Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001444.1 Hibiscus syriacus cultivar Beakdansim tig00002793_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: 2564052
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 12
Found at i:288447 original size:3 final size:3
Alignment explanation
Indices: 288439--288463 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
288429 AAAGGCAACA
288439 AAG AAG AAG AAG AAG AAG AAG AAG A
1 AAG AAG AAG AAG AAG AAG AAG AAG A
288464 CATGCTGATG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:290407 original size:54 final size:55
Alignment explanation
Indices: 290325--290429 Score: 203
Period size: 54 Copynumber: 1.9 Consensus size: 55
290315 TTTGTTTTGG
290325 AATAATTCATAAAATTCATCATAAGACC-TTTTAGTGAAAAAATAAAAAATAAAA
1 AATAATTCATAAAATTCATCATAAGACCTTTTTAGTGAAAAAATAAAAAATAAAA
290379 AATAATTCATAAAATTCATCATAAGACCTTTTTAGTGAAAAAATAAAAAAT
1 AATAATTCATAAAATTCATCATAAGACCTTTTTAGTGAAAAAATAAAAAAT
290430 TAAATTAGAT
Statistics
Matches: 50, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
54 28 0.56
55 22 0.44
ACGTcount: A:0.55, C:0.10, G:0.06, T:0.30
Consensus pattern (55 bp):
AATAATTCATAAAATTCATCATAAGACCTTTTTAGTGAAAAAATAAAAAATAAAA
Found at i:306929 original size:17 final size:17
Alignment explanation
Indices: 306907--306956 Score: 54
Period size: 17 Copynumber: 3.1 Consensus size: 17
306897 AAATTCTTCT
306907 AACATTCATAGAAACCA
1 AACATTCATAGAAACCA
*
306924 AACA-T--TA-ATACTCA
1 AACATTCATAGAAAC-CA
306938 AACATTCATAGAAACCA
1 AACATTCATAGAAACCA
306955 AA
1 AA
306957 ACATGAACAA
Statistics
Matches: 26, Mismatches: 2, Indels: 10
0.68 0.05 0.26
Matches are distributed among these distances:
13 3 0.12
14 8 0.31
15 1 0.04
16 1 0.04
17 10 0.38
18 3 0.12
ACGTcount: A:0.54, C:0.22, G:0.04, T:0.20
Consensus pattern (17 bp):
AACATTCATAGAAACCA
Found at i:307290 original size:2 final size:2
Alignment explanation
Indices: 307253--307279 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
307243 TATTTTTTTA
307253 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
307280 GATGGATATA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:311687 original size:25 final size:27
Alignment explanation
Indices: 311636--311690 Score: 87
Period size: 25 Copynumber: 2.1 Consensus size: 27
311626 TCTTAATTCA
311636 TTATGAGAAAAATAAATAATCTGTAAC
1 TTATGAGAAAAATAAATAATCTGTAAC
*
311663 TTATGAG-AAAA-AAATAATCTTTAAC
1 TTATGAGAAAAATAAATAATCTGTAAC
311688 TTA
1 TTA
311691 GAAAAACACT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
25 16 0.59
26 4 0.15
27 7 0.26
ACGTcount: A:0.51, C:0.07, G:0.09, T:0.33
Consensus pattern (27 bp):
TTATGAGAAAAATAAATAATCTGTAAC
Found at i:312738 original size:2 final size:2
Alignment explanation
Indices: 312725--312777 Score: 51
Period size: 2 Copynumber: 28.5 Consensus size: 2
312715 ATAATCCATA
*
312725 AT AT AA AT AT AT AT -T AT AT -T AT AT -T AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* *
312764 A- AT AA AA AT AT AT A
1 AT AT AT AT AT AT AT A
312778 AACTAACCGG
Statistics
Matches: 43, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
1 4 0.09
2 39 0.91
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:316027 original size:15 final size:14
Alignment explanation
Indices: 315986--316017 Score: 64
Period size: 14 Copynumber: 2.3 Consensus size: 14
315976 ACAGATTTCG
315986 GATTAAAATTATAT
1 GATTAAAATTATAT
316000 GATTAAAATTATAT
1 GATTAAAATTATAT
316014 GATT
1 GATT
316018 TAATTTTATA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.47, C:0.00, G:0.09, T:0.44
Consensus pattern (14 bp):
GATTAAAATTATAT
Found at i:324583 original size:15 final size:15
Alignment explanation
Indices: 324559--324592 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
324549 CTGTAGGACC
324559 ACTACATCCCGAAGG
1 ACTACATCCCGAAGG
*
324574 ACTACGTCCCGAAGG
1 ACTACATCCCGAAGG
324589 ACTA
1 ACTA
324593 TTATACCCTC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.32, C:0.32, G:0.21, T:0.15
Consensus pattern (15 bp):
ACTACATCCCGAAGG
Found at i:325188 original size:64 final size:64
Alignment explanation
Indices: 325119--325275 Score: 176
Period size: 64 Copynumber: 2.5 Consensus size: 64
325109 TAATGAAGGT
* * * **
325119 ATGCATCGATGCACTACTTGTGCATCGGTGCA-TAAAATGCATTTGAT-GTTTTATTATTAATGG
1 ATGCATCGATGCACTACTTATGCATCGATGCACT-AAATGCATTCGATCGTTTTATT-TTAAAAG
325182 A
64 A
* * *
325183 ATGCATCGATGCA-TGCCTTATGCATCGATGCACTAATTGCATTCGATCTTTTTATTTTAAAAGA
1 ATGCATCGATGCACT-ACTTATGCATCGATGCACTAAATGCATTCGATCGTTTTATTTTAAAAGA
* *
325247 GTGCATCGATGCACTACCTATGCATCGAT
1 ATGCATCGATGCACTACTTATGCATCGAT
325276 ACACCTTCAA
Statistics
Matches: 78, Mismatches: 11, Indels: 8
0.80 0.11 0.08
Matches are distributed among these distances:
63 1 0.01
64 68 0.87
65 9 0.12
ACGTcount: A:0.27, C:0.18, G:0.18, T:0.36
Consensus pattern (64 bp):
ATGCATCGATGCACTACTTATGCATCGATGCACTAAATGCATTCGATCGTTTTATTTTAAAAGA
Found at i:328164 original size:82 final size:81
Alignment explanation
Indices: 328025--328231 Score: 200
Period size: 82 Copynumber: 2.5 Consensus size: 81
328015 TCGACATTCT
* ** * * **
328025 TGAAAAACACCACTATTAACGAACCCTATTGCAGTATTTGTATAAAAAAGCCACTAAAGTA-TCA
1 TGAAAAAAACCACTATCCATGAA-CCTATTGCCGCGTTTGTATAAAAAAGCCACTAAAGTACT-A
* * *
328089 CTATGTCACGGCATTTGT
64 ATATGTCACAGCATTTGC
* ** * * *
328107 TGAAAAAAGCCACTATGGATGAACCTTATTGCCGCGTTTGTATAAAAACGTCGCTAAAGTACTAA
1 TGAAAAAAACCACTATCCATGAACC-TATTGCCGCGTTTGTATAAAAAAGCCACTAAAGTACTAA
* * *
328172 TCTGTCACATCGTTTGC
65 TATGTCACAGCATTTGC
*
328189 TGAAAAAAACCACTATCCATGAACCTATTGCGGCGTTTGTATA
1 TGAAAAAAACCACTATCCATGAACCTATTGCCGCGTTTGTATA
328232 GAAATGCTGC
Statistics
Matches: 102, Mismatches: 21, Indels: 5
0.80 0.16 0.04
Matches are distributed among these distances:
81 19 0.19
82 82 0.80
83 1 0.01
ACGTcount: A:0.35, C:0.21, G:0.16, T:0.29
Consensus pattern (81 bp):
TGAAAAAAACCACTATCCATGAACCTATTGCCGCGTTTGTATAAAAAAGCCACTAAAGTACTAAT
ATGTCACAGCATTTGC
Found at i:328252 original size:82 final size:82
Alignment explanation
Indices: 328102--328261 Score: 207
Period size: 82 Copynumber: 2.0 Consensus size: 82
328092 TGTCACGGCA
* * ** *
328102 TTTGTTGAAAAAAGCCACTATGGATGAACCTTATTGCCGCGTTTGTATAAAAACGTCGCTAAAGT
1 TTTGCTGAAAAAAACCACTATCCATGAACCTTATTGCCGCGTTTGTATAAAAACGTCGCTAAAAT
328167 ACTAATCTGTCACATCG
66 ACTAATCTGTCACATCG
* * *
