACCTAATGAAA--TTTAAGCCTAGTTTAGCTGGCACCCAATG-AAATTTAA
17856620 GC
63 GC
* ** * * * * *
17856622 CTAATTTAACTGGCACCCAATGAAAATTTAAGCCTAATGTAGCTGGCACTCAATGAAAATTTAAA
1 CTAGTTTAGTTGGCACCTAATG-AAATTTAAGCCTAGTTTAGCTGGCACCCAATG-AAATTTAAG
17856687 C
64 C
* * * *
17856688 CCAGCTTAGTTGGCATCC-AATGAAATTTAAGTCC-AGTTTAGCTGGCACCTAATGAAATTTAAT
1 CTAGTTTAGTTGGCA-CCTAATGAAATTTAAG-CCTAGTTTAGCTGGCACCCAATGAAATTTAAG
17856751 C
64 C
* * * * * * * * * * *
17856752 CCAGTATAGCTGGCACTTAATAAAGACTTAAGCCCAATGTAACTGGCACTCAATGAAGATTTAAG
1 CTAGTTTAGTTGGCACCTAATGAA-ATTTAAGCCTAGTTTAGCTGGCACCCAATGAA-ATTTAAG
17856817 C
64 C
* * ** * * ** *
17856818 CTAGTTTAGCTAGCATTTAATGAAATTTGAGCCCAGTTTAGCTGGCATTCAATGAAATTTTAATC
1 CTAGTTTAGTTGGCACCTAATGAAATTTAAGCCTAGTTTAGCTGGCACCCAATGAAA-TTTAAGC
* * * * ** * * *
17856883 CTAGTTTAGCTGGTATCC-AATGAAAGTTAAGCCCAACTTAGCTAGTACTCAATGAAAATTTAAG
1 CTAGTTTAGTTGGCA-CCTAATGAAATTTAAGCCTAGTTTAGCTGGCACCCAATG-AAATTTAAG
17856947 C
64 C
17856948 C
1 C
17856949 AAACTTAACT
Statistics
Matches: 457, Mismatches: 102, Indels: 57
0.74 0.17 0.09
Matches are distributed among these distances:
63 5 0.01
64 47 0.10
65 282 0.62
66 118 0.26
67 2 0.00
68 3 0.01
ACGTcount: A:0.35, C:0.18, G:0.17, T:0.30
Consensus pattern (64 bp):
CTAGTTTAGTTGGCACCTAATGAAATTTAAGCCTAGTTTAGCTGGCACCCAATGAAATTTAAGC
Found at i:17856904 original size:33 final size:31
Alignment explanation
Indices: 17856296--17856948 Score: 344
Period size: 33 Copynumber: 20.0 Consensus size: 31
17856286 AGTTTTAACT
* * * *
17856296 CTAGTGTAGTTGGCACTTAATGAAGATTTGAGC
1 CTAGTTTAGCTGGCAC-CAATGAA-ATTTAAGC
**
17856329 CTAGAGTAGCTGGCACCCAATGAAGATTTAAGC
1 CTAGTTTAGCTGGCA-CCAATGAA-ATTTAAGC
* * *
17856362 CTAGTTTAGTTAGCACCTAATGAGATTTAAGC
1 CTAGTTTAGCTGGCACC-AATGAAATTTAAGC
*
17856394 CTAGTTTAGCTGGCGCTCAAT-AAAGTTTTAAGC
1 CTAGTTTAGCTGGCAC-CAATGAAA--TTTAAGC
* ** * *
17856427 CCAAATTATCTGGAACCAATGAAAATTTAAG-
1 CTAGTTTAGCTGGCACCAATG-AAATTTAAGC
* * *
17856458 CTCAGTTT-GACTGGAATCCAATGAAATTTTAGG
1 CT-AGTTTAG-CTGGCA-CCAATGAAATTTAAGC
** * *
17856491 CTCAAATTATCTAGCACCAATGAAAATTTAAGC
1 CT-AGTTTAGCTGGCACCAATG-AAATTTAAGC
* * * * *
17856524 CCAATTTGGTTGACATCCAATGGAAATTTAAGC
1 CTAGTTTAGCTGGCA-CCAAT-GAAATTTAAGC
* * ** *
17856557 CCAGATTATTTGGCACTAAT-AAAGTTTTAAGC
1 CTAGTTTAGCTGGCACCAATGAAA--TTTAAGC
* *
17856589 CTAGTTTAGCTAGCACCAAATGAAAAATTAAGC
1 CTAGTTTAGCTGGCACC-AATG-AAATTTAAGC
* *
17856622 CTAATTTAACTGGCACCCAATGAAAATTTAAGC
1 CTAGTTTAGCTGGCA-CCAATG-AAATTTAAGC
* * *
17856655 CTAATGTAGCTGGCACTCAATGAAAATTTAAAC
1 CTAGTTTAGCTGGCAC-CAATG-AAATTTAAGC
* * *
17856688 CCAGCTTAGTTGGCATCCAATGAAATTTAAGTC
1 CTAGTTTAGCTGGCA-CCAATGAAATTTAAG-C
*
17856721 C-AGTTTAGCTGGCACCTAATGAAATTTAATC
1 CTAGTTTAGCTGGCACC-AATGAAATTTAAGC
* * * * *
17856752 CCAGTATAGCTGGCACTTAATAAAGACTTAAGC
1 CTAGTTTAGCTGGCAC-CAATGAA-ATTTAAGC
* * * *
17856785 CCAATGTAACTGGCACTCAATGAAGATTTAAGC
1 CTAGTTTAGCTGGCAC-CAATGAA-ATTTAAGC
* ** *
17856818 CTAGTTTAGCTAGCATTTAATGAAATTTGAGC
1 CTAGTTTAGCTGGCA-CCAATGAAATTTAAGC
* * *
17856850 CCAGTTTAGCTGGCATTCAATGAAATTTTAATC
1 CTAGTTTAGCTGGCA-CCAATGAAA-TTTAAGC
* *
17856883 CTAGTTTAGCTGGTATCCAATGAAAGTTAAGC
1 CTAGTTTAGCTGGCA-CCAATGAAATTTAAGC
* ** * *
17856915 CCAACTTAGCTAGTACTCAATGAAAATTTAAGC
1 CTAGTTTAGCTGGCAC-CAATG-AAATTTAAGC
17856948 C
1 C
17856949 AAACTTAACT
Statistics
Matches: 487, Mismatches: 101, Indels: 64
0.75 0.15 0.10
Matches are distributed among these distances:
30 3 0.01
31 8 0.02
32 188 0.39
33 277 0.57
34 8 0.02
35 3 0.01
ACGTcount: A:0.35, C:0.18, G:0.17, T:0.30
Consensus pattern (31 bp):
CTAGTTTAGCTGGCACCAATGAAATTTAAGC
Found at i:17856954 original size:33 final size:32
Alignment explanation
Indices: 17856900--17856962 Score: 90
Period size: 33 Copynumber: 1.9 Consensus size: 32
17856890 AGCTGGTATC
* *
17856900 CAATGAAAGTTAAGCCCAACTTAGCTAGTACT
1 CAATGAAAGTTAAGCCAAACTTAACTAGTACT
*
17856932 CAATGAAAATTTAAGCCAAACTTAACTAGTA
1 CAATG-AAAGTTAAGCCAAACTTAACTAGTA
17856963 TAAGTCTAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
32 5 0.19
33 22 0.81
ACGTcount: A:0.43, C:0.19, G:0.13, T:0.25
Consensus pattern (32 bp):
CAATGAAAGTTAAGCCAAACTTAACTAGTACT
Found at i:17857059 original size:31 final size:31
Alignment explanation
Indices: 17857024--17857083 Score: 77
Period size: 31 Copynumber: 1.9 Consensus size: 31
17857014 CAGATAATGG
**
17857024 CACTTCATTTGACTTGT-GCTTTAATCCTGGT
1 CACTTCATTCAACTTGTAG-TTTAATCCTGGT
*
17857055 CACTTTATTCAACTTGTAGTTTAATCCTG
1 CACTTCATTCAACTTGTAGTTTAATCCTG
17857084 ATCATCCTTA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
31 24 0.96
32 1 0.04
ACGTcount: A:0.20, C:0.22, G:0.13, T:0.45
Consensus pattern (31 bp):
CACTTCATTCAACTTGTAGTTTAATCCTGGT
Found at i:17857536 original size:19 final size:18
Alignment explanation
Indices: 17857513--17857598 Score: 74
Period size: 16 Copynumber: 4.9 Consensus size: 18
17857503 ATTGGCCATA
17857513 TAAAAAATAATTAAAAAT
1 TAAAAAATAATTAAAAAT
*
17857531 T-AAAAA-AATTAATAAT
1 TAAAAAATAATTAAAAAT
* *
17857547 TAATAATATAATTAATAA-
1 TAA-AAAATAATTAAAAAT
*
17857565 TAAAAAAT-ACTAAAAAT
1 TAAAAAATAATTAAAAAT
*
17857582 CAAAACAATAA-TAAAAA
1 TAAAA-AATAATTAAAAA
17857599 GCTTGCTCGA
Statistics
Matches: 56, Mismatches: 6, Indels: 12
0.76 0.08 0.16
Matches are distributed among these distances:
16 16 0.29
17 14 0.25
18 16 0.29
19 10 0.18
ACGTcount: A:0.70, C:0.03, G:0.00, T:0.27
Consensus pattern (18 bp):
TAAAAAATAATTAAAAAT
Found at i:17857559 original size:12 final size:12
Alignment explanation
Indices: 17857542--17857566 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
17857532 AAAAAAATTA
17857542 ATAATTAATAAT
1 ATAATTAATAAT
17857554 ATAATTAATAAT
1 ATAATTAATAAT
17857566 A
1 A
17857567 AAAAATACTA
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:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (12 bp):
ATAATTAATAAT
Found at i:17858723 original size:26 final size:25
Alignment explanation
Indices: 17858668--17858743 Score: 64
Period size: 27 Copynumber: 2.9 Consensus size: 25
17858658 CCCTACGATC
* *
17858668 AAAACTCTAAATGGAAACCCCAATGTT
1 AAAA-TCTAAAT-GAAACCCTAAAGTT
17858695 AAAATCTAAAATCGAAACCCTAAAG-T
1 AAAATCT-AAAT-GAAACCCTAAAGTT
* *
17858721 AAAACCTTAAGTGAAACCCTAAA
1 AAAATC-TAAATGAAACCCTAAA
17858744 CTCAAAACCC
Statistics
Matches: 42, Mismatches: 5, Indels: 6
0.79 0.09 0.11
Matches are distributed among these distances:
25 11 0.26
26 12 0.29
27 19 0.45
ACGTcount: A:0.50, C:0.21, G:0.09, T:0.20
Consensus pattern (25 bp):
AAAATCTAAATGAAACCCTAAAGTT
Found at i:17860277 original size:345 final size:345
Alignment explanation
Indices: 17859646--17860333 Score: 1304
Period size: 345 Copynumber: 2.0 Consensus size: 345
17859636 TTTGTAGACC
17859646 TAAATTATCTTTTTAATAAAATTTAAACCTCATTTTATTGTTTTATTAAAAAGATAAATTTCTAG
1 TAAATTATCTTTTTAATAAAATTTAAACCTCATTTTATTGTTTTATTAAAAAGATAAATTTCTAG
17859711 GTGGTCAATCACACCCTAAAAAAGATTGGTGGCAACTCCTCACATTTTTCACAATGTTAAATGAT
66 GTGGTCAATCACACCCTAAAAAAGATTGGTGGCAACTCCTCACATTTTTCACAATGTTAAATGAT
* *
17859776 TACGTCTAGTGATCAAATCTCTGGATCGATACTTTATGACAATCACCCTTGCTACAAACCATACG
131 TACGTCTAGTGATCAAATCTCTGGATCAATACTTTATGACAATCACCCTTGCTACAAACCACACG
17859841 ATTGATTTAGTTGGTTGAATTTGTTGGATCAAGCATGGGTTAATGGAATAAAACAACTATGGAGA
196 ATTGATTTAGTTGGTTGAATTTGTTGGATCAAGCATGGGTTAATGGAATAAAACAACTATGGAGA
* *
17859906 TAGTAGTTCCCTTTTGAAAATCACAAAAAATTAAAAACAACTAATATGAAAAATTATGGAAATAA
261 TAGTAGTTCCCTCTTGAAAATCACAAAAAATTAAAAACAACTAATATGAAAAATTATAGAAATAA
17859971 ACATGAAAATGCATGAAAGA
326 ACATGAAAATGCATGAAAGA
*
17859991 TAAATTATCTTTTTAATAAAATTTAAACCTCATTTTATTGTTTTATTAAAAAGATAAATTTTTAG
1 TAAATTATCTTTTTAATAAAATTTAAACCTCATTTTATTGTTTTATTAAAAAGATAAATTTCTAG
* * *
17860056 GTGGTCAATCACACCTTAAAAAAGATTGGTGGCAACTCCTCATATTTTTCACAATTTTAAATGAT
66 GTGGTCAATCACACCCTAAAAAAGATTGGTGGCAACTCCTCACATTTTTCACAATGTTAAATGAT
17860121 TACGTCTAGTGATCAAATCTCTGGATCAATACTTTATGACAATCACCCTTGCTACAAACCACACG
131 TACGTCTAGTGATCAAATCTCTGGATCAATACTTTATGACAATCACCCTTGCTACAAACCACACG
17860186 ATTGATTTAGTTGGTTGAATTTGTTGGATCAAGCATGGGTTAATGGAATAAAACAACTATGGAGA
196 ATTGATTTAGTTGGTTGAATTTGTTGGATCAAGCATGGGTTAATGGAATAAAACAACTATGGAGA
17860251 TAGTAGTTCCCTCTTGAAAATCACAAAAAATTAAAAACAACTAATATGAAAAATTATAGAAATAA
261 TAGTAGTTCCCTCTTGAAAATCACAAAAAATTAAAAACAACTAATATGAAAAATTATAGAAATAA
17860316 ACATGAAAATGCATGAAA
326 ACATGAAAATGCATGAAA
17860334 AAAGGGATAA
Statistics
Matches: 335, Mismatches: 8, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
345 335 1.00
ACGTcount: A:0.39, C:0.14, G:0.14, T:0.33
Consensus pattern (345 bp):
TAAATTATCTTTTTAATAAAATTTAAACCTCATTTTATTGTTTTATTAAAAAGATAAATTTCTAG
GTGGTCAATCACACCCTAAAAAAGATTGGTGGCAACTCCTCACATTTTTCACAATGTTAAATGAT
TACGTCTAGTGATCAAATCTCTGGATCAATACTTTATGACAATCACCCTTGCTACAAACCACACG
ATTGATTTAGTTGGTTGAATTTGTTGGATCAAGCATGGGTTAATGGAATAAAACAACTATGGAGA
TAGTAGTTCCCTCTTGAAAATCACAAAAAATTAAAAACAACTAATATGAAAAATTATAGAAATAA
ACATGAAAATGCATGAAAGA
Found at i:17861145 original size:144 final size:144
Alignment explanation
Indices: 17860730--17861146 Score: 389
Period size: 144 Copynumber: 2.9 Consensus size: 144
17860720 TTTTTGTGAT
* * * * * * *
17860730 TTTAATGCATCAAAAATCATAAAATAATATCAAAACATGATTTGTAGC-TTTTCACAACAAAC-G
1 TTTAATGCACCAAAAATCATGAAATAATATCAAAACAAGATCTGAAGCTTTTTCAGAA-AAACTA
* * * * * *
17860793 A-CTATGGGAAGGTCAAATTACGAAAATACCTTTAAAAGGTATTTTCATAATTTCACTCCTTTTC
65 ACCT-TCGAAAGGTCAAATTACGAAAATACCCTTAAAGGGTATTTTAATAATTTCACACC-TTTC
**
17860857 GAGGTGTGATCAAGGTG
128 GAGGTGCAATCAAGGTG
* * * *
17860874 TTTAATGCACCAAAAATCATGAAATAATATCAAAACAAGATCTGGAGCTTTTTGAGAAAAATTGA
1 TTTAATGCACCAAAAATCATGAAATAATATCAAAACAAGATCTGAAGCTTTTTCAGAAAAACTAA
* ** * * * **
17860939 CCTTGGAAAAATCAAATTACAAAAATAGCCC-TAAAGGGTATATTATTAATTTCACATATTTCGA
66 CCTTCGAAAGGTCAAATTACGAAAATA-CCCTTAAAGGGTATTTTAATAATTTCACACCTTTCGA
17861003 GGTGCAATCAAGGCT-
130 GGTGCAATCAAGG-TG
* * * * **
17861018 TTTAATGTATCAAAAATCATGAAATAGTATCAAAACATGATCTGAAATTTTTTTCA-AAAAACTA
1 TTTAATGCACCAAAAATCATGAAATAATATCAAAACAAGATCTG-AAGCTTTTTCAGAAAAACTA
* ** *
17861082 ACC-TCGAAAGGGTCAAATTATGAAAATACCCTTAAAGGGTATTTTGGTAATATCACACCTTTCG
65 ACCTTCGAAA-GGTCAAATTACGAAAATACCCTTAAAGGGTATTTTAATAATTTCACACCTTTCG
17861146 A
129 A
17861147 AGTGTAATAA
Statistics
Matches: 222, Mismatches: 43, Indels: 16
0.79 0.15 0.06
Matches are distributed among these distances:
143 8 0.04
144 153 0.69
145 57 0.26
146 4 0.02
ACGTcount: A:0.41, C:0.15, G:0.14, T:0.31
Consensus pattern (144 bp):
TTTAATGCACCAAAAATCATGAAATAATATCAAAACAAGATCTGAAGCTTTTTCAGAAAAACTAA
CCTTCGAAAGGTCAAATTACGAAAATACCCTTAAAGGGTATTTTAATAATTTCACACCTTTCGAG
GTGCAATCAAGGTG
