Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009235.1 Hibiscus syriacus cultivar Beakdansim tig00112857_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: 1478786
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 1 of 6
Found at i:9259 original size:20 final size:20
Alignment explanation
Indices: 9230--9275 Score: 83
Period size: 20 Copynumber: 2.3 Consensus size: 20
9220 AACAGTATCT
*
9230 GAAAGCGGAAAAACATTTTC
1 GAAAGGGGAAAAACATTTTC
9250 GAAAGGGGAAAAACATTTTC
1 GAAAGGGGAAAAACATTTTC
9270 GAAAGG
1 GAAAGG
9276 TGAGCTAGGC
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.46, C:0.11, G:0.26, T:0.17
Consensus pattern (20 bp):
GAAAGGGGAAAAACATTTTC
Found at i:10337 original size:7 final size:7
Alignment explanation
Indices: 10325--10361 Score: 58
Period size: 7 Copynumber: 5.4 Consensus size: 7
10315 GTTAAAGGAA
10325 GTCAACG
1 GTCAACG
10332 GTCAACG
1 GTCAACG
*
10339 GTC-ACA
1 GTCAACG
10345 GTCAACG
1 GTCAACG
10352 GTCAACG
1 GTCAACG
10359 GTC
1 GTC
10362 GGGTCGGGTC
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
6 5 0.19
7 22 0.81
ACGTcount: A:0.27, C:0.30, G:0.27, T:0.16
Consensus pattern (7 bp):
GTCAACG
Found at i:10349 original size:20 final size:20
Alignment explanation
Indices: 10324--10361 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
10314 GGTTAAAGGA
10324 AGTCAACGGTCAACGGTCAC
1 AGTCAACGGTCAACGGTCAC
10344 AGTCAACGGTCAACGGTC
1 AGTCAACGGTCAACGGTC
10362 GGGTCGGGTC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.29, C:0.29, G:0.26, T:0.16
Consensus pattern (20 bp):
AGTCAACGGTCAACGGTCAC
Found at i:17209 original size:18 final size:17
Alignment explanation
Indices: 17186--17219 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
17176 AATTAACGTT
17186 TATTCTAGATGAAAAAAA
1 TATTCTAGAT-AAAAAAA
*
17204 TATTCTATATAAAAAA
1 TATTCTAGATAAAAAA
17220 GCATATTTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.56, C:0.06, G:0.06, T:0.32
Consensus pattern (17 bp):
TATTCTAGATAAAAAAA
Found at i:18266 original size:23 final size:23
Alignment explanation
Indices: 18214--18267 Score: 63
Period size: 23 Copynumber: 2.3 Consensus size: 23
18204 TAAATGTTCA
*
18214 ATTCATTTAACATTCACGAACAT
1 ATTCGTTTAACATTCACGAACAT
* ** *
18237 ATGCGTTTAACATTCGTGAATAT
1 ATTCGTTTAACATTCACGAACAT
18260 ATTCGTTT
1 ATTCGTTT
18268 GGCATTTGTA
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.31, C:0.17, G:0.11, T:0.41
Consensus pattern (23 bp):
ATTCGTTTAACATTCACGAACAT
Found at i:18380 original size:21 final size:23
Alignment explanation
Indices: 18339--18380 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
18329 CCACTAATCC
18339 TTAAGCTCTAAAAGTTTCACAGT
1 TTAAGCTCTAAAAGTTTCACAGT
*
18362 TTAAGCT-TCAAAG-TTCACA
1 TTAAGCTCTAAAAGTTTCACA
18381 TTGTGTTTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 6 0.33
22 5 0.28
23 7 0.39
ACGTcount: A:0.36, C:0.19, G:0.12, T:0.33
Consensus pattern (23 bp):
TTAAGCTCTAAAAGTTTCACAGT
Found at i:21223 original size:21 final size:21
Alignment explanation
Indices: 21181--21223 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
21171 TTTCTGGGCT
* *
21181 AGGGGAATCGGTACCCATTCA
1 AGGGGAATCGATACCCACTCA
* *
21202 AGGGGAATCGATCCCCCCTCA
1 AGGGGAATCGATACCCACTCA
21223 A
1 A
21224 ACGAATATGA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.28, C:0.30, G:0.26, T:0.16
Consensus pattern (21 bp):
AGGGGAATCGATACCCACTCA
Found at i:22406 original size:30 final size:30
Alignment explanation
Indices: 22345--22504 Score: 230
Period size: 30 Copynumber: 5.3 Consensus size: 30
22335 CTAAGGAACA
* * ***
22345 TATGGATAGTTTACCTAGGTTCTTCGGGACC
1 TATGGATAG-TTACCGAGGATCTTTATGACC
22376 TATGGATAGTTACCGAGGATCTTTATGACC
1 TATGGATAGTTACCGAGGATCTTTATGACC
22406 TATGGATAGTTACCGAGGATCTTTATGACC
1 TATGGATAGTTACCGAGGATCTTTATGACC
*
22436 TCTGGATAGTTACCGAGGATCTTTATGACC
1 TATGGATAGTTACCGAGGATCTTTATGACC
* *
22466 TCTGGATAGTTACCAAGGATCTTTATGACC
1 TATGGATAGTTACCGAGGATCTTTATGACC
*
22496 TCTGGATAG
1 TATGGATAG
22505 GTCTTTCGGA
Statistics
Matches: 122, Mismatches: 7, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
30 113 0.93
31 9 0.07
ACGTcount: A:0.24, C:0.18, G:0.24, T:0.34
Consensus pattern (30 bp):
TATGGATAGTTACCGAGGATCTTTATGACC
Found at i:24508 original size:21 final size:22
Alignment explanation
Indices: 24464--24509 Score: 76
Period size: 22 Copynumber: 2.1 Consensus size: 22
24454 TTTTATGTGA
*
24464 ATTATTTTTTATGAGTTTTAAT
1 ATTATTTTTGATGAGTTTTAAT
24486 ATTATTTTTGATGAGTTTT-AT
1 ATTATTTTTGATGAGTTTTAAT
24507 ATT
1 ATT
24510 TTTAATTTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 5 0.22
22 18 0.78
ACGTcount: A:0.26, C:0.00, G:0.11, T:0.63
Consensus pattern (22 bp):
ATTATTTTTGATGAGTTTTAAT
Found at i:30354 original size:30 final size:30
Alignment explanation
Indices: 30318--30376 Score: 82
Period size: 30 Copynumber: 2.0 Consensus size: 30
30308 AATGGGATGG
*
30318 GAAAAACCGTTTATGCTAAACGGGGACGGA
1 GAAAAACCGTTTATGCTAAACGGAGACGGA
* * *
30348 GAAAAACTGTTTATGTTAAATGGAGACGG
1 GAAAAACCGTTTATGCTAAACGGAGACGG
30377 GTTTAGTAAT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.37, C:0.12, G:0.29, T:0.22
Consensus pattern (30 bp):
GAAAAACCGTTTATGCTAAACGGAGACGGA
Found at i:31852 original size:69 final size:69
Alignment explanation
Indices: 31773--32282 Score: 750
Period size: 69 Copynumber: 7.4 Consensus size: 69
31763 GATGTTGAAC
* * *
31773 GTAATGGAGATGATAATTGAAGTGGAGAAGTGGATGGTAGTGATTGAAGTGAAGTAGATAGTGGT
1 GTAATGGAGATGATAATTGAAGTGGAGAAGTGGATGATGGTGATTGAAGTGAAGTAGATGGTGGT
*
31838 AGAT
66 GGAT
* * *
31842 GTAATGGAGATGATAATTGAAGTGGAGAAGTGGATGATGGTGCTTGAAGTGAAGCATATGGTGGT
1 GTAATGGAGATGATAATTGAAGTGGAGAAGTGGATGATGGTGATTGAAGTGAAGTAGATGGTGGT
31907 GGAT
66 GGAT
* * * *
31911 ATAATGGAGATGATAATTGAAGTGGAGAAGTGGATGGTGGTGATCGAAGTGAATTAGATGGTGGT
1 GTAATGGAGATGATAATTGAAGTGGAGAAGTGGATGATGGTGATTGAAGTGAAGTAGATGGTGGT
31976 GGAT
66 GGAT
* * ** * *
31980 GTAATGGAGATGATAACTGAAATGGAGAAGTGGATGATAATGGTTGAAGTGAAGTAGATAGTGGT
1 GTAATGGAGATGATAATTGAAGTGGAGAAGTGGATGATGGTGATTGAAGTGAAGTAGATGGTGGT
*
32045 AGAT
66 GGAT
* * *
32049 GTAATGGAGATGATAATTGAAGTGGAGAAGTGGATGATGGTGCTTGAAGTGAAGCATATGGTGGT
1 GTAATGGAGATGATAATTGAAGTGGAGAAGTGGATGATGGTGATTGAAGTGAAGTAGATGGTGGT
*
32114 GAAT
66 GGAT
* * *
32118 ATAATGGAGATGATAATTGAAGTGGAGAAGTGGATGGTGGTGATTGAAGTGAATTAGATGGTGGT
1 GTAATGGAGATGATAATTGAAGTGGAGAAGTGGATGATGGTGATTGAAGTGAAGTAGATGGTGGT
32183 GGAT
66 GGAT
* * ** *
32187 GTAATGGAGATGATAACTGAAATGGAGAAGTGGATGATAATGGTTGAAGTGAAGTAGATGGTGGT
1 GTAATGGAGATGATAATTGAAGTGGAGAAGTGGATGATGGTGATTGAAGTGAAGTAGATGGTGGT
32252 GGAT
66 GGAT
32256 GTAATGGAGATGATAATTGAAGTGGAG
1 GTAATGGAGATGATAATTGAAGTGGAG
32283 GAGATGCCAA
Statistics
Matches: 389, Mismatches: 52, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
69 389 1.00
ACGTcount: A:0.34, C:0.01, G:0.38, T:0.27
Consensus pattern (69 bp):
GTAATGGAGATGATAATTGAAGTGGAGAAGTGGATGATGGTGATTGAAGTGAAGTAGATGGTGGT
GGAT
Found at i:32128 original size:207 final size:207
Alignment explanation
Indices: 31773--32282 Score: 939
Period size: 207 Copynumber: 2.5 Consensus size: 207
31763 GATGTTGAAC
* * * * *
31773 GTAATGGAGATGATAATTGAAGTGGAGAAGTGGATGGTAGTGATTGAAGTGAAGTAGATAGTGGT
1 GTAATGGAGATGATAACTGAAATGGAGAAGTGGATGATAATGGTTGAAGTGAAGTAGATAGTGGT
31838 AGATGTAATGGAGATGATAATTGAAGTGGAGAAGTGGATGATGGTGCTTGAAGTGAAGCATATGG
66 AGATGTAATGGAGATGATAATTGAAGTGGAGAAGTGGATGATGGTGCTTGAAGTGAAGCATATGG
*
31903 TGGTGGATATAATGGAGATGATAATTGAAGTGGAGAAGTGGATGGTGGTGATCGAAGTGAATTAG
131 TGGTGAATATAATGGAGATGATAATTGAAGTGGAGAAGTGGATGGTGGTGATCGAAGTGAATTAG
31968 ATGGTGGTGGAT
196 ATGGTGGTGGAT
31980 GTAATGGAGATGATAACTGAAATGGAGAAGTGGATGATAATGGTTGAAGTGAAGTAGATAGTGGT
1 GTAATGGAGATGATAACTGAAATGGAGAAGTGGATGATAATGGTTGAAGTGAAGTAGATAGTGGT
32045 AGATGTAATGGAGATGATAATTGAAGTGGAGAAGTGGATGATGGTGCTTGAAGTGAAGCATATGG
66 AGATGTAATGGAGATGATAATTGAAGTGGAGAAGTGGATGATGGTGCTTGAAGTGAAGCATATGG
*
32110 TGGTGAATATAATGGAGATGATAATTGAAGTGGAGAAGTGGATGGTGGTGATTGAAGTGAATTAG
131 TGGTGAATATAATGGAGATGATAATTGAAGTGGAGAAGTGGATGGTGGTGATCGAAGTGAATTAG
32175 ATGGTGGTGGAT
196 ATGGTGGTGGAT
*
32187 GTAATGGAGATGATAACTGAAATGGAGAAGTGGATGATAATGGTTGAAGTGAAGTAGATGGTGGT
1 GTAATGGAGATGATAACTGAAATGGAGAAGTGGATGATAATGGTTGAAGTGAAGTAGATAGTGGT
*
32252 GGATGTAATGGAGATGATAATTGAAGTGGAG
66 AGATGTAATGGAGATGATAATTGAAGTGGAG
32283 GAGATGCCAA
Statistics
Matches: 294, Mismatches: 9, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
207 294 1.00
ACGTcount: A:0.34, C:0.01, G:0.38, T:0.27
Consensus pattern (207 bp):
GTAATGGAGATGATAACTGAAATGGAGAAGTGGATGATAATGGTTGAAGTGAAGTAGATAGTGGT
AGATGTAATGGAGATGATAATTGAAGTGGAGAAGTGGATGATGGTGCTTGAAGTGAAGCATATGG
TGGTGAATATAATGGAGATGATAATTGAAGTGGAGAAGTGGATGGTGGTGATCGAAGTGAATTAG
ATGGTGGTGGAT
Found at i:35392 original size:2 final size:2
Alignment explanation
Indices: 35385--35446 Score: 124
Period size: 2 Copynumber: 31.0 Consensus size: 2
35375 CTTATTTGCT
35385 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
35427 GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA
35447 AGAATTAAAA
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 60 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:37397 original size:21 final size:21
Alignment explanation
Indices: 37379--37424 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
37369 TTTAATAAAC
37379 TTTAACAATCATTTTATAATA
1 TTTAACAATCATTTTATAATA
* *
37400 TTTAATAATCATTCTATAAT-
1 TTTAACAATCATTTTATAATA
37420 TTTAA
1 TTTAA
37425 AAGTTTAATG
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 5 0.22
21 18 0.78
ACGTcount: A:0.41, C:0.09, G:0.00, T:0.50
Consensus pattern (21 bp):
TTTAACAATCATTTTATAATA
Found at i:41634 original size:18 final size:18
Alignment explanation
Indices: 41611--41648 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
41601 AAGAAAAAGC
41611 AAACATGAAATGTGAACT
1 AAACATGAAATGTGAACT
*
41629 AAACATGAGATGTGAACT
1 AAACATGAAATGTGAACT
41647 AA
1 AA
41649 GTACTGCCAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.50, C:0.11, G:0.18, T:0.21
Consensus pattern (18 bp):
AAACATGAAATGTGAACT
Found at i:46342 original size:19 final size:21
Alignment explanation
Indices: 46299--46350 Score: 81
Period size: 19 Copynumber: 2.6 Consensus size: 21
46289 GAAACCCCTT
46299 TGAAAATACATGATTTTTAAA
1 TGAAAATACATGATTTTTAAA
46320 TGAAAATACATGA-TTTT-AA
1 TGAAAATACATGATTTTTAAA
*
46339 TGAAGATACATG
1 TGAAAATACATG
46351 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:50523 original size:19 final size:21
Alignment explanation
Indices: 50480--50531 Score: 81
Period size: 19 Copynumber: 2.6 Consensus size: 21
50470 TAAACCCCTT
50480 TGAAAATACATGATTTTTAAA
1 TGAAAATACATGATTTTTAAA
50501 TGAAAATACATGA-TTTT-AA
1 TGAAAATACATGATTTTTAAA
*
50520 TGAAGATACATG
1 TGAAAATACATG
50532 CTCTTGGCTG
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:57396 original size:24 final size:25
Alignment explanation
Indices: 57368--57444 Score: 70
Period size: 24 Copynumber: 3.2 Consensus size: 25
57358 AAATATTTTA
* *
57368 TCTGATTTC-CGACTTGAATTTTGT
1 TCTGATTTCACGACCTGAATTCTGT
* *
57392 TCTGA-TACATGACCTGAATTCTGT
1 TCTGATTTCACGACCTGAATTCTGT
* * *
57416 TCTGATTTC-TGATCTGGATTCTGT
1 TCTGATTTCACGACCTGAATTCTGT
57440 TCTGA
1 TCTGA
57445 CTTCTGTTTT
Statistics
Matches: 44, Mismatches: 7, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
23 2 0.05
24 40 0.91
25 2 0.05
ACGTcount: A:0.18, C:0.18, G:0.18, T:0.45
Consensus pattern (25 bp):
TCTGATTTCACGACCTGAATTCTGT
Found at i:57420 original size:12 final size:12
Alignment explanation
Indices: 57405--57462 Score: 62
Period size: 12 Copynumber: 4.8 Consensus size: 12
57395 GATACATGAC
57405 CTGAATTCTGTT
1 CTGAATTCTGTT
* *
57417 CTGATTTCTGAT
1 CTGAATTCTGTT
*
57429 CTGGATTCTGTT
1 CTGAATTCTGTT
*
57441 CTGACTTCTGTT
1 CTGAATTCTGTT
* *
57453 TTGATTTCTG
1 CTGAATTCTG
57463 ATATCTCCGT
Statistics
Matches: 37, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
12 37 1.00
ACGTcount: A:0.12, C:0.17, G:0.19, T:0.52
Consensus pattern (12 bp):
CTGAATTCTGTT
Found at i:57639 original size:2 final size:2
Alignment explanation
Indices: 57632--57662 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
57622 GGGATGGGGG
57632 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
57663 GTTTTAAAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:60483 original size:9 final size:9
Alignment explanation
Indices: 60471--60521 Score: 54
Period size: 9 Copynumber: 6.0 Consensus size: 9
60461 AATATTTTGC
60471 ATTTAATTT
1 ATTTAATTT
*
60480 ATTTAA-GT
1 ATTTAATTT
60488 ATTTAATTT
1 ATTTAATTT
60497 ATTTAA--T
1 ATTTAATTT
*
60504 ATTTTATTT
1 ATTTAATTT
*
60513 AATTAATTT
1 ATTTAATTT
60522 TTTTGCAGAT
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
7 6 0.18
8 7 0.21
9 21 0.62
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (9 bp):
ATTTAATTT
Found at i:60493 original size:17 final size:16
Alignment explanation
Indices: 60471--60519 Score: 71
Period size: 16 Copynumber: 3.0 Consensus size: 16
60461 AATATTTTGC
60471 ATTTAATTTATTTAAGT
1 ATTTAATTTATTTAA-T
60488 ATTTAATTTATTTAAT
1 ATTTAATTTATTTAAT
* *
60504 ATTTTATTTAATTAAT
1 ATTTAATTTATTTAAT
60520 TTTTTTGCAG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
16 15 0.50
17 15 0.50
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (16 bp):
ATTTAATTTATTTAAT
Found at i:62788 original size:19 final size:19
Alignment explanation
Indices: 62764--62835 Score: 144
Period size: 19 Copynumber: 3.8 Consensus size: 19
62754 GAATGTCGTC
62764 AGTGCATCGATGCATAAGG
1 AGTGCATCGATGCATAAGG
62783 AGTGCATCGATGCATAAGG
1 AGTGCATCGATGCATAAGG
62802 AGTGCATCGATGCATAAGG
1 AGTGCATCGATGCATAAGG
62821 AGTGCATCGATGCAT
1 AGTGCATCGATGCAT
62836 TTCTAATAAA
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 53 1.00
ACGTcount: A:0.31, C:0.17, G:0.31, T:0.22
Consensus pattern (19 bp):
AGTGCATCGATGCATAAGG
Found at i:63621 original size:149 final size:147
Alignment explanation
Indices: 63353--63653 Score: 557
Period size: 149 Copynumber: 2.0 Consensus size: 147
63343 GGGTAGAGGG
*
63353 TCTACGCGGTCCTTCGGGATATATATATTCTGTGGAATATGTGTGAAGTCTTGTAAGACACATAC
1 TCTACGCGGTCCTTCGGGATATATATATTCTGTGGAACATGTGTGAAGTCTTGTAAGACACATAC
63418 TTGATCCCTAGTATATGTATATGATTCTTAAGGAATGATATGTGGTCCTTATGGACATTATTATA
66 TTGATCCCTAGTATATGTATATGATTCTTAAGGAATGATATGTGGTCCTTATGGACATTATTATA
*
63483 TGGCACTACGGTGCAAT
131 TGGCACTAAGGTGCAAT
63500 TCTACGCGGTCCTTCGGGATATATATATATTCTGTGGAACATGTGTGAAGTCTTGTAAGACACAT
1 TCTACGCGGTCCTTCGGG--ATATATATATTCTGTGGAACATGTGTGAAGTCTTGTAAGACACAT
*
63565 ACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATGATATGTGGTCCTTATGGACTTTATTA
64 ACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATGATATGTGGTCCTTATGGACATTATTA
63630 TATGGCACTAAGGTGCAAT
129 TATGGCACTAAGGTGCAAT
63649 TCTAC
1 TCTAC
63654 ATGGCACTTC
Statistics
Matches: 149, Mismatches: 3, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
147 18 0.12
149 131 0.88
ACGTcount: A:0.27, C:0.15, G:0.21, T:0.36
Consensus pattern (147 bp):
TCTACGCGGTCCTTCGGGATATATATATTCTGTGGAACATGTGTGAAGTCTTGTAAGACACATAC
TTGATCCCTAGTATATGTATATGATTCTTAAGGAATGATATGTGGTCCTTATGGACATTATTATA
TGGCACTAAGGTGCAAT
Found at i:65662 original size:200 final size:201
Alignment explanation
Indices: 65311--65969 Score: 1034
Period size: 200 Copynumber: 3.2 Consensus size: 201
65301 GACATACGCT
*
65311 TTATGGGTTTCGATGTTTCTGGGATCGATACTTTTTATAAATGGATCGACACTTTATGGGTTCAC
1 TTATGGGTTTCGATGTTTCTGGGATCGATACTTTTTATAAATGGATCGACACTTTATGGGTGCAC
*
65376 CCTTTTTGTGCATTCATTCTGGACAAAAAGTATCGACACAAAATTAAAAAGTGTCGATACATGTT
66 CCTTTTTGTGCATTCATTCTGGACAAAAAGTATTGACACAAAATTAAAAAGTGTCGATACATGTT
* * * *
65441 GTAGACCTATTCTCTCATAAAACCAGTATATTTATACCGGTTACATTGAAAATTTACCTATTATA
131 GTAGACCTATTCTTTCATAAAACCGGTATATTTATACCGGTTACATTGAAAAATTACCTATTACA
65506 TTATAC
196 TTATAC
* * *
65512 TTATGGATTTCGATGTTTTTGGGATCTATACTTTTTATAAATGGATCGACACTTTATGGGTGCAC
1 TTATGGGTTTCGATGTTTCTGGGATCGATACTTTTTATAAATGGATCGACACTTTATGGGTGCAC
* *
65577 CCTTTTTG-GCATTCATTCTAGACCAAAAGTATTGACACAAAATTAAAAAGTGTCGATACATGTT
66 CCTTTTTGTGCATTCATTCTGGACAAAAAGTATTGACACAAAATTAAAAAGTGTCGATACATGTT
* *
65641 GTAGGCCTATTCTTTCATAAAATCGGTATATTTATACCGGTTACATTGAAAAATTACCTATTACA
131 GTAGACCTATTCTTTCATAAAACCGGTATATTTATACCGGTTACATTGAAAAATTACCTATTACA
65706 TTATAC
196 TTATAC
* * *
65712 TTATGGGTTTCGATGTTTCTGGGATCGATATTTTTTTATAAATGGATCGACACTTTATAGTTGCA
1 TTATGGGTTTCGATGTTTCTGGGATCGATA-CTTTTTATAAATGGATCGACACTTTATGGGTGCA
* * *
65777 CCCTTTTTGTGCATTTATTCTGGACAAAAAGTATCAGTATCGACACAAAATAAAAAAGTGTCAAT
65 CCCTTTTTGTGCATTCATTCTGGACAAAAAG--T-A-T-T-GACACAAAATTAAAAAGTGTCGAT
*
65842 ACATGTTGTAGACCTATT-TTCTCATAAAACCGGTATATTTATACCGGTTAGATTGAAAAATTAC
124 ACATGTTGTAGACCTATTCTT-TCATAAAACCGGTATATTTATACCGGTTACATTGAAAAATTAC
65906 CTATTACATTATAC
188 CTATTACATTATAC
* *
65920 TTATGGGTTTCGATGTTTCTGAGATCGATACTTTTTATATATGGATCGAC
1 TTATGGGTTTCGATGTTTCTGGGATCGATACTTTTTATAAATGGATCGAC
65970 TCATATGCTT
Statistics
Matches: 419, Mismatches: 30, Indels: 12
0.91 0.07 0.03
Matches are distributed among these distances:
200 145 0.35
201 109 0.26
202 18 0.04
204 1 0.00
205 1 0.00
206 1 0.00
207 21 0.05
208 123 0.29
ACGTcount: A:0.31, C:0.15, G:0.16, T:0.38
Consensus pattern (201 bp):
TTATGGGTTTCGATGTTTCTGGGATCGATACTTTTTATAAATGGATCGACACTTTATGGGTGCAC
CCTTTTTGTGCATTCATTCTGGACAAAAAGTATTGACACAAAATTAAAAAGTGTCGATACATGTT
GTAGACCTATTCTTTCATAAAACCGGTATATTTATACCGGTTACATTGAAAAATTACCTATTACA
TTATAC
Found at i:66302 original size:19 final size:19
Alignment explanation
Indices: 66278--66326 Score: 98
Period size: 19 Copynumber: 2.6 Consensus size: 19
66268 TTACATTCAC
66278 ATACAAAATTATAAATCGT
1 ATACAAAATTATAAATCGT
66297 ATACAAAATTATAAATCGT
1 ATACAAAATTATAAATCGT
66316 ATACAAAATTA
1 ATACAAAATTA
66327 ACCCTACATT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 30 1.00
ACGTcount: A:0.55, C:0.10, G:0.04, T:0.31
Consensus pattern (19 bp):
ATACAAAATTATAAATCGT
Found at i:68151 original size:33 final size:33
Alignment explanation
Indices: 68114--68177 Score: 110
Period size: 33 Copynumber: 1.9 Consensus size: 33
68104 TCTTAAGATT
*
68114 ACCCCTTAACACCTCAACTTCTTTCACCACTTC
1 ACCCCTCAACACCTCAACTTCTTTCACCACTTC
*
68147 ACCCCTCAACACCTCTACTTCTTTCACCACT
1 ACCCCTCAACACCTCAACTTCTTTCACCACT
68178 CCATCTATTT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.23, C:0.47, G:0.00, T:0.30
Consensus pattern (33 bp):
ACCCCTCAACACCTCAACTTCTTTCACCACTTC
Found at i:68251 original size:21 final size:21
Alignment explanation
Indices: 68226--68269 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
68216 CCCCTTATGC
68226 CTCTCAAGTGTCTCTTCAACT
1 CTCTCAAGTGTCTCTTCAACT
* *
68247 CTCTCAAGTTTCTCTTCGACT
1 CTCTCAAGTGTCTCTTCAACT
68268 CT
1 CT
68270 TAATTGTCTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.34, G:0.09, T:0.41
Consensus pattern (21 bp):
CTCTCAAGTGTCTCTTCAACT
Found at i:70522 original size:20 final size:20
Alignment explanation
Indices: 70476--70522 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 20
70466 TCCGGTAGCG
70476 CTTTACCGGTTTTATCATTT
1 CTTTACCGGTTTTATCATTT
** *
70496 CAATACCGGTTTTGTCATATT
1 CTTTACCGGTTTTATCAT-TT
70517 -TTTACC
1 CTTTACC
70523 TATTATATAT
Statistics
Matches: 21, Mismatches: 5, Indels: 2
0.75 0.18 0.07
Matches are distributed among these distances:
20 19 0.90
21 2 0.10
ACGTcount: A:0.19, C:0.21, G:0.11, T:0.49
Consensus pattern (20 bp):
CTTTACCGGTTTTATCATTT
Found at i:74713 original size:20 final size:20
Alignment explanation
Indices: 74690--74749 Score: 66
Period size: 20 Copynumber: 3.0 Consensus size: 20
74680 ATCTAAGACG
*
74690 TTTCATTGTGTTCTAGAACT
1 TTTCATTGTGTTCTAGAACC
** * *
74710 TTTCATAATGTTCTTGATCC
1 TTTCATTGTGTTCTAGAACC
*
74730 TTCCATTGTGTTCTAGAACC
1 TTTCATTGTGTTCTAGAACC
74750 ATTAGTTATA
Statistics
Matches: 30, Mismatches: 10, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.20, C:0.20, G:0.13, T:0.47
Consensus pattern (20 bp):
TTTCATTGTGTTCTAGAACC
Found at i:87048 original size:10 final size:10
Alignment explanation
Indices: 87009--87047 Score: 60
Period size: 10 Copynumber: 3.9 Consensus size: 10
86999 ACCGAACACC
87009 AAAAACAACA
1 AAAAACAACA
87019 AAAAACAACA
1 AAAAACAACA
*
87029 AAAAACAACC
1 AAAAACAACA
*
87039 GAAAACAAC
1 AAAAACAAC
87048 CCTAAACAAC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
10 27 1.00
ACGTcount: A:0.74, C:0.23, G:0.03, T:0.00
Consensus pattern (10 bp):
AAAAACAACA
Found at i:92089 original size:15 final size:15
Alignment explanation
Indices: 92069--92100 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
92059 AAACACCAGG
92069 ATGGAATCCCATGGC
1 ATGGAATCCCATGGC
92084 ATGGAATCCCATGGC
1 ATGGAATCCCATGGC
92099 AT
1 AT
92101 TAGTCTATAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.28, C:0.25, G:0.25, T:0.22
Consensus pattern (15 bp):
ATGGAATCCCATGGC
Found at i:94437 original size:2 final size:2
Alignment explanation
Indices: 94430--94467 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
94420 TCTGATGTGA
94430 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
94468 GTTGATGGAG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:94508 original size:19 final size:19
Alignment explanation
Indices: 94484--94521 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
94474 GGAGATGGGG
* *
94484 GCATTAGGATACAGATGAA
1 GCATTAGGACACAAATGAA
94503 GCATTAGGACACAAATGAA
1 GCATTAGGACACAAATGAA
94522 TGGAAGGAGA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.45, C:0.13, G:0.24, T:0.18
Consensus pattern (19 bp):
GCATTAGGACACAAATGAA
Found at i:105945 original size:19 final size:19
Alignment explanation
Indices: 105917--105977 Score: 86
Period size: 19 Copynumber: 3.2 Consensus size: 19
105907 AACCCGATCC
*
105917 GACCCGTTGATTTTGACCT
1 GACCCATTGATTTTGACCT
*
105936 GACCCATTGATTTTGACCC
1 GACCCATTGATTTTGACCT
* *
105955 GACCCATTGAATTTGACAT
1 GACCCATTGATTTTGACCT
105974 GACC
1 GACC
105978 TGTTGACTGT
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 37 1.00
ACGTcount: A:0.23, C:0.28, G:0.18, T:0.31
Consensus pattern (19 bp):
GACCCATTGATTTTGACCT
Found at i:111192 original size:19 final size:20
Alignment explanation
Indices: 111149--111193 Score: 56
Period size: 19 Copynumber: 2.3 Consensus size: 20
111139 ATAATATCAC
*
111149 GATGATAATTTTATAAATTT
1 GATGATAATTCTATAAATTT
* *
111169 AATGAT-ATTCTATAATTTT
1 GATGATAATTCTATAAATTT
111188 GATGAT
1 GATGAT
111194 TATTAAATTA
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
19 16 0.76
20 5 0.24
ACGTcount: A:0.38, C:0.02, G:0.11, T:0.49
Consensus pattern (20 bp):
GATGATAATTCTATAAATTT
Found at i:114437 original size:22 final size:21
Alignment explanation
Indices: 114412--114452 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
114402 TATAAAAAAT
114412 TATTTTTATTAAATATTTTTGG
1 TATTTTTATTAAAT-TTTTTGG
*
114434 TATTTTTATTTAATTTTTT
1 TATTTTTATTAAATTTTTT
114453 AAATAACTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.24, C:0.00, G:0.05, T:0.71
Consensus pattern (21 bp):
TATTTTTATTAAATTTTTTGG
Found at i:123812 original size:37 final size:36
Alignment explanation
Indices: 123753--123872 Score: 181
Period size: 35 Copynumber: 3.3 Consensus size: 36
123743 ATCTCATTAT
*
123753 CATTTTTC-AACAAACATCTACCAAACTTTGAAAAAC
1 CATTTTTCAAAGAAACATCTACCAAACTTTG-AAAAC
* *
123789 TATTTTTCAAAGAAACATTTACCAAACTTTGAAAAC
1 CATTTTTCAAAGAAACATCTACCAAACTTTGAAAAC
123825 CA-TTTTCAAAGAAACATCTACCAAACTTTGAAAAC
1 CATTTTTCAAAGAAACATCTACCAAACTTTGAAAAC
123860 CATTTTTTCAAAG
1 CA-TTTTTCAAAG
123873 TTGGTTACCA
Statistics
Matches: 76, Mismatches: 5, Indels: 5
0.88 0.06 0.06
Matches are distributed among these distances:
35 34 0.45
36 13 0.17
37 29 0.38
ACGTcount: A:0.43, C:0.21, G:0.05, T:0.31
Consensus pattern (36 bp):
CATTTTTCAAAGAAACATCTACCAAACTTTGAAAAC
Found at i:123828 original size:21 final size:21
Alignment explanation
Indices: 123804--123864 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
123794 TTCAAAGAAA
123804 CATTTACCAAACTTTGAAAAC
1 CATTTACCAAACTTTGAAAAC
*
123825 CATTT-TCAAA----G-AAA-
1 CATTTACCAAACTTTGAAAAC
*
123839 CATCTACCAAACTTTGAAAAC
1 CATTTACCAAACTTTGAAAAC
123860 CATTT
1 CATTT
123865 TTTCAAAGTT
Statistics
Matches: 29, Mismatches: 4, Indels: 14
0.62 0.09 0.30
Matches are distributed among these distances:
14 4 0.14
15 7 0.24
16 1 0.03
19 1 0.03
20 7 0.24
21 9 0.31
ACGTcount: A:0.43, C:0.23, G:0.05, T:0.30
Consensus pattern (21 bp):
CATTTACCAAACTTTGAAAAC
Found at i:123882 original size:35 final size:36
Alignment explanation
Indices: 123755--123899 Score: 158
Period size: 35 Copynumber: 4.1 Consensus size: 36
123745 CTCATTATCA
* *
123755 TTTTTC-AACAAACATCTACCAAACTTTGAAAAAC-T
1 TTTTTCAAAGAAACAT-TACCAAACTTTGAAAACCAT
123790 ATTTTTCAAAGAAACATTTACCAAACTTTGAAAACCA-
1 -TTTTTCAAAGAAACA-TTACCAAACTTTGAAAACCAT
123827 -TTTTCAAAGAAACATCTACCAAACTTTGAAAACCAT
1 TTTTTCAAAGAAACAT-TACCAAACTTTGAAAACCAT
****
123863 TTTTTCAAAG-TTGGTTACCAAAC-TTGAAAACCAT
1 TTTTTCAAAGAAACATTACCAAACTTTGAAAACCAT
123897 TTT
1 TTT
123900 AATACTTTCA
Statistics
Matches: 97, Mismatches: 6, Indels: 14
0.83 0.05 0.12
Matches are distributed among these distances:
34 15 0.15
35 41 0.42
36 7 0.07
37 33 0.34
38 1 0.01
ACGTcount: A:0.41, C:0.20, G:0.06, T:0.32
Consensus pattern (36 bp):
TTTTTCAAAGAAACATTACCAAACTTTGAAAACCAT
Found at i:131547 original size:17 final size:17
Alignment explanation
Indices: 131507--131547 Score: 73
Period size: 17 Copynumber: 2.4 Consensus size: 17
131497 GTCTTCCTTG
*
131507 TTCTTGCGCCGATTTTC
1 TTCTTGTGCCGATTTTC
131524 TTCTTGTGCCGATTTTC
1 TTCTTGTGCCGATTTTC
131541 TTCTTGT
1 TTCTTGT
131548 ATAATAGCAG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.05, C:0.24, G:0.17, T:0.54
Consensus pattern (17 bp):
TTCTTGTGCCGATTTTC
Found at i:132923 original size:29 final size:29
Alignment explanation
Indices: 132848--132923 Score: 75
Period size: 29 Copynumber: 2.6 Consensus size: 29
132838 TTTTGGCGAT
* * *
132848 TTTCCCGATATATCACCGTTGAACAGTATA
1 TTTCCCGATCTAACACCGTTCAACA-TATA
*
132878 TTTCCCGATC-ATGCACCGTTCAGAC-TATA
1 TTTCCCGATCTA-ACACCGTTCA-ACATATA
132907 TTTCCCGATCTAACACC
1 TTTCCCGATCTAACACC
132924 ATTTGCAGAA
Statistics
Matches: 39, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
29 19 0.49
30 18 0.46
31 2 0.05
ACGTcount: A:0.26, C:0.30, G:0.12, T:0.32
Consensus pattern (29 bp):
TTTCCCGATCTAACACCGTTCAACATATA
Found at i:139840 original size:16 final size:16
Alignment explanation
Indices: 139816--139849 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
139806 TATCGCCGAC
*
139816 CGAATTTCACTATTCA
1 CGAAATTCACTATTCA
139832 CGAAATTCACTATTCA
1 CGAAATTCACTATTCA
139848 CG
1 CG
139850 TGAATAGTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.32, C:0.26, G:0.09, T:0.32
Consensus pattern (16 bp):
CGAAATTCACTATTCA
Found at i:142315 original size:3 final size:3
Alignment explanation
Indices: 142283--142326 Score: 52
Period size: 3 Copynumber: 14.7 Consensus size: 3
142273 ACATGCAAAT
* * * *
142283 TAG TAA TAG TAA TAG TAA TAG TAA TAG TAG TAG TAG TAG TAG TA
1 TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TA
142327 AAAATACTTA
Statistics
Matches: 33, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.43, C:0.00, G:0.23, T:0.34
Consensus pattern (3 bp):
TAG
Found at i:142326 original size:6 final size:6
Alignment explanation
Indices: 142283--142323 Score: 64
Period size: 6 Copynumber: 6.8 Consensus size: 6
142273 ACATGCAAAT
* *
142283 TAGTAA TAGTAA TAGTAA TAGTAA TAGTAG TAGTAG TAGTA
1 TAGTAA TAGTAA TAGTAA TAGTAA TAGTAA TAGTAA TAGTA
142324 GTAAAAATAC
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 34 1.00
ACGTcount: A:0.44, C:0.00, G:0.22, T:0.34
Consensus pattern (6 bp):
TAGTAA
Found at i:143312 original size:14 final size:14
Alignment explanation
Indices: 143293--143320 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
143283 GAAATTAAAA
143293 AAATTACATCTTTT
1 AAATTACATCTTTT
143307 AAATTACATCTTTT
1 AAATTACATCTTTT
143321 CATTTAAACC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.36, C:0.14, G:0.00, T:0.50
Consensus pattern (14 bp):
AAATTACATCTTTT
Found at i:143470 original size:17 final size:17
Alignment explanation
Indices: 143450--143482 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
143440 TAATTTTCCA
143450 ATAAGTAAA-ATTTATTT
1 ATAA-TAAATATTTATTT
143467 ATAATAAATATTTATT
1 ATAATAAATATTTATT
143483 GTCATTAATT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (17 bp):
ATAATAAATATTTATTT
Found at i:152091 original size:22 final size:21
Alignment explanation
Indices: 152059--152122 Score: 67
Period size: 22 Copynumber: 3.0 Consensus size: 21
152049 CTACCAAAAG