328184 TTTGCTGAAAAAAACCACTATCCATGAACC-TATTGCGGCGTTTGTATAGAAATG-CTGCTTAAA
1 TTTGCTGAAAAAAACCACTATCCATGAACCTTATTGCCGCGTTTGTATAAAAACGTC-GC-TAAA
*
328247 ATACTACTCTGTCAC
64 ATACTAATCTGTCAC
328262 GGTAGTTCTA
Statistics
Matches: 67, Mismatches: 9, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
80 1 0.01
81 23 0.34
82 43 0.64
ACGTcount: A:0.32, C:0.21, G:0.17, T:0.31
Consensus pattern (82 bp):
TTTGCTGAAAAAAACCACTATCCATGAACCTTATTGCCGCGTTTGTATAAAAACGTCGCTAAAAT
ACTAATCTGTCACATCG
Found at i:332264 original size:10 final size:10
Alignment explanation
Indices: 332246--332314 Score: 57
Period size: 10 Copynumber: 6.2 Consensus size: 10
332236 TATATTTTCA
332246 TTTATGTTCG
1 TTTATGTTCG
*
332256 TTTACGTTCG
1 TTTATGTTCG
*
332266 TTTATGTTCATT
1 TTTATGTTC--G
332278 TATTATGTTCG
1 T-TTATGTTCG
332289 TTTACATTTGTTCG
1 TTT--A--TGTTCG
332303 TTTATGTTCG
1 TTTATGTTCG
332313 TT
1 TT
332315 CATTTGTGTC
Statistics
Matches: 48, Mismatches: 4, Indels: 14
0.73 0.06 0.21
Matches are distributed among these distances:
10 27 0.56
11 1 0.02
12 3 0.06
13 8 0.17
14 9 0.19
ACGTcount: A:0.13, C:0.12, G:0.16, T:0.59
Consensus pattern (10 bp):
TTTATGTTCG
Found at i:344044 original size:65 final size:64
Alignment explanation
Indices: 343914--344135 Score: 252
Period size: 64 Copynumber: 3.5 Consensus size: 64
343904 TTGAAGGTGT
** * * * * *
343914 ATCGATGCATTGGTAGTGCATCAATGCA-CTCTTTTAA-AATAAAAACATCGAATGCAATTCATG
1 ATCGATGCATAAGTAGTGCATCGATGCATCCCATTTAATAAT--AAACATCGAATACAATTGATG
343977 C
64 C
*
343978 ATCGATGCATAAGTAGTGCATCGATGCATCCCATTTAATAATGAAACATCGAATACAATTGGTGC
1 ATCGATGCATAAGTAGTGCATCGATGCATCCCATTTAATAAT-AAACATCGAATACAATTGATGC
* * ** *
344043 ATCGATGCATAAGGAGTGCATCGATGCATCCCA-TCAATAATAATACATCGAATACCTTTTATGC
1 ATCGATGCATAAGTAGTGCATCGATGCATCCCATTTAATAATAA-ACATCGAATACAATTGATGC
* *
344107 ACCGATGCATCAGTAGTGCATCGATGCAT
1 ATCGATGCATAAGTAGTGCATCGATGCAT
344136 ACCTTCATTA
Statistics
Matches: 137, Mismatches: 18, Indels: 6
0.85 0.11 0.04
Matches are distributed among these distances:
63 2 0.01
64 74 0.54
65 58 0.42
66 3 0.02
ACGTcount: A:0.34, C:0.20, G:0.18, T:0.28
Consensus pattern (64 bp):
ATCGATGCATAAGTAGTGCATCGATGCATCCCATTTAATAATAAACATCGAATACAATTGATGC
Found at i:344115 original size:64 final size:65
Alignment explanation
Indices: 343956--344135 Score: 247
Period size: 65 Copynumber: 2.8 Consensus size: 65
343946 TTTAAAATAA
* * *
343956 AAACATCGAATGCAATTCATGCATCGATGCATAAGTAGTGCATCGATGCATCCCATTTAATAATG
1 AAACATCGAATACAATTGATGCATCGATGCATAAGTAGTGCATCGATGCATCCCATTCAATAATG
* *
344021 AAACATCGAATACAATTGGTGCATCGATGCATAAGGAGTGCATCGATGCATCCCA-TCAATAAT-
1 AAACATCGAATACAATTGATGCATCGATGCATAAGTAGTGCATCGATGCATCCCATTCAATAATG
** * * *
344084 AATACATCGAATACCTTTTATGCACCGATGCATCAGTAGTGCATCGATGCAT
1 AA-ACATCGAATACAATTGATGCATCGATGCATAAGTAGTGCATCGATGCAT
344136 ACCTTCATTA
Statistics
Matches: 102, Mismatches: 12, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
63 2 0.02
64 49 0.48
65 51 0.50
ACGTcount: A:0.34, C:0.21, G:0.18, T:0.27
Consensus pattern (65 bp):
AAACATCGAATACAATTGATGCATCGATGCATAAGTAGTGCATCGATGCATCCCATTCAATAATG
Found at i:344461 original size:12 final size:12
Alignment explanation
Indices: 344443--344478 Score: 63
Period size: 12 Copynumber: 3.0 Consensus size: 12
344433 TATATATGTT
344443 CATGTGATATGA
1 CATGTGATATGA
*
344455 TATGTGATATGA
1 CATGTGATATGA
344467 CATGTGATATGA
1 CATGTGATATGA
344479 GAACATGATA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.33, C:0.06, G:0.25, T:0.36
Consensus pattern (12 bp):
CATGTGATATGA
Found at i:344500 original size:23 final size:26
Alignment explanation
Indices: 344443--344511 Score: 85
Period size: 24 Copynumber: 2.8 Consensus size: 26
344433 TATATATGTT
**
344443 CATGTGATAT--GATATGTGATATGA
1 CATGTGATATGAGATACATGATATGA
344467 CATGTGATATGAGA-ACATGATATGA
1 CATGTGATATGAGATACATGATATGA
344492 -A-GTGATATGAGATACATGAT
1 CATGTGATATGAGATACATGAT
344512 CACAAGAGAA
Statistics
Matches: 40, Mismatches: 2, Indels: 6
0.83 0.04 0.12
Matches are distributed among these distances:
23 11 0.28
24 18 0.45
25 9 0.22
26 2 0.05
ACGTcount: A:0.38, C:0.06, G:0.25, T:0.32
Consensus pattern (26 bp):
CATGTGATATGAGATACATGATATGA
Found at i:344643 original size:15 final size:15
Alignment explanation
Indices: 344623--344655 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
344613 TAGGGTATAA
344623 TAGTCCTTCGGGATG
1 TAGTCCTTCGGGATG
344638 TAGTCCTTCGGGATG
1 TAGTCCTTCGGGATG
344653 TAG
1 TAG
344656 GGGTCCTATG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.15, C:0.18, G:0.33, T:0.33
Consensus pattern (15 bp):
TAGTCCTTCGGGATG
Found at i:383263 original size:27 final size:27
Alignment explanation
Indices: 383200--383275 Score: 75
Period size: 27 Copynumber: 2.9 Consensus size: 27
383190 AATAAATTTT
*
383200 AAAAT-AAAAT-ATATATTTTTAAATG
1 AAAATAAAAATAAAATATTTTTAAATG
* *
383225 AAAATAAAAATAAGATATTTTTAAATT
1 AAAATAAAAATAAAATATTTTTAAATG
** * *
383252 AAGTTAATAATAAAATATATTTAA
1 AAAATAAAAATAAAATATTTTTAA
383276 TAACTTACTA
Statistics
Matches: 42, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
25 5 0.12
26 5 0.12
27 32 0.76
ACGTcount: A:0.58, C:0.00, G:0.04, T:0.38
Consensus pattern (27 bp):
AAAATAAAAATAAAATATTTTTAAATG
Found at i:384629 original size:516 final size:516
Alignment explanation
Indices: 383657--384689 Score: 2048
Period size: 516 Copynumber: 2.0 Consensus size: 516
383647 TCAGTCGTAA
* *
383657 ATTCAAAGTTTAAATTAGGATTTGTCTTTGTTTTTAGGATTTAATTCAAACAAATTCTAAGAATT
1 ATTCAAAGTTTAAATTAGGATTTATCTTTGTTTTTAGGATTTAATTCAAACAAATTCCAAGAATT
383722 ATATGTTATCATTTCTACTACATTTTTAAGATTTTAGGAGAGTATAAATACCCCATCAAGGCAAG
66 ATATGTTATCATTTCTACTACATTTTTAAGATTTTAGGAGAGTATAAATACCCCATCAAGGCAAG
383787 CTCAAAAGCATCATCTCTCATATCTTGAATTCTTTTGTTTCTTCTTTTAGTTTTATAAAATTTAT
131 CTCAAAAGCATCATCTCTCATATCTTGAATTCTTTTGTTTCTTCTTTTAGTTTTATAAAATTTAT
383852 TTTCTTTTTTACTTTCTCTTTTCTTTACTTTTCCTTAAAAGTTTTCTTTACTTTTGAATGCTAAG
196 TTTCTTTTTTACTTTCTCTTTTCTTTACTTTTCCTTAAAAGTTTTCTTTACTTTTGAATGCTAAG
383917 TATGGCTTCTATTATGCTTAGCTAAGATTTTCATAAGCCAAAGGCTGAAGCGATGACTCAATTCT
261 TATGGCTTCTATTATGCTTAGCTAAGATTTTCATAAGCCAAAGGCTGAAGCGATGACTCAATTCT
383982 GATCGTGAGAATAGAAAAACACCTCATACCCTTCTAATTACATTTTCAGTTTTCTGGAATCAAGG
326 GATCGTGAGAATAGAAAAACACCTCATACCCTTCTAATTACATTTTCAGTTTTCTGGAATCAAGG
384047 ATTGACAATCAACCATCCTTTTATAATTGAAAACATTTTCTTTTCAAAAAATACACGTTGTATTG