Found at i:17865558 original size:20 final size:20
Alignment explanation
Indices: 17865533--17865573 Score: 66
Period size: 20 Copynumber: 2.0 Consensus size: 20
17865523 GTGTTTTGGT
17865533 TGTTTAA-TCATGCTTTAAAG
1 TGTTTAATTCATG-TTTAAAG
17865553 TGTTTAATTCATGTTTAAAG
1 TGTTTAATTCATGTTTAAAG
17865573 T
1 T
17865574 TGATTTGACC
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 15 0.75
21 5 0.25
ACGTcount: A:0.29, C:0.07, G:0.15, T:0.49
Consensus pattern (20 bp):
TGTTTAATTCATGTTTAAAG
Found at i:17869031 original size:18 final size:18
Alignment explanation
Indices: 17868998--17869045 Score: 62
Period size: 18 Copynumber: 2.6 Consensus size: 18
17868988 GAAAGTTATA
17868998 TTTTCAAAATGAAAAATG
1 TTTTCAAAATGAAAAATG
17869016 TTTTCTAAAATG-AAAATG
1 TTTTC-AAAATGAAAAATG
*
17869034 TATTGCAAAATG
1 T-TTTCAAAATG
17869046 GTAACTTTCT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
18 18 0.67
19 9 0.33
ACGTcount: A:0.46, C:0.06, G:0.12, T:0.35
Consensus pattern (18 bp):
TTTTCAAAATGAAAAATG
Found at i:17876556 original size:28 final size:28
Alignment explanation
Indices: 17876503--17876557 Score: 76
Period size: 27 Copynumber: 2.0 Consensus size: 28
17876493 CATCAACTAG
*
17876503 TTGGATTTGGCTATATCTCCTTGCATGA
1 TTGGATTTGGCTATATCTCCATGCATGA
*
17876531 TTGG-TTTGGCTCTATCTCCCATGCATG
1 TTGGATTTGGCTATATCT-CCATGCATG
17876558 GTCGAATTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
27 12 0.50
28 12 0.50
ACGTcount: A:0.15, C:0.22, G:0.22, T:0.42
Consensus pattern (28 bp):
TTGGATTTGGCTATATCTCCATGCATGA
Found at i:17886938 original size:14 final size:15
Alignment explanation
Indices: 17886911--17886939 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
17886901 AGGCCATTCA
17886911 CCTCATTTCATTATC
1 CCTCATTTCATTATC
17886926 CCTCATTTC-TTATC
1 CCTCATTTCATTATC
17886940 TCTTCTCTCT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 5 0.36
15 9 0.64
ACGTcount: A:0.17, C:0.34, G:0.00, T:0.48
Consensus pattern (15 bp):
CCTCATTTCATTATC
Found at i:17894500 original size:23 final size:23
Alignment explanation
Indices: 17894470--17894519 Score: 100
Period size: 23 Copynumber: 2.2 Consensus size: 23
17894460 TAGGAACCAT
17894470 AGGTGCTATTAACTCGATTAAAA
1 AGGTGCTATTAACTCGATTAAAA
17894493 AGGTGCTATTAACTCGATTAAAA
1 AGGTGCTATTAACTCGATTAAAA
17894516 AGGT
1 AGGT
17894520 TATTGAATAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.38, C:0.12, G:0.20, T:0.30
Consensus pattern (23 bp):
AGGTGCTATTAACTCGATTAAAA
Found at i:17896018 original size:32 final size:32
Alignment explanation
Indices: 17895904--17896026 Score: 106
Period size: 32 Copynumber: 3.8 Consensus size: 32
17895894 TAATAAATCT
* * * *
17895904 ATTTTTTAAAATGTTATCAAAAATTTTTACTTA
1 ATTTTTTAAAATGATAT-AGAAATTTTAATTTA
* ** *
17895937 ATATTTTAAAATGATAT-GAGGTTTTTTATTTA
1 ATTTTTTAAAATGATATAGA-AATTTTAATTTA
***
17895969 ATTTTTTAAACCAATATAGAAATTTTAATTTA
1 ATTTTTTAAAATGATATAGAAATTTTAATTTA
*
17896001 ATTTTCTAAAATGATATAG-AATTTTA
1 ATTTTTTAAAATGATATAGAAATTTTA
17896027 CAAAATTTCA
Statistics
Matches: 71, Mismatches: 17, Indels: 6
0.76 0.18 0.06
Matches are distributed among these distances:
31 8 0.11
32 46 0.65
33 17 0.24
ACGTcount: A:0.40, C:0.04, G:0.07, T:0.50
Consensus pattern (32 bp):
ATTTTTTAAAATGATATAGAAATTTTAATTTA
Found at i:17900523 original size:7 final size:7
Alignment explanation
Indices: 17900511--17900655 Score: 69
Period size: 7 Copynumber: 22.3 Consensus size: 7
17900501 TCATATGCAT
17900511 CCCTAAA
1 CCCTAAA
17900518 CCCTAAA
1 CCCTAAA
17900525 -CCTAAA
1 CCCTAAA
**
17900531 AGCTAAA
1 CCCTAAA
17900538 CCCTAAA
1 CCCTAAA
***
17900545 TTGT-AA
1 CCCTAAA
*
17900551 CCCAAAA
1 CCCTAAA
17900558 CCCTAAA
1 CCCTAAA
* *
17900565 TCCTATA
1 CCCTAAA
17900572 -CCTAAA
1 CCCTAAA
*
17900578 -CCAAAA
1 CCCTAAA
17900584 CCC--AA
1 CCCTAAA
*
17900589 CCTTAAA
1 CCCTAAA
17900596 CCCTAAA
1 CCCTAAA
17900603 CCCTAAA
1 CCCTAAA
*
17900610 ACC-AAA
1 CCCTAAA
* *
17900616 ACCTTAA
1 CCCTAAA
*
17900623 -CCTAGA
1 CCCTAAA
17900629 CCCTAAA
1 CCCTAAA
*
17900636 ---TCAA
1 CCCTAAA
17900640 CCCTAAA
1 CCCTAAA
*
17900647 CCTTAAA
1 CCCTAAA
17900654 CC
1 CC
17900656 AACCCCAAAT
Statistics
Matches: 103, Mismatches: 25, Indels: 20
0.70 0.17 0.14
Matches are distributed among these distances:
4 3 0.03
5 4 0.04
6 28 0.27
7 68 0.66
ACGTcount: A:0.45, C:0.36, G:0.02, T:0.17
Consensus pattern (7 bp):
CCCTAAA
Found at i:17900530 original size:13 final size:13
Alignment explanation
Indices: 17900512--17900624 Score: 61
Period size: 13 Copynumber: 8.6 Consensus size: 13
17900502 CATATGCATC
17900512 CCTAAACCCTAAA
1 CCTAAACCCTAAA
**
17900525 CCTAAAAGCTAAA
1 CCTAAACCCTAAA
*** *
17900538 CCCTAAATTGTAAC
1 -CCTAAACCCTAAA
*
17900552 CCAAAACCCTAAA
1 CCTAAACCCTAAA
*
17900565 TCCTATA-CCTAAA
1 -CCTAAACCCTAAA
*
17900578 CCAAAACCC--AA
1 CCTAAACCCTAAA
17900589 CCTTAAACCCTAAA
1 CC-TAAACCCTAAA
* *
17900603 CCCTAAAACCAAAA
1 -CCTAAACCCTAAA
*
17900617 CCTTAACC
1 CCTAAACC
17900625 TAGACCCTAA
Statistics
Matches: 73, Mismatches: 20, Indels: 14
0.68 0.19 0.13
Matches are distributed among these distances:
11 4 0.05
12 10 0.14
13 33 0.45
14 24 0.33
15 2 0.03
ACGTcount: A:0.46, C:0.35, G:0.02, T:0.17
Consensus pattern (13 bp):
CCTAAACCCTAAA
Found at i:17900578 original size:20 final size:19
Alignment explanation
Indices: 17900512--17900608 Score: 65
Period size: 20 Copynumber: 5.0 Consensus size: 19
17900502 CATATGCATC
17900512 CCTAAACCCTAAA-CCTAAAA
1 CCTAAACCCTAAATCCT--AA
* **
17900532 GCTAAACCCTAAATTGTAA
1 CCTAAACCCTAAATCCTAA
*
17900551 CCCAAAACCCTAAATCCTATA
1 -CCTAAACCCTAAATCCTA-A
* *
17900572 CCTAAA-CC-AAAACCCAA
1 CCTAAACCCTAAATCCTAA
*
17900589 CCTTAAACCCTAAACCCTAA
1 CC-TAAACCCTAAATCCTAA
17900609 AACCAAAACC
Statistics
Matches: 59, Mismatches: 12, Indels: 12
0.71 0.14 0.14
Matches are distributed among these distances:
17 3 0.05
18 10 0.17
19 6 0.10
20 38 0.64
21 2 0.03
ACGTcount: A:0.45, C:0.35, G:0.02, T:0.18
Consensus pattern (19 bp):
CCTAAACCCTAAATCCTAA
Found at i:17900675 original size:19 final size:18
Alignment explanation
Indices: 17900637--17900676 Score: 53
Period size: 19 Copynumber: 2.2 Consensus size: 18
17900627 GACCCTAAAT
* *
17900637 CAACCCTAAACCTTAAAC
1 CAACCCCAAACCTAAAAC
17900655 CAACCCCAAATCCTAAAAC
1 CAACCCCAAA-CCTAAAAC
17900674 CAA
1 CAA
17900677 TTTGATCCCA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 9 0.47
19 10 0.53
ACGTcount: A:0.47, C:0.40, G:0.00, T:0.12
Consensus pattern (18 bp):
CAACCCCAAACCTAAAAC
Found at i:17903639 original size:41 final size:40
Alignment explanation
Indices: 17903594--17903730 Score: 159
Period size: 40 Copynumber: 3.4 Consensus size: 40
17903584 TTAAACTTGC
* *
17903594 TCAAACAATCTAAGATTTTGCCCAAAGGTCTTGGAAATCAT
1 TCAAA-AATCTAAGATTTTGCCTAGAGGTCTTGGAAATCAT
* * * * * * *
17903635 TCAAATATATAAGACTTTGCTTGGAGGTCTTAGAAATAAT
1 TCAAAAATCTAAGATTTTGCCTAGAGGTCTTGGAAATCAT
*
17903675 TCAAAAATCTAAGATTTTTCCTAGAGGTCTTGGAAATCAT
1 TCAAAAATCTAAGATTTTGCCTAGAGGTCTTGGAAATCAT
17903715 TCCAAAAAT-TAAGATT
1 T-CAAAAATCTAAGATT
17903731 CTATCTTGAG
Statistics
Matches: 78, Mismatches: 17, Indels: 3
0.80 0.17 0.03
Matches are distributed among these distances:
40 66 0.85
41 12 0.15
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.33
Consensus pattern (40 bp):
TCAAAAATCTAAGATTTTGCCTAGAGGTCTTGGAAATCAT
Found at i:17903742 original size:40 final size:38
Alignment explanation
Indices: 17903619--17903745 Score: 130
Period size: 40 Copynumber: 3.2 Consensus size: 38
17903609 TTTTGCCCAA
* *
17903619 AGGTCTTGGAAATCATTCAAATATATAAGACTTTGCTTGG
1 AGGTCTTGGAAATCATTCAAAAATATAAGA-TTTTCTT-G
* * * *
17903659 AGGTCTTAGAAATAATTCAAAAATCTAAGATTTTTCCTAG
1 AGGTCTTGGAAATCATTCAAAAATATAAGA-TTTT-CTTG
17903699 AGGTCTTGGAAATCATTCCAAAAAT-TAAGATTCTATCTTG
1 AGGTCTTGGAAATCATT-CAAAAATATAAGATT-T-TCTTG
17903739 AGGTCTT
1 AGGTCTT
17903746 TCAAATATTG
Statistics
Matches: 73, Mismatches: 10, Indels: 8
0.80 0.11 0.09
Matches are distributed among these distances:
39 2 0.03
40 61 0.84
41 10 0.14
ACGTcount: A:0.35, C:0.13, G:0.17, T:0.35
Consensus pattern (38 bp):
AGGTCTTGGAAATCATTCAAAAATATAAGATTTTCTTG
Found at i:17904077 original size:19 final size:20
Alignment explanation
Indices: 17904038--17904079 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
17904028 AAGTTTTGTC
*
17904038 TAATTTTGACTTTATTTGAT
1 TAATTTTGACTTTAGTTGAT
17904058 TAATTTTGACTTT-GTTGAT
1 TAATTTTGACTTTAGTTGAT
17904077 TAA
1 TAA
17904080 GTTCAACAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
19 8 0.38
20 13 0.62
ACGTcount: A:0.26, C:0.05, G:0.12, T:0.57
Consensus pattern (20 bp):
TAATTTTGACTTTAGTTGAT
Found at i:17905876 original size:6 final size:7
Alignment explanation
Indices: 17905856--17905881 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
17905846 TAAATATATA
17905856 TAATTTT
1 TAATTTT
17905863 TAATTTT
1 TAATTTT
17905870 TAATTTT
1 TAATTTT
17905877 TAATT
1 TAATT
17905882 GGCTTCCTCA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (7 bp):
TAATTTT
Found at i:17908236 original size:22 final size:21
Alignment explanation
Indices: 17908205--17908254 Score: 57
Period size: 22 Copynumber: 2.4 Consensus size: 21
17908195 TACGTGAAAT
*
17908205 TAAAAGAAAAAATTACAAAAAA
1 TAAAAAAAAAAATTA-AAAAAA
* *
17908227 TAAAAAAAAAACTTAAAAAGA
1 TAAAAAAAAAAATTAAAAAAA
17908248 -AAAAAAA
1 TAAAAAAA
17908255 TATGAAAAGC
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
20 7 0.28
21 5 0.20
22 13 0.52
ACGTcount: A:0.80, C:0.04, G:0.04, T:0.12
Consensus pattern (21 bp):
TAAAAAAAAAAATTAAAAAAA
Found at i:17908310 original size:17 final size:17
Alignment explanation
Indices: 17908290--17908322 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
17908280 AATAAAATTT
17908290 TCTAA-AAATTTAAAAAA
1 TCTAAGAAA-TTAAAAAA
17908307 TCTAAGAAATTAAAAA
1 TCTAAGAAATTAAAAA
17908323 CTTATAGAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 12 0.80
18 3 0.20
ACGTcount: A:0.64, C:0.06, G:0.03, T:0.27
Consensus pattern (17 bp):
TCTAAGAAATTAAAAAA
Found at i:17908427 original size:7 final size:7
Alignment explanation
Indices: 17908406--17908451 Score: 60
Period size: 7 Copynumber: 6.6 Consensus size: 7
17908396 AGAAAATGTG
17908406 AAAATTA
1 AAAATTA
17908413 AAAA--A
1 AAAATTA
17908418 AAAATTA
1 AAAATTA
17908425 AAAATTA
1 AAAATTA
17908432 AAAATCTA
1 AAAAT-TA
17908440 AAAGATTA
1 AAA-ATTA
17908448 AAAA
1 AAAA
17908452 ATCTCAATTT
Statistics
Matches: 35, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
5 5 0.14
7 18 0.51
8 10 0.29
9 2 0.06
ACGTcount: A:0.74, C:0.02, G:0.02, T:0.22
Consensus pattern (7 bp):
AAAATTA
Found at i:17908586 original size:17 final size:17
Alignment explanation
Indices: 17908549--17908623 Score: 66
Period size: 17 Copynumber: 4.4 Consensus size: 17
17908539 AAGAATAAAA
* *
17908549 AAAAAAGTGAAAAAATA
1 AAAAAATTGAAAAAATT
*
17908566 AAAAAATTGAAAACATT
1 AAAAAATTGAAAAAATT
17908583 -AAAAATTAGTAAAAAATT
1 AAAAAATT-G-AAAAAATT
17908601 CAAAAAATATG--AAAATT
1 -AAAAAAT-TGAAAAAATT
17908618 AAAAAA
1 AAAAAA
17908624 ATCTATAAAT
Statistics
Matches: 49, Mismatches: 4, Indels: 11
0.77 0.06 0.17
Matches are distributed among these distances:
16 13 0.27
17 21 0.43
18 7 0.14
20 7 0.14
21 1 0.02
ACGTcount: A:0.71, C:0.03, G:0.07, T:0.20
Consensus pattern (17 bp):
AAAAAATTGAAAAAATT
Found at i:17908838 original size:28 final size:26
Alignment explanation
Indices: 17908793--17908847 Score: 67
Period size: 27 Copynumber: 2.0 Consensus size: 26
17908783 TTTTTCAAAA
17908793 TTTTGAATTTTATAATTTCTTCAATTT
1 TTTTGAATTTTATAATTT-TTCAATTT
*
17908820 TTTTGGAATTTTA-AGATTTTTTAATTT
1 TTTT-GAATTTTATA-ATTTTTCAATTT
17908847 T
1 T
17908848 CCATTTTTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
27 13 0.52
28 12 0.48
ACGTcount: A:0.25, C:0.04, G:0.07, T:0.64
Consensus pattern (26 bp):
TTTTGAATTTTATAATTTTTCAATTT
Found at i:17908952 original size:8 final size:8
Alignment explanation
Indices: 17908934--17909021 Score: 54
Period size: 8 Copynumber: 10.8 Consensus size: 8
17908924 TTCTTCAAAT
17908934 TTTTATATA
1 TTTT-TATA
17908943 TTTTTATA
1 TTTTTATA
17908951 TTTTTATGA
1 TTTTTAT-A
*
17908960 TTTTTTGAAA
1 -TTTTT-ATA
*
17908970 TTTTTAGA
1 TTTTTATA
*
17908978 TTTTTAGA
1 TTTTTATA
* *
17908986 -GTTTCTA
1 TTTTTATA
*
17908993 TTTTTAGA
1 TTTTTATA
*
17909001 TATTT-TA
1 TTTTTATA
*
17909008 TTTTTGTA
1 TTTTTATA
17909016 TTTTTA
1 TTTTTA
17909022 ACATTTTAAT
Statistics
Matches: 62, Mismatches: 12, Indels: 11
0.73 0.14 0.13
Matches are distributed among these distances:
7 9 0.15
8 36 0.58
9 10 0.16
10 6 0.10
11 1 0.02
ACGTcount: A:0.24, C:0.01, G:0.08, T:0.67
Consensus pattern (8 bp):
TTTTTATA
Found at i:17908955 original size:18 final size:19
Alignment explanation
Indices: 17908930--17908982 Score: 67
Period size: 18 Copynumber: 2.9 Consensus size: 19
17908920 TAATTTCTTC
17908930 AAATTTTTAT-ATATTTTT-
1 AAATTTTTATGAT-TTTTTG
*
17908948 ATATTTTTATGATTTTTTG
1 AAATTTTTATGATTTTTTG
17908967 AAATTTTTA-GATTTTT
1 AAATTTTTATGATTTTT
17908983 AGAGTTTCTA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
18 21 0.68
19 10 0.32
ACGTcount: A:0.28, C:0.00, G:0.06, T:0.66
Consensus pattern (19 bp):
AAATTTTTATGATTTTTTG
Found at i:17911396 original size:15 final size:15
Alignment explanation
Indices: 17911360--17911402 Score: 68
Period size: 15 Copynumber: 2.8 Consensus size: 15
17911350 TAATGTTATG
17911360 TTAATTAAAATATAAA
1 TTAATTAAAAT-TAAA
*
17911376 TTAATTAAAATTAAT
1 TTAATTAAAATTAAA
17911391 TTAATTAAAATT
1 TTAATTAAAATT
17911403 TGAATAATAT
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
15 15 0.58
16 11 0.42
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (15 bp):
TTAATTAAAATTAAA
Found at i:17911410 original size:15 final size:15
Alignment explanation
Indices: 17911360--17911403 Score: 54
Period size: 16 Copynumber: 2.9 Consensus size: 15
17911350 TAATGTTATG
*
17911360 TTAATTAAAATATAAA
1 TTAATTAAAAT-TTAA
17911376 TTAATTAAAA-TTAA
1 TTAATTAAAATTTAA
17911390 TTTAATTAAAATTT
1 -TTAATTAAAATTT
17911404 GAATAATATC
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
14 3 0.12
15 10 0.40
16 12 0.48
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (15 bp):
TTAATTAAAATTTAA
Found at i:17911727 original size:4 final size:4
Alignment explanation
Indices: 17911718--17911742 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
17911708 AAGCAAATCT
17911718 TTTA TTTA TTTA TTTA TTTA TTTA T
1 TTTA TTTA TTTA TTTA TTTA TTTA T
17911743 CATAACAAAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
TTTA
Found at i:17912423 original size:14 final size:15
Alignment explanation
Indices: 17912404--17912436 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
17912394 AATAAAAAAT
17912404 AAATTTTT-TTCTTA
1 AAATTTTTATTCTTA
*
17912418 AAATTTTTATTTTTA
1 AAATTTTTATTCTTA
17912433 AAAT
1 AAAT
17912437 AAAAAATAAC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 8 0.47
15 9 0.53
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.61
Consensus pattern (15 bp):
AAATTTTTATTCTTA
Found at i:17914154 original size:399 final size:397
Alignment explanation
Indices: 17913682--17914479 Score: 1375
Period size: 399 Copynumber: 2.0 Consensus size: 397
17913672 CATTTTTGTC
*
17913682 AAAACTCCAAAATTTTATATATATGTTTATCTTTTATTTTTTATCTCTCTTCTTTACTTTGAATT
1 AAAACTCCAAAATTATATATATATGTTTATCTTTTATTTTTTATCTCTCTTCTTTACTTTGAATT
* *
17913747 TTTTATAATTTTTTACAAAAACCATTTATAATTTTTAAAACTAAAAATTTACTAACAAGATTTCA
66 TTTTATAATTTTTTACAAAAACCATTTATAATTTTTAAAAATAAAAATATACTAACAAGATTTCA
* *
17913812 TATATTTTATATTTTTAAACTATTCTATATTATGATTTTCAATAGCAATTATATAAAAATTAATG
131 TATATTTAATATTTTTAAACTATTCTATATTATGATTTTCAAGAGCAATTATATAAAAATTAATG
* * * * *
17913877 AAAAATGAAGAAAGAGAAAATAAATTTGAGACAAATAAGTATAGTAAAACGAAATTATATTTCTC
196 AAAAATGAAGAAAGAGAAAATAAATTTGAGACAAATAAGAATAATAAAAAGAAATTAAATTTATC
*
17913942 ATTTTTCCTTTTTATAATATTTTTATTTCTCCTTATTTCTCTC-TTTCTTTTTATTAAATAATCC
261 ATTTTTCCTTTTTATAATA-TTTTATTTCTCCGTATTTCTCTCTTTTCTTTTTATTAAATAATCC
* *
17914006 AATATATTTTTACTTAATGTAAAAAC-AAAAAAACTAATTCACTAAATATATAATTGTAAATTGT
325 AATATATTTTTACTCAATGTAAAAACAAAAAAAACTAATT-ACTAAATATATAATTGTAAA-TGG
17914070 TTTTTTAATT
388 TTTTTTAATT
*
17914080 AAAACTCCAAAATTATATATATATGTTTATCTTTTTTCTTTTTATCTCTCTTCTTTACTTTGAAT
1 AAAACTCCAAAATTATATATATATGTTTATCTTTTAT-TTTTTATCTCTCTTCTTTACTTTGAAT
* *
17914145 TTTTTATAATTTTTTACAGAAGCCATTTATAATTTTTAAAAATAAAAATATACTAACAAGATTTC
65 TTTTTATAATTTTTTACAAAAACCATTTATAATTTTTAAAAATAAAAATATACTAACAAGATTTC
*
17914210 ATATATTTAATATTTTTAAACTATTCTATATTGTGATTTTCAAGAGCAATTATATAAAAATTAAT
130 ATATATTTAATATTTTTAAACTATTCTATATTATGATTTTCAAGAGCAATTATATAAAAATTAAT
* *
17914275 GAAAAATGAAGAAAGGGAAAATATATTTGAGACAAATAAGAATAATAAAAAGAAATTAAATTTAT
195 GAAAAATGAAGAAAGAGAAAATAAATTTGAGACAAATAAGAATAATAAAAAGAAATTAAATTTAT
17914340 CATTTTTCCTTTTTATAATATTTTATTTCTCCGTATTTCTCTCTTTTCTTTTTATTAAATAATCC
260 CATTTTTCCTTTTTATAATATTTTATTTCTCCGTATTTCTCTCTTTTCTTTTTATTAAATAATCC
17914405 AATATATTTTTACTCAATGTAAAAACAAAAAAAACTAATTACTAAATATATAATTGTAAATGGTT
325 AATATATTTTTACTCAATGTAAAAACAAAAAAAACTAATTACTAAATATATAATTGTAAATGGTT
17914470 TTTTAATT
390 TTTTAATT
17914478 AA
1 AA
17914480 TTAAAATTAA
Statistics
Matches: 378, Mismatches: 19, Indels: 6
0.94 0.05 0.01
Matches are distributed among these distances:
398 71 0.19
399 294 0.78
400 13 0.03
ACGTcount: A:0.40, C:0.10, G:0.05, T:0.45
Consensus pattern (397 bp):
AAAACTCCAAAATTATATATATATGTTTATCTTTTATTTTTTATCTCTCTTCTTTACTTTGAATT
TTTTATAATTTTTTACAAAAACCATTTATAATTTTTAAAAATAAAAATATACTAACAAGATTTCA
TATATTTAATATTTTTAAACTATTCTATATTATGATTTTCAAGAGCAATTATATAAAAATTAATG
AAAAATGAAGAAAGAGAAAATAAATTTGAGACAAATAAGAATAATAAAAAGAAATTAAATTTATC
ATTTTTCCTTTTTATAATATTTTATTTCTCCGTATTTCTCTCTTTTCTTTTTATTAAATAATCCA
ATATATTTTTACTCAATGTAAAAACAAAAAAAACTAATTACTAAATATATAATTGTAAATGGTTT
TTTAATT
Found at i:17914557 original size:16 final size:17
Alignment explanation
Indices: 17914527--17914560 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
17914517 CAAAAACTCG
17914527 TTTTCTCTTTATTCTTT
1 TTTTCTCTTTATTCTTT
*
17914544 TTTTTTCTTT-TTCTTT
1 TTTTCTCTTTATTCTTT
17914560 T
1 T
17914561 AGTTTTATAC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.03, C:0.15, G:0.00, T:0.82
Consensus pattern (17 bp):
TTTTCTCTTTATTCTTT
Found at i:17915784 original size:20 final size:21
Alignment explanation
Indices: 17915759--17915811 Score: 72
Period size: 20 Copynumber: 2.5 Consensus size: 21
17915749 TTTACAAAAT
17915759 AAATCATGCAAATATC-ATAA
1 AAATCATGCAAATATCAATAA
*
17915779 AAATCAAGCAAATATCAAATAA
1 AAATCATGCAAATATC-AATAA
*
17915801 AAATCTTGCAA
1 AAATCATGCAA
17915812 GGGTATCATG
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
20 15 0.54
22 13 0.46
ACGTcount: A:0.57, C:0.15, G:0.06, T:0.23
Consensus pattern (21 bp):
AAATCATGCAAATATCAATAA
Found at i:17915933 original size:27 final size:25
Alignment explanation
Indices: 17915884--17915935 Score: 68
Period size: 25 Copynumber: 2.0 Consensus size: 25
17915874 ATGTAAAATA
* *
17915884 TCATGCAAATATATATGATAATCAT
1 TCATGCAAAAATATATAATAATCAT
17915909 TCATGCAAAAATATTATAATAAATCAT
1 TCATGCAAAAATA-TATAAT-AATCAT
17915936 ACAAATAATT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
25 12 0.52
26 5 0.22
27 6 0.26
ACGTcount: A:0.48, C:0.12, G:0.06, T:0.35
Consensus pattern (25 bp):
TCATGCAAAAATATATAATAATCAT
Found at i:17915935 original size:23 final size:23
Alignment explanation
Indices: 17915883--17915964 Score: 76
Period size: 23 Copynumber: 3.5 Consensus size: 23
17915873 CATGTAAAAT
* *
17915883 ATCATGCAAATATATATGATAATCA
1 ATCATGCAAA-A-ATATTATAATAA
*
17915908 TTCATGCAAAAATATTATAATAA
1 ATCATGCAAAAATATTATAATAA
* * *
17915931 ATCATACAAATA-ATTATCATAAA
1 ATCATGCAAAAATATTATAAT-AA
17915954 ATCATGCAAAA
1 ATCATGCAAAA
17915965 TACATATCAT
Statistics
Matches: 47, Mismatches: 9, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
22 7 0.15
23 30 0.64
24 1 0.02
25 9 0.19
ACGTcount: A:0.52, C:0.12, G:0.05, T:0.30
Consensus pattern (23 bp):
ATCATGCAAAAATATTATAATAA
Found at i:17915952 original size:22 final size:23
Alignment explanation
Indices: 17915916--17915977 Score: 67
Period size: 23 Copynumber: 2.7 Consensus size: 23
17915906 CATTCATGCA
*
17915916 AAAAT-ATTATAATAAATCATAC
1 AAAATAATTATCATAAATCATAC
*
17915938 -AAATAATTATCATAAAATCATGC
1 AAAATAATTATCAT-AAATCATAC
17915961 AAAATACA-TATCATAAA
1 AAAATA-ATTATCATAAA
17915978 AATCATTAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 7
0.79 0.05 0.16
Matches are distributed among these distances:
21 4 0.12
22 7 0.21
23 11 0.32
24 11 0.32
25 1 0.03
ACGTcount: A:0.58, C:0.11, G:0.02, T:0.29
Consensus pattern (23 bp):
AAAATAATTATCATAAATCATAC
Found at i:17915972 original size:24 final size:24
Alignment explanation
Indices: 17915924--17915983 Score: 70
Period size: 24 Copynumber: 2.5 Consensus size: 24
17915914 CAAAAATATT
17915924 ATAATAAATCATACAAATAATTATC
1 ATAA-AAATCATACAAATAATTATC
*
17915949 AT-AAAATCATGCAAAATACA-TATC
1 ATAAAAATCATAC-AAATA-ATTATC
17915973 ATAAAAATCAT
1 ATAAAAATCAT
17915984 TAAAAAATGC
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
23 8 0.26
24 12 0.39
25 11 0.35
