Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009399.1 Hibiscus syriacus cultivar Beakdansim tig00113326_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: 409278
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.32
Found at i:2348 original size:14 final size:14
Alignment explanation
Indices: 2329--2361 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
2319 AAAGCACTCA
2329 AAAAGAAGAA-AAAG
1 AAAAGAA-AAGAAAG
2343 AAAAGAAAAGAAAG
1 AAAAGAAAAGAAAG
2357 AAAAG
1 AAAAG
2362 TTGGAAGCAC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 2 0.11
14 16 0.89
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (14 bp):
AAAAGAAAAGAAAG
Found at i:6554 original size:14 final size:14
Alignment explanation
Indices: 6535--6567 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
6525 AAAGCACTCA
6535 AAAAGAAGAA-AAAG
1 AAAAGAA-AAGAAAG
6549 AAAAGAAAAGAAAG
1 AAAAGAAAAGAAAG
6563 AAAAG
1 AAAAG
6568 TTGGAAGCAC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 2 0.11
14 16 0.89
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (14 bp):
AAAAGAAAAGAAAG
Found at i:10758 original size:14 final size:14
Alignment explanation
Indices: 10739--10771 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
10729 AAAGCACTCA
10739 AAAAGAAGAA-AAAG
1 AAAAGAA-AAGAAAG
10753 AAAAGAAAAGAAAG
1 AAAAGAAAAGAAAG
10767 AAAAG
1 AAAAG
10772 TTGGAAGCAC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 2 0.11
14 16 0.89
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (14 bp):
AAAAGAAAAGAAAG
Found at i:16988 original size:35 final size:37
Alignment explanation
Indices: 16942--17021 Score: 119
Period size: 35 Copynumber: 2.2 Consensus size: 37
16932 TTTGAGAATT
* *
16942 TGGTGATGATATTGGCGTGAT-ATGG-TGATGGACTA
1 TGGTGATGATATAGGCGTGATAATGGAAGATGGACTA
*
16977 TGGTGATGATATAGGCGTGATAATGGAAGATGGATTA
1 TGGTGATGATATAGGCGTGATAATGGAAGATGGACTA
17014 TGGTGATG
1 TGGTGATG
17022 GAAATAGTAT
Statistics
Matches: 40, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
35 20 0.50
36 4 0.10
37 16 0.40
ACGTcount: A:0.26, C:0.04, G:0.38, T:0.33
Consensus pattern (37 bp):
TGGTGATGATATAGGCGTGATAATGGAAGATGGACTA
Found at i:22257 original size:18 final size:19
Alignment explanation
Indices: 22236--22280 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 19
22226 ACTTCTCTTT
22236 TTCTTTTCT-TTTCTTT-TC
1 TTCTTTTCTATTT-TTTCTC
22254 TTCTTTTCTGATTTTTTCTC
1 TTCTTTTCT-ATTTTTTCTC
22274 TTCTTTT
1 TTCTTTT
22281 TGCACTCCAA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
18 9 0.38
19 3 0.12
20 12 0.50
ACGTcount: A:0.02, C:0.20, G:0.02, T:0.76
Consensus pattern (19 bp):
TTCTTTTCTATTTTTTCTC
Found at i:38765 original size:28 final size:27
Alignment explanation
Indices: 38725--38777 Score: 97
Period size: 28 Copynumber: 1.9 Consensus size: 27
38715 AAGGTTAAAA
38725 GGTTATGATATAGGGTAGGAATAGAAAT
1 GGTTATGATATAGGGTAGGAA-AGAAAT
38753 GGTTATGATATAGGGTAGGAAAGAA
1 GGTTATGATATAGGGTAGGAAAGAA
38778 GAAGAGTAAG
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
27 4 0.16
28 21 0.84
ACGTcount: A:0.40, C:0.00, G:0.34, T:0.26
Consensus pattern (27 bp):
GGTTATGATATAGGGTAGGAAAGAAAT
Found at i:40027 original size:20 final size:21
Alignment explanation
Indices: 39985--40028 Score: 54
Period size: 20 Copynumber: 2.1 Consensus size: 21
39975 ATTCGGCTAG
** *
39985 ATACATGTCTTTTTAATGGAA
1 ATACATGTCTTTAAAATGAAA
40006 ATACATGTC-TTAAAATGAAA
1 ATACATGTCTTTAAAATGAAA
40026 ATA
1 ATA
40029 GATGATGCTT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
20 11 0.55
21 9 0.45
ACGTcount: A:0.43, C:0.09, G:0.11, T:0.36
Consensus pattern (21 bp):
ATACATGTCTTTAAAATGAAA
Found at i:41308 original size:30 final size:31
Alignment explanation
Indices: 41256--41315 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 31
41246 CATAGCTTTA
**
41256 TATTATGTTTACATATGTTTTAGAT-TCATT
1 TATTATGTTTACATATCATTTAGATATCATT
* *
41286 TATTATGTTTGCATTTCATTTAGATATCAT
1 TATTATGTTTACATATCATTTAGATATCAT
41316 GGCAGCATGT
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:0.27, C:0.08, G:0.10, T:0.55
Consensus pattern (31 bp):
TATTATGTTTACATATCATTTAGATATCATT
Found at i:42252 original size:19 final size:20
Alignment explanation
Indices: 42228--42277 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
42218 GGCCAAGAGC
* *
42228 ATGTATCTTCAT-TAAAATA
1 ATGTATTTTCATCAAAAATA
*
42247 ATGTATTTTCATCAAAAATC
1 ATGTATTTTCATCAAAAATA
42267 ATGTATTTTCA
1 ATGTATTTTCA
42278 AAGGGGTTTC
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
19 11 0.41
20 16 0.59
ACGTcount: A:0.38, C:0.12, G:0.06, T:0.44
Consensus pattern (20 bp):
ATGTATTTTCATCAAAAATA
Found at i:42728 original size:20 final size:20
Alignment explanation
Indices: 42692--42729 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
42682 TTTTTATTTA
*
42692 TTTCATTTCTATTCTTATTC
1 TTTCATTTCCATTCTTATTC
42712 TTTCA-TTCCATTACTTAT
1 TTTCATTTCCATT-CTTAT
42730 ATTATTATTC
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 6 0.38
20 10 0.62
ACGTcount: A:0.18, C:0.21, G:0.00, T:0.61
Consensus pattern (20 bp):
TTTCATTTCCATTCTTATTC
Found at i:43610 original size:21 final size:21
Alignment explanation
Indices: 43570--43610 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
43560 AAGGAAGATT
*
43570 AAATGAAATGATAAAGATAAG
1 AAATGAAATGATAAAAATAAG
43591 AAATGAAATGA-AATAAATAA
1 AAATGAAATGATAA-AAATAA
43611 AGGATAGAGA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 2 0.11
21 16 0.89
ACGTcount: A:0.66, C:0.00, G:0.15, T:0.20
Consensus pattern (21 bp):
AAATGAAATGATAAAAATAAG
Found at i:43659 original size:22 final size:21
Alignment explanation
Indices: 43633--43674 Score: 66
Period size: 22 Copynumber: 2.0 Consensus size: 21
43623 GCTGCAGAAT
43633 TGATGGTCTTGATGGATGAAAA
1 TGATGGTCTTGAT-GATGAAAA
*
43655 TGATGGTGTTGATGATGAAA
1 TGATGGTCTTGATGATGAAA
43675 TGGAGATGTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 7 0.37
22 12 0.63
ACGTcount: A:0.31, C:0.02, G:0.33, T:0.33
Consensus pattern (21 bp):
TGATGGTCTTGATGATGAAAA
Found at i:48969 original size:33 final size:33
Alignment explanation
Indices: 48890--48993 Score: 95
Period size: 33 Copynumber: 3.1 Consensus size: 33
48880 ATACAATCTG
* *
48890 TCCATCACCATTATCACGCCTATATCATCA-CCATAT
1 TCCATCACCA-TATCACGCCAATAACATCATCC---T
48926 TCCATCACCATATCACGCCAATAACATCATCCT
1 TCCATCACCATATCACGCCAATAACATCATCCT
* * * *
48959 TCCATTACCATTTCATCACCATTAA-ATCATCCT
1 TCCATCACCATATCA-CGCCAATAACATCATCCT
48992 TC
1 TC
48994 ATTCATCAAC
Statistics
Matches: 60, Mismatches: 6, Indels: 7
0.82 0.08 0.10
Matches are distributed among these distances:
33 24 0.40
34 7 0.12
35 17 0.28
36 12 0.20
ACGTcount: A:0.31, C:0.37, G:0.02, T:0.31
Consensus pattern (33 bp):
TCCATCACCATATCACGCCAATAACATCATCCT
Found at i:49363 original size:12 final size:12
Alignment explanation
Indices: 49349--49378 Score: 51
Period size: 12 Copynumber: 2.4 Consensus size: 12
49339 AAGCAACAAG
49349 AAAGAAGAAAAGA
1 AAAG-AGAAAAGA
49362 AAAGAGAAAAGA
1 AAAGAGAAAAGA
49374 AAAGA
1 AAAGA
49379 CTCCTACAAC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 13 0.76
13 4 0.24
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (12 bp):
AAAGAGAAAAGA
Found at i:53436 original size:33 final size:33
Alignment explanation
Indices: 53357--53460 Score: 95
Period size: 33 Copynumber: 3.1 Consensus size: 33
