Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold301
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: 562684
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.32
File 1 of 4
Found at i:711 original size:20 final size:21
Alignment explanation
Indices: 664--716 Score: 65
Period size: 20 Copynumber: 2.6 Consensus size: 21
654 ACCAATCACC
*
664 TGTATCGATACATTCTTTGCA
1 TGTATCGATACATTCTGTGCA
*
685 AGTATCGATACATT-TG-GTCA
1 TGTATCGATACATTCTGTG-CA
705 TGTATCGATACA
1 TGTATCGATACA
717 ATGTATCGAT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
19 1 0.04
20 14 0.50
21 13 0.46
ACGTcount: A:0.28, C:0.17, G:0.17, T:0.38
Consensus pattern (21 bp):
TGTATCGATACATTCTGTGCA
Found at i:722 original size:13 final size:13
Alignment explanation
Indices: 704--728 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
694 ACATTTGGTC
704 ATGTATCGATACA
1 ATGTATCGATACA
717 ATGTATCGATAC
1 ATGTATCGATAC
729 TGTGCATTCT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:4723 original size:13 final size:13
Alignment explanation
Indices: 4705--4740 Score: 72
Period size: 13 Copynumber: 2.8 Consensus size: 13
4695 CTTTTGAAAG
4705 TTTGAAAATATGA
1 TTTGAAAATATGA
4718 TTTGAAAATATGA
1 TTTGAAAATATGA
4731 TTTGAAAATA
1 TTTGAAAATA
4741 GAGGATTTTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.47, C:0.00, G:0.14, T:0.39
Consensus pattern (13 bp):
TTTGAAAATATGA
Found at i:7784 original size:3 final size:3
Alignment explanation
Indices: 7776--7806 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
7766 TCTGAGTCAC
*
7776 CAT CAT CAT CAT CAT CAT CAT CTT CAT CAT C
1 CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT C
7807 CTTGATGGTT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.29, C:0.35, G:0.00, T:0.35
Consensus pattern (3 bp):
CAT
Found at i:9431 original size:13 final size:13
Alignment explanation
Indices: 9413--9438 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
9403 AATTTGGTCA
9413 TGTATCGATACAT
1 TGTATCGATACAT
9426 TGTATCGATACAT
1 TGTATCGATACAT
9439 CTTGTGTGTA
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:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:9545 original size:20 final size:21
Alignment explanation
Indices: 9498--9550 Score: 65
Period size: 20 Copynumber: 2.6 Consensus size: 21
9488 ACCAATCACC
*
9498 TGTATCGATACATTCTTTGCA
1 TGTATCGATACATTCTGTGCA
*
9519 AGTATCGATACATT-TG-GTCA
1 TGTATCGATACATTCTGTG-CA
9539 TGTATCGATACA
1 TGTATCGATACA
9551 ATGTATCGAT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
19 1 0.04
20 14 0.50
21 13 0.46
ACGTcount: A:0.28, C:0.17, G:0.17, T:0.38
Consensus pattern (21 bp):
TGTATCGATACATTCTGTGCA
Found at i:9556 original size:13 final size:13
Alignment explanation
Indices: 9538--9562 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
9528 ACATTTGGTC
9538 ATGTATCGATACA
1 ATGTATCGATACA
9551 ATGTATCGATAC
1 ATGTATCGATAC
9563 TGTGCATTCT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:11292 original size:31 final size:28
Alignment explanation
Indices: 11208--11281 Score: 96
Period size: 28 Copynumber: 2.6 Consensus size: 28
11198 TTTCATAATC
* * *
11208 GGGGGTACTCCAACCCCGTTATTTCAT-T
1 GGGGATACTCTAACCCCGTTATTTC-TGA
*
11236 GGGGATACTCTAATCCCGTTATTTCTGA
1 GGGGATACTCTAACCCCGTTATTTCTGA
11264 GGGGATACTCTAACCCCG
1 GGGGATACTCTAACCCCG
11282 ATTTTATTTC
Statistics
Matches: 40, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
27 1 0.03
28 39 0.98
ACGTcount: A:0.20, C:0.27, G:0.23, T:0.30
Consensus pattern (28 bp):
GGGGATACTCTAACCCCGTTATTTCTGA
Found at i:11334 original size:51 final size:51
Alignment explanation
Indices: 11266--11380 Score: 160
Period size: 51 Copynumber: 2.3 Consensus size: 51
11256 ATTTCTGAGG
*
11266 GGATACTCTAACCCCGATTTTA-TTTCTAAAAAACCAATTTTTCACAATCGA
1 GGATACTCCAACCCCGATTTTATTTTC-AAAAAACCAATTTTTCACAATCGA
* * * *
11317 GGATACTCCAACTCCGATTTTATTTTCAAAACACCAATTTTTCACAATTGG
1 GGATACTCCAACCCCGATTTTATTTTCAAAAAACCAATTTTTCACAATCGA
*
11368 GGATACTCTAACC
1 GGATACTCCAACC
11381 TCGGTATTTC
Statistics
Matches: 56, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
51 52 0.93
52 4 0.07
ACGTcount: A:0.33, C:0.24, G:0.10, T:0.33
Consensus pattern (51 bp):
GGATACTCCAACCCCGATTTTATTTTCAAAAAACCAATTTTTCACAATCGA
Found at i:11341 original size:110 final size:110
Alignment explanation
Indices: 11123--11328 Score: 249
Period size: 110 Copynumber: 1.9 Consensus size: 110
11113 ATTTTTCACA
* *
11123 ATTGGGGATACTCCAACCTCGTTATTTCCGAGGGGATACTCCAACCCTGGCTTTATATCTAACAA
1 ATTGGGGATACTCCAACCTCGTTATTTCCGAGGGGATACTCCAACCCCGACTTTATATCTAACAA
*** * * * *
11188 TATTGATTTCTTTCATAATCGGGGGTACTCCAACCCCGTTATTTC
66 TAACCAATTCTTTCACAATCGAGGATACTCCAACCCCGTTATTTC
* * * * *
11233 ATTGGGGATACTCTAATCC-CGTTATTTCTGAGGGGATACTCTAACCCCGATTTTATTTCTAA-A
1 ATTGGGGATACTCCAA-CCTCGTTATTTCCGAGGGGATACTCCAACCCCGACTTTATATCTAACA
11296 A-AACCAATT-TTTCACAATCGAGGATACTCCAAC
65 ATAACCAATTCTTTCACAATCGAGGATACTCCAAC
11329 TCCGATTTTA
Statistics
Matches: 81, Mismatches: 14, Indels: 5
0.81 0.14 0.05
Matches are distributed among these distances:
107 21 0.26
108 4 0.05
109 2 0.02
110 52 0.64
111 2 0.02
ACGTcount: A:0.27, C:0.24, G:0.16, T:0.33
Consensus pattern (110 bp):
ATTGGGGATACTCCAACCTCGTTATTTCCGAGGGGATACTCCAACCCCGACTTTATATCTAACAA
TAACCAATTCTTTCACAATCGAGGATACTCCAACCCCGTTATTTC
Found at i:11478 original size:79 final size:78
Alignment explanation
Indices: 11391--11594 Score: 230
Period size: 79 Copynumber: 2.6 Consensus size: 78
11381 TCGGTATTTC
* * * *
11391 ATCAGGGATACTCCAACCCCGTTATTTTTGTGGGAATACTCCAACCCCAACCTTATTTTTAAAGC
1 ATCAGGGATACTCCAACCCCGTTATTTTCGAGGGAATACTCCAACCCCAACCTTATTTTCAAAAC
*
11456 ATTAATTTCCCACA
66 ATCAATTTCCC-CA
* * * **
11470 ATCGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCCTAATTTTATTTTCAAAAC
1 ATCAGGGATACTCCAACCCCGTTATTTTCGAGGGAATACTCCAACCCCAACCTTATTTTCAAAAC
* * *
11535 GTCAATTTCTCTA
66 ATCAATTTCCCCA
* * * *
11548 ATCAAGGATACTCCAACCCTGTTATTTTCAAAGGG-ATACTCTAACCC
1 ATCAGGGATACTCCAACCCCGTTATTTTC-GAGGGAATACTCCAACCC
11595 TAATTTTATT
Statistics
Matches: 106, Mismatches: 18, Indels: 3
0.83 0.14 0.02
Matches are distributed among these distances:
78 38 0.36
79 68 0.64
ACGTcount: A:0.29, C:0.27, G:0.13, T:0.31
Consensus pattern (78 bp):
ATCAGGGATACTCCAACCCCGTTATTTTCGAGGGAATACTCCAACCCCAACCTTATTTTCAAAAC
ATCAATTTCCCCA
Found at i:11486 original size:158 final size:158
Alignment explanation
Indices: 11198--11486 Score: 353
Period size: 158 Copynumber: 1.8 Consensus size: 158
11188 TATTGATTTC
* * * ** * *
11198 TTTCATAATCGGGGGTACTCCAACCCCGTTATTTCATTGGGGATACTCTAATCCCGTTATTTCTG
1 TTTCACAATCGGGGATACTCCAACCCCGGTATTTCATCAGGGATACTCCAACCCCGTTATTTCTG
* * * ** **
11263 AGGGGATACTCTAACCCCGATTTTATTTCTAAAAAACCAATTTTTCACAATCGAGGATACTCCAA
66 AGGGAATACTCCAACCCCAACCTTATTTCTAAAAAACCAATTTCCCACAATCGAGGATACTCCAA
11328 CTCCGATTTTATTTTCAAAACACCAATT
131 CTCCGATTTTATTTTCAAAACACCAATT
* * * *
11356 TTTCACAATTGGGGATACTCTAACCTCGGTATTTCATCAGGGATACTCCAACCCCGTTATTTTTG
1 TTTCACAATCGGGGATACTCCAACCCCGGTATTTCATCAGGGATACTCCAACCCCGTTATTTCTG
* * ** ** *
11421 TGGGAATACTCCAACCCCAACCTTATTTTTAAAGCATTAATTTCCCACAATCGGGGATACTCCAA
66 AGGGAATACTCCAACCCCAACCTTATTTCTAAAAAACCAATTTCCCACAATCGAGGATACTCCAA
11486 C
131 C
11487 CCCGTTATTT
Statistics
Matches: 106, Mismatches: 25, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
158 106 1.00
ACGTcount: A:0.28, C:0.25, G:0.14, T:0.33
Consensus pattern (158 bp):
TTTCACAATCGGGGATACTCCAACCCCGGTATTTCATCAGGGATACTCCAACCCCGTTATTTCTG
AGGGAATACTCCAACCCCAACCTTATTTCTAAAAAACCAATTTCCCACAATCGAGGATACTCCAA
CTCCGATTTTATTTTCAAAACACCAATT
Found at i:23725 original size:13 final size:13
Alignment explanation
Indices: 23707--23731 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
23697 TAAAGATCAG
23707 TGTATCGATACAA
1 TGTATCGATACAA
23720 TGTATCGATACA
1 TGTATCGATACA
23732 TTGGAGTAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:23794 original size:13 final size:13
Alignment explanation
Indices: 23776--23827 Score: 50
Period size: 13 Copynumber: 3.5 Consensus size: 13
23766 AGCTTCGTAG
23776 CGATACATTGTAT
1 CGATACATTGTAT
23789 CGATACAACACTTATGTAT
1 CGAT---ACA-TT--GTAT
23808 CGATACATTGTAT
1 CGATACATTGTAT
23821 CGATACA
1 CGATACA
23828 AACCATTGAA
Statistics
Matches: 33, Mismatches: 0, Indels: 12
0.73 0.00 0.27
Matches are distributed among these distances:
13 15 0.45
15 2 0.06
16 6 0.18
17 2 0.06
19 8 0.24
ACGTcount: A:0.35, C:0.19, G:0.13, T:0.33
Consensus pattern (13 bp):
CGATACATTGTAT
Found at i:27077 original size:51 final size:51
Alignment explanation
Indices: 27020--27416 Score: 290
Period size: 51 Copynumber: 7.6 Consensus size: 51
27010 TTAAGTTTCT
*
27020 CAATTTTTCATAATCGGGGATACTCCAACCCCGATTTTATTTTCAAAACAC
1 CAATTTTTCATAATCGGGGATACTCCAACCCCGATTTTATTTCCAAAACAC
* * * *
27071 CAATTTTCCTTTAATCGGGGATACTCCAACTCCGACTTTATTTCCAAAAACAC
1 CAATTTTTC-ATAATCGGGGATACTCCAACCCCGATTTTATTTCC-AAAACAC
* * * * ***** * *
27124 CAATTTTTCACAATCGAGGATACTCCAACCTCGTTATTTCATCGGGGATACTC
1 CAATTTTTCATAATCGGGGATACTCCAACCCCG--ATTTTATTTCCAAAACAC
** * * **** * ** * *
27177 CAACCCCGTTACCTCCGAGGGGATACTCAAACCCCGGCTTTATTTCCAAAATAT
1 CAA---TTTTTCATAATCGGGGATACTCCAACCCCGATTTTATTTCCAAAACAC
** * * * *
27231 TGATTTCTCATAATCGAGGATAATCCAACCCCGTTTTTATTTCCAAAACAC
1 CAATTTTTCATAATCGGGGATACTCCAACCCCGATTTTATTTCCAAAACAC
* * * * *
27282 TAATTTTCCACAATCGGGGATACTCCAACCCCGGTTTTATTTTCAAAACAC
1 CAATTTTTCATAATCGGGGATACTCCAACCCCGATTTTATTTCCAAAACAC
* * *
27333 CAATTTTTCTTTAATCGGGGATACTCCAACTCCGATTTTATTTCAAAAAACAC
1 CAATTTTTC-ATAATCGGGGATACTCCAACCCCGATTTTATTTC-CAAAACAC
* * *
27386 CAATTTTTTCACAATCGAGGATACTCTAACC
1 CAA-TTTTTCATAATCGGGGATACTCCAACC
27417 TCATTATTTC
Statistics
Matches: 253, Mismatches: 83, Indels: 18
0.71 0.23 0.05
Matches are distributed among these distances:
51 90 0.36
52 79 0.31
53 48 0.19
54 18 0.07
56 18 0.07
ACGTcount: A:0.30, C:0.27, G:0.11, T:0.32
Consensus pattern (51 bp):
CAATTTTTCATAATCGGGGATACTCCAACCCCGATTTTATTTCCAAAACAC
Found at i:27504 original size:263 final size:262
Alignment explanation
Indices: 27021--27507 Score: 857
Period size: 263 Copynumber: 1.9 Consensus size: 262
27011 TAAGTTTCTC
* *
27021 AATTTTTCATAATCGGGGATACTCCAACCCCGATTTTATTTTCAAAACACCAATTTTCCTTTAAT
1 AATTTTCCACAATCGGGGATACTCCAACCCCGATTTTATTTTCAAAACACCAATTTTCCTTTAAT
*
27086 CGGGGATACTCCAACTCCGACTTTATTTCCAAAAACACCAATTTTTCACAATCGAGGATACTCCA
66 CGGGGATACTCCAACTCCGACTTTATTTCAAAAAACACCAATTTTTCACAATCGAGGATACTCCA
* *
27151 ACCTCGTTATTTCATCGGGGATACTCCAACCCCGTTACCTCCGAGGGGATACTCAAACCCCGGCT
131 ACCTCATTATTTCATCGGGGATACTCCAACCCCGTTACCTCCGAGGGGATACTCAAACCCCAGCT
*
27216 TTATTTCCAAAATATTGATTTCTCATAATCGAGGATAATCCAACCCCGTTTTTATTTCCAAAACA
196 TTATTCCCAAAATATTGATTTCTCATAATCGAGGATAATCCAACCCCGTTTTTATTTCCAAAACA
27281 CT
261 CT
* *
27283 AATTTTCCACAATCGGGGATACTCCAACCCCGGTTTTATTTTCAAAACACCAATTTTTCTTTAAT
1 AATTTTCCACAATCGGGGATACTCCAACCCCGATTTTATTTTCAAAACACCAATTTTCCTTTAAT
* *
27348 CGGGGATACTCCAACTCCGATTTTATTTCAAAAAACACCAATTTTTTCACAATCGAGGATACTCT
66 CGGGGATACTCCAACTCCGACTTTATTTCAAAAAACACCAA-TTTTTCACAATCGAGGATACTCC
* *
27413 AACCTCATTATTTCATCGGGGATACTCCAACCCCGTTACCTCGGAGGGGATACTCCAACCCCAGC
130 AACCTCATTATTTCATCGGGGATACTCCAACCCCGTTACCTCCGAGGGGATACTCAAACCCCAGC
27478 TTTATTCCCAAAATATTGATTTCTCATAAT
195 TTTATTCCCAAAATATTGATTTCTCATAAT
27508 TAGGGATAGT
Statistics
Matches: 212, Mismatches: 12, Indels: 1
0.94 0.05 0.00
Matches are distributed among these distances:
262 100 0.47
263 112 0.53
ACGTcount: A:0.29, C:0.27, G:0.12, T:0.32
Consensus pattern (262 bp):
AATTTTCCACAATCGGGGATACTCCAACCCCGATTTTATTTTCAAAACACCAATTTTCCTTTAAT
CGGGGATACTCCAACTCCGACTTTATTTCAAAAAACACCAATTTTTCACAATCGAGGATACTCCA
ACCTCATTATTTCATCGGGGATACTCCAACCCCGTTACCTCCGAGGGGATACTCAAACCCCAGCT
TTATTCCCAAAATATTGATTTCTCATAATCGAGGATAATCCAACCCCGTTTTTATTTCCAAAACA
CT
Found at i:37423 original size:84 final size:85
Alignment explanation
Indices: 37303--37474 Score: 233
Period size: 84 Copynumber: 2.0 Consensus size: 85
37293 AAATTTTTCA
* * *
37303 TTTTAGGGAAACTCCATCCTCACTATTCTGAGGGGATACTCT-ACCCCCGATCTT-TAAAAAACT
1 TTTTAGGGAAACTCCATCCTCACTATTCTAAAGGGATACTCTGA-CCCCGATCTTCAAAAAAACT
* *
37366 TAAATTTTTGCTTTATATAAT
65 TAAACTTTTCCTTTATATAAT
* *
37387 TTTTAGGGAAACTCCATCCGT-ACTCTTCTAAAGGGATACTCTGACCTCGATCTTCAAAAAAACT
1 TTTTAGGGAAACTCCATCC-TCACTATTCTAAAGGGATACTCTGACCCCGATCTTCAAAAAAACT
*
37451 TAAACTTTTCCTTTGTATAAT
65 TAAACTTTTCCTTTATATAAT
37472 TTT
1 TTT
37475 ATCTTTAGGG
Statistics
Matches: 77, Mismatches: 8, Indels: 5
0.86 0.09 0.06
Matches are distributed among these distances:
84 46 0.60
85 31 0.40
ACGTcount: A:0.30, C:0.22, G:0.12, T:0.37
Consensus pattern (85 bp):
TTTTAGGGAAACTCCATCCTCACTATTCTAAAGGGATACTCTGACCCCGATCTTCAAAAAAACTT
AAACTTTTCCTTTATATAAT
Found at i:40513 original size:13 final size:13
Alignment explanation
Indices: 40495--40520 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
40485 ACATTTTAGG
40495 ATGTATCGATACA
1 ATGTATCGATACA
40508 ATGTATCGATACA
1 ATGTATCGATACA
40521 TATTGTGTGT
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:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:40515 original size:33 final size:32
Alignment explanation
Indices: 40473--40540 Score: 102
Period size: 33 Copynumber: 2.1 Consensus size: 32
40463 CGTTACAAGC
*
40473 CAATGTATCGATACATTTTAG-GATGTATCGATA
1 CAATGTATCGATACATATT-GTG-TGTATCGATA
40506 CAATGTATCGATACATATTGTGTGTATCGATA
1 CAATGTATCGATACATATTGTGTGTATCGATA
40538 CAA
1 CAA
40541 ACAGTTAAGG
Statistics
Matches: 33, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
32 14 0.42
33 19 0.58
ACGTcount: A:0.34, C:0.13, G:0.18, T:0.35
Consensus pattern (32 bp):
CAATGTATCGATACATATTGTGTGTATCGATA
Found at i:40639 original size:13 final size:13
Alignment explanation
Indices: 40621--40645 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
40611 ACATTTGGTC
40621 ATGTATCGATACA
1 ATGTATCGATACA
40634 ATGTATCGATAC
1 ATGTATCGATAC
40646 TGTGCAATCT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:41245 original size:22 final size:22
Alignment explanation
Indices: 41202--41246 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
41192 TTTTCTTTTC
* *
41202 TCTCCCCTTTAATCAAAAAATT
1 TCTCCCCCTGAATCAAAAAATT
41224 TCTCCCCCTGAAT-AAAATAATT
1 TCTCCCCCTGAATCAAAA-AATT
41246 T
1 T
41247 AACAATTTCG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 4 0.20
22 16 0.80
ACGTcount: A:0.36, C:0.27, G:0.02, T:0.36
Consensus pattern (22 bp):
TCTCCCCCTGAATCAAAAAATT
Found at i:49314 original size:19 final size:20
Alignment explanation
Indices: 49271--49322 Score: 72
Period size: 19 Copynumber: 2.6 Consensus size: 20
49261 CACACCCATA
*
49271 TGTATCGATACATTATGCTT
1 TGTATCGATACATTATGCAT
49291 TGTATCGATACATGT-T-CAT
1 TGTATCGATACAT-TATGCAT
49310 TGTATCGATACAT
1 TGTATCGATACAT
49323 AGACAATTGT
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
19 15 0.50
20 14 0.47
21 1 0.03
ACGTcount: A:0.27, C:0.15, G:0.15, T:0.42
Consensus pattern (20 bp):
TGTATCGATACATTATGCAT
Found at i:49333 original size:20 final size:19
Alignment explanation
Indices: 49271--49335 Score: 62
Period size: 20 Copynumber: 3.3 Consensus size: 19
49261 CACACCCATA
*
49271 TGTATCGATACAT-TATGCTT
1 TGTATCGATACATGTA--CAT
*
49291 TGTATCGATACATGTTCAT
1 TGTATCGATACATGTACAT
49310 TGTATCGATACATAG-ACAAT
1 TGTATCGATACAT-GTAC-AT
49330 TGTATC
1 TGTATC
49336 TGAAAGCTCA
Statistics
Matches: 39, Mismatches: 3, Indels: 6
0.81 0.06 0.12
Matches are distributed among these distances:
19 16 0.41
20 22 0.56
21 1 0.03
ACGTcount: A:0.29, C:0.15, G:0.15, T:0.40
Consensus pattern (19 bp):
TGTATCGATACATGTACAT
Found at i:58227 original size:9 final size:9
Alignment explanation
Indices: 58213--58242 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
58203 GAAGAAGATG
58213 CTCCTCTTC
1 CTCCTCTTC
58222 CTCCTCTTC
1 CTCCTCTTC
58231 CT-CTCTTC
1 CTCCTCTTC
58239 CTCC
1 CTCC
58243 ACCCAAAGCT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
8 8 0.40
9 12 0.60
ACGTcount: A:0.00, C:0.57, G:0.00, T:0.43
Consensus pattern (9 bp):
CTCCTCTTC
Found at i:59345 original size:20 final size:20
Alignment explanation
Indices: 59322--59395 Score: 107
Period size: 20 Copynumber: 3.8 Consensus size: 20
59312 ACATTATGCT
59322 TTGTATCGATACATGGACAA
1 TTGTATCGATACATGGACAA
*
59342 TTGTATCGATACATTGA-ACA
1 TTGTATCGATACATGGACA-A
59362 -TGTATCGATACATGGACAA
1 TTGTATCGATACATGGACAA
*
59381 TTGTATTGATACATG
1 TTGTATCGATACATG
59396 AAACTAGCAG
Statistics
Matches: 48, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
19 17 0.35
20 31 0.65
ACGTcount: A:0.34, C:0.14, G:0.19, T:0.34
Consensus pattern (20 bp):
TTGTATCGATACATGGACAA
Found at i:64421 original size:50 final size:51
Alignment explanation
Indices: 64359--64466 Score: 164
Period size: 51 Copynumber: 2.1 Consensus size: 51
64349 TAAACAGTAC
*
64359 ATGTATCGATACATTTT-GTTTTCTACCCAGATATATCGATACATTTTTCA
1 ATGTATCAATACATTTTAGTTTTCTACCCAGATATATCGATACATTTTTCA
* * * *
64409 ATGTATCAATACATTTTATTTTTTTACCCAGATGTATCGATACATTTTTTA
1 ATGTATCAATACATTTTAGTTTTCTACCCAGATATATCGATACATTTTTCA
64460 ATGTATC
1 ATGTATC
64467 GATGCATCTA
Statistics
Matches: 52, Mismatches: 5, Indels: 1
0.90 0.09 0.02
Matches are distributed among these distances:
50 16 0.31
51 36 0.69
ACGTcount: A:0.29, C:0.16, G:0.09, T:0.46
Consensus pattern (51 bp):
ATGTATCAATACATTTTAGTTTTCTACCCAGATATATCGATACATTTTTCA
Found at i:73048 original size:87 final size:86
Alignment explanation
Indices: 72946--73256 Score: 256
Period size: 87 Copynumber: 3.6 Consensus size: 86
72936 TTAAGAATGG
* *
72946 GGTTGGAGTGTCCCCTCGAAGGAGTGGGAATAGAGTTTCCCCAAAAATAAAATTATACGAAGAAT
1 GGTTGGAGTATCCCCTCGAA-GAGTGGGGATAGAGTTTCCCC-AAAATAAAATTATACGAAGAAT
* *
73011 AACTTGAATTTTTGTTGGAACGG
64 AAATTGAATTTTTGTTGGAACGA
* * * * * * **
73034 GGTTAGAGTA-CCCCTCAAAATAGTAGGGATGGAGTTTCCCCCAAAGATTAAATTCCACGAAG--
1 GGTTGGAGTATCCCCTC-GAAGAGTGGGGATAGAGTTT-CCCCAAA-ATAAAATTATACGAAGAA
* * * *
73096 TAAATTTAAATTTTGTTAGAACAA
63 TAAATTGAATTTTTGTTGGAACGA
* * * *** * *
73120 GGTTGGAGTATCCCTTTAGAATG-GTGGGGATGGAGTTTCCCCATTGTTAAATTATGCGAAGGAA
1 GGTTGGAGTATCCC-CTCGAA-GAGTGGGGATAGAGTTTCCCCAAAATAAAATTATACGAA-GAA
*
73184 -AATTTGAATTTTTGTTAGG-ACGA
63 TAAATTGAATTTTTGTT-GGAACGA
*
73207 GGTTGGAGTATCCCCTCAGAATAGTGGGGATAGAGTTTCCCCAAAATAAA
1 GGTTGGAGTATCCCCTC-GAAGAGTGGGGATAGAGTTTCCCCAAAATAAA
73257 CTTTTTTTAA
Statistics
Matches: 170, Mismatches: 41, Indels: 25
0.72 0.17 0.11
Matches are distributed among these distances:
85 11 0.06
86 34 0.20
87 96 0.56
88 29 0.17
ACGTcount: A:0.32, C:0.14, G:0.25, T:0.29
Consensus pattern (86 bp):
GGTTGGAGTATCCCCTCGAAGAGTGGGGATAGAGTTTCCCCAAAATAAAATTATACGAAGAATAA
ATTGAATTTTTGTTGGAACGA
Found at i:76648 original size:73 final size:74
Alignment explanation
Indices: 76518--77218 Score: 533
Period size: 74 Copynumber: 9.6 Consensus size: 74
76508 AAGGTAGGTC
** * * * *
76518 GATGCCACCAGCTTGTGTGGGC-TTCGA-AAAAAGAAAAGGCATCTTGCTCTTTGAGGACTGAGA
1 GATGCCACCAGCTTGTGTGGGCTTTAAAGAAAAAGAAAAGACATCCTGCTCTTTAAGGACTGAAA
76581 AAGATAAAT
66 AAGATAAAT
* * * * * * *
76590 GATTCCACTAACTTGTGTGGGCTTTAAAGAAAAA-AAATGATATCTTGCTCTTTAAGGACTAAAA
1 GATGCCACCAGCTTGTGTGGGCTTTAAAGAAAAAGAAAAGACATCCTGCTCTTTAAGGACTGAAA
76654 AAGATAAAT
66 AAGATAAAT
* * ** **** ** * *
76663 GATGCCACCAACTTATGCTTTTTGAAGAAAATGAAAAA-AAAAGATGTCCTCCTCTTTGAGGACT
1 GATGCCACCAGC-T-TG-TGTGGGCTTTAAA-GAAAAAGAAAAGACATCCTGCTCTTTAAGGACT
*
76727 AAAAAAGATAAAT
62 GAAAAAGATAAAT
* * * **
76740 GATGCCACCAGCTTGTGTGGGCTTTAAAGAGAAAA-AAAAGGCGTCCTGCTTTTTGGGGACTG-A
1 GATGCCACCAGCTTGTGTGGGCTTTAAAGA-AAAAGAAAAGACATCCTGCTCTTTAAGGACTGAA
76803 AAAGATAAAT
65 AAAGATAAAT
* * ** * *
76813 GATGCCACTAGCTTGTGTGGGCTTT---G---AAG-AAAGGCATTATGCTCTTTGAA-AACCGAA
1 GATGCCACCAGCTTGTGTGGGCTTTAAAGAAAAAGAAAAGACATCCTGCTCTTT-AAGGACTGAA
76870 AAAGATAAAT
65 AAAGATAAAT
* * * * * * *
76880 AATGTCACCAGCTTGTGTGAGCTTTGAAGAAAAAGAAAAGGCATCCTACTCTTCAAGGACTG-AA
1 GATGCCACCAGCTTGTGTGGGCTTTAAAGAAAAAGAAAAGACATCCTGCTCTTTAAGGACTGAAA
76944 AAGATAAAT
66 AAGATAAAT
* * * * *
76953 GATGCCACCAGCTTATGTGGGCTTTGAAAAAAAAAGAAAAAACGTCTTGCTCTTTGAA-GACT-A
1 GATGCCACCAGCTTGTGTGGGCTTT-AAAGAAAAAGAAAAGACATCCTGCTCTTT-AAGGACTGA
*
77016 GAAAAGATAACT
64 -AAAAGATAAAT
* * * * ** * *
77028 GATGCCACCAGCTTGTATAGGCATTGAAGAAAAAGAAAA-AGTGTCCTACTCTTTAAGGACTAAA
1 GATGCCACCAGCTTGTGTGGGCTTTAAAGAAAAAGAAAAGA-CATCCTGCTCTTTAAGGACTGAA
77092 AAAGATAAAT
65 AAAGATAAAT
* * * * *
77102 GATGCCACTAACTTGTGTGGGCTTTTAGAGAAAAAGAAAAGGCATCCTGCTCTTTGAGGACTG-A
1 GATGCCACCAGCTTGTGTGGGC-TTTAAAGAAAAAGAAAAGACATCCTGCTCTTTAAGGACTGAA
77166 AAAGATAAAT
65 AAAGATAAAT
* * ** *
77176 AATGCCACCAACTTGCATGGGCTTTCGAAA-AAGAAGAAAAGAC
1 GATGCCACCAGCTTGTGTGGGCTTT--AAAGAAAAAGAAAAGAC
77219 GCCCTACTCA
Statistics
Matches: 499, Mismatches: 101, Indels: 56
0.76 0.15 0.09
Matches are distributed among these distances:
66 19 0.04
67 32 0.06
70 2 0.00
72 19 0.04
73 126 0.25
74 173 0.35
75 70 0.14
76 7 0.01
77 51 0.10
ACGTcount: A:0.38, C:0.16, G:0.21, T:0.25
Consensus pattern (74 bp):
GATGCCACCAGCTTGTGTGGGCTTTAAAGAAAAAGAAAAGACATCCTGCTCTTTAAGGACTGAAA