152059 GTAAAGAAAACATGTCACAAA
1 GTAAAGAAAACATGTCACAAA
* *
152080 GTAAAGATAAACGTGTCATAAA
1 GTAAAGA-AAACATGTCACAAA
* * *
152102 -TATATAAAACATATCACAAA
1 GTAAAGAAAACATGTCACAAA
152122 G
1 G
152123 ACATAATTAT
Statistics
Matches: 34, Mismatches: 7, Indels: 4
0.76 0.16 0.09
Matches are distributed among these distances:
20 11 0.32
21 11 0.32
22 12 0.35
ACGTcount: A:0.55, C:0.12, G:0.12, T:0.20
Consensus pattern (21 bp):
GTAAAGAAAACATGTCACAAA
Found at i:152298 original size:2 final size:2
Alignment explanation
Indices: 152282--152314 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
152272 TAAGAAATTT
152282 TA TA T- TA TA -A TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
152315 GATCAATTGG
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
1 2 0.07
2 27 0.93
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:152813 original size:17 final size:18
Alignment explanation
Indices: 152774--152812 Score: 60
Period size: 20 Copynumber: 2.1 Consensus size: 18
152764 AGTGTCCAAT
152774 AATAATAAAACTGGTAGAAA
1 AATAATAAAACTGGT--AAA
152794 AATAATAAAACTGGTAAA
1 AATAATAAAACTGGTAAA
152812 A
1 A
152813 TGCTCAATAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 4 0.21
20 15 0.79
ACGTcount: A:0.62, C:0.05, G:0.13, T:0.21
Consensus pattern (18 bp):
AATAATAAAACTGGTAAA
Found at i:161741 original size:71 final size:71
Alignment explanation
Indices: 161539--161752 Score: 349
Period size: 72 Copynumber: 3.0 Consensus size: 71
161529 CCTTAACTAG
* * *
161539 ATCTATTTCATTAAT-CGTTCATGCCACAAACACACAAATGAGTTGGCATGTGAGGCATGCACCT
1 ATCTATTTTATTAATCCCTTCATGCCACAAACACACAAAGGAGTTGGCATGTGAGGCATGCACCT
161603 ACATAC
66 ACATAC
* *
161609 ATTTATTTTATTAATCCCCTTCATGCCACAAACACACAAAGGAGTTGGCATGCGAGGCATGCACC
1 ATCTATTTTATTAAT-CCCTTCATGCCACAAACACACAAAGGAGTTGGCATGTGAGGCATGCACC
161674 TACATAC
65 TACATAC
* *
161681 ATCTATTTTATTAATCCCTTCATTCCACAAACACACAAAGGAGTTGGCATGTGAGACATGCACCT
1 ATCTATTTTATTAATCCCTTCATGCCACAAACACACAAAGGAGTTGGCATGTGAGGCATGCACCT
161746 ACATAC
66 ACATAC
161752 A
1 A
161753 CAATGAAATA
Statistics
Matches: 133, Mismatches: 9, Indels: 3
0.92 0.06 0.02
Matches are distributed among these distances:
70 13 0.10
71 54 0.41
72 66 0.50
ACGTcount: A:0.33, C:0.25, G:0.14, T:0.27
Consensus pattern (71 bp):
ATCTATTTTATTAATCCCTTCATGCCACAAACACACAAAGGAGTTGGCATGTGAGGCATGCACCT
ACATAC
Found at i:169583 original size:135 final size:137
Alignment explanation
Indices: 169387--169670 Score: 376
Period size: 144 Copynumber: 2.0 Consensus size: 137
169377 AATTCCATAG
* * * * *
169387 CCTCTCCCACGACCTCCTTGTTGGGACTGTGAGGCCCAACCTCTTCCCCCCGGGTAGCCT-CCAC
1 CCTCCCCCACGACCACCTTGTTGGGACTGTGAGACCCAACCTCTTCCCCCCGGATAACCTCCCAC
* *
169451 CTTGTCC-TTGTTGAGGACGTTGGGGACCACGACCACTGCCACCGCCAGTGTCATGGGACTGAGA
66 CTTGTCCTTTGTTGAGGAAGTTGGGGACCACGACCACTGCCACCACCAGTGTCATGGGACTGAGA
*
169515 GCTCTCA
131 GCCCTCA
*
169522 CCTCCCCCACGACCACCTTGTTGGGACTGTG-GAACCCAACCTCTTCCCCCCGTATAACCTCCAC
1 CCTCCCCCACGACCACCTTGTTGGGACTGTGAG-ACCCAACCTCTTCCCCCCGGATAACCT----
*
169586 GCCCACCTTGTCCTTGTTGTTGAGGAAGTTGGGGACCATGACCACTGCCACCACCAGTGTCATGG
61 -CCCACCTTGTCC-T-TTGTTGAGGAAGTTGGGGACCACGACCACTGCCACCACCAGTGTCATGG
*
169651 GACTGAGATCCCTCA
123 GACTGAGAGCCCTCA
169666 CCTCC
1 CCTCC
169671 GCCAGAGGGA
Statistics
Matches: 128, Mismatches: 11, Indels: 11
0.85 0.07 0.07
Matches are distributed among these distances:
134 1 0.01
135 52 0.41
141 11 0.09
144 64 0.50
ACGTcount: A:0.17, C:0.38, G:0.23, T:0.22
Consensus pattern (137 bp):
CCTCCCCCACGACCACCTTGTTGGGACTGTGAGACCCAACCTCTTCCCCCCGGATAACCTCCCAC
CTTGTCCTTTGTTGAGGAAGTTGGGGACCACGACCACTGCCACCACCAGTGTCATGGGACTGAGA
GCCCTCA
Found at i:172041 original size:12 final size:12
Alignment explanation
Indices: 172024--172053 Score: 60
Period size: 12 Copynumber: 2.5 Consensus size: 12
172014 TTAGAAGGAT
172024 GCAAACTAAGGG
1 GCAAACTAAGGG
172036 GCAAACTAAGGG
1 GCAAACTAAGGG
172048 GCAAAC
1 GCAAAC
172054 ATTTTCCCAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.43, C:0.20, G:0.30, T:0.07
Consensus pattern (12 bp):
GCAAACTAAGGG
Found at i:173265 original size:18 final size:18
Alignment explanation
Indices: 173242--173277 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
173232 AAAGAAAGGG
173242 GGCTCAAATTCTCATGCA
1 GGCTCAAATTCTCATGCA
173260 GGCTCAAATTCTCATGCA
1 GGCTCAAATTCTCATGCA
173278 ACCTATCTCA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.28, C:0.28, G:0.17, T:0.28
Consensus pattern (18 bp):
GGCTCAAATTCTCATGCA
Found at i:175596 original size:13 final size:13
Alignment explanation
Indices: 175578--175602 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
175568 TATTTTCATC
175578 ATTTTTTATTTTT
1 ATTTTTTATTTTT
175591 ATTTTTTATTTT
1 ATTTTTTATTTT
175603 GTAGGTTCTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (13 bp):
ATTTTTTATTTTT
Found at i:178666 original size:17 final size:17
Alignment explanation
Indices: 178644--178682 Score: 71
Period size: 17 Copynumber: 2.4 Consensus size: 17
178634 TGAATCAAAT
178644 TAATTAGATATTATTTA
1 TAATTAGATATTATTTA
178661 TAATTAGATATTATTTA
1 TAATTAGATATTATTTA
178678 -AATTA
1 TAATTA
178683 ATTGTAAATT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
16 5 0.23
17 17 0.77
ACGTcount: A:0.44, C:0.00, G:0.05, T:0.51
Consensus pattern (17 bp):
TAATTAGATATTATTTA
Found at i:180704 original size:28 final size:28
Alignment explanation
Indices: 180664--180735 Score: 117
Period size: 28 Copynumber: 2.6 Consensus size: 28
180654 GCGTAGAATT
180664 TGTCCCGAAGGACCACATATAACACATA
1 TGTCCCGAAGGACCACATATAACACATA
* *
180692 TGTCCCGAAGGACCAAATATAACATATA
1 TGTCCCGAAGGACCACATATAACACATA
*
180720 TATCCCGAAGGACCAC
1 TGTCCCGAAGGACCAC
180736 TATGTCCCGA
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
28 40 1.00
ACGTcount: A:0.39, C:0.28, G:0.15, T:0.18
Consensus pattern (28 bp):
TGTCCCGAAGGACCACATATAACACATA
Found at i:181572 original size:24 final size:21
Alignment explanation
Indices: 181519--181592 Score: 75
Period size: 20 Copynumber: 3.6 Consensus size: 21
181509 TTTCCCATTG
*
181519 AAGTGCATCGGTGCATTCTAC
1 AAGTGCATCGATGCATTCTAC
181540 -AGTGCATCGATGCATTCTTTAAC
1 AAGTGCATCGATGCATTC--T-AC
181563 AAGTGCATCGATGCA--CTAC
1 AAGTGCATCGATGCATTCTAC
*
181582 CA-TGCATCGAT
1 AAGTGCATCGAT
181593 ACACAATTTA
Statistics
Matches: 47, Mismatches: 2, Indels: 11
0.78 0.03 0.18
Matches are distributed among these distances:
18 9 0.19
19 3 0.06
20 17 0.36
22 2 0.04
23 2 0.04
24 14 0.30
ACGTcount: A:0.27, C:0.24, G:0.20, T:0.28
Consensus pattern (21 bp):
AAGTGCATCGATGCATTCTAC
Found at i:182749 original size:26 final size:26
Alignment explanation
Indices: 182720--182776 Score: 96
Period size: 26 Copynumber: 2.2 Consensus size: 26
182710 GTGATATCTT
*
182720 ACTCAACTTTTTGAACTCATACTCTC
1 ACTCAACTTTTCGAACTCATACTCTC
*
182746 ACTCAACTTTTCGAACTCATACTCTT
1 ACTCAACTTTTCGAACTCATACTCTC
182772 ACTCA
1 ACTCA
182777 TACACAGTAC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.28, C:0.32, G:0.04, T:0.37
Consensus pattern (26 bp):
ACTCAACTTTTCGAACTCATACTCTC
Found at i:185217 original size:20 final size:20
Alignment explanation
Indices: 185184--185221 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
185174 TTCCCATTGA
* *
185184 AGTGCGTCGGTGCATTCTAC
1 AGTGCATCGATGCATTCTAC
185204 AGTGCATCGATGCATTCT
1 AGTGCATCGATGCATTCT
185222 TTAACAAGTG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.18, C:0.24, G:0.26, T:0.32
Consensus pattern (20 bp):
AGTGCATCGATGCATTCTAC
Found at i:187371 original size:19 final size:20
Alignment explanation
Indices: 187329--187375 Score: 57
Period size: 19 Copynumber: 2.5 Consensus size: 20
187319 ACAATTAATG
187329 TAAA-ACATATAATCACATA
1 TAAACACATATAATCACATA
187348 T-AACACATATAAT-A-ATAA
1 TAAACACATATAATCACAT-A
187366 TAAACACATA
1 TAAACACATA
187376 ATCTTATTCG
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
17 2 0.08
18 5 0.20
19 18 0.72
ACGTcount: A:0.60, C:0.15, G:0.00, T:0.26
Consensus pattern (20 bp):
TAAACACATATAATCACATA
Found at i:190495 original size:23 final size:23
Alignment explanation
Indices: 190461--190528 Score: 91
Period size: 23 Copynumber: 3.0 Consensus size: 23
190451 CATCTTATAT
190461 GGCACTTCGGTGCATTTCTACGC
1 GGCACTTCGGTGCATTTCTACGC
* * * *
190484 GGCACTTAGGTGCAATTCTATGT
1 GGCACTTCGGTGCATTTCTACGC
*
190507 GGCACTTCGGTGCATTTATACG
1 GGCACTTCGGTGCATTTCTACG
190529 AGCTATGGTG
Statistics
Matches: 37, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.18, C:0.24, G:0.26, T:0.32
Consensus pattern (23 bp):
GGCACTTCGGTGCATTTCTACGC
Found at i:195574 original size:23 final size:23
Alignment explanation
Indices: 195545--195589 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
195535 CACTTCGATT
195545 TTCTATGCGGCACTTAGGTGCAA
1 TTCTATGCGGCACTTAGGTGCAA
* *
195568 TTCTATGTGGCACTTCGGTGCA
1 TTCTATGCGGCACTTAGGTGCA
195590 TTTATACGAG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.18, C:0.22, G:0.27, T:0.33
Consensus pattern (23 bp):
TTCTATGCGGCACTTAGGTGCAA
Found at i:205681 original size:30 final size:31
Alignment explanation
Indices: 205632--205690 Score: 84
Period size: 30 Copynumber: 1.9 Consensus size: 31
205622 TTCTTAGATG
*
205632 ATTACAAAATGGTAATTAAAATTATCAAACT
1 ATTACAAAATGATAATTAAAATTATCAAACT
* *
205663 ATTAC-AAATGATAGTTAAACTTATCAAA
1 ATTACAAAATGATAATTAAAATTATCAAA
205691 GTTCATTACC
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
30 20 0.80
31 5 0.20
ACGTcount: A:0.51, C:0.10, G:0.07, T:0.32
Consensus pattern (31 bp):
ATTACAAAATGATAATTAAAATTATCAAACT
Found at i:216900 original size:29 final size:29
Alignment explanation
Indices: 216867--216940 Score: 87
Period size: 29 Copynumber: 2.6 Consensus size: 29
216857 AATTAGTTTT
*
216867 CTGGAAATTGAATT-TTGGAAAATGAAATA
1 CTGGAAATTGAATTACTGGAAAATG-AATA
* *
216896 CTGGAAATTGAATTACTGGAAATTGAATT
1 CTGGAAATTGAATTACTGGAAAATGAATA
* *
216925 CTGGAAAATAAATTAC
1 CTGGAAATTGAATTAC
216941 ATTTTTTGAA
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
29 31 0.79
30 8 0.21
ACGTcount: A:0.43, C:0.07, G:0.19, T:0.31
Consensus pattern (29 bp):
CTGGAAATTGAATTACTGGAAAATGAATA
Found at i:216933 original size:15 final size:14
Alignment explanation
Indices: 216865--216931 Score: 89
Period size: 15 Copynumber: 4.6 Consensus size: 14
216855 GTAATTAGTT
216865 TTCTGGAAATTGAA
1 TTCTGGAAATTGAA
* *
216879 TTTTGGAAAATGAAA
1 TTCTGGAAATTG-AA
*
216894 TACTGGAAATTGAA
1 TTCTGGAAATTGAA
216908 TTACTGGAAATTGAA
1 TT-CTGGAAATTGAA
216923 TTCTGGAAA
1 TTCTGGAAA
216932 ATAAATTACA
Statistics
Matches: 45, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
14 20 0.44
15 25 0.56
ACGTcount: A:0.40, C:0.06, G:0.21, T:0.33
Consensus pattern (14 bp):
TTCTGGAAATTGAA
Found at i:217297 original size:23 final size:23
Alignment explanation
Indices: 217271--217315 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
217261 AGTGTTATAT
217271 TATATTTTAAAAATATTAATTAG
1 TATATTTTAAAAATATTAATTAG
* *
217294 TATATTTTAAATATATTTATTA
1 TATATTTTAAAAATATTAATTA
217316 AAATATTATT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.53
Consensus pattern (23 bp):
TATATTTTAAAAATATTAATTAG
Found at i:217321 original size:23 final size:23
Alignment explanation
Indices: 217272--217340 Score: 68
Period size: 23 Copynumber: 3.0 Consensus size: 23
217262 GTGTTATATT
* * **
217272 ATATTTTAAAAATATTAATTAGT
1 ATATTTTAAATATATTTATTAAA
217295 ATATTTTAAATATATTTATTAAA
1 ATATTTTAAATATATTTATTAAA
*
217318 ATATTATTATAT-TATTATATTAA
1 ATATT-TTAAATATATT-TATTAA
217341 TATTAAATAT
Statistics
Matches: 39, Mismatches: 5, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
23 28 0.72
24 11 0.28
ACGTcount: A:0.46, C:0.00, G:0.01, T:0.52
Consensus pattern (23 bp):
ATATTTTAAATATATTTATTAAA
Found at i:217344 original size:34 final size:34
Alignment explanation
Indices: 217265--217344 Score: 80
Period size: 35 Copynumber: 2.4 Consensus size: 34
217255 AGTATTAGTG
217265 TTATATT-ATATTTTAAAAATATTAATTAGTATA
1 TTATATTAATATTTTAAAAATATTAATTAGTATA
*
217298 TT-T-TAAATATATTTATTAAAATATT-ATTA-TATTA
1 TTATATTAATAT-TTTA--AAAATATTAATTAGTA-TA
217332 TTATATTAATATT
1 TTATATTAATATT
217345 AAATATATAA
Statistics
Matches: 38, Mismatches: 2, Indels: 12
0.73 0.04 0.23
Matches are distributed among these distances:
31 1 0.03
32 5 0.13
33 8 0.21
34 8 0.21
35 10 0.26
36 6 0.16
ACGTcount: A:0.44, C:0.00, G:0.01, T:0.55
Consensus pattern (34 bp):
TTATATTAATATTTTAAAAATATTAATTAGTATA
Found at i:217351 original size:23 final size:22
Alignment explanation
Indices: 217277--217352 Score: 61
Period size: 23 Copynumber: 3.5 Consensus size: 22
217267 ATATTATATT
* *
217277 TTAAAAATATTAATTAGTAT-ATT
1 TTAAATATATT-ATTA-TATAATA
217300 TTAAATATATTTATTA-A-AATA
1 TTAAATATA-TTATTATATAATA
*
217321 TT-ATTATATTATTATATTAATA
1 TTAAATATATTATTATA-TAATA
217343 TTAAATATAT
1 TTAAATATAT
217353 AAATAATATT
Statistics
Matches: 43, Mismatches: 4, Indels: 12
0.73 0.07 0.20
Matches are distributed among these distances:
19 6 0.14
20 6 0.14
21 5 0.12
22 6 0.14
23 18 0.42
24 2 0.05
ACGTcount: A:0.47, C:0.00, G:0.01, T:0.51
Consensus pattern (22 bp):
TTAAATATATTATTATATAATA
Found at i:217361 original size:54 final size:55
Alignment explanation
Indices: 217303--217498 Score: 137
Period size: 58 Copynumber: 3.6 Consensus size: 55
217293 GTATATTTTA
217303 AATATATTTATTAA-AATATT-ATTATATTATTATATTAATATTAAATATATAA-AT
1 AATATATTTATTAATAAT-TTAATTATATTATTATATTAA-ATTAAATATATAATAT
* * * *
217357 AATATTATTCATTATTAATAATTTAATAATATTATTTCTATGAAATT-AATAAATAATAT
1 AATA-TA-T--TTATTAATAATTTAATTATATTA-TTATATTAAATTAAATATATAATAT
* *
217416 AA-AT-TTTATTAATAATTT-ATTATA-TA-T-TATTAAAATAAAAATATAATAT
1 AATATATTTATTAATAATTTAATTATATTATTATATTAAATTAAATATATAATAT
** * * *
217465 CTTATA-TTATT-ACAATATTGATTATTTTATTATA
1 AATATATTTATTAATAAT-TTAATTATATTATTATA
217499 ATATTAAAAA
Statistics
Matches: 113, Mismatches: 13, Indels: 32
0.72 0.08 0.20
Matches are distributed among these distances:
48 7 0.06
49 15 0.13
50 9 0.08
51 7 0.06
52 7 0.06
53 14 0.12
54 6 0.05
55 3 0.03
56 1 0.01
57 1 0.01
58 18 0.16
59 18 0.16
60 7 0.06
ACGTcount: A:0.47, C:0.02, G:0.01, T:0.49
Consensus pattern (55 bp):
AATATATTTATTAATAATTTAATTATATTATTATATTAAATTAAATATATAATAT
Found at i:217494 original size:20 final size:20
Alignment explanation
Indices: 217466--217503 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
217456 ATATAATATC
217466 TTATATTATTACAATATTGA
1 TTATATTATTACAATATTGA
* *
217486 TTATTTTATTATAATATT
1 TTATATTATTACAATATT
217504 AAAAATATAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.37, C:0.03, G:0.03, T:0.58
Consensus pattern (20 bp):
TTATATTATTACAATATTGA
Found at i:217540 original size:28 final size:27
Alignment explanation
Indices: 217485--217542 Score: 80
Period size: 28 Copynumber: 2.1 Consensus size: 27
217475 TACAATATTG
* *
217485 ATTATTTTATTATAATATTAAAAATAT
1 ATTATATTATTAGAATATTAAAAATAT
*
217512 ATTATATTATTAGATATATTAATAATAT
1 ATTATATTATTAGA-ATATTAAAAATAT
217540 ATT
1 ATT
217543 TTAAATATTT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
27 12 0.44
28 15 0.56
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.52
Consensus pattern (27 bp):
ATTATATTATTAGAATATTAAAAATAT
Found at i:217555 original size:22 final size:23
Alignment explanation
Indices: 217507--217568 Score: 72
Period size: 22 Copynumber: 2.6 Consensus size: 23
217497 TAATATTAAA
*
217507 AATATATTATATTATTAGATATATT
1 AATA-ATTATATT-TTAAATATATT
*
217532 AATAA-TATATTTTAAATATTTT
1 AATAATTATATTTTAAATATATT
217554 AATAATTAATATTTT
1 AATAATT-ATATTTT
217569 GATTAAAATG
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
22 14 0.42
23 7 0.21
24 8 0.24
25 4 0.12
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (23 bp):
AATAATTATATTTTAAATATATT
Found at i:221591 original size:201 final size:201
Alignment explanation
Indices: 220985--221978 Score: 1783
Period size: 201 Copynumber: 4.9 Consensus size: 201
220975 TTTATCCGGC
* *
220985 TTGTTATGACTTTAAAAACGACGTTGAAGATGCATTTTCAAGTTTATATGTATACTAGTAATATG
1 TTGTTAGGACTTTAAAAACGACGTTGAAGATGCATTTTCAAGTTTGTATGTATACTAGTAATATG
221050 TAACAATTATGGATATGAACCATTGATATTTATTAGATCAAATTATTTAAATTACTCATACGAAA
66 TAACAATTATGGATATGAACCATTGATATTTATTAGATCAAATTATTTAAATTACTCATACGAAA
* *
221115 ATGATCAAACAATTGAAGGACGGAATTCATGATTAAATAAAAAATCATATACAAAAATGATAAAG
131 ATGATCAAACAATTGAAGGACGGAATTCATGATTAAATCAAAAATCATATACGAAAATGATAAAG
221180 GAATTA
196 GAATTA
* * *
221186 TTGTTAAGACTCTAAAAACGACGTTGAATATGCATTTTCAAGTTTGTATGTATACTAGTAATATG
1 TTGTTAGGACTTTAAAAACGACGTTGAAGATGCATTTTCAAGTTTGTATGTATACTAGTAATATG
221251 TAACAATTATGGATATGAACCATTGATATTTATTAGATCAAA-TATTTAAATTACTCATACGAAA
66 TAACAATTATGGATATGAACCATTGATATTTATTAGATCAAATTATTTAAATTACTCATACGAAA
221315 ATGATCAAACAATTGAAGGACGGAATTCATGATTAAATCAAAAATCATATACGAAAATGATAAAG
131 ATGATCAAACAATTGAAGGACGGAATTCATGATTAAATCAAAAATCATATACGAAAATGATAAAG
221380 GAATTA
196 GAATTA
* *
221386 TTGTTAGGCCTTTAAAAATGACGTTGAAGATGCATTTTCAAGTTTGTATGTATACTAGTAATATG
1 TTGTTAGGACTTTAAAAACGACGTTGAAGATGCATTTTCAAGTTTGTATGTATACTAGTAATATG
* *
221451 TAACAATTATGGCTATGAACCATTGATATTTATTAGATCAAATTATTTAAATTACTCGTACGAAA
66 TAACAATTATGGATATGAACCATTGATATTTATTAGATCAAATTATTTAAATTACTCATACGAAA
*
221516 ATGATCAAACAATTGAAGGACGAAATTCATGATTAAATCAAAAATCATATACGAAAATGATAAAG
131 ATGATCAAACAATTGAAGGACGGAATTCATGATTAAATCAAAAATCATATACGAAAATGATAAAG
221581 GAATTA
196 GAATTA
* *
221587 TTGTTAGGATTTTAAAAATGACGTTGAAGATGCATTTTCAAGTTTGTATGTATACTAGTAATATG
1 TTGTTAGGACTTTAAAAACGACGTTGAAGATGCATTTTCAAGTTTGTATGTATACTAGTAATATG
221652 TAACAATTATGGATATGAACCATTGATATTTATTAGATCAAATTATTTAAATTACTCATACGAAA
66 TAACAATTATGGATATGAACCATTGATATTTATTAGATCAAATTATTTAAATTACTCATACGAAA
* *
221717 ATTATCAAACAATTGAAGGACGAAATTCATGATTAAATCAAAAATCATATACGAAAATGATAAAG
131 ATGATCAAACAATTGAAGGACGGAATTCATGATTAAATCAAAAATCATATACGAAAATGATAAAG
*
221782 GAATCA
196 GAATTA
**
221788 TTGTTAGGACTTTAAAAACGACGACGAAGATGCATTTTCAAGTTTGTATGTATACTAGTAATATG
1 TTGTTAGGACTTTAAAAACGACGTTGAAGATGCATTTTCAAGTTTGTATGTATACTAGTAATATG
* *
221853 CAACAATTATGGATATGAACCATTGATATTTATTAGATCAAATTATTTAAATTACTCGTACGAAA
66 TAACAATTATGGATATGAACCATTGATATTTATTAGATCAAATTATTTAAATTACTCATACGAAA
221918 ATGATCAAACAATTTGAAGGACGGAATTCATGATTAAATCAAAAATCATATACGAAAATGA
131 ATGATCAAACAA-TTGAAGGACGGAATTCATGATTAAATCAAAAATCATATACGAAAATGA
221979 AGTAGATGTT
Statistics
Matches: 763, Mismatches: 28, Indels: 3
0.96 0.04 0.00
Matches are distributed among these distances:
200 192 0.25
201 524 0.69
202 47 0.06
ACGTcount: A:0.42, C:0.10, G:0.14, T:0.33
Consensus pattern (201 bp):
TTGTTAGGACTTTAAAAACGACGTTGAAGATGCATTTTCAAGTTTGTATGTATACTAGTAATATG
TAACAATTATGGATATGAACCATTGATATTTATTAGATCAAATTATTTAAATTACTCATACGAAA
ATGATCAAACAATTGAAGGACGGAATTCATGATTAAATCAAAAATCATATACGAAAATGATAAAG
GAATTA
Found at i:237540 original size:20 final size:20
Alignment explanation
Indices: 237517--237657 Score: 106
Period size: 20 Copynumber: 7.0 Consensus size: 20
237507 GTTTCCAGAT
*
237517 TCGCAACGCGATTCTGACTA
1 TCGCAATGCGATTCTGACTA
* *
237537 TCGCATTGCGATTTTCCGACTA
1 TCGCAATGCGA--TTCTGACTA
* * *
237559 TCGCAATGCGAATATGTA-AA
1 TCGCAATGCGATTCTG-ACTA
* * *
237579 TCGCAATGCGAATATGTA-AA
1 TCGCAATGCGATTCTG-ACTA
*
237599 TCGCAATGCGATTATGACTA
1 TCGCAATGCGATTCTGACTA
* * *
237619 TCGCAACGCGATTCTGAATG
1 TCGCAATGCGATTCTGACTA
*
237639 TCGCAACGCGATTCTGACT
1 TCGCAATGCGATTCTGACT
237658 GTCGTAACAC
Statistics
Matches: 102, Mismatches: 15, Indels: 8
0.82 0.12 0.06
Matches are distributed among these distances:
19 1 0.01
20 82 0.80
21 1 0.01
22 18 0.18
ACGTcount: A:0.28, C:0.23, G:0.21, T:0.28
Consensus pattern (20 bp):
TCGCAATGCGATTCTGACTA
Found at i:238517 original size:24 final size:24
Alignment explanation
Indices: 238485--238538 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
238475 GTATTCGAAA
238485 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATCTTGGTCAATACCCGGAC
* *
238509 TTTGATCTTGGTCAATACTCGGAT
1 TTTGATCTTGGTCAATACCCGGAC
238533 TTTGAT
1 TTTGAT
238539 TATGTTTCAG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.20, C:0.19, G:0.20, T:0.41
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACCCGGAC
Found at i:240809 original size:18 final size:18
Alignment explanation
Indices: 240786--240820 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
240776 AGAAAAAGGC
*
240786 AATCAAAATCGCAATCAA
1 AATCAAAATCCCAATCAA
240804 AATCAAAATCCCAATCA
1 AATCAAAATCCCAATCA
240821 CAACCGGCTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.54, C:0.26, G:0.03, T:0.17
Consensus pattern (18 bp):
AATCAAAATCCCAATCAA
Found at i:241132 original size:140 final size:140
Alignment explanation
Indices: 240880--241149 Score: 504
Period size: 140 Copynumber: 1.9 Consensus size: 140
240870 AAACGTTGTA
*
240880 TTATGTGTAAACTTTTAAAATTTTCAGTTAGGCATGTATTAGTAACTTGAGTTTGAACATTGCTA
1 TTATGTGTAAACTTTTAAAATTTTCAGTTAGGCATGTATTAGTAACTTGAGTATGAACATTGCTA
* *
240945 TGATCTGTTCAGTTGTTATCAGTTATTACACATTCATTTGAATATCGCAACGCGAATTTGACTAT
66 TGATATGTTCAGTTGTTATCACTTATTACACATTCATTTGAATATCGCAACGCGAATTTGACTAT
241010 TATGTGTATT
131 TATGTGTATT
*
241020 TTATGTGTAAACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTTGAGTATGAACATTGCTA
1 TTATGTGTAAACTTTTAAAATTTTCAGTTAGGCATGTATTAGTAACTTGAGTATGAACATTGCTA
241085 TGATATGTTCAGTTGTTATCACTTATTACACATTCATTTGAATATCGCAACGCGAATTTGACTAT
66 TGATATGTTCAGTTGTTATCACTTATTACACATTCATTTGAATATCGCAACGCGAATTTGACTAT
241150 CGCAATGCAA
Statistics
Matches: 126, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
140 126 1.00
ACGTcount: A:0.29, C:0.13, G:0.16, T:0.42
Consensus pattern (140 bp):
TTATGTGTAAACTTTTAAAATTTTCAGTTAGGCATGTATTAGTAACTTGAGTATGAACATTGCTA
TGATATGTTCAGTTGTTATCACTTATTACACATTCATTTGAATATCGCAACGCGAATTTGACTAT
TATGTGTATT
Found at i:241145 original size:20 final size:20
Alignment explanation
Indices: 241120--241324 Score: 191
Period size: 20 Copynumber: 10.8 Consensus size: 20
241110 TTACACATTC
*
241120 ATTTGAATATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
* *
241140 ATTTGACTATCGCAATGCAA
1 ATTTGACTATCGCAACGCGA
* *
241160 ATTTGAATATCGCAACTC-A
1 ATTTGACTATCGCAACGCGA
*
241179 A----A-AATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
* *
241194 ATTTGACTATCGCAACACAA
1 ATTTGACTATCGCAACGCGA
*
241214 ATATGACTATCGCAACGC-A
1 ATTTGACTATCGCAACGCGA
* *
241233 A----A-AATCGCAACACGA
1 ATTTGACTATCGCAACGCGA
*
241248 ATTTGTCTATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
241268 ATTTGACTATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
* * *
241288 ATTTGATTATCGCAACGGGT
1 ATTTGACTATCGCAACGCGA
241308 ATTTGACTATCGCAACG
1 ATTTGACTATCGCAACG
241325 AGAAAATCGC
Statistics
Matches: 150, Mismatches: 23, Indels: 24
0.76 0.12 0.12
Matches are distributed among these distances:
14 18 0.12
15 6 0.04
19 5 0.03
20 121 0.81
ACGTcount: A:0.35, C:0.23, G:0.17, T:0.25
Consensus pattern (20 bp):
ATTTGACTATCGCAACGCGA
Found at i:241197 original size:34 final size:34
Alignment explanation
Indices: 241148--241214 Score: 98
Period size: 34 Copynumber: 2.0 Consensus size: 34
241138 GAATTTGACT
* *
241148 ATCGCAATGCAAATTTGAATATCGCAACTCAAAA
1 ATCGCAACGCAAATTTGAATATCGCAACACAAAA
* *
241182 ATCGCAACGCGAATTTGACTATCGCAACACAAA
1 ATCGCAACGCAAATTTGAATATCGCAACACAAA
241215 TATGACTATC
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
34 29 1.00
ACGTcount: A:0.42, C:0.24, G:0.13, T:0.21
Consensus pattern (34 bp):
ATCGCAACGCAAATTTGAATATCGCAACACAAAA
Found at i:241215 original size:54 final size:54
Alignment explanation
Indices: 241128--241285 Score: 244
Period size: 54 Copynumber: 2.9 Consensus size: 54
241118 TCATTTGAAT
* * *
241128 ATCGCAACGCGAATTTGACTATCGCAATGCAAATTTGAATATCGCAACTCAAAA
1 ATCGCAACGCGAATTTGACTATCGCAACGCAAATTTGACTATCGCAACGCAAAA
* *
241182 ATCGCAACGCGAATTTGACTATCGCAACACAAATATGACTATCGCAACGCAAAA
1 ATCGCAACGCGAATTTGACTATCGCAACGCAAATTTGACTATCGCAACGCAAAA
* * *
241236 ATCGCAACACGAATTTGTCTATCGCAACGCGAATTTGACTATCGCAACGC
1 ATCGCAACGCGAATTTGACTATCGCAACGCAAATTTGACTATCGCAACGC
241286 GAATTTGATT
Statistics
Matches: 94, Mismatches: 10, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
54 94 1.00
ACGTcount: A:0.37, C:0.25, G:0.16, T:0.22
Consensus pattern (54 bp):
ATCGCAACGCGAATTTGACTATCGCAACGCAAATTTGACTATCGCAACGCAAAA
Found at i:241291 original size:94 final size:93
Alignment explanation
Indices: 241182--241373 Score: 244
Period size: 94 Copynumber: 2.1 Consensus size: 93
241172 CAACTCAAAA
241182 ATCGCAACGCGAATTTGACTATCGCAACACAAATATGACTATCGCAACGCA-AAAATCGCAACA-
1 ATCGCAACGCGAATTTGACTATCGCAACACAAATATGACTATCGCAACG-AGAAAATCGCAA-AG
* *
241245 CGAATTTGTCTATCGCAACGCGAATTTGACT
64 CGAATTAGACTATCGCAACGCGAA-TTGACT
* **** * *
241276 ATCGCAACGCGAATTTGATTATCGCAACGGGTATTTGACTATCGCAACGAGAAAATCGCAAAGTG
1 ATCGCAACGCGAATTTGACTATCGCAACACAAATATGACTATCGCAACGAGAAAATCGCAAAGCG
*
241341 TATTAGACTATCGCAACGCGAATTGACT
66 AATTAGACTATCGCAACGCGAATTGACT
*
241369 TTCGC
1 ATCGC
241374 GTTGCGATTT
Statistics
Matches: 85, Mismatches: 11, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
93 12 0.14
94 73 0.86
ACGTcount: A:0.34, C:0.23, G:0.19, T:0.24
Consensus pattern (93 bp):
ATCGCAACGCGAATTTGACTATCGCAACACAAATATGACTATCGCAACGAGAAAATCGCAAAGCG
AATTAGACTATCGCAACGCGAATTGACT
Found at i:241334 original size:74 final size:74
Alignment explanation
Indices: 241120--241373 Score: 212
Period size: 74 Copynumber: 3.4 Consensus size: 74
241110 TTACACATTC
* * * *
241120 ATTTGAATATCGCAACGCGAATTTGACTATCGCAATGCAAATTTGAATATCGCAACTCA-AAAAT
1 ATTTGACTATCGCAACGCGAATTTGACTATCGCAACGAAAATTTGACTATCGCAAC-CAGAAAAT
241184 CGCAACGCGA
65 CGCAACGCGA
* * * * * *** ***
241194 ATTTGACTATCGCAACACAAATATGACTATCGCAACGCAAAAATCGCAAC-A-CG-AATTTGTCT
1 ATTTGACTATCGCAACGCGAATTTGACTATCGCAACG-AAAATTTG--ACTATCGCAACCAGAAA
241256 ATCGCAACGCGA
63 ATCGCAACGCGA
* *** *
241268 ATTTGACTATCGCAACGCGAATTTGATTATCGCAACGGGTATTTGACTATCGCAACGAGAAAATC
1 ATTTGACTATCGCAACGCGAATTTGACTATCGCAACGAAAATTTGACTATCGCAACCAGAAAATC
* * *
241333 GCAAAGTGT
66 GCAACGCGA
* *
241342 ATTAGACTATCGCAACGCGAA-TTGACTTTCGC
1 ATTTGACTATCGCAACGCGAATTTGACTATCGC
241374 GTTGCGATTT
Statistics
Matches: 137, Mismatches: 36, Indels: 15
0.73 0.19 0.08
Matches are distributed among these distances:
71 2 0.01
72 1 0.01
73 14 0.10
74 111 0.81
75 7 0.05
76 1 0.01
77 1 0.01
ACGTcount: A:0.35, C:0.22, G:0.18, T:0.25
Consensus pattern (74 bp):
ATTTGACTATCGCAACGCGAATTTGACTATCGCAACGAAAATTTGACTATCGCAACCAGAAAATC
GCAACGCGA
Found at i:241392 original size:20 final size:20
Alignment explanation
Indices: 241363--241420 Score: 80
Period size: 20 Copynumber: 2.9 Consensus size: 20
241353 GCAACGCGAA
241363 TTGACTTTCGCGTTGCGATT
1 TTGACTTTCGCGTTGCGATT
* *
241383 TTGTCTTTCGCATTGCGATT
1 TTGACTTTCGCGTTGCGATT
* *
241403 TTGAGTTTAGCGTTGCGA
1 TTGACTTTCGCGTTGCGA
241421 AAGTGTACAT
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.12, C:0.17, G:0.26, T:0.45
Consensus pattern (20 bp):
TTGACTTTCGCGTTGCGATT
Found at i:241579 original size:14 final size:14
Alignment explanation
Indices: 241519--241580 Score: 61
Period size: 14 Copynumber: 4.3 Consensus size: 14
241509 CACAAATAAG
*
241519 AATTATTTACACATC
1 AATT-TTTACAAATC
**
241534 AATATTAAACAAATC
1 AAT-TTTTACAAATC
*
241549 AACTTTTACAAATC
1 AATTTTTACAAATC
*
241563 AATTTTTATAAATC
1 AATTTTTACAAATC
241577 AATT
1 AATT
241581 AAACAAGCAA
Statistics
Matches: 38, Mismatches: 8, Indels: 3
0.78 0.16 0.06
Matches are distributed among these distances:
14 25 0.66
15 12 0.32
16 1 0.03
ACGTcount: A:0.47, C:0.15, G:0.00, T:0.39
Consensus pattern (14 bp):
AATTTTTACAAATC
Found at i:243059 original size:21 final size:20
Alignment explanation
Indices: 242978--243075 Score: 61
Period size: 21 Copynumber: 4.7 Consensus size: 20
242968 GAATGTTGGG
* * *
242978 AGGGACCTCTTCAACGATGAC
1 AGGGGCCTCTTGAACGAT-AA
* * **
242999 AGTGGCCTCTTGAACGGTGGG
1 AGGGGCCTCTTGAACGAT-AA
* **
243020 AGGGGACTCTTGAGGGATAA
1 AGGGGCCTCTTGAACGATAA
243040 TAGGGGCCTCTTGAACGATAA
1 -AGGGGCCTCTTGAACGATAA
*
243061 GGGAGGCCTCTTGAA
1 AGG-GGCCTCTTGAA
243076 TGATGACAGG
Statistics
Matches: 58, Mismatches: 17, Indels: 4
0.73 0.22 0.05
Matches are distributed among these distances:
20 2 0.03
21 56 0.97
ACGTcount: A:0.24, C:0.19, G:0.35, T:0.21
Consensus pattern (20 bp):
AGGGGCCTCTTGAACGATAA
Found at i:243594 original size:18 final size:18
Alignment explanation
Indices: 243571--243637 Score: 80
Period size: 20 Copynumber: 3.5 Consensus size: 18
243561 GAAACTTAAA
*
243571 ATCGCAACACGAATGACT
1 ATCGCAACGCGAATGACT
243589 ATCGCAACGCGAAAATGACT
1 ATCGCAACGCG--AATGACT
243609 ATCGCAACGCGAATTTGACT
1 ATCGCAACGCGAA--TGACT
*
243629 AGCGCAACG
1 ATCGCAACG
243638 AGAGAATCGC
Statistics
Matches: 43, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
18 12 0.28
20 31 0.72
ACGTcount: A:0.36, C:0.27, G:0.21, T:0.16
Consensus pattern (18 bp):
ATCGCAACGCGAATGACT
Found at i:243607 original size:20 final size:20
Alignment explanation
Indices: 243582--243637 Score: 85
Period size: 20 Copynumber: 2.8 Consensus size: 20
243572 TCGCAACACG
243582 AATGACTATCGCAACGCGAA
1 AATGACTATCGCAACGCGAA
243602 AATGACTATCGCAACGCGAA
1 AATGACTATCGCAACGCGAA
** *
243622 TTTGACTAGCGCAACG
1 AATGACTATCGCAACG
243638 AGAGAATCGC
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.36, C:0.25, G:0.21, T:0.18
Consensus pattern (20 bp):
AATGACTATCGCAACGCGAA
Found at i:243740 original size:20 final size:20
Alignment explanation
Indices: 243680--243740 Score: 104
Period size: 20 Copynumber: 3.0 Consensus size: 20
243670 GCGATTCTTT
243680 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCATTTTCG
* *
243700 AGTTACGATAGTCATTTTCG
1 CGTTGCGATAGTCATTTTCG
243720 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCATTTTCG
243740 C
1 C
243741 ACTGCGAAAG
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 37 1.00
ACGTcount: A:0.18, C:0.20, G:0.23, T:0.39
Consensus pattern (20 bp):
CGTTGCGATAGTCATTTTCG
Found at i:243746 original size:20 final size:20
Alignment explanation
Indices: 243682--243747 Score: 89
Period size: 20 Copynumber: 3.3 Consensus size: 20
243672 GATTCTTTCG
243682 TTGCGATAGTCATTTTCG-A
1 TTGCGATAGTCATTTTCGCA
* *
243701 GTTACGATAGTCATTTTCGCG
1 -TTGCGATAGTCATTTTCGCA
243722 TTGCGATAGTCATTTTCGCA
1 TTGCGATAGTCATTTTCGCA
*
243742 CTGCGA
1 TTGCGA
243748 AAGTAAACTA
Statistics
Matches: 40, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
20 40 1.00
ACGTcount: A:0.20, C:0.20, G:0.23, T:0.38
Consensus pattern (20 bp):
TTGCGATAGTCATTTTCGCA
Found at i:243917 original size:18 final size:18
Alignment explanation
Indices: 243894--243943 Score: 100
Period size: 18 Copynumber: 2.8 Consensus size: 18
243884 TTTACTAAGC
243894 AATCTAAGTGAAATGGTT
1 AATCTAAGTGAAATGGTT
243912 AATCTAAGTGAAATGGTT
1 AATCTAAGTGAAATGGTT
243930 AATCTAAGTGAAAT
1 AATCTAAGTGAAAT
243944 TACGAGTAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 32 1.00
ACGTcount: A:0.42, C:0.06, G:0.20, T:0.32
Consensus pattern (18 bp):
AATCTAAGTGAAATGGTT
Found at i:245676 original size:20 final size:20
Alignment explanation
Indices: 245653--245738 Score: 93
Period size: 20 Copynumber: 4.3 Consensus size: 20
245643 TCTGAAACTT
245653 AAAATCGCAACACGAAAATG
1 AAAATCGCAACACGAAAATG
245673 AAAATCGCAACACGAAAATG
1 AAAATCGCAACACGAAAATG
** * **
245693 ACTATCGCAACGCGAATTTG
1 AAAATCGCAACACGAAAATG
* * *
245713 ACAATCGCAACGCGAAACT-
1 AAAATCGCAACACGAAAATG
245732 AAAATCG
1 AAAATCG
245739 TATTGCGATT
Statistics
Matches: 57, Mismatches: 9, Indels: 1
0.85 0.13 0.01
Matches are distributed among these distances:
19 6 0.11
20 51 0.89
ACGTcount: A:0.47, C:0.23, G:0.16, T:0.14
Consensus pattern (20 bp):
AAAATCGCAACACGAAAATG
Found at i:246351 original size:20 final size:20
Alignment explanation
Indices: 246321--246434 Score: 147
Period size: 20 Copynumber: 5.7 Consensus size: 20
246311 GCGCTTTGAA
*
246321 AATCGCATTGCGATAGTCAG
1 AATCGCGTTGCGATAGTCAG
* *
246341 CATCGCGTTGCGACAGTCAG
1 AATCGCGTTGCGATAGTCAG
*
246361 AATCGCGTTGCGGTAGTCAG
1 AATCGCGTTGCGATAGTCAG
* *
246381 AATCTCGTTGCAATAGTCAG
1 AATCGCGTTGCGATAGTCAG
*
246401 AATCGCGTTGCGATAGTCAT
1 AATCGCGTTGCGATAGTCAG
* *
246421 ACTCGCATTGCGAT
1 AATCGCGTTGCGAT
246435 TTACATATTC
Statistics
Matches: 80, Mismatches: 14, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 80 1.00
ACGTcount: A:0.25, C:0.23, G:0.26, T:0.26
Consensus pattern (20 bp):
AATCGCGTTGCGATAGTCAG
Found at i:246457 original size:60 final size:60
Alignment explanation
Indices: 246321--246458 Score: 152
Period size: 60 Copynumber: 2.3 Consensus size: 60
246311 GCGCTTTGAA
* * *
246321 AATCGCATTGCGATAGTCAGCATCGCGTTGCGACAGTCAGAATCGCGTTGCGGTAGTCAG
1 AATCGCATTGCGATAGTCAGAATCGCGTTGCGACAGTCAGAATCGCATTGCGATAGTCAG
* * * * * * * *
246381 AATCTCGTTGCAATAGTCAGAATCGCGTTGCGATAGTCATACTCGCATTGCGAT-TTACAT
1 AATCGCATTGCGATAGTCAGAATCGCGTTGCGACAGTCAGAATCGCATTGCGATAGT-CAG
*
246441 ATTCGCATTGCGATAGTC
1 AATCGCATTGCGATAGTC
246459 GGAAAATCGC
Statistics
Matches: 62, Mismatches: 15, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
59 1 0.02
60 61 0.98
ACGTcount: A:0.25, C:0.22, G:0.25, T:0.28
Consensus pattern (60 bp):
AATCGCATTGCGATAGTCAGAATCGCGTTGCGACAGTCAGAATCGCATTGCGATAGTCAG
Found at i:246524 original size:41 final size:40
Alignment explanation
Indices: 246472--246558 Score: 97
Period size: 40 Copynumber: 2.1 Consensus size: 40
246462 AAATCGCAAC
* *
246472 GCGAATTTGGAAAATCGCA-ATGCGATAGTCAGA-ATCGCGTT
1 GCGAATCTGGAAAAT-G-ATATGCGATA-CCAGAGATCGCGTT
* *
246513 GCGAATCTGGAAACTGATTTGCGATACCAGAGATCGCGTT
1 GCGAATCTGGAAAATGATATGCGATACCAGAGATCGCGTT
246553 GCGAAT
1 GCGAAT
246559 TATCGATCGC
Statistics
Matches: 40, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
39 5 0.12
40 22 0.55
41 13 0.32
ACGTcount: A:0.30, C:0.18, G:0.28, T:0.24
Consensus pattern (40 bp):
GCGAATCTGGAAAATGATATGCGATACCAGAGATCGCGTT
Found at i:255893 original size:29 final size:29
Alignment explanation
Indices: 255849--255909 Score: 86
Period size: 29 Copynumber: 2.1 Consensus size: 29
255839 ATGGGCATAG
* *
255849 TCCTCATCTTGATTCTGCATGGGATTATA
1 TCCTCATCCTGATTCTGCAAGGGATTATA
* *
255878 TCCTCATCCTGTTTCTGCAAGGGATTGTA
1 TCCTCATCCTGATTCTGCAAGGGATTATA
255907 TCC
1 TCC
255910 CCGCTTTGTT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.18, C:0.25, G:0.18, T:0.39
Consensus pattern (29 bp):
TCCTCATCCTGATTCTGCAAGGGATTATA
Found at i:260465 original size:3 final size:3
Alignment explanation
Indices: 260445--260479 Score: 52
Period size: 3 Copynumber: 11.3 Consensus size: 3
260435 AATGTAATTT
*
260445 ATA ATTA ATA ATA GTA ATA ATA ATA ATA ATA ATA A
1 ATA A-TA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
260480 AATTAAAATT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
3 26 0.90
4 3 0.10
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:261096 original size:17 final size:17
Alignment explanation
Indices: 261069--261101 Score: 50
Period size: 16 Copynumber: 1.9 Consensus size: 17
261059 ATCAATTTTA
261069 ATTTTAATTT-ATTCTT
1 ATTTTAATTTAATTCTT
261085 ATTTTAAATTTAATTCT
1 ATTTT-AATTTAATTCT
261102 AATATAATAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 5 0.33
17 5 0.33
18 5 0.33
ACGTcount: A:0.30, C:0.06, G:0.00, T:0.64
Consensus pattern (17 bp):
ATTTTAATTTAATTCTT
Found at i:266581 original size:22 final size:22
Alignment explanation
Indices: 266553--266597 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
266543 AAAAAATAAA
* *
266553 TAAATAAAGTTAAACAATTACC
1 TAAATAAAGGTAAACAACTACC
266575 TAAATAAAGGTAAACAACTACC
1 TAAATAAAGGTAAACAACTACC
266597 T
1 T
266598 TGCAACCATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.53, C:0.16, G:0.07, T:0.24
Consensus pattern (22 bp):
TAAATAAAGGTAAACAACTACC
Found at i:270990 original size:19 final size:17
Alignment explanation
Indices: 270964--271016 Score: 54
Period size: 19 Copynumber: 3.1 Consensus size: 17
270954 ATTTCACAAA
270964 TATATTTTATAAAAATT
1 TATATTTTATAAAAATT
* * *
270981 ATCTTATTTTTTAAATATT
1 -T-ATATTTTATAAAAATT
271000 TATATTTTA-AAAAATT
1 TATATTTTATAAAAATT
271016 T
1 T
271017 GTAAACTTTT
Statistics
Matches: 28, Mismatches: 6, Indels: 4
0.74 0.16 0.11
Matches are distributed among these distances:
16 7 0.25
17 6 0.21
18 2 0.07
19 13 0.46
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.57
Consensus pattern (17 bp):
TATATTTTATAAAAATT
Found at i:271082 original size:2 final size:2
Alignment explanation
Indices: 271075--271099 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
271065 TAAAAGTTAT
271075 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
271100 TATCTTGTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:279919 original size:60 final size:60
Alignment explanation
Indices: 279846--279959 Score: 149
Period size: 60 Copynumber: 1.9 Consensus size: 60
279836 CGGTTATCTT
* *
279846 ACTATAGGATATTGCTTTATTAAGTCCCTCGACAATTAAAAGTTACAAAATGGTTCTCAG
1 ACTATAGGATATTGCATTATTAAGTCCCTCAACAATTAAAAGTTACAAAATGGTTCTCAG
* * * * *
279906 ACTATA-GAGTATTGCATTGTTGAGTCCTTCAACTATTAAAAGTTGCAAAATGGT
1 ACTATAGGA-TATTGCATTATTAAGTCCCTCAACAATTAAAAGTTACAAAATGGT
279960 CACCCGATTA
Statistics
Matches: 46, Mismatches: 7, Indels: 2
0.84 0.13 0.04
Matches are distributed among these distances:
59 2 0.04
60 44 0.96
ACGTcount: A:0.34, C:0.15, G:0.17, T:0.34
Consensus pattern (60 bp):
ACTATAGGATATTGCATTATTAAGTCCCTCAACAATTAAAAGTTACAAAATGGTTCTCAG
Found at i:281272 original size:29 final size:31
Alignment explanation
Indices: 281218--281279 Score: 83
Period size: 29 Copynumber: 2.1 Consensus size: 31
281208 ATGAACAAGA
281218 TATATAATCTAAATTTATATAAATTTGTATT
1 TATATAATCTAAATTTATATAAATTTGTATT
* * *
281249 TATATAATCT-TATTT-TATTAATTTTTATT
1 TATATAATCTAAATTTATATAAATTTGTATT
281278 TA
1 TA
281280 AAAGATAAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
29 14 0.50
30 4 0.14
31 10 0.36
ACGTcount: A:0.37, C:0.03, G:0.02, T:0.58
Consensus pattern (31 bp):
TATATAATCTAAATTTATATAAATTTGTATT
Found at i:281279 original size:14 final size:15
Alignment explanation
Indices: 281230--281279 Score: 50
Period size: 14 Copynumber: 3.3 Consensus size: 15
281220 TATAATCTAA
*
281230 ATTTATATAAATTTGT
1 ATTTATAT-AATTTTT
*
281246 ATTTATATAA-TCTT
1 ATTTATATAATTTTT
281260 ATTT-TATTAATTTTT
1 ATTTATA-TAATTTTT
281275 ATTTA
1 ATTTA