53347 ATACAATCTG
* *
53357 TCCATCACCATTATCACGCCTATATCATCA-CCATAT
1 TCCATCACCA-TATCACGCCAATAACATCATCC---T
53393 TCCATCACCATATCACGCCAATAACATCATCCT
1 TCCATCACCATATCACGCCAATAACATCATCCT
* * * *
53426 TCCATTACCATTTCATCACCATTAA-ATCATCCT
1 TCCATCACCATATCA-CGCCAATAACATCATCCT
53459 TC
1 TC
53461 ATTCATCAAC
Statistics
Matches: 60, Mismatches: 6, Indels: 7
0.82 0.08 0.10
Matches are distributed among these distances:
33 24 0.40
34 7 0.12
35 17 0.28
36 12 0.20
ACGTcount: A:0.31, C:0.37, G:0.02, T:0.31
Consensus pattern (33 bp):
TCCATCACCATATCACGCCAATAACATCATCCT
Found at i:55517 original size:18 final size:17
Alignment explanation
Indices: 55496--55575 Score: 53
Period size: 18 Copynumber: 4.6 Consensus size: 17
55486 CCTTGGCTTG
55496 CTTTCTTTTTGAATTTTT
1 CTTTCTTTTTG-ATTTTT
55514 CTTT-TTCTTT--TCTTTT
1 CTTTCTT-TTTGAT-TTTT
*
55530 -ATTCTTTTCTGATTTTT
1 CTTTCTTTT-TGATTTTT
*
55547 CTCTTC-TTTTGTCTTTTT
1 CT-TTCTTTTTG-ATTTTT
55565 CTTTCTTTTTG
1 CTTTCTTTTTG
55576 CACTCCAATT
Statistics
Matches: 49, Mismatches: 3, Indels: 20
0.68 0.04 0.28
Matches are distributed among these distances:
15 5 0.10
16 7 0.14
17 11 0.22
18 23 0.47
19 3 0.06
ACGTcount: A:0.05, C:0.16, G:0.05, T:0.74
Consensus pattern (17 bp):
CTTTCTTTTTGATTTTT
Found at i:55534 original size:13 final size:12
Alignment explanation
Indices: 55510--55568 Score: 57
Period size: 13 Copynumber: 4.7 Consensus size: 12
55500 CTTTTTGAAT
55510 TTTTC-TTTTTC
1 TTTTCTTTTTTC
55521 TTTTCTTTTATTC
1 TTTTCTTTT-TTC
55534 TTTTCTGATTTTTC
1 TTTTCT--TTTTTC
* *
55548 TCTTCTTTTGTC
1 TTTTCTTTTTTC
55560 TTTTTCTTT
1 -TTTTCTTT
55569 CTTTTTGCAC
Statistics
Matches: 40, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
11 5 0.12
12 8 0.20
13 16 0.40
14 8 0.20
15 3 0.08
ACGTcount: A:0.03, C:0.17, G:0.03, T:0.76
Consensus pattern (12 bp):
TTTTCTTTTTTC
Found at i:63647 original size:59 final size:59
Alignment explanation
Indices: 63575--63692 Score: 218
Period size: 59 Copynumber: 2.0 Consensus size: 59
63565 TAAAAATGTG
* *
63575 AACTGTAGGTTATTTAATATTCAGTATGTAATATATTAAACAACCTATTATCTAAGGGT
1 AACTATAGGTTATTTAATATTCAATATGTAATATATTAAACAACCTATTATCTAAGGGT
63634 AACTATAGGTTATTTAATATTCAATATGTAATATATTAAACAACCTATTATCTAAGGGT
1 AACTATAGGTTATTTAATATTCAATATGTAATATATTAAACAACCTATTATCTAAGGGT
63693 TCTTTCTCAT
Statistics
Matches: 57, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
59 57 1.00
ACGTcount: A:0.39, C:0.10, G:0.12, T:0.39
Consensus pattern (59 bp):
AACTATAGGTTATTTAATATTCAATATGTAATATATTAAACAACCTATTATCTAAGGGT
Found at i:75267 original size:30 final size:33
Alignment explanation
Indices: 75208--75268 Score: 92
Period size: 32 Copynumber: 1.9 Consensus size: 33
75198 TTGATAACAT
*
75208 TTCTATCCATTTCGTTTCTTATCATTTCCATTC
1 TTCTATCCATTTCGTATCTTATCATTTCCATTC
75241 TTCT-TCCATTTCGTAT-TTAT-ATTTCCAT
1 TTCTATCCATTTCGTATCTTATCATTTCCAT
75269 CTTAATAATT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
30 8 0.30
31 4 0.15
32 11 0.41
33 4 0.15
ACGTcount: A:0.16, C:0.25, G:0.03, T:0.56
Consensus pattern (33 bp):
TTCTATCCATTTCGTATCTTATCATTTCCATTC
Found at i:75756 original size:17 final size:17
Alignment explanation
Indices: 75705--75759 Score: 51
Period size: 17 Copynumber: 3.4 Consensus size: 17
75695 GTAAGTTATC
* *
75705 TTCACTTTC-TTACTAT
1 TTCATTTTCTTTAGTAT
*
75721 TTCA-TTTCTTTAGTCT
1 TTCATTTTCTTTAGTAT
* *
75737 TTCATTTTTTTTATTAT
1 TTCATTTTCTTTAGTAT
75754 TTCATT
1 TTCATT
75760 ACCATATATT
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
15 4 0.12
16 13 0.41
17 15 0.47
ACGTcount: A:0.16, C:0.16, G:0.02, T:0.65
Consensus pattern (17 bp):
TTCATTTTCTTTAGTAT
Found at i:84297 original size:24 final size:24
Alignment explanation
Indices: 84252--84298 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
84242 CTTTTCTTCT
*
84252 TTTTGAGTGTTGGATTTTTCTTTC
1 TTTTGAGTGTTGGATTTGTCTTTC
*
84276 TTTTGAGTGCTTTG-TTTGTCTTT
1 TTTTGAGTG-TTGGATTTGTCTTT
84299 GCTGGATTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 17 0.85
25 3 0.15
ACGTcount: A:0.06, C:0.09, G:0.21, T:0.64
Consensus pattern (24 bp):
TTTTGAGTGTTGGATTTGTCTTTC
Found at i:86365 original size:1 final size:1
Alignment explanation
Indices: 86361--86396 Score: 54
Period size: 1 Copynumber: 36.0 Consensus size: 1
86351 TCCGAAAATT
* *
86361 AAAAAAAAAAAAAAAAAAAAAAAAGAAAAAGAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
86397 GAATTCTGGT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
1 31 1.00
ACGTcount: A:0.94, C:0.00, G:0.06, T:0.00
Consensus pattern (1 bp):
A
Found at i:95067 original size:16 final size:16
Alignment explanation
Indices: 95033--95081 Score: 53
Period size: 16 Copynumber: 2.9 Consensus size: 16
95023 GTAAGTTATC
* * *
95033 TTCACTTTCTTACTAT
1 TTCATTTTCTTATTCT
95049 TTCATTTTCTTATTCT
1 TTCATTTTCTTATTCT
95065 TTCATCTATTCTTATTC
1 TTCAT-T-TTCTTATTC
95082 CATTGCCTTA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
16 18 0.64
17 1 0.04
18 9 0.32
ACGTcount: A:0.16, C:0.22, G:0.00, T:0.61
Consensus pattern (16 bp):
TTCATTTTCTTATTCT
Found at i:97800 original size:19 final size:19
Alignment explanation
Indices: 97776--97825 Score: 82
Period size: 19 Copynumber: 2.6 Consensus size: 19
97766 GAAACCCCTT
*
97776 TGAAAATACATGATTTTGA
1 TGAAAATACATGATTTTAA
97795 TGAAAATACATGATTTTAA
1 TGAAAATACATGATTTTAA
*
97814 TGAAGATACATG
1 TGAAAATACATG
97826 CTCTTGGCCG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.44, C:0.06, G:0.16, T:0.34
Consensus pattern (19 bp):
TGAAAATACATGATTTTAA
Found at i:109627 original size:18 final size:19
Alignment explanation
Indices: 109606--109650 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 19
109596 ACTTCTCTTT
109606 TTCTTTTCT-TTTCTTT-TC
1 TTCTTTTCTATTT-TTTCTC
109624 TTCTTTTCTGATTTTTTCTC
1 TTCTTTTCT-ATTTTTTCTC
109644 TTCTTTT
1 TTCTTTT
109651 TGCACTCCAA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
18 9 0.38
19 3 0.12
20 12 0.50
ACGTcount: A:0.02, C:0.20, G:0.02, T:0.76
Consensus pattern (19 bp):
TTCTTTTCTATTTTTTCTC
Found at i:111953 original size:24 final size:24
Alignment explanation
Indices: 111929--111983 Score: 69
Period size: 23 Copynumber: 2.4 Consensus size: 24
111919 AAAAATCAGA
*
111929 AAAG-AAAATGAAGCACTCAAAAG
1 AAAGAAAAATCAAGCACTCAAAAG
* *
111952 AAAGAAAAATCCAGCACTC-AAAC
1 AAAGAAAAATCAAGCACTCAAAAG
111975 AAAGAAAAA
1 AAAGAAAAA
111984 GCAAAGAAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
23 16 0.57
24 12 0.43
ACGTcount: A:0.64, C:0.16, G:0.13, T:0.07
Consensus pattern (24 bp):
AAAGAAAAATCAAGCACTCAAAAG
Found at i:111956 original size:23 final size:22
Alignment explanation
Indices: 111929--111982 Score: 63
Period size: 24 Copynumber: 2.4 Consensus size: 22
111919 AAAAATCAGA
* *
111929 AAAGAAAATGAAGCACTCAAAAG
1 AAAGAAAATCAAGCACTC-AAAC
*
111952 AAAGAAAAATCCAGCACTCAAAC
1 AAAG-AAAATCAAGCACTCAAAC
111975 AAAGAAAA
1 AAAGAAAA
111983 AGCAAAGAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
22 4 0.15
23 11 0.41
24 12 0.44
ACGTcount: A:0.63, C:0.17, G:0.13, T:0.07
Consensus pattern (22 bp):
AAAGAAAATCAAGCACTCAAAC
Found at i:115820 original size:15 final size:14
Alignment explanation
Indices: 115800--115834 Score: 52
Period size: 15 Copynumber: 2.4 Consensus size: 14
115790 TGTAGGAGTC
115800 TTTTTCTTTTATTTT
1 TTTTTCTTTT-TTTT
115815 TTTTTCTTTTTTTT
1 TTTTTCTTTTTTTT
115829 TCTTTT
1 T-TTTT