AAGATAAAT
Found at i:76966 original size:140 final size:141
Alignment explanation
Indices: 76728--77273 Score: 460
Period size: 148 Copynumber: 3.8 Consensus size: 141
76718 TTGAGGACTA
* * * *
76728 AAAAAGATAAATGATGCCACCAGCTTGTGTGGGCTTTAAAGAGAAAA-AAAAGGCGTCCTGCTTT
1 AAAAAGATAAATGATGCCACCAGCTTGTGTGAGCTTTGAAGA-AAAAGAAAAGGCGTCCTACTCT
** **
76792 TTGGGGACTGAAAAGATAAATGATGCCACTAGCTTGTGTGGGCTTTG-AAG-AAAGGCAT-TATG
65 TTAAGGACTGAAAAGATAAATGATGCCACTAGCTTGTGTGGGCTTTGAAAGAAAAAACATCT-TG
76854 CTCTTTGAAAACCG
129 CTCTTTGAAAA-CG
* * *
76868 AAAAAGATAAATAATGTCACCAGCTTGTGTGAGCTTTGAAGAAAAAGAAAAGGCATCCTACTCTT
1 AAAAAGATAAATGATGCCACCAGCTTGTGTGAGCTTTGAAGAAAAAGAAAAGGCGTCCTACTCTT
* * * *
76933 CAAGGACTGAAAAGATAAATGATGCCACCAGCTTATGTGGGCTTTGAAAAAAAAAGAAAAAACGT
66 TAAGGACTGAAAAGATAAATGATGCCACTAGCTTGTGTGGGCTTTG------AAAGAAAAAACAT
* *
76998 CTTGCTCTTTGAAGACT
125 CTTGCTCTTTGAAAACG
* * * * *
77015 AGAAAAGATAACTGATGCCACCAGCTTGTAT-AGGCATTGAAGAAAAAGAAAAAGTGTCCTACTC
1 A-AAAAGATAAATGATGCCACCAGCTTGTGTGA-GCTTTGAAGAAAAAGAAAAGGCGTCCTACTC
* * *
77079 TTTAAGGACTAAAAAAGATAAATGATGCCACTAACTTGTGTGGGCTTTTAGAGAAAAAGAAAAGG
64 TTTAAGGACT-GAAAAGATAAATGATGCCACTAGCTTGTGTGGGC-TTT-GA-AAGAA-AAAA--
* **
77144 CATCCTGCTCTTTGAGGACTG
122 CATCTTGCTCTTTGAAAAC-G
* * ** * * *
77165 -AAAAGATAAATAATGCCACCAACTTGCATGGGCTTTCGAA-AAAGAAGAAAAGACGCCCTACTC
1 AAAAAGATAAATGATGCCACCAGCTTGTGTGAGCTTT-GAAGAAA-AAGAAAAGGCGTCCTACTC
*
77228 -------A-TTAAAAGATAAATGATG-CACTAGCTTGTGTGGGCTTTG-AAGAAAA
64 TTTAAGGACTGAAAAGATAAATGATGCCACTAGCTTGTGTGGGCTTTGAAAGAAAA
77274 GAAAAAGCGT
Statistics
Matches: 335, Mismatches: 48, Indels: 52
0.77 0.11 0.12
Matches are distributed among these distances:
134 2 0.01
135 4 0.01
137 1 0.00
138 3 0.01
139 20 0.06
140 109 0.33
141 1 0.00
142 1 0.00
145 1 0.00
146 4 0.01
147 10 0.03
148 110 0.33
149 65 0.19
150 3 0.01
151 1 0.00
ACGTcount: A:0.38, C:0.16, G:0.22, T:0.24
Consensus pattern (141 bp):
AAAAAGATAAATGATGCCACCAGCTTGTGTGAGCTTTGAAGAAAAAGAAAAGGCGTCCTACTCTT
TAAGGACTGAAAAGATAAATGATGCCACTAGCTTGTGTGGGCTTTGAAAGAAAAAACATCTTGCT
CTTTGAAAACG
Found at i:76987 original size:74 final size:74
Alignment explanation
Indices: 76869--77305 Score: 375
Period size: 74 Copynumber: 6.1 Consensus size: 74
76859 TGAAAACCGA
* * * *
76869 AAAAGATAAATAATGTCACCAGCTTGTGTGAGCTTTGAAGAAAAAGAAAAGGCATCCTACTCTTC
1 AAAAGATAAATGATGCCACCAGCTTGTGTGGGCTTTGAAGAAAAAGAAAAGGCATCCTACTCTTT
76934 AAGGACT-G
66 AAGGACTAG
* * ** * * *
76942 AAAAGATAAATGATGCCACCAGCTTATGTGGGCTTTGAAAAAAAAAGAAAAAACGTCTTGCTCTT
1 AAAAGATAAATGATGCCACCAGCTTGTGTGGGCTTTG-AAGAAAAAGAAAAGGCATCCTACTCTT
77007 TGAA-GACTAG
65 T-AAGGACTAG
* * * * * **
77017 AAAAGATAACTGATGCCACCAGCTTGTATAGGCATTGAAGAAAAAGAAAAAGTGTCCTACTCTTT
1 AAAAGATAAATGATGCCACCAGCTTGTGTGGGCTTTGAAGAAAAAGAAAAGGCATCCTACTCTTT
*
77082 AAGGACTAA
66 AAGGACTAG
* * * *
77091 AAAAGATAAATGATGCCACTAACTTGTGTGGGCTTTTAGAGAAAAAGAAAAGGCATCCTGCTCTT
1 AAAAGATAAATGATGCCACCAGCTTGTGTGGGCTTTGA-AGAAAAAGAAAAGGCATCCTACTCTT
*
77156 TGAGGACT-G
65 TAAGGACTAG
* * ** * **
77165 AAAAGATAAATAATGCCACCAACTTGCATGGGCTTTCGAA-AAAGAAGAAAAGACGCCCTACTC-
1 AAAAGATAAATGATGCCACCAGCTTGTGTGGGCTTT-GAAGAAA-AAGAAAAGGCATCCTACTCT
*
77228 ------A-T-T
64 TTAAGGACTAG
* * * * *
77231 AAAAGATAAATGATG-CACTAGCTTGTGTGGGCTTTGAAG-AAAAGAAAAAGCGTCCTAATTTTT
1 AAAAGATAAATGATGCCACCAGCTTGTGTGGGCTTTGAAGAAAAAGAAAAGGCATCCTACTCTTT
*
77294 GAGGACT-G
66 AAGGACTAG
77302 AAAA
1 AAAA
77306 AGACGAATAA
Statistics
Matches: 292, Mismatches: 56, Indels: 34
0.76 0.15 0.09
Matches are distributed among these distances:
63 14 0.05
64 5 0.02
65 16 0.05
66 15 0.05
67 1 0.00
70 1 0.00
71 5 0.02
73 38 0.13
74 132 0.45
75 65 0.22
ACGTcount: A:0.40, C:0.16, G:0.21, T:0.24
Consensus pattern (74 bp):
AAAAGATAAATGATGCCACCAGCTTGTGTGGGCTTTGAAGAAAAAGAAAAGGCATCCTACTCTTT
AAGGACTAG
Found at i:77215 original size:223 final size:218
Alignment explanation
Indices: 76518--77286 Score: 704
Period size: 223 Copynumber: 3.5 Consensus size: 218
76508 AAGGTAGGTC
* ** *
76518 GATGCCACCAGCTTGTGTGGGCTTCG-AAAA-AAGAAAAGGCATCTTGCTCTTTGAGGACTGAGA
1 GATGCCACCAGCTTGTGTGGGCTTTGAAAAAGAAGAAAAAACGTCTTGCTCTTTGAGGACTGA-A
* * * * * *
76581 AAGATAAATGATTCCACTAACTTGTGTGGGCTTTAAAGAAAA-AAAATGATATCTTGCTCTTTAA
65 AAGATAAATGATGCCACTAGCTTGTGTGGGCTTTGAAGAAAAGAAAAAG-TGTCCT-CTCTTTAA
*
76645 GGACTAAAAAAGATAAATGATGCCACCAAC-T-TAT-GCTTTTTGAAGAAAATGAAAAA-AAAAG
128 GGACTAAAAAAGATAAATGATGCCACCAACTTGTGTGGC-TTTT--AG---A-GAAAAAGAAAAG
*** * *
76706 ATGTCCTCCTCTTTGAGGACTAAAAAAGATAAAT
186 GCATCCTACTCTTTGAGGACT-GAAAAGATAAAT
* * * *
76740 GATGCCACCAGCTTGTGTGGGCTTT-AAAGAGAA-AAAAAAGGCGTCCTGCTTTTTGGGGACTGA
1 GATGCCACCAGCTTGTGTGGGCTTTGAAAAAGAAGAAAAAA--CGTCTTGCTCTTTGAGGACTGA
* * ** *
76803 AAAGATAAATGATGCCACTAGCTTGTGTGGGCTTTGAAGAAAGGCATTA-TG--CTCT-TTGAA-
64 AAAGATAAATGATGCCACTAGCTTGTGTGGGCTTTGAAGAAAAGAAAAAGTGTCCTCTCTTTAAG
* ** * * * *
76863 AACCGAAAAAGATAAATAATGTCACCAGCTTGTGTGAGCTTTGA-AGAAAAAGAAAAGGCATCCT
129 GACTAAAAAAGATAAATGATGCCACCAACTTGTGTG-GCTTTTAGAGAAAAAGAAAAGGCATCCT
**
76927 ACTCTTCAAGGACTGAAAAGATAAAT
193 ACTCTTTGAGGACTGAAAAGATAAAT
* * *
76953 GATGCCACCAGCTTATGTGGGCTTTGAAAAAAAAAGAAAAAACGTCTTGCTCTTTGAAGACTAGA
1 GATGCCACCAGCTTGTGTGGGCTTTG-AAAAAGAAGAAAAAACGTCTTGCTCTTTGAGGACT-GA
* * * * *
77018 AAAGATAACTGATGCCACCAGCTTGTATAGGCATTGAAGAAAAAGAAAAAGTGTCCTACTCTTTA
64 AAAGATAAATGATGCCACTAGCTTGTGTGGGCTTTGAAG-AAAAGAAAAAGTGTCCT-CTCTTTA
*
77083 AGGACTAAAAAAGATAAATGATGCCACTAACTTGTGTGGGCTTTTAGAGAAAAAGAAAAGGCATC
127 AGGACTAAAAAAGATAAATGATGCCACCAACTTGTGT-GGCTTTTAGAGAAAAAGAAAAGGCATC
*
77148 CTGCTCTTTGAGGACTGAAAAGATAAAT
191 CTACTCTTTGAGGACTGAAAAGATAAAT
* * ** * * * * *
77176 AATGCCACCAACTTGCATGGGCTTTCGAAAAAGAAGAAAAGACGCCCTACTC-------A-TTAA
1 GATGCCACCAGCTTGTGTGGGCTTT-GAAAAAGAAGAAAAAACGTCTTGCTCTTTGAGGACTGAA
*
77233 AAGATAAATGATG-CACTAGCTTGTGTGGGCTTTGAAGAAAAGAAAAAGCGTCCT
65 AAGATAAATGATGCCACTAGCTTGTGTGGGCTTTGAAGAAAAGAAAAAGTGTCCT
77287 AATTTTTGAG
Statistics
Matches: 444, Mismatches: 79, Indels: 58
0.76 0.14 0.10
Matches are distributed among these distances:
212 16 0.04
213 61 0.14
214 51 0.11
215 43 0.10
216 13 0.03
217 25 0.06
218 6 0.01
219 6 0.01
220 6 0.01
221 6 0.01
222 66 0.15
223 125 0.28
224 20 0.05
ACGTcount: A:0.38, C:0.16, G:0.21, T:0.25
Consensus pattern (218 bp):
GATGCCACCAGCTTGTGTGGGCTTTGAAAAAGAAGAAAAAACGTCTTGCTCTTTGAGGACTGAAA
AGATAAATGATGCCACTAGCTTGTGTGGGCTTTGAAGAAAAGAAAAAGTGTCCTCTCTTTAAGGA
CTAAAAAAGATAAATGATGCCACCAACTTGTGTGGCTTTTAGAGAAAAAGAAAAGGCATCCTACT
CTTTGAGGACTGAAAAGATAAAT
Found at i:78655 original size:168 final size:167
Alignment explanation
Indices: 78433--78827 Score: 480
Period size: 168 Copynumber: 2.4 Consensus size: 167
78423 AATTACAGGA
*
78433 TTTTCTACTCCGTAAAA-TTTTTCGAGAGGA-TTTTCATTGGTTTAAAATTTTTAAAATTCATCA
1 TTTTCTACTTCGTAAAATTTTTTCGAG-GGATTTTTC-TTGGTTTAAAATTTTTAAAATTCATCA
* ** * *
78496 AATATTATTATTTATTTCATATTAAATTGGTTTTT-AAAAATTCATTGATTTGCA-TGAGTTTTA
64 AATATTATTATTTATTTCAAATTAAA-TCATTTTTCAAAAATTCATTCATTTGCATTCAGTTTTA
* *
78559 AATTTTTTCCTTAAAATTCCCCTATATT-CCAAAATACGGAG
128 AATTTTTTCCTTAAAA-TCCCC-ATATTCCCAAAAAACCGAG
* **
78600 TTTTCTACTTTGTAAAATTTTTTTCGAGGGATTTTTCTTGGTTTCTAATTTTTAAAATTCATCAA
1 TTTTCTACTTCGTAAAA-TTTTTTCGAGGGATTTTTCTTGGTTTAAAATTTTTAAAATTCATCAA
* * * *
78665 ATATTATTATTTATTTCAAATTAAATCATTTTTCAAAAATTCATTCATTTTCATTCATTTTTGAT
65 ATATTATTATTTATTTCAAATTAAATCATTTTTCAAAAATTCATTCATTTGCATTCAGTTTTAAA
* * *
78730 TTTTTTCTTTAAAATGCCCATTTTCCCAAAAAACCGAG
130 TTTTTTCCTTAAAATCCCCATATTCCCAAAAAACCGAG
* * * * *
78768 TTTTCTACTTCAT-AAATTTTTTGGGGGGATTTTTCTT-GATTAAAATTTTTAAAGTTCATC
1 TTTTCTACTTCGTAAAATTTTTTCGAGGGATTTTTCTTGGTTTAAAATTTTTAAAATTCATC
78828 TAACACTGTC
Statistics
Matches: 196, Mismatches: 26, Indels: 14
0.83 0.11 0.06
Matches are distributed among these distances:
165 19 0.10
166 19 0.10
167 28 0.14
168 96 0.49
169 34 0.17
ACGTcount: A:0.30, C:0.12, G:0.09, T:0.49
Consensus pattern (167 bp):
TTTTCTACTTCGTAAAATTTTTTCGAGGGATTTTTCTTGGTTTAAAATTTTTAAAATTCATCAAA
TATTATTATTTATTTCAAATTAAATCATTTTTCAAAAATTCATTCATTTGCATTCAGTTTTAAAT
TTTTTCCTTAAAATCCCCATATTCCCAAAAAACCGAG
Found at i:79031 original size:5 final size:5
Alignment explanation
Indices: 79023--79048 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
79013 TATTTTTAAA
79023 AATTT AATTT AATTT AATTT AATTT A
1 AATTT AATTT AATTT AATTT AATTT A
79049 TTTTCTTCAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (5 bp):
AATTT
Found at i:79246 original size:12 final size:12
Alignment explanation
Indices: 79226--79258 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
79216 ATGGCTTGGG
79226 AAATGGAAAAATA
1 AAAT-GAAAAATA
79239 AAATGAAAAATA
1 AAATGAAAAATA
79251 AAA-GAAAA
1 AAATGAAAA
79259 TGGAAAACTC
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 5 0.25
12 11 0.55
13 4 0.20
ACGTcount: A:0.76, C:0.00, G:0.12, T:0.12
Consensus pattern (12 bp):
AAATGAAAAATA
Found at i:79406 original size:10 final size:10
Alignment explanation
Indices: 79383--79419 Score: 58
Period size: 10 Copynumber: 3.8 Consensus size: 10
79373 AGTGGAGAGA
79383 AAAGAAAAAG
1 AAAGAAAAAG
79393 -AAGAAAAAG
1 AAAGAAAAAG
79402 AAAGAAAAAG
1 AAAGAAAAAG
*
79412 AGAGAAAA
1 AAAGAAAA
79420 CAGGAAAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
9 9 0.36
10 16 0.64
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (10 bp):
AAAGAAAAAG
Found at i:82701 original size:79 final size:78
Alignment explanation
Indices: 82494--82711 Score: 253
Period size: 79 Copynumber: 2.8 Consensus size: 78
82484 ACAACAGGGC
* * * * *
82494 TGGAGTATCCTCAATTATAGAAAATCGGTGTTTT-GAAAATAAAATCGGGGTTGGAGTATCCCTT
1 TGGAGTATCCCCGATTGTAGAAAATCGGTGTTTTAG-AAATAAAATAGGGGTTGGAGTATCCCGT
*
82558 GAAAATAACGGGGT
65 GAAAATAACGAGGT
* * * * ***
82572 TGGAGTAT-CCTGATTGTGGAAAATCGATGCTTTAGAAATAAGGCCA-GGGTTGGAGTATCCTCG
1 TGGAGTATCCCCGATTGTAGAAAATCGGTGTTTTAGAAATAA-AATAGGGGTTGGAGTATCC-CG
82635 TGAAAATAACGAGGT
64 TGAAAATAACGAGGT
* *
82650 TGGAGTATCCCCGATTGTAAAAAATTGGTGTTTTAGAAATAAAATAGGGGTTGGAGTATCCC
1 TGGAGTATCCCCGATTGTAGAAAATCGGTGTTTTAGAAATAAAATAGGGGTTGGAGTATCCC
82712 CGATTGTGAG
Statistics
Matches: 113, Mismatches: 22, Indels: 10
0.78 0.15 0.07
Matches are distributed among these distances:
77 38 0.34
78 34 0.30
79 41 0.36
ACGTcount: A:0.32, C:0.12, G:0.27, T:0.29
Consensus pattern (78 bp):
TGGAGTATCCCCGATTGTAGAAAATCGGTGTTTTAGAAATAAAATAGGGGTTGGAGTATCCCGTG
AAAATAACGAGGT
Found at i:82711 original size:51 final size:51
Alignment explanation
Indices: 82647--82763 Score: 144
Period size: 51 Copynumber: 2.3 Consensus size: 51
82637 AAAATAACGA
*** * *
82647 GGTTGGAGTATCCCCGATTGTAAAAAATTGGTGTTTTAGAAATAAAATAGG
1 GGTTGGAGTATCCCCGATTGTAAAAAATCAATATTTTAGAAATAAAACAGG
* * * *
82698 GGTTGGAGTATCCCCGATTGTGAGAAATCAATATTTTAGAAATAAAGCCGG
1 GGTTGGAGTATCCCCGATTGTAAAAAATCAATATTTTAGAAATAAAACAGG
*
82749 GGTTGGTGTATCCCC
1 GGTTGGAGTATCCCC
82764 TCGAAAATAA
Statistics
Matches: 56, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
51 56 1.00
ACGTcount: A:0.31, C:0.13, G:0.26, T:0.30
Consensus pattern (51 bp):
GGTTGGAGTATCCCCGATTGTAAAAAATCAATATTTTAGAAATAAAACAGG
Found at i:82736 original size:130 final size:131
Alignment explanation
Indices: 82567--82840 Score: 328
Period size: 130 Copynumber: 2.1 Consensus size: 131
82557 TGAAAATAAC
* * * *
82567 GGGGTTGGAGTAT-CCTGATTGTGGAAAATCGATGCTTTAGAAATAAGGCCAGGGTTGGAGTATC
1 GGGGTTGGAGTATCCCCGATTGTGGAAAATCAATACTTTAGAAATAAAGCCAGGGTTGGAGTATC
* * *
82631 CTCGT-GAAAATAACGAGG-TTGGAGTATCCCCGATTGTAAAAAATTGG-TGTTTTAGAAATAAA
66 C-CCTCGAAAATAA-GAGGATTGGAATATCCCCGATTATAAAAAA-TGGATGTTTTAGAAATAAA
82693 AT-A
128 ATCA
* * *
82696 GGGGTTGGAGTATCCCCGATTGT-GAGAAATCAATATTTTAGAAATAAAGCCGGGGTTGGTGTAT
1 GGGGTTGGAGTATCCCCGATTGTGGA-AAATCAATACTTTAGAAATAAAGCCAGGGTTGGAGTAT
* * * *
82760 CCCCTCGAAAATAAGGGGATTGGAATATCGCCGATTATGAAAAATGGATGTTTTGGAAATAAAAT
65 CCCCTCGAAAATAAGAGGATTGGAATATCCCCGATTATAAAAAATGGATGTTTTAGAAATAAAAT
82825 CA
130 CA
*
82827 -GAGTTGGAGTATCC
1 GGGGTTGGAGTATCC
82841 TCGAGATGAA
Statistics
Matches: 124, Mismatches: 15, Indels: 11
0.83 0.10 0.07
Matches are distributed among these distances:
129 23 0.19
130 100 0.81
131 1 0.01
ACGTcount: A:0.32, C:0.12, G:0.28, T:0.28
Consensus pattern (131 bp):
GGGGTTGGAGTATCCCCGATTGTGGAAAATCAATACTTTAGAAATAAAGCCAGGGTTGGAGTATC
CCCTCGAAAATAAGAGGATTGGAATATCCCCGATTATAAAAAATGGATGTTTTAGAAATAAAATC
A
Found at i:85207 original size:13 final size:13
Alignment explanation
Indices: 85189--85216 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
85179 GTAAACCCAG
85189 AATGTATCGATAC
1 AATGTATCGATAC
85202 AATGTATCGATAC
1 AATGTATCGATAC
85215 AA
1 AA
85217 CTAGGTAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.43, C:0.14, G:0.14, T:0.29
Consensus pattern (13 bp):
AATGTATCGATAC
Found at i:85224 original size:42 final size:43
Alignment explanation
Indices: 85160--85248 Score: 135
Period size: 43 Copynumber: 2.1 Consensus size: 43
85150 TACATTGAAA
* *
85160 AATGCATCGATACATCTGGGT-AAACCCAGAATGTATCGATAC
1 AATGCATCGATACAACTAGGTAAAACCCAGAATGTATCGATAC
* *
85202 AATGTATCGATACAACTAGGTAAAACCCAGAATTTATCGATAC
1 AATGCATCGATACAACTAGGTAAAACCCAGAATGTATCGATAC
85245 AATG
1 AATG
85249 AACAATGTAT
Statistics
Matches: 42, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
42 18 0.43
43 24 0.57
ACGTcount: A:0.39, C:0.19, G:0.17, T:0.25
Consensus pattern (43 bp):
AATGCATCGATACAACTAGGTAAAACCCAGAATGTATCGATAC
Found at i:86133 original size:19 final size:20
Alignment explanation
Indices: 86109--86161 Score: 72
Period size: 19 Copynumber: 2.7 Consensus size: 20
86099 CAAACCCAGA
**
86109 TGTATCGATACATGTTC-AT
1 TGTATCGATACATGGACAAT
86128 TGTATCGATACATGGACAAT
1 TGTATCGATACATGGACAAT
*
86148 TGTATCGGTACATG
1 TGTATCGATACATG
86162 AAACTGGCAG
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 15 0.50
20 15 0.50
ACGTcount: A:0.28, C:0.15, G:0.21, T:0.36
Consensus pattern (20 bp):
TGTATCGATACATGGACAAT
Found at i:86227 original size:33 final size:33
Alignment explanation
Indices: 86190--86257 Score: 102
Period size: 33 Copynumber: 2.1 Consensus size: 33
86180 CTACCACTAT
86190 TTATATCAATACATG-GCACATTGTATCGATACA
1 TTATATCAATACATGAGCA-ATTGTATCGATACA
* *
86223 TTATATCGATACATGATCAATTGTATCGATACA
1 TTATATCAATACATGAGCAATTGTATCGATACA
86256 TT
1 TT
86258 GCTTCAAACG
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
33 30 0.94
34 2 0.06
ACGTcount: A:0.35, C:0.16, G:0.12, T:0.37
Consensus pattern (33 bp):
TTATATCAATACATGAGCAATTGTATCGATACA
Found at i:86229 original size:13 final size:13
Alignment explanation
Indices: 86207--86236 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
86197 AATACATGGC
*
86207 ACATTGTATCGAT
1 ACATTATATCGAT
86220 ACATTATATCGAT
1 ACATTATATCGAT
86233 ACAT
1 ACAT
86237 GATCAATTGT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.37, C:0.17, G:0.10, T:0.37
Consensus pattern (13 bp):
ACATTATATCGAT
Found at i:88513 original size:19 final size:18
Alignment explanation
Indices: 88488--88552 Score: 77
Period size: 19 Copynumber: 3.8 Consensus size: 18
88478 ATTTCAACGA
88488 TTTGTATCGATACATAAG
1 TTTGTATCGATACATAAG
88506 TGTTGTATCGATAC--AA-
1 T-TTGTATCGATACATAAG
88522 --TGTATCGATACATAAG
1 TTTGTATCGATACATAAG
88538 TTTTGTATCGATACA
1 -TTTGTATCGATACA
88553 ATGTATCGCT
Statistics
Matches: 40, Mismatches: 0, Indels: 13
0.75 0.00 0.25
Matches are distributed among these distances:
13 11 0.28
15 2 0.05
17 2 0.05
18 1 0.03
19 24 0.60
ACGTcount: A:0.32, C:0.12, G:0.17, T:0.38
Consensus pattern (18 bp):
TTTGTATCGATACATAAG
Found at i:88526 original size:32 final size:32
Alignment explanation
Indices: 88490--88565 Score: 134
Period size: 32 Copynumber: 2.4 Consensus size: 32
88480 TTCAACGATT
88490 TGTATCGATACATAAGTGTTGTATCGATACAA
1 TGTATCGATACATAAGTGTTGTATCGATACAA
*
88522 TGTATCGATACATAAGTTTTGTATCGATACAA
1 TGTATCGATACATAAGTGTTGTATCGATACAA
*
88554 TGTATCGCTACA
1 TGTATCGATACA
88566 AAACTACTGC
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
32 42 1.00
ACGTcount: A:0.33, C:0.14, G:0.17, T:0.36
Consensus pattern (32 bp):
TGTATCGATACATAAGTGTTGTATCGATACAA
Found at i:88527 original size:13 final size:13
Alignment explanation
Indices: 88509--88566 Score: 53
Period size: 13 Copynumber: 4.0 Consensus size: 13
88499 ACATAAGTGT
88509 TGTATCGATACAA
1 TGTATCGATACAA
88522 TGTATCGATACATAA
1 TGTATCGATAC--AA
88537 GTTTTGTATCGATACAA
1 ----TGTATCGATACAA
*
88554 TGTATCGCTACAA
1 TGTATCGATACAA
88567 AACTACTGCC
Statistics
Matches: 38, Mismatches: 1, Indels: 12
0.75 0.02 0.24
Matches are distributed among these distances:
13 23 0.61
15 2 0.05
17 2 0.05
19 11 0.29
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:88646 original size:52 final size:52
Alignment explanation
Indices: 88604--88732 Score: 231
Period size: 52 Copynumber: 2.5 Consensus size: 52
88594 CACTGATCTT
* *
88604 TGTATCGATACATGCAGGCAAATTTGTCCAGATGTATTGATACACTATGAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATGAAA
*
88656 TGTATCGATACATACAGGCAAATTTGCCCAGATGTATCGATACACTATGAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATGAAA
88708 TGTATCGATACATGCAGGCAAATTT
1 TGTATCGATACATGCAGGCAAATTT
88733 TTATATTTCG
Statistics
Matches: 73, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
52 73 1.00
ACGTcount: A:0.35, C:0.17, G:0.19, T:0.29
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATGAAA
Found at i:97594 original size:19 final size:20
Alignment explanation
Indices: 97549--97600 Score: 79
Period size: 20 Copynumber: 2.6 Consensus size: 20
97539 TTACAAGCCA
*
97549 ATGTATCGATACATTTTGGG
1 ATGTATCGATACATATTGGG
*
97569 ATGTATCGATACATATTGTG
1 ATGTATCGATACATATTGGG
97589 -TGTATCGATACA
1 ATGTATCGATACA
97601 AACAGTTAAG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 12 0.40
20 18 0.60
ACGTcount: A:0.29, C:0.12, G:0.21, T:0.38
Consensus pattern (20 bp):
ATGTATCGATACATATTGGG
Found at i:97700 original size:13 final size:13
Alignment explanation
Indices: 97682--97706 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
97672 ACATTTGGTC
97682 ATGTATCGATACA
1 ATGTATCGATACA
97695 ATGTATCGATAC
1 ATGTATCGATAC
97707 TGTGCAATAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:97943 original size:63 final size:63
Alignment explanation
Indices: 97865--98013 Score: 271
Period size: 63 Copynumber: 2.4 Consensus size: 63
97855 TTTCCTTATC
*
97865 TCTCCCCCTTAATCAAAAAATTTCTCCCCCTTAATAAAGCAATTTCACAATTACAAGTTTCTT
1 TCTCCCCCTTAATCAAAAAATTTCTCCCCCTTAATAAAGCAATTTCACAATTACAACTTTCTT
97928 TCTCCCCCTTAATCAAAAAATTTCTCCCCCTTAATAAAGCAATTTCACAATTACAACTTTCTT
1 TCTCCCCCTTAATCAAAAAATTTCTCCCCCTTAATAAAGCAATTTCACAATTACAACTTTCTT
* *
97991 TCTCCCCCTTAAGCATAAAATTT
1 TCTCCCCCTTAATCAAAAAATTT
98014 AATTACAGAG
Statistics
Matches: 83, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
63 83 1.00
ACGTcount: A:0.33, C:0.30, G:0.03, T:0.35
Consensus pattern (63 bp):
TCTCCCCCTTAATCAAAAAATTTCTCCCCCTTAATAAAGCAATTTCACAATTACAACTTTCTT
Found at i:99847 original size:13 final size:13
Alignment explanation
Indices: 99829--99890 Score: 90
Period size: 13 Copynumber: 4.8 Consensus size: 13
99819 ATAAACCCTT
99829 TGTATCGATA-AA
1 TGTATCGATACAA
99841 CTGTATCGATACAA
1 -TGTATCGATACAA
* *
99855 TGTCTCGATACAC
1 TGTATCGATACAA
99868 TGTATCGATACAA
1 TGTATCGATACAA
99881 TGTATCGATA
1 TGTATCGATA
99891 TAGAGAATGC
Statistics
Matches: 44, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
13 42 0.95
14 2 0.05
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:99869 original size:26 final size:26
Alignment explanation
Indices: 99829--99890 Score: 106
Period size: 26 Copynumber: 2.4 Consensus size: 26
99819 ATAAACCCTT
99829 TGTATCGATAAACTGTATCGATACAA
1 TGTATCGATAAACTGTATCGATACAA
* *
99855 TGTCTCGATACACTGTATCGATACAA
1 TGTATCGATAAACTGTATCGATACAA
99881 TGTATCGATA
1 TGTATCGATA
99891 TAGAGAATGC
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 33 1.00
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.32
Consensus pattern (26 bp):
TGTATCGATAAACTGTATCGATACAA
Found at i:100108 original size:8 final size:8
Alignment explanation
Indices: 100090--100120 Score: 53
Period size: 8 Copynumber: 3.8 Consensus size: 8
100080 TTTTCAACAT
100090 CAAACATCA
1 CAAA-ATCA
100099 CAAAATCA
1 CAAAATCA
100107 CAAAATCA
1 CAAAATCA
100115 CAAAAT
1 CAAAAT
100121 TTAATCAAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
8 18 0.82
9 4 0.18
ACGTcount: A:0.61, C:0.26, G:0.00, T:0.13
Consensus pattern (8 bp):
CAAAATCA
Found at i:106146 original size:21 final size:21
Alignment explanation
Indices: 106120--106194 Score: 118
Period size: 21 Copynumber: 3.7 Consensus size: 21
106110 CTGCCAGTTT
106120 CATGTATCGATACAATTTGGG
1 CATGTATCGATACAATTTGGG
106141 CATGTATCGATACAATTTGGG
1 CATGTATCGATACAATTTGGG
**
106162 CATGTATCGATACAA--TGAA
1 CATGTATCGATACAATTTGGG
106181 CATGTATCGATACA
1 CATGTATCGATACA
106195 CTGTATCGAT
Statistics
Matches: 52, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
19 16 0.31
21 36 0.69
ACGTcount: A:0.33, C:0.16, G:0.20, T:0.31
Consensus pattern (21 bp):
CATGTATCGATACAATTTGGG
Found at i:106201 original size:13 final size:13
Alignment explanation