391 ATTGACAATCAACCATCCTTTTATAATTGAAAACATTTTCTTTTCAAAAAATACACGTTGTATTG
384112 ATTGCAATTTCGATTAATAGTTGGGAGATAAGATCGACTTGTAGCATATTCGATTTCCGGT
456 ATTGCAATTTCGATTAATAGTTGGGAGATAAGATCGACTTGTAGCATATTCGATTTCCGGT
384173 ATTCAAAGTTTAAATTAGGATTTATCTTTGTTTTTAGGATTTAATTCAAACAAATTCCAAGAATT
1 ATTCAAAGTTTAAATTAGGATTTATCTTTGTTTTTAGGATTTAATTCAAACAAATTCCAAGAATT
384238 ATATGTTATCATTTCTACTACATTTTTAAGATTTTAGGAGAGTATAAATACCCCATCAAGGCAAG
66 ATATGTTATCATTTCTACTACATTTTTAAGATTTTAGGAGAGTATAAATACCCCATCAAGGCAAG
384303 CTCAAAAGCATCATCTCTCATATCTTGAATTCTTTTGTTTCTTCTTTTAGTTTTATAAAATTTAT
131 CTCAAAAGCATCATCTCTCATATCTTGAATTCTTTTGTTTCTTCTTTTAGTTTTATAAAATTTAT
384368 TTTCTTTTTTACTTTCTCTTTTCTTTACTTTTCCTTAAAAGTTTTCTTTACTTTTGAATGCTAAG
196 TTTCTTTTTTACTTTCTCTTTTCTTTACTTTTCCTTAAAAGTTTTCTTTACTTTTGAATGCTAAG
384433 TATGGCTTCTATTATGCTTAGCTAAGATTTTCATAAGCCAAAGGCTGAAGCGATGACTCAATTCT
261 TATGGCTTCTATTATGCTTAGCTAAGATTTTCATAAGCCAAAGGCTGAAGCGATGACTCAATTCT
384498 GATCGTGAGAATAGAAAAACACCTCATACCCTTCTAATTACATTTTCAGTTTTCTGGAATCAAGG
326 GATCGTGAGAATAGAAAAACACCTCATACCCTTCTAATTACATTTTCAGTTTTCTGGAATCAAGG
384563 ATTGACAATCAACCATCCTTTTATAATTGAAAACATTTTCTTTTCAAAAAATACACGTTGTATTG
391 ATTGACAATCAACCATCCTTTTATAATTGAAAACATTTTCTTTTCAAAAAATACACGTTGTATTG
384628 ATTGCAATTTCGATTAATAGTTGGGAGATAAGATCGACTTGTAGCATATTCGATTTCCGGT
456 ATTGCAATTTCGATTAATAGTTGGGAGATAAGATCGACTTGTAGCATATTCGATTTCCGGT
384689 A
1 A
384690 AACACACTTA
Statistics
Matches: 515, Mismatches: 2, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
516 515 1.00
ACGTcount: A:0.30, C:0.16, G:0.13, T:0.41
Consensus pattern (516 bp):
ATTCAAAGTTTAAATTAGGATTTATCTTTGTTTTTAGGATTTAATTCAAACAAATTCCAAGAATT
ATATGTTATCATTTCTACTACATTTTTAAGATTTTAGGAGAGTATAAATACCCCATCAAGGCAAG
CTCAAAAGCATCATCTCTCATATCTTGAATTCTTTTGTTTCTTCTTTTAGTTTTATAAAATTTAT
TTTCTTTTTTACTTTCTCTTTTCTTTACTTTTCCTTAAAAGTTTTCTTTACTTTTGAATGCTAAG
TATGGCTTCTATTATGCTTAGCTAAGATTTTCATAAGCCAAAGGCTGAAGCGATGACTCAATTCT
GATCGTGAGAATAGAAAAACACCTCATACCCTTCTAATTACATTTTCAGTTTTCTGGAATCAAGG
ATTGACAATCAACCATCCTTTTATAATTGAAAACATTTTCTTTTCAAAAAATACACGTTGTATTG
ATTGCAATTTCGATTAATAGTTGGGAGATAAGATCGACTTGTAGCATATTCGATTTCCGGT
Found at i:385374 original size:19 final size:19
Alignment explanation
Indices: 385350--385395 Score: 83
Period size: 19 Copynumber: 2.4 Consensus size: 19
385340 AGAAGAATTT
385350 GATCTAGAAATCAAAGCAC
1 GATCTAGAAATCAAAGCAC
385369 GATCTAGAAATCAAAGCAC
1 GATCTAGAAATCAAAGCAC
*
385388 GAGCTAGA
1 GATCTAGA
385396 CGAATCCACA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.46, C:0.20, G:0.20, T:0.15
Consensus pattern (19 bp):
GATCTAGAAATCAAAGCAC
Found at i:390692 original size:16 final size:17
Alignment explanation
Indices: 390671--390703 Score: 59
Period size: 16 Copynumber: 2.0 Consensus size: 17
390661 CCCATTTTTA
390671 ATTTTTAA-TTTTATTC
1 ATTTTTAATTTTTATTC
390687 ATTTTTAATTTTTATTC
1 ATTTTTAATTTTTATTC
390704 GTAATTTTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.50
17 8 0.50
ACGTcount: A:0.24, C:0.06, G:0.00, T:0.70
Consensus pattern (17 bp):
ATTTTTAATTTTTATTC
Found at i:396297 original size:22 final size:22
Alignment explanation
Indices: 396269--396321 Score: 72
Period size: 22 Copynumber: 2.4 Consensus size: 22
396259 TTCCATTTCG
396269 CGTTGCGATAGT-TGAAAGTTGT
1 CGTTGCGATAGTCT-AAAGTTGT
* *
396291 TGTTGCGATAGTCTACAGTTGT
1 CGTTGCGATAGTCTAAAGTTGT
396313 CGTTGCGAT
1 CGTTGCGAT
396322 TTTCCAAATT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
22 26 0.96
23 1 0.04
ACGTcount: A:0.19, C:0.13, G:0.30, T:0.38
Consensus pattern (22 bp):
CGTTGCGATAGTCTAAAGTTGT
Found at i:396488 original size:20 final size:20
Alignment explanation
Indices: 396463--396559 Score: 122
Period size: 20 Copynumber: 4.8 Consensus size: 20
396453 CGACCCGACT
396463 ATCGCAACGCGAAATGGAAA
1 ATCGCAACGCGAAATGGAAA
** ** *
396483 ATCGCAACGCGATTTTCAACT
1 ATCGCAACGCGAAATGGAA-A
*
396504 ATCGCAACGCGAACTGGAAA
1 ATCGCAACGCGAAATGGAAA
*
396524 ATCGCAACGCGAAATGAAAA
1 ATCGCAACGCGAAATGGAAA
396544 ATCGCAACGCGAAATG
1 ATCGCAACGCGAAATG
396560 CAACGCGAAT
Statistics
Matches: 64, Mismatches: 12, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
20 49 0.77
21 15 0.23
ACGTcount: A:0.40, C:0.24, G:0.22, T:0.14
Consensus pattern (20 bp):
ATCGCAACGCGAAATGGAAA
Found at i:397375 original size:21 final size:21
Alignment explanation
Indices: 397347--397395 Score: 91
Period size: 21 Copynumber: 2.4 Consensus size: 21
397337 AACCCCTGGT
397347 TTTC-AAAACTATTCATTCAG
1 TTTCGAAAACTATTCATTCAG
397367 TTTCGAAAACTATTCATTCAG
1 TTTCGAAAACTATTCATTCAG
397388 TTTCGAAA
1 TTTCGAAA
397396 TCTCCTTTTA
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
20 4 0.14
21 24 0.86
ACGTcount: A:0.35, C:0.18, G:0.08, T:0.39
Consensus pattern (21 bp):
TTTCGAAAACTATTCATTCAG
Found at i:397871 original size:23 final size:24
Alignment explanation
Indices: 397835--397881 Score: 87
Period size: 23 Copynumber: 2.0 Consensus size: 24
397825 GAAATTTCAG
397835 TGAGTAAAATTAGAAAAATTATAA
1 TGAGTAAAATTAGAAAAATTATAA
397859 TGAGT-AAATTAGAAAAATTATAA
1 TGAGTAAAATTAGAAAAATTATAA
397882 GTACACTGAG
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
23 18 0.78
24 5 0.22
ACGTcount: A:0.57, C:0.00, G:0.13, T:0.30
Consensus pattern (24 bp):
TGAGTAAAATTAGAAAAATTATAA
Found at i:400873 original size:14 final size:14
Alignment explanation
Indices: 400854--400880 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
400844 TTTTAAAATT
400854 CAAAATATTTTTTA
1 CAAAATATTTTTTA
400868 CAAAATATTTTTT
1 CAAAATATTTTTT
400881 TTAATTTTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.41, C:0.07, G:0.00, T:0.52
Consensus pattern (14 bp):
CAAAATATTTTTTA
Found at i:403214 original size:2 final size:2
Alignment explanation
Indices: 403209--403243 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
403199 CGTGTGTGTG
403209 TA TA 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 TA TA T
403244 TATGTGCTTA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:406114 original size:20 final size:20
Alignment explanation
Indices: 406091--406136 Score: 83
Period size: 20 Copynumber: 2.3 Consensus size: 20
406081 GGACGAACCT
406091 GAGCAATTGAGGCATACCGG
1 GAGCAATTGAGGCATACCGG
*
406111 GAGCAATTGAGGCATGCCGG
1 GAGCAATTGAGGCATACCGG
406131 GAGCAA
1 GAGCAA
406137 GAAGCAGAAA
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:0.30, C:0.20, G:0.37, T:0.13