ACGTcount: A:0.57, C:0.13, G:0.02, T:0.28
Consensus pattern (24 bp):
ATAAAAATCATACAAATAATTATC
Found at i:17915988 original size:24 final size:23
Alignment explanation
Indices: 17915918--17915988 Score: 65
Period size: 24 Copynumber: 3.0 Consensus size: 23
17915908 TTCATGCAAA
*
17915918 AATATTATAATAAATCA-TACAAAT
1 AATATCATAA-AAATCATTA-AAAT
*
17915942 AATTATCAT-AAAATCATGCAAAAT
1 AA-TATCATAAAAATCAT-TAAAAT
17915966 ACATATCATAAAAATCATTAAAA
1 A-ATATCATAAAAATCATTAAAA
17915989 AATGCAAACA
Statistics
Matches: 39, Mismatches: 3, Indels: 10
0.75 0.06 0.19
Matches are distributed among these distances:
23 6 0.15
24 18 0.46
25 15 0.38
ACGTcount: A:0.58, C:0.11, G:0.01, T:0.30
Consensus pattern (23 bp):
AATATCATAAAAATCATTAAAAT
Found at i:17915989 original size:25 final size:24
Alignment explanation
Indices: 17915918--17915989 Score: 67
Period size: 25 Copynumber: 3.0 Consensus size: 24
17915908 TTCATGCAAA
* *
17915918 AATATTATAATAAATCA-TACAAAT
1 AATATCATAA-AAATCATTAAAAAT
**
17915942 AATTATCAT-AAAATCATGCAAAAT
1 AA-TATCATAAAAATCATTAAAAAT
17915966 ACATATCATAAAAATCATTAAAAA
1 A-ATATCATAAAAATCATTAAAAA
17915990 ATGCAAACAA
Statistics
Matches: 38, Mismatches: 6, Indels: 7
0.75 0.12 0.14
Matches are distributed among these distances:
23 6 0.16
24 14 0.37
25 18 0.47
ACGTcount: A:0.58, C:0.11, G:0.01, T:0.29
Consensus pattern (24 bp):
AATATCATAAAAATCATTAAAAAT
Found at i:17916533 original size:21 final size:22
Alignment explanation
Indices: 17916495--17916547 Score: 99
Period size: 22 Copynumber: 2.5 Consensus size: 22
17916485 TCCGAAATTA
17916495 ATAAAATATTATTTTTTTAAAT
1 ATAAAATATTATTTTTTTAAAT
17916517 ATAAAATATTATTTTTTTAAAT
1 ATAAAATATTATTTTTTTAAAT
17916539 AT-AAATATT
1 ATAAAATATT
17916548 TAAAAATATC
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
21 7 0.23
22 24 0.77
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (22 bp):
ATAAAATATTATTTTTTTAAAT
Found at i:17918312 original size:32 final size:32
Alignment explanation
Indices: 17918276--17918336 Score: 88
Period size: 32 Copynumber: 1.9 Consensus size: 32
17918266 TTAATATTTT
*
17918276 CAAATAAAATAAT-ATTTAATTTTTAATAATAC
1 CAAATAAAATAATCA-TTAATTGTTAATAATAC
*
17918308 CAAATAAAATGATCATTAATTGTTAATAA
1 CAAATAAAATAATCATTAATTGTTAATAA
17918337 AAATAATTTG
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
32 25 0.96
33 1 0.04
ACGTcount: A:0.52, C:0.07, G:0.03, T:0.38
Consensus pattern (32 bp):
CAAATAAAATAATCATTAATTGTTAATAATAC
Found at i:17920713 original size:22 final size:22
Alignment explanation
Indices: 17920666--17920707 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
17920656 ATTTATAACG
**
17920666 TATAAAATATAAATTTTTAATA
1 TATAAAATATAAATTTGAAATA
*
17920688 TATAAAATATATATTTGAAA
1 TATAAAATATAAATTTGAAA
17920708 GTTATATTTT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (22 bp):
TATAAAATATAAATTTGAAATA
Found at i:17922183 original size:19 final size:19
Alignment explanation
Indices: 17922161--17922208 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 19
17922151 ATTTTTTATG
*
17922161 TAATTTATATTAT-AAAAAT
1 TAATTTAT-TTATCAAAAAA
17922180 TAATTTATTTATCAAAAAA
1 TAATTTATTTATCAAAAAA
17922199 TATATTTATT
1 TA-ATTTATT
17922209 ACTTTAATAA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
18 4 0.15
19 15 0.58
20 7 0.27
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (19 bp):
TAATTTATTTATCAAAAAA
Found at i:17922199 original size:20 final size:17
Alignment explanation
Indices: 17922161--17922207 Score: 51
Period size: 16 Copynumber: 2.7 Consensus size: 17
17922151 ATTTTTTATG
17922161 TAATTTATATTATAAAAA
1 TAATTTAT-TTATAAAAA
*
17922179 TTAATTTATTTATCAAAA
1 -TAATTTATTTATAAAAA
*
17922197 -AATATATTTAT
1 TAATTTATTTAT
17922208 TACTTTAATA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
16 10 0.38
18 8 0.31
19 8 0.31
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (17 bp):
TAATTTATTTATAAAAA
Found at i:17922278 original size:3 final size:3
Alignment explanation
Indices: 17922270--17922295 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
17922260 TATTTAATAG
17922270 ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT AT
17922296 CAAGGTTACA
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:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:17925696 original size:25 final size:25
Alignment explanation
Indices: 17925646--17925696 Score: 59
Period size: 25 Copynumber: 2.0 Consensus size: 25
17925636 CCTAATCTTG
* *
17925646 TAAAAACTTCACCTATTTATAACCA
1 TAAAAACTTCACCTATTAAGAACCA
*
17925671 TAAAAACTT-GCCTATTAAGAATCCA
1 TAAAAACTTCACCTATTAAGAA-CCA
17925696 T
1 T
17925697 TTCTTTTTAG
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
24 9 0.41
25 13 0.59
ACGTcount: A:0.43, C:0.22, G:0.04, T:0.31
Consensus pattern (25 bp):
TAAAAACTTCACCTATTAAGAACCA
Found at i:17925772 original size:22 final size:22
Alignment explanation
Indices: 17925747--17925792 Score: 65
Period size: 22 Copynumber: 2.1 Consensus size: 22
17925737 TCAAGTAATA
* *
17925747 TCTAACAAATTTTAAACAAATC
1 TCTAACAAATCTCAAACAAATC
*
17925769 TCTAACAAATCTCAAACAGATC
1 TCTAACAAATCTCAAACAAATC
17925791 TC
1 TC
17925793 CTATGAGATT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.46, C:0.24, G:0.02, T:0.28
Consensus pattern (22 bp):
TCTAACAAATCTCAAACAAATC
Found at i:17930551 original size:20 final size:20
Alignment explanation
Indices: 17930515--17930552 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
17930505 ACACAAGCAT
*
17930515 TCTTAGCAAATTCATCACAA
1 TCTTAGCAAATTAATCACAA
17930535 TCTTAGCACAA-TAATCAC
1 TCTTAGCA-AATTAATCAC
17930553 TTATCAACAA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 14 0.88
21 2 0.12
ACGTcount: A:0.39, C:0.26, G:0.05, T:0.29
Consensus pattern (20 bp):
TCTTAGCAAATTAATCACAA
Found at i:17937593 original size:21 final size:24
Alignment explanation
Indices: 17937567--17937613 Score: 73
Period size: 24 Copynumber: 2.1 Consensus size: 24
17937557 TAAACATCAA
17937567 CAATAGC-AC-CT-TGGTTAGCAT
1 CAATAGCAACACTCTGGTTAGCAT
17937588 CAATAGCAACACTCTGGTTAGCAT
1 CAATAGCAACACTCTGGTTAGCAT
17937612 CA
1 CA
17937614 GCAATAGCAA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
21 7 0.30
22 2 0.09
23 2 0.09
24 12 0.52
ACGTcount: A:0.32, C:0.26, G:0.17, T:0.26
Consensus pattern (24 bp):
CAATAGCAACACTCTGGTTAGCAT
Found at i:17942651 original size:26 final size:26
Alignment explanation
Indices: 17942621--17942670 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
17942611 ATTGAAAGAA
17942621 AGAAA-ATTGTAAGGTTGAGAAAGGCT
1 AGAAAGATTGTAAGGTT-AGAAAGGCT
* *
17942647 AGAAAGTTTTTAAGGTTAGAAAGG
1 AGAAAGATTGTAAGGTTAGAAAGG
17942671 TTAGGTCGAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
26 12 0.57
27 9 0.43
ACGTcount: A:0.42, C:0.02, G:0.30, T:0.26
Consensus pattern (26 bp):
AGAAAGATTGTAAGGTTAGAAAGGCT
Found at i:17944720 original size:22 final size:22
Alignment explanation
Indices: 17944692--17944734 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
17944682 TTGATAATGA
*
17944692 ATACTTAATTTTGATATTTTAG
1 ATACTTAATTTTAATATTTTAG
*
17944714 ATACTTACTTTTAATATTTTA
1 ATACTTAATTTTAATATTTTA
17944735 AAATTTTTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.33, C:0.07, G:0.05, T:0.56
Consensus pattern (22 bp):
ATACTTAATTTTAATATTTTAG
Found at i:17948859 original size:23 final size:23
Alignment explanation
Indices: 17948833--17948878 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
17948823 TCATAGAAGG
17948833 TTCAAAATTCACATGAAAAGTTT
1 TTCAAAATTCACATGAAAAGTTT
* * *
17948856 TTCAAGATTCACATTAAAGGTTT
1 TTCAAAATTCACATGAAAAGTTT
17948879 GGAACTCACA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.39, C:0.13, G:0.11, T:0.37
Consensus pattern (23 bp):
TTCAAAATTCACATGAAAAGTTT
Found at i:17949180 original size:139 final size:138
Alignment explanation
Indices: 17948958--17949213 Score: 325
Period size: 139 Copynumber: 1.8 Consensus size: 138
17948948 TTGAAGGATC
* * ** * ** **
17948958 GAGATTCACACCAAAAGGTTCTTGAGGTTCACATTGAGATTCGTATCAAGTCTTTAAGATTTGCA
1 GAGATTCACACCAAAAGGTTCTCGAGATTCACATCAAGAATCACATCAAGTCTCCAAGATTTGCA
* * *
17949023 TCAAAAGTTCAAGATTCACACTGAAAGGTTTTTAATATTCACATCATAAGTCTTCGATATTCCAA
66 TCAAAAGTTCAAGATTCACACTAAAAGGTTCTTAAGATTCACAT--TAAGTCTTCGATATTCCAA
17949088 TCGAATGTTT
129 TCGAATGTTT
* *
17949098 GAGATTCACACC-AAATGTTCTCGAGATTCACATCAAGAATCACATTAAGTCTCCAAGATTTGCA
1 GAGATTCACACCAAAAGGTTCTCGAGATTCACATCAAGAATCACATCAAGTCTCCAAGATTTGCA
** * *
17949162 TCAAAAGTTCTGGTTTCACATTAAAAGGTTCTTAAGATTCACATTAAGTCTT
66 TCAAAAGTTCAAGATTCACACTAAAAGGTTCTTAAGATTCACATTAAGTCTT
17949214 TGCATTATAG
Statistics
Matches: 98, Mismatches: 18, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
137 8 0.08
139 78 0.80
140 12 0.12
ACGTcount: A:0.34, C:0.18, G:0.15, T:0.33
Consensus pattern (138 bp):
GAGATTCACACCAAAAGGTTCTCGAGATTCACATCAAGAATCACATCAAGTCTCCAAGATTTGCA
TCAAAAGTTCAAGATTCACACTAAAAGGTTCTTAAGATTCACATTAAGTCTTCGATATTCCAATC
GAATGTTT
Found at i:17949259 original size:20 final size:21
Alignment explanation
Indices: 17949231--17949269 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
17949221 TAGGTTTTCA
*
17949231 AGATTCACATCGA-AGGTTTG
1 AGATACACATCGATAGGTTTG
17949251 AGATACACATCGATAGGTT
1 AGATACACATCGATAGGTT
17949270 CTCGACATTC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.33, C:0.15, G:0.23, T:0.28
Consensus pattern (21 bp):
AGATACACATCGATAGGTTTG
Found at i:17949283 original size:23 final size:20
Alignment explanation
Indices: 17949233--17949283 Score: 57
Period size: 20 Copynumber: 2.4 Consensus size: 20
17949223 GGTTTTCAAG
*
17949233 ATTCACATCGAAGGTTTGAG
1 ATTCACATCGAAGGTTTGAC
*
17949253 ATACACATCGATAGGTTCTCGAC
1 ATTCACATCGA-AGGTT-T-GAC
17949276 ATTCACAT
1 ATTCACAT
17949284 TGTGATTTGT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
20 10 0.40
21 5 0.20
22 1 0.04
23 9 0.36
ACGTcount: A:0.31, C:0.22, G:0.18, T:0.29
Consensus pattern (20 bp):
ATTCACATCGAAGGTTTGAC
Found at i:17949559 original size:21 final size:22
Alignment explanation
Indices: 17949533--17949574 Score: 59
Period size: 23 Copynumber: 1.9 Consensus size: 22
17949523 TATTTGCATC
*
17949533 AAAGG-TTCAGGATTCACATAG
1 AAAGGTTTCAAGATTCACATAG
17949554 AAAGGTTTTCAAGATTCACAT
1 AAAGG-TTTCAAGATTCACAT
17949575 CGGGTCTTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 5 0.28
23 13 0.72
ACGTcount: A:0.38, C:0.14, G:0.19, T:0.29
Consensus pattern (22 bp):
AAAGGTTTCAAGATTCACATAG
Found at i:17949612 original size:78 final size:78
Alignment explanation
Indices: 17949461--17949641 Score: 181