115835 TGTTGCTTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 5 0.26
15 14 0.74
ACGTcount: A:0.03, C:0.09, G:0.00, T:0.89
Consensus pattern (14 bp):
TTTTTCTTTTTTTT
Found at i:115824 original size:9 final size:10
Alignment explanation
Indices: 115798--115835 Score: 58
Period size: 10 Copynumber: 3.7 Consensus size: 10
115788 GATGTAGGAG
115798 TCTTTTTCTTT
1 TCTTTTT-TTT
*
115809 TATTTTTTTT
1 TCTTTTTTTT
115819 TCTTTTTTTT
1 TCTTTTTTTT
115829 TCTTTTT
1 TCTTTTT
115836 GTTGCTTTTA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
10 19 0.76
11 6 0.24
ACGTcount: A:0.03, C:0.11, G:0.00, T:0.87
Consensus pattern (10 bp):
TCTTTTTTTT
Found at i:120110 original size:33 final size:33
Alignment explanation
Indices: 120031--120134 Score: 95
Period size: 33 Copynumber: 3.1 Consensus size: 33
120021 ATACAATCTG
* *
120031 TCCATCACCATTATCACGCCTATATCATCA-CCATAT
1 TCCATCACCA-TATCACGCCAATAACATCATCC---T
120067 TCCATCACCATATCACGCCAATAACATCATCCT
1 TCCATCACCATATCACGCCAATAACATCATCCT
* * * *
120100 TCCATTACCATTTCATCACCATTAA-ATCATCCT
1 TCCATCACCATATCA-CGCCAATAACATCATCCT
120133 TC
1 TC
120135 ATTCATCAAC
Statistics
Matches: 60, Mismatches: 6, Indels: 7
0.82 0.08 0.10
Matches are distributed among these distances:
33 24 0.40
34 7 0.12
35 17 0.28
36 12 0.20
ACGTcount: A:0.31, C:0.37, G:0.02, T:0.31
Consensus pattern (33 bp):
TCCATCACCATATCACGCCAATAACATCATCCT
Found at i:120578 original size:14 final size:15
Alignment explanation
Indices: 120544--120590 Score: 51
Period size: 14 Copynumber: 3.1 Consensus size: 15
120534 AATTTGGAGT
120544 GCAAAAGAAAGAAAA
1 GCAAAAGAAAGAAAA
*
120559 GAAAAAG-AAGAAAA
1 GCAAAAGAAAGAAAA
*
120573 TCAAAAGCAAAAGAAAA
1 GCAAAAG--AAAGAAAA
120590 G
1 G
120591 TGAAGCAAGT
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:124081 original size:33 final size:33
Alignment explanation
Indices: 124002--124105 Score: 95
Period size: 33 Copynumber: 3.1 Consensus size: 33
123992 ATACAATCTG
* *
124002 TCCATCACCATTATCACGCCTATATCATCA-CCATAT
1 TCCATCACCA-TATCACGCCAATAACATCATCC---T
124038 TCCATCACCATATCACGCCAATAACATCATCCT
1 TCCATCACCATATCACGCCAATAACATCATCCT
* * * *
124071 TCCATTACCATTTCATCACCATTAA-ATCATCCT
1 TCCATCACCATATCA-CGCCAATAACATCATCCT
124104 TC
1 TC
124106 ATTCATCAAC
Statistics
Matches: 60, Mismatches: 6, Indels: 7
0.82 0.08 0.10
Matches are distributed among these distances:
33 24 0.40
34 7 0.12
35 17 0.28
36 12 0.20
ACGTcount: A:0.31, C:0.37, G:0.02, T:0.31
Consensus pattern (33 bp):
TCCATCACCATATCACGCCAATAACATCATCCT
Found at i:127263 original size:10 final size:10
Alignment explanation
Indices: 127248--127291 Score: 63
Period size: 10 Copynumber: 4.3 Consensus size: 10
127238 GTGATTCAAC
127248 TTTCTTTCTT
1 TTTCTTTCTT
127258 TTTCTTT-TCT
1 TTTCTTTCT-T
127268 TTTCTTTTCTT
1 TTTC-TTTCTT
127279 TTTCTTTCTT
1 TTTCTTTCTT
127289 TTT
1 TTT
127292 GAGTGCTTTC
Statistics
Matches: 31, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
9 1 0.03
10 21 0.68
11 8 0.26
12 1 0.03
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (10 bp):
TTTCTTTCTT
Found at i:127267 original size:5 final size:5
Alignment explanation
Indices: 127248--127290 Score: 54
Period size: 5 Copynumber: 8.6 Consensus size: 5
127238 GTGATTCAAC
127248 TTTC- TTTCTT TTTCT TTTCT TTTCT TTTCT TTT-T CTTTCT TTT
1 TTTCT TTTC-T TTTCT TTTCT TTTCT TTTCT TTTCT -TTTCT TTT
127291 TGAGTGCTTT
Statistics
Matches: 35, Mismatches: 0, Indels: 7
0.83 0.00 0.17
Matches are distributed among these distances:
4 5 0.14
5 25 0.71
6 5 0.14
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (5 bp):
TTTCT
Found at i:127268 original size:15 final size:16
Alignment explanation
Indices: 127248--127291 Score: 65
Period size: 15 Copynumber: 2.8 Consensus size: 16
127238 GTGATTCAAC
127248 TTTCTTTCTTTTTC-T
1 TTTCTTTCTTTTTCTT
127263 TTTCTTT-TCTTTTCTT
1 TTTCTTTCT-TTTTCTT
127279 TTTCTTTCTTTTT
1 TTTCTTTCTTTTT
127292 GAGTGCTTTC
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
14 1 0.04
15 12 0.46
16 12 0.46
17 1 0.04
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (16 bp):
TTTCTTTCTTTTTCTT
Found at i:144070 original size:19 final size:20
Alignment explanation
Indices: 144024--144073 Score: 66
Period size: 19 Copynumber: 2.5 Consensus size: 20
144014 AAACCCCTTT
* *
144024 GAAAATACATGATTTTTGAT
1 GAAAATACATGATTTTTAAC
144044 GAAAATACATGA-TTTTAAC
1 GAAAATACATGATTTTTAAC
*
144063 GAAGATACATG
1 GAAAATACATG
144074 CTCTTAGCCG
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
19 15 0.56
20 12 0.44
ACGTcount: A:0.44, C:0.08, G:0.16, T:0.32
Consensus pattern (20 bp):
GAAAATACATGATTTTTAAC
Found at i:145024 original size:30 final size:31
Alignment explanation
Indices: 144983--145042 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 31
144973 ACATGCTGCC
**
144983 ATGATATCTAAATGAAATGCAAACATAATAA
1 ATGATATCTAAAACAAATGCAAACATAATAA
* *
145014 ATGA-ATCTAAAACATATGTAAACATAATA
1 ATGATATCTAAAACAAATGCAAACATAATA
145043 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:0.55, C:0.10, G:0.08, T:0.27
Consensus pattern (31 bp):
ATGATATCTAAAACAAATGCAAACATAATAA
Found at i:148263 original size:19 final size:20
Alignment explanation
Indices: 148220--148272 Score: 63
Period size: 19 Copynumber: 2.6 Consensus size: 20
148210 GAAACCCCTT
*
148220 TGAAAATACATGATTTTTTTTA
1 TGAAAATACATGA--TTTTTAA
148242 TGAAAATACATGA-TTTTAA
1 TGAAAATACATGATTTTTAA
*
148261 TGAAGATACATG
1 TGAAAATACATG
148273 CTCTTGGCCG
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
19 16 0.55
22 13 0.45
ACGTcount: A:0.42, C:0.06, G:0.13, T:0.40
Consensus pattern (20 bp):
TGAAAATACATGATTTTTAA
Found at i:150415 original size:29 final size:27
Alignment explanation
Indices: 150368--150426 Score: 82
Period size: 29 Copynumber: 2.1 Consensus size: 27
150358 AGAAAAAAAT
*
150368 GGAAAGGTAGAAGAAAGGATAATGAAA
1 GGAAAGGTAGAAGAAAGGAAAATGAAA
*
150395 GGAAATGGTTGAAGACAAGGAAAATGAAA
1 GGAAA-GGTAGAAGA-AAGGAAAATGAAA
150424 GGA
1 GGA
150427 TAGAAAATGA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
27 5 0.18
28 8 0.29
29 15 0.54
ACGTcount: A:0.53, C:0.02, G:0.34, T:0.12
Consensus pattern (27 bp):
GGAAAGGTAGAAGAAAGGAAAATGAAA
Found at i:150625 original size:19 final size:18
Alignment explanation
Indices: 150603--150647 Score: 56
Period size: 19 Copynumber: 2.5 Consensus size: 18
150593 CCTTTTCTTT
*
150603 TCTTCTTTTCTGATTTTTC
1 TCTTCTTTTAT-ATTTTTC
*
150622 TCTTCTTTTATCTTTTTC
1 TCTTCTTTTATATTTTTC
150640 T-TTCTTTT
1 TCTTCTTTT
150648 TGCACTCCAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
17 7 0.29
18 7 0.29
19 10 0.42
ACGTcount: A:0.04, C:0.20, G:0.02, T:0.73
Consensus pattern (18 bp):
TCTTCTTTTATATTTTTC
Found at i:150643 original size:22 final size:20
Alignment explanation
Indices: 150590--150644 Score: 51
Period size: 19 Copynumber: 2.8 Consensus size: 20
150580 TTTCTTTTTC
*
150590 TTTCCTTTTCTTT-TCTTCT
1 TTTCTTTTTCTTTCTCTTCT
**
150609 TTTCTGATT-TTTCTCTTCTT
1 TTTCTTTTTCTTTCTCTTC-T
150629 TTATCTTTTTCTTTCT
1 TT-TCTTTTTCTTTCT
150645 TTTTGCACTC
Statistics
Matches: 27, Mismatches: 5, Indels: 5
0.73 0.14 0.14
Matches are distributed among these distances:
18 3 0.11
19 11 0.41
20 3 0.11
21 5 0.19
22 5 0.19
ACGTcount: A:0.04, C:0.22, G:0.02, T:0.73
Consensus pattern (20 bp):
TTTCTTTTTCTTTCTCTTCT
Found at i:150952 original size:19 final size:20
Alignment explanation