Consensus pattern (20 bp):
GAGCAATTGAGGCATACCGG
Found at i:406541 original size:15 final size:16
Alignment explanation
Indices: 406510--406549 Score: 55
Period size: 16 Copynumber: 2.5 Consensus size: 16
406500 AAAGAAAAGC
*
406510 AAAGAACAAGAATC-AA
1 AAAGAA-AAGAAGCAAA
406526 AAAGAAAAGAAGCAAA
1 AAAGAAAAGAAGCAAA
406542 AAAGAAAA
1 AAAGAAAA
406550 AACAAAGAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 6 0.27
16 16 0.73
ACGTcount: A:0.75, C:0.07, G:0.15, T:0.03
Consensus pattern (16 bp):
AAAGAAAAGAAGCAAA
Found at i:407630 original size:32 final size:32
Alignment explanation
Indices: 407594--407667 Score: 85
Period size: 32 Copynumber: 2.3 Consensus size: 32
407584 GCATCTTTAA
* *
407594 AGATTCAACAATAAATGTTGGGGTATATTTGG
1 AGATTCAACAATAAATATTGGGGCATATTTGG
* * * *
407626 AGATTCAATATTGAATATTGTGGCATATTTGG
1 AGATTCAACAATAAATATTGGGGCATATTTGG
*
407658 GGATTCAACA
1 AGATTCAACA
407668 TCCTGATGCA
Statistics
Matches: 34, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
32 34 1.00
ACGTcount: A:0.34, C:0.08, G:0.23, T:0.35
Consensus pattern (32 bp):
AGATTCAACAATAAATATTGGGGCATATTTGG
Found at i:408273 original size:43 final size:43
Alignment explanation
Indices: 408220--408365 Score: 202
Period size: 43 Copynumber: 3.4 Consensus size: 43
408210 ATGAAGGGGT
*
408220 CATCCGCGATTTCAACTCCACGACGGAGGATATCGTACCCACA
1 CATCCACGATTTCAACTCCACGACGGAGGATATCGTACCCACA
* *
408263 CATCCACGATTTTAACTCCACGACGGAGGATATCGTACCAACA
1 CATCCACGATTTCAACTCCACGACGGAGGATATCGTACCCACA
* * * * *
408306 GATCCACGATTTCAACTCCACAATGGAGGATATCGTGCCCATA
1 CATCCACGATTTCAACTCCACGACGGAGGATATCGTACCCACA
* *
408349 CATTCACGGTTTCAACT
1 CATCCACGATTTCAACT
408366 TCACAACGAA
Statistics
Matches: 90, Mismatches: 13, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
43 90 1.00
ACGTcount: A:0.29, C:0.31, G:0.17, T:0.23
Consensus pattern (43 bp):
CATCCACGATTTCAACTCCACGACGGAGGATATCGTACCCACA
Found at i:408384 original size:86 final size:86
Alignment explanation
Indices: 408221--408385 Score: 215
Period size: 86 Copynumber: 1.9 Consensus size: 86
408211 TGAAGGGGTC
* * * *
408221 ATCCGCGATTTCAACTCCACGACGGAGGATATCGTACCCACACATCCACGATTTTAACTCCACGA
1 ATCCACGATTTCAACTCCACAACGGAGGATATCGTACCCACACATCCACGATTTCAACTCCACAA
*
408286 CGGAGGATATCGTACCAACAG
66 CGAAGGATATCGTACCAACAG
* * * * * *
408307 ATCCACGATTTCAACTCCACAATGGAGGATATCGTGCCCATACATTCACGGTTTCAACTTCACAA
1 ATCCACGATTTCAACTCCACAACGGAGGATATCGTACCCACACATCCACGATTTCAACTCCACAA
408372 CGAAGGGA-ATCGTA
66 CGAA-GGATATCGTA
408386 TACACGAGCA
Statistics
Matches: 67, Mismatches: 11, Indels: 2
0.84 0.14 0.03
Matches are distributed among these distances:
86 64 0.96
87 3 0.04
ACGTcount: A:0.31, C:0.29, G:0.18, T:0.22
Consensus pattern (86 bp):
ATCCACGATTTCAACTCCACAACGGAGGATATCGTACCCACACATCCACGATTTCAACTCCACAA
CGAAGGATATCGTACCAACAG
Found at i:408997 original size:121 final size:121
Alignment explanation
Indices: 408828--409048 Score: 352
Period size: 121 Copynumber: 1.8 Consensus size: 121
408818 TACAACTTAA
* * * * *
408828 CTTGGATTTCAACTTCTCGATGAAGGATATCCAATTCAAGGTTTAACTTCACGACGAAGGGGTCA
1 CTTGGATTTCAACTTCACGACGAAGGATATCCAATTCAAGGCTCAACTTCACAACGAAGGGGTCA
*
408893 TCCACGATTTCAACTTCACGATGAAGGATATCGTGTCCACCAGCATCAATGCAACC
66 TCCACGATTTCAACTTCACGACGAAGGATATCGTGTCCACCAGCATCAATGCAACC
* * *
408949 CTTGGATTTCAACTTCACGACGAAGGATATCCAATTCGAGGCTCAACTTCACAATGAATGGGTCA
1 CTTGGATTTCAACTTCACGACGAAGGATATCCAATTCAAGGCTCAACTTCACAACGAAGGGGTCA
*
409014 TTCACGATTTCAACTTCACGACGAAGGATATCGTG
66 TCCACGATTTCAACTTCACGACGAAGGATATCGTG
409049 CTCATTTGCA
Statistics
Matches: 90, Mismatches: 10, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
121 90 1.00
ACGTcount: A:0.30, C:0.24, G:0.19, T:0.27
Consensus pattern (121 bp):
CTTGGATTTCAACTTCACGACGAAGGATATCCAATTCAAGGCTCAACTTCACAACGAAGGGGTCA
TCCACGATTTCAACTTCACGACGAAGGATATCGTGTCCACCAGCATCAATGCAACC
Found at i:409191 original size:84 final size:84
Alignment explanation
Indices: 409050--409506 Score: 434
Period size: 84 Copynumber: 5.4 Consensus size: 84
409040 GATATCGTGC
* * * *
409050 TCATTTGCACCTTAGCTCAAGGCAAGAAGGGTTATCTG-CTAACAAAAGACCTTCGAGTTCGATT
1 TCATTTGCAGCATAACTCAAGGCGAGAAGGGTTATCTGTC-AACAAAAGACCTTCGAGTTCGATT
409114 ATACTCAGCTCAAAGGCACA
65 ATACTCAGCTCAAAGGCACA
* * * * * * * * * *
409134 TCATTTGTAGTATAGCTTAAGTCGAGAAGGGCTATCTGCCAACCAAAGACCTTCGAGTTTGACTA
1 TCATTTGCAGCATAACTCAAGGCGAGAAGGGTTATCTGTCAACAAAAGACCTTCGAGTTCGATTA
** * *
409199 CGCTCAGCTCCAAGGCACG
66 TACTCAGCTCAAAGGCACA
* * *
409218 TCATTTGCAGCATAACTCAAGGCTAGAAGGGTTATCTGTCAATAAAAGACCTTCGAGTTCAATTA
1 TCATTTGCAGCATAACTCAAGGCGAGAAGGGTTATCTGTCAACAAAAGACCTTCGAGTTCGATTA
* * * *
409283 TATTCAACTCAAAGGAATA
66 TACTCAGCTCAAAGGCACA
* * * ** * * * * *
409302 TCATTTGCAGTATAGCTTAAGTTGATAAGAGTTATCTGTCATC-AAATACCTTCAAGATTCGATT
1 TCATTTGCAGCATAACTCAAGGCGAGAAGGGTTATCTGTCAACAAAAGACCTTCGAG-TTCGATT
* * * *
409366 -TCATTCAGTTCCAAGGCACG
65 AT-ACTCAGCTCAAAGGCACA
* *
409386 TCATTTGCAGCATAACTCAAGGCTAGAAGGGTTATCTGTCAACAAAAGACCTTTTGAGTTCGATT
1 TCATTTGCAGCATAACTCAAGGCGAGAAGGGTTATCTGTCAACAAAAGACC-TTCGAGTTCGATT
* * *
409451 ACACTCAGCTTAAAGACACA
65 ATACTCAGCTCAAAGGCACA
* * *
409471 TCTTTTGCAGCATAACTCAAGGCTAGAAGGATTATC
1 TCATTTGCAGCATAACTCAAGGCGAGAAGGGTTATC
409507 CACCAACATC
Statistics
Matches: 291, Mismatches: 76, Indels: 11
0.77 0.20 0.03
Matches are distributed among these distances:
83 12 0.04
84 215 0.74
85 60 0.21
86 4 0.01
ACGTcount: A:0.32, C:0.21, G:0.19, T:0.28
Consensus pattern (84 bp):
TCATTTGCAGCATAACTCAAGGCGAGAAGGGTTATCTGTCAACAAAAGACCTTCGAGTTCGATTA
TACTCAGCTCAAAGGCACA
Found at i:409381 original size:168 final size:168
Alignment explanation
Indices: 409050--409480 Score: 526
Period size: 168 Copynumber: 2.6 Consensus size: 168
409040 GATATCGTGC
* * * * *
409050 TCATTTGCACCTTAGCTCAAGGCAAGAAGGGTTATCTG-CTAACAAAAGACCTTCGAGTTCGATT
1 TCATTTGCAGCATAACTCAAGGCTAGAAGGGTTATCTGTC-AACAAAAGACCTTCGAGTTCAATT
* * * *
409114 ATACTCAGCTCAAAGGCACATCATTTGTAGTATAGCTTAAGTCGAGAAGGGCTATCTGCCAACCA
65 ATACTCAACTCAAAGGAACATCATTTGCAGTATAGCTTAAGTCGAGAAGAGCTATCTGCCAACCA
* * *
409179 AAGACCTTCGAGTTTGACTACGCTCAGCTCCAAGGCACG
130 AAGACCTTCAAGTTCGACTACACTCAGCTCCAAGGCACG
*
409218 TCATTTGCAGCATAACTCAAGGCTAGAAGGGTTATCTGTCAATAAAAGACCTTCGAGTTCAATTA
1 TCATTTGCAGCATAACTCAAGGCTAGAAGGGTTATCTGTCAACAAAAGACCTTCGAGTTCAATTA
* * * * * * *