Period size: 78 Copynumber: 2.3 Consensus size: 78
17949451 ACATGGAAAA
* ** * *
17949461 TTCA-GATTCACATTGAAAGGTCCTCGAGATTCGCATCGAGTCTTCACATCATAAGTCTTAGATA
1 TTCAGGATTCACATAGAAAGGTTTTCAAGATTCACATCGAGTCTTCACATCATAAGTCTTAGATA
* *
17949525 TTTGCATCAAAGG-
66 TTCGAATC-AAGGT
* * *
17949538 TTCAGGATTCACATAGAAAGGTTTTCAAGATTCACATCGGGTCTTTACATCATAGGTCTTCA-AG
1 TTCAGGATTCACATAGAAAGGTTTTCAAGATTCACATCGAGTCTTCACATCATAAGTCTT-AGA-
17949602 T-TTCGAATCAAGGT
64 TATTCGAATCAAGGT
** **
17949616 TTTGGGATTCACACCGAAAGGTTTTC
1 TTCAGGATTCACATAGAAAGGTTTTC
17949642 GAGGTTCATA
Statistics
Matches: 86, Mismatches: 14, Indels: 7
0.80 0.13 0.07
Matches are distributed among these distances:
77 8 0.09
78 76 0.88
79 2 0.02
ACGTcount: A:0.29, C:0.19, G:0.19, T:0.33
Consensus pattern (78 bp):
TTCAGGATTCACATAGAAAGGTTTTCAAGATTCACATCGAGTCTTCACATCATAAGTCTTAGATA
TTCGAATCAAGGT
Found at i:17950106 original size:36 final size:36
Alignment explanation
Indices: 17950066--17950203 Score: 125
Period size: 36 Copynumber: 3.8 Consensus size: 36
17950056 TCATGTCCTA
* *
17950066 AATGCACA-TATCAATTAAAATTAATGTGATACCTTG
1 AATGCA-AGTATCAATGAAAATTAATGTCATACCTTG
* *
17950102 AATGCAAGTATTAATGAAAATTAATGTCATATCTTG
1 AATGCAAGTATCAATGAAAATTAATGTCATACCTTG
* * * * * *
17950138 GATACTAGTATCAATGGAAATCAATGTCATATCTTG
1 AATGCAAGTATCAATGAAAATTAATGTCATACCTTG
* * * * *
17950174 GATACTAGTATCAATGGAAATCAATGTCAT
1 AATGCAAGTATCAATGAAAATTAATGTCAT
17950204 GCACCCCTAA
Statistics
Matches: 91, Mismatches: 10, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
35 1 0.01
36 90 0.99
ACGTcount: A:0.40, C:0.12, G:0.14, T:0.33
Consensus pattern (36 bp):
AATGCAAGTATCAATGAAAATTAATGTCATACCTTG
Found at i:17956810 original size:3 final size:3
Alignment explanation
Indices: 17956802--17956832 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
17956792 TGATAAAGGA
*
17956802 AAT AAT AAT AAA AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
17956833 GTAAAAGTAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (3 bp):
AAT
Found at i:17956822 original size:12 final size:12
Alignment explanation
Indices: 17956801--17956838 Score: 58
Period size: 12 Copynumber: 3.2 Consensus size: 12
17956791 ATGATAAAGG
17956801 AAATAATAATAA
1 AAATAATAATAA
17956813 AAATAATAATAA
1 AAATAATAATAA
* *
17956825 TAATAATAGTAA
1 AAATAATAATAA
17956837 AA
1 AA
17956839 GTAAAAACTG
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.71, C:0.00, G:0.03, T:0.26
Consensus pattern (12 bp):
AAATAATAATAA
Found at i:17958400 original size:5 final size:5
Alignment explanation
Indices: 17958386--17958445 Score: 52
Period size: 5 Copynumber: 11.6 Consensus size: 5
17958376 TTCAATCACT
* *
17958386 AAAT- AAATA AAATA AAATA AAACA AAA-A AATTA GAAACTA AAATCA
1 AAATA AAATA AAATA AAATA AAATA AAATA AAATA -AAA-TA AAAT-A
17958432 AAATCA AAATA AAA
1 AAAT-A AAATA AAA
17958446 AATCAAACAA
Statistics
Matches: 48, Mismatches: 3, Indels: 9
0.80 0.05 0.15
Matches are distributed among these distances:
4 7 0.15
5 23 0.48
6 16 0.33
7 2 0.04
ACGTcount: A:0.75, C:0.07, G:0.02, T:0.17
Consensus pattern (5 bp):
AAATA
Found at i:17958686 original size:25 final size:24
Alignment explanation
Indices: 17958652--17958706 Score: 74
Period size: 25 Copynumber: 2.2 Consensus size: 24
17958642 TTTCTTTAAC
* * *
17958652 CAAAATAAATCACAAATTTAAAAT
1 CAAAATAAATAAAAAAATTAAAAT
17958676 CAAAACTAAATAAAAAAATTAAAAT
1 CAAAA-TAAATAAAAAAATTAAAAT
17958701 CAAAAT
1 CAAAAT
17958707 CAACATTGAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
24 6 0.22
25 21 0.78
ACGTcount: A:0.67, C:0.11, G:0.00, T:0.22
Consensus pattern (24 bp):
CAAAATAAATAAAAAAATTAAAAT
Found at i:17958723 original size:18 final size:16
Alignment explanation
Indices: 17958669--17958740 Score: 60
Period size: 18 Copynumber: 4.4 Consensus size: 16
17958659 AATCACAAAT
*
17958669 TTAAAATCAAAACTAAA
1 TTAAAATC-AAATTAAA
17958686 -TAAAA--AAATTAAAA
1 TTAAAATCAAATT-AAA
*
17958700 TCAAAATCAACATTGAAA
1 TTAAAATCAA-ATT-AAA
17958718 TTAAAATCAAATTACAA
1 TTAAAATCAAATTA-AA
17958735 TTAAAA
1 TTAAAA
17958741 ATTTTGGGCC
Statistics
Matches: 45, Mismatches: 4, Indels: 12
0.74 0.07 0.20
Matches are distributed among these distances:
13 4 0.09
14 3 0.07
15 4 0.09
16 6 0.13
17 13 0.29
18 15 0.33
ACGTcount: A:0.64, C:0.10, G:0.01, T:0.25
Consensus pattern (16 bp):
TTAAAATCAAATTAAA
Found at i:17959376 original size:33 final size:33
Alignment explanation
Indices: 17959288--17959376 Score: 90
Period size: 33 Copynumber: 2.7 Consensus size: 33
17959278 TTCAGTTTCA
* * * *
17959288 CAAGAATTCTAGATTCGCAAGGATGGAAGATTTG
1 CAAGAACTC-AGATTCGTAAGAATGGAAAATTTG
* *
17959322 CAAGAACTCAAATT-TTAAAGAATGGAAAATTTG
1 CAAGAACTCAGATTCGT-AAGAATGGAAAATTTG
*
17959355 TAAGAACTCAGATTCGTAAGAA
1 CAAGAACTCAGATTCGTAAGAA
17959377 ATTCAATTTC
Statistics
Matches: 44, Mismatches: 9, Indels: 5
0.76 0.16 0.09
Matches are distributed among these distances:
33 35 0.80
34 9 0.20
ACGTcount: A:0.43, C:0.11, G:0.20, T:0.26
Consensus pattern (33 bp):
CAAGAACTCAGATTCGTAAGAATGGAAAATTTG
Found at i:17959754 original size:43 final size:45
Alignment explanation
Indices: 17959669--17959772 Score: 122
Period size: 43 Copynumber: 2.4 Consensus size: 45
17959659 ACATCTAGAA
*
17959669 TTCAAAGATTCTCATTCGAAAAATTTAGAGATTCACACCCAAAAG
1 TTCAAAGATTCTCATTCGAAAAACTTAGAGATTCACACCCAAAAG
* * * * * *
17959714 TT-AAAGATTTTTATTC-AAAAACTTAGGGATTCATATCCAAAAT
1 TTCAAAGATTCTCATTCGAAAAACTTAGAGATTCACACCCAAAAG
*
17959757 TTCAAAGATTCACATT
1 TTCAAAGATTCTCATT
17959773 AAAAAAAATT
Statistics
Matches: 48, Mismatches: 10, Indels: 3
0.79 0.16 0.05
Matches are distributed among these distances:
43 24 0.50
44 22 0.46
45 2 0.04
ACGTcount: A:0.41, C:0.16, G:0.10, T:0.33
Consensus pattern (45 bp):
TTCAAAGATTCTCATTCGAAAAACTTAGAGATTCACACCCAAAAG
Found at i:17959777 original size:43 final size:44
Alignment explanation
Indices: 17959669--17959778 Score: 123
Period size: 44 Copynumber: 2.5 Consensus size: 44
17959659 ACATCTAGAA
*
17959669 TTCAAAGATTCTCATTCGAAAAATTTAGAGATTCACACCCAAAAG
1 TTCAAAGATTCTCATTC-AAAAACTTAGAGATTCACACCCAAAAG
* * * * * *
17959714 TT-AAAGATTTTTATTCAAAAACTTAGGGATTCATATCCAAAAT
1 TTCAAAGATTCTCATTCAAAAACTTAGAGATTCACACCCAAAAG
* *
17959757 TTCAAAGATTCACATTAAAAAA
1 TTCAAAGATTCTCATTCAAAAA
17959779 AATTTATGAT
Statistics
Matches: 53, Mismatches: 11, Indels: 3
0.79 0.16 0.04
Matches are distributed among these distances:
43 24 0.45
44 27 0.51
45 2 0.04
ACGTcount: A:0.45, C:0.15, G:0.09, T:0.31
Consensus pattern (44 bp):
TTCAAAGATTCTCATTCAAAAACTTAGAGATTCACACCCAAAAG
Found at i:17959825 original size:24 final size:23
Alignment explanation
Indices: 17959752--17959832 Score: 74
Period size: 23 Copynumber: 3.4 Consensus size: 23
17959742 ATTCATATCC
* *
17959752 AAAATTTCAAAGATTCACATTAAA
1 AAAATTTTAAAGATTCTCATT-AA
* * *
17959776 AAAAATTT-ATGATTTCTCATTCA
1 AAAATTTTAAAGA-TTCTCATTAA
*
17959799 AAATTTTTAAAGATTCTCATTAA
1 AAAATTTTAAAGATTCTCATTAA
17959822 AAAACTTTTAA
1 AAAA-TTTTAA
17959833 GGTATCACAT
Statistics
Matches: 44, Mismatches: 10, Indels: 6
0.73 0.17 0.10
Matches are distributed among these distances:
23 22 0.50
24 22 0.50
ACGTcount: A:0.47, C:0.11, G:0.04, T:0.38
Consensus pattern (23 bp):
AAAATTTTAAAGATTCTCATTAA
Found at i:17961315 original size:25 final size:25
Alignment explanation
Indices: 17961287--17961335 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
17961277 GCCTCATCAA
17961287 TTTCTT-CTTCATTTTTTTCGTTTTC
1 TTTCTTAC-TCATTTTTTTCGTTTTC
* *
17961312 TTTCTTACTCTTTTTTTTCTTTTT
1 TTTCTTACTCATTTTTTTCGTTTT
17961336 TTTTTGCTCT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 20 0.95
26 1 0.05
ACGTcount: A:0.04, C:0.18, G:0.02, T:0.76
Consensus pattern (25 bp):
TTTCTTACTCATTTTTTTCGTTTTC
Found at i:17961345 original size:23 final size:25
Alignment explanation
Indices: 17961298--17961348 Score: 70
Period size: 23 Copynumber: 2.1 Consensus size: 25
17961288 TTCTTCTTCA
17961298 TTTTTTTCGTTTTCTTTCTTACTCT
1 TTTTTTTCGTTTTCTTTCTTACTCT
* *
17961323 TTTTTTTC-TTTT-TTTTTTGCTCT
1 TTTTTTTCGTTTTCTTTCTTACTCT
17961346 TTT
1 TTT
17961349 GATCAGTTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
23 12 0.50
24 4 0.17
25 8 0.33
ACGTcount: A:0.02, C:0.16, G:0.04, T:0.78
Consensus pattern (25 bp):
TTTTTTTCGTTTTCTTTCTTACTCT
Found at i:17965360 original size:6 final size:6
Alignment explanation
Indices: 17965338--17965393 Score: 51
Period size: 6 Copynumber: 8.7 Consensus size: 6
17965328 TAAAAAACAT
*
17965338 AAAATA AGAATAA AAAATTAA AAAATTA AAAACT- AAAATA AAAATA AAAATA
1 AAAATA AAAAT-A AAAA-T-A AAAA-TA AAAA-TA AAAATA AAAATA AAAATA
17965390 AAAA
1 AAAA
17965394 ATCAAATGAA
Statistics
Matches: 44, Mismatches: 3, Indels: 6
0.83 0.06 0.11
Matches are distributed among these distances:
5 1 0.02
6 24 0.55
7 10 0.23
8 9 0.20
ACGTcount: A:0.79, C:0.02, G:0.02, T:0.18
Consensus pattern (6 bp):
AAAATA
Found at i:17965376 original size:34 final size:33
Alignment explanation
Indices: 17965330--17965395 Score: 98
Period size: 34 Copynumber: 2.0 Consensus size: 33
17965320 TCACTAAGTA
*
17965330 AAAAACATAAAATAAGAATAAAAAATTAAAAAATT
1 AAAAACATAAAATAAAAAT-AAAAA-TAAAAAATT
17965365 AAAAAC-TAAAATAAAAATAAAAATAAAAAAT
1 AAAAACATAAAATAAAAATAAAAATAAAAAAT
17965396 CAAATGAAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
32 8 0.27
33 5 0.17
34 11 0.37
35 6 0.20
ACGTcount: A:0.77, C:0.03, G:0.02, T:0.18
Consensus pattern (33 bp):
AAAAACATAAAATAAAAATAAAAATAAAAAATT
Found at i:17965381 original size:13 final size:12
Alignment explanation
Indices: 17965338--17965411 Score: 53
Period size: 13 Copynumber: 5.8 Consensus size: 12
17965328 TAAAAAACAT
17965338 AAAATAAGAATAA
1 AAAATAA-AATAA
17965351 AAAATTAAAAAATTAA
1 AAAA-T--AAAA-TAA
*
17965367 AAACTAAAAT-A
1 AAAATAAAATAA
17965378 AAAATAAAAATAA
1 AAAAT-AAAATAA
*
17965391 AAAATCAAATGAA
1 AAAATAAAAT-AA
17965404 AAAA-AAAA
1 AAAATAAAA
17965412 GGAAAAACCT
Statistics
Matches: 50, Mismatches: 4, Indels: 15
0.72 0.06 0.22
Matches are distributed among these distances:
11 5 0.10
12 13 0.26
13 20 0.40
14 1 0.02
15 3 0.06
16 8 0.16
ACGTcount: A:0.78, C:0.03, G:0.03, T:0.16
Consensus pattern (12 bp):
AAAATAAAATAA
Found at i:17965417 original size:24 final size:24
Alignment explanation
Indices: 17965373--17965418 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
17965363 TTAAAAACTA
*
17965373 AAATAAAAATAAAAATAAAAAATC
1 AAATAAAAATAAAAAGAAAAAATC
*
17965397 AAATGAAAAA-AAAAAGGAAAAA
1 AAAT-AAAAATAAAAAGAAAAAA
17965419 CCTGCGATTA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
24 14 0.74
25 5 0.26
ACGTcount: A:0.80, C:0.02, G:0.07, T:0.11
Consensus pattern (24 bp):
AAATAAAAATAAAAAGAAAAAATC
Found at i:17966044 original size:21 final size:21
Alignment explanation
Indices: 17965969--17966045 Score: 57
Period size: 21 Copynumber: 3.5 Consensus size: 21
17965959 TATTGCCTGC
17965969 TCATTTATAAGGATTGAATCCCTT
1 TCATTTATAA--ATT-AATCCCTT
* ** *
17965993 TCAATTTAGAAAATTAATTTC-A
1 TC-ATTTA-TAAATTAATCCCTT
*
17966015 TCGTTTATAAATTAATCCCTT
1 TCATTTATAAATTAATCCCTT
17966036 TCATTTATAA
1 TCATTTATAA
17966046 TTCAAATTCT
Statistics
Matches: 40, Mismatches: 10, Indels: 9
0.68 0.17 0.15
Matches are distributed among these distances:
20 9 0.22
21 13 0.32
22 2 0.05
23 4 0.10
24 5 0.12
25 5 0.12
26 2 0.05
ACGTcount: A:0.35, C:0.14, G:0.06, T:0.44
Consensus pattern (21 bp):
TCATTTATAAATTAATCCCTT
Found at i:17971712 original size:15 final size:15
Alignment explanation
Indices: 17971689--17971720 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
17971679 TAAATCAAAT
*
17971689 AATATAAAAATAAAA
1 AATAAAAAAATAAAA
17971704 AATAAAAAAATAAAA
1 AATAAAAAAATAAAA
17971719 AA
1 AA
17971721 ACATCAAAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (15 bp):
AATAAAAAAATAAAA
Found at i:17971719 original size:9 final size:8
Alignment explanation
Indices: 17971689--17971721 Score: 50
Period size: 8 Copynumber: 4.2 Consensus size: 8
17971679 TAAATCAAAT
*
17971689 AATATAAA
1 AATAAAAA
17971697 AAT-AAAA
1 AATAAAAA
17971704 AATAAAAA
1 AATAAAAA
17971712 AATAAAAA
1 AATAAAAA
17971720 AA
1 AA
17971722 CATCAAAATA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
7 6 0.26
8 17 0.74
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (8 bp):
AATAAAAA
Found at i:17971729 original size:24 final size:25
Alignment explanation
Indices: 17971702--17971749 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 25
17971692 ATAAAAATAA
17971702 AAAATA-AAAAAATAAAAAAACATC
1 AAAATATAAAAAATAAAAAAACATC
* * *
17971726 AAAATATCAAAATTAAAAACACAT
1 AAAATATAAAAAATAAAAAAACAT
17971750 ATAATAGTAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
24 6 0.30
25 14 0.70
ACGTcount: A:0.73, C:0.10, G:0.00, T:0.17
Consensus pattern (25 bp):
AAAATATAAAAAATAAAAAAACATC
Found at i:17971765 original size:12 final size:12
Alignment explanation
Indices: 17971748--17971784 Score: 56
Period size: 12 Copynumber: 3.1 Consensus size: 12
17971738 TTAAAAACAC
17971748 ATATAATAGTAA
1 ATATAATAGTAA
*
17971760 ATATAATAGGAA
1 ATATAATAGTAA
*
17971772 ATATAATAATAA
1 ATATAATAGTAA
17971784 A
1 A
17971785 ATAGTGATAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.62, C:0.00, G:0.08, T:0.30
Consensus pattern (12 bp):
ATATAATAGTAA
Found at i:17973405 original size:12 final size:12
Alignment explanation
Indices: 17973388--17973461 Score: 57
Period size: 12 Copynumber: 6.2 Consensus size: 12
17973378 TTGCTTATGG
17973388 TTTAGGGTTTCA
1 TTTAGGGTTTCA
17973400 TTTAGGG--T--
1 TTTAGGGTTTCA
* *
17973408 TTTAAGATTTCA
1 TTTAGGGTTTCA
*
17973420 TTTAGGGTTTTAA
1 TTTAGGG-TTTCA
17973433 TTTTAAGGGTTTCA
1 -TTT-AGGGTTTCA
*
17973447 TTTAGGGTTTAA
1 TTTAGGGTTTCA
17973459 TTT
1 TTT
17973462 TTTAAAGTTT
Statistics
Matches: 48, Mismatches: 7, Indels: 14
0.70 0.10 0.20
Matches are distributed among these distances:
8 5 0.10
10 2 0.04
12 23 0.48
13 7 0.15
14 7 0.15
15 4 0.08
ACGTcount: A:0.22, C:0.04, G:0.22, T:0.53
Consensus pattern (12 bp):
TTTAGGGTTTCA
Found at i:17973418 original size:20 final size:20
Alignment explanation
Indices: 17973395--17973432 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
17973385 TGGTTTAGGG
17973395 TTTCATTTAGGGTTTTAAGA
1 TTTCATTTAGGGTTTTAAGA
17973415 TTTCATTTAGGGTTTTAA
1 TTTCATTTAGGGTTTTAA
17973433 TTTTAAGGGT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.24, C:0.05, G:0.18, T:0.53
Consensus pattern (20 bp):
TTTCATTTAGGGTTTTAAGA
Found at i:17973448 original size:27 final size:26
Alignment explanation
Indices: 17973407--17973498 Score: 114
Period size: 27 Copynumber: 3.5 Consensus size: 26
17973397 TCATTTAGGG
*
17973407 TTTTAAGATTTCATTTAGGGTTTTAA
1 TTTTAAGGTTTCATTTAGGGTTTTAA
17973433 TTTTAAGGGTTTCATTTAGGG-TTTAA
1 TTTTAA-GGTTTCATTTAGGGTTTTAA
* *
17973459 TTTTTTAAAGTTTCATTTAGAGTTTTAA
1 --TTTTAAGGTTTCATTTAGGGTTTTAA
*
17973487 TTTTAAAGTTTC
1 TTTTAAGGTTTC
17973499 GAGTTTCATT
Statistics
Matches: 59, Mismatches: 3, Indels: 8
0.84 0.04 0.11
Matches are distributed among these distances:
26 23 0.39
27 25 0.42
28 11 0.19
ACGTcount: A:0.26, C:0.04, G:0.15, T:0.54
Consensus pattern (26 bp):
TTTTAAGGTTTCATTTAGGGTTTTAA
Found at i:17973497 original size:26 final size:25
Alignment explanation
Indices: 17973407--17973498 Score: 105
Period size: 26 Copynumber: 3.5 Consensus size: 25
17973397 TCATTTAGGG
17973407 TTTT-AAGATTTCATTTAGGGTTTTAA
1 TTTTAAAG-TTTCATTTA-GGTTTTAA
* *
17973433 TTTTAAGGGTTTCATTTAGGGTTTAA
1 TTTTAA-AGTTTCATTTAGGTTTTAA
17973459 TTTTTTAAAGTTTCATTTAGAGTTTTAA
1 --TTTTAAAGTTTCATTTAG-GTTTTAA
17973487 TTTTAAAGTTTC
1 TTTTAAAGTTTC
17973499 GAGTTTCATT
Statistics
Matches: 57, Mismatches: 4, Indels: 10
0.80 0.06 0.14
Matches are distributed among these distances:
26 23 0.40
27 21 0.37
28 13 0.23
ACGTcount: A:0.26, C:0.04, G:0.15, T:0.54
Consensus pattern (25 bp):
TTTTAAAGTTTCATTTAGGTTTTAA
Found at i:17973973 original size:20 final size:20
Alignment explanation
Indices: 17973944--17973983 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
17973934 CATGGAATTT
*
17973944 AAATTGTAATTAAACTTAGA
1 AAATTATAATTAAACTTAGA
17973964 AAATTATAATTAAACTTAGA
1 AAATTATAATTAAACTTAGA
17973984 CAACATGAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.53, C:0.05, G:0.07, T:0.35
Consensus pattern (20 bp):
AAATTATAATTAAACTTAGA
Found at i:17974043 original size:65 final size:65
Alignment explanation
Indices: 17973970--17974094 Score: 178
Period size: 65 Copynumber: 1.9 Consensus size: 65
17973960 TAGAAAATTA
* * * *
17973970 TAATTAAACTTAGACAACATGAAAGAAATCTGTATGGAATTTGAAAGCATTTGTTTTCTTCTTGG
1 TAATTAAACTCAGACAACATGAAAGAAATCTGCATGAAATTTAAAAGCATTTGTTTTCTTCTTGG
* * * *
17974035 TAATTAAACTCATACAACATGAAAGAAATTTGCATGAAATTTAAAAGTATTTTTTTTCTT
1 TAATTAAACTCAGACAACATGAAAGAAATCTGCATGAAATTTAAAAGCATTTGTTTTCTT
17974095 GGTATGGTGA
Statistics
Matches: 52, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
65 52 1.00
ACGTcount: A:0.38, C:0.10, G:0.13, T:0.38
Consensus pattern (65 bp):
TAATTAAACTCAGACAACATGAAAGAAATCTGCATGAAATTTAAAAGCATTTGTTTTCTTCTTGG
Found at i:17976985 original size:19 final size:20
Alignment explanation
Indices: 17976940--17976989 Score: 52
Period size: 19 Copynumber: 2.6 Consensus size: 20
17976930 TTTAATAATG
17976940 TTTGTTTTATTTTTTAATTC
1 TTTGTTTTATTTTTTAATTC
* *
17976960 -TTGGTTT-TTTTTTATATTT
1 TTTGTTTTATTTTTTA-ATTC
17976979 TTTG-TTTATTT
1 TTTGTTTTATTT
17976990 AGTTTTTTAT
Statistics
Matches: 25, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
18 7 0.28
19 12 0.48
20 6 0.24
ACGTcount: A:0.12, C:0.02, G:0.08, T:0.78
Consensus pattern (20 bp):
TTTGTTTTATTTTTTAATTC
Found at i:17982281 original size:153 final size:153
Alignment explanation
Indices: 17982074--17982381 Score: 510
Period size: 153 Copynumber: 2.0 Consensus size: 153
17982064 TCTTACATAA
*
17982074 AAAATGCCATTACTGTTAAACACACTTCAACCATAAGTTATTTATGCATTTCAAGCATGGCAATA
1 AAAATGCCATTACTGTTAAACACACTTCAACCATAAGTTATTTATGCATATCAAGCATGGCAATA
* *
17982139 AAGATTGGACACATGTAATATCATGTAATAGGAGCAATCTAAACTATTAAAATAGAACAATAATT
66 AAGATTGGACACATGTAATAACATGTAATAGGAACAATCTAAACTATTAAAATAGAACAATAATT
17982204 GTAAATTTGCACTTTTGCCTTTT
131 GTAAATTTGCACTTTTGCCTTTT
*
17982227 AAAATGCTATTACTGTTAAACACACTTCAACCAT-AGCTTATTTATGCATATCAAGCATGGCAAT
1 AAAATGCCATTACTGTTAAACACACTTCAACCATAAG-TTATTTATGCATATCAAGCATGGCAAT
* * * *
17982291 AAAGATTGGACATATGTAATAACATGTAATATGAACAATCTCAACTGTTAAAATAGAACAATAAT
65 AAAGATTGGACACATGTAATAACATGTAATAGGAACAATCTAAACTATTAAAATAGAACAATAAT
* *
17982356 TGTAAATTTGCATTTTTTCCTTTT
130 TGTAAATTTGCACTTTTGCCTTTT
17982380 AA
1 AA
17982382 CATTACAAAA
Statistics
Matches: 144, Mismatches: 10, Indels: 2
0.92 0.06 0.01
Matches are distributed among these distances:
152 2 0.01
153 142 0.99
ACGTcount: A:0.40, C:0.15, G:0.12, T:0.33
Consensus pattern (153 bp):
AAAATGCCATTACTGTTAAACACACTTCAACCATAAGTTATTTATGCATATCAAGCATGGCAATA
AAGATTGGACACATGTAATAACATGTAATAGGAACAATCTAAACTATTAAAATAGAACAATAATT
GTAAATTTGCACTTTTGCCTTTT
Found at i:17982931 original size:162 final size:162
Alignment explanation
Indices: 17982684--17983953 Score: 1052
Period size: 162 Copynumber: 7.9 Consensus size: 162
17982674 CAAAATTATA
* * * * * *
17982684 TTTTT-ACCCTTTAACAGCA-AAACATAGTCCTAAAAAGACATAAACGGTAACATTTTCACACAT
1 TTTTTGACCTTTTAACAGCATAAA-AAAGTGCTAAACAGACATAAACAGTAACTTTTTCACACAT
*
17982747 ATCAA-CAATGGAAACCAAGTTCAATTATTCTGACAAGTTTAATATCATGTATTAAAGCTATCTA
65 ATCAATC-ATGGAAACCAAGTTCAATCATTCTGACAAGTTTAATATCATGTATTAAAGCTATCTA
17982811 AACTGTTAAAATAGAATAATAAACATAAATTTGC
129 AACTGTTAAAATAGAATAATAAACATAAATTTGC
** * *
17982845 TTTTTGACCTTTTAACATTATAAAAAAGTGCTAAACAGACATATACAGTAACTTTTTCACACCTA
1 TTTTTGACCTTTTAACAGCATAAAAAAGTGCTAAACAGACATAAACAGTAACTTTTTCACACATA
* * * *
17982910 TCAATCATGAAAACTAAGTTCAATCATTC-GAAAAGGTTTAATATCATGTATTTAAGCTATCTAA
66 TCAATCATGGAAACCAAGTTCAATCATTCTGACAA-GTTTAATATCATGTATTAAAGCTATCTAA
** * *
17982974 ACTGTTAAAACGGAATAATAAACAAAAATTTAC
130 ACTGTTAAAATAGAATAATAAACATAAATTTGC
* * * * * * *
17983007 ATTTTGGCCTTTTAACAGCATAAAAAAATACTAAACAGACATAAATAGTAATTTTTTCACACATT
1 TTTTTGACCTTTTAACAGCATAAAAAAGTGCTAAACAGACATAAACAGTAACTTTTTCACACATA
* * ** * * *
17983072 TCAATCGTGGAAACCAAGTTCAACCATTCAAAAAAGTTTAATATCATGTATTTAAGATATCTAAA
66 TCAATCATGGAAACCAAGTTCAATCATTCTGACAAGTTTAATATCATGTATTAAAGCTATCTAAA
* * **
17983137 TTGTTAAAACATA-AAT-AT-AACTATAAGTTTATA
131 CTGTT-AAA-ATAGAATAATAAAC-ATAAATTT-GC
* ** * * * * *
17983170 TTTTTG-CCCTTTAATGGCATAACAAAGTCCTAAAAAGACATACAA-GGTAACATTTTCACACAT
1 TTTTTGACCTTTTAACAGCATAAAAAAGTGCTAAACAGACATA-AACAGTAACTTTTTCACACAT
** * **
17983233 ATCAGCCATGGAAACCAAGTTTAATCATT-TGGACAAGTTTAATATCATGTATTGAAA-CTATAA
65 ATCAATCATGGAAACCAAGTTCAATCATTCT-GACAAGTTTAATATCATGTATT-AAAGCTATCT
* * * *
17983296 AAAATGTTAAAATAGAAGAGT-AACACAAATTTG-
128 AAACTGTTAAAATAGAATAATAAACATAAATTTGC
* * ** *
17983329 TATTTTGGCCTTTTAACAGTGC-T-AAAAAGTGTTAAACAGACATAAATGGTAACTTTTTTACAC
1 T-TTTTGACCTTTTAACA--GCATAAAAAAGTGCTAAACAGACATAAACAGTAACTTTTTCACAC
* * * * * * *
17983392 ATATCAATCATGAAAACCAAGTTCAATCATTC-AAAAATATTTAATATCATATTTTAAAACTATC
63 ATATCAATCATGGAAACCAAGTTCAATCATTCTGACAA-GTTTAATATCATGTATTAAAGCTATC
* ** *
17983456 TAAACTGTTAGAATAGAATAATAAATGTAAATTTTC
127 TAAACTGTTAAAATAGAATAATAAACATAAATTTGC
* * * * *
17983492 ATTTT-AGCCCTTTAACAGCACAAAAAA-T-CTTAAATAGACATAAAC-GATAACTTTTTTTACA
1 TTTTTGA-CCTTTTAACAGCATAAAAAAGTGC-TAAACAGACATAAACAG-TAAC-TTTTTCACA
* ** * ** * * *
17983553 CATATCAACCATACAAACTAAGTTCAATCATTCAAATAAGTTTAATATCATTTATTGAAGCTATC
62 CATATCAATCATGGAAACCAAGTTCAATCATTCTGACAAGTTTAATATCATGTATTAAAGCTATC
* * *
17983618 TAAACTGTTAAAATGGAATAATAAA-AGCAATTTTGC
127 TAAACTGTTAAAATAGAATAATAAACA-TAAATTTGC
* * * * * *
17983654 ATTTTGGCCTTTTAATAGCA-CAAAAAGTGCTAAACAAACATAAACAATAACTTTTTTCACA-A-
1 TTTTTGACCTTTTAACAGCATAAAAAAGTGCTAAACAGACATAAACAGTAAC-TTTTTCACACAT
* * * * *
17983716 ATCAATCATGGAAACCAAGTTCAATCATTCGGGCAAATTTAATATCATGTATTTAAGTTATCTAA
65 ATCAATCATGGAAACCAAGTTCAATCATTCTGACAAGTTTAATATCATGTATTAAAGCTATCTAA
* ***
17983781 ACTGTTAAAACATA-AAT-ATAACTGCA-AAATTAAA
130 ACTGTT-AAA-ATAGAATAATAA--ACATAAATTTGC
* * * * * * * **
17983815 TTTTT-ACCCTATAACGGCACAAACAAAGTCCTAAAAAGATATAAATGGTAACTTTTTCACACAT
1 TTTTTGACCTTTTAACAGCATAAA-AAAGTGCTAAACAGACATAAACAGTAACTTTTTCACACAT
* * *
17983879 ATCAA-CAATGGAAACCAAGTTCAATCATT-TAGGCAAGTTTAATATAATGTATTAAAGCTATCC
65 ATCAATC-ATGGAAACCAAGTTCAATCATTCT-GACAAGTTTAATATCATGTATTAAAGCTATCT
*
17983942 AAACTATTAAAA
128 AAACTGTTAAAA
17983954 CAAAAAAATA
Statistics
Matches: 891, Mismatches: 171, Indels: 94
0.77 0.15 0.08
Matches are distributed among these distances:
159 1 0.00
160 91 0.10
161 173 0.19
162 533 0.60
163 92 0.10
164 1 0.00
ACGTcount: A:0.43, C:0.15, G:0.10, T:0.32
Consensus pattern (162 bp):
TTTTTGACCTTTTAACAGCATAAAAAAGTGCTAAACAGACATAAACAGTAACTTTTTCACACATA
TCAATCATGGAAACCAAGTTCAATCATTCTGACAAGTTTAATATCATGTATTAAAGCTATCTAAA
CTGTTAAAATAGAATAATAAACATAAATTTGC
Found at i:17984001 original size:323 final size:321
Alignment explanation
Indices: 17982442--17984030 Score: 1361
Period size: 323 Copynumber: 4.9 Consensus size: 321
17982432 CAAATTGAAA
* * * * * *
17982442 AAACCAAGTTCAATCATTTGGACAAGTTTAATATCATGTATTAAAGTTACCAAAACTGTTAAAAT
1 AAACCAAGTTCAATCA-TTCGACAAATTTAATATCATGTATTTAAGCTATCTAAACTGTTAAAA-
** * * *
17982507 ATAAATATAACTATAAAATTACATTTTTA-CCTTTAGTGGTACAATAAAGTCTTAAAAAGACATA
64 ATAAATATAACTATAAAATTACATTTTTACCCTTTAACGGCACAAAAAAGTCCTAAAAAGACATA
* * * * *
17982571 AACGATATCTTTTTCACACATATCAATCATGGAAACCAAGTTCAATAATTTAAATAAG--T--T-
129 AACGGTAACTTTTTCACACATATCAA-CATGGAAACCAAGTTCAATCATTTAGACAAGTTTAATA
* * * * * * * ** *
17982631 T-ATGTGTTGAAGCTAT-CTAA-TAGTAAAAACATAAAAATAACTACAAAATTATATTTTTACCC
193 TCATGTATTAAAGCTATCCAAACT-GTTAAAACAGAAAAATAAC-ACAAATTTACATTTTGGCCT
* *
17982693 TTTAA-CAGCA-AAACATAGTCCTAAA-AAGACATAAACGGTAAC-ATTTTCACACATATCAA-C
256 TTTAATCAGCACAAA-A-AGTGCTAAACAA-ACATAAACGGTAACTTTTTTCACACATATCAATC
17982753 AATGG
318 -ATGG
* * *
17982758 AAACCAAGTTCAATTATTCTGACAAGTTTAATATCATGTATTAAAGCTATCTAAACTGTT-AAAA
1 AAACCAAGTTCAATCATTC-GACAAATTTAATATCATGTATTTAAGCTATCTAAACTGTTAAAAA
* * * *** * * *
17982822 TAGAATAATAAAC-ATAAATTTGC-TTTTTGACCTTTTAACATTATAAAAAAGTGCTAAACAGAC
65 TA-AAT-AT-AACTATAAAATTACATTTTT-ACCCTTTAACGGCACAAAAAAGTCCTAAAAAGAC
* * * * * * *
17982885 ATATACAGTAACTTTTTCACACCTATCAATCATGAAAACTAAGTTCAATCA-TTCGAAAAGGTTT
126 ATAAACGGTAACTTTTTCACACATATCAA-CATGGAAACCAAGTTCAATCATTTAGACAA-GTTT
* * * * *
17982949 AATATCATGTATTTAAGCTATCTAAACTGTTAAAACGGAATAATAAACAAAAATTTACATTTTGG
189 AATATCATGTATTAAAGCTATCCAAACTGTTAAAACAGAAAAAT-AACACAAATTTACATTTTGG
* * * * ** *
17983014 CCTTTTAA-CAGCATAAAAAAATACTAAACAGACATAAATAGTAA-TTTTTTCACACATTTCAAT
253 CCTTTTAATCAGCA-CAAAAAGTGCTAAACAAACATAAACGGTAACTTTTTTCACACATATCAAT
*
17983077 CGTGG
317 CATGG
* * * * *
17983082 AAACCAAGTTCAACCATTCAAAAAAGTTTAATATCATGTATTTAAGATATCTAAATTGTTAAAAC
1 AAACCAAGTTCAATCATTCGACAAA-TTTAATATCATGTATTTAAGCTATCTAAACTGTTAAAA-
** * * * * *
17983147 ATAAATATAACTATAAGTTTATATTTTTGCCCTTTAATGGCATAACAAAGTCCTAAAAAGACATA
64 ATAAATATAACTATAAAATTACATTTTTACCCTTTAACGGCACAAAAAAGTCCTAAAAAGACATA
* * * *
17983212 CAA-GGTAACATTTTCACACATATCAGCCATGGAAACCAAGTTTAATCATTTGGACAAGTTTAAT
129 -AACGGTAACTTTTTCACACATATCA-ACATGGAAACCAAGTTCAATCATTTAGACAAGTTTAAT
** * * * * **
17983276 ATCATGTATTGAAA-CTATAAAAAATGTTAAAATAGAAGAGTAACACAAATTTGTATTTTGGCCT
192 ATCATGTATT-AAAGCTATCCAAACTGTTAAAACAGAAAAATAACACAAATTTACATTTTGGCCT
** * * *
17983340 TTTAA-CAGTGCTAAAAAGTGTTAAACAGACATAAATGGTAACTTTTTT-ACACATATCAATCAT
256 TTTAATCAGCAC-AAAAAGTGCTAAACAAACATAAACGGTAACTTTTTTCACACATATCAATCAT
*
17983403 GA
320 GG
* * * * *
17983405 AAACCAAGTTCAATCATTCAAAAATATTTAATATCATAT-TTTAAAACTATCTAAACTGTT-AGA
1 AAACCAAGTTCAATCATTCGACAA-ATTTAATATCATGTATTT-AAGCTATCTAAACTGTTAAAA
* * * * * * *
17983468 ATAGAATAATAAATGTAAATTTTCA-TTTTAGCCCTTTAACAGCACAAAAAA-TCTTAAATAGAC
64 ATA-AAT-ATAACTATAAAATTACATTTTTA-CCCTTTAACGGCACAAAAAAGTCCTAAAAAGAC
* * ** * * * *
17983531 ATAAACGATAACTTTTTTTACACATATCAACCATACAAACTAAGTTCAATCATTCAAATAAGTTT
126 ATAAACGGTAAC-TTTTTCACACATATCAA-CATGGAAACCAAGTTCAATCATTTAGACAAGTTT
* * * ** * * * *
17983596 AATATCATTTATTGAAGCTATCTAAACTGTTAAAATGGAATAATAAAAGCAATTTTGCATTTTGG
189 AATATCATGTATTAAAGCTATCCAAACTGTTAAAACAGAAAAATAACA-CAAATTTACATTTTGG
**
17983661 CCTTTTAAT-AGCACAAAAAGTGCTAAACAAACATAAACAATAACTTTTTTCACA-A-ATCAATC
253 CCTTTTAATCAGCACAAAAAGTGCTAAACAAACATAAACGGTAACTTTTTTCACACATATCAATC
17983723 ATGG
318 ATGG
* *
17983727 AAACCAAGTTCAATCATTCGGGCAAATTTAATATCATGTATTTAAGTTATCTAAACTGTTAAAAC
1 AAACCAAGTTCAATCATTC-GACAAATTTAATATCATGTATTTAAGCTATCTAAACTGTTAAAA-
** * * *
17983792 ATAAATATAACTGCAAAATTAAATTTTTACCCTATAACGGCACAAACAAAGTCCTAAAAAGATAT
64 ATAAATATAACTATAAAATTACATTTTTACCCTTTAACGGCACAAA-AAAGTCCTAAAAAGACAT
* *
17983857 AAATGGTAACTTTTTCACACATATCAACAATGGAAACCAAGTTCAATCATTTAGGCAAGTTTAAT
128 AAACGGTAACTTTTTCACACATATCAAC-ATGGAAACCAAGTTCAATCATTTAGACAAGTTTAAT
* * * * * * *
17983922 ATAATGTATTAAAGCTATCCAAACTATTAAAACAAAAAAATAACTGCATATTTACATTTTTGCCA
192 ATCATGTATTAAAGCTATCCAAACTGTTAAAACAGAAAAATAAC-ACAAATTTACATTTTGGCCT
* * *
17983987 TTTAATGA-CACAAAAAGTGCTAAACAAATATAAACGATAACTTT
256 TTTAATCAGCACAAAAAGTGCTAAACAAACATAAACGGTAACTTT
17984031 CTTATTTGAT
Statistics
Matches: 1024, Mismatches: 195, Indels: 101
0.78 0.15 0.08
Matches are distributed among these distances:
314 3 0.00
315 13 0.01
316 68 0.07
317 69 0.07
319 1 0.00
321 6 0.01
322 118 0.12
323 422 0.41
324 291 0.28
325 27 0.03
326 6 0.01
ACGTcount: A:0.44, C:0.15, G:0.09, T:0.32
Consensus pattern (321 bp):
AAACCAAGTTCAATCATTCGACAAATTTAATATCATGTATTTAAGCTATCTAAACTGTTAAAAAT
AAATATAACTATAAAATTACATTTTTACCCTTTAACGGCACAAAAAAGTCCTAAAAAGACATAAA
CGGTAACTTTTTCACACATATCAACATGGAAACCAAGTTCAATCATTTAGACAAGTTTAATATCA
TGTATTAAAGCTATCCAAACTGTTAAAACAGAAAAATAACACAAATTTACATTTTGGCCTTTTAA
TCAGCACAAAAAGTGCTAAACAAACATAAACGGTAACTTTTTTCACACATATCAATCATGG
Found at i:17984001 original size:485 final size:479
Alignment explanation
Indices: 17982367--17984030 Score: 1463
Period size: 485 Copynumber: 3.5 Consensus size: 479
17982357 GTAAATTTGC
* * * * ** * *
17982367 ATTTTTTCCTTTTAACATTAC-AAAAAGT-CTTAAACATATATAAATCTTAACTTATTCATACAT
1 ATTTTTACCTTTTAACAGTACAAAAAAGTGC-TAAACAGACATAAATGGTAACTTTTTCACACAT
* * *
17982430 ATCAA--ATTGAAAAAACCAAGTTCAATCATTTGGACAA-GTTTAATATCATGTATTAAAGTTA-
65 ATCAATCA-TG--AAAACCAAGTTCAATCATTTAGAAAAGGTTTAATATCATGTATTAAAGCTAT
* * * * * *** * *
17982491 CCAAAACTGTTAAAATATAAATATAACTATAAAATTACATTTTTACCTTTAGTGGTACAATAAAG
127 CC-AAACTGTTAAAACAGAAAAATAACTATAAATTTACATTTTTGCCTTTAACAGCACAA-AAAA
* * *
17982556 T-CTTAAAAAGACATAAACGATATC-TTTTTCACACATATCAATCATGGAAACCAAGTTCAATAA
190 TAC-TAAACAGACATAAACGATAACTTTTTTCACACATATCAATCATGGAAACCAAGTTCAATCA
* * *
17982619 TTTAAATAAG--T--T-T-ATGTGTTGAAGCTATCT-AATAGTAAAAACATAAA-AATAACTACA
254 TTCAAATAAGTTTAATATCATGTATTGAAGCTATCTAAAT-GT-TAAA-ATAAATAATAACTACA
* * * **
17982676 AAATTATATTTTTACCCTTTAACAGCAAAACATAGTCCTAAAAAGACATAAACGGTAACATTTTC
316 AATTTATATTTTTGCCCTTTAATAGCAAAA-A-AGTCCTAAAAAGACATAAACAATAACATTTTC
* *
17982741 ACACATATCAACAATGGAAACCAAGTTCAATTATTCTGACAAGTTTAATATCATGTATTAAAGCT
379 ACACATATCAAC-ATGGAAACCAAGTTCAATCATTCGGACAAGTTTAATATCATGTATTAAAGCT
**
17982806 ATCTAAACTGTTAAAATAGAATAATAA-ACATAAATTTG
443 ATCTAAACTGTTAAAATAGAAT-ATAACACA-AAATTAA
* * * * ** *
17982844 CTTTTTGACCTTTTAACATTATAAAAAAGTGCTAAACAGACATATACAGTAACTTTTTCACACCT
1 ATTTTT-ACCTTTTAACAGTACAAAAAAGTGCTAAACAGACATAAATGGTAACTTTTTCACACAT
* * * *
17982909 ATCAATCATGAAAACTAAGTTCAATCA-TTCGAAAAGGTTTAATATCATGTATTTAAGCTATCTA
65 ATCAATCATGAAAACCAAGTTCAATCATTTAGAAAAGGTTTAATATCATGTATTAAAGCTATCCA
* * * * *
17982973 AACTGTTAAAACGGAATAATAAAC-AAAAATTTACATTTTGGCCTTTTAACAGCATAAAAAAATA
130 AACTGTTAAAACAGAAAAAT-AACTATAAATTTACATTTTTGCC-TTTAACAGCA-CAAAAAATA
* * * *
17983037 CTAAACAGACATAAA-TAGTAA-TTTTTTCACACATTTCAATCGTGGAAACCAAGTTCAACCATT
192 CTAAACAGACATAAACGA-TAACTTTTTTCACACATATCAATCATGGAAACCAAGTTCAATCATT
* * * * *
17983100 CAAAAAAGTTTAATATCATGTATTTAAGATATCTAAATTGTTAAAACATAAAT-ATAACTATAAG
256 CAAATAAGTTTAATATCATGTATTGAAGCTATCTAAA-TGTT-AAA-ATAAATAATAACTACAAA
*
17983164 TTTATATTTTTGCCCTTTAATGGCATAACAAAGTCCTAAAAAGACAT--ACAAGGTAACATTTTC
318 TTTATATTTTTGCCCTTTAATAGCA-AA-AAAGTCCTAAAAAGACATAAACAA--TAACATTTTC
* * *
17983227 ACACATATCAGCCATGGAAACCAAGTTTAATCATTTGGACAAGTTTAATATCATGTATTGAAA-C
379 ACACATATCA-ACATGGAAACCAAGTTCAATCATTCGGACAAGTTTAATATCATGTATT-AAAGC
** * * * **
17983291 TATAAAAAATGTTAAAATAGAAGAGTAACACAAATTTGT
442 TATCTAAACTGTTAAAATAGAATA-TAACACAAAATTAA
** * * * *
17983330 ATTTTGGCCTTTTAACAGTGCTAAAAAGTGTTAAACAGACATAAATGGTAACTTTTTTACACATA
1 ATTTTTACCTTTTAACAGTACAAAAAAGTGCTAAACAGACATAAATGGTAACTTTTTCACACATA
* ** * * * *
17983395 TCAATCATGAAAACCAAGTTCAATCATTCA-AAAATATTTAATATCATATTTTAAAACTATCTAA
66 TCAATCATGAAAACCAAGTTCAATCATTTAGAAAAGGTTTAATATCATGTATTAAAGCTATCCAA
* * * * * * *
17983459 ACTGTTAGAATAGAATAATAAATGTAAATTTTCATTTTAGCCCTTTAACAGCACAAAAAAT-CTT
131 ACTGTTAAAACAGAAAAATAACTATAAATTTACATTTTTG-CCTTTAACAGCACAAAAAATAC-T
* * * ** *
17983523 AAATAGACATAAACGATAACTTTTTTTACACATATCAACCATACAAACTAAGTTCAATCATTCAA
194 AAACAGACATAAACGATAACTTTTTTCACACATATCAATCATGGAAACCAAGTTCAATCATTCAA
* * * *
17983588 ATAAGTTTAATATCATTTATTGAAGCTATCTAAACTGTTAAAATGGAATAATAA-AAGCAATTTT
259 ATAAGTTTAATATCATGTATTGAAGCTATCTAAA-TGTTAAAAT-AAATAATAACTA-CAAATTT
** * * * *
17983652 GCATTTTGGCCTTTTAATAGCACAAAAAGTGCTAAACAA-ACATAAACAATAACTTTTTTCACA-
321 ATATTTTTGCCCTTTAATAGCA-AAAAAGTCCTAAA-AAGACATAAACAATAAC-ATTTTCACAC
* * * *
17983715 A-ATCAATCATGGAAACCAAGTTCAATCATTCGGGCAAATTTAATATCATGTATTTAAGTTATCT
383 ATATCAA-CATGGAAACCAAGTTCAATCATTCGGACAAGTTTAATATCATGTATTAAAGCTATCT
*
17983779 AAACTGTTAAAACATA-AATATAACTGCAAAATTAA
447 AAACTGTT-AAA-ATAGAATATAAC-ACAAAATTAA
* * * * * * *
17983814 ATTTTTACCCTATAACGGCACAAACAAAGTCCTAAAAAGATATAAATGGTAACTTTTTCACACAT
1 ATTTTTACCTTTTAACAGTACAAA-AAAGTGCTAAACAGACATAAATGGTAACTTTTTCACACAT
* ** *
17983879 ATCAA-CAATGGAAACCAAGTTCAATCATTTAGGCAA-GTTTAATATAATGTATTAAAGCTATCC
65 ATCAATC-ATGAAAACCAAGTTCAATCATTTAGAAAAGGTTTAATATCATGTATTAAAGCTATCC
* * ** * * * *
17983942 AAACTATTAAAACAAAAAAATAACTGCATATTTACATTTTTGCCATTTAA-TGACACAAAAAGTG
129 AAACTGTTAAAACAGAAAAATAACTATAAATTTACATTTTTGCC-TTTAACAG-CACAAAAAATA
* *
17984006 CTAAACAAATATAAACGATAACTTT
192 CTAAACAGACATAAACGATAACTTT
17984031 CTTATTTGAT
Statistics
Matches: 955, Mismatches: 177, Indels: 102
0.77 0.14 0.08
Matches are distributed among these distances:
477 11 0.01
478 83 0.09
479 108 0.11
480 6 0.01
481 2 0.00
482 2 0.00
483 65 0.07
484 86 0.09
485 418 0.44
486 162 0.17
487 11 0.01
488 1 0.00
ACGTcount: A:0.44, C:0.15, G:0.09, T:0.32
Consensus pattern (479 bp):
ATTTTTACCTTTTAACAGTACAAAAAAGTGCTAAACAGACATAAATGGTAACTTTTTCACACATA
TCAATCATGAAAACCAAGTTCAATCATTTAGAAAAGGTTTAATATCATGTATTAAAGCTATCCAA
ACTGTTAAAACAGAAAAATAACTATAAATTTACATTTTTGCCTTTAACAGCACAAAAAATACTAA
ACAGACATAAACGATAACTTTTTTCACACATATCAATCATGGAAACCAAGTTCAATCATTCAAAT
AAGTTTAATATCATGTATTGAAGCTATCTAAATGTTAAAATAAATAATAACTACAAATTTATATT
TTTGCCCTTTAATAGCAAAAAAGTCCTAAAAAGACATAAACAATAACATTTTCACACATATCAAC
ATGGAAACCAAGTTCAATCATTCGGACAAGTTTAATATCATGTATTAAAGCTATCTAAACTGTTA
AAATAGAATATAACACAAAATTAA
Found at i:17985112 original size:13 final size:13
Alignment explanation
Indices: 17985077--17985123 Score: 58
Period size: 13 Copynumber: 3.5 Consensus size: 13
17985067 CAAACATTGT
**
17985077 ATATATAACCAAC
1 ATATATAAAGAAC
17985090 TATATATAAAGAAC
1 -ATATATAAAGAAC
*
17985104 ATATCTAAAGAAC
1 ATATATAAAGAAC
17985117 ATATATA
1 ATATATA
17985124 CACTTTGAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
13 18 0.62
14 11 0.38
ACGTcount: A:0.55, C:0.13, G:0.04, T:0.28
Consensus pattern (13 bp):
ATATATAAAGAAC
Found at i:17987371 original size:21 final size:21
Alignment explanation
Indices: 17987347--17987390 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
17987337 CATTATCATT
*
17987347 TTGAATATCTA-CATTACCAAC
1 TTGAATAT-TAGCATCACCAAC
*
17987368 TTGAGTATTAGCATCACCAAC
1 TTGAATATTAGCATCACCAAC
17987389 TT
1 TT
17987391 AAGGAATAGG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 2 0.10
21 18 0.90
ACGTcount: A:0.34, C:0.23, G:0.09, T:0.34
Consensus pattern (21 bp):
TTGAATATTAGCATCACCAAC
Found at i:17998013 original size:42 final size:42
Alignment explanation
Indices: 17997933--17998013 Score: 110
Period size: 42 Copynumber: 1.9 Consensus size: 42
17997923 TTCTATATAA
* * *
17997933 AAAATCAATCGATCCATTTTTAGGGGATCGATCCATTTTTTG
1 AAAACCAATCGATCCATTTTTAGGGGATCAATCAATTTTTTG
*
17997975 AAAACCAATCGATCCATTTTTAATGGG-TCAATCAATTTT
1 AAAACCAATCGATCCATTTTT-AGGGGATCAATCAATTTT
17998014 AGGTTTTTAC
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
42 30 0.88
43 4 0.12
ACGTcount: A:0.32, C:0.17, G:0.14, T:0.37
Consensus pattern (42 bp):
AAAACCAATCGATCCATTTTTAGGGGATCAATCAATTTTTTG
Found at i:17998726 original size:18 final size:18
Alignment explanation
Indices: 17998686--17998817 Score: 110
Period size: 18 Copynumber: 7.4 Consensus size: 18
17998676 TGAAACTTAC
*
17998686 GAATCTTT-ATACACTTGT
1 GAATCTTTGA-ACTCTTGT
* *
17998704 AAATCTTTGAACTCTTAT
1 GAATCTTTGAACTCTTGT
* *
17998722 GAATCTCTAAACAT-TTGT
1 GAATCTTTGAAC-TCTTGT
*
17998740 GAATCTTTGAACTCTTGC
1 GAATCTTTGAACTCTTGT
*
17998758 GAATCTTTAAACTCTTGT
1 GAATCTTTGAACTCTTGT
* *
17998776 GAATCTTTGAA-ACTTGC
1 GAATCTTTGAACTCTTGT
* **
17998793 CAATCTTT-AAAGCTTGT
1 GAATCTTTGAACTCTTGT
17998810 GAATCTTT
1 GAATCTTT
17998818 AAAACTTGCA
Statistics
Matches: 91, Mismatches: 19, Indels: 9
0.76 0.16 0.08
Matches are distributed among these distances:
16 2 0.02
17 23 0.25
18 64 0.70
19 2 0.02
ACGTcount: A:0.29, C:0.17, G:0.12, T:0.42
Consensus pattern (18 bp):
GAATCTTTGAACTCTTGT
Found at i:17998727 original size:36 final size:36
Alignment explanation
Indices: 17998597--17998817 Score: 145
Period size: 36 Copynumber: 6.4 Consensus size: 36
17998587 TCTCCTAAAT
* *
17998597 CTTGCAAATCTTTG-ACTCTTACGAATCTTTGAA-A
1 CTTGTAAATCTTTGAACTCTTACGAATCTTTAAACA
* * * * * * *
17998631 CTTGCAAATATCTGAGCT-TGT--GAATCGTTGAA-G
1 CTTGTAAATCTTTGAACTCT-TACGAATCTTTAAACA
* * * *
17998664 CTTGCAAATTTTTGAA-ACTTACGAATCTTTATACA
1 CTTGTAAATCTTTGAACTCTTACGAATCTTTAAACA
* *
17998699 CTTGTAAATCTTTGAACTCTTATGAATCTCTAAACA
1 CTTGTAAATCTTTGAACTCTTACGAATCTTTAAACA
* * * *
17998735 TTTGTGAATCTTTGAACTCTTGCGAATCTTTAAACT
1 CTTGTAAATCTTTGAACTCTTACGAATCTTTAAACA
* * * * *
17998771 CTTGTGAATCTTTGAA-ACTTGCCAATCTTTAAA-G
1 CTTGTAAATCTTTGAACTCTTACGAATCTTTAAACA
*
17998805 CTTGTGAATCTTT
1 CTTGTAAATCTTT
17998818 AAAACTTGCA
Statistics
Matches: 151, Mismatches: 29, Indels: 14
0.78 0.15 0.07
Matches are distributed among these distances:
32 1 0.01
33 24 0.16
34 34 0.23
35 32 0.21
36 60 0.40
ACGTcount: A:0.29, C:0.18, G:0.14, T:0.40
Consensus pattern (36 bp):
CTTGTAAATCTTTGAACTCTTACGAATCTTTAAACA
Found at i:17998797 original size:17 final size:17
Alignment explanation
Indices: 17998619--17998924 Score: 174
Period size: 17 Copynumber: 17.7 Consensus size: 17
17998609 TGACTCTTAC
*
17998619 GAATCTTTGAAACTTGC
1 GAATCTTTGAAACTTGT
* * * *
17998636 AAATATCTG-AGCTTGT
1 GAATCTTTGAAACTTGT
* * *
17998652 GAATCGTTGAAGCTTGC
1 GAATCTTTGAAACTTGT
* * **
17998669 AAATTTTTGAAACTTAC
1 GAATCTTTGAAACTTGT
17998686 GAATCTTT-ATACACTTGT
1 GAATCTTTGA-A-ACTTGT
* * *
17998704 AAATCTTTGAACTCTTAT
1 GAATCTTTGAA-ACTTGT
*
17998722 GAATCTCT-AAACATTTGT
1 GAATCTTTGAAAC--TTGT
* *
17998740 GAATCTTTGAACTCTTGC
1 GAATCTTTGAA-ACTTGT
17998758 GAATCTTT-AAACTCTTGT
1 GAATCTTTGAAA--CTTGT
*
17998776 GAATCTTTGAAACTTGC
1 GAATCTTTGAAACTTGT
*
17998793 CAATCTTT-AAAGCTTGT
1 GAATCTTTGAAA-CTTGT
*
17998810 GAATCTTTAAAACTTG-
1 GAATCTTTGAAACTTGT
* * * *
17998826 CATATCTTTTAAAATTAT
1 GA-ATCTTTGAAACTTGT
* * *
17998844 AAATCTTTGAAATTTAT
1 GAATCTTTGAAACTTGT
17998861 GAATCTTTGAAACTTGT
1 GAATCTTTGAAACTTGT
* * *
17998878 GAAACTCTAAGAACTTGT
1 GAATCTTTGA-AACTTGT
17998896 GAATCTTTGAAACTTGT
1 GAATCTTTGAAACTTGT
* *
17998913 GGATCTATGAAA
1 GAATCTTTGAAA
17998925 TTTACGAATA
Statistics
Matches: 220, Mismatches: 53, Indels: 32
0.72 0.17 0.10
Matches are distributed among these distances:
16 16 0.07
17 123 0.56
18 74 0.34
19 6 0.03
20 1 0.00
ACGTcount: A:0.32, C:0.15, G:0.14, T:0.39
Consensus pattern (17 bp):
GAATCTTTGAAACTTGT
Found at i:17998814 original size:34 final size:35
Alignment explanation
Indices: 17998674--17998834 Score: 137
Period size: 36 Copynumber: 4.6 Consensus size: 35
17998664 CTTGCAAATT
* * * * *
17998674 TTTGAAACTTACGAATCTTTATACACTTGTAAATC
1 TTTGAAACTTGCCAATCTTTAAACGCTTGTGAATC
* *** * **
17998709 TTTGAACTCTTATGAATCTCTAAACATTTGTGAATC
1 TTTGAA-ACTTGCCAATCTTTAAACGCTTGTGAATC
* * *
17998745 TTTGAACTCTTGCGAATCTTTAAACTCTTGTGAATC
1 TTTGAA-ACTTGCCAATCTTTAAACGCTTGTGAATC
17998781 TTTGAAACTTGCCAATCTTTAAA-GCTTGTGAATC
1 TTTGAAACTTGCCAATCTTTAAACGCTTGTGAATC
*
17998815 TTTAAAACTTG-CATATCTTT
1 TTTGAAACTTGCCA-ATCTTT
17998835 TAAAATTATA
Statistics
Matches: 109, Mismatches: 15, Indels: 5
0.84 0.12 0.04
Matches are distributed among these distances:
33 2 0.02
34 26 0.24
35 21 0.19
36 60 0.55
ACGTcount: A:0.30, C:0.17, G:0.11, T:0.42
Consensus pattern (35 bp):
TTTGAAACTTGCCAATCTTTAAACGCTTGTGAATC
Found at i:17999004 original size:18 final size:18
Alignment explanation
Indices: 17998936--17999014 Score: 77
Period size: 18 Copynumber: 4.3 Consensus size: 18
17998926 TTACGAATAT
* *
17998936 TAAACTCTAACGAATCTC
1 TAAACTCTTACAAATCTC
* * **
17998954 TTAACACTTACAAATCAA
1 TAAACTCTTACAAATCTC
17998972 TAAACTCTTACAAATCTC
1 TAAACTCTTACAAATCTC
**
17998990 TAAACTCTTGTAAATCTC
1 TAAACTCTTACAAATCTC
17999008 TGAAACT
1 T-AAACT
17999015 TACCTTTGAA
Statistics
Matches: 48, Mismatches: 12, Indels: 1
0.79 0.20 0.02
Matches are distributed among these distances:
18 43 0.90
19 5 0.10
ACGTcount: A:0.41, C:0.24, G:0.04, T:0.32
Consensus pattern (18 bp):
TAAACTCTTACAAATCTC
Found at i:17999052 original size:17 final size:17
Alignment explanation
Indices: 17999031--17999110 Score: 88
Period size: 17 Copynumber: 4.6 Consensus size: 17
17999021 TGAAGCTTAA
17999031 GAATCTCTGAAACTTGT
1 GAATCTCTGAAACTTGT
* * *
17999048 AAATCTCTAAACACTTAT
1 GAATCTCTGAA-ACTTGT
* *
17999066 GAATCTTTGAAGCTTGT
1 GAATCTCTGAAACTTGT
*
17999083 GAATCTCTAAAACTTGT
1 GAATCTCTGAAACTTGT
*
17999100 GAATCTTTGAA
1 GAATCTCTGAA
17999111 TGTTACAAAT
Statistics
Matches: 49, Mismatches: 13, Indels: 2
0.77 0.20 0.03
Matches are distributed among these distances:
17 36 0.73
18 13 0.27
ACGTcount: A:0.34, C:0.16, G:0.14, T:0.36
Consensus pattern (17 bp):
GAATCTCTGAAACTTGT
Found at i:17999082 original size:35 final size:34
Alignment explanation
Indices: 17999026--17999110 Score: 116
Period size: 35 Copynumber: 2.5 Consensus size: 34
17999016 ACCTTTGAAG
* *
17999026 CTTAAGAATCTCTGAAACTTGTAAATCTCTAAACA
1 CTTATGAATCTTTGAAACTTGTAAATCTCTAAA-A
* *
17999061 CTTATGAATCTTTGAAGCTTGTGAATCTCTAAAA
1 CTTATGAATCTTTGAAACTTGTAAATCTCTAAAA
*
17999095 CTTGTGAATCTTTGAA
1 CTTATGAATCTTTGAA
17999111 TGTTACAAAT
Statistics
Matches: 45, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
34 16 0.36
35 29 0.64
ACGTcount: A:0.34, C:0.16, G:0.13, T:0.36
Consensus pattern (34 bp):
CTTATGAATCTTTGAAACTTGTAAATCTCTAAAA
Found at i:17999121 original size:17 final size:18
Alignment explanation
Indices: 17999101--17999147 Score: 53
Period size: 17 Copynumber: 2.7 Consensus size: 18
17999091 AAAACTTGTG
*
17999101 AATCTTTGAA-TGTTACA
1 AATCTTTAAACTGTTACA
*
17999118 AATCTTTAAACTTTTACA
1 AATCTTTAAACTGTTACA
17999136 AAT-TTTAGAACT
1 AATCTTTA-AACT
17999148 TTTATGAATC
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
17 13 0.50
18 13 0.50
ACGTcount: A:0.38, C:0.13, G:0.06, T:0.43
Consensus pattern (18 bp):
AATCTTTAAACTGTTACA
Found at i:17999122 original size:34 final size:35
Alignment explanation
Indices: 17999048--17999128 Score: 94
Period size: 34 Copynumber: 2.3 Consensus size: 35
17999038 TGAAACTTGT
**
17999048 AAATCTCTAAACACTTATGAATCTTTGAAGCTTGT
1 AAATCTCTAAACACTTATGAATCTTTGAAGCTTAC
* *
17999083 GAATCTCTAAA-ACTTGTGAATCTTTGAATG-TTAC
1 AAATCTCTAAACACTTATGAATCTTTGAA-GCTTAC
*
17999117 AAATCTTTAAAC
1 AAATCTCTAAAC
17999129 TTTTACAAAT
Statistics
Matches: 38, Mismatches: 6, Indels: 4
0.79 0.12 0.08
Matches are distributed among these distances:
34 27 0.71
35 11 0.29
ACGTcount: A:0.36, C:0.16, G:0.11, T:0.37
Consensus pattern (35 bp):
AAATCTCTAAACACTTATGAATCTTTGAAGCTTAC
Done.