Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold384
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: 365111
ACGTcount: A:0.31, C:0.16, G:0.15, T:0.31
Warning! 24399 characters in sequence are not A, C, G, or T
File 1 of 2
Found at i:543 original size:48 final size:48
Alignment explanation
Indices: 472--617 Score: 175
Period size: 48 Copynumber: 3.0 Consensus size: 48
462 TACTATGCAT
*
472 ACCAATATTCTGTTAAGATACAAGGGTGGCATAGACTGTGTGCAGGCC
1 ACCAATATTCTGTTAAGATACAAGGGTGGCACAGACTGTGTGCAGGCC
* *
520 ACCAATATTCTGTTAAGATACAAGGGTGGCACGGACTTTGTGCAGGCC
1 ACCAATATTCTGTTAAGATACAAGGGTGGCACAGACTGTGTGCAGGCC
* * * ** * * * * *
568 ACCGAGAGTCTGTTATTACACAAAGGTGGTACGGACTGTGTGTAGGCC
1 ACCAATATTCTGTTAAGATACAAGGGTGGCACAGACTGTGTGCAGGCC
616 AC
1 AC
618 TGAGAAATCT
Statistics
Matches: 85, Mismatches: 13, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
48 85 1.00
ACGTcount: A:0.27, C:0.20, G:0.28, T:0.25
Consensus pattern (48 bp):
ACCAATATTCTGTTAAGATACAAGGGTGGCACAGACTGTGTGCAGGCC
Found at i:2499 original size:51 final size:51
Alignment explanation
Indices: 2421--2552 Score: 176
Period size: 51 Copynumber: 2.6 Consensus size: 51
2411 TTACAGGTCG
*
2421 CATGTGTAGTACTATGTGCAGGCTACTATGCGTACCGGATAGT-TTCGATCA
1 CATGTGTAGTACTATGTGCAGGCTACTATGCGTACCGGATAGTAAT-GATCA
* * * * * *
2472 CGTGTGTAGTACTATGTGCAGGCTACTACGTGTATCGGATGGTAATGGTCA
1 CATGTGTAGTACTATGTGCAGGCTACTATGCGTACCGGATAGTAATGATCA
*
2523 CATGTGTAGTACTATGTGTAGGCTACTATG
1 CATGTGTAGTACTATGTGCAGGCTACTATG
2553 TGAACCAAAC
Statistics
Matches: 70, Mismatches: 10, Indels: 2
0.85 0.12 0.02
Matches are distributed among these distances:
51 69 0.99
52 1 0.01
ACGTcount: A:0.23, C:0.17, G:0.28, T:0.33
Consensus pattern (51 bp):
CATGTGTAGTACTATGTGCAGGCTACTATGCGTACCGGATAGTAATGATCA
Found at i:2720 original size:23 final size:22
Alignment explanation
Indices: 2694--2737 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 22
2684 AATTGACTAA
2694 GTGT-AATTGAATAATGAATATAG
1 GTGTAAATTGAAT--TGAATATAG
2717 GTGTGAAATTGAATTGAATAT
1 GTGT-AAATTGAATTGAATAT
2738 CTACTTAGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
23 11 0.58
25 8 0.42
ACGTcount: A:0.41, C:0.00, G:0.23, T:0.36
Consensus pattern (22 bp):
GTGTAAATTGAATTGAATATAG
Found at i:3061 original size:9 final size:10
Alignment explanation
Indices: 3040--3064 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
3030 CTGACTTTGG
3040 AAAATTGTAA
1 AAAATTGTAA
3050 AAAATTGTAA
1 AAAATTGTAA
3060 AAAAT
1 AAAAT
3065 AATTATGGGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.64, C:0.00, G:0.08, T:0.28
Consensus pattern (10 bp):
AAAATTGTAA
Found at i:5539 original size:27 final size:26
Alignment explanation
Indices: 5491--5541 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 26
5481 TAGAATTAAT
*
5491 TTGTTATTCATCATTTGCTTTGTATA
1 TTGTTAATCATCATTTGCTTTGTATA
5517 TTGTTAATCAATCATATTG-TTTGTA
1 TTGTTAATC-ATCAT-TTGCTTTGTA
5542 AGAATTTCAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
26 8 0.36
27 11 0.50
28 3 0.14
ACGTcount: A:0.24, C:0.10, G:0.12, T:0.55
Consensus pattern (26 bp):
TTGTTAATCATCATTTGCTTTGTATA
Found at i:13300 original size:3 final size:3
Alignment explanation
Indices: 13294--13346 Score: 106
Period size: 3 Copynumber: 17.7 Consensus size: 3
13284 TTGCGTCCAT
13294 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
13342 TTA TT
1 TTA TT
13347 TGTGGTTCTG
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 50 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:13606 original size:29 final size:30
Alignment explanation
Indices: 13565--13634 Score: 88
Period size: 29 Copynumber: 2.3 Consensus size: 30
13555 AATGATAACG
* *
13565 TAAGTGACCAAAACGTAACAT-TTCAAATA
1 TAAGTGACTAAAACGTAACATAGTCAAATA
*
13594 TAAGTGACTAAAATGTAACATGAGTCAAATA
1 TAAGTGACTAAAACGTAACAT-AGTCAAATA
*
13625 AAAGTGACTA
1 TAAGTGACTA
13635 TGTTGATAGT
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
29 19 0.54
31 16 0.46
ACGTcount: A:0.49, C:0.13, G:0.14, T:0.24
Consensus pattern (30 bp):
TAAGTGACTAAAACGTAACATAGTCAAATA
Found at i:16609 original size:21 final size:22
Alignment explanation
Indices: 16574--16614 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
16564 TTCTTTATTT
**
16574 TAATATTATTTTAA-TATTGGC
1 TAATATTATCATAATTATTGGC
16595 TAATATTATCATAATTATTG
1 TAATATTATCATAATTATTG
16615 ATATCAATTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 12 0.71
22 5 0.29
ACGTcount: A:0.37, C:0.05, G:0.07, T:0.51
Consensus pattern (22 bp):
TAATATTATCATAATTATTGGC
Found at i:29318 original size:44 final size:45
Alignment explanation
Indices: 28981--29430 Score: 210
Period size: 44 Copynumber: 10.3 Consensus size: 45
28971 AAGATTATAG
* ** * *
28981 ATCTTATC-TCCCTAAGCAATAGTGGAGCAGATCGAAGACGGCGA
1 ATCTTATCTTCCCTAAGCAGTAGTGGAATAGATTGAAGACGACGA
* * * * *
29025 ATCTTATCTTCCC-CAGGAGTAG-GGAAACAGATTTAAG-CCAC-A
1 ATCTTATCTTCCCTAAGCAGTAGTGG-AATAGATTGAAGACGACGA
* * * *
29067 AGTCTTAT-TTCCCTGAGCAGTAGTGGAATAGGTTGGAGACTACCG-
1 A-TCTTATCTTCCCTAAGCAGTAGTGGAATAGATTGAAGACGA-CGA
* ** * **
29112 ATCTTATC-TCCCTAAGCAATAGTGGAGCAGATCGAAGACGGTGA
1 ATCTTATCTTCCCTAAGCAGTAGTGGAATAGATTGAAGACGACGA
* * * *
29156 ATCTTATCTTCCCT-AGGAGTAG-GGAAATAGATTTAA-CCCAC-A
1 ATCTTATCTTCCCTAAGCAGTAGTGG-AATAGATTGAAGACGACGA
* * * * * *
29198 AGTCCTAT-TTCCCTGAGCAGCAGTGGAATAGGTTGGAGACTAC-A
1 A-TCTTATCTTCCCTAAGCAGTAGTGGAATAGATTGAAGACGACGA
* * * *
29242 GATCTTATC-TCCCTAAGCAATAGTGGAGTAGATCGAAGACGGCGA
1 -ATCTTATCTTCCCTAAGCAGTAGTGGAATAGATTGAAGACGACGA
* * * *
29287 ATCTTATCTTCCCT-AGGAGTAG-GGAAATAGATTTAAG-CCACTA
1 ATCTTATCTTCCCTAAGCAGTAGTGG-AATAGATTGAAGACGACGA
* * * **
29330 GTCTTATC-TCCCT-GGTCAGCAGTGGGACAT-G-TTGAAGATTAC-A
1 ATCTTATCTTCCCTAAG-CAGTAGT-GGA-ATAGATTGAAGACGACGA
* ** *
29373 GATCTTATC-TCCCTAAGTAGTAGTGGAGCAGATTGAAGACGGCGA
1 -ATCTTATCTTCCCTAAGCAGTAGTGGAATAGATTGAAGACGACGA
29418 ATCTTATCTTCCC
1 ATCTTATCTTCCC
29431 CAGGAGTAGG
Statistics
Matches: 297, Mismatches: 77, Indels: 63
0.68 0.18 0.14
Matches are distributed among these distances:
42 21 0.07
43 74 0.25
44 174 0.59
45 28 0.09
ACGTcount: A:0.29, C:0.21, G:0.24, T:0.26
Consensus pattern (45 bp):
ATCTTATCTTCCCTAAGCAGTAGTGGAATAGATTGAAGACGACGA
Found at i:29466 original size:131 final size:131
Alignment explanation
Indices: 28805--29455 Score: 991
Period size: 131 Copynumber: 5.0 Consensus size: 131
28795 CAAAGACACT
*
28805 AGTCCTATCTCCCTGGTCAGCAGTGGGATAGGTTGAAGATTACAGATCTTAGCTCCCTAAGCAAT
1 AGTCCTATCTCCCTGGTCAGCAGTGGGATAGGTTGAAGATTACAGATCTTATCTCCCTAAGCAAT
*
28870 AGTGGAGCAGATCGAAGATGGCGAATCTTATCTTCCCCAGGAGTAGGGAAATAGATTTAAGCCAC
66 AGTGGAGCAGATCGAAGACGGCGAATCTTATCTTCCCCAGGAGTAGGGAAATAGATTTAAGCCAC
*
28935 T
131 A
* *
28936 AGTCCTATCTCCCTGGTCAGCAGTAGGATAGGTTGAAGATTATAGATCTTATCTCCCTAAGCAAT
1 AGTCCTATCTCCCTGGTCAGCAGTGGGATAGGTTGAAGATTACAGATCTTATCTCCCTAAGCAAT
*
29001 AGTGGAGCAGATCGAAGACGGCGAATCTTATCTTCCCCAGGAGTAGGGAAACAGATTTAAGCCAC
66 AGTGGAGCAGATCGAAGACGGCGAATCTTATCTTCCCCAGGAGTAGGGAAATAGATTTAAGCCAC
29066 A
131 A
* * * * * * *
29067 AGTCTTATTTCCCTGAG-CAGTAGTGGAATAGGTTGGAGACTACCGATCTTATCTCCCTAAGCAA
1 AGTCCTATCTCCCTG-GTCAGCAGTGGGATAGGTTGAAGATTACAGATCTTATCTCCCTAAGCAA
* * *
29131 TAGTGGAGCAGATCGAAGACGGTGAATCTTATCTTCCCTAGGAGTAGGGAAATAGATTTAACCCA
65 TAGTGGAGCAGATCGAAGACGGCGAATCTTATCTTCCCCAGGAGTAGGGAAATAGATTTAAGCCA
29196 CA
130 CA
* * * *
29198 AGTCCTATTTCCCTGAG-CAGCAGTGGAATAGGTTGGAGACTACAGATCTTATCTCCCTAAGCAA
1 AGTCCTATCTCCCTG-GTCAGCAGTGGGATAGGTTGAAGATTACAGATCTTATCTCCCTAAGCAA
* *
29262 TAGTGGAGTAGATCGAAGACGGCGAATCTTATCTTCCCTAGGAGTAGGGAAATAGATTTAAGCCA
65 TAGTGGAGCAGATCGAAGACGGCGAATCTTATCTTCCCCAGGAGTAGGGAAATAGATTTAAGCCA
*
29327 CT
130 CA
* * * * *
29329 AGTCTTATCTCCCTGGTCAGCAGTGGGACATGTTGAAGATTACAGATCTTATCTCCCTAAGTAGT
1 AGTCCTATCTCCCTGGTCAGCAGTGGGATAGGTTGAAGATTACAGATCTTATCTCCCTAAGCAAT
* **
29394 AGTGGAGCAGATTGAAGACGGCGAATCTTATCTTCCCCAGGAGTAGGGAAGCAGATTTAAGC
66 AGTGGAGCAGATCGAAGACGGCGAATCTTATCTTCCCCAGGAGTAGGGAAATAGATTTAAGC
29456 GACGAGTCTT
Statistics
Matches: 478, Mismatches: 40, Indels: 4
0.92 0.08 0.01
Matches are distributed among these distances:
130 1 0.00
131 476 1.00
132 1 0.00
ACGTcount: A:0.29, C:0.20, G:0.25, T:0.26
Consensus pattern (131 bp):
AGTCCTATCTCCCTGGTCAGCAGTGGGATAGGTTGAAGATTACAGATCTTATCTCCCTAAGCAAT
AGTGGAGCAGATCGAAGACGGCGAATCTTATCTTCCCCAGGAGTAGGGAAATAGATTTAAGCCAC
A
Found at i:31221 original size:21 final size:22
Alignment explanation
Indices: 31186--31226 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
31176 TTCTTTATTT
**
31186 TAATATTATTTTAA-TATTGGC
1 TAATATTATCATAATTATTGGC
31207 TAATATTATCATAATTATTG
1 TAATATTATCATAATTATTG
31227 ATATTAATTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 12 0.71
22 5 0.29
ACGTcount: A:0.37, C:0.05, G:0.07, T:0.51
Consensus pattern (22 bp):
TAATATTATCATAATTATTGGC
Found at i:31687 original size:40 final size:40
Alignment explanation
Indices: 31650--31729 Score: 151
Period size: 40 Copynumber: 2.0 Consensus size: 40
31640 AGAGAATTGT
31650 GCCCTAACTTACTGGGCTTCAATTCTTCTCGATGAATTTA
1 GCCCTAACTTACTGGGCTTCAATTCTTCTCGATGAATTTA
*
31690 GCCCTGACTTACTGGGCTTCAATTCTTCTCGATGAATTTA
1 GCCCTAACTTACTGGGCTTCAATTCTTCTCGATGAATTTA
31730 TATCATCAAG
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
40 39 1.00
ACGTcount: A:0.21, C:0.25, G:0.16, T:0.38
Consensus pattern (40 bp):
GCCCTAACTTACTGGGCTTCAATTCTTCTCGATGAATTTA
Found at i:32649 original size:16 final size:17
Alignment explanation
Indices: 32630--32680 Score: 52
Period size: 18 Copynumber: 3.0 Consensus size: 17
32620 ATATTGTAGA
32630 ATATATAA-AAAAATAT
1 ATATATAAGAAAAATAT
*
32646 ATATGA-AATATAAAATAT
1 ATAT-ATAAGA-AAAATAT
*
32664 ATACATAAGAAAAATAT
1 ATATATAAGAAAAATAT
32681 GGATTTTAAG
Statistics
Matches: 29, Mismatches: 2, Indels: 7
0.76 0.05 0.18
Matches are distributed among these distances:
16 6 0.21
17 10 0.34
18 13 0.45
ACGTcount: A:0.65, C:0.02, G:0.04, T:0.29
Consensus pattern (17 bp):
ATATATAAGAAAAATAT
Found at i:32775 original size:26 final size:26
Alignment explanation
Indices: 32743--32805 Score: 72
Period size: 26 Copynumber: 2.4 Consensus size: 26
32733 GTATGAAAAT
**
32743 ATGTGTATATATGTACATAAATTAAA
1 ATGTGTATATACATACATAAATTAAA
* *
32769 ATGTGTATATGCATATATAAATTAAA
1 ATGTGTATATACATACATAAATTAAA
* *
32795 AAGTATATATA
1 ATGTGTATATA
32806 AAAAAAAGTG
Statistics
Matches: 30, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
26 30 1.00