Indices: 106183--106207 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
106173 ACAATGAACA
106183 TGTATCGATACAC
1 TGTATCGATACAC
106196 TGTATCGATACA
1 TGTATCGATACA
106208 AAGCAGCATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.20, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAC
Found at i:106223 original size:33 final size:32
Alignment explanation
Indices: 106164--106227 Score: 101
Period size: 33 Copynumber: 2.0 Consensus size: 32
106154 AATTTGGGCA
*
106164 TGTATCGATACAATGAACATGTATCGATACAC
1 TGTATCGATACAAAGAACATGTATCGATACAC
*
106196 TGTATCGATACAAAGCAGCATGTATCGATACA
1 TGTATCGATACAAAG-AACATGTATCGATACA
106228 ACATCTCGGT
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 14 0.48
33 15 0.52
ACGTcount: A:0.38, C:0.19, G:0.17, T:0.27
Consensus pattern (32 bp):
TGTATCGATACAAAGAACATGTATCGATACAC
Found at i:107345 original size:21 final size:19
Alignment explanation
Indices: 107316--107357 Score: 57
Period size: 19 Copynumber: 2.1 Consensus size: 19
107306 TTTTAACCGA
107316 TTATCAAAGGGGAGAAATTTT
1 TTATCAAA-GGGA-AAATTTT
*
107337 TTATTAAAGGGAAAATTTT
1 TTATCAAAGGGAAAATTTT
107356 TT
1 TT
107358 TAACGAGAGC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 9 0.45
20 4 0.20
21 7 0.35
ACGTcount: A:0.38, C:0.02, G:0.19, T:0.40
Consensus pattern (19 bp):
TTATCAAAGGGAAAATTTT
Found at i:107993 original size:13 final size:13
Alignment explanation
Indices: 107975--107999 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
107965 ACATGGCACA
107975 TTGTATCGATACC
1 TTGTATCGATACC
107988 TTGTATCGATAC
1 TTGTATCGATAC
108000 ATGATTAATT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.24, C:0.20, G:0.16, T:0.40
Consensus pattern (13 bp):
TTGTATCGATACC
Found at i:111354 original size:7 final size:7
Alignment explanation
Indices: 111344--111401 Score: 52
Period size: 7 Copynumber: 8.9 Consensus size: 7
111334 TAAAAAAGCA
111344 AAAAAAC
1 AAAAAAC
111351 AAAAAAC
1 AAAAAAC
111358 --AAAA-
1 AAAAAAC
*
111362 AAAAAGC
1 AAAAAAC
111369 AAAAAAC
1 AAAAAAC
111376 AAAAAA-
1 AAAAAAC
* *
111382 AAACAAT
1 AAAAAAC
*
111389 AACAAAC
1 AAAAAAC
111396 AAAAAA
1 AAAAAA
111402 GGGGAGGAAA
Statistics
Matches: 40, Mismatches: 7, Indels: 8
0.73 0.13 0.15
Matches are distributed among these distances:
5 4 0.10
6 8 0.20
7 28 0.70
ACGTcount: A:0.84, C:0.12, G:0.02, T:0.02
Consensus pattern (7 bp):
AAAAAAC
Found at i:111356 original size:10 final size:10
Alignment explanation
Indices: 111335--111401 Score: 55
Period size: 10 Copynumber: 6.4 Consensus size: 10
111325 ATCTTTCGTT
*
111335 AAAAAAGCAA
1 AAAAAAACAA
111345 AAAAACAA-AA
1 AAAAA-AACAA
*
111355 AACAAAAAAAA
1 AA-AAAAACAA
111366 AGCAAAAAACAA
1 A--AAAAAACAA
111378 AAAAAAACAA
1 AAAAAAACAA
* *
111388 TAACAAACAA
1 AAAAAAACAA
111398 AAAA
1 AAAA
111402 GGGGAGGAAA
Statistics
Matches: 46, Mismatches: 6, Indels: 10
0.74 0.10 0.16
Matches are distributed among these distances:
10 30 0.65
11 7 0.15
12 8 0.17
13 1 0.02
ACGTcount: A:0.84, C:0.12, G:0.03, T:0.01
Consensus pattern (10 bp):
AAAAAAACAA
Found at i:111356 original size:18 final size:16
Alignment explanation
Indices: 111343--111383 Score: 64
Period size: 17 Copynumber: 2.4 Consensus size: 16
111333 TTAAAAAAGC
111343 AAAAAAACAAAAAACAA
1 AAAAAAACAAAAAAC-A
111360 AAAAAAAGCAAAAAACA
1 AAAAAAA-CAAAAAACA
111377 AAAAAAA
1 AAAAAAA
111384 ACAATAACAA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
17 15 0.65
18 8 0.35
ACGTcount: A:0.88, C:0.10, G:0.02, T:0.00
Consensus pattern (16 bp):
AAAAAAACAAAAAACA
Found at i:111384 original size:18 final size:17
Alignment explanation
Indices: 111343--111401 Score: 84
Period size: 18 Copynumber: 3.4 Consensus size: 17
111333 TTAAAAAAGC
111343 AAAAAAACAAAAAACAA
1 AAAAAAACAAAAAACAA
111360 AAAAAAAGCAAAAAACAA
1 AAAAAAA-CAAAAAACAA
*
111378 AAAAAAAC-AATAACAA
1 AAAAAAACAAAAAACAA
111394 ACAAAAAA
1 A-AAAAAA
111402 GGGGAGGAAA
Statistics
Matches: 39, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
16 8 0.21
17 14 0.36
18 17 0.44
ACGTcount: A:0.85, C:0.12, G:0.02, T:0.02
Consensus pattern (17 bp):
AAAAAAACAAAAAACAA
Found at i:113025 original size:32 final size:32
Alignment explanation
Indices: 112980--113267 Score: 307
Period size: 32 Copynumber: 9.0 Consensus size: 32
112970 CTAGTGGAGA
112980 AACCTTCTTCAAAGCCCACACAAGTTGGTGGC
1 AACCTTCTTCAAAGCCCACACAAGTTGGTGGC
* * *
113012 AACTTTCTTCAAAGCCCACCCAAGTTAGTGGC
1 AACCTTCTTCAAAGCCCACACAAGTTGGTGGC
113044 AACC-TCTTCAAAAGCCCACACAAGTTGGTGGC
1 AACCTTCTTC-AAAGCCCACACAAGTTGGTGGC
* *
113076 AACTTTCTTCAAAGCCCACATAAGTTGGTGGC
1 AACCTTCTTCAAAGCCCACACAAGTTGGTGGC
* * * * * *
113108 ATCCTTTTTCAAAGCCCATACAAGTCGATGCC
1 AACCTTCTTCAAAGCCCACACAAGTTGGTGGC
** *
113140 AACC-TCTTCAAAAGCCCACACAAGTCAGTGGT
1 AACCTTCTTC-AAAGCCCACACAAGTTGGTGGC
* * * *
113172 AACCCT-TTCAAAGCCTACACAAGCTGGTGGT
1 AACCTTCTTCAAAGCCCACACAAGTTGGTGGC
* * * *
113203 AACCCTTCAT-AAAGCCCACAAAAGTCGATGGC
1 AA-CCTTCTTCAAAGCCCACACAAGTTGGTGGC
113235 AACCTT-TTCAAAAGCCCACACAAGTTGGTGGC
1 AACCTTCTTC-AAAGCCCACACAAGTTGGTGGC
113267 A
1 A
113268 TCTCCATCTT
Statistics
Matches: 209, Mismatches: 39, Indels: 16
0.79 0.15 0.06
Matches are distributed among these distances:
30 1 0.00
31 33 0.16
32 168 0.80
33 7 0.03
ACGTcount: A:0.31, C:0.30, G:0.17, T:0.22
Consensus pattern (32 bp):
AACCTTCTTCAAAGCCCACACAAGTTGGTGGC
Found at i:113148 original size:96 final size:95
Alignment explanation
Indices: 112980--113267 Score: 348
Period size: 96 Copynumber: 3.0 Consensus size: 95
112970 CTAGTGGAGA
* * *
112980 AACCTTCTTCAAAGCCCACACAAGTTGGTGGCAACTTTCTTCAAAGCCCACCCAAGT-TAGTGGC
1 AACCTTCTTCAAAGCCCACACAAGTTGGTGGCACCTTT-TTCAAAGCCCACACAAGTCGA-TGGC
113044 AACCTCTTCAAAAGCCCACACAAGTTGGTGGC
64 AACCTCTTCAAAAGCCCACACAAGTTGGTGGC
* * * *
113076 AACTTTCTTCAAAGCCCACATAAGTTGGTGGCATCCTTTTTCAAAGCCCATACAAGTCGATGCCA
1 AACCTTCTTCAAAGCCCACACAAGTTGGTGGCA-CCTTTTTCAAAGCCCACACAAGTCGATGGCA
** *
113141 ACCTCTTCAAAAGCCCACACAAGTCAGTGGT
65 ACCTCTTCAAAAGCCCACACAAGTTGGTGGC
* * * * ** *
113172 AACCCT-TTCAAAGCCTACACAAGCTGGTGGTAACCCTTCAT-AAAGCCCACAAAAGTCGATGGC
1 AACCTTCTTCAAAGCCCACACAAGTTGGTGG-CA-CCTTTTTCAAAGCCCACACAAGTCGATGGC
*
113235 AACCTTTTCAAAAGCCCACACAAGTTGGTGGC
64 AACCTCTTCAAAAGCCCACACAAGTTGGTGGC
113267 A
1 A
113268 TCTCCATCTT
Statistics
Matches: 163, Mismatches: 26, Indels: 7
0.83 0.13 0.04
Matches are distributed among these distances:
95 69 0.42
96 89 0.55
97 5 0.03
ACGTcount: A:0.31, C:0.30, G:0.17, T:0.22
Consensus pattern (95 bp):
AACCTTCTTCAAAGCCCACACAAGTTGGTGGCACCTTTTTCAAAGCCCACACAAGTCGATGGCAA
CCTCTTCAAAAGCCCACACAAGTTGGTGGC
Found at i:113345 original size:49 final size:49
Alignment explanation
Indices: 113263--113363 Score: 130
Period size: 49 Copynumber: 2.1 Consensus size: 49
113253 CACAAGTTGG
* * *
113263 TGGCATCTCCATCTTTAAGTCCAATGTCCTTGGCCTTGCATCAGCACAT
1 TGGCACCTCCATCTTTAAGTCCAATATCCTTGGCCTTGAATCAGCACAT
* ** * *
113312 TGGCACCTTCATCTTTAAGTCTGATATCGTTGGCCTTGAATCAGCATAT
1 TGGCACCTCCATCTTTAAGTCCAATATCCTTGGCCTTGAATCAGCACAT
113361 TGG
1 TGG
113364 TAACTATAAC
Statistics
Matches: 44, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
49 44 1.00
ACGTcount: A:0.21, C:0.26, G:0.19, T:0.35
Consensus pattern (49 bp):
TGGCACCTCCATCTTTAAGTCCAATATCCTTGGCCTTGAATCAGCACAT
Found at i:114245 original size:19 final size:20
Alignment explanation
Indices: 114221--114273 Score: 83
Period size: 19 Copynumber: 2.7 Consensus size: 20
114211 ACAATTTGTC
114221 CATGTATCGATACAATGA-A-
1 CATGTATCGATACAA-GACAG
114240 CATGTATCGATACAAGACAG
1 CATGTATCGATACAAGACAG
114260 CATGTATCGATACA
1 CATGTATCGATACA
114274 TCTGGGTGTG
Statistics
Matches: 32, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
18 2 0.06
19 16 0.50
20 14 0.44
ACGTcount: A:0.40, C:0.19, G:0.17, T:0.25
Consensus pattern (20 bp):
CATGTATCGATACAAGACAG
Found at i:114852 original size:22 final size:18
Alignment explanation
Indices: 114804--114856 Score: 61
Period size: 19 Copynumber: 2.7 Consensus size: 18
114794 TCCTAAAAAA
114804 TTCTCCCCCTTAAACGAT
1 TTCTCCCCCTTAAACGAT
114822 TATCTCCCCCTTAAACAGTTAT
1 T-TCTCCCCCTTAAAC-G--AT
114844 CTTCTCCCCCTTA
1 -TTCTCCCCCTTA
114857 TGTAAAAATT
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
18 1 0.03
19 14 0.47
20 1 0.03
22 13 0.43
23 1 0.03
ACGTcount: A:0.21, C:0.40, G:0.04, T:0.36
Consensus pattern (18 bp):
TTCTCCCCCTTAAACGAT
Found at i:116701 original size:13 final size:13
Alignment explanation
Indices: 116683--116711 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
116673 AAATAGTACC
116683 CAATGTATCGATA
1 CAATGTATCGATA
116696 CAATGTATCGATA
1 CAATGTATCGATA
116709 CAA
1 CAA
116712 GGAATGTTGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.41, C:0.17, G:0.14, T:0.28
Consensus pattern (13 bp):
CAATGTATCGATA
Found at i:123822 original size:51 final size:52
Alignment explanation
Indices: 123738--123861 Score: 198
Period size: 51 Copynumber: 2.4 Consensus size: 52
123728 ATATGAAAAG
* *
123738 TTGCTTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCA-AT
1 TTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCACAT
*
123789 TTGCCTGCATGTATCGATACACTTT-ATAATGTATCGATACATCTGGGTACAT
1 TTGCCTGCATGTATCGATACA-TTTAATAATGTATCGATACATCTGGGCACAT
123841 TTGCCTGCATGTATCGATACA
1 TTGCCTGCATGTATCGATACA
123862 AAGATCGGTG
Statistics
Matches: 68, Mismatches: 3, Indels: 3
0.92 0.04 0.04
Matches are distributed among these distances:
51 42 0.62
52 26 0.38
ACGTcount: A:0.27, C:0.19, G:0.19, T:0.36
Consensus pattern (52 bp):
TTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCACAT
Found at i:123874 original size:52 final size:51
Alignment explanation
Indices: 123738--123881 Score: 166
Period size: 51 Copynumber: 2.8 Consensus size: 51
123728 ATATGAAAAG
* **
123738 TTGCTTGCATGTATCGATACATTTA-ATAGTGTATCGATACATCTGGGCAAT
1 TTGCCTGCATGTATCGATACA-CAAGATAGTGTATCGATACATCTGGGCAAT
*** * *
123789 TTGCCTGCATGTATCGATACACTTTATAATGTATCGATACATCTGGGTACAT
1 TTGCCTGCATGTATCGATACACAAGATAGTGTATCGATACATCTGGGCA-AT
*
123841 TTGCCTGCATGTATCGATACA-AAGATCGGTGTATCGATACA
1 TTGCCTGCATGTATCGATACACAAGAT-AGTGTATCGATACA
123882 ATGTATCGAT
Statistics
Matches: 80, Mismatches: 10, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
50 1 0.01
51 44 0.55
52 35 0.44
ACGTcount: A:0.28, C:0.18, G:0.19, T:0.35
Consensus pattern (51 bp):
TTGCCTGCATGTATCGATACACAAGATAGTGTATCGATACATCTGGGCAAT
Found at i:123888 original size:13 final size:13
Alignment explanation
Indices: 123870--123894 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
123860 CAAAGATCGG
123870 TGTATCGATACAA
1 TGTATCGATACAA
123883 TGTATCGATACA
1 TGTATCGATACA
123895 TTTGAGTAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:123975 original size:13 final size:13
Alignment explanation
Indices: 123957--123981 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
123947 CAAAGAAATA
123957 TGTATCGATACAT
1 TGTATCGATACAT
123970 TGTATCGATACA
1 TGTATCGATACA
123982 ACACTTTATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:126631 original size:52 final size:52
Alignment explanation
Indices: 126546--126670 Score: 207
Period size: 52 Copynumber: 2.4 Consensus size: 52
126536 ATATGAAAAG
* * *
126546 TTGCTTGCATGTATCGATACATTTAATAGTGTATCGATACTTCTGGGCAAAT
1 TTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAAT
126598 TTGCCTGCATGTATCGATACACTTT-ATAATGTATCGATACATCTGGGCAAAT
1 TTGCCTGCATGTATCGATACA-TTTAATAATGTATCGATACATCTGGGCAAAT
126650 TTGCCTGCATGTATCGATACA
1 TTGCCTGCATGTATCGATACA
126671 AAGATCAGTG
Statistics
Matches: 69, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
52 66 0.96
53 3 0.04
ACGTcount: A:0.27, C:0.18, G:0.18, T:0.36
Consensus pattern (52 bp):
TTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAAT
Found at i:126683 original size:52 final size:51
Alignment explanation
Indices: 126546--126690 Score: 202
Period size: 52 Copynumber: 2.8 Consensus size: 51
126536 ATATGAAAAG
* *
126546 TTGCTTGCATGTATCGATACATTTAATAGTGTATCGATACTTCTGGGCAAAT
1 TTGCCTGCATGTATCGATACA-TTAATAGTGTATCGATACATCTGGGCAAAT
* *
126598 TTGCCTGCATGTATCGATACACTTTATAATGTATCGATACATCTGGGCAAAT
1 TTGCCTGCATGTATCGATACA-TTAATAGTGTATCGATACATCTGGGCAAAT
*
126650 TTGCCTGCATGTATCGATACA-AAGATCAGTGTATCGATACA
1 TTGCCTGCATGTATCGATACATTA-AT-AGTGTATCGATACA
126691 ATGTATCGAT
Statistics
Matches: 83, Mismatches: 8, Indels: 4
0.87 0.08 0.04
Matches are distributed among these distances:
51 2 0.02
52 81 0.98
ACGTcount: A:0.29, C:0.18, G:0.19, T:0.34
Consensus pattern (51 bp):
TTGCCTGCATGTATCGATACATTAATAGTGTATCGATACATCTGGGCAAAT
Found at i:126697 original size:13 final size:13
Alignment explanation
Indices: 126679--126703 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
126669 CAAAGATCAG
126679 TGTATCGATACAA
1 TGTATCGATACAA
126692 TGTATCGATACA
1 TGTATCGATACA
126704 TTTGAGTAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:126781 original size:33 final size:33
Alignment explanation
Indices: 126744--126810 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
126734 AGTAGCTTAA
126744 ATTGTATCGATACAAAAAAATATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
* ***
126777 ATTGTATCGATACAACACTTTATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
126810 A
1 A
126811 AATCGTTGAA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.40, C:0.15, G:0.12, T:0.33
Consensus pattern (33 bp):
ATTGTATCGATACAAAAAAATATGTATCGATAC
Found at i:126784 original size:13 final size:13
Alignment explanation
Indices: 126766--126790 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
126756 CAAAAAAATA
126766 TGTATCGATACAT
1 TGTATCGATACAT
126779 TGTATCGATACA
1 TGTATCGATACA
126791 ACACTTTATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:138131 original size:49 final size:49
Alignment explanation
Indices: 137954--138428 Score: 618
Period size: 49 Copynumber: 9.9 Consensus size: 49
137944 AAGATGAGAA
* *
137954 AAAGGATGTCAATGTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGAT
1 AAAGG-TGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAT
*
138004 GGAAAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAT
1 ---AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAT
*
138056 GAA-GTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAT
1 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAT
*
138104 AAAGGTGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGAT
1 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAT
* *
138153 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGAC-T-----T
1 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAT
* *
138196 AAAGGTGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGGT
1 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAT
* *
138245 -GAGGTGCCAATGTGCTGATTCAAGGCTAGCTACATTGGACTTAAAGAT
1 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAT
* * * * *
138293 GAAGGTGCCAATATGCTGATTCAGGGCCAGCGATATTGGAC-T-----T
1 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAT
* * *
138336 AAAGGTGCCAATTTGTTGATTCAAGGCCAGCTACATTGGACTTAAAGAA
1 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAT
* * *
138385 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGGCTTA
1 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTA
138429 GAAGGGTTGC
Statistics
Matches: 374, Mismatches: 34, Indels: 32
0.85 0.08 0.07
Matches are distributed among these distances:
43 75 0.20
44 2 0.01
48 92 0.25
49 159 0.43
52 41 0.11
53 5 0.01
ACGTcount: A:0.32, C:0.18, G:0.25, T:0.25
Consensus pattern (49 bp):
AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAT
Found at i:138238 original size:189 final size:184
Alignment explanation
Indices: 138006--138428 Score: 596
Period size: 189 Copynumber: 2.2 Consensus size: 184
137996 TTAAAGATGG
138006 AAAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGTGCCAATGTGC
1 AAAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGTGCCAATGTGC
* *
138071 TGATTCAAGGCCAGCTACATTGGACTTAAAGATAAAGGTGCCAATGTGCTGAGTCAAGGCCAGCT
66 TGATTCAAGGCCAGCTACATTGGACTTAAAGATAAAGGTGCCAATATGCTGAGTCAAGGCCAGCG
*
138136 ACATTGGACTTAAAGATAAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTT
131 ACATTGGAC-T-----TAAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTT
* * * *
138196 -AAAGGTGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGGTGAGGTGCCAATGTGC
1 AAAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGTGCCAATGTGC
* * * *
138260 TGATTCAAGGCTAGCTACATTGGACTTAAAGATGAAGGTGCCAATATGCTGATTCAGGGCCAGCG
66 TGATTCAAGGCCAGCTACATTGGACTTAAAGATAAAGGTGCCAATATGCTGAGTCAAGGCCAGCG
* * *
138325 ATATTGGACTTAAAGGTGCCAATTTGTTGATTCAAGGCCAGCTACATTGGACTT
131 ACATTGGACTTAAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTT
* *
138379 AAAGAAAAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGGCTTA
1 -----AAAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTTA
138429 GAAGGGTTGC
Statistics
Matches: 209, Mismatches: 18, Indels: 13
0.87 0.08 0.05
Matches are distributed among these distances:
183 41 0.20
188 1 0.00
189 167 0.80
ACGTcount: A:0.31, C:0.18, G:0.26, T:0.25
Consensus pattern (184 bp):
AAAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGTGCCAATGTGC
TGATTCAAGGCCAGCTACATTGGACTTAAAGATAAAGGTGCCAATATGCTGAGTCAAGGCCAGCG
ACATTGGACTTAAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTT
Found at i:138469 original size:32 final size:32
Alignment explanation
Indices: 138421--138621 Score: 325
Period size: 32 Copynumber: 6.2 Consensus size: 32
138411 CCAGCTATAT
138421 TGGGC-TTAGA-AGGGTTGCCACCGACTTGTG
1 TGGGCTTTAGAGAGGGTTGCCACCGACTTGTG
138451 TGGGCTTTAGAGAGGGTTGCCACCGACTTGTG
1 TGGGCTTTAGAGAGGGTTGCCACCGACTTGTG
*
138483 TGGGCTTTAGAGAGGGTTGCCACCAACTTGTG
1 TGGGCTTTAGAGAGGGTTGCCACCGACTTGTG
138515 TGGGCTTTAGAGAGGGTTGCCACCGACTTGTG
1 TGGGCTTTAGAGAGGGTTGCCACCGACTTGTG
* * *
138547 TAGGCTTTAGAAGAAGGTTGCCACCGACTTATG
1 TGGGCTTTAG-AGAGGGTTGCCACCGACTTGTG
138580 TGGGCTTTAGAGAAGGGTTTGCCACCGACTTGTG
1 TGGGCTTTAGAG-AGGG-TTGCCACCGACTTGTG
138614 TGGGCTTT
1 TGGGCTTT
138622 GAAAAGAACA
Statistics
Matches: 158, Mismatches: 8, Indels: 6
0.92 0.05 0.03
Matches are distributed among these distances:
30 5 0.03
31 5 0.03
32 93 0.59
33 32 0.20
34 23 0.15
ACGTcount: A:0.18, C:0.18, G:0.35, T:0.29
Consensus pattern (32 bp):
TGGGCTTTAGAGAGGGTTGCCACCGACTTGTG
Found at i:146656 original size:52 final size:52
Alignment explanation
Indices: 146569--146693 Score: 198
Period size: 52 Copynumber: 2.4 Consensus size: 52
146559 ATATGAAAAG
* * * *
146569 TTGCTTGCATGTATCGAGACATTTAATAGTGTATCGATACATCTGGGCAAAT
1 TTGCCTGCATGTATCGATACATTTAATAATATATCGATACATCTGGGCAAAT
146621 TTGCCTGCATGTATCGATACAGTTT-ATAATATATCGATACATCTGGGCAAAT
1 TTGCCTGCATGTATCGATACA-TTTAATAATATATCGATACATCTGGGCAAAT
146673 TTGCCTGCATGTATCGATACA
1 TTGCCTGCATGTATCGATACA
146694 AAGATCAGTG
Statistics
Matches: 68, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
52 65 0.96
53 3 0.04
ACGTcount: A:0.29, C:0.18, G:0.19, T:0.34
Consensus pattern (52 bp):
TTGCCTGCATGTATCGATACATTTAATAATATATCGATACATCTGGGCAAAT
Found at i:146708 original size:52 final size:52
Alignment explanation
Indices: 146594--146713 Score: 179
Period size: 52 Copynumber: 2.3 Consensus size: 52
146584 GAGACATTTA
***
146594 ATAGTGTATCGATACATCTGGGCAAATTTGCCTGCATGTATCGATACAGTTT
1 ATAGTGTATCGATACATCTGGGCAAATTTGCCTGCATGTATCGATACAGAAG
* *
146646 ATAATATATCGATACATCTGGGCAAATTTGCCTGCATGTATCGATACA-AAG
1 ATAGTGTATCGATACATCTGGGCAAATTTGCCTGCATGTATCGATACAGAAG
146697 ATCAGTGTATCGATACA
1 AT-AGTGTATCGATACA
146714 ATGTATCGAT
Statistics
Matches: 60, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
51 2 0.03
52 58 0.97
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.32
Consensus pattern (52 bp):
ATAGTGTATCGATACATCTGGGCAAATTTGCCTGCATGTATCGATACAGAAG
Found at i:146720 original size:13 final size:13
Alignment explanation
Indices: 146702--146726 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
146692 CAAAGATCAG
146702 TGTATCGATACAA
1 TGTATCGATACAA
146715 TGTATCGATACA
1 TGTATCGATACA
146727 TTTGAGTAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:146807 original size:13 final size:13
Alignment explanation
Indices: 146789--146813 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
146779 CAAAAAAATA
146789 TGTATCGATACAT
1 TGTATCGATACAT
146802 TGTATCGATACA
1 TGTATCGATACA
146814 ACACTTTATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:149224 original size:33 final size:32
Alignment explanation
Indices: 149164--149228 Score: 94
Period size: 33 Copynumber: 2.0 Consensus size: 32
149154 CAATTTGCCC
*
149164 ATGTATCGATACAATGAACATGTATCGATACA
1 ATGTATCGATACAAGGAACATGTATCGATACA
* *
149196 ATGTATCGGTACAAGGCAGCATGTATCGATACA
1 ATGTATCGATACAAGG-AACATGTATCGATACA
149229 TCTAGGTGTG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 14 0.48
33 15 0.52
ACGTcount: A:0.37, C:0.17, G:0.20, T:0.26
Consensus pattern (32 bp):
ATGTATCGATACAAGGAACATGTATCGATACA
Found at i:149720 original size:61 final size:61
Alignment explanation
Indices: 149609--149736 Score: 161
Period size: 61 Copynumber: 2.1 Consensus size: 61
149599 ACATTTTTTG
* * * *
149609 CATCTTTAAGCCCAATATCATTGGCCTTGAATCAACATATTGGCACCTTTATCA-TCATTCT
1 CATCTTTAAGCACAATATCATTAGCCCTGAATCAACACATTGGCACCTTTATCACTC-TTCT
* * *
149670 CATCTTTAAGCACAATATC-TCTAGCCCTGAATCAGCACATTTGCATCTTTATCACTCTTCT
1 CATCTTTAAGCACAATATCAT-TAGCCCTGAATCAACACATTGGCACCTTTATCACTCTTCT
149731 CATCTT
1 CATCTT
149737 CATCATCTTT
Statistics
Matches: 58, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
60 1 0.02
61 55 0.95
62 2 0.03
ACGTcount: A:0.27, C:0.28, G:0.09, T:0.37
Consensus pattern (61 bp):
CATCTTTAAGCACAATATCATTAGCCCTGAATCAACACATTGGCACCTTTATCACTCTTCT
Found at i:153886 original size:15 final size:16
Alignment explanation
Indices: 153866--153898 Score: 52
Period size: 14 Copynumber: 2.2 Consensus size: 16
153856 GAAAAAAAAC
153866 AAAAAAAT-AATAAAT
1 AAAAAAATAAATAAAT
153881 -AAAAAATAAATAAAT
1 AAAAAAATAAATAAAT
153896 AAA
1 AAA
153899 TCAAATGAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 3
0.84 0.00 0.16
Matches are distributed among these distances:
14 7 0.44
15 7 0.44
16 2 0.12
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (16 bp):
AAAAAAATAAATAAAT
Found at i:155462 original size:85 final size:85
Alignment explanation
Indices: 155360--155576 Score: 246
Period size: 83 Copynumber: 2.6 Consensus size: 85
155350 TACCTTTATG
* * * *
155360 GTGACCTGTCAGCTTAGTCTCCAGTTAACCTTCATCTCATTGTTTACCTGTAAGCTCAGTCCTTA
1 GTGACCTATCAGCTTAGTCTTCAGTCAACCTTCATCTCATTGTTTACCTGTAAGCTCAGTCC-CA
155425 C-TAAACCCATTA-TCCCTACGA
65 CGTAAACCCATTACT-CCTA-GA
* * * * ** *
155446 -TGACCTATCAGGTTAGTCTTCTGCCAACC-T-ATCTCATTATTTACCTGTCGGCTCAGTCCCCC
1 GTGACCTATCAGCTTAGTCTTCAGTCAACCTTCATCTCATTGTTTACCTGTAAGCTCAGTCCCAC
*
155508 GTAAACCCATTACTCCTATA
66 GTAAACCCATTACTCCTAGA
* *
155528 GTGACCTATCAGCTCAGTCTTCGGTCAACCTTCATCTCATTGTTTACCT
1 GTGACCTATCAGCTTAGTCTTCAGTCAACCTTCATCTCATTGTTTACCT
155577 ATCAACTTGG
Statistics
Matches: 109, Mismatches: 17, Indels: 11
0.80 0.12 0.08
Matches are distributed among these distances:
82 2 0.02
83 66 0.61
84 3 0.03
85 38 0.35
ACGTcount: A:0.22, C:0.31, G:0.13, T:0.34
Consensus pattern (85 bp):
GTGACCTATCAGCTTAGTCTTCAGTCAACCTTCATCTCATTGTTTACCTGTAAGCTCAGTCCCAC
GTAAACCCATTACTCCTAGA
Found at i:155746 original size:128 final size:131
Alignment explanation
Indices: 155517--155847 Score: 384
Period size: 128 Copynumber: 2.5 Consensus size: 131
155507 CGTAAACCCA
* * * * *
155517 TTACTCCTATAGTGACCTATCAGCTCAGTCTTCGGTCAACCTTCATCTCATTGTTTACCTATCAA
1 TTACCCCTATGGTGACCTATCAGCTCAGTCTTCGGTCAACCTTCATCTTATTGTTTACCTGTCGA
* *
155582 CTTGGTCTCGAGAAACACCTTTTATCCCTTACCTACC-T-ATG-GA-CTCAGTCCTAAGAGACAC
66 CTTAGTCTCGAGAAACACCTTTTATCCCTTACCTACCGTCATGTCAGCTCAGTCCTAAGAGACAC
155643 C
131 C
* * * * * *
155644 TTTACCCCTATGGTGACTTATCCGCTCAATCTTCGATCAACCTTCATCTTATTATTTACTTGTCG
1 -TTACCCCTATGGTGACCTATCAGCTCAGTCTTCGGTCAACCTTCATCTTATTGTTTACCTGTCG
* ** ** * *
155709 GCTTAGTCTCGAGAAACACCTTTTATCTTTTGTCTACCTGTCATGTCAGCTCAGTCTTAGGAGAC
65 ACTTAGTCTCGAGAAACACCTTTTATCCCTTACCTACC-GTCATGTCAGCTCAGTCCTAAGAGAC
155774 ACC
129 ACC
* * * *
155777 TTATCCCT-TGGTGACCTGTCAACTCAGTCTCCGGTCAACCTTCATCTTATTGTTTACCTGTCGA
1 TTACCCCTATGGTGACCTATCAGCTCAGTCTTCGGTCAACCTTCATCTTATTGTTTACCTGTCGA
*
155841 CTCAGTC
66 CTTAGTC
155848 CTCGGTAAAC
Statistics
Matches: 166, Mismatches: 32, Indels: 7
0.81 0.16 0.03
Matches are distributed among these distances:
128 85 0.51
130 1 0.01
131 55 0.33
132 8 0.05
133 17 0.10
ACGTcount: A:0.21, C:0.29, G:0.14, T:0.35
Consensus pattern (131 bp):
TTACCCCTATGGTGACCTATCAGCTCAGTCTTCGGTCAACCTTCATCTTATTGTTTACCTGTCGA
CTTAGTCTCGAGAAACACCTTTTATCCCTTACCTACCGTCATGTCAGCTCAGTCCTAAGAGACAC
C
Found at i:156017 original size:42 final size:41
Alignment explanation
Indices: 155959--156141 Score: 145
Period size: 42 Copynumber: 4.4 Consensus size: 41
155949 TCTCTTGGTG
* *
155959 ACCTGTTAGCTTAGTCTCC-AGTCAACCTTCATCTCTTTGTTT
1 ACCTGTCAGCTCAGTCTCCGA-TCAACCTTCATC-CTTTGTTT
* * *
156001 ACTTGTCAGCTCAGTCTTCGATCAATCTTCATCCTTTGTTT
1 ACCTGTCAGCTCAGTCTCCGATCAACCTTCATCCTTTGTTT
* * * * * * * *
156042 ACCTATCAACTCAGTCCCCGGTAAACCCTTACA-CCTATGGTG
1 ACCTGTCAGCTCAGTCTCCGATCAA-CCTT-CATCCTTTGTTT
* * * *
156084 ACCTGTTAGCTCAGTCCCCGATCAAGCTTCATCTCCTTGTTT
1 ACCTGTCAGCTCAGTCTCCGATCAACCTTCATC-CTTTGTTT
*
156126 ACCTGTCAGCTTAGTC
1 ACCTGTCAGCTCAGTC
156142 CCTGGTAAAC
Statistics
Matches: 108, Mismatches: 28, Indels: 10
0.74 0.19 0.07
Matches are distributed among these distances:
40 2 0.02
41 30 0.28
42 73 0.68
43 3 0.03
ACGTcount: A:0.19, C:0.31, G:0.14, T:0.36
Consensus pattern (41 bp):
ACCTGTCAGCTCAGTCTCCGATCAACCTTCATCCTTTGTTT
Found at i:156183 original size:211 final size:211
Alignment explanation
Indices: 155793--156213 Score: 452
Period size: 211 Copynumber: 2.0 Consensus size: 211
155783 CTTGGTGACC
* * * * *
155793 TGTCAACTCAGTCTCCGGTCAACCTTCATCTTATTGTTTACCTGTCGACTCAGTCCTCGGTAAAC
1 TGTCAACTCAGTCTCCGATCAACCTTCATCCTATTGTTTACCTATCAACTCAGTCCCCGGTAAAC
* *** * * * **
155858 CCATTACCCCTATGGTGACCAATCAGCTCAGTCTTTGGCCAATCTTTATCTTTTTGTTAACCTAT
66 CCATTACACCTATGGTGACCAATCAGCTCAGTCCCCGACCAAGCTTCATCTCCTTGTTAACCTAT
** * * * * * *
155923 TTGCTTTGTCTCGGGAGACACCCTTATCTCTTGGTGACCTGTTAGCTTAGTCTCCAGTCAACCT-
131 CAGCTTAGTCCCGGGAAACACCCTTACCTCTTGGTGACCTATCAGCTTAGTCTCCAGTCAACCTC
*
155987 TCATCTCTTTGTTTACT
196 T-ATCTCATTGTTTACT
* * *
156004 TGTCAGCTCAGTCTTCGATCAATCTTCATCCT-TTGTTTACCTATCAACTCAGTCCCCGGTAAAC
1 TGTCAACTCAGTCTCCGATCAACCTTCATCCTATTGTTTACCTATCAACTCAGTCCCCGGTAAAC
** * * * *
156068 CC-TTACACCTATGGTGACCTGTTAGCTCAGTCCCCGATCAAGCTTCATCTCCTTGTTTACCTGT
66 CCATTACACCTATGGTGACCAATCAGCTCAGTCCCCGACCAAGCTTCATCTCCTTGTTAACCTAT
* * * ***
156132 CAGCTTAGTCCCTGGTAAACCCCCTTACCTTTTTGGTGACCTATCAGCTTAGTCTTTTGTCAACC
131 CAGCTTAGTCCC-GGGAAACACCCTTACC-TCTTGGTGACCTATCAGCTTAGTCTCCAGTCAACC
156197 TCTATCTCATTGTTTAC
194 TCTATCTCATTGTTTAC
156214 CCGTCGGCCT
Statistics
Matches: 169, Mismatches: 38, Indels: 6
0.79 0.18 0.03
Matches are distributed among these distances:
209 55 0.33
210 43 0.25
211 70 0.41
212 1 0.01
ACGTcount: A:0.19, C:0.30, G:0.14, T:0.37
Consensus pattern (211 bp):
TGTCAACTCAGTCTCCGATCAACCTTCATCCTATTGTTTACCTATCAACTCAGTCCCCGGTAAAC
CCATTACACCTATGGTGACCAATCAGCTCAGTCCCCGACCAAGCTTCATCTCCTTGTTAACCTAT
CAGCTTAGTCCCGGGAAACACCCTTACCTCTTGGTGACCTATCAGCTTAGTCTCCAGTCAACCTC
TATCTCATTGTTTACT
Found at i:157440 original size:13 final size:13
Alignment explanation
Indices: 157411--157439 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
157401 CATAGCTTGG
157411 AAAATGGAAAAAT
1 AAAATGGAAAAAT
157424 AAAAT-GAAAAAT
1 AAAATGGAAAAAT
157436 AAAA
1 AAAA
157440 AAAAATGGAG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 11 0.69
13 5 0.31
ACGTcount: A:0.76, C:0.00, G:0.10, T:0.14
Consensus pattern (13 bp):
AAAATGGAAAAAT
Found at i:157583 original size:14 final size:14
Alignment explanation
Indices: 157566--157610 Score: 56
Period size: 14 Copynumber: 3.1 Consensus size: 14
157556 AAAACTGGAG
157566 AGAAAAAAA-AAAGA
1 AGAAAAAAAGAAA-A
157580 AGAAAAAAAGAAAA
1 AGAAAAAAAGAAAA
157594 AGACAAAAAAGGAAAA
1 AGA-AAAAAA-GAAAA
157610 A
1 A
157611 TCAAAGAAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
14 13 0.46
15 9 0.32
16 6 0.21
ACGTcount: A:0.82, C:0.02, G:0.16, T:0.00
Consensus pattern (14 bp):
AGAAAAAAAGAAAA
Found at i:157601 original size:16 final size:17
Alignment explanation
Indices: 157568--157610 Score: 54
Period size: 16 Copynumber: 2.6 Consensus size: 17
157558 AACTGGAGAG
*
157568 AAAAA-AAAAAGAAGAA
1 AAAAAGAAAAAGAACAA
157584 AAAAAGAAAAAG-ACAA
1 AAAAAGAAAAAGAACAA
*
157600 AAAAGGAAAAA
1 AAAAAGAAAAA
157611 TCAAAGAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
16 18 0.75
17 6 0.25
ACGTcount: A:0.84, C:0.02, G:0.14, T:0.00
Consensus pattern (17 bp):
AAAAAGAAAAAGAACAA
Found at i:158482 original size:7 final size:7
Alignment explanation
Indices: 158459--158499 Score: 50
Period size: 7 Copynumber: 5.9 Consensus size: 7
158449 GAAATTTTTA
158459 AAATAAT
1 AAATAAT
158466 -AAT-AT
1 AAATAAT
158471 AAAATAAT
1 -AAATAAT
158479 AAATAATT
1 AAATAA-T
158487 AAATAAT
1 AAATAAT
158494 AAATAA
1 AAATAA
158500 ATTCTTTTTC
Statistics
Matches: 30, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
5 2 0.07
6 3 0.10
7 16 0.53
8 9 0.30
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (7 bp):
AAATAAT
Found at i:160942 original size:13 final size:13
Alignment explanation
Indices: 160924--160949 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
160914 TACACCAAGT
160924 ATGTATCGATACA
1 ATGTATCGATACA
160937 ATGTATCGATACA
1 ATGTATCGATACA
160950 CAAAAAAATG
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:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:163203 original size:21 final size:21
Alignment explanation
Indices: 163170--163214 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
163160 TTGCAAGTTG
*
163170 AAATAAAGAAGTTGGCTAATGA
1 AAATAAAGAAGTTAGCTAA-GA
*
163192 AAATAATG-AGTTAGCTAAGA
1 AAATAAAGAAGTTAGCTAAGA
163212 AAA
1 AAA
163215 ATGAAAAATT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 9 0.43
22 7 0.33
ACGTcount: A:0.53, C:0.04, G:0.20, T:0.22
Consensus pattern (21 bp):
AAATAAAGAAGTTAGCTAAGA
Found at i:165037 original size:15 final size:15
Alignment explanation
Indices: 165017--165055 Score: 60
Period size: 15 Copynumber: 2.6 Consensus size: 15
165007 TAAAAATGTC
*
165017 CAAAATGAGGAAGCT
1 CAAAATGAAGAAGCT
165032 CAAAATGAAGAAGCT
1 CAAAATGAAGAAGCT
*
165047 CCAAATGAA
1 CAAAATGAA
165056 ATTGATGAAC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.51, C:0.15, G:0.21, T:0.13
Consensus pattern (15 bp):
CAAAATGAAGAAGCT
Found at i:167300 original size:20 final size:20
Alignment explanation
Indices: 167257--167302 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 20
167247 AAATCTTTTG
167257 CAAAATACTTGTTTTTCACTT
1 CAAAATACTTGTTTTTCAC-T
*
167278 CAAATTACTTCGTTTTTCA-T
1 CAAAATACTT-GTTTTTCACT
167298 CAAAA
1 CAAAA
167303 CCAGCATCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
20 5 0.23
21 9 0.41
22 8 0.36
ACGTcount: A:0.33, C:0.20, G:0.04, T:0.43
Consensus pattern (20 bp):
CAAAATACTTGTTTTTCACT
Found at i:169320 original size:18 final size:18
Alignment explanation
Indices: 169297--169333 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
169287 AAGGGGGAGA
169297 TTGTTAGGATCTTGGTTT
1 TTGTTAGGATCTTGGTTT
*
169315 TTGTTAGGATTTTGGTTT
1 TTGTTAGGATCTTGGTTT
169333 T
1 T
169334 GATATAACAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.11, C:0.03, G:0.27, T:0.59
Consensus pattern (18 bp):
TTGTTAGGATCTTGGTTT
Found at i:169550 original size:21 final size:21
Alignment explanation
Indices: 169517--169557 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
169507 CTAAGTAAAA
169517 ATACGTATTGTATCAATACAT
1 ATACGTATTGTATCAATACAT
*
169538 ATAC-TATTGGTATTAATACA
1 ATACGTATT-GTATCAATACA
169558 CAAGGTTGAC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.39, C:0.12, G:0.10, T:0.39
Consensus pattern (21 bp):
ATACGTATTGTATCAATACAT
Found at i:169622 original size:20 final size:20
Alignment explanation
Indices: 169597--169667 Score: 74
Period size: 20 Copynumber: 3.5 Consensus size: 20
169587 ACCCTGAAAA
169597 GTATCGATACACATATAAAT
1 GTATCGATACACATATAAAT
* **
169617 GTATCGATACAAAT-TGCAT
1 GTATCGATACACATATAAAT
*
169636 AGTATCGATACACA-AAAATAT
1 -GTATCGATACACATATAA-AT
169657 GTATCGATACA
1 GTATCGATACA
169668 AGACATTGGC
Statistics
Matches: 41, Mismatches: 7, Indels: 6
0.76 0.13 0.11
Matches are distributed among these distances:
19 3 0.07
20 36 0.88
21 2 0.05
ACGTcount: A:0.44, C:0.15, G:0.13, T:0.28
Consensus pattern (20 bp):
GTATCGATACACATATAAAT
Found at i:169717 original size:53 final size:53
Alignment explanation
Indices: 169637--169773 Score: 229
Period size: 53 Copynumber: 2.6 Consensus size: 53
169627 AAATTGCATA
*
169637 GTATCGATACACAAAAATATGTATCGATACAAGACATTGGCAGTAGCCAAATTT
1 GTATCGATACAC-AAAATATGTATCGATACAAGACATTGGCAGTACCCAAATTT
* * *
169691 GTATCGATACACACAATATGTATCGATACAGGTCATTGGCAGTACCCAAATTT
1 GTATCGATACACAAAATATGTATCGATACAAGACATTGGCAGTACCCAAATTT
169744 GTATCGATACACAAAATATGTATCGATACA
1 GTATCGATACACAAAATATGTATCGATACA
169774 TTGGAAGTAG
Statistics
Matches: 78, Mismatches: 5, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
53 66 0.85
54 12 0.15
ACGTcount: A:0.39, C:0.18, G:0.16, T:0.27
Consensus pattern (53 bp):
GTATCGATACACAAAATATGTATCGATACAAGACATTGGCAGTACCCAAATTT
Found at i:169816 original size:10 final size:10
Alignment explanation
Indices: 169797--169827 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
169787 AATCTCATTT
169797 TCACTGTTCA
1 TCACTGTTCA
*
169807 TCACTATTCA
1 TCACTGTTCA
169817 TCACTGTTCA
1 TCACTGTTCA
169827 T
1 T
169828 GTATCGATAC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.23, C:0.29, G:0.06, T:0.42
Consensus pattern (10 bp):
TCACTGTTCA
Found at i:169849 original size:21 final size:22
Alignment explanation
Indices: 169815--169870 Score: 105
Period size: 21 Copynumber: 2.6 Consensus size: 22
169805 CATCACTATT
169815 CATCACTGTTCATGTATCGATA
1 CATCACTGTTCATGTATCGATA
169837 CATCACT-TTCATGTATCGATA
1 CATCACTGTTCATGTATCGATA
169858 CATCACTGTTCAT
1 CATCACTGTTCAT
169871 AGATCACTGT
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
21 21 0.64
22 12 0.36
ACGTcount: A:0.27, C:0.25, G:0.11, T:0.38
Consensus pattern (22 bp):
CATCACTGTTCATGTATCGATA
Found at i:169971 original size:13 final size:13
Alignment explanation
Indices: 169953--169978 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
169943 ACATATTTGT
169953 GTGTATCGATACA
1 GTGTATCGATACA
169966 GTGTATCGATACA
1 GTGTATCGATACA
169979 TCATAAATAG
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:0.31, C:0.15, G:0.23, T:0.31
Consensus pattern (13 bp):
GTGTATCGATACA
Found at i:170521 original size:34 final size:35
Alignment explanation
Indices: 170458--170524 Score: 102
Period size: 37 Copynumber: 1.9 Consensus size: 35
170448 CTAAGTGATT
170458 GAGAGGTTCTATCTTAGCCTTTGAAAAAGATAGAGA
1 GAGAGGTTCTATCTTAGCCTTTG-AAAAGATAGAGA
170494 GAGAGGTTTCTATCTTAGCC-TTG-AAAGATAG
1 GAGAGG-TTCTATCTTAGCCTTTGAAAAGATAG
170525 TGTTGTAAGG
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
34 8 0.27
36 9 0.30
37 13 0.43
ACGTcount: A:0.33, C:0.12, G:0.25, T:0.30
Consensus pattern (35 bp):
GAGAGGTTCTATCTTAGCCTTTGAAAAGATAGAGA
Found at i:173630 original size:13 final size:13
Alignment explanation
Indices: 173612--173636 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
173602 TTTTCCAGAT
173612 TGTATCGATACAA
1 TGTATCGATACAA
173625 TGTATCGATACA
1 TGTATCGATACA
173637 TTGCTTCAGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:174662 original size:31 final size:31
Alignment explanation
Indices: 174627--174687 Score: 104
Period size: 31 Copynumber: 2.0 Consensus size: 31
174617 TTGATTATTT
* *
174627 GTTATAAAGGAAGAAACTGAAAATATTGAAA
1 GTTATAAAGGAAGAAACTAAAAACATTGAAA
174658 GTTATAAAGGAAGAAACTAAAAACATTGAA
1 GTTATAAAGGAAGAAACTAAAAACATTGAA
174688 GAATATTGGT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.56, C:0.05, G:0.18, T:0.21
Consensus pattern (31 bp):
GTTATAAAGGAAGAAACTAAAAACATTGAAA
Found at i:175308 original size:21 final size:21
Alignment explanation
Indices: 175275--175315 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
175265 CTAAGTAAAA
175275 ATACGTATTGTATCAATACAT
1 ATACGTATTGTATCAATACAT
*
175296 ATAC-TATTGGTATTAATACA
1 ATACGTATT-GTATCAATACA
175316 CAAGGTTGAC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.39, C:0.12, G:0.10, T:0.39
Consensus pattern (21 bp):
ATACGTATTGTATCAATACAT
Found at i:175380 original size:20 final size:20
Alignment explanation
Indices: 175355--175425 Score: 74
Period size: 20 Copynumber: 3.5 Consensus size: 20
175345 ACCCTGAAAA
175355 GTATCGATACACATATAAAT
1 GTATCGATACACATATAAAT
* **
175375 GTATCGATACAAAT-TGCAT
1 GTATCGATACACATATAAAT
*
175394 AGTATCGATACACA-AAAATAT
1 -GTATCGATACACATATAA-AT
175415 GTATCGATACA
1 GTATCGATACA
175426 AGACATTGGC
Statistics
Matches: 41, Mismatches: 7, Indels: 6
0.76 0.13 0.11
Matches are distributed among these distances:
19 3 0.07
20 36 0.88
21 2 0.05
ACGTcount: A:0.44, C:0.15, G:0.13, T:0.28
Consensus pattern (20 bp):
GTATCGATACACATATAAAT
Found at i:175475 original size:53 final size:53
Alignment explanation
Indices: 175395--175531 Score: 229
Period size: 53 Copynumber: 2.6 Consensus size: 53
175385 AAATTGCATA
*
175395 GTATCGATACACAAAAATATGTATCGATACAAGACATTGGCAGTAGCCAAATTT
1 GTATCGATACAC-AAAATATGTATCGATACAAGACATTGGCAGTACCCAAATTT
* * *
175449 GTATCGATACACACAATATGTATCGATACAGGTCATTGGCAGTACCCAAATTT
1 GTATCGATACACAAAATATGTATCGATACAAGACATTGGCAGTACCCAAATTT
175502 GTATCGATACACAAAATATGTATCGATACA
1 GTATCGATACACAAAATATGTATCGATACA
175532 TTGGAAGTAG
Statistics
Matches: 78, Mismatches: 5, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
53 66 0.85
54 12 0.15
ACGTcount: A:0.39, C:0.18, G:0.16, T:0.27
Consensus pattern (53 bp):
GTATCGATACACAAAATATGTATCGATACAAGACATTGGCAGTACCCAAATTT
Found at i:175574 original size:10 final size:10
Alignment explanation
Indices: 175555--175585 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
175545 AATCTCATTT
175555 TCACTGTTCA
1 TCACTGTTCA
*
175565 TCACTATTCA
1 TCACTGTTCA
175575 TCACTGTTCA
1 TCACTGTTCA
175585 T
1 T
175586 GTATCGATAC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.23, C:0.29, G:0.06, T:0.42
Consensus pattern (10 bp):
TCACTGTTCA
Found at i:175607 original size:21 final size:22
Alignment explanation
Indices: 175573--175628 Score: 105
Period size: 21 Copynumber: 2.6 Consensus size: 22
175563 CATCACTATT
175573 CATCACTGTTCATGTATCGATA
1 CATCACTGTTCATGTATCGATA
175595 CATCACT-TTCATGTATCGATA
1 CATCACTGTTCATGTATCGATA
175616 CATCACTGTTCAT
1 CATCACTGTTCAT
175629 AGATCACTGT
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
21 21 0.64
22 12 0.36
ACGTcount: A:0.27, C:0.25, G:0.11, T:0.38
Consensus pattern (22 bp):
CATCACTGTTCATGTATCGATA
Found at i:175729 original size:13 final size:13
Alignment explanation
Indices: 175711--175736 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
175701 ACATATTTGT
175711 GTGTATCGATACA
1 GTGTATCGATACA
175724 GTGTATCGATACA
1 GTGTATCGATACA
175737 TCATAAATAG
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:0.31, C:0.15, G:0.23, T:0.31
Consensus pattern (13 bp):
GTGTATCGATACA
Found at i:176279 original size:34 final size:35
Alignment explanation
Indices: 176216--176282 Score: 102
Period size: 37 Copynumber: 1.9 Consensus size: 35
176206 CTAAGTGATT
176216 GAGAGGTTCTATCTTAGCCTTTGAAAAAGATAGAGA
1 GAGAGGTTCTATCTTAGCCTTTG-AAAAGATAGAGA
176252 GAGAGGTTTCTATCTTAGCC-TTG-AAAGATAG
1 GAGAGG-TTCTATCTTAGCCTTTGAAAAGATAG
176283 TGTTGTAAGG
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
34 8 0.27
36 9 0.30
37 13 0.43
ACGTcount: A:0.33, C:0.12, G:0.25, T:0.30
Consensus pattern (35 bp):
GAGAGGTTCTATCTTAGCCTTTGAAAAGATAGAGA
Found at i:176835 original size:20 final size:21
Alignment explanation
Indices: 176812--176864 Score: 72
Period size: 20 Copynumber: 2.6 Consensus size: 21
176802 ACAATTCAAA
** *
176812 GTATCGATACATGTTACA-AT
1 GTATCGATACATGAAAAAGAT
176832 GTATCGATACATGAAAAAGAT
1 GTATCGATACATGAAAAAGAT
176853 GTATCGATACAT
1 GTATCGATACAT
176865 TTCTTGGCAG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 15 0.52
21 14 0.48
ACGTcount: A:0.40, C:0.13, G:0.17, T:0.30
Consensus pattern (21 bp):
GTATCGATACATGAAAAAGAT
Found at i:178401 original size:20 final size:20
Alignment explanation
Indices: 178358--178401 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
178348 TTCAAGTGCA
*
178358 TGTATCGATACATTATGAAT
1 TGTATCGATACATTAGGAAT
178378 TGTATCGATACATT-GGAAT
1 TGTATCGATACATTAGGAAT
178397 GTGTA
1 -TGTA
178402 AGTGCGAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 4 0.18
20 18 0.82
ACGTcount: A:0.32, C:0.09, G:0.20, T:0.39
Consensus pattern (20 bp):
TGTATCGATACATTAGGAAT
Found at i:178730 original size:19 final size:19
Alignment explanation
Indices: 178703--178770 Score: 76
Period size: 19 Copynumber: 3.9 Consensus size: 19
178693 AATTCAACAA
178703 TTTGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
*
178722 TTTGCATCGATAC--AA--
1 TTTGTATCGATACATAAGT
178737 --TGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
*
178754 ATTGTATCGATACATAA
1 TTTGTATCGATACATAA
178771 TTAGTTACTG
Statistics
Matches: 41, Mismatches: 2, Indels: 12
0.75 0.04 0.22
Matches are distributed among these distances:
13 10 0.24
15 2 0.05
17 2 0.05
19 27 0.66
ACGTcount: A:0.35, C:0.13, G:0.15, T:0.37
Consensus pattern (19 bp):
TTTGTATCGATACATAAGT
Found at i:178746 original size:32 final size:32
Alignment explanation
Indices: 178705--178767 Score: 108
Period size: 32 Copynumber: 2.0 Consensus size: 32
178695 TTCAACAATT
*
178705 TGTATCGATACATAAGTTTTGCATCGATACAA
1 TGTATCGATACATAAGTATTGCATCGATACAA
*
178737 TGTATCGATACATAAGTATTGTATCGATACA
1 TGTATCGATACATAAGTATTGCATCGATACA
178768 TAATTAGTTA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.35, C:0.14, G:0.16, T:0.35
Consensus pattern (32 bp):
TGTATCGATACATAAGTATTGCATCGATACAA
Done.