Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009626.1 Hibiscus syriacus cultivar Beakdansim tig00117018_pilon, 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: 478969
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
File 1 of 3
Found at i:8 original size:3 final size:3
Alignment explanation
Indices: 1--256 Score: 322
Period size: 3 Copynumber: 87.3 Consensus size: 3
1 AAG AAG AAG -AG AAG AAG AAG AA- AAG AAG AA- AGAG AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG A-AG AAG AAG AAG
*
44 AAG AAG AAG AA- AAG AAG AAG -AG AGG AAG AAG AAG AAG AA- AGAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG A-AG
* * *
87 AAG AAG AAG AAA AAG AAG AAG AAG AAG AAG AAG AAG AGAT AAA AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG A-AG AAG AAG
133 AAG AA- AAG AAG AA- AAG -AG AAG AAG AAG AAG AAG AAG AA- AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
177 AAG AAG AAG AAGG AAG -AG AAG AAG AAG -AG AAAG AAG -AG AAG AAG
1 AAG AAG AAG AA-G AAG AAG AAG AAG AAG AAG -AAG AAG AAG AAG AAG
221 AAAG AAG AAG AAG AAG AAG AAG AAG AAG AAAG AAG A
1 -AAG AAG AAG AAG AAG AAG AAG AAG AAG -AAG AAG A
257 TAGTTCAATT
Statistics
Matches: 226, Mismatches: 7, Indels: 40
0.83 0.03 0.15
Matches are distributed among these distances:
2 24 0.11
3 187 0.83
4 15 0.07
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:351 original size:3 final size:3
Alignment explanation
Indices: 345--388 Score: 79
Period size: 3 Copynumber: 14.3 Consensus size: 3
335 TTATATATAT
345 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA T
389 ATTTATTAAT
Statistics
Matches: 40, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
3 37 0.93
4 3 0.08
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:394 original size:9 final size:9
Alignment explanation
Indices: 332--396 Score: 64
Period size: 9 Copynumber: 7.0 Consensus size: 9
322 TCTTTTTTTT
332 TATTTATATA
1 TATTTAT-TA
342 TATTTATTA
1 TATTTATTA
351 T-TATTATTA
1 TAT-TTATTA
360 T-TATTATTA
1 TAT-TTATTA
369 TTATTTATTA
1 -TATTTATTA
379 T-TATTATTA
1 TAT-TTATTA
388 TATTTATTA
1 TATTTATTA
397 ATTACATATT
Statistics
Matches: 50, Mismatches: 0, Indels: 11
0.82 0.00 0.18
Matches are distributed among these distances:
8 2 0.04
9 32 0.64
10 15 0.30
11 1 0.02
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (9 bp):
TATTTATTA
Found at i:3993 original size:33 final size:33
Alignment explanation
Indices: 3913--3985 Score: 146
Period size: 33 Copynumber: 2.2 Consensus size: 33
3903 TTGGGTAGAT
3913 AGCATGTCCGGGTAGGATTGTTATTTAATTGAA
1 AGCATGTCCGGGTAGGATTGTTATTTAATTGAA
3946 AGCATGTCCGGGTAGGATTGTTATTTAATTGAA
1 AGCATGTCCGGGTAGGATTGTTATTTAATTGAA
3979 AGCATGT
1 AGCATGT
3986 TTGGGTAGAT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 40 1.00
ACGTcount: A:0.27, C:0.10, G:0.27, T:0.36
Consensus pattern (33 bp):
AGCATGTCCGGGTAGGATTGTTATTTAATTGAA
Found at i:7705 original size:4 final size:4
Alignment explanation
Indices: 7696--7747 Score: 76
Period size: 4 Copynumber: 14.0 Consensus size: 4
7686 AAAAGTATAC
7696 ACAT ACAT ACAT ACAT AC-- ACAT ACAT ACAT ACAT ACAT AC-- ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
7740 ACAT ACAT
1 ACAT ACAT
7748 GATACATAAA
Statistics
Matches: 44, Mismatches: 0, Indels: 8
0.85 0.00 0.15
Matches are distributed among these distances:
2 4 0.09
4 40 0.91
ACGTcount: A:0.50, C:0.27, G:0.00, T:0.23
Consensus pattern (4 bp):
ACAT
Found at i:7715 original size:18 final size:18
Alignment explanation
Indices: 7692--7747 Score: 94
Period size: 18 Copynumber: 3.1 Consensus size: 18
7682 CGAGAAAAGT
7692 ATACACATACATACATAC
1 ATACACATACATACATAC
7710 ATACACATACATACATAC
1 ATACACATACATACATAC
* *
7728 ATACATACACATACATAC
1 ATACACATACATACATAC
7746 AT
1 AT
7748 GATACATAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 36 1.00
ACGTcount: A:0.50, C:0.27, G:0.00, T:0.23
Consensus pattern (18 bp):
ATACACATACATACATAC
Found at i:7722 original size:22 final size:22
Alignment explanation
Indices: 7696--7755 Score: 104
Period size: 22 Copynumber: 2.8 Consensus size: 22
7686 AAAAGTATAC
7696 ACATACATACATACATACACAT
1 ACATACATACATACATACACAT
7718 ACATACATACATACATACACAT
1 ACATACATACATACATACACAT
*
7740 ACATACAT-GATACATA
1 ACATACATACATACATA
7756 AAATTTGTAT
Statistics
Matches: 37, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
21 7 0.19
22 30 0.81
ACGTcount: A:0.50, C:0.25, G:0.02, T:0.23
Consensus pattern (22 bp):
ACATACATACATACATACACAT
Found at i:8320 original size:34 final size:36
Alignment explanation
Indices: 8236--8333 Score: 128
Period size: 36 Copynumber: 2.8 Consensus size: 36
8226 TTGTTTCCTC
* *
8236 AAAAACAAACTTTGTCTCGCTTGAGACAATTTCTCT
1 AAAAACAAATTTTGTCTCGCTTGAGACAATATCTCT
** *
8272 AAAAACAAATTTTGTCTCATTTGAGACTATATCT-T
1 AAAAACAAATTTTGTCTCGCTTGAGACAATATCTCT
*
8307 -AAAGCAAATTTTGTCTCGCTTGAGACA
1 AAAAACAAATTTTGTCTCGCTTGAGACA
8334 TCATTTTCTC
Statistics
Matches: 53, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
34 23 0.43
35 1 0.02
36 29 0.55
ACGTcount: A:0.35, C:0.18, G:0.12, T:0.35
Consensus pattern (36 bp):
AAAAACAAATTTTGTCTCGCTTGAGACAATATCTCT
Found at i:8619 original size:29 final size:28
Alignment explanation
Indices: 8585--8831 Score: 175
Period size: 29 Copynumber: 8.6 Consensus size: 28
8575 GTTTCTCTTG
8585 AAAAAATCTTTGAGTTTGTTCCTTTTGA
1 AAAAAATCTTTGAGTTTGTTCCTTTTGA
*
8613 ATAAAAATCTTGGAGTTTGTTCCTTTTGA
1 A-AAAAATCTTTGAGTTTGTTCCTTTTGA
* *
8642 ATAAATATCTTTGAG-TTGTTTCTTTTG-
1 A-AAAAATCTTTGAGTTTGTTCCTTTTGA
* * **
8669 -AAAAATCTTTGAGTCTATTTATTTTGA
1 AAAAAATCTTTGAGTTTGTTCCTTTTGA
* *** * *
8696 AACAAAGTTTTGTCTCTCTTGAGACAGTTTCTCTTG-
1 AA-AAA-------ATCT-TTGAGTTTGTTCCTTTTGA
*
8732 AAAAAATATTTGAGTTTGTTCCTTTTGA
1 AAAAAATCTTTGAGTTTGTTCCTTTTGA
*
8760 ATAAAAATCTTGGAGTTTGTTCCTTTTGA
1 A-AAAAATCTTTGAGTTTGTTCCTTTTGA
* *
8789 ATAAATATCTTTGAG-TTGTTTCTTTTG-
1 A-AAAAATCTTTGAGTTTGTTCCTTTTGA
8816 -AAAAATCTTTGAGTTT
1 AAAAAATCTTTGAGTTT
8832 ATTTATTTTG
Statistics
Matches: 176, Mismatches: 27, Indels: 34
0.74 0.11 0.14
Matches are distributed among these distances:
25 24 0.14
26 11 0.06
27 13 0.07
28 27 0.15
29 80 0.45
35 3 0.02
36 5 0.03
37 13 0.07
ACGTcount: A:0.28, C:0.10, G:0.15, T:0.47
Consensus pattern (28 bp):
AAAAAATCTTTGAGTTTGTTCCTTTTGA
Found at i:8694 original size:54 final size:54
Alignment explanation
Indices: 8582--8697 Score: 128
Period size: 54 Copynumber: 2.1 Consensus size: 54
8572 ACAGTTTCTC
* * *
8582 TTGAAAAAATCTTTGAGTTTGTTCCTTTTGAATAAAAATCTTGGAGTTTGTTCCTT
1 TTGAAAAAATCTTTGAGTTTGTTCCTTTTG-A-AAAAATCTTGGAGTCTATTCATT
* * *
8638 TTGAATAAATATCTTTGAG-TTGTTTCTTTTG-AAAAATCTTTGAGTCTATTTATT
1 TTGAA-AAA-ATCTTTGAGTTTGTTCCTTTTGAAAAAATCTTGGAGTCTATTCATT
8692 TTGAAA
1 TTGAAA
8698 CAAAGTTTTG
Statistics
Matches: 52, Mismatches: 6, Indels: 7
0.80 0.09 0.11
Matches are distributed among these distances:
53 1 0.02
54 23 0.44
56 5 0.10
57 14 0.27
58 9 0.17
ACGTcount: A:0.28, C:0.09, G:0.15, T:0.48
Consensus pattern (54 bp):
TTGAAAAAATCTTTGAGTTTGTTCCTTTTGAAAAAATCTTGGAGTCTATTCATT
Found at i:8722 original size:147 final size:147
Alignment explanation
Indices: 8556--8890 Score: 604
Period size: 147 Copynumber: 2.3 Consensus size: 147
8546 AAACGATTTT
*
8556 TTTTGTCTCTCTTGCGACAGTTTCTCTTGAAAAAATCTTTGAGTTTGTTCCTTTTGAATAAAAAT
1 TTTTGTCTCTCTTGAGACAGTTTCTCTTGAAAAAATCTTTGAGTTTGTTCCTTTTGAATAAAAAT
8621 CTTGGAGTTTGTTCCTTTTGAATAAATATCTTTGAGTTGTTTCTTTTGAAAAATCTTTGAGTCTA
66 CTTGGAGTTTGTTCCTTTTGAATAAATATCTTTGAGTTGTTTCTTTTGAAAAATCTTTGAGTCTA
8686 TTTATTTTGAAACAAAG
131 TTTATTTTGAAACAAAG
*
8703 TTTTGTCTCTCTTGAGACAGTTTCTCTTGAAAAAATATTTGAGTTTGTTCCTTTTGAATAAAAAT
1 TTTTGTCTCTCTTGAGACAGTTTCTCTTGAAAAAATCTTTGAGTTTGTTCCTTTTGAATAAAAAT
*
8768 CTTGGAGTTTGTTCCTTTTGAATAAATATCTTTGAGTTGTTTCTTTTGAAAAATCTTTGAGTTTA
66 CTTGGAGTTTGTTCCTTTTGAATAAATATCTTTGAGTTGTTTCTTTTGAAAAATCTTTGAGTCTA
8833 TTTATTTTGAAACAAAG
131 TTTATTTTGAAACAAAG
* *
8850 TTTTGTCTCTCTTGAGACA-ATT-TCGTG-AAAAATCTTTGAGT
1 TTTTGTCTCTCTTGAGACAGTTTCTCTTGAAAAAATCTTTGAGT
8891 CTGAAACAAA
Statistics
Matches: 182, Mismatches: 6, Indels: 3
0.95 0.03 0.02
Matches are distributed among these distances:
144 13 0.07
145 4 0.02
146 2 0.01
147 163 0.90
ACGTcount: A:0.26, C:0.12, G:0.15, T:0.47
Consensus pattern (147 bp):
TTTTGTCTCTCTTGAGACAGTTTCTCTTGAAAAAATCTTTGAGTTTGTTCCTTTTGAATAAAAAT
CTTGGAGTTTGTTCCTTTTGAATAAATATCTTTGAGTTGTTTCTTTTGAAAAATCTTTGAGTCTA
TTTATTTTGAAACAAAG
Found at i:8962 original size:28 final size:28
Alignment explanation
Indices: 8931--8998 Score: 95
Period size: 27 Copynumber: 2.5 Consensus size: 28
8921 ATTTTGTGAA
*
8931 AAAAAAATCTTTGAGATTGTTTCTTTTG
1 AAAAAAATCTTTGAGATTGTTTCTTTGG
*
8959 -AAAAAATCTTTGAGTTTGTTTCTTTGG
1 AAAAAAATCTTTGAGATTGTTTCTTTGG
8986 AAACAAAAT-TTTG
1 AAA-AAAATCTTTG
8999 TCTCTCTTAA
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
27 25 0.69
28 6 0.17
29 5 0.14
ACGTcount: A:0.34, C:0.07, G:0.15, T:0.44
Consensus pattern (28 bp):
AAAAAAATCTTTGAGATTGTTTCTTTGG
Found at i:8984 original size:26 final size:27
Alignment explanation
Indices: 8932--8988 Score: 96
Period size: 27 Copynumber: 2.1 Consensus size: 27
8922 TTTTGTGAAA
8932 AAAAAATCTTTGAGATTGTTTCTTTTG
1 AAAAAATCTTTGAGATTGTTTCTTTTG
* *
8959 AAAAAATCTTTGAGTTTGTTTCTTTGG
1 AAAAAATCTTTGAGATTGTTTCTTTTG
8986 AAA
1 AAA
8989 CAAAATTTTG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.32, C:0.07, G:0.16, T:0.46
Consensus pattern (27 bp):
AAAAAATCTTTGAGATTGTTTCTTTTG
Found at i:9027 original size:37 final size:37
Alignment explanation
Indices: 8976--9104 Score: 110
Period size: 37 Copynumber: 3.6 Consensus size: 37
8966 CTTTGAGTTT
*
8976 GTTTCTTTGGAAACAAAATTTTGTCTCTCTTAAGATA
1 GTTTCTTTGAAAACAAAATTTTGTCTCTCTTAAGATA
* * * * *
9013 GTTTCTTTTAAAACAAAA------ATCT-TTGAGTTT
1 GTTTCTTTGAAAACAAAATTTTGTCTCTCTTAAGATA
*
9043 GTTTCTTTGGAAACAAAATTTTGTCTCTCTTAAGATA
1 GTTTCTTTGAAAACAAAATTTTGTCTCTCTTAAGATA
* *
9080 ATTTCTTTTGAAAAAAAAATCTTTG
1 GTTTC-TTTGAAAACAAAAT-TTTG
9105 AATCTGTTTC
Statistics
Matches: 68, Mismatches: 15, Indels: 16
0.69 0.15 0.16
Matches are distributed among these distances:
30 21 0.31
31 3 0.04
36 3 0.04
37 25 0.37
38 12 0.18
39 4 0.06
ACGTcount: A:0.33, C:0.12, G:0.12, T:0.44
Consensus pattern (37 bp):
GTTTCTTTGAAAACAAAATTTTGTCTCTCTTAAGATA
Found at i:9035 original size:67 final size:66
Alignment explanation
Indices: 8959--9181 Score: 274
Period size: 67 Copynumber: 3.3 Consensus size: 66
8949 GTTTCTTTTG
8959 AAAAAATCTTTGAGTTTGTTTCTTTGGAAACAAAATTTTGTCTCTCTTAAGATAGTTTCTTTTAA
1 AAAAAATCTTTGAGTTTGTTTCTTTGGAAACAAAATTTTGTCTCTCTTAAGATAGTTTCTTTTAA
9024 A
66 A
*
9025 ACAAAAATCTTTGAGTTTGTTTCTTTGGAAACAAAATTTTGTCTCTCTTAAGATAATTTCTTTTG
1 A-AAAAATCTTTGAGTTTGTTTCTTTGGAAACAAAATTTTGTCTCTCTTAAGATAGTTTCTTTT-
9090 AAA
64 AAA
* * * * * ** *
9093 AAAAAATCTTTGAATCTGTTTCTCTT--AAA-ATGAATTTTGTATCTCTTGAGGCAGTTTC-TCT
1 AAAAAATCTTTGAGTTTGTTTCT-TTGGAAACA-AAATTTTGTCTCTCTTAAGATAGTTTCTTTT
9154 AGAA
64 A-AA
9158 ATACAAAATCTTTGAGTTTGTTTC
1 A-A-AAAATCTTTGAGTTTGTTTC
9182 ACTTGAAATA
Statistics
Matches: 138, Mismatches: 12, Indels: 13
0.85 0.07 0.08
Matches are distributed among these distances:
64 1 0.01
65 6 0.04
66 26 0.19
67 99 0.72
68 6 0.04
ACGTcount: A:0.31, C:0.12, G:0.13, T:0.44
Consensus pattern (66 bp):
AAAAAATCTTTGAGTTTGTTTCTTTGGAAACAAAATTTTGTCTCTCTTAAGATAGTTTCTTTTAA
A
Found at i:9151 original size:66 final size:66
Alignment explanation
Indices: 8944--9193 Score: 246
Period size: 67 Copynumber: 3.8 Consensus size: 66
8934 AAAATCTTTG
*
8944 AGATTGTTTCTTTTG---AAAAAATCTTTGAGTTTGTTTCT-TTGGAAACA-AAATTTTGTCTCT
1 AGATAGTTTCTTTTGAAAAAAAAATCTTTGAGTTTGTTTCTCTT--AAA-ATAAATTTTGTCTCT
9004 CTTA
63 CTTA
9008 AGATAGTTTCTTTT-AAAACAAAAATCTTTGAGTTTGTTTCT-TTGGAAACA-AAATTTTGTCTC
1 AGATAGTTTCTTTTGAAAA-AAAAATCTTTGAGTTTGTTTCTCTT--AAA-ATAAATTTTGTCTC
9070 TCTTA
62 TCTTA
* * * * *
9075 AGATAATTTCTTTTGAAAAAAAAATCTTTGAATCTGTTTCTCTTAAAATGAATTTTGTATCTCTT
1 AGATAGTTTCTTTTGAAAAAAAAATCTTTGAGTTTGTTTCTCTTAAAATAAATTTTGTCTCTCTT
*
9140 G
66 A
** * * * * *
9141 AGGCAGTTTCTCTAGAAATACAAAATCTTTGAGTTTGTTTCACTTGAAATAAA
1 AGATAGTTTCTTTTGAAA-AAAAAATCTTTGAGTTTGTTTCTCTTAAAATAAA
9194 ACCATTTTTG
Statistics
Matches: 160, Mismatches: 18, Indels: 13
0.84 0.09 0.07
Matches are distributed among these distances:
64 13 0.08
65 1 0.01
66 31 0.19
67 109 0.68
68 6 0.04
ACGTcount: A:0.32, C:0.12, G:0.13, T:0.44
Consensus pattern (66 bp):
AGATAGTTTCTTTTGAAAAAAAAATCTTTGAGTTTGTTTCTCTTAAAATAAATTTTGTCTCTCTT
A
Found at i:9759 original size:40 final size:40
Alignment explanation
Indices: 9704--9942 Score: 115
Period size: 40 Copynumber: 5.6 Consensus size: 40
9694 TGGCCAGTAG
* *
9704 TCCTCATCACATAGGAACCGTGTCATCCCCTGACCAGATC
1 TCCTCATCACGTAGGAACCGTGTCATCCCCTGACCAGACC
* * * * *
9744 TCCTCATCATGTAGGAGCCATGTCA-ACCATAGATAACCAG-CC
1 TCCTCATCACGTAGGAACCGTGTCATCCCCT-G---ACCAGACC
* *
9786 GTCCTCATCACGTAGGAACCGTGTTATCGCCCTACCTAAAGATGTCCAGAAC
1 -TCCTCATCACGTAGGAACCGTGTCAT---CC--CCT---GA---CCAGACC
* * * * *
9838 TCTTCATCATGTATGAGCAGTGTCATCCCCTGACCAGACC
1 TCCTCATCACGTAGGAACCGTGTCATCCCCTGACCAGACC
* ** *
9878 TCCTCATCACGTAGGATCCGTGTCATCCTAGATAACCAG-CC
1 TCCTCATCACGTAGGAACCGTGTCATCC--CCTGACCAGACC
*
9919 GTCCTCATCACGTAGGAATCGTGT
1 -TCCTCATCACGTAGGAACCGTGT
9943 TATCACTCCT
Statistics
Matches: 148, Mismatches: 31, Indels: 38
0.68 0.14 0.18
Matches are distributed among these distances:
39 3 0.02
40 51 0.34
41 2 0.01
42 28 0.19
43 28 0.19
46 3 0.02
47 1 0.01
48 3 0.02
49 2 0.01
51 26 0.18
52 1 0.01
ACGTcount: A:0.26, C:0.32, G:0.18, T:0.24
Consensus pattern (40 bp):
TCCTCATCACGTAGGAACCGTGTCATCCCCTGACCAGACC
Found at i:9968 original size:133 final size:134
Alignment explanation
Indices: 9723--10035 Score: 495
Period size: 133 Copynumber: 2.3 Consensus size: 134
9713 CATAGGAACC
*
9723 GTGTCATCCCCTGACCAGATCTCCTCATCATGTAGGAGCCATGTCAACCATAGATAACCAGCCGT
1 GTGTCATCCCCTGACCAGATCTCCTCATCATGTAGGAACCATGTCAACCATAGATAACCAGCCGT
* *
9788 CCTCATCACGTAGGAACCGTGTTATCGCCCTACCTAAAGATGTCCAGAACTCTTCATCATGTATG
66 CCTCATCACGTAGGAACCGTGTTATCACCCTACCTAAAGATGACCAGAACTCTTCATCATGTATG
9853 AGCA
131 AGCA
* * * * *
9857 GTGTCATCCCCTGACCAGACCTCCTCATCACGTAGGATCCGTGTCATCC-TAGATAACCAGCCGT
1 GTGTCATCCCCTGACCAGATCTCCTCATCATGTAGGAACCATGTCAACCATAGATAACCAGCCGT
*
9921 CCTCATCACGTAGGAATCGTGTTATCACTCCT-CCTAAAGATGACCAGAACTCTTCATCATGTAT
66 CCTCATCACGTAGGAACCGTGTTATCAC-CCTACCTAAAGATGACCAGAACTCTTCATCATGTAT
9985 GAGCA
130 GAGCA
* * *
9990 GTGTCATCCCTTGACCAGATTTCCTCATCATGTAGGAACCTTGTCA
1 GTGTCATCCCCTGACCAGATCTCCTCATCATGTAGGAACCATGTCA
10036 CTTTTAGACG
Statistics
Matches: 164, Mismatches: 14, Indels: 3
0.91 0.08 0.02
Matches are distributed among these distances:
133 117 0.71
134 47 0.29
ACGTcount: A:0.26, C:0.31, G:0.18, T:0.26
Consensus pattern (134 bp):
GTGTCATCCCCTGACCAGATCTCCTCATCATGTAGGAACCATGTCAACCATAGATAACCAGCCGT
CCTCATCACGTAGGAACCGTGTTATCACCCTACCTAAAGATGACCAGAACTCTTCATCATGTATG
AGCA
Found at i:10252 original size:3 final size:3
Alignment explanation
Indices: 10246--10283 Score: 67
Period size: 3 Copynumber: 12.3 Consensus size: 3
10236 TTATATATAT
10246 TTA TTA TTA TTA TTA TTA TTA TTA TTTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA T
10284 GGTTATTAAT
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 31 0.91
4 3 0.09
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:10289 original size:19 final size:19
Alignment explanation
Indices: 10232--10295 Score: 64
Period size: 19 Copynumber: 3.5 Consensus size: 19
10222 GGTCTTTTTT
10232 TTATTTA-TATATATT-T-A
1 TTATTTATTAT-TATTATGA
*
10249 TTA-TTATTATTATTATTA
1 TTATTTATTATTATTATGA
*
10267 TTATTTATTATTATTATGG
1 TTATTTATTATTATTATGA
*
10286 TTATTAATTA
1 TTATTTATTA
10296 CATATTACAA
Statistics
Matches: 40, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
16 7 0.17
17 7 0.17
18 4 0.10
19 22 0.55
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.64
Consensus pattern (19 bp):
TTATTTATTATTATTATGA
Found at i:10289 original size:25 final size:25
Alignment explanation
Indices: 10243--10291 Score: 80
Period size: 25 Copynumber: 2.0 Consensus size: 25
10233 TATTTATATA
*
10243 TATTTATTATTATTATTATTATTAT
1 TATTTATTATTATTATGATTATTAT
*
10268 TATTTATTATTATTATGGTTATTA
1 TATTTATTATTATTATGATTATTA
10292 ATTACATATT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.31, C:0.00, G:0.04, T:0.65
Consensus pattern (25 bp):
TATTTATTATTATTATGATTATTAT
Found at i:13120 original size:32 final size:32
Alignment explanation
Indices: 13079--13196 Score: 159
Period size: 32 Copynumber: 3.7 Consensus size: 32
13069 TGAATTTAGA
*
13079 AGTTAAATTGATATTTTATCTAAAGTTTTAAG
1 AGTTAAATTAATATTTTATCTAAAGTTTTAAG
*
13111 AGTTAAATTGATATTTTATCTAAAGTTTTAAG
1 AGTTAAATTAATATTTTATCTAAAGTTTTAAG
* * *
13143 AGTTAAATTAATATTTTATTTTAAAG--GTAAA
1 AGTTAAATTAATATTTTA-TCTAAAGTTTTAAG
*
13174 AATTAAATTAATATTTTATCTAA
1 AGTTAAATTAATATTTTATCTAA
13197 TATTCATGAG
Statistics
Matches: 79, Mismatches: 6, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
30 4 0.05
31 20 0.25
32 49 0.62
33 6 0.08
ACGTcount: A:0.42, C:0.03, G:0.09, T:0.47
Consensus pattern (32 bp):
AGTTAAATTAATATTTTATCTAAAGTTTTAAG
Found at i:19510 original size:18 final size:18
Alignment explanation
Indices: 19487--19525 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
19477 CTCCTAAAAA
19487 TTTAAAATTATTATATAT
1 TTTAAAATTATTATATAT
* *
19505 TTTAAAATTTTTATATGT
1 TTTAAAATTATTATATAT
19523 TTT
1 TTT
19526 TTATTAAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.36, C:0.00, G:0.03, T:0.62
Consensus pattern (18 bp):
TTTAAAATTATTATATAT
Found at i:20950 original size:16 final size:16
Alignment explanation
Indices: 20931--20964 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
20921 CAATATAAGA
20931 ATAAAAATATATTTAT
1 ATAAAAATATATTTAT
*
20947 ATAAAAGTATATTTAT
1 ATAAAAATATATTTAT
20963 AT
1 AT
20965 TTAGATGTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.44
Consensus pattern (16 bp):
ATAAAAATATATTTAT
Found at i:21038 original size:16 final size:18
Alignment explanation
Indices: 21006--21039 Score: 54
Period size: 16 Copynumber: 2.0 Consensus size: 18
20996 TATTAATGTA
21006 TGAATCATTTATATTTTT
1 TGAATCATTTATATTTTT
21024 TGAAT-ATTT-TATTTTT
1 TGAATCATTTATATTTTT
21040 AATAAGAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.44
17 4 0.25
18 5 0.31
ACGTcount: A:0.26, C:0.03, G:0.06, T:0.65
Consensus pattern (18 bp):
TGAATCATTTATATTTTT
Found at i:21514 original size:20 final size:20
Alignment explanation
Indices: 21489--21532 Score: 88
Period size: 20 Copynumber: 2.2 Consensus size: 20
21479 CAAATTTTAT
21489 TTCTTTGTAACTTAATTTTC
1 TTCTTTGTAACTTAATTTTC
21509 TTCTTTGTAACTTAATTTTC
1 TTCTTTGTAACTTAATTTTC
21529 TTCT
1 TTCT
21533 AATTAGGTGG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.18, C:0.16, G:0.05, T:0.61
Consensus pattern (20 bp):
TTCTTTGTAACTTAATTTTC
Found at i:21585 original size:23 final size:21
Alignment explanation
Indices: 21559--21605 Score: 58
Period size: 23 Copynumber: 2.1 Consensus size: 21
21549 GTGTCACCAA
21559 TAACACATATCATGATCATGTGT
1 TAACACATATCA-GATCATG-GT
* *
21582 TAACACATGTCAGATCCTGGT
1 TAACACATATCAGATCATGGT
21603 TAA
1 TAA
21606 ATGATTAATT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 5 0.23
22 6 0.27
23 11 0.50
ACGTcount: A:0.34, C:0.19, G:0.15, T:0.32
Consensus pattern (21 bp):
TAACACATATCAGATCATGGT
Found at i:21717 original size:130 final size:130
Alignment explanation
Indices: 21532--21779 Score: 433
Period size: 130 Copynumber: 1.9 Consensus size: 130
21522 AATTTTCTTC
*
21532 TAATTAGGTGGTGACATGTGTCACCAATAACACATATCATGATCATGTGTTAACACATGTCAGAT
1 TAATTAGGTGGTGACATGTGTCACCAATAACACATATCATGATCATGTGCTAACACATGTCAGAT
** *
21597 CCTGGTTAAATGATTAATTTATTAAATTTTATTTAATTTAGGACCAAATTGATAGCATATATAAA
66 CCTAATTAAATGATTAATTTATTAAATTCTATTTAATTTAGGACCAAATTGATAGCATATATAAA
* * *
21662 TAATTAGGTGGTGACATGTGTCACCAATGACACGTGTCATGATCATGTGCTAACACATGTCAGAT
1 TAATTAGGTGGTGACATGTGTCACCAATAACACATATCATGATCATGTGCTAACACATGTCAGAT
21727 CCTAATTAAATGATTAATTTATTAAATTCTATTTAATTTAGGACCAAATTGAT
66 CCTAATTAAATGATTAATTTATTAAATTCTATTTAATTTAGGACCAAATTGAT
21780 TATATAAATA
Statistics
Matches: 111, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
130 111 1.00
ACGTcount: A:0.35, C:0.13, G:0.15, T:0.36
Consensus pattern (130 bp):
TAATTAGGTGGTGACATGTGTCACCAATAACACATATCATGATCATGTGCTAACACATGTCAGAT
CCTAATTAAATGATTAATTTATTAAATTCTATTTAATTTAGGACCAAATTGATAGCATATATAAA
Found at i:22226 original size:35 final size:35
Alignment explanation
Indices: 22176--22251 Score: 125
Period size: 35 Copynumber: 2.2 Consensus size: 35
22166 AATTGAATTT
* *
22176 AATTGAATTATTTTGGAATTTAGGGTTTAGAATGA
1 AATTGAATTACTTTGGAAATTAGGGTTTAGAATGA
*
22211 AATTGAATTACTTTGGAAATTGGGGTTTAGAATGA
1 AATTGAATTACTTTGGAAATTAGGGTTTAGAATGA
22246 AATTGA
1 AATTGA
22252 GGATTGTTTT
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
35 38 1.00
ACGTcount: A:0.36, C:0.01, G:0.24, T:0.39
Consensus pattern (35 bp):
AATTGAATTACTTTGGAAATTAGGGTTTAGAATGA
Found at i:23840 original size:3 final size:3
Alignment explanation
Indices: 23832--23904 Score: 146
Period size: 3 Copynumber: 24.3 Consensus size: 3
23822 AATTGAGTTG
23832 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
23880 ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA A
23905 ACAACAACAA
Statistics
Matches: 70, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 70 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:30450 original size:23 final size:23
Alignment explanation
Indices: 30424--30467 Score: 72
Period size: 23 Copynumber: 1.9 Consensus size: 23
30414 AACAATCAAA
30424 ATGCAT-AAAGAACATACTAAAAC
1 ATGCATAAAAG-ACATACTAAAAC
30447 ATGCATAAAAGACATACTAAA
1 ATGCATAAAAGACATACTAAA
30468 CACTCTAAGA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
23 16 0.80
24 4 0.20
ACGTcount: A:0.57, C:0.16, G:0.09, T:0.18
Consensus pattern (23 bp):
ATGCATAAAAGACATACTAAAAC
Found at i:35032 original size:42 final size:42
Alignment explanation
Indices: 34947--35039 Score: 114
Period size: 42 Copynumber: 2.2 Consensus size: 42
34937 TTAAGGGAAT
* * * * *
34947 GGATCAATCCTTTTCATCAATGGATCAATCATTTTGGTGAAG
1 GGATCGATCCTTTACATCAAGGGATCAATCATTTTCGTCAAG
* * *
34989 GGATCGATCCTTTACATCTAGGGATCGATCATTTTCTTCAAG
1 GGATCGATCCTTTACATCAAGGGATCAATCATTTTCGTCAAG
35031 GGATCGATC
1 GGATCGATC
35040 TAAAACTTAC
Statistics
Matches: 43, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
42 43 1.00
ACGTcount: A:0.26, C:0.19, G:0.20, T:0.34
Consensus pattern (42 bp):
GGATCGATCCTTTACATCAAGGGATCAATCATTTTCGTCAAG
Found at i:35036 original size:21 final size:21
Alignment explanation
Indices: 34947--35039 Score: 87
Period size: 21 Copynumber: 4.4 Consensus size: 21
34937 TTAAGGGAAT
* * *
34947 GGATCAATCCTTTTCATCAAT
1 GGATCGATCATTTTCATCAAG
* ** *
34968 GGATCAATCATTTTGGTGAAG
1 GGATCGATCATTTTCATCAAG
* * *
34989 GGATCGATCCTTTACATCTAG
1 GGATCGATCATTTTCATCAAG
*
35010 GGATCGATCATTTTCTTCAAG
1 GGATCGATCATTTTCATCAAG
35031 GGATCGATC
1 GGATCGATC
35040 TAAAACTTAC
Statistics
Matches: 56, Mismatches: 16, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
21 56 1.00
ACGTcount: A:0.26, C:0.19, G:0.20, T:0.34
Consensus pattern (21 bp):
GGATCGATCATTTTCATCAAG
Found at i:35434 original size:21 final size:21
Alignment explanation
Indices: 35409--35462 Score: 72
Period size: 21 Copynumber: 2.6 Consensus size: 21
35399 GCTACCATTG
* *
35409 ATTGTCATGTTAGCATCATAA
1 ATTGTCATGTCAGCACCATAA
* *
35430 ATTGTCATGTCAGTACCGTAA
1 ATTGTCATGTCAGCACCATAA
35451 ATTGTCATGTCA
1 ATTGTCATGTCA
35463 ACACTGTAAC
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.30, C:0.17, G:0.17, T:0.37
Consensus pattern (21 bp):
ATTGTCATGTCAGCACCATAA
Found at i:35471 original size:21 final size:21
Alignment explanation
Indices: 35409--35471 Score: 63
Period size: 21 Copynumber: 3.0 Consensus size: 21
35399 GCTACCATTG
* * * *
35409 ATTGTCATGTTAGCATCATAA
1 ATTGTCATGTCAACACCGTAA
**
35430 ATTGTCATGTCAGTACCGTAA
1 ATTGTCATGTCAACACCGTAA
*
35451 ATTGTCATGTCAACACTGTAA
1 ATTGTCATGTCAACACCGTAA
35472 CAGTCAACGA
Statistics
Matches: 35, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.32, C:0.17, G:0.16, T:0.35
Consensus pattern (21 bp):
ATTGTCATGTCAACACCGTAA
Found at i:35811 original size:21 final size:21
Alignment explanation
Indices: 35781--35820 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
35771 AATTAGTTAA
*
35781 AAAATTAAAGACAAATTATTT
1 AAAATAAAAGACAAATTATTT
**
35802 AAAATAAAAGGTAAATTAT
1 AAAATAAAAGACAAATTAT
35821 ACCATTGACC
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.60, C:0.03, G:0.07, T:0.30
Consensus pattern (21 bp):
AAAATAAAAGACAAATTATTT
Found at i:38156 original size:34 final size:37
Alignment explanation
Indices: 38112--38213 Score: 158
Period size: 34 Copynumber: 2.8 Consensus size: 37
38102 TTTCGTCCTA
*
38112 CTAGGATTCAAACTCCTAAAAATAGGATAGA-A-TTT
1 CTAGGATTCAAACTCCTAAAAATATGATAGACATTTT
38147 -TAGGATTCAAACTCCTAAAAATATGATA-ACATTTT
1 CTAGGATTCAAACTCCTAAAAATATGATAGACATTTT
38182 GCTAGGATTCAAACTCCTAAAAATATGATAGA
1 -CTAGGATTCAAACTCCTAAAAATATGATAGA
38214 GTTCTACTAA
Statistics
Matches: 61, Mismatches: 1, Indels: 7
0.88 0.01 0.10
Matches are distributed among these distances:
33 1 0.02
34 28 0.46
35 3 0.05
37 28 0.46
38 1 0.02
ACGTcount: A:0.43, C:0.15, G:0.13, T:0.29
Consensus pattern (37 bp):
CTAGGATTCAAACTCCTAAAAATATGATAGACATTTT
Found at i:38237 original size:37 final size:37
Alignment explanation
Indices: 38109--38239 Score: 162
Period size: 37 Copynumber: 3.6 Consensus size: 37
38099 ATTTTTCGTC
*
38109 CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
1 CTACTAGGATTCAAACTCCTAAAAATATGATAGAATT
38146 -T--TAGGATTCAAACTCCTAAAAATATGATA-ACATT
1 CTACTAGGATTCAAACTCCTAAAAATATGATAGA-ATT
* * *
38180 TTGCTAGGATTCAAACTCCTAAAAATATGATAGAGTT
1 CTACTAGGATTCAAACTCCTAAAAATATGATAGAATT
* * *
38217 CTACTAAGATTTAAATTCCTAAA
1 CTACTAGGATTCAAACTCCTAAA
38240 GATAGGATCC
Statistics
Matches: 82, Mismatches: 7, Indels: 10
0.83 0.07 0.10
Matches are distributed among these distances:
33 1 0.01
34 30 0.37
35 1 0.01
36 1 0.01
37 48 0.59
38 1 0.01
ACGTcount: A:0.42, C:0.15, G:0.11, T:0.31
Consensus pattern (37 bp):
CTACTAGGATTCAAACTCCTAAAAATATGATAGAATT
Found at i:38644 original size:18 final size:17
Alignment explanation
Indices: 38605--38647 Score: 61
Period size: 18 Copynumber: 2.5 Consensus size: 17
38595 ATTATATGGA
38605 TATT-TTATTCATTTAT
1 TATTATTATTCATTTAT
*
38621 TTTTATTATTCATGTTAT
1 TATTATTATTCAT-TTAT
38639 TATTATTAT
1 TATTATTAT
38648 ATGTATATAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
16 3 0.13
17 8 0.35
18 12 0.52
ACGTcount: A:0.26, C:0.05, G:0.02, T:0.67
Consensus pattern (17 bp):
TATTATTATTCATTTAT
Found at i:42347 original size:16 final size:16
Alignment explanation
Indices: 42321--42373 Score: 54
Period size: 17 Copynumber: 3.2 Consensus size: 16
42311 AGATCCAATT
42321 AAGAACAAAAAAG-AA
1 AAGAACAAAAAAGCAA
42336 AAGAAGCAAAAAAGCAA
1 AAGAA-CAAAAAAGCAA
* * *
42353 AAAAAAAAACAAAGAAA
1 AAGAACAAA-AAAGCAA
42370 AAGA
1 AAGA
42374 GAAACAAGAA
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
15 5 0.16
16 11 0.35
17 15 0.48
ACGTcount: A:0.79, C:0.08, G:0.13, T:0.00
Consensus pattern (16 bp):
AAGAACAAAAAAGCAA
Found at i:42370 original size:23 final size:23
Alignment explanation
Indices: 42344--42394 Score: 59
Period size: 23 Copynumber: 2.2 Consensus size: 23
42334 AAAAGAAGCA
42344 AAAAAGCAAAAAAAAAAAC-AAAG
1 AAAAAG-AAAAAAAAAAACAAAAG
* * *
42367 AAAAAGAGAAACAAGAACAAAAG
1 AAAAAGAAAAAAAAAAACAAAAG
42390 AAAAA
1 AAAAA
42395 AAGAGTAAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
22 9 0.38
23 15 0.62
ACGTcount: A:0.80, C:0.08, G:0.12, T:0.00
Consensus pattern (23 bp):
AAAAAGAAAAAAAAAAACAAAAG
Found at i:42370 original size:24 final size:24
Alignment explanation
Indices: 42326--42397 Score: 58
Period size: 24 Copynumber: 3.0 Consensus size: 24
42316 CAATTAAGAA
* *
42326 CAAAAAAGAAAAGAAGCAAAAAAG
1 CAAAAAAAAAAAAAAGCAAAAAAG
42350 CAAAAAAAAAAACAAAG-AAAAAGAG
1 CAAAAAAAAAAA-AAAGCAAAAA-AG
* * * *
42375 -AAACAAGAACAAAAGAAAAAAAG
1 CAAAAAAAAAAAAAAGCAAAAAAG
42398 AGTAAAAATC
Statistics
Matches: 40, Mismatches: 5, Indels: 7
0.77 0.10 0.13
Matches are distributed among these distances:
23 6 0.15
24 29 0.73
25 5 0.12
ACGTcount: A:0.78, C:0.08, G:0.14, T:0.00
Consensus pattern (24 bp):
CAAAAAAAAAAAAAAGCAAAAAAG
Found at i:43081 original size:22 final size:22
Alignment explanation
Indices: 43056--43126 Score: 117
Period size: 22 Copynumber: 3.2 Consensus size: 22
43046 CCATCAATCT
43056 TTTGAGCATCCAAA-GTCAAACC
1 TTTGAGCAT-CAAATGTCAAACC
43078 TTTGAGCATCAAATGTCAAACC
1 TTTGAGCATCAAATGTCAAACC
*
43100 TTTGAGCATCAAATGCCAAACC
1 TTTGAGCATCAAATGTCAAACC
43122 TTTGA
1 TTTGA
43127 CCAAACACAA
Statistics
Matches: 47, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
21 4 0.09
22 43 0.91
ACGTcount: A:0.35, C:0.24, G:0.14, T:0.27
Consensus pattern (22 bp):
TTTGAGCATCAAATGTCAAACC
Found at i:43562 original size:17 final size:18
Alignment explanation
Indices: 43540--43574 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
43530 TTTAACATCA
*
43540 ATATTGGGGCAT-TTTGG
1 ATATTGAGGCATCTTTGG
43557 ATATTGAGGCATCTTTGG
1 ATATTGAGGCATCTTTGG
43575 GGATTCAACA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 11 0.69
18 5 0.31
ACGTcount: A:0.20, C:0.09, G:0.31, T:0.40
Consensus pattern (18 bp):
ATATTGAGGCATCTTTGG
Found at i:45708 original size:15 final size:15
Alignment explanation
Indices: 45688--45717 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
45678 AGCTGGGTGT
*
45688 GCGGATGCGGGGCGG
1 GCGGATGCAGGGCGG
45703 GCGGATGCAGGGCGG
1 GCGGATGCAGGGCGG
45718 ATGCGGGGCG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.10, C:0.20, G:0.63, T:0.07
Consensus pattern (15 bp):
GCGGATGCAGGGCGG
Found at i:47115 original size:20 final size:20
Alignment explanation
Indices: 47074--47115 Score: 50
Period size: 20 Copynumber: 2.1 Consensus size: 20
47064 ATATAAAAGG
*
47074 TAAATTATACGTTTTGTACT
1 TAAATTATACGTTTTATACT
*
47094 TAAATTATCAC-TTTTATCCT
1 TAAATTAT-ACGTTTTATACT
47114 TA
1 TA
47116 CGTGACATGA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 17 0.89
21 2 0.11
ACGTcount: A:0.31, C:0.14, G:0.05, T:0.50
Consensus pattern (20 bp):
TAAATTATACGTTTTATACT
Found at i:49504 original size:20 final size:21
Alignment explanation
Indices: 49479--49571 Score: 100
Period size: 21 Copynumber: 4.5 Consensus size: 21
49469 TTTTCCCAAT
*
49479 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
49499 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
*
49520 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
49540 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
49561 TCGCAATGCGA
1 TCGCAATGCGA
49572 TACTGACTAT
Statistics
Matches: 58, Mismatches: 13, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
20 27 0.47
21 31 0.53
ACGTcount: A:0.40, C:0.18, G:0.25, T:0.17
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:49524 original size:41 final size:41
Alignment explanation
Indices: 49479--49571 Score: 186
Period size: 41 Copynumber: 2.3 Consensus size: 41
49469 TTTTCCCAAT
49479 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
49520 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
49561 TCGCAATGCGA
1 TCGCAATGCGA
49572 TACTGACTAT
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.40, C:0.18, G:0.25, T:0.17
Consensus pattern (41 bp):
TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
Found at i:49584 original size:41 final size:41
Alignment explanation
Indices: 49498--49632 Score: 132
Period size: 41 Copynumber: 3.3 Consensus size: 41
49488 GAATAAGTAA
* *
49498 ATCGCAACGCGAATTGGGAAAATCGCAATGCGAATA-AGTA-A
1 ATCGCAACGCGAATTGGGAAAATCGCAATGCG-ATACTG-ACT
49539 ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTGACT
1 ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTGACT
* * ** * * *
49580 ATCGCAATGCGATAAT-ACAAAATCGCAACGAGATACTTACT
1 ATCGCAACGCGA-ATTGGGAAAATCGCAATGCGATACTGACT
*
49621 TTCGCAACGCGA
1 ATCGCAACGCGA
49633 TACTGACTTT
Statistics
Matches: 80, Mismatches: 11, Indels: 6
0.82 0.11 0.06
Matches are distributed among these distances:
40 4 0.05
41 74 0.93
42 2 0.03
ACGTcount: A:0.38, C:0.21, G:0.21, T:0.19
Consensus pattern (41 bp):
ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTGACT
Found at i:49585 original size:20 final size:20
Alignment explanation
Indices: 49560--49674 Score: 115
Period size: 20 Copynumber: 5.7 Consensus size: 20
49550 AATTGGGAAA
*
49560 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* * *
49580 ATCGCAATGCGATAAT-ACAAA
1 ATCGCAACGCGATACTGAC--T
* *
49601 ATCGCAACGAGATACTTACT
1 ATCGCAACGCGATACTGACT
*
49621 TTCGCAACGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* *
49641 TTCGCAACGCGATTCTGACT
1 ATCGCAACGCGATACTGACT
*
49661 TTCGCAACGCGATA
1 ATCGCAACGCGATA
49675 ATACATAATC
Statistics
Matches: 81, Mismatches: 11, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
19 2 0.02
20 64 0.79
21 13 0.16
22 2 0.02
ACGTcount: A:0.31, C:0.26, G:0.18, T:0.24
Consensus pattern (20 bp):
ATCGCAACGCGATACTGACT
Found at i:49633 original size:41 final size:41
Alignment explanation
Indices: 49557--49688 Score: 151
Period size: 41 Copynumber: 3.2 Consensus size: 41
49547 GCGAATTGGG
* * *
49557 AAAATCGCAATGCGATACTGACTATCGCAATGCGATAATAC
1 AAAATCGCAACGCGATACTGACTTTCGCAACGCGATAATAC
* * *
49598 AAAATCGCAACGAGATACTTACTTTCGCAACGCGATACTGAC
1 AAAATCGCAACGCGATACTGACTTTCGCAACGCGATAAT-AC
** *
49640 --TTTCGCAACGCGATTCTGACTTTCGCAACGCGATAATAC
1 AAAATCGCAACGCGATACTGACTTTCGCAACGCGATAATAC
*
49679 ATAATCGCAA
1 AAAATCGCAA
49689 TACGATTTTC
Statistics
Matches: 74, Mismatches: 14, Indels: 6
0.79 0.15 0.06
Matches are distributed among these distances:
39 2 0.03
40 31 0.42
41 39 0.53
42 2 0.03
ACGTcount: A:0.35, C:0.25, G:0.17, T:0.23
Consensus pattern (41 bp):
AAAATCGCAACGCGATACTGACTTTCGCAACGCGATAATAC
Found at i:49890 original size:22 final size:22
Alignment explanation
Indices: 49862--49905 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
49852 CACTCTCTCA
49862 CCCATCTCCGACGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
*
49884 CCCATCTCCGGCGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
49906 TATCTCCATC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.20, C:0.45, G:0.16, T:0.18
Consensus pattern (22 bp):
CCCATCTCCGACGAAATCCGTC
Found at i:50205 original size:19 final size:20
Alignment explanation
Indices: 50145--50207 Score: 76
Period size: 20 Copynumber: 3.2 Consensus size: 20
50135 GCGATTTTAG
50145 TTTCGCGTTGCGATAGTCGA-
1 TTTCGCGTTGCGATAGTC-AT
*
50165 ATTCGCGTTGCGATAGTCAT
1 TTTCGCGTTGCGATAGTCAT
* *
50185 TTTCGTGTTGCGAT-TTCAT
1 TTTCGCGTTGCGATAGTCAT
50204 TTTC
1 TTTC
50208 AGAAAATTCT
Statistics
Matches: 38, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
19 9 0.24
20 29 0.76
ACGTcount: A:0.14, C:0.19, G:0.24, T:0.43
Consensus pattern (20 bp):
TTTCGCGTTGCGATAGTCAT
Found at i:51533 original size:18 final size:18
Alignment explanation
Indices: 51512--51556 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
51502 TCCACTTCGG
*
51512 GAGCCATCACCTCGCCCA
1 GAGCCATCACCTCACCCA
*
51530 GAGCTATCACCTCACCCA
1 GAGCCATCACCTCACCCA
51548 GAGCCATCA
1 GAGCCATCA
51557 TCTGATCGAC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.27, C:0.44, G:0.16, T:0.13
Consensus pattern (18 bp):
GAGCCATCACCTCACCCA
Found at i:52092 original size:19 final size:20
Alignment explanation
Indices: 52038--52104 Score: 73
Period size: 20 Copynumber: 3.4 Consensus size: 20
52028 TAGTTTACTT
* *
52038 TCGCAACACGAAAATGACTA
1 TCGCAACGCGGAAATGACTA
*
52058 TCGCAACGCGGAAATGGCTA
1 TCGCAACGCGGAAATGACTA
* **
52078 TCGCAATGC-GAAATGAAAA
1 TCGCAACGCGGAAATGACTA
52097 TCGCAACG
1 TCGCAACG
52105 ACAAAATCGC
Statistics
Matches: 39, Mismatches: 8, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
19 14 0.36
20 25 0.64
ACGTcount: A:0.39, C:0.24, G:0.22, T:0.15
Consensus pattern (20 bp):
TCGCAACGCGGAAATGACTA
Found at i:52112 original size:14 final size:14
Alignment explanation
Indices: 52093--52150 Score: 62
Period size: 14 Copynumber: 3.9 Consensus size: 14
52083 ATGCGAAATG
52093 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
52107 AAAATCGCAACGCGAA
1 AAAATCGCAA--CGAC
*
52123 ATGAAATCACAACGAC
1 A--AAATCGCAACGAC
52139 AAAATCGCAACG
1 AAAATCGCAACG
52151 CGAAATGAAA
Statistics
Matches: 36, Mismatches: 4, Indels: 8
0.75 0.08 0.17
Matches are distributed among these distances:
14 20 0.56
16 8 0.22
18 8 0.22
ACGTcount: A:0.50, C:0.26, G:0.16, T:0.09
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:52122 original size:33 final size:33
Alignment explanation
Indices: 52077--52167 Score: 157
Period size: 32 Copynumber: 2.8 Consensus size: 33
52067 GGAAATGGCT
*
52077 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGACAAA
*
52110 ATCGCAACGCGAAATG-AAATCACAACGACAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGACAAA
52142 ATCGCAACGCGAAATGAAAATCGCAA
1 ATCGCAACGCGAAATGAAAATCGCAA
52168 TGCGATTTGT
Statistics
Matches: 54, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
32 31 0.57
33 23 0.43
ACGTcount: A:0.48, C:0.23, G:0.18, T:0.11
Consensus pattern (33 bp):
ATCGCAACGCGAAATGAAAATCGCAACGACAAA
Found at i:52135 original size:18 final size:18
Alignment explanation
Indices: 52038--52172 Score: 79
Period size: 19 Copynumber: 7.6 Consensus size: 18
52028 TAGTTTACTT
* *
52038 TCGCAACACGAAAATGACTA
1 TCGCAACGCG-AAATGA-AA
**
52058 TCGCAACGCGGAAATGGCTA
1 TCGCAACGC-GAAAT-GAAA
*
52078 TCGCAATGCGAAATGAAAA
1 TCGCAACGCGAAATG-AAA
*
52097 TCGCAA--CGACA--AAA
1 TCGCAACGCGAAATGAAA
52111 TCGCAACGCGAAATGAAA
1 TCGCAACGCGAAATGAAA
* *
52129 TCACAA--CGACA--AAA
1 TCGCAACGCGAAATGAAA
52143 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATG-AAA
*
52162 TCGCAATGCGA
1 TCGCAACGCGA
52173 TTTGTGTTTC
Statistics
Matches: 91, Mismatches: 12, Indels: 25
0.71 0.09 0.20
Matches are distributed among these distances:
14 17 0.19
16 12 0.13
17 4 0.04
18 9 0.10
19 25 0.27
20 22 0.24
21 2 0.02
ACGTcount: A:0.44, C:0.24, G:0.20, T:0.13
Consensus pattern (18 bp):
TCGCAACGCGAAATGAAA
Found at i:52207 original size:14 final size:14
Alignment explanation
Indices: 52184--52241 Score: 62
Period size: 14 Copynumber: 3.9 Consensus size: 14
52174 TTGTGTTTCG
52184 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
* *
52198 CGTTGTGATTTCATTT
1 CGTTGCGATTT--TGT
52214 CGCGTTGCGATTTTGT
1 --CGTTGCGATTTTGT
52230 CGTTGCGATTTT
1 CGTTGCGATTTT
52242 CATTTCGCAT
Statistics
Matches: 36, Mismatches: 4, Indels: 8
0.75 0.08 0.17
Matches are distributed among these distances:
14 22 0.61
16 4 0.11
18 10 0.28
ACGTcount: A:0.09, C:0.16, G:0.26, T:0.50
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:52215 original size:32 final size:33
Alignment explanation
Indices: 52179--52257 Score: 133
Period size: 32 Copynumber: 2.4 Consensus size: 33
52169 GCGATTTGTG
*
52179 TTTCGCGTTGCGATTTTGTCGTTGTGA-TTTCA
1 TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
52211 TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
1 TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
*
52244 TTTCGCATTGCGAT
1 TTTCGCGTTGCGAT
52258 AGCCATTTCC
Statistics
Matches: 44, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
32 26 0.59
33 18 0.41
ACGTcount: A:0.10, C:0.18, G:0.24, T:0.48
Consensus pattern (33 bp):
TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
Found at i:52256 original size:19 final size:19
Alignment explanation
Indices: 52230--52296 Score: 89
Period size: 19 Copynumber: 3.5 Consensus size: 19
52220 GCGATTTTGT
**
52230 CGTTGCGATTTTCATTTCG
1 CGTTGCGATAGTCATTTCG
* *
52249 CATTGCGATAGCCATTTCCG
1 CGTTGCGATAGTCATTT-CG
52269 CGTTGCGATAGTCATTTCG
1 CGTTGCGATAGTCATTTCG
52288 CGTTGCGAT
1 CGTTGCGAT
52297 TTTAAGTTTC
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
19 24 0.59
20 17 0.41
ACGTcount: A:0.15, C:0.24, G:0.24, T:0.37
Consensus pattern (19 bp):
CGTTGCGATAGTCATTTCG
Found at i:52276 original size:20 final size:19
Alignment explanation
Indices: 52242--52296 Score: 83
Period size: 20 Copynumber: 2.8 Consensus size: 19
52232 TTGCGATTTT
*
52242 CATTTCGCATTGCGATAGC
1 CATTTCGCGTTGCGATAGC
*
52261 CATTTCCGCGTTGCGATAGT
1 CATTT-CGCGTTGCGATAGC
52281 CATTTCGCGTTGCGAT
1 CATTTCGCGTTGCGAT
52297 TTTAAGTTTC
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
19 16 0.48
20 17 0.52
ACGTcount: A:0.16, C:0.25, G:0.24, T:0.35
Consensus pattern (19 bp):
CATTTCGCGTTGCGATAGC
Found at i:54183 original size:14 final size:14
Alignment explanation
Indices: 54164--54199 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
54154 ATTGTTTAAT
54164 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
* *
54178 TGATTTGTAAATGT
1 TGATTTGTAAAAGA
54192 TGATTTGT
1 TGATTTGT
54200 TTAATTGATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.22, T:0.47
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:54325 original size:14 final size:14
Alignment explanation
Indices: 54306--54359 Score: 54
Period size: 14 Copynumber: 3.5 Consensus size: 14
54296 CGAAATGGCT
*
54306 ATCGCAACGAGAGA
1 ATCGCAACGAGAAA
54320 ATCGCAATGCGAAATGAAA
1 ATCGCAA--CG--A-GAAA
54339 ATCGCAACGAGAAA
1 ATCGCAACGAGAAA
54353 ATCGCAA
1 ATCGCAA
54360 TGCGATTTTC
Statistics
Matches: 34, Mismatches: 1, Indels: 10
0.76 0.02 0.22
Matches are distributed among these distances:
14 18 0.53
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.29
ACGTcount: A:0.46, C:0.20, G:0.22, T:0.11
Consensus pattern (14 bp):
ATCGCAACGAGAAA
Found at i:54343 original size:19 final size:17
Alignment explanation
Indices: 54319--54364 Score: 53
Period size: 14 Copynumber: 2.8 Consensus size: 17
54309 GCAACGAGAG
54319 AATCGCAATGCGAAATGAA
1 AATCGCAATGCG-AA-GAA
54338 AATCGCAA--CG-AGAA
1 AATCGCAATGCGAAGAA
54352 AATCGCAATGCGA
1 AATCGCAATGCGA
54365 TTTTCATTTC
Statistics
Matches: 24, Mismatches: 0, Indels: 8
0.75 0.00 0.25
Matches are distributed among these distances:
14 11 0.46
15 1 0.04
16 2 0.08
17 2 0.08
19 8 0.33
ACGTcount: A:0.46, C:0.20, G:0.22, T:0.13
Consensus pattern (17 bp):
AATCGCAATGCGAAGAA
Found at i:54378 original size:33 final size:33
Alignment explanation
Indices: 54287--54364 Score: 120
Period size: 33 Copynumber: 2.4 Consensus size: 33
54277 AAAACAGACT
*** *
54287 ATCGCAATGCGAAATGGCTATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAAA
54320 ATCGCAATGCGAAATGAAAATCGCAACGAGAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAAA
54353 ATCGCAATGCGA
1 ATCGCAATGCGA
54365 TTTTCATTTC
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 41 1.00
ACGTcount: A:0.41, C:0.21, G:0.24, T:0.14
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAAA
Found at i:54408 original size:20 final size:20
Alignment explanation
Indices: 54383--54460 Score: 147
Period size: 20 Copynumber: 3.9 Consensus size: 20
54373 TCGCAATGCG
*
54383 ATTTTCTCGTTGCGATAGCC
1 ATTTTCGCGTTGCGATAGCC
54403 ATTTTCGCGTTGCGATAGCC
1 ATTTTCGCGTTGCGATAGCC
54423 ATTTTCGCGTTGCGATAGCC
1 ATTTTCGCGTTGCGATAGCC
54443 ATTTTCGCGTTGCGATAG
1 ATTTTCGCGTTGCGATAG
54461 TCAAATGAAT
Statistics
Matches: 57, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
20 57 1.00
ACGTcount: A:0.15, C:0.23, G:0.24, T:0.37
Consensus pattern (20 bp):
ATTTTCGCGTTGCGATAGCC
Found at i:55544 original size:24 final size:24
Alignment explanation
Indices: 55517--55570 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 24
55507 GTATTCGAAA
* * *
55517 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATATTGGTAAATACACGGAC
*
55541 TTTGATATTGGTAAATACACGGAT
1 TTTGATATTGGTAAATACACGGAC
55565 TTTGAT
1 TTTGAT
55571 GATGTTTCAG
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.26, C:0.15, G:0.20, T:0.39
Consensus pattern (24 bp):
TTTGATATTGGTAAATACACGGAC
Found at i:55762 original size:12 final size:12
Alignment explanation
Indices: 55745--55769 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
55735 ATATAATCCT
55745 GAAGAAGAAAAA
1 GAAGAAGAAAAA
55757 GAAGAAGAAAAA
1 GAAGAAGAAAAA
55769 G
1 G
55770 TCCCCGAAGA
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:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:58101 original size:33 final size:33
Alignment explanation
Indices: 58059--58185 Score: 202
Period size: 33 Copynumber: 3.8 Consensus size: 33
58049 GAAAATTACT
58059 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
**
58092 ATCGCAATGCGAAATGAAAATCGCAACGCTA-A
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
* *
58124 TTTCGCAATGCGAAATGAAAATCGCAACGAGGGA
1 -ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
58158 ATCGCAATGCGAAATGAAAATCGCAACG
1 ATCGCAATGCGAAATGAAAATCGCAACG
58186 CAAATTTAAT
Statistics
Matches: 85, Mismatches: 7, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
32 1 0.01
33 83 0.98
34 1 0.01
ACGTcount: A:0.43, C:0.20, G:0.23, T:0.15
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:58166 original size:66 final size:66
Alignment explanation
Indices: 58060--58192 Score: 248
Period size: 66 Copynumber: 2.0 Consensus size: 66
58050 AAAATTACTA
*
58060 TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCTAAT
1 TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCAAAT
58125 T
66 T
*
58126 TCGCAATGCGAAATGAAAATCGCAACGAGGGAATCGCAATGCGAAATGAAAATCGCAACGCAAAT
1 TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCAAAT
58191 T
66 T
58192 T
1 T
58193 AATTTCACGT
Statistics
Matches: 65, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
66 65 1.00
ACGTcount: A:0.42, C:0.20, G:0.22, T:0.17
Consensus pattern (66 bp):
TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCAAAT
T
Found at i:58387 original size:14 final size:14
Alignment explanation
Indices: 58368--58404 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
58358 CATCAATTAA
58368 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
58382 ACAAATCACCTTTT
1 ACAAATCAACTTTT
58396 ACAAATCAA
1 ACAAATCAA
58405 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.24, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:59826 original size:21 final size:21
Alignment explanation
Indices: 59760--59826 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
59750 GTGAATCGGG
*
59760 CTCTTGAATGGTGGGA-GGGA
1 CTCTTGAACGGTGGGAGGGGA
* * ** * *
59780 CCTCTTCAACGATGACAGTGGC
1 -CTCTTGAACGGTGGGAGGGGA
59802 CTCTTGAACGGTGGGAGGGGA
1 CTCTTGAACGGTGGGAGGGGA
59823 CTCT
1 CTCT
59827 CGAGGAATGA
Statistics
Matches: 32, Mismatches: 13, Indels: 2
0.68 0.28 0.04
Matches are distributed among these distances:
21 30 0.94
22 2 0.06
ACGTcount: A:0.19, C:0.21, G:0.36, T:0.24
Consensus pattern (21 bp):
CTCTTGAACGGTGGGAGGGGA
Found at i:59845 original size:42 final size:41
Alignment explanation
Indices: 59760--59882 Score: 113
Period size: 42 Copynumber: 2.9 Consensus size: 41
59750 GTGAATCGGG
* * * *
59760 CTCTTGAATGGTGGGA-GGGACCTCTTCAACGATGACAGTGGC
1 CTCTTGAACGGTGGGAGGGGA-CTC-TCGAGGATGACAGGGGC
*
59802 CTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGGGGC
1 CTCTTGAACGGTGGGAGGGGACTCTCGAGG-ATGACAGGGGC
* * * * *
59844 CTCTTCAACGATAGGAGTGGACTCTTGAGGGATGACAGG
1 CTCTTGAACGGTGGGAGGGGACTCTCGA-GGATGACAGG
59883 CGAGTCGGGC
Statistics
Matches: 67, Mismatches: 11, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
41 4 0.06
42 57 0.85
43 6 0.09
ACGTcount: A:0.23, C:0.19, G:0.37, T:0.22
Consensus pattern (41 bp):
CTCTTGAACGGTGGGAGGGGACTCTCGAGGATGACAGGGGC
Found at i:61922 original size:20 final size:19
Alignment explanation
Indices: 61891--62084 Score: 94
Period size: 19 Copynumber: 10.8 Consensus size: 19
61881 TCTTTTGGTT
61891 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGA
*
61910 GATAATGAGAATCGCAACGCA
1 GA-AATGAAAATCGCAACG-A
**
61931 GAAATGACTATCGCAAC--
1 GAAATGAAAATCGCAACGA
*
61948 G--AT-AGAATCGCAACGA
1 GAAATGAAAATCGCAACGA
*
61964 G--A-G--AATCGCAACGC
1 GAAATGAAAATCGCAACGA
**
61978 GAAATGACTATCG---CGA
1 GAAATGAAAATCGCAACGA
** * *
61994 -CCA-GACAATCGCAACGC
1 GAAATGAAAATCGCAACGA
*
62011 GAAATGAAAATCGCAACCGC
1 GAAATGAAAATCGCAA-CGA
* *
62031 GAAATAAAAATCGCAACGC
1 GAAATGAAAATCGCAACGA
* *
62050 GAAATAAAAATCGCAACGC
1 GAAATGAAAATCGCAACGA
* *
62069 GAAATAAAAATTGCAA
1 GAAATGAAAATCGCAA
62085 TGCGATTTTT
Statistics
Matches: 142, Mismatches: 17, Indels: 32
0.74 0.09 0.17
Matches are distributed among these distances:
14 27 0.19
15 3 0.02
16 5 0.04
17 4 0.03
18 1 0.01
19 53 0.37
20 46 0.32
21 3 0.02
ACGTcount: A:0.46, C:0.22, G:0.20, T:0.12
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGA
Found at i:61959 original size:14 final size:14
Alignment explanation
Indices: 61940--61976 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
61930 AGAAATGACT
*
61940 ATCGCAACGATAGA
1 ATCGCAACGAGAGA
61954 ATCGCAACGAGAGA
1 ATCGCAACGAGAGA
61968 ATCGCAACG
1 ATCGCAACG
61977 CGAAATGACT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.41, C:0.24, G:0.24, T:0.11
Consensus pattern (14 bp):
ATCGCAACGAGAGA
Found at i:61991 original size:47 final size:48
Alignment explanation
Indices: 61916--62009 Score: 145
Period size: 47 Copynumber: 2.0 Consensus size: 48
61906 ACGAGATAAT
* * *
61916 GAGAATCGCAACGCAGAAATGACTATCGCAACGATAGAATCGCAACGA
1 GAGAATCGCAACGCAGAAATGACTATCGCAACCAGACAATCGCAACGA
*
61964 GAGAATCGCAACGC-GAAATGACTATCGCGACCAGACAATCGCAACG
1 GAGAATCGCAACGCAGAAATGACTATCGCAACCAGACAATCGCAACG
62010 CGAAATGAAA
Statistics
Matches: 42, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
47 28 0.67
48 14 0.33
ACGTcount: A:0.39, C:0.26, G:0.23, T:0.12
Consensus pattern (48 bp):
GAGAATCGCAACGCAGAAATGACTATCGCAACCAGACAATCGCAACGA
Found at i:62022 original size:19 final size:19
Alignment explanation
Indices: 62000--62089 Score: 144
Period size: 19 Copynumber: 4.7 Consensus size: 19
61990 GCGACCAGAC
*
62000 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATAAA
62019 AATCGCAACCGCGAAATAAA
1 AATCGCAA-CGCGAAATAAA
62039 AATCGCAACGCGAAATAAA
1 AATCGCAACGCGAAATAAA
62058 AATCGCAACGCGAAATAAA
1 AATCGCAACGCGAAATAAA
* *
62077 AATTGCAATGCGA
1 AATCGCAACGCGA
62090 TTTTTGTTTC
Statistics
Matches: 67, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
19 49 0.73
20 18 0.27
ACGTcount: A:0.49, C:0.21, G:0.18, T:0.12
Consensus pattern (19 bp):
AATCGCAACGCGAAATAAA
Found at i:62024 original size:33 final size:33
Alignment explanation
Indices: 61953--62028 Score: 107
Period size: 33 Copynumber: 2.3 Consensus size: 33
61943 GCAACGATAG
* * *
61953 AATCGCAACGAGAGAATCGCAACGCGAAATGAC
1 AATCGCAACCAGACAATCGCAACGCGAAATGAA
* *
61986 TATCGCGACCAGACAATCGCAACGCGAAATGAA
1 AATCGCAACCAGACAATCGCAACGCGAAATGAA
62019 AATCGCAACC
1 AATCGCAACC
62029 GCGAAATAAA
Statistics
Matches: 36, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.41, C:0.28, G:0.21, T:0.11
Consensus pattern (33 bp):
AATCGCAACCAGACAATCGCAACGCGAAATGAA
Found at i:62043 original size:39 final size:38
Alignment explanation
Indices: 62000--62089 Score: 144
Period size: 39 Copynumber: 2.3 Consensus size: 38
61990 GCGACCAGAC
*
62000 AATCGCAACGCGAAATGAAAATCGCAACCGCGAAATAAA
1 AATCGCAACGCGAAATAAAAATCGCAA-CGCGAAATAAA
62039 AATCGCAACGCGAAATAAAAATCGCAACGCGAAATAAA
1 AATCGCAACGCGAAATAAAAATCGCAACGCGAAATAAA
* *
62077 AATTGCAATGCGA
1 AATCGCAACGCGA
62090 TTTTTGTTTC
Statistics
Matches: 48, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
38 22 0.46
39 26 0.54
ACGTcount: A:0.49, C:0.21, G:0.18, T:0.12
Consensus pattern (38 bp):
AATCGCAACGCGAAATAAAAATCGCAACGCGAAATAAA
Found at i:62689 original size:20 final size:20
Alignment explanation
Indices: 62664--62716 Score: 88
Period size: 20 Copynumber: 2.6 Consensus size: 20
62654 GCGCTATGTA
62664 AATCGCGTTGCGAAAGTCAG
1 AATCGCGTTGCGAAAGTCAG
62684 AATCGCGTTGCGAAAGTCAG
1 AATCGCGTTGCGAAAGTCAG
* *
62704 TATCTCGTTGCGA
1 AATCGCGTTGCGA
62717 TTTTGTATTA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.26, C:0.21, G:0.28, T:0.25
Consensus pattern (20 bp):
AATCGCGTTGCGAAAGTCAG
Found at i:62750 original size:20 final size:20
Alignment explanation
Indices: 62725--62778 Score: 99
Period size: 20 Copynumber: 2.7 Consensus size: 20
62715 GATTTTGTAT
62725 TATCGCATTGCGATAGTAAG
1 TATCGCATTGCGATAGTAAG
*
62745 TATCGCATTGCGATAGTCAG
1 TATCGCATTGCGATAGTAAG
62765 TATCGCATTGCGAT
1 TATCGCATTGCGAT
62779 TTCCCAATTC
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.26, C:0.19, G:0.24, T:0.31
Consensus pattern (20 bp):
TATCGCATTGCGATAGTAAG
Found at i:62763 original size:61 final size:61
Alignment explanation
Indices: 62665--62780 Score: 160
Period size: 61 Copynumber: 1.9 Consensus size: 61
62655 CGCTATGTAA
* * * * *
62665 ATCGCGTTGCGAAAGTCAGAATCGCGTTGCGAAAGTCAGTATCTCGTTGCGATTTTGTATT
1 ATCGCATTGCGAAAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTTGTATT
* * *
62726 ATCGCATTGCGATAGTAAGTATCGCATTGCGATAGTCAGTATCGCATTGCGATTT
1 ATCGCATTGCGAAAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTT
62781 CCCAATTCAC
Statistics
Matches: 47, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
61 47 1.00
ACGTcount: A:0.24, C:0.18, G:0.25, T:0.33
Consensus pattern (61 bp):
ATCGCATTGCGAAAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTTGTATT
Found at i:62815 original size:20 final size:20
Alignment explanation
Indices: 62767--62817 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
62757 ATAGTCAGTA
*
62767 TCGCATTGCGATTTCCCAAT
1 TCGCATTGCGATTTACCAAT
* * **
62787 TCACGTTGCGATTTACTTAT
1 TCGCATTGCGATTTACCAAT
62807 TCGCATTGCGA
1 TCGCATTGCGA
62818 ATTGGGAAAA
Statistics
Matches: 24, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.20, C:0.25, G:0.18, T:0.37
Consensus pattern (20 bp):
TCGCATTGCGATTTACCAAT
Found at i:62888 original size:21 final size:21
Alignment explanation
Indices: 62848--62888 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
62838 ACTGTATACC
**
62848 ATCGCAACGCGATTTCCAACT
1 ATCGCAACGCGAAATCCAACT
*
62869 ATCGCAACGCGAAATGCAAC
1 ATCGCAACGCGAAATCCAAC
62889 GCGAATTTGC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.34, C:0.32, G:0.17, T:0.17
Consensus pattern (21 bp):
ATCGCAACGCGAAATCCAACT
Found at i:64459 original size:27 final size:27
Alignment explanation
Indices: 64393--64450 Score: 88
Period size: 25 Copynumber: 2.3 Consensus size: 27
64383 GAACCGAGTA
64393 AAACGGTTCGG--TTCGGTTCGGCTTT
1 AAACGGTTCGGTTTTCGGTTCGGCTTT
64418 AAACGGTTCGGTTTTCGGTTCGG-TTT
1 AAACGGTTCGGTTTTCGGTTCGGCTTT
64444 AAA-GGTT
1 AAACGGTT
64451 TCATTTTTTT
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
25 15 0.48
26 6 0.19
27 10 0.32
ACGTcount: A:0.16, C:0.16, G:0.31, T:0.38
Consensus pattern (27 bp):
AAACGGTTCGGTTTTCGGTTCGGCTTT
Found at i:64609 original size:19 final size:18
Alignment explanation
Indices: 64577--64645 Score: 72
Period size: 19 Copynumber: 3.8 Consensus size: 18
64567 TTCATTGAAA
64577 AACCGAAAAACCGAACCG
1 AACCGAAAAACCGAACCG
64595 AACCGAAAAATCCGAACCG
1 AACCGAAAAA-CCGAACCG
*
64614 TTAA---AAAACCCGAACCG
1 --AACCGAAAAACCGAACCG
64631 AACCGAAAAAACCGA
1 AACCG-AAAAACCGA
64646 TTTCGGTTTT
Statistics
Matches: 42, Mismatches: 2, Indels: 13
0.74 0.04 0.23
Matches are distributed among these distances:
15 2 0.05
17 8 0.19
18 14 0.33
19 16 0.38
21 2 0.05
ACGTcount: A:0.51, C:0.30, G:0.14, T:0.04
Consensus pattern (18 bp):
AACCGAAAAACCGAACCG
Found at i:69052 original size:16 final size:18
Alignment explanation
Indices: 69030--69069 Score: 64
Period size: 18 Copynumber: 2.3 Consensus size: 18
69020 AGTTAAAAAT
69030 AAAAAAA-ATAAGCCTTC
1 AAAAAAATATAAGCCTTC
*
69047 AAAAAAATATAAGCCTTG
1 AAAAAAATATAAGCCTTC
69065 AAAAA
1 AAAAA
69070 CTCAAACTCG
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
17 7 0.33
18 14 0.67
ACGTcount: A:0.62, C:0.12, G:0.07, T:0.17
Consensus pattern (18 bp):
AAAAAAATATAAGCCTTC
Found at i:69977 original size:3 final size:3
Alignment explanation
Indices: 69969--70033 Score: 123
Period size: 3 Copynumber: 22.0 Consensus size: 3
69959 TACTTTACCC
69969 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
70017 TTA TTA TTA TTA -TA TTA
1 TTA TTA TTA TTA TTA TTA
70034 ATCTTAGGCT
Statistics
Matches: 61, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
2 2 0.03
3 59 0.97
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:72606 original size:16 final size:16
Alignment explanation
Indices: 72572--72611 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
72562 ATTTTAGCCA
**
72572 AACCGAAAGTAACTTG
1 AACCGAAAGTAACAAG
*
72588 AACTGAAAGTAACAAG
1 AACCGAAAGTAACAAG
72604 AACCGAAA
1 AACCGAAA
72612 CCGACTCAAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.53, C:0.17, G:0.17, T:0.12
Consensus pattern (16 bp):
AACCGAAAGTAACAAG
Found at i:72652 original size:16 final size:15
Alignment explanation
Indices: 72624--72657 Score: 50
Period size: 16 Copynumber: 2.2 Consensus size: 15
72614 GACTCAAATT
72624 TAATCAAACCGAAAG
1 TAATCAAACCGAAAG
*
72639 TAATCCAAATCGAAAG
1 TAAT-CAAACCGAAAG
72655 TAA
1 TAA
72658 CCCGAACCGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 4 0.24
16 13 0.76
ACGTcount: A:0.53, C:0.18, G:0.12, T:0.18
Consensus pattern (15 bp):
TAATCAAACCGAAAG
Found at i:72668 original size:16 final size:16
Alignment explanation
Indices: 72628--72670 Score: 59
Period size: 16 Copynumber: 2.7 Consensus size: 16
72618 CAAATTTAAT
*
72628 CAAACCGAAAGTAATC
1 CAAACCGAAAGTAACC
*
72644 CAAATCGAAAGTAACC
1 CAAACCGAAAGTAACC
*
72660 CGAACCGAAAG
1 CAAACCGAAAG
72671 CAATTGAACC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.49, C:0.26, G:0.16, T:0.09
Consensus pattern (16 bp):
CAAACCGAAAGTAACC
Found at i:72790 original size:2 final size:2
Alignment explanation
Indices: 72740--72773 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
72730 ATCTTTTTAA
72740 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
72774 CAATAATTCT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:75887 original size:19 final size:19
Alignment explanation
Indices: 75832--75891 Score: 59
Period size: 19 Copynumber: 3.2 Consensus size: 19
75822 TATAATACTT
75832 TAATCTTTTGGTGTTTTAA
1 TAATCTTTTGGTGTTTTAA
*** * *
75851 TAA-AAATTGATAGGTTTAA
1 TAATCTTTTGGT-GTTTTAA
75870 TAATCTTTTGGTGTTTTAA
1 TAATCTTTTGGTGTTTTAA
75889 TAA
1 TAA
75892 AAAAAATTGG
Statistics
Matches: 29, Mismatches: 10, Indels: 4
0.67 0.23 0.09
Matches are distributed among these distances:
18 4 0.14
19 21 0.72
20 4 0.14
ACGTcount: A:0.32, C:0.03, G:0.15, T:0.50
Consensus pattern (19 bp):
TAATCTTTTGGTGTTTTAA
Found at i:75909 original size:41 final size:39
Alignment explanation
Indices: 75832--75948 Score: 173
Period size: 41 Copynumber: 3.0 Consensus size: 39
75822 TATAATACTT
*
75832 TAATCTTTTGGTGTTTTAAT-AAAAATTGATAGGTTTAA
1 TAATCTTTTGGTGTTTTAATAAAAAATTGGTAGGTTTAA
*
75870 TAATCTTTTGGTGTTTTAATAAAAAAAATTGGTAGGTTTAG
1 TAATCTTTTGGTGTTTTAAT--AAAAAATTGGTAGGTTTAA
* *
75911 TAATCTTTTAGTGTTTTAATAAAAATTTGGTAGGTTTA
1 TAATCTTTTGGTGTTTTAATAAAAAATTGGTAGGTTTA
75949 GAAAAATATT
Statistics
Matches: 72, Mismatches: 4, Indels: 5
0.89 0.05 0.06
Matches are distributed among these distances:
38 20 0.28
39 17 0.24
41 35 0.49
ACGTcount: A:0.33, C:0.03, G:0.17, T:0.47
Consensus pattern (39 bp):
TAATCTTTTGGTGTTTTAATAAAAAATTGGTAGGTTTAA
Found at i:75969 original size:21 final size:20
Alignment explanation
Indices: 75931--75971 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 20
75921 GTGTTTTAAT
*
75931 AAAAATTTGGTAGGTTTAGA
1 AAAAATTTGGTAGATTTAGA
*
75951 AAAATATTTGGTATATTTAGA
1 AAAA-ATTTGGTAGATTTAGA
75972 CTAACCCTTG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.41, C:0.00, G:0.20, T:0.39
Consensus pattern (20 bp):
AAAAATTTGGTAGATTTAGA
Found at i:77492 original size:21 final size:21
Alignment explanation
Indices: 77459--77510 Score: 52
Period size: 21 Copynumber: 2.5 Consensus size: 21
77449 ATCTAATTTG
* *
77459 TTTAAATTATTTAAAT-TTCAA
1 TTTAATTTTTTTAAATATT-AA
*
77480 TTTAATTTTTTTACATATTAA
1 TTTAATTTTTTTAAATATTAA
*
77501 TTTTATTTTT
1 TTTAATTTTT
77511 CTTTGAATTT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
21 24 0.92
22 2 0.08
ACGTcount: A:0.33, C:0.04, G:0.00, T:0.63
Consensus pattern (21 bp):
TTTAATTTTTTTAAATATTAA
Found at i:88295 original size:20 final size:18
Alignment explanation
Indices: 88260--88299 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 18
88250 AATAAAAAAT
88260 AAATTATTTGAAATATTAA
1 AAATTATTTGAAATA-TAA
88279 AAATTATTTGAAAATATAA
1 AAATTATTTG-AAATATAA
88298 AA
1 AA
88300 GTTAAAGTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
19 15 0.75
20 5 0.25
ACGTcount: A:0.57, C:0.00, G:0.05, T:0.38
Consensus pattern (18 bp):
AAATTATTTGAAATATAA
Found at i:95965 original size:5 final size:5
Alignment explanation
Indices: 95928--95963 Score: 63
Period size: 5 Copynumber: 7.2 Consensus size: 5
95918 AAATAGTTGC
*
95928 GTGGG GTGGG GTGGG GTGGG GTGGG GTGGG GAGGG G
1 GTGGG GTGGG GTGGG GTGGG GTGGG GTGGG GTGGG G
95964 AGATCAGATC
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
5 30 1.00
ACGTcount: A:0.03, C:0.00, G:0.81, T:0.17
Consensus pattern (5 bp):
GTGGG
Found at i:96865 original size:18 final size:18
Alignment explanation
Indices: 96842--96876 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
96832 ATGTAAGGCT
* *
96842 TTTTTCTATTTTTAAACC
1 TTTTTCGATTGTTAAACC
96860 TTTTTCGATTGTTAAAC
1 TTTTTCGATTGTTAAAC
96877 ATGAGAGTAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.23, C:0.14, G:0.06, T:0.57
Consensus pattern (18 bp):
TTTTTCGATTGTTAAACC
Found at i:98514 original size:3 final size:3
Alignment explanation
Indices: 98508--98532 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
98498 GTTTTTTTAA
98508 AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT A
98533 GCTATCATAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:100621 original size:21 final size:21
Alignment explanation
Indices: 100596--100669 Score: 107
Period size: 21 Copynumber: 3.6 Consensus size: 21
100586 TTTGGAATAA
100596 ATCGCAACGCGAACTTCGACT
1 ATCGCAACGCGAACTTCGACT
100617 ATCGCAACGCGAACTTCGACT
1 ATCGCAACGCGAACTTCGACT
* *
100638 ATCGCAA--CGAATTTGGACT
1 ATCGCAACGCGAACTTCGACT
*
100657 ATCGCAATGCGAA
1 ATCGCAACGCGAA
100670 TATGTAAATC
Statistics
Matches: 49, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
19 17 0.35
21 32 0.65
ACGTcount: A:0.31, C:0.28, G:0.20, T:0.20
Consensus pattern (21 bp):
ATCGCAACGCGAACTTCGACT
Found at i:100703 original size:21 final size:22
Alignment explanation
Indices: 100596--100710 Score: 79
Period size: 21 Copynumber: 5.6 Consensus size: 22
100586 TTTGGAATAA
*
100596 ATCGCAACGCGA-ACTTCGACT
1 ATCGCAATGCGATACTTCGACT
*
100617 ATCGCAACGCGA-ACTTCGACT
1 ATCGCAATGCGATACTTCGACT
* *
100638 ATCGCAA--CGA-ATTTGGACT
1 ATCGCAATGCGATACTTCGACT
*
100657 ATCGCAATGCGA-A-TAT-GTA-A
1 ATCGCAATGCGATACT-TCG-ACT
*
100677 ATCGCAATGCGATA-GTCGACT
1 ATCGCAATGCGATACTTCGACT
*
100698 ATCGCATTGCGAT
1 ATCGCAATGCGAT
100711 TTATATATTC
Statistics
Matches: 81, Mismatches: 6, Indels: 14
0.80 0.06 0.14
Matches are distributed among these distances:
19 17 0.21
20 16 0.20
21 48 0.59
ACGTcount: A:0.30, C:0.25, G:0.21, T:0.23
Consensus pattern (22 bp):
ATCGCAATGCGATACTTCGACT
Found at i:100751 original size:21 final size:21
Alignment explanation
Indices: 100722--100762 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
100712 TATATATTCA
*
100722 CATTGCGATAGTCCAAGTTCG
1 CATTACGATAGTCCAAGTTCG
*
100743 CATTACGATAGTCGAAGTTC
1 CATTACGATAGTCCAAGTTC
100763 ACGTTGCGAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.27, C:0.22, G:0.22, T:0.29
Consensus pattern (21 bp):
CATTACGATAGTCCAAGTTCG
Found at i:101098 original size:52 final size:52
Alignment explanation
Indices: 101028--101130 Score: 188
Period size: 52 Copynumber: 2.0 Consensus size: 52
101018 AAATTGGACA
*
101028 CATAGAAATAGGAAACTAGCCTAGAGTTAGGGGATTACAACTAATTACAAGG
1 CATAAAAATAGGAAACTAGCCTAGAGTTAGGGGATTACAACTAATTACAAGG
*
101080 CATAAAAATAGGAGACTAGCCTAGAGTTAGGGGATTACAACTAATTACAAG
1 CATAAAAATAGGAAACTAGCCTAGAGTTAGGGGATTACAACTAATTACAAG
101131 AATATTATAA
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 49 1.00
ACGTcount: A:0.43, C:0.14, G:0.22, T:0.21
Consensus pattern (52 bp):
CATAAAAATAGGAAACTAGCCTAGAGTTAGGGGATTACAACTAATTACAAGG
Found at i:105684 original size:52 final size:52
Alignment explanation
Indices: 105622--105724 Score: 197
Period size: 52 Copynumber: 2.0 Consensus size: 52
105612 AAATTGGACA
105622 CATAGAAATAGGAAACTAGCCTAGAGTTAGGGGATTACAACTAATTACAAGG
1 CATAGAAATAGGAAACTAGCCTAGAGTTAGGGGATTACAACTAATTACAAGG
*
105674 CATAGAAATAGGAGACTAGCCTAGAGTTAGGGGATTACAACTAATTACAAG
1 CATAGAAATAGGAAACTAGCCTAGAGTTAGGGGATTACAACTAATTACAAG
105725 AATATTATAA
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
52 50 1.00
ACGTcount: A:0.42, C:0.14, G:0.23, T:0.21
Consensus pattern (52 bp):
CATAGAAATAGGAAACTAGCCTAGAGTTAGGGGATTACAACTAATTACAAGG
Found at i:106732 original size:29 final size:29
Alignment explanation
Indices: 106666--106733 Score: 75
Period size: 29 Copynumber: 2.3 Consensus size: 29
106656 AATAAAATAA
*
106666 AGTTTATATAAATTATCACTGAAAACCAT
1 AGTTTACATAAATTATCACTGAAAACCAT
** *
106695 AGTGCACATAAATTATCA-TTAATAACCAT
1 AGTTTACATAAATTATCACTGAA-AACCAT
*
106724 ATTTTACATA
1 AGTTTACATA
106734 GGAGTAAAAT
Statistics
Matches: 31, Mismatches: 7, Indels: 2
0.77 0.17 0.05
Matches are distributed among these distances:
28 3 0.10
29 28 0.90
ACGTcount: A:0.44, C:0.15, G:0.06, T:0.35
Consensus pattern (29 bp):
AGTTTACATAAATTATCACTGAAAACCAT
Found at i:108522 original size:26 final size:26
Alignment explanation
Indices: 108477--108531 Score: 67
Period size: 27 Copynumber: 2.1 Consensus size: 26
108467 ACTTTAAGTC
*
108477 TTTAATTTTTTTTAATTATAATAAATA
1 TTTAATTTTGTTTAATTAT-ATAAATA
* *
108504 TTTAATTTTGTTTGA-TATATCAATA
1 TTTAATTTTGTTTAATTATATAAATA
108529 TTT
1 TTT
108532 CGTTGATTAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
25 9 0.36
26 3 0.12
27 13 0.52
ACGTcount: A:0.35, C:0.02, G:0.04, T:0.60
Consensus pattern (26 bp):
TTTAATTTTGTTTAATTATATAAATA
Found at i:108855 original size:23 final size:22
Alignment explanation
Indices: 108808--108857 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 22
108798 AATCGTAATA
* *
108808 AAATAATTAAAATTTTATTATC
1 AAATAATTAAAATTTTATAAAC
108830 AAATAATTAAAAATATTTA-AAAC
1 AAATAATT-AAAAT-TTTATAAAC
108853 AAATA
1 AAATA
108858 TTATTCTATA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
22 8 0.33
23 12 0.50
24 4 0.17
ACGTcount: A:0.60, C:0.04, G:0.00, T:0.36
Consensus pattern (22 bp):
AAATAATTAAAATTTTATAAAC
Found at i:112407 original size:48 final size:48
Alignment explanation
Indices: 112335--112427 Score: 150
Period size: 48 Copynumber: 1.9 Consensus size: 48
112325 GTACAAGAGA
* * * *
112335 CCCTTGTGCTTTTAAAAAATCTTAATGTGGTCCTTAAATTATTTTAGG
1 CCCTTGTACTTTAAAAAAAACTTAATATGGTCCTTAAATTATTTTAGG
112383 CCCTTGTACTTTAAAAAAAACTTAATATGGTCCTTAAATTATTTT
1 CCCTTGTACTTTAAAAAAAACTTAATATGGTCCTTAAATTATTTT
112428 TGCATTCAAT
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
48 41 1.00
ACGTcount: A:0.31, C:0.15, G:0.11, T:0.43
Consensus pattern (48 bp):
CCCTTGTACTTTAAAAAAAACTTAATATGGTCCTTAAATTATTTTAGG
Found at i:112706 original size:2 final size:2
Alignment explanation
Indices: 112699--112730 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
112689 CTAAAATTTA
112699 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
112731 CATTATTTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:113226 original size:21 final size:21
Alignment explanation
Indices: 113200--113275 Score: 100
Period size: 21 Copynumber: 3.7 Consensus size: 21
113190 TGCGATAAGT
113200 AAATCGCAACGCGAATTGGGA
1 AAATCGCAACGCGAATTGGGA
* ** *
113221 AAATCGCAATGCGAA-TAAGT
1 AAATCGCAACGCGAATTGGGA
113241 AAATCGCAACGCGAATTGGGA
1 AAATCGCAACGCGAATTGGGA
*
113262 AAATCGCAATGCGA
1 AAATCGCAACGCGA
113276 TACTGACTAT
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 16 0.36
21 29 0.64
ACGTcount: A:0.41, C:0.18, G:0.25, T:0.16
Consensus pattern (21 bp):
AAATCGCAACGCGAATTGGGA
Found at i:113245 original size:41 final size:41
Alignment explanation
Indices: 113184--113275 Score: 177
Period size: 41 Copynumber: 2.3 Consensus size: 41
113174 TTTTCCCAAT
113184 TCGCAATGCG-ATAAGTAAATCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
113224 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
113265 TCGCAATGCGA
1 TCGCAATGCGA
113276 TACTGACTAT
Statistics
Matches: 51, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
40 10 0.20
41 41 0.80
ACGTcount: A:0.39, C:0.18, G:0.25, T:0.17
Consensus pattern (41 bp):
TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
Found at i:113246 original size:20 final size:21
Alignment explanation
Indices: 113184--113275 Score: 91
Period size: 21 Copynumber: 4.5 Consensus size: 21
113174 TTTTCCCAAT
*
113184 TCGCAATGCG-A-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
113203 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
*
113224 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
113244 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
113265 TCGCAATGCGA
1 TCGCAATGCGA
113276 TACTGACTAT
Statistics
Matches: 57, Mismatches: 13, Indels: 4
0.77 0.18 0.05
Matches are distributed among these distances:
19 9 0.16
20 17 0.30
21 31 0.54
ACGTcount: A:0.39, C:0.18, G:0.25, T:0.17
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:113288 original size:41 final size:41
Alignment explanation
Indices: 113202--113336 Score: 132
Period size: 41 Copynumber: 3.3 Consensus size: 41
113192 CGATAAGTAA
* *
113202 ATCGCAACGCGAATTGGGAAAATCGCAATGCGAATA-AGTA-A
1 ATCGCAACGCGAATTGGGAAAATCGCAATGCG-ATACTG-ACT
113243 ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTGACT
1 ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTGACT
* * ** * * *
113284 ATCGCAATGCGATAAT-AAAAAATCGCAACGAGATACTTACT
1 ATCGCAACGCGA-ATTGGGAAAATCGCAATGCGATACTGACT
*
113325 TTCGCAACGCGA
1 ATCGCAACGCGA
113337 TACTGACTTT
Statistics
Matches: 80, Mismatches: 11, Indels: 6
0.82 0.11 0.06
Matches are distributed among these distances:
40 4 0.05
41 74 0.93
42 2 0.03
ACGTcount: A:0.39, C:0.21, G:0.21, T:0.19
Consensus pattern (41 bp):
ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTGACT
Found at i:113289 original size:20 final size:20
Alignment explanation
Indices: 113264--113358 Score: 91
Period size: 20 Copynumber: 4.7 Consensus size: 20
113254 AATTGGGAAA
*
113264 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* * * **
113284 ATCGCAATGCGATAATAAAAA
1 ATCGCAACGCGATACT-GACT
* *
113305 ATCGCAACGAGATACTTACT
1 ATCGCAACGCGATACTGACT
*
113325 TTCGCAACGCGATACTGACT
1 ATCGCAACGCGATACTGACT
*
113345 TTCGCAACGCGATA
1 ATCGCAACGCGATA
113359 ATACATAATC
Statistics
Matches: 61, Mismatches: 13, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
20 47 0.77
21 14 0.23
ACGTcount: A:0.35, C:0.24, G:0.18, T:0.23
Consensus pattern (20 bp):
ATCGCAACGCGATACTGACT
Found at i:113574 original size:22 final size:22
Alignment explanation
Indices: 113546--113589 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
113536 CACTCTCTCA
113546 CCCATCTCCGACGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
*
113568 CCCATCTCCGGCGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
113590 TATCTCCATC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.20, C:0.45, G:0.16, T:0.18
Consensus pattern (22 bp):
CCCATCTCCGACGAAATCCGTC
Found at i:113878 original size:20 final size:20
Alignment explanation
Indices: 113853--113890 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
113843 CGATTCTCTC
113853 GTTGCGATAGTCATTTTCGT
1 GTTGCGATAGTCATTTTCGT
**
113873 GTTGCGATTTTCATTTTC
1 GTTGCGATAGTCATTTTC
113891 AGAAACTATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.13, C:0.16, G:0.21, T:0.50
Consensus pattern (20 bp):
GTTGCGATAGTCATTTTCGT
Found at i:115232 original size:18 final size:18
Alignment explanation
Indices: 115206--115250 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
115196 CTCCACTTCG
*
115206 GAGCCATCACCTCGCCCA
1 GAGCCATCACCTCACCCA
*
115224 GAGCTATCACCTCACCCA
1 GAGCCATCACCTCACCCA
115242 GAGCCATCA
1 GAGCCATCA
115251 TCTGATCGAC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.27, C:0.44, G:0.16, T:0.13
Consensus pattern (18 bp):
GAGCCATCACCTCACCCA
Found at i:115753 original size:20 final size:20
Alignment explanation
Indices: 115728--115773 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
115718 TAGTTTACTT
115728 TCGCAACACGAAAATGACTA
1 TCGCAACACGAAAATGACTA
* * *
115748 TCGCAACGCGGAAATGGCTA
1 TCGCAACACGAAAATGACTA
115768 TCGCAA
1 TCGCAA
115774 TGCGAAATAA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.37, C:0.26, G:0.22, T:0.15
Consensus pattern (20 bp):
TCGCAACACGAAAATGACTA
Done.