Indices: 150913--150952 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 20
150903 GAATAATAAT
150913 ATAAGTAATGAAAAGAAATA
1 ATAAGTAATGAAAAGAAATA
*
150933 ATAAG-AATGAAATGAAATA
1 ATAAGTAATGAAAAGAAATA
150952 A
1 A
150953 GGATGGGATA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 14 0.74
20 5 0.26
ACGTcount: A:0.65, C:0.00, G:0.15, T:0.20
Consensus pattern (20 bp):
ATAAGTAATGAAAAGAAATA
Found at i:163904 original size:35 final size:35
Alignment explanation
Indices: 163865--163956 Score: 121
Period size: 35 Copynumber: 2.6 Consensus size: 35
163855 ATTGGTGGTT
*
163865 ATATAGGCGTTAAATGGTGATAGAAGATGGTAATG
1 ATATAGGCGTGAAATGGTGATAGAAGATGGTAATG
* * * *
163900 ATATAGGCGTGCAATGGTAATGGAAGATGGTGATG
1 ATATAGGCGTGAAATGGTGATAGAAGATGGTAATG
*
163935 TTATAGGCGTGAAGATGGTGAT
1 ATATAGGCGTGAA-ATGGTGAT
163957 GTTTAGGTAG
Statistics
Matches: 48, Mismatches: 8, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
35 41 0.85
36 7 0.15
ACGTcount: A:0.33, C:0.04, G:0.35, T:0.28
Consensus pattern (35 bp):
ATATAGGCGTGAAATGGTGATAGAAGATGGTAATG
Found at i:166867 original size:33 final size:33
Alignment explanation
Indices: 166825--166893 Score: 86
Period size: 33 Copynumber: 2.1 Consensus size: 33
166815 GTTGATGAAT
*
166825 GAAGGATGAT-TTAATGGTGATGAAATGGTAATG
1 GAAGGATGATGTTAATGGCG-TGAAATGGTAATG
* * *
166858 GAAGGATGATGTTATTGGCGTGATATGGTGATG
1 GAAGGATGATGTTAATGGCGTGAAATGGTAATG
166891 GAA
1 GAA
166894 TATGGTGATG
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
33 24 0.77
34 7 0.23
ACGTcount: A:0.32, C:0.01, G:0.36, T:0.30
Consensus pattern (33 bp):
GAAGGATGATGTTAATGGCGTGAAATGGTAATG
Found at i:168988 original size:26 final size:26
Alignment explanation
Indices: 168952--169038 Score: 129
Period size: 26 Copynumber: 3.3 Consensus size: 26
168942 TAGGGTCTAA
* *
168952 AAATGGCTATGGTAGGGGTAGGATAG
1 AAATGGTTATGATAGGGGTAGGATAG
*
168978 AAATGGTTATGATAGGGGTCGGATAG
1 AAATGGTTATGATAGGGGTAGGATAG
*
169004 AAATGGTTATGATAGGGGTAGGATGG
1 AAATGGTTATGATAGGGGTAGGATAG
*
169030 AAAAGGTTA
1 AAATGGTTA
169039 AGAAGTGGAT
Statistics
Matches: 55, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
26 55 1.00
ACGTcount: A:0.33, C:0.02, G:0.39, T:0.25
Consensus pattern (26 bp):
AAATGGTTATGATAGGGGTAGGATAG
Found at i:169836 original size:36 final size:35
Alignment explanation
Indices: 169742--169847 Score: 142
Period size: 35 Copynumber: 3.0 Consensus size: 35
169732 ATTAGTGGTT
* *
169742 ATATAGGCGTGAAATGGTGATAGAAGATGGTAATG
1 ATATAGGCGTGAAATGGTGATGGAAGATGGTGATG
* * *
169777 ATATAGGTGTGCAATGGTAATGGAAGATGGTGAT-
1 ATATAGGCGTGAAATGGTGATGGAAGATGGTGATG
169811 ATTATAGGCGTGAAAATGGTGATGGAAGATGGTGATG
1 A-TATAGGCGTG-AAATGGTGATGGAAGATGGTGATG
169848 TTTACGTAGT
Statistics
Matches: 60, Mismatches: 8, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
34 1 0.02
35 38 0.63
36 21 0.35
ACGTcount: A:0.34, C:0.03, G:0.36, T:0.27
Consensus pattern (35 bp):
ATATAGGCGTGAAATGGTGATGGAAGATGGTGATG
Found at i:171329 original size:19 final size:19
Alignment explanation
Indices: 171285--171332 Score: 78
Period size: 19 Copynumber: 2.5 Consensus size: 19
171275 GAAATCCCTT
*
171285 TGAAAAGACATGATTTTAA
1 TGAAAATACATGATTTTAA
*
171304 TGAAAATACATTATTTTAA
1 TGAAAATACATGATTTTAA
171323 TGAAAATACA
1 TGAAAATACA
171333 CGCTCTTAGC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.50, C:0.06, G:0.10, T:0.33
Consensus pattern (19 bp):
TGAAAATACATGATTTTAA
Found at i:176489 original size:14 final size:14
Alignment explanation
Indices: 176470--176502 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
176460 GTGCTTCCAA
176470 CTTTTCTTTCTT-TT
1 CTTTTCTTT-TTCTT
176484 CTTTTCTTTTTCTT
1 CTTTTCTTTTTCTT
176498 CTTTT
1 CTTTT
176503 TGAGTGCTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 2 0.11
14 16 0.89
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (14 bp):
CTTTTCTTTTTCTT
Found at i:179893 original size:33 final size:33
Alignment explanation
Indices: 179851--179919 Score: 86
Period size: 33 Copynumber: 2.1 Consensus size: 33
179841 GGTGATGAAT
*
179851 GAAGGATGAT-TTAATGGTGATGAAATGGTAATG
1 GAAGGATGATGTTAATGGCG-TGAAATGGTAATG
* * *
179884 GAAGGATGATGTTATTGGCGTGATATGGTGATG
1 GAAGGATGATGTTAATGGCGTGAAATGGTAATG
179917 GAA
1 GAA
179920 TATGGTGATG
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
33 24 0.77
34 7 0.23
ACGTcount: A:0.32, C:0.01, G:0.36, T:0.30
Consensus pattern (33 bp):
GAAGGATGATGTTAATGGCGTGAAATGGTAATG
Found at i:183436 original size:17 final size:16
Alignment explanation
Indices: 183406--183456 Score: 52
Period size: 17 Copynumber: 3.1 Consensus size: 16
183396 GTAGGAGTCT
183406 TTTTCTTTTATCTTTTG
1 TTTTCTTTT-TCTTTTG
183423 TTTTCTTCTTTCTTGTTG
1 TTTTCTT-TTTCTT-TTG
*
183441 CTTT-TTTTT-TTTTG
1 TTTTCTTTTTCTTTTG
183455 TT
1 TT
183457 GTTGTAGCAC
Statistics
Matches: 30, Mismatches: 2, Indels: 7
0.77 0.05 0.18
Matches are distributed among these distances:
14 4 0.13
15 2 0.07
16 3 0.10
17 13 0.43
18 8 0.27
ACGTcount: A:0.02, C:0.12, G:0.08, T:0.78
Consensus pattern (16 bp):
TTTTCTTTTTCTTTTG
Found at i:183841 original size:33 final size:33
Alignment explanation
Indices: 183799--183867 Score: 86
Period size: 33 Copynumber: 2.1 Consensus size: 33
183789 GGTGATGAAT
*
183799 GAAGGATGAT-TTAATGGTGATGAAATGGTAATG
1 GAAGGATGATGTTAATGGCG-TGAAATGGTAATG
* * *
183832 GAAGGATGATGTTATTGGCGTGATATGGTGATG
1 GAAGGATGATGTTAATGGCGTGAAATGGTAATG
183865 GAA
1 GAA
183868 TATGGTGATG
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
33 24 0.77
34 7 0.23
ACGTcount: A:0.32, C:0.01, G:0.36, T:0.30
Consensus pattern (33 bp):
GAAGGATGATGTTAATGGCGTGAAATGGTAATG
Found at i:189365 original size:72 final size:71
Alignment explanation
Indices: 189247--189385 Score: 165
Period size: 72 Copynumber: 1.9 Consensus size: 71
189237 AATACATCCT
* * * * * *
189247 TTGGCTGAATTCATCCCACCTTGTATGAACTTGTTGATTTGTCTTCTATGGATGAATGTTCATGA
1 TTGGCTGAATTCATCCCACCTTGTATGAACATGCTGATTTGGCTTCT-TGCATGAATATGCATGA
189312 ATGTATC
65 ATGTATC
* *
189319 TTGGCTGAAATTCTTCCC-CCTTGTGTGAACATGACT-ATTTGGCTTCTTGCATGAATATGCATG
1 TTGGCTG-AATTCATCCCACCTTGTATGAACATG-CTGATTTGGCTTCTTGCATGAATATGCATG
189382 AATG
64 AATG
189386 GATGAATTTA
Statistics
Matches: 57, Mismatches: 8, Indels: 5
0.81 0.11 0.07
Matches are distributed among these distances:
71 17 0.30
72 30 0.53
73 10 0.18
ACGTcount: A:0.22, C:0.18, G:0.20, T:0.40
Consensus pattern (71 bp):
TTGGCTGAATTCATCCCACCTTGTATGAACATGCTGATTTGGCTTCTTGCATGAATATGCATGAA
TGTATC
Found at i:201059 original size:11 final size:11
Alignment explanation
Indices: 201045--201100 Score: 51
Period size: 13 Copynumber: 4.7 Consensus size: 11
201035 TCTTTTTGAA
201045 TTCTTTTTCTT
1 TTCTTTTTCTT
201056 TTCTTTTCTTCTT
1 TTC-TTT-TTCTT
*
201069 TTCTTCTTCTTTT
1 TTCTT-TT-TCTT
201082 TGTCTTTTTC-T
1 T-TCTTTTTCTT
201093 TTCTTTTT
1 TTCTTTTT
201101 GCACTCCAAT
Statistics
Matches: 38, Mismatches: 2, Indels: 11
0.75 0.04 0.22
Matches are distributed among these distances:
10 7 0.18
11 5 0.13
12 7 0.18
13 15 0.39
14 4 0.11
ACGTcount: A:0.00, C:0.20, G:0.02, T:0.79
Consensus pattern (11 bp):
TTCTTTTTCTT
Found at i:201069 original size:19 final size:18
Alignment explanation
Indices: 201045--201100 Score: 71
Period size: 18 Copynumber: 3.1 Consensus size: 18
201035 TCTTTTTGAA
201045 TTCTTTTTCTTTTCTTTT
1 TTCTTTTTCTTTTCTTTT
201063 CTTC-TTTTCTTCTTCTTTT
1 -TTCTTTTTCTT-TTCTTTT
201082 TGTCTTTTTC-TTTCTTTT
1 T-TCTTTTTCTTTTCTTTT
201100 T
1 T
201101 GCACTCCAAT
Statistics
Matches: 34, Mismatches: 0, Indels: 7
0.83 0.00 0.17
Matches are distributed among these distances:
18 16 0.47
19 13 0.38
20 5 0.15
ACGTcount: A:0.00, C:0.20, G:0.02, T:0.79
Consensus pattern (18 bp):
TTCTTTTTCTTTTCTTTT
Found at i:201478 original size:20 final size:21
Alignment explanation
Indices: 201441--201479 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
201431 GATGGTCTTG
*
201441 ATGAAGGATGTTGATGATGAA
1 ATGAAGGATGGTGATGATGAA
*
201462 ATGAA-GATGGTGGTGATG
1 ATGAAGGATGGTGATGATG
201480 TTGTATCTCA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 11 0.69
21 5 0.31
ACGTcount: A:0.33, C:0.00, G:0.38, T:0.28
Consensus pattern (21 bp):
ATGAAGGATGGTGATGATGAA
Found at i:205229 original size:20 final size:20
Alignment explanation
Indices: 205199--205244 Score: 74
Period size: 20 Copynumber: 2.2 Consensus size: 20
205189 CTCATCCATG
205199 CATGTCTTCATTAATTCCTCC
1 CATG-CTTCATTAATTCCTCC
*
205220 TATGCTTCATTAATTCCTCC
1 CATGCTTCATTAATTCCTCC
205240 CATGC
1 CATGC
205245 ATAAGTCTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 20 0.87
21 3 0.13
ACGTcount: A:0.20, C:0.33, G:0.07, T:0.41
Consensus pattern (20 bp):
CATGCTTCATTAATTCCTCC
Found at i:219580 original size:33 final size:33
Alignment explanation
Indices: 219536--219604 Score: 86
Period size: 33 Copynumber: 2.1 Consensus size: 33
219526 AATCACCATA
*
219536 TTCCATCACCATATCA-CGCCAATAACATCATCC
1 TTCCATCACCATATCATCACCAATAA-ATCATCC
* * *
219569 TTCCATTACCATTTCATCACCATTAAATCATCC
1 TTCCATCACCATATCATCACCAATAAATCATCC
219602 TTC
1 TTC
219605 ATTCATCAAC
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
33 24 0.77
34 7 0.23
ACGTcount: A:0.30, C:0.36, G:0.01, T:0.32
Consensus pattern (33 bp):
TTCCATCACCATATCATCACCAATAAATCATCC
Found at i:222440 original size:21 final size:22
Alignment explanation
Indices: 222415--222467 Score: 58
Period size: 21 Copynumber: 2.5 Consensus size: 22
222405 AGTGCAAAAG
222415 GAAAAGAAAAGAT-A-AAAAGAA
1 GAAAAGAAAA-ATCAGAAAAGAA
*
222436 GAAAA-AAAATTCAGAAAAGAA
1 GAAAAGAAAAATCAGAAAAGAA
*
222457 TAAAAGAAAAA
1 GAAAAGAAAAA
222468 GACAATCAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
19 1 0.04
20 5 0.19
21 16 0.62
22 4 0.15
ACGTcount: A:0.75, C:0.02, G:0.15, T:0.08
Consensus pattern (22 bp):
GAAAAGAAAAATCAGAAAAGAA
Found at i:223729 original size:19 final size:21
Alignment explanation
Indices: 223686--223737 Score: 81
Period size: 19 Copynumber: 2.6 Consensus size: 21
223676 TGAAACCCTT
223686 TGAAAATACATGATTTTTAAA
1 TGAAAATACATGATTTTTAAA
223707 TGAAAATACATGA-TTTT-AA
1 TGAAAATACATGATTTTTAAA
*
223726 TGAAGATACATG
1 TGAAAATACATG
223738 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:224756 original size:30 final size:31
Alignment explanation
Indices: 224716--224775 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 31
224706 ACATGCTGCC
**
224716 ATGATATCTAAATGAAATGCAAACATAATAA
1 ATGATATCTAAAACAAATGCAAACATAATAA
* *
224747 ATGA-ATCTAAAACATATGTAAACATAATA
1 ATGATATCTAAAACAAATGCAAACATAATA
224776 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:0.55, C:0.10, G:0.08, T:0.27
Consensus pattern (31 bp):
ATGATATCTAAAACAAATGCAAACATAATAA
Found at i:231034 original size:18 final size:19
Alignment explanation
Indices: 230992--231047 Score: 57
Period size: 18 Copynumber: 3.1 Consensus size: 19
230982 CAAGTGCTGC
*
230992 AACAAAAGAAACAA-AAAG
1 AACAAAAGAAAGAAGAAAG
231010 AGA-AAAAGAAAGAAGAAA-
1 A-ACAAAAGAAAGAAGAAAG
*
231028 AACAAAAAAAAG-AGAAAG
1 AACAAAAGAAAGAAGAAAG
231046 AA
1 AA
231048 AAGACTCCTA
Statistics
Matches: 32, Mismatches: 2, Indels: 8
0.76 0.05 0.19
Matches are distributed among these distances:
17 6 0.19
18 22 0.69
19 4 0.12
ACGTcount: A:0.79, C:0.05, G:0.16, T:0.00
Consensus pattern (19 bp):
AACAAAAGAAAGAAGAAAG
Found at i:231282 original size:16 final size:16
Alignment explanation
Indices: 231243--231301 Score: 59
Period size: 16 Copynumber: 3.6 Consensus size: 16
231233 GAGTTATAAG
231243 TTATCTTCACTTTC-TTA
1 TTAT-TTCA-TTTCTTTA
*
231260 CTATTTCATTTCTTTA
1 TTATTTCATTTCTTTA
*
231276 GTT-TTTCATTTTTTTA
1 -TTATTTCATTTCTTTA
231292 TTATTTCATT
1 TTATTTCATT
231302 ACCATATCTT
Statistics
Matches: 36, Mismatches: 3, Indels: 7
0.78 0.07 0.15
Matches are distributed among these distances:
15 6 0.17
16 26 0.72
17 4 0.11
ACGTcount: A:0.17, C:0.15, G:0.02, T:0.66
Consensus pattern (16 bp):
TTATTTCATTTCTTTA
Found at i:234210 original size:14 final size:13
Alignment explanation
Indices: 234193--234242 Score: 52
Period size: 14 Copynumber: 3.9 Consensus size: 13
234183 GTGCAAAAAG
234193 AAAGAAAAAGACAA
1 AAAGAAAAAGA-AA
*
234207 AAAGAAGAAGAAA
1 AAAGAAAAAGAAA
234220 AGAAG-AAAAG--A
1 A-AAGAAAAAGAAA
234231 AAAGAAAAAGAA
1 AAAGAAAAAGAA
234243 TTCAAAAAGA
Statistics
Matches: 30, Mismatches: 2, Indels: 9
0.73 0.05 0.22
Matches are distributed among these distances:
10 3 0.10
11 7 0.23
13 7 0.23
14 13 0.43
ACGTcount: A:0.78, C:0.02, G:0.20, T:0.00
Consensus pattern (13 bp):
AAAGAAAAAGAAA
Found at i:234239 original size:19 final size:18
Alignment explanation
Indices: 234187--234242 Score: 71
Period size: 19 Copynumber: 3.1 Consensus size: 18
234177 ATTGGAGTGC
234187 AAAAAG-AAAGAAAAAGA
1 AAAAAGAAAAGAAAAAGA
234204 CAAAAAGAAGAAG-AAAAGA
1 -AAAAAGAA-AAGAAAAAGA
234223 AGAAAAGAAAAGAAAAAGA
1 A-AAAAGAAAAGAAAAAGA
234242 A
1 A
234243 TTCAAAAAGA
Statistics
Matches: 34, Mismatches: 0, Indels: 7
0.83 0.00 0.17
Matches are distributed among these distances:
18 10 0.29
19 21 0.62
20 3 0.09
ACGTcount: A:0.79, C:0.02, G:0.20, T:0.00
Consensus pattern (18 bp):
AAAAAGAAAAGAAAAAGA
Found at i:234240 original size:11 final size:11
Alignment explanation
Indices: 234187--234242 Score: 51
Period size: 11 Copynumber: 4.7 Consensus size: 11
234177 ATTGGAGTGC
234187 AAAAAG-AAAG
1 AAAAAGAAAAG
234197 AAAAAGACAAAAAG
1 AAAAAG---AAAAG
*
234211 AAGAAGAAAAG
1 AAAAAGAAAAG
234222 AAGAAAAGAAAAG
1 -A-AAAAGAAAAG
234235 AAAAAGAA
1 AAAAAGAA
234243 TTCAAAAAGA
Statistics
Matches: 38, Mismatches: 2, Indels: 11
0.75 0.04 0.22
Matches are distributed among these distances:
10 6 0.16
11 12 0.32
12 2 0.05
13 9 0.24
14 9 0.24
ACGTcount: A:0.79, C:0.02, G:0.20, T:0.00
Consensus pattern (11 bp):
AAAAAGAAAAG
Found at i:237928 original size:14 final size:14
Alignment explanation
Indices: 237909--237941 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
237899 AAAGCACTCA
237909 AAAAGAAGAA-AAAG
1 AAAAGAA-AAGAAAG
237923 AAAAGAAAAGAAAG
1 AAAAGAAAAGAAAG
237937 AAAAG
1 AAAAG
237942 TTGGAAGCAC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 2 0.11
14 16 0.89
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (14 bp):
AAAAGAAAAGAAAG
Found at i:242141 original size:14 final size:14
Alignment explanation
Indices: 242122--242154 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
242112 AAAGCACTCA
242122 AAAAGAAGAA-AAAG
1 AAAAGAA-AAGAAAG
242136 AAAAGAAAAGAAAG
1 AAAAGAAAAGAAAG
242150 AAAAG
1 AAAAG
242155 TTGGAAGCAC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 2 0.11
14 16 0.89
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (14 bp):
AAAAGAAAAGAAAG
Found at i:256482 original size:20 final size:20
Alignment explanation
Indices: 256446--256483 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
256436 GGGTAATAAT
256446 ATAAGTAATGAAAGAAAAGA
1 ATAAGTAATGAAAGAAAAGA
256466 ATAAG-AATGAAATGAAAA
1 ATAAGTAATGAAA-GAAAA
256484 AAAAATTATA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 7 0.41
20 10 0.59
ACGTcount: A:0.66, C:0.00, G:0.18, T:0.16
Consensus pattern (20 bp):
ATAAGTAATGAAAGAAAAGA
Found at i:270261 original size:19 final size:22
Alignment explanation
Indices: 270239--270286 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 22
270229 CTTTTTGAAC
270239 TTCTCTTT-TTCTTTT-T-TTT
1 TTCTCTTTCTTCTTTTCTATTT
270258 TTCT-TTTCTTCTTTTCTGATTT
1 TTCTCTTTCTTCTTTTCT-ATTT
270280 TTCTCTT
1 TTCTCTT
270287 CTTTTTGCAC
Statistics
Matches: 24, Mismatches: 0, Indels: 6
0.80 0.00 0.20
Matches are distributed among these distances:
18 3 0.12
19 11 0.46
20 1 0.04
22 7 0.29
23 2 0.08
ACGTcount: A:0.02, C:0.19, G:0.02, T:0.77
Consensus pattern (22 bp):
TTCTCTTTCTTCTTTTCTATTT
Found at i:273587 original size:13 final size:13
Alignment explanation
Indices: 273566--273603 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 13
273556 TTTTTTGAAC
273566 TTCTCTTTTTCTTT
1 TTCT-TTTTTCTTT
273580 TTCTTTTTTC-TT
1 TTCTTTTTTCTTT
273592 TTCTTCTTTTCT
1 TTCTT-TTTTCT
273604 GATTTTTCTC
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
12 7 0.32
13 11 0.50
14 4 0.18
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (13 bp):
TTCTTTTTTCTTT
Found at i:278164 original size:10 final size:9
Alignment explanation
Indices: 278148--278180 Score: 50
Period size: 10 Copynumber: 3.7 Consensus size: 9
278138 TTTAAACTTC
278148 TCTTTTTTT
1 TCTTTTTTT
278157 TCCTTTTTTT
1 T-CTTTTTTT
278167 TC-TTTTTT
1 TCTTTTTTT
278175 TCTTTT
1 TCTTTT
278181 CTTCTTTTCT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
8 8 0.36
9 5 0.23
10 9 0.41
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (9 bp):
TCTTTTTTT
Found at i:278188 original size:22 final size:21
Alignment explanation
Indices: 278164--278205 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 21
278154 TTTTCCTTTT
*
278164 TTTTCTTTTTTTCTTTTCTTC
1 TTTTCTATTTTTCTTTTCTTC
*
278185 TTTTCTGATTTTTCTCTTCTT
1 TTTTCT-ATTTTTCTTTTCTT
278206 TTTGCACTCC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 6 0.33
22 12 0.67
ACGTcount: A:0.02, C:0.19, G:0.02, T:0.76
Consensus pattern (21 bp):
TTTTCTATTTTTCTTTTCTTC
Found at i:281087 original size:20 final size:20
Alignment explanation
Indices: 281051--281088 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
281041 TTTTTATTTA
*
281051 TTTCATTTCTATTCTTATTC
1 TTTCATTTCCATTCTTATTC
281071 TTTCA-TTCCATTACTTAT
1 TTTCATTTCCATT-CTTAT
281089 ATTATTATTC
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 6 0.38
20 10 0.62
ACGTcount: A:0.18, C:0.21, G:0.00, T:0.61
Consensus pattern (20 bp):
TTTCATTTCCATTCTTATTC
Found at i:281408 original size:18 final size:18
Alignment explanation
Indices: 281356--281400 Score: 56
Period size: 20 Copynumber: 2.4 Consensus size: 18
281346 TTGGAGTGCA
281356 AAAAGAAGAGAAA-AAATCAG
1 AAAAGAAGA-AAAGAAA--AG
281376 AAAAGAAGAAAAGAAAAG
1 AAAAGAAGAAAAGAAAAG
281394 AAAAGAA
1 AAAAGAA
281401 AAAGAGAAGT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
18 9 0.38
19 3 0.12
20 12 0.50
ACGTcount: A:0.76, C:0.02, G:0.20, T:0.02
Consensus pattern (18 bp):
AAAAGAAGAAAAGAAAAG
Found at i:285654 original size:20 final size:20
Alignment explanation
Indices: 285618--285655 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
285608 TTTTTATTTA
*
285618 TTTCATTTCTATTCTTATTC
1 TTTCATTTCCATTCTTATTC
285638 TTTCA-TTCCATTACTTAT
1 TTTCATTTCCATT-CTTAT
285656 ATTATTATTC
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 6 0.38
20 10 0.62
ACGTcount: A:0.18, C:0.21, G:0.00, T:0.61
Consensus pattern (20 bp):
TTTCATTTCCATTCTTATTC
Found at i:286683 original size:19 final size:20
Alignment explanation
Indices: 286659--286704 Score: 76
Period size: 20 Copynumber: 2.4 Consensus size: 20
286649 GAACTGTATC
*
286659 ATTTTCATT-AAAGTCATGT
1 ATTTTCATTAAAAATCATGT
286678 ATTTTCATTAAAAATCATGT
1 ATTTTCATTAAAAATCATGT
286698 ATTTTCA
1 ATTTTCA
286705 AAGGGATTTC
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
19 9 0.36
20 16 0.64
ACGTcount: A:0.35, C:0.11, G:0.07, T:0.48
Consensus pattern (20 bp):
ATTTTCATTAAAAATCATGT
Found at i:290922 original size:33 final size:33
Alignment explanation
Indices: 290880--290948 Score: 86
Period size: 33 Copynumber: 2.1 Consensus size: 33
290870 GTTGATGAAT
*
290880 GAAGGATGAT-TTAATGGTGATGAAATGGTAATG
1 GAAGGATGATGTTAATGGCG-TGAAATGGTAATG
* * *
290913 GAAGGATGATGTTATTGGCGTGATATGGTGATG
1 GAAGGATGATGTTAATGGCGTGAAATGGTAATG
290946 GAA
1 GAA
290949 TATGGTGATG
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
33 24 0.77
34 7 0.23
ACGTcount: A:0.32, C:0.01, G:0.36, T:0.30
Consensus pattern (33 bp):
GAAGGATGATGTTAATGGCGTGAAATGGTAATG
Found at i:295383 original size:33 final size:33
Alignment explanation
Indices: 295341--295409 Score: 86
Period size: 33 Copynumber: 2.1 Consensus size: 33
295331 GTTGATGAAT
*
295341 GAAGGATGAT-TTAATGGTGATGAAATGGTAATG
1 GAAGGATGATGTTAATGGCG-TGAAATGGTAATG
* * *
295374 GAAGGATGATGTTATTGGCGTGATATGGTGATG
1 GAAGGATGATGTTAATGGCGTGAAATGGTAATG
295407 GAA
1 GAA
295410 TATGGTGATG
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
33 24 0.77
34 7 0.23
ACGTcount: A:0.32, C:0.01, G:0.36, T:0.30
Consensus pattern (33 bp):
GAAGGATGATGTTAATGGCGTGAAATGGTAATG
Found at i:297505 original size:2 final size:2
Alignment explanation
Indices: 297498--297568 Score: 142
Period size: 2 Copynumber: 35.5 Consensus size: 2
297488 TGGCAGTGGA
297498 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
297540 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
297569 ATTTGGTGAT
Statistics
Matches: 69, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 69 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:300213 original size:43 final size:44
Alignment explanation
Indices: 300165--300250 Score: 165
Period size: 43 Copynumber: 2.0 Consensus size: 44
300155 AAATCCTTTG
300165 AAGATGGCGTTGGTGTGCTCACATCAT-CCCCCTTCTTTTATGC
1 AAGATGGCGTTGGTGTGCTCACATCATCCCCCCTTCTTTTATGC
300208 AAGATGGCGTTGGTGTGCTCACATCATCCCCCCTTCTTTTATG
1 AAGATGGCGTTGGTGTGCTCACATCATCCCCCCTTCTTTTATG
300251 TGATTTGTCC
Statistics
Matches: 42, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
43 27 0.64
44 15 0.36
ACGTcount: A:0.16, C:0.28, G:0.21, T:0.35
Consensus pattern (44 bp):
AAGATGGCGTTGGTGTGCTCACATCATCCCCCCTTCTTTTATGC
Found at i:322379 original size:18 final size:18
Alignment explanation
Indices: 322328--322381 Score: 67
Period size: 18 Copynumber: 3.1 Consensus size: 18
322318 ATTGGAGTGC
*
322328 AAAAAAAAG-ACAAAAAG
1 AAAAAAAAGTTCAAAAAG
*
322345 AAAAAAAAATT-AGAAAAG
1 AAAAAAAAGTTCA-AAAAG
322363 AAAAAAAAGTTCAAAAAG
1 AAAAAAAAGTTCAAAAAG
322381 A
1 A
322382 GAAAGAAAGC
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
17 9 0.29
18 21 0.68
19 1 0.03
ACGTcount: A:0.78, C:0.04, G:0.11, T:0.07
Consensus pattern (18 bp):
AAAAAAAAGTTCAAAAAG
Found at i:325403 original size:14 final size:14
Alignment explanation
Indices: 325384--325426 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
325374 ATAAGATACT
* *
325384 ATCTATTCATCATC
1 ATCTATCCATCACC
325398 ATCTATCCATCACC
1 ATCTATCCATCACC
*
325412 ATC-CTCCATCACC
1 ATCTATCCATCACC
325425 AT
1 AT
325427 TCACACCTAT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