409283 TATTCAACTCAAAGGAATATCATTTGCAGTATAGCTTAAGTTGATAAGAGTTATCTGTC-ATCAA
66 TACTCAACTCAAAGGAACATCATTTGCAGTATAGCTTAAGTCGAGAAGAGCTATCTGCCAACCAA
* * * * *
409347 ATACCTTCAAGATTCGATTTCATTCAGTTCCAAGGCACG
131 AGACCTTCAAG-TTCGACTACACTCAGCTCCAAGGCACG
* *
409386 TCATTTGCAGCATAACTCAAGGCTAGAAGGGTTATCTGTCAACAAAAGACCTTTTGAGTTCGATT
1 TCATTTGCAGCATAACTCAAGGCTAGAAGGGTTATCTGTCAACAAAAGACC-TTCGAGTTCAATT
* * * *
409451 ACACTCAGCTTAAA-GACACATCTTTTGCAG
65 ATACTCAACTCAAAGGA-ACATCATTTGCAG
409481 CATAACTCAA
Statistics
Matches: 225, Mismatches: 34, Indels: 7
0.85 0.13 0.03
Matches are distributed among these distances:
167 13 0.06
168 179 0.80
169 33 0.15
ACGTcount: A:0.32, C:0.21, G:0.19, T:0.29
Consensus pattern (168 bp):
TCATTTGCAGCATAACTCAAGGCTAGAAGGGTTATCTGTCAACAAAAGACCTTCGAGTTCAATTA
TACTCAACTCAAAGGAACATCATTTGCAGTATAGCTTAAGTCGAGAAGAGCTATCTGCCAACCAA
AGACCTTCAAGTTCGACTACACTCAGCTCCAAGGCACG
Found at i:414125 original size:31 final size:32
Alignment explanation
Indices: 414071--414136 Score: 125
Period size: 31 Copynumber: 2.1 Consensus size: 32
414061 ACATTTTTGT
414071 ATACCTTTTTGGGGATTTTTTTACCAAATTTA
1 ATACCTTTTTGGGGATTTTTTTACCAAATTTA
414103 ATACCTTTTTGGGGA-TTTTTTACCAAATTTA
1 ATACCTTTTTGGGGATTTTTTTACCAAATTTA
414134 ATA
1 ATA
414137 AACTGGGTCA
Statistics
Matches: 34, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
31 19 0.56
32 15 0.44
ACGTcount: A:0.27, C:0.12, G:0.12, T:0.48
Consensus pattern (32 bp):
ATACCTTTTTGGGGATTTTTTTACCAAATTTA
Found at i:430637 original size:21 final size:21
Alignment explanation
Indices: 430611--430659 Score: 71
Period size: 21 Copynumber: 2.3 Consensus size: 21
430601 GATTCTGCGG
* *
430611 TTGAGAAGGCATGAGAAGCAA
1 TTGAGAAGACACGAGAAGCAA
*
430632 TTGAGAAGACACGGGAAGCAA
1 TTGAGAAGACACGAGAAGCAA
430653 TTGAGAA
1 TTGAGAA
430660 TGAAAATGAT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.43, C:0.10, G:0.33, T:0.14
Consensus pattern (21 bp):
TTGAGAAGACACGAGAAGCAA
Found at i:430807 original size:16 final size:17
Alignment explanation
Indices: 430786--430820 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
430776 GGAAACAAGT
430786 AAAGAAAGTATGG-GTG
1 AAAGAAAGTATGGAGTG
*
430802 AAAGAAAGTCTGGAGTG
1 AAAGAAAGTATGGAGTG
430819 AA
1 AA
430821 GTAATAGTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 12 0.71
17 5 0.29
ACGTcount: A:0.46, C:0.03, G:0.34, T:0.17
Consensus pattern (17 bp):
AAAGAAAGTATGGAGTG
Found at i:435733 original size:21 final size:21
Alignment explanation
Indices: 435707--435755 Score: 89
Period size: 21 Copynumber: 2.3 Consensus size: 21
435697 GATTCTGCGG
*
435707 TTGAGAAGGCATGGGAAGCAA
1 TTGAGAAGACATGGGAAGCAA
435728 TTGAGAAGACATGGGAAGCAA
1 TTGAGAAGACATGGGAAGCAA
435749 TTGAGAA
1 TTGAGAA
435756 TGAAAATGAT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.41, C:0.08, G:0.35, T:0.16
Consensus pattern (21 bp):
TTGAGAAGACATGGGAAGCAA
Found at i:435902 original size:16 final size:17
Alignment explanation
Indices: 435881--435915 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
435871 GGAAACAAGT
435881 AAAGAAAGTATGG-GTG
1 AAAGAAAGTATGGAGTG
*
435897 AAAGAAAGTCTGGAGTG
1 AAAGAAAGTATGGAGTG
435914 AA
1 AA
435916 GTAATAGTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 12 0.71
17 5 0.29
ACGTcount: A:0.46, C:0.03, G:0.34, T:0.17
Consensus pattern (17 bp):
AAAGAAAGTATGGAGTG
Found at i:440762 original size:22 final size:22
Alignment explanation
Indices: 440737--440778 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
440727 AAGAGTTATT
* *
440737 TGATTTAATTCCAGGGGTTACA
1 TGATATAATTCCAGGAGTTACA
*
440759 TGATATAATTTCAGGAGTTA
1 TGATATAATTCCAGGAGTTA
440779 TAACAGCTGA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.31, C:0.10, G:0.21, T:0.38
Consensus pattern (22 bp):
TGATATAATTCCAGGAGTTACA
Found at i:444827 original size:169 final size:171
Alignment explanation
Indices: 444548--444891 Score: 647
Period size: 169 Copynumber: 2.0 Consensus size: 171
444538 TTCGAACTCC
444548 TTATGACCCTAGCGTACATCTAGTTAGGAATAAAGGAAGTAGCGTTTCCCAAAGTGAATATGCTA
1 TTATGACCCTAGCGTACATCTAGTTAGGAATAAAGGAAGTAGCGTTTCCCAAAGTGAATATGCTA
444613 AATTAATCGGAAGCTTAATGTTCTTAATGAACTATACTCAGCCTGATATTGCTTATGATGTGAGT
66 AATTAATCGGAAGCTTAATGTTCTTAATGAACTATACTCAGCCTGATATTGCTTATGATGTGAGT
444678 AGA-AGGAGATATACTCATAAT-TGAGTGGTGAGCACTGGA
131 AGACAGGAGATATACTCATAATCTGAGTGGTGAGCACTGGA
444717 TTATGACCCTAGCGTACATCTAGTTAGGAATAAAGGAAGTAGCGTTTCCCAAAGTGAATATGCTA
1 TTATGACCCTAGCGTACATCTAGTTAGGAATAAAGGAAGTAGCGTTTCCCAAAGTGAATATGCTA
444782 AATTAATCGGAAGCTTAATGTTCTTAATGAACTATACTCAGCCTGATATTGCTTATGATGTGAGT
66 AATTAATCGGAAGCTTAATGTTCTTAATGAACTATACTCAGCCTGATATTGCTTATGATGTGAGT
*
444847 AGACTGAGTAGATATACTCATAATCTGAGTGGTGAGCACTGGA
131 AGAC--AGGAGATATACTCATAATCTGAGTGGTGAGCACTGGA
444890 TT
1 TT
444892 GCTCTTAAAC
Statistics
Matches: 170, Mismatches: 1, Indels: 4
0.97 0.01 0.02
Matches are distributed among these distances:
169 133 0.78
172 17 0.10
173 20 0.12
ACGTcount: A:0.33, C:0.15, G:0.22, T:0.31
Consensus pattern (171 bp):
TTATGACCCTAGCGTACATCTAGTTAGGAATAAAGGAAGTAGCGTTTCCCAAAGTGAATATGCTA
AATTAATCGGAAGCTTAATGTTCTTAATGAACTATACTCAGCCTGATATTGCTTATGATGTGAGT
AGACAGGAGATATACTCATAATCTGAGTGGTGAGCACTGGA
Found at i:446793 original size:337 final size:337
Alignment explanation
Indices: 446178--446810 Score: 1160
Period size: 337 Copynumber: 1.9 Consensus size: 337
446168 GAAAGTTCCA
*
446178 GACTAGTTTCACTTATCTAAGAGAATGATTGCTCATCATCACTATGTACTAGTTTCAGATACGTT
1 GACTAGTTTCACTTATCTAAGAGAATGATTGCTCATCATCACTATGTACTAGTTCCAGATACGTT
*
446243 TACTAGTGCTTAAGCAACTAATCTCGCTATTGCTCTTCTGGAAAGTTTGTTTTCGAGTTTCAAAA
66 CACTAGTGCTTAAGCAACTAATCTCGCTATTGCTCTTCTGGAAAGTTTGTTTTCGAGTTTCAAAA
446308 GATTTCTTTCGCATTAGTGGGGGAATGTTGATAATGCTCAATCCCACATAGTATTGGAAACACTA
131 GATTTCTTTCGCATTAGTGGGGGAATGTTGATAATGCTCAATCCCACATAGTATTGGAAACACTA
*
446373 TTGGGAATGGTATTTAAGGCTTGGCTTTCCCACTTCCTTGTTGAGTGATAGAGAACAAGGGGGAC
196 TTGGGAATGGTATTTAAGGCTTGGCTTTCCCACTTCCTTGTTGAGTGATAGAGAACAAGGAGGAC
446438 TCTCGCGCACCGCCGCCGCCGTCCGTCTCGTCTCGTTTTGGCTTGGCTCGGCACGGCACGGCACG
261 TCTCGCGCACCGCCGCCGCCGTCCGTCTCGTCTCGTTTTGGCTTGGCTCGGCACGGCACGGCACG
446503 GCTCGTGGTCGT
326 GCTCGTGGTCGT
446515 GACTAGTTTCACTTATCTAAGAGAATGATTGCTCATCATCACTATGTACTTA-TTCCAGATACGT
1 GACTAGTTTCACTTATCTAAGAGAATGATTGCTCATCATCACTATGTAC-TAGTTCCAGATACGT
**
446579 TCACTAGTGCTTAAGCAACTAATCTCGCTATTGCTCTTCTGGAAAGTTTGTTTTCGAGTTTCTGA
65 TCACTAGTGCTTAAGCAACTAATCTCGCTATTGCTCTTCTGGAAAGTTTGTTTTCGAGTTTCAAA
* * *
446644 AGATTTCTTTCGCATTAGTGGGGGAATGTTGGTAATGCTCAATCTCACTTAGTATTGGAAACACT
130 AGATTTCTTTCGCATTAGTGGGGGAATGTTGATAATGCTCAATCCCACATAGTATTGGAAACACT
* *
446709 ATTGGGAATGGTATTTAAGGCTTGGCTTTTCCACTTTCTTGTTGAGTGATAGAGAACAAGGAGGA
195 ATTGGGAATGGTATTTAAGGCTTGGCTTTCCCACTTCCTTGTTGAGTGATAGAGAACAAGGAGGA
446774 CTCTCGCGCACCGCCGCCGCCGTCCGTCTCGTCTCGT
260 CTCTCGCGCACCGCCGCCGCCGTCCGTCTCGTCTCGT
446811 CTCGGTACGG
Statistics
Matches: 285, Mismatches: 10, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
337 283 0.99
338 2 0.01
ACGTcount: A:0.22, C:0.22, G:0.23, T:0.33
Consensus pattern (337 bp):
GACTAGTTTCACTTATCTAAGAGAATGATTGCTCATCATCACTATGTACTAGTTCCAGATACGTT
CACTAGTGCTTAAGCAACTAATCTCGCTATTGCTCTTCTGGAAAGTTTGTTTTCGAGTTTCAAAA
GATTTCTTTCGCATTAGTGGGGGAATGTTGATAATGCTCAATCCCACATAGTATTGGAAACACTA
TTGGGAATGGTATTTAAGGCTTGGCTTTCCCACTTCCTTGTTGAGTGATAGAGAACAAGGAGGAC
TCTCGCGCACCGCCGCCGCCGTCCGTCTCGTCTCGTTTTGGCTTGGCTCGGCACGGCACGGCACG
GCTCGTGGTCGT
Found at i:447148 original size:22 final size:22
Alignment explanation
Indices: 447123--447180 Score: 62
Period size: 22 Copynumber: 2.6 Consensus size: 22
447113 ATATCAGGAG
* *
447123 TTACAGGAGTTATTTGATTTAA
1 TTACAGGAGTTATATGATATAA
* *
447145 TTACAGGGGTTACATGATATAA
1 TTACAGGAGTTATATGATATAA
* *
447167 TTTCAAGAGTTATA
1 TTACAGGAGTTATA
447181 ACAGCTGAAT
Statistics
Matches: 28, Mismatches: 8, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.34, C:0.07, G:0.19, T:0.40
Consensus pattern (22 bp):
TTACAGGAGTTATATGATATAA
Found at i:449707 original size:14 final size:13
Alignment explanation
Indices: 449688--449725 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 13
449678 CTAAACATGG
449688 GAAGAATGAAAGAA
1 GAAGAATGAAA-AA
449702 GAAGAATGGAAAAA
1 GAAGAAT-GAAAAA
449716 GAAGAA-GAAA
1 GAAGAATGAAA
449726 TTGGTGTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
12 4 0.17
14 15 0.65
15 4 0.17
ACGTcount: A:0.66, C:0.00, G:0.29, T:0.05
Consensus pattern (13 bp):
GAAGAATGAAAAA
Found at i:450359 original size:30 final size:32
Alignment explanation
Indices: 450313--450390 Score: 88
Period size: 33 Copynumber: 2.4 Consensus size: 32
450303 TTTAAATAGT
450313 TATTATATTTTATATT-AAT-ATAATTATATAAA
1 TATTAT-TTTT-TATTAAATAATAATTATATAAA
* *
450345 TATTATTTTTTATTAAAATAATATTTATATAAT
1 TATTATTTTTTATT-AAATAATAATTATATAAA
450378 TATTATTTATTTA
1 TATTATTT-TTTA
450391 AATTTATTAA
Statistics
Matches: 40, Mismatches: 2, Indels: 6
0.83 0.04 0.12
Matches are distributed among these distances:
30 4 0.10
31 4 0.10
32 9 0.22
33 19 0.47
34 4 0.10
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (32 bp):
TATTATTTTTTATTAAATAATAATTATATAAA
Found at i:450382 original size:33 final size:30
Alignment explanation
Indices: 450303--450390 Score: 86
Period size: 33 Copynumber: 2.7 Consensus size: 30
450293 CAGTTATTTT
* *
450303 TTTAAATAGTTATTATATTTTATATTAATATA
1 TTTATATAATTATTAT-TTTT-TATTAATATA
* *
450335 ATTATATAAATATTATTTTTTATTAAAATAATA
1 TTTATATAATTATTATTTTTTATT--AAT-ATA
450368 TTTATATAATTATTATTTATTTA
1 TTTATATAATTATTATTT-TTTA
450391 AATTTATTAA
Statistics
Matches: 46, Mismatches: 6, Indels: 6
0.79 0.10 0.10
Matches are distributed among these distances:
30 4 0.09
31 4 0.09
32 15 0.33
33 19 0.41
34 4 0.09
ACGTcount: A:0.42, C:0.00, G:0.01, T:0.57
Consensus pattern (30 bp):
TTTATATAATTATTATTTTTTATTAATATA
Found at i:450384 original size:15 final size:14
Alignment explanation
Indices: 450346--450428 Score: 53
Period size: 15 Copynumber: 5.7 Consensus size: 14
450336 TTATATAAAT
*
450346 ATTATTTTTTATTAA
1 ATTATTATTTATT-A
* *
450361 AATAATATTTATATA
1 ATTATTATTTAT-TA
450376 ATTATTATTTATTTA
1 ATTATTATTTA-TTA
* *
450391 AAT-TTATTAATTA
1 ATTATTATTTATTA
*
450404 ATTATT-TTTGTGCTA
1 ATTATTATTTAT--TA
450419 ATTATTATTT
1 ATTATTATTT
450429 TTTGTCTACA
Statistics
Matches: 52, Mismatches: 10, Indels: 11
0.71 0.14 0.15
Matches are distributed among these distances:
13 8 0.15
14 8 0.15
15 31 0.60
16 5 0.10
ACGTcount: A:0.36, C:0.01, G:0.02, T:0.60
Consensus pattern (14 bp):
ATTATTATTTATTA
Found at i:453867 original size:25 final size:25
Alignment explanation
Indices: 453833--453892 Score: 84
Period size: 25 Copynumber: 2.4 Consensus size: 25
453823 ATTATCATTA
453833 ATTTAGGTATGTACAATAACTACAT
1 ATTTAGGTATGTACAATAACTACAT
****
453858 ATTTAGGTATGTTTGTTAACTACAT
1 ATTTAGGTATGTACAATAACTACAT
453883 ATTTAGGTAT
1 ATTTAGGTAT
453893 ATATACTTTG
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
25 31 1.00
ACGTcount: A:0.33, C:0.08, G:0.15, T:0.43
Consensus pattern (25 bp):
ATTTAGGTATGTACAATAACTACAT
Found at i:454270 original size:23 final size:23
Alignment explanation
Indices: 454239--454311 Score: 101
Period size: 23 Copynumber: 3.2 Consensus size: 23
454229 ATAGGTAAAA
*
454239 ATATGATGTAATAGGTAGCGCTT
1 ATATAATGTAATAGGTAGCGCTT
* *
454262 ATATAATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTAGCGCTT
* *
454285 ATATAATGTAATAGGTAGTGGTT
1 ATATAATGTAATAGGTAGCGCTT
454308 ATAT
1 ATAT
454312 TGTAAAGTAT
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 44 1.00
ACGTcount: A:0.34, C:0.04, G:0.22, T:0.40
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCGCTT
Found at i:454599 original size:25 final size:25
Alignment explanation
Indices: 454571--454620 Score: 91
Period size: 25 Copynumber: 2.0 Consensus size: 25
454561 AAATCAATTA
*
454571 AACATTGTTGTGGGTACATTATTTG
1 AACATTGTTATGGGTACATTATTTG
454596 AACATTGTTATGGGTACATTATTTG
1 AACATTGTTATGGGTACATTATTTG
454621 GAAAAATAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.26, C:0.08, G:0.22, T:0.44
Consensus pattern (25 bp):
AACATTGTTATGGGTACATTATTTG
Found at i:455027 original size:18 final size:18
Alignment explanation
Indices: 455006--455042 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
454996 GTAATTGGAG
455006 TTTGAATTTAAATTTCAA
1 TTTGAATTTAAATTTCAA
* *
455024 TTTGAGTTTGAATTTCAA
1 TTTGAATTTAAATTTCAA
455042 T
1 T
455043 ATATATTTCG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.32, C:0.05, G:0.11, T:0.51
Consensus pattern (18 bp):
TTTGAATTTAAATTTCAA
Found at i:455050 original size:24 final size:24
Alignment explanation
Indices: 454998--455044 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
454988 TTTCATATGT
* *
454998 AATTGGAGTTTGAATTTAAATTTC
1 AATTTGAGTTTGAATTTAAATATC
*
455022 AATTTGAGTTTGAATTTCAATAT
1 AATTTGAGTTTGAATTTAAATAT
455045 ATATTTCGGC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.34, C:0.04, G:0.15, T:0.47
Consensus pattern (24 bp):
AATTTGAGTTTGAATTTAAATATC
Found at i:455356 original size:39 final size:39
Alignment explanation
Indices: 455313--455399 Score: 147
Period size: 39 Copynumber: 2.2 Consensus size: 39
455303 TTCGATGCTC
*
455313 ATCAAAATCCAAAGCTCATATGGTGCCAAGCAAAAGGAA
1 ATCAAAATCCAAAGCTCATATGATGCCAAGCAAAAGGAA
* *
455352 ATCAAAATCCAAATCTCATATGATGTCAAGCAAAAGGAA
1 ATCAAAATCCAAAGCTCATATGATGCCAAGCAAAAGGAA
455391 ATCAAAATC
1 ATCAAAATC
455400 TACAACTTGA
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
39 45 1.00
ACGTcount: A:0.48, C:0.20, G:0.14, T:0.18
Consensus pattern (39 bp):
ATCAAAATCCAAAGCTCATATGATGCCAAGCAAAAGGAA
Found at i:455847 original size:21 final size:21
Alignment explanation
Indices: 455821--455875 Score: 92
Period size: 21 Copynumber: 2.6 Consensus size: 21
455811 TAAAAATATG
455821 ATGTAATAGGTAGCGCTTATA
1 ATGTAATAGGTAGCGCTTATA
* *
455842 ATGTAATAGGTATCGTTTATA
1 ATGTAATAGGTAGCGCTTATA
455863 ATGTAATAGGTAG
1 ATGTAATAGGTAG
455876 TGGTTATTGT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.35, C:0.05, G:0.24, T:0.36
Consensus pattern (21 bp):
ATGTAATAGGTAGCGCTTATA
Found at i:455882 original size:21 final size:21
Alignment explanation
Indices: 455821--455882 Score: 81
Period size: 21 Copynumber: 3.0 Consensus size: 21
455811 TAAAAATATG
*
455821 ATGTAATAGGTAGCGCTTATA
1 ATGTAATAGGTAGTGCTTATA
*
455842 ATGTAATAGGTA-TCGTTTATA
1 ATGTAATAGGTAGT-GCTTATA
*
455863 ATGTAATAGGTAGTGGTTAT
1 ATGTAATAGGTAGTGCTTAT
455883 TGTAAAGTAT
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
21 35 0.97
22 1 0.03
ACGTcount: A:0.32, C:0.05, G:0.24, T:0.39
Consensus pattern (21 bp):
ATGTAATAGGTAGTGCTTATA
Found at i:456230 original size:107 final size:107
Alignment explanation
Indices: 456082--456296 Score: 412
Period size: 107 Copynumber: 2.0 Consensus size: 107
456072 ACAATCAAAT
*
456082 AATTTTTTGTGCAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACAATATTAAA
1 AATTTTTTGTGCAAATGAAATTATTAAATTAATATTATAGGTGGAAAACATGAAACAATATTAAA
456147 AAAAATTGAAACATAAATTACATAACTTTAAAAGAAGTATCG
66 AAAAATTGAAACATAAATTACATAACTTTAAAAGAAGTATCG
*
456189 AATTTTTTGTGCAAATGAAATTATTAAATTAATATTATAGGTGGAAAACATGAAACACTATTAAA
1 AATTTTTTGTGCAAATGAAATTATTAAATTAATATTATAGGTGGAAAACATGAAACAATATTAAA
456254 AAAAATTGAAACATAAATTACATAACTTTAAAAGAAGTATCG
66 AAAAATTGAAACATAAATTACATAACTTTAAAAGAAGTATCG
456296 A
1 A
456297 TCCTTTTTAT
Statistics
Matches: 106, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
107 106 1.00
ACGTcount: A:0.50, C:0.07, G:0.12, T:0.32
Consensus pattern (107 bp):
AATTTTTTGTGCAAATGAAATTATTAAATTAATATTATAGGTGGAAAACATGAAACAATATTAAA
AAAAATTGAAACATAAATTACATAACTTTAAAAGAAGTATCG
Found at i:456377 original size:23 final size:23
Alignment explanation
Indices: 456342--456414 Score: 83
Period size: 23 Copynumber: 3.2 Consensus size: 23
456332 ATATGTAAAA
*
456342 ATATGATGTAATAGGTAGCGCTT
1 ATATAATGTAATAGGTAGCGCTT
* * *
456365 ATATAATGCAATAGGTATCGTTT
1 ATATAATGTAATAGGTAGCGCTT
* * *
456388 ATACAATGTAATAGGTAGTGGTT
1 ATATAATGTAATAGGTAGCGCTT
456411 ATAT
1 ATAT
456415 TGTAAAGTAT
Statistics
Matches: 40, Mismatches: 10, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
23 40 1.00
ACGTcount: A:0.34, C:0.07, G:0.22, T:0.37
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCGCTT
Found at i:456698 original size:23 final size:23
Alignment explanation
Indices: 456667--456739 Score: 92
Period size: 23 Copynumber: 3.2 Consensus size: 23
456657 ATAGGTAAAA
*
456667 ATATGATGTAATAGGTAGCGCTT
1 ATATAATGTAATAGGTAGCGCTT
* * *
456690 ATATAATGTAATATGTATCGTTT
1 ATATAATGTAATAGGTAGCGCTT
* *
456713 ATATAATGTAATAGGTAGTGGTT
1 ATATAATGTAATAGGTAGCGCTT
456736 ATAT
1 ATAT
456740 TGTAAAGTAT
Statistics
Matches: 42, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 42 1.00
ACGTcount: A:0.34, C:0.04, G:0.21, T:0.41
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCGCTT
Found at i:456816 original size:295 final size:293
Alignment explanation
Indices: 456463--457059 Score: 1035
Period size: 295 Copynumber: 2.0 Consensus size: 293
456453 TTTTTCACTA
456463 TTAT-TAAATTAAAAATTCTAAATATTATTTTATAAATATCAAACAATCAAATAATTTTTTGTGC
1 TTATATAAATTAAAAATTCTAAATATTATTTTATAAATATCAAACAATCAAATAATTTTTTGTGC
456527 AAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAAATTGAAAC
66 AAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAAATTGAAA-
** *
456592 ATAAATTTTATAACTTT-AAAGAAGTATCGATCCTTTTTATAAAAAGTATGGACACTTTCAATAT
130 ATAAATTACATAACTTTAAAAGAAATATCGATCCTTTTTAT-AAAAGTATGGACACTTTC-A-AT
*
456656 AATAGGTAAAAATATGATGTAATAGGTAGCGCTTATATAATGTAATATGTATCGTTTATATAATG
192 AATAGGTAAAAA-ATGATGTAATAGGTAGCGCTTATATAATGTAATAGGTATCGTTTATATAATG
*
456721 TAATAGGTAGTGGTTATATTGTAAAGTATCTATCCTTT
256 TAATAGGTAGTGGTTATATTGTAAAGTATCTATCATTT
456759 TTATATAAATT-AAAATTCTAAATATT-TTTTATAAA-ATCAAAACAATCAAATAATTTTTTGTG
1 TTATATAAATTAAAAATTCTAAATATTATTTTATAAATATC-AAACAATCAAATAATTTTTTGTG
456821 CAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAAATTGAAA
65 CAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAAATTGAAA
*
456886 ATAAATTACATAACTTTAAAAGAAATATCGATCCTTTTTATAAAAGTATGGACGCTTTCAATAAT
130 ATAAATTACATAACTTTAAAAGAAATATCGATCCTTTTTATAAAAGTATGGACACTTTCAATAAT
456951 AGGTAAAAAATGATGTAATAGGTAGCGCTTATATAATGTAATAGGTATCGTTTATATAATGTAAT
195 AGGTAAAAAATGATGTAATAGGTAGCGCTTATATAATGTAATAGGTATCGTTTATATAATGTAAT
457016 AGGTAGTGGTTATATTGTAAAGTATCTATCATTT
260 AGGTAGTGGTTATATTGTAAAGTATCTATCATTT
*
457050 TTTTA-AAATT
1 TTATATAAATT
457060 GTCTATACTT
Statistics
Matches: 291, Mismatches: 7, Indels: 12
0.94 0.02 0.04
Matches are distributed among these distances:
290 5 0.02
291 92 0.32
292 14 0.05
293 1 0.00
294 35 0.12
295 119 0.41
296 19 0.07
297 6 0.02
ACGTcount: A:0.43, C:0.07, G:0.12, T:0.38
Consensus pattern (293 bp):
TTATATAAATTAAAAATTCTAAATATTATTTTATAAATATCAAACAATCAAATAATTTTTTGTGC
AAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAAATTGAAAA
TAAATTACATAACTTTAAAAGAAATATCGATCCTTTTTATAAAAGTATGGACACTTTCAATAATA
GGTAAAAAATGATGTAATAGGTAGCGCTTATATAATGTAATAGGTATCGTTTATATAATGTAATA
GGTAGTGGTTATATTGTAAAGTATCTATCATTT
Found at i:456989 original size:23 final size:23
Alignment explanation
Indices: 456963--457030 Score: 100
Period size: 23 Copynumber: 3.0 Consensus size: 23
456953 GTAAAAAATG
456963 ATGTAATAGGTAGCGCTTATATA
1 ATGTAATAGGTAGCGCTTATATA
* *
456986 ATGTAATAGGTATCGTTTATATA
1 ATGTAATAGGTAGCGCTTATATA
* *
457009 ATGTAATAGGTAGTGGTTATAT
1 ATGTAATAGGTAGCGCTTATAT
457031 TGTAAAGTAT
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 40 1.00
ACGTcount: A:0.34, C:0.04, G:0.22, T:0.40
Consensus pattern (23 bp):
ATGTAATAGGTAGCGCTTATATA
Found at i:457511 original size:23 final size:23
Alignment explanation
Indices: 457441--457511 Score: 97
Period size: 23 Copynumber: 3.1 Consensus size: 23
457431 AAATAGGTAA
* *
457441 ATATAAGCGTTACCTATTACATT
1 ATATAAGCGCTACCTATTATATT
*
457464 ATATACGCGCTACCTATTATATT
1 ATATAAGCGCTACCTATTATATT
* *
457487 ATATAAGCGCTACCTAGTATGTT
1 ATATAAGCGCTACCTATTATATT
457510 AT
1 AT
457512 TGTACTTTAT
Statistics
Matches: 42, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 42 1.00
ACGTcount: A:0.32, C:0.18, G:0.11, T:0.38
Consensus pattern (23 bp):
ATATAAGCGCTACCTATTATATT
Found at i:463179 original size:13 final size:13
Alignment explanation
Indices: 463161--463199 Score: 62
Period size: 13 Copynumber: 3.1 Consensus size: 13
463151 TCATATTTTG
463161 TTATATTATATAA
1 TTATATTATATAA
*
463174 TTATATTGTATAA
1 TTATATTATATAA
463187 TTATA-TATATAA
1 TTATATTATATAA
463199 T
1 T
463200 ATTATTAATA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
12 7 0.29
13 17 0.71
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.54
Consensus pattern (13 bp):
TTATATTATATAA
Found at i:463208 original size:21 final size:21
Alignment explanation
Indices: 463165--463208 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
463155 ATTTTGTTAT
* *
463165 ATTATATAATTATATTGTATA
1 ATTATATAATAATATTATATA
463186 ATTATATATATAATATTAT-TA
1 ATTATATA-ATAATATTATATA
463207 AT
1 AT
463209 ATTATTTCTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 12 0.60
22 8 0.40
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (21 bp):
ATTATATAATAATATTATATA
Found at i:464254 original size:2 final size:2
Alignment explanation
Indices: 464247--464279 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
464237 TTAATTCATT
464247 TA 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 TA T
464280 TATTTTTTAG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:464486 original size:14 final size:15
Alignment explanation
Indices: 464467--464499 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
464457 TTTACGTATA
464467 TTATATT-CATTTGT
1 TTATATTACATTTGT
*
464481 TTATATTACATTTTT
1 TTATATTACATTTGT
464496 TTAT
1 TTAT
464500 TTATTATTTC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 7 0.41
15 10 0.59
ACGTcount: A:0.24, C:0.06, G:0.03, T:0.67
Consensus pattern (15 bp):
TTATATTACATTTGT
Found at i:465734 original size:28 final size:28
Alignment explanation
Indices: 465700--465757 Score: 82
Period size: 28 Copynumber: 2.0 Consensus size: 28
465690 ATAAGTAAAA
465700 ATATATAATCTAAATATTAAAT-ATATATAT
1 ATATATAA-CTAAAT-TTAAATGATA-ATAT
465730 ATATATAACTAAATTTAAATGATAATAT
1 ATATATAACTAAATTTAAATGATAATAT
465758 CGCTCAAGCA
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
28 10 0.37
29 9 0.33
30 8 0.30
ACGTcount: A:0.53, C:0.03, G:0.02, T:0.41
Consensus pattern (28 bp):
ATATATAACTAAATTTAAATGATAATAT
Found at i:466139 original size:2 final size:2
Alignment explanation
Indices: 466132--466180 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
466122 ATACTGCTTG
466132 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
466174 TA TA TA T
1 TA TA TA T
466181 TTCACATATT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:468935 original size:21 final size:20
Alignment explanation
Indices: 468909--469121 Score: 112
Period size: 21 Copynumber: 10.7 Consensus size: 20
468899 CATATTCGCA
468909 TTGCGATATTCCAAGTTCACG
1 TTGCGATATTCCAAGTTC-CG
*
468930 TTGCGATTTATTCCAGGTT-CG
1 TTGCGA--TATTCCAAGTTCCG
* *
468951 TTGCGATAGTCGAAGTTCGCG
1 TTGCGATATTCCAAGTTC-CG
*
468972 TTGCGATTTATTCCAAATT-CG
1 TTGCGA--TATTCCAAGTTCCG
*
468993 TTGCGATAGTCCAAGTTCACG
1 TTGCGATATTCCAAGTTC-CG
469014 TTGCG--------A-TT-CG
1 TTGCGATATTCCAAGTTCCG
* *
469024 TTGCGATAGTCGAAGTTCGCG
1 TTGCGATATTCCAAGTTC-CG
* *
469045 TTGCGATTTATTACAAATT-CG
1 TTGCGA--TATTCCAAGTTCCG
*
469066 TTGCGATAGTCCAAGTTCTCG
1 TTGCGATATTCCAAGTTC-CG
469087 TTGCGATTTATTCCAAGTT-CG
1 TTGCGA--TATTCCAAGTTCCG
*
469108 TTGCGATAGTCCAA
1 TTGCGATATTCCAA
469122 AATCGCAACG
Statistics
Matches: 149, Mismatches: 18, Indels: 52
0.68 0.08 0.24
Matches are distributed among these distances:
10 7 0.05
12 2 0.01
13 1 0.01
18 1 0.01
19 34 0.23
21 69 0.46
23 35 0.23
ACGTcount: A:0.21, C:0.20, G:0.23, T:0.36
Consensus pattern (20 bp):
TTGCGATATTCCAAGTTCCG
Found at i:468967 original size:42 final size:42
Alignment explanation
Indices: 468909--469121 Score: 259
Period size: 42 Copynumber: 5.3 Consensus size: 42
468899 CATATTCGCA
* **
468909 TTGCGATATTCCAAGTTCACGTTGCGATTTATTCCAGGTTCG
1 TTGCGATAGTCCAAGTTCACGTTGCGATTTATTCCAAATTCG
* *
468951 TTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTCG
1 TTGCGATAGTCCAAGTTCACGTTGCGATTTATTCCAAATTCG
468993 TTGCGATAGTCCAAGTTCACGTTGCG-----------ATTCG
1 TTGCGATAGTCCAAGTTCACGTTGCGATTTATTCCAAATTCG
* * *
469024 TTGCGATAGTCGAAGTTCGCGTTGCGATTTATTACAAATTCG
1 TTGCGATAGTCCAAGTTCACGTTGCGATTTATTCCAAATTCG
* *
469066 TTGCGATAGTCCAAGTTCTCGTTGCGATTTATTCCAAGTTCG
1 TTGCGATAGTCCAAGTTCACGTTGCGATTTATTCCAAATTCG
469108 TTGCGATAGTCCAA
1 TTGCGATAGTCCAA
469122 AATCGCAACG
Statistics
Matches: 147, Mismatches: 13, Indels: 22
0.81 0.07 0.12
Matches are distributed among these distances:
31 29 0.20
42 118 0.80
ACGTcount: A:0.21, C:0.20, G:0.23, T:0.36
Consensus pattern (42 bp):
TTGCGATAGTCCAAGTTCACGTTGCGATTTATTCCAAATTCG
Found at i:469026 original size:31 final size:31
Alignment explanation
Indices: 468988--469052 Score: 112
Period size: 31 Copynumber: 2.1 Consensus size: 31
468978 TTTATTCCAA
468988 ATTCGTTGCGATAGTCCAAGTTCACGTTGCG
1 ATTCGTTGCGATAGTCCAAGTTCACGTTGCG
* *
469019 ATTCGTTGCGATAGTCGAAGTTCGCGTTGCG
1 ATTCGTTGCGATAGTCCAAGTTCACGTTGCG
469050 ATT
1 ATT
469053 TATTACAAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.18, C:0.20, G:0.28, T:0.34
Consensus pattern (31 bp):
ATTCGTTGCGATAGTCCAAGTTCACGTTGCG
Found at i:469066 original size:73 final size:73
Alignment explanation
Indices: