Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004985.1 Hibiscus syriacus cultivar Beakdansim tig00011185_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 383687
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.32
File 1 of 2
Found at i:776 original size:35 final size:36
Alignment explanation
Indices: 729--796 Score: 93
Period size: 35 Copynumber: 1.9 Consensus size: 36
719 ATTTATAAGT
729 TGGTGATAATATAGACAAGAT-ATGGTGATGGAATA
1 TGGTGATAATATAGACAAGATAATGGTGATGGAATA
* * **
764 TGGTGATGATATAGGCGTGATAATGGTGATGGA
1 TGGTGATAATATAGACAAGATAATGGTGATGGA
797 CAGATTGTAT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
35 17 0.61
36 11 0.39
ACGTcount: A:0.34, C:0.03, G:0.34, T:0.29
Consensus pattern (36 bp):
TGGTGATAATATAGACAAGATAATGGTGATGGAATA
Found at i:2991 original size:15 final size:16
Alignment explanation
Indices: 2960--3000 Score: 57
Period size: 15 Copynumber: 2.6 Consensus size: 16
2950 CAAAAGCAAC
*
2960 AAAAGAGAAACAGAAAG
1 AAAAGA-AAACAAAAAG
2977 AAAA-AAAACAAAAAG
1 AAAAGAAAACAAAAAG
2992 AAAAGAAAA
1 AAAAGAAAA
3001 AGACTCCTAC
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
15 13 0.59
16 5 0.23
17 4 0.18
ACGTcount: A:0.80, C:0.05, G:0.15, T:0.00
Consensus pattern (16 bp):
AAAAGAAAACAAAAAG
Found at i:5725 original size:35 final size:36
Alignment explanation
Indices: 5678--5745 Score: 120
Period size: 35 Copynumber: 1.9 Consensus size: 36
5668 ATTTATAAGT
5678 TGGTGATAATATAGGCGTGAT-ATGGTGATGGAATA
1 TGGTGATAATATAGGCGTGATAATGGTGATGGAATA
*
5713 TGGTGATGATATAGGCGTGATAATGGTGATGGA
1 TGGTGATAATATAGGCGTGATAATGGTGATGGA
5746 CAGATTGTAT
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
35 20 0.65
36 11 0.35
ACGTcount: A:0.29, C:0.03, G:0.37, T:0.31
Consensus pattern (36 bp):
TGGTGATAATATAGGCGTGATAATGGTGATGGAATA
Found at i:10121 original size:24 final size:22
Alignment explanation
Indices: 10077--10123 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 22
10067 ATTTATTAGT
10077 TGGTGATAATATAGGTGTGATA
1 TGGTGATAATATAGGTGTGATA
10099 TGGTGATGGAATAT-GGTGATGATA
1 TGGTGAT--AATATAGGTG-TGATA
10123 T
1 T
10124 AGGCGTGATA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
22 7 0.32
23 4 0.18
24 11 0.50
ACGTcount: A:0.30, C:0.00, G:0.34, T:0.36
Consensus pattern (22 bp):
TGGTGATAATATAGGTGTGATA
Found at i:10124 original size:35 final size:36
Alignment explanation
Indices: 10077--10144 Score: 111
Period size: 35 Copynumber: 1.9 Consensus size: 36
10067 ATTTATTAGT
*
10077 TGGTGATAATATAGGTGTGAT-ATGGTGATGGAATA
1 TGGTGATAATATAGGCGTGATAATGGTGATGGAATA
*
10112 TGGTGATGATATAGGCGTGATAATGGTGATGGA
1 TGGTGATAATATAGGCGTGATAATGGTGATGGA
10145 CAAATTGTAT
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
35 19 0.63
36 11 0.37
ACGTcount: A:0.29, C:0.01, G:0.37, T:0.32
Consensus pattern (36 bp):
TGGTGATAATATAGGCGTGATAATGGTGATGGAATA
Found at i:18407 original size:22 final size:23
Alignment explanation
Indices: 18361--18407 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 23
18351 TATCACGCCT
18361 ATATCATCACTATATTCCATCACC
1 ATATCATCACTATATT-CATCACC
18385 ATATCACTC-CTATATT-ATCACC
1 ATATCA-TCACTATATTCATCACC
18407 A
1 A
18408 ACTTCTAAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
22 7 0.32
24 13 0.59
25 2 0.09
ACGTcount: A:0.34, C:0.32, G:0.00, T:0.34
Consensus pattern (23 bp):
ATATCATCACTATATTCATCACC
Found at i:25055 original size:19 final size:21
Alignment explanation
Indices: 25031--25082 Score: 81
Period size: 21 Copynumber: 2.6 Consensus size: 21
25021 CGGCCAAGAG
*
25031 CATGTATCTTCA-TTAAAA-T
1 CATGTATTTTCATTTAAAAGT
25050 CATGTATTTTCATTTAAAAGT
1 CATGTATTTTCATTTAAAAGT
25071 CATGTATTTTCA
1 CATGTATTTTCA
25083 AAGAGTTTTC
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 11 0.37
20 6 0.20
21 13 0.43
ACGTcount: A:0.33, C:0.13, G:0.08, T:0.46
Consensus pattern (21 bp):
CATGTATTTTCATTTAAAAGT
Found at i:27168 original size:35 final size:37
Alignment explanation
Indices: 27099--27178 Score: 119
Period size: 35 Copynumber: 2.2 Consensus size: 37
27089 ATACTATTTC
*
27099 CATCACCATAATCCATCTTCCATTATCACGCCTATAT
1 CATCACCATAATCCATCTACCATTATCACGCCTATAT
* *
27136 CATCACCATAGTCCATC-ACCA-TATCACTCCTATAT
1 CATCACCATAATCCATCTACCATTATCACGCCTATAT
27171 CATCACCA
1 CATCACCA
27179 AATTCTCAAA
Statistics
Matches: 40, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
35 21 0.52
36 3 0.08
37 16 0.40
ACGTcount: A:0.31, C:0.38, G:0.03, T:0.29
Consensus pattern (37 bp):
CATCACCATAATCCATCTACCATTATCACGCCTATAT
Found at i:31131 original size:35 final size:37
Alignment explanation
Indices: 31062--31141 Score: 119
Period size: 35 Copynumber: 2.2 Consensus size: 37
31052 ATACTATTTC
*
31062 CATCACCATAATCCATCTTCCATTATCACGCCTATAT
1 CATCACCATAATCCATCTACCATTATCACGCCTATAT
* *
31099 CTTCACCATAGTCCATC-ACCA-TATCACGCCTATAT
1 CATCACCATAATCCATCTACCATTATCACGCCTATAT
31134 CATCACCA
1 CATCACCA
31142 AATTCTCAAA
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
35 21 0.54
36 3 0.08
37 15 0.38
ACGTcount: A:0.30, C:0.38, G:0.04, T:0.29
Consensus pattern (37 bp):
CATCACCATAATCCATCTACCATTATCACGCCTATAT
Found at i:32435 original size:19 final size:21
Alignment explanation
Indices: 32411--32461 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
32401 GGCCAAGAGC
*
32411 ATGTATCTTCA-TTAAAA-TA
1 ATGTATTTTCATTTAAAAGTA
*
32430 ATGTATTTTCATTTAAAAGTC
1 ATGTATTTTCATTTAAAAGTA
32451 ATGTATTTTCA
1 ATGTATTTTCA
32462 AAGGGGTTTC
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
19 10 0.36
20 6 0.21
21 12 0.43
ACGTcount: A:0.35, C:0.10, G:0.08, T:0.47
Consensus pattern (21 bp):
ATGTATTTTCATTTAAAAGTA
Found at i:34628 original size:17 final size:17
Alignment explanation
Indices: 34606--34649 Score: 56
Period size: 17 Copynumber: 2.6 Consensus size: 17
34596 GTAGGAGTCT
34606 TTTTCTTTTCTCTT-TTG
1 TTTTCTTTT-TCTTGTTG
34623 TTTTCTTCTTTCTTGTTG
1 TTTTCTT-TTTCTTGTTG
34641 TTTT-TTTTT
1 TTTTCTTTTT
34650 AGCACTTTGA
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
16 3 0.12
17 13 0.52
18 9 0.36
ACGTcount: A:0.00, C:0.14, G:0.07, T:0.80
Consensus pattern (17 bp):
TTTTCTTTTTCTTGTTG
Found at i:36089 original size:19 final size:21
Alignment explanation
Indices: 36065--36116 Score: 81
Period size: 21 Copynumber: 2.6 Consensus size: 21
36055 CGGCCAAGAG
*
36065 CATGTATCTTCA-TT-AAAAT
1 CATGTATTTTCATTTAAAAAT
36084 CATGTATTTTCATTTAAAAAT
1 CATGTATTTTCATTTAAAAAT
36105 CATGTATTTTCA
1 CATGTATTTTCA
36117 AAGGGGTTTC
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 11 0.37
20 2 0.07
21 17 0.57
ACGTcount: A:0.35, C:0.13, G:0.06, T:0.46
Consensus pattern (21 bp):
CATGTATTTTCATTTAAAAAT
Found at i:38630 original size:7 final size:6
Alignment explanation
Indices: 38613--38672 Score: 56
Period size: 6 Copynumber: 10.5 Consensus size: 6
38603 GTGCAAAAAG
* * *
38613 AAAGAA AAAGACA AAAG-A AGAGAA AAAGAA GAA-AA GAAG-A AAAG-A
1 AAAGAA AAAGA-A AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA
38658 AAAGAA AAAGAA AAA
1 AAAGAA AAAGAA AAA
38673 TTCAAAAAGA
Statistics
Matches: 46, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
5 18 0.39
6 23 0.50
7 5 0.11
ACGTcount: A:0.78, C:0.02, G:0.20, T:0.00
Consensus pattern (6 bp):
AAAGAA
Found at i:38638 original size:27 final size:28
Alignment explanation
Indices: 38607--38670 Score: 87
Period size: 27 Copynumber: 2.3 Consensus size: 28
38597 ATTGGAGTGC
*
38607 AAAAAGAAAGAAAA-AGACAAAAGAAGAG
1 AAAAAGAAAGAAAAGA-ACAAAAGAAAAG
*
38635 AAAAAG-AAGAAAAGAAGAAAAGAAAAG
1 AAAAAGAAAGAAAAGAACAAAAGAAAAG
38662 AAAAAGAAA
1 AAAAAGAAA
38671 AATTCAAAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
27 23 0.72
28 9 0.28
ACGTcount: A:0.78, C:0.02, G:0.20, T:0.00
Consensus pattern (28 bp):
AAAAAGAAAGAAAAGAACAAAAGAAAAG
Found at i:38666 original size:11 final size:11
Alignment explanation
Indices: 38607--38671 Score: 55
Period size: 11 Copynumber: 5.9 Consensus size: 11
38597 ATTGGAGTGC
38607 AAAAAG-AAAG
1 AAAAAGAAAAG
*
38617 AAAAAGACAA-
1 AAAAAGAAAAG
*
38627 AAGAAGAGAAA-
1 AAAAAGA-AAAG
*
38638 AAGAAGAAAAG
1 AAAAAGAAAAG
38649 AAGAAAAGAAAAG
1 -A-AAAAGAAAAG
38662 AAAAAGAAAA
1 AAAAAGAAAA
38672 ATTCAAAAAG
Statistics
Matches: 46, Mismatches: 4, Indels: 9
0.78 0.07 0.15
Matches are distributed among these distances:
10 15 0.33
11 20 0.43
12 2 0.04
13 9 0.20
ACGTcount: A:0.78, C:0.02, G:0.20, T:0.00
Consensus pattern (11 bp):
AAAAAGAAAAG
Found at i:39955 original size:24 final size:24
Alignment explanation
Indices: 39940--39993 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 24
39930 AAAATCATGG
*
39940 CTTTTGAAAAACCAAAAGATGTGA
1 CTTTTGAAAAACCAAAAGATATGA
* * **
39964 CTTTTGAAGAACCAATAGCCATGA
1 CTTTTGAAAAACCAAAAGATATGA
39988 CTTTTG
1 CTTTTG
39994 GTGATTCACA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.37, C:0.17, G:0.17, T:0.30
Consensus pattern (24 bp):
CTTTTGAAAAACCAAAAGATATGA
Found at i:42255 original size:19 final size:20
Alignment explanation
Indices: 42217--42259 Score: 61
Period size: 19 Copynumber: 2.2 Consensus size: 20
42207 GAAACCCCTT
*
42217 TGAAAACACATGATTTTTAA
1 TGAAAACACATGAATTTTAA
*
42237 TGAAAATACAT-AATTTTAA
1 TGAAAACACATGAATTTTAA
42256 TGAA
1 TGAA
42260 GATAAATGCT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 11 0.52
20 10 0.48
ACGTcount: A:0.49, C:0.07, G:0.09, T:0.35
Consensus pattern (20 bp):
TGAAAACACATGAATTTTAA
Found at i:45438 original size:15 final size:15
Alignment explanation
Indices: 45411--45449 Score: 55
Period size: 14 Copynumber: 2.7 Consensus size: 15
45401 CACTTTTCTT
45411 TTTCTTTTAT-TTTTC
1 TTTCTTTT-TCTTTTC
45426 -TTCTTTTTCTTTTC
1 TTTCTTTTTCTTTTC
45440 TTTCTTTTTC
1 TTTCTTTTTC
45450 ACTCCAATTT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
13 1 0.05
14 12 0.55
15 9 0.41
ACGTcount: A:0.03, C:0.18, G:0.00, T:0.79
Consensus pattern (15 bp):
TTTCTTTTTCTTTTC
Found at i:45440 original size:11 final size:11
Alignment explanation
Indices: 45403--45442 Score: 57
Period size: 11 Copynumber: 3.8 Consensus size: 11
45393 ACTTTCTTCA
45403 CTTTTCTTTTT
1 CTTTTCTTTTT
*
45414 CTTTTATTTTT
1 CTTTTCTTTTT
45425 C--TTCTTTTT
1 CTTTTCTTTTT
45434 CTTTTCTTT
1 CTTTTCTTT
45443 CTTTTTCACT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
9 8 0.32
11 17 0.68
ACGTcount: A:0.03, C:0.17, G:0.00, T:0.80
Consensus pattern (11 bp):
CTTTTCTTTTT
Found at i:46334 original size:19 final size:20
Alignment explanation
Indices: 46296--46338 Score: 61
Period size: 19 Copynumber: 2.2 Consensus size: 20
46286 GAAACCCCTT
*
46296 TGAAAACACATGATTTTTAA
1 TGAAAACACATGAATTTTAA
*
46316 TGAAAATACAT-AATTTTAA
1 TGAAAACACATGAATTTTAA
46335 TGAA
1 TGAA
46339 GATAAATGCT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 11 0.52
20 10 0.48
ACGTcount: A:0.49, C:0.07, G:0.09, T:0.35
Consensus pattern (20 bp):
TGAAAACACATGAATTTTAA
Found at i:48387 original size:36 final size:36
Alignment explanation
Indices: 48335--48447 Score: 165
Period size: 36 Copynumber: 3.2 Consensus size: 36
48325 GATACTATTT
* *
48335 TCATCACCATAATCCATCTCCATTATCGCGCCTATA
1 TCATCACCATAATCCATCACCATTATCACGCCTATA
*
48371 TCATCACCATAGTCCATCACCATTATCACGCCTATA
1 TCATCACCATAATCCATCACCATTATCACGCCTATA
* *
48407 TCATCACCATATTCCATCACCA-TATCACGCCAATA
1 TCATCACCATAATCCATCACCATTATCACGCCTATA
*
48442 ACATCA
1 TCATCA
48448 TATTTCCATT
Statistics
Matches: 71, Mismatches: 6, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
35 17 0.24
36 54 0.76
ACGTcount: A:0.32, C:0.36, G:0.04, T:0.27
Consensus pattern (36 bp):
TCATCACCATAATCCATCACCATTATCACGCCTATA
Found at i:48390 original size:13 final size:11
Alignment explanation
Indices: 48368--48433 Score: 62
Period size: 13 Copynumber: 5.5 Consensus size: 11
48358 TATCGCGCCT
48368 ATATCATCACC
1 ATATCATCACC
48379 ATAGTCCATCACC
1 ATA-T-CATCACC
*
48392 ATTATCA-CGCC
1 A-TATCATCACC
48403 TATATCATCACC
1 -ATATCATCACC
48415 ATATTCCATCACC
1 ATA-T-CATCACC
48428 ATATCA
1 ATATCA
48434 CGCCAATAAC
Statistics
Matches: 46, Mismatches: 2, Indels: 14
0.74 0.03 0.23
Matches are distributed among these distances:
11 16 0.35
12 9 0.20
13 19 0.41
14 2 0.04
ACGTcount: A:0.33, C:0.35, G:0.03, T:0.29
Consensus pattern (11 bp):
ATATCATCACC
Found at i:48867 original size:17 final size:17
Alignment explanation
Indices: 48839--48879 Score: 52
Period size: 17 Copynumber: 2.5 Consensus size: 17
48829 AAAAGCAACA
48839 AAAAG-AAA-AAAAGA-
1 AAAAGAAAACAAAAGAG
48853 AAGAAGAAAACAAAAGAG
1 AA-AAGAAAACAAAAGAG
48871 AAAAGAAAA
1 AAAAGAAAA
48880 AGACTCCTAC
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
14 2 0.09
15 3 0.13
16 3 0.13
17 13 0.57
18 2 0.09
ACGTcount: A:0.80, C:0.02, G:0.17, T:0.00
Consensus pattern (17 bp):
AAAAGAAAACAAAAGAG
Found at i:48929 original size:14 final size:15
Alignment explanation
Indices: 48906--48949 Score: 54
Period size: 14 Copynumber: 2.9 Consensus size: 15
48896 TTTGGAGCGC
48906 AAAAGAAAGAAAATA
1 AAAAGAAAGAAAATA
*
48921 AAAAG-AAGAAAATC
1 AAAAGAAAGAAAATA
48935 AAAAGCAAAAGAAAA
1 AAAAG--AAAGAAAA
48950 GTTAAGCAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
14 13 0.52
15 5 0.20
17 7 0.28
ACGTcount: A:0.77, C:0.05, G:0.14, T:0.05
Consensus pattern (15 bp):
AAAAGAAAGAAAATA
Found at i:52243 original size:36 final size:36
Alignment explanation
Indices: 52191--52303 Score: 165
Period size: 36 Copynumber: 3.2 Consensus size: 36
52181 GATACTATTT
* *
52191 TCATCACCATAATCCATCTCCATTATCGCGCCTATA
1 TCATCACCATAATCCATCACCATTATCACGCCTATA
*
52227 TCATCACCATAGTCCATCACCATTATCACGCCTATA
1 TCATCACCATAATCCATCACCATTATCACGCCTATA
* *
52263 TCATCACCATATTCCATCACCA-TATCACGCCAATA
1 TCATCACCATAATCCATCACCATTATCACGCCTATA
*
52298 ACATCA
1 TCATCA
52304 TCTTTCCATT
Statistics
Matches: 71, Mismatches: 6, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
35 17 0.24
36 54 0.76
ACGTcount: A:0.32, C:0.36, G:0.04, T:0.27
Consensus pattern (36 bp):
TCATCACCATAATCCATCACCATTATCACGCCTATA
Found at i:52246 original size:13 final size:11
Alignment explanation
Indices: 52224--52289 Score: 62
Period size: 13 Copynumber: 5.5 Consensus size: 11
52214 TATCGCGCCT
52224 ATATCATCACC
1 ATATCATCACC
52235 ATAGTCCATCACC
1 ATA-T-CATCACC
*
52248 ATTATCA-CGCC
1 A-TATCATCACC
52259 TATATCATCACC
1 -ATATCATCACC
52271 ATATTCCATCACC
1 ATA-T-CATCACC
52284 ATATCA
1 ATATCA
52290 CGCCAATAAC
Statistics
Matches: 46, Mismatches: 2, Indels: 14
0.74 0.03 0.23
Matches are distributed among these distances:
11 16 0.35
12 9 0.20
13 19 0.41
14 2 0.04
ACGTcount: A:0.33, C:0.35, G:0.03, T:0.29
Consensus pattern (11 bp):
ATATCATCACC
Found at i:55302 original size:11 final size:11
Alignment explanation
Indices: 55286--55325 Score: 57
Period size: 11 Copynumber: 3.8 Consensus size: 11
55276 ACCTTCTTCA
55286 CTTTTCTTTTT
1 CTTTTCTTTTT
55297 CTTTTCTTTTT
1 CTTTTCTTTTT
*
55308 C--ATCTTTTT
1 CTTTTCTTTTT
55317 CTTTTCTTT
1 CTTTTCTTT
55326 CTTTGGCACT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
9 8 0.32
11 17 0.68
ACGTcount: A:0.03, C:0.20, G:0.00, T:0.78
Consensus pattern (11 bp):
CTTTTCTTTTT
Found at i:56216 original size:19 final size:20
Alignment explanation
Indices: 56180--56222 Score: 70
Period size: 19 Copynumber: 2.2 Consensus size: 20
56170 GAAACCCCTT
56180 TGAAAACACATGATTTTTAA
1 TGAAAACACATGATTTTTAA
*
56200 TGAAAATACAT-ATTTTTAA
1 TGAAAACACATGATTTTTAA
56219 TGAA
1 TGAA
56223 GATAAATGCT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
19 12 0.55
20 10 0.45
ACGTcount: A:0.47, C:0.07, G:0.09, T:0.37
Consensus pattern (20 bp):
TGAAAACACATGATTTTTAA
Found at i:57117 original size:19 final size:20
Alignment explanation
Indices: 57060--57109 Score: 61
Period size: 19 Copynumber: 2.6 Consensus size: 20
57050 ATAATGGGTT
*
57060 TAAGAAATGAATAAT-AAT-A
1 TAAGTAATGAA-AATAAATAA
57079 TAAGTAATGAAAATAAATAA
1 TAAGTAATGAAAATAAATAA
57099 TAAG-AATGAAA
1 TAAGTAATGAAA
57110 TGAAATAAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
18 3 0.11
19 20 0.71
20 5 0.18
ACGTcount: A:0.64, C:0.00, G:0.12, T:0.24
Consensus pattern (20 bp):
TAAGTAATGAAAATAAATAA
Found at i:61358 original size:20 final size:20
Alignment explanation
Indices: 61335--61390 Score: 58
Period size: 20 Copynumber: 2.8 Consensus size: 20
61325 TTTGAAATCT
61335 TTTTCTTTTTTTTCTTCTTC
1 TTTTCTTTTTTTTCTTCTTC
*** *
61355 TTTTCTGAATTTTCTTCTTT
1 TTTTCTTTTTTTTCTTCTTC
* *
61375 TTTTATTTTCTTTCTT
1 TTTTCTTTTTTTTCTT
61391 TTTGCACTCC
Statistics
Matches: 27, Mismatches: 9, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.05, C:0.16, G:0.02, T:0.77
Consensus pattern (20 bp):
TTTTCTTTTTTTTCTTCTTC
Found at i:61373 original size:32 final size:34
Alignment explanation
Indices: 61321--61394 Score: 93
Period size: 32 Copynumber: 2.2 Consensus size: 34
61311 TTGCTTTTTC
61321 TCTTTTTGAAATCTTTTTCTTTTTTT-TCTTC-T
1 TCTTTTTGAAATCTTTTTCTTTTTTTATCTTCTT
*
61353 TCTTTTCTG-AAT-TTTCTTCTTTTTTTATTTTCTT
1 TCTTTT-TGAAATCTTT-TTCTTTTTTTATCTTCTT
61387 TCTTTTTG
1 TCTTTTTG
61395 CACTCCAATT
Statistics
Matches: 37, Mismatches: 1, Indels: 7
0.82 0.02 0.16
Matches are distributed among these distances:
31 3 0.08
32 19 0.51
33 8 0.22
34 7 0.19
ACGTcount: A:0.08, C:0.15, G:0.04, T:0.73
Consensus pattern (34 bp):
TCTTTTTGAAATCTTTTTCTTTTTTTATCTTCTT
Found at i:61389 original size:17 final size:16
Alignment explanation
Indices: 61337--61393 Score: 62
Period size: 17 Copynumber: 3.5 Consensus size: 16
61327 TGAAATCTTT
*
61337 TTCTTTTTTT-TCTTC
1 TTCTTTTTTTATTTTC
**
61352 TTCTTTTCTGAATTTTC
1 TTCTTTT-TTTATTTTC
61369 TTCTTTTTTTATTTTC
1 TTCTTTTTTTATTTTC
61385 TTTCTTTTT
1 -TTCTTTTT
61394 GCACTCCAAT
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
15 7 0.21
16 8 0.24
17 19 0.56
ACGTcount: A:0.05, C:0.16, G:0.02, T:0.77
Consensus pattern (16 bp):
TTCTTTTTTTATTTTC
Found at i:61703 original size:19 final size:20
Alignment explanation
Indices: 61646--61695 Score: 61
Period size: 19 Copynumber: 2.6 Consensus size: 20
61636 ATAATGGGTT
*
61646 TAAGAAATGAATAAT-AAT-A
1 TAAGTAATGAA-AATAAATAA
61665 TAAGTAATGAAAATAAATAA
1 TAAGTAATGAAAATAAATAA
61685 TAAG-AATGAAA
1 TAAGTAATGAAA
61696 TGAAATAAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
18 3 0.11
19 20 0.71
20 5 0.18
ACGTcount: A:0.64, C:0.00, G:0.12, T:0.24
Consensus pattern (20 bp):
TAAGTAATGAAAATAAATAA
Found at i:65644 original size:11 final size:11
Alignment explanation
Indices: 65628--65667 Score: 57
Period size: 11 Copynumber: 3.8 Consensus size: 11
65618 ACTTTCTTCA
65628 CTTTTCTTTTT
1 CTTTTCTTTTT
65639 CTTTTCTTTTT
1 CTTTTCTTTTT
*
65650 C--TTATTTTT
1 CTTTTCTTTTT
65659 CTTTTCTTT
1 CTTTTCTTT
65668 CTTTGGCACT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
9 8 0.32
11 17 0.68
ACGTcount: A:0.03, C:0.17, G:0.00, T:0.80
Consensus pattern (11 bp):
CTTTTCTTTTT
Found at i:65891 original size:21 final size:19
Alignment explanation
Indices: 65843--65894 Score: 68
Period size: 21 Copynumber: 2.6 Consensus size: 19
65833 CGGCCAAGAG
*
65843 CATGTATCTTCATTAAAAT
1 CATGTATTTTCATTAAAAT
*
65862 CATGAATTTTCATTTAAAAGT
1 CATGTATTTTCA-TTAAAA-T
65883 CATGTATTTTCA
1 CATGTATTTTCA
65895 AAGGGGTTTC
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
19 10 0.36
20 6 0.21
21 12 0.43
ACGTcount: A:0.35, C:0.13, G:0.08, T:0.44
Consensus pattern (19 bp):
CATGTATTTTCATTAAAAT
Found at i:66328 original size:19 final size:20
Alignment explanation
Indices: 66304--66344 Score: 57
Period size: 19 Copynumber: 2.1 Consensus size: 20
66294 ATCCCTTTCT
66304 TTATTTCACTTCA-TTATTA
1 TTATTTCACTTCATTTATTA
**
66323 TTATTTCTTTTCATTTATTA
1 TTATTTCACTTCATTTATTA
66343 TT
1 TT
66345 CACTTTATTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 11 0.58
20 8 0.42
ACGTcount: A:0.22, C:0.12, G:0.00, T:0.66
Consensus pattern (20 bp):
TTATTTCACTTCATTTATTA
Found at i:71251 original size:23 final size:22
Alignment explanation
Indices: 71225--71268 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
71215 TATTTTGCAA
71225 ATTTCTTCACTTCTTTTTCTTTG
1 ATTTCTTC-CTTCTTTTTCTTTG
* *
71248 ATTTTTTCCTTGTTTTTCTTT
1 ATTTCTTCCTTCTTTTTCTTT
71269 TCTTTCTTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 12 0.63
23 7 0.37
ACGTcount: A:0.07, C:0.18, G:0.05, T:0.70
Consensus pattern (22 bp):
ATTTCTTCCTTCTTTTTCTTTG
Found at i:71327 original size:18 final size:18
Alignment explanation
Indices: 71304--71343 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
71294 TGTAGGAGTC
71304 TTTTCTT-TTGCTTTTTGT
1 TTTTCTTCTTGC-TTTTGT
*
71322 TTTTCTTCTTTCTTTTGT
1 TTTTCTTCTTGCTTTTGT
71340 TTTT
1 TTTT
71344 TGTTGCAGCA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 17 0.85
19 3 0.15
ACGTcount: A:0.00, C:0.12, G:0.07, T:0.80
Consensus pattern (18 bp):
TTTTCTTCTTGCTTTTGT
Found at i:71892 original size:26 final size:26
Alignment explanation
Indices: 71862--71922 Score: 113
Period size: 26 Copynumber: 2.3 Consensus size: 26
71852 AATCATATAG
71862 TATGCAAGCGAATGGTAACATATGAT
1 TATGCAAGCGAATGGTAACATATGAT
71888 TATGCAAGCGAATGGTAACATATGAT
1 TATGCAAGCGAATGGTAACATATGAT
*
71914 TATTCAAGC
1 TATGCAAGC
71923 ATAGTTTAAA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 34 1.00
ACGTcount: A:0.38, C:0.13, G:0.21, T:0.28
Consensus pattern (26 bp):
TATGCAAGCGAATGGTAACATATGAT
Found at i:76539 original size:36 final size:36
Alignment explanation
Indices: 76487--76599 Score: 165
Period size: 36 Copynumber: 3.2 Consensus size: 36
76477 GATACTATTT
* *
76487 TCATCACCATAATCCATCTCCATTATCGCGCCTATA
1 TCATCACCATAATCCATCACCATTATCACGCCTATA
*
76523 TCATCACCATAGTCCATCACCATTATCACGCCTATA
1 TCATCACCATAATCCATCACCATTATCACGCCTATA
* *
76559 TCATCACCATATTCCATCACCA-TATCACGCCAATA
1 TCATCACCATAATCCATCACCATTATCACGCCTATA
*
76594 ACATCA
1 TCATCA
76600 TCTTTCCATT
Statistics
Matches: 71, Mismatches: 6, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
35 17 0.24
36 54 0.76
ACGTcount: A:0.32, C:0.36, G:0.04, T:0.27
Consensus pattern (36 bp):
TCATCACCATAATCCATCACCATTATCACGCCTATA
Found at i:76542 original size:13 final size:11
Alignment explanation
Indices: 76520--76585 Score: 62
Period size: 13 Copynumber: 5.5 Consensus size: 11
76510 TATCGCGCCT
76520 ATATCATCACC
1 ATATCATCACC
76531 ATAGTCCATCACC
1 ATA-T-CATCACC
*
76544 ATTATCA-CGCC
1 A-TATCATCACC
76555 TATATCATCACC
1 -ATATCATCACC
76567 ATATTCCATCACC
1 ATA-T-CATCACC
76580 ATATCA
1 ATATCA
76586 CGCCAATAAC
Statistics
Matches: 46, Mismatches: 2, Indels: 14
0.74 0.03 0.23
Matches are distributed among these distances:
11 16 0.35
12 9 0.20
13 19 0.41
14 2 0.04
ACGTcount: A:0.33, C:0.35, G:0.03, T:0.29
Consensus pattern (11 bp):
ATATCATCACC
Found at i:77084 original size:14 final size:15
Alignment explanation
Indices: 77050--77096 Score: 51
Period size: 14 Copynumber: 3.1 Consensus size: 15
77040 AATTTGGAGT
77050 GCAAAAGAAAGAAAA
1 GCAAAAGAAAGAAAA
*
77065 GAAAAAG-AAGAAAA
1 GCAAAAGAAAGAAAA
*
77079 TCAAAAGCAAAAGAAAA
1 GCAAAAG--AAAGAAAA
77096 G
1 G
77097 TGAAACAAAG
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
14 12 0.48
15 6 0.24
17 7 0.28
ACGTcount: A:0.72, C:0.06, G:0.19, T:0.02
Consensus pattern (15 bp):
GCAAAAGAAAGAAAA
Found at i:78694 original size:24 final size:23
Alignment explanation
Indices: 78651--78703 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 23
78641 AGCATAAAAT
*
78651 CATGAATTTTCATGATCCAATGGA
1 CATGAATTTT-ATGATCCAAGGGA
78675 CATGAATTTT-TGGATGCCAAGGGA
1 CATGAATTTTAT-GAT-CCAAGGGA
78699 CATGA
1 CATGA
78704 TCATTCAAAG
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
22 1 0.04
23 3 0.12
24 22 0.85
ACGTcount: A:0.32, C:0.15, G:0.23, T:0.30
Consensus pattern (23 bp):
CATGAATTTTATGATCCAAGGGA
Found at i:80567 original size:36 final size:36
Alignment explanation
Indices: 80515--80613 Score: 155
Period size: 36 Copynumber: 2.8 Consensus size: 36
80505 GATACTATTT
* *
80515 TCATCACCATAATCCATCTCCATTATCGCGCCTATA
1 TCATCACCATAATCCATCACCATTATCACGCCTATA
*
80551 TCATCACCATAGTCCATCACCATTATCACGCCTATA
1 TCATCACCATAATCCATCACCATTATCACGCCTATA
*
80587 TCATCACCATATTCCATCACCA-TATCA
1 TCATCACCATAATCCATCACCATTATCA
80614 TGCCAGTAAC
Statistics
Matches: 59, Mismatches: 4, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
35 5 0.08
36 54 0.92
ACGTcount: A:0.30, C:0.36, G:0.04, T:0.29
Consensus pattern (36 bp):
TCATCACCATAATCCATCACCATTATCACGCCTATA
Found at i:80570 original size:13 final size:11
Alignment explanation
Indices: 80548--80614 Score: 64
Period size: 13 Copynumber: 5.6 Consensus size: 11
80538 TATCGCGCCT
80548 ATATCATCACC
1 ATATCATCACC
80559 ATAGTCCATCACC
1 ATA-T-CATCACC
*
80572 ATTATCA-CGCC
1 A-TATCATCACC
80583 TATATCATCACC
1 -ATATCATCACC
80595 ATATTCCATCACC
1 ATA-T-CATCACC
80608 ATATCAT
1 ATATCAT
80615 GCCAGTAACA
Statistics
Matches: 47, Mismatches: 2, Indels: 14
0.75 0.03 0.22
Matches are distributed among these distances:
11 17 0.36
12 9 0.19
13 19 0.40
14 2 0.04
ACGTcount: A:0.33, C:0.34, G:0.03, T:0.30
Consensus pattern (11 bp):
ATATCATCACC
Found at i:80661 original size:33 final size:33
Alignment explanation
Indices: 80598--80662 Score: 78
Period size: 33 Copynumber: 2.0 Consensus size: 33
80588 CATCACCATA
*
80598 TTCCATCACCATATCATGCCAGTAACATCATCT
1 TTCCATCACCATATCATACCAGTAACATCATCT
* * *
80631 TTCCATTACCATTTCATCACCATTAA-ATCATC
1 TTCCATCACCATATCAT-ACCAGTAACATCATC
80663 CTTCATTCAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
33 21 0.78
34 6 0.22
ACGTcount: A:0.31, C:0.32, G:0.03, T:0.34
Consensus pattern (33 bp):
TTCCATCACCATATCATACCAGTAACATCATCT
Found at i:81054 original size:13 final size:13
Alignment explanation
Indices: 81018--81055 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 13
81008 CAAAAAAAAG
81018 AAACAAGAAAGAAGA
1 AAACAA-AAAG-AGA
81033 AAAC-AAAAGAGA
1 AAACAAAAAGAGA
81045 AAACAAAAAGA
1 AAACAAAAAGA
81056 CTCCTACATC
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
12 7 0.32
13 10 0.45
14 1 0.05
15 4 0.18
ACGTcount: A:0.76, C:0.08, G:0.16, T:0.00
Consensus pattern (13 bp):
AAACAAAAAGAGA
Found at i:81104 original size:14 final size:15
Alignment explanation
Indices: 81078--81122 Score: 65
Period size: 14 Copynumber: 2.9 Consensus size: 15
81068 ATTTGGAGTG
81078 CAAAAGAAAGAAAAT
1 CAAAAGAAAGAAAAT
81093 CAAAAG-AAGAAAAT
1 CAAAAGAAAGAAAAT
81107 CAAAAGCAAAAGAAAA
1 CAAAAG--AAAGAAAA
81123 GTGAAACAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
14 14 0.52
15 6 0.22
17 7 0.26
ACGTcount: A:0.73, C:0.09, G:0.13, T:0.04
Consensus pattern (15 bp):
CAAAAGAAAGAAAAT
Found at i:82719 original size:24 final size:23
Alignment explanation
Indices: 82676--82728 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 23
82666 AGCATAAAAT
*
82676 CATGAATTTTCATGATCCAATGGA
1 CATGAATTTT-ATGATCCAAGGGA
82700 CATGAATTTT-TGGATGCCAAGGGA
1 CATGAATTTTAT-GAT-CCAAGGGA
82724 CATGA
1 CATGA
82729 TCATTCAAAG
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
22 1 0.04
23 3 0.12
24 22 0.85
ACGTcount: A:0.32, C:0.15, G:0.23, T:0.30
Consensus pattern (23 bp):
CATGAATTTTATGATCCAAGGGA
Found at i:84594 original size:36 final size:36
Alignment explanation
Indices: 84542--84640 Score: 155
Period size: 36 Copynumber: 2.8 Consensus size: 36
84532 GATACTATTT
* *
84542 TCATCACCATAATCCATCTCCATTATCGCGCCTATA
1 TCATCACCATAATCCATCACCATTATCACGCCTATA
*
84578 TCATCACCATAGTCCATCACCATTATCACGCCTATA
1 TCATCACCATAATCCATCACCATTATCACGCCTATA
*
84614 TCATCACCATATTCCATCACCA-TATCA
1 TCATCACCATAATCCATCACCATTATCA
84641 TGCCAGTAAC
Statistics
Matches: 59, Mismatches: 4, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
35 5 0.08
36 54 0.92
ACGTcount: A:0.30, C:0.36, G:0.04, T:0.29
Consensus pattern (36 bp):
TCATCACCATAATCCATCACCATTATCACGCCTATA
Found at i:84597 original size:13 final size:11
Alignment explanation
Indices: 84575--84641 Score: 64
Period size: 13 Copynumber: 5.6 Consensus size: 11
84565 TATCGCGCCT
84575 ATATCATCACC
1 ATATCATCACC
84586 ATAGTCCATCACC
1 ATA-T-CATCACC
*
84599 ATTATCA-CGCC
1 A-TATCATCACC
84610 TATATCATCACC
1 -ATATCATCACC
84622 ATATTCCATCACC
1 ATA-T-CATCACC
84635 ATATCAT
1 ATATCAT
84642 GCCAGTAACA
Statistics
Matches: 47, Mismatches: 2, Indels: 14
0.75 0.03 0.22
Matches are distributed among these distances:
11 17 0.36
12 9 0.19
13 19 0.40
14 2 0.04
ACGTcount: A:0.33, C:0.34, G:0.03, T:0.30
Consensus pattern (11 bp):
ATATCATCACC
Found at i:84688 original size:33 final size:33
Alignment explanation
Indices: 84625--84689 Score: 78
Period size: 33 Copynumber: 2.0 Consensus size: 33
84615 CATCACCATA
*
84625 TTCCATCACCATATCATGCCAGTAACATCATCT
1 TTCCATCACCATATCATACCAGTAACATCATCT
* * *
84658 TTCCATTACCATTTCATCACCATTAA-ATCATC
1 TTCCATCACCATATCAT-ACCAGTAACATCATC
84690 CTTCATTCAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
33 21 0.78
34 6 0.22
ACGTcount: A:0.31, C:0.32, G:0.03, T:0.34
Consensus pattern (33 bp):
TTCCATCACCATATCATACCAGTAACATCATCT
Found at i:85131 original size:14 final size:15
Alignment explanation
Indices: 85105--85149 Score: 65
Period size: 14 Copynumber: 2.9 Consensus size: 15
85095 ATTTGGAGTG
85105 CAAAAGAAAGAAAAT
1 CAAAAGAAAGAAAAT
85120 CAAAAG-AAGAAAAT
1 CAAAAGAAAGAAAAT
85134 CAAAAGCAAAAGAAAA
1 CAAAAG--AAAGAAAA
85150 GTGAAACAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
14 14 0.52
15 6 0.22
17 7 0.26
ACGTcount: A:0.73, C:0.09, G:0.13, T:0.04
Consensus pattern (15 bp):
CAAAAGAAAGAAAAT
Found at i:90587 original size:18 final size:18
Alignment explanation
Indices: 90523--90587 Score: 57
Period size: 16 Copynumber: 3.8 Consensus size: 18
90513 GAACTTCTCT
*
90523 TTTTCTTTTCTTTTAT-TA
1 TTTTC-TTTCTTTTTTGTA
*
90541 TTTTC-TTCATTTTTG-A
1 TTTTCTTTCTTTTTTGTA
* *
90557 TTTT-TTTCCTTTTTGTC
1 TTTTCTTTCTTTTTTGTA
90574 TTTTCTTTCTTTTT
1 TTTTCTTTCTTTTT
90588 GCACTCCAAT
Statistics
Matches: 38, Mismatches: 5, Indels: 8
0.75 0.10 0.16
Matches are distributed among these distances:
16 21 0.55
17 4 0.11
18 13 0.34
ACGTcount: A:0.06, C:0.14, G:0.03, T:0.77
Consensus pattern (18 bp):
TTTTCTTTCTTTTTTGTA
Found at i:96482 original size:23 final size:24
Alignment explanation
Indices: 96452--96504 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 24
96442 AAAAATAGAA
*
96452 AAGAAA-TTAAAGCACTCCAAAAG
1 AAGAAATTTAAAGCACTCAAAAAG
**
96475 AAGAAATTTCCAGCACTCAAAAAG
1 AAGAAATTTAAAGCACTCAAAAAG
96499 AAGAAA
1 AAGAAA
96505 AGGAAAGAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
23 6 0.23
24 20 0.77
ACGTcount: A:0.57, C:0.17, G:0.13, T:0.13
Consensus pattern (24 bp):
AAGAAATTTAAAGCACTCAAAAAG
Found at i:101188 original size:23 final size:24
Alignment explanation
Indices: 101159--101211 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 24
101149 AAAAATAGAA
*
101159 AAGAAA-TTAAAGCACTCCAAAAG
1 AAGAAATTTAAAGCACTCAAAAAG
**
101182 AAGAAATTTCCAGCACTCAAAAAG
1 AAGAAATTTAAAGCACTCAAAAAG
101206 AAGAAA
1 AAGAAA
101212 AGCAAAGAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
23 6 0.23
24 20 0.77
ACGTcount: A:0.57, C:0.17, G:0.13, T:0.13
Consensus pattern (24 bp):
AAGAAATTTAAAGCACTCAAAAAG
Found at i:107587 original size:13 final size:11
Alignment explanation
Indices: 107568--107630 Score: 65
Period size: 13 Copynumber: 5.4 Consensus size: 11
107558 TACATTCTGT
107568 TCATCACCATA
1 TCATCACCATA
107579 GTCCATCACCATA
1 -T-CATCACCATA
*
107592 TCA-CGCCTATA
1 TCATCACC-ATA
107603 TCATCACCATA
1 TCATCACCATA
107614 CTCCATCACCATA
1 -T-CATCACCATA
107627 TCAT
1 TCAT
107631 GCCTAAATCA
Statistics
Matches: 44, Mismatches: 2, Indels: 11
0.77 0.04 0.19
Matches are distributed among these distances:
10 3 0.07
11 14 0.32
12 7 0.16
13 20 0.45
ACGTcount: A:0.32, C:0.38, G:0.03, T:0.27
Consensus pattern (11 bp):
TCATCACCATA
Found at i:107654 original size:35 final size:35
Alignment explanation
Indices: 107568--107646 Score: 131
Period size: 35 Copynumber: 2.3 Consensus size: 35
107558 TACATTCTGT
* *
107568 TCATCACCATAGTCCATCACCATATCACGCCTATA
1 TCATCACCATACTCCATCACCATATCACGCCTAAA
*
107603 TCATCACCATACTCCATCACCATATCATGCCTAAA
1 TCATCACCATACTCCATCACCATATCACGCCTAAA
107638 TCATCACCA
1 TCATCACCA
107647 AATTCCATTT
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
35 41 1.00
ACGTcount: A:0.33, C:0.38, G:0.04, T:0.25
Consensus pattern (35 bp):
TCATCACCATACTCCATCACCATATCACGCCTAAA
Found at i:115690 original size:24 final size:24
Alignment explanation
Indices: 115663--115717 Score: 60
Period size: 24 Copynumber: 2.3 Consensus size: 24
115653 CCAACTTTTC
115663 TTTCTTTTTTCTTC-TTTTGAGTG
1 TTTCTTTTTTCTTCTTTTTGAGTG
**
115686 TTT-TCAATTTCTTCTTTTTGAGTG
1 TTTCT-TTTTTCTTCTTTTTGAGTG
*
115710 CTTCTTTT
1 TTTCTTTT
115718 CTAATTTTTC
Statistics
Matches: 24, Mismatches: 5, Indels: 5
0.71 0.15 0.15
Matches are distributed among these distances:
22 1 0.04
23 10 0.42
24 12 0.50
25 1 0.04
ACGTcount: A:0.07, C:0.15, G:0.11, T:0.67
Consensus pattern (24 bp):
TTTCTTTTTTCTTCTTTTTGAGTG
Found at i:119925 original size:19 final size:20
Alignment explanation
Indices: 119884--119934 Score: 77
Period size: 19 Copynumber: 2.6 Consensus size: 20
119874 GAAACCCCTT
*
119884 TGAAAATACATGATTTTTGA
1 TGAAAATACATGATTTTTAA
119904 TGAAAATACATGA-TTTTAA
1 TGAAAATACATGATTTTTAA
*
119923 TGAAGATACATG
1 TGAAAATACATG
119935 CTCTTGGCCG
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 16 0.55
20 13 0.45
ACGTcount: A:0.43, C:0.06, G:0.16, T:0.35
Consensus pattern (20 bp):
TGAAAATACATGATTTTTAA
Found at i:120659 original size:20 final size:21
Alignment explanation
Indices: 120617--120659 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 21
120607 ATGATCATCA
* * *
120617 ATAAGCTAAGATAACATGTAT
1 ATAAGCTAAGATAAAAGGCAT
120638 ATAAGCT-AGATAAAAGGCAT
1 ATAAGCTAAGATAAAAGGCAT
120658 AT
1 AT
120660 GACGTTTATG
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
20 12 0.63
21 7 0.37
ACGTcount: A:0.49, C:0.09, G:0.16, T:0.26
Consensus pattern (21 bp):
ATAAGCTAAGATAAAAGGCAT
Found at i:127645 original size:51 final size:51
Alignment explanation
Indices: 127588--127689 Score: 186
Period size: 51 Copynumber: 2.0 Consensus size: 51
127578 TCCACACTCA
*
127588 AGCTAGCTTGGAAGGAGACACATGCACCCCCAAGTTGGAGCACATGACCAG
1 AGCTAGCTTAGAAGGAGACACATGCACCCCCAAGTTGGAGCACATGACCAG
*
127639 AGCTAGCTTAGAAGGAGACACATGCACGCCCAAGTTGGAGCACATGACCAG
1 AGCTAGCTTAGAAGGAGACACATGCACCCCCAAGTTGGAGCACATGACCAG
127690 CCATAATTCT
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
51 49 1.00
ACGTcount: A:0.32, C:0.26, G:0.27, T:0.14
Consensus pattern (51 bp):
AGCTAGCTTAGAAGGAGACACATGCACCCCCAAGTTGGAGCACATGACCAG
Found at i:132858 original size:30 final size:30
Alignment explanation
Indices: 132819--132899 Score: 153
Period size: 30 Copynumber: 2.7 Consensus size: 30
132809 CACTAAGGAA
*
132819 AGCTCAACTTAGCTGGAGGAGCTAGCATAT
1 AGCTTAACTTAGCTGGAGGAGCTAGCATAT
132849 AGCTTAACTTAGCTGGAGGAGCTAGCATAT
1 AGCTTAACTTAGCTGGAGGAGCTAGCATAT
132879 AGCTTAACTTAGCTGGAGGAG
1 AGCTTAACTTAGCTGGAGGAG
132900 AGATTTGGAC
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
30 50 1.00
ACGTcount: A:0.30, C:0.17, G:0.28, T:0.25
Consensus pattern (30 bp):
AGCTTAACTTAGCTGGAGGAGCTAGCATAT
Found at i:134148 original size:23 final size:23
Alignment explanation
Indices: 134122--134170 Score: 71
Period size: 23 Copynumber: 2.1 Consensus size: 23
134112 ATCAGAAAAC
* *
134122 AAATTGAAGCACTCCAAAAGAAG
1 AAATTCAAGCACTCAAAAAGAAG
*
134145 AAATTCCAGCACTCAAAAAGAAG
1 AAATTCAAGCACTCAAAAAGAAG
134168 AAA
1 AAA
134171 AGCAAAGAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.55, C:0.18, G:0.14, T:0.12
Consensus pattern (23 bp):
AAATTCAAGCACTCAAAAAGAAG
Found at i:134182 original size:5 final size:5
Alignment explanation
Indices: 134165--134200 Score: 63
Period size: 5 Copynumber: 7.2 Consensus size: 5
134155 ACTCAAAAAG
*
134165 AAGAA AAGCA AAGAA AAGAA AAGAA AAGAA AAGAA A
1 AAGAA AAGAA AAGAA AAGAA AAGAA AAGAA AAGAA A
134201 GAAGTTGAAG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
5 29 1.00
ACGTcount: A:0.78, C:0.03, G:0.19, T:0.00
Consensus pattern (5 bp):
AAGAA
Found at i:139608 original size:23 final size:25
Alignment explanation
Indices: 139569--139622 Score: 76
Period size: 23 Copynumber: 2.2 Consensus size: 25
139559 TCTTTTTCTT
139569 TTTCTTCCTTTTTGAGTGCTTTCAA
1 TTTCTTCCTTTTTGAGTGCTTTCAA
* *
139594 TTTCTT-C-TTTTGAGTGCTTTGAT
1 TTTCTTCCTTTTTGAGTGCTTTCAA
139617 TTTCTT
1 TTTCTT
139623 TGCTGGATTT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
23 20 0.74
24 1 0.04
25 6 0.22
ACGTcount: A:0.09, C:0.17, G:0.13, T:0.61
Consensus pattern (25 bp):
TTTCTTCCTTTTTGAGTGCTTTCAA
Found at i:143589 original size:24 final size:24
Alignment explanation
Indices: 143562--143616 Score: 69
Period size: 24 Copynumber: 2.3 Consensus size: 24
143552 CCAACTTTTC
143562 TTTCTTTTTTCTTC-TTTTGAGTG
1 TTTCTTTTTTCTTCTTTTTGAGTG
**
143585 TTT-TCAATTTCTTCTTTTTGAGTG
1 TTTCT-TTTTTCTTCTTTTTGAGTG
143609 TTTCTTTT
1 TTTCTTTT
143617 CTGATTTTAC
Statistics
Matches: 25, Mismatches: 4, Indels: 5
0.74 0.12 0.15
Matches are distributed among these distances:
22 1 0.04
23 10 0.40
24 13 0.52
25 1 0.04
ACGTcount: A:0.07, C:0.13, G:0.11, T:0.69
Consensus pattern (24 bp):
TTTCTTTTTTCTTCTTTTTGAGTG
Found at i:143624 original size:22 final size:24
Alignment explanation
Indices: 143576--143624 Score: 57
Period size: 22 Copynumber: 2.1 Consensus size: 24
143566 TTTTTTCTTC
**
143576 TTTTGAGTGTTTTCAATTTCTTCT
1 TTTTGAGTGTTTTCAATTTCTGAT
*
143600 TTTTGAGTG-TTTC-TTTTCTGAT
1 TTTTGAGTGTTTTCAATTTCTGAT
143622 TTT
1 TTT
143625 ACTTGATACG
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
22 9 0.41
23 4 0.18
24 9 0.41
ACGTcount: A:0.10, C:0.10, G:0.14, T:0.65
Consensus pattern (24 bp):
TTTTGAGTGTTTTCAATTTCTGAT
Found at i:146663 original size:13 final size:11
Alignment explanation
Indices: 146644--146703 Score: 50
Period size: 13 Copynumber: 5.1 Consensus size: 11
146634 TACAATCTGT
146644 TCATCACCATA
1 TCATCACCATA
*
146655 GTCCATCACCGTA
1 -T-CATCACCATA
*
146668 TCA-CGCCTATA
1 TCATCACC-ATA
146679 TCATCACCATA
1 TCATCACCATA
146690 GTCTATCACCATA
1 -TC-ATCACCATA
146703 T
1 T
146704 AACGCCTAAA
Statistics
Matches: 39, Mismatches: 4, Indels: 10
0.74 0.08 0.19
Matches are distributed among these distances:
10 3 0.08
11 10 0.26
12 8 0.21
13 18 0.46
ACGTcount: A:0.30, C:0.35, G:0.07, T:0.28
Consensus pattern (11 bp):
TCATCACCATA
Found at i:146690 original size:35 final size:35
Alignment explanation
Indices: 146644--146722 Score: 122
Period size: 35 Copynumber: 2.3 Consensus size: 35
146634 TACAATCTGT
* * *
146644 TCATCACCATAGTCCATCACCGTATCACGCCTATA
1 TCATCACCATAGTCCATCACCATATAACGCCTAAA
*
146679 TCATCACCATAGTCTATCACCATATAACGCCTAAA
1 TCATCACCATAGTCCATCACCATATAACGCCTAAA
146714 TCATCACCA
1 TCATCACCA
146723 AATTCCATTT
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
35 40 1.00
ACGTcount: A:0.33, C:0.35, G:0.06, T:0.25
Consensus pattern (35 bp):
TCATCACCATAGTCCATCACCATATAACGCCTAAA
Found at i:146885 original size:15 final size:15
Alignment explanation
Indices: 146865--146896 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
146855 TTGATAACAT
146865 TTCTTTCCATTTCAA
1 TTCTTTCCATTTCAA
146880 TTCTTTCCATTTCAA
1 TTCTTTCCATTTCAA
146895 TT
1 TT
146897 TACTTTTCAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.19, C:0.25, G:0.00, T:0.56
Consensus pattern (15 bp):
TTCTTTCCATTTCAA
Found at i:152172 original size:13 final size:11
Alignment explanation
Indices: 152153--152215 Score: 65
Period size: 13 Copynumber: 5.4 Consensus size: 11
152143 TACAATCTGT
152153 TCATCACCATA
1 TCATCACCATA
152164 GTCCATCACCATA
1 -T-CATCACCATA
*
152177 TCA-CGCCTATA
1 TCATCACC-ATA
152188 TCATCACCATA
1 TCATCACCATA
152199 CTCCATCACCATA
1 -T-CATCACCATA
152212 TCAT
1 TCAT
152216 GCCTAAATCA
Statistics
Matches: 44, Mismatches: 2, Indels: 11
0.77 0.04 0.19
Matches are distributed among these distances:
10 3 0.07
11 14 0.32
12 7 0.16
13 20 0.45
ACGTcount: A:0.32, C:0.38, G:0.03, T:0.27
Consensus pattern (11 bp):
TCATCACCATA
Found at i:152204 original size:35 final size:35
Alignment explanation
Indices: 152153--152229 Score: 127
Period size: 35 Copynumber: 2.2 Consensus size: 35
152143 TACAATCTGT
* *
152153 TCATCACCATAGTCCATCACCATATCACGCCTATA
1 TCATCACCATACTCCATCACCATATCACGCCTAAA
*
152188 TCATCACCATACTCCATCACCATATCATGCCTAAA
1 TCATCACCATACTCCATCACCATATCACGCCTAAA
152223 TCATCAC
1 TCATCAC
152230 TAAATTCCAT
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
35 39 1.00
ACGTcount: A:0.32, C:0.38, G:0.04, T:0.26
Consensus pattern (35 bp):
TCATCACCATACTCCATCACCATATCACGCCTAAA
Found at i:152239 original size:35 final size:35
Alignment explanation
Indices: 152153--152239 Score: 111
Period size: 35 Copynumber: 2.5 Consensus size: 35
152143 TACAATCTGT
* * *
152153 TCATCACCATAGTCCATCACCATATCACGCCTATA
1 TCATCACCAAACTCCATCACCATATCACGCCTAAA
* *
152188 TCATCACCATACTCCATCACCATATCATGCCTAAA
1 TCATCACCAAACTCCATCACCATATCACGCCTAAA
* *
152223 TCATCACTAAATTCCAT
1 TCATCACCAAACTCCAT
152240 TTCCATTTCT
Statistics
Matches: 46, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
35 46 1.00
ACGTcount: A:0.33, C:0.36, G:0.03, T:0.28
Consensus pattern (35 bp):
TCATCACCAAACTCCATCACCATATCACGCCTAAA
Found at i:155435 original size:24 final size:25
Alignment explanation
Indices: 155399--155446 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 25
155389 CACCATGATC
* * *
155399 TGCATTTTATTCAGTTTCTTCATCT
1 TGCATTGTATTCAGGTTCCTCATCT
155424 TGCATTGT-TTCAGGTTCCTCATC
1 TGCATTGTATTCAGGTTCCTCATC
155447 AAAAATAGGC
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
24 13 0.65
25 7 0.35
ACGTcount: A:0.15, C:0.23, G:0.12, T:0.50
Consensus pattern (25 bp):
TGCATTGTATTCAGGTTCCTCATCT
Found at i:160274 original size:24 final size:24
Alignment explanation
Indices: 160247--160301 Score: 60
Period size: 24 Copynumber: 2.3 Consensus size: 24
160237 CCAACTTTTC
160247 TTTCTTTTTTCTTC-TTTTGAGTG
1 TTTCTTTTTTCTTCTTTTTGAGTG
**
160270 TTT-TCAATTTCTTCTTTTTGAGTG
1 TTTCT-TTTTTCTTCTTTTTGAGTG
*
160294 CTTCTTTT
1 TTTCTTTT
160302 CTGATTTTTC
Statistics
Matches: 24, Mismatches: 5, Indels: 5
0.71 0.15 0.15
Matches are distributed among these distances:
22 1 0.04
23 10 0.42
24 12 0.50
25 1 0.04
ACGTcount: A:0.07, C:0.15, G:0.11, T:0.67
Consensus pattern (24 bp):
TTTCTTTTTTCTTCTTTTTGAGTG
Found at i:165179 original size:19 final size:20
Alignment explanation
Indices: 165138--165188 Score: 77
Period size: 19 Copynumber: 2.6 Consensus size: 20
165128 GAAACCCCTT
*
165138 TGAAAATACATGAGTTTTGA
1 TGAAAATACATGAGTTTTAA
165158 TGAAAATACATGA-TTTTAA
1 TGAAAATACATGAGTTTTAA
*
165177 TGAAGATACATG
1 TGAAAATACATG
165189 CTCTTGGCCA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 16 0.55
20 13 0.45
ACGTcount: A:0.43, C:0.06, G:0.18, T:0.33
Consensus pattern (20 bp):
TGAAAATACATGAGTTTTAA
Found at i:166120 original size:30 final size:31
Alignment explanation
Indices: 166080--166139 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 31
166070 ACATGCTGCC
**
166080 ATGATATCTAAATGAAATGAAAACATAATAA
1 ATGATATCTAAAACAAATGAAAACATAATAA
* *
166111 ATGA-ATCTAAAACATATGTAAACATAATA
1 ATGATATCTAAAACAAATGAAAACATAATA
166140 TAAAGCTAAG
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
30 21 0.84
31 4 0.16
ACGTcount: A:0.57, C:0.08, G:0.08, T:0.27
Consensus pattern (31 bp):
ATGATATCTAAAACAAATGAAAACATAATAA
Found at i:166458 original size:21 final size:21
Alignment explanation
Indices: 166418--166458 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
166408 TTTTTGAAAT
*
166418 TATTCTTTTTTTCTTTTCTTC
1 TATTCTTTTTTTCTTGTCTTC
166439 TATTCTGTTTTTT-TTGTCTT
1 TATTCT-TTTTTTCTTGTCTT
166459 TTCTTTCTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 12 0.67
22 6 0.33
ACGTcount: A:0.05, C:0.15, G:0.05, T:0.76
Consensus pattern (21 bp):
TATTCTTTTTTTCTTGTCTTC
Found at i:173397 original size:51 final size:51
Alignment explanation
Indices: 173340--173441 Score: 177
Period size: 51 Copynumber: 2.0 Consensus size: 51
173330 TCCACACTCA
* *
173340 AGCTAGCTTGGAAGGAGACACATGCATCCCCAAGTTGGAGCACATGACCAG
1 AGCTAGCTTAGAAGGAGAAACATGCATCCCCAAGTTGGAGCACATGACCAG
*
173391 AGCTAGCTTAGAAGGAGAAACATGCATGCCCAAGTTGGAGCACATGACCAG
1 AGCTAGCTTAGAAGGAGAAACATGCATCCCCAAGTTGGAGCACATGACCAG
173442 CCATAATTCC
Statistics
Matches: 48, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
51 48 1.00
ACGTcount: A:0.33, C:0.24, G:0.27, T:0.16
Consensus pattern (51 bp):
AGCTAGCTTAGAAGGAGAAACATGCATCCCCAAGTTGGAGCACATGACCAG
Found at i:179901 original size:5 final size:5
Alignment explanation
Indices: 179891--179921 Score: 62
Period size: 5 Copynumber: 6.2 Consensus size: 5
179881 ACTCAAAAAG
179891 AAGAA AAGAA AAGAA AAGAA AAGAA AAGAA A
1 AAGAA AAGAA AAGAA AAGAA AAGAA AAGAA A
179922 GAAGTTAAAG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 26 1.00
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (5 bp):
AAGAA
Found at i:189434 original size:35 final size:36
Alignment explanation
Indices: 189367--189434 Score: 93
Period size: 35 Copynumber: 1.9 Consensus size: 36
189357 ATACAATCTG
*
189367 TCCATCACCATTATCACGCCTATATCATCACCATAT
1 TCCATCACCATTATCACGCCTATATCAGCACCATAT
* * *
189403 TCCATCACCA-TCTCACTCCTATATTAGCACCA
1 TCCATCACCATTATCACGCCTATATCAGCACCA
189435 ACTTATAAAT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
35 18 0.64
36 10 0.36
ACGTcount: A:0.29, C:0.38, G:0.03, T:0.29
Consensus pattern (36 bp):
TCCATCACCATTATCACGCCTATATCAGCACCATAT
Found at i:190064 original size:24 final size:25
Alignment explanation
Indices: 190020--190069 Score: 68
Period size: 24 Copynumber: 2.0 Consensus size: 25
190010 TTACTATTTC
*
190020 ATTTCATTTTCTTTCATCTTTTCTT
1 ATTTCATTTACTTTCATCTTTTCTT
190045 ATTTCA-TTACTTT-ATCCTTTTCTT
1 ATTTCATTTACTTTCAT-CTTTTCTT
190069 A
1 A
190070 ACCTTTTTTA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
23 2 0.09
24 15 0.65
25 6 0.26
ACGTcount: A:0.16, C:0.20, G:0.00, T:0.64
Consensus pattern (25 bp):
ATTTCATTTACTTTCATCTTTTCTT
Found at i:201105 original size:23 final size:25
Alignment explanation
Indices: 201066--201119 Score: 76
Period size: 23 Copynumber: 2.2 Consensus size: 25
201056 TCTTTTTCTT
201066 TTTCTTCCTTTTTGAGTGCTTTCAA
1 TTTCTTCCTTTTTGAGTGCTTTCAA
* *
201091 TTTCTT-C-TTTTGAGTGCTTTGAT
1 TTTCTTCCTTTTTGAGTGCTTTCAA
201114 TTTCTT
1 TTTCTT
201120 TGCTGGATTT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
23 20 0.74
24 1 0.04
25 6 0.22
ACGTcount: A:0.09, C:0.17, G:0.13, T:0.61
Consensus pattern (25 bp):
TTTCTTCCTTTTTGAGTGCTTTCAA
Found at i:203676 original size:23 final size:24
Alignment explanation
Indices: 203637--203690 Score: 74
Period size: 23 Copynumber: 2.2 Consensus size: 24
203627 TCTTTTTCTT
203637 TTTCTTTCTTTTTGAGTGCTTTCAA
1 TTTC-TTCTTTTTGAGTGCTTTCAA
* *
203662 TTTCTTC-TTTTGAGTGCTTTGAT
1 TTTCTTCTTTTTGAGTGCTTTCAA
203685 TTTCTT
1 TTTCTT
203691 TGCTGGATTT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
23 20 0.74
24 3 0.11
25 4 0.15
ACGTcount: A:0.09, C:0.15, G:0.13, T:0.63
Consensus pattern (24 bp):
TTTCTTCTTTTTGAGTGCTTTCAA
Found at i:228848 original size:15 final size:16
Alignment explanation
Indices: 228775--228847 Score: 55
Period size: 16 Copynumber: 4.5 Consensus size: 16
228765 GGGTTAAAAA
228775 TATTATCTTTAGTT-AT
1 TATTAT-TTTAGTTCAT
*
228791 TATTATTTTAGAGTT-AA
1 TATTATTTT--AGTTCAT
*
228808 GA-TATGTTTAGTTCAT
1 TATTAT-TTTAGTTCAT
228824 TATTATTTTA-TTCAT
1 TATTATTTTAGTTCAT
228839 TAGTTATTT
1 TA-TTATTT
228848 AGGACCTTTA
Statistics
Matches: 47, Mismatches: 4, Indels: 12
0.75 0.06 0.19
Matches are distributed among these distances:
15 14 0.30
16 21 0.45
17 12 0.26
ACGTcount: A:0.27, C:0.04, G:0.10, T:0.59
Consensus pattern (16 bp):
TATTATTTTAGTTCAT
Found at i:232893 original size:14 final size:14
Alignment explanation
Indices: 232874--232900 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
232864 AACAACTCCA
232874 CATGCTTTATAGTT
1 CATGCTTTATAGTT
232888 CATGCTTTATAGT
1 CATGCTTTATAGT
232901 CGAAACCAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.22, C:0.15, G:0.15, T:0.48
Consensus pattern (14 bp):
CATGCTTTATAGTT
Found at i:238378 original size:24 final size:21
Alignment explanation
Indices: 238344--238386 Score: 50
Period size: 23 Copynumber: 1.9 Consensus size: 21
238334 TCCACAAGAT
*
238344 ATGTCCTTTGACATTTCAAAGG
1 ATGTCCTTTGA-AATTCAAAGG
238366 ATGTACCTCTTGAAATTCAAA
1 ATGT-CCT-TTGAAATTCAAA
238387 AGAATGAGCC
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
22 4 0.22
23 10 0.56
24 4 0.22
ACGTcount: A:0.33, C:0.19, G:0.14, T:0.35
Consensus pattern (21 bp):
ATGTCCTTTGAAATTCAAAGG
Found at i:241818 original size:23 final size:25
Alignment explanation
Indices: 241779--241832 Score: 76
Period size: 23 Copynumber: 2.2 Consensus size: 25
241769 TCTTTTTCTT
241779 TTTCTTCCTTTTTGAGTGCTTTCAA
1 TTTCTTCCTTTTTGAGTGCTTTCAA
* *
241804 TTTCTT-C-TTTTGAGTGCTTTGAT
1 TTTCTTCCTTTTTGAGTGCTTTCAA
241827 TTTCTT
1 TTTCTT
241833 TGCTGGATTT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
23 20 0.74
24 1 0.04
25 6 0.22
ACGTcount: A:0.09, C:0.17, G:0.13, T:0.61
Consensus pattern (25 bp):
TTTCTTCCTTTTTGAGTGCTTTCAA
Found at i:255951 original size:20 final size:20
Alignment explanation
Indices: 255928--255972 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
255918 TTTTTTGAAA
*
255928 TTTTGGCTTTTTTGGCTTTT
1 TTTTGGCTTTTTTGGCCTTT
** *
255948 TTTTGTTTTTTTTTGCCTTT
1 TTTTGGCTTTTTTGGCCTTT
255968 TTTTG
1 TTTTG
255973 TTGTTTTTGA
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:0.00, C:0.09, G:0.16, T:0.76
Consensus pattern (20 bp):
TTTTGGCTTTTTTGGCCTTT
Found at i:255973 original size:20 final size:21
Alignment explanation
Indices: 255935--255980 Score: 67
Period size: 20 Copynumber: 2.2 Consensus size: 21
255925 AAATTTTGGC
*
255935 TTTTTTGGCTTTTTTTTGTT-
1 TTTTTTGGCCTTTTTTTGTTG
*
255955 TTTTTTTGCCTTTTTTTGTTG
1 TTTTTTGGCCTTTTTTTGTTG
255976 TTTTT
1 TTTTT
255981 GAAAAAAATA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 18 0.78
21 5 0.22
ACGTcount: A:0.00, C:0.07, G:0.13, T:0.80
Consensus pattern (21 bp):
TTTTTTGGCCTTTTTTTGTTG
Found at i:264671 original size:36 final size:36
Alignment explanation
Indices: 264620--264717 Score: 153
Period size: 36 Copynumber: 2.8 Consensus size: 36
264610 CTTAATTCGT
*
264620 ACCATTATCACGCCTATATCATCACCATAGTCCATC
1 ACCATTATCACGCCTATATCATCACCATAGTCAATC
* *
264656 ACCATTATCATGCCTATATCATCACCATATTCAATC
1 ACCATTATCACGCCTATATCATCACCATAGTCAATC
*
264692 ACCA-TATCACGCCTATATTATCACCA
1 ACCATTATCACGCCTATATCATCACCA
264718 ACTTATAAAT
Statistics
Matches: 57, Mismatches: 5, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
35 20 0.35
36 37 0.65
ACGTcount: A:0.33, C:0.34, G:0.04, T:0.30
Consensus pattern (36 bp):
ACCATTATCACGCCTATATCATCACCATAGTCAATC
Found at i:266621 original size:90 final size:91
Alignment explanation
Indices: 266467--266648 Score: 276
Period size: 90 Copynumber: 2.0 Consensus size: 91
266457 CCTAGAACAC
*
266467 CCATGTGCCTTGCATATGACCAGCCCCCATGTGCCTTGCATGAGGATCATTTAGGCGCCAAGATG
1 CCATGTGCCTTGCATATGAACAGCCCCCATGTGCCTTGCATGAGGATCATTTAGGCGCCAAGATG
*
266532 AAGAGTTCTCTCCCTATTCGGCCAAG
66 AAGAGCTCTCTCCCTATTCGGCCAAG
** * * * * *
266558 CCATGTGTTTTGCATGTGAACAG-CCCCATGTGCCTTGCATGTGGTTTATTTAGGGGCCAAGATG
1 CCATGTGCCTTGCATATGAACAGCCCCCATGTGCCTTGCATGAGGATCATTTAGGCGCCAAGATG
266622 AAGAGCTCTCTCCCTATTCGGCCAAG
66 AAGAGCTCTCTCCCTATTCGGCCAAG
266648 C
1 C
266649 ATCATTTCCC
Statistics
Matches: 82, Mismatches: 9, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
90 63 0.77
91 19 0.23
ACGTcount: A:0.21, C:0.27, G:0.24, T:0.27
Consensus pattern (91 bp):
CCATGTGCCTTGCATATGAACAGCCCCCATGTGCCTTGCATGAGGATCATTTAGGCGCCAAGATG
AAGAGCTCTCTCCCTATTCGGCCAAG
Found at i:267489 original size:24 final size:23
Alignment explanation
Indices: 267431--267490 Score: 59
Period size: 23 Copynumber: 2.6 Consensus size: 23
267421 AAAATCAGCA
*
267431 AAGAAAATA-AAAGCACTCAAAAT
1 AAGAAAA-AGAAAGCACTCAAAAG
* **
267454 AATAAATTGAAAGCACTCGAAAAG
1 AAGAAAAAGAAAGCACTC-AAAAG
267478 AAGAAAAAGAAAG
1 AAGAAAAAGAAAG
267491 AAAGAAAAGT
Statistics
Matches: 28, Mismatches: 7, Indels: 3
0.74 0.18 0.08
Matches are distributed among these distances:
23 14 0.50
24 14 0.50
ACGTcount: A:0.63, C:0.10, G:0.15, T:0.12
Consensus pattern (23 bp):
AAGAAAAAGAAAGCACTCAAAAG
Found at i:274312 original size:25 final size:22
Alignment explanation
Indices: 274268--274313 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
274258 AGGATTATGC
274268 ATTATCTTTTAGGATTAGATTT
1 ATTATCTTTTAGGATTAGATTT
*
274290 ATTATTTTATTAGGAATTAAGATT
1 ATTATCTT-TTAGG-ATT-AGATT
274314 GGGTTAAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
22 7 0.35
23 5 0.25
24 3 0.15
25 5 0.25
ACGTcount: A:0.33, C:0.02, G:0.13, T:0.52
Consensus pattern (22 bp):
ATTATCTTTTAGGATTAGATTT
Found at i:276371 original size:17 final size:19
Alignment explanation
Indices: 276349--276391 Score: 63
Period size: 17 Copynumber: 2.4 Consensus size: 19
276339 TTGTTTTTCA
*
276349 AAAAAAAAT-AAACAAA-C
1 AAAAAAAATAAAAAAAAGC
276366 AAAAAAAATAAAAAAAAGC
1 AAAAAAAATAAAAAAAAGC
276385 AAAAAAA
1 AAAAAAA
276392 GCAAAATTTC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 9 0.39
18 6 0.26
19 8 0.35
ACGTcount: A:0.86, C:0.07, G:0.02, T:0.05
Consensus pattern (19 bp):
AAAAAAAATAAAAAAAAGC
Found at i:286022 original size:5 final size:5
Alignment explanation
Indices: 286008--286042 Score: 63
Period size: 5 Copynumber: 7.2 Consensus size: 5
285998 GTGCTTCAAC
286008 TTTC- TTTCT TTTCT TTTCT TTTCT TTTCT TTTCT T
1 TTTCT TTTCT TTTCT TTTCT TTTCT TTTCT TTTCT T
286043 ATTTTTGAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
4 4 0.13
5 26 0.87
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (5 bp):
TTTCT
Found at i:289921 original size:23 final size:25
Alignment explanation
Indices: 289882--289935 Score: 76
Period size: 23 Copynumber: 2.2 Consensus size: 25
289872 TCTTTTTCTT
289882 TTTCTTCCTTTTTGAGTGCTTTCAA
1 TTTCTTCCTTTTTGAGTGCTTTCAA
* *
289907 TTTCTT-C-TTTTGAGTGCTTTGAT
1 TTTCTTCCTTTTTGAGTGCTTTCAA
289930 TTTCTT
1 TTTCTT
289936 TGCTGGATTT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
23 20 0.74
24 1 0.04
25 6 0.22
ACGTcount: A:0.09, C:0.17, G:0.13, T:0.61
Consensus pattern (25 bp):
TTTCTTCCTTTTTGAGTGCTTTCAA
Found at i:292993 original size:23 final size:25
Alignment explanation
Indices: 292954--293007 Score: 76
Period size: 23 Copynumber: 2.2 Consensus size: 25
292944 TCTTTTTCTT
292954 TTTCTTCCTTTTTGAGTGCTTTCAA
1 TTTCTTCCTTTTTGAGTGCTTTCAA
* *
292979 TTTCTT-C-TTTTGAGTGCTTTGAT
1 TTTCTTCCTTTTTGAGTGCTTTCAA
293002 TTTCTT
1 TTTCTT
293008 TGCTGGATTT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
23 20 0.74
24 1 0.04
25 6 0.22
ACGTcount: A:0.09, C:0.17, G:0.13, T:0.61
Consensus pattern (25 bp):
TTTCTTCCTTTTTGAGTGCTTTCAA
Found at i:299639 original size:17 final size:17
Alignment explanation
Indices: 299617--299667 Score: 59
Period size: 17 Copynumber: 3.0 Consensus size: 17
299607 AATTGTAGTG
299617 CAAAAAGAAAGAAAAGA
1 CAAAAAGAAAGAAAAGA
**
299634 CAAAAAG-AAGAAAATT
1 CAAAAAGAAAGAAAAGA
*
299650 CAGAAAAGAAAAAAAAGA
1 CA-AAAAGAAAGAAAAGA
299668 AAATGATTTC
Statistics
Matches: 27, Mismatches: 5, Indels: 3
0.77 0.14 0.09
Matches are distributed among these distances:
16 9 0.33
17 12 0.44
18 6 0.22
ACGTcount: A:0.75, C:0.06, G:0.16, T:0.04
Consensus pattern (17 bp):
CAAAAAGAAAGAAAAGA
Found at i:299647 original size:25 final size:23
Alignment explanation
Indices: 299619--299670 Score: 59
Period size: 25 Copynumber: 2.2 Consensus size: 23
299609 TTGTAGTGCA
299619 AAAAGAAAGAAAAGACAAAAAGAAG
1 AAAAGAAAGAAAAGA-AAAAA-AAG
***
299644 AAAATTCAGAAAAGAAAAAAAAG
1 AAAAGAAAGAAAAGAAAAAAAAG
299667 AAAA
1 AAAA
299671 TGATTTCAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
23 7 0.29
24 5 0.21
25 12 0.50
ACGTcount: A:0.77, C:0.04, G:0.15, T:0.04
Consensus pattern (23 bp):
AAAAGAAAGAAAAGAAAAAAAAG
Found at i:299667 original size:23 final size:25
Alignment explanation
Indices: 299626--299671 Score: 78
Period size: 23 Copynumber: 1.9 Consensus size: 25
299616 GCAAAAAGAA
299626 AGAAAAGACAAAAAGAAGAAAATTC
1 AGAAAAGACAAAAAGAAGAAAATTC
299651 AGAAAAGA-AAAAA-AAGAAAAT
1 AGAAAAGACAAAAAGAAGAAAAT
299672 GATTTCAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
23 8 0.38
24 5 0.24
25 8 0.38
ACGTcount: A:0.74, C:0.04, G:0.15, T:0.07
Consensus pattern (25 bp):
AGAAAAGACAAAAAGAAGAAAATTC
Found at i:301234 original size:15 final size:17
Alignment explanation
Indices: 301209--301242 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
301199 TAAAGGTCCT
301209 AAATAACTAATAAA-TA
1 AAATAACTAATAAACTA
301225 AAATAA-TAATAAACTA
1 AAATAACTAATAAACTA
301241 AA
1 AA
301243 CATATATTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 7 0.41
16 10 0.59
ACGTcount: A:0.71, C:0.06, G:0.00, T:0.24
Consensus pattern (17 bp):
AAATAACTAATAAACTA
Found at i:301330 original size:25 final size:22
Alignment explanation
Indices: 301302--301347 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
301292 TTTTTAACCC
301302 AATCTTAATTCCTAATAAAATAATA
1 AATC-TAA-TCCTAA-AAAATAATA
*
301327 AATCTAATCCTAAAAGATAAT
1 AATCTAATCCTAAAAAATAAT
301348 GCATCATCCT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
22 7 0.35
23 6 0.30
24 3 0.15
25 4 0.20
ACGTcount: A:0.52, C:0.13, G:0.02, T:0.33
Consensus pattern (22 bp):
AATCTAATCCTAAAAAATAATA
Found at i:305942 original size:15 final size:17
Alignment explanation
Indices: 305917--305950 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
305907 TAAAGGTCAT
305917 AAATAACTAATAAA-TA
1 AAATAACTAATAAACTA
305933 AAATAA-TAATAAACTA
1 AAATAACTAATAAACTA
305949 AA
1 AA
305951 CATATTTTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 7 0.41
16 10 0.59
ACGTcount: A:0.71, C:0.06, G:0.00, T:0.24
Consensus pattern (17 bp):
AAATAACTAATAAACTA
Found at i:306004 original size:45 final size:48
Alignment explanation
Indices: 305923--306034 Score: 117
Period size: 45 Copynumber: 2.3 Consensus size: 48
305913 TCATAAATAA
*
305923 CTAATAAATAAAATAATAATAAACTAAACATATTTTAA-C-TC-TAATTC
1 CTAATAAAT--AATAATAATAAACGAAACATATTTTAACCATCTTAATTC
305970 CTAATAAATAATAATAACTAAA-GAAA-ATATTTTTAACCCAATCTTAATTC
1 CTAATAAATAATAATAA-TAAACGAAACATA-TTTTAA-CC-ATCTTAATTC
306020 CTAATAAAATAATAA
1 CTAAT-AAATAATAA
306035 ATCTAATCCT
Statistics
Matches: 56, Mismatches: 1, Indels: 12
0.81 0.01 0.17
Matches are distributed among these distances:
44 3 0.05
45 17 0.30
46 4 0.07
47 10 0.18
49 2 0.04
50 11 0.20
51 9 0.16
ACGTcount: A:0.54, C:0.12, G:0.01, T:0.33
Consensus pattern (48 bp):
CTAATAAATAATAATAATAAACGAAACATATTTTAACCATCTTAATTC
Found at i:306037 original size:25 final size:22
Alignment explanation
Indices: 306009--306054 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
305999 TTTTTAACCC
306009 AATCTTAATTCCTAATAAAATAATA
1 AATC-TAA-TCCTAA-AAAATAATA
*
306034 AATCTAATCCTAAAAGATAAT
1 AATCTAATCCTAAAAAATAAT
306055 GCATCATCCT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
22 7 0.35
23 6 0.30
24 3 0.15
25 4 0.20
ACGTcount: A:0.52, C:0.13, G:0.02, T:0.33
Consensus pattern (22 bp):
AATCTAATCCTAAAAAATAATA
Found at i:316269 original size:23 final size:25
Alignment explanation
Indices: 316227--316280 Score: 67
Period size: 23 Copynumber: 2.2 Consensus size: 25
316217 TCTTTTTCTT
316227 TTTCTTCCTTTTTGAGTGCTTTCAA
1 TTTCTTCCTTTTTGAGTGCTTTCAA
* * *
316252 TTTCTT-C-TTTTGATTGCTTTGAT
1 TTTCTTCCTTTTTGAGTGCTTTCAA
316275 TTTCTT
1 TTTCTT
316281 TGCTGGATTT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
23 19 0.73
24 1 0.04
25 6 0.23
ACGTcount: A:0.09, C:0.17, G:0.11, T:0.63
Consensus pattern (25 bp):
TTTCTTCCTTTTTGAGTGCTTTCAA
Found at i:327949 original size:19 final size:21
Alignment explanation
Indices: 327906--327957 Score: 81
Period size: 19 Copynumber: 2.6 Consensus size: 21
327896 GAAACCCCTT
327906 TGAAAATACATGATTTTTAAA
1 TGAAAATACATGATTTTTAAA
327927 TGAAAATACATGA-TTTT-AA
1 TGAAAATACATGATTTTTAAA
*
327946 TGAAGATACATG
1 TGAAAATACATG
327958 CTCTTGGCCG
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 13 0.43
20 4 0.13
21 13 0.43
ACGTcount: A:0.46, C:0.06, G:0.13, T:0.35
Consensus pattern (21 bp):
TGAAAATACATGATTTTTAAA
Found at i:331153 original size:8 final size:8
Alignment explanation
Indices: 331142--331174 Score: 57
Period size: 8 Copynumber: 4.1 Consensus size: 8
331132 TCTTTTTCTT
*
331142 TTCTTTTA
1 TTCTTTTC
331150 TTCTTTTC
1 TTCTTTTC
331158 TTCTTTTC
1 TTCTTTTC
331166 TTCTTTTC
1 TTCTTTTC
331174 T
1 T
331175 GATTTTTCTC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
8 24 1.00
ACGTcount: A:0.03, C:0.21, G:0.00, T:0.76
Consensus pattern (8 bp):
TTCTTTTC
Found at i:331174 original size:13 final size:12
Alignment explanation
Indices: 331129--331167 Score: 51
Period size: 13 Copynumber: 3.0 Consensus size: 12
331119 CTTTTTGAAC
331129 TTCTCTTTTTCTT
1 TTCT-TTTTTCTT
331142 TTCTTTTATTCTT
1 TTCTTTT-TTCTT
331155 TTCTTCTTTTCTT
1 TTCTT-TTTTCTT
331168 CTTTTCTGAT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
12 3 0.12
13 19 0.79
14 2 0.08
ACGTcount: A:0.03, C:0.21, G:0.00, T:0.77
Consensus pattern (12 bp):
TTCTTTTTTCTT
Found at i:335679 original size:8 final size:8
Alignment explanation
Indices: 335666--335713 Score: 53
Period size: 8 Copynumber: 5.9 Consensus size: 8
335656 AATTTTCTTT
335666 TTCTTTTC
1 TTCTTTTC
335674 TTCTTTTC
1 TTCTTTTC
**
335682 TGATTTTC
1 TTCTTTTC
335690 TTCTTTT-
1 TTCTTTTC
335697 TGTCTTTTC
1 T-TCTTTTC
335706 TTTCTTTT
1 -TTCTTTT
335714 TGCACTCCAA
Statistics
Matches: 33, Mismatches: 4, Indels: 5
0.79 0.10 0.12
Matches are distributed among these distances:
7 1 0.03
8 25 0.76
9 6 0.18
10 1 0.03
ACGTcount: A:0.02, C:0.19, G:0.04, T:0.75
Consensus pattern (8 bp):
TTCTTTTC
Found at i:335704 original size:16 final size:16
Alignment explanation
Indices: 335663--335715 Score: 65
Period size: 16 Copynumber: 3.3 Consensus size: 16
335653 ATGAATTTTC
335663 TTTT-TCTTTTCTTCT
1 TTTTGTCTTTTCTTCT
*
335678 TTTCTG-ATTTTCTTCT
1 TTT-TGTCTTTTCTTCT
335694 TTTTGTCTTTTCTTTCT
1 TTTTGTCTTTTC-TTCT
335711 TTTTG
1 TTTTG
335716 CACTCCAATT
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
15 5 0.16
16 18 0.56
17 9 0.28
ACGTcount: A:0.02, C:0.17, G:0.06, T:0.75
Consensus pattern (16 bp):
TTTTGTCTTTTCTTCT
Found at i:338190 original size:19 final size:21
Alignment explanation
Indices: 338147--338198 Score: 81
Period size: 19 Copynumber: 2.6 Consensus size: 21
338137 GAAACCCCTT
338147 TGAAAATACATGATTTTTAAA
1 TGAAAATACATGATTTTTAAA
338168 TGAAAATACATGA-TTTT-AA
1 TGAAAATACATGATTTTTAAA
*
338187 TGAAGATACATG
1 TGAAAATACATG
338199 CTCTTGGCAG
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 13 0.43
20 4 0.13
21 13 0.43
ACGTcount: A:0.46, C:0.06, G:0.13, T:0.35
Consensus pattern (21 bp):
TGAAAATACATGATTTTTAAA
Found at i:344153 original size:90 final size:91
Alignment explanation
Indices: 343999--344180 Score: 285
Period size: 90 Copynumber: 2.0 Consensus size: 91
343989 CCTAGAACAC
*
343999 CCATGTGCCTTGCATATGACCAGCCCCCATGTGCCTTGCATGAGGATCATTTAGGCGCCAAGATG
1 CCATGTGCCTTGCATATGAACAGCCCCCATGTGCCTTGCATGAGGATCATTTAGGCGCCAAGATG
*
344064 AAGAGTTCTCTCCCTATTCGGCCAAG
66 AAGAGCTCTCTCCCTATTCGGCCAAG
** * * * *
344090 CCATGTGTTTTGCATGTGAACAG-CCCCATGTGCCTTGCATGTGGTTTATTTAGGCGCCAAGATG
1 CCATGTGCCTTGCATATGAACAGCCCCCATGTGCCTTGCATGAGGATCATTTAGGCGCCAAGATG
344154 AAGAGCTCTCTCCCTATTCGGCCAAG
66 AAGAGCTCTCTCCCTATTCGGCCAAG
344180 C
1 C
344181 ATCATTTCCC
Statistics
Matches: 83, Mismatches: 8, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
90 64 0.77
91 19 0.23
ACGTcount: A:0.21, C:0.28, G:0.24, T:0.27
Consensus pattern (91 bp):
CCATGTGCCTTGCATATGAACAGCCCCCATGTGCCTTGCATGAGGATCATTTAGGCGCCAAGATG
AAGAGCTCTCTCCCTATTCGGCCAAG
Found at i:344991 original size:23 final size:24
Alignment explanation
Indices: 344964--345017 Score: 74
Period size: 23 Copynumber: 2.3 Consensus size: 24
344954 AAAATCAGCA
*
344964 AAGAAAATAAAAGCACTC-AAAAT
1 AAGAAAATAAAAGCACTCGAAAAG
* *
344987 AAGAAATTGAAAGCACTCGAAAAG
1 AAGAAAATAAAAGCACTCGAAAAG
345011 AAGAAAA
1 AAGAAAA
345018 AGAAAGAAAG
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
23 16 0.62
24 10 0.38
ACGTcount: A:0.63, C:0.11, G:0.15, T:0.11
Consensus pattern (24 bp):
AAGAAAATAAAAGCACTCGAAAAG
Found at i:347804 original size:11 final size:13
Alignment explanation
Indices: 347772--347801 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
347762 TGGCCAAAGA
347772 TGAAAAGGTATGT
1 TGAAAAGGTATGT
347785 TGAAAAGGTATG-
1 TGAAAAGGTATGT
347797 TGAAA
1 TGAAA
347802 GGTGTTTATT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 5 0.29
13 12 0.71
ACGTcount: A:0.43, C:0.00, G:0.30, T:0.27
Consensus pattern (13 bp):
TGAAAAGGTATGT
Found at i:351457 original size:9 final size:9
Alignment explanation
Indices: 351443--351576 Score: 61
Period size: 10 Copynumber: 14.0 Consensus size: 9
351433 AAATCGCTCA
351443 AACCGGTTT
1 AACCGGTTT
351452 AACCGGTTTT
1 AACCGG-TTT
**
351462 CAAATGGTTCT
1 -AACCGGTT-T
*
351473 GACCGGTTT
1 AACCGGTTT
*
351482 GACCGGTTT
1 AACCGGTTT
*
351491 CAACCGGTTCG
1 -AACCGGTT-T
351502 AACCGGTTT
1 AACCGGTTT
* *
351511 GACCGGTCTG
1 AACCGGT-TT
*
351521 AATCGGTTT
1 AACCGGTTT
* *
351530 GACCGGTCTG
1 AACCGGT-TT
*
351540 AATCGGTTT
1 AACCGGTTT
* *
351549 GACCGGTCTG
1 AACCGGT-TT
*
351559 AGCCGGTTT
1 AACCGGTTT
*
351568 GACCGGTTT
1 AACCGGTTT
351577 GACCCGACCC
Statistics
Matches: 90, Mismatches: 27, Indels: 16
0.68 0.20 0.12
Matches are distributed among these distances:
9 42 0.47
10 43 0.48
11 5 0.06
ACGTcount: A:0.16, C:0.23, G:0.29, T:0.31
Consensus pattern (9 bp):
AACCGGTTT
Found at i:351496 original size:19 final size:19
Alignment explanation
Indices: 351467--351574 Score: 130
Period size: 19 Copynumber: 5.6 Consensus size: 19
351457 GTTTTCAAAT
*
351467 GGTTCTGACCGGTTTG-ACC
1 GGTT-TGACCGGTCTGAACC
*
351486 GGTTTCAACCGGT-TCGAACC
1 GGTTT-GACCGGTCT-GAACC
*
351506 GGTTTGACCGGTCTGAATC
1 GGTTTGACCGGTCTGAACC
*
351525 GGTTTGACCGGTCTGAATC
1 GGTTTGACCGGTCTGAACC
*
351544 GGTTTGACCGGTCTGAGCC
1 GGTTTGACCGGTCTGAACC
351563 GGTTTGACCGGT
1 GGTTTGACCGGT
351575 TTGACCCGAC
Statistics
Matches: 80, Mismatches: 5, Indels: 8
0.86 0.05 0.09
Matches are distributed among these distances:
18 2 0.03
19 69 0.86
20 9 0.11
ACGTcount: A:0.14, C:0.24, G:0.32, T:0.30
Consensus pattern (19 bp):
GGTTTGACCGGTCTGAACC
Found at i:351517 original size:38 final size:38
Alignment explanation
Indices: 351444--351575 Score: 133
Period size: 38 Copynumber: 3.4 Consensus size: 38
351434 AATCGCTCAA
* * * ** *
351444 ACCGGTTTAACCGGTTTTCAAATGGTTCTGACCGGTTTG
1 ACCGGTTTGACCGGTTCTGAACCGGTT-TGACCGGTCTG
*
351483 ACCGGTTTCAACCGGTTC-GAACCGGTTTGACCGGTCTG
1 ACCGGTTT-GACCGGTTCTGAACCGGTTTGACCGGTCTG
* *
351521 AATCGGTTTGACCGG-TCTGAATCGGTTTGACCGGTCTG
1 -ACCGGTTTGACCGGTTCTGAACCGGTTTGACCGGTCTG
351559 AGCCGGTTTGACCGGTT
1 A-CCGGTTTGACCGGTT
351576 TGACCCGACC
Statistics
Matches: 79, Mismatches: 9, Indels: 10
0.81 0.09 0.10
Matches are distributed among these distances:
37 3 0.04
38 46 0.58
39 22 0.28
40 8 0.10
ACGTcount: A:0.16, C:0.23, G:0.30, T:0.31
Consensus pattern (38 bp):
ACCGGTTTGACCGGTTCTGAACCGGTTTGACCGGTCTG
Done.