Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008319.1 Hibiscus syriacus cultivar Beakdansim tig00111022_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: 4819703
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 1 of 21
Found at i:769 original size:31 final size:31
Alignment explanation
Indices: 714--772 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
704 TTAGGTCCAT
* *
714 AAGGAATTACCAGTCGGTGATGAACCTATAC
1 AAGGAATTACCAGTCAGCGATGAACCTATAC
745 AAGGAATTACCAGT-AGCGATTGAACCTA
1 AAGGAATTACCAGTCAGCGA-TGAACCTA
773 CCAGAGTCTT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
30 3 0.12
31 22 0.88
ACGTcount: A:0.37, C:0.19, G:0.22, T:0.22
Consensus pattern (31 bp):
AAGGAATTACCAGTCAGCGATGAACCTATAC
Found at i:13056 original size:14 final size:15
Alignment explanation
Indices: 13037--13067 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
13027 ATTAATTAAA
13037 TATTTTATGTT-ATT
1 TATTTTATGTTAATT
13051 TATTTTATGTTAATT
1 TATTTTATGTTAATT
13066 TA
1 TA
13068 GTTTGTTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 11 0.69
15 5 0.31
ACGTcount: A:0.26, C:0.00, G:0.06, T:0.68
Consensus pattern (15 bp):
TATTTTATGTTAATT
Found at i:19942 original size:13 final size:13
Alignment explanation
Indices: 19924--19949 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
19914 ATTATCGGTT
19924 TTGACCCGACCCG
1 TTGACCCGACCCG
19937 TTGACCCGACCCG
1 TTGACCCGACCCG
19950 ACCCGACCGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.15, C:0.46, G:0.23, T:0.15
Consensus pattern (13 bp):
TTGACCCGACCCG
Found at i:20083 original size:28 final size:28
Alignment explanation
Indices: 19981--20141 Score: 173
Period size: 29 Copynumber: 5.6 Consensus size: 28
19971 CGTTGACCGA
* * *
19981 GTGACATTTTGGGAATTAATTTGAAAGGG
1 GTGATATTTTGGGAATTAATTCGAAA-AG
* *
20010 GTGTTATTTTGGGAATTAATTCG-AAAT
1 GTGATATTTTGGGAATTAATTCGAAAAG
*
20037 GTGTACTATTTTGGGAATTAATTCGAAAAT
1 GTG-A-TATTTTGGGAATTAATTCGAAAAG
20067 GTGATATTTTGGGAATTTAATTCGAAAA-
1 GTGATATTTTGGGAA-TTAATTCGAAAAG
* *
20095 GTGCTATTTTGGGAATTTAAATCGAAAAG
1 GTGATATTTTGGGAA-TTAATTCGAAAAG
* *
20124 GTGCTATTTTGGTAATTA
1 GTGATATTTTGGGAATTA
20142 TTTAAGAAAT
Statistics
Matches: 118, Mismatches: 9, Indels: 11
0.86 0.07 0.08
Matches are distributed among these distances:
27 3 0.03
28 42 0.36
29 66 0.56
30 7 0.06
ACGTcount: A:0.32, C:0.05, G:0.24, T:0.40
Consensus pattern (28 bp):
GTGATATTTTGGGAATTAATTCGAAAAG
Found at i:20120 original size:57 final size:57
Alignment explanation
Indices: 19980--20140 Score: 193
Period size: 57 Copynumber: 2.8 Consensus size: 57
19970 CCGTTGACCG
* * * *
19980 AGTGAC-ATTTTGGGAATTAATTTGAAAGGGGTGTTATTTTGGGAA-TTAATTCGAAA
1 AGTGACTATTTTGGGAATTAAATCGAAA-AGGTGATATTTTGGGAATTTAATTCGAAA
* * *
20036 TGTGTACTATTTTGGGAATTAATTCGAAAATGTGATATTTTGGGAATTTAATTCGAAA
1 AGTG-ACTATTTTGGGAATTAAATCGAAAAGGTGATATTTTGGGAATTTAATTCGAAA
* *
20094 AGTG-CTATTTTGGGAATTTAAATCGAAAAGGTGCTATTTTGGTAATT
1 AGTGACTATTTTGGGAA-TTAAATCGAAAAGGTGATATTTTGGGAATT
20141 ATTTAAGAAA
Statistics
Matches: 91, Mismatches: 10, Indels: 7
0.84 0.09 0.06
Matches are distributed among these distances:
56 15 0.16
57 42 0.46
58 34 0.37
ACGTcount: A:0.32, C:0.05, G:0.24, T:0.40
Consensus pattern (57 bp):
AGTGACTATTTTGGGAATTAAATCGAAAAGGTGATATTTTGGGAATTTAATTCGAAA
Found at i:20150 original size:29 final size:28
Alignment explanation
Indices: 19986--20161 Score: 165
Period size: 29 Copynumber: 6.1 Consensus size: 28
19976 ACCGAGTGAC
* * *
19986 ATTTTGGGAATTAATTTGAAAGGGGTGTT
1 ATTTTGGGAATTAATTAGAAA-AGGTGCT
* * *
20015 ATTTTGGGAATTAATTCGAAATGTGTACT
1 ATTTTGGGAATTAATTAGAAAAG-GTGCT
* * *
20044 ATTTTGGGAATTAATTCGAAAATGTGAT
1 ATTTTGGGAATTAATTAGAAAAGGTGCT
*
20072 ATTTTGGGAATTTAATTCGAAAA-GTGCT
1 ATTTTGGGAA-TTAATTAGAAAAGGTGCT
* *
20100 ATTTTGGGAATTTAAATCGAAAAGGTGCT
1 ATTTTGGGAA-TTAATTAGAAAAGGTGCT
* * *
20129 ATTTTGGTAATTATTTAAGAAATGGTGCT
1 ATTTTGGGAATTAATT-AGAAAAGGTGCT
20158 ATTT
1 ATTT
20162 CTGTAAAATG
Statistics
Matches: 128, Mismatches: 15, Indels: 8
0.85 0.10 0.05
Matches are distributed among these distances:
28 44 0.34
29 84 0.66
ACGTcount: A:0.32, C:0.05, G:0.23, T:0.41
Consensus pattern (28 bp):
ATTTTGGGAATTAATTAGAAAAGGTGCT
Found at i:21288 original size:117 final size:117
Alignment explanation
Indices: 21074--21365 Score: 428
Period size: 117 Copynumber: 2.5 Consensus size: 117
21064 GGAAGTATTT
* *
21074 CAGGCTCCTTTGCTGTGTGCTCAGGGTAAGTCCTTACTGGTGTGCAGGTGGGTGTATGGTTATGG
1 CAGGCTCCTTTGCTGTGTGCTTAAGGTAAGTCCTTACTGGTGTGCAGGTGGGTGTATGGTTATGG
* * * *
21139 GGAACCTACACATTGTAGTGATTGGAGTGACTGGATGGGGAAGTTATTACTG
66 GGAACCTACACATTATAGTGATTGGAGCGACTGGATAGAGAAGTTATTACTG
* *
21191 CAGGCTCCTTTGCTGTGTGCTTAAGGAAAGTCCTTACTGGTGTGCAGGTGGGTGTATGGTTCTGG
1 CAGGCTCCTTTGCTGTGTGCTTAAGGTAAGTCCTTACTGGTGTGCAGGTGGGTGTATGGTTATGG
*
21256 GGAACCTACACATTATAGTGA-TGGAAGCGACTGGATAGAGACGTTATTACTG
66 GGAACCTACACATTATAGTGATTGG-AGCGACTGGATAGAGAAGTTATTACTG
** *
21308 CAGGCTCCTCAGCT-TCGTGCTT-AGAGTAAGTCCTTATTGGTGTGCAGGTGGGTGTATG
1 CAGGCTCCTTTGCTGT-GTGCTTAAG-GTAAGTCCTTACTGGTGTGCAGGTGGGTGTATG
21366 TTCGGGAAAA
Statistics
Matches: 159, Mismatches: 13, Indels: 6
0.89 0.07 0.03
Matches are distributed among these distances:
116 6 0.04
117 153 0.96
ACGTcount: A:0.20, C:0.16, G:0.33, T:0.31
Consensus pattern (117 bp):
CAGGCTCCTTTGCTGTGTGCTTAAGGTAAGTCCTTACTGGTGTGCAGGTGGGTGTATGGTTATGG
GGAACCTACACATTATAGTGATTGGAGCGACTGGATAGAGAAGTTATTACTG
Found at i:27489 original size:13 final size:13
Alignment explanation
Indices: 27471--27496 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
27461 TTGACCGGTT
27471 TTAACCCGACCCG
1 TTAACCCGACCCG
27484 TTAACCCGACCCG
1 TTAACCCGACCCG
27497 ACGTTAACAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.23, C:0.46, G:0.15, T:0.15
Consensus pattern (13 bp):
TTAACCCGACCCG
Found at i:27554 original size:29 final size:29
Alignment explanation
Indices: 27521--27697 Score: 182
Period size: 29 Copynumber: 6.1 Consensus size: 29
27511 CCGTTGACAC
* *
27521 ATTTTGGGAATTAATTTGAAATGGGTGTT
1 ATTTTGGGAATTAATTCGAAATGGGTGCT
*
27550 ATTTTGGGAATTAATTCGAAATGGGTACT
1 ATTTTGGGAATTAATTCGAAATGGGTGCT
*
27579 ATTTTGGGAATTAATTCGAAAAT-GGTGAT
1 ATTTTGGGAATTAATTCG-AAATGGGTGCT
*
27608 ATTTTGGGAATTTAATTCGAAA--AGTGCT
1 ATTTTGGGAA-TTAATTCGAAATGGGTGCT
* * *
27636 ATTTTGGGAATTTAATTTGAAA-AGGTGTT
1 ATTTTGGGAA-TTAATTCGAAATGGGTGCT
* * ** *
27665 ATTTTGGTAATTATTTTAAAAAGGGTGCT
1 ATTTTGGGAATTAATTCGAAATGGGTGCT
27694 ATTT
1 ATTT
27698 CTGTAAAATG
Statistics
Matches: 129, Mismatches: 15, Indels: 8
0.85 0.10 0.05
Matches are distributed among these distances:
28 34 0.26
29 83 0.64
30 12 0.09
ACGTcount: A:0.31, C:0.03, G:0.23, T:0.42
Consensus pattern (29 bp):
ATTTTGGGAATTAATTCGAAATGGGTGCT
Found at i:27695 original size:58 final size:57
Alignment explanation
Indices: 27521--27697 Score: 223
Period size: 58 Copynumber: 3.1 Consensus size: 57
27511 CCGTTGACAC
* * *
27521 ATTTTGGGAATTAATTTGAAATGGGTGTTATTTTGGGAATTAATTCGAAATGGGTACT
1 ATTTTGGGAATTAATTTGAAA-AGGTGTTATTTTGGGAATTAATTCGAAAAGGGTGCT
* *
27579 ATTTTGGGAATTAATTCGAAAATGGTGATATTTTGGGAATTTAATTCGAAAA--GTGCT
1 ATTTTGGGAATTAATTTGAAAA-GGTGTTATTTTGGGAA-TTAATTCGAAAAGGGTGCT
* * **
27636 ATTTTGGGAATTTAATTTGAAAAGGTGTTATTTTGGTAATTATTTTAAAAAGGGTGCT
1 ATTTTGGGAA-TTAATTTGAAAAGGTGTTATTTTGGGAATTAATTCGAAAAGGGTGCT
27694 ATTT
1 ATTT
27698 CTGTAAAATG
Statistics
Matches: 103, Mismatches: 11, Indels: 10
0.83 0.09 0.08
Matches are distributed among these distances:
56 9 0.09
57 28 0.27
58 55 0.53
59 11 0.11
ACGTcount: A:0.31, C:0.03, G:0.23, T:0.42
Consensus pattern (57 bp):
ATTTTGGGAATTAATTTGAAAAGGTGTTATTTTGGGAATTAATTCGAAAAGGGTGCT
Found at i:28828 original size:117 final size:116
Alignment explanation
Indices: 28614--28905 Score: 451
Period size: 117 Copynumber: 2.5 Consensus size: 116
28604 GGAAGTATTT
*
28614 CAGGCTCCTTTGCTGTGTGCTCAGGGTAAGTCCTTACTGGTGTGCAGGTGGGTGTATGGTTCTGG
1 CAGGCTCCTTTGC-GTGTGCTTAGGGTAAGTCCTTACTGGTGTGCAGGTGGGTGTATGGTTCTGG
* * *
28679 GGAACCTACACATTGTAGTGATTGGAGTGACTGGATGGGGAAGTTATTACTG
65 GGAACCTACACATTGTAGTGATTGGAGCGACTGGATAGAGAAGTTATTACTG
*
28731 CAGGCTCCTTTGCAGTGTGCTTAGGGAAAGTCCTTACTGGTGTGCAGGTGGGTGTATGGTTCTGG
1 CAGGCTCCTTTGC-GTGTGCTTAGGGTAAGTCCTTACTGGTGTGCAGGTGGGTGTATGGTTCTGG
*
28796 GGAACCTACACATTGTAGTGA-TGGAAGCGACTGGATAGAGACGTTATTACTG
65 GGAACCTACACATTGTAGTGATTGG-AGCGACTGGATAGAGAAGTTATTACTG
** * *
28848 CAGGCTCCTCAGCTTCGTGCTTAGGGTAAGTCCTTACTGGTGTGAAGGTGGGTGTATG
1 CAGGCTCCTTTGCGT-GTGCTTAGGGTAAGTCCTTACTGGTGTGCAGGTGGGTGTATG
28906 TTCGGGAAAA
Statistics
Matches: 161, Mismatches: 12, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
116 4 0.02
117 157 0.98
ACGTcount: A:0.19, C:0.16, G:0.34, T:0.30
Consensus pattern (116 bp):
CAGGCTCCTTTGCGTGTGCTTAGGGTAAGTCCTTACTGGTGTGCAGGTGGGTGTATGGTTCTGGG
GAACCTACACATTGTAGTGATTGGAGCGACTGGATAGAGAAGTTATTACTG
Found at i:32629 original size:14 final size:15
Alignment explanation
Indices: 32610--32640 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
32600 ATTAATTAAA
32610 TATTTTATGTT-ATT
1 TATTTTATGTTAATT
32624 TATTTTATGTTAATT
1 TATTTTATGTTAATT
32639 TA
1 TA
32641 GTTTGTTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 11 0.69
15 5 0.31
ACGTcount: A:0.26, C:0.00, G:0.06, T:0.68
Consensus pattern (15 bp):
TATTTTATGTTAATT
Found at i:34455 original size:29 final size:29
Alignment explanation
Indices: 34421--34479 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
34411 CCTAAATTAA
34421 TTTGATGTCATTGCTTACATCAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
34450 TTTGATGTCATTGCTTACATCAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
34479 T
1 T
34480 AGGTGAAAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.24, C:0.14, G:0.14, T:0.49
Consensus pattern (29 bp):
TTTGATGTCATTGCTTACATCAATTTAGT
Found at i:39141 original size:29 final size:29
Alignment explanation
Indices: 39107--39165 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
39097 CCTAAATTAA
39107 TTTGATGTCATTGCTTACATCAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
39136 TTTGATGTCATTGCTTACATCAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
39165 T
1 T
39166 AGGTGAAAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.24, C:0.14, G:0.14, T:0.49
Consensus pattern (29 bp):
TTTGATGTCATTGCTTACATCAATTTAGT
Found at i:45545 original size:17 final size:17
Alignment explanation
Indices: 45508--45546 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
45498 TATTATTTTT
*
45508 AATTTAAATTTATAATG
1 AATTTAAATTTATAATA
* *
45525 AATTTATATTTATTATA
1 AATTTAAATTTATAATA
45542 AATTT
1 AATTT
45547 TTATAATGCA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.54
Consensus pattern (17 bp):
AATTTAAATTTATAATA
Found at i:47071 original size:21 final size:22
Alignment explanation
Indices: 47045--47113 Score: 99
Period size: 21 Copynumber: 3.3 Consensus size: 22
47035 CAATCTCCGT
47045 AGGGTTACATTCCTAGCCCT-C
1 AGGGTTACATTCCTAGCCCTCC
*
47066 AGGGTTACATTCTTAGCCCTCC
1 AGGGTTACATTCCTAGCCCTCC
*
47088 A-GGTTACATTCCTAG-CCTGC
1 AGGGTTACATTCCTAGCCCTCC
47108 AGGGTT
1 AGGGTT
47114 TTATGACACC
Statistics
Matches: 43, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
20 5 0.12
21 36 0.84
22 2 0.05
ACGTcount: A:0.19, C:0.29, G:0.22, T:0.30
Consensus pattern (22 bp):
AGGGTTACATTCCTAGCCCTCC
Found at i:47666 original size:34 final size:34
Alignment explanation
Indices: 47623--47695 Score: 110
Period size: 34 Copynumber: 2.1 Consensus size: 34
47613 TTAAATGTTT
* *
47623 TTAATATACAGATTATAATATTCGAAATTTAAAA
1 TTAAAATACAAATTATAATATTCGAAATTTAAAA
**
47657 TTAAAATACAAATTATGGTATTCGAAATTTAAAA
1 TTAAAATACAAATTATAATATTCGAAATTTAAAA
47691 TTAAA
1 TTAAA
47696 TTCAACTTAA
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.51, C:0.05, G:0.07, T:0.37
Consensus pattern (34 bp):
TTAAAATACAAATTATAATATTCGAAATTTAAAA
Found at i:47933 original size:23 final size:22
Alignment explanation
Indices: 47904--48006 Score: 72
Period size: 23 Copynumber: 4.8 Consensus size: 22
47894 TTATCACTTC
*
47904 ACATTTATTCAATTTATCCATA
1 ACATTTATCCAATTTATCCATA
* *
47926 ACATTTTATCCAATATATTCA-A
1 ACA-TTTATCCAATTTATCCATA
* *
47948 ACA---A-CCAATTGATCACTTA
1 ACATTTATCCAATTTATC-CATA
* *
47967 ACATTTATTCAATTTATTCATA
1 ACATTTATCCAATTTATCCATA
*
47989 ACATTTTATCCAAATTAT
1 ACA-TTTATCCAATTTAT
48007 TCAAACTTCA
Statistics
Matches: 60, Mismatches: 13, Indels: 15
0.68 0.15 0.17
Matches are distributed among these distances:
17 7 0.12
18 2 0.03
19 4 0.07
22 14 0.23
23 33 0.55
ACGTcount: A:0.39, C:0.18, G:0.01, T:0.42
Consensus pattern (22 bp):
ACATTTATCCAATTTATCCATA
Found at i:47989 original size:63 final size:63
Alignment explanation
Indices: 47888--48012 Score: 200
Period size: 63 Copynumber: 2.0 Consensus size: 63
47878 CAATGTCACG
*
47888 ACCAACTTATCACTTCACATTTATTCAATTTATCCATAACATTTTATCC-AATATATTCAAACA
1 ACCAACTTATCACTTAACATTTATTCAATTTATCCATAACATTTTATCCAAAT-TATTCAAACA
*
47951 ACCAA-TTGATCACTTAACATTTATTCAATTTATTCATAACATTTTATCCAAATTATTCAAAC
1 ACCAACTT-ATCACTTAACATTTATTCAATTTATCCATAACATTTTATCCAAATTATTCAAAC
48013 TTCACATAAC
Statistics
Matches: 58, Mismatches: 2, Indels: 4
0.91 0.03 0.06
Matches are distributed among these distances:
62 2 0.03
63 53 0.91
64 3 0.05
ACGTcount: A:0.38, C:0.22, G:0.01, T:0.39
Consensus pattern (63 bp):
ACCAACTTATCACTTAACATTTATTCAATTTATCCATAACATTTTATCCAAATTATTCAAACA
Found at i:48436 original size:137 final size:136
Alignment explanation
Indices: 48144--48503 Score: 567
Period size: 137 Copynumber: 2.6 Consensus size: 136
48134 CCATCAATCT
48144 ATAGTTCCTCGGGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAAT
1 ATAGTTCC-CGGGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAAT
* * * * *
48209 CGAAGGTGCGCCCTCAGGAACGCGCTTTCACCACTTTGCCAAGTCCCCTCAGAAATAATCGGTAC
65 CGAAGGTGCACCC-CGGGAACACGCTTCCACCACTTTGCCAAGTCCCCTCAGAAATAATAGGTAC
* *
48274 TGGCATTA
129 TGACATGA
48282 ATAGTTCCCCGGGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAAT
1 ATAGTT-CCCGGGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAAT
48347 CGAAGGTGCACCCCGGGAACACGCTTCCACCACTTTGCCAAGTCCCCTCAGAAATAATAGGTACT
65 CGAAGGTGCACCCCGGGAACACGCTTCCACCACTTTGCCAAGTCCCCTCAGAAATAATAGGTACT
*
48412 TACATGA
130 GACATGA
* *
48419 ATAGTTCTCCGGGGGACATGAGTGGCATAATAGGGCAATGATAACATATTCTTTGACAAAATAAT
1 ATAGTTC-CCGGGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAAT
* *
48484 CGAAGGCGCGCCCCCGGGAA
65 CGAAGGTGC-ACCCCGGGAA
48504 TGCGCCTTCA
Statistics
Matches: 207, Mismatches: 12, Indels: 6
0.92 0.05 0.03
Matches are distributed among these distances:
136 1 0.00
137 121 0.58
138 83 0.40
139 2 0.01
ACGTcount: A:0.32, C:0.23, G:0.23, T:0.23
Consensus pattern (136 bp):
ATAGTTCCCGGGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAATC
GAAGGTGCACCCCGGGAACACGCTTCCACCACTTTGCCAAGTCCCCTCAGAAATAATAGGTACTG
ACATGA
Found at i:51696 original size:21 final size:21
Alignment explanation
Indices: 51670--51711 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
51660 AATAATTAAT
*
51670 ATTATTTATTATAAAAAATTA
1 ATTATTAATTATAAAAAATTA
* *
51691 ATTATTAATTTTAAAATATTA
1 ATTATTAATTATAAAAAATTA
51712 TAATAATTCC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (21 bp):
ATTATTAATTATAAAAAATTA
Found at i:54948 original size:18 final size:18
Alignment explanation
Indices: 54925--54995 Score: 124
Period size: 18 Copynumber: 3.9 Consensus size: 18
54915 ACTGAATATT
*
54925 TGTCCCGAATGACCACTA
1 TGTCCCGAAGGACCACTA
54943 TGTCCCGAAGGACCACTA
1 TGTCCCGAAGGACCACTA
54961 TGTCCCGAAGGACCACTA
1 TGTCCCGAAGGACCACTA
*
54979 TGTCTCGAAGGACCACT
1 TGTCCCGAAGGACCACT
54996 GATAATCCCT
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 51 1.00
ACGTcount: A:0.27, C:0.32, G:0.21, T:0.20
Consensus pattern (18 bp):
TGTCCCGAAGGACCACTA
Found at i:59481 original size:23 final size:23
Alignment explanation
Indices: 59444--59516 Score: 85
Period size: 23 Copynumber: 3.2 Consensus size: 23
59434 CAGCTCGTAT
*
59444 AAATGCACCGGAGTGCCATGTAG
1 AAATGCACCGAAGTGCCATGTAG
* **
59467 AATTGCACCGAAGTGCCGCGTAG
1 AAATGCACCGAAGTGCCATGTAG
* *
59490 AAATGCACCGTAGTGCCATATA-
1 AAATGCACCGAAGTGCCATGTAG
59512 AAATG
1 AAATG
59517 TCCCTAAGGA
Statistics
Matches: 41, Mismatches: 9, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
22 5 0.12
23 36 0.88
ACGTcount: A:0.33, C:0.22, G:0.26, T:0.19
Consensus pattern (23 bp):
AAATGCACCGAAGTGCCATGTAG
Found at i:60696 original size:20 final size:19
Alignment explanation
Indices: 60671--60709 Score: 51
Period size: 20 Copynumber: 2.0 Consensus size: 19
60661 TCTTTTATAT
60671 TAATATAATTTATTATCATC
1 TAATATAATTTA-TATCATC
**
60691 TAATATGGTTTATATCATC
1 TAATATAATTTATATCATC
60710 ATAACATAAC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 7 0.41
20 10 0.59
ACGTcount: A:0.36, C:0.10, G:0.05, T:0.49
Consensus pattern (19 bp):
TAATATAATTTATATCATC
Found at i:66477 original size:58 final size:58
Alignment explanation
Indices: 66407--66516 Score: 211
Period size: 58 Copynumber: 1.9 Consensus size: 58
66397 TGTCCCGAAT
66407 GACCACTGATAATCCCTCGACTCTTGGTATGCCAATTATACATGCAGCTCTCCCAAAG
1 GACCACTGATAATCCCTCGACTCTTGGTATGCCAATTATACATGCAGCTCTCCCAAAG
*
66465 GACCACTGATAATCCCTCGACTCTTGGTATGCCAATTATACCTGCAGCTCTC
1 GACCACTGATAATCCCTCGACTCTTGGTATGCCAATTATACATGCAGCTCTC
66517 ATATTAAATA
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
58 51 1.00
ACGTcount: A:0.25, C:0.32, G:0.15, T:0.27
Consensus pattern (58 bp):
GACCACTGATAATCCCTCGACTCTTGGTATGCCAATTATACATGCAGCTCTCCCAAAG
Found at i:71849 original size:30 final size:31
Alignment explanation
Indices: 71810--71883 Score: 80
Period size: 30 Copynumber: 2.4 Consensus size: 31
71800 GTTTTTCAAA
*
71810 AAAATATATATAAACTAATTTTTTTA-AATAT
1 AAAATATATAT-AACAAATTTTTTTATAATAT
* *
71841 AAAA-ATATATACCAAATTTTTTTATATTAT
1 AAAATATATATAACAAATTTTTTTATAATAT
71871 AAAACTATTATAT
1 AAAA-TA-TATAT
71884 GATTGATAAT
Statistics
Matches: 36, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
29 12 0.33
30 14 0.39
31 4 0.11
32 1 0.03
33 5 0.14
ACGTcount: A:0.50, C:0.05, G:0.00, T:0.45
Consensus pattern (31 bp):
AAAATATATATAACAAATTTTTTTATAATAT
Found at i:72324 original size:21 final size:20
Alignment explanation
Indices: 72289--72341 Score: 56
Period size: 21 Copynumber: 2.6 Consensus size: 20
72279 TAAAAAATTC
*
72289 GTGAAAATTAA-ATTAAAAA
1 GTGAAATTTAAGATTAAAAA
*
72308 -TGTAAATGTTAAGATTACAAA
1 GTG-AAAT-TTAAGATTAAAAA
72329 GTGAAATTTAAGA
1 GTGAAATTTAAGA
72342 GGTCCATTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 7
0.76 0.05 0.19
Matches are distributed among these distances:
18 2 0.07
19 3 0.11
20 10 0.36
21 11 0.39
22 2 0.07
ACGTcount: A:0.53, C:0.02, G:0.15, T:0.30
Consensus pattern (20 bp):
GTGAAATTTAAGATTAAAAA
Found at i:72341 original size:20 final size:19
Alignment explanation
Indices: 72289--72341 Score: 54
Period size: 20 Copynumber: 2.7 Consensus size: 19
72279 TAAAAAATTC
*
72289 GTGAAAATTAA-ATTAAAA
1 GTGAAATTTAAGATTAAAA
*
72307 ATGTAAATGTTAAGATTACAAA
1 GTG-AAAT-TTAAGATTA-AAA
72329 GTGAAATTTAAGA
1 GTGAAATTTAAGA
72342 GGTCCATTTT
Statistics
Matches: 28, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
18 2 0.07
19 3 0.11
20 10 0.36
21 8 0.29
22 5 0.18
ACGTcount: A:0.53, C:0.02, G:0.15, T:0.30
Consensus pattern (19 bp):
GTGAAATTTAAGATTAAAA
Found at i:76593 original size:39 final size:39
Alignment explanation
Indices: 76531--76608 Score: 129
Period size: 39 Copynumber: 2.0 Consensus size: 39
76521 TTTGAGTCCT
76531 TTCTGTCTGTGATTAATGCGATGTTTGATATTCGAGTTG
1 TTCTGTCTGTGATTAATGCGATGTTTGATATTCGAGTTG
* * *
76570 TTCTGTCTGTGATTAGTGTGATGTTTGATATTTGAGTTG
1 TTCTGTCTGTGATTAATGCGATGTTTGATATTCGAGTTG
76609 GTTTGTTCTC
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
39 36 1.00
ACGTcount: A:0.17, C:0.08, G:0.27, T:0.49
Consensus pattern (39 bp):
TTCTGTCTGTGATTAATGCGATGTTTGATATTCGAGTTG
Found at i:82159 original size:27 final size:27
Alignment explanation
Indices: 82128--82181 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
82118 CTAAATCTTA
82128 AAACTGATTGTTCAATGACAAAATTCC
1 AAACTGATTGTTCAATGACAAAATTCC
82155 AAACTGATTGTTCAATGACAAAATTCC
1 AAACTGATTGTTCAATGACAAAATTCC
82182 CAAAAATTTG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.41, C:0.19, G:0.11, T:0.30
Consensus pattern (27 bp):
AAACTGATTGTTCAATGACAAAATTCC
Found at i:93856 original size:50 final size:50
Alignment explanation
Indices: 93781--93908 Score: 229
Period size: 50 Copynumber: 2.6 Consensus size: 50
93771 TGAGAACTAG
*
93781 ATAAACGAGCTTGTTCGTGAACATAAATGAAGGACTCAATAAACAAGCTT
1 ATAAACGAGCTTGTTCGTGAACATAAACGAAGGACTCAATAAACAAGCTT
*
93831 ATAAACGAGCTTGTTCGTGAACATAAACGAATGACTCAATAAACAAGCTT
1 ATAAACGAGCTTGTTCGTGAACATAAACGAAGGACTCAATAAACAAGCTT
*
93881 ATAAACGAGCTTGTTCGTGAGCATAAAC
1 ATAAACGAGCTTGTTCGTGAACATAAAC
93909 AAACCAAACA
Statistics
Matches: 75, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
50 75 1.00
ACGTcount: A:0.41, C:0.17, G:0.18, T:0.24
Consensus pattern (50 bp):
ATAAACGAGCTTGTTCGTGAACATAAACGAAGGACTCAATAAACAAGCTT
Found at i:96208 original size:13 final size:13
Alignment explanation
Indices: 96190--96216 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
96180 TCAAAACATC
96190 AAAAAATATATAA
1 AAAAAATATATAA
96203 AAAAAATATATAA
1 AAAAAATATATAA
96216 A
1 A
96217 TCTTAGTTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (13 bp):
AAAAAATATATAA
Found at i:96331 original size:35 final size:35
Alignment explanation
Indices: 96259--96332 Score: 103
Period size: 35 Copynumber: 2.1 Consensus size: 35
96249 ATATATTATT
**
96259 TTGAAGTATTTTAGAATTTAGGGTTTAGAATGTAA
1 TTGAAGTATTTTAGAATTTAGGGTTTAGAATAAAA
* * *
96294 TTGAATTATTTTGGAATTTGGGGTTTAGAATAAAA
1 TTGAAGTATTTTAGAATTTAGGGTTTAGAATAAAA
96329 TTGA
1 TTGA
96333 GGACTATTTT
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
35 34 1.00
ACGTcount: A:0.34, C:0.00, G:0.23, T:0.43
Consensus pattern (35 bp):
TTGAAGTATTTTAGAATTTAGGGTTTAGAATAAAA
Found at i:105429 original size:22 final size:22
Alignment explanation
Indices: 105387--105451 Score: 64
Period size: 22 Copynumber: 3.0 Consensus size: 22
105377 GACTTTTTTT
*
105387 GTCAAAGTCAACGGT-TAGATCA
1 GTCAAAGTCAATGGTCT-GATCA
*
105409 GTCAAAGTCAATGGTCTGATCG
1 GTCAAAGTCAATGGTCTGATCA
*
105431 GTCAACGATCAAT--TCTGATCA
1 GTCAAAG-TCAATGGTCTGATCA
105452 AAGTCAACGG
Statistics
Matches: 37, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
21 7 0.19
22 24 0.65
23 6 0.16
ACGTcount: A:0.32, C:0.20, G:0.22, T:0.26
Consensus pattern (22 bp):
GTCAAAGTCAATGGTCTGATCA
Found at i:112100 original size:30 final size:29
Alignment explanation
Indices: 112066--112146 Score: 76
Period size: 28 Copynumber: 2.7 Consensus size: 29
112056 TTGTAAAAGT
112066 TTTAAAGAGCATAAAAGAAAATAAGATAAA
1 TTTAAAGAGCATAAAA-AAAATAAGATAAA
* *
112096 TTT-AAG-GCAAAAAAAAGAAGAAGATAAA
1 TTTAAAGAGCATAAAAAA-AATAAGATAAA
**
112124 TGTTGAAAGAAAATAAAAAAAAT
1 T-TT-AAAGAGCATAAAAAAAAT
112147 TAAAGATTTT
Statistics
Matches: 40, Mismatches: 6, Indels: 9
0.73 0.11 0.16
Matches are distributed among these distances:
27 2 0.05
28 18 0.45
29 5 0.12
30 3 0.08
31 5 0.12
32 7 0.17
ACGTcount: A:0.64, C:0.02, G:0.15, T:0.19
Consensus pattern (29 bp):
TTTAAAGAGCATAAAAAAAATAAGATAAA
Found at i:120114 original size:72 final size:73
Alignment explanation
Indices: 119996--120136 Score: 205
Period size: 72 Copynumber: 1.9 Consensus size: 73
119986 AAAATGGGGC
* ** * * *
119996 CCCATTAAATTACTATATTTTTTAGTTTTTTAAATAAAAAATTATGTTT-AAAATATTTTTTAAT
1 CCCACTAAATTACTATATTTTCAAGTATTTAAAATAAAAAAATATGTTTAAAAATATTTTTTAAT
120060 TATTGAGG
66 TATTGAGG
120068 CCCACTAAATTA-TCATATTTTCAAGTATTTAAAATAAAAAAATATGTTTAAAAATATTTTTTAA
1 CCCACTAAATTACT-ATATTTTCAAGTATTTAAAATAAAAAAATATGTTTAAAAATATTTTTTAA
120132 TTATT
65 TTATT
120137 AAACTTAAAA
Statistics
Matches: 61, Mismatches: 6, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
71 1 0.02
72 41 0.67
73 19 0.31
ACGTcount: A:0.41, C:0.07, G:0.05, T:0.47
Consensus pattern (73 bp):
CCCACTAAATTACTATATTTTCAAGTATTTAAAATAAAAAAATATGTTTAAAAATATTTTTTAAT
TATTGAGG
Found at i:122651 original size:36 final size:36
Alignment explanation
Indices: 122577--122648 Score: 90
Period size: 36 Copynumber: 2.0 Consensus size: 36
122567 TAATATAGTG
* ** **
122577 TTTGAAGATTTAAATCTAATCTTTTTATTTTTAAAA
1 TTTGAAGATTTAAATCTAACCTTAATATGATTAAAA
122613 TTTGAAGATTTAAATCTAACCATTAATATGATTAAA
1 TTTGAAGATTTAAATCTAACC-TTAATATGATTAAA
122649 TTTAACTTTA
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
36 20 0.67
37 10 0.33
ACGTcount: A:0.40, C:0.07, G:0.07, T:0.46
Consensus pattern (36 bp):
TTTGAAGATTTAAATCTAACCTTAATATGATTAAAA
Found at i:124177 original size:20 final size:20
Alignment explanation
Indices: 124152--124198 Score: 76
Period size: 20 Copynumber: 2.4 Consensus size: 20
124142 TTCGTGCATG
*
124152 GATGCACAGCAGGATGAATC
1 GATGCACAACAGGATGAATC
*
124172 GATGCACAACAGGATGCATC
1 GATGCACAACAGGATGAATC
124192 GATGCAC
1 GATGCAC
124199 TAAGTGCATT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.34, C:0.23, G:0.28, T:0.15
Consensus pattern (20 bp):
GATGCACAACAGGATGAATC
Found at i:124286 original size:21 final size:21
Alignment explanation
Indices: 124218--124338 Score: 156
Period size: 21 Copynumber: 5.7 Consensus size: 21
124208 TCAAAATGGA
*
124218 GTGCATGGATGCACTGCA-TG
1 GTGCATGGATGCACTGCAGGG
* *
124238 GTGCATCGATGCACTAG-TGGCAG
1 GTGCATGGATGCACT-GCAGG--G
124261 GTGCATGGATGCACTGCAGGG
1 GTGCATGGATGCACTGCAGGG
124282 GTGCATGGATGCACTGCAGGG
1 GTGCATGGATGCACTGCAGGG
*
124303 GTGCATTGATGCACTGCAGGG
1 GTGCATGGATGCACTGCAGGG
*
124324 GTGCATTGATGCACT
1 GTGCATGGATGCACT
124339 TTGACACCCT
Statistics
Matches: 90, Mismatches: 6, Indels: 9
0.86 0.06 0.09
Matches are distributed among these distances:
20 14 0.16
21 58 0.64
22 1 0.01
23 17 0.19
ACGTcount: A:0.20, C:0.20, G:0.37, T:0.23
Consensus pattern (21 bp):
GTGCATGGATGCACTGCAGGG
Found at i:126766 original size:31 final size:30
Alignment explanation
Indices: 126743--126832 Score: 94
Period size: 29 Copynumber: 3.0 Consensus size: 30
126733 AAATTATAAT
126743 TTATATTTTAAATTAATTTTTAAATT-TTC
1 TTATATTTTAAATTAATTTTTAAATTATTC
* * * * *
126772 TAAAATTTTATATTATTTTTTAAAATATGTC
1 TTATATTTTAAATTAATTTTTAAATTAT-TC
* *
126803 TTTTATTCTAAATTAATTTTTAAA-TATTC
1 TTATATTTTAAATTAATTTTTAAATTATTC
126832 T
1 T
126833 AATCTCTTCT
Statistics
Matches: 48, Mismatches: 11, Indels: 4
0.76 0.17 0.06
Matches are distributed among these distances:
29 24 0.50
30 4 0.08
31 20 0.42
ACGTcount: A:0.36, C:0.04, G:0.01, T:0.59
Consensus pattern (30 bp):
TTATATTTTAAATTAATTTTTAAATTATTC
Found at i:127522 original size:2 final size:2
Alignment explanation
Indices: 127515--127548 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
127505 TGAATATACA
127515 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
127549 CAAAATAAAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:134842 original size:33 final size:33
Alignment explanation
Indices: 134776--134860 Score: 89
Period size: 33 Copynumber: 2.6 Consensus size: 33
134766 ATACATATGT
* ** * *
134776 TCATCTCTCATAAATTTATGGAGGAATTTATAA
1 TCATCTCTCATAAAATTACAGAGAAATTCATAA
*
134809 TCATGTCTCATAAAATTACAGAGAAATTCATAA
1 TCATCTCTCATAAAATTACAGAGAAATTCATAA
* * *
134842 TCACCTTTTATAAAATTAC
1 TCATCTCTCATAAAATTAC
134861 TAAAGAATTG
Statistics
Matches: 42, Mismatches: 10, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
33 42 1.00
ACGTcount: A:0.40, C:0.15, G:0.08, T:0.36
Consensus pattern (33 bp):
TCATCTCTCATAAAATTACAGAGAAATTCATAA
Found at i:136106 original size:260 final size:260
Alignment explanation
Indices: 135558--136336 Score: 1445
Period size: 260 Copynumber: 3.0 Consensus size: 260
135548 CCTTCTCTTG
*
135558 ACATGATTTTTGGAAGACTTGTTTAATTTATCAGAGTTAAATTTATTGTCAAACAGTCATATTCA
1 ACATGATTTTTGGAAGATTTGTTTAATTTATCAGAGTTAAATTTATTGTCAAACAGTCATATTCA
135623 TTCAACTTGTCAACCGACGAGTAGCAATCATGATCTTAAATCTGACACGAACACTAAGGATCACT
66 TTCAACTTGTCAACCGACGAGTAGCAATCATGATCTTAAATCTGACACGAACACTAAGGATCACT
* * * *
135688 ATAAAATCATTCAACCAATACTGA--GGGAGGGGACTTTTAGACTGAGAATTTTCCTTCTTATAA
131 ATAAAATCCTTCAACCAATACTGAGGGGGGGGGGACTTTTTGACTGAGAATTTTCCTTCTTATGA
* *
135751 TGAAATTCCACTTCATCTCAAAAAATCTCCTTAACCAAATGATTTGAGTCTTCTGTAACTTCATT
196 TGAAATTCCACTTCATCTCAAAAAATCTCCTTGACCAAATGATTTGAGTCGTCTGTAACTTCATT
*
135816 ACATGATTTTTGGAAGATTTGTTTAATTTATCATAGTTAAATTTATTGTCAAACAGTCATATTCA
1 ACATGATTTTTGGAAGATTTGTTTAATTTATCAGAGTTAAATTTATTGTCAAACAGTCATATTCA
135881 TTCAACTTGTCAACCGACGAGTAGCAATCATGATCTTAAATCTGACACGAACACTAAGGATCACT
66 TTCAACTTGTCAACCGACGAGTAGCAATCATGATCTTAAATCTGACACGAACACTAAGGATCACT
135946 ATAAAATCCTTCAACCAATACTGAGGGGGGGGGGACTTTTTGACTGAGAATTTTCCTTCTTATGA
131 ATAAAATCCTTCAACCAATACTGAGGGGGGGGGGACTTTTTGACTGAGAATTTTCCTTCTTATGA
*
136011 TGAAATTCCACTTCATCTCAAAAAATCTCCTTGACCAAATGATTTGAGTCGTATGTAACTTCATT
196 TGAAATTCCACTTCATCTCAAAAAATCTCCTTGACCAAATGATTTGAGTCGTCTGTAACTTCATT
*
136076 ACATGATTTTTGGAAGATTTGTTTAATTTATCAGAGTTAAATTTATTGTCAAACTGTCATATTCA
1 ACATGATTTTTGGAAGATTTGTTTAATTTATCAGAGTTAAATTTATTGTCAAACAGTCATATTCA
*
136141 TTCAACTTGTCAACCGAAGAGTAGCAATCATGATCTTAAATCTGACACGAACACTAAGGATCACT
66 TTCAACTTGTCAACCGACGAGTAGCAATCATGATCTTAAATCTGACACGAACACTAAGGATCACT
136206 ATAAAATCCTTCAACCAATACTGAGGGGGGGGGGACTTTTTGACTGAGAATTTTCCTTCTTATGA
131 ATAAAATCCTTCAACCAATACTGAGGGGGGGGGGACTTTTTGACTGAGAATTTTCCTTCTTATGA
136271 TGAAATTCCACTTCATCTCAAAAAATCTCCTTGACCAAATGATTTGAGTCGTCTGTAACTTCATT
196 TGAAATTCCACTTCATCTCAAAAAATCTCCTTGACCAAATGATTTGAGTCGTCTGTAACTTCATT
136336 A
1 A
136337 GTTGAACCAT
Statistics
Matches: 506, Mismatches: 13, Indels: 2
0.97 0.02 0.00
Matches are distributed among these distances:
258 151 0.30
260 355 0.70
ACGTcount: A:0.33, C:0.18, G:0.15, T:0.34
Consensus pattern (260 bp):
ACATGATTTTTGGAAGATTTGTTTAATTTATCAGAGTTAAATTTATTGTCAAACAGTCATATTCA
TTCAACTTGTCAACCGACGAGTAGCAATCATGATCTTAAATCTGACACGAACACTAAGGATCACT
ATAAAATCCTTCAACCAATACTGAGGGGGGGGGGACTTTTTGACTGAGAATTTTCCTTCTTATGA
TGAAATTCCACTTCATCTCAAAAAATCTCCTTGACCAAATGATTTGAGTCGTCTGTAACTTCATT
Found at i:138640 original size:41 final size:41
Alignment explanation
Indices: 138577--138665 Score: 101
Period size: 41 Copynumber: 2.2 Consensus size: 41
138567 TTAGTTGTAT
* *
138577 TTTAGTGGCTTTTTTGATCAAAC-ACTGATAAATACTCATAC
1 TTTAGTGACGTTTTTGATCAAACGACT-ATAAATACTCATAC
* * *
138618 TTTAGTGACGTTTTT-ATACAAACGCCTCTAAATACTCATAT
1 TTTAGTGACGTTTTTGAT-CAAACGACTATAAATACTCATAC
138659 TTTAGTG
1 TTTAGTG
138666 GTATTTTTAT
Statistics
Matches: 41, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
40 2 0.05
41 37 0.90
42 2 0.05
ACGTcount: A:0.30, C:0.17, G:0.12, T:0.40
Consensus pattern (41 bp):
TTTAGTGACGTTTTTGATCAAACGACTATAAATACTCATAC
Found at i:138673 original size:41 final size:41
Alignment explanation
Indices: 138605--138731 Score: 157
Period size: 41 Copynumber: 3.1 Consensus size: 41
138595 CAAACACTGA
* * * *
138605 TAAATACTCATACTTTAGT-GACGTTTTTATACAAACGCCTC
1 TAAATACTCATAATTTAGTGGA-ATTTTTATATAAACGCCGC
* *
138646 TAAATACTCATATTTTAGTGGTATTTTTATATAAACGCCGC
1 TAAATACTCATAATTTAGTGGAATTTTTATATAAACGCCGC
* * *
138687 TAAAGATTCATAATTTAGTGGAATTTTTATATAAACACCGC
1 TAAATACTCATAATTTAGTGGAATTTTTATATAAACGCCGC
138728 TAAA
1 TAAA
138732 GATTCCTACT
Statistics
Matches: 75, Mismatches: 10, Indels: 2
0.86 0.11 0.02
Matches are distributed among these distances:
41 74 0.99
42 1 0.01
ACGTcount: A:0.35, C:0.16, G:0.11, T:0.38
Consensus pattern (41 bp):
TAAATACTCATAATTTAGTGGAATTTTTATATAAACGCCGC
Found at i:139526 original size:33 final size:34
Alignment explanation
Indices: 139476--139541 Score: 116
Period size: 33 Copynumber: 2.0 Consensus size: 34
139466 CCCATGTTCA
139476 AAGTTTGGCCACCAACCAAGATGAAATTTCCAAT
1 AAGTTTGGCCACCAACCAAGATGAAATTTCCAAT
*
139510 AAGTTT-GCCACTAACCAAGATGAAATTTCCAA
1 AAGTTTGGCCACCAACCAAGATGAAATTTCCAA
139542 CTTGCCAACT
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
33 25 0.81
34 6 0.19
ACGTcount: A:0.39, C:0.23, G:0.14, T:0.24
Consensus pattern (34 bp):
AAGTTTGGCCACCAACCAAGATGAAATTTCCAAT
Found at i:147596 original size:21 final size:21
Alignment explanation
Indices: 147572--147630 Score: 75
Period size: 21 Copynumber: 2.8 Consensus size: 21
147562 TGATTTATTA
*
147572 TTATGGATTTCAATTTTCTTG
1 TTATGGATTTCAAGTTTCTTG
* *
147593 TTATGGATTTGAAGTTTGTTG
1 TTATGGATTTCAAGTTTCTTG
147614 TTAT-GATTGTCAAGTTT
1 TTATGGATT-TCAAGTTT
147631 ATTGGTTAAC
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
20 4 0.12
21 29 0.88
ACGTcount: A:0.20, C:0.05, G:0.20, T:0.54
Consensus pattern (21 bp):
TTATGGATTTCAAGTTTCTTG
Found at i:147892 original size:44 final size:43
Alignment explanation
Indices: 147823--147914 Score: 125
Period size: 44 Copynumber: 2.1 Consensus size: 43
147813 TTCTAAATTC
*
147823 ACAAACGACACTATATGATATAACATTTAGCGGCATTTTTGGG
1 ACAAACGACACTATATGATAGAACATTTAGCGGCATTTTTGGG
*
147866 AACAAACG-CAACTATATG-TCAGAACATTTAGTGGCATTTTTGGG
1 -ACAAACGAC-ACTATATGAT-AGAACATTTAGCGGCATTTTTGGG
147910 ACAAA
1 ACAAA
147915 ACGCCACAAA
Statistics
Matches: 44, Mismatches: 2, Indels: 5
0.86 0.04 0.10
Matches are distributed among these distances:
43 7 0.16
44 37 0.84
ACGTcount: A:0.37, C:0.16, G:0.18, T:0.28
Consensus pattern (43 bp):
ACAAACGACACTATATGATAGAACATTTAGCGGCATTTTTGGG
Found at i:150275 original size:32 final size:32
Alignment explanation
Indices: 150239--150323 Score: 102
Period size: 32 Copynumber: 2.7 Consensus size: 32
150229 ACTTATCGCG
*
150239 TCATCATCTTAGGTGATGTAACACATGCCATA
1 TCATCATCTTAGATGATGTAACACATGCCATA
* *
150271 TCATCATCTTA-ATTGATGTAACACATGTCATG
1 TCATCATCTTAGA-TGATGTAACACATGCCATA
*
150303 TCAT-AGCATTAGATGATGTAA
1 TCATCATC-TTAGATGATGTAA
150324 TATATCAATA
Statistics
Matches: 46, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
31 2 0.04
32 43 0.93
33 1 0.02
ACGTcount: A:0.33, C:0.18, G:0.15, T:0.34
Consensus pattern (32 bp):
TCATCATCTTAGATGATGTAACACATGCCATA
Found at i:155329 original size:23 final size:23
Alignment explanation
Indices: 155283--155329 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
155273 AACTATATAG
** **
155283 ATGAACATGTTGGCGAACGTTAA
1 ATGAACATGTTCCCGAACACTAA
155306 ATGAACATGTTCCCGAACACTAA
1 ATGAACATGTTCCCGAACACTAA
155329 A
1 A
155330 CAAACCAACA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.38, C:0.19, G:0.19, T:0.23
Consensus pattern (23 bp):
ATGAACATGTTCCCGAACACTAA
Found at i:167366 original size:29 final size:29
Alignment explanation
Indices: 167323--167478 Score: 132
Period size: 29 Copynumber: 5.6 Consensus size: 29
167313 CCTTTTTAAG
*
167323 AAATATTTACCAAAATATCATCATTTTCA
1 AAATAATTACCAAAATATCATCATTTTCA
* *
167352 AAATAATTACTAAAATATCAT--TTTTTA
1 AAATAATTACCAAAATATCATCATTTTCA
* *
167379 AAGAAAATTA-CTAAAT-T-ATCA-TTT-A
1 AA-ATAATTACCAAAATATCATCATTTTCA
* * *
167404 TAAA-AATTACAAAAATAGCA-CTATTTTTA
1 -AAATAATTACCAAAATATCATC-ATTTTCA
* *
167433 AAATAATTACCAGAATATCACCATTTTCA
1 AAATAATTACCAAAATATCATCATTTTCA
167462 AAATAATTACCAAAATA
1 AAATAATTACCAAAATA
167479 CCACTCGATT
Statistics
Matches: 101, Mismatches: 14, Indels: 24
0.73 0.10 0.17
Matches are distributed among these distances:
24 5 0.05
25 8 0.08
26 7 0.07
27 13 0.13
28 12 0.12
29 55 0.54
30 1 0.01
ACGTcount: A:0.50, C:0.13, G:0.02, T:0.35
Consensus pattern (29 bp):
AAATAATTACCAAAATATCATCATTTTCA
Found at i:167388 original size:28 final size:28
Alignment explanation
Indices: 167315--167402 Score: 90
Period size: 28 Copynumber: 3.1 Consensus size: 28
167305 GTTATCACCC
*
167315 TTTTT-AAGAAATATTTACCAAAATATCAT
1 TTTTTAAAGAAA-A-TTACTAAAATATCAT
* *
167344 CATTTTCAAA-ATAATTACTAAAATATCAT
1 --TTTTTAAAGAAAATTACTAAAATATCAT
*
167373 TTTTTAAAGAAAATTACTAAATTATCAT
1 TTTTTAAAGAAAATTACTAAAATATCAT
167401 TT
1 TT
167403 ATAAAAATTA
Statistics
Matches: 49, Mismatches: 6, Indels: 7
0.79 0.10 0.11
Matches are distributed among these distances:
27 7 0.14
28 19 0.39
29 14 0.29
30 1 0.02
31 6 0.12
32 2 0.04
ACGTcount: A:0.45, C:0.10, G:0.02, T:0.42
Consensus pattern (28 bp):
TTTTTAAAGAAAATTACTAAAATATCAT
Found at i:168266 original size:2 final size:2
Alignment explanation
Indices: 168259--168285 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
168249 AAATTTCAAT
168259 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
168286 TCCCAATTTC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:172405 original size:22 final size:22
Alignment explanation
Indices: 172377--172421 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
172367 GGGGTTGAGG
172377 CCTGATTGTGTTACATTCAATA
1 CCTGATTGTGTTACATTCAATA
172399 CCTGATTGTGTTACATTCAATA
1 CCTGATTGTGTTACATTCAATA
172421 C
1 C
172422 TTTGATAGAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.27, C:0.20, G:0.13, T:0.40
Consensus pattern (22 bp):
CCTGATTGTGTTACATTCAATA
Found at i:173300 original size:27 final size:27
Alignment explanation
Indices: 173269--173336 Score: 122
Period size: 27 Copynumber: 2.6 Consensus size: 27
173259 TCTATTTACA
173269 AAATCATATCTCTATAGGAATGGTAAC
1 AAATCATATCTCTATAGGAATGGTAAC
173296 AAATCATATCTCTATAGGAATGGTAAC
1 AAATCATATCTCTATAGGAATGGTAAC
173323 AAATC--ATCTCTATA
1 AAATCATATCTCTATA
173337 ATTCCTACAC
Statistics
Matches: 41, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
25 9 0.22
27 32 0.78
ACGTcount: A:0.41, C:0.16, G:0.12, T:0.31
Consensus pattern (27 bp):
AAATCATATCTCTATAGGAATGGTAAC
Found at i:178544 original size:27 final size:29
Alignment explanation
Indices: 178513--178577 Score: 80
Period size: 30 Copynumber: 2.3 Consensus size: 29
178503 AATATAATTT
178513 TTAATTTTTT-AT-TAATAAAATAAAATA
1 TTAATTTTTTAATATAATAAAATAAAATA
* *
178540 TTAATTTATTTAATATAATGACATAAAATA
1 TTAATTT-TTTAATATAATAAAATAAAATA
*
178570 TAAATTTT
1 TTAATTTT
178578 AATTTAATAT
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
27 7 0.22
28 3 0.09
29 3 0.09
30 19 0.59
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.48
Consensus pattern (29 bp):
TTAATTTTTTAATATAATAAAATAAAATA
Found at i:178592 original size:35 final size:35
Alignment explanation
Indices: 178527--178593 Score: 91
Period size: 35 Copynumber: 1.9 Consensus size: 35
178517 TTTTTTATTA
*
178527 ATAAAATAAAATATTAATTTATTTAATATAATGAC
1 ATAAAATAAAATATTAATTTATATAATATAATGAC
* *
178562 ATAAAATATAAATTTTAATTTA-ATATTATAAT
1 ATAAAATA-AAATATTAATTTATATAATATAAT
178594 ATTGGTATTT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
35 16 0.57
36 12 0.43
ACGTcount: A:0.54, C:0.01, G:0.01, T:0.43
Consensus pattern (35 bp):
ATAAAATAAAATATTAATTTATATAATATAATGAC
Found at i:181531 original size:3 final size:3
Alignment explanation
Indices: 181523--181605 Score: 139
Period size: 3 Copynumber: 27.7 Consensus size: 3
181513 TACCATCCTT
*
181523 TTA TTA TTA TTA TTA TTA TTA TTA TTA TCA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* *
181571 TTA TTA TTA TAA ATA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
181606 TTTTTTTGAT
Statistics
Matches: 74, Mismatches: 6, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
3 74 1.00
ACGTcount: A:0.35, C:0.01, G:0.00, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:181718 original size:3 final size:3
Alignment explanation
Indices: 181710--181748 Score: 60
Period size: 3 Copynumber: 13.0 Consensus size: 3
181700 AAGAAAACTT
* *
181710 TTA TTA TTA TTA TTA TTA TTA TTA TTA TAA ATA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
181749 AGGTAAACTA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:197256 original size:14 final size:15
Alignment explanation
Indices: 197239--197272 Score: 54
Period size: 14 Copynumber: 2.4 Consensus size: 15
197229 ATTTAATTTA
197239 AATTATTA-ACTAAT
1 AATTATTATACTAAT
197253 AATTA-TATACTAAT
1 AATTATTATACTAAT
197267 AATTAT
1 AATTAT
197273 AGAAATAAAG
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
13 2 0.11
14 16 0.89
ACGTcount: A:0.50, C:0.06, G:0.00, T:0.44
Consensus pattern (15 bp):
AATTATTATACTAAT
Found at i:204464 original size:29 final size:29
Alignment explanation
Indices: 204422--204489 Score: 127
Period size: 29 Copynumber: 2.3 Consensus size: 29
204412 TTTATACACT
204422 ACCCTAAACCATAATCCCATAACCTTTTA
1 ACCCTAAACCATAATCCCATAACCTTTTA
*
204451 ACCCTAAACCATAATCTCATAACCTTTTA
1 ACCCTAAACCATAATCCCATAACCTTTTA
204480 ACCCTAAACC
1 ACCCTAAACC
204490 CTAAACTCTA
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 38 1.00
ACGTcount: A:0.38, C:0.35, G:0.00, T:0.26
Consensus pattern (29 bp):
ACCCTAAACCATAATCCCATAACCTTTTA
Found at i:208297 original size:11 final size:11
Alignment explanation
Indices: 208281--208323 Score: 59
Period size: 11 Copynumber: 3.7 Consensus size: 11
208271 TGTTATTACA
208281 ATCACAATAGT
1 ATCACAATAGT
*
208292 ATCACAATCATGA
1 ATCACAAT-A-GT
208305 ATCACAATAGT
1 ATCACAATAGT
208316 ATCACAAT
1 ATCACAAT
208324 CATGAATATA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
11 17 0.61
12 2 0.07
13 9 0.32
ACGTcount: A:0.47, C:0.21, G:0.07, T:0.26
Consensus pattern (11 bp):
ATCACAATAGT
Found at i:208308 original size:24 final size:24
Alignment explanation
Indices: 208280--208330 Score: 102
Period size: 24 Copynumber: 2.1 Consensus size: 24
208270 ATGTTATTAC
208280 AATCACAATAGTATCACAATCATG
1 AATCACAATAGTATCACAATCATG
208304 AATCACAATAGTATCACAATCATG
1 AATCACAATAGTATCACAATCATG
208328 AAT
1 AAT
208331 ATATTTCCTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.47, C:0.20, G:0.08, T:0.25
Consensus pattern (24 bp):
AATCACAATAGTATCACAATCATG
Found at i:208720 original size:30 final size:30
Alignment explanation
Indices: 208686--208757 Score: 72
Period size: 30 Copynumber: 2.4 Consensus size: 30
208676 AATAATCATC
* *
208686 AAATTCTCAAATGATTATAAAATGACCATT
1 AAATTATCAAATGATTACAAAATGACCATT
** * *
208716 AAATTATTGAATTATTACAAAATGATCATT
1 AAATTATCAAATGATTACAAAATGACCATT
*
208746 AAAACTATCAAA
1 -AAATTATCAAA
208758 ACATATTATT
Statistics
Matches: 32, Mismatches: 9, Indels: 1
0.76 0.21 0.02
Matches are distributed among these distances:
30 24 0.75
31 8 0.25
ACGTcount: A:0.50, C:0.11, G:0.06, T:0.33
Consensus pattern (30 bp):
AAATTATCAAATGATTACAAAATGACCATT
Found at i:211627 original size:23 final size:23
Alignment explanation
Indices: 211601--211669 Score: 84
Period size: 23 Copynumber: 3.0 Consensus size: 23
211591 CACCACAGCT
* *
211601 CGTATAATTACACCGAAGTGCCA
1 CGTAGAATTGCACCGAAGTGCCA
* * *
211624 CGTAGAATTGCACCGGAGTACCG
1 CGTAGAATTGCACCGAAGTGCCA
*
211647 CGTAGAATTGCACCGTAGTGCCA
1 CGTAGAATTGCACCGAAGTGCCA
211670 TATAATAATG
Statistics
Matches: 38, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 38 1.00
ACGTcount: A:0.29, C:0.26, G:0.25, T:0.20
Consensus pattern (23 bp):
CGTAGAATTGCACCGAAGTGCCA
Found at i:211856 original size:103 final size:103
Alignment explanation
Indices: 211685--211902 Score: 409
Period size: 103 Copynumber: 2.1 Consensus size: 103
211675 TAATGTCCAT
* *
211685 AAGGACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
211750 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
*
211788 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
211853 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
211891 AAGGACCACATA
1 AAGGACCACATA
211903 GACCCTCGAC
Statistics
Matches: 112, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
103 112 1.00
ACGTcount: A:0.37, C:0.24, G:0.14, T:0.26
Consensus pattern (103 bp):
AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
Found at i:212043 original size:24 final size:24
Alignment explanation
Indices: 212015--212067 Score: 65
Period size: 24 Copynumber: 2.2 Consensus size: 24
212005 TGTAGTTCTT
*
212015 TCACATAGCTCATCGT-CATATAAA
1 TCACATAGCACAT-GTACATATAAA
*
212039 TCACATATCACATGTACATATAAA
1 TCACATAGCACATGTACATATAAA
212063 -CACAT
1 TCACAT
212068 GGTTCACTTA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
23 7 0.27
24 19 0.73
ACGTcount: A:0.42, C:0.25, G:0.06, T:0.28
Consensus pattern (24 bp):
TCACATAGCACATGTACATATAAA
Found at i:218692 original size:2 final size:2
Alignment explanation
Indices: 218685--218728 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
218675 TTAAATTATC
218685 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
218727 AT
1 AT
218729 TATTTGTATT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:227679 original size:2 final size:2
Alignment explanation
Indices: 227672--227705 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
227662 ACCAAATTAC
227672 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
227706 CAACACTTTA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:228400 original size:243 final size:243
Alignment explanation
Indices: 227972--228452 Score: 818
Period size: 243 Copynumber: 2.0 Consensus size: 243
227962 AGAGTGACAT
* * *
227972 AATTACAGCTAAACATAAACGTCAGTATTAAAATTGATAAAATTGAAACGTCAGTGACATAAACG
1 AATTACAGCTAAACATAAACGTCAGTATTAAAATTGACAAAATTGAAACGGCAATGACATAAACG
*
228037 AGCCCACAATTAAAGGTGAGTGGTACTTGAAGTAGTTAACCCTAAAATTTATATTATCTAAATCA
66 AGCCCACAATTAAAGGTGAGTGATACTTGAAGTAGTTAACCCTAAAATTTATATTATCTAAATCA
*
228102 ATACAGGTTACATACTTGATCTGGTGGGTGAGCCTTCTAGTAGAGACATTTTACATATACAAATA
131 ATACAGGTTACATACTTGATCTGGTGGGCGAGCCTTCTAGTAGAGACATTTTACATATACAAATA
*
228167 CTCAAATTTGATATATACTTAAATGATATCATATTATTTACTAGTTCA
196 ATCAAATTTGATATATACTTAAATGATATCATATTATTTACTAGTTCA
*
228215 AATTACAGCTAAACATAAACGTCAGTGTTAAAATTGACAAAATTGAAACGGCAATGACATAAACG
1 AATTACAGCTAAACATAAACGTCAGTATTAAAATTGACAAAATTGAAACGGCAATGACATAAACG
** * * * * *
228280 AGCCCACGCTTAAAGGTTAGTGATATTTGAAGTAGTTAACCCTAAAATTTGTATTATCTAATTCG
66 AGCCCACAATTAAAGGTGAGTGATACTTGAAGTAGTTAACCCTAAAATTTATATTATCTAAATCA
*
228345 ATTCAGGTTACATACTTGATCTGGTGGGCGAGCCTTCTAGTAGAGACATTTTACATATACAAATA
131 ATACAGGTTACATACTTGATCTGGTGGGCGAGCCTTCTAGTAGAGACATTTTACATATACAAATA
*
228410 ATCAAATTTGATATATACTTAAATTATATCATATTATTTACTA
196 ATCAAATTTGATATATACTTAAATGATATCATATTATTTACTA
228453 CTTAAACTAA
Statistics
Matches: 222, Mismatches: 16, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
243 222 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.32
Consensus pattern (243 bp):
AATTACAGCTAAACATAAACGTCAGTATTAAAATTGACAAAATTGAAACGGCAATGACATAAACG
AGCCCACAATTAAAGGTGAGTGATACTTGAAGTAGTTAACCCTAAAATTTATATTATCTAAATCA
ATACAGGTTACATACTTGATCTGGTGGGCGAGCCTTCTAGTAGAGACATTTTACATATACAAATA
ATCAAATTTGATATATACTTAAATGATATCATATTATTTACTAGTTCA
Found at i:228546 original size:18 final size:17
Alignment explanation
Indices: 228510--228551 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
228500 ATTTTTGGTC
228510 TTTTATGATTAAATATT
1 TTTTATGATTAAATATT
* *
228527 TTTTATTATTACAT-TAT
1 TTTTATGATTAAATAT-T
228544 TTTTATGA
1 TTTTATGA
228552 ATTTTAAGTC
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
16 1 0.05
17 20 0.95
ACGTcount: A:0.31, C:0.02, G:0.05, T:0.62
Consensus pattern (17 bp):
TTTTATGATTAAATATT
Found at i:247024 original size:15 final size:15
Alignment explanation
Indices: 247006--247038 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
246996 AAATTCTAAA
247006 TATTTA-AATAAAAAT
1 TATTTATAA-AAAAAT
247021 TATTTATAAAAAAAT
1 TATTTATAAAAAAAT
247036 TAT
1 TAT
247039 ATTTGTTGAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 15 0.88
16 2 0.12
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (15 bp):
TATTTATAAAAAAAT
Found at i:253096 original size:29 final size:29
Alignment explanation
Indices: 253064--253158 Score: 70
Period size: 29 Copynumber: 3.2 Consensus size: 29
253054 AATTAGTTCT
253064 TAAACTTTTAACTATTTCAATTTCATCCC
1 TAAACTTTTAACTATTTCAATTTCATCCC
* * * *
253093 TAAAC-TATGACTATCATTCTAAATTAAT-CC
1 TAAACTTTTAACTAT--TTC-AATTTCATCCC
*
253123 TCAAAATTTTAAAC-ATTTCAATTTCATCCC
1 T-AAACTTTT-AACTATTTCAATTTCATCCC
*
253153 CAAACT
1 TAAACT
253159 ATGCATTTAT
Statistics
Matches: 48, Mismatches: 11, Indels: 14
0.66 0.15 0.19
Matches are distributed among these distances:
28 7 0.15
29 15 0.31
30 11 0.23
31 9 0.19
32 4 0.08
33 2 0.04
ACGTcount: A:0.37, C:0.23, G:0.01, T:0.39
Consensus pattern (29 bp):
TAAACTTTTAACTATTTCAATTTCATCCC
Found at i:254342 original size:31 final size:31
Alignment explanation
Indices: 254282--254346 Score: 85
Period size: 31 Copynumber: 2.1 Consensus size: 31
254272 TAACCGAATT
* **
254282 AACCAAACTTTTTTTCTTTAACCGTTAACCG
1 AACCAAACTTTTTTTCTTTAAACACTAACCG
* *
254313 AACCAAACTTTTTTTTTTTAAATACTAACCG
1 AACCAAACTTTTTTTCTTTAAACACTAACCG
254344 AAC
1 AAC
254347 TGAATACATT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.34, C:0.23, G:0.05, T:0.38
Consensus pattern (31 bp):
AACCAAACTTTTTTTCTTTAAACACTAACCG
Found at i:271954 original size:4 final size:4
Alignment explanation
Indices: 271947--271997 Score: 84
Period size: 4 Copynumber: 12.8 Consensus size: 4
271937 TATATATATA
* *
271947 TATG TATG TATG TATG TATG TACG TATG TATG TATG TATG TATA TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
271995 TAT
1 TAT
271998 ATGGGCCACA
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
4 43 1.00
ACGTcount: A:0.27, C:0.02, G:0.22, T:0.49
Consensus pattern (4 bp):
TATG
Found at i:272879 original size:58 final size:58
Alignment explanation
Indices: 272760--272885 Score: 137
Period size: 58 Copynumber: 2.1 Consensus size: 58
272750 ATAGTTAAGT
* * *
272760 GACCATTTTGTAACTTTTAATAGTCGATGGACTCAATAGAACAACACCCTATAATCGGGG
1 GACCATTTCGTAAC--TTAATAGTCGATGGACTAAATAGAACAACACCCTATAATCAGGG
* * * * * *
272820 GATCATTTCGTAACTTAATAGTCAGA-GGACTAAATATATCAACGCCCTATAGTTAGGG
1 GACCATTTCGTAACTTAATAGTC-GATGGACTAAATAGAACAACACCCTATAATCAGGG
272878 GACCATTT
1 GACCATTT
272886 ATATACTTTA
Statistics
Matches: 55, Mismatches: 10, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
58 41 0.75
59 2 0.04
60 12 0.22
ACGTcount: A:0.33, C:0.19, G:0.18, T:0.29
Consensus pattern (58 bp):
GACCATTTCGTAACTTAATAGTCGATGGACTAAATAGAACAACACCCTATAATCAGGG
Found at i:277849 original size:18 final size:18
Alignment explanation
Indices: 277806--277897 Score: 103
Period size: 18 Copynumber: 5.0 Consensus size: 18
277796 GAGGGATTAT
* *
277806 TAGTGGTCATTCGGAATAA
1 TAGTGGTCATTCGGGA-CA
* *
277825 TTAGTGGTCCTTCGAGACA
1 -TAGTGGTCATTCGGGACA
277844 TAGTGGTCATTCGGGACA
1 TAGTGGTCATTCGGGACA
*
277862 TAATGGTCATTCGGGACA
1 TAGTGGTCATTCGGGACA
* *
277880 TAGTGGTCCTTCGTGACA
1 TAGTGGTCATTCGGGACA
277898 AATATTCAGT
Statistics
Matches: 62, Mismatches: 10, Indels: 2
0.84 0.14 0.03
Matches are distributed among these distances:
18 48 0.77
19 1 0.02
20 13 0.21
ACGTcount: A:0.24, C:0.17, G:0.28, T:0.30
Consensus pattern (18 bp):
TAGTGGTCATTCGGGACA
Found at i:284730 original size:20 final size:18
Alignment explanation
Indices: 284681--284736 Score: 60
Period size: 20 Copynumber: 2.9 Consensus size: 18
284671 AGGGATTATC
284681 AGTGGTCTTTCGGGAC-AT
1 AGTGGTC-TTCGGGACAAT
*
284699 AGTGGTTCTTCGGAACAATT
1 AGTGG-TCTTCGGGACAA-T
284719 AGTGGTCATTCGGGACAA
1 AGTGGTC-TTCGGGACAA
284737 ATATTCAGTG
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
18 12 0.38
19 5 0.16
20 15 0.47
ACGTcount: A:0.23, C:0.16, G:0.30, T:0.30
Consensus pattern (18 bp):
AGTGGTCTTCGGGACAAT
Found at i:287506 original size:23 final size:23
Alignment explanation
Indices: 287480--287527 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 23
287470 ATAAAGTACA
*
287480 ATAACATACTAGGTAGCGCTTAT
1 ATAACATAATAGGTAGCGCTTAT
**
287503 ATAATGTAATAGGTAGCGCTTAT
1 ATAACATAATAGGTAGCGCTTAT
287526 AT
1 AT
287528 TTACCTATTT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.35, C:0.12, G:0.19, T:0.33
Consensus pattern (23 bp):
ATAACATAATAGGTAGCGCTTAT
Found at i:287969 original size:21 final size:22
Alignment explanation
Indices: 287944--287995 Score: 77
Period size: 23 Copynumber: 2.3 Consensus size: 22
287934 ACACTTTACA
*
287944 ATATAACCACTACCTATTACATT
1 ATATAAACA-TACCTATTACATT
287967 ATATAAACGATACCTATTACATT
1 ATATAAAC-ATACCTATTACATT
287990 ATATAA
1 ATATAA
287996 GGGCTACCTA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
23 26 0.96
24 1 0.04
ACGTcount: A:0.44, C:0.19, G:0.02, T:0.35
Consensus pattern (22 bp):
ATATAAACATACCTATTACATT
Found at i:287980 original size:23 final size:23
Alignment explanation
Indices: 287954--288016 Score: 90
Period size: 23 Copynumber: 2.7 Consensus size: 23
287944 ATATAACCAC
287954 TACCTATTACATTATATAAACGA
1 TACCTATTACATTATATAAACGA
** *
287977 TACCTATTACATTATATAAGGGC
1 TACCTATTACATTATATAAACGA
*
288000 TACCTATTACATCATAT
1 TACCTATTACATTATAT
288017 GTTTACCTAT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.38, C:0.19, G:0.06, T:0.37
Consensus pattern (23 bp):
TACCTATTACATTATATAAACGA
Found at i:288474 original size:39 final size:39
Alignment explanation
Indices: 288420--288506 Score: 156
Period size: 39 Copynumber: 2.2 Consensus size: 39
288410 TCAAGTTGTA
*
288420 GATTTTGATTTCCTTTTGCTTGGCATCATATGAGATTTG
1 GATTTTGATTTCCTTTTGCTTGGCACCATATGAGATTTG
*
288459 GATTTTGATTTCCTTTTGCTTGGCACCATATGAGCTTTG
1 GATTTTGATTTCCTTTTGCTTGGCACCATATGAGATTTG
288498 GATTTTGAT
1 GATTTTGAT
288507 GAGCATCGGA
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
39 46 1.00
ACGTcount: A:0.17, C:0.14, G:0.21, T:0.48
Consensus pattern (39 bp):
GATTTTGATTTCCTTTTGCTTGGCACCATATGAGATTTG
Found at i:288787 original size:18 final size:18
Alignment explanation
Indices: 288764--288800 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
288754 CGAAATATAT
288764 ATTGAAATTCAAACTCAA
1 ATTGAAATTCAAACTCAA
* *
288782 ATTGAAATTTAAATTCAA
1 ATTGAAATTCAAACTCAA
288800 A
1 A
288801 CTCCAATTAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.51, C:0.11, G:0.05, T:0.32
Consensus pattern (18 bp):
ATTGAAATTCAAACTCAA
Found at i:289229 original size:25 final size:25
Alignment explanation
Indices: 289189--289239 Score: 75
Period size: 25 Copynumber: 2.0 Consensus size: 25
289179 TTTTTCCAAA
* *
289189 TAATGTACCCATAACAATGTTCAAT
1 TAATGTACACACAACAATGTTCAAT
*
289214 TAATGTACACACAACAATGTTTAAT
1 TAATGTACACACAACAATGTTCAAT
289239 T
1 T
289240 GATTTGTTGT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.41, C:0.18, G:0.08, T:0.33
Consensus pattern (25 bp):
TAATGTACACACAACAATGTTCAAT
Found at i:289575 original size:23 final size:22
Alignment explanation
Indices: 289513--289584 Score: 90
Period size: 23 Copynumber: 3.2 Consensus size: 22
289503 ACACTTTACA
*
289513 ATATAACCACTACCTATTACATT
1 ATATAA-CGCTACCTATTACATT
*
289536 ATATAACGATACCTATTACATT
1 ATATAACGCTACCTATTACATT
* *
289558 ATATAAGGGCTACCTATTACATC
1 ATATAA-CGCTACCTATTACATT
289581 ATAT
1 ATAT
289585 GTTTACCTAT
Statistics
Matches: 43, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
22 20 0.47
23 23 0.53
ACGTcount: A:0.39, C:0.21, G:0.06, T:0.35
Consensus pattern (22 bp):
ATATAACGCTACCTATTACATT
Found at i:289973 original size:21 final size:22
Alignment explanation
Indices: 289948--289999 Score: 77
Period size: 23 Copynumber: 2.3 Consensus size: 22
289938 ACACTTTACA
*
289948 ATATAACCACTACCTATTACATT
1 ATATAAACA-TACCTATTACATT
289971 ATATAAACGATACCTATTACATT
1 ATATAAAC-ATACCTATTACATT
289994 ATATAA
1 ATATAA
290000 GGGCTACCTA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
23 26 0.96
24 1 0.04
ACGTcount: A:0.44, C:0.19, G:0.02, T:0.35
Consensus pattern (22 bp):
ATATAAACATACCTATTACATT
Found at i:289984 original size:23 final size:23
Alignment explanation
Indices: 289958--290020 Score: 90
Period size: 23 Copynumber: 2.7 Consensus size: 23
289948 ATATAACCAC
289958 TACCTATTACATTATATAAACGA
1 TACCTATTACATTATATAAACGA
** *
289981 TACCTATTACATTATATAAGGGC
1 TACCTATTACATTATATAAACGA
*
290004 TACCTATTACATCATAT
1 TACCTATTACATTATAT
290021 GTTTACCTAT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.38, C:0.19, G:0.06, T:0.37
Consensus pattern (23 bp):
TACCTATTACATTATATAAACGA
Found at i:290262 original size:435 final size:435
Alignment explanation
Indices: 289274--290577 Score: 2520
Period size: 435 Copynumber: 3.0 Consensus size: 435
289264 GAATTATTTG
*
289274 ATTTAATAATTTCATTTGCACAAAAAATTATTTGATTGTTTTGATATTTTATAAAATAATATTTA
1 ATTTAATAATTTCATTTGCACAAAAAATTATTTGATTGTTTTGATATTTTATAAAATATTATTTA
*
289339 GAATTTTTAATTTAATAATAATATATATCGTAACGTAAAAAATAAATCATTATACGCCTATAATT
66 GAATTTTTAATTTAATAATAATATATATCGTAACGTAAAAAATAAATCATTAGACGCCTATAATT
289404 ACTAAATTAATATCTTAAAACTCACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTG
131 ACTAAATTAATATCTTAAAACTCACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTG
289469 AAAAAAAGTATGGACACTTTTATAAAAAGGATAGACACTTTACAATATAACCACTACCTATTACA
196 -AAAAAAGTATGGACACTTTTATAAAAAGGATAGACACTTTACAATATAACCACTACCTATTACA
289534 TTATAT-AACGATACCTATTACATTATATAAGGGCTACCTATTACATCATATGTTTACCTATTAT
260 TTATATAAACGATACCTATTACATTATATAAGGGCTACCTATTACATCATATGTTTACCTATTAT
289598 ATTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTTTTTTAAAAGTTATGTAATTTATG
325 ATTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTTTTTTAAAAGTTATGTAATTTATG
*
289663 TTTCAATTTTTTTTAACATTGTTTCATGTTTTCCACCTACAATATTA
390 TTTCAA-TTTTTTTAACAGTGTTTCATGTTTTCCACCTACAATATTA
289710 ATTTAATAATTTCATTTGCACAAAAAATTATTTGATTGTTTTGATATTTTATAAAATATTATTTA
1 ATTTAATAATTTCATTTGCACAAAAAATTATTTGATTGTTTTGATATTTTATAAAATATTATTTA
289775 GAATTTTTAATTTAATAATAATATATATCGTAACGTAAAAAATAAATCATTAGACGCCTATAATT
66 GAATTTTTAATTTAATAATAATATATATCGTAACGTAAAAAATAAATCATTAGACGCCTATAATT
289840 ACTAAATTAATATCTTAAAACTCACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTG
131 ACTAAATTAATATCTTAAAACTCACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTG
289905 AAAAAAGTATGGACACTTTTATAAAAAGGATAGACACTTTACAATATAACCACTACCTATTACAT
196 AAAAAAGTATGGACACTTTTATAAAAAGGATAGACACTTTACAATATAACCACTACCTATTACAT
289970 TATATAAACGATACCTATTACATTATATAAGGGCTACCTATTACATCATATGTTTACCTATTATA
261 TATATAAACGATACCTATTACATTATATAAGGGCTACCTATTACATCATATGTTTACCTATTATA
290035 TTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTTTTTTAAAAGTTATGTAATTTATGT
326 TTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTTTTTTAAAAGTTATGTAATTTATGT
290100 TTCAATTTTTTTAACAGTGTTTCATGTTTTCCACCTACAATATTA
391 TTCAATTTTTTTAACAGTGTTTCATGTTTTCCACCTACAATATTA
290145 ATTTAATAATTTCATTTGCACAAAAAATTATTTGATTGTTTTGATATTTTATAAAATATTATTTA
1 ATTTAATAATTTCATTTGCACAAAAAATTATTTGATTGTTTTGATATTTTATAAAATATTATTTA
290210 GAATTTTTAATTTAATAATAATATATATCGTAACGTAAAAAATAAATCATTAGACGCCTATAATT
66 GAATTTTTAATTTAATAATAATATATATCGTAACGTAAAAAATAAATCATTAGACGCCTATAATT
*
290275 ATTAAATTAATATCTTAAAACTCACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTG
131 ACTAAATTAATATCTTAAAACTCACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTG
* *
290340 AAAAAAGTATGGGCACTTTTATAAAAAGGATAGACACTTTACAATATAATCACTACCTATTACAT
196 AAAAAAGTATGGACACTTTTATAAAAAGGATAGACACTTTACAATATAACCACTACCTATTACAT
*
290405 TATATAAACGATACCTATTACATTATATAAGGGCTACATATTACATCATATGTTTACCTATTATA
261 TATATAAACGATACCTATTACATTATATAAGGGCTACCTATTACATCATATGTTTACCTATTATA
290470 TTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTTTTTTAAAAGTTATGTAATTTATGT
326 TTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTTTTTTAAAAGTTATGTAATTTATGT
290535 TTCAATTTTTTTAACAGTGTTTCATGTTTTCCACCTACAATAT
391 TTCAATTTTTTTAACAGTGTTTCATGTTTTCCACCTACAATAT
290578 GAGCTTTGGA
Statistics
Matches: 860, Mismatches: 7, Indels: 3
0.99 0.01 0.00
Matches are distributed among these distances:
435 538 0.63
436 322 0.37
ACGTcount: A:0.39, C:0.13, G:0.08, T:0.40
Consensus pattern (435 bp):
ATTTAATAATTTCATTTGCACAAAAAATTATTTGATTGTTTTGATATTTTATAAAATATTATTTA
GAATTTTTAATTTAATAATAATATATATCGTAACGTAAAAAATAAATCATTAGACGCCTATAATT
ACTAAATTAATATCTTAAAACTCACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTG
AAAAAAGTATGGACACTTTTATAAAAAGGATAGACACTTTACAATATAACCACTACCTATTACAT
TATATAAACGATACCTATTACATTATATAAGGGCTACCTATTACATCATATGTTTACCTATTATA
TTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTTTTTTAAAAGTTATGTAATTTATGT
TTCAATTTTTTTAACAGTGTTTCATGTTTTCCACCTACAATATTA
Found at i:290446 original size:23 final size:23
Alignment explanation
Indices: 290383--290455 Score: 83
Period size: 23 Copynumber: 3.2 Consensus size: 23
290373 ACACTTTACA
* *
290383 ATATAATCACTACCTATTACATT
1 ATATAAACGCTACCTATTACATT
*
290406 ATATAAACGATACCTATTACATT
1 ATATAAACGCTACCTATTACATT
** * *
290429 ATATAAGGGCTACATATTACATC
1 ATATAAACGCTACCTATTACATT
290452 ATAT
1 ATAT
290456 GTTTACCTAT
Statistics
Matches: 42, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 42 1.00
ACGTcount: A:0.41, C:0.18, G:0.05, T:0.36
Consensus pattern (23 bp):
ATATAAACGCTACCTATTACATT
Found at i:290876 original size:18 final size:18
Alignment explanation
Indices: 290853--290889 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
290843 CGAAATATAT
290853 ATTGAAATTCAAACTCAA
1 ATTGAAATTCAAACTCAA
* *
290871 ATTGAAATTTAAATTCAA
1 ATTGAAATTCAAACTCAA
290889 A
1 A
290890 CTCCAATTAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.51, C:0.11, G:0.05, T:0.32
Consensus pattern (18 bp):
ATTGAAATTCAAACTCAA
Found at i:291318 original size:25 final size:25
Alignment explanation
Indices: 291278--291328 Score: 75
Period size: 25 Copynumber: 2.0 Consensus size: 25
291268 TTTTTCCAAA
* *
291278 TAATGTACCCATAACAATGTTCAAT
1 TAATGTACACACAACAATGTTCAAT
*
291303 TAATGTACACACAACAATGTTTAAT
1 TAATGTACACACAACAATGTTCAAT
291328 T
1 T
291329 GATTTGTTGT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.41, C:0.18, G:0.08, T:0.33
Consensus pattern (25 bp):
TAATGTACACACAACAATGTTCAAT
Found at i:291625 original size:21 final size:22
Alignment explanation
Indices: 291600--291651 Score: 77
Period size: 23 Copynumber: 2.3 Consensus size: 22
291590 ACACTTTACA
*
291600 ATATAACCACTACCTATTACATT
1 ATATAAACA-TACCTATTACATT
291623 ATATAAACGATACCTATTACATT
1 ATATAAAC-ATACCTATTACATT
291646 ATATAA
1 ATATAA
291652 GGGCTACCTA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
23 26 0.96
24 1 0.04
ACGTcount: A:0.44, C:0.19, G:0.02, T:0.35
Consensus pattern (22 bp):
ATATAAACATACCTATTACATT
Found at i:291636 original size:23 final size:23
Alignment explanation
Indices: 291610--291672 Score: 90
Period size: 23 Copynumber: 2.7 Consensus size: 23
291600 ATATAACCAC
291610 TACCTATTACATTATATAAACGA
1 TACCTATTACATTATATAAACGA
** *
291633 TACCTATTACATTATATAAGGGC
1 TACCTATTACATTATATAAACGA
*
291656 TACCTATTACATCATAT
1 TACCTATTACATTATAT
291673 GTTTACCTAT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.38, C:0.19, G:0.06, T:0.37
Consensus pattern (23 bp):
TACCTATTACATTATATAAACGA
Found at i:292098 original size:23 final size:23
Alignment explanation
Indices: 292035--292107 Score: 83
Period size: 23 Copynumber: 3.2 Consensus size: 23
292025 ACACTTTACA
* *
292035 ATATAACCACTACCTATTACATT
1 ATATAAACGCTACCTATTACATT
*
292058 ATATAAACGATACCTATTACATT
1 ATATAAACGCTACCTATTACATT
** * *
292081 ATATAAGGGCTACATATTACATC
1 ATATAAACGCTACCTATTACATT
292104 ATAT
1 ATAT
292108 GTTTACCTAT
Statistics
Matches: 42, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 42 1.00
ACGTcount: A:0.41, C:0.19, G:0.05, T:0.34
Consensus pattern (23 bp):
ATATAAACGCTACCTATTACATT
Found at i:292194 original size:435 final size:434
Alignment explanation
Indices: 291363--292229 Score: 1707
Period size: 435 Copynumber: 2.0 Consensus size: 434
291353 GAATTATTTG
291363 ATTTAATAATTTCATTTGCACAAAAATTATTTGATTGTTTTGATATTTTATAAAATATTATTTAG
1 ATTTAATAATTTCATTTGCACAAAAATTATTTGATTGTTTTGATATTTTATAAAATATTATTTAG
291428 AATTTTTAATTTAATAATAATATATATCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTA
66 AATTTTTAATTTAATAATAATATATATCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTA
291493 CTAAATTAATATCTTAAAACTCACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGA
131 CTAAATTAATATCTTAAAACTCACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGA
291558 AAAAAGTATGGACACTTTTATAAAAAGGATAGACACTTTACAATATAACCACTACCTATTACATT
196 AAAAAGTATGGACACTTTTATAAAAAGGATAGACACTTTACAATATAACCACTACCTATTACATT
*
291623 ATATAAACGATACCTATTACATTATATAAGGGCTACCTATTACATCATATGTTTACCTATTATAT
261 ATATAAACGATACCTATTACATTATATAAGGGCTACATATTACATCATATGTTTACCTATTATAT
291688 TGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTTTTTTAAAAGTTATGTAATTTATGTT
326 TGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTTTTTTAAAAGTTATGTAATTTATGTT
291753 TCAATTTTTTTAACAGTGTTTCATGTTTTCCACCTACAATATTA
391 TCAATTTTTTTAACAGTGTTTCATGTTTTCCACCTACAATATTA
291797 ATTTAATAATTTCATTTGCACAAAAAATTATTTGATTGTTTTGATATTTTATAAAATATTATTTA
1 ATTTAATAATTTCATTTGCAC-AAAAATTATTTGATTGTTTTGATATTTTATAAAATATTATTTA
291862 GAATTTTTAATTTAATAATAATATATATCGTAACGTAAAAAATAAATCATTAGACGCCTATAATT
65 GAATTTTTAATTTAATAATAATATATATCGTAACGTAAAAAATAAATCATTAGACGCCTATAATT
291927 ACTAAATTAATATCTTAAAACTCACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTG
130 ACTAAATTAATATCTTAAAACTCACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTG
*
291992 AAAAAAGTATGGGCACTTTTATAAAAAGGATAGACACTTTACAATATAACCACTACCTATTACAT
195 AAAAAAGTATGGACACTTTTATAAAAAGGATAGACACTTTACAATATAACCACTACCTATTACAT
292057 TATATAAACGATACCTATTACATTATATAAGGGCTACATATTACATCATATGTTTACCTATTATA
260 TATATAAACGATACCTATTACATTATATAAGGGCTACATATTACATCATATGTTTACCTATTATA
292122 TTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTTTTTTAAAAGTTATGTAATTTATGT
325 TTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTTTTTTAAAAGTTATGTAATTTATGT
292187 TTCAATTTTTTTAACAGTGTTTCATGTTTTCCACCTACAATAT
390 TTCAATTTTTTTAACAGTGTTTCATGTTTTCCACCTACAATAT
292230 GAGCTTTGGA
Statistics
Matches: 430, Mismatches: 2, Indels: 1
0.99 0.00 0.00
Matches are distributed among these distances:
434 21 0.05
435 409 0.95
ACGTcount: A:0.39, C:0.13, G:0.08, T:0.40
Consensus pattern (434 bp):
ATTTAATAATTTCATTTGCACAAAAATTATTTGATTGTTTTGATATTTTATAAAATATTATTTAG
AATTTTTAATTTAATAATAATATATATCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTA
CTAAATTAATATCTTAAAACTCACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGA
AAAAAGTATGGACACTTTTATAAAAAGGATAGACACTTTACAATATAACCACTACCTATTACATT
ATATAAACGATACCTATTACATTATATAAGGGCTACATATTACATCATATGTTTACCTATTATAT
TGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTTTTTTAAAAGTTATGTAATTTATGTT
TCAATTTTTTTAACAGTGTTTCATGTTTTCCACCTACAATATTA
Found at i:292528 original size:18 final size:18
Alignment explanation
Indices: 292505--292541 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
292495 CGAAATATAT
292505 ATTGAAATTCAAACTCAA
1 ATTGAAATTCAAACTCAA
* *
292523 ATTGAAATTTAAATTCAA
1 ATTGAAATTCAAACTCAA
292541 A
1 A
292542 CTCCAATTAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.51, C:0.11, G:0.05, T:0.32
Consensus pattern (18 bp):
ATTGAAATTCAAACTCAA
Found at i:292970 original size:25 final size:25
Alignment explanation
Indices: 292930--292980 Score: 75
Period size: 25 Copynumber: 2.0 Consensus size: 25
292920 TTTTTCCAAA
* *
292930 TAATGTACCCATAACAATGTTCAAT
1 TAATGTACACACAACAATGTTCAAT
*
292955 TAATGTACACACAACAATGTTTAAT
1 TAATGTACACACAACAATGTTCAAT
292980 T
1 T
292981 GATTTGTTGT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.41, C:0.18, G:0.08, T:0.33
Consensus pattern (25 bp):
TAATGTACACACAACAATGTTCAAT
Found at i:293278 original size:21 final size:22
Alignment explanation
Indices: 293253--293304 Score: 77
Period size: 23 Copynumber: 2.3 Consensus size: 22
293243 ACACTTTACA
*
293253 ATATAACCACTACCTATTACATT
1 ATATAAACA-TACCTATTACATT
293276 ATATAAACGATACCTATTACATT
1 ATATAAAC-ATACCTATTACATT
293299 ATATAA
1 ATATAA
293305 GGGCTACCTA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
23 26 0.96
24 1 0.04
ACGTcount: A:0.44, C:0.19, G:0.02, T:0.35
Consensus pattern (22 bp):
ATATAAACATACCTATTACATT
Found at i:293289 original size:23 final size:23
Alignment explanation
Indices: 293263--293325 Score: 90
Period size: 23 Copynumber: 2.7 Consensus size: 23
293253 ATATAACCAC
293263 TACCTATTACATTATATAAACGA
1 TACCTATTACATTATATAAACGA
** *
293286 TACCTATTACATTATATAAGGGC
1 TACCTATTACATTATATAAACGA
*
293309 TACCTATTACATCATAT
1 TACCTATTACATTATAT
293326 GTTTACCTAT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.38, C:0.19, G:0.06, T:0.37
Consensus pattern (23 bp):
TACCTATTACATTATATAAACGA
Found at i:293724 original size:25 final size:24
Alignment explanation
Indices: 293665--293731 Score: 80
Period size: 25 Copynumber: 2.7 Consensus size: 24
293655 TCACTCAAAA
*
293665 TATGTATATACCTAAATATGTAGT
1 TATGTACATACCTAAATATGTAGT
***
293689 TAACAACCATACCTAAATATGTAGT
1 TATGTA-CATACCTAAATATGTAGT
293714 TATTGTACATACCTAAAT
1 TA-TGTACATACCTAAAT
293732 TTAATGATAA
Statistics
Matches: 34, Mismatches: 7, Indels: 3
0.77 0.16 0.07
Matches are distributed among these distances:
24 3 0.09
25 30 0.88
26 1 0.03
ACGTcount: A:0.40, C:0.15, G:0.09, T:0.36
Consensus pattern (24 bp):
TATGTACATACCTAAATATGTAGT
Found at i:296511 original size:183 final size:184
Alignment explanation
Indices: 296199--296729 Score: 904
Period size: 183 Copynumber: 2.9 Consensus size: 184
296189 TTCAAATTAC
* * *
296199 CGACACTTTTTTAAATGGTATCGACACATTTTTCTTCCAATCTGGACATAAAGTATCGACACAAT
1 CGACACTTTTTTAAATCGTATCGACACATTTTTCTTCCAATATGGACATAAAGTACCGACACAAT
* *
296264 ATTATAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGGTATATTTATACCGGTT
66 ATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAAACCGGTATATTTATACCGGTT
*
296329 ATATTACAAAATTATCTATTACATTATAAATCTGGGTTCCGATGTGTAAA-TAT
131 ATATTACAAAATTATCTATTACATTATAAATATGGGTTCCGATGTGTAAACTAT
*
296382 CGATACTTTTTTAAATCGTATCGACACATTTTTCTTCCAATATGGACATAAAGTACCGACACAAT
1 CGACACTTTTTTAAATCGTATCGACACATTTTTCTTCCAATATGGACATAAAGTACCGACACAAT
*
296447 ATTAAAAAGTGTCGATATAGGTTGTAGGCCTATTCGCGCATAAAACCGGTATATTTATACCGGTT
66 ATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAAACCGGTATATTTATACCGGTT
* *
296512 ATATTACAAAATTATCTATTACATTATAATTATGGGTTCCGATGTGTAAACTGT
131 ATATTACAAAATTATCTATTACATTATAAATATGGGTTCCGATGTGTAAACTAT
296566 CGACACTTTTTTTAAATCGTATCGACACATTTTTCTTCCAATATGGACATAAAGTACCGACACAA
1 CGACAC-TTTTTTAAATCGTATCGACACATTTTTCTTCCAATATGGACATAAAGTACCGACACAA
296631 TATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAAACCGGTATATTTATACCGGT
65 TATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAAACCGGTATATTTATACCGGT
* * * **
296696 TATATTGCAAATTTACCTATTTTATTAT-AATATG
130 TATATTACAAAATTATCTATTACATTATAAATATG
296730 TTGAAAGTGT
Statistics
Matches: 328, Mismatches: 18, Indels: 3
0.94 0.05 0.01
Matches are distributed among these distances:
183 171 0.52
184 12 0.04
185 145 0.44
ACGTcount: A:0.33, C:0.17, G:0.14, T:0.36
Consensus pattern (184 bp):
CGACACTTTTTTAAATCGTATCGACACATTTTTCTTCCAATATGGACATAAAGTACCGACACAAT
ATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAAACCGGTATATTTATACCGGTT
ATATTACAAAATTATCTATTACATTATAAATATGGGTTCCGATGTGTAAACTAT
Found at i:311923 original size:13 final size:13
Alignment explanation
Indices: 311896--311937 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
311886 ATATATGTTA
*
311896 TTTTACAATTTGT
1 TTTTCCAATTTGT
*
311909 TTATTCTAA-TTGT
1 TT-TTCCAATTTGT
311922 TTTTCCAATTTGT
1 TTTTCCAATTTGT
311935 TTT
1 TTT
311938 ATAACATCAG
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
12 5 0.21
13 15 0.62
14 4 0.17
ACGTcount: A:0.19, C:0.10, G:0.07, T:0.64
Consensus pattern (13 bp):
TTTTCCAATTTGT
Found at i:313758 original size:6 final size:6
Alignment explanation
Indices: 313749--313778 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
313739 GGGTTGGGAA
313749 TTGGAC TTGGAC TTGGAC TTGGAC TTGGAC
1 TTGGAC TTGGAC TTGGAC TTGGAC TTGGAC
313779 GTAGCCGTTC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.17, C:0.17, G:0.33, T:0.33
Consensus pattern (6 bp):
TTGGAC
Found at i:314241 original size:56 final size:57
Alignment explanation
Indices: 314180--314289 Score: 127
Period size: 57 Copynumber: 1.9 Consensus size: 57
314170 AGTTTTAAAT
* * *
314180 TTTGA-TCATGATTATTTTAAATAAT-TAAATTTTATAA-AATATATATTTAAAAACTA
1 TTTGATTCAAGATT-TTTTAAAAAATATAAATTTTATAATAATAAAT-TTTAAAAACTA
* * *
314236 TTTGATTTAAGATTTTTTAAAAAATATATATTTTTTAATAATAAATTTTAAAAA
1 TTTGATTCAAGATTTTTTAAAAAATATAAATTTTATAATAATAAATTTTAAAAA
314290 ATAACGAGTC
Statistics
Matches: 45, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
56 15 0.33
57 24 0.53
58 6 0.13
ACGTcount: A:0.46, C:0.02, G:0.04, T:0.48
Consensus pattern (57 bp):
TTTGATTCAAGATTTTTTAAAAAATATAAATTTTATAATAATAAATTTTAAAAACTA
Found at i:327056 original size:21 final size:21
Alignment explanation
Indices: 327030--327074 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
327020 GATTTCTGGG
* *
327030 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
327051 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
327072 CAA
1 CAA
327075 ACGAATAACA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:328815 original size:149 final size:149
Alignment explanation
Indices: 328628--328942 Score: 560
Period size: 149 Copynumber: 2.1 Consensus size: 149
328618 GAGTCGAGGG
* * *
328628 TCTACGCGATCCTTCGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTTGAAAGACACAT
1 TCTACGCGGTCCTTCGGGACATATATATATTCTGTGGAACATGTGTGAAGTCTTGAAAGACACAT
328693 ACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATAATATGTGGTCCTTATGGACATTATTA
66 ACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATAATATGTGGTCCTTATGGACATTATTA
328758 TATGGCACTACGGTGCAAT
131 TATGGCACTACGGTGCAAT
*
328777 TCTACGCGGTCCTTCGGGATATATATATATTCTGTGGAACATGTGTGAAGTCTTGAAAGACACAT
1 TCTACGCGGTCCTTCGGGACATATATATATTCTGTGGAACATGTGTGAAGTCTTGAAAGACACAT
*
328842 ACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATAATATGTGGTCCTTATGGACATTGTTA
66 ACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATAATATGTGGTCCTTATGGACATTATTA
*
328907 TATGGCACTACGGTGTAAT
131 TATGGCACTACGGTGCAAT
328926 TCTACGCGG-CACTTCGG
1 TCTACGCGGTC-CTTCGG
328943 TGCAATTATA
Statistics
Matches: 159, Mismatches: 6, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
148 1 0.01
149 158 0.99
ACGTcount: A:0.28, C:0.17, G:0.21, T:0.35
Consensus pattern (149 bp):
TCTACGCGGTCCTTCGGGACATATATATATTCTGTGGAACATGTGTGAAGTCTTGAAAGACACAT
ACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATAATATGTGGTCCTTATGGACATTATTA
TATGGCACTACGGTGCAAT
Found at i:328943 original size:23 final size:23
Alignment explanation
Indices: 328910--328954 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
328900 ATTGTTATAT
* *
328910 GGCACTACGGTGTAATTCTACGC
1 GGCACTACGGTGCAATTATACGC
*
328933 GGCACTTCGGTGCAATTATACG
1 GGCACTACGGTGCAATTATACG
328955 AGCTGTGGTG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.22, C:0.24, G:0.27, T:0.27
Consensus pattern (23 bp):
GGCACTACGGTGCAATTATACGC
Found at i:330497 original size:30 final size:28
Alignment explanation
Indices: 330462--330533 Score: 90
Period size: 28 Copynumber: 2.5 Consensus size: 28
330452 AAATATTTGA
* **
330462 AATATTTGTTATTATGGTTTTACTTTTTTT
1 AATATTTATTATTATGGGCTTA--TTTTTT
*
330492 AATATTTATTATTTTGGGCTTATTTTTT
1 AATATTTATTATTATGGGCTTATTTTTT
330520 AATATTTATTATTA
1 AATATTTATTATTA
330534 GGACCTATTT
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
28 19 0.51
30 18 0.49
ACGTcount: A:0.25, C:0.03, G:0.08, T:0.64
Consensus pattern (28 bp):
AATATTTATTATTATGGGCTTATTTTTT
Found at i:330550 original size:28 final size:28
Alignment explanation
Indices: 330486--330550 Score: 69
Period size: 28 Copynumber: 2.3 Consensus size: 28
330476 TGGTTTTACT
* * * *
330486 TTTTTTAATATTTATTATTTTGGGCTTA
1 TTTTATAATATTTATTATTTAGGACCTA
*
330514 TTTTTTAATATTTATTA-TTAGGACCTA
1 TTTTATAATATTTATTATTTAGGACCTA
330541 TTTTCATAAT
1 TTTT-ATAAT
330551 TTATTTTTAT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
27 11 0.34
28 21 0.66
ACGTcount: A:0.26, C:0.06, G:0.08, T:0.60
Consensus pattern (28 bp):
TTTTATAATATTTATTATTTAGGACCTA
Found at i:330747 original size:29 final size:30
Alignment explanation
Indices: 330714--330787 Score: 82
Period size: 29 Copynumber: 2.5 Consensus size: 30
330704 TTCTAATATT
* *
330714 TATTTGTTGTTATGAATTTAATA-TTTTAA
1 TATTTGTTATTATGAATTCAATATTTTTAA
* *
330743 TATTT-TTATT-GGAGGTTCAATATTTTTAA
1 TATTTGTTATTATGA-ATTCAATATTTTTAA
330772 TATTTGTTATTATGAA
1 TATTTGTTATTATGAA
330788 AATACTGTTA
Statistics
Matches: 35, Mismatches: 6, Indels: 7
0.73 0.12 0.15
Matches are distributed among these distances:
27 2 0.06
28 10 0.29
29 16 0.46
30 5 0.14
31 2 0.06
ACGTcount: A:0.30, C:0.01, G:0.12, T:0.57
Consensus pattern (30 bp):
TATTTGTTATTATGAATTCAATATTTTTAA
Found at i:331259 original size:14 final size:14
Alignment explanation
Indices: 331240--331266 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
331230 GTATGCATCT
331240 AAATCAAACCCAAG
1 AAATCAAACCCAAG
331254 AAATCAAACCCAA
1 AAATCAAACCCAA
331267 CATAGTTCTT
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:0.59, C:0.30, G:0.04, T:0.07
Consensus pattern (14 bp):
AAATCAAACCCAAG
Found at i:332053 original size:150 final size:147
Alignment explanation
Indices: 331878--332267 Score: 585
Period size: 150 Copynumber: 2.7 Consensus size: 147
331868 CAACAACTTT
*
331878 TTTATCCTCGGCCTTCTTTTCCTCTACATTTTCATCAACCTTCTTCTCCTCAATTCGATCCACAA
1 TTTATCCTCGGCCTTCTTTTCCTCTACATTTTCATCAACCTTCTTCACCTCAATTCGATCCACAA
*
331943 CCTTGTCATCTTGAGCTTCACTGATCTTCTTGGTTTTCTCTTTGACAACTTTCGAAGTTTGTGAT
66 CCTTGTCATCTTGAGCTTCACTGATCTTCTT-G--TTCTCTTTGACAACTTTCGAAGTTCGTGAT
*
332008 GCACTTGGTGGTTCAACACA
128 GCACTTGGTCGTTCAACACA
* *
332028 TTTATCCTCAGCCTTCTTTTCCTCTACATTTTCATCAACCTTCTTCACCTCGATTCGATCCACAA
1 TTTATCCTCGGCCTTCTTTTCCTCTACATTTTCATCAACCTTCTTCACCTCAATTCGATCCACAA
332093 CCTTGTCATCTTGAGCTTCACTGATCTTC---TTCTCTTTGACAACTTTCGAAGTTCGTGATGCA
66 CCTTGTCATCTTGAGCTTCACTGATCTTCTTGTTCTCTTTGACAACTTTCGAAGTTCGTGATGCA
*
332155 CTTGGTCGTTCAACATA
131 CTTGGTCGTTCAACACA
* * * * * *
332172 TTTATCCTCGGCCTTCTTATCTTCTACGTTTTCGTCAA-C--CTTCACCTCAATTTGGTCCACAA
1 TTTATCCTCGGCCTTCTTTTCCTCTACATTTTCATCAACCTTCTTCACCTCAATTCGATCCACAA
* *
332234 CCTTGTTATCTAGAGCTTCACTGATCTTCTTGTT
66 CCTTGTCATCTTGAGCTTCACTGATCTTCTTGTT
332268 ATTGTTCTTC
Statistics
Matches: 221, Mismatches: 16, Indels: 12
0.89 0.06 0.05
Matches are distributed among these distances:
141 47 0.21
143 1 0.00
144 82 0.37
150 91 0.41
ACGTcount: A:0.18, C:0.29, G:0.12, T:0.41
Consensus pattern (147 bp):
TTTATCCTCGGCCTTCTTTTCCTCTACATTTTCATCAACCTTCTTCACCTCAATTCGATCCACAA
CCTTGTCATCTTGAGCTTCACTGATCTTCTTGTTCTCTTTGACAACTTTCGAAGTTCGTGATGCA
CTTGGTCGTTCAACACA
Found at i:332078 original size:27 final size:28
Alignment explanation
Indices: 332025--332078 Score: 65
Period size: 27 Copynumber: 2.0 Consensus size: 28
332015 GTGGTTCAAC
* * **
332025 ACATTTATCCTCAGCCTTCTTTTCCTCT
1 ACATTTATCATCAACCTTCTTCACCTCT
332053 ACATTT-TCATCAACCTTCTTCACCTC
1 ACATTTATCATCAACCTTCTTCACCTC
332079 GATTCGATCC
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
27 16 0.73
28 6 0.27
ACGTcount: A:0.19, C:0.37, G:0.02, T:0.43
Consensus pattern (28 bp):
ACATTTATCATCAACCTTCTTCACCTCT
Found at i:333753 original size:15 final size:15
Alignment explanation
Indices: 333733--333774 Score: 66
Period size: 17 Copynumber: 2.7 Consensus size: 15
333723 AAATTTAAGT
333733 TATAAAATTAACGAG
1 TATAAAATTAACGAG
333748 TATAAAATATTAACGAG
1 TAT-AAA-ATTAACGAG
333765 TATAAAATTA
1 TATAAAATTA
333775 TCTTCGGATA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
15 7 0.28
16 6 0.24
17 12 0.48
ACGTcount: A:0.55, C:0.05, G:0.10, T:0.31
Consensus pattern (15 bp):
TATAAAATTAACGAG
Found at i:333761 original size:17 final size:17
Alignment explanation
Indices: 333739--333772 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
333729 AAGTTATAAA
333739 ATTAACGAGTATAAAAT
1 ATTAACGAGTATAAAAT
333756 ATTAACGAGTATAAAAT
1 ATTAACGAGTATAAAAT
333773 TATCTTCGGA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.53, C:0.06, G:0.12, T:0.29
Consensus pattern (17 bp):
ATTAACGAGTATAAAAT
Found at i:335194 original size:16 final size:16
Alignment explanation
Indices: 335151--335206 Score: 51
Period size: 16 Copynumber: 3.3 Consensus size: 16
335141 AGAGAATTGA
*
335151 TTAAAAAT-ATTATTT
1 TTAAAAATAAATATTT
*
335166 TTAAAAAATAATAATTTTTT
1 TT-AAAAAT-A-AA-TATTT
335186 TTAAAAATAAATATTT
1 TTAAAAATAAATATTT
335202 TTAAA
1 TTAAA
335207 CTCTTTTTTT
Statistics
Matches: 33, Mismatches: 3, Indels: 9
0.73 0.07 0.20
Matches are distributed among these distances:
15 2 0.06
16 15 0.45
17 2 0.06
18 1 0.03
19 7 0.21
20 6 0.18
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (16 bp):
TTAAAAATAAATATTT
Found at i:335198 original size:20 final size:19
Alignment explanation
Indices: 335156--335203 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 19
335146 ATTGATTAAA
*
335156 AATATTATTTTTAAAAAAT
1 AATATTTTTTTTAAAAAAT
335175 AATAATTTTTTTT-AAAAAT
1 AAT-ATTTTTTTTAAAAAAT
335194 AAATATTTTT
1 -AATATTTTT
335204 AAACTCTTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
19 15 0.58
20 11 0.42
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (19 bp):
AATATTTTTTTTAAAAAAT
Found at i:335201 original size:19 final size:18
Alignment explanation
Indices: 335153--335203 Score: 66
Period size: 20 Copynumber: 2.7 Consensus size: 18
335143 AGAATTGATT
*
335153 AAAAATATTATTTTTAAA
1 AAAAATATTTTTTTTAAA
335171 AAATAATAATTTTTTTTAAA
1 AAA-AAT-ATTTTTTTTAAA
335191 AATAAATATTTTT
1 AA-AAATATTTTT
335204 AAACTCTTTT
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
18 3 0.10
19 9 0.31
20 16 0.55
21 1 0.03
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (18 bp):
AAAAATATTTTTTTTAAA
Found at i:342166 original size:27 final size:27
Alignment explanation
Indices: 342128--342181 Score: 90
Period size: 27 Copynumber: 2.0 Consensus size: 27
342118 AGGGCAGGGA
*
342128 GATGTCCTATATGGGTATCACAATGTC
1 GATGTCCCATATGGGTATCACAATGTC
*
342155 GATGTCCCATATGGGTATCTCAATGTC
1 GATGTCCCATATGGGTATCACAATGTC
342182 TCTTTATTTC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.24, C:0.20, G:0.22, T:0.33
Consensus pattern (27 bp):
GATGTCCCATATGGGTATCACAATGTC
Found at i:343121 original size:21 final size:20
Alignment explanation
Indices: 343097--343195 Score: 85
Period size: 21 Copynumber: 4.8 Consensus size: 20
343087 ATAGTATAAG
343097 TATACTTATAAATAATATTAA
1 TATA-TTATAAATAATATTAA
* * * *
343118 TATATACAAAAATATTATTTA
1 TATAT-TATAAATAATATTAA
**
343139 TATATTAATACAA-AATACAAA
1 TATATT-ATA-AATAATATTAA
*
343160 TATATTATAATTAATATTAA
1 TATATTATAAATAATATTAA
343180 TATA-TATAAATAATAT
1 TATATTATAAATAATAT
343196 ATTTTATATA
Statistics
Matches: 60, Mismatches: 14, Indels: 10
0.71 0.17 0.12
Matches are distributed among these distances:
19 12 0.20
20 14 0.23
21 32 0.53
22 2 0.03
ACGTcount: A:0.55, C:0.04, G:0.00, T:0.41
Consensus pattern (20 bp):
TATATTATAAATAATATTAA
Done.