Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007101.1 Hibiscus syriacus cultivar Beakdansim tig00018555_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: 142622
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.32
Found at i:747 original size:31 final size:31
Alignment explanation
Indices: 709--773 Score: 85
Period size: 31 Copynumber: 2.1 Consensus size: 31
699 AGAGTCGAGG
*
709 GTTTACCTATGTTCTAAGGAACATATGGACA
1 GTTTACCTAGGTTCTAAGGAACATATGGACA
** * *
740 GTTTACCTAGGTTCTTCGGGACCTATGGACA
1 GTTTACCTAGGTTCTAAGGAACATATGGACA
771 GTT
1 GTT
774 ACCGAGGATC
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.25, C:0.18, G:0.23, T:0.34
Consensus pattern (31 bp):
GTTTACCTAGGTTCTAAGGAACATATGGACA
Found at i:793 original size:30 final size:30
Alignment explanation
Indices: 732--807 Score: 80
Period size: 30 Copynumber: 2.5 Consensus size: 30
722 CTAAGGAACA
* * *
732 TATGGACAGTTTACCTAGGTTCTTCGGGACC
1 TATGGACAG-TTACCGAGGATCTTCAGGACC
* *
763 TATGGACAGTTACCGAGGATCTTTATGACC
1 TATGGACAGTTACCGAGGATCTTCAGGACC
* *
793 TCTGGATAGTTACCG
1 TATGGACAGTTACCG
808 GGGTCTGTGT
Statistics
Matches: 38, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
30 29 0.76
31 9 0.24
ACGTcount: A:0.22, C:0.21, G:0.25, T:0.32
Consensus pattern (30 bp):
TATGGACAGTTACCGAGGATCTTCAGGACC
Found at i:824 original size:29 final size:30
Alignment explanation
Indices: 759--830 Score: 92
Period size: 29 Copynumber: 2.4 Consensus size: 30
749 GGTTCTTCGG
* * *
759 GACCTATGGACAGTTACCGAGGATCTTTAT
1 GACCTCTGGATAGTTACCGAGGATCTGTAT
* *
789 GACCTCTGGATAGTTACCG-GGGTCTGTGT
1 GACCTCTGGATAGTTACCGAGGATCTGTAT
818 GACCTCTGGATAG
1 GACCTCTGGATAG
831 GTCCTTCGGA
Statistics
Matches: 37, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
29 20 0.54
30 17 0.46
ACGTcount: A:0.21, C:0.21, G:0.29, T:0.29
Consensus pattern (30 bp):
GACCTCTGGATAGTTACCGAGGATCTGTAT
Found at i:2965 original size:26 final size:27
Alignment explanation
Indices: 2934--2992 Score: 111
Period size: 26 Copynumber: 2.2 Consensus size: 27
2924 CCAAGCCATG
2934 TGGCTTCAAAACCATCTC-AATCATTC
1 TGGCTTCAAAACCATCTCAAATCATTC
2960 TGGCTTCAAAACCATCTCAAATCATTC
1 TGGCTTCAAAACCATCTCAAATCATTC
2987 TGGCTT
1 TGGCTT
2993 TCTCTCAATA
Statistics
Matches: 32, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
26 18 0.56
27 14 0.44
ACGTcount: A:0.29, C:0.29, G:0.10, T:0.32
Consensus pattern (27 bp):
TGGCTTCAAAACCATCTCAAATCATTC
Found at i:6176 original size:37 final size:36
Alignment explanation
Indices: 6120--6236 Score: 166
Period size: 35 Copynumber: 3.2 Consensus size: 36
6110 CCCATTCCTA
* *
6120 TTTTC-AACAAACATCTACCAAACTTTGAAAAACTAT
1 TTTTCAAAGAAACATTTACCAAACTTTGAAAAAC-AT
*
6156 TTTTCAAAGAAACATTTACCAAACTTTGAAAACCA-
1 TTTTCAAAGAAACATTTACCAAACTTTGAAAAACAT
*
6191 TTTTCAAAGAAACATTTACCAAACTTTGAAAATCATT
1 TTTTCAAAGAAACATTTACCAAACTTTGAAAAACA-T
6228 TTTTCAAAG
1 TTTTCAAAG
6237 TTGGTTACCA
Statistics
Matches: 74, Mismatches: 4, Indels: 5
0.89 0.05 0.06
Matches are distributed among these distances:
35 34 0.46
36 6 0.08
37 34 0.46
ACGTcount: A:0.44, C:0.19, G:0.05, T:0.32
Consensus pattern (36 bp):
TTTTCAAAGAAACATTTACCAAACTTTGAAAAACAT
Found at i:6192 original size:21 final size:20
Alignment explanation
Indices: 6165--6228 Score: 59
Period size: 20 Copynumber: 3.4 Consensus size: 20
6155 TTTTTCAAAG
6165 AAACATTTACCAAACTTTGA
1 AAACATTTACCAAACTTTGA
*
6185 AAACCATTT-TCAAA----G-
1 AAA-CATTTACCAAACTTTGA
6200 AAACATTTACCAAACTTTGA
1 AAACATTTACCAAACTTTGA
6220 AAATCATTT
1 AAA-CATTT
6229 TTTCAAAGTT
Statistics
Matches: 34, Mismatches: 2, Indels: 15
0.67 0.04 0.29
Matches are distributed among these distances:
14 5 0.15
15 7 0.21
16 1 0.03
19 1 0.03
20 10 0.29
21 10 0.29
ACGTcount: A:0.45, C:0.19, G:0.05, T:0.31
Consensus pattern (20 bp):
AAACATTTACCAAACTTTGA
Found at i:10771 original size:35 final size:36
Alignment explanation
Indices: 10688--10779 Score: 134
Period size: 37 Copynumber: 2.6 Consensus size: 36
10678 ACCCATTCCT
* * *
10688 ATTTTC-AACAAACATCTACCAAACTTTGAAAATCT
1 ATTTTCAAAGAAACATTTACCAAACTTTGAAAATCC
10723 ATTTTTCAAAGAAACATTTACCAAACTTTGAAAA-CC
1 A-TTTTCAAAGAAACATTTACCAAACTTTGAAAATCC
10759 ATTTTCAAAGAAACATTTACC
1 ATTTTCAAAGAAACATTTACC
10780 TGAAAACCAT
Statistics
Matches: 52, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
35 21 0.40
36 7 0.13
37 24 0.46
ACGTcount: A:0.43, C:0.21, G:0.04, T:0.32
Consensus pattern (36 bp):
ATTTTCAAAGAAACATTTACCAAACTTTGAAAATCC
Found at i:14844 original size:16 final size:17
Alignment explanation
Indices: 14817--14849 Score: 59
Period size: 16 Copynumber: 2.0 Consensus size: 17
14807 GTATTGTCGG
14817 CAAAATTTTACTATTCA
1 CAAAATTTTACTATTCA
14834 CAAAA-TTTACTATTCA
1 CAAAATTTTACTATTCA
14850 TTGAATAGTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 11 0.69
17 5 0.31
ACGTcount: A:0.42, C:0.18, G:0.00, T:0.39
Consensus pattern (17 bp):
CAAAATTTTACTATTCA
Found at i:15286 original size:26 final size:27
Alignment explanation
Indices: 15254--15304 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 27
15244 CCCATTCCTA
*
15254 TTTTC-AACAAACATCTATCAAACTAT
1 TTTTCAAACAAACATCTACCAAACTAT
* *
15280 TTTTCAAAGAAACATTTACCAAACT
1 TTTTCAAACAAACATCTACCAAACT
15305 TTGAAAACCA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
26 5 0.24
27 16 0.76
ACGTcount: A:0.43, C:0.22, G:0.02, T:0.33
Consensus pattern (27 bp):
TTTTCAAACAAACATCTACCAAACTAT
Found at i:15319 original size:35 final size:37
Alignment explanation
Indices: 15278--15360 Score: 152
Period size: 35 Copynumber: 2.3 Consensus size: 37
15268 CTATCAAACT
15278 ATTTTTCAAAGAAACATTTACCAAACTTTGAAAACC-
1 ATTTTTCAAAGAAACATTTACCAAACTTTGAAAACCA
15314 A-TTTTCAAAGAAACATTTACCAAACTTTGAAAACCA
1 ATTTTTCAAAGAAACATTTACCAAACTTTGAAAACCA
15350 ATTTTTCAAAG
1 ATTTTTCAAAG
15361 TTGGTTACCA
Statistics
Matches: 45, Mismatches: 0, Indels: 3
0.94 0.00 0.06
Matches are distributed among these distances:
35 34 0.76
36 2 0.04
37 9 0.20
ACGTcount: A:0.45, C:0.18, G:0.06, T:0.31
Consensus pattern (37 bp):
ATTTTTCAAAGAAACATTTACCAAACTTTGAAAACCA
Found at i:15369 original size:35 final size:35
Alignment explanation
Indices: 15273--15387 Score: 128
Period size: 35 Copynumber: 3.3 Consensus size: 35
15263 AACATCTATC
* *
15273 AAACTATTTTTCAAAGAAACATTTACCAAACTTTGA
1 AAACCATTTTTCAAAG-AACAGTTACCAAACTTTGA
*
15309 AAACCA-TTTTCAAAGAAACATTTACCAAACTTTGA
1 AAACCATTTTTCAAAG-AACAGTTACCAAACTTTGA
***
15344 AAACCAATTTTTCAAAG-TTGGTTACCAAAC-TTGA
1 AAACC-ATTTTTCAAAGAACAGTTACCAAACTTTGA
15378 AAACCATTTT
1 AAACCATTTT
15388 AATACTTTCA
Statistics
Matches: 72, Mismatches: 5, Indels: 7
0.86 0.06 0.08
Matches are distributed among these distances:
33 5 0.07
34 9 0.12
35 43 0.60
36 6 0.08
37 9 0.12
ACGTcount: A:0.43, C:0.18, G:0.07, T:0.32
Consensus pattern (35 bp):
AAACCATTTTTCAAAGAACAGTTACCAAACTTTGA
Found at i:17984 original size:13 final size:13
Alignment explanation
Indices: 17966--17991 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
17956 GTCCGATTTA
17966 CCATTCATCAAAC
1 CCATTCATCAAAC
17979 CCATTCATCAAAC
1 CCATTCATCAAAC
17992 ATGTATAAAC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.38, G:0.00, T:0.23
Consensus pattern (13 bp):
CCATTCATCAAAC
Found at i:20855 original size:6 final size:6
Alignment explanation
Indices: 20844--20870 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
20834 CGGCTACGAG
20844 TTCCGA TTCCGA TTCCGA TTCCGA TTC
1 TTCCGA TTCCGA TTCCGA TTCCGA TTC
20871 GGCAGTGGGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.15, C:0.33, G:0.15, T:0.37
Consensus pattern (6 bp):
TTCCGA
Found at i:23815 original size:228 final size:228
Alignment explanation
Indices: 23605--24260 Score: 990
Period size: 228 Copynumber: 2.9 Consensus size: 228
23595 AACCAAATGA
* * * *
23605 AGGGTCGACTCCTTTTGGATGTTGTAATCGGCCAAGGTACGACCGTCCTCGAGCTGTTTTCCGGC
1 AGGGTCGACTCCTTCTGGATGTTGTAGTCGGCCAAGGTACGGCCGTCCTCGAGCTGCTTTCCGGC
* *
23670 GAAGATGAGACGTTGCTGGTCCGGTGGGATCCCTTCCTTGTCTTGGATCTTGGCCTTGACGTTGT
66 GAAGATAAGACGTTGCTGGTCCGGTGGGATTCCTTCCTTGTCTTGGATCTTGGCCTTGACGTTGT
* *
23735 CGATGGTGTCGGAGCTCTCGACTTCCAAGGTGATTGTCTTGCCCGTCAGGGTTTTCACGAAGATC
131 CGATGGTGTCGGAGCTCTCGACCTCCAAGGTGATTGTCTTGCCGGTCAGGGTTTTCACGAAGATC
23800 TGCATGCCTCCACGAAGACGGAGGACCAGGTGG
196 TGCATGCCTCCACGAAGACGGAGGACCAGGTGG
* * * *
23833 AGGGTCGACTCCTTCTGGATGTTATAGTCCGCCAAGGTACGGCCGTCCTCGAGTTGCTTCCCGGC
1 AGGGTCGACTCCTTCTGGATGTTGTAGTCGGCCAAGGTACGGCCGTCCTCGAGCTGCTTTCCGGC
* * *
23898 GAAGATCAG-CCTCTGCTGGTCTGGTGGGATTCCTTCCTTGTCTTGGATCTTGGCCTTGACGTTG
66 GAAGATAAGACGT-TGCTGGTCCGGTGGGATTCCTTCCTTGTCTTGGATCTTGGCCTTGACGTTG
* * *
23962 TCGATGGTGTCGGAGCTCTCGACCTCCAAGGTGATGGTTTTGCCGGTAAGGGTTTTCACGAAGAT
130 TCGATGGTGTCGGAGCTCTCGACCTCCAAGGTGATTGTCTTGCCGGTCAGGGTTTTCACGAAGAT
* *
24027 TTGCATGCCTCCACGAAGACGGAGGACGAGGTGG
195 CTGCATGCCTCCACGAAGACGGAGGACCAGGTGG
*
24061 AGGGTTGACTCCTTCTGGATGTTGTAGTCGGCCAAGGTACGGCCGTCCTCGAGCTGCTTTCCGGC
1 AGGGTCGACTCCTTCTGGATGTTGTAGTCGGCCAAGGTACGGCCGTCCTCGAGCTGCTTTCCGGC
* * * * * * *
24126 AAAGATAAGACGCTGTTGGTCCGGAGGAATTCCTTCCTTGTCTTGGATCTTCGCCTTGACGTTAT
66 GAAGATAAGACGTTGCTGGTCCGGTGGGATTCCTTCCTTGTCTTGGATCTTGGCCTTGACGTTGT
* * * * * *
24191 CAATGGTGTCGGAGCTCTCAACCTCGAGGGTGATTGTCTTGCCGGTCAGGGTCTTAACGAAGATC
131 CGATGGTGTCGGAGCTCTCGACCTCCAAGGTGATTGTCTTGCCGGTCAGGGTTTTCACGAAGATC
24256 TGCAT
196 TGCAT
24261 CTTGTTTGGT
Statistics
Matches: 382, Mismatches: 44, Indels: 4
0.89 0.10 0.01
Matches are distributed among these distances:
227 2 0.01
228 379 0.99
229 1 0.00
ACGTcount: A:0.16, C:0.24, G:0.31, T:0.29
Consensus pattern (228 bp):
AGGGTCGACTCCTTCTGGATGTTGTAGTCGGCCAAGGTACGGCCGTCCTCGAGCTGCTTTCCGGC
GAAGATAAGACGTTGCTGGTCCGGTGGGATTCCTTCCTTGTCTTGGATCTTGGCCTTGACGTTGT
CGATGGTGTCGGAGCTCTCGACCTCCAAGGTGATTGTCTTGCCGGTCAGGGTTTTCACGAAGATC
TGCATGCCTCCACGAAGACGGAGGACCAGGTGG
Found at i:24206 original size:456 final size:456
Alignment explanation
Indices: 23434--24260 Score: 1120
Period size: 456 Copynumber: 1.8 Consensus size: 456
23424 TTCCAATTGT
*
23434 TTCCCAGCGAAAATCAACCTCTGCTGGTCTGGGGGAATCCCTTCTTTGTCCTGAATCTTCGCCTT
1 TTCCCAGCGAAAATCAACCTCTGCTGGTCTGGGGGAATCCCTTCCTTGTCCTGAATCTTCGCCTT
*
23499 GACATTATCAATCGTATCAGAACTCTCCACCTCCAGAGTAATGGTTTTCCCGGTCAAAGTTTTGA
66 GACATTATCAATCGTATCAGAACTCTCCACCTCCAGAGTAATGGTTTTCCCGGTCAAAGTTTTCA
* * *
23564 CGAAGATCTGCATCCCGCCACGAAGCCTCAAAACCAAATGAAGGGTCGACTCCTTTTGGATGTTG
131 CGAAGATCTGCATCCCGCCACGAAGACGCAAAACCAAATGAAGGGTCGACTCCTTCTGGATGTTG
* * * *
23629 TAATCGGCCAAGGTACGACCGTCCTCGAGCTGTTTTCCGGCGAAGATGAGACGTTGCTGGTCCGG
196 TAATCGGCCAAGGTACGACCGTCCTCGAGCTGCTTTCCGGCAAAGATAAGACGCTGCTGGTCCGG
* * * * * * *
23694 TGGGATCCCTTCCTTGTCTTGGATCTTGGCCTTGACGTTGTCGATGGTGTCGGAGCTCTCGACTT
261 AGGAATCCCTTCCTTGTCTTGGATCTTCGCCTTGACGTTATCAATGGTGTCGGAGCTCTCAACCT
* *
23759 CCAAGGTGATTGTCTTGCCCGTCAGGGTTTTCACGAAGATCTGCATGCCTCCACGAAGACGGAGG
326 CCAAGGTGATTGTCTTGCCCGTCAGGGTCTTAACGAAGATCTGCATGCCTCCACGAAGACGGAGG
23824 ACCAGGTGGAGGGTCGACTCCTTCTGGATGTTATAGTCCGCCAAGGTACGGCCGTCCTCGAGTTG
391 ACCAGGTGGAGGGTCGACTCCTTCTGGATGTTATAGTCCGCCAAGGTACGGCCGTCCTCGAGTTG
23889 C
456 C
* * * * * * *
23890 TTCCCGGCGAAGATCAGCCTCTGCTGGTCTGGTGGG-ATTCCTTCCTTGTCTTGGATCTTGGCCT
1 TTCCCAGCGAAAATCAACCTCTGCTGGTCTGG-GGGAATCCCTTCCTTGTCCTGAATCTTCGCCT
* * * * * * * * * * *
23954 TGACGTTGTCGATGGTGTCGGAGCTCTCGACCTCCA-AGGTGATGGTTTTGCCGGT-AAGGGTTT
65 TGACATTATCAATCGTATCAGAACTCTCCACCTCCAGA-GTAATGGTTTTCCCGGTCAA-AGTTT
* * * * ** * ** * *
24017 TCACGAAGATTTGCATGCCTCCACGAAGACGGAGGACGAGGTGGAGGGTTGACTCCTTCTGGATG
128 TCACGAAGATCTGCATCCCGCCACGAAGACGCAAAACCAAATGAAGGGTCGACTCCTTCTGGATG
* * *
24082 TTGTAGTCGGCCAAGGTACGGCCGTCCTCGAGCTGCTTTCCGGCAAAGATAAGACGCTGTTGGTC
193 TTGTAATCGGCCAAGGTACGACCGTCCTCGAGCTGCTTTCCGGCAAAGATAAGACGCTGCTGGTC
*
24147 CGGAGGAATTCCTTCCTTGTCTTGGATCTTCGCCTTGACGTTATCAATGGTGTCGGAGCTCTCAA
258 CGGAGGAATCCCTTCCTTGTCTTGGATCTTCGCCTTGACGTTATCAATGGTGTCGGAGCTCTCAA
* * *
24212 CCTCGAGGGTGATTGTCTTGCCGGTCAGGGTCTTAACGAAGATCTGCAT
323 CCTCCAAGGTGATTGTCTTGCCCGTCAGGGTCTTAACGAAGATCTGCAT
24261 CTTGTTTGGT
Statistics
Matches: 314, Mismatches: 54, Indels: 6
0.84 0.14 0.02
Matches are distributed among these distances:
455 3 0.01
456 308 0.98
457 3 0.01
ACGTcount: A:0.18, C:0.25, G:0.28, T:0.28
Consensus pattern (456 bp):
TTCCCAGCGAAAATCAACCTCTGCTGGTCTGGGGGAATCCCTTCCTTGTCCTGAATCTTCGCCTT
GACATTATCAATCGTATCAGAACTCTCCACCTCCAGAGTAATGGTTTTCCCGGTCAAAGTTTTCA
CGAAGATCTGCATCCCGCCACGAAGACGCAAAACCAAATGAAGGGTCGACTCCTTCTGGATGTTG
TAATCGGCCAAGGTACGACCGTCCTCGAGCTGCTTTCCGGCAAAGATAAGACGCTGCTGGTCCGG
AGGAATCCCTTCCTTGTCTTGGATCTTCGCCTTGACGTTATCAATGGTGTCGGAGCTCTCAACCT
CCAAGGTGATTGTCTTGCCCGTCAGGGTCTTAACGAAGATCTGCATGCCTCCACGAAGACGGAGG
ACCAGGTGGAGGGTCGACTCCTTCTGGATGTTATAGTCCGCCAAGGTACGGCCGTCCTCGAGTTG
C
Found at i:25305 original size:27 final size:24
Alignment explanation
Indices: 25246--25306 Score: 63
Period size: 23 Copynumber: 2.5 Consensus size: 24
25236 TCAGTATTAA
25246 TAAA-ATTTATTTACTAAATTTAT
1 TAAATATTTATTTACTAAATTTAT
* *
25269 TAGATA-TTATTTATCTGAAATATTTT
1 TAAATATTTATTTA-CT-AAAT-TTAT
25295 TAAATATTTATT
1 TAAATATTTATT
25307 ATTGAACAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
23 10 0.33
24 3 0.10
25 4 0.13
26 8 0.27
27 5 0.17
ACGTcount: A:0.39, C:0.03, G:0.03, T:0.54
Consensus pattern (24 bp):
TAAATATTTATTTACTAAATTTAT
Found at i:26350 original size:23 final size:23
Alignment explanation
Indices: 26322--26384 Score: 72
Period size: 23 Copynumber: 2.7 Consensus size: 23
26312 TATTCATGTT
** *
26322 CGTTCATTTAATGTTTGTAAATA
1 CGTTCATTTAATGTTTACAAACA
* * *
26345 TGTTCATTTAACGTTTACGAACA
1 CGTTCATTTAATGTTTACAAACA
26368 CGTTCATTTAATGTTTA
1 CGTTCATTTAATGTTTA
26385 ACAACCGAAA
Statistics
Matches: 32, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.29, C:0.13, G:0.13, T:0.46
Consensus pattern (23 bp):
CGTTCATTTAATGTTTACAAACA
Found at i:29422 original size:67 final size:67
Alignment explanation
Indices: 29314--29445 Score: 210
Period size: 67 Copynumber: 2.0 Consensus size: 67
29304 CGTAGTGCTG
*
29314 TGACACATAAGGTCGTGCCCACCACCTGCACTAAGTGTCCTTACACATTATAGTGCTAAATCAAA
1 TGACACATAAGGTCGTGCCCACCACCTGCACTAAGTGTCCTTACACACTATAGTGCTAAATCAAA
29379 TA
66 TA
* * * * *
29381 TGACACTTAAGGTTGTGCCCACCACCTGTACTAAGTGTCCTTACACACTATAGTGTTGAATCAAA
1 TGACACATAAGGTCGTGCCCACCACCTGCACTAAGTGTCCTTACACACTATAGTGCTAAATCAAA
29446 CCTGCAACCA
Statistics
Matches: 59, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
67 59 1.00
ACGTcount: A:0.31, C:0.26, G:0.16, T:0.27
Consensus pattern (67 bp):
TGACACATAAGGTCGTGCCCACCACCTGCACTAAGTGTCCTTACACACTATAGTGCTAAATCAAA
TA
Found at i:35487 original size:21 final size:21
Alignment explanation
Indices: 35461--35504 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
35451 ATTTCTGGGT
* *
35461 AAGGGGAATCGGTACCCATTC
1 AAGGGGAACCGATACCCATTC
*
35482 AAGGGGAACCGATACCCCTTC
1 AAGGGGAACCGATACCCATTC
35503 AA
1 AA
35505 ACGACAGAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.32, C:0.27, G:0.25, T:0.16
Consensus pattern (21 bp):
AAGGGGAACCGATACCCATTC
Found at i:36058 original size:23 final size:24
Alignment explanation
Indices: 36015--36061 Score: 78
Period size: 23 Copynumber: 2.0 Consensus size: 24
36005 ACATGGCCTG
*
36015 TGATATGAAAGTGTATATGTGAAA
1 TGATATGAAAGTATATATGTGAAA
36039 TGATATGAAA-TATATATGTGAAA
1 TGATATGAAAGTATATATGTGAAA
36062 ACAAGTATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
23 12 0.55
24 10 0.45
ACGTcount: A:0.45, C:0.00, G:0.21, T:0.34
Consensus pattern (24 bp):
TGATATGAAAGTATATATGTGAAA
Found at i:36277 original size:31 final size:31
Alignment explanation
Indices: 36239--36394 Score: 260
Period size: 31 Copynumber: 5.0 Consensus size: 31
36229 AGGGTCGAGG
36239 GTTTACCTATGTTCTTCGGAACATATGGACT
1 GTTTACCTATGTTCTTCGGAACATATGGACT
36270 GTTTACCTATGTTCTTCGGAACATATGGACT
1 GTTTACCTATGTTCTTCGGAACATATGGACT
36301 GTTTACCTATGTTCTTCGGAACATATGGACT
1 GTTTACCTATGTTCTTCGGAACATATGGACT
* *
36332 GTTTACCTATGTCCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGAACATATGGACT
* *
36363 GATTACCTAGGTTCTTCGGAATC-TATGGACT
1 GTTTACCTATGTTCTTCGGAA-CATATGGACT
36394 G
1 G
36395 GTCCTTCGGG
Statistics
Matches: 118, Mismatches: 6, Indels: 2
0.94 0.05 0.02
Matches are distributed among these distances:
31 117 0.99
32 1 0.01
ACGTcount: A:0.22, C:0.20, G:0.21, T:0.37
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGGAACATATGGACT
Found at i:39419 original size:21 final size:21
Alignment explanation
Indices: 39393--39436 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
39383 ATTTCTGGGT
* *
39393 AAGGGGAATCGGTACCCATTC
1 AAGGGGAACCGATACCCATTC
*
39414 AAGGGGAACCGATACCCCTTC
1 AAGGGGAACCGATACCCATTC
39435 AA
1 AA
39437 ACGACAGAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.32, C:0.27, G:0.25, T:0.16
Consensus pattern (21 bp):
AAGGGGAACCGATACCCATTC
Found at i:39991 original size:23 final size:24
Alignment explanation
Indices: 39948--39994 Score: 78
Period size: 23 Copynumber: 2.0 Consensus size: 24
39938 ACATGGCCTG
*
39948 TGATATGAAAGTGTATATGTGAAA
1 TGATATGAAAGTATATATGTGAAA
39972 TGATATGAAA-TATATATGTGAAA
1 TGATATGAAAGTATATATGTGAAA
39995 ACAAGTATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
23 12 0.55
24 10 0.45
ACGTcount: A:0.45, C:0.00, G:0.21, T:0.34
Consensus pattern (24 bp):
TGATATGAAAGTATATATGTGAAA
Found at i:40210 original size:31 final size:31
Alignment explanation
Indices: 40172--40327 Score: 260
Period size: 31 Copynumber: 5.0 Consensus size: 31
40162 AGGGTCGAGG
40172 GTTTACCTATGTTCTTCGGAACATATGGACT
1 GTTTACCTATGTTCTTCGGAACATATGGACT
40203 GTTTACCTATGTTCTTCGGAACATATGGACT
1 GTTTACCTATGTTCTTCGGAACATATGGACT
40234 GTTTACCTATGTTCTTCGGAACATATGGACT
1 GTTTACCTATGTTCTTCGGAACATATGGACT
* *
40265 GTTTACCTATGTCCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGAACATATGGACT
* *
40296 GATTACCTAGGTTCTTCGGAATC-TATGGACT
1 GTTTACCTATGTTCTTCGGAA-CATATGGACT
40327 G
1 G
40328 GTCCTTCGGA
Statistics
Matches: 118, Mismatches: 6, Indels: 2
0.94 0.05 0.02
Matches are distributed among these distances:
31 117 0.99
32 1 0.01
ACGTcount: A:0.22, C:0.20, G:0.21, T:0.37
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGGAACATATGGACT
Found at i:51007 original size:21 final size:21
Alignment explanation
Indices: 50981--51039 Score: 66
Period size: 20 Copynumber: 2.8 Consensus size: 21
50971 GGTGTCAAAA
*
50981 TGCATCCATGCACCCCTACAG
1 TGCATCCATGCACCCATACAG
* **
51002 TGCATCGATGCA-CCATGTAG
1 TGCATCCATGCACCCATACAG
51022 TGCATCCATGCACTCCAT
1 TGCATCCATGCAC-CCAT
51040 TTCGAATGCA
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
20 16 0.52
21 11 0.35
22 4 0.13
ACGTcount: A:0.24, C:0.36, G:0.17, T:0.24
Consensus pattern (21 bp):
TGCATCCATGCACCCATACAG
Found at i:51125 original size:20 final size:20
Alignment explanation
Indices: 51054--51126 Score: 76
Period size: 20 Copynumber: 3.6 Consensus size: 20
51044 AATGCAATTA
*
51054 GTGCATCGATGCATCCTGCT
1 GTGCATCGATGCATCTTGCT
* *
51074 ATGCATCGATGCATCTTGCC
1 GTGCATCGATGCATCTTGCT
* *
51094 GT-CTATCAATGCATCTTGTT
1 GTGC-ATCGATGCATCTTGCT
*
51114 GTGCATCCATGCA
1 GTGCATCGATGCA
51127 CCAAGGCTGC
Statistics
Matches: 43, Mismatches: 8, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
19 1 0.02
20 41 0.95
21 1 0.02
ACGTcount: A:0.19, C:0.27, G:0.21, T:0.33
Consensus pattern (20 bp):
GTGCATCGATGCATCTTGCT
Found at i:54408 original size:30 final size:30
Alignment explanation
Indices: 54373--54429 Score: 96
Period size: 30 Copynumber: 1.9 Consensus size: 30
54363 ACAATTTAAG
*
54373 ACAAAATGGTTTTGGACTTGAATTGAATTT
1 ACAAAATGGTTTTGGACTTCAATTGAATTT
*
54403 ACAAAATGTTTTTGGACTTCAATTGAA
1 ACAAAATGGTTTTGGACTTCAATTGAA
54430 GTTTTAAAAG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.35, C:0.09, G:0.18, T:0.39
Consensus pattern (30 bp):
ACAAAATGGTTTTGGACTTCAATTGAATTT
Found at i:54631 original size:20 final size:20
Alignment explanation
Indices: 54602--54673 Score: 101
Period size: 20 Copynumber: 3.6 Consensus size: 20
54592 ATGCAAATAA
54602 TGCATCGATGCATCCTGTCG
1 TGCATCGATGCATCCTGTCG
* *
54622 TGCATTGATGCATCATGTCG
1 TGCATCGATGCATCCTGTCG
54642 TGCATCGATGCATCCTG-CTG
1 TGCATCGATGCATCCTGTC-G
*
54662 TGCATCCATGCA
1 TGCATCGATGCA
54674 CCAAGGCTGT
Statistics
Matches: 46, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
19 1 0.02
20 45 0.98
ACGTcount: A:0.18, C:0.28, G:0.24, T:0.31
Consensus pattern (20 bp):
TGCATCGATGCATCCTGTCG
Found at i:55079 original size:34 final size:32
Alignment explanation
Indices: 55040--55109 Score: 95
Period size: 34 Copynumber: 2.1 Consensus size: 32
55030 TTTTGTAAAG
* *
55040 GGGAAAGGTTCTAGCTTATCCCGTGTAAAAGCTA
1 GGGAAAGGTTCTAGCTTAGCCCG-G-AAAAACTA
*
55074 GGGAAAGGTTCTAGTTTAGCCCGGAAAAACTA
1 GGGAAAGGTTCTAGCTTAGCCCGGAAAAACTA
55106 GGGA
1 GGGA
55110 GTTGTAAGGT
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
32 11 0.33
33 1 0.03
34 21 0.64
ACGTcount: A:0.31, C:0.16, G:0.30, T:0.23
Consensus pattern (32 bp):
GGGAAAGGTTCTAGCTTAGCCCGGAAAAACTA
Found at i:60669 original size:23 final size:22
Alignment explanation
Indices: 60628--60708 Score: 103
Period size: 23 Copynumber: 3.7 Consensus size: 22
60618 TAGTGCATGA
60628 GGAATCGATACCCCC-TTGAAGG
1 GGAATCGATACCCCCTTTGAA-G
* *
60650 GGAACCGATTCCCCCTTTGAATG
1 GGAATCGATACCCCCTTTGAA-G
*
60673 GGAATCGATTCCCCCTTTG-AG
1 GGAATCGATACCCCCTTTGAAG
60694 GGAATCGATACCCCC
1 GGAATCGATACCCCC
60709 ACAGGGTCTA
Statistics
Matches: 53, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
21 15 0.28
22 14 0.26
23 24 0.45
ACGTcount: A:0.23, C:0.31, G:0.23, T:0.22
Consensus pattern (22 bp):
GGAATCGATACCCCCTTTGAAG
Found at i:62900 original size:16 final size:16
Alignment explanation
Indices: 62879--62909 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
62869 AAAAGGGGGA
*
62879 GAAGTGTTATAGTAAG
1 GAAGTGTTAAAGTAAG
62895 GAAGTGTTAAAGTAA
1 GAAGTGTTAAAGTAA
62910 AGGGGAGTAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.42, C:0.00, G:0.29, T:0.29
Consensus pattern (16 bp):
GAAGTGTTAAAGTAAG
Found at i:73044 original size:20 final size:20
Alignment explanation
Indices: 72997--73226 Score: 185
Period size: 20 Copynumber: 11.2 Consensus size: 20
72987 AATGACCAAC
* *
72997 AAAATCGCAACGCGATAT-C
1 AAAATCGCAACGCGATTTAG
*
73016 AAAACCGCAACGCGATTTAG
1 AAAATCGCAACGCGATTTAG
* * **
73036 AAAAGCGCAACGTTGA-AAAG
1 AAAATCGCAACG-CGATTTAG
* **
73056 AAGATCGCAACGCGATCTTCC
1 AAAATCGCAACGCGAT-TTAG
* * *
73077 AAGAATCGCAATGCGATTCAT
1 AA-AATCGCAACGCGATTTAG
*
73098 AAAATCGCAACGCGATTAAG
1 AAAATCGCAACGCGATTTAG
*
73118 AAAATCGCAACGCGATTCAG
1 AAAATCGCAACGCGATTTAG
**
73138 AAAATCGCAACGCGATCTTCC
1 AAAATCGCAACGCGAT-TTAG
*
73159 AAGAATCGCAACGCGATTAAG
1 AA-AATCGCAACGCGATTTAG
* **
73180 GAAATCGCAACGCGATCTTCC
1 AAAATCGCAACGCGAT-TTAG
*
73201 AAGAATCGCAACGCGATTCAG
1 AA-AATCGCAACGCGATTTAG
73222 AAAAT
1 AAAAT
73227 GAGTAAATTC
Statistics
Matches: 165, Mismatches: 37, Indels: 17
0.75 0.17 0.08
Matches are distributed among these distances:
19 18 0.11
20 90 0.55
21 17 0.10
22 40 0.24
ACGTcount: A:0.40, C:0.24, G:0.20, T:0.17
Consensus pattern (20 bp):
AAAATCGCAACGCGATTTAG
Found at i:73106 original size:42 final size:42
Alignment explanation
Indices: 73054--73226 Score: 260
Period size: 42 Copynumber: 4.2 Consensus size: 42
73044 AACGTTGAAA
* *
73054 AGAAGATCGCAACGCGATCTTCCAAGAATCGCAATGCGATTC
1 AGAAAATCGCAACGCGATCTTCCAAGAATCGCAACGCGATTC
* ***
73096 ATAAAATCGCAACGCGAT-TAAGAA-AATCGCAACGCGATTC
1 AGAAAATCGCAACGCGATCTTCCAAGAATCGCAACGCGATTC
*
73136 AGAAAATCGCAACGCGATCTTCCAAGAATCGCAACGCGATTA
1 AGAAAATCGCAACGCGATCTTCCAAGAATCGCAACGCGATTC
*
73178 AGGAAATCGCAACGCGATCTTCCAAGAATCGCAACGCGATTC
1 AGAAAATCGCAACGCGATCTTCCAAGAATCGCAACGCGATTC
73220 AGAAAAT
1 AGAAAAT
73227 GAGTAAATTC
Statistics
Matches: 115, Mismatches: 14, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
40 32 0.28
41 6 0.05
42 77 0.67
ACGTcount: A:0.38, C:0.25, G:0.20, T:0.17
Consensus pattern (42 bp):
AGAAAATCGCAACGCGATCTTCCAAGAATCGCAACGCGATTC
Found at i:73145 original size:82 final size:81
Alignment explanation
Indices: 72999--73226 Score: 282
Period size: 82 Copynumber: 2.8 Consensus size: 81
72989 TGACCAACAA
* * * ** *
72999 AATCGCAACGCGA-TATCAAAACCGCAACGCGATTTAGAAAAGCGCAACGTTGA-AAAGAAGATC
1 AATCGCAACGCGATTAT-AAAATCGCAACGCGATTTAGAAAATCGCAACG-CGATTCAGAAAATC
73062 GCAACGCGATCTTCCAAG
64 GCAACGCGATCTTCCAAG
* *
73080 AATCGCAATGCGATTCATAAAATCGCAACGCGATTAAGAAAATCGCAACGCGATTCAGAAAATCG
1 AATCGCAACGCGATT-ATAAAATCGCAACGCGATTTAGAAAATCGCAACGCGATTCAGAAAATCG
73145 CAACGCGATCTTCCAAG
65 CAACGCGATCTTCCAAG
**
73162 AATCGCAACGCGATTA-AGGAAATCGCAACGCGATCTTCCAAGAATCGCAACGCGATTCAGAAAA
1 AATCGCAACGCGATTATA--AAATCGCAACGCGAT-TTAGAA-AATCGCAACGCGATTCAGAAAA
73226 T
62 T
73227 GAGTAAATTC
Statistics
Matches: 128, Mismatches: 12, Indels: 11
0.85 0.08 0.07
Matches are distributed among these distances:
80 1 0.01
81 15 0.12
82 84 0.66
83 5 0.04
84 23 0.18
ACGTcount: A:0.39, C:0.25, G:0.20, T:0.17
Consensus pattern (81 bp):
AATCGCAACGCGATTATAAAATCGCAACGCGATTTAGAAAATCGCAACGCGATTCAGAAAATCGC
AACGCGATCTTCCAAG
Found at i:73333 original size:6 final size:6
Alignment explanation
Indices: 73322--73414 Score: 144
Period size: 6 Copynumber: 16.5 Consensus size: 6
73312 GACACGTATT
73322 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
73370 ACCACG ACCACG ACC-CG ACC-CG ACC-CG ACC-CG ACC-CG ACC-CG
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
73412 ACC
1 ACC
73415 CGAGACGAGA
Statistics
Matches: 87, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
5 30 0.34
6 57 0.66
ACGTcount: A:0.29, C:0.54, G:0.17, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:73934 original size:6 final size:6
Alignment explanation
Indices: 73908--74027 Score: 219
Period size: 6 Copynumber: 20.5 Consensus size: 6
73898 TCTCGTCTCG
73908 GGTCG- GGTCG- GGTCG- GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
73953 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
74001 GGTCGT GGTCGT GGTCGT GGTCGT GGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGT
74028 AATACGTGTC
Statistics
Matches: 114, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
5 15 0.13
6 99 0.87
ACGTcount: A:0.00, C:0.17, G:0.52, T:0.32
Consensus pattern (6 bp):
GGTCGT
Found at i:74074 original size:20 final size:20
Alignment explanation
Indices: 74049--74181 Score: 108
Period size: 20 Copynumber: 6.6 Consensus size: 20
74039 TCGACACGTC
74049 CGTTGCGATTTTCTTAATCG
1 CGTTGCGATTTTCTTAATCG
***
74069 CGTTGCGATTCTTGGAAGATCG
1 CGTTGCGATT-TTCTTA-ATCG
* *
74091 CGTTGCGATTTTCTGAATCA
1 CGTTGCGATTTTCTTAATCG
* * *
74111 CGTTGCGATCTTCTT-TTCAA
1 CGTTGCGATTTTCTTAATC-G
* *
74131 CGTTGCGCTTTTCTAAATCG
1 CGTTGCGATTTTCTTAATCG
* **
74151 CGTTGCGGTTTTGAT-ATCG
1 CGTTGCGATTTTCTTAATCG
74170 CGTTGCGATTTT
1 CGTTGCGATTTT
74182 GTTGGTCATT
Statistics
Matches: 89, Mismatches: 20, Indels: 9
0.75 0.17 0.08
Matches are distributed among these distances:
19 17 0.19
20 50 0.56
21 8 0.09
22 14 0.16
ACGTcount: A:0.15, C:0.20, G:0.23, T:0.41
Consensus pattern (20 bp):
CGTTGCGATTTTCTTAATCG
Found at i:75631 original size:29 final size:30
Alignment explanation
Indices: 75562--75632 Score: 74
Period size: 29 Copynumber: 2.4 Consensus size: 30
75552 TACATCATTC
*
75562 TTCACTGAAC-TTTACTCTATCTTATTTTG
1 TTCACTGAACTTTTAATCTATCTTATTTTG
* * * * *
75591 CTCACCGTACTTTTAATTTTTC-TATTTTG
1 TTCACTGAACTTTTAATCTATCTTATTTTG
75620 TTCACTGAACTTT
1 TTCACTGAACTTT
75633 ACTGATTGAA
Statistics
Matches: 32, Mismatches: 9, Indels: 2
0.74 0.21 0.05
Matches are distributed among these distances:
29 24 0.75
30 8 0.25
ACGTcount: A:0.20, C:0.21, G:0.07, T:0.52
Consensus pattern (30 bp):
TTCACTGAACTTTTAATCTATCTTATTTTG
Found at i:82941 original size:60 final size:60
Alignment explanation
Indices: 82828--82944 Score: 148
Period size: 60 Copynumber: 1.9 Consensus size: 60
82818 ATATTTGGAT
* * *
82828 GACCATTTTATAACTTTTAATAGTTGAGGGACTCAAGAAAGCAATGTCCTATAATCGAAG
1 GACCATTTTATAACTTTTAATAGTCGAGGGACTCAACAAAACAATGTCCTATAATCGAAG
* * *
82888 GACCATTTTGTAACTTTTAATAGTCG-GGATACTCAACAAAACAACT-TCTTATAATCG
1 GACCATTTTATAACTTTTAATAGTCGAGG-GACTCAACAAAACAA-TGTCCTATAATCG
82945 GAAACCATTT
Statistics
Matches: 49, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
59 2 0.04
60 46 0.94
61 1 0.02
ACGTcount: A:0.36, C:0.17, G:0.15, T:0.32
Consensus pattern (60 bp):
GACCATTTTATAACTTTTAATAGTCGAGGGACTCAACAAAACAATGTCCTATAATCGAAG
Found at i:87210 original size:18 final size:16
Alignment explanation
Indices: 87178--87208 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
87168 TAAAACTCGA
87178 CTCGAACTCAAAAAAG
1 CTCGAACTCAAAAAAG
87194 CTCGAACTCAAAAAA
1 CTCGAACTCAAAAAA
87209 AAAAAATTCA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.52, C:0.26, G:0.10, T:0.13
Consensus pattern (16 bp):
CTCGAACTCAAAAAAG
Found at i:87272 original size:23 final size:22
Alignment explanation
Indices: 87244--87296 Score: 79
Period size: 23 Copynumber: 2.4 Consensus size: 22
87234 CTCGAGACTC
*
87244 AAGCTCGATTGAAGCTCAATATT
1 AAGCTCGATTCAAGCTCAATA-T
*
87267 GAGCTCGATTCAAGCTCAATAT
1 AAGCTCGATTCAAGCTCAATAT
87289 AAGCTCGA
1 AAGCTCGA
87297 CAGGTTAAGT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
22 8 0.30
23 19 0.70
ACGTcount: A:0.34, C:0.21, G:0.19, T:0.26
Consensus pattern (22 bp):
AAGCTCGATTCAAGCTCAATAT
Found at i:89317 original size:21 final size:21
Alignment explanation
Indices: 89293--89335 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
89283 AACTTAAACC
* *
89293 CTAACCCCTAAAATCTAAAAT
1 CTAAACCCTAAAACCTAAAAT
*
89314 CTAAACCCTAAAACCTTAAAT
1 CTAAACCCTAAAACCTAAAAT
89335 C
1 C
89336 CTATAACATA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.47, C:0.30, G:0.00, T:0.23
Consensus pattern (21 bp):
CTAAACCCTAAAACCTAAAAT
Found at i:89334 original size:28 final size:29
Alignment explanation
Indices: 89287--89359 Score: 80
Period size: 28 Copynumber: 2.6 Consensus size: 29
89277 GTACATAACT
** *
89287 TAAACCCTAACCCCTAAAAT-CTAAAATC-
1 TAAACCCTAAAACCTTAAATCCTAAAA-CA
*
89315 TAAACCCTAAAACCTTAAATCCTATAACA
1 TAAACCCTAAAACCTTAAATCCTAAAACA
89344 TAAACCCT-AAACCTTA
1 TAAACCCTAAAACCTTA
89360 TCACATAATT
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
28 26 0.67
29 13 0.33
ACGTcount: A:0.47, C:0.30, G:0.00, T:0.23
Consensus pattern (29 bp):
TAAACCCTAAAACCTTAAATCCTAAAACA
Found at i:89348 original size:21 final size:21
Alignment explanation
Indices: 89324--89367 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
89314 CTAAACCCTA
*
89324 AAACCTTAAATCC-TATAACAT
1 AAACCCTAAA-CCTTATAACAT
*
89345 AAACCCTAAACCTTATCACAT
1 AAACCCTAAACCTTATAACAT
89366 AA
1 AA
89368 TTAGAAGGAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 2 0.10
21 18 0.90
ACGTcount: A:0.48, C:0.27, G:0.00, T:0.25
Consensus pattern (21 bp):
AAACCCTAAACCTTATAACAT
Found at i:90085 original size:14 final size:14
Alignment explanation
Indices: 90068--90108 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
90058 TTTATTCATC
90068 AATAATGTATTTTT
1 AATAATGTATTTTT
90082 AAT-A--TATTTTT
1 AATAATGTATTTTT
*
90093 AATAATGTAATTTT
1 AATAATGTATTTTT
90107 AA
1 AA
90109 AAAATCTAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 6
0.77 0.03 0.20
Matches are distributed among these distances:
11 10 0.43
12 1 0.04
13 1 0.04
14 11 0.48
ACGTcount: A:0.41, C:0.00, G:0.05, T:0.54
Consensus pattern (14 bp):
AATAATGTATTTTT
Found at i:97000 original size:81 final size:81
Alignment explanation
Indices: 96860--97017 Score: 271
Period size: 81 Copynumber: 2.0 Consensus size: 81
96850 GTCTCTTGCA
* * *
96860 CAACTGGCTCGGTAGCTTCCTGCTCTACACCTCTGTGAGAGCTTGTCGATCCGCCATTTCGTGTG
1 CAACCGGCTCAGTAACTTCCTGCTCTACACCTCTGTGAGAGCTTGTCGATCCGCCATTTCGTGTG
96925 CGAACCATTCTTGGTG
66 CGAACCATTCTTGGTG
* *
96941 CAACCGGCTCAGTAACTTCCTGCTCTACACCTCTGTGAGAGCTTGTTGCTCCGCCATTTCGTGTG
1 CAACCGGCTCAGTAACTTCCTGCTCTACACCTCTGTGAGAGCTTGTCGATCCGCCATTTCGTGTG
97006 CGAACCATTCTT
66 CGAACCATTCTT
97018 TGTAACTCGC
Statistics
Matches: 72, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
81 72 1.00
ACGTcount: A:0.16, C:0.31, G:0.22, T:0.31
Consensus pattern (81 bp):
CAACCGGCTCAGTAACTTCCTGCTCTACACCTCTGTGAGAGCTTGTCGATCCGCCATTTCGTGTG
CGAACCATTCTTGGTG
Found at i:97191 original size:55 final size:54
Alignment explanation
Indices: 97130--97432 Score: 324
Period size: 54 Copynumber: 5.5 Consensus size: 54
97120 TGCTAGAATT
*
97130 AATGATTGAGCACCTCTGTGCTTCAATCGAGAGCTGACACCTCTGTGTAGCCAA
1 AATGATTGAGCACCTCTGTGCTTCAATCGAGAGCTGACACCTCTGTGCAGCCAA
* **
97184 AAGTGATTGAGCACCTCTGTGCTT-AATCGAGAAACTGACACCTCTGTGCAGTTAAAAA
1 AA-TGATTGAGCACCTCTGTGCTTCAATCGAG-AGCTGACACCTCTGTGCAG---CCAA
* ** * * *
97242 AATGACTGAGCACCTCTGTGCTTCAGCCGGGAGCTGACACCTCTGTGTAGCTAA
1 AATGATTGAGCACCTCTGTGCTTCAATCGAGAGCTGACACCTCTGTGCAGCCAA
*
97296 GATGATTGAGCACCTCTGTGCTTCAATCGAG-GACTGACACCTCTGTGCAGCCAA
1 AATGATTGAGCACCTCTGTGCTTCAATCGAGAG-CTGACACCTCTGTGCAGCCAA
* * * * * * * **
97350 CTATGACTGAGCACCTCTGTGCTTCAATCTAAATTCTGGCACCTCTGTGCA-TCGG
1 -AATGATTGAGCACCTCTGTGCTTCAATCGAGA-GCTGACACCTCTGTGCAGCCAA
*
97405 AATGATTGAGCACCTCTGTGCTACAATC
1 AATGATTGAGCACCTCTGTGCTTCAATC
97433 TAAAATCAAG
Statistics
Matches: 208, Mismatches: 31, Indels: 20
0.80 0.12 0.08
Matches are distributed among these distances:
53 1 0.00
54 81 0.39
55 66 0.32
56 15 0.07
57 37 0.18
58 8 0.04
ACGTcount: A:0.25, C:0.26, G:0.22, T:0.26
Consensus pattern (54 bp):
AATGATTGAGCACCTCTGTGCTTCAATCGAGAGCTGACACCTCTGTGCAGCCAA
Found at i:97336 original size:27 final size:28
Alignment explanation
Indices: 97136--97378 Score: 127
Period size: 27 Copynumber: 8.8 Consensus size: 28
97126 AATTAATGAT
97136 TGAGCACCTCTGTGCTTCAATCGA-GAGC
1 TGAGCACCTCTGTGCTTCAATCGAGGA-C
* * *
97164 TGA-CACCTCTGTG-TAGCCAA--AAGTGAT
1 TGAGCACCTCTGTGCT--TCAATCGAG-GAC
*
97191 TGAGCACCTCTGTGCTT-AATCGAGAAAC
1 TGAGCACCTCTGTGCTTCAATCGAG-GAC
* *** *
97219 TGA-CACCTCTGTGCAGTTAAAAAAATGAC
1 TGAGCACCTCTGTGC--TTCAATCGAGGAC
**
97248 TGAGCACCTCTGTGCTTCAGCCG-GGAGC
1 TGAGCACCTCTGTGCTTCAATCGAGGA-C
* * *
97276 TGA-CACCTCTGTG-TAGCTAA--GATGAT
1 TGAGCACCTCTGTGCT-TC-AATCGAGGAC
97302 TGAGCACCTCTGTGCTTCAATCGAGGAC
1 TGAGCACCTCTGTGCTTCAATCGAGGAC
** * *
97330 TGA-CACCTCTGTGCAGCCAA-CTATGAC
1 TGAGCACCTCTGTGC-TTCAATCGAGGAC
97357 TGAGCACCTCTGTGCTTCAATC
1 TGAGCACCTCTGTGCTTCAATC
97379 TAAATTCTGG
Statistics
Matches: 160, Mismatches: 32, Indels: 46
0.67 0.13 0.19
Matches are distributed among these distances:
26 11 0.07
27 72 0.45
28 55 0.34
29 8 0.05
30 14 0.09
ACGTcount: A:0.25, C:0.27, G:0.23, T:0.26
Consensus pattern (28 bp):
TGAGCACCTCTGTGCTTCAATCGAGGAC
Found at i:100422 original size:31 final size:31
Alignment explanation
Indices: 100347--100422 Score: 73
Period size: 31 Copynumber: 2.4 Consensus size: 31
100337 TATGTACTTT
* *
100347 GACATTATATCATATTATCACTTTATACAAAC
1 GACA-TATATCACATTATCACTTTAAACAAAC
* * *
100379 GACTTTTGTCACATTATCACTTTAAACAAA-
1 GACATATATCACATTATCACTTTAAACAAAC
*
100409 TATCATATATCACA
1 GA-CATATATCACA
100423 ATTTCATTTT
Statistics
Matches: 34, Mismatches: 9, Indels: 3
0.74 0.20 0.07
Matches are distributed among these distances:
30 1 0.03
31 30 0.88
32 3 0.09
ACGTcount: A:0.39, C:0.20, G:0.04, T:0.37
Consensus pattern (31 bp):
GACATATATCACATTATCACTTTAAACAAAC
Found at i:101515 original size:30 final size:30
Alignment explanation
Indices: 101479--101571 Score: 177
Period size: 30 Copynumber: 3.1 Consensus size: 30
101469 GGATGCTTTT
*
101479 ATTTTGACCACCGTATTAGAGAAATCGTTC
1 ATTTTGACCACCGTGTTAGAGAAATCGTTC
101509 ATTTTGACCACCGTGTTAGAGAAATCGTTC
1 ATTTTGACCACCGTGTTAGAGAAATCGTTC
101539 ATTTTGACCACCGTGTTAGAGAAATCGTTC
1 ATTTTGACCACCGTGTTAGAGAAATCGTTC
101569 ATT
1 ATT
101572 ATTTTCACAC
Statistics
Matches: 62, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
30 62 1.00
ACGTcount: A:0.28, C:0.19, G:0.18, T:0.34
Consensus pattern (30 bp):
ATTTTGACCACCGTGTTAGAGAAATCGTTC
Found at i:104922 original size:17 final size:17
Alignment explanation
Indices: 104897--104956 Score: 70
Period size: 17 Copynumber: 3.5 Consensus size: 17
104887 AAAATATGTA
104897 AAAAT-ATAATATTAAT
1 AAAATAATAATATTAAT
*
104913 AAAATAATAATATAAAT
1 AAAATAATAATATTAAT
104930 ATAAA-AATAATAATTAAT
1 A-AAATAATAAT-ATTAAT
104948 AATAATAAT
1 AA-AATAAT
104957 TTAAAAAAGA
Statistics
Matches: 37, Mismatches: 2, Indels: 7
0.80 0.04 0.15
Matches are distributed among these distances:
16 5 0.14
17 18 0.49
18 11 0.30
19 3 0.08
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (17 bp):
AAAATAATAATATTAAT
Found at i:104923 original size:3 final size:3
Alignment explanation
Indices: 104902--104956 Score: 53
Period size: 3 Copynumber: 18.7 Consensus size: 3
104892 ATGTAAAAAT
* *
104902 ATA ATA TTA ATA A-A ATA ATA AT- ATA A-A TATA AAA ATA ATA ATTA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA -ATA ATA ATA ATA A-TA
104946 ATA ATA ATA AT
1 ATA ATA ATA AT
104957 TTAAAAAAGA
Statistics
Matches: 43, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
2 5 0.12
3 34 0.79
4 4 0.09
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
ATA
Found at i:104955 original size:28 final size:28
Alignment explanation
Indices: 104898--104954 Score: 78
Period size: 28 Copynumber: 2.0 Consensus size: 28
104888 AAATATGTAA
* *
104898 AAATATAATATTAATAAAATAATAATAT
1 AAATATAAAAATAATAAAATAATAATAT
104926 AAATATAAAAATAATAATTAATAATAATA
1 AAATATAAAAATAATAA--AATAATAATA
104955 ATTTAAAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 15 0.60
30 10 0.40
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (28 bp):
AAATATAAAAATAATAAAATAATAATAT
Found at i:105428 original size:43 final size:43
Alignment explanation
Indices: 105252--105478 Score: 138
Period size: 43 Copynumber: 5.4 Consensus size: 43
105242 ATAACTCGGT
* *
105252 TCCTACGTGATGAGGACGGCTGGTTATCTATGGT-TGACACGGC
1 TCCTACGTGATGAGGA-GGCTGATTATCTAAGGTATGACACGGC
** *
105295 TCCTACGTGATGAGGA----GATTAGGT-CGGTGATGACACGGC
1 TCCTACGTGATGAGGAGGCTGATTATCTAAGGT-ATGACACGGC
* * * * * * * * *
105334 TCATACATGATGAAGAGTTCTGGTCATATAAAGGTGATAACACGGT
1 TCCTACGTGATGAGGAG-GCTGATTATCT-AAGGT-ATGACACGGC
*
105380 TCCTACGTGATGAGGACGGCTGATTATCTAAGGT-TGACGCGGC
1 TCCTACGTGATGAGGA-GGCTGATTATCTAAGGTATGACACGGC
*
105423 TCCTACGTGATGAGGA----GATCTAGTC-AAGAG-ATGACACGGT
1 TCCTACGTGATGAGGAGGCTGAT-TA-TCTAAG-GTATGACACGGC
105463 TCCTACGTGATGAGGA
1 TCCTACGTGATGAGGA
105479 CGACTGGCGA
Statistics
Matches: 144, Mismatches: 26, Indels: 31
0.72 0.13 0.15
Matches are distributed among these distances:
37 3 0.02
38 8 0.06
39 27 0.19
40 26 0.18
43 38 0.26
44 4 0.03
45 5 0.03
46 32 0.22
47 1 0.01
ACGTcount: A:0.26, C:0.18, G:0.31, T:0.26
Consensus pattern (43 bp):
TCCTACGTGATGAGGAGGCTGATTATCTAAGGTATGACACGGC
Found at i:105501 original size:128 final size:125
Alignment explanation
Indices: 105144--105501 Score: 340
Period size: 128 Copynumber: 2.7 Consensus size: 125
105134 GTTCGGGTCG
* * * * * * * * *
105144 TCTAAGGGTGACACAGATCCTACATGATGGGGATATTTGGTCGGGGGATGACACGGTTCCTACGT
1 TCTAAGGTTGACACGGCTCCTACGTGATGAGGAGATTAGGTC-AGAGATGACACGGTTCCTACGT
* * *
105209 GATGAGGATGGCTGACCATCTTTAAGAGTGGGGATAACTCGGTTCCTACGTGATGAGGACGGCTG
65 GATGAGGA-GACTG-GCATCTTT---A---GGGATAACACGGTTCCTACGTGATGAGGACGGCTG
*
105274 GTTA
122 ATTA
* * * * * *
105278 TCTATGGTTGACACGGCTCCTACGTGATGAGGAGATTAGGTCGGTGATGACACGGCTCATACATG
1 TCTAAGGTTGACACGGCTCCTACGTGATGAGGAGATTAGGTCAGAGATGACACGGTTCCTACGTG
* * * **
105343 ATGAAGAGTTCTGGTCATATAAAGGTGATAACACGGTTCCTACGTGATGAGGACGGCTGATTA
66 ATGAGGAG-ACTGG-CATCTTTAGG-GATAACACGGTTCCTACGTGATGAGGACGGCTGATTA
*
105406 TCTAAGGTTGACGCGGCTCCTACGTGATGAGGAGATCTA-GTCAAGAGATGACACGGTTCCTACG
1 TCTAAGGTTGACACGGCTCCTACGTGATGAGGAGAT-TAGGTC-AGAGATGACACGGTTCCTACG
105470 TGATGAGGACGACTGGCGATCTTTAGGGATAA
64 TGATGAGGA-GACTGGC-ATCTTTAGGGATAA
105502 GGGTTTCAAG
Statistics
Matches: 185, Mismatches: 32, Indels: 20
0.78 0.14 0.08
Matches are distributed among these distances:
127 2 0.01
128 78 0.42
129 36 0.19
130 2 0.01
132 1 0.01
133 32 0.17
134 34 0.18
ACGTcount: A:0.25, C:0.18, G:0.32, T:0.26
Consensus pattern (125 bp):
TCTAAGGTTGACACGGCTCCTACGTGATGAGGAGATTAGGTCAGAGATGACACGGTTCCTACGTG
ATGAGGAGACTGGCATCTTTAGGGATAACACGGTTCCTACGTGATGAGGACGGCTGATTA
Found at i:105597 original size:31 final size:28
Alignment explanation
Indices: 105524--105600 Score: 102
Period size: 28 Copynumber: 2.6 Consensus size: 28
105514 AAACCGACTT
105524 AAAGATTTGTTTCAAAAGAAACAAACCC
1 AAAGATTTGTTTCAAAAGAAACAAACCC
*
105552 AAAGATTTGTTTCAAGAA-AAACAAACTC
1 AAAGATTTGTTTCAA-AAGAAACAAACCC
105580 AAAGATGATATGTTTCAAAAG
1 AAAGAT--T-TGTTTCAAAAG
105601 CAACTGTCTC
Statistics
Matches: 43, Mismatches: 1, Indels: 7
0.84 0.02 0.14
Matches are distributed among these distances:
28 30 0.70
29 2 0.05
30 3 0.07
31 8 0.19
ACGTcount: A:0.49, C:0.13, G:0.13, T:0.25
Consensus pattern (28 bp):
AAAGATTTGTTTCAAAAGAAACAAACCC
Found at i:105746 original size:35 final size:35
Alignment explanation
Indices: 105707--105786 Score: 92
Period size: 36 Copynumber: 2.3 Consensus size: 35
105697 GGGAAATGAT
* *
105707 CTCAAAGATGTTTG-TTTTGTTT-CAAAGGAAACAGA
1 CTCAAAGATG-GTGATTTTGTTTCCAAA-GAAACAAA
*
105742 CTCAAAGATGGTGAATTTTGTTTCCACAGAAACAAA
1 CTCAAAGATGGTG-ATTTTGTTTCCAAAGAAACAAA
105778 CTCAAAGAT
1 CTCAAAGAT
105787 TTTTCTCAAA
Statistics
Matches: 39, Mismatches: 3, Indels: 5
0.83 0.06 0.11
Matches are distributed among these distances:
34 2 0.05
35 10 0.26
36 24 0.62
37 3 0.08
ACGTcount: A:0.38, C:0.15, G:0.17, T:0.30
Consensus pattern (35 bp):
CTCAAAGATGGTGATTTTGTTTCCAAAGAAACAAA
Found at i:105955 original size:31 final size:30
Alignment explanation
Indices: 105891--105965 Score: 82
Period size: 31 Copynumber: 2.4 Consensus size: 30
105881 TGAAAATTCG
* *
105891 TTTCAAGGGAAACGACTCAAAGATGGTTTTA
1 TTTCAAGAGAAACAACTCAAAGAT-GTTTTA
105922 TTTCAAGAGAAACAAACTCAAAGAT-TTTGTA
1 TTTCAAGAGAAAC-AACTCAAAGATGTTT-TA
105953 TTT-ATAGAGAAAC
1 TTTCA-AGAGAAAC
105966 TGCCTCAAGG
Statistics
Matches: 39, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
30 4 0.10
31 25 0.64
32 10 0.26
ACGTcount: A:0.41, C:0.12, G:0.17, T:0.29
Consensus pattern (30 bp):
TTTCAAGAGAAACAACTCAAAGATGTTTTA
Found at i:106245 original size:28 final size:28
Alignment explanation
Indices: 106144--106237 Score: 91
Period size: 28 Copynumber: 3.3 Consensus size: 28
106134 TTTTTTTTTT
* *
106144 AAAGAAATAGACTCAAAGATGATTTTGTTA
1 AAAGAAACAGACTCAAAGATG-TTTT-TCA
** *
106174 GTAGAAACAAACTCAAAGATGTTTTTCA
1 AAAGAAACAGACTCAAAGATGTTTTTCA
*
106202 AAAGGAACAGACTCAAAGAT-TTGTTTCA
1 AAAGAAACAGACTCAAAGATGTT-TTTCA
*
106230 AGAGAAAC
1 AAAGAAAC
106238 TGTCTCAATA
Statistics
Matches: 52, Mismatches: 11, Indels: 4
0.78 0.16 0.06
Matches are distributed among these distances:
27 2 0.04
28 29 0.56
29 4 0.08
30 17 0.33
ACGTcount: A:0.46, C:0.12, G:0.17, T:0.26
Consensus pattern (28 bp):
AAAGAAACAGACTCAAAGATGTTTTTCA
Found at i:106336 original size:64 final size:63
Alignment explanation
Indices: 106197--106367 Score: 207
Period size: 64 Copynumber: 2.6 Consensus size: 63
106187 CAAAGATGTT
* * * *
106197 TTTCAAAAGGAACAGACTCAAAGATTTGTTTCAAGAGAAACTGTCTCAATAAAGACAAAATTTG
1 TTTCAAAAGAAACAAACTCAAAGATTT-TTTCAAAAGAAACTGTCTCAAGAAAGACAAAATTTG
* * * * *
106261 TTTTAAGAGAAACATACTCAAAGATTTTTTCAAAAGAAATTGTCTCAAGAGAGACAAAATTTTG
1 TTTCAAAAGAAACAAACTCAAAGATTTTTTCAAAAGAAACTGTCTCAAGAAAGACAAAA-TTTG
*
106325 TTTCCAAAGAAACAAACTCAAAGATTTTTATTTCAAAAGAAAC
1 TTTCAAAAGAAACAAACTCAAAGA--TTT-TTTCAAAAGAAAC
106368 AACTCAAAGA
Statistics
Matches: 90, Mismatches: 13, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
63 28 0.31
64 47 0.52
66 3 0.03
67 12 0.13
ACGTcount: A:0.45, C:0.13, G:0.13, T:0.29
Consensus pattern (63 bp):
TTTCAAAAGAAACAAACTCAAAGATTTTTTCAAAAGAAACTGTCTCAAGAAAGACAAAATTTG
Found at i:106346 original size:186 final size:183
Alignment explanation
Indices: 106116--106455 Score: 452
Period size: 186 Copynumber: 1.8 Consensus size: 183
106106 TCATTAAAAC
* ** * * **
106116 TGTCTCAAGAGAGACAAATTTTTTTTTTAAAGAAATAGACTCAAAGATGATTTT-GTT-AGTAGA
1 TGTCTCAAGAGAGACAAATTTTGTTTCCAAAGAAACAAACTCAAAGAT--TTTTAGTTCAAAAGA
*
106179 AACAAACTCAAAGATGTTT-TTCAAAAGGAACAGACTCAAAGATTTGTTTCAAGAGAAACTGTCT
64 AAC-AACTCAAAGATGTTTATTCAAAAGGAACAAACTCAAAGATTT-TTT-AAGAGAAACTGTCT
* * *
106243 CAATAAAGACAAAATTTGTTTTAAGAGAAACATACTCAAAGATTTTTTCAAAAGAAAT
126 CAAGAAAGACAAAAATCGTTTTAAGAGAAACATACTCAAAGATTTTTTCAAAAGAAAT
*
106301 TGTCTCAAGAGAGACAAAATTTTGTTTCCAAAGAAACAAACTCAAAGATTTTTATTTCAAAAGAA
1 TGTCTCAAGAGAGAC-AAATTTTGTTTCCAAAGAAACAAACTCAAAGATTTTTAGTTCAAAAGAA
* * *
106366 ACAACTCAAAGATTTTTATTCGAAAGGAACAAACTCAAAGATTTTTTAAGAGAAACTGTTTCAAG
65 ACAACTCAAAGATGTTTATTCAAAAGGAACAAACTCAAAGATTTTTTAAGAGAAACTGTCTCAAG
**
106431 AGGGACAAAAATCGTTTTAAGAGAA
130 AAAGACAAAAATCGTTTTAAGAGAA
106456 CAAGATTCAA
Statistics
Matches: 134, Mismatches: 17, Indels: 9
0.84 0.11 0.06
Matches are distributed among these distances:
184 41 0.31
185 34 0.25
186 59 0.44
ACGTcount: A:0.44, C:0.12, G:0.15, T:0.29
Consensus pattern (183 bp):
TGTCTCAAGAGAGACAAATTTTGTTTCCAAAGAAACAAACTCAAAGATTTTTAGTTCAAAAGAAA
CAACTCAAAGATGTTTATTCAAAAGGAACAAACTCAAAGATTTTTTAAGAGAAACTGTCTCAAGA
AAGACAAAAATCGTTTTAAGAGAAACATACTCAAAGATTTTTTCAAAAGAAAT
Found at i:106366 original size:30 final size:30
Alignment explanation
Indices: 106320--106411 Score: 134
Period size: 29 Copynumber: 3.1 Consensus size: 30
106310 AGAGACAAAA
* *
106320 TTTTGTTTCCAAAGAAACAAACTCAAAGAT
1 TTTTATTTCAAAAGAAACAAACTCAAAGAT
106350 TTTTATTTCAAAAGAAAC-AACTCAAAGAT
1 TTTTATTTCAAAAGAAACAAACTCAAAGAT
* *
106379 TTTTA-TTCGAAAGGAACAAACTCAAAGAT
1 TTTTATTTCAAAAGAAACAAACTCAAAGAT
106408 TTTT
1 TTTT
106412 TAAGAGAAAC
Statistics
Matches: 57, Mismatches: 4, Indels: 3
0.89 0.06 0.05
Matches are distributed among these distances:
28 10 0.18
29 31 0.54
30 16 0.28
ACGTcount: A:0.43, C:0.14, G:0.10, T:0.33
Consensus pattern (30 bp):
TTTTATTTCAAAAGAAACAAACTCAAAGAT
Found at i:107206 original size:4 final size:4
Alignment explanation
Indices: 107199--107283 Score: 106
Period size: 4 Copynumber: 22.2 Consensus size: 4
107189 ATCATATATA
* * *
107199 TATG TATG --TG TATG TATG TATG TTTG TATG TATG TATG TTTG TTTG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
*
107245 TATG TATG TATG TA-- TATG TATG TATG TATA TATG TATG T
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG T
107284 TTTTCTTGAT
Statistics
Matches: 71, Mismatches: 6, Indels: 8
0.84 0.07 0.09
Matches are distributed among these distances:
2 4 0.06
4 67 0.94
ACGTcount: A:0.22, C:0.00, G:0.24, T:0.54
Consensus pattern (4 bp):
TATG
Found at i:107553 original size:19 final size:20
Alignment explanation
Indices: 107520--107567 Score: 87
Period size: 20 Copynumber: 2.4 Consensus size: 20
107510 ACTTATCTTG
107520 TTTGAAAATGTTTTTCTTCT
1 TTTGAAAATGTTTTTCTTCT
*
107540 TTTGAAAATGTTTTTCTTGT
1 TTTGAAAATGTTTTTCTTCT
107560 TTTGAAAA
1 TTTGAAAA
107568 CCACTTGACG
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.25, C:0.06, G:0.12, T:0.56
Consensus pattern (20 bp):
TTTGAAAATGTTTTTCTTCT
Found at i:112407 original size:19 final size:19
Alignment explanation
Indices: 112350--112412 Score: 53
Period size: 19 Copynumber: 3.4 Consensus size: 19
112340 CCAAAATATG
*
112350 TAAAAA-TATAA-TATTAA
1 TAAAAATTATAATTAATAA
*
112367 T-AAAATAATAATATAA-ATA
1 TAAAAATTATAAT-TAATA-A
112386 TAAAAATTATAATTAATAA
1 TAAAAATTATAATTAATAA
*
112405 TAATAATT
1 TAAAAATT
112413 TAAAAAAGAC
Statistics
Matches: 36, Mismatches: 4, Indels: 10
0.72 0.08 0.20
Matches are distributed among these distances:
16 4 0.11
17 5 0.14
18 1 0.03
19 15 0.42
20 11 0.31
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (19 bp):
TAAAAATTATAATTAATAA
Found at i:112798 original size:19 final size:21
Alignment explanation
Indices: 112765--112807 Score: 63
Period size: 20 Copynumber: 2.1 Consensus size: 21
112755 TAAAAATTTC
*
112765 TTTAAAAATTATTGAATAT-T
1 TTTAAAAAATATTGAATATAT
112785 TTTAAAAAAT-TTGAATATAT
1 TTTAAAAAATATTGAATATAT
112805 TTT
1 TTT
112808 TTAAATTTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 8 0.38
20 13 0.62
ACGTcount: A:0.44, C:0.00, G:0.05, T:0.51
Consensus pattern (21 bp):
TTTAAAAAATATTGAATATAT
Found at i:117003 original size:15 final size:15
Alignment explanation
Indices: 116974--117013 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
116964 TTGGTTTCCA
*
116974 TCATGTTA-CTAATT
1 TCATGTTATTTAATT
116988 TCATGTTATTTAATT
1 TCATGTTATTTAATT
*
117003 TCATTTTATTT
1 TCATGTTATTT
117014 TCAGATATAT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 8 0.35
15 15 0.65
ACGTcount: A:0.25, C:0.10, G:0.05, T:0.60
Consensus pattern (15 bp):
TCATGTTATTTAATT
Found at i:119281 original size:60 final size:60
Alignment explanation
Indices: 119213--119349 Score: 159
Period size: 60 Copynumber: 2.3 Consensus size: 60
119203 GACAATTTTG
* * * * * * *
119213 TAACTTTTAATAGTTAGAGGACTAAACAAAGCAACATCCTATAGTCGGGGGATCACTTT-A
1 TAACTTTTAATAGTCAAAGAACTAAACAAAGAAACACCCTATAATCGAGGGATCA-TTTCA
* * * *
119273 TAACTTTTAATAGTCAAAGAACTCAACAAAGAAATACCCTATAATCGATGGATCATTTCG
1 TAACTTTTAATAGTCAAAGAACTAAACAAAGAAACACCCTATAATCGAGGGATCATTTCA
119333 TAACTTTTAATAGTCAA
1 TAACTTTTAATAGTCAA
119350 TAAACTCAAC
Statistics
Matches: 65, Mismatches: 11, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
59 3 0.05
60 62 0.95
ACGTcount: A:0.39, C:0.17, G:0.14, T:0.30
Consensus pattern (60 bp):
TAACTTTTAATAGTCAAAGAACTAAACAAAGAAACACCCTATAATCGAGGGATCATTTCA
Found at i:122001 original size:23 final size:23
Alignment explanation
Indices: 121934--121989 Score: 67
Period size: 23 Copynumber: 2.4 Consensus size: 23
121924 CACCACAGCT
* ** * *
121934 CGTATAATTGCACCAAAGTACCA
1 CGTAGAATTGCACCGGAGTGCCG
121957 CGTAGAATTGCACCGGAGTGCCG
1 CGTAGAATTGCACCGGAGTGCCG
121980 CGTAGAATTG
1 CGTAGAATTG
121990 GATCGTAGTG
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.30, C:0.23, G:0.25, T:0.21
Consensus pattern (23 bp):
CGTAGAATTGCACCGGAGTGCCG
Found at i:122255 original size:30 final size:30
Alignment explanation
Indices: 122219--122280 Score: 106
Period size: 30 Copynumber: 2.1 Consensus size: 30
122209 TTGTATCGCG
* *
122219 TAGACATATTATTTTCATACCTTTATCACA
1 TAGACATATCATTTCCATACCTTTATCACA
122249 TAGACATATCATTTCCATACCTTTATCACA
1 TAGACATATCATTTCCATACCTTTATCACA
122279 TA
1 TA
122281 ACTGATATAA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.34, C:0.23, G:0.03, T:0.40
Consensus pattern (30 bp):
TAGACATATCATTTCCATACCTTTATCACA
Found at i:122838 original size:21 final size:21
Alignment explanation
Indices: 122812--122867 Score: 85
Period size: 21 Copynumber: 2.7 Consensus size: 21
122802 TTATCATTGA
*
122812 TGCATCGGTTCACAATGAATG
1 TGCATCGGTGCACAATGAATG
*
122833 TGCATCGGTGCATAATGAATG
1 TGCATCGGTGCACAATGAATG
*
122854 TGCATCGATGCACA
1 TGCATCGGTGCACA
122868 TTGCCCAGAA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.29, C:0.20, G:0.25, T:0.27
Consensus pattern (21 bp):
TGCATCGGTGCACAATGAATG
Found at i:126331 original size:21 final size:21
Alignment explanation
Indices: 126306--126345 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
126296 CCTTTTCTAA
* *
126306 TAACTCTTGCAATTGTTTCTT
1 TAACTCTTACAATTCTTTCTT
126327 TAACTCTTACAATTCTTTC
1 TAACTCTTACAATTCTTTC
126346 GGAGCCATCC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.23, C:0.23, G:0.05, T:0.50
Consensus pattern (21 bp):
TAACTCTTACAATTCTTTCTT
Found at i:128977 original size:23 final size:23
Alignment explanation
Indices: 128910--128965 Score: 76
Period size: 23 Copynumber: 2.4 Consensus size: 23
128900 CACCACAACT
* **
128910 CGTATAATTGCACCAAAGTGCCA
1 CGTAGAATTGCACCGGAGTGCCA
*
128933 CGTAGAATTGCACCGGAGTGCCG
1 CGTAGAATTGCACCGGAGTGCCA
128956 CGTAGAATTG
1 CGTAGAATTG
128966 GATCGTAGTG
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.29, C:0.23, G:0.27, T:0.21
Consensus pattern (23 bp):
CGTAGAATTGCACCGGAGTGCCA
Found at i:129228 original size:30 final size:30
Alignment explanation
Indices: 129192--129253 Score: 99
Period size: 30 Copynumber: 2.1 Consensus size: 30
129182 TTGTATCGCG
*
129192 TAGACATATTATTGT-CATACCTTTATCACA
1 TAGACATATCATT-TCCATACCTTTATCACA
129222 TAGACATATCATTTCCATACCTTTATCACA
1 TAGACATATCATTTCCATACCTTTATCACA
129252 TA
1 TA
129254 ACTCATATAA
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
29 1 0.03
30 29 0.97
ACGTcount: A:0.34, C:0.23, G:0.05, T:0.39
Consensus pattern (30 bp):
TAGACATATCATTTCCATACCTTTATCACA
Found at i:129778 original size:21 final size:21
Alignment explanation
Indices: 129749--129802 Score: 72
Period size: 21 Copynumber: 2.6 Consensus size: 21
129739 TTATCATTGA
* *
129749 TGCACCGGTTCACAATGAATG
1 TGCATCGGTGCACAATGAATG
*
129770 TGCATCGGTGCATAATGAATG
1 TGCATCGGTGCACAATGAATG
*
129791 TGCATCGATGCA
1 TGCATCGGTGCA
129803 TATTGCCCAG
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:0.28, C:0.20, G:0.26, T:0.26
Consensus pattern (21 bp):
TGCATCGGTGCACAATGAATG
Found at i:129803 original size:21 final size:21
Alignment explanation
Indices: 129762--129804 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
129752 ACCGGTTCAC
*
129762 AATGAATGTGCATCGGTGCAT
1 AATGAATGTGCATCGATGCAT
129783 AATGAATGTGCATCGATGCAT
1 AATGAATGTGCATCGATGCAT
129804 A
1 A
129805 TTGCCCAGAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.33, C:0.14, G:0.26, T:0.28
Consensus pattern (21 bp):
AATGAATGTGCATCGATGCAT
Found at i:135806 original size:12 final size:12
Alignment explanation
Indices: 135789--135818 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
135779 AGTAAAATAG
135789 CATAAAAATAAA
1 CATAAAAATAAA
*
135801 CATAAATATAAA
1 CATAAAAATAAA
135813 CATAAA
1 CATAAA
135819 GCACTCTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.70, C:0.10, G:0.00, T:0.20
Consensus pattern (12 bp):
CATAAAAATAAA
Found at i:135857 original size:10 final size:11
Alignment explanation
Indices: 135840--135869 Score: 60
Period size: 11 Copynumber: 2.7 Consensus size: 11
135830 TCCTTTTTTT
135840 TTCTTTTTATC
1 TTCTTTTTATC
135851 TTCTTTTTATC
1 TTCTTTTTATC
135862 TTCTTTTT
1 TTCTTTTT
135870 TTCTGCTGGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.07, C:0.17, G:0.00, T:0.77
Consensus pattern (11 bp):
TTCTTTTTATC
Found at i:136893 original size:30 final size:30
Alignment explanation
Indices: 136857--136913 Score: 78
Period size: 30 Copynumber: 1.9 Consensus size: 30
136847 TTAACTAGTT
*
136857 GAACCAAAAATCTACTGTTGTTTTTTTTTC
1 GAACCAAAAATCTACTGTTATTTTTTTTTC
* * *
136887 GAACCAAAATTGTATTGTTATTTTTTT
1 GAACCAAAAATCTACTGTTATTTTTTT
136914 ACACTGCACT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 23 1.00
ACGTcount: A:0.28, C:0.12, G:0.11, T:0.49
Consensus pattern (30 bp):
GAACCAAAAATCTACTGTTATTTTTTTTTC
Found at i:137311 original size:5 final size:6
Alignment explanation
Indices: 137290--137319 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
137280 AAAATCAAAG
*
137290 AAAAAT AAAAAC AAAAAT AAAAAT AAAAAT
1 AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT
137320 TGAACAAACG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.83, C:0.03, G:0.00, T:0.13
Consensus pattern (6 bp):
AAAAAT
Found at i:141237 original size:72 final size:72
Alignment explanation
Indices: 141161--141302 Score: 284
Period size: 72 Copynumber: 2.0 Consensus size: 72
141151 CTTAAAATTA
141161 TTTAAACTAAAAATACTAAAAACAAATATAAGATAAAATATAATATAATATAATATTTAAACTAA
1 TTTAAACTAAAAATACTAAAAACAAATATAAGATAAAATATAATATAATATAATATTTAAACTAA
141226 TATCTGT
66 TATCTGT
141233 TTTAAACTAAAAATACTAAAAACAAATATAAGATAAAATATAATATAATATAATATTTAAACTAA
1 TTTAAACTAAAAATACTAAAAACAAATATAAGATAAAATATAATATAATATAATATTTAAACTAA
141298 TATCT
66 TATCT
141303 TAAAACATGA
Statistics
Matches: 70, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
72 70 1.00
ACGTcount: A:0.58, C:0.07, G:0.02, T:0.33
Consensus pattern (72 bp):
TTTAAACTAAAAATACTAAAAACAAATATAAGATAAAATATAATATAATATAATATTTAAACTAA
TATCTGT
Done.