13 11 0.42
14 15 0.58
ACGTcount: A:0.28, C:0.40, G:0.00, T:0.33
Consensus pattern (14 bp):
ATCTATCCATCACC
Found at i:330118 original size:19 final size:20
Alignment explanation
Indices: 330090--330129 Score: 73
Period size: 19 Copynumber: 2.0 Consensus size: 20
330080 GAATAATAAT
330090 ATAAGTAATGAAATGAAATA
1 ATAAGTAATGAAATGAAATA
330110 ATAAG-AATGAAATGAAATA
1 ATAAGTAATGAAATGAAATA
330129 A
1 A
330130 AGAAAGGATG
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 15 0.75
20 5 0.25
ACGTcount: A:0.62, C:0.00, G:0.15, T:0.23
Consensus pattern (20 bp):
ATAAGTAATGAAATGAAATA
Found at i:337657 original size:24 final size:24
Alignment explanation
Indices: 337629--337680 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
337619 AAAAATCAGC
* **
337629 AAAGAAAAGTCAAGCACTCCAAAA
1 AAAGAAAAGTCAAGAACTAAAAAA
337653 AAAGAAAAGTCAAGAACTAAAAAA
1 AAAGAAAAGTCAAGAACTAAAAAA
337677 AAAG
1 AAAG
337681 TTGAATCACT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.65, C:0.13, G:0.13, T:0.08
Consensus pattern (24 bp):
AAAGAAAAGTCAAGAACTAAAAAA
Found at i:339536 original size:11 final size:13
Alignment explanation
Indices: 339504--339533 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
339494 TGGCCAAAGA
339504 TGAAAAGGTATGT
1 TGAAAAGGTATGT
339517 TGAAAAGGTATG-
1 TGAAAAGGTATGT
339529 TGAAA
1 TGAAA
339534 GGTGTTTAGT
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:342780 original size:28 final size:28
Alignment explanation
Indices: 342740--342801 Score: 76
Period size: 28 Copynumber: 2.2 Consensus size: 28
342730 AAAGAAATAA
*
342740 AAGACAAAAAGAAGAAA-A-TTCATAAAAG
1 AAGAAAAAAAGAA-AAAGATTTCA-AAAAG
342768 AAGAAAAAAAGAAAAAGATTTCAAAAAG
1 AAGAAAAAAAGAAAAAGATTTCAAAAAG
342796 -AGAAAA
1 AAGAAAA
342802 GCAAGCCAAG
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
27 9 0.29
28 18 0.58
29 4 0.13
ACGTcount: A:0.71, C:0.05, G:0.15, T:0.10
Consensus pattern (28 bp):
AAGAAAAAAAGAAAAAGATTTCAAAAAG
Found at i:345351 original size:30 final size:31
Alignment explanation
Indices: 345299--345358 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 31
345289 CTTAGCTTTA
**
345299 TATTATGTTTACATATGTTTTAGAT-TCATT
1 TATTATGTTTACATATCATTTAGATATCATT
* *
345329 TATTATGTTTGCATTTCATTTAGATATCAT
1 TATTATGTTTACATATCATTTAGATATCAT
345359 GGCAGCATGT
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:0.27, C:0.08, G:0.10, T:0.55
Consensus pattern (31 bp):
TATTATGTTTACATATCATTTAGATATCATT
Found at i:346290 original size:19 final size:21
Alignment explanation
Indices: 346266--346317 Score: 81
Period size: 21 Copynumber: 2.6 Consensus size: 21
346256 CGGCCAAGAG
*
346266 CATGTATCTTCA-TT-AAAAT
1 CATGTATTTTCATTTAAAAAT
346285 CATGTATTTTCATTTAAAAAT
1 CATGTATTTTCATTTAAAAAT
346306 CATGTATTTTCA
1 CATGTATTTTCA
346318 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:349581 original size:30 final size:31
Alignment explanation
Indices: 349529--349588 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 31
349519 CTTAGCTTTA
**
349529 TATTATGTTTACATATGTTTTAGAT-TCATT
1 TATTATGTTTACATATCATTTAGATATCATT
* *
349559 TATTATGTTTGCATTTCATTTAGATATCAT
1 TATTATGTTTACATATCATTTAGATATCAT
349589 GGCAGCATGT
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:0.27, C:0.08, G:0.10, T:0.55
Consensus pattern (31 bp):
TATTATGTTTACATATCATTTAGATATCATT
Found at i:350518 original size:19 final size:21
Alignment explanation
Indices: 350494--350545 Score: 81
Period size: 21 Copynumber: 2.6 Consensus size: 21
350484 CGGCCAAGAG
*
350494 CATGTATCTTCA-TT-AAAAT
1 CATGTATTTTCATTTAAAAAT
350513 CATGTATTTTCATTTAAAAAT
1 CATGTATTTTCATTTAAAAAT
350534 CATGTATTTTCA
1 CATGTATTTTCA
350546 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:357538 original size:19 final size:19
Alignment explanation
Indices: 357510--357549 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
357500 ATCCATCTCT
*
357510 TCCATCAATTCCGCAGCCA
1 TCCATAAATTCCGCAGCCA
* *
357529 TCCATAAATTTCGCAGTCA
1 TCCATAAATTCCGCAGCCA
357548 TC
1 TC
357550 TCTATCCTTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.28, C:0.35, G:0.10, T:0.28
Consensus pattern (19 bp):
TCCATAAATTCCGCAGCCA
Found at i:357586 original size:19 final size:20
Alignment explanation
Indices: 357562--357601 Score: 57
Period size: 19 Copynumber: 2.0 Consensus size: 20
357552 TATCCTTTCT
357562 TTATTTCATTTT-ATT-CTTA
1 TTATTTC-TTTTCATTACTTA
357581 TTATTTCTTTTCATTACTTA
1 TTATTTCTTTTCATTACTTA
357601 T
1 T
357602 ATTATTATTC
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 4 0.21
19 10 0.53
20 5 0.26
ACGTcount: A:0.20, C:0.12, G:0.00, T:0.68
Consensus pattern (20 bp):
TTATTTCTTTTCATTACTTA
Found at i:361301 original size:19 final size:21
Alignment explanation
Indices: 361258--361309 Score: 81
Period size: 19 Copynumber: 2.6 Consensus size: 21
361248 GAAACCCCTT
361258 TGAAAATACATGATTTTTAAA
1 TGAAAATACATGATTTTTAAA
361279 TGAAAATACATGA-TTTT-AA
1 TGAAAATACATGATTTTTAAA
*
361298 TGAAGATACATG
1 TGAAAATACATG
361310 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:362258 original size:30 final size:31
Alignment explanation
Indices: 362218--362277 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 31
362208 ACATGCTGCC
**
362218 ATGATATCTAAATGAAATGCAAACATAATAA
1 ATGATATCTAAAACAAATGCAAACATAATAA
* *
362249 ATGA-ATCTAAAACATATGTAAACATAATA
1 ATGATATCTAAAACAAATGCAAACATAATA
362278 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:0.55, C:0.10, G:0.08, T:0.27
Consensus pattern (31 bp):
ATGATATCTAAAACAAATGCAAACATAATAA
Found at i:364731 original size:11 final size:11
Alignment explanation
Indices: 364717--364772 Score: 51
Period size: 13 Copynumber: 4.7 Consensus size: 11
364707 TCTTTTTGAA
364717 TTCTTTTTCTT
1 TTCTTTTTCTT
364728 TTCTTTTCTTCTT
1 TTC-TTT-TTCTT
*
364741 TTCTTCTTCTTTT
1 TTCTT-TT-TCTT
364754 TGTCTTTTTC-T
1 T-TCTTTTTCTT
364765 TTCTTTTT
1 TTCTTTTT
364773 GCACTCCAAT
Statistics
Matches: 38, Mismatches: 2, Indels: 11
0.75 0.04 0.22
Matches are distributed among these distances:
10 7 0.18
11 5 0.13
12 7 0.18
13 15 0.39
14 4 0.11
ACGTcount: A:0.00, C:0.20, G:0.02, T:0.79
Consensus pattern (11 bp):
TTCTTTTTCTT
Found at i:364741 original size:19 final size:18
Alignment explanation
Indices: 364717--364772 Score: 71
Period size: 18 Copynumber: 3.1 Consensus size: 18
364707 TCTTTTTGAA
364717 TTCTTTTTCTTTTCTTTT
1 TTCTTTTTCTTTTCTTTT
364735 CTTC-TTTTCTTCTTCTTTT
1 -TTCTTTTTCTT-TTCTTTT
364754 TGTCTTTTTC-TTTCTTTT
1 T-TCTTTTTCTTTTCTTTT
364772 T
1 T
364773 GCACTCCAAT
Statistics
Matches: 34, Mismatches: 0, Indels: 7
0.83 0.00 0.17
Matches are distributed among these distances:
18 16 0.47
19 13 0.38
20 5 0.15
ACGTcount: A:0.00, C:0.20, G:0.02, T:0.79
Consensus pattern (18 bp):
TTCTTTTTCTTTTCTTTT
Found at i:365523 original size:21 final size:19
Alignment explanation
Indices: 365497--365546 Score: 64
Period size: 21 Copynumber: 2.5 Consensus size: 19
365487 GAAACCCCTT
365497 TGAAAATACACGATTTTTAAA
1 TGAAAATACACGA-TTTT-AA
*
365518 TGAAAATACATGATTTTAA
1 TGAAAATACACGATTTTAA
*
365537 TGAAGATACA
1 TGAAAATACA
365547 TGCTCTTGGC
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
19 11 0.41
20 4 0.15
21 12 0.44
ACGTcount: A:0.48, C:0.08, G:0.12, T:0.32
Consensus pattern (19 bp):
TGAAAATACACGATTTTAA
Found at i:365540 original size:19 final size:21
Alignment explanation
Indices: 365497--365548 Score: 72
Period size: 19 Copynumber: 2.6 Consensus size: 21
365487 GAAACCCCTT
*
365497 TGAAAATACACGATTTTTAAA
1 TGAAAATACATGATTTTTAAA
365518 TGAAAATACATGA-TTTT-AA
1 TGAAAATACATGATTTTTAAA
*
365537 TGAAGATACATG
1 TGAAAATACATG
365549 CTCTTGGCCG
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
19 13 0.45
20 4 0.14
21 12 0.41
ACGTcount: A:0.46, C:0.08, G:0.13, T:0.33
Consensus pattern (21 bp):
TGAAAATACATGATTTTTAAA
Found at i:366497 original size:30 final size:31
Alignment explanation
Indices: 366457--366516 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 31
366447 ACATGCTGCC
**
366457 ATGATATCTAAATGAAATGCAAACATAATAA
1 ATGATATCTAAAACAAATGCAAACATAATAA
* *
366488 ATGA-ATCTAAAACATATGTAAACATAATA
1 ATGATATCTAAAACAAATGCAAACATAATA
366517 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:0.55, C:0.10, G:0.08, T:0.27
Consensus pattern (31 bp):
ATGATATCTAAAACAAATGCAAACATAATAA
Found at i:368280 original size:19 final size:20
Alignment explanation
Indices: 368251--368292 Score: 59
Period size: 19 Copynumber: 2.1 Consensus size: 20
368241 AGTAGGAGAC
* *
368251 TTTTTCTTTTCTTTTTGGTT
1 TTTTTCTTTTCTTGTTGCTT
368271 TTTTTC-TTTCTTGTTGCTT
1 TTTTTCTTTTCTTGTTGCTT
368290 TTT
1 TTT
368293 GTTGTAGCAC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 14 0.70
20 6 0.30
ACGTcount: A:0.00, C:0.12, G:0.10, T:0.79
Consensus pattern (20 bp):
TTTTTCTTTTCTTGTTGCTT
Found at i:370891 original size:31 final size:31
Alignment explanation
Indices: 370853--370966 Score: 176
Period size: 31 Copynumber: 3.7 Consensus size: 31
370843 TCACTTAAGG
370853 AGCTTCAACTTAGCTGGAGGAGCTAGCATCT
1 AGCTTCAACTTAGCTGGAGGAGCTAGCATCT
370884 AGCTTCAACTTAGCTGGAGGAGCTAGCATCT
1 AGCTTCAACTTAGCTGGAGGAGCTAGCATCT
* *
370915 AGCTTCAACTTAGCTAGAGGAGCTAGTATCT
1 AGCTTCAACTTAGCTGGAGGAGCTAGCATCT
* * *
370946 AGC-TGAACTAAGTTGGAGGAG
1 AGCTTCAACTTAGCTGGAGGAG
370967 AGCTTTGGAC
Statistics
Matches: 77, Mismatches: 6, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
30 14 0.18
31 63 0.82
ACGTcount: A:0.28, C:0.19, G:0.27, T:0.25
Consensus pattern (31 bp):
AGCTTCAACTTAGCTGGAGGAGCTAGCATCT
Found at i:371747 original size:26 final size:26
Alignment explanation
Indices: 371718--371768 Score: 102
Period size: 26 Copynumber: 2.0 Consensus size: 26
371708 CACTACTATT
371718 TCTCATATCATAAATAGCCTACCATG
1 TCTCATATCATAAATAGCCTACCATG
371744 TCTCATATCATAAATAGCCTACCAT
1 TCTCATATCATAAATAGCCTACCAT
371769 TTCACCTTGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.35, C:0.27, G:0.06, T:0.31
Consensus pattern (26 bp):
TCTCATATCATAAATAGCCTACCATG
Found at i:372026 original size:25 final size:26
Alignment explanation
Indices: 371981--372030 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 26
371971 AAATAAATTG
* *
371981 AAGCACTCCAAAAGAAGAAAAAAATC
1 AAGCACTCCAAAAAAAAAAAAAAATC
*
372007 AAGCACTCAAAAAAAAAAAAAAAA
1 AAGCACTCCAAAAAAAAAAAAAAA
372031 AAGAAAAGAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.70, C:0.16, G:0.08, T:0.06
Consensus pattern (26 bp):
AAGCACTCCAAAAAAAAAAAAAAATC
Found at i:377021 original size:36 final size:35
Alignment explanation
Indices: 376970--377080 Score: 152
Period size: 35 Copynumber: 3.2 Consensus size: 35
376960 TAAGATACTA
*
376970 CCTA-AACATCACCATCTTCCATCACCATTTTCATG
1 CCTATAACATCACCATCTTCCATCACCA-TTTCACG
* *
377005 CCTATAACATCACCATCTTCCATTACCATTGCACG
1 CCTATAACATCACCATCTTCCATCACCATTTCACG
* * *
377040 CCTATATCATTACCATCTTCTATCACCATTTCACG
1 CCTATAACATCACCATCTTCCATCACCATTTCACG
377075 CCTATA
1 CCTATA
377081 TAACCACCAA
Statistics
Matches: 67, Mismatches: 8, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
35 45 0.67
36 22 0.33
ACGTcount: A:0.28, C:0.36, G:0.04, T:0.32
Consensus pattern (35 bp):
CCTATAACATCACCATCTTCCATCACCATTTCACG
Found at i:379712 original size:22 final size:22
Alignment explanation
Indices: 379668--379711 Score: 81
Period size: 21 Copynumber: 2.0 Consensus size: 22
379658 TAAGAAATTC
379668 ATCCTGAAAATTAAAAAAAAAA
1 ATCCTGAAAATTAAAAAAAAAA
379690 ATCC-GAAAATTAAAAAAAAAA
1 ATCCTGAAAATTAAAAAAAAAA
379711 A
1 A
379712 AGAAAAGAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
21 18 0.82
22 4 0.18
ACGTcount: A:0.70, C:0.09, G:0.05, T:0.16
Consensus pattern (22 bp):
ATCCTGAAAATTAAAAAAAAAA
Found at i:386892 original size:19 final size:20
Alignment explanation
Indices: 386856--386895 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
386846 GAATAATAAT
386856 ATAAGTAATGAAAAGAAATA
1 ATAAGTAATGAAAAGAAATA
* *
386876 ATAAG-AATGATATGAAATA
1 ATAAGTAATGAAAAGAAATA
386895 A
1 A
386896 GGAAATGATA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 13 0.72
20 5 0.28
ACGTcount: A:0.62, C:0.00, G:0.15, T:0.23
Consensus pattern (20 bp):
ATAAGTAATGAAAAGAAATA
Found at i:391087 original size:13 final size:12
Alignment explanation
Indices: 391071--391127 Score: 53
Period size: 13 Copynumber: 4.7 Consensus size: 12
391061 TTTTTTGAAC
391071 TTCTCTTTTTCTT
1 TTCT-TTTTTCTT
391084 TTCTTTTCTTCTT
1 TTCTTTT-TTCTT
391097 TTCTTTTTT-TT
1 TTCTTTTTTCTT
* ** *
391108 ATGATTTTTCTC
1 TTCTTTTTTCTT
391120 TTCTTTTT
1 TTCTTTTT
391128 GCACTCCAAT
Statistics
Matches: 35, Mismatches: 7, Indels: 5
0.74 0.15 0.11
Matches are distributed among these distances:
11 8 0.23
12 11 0.31
13 16 0.46
ACGTcount: A:0.04, C:0.18, G:0.02, T:0.77
Consensus pattern (12 bp):
TTCTTTTTTCTT
Found at i:391429 original size:19 final size:20
Alignment explanation
Indices: 391393--391432 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
391383 GAATAATAAT
391393 ATAAGTAATGAAAAGAAATA
1 ATAAGTAATGAAAAGAAATA
* *
391413 ATAAG-AATGATATGAAATA
1 ATAAGTAATGAAAAGAAATA
391432 A
1 A
391433 GGAAATGATA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 13 0.72
20 5 0.28
ACGTcount: A:0.62, C:0.00, G:0.15, T:0.23
Consensus pattern (20 bp):
ATAAGTAATGAAAAGAAATA
Found at i:395238 original size:34 final size:34
Alignment explanation
Indices: 395195--395287 Score: 132
Period size: 34 Copynumber: 2.7 Consensus size: 34
395185 ATGGTAATGG
*
395195 AATGGTGATGATATAGGTGTGAAATAGTGATAGA
1 AATGGTGATGATATAGGCGTGAAATAGTGATAGA
* * * *
395229 AATGGTGATGATATAGGCATGCAATGGTGATGGA
1 AATGGTGATGATATAGGCGTGAAATAGTGATAGA
395263 AGATGGTGATGATATAGGCGTGAAA
1 A-ATGGTGATGATATAGGCGTGAAA
395288 ATGGTGATGA
Statistics
Matches: 51, Mismatches: 7, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
34 30 0.59
35 21 0.41
ACGTcount: A:0.35, C:0.03, G:0.34, T:0.27
Consensus pattern (34 bp):
AATGGTGATGATATAGGCGTGAAATAGTGATAGA
Found at i:396801 original size:17 final size:17
Alignment explanation
Indices: 396779--396812 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
396769 GTGTTTGGGC
396779 GCCAATTTGATGTCACA
1 GCCAATTTGATGTCACA
396796 GCCAATTTGATGTCACA
1 GCCAATTTGATGTCACA
396813 TGAAGTGCAC
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:0.29, C:0.24, G:0.18, T:0.29
Consensus pattern (17 bp):
GCCAATTTGATGTCACA
Found at i:399892 original size:14 final size:14
Alignment explanation
Indices: 399873--399907 Score: 61
Period size: 14 Copynumber: 2.5 Consensus size: 14
399863 GTGATTCAAC
*
399873 TTTCTTTCTTTTCT
1 TTTCTTTCTTTGCT
399887 TTTCTTTCTTTGCT
1 TTTCTTTCTTTGCT
399901 TTTCTTT
1 TTTCTTT
399908 TTGAGTGCTG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.00, C:0.20, G:0.03, T:0.77
Consensus pattern (14 bp):
TTTCTTTCTTTGCT
Done.