Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008756.1 Hibiscus syriacus cultivar Beakdansim tig00111848_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: 4584045
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 9 of 21
Found at i:1849270 original size:30 final size:30
Alignment explanation
Indices: 1849223--1849281 Score: 102
Period size: 29 Copynumber: 2.0 Consensus size: 30
1849213 AAACATTGAA
1849223 TAAATTCAATTAAGTCCAAAAA-CATTTTG
1 TAAATTCAATTAAGTCCAAAAACCATTTTG
1849252 TAAATTCAATTCAAGTCCAAAAACCATTTT
1 TAAATTCAATT-AAGTCCAAAAACCATTTT
1849282 TCCTTAAATT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
29 11 0.39
30 11 0.39
31 6 0.21
ACGTcount: A:0.44, C:0.17, G:0.05, T:0.34
Consensus pattern (30 bp):
TAAATTCAATTAAGTCCAAAAACCATTTTG
Found at i:1860977 original size:78 final size:78
Alignment explanation
Indices: 1860848--1860998 Score: 257
Period size: 78 Copynumber: 1.9 Consensus size: 78
1860838 GACCATCCTA
1860848 AAAAGTGATCATCAAACTCATTTACATCAAGTTCATTTCGATCATGCAGAAGCATGATTATGTTG
1 AAAAGTGATCATCAAACTCATTTACATCAAGTTCATTTCGATCATGCAGAAGCATGATTATGTTG
1860913 GAGAGTTTGACAT
66 GAGAGTTTGACAT
** * * *
1860926 AAAAGTGATCATCAAGTTCATTTACATCGAGTTCATTTCGGTCATGCAGAAGCATGGTTATGTTG
1 AAAAGTGATCATCAAACTCATTTACATCAAGTTCATTTCGATCATGCAGAAGCATGATTATGTTG
1860991 GAGAGTTT
66 GAGAGTTT
1860999 ATGCCGATGA
Statistics
Matches: 68, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
78 68 1.00
ACGTcount: A:0.32, C:0.15, G:0.21, T:0.33
Consensus pattern (78 bp):
AAAAGTGATCATCAAACTCATTTACATCAAGTTCATTTCGATCATGCAGAAGCATGATTATGTTG
GAGAGTTTGACAT
Found at i:1869801 original size:111 final size:111
Alignment explanation
Indices: 1869578--1870043 Score: 641
Period size: 111 Copynumber: 4.2 Consensus size: 111
1869568 GGGAAAATTA
* * * * * * * **
1869578 AATCAGGGTAGACTTGTTCCATTATTACTTATGGAATATCAAATCTGGAAAGAGATTTGATCTGT
1 AATCAAGGTAGACTTGTTCCACTGTCACTCAGGGAATATCAAATCTTGAAAGAGA-GGGATCTGT
* *
1869643 TCCACTT-CTCCTGAGGGAATATCAGATCTAGGAAAGTTGATCCATTG
65 TCCACTTCCT-CTGAGGGAATATCAGATCTGGGAAAGTTGATTCATTG
* * *
1869690 AATCAGGGTAGAATTGTTCCACTGTCGCTCAGGGAATATCAAATCTTGAAAGAGAGGGATCTGTT
1 AATCAAGGTAGACTTGTTCCACTGTCACTCAGGGAATATCAAATCTTGAAAGAGAGGGATCTGTT
* *
1869755 CCACTTCCTCTGAGGGAATATCATATCTGGGAAAGTTGATTTATTG
66 CCACTTCCTCTGAGGGAATATCAGATCTGGGAAAGTTGATTCATTG
* ** *
1869801 AATCAAGGTAGATTTGTTCCGTTGTCATTCAGGGAATATCAAATCTTG-AA-AGAGGGATCTGTT
1 AATCAAGGTAGACTTGTTCCACTGTCACTCAGGGAATATCAAATCTTGAAAGAGAGGGATCTGTT
* *
1869864 CCACTTTCTCTGAGGGAATATCAGATCTGGCAAAGTTGATTCATTG
66 CCACTTCCTCTGAGGGAATATCAGATCTGGGAAAGTTGATTCATTG
** * *
1869910 AATCAAGGTAGACTTGTTCTGCTGTCACTCAAGGAATACCAAATCTTGAAAGAGAGGGATCTGTT
1 AATCAAGGTAGACTTGTTCCACTGTCACTCAGGGAATATCAAATCTTGAAAGAGAGGGATCTGTT
1869975 CCACTTCCTCTGAGGGAATATCAGATCTGGGAAAGTTGATTCATTG
66 CCACTTCCTCTGAGGGAATATCAGATCTGGGAAAGTTGATTCATTG
* *
1870021 AATCAAAGCAGACTTGTTCCACT
1 AATCAAGGTAGACTTGTTCCACT
1870044 TACTATGAAT
Statistics
Matches: 315, Mismatches: 36, Indels: 7
0.88 0.10 0.02
Matches are distributed among these distances:
109 97 0.31
110 4 0.01
111 165 0.52
112 49 0.16
ACGTcount: A:0.30, C:0.17, G:0.22, T:0.31
Consensus pattern (111 bp):
AATCAAGGTAGACTTGTTCCACTGTCACTCAGGGAATATCAAATCTTGAAAGAGAGGGATCTGTT
CCACTTCCTCTGAGGGAATATCAGATCTGGGAAAGTTGATTCATTG
Found at i:1869976 original size:220 final size:221
Alignment explanation
Indices: 1869610--1870040 Score: 670
Period size: 220 Copynumber: 1.9 Consensus size: 221
1869600 TATTACTTAT
*
1869610 GGAATATCAAATCTGGAAAGAGATTTGATCTGTTCCACTTCTCCTGAGGGAATATCAGATCTAGG
1 GGAATATCAAATCTGGAAAGAG--TGGATCTGTTCCACTTCTCCTGAGGGAATATCAGATCTAGG
* * * *
1869675 AAAGTTGATCCATTGAATCAGGGTAGAATTGTTCCACTGTCGCTCAGGGAATATCAAATCTTGAA
64 AAAGTTGATCCATTGAATCAAGGTAGAATTGTTCCACTGTCACTCAAGGAATACCAAATCTTGAA
* *
1869740 AGAGAGGGATCTGTTCCACTTCCTCTGAGGGAATATCATATCTGGGAAAGTTGATTTATTGAATC
129 AGAGAGGGATCTGTTCCACTTCCTCTGAGGGAATATCAGATCTGGGAAAGTTGATTCATTGAATC
* * *
1869805 AAGGTAGATTTGTTCCGTTGTCATTCAG
194 AAAGCAGACTTGTTCCGTTGTCATTCAG
*
1869833 GGAATATCAAATCTTGAAAGAG-GGATCTGTTCCACTT-TCTCTGAGGGAATATCAGATCT-GGC
1 GGAATATCAAATCTGGAAAGAGTGGATCTGTTCCACTTCTC-CTGAGGGAATATCAGATCTAGG-
* * **
1869895 AAAGTTGATTCATTGAATCAAGGTAGACTTGTTCTGCTGTCACTCAAGGAATACCAAATCTTGAA
64 AAAGTTGATCCATTGAATCAAGGTAGAATTGTTCCACTGTCACTCAAGGAATACCAAATCTTGAA
1869960 AGAGAGGGATCTGTTCCACTTCCTCTGAGGGAATATCAGATCTGGGAAAGTTGATTCATTGAATC
129 AGAGAGGGATCTGTTCCACTTCCTCTGAGGGAATATCAGATCTGGGAAAGTTGATTCATTGAATC
1870025 AAAGCAGACTTGTTCC
194 AAAGCAGACTTGTTCC
1870041 ACTTACTATG
Statistics
Matches: 191, Mismatches: 15, Indels: 7
0.90 0.07 0.03
Matches are distributed among these distances:
219 4 0.02
220 166 0.87
223 21 0.11
ACGTcount: A:0.30, C:0.17, G:0.23, T:0.30
Consensus pattern (221 bp):
GGAATATCAAATCTGGAAAGAGTGGATCTGTTCCACTTCTCCTGAGGGAATATCAGATCTAGGAA
AGTTGATCCATTGAATCAAGGTAGAATTGTTCCACTGTCACTCAAGGAATACCAAATCTTGAAAG
AGAGGGATCTGTTCCACTTCCTCTGAGGGAATATCAGATCTGGGAAAGTTGATTCATTGAATCAA
AGCAGACTTGTTCCGTTGTCATTCAG
Found at i:1870086 original size:66 final size:66
Alignment explanation
Indices: 1869971--1870485 Score: 899
Period size: 66 Copynumber: 7.8 Consensus size: 66
1869961 GAGAGGGATC
* * * * *
1869971 TGTTCCACTTCCTCTG-AGGGAATATCAGATCTGGGA-AAGTTGATTCATTGAATCAAAGCAGAC
1 TGTTCCACTTACTCTGAAGGGAATATCAAATCTTGGAGAAGTTGATCCATTGAATCGAAGCAGAC
1870034 T
66 T
* * * *
1870035 TGTTCCACTTACTATGAATGGAATATCAAATCTTGGAGAAATTGATCCATTGAATCAAAGCAGAC
1 TGTTCCACTTACTCTGAAGGGAATATCAAATCTTGGAGAAGTTGATCCATTGAATCGAAGCAGAC
1870100 T
66 T
* * *
1870101 TGTTCCACTTACTCTAAAGGGAATATCAAATATTGGAGAAGTTGGTCCATTGAATCGAAGCAGAC
1 TGTTCCACTTACTCTGAAGGGAATATCAAATCTTGGAGAAGTTGATCCATTGAATCGAAGCAGAC
1870166 T
66 T
1870167 TGTTCCACTTACTCTGAAGGGAATATCAAATCTTGGAGAAGTTGATCCATTGAATCGAAGCAGAC
1 TGTTCCACTTACTCTGAAGGGAATATCAAATCTTGGAGAAGTTGATCCATTGAATCGAAGCAGAC
1870232 T
66 T
1870233 TGTTCCACTTACTCTGAAGGGAATATCAAATCTTGGAGAAGTTGATCCATTGAATCGAAGCAGAC
1 TGTTCCACTTACTCTGAAGGGAATATCAAATCTTGGAGAAGTTGATCCATTGAATCGAAGCAGAC
1870298 T
66 T
*
1870299 TGTTCCACTTACTCTGAAGGGAATATCAAATCTTGGAGAAGTTGATCCATTGAATTGAAGCAGAC
1 TGTTCCACTTACTCTGAAGGGAATATCAAATCTTGGAGAAGTTGATCCATTGAATCGAAGCAGAC
1870364 T
66 T
1870365 TGTTCCACTTACTCTGAAGGGAATATCAAATCTTGGAGAAGTTGATCCATTGAATCGAAGCAGAC
1 TGTTCCACTTACTCTGAAGGGAATATCAAATCTTGGAGAAGTTGATCCATTGAATCGAAGCAGAC
1870430 T
66 T
1870431 TGTTCCACTTACTCTGAAGGGAATATCAAATCTTGGAGAAGTTGATCCATTGAAT
1 TGTTCCACTTACTCTGAAGGGAATATCAAATCTTGGAGAAGTTGATCCATTGAAT
1870486 TGGGATCGAA
Statistics
Matches: 430, Mismatches: 19, Indels: 2
0.95 0.04 0.00
Matches are distributed among these distances:
64 14 0.03
65 17 0.04
66 399 0.93
ACGTcount: A:0.32, C:0.17, G:0.21, T:0.30
Consensus pattern (66 bp):
TGTTCCACTTACTCTGAAGGGAATATCAAATCTTGGAGAAGTTGATCCATTGAATCGAAGCAGAC
T
Found at i:1875201 original size:4 final size:4
Alignment explanation
Indices: 1875158--1875216 Score: 50
Period size: 4 Copynumber: 14.8 Consensus size: 4
1875148 TCCCATATCA
* * * *
1875158 AAAT AGAAT GAAAT -AAT -AAT ATAT AAAA AAAG AAAG AAAT AAAT AAAT
1 AAAT A-AAT -AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT
1875206 AAAT AAAT AAA
1 AAAT AAAT AAA
1875217 AGAATGGAAA
Statistics
Matches: 47, Mismatches: 5, Indels: 6
0.81 0.09 0.10
Matches are distributed among these distances:
3 6 0.13
4 34 0.72
5 6 0.13
6 1 0.02
ACGTcount: A:0.73, C:0.00, G:0.07, T:0.20
Consensus pattern (4 bp):
AAAT
Found at i:1878832 original size:11 final size:11
Alignment explanation
Indices: 1878818--1878847 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
1878808 TGCAATGTAG
1878818 ATGCAATATGA
1 ATGCAATATGA
*
1878829 ATGCAAGATGA
1 ATGCAATATGA
1878840 ATGCAATA
1 ATGCAATA
1878848 CAAGGTGTTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.47, C:0.10, G:0.20, T:0.23
Consensus pattern (11 bp):
ATGCAATATGA
Found at i:1881257 original size:15 final size:17
Alignment explanation
Indices: 1881227--1881258 Score: 50
Period size: 15 Copynumber: 2.0 Consensus size: 17
1881217 TTAGTAGATC
1881227 CTACCCAGTCATGATTT
1 CTACCCAGTCATGATTT
1881244 CTACCCA-T-ATGATTT
1 CTACCCAGTCATGATTT
1881259 TGTTATTCAC
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 7 0.47
16 1 0.07
17 7 0.47
ACGTcount: A:0.25, C:0.28, G:0.09, T:0.38
Consensus pattern (17 bp):
CTACCCAGTCATGATTT
Found at i:1881952 original size:40 final size:40
Alignment explanation
Indices: 1881908--1881988 Score: 162
Period size: 40 Copynumber: 2.0 Consensus size: 40
1881898 AAAGCATTCA
1881908 AAACTTATTTAAAACAAAACAAGGGATCAAAAACCAAATT
1 AAACTTATTTAAAACAAAACAAGGGATCAAAAACCAAATT
1881948 AAACTTATTTAAAACAAAACAAGGGATCAAAAACCAAATT
1 AAACTTATTTAAAACAAAACAAGGGATCAAAAACCAAATT
1881988 A
1 A
1881989 GAACGAACTT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 41 1.00
ACGTcount: A:0.58, C:0.15, G:0.07, T:0.20
Consensus pattern (40 bp):
AAACTTATTTAAAACAAAACAAGGGATCAAAAACCAAATT
Found at i:1883767 original size:3 final size:3
Alignment explanation
Indices: 1883738--1883837 Score: 71
Period size: 3 Copynumber: 34.0 Consensus size: 3
1883728 TGTTCCTTTT
* *
1883738 TTA TT- TTA ATA TTA TT- TTAA TTA -TA TTA TTA TTA ATA TTA TTA
1 TTA TTA TTA TTA TTA TTA TT-A TTA TTA TTA TTA TTA TTA TTA TTA
* * * * * * * * *
1883781 TTA ATA ATA TTA TTA CTA ATA ATA ATA ATA ATA ATA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1883829 TTA TTA TTA
1 TTA TTA TTA
1883838 CAGGCCCAAA
Statistics
Matches: 84, Mismatches: 9, Indels: 8
0.83 0.09 0.08
Matches are distributed among these distances:
2 6 0.07
3 76 0.90
4 2 0.02
ACGTcount: A:0.43, C:0.01, G:0.00, T:0.56
Consensus pattern (3 bp):
TTA
Found at i:1886653 original size:22 final size:21
Alignment explanation
Indices: 1886620--1886661 Score: 66
Period size: 22 Copynumber: 2.0 Consensus size: 21
1886610 TCCTTTCTCA
*
1886620 TTTTTATTCATTTTATATTAT
1 TTTTTATGCATTTTATATTAT
1886641 TTTTTCATGCATTTTATATTA
1 TTTTT-ATGCATTTTATATTA
1886662 ATTTCTTTTG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 5 0.26
22 14 0.74
ACGTcount: A:0.24, C:0.07, G:0.02, T:0.67
Consensus pattern (21 bp):
TTTTTATGCATTTTATATTAT
Found at i:1888789 original size:16 final size:16
Alignment explanation
Indices: 1888770--1888818 Score: 52
Period size: 16 Copynumber: 3.3 Consensus size: 16
1888760 AGTGGAAGCC
1888770 TTATACTCATATTATA
1 TTATACTCATATTATA
*
1888786 TTATA-T-ATA-CA-A
1 TTATACTCATATTATA
*
1888798 TAATACTCATATTATA
1 TTATACTCATATTATA
1888814 TTATA
1 TTATA
1888819 TATACAATAA
Statistics
Matches: 25, Mismatches: 4, Indels: 8
0.68 0.11 0.22
Matches are distributed among these distances:
12 5 0.20
13 2 0.08
14 6 0.24
15 2 0.08
16 10 0.40
ACGTcount: A:0.43, C:0.10, G:0.00, T:0.47
Consensus pattern (16 bp):
TTATACTCATATTATA
Found at i:1888812 original size:28 final size:28
Alignment explanation
Indices: 1888772--1888828 Score: 114
Period size: 28 Copynumber: 2.0 Consensus size: 28
1888762 TGGAAGCCTT
1888772 ATACTCATATTATATTATATATACAATA
1 ATACTCATATTATATTATATATACAATA
1888800 ATACTCATATTATATTATATATACAATA
1 ATACTCATATTATATTATATATACAATA
1888828 A
1 A
1888829 AGCTTGAGTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.47, C:0.11, G:0.00, T:0.42
Consensus pattern (28 bp):
ATACTCATATTATATTATATATACAATA
Found at i:1888909 original size:10 final size:10
Alignment explanation
Indices: 1888894--1888938 Score: 56
Period size: 10 Copynumber: 4.5 Consensus size: 10
1888884 TTTCAAATAG
1888894 AAAAAAGAAA
1 AAAAAAGAAA
1888904 AAAAAAGAAA
1 AAAAAAGAAA
1888914 AAGAAAA-AAA
1 AA-AAAAGAAA
* *
1888924 GAGAAAGAAA
1 AAAAAAGAAA
1888934 AAAAA
1 AAAAA
1888939 GAGGTTATAA
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
9 3 0.10
10 22 0.76
11 4 0.14
ACGTcount: A:0.87, C:0.00, G:0.13, T:0.00
Consensus pattern (10 bp):
AAAAAAGAAA
Found at i:1888920 original size:15 final size:15
Alignment explanation
Indices: 1888895--1888940 Score: 67
Period size: 14 Copynumber: 3.1 Consensus size: 15
1888885 TTCAAATAGA
1888895 AAAAAGAAAAAAAAAG
1 AAAAAG-AAAAAAAAG
1888911 AAAAAG-AAAAAAAG
1 AAAAAGAAAAAAAAG
*
1888925 AGAAAGAAAAAAAAG
1 AAAAAGAAAAAAAAG
1888940 A
1 A
1888941 GGTTATAAAG
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
14 13 0.46
15 9 0.32
16 6 0.21
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (15 bp):
AAAAAGAAAAAAAAG
Found at i:1888922 original size:23 final size:22
Alignment explanation
Indices: 1888892--1888940 Score: 62
Period size: 24 Copynumber: 2.1 Consensus size: 22
1888882 AGTTTCAAAT
1888892 AGAAAAAAGAAAAAAAAAGAAAA
1 AGAAAAAAGAAAAAAAAA-AAAA
* *
1888915 AGAAAAAAAGAGAAAGAAAAAAA
1 AG-AAAAAAGAAAAAAAAAAAAA
1888938 AGA
1 AGA
1888941 GGTTATAAAG
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
22 1 0.04
23 8 0.35
24 14 0.61
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (22 bp):
AGAAAAAAGAAAAAAAAAAAAA
Found at i:1888941 original size:15 final size:15
Alignment explanation
Indices: 1888897--1888941 Score: 65
Period size: 15 Copynumber: 3.0 Consensus size: 15
1888887 CAAATAGAAA
1888897 AAAGAAAAAAAA-AG
1 AAAGAAAAAAAAGAG
*
1888911 AAAAAGAAAAAAAGAG
1 AAAGA-AAAAAAAGAG
1888927 AAAGAAAAAAAAGAG
1 AAAGAAAAAAAAGAG
1888942 GTTATAAAGA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
14 4 0.15
15 17 0.63
16 6 0.22
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (15 bp):
AAAGAAAAAAAAGAG
Found at i:1891392 original size:123 final size:123
Alignment explanation
Indices: 1891173--1891825 Score: 973
Period size: 123 Copynumber: 5.3 Consensus size: 123
1891163 TCGATGGATA
* *
1891173 AACATTTCCAGAAGGAGTTCGTAATAAGAAGAACTCATCTGAAGATGAAGAATAAGTTCATAATC
1 AACATTTCCAGAAGGAGTTCGTAATAAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAATC
* * * *
1891238 TGAAGAACTTATTCAACTTTTTGCTCGACTCTATCGTAGAAGGAAATAGAGCAGCATC
66 TGAAGAACTTGTTCAACCTTTTGCTCGATTCTATCGCAGAAGGAAATAGAGCAGCATC
*
1891296 AACATTTCCAGAAGGAGTTCGTAATAAGAAGAACTCATCTGAAGAGGAAGAAAAAGTTCATAATC
1 AACATTTCCAGAAGGAGTTCGTAATAAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAATC
* * *
1891361 TGAAGAACTTATTCAACCTTTTGCTCGACTCTATCGCAGAAGGAAATAGAGCAACATC
66 TGAAGAACTTGTTCAACCTTTTGCTCGATTCTATCGCAGAAGGAAATAGAGCAGCATC
* * *
1891419 AATATTTCCAGAAGGAGTTCGTAATAAGAAGAACTCATCTGAAGAGGAAGAGGAAGTTCATAATT
1 AACATTTCCAGAAGGAGTTCGTAATAAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAATC
* * * *
1891484 TGAAGAACTTGTTCAACCTTTTTGCTCGATTCTATCGCATAATGATATATAGCAGCATC
66 TGAAGAACTTGTTCAACC-TTTTGCTCGATTCTATCGCAGAAGGAAATAGAGCAGCATC
* * * *
1891543 AAACATTTCCAAAAGGAGTTCGTAATAAGAAGAACTCATCTGAAGAGGAACAGGAAGTTCGTAAT
1 -AACATTTCCAGAAGGAGTTCGTAATAAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAAT
* * * * *
1891608 CTGAAGAACTTGTTCAACTTTTTTGCTCGATTTTATCACAGAAGGAGATAGAGCAGTATC
65 CTGAAGAACTTGTTCAAC-CTTTTGCTCGATTCTATCGCAGAAGGAAATAGAGCAGCATC
* *
1891668 AACATTTCCAGAAGGAGTTCGTAATAAGAAGAACTCATCTAAAGAGGAAGTAGAAGTTCATAATC
1 AACATTTCCAGAAGGAGTTCGTAATAAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAATC
* * * *
1891733 TGAAGAACTTGTTCAACCTTTTGCTCGATTCTATCACAGAAGGAGATGGAGCAACATC
66 TGAAGAACTTGTTCAACCTTTTGCTCGATTCTATCGCAGAAGGAAATAGAGCAGCATC
* *
1891791 AACATTTCTAGAAGGAGTTCATAATAAGAAGAACT
1 AACATTTCCAGAAGGAGTTCGTAATAAGAAGAACT
1891826 TCAAAATAAG
Statistics
Matches: 485, Mismatches: 42, Indels: 6
0.91 0.08 0.01
Matches are distributed among these distances:
123 265 0.55
124 110 0.23
125 110 0.23
ACGTcount: A:0.38, C:0.16, G:0.19, T:0.26
Consensus pattern (123 bp):
AACATTTCCAGAAGGAGTTCGTAATAAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAATC
TGAAGAACTTGTTCAACCTTTTGCTCGATTCTATCGCAGAAGGAAATAGAGCAGCATC
Found at i:1891828 original size:17 final size:17
Alignment explanation
Indices: 1891808--1891842 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
1891798 CTAGAAGGAG
*
1891808 TTCATAATAAGAAGAAC
1 TTCAAAATAAGAAGAAC
1891825 TTCAAAATAAGAAGAAC
1 TTCAAAATAAGAAGAAC
1891842 T
1 T
1891843 CATCTGAAGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.54, C:0.11, G:0.11, T:0.23
Consensus pattern (17 bp):
TTCAAAATAAGAAGAAC
Found at i:1891932 original size:140 final size:140
Alignment explanation
Indices: 1891690--1891965 Score: 446
Period size: 140 Copynumber: 2.0 Consensus size: 140
1891680 AGGAGTTCGT
* *
1891690 AATAAGAAGAACTCATCTAAAGAGGAAGTAGAAGTTCATAATCTGAAGAACTTGTTCAACCTTTT
1 AATAAGAAGAACTCATCTAAAGAGAAAGTAGAAGTTCATAATCTGAAGAACTTATTCAACCTTTT
* * * *
1891755 GCTCGATTCTATCACAGAAGGAGATGGAGCAACATCAACATTTCTAGAAGGAGTTCATAATAAGA
66 GCTCGACTCTATCACAGAAGGAGATAGAGCAAAATCAACATTTCCAGAAGGAGTTCATAATAAGA
1891820 AGAACTTCAA
131 AGAACTTCAA
* *
1891830 AATAAGAAGAACTCATCTGAAGAGAAAGTAGAAGTTCATAATCTGAAGAAGTTATTCAACCTTTT
1 AATAAGAAGAACTCATCTAAAGAGAAAGTAGAAGTTCATAATCTGAAGAACTTATTCAACCTTTT
**
1891895 GCTCGACTCTATCGTAGAAGGAGATAGAG-AAGAATCAACATTTCCAGAAGGAGTTCATAATAAG
66 GCTCGACTCTATCACAGAAGGAGATAGAGCAA-AATCAACATTTCCAGAAGGAGTTCATAATAAG
1891959 AAGAACT
130 AAGAACT
1891966 CATCTGAAGA
Statistics
Matches: 125, Mismatches: 10, Indels: 2
0.91 0.07 0.01
Matches are distributed among these distances:
139 2 0.02
140 123 0.98
ACGTcount: A:0.41, C:0.15, G:0.19, T:0.25
Consensus pattern (140 bp):
AATAAGAAGAACTCATCTAAAGAGAAAGTAGAAGTTCATAATCTGAAGAACTTATTCAACCTTTT
GCTCGACTCTATCACAGAAGGAGATAGAGCAAAATCAACATTTCCAGAAGGAGTTCATAATAAGA
AGAACTTCAA
Found at i:1891986 original size:123 final size:120
Alignment explanation
Indices: 1891825--1892085 Score: 396
Period size: 123 Copynumber: 2.1 Consensus size: 120
1891815 TAAGAAGAAC
* * *
1891825 TTCAAAATAAGAAGAACTCATCTGAAGAGAAAGTAGAAGTTCATAATCTGAAGAAGTTATTCAAC
1 TTCATAATAAGAAGAACTCATCTGAAGAGAAAGAAGAAGTTCATAATCTGAAGAACTTATTCAAC
**
1891890 CTTTTGCTCGACTCTATCGTAGAAGGAGATAGAGAAGAATCAACATTTCCAGAAGGAG
66 CTTTTGCTCGACTC-ATCACAGAAGGAGATAGAGAAGAATC-A-ATTTCCAGAAGGAG
*
1891948 TTCATAATAAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAATCTGAAGAACTTATTCAAC
1 TTCATAATAAGAAGAACTCATCTGAAGAGAAAGAAGAAGTTCATAATCTGAAGAACTTATTCAAC
* ** **
1892013 CTTTTGCTCGACTCATCACAGAATGAGATAGATCATCATCAATTTCCAGAAGGAG
66 CTTTTGCTCGACTCATCACAGAAGGAGATAGAGAAGAATCAATTTCCAGAAGGAG
1892068 TTCATAATAAGAAGAACT
1 TTCATAATAAGAAGAACT
1892086 AGTTCAACCT
Statistics
Matches: 127, Mismatches: 11, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
120 32 0.25
121 1 0.01
122 19 0.15
123 75 0.59
ACGTcount: A:0.41, C:0.16, G:0.18, T:0.25
Consensus pattern (120 bp):
TTCATAATAAGAAGAACTCATCTGAAGAGAAAGAAGAAGTTCATAATCTGAAGAACTTATTCAAC
CTTTTGCTCGACTCATCACAGAAGGAGATAGAGAAGAATCAATTTCCAGAAGGAG
Found at i:1892391 original size:3 final size:3
Alignment explanation
Indices: 1892362--1892434 Score: 64
Period size: 3 Copynumber: 25.0 Consensus size: 3
1892352 TGTCCCTTTT
* * *
1892362 TTA TT- TTA ATA TTA TT- TTAA TTA -TA TTA TTA ATA TTA ATA TTA
1 TTA TTA TTA TTA TTA TTA TT-A TTA TTA TTA TTA TTA TTA TTA TTA
*
1892405 TTA CTA TTA TTCA -TA TTA TTA TTA TTA TTA
1 TTA TTA TTA TT-A TTA TTA TTA TTA TTA TTA
1892435 CAGGACTAAA
Statistics
Matches: 56, Mismatches: 8, Indels: 12
0.74 0.11 0.16
Matches are distributed among these distances:
2 7 0.12
3 46 0.82
4 3 0.05
ACGTcount: A:0.37, C:0.03, G:0.00, T:0.60
Consensus pattern (3 bp):
TTA
Found at i:1896204 original size:45 final size:45
Alignment explanation
Indices: 1896127--1896220 Score: 143
Period size: 45 Copynumber: 2.1 Consensus size: 45
1896117 CACTAACTTG
** *
1896127 ACGACATAATTTAAATAAAGAATCAATCCACAAAATACAAGTCAA
1 ACGACATAAAGTAAATAAAGAACCAATCCACAAAATACAAGTCAA
* *
1896172 ACGACATAAAGTAAATAGAGAACCAATGCACAAAATACAAGTCAA
1 ACGACATAAAGTAAATAAAGAACCAATCCACAAAATACAAGTCAA
1896217 ACGA
1 ACGA
1896221 TTCTAGAATC
Statistics
Matches: 44, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
45 44 1.00
ACGTcount: A:0.55, C:0.18, G:0.11, T:0.16
Consensus pattern (45 bp):
ACGACATAAAGTAAATAAAGAACCAATCCACAAAATACAAGTCAA
Found at i:1896390 original size:29 final size:29
Alignment explanation
Indices: 1896358--1896415 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 29
1896348 CGATAACACC
*
1896358 TTATAATCAG-GAATCATTTTATAACTTTT
1 TTATAATCAGAGAAT-ATGTTATAACTTTT
* *
1896387 TTATAATTAGAGACTATGTTATAACTTTT
1 TTATAATCAGAGAATATGTTATAACTTTT
1896416 AATAGTTGGG
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 22 0.88
30 3 0.12
ACGTcount: A:0.34, C:0.09, G:0.09, T:0.48
Consensus pattern (29 bp):
TTATAATCAGAGAATATGTTATAACTTTT
Found at i:1899497 original size:14 final size:14
Alignment explanation
Indices: 1899478--1899511 Score: 52
Period size: 14 Copynumber: 2.4 Consensus size: 14
1899468 TGTGAGTATT
1899478 TATTATG-ATTAAAA
1 TATTATGTATT-AAA
1899492 TATTATGTATTAAA
1 TATTATGTATTAAA
1899506 TATTAT
1 TATTAT
1899512 TTTAGTTTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 16 0.84
15 3 0.16
ACGTcount: A:0.44, C:0.00, G:0.06, T:0.50
Consensus pattern (14 bp):
TATTATGTATTAAA
Found at i:1903807 original size:3 final size:3
Alignment explanation
Indices: 1903790--1903841 Score: 70
Period size: 3 Copynumber: 17.0 Consensus size: 3
1903780 CGAGTCTTTT
*
1903790 TTA TT- TTA TTTA TTA TTA TTA TTA TTA TTA TTA TTA TTA CTAA TTA
1 TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA
1903836 TTA TTA
1 TTA TTA
1903842 CATTATTTTT
Statistics
Matches: 44, Mismatches: 2, Indels: 6
0.85 0.04 0.12
Matches are distributed among these distances:
2 2 0.05
3 37 0.84
4 5 0.11
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:1905359 original size:30 final size:30
Alignment explanation
Indices: 1905297--1905362 Score: 82
Period size: 30 Copynumber: 2.2 Consensus size: 30
1905287 TGCCATTATA
**
1905297 GTCCTTTAAGTTTCAGTTTTTACTATTTTT
1 GTCCTTTAAGTTTCAGTTTTTACTATGGTT
1905327 GTCCTTTAAGTTATCA-TTTTT-CTTATGGTT
1 GTCCTTTAAGTT-TCAGTTTTTAC-TATGGTT
1905357 GTCCTT
1 GTCCTT
1905363 GTAATTTTAA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
29 1 0.03
30 28 0.88
31 3 0.09
ACGTcount: A:0.15, C:0.15, G:0.12, T:0.58
Consensus pattern (30 bp):
GTCCTTTAAGTTTCAGTTTTTACTATGGTT
Found at i:1909710 original size:20 final size:21
Alignment explanation
Indices: 1909685--1909731 Score: 62
Period size: 20 Copynumber: 2.3 Consensus size: 21
1909675 TATCGAGAAA
*
1909685 ACATACAACA-ACACATACAT
1 ACATACAACATACACACACAT
*
1909705 ACATAC-ACATACATACACAT
1 ACATACAACATACACACACAT
1909725 ACATACA
1 ACATACA
1909732 TGATACATGA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
19 3 0.13
20 20 0.87
ACGTcount: A:0.53, C:0.30, G:0.00, T:0.17
Consensus pattern (21 bp):
ACATACAACATACACACACAT
Found at i:1909714 original size:10 final size:10
Alignment explanation
Indices: 1909701--1909731 Score: 62
Period size: 10 Copynumber: 3.1 Consensus size: 10
1909691 AACAACACAT
1909701 ACATACATAC
1 ACATACATAC
1909711 ACATACATAC
1 ACATACATAC
1909721 ACATACATAC
1 ACATACATAC
1909731 A
1 A
1909732 TGATACATGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.52, C:0.29, G:0.00, T:0.19
Consensus pattern (10 bp):
ACATACATAC
Found at i:1910326 original size:28 final size:28
Alignment explanation
Indices: 1910289--1910353 Score: 78
Period size: 30 Copynumber: 2.3 Consensus size: 28
1910279 GTATGCTCAT
1910289 TTTAAAAAAA-ATAATTAAGTCTATTTC
1 TTTAAAAAAACATAATTAAGTCTATTTC
* **
1910316 TCTTAACAAAATCATCTTTAAGTCTATTTC
1 T-TTAA-AAAAACATAATTAAGTCTATTTC
1910346 TTTAAAAA
1 TTTAAAAA
1910354 CAAATTTTGT
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
27 1 0.03
28 7 0.22
29 8 0.25
30 16 0.50
ACGTcount: A:0.43, C:0.12, G:0.03, T:0.42
Consensus pattern (28 bp):
TTTAAAAAAACATAATTAAGTCTATTTC
Found at i:1910580 original size:65 final size:65
Alignment explanation
Indices: 1910453--1910581 Score: 147
Period size: 65 Copynumber: 2.0 Consensus size: 65
1910443 TAACCCATCG
* * ** * *
1910453 TTGAGTCTGTTTCTTTGGAAACAAAATTTTGTCTCTCTTGAGACATTTTCTTTTGAGAAAAATCT
1 TTGAGTATGTTTCTATGGAAACAAAATTTTACCTCTCTTGAGACATTTTCCTTTGAAAAAAATCT
*
1910518 TTGAGTATGTTTCTATGGAAACAAAA-TTTACCATCT-TTGAG-TATGTTTCCTTTGAAACAAAA
1 TTGAGTATGTTTCTATGGAAACAAAATTTTACC-TCTCTTGAGACAT-TTTCCTTTGAAA-AAAA
1910580 TC
63 TC
1910582 ATCTTTGAGA
Statistics
Matches: 54, Mismatches: 7, Indels: 6
0.81 0.10 0.09
Matches are distributed among these distances:
63 2 0.04
64 19 0.35
65 33 0.61
ACGTcount: A:0.29, C:0.14, G:0.15, T:0.42
Consensus pattern (65 bp):
TTGAGTATGTTTCTATGGAAACAAAATTTTACCTCTCTTGAGACATTTTCCTTTGAAAAAAATCT
Found at i:1910590 original size:32 final size:34
Alignment explanation
Indices: 1910514--1910590 Score: 97
Period size: 36 Copynumber: 2.3 Consensus size: 34
1910504 TTTGAGAAAA
1910514 ATCTTTGAGTATGTTTCTATGGAAACAAAATTTACC
1 ATCTTTGAGTATGTTTCTATGGAAACAAAA-TTA-C
*
1910550 ATCTTTGAGTATGTTTCCT-TTGAAACAAAA-T-C
1 ATCTTTGAGTATGTTT-CTATGGAAACAAAATTAC
1910582 ATCTTTGAG
1 ATCTTTGAG
1910591 ATTATTTCCC
Statistics
Matches: 39, Mismatches: 1, Indels: 6
0.85 0.02 0.13
Matches are distributed among these distances:
32 10 0.26
34 1 0.03
36 26 0.67
37 2 0.05
ACGTcount: A:0.31, C:0.14, G:0.14, T:0.40
Consensus pattern (34 bp):
ATCTTTGAGTATGTTTCTATGGAAACAAAATTAC
Found at i:1910599 original size:32 final size:32
Alignment explanation
Indices: 1910549--1910609 Score: 79
Period size: 32 Copynumber: 1.9 Consensus size: 32
1910539 CAAAATTTAC
* * *
1910549 CATCTTTGAGTATGTTTCCTTTGAAACAAAAT
1 CATCTTTGAGTATATTTCCCTTAAAACAAAAT
1910581 CATCTTTGAG-ATTATTTCCCTTAAAACAA
1 CATCTTTGAGTA-TATTTCCCTTAAAACAA
1910610 GTTTTGTTTC
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
31 1 0.04
32 24 0.96
ACGTcount: A:0.33, C:0.18, G:0.10, T:0.39
Consensus pattern (32 bp):
CATCTTTGAGTATATTTCCCTTAAAACAAAAT
Found at i:1910708 original size:67 final size:66
Alignment explanation
Indices: 1910568--1910722 Score: 168
Period size: 67 Copynumber: 2.3 Consensus size: 66
1910558 GTATGTTTCC
* * * ** *
1910568 TTTGAAACAAAATCATCTTTGAGATTATTTCCCTTAAAACAAGTTTTGTTTCTTTTGAGATAGTT
1 TTTGAAACACAA--ATCTTTGAGATCATTTCCCTTAAAACAAGTTTTGTCTCCCTTGAGACAGTT
*
1910633 TCT
64 TAT
* * ** *
1910636 CTTGAAACACAAATCTTTGAGATCGTTTCCCTTGAAATGAATTTTTGTCTCCCTTGAGACAGTTT
1 TTTGAAACACAAATCTTTGAGATCATTTCCCTT-AAAACAAGTTTTGTCTCCCTTGAGACAGTTT
1910701 AT
65 AT
1910703 TTTGAAACACAAA-CTTTGAG
1 TTTGAAACACAAATCTTTGAG
1910723 TTTGTTTCTA
Statistics
Matches: 73, Mismatches: 13, Indels: 4
0.81 0.14 0.04
Matches are distributed among these distances:
66 26 0.36
67 37 0.51
68 10 0.14
ACGTcount: A:0.30, C:0.16, G:0.14, T:0.41
Consensus pattern (66 bp):
TTTGAAACACAAATCTTTGAGATCATTTCCCTTAAAACAAGTTTTGTCTCCCTTGAGACAGTTTA
T
Found at i:1910739 original size:29 final size:29
Alignment explanation
Indices: 1910707--1910777 Score: 81
Period size: 29 Copynumber: 2.5 Consensus size: 29
1910697 GTTTATTTTG
* * * *
1910707 AAACACAAACTTTGAGTTTGTTTCTATTA
1 AAACACAAATTTTGAGATCGCTTCTATTA
* *
1910736 AAACACCAATTTTGAGATCGCTTCTATTG
1 AAACACAAATTTTGAGATCGCTTCTATTA
1910765 AAACA-AAATTTTG
1 AAACACAAATTTTG
1910778 TCTCTCTTGA
Statistics
Matches: 35, Mismatches: 7, Indels: 1
0.81 0.16 0.02
Matches are distributed among these distances:
28 7 0.20
29 28 0.80
ACGTcount: A:0.37, C:0.15, G:0.11, T:0.37
Consensus pattern (29 bp):
AAACACAAATTTTGAGATCGCTTCTATTA
Found at i:1910787 original size:95 final size:96
Alignment explanation
Indices: 1910621--1910795 Score: 235
Period size: 95 Copynumber: 1.8 Consensus size: 96
1910611 TTTTGTTTCT
* * * * ** *
1910621 TTTGAGATAGTTTCTCTTGAAACACAAATCTTTGAGATCGTTTCCCTTGAAATGAATTTTTGTCT
1 TTTGAGATAGTTTCTATTAAAACACAAATCTTTGAGATCGCTTCCATTGAAACAAAATTTTGTCT
1910686 CCCTTGAGACAGTTTATTTTGAAACACAAAC
66 CCCTTGAGACAGTTTATTTTGAAACACAAAC
* * * *
1910717 TTTGAGTTTGTTTCTATTAAAACACCAAT-TTTGAGATCGCTTCTATTGAAACAAAATTTTGTCT
1 TTTGAGATAGTTTCTATTAAAACACAAATCTTTGAGATCGCTTCCATTGAAACAAAATTTTGTCT
*
1910781 CTCTTGAGACAGTTT
66 CCCTTGAGACAGTTT
1910796 CTCTTAAAAC
Statistics
Matches: 67, Mismatches: 12, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
95 43 0.64
96 24 0.36
ACGTcount: A:0.29, C:0.17, G:0.14, T:0.41
Consensus pattern (96 bp):
TTTGAGATAGTTTCTATTAAAACACAAATCTTTGAGATCGCTTCCATTGAAACAAAATTTTGTCT
CCCTTGAGACAGTTTATTTTGAAACACAAAC
Found at i:1910949 original size:29 final size:29
Alignment explanation
Indices: 1910870--1910957 Score: 106
Period size: 29 Copynumber: 3.1 Consensus size: 29
1910860 CTTTTGAAAC
* * *
1910870 ACATCATCTCTGAGTTTGTTTTTCTTGAA
1 ACATCATCTTTGAGTCTGTTTCTCTTGAA
* * *
1910899 ACA-AATCCTTGAATCTGTTTCTCTTGAA
1 ACATCATCTTTGAGTCTGTTTCTCTTGAA
*
1910927 ACATCATCTTTGAGTCGGTTTCTCTTGAA
1 ACATCATCTTTGAGTCTGTTTCTCTTGAA
1910956 AC
1 AC
1910958 CATAATCCCT
Statistics
Matches: 48, Mismatches: 10, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
28 22 0.46
29 26 0.54
ACGTcount: A:0.24, C:0.20, G:0.14, T:0.42
Consensus pattern (29 bp):
ACATCATCTTTGAGTCTGTTTCTCTTGAA
Found at i:1912084 original size:3 final size:3
Alignment explanation
Indices: 1912065--1912114 Score: 57
Period size: 3 Copynumber: 16.0 Consensus size: 3
1912055 GGGTCTTTTT
*
1912065 TTA TT- TTA TTTA TTTA TTA TTA TTA TTA TTA TTA TTA GTAA TTA TTA
1 TTA TTA TTA -TTA -TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA
1912112 TTA
1 TTA
1912115 CATCATTTTT
Statistics
Matches: 42, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
2 2 0.05
3 31 0.74
4 9 0.21
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:1912415 original size:53 final size:53
Alignment explanation
Indices: 1912335--1912442 Score: 207
Period size: 53 Copynumber: 2.0 Consensus size: 53
1912325 GGTTTTTAAA
1912335 ACCCTAACCCTAGGGTATGGTTATGCCACCACCATCTGCTGTTACTGCCACCC
1 ACCCTAACCCTAGGGTATGGTTATGCCACCACCATCTGCTGTTACTGCCACCC
*
1912388 ACCCTAACCCTAGGGTATGGTTATGCCACCACCGTCTGCTGTTACTGCCACCC
1 ACCCTAACCCTAGGGTATGGTTATGCCACCACCATCTGCTGTTACTGCCACCC
1912441 AC
1 AC
1912443 TGACGCCGCT
Statistics
Matches: 54, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
53 54 1.00
ACGTcount: A:0.20, C:0.38, G:0.18, T:0.24
Consensus pattern (53 bp):
ACCCTAACCCTAGGGTATGGTTATGCCACCACCATCTGCTGTTACTGCCACCC
Found at i:1913728 original size:30 final size:30
Alignment explanation
Indices: 1913694--1913758 Score: 87
Period size: 30 Copynumber: 2.2 Consensus size: 30
1913684 GCCACTGTAA
* *
1913694 TCCTTTAAGTTTCAATTTTTGC-TATTTTGG
1 TCCTTTAAGTTACAATTTTT-CTTATTGTGG
*
1913724 TCCTTTAAGTTACTATTTTTCTTATTGTGG
1 TCCTTTAAGTTACAATTTTTCTTATTGTGG
1913754 TCCTT
1 TCCTT
1913759 GTAATTTTAA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
29 1 0.03
30 30 0.97
ACGTcount: A:0.15, C:0.15, G:0.12, T:0.57
Consensus pattern (30 bp):
TCCTTTAAGTTACAATTTTTCTTATTGTGG
Found at i:1914044 original size:21 final size:21
Alignment explanation
Indices: 1914018--1914302 Score: 116
Period size: 21 Copynumber: 13.7 Consensus size: 21
1914008 CATATTCGCA
*
1914018 TTGCGATAGTCCACGTTCACG
1 TTGCGATAGTCCAAGTTCACG
* *
1914039 TTGCGATAGTCGAAGTTCGCG
1 TTGCGATAGTCCAAGTTCACG
* *
1914060 TTGCGATTTATTCCAAATTCA--
1 TTGCGA--TAGTCCAAGTTCACG
* *
1914081 TTGCGATTTATTCCAAATT--CG
1 TTGCGA--TAGTCCAAGTTCACG
* * *
1914102 TTGCAATTTATTCCAAATT--CG
1 TTGCGA--TAGTCCAAGTTCACG
* * *
1914123 TTGTGATTTATTCCAAATT--CG
1 TTGCGA--TAGTCCAAGTTCACG
*
1914144 TTGCGATAGTCCAAGTTCGCG
1 TTGCGATAGTCCAAGTTCACG
*
1914165 TTGCGATTTATTCCAAGTTCA--
1 TTGCGA--TAGTCCAAGTTCACG
* *
1914186 TTGCGATAGTCGAAGTTCGCG
1 TTGCGATAGTCCAAGTTCACG
* *
1914207 TTGCGATTTATTCCAAATT--CG
1 TTGCGA--TAGTCCAAGTTCACG
1914228 TTGCGATAGTCCAAGTT--CG
1 TTGCGATAGTCCAAGTTCACG
* *
1914247 TTGCGATAGTCGAAGTTCGCG
1 TTGCGATAGTCCAAGTTCACG
* * *
1914268 TTGCAATTTATTCCAAATT--CG
1 TTGCGA--TAGTCCAAGTTCACG
1914289 TTGCGATAGTCCAA
1 TTGCGATAGTCCAA
1914303 AATCGCAACG
Statistics
Matches: 218, Mismatches: 30, Indels: 34
0.77 0.11 0.12
Matches are distributed among these distances:
19 53 0.24
21 129 0.59
23 36 0.17
ACGTcount: A:0.23, C:0.20, G:0.20, T:0.36
Consensus pattern (21 bp):
TTGCGATAGTCCAAGTTCACG
Found at i:1914148 original size:84 final size:82
Alignment explanation
Indices: 1914071--1914295 Score: 269
Period size: 84 Copynumber: 2.7 Consensus size: 82
1914061 TGCGATTTAT
* * * *
1914071 TCCAAATTCATTGCGATTTATTCCAAATTCGTTGCAATTTATTCCAAATTCGTTGTGATTTATTC
1 TCCAAGTTCGTTGCGATTTATTCCAAGTTCGTTGCAATTTATTCCAAATTCGTTGCGATTTATTC
1914136 CAAATTCGTTGCGATAG
66 CAAATTCGTTGCGATAG
* * * * *
1914153 TCCAAGTTCGCGTTGCGATTTATTCCAAGTTCATTGCGA--TAGTCGAAGTTCGCGTTGCGATTT
1 TCCAAGTT--CGTTGCGATTTATTCCAAGTTCGTTGCAATTTATTCCAAATT--CGTTGCGATTT
1914216 ATTCCAAATTCGTTGCGATAG
62 ATTCCAAATTCGTTGCGATAG
* *
1914237 TCCAAGTTCGTTGCGA--TAGTCGAAGTTCGCGTTGCAATTTATTCCAAATTCGTTGCGAT
1 TCCAAGTTCGTTGCGATTTATTCCAAGTT--CGTTGCAATTTATTCCAAATTCGTTGCGAT
1914296 AGTCCAAAAT
Statistics
Matches: 119, Mismatches: 16, Indels: 16
0.79 0.11 0.11
Matches are distributed among these distances:
80 9 0.08
82 38 0.32
84 72 0.61
ACGTcount: A:0.24, C:0.20, G:0.19, T:0.38
Consensus pattern (82 bp):
TCCAAGTTCGTTGCGATTTATTCCAAGTTCGTTGCAATTTATTCCAAATTCGTTGCGATTTATTC
CAAATTCGTTGCGATAG
Found at i:1914255 original size:61 final size:62
Alignment explanation
Indices: 1914081--1914302 Score: 240
Period size: 61 Copynumber: 3.6 Consensus size: 62
1914071 TCCAAATTCA
* * * * * * *
1914081 TTGCGATTTATTCCAAATTCGTTGCAATTTATTCCAAATTCGTTGTGATTTATTCCAAATT--CG
1 TTGCGATTTATTCCAAATTCGTTGCGA-TTAGTCCAAGTTCGTTGCGA--TAGTCGAAGTTCGCG
* * * *
1914144 TTGCGA--TAGTCCAAGTTCGCGTTGCGATTTATTCCAAGTTCATTGCGATAGTCGAAGTTCGCG
1 TTGCGATTTATTCCAAATT--CGTTGCGA-TTAGTCCAAGTTCGTTGCGATAGTCGAAGTTCGCG
1914207 TTGCGATTTATTCCAAATTCGTTGCGA-TAGTCCAAGTTCGTTGCGATAGTCGAAGTTCGCG
1 TTGCGATTTATTCCAAATTCGTTGCGATTAGTCCAAGTTCGTTGCGATAGTCGAAGTTCGCG
*
1914268 TTGCAATTTATTCCAAATTCGTTGCGA-TAGTCCAA
1 TTGCGATTTATTCCAAATTCGTTGCGATTAGTCCAA
1914303 AATCGCAACG
Statistics
Matches: 139, Mismatches: 14, Indels: 14
0.83 0.08 0.08
Matches are distributed among these distances:
61 83 0.60
63 47 0.34
65 9 0.06
ACGTcount: A:0.23, C:0.19, G:0.20, T:0.37
Consensus pattern (62 bp):
TTGCGATTTATTCCAAATTCGTTGCGATTAGTCCAAGTTCGTTGCGATAGTCGAAGTTCGCG
Found at i:1914399 original size:6 final size:6
Alignment explanation
Indices: 1914388--1914424 Score: 74
Period size: 6 Copynumber: 6.2 Consensus size: 6
1914378 GACACGTATT
1914388 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG A
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG A
1914425 GACGGGACAG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 31 1.00
ACGTcount: A:0.35, C:0.49, G:0.16, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:1914952 original size:12 final size:11
Alignment explanation
Indices: 1914922--1914955 Score: 52
Period size: 12 Copynumber: 3.1 Consensus size: 11
1914912 CCGTCTCGTC
1914922 TCGGGTCG-GG
1 TCGGGTCGTGG
1914932 TCGGGTCGTGG
1 TCGGGTCGTGG
1914943 TCGTGGTCGTGG
1 TCG-GGTCGTGG
1914955 T
1 T
1914956 AATACGTGTC
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
10 8 0.36
11 5 0.23
12 9 0.41
ACGTcount: A:0.00, C:0.18, G:0.53, T:0.29
Consensus pattern (11 bp):
TCGGGTCGTGG
Found at i:1915083 original size:21 final size:21
Alignment explanation
Indices: 1915054--1915211 Score: 100
Period size: 21 Copynumber: 7.6 Consensus size: 21
1915044 TTTGGAATAA
1915054 ATCGCAACGCGAACTTTGACT
1 ATCGCAACGCGAACTTTGACT
* *
1915075 ATCACAA--CGAA-TTTGGAAT
1 ATCGCAACGCGAACTTT-GACT
*
1915094 AAATCGCAACGCGAACTTCGACT
1 --ATCGCAACGCGAACTTTGACT
*
1915117 ATCGCAA--CGAA-TTTGGAAT
1 ATCGCAACGCGAACTTT-GACT
* *
1915136 AAATCCCAACGCGAACTTCGACT
1 --ATCGCAACGCGAACTTTGACT
**
1915159 ATCGCAA--CGAA-TTTGGAAA
1 ATCGCAACGCGAACTTT-GACT
*
1915178 ATCGCAACGCGAACTTGGACT
1 ATCGCAACGCGAACTTTGACT
*
1915199 ATCGCAATGCGAA
1 ATCGCAACGCGAA
1915212 TATGTAAATC
Statistics
Matches: 103, Mismatches: 18, Indels: 32
0.67 0.12 0.21
Matches are distributed among these distances:
18 7 0.07
19 27 0.26
21 49 0.48
22 2 0.02
23 14 0.14
24 4 0.04
ACGTcount: A:0.35, C:0.25, G:0.19, T:0.21
Consensus pattern (21 bp):
ATCGCAACGCGAACTTTGACT
Found at i:1915212 original size:42 final size:42
Alignment explanation
Indices: 1915040--1915205 Score: 282
Period size: 42 Copynumber: 4.0 Consensus size: 42
1915030 CCAGCCGTTG
* *
1915040 CGAATTTGGAATAAATCGCAACGCGAACTTTGACTATCACAA
1 CGAATTTGGAATAAATCGCAACGCGAACTTCGACTATCGCAA
1915082 CGAATTTGGAATAAATCGCAACGCGAACTTCGACTATCGCAA
1 CGAATTTGGAATAAATCGCAACGCGAACTTCGACTATCGCAA
*
1915124 CGAATTTGGAATAAATCCCAACGCGAACTTCGACTATCGCAA
1 CGAATTTGGAATAAATCGCAACGCGAACTTCGACTATCGCAA
*
1915166 CGAATTTGG-A-AAATCGCAACGCGAACTTGGACTATCGCAA
1 CGAATTTGGAATAAATCGCAACGCGAACTTCGACTATCGCAA
1915206 TGCGAATATG
Statistics
Matches: 119, Mismatches: 5, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
40 28 0.24
41 1 0.01
42 90 0.76
ACGTcount: A:0.36, C:0.23, G:0.19, T:0.22
Consensus pattern (42 bp):
CGAATTTGGAATAAATCGCAACGCGAACTTCGACTATCGCAA
Found at i:1915224 original size:20 final size:20
Alignment explanation
Indices: 1915199--1915250 Score: 104
Period size: 20 Copynumber: 2.6 Consensus size: 20
1915189 AACTTGGACT
1915199 ATCGCAATGCGAATATGTAA
1 ATCGCAATGCGAATATGTAA
1915219 ATCGCAATGCGAATATGTAA
1 ATCGCAATGCGAATATGTAA
1915239 ATCGCAATGCGA
1 ATCGCAATGCGA
1915251 TAGTCGAAGT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.38, C:0.17, G:0.21, T:0.23
Consensus pattern (20 bp):
ATCGCAATGCGAATATGTAA
Found at i:1915270 original size:21 final size:21
Alignment explanation
Indices: 1915240--1915279 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
1915230 AATATGTAAA
1915240 TCGCAATGCGATAGTCGAAGT
1 TCGCAATGCGATAGTCGAAGT
*
1915261 TCGCATTGCGATAGTCGAA
1 TCGCAATGCGATAGTCGAA
1915280 TTTGGAAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.28, C:0.20, G:0.28, T:0.25
Consensus pattern (21 bp):
TCGCAATGCGATAGTCGAAGT
Found at i:1915312 original size:21 final size:21
Alignment explanation
Indices: 1915288--1915342 Score: 83
Period size: 21 Copynumber: 2.6 Consensus size: 21
1915278 AATTTGGAAA
*
1915288 ATCGCAACGCGAACTTCGACC
1 ATCGCAATGCGAACTTCGACC
* *
1915309 ATCGCAATGCGAACTTGGACT
1 ATCGCAATGCGAACTTCGACC
1915330 ATCGCAATGCGAA
1 ATCGCAATGCGAA
1915343 TATGTAAATC
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.31, C:0.29, G:0.22, T:0.18
Consensus pattern (21 bp):
ATCGCAATGCGAACTTCGACC
Found at i:1915371 original size:111 final size:111
Alignment explanation
Indices: 1915166--1915501 Score: 541
Period size: 111 Copynumber: 3.0 Consensus size: 111
1915156 ACTATCGCAA
* * *
1915166 CGAATTTGGAAAATCGCAACGCGAACTTGGACTATCGCAATGCGAA-TATGTA-AATCGCAATGC
1 CGAATTTGGAAAATCGCAACGCGAACTTCGACTATCGCAATGCGAACT-TGGACTATCGCAATGC
* *
1915229 GAATATGTAAATCGCAATGCGATAGTCGAAGTTCGCATTGCGATAGT
65 GAATATGTAAATCACAATGCGATAGTCGAAGTTCGCGTTGCGATAGT
*
1915276 CGAATTTGGAAAATCGCAACGCGAACTTCGACCATCGCAATGCGAACTTGGACTATCGCAATGCG
1 CGAATTTGGAAAATCGCAACGCGAACTTCGACTATCGCAATGCGAACTTGGACTATCGCAATGCG
*
1915341 AATATGTAAATCCCAATGCGATAGTCGAAGTTCGCGTTGCGATAGT
66 AATATGTAAATCACAATGCGATAGTCGAAGTTCGCGTTGCGATAGT
* * *
1915387 TGAATTTGGAAAATCGCAACTCGAACTTCGACTATCGCAATGCAAACTTGGACTATCGCAATGCG
1 CGAATTTGGAAAATCGCAACGCGAACTTCGACTATCGCAATGCGAACTTGGACTATCGCAATGCG
* *
1915452 AATATGTAAATCACAATGCGATGGTCGAAGTTCGCGTTGCGATTGT
66 AATATGTAAATCACAATGCGATAGTCGAAGTTCGCGTTGCGATAGT
1915498 CGAA
1 CGAA
1915502 GTTCGCGTTG
Statistics
Matches: 210, Mismatches: 14, Indels: 3
0.93 0.06 0.01
Matches are distributed among these distances:
110 47 0.22
111 163 0.78
ACGTcount: A:0.32, C:0.20, G:0.23, T:0.25
Consensus pattern (111 bp):
CGAATTTGGAAAATCGCAACGCGAACTTCGACTATCGCAATGCGAACTTGGACTATCGCAATGCG
AATATGTAAATCACAATGCGATAGTCGAAGTTCGCGTTGCGATAGT
Found at i:1915425 original size:21 final size:21
Alignment explanation
Indices: 1915410--1915450 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
1915400 TCGCAACTCG
1915410 AACTTCGACTATCGCAATGCA
1 AACTTCGACTATCGCAATGCA
*
1915431 AACTTGGACTATCGCAATGC
1 AACTTCGACTATCGCAATGC
1915451 GAATATGTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.32, C:0.27, G:0.17, T:0.24
Consensus pattern (21 bp):
AACTTCGACTATCGCAATGCA
Found at i:1915494 original size:21 final size:21
Alignment explanation
Indices: 1915468--1915514 Score: 85
Period size: 21 Copynumber: 2.2 Consensus size: 21
1915458 TAAATCACAA
1915468 TGCGATGGTCGAAGTTCGCGT
1 TGCGATGGTCGAAGTTCGCGT
*
1915489 TGCGATTGTCGAAGTTCGCGT
1 TGCGATGGTCGAAGTTCGCGT
1915510 TGCGA
1 TGCGA
1915515 ATCTGGAAAC
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.15, C:0.19, G:0.36, T:0.30
Consensus pattern (21 bp):
TGCGATGGTCGAAGTTCGCGT
Found at i:1915714 original size:19 final size:19
Alignment explanation
Indices: 1915673--1915716 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 19
1915663 TTTAAATCTG
**
1915673 TATGTATATATTTGTATGT
1 TATGTATATATTTGTATCA
1915692 TATGTAT-TCATTTGTATCA
1 TATGTATAT-ATTTGTATCA
1915711 TATGTA
1 TATGTA
1915717 ATTAAATATG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
18 1 0.05
19 21 0.95
ACGTcount: A:0.27, C:0.05, G:0.14, T:0.55
Consensus pattern (19 bp):
TATGTATATATTTGTATCA
Found at i:1918314 original size:22 final size:22
Alignment explanation
Indices: 1918286--1918333 Score: 96
Period size: 22 Copynumber: 2.2 Consensus size: 22
1918276 GATTGCTGAT
1918286 TGCTCCTTAATAGCAAATGAGG
1 TGCTCCTTAATAGCAAATGAGG
1918308 TGCTCCTTAATAGCAAATGAGG
1 TGCTCCTTAATAGCAAATGAGG
1918330 TGCT
1 TGCT
1918334 TGACGACCTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.29, C:0.19, G:0.23, T:0.29
Consensus pattern (22 bp):
TGCTCCTTAATAGCAAATGAGG
Found at i:1923750 original size:21 final size:19
Alignment explanation
Indices: 1923721--1923759 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 19
1923711 AAATTTAACT
1923721 CAACATTTTTATTTGCTTTAA
1 CAACATTTTT-TTTG-TTTAA
*
1923742 CAACTTTTTTTTTGTTTA
1 CAACATTTTTTTTGTTTA
1923760 TATTTGTACA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 4 0.24
20 4 0.24
21 9 0.53
ACGTcount: A:0.23, C:0.13, G:0.05, T:0.59
Consensus pattern (19 bp):
CAACATTTTTTTTGTTTAA
Found at i:1923755 original size:20 final size:20
Alignment explanation
Indices: 1923721--1923759 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
1923711 AAATTTAACT
1923721 CAACATTTTTATTTGCTTTAA
1 CAACATTTTTATTTG-TTTAA
*
1923742 CAAC-TTTTTTTTTGTTTA
1 CAACATTTTTATTTGTTTA
1923760 TATTTGTACA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 4 0.24
20 9 0.53
21 4 0.24
ACGTcount: A:0.23, C:0.13, G:0.05, T:0.59
Consensus pattern (20 bp):
CAACATTTTTATTTGTTTAA
Found at i:1944220 original size:11 final size:11
Alignment explanation
Indices: 1944204--1944228 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
1944194 GCAATATGCT
1944204 AAAAAATGAAA
1 AAAAAATGAAA
1944215 AAAAAATGAAA
1 AAAAAATGAAA
1944226 AAA
1 AAA
1944229 TGACAATACA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.84, C:0.00, G:0.08, T:0.08
Consensus pattern (11 bp):
AAAAAATGAAA
Found at i:1955313 original size:20 final size:20
Alignment explanation
Indices: 1955288--1955347 Score: 120
Period size: 20 Copynumber: 3.0 Consensus size: 20
1955278 AAACACACGG
1955288 GGAAAGGATTTTTGCATTGA
1 GGAAAGGATTTTTGCATTGA
1955308 GGAAAGGATTTTTGCATTGA
1 GGAAAGGATTTTTGCATTGA
1955328 GGAAAGGATTTTTGCATTGA
1 GGAAAGGATTTTTGCATTGA
1955348 ATGCAATATC
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 40 1.00
ACGTcount: A:0.30, C:0.05, G:0.30, T:0.35
Consensus pattern (20 bp):
GGAAAGGATTTTTGCATTGA
Found at i:1962590 original size:54 final size:54
Alignment explanation
Indices: 1962504--1962991 Score: 523
Period size: 54 Copynumber: 9.0 Consensus size: 54
1962494 AATGTATATG
* ** *
1962504 TTGT-AATTACCATATCGGTACTATGTGTGCAACCTACGTAATTCATAATGAGCT
1 TTGTGAATTACCGTATCGACACTATGTGTGCAACCCACGTAATTCATAATGAG-T
* * * *
1962558 TT-TGAATTACCGTATCAATACTATGTGTGCAACCCACATAATTCATAATGAGC
1 TTGTGAATTACCGTATCGACACTATGTGTGCAACCCACGTAATTCATAATGAGT
* * * *
1962611 TTGTGAATTACCGTATTGGCACTATGTGTGCAACCCACATATTTCATAATGAGT
1 TTGTGAATTACCGTATCGACACTATGTGTGCAACCCACGTAATTCATAATGAGT
* ** ** * *
1962665 TTGGGAATTACCGTATCGGTAGAATGTATGCAACCCACGTAATTCATAATAAGT
1 TTGTGAATTACCGTATCGACACTATGTGTGCAACCCACGTAATTCATAATGAGT
* * ** * * *
1962719 TTTTGAATTATCGTATCGGTACTATGTATGCAACCCACATAATTCATAATAAGT
1 TTGTGAATTACCGTATCGACACTATGTGTGCAACCCACGTAATTCATAATGAGT
* *
1962773 TTGTGAATTAACGTATC-ACCACTATGTTGTGCAACCCACTTAATTCATAATGAGT
1 TTGTGAATTACCGTATCGA-CACTATG-TGTGCAACCCACGTAATTCATAATGAGT
* * *
1962828 TTGTGAATTAGCGTATCGACACTATGTGTACAACCCATGTAATTCATAATGAGT
1 TTGTGAATTACCGTATCGACACTATGTGTGCAACCCACGTAATTCATAATGAGT
** * * * * *
1962882 TTACGAATTACCGTATCGACATTATGTGTACAACCTACGCAATTCATAATTAGT
1 TTGTGAATTACCGTATCGACACTATGTGTGCAACCCACGTAATTCATAATGAGT
** * * * *
1962936 TTGTGAATTAATGTATCGACACTATGTGAGCAAAACCACATAATTTATAATGAGT
1 TTGTGAATTACCGTATCGACACTATGTGTGC-AACCCACGTAATTCATAATGAGT
1962991 T
1 T
1962992 GAAATATTAA
Statistics
Matches: 369, Mismatches: 59, Indels: 11
0.84 0.13 0.03
Matches are distributed among these distances:
53 3 0.01
54 299 0.81
55 66 0.18
56 1 0.00
ACGTcount: A:0.32, C:0.18, G:0.16, T:0.34
Consensus pattern (54 bp):
TTGTGAATTACCGTATCGACACTATGTGTGCAACCCACGTAATTCATAATGAGT
Found at i:1962899 original size:163 final size:160
Alignment explanation
Indices: 1962508--1962991 Score: 563
Period size: 163 Copynumber: 3.0 Consensus size: 160
1962498 TATATGTTGT
* ** *
1962508 AATTACCATATCGGTACTATGTGTGCAACCTACGTAATTCATAATGAGCTTTTGAATTACCGTAT
1 AATTACCGTATCGACACTATGTGTGCAACCCACGTAATTCATAATGAG-TTTTGAATTACCGTAT
* * * * **
1962573 CAATACTATGTGTGCAACCCACATAATTCATAATGAGCTTGTGAATTACCGTATTGGCACTATGT
65 CGATACTATGTGTGCAACCCACATAATTCATAATAAGTTTGTGAATTAACGTA-TCACACTATGT
*
1962638 GTGCAACCCACATATTTCATAATGAGTTTGGG
129 GTGCAACCCACATAATTCATAATGAGTTTGGG
** ** * * *
1962670 AATTACCGTATCGGTAGAATGTATGCAACCCACGTAATTCATAATAAGTTTTTGAATTATCGTAT
1 AATTACCGTATCGACACTATGTGTGCAACCCACGTAATTCATAATGAG-TTTTGAATTACCGTAT
* *
1962735 CGGTACTATGTATGCAACCCACATAATTCATAATAAGTTTGTGAATTAACGTATCACCACTATGT
65 CGATACTATGTGTGCAACCCACATAATTCATAATAAGTTTGTGAATTAACGTATCA-CACTATG-
* *
1962800 TGTGCAACCCACTTAATTCATAATGAGTTTGTG
128 TGTGCAACCCACATAATTCATAATGAGTTTGGG
* * * *
1962833 AATTAGCGTATCGACACTATGTGTACAACCCATGTAATTCATAATGAGTTTACGAATTACCGTAT
1 AATTACCGTATCGACACTATGTGTGCAACCCACGTAATTCATAATGAGTTT-TGAATTACCGTAT
* * * * ** * *
1962898 CGACATTATGTGTACAACCTACGCAATTCATAATTAGTTTGTGAATTAATGTATCGACACTATGT
65 CGATACTATGTGTGCAACCCACATAATTCATAATAAGTTTGTGAATTAACGTATC-ACACTATGT
* * *
1962963 GAGCAAAACCACATAATTTATAATGAGTT
129 GTGC-AACCCACATAATTCATAATGAGTT
1962992 GAAATATTAA
Statistics
Matches: 273, Mismatches: 44, Indels: 9
0.84 0.13 0.03
Matches are distributed among these distances:
161 1 0.00
162 118 0.43
163 153 0.56
164 1 0.00
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33
Consensus pattern (160 bp):
AATTACCGTATCGACACTATGTGTGCAACCCACGTAATTCATAATGAGTTTTGAATTACCGTATC
GATACTATGTGTGCAACCCACATAATTCATAATAAGTTTGTGAATTAACGTATCACACTATGTGT
GCAACCCACATAATTCATAATGAGTTTGGG
Found at i:1973915 original size:54 final size:54
Alignment explanation
Indices: 1973844--1974149 Score: 386
Period size: 54 Copynumber: 5.7 Consensus size: 54
1973834 TACCATATTA
*
1973844 GCACTATGTGTGCAACCCACGTAATTCATATTGAGTTTGTGAATTA-CAGTATCG
1 GCACTATGTGTGCAACCCACGTAATTCATAATGAGTTTGTGAATTATC-GTATCG
* * *
1973898 GCACTATG-GTTGTAACCCACGTAATTCATAATAAG--TGTGAATTATCATATCG
1 GCACTATGTG-TGCAACCCACGTAATTCATAATGAGTTTGTGAATTATCGTATCG
* *
1973950 GCACTATGTGTGCAAGCCACGTAAATCATAATGAGTTTGTGAATTATCGTATCG
1 GCACTATGTGTGCAACCCACGTAATTCATAATGAGTTTGTGAATTATCGTATCG
* * *
1974004 ACACTATGTGTGCAAGCCACGTAAATCATAATGAGTTTGTGAATTATCGTATCG
1 GCACTATGTGTGCAACCCACGTAATTCATAATGAGTTTGTGAATTATCGTATCG
* * ** * *
1974058 ACATTATGTGTGCAACCCACAAAATTCATAATGAGTTTGTGAATTACCGTATAG
1 GCACTATGTGTGCAACCCACGTAATTCATAATGAGTTTGTGAATTATCGTATCG
* ** *
1974112 GCACTATGTGTGCAAAACCACAAAATTTATAATGAGTT
1 GCACTATGTGTGC-AACCCACGTAATTCATAATGAGTT
1974150 AAAATATTAA
Statistics
Matches: 225, Mismatches: 21, Indels: 11
0.88 0.08 0.04
Matches are distributed among these distances:
52 43 0.19
53 3 0.01
54 157 0.70
55 22 0.10
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.32
Consensus pattern (54 bp):
GCACTATGTGTGCAACCCACGTAATTCATAATGAGTTTGTGAATTATCGTATCG
Found at i:1974024 original size:106 final size:106
Alignment explanation
Indices: 1973826--1974126 Score: 376
Period size: 106 Copynumber: 2.8 Consensus size: 106
1973816 AAATGTATAT
* ** * *
1973826 GTTGT-AATTACCATATTAGCACTATGTGTGCAACCCACGTAATTCATATTGAGTTTGTGAATTA
1 GTTGTGAATTATCATATCGGCACTATGTGTGCAACCCACGTAAATCATAATGAGTTTGTGAATTA
* *
1973890 CAGTATCGGCACTATG-GTTGTAACCCACGTAATTCATAATAA
66 C-GTATCGGCACTATGTG-TGCAACCCACGTAAATCATAATAA
*
1973932 G-TGTGAATTATCATATCGGCACTATGTGTGCAAGCCACGTAAATCATAATGAGTTTGTGAATTA
1 GTTGTGAATTATCATATCGGCACTATGTGTGCAACCCACGTAAATCATAATGAGTTTGTGAATTA
* * *
1973996 TCGTATCGACACTATGTGTGCAAGCCACGTAAATCATAATGA
66 -CGTATCGGCACTATGTGTGCAACCCACGTAAATCATAATAA
* * * *
1974038 GTTTGTGAATTATCGTATCGACATTATGTGTGCAACCCAC-AAAATTCATAATGAGTTTGTGAAT
1 G-TTGTGAATTATCATATCGGCACTATGTGTGCAACCCACGTAAA-TCATAATGAGTTTGTGAAT
*
1974102 TACCGTATAGGCACTATGTGTGCAA
64 TA-CGTATCGGCACTATGTGTGCAA
1974127 AACCACAAAA
Statistics
Matches: 170, Mismatches: 19, Indels: 10
0.85 0.10 0.05
Matches are distributed among these distances:
105 3 0.02
106 88 0.52
107 5 0.03
108 74 0.44
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.33
Consensus pattern (106 bp):
GTTGTGAATTATCATATCGGCACTATGTGTGCAACCCACGTAAATCATAATGAGTTTGTGAATTA
CGTATCGGCACTATGTGTGCAACCCACGTAAATCATAATAA
Found at i:1976125 original size:18 final size:18
Alignment explanation
Indices: 1976102--1976137 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
1976092 AAAAACCAAG
1976102 AAATGAAAGAGTAATTAA
1 AAATGAAAGAGTAATTAA
* *
1976120 AAATGAAATATTAATTAA
1 AAATGAAAGAGTAATTAA
1976138 TTTGAGCACT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.61, C:0.00, G:0.11, T:0.28
Consensus pattern (18 bp):
AAATGAAAGAGTAATTAA
Found at i:1995831 original size:14 final size:14
Alignment explanation
Indices: 1995812--1995838 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
1995802 TTCATGTGAT
1995812 ATGGGCATCATCAC
1 ATGGGCATCATCAC
1995826 ATGGGCATCATCA
1 ATGGGCATCATCA
1995839 ATCTGGGCCC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.30, C:0.26, G:0.22, T:0.22
Consensus pattern (14 bp):
ATGGGCATCATCAC
Found at i:1997524 original size:3 final size:3
Alignment explanation
Indices: 1997516--1997557 Score: 84
Period size: 3 Copynumber: 14.0 Consensus size: 3
1997506 GTCAAAAAAT
1997516 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
1997558 TTATTATTAT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:1997562 original size:3 final size:3
Alignment explanation
Indices: 1997556--1997603 Score: 87
Period size: 3 Copynumber: 15.7 Consensus size: 3
1997546 ATAATAATAA
1997556 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T-AT TAT
1997602 TA
1 TA
1997604 ACCCACCACT
Statistics
Matches: 44, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
3 41 0.93
4 3 0.07
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:1997644 original size:22 final size:22
Alignment explanation
Indices: 1997619--1997660 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
1997609 CCACTATCCC
*
1997619 CTAAAACGCACTCAATCCACTA
1 CTAAAACCCACTCAATCCACTA
1997641 CTAAAACCCACTCAATCCAC
1 CTAAAACCCACTCAATCCAC
1997661 CAACCCACTA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.40, C:0.40, G:0.02, T:0.17
Consensus pattern (22 bp):
CTAAAACCCACTCAATCCACTA
Found at i:1998510 original size:12 final size:13
Alignment explanation
Indices: 1998493--1998521 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
1998483 AATCGAATGT
1998493 TTTTAATTTT-AA
1 TTTTAATTTTCAA
1998505 TTTTAATTTTCAA
1 TTTTAATTTTCAA
1998518 TTTT
1 TTTT
1998522 TCGTAATTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 10 0.62
13 6 0.38
ACGTcount: A:0.28, C:0.03, G:0.00, T:0.69
Consensus pattern (13 bp):
TTTTAATTTTCAA
Found at i:2002544 original size:110 final size:106
Alignment explanation
Indices: 2002393--2002614 Score: 259
Period size: 106 Copynumber: 2.1 Consensus size: 106
2002383 ATATTGGACT
* * * * *
2002393 CAAGATCAACTTCACAACGAAGGGGCGATTGATTGTCAACAAATAACTTTT-CATTTTCATTCAG
1 CAAGCTCAACTTCACAACGAAGGGGCGACTGACTGTCAACAAACAA-TTTTCCA--GT--TTCAG
* *
2002457 AGTCAATTTCAACTTCATAG-CAAAGGATATTAGACTCGAGACAGCA
61 AGCCAATTTCAACTTCA-AGACAAAGGATATTAGACTCGAAACAGCA
* * *
2002503 CAAGCTCAACTTCACAACGAAGGGGTGGCTGGCTGTCAACAAACAATTTTCCAGTTTCAGAGCCA
1 CAAGCTCAACTTCACAACGAAGGGGCGACTGACTGTCAACAAACAATTTTCCAGTTTCAGAGCCA
* * *
2002568 ATTTCAACTTCACGACGAAGGATATTGGACTCGAAACAGCA
66 ATTTCAACTTCAAGACAAAGGATATTAGACTCGAAACAGCA
2002609 CAAGCT
1 CAAGCT
2002615 TGGATTTAAA
Statistics
Matches: 97, Mismatches: 13, Indels: 8
0.82 0.11 0.07
Matches are distributed among these distances:
105 1 0.01
106 50 0.52
108 1 0.01
109 4 0.04
110 41 0.42
ACGTcount: A:0.35, C:0.23, G:0.18, T:0.24
Consensus pattern (106 bp):
CAAGCTCAACTTCACAACGAAGGGGCGACTGACTGTCAACAAACAATTTTCCAGTTTCAGAGCCA
ATTTCAACTTCAAGACAAAGGATATTAGACTCGAAACAGCA
Found at i:2003007 original size:254 final size:249
Alignment explanation
Indices: 2002550--2003024 Score: 567
Period size: 254 Copynumber: 1.9 Consensus size: 249
2002540 AACAAACAAT
*
2002550 TTTCCAGTTTCAGAGCCAATTTCAACTTCACGACGAAGGATATTGGACTCGAAACAGCACAAGCT
1 TTTCCAGTTTCAGAGCCAATTTCAACTTCACGACGAAGGATATTGGACTCGAAACAGCACAAACT
* * **
2002615 TGGATTTAAACTTCACGACGAAGGATATTCAAGTCAAGGCTCAACTTCACGACGAAGGGGCCACT
66 TGGATTTAAACTTCACGACGAAGGATATCCAACTCAAGGCTCAACTTCACGACGAAGGAACCACT
* * ** * * * *
2002680 CGCGGTTTCAAATTCATGACGAAGGGAATCGTGCACACAATAAACATCCGTCTCTAGATTGGATT
131 CACGATTTCAAATTCACAAAGAAGGGAATCATGCACACAAGAAACATCCATCTCTAGATTGGATT
2002745 TCAACTTCACAACGAAGGATATCCAACTCAAAGAAGGAGTATCTTTCAATAAAC
196 TCAACTTCACAACGAAGGATATCCAACTCAAAGAAGGAGTATCTTTCAATAAAC
** * *
2002799 TTTCCAGTTTCAGAGTTAATTTTAACTTCAC-AGCGAAGGATATTGGACTCGAAACATCACAACT
1 TTTCCAGTTTCAGAGCCAATTTCAACTTCACGA-CGAAGGATATTGGACTCGAAACAGCACAA--
* * * * *
2002863 TACATTGGATTTCAACTTCACGATGAATGATATCCAACTCCAAGGTTCAACTTCATGACGAAGGA
63 -AC-TTGGATTTAAACTTCACGACGAAGGATATCCAACT-CAAGGCTCAACTTCACGACGAAGGA
* * * * * * * * *
2002928 ACCA-TATATGATTTCAACTTCACAAAGAAGGGAATCATGCTCACTAGCAACATTCATGTTTAGA
125 ACCACT-CACGATTTCAAATTCACAAAGAAGGGAATCATGCACACAAGAAACATCCATCTCTAGA
* * *
2002992 TTGGATTTTAACTTCACGATGAAGGATATCCAA
189 TTGGATTTCAACTTCACAACGAAGGATATCCAA
2003025 TTCCAGGCTC
Statistics
Matches: 185, Mismatches: 34, Indels: 9
0.81 0.15 0.04
Matches are distributed among these distances:
248 1 0.01
249 56 0.30
252 1 0.01
253 31 0.17
254 96 0.52
ACGTcount: A:0.34, C:0.21, G:0.18, T:0.27
Consensus pattern (249 bp):
TTTCCAGTTTCAGAGCCAATTTCAACTTCACGACGAAGGATATTGGACTCGAAACAGCACAAACT
TGGATTTAAACTTCACGACGAAGGATATCCAACTCAAGGCTCAACTTCACGACGAAGGAACCACT
CACGATTTCAAATTCACAAAGAAGGGAATCATGCACACAAGAAACATCCATCTCTAGATTGGATT
TCAACTTCACAACGAAGGATATCCAACTCAAAGAAGGAGTATCTTTCAATAAAC
Found at i:2003102 original size:124 final size:125
Alignment explanation
Indices: 2002866--2003104 Score: 320
Period size: 124 Copynumber: 1.9 Consensus size: 125
2002856 CACAACTTAC
* * * *
2002866 ATTGGATTTCAACTTCACGATGAATGATATCCAACTCCAAGGTTCAACTTCATGACGAAGGAACC
1 ATTGGATTTCAACTTCACGATGAAGGATATCCAACTCCAAGGCTCAACTTCACGACAAAGGAACC
*
2002931 ATATATGATTTCAACTTCACAAAGAAGGGAATCATGCTCACTAGCAACATTCATGTTTAG
66 ATACATGATTTCAACTTCACAAAGAAGGGAATCATGCTCACTAGCAACATTCATGTTTAG
* * **
2002991 ATTGGATTTTAACTTCACGATGAAGGATATCCAATTCC-AGGCTCAACTTCACGACAAAGGGGCC
1 ATTGGATTTCAACTTCACGATGAAGGATATCCAACTCCAAGGCTCAACTTCACGACAAAGGAACC
* * * * * *
2003055 ATCCATGATTTCAACTTTACGAAGAA-GGATATCATGTTCATTTGCAACAT
66 ATACATGATTTCAACTTCACAAAGAAGGGA-ATCATGCTCACTAGCAACAT
2003105 AGCTCAAAAC
Statistics
Matches: 98, Mismatches: 15, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
123 3 0.03
124 60 0.61
125 35 0.36
ACGTcount: A:0.34, C:0.21, G:0.17, T:0.28
Consensus pattern (125 bp):
ATTGGATTTCAACTTCACGATGAAGGATATCCAACTCCAAGGCTCAACTTCACGACAAAGGAACC
ATACATGATTTCAACTTCACAAAGAAGGGAATCATGCTCACTAGCAACATTCATGTTTAG
Found at i:2003235 original size:84 final size:85
Alignment explanation
Indices: 2003131--2003296 Score: 237
Period size: 84 Copynumber: 2.0 Consensus size: 85
2003121 GGCTATTTTG
* * * * *
2003131 CAACAAAAGACCTTCGAGTTCGACTACGCTCAAT-TCTAAGGCACATTA-TTTGCAGCATAACTC
1 CAACAAAAGACCTTCGAGTTCAACTACACTC-ATCTCAAAGGCACATCATTTTACAGCATAACTC
2003194 AAGGCTAGAAGGATTATCTGC
65 AAGGCTAGAAGGATTATCTGC
* *
2003215 CAACAAAAGACCTTCGAGTTCAACTATACTCATCTCAAAGGCACATCATTTTACAGCATAGCTCA
1 CAACAAAAGACCTTCGAGTTCAACTACACTCATCTCAAAGGCACATCATTTTACAGCATAACTCA
*
2003280 AGGCTAGAAGGGTTATC
66 AGGCTAGAAGGATTATC
2003297 CGTCAATAAA
Statistics
Matches: 72, Mismatches: 8, Indels: 3
0.87 0.10 0.04
Matches are distributed among these distances:
83 2 0.03
84 40 0.56
85 30 0.42
ACGTcount: A:0.34, C:0.24, G:0.17, T:0.25
Consensus pattern (85 bp):
CAACAAAAGACCTTCGAGTTCAACTACACTCATCTCAAAGGCACATCATTTTACAGCATAACTCA
AGGCTAGAAGGATTATCTGC
Found at i:2003651 original size:3 final size:3
Alignment explanation
Indices: 2003643--2003680 Score: 58
Period size: 3 Copynumber: 12.0 Consensus size: 3
2003633 ATAGATTTCA
2003643 CTT CTT CTT CTT CTTT CTT CTT CTT CTTT CTT CTT CTT
1 CTT CTT CTT CTT C-TT CTT CTT CTT C-TT CTT CTT CTT
2003681 TACCATTAAG
Statistics
Matches: 33, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
3 27 0.82
4 6 0.18
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
CTT
Found at i:2003662 original size:10 final size:10
Alignment explanation
Indices: 2003643--2003681 Score: 55
Period size: 10 Copynumber: 4.0 Consensus size: 10
2003633 ATAGATTTCA
2003643 CTTCTTC-TT
1 CTTCTTCTTT
2003652 CTTCTT-TCTT
1 CTTCTTCT-TT
2003662 CTTCTTCTTT
1 CTTCTTCTTT
2003672 CTTCTTCTTT
1 CTTCTTCTTT
2003682 ACCATTAAGA
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
9 6 0.22
10 20 0.74
11 1 0.04
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (10 bp):
CTTCTTCTTT
Found at i:2003662 original size:13 final size:13
Alignment explanation
Indices: 2003644--2003680 Score: 74
Period size: 13 Copynumber: 2.8 Consensus size: 13
2003634 TAGATTTCAC
2003644 TTCTTCTTCTTCT
1 TTCTTCTTCTTCT
2003657 TTCTTCTTCTTCT
1 TTCTTCTTCTTCT
2003670 TTCTTCTTCTT
1 TTCTTCTTCTT
2003681 TACCATTAAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (13 bp):
TTCTTCTTCTTCT
Found at i:2005027 original size:22 final size:22
Alignment explanation
Indices: 2004987--2005053 Score: 62
Period size: 23 Copynumber: 3.0 Consensus size: 22
2004977 AAGCTTATAT
* *
2004987 GGCACTACGCTGCAATTCTACGC
1 GGCACTTCG-TGCATTTCTACGC
* *
2005010 GGCACTTCGTGCATTTCTATGT
1 GGCACTTCGTGCATTTCTACGC
* *
2005032 GGCACATCGGTGCATTTATACG
1 GGCACTTC-GTGCATTTCTACG
2005054 AGCTGTGGTG
Statistics
Matches: 36, Mismatches: 7, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
22 17 0.47
23 19 0.53
ACGTcount: A:0.19, C:0.27, G:0.24, T:0.30
Consensus pattern (22 bp):
GGCACTTCGTGCATTTCTACGC
Found at i:2011191 original size:20 final size:20
Alignment explanation
Indices: 2011166--2011218 Score: 106
Period size: 20 Copynumber: 2.6 Consensus size: 20
2011156 ATAGGATTTA
2011166 TGCATCGATGCATGGTGTGG
1 TGCATCGATGCATGGTGTGG
2011186 TGCATCGATGCATGGTGTGG
1 TGCATCGATGCATGGTGTGG
2011206 TGCATCGATGCAT
1 TGCATCGATGCAT
2011219 ACCTTCATTA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.17, C:0.17, G:0.36, T:0.30
Consensus pattern (20 bp):
TGCATCGATGCATGGTGTGG
Found at i:2011913 original size:23 final size:23
Alignment explanation
Indices: 2011846--2011905 Score: 93
Period size: 23 Copynumber: 2.6 Consensus size: 23
2011836 AAGCTTATAT
*
2011846 GGCACTACGGTGCAATTCTACGC
1 GGCACTTCGGTGCAATTCTACGC
*
2011869 GGCACTTCGGTGCAATTCTACGT
1 GGCACTTCGGTGCAATTCTACGC
*
2011892 GGTACTTCGGTGCA
1 GGCACTTCGGTGCA
2011906 TTTATACGAG
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.18, C:0.27, G:0.28, T:0.27
Consensus pattern (23 bp):
GGCACTTCGGTGCAATTCTACGC
Found at i:2012998 original size:22 final size:21
Alignment explanation
Indices: 2012936--2012995 Score: 93
Period size: 22 Copynumber: 2.8 Consensus size: 21
2012926 CCACTATCCC
2012936 CTAAAACCCACTCAACCACCA
1 CTAAAACCCACTCAACCACCA
*
2012957 CTAAAACCCACTCAATCCACTA
1 CTAAAACCCACTCAA-CCACCA
*
2012979 CTAAAACTCACTCAACC
1 CTAAAACCCACTCAACC
2012996 CACCTAACCC
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
21 17 0.47
22 19 0.53
ACGTcount: A:0.42, C:0.43, G:0.00, T:0.15
Consensus pattern (21 bp):
CTAAAACCCACTCAACCACCA
Found at i:2013672 original size:13 final size:14
Alignment explanation
Indices: 2013648--2013716 Score: 51
Period size: 13 Copynumber: 5.1 Consensus size: 14
2013638 TTAAATGTCC
2013648 TTTAAGTTTTTTT-T
1 TTTAA-TTTTTTTAT
2013662 TTTAATTTTTTTAT
1 TTTAATTTTTTTAT
**
2013676 TTT-ATTTTCCCT-T
1 TTTAATTTT-TTTAT
2013689 TTT-ATTTTTTTAT
1 TTTAATTTTTTTAT
2013702 TATT-A-TTTTTTAT
1 T-TTAATTTTTTTAT
2013715 TT
1 TT
2013717 AACATTGTTT
Statistics
Matches: 47, Mismatches: 4, Indels: 10
0.77 0.07 0.16
Matches are distributed among these distances:
12 2 0.04
13 32 0.68
14 13 0.28
ACGTcount: A:0.16, C:0.04, G:0.01, T:0.78
Consensus pattern (14 bp):
TTTAATTTTTTTAT
Found at i:2016711 original size:81 final size:80
Alignment explanation
Indices: 2016506--2016745 Score: 329
Period size: 81 Copynumber: 3.0 Consensus size: 80
2016496 AAACTTGATT
* * *
2016506 TGTGCCTCTTTTTTGGGTAGACAGATCAATTTTGGTAGACGTGTTTGTTCCACTATTCTTTCAGG
1 TGTGCCT-TTTTTTGGGTAGACAGATCAATTTTGGAAGACGTGTCTGCTCCACTATTCTTTCAGG
* *
2016571 GACATAACACTCGATA
65 GAGATAAGACTCGATA
* * * *
2016587 TGTGCCTTTTTCCT-GGTAGACAGATCAATTTTGGAAGATGTGTCTGCTACACTATTCTTTCAAG
1 TGTGCCTTTTT-TTGGGTAGACAGATCAATTTTGGAAGACGTGTCTGCTCCACTATTCTTTCAGG
*
2016651 GAGATAAGACTCGATC
65 GAGATAAGACTCGATA
* * *
2016667 TGTGCCTATTTTTTGGGTAGACATATCAATTTTGGAAGACGTGTCTGCTCCATTATTCATTCAGG
1 TGTGCCT-TTTTTTGGGTAGACAGATCAATTTTGGAAGACGTGTCTGCTCCACTATTCTTTCAGG
2016732 GAGATAAGACTCGA
65 GAGATAAGACTCGA
2016746 GATTGATTTG
Statistics
Matches: 139, Mismatches: 17, Indels: 6
0.86 0.10 0.04
Matches are distributed among these distances:
80 69 0.50
81 70 0.50
ACGTcount: A:0.24, C:0.18, G:0.22, T:0.36
Consensus pattern (80 bp):
TGTGCCTTTTTTTGGGTAGACAGATCAATTTTGGAAGACGTGTCTGCTCCACTATTCTTTCAGGG
AGATAAGACTCGATA
Found at i:2033394 original size:215 final size:216
Alignment explanation
Indices: 2033016--2033441 Score: 626
Period size: 215 Copynumber: 2.0 Consensus size: 216
2033006 TTTGATAGTC
* * * * *
2033016 CAATTTTGGAAATAATTTACTGCATAAGAAACTTTGGAAATTGCTTTCTTACTTTTCAAAAATTT
1 CAATTTTGGAAATAATCTACTGCATAAGAAACTTTGCAAATAGCTTTCATACATTTCAAAAATTT
* * * *
2033081 CATTTTCTGAAAACATTAAATGAGAAGCTTTGGAAATCGCTTTCTCATTTTTTGAAAGTCACGTG
66 CATTTTCTGAAAACATTAAATGAGAAACTTTGGAAATCACTTTCTCAGTTTTTGAAAGTCACATG
* * * *
2033146 AAAATATCCTGCCCGGAGGTCTTATATATGGCCCGAAGGACTTATCATCTTGCTCGGAAA-CCTG
131 AAAACATCCTACCCGAAGGTCTTATAGATGGCCCGAAGGACTTATCATCTTGCTC-GAAAGCCTG
*
2033210 ACAAATGGCCCGAAGGAATTAT
195 ACAAATGACCCGAAGGAATTAT
*
2033232 CAATTTTGGAAATAGTCTACTAAG-A-AAGAAACTTTGCAAATAGCTTTCATA-ATTTCAAAAAT
1 CAATTTTGGAAATAATCTACT--GCATAAGAAACTTTGCAAATAGCTTTCATACATTTCAAAAAT
2033294 TTCATTTTCTGAAAACATTAAATGAGAAACTTTGGAAATCACTTTCTCAGTTTTTGAAAGTCACA
64 TTCATTTTCTGAAAACATTAAATGAGAAACTTTGGAAATCACTTTCTCAGTTTTTGAAAGTCACA
* * *
2033359 TGAAAACATCCTACCTGAAGGTCTTATCGATGGCCCGAATGACTTATCATCTTGCTCGAAAGCCT
129 TGAAAACATCCTACCCGAAGGTCTTATAGATGGCCCGAAGGACTTATCATCTTGCTCGAAAGCCT
*
2033424 GACAGATGACCCGAAGGA
194 GACAAATGACCCGAAGGA
2033442 TTTAATCATC
Statistics
Matches: 188, Mismatches: 19, Indels: 7
0.88 0.09 0.03
Matches are distributed among these distances:
214 4 0.02
215 140 0.74
216 42 0.22
217 1 0.01
218 1 0.01
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.32
Consensus pattern (216 bp):
CAATTTTGGAAATAATCTACTGCATAAGAAACTTTGCAAATAGCTTTCATACATTTCAAAAATTT
CATTTTCTGAAAACATTAAATGAGAAACTTTGGAAATCACTTTCTCAGTTTTTGAAAGTCACATG
AAAACATCCTACCCGAAGGTCTTATAGATGGCCCGAAGGACTTATCATCTTGCTCGAAAGCCTGA
CAAATGACCCGAAGGAATTAT
Found at i:2035414 original size:21 final size:20
Alignment explanation
Indices: 2035390--2035429 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 20
2035380 TCTCTCACTT
2035390 TTTTCCTTTTTCCTCTTTTTC
1 TTTTCCTTTTT-CTCTTTTTC
*
2035411 TTTTTCTTTTTCTCTTTTT
1 TTTTCCTTTTTCTCTTTTT
2035430 TATTTTATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 8 0.44
21 10 0.56
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.78
Consensus pattern (20 bp):
TTTTCCTTTTTCTCTTTTTC
Found at i:2035429 original size:9 final size:9
Alignment explanation
Indices: 2035387--2035504 Score: 53
Period size: 9 Copynumber: 12.8 Consensus size: 9
2035377 ATTTCTCTCA
2035387 CTTTTTTC-
1 CTTTTTTCT
*
2035395 CTTTTTCCT
1 CTTTTTTCT
*
2035404 CTTTTTCTTT
1 CTTTTT-TCT
*
2035414 TTCTTTTTCT
1 CT-TTTTTCT
*
2035424 CTTTTTTAT
1 CTTTTTTCT
* *
2035433 TTTATATTTTT
1 CTT-T-TTTCT
* * *
2035444 ATTTTATAT
1 CTTTTTTCT
2035453 -TTTTTTCT
1 CTTTTTTCT
*
2035461 ATTTTTTCT
1 CTTTTTTCT
*
2035470 ATTTTTTCCT
1 CTTTTTT-CT
2035480 CTTTTTT-T
1 CTTTTTTCT
*
2035488 CTTTTTTTT
1 CTTTTTTCT
2035497 CCTTTTTT
1 -CTTTTTT
2035505 TTTTCTATAT
Statistics
Matches: 86, Mismatches: 15, Indels: 16
0.74 0.13 0.14
Matches are distributed among these distances:
8 21 0.24
9 33 0.38
10 22 0.26
11 10 0.12
ACGTcount: A:0.07, C:0.15, G:0.00, T:0.78
Consensus pattern (9 bp):
CTTTTTTCT
Found at i:2035430 original size:21 final size:21
Alignment explanation
Indices: 2035405--2035529 Score: 69
Period size: 21 Copynumber: 5.8 Consensus size: 21
2035395 CTTTTTCCTC
*
2035405 TTTTTCTTTTTCTTTTTCTCT
1 TTTTTCTTTTTCTTTTTCTAT
* *
2035426 TTTTTATTTTAT-ATTTT-TAT
1 TTTTTCTTTT-TCTTTTTCTAT
*
2035446 TTTATATTTTTTTCTATTTTTTCTAT
1 TTT-T-TCTTTTTC---TTTTTCTAT
* * *
2035472 TTTTTCCTCTT-TTTTTCTTT
1 TTTTTCTTTTTCTTTTTCTAT
2035492 TTTTTCCTTTTT-TTTTTCTAT
1 TTTTT-CTTTTTCTTTTTCTAT
* * *
2035513 ATTTTCTCTTTATTTTT
1 TTTTTCTTTTTCTTTTT
2035530 ACAAATTTAT
Statistics
Matches: 80, Mismatches: 14, Indels: 20
0.70 0.12 0.18
Matches are distributed among these distances:
20 23 0.29
21 36 0.45
22 6 0.08
24 4 0.05
25 5 0.06
26 6 0.08
ACGTcount: A:0.09, C:0.12, G:0.00, T:0.79
Consensus pattern (21 bp):
TTTTTCTTTTTCTTTTTCTAT
Found at i:2035435 original size:20 final size:18
Alignment explanation
Indices: 2035396--2035508 Score: 79
Period size: 19 Copynumber: 6.1 Consensus size: 18
2035386 ACTTTTTTCC
*
2035396 TTTTTCCTCTTTTTCTTTT
1 TTTTTTCTCTTTTT-TTTT
2035415 TCTTTTTCTCTTTTTTATTT
1 T-TTTTTCTCTTTTTT-TTT
* * *
2035435 TATATTTT-T-ATTTTATAT
1 T-T-TTTTCTCTTTTTTTTT
* *
2035453 TTTTTTCTATTTTTTCTAT
1 TTTTTTCTCTTTTTT-TTT
*
2035472 TTTTTCCTCTTTTTTTCTT
1 TTTTTTCTCTTTTTTT-TT
2035491 TTTTTTC-CTTTTTTTTT
1 TTTTTTCTCTTTTTTTTT
2035508 T
1 T
2035509 CTATATTTTC
Statistics
Matches: 76, Mismatches: 11, Indels: 16
0.74 0.11 0.16
Matches are distributed among these distances:
16 4 0.05
17 5 0.07
18 16 0.21
19 29 0.38
20 18 0.24
21 4 0.05
ACGTcount: A:0.07, C:0.13, G:0.00, T:0.80
Consensus pattern (18 bp):
TTTTTTCTCTTTTTTTTT
Found at i:2035442 original size:13 final size:13
Alignment explanation
Indices: 2035426--2035474 Score: 64
Period size: 13 Copynumber: 3.8 Consensus size: 13
2035416 CTTTTTCTCT
2035426 TTTTTATTTTATA
1 TTTTTATTTTATA
2035439 TTTTTATTTTATA
1 TTTTTATTTTATA
* *
2035452 TTTTT-TTCTATT
1 TTTTTATTTTATA
2035464 TTTTCTATTTT
1 TTTT-TATTTT
2035475 TTCCTCTTTT
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
12 9 0.29
13 19 0.61
14 3 0.10
ACGTcount: A:0.16, C:0.04, G:0.00, T:0.80
Consensus pattern (13 bp):
TTTTTATTTTATA
Found at i:2035463 original size:10 final size:10
Alignment explanation
Indices: 2035445--2035517 Score: 69
Period size: 10 Copynumber: 7.2 Consensus size: 10
2035435 TATATTTTTA
*
2035445 TTTTATATTT
1 TTTTCTATTT
2035455 TTTTCTA-TT
1 TTTTCTATTT
2035464 TTTTCTATTT
1 TTTTCTATTT
* *
2035474 TTTCCTCTTT
1 TTTTCTATTT
2035484 TTTTCT-TTT
1 TTTTCTATTT
*
2035493 TTTTCCTTTTTT
1 TTTT-C-TATTT
2035505 TTTTCTATATT
1 TTTTCTAT-TT
2035516 TT
1 TT
2035518 CTCTTTATTT
Statistics
Matches: 53, Mismatches: 5, Indels: 9
0.79 0.07 0.13
Matches are distributed among these distances:
9 16 0.30
10 24 0.45
11 6 0.11
12 7 0.13
ACGTcount: A:0.08, C:0.12, G:0.00, T:0.79
Consensus pattern (10 bp):
TTTTCTATTT
Found at i:2035526 original size:11 final size:10
Alignment explanation
Indices: 2035452--2035528 Score: 61
Period size: 10 Copynumber: 7.7 Consensus size: 10
2035442 TTATTTTATA
2035452 TTTTTTTCT-
1 TTTTTTTCTC
* *
2035461 ATTTTTTCTA
1 TTTTTTTCTC
*
2035471 TTTTTTCCTC
1 TTTTTTTCTC
2035481 TTTTTTTCT-
1 TTTTTTTCTC
2035490 TTTTTTTC-C
1 TTTTTTTCTC
*
2035499 TTTTTTTTTTC
1 -TTTTTTTCTC
*
2035510 TATATTTTCTC
1 T-TTTTTTCTC
2035521 TTTATTTT
1 TTT-TTTT
2035529 TACAAATTTA
Statistics
Matches: 53, Mismatches: 9, Indels: 10
0.74 0.12 0.14
Matches are distributed among these distances:
9 16 0.30
10 24 0.45
11 13 0.25
ACGTcount: A:0.06, C:0.14, G:0.00, T:0.79
Consensus pattern (10 bp):
TTTTTTTCTC
Found at i:2036306 original size:54 final size:54
Alignment explanation
Indices: 2036223--2036486 Score: 386
Period size: 54 Copynumber: 4.9 Consensus size: 54
2036213 CATAAACATA
* *
2036223 GTTCATCAACATATGATGAATT-TCGTGGGTTGCACACTTAGTGCCTATACGGTT
1 GTTCATCAACATATGATGAATTCT-ATGGGTTGCACACTTAGTGCCTATACGGTC
*
2036277 GTTCATCAACGTATGATGAATTCTATGGGTTGCACACTTAGTGCCTATACGGTC
1 GTTCATCAACATATGATGAATTCTATGGGTTGCACACTTAGTGCCTATACGGTC
* * *
2036331 GTTCATCAACATATGATGAATTTTATGGGTTGCACACTTAGTGTCTATATGGTC
1 GTTCATCAACATATGATGAATTCTATGGGTTGCACACTTAGTGCCTATACGGTC
* * * **
2036385 ATTCATCAATATATGTTGAATTCCGTGGGTTGCACACTTAGTGCCTATACGGTC
1 GTTCATCAACATATGATGAATTCTATGGGTTGCACACTTAGTGCCTATACGGTC
* * *
2036439 GTTCATTAACATATAATGAATTTTATGGGTTGCACACTTAGTGCCTAT
1 GTTCATCAACATATGATGAATTCTATGGGTTGCACACTTAGTGCCTAT
2036487 GGTACACATA
Statistics
Matches: 186, Mismatches: 23, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
54 185 0.99
55 1 0.01
ACGTcount: A:0.25, C:0.18, G:0.20, T:0.36
Consensus pattern (54 bp):
GTTCATCAACATATGATGAATTCTATGGGTTGCACACTTAGTGCCTATACGGTC
Found at i:2044665 original size:21 final size:21
Alignment explanation
Indices: 2044640--2044679 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
2044630 AAGACTATTT
2044640 TCATTTTTCA-ATTTTGAAACA
1 TCATTTTT-ATATTTTGAAACA
2044661 TCATTTTTATATTTTGAAA
1 TCATTTTTATATTTTGAAA
2044680 ATAGAGTCTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 1 0.06
21 17 0.94
ACGTcount: A:0.33, C:0.10, G:0.05, T:0.53
Consensus pattern (21 bp):
TCATTTTTATATTTTGAAACA
Found at i:2050223 original size:31 final size:33
Alignment explanation
Indices: 2050171--2050233 Score: 87
Period size: 31 Copynumber: 2.0 Consensus size: 33
2050161 ACCTAGAAAA
*
2050171 AGTCAATGGTCGGTCAGCGGT-CTGGTCAACGAC
1 AGTCAATGGTCGGTCAACGGTCCT-GTCAACGAC
2050204 AGTCAAT-G-CGGTCAACGGTCCTGTCAACGA
1 AGTCAATGGTCGGTCAACGGTCCTGTCAACGA
2050234 TCAACAGGTC
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
31 18 0.64
32 3 0.11
33 7 0.25
ACGTcount: A:0.24, C:0.25, G:0.30, T:0.21
Consensus pattern (33 bp):
AGTCAATGGTCGGTCAACGGTCCTGTCAACGAC
Found at i:2052966 original size:17 final size:17
Alignment explanation
Indices: 2052944--2052986 Score: 86
Period size: 17 Copynumber: 2.5 Consensus size: 17
2052934 CAAGAATCCT
2052944 TCATCGAAAGGAGATTA
1 TCATCGAAAGGAGATTA
2052961 TCATCGAAAGGAGATTA
1 TCATCGAAAGGAGATTA
2052978 TCATCGAAA
1 TCATCGAAA
2052987 ACAACATGAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 26 1.00
ACGTcount: A:0.42, C:0.14, G:0.21, T:0.23
Consensus pattern (17 bp):
TCATCGAAAGGAGATTA
Found at i:2057708 original size:24 final size:24
Alignment explanation
Indices: 2057668--2057719 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
2057658 TTTGGTTAAG
*
2057668 AAAA-AATGAAATATAAAAAATAT
1 AAAATAATAAAATATAAAAAATAT
* *
2057691 AAAATAATAAAATTTAAAAAATTT
1 AAAATAATAAAATATAAAAAATAT
2057715 AAAAT
1 AAAAT
2057720 TTAGTATTAA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
23 4 0.16
24 21 0.84
ACGTcount: A:0.71, C:0.00, G:0.02, T:0.27
Consensus pattern (24 bp):
AAAATAATAAAATATAAAAAATAT
Found at i:2059675 original size:19 final size:20
Alignment explanation
Indices: 2059651--2059693 Score: 61
Period size: 19 Copynumber: 2.2 Consensus size: 20
2059641 TGTAACCCTT
*
2059651 TGAAAATGCACGAG-TTTAA
1 TGAAAATACACGAGTTTTAA
*
2059670 TGAAAATACATGAGTTTTAA
1 TGAAAATACACGAGTTTTAA
2059690 TGAA
1 TGAA
2059694 TTTACATGCT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 12 0.57
20 9 0.43
ACGTcount: A:0.44, C:0.07, G:0.19, T:0.30
Consensus pattern (20 bp):
TGAAAATACACGAGTTTTAA
Found at i:2073622 original size:14 final size:14
Alignment explanation
Indices: 2073603--2073632 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
2073593 GTAGGATATG
2073603 AATTAAATAAAATT
1 AATTAAATAAAATT
*
2073617 AATTAATTAAAATT
1 AATTAAATAAAATT
2073631 AA
1 AA
2073633 CAACAAAATT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (14 bp):
AATTAAATAAAATT
Found at i:2076365 original size:40 final size:40
Alignment explanation
Indices: 2076320--2076408 Score: 160
Period size: 40 Copynumber: 2.2 Consensus size: 40
2076310 TTGATAATAG
*
2076320 TATCGGTACCACATGAACAGTACCAATATTGTTCTTCCAA
1 TATCGGTACCACATGAACAGTACCAATATTGTTATTCCAA
2076360 TATCGGTACCACATGAACAGTACCAATATTGTTATTCCAA
1 TATCGGTACCACATGAACAGTACCAATATTGTTATTCCAA
*
2076400 TATTGGTAC
1 TATCGGTAC
2076409 TTGATAATCC
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
40 47 1.00
ACGTcount: A:0.33, C:0.22, G:0.13, T:0.31
Consensus pattern (40 bp):
TATCGGTACCACATGAACAGTACCAATATTGTTATTCCAA
Found at i:2076500 original size:20 final size:20
Alignment explanation
Indices: 2076475--2076517 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
2076465 TCTAAGAGCC
*
2076475 CATTTAGAATCATATAGATG
1 CATTTAGAAGCATATAGATG
*
2076495 CATTTAGAAGCATATAGTTG
1 CATTTAGAAGCATATAGATG
2076515 CAT
1 CAT
2076518 GTGGTGGAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.37, C:0.12, G:0.16, T:0.35
Consensus pattern (20 bp):
CATTTAGAAGCATATAGATG
Found at i:2076917 original size:23 final size:24
Alignment explanation
Indices: 2076868--2076921 Score: 74
Period size: 23 Copynumber: 2.3 Consensus size: 24
2076858 CGAGTACTCA
* *
2076868 GCCAGCTACCCAGGATGGACCATT
1 GCCAGCTACCCAGGAGGGACCACT
*
2076892 GCCAGCTGCCCAGG-GGGACCACT
1 GCCAGCTACCCAGGAGGGACCACT
2076915 GCCAGCT
1 GCCAGCT
2076922 CTACCCACCC
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
23 14 0.52
24 13 0.48
ACGTcount: A:0.20, C:0.37, G:0.30, T:0.13
Consensus pattern (24 bp):
GCCAGCTACCCAGGAGGGACCACT
Found at i:2078048 original size:20 final size:22
Alignment explanation
Indices: 2078023--2078062 Score: 66
Period size: 20 Copynumber: 1.9 Consensus size: 22
2078013 ATATTACCAT
2078023 CATTACAT-TT-CCACAACAGC
1 CATTACATCTTGCCACAACAGC
2078043 CATTACATCTTGCCACAACA
1 CATTACATCTTGCCACAACA
2078063 TTCTCATTTG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 8 0.44
21 2 0.11
22 8 0.44
ACGTcount: A:0.35, C:0.35, G:0.05, T:0.25
Consensus pattern (22 bp):
CATTACATCTTGCCACAACAGC
Found at i:2087488 original size:20 final size:20
Alignment explanation
Indices: 2087463--2087505 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
2087453 TCTAAGAGCC
*
2087463 CATTTAGAATCATATAGATG
1 CATTTAGAAGCATATAGATG
* *
2087483 CATTTAGGAGCATATAGTTG
1 CATTTAGAAGCATATAGATG
2087503 CAT
1 CAT
2087506 ATGCTAGAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.35, C:0.12, G:0.19, T:0.35
Consensus pattern (20 bp):
CATTTAGAAGCATATAGATG
Found at i:2093598 original size:21 final size:21
Alignment explanation
Indices: 2093572--2093619 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
2093562 TTTAATTTGT
2093572 GTTTATAATTTAAT-GTTTAGG
1 GTTTATAATTT-ATGGTTTAGG
* *
2093593 GTTTATTATTTTTGGTTTAGG
1 GTTTATAATTTATGGTTTAGG
2093614 GTTTAT
1 GTTTAT
2093620 TTCTTTTTAG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 1 0.04
21 23 0.96
ACGTcount: A:0.21, C:0.00, G:0.21, T:0.58
Consensus pattern (21 bp):
GTTTATAATTTATGGTTTAGG
Found at i:2093836 original size:24 final size:23
Alignment explanation
Indices: 2093809--2093904 Score: 63
Period size: 24 Copynumber: 4.2 Consensus size: 23
2093799 ATGAAAGAAT
2093809 ATAAACGAACGAATGTAAACGAAC
1 ATAAACGAAC-AATGTAAACGAAC
* *** *
2093833 ATAAATGAACACCATAAACAAAC
1 ATAAACGAACAATGTAAACGAAC
* *
2093856 GTAAATGAAC-A--TAAACGAAC
1 ATAAACGAACAATGTAAACGAAC
* * *
2093876 AAAAACAAACGAATGTAGACGAAC
1 ATAAACGAAC-AATGTAAACGAAC
2093900 ATAAA
1 ATAAA
2093905 TGAGCACAAT
Statistics
Matches: 54, Mismatches: 14, Indels: 8
0.71 0.18 0.11
Matches are distributed among these distances:
20 14 0.26
22 1 0.02
23 18 0.33
24 21 0.39
ACGTcount: A:0.58, C:0.17, G:0.12, T:0.12
Consensus pattern (23 bp):
ATAAACGAACAATGTAAACGAAC
Found at i:2093985 original size:23 final size:23
Alignment explanation
Indices: 2093949--2093993 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
2093939 AAAACCTTCA
*
2093949 CAAACATAACAAATGAACATAAT
1 CAAACAAAACAAATGAACATAAT
*
2093972 CAAACAAAATAAATGAACATAA
1 CAAACAAAACAAATGAACATAA
2093994 ACGAACGTAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.64, C:0.16, G:0.04, T:0.16
Consensus pattern (23 bp):
CAAACAAAACAAATGAACATAAT
Found at i:2095879 original size:17 final size:17
Alignment explanation
Indices: 2095857--2095928 Score: 72
Period size: 17 Copynumber: 4.2 Consensus size: 17
2095847 AATTAAGAGT
*
2095857 TAGTTTAATAAATGCAC
1 TAGTTTAATAAATGAAC
* *
2095874 TAGTTTGATGAATGAAC
1 TAGTTTAATAAATGAAC
*
2095891 TAGTTTAATTAATGAAC
1 TAGTTTAATAAATGAAC
* * *
2095908 TAACTTTATTCAATGAAC
1 T-AGTTTAATAAATGAAC
2095926 TAG
1 TAG
2095929 ATGCATGAAT
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
17 31 0.69
18 14 0.31
ACGTcount: A:0.39, C:0.10, G:0.14, T:0.38
Consensus pattern (17 bp):
TAGTTTAATAAATGAAC
Found at i:2095922 original size:18 final size:18
Alignment explanation
Indices: 2095884--2095927 Score: 56
Period size: 18 Copynumber: 2.5 Consensus size: 18
2095874 TAGTTTGATG
*
2095884 AATGAACT-AGTTTAATT
1 AATGAACTAACTTTAATT
2095901 AATGAACTAACTTT-ATT
1 AATGAACTAACTTTAATT
2095918 CAATGAACTA
1 -AATGAACTA
2095928 GATGCATGAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
17 11 0.46
18 13 0.54
ACGTcount: A:0.43, C:0.11, G:0.09, T:0.36
Consensus pattern (18 bp):
AATGAACTAACTTTAATT
Found at i:2097086 original size:15 final size:15
Alignment explanation
Indices: 2097066--2097102 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
2097056 ACAAACAATT
2097066 TCTTTTTCAAACTCA
1 TCTTTTTCAAACTCA
**
2097081 TCTTTTTCACTCTCA
1 TCTTTTTCAAACTCA
2097096 TCTTTTT
1 TCTTTTT
2097103 TTTGAATTTC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.16, C:0.27, G:0.00, T:0.57
Consensus pattern (15 bp):
TCTTTTTCAAACTCA
Found at i:2099687 original size:17 final size:17
Alignment explanation
Indices: 2099626--2099707 Score: 71
Period size: 17 Copynumber: 4.8 Consensus size: 17
2099616 TGCATGAAAC
*
2099626 AATTAA-GAGCTAGTTT
1 AATTAATGAACTAGTTT
2099642 AA-TAATTGAACTAGTTT
1 AATTAA-TGAACTAGTTT
* *
2099659 AATGAATAAACTAGTTT
1 AATTAATGAACTAGTTT
* *
2099676 AATTCATGAACTAACTTT
1 AATTAATGAACT-AGTTT
2099694 -ATTCAATGAACTAG
1 AATT-AATGAACTAG
2099708 ATGCATGAAT
Statistics
Matches: 52, Mismatches: 9, Indels: 9
0.74 0.13 0.13
Matches are distributed among these distances:
15 3 0.06
16 2 0.04
17 34 0.65
18 13 0.25
ACGTcount: A:0.41, C:0.10, G:0.12, T:0.37
Consensus pattern (17 bp):
AATTAATGAACTAGTTT
Found at i:2100119 original size:28 final size:28
Alignment explanation
Indices: 2100074--2100128 Score: 83
Period size: 28 Copynumber: 2.0 Consensus size: 28
2100064 CGAAATGGCA
* *
2100074 TTCAAAGGCACGCGCCCTACAACGCGCT
1 TTCAAAGGCACGCCCCCTAAAACGCGCT
*
2100102 TTCAAAGGCTCGCCCCCTAAAACGCGC
1 TTCAAAGGCACGCCCCCTAAAACGCGC
2100129 CTTACACTGT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.25, C:0.40, G:0.20, T:0.15
Consensus pattern (28 bp):
TTCAAAGGCACGCCCCCTAAAACGCGCT
Found at i:2100192 original size:15 final size:15
Alignment explanation
Indices: 2100172--2100204 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
2100162 CGTCCTGTGA
2100172 AACAAGTCTTCGTGC
1 AACAAGTCTTCGTGC
2100187 AACAAGTCTTCGTGC
1 AACAAGTCTTCGTGC
2100202 AAC
1 AAC
2100205 GTAGGTAATG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.30, C:0.27, G:0.18, T:0.24
Consensus pattern (15 bp):
AACAAGTCTTCGTGC
Found at i:2102354 original size:55 final size:56
Alignment explanation
Indices: 2102254--2102364 Score: 170
Period size: 56 Copynumber: 2.0 Consensus size: 56
2102244 AATGTTTAAC
* * *
2102254 ATTTTCGGCAAAACGTTATATAAAACATTATTTTTTTCTATTAGAAATGTTAATAT
1 ATTTCCGGCAAAACGCTATATAAAACATTATTTTTTTCTACTAGAAATGTTAATAT
* *
2102310 ATTTCCGGTAAAACGCTATGTAAAACATTA-TTTTTTCTACTAGAAATGTTAATAT
1 ATTTCCGGCAAAACGCTATATAAAACATTATTTTTTTCTACTAGAAATGTTAATAT
2102365 TAGGCGCTAC
Statistics
Matches: 50, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
55 24 0.48
56 26 0.52
ACGTcount: A:0.37, C:0.11, G:0.10, T:0.42
Consensus pattern (56 bp):
ATTTCCGGCAAAACGCTATATAAAACATTATTTTTTTCTACTAGAAATGTTAATAT
Found at i:2103680 original size:3 final size:3
Alignment explanation
Indices: 2103672--2103745 Score: 87
Period size: 3 Copynumber: 25.0 Consensus size: 3
2103662 TTTAAAATTG
* * * * *
2103672 TTA TTA TTA TTA TTA TAA TTA TAA GTA TTA TTA TTA TTA TAA TTA TAA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
*
2103720 GTA TTA TTA TTA TTA -TA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA
2103746 ATAAATAATT
Statistics
Matches: 58, Mismatches: 12, Indels: 2
0.81 0.17 0.03
Matches are distributed among these distances:
2 2 0.03
3 56 0.97
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (3 bp):
TTA
Found at i:2103705 original size:24 final size:24
Alignment explanation
Indices: 2103673--2103740 Score: 129
Period size: 24 Copynumber: 2.9 Consensus size: 24
2103663 TTAAAATTGT
2103673 TATTATTATTATTATAATTATAAG
1 TATTATTATTATTATAATTATAAG
2103697 TATTATTATTATTATAATTATAAG
1 TATTATTATTATTATAATTATAAG
2103721 TATTATTATTATTAT-ATTAT
1 TATTATTATTATTATAATTAT
2103741 TATTAATAAA
Statistics
Matches: 44, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
23 5 0.11
24 39 0.89
ACGTcount: A:0.40, C:0.00, G:0.03, T:0.57
Consensus pattern (24 bp):
TATTATTATTATTATAATTATAAG
Found at i:2105257 original size:16 final size:17
Alignment explanation
Indices: 2105217--2105258 Score: 50
Period size: 16 Copynumber: 2.5 Consensus size: 17
2105207 GTTCTATTCA
*
2105217 AATTATTATATTTTTCTT
1 AATT-TTATATTTATCTT
*
2105235 CATTTTATATTTAT-TT
1 AATTTTATATTTATCTT
2105251 AATTTTAT
1 AATTTTAT
2105259 TCATATTAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
16 9 0.43
17 9 0.43
18 3 0.14
ACGTcount: A:0.29, C:0.05, G:0.00, T:0.67
Consensus pattern (17 bp):
AATTTTATATTTATCTT
Found at i:2113282 original size:54 final size:55
Alignment explanation
Indices: 2113221--2113639 Score: 460
Period size: 54 Copynumber: 7.7 Consensus size: 55
2113211 TATGTAGAAT
* ** *
2113221 CCATAGGAAAGGATGAATGTGGCGTCAAATGTATTACGAACATCTGTACAGAAGA
1 CCATATGAAAGGATGAATGTGTTGTCAAATGTTTTACGAACATCTGTACAGAAGA
* * * * *
2113276 -CGTAGGAAAGGATAAATGTGTTGTCAAATGTTTTACAAACATCTGTGCAGAA-A
1 CCATATGAAAGGATGAATGTGTTGTCAAATGTTTTACGAACATCTGTACAGAAGA
* * * * * * *
2113329 CCACATGAAAGGATGAATGTGTTGTCAAATATATTACAAACATATGTATAAAAGA
1 CCATATGAAAGGATGAATGTGTTGTCAAATGTTTTACGAACATCTGTACAGAAGA
* * * *
2113384 -CATAAGAAATGATGAATGTGTTGTCAAATGTTTTACGAACATCTGTGCA-AAAA
1 CCATATGAAAGGATGAATGTGTTGTCAAATGTTTTACGAACATCTGTACAGAAGA
* * * *
2113437 CCATATGAAAGGATGAATGTGTAGTCAAATATATTACGAACATCTGTATAGAAGA
1 CCATATGAAAGGATGAATGTGTTGTCAAATGTTTTACGAACATCTGTACAGAAGA
*
2113492 CACA-A-GAAATGATGAATGTGTTGTCAAATGTTTTACGAACATCTGTACAGAA-A
1 C-CATATGAAAGGATGAATGTGTTGTCAAATGTTTTACGAACATCTGTACAGAAGA
* *
2113545 CCACATGAAAGGATGAATGTGTTGTCAAATGTTTTACGAACATCTG-AGAAGAAG-
1 CCATATGAAAGGATGAATGTGTTGTCAAATGTTTTACGAACATCTGTA-CAGAAGA
* * * * * *
2113599 CCACAGGAAATGATGAATGTGTTGCCAAATTTTTTATGAAC
1 CCATATGAAAGGATGAATGTGTTGTCAAATGTTTTACGAAC
2113640 CAGTGATTAT
Statistics
Matches: 308, Mismatches: 47, Indels: 19
0.82 0.13 0.05
Matches are distributed among these distances:
52 2 0.01
53 8 0.03
54 290 0.94
55 6 0.02
56 2 0.01
ACGTcount: A:0.39, C:0.12, G:0.21, T:0.27
Consensus pattern (55 bp):
CCATATGAAAGGATGAATGTGTTGTCAAATGTTTTACGAACATCTGTACAGAAGA
Found at i:2113402 original size:108 final size:108
Alignment explanation
Indices: 2113204--2113634 Score: 558
Period size: 108 Copynumber: 4.0 Consensus size: 108
2113194 CGTCACTGGT
* * * * * ** *
2113204 AAACATCTATGTAGAATCCATAGGAAAGGATGAATGTGGCGTCAAATGTATTACGAACATCTGTA
1 AAACATCTGTGCAGAAACCACATGAAAGGATGAATGTGTTGTCAAATATATTACGAACATCTGTA
* * ** * * *
2113269 CAGAAGACGTAGGAAAGGATAAATGTGTTGTCAAATGTTTTAC
66 TAAAAGACACAAGAAATGATGAATGTGTTGTCAAATGTTTTAC
* *
2113312 AAACATCTGTGCAGAAACCACATGAAAGGATGAATGTGTTGTCAAATATATTACAAACATATGTA
1 AAACATCTGTGCAGAAACCACATGAAAGGATGAATGTGTTGTCAAATATATTACGAACATCTGTA
*
2113377 TAAAAGACATAAGAAATGATGAATGTGTTGTCAAATGTTTTAC
66 TAAAAGACACAAGAAATGATGAATGTGTTGTCAAATGTTTTAC
* * * *
2113420 GAACATCTGTGCAAAAACCATATGAAAGGATGAATGTGTAGTCAAATATATTACGAACATCTGTA
1 AAACATCTGTGCAGAAACCACATGAAAGGATGAATGTGTTGTCAAATATATTACGAACATCTGTA
*
2113485 TAGAAGACACAAGAAATGATGAATGTGTTGTCAAATGTTTTAC
66 TAAAAGACACAAGAAATGATGAATGTGTTGTCAAATGTTTTAC
* * * *
2113528 GAACATCTGTACAGAAACCACATGAAAGGATGAATGTGTTGTCAAATGTTTTACGAACATCTG-A
1 AAACATCTGTGCAGAAACCACATGAAAGGATGAATGTGTTGTCAAATATATTACGAACATCTGTA
* * * * *
2113592 GAAGAAGCCACAGGAAATGATGAATGTGTTGCCAAATTTTTTA
66 TAA-AAGACACAAGAAATGATGAATGTGTTGTCAAATGTTTTA
2113635 TGAACCAGTG
Statistics
Matches: 286, Mismatches: 36, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
107 2 0.01
108 284 0.99
ACGTcount: A:0.40, C:0.12, G:0.20, T:0.28
Consensus pattern (108 bp):
AAACATCTGTGCAGAAACCACATGAAAGGATGAATGTGTTGTCAAATATATTACGAACATCTGTA
TAAAAGACACAAGAAATGATGAATGTGTTGTCAAATGTTTTAC
Found at i:2114038 original size:22 final size:22
Alignment explanation
Indices: 2114007--2114061 Score: 85
Period size: 22 Copynumber: 2.5 Consensus size: 22
2113997 ATCTACATTC
2114007 TTCAAAGATGATAGATTCTCACT
1 TTCAAAGATGATAGATTCTC-CT
*
2114030 TT-AAAGATGATAGATTCTCTT
1 TTCAAAGATGATAGATTCTCCT
2114051 TTCAAAGATGA
1 TTCAAAGATGA
2114062 AAGCTTTATT
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
21 3 0.10
22 25 0.83
23 2 0.07
ACGTcount: A:0.36, C:0.13, G:0.15, T:0.36
Consensus pattern (22 bp):
TTCAAAGATGATAGATTCTCCT
Found at i:2114865 original size:76 final size:74
Alignment explanation
Indices: 2114767--2114909 Score: 216
Period size: 76 Copynumber: 1.9 Consensus size: 74
2114757 CTTCAGTGCA
* * *
2114767 TGATGTTTTCATAGCCTTCGGGTCATATGTAA-GCCTTACAGTGCATGATGTTTTCAAAAAGCCT
1 TGATATTTTCAAAGCCTTCGGGTCATATGTAATACCTT-CAGTGCATGATGTTTTC-AAAA-CCT
2114831 TCGGGAGCTTTT
63 TCGGGAGCTTTT
*
2114843 TGATATTTTCAAAGCCTTCGGGTCATCTGTAATACCTTCAGTGCATGATGTTTTCAAAACCTTCG
1 TGATATTTTCAAAGCCTTCGGGTCATATGTAATACCTTCAGTGCATGATGTTTTCAAAACCTTCG
2114908 GG
66 GG
2114910 TCATCCATAA
Statistics
Matches: 62, Mismatches: 4, Indels: 4
0.89 0.06 0.06
Matches are distributed among these distances:
74 8 0.13
75 4 0.06
76 46 0.74
77 4 0.06
ACGTcount: A:0.23, C:0.20, G:0.21, T:0.36
Consensus pattern (74 bp):
TGATATTTTCAAAGCCTTCGGGTCATATGTAATACCTTCAGTGCATGATGTTTTCAAAACCTTCG
GGAGCTTTT
Found at i:2114899 original size:45 final size:45
Alignment explanation
Indices: 2114843--2114956 Score: 147
Period size: 45 Copynumber: 2.5 Consensus size: 45
2114833 GGGAGCTTTT
* ** * *
2114843 TGATATTTTCAAAGCCTTCGGGTCATCTGTAATACCTTCAGTGCA
1 TGATGTTTTCAAAGCCTTCGGGTCATCCATAAAACCTACAGTGCA
*
2114888 TGATGTTTTCAAAACCTTCGGGTCATCCATAAAACCTACAGTGCA
1 TGATGTTTTCAAAGCCTTCGGGTCATCCATAAAACCTACAGTGCA
*
2114933 GGATGTTTTCAAAAAGCCTTCGGG
1 TGATGTTTTC--AAAGCCTTCGGG
2114957 AGCTTTTTGA
Statistics
Matches: 59, Mismatches: 8, Indels: 2
0.86 0.12 0.03
Matches are distributed among these distances:
45 48 0.81
47 11 0.19
ACGTcount: A:0.27, C:0.22, G:0.19, T:0.32
Consensus pattern (45 bp):
TGATGTTTTCAAAGCCTTCGGGTCATCCATAAAACCTACAGTGCA
Done.