ACGTcount: A:0.48, C:0.03, G:0.11, T:0.38
Consensus pattern (26 bp):
ATGTGTATATACATACATAAATTAAA
Found at i:32811 original size:16 final size:17
Alignment explanation
Indices: 32781--32814 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
32771 GTGTATATGC
32781 ATATATAAATTAAAAAGT
1 ATATATAAA-TAAAAAGT
32799 ATATATAAA-AAAAAGT
1 ATATATAAATAAAAAGT
32815 GGGTATATAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.44
18 9 0.56
ACGTcount: A:0.65, C:0.00, G:0.06, T:0.29
Consensus pattern (17 bp):
ATATATAAATAAAAAGT
Found at i:32890 original size:3 final size:3
Alignment explanation
Indices: 32876--33067 Score: 350
Period size: 3 Copynumber: 63.7 Consensus size: 3
32866 GGTATAAATA
32876 AAT AAGT AAT AAT AAT -AT CAAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AA-T AAT AAT AAT AAT -AAT AAT AAT AAT AAT AAT AAT AAT AAT
32922 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
32970 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
*
33018 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT GAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
33066 AA
1 AA
33068 CGATAGTAAA
Statistics
Matches: 184, Mismatches: 2, Indels: 6
0.96 0.01 0.03
Matches are distributed among these distances:
2 2 0.01
3 177 0.96
4 5 0.03
ACGTcount: A:0.66, C:0.01, G:0.01, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:34851 original size:45 final size:45
Alignment explanation
Indices: 34693--34852 Score: 139
Period size: 45 Copynumber: 3.6 Consensus size: 45
34683 ATTTTAATTC
* *
34693 GCTCCATTGCAACTTCAGGGAGAT-AGGATT-AGTA-GTTTCAGTCT
1 GCTCCACTGCAACTTCAGGGAGATAAGGATTGA-TATG-ATCAGTCT
* * * *
34737 GCTCCACTACAACTTCAGGGAGATAAGGCTCGCTAT-ATTCAGTCT
1 GCTCCACTGCAACTTCAGGGAGATAAGGATTGATATGA-TCAGTCT
* ** * ** * *
34782 ACTTTACTGCAACCTCAGTAAGATAAGGTTTGATATGATCAATCT
1 GCTCCACTGCAACTTCAGGGAGATAAGGATTGATATGATCAGTCT
34827 GCTCCACTGCAACTTCAGGGAGATAA
1 GCTCCACTGCAACTTCAGGGAGATAA
34853 AACTTGTCAT
Statistics
Matches: 88, Mismatches: 23, Indels: 9
0.73 0.19 0.08
Matches are distributed among these distances:
44 22 0.25
45 65 0.74
46 1 0.01
ACGTcount: A:0.29, C:0.22, G:0.21, T:0.29
Consensus pattern (45 bp):
GCTCCACTGCAACTTCAGGGAGATAAGGATTGATATGATCAGTCT
Found at i:35176 original size:44 final size:44
Alignment explanation
Indices: 35095--35199 Score: 111
Period size: 44 Copynumber: 2.4 Consensus size: 44
35085 GGACTCATAT
* * * * * *
35095 CTTCAACTTGCCCAACTGCAACTTCAGGGGGATAAGGTTAGTGA
1 CTTCAACCTGCTCTACTGCAACTTCAGAGAGACAAGGTTAGTGA
* * *
35139 CTTCAACCTGCTCTACTGCAGCTTCAGAGAGACAAGGTTTGTTA
1 CTTCAACCTGCTCTACTGCAACTTCAGAGAGACAAGGTTAGTGA
* *
35183 TTTCAACCTACTCTACT
1 CTTCAACCTGCTCTACT
35200 ACGCCTTCGA
Statistics
Matches: 50, Mismatches: 11, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
44 50 1.00
ACGTcount: A:0.26, C:0.26, G:0.19, T:0.30
Consensus pattern (44 bp):
CTTCAACCTGCTCTACTGCAACTTCAGAGAGACAAGGTTAGTGA
Found at i:35214 original size:44 final size:44
Alignment explanation
Indices: 35140--35229 Score: 112
Period size: 44 Copynumber: 2.0 Consensus size: 44
35130 GGTTAGTGAC
* * *
35140 TTCAACCTGCTCTACTGCAGCTTCAGAGAGACAAGGTTTGTTAT
1 TTCAACCTACTCTACTACAGCTTCAGAGAGACAAGGTTTGTAAT
*
35184 TTCAACCTACTCTACTAC-GCCTTC-GAAGAGATAAGGTTTGTAAT
1 TTCAACCTACTCTACTACAG-CTTCAG-AGAGACAAGGTTTGTAAT
35228 TT
1 TT
35230 ATAGCTTCCA
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
43 2 0.05
44 38 0.95
ACGTcount: A:0.27, C:0.22, G:0.18, T:0.33
Consensus pattern (44 bp):
TTCAACCTACTCTACTACAGCTTCAGAGAGACAAGGTTTGTAAT
Found at i:35844 original size:24 final size:24
Alignment explanation
Indices: 35790--35847 Score: 62
Period size: 24 Copynumber: 2.4 Consensus size: 24
35780 TGGATTGCCC
*
35790 CCACTGTAATATTTAAAGTTCAAT
1 CCACTGTAATATTCAAAGTTCAAT
* * * * *
35814 CCGCTGTAATCTTCAAGGTTTAGT
1 CCACTGTAATATTCAAAGTTCAAT
35838 CCACTGTAAT
1 CCACTGTAAT
35848 TTTGGGACAT
Statistics
Matches: 27, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.29, C:0.21, G:0.14, T:0.36
Consensus pattern (24 bp):
CCACTGTAATATTCAAAGTTCAAT
Found at i:36490 original size:97 final size:97
Alignment explanation
Indices: 36319--36606 Score: 490
Period size: 97 Copynumber: 3.0 Consensus size: 97
36309 GAAAACTGCT
* * *
36319 TGAAAAAGATTATCACAATGGACAAGATGAAATTTTATTGAGAA-CAAAGCTTGAAATGAATAAA
1 TGAAAAAGATTATCACAATGGATAAGATGAAATTTTATTGA-AAGCACAGCTCGAAATGAATAAA
* *
36383 TTAATGAAGATAGCAAATTTTTCT-AGAATAAGA
65 TTAATCAAGATAGCAAATTTTGCTAAG-ATAAGA
36416 TGAAAAAGATTATCACAATGGATAAGATGAAATTTTATTGAAAGCACAGCTCGAAATGAATAAAT
1 TGAAAAAGATTATCACAATGGATAAGATGAAATTTTATTGAAAGCACAGCTCGAAATGAATAAAT
*
36481 TAATCAAGATAGAAAATTTTGCTAAGATAAGA
66 TAATCAAGATAGCAAATTTTGCTAAGATAAGA
36513 TGAAAAAGATTATCACAATGGATAAGATGAAATTTTATTGAAAGCACAGCTCGAAATGAATAAAT
1 TGAAAAAGATTATCACAATGGATAAGATGAAATTTTATTGAAAGCACAGCTCGAAATGAATAAAT
36578 TAATCAAGATAGCAAATTTTGCTAAGATA
66 TAATCAAGATAGCAAATTTTGCTAAGATA
36607 CGAAATGAAT
Statistics
Matches: 182, Mismatches: 7, Indels: 4
0.94 0.04 0.02
Matches are distributed among these distances:
96 2 0.01
97 178 0.98
98 2 0.01
ACGTcount: A:0.48, C:0.08, G:0.16, T:0.27
Consensus pattern (97 bp):
TGAAAAAGATTATCACAATGGATAAGATGAAATTTTATTGAAAGCACAGCTCGAAATGAATAAAT
TAATCAAGATAGCAAATTTTGCTAAGATAAGA
Found at i:36952 original size:22 final size:22
Alignment explanation
Indices: 36912--36953 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
36902 TTTCTTATTA
*
36912 TTATTTTTTTCCTTGTTTTTCT
1 TTATTTTTTTCCTTATTTTTCT
36934 TTATTTTTCTT-CTTATTTTT
1 TTATTTTT-TTCCTTATTTTT
36954 TGAACATTCT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 16 0.89
23 2 0.11
ACGTcount: A:0.07, C:0.12, G:0.02, T:0.79
Consensus pattern (22 bp):
TTATTTTTTTCCTTATTTTTCT
Found at i:42099 original size:26 final size:26
Alignment explanation
Indices: 42067--42116 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 26
42057 GTATGAAAAT
*
42067 ATGTGTATATATGTACATAAATTAAA
1 ATGTGTATATATATACATAAATTAAA
* *
42093 ATGTGTATATGTATATATAAATTA
1 ATGTGTATATATATACATAAATTA
42117 TAAAGTATAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.44, C:0.02, G:0.12, T:0.42
Consensus pattern (26 bp):
ATGTGTATATATATACATAAATTAAA
Found at i:42127 original size:26 final size:24
Alignment explanation
Indices: 42070--42128 Score: 66
Period size: 26 Copynumber: 2.4 Consensus size: 24
42060 TGAAAATATG
42070 TGTATATATGTACATAAATTAAAA
1 TGTATATATGTACATAAATTAAAA
* *
42094 TGTGTATATGTATATATAAATTATAAA
1 TGTATATATG--TACATAAATTA-AAA
42121 -GTATATAT
1 TGTATATAT
42129 CAAGGATGTA
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
24 9 0.31
26 17 0.59
27 3 0.10
ACGTcount: A:0.46, C:0.02, G:0.10, T:0.42
Consensus pattern (24 bp):
TGTATATATGTACATAAATTAAAA
Found at i:46214 original size:40 final size:40
Alignment explanation
Indices: 46155--46303 Score: 149
Period size: 41 Copynumber: 3.6 Consensus size: 40
46145 ATACACGAGA
* * *
46155 CTTCGGCTATTTATTGCACTTAGTGTGCGA-TTTGGAATAG
1 CTTCGGCTATATATGGCACTTAGTGTGCGAGATT-GAATAG
*
46195 CTTCGGCTATATATGGCACTTAGTGTGCGAGACTGAGATAG
1 CTTCGGCTATATATGGCACTTAGTGTGCGAGATTGA-ATAG
* * * * *
46236 CTTTGGCTATGTAAGGCACTTAGTGTGTGAGATTATAATAG
1 CTTCGGCTATATATGGCACTTAGTGTGCGAGATT-GAATAG
*
46277 CTTCGGCTATGCA-ATGGCAATTAGTGT
1 CTTCGGCTAT--ATATGGCACTTAGTGT
46304 ACGAAACATT
Statistics
Matches: 90, Mismatches: 14, Indels: 8
0.80 0.12 0.07
Matches are distributed among these distances:
40 30 0.33
41 47 0.52
42 13 0.14
ACGTcount: A:0.23, C:0.15, G:0.27, T:0.35
Consensus pattern (40 bp):
CTTCGGCTATATATGGCACTTAGTGTGCGAGATTGAATAG
Found at i:47003 original size:46 final size:46
Alignment explanation
Indices: 46950--47192 Score: 387
Period size: 46 Copynumber: 5.2 Consensus size: 46
46940 ATATGTTATG
46950 ATGCTGTCCAATTTGAGCATATTAATGCTGTCCAATTTGATGTATA
1 ATGCTGTCCAATTTGAGCATATTAATGCTGTCCAATTTGATGTATA
* * *
46996 ATGCTGTCCATTTTGAGCATATTGATGTTGTCCAATTTGATGTATA
1 ATGCTGTCCAATTTGAGCATATTAATGCTGTCCAATTTGATGTATA
*
47042 ATGCTGTCCAATTTGAGCATATTAAAGCTGTCCAATTTGATGTATA
1 ATGCTGTCCAATTTGAGCATATTAATGCTGTCCAATTTGATGTATA
* * *
47088 ATGCTGTCCATTTTGAGCATATTGATGGCTGTCTAATTTGATGTATA
1 ATGCTGTCCAATTTGAGCATATTAAT-GCTGTCCAATTTGATGTATA
* *
47135 ATGCTATCCATTTTGAGCATATTAATGCTGTCCAATTTGATGTATAA
1 ATGCTGTCCAATTTGAGCATATTAATGCTGTCCAATTTGATGTAT-A
47182 ATGCTGTCCAA
1 ATGCTGTCCAA
47193 AACAGGGCAG
Statistics
Matches: 179, Mismatches: 16, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
46 126 0.70
47 53 0.30
ACGTcount: A:0.27, C:0.15, G:0.18, T:0.40
Consensus pattern (46 bp):
ATGCTGTCCAATTTGAGCATATTAATGCTGTCCAATTTGATGTATA
Found at i:48347 original size:26 final size:26
Alignment explanation
Indices: 48318--48369 Score: 86
Period size: 26 Copynumber: 2.0 Consensus size: 26
48308 AATTACATTA
* *
48318 GGTTAATTTTATGTAAGTAATTTATT
1 GGTTAATTTAAGGTAAGTAATTTATT
48344 GGTTAATTTAAGGTAAGTAATTTATT
1 GGTTAATTTAAGGTAAGTAATTTATT
48370 TAGTTTAATC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.17, T:0.50
Consensus pattern (26 bp):
GGTTAATTTAAGGTAAGTAATTTATT
Found at i:49920 original size:20 final size:21
Alignment explanation
Indices: 49895--49948 Score: 65
Period size: 22 Copynumber: 2.6 Consensus size: 21
49885 TAGTTTTAGG
* *
49895 GTCTCGAGACAAGTGG-CTTT
1 GTCTCGAGACAAGGGGTCATT
49915 GTCTCGAGACATAGGGGTCATT
1 GTCTCGAGACA-AGGGGTCATT
*
49937 ATCTCGAGACAA
1 GTCTCGAGACAA
49949 TCGACAAGTT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
20 11 0.38
21 5 0.17
22 13 0.45
ACGTcount: A:0.26, C:0.20, G:0.28, T:0.26
Consensus pattern (21 bp):
GTCTCGAGACAAGGGGTCATT
Found at i:56618 original size:116 final size:116
Alignment explanation
Indices: 56406--56638 Score: 306
Period size: 116 Copynumber: 2.0 Consensus size: 116
56396 TGATCTTAAA
* *
56406 TCGAATGAACTTAGGTTGCAATCTTAAATCAGCGAAACTTAACAATATCAGTTATGATCTTAAAT
1 TCGAATGAACTTAGGTTACAATCTTAAATCAGCGAAACTTAACAATATCAGCTATGATCTTAAAT
* ** * * *
56471 CAGCGAGCTGTTTGGAGTTAGGATTTCAGATCAACTAACTCAAATAAAATT
66 CAGCGAGCTATTCAGAGTTAGGATCTAAGATCAACAAACTCAAATAAAATT
* * * * *
56522 TCGAATGAGCTTAGGTTACGATCTTAAATCATCGAACCTTAACAATATTAGCTATGATCTTAAAT
1 TCGAATGAACTTAGGTTACAATCTTAAATCAGCGAAACTTAACAATATCAGCTATGATCTTAAAT
* * *
56587 TAGTGAGTTATTCAGAGTT-GCGATCTAAGATCAACAAACTCAAATAAAATT
66 CAGCGAGCTATTCAGAGTTAG-GATCTAAGATCAACAAACTCAAATAAAATT
56638 T
1 T
56639 GTTCACAATC
Statistics
Matches: 100, Mismatches: 16, Indels: 2
0.85 0.14 0.02
Matches are distributed among these distances:
115 1 0.01
116 99 0.99
ACGTcount: A:0.37, C:0.15, G:0.15, T:0.32
Consensus pattern (116 bp):
TCGAATGAACTTAGGTTACAATCTTAAATCAGCGAAACTTAACAATATCAGCTATGATCTTAAAT
CAGCGAGCTATTCAGAGTTAGGATCTAAGATCAACAAACTCAAATAAAATT
Found at i:56761 original size:132 final size:132
Alignment explanation
Indices: 56522--57040 Score: 628
Period size: 132 Copynumber: 3.9 Consensus size: 132
56512 AAATAAAATT
* * * * * * **
56522 TCGAATGAGCTTAGGTTACGATCTTAAATCATCGAACCTTAACAATATTAGCTATGATCTTAAAT
1 TCGAATGAACTTAGGTTGCAATATTAAATCAGCGAACCTTAACAATATCAGCTGCGATCTTAAAT
* * * * **
56587 TAGTGAGTTATTCAGAGTTGCGATCTAAGATCAACAAACTCAAATAAAATTTGTTCACAATCTTA
66 TAGCGAGCTATTCAGAGTTGCGATCTGAGATCAACTAACTCAAATAAAATTTGTTCATGATCTTA
56652 AA
131 AA
* * * * * *
56654 TTGAATGAACTTAGGTTGCGATATTAAATCAGCTAACCTTAACAACATCAGCTGTGATATTAAAT
1 TCGAATGAACTTAGGTTGCAATATTAAATCAGCGAACCTTAACAATATCAGCTGCGATCTTAAAT
* * * *
56719 TAGCGAGTTGTTCGGAGTTGCGATCTGAGATCAACTAACTCAAATAAAATTTGTTCATGGTCTTA
66 TAGCGAGCTATTCAGAGTTGCGATCTGAGATCAACTAACTCAAATAAAATTTGTTCATGATCTTA
56784 AA
131 AA
* * *
56786 TCGAATGAACTTAGGTTGCAATCTTAAATCAGTGAACCTTAACAATATCAGTTGCGATCTTAAAT
1 TCGAATGAACTTAGGTTGCAATATTAAATCAGCGAACCTTAACAATATCAGCTGCGATCTTAAAT
* * * *
56851 TAGCAAGCTGTT-TGAAGTTGCGATCTTG-GATCAACTAACTCAAATAAAATTTGTTCTTGATCT
66 TAGCGAGCTATTCAG-AGTTGCGATC-TGAGATCAACTAACTCAAATAAAATTTGTTCATGATCT
56914 TAAA
129 TAAA
* * * * * *
56918 CCGAATGAACTTAGGTTGCAATATTAAATTAACGAACCTTAACAATATCAGTTGCAATCTTAAAC
1 TCGAATGAACTTAGGTTGCAATATTAAATCAGCGAACCTTAACAATATCAGCTGCGATCTTAAAT
* * * * *
56983 CAGCGAGCTATTAAGAGTTGCAATATGAGATCAGCTAACTCAAATAAAATTTGTTCAT
66 TAGCGAGCTATTCAGAGTTGCGATCTGAGATCAACTAACTCAAATAAAATTTGTTCAT
57041 AAATTAAAGT
Statistics
Matches: 336, Mismatches: 47, Indels: 8
0.86 0.12 0.02
Matches are distributed among these distances:
131 3 0.01
132 330 0.98
133 3 0.01
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (132 bp):
TCGAATGAACTTAGGTTGCAATATTAAATCAGCGAACCTTAACAATATCAGCTGCGATCTTAAAT
TAGCGAGCTATTCAGAGTTGCGATCTGAGATCAACTAACTCAAATAAAATTTGTTCATGATCTTA
AA
Found at i:66881 original size:36 final size:36
Alignment explanation
Indices: 66834--66915 Score: 157
Period size: 36 Copynumber: 2.3 Consensus size: 36
66824 CACTATTTGT
66834 GCACGAAATAGACAACCTACTGAAGGAAAGATACTA
1 GCACGAAATAGACAACCTACTGAAGGAAAGATACTA
66870 GCACGAAATAGACAACCTACTGAAGGAAAGATACTA
1 GCACGAAATAGACAACCTACTGAAGGAAAGATACTA
66906 GCAC-AAATAG
1 GCACGAAATAG
66916 TGCATCATCG
Statistics
Matches: 46, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
35 6 0.13
36 40 0.87
ACGTcount: A:0.48, C:0.20, G:0.20, T:0.13
Consensus pattern (36 bp):
GCACGAAATAGACAACCTACTGAAGGAAAGATACTA
Found at i:66947 original size:43 final size:43
Alignment explanation
Indices: 66900--66988 Score: 99
Period size: 43 Copynumber: 2.1 Consensus size: 43
66890 TGAAGGAAAG
* * *
66900 ATACTAGCACA-AATAGTGCATCATCGGACAAACTGAAGCAATT
1 ATACTAGCACACAA-AGTGCACCATCGGACAAACCGAACCAATT
* * * *
66943 ATACTGGCACACGAGGTGCACCATTGGACAAACCGAACCAATT
1 ATACTAGCACACAAAGTGCACCATCGGACAAACCGAACCAATT
66986 ATA
1 ATA
66989 TTGGCATGCA
Statistics
Matches: 38, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
43 37 0.97
44 1 0.03
ACGTcount: A:0.39, C:0.24, G:0.18, T:0.19
Consensus pattern (43 bp):
ATACTAGCACACAAAGTGCACCATCGGACAAACCGAACCAATT
Found at i:67005 original size:43 final size:42
Alignment explanation
Indices: 66914--67019 Score: 124
Period size: 43 Copynumber: 2.5 Consensus size: 42
66904 TAGCACAAAT
* *
66914 AGTGCATCATCGGACAAACTGAAGCAATTATACTGGCACACG
1 AGTGCATCATCGGACAAACCGAACCAATTATACTGGCACACG
* * *
66956 AGGTGCACCATTGGACAAACCGAACCAATTATATTGGCATGCAC-
1 A-GTGCATCATCGGACAAACCGAACCAATTATACTGGCA--CACG
*
67000 AGTGCATCATCGGATAAACC
1 AGTGCATCATCGGACAAACC
67020 AAAGTAATCA
Statistics
Matches: 53, Mismatches: 8, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
42 1 0.02
43 48 0.91
44 1 0.02
45 3 0.06
ACGTcount: A:0.35, C:0.25, G:0.21, T:0.20
Consensus pattern (42 bp):
AGTGCATCATCGGACAAACCGAACCAATTATACTGGCACACG
Found at i:68793 original size:22 final size:22
Alignment explanation
Indices: 68751--68794 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
68741 TGTAGAAAAA
*
68751 TAAATAAAATAAAAAATTAAAT
1 TAAATAAAATAAAAAACTAAAT
*
68773 TAAATTAAAA-AAATAACTAAAT
1 TAAA-TAAAATAAAAAACTAAAT
68795 ATATGGTTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 14 0.74
23 5 0.26
ACGTcount: A:0.70, C:0.02, G:0.00, T:0.27
Consensus pattern (22 bp):
TAAATAAAATAAAAAACTAAAT
Found at i:68794 original size:17 final size:17
Alignment explanation
Indices: 68746--68794 Score: 62
Period size: 18 Copynumber: 2.8 Consensus size: 17
68736 AATTATGTAG
*
68746 AAAAATAAATAAAATAA
1 AAAAATAAATAAATTAA
*
68763 AAAATTAAATTAAATTAA
1 AAAAATAAA-TAAATTAA
*
68781 AAAAATAACTAAAT
1 AAAAATAAATAAAT
68795 ATATGGTTAA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
17 13 0.48
18 14 0.52
ACGTcount: A:0.73, C:0.02, G:0.00, T:0.24
Consensus pattern (17 bp):
AAAAATAAATAAATTAA
Found at i:70022 original size:21 final size:21
Alignment explanation
Indices: 69981--70022 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
69971 TCGTCTCAGA
* *
69981 TTATTGGGTTTTGCTTTTTAT
1 TTATTGGGTTATGCTTATTAT
70002 TTATTGGGTTAATGC-TATTAT
1 TTATTGGGTT-ATGCTTATTAT
70023 CTTTAAGTTG
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 15 0.83
22 3 0.17
ACGTcount: A:0.17, C:0.05, G:0.19, T:0.60
Consensus pattern (21 bp):
TTATTGGGTTATGCTTATTAT
Found at i:73088 original size:107 final size:108
Alignment explanation
Indices: 72957--73172 Score: 425
Period size: 107 Copynumber: 2.0 Consensus size: 108
72947 TATTATAAAA
72957 AATAAATATTTATATTTAAAATAGCGAAAGTGTCTTAAATTTTTTATATAAAAATATTTTTTTTA
1 AATAAATATTTATATTTAAAATAGCGAAAGTGTCTTAAATTTTTTATATAAAAATATTTTTTTTA
73022 AAATACTACATAAGATAAAAGTCTAGAAATTAAAAGAAATTGC
66 AAATACTACATAAGATAAAAGTCTAGAAATTAAAAGAAATTGC
73065 AATAAATATTT-TATTTAAAATAGCGAAAGTGTCTTAAATTTTTTATATAAAAATATTTTTTTTA
1 AATAAATATTTATATTTAAAATAGCGAAAGTGTCTTAAATTTTTTATATAAAAATATTTTTTTTA
73129 AAATACTACATAAGATAAAAGTCTAGAAATTAAAAGAAATTGC
66 AAATACTACATAAGATAAAAGTCTAGAAATTAAAAGAAATTGC
73172 A
1 A
73173 TATTGTACTT
Statistics
Matches: 108, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
107 97 0.90
108 11 0.10
ACGTcount: A:0.48, C:0.06, G:0.08, T:0.38
Consensus pattern (108 bp):
AATAAATATTTATATTTAAAATAGCGAAAGTGTCTTAAATTTTTTATATAAAAATATTTTTTTTA
AAATACTACATAAGATAAAAGTCTAGAAATTAAAAGAAATTGC
Found at i:73562 original size:22 final size:21
Alignment explanation
Indices: 73531--73587 Score: 82
Period size: 21 Copynumber: 2.8 Consensus size: 21
73521 AATTTTAAAA
*
73531 ATATTTAAAAAT-ATTTTTTT
1 ATATTTAAAAATAATTTTTAT
73551 ATGATTTAAAAATAATTTTTAT
1 AT-ATTTAAAAATAATTTTTAT
73573 ATATTTAAAAA-AATT
1 ATATTTAAAAATAATT
73588 AATTAAATCC
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
20 6 0.18
21 19 0.56
22 9 0.26
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (21 bp):
ATATTTAAAAATAATTTTTAT
Found at i:85614 original size:14 final size:14
Alignment explanation
Indices: 85595--85624 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
85585 TGACCCATCA
*
85595 TTCTTTTTTTCTTT
1 TTCTTTTTCTCTTT
85609 TTCTTTTTCTCTTT
1 TTCTTTTTCTCTTT
85623 TT
1 TT
85625 ACTTCTGTTT
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:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (14 bp):
TTCTTTTTCTCTTT
Found at i:90164 original size:26 final size:25
Alignment explanation
Indices: 90108--90194 Score: 95
Period size: 26 Copynumber: 3.4 Consensus size: 25
90098 AGCCAATATT
90108 GGGAAGCTC-CGAAGAGCCATTAATC
1 GGGAAGCTCACGAAGAGCC-TTAATC
** *
90133 AAGAAGCTCACAAAGAGCCTTTAATC
1 GGGAAGCTCACGAAGAGCC-TTAATC
*
90159 GGGAAGCTCACGAAGAGCCATATATC
1 GGGAAGCTCACGAAGAGCCTTA-ATC
*
90185 GGGATGCTCA
1 GGGAAGCTCA
90195 TAAGAACTGT
Statistics
Matches: 51, Mismatches: 9, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
25 9 0.18
26 42 0.82
ACGTcount: A:0.34, C:0.23, G:0.25, T:0.17
Consensus pattern (25 bp):
GGGAAGCTCACGAAGAGCCTTAATC
Found at i:91222 original size:13 final size:13
Alignment explanation
Indices: 91206--91233 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
91196 TTTTATTTTA
91206 TTATTTTTCATCT
1 TTATTTTTCATCT
91219 TTATTTTTCATCT
1 TTATTTTTCATCT
91232 TT
1 TT
91234 CCAATTTTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.14, C:0.14, G:0.00, T:0.71
Consensus pattern (13 bp):
TTATTTTTCATCT
Found at i:104201 original size:18 final size:17
Alignment explanation
Indices: 104178--104212 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
104168 GAATGTTAGA
104178 GTATTTTATAAAATTATT
1 GTATTTTA-AAAATTATT
*
104196 GTATTTTAAAATTTATT
1 GTATTTTAAAAATTATT
104213 TAGAAAAATA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.37, C:0.00, G:0.06, T:0.57
Consensus pattern (17 bp):
GTATTTTAAAAATTATT
Found at i:114562 original size:18 final size:18
Alignment explanation
Indices: 114541--114575 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
114531 CAAAAAATAA
*
114541 AAAATACATAAAATTTAG
1 AAAACACATAAAATTTAG
*
114559 AAAACATATAAAATTTA
1 AAAACACATAAAATTTA
114576 TTCCACCATG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.63, C:0.06, G:0.03, T:0.29
Consensus pattern (18 bp):
AAAACACATAAAATTTAG
Found at i:117843 original size:25 final size:25
Alignment explanation
Indices: 117796--117846 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
117786 GACCAGACAG
**
117796 AATACGCCACAAAGGTGACATACAA
1 AATACGCCACAAAGGCAACATACAA
* *
117821 AATACGCCACAATGGCAATATACAA
1 AATACGCCACAAAGGCAACATACAA
117846 A
1 A
117847 GTATTTCATA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.49, C:0.24, G:0.14, T:0.14
Consensus pattern (25 bp):
AATACGCCACAAAGGCAACATACAA
Found at i:123117 original size:2 final size:2
Alignment explanation
Indices: 123110--123138 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
123100 AATATGAACC
123110 TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
123139 CTTTATGTCG
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:131195 original size:21 final size:21
Alignment explanation
Indices: 131170--131231 Score: 61
Period size: 21 Copynumber: 2.9 Consensus size: 21
131160 AATAATTAAC
131170 TTTAAATAAATTCAAAATAAA
1 TTTAAATAAATTCAAAATAAA
** * *
131191 TTTAAATTTATTCAATAATCAT
1 TTTAAATAAATTCAA-AATAAA
* *
131213 TTTAAATAACTTAAAAATA
1 TTTAAATAAATTCAAAATA
131232 CTATACAAAT
Statistics
Matches: 31, Mismatches: 9, Indels: 2
0.74 0.21 0.05
Matches are distributed among these distances:
21 16 0.52
22 15 0.48
ACGTcount: A:0.53, C:0.06, G:0.00, T:0.40
Consensus pattern (21 bp):
TTTAAATAAATTCAAAATAAA
Found at i:133949 original size:53 final size:51
Alignment explanation
Indices: 133808--134021 Score: 184
Period size: 52 Copynumber: 4.0 Consensus size: 51
133798 CCCCCTCAAA
*
133808 TCCTTTTACTTT-TCCCCTAAAAATTTTACTTCCCCCAAATCCCCAAAAACTTTTTT
1 TCCTTTTACTTTCT-CCC-AAAACTTTTACTTCCCCCAAA-CCCCAAAAA---TTTT
* * * *
133864 TCTTTTTGA-TTTC-CTGCAAAAGTTTTACTTCCCCCAAACCCCTAAAAAATTT
1 TCCTTTT-ACTTTCTC-CCAAAACTTTTACTTCCCCCAAACCCC-AAAAATTTT
**
133916 TCCTTTTACTTTCTCCCTAAAACTTTTACTT-CCCCAAACTCCCAAATTTTTTT
1 TCCTTTTACTTTCTCCC-AAAACTTTTACTTCCCCCAAAC-CCCAAA-AATTTT
* * * *
133969 TCCTTTTGCTTTCTCTCAAAACTTTTACTTCCTCCGAACCCCAAAAACTTTT
1 TCCTTTTACTTTCTCCCAAAACTTTTACTTCCCCCAAACCCCAAAAA-TTTT
134021 T
1 T
134022 TTTGAATTTA
Statistics
Matches: 131, Mismatches: 16, Indels: 26
0.76 0.09 0.15
Matches are distributed among these distances:
51 1 0.01
52 49 0.37
53 40 0.31
54 4 0.03
55 26 0.20
56 10 0.08
57 1 0.01
ACGTcount: A:0.25, C:0.31, G:0.02, T:0.42
Consensus pattern (51 bp):
TCCTTTTACTTTCTCCCAAAACTTTTACTTCCCCCAAACCCCAAAAATTTT
Found at i:134022 original size:53 final size:53
Alignment explanation
Indices: 133826--134022 Score: 206
Period size: 53 Copynumber: 3.7 Consensus size: 53
133816 CTTTTCCCCT
* * *
133826 AAAAATTTTACTTCCCCCAAATCCCCAAAAACTTTTTTTCTTTTTGATTTC-CTGC
1 AAAACTTTTACTTCCCCCAAA-CCCCAAAAAC-TTTTTTCCTTTTGCTTTCTCT-C
* * * *
133881 AAAAGTTTTACTTCCCCCAAACCCCTAAAAA--ATTTTCCTTTTACTTTCTCCC
1 AAAACTTTTACTTCCCCCAAACCCC-AAAAACTTTTTTCCTTTTGCTTTCTCTC
**
133933 TAAAACTTTTACTT-CCCCAAACTCCC-AAATTTTTTTTCCTTTTGCTTTCTCTC
1 -AAAACTTTTACTTCCCCCAAAC-CCCAAAAACTTTTTTCCTTTTGCTTTCTCTC
* *
133986 AAAACTTTTACTTCCTCCGAACCCCAAAAACTTTTTT
1 AAAACTTTTACTTCCCCCAAACCCCAAAAACTTTTTT
134023 TTGAATTTAT
Statistics
Matches: 119, Mismatches: 15, Indels: 18
0.78 0.10 0.12
Matches are distributed among these distances:
51 3 0.03
52 38 0.32
53 49 0.41
54 4 0.03
55 25 0.21
ACGTcount: A:0.27, C:0.30, G:0.03, T:0.41
Consensus pattern (53 bp):
AAAACTTTTACTTCCCCCAAACCCCAAAAACTTTTTTCCTTTTGCTTTCTCTC
Found at i:144126 original size:47 final size:47
Alignment explanation
Indices: 144070--145020 Score: 1679
Period size: 47 Copynumber: 20.3 Consensus size: 47
144060 ATAACATGCT
144070 CAAAA-TGGACAGCATTATACATCAAATTAGACAGCTTAAATATACC
1 CAAAATTGGACAGCATTATACATCAAATTAGACAGCTTAAATATACC
144116 CAAAATTGGACAGCATTATACATCAAATTAGACAGCTTAAATATACC
1 CAAAATTGGACAGCATTATACATCAAATTAGACAGCTTAAATATACC
144163 CAAAATTGGACAGCATTATACATCAAATTAGACAGCTTAAATATACC
1 CAAAATTGGACAGCATTATACATCAAATTAGACAGCTTAAATATACC
144210 CAAAATTGGACAGCATTATACATCAAATTAGACAGCTTAAATATACC
1 CAAAATTGGACAGCATTATACATCAAATTAGACAGCTTAAATATACC
144257 CAAAATTGGACAGCATTATACATCAAATTAGACAGCTTAAATATACC
1 CAAAATTGGACAGCATTATACATCAAATTAGACAGCTTAAATATACC
144304 CAAAATTGGACAGCATTATACATCAAATTAGACAGCTTAAATATACC
1 CAAAATTGGACAGCATTATACATCAAATTAGACAGCTTAAATATACC
144351 CAAAATTGGACAGCATTATACATCAAATTAGACAGCTTAAATATACC
1 CAAAATTGGACAGCATTATACATCAAATTAGACAGCTTAAATATACC
144398 CAAAATTGGACAGCATTATACATCAAATTAGACAGCTTAAATATACC
1 CAAAATTGGACAGCATTATACATCAAATTAGACAGCTTAAATATACC
144445 CAAAATTGGACAGCATTATACATCAAATTAGACAGCTTAAATATACC
1 CAAAATTGGACAGCATTATACATCAAATTAGACAGCTTAAATATACC
144492 CAAAATTGGACAGCATTATACATCAAATTAGACAGCTTAAATATACC
1 CAAAATTGGACAGCATTATACATCAAATTAGACAGCTTAAATATACC
144539 CAAAATTGGACAGCATTATACATCAAATTAGACAGCTTAAATATACC
1 CAAAATTGGACAGCATTATACATCAAATTAGACAGCTTAAATATACC
*
144586 CAAAATTGGACAGCATTATACATCAAATTAGACAGCTTAAATATACT
1 CAAAATTGGACAGCATTATACATCAAATTAGACAGCTTAAATATACC
* *
144633 CACAATTGGACAGCATTATACATCAAATTAGACAGCTTAAATATACT
1 CAAAATTGGACAGCATTATACATCAAATTAGACAGCTTAAATATACC
* *
144680 CACAATTGGACAGCATTATACATCAAATTAGACAGCTTAAATATACT
1 CAAAATTGGACAGCATTATACATCAAATTAGACAGCTTAAATATACC
* *
144727 CACAATTGGACAGCATTATACATCAAATTAGACAGCTTAAATATACT
1 CAAAATTGGACAGCATTATACATCAAATTAGACAGCTTAAATATACC
* *
144774 CACAATTGGACAGCATTATACATCAAATTAGACAGCTTAAATATACT
1 CAAAATTGGACAGCATTATACATCAAATTAGACAGCTTAAATATACC
* *
144821 CACAATTGGACAGCATTATACATCAAATTAGACAGCTTAAATATACT
1 CAAAATTGGACAGCATTATACATCAAATTAGACAGCTTAAATATACC
* *
144868 CACAATTGGACAGCATTATACATCAAATTAGACAGCTTAAATATACT
1 CAAAATTGGACAGCATTATACATCAAATTAGACAGCTTAAATATACC
* *
144915 CACAATTGGACAGCATTATACATCAAATTAGACAGCTTAAATATACT
1 CAAAATTGGACAGCATTATACATCAAATTAGACAGCTTAAATATACC
* * * * * * * * *
144962 CACAATTGGACAGCATTATATATTAAAATGGACAGCATCAATACACT
1 CAAAATTGGACAGCATTATACATCAAATTAGACAGCTTAAATATACC
145009 CAAAATTGGACA
1 CAAAATTGGACA
145021 TCAAATTTGG
Statistics
Matches: 894, Mismatches: 10, Indels: 1
0.99 0.01 0.00
Matches are distributed among these distances:
46 5 0.01
47 889 0.99
ACGTcount: A:0.44, C:0.19, G:0.11, T:0.26
Consensus pattern (47 bp):
CAAAATTGGACAGCATTATACATCAAATTAGACAGCTTAAATATACC
Found at i:154505 original size:24 final size:23
Alignment explanation
Indices: 154477--154534 Score: 73
Period size: 23 Copynumber: 2.5 Consensus size: 23
154467 ATATAATACA
154477 TCAAAAATATT-AAAATAAATATTT
1 TCAAAAATATTAAAAAT-AA-ATTT
*
154501 TCAAACATATTAAAAATAAATTT
1 TCAAAAATATTAAAAATAAATTT
*
154524 TAAAAAATATT
1 TCAAAAATATT
154535 TATACTTAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
23 13 0.43
24 12 0.40
25 5 0.17
ACGTcount: A:0.59, C:0.05, G:0.00, T:0.36
Consensus pattern (23 bp):
TCAAAAATATTAAAAATAAATTT
Found at i:157109 original size:6 final size:6
Alignment explanation
Indices: 157095--157134 Score: 53
Period size: 6 Copynumber: 6.7 Consensus size: 6
157085 ATAAATGGAT
* * *
157095 CATTTC CATTCC CATTCC CATTCC CATTCC TATTTC CATT
1 CATTCC CATTCC CATTCC CATTCC CATTCC CATTCC CATT
157135 TTTGGAAACC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
6 30 1.00
ACGTcount: A:0.17, C:0.40, G:0.00, T:0.42
Consensus pattern (6 bp):
CATTCC
Found at i:164078 original size:26 final size:25
Alignment explanation
Indices: 164037--164086 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 25
164027 CTGGAACATA
164037 CATCCTTCCCATAAATCAAAGTTTGC
1 CATCCTTCCCATAAAT-AAAGTTTGC
*
164063 CATCCTTTCCCA-AAATGAAGTTTG
1 CATCC-TTCCCATAAATAAAGTTTG
164087 TAGTATCTCT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
25 7 0.32
26 9 0.41
27 6 0.27
ACGTcount: A:0.30, C:0.28, G:0.10, T:0.32
Consensus pattern (25 bp):
CATCCTTCCCATAAATAAAGTTTGC
Found at i:164202 original size:28 final size:28
Alignment explanation
Indices: 164162--164217 Score: 112
Period size: 28 Copynumber: 2.0 Consensus size: 28
164152 AAAATATGAG
164162 AAAGAAAGGAAGGTTGGGCAGTCAATTT
1 AAAGAAAGGAAGGTTGGGCAGTCAATTT
164190 AAAGAAAGGAAGGTTGGGCAGTCAATTT
1 AAAGAAAGGAAGGTTGGGCAGTCAATTT
164218 TACAAGCAGC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.39, C:0.07, G:0.32, T:0.21
Consensus pattern (28 bp):
AAAGAAAGGAAGGTTGGGCAGTCAATTT
Found at i:179041 original size:77 final size:77
Alignment explanation
Indices: 178950--179105 Score: 233
Period size: 77 Copynumber: 2.0 Consensus size: 77
178940 TCATTTGTGC
* * *
178950 ATGGCAAGACTCAAATATAGACTATGAAAGTTACG-GGGCCTTAACCTTGTAAACACAACTAATG
1 ATGGCAAGACTCAAACATAGACTATGAAAGTT-CGAGGGCCTTAACCTTGTAAACACAACCAAGG
179014 CATCATTGATAAA
65 CATCATTGATAAA
* * * *
179027 ATGGCGAGCCTCAAACATAGACTATGGAAGTTTGAGGGCCTTAACCTTGTAAACACAACCAAGGC
1 ATGGCAAGACTCAAACATAGACTATGAAAGTTCGAGGGCCTTAACCTTGTAAACACAACCAAGGC
179092 ATCATTGATAAA
66 ATCATTGATAAA
179104 AT
1 AT
179106 TAAATTATAT
Statistics
Matches: 71, Mismatches: 7, Indels: 2
0.89 0.09 0.03
Matches are distributed among these distances:
76 1 0.01
77 70 0.99
ACGTcount: A:0.38, C:0.19, G:0.19, T:0.24
Consensus pattern (77 bp):
ATGGCAAGACTCAAACATAGACTATGAAAGTTCGAGGGCCTTAACCTTGTAAACACAACCAAGGC
ATCATTGATAAA
Found at i:183621 original size:3 final size:3
Alignment explanation
Indices: 183613--183642 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
183603 AGTTTCAACT
183613 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA
1 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA
183643 GATTTCAACA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.33, G:0.00, T:0.33
Consensus pattern (3 bp):
TCA
Found at i:185558 original size:7 final size:7
Alignment explanation
Indices: 185546--185588 Score: 50
Period size: 7 Copynumber: 6.1 Consensus size: 7
185536 TTTAAGAAGG
185546 TCCCAAC
1 TCCCAAC
185553 TCCCAAC
1 TCCCAAC
*
185560 TCTCAAC
1 TCCCAAC
*
185567 TCTCAAC
1 TCCCAAC
*
185574 TCTCAAC
1 TCCCAAC
*
185581 CCCCAAC
1 TCCCAAC
185588 T
1 T
185589 TATATTTTAT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
7 32 1.00
ACGTcount: A:0.28, C:0.51, G:0.00, T:0.21
Consensus pattern (7 bp):
TCCCAAC
Found at i:185568 original size:14 final size:14
Alignment explanation
Indices: 185549--185588 Score: 62
Period size: 14 Copynumber: 2.9 Consensus size: 14
185539 AAGAAGGTCC
185549 CAACTCCCAACTCT
1 CAACTCCCAACTCT
*
185563 CAACTCTCAACTCT
1 CAACTCCCAACTCT
*
185577 CAACCCCCAACT
1 CAACTCCCAACT
185589 TATATTTTAT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.30, C:0.50, G:0.00, T:0.20
Consensus pattern (14 bp):
CAACTCCCAACTCT
Found at i:185823 original size:16 final size:16
Alignment explanation
Indices: 185773--185823 Score: 50
Period size: 16 Copynumber: 3.2 Consensus size: 16
185763 TGGTTGGGAG
*
185773 AATGGAATAAAGCTGT
1 AATGGAATAGAGCTGT
* *
185789 AATGGAATATGA-TTAT
1 AATGGAATA-GAGCTGT
*
185805 AATTGAATAGAGCTGT
1 AATGGAATAGAGCTGT
185821 AAT
1 AAT
185824 AGTAGTGATC
Statistics
Matches: 27, Mismatches: 6, Indels: 4
0.73 0.16 0.11
Matches are distributed among these distances:
15 2 0.07
16 24 0.89
17 1 0.04
ACGTcount: A:0.43, C:0.04, G:0.22, T:0.31
Consensus pattern (16 bp):
AATGGAATAGAGCTGT
Found at i:199005 original size:14 final size:14
Alignment explanation
Indices: 198986--199043 Score: 107
Period size: 14 Copynumber: 4.1 Consensus size: 14
198976 TAGCTCTCTC
198986 TTTTTTTTCACAAT
1 TTTTTTTTCACAAT
199000 TTTTTTTTCACAAT
1 TTTTTTTTCACAAT
*
199014 TTTTTTTTCAAAAT
1 TTTTTTTTCACAAT
199028 TTTTTTTTCACAAT
1 TTTTTTTTCACAAT
199042 TT
1 TT
199044 GATATCCAAT
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 42 1.00
ACGTcount: A:0.22, C:0.12, G:0.00, T:0.66
Consensus pattern (14 bp):
TTTTTTTTCACAAT
Found at i:199058 original size:28 final size:28
Alignment explanation
Indices: 198997--199052 Score: 76
Period size: 28 Copynumber: 2.0 Consensus size: 28
198987 TTTTTTTCAC
** * *
198997 AATTTTTTTTTCACAATTTTTTTTTCAA
1 AATTTTTTTTTCACAATTTGATATCCAA
199025 AATTTTTTTTTCACAATTTGATATCCAA
1 AATTTTTTTTTCACAATTTGATATCCAA
199053 TCTTTTAAGT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.29, C:0.12, G:0.02, T:0.57
Consensus pattern (28 bp):
AATTTTTTTTTCACAATTTGATATCCAA
Found at i:199097 original size:11 final size:11
Alignment explanation
Indices: 199081--199121 Score: 55
Period size: 11 Copynumber: 3.6 Consensus size: 11
199071 AAACTAGTTT
199081 TTTTTTTAGAA
1 TTTTTTTAGAA
*
199092 TTTTTTTTGAA
1 TTTTTTTAGAA
*
199103 TTTTTTTAAAA
1 TTTTTTTAGAA
199114 GTTTTTTT
1 -TTTTTTT
199122 TAAAGAAACT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
11 19 0.73
12 7 0.27
ACGTcount: A:0.22, C:0.00, G:0.07, T:0.71
Consensus pattern (11 bp):
TTTTTTTAGAA
Found at i:199126 original size:12 final size:11
Alignment explanation
Indices: 199080--199125 Score: 56
Period size: 12 Copynumber: 4.0 Consensus size: 11
199070 GAAACTAGTT
199080 TTTTTTTTAGAA
1 TTTTTTTTA-AA
*
199092 TTTTTTTTGAA
1 TTTTTTTTAAA
*
199103 TTTTTTTAAAA
1 TTTTTTTTAAA
199114 GTTTTTTTTAAA
1 -TTTTTTTTAAA
199126 GAAACTACTA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
11 11 0.38
12 18 0.62
ACGTcount: A:0.26, C:0.00, G:0.07, T:0.67
Consensus pattern (11 bp):
TTTTTTTTAAA
Found at i:201680 original size:67 final size:67
Alignment explanation
Indices: 201568--201695 Score: 220
Period size: 67 Copynumber: 1.9 Consensus size: 67
201558 TTCAAGTTAA
201568 AAACCTCCATTAACTAGAAATAAAAAAGGATTCAATGACAAGATTTATATATTTAAACAAAAAAT
1 AAACCTCCATTAACTAGAAATAAAAAAGGATTCAATGACAAGATTTATATATTTAAACAAAAAAT
201633 AG
66 AG
* * * *
201635 AAACCTTCATTTACTGGAAATAAAAAAGGATTCAATGACAGGATTTATATATTTAAACAAA
1 AAACCTCCATTAACTAGAAATAAAAAAGGATTCAATGACAAGATTTATATATTTAAACAAA
201696 GAATTTGTCC
Statistics
Matches: 57, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
67 57 1.00
ACGTcount: A:0.51, C:0.12, G:0.10, T:0.27
Consensus pattern (67 bp):
AAACCTCCATTAACTAGAAATAAAAAAGGATTCAATGACAAGATTTATATATTTAAACAAAAAAT
AG
Found at i:205406 original size:135 final size:134
Alignment explanation
Indices: 205178--205522 Score: 412
Period size: 135 Copynumber: 2.6 Consensus size: 134
205168 CGAAATGAGA
* ** *
205178 AAGACTATAGTTGAAAGATACTATGATACTAAATCGGAATGAATAAGACTATAGTTGAAAGATAC
1 AAGACCATAGTTGAAAGATACTATGGCACTAAATCGGAATGAATAAGACCATAGTTGAAAGATAC
205243 TATGGCACTAAACTGGAAATGTGTAAGACCGTAGTTGAAAGATACTATGGCACTAAA-CTGGAAA
66 TATGGCACTAAACTGGAAATGTGTAAGACCGTAGTTGAAAGATACTATGGCACTAAATCT-GAAA
* **
205307 TGTGT
130 CGAAT
* ** * *
205312 AAGACCGTAGTTGAAAGATACTATGGCACTAAA-CTGGAAATGTGTAAGACCGTGGTTGAAAGAT
1 AAGACCATAGTTGAAAGATACTATGGCACTAAATC-GG-AATGAATAAGACCATAGTTGAAAGAT
* *
205376 ACTATGGCACTAAACTGGAAATGTGTAAGACCGTAGTTGAAAGATACTATGGCATTAAATCTGAT
64 ACTATGGCACTAAACTGGAAATGTGTAAGACCGTAGTTGAAAGATACTATGGCACTAAATCTGAA
205441 ACGAAT
129 ACGAAT
* * * *
205447 AAGACCATAGTTCAAAGATATTATGGCA-TCACAT-GGATAATG-ATCAATACCATAGTTGAAAG
1 AAGACCATAGTTGAAAGATACTATGGCACT-AAATCGG--AATGAAT-AAGACCATAGTTGAAAG
* *
205509 ATACTGTGACACTA
62 ATACTATGGCACTA
205523 CTTCGGAAAT
Statistics
Matches: 179, Mismatches: 25, Indels: 13
0.82 0.12 0.06
Matches are distributed among these distances:
133 1 0.01
134 35 0.20
135 141 0.79
136 2 0.01
ACGTcount: A:0.40, C:0.13, G:0.21, T:0.26
Consensus pattern (134 bp):
AAGACCATAGTTGAAAGATACTATGGCACTAAATCGGAATGAATAAGACCATAGTTGAAAGATAC
TATGGCACTAAACTGGAAATGTGTAAGACCGTAGTTGAAAGATACTATGGCACTAAATCTGAAAC
GAAT
Found at i:205475 original size:45 final size:45
Alignment explanation
Indices: 205185--205474 Score: 406
Period size: 45 Copynumber: 6.5 Consensus size: 45
205175 AGAAAGACTA
** ** **
205185 TAGTTGAAAGATACTATGATACTAAA-TCGG-AATGAATAAGACTA
1 TAGTTGAAAGATACTATGGCACTAAACT-GGAAATGTGTAAGACCG
205229 TAGTTGAAAGATACTATGGCACTAAACTGGAAATGTGTAAGACCG
1 TAGTTGAAAGATACTATGGCACTAAACTGGAAATGTGTAAGACCG
205274 TAGTTGAAAGATACTATGGCACTAAACTGGAAATGTGTAAGACCG
1 TAGTTGAAAGATACTATGGCACTAAACTGGAAATGTGTAAGACCG
205319 TAGTTGAAAGATACTATGGCACTAAACTGGAAATGTGTAAGACCG
1 TAGTTGAAAGATACTATGGCACTAAACTGGAAATGTGTAAGACCG
*
205364 TGGTTGAAAGATACTATGGCACTAAACTGGAAATGTGTAAGACCG
1 TAGTTGAAAGATACTATGGCACTAAACTGGAAATGTGTAAGACCG
* * * ** *
205409 TAGTTGAAAGATACTATGGCATTAAATCT-GATACGAATAAGACCA
1 TAGTTGAAAGATACTATGGCACTAAA-CTGGAAATGTGTAAGACCG
* *
205454 TAGTTCAAAGATATTATGGCA
1 TAGTTGAAAGATACTATGGCA
205475 TCACATGGAT
Statistics
Matches: 227, Mismatches: 16, Indels: 5
0.92 0.06 0.02
Matches are distributed among these distances:
44 26 0.11
45 199 0.88
46 2 0.01
ACGTcount: A:0.39, C:0.12, G:0.22, T:0.26
Consensus pattern (45 bp):
TAGTTGAAAGATACTATGGCACTAAACTGGAAATGTGTAAGACCG
Found at i:205503 original size:90 final size:90
Alignment explanation
Indices: 205185--205522 Score: 400
Period size: 90 Copynumber: 3.8 Consensus size: 90
205175 AGAAAGACTA
** ** *
205185 TAGTTGAAAGATACTATGATACTAAA-TCGG-AATGAATAAGACTATAGTTGAAAGATACTATGG
1 TAGTTGAAAGATACTATGGCACTAAACT-GGAAATGTGTAAGACCATAGTTGAAAGATACTATGG
205248 CACTAAACTGGAAATGTGTAAGACCG
65 CACTAAACTGGAAATGTGTAAGACCG
*
205274 TAGTTGAAAGATACTATGGCACTAAACTGGAAATGTGTAAGACCGTAGTTGAAAGATACTATGGC
1 TAGTTGAAAGATACTATGGCACTAAACTGGAAATGTGTAAGACCATAGTTGAAAGATACTATGGC
205339 ACTAAACTGGAAATGTGTAAGACCG
66 ACTAAACTGGAAATGTGTAAGACCG
* *
205364 TGGTTGAAAGATACTATGGCACTAAACTGGAAATGTGTAAGACCGTAGTTGAAAGATACTATGGC
1 TAGTTGAAAGATACTATGGCACTAAACTGGAAATGTGTAAGACCATAGTTGAAAGATACTATGGC
* * * ** *
205429 ATTAAATCT-GATACGAATAAGACCA
66 ACTAAA-CTGGAAATGTGTAAGACCG
* * * * * *
205454 TAGTTCAAAGATATTATGGCA-T-CACATGGATAATGAT-CAATACCATAGTTGAAAGATACTGT
1 TAGTTGAAAGATACTATGGCACTAAAC-TGGA-AATG-TGTAAGACCATAGTTGAAAGATACTAT
*
205516 GACACTA
63 GGCACTA
205523 CTTCGGAAAT
Statistics
Matches: 220, Mismatches: 23, Indels: 11
0.87 0.09 0.04
Matches are distributed among these distances:
88 2 0.01
89 31 0.14
90 184 0.84
91 3 0.01
ACGTcount: A:0.39, C:0.13, G:0.22, T:0.26
Consensus pattern (90 bp):
TAGTTGAAAGATACTATGGCACTAAACTGGAAATGTGTAAGACCATAGTTGAAAGATACTATGGC
ACTAAACTGGAAATGTGTAAGACCG
Found at i:205544 original size:45 final size:44
Alignment explanation
Indices: 205178--205549 Score: 358
Period size: 45 Copynumber: 8.3 Consensus size: 44
205168 CGAAATGAGA
* ** * *
205178 AAGACTATAGTTGAAAGATACTATGATACTAAATCGG-AATGAAT
1 AAGACCATAGTTGAAAGATACTATGGCACTAACT-GGAAATGTAT
* *
205222 AAGACTATAGTTGAAAGATACTATGGCACTAAACTGGAAATGTGT
1 AAGACCATAGTTGAAAGATACTATGGCACT-AACTGGAAATGTAT
* *
205267 AAGACCGTAGTTGAAAGATACTATGGCACTAAACTGGAAATGTGT
1 AAGACCATAGTTGAAAGATACTATGGCACT-AACTGGAAATGTAT
* *
205312 AAGACCGTAGTTGAAAGATACTATGGCACTAAACTGGAAATGTGT
1 AAGACCATAGTTGAAAGATACTATGGCACT-AACTGGAAATGTAT
* * *
205357 AAGACCGTGGTTGAAAGATACTATGGCACTAAACTGGAAATGTGT
1 AAGACCATAGTTGAAAGATACTATGGCACT-AACTGGAAATGTAT
* * * * *
205402 AAGACCGTAGTTGAAAGATACTATGGCATTAAATCT-GATACGAAT
1 AAGACCATAGTTGAAAGATACTATGGCACT-AA-CTGGAAATGTAT
* * *
205447 AAGACCATAGTTCAAAGATATTATGGCA-TCACATGGATAATG-AT
1 AAGACCATAGTTGAAAGATACTATGGCACTAAC-TGGA-AATGTAT
* * * *
205491 CAATACCATAGTTGAAAGATACTGTGACACT-ACTTCGGAAATGCAT
1 -AAGACCATAGTTGAAAGATACTATGGCACTAAC-T-GGAAATGTAT
*
205537 AAGACCATGGTTG
1 AAGACCATAGTTG
205550 GAATATATCA
Statistics
Matches: 290, Mismatches: 28, Indels: 19
0.86 0.08 0.06
Matches are distributed among these distances:
42 1 0.00
43 2 0.01
44 35 0.12
45 244 0.84
46 8 0.03
ACGTcount: A:0.39, C:0.13, G:0.22, T:0.26
Consensus pattern (44 bp):
AAGACCATAGTTGAAAGATACTATGGCACTAACTGGAAATGTAT
Found at i:211774 original size:25 final size:25
Alignment explanation
Indices: 211742--211791 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
211732 ATCTTCTTTA
211742 CTTAGATTCTTCCATTTTCTTTTGT
1 CTTAGATTCTTCCATTTTCTTTTGT
211767 CTTAGATTCTTCCATTTTCTTTTGT
1 CTTAGATTCTTCCATTTTCTTTTGT
211792 TTTTCTATCT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.12, C:0.20, G:0.08, T:0.60
Consensus pattern (25 bp):
CTTAGATTCTTCCATTTTCTTTTGT
Found at i:213802 original size:19 final size:19
Alignment explanation
Indices: 213766--213802 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
213756 CACATGTCAT
*
213766 GTATCACTATCTAGTCCAC
1 GTATCACTATCTAATCCAC
*
213785 GTATCACTATTTAATCCA
1 GTATCACTATCTAATCCA
213803 TGTTAGTTTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.30, C:0.27, G:0.08, T:0.35
Consensus pattern (19 bp):
GTATCACTATCTAATCCAC
Found at i:214214 original size:21 final size:20
Alignment explanation
Indices: 214185--214225 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 20
214175 ACATATGAAA
*
214185 TATAAATTTGGAATATAATTT
1 TATAAATTTGAAATA-AATTT
*
214206 TATATATTTGAAATAAATTT
1 TATAAATTTGAAATAAATTT
214226 CAATAACAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.44, C:0.00, G:0.07, T:0.49
Consensus pattern (20 bp):
TATAAATTTGAAATAAATTT
Found at i:214265 original size:15 final size:16
Alignment explanation
Indices: 214233--214265 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
214223 TTTCAATAAC
214233 AAATATACTTAATATA
1 AAATATACTTAATATA
*
214249 AAATATA-TTAGTATA
1 AAATATACTTAATATA
214264 AA
1 AA
214266 TAAAGATTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 9 0.56
16 7 0.44
ACGTcount: A:0.58, C:0.03, G:0.03, T:0.36
Consensus pattern (16 bp):
AAATATACTTAATATA
Found at i:217280 original size:42 final size:43
Alignment explanation
Indices: 217133--217341 Score: 241
Period size: 43 Copynumber: 4.9 Consensus size: 43
217123 TAATTGTTAC
* *
217133 ACGGTGGAATCAGCACTTAGCAACCACC-TTAAAATCAATGAT
1 ACGGTGGAATCAGCACTTAGCAACCACCTTTACATTCAATGAT
* * *
217175 ACGG-GGAATCAGCACATAGCAACC-CCTTTCACAGTCAAGGAT
1 ACGGTGGAATCAGCACTTAGCAACCACCTTT-ACATTCAATGAT
* *
217217 ACGGTGGAATCAGCACTTAGCAACCACCGTTATATTCAATGAT
1 ACGGTGGAATCAGCACTTAGCAACCACCTTTACATTCAATGAT
* * *
217260 GCGG-GGAATCAGCACATAGCAACC-CCTTTCACAGTT-AAGGAT
1 ACGGTGGAATCAGCACTTAGCAACCACCTTT-ACA-TTCAATGAT
* *
217302 ATGGTGGAATCAGCACTTAGCAACCACCTTTATATTCAAT
1 ACGGTGGAATCAGCACTTAGCAACCACCTTTACATTCAAT
217342 TATGCAGATT
Statistics
Matches: 139, Mismatches: 19, Indels: 17
0.79 0.11 0.10
Matches are distributed among these distances:
40 2 0.01
41 25 0.18
42 47 0.34
43 56 0.40
44 9 0.06
ACGTcount: A:0.33, C:0.25, G:0.19, T:0.22
Consensus pattern (43 bp):
ACGGTGGAATCAGCACTTAGCAACCACCTTTACATTCAATGAT
Found at i:217280 original size:85 final size:84
Alignment explanation
Indices: 217133--217346 Score: 356
Period size: 85 Copynumber: 2.5 Consensus size: 84
217123 TAATTGTTAC
* * *
217133 ACGGTGGAATCAGCACTTAGCAACCACCTTAAAATCAATGATACGGGGAATCAGCACATAGCAAC
1 ACGGTGGAATCAGCACTTAGCAACCACCTTATATTCAATGATGCGGGGAATCAGCACATAGCAAC
217198 CCCTTTCACAGTCAAGGAT
66 CCCTTTCACAGTCAAGGAT
217217 ACGGTGGAATCAGCACTTAGCAACCACCGTTATATTCAATGATGCGGGGAATCAGCACATAGCAA
1 ACGGTGGAATCAGCACTTAGCAACCACC-TTATATTCAATGATGCGGGGAATCAGCACATAGCAA
*
217282 CCCCTTTCACAGTTAAGGAT
65 CCCCTTTCACAGTCAAGGAT
* *
217302 ATGGTGGAATCAGCACTTAGCAACCACCTTTATATTCAATTATGC
1 ACGGTGGAATCAGCACTTAGCAACCACC-TTATATTCAATGATGC
217347 AGATTCACAT
Statistics
Matches: 122, Mismatches: 7, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
84 28 0.23
85 94 0.77
ACGTcount: A:0.33, C:0.25, G:0.19, T:0.23
Consensus pattern (84 bp):
ACGGTGGAATCAGCACTTAGCAACCACCTTATATTCAATGATGCGGGGAATCAGCACATAGCAAC
CCCTTTCACAGTCAAGGAT
Found at i:217432 original size:51 final size:51
Alignment explanation
Indices: 217356--217546 Score: 246
Period size: 51 Copynumber: 3.8 Consensus size: 51
217346 CAGATTCACA
* *
217356 TAGTAGCATGCACATAGTACTACACATGTGACCATCACTATCCGGTACACG
1 TAGTAGCCTGCACATAGTACTACACACGTGACCATCACTATCCGGTACACG
* * *
217407 TAGTAGCCTGCACATAGTACTACACACGTGATCGA--AGCTATCCGGTACGCA
1 TAGTAGCCTGCACATAGTACTACACACGTGA-CCATCA-CTATCCGGTACACG
* * *
217458 TAGTAGCCTGCACATAGTACTACACATGCGACCTATCA-T-TCTGGTACACG
1 TAGTAGCCTGCACATAGTACTACACACGTGACC-ATCACTATCCGGTACACG
*
217508 TAGTAGCCTACACATAGTACTACACACGTGACCATCACT
1 TAGTAGCCTGCACATAGTACTACACACGTGACCATCACT
217547 TTCACTTTCA
Statistics
Matches: 120, Mismatches: 14, Indels: 13
0.82 0.10 0.09
Matches are distributed among these distances:
49 4 0.03
50 41 0.34
51 72 0.60
52 2 0.02
53 1 0.01
ACGTcount: A:0.30, C:0.28, G:0.18, T:0.24
Consensus pattern (51 bp):
TAGTAGCCTGCACATAGTACTACACACGTGACCATCACTATCCGGTACACG
Found at i:217530 original size:101 final size:102
Alignment explanation
Indices: 217354--217538 Score: 311
Period size: 101 Copynumber: 1.8 Consensus size: 102
217344 TGCAGATTCA
* *
217354 CATAGTAGCATGCACATAGTACTACACATGTGACCATCACTATCCGGTACACGTAGTAGCCTGCA
1 CATAGTAGCATGCACATAGTACTACACATGCGACCATCACTATCCGGTACACGTAGTAGCCTACA
217419 CATAGTACTACACACGTGATCGAAGCTATCCGGTACG
66 CATAGTACTACACACGTGATCGAAGCTATCCGGTACG
* *
217456 CATAGTAGCCTGCACATAGTACTACACATGCGACCTATCA-T-TCTGGTACACGTAGTAGCCTAC
1 CATAGTAGCATGCACATAGTACTACACATGCGACC-ATCACTATCCGGTACACGTAGTAGCCTAC
217519 ACATAGTACTACACACGTGA
65 ACATAGTACTACACACGTGA
217539 CCATCACTTT
Statistics
Matches: 78, Mismatches: 4, Indels: 3
0.92 0.05 0.04
Matches are distributed among these distances:
101 40 0.51
102 34 0.44
103 4 0.05
ACGTcount: A:0.31, C:0.28, G:0.18, T:0.23
Consensus pattern (102 bp):
CATAGTAGCATGCACATAGTACTACACATGCGACCATCACTATCCGGTACACGTAGTAGCCTACA
CATAGTACTACACACGTGATCGAAGCTATCCGGTACG
Found at i:222189 original size:42 final size:43
Alignment explanation
Indices: 222143--222249 Score: 148
Period size: 42 Copynumber: 2.5 Consensus size: 43
222133 TGGAAACCTG
*
222143 TAAGGGTTAAACGGAAGCTCATAAA-AGCTGAAC-GAAAACCCA
1 TAAGGGTTAAACTGAAGCTCATAAATAGCTGAACTG-AAACCCA
*
222185 TAAGGGTTAAATTGAAGCTCA-AAATAGCTGAACTGAAACCCA
1 TAAGGGTTAAACTGAAGCTCATAAATAGCTGAACTGAAACCCA
* *
222227 GAAGGGTTAAACTGAAACTCATA
1 TAAGGGTTAAACTGAAGCTCATA
222250 TGAGATAACT
Statistics
Matches: 57, Mismatches: 5, Indels: 5
0.85 0.07 0.07
Matches are distributed among these distances:
41 3 0.05
42 52 0.91
43 2 0.04
ACGTcount: A:0.44, C:0.17, G:0.21, T:0.19
Consensus pattern (43 bp):
TAAGGGTTAAACTGAAGCTCATAAATAGCTGAACTGAAACCCA
Found at i:222261 original size:20 final size:20
Alignment explanation
Indices: 222236--222277 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
222226 AGAAGGGTTA
222236 AACTGAAACTCAT-ATGAGAT
1 AACTGAAACTCATGA-GAGAT
*
222256 AACTGAAGCTCATGAGAGAT
1 AACTGAAACTCATGAGAGAT
222276 AA
1 AA
222278 ACGGAAAGCA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 19 0.95
21 1 0.05
ACGTcount: A:0.45, C:0.14, G:0.19, T:0.21
Consensus pattern (20 bp):
AACTGAAACTCATGAGAGAT
Found at i:224677 original size:20 final size:20
Alignment explanation
Indices: 224644--224693 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 20
224634 GTTGATGAGA
* * *
224644 AAAAAATAATTATAAGTTAT
1 AAAAATTAAATATAAATTAT
*
224664 AAAAATTAAATATAAATTTT
1 AAAAATTAAATATAAATTAT
*
224684 AAAAGTTAAA
1 AAAAATTAAA
224694 AAAAAAAGTA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.62, C:0.00, G:0.04, T:0.34
Consensus pattern (20 bp):
AAAAATTAAATATAAATTAT
Found at i:231602 original size:29 final size:30
Alignment explanation
Indices: 231560--231631 Score: 103
Period size: 29 Copynumber: 2.4 Consensus size: 30
231550 ATTAAGAATA
* *
231560 CAATCAATTAAGCCCTTAATTGTAAA-TT-G
1 CAATCAATTGAGCCATTAATTG-AAAGTTGG
231589 CAATCAATTGAGCCATTAATTGAAAGTTGG
1 CAATCAATTGAGCCATTAATTGAAAGTTGG
231619 CAATCAATTGAGC
1 CAATCAATTGAGC
231632 TCCTAAAATA
Statistics
Matches: 39, Mismatches: 2, Indels: 3
0.89 0.05 0.07
Matches are distributed among these distances:
28 3 0.08
29 22 0.56
30 14 0.36
ACGTcount: A:0.38, C:0.17, G:0.15, T:0.31
Consensus pattern (30 bp):
CAATCAATTGAGCCATTAATTGAAAGTTGG
Found at i:233681 original size:85 final size:86
Alignment explanation
Indices: 233538--233698 Score: 254
Period size: 85 Copynumber: 1.9 Consensus size: 86
233528 AGATAAAAAC
* *
233538 ATTTGCAGTTACTGCCACTTGTTGTGAGTGCACAACATGGTTTCAGATTAAACAAACTGCCACTG
1 ATTTGCAGTTACTGCCACTTGTTGTGAGTGCACAACATGATTGCAGATTAAACAAACTGCCACTG
233603 GG-TTTGTGGACGAACCACAT
66 GGTTTTGTGGACGAACCACAT
* * *
233623 ATTTGCAGTTATTGTCACTTGTTGTGAGTGCACAACAT-ATTCGCAGATTAAACAAACTGTCACT
1 ATTTGCAGTTACTGCCACTTGTTGTGAGTGCACAACATGATT-GCAGATTAAACAAACTGCCACT
233687 GGGTTTTGTGGA
65 GGGTTTTGTGGA
233699 TGGGCAACCA
Statistics
Matches: 69, Mismatches: 5, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
84 2 0.03
85 59 0.86
86 8 0.12
ACGTcount: A:0.27, C:0.19, G:0.22, T:0.32
Consensus pattern (86 bp):
ATTTGCAGTTACTGCCACTTGTTGTGAGTGCACAACATGATTGCAGATTAAACAAACTGCCACTG
GGTTTTGTGGACGAACCACAT
Found at i:237026 original size:21 final size:21
Alignment explanation
Indices: 237002--237044 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
236992 AAATCCCAAA
237002 TTTTCTTCCTTTCCTTCCCTT
1 TTTTCTTCCTTTCCTTCCCTT
* * * *
237023 TTTTTTTCTTTTTCTTTCCTT
1 TTTTCTTCCTTTCCTTCCCTT
237044 T
1 T
237045 CCTTCTTTCC
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (21 bp):
TTTTCTTCCTTTCCTTCCCTT
Found at i:241748 original size:18 final size:19
Alignment explanation
Indices: 241722--241758 Score: 51
Period size: 18 Copynumber: 2.0 Consensus size: 19
241712 TTATTATATC
241722 TTATCATTTT-TTAGATTAA
1 TTATCATTTTATT-GATTAA
241741 TTAT-ATTTTATTGATTAA
1 TTATCATTTTATTGATTAA
241759 ATACTATAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
18 11 0.65
19 6 0.35
ACGTcount: A:0.32, C:0.03, G:0.05, T:0.59
Consensus pattern (19 bp):
TTATCATTTTATTGATTAA
Found at i:242018 original size:24 final size:26
Alignment explanation
Indices: 241966--242031 Score: 72
Period size: 24 Copynumber: 2.7 Consensus size: 26
241956 TATAGAGGTA
241966 AACAT-AGTAATAAATAATTTATAAT
1 AACATAAGTAATAAATAATTTATAAT
241991 -ACATAAGTAA-AAAT-A-TTATGAAT
1 AACATAAGTAATAAATAATTTAT-AAT
*
242014 AACATAA-AAATAAATAAT
1 AACATAAGTAATAAATAAT
242032 GATAATAGTA
Statistics
Matches: 34, Mismatches: 1, Indels: 11
0.74 0.02 0.24
Matches are distributed among these distances:
22 4 0.12
23 6 0.18
24 18 0.53
25 6 0.18
ACGTcount: A:0.61, C:0.05, G:0.05, T:0.30
Consensus pattern (26 bp):
AACATAAGTAATAAATAATTTATAAT
Found at i:244844 original size:20 final size:20
Alignment explanation
Indices: 244816--244860 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
244806 ATATATTTAC
*
244816 ATTATTTTAATTTAATATTT
1 ATTAATTTAATTTAATATTT
* **
244836 ATTAATTTAGTTTTTTATTT
1 ATTAATTTAATTTAATATTT
244856 ATTAA
1 ATTAA
244861 AATATTACAT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.64
Consensus pattern (20 bp):
ATTAATTTAATTTAATATTT
Found at i:247490 original size:25 final size:25
Alignment explanation
Indices: 247462--247532 Score: 97
Period size: 25 Copynumber: 2.8 Consensus size: 25
247452 CTCTTCCGAG
247462 CTGAATAACGGGAAGCTCATACGAC
1 CTGAATAACGGGAAGCTCATACGAC
* * * *
247487 CTGAGTAACAGGAAGCTCATGCGAG
1 CTGAATAACGGGAAGCTCATACGAC
*
247512 CTGTATAACGGGAAGCTCATA
1 CTGAATAACGGGAAGCTCATA
247533 TAAGTTGTGG
Statistics
Matches: 38, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 38 1.00
ACGTcount: A:0.34, C:0.21, G:0.27, T:0.18
Consensus pattern (25 bp):
CTGAATAACGGGAAGCTCATACGAC
Found at i:247867 original size:15 final size:16
Alignment explanation
Indices: 247847--247876 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
247837 CGAATGAATT
247847 TAACTCA-ATTCAATA
1 TAACTCATATTCAATA
247862 TAACTCATATTCAAT
1 TAACTCATATTCAAT
247877 TTAGTCCAAC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.43, C:0.20, G:0.00, T:0.37
Consensus pattern (16 bp):
TAACTCATATTCAATA
Found at i:251966 original size:17 final size:17
Alignment explanation
Indices: 251940--251979 Score: 71
Period size: 17 Copynumber: 2.4 Consensus size: 17
251930 TCGTACGCTC
*
251940 AATTAAGGCTCAAATTT
1 AATTACGGCTCAAATTT
251957 AATTACGGCTCAAATTT
1 AATTACGGCTCAAATTT
251974 AATTAC
1 AATTAC
251980 ATTTCATAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.40, C:0.15, G:0.10, T:0.35
Consensus pattern (17 bp):
AATTACGGCTCAAATTT
Found at i:252193 original size:15 final size:18
Alignment explanation
Indices: 252156--252196 Score: 52
Period size: 19 Copynumber: 2.4 Consensus size: 18
252146 TGTTTAACTT
252156 TTAATTAATCATAATTAAC
1 TTAATTAATCAT-ATTAAC
252175 TTAATTAATC-T-TTAA-
1 TTAATTAATCATATTAAC
252190 TTAATTA
1 TTAATTA
252197 GTTTTTAATC
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
15 7 0.32
16 4 0.18
18 1 0.05
19 10 0.45
ACGTcount: A:0.44, C:0.07, G:0.00, T:0.49
Consensus pattern (18 bp):
TTAATTAATCATATTAAC
Found at i:256849 original size:5 final size:5
Alignment explanation
Indices: 256839--256871 Score: 66
Period size: 5 Copynumber: 6.6 Consensus size: 5
256829 ATCTTGTAAA
256839 GATTT GATTT GATTT GATTT GATTT GATTT GAT
1 GATTT GATTT GATTT GATTT GATTT GATTT GAT
256872 GTAATCTTGT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 28 1.00
ACGTcount: A:0.21, C:0.00, G:0.21, T:0.58
Consensus pattern (5 bp):
GATTT
Found at i:257533 original size:17 final size:18
Alignment explanation
Indices: 257501--257534 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
257491 TCAAAAAATT
257501 ATTTAAAAAATAATAAAG
1 ATTTAAAAAATAATAAAG
257519 ATTTAAAAAAT-ATAAA
1 ATTTAAAAAATAATAAA
257535 AAATTAATTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.68, C:0.00, G:0.03, T:0.29
Consensus pattern (18 bp):
ATTTAAAAAATAATAAAG
Found at i:257541 original size:17 final size:18
Alignment explanation
Indices: 257503--257541 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 18
257493 AAAAAATTAT
* *
257503 TTAAAAAATAATAAAGAT
1 TTAAAAAATAATAAAAAA
257521 TTAAAAAAT-ATAAAAAA
1 TTAAAAAATAATAAAAAA
257538 TTAA
1 TTAA
257542 TTAATTACTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 10 0.53
18 9 0.47
ACGTcount: A:0.69, C:0.00, G:0.03, T:0.28
Consensus pattern (18 bp):
TTAAAAAATAATAAAAAA
Found at i:261637 original size:19 final size:19
Alignment explanation
Indices: 261613--261650 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
261603 TATAGAGTGG
261613 TGATGGATTCAATAACATC
1 TGATGGATTCAATAACATC
*
261632 TGATGGATTTAATAACATC
1 TGATGGATTCAATAACATC
261651 CACTCTCGCC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.37, C:0.13, G:0.16, T:0.34
Consensus pattern (19 bp):
TGATGGATTCAATAACATC
Found at i:264048 original size:16 final size:17
Alignment explanation
Indices: 264032--264067 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 17
264022 AAGGTATTAA
264032 TTATTATAAAATATAATC
1 TTATTATAAAATATAA-C
264050 TTATTATAAAATA-AAC
1 TTATTATAAAATATAAC
264066 TT
1 TT
264068 TGATTGTCAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 3 0.17
17 2 0.11
18 13 0.72
ACGTcount: A:0.50, C:0.06, G:0.00, T:0.44
Consensus pattern (17 bp):
TTATTATAAAATATAAC
Found at i:267073 original size:29 final size:30
Alignment explanation
Indices: 267027--267102 Score: 91
Period size: 29 Copynumber: 2.5 Consensus size: 30
267017 ATATGTGTCA
* *
267027 TCAACAAATAAATTAAAACTTT-TAAAAAT
1 TCAAAAAATAAATAAAAACTTTATAAAAAT
* *
267056 TCAAAAAATATATAAAAAGTTTATAAAAAT
1 TCAAAAAATAAATAAAAACTTTATAAAAAT
*
267086 TCAAAAAAAAAAGTAAA
1 TCAAAAAATAAA-TAAA
267103 TGTAAATGTA
Statistics
Matches: 39, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
29 18 0.46
30 17 0.44
31 4 0.10
ACGTcount: A:0.64, C:0.07, G:0.03, T:0.26
Consensus pattern (30 bp):
TCAAAAAATAAATAAAAACTTTATAAAAAT
Found at i:269981 original size:16 final size:16
Alignment explanation
Indices: 269952--269984 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
269942 TGGTTTTGTC
269952 TATATATTTTAATTTT
1 TATATATTTTAATTTT
*
269968 TATAT-TTTTAAATTT
1 TATATATTTTAATTTT
269983 TA
1 TA
269985 AAATTTCAGT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 11 0.69
16 5 0.31
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (16 bp):
TATATATTTTAATTTT
Found at i:277908 original size:20 final size:18
Alignment explanation
Indices: 277876--277912 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 18
277866 CATTTTTATA
277876 TTTTTTTATATTTCTAAT
1 TTTTTTTATATTTCTAAT
277894 TTTTTTTACTAATTTCTAA
1 TTTTTTTA-T-ATTTCTAA
277913 AATTTTATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 8 0.47
19 1 0.06
20 8 0.47
ACGTcount: A:0.24, C:0.08, G:0.00, T:0.68
Consensus pattern (18 bp):
TTTTTTTATATTTCTAAT
Found at i:278980 original size:17 final size:17
Alignment explanation
Indices: 278958--278991 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
278948 CGTGACCACA
278958 CGTGTGCCACACACGGG
1 CGTGTGCCACACACGGG
*
278975 CGTGTGCCGCACACGGG
1 CGTGTGCCACACACGGG
278992 GGGTTCATAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.15, C:0.35, G:0.38, T:0.12
Consensus pattern (17 bp):
CGTGTGCCACACACGGG
Found at i:281335 original size:30 final size:30
Alignment explanation
Indices: 281286--281343 Score: 73
Period size: 30 Copynumber: 1.9 Consensus size: 30
281276 TGTAGGTATA
* *
281286 AAAATTTTAAATTAAATAAATAATATGGAAG
1 AAAATTTTAAAATAAATAAA-AAAATGGAAG
*
281317 AAAA-TTTAAAATAGATAAAAAAATGGA
1 AAAATTTTAAAATAAATAAAAAAATGGA
281344 GTTAAAAATA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 7 0.29
30 13 0.54
31 4 0.17
ACGTcount: A:0.62, C:0.00, G:0.10, T:0.28
Consensus pattern (30 bp):
AAAATTTTAAAATAAATAAAAAAATGGAAG
Found at i:284048 original size:44 final size:45
Alignment explanation
Indices: 283921--284059 Score: 126
Period size: 45 Copynumber: 3.1 Consensus size: 45
283911 TGAACTAGTG
* * * *
283921 CTTCAATCTACTCCACTGCATCTTCAGTGAGATAAGATTTGCCAT
1 CTTCAGTCTACTCCACTGCAACTTCAGGGAGATAAGACTTGCCAT
* **
283966 CTTCAGTCTAC-CTCACTGCAA-TTCCA-GGAGGATCAGACTTG-TTT
1 CTTCAGTCTACTC-CACTGCAACTT-CAGGGA-GATAAGACTTGCCAT
* *
284010 CATT-AGTCTACTCCACTGCAACTTCAGGGAGATAAGACTTTCAAT
1 C-TTCAGTCTACTCCACTGCAACTTCAGGGAGATAAGACTTGCCAT
284055 CTTCA
1 CTTCA
284060 ATTTATTTCA
Statistics
Matches: 74, Mismatches: 11, Indels: 18
0.72 0.11 0.17
Matches are distributed among these distances:
44 35 0.47
45 39 0.53
ACGTcount: A:0.27, C:0.27, G:0.15, T:0.32
Consensus pattern (45 bp):
CTTCAGTCTACTCCACTGCAACTTCAGGGAGATAAGACTTGCCAT
Found at i:284541 original size:305 final size:306
Alignment explanation
Indices: 284172--284738 Score: 917
Period size: 305 Copynumber: 1.9 Consensus size: 306
284162 TTCTTAGGGA
*
284172 GATAAGACCTACTTACTTAGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTAGATACGATCTG
1 GATAAGACCTACTTACTTAGTCTGCTCCACTGCAACTTCAGGGAGATAAAACTAGATACGATCTG
* *
284237 CTCTCTGCAACTTCAGAGAGTTAAGATCTGAGATTTTAATCCGCTCCACTGCAACTTCAGGGAGA
66 CTCTCTGCAACTTCAGAAAGATAAGATCTGAGATTTTAATCCGCTCCACTGCAACTTCAGGGAGA
284302 TAGGATTGTCGGCTTTAATCTGCTCCACTACAACTTTAGGGAGATAAGATTTGCCATCTTCAGTC
131 TAGGATTGTCGGCTTTAATCTGCTCCACTACAACTTTAGGGAGATAAGATTTGCCATCTTCAGTC
* *
284367 TGCC-CACTACAACTTCAAGGA-GATAGGA-TTGAC-GGCTTTAATCTGCTCCACTGCAACTTCA
196 TGCCTCACTACAACTTC-AGGAGGATAAGACTTG-CTGAC-TTAATCTGCTCCACTGCAACTTCA
284428 GGGAGGTAAGATTTGCCATCTTCAGTCTGCCTCACTGCAACTTCAGGAG
258 GGGAGGTAAGATTTGCCATCTTCAGTCTGCCTCACTGCAACTTCAGGAG
* * *
284477 GATAAGACTTGCTTACTTAGTCTGCTCCACTGCAACTTCAGGGAGATAAAACTAGATGCGATCTG
1 GATAAGACCTACTTACTTAGTCTGCTCCACTGCAACTTCAGGGAGATAAAACTAGATACGATCTG
* * *
284542 CTCTCTGCAACTTTAGAAAGATAAGATCTGAGATTTTAATCCGCTCTACTGTAACTTCAGGGAGA
66 CTCTCTGCAACTTCAGAAAGATAAGATCTGAGATTTTAATCCGCTCCACTGCAACTTCAGGGAGA
* * *
284607 TAGGATTGTCGGTTTTAATCTGCTCCACTGCAACTTTAGGGAGATAAGATTTGCCATTTTCAGTC
131 TAGGATTGTCGGCTTTAATCTGCTCCACTACAACTTTAGGGAGATAAGATTTGCCATCTTCAGTC
* * * *
284672 TGCCTCACTGCAACTTCAGGAGGATAAGACTTGCTTACTTAGTTTGCTCCACTGCAACTTCAGGG
196 TGCCTCACTACAACTTCAGGAGGATAAGACTTGCTGACTTAATCTGCTCCACTGCAACTTCAGGG
284737 AG
261 AG
284739 ATAAAACTAG
Statistics
Matches: 240, Mismatches: 18, Indels: 7
0.91 0.07 0.03
Matches are distributed among these distances:
305 191 0.80
306 45 0.19
307 4 0.02
ACGTcount: A:0.27, C:0.23, G:0.21, T:0.29
Consensus pattern (306 bp):
GATAAGACCTACTTACTTAGTCTGCTCCACTGCAACTTCAGGGAGATAAAACTAGATACGATCTG
CTCTCTGCAACTTCAGAAAGATAAGATCTGAGATTTTAATCCGCTCCACTGCAACTTCAGGGAGA
TAGGATTGTCGGCTTTAATCTGCTCCACTACAACTTTAGGGAGATAAGATTTGCCATCTTCAGTC
TGCCTCACTACAACTTCAGGAGGATAAGACTTGCTGACTTAATCTGCTCCACTGCAACTTCAGGG
AGGTAAGATTTGCCATCTTCAGTCTGCCTCACTGCAACTTCAGGAG
Found at i:284812 original size:44 final size:44
Alignment explanation
Indices: 284192--284830 Score: 336
Period size: 44 Copynumber: 14.8 Consensus size: 44
284182 ACTTACTTAG
* ***
284192 TCTGCTCCACTGCAACTTCAGGGAGATAAGA-CT-AGA-TACGA
1 TCTGCTCCACTGCAACTTCAGGAAGATAAGATCTGAGATTTTAA
* *
284233 TCTGCT-CTCTGCAACTTCA-GAGAGTTAAGATCTGAGATTTTAA
1 TCTGCTCCACTGCAACTTCAGGA-AGATAAGATCTGAGATTTTAA
* * * * **
284276 TCCGCTCCACTGCAACTTCAGGGAGATAGGAT-TGTCGGCTTTAA
1 TCTGCTCCACTGCAACTTCAGGAAGATAAGATCTG-AGATTTTAA
* * * * ** * *
284320 TCTGCTCCACTACAACTTTAGGGAGATAAGATTTGCCATCTTCAG
1 TCTGCTCCACTGCAACTTCAGGAAGATAAGATCTGAGAT-TTTAA
* * **
284365 TCTGC-CCACTACAACTTCAAGG-AGATAGGAT-TGACGGCTTTAA
1 TCTGCTCCACTGCAACTTC-AGGAAGATAAGATCTGA-GATTTTAA
* * * ** * *
284408 TCTGCTCCACTGCAACTTCAGGGAGGTAAGATTTGCCATCTTCAG
1 TCTGCTCCACTGCAACTTCAGGAAGATAAGATCTGAGAT-TTTAA
* * * *
284453 TCTGC-CTCACTGCAACTTCAGGAGGATAAGA-CT-TGCTTACTTAG
1 TCTGCTC-CACTGCAACTTCAGGAAGATAAGATCTGAGATT--TTAA
* * ***
284497 TCTGCTCCACTGCAACTTCAGGGAGATAA-AACT-AGA-TGCGA
1 TCTGCTCCACTGCAACTTCAGGAAGATAAGATCTGAGATTTTAA
* * *
284538 TCTGCT-CTCTGCAACTTTAGAAAGATAAGATCTGAGATTTTAA
1 TCTGCTCCACTGCAACTTCAGGAAGATAAGATCTGAGATTTTAA
* * * * * * *
284581 TCCGCTCTACTGTAACTTCAGGGAGATAGGAT-TGTCGGTTTTAA
1 TCTGCTCCACTGCAACTTCAGGAAGATAAGATCTG-AGATTTTAA
* * * ** *
284625 TCTGCTCCACTGCAACTTTAGGGAGATAAGATTTGCCATTTTCAG
1 TCTGCTCCACTGCAACTTCAGGAAGATAAGATCTGAGATTTT-AA
* * * *
284670 TCTGC-CTCACTGCAACTTCAGGAGGATAAGA-CT-TGCTTACTTAG
1 TCTGCTC-CACTGCAACTTCAGGAAGATAAGATCTGAGATT--TTAA
* * * ***
284714 TTTGCTCCACTGCAACTTCAGGGAGATAA-AACT-AGA-TGCGA
1 TCTGCTCCACTGCAACTTCAGGAAGATAAGATCTGAGATTTTAA
* * *
284755 TCTGCT-CTCTGCAACTTTAGAAAGATAAGATCTGAGATTTTAA
1 TCTGCTCCACTGCAACTTCAGGAAGATAAGATCTGAGATTTTAA
* * *
284798 TCCGCTCCACTGCAACTTCAGGGAGATAGGATC
1 TCTGCTCCACTGCAACTTCAGGAAGATAAGATC
284831 CCGGCCACTA
Statistics
Matches: 449, Mismatches: 113, Indels: 69
0.71 0.18 0.11
Matches are distributed among these distances:
39 1 0.00
40 55 0.12
41 25 0.06
42 10 0.02
43 45 0.10
44 235 0.52
45 78 0.17
ACGTcount: A:0.27, C:0.23, G:0.21, T:0.29
Consensus pattern (44 bp):
TCTGCTCCACTGCAACTTCAGGAAGATAAGATCTGAGATTTTAA
Found at i:284845 original size:217 final size:217
Alignment explanation
Indices: 284370--284829 Score: 830
Period size: 217 Copynumber: 2.1 Consensus size: 217
284360 TTCAGTCTGC
* * *
284370 CCACTACAACTTCAAGGAGATAGGATTGACGGCTTTAATCTGCTCCACTGCAACTTCAGGGAGGT
1 CCACTGCAACTTCAGGGAGATAGGATTGACGGCTTTAATCTGCTCCACTGCAACTTCAGGGAGAT
284435 AAGATTTGCCATCTTCAGTCTGCCTCACTGCAACTTCAGGAGGATAAGACTTGCTTACTTAGTCT
66 AAGATTTGCCATCTTCAGTCTGCCTCACTGCAACTTCAGGAGGATAAGACTTGCTTACTTAGTCT
284500 GCTCCACTGCAACTTCAGGGAGATAAAACTAGATGCGATCTGCTCTCTGCAACTTTAGAAAGATA
131 GCTCCACTGCAACTTCAGGGAGATAAAACTAGATGCGATCTGCTCTCTGCAACTTTAGAAAGATA
284565 AGATCTGAGATTTTAATCCGCT
196 AGATCTGAGATTTTAATCCGCT
* * * * *
284587 CTACTGTAACTTCAGGGAGATAGGATTGTCGGTTTTAATCTGCTCCACTGCAACTTTAGGGAGAT
1 CCACTGCAACTTCAGGGAGATAGGATTGACGGCTTTAATCTGCTCCACTGCAACTTCAGGGAGAT
* *
284652 AAGATTTGCCATTTTCAGTCTGCCTCACTGCAACTTCAGGAGGATAAGACTTGCTTACTTAGTTT
66 AAGATTTGCCATCTTCAGTCTGCCTCACTGCAACTTCAGGAGGATAAGACTTGCTTACTTAGTCT
284717 GCTCCACTGCAACTTCAGGGAGATAAAACTAGATGCGATCTGCTCTCTGCAACTTTAGAAAGATA
131 GCTCCACTGCAACTTCAGGGAGATAAAACTAGATGCGATCTGCTCTCTGCAACTTTAGAAAGATA
284782 AGATCTGAGATTTTAATCCGCT
196 AGATCTGAGATTTTAATCCGCT
284804 CCACTGCAACTTCAGGGAGATAGGAT
1 CCACTGCAACTTCAGGGAGATAGGAT
284830 CCCGGCCACT
Statistics
Matches: 231, Mismatches: 12, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
217 231 1.00
ACGTcount: A:0.28, C:0.22, G:0.21, T:0.29
Consensus pattern (217 bp):
CCACTGCAACTTCAGGGAGATAGGATTGACGGCTTTAATCTGCTCCACTGCAACTTCAGGGAGAT
AAGATTTGCCATCTTCAGTCTGCCTCACTGCAACTTCAGGAGGATAAGACTTGCTTACTTAGTCT
GCTCCACTGCAACTTCAGGGAGATAAAACTAGATGCGATCTGCTCTCTGCAACTTTAGAAAGATA
AGATCTGAGATTTTAATCCGCT
Found at i:298314 original size:22 final size:23
Alignment explanation
Indices: 298281--298339 Score: 77
Period size: 24 Copynumber: 2.6 Consensus size: 23
298271 AGAATGATAC
*
298281 ATGA-AAACTTAAAATAAT-TAT
1 ATGATAAATTTAAAATAATATAT
298302 ATGATAAATTTAAAATAATAATAT
1 ATGATAAATTTAAAATAAT-ATAT
*
298326 GTGATAAATTTAAA
1 ATGATAAATTTAAA
298340 CAACATTCAT
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
21 4 0.12
22 13 0.39
24 16 0.48
ACGTcount: A:0.56, C:0.02, G:0.07, T:0.36
Consensus pattern (23 bp):
ATGATAAATTTAAAATAATATAT
Found at i:299808 original size:164 final size:165
Alignment explanation
Indices: 299526--299854 Score: 651
Period size: 164 Copynumber: 2.0 Consensus size: 165
299516 TGGGTCACTG
299526 TAATATGGACATTTTGGACATTTAATATATTTATTTTTGTTTTTATTATCCATATTGGGTCGGGC
1 TAATATGGACATTTTGGACATTTAATATATTTATTTTTGTTTTTATTATCCATATTGGGTCGGGC
299591 AATATTGGGCTATTACAGTATTTATAGGGACTATGGTATAATTTTAGTATGGGTTTTCGTAAATT
66 AATATTGGGCTATTACAGTATTTATAGGGACTATGGTATAATTTTAGTATGGGTTTTCGTAAATT
299656 GATTTTGGACCGAATTTTAGAAACTGCGGAATTAT
131 GATTTTGGACCGAATTTTAGAAACTGCGGAATTAT
299691 TAATATGGAC-TTTTGGACATTTAATATATTTATTTTTGTTTTTATTATCCATATTGGGTCGGGC
1 TAATATGGACATTTTGGACATTTAATATATTTATTTTTGTTTTTATTATCCATATTGGGTCGGGC
299755 AATATTGGGCTATTACAGTATTTATAGGGACTATGGTATAATTTTAGTATGGGTTTTCGTAAATT
66 AATATTGGGCTATTACAGTATTTATAGGGACTATGGTATAATTTTAGTATGGGTTTTCGTAAATT
299820 GATTTTGGACCGAATTTTAGAAACTGCGGAATTAT
131 GATTTTGGACCGAATTTTAGAAACTGCGGAATTAT
299855 ATTTCCTAAT
Statistics
Matches: 164, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
164 154 0.94
165 10 0.06
ACGTcount: A:0.28, C:0.09, G:0.20, T:0.44
Consensus pattern (165 bp):
TAATATGGACATTTTGGACATTTAATATATTTATTTTTGTTTTTATTATCCATATTGGGTCGGGC
AATATTGGGCTATTACAGTATTTATAGGGACTATGGTATAATTTTAGTATGGGTTTTCGTAAATT
GATTTTGGACCGAATTTTAGAAACTGCGGAATTAT
Found at i:300391 original size:17 final size:18
Alignment explanation
Indices: 300369--300403 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
300359 GTTTTTATAC
*
300369 CTTTTT-AATAATTTTTA
1 CTTTTTAAATAAATTTTA
300386 CTTTTTAAATAAATTTTA
1 CTTTTTAAATAAATTTTA
300404 TAATTTTTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.34, C:0.06, G:0.00, T:0.60
Consensus pattern (18 bp):
CTTTTTAAATAAATTTTA
Found at i:300391 original size:18 final size:20
Alignment explanation
Indices: 300342--300414 Score: 62
Period size: 19 Copynumber: 3.8 Consensus size: 20
300332 ATTAATTAAT
* **
300342 TTTTAAAATTTTTT-ATAGT
1 TTTTATAATTTTTTAATAAA
**
300361 TTTTATACCTTTTTAAT-AA
1 TTTTATAATTTTTTAATAAA
* *
300380 TTTT-TACTTTTTAAATAAA
1 TTTTATAATTTTTTAATAAA
300399 TTTTATAATTTTTTAA
1 TTTTATAATTTTTTAA
300415 ACTTTTAAAT
Statistics
Matches: 42, Mismatches: 9, Indels: 5
0.75 0.16 0.09
Matches are distributed among these distances:
18 10 0.24
19 21 0.50
20 11 0.26
ACGTcount: A:0.33, C:0.04, G:0.01, T:0.62
Consensus pattern (20 bp):
TTTTATAATTTTTTAATAAA
Found at i:316778 original size:14 final size:12
Alignment explanation
Indices: 316759--316802 Score: 52
Period size: 13 Copynumber: 3.4 Consensus size: 12
316749 GCCACAAGGA
316759 AAAAAGAGAGAAAG
1 AAAAAGA-A-AAAG
*
316773 AAAAAGAAAAAA
1 AAAAAGAAAAAG
316785 AGAAAAGAAAAAG
1 A-AAAAGAAAAAG
316798 AAAAA
1 AAAAA
316803 ACAAACACCC
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
12 8 0.30
13 12 0.44
14 7 0.26
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (12 bp):
AAAAAGAAAAAG
Found at i:316780 original size:6 final size:6
Alignment explanation
Indices: 316759--316802 Score: 52
Period size: 6 Copynumber: 6.8 Consensus size: 6
316749 GCCACAAGGA
*
316759 AAAAAG AGAGAAAG AAAAAG AAAAAA AGAAAAG AAAAAG AAAAA
1 AAAAAG A-A-AAAG AAAAAG AAAAAG A-AAAAG AAAAAG AAAAA
316803 ACAAACACCC
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
6 21 0.64
7 7 0.21
8 5 0.15
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (6 bp):
AAAAAG
Found at i:316790 original size:13 final size:14
Alignment explanation
Indices: 316759--316796 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
316749 GCCACAAGGA
* *
316759 AAAAAGAGAGAAAG
1 AAAAAGAAAAAAAG
316773 AAAAAGAAAAAAAG
1 AAAAAGAAAAAAAG
316787 -AAAAGAAAAA
1 AAAAAGAAAAA
316797 GAAAAAACAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
13 10 0.45
14 12 0.55
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (14 bp):
AAAAAGAAAAAAAG
Found at i:316831 original size:9 final size:9
Alignment explanation
Indices: 316817--316842 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
316807 ACACCCAAAG
316817 TTCCTAAAA
1 TTCCTAAAA
316826 TTCCTAAAA
1 TTCCTAAAA
316835 TTCCTAAA
1 TTCCTAAA
316843 CCTTTTTCTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.42, C:0.23, G:0.00, T:0.35
Consensus pattern (9 bp):
TTCCTAAAA
Found at i:326810 original size:20 final size:21
Alignment explanation
Indices: 326777--326816 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
326767 GGCTGGTGGT
*
326777 CAAATTTAACAAAATAAAGTC
1 CAAATTTAACAAAAAAAAGTC
*
326798 CAAA-TTAAGAAAAAAAAGT
1 CAAATTTAACAAAAAAAAGT
326817 AAACGTTGAG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.62, C:0.10, G:0.07, T:0.20
Consensus pattern (21 bp):
CAAATTTAACAAAAAAAAGTC
Found at i:329771 original size:30 final size:32
Alignment explanation
Indices: 329708--329774 Score: 93
Period size: 32 Copynumber: 2.2 Consensus size: 32
329698 TAATTTATGC
**
329708 AAAATAAATATTAAATATATAGTTTATTTTAA
1 AAAATAAATATTAAATATATAGTTTATACTAA
*
329740 AAAATATATATTAAATATATA-TTTA-ACTAA
1 AAAATAAATATTAAATATATAGTTTATACTAA
329770 AAAAT
1 AAAAT
329775 TGCATTCAAC
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
30 8 0.25
31 4 0.12
32 20 0.62
ACGTcount: A:0.57, C:0.01, G:0.01, T:0.40
Consensus pattern (32 bp):
AAAATAAATATTAAATATATAGTTTATACTAA
Found at i:332670 original size:28 final size:28
Alignment explanation
Indices: 332613--332672 Score: 77
Period size: 28 Copynumber: 2.1 Consensus size: 28
332603 TTATGTTATA
*
332613 AAATAATATTATATTAATTATATATGTT
1 AAATAATATTATATTAATTATATATATT
* *
332641 AAATAATATATATATTTA-TATTTATATT
1 AAATAATAT-TATATTAATTATATATATT
332669 AAAT
1 AAAT
332673 TACTAATTCA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
28 21 0.75
29 7 0.25
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (28 bp):
AAATAATATTATATTAATTATATATATT
Found at i:332872 original size:17 final size:17
Alignment explanation
Indices: 332830--332872 Score: 52
Period size: 17 Copynumber: 2.5 Consensus size: 17
332820 AGTGTATTAT
332830 ATATGTAATTTTAAAAAG
1 ATAT-TAATTTTAAAAAG
*
332848 ATAATAATTTTAAATAA-
1 ATATTAATTTTAAA-AAG
332865 ATATTAAT
1 ATATTAAT
332873 CTAAGAAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
17 17 0.77
18 5 0.23
ACGTcount: A:0.53, C:0.00, G:0.05, T:0.42
Consensus pattern (17 bp):
ATATTAATTTTAAAAAG
Found at i:350470 original size:18 final size:17
Alignment explanation
Indices: 350434--350481 Score: 60
Period size: 18 Copynumber: 2.6 Consensus size: 17
350424 AAAATATTTC
350434 TTTTGATAATCAAAAGATA
1 TTTT-ATAAT-AAAAGATA
350453 TTTTATAATAAAATGATA
1 TTTTATAATAAAA-GATA
*
350471 TTTTGTAATAA
1 TTTTATAATAA
350482 TTAGTATCAG
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
17 4 0.15
18 19 0.70
19 4 0.15
ACGTcount: A:0.46, C:0.02, G:0.08, T:0.44
Consensus pattern (17 bp):
TTTTATAATAAAAGATA
Found at i:359120 original size:13 final size:13
Alignment explanation
Indices: 359099--359130 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
359089 GCTTGGATCA
*
359099 TCATCAAATAAAT
1 TCATAAAATAAAT
359112 TCATAAAATAAAT
1 TCATAAAATAAAT
359125 TCATAA
1 TCATAA
359131 TTGCTGGAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.56, C:0.12, G:0.00, T:0.31
Consensus pattern (13 bp):
TCATAAAATAAAT
Found at i:359377 original size:30 final size:30
Alignment explanation
Indices: 359342--359399 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
359332 CCTCGACTCT
*
359342 AACTTTTTCAAAATTACAATTTTGCCCCTA
1 AACTTTTACAAAATTACAATTTTGCCCCTA
* *
359372 AACTTTTACATAATTACATTTTTGCCCC
1 AACTTTTACAAAATTACAATTTTGCCCC
359400 AAGGCTCGGA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.31, C:0.24, G:0.03, T:0.41
Consensus pattern (30 bp):
AACTTTTACAAAATTACAATTTTGCCCCTA
Found at i:360080 original size:13 final size:13
Alignment explanation
Indices: 360062--360096 Score: 61
Period size: 13 Copynumber: 2.7 Consensus size: 13
360052 GCCCAAACGT
360062 CGAAATTTTTGAA
1 CGAAATTTTTGAA
*
360075 CGAAATTTTTTAA
1 CGAAATTTTTGAA
360088 CGAAATTTT
1 CGAAATTTT
360097 CATAAAATCA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.37, C:0.09, G:0.11, T:0.43
Consensus pattern (13 bp):
CGAAATTTTTGAA
Found at i:361860 original size:12 final size:12
Alignment explanation
Indices: 361843--361872 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
361833 TACACTTGCT
361843 GAGTTTAATATA
1 GAGTTTAATATA
361855 GAGTTTAATATA
1 GAGTTTAATATA
*
361867 GCGTTT
1 GAGTTT
361873 CCTTTATCGC
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:0.33, C:0.03, G:0.20, T:0.43
Consensus pattern (12 bp):
GAGTTTAATATA
Found at i:361972 original size:20 final size:20
Alignment explanation
Indices: 361947--361990 Score: 88
Period size: 20 Copynumber: 2.2 Consensus size: 20
361937 TATGGATGAT
361947 TTTTTTCTACTTGGCCCTTC
1 TTTTTTCTACTTGGCCCTTC
361967 TTTTTTCTACTTGGCCCTTC
1 TTTTTTCTACTTGGCCCTTC
361987 TTTT
1 TTTT
361991 GTGTTCTATG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.05, C:0.27, G:0.09, T:0.59
Consensus pattern (20 bp):
TTTTTTCTACTTGGCCCTTC
Done.