281280 AAAGATAAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
13 2 0.07
14 9 0.32
15 9 0.32
16 8 0.29
ACGTcount: A:0.34, C:0.02, G:0.02, T:0.62
Consensus pattern (15 bp):
ATTTATATAATTTTT
Found at i:284862 original size:21 final size:21
Alignment explanation
Indices: 284837--284883 Score: 94
Period size: 21 Copynumber: 2.2 Consensus size: 21
284827 ACGGATGCAG
284837 CAGAAGCTAGAGAAAAGCCAT
1 CAGAAGCTAGAGAAAAGCCAT
284858 CAGAAGCTAGAGAAAAGCCAT
1 CAGAAGCTAGAGAAAAGCCAT
284879 CAGAA
1 CAGAA
284884 CTTGCAGGGC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.49, C:0.19, G:0.23, T:0.09
Consensus pattern (21 bp):
CAGAAGCTAGAGAAAAGCCAT
Found at i:290763 original size:3 final size:3
Alignment explanation
Indices: 290755--290792 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
290745 CGAACCAAAT
290755 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
290793 AGACAATGCT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:297052 original size:8 final size:8
Alignment explanation
Indices: 297039--297079 Score: 57
Period size: 8 Copynumber: 5.2 Consensus size: 8
297029 CTCATTTTCA
297039 GAGAATTT
1 GAGAATTT
297047 GAGAATTT
1 GAGAATTT
*
297055 -AGAGTTT
1 GAGAATTT
*
297062 GGGAATTT
1 GAGAATTT
297070 GAGAATTT
1 GAGAATTT
297078 GA
1 GA
297080 AAGCTTGTGA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
7 6 0.21
8 22 0.79
ACGTcount: A:0.34, C:0.00, G:0.29, T:0.37
Consensus pattern (8 bp):
GAGAATTT
Found at i:297385 original size:128 final size:128
Alignment explanation
Indices: 297150--297649 Score: 921
Period size: 128 Copynumber: 3.9 Consensus size: 128
297140 TAATCGGAGT
297150 ACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCA-AGAATATGTTAT
1 ACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTAT
* *
297214 AATTACCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
66 CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
*
297277 ACTATTCACATGAAGGCGCGTTCCCGGGGGCACGCCTTCCATTATTTTGTCAGAGAATATGTTAT
1 ACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTAT
*
297342 CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACATATTATTTC
66 CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
* * *
297405 ACTATTCACATGAAGGCGCATTCCTGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATATTAT
1 ACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTAT
*
297470 CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAATACCTATTATTTC
66 CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
297533 ACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTAT
1 ACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTAT
297598 CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTA
66 CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTA
297650 AATCAGGTAA
Statistics
Matches: 358, Mismatches: 14, Indels: 1
0.96 0.04 0.00
Matches are distributed among these distances:
127 51 0.14
128 307 0.86
ACGTcount: A:0.24, C:0.24, G:0.19, T:0.33
Consensus pattern (128 bp):
ACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTAT
CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
Found at i:298087 original size:34 final size:34
Alignment explanation
Indices: 298049--298149 Score: 139
Period size: 34 Copynumber: 3.0 Consensus size: 34
298039 AAATTTAATG
*
298049 TTAAATTTCGAATACTATAATTTATATTTTAAAT
1 TTAAATTTCGAATAATATAATTTATATTTTAAAT
* * * *
298083 TTAAATTTCGAATAATATTATTTTTATTTTTATT
1 TTAAATTTCGAATAATATAATTTATATTTTAAAT
* *
298117 TTAAATTTTGAATAATATAATTTGTATTTTAAA
1 TTAAATTTCGAATAATATAATTTATATTTTAAA
298150 AACATTTATC
Statistics
Matches: 57, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
34 57 1.00
ACGTcount: A:0.39, C:0.03, G:0.04, T:0.54
Consensus pattern (34 bp):
TTAAATTTCGAATAATATAATTTATATTTTAAAT
Found at i:298700 original size:21 final size:20
Alignment explanation
Indices: 298671--298777 Score: 119
Period size: 21 Copynumber: 5.2 Consensus size: 20
298661 GGTGTAAAAC
*
298671 CCTGTGGGCT-AGACATGTAA
1 CCTGCGGGCTCAGA-ATGTAA
298691 CCTGGCGGGCT-AGGAATGTAA
1 CCT-GCGGGCTCA-GAATGTAA
*
298712 CCCTGCGGGCTCGGAATGTAA
1 -CCTGCGGGCTCAGAATGTAA
*
298733 CCATGCGGGCTCAGAATATAA
1 CC-TGCGGGCTCAGAATGTAA
298754 CCCTGCGGGCTCAGAATGTAA
1 -CCTGCGGGCTCAGAATGTAA
298775 CCT
1 CCT
298778 TGTGGAGATG
Statistics
Matches: 76, Mismatches: 5, Indels: 12
0.82 0.05 0.13
Matches are distributed among these distances:
20 8 0.11
21 61 0.80
22 7 0.09
ACGTcount: A:0.24, C:0.25, G:0.30, T:0.21
Consensus pattern (20 bp):
CCTGCGGGCTCAGAATGTAA
Found at i:298731 original size:42 final size:41
Alignment explanation
Indices: 298668--298777 Score: 143
Period size: 42 Copynumber: 2.6 Consensus size: 41
298658 TATGGTGTAA
* *
298668 AACCCTGTGGGCT-AGACATGTAACCTGGCGGGCT-AGGAATGT
1 AACCCTGCGGGCTCAGA-ATGTAACCT-GCGGGCTCA-GAATAT
*
298710 AACCCTGCGGGCTCGGAATGTAACCATGCGGGCTCAGAATAT
1 AACCCTGCGGGCTCAGAATGTAACC-TGCGGGCTCAGAATAT
298752 AACCCTGCGGGCTCAGAATGTAACCT
1 AACCCTGCGGGCTCAGAATGTAACCT
298778 TGTGGAGATG
Statistics
Matches: 61, Mismatches: 4, Indels: 7
0.85 0.06 0.10
Matches are distributed among these distances:
41 1 0.02
42 56 0.92
43 4 0.07
ACGTcount: A:0.25, C:0.25, G:0.29, T:0.20
Consensus pattern (41 bp):
AACCCTGCGGGCTCAGAATGTAACCTGCGGGCTCAGAATAT
Found at i:298813 original size:21 final size:21
Alignment explanation
Indices: 298789--298833 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
298779 GTGGAGATGA
* *
298789 CATATAAACTGGTGGGCTTGG
1 CATATAAACTGGAGGGCTGGG
* *
298810 CATATGAAGTGGAGGGCTGGG
1 CATATAAACTGGAGGGCTGGG
298831 CAT
1 CAT
298834 GTACCCCTAC
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.24, C:0.13, G:0.38, T:0.24
Consensus pattern (21 bp):
CATATAAACTGGAGGGCTGGG
Found at i:300601 original size:31 final size:32
Alignment explanation
Indices: 300565--300633 Score: 79
Period size: 31 Copynumber: 2.2 Consensus size: 32
300555 CTAAATAAAT
* *
300565 AATAATTATATAAAT-ATTATTTTAATAAAAA
1 AATAATTATATAAATAAATATATTAATAAAAA
* *
300596 AATAA-TATTTACATAAATATATTAATAAAAA
1 AATAATTATATAAATAAATATATTAATAAAAA
300627 ATATAAT
1 A-ATAAT
300634 AACTATTTAA
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
30 7 0.23
31 20 0.65
32 4 0.13
ACGTcount: A:0.59, C:0.01, G:0.00, T:0.39
Consensus pattern (32 bp):
AATAATTATATAAATAAATATATTAATAAAAA
Found at i:300601 original size:34 final size:31
Alignment explanation
Indices: 300556--300644 Score: 97
Period size: 34 Copynumber: 2.7 Consensus size: 31
300546 TTAATAATTC
*
300556 TAAATAAATAATAATTATATAAATATTATTTTAA
1 TAAAAAAATAATAATTATATAAATA-TA--TTAA
* *
300590 TAAAAAAATAATATTTACATAAATATATTAA
1 TAAAAAAATAATAATTATATAAATATATTAA
* *
300621 TAAAAAATATAATAACTATTTAAA
1 TAAAAAA-ATAATAATTATATAAA
300645 AAAATACTAA
Statistics
Matches: 47, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
31 11 0.23
32 12 0.26
33 2 0.04
34 22 0.47
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (31 bp):
TAAAAAAATAATAATTATATAAATATATTAA
Found at i:310727 original size:32 final size:32
Alignment explanation
Indices: 310684--310765 Score: 105
Period size: 32 Copynumber: 2.6 Consensus size: 32
310674 ATAATAAATT
310684 ATAAAATTTTAATGATTATTGTATAAT-GTTTTG
1 ATAAAA-TTTAATGATTATTGTATAATAG-TTTG
* * *
310717 ATAAAATTTAATGATAATTTTGTAATAGTTTG
1 ATAAAATTTAATGATTATTGTATAATAGTTTG
310749 AT-AAATTTAATGATTAT
1 ATAAAATTTAATGATTAT
310766 CTTTTAACTA
Statistics
Matches: 44, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
31 14 0.32
32 23 0.52
33 7 0.16
ACGTcount: A:0.40, C:0.00, G:0.11, T:0.49
Consensus pattern (32 bp):
ATAAAATTTAATGATTATTGTATAATAGTTTG
Found at i:323298 original size:17 final size:18
Alignment explanation
Indices: 323271--323305 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
323261 TATTTATTTT
*
323271 AATTTATTAAATAAATTA
1 AATTTATTAAAAAAATTA
323289 AATTTA-TAAAAAAATTA
1 AATTTATTAAAAAAATTA
323306 TTATGGGATA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 10 0.62
18 6 0.38
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (18 bp):
AATTTATTAAAAAAATTA
Found at i:327049 original size:31 final size:31
Alignment explanation
Indices: 327013--327078 Score: 114
Period size: 31 Copynumber: 2.1 Consensus size: 31
327003 AAAAGATTGG
*
327013 TTAATTTATAATTAAACTTCAAATTTTAAGT
1 TTAATTTATAATAAAACTTCAAATTTTAAGT
*
327044 TTAATTTATAATAAAACTTCGAATTTTAAGT
1 TTAATTTATAATAAAACTTCAAATTTTAAGT
327075 TTAA
1 TTAA
327079 AAAGTTAAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.42, C:0.06, G:0.05, T:0.47
Consensus pattern (31 bp):
TTAATTTATAATAAAACTTCAAATTTTAAGT
Found at i:337799 original size:23 final size:25
Alignment explanation
Indices: 337763--337822 Score: 61
Period size: 26 Copynumber: 2.4 Consensus size: 25
337753 AAAAAGTATA
* *
337763 AAAATAGTACATTA-AAAT-ATAAT
1 AAAATAATAAATTACAAATAATAAT
*
337786 AAAATAATAAATTATCAAATAATTAT
1 AAAATAATAAATTA-CAAATAATAAT
*
337812 AATATAATAAA
1 AAAATAATAAA
337823 AAACTTACCT
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
23 12 0.40
25 4 0.13
26 14 0.47
ACGTcount: A:0.63, C:0.03, G:0.02, T:0.32
Consensus pattern (25 bp):
AAAATAATAAATTACAAATAATAAT
Found at i:343867 original size:24 final size:24
Alignment explanation
Indices: 343821--343868 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
343811 TTAGTAATCC
* *
343821 GTTCGTTTATATTTATTTATTTAT
1 GTTCGTTTATATTCATTCATTTAT
* *
343845 GTTCGTTTATGTTCATTCGTTTAT
1 GTTCGTTTATATTCATTCATTTAT
343869 ACTAGTTTGT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.17, C:0.08, G:0.12, T:0.62
Consensus pattern (24 bp):
GTTCGTTTATATTCATTCATTTAT
Done.