Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012572.1 Kokia drynarioides strain JFW-HI SEQ_127581, 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: 420729
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 120 characters in sequence are not A, C, G, or T
File 1 of 2
Found at i:8002 original size:190 final size:190
Alignment explanation
Indices: 7676--8025 Score: 628
Period size: 190 Copynumber: 1.8 Consensus size: 190
7666 ACTCTTTAAG
* *
7676 AAGAGAGACAACTTATGTATAAAAGGTCATTGGTTATATACCTATTGTACAGCTGGAAAATAAGA
1 AAGAGAGACAACTTATGTATAAAAGATCATTGGTTATATACCTATTGTACAACTGGAAAATAAGA
** * *
7741 TTTACTCTCAAAGTTTGTTATTAATAAATGCCATGCATTTGAAGATTTTGGCATATTCCCTTAAG
66 TCCACTCTCAAAGTTTGCTATTAATAAATGCCATGCATTTGAAGATTTTGGCATATTCCCTTAAA
*
7806 CGAATATTGCATATAATTATTTGAAAATTATAAACTTCACATAAGTTGTCTCTCTTCTTA
131 CGAATATTGCATATAATTACTTGAAAATTATAAACTTCACATAAGTTGTCTCTCTTCTTA
*
7866 AAGAGAGACAACTTATGTATAAAAGATCATTGGTTATATACCTATTGTACAATTGGAAAATAAGA
1 AAGAGAGACAACTTATGTATAAAAGATCATTGGTTATATACCTATTGTACAACTGGAAAATAAGA
7931 TCCACTCTCAAAGTTTGCTATTAATAAATGCCATGCATTTGAAGATTTTGGCATATTCCCTTAAA
66 TCCACTCTCAAAGTTTGCTATTAATAAATGCCATGCATTTGAAGATTTTGGCATATTCCCTTAAA
7996 CGAATATTGCATATAATTACTTGAAAATTA
131 CGAATATTGCATATAATTACTTGAAAATTA
8026 AATTATATGA
Statistics
Matches: 152, Mismatches: 8, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
190 152 1.00
ACGTcount: A:0.37, C:0.14, G:0.14, T:0.35
Consensus pattern (190 bp):
AAGAGAGACAACTTATGTATAAAAGATCATTGGTTATATACCTATTGTACAACTGGAAAATAAGA
TCCACTCTCAAAGTTTGCTATTAATAAATGCCATGCATTTGAAGATTTTGGCATATTCCCTTAAA
CGAATATTGCATATAATTACTTGAAAATTATAAACTTCACATAAGTTGTCTCTCTTCTTA
Found at i:11352 original size:18 final size:19
Alignment explanation
Indices: 11318--11353 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
11308 TTATTTTATT
*
11318 TAAATTTAATTATAAAATA
1 TAAATTTAATGATAAAATA
11337 TAAATTTAA-GATAAAAT
1 TAAATTTAATGATAAAAT
11354 TATTTTTTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.39
Consensus pattern (19 bp):
TAAATTTAATGATAAAATA
Found at i:11560 original size:14 final size:14
Alignment explanation
Indices: 11538--11568 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
11528 TTAACTAACT
11538 AATAATTTTTTTTA
1 AATAATTTTTTTTA
*
11552 AATATTTTTTTTTA
1 AATAATTTTTTTTA
11566 AAT
1 AAT
11569 TTGAGGTATG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (14 bp):
AATAATTTTTTTTA
Found at i:13960 original size:7 final size:7
Alignment explanation
Indices: 13948--13974 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
13938 ATCTGCATGT
13948 ATATATA
1 ATATATA
13955 ATATATA
1 ATATATA
13962 ATATATA
1 ATATATA
13969 ATATAT
1 ATATAT
13975 TTAAAAACAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (7 bp):
ATATATA
Found at i:14396 original size:20 final size:20
Alignment explanation
Indices: 14371--14410 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
14361 TTTGATTTTA
*
14371 AATTT-ATTTATAATTATAAT
1 AATTTAATTT-TAACTATAAT
14391 AATTTAATTTTAACTATAAT
1 AATTTAATTTTAACTATAAT
14411 TATTAAAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 14 0.78
21 4 0.22
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.53
Consensus pattern (20 bp):
AATTTAATTTTAACTATAAT
Found at i:24718 original size:25 final size:24
Alignment explanation
Indices: 24690--24737 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 24
24680 ATTAAAAATA
24690 TTAAAAACATT-AAAATAAATATTTC
1 TTAAAAA-ATTAAAAATAAA-ATTTC
*
24715 TTAACAAATTAAAAATAAAATTT
1 TTAAAAAATTAAAAATAAAATTT
24738 TAAAAATATG
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
24 7 0.33
25 14 0.67
ACGTcount: A:0.58, C:0.06, G:0.00, T:0.35
Consensus pattern (24 bp):
TTAAAAAATTAAAAATAAAATTTC
Found at i:24897 original size:19 final size:21
Alignment explanation
Indices: 24875--24922 Score: 55
Period size: 22 Copynumber: 2.3 Consensus size: 21
24865 GTGCAATAGT
24875 AACAAAATAGAA-A-GAAAAC
1 AACAAAATAGAACATGAAAAC
* *
24894 AACAAGAATATAACATTAAAAC
1 AACAA-AATAGAACATGAAAAC
24916 AACAAAA
1 AACAAAA
24923 ATAAATTTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
19 5 0.21
20 6 0.25
21 3 0.12
22 10 0.42
ACGTcount: A:0.71, C:0.12, G:0.06, T:0.10
Consensus pattern (21 bp):
AACAAAATAGAACATGAAAAC
Found at i:25137 original size:13 final size:14
Alignment explanation
Indices: 25121--25167 Score: 55
Period size: 13 Copynumber: 3.5 Consensus size: 14
25111 AAAACTTTCA
25121 ATAAATA-AAAAAT
1 ATAAATATAAAAAT
25134 ATAAA-ATAAAAAT
1 ATAAATATAAAAAT
*
25147 ATTAAATATTAAAAT
1 A-TAAATATAAAAAT
25162 A-AAATA
1 ATAAATA
25168 AATATTTTTT
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
12 1 0.03
13 17 0.57
14 4 0.13
15 8 0.27
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (14 bp):
ATAAATATAAAAAT
Found at i:26116 original size:7 final size:7
Alignment explanation
Indices: 26104--26133 Score: 51
Period size: 7 Copynumber: 4.3 Consensus size: 7
26094 TCATTGTACT
26104 TTAAGAA
1 TTAAGAA
26111 TTAAGAA
1 TTAAGAA
26118 TTAAGAA
1 TTAAGAA
*
26125 TTAAAAA
1 TTAAGAA
26132 TT
1 TT
26134 CAAACTTCTT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.57, C:0.00, G:0.10, T:0.33
Consensus pattern (7 bp):
TTAAGAA
Found at i:26282 original size:18 final size:19
Alignment explanation
Indices: 26259--26296 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
26249 TTAATTATTA
*
26259 TAATAAATAAA-AAAATAT
1 TAATAAAAAAATAAAATAT
26277 TAATAAAAAAATAAAATAT
1 TAATAAAAAAATAAAATAT
26296 T
1 T
26297 TTAATTTTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 10 0.56
19 8 0.44
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (19 bp):
TAATAAAAAAATAAAATAT
Found at i:26300 original size:21 final size:20
Alignment explanation
Indices: 26254--26301 Score: 55
Period size: 18 Copynumber: 2.5 Consensus size: 20
26244 ATAGTTTAAT
* *
26254 TATTATAATAAATAAAAAAA
1 TATTTTAATAAAAAAAAAAA
26274 TA--TTAATAAAAAAATAAAA
1 TATTTTAATAAAAAAA-AAAA
26293 TATTTTAAT
1 TATTTTAAT
26302 TTTTAACCTA
Statistics
Matches: 23, Mismatches: 2, Indels: 5
0.77 0.07 0.17
Matches are distributed among these distances:
18 10 0.43
19 6 0.26
20 2 0.09
21 5 0.22
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (20 bp):
TATTTTAATAAAAAAAAAAA
Found at i:27627 original size:13 final size:13
Alignment explanation
Indices: 27609--27633 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
27599 GTCCTTTAGG
27609 GATTCTTTTATTC
1 GATTCTTTTATTC
27622 GATTCTTTTATT
1 GATTCTTTTATT
27634 ATGAAATTAC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.16, C:0.12, G:0.08, T:0.64
Consensus pattern (13 bp):
GATTCTTTTATTC
Found at i:37045 original size:29 final size:30
Alignment explanation
Indices: 37012--37068 Score: 89
Period size: 29 Copynumber: 1.9 Consensus size: 30
37002 AGAATGAACG
37012 TGTAATTGTATACATG-AATTTTGATTTTA
1 TGTAATTGTATACATGAAATTTTGATTTTA
* *
37041 TGTAATTTTATATATGAAATTTTGATTT
1 TGTAATTGTATACATGAAATTTTGATTT
37069 GAATCAATTC
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
29 14 0.56
30 11 0.44
ACGTcount: A:0.32, C:0.02, G:0.12, T:0.54
Consensus pattern (30 bp):
TGTAATTGTATACATGAAATTTTGATTTTA
Found at i:37884 original size:60 final size:60
Alignment explanation
Indices: 37811--38011 Score: 213
Period size: 60 Copynumber: 3.1 Consensus size: 60
37801 TTAGTGTTTG
*
37811 AAAATTATCTTAATATTAATCTTACAAAAGTTATCGATGGTGATGGCGGTATTCTTTTCA
1 AAAATTATATTAATATTAATCTTACAAAAGTTATCGATGGTGATGGCGGTATTCTTTTCA
* * *
37871 AAAATTATATTAATATCAATCTTACTATCAATCTTACAAAAGTTATCAATGGTGCTGGCGATATT
1 AAAA-T-TA-T-AT-T-AA---TA-T-T-AATCTTACAAAAGTTATCGATGGTGATGGCGGTATT
37936 CTTTTCA
54 CTTTTCA
* * * *
37943 AAAATTATATTTATATCAATCTTACAAAAGTTATCGATGGTGATGACGGTATTCTTTTAA
1 AAAATTATATTAATATTAATCTTACAAAAGTTATCGATGGTGATGGCGGTATTCTTTTCA
*
38003 AAAACTATA
1 AAAATTATA
38012 ATCAAATCAA
Statistics
Matches: 117, Mismatches: 12, Indels: 24
0.76 0.08 0.16
Matches are distributed among these distances:
60 50 0.43
61 1 0.01
62 3 0.03
63 3 0.03
64 1 0.01
65 1 0.01
66 3 0.03
67 1 0.01
68 2 0.02
69 3 0.03
70 3 0.03
71 2 0.02
72 44 0.38
ACGTcount: A:0.37, C:0.12, G:0.12, T:0.39
Consensus pattern (60 bp):
AAAATTATATTAATATTAATCTTACAAAAGTTATCGATGGTGATGGCGGTATTCTTTTCA
Found at i:37936 original size:72 final size:72
Alignment explanation
Indices: 37817--37967 Score: 248
Period size: 72 Copynumber: 2.1 Consensus size: 72
37807 TTTGAAAATT
* * * *
37817 ATCTTAATATTAATCTTACAAAAGTTATCGATGGTGATGGCGGTATTCTTTTCAAAAATTATATT
1 ATCTTACTATCAATCTTACAAAAGTTATCAATGGTGATGGCGATATTCTTTTCAAAAATTATATT
37882 AATATCA
66 AATATCA
*
37889 ATCTTACTATCAATCTTACAAAAGTTATCAATGGTGCTGGCGATATTCTTTTCAAAAATTATATT
1 ATCTTACTATCAATCTTACAAAAGTTATCAATGGTGATGGCGATATTCTTTTCAAAAATTATATT
*
37954 TATATCA
66 AATATCA
37961 ATCTTAC
1 ATCTTAC
37968 AAAAGTTATC
Statistics
Matches: 73, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
72 73 1.00
ACGTcount: A:0.35, C:0.14, G:0.11, T:0.40
Consensus pattern (72 bp):
ATCTTACTATCAATCTTACAAAAGTTATCAATGGTGATGGCGATATTCTTTTCAAAAATTATATT
AATATCA
Found at i:38592 original size:28 final size:27
Alignment explanation
Indices: 38543--38605 Score: 74
Period size: 28 Copynumber: 2.3 Consensus size: 27
38533 CAGGGCCAAC
* *
38543 CATATATTATTCAGGCGACAGAGCTGA
1 CATATATCATTCAGGCGACAGAACTGA
38570 TCATATATCATTCAGGC-AGCAGAACTGA
1 -CATATATCATTCAGGCGA-CAGAACTGA
38598 CTATATAT
1 C-ATATAT
38606 AGAAGCTAAC
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
27 2 0.06
28 29 0.94
ACGTcount: A:0.35, C:0.19, G:0.17, T:0.29
Consensus pattern (27 bp):
CATATATCATTCAGGCGACAGAACTGA
Found at i:42725 original size:31 final size:29
Alignment explanation
Indices: 42640--42758 Score: 78
Period size: 30 Copynumber: 3.9 Consensus size: 29
42630 CATAAACTCC
* *
42640 TAACCTTTATAAAAATGCTCAAATAAAGGT
1 TAACCTTT-TAAAAATACTCAAATAAGGGT
* ** **
42670 CAAATTTTTCAAAACGA-TCAAATAAGGGTT
1 TAACCTTTT-AAAAATACTCAAATAAGGG-T
**
42700 TAACCTTTTCAAAAATACTCAAATAATGGCC
1 TAACCTTTT-AAAAATACTCAAATAA-GGGT
* *
42731 AAACATTTTAAAAAGTACTCAAATAAGG
1 TAACCTTTTAAAAA-TACTCAAATAAGG
42759 ACTTATCAAA
Statistics
Matches: 68, Mismatches: 16, Indels: 10
0.72 0.17 0.11
Matches are distributed among these distances:
29 11 0.16
30 29 0.43
31 26 0.38
32 2 0.03
ACGTcount: A:0.46, C:0.15, G:0.10, T:0.29
Consensus pattern (29 bp):
TAACCTTTTAAAAATACTCAAATAAGGGT
Found at i:52039 original size:22 final size:22
Alignment explanation
Indices: 51989--52040 Score: 59
Period size: 22 Copynumber: 2.4 Consensus size: 22
51979 GCAAAGTATA
** *
51989 ATATGTATGTATGTGTATGTGT
1 ATATGTATGTACATGTATATGT
*
52011 ATTTGTATGTACATGTATATGT
1 ATATGTATGTACATGTATATGT
*
52033 CTATGTAT
1 ATATGTAT
52041 ATGTGAATGA
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.25, C:0.04, G:0.21, T:0.50
Consensus pattern (22 bp):
ATATGTATGTACATGTATATGT
Found at i:55384 original size:7 final size:7
Alignment explanation
Indices: 55372--55418 Score: 51
Period size: 7 Copynumber: 6.7 Consensus size: 7
55362 TAAAACAATA
55372 TTATTTT
1 TTATTTT
55379 TTATTTT
1 TTATTTT
*
55386 TTATTTA
1 TTATTTT
*
55393 ATATTTT
1 TTATTTT
55400 TATATTTT
1 T-TATTTT
*
55408 TT-TTAT
1 TTATTTT
55414 TTATT
1 TTATT
55419 AAAATTTTAT
Statistics
Matches: 33, Mismatches: 5, Indels: 4
0.79 0.12 0.10
Matches are distributed among these distances:
6 5 0.15
7 21 0.64
8 7 0.21
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (7 bp):
TTATTTT
Found at i:55407 original size:27 final size:26
Alignment explanation
Indices: 55372--55432 Score: 70
Period size: 27 Copynumber: 2.3 Consensus size: 26
55362 TAAAACAATA
* *
55372 TTATTTTTTATTT-TTTATTTAATATTT
1 TTATATTTTATTTATTTA-TTAA-AATT
*
55399 TTATATTTTTTTTATTTATTAAAATT
1 TTATATTTTATTTATTTATTAAAATT
55425 TTATATTT
1 TTATATTT
55433 AAGCATCTTA
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
26 11 0.37
27 15 0.50
28 4 0.13
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (26 bp):
TTATATTTTATTTATTTATTAAAATT
Found at i:58202 original size:20 final size:21
Alignment explanation
Indices: 58177--58216 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
58167 AAAATATAAT
58177 ATATATAAAATT-TCATAAAA
1 ATATATAAAATTATCATAAAA
*
58197 ATATATAATATTATCATAAA
1 ATATATAAAATTATCATAAA
58217 TACAAATATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 11 0.61
21 7 0.39
ACGTcount: A:0.57, C:0.05, G:0.00, T:0.38
Consensus pattern (21 bp):
ATATATAAAATTATCATAAAA
Found at i:59811 original size:16 final size:16
Alignment explanation
Indices: 59775--59805 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
59765 TAAAATTACA
59775 AAAAAAAAAAAAATTG
1 AAAAAAAAAAAAATTG
59791 AAAAAAAAAAAAATT
1 AAAAAAAAAAAAATT
59806 TTAAAATTAC
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:0.84, C:0.00, G:0.03, T:0.13
Consensus pattern (16 bp):
AAAAAAAAAAAAATTG
Found at i:61069 original size:15 final size:15
Alignment explanation
Indices: 61022--61082 Score: 61
Period size: 15 Copynumber: 4.1 Consensus size: 15
61012 CCGTTCGTTC
* *
61022 CCTTGTCATCTGTGT
1 CCTTGCCATTTGTGT
*
61037 CCTTGCCATTCAGT-T
1 CCTTGCCATT-TGTGT
*
61052 CCTTGTCATTTGTGT
1 CCTTGCCATTTGTGT
*
61067 CCTTGCCGTTTGTGT
1 CCTTGCCATTTGTGT
61082 C
1 C
61083 TTTCTGCTGG
Statistics
Matches: 37, Mismatches: 7, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
14 2 0.05
15 33 0.89
16 2 0.05
ACGTcount: A:0.07, C:0.28, G:0.20, T:0.46
Consensus pattern (15 bp):
CCTTGCCATTTGTGT
Found at i:61209 original size:26 final size:26
Alignment explanation
Indices: 61179--61232 Score: 108
Period size: 26 Copynumber: 2.1 Consensus size: 26
61169 TTGATTCAAT
61179 AAATAAAATATTGTTATAGTAAAAAG
1 AAATAAAATATTGTTATAGTAAAAAG
61205 AAATAAAATATTGTTATAGTAAAAAG
1 AAATAAAATATTGTTATAGTAAAAAG
61231 AA
1 AA
61233 CAAAATGAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.59, C:0.00, G:0.11, T:0.30
Consensus pattern (26 bp):
AAATAAAATATTGTTATAGTAAAAAG
Found at i:61237 original size:25 final size:26
Alignment explanation
Indices: 61183--61238 Score: 96
Period size: 26 Copynumber: 2.2 Consensus size: 26
61173 TTCAATAAAT
*
61183 AAAATATTGTTATAGTAAAAAGAAAT
1 AAAATATTGTTATAGTAAAAAGAAAC
61209 AAAATATTGTTATAGTAAAAAG-AAC
1 AAAATATTGTTATAGTAAAAAGAAAC
61234 AAAAT
1 AAAAT
61239 GAAAACTCTC
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
25 7 0.24
26 22 0.76
ACGTcount: A:0.59, C:0.02, G:0.11, T:0.29
Consensus pattern (26 bp):
AAAATATTGTTATAGTAAAAAGAAAC
Found at i:63547 original size:23 final size:23
Alignment explanation
Indices: 63500--63552 Score: 72
Period size: 23 Copynumber: 2.3 Consensus size: 23
63490 AGATTTAAAC
*
63500 AAATATTCATATTTATATTGTTA
1 AAATATTCATATTTATATTGATA
*
63523 AAATATTCATATTTTGTATT-ATA
1 AAATATTCATA-TTTATATTGATA
63546 AAATATT
1 AAATATT
63553 TATTACTAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
23 20 0.74
24 7 0.26
ACGTcount: A:0.42, C:0.04, G:0.04, T:0.51
Consensus pattern (23 bp):
AAATATTCATATTTATATTGATA
Found at i:63671 original size:19 final size:19
Alignment explanation
Indices: 63634--63673 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
63624 AAATATTTAG
*
63634 AATGTTAAAAGGTATTATT
1 AATGTTAAAAGGTAGTATT
**
63653 AATGTTAAAATTTAGTATT
1 AATGTTAAAAGGTAGTATT
63672 AA
1 AA
63674 AATAAAATTG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.45, C:0.00, G:0.12, T:0.42
Consensus pattern (19 bp):
AATGTTAAAAGGTAGTATT
Found at i:70417 original size:5 final size:5
Alignment explanation
Indices: 70407--70438 Score: 55
Period size: 5 Copynumber: 6.4 Consensus size: 5
70397 TAGAATGTTT
*
70407 GGAGA GGAGA GGAGA GGAGA GGAAA GGAGA GG
1 GGAGA GGAGA GGAGA GGAGA GGAGA GGAGA GG
70439 GGGGAAAGAT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
5 25 1.00
ACGTcount: A:0.41, C:0.00, G:0.59, T:0.00
Consensus pattern (5 bp):
GGAGA
Found at i:72364 original size:9 final size:9
Alignment explanation
Indices: 72350--72393 Score: 52
Period size: 10 Copynumber: 4.6 Consensus size: 9
72340 TTTTAGAAAA
72350 TTTTTAAAT
1 TTTTTAAAT
72359 TTTTTAAACT
1 TTTTTAAA-T
*
72369 TTTTTATAT
1 TTTTTAAAT
72378 ATTTTTAGAAT
1 -TTTTTA-AAT
72389 TTTTT
1 TTTTT
72394 CATAAAAATA
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
9 9 0.30
10 19 0.63
11 2 0.07
ACGTcount: A:0.27, C:0.02, G:0.02, T:0.68
Consensus pattern (9 bp):
TTTTTAAAT
Found at i:72423 original size:18 final size:19
Alignment explanation
Indices: 72402--72438 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
72392 TTCATAAAAA
72402 TATAAAT-TTTAGAATTTT
1 TATAAATATTTAGAATTTT
*
72420 TATAAATATTTTGAATTTT
1 TATAAATATTTAGAATTTT
72439 AAAAATTATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 7 0.41
19 10 0.59
ACGTcount: A:0.38, C:0.00, G:0.05, T:0.57
Consensus pattern (19 bp):
TATAAATATTTAGAATTTT
Found at i:72439 original size:18 final size:18
Alignment explanation
Indices: 72402--72455 Score: 56
Period size: 19 Copynumber: 2.9 Consensus size: 18
72392 TTCATAAAAA
*
72402 TATAAAT-TTTAGAATTTT
1 TATAAATATTTTGAA-TTT
72420 TATAAATATTTTGAATTT
1 TATAAATATTTTGAATTT
* *
72438 TAAAAATTATTTTAAATT
1 TATAAA-TATTTTGAATT
72456 ATTTTGTAGA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
18 15 0.48
19 16 0.52
ACGTcount: A:0.43, C:0.00, G:0.04, T:0.54
Consensus pattern (18 bp):
TATAAATATTTTGAATTT
Found at i:72552 original size:9 final size:9
Alignment explanation
Indices: 72538--72573 Score: 54
Period size: 9 Copynumber: 4.0 Consensus size: 9
72528 ACACCAACAT
*
72538 GTTATTTAA
1 GTTATTCAA
72547 GTTATTCAA
1 GTTATTCAA
*
72556 ATTATTCAA
1 GTTATTCAA
72565 GTTATTCAA
1 GTTATTCAA
72574 ATTGTAAAGT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
9 24 1.00
ACGTcount: A:0.36, C:0.08, G:0.08, T:0.47
Consensus pattern (9 bp):
GTTATTCAA
Found at i:72566 original size:18 final size:18
Alignment explanation
Indices: 72539--72576 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
72529 CACCAACATG
*
72539 TTATTTAAGTTATTCAAA
1 TTATTCAAGTTATTCAAA
72557 TTATTCAAGTTATTCAAA
1 TTATTCAAGTTATTCAAA
72575 TT
1 TT
72577 GTAAAGTTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.37, C:0.08, G:0.05, T:0.50
Consensus pattern (18 bp):
TTATTCAAGTTATTCAAA
Found at i:81292 original size:48 final size:48
Alignment explanation
Indices: 81228--81323 Score: 174
Period size: 48 Copynumber: 2.0 Consensus size: 48
81218 ACACAATATA
81228 TAATATTTTTTAAAATCAAAACTAAATTAACATAATTTATAAATATTG
1 TAATATTTTTTAAAATCAAAACTAAATTAACATAATTTATAAATATTG
* *
81276 TAATTTTTTTTAAAATCAAAACTAAATTAATATAATTTATAAATATTG
1 TAATATTTTTTAAAATCAAAACTAAATTAACATAATTTATAAATATTG
81324 AAAGTTAAAA
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
48 46 1.00
ACGTcount: A:0.49, C:0.05, G:0.02, T:0.44
Consensus pattern (48 bp):
TAATATTTTTTAAAATCAAAACTAAATTAACATAATTTATAAATATTG
Found at i:81333 original size:43 final size:45
Alignment explanation
Indices: 81237--81334 Score: 128
Period size: 48 Copynumber: 2.2 Consensus size: 45
81227 ATAATATTTT
**
81237 TTAAAATCAAAACTAAATTAACATAATTTATAAATATTGTAATTTTTT
1 TTAAAATCAAAACTAAATTAACATAATTTATAAATATTGTAA---TAG
*
81285 TTAAAATCAAAACTAAATTAATATAATTTATAAATATTG-AA-AG
1 TTAAAATCAAAACTAAATTAACATAATTTATAAATATTGTAATAG
81328 TTAAAAT
1 TTAAAAT
81335 TACTATAATG
Statistics
Matches: 47, Mismatches: 3, Indels: 5
0.85 0.05 0.09
Matches are distributed among these distances:
43 7 0.15
47 2 0.04
48 38 0.81
ACGTcount: A:0.52, C:0.05, G:0.03, T:0.40
Consensus pattern (45 bp):
TTAAAATCAAAACTAAATTAACATAATTTATAAATATTGTAATAG
Found at i:85252 original size:5 final size:5
Alignment explanation
Indices: 85242--85266 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
85232 GTATATACCA
85242 TTATT TTATT TTATT TTATT TTATT
1 TTATT TTATT TTATT TTATT TTATT
85267 AGCTTATGTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (5 bp):
TTATT
Found at i:87908 original size:24 final size:24
Alignment explanation
Indices: 87876--87923 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
87866 TGTTATCTTC
87876 ATTCATATATGCAAGTCAAAGCCA
1 ATTCATATATGCAAGTCAAAGCCA
87900 ATTCATATATGCAAGTCAAAGCCA
1 ATTCATATATGCAAGTCAAAGCCA
87924 CTTTAAATCC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.42, C:0.21, G:0.12, T:0.25
Consensus pattern (24 bp):
ATTCATATATGCAAGTCAAAGCCA
Found at i:88602 original size:18 final size:17
Alignment explanation
Indices: 88579--88634 Score: 66
Period size: 16 Copynumber: 3.5 Consensus size: 17
88569 ATTTTCTTTT
88579 AATTAATTAAGAAATTTC
1 AATTAATTAA-AAATTTC
88597 AATTAATT--AAATTT-
1 AATTAATTAAAAATTTC
*
88611 AATTAATTAAAAA-ATC
1 AATTAATTAAAAATTTC
88627 AATTAATT
1 AATTAATT
88635 TACTTGGTTG
Statistics
Matches: 34, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
14 8 0.24
15 7 0.21
16 11 0.32
18 8 0.24
ACGTcount: A:0.54, C:0.04, G:0.02, T:0.41
Consensus pattern (17 bp):
AATTAATTAAAAATTTC
Found at i:88613 original size:32 final size:30
Alignment explanation
Indices: 88576--88634 Score: 91
Period size: 32 Copynumber: 1.9 Consensus size: 30
88566 AACATTTTCT
*
88576 TTTAATTAATTAAGAAATTTCAATTAATTAAA
1 TTTAATTAATTAA-AAA-ATCAATTAATTAAA
88608 TTTAATTAATTAAAAAATCAATTAATT
1 TTTAATTAATTAAAAAATCAATTAATT
88635 TACTTGGTTG
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
30 10 0.38
31 3 0.12
32 13 0.50
ACGTcount: A:0.51, C:0.03, G:0.02, T:0.44
Consensus pattern (30 bp):
TTTAATTAATTAAAAAATCAATTAATTAAA
Found at i:88618 original size:14 final size:14
Alignment explanation
Indices: 88581--88621 Score: 57
Period size: 14 Copynumber: 2.9 Consensus size: 14
88571 TTTCTTTTAA
*
88581 TTAATTAA-GAAAT
1 TTAATTAATTAAAT
88594 TTCAATTAATTAAAT
1 TT-AATTAATTAAAT
88609 TTAATTAATTAAA
1 TTAATTAATTAAA
88622 AAATCAATTA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
13 2 0.08
14 17 0.68
15 6 0.24
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.44
Consensus pattern (14 bp):
TTAATTAATTAAAT
Found at i:101310 original size:48 final size:48
Alignment explanation
Indices: 101252--101351 Score: 164
Period size: 48 Copynumber: 2.1 Consensus size: 48
101242 TGTCACCTAT
* * *
101252 ATTTTAATTTGGATTAATTATTTGTTTGTGTGAAATTGTAAAATATAA
1 ATTTGAATTTGAATTAATTATTTGTTTGTGTCAAATTGTAAAATATAA
*
101300 ATTTGAATTTGAATTAATTATTTGTTTGTGTCAAATTGTAAAGTATAA
1 ATTTGAATTTGAATTAATTATTTGTTTGTGTCAAATTGTAAAATATAA
101348 ATTT
1 ATTT
101352 AAAGCTTAAA
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
48 48 1.00
ACGTcount: A:0.35, C:0.01, G:0.14, T:0.50
Consensus pattern (48 bp):
ATTTGAATTTGAATTAATTATTTGTTTGTGTCAAATTGTAAAATATAA
Found at i:103904 original size:30 final size:30
Alignment explanation
Indices: 103870--103930 Score: 104
Period size: 30 Copynumber: 2.0 Consensus size: 30
103860 AGCCCAAATG
**
103870 ACTTAAATAAAAACTTTTGAATAGTTCAAT
1 ACTTAAATAAAAACTTTCAAATAGTTCAAT
103900 ACTTAAATAAAAACTTTCAAATAGTTCAAT
1 ACTTAAATAAAAACTTTCAAATAGTTCAAT
103930 A
1 A
103931 ATCATTTTAT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.49, C:0.11, G:0.05, T:0.34
Consensus pattern (30 bp):
ACTTAAATAAAAACTTTCAAATAGTTCAAT
Found at i:105546 original size:27 final size:29
Alignment explanation
Indices: 105498--105557 Score: 79
Period size: 27 Copynumber: 2.1 Consensus size: 29
105488 TTAAATAAAA
105498 AAAATAAAGAGACTTAATATTTTAAAATT
1 AAAATAAAGAGACTTAATATTTTAAAATT
* * *
105527 AAAATATATAGAC-TAA-ATTTTAAATTT
1 AAAATAAAGAGACTTAATATTTTAAAATT
105554 AAAA
1 AAAA
105558 AAACAAAAAC
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
27 14 0.50
28 3 0.11
29 11 0.39
ACGTcount: A:0.57, C:0.03, G:0.05, T:0.35
Consensus pattern (29 bp):
AAAATAAAGAGACTTAATATTTTAAAATT
Found at i:119785 original size:26 final size:26
Alignment explanation
Indices: 119756--119809 Score: 99
Period size: 26 Copynumber: 2.1 Consensus size: 26
119746 ATTTAAAACT
119756 ATTCATAGTCTCTTCTCAACCCATAA
1 ATTCATAGTCTCTTCTCAACCCATAA
*
119782 ATTCATAGTCTCTTCTCAACCTATAA
1 ATTCATAGTCTCTTCTCAACCCATAA
119808 AT
1 AT
119810 AGAAAGATAA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.31, C:0.28, G:0.04, T:0.37
Consensus pattern (26 bp):
ATTCATAGTCTCTTCTCAACCCATAA
Found at i:121055 original size:24 final size:24
Alignment explanation
Indices: 121028--121080 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
121018 AAAATTTGAC
* * *
121028 TGAAGCAAATAAATATAATTTAAT
1 TGAAACAAATAAACAGAATTTAAT
*
121052 TGAAACAAATAAACAGAGTTTAAT
1 TGAAACAAATAAACAGAATTTAAT
121076 TGAAA
1 TGAAA
121081 GATTATTTTT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.55, C:0.06, G:0.11, T:0.28
Consensus pattern (24 bp):
TGAAACAAATAAACAGAATTTAAT
Found at i:123194 original size:24 final size:25
Alignment explanation
Indices: 123141--123212 Score: 92
Period size: 25 Copynumber: 2.8 Consensus size: 25
123131 CAAAGTACTT
*
123141 AACAGAAGCGCATAAGTGCTAGGGA
1 AACAGAAGCACATAAGTGCTAGGGA
123166 AACAGAAGCACATAAGTGCT-GGGA
1 AACAGAAGCACATAAGTGCTAGGGA
* *
123190 AACAGTAGGCACACACAGTGCTA
1 AACAG-AAGCACATA-AGTGCTA
123213 AACATGCTAA
Statistics
Matches: 41, Mismatches: 3, Indels: 4
0.85 0.06 0.08
Matches are distributed among these distances:
24 9 0.22
25 26 0.63
26 6 0.15
ACGTcount: A:0.40, C:0.19, G:0.28, T:0.12
Consensus pattern (25 bp):
AACAGAAGCACATAAGTGCTAGGGA
Found at i:123860 original size:11 final size:11
Alignment explanation
Indices: 123833--123863 Score: 55
Period size: 10 Copynumber: 2.9 Consensus size: 11
123823 TCAGCCTCTA
123833 ATAATTTTTCT
1 ATAATTTTTCT
123844 AT-ATTTTTCT
1 ATAATTTTTCT
123854 ATAATTTTTC
1 ATAATTTTTC
123864 AAAGTCAGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
10 10 0.53
11 9 0.47
ACGTcount: A:0.26, C:0.10, G:0.00, T:0.65
Consensus pattern (11 bp):
ATAATTTTTCT
Found at i:126404 original size:21 final size:21
Alignment explanation
Indices: 126375--126421 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 21
126365 ACTTTCATCA
*
126375 TTAAGCTTTAATTAA-CTATTT
1 TTAACCTTT-ATTAACCTATTT
126396 TTAACCTTTATTAAGCCTATTT
1 TTAACCTTTATTAA-CCTATTT
126418 TTAA
1 TTAA
126422 ACAATATAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
20 5 0.22
21 8 0.35
22 10 0.43
ACGTcount: A:0.32, C:0.13, G:0.04, T:0.51
Consensus pattern (21 bp):
TTAACCTTTATTAACCTATTT
Found at i:131761 original size:24 final size:24
Alignment explanation
Indices: 131729--131776 Score: 87
Period size: 24 Copynumber: 2.0 Consensus size: 24
131719 GTGCACTTGG
*
131729 TGTGTTATTGCTCAGCCCCTATTT
1 TGTGGTATTGCTCAGCCCCTATTT
131753 TGTGGTATTGCTCAGCCCCTATTT
1 TGTGGTATTGCTCAGCCCCTATTT
131777 GCATGCAATC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.12, C:0.25, G:0.19, T:0.44
Consensus pattern (24 bp):
TGTGGTATTGCTCAGCCCCTATTT
Found at i:143395 original size:3 final size:3
Alignment explanation
Indices: 143387--143421 Score: 63
Period size: 3 Copynumber: 12.0 Consensus size: 3
143377 AGTATTAAAA
143387 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T-T TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
143422 ACAAAAAAGA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.06
3 29 0.94
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TAT
Found at i:145730 original size:2 final size:2
Alignment explanation
Indices: 145723--145754 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
145713 TGATTGTAAT
145723 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
145755 ATTATGGAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:147393 original size:28 final size:28
Alignment explanation
Indices: 147353--147414 Score: 81
Period size: 28 Copynumber: 2.2 Consensus size: 28
147343 AAATGAGACT
147353 TTTTGGATACTCG-GGGCCAAAATGGTAA
1 TTTTGGATACTCGAGGG-CAAAATGGTAA
* * *
147381 TTTTGGATTCTCGAGGGTAAAATGGTAG
1 TTTTGGATACTCGAGGGCAAAATGGTAA
147409 TTTTGG
1 TTTTGG
147415 GAAAATTTAG
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
28 27 0.90
29 3 0.10
ACGTcount: A:0.24, C:0.10, G:0.31, T:0.35
Consensus pattern (28 bp):
TTTTGGATACTCGAGGGCAAAATGGTAA
Found at i:147454 original size:58 final size:57
Alignment explanation
Indices: 147371--147837 Score: 390
Period size: 59 Copynumber: 8.0 Consensus size: 57
147361 ACTCGGGGCC
* * * **
147371 AAAATGGTAATTTTGGA-TTCTCGAGGGTAAAATGGTAGTTTTGGGAAAATTTAGGGTTT
1 AAAATGG-AATTTTGGACAT-TCGAGGGTAAAATGGTAATTTT-GGAAAATTTGGGGTAA
* * * * * *
147430 AAAATGGAATTTTAGACATCCGAGGGTAAAACGGTAATTTTTAGAAAA-TCGGGATAA
1 AAAATGGAATTTTGGACATTCGAGGGTAAAATGGTAA-TTTTGGAAAATTTGGGGTAA
* * * * *
147487 AAAA-AGATTTTTTTGGACATTCGAGGGTAAAATGGTAATTTTTGAGAGTTTCGGGGTAA
1 AAAATGGA--ATTTTGGACATTCGAGGGTAAAATGGTAATTTTGGAAAATTT-GGGGTAA
* **
147546 AAAATGGAGTTTTGGACATTCGAGGGTAAAAAT-GTAATTTTTGGAAGTTTTGGGGTAA
1 AAAATGGAATTTTGGACATTCGAGGGT-AAAATGGTAA-TTTTGGAAAATTTGGGGTAA
* * * *
147604 AAAATGGAGTTTTTGGACA-TCTGAGGGTAAAATGGTAATTTTTGAAAATTTTGAGGTCA
1 AAAATGGA-ATTTTGGACATTC-GAGGGTAAAATGGTAATTTTGGAAAA-TTTGGGGTAA
** **
147663 AAAATGGAATTTTTGGAGGTTCGAGGGTAAAAAT-GTAATTTTTGGAAGTTTTGGGGTAA
1 AAAATGGAA-TTTTGGACATTCGAGGGT-AAAATGGTAA-TTTTGGAAAATTTGGGGTAA
* * * *
147722 AAAATGGAGTTTTTGGACATTTGAGGGTAAAATGGTAATTTTTGAAAATTTTGAGGTAA
1 AAAATGGA-ATTTTGGACATTCGAGGGTAAAATGGTAATTTTGGAAAA-TTTGGGGTAA
** **
147781 AAAATGGAATTTTTGGAGGTTCGAGGGTAAAAAT-GTAATTTTTGGAAGTTTTGGGGT
1 AAAATGGAA-TTTTGGACATTCGAGGGT-AAAATGGTAA-TTTTGGAAAATTTGGGGT
147838 CTAAAATAGA
Statistics
Matches: 328, Mismatches: 57, Indels: 46
0.76 0.13 0.11
Matches are distributed among these distances:
56 2 0.01
57 15 0.05
58 117 0.36
59 166 0.51
60 28 0.09
ACGTcount: A:0.34, C:0.04, G:0.28, T:0.35
Consensus pattern (57 bp):
AAAATGGAATTTTGGACATTCGAGGGTAAAATGGTAATTTTGGAAAATTTGGGGTAA
Found at i:147518 original size:29 final size:28
Alignment explanation
Indices: 147486--147635 Score: 76
Period size: 29 Copynumber: 5.1 Consensus size: 28
147476 AATCGGGATA
147486 AAAAAAGATTTTTTTGGACATTCGAGGGT
1 AAAAAAGA-TTTTTTGGACATTCGAGGGT
** * **
147515 AAAATGGTAATTTTTGAGAGTTTCG-GGGT
1 AAAAAAG-ATTTTTTG-GACATTCGAGGGT
*
147544 AAAAAATGGA-GTTTTGGACATTCGAGGGT
1 AAAAAA--GATTTTTTGGACATTCGAGGGT
* * *
147573 AAAAATGTAATTTTTGGA-AGTTTTG-GGGT
1 AAAAAAG-ATTTTTTGGACA--TTCGAGGGT
*
147602 AAAAAATGGAGTTTTTGGACA-TCTGAGGGT
1 AAAAAA--GATTTTTTGGACATTC-GAGGGT
147632 AAAA
1 AAAA
147636 TGGTAATTTT
Statistics
Matches: 91, Mismatches: 16, Indels: 27
0.68 0.12 0.20
Matches are distributed among these distances:
27 1 0.01
28 9 0.10
29 50 0.55
30 28 0.31
31 3 0.03
ACGTcount: A:0.34, C:0.05, G:0.28, T:0.33
Consensus pattern (28 bp):
AAAAAAGATTTTTTGGACATTCGAGGGT
Found at i:147621 original size:59 final size:59
Alignment explanation
Indices: 147496--147962 Score: 470
Period size: 59 Copynumber: 7.9 Consensus size: 59
147486 AAAAAAGATT
*
147496 TTTTTGGACATTCGAGGGT-AAAATGGTAATTTTT-GAGAGTTTCGGGGTAAAAAATGGAG
1 TTTTTGGACATTCGAGGGTAAAAAT-GTAATTTTTGGA-AGTTTTGGGGTAAAAAATGGAG
147555 -TTTTGGACATTCGAGGGTAAAAATGTAATTTTTGGAAGTTTTGGGGTAAAAAATGGAG
1 TTTTTGGACATTCGAGGGTAAAAATGTAATTTTTGGAAGTTTTGGGGTAAAAAATGGAG
* * * * *
147613 TTTTTGGACA-TCTGAGGGT-AAAATGGTAATTTTTGAAAATTTTGAGGTCAAAAATGGAA
1 TTTTTGGACATTC-GAGGGTAAAAAT-GTAATTTTTGGAAGTTTTGGGGTAAAAAATGGAG
**
147672 TTTTTGGAGGTTCGAGGGTAAAAATGTAATTTTTGGAAGTTTTGGGGTAAAAAATGGAG
1 TTTTTGGACATTCGAGGGTAAAAATGTAATTTTTGGAAGTTTTGGGGTAAAAAATGGAG
* * * * *
147731 TTTTTGGACATTTGAGGGT-AAAATGGTAATTTTTGAAAATTTTGAGGTAAAAAATGGAA
1 TTTTTGGACATTCGAGGGTAAAAAT-GTAATTTTTGGAAGTTTTGGGGTAAAAAATGGAG
** ** * *
147790 TTTTTGGAGGTTCGAGGGTAAAAATGTAATTTTTGGAAGTTTTGGGGTCTAAAATAGAAAT
1 TTTTTGGACATTCGAGGGTAAAAATGTAATTTTTGGAAGTTTTGGGGTAAAAAAT-G-GAG
* * * * * *
147851 TTTTTTGA-AGCTT-GGGGGTTAAAAAT-TAAGTTTTGAAAGTTTTAGGGTTAAAAATGGA-
1 TTTTTGGACA--TTCGAGGG-TAAAAATGTAATTTTTGGAAGTTTTGGGGTAAAAAATGGAG
* * * * **
147909 TTTTTTGAAAGTTCGA-GGTCAAAATTGGAATTTTTGGAAGTTCGGGGGTAAAAA
1 TTTTTGGACA-TTCGAGGGT-AAAAATGTAATTTTTGGAAGTTTTGGGGTAAAAA
147963 TGTAATTTTG
Statistics
Matches: 341, Mismatches: 49, Indels: 36
0.80 0.12 0.08
Matches are distributed among these distances:
57 1 0.00
58 77 0.23
59 204 0.60
60 14 0.04
61 36 0.11
62 9 0.03
ACGTcount: A:0.33, C:0.03, G:0.28, T:0.36
Consensus pattern (59 bp):
TTTTTGGACATTCGAGGGTAAAAATGTAATTTTTGGAAGTTTTGGGGTAAAAAATGGAG
Found at i:147837 original size:29 final size:29
Alignment explanation
Indices: 147511--147980 Score: 270
Period size: 29 Copynumber: 15.9 Consensus size: 29
147501 GGACATTCGA
*
147511 GGGT-AAAATGGTAATTTTT-GAGAGTTTCG
1 GGGTAAAAAT-GTAATTTTTGGA-AGTTTTG
* * *
147540 GGGTAAAAAATG-GAGTTTTGGACA--TTCG
1 GGGT-AAAAATGTAATTTTTGGA-AGTTTTG
147568 AGGGTAAAAATGTAATTTTTGGAAGTTTTG
1 -GGGTAAAAATGTAATTTTTGGAAGTTTTG
* * *
147598 GGGTAAAAAATGGAGTTTTTGGACA--TCTG
1 GGGT-AAAAATGTAATTTTTGGA-AGTTTTG
* *
147627 AGGGT-AAAATGGTAATTTTTGAAAATTTTG
1 -GGGTAAAAAT-GTAATTTTTGGAAGTTTTG
* * * *
147657 AGGTCAAAAATGGAATTTTTGG-AGGTTCG
1 GGGT-AAAAATGTAATTTTTGGAAGTTTTG
147686 AGGGTAAAAATGTAATTTTTGGAAGTTTTG
1 -GGGTAAAAATGTAATTTTTGGAAGTTTTG
* *
147716 GGGTAAAAAATGGAGTTTTTGGACA--TTTG
1 GGGT-AAAAATGTAATTTTTGGA-AGTTTTG
* *
147745 AGGGT-AAAATGGTAATTTTTGAAAATTTTG
1 -GGGTAAAAAT-GTAATTTTTGGAAGTTTTG
* * * *
147775 AGGTAAAAAATGGAATTTTTGG-AGGTTCG
1 GGGT-AAAAATGTAATTTTTGGAAGTTTTG
147804 AGGGTAAAAATGTAATTTTTGGAAGTTTTG
1 -GGGTAAAAATGTAATTTTTGGAAGTTTTG
* * * * *
147834 GGGTCTAAAATAGAAATTTTTTTGAAGCTTGG
1 GGGT-AAAAAT-GTAA-TTTTTGGAAGTTTTG
* *
147866 GGGTTAAAAAT-TAAGTTTTGAAAGTTTTAG
1 GGG-TAAAAATGTAATTTTTGGAAGTTTT-G
* * * * *
147896 GGTTAAAAATGGATTTTTTGAAAG-TTCG
1 GGGTAAAAATGTAATTTTTGGAAGTTTTG
* * * **
147924 AGGTCAAAATTGGAATTTTTGGAAGTTCGG
1 GGGT-AAAAATGTAATTTTTGGAAGTTTTG
147954 GGGTAAAAATGTAA-TTTTGGATAGTTT
1 GGGTAAAAATGTAATTTTTGGA-AGTTT
147981 AGGGATTTCC
Statistics
Matches: 339, Mismatches: 66, Indels: 72
0.71 0.14 0.15
Matches are distributed among these distances:
28 34 0.10
29 151 0.45
30 113 0.33
31 20 0.06
32 20 0.06
33 1 0.00
ACGTcount: A:0.33, C:0.03, G:0.28, T:0.37
Consensus pattern (29 bp):
GGGTAAAAATGTAATTTTTGGAAGTTTTG
Found at i:147844 original size:118 final size:118
Alignment explanation
Indices: 147496--147837 Score: 587
Period size: 118 Copynumber: 2.9 Consensus size: 118
147486 AAAAAAGATT
* * * * * *
147496 TTTTTGGACATTCGAGGGTAAAATGGTAATTTTTGAGAGTTTCGGGGTAAAAAATGG-AGTTTTG
1 TTTTTGGACATTTGAGGGTAAAATGGTAATTTTTGAAAATTTTGAGGTAAAAAATGGAATTTTTG
**
147560 GACATTCGAGGGTAAAAATGTAATTTTTGGAAGTTTTGGGGTAAAAAATGGAG
66 GAGGTTCGAGGGTAAAAATGTAATTTTTGGAAGTTTTGGGGTAAAAAATGGAG
* *
147613 TTTTTGGACATCTGAGGGTAAAATGGTAATTTTTGAAAATTTTGAGGTCAAAAATGGAATTTTTG
1 TTTTTGGACATTTGAGGGTAAAATGGTAATTTTTGAAAATTTTGAGGTAAAAAATGGAATTTTTG
147678 GAGGTTCGAGGGTAAAAATGTAATTTTTGGAAGTTTTGGGGTAAAAAATGGAG
66 GAGGTTCGAGGGTAAAAATGTAATTTTTGGAAGTTTTGGGGTAAAAAATGGAG
147731 TTTTTGGACATTTGAGGGTAAAATGGTAATTTTTGAAAATTTTGAGGTAAAAAATGGAATTTTTG
1 TTTTTGGACATTTGAGGGTAAAATGGTAATTTTTGAAAATTTTGAGGTAAAAAATGGAATTTTTG
147796 GAGGTTCGAGGGTAAAAATGTAATTTTTGGAAGTTTTGGGGT
66 GAGGTTCGAGGGTAAAAATGTAATTTTTGGAAGTTTTGGGGT
147838 CTAAAATAGA
Statistics
Matches: 212, Mismatches: 12, Indels: 1
0.94 0.05 0.00
Matches are distributed among these distances:
117 50 0.24
118 162 0.76
ACGTcount: A:0.32, C:0.03, G:0.29, T:0.36
Consensus pattern (118 bp):
TTTTTGGACATTTGAGGGTAAAATGGTAATTTTTGAAAATTTTGAGGTAAAAAATGGAATTTTTG
GAGGTTCGAGGGTAAAAATGTAATTTTTGGAAGTTTTGGGGTAAAAAATGGAG
Found at i:149329 original size:30 final size:28
Alignment explanation
Indices: 149293--149467 Score: 138
Period size: 30 Copynumber: 5.9 Consensus size: 28
149283 GTCTCCTTTC
*
149293 AAAAATT-CAATTTTTGACCTAAAAACTTTT
1 AAAAATTAC-ATTTTT-ACCT-AAAACTTCT
**
149323 AAAAATTACATTTTTACCCCAAACTTCT
1 AAAAATTACATTTTTACCTAAAACTTCT
*
149351 AAAAATTCCATTTTTAACCCTAAAACTTCT
1 AAAAATTACATTTTT-A-CCTAAAACTTCT
*** * *
149381 AAAAATTACATTTTTACCCCCGAACATCC
1 AAAAATTACATTTTTA-CCTAAAACTTCT
* *
149410 AAAAATTCCATTTTTGACCTCGAAACTT-T
1 AAAAATTACATTTTT-ACCT-AAAACTTCT
149439 CAAAAATTACATTTTTACCACTAAAACTT
1 -AAAAATTACATTTTTA-C-CTAAAACTT
149468 AAAAACTCCA
Statistics
Matches: 117, Mismatches: 20, Indels: 16
0.76 0.13 0.10
Matches are distributed among these distances:
28 21 0.18
29 30 0.26
30 63 0.54
31 3 0.03
ACGTcount: A:0.40, C:0.22, G:0.02, T:0.35
Consensus pattern (28 bp):
AAAAATTACATTTTTACCTAAAACTTCT
Found at i:149336 original size:29 final size:29
Alignment explanation
Indices: 149304--149484 Score: 120
Period size: 29 Copynumber: 6.2 Consensus size: 29
149294 AAAATTCAAT
* *
149304 TTTTGACCTAAAAACTTTTAAAAATTACA
1 TTTTGACCTCAAAACTTCTAAAAATTACA
* * *
149333 TTTTTACC-CCAAACTTCTAAAAATTCCA
1 TTTTGACCTCAAAACTTCTAAAAATTACA
*
149361 TTTTTAACC-CTAAAACTTCTAAAAATTACA
1 -TTTTGACCTC-AAAACTTCTAAAAATTACA
* * ** * * *
149391 TTTTTACCCCCGAACATCCAAAAATTCCA
1 TTTTGACCTCAAAACTTCTAAAAATTACA
*
149420 TTTTTGACCTCGAAACTT-TCAAAAATTACA
1 -TTTTGACCTCAAAACTTCT-AAAAATTACA
* * * *
149450 TTTTTACCACTAAAAC-T-TAAAAACTCCA
1 TTTTGACCTC-AAAACTTCTAAAAATTACA
149478 TTTTGAC
1 TTTTGAC
149485 TCTTTTTTTT
Statistics
Matches: 119, Mismatches: 27, Indels: 13
0.75 0.17 0.08
Matches are distributed among these distances:
28 30 0.25
29 46 0.39
30 43 0.36
ACGTcount: A:0.39, C:0.23, G:0.03, T:0.35
Consensus pattern (29 bp):
TTTTGACCTCAAAACTTCTAAAAATTACA
Found at i:149421 original size:59 final size:58
Alignment explanation
Indices: 149292--149457 Score: 219
Period size: 59 Copynumber: 2.8 Consensus size: 58
149282 TGTCTCCTTT
* *
149292 CAAAAATTCAATTTTTGACCTAAAAACTTTTAAAAATTACATTTTTA-CCCCAAACTTC
1 CAAAAATTCCATTTTTGACCTAAAAAC-TTTAAAAATTACATTTTTACCCCCAAACATC
* * *
149350 TAAAAATTCCATTTTTAACCCT-AAAACTTCTAAAAATTACATTTTTACCCCCGAACATC
1 CAAAAATTCCATTTTTGA-CCTAAAAACTT-TAAAAATTACATTTTTACCCCCAAACATC
**
149409 CAAAAATTCCATTTTTGACCTCGAAACTTTCAAAAATTACATTTTTACC
1 CAAAAATTCCATTTTTGACCTAAAAACTTT-AAAAATTACATTTTTACC
149458 ACTAAAACTT
Statistics
Matches: 95, Mismatches: 8, Indels: 9
0.85 0.07 0.08
Matches are distributed among these distances:
57 2 0.02
58 41 0.43
59 52 0.55
ACGTcount: A:0.39, C:0.23, G:0.02, T:0.36
Consensus pattern (58 bp):
CAAAAATTCCATTTTTGACCTAAAAACTTTAAAAATTACATTTTTACCCCCAAACATC
Found at i:155121 original size:7 final size:7
Alignment explanation
Indices: 155109--155186 Score: 56
Period size: 7 Copynumber: 11.0 Consensus size: 7
155099 AGATGCAATG
155109 AAGAAAA
1 AAGAAAA
155116 AAGAAAA
1 AAGAAAA
155123 AAG-AAA
1 AAGAAAA
155129 AAGAAAGA
1 AAGAAA-A
*
155137 AA-AAAG
1 AAGAAAA
155143 AAGAAAA
1 AAGAAAA
155150 ATAGGAAAGA
1 A-A-GAAA-A
*
155160 AA-ATAGA
1 AAGA-AAA
155167 AA-AAAA
1 AAGAAAA
*
155173 AGGAAAA
1 AAGAAAA
155180 AAGAAAA
1 AAGAAAA
155187 GGAGAGGTCG
Statistics
Matches: 57, Mismatches: 6, Indels: 16
0.72 0.08 0.20
Matches are distributed among these distances:
6 11 0.19
7 34 0.60
8 5 0.09
9 5 0.09
10 2 0.04
ACGTcount: A:0.79, C:0.00, G:0.18, T:0.03
Consensus pattern (7 bp):
AAGAAAA
Found at i:155137 original size:17 final size:17
Alignment explanation
Indices: 155115--155185 Score: 65
Period size: 17 Copynumber: 4.2 Consensus size: 17
155105 AATGAAGAAA
155115 AAAGAAAAAAGAAAAAG
1 AAAGAAAAAAGAAAAAG
*
155132 AAAGAAAAAAGAAGAA-
1 AAAGAAAAAAGAAAAAG
* **
155148 AAATAGGAAAGAAAATAG
1 AAAGAAAAAAGAAAA-AG
*
155166 AAA-AAAAAGGAAAAAAG
1 AAAGAAAAAAG-AAAAAG
155183 AAA
1 AAA
155186 AGGAGAGGTC
Statistics
Matches: 43, Mismatches: 8, Indels: 6
0.75 0.14 0.11
Matches are distributed among these distances:
16 11 0.26
17 25 0.58
18 7 0.16
ACGTcount: A:0.79, C:0.00, G:0.18, T:0.03
Consensus pattern (17 bp):
AAAGAAAAAAGAAAAAG
Found at i:155158 original size:27 final size:24
Alignment explanation
Indices: 155109--155171 Score: 83
Period size: 23 Copynumber: 2.7 Consensus size: 24
155099 AGATGCAATG
155109 AAGAAAAAAGAAAAAAGAAAAAGA
1 AAGAAAAAAGAAAAAAGAAAAAGA
* * *
155133 AAGAAAAAAGAAGAAA-AATAGGA
1 AAGAAAAAAGAAAAAAGAAAAAGA
*
155156 AAGAAAATAGAAAAAA
1 AAGAAAAAAGAAAAAA
155172 AAGGAAAAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
23 19 0.56
24 15 0.44
ACGTcount: A:0.79, C:0.00, G:0.17, T:0.03
Consensus pattern (24 bp):
AAGAAAAAAGAAAAAAGAAAAAGA
Found at i:155178 original size:10 final size:9
Alignment explanation
Indices: 155119--155186 Score: 66
Period size: 10 Copynumber: 7.2 Consensus size: 9
155109 AAGAAAAAAG
155119 AAAAAAGAA
1 AAAAAAGAA
155128 AAAGAAAGAA
1 AAA-AAAGAA
155138 AAAAGAAGAA
1 AAAA-AAGAA
* *
155148 AAATAGGAA
1 AAAAAAGAA
155157 AGAAAATAGAA
1 A-AAAA-AGAA
*
155168 AAAAAAG-G
1 AAAAAAGAA
155176 AAAAAAGAA
1 AAAAAAGAA
155185 AA
1 AA
155187 GGAGAGGTCG
Statistics
Matches: 48, Mismatches: 6, Indels: 10
0.75 0.09 0.16
Matches are distributed among these distances:
8 7 0.15
9 13 0.27
10 24 0.50
11 4 0.08
ACGTcount: A:0.79, C:0.00, G:0.18, T:0.03
Consensus pattern (9 bp):
AAAAAAGAA
Found at i:156532 original size:48 final size:49
Alignment explanation
Indices: 156389--156579 Score: 251
Period size: 48 Copynumber: 3.9 Consensus size: 49
156379 CAGGTTTGAC
* * *
156389 AGGGAAAGATCTAAGACCGCAACAGCAGATCCAGTACCACAAAAACACGA
1 AGGGAAAGATCTAAGACCGCAACGGCGGATCCAGTACCACAAAGACAC-A
* * * *
156439 TGGGAAAGATCTAAGACCGTAACGGCGGATCCAGTACCGCTAAGACACA
1 AGGGAAAGATCTAAGACCGCAACGGCGGATCCAGTACCACAAAGACACA
* * * *
156488 AGGGAAAGATCTAAG-CTGCGATGGCGGATCCAGTATCACAAAGACACA
1 AGGGAAAGATCTAAGACCGCAACGGCGGATCCAGTACCACAAAGACACA
*
156536 AGGAAAAGATCTAAG-CCGCAACGGCGGATCCAGTACCACAAAGA
1 AGGGAAAGATCTAAGACCGCAACGGCGGATCCAGTACCACAAAGA
156580 TTTGAAGGGA
Statistics
Matches: 121, Mismatches: 20, Indels: 2
0.85 0.14 0.01
Matches are distributed among these distances:
48 65 0.54
49 15 0.12
50 41 0.34
ACGTcount: A:0.40, C:0.24, G:0.25, T:0.12
Consensus pattern (49 bp):
AGGGAAAGATCTAAGACCGCAACGGCGGATCCAGTACCACAAAGACACA
Found at i:156564 original size:96 final size:99
Alignment explanation
Indices: 156389--156572 Score: 257
Period size: 98 Copynumber: 1.9 Consensus size: 99
156379 CAGGTTTGAC
* *
156389 AGGGAAAGATCTAAGACCGCAACAGCAGATCCAGTACCACAAAAACACGATGGGAAAGATCTAAG
1 AGGGAAAGATCTAAGACCGCAACAGCAGATCCAGTACCACAAAAACACGAAGGAAAAGATCTAAG
*
156454 ACCGTAACGGCGGATCCAGTACCGCTAAGACACA
66 ACCGCAACGGCGGATCCAGTACCGCTAAGACACA
* * ** * * *
156488 AGGGAAAGATCTAAG-CTGCGATGGCGGATCCAGTATCACAAAGACAC-AAGGAAAAGATCTAAG
1 AGGGAAAGATCTAAGACCGCAACAGCAGATCCAGTACCACAAAAACACGAAGGAAAAGATCTAAG
156551 -CCGCAACGGCGGATCCAGTACC
66 ACCGCAACGGCGGATCCAGTACC
156573 ACAAAGATTT
Statistics
Matches: 75, Mismatches: 10, Indels: 3
0.85 0.11 0.03
Matches are distributed among these distances:
96 21 0.28
97 14 0.19
98 25 0.33
99 15 0.20
ACGTcount: A:0.39, C:0.24, G:0.25, T:0.12
Consensus pattern (99 bp):
AGGGAAAGATCTAAGACCGCAACAGCAGATCCAGTACCACAAAAACACGAAGGAAAAGATCTAAG
ACCGCAACGGCGGATCCAGTACCGCTAAGACACA
Found at i:156824 original size:100 final size:102
Alignment explanation
Indices: 156697--156950 Score: 395
Period size: 100 Copynumber: 2.5 Consensus size: 102
156687 TCAGATAAAA
156697 AAAACAATAGCAAGTCTTTATCTCTCTGAAGTTGTAGTAAGAGCAAGATGAAGCTTC-AAACATC
1 AAAACAATAGCAAGTCTTTATCTCTCTGAAGTTGTAGTAAGAGCAAGATGAAGCTTCAAAACATC
* *
156761 AATTCCTATCCTCTTGAAGTTATAGGAAAGTTGGATT
66 AATTCCTACCCTCTTGAAGTTACAGGAAAGTTGGATT
* * *
156798 -AAACAATAGCAAGTCTTTCTTTCTCTGACGTTGTAGTAAGAGCAAGATGAAGCTTCAAAACATC
1 AAAACAATAGCAAGTCTTTATCTCTCTGAAGTTGTAGTAAGAGCAAGATGAAGCTTCAAAACATC
* *
156862 AATTCCTACCCTCTTGAAGTTGCAGTAAAGTTGGATT
66 AATTCCTACCCTCTTGAAGTTACAGGAAAGTTGGATT
* * * *
156899 AAAACATTAGTAAGTCTTTATCTCTCTGAAGTTGTTGTAAAAGCAAGATGAA
1 AAAACAATAGCAAGTCTTTATCTCTCTGAAGTTGTAGTAAGAGCAAGATGAA
156951 ACCTCGACAC
Statistics
Matches: 137, Mismatches: 14, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
100 53 0.39
101 40 0.29
102 44 0.32
ACGTcount: A:0.35, C:0.16, G:0.18, T:0.31
Consensus pattern (102 bp):
AAAACAATAGCAAGTCTTTATCTCTCTGAAGTTGTAGTAAGAGCAAGATGAAGCTTCAAAACATC
AATTCCTACCCTCTTGAAGTTACAGGAAAGTTGGATT
Found at i:157140 original size:39 final size:39
Alignment explanation
Indices: 157092--157298 Score: 128
Period size: 39 Copynumber: 5.3 Consensus size: 39
157082 CAGCCATTTG
*
157092 ATCTTTTACCCCGAGCCTGGGGCAGATCATCATCAACCA
1 ATCTCTTACCCCGAGCCTGGGGCAGATCATCATCAACCA
* ** * * * * ****
157131 ATCTCTTACCTCGAGCCTAAGGCATATTATAACCATTTG
1 ATCTCTTACCCCGAGCCTGGGGCAGATCATCATCAACCA
* ** * *
157170 ATCTTTTACCCCGAGTTTGGGGCAGATCATCGTTAACCA
1 ATCTCTTACCCCGAGCCTGGGGCAGATCATCATCAACCA
** * * ** *
157209 ATCTCTTACCCCGAGCAAGGGGCAGATTA-CAACCATTCG
1 ATCTCTTACCCCGAGCCTGGGGCAGATCATC-ATCAACCA
* * * * *
157248 ATCTCTTACCCCAAACTTAGGGCAGATCACCATCAACCA
1 ATCTCTTACCCCGAGCCTGGGGCAGATCATCATCAACCA
157287 ATCTCTTTACCC
1 ATCTC-TTACCC
157299 TGATCACGGG
Statistics
Matches: 116, Mismatches: 49, Indels: 5
0.68 0.29 0.03
Matches are distributed among these distances:
38 1 0.01
39 108 0.93
40 7 0.06
ACGTcount: A:0.27, C:0.31, G:0.15, T:0.27
Consensus pattern (39 bp):
ATCTCTTACCCCGAGCCTGGGGCAGATCATCATCAACCA
Found at i:157191 original size:78 final size:77
Alignment explanation
Indices: 157042--157298 Score: 273
Period size: 78 Copynumber: 3.3 Consensus size: 77
157032 AGTGAAGTTA
* * ** ** * * *
157042 CATCACCAACCAATCTATTACCTTGAGCCTGGGCAGGTTGCAGCCATTTGATCTTTTACCCCGAG
1 CATCATCAACCAATCTCTTACCCCGAGCAAGGGCAGATTACAACCATTTGATCTTTTACCCCGAG
*
157107 CCTGGGGCAGAT
66 CTTGGGGCAGAT
* * *
157119 CATCATCAACCAATCTCTTACCTCGAGCCTAA-GGCATATTATAACCATTTGATCTTTTACCCCG
1 CATCATCAACCAATCTCTTACCCCGAG-C-AAGGGCAGATTACAACCATTTGATCTTTTACCCCG
*
157183 AGTTTGGGGCAGAT
64 AGCTTGGGGCAGAT
* * * * *
157197 CATCGTTAACCAATCTCTTACCCCGAGCAAGGGGCAGATTACAACCATTCGATCTCTTACCCCAA
1 CATCATCAACCAATCTCTTACCCCGAGCAA-GGGCAGATTACAACCATTTGATCTTTTACCCCGA
* *
157262 ACTTAGGGCAGAT
65 GCTTGGGGCAGAT
*
157275 CACCATCAACCAATCTCTTTACCC
1 CATCATCAACCAATCTC-TTACCC
157299 TGATCACGGG
Statistics
Matches: 149, Mismatches: 26, Indels: 8
0.81 0.14 0.04
Matches are distributed among these distances:
76 2 0.01
77 25 0.17
78 116 0.78
79 6 0.04
ACGTcount: A:0.26, C:0.31, G:0.16, T:0.26
Consensus pattern (77 bp):
CATCATCAACCAATCTCTTACCCCGAGCAAGGGCAGATTACAACCATTTGATCTTTTACCCCGAG
CTTGGGGCAGAT
Found at i:157673 original size:201 final size:201
Alignment explanation
Indices: 157328--158172 Score: 1122
Period size: 201 Copynumber: 4.2 Consensus size: 201
157318 GATTATCCAT
* * *
157328 AAGTGAGGCGGTCATCTTCCTGATGAGATAAATAGAAGTATACTAACTCAAGGCTCAAAGTGAGC
1 AAGTGAGGCGGTCATCTTCCTGATGAGATACAGAGAAGTATACCAACTCAAGGCTCAAAGTGAGC
* * * *
157393 AAATCTTTGAACACTAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAACAATAAAATGGTTAG
66 AAATCTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCAATAAAATGGTTAG
* * *
157458 CTTCTTGATGAGATACTGAGAAGTGGACCAAATTTGCCTTCCTGGTGAGATACAGAGAAGCGAAT
131 CTTCCTGATGAGATACTGAGAAGTGGACCAAATTCGCCTTCCTAGTGAGATACAGAGAAGCGAAT
157523 TGAAAC
196 TGAAAC
* *
157529 AAGTGAGTCGGTCATCTTCCTGATGAGATACAGAGAAGTATACCAACTCAAGGCTCAAAGTGAAC
1 AAGTGAGGCGGTCATCTTCCTGATGAGATACAGAGAAGTATACCAACTCAAGGCTCAAAGTGAGC
* * *
157594 AAATCTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGAAGGTCGAAGTAATAAAATAGTTAG
66 AAATCTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCAATAAAATGGTTAG
*
157659 CTTCCTGATGAGATACTGAGAAGTGGACCAAATTCGCCTTCCTAGTGCGATACAGAGAAGCGAAT
131 CTTCCTGATGAGATACTGAGAAGTGGACCAAATTCGCCTTCCTAGTGAGATACAGAGAAGCGAAT
157724 TGAAAC
196 TGAAAC
*
157730 AAGTGAGGCGGTCATCTTCCTGATGAGATATAGAGAAGTATACCAACTCAAGGCTCAAAGTGAGC
1 AAGTGAGGCGGTCATCTTCCTGATGAGATACAGAGAAGTATACCAACTCAAGGCTCAAAGTGAGC
*
157795 AAATCTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGTAATAAAATGGTTAG
66 AAATCTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCAATAAAATGGTTAG
* * *
157860 CTTCCTGATGAGATACTGAGAAGTGGACCAAATTCGCCTTCCTAATGAGATACAAAGAAGCGGAT
131 CTTCCTGATGAGATACTGAGAAGTGGACCAAATTCGCCTTCCTAGTGAGATACAGAGAAGCGAAT
**
157925 CAAAAC
196 TGAAAC
* * * * * *
157931 AAGT-AGCGCGGTCCTCTTCCTGATGAGATACTA-AGAAGAAGACCAAATCAA-ACCCACACTCG
1 AAGTGAG-GCGGTCATCTTCCTGATGAGATAC-AGAGAAGTATACCAACTCAAGGCTCA-A----
** * *
157993 ATGTGAGTGAATCTTCGAACCCCAACTTCCTGATGAGATACTGAAAAGCAGGTCGAAGCAATAAA
59 A-GTGAGCAAATCTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCAATAAA
* * * * * * * * *
158058 GTGGTTAGCTTCCTGATGTGATACTAAGAAGTGAACCAAATCCGTCTTCCT-GATGAAACATAGA
123 ATGGTTAGCTTCCTGATGAGATACTGAGAAGTGGACCAAATTCGCCTTCCTAG-TGAGATACAGA
* * **
158122 GAAGTGGATCAAAAC
187 GAAGCGAATTGAAAC
* ** * *
158137 AAGTGACGCGACCATCTTCTTGATGAGATACTGAGA
1 AAGTGAGGCGGTCATCTTCCTGATGAGATACAGAGA
158173 CGAAGACCAA
Statistics
Matches: 576, Mismatches: 57, Indels: 17
0.89 0.09 0.03
Matches are distributed among these distances:
200 5 0.01
201 417 0.72
202 1 0.00
205 1 0.00
206 151 0.26
207 1 0.00
ACGTcount: A:0.35, C:0.19, G:0.23, T:0.23
Consensus pattern (201 bp):
AAGTGAGGCGGTCATCTTCCTGATGAGATACAGAGAAGTATACCAACTCAAGGCTCAAAGTGAGC
AAATCTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCAATAAAATGGTTAG
CTTCCTGATGAGATACTGAGAAGTGGACCAAATTCGCCTTCCTAGTGAGATACAGAGAAGCGAAT
TGAAAC
Found at i:158543 original size:17 final size:17
Alignment explanation
Indices: 158521--158563 Score: 68
Period size: 17 Copynumber: 2.5 Consensus size: 17
158511 AACTTTTAAT
*
158521 TTTTAAATTTTAATTTA
1 TTTTAAATTTGAATTTA
158538 TTTTAAATTTGAATTTA
1 TTTTAAATTTGAATTTA
*
158555 TTTTGAATT
1 TTTTAAATT
158564 AAAAATTATT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.05, T:0.63
Consensus pattern (17 bp):
TTTTAAATTTGAATTTA
Found at i:159239 original size:3 final size:3
Alignment explanation
Indices: 159231--159288 Score: 64
Period size: 3 Copynumber: 19.0 Consensus size: 3
159221 TTAAAACGTC
* *
159231 AAT AAT AAT AAT AAT AGT AAT AAT AAGT AAT ATT AAT AAT AATT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AA-T AAT AAT AAT AAT AA-T AAT
*
159278 AA- AAA AAT AAT
1 AAT AAT AAT AAT
159289 CGAAGAGCCA
Statistics
Matches: 47, Mismatches: 5, Indels: 6
0.81 0.09 0.10
Matches are distributed among these distances:
2 2 0.04
3 39 0.83
4 6 0.13
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:159267 original size:16 final size:15
Alignment explanation
Indices: 159233--159278 Score: 65
Period size: 16 Copynumber: 2.9 Consensus size: 15
159223 AAAACGTCAA
159233 TAATAATAATAATAG
1 TAATAATAATAATAG
*
159248 TAATAATAAGTAATAT
1 TAATAATAA-TAATAG
159264 TAATAATAATTAATA
1 TAATAATAA-TAATA
159279 AAAAAATAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
15 9 0.32
16 19 0.68
ACGTcount: A:0.59, C:0.00, G:0.04, T:0.37
Consensus pattern (15 bp):
TAATAATAATAATAG
Found at i:159459 original size:22 final size:22
Alignment explanation
Indices: 159413--159459 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
159403 AGAGATAAAC
** *
159413 AAAGGGATTAAAAAGGAAATGA
1 AAAGGGATTAAAAAACAAATAA
*
159435 AAAGGGATTAAAAAACATATAA
1 AAAGGGATTAAAAAACAAATAA
159457 AAA
1 AAA
159460 AGAGAGGAAT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.64, C:0.02, G:0.19, T:0.15
Consensus pattern (22 bp):
AAAGGGATTAAAAAACAAATAA
Found at i:160460 original size:29 final size:29
Alignment explanation
Indices: 160398--160463 Score: 73
Period size: 29 Copynumber: 2.3 Consensus size: 29
160388 TAAACTGTCA
*
160398 AAAAATTATAATTTTACCCCTTTAACTTC
1 AAAAATTATAATTTTACCCCTTGAACTTC
* *
160427 CAAAATTATATTTTTGA-CCC-TGAACTTC
1 AAAAATTATAATTTT-ACCCCTTGAACTTC
160455 TAAAAATTA
1 -AAAAATTA
160464 CATTGATGCC
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
28 7 0.23
29 23 0.74
30 1 0.03
ACGTcount: A:0.39, C:0.18, G:0.03, T:0.39
Consensus pattern (29 bp):
AAAAATTATAATTTTACCCCTTGAACTTC
Found at i:160510 original size:30 final size:29
Alignment explanation
Indices: 160476--160657 Score: 120
Period size: 30 Copynumber: 6.2 Consensus size: 29
160466 TTGATGCCCG
*
160476 AACTTTCAAAGATTCCATTTTTAACCCCAA
1 AACTTTCAAAAATTCCATTTTT-ACCCCAA
** * *
160506 AACTTTTGAAAATTGCATTTTTACCCCTAG
1 AACTTTCAAAAATTCCATTTTTACCCC-AA
* **
160536 AA-TTCCAAAAATTCCATTTTTGACCTTAA
1 AACTTTCAAAAATTCCATTTTT-ACCCCAA
*
160565 AACTTTCAAAAATTACATTTTTACCCTCAA
1 AACTTTCAAAAATTCCATTTTTACCC-CAA
* * *** * *
160595 AA--TTCCAAATTTTTTTTTTTGATCCCGA
1 AACTTTCAAAAATTCCATTTTT-ACCCCAA
*
160623 AACTTTCAAAAATTAC-TTTCTTACCCCTAA
1 AACTTTCAAAAATTCCATTT-TTACCCC-AA
160653 AACTT
1 AACTT
160658 AAAACTCCAT
Statistics
Matches: 114, Mismatches: 29, Indels: 18
0.71 0.18 0.11
Matches are distributed among these distances:
28 17 0.15
29 36 0.32
30 61 0.54
ACGTcount: A:0.35, C:0.23, G:0.04, T:0.39
Consensus pattern (29 bp):
AACTTTCAAAAATTCCATTTTTACCCCAA
Found at i:160546 original size:29 final size:28
Alignment explanation
Indices: 160514--160603 Score: 99
Period size: 29 Copynumber: 3.1 Consensus size: 28
160504 AAAACTTTTG
* *
160514 AAAATTGCATTTTTACCCCTAGAATTCCA
1 AAAATTACATTTTTA-CCCTAAAATTCCA
* * *
160543 AAAATTCCATTTTTGACCTTAAAACTTTCA
1 AAAATTACATTTTT-ACCCTAAAA-TTCCA
160573 AAAATTACATTTTTACCCTCAAAATTCCA
1 AAAATTACATTTTTACCCT-AAAATTCCA
160602 AA
1 AA
160604 TTTTTTTTTT
Statistics
Matches: 51, Mismatches: 7, Indels: 6
0.80 0.11 0.09
Matches are distributed among these distances:
29 29 0.57
30 22 0.43
ACGTcount: A:0.39, C:0.22, G:0.03, T:0.36
Consensus pattern (28 bp):
AAAATTACATTTTTACCCTAAAATTCCA
Found at i:160556 original size:59 final size:59
Alignment explanation
Indices: 160482--160648 Score: 160
Period size: 59 Copynumber: 2.8 Consensus size: 59
160472 CCCGAACTTT
* ** * *
160482 CAAAGATTCCATTTTTAACCCCAAAACTTTTGAAAATTGCATTTTTACCC-CTAGAATTC
1 CAAAAATTCCATTTTTAACCCCAAAACTTTCAAAAATTACATTTTTACCCTC-AAAATTC
* **
160541 CAAAAATTCCATTTTTGACCTTAAAACTTTCAAAAATTACATTTTTACCCTCAAAATTC
1 CAAAAATTCCATTTTTAACCCCAAAACTTTCAAAAATTACATTTTTACCCTCAAAATTC
* *** * * *
160600 C-AAATTTTTTTTTTTGATCCCGAAACTTTCAAAAATTAC-TTTCTTACCC
1 CAAAAATTCCATTTTTAACCCCAAAACTTTCAAAAATTACATTT-TTACCC
160649 CTAAAACTTA
Statistics
Matches: 90, Mismatches: 16, Indels: 5
0.81 0.14 0.05
Matches are distributed among these distances:
57 3 0.03
58 36 0.40
59 50 0.56
60 1 0.01
ACGTcount: A:0.34, C:0.23, G:0.04, T:0.39
Consensus pattern (59 bp):
CAAAAATTCCATTTTTAACCCCAAAACTTTCAAAAATTACATTTTTACCCTCAAAATTC
Found at i:160717 original size:30 final size:30
Alignment explanation
Indices: 160683--160760 Score: 81
Period size: 30 Copynumber: 2.6 Consensus size: 30
160673 CCCTTTTTTC
160683 AAAATTACCATTTTACCCCCGA-ACTTCCA
1 AAAATTACCATTTTACCCCCGATACTTCCA
* * **
160712 AAAAAT-CCATTTTTGA-CCTCGATTTTTCCA
1 AAAATTACCA-TTTT-ACCCCCGATACTTCCA
160742 AAAATTACCATTTTACCCC
1 AAAATTACCATTTTACCCC
160761 AAGATATCTA
Statistics
Matches: 38, Mismatches: 6, Indels: 9
0.72 0.11 0.17
Matches are distributed among these distances:
28 3 0.08
29 15 0.39
30 17 0.45
31 3 0.08
ACGTcount: A:0.33, C:0.29, G:0.04, T:0.33
Consensus pattern (30 bp):
AAAATTACCATTTTACCCCCGATACTTCCA
Found at i:160774 original size:59 final size:57
Alignment explanation
Indices: 160683--160845 Score: 136
Period size: 58 Copynumber: 2.8 Consensus size: 57
160673 CCCTTTTTTC
* * * *
160683 AAAATTACCATTTTACCCCCGAACTTCCAAAAAAT-CCATTTTTGA-CCTCGATTTTTCCA
1 AAAATTACCATTTTACCCCAGAAC-TCC-AAAAATCCCA-TTTTAACCCT-AAATTTTCCA
* *
160742 AAAATTACCATTTTACCCCAAGATA-TCTAAAAATCCCATTTTAACCCTAAATTTTCCC
1 AAAATTACCATTTTACCCC-AGA-ACTCCAAAAATCCCATTTTAACCCTAAATTTTCCA
* * * * *
160800 AAAATTACCATTTTGCCCTAGAGAGTCCAAAATTACCA-TTTAACCC
1 AAAATTACCATTTTACCCCAGA-ACTCCAAAAATCCCATTTTAACCC
160846 CCAGGTATCC
Statistics
Matches: 87, Mismatches: 12, Indels: 12
0.78 0.11 0.11
Matches are distributed among these distances:
57 12 0.14
58 45 0.52
59 27 0.31
60 2 0.02
61 1 0.01
ACGTcount: A:0.36, C:0.28, G:0.05, T:0.32
Consensus pattern (57 bp):
AAAATTACCATTTTACCCCAGAACTCCAAAAATCCCATTTTAACCCTAAATTTTCCA
Found at i:163526 original size:13 final size:13
Alignment explanation
Indices: 163508--163551 Score: 52
Period size: 13 Copynumber: 3.3 Consensus size: 13
163498 CCTAATATTT
163508 ATTTTTTTTCTTG
1 ATTTTTTTTCTTG
*
163521 ATTTTTTTGCTTTG
1 ATTTTTTTTC-TTG
* *
163535 TTTTTTTTTCTTT
1 ATTTTTTTTCTTG
163548 ATTT
1 ATTT
163552 CCATTATTTC
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
13 14 0.56
14 11 0.44
ACGTcount: A:0.07, C:0.07, G:0.07, T:0.80
Consensus pattern (13 bp):
ATTTTTTTTCTTG
Found at i:164396 original size:81 final size:81
Alignment explanation
Indices: 164260--164436 Score: 327
Period size: 81 Copynumber: 2.2 Consensus size: 81
164250 TTCTCCTCCG
* *
164260 CACTATCCACAACAAGTATCACCATCTGTAGGTTATCCGCAACCCCCGATTGTGTCACCCGTGGT
1 CACTATCCACAACAAATATCACCATCTGTAGGTTATCCGCAACCCCCGATAGTGTCACCCGTGGT
164325 GGCATATCCGGATCCC
66 GGCATATCCGGATCCC
*
164341 CACTATCCACAACAAATATCACCATCTGTAGGTTATCCGCAACCCCCGGTAGTGTCACCCGTGGT
1 CACTATCCACAACAAATATCACCATCTGTAGGTTATCCGCAACCCCCGATAGTGTCACCCGTGGT
164406 GGCATATCCGGATCCC
66 GGCATATCCGGATCCC
164422 CACTATCCACAACAA
1 CACTATCCACAACAA
164437 GTAGCACCCT
Statistics
Matches: 93, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
81 93 1.00
ACGTcount: A:0.26, C:0.35, G:0.17, T:0.22
Consensus pattern (81 bp):
CACTATCCACAACAAATATCACCATCTGTAGGTTATCCGCAACCCCCGATAGTGTCACCCGTGGT
GGCATATCCGGATCCC
Found at i:167167 original size:31 final size:31
Alignment explanation
Indices: 167132--167229 Score: 94
Period size: 31 Copynumber: 3.2 Consensus size: 31
167122 TCACGTTAAG
167132 TTTTGAAGTAATTAATTATATTTTTTAAAAA
1 TTTTGAAGTAATTAATTATATTTTTTAAAAA
* * *
167163 TTTTG-AGT-GTTCAATTAAAATTTTTCAAAAA
1 TTTTGAAGTAATT-AATT-ATATTTTTTAAAAA
** * *
167194 TTTTGAAAAAATTAATGATAATTTTT-AAAA
1 TTTTGAAGTAATTAATTATATTTTTTAAAAA
167224 TTTTGA
1 TTTTGA
167230 GGGTTCAATT
Statistics
Matches: 53, Mismatches: 10, Indels: 9
0.74 0.14 0.12
Matches are distributed among these distances:
29 2 0.04
30 17 0.32
31 28 0.53
32 4 0.08
33 2 0.04
ACGTcount: A:0.42, C:0.02, G:0.08, T:0.48
Consensus pattern (31 bp):
TTTTGAAGTAATTAATTATATTTTTTAAAAA
Found at i:167243 original size:61 final size:61
Alignment explanation
Indices: 167132--167252 Score: 172
Period size: 61 Copynumber: 2.0 Consensus size: 61
167122 TCACGTTAAG
** * * * *
167132 TTTTGAAGTAATTAATTATATTTTTTAAAAATTTTGAGTGTTCAATTAAAATTTTTCAAAAA
1 TTTTGAAAAAATTAATGATAATTTTTAAAAATTTTGAGGGTTCAATTAAAA-ATTTCAAAAA
167194 TTTTGAAAAAATTAATGATAATTTTT-AAAATTTTGAGGGTTCAATTAAAAATTTCAAAA
1 TTTTGAAAAAATTAATGATAATTTTTAAAAATTTTGAGGGTTCAATTAAAAATTTCAAAA
167253 CTTTGATAGA
Statistics
Matches: 53, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
60 8 0.15
61 23 0.43
62 22 0.42
ACGTcount: A:0.43, C:0.03, G:0.09, T:0.45
Consensus pattern (61 bp):
TTTTGAAAAAATTAATGATAATTTTTAAAAATTTTGAGGGTTCAATTAAAAATTTCAAAAA
Found at i:168723 original size:17 final size:17
Alignment explanation
Indices: 168701--168743 Score: 68
Period size: 17 Copynumber: 2.5 Consensus size: 17
168691 AACTTTTAAT
*
168701 TTTTAAATTTTAATTTA
1 TTTTAAATTTGAATTTA
168718 TTTTAAATTTGAATTTA
1 TTTTAAATTTGAATTTA
*
168735 TTTTGAATT
1 TTTTAAATT
168744 AAAAATTATT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.05, T:0.63
Consensus pattern (17 bp):
TTTTAAATTTGAATTTA
Found at i:169419 original size:3 final size:3
Alignment explanation
Indices: 169411--169468 Score: 64
Period size: 3 Copynumber: 19.0 Consensus size: 3
169401 TTAAAACGTC
* *
169411 AAT AAT AAT AAT AAT AGT AAT AAT AAGT AAT ATT AAT AAT AATT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AA-T AAT AAT AAT AAT AA-T AAT
*
169458 AA- AAA AAT AAT
1 AAT AAT AAT AAT
169469 CGAAGAGCCA
Statistics
Matches: 47, Mismatches: 5, Indels: 6
0.81 0.09 0.10
Matches are distributed among these distances:
2 2 0.04
3 39 0.83
4 6 0.13
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:169447 original size:16 final size:15
Alignment explanation
Indices: 169413--169458 Score: 65
Period size: 16 Copynumber: 2.9 Consensus size: 15
169403 AAAACGTCAA
169413 TAATAATAATAATAG
1 TAATAATAATAATAG
*
169428 TAATAATAAGTAATAT
1 TAATAATAA-TAATAG
169444 TAATAATAATTAATA
1 TAATAATAA-TAATA
169459 AAAAAATAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
15 9 0.32
16 19 0.68
ACGTcount: A:0.59, C:0.00, G:0.04, T:0.37
Consensus pattern (15 bp):
TAATAATAATAATAG
Found at i:169639 original size:22 final size:22
Alignment explanation
Indices: 169593--169639 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
169583 AGAGATAAAC
** *
169593 AAAGGGATTAAAAAGGAAATGA
1 AAAGGGATTAAAAAACAAATAA
*
169615 AAAGGGATTAAAAAACATATAA
1 AAAGGGATTAAAAAACAAATAA
169637 AAA
1 AAA
169640 AGAGAGGAAT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.64, C:0.02, G:0.19, T:0.15
Consensus pattern (22 bp):
AAAGGGATTAAAAAACAAATAA
Found at i:170640 original size:29 final size:29
Alignment explanation
Indices: 170578--170643 Score: 73
Period size: 29 Copynumber: 2.3 Consensus size: 29
170568 TAAACTGTCA
*
170578 AAAAATTATAATTTTACCCCTTTAACTTC
1 AAAAATTATAATTTTACCCCTTGAACTTC
* *
170607 CAAAATTATATTTTTGA-CCC-TGAACTTC
1 AAAAATTATAATTTT-ACCCCTTGAACTTC
170635 TAAAAATTA
1 -AAAAATTA
170644 CATTGATGCC
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
28 7 0.23
29 23 0.74
30 1 0.03
ACGTcount: A:0.39, C:0.18, G:0.03, T:0.39
Consensus pattern (29 bp):
AAAAATTATAATTTTACCCCTTGAACTTC
Found at i:170690 original size:30 final size:29
Alignment explanation
Indices: 170656--170837 Score: 120
Period size: 30 Copynumber: 6.2 Consensus size: 29
170646 TTGATGCCCG
*
170656 AACTTTCAAAGATTCCATTTTTAACCCCAA
1 AACTTTCAAAAATTCCATTTTT-ACCCCAA
** * *
170686 AACTTTTGAAAATTGCATTTTTACCCCTAG
1 AACTTTCAAAAATTCCATTTTTACCCC-AA
* **
170716 AA-TTCCAAAAATTCCATTTTTGACCTTAA
1 AACTTTCAAAAATTCCATTTTT-ACCCCAA
*
170745 AACTTTCAAAAATTACATTTTTACCCTCAA
1 AACTTTCAAAAATTCCATTTTTACCC-CAA
* * *** * *
170775 AA--TTCCAAATTTTTTTTTTTGATCCCGA
1 AACTTTCAAAAATTCCATTTTT-ACCCCAA
*
170803 AACTTTCAAAAATTAC-TTTCTTACCCCTAA
1 AACTTTCAAAAATTCCATTT-TTACCCC-AA
170833 AACTT
1 AACTT
170838 AAAACTCCAT
Statistics
Matches: 114, Mismatches: 29, Indels: 18
0.71 0.18 0.11
Matches are distributed among these distances:
28 17 0.15
29 36 0.32
30 61 0.54
ACGTcount: A:0.35, C:0.23, G:0.04, T:0.39
Consensus pattern (29 bp):
AACTTTCAAAAATTCCATTTTTACCCCAA
Found at i:170726 original size:29 final size:28
Alignment explanation
Indices: 170694--170783 Score: 99
Period size: 29 Copynumber: 3.1 Consensus size: 28
170684 AAAACTTTTG
* *
170694 AAAATTGCATTTTTACCCCTAGAATTCCA
1 AAAATTACATTTTTA-CCCTAAAATTCCA
* * *
170723 AAAATTCCATTTTTGACCTTAAAACTTTCA
1 AAAATTACATTTTT-ACCCTAAAA-TTCCA
170753 AAAATTACATTTTTACCCTCAAAATTCCA
1 AAAATTACATTTTTACCCT-AAAATTCCA
170782 AA
1 AA
170784 TTTTTTTTTT
Statistics
Matches: 51, Mismatches: 7, Indels: 6
0.80 0.11 0.09
Matches are distributed among these distances:
29 29 0.57
30 22 0.43
ACGTcount: A:0.39, C:0.22, G:0.03, T:0.36
Consensus pattern (28 bp):
AAAATTACATTTTTACCCTAAAATTCCA
Found at i:170736 original size:59 final size:59
Alignment explanation
Indices: 170662--170828 Score: 160
Period size: 59 Copynumber: 2.8 Consensus size: 59
170652 CCCGAACTTT
* ** * *
170662 CAAAGATTCCATTTTTAACCCCAAAACTTTTGAAAATTGCATTTTTACCC-CTAGAATTC
1 CAAAAATTCCATTTTTAACCCCAAAACTTTCAAAAATTACATTTTTACCCTC-AAAATTC
* **
170721 CAAAAATTCCATTTTTGACCTTAAAACTTTCAAAAATTACATTTTTACCCTCAAAATTC
1 CAAAAATTCCATTTTTAACCCCAAAACTTTCAAAAATTACATTTTTACCCTCAAAATTC
* *** * * *
170780 C-AAATTTTTTTTTTTGATCCCGAAACTTTCAAAAATTAC-TTTCTTACCC
1 CAAAAATTCCATTTTTAACCCCAAAACTTTCAAAAATTACATTT-TTACCC
170829 CTAAAACTTA
Statistics
Matches: 90, Mismatches: 16, Indels: 5
0.81 0.14 0.05
Matches are distributed among these distances:
57 3 0.03
58 36 0.40
59 50 0.56
60 1 0.01
ACGTcount: A:0.34, C:0.23, G:0.04, T:0.39
Consensus pattern (59 bp):
CAAAAATTCCATTTTTAACCCCAAAACTTTCAAAAATTACATTTTTACCCTCAAAATTC
Found at i:170897 original size:30 final size:30
Alignment explanation
Indices: 170863--170940 Score: 81
Period size: 30 Copynumber: 2.6 Consensus size: 30
170853 CCCTTTTTTC
170863 AAAATTACCATTTTACCCCCGA-ACTTCCA
1 AAAATTACCATTTTACCCCCGATACTTCCA
* * **
170892 AAAAAT-CCATTTTTGA-CCTCGATTTTTCCA
1 AAAATTACCA-TTTT-ACCCCCGATACTTCCA
170922 AAAATTACCATTTTACCCC
1 AAAATTACCATTTTACCCC
170941 AAGATATCTA
Statistics
Matches: 38, Mismatches: 6, Indels: 9
0.72 0.11 0.17
Matches are distributed among these distances:
28 3 0.08
29 15 0.39
30 17 0.45
31 3 0.08
ACGTcount: A:0.33, C:0.29, G:0.04, T:0.33
Consensus pattern (30 bp):
AAAATTACCATTTTACCCCCGATACTTCCA
Found at i:170954 original size:59 final size:57
Alignment explanation
Indices: 170863--171025 Score: 136
Period size: 58 Copynumber: 2.8 Consensus size: 57
170853 CCCTTTTTTC
* * * *
170863 AAAATTACCATTTTACCCCCGAACTTCCAAAAAAT-CCATTTTTGA-CCTCGATTTTTCCA
1 AAAATTACCATTTTACCCCAGAAC-TCC-AAAAATCCCA-TTTTAACCCT-AAATTTTCCA
* *
170922 AAAATTACCATTTTACCCCAAGATA-TCTAAAAATCCCATTTTAACCCTAAATTTTCCC
1 AAAATTACCATTTTACCCC-AGA-ACTCCAAAAATCCCATTTTAACCCTAAATTTTCCA
* * * * *
170980 AAAATTACCATTTTGCCCTAGAGAGTCCAAAATTACCA-TTTAACCC
1 AAAATTACCATTTTACCCCAGA-ACTCCAAAAATCCCATTTTAACCC
171026 CCAGGTATCC
Statistics
Matches: 87, Mismatches: 12, Indels: 12
0.78 0.11 0.11
Matches are distributed among these distances:
57 12 0.14
58 45 0.52
59 27 0.31
60 2 0.02
61 1 0.01
ACGTcount: A:0.36, C:0.28, G:0.05, T:0.32
Consensus pattern (57 bp):
AAAATTACCATTTTACCCCAGAACTCCAAAAATCCCATTTTAACCCTAAATTTTCCA
Found at i:173706 original size:13 final size:13
Alignment explanation
Indices: 173688--173731 Score: 52
Period size: 13 Copynumber: 3.3 Consensus size: 13
173678 CCTAATATTT
173688 ATTTTTTTTCTTG
1 ATTTTTTTTCTTG
*
173701 ATTTTTTTGCTTTG
1 ATTTTTTTTC-TTG
* *
173715 TTTTTTTTTCTTT
1 ATTTTTTTTCTTG
173728 ATTT
1 ATTT
173732 CCATTATTTC
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
13 14 0.56
14 11 0.44
ACGTcount: A:0.07, C:0.07, G:0.07, T:0.80
Consensus pattern (13 bp):
ATTTTTTTTCTTG
Found at i:174576 original size:81 final size:81
Alignment explanation
Indices: 174440--174616 Score: 327
Period size: 81 Copynumber: 2.2 Consensus size: 81
174430 TTCTCCTCCG
* *
174440 CACTATCCACAACAAGTATCACCATCTGTAGGTTATCCGCAACCCCCGATTGTGTCACCCGTGGT
1 CACTATCCACAACAAATATCACCATCTGTAGGTTATCCGCAACCCCCGATAGTGTCACCCGTGGT
174505 GGCATATCCGGATCCC
66 GGCATATCCGGATCCC
*
174521 CACTATCCACAACAAATATCACCATCTGTAGGTTATCCGCAACCCCCGGTAGTGTCACCCGTGGT
1 CACTATCCACAACAAATATCACCATCTGTAGGTTATCCGCAACCCCCGATAGTGTCACCCGTGGT
174586 GGCATATCCGGATCCC
66 GGCATATCCGGATCCC
174602 CACTATCCACAACAA
1 CACTATCCACAACAA
174617 GTAGCACCCT
Statistics
Matches: 93, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
81 93 1.00
ACGTcount: A:0.26, C:0.35, G:0.17, T:0.22
Consensus pattern (81 bp):
CACTATCCACAACAAATATCACCATCTGTAGGTTATCCGCAACCCCCGATAGTGTCACCCGTGGT
GGCATATCCGGATCCC
Found at i:177347 original size:31 final size:31
Alignment explanation
Indices: 177312--177409 Score: 94
Period size: 31 Copynumber: 3.2 Consensus size: 31
177302 TCACGTTAAG
177312 TTTTGAAGTAATTAATTATATTTTTTAAAAA
1 TTTTGAAGTAATTAATTATATTTTTTAAAAA
* * *
177343 TTTTG-AGT-GTTCAATTAAAATTTTTCAAAAA
1 TTTTGAAGTAATT-AATT-ATATTTTTTAAAAA
** * *
177374 TTTTGAAAAAATTAATGATAATTTTT-AAAA
1 TTTTGAAGTAATTAATTATATTTTTTAAAAA
177404 TTTTGA
1 TTTTGA
177410 GGGTTCAATT
Statistics
Matches: 53, Mismatches: 10, Indels: 9
0.74 0.14 0.12
Matches are distributed among these distances:
29 2 0.04
30 17 0.32
31 28 0.53
32 4 0.08
33 2 0.04
ACGTcount: A:0.42, C:0.02, G:0.08, T:0.48
Consensus pattern (31 bp):
TTTTGAAGTAATTAATTATATTTTTTAAAAA
Found at i:177423 original size:61 final size:61
Alignment explanation
Indices: 177312--177432 Score: 172
Period size: 61 Copynumber: 2.0 Consensus size: 61
177302 TCACGTTAAG
** * * * *
177312 TTTTGAAGTAATTAATTATATTTTTTAAAAATTTTGAGTGTTCAATTAAAATTTTTCAAAAA
1 TTTTGAAAAAATTAATGATAATTTTTAAAAATTTTGAGGGTTCAATTAAAA-ATTTCAAAAA
177374 TTTTGAAAAAATTAATGATAATTTTT-AAAATTTTGAGGGTTCAATTAAAAATTTCAAAA
1 TTTTGAAAAAATTAATGATAATTTTTAAAAATTTTGAGGGTTCAATTAAAAATTTCAAAA
177433 CTTTGATAGA
Statistics
Matches: 53, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
60 8 0.15
61 23 0.43
62 22 0.42
ACGTcount: A:0.43, C:0.03, G:0.09, T:0.45
Consensus pattern (61 bp):
TTTTGAAAAAATTAATGATAATTTTTAAAAATTTTGAGGGTTCAATTAAAAATTTCAAAAA
Found at i:181586 original size:18 final size:18
Alignment explanation
Indices: 181561--181599 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 18
181551 CTTATATTAT
181561 ATATATATATATATTAAAAA
1 ATATATA-ATATA-TAAAAA
181581 ATATATAATATATAAAAA
1 ATATATAATATATAAAAA
181599 A
1 A
181600 ACTAAAAATA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 7 0.37
19 5 0.26
20 7 0.37
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (18 bp):
ATATATAATATATAAAAA
Found at i:181609 original size:19 final size:19
Alignment explanation
Indices: 181569--181620 Score: 54
Period size: 19 Copynumber: 2.7 Consensus size: 19
181559 ATATATATAT
* *
181569 ATATATTAAAAAATATATA
1 ATATATAAAAAAATATAAA
181588 ATATATAAAAAAACTA-AAA
1 ATATATAAAAAAA-TATAAA
181607 ATAT-TAAAATAAAT
1 ATATATAAAA-AAAT
181621 GCTTCTCAAC
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
18 6 0.21
19 21 0.72
20 2 0.07
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (19 bp):
ATATATAAAAAAATATAAA
Found at i:181806 original size:24 final size:23
Alignment explanation
Indices: 181753--181806 Score: 54
Period size: 24 Copynumber: 2.2 Consensus size: 23
181743 TATAATATTC
*
181753 AAACAATAATAACAAAATATAGTA
1 AAAC-ATAATAACAAAATATAGCA
**
181777 ACAACATAATAATGAAATAATAGCA
1 A-AACATAATAACAAAAT-ATAGCA
181802 AAACA
1 AAACA
181807 GTGAAAAAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
24 16 0.64
25 9 0.36
ACGTcount: A:0.65, C:0.11, G:0.06, T:0.19
Consensus pattern (23 bp):
AAACATAATAACAAAATATAGCA
Found at i:182464 original size:5 final size:5
Alignment explanation
Indices: 182450--182482 Score: 57
Period size: 5 Copynumber: 6.6 Consensus size: 5
182440 GATACCAAAT
*
182450 CAGAC CAGAC TAGAC CAGAC CAGAC CAGAC CAG
1 CAGAC CAGAC CAGAC CAGAC CAGAC CAGAC CAG
182483 TCAAGTTTCT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
5 26 1.00
ACGTcount: A:0.39, C:0.36, G:0.21, T:0.03
Consensus pattern (5 bp):
CAGAC
Found at i:182735 original size:51 final size:50
Alignment explanation
Indices: 182651--183302 Score: 456
Period size: 51 Copynumber: 12.9 Consensus size: 50
182641 GAGCCAGCAG
* * * * *
182651 CAGCATCGACCTCCTCGAGAAAGTTATCAGAGTTCTGTTAATCTTCAACAA
1 CAGCATCGGCCTCCTCGGGAAAGTTAT-AGAGTTCAGATCATCTTCAACAA
* *
182702 CAGCATCGGCCTCCTCGGGAAACTTATAGGAGTTCTGATCATCTTCAACAA
1 CAGCATCGGCCTCCTCGGGAAAGTTATA-GAGTTCAGATCATCTTCAACAA
* * * * *
182753 CAGCATCAG---CCTCGAGAAACTTATAAGAGCTCAGATCATATTCAACAA
1 CAGCATCGGCCTCCTCGGGAAAGTTAT-AGAGTTCAGATCATCTTCAACAA
* * * * *
182801 CAGCATCGGCCTCATTGGGAAACTAATGAGAGTTCTGATCATCTTCAACAA
1 CAGCATCGGCCTCCTCGGGAAAGTTAT-AGAGTTCAGATCATCTTCAACAA
* ** * * *
182852 AAGCA---GCAACCTCGGGAAAGTTATAGAAGCTCAGGTCATATTCAACAA
1 CAGCATCGGCCTCCTCGGGAAAGTTATAG-AGTTCAGATCATCTTCAACAA
* * * * * *
182900 CAGCATTGTCCTCCTCGAGAAAGTTATCAGAGTCCAAATCATCTCCAACAA
1 CAGCATCGGCCTCCTCGGGAAAGTTAT-AGAGTTCAGATCATCTTCAACAA
* * * *
182951 CAGCATC-G--ACCTCGGGAAACTTATAAGAGCTCAGATCATATTCAACAA
1 CAGCATCGGCCTCCTCGGGAAAGTTAT-AGAGTTCAGATCATCTTCAACAA
* * * *
182999 CAGCATCAGCCTCCTCGGGAGAGTTATCAGAGTTCCGATCATCTTCATCAA
1 CAGCATCGGCCTCCTCGGGAAAGTTAT-AGAGTTCAGATCATCTTCAACAA
* *
183050 CAACATCGCCAGCCTCCTCGGGAAAGTTATCAGAGTTCTGATCATCTTCAACAA
1 CAGCATCG---GCCTCCTCGGGAAAGTTAT-AGAGTTCAGATCATCTTCAACAA
** ** * * * *
183104 CAGCAAT-ATCAGCCTCGAGAAAGTTATCAG-GACTCGGAACATCTTCAACAA
1 CAGC-ATCGGCCTCCTCGGGAAAGTTAT-AGAG-TTCAGATCATCTTCAACAA
* *
183155 CAGCAACGGCCTCCTCGAGAAAGTTATCAGAGTTCCA-ATCATCTTCAACAA
1 CAGCATCGGCCTCCTCGGGAAAGTTAT-AGAGTT-CAGATCATCTTCAACAA
* * *
183206 CAGCAACAGCCT--TC-GGAAAGTTATCATCAGAGTTCCA-ATCATCTTCAACAG
1 CAGCATCGGCCTCCTCGGGAAAG-T-T-AT-AGAGTT-CAGATCATCTTCAACAA
* * * * *
183257 CAGCAGCGTCAGT-CTCGGGAAAGTTATCAGAGCTCCGATCATCTTC
1 CAGCATCGGC-CTCCTCGGGAAAGTTAT-AGAGTTCAGATCATCTTC
183303 CTCCTCGAGA
Statistics
Matches: 482, Mismatches: 91, Indels: 56
0.77 0.14 0.09
Matches are distributed among these distances:
47 2 0.00
48 118 0.24
49 5 0.01
50 5 0.01
51 292 0.61
52 6 0.01
53 3 0.01
54 49 0.10
55 2 0.00
ACGTcount: A:0.33, C:0.27, G:0.18, T:0.23
Consensus pattern (50 bp):
CAGCATCGGCCTCCTCGGGAAAGTTATAGAGTTCAGATCATCTTCAACAA
Found at i:182834 original size:99 final size:99
Alignment explanation
Indices: 182694--183108 Score: 467
Period size: 99 Copynumber: 4.1 Consensus size: 99
182684 TCTGTTAATC
182694 TTCAACAACAGCATCGGCCTCCTCGGGAAACTTAT-AGGAGTTCTGATCATCTTCAACAACAGCA
1 TTCAACAACAGCATCGGCCTCCTCGGGAAACTTATCA-GAGTTCTGATCATCTTCAACAACAGCA
*
182758 TCAGCCTCGAGAAACTTATAAGAGCTCAGATCATA
65 TCAGCCTCGGGAAACTTATAAGAGCTCAGATCATA
* * * * * *
182793 TTCAACAACAGCATCGGCCTCATTGGGAAACTAATGAGAGTTCTGATCATCTTCAACAAAAGCAG
1 TTCAACAACAGCATCGGCCTCCTCGGGAAACTTATCAGAGTTCTGATCATCTTCAACAACAGCAT
* * *
182858 CAACCTCGGGAAAGTTAT-AGAAGCTCAGGTCATA
66 CAGCCTCGGGAAACTTATAAG-AGCTCAGATCATA
* * * * * ** *
182892 TTCAACAACAGCATTGTCCTCCTCGAGAAAGTTATCAGAGTCCAAATCATCTCCAACAACAGCAT
1 TTCAACAACAGCATCGGCCTCCTCGGGAAACTTATCAGAGTTCTGATCATCTTCAACAACAGCAT
182957 C-GACCTCGGGAAACTTATAAGAGCTCAGATCATA
66 CAG-CCTCGGGAAACTTATAAGAGCTCAGATCATA
* * * * * *
182991 TTCAACAACAGCATCAGCCTCCTCGGGAGAGTTATCAGAGTTCCGATCATCTTCATCAACAACAT
1 TTCAACAACAGCATCGGCCTCCTCGGGAAACTTATCAGAGTTCTGATCATCTTCAACAACAGCAT
* * * * *
183056 CGCCAGCCTCCTCGGGAAAGTTATCAGAGTTCTGATCATC
66 ---CAG---CCTCGGGAAACTTATAAGAGCTCAGATCATA
183096 TTCAACAACAGCA
1 TTCAACAACAGCA
183109 ATATCAGCCT
Statistics
Matches: 263, Mismatches: 43, Indels: 14
0.82 0.13 0.04
Matches are distributed among these distances:
98 2 0.01
99 217 0.83
100 3 0.01
102 1 0.00
103 1 0.00
105 39 0.15
ACGTcount: A:0.33, C:0.27, G:0.17, T:0.23
Consensus pattern (99 bp):
TTCAACAACAGCATCGGCCTCCTCGGGAAACTTATCAGAGTTCTGATCATCTTCAACAACAGCAT
CAGCCTCGGGAAACTTATAAGAGCTCAGATCATA
Found at i:183188 original size:156 final size:153
Alignment explanation
Indices: 182909--183207 Score: 386
Period size: 156 Copynumber: 1.9 Consensus size: 153
182899 ACAGCATTGT
*
182909 CCTCCTCGAGAAAGTTATCAGAGTCCAAATCATCTCCAACAACAGCATCGACCTCGGGAAACTTA
1 CCTCCTCGAGAAAGTTATCAGAGTCCAAATCATCTCCAACAACAGCATCGACCTCGAGAAACTTA
* * * * *
182974 TAAGAGCTCAGATCATATTCAACAACAGCATCAGCCTCCTCGGGAGAGTTATCAGAGTTCCGATC
66 TAAGAGCTCAGAACATATTCAACAACAGCAACAGCCTCCTCGAGAAAGTTATCAGAGTTCCAATC
*
183039 ATCTTCATCAACAACATCGCCAG
131 ATCTTCAACAACAACATCGCCAG
* * ** *
183062 CCTCCTCGGGAAAGTTATCAGAGTTCTGATCATCTTCAACAACAGCAATATC-AGCCTCGAGAAA
1 CCTCCTCGAGAAAGTTATCAGAGTCCAAATCATCTCCAACAACAGC---ATCGA-CCTCGAGAAA
* * * * *
183126 GTTATCAG-GACTCGGAACATCTTCAACAACAGCAACGGCCTCCTCGAGAAAGTTATCAGAGTTC
62 CTTATAAGAG-CTCAGAACATATTCAACAACAGCAACAGCCTCCTCGAGAAAGTTATCAGAGTTC
183190 CAATCATCTTCAACAACA
126 CAATCATCTTCAACAACA
183208 GCAACAGCCT
Statistics
Matches: 124, Mismatches: 17, Indels: 7
0.84 0.11 0.05
Matches are distributed among these distances:
153 41 0.33
155 2 0.02
156 81 0.65
ACGTcount: A:0.33, C:0.28, G:0.16, T:0.22
Consensus pattern (153 bp):
CCTCCTCGAGAAAGTTATCAGAGTCCAAATCATCTCCAACAACAGCATCGACCTCGAGAAACTTA
TAAGAGCTCAGAACATATTCAACAACAGCAACAGCCTCCTCGAGAAAGTTATCAGAGTTCCAATC
ATCTTCAACAACAACATCGCCAG
Found at i:183330 original size:36 final size:36
Alignment explanation
Indices: 183270--183338 Score: 93
Period size: 36 Copynumber: 1.9 Consensus size: 36
183260 CAGCGTCAGT
* * * *
183270 CTCGGGAAAGTTATCAGAGCTCCGATCATCTTCCTC
1 CTCGAGAAAGTTATCAAAACTCCGATCACCTTCCTC
*
183306 CTCGAGAAAGTTATCAAAATTCCGATCACCTTC
1 CTCGAGAAAGTTATCAAAACTCCGATCACCTTC
183339 AACAACAGCA
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
36 28 1.00
ACGTcount: A:0.28, C:0.29, G:0.16, T:0.28
Consensus pattern (36 bp):
CTCGAGAAAGTTATCAAAACTCCGATCACCTTCCTC
Found at i:185943 original size:10 final size:11
Alignment explanation
Indices: 185928--185964 Score: 51
Period size: 10 Copynumber: 3.5 Consensus size: 11
185918 TTTTATTTAA
185928 TATATCTATAT
1 TATATCTATAT
185939 T-TATCTAT-T
1 TATATCTATAT
185948 TATATCTATAT
1 TATATCTATAT
185959 CTATAT
1 -TATAT
185965 ATTTTCACTT
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
9 2 0.09
10 14 0.61
11 2 0.09
12 5 0.22
ACGTcount: A:0.32, C:0.11, G:0.00, T:0.57
Consensus pattern (11 bp):
TATATCTATAT
Found at i:185953 original size:20 final size:20
Alignment explanation
Indices: 185928--185968 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
185918 TTTTATTTAA
* *
185928 TATATCTATATTTATCTATT
1 TATATCTATATCTATATATT
185948 TATATCTATATCTATATATT
1 TATATCTATATCTATATATT
185968 T
1 T
185969 TCACTTCCTC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.32, C:0.10, G:0.00, T:0.59
Consensus pattern (20 bp):
TATATCTATATCTATATATT
Found at i:193205 original size:15 final size:15
Alignment explanation
Indices: 193175--193203 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
193165 AAAAAAAAGT
193175 TAAAAAAACATAAAA
1 TAAAAAAACATAAAA
193190 TAAAAAAA-ATAAAA
1 TAAAAAAACATAAAA
193204 ATGCTCAGAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 6 0.43
15 8 0.57
ACGTcount: A:0.83, C:0.03, G:0.00, T:0.14
Consensus pattern (15 bp):
TAAAAAAACATAAAA
Found at i:196319 original size:30 final size:30
Alignment explanation
Indices: 196283--196357 Score: 123
Period size: 30 Copynumber: 2.5 Consensus size: 30
196273 GGCCATGTTT
196283 TAATAGGAAAATTTTAGATAGATTAAAAAG
1 TAATAGGAAAATTTTAGATAGATTAAAAAG
196313 TAATAGGAAAATTTTAGATAGATTAAAAAG
1 TAATAGGAAAATTTTAGATAGATTAAAAAG
* *
196343 AAATAAGAATAATTT
1 TAATAGGAA-AATTT
196358 AGGCATTAAA
Statistics
Matches: 42, Mismatches: 2, Indels: 1
0.93 0.04 0.02
Matches are distributed among these distances:
30 37 0.88
31 5 0.12
ACGTcount: A:0.55, C:0.00, G:0.15, T:0.31
Consensus pattern (30 bp):
TAATAGGAAAATTTTAGATAGATTAAAAAG
Found at i:197359 original size:22 final size:22
Alignment explanation
Indices: 197332--197375 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
197322 TAATATTTAT
*
197332 ATTAAAT-CATTAATCCAAAACA
1 ATTAAATCCATT-ACCCAAAACA
197354 ATTAAATCCATTACCCAAAACA
1 ATTAAATCCATTACCCAAAACA
197376 TAAAAAAATG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 16 0.80
23 4 0.20
ACGTcount: A:0.52, C:0.23, G:0.00, T:0.25
Consensus pattern (22 bp):
ATTAAATCCATTACCCAAAACA
Found at i:198318 original size:192 final size:192
Alignment explanation
Indices: 197991--198376 Score: 745
Period size: 192 Copynumber: 2.0 Consensus size: 192
197981 AACACATTCA
197991 AATCATGATATACAATTTAATCCGAGTCTCGGTCGAGCTTAGGAAAGCTCTTTTGATGACCCAAA
1 AATCATGATATACAATTTAATCCGAGTCTCGGTCGAGCTTAGGAAAGCTCTTTTGATGACCCAAA
*
198056 CATGAAATAGGACCAAATTGTAAAGTTGTAAAAGTTTAGGACCAACATCGTCACTCAATATGTCA
66 CATGAAATAGGACCAAATTATAAAGTTGTAAAAGTTTAGGACCAACATCGTCACTCAATATGTCA
* *
198121 CGTCGCTACATCACAAACTATTGGCCACCGTTGCGACAAGGGAAATTGATCGTCGTAACGAG
131 CGTCGCGACATCACAAACTATTGGCCACCATTGCGACAAGGGAAATTGATCGTCGTAACGAG
198183 AATCATGATATACAATTTAATCCGAGTCTCGGTCGAGCTTAGGAAAGCTCTTTTGATGACCCAAA
1 AATCATGATATACAATTTAATCCGAGTCTCGGTCGAGCTTAGGAAAGCTCTTTTGATGACCCAAA
198248 CATGAAATAGGACCAAATTATAAAGTTGTAAAAGTTTAGGACCAACATCGTCACTCAATATGTCA
66 CATGAAATAGGACCAAATTATAAAGTTGTAAAAGTTTAGGACCAACATCGTCACTCAATATGTCA
198313 CGTCGCGACATCACAAACTATTGGCCACCATTGCGACAAGGGAAATTGATCGTCGTAACGAG
131 CGTCGCGACATCACAAACTATTGGCCACCATTGCGACAAGGGAAATTGATCGTCGTAACGAG
198375 AA
1 AA
198377 CCTTGCTTTT
Statistics
Matches: 191, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
192 191 1.00
ACGTcount: A:0.35, C:0.21, G:0.19, T:0.25
Consensus pattern (192 bp):
AATCATGATATACAATTTAATCCGAGTCTCGGTCGAGCTTAGGAAAGCTCTTTTGATGACCCAAA
CATGAAATAGGACCAAATTATAAAGTTGTAAAAGTTTAGGACCAACATCGTCACTCAATATGTCA
CGTCGCGACATCACAAACTATTGGCCACCATTGCGACAAGGGAAATTGATCGTCGTAACGAG
Found at i:199712 original size:2 final size:2
Alignment explanation
Indices: 199657--199693 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
199647 ATTGAAATTA
199657 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
199694 GAATTATAAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:200887 original size:23 final size:23
Alignment explanation
Indices: 200808--200889 Score: 58
Period size: 23 Copynumber: 3.3 Consensus size: 23
200798 TTTTATCTAA
200808 TATAAATAAGGGTATTTTAGAAG
1 TATAAATAAGGGTATTTTAGAAG
* * *
200831 TATAAAAAATTAATAGGAATTTTTATCTAA-
1 TAT---AAA-TAA-GGGTA-TTTTA--GAAG
200861 TATAAATAAGGGTATTTTAGAAG
1 TATAAATAAGGGTATTTTAGAAG
200884 TATAAA
1 TATAAA
200890 AAATTAATAG
Statistics
Matches: 44, Mismatches: 6, Indels: 18
0.65 0.09 0.26
Matches are distributed among these distances:
22 2 0.05
23 9 0.20
24 5 0.11
25 3 0.07
26 6 0.14
27 6 0.14
28 3 0.07
29 5 0.11
30 3 0.07
31 2 0.05
ACGTcount: A:0.48, C:0.01, G:0.15, T:0.37
Consensus pattern (23 bp):
TATAAATAAGGGTATTTTAGAAG
Found at i:200921 original size:53 final size:53
Alignment explanation
Indices: 200796--200908 Score: 217
Period size: 53 Copynumber: 2.1 Consensus size: 53
200786 ATTATTAGTT
200796 ATTTTTATCTAATATAAATAAGGGTATTTTAGAAGTATAAAAAATTAATAGGA
1 ATTTTTATCTAATATAAATAAGGGTATTTTAGAAGTATAAAAAATTAATAGGA
200849 ATTTTTATCTAATATAAATAAGGGTATTTTAGAAGTATAAAAAATTAATAGGA
1 ATTTTTATCTAATATAAATAAGGGTATTTTAGAAGTATAAAAAATTAATAGGA
200902 ATATTTT
1 AT-TTTT
200909 TTTTGGTAAA
Statistics
Matches: 59, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
53 55 0.93
54 4 0.07
ACGTcount: A:0.46, C:0.02, G:0.12, T:0.40
Consensus pattern (53 bp):
ATTTTTATCTAATATAAATAAGGGTATTTTAGAAGTATAAAAAATTAATAGGA
Found at i:202051 original size:29 final size:27
Alignment explanation
Indices: 201988--202051 Score: 67
Period size: 29 Copynumber: 2.3 Consensus size: 27
201978 TTCGGTCCAA
*
201988 ATATATTATGTTGTAAAAAAATATTAT
1 ATATATTATGTTATAAAAAAATATTAT
* *
202015 AT-TAATTATGTATATTAAATAATAATTAT
1 ATAT-ATTATGT-TATAAAAAAAT-ATTAT
202044 ATATATTA
1 ATATATTA
202052 ATATTTATAT
Statistics
Matches: 30, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
26 1 0.03
27 9 0.30
28 8 0.27
29 11 0.37
30 1 0.03
ACGTcount: A:0.48, C:0.00, G:0.05, T:0.47
Consensus pattern (27 bp):
ATATATTATGTTATAAAAAAATATTAT
Found at i:202193 original size:32 final size:33
Alignment explanation
Indices: 202156--202229 Score: 87
Period size: 36 Copynumber: 2.2 Consensus size: 33
202146 AAAATTTAGA
*
202156 ATTTATATT-TAATACAATAAAATGTTTATTAT
1 ATTTATATTCTAATACAATAAAATATTTATTAT
* *
202188 ATTTATTTTTTTCTAATATAATAAAATATTTATTAT
1 ATTTA---TATTCTAATACAATAAAATATTTATTAT
202224 ATTTAT
1 ATTTAT
202230 GGTTGTGTTT
Statistics
Matches: 35, Mismatches: 3, Indels: 7
0.78 0.07 0.16
Matches are distributed among these distances:
32 5 0.14
33 1 0.03
35 3 0.09
36 26 0.74
ACGTcount: A:0.41, C:0.03, G:0.01, T:0.55
Consensus pattern (33 bp):
ATTTATATTCTAATACAATAAAATATTTATTAT
Found at i:207512 original size:24 final size:24
Alignment explanation
Indices: 207485--207541 Score: 78
Period size: 24 Copynumber: 2.4 Consensus size: 24
207475 TATCTTTTAG
*
207485 TTAAACTCTATTTATTTGTTTCAA
1 TTAAACTCTATTTATTTATTTCAA
* * *
207509 TTAAACTCTGTTTATTTATTTGAG
1 TTAAACTCTATTTATTTATTTCAA
207533 TTAAACTCT
1 TTAAACTCT
207542 TATTAGTCTA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.28, C:0.12, G:0.07, T:0.53
Consensus pattern (24 bp):
TTAAACTCTATTTATTTATTTCAA
Found at i:215853 original size:18 final size:19
Alignment explanation
Indices: 215806--215855 Score: 52
Period size: 17 Copynumber: 2.7 Consensus size: 19
215796 TCTTTTATGT
*
215806 TCTTTTAACTTTT-CATTTT
1 TCTTTT-ACTTTTCCATTTC
*
215825 TCCTTTA-TTTTCCA-TTC
1 TCTTTTACTTTTCCATTTC
215842 TCTTTTACTTTTCC
1 TCTTTTACTTTTCC
215856 CTTTGGTTTC
Statistics
Matches: 26, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
17 12 0.46
18 9 0.35
19 5 0.19
ACGTcount: A:0.12, C:0.24, G:0.00, T:0.64
Consensus pattern (19 bp):
TCTTTTACTTTTCCATTTC
Found at i:218737 original size:44 final size:44
Alignment explanation
Indices: 218643--218738 Score: 113
Period size: 44 Copynumber: 2.2 Consensus size: 44
218633 TTGCCATTTT
* *
218643 GGCTTGCACCCACTCGATCTTGCATTTAGACTATCCGCCGCTTC
1 GGCTTGCACCCACTCGATCTTGCATTTAGACTATCCGCCACCTC
* * * **
218687 GACTTGCACCCACTCGGGT-TTGCATTTAGACTGTTTGCCACCTC
1 GGCTTGCACCCACTC-GATCTTGCATTTAGACTATCCGCCACCTC
218731 GGCTTGCA
1 GGCTTGCA
218739 ATTCGACAGG
Statistics
Matches: 43, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
44 41 0.95
45 2 0.05
ACGTcount: A:0.16, C:0.33, G:0.21, T:0.30
Consensus pattern (44 bp):
GGCTTGCACCCACTCGATCTTGCATTTAGACTATCCGCCACCTC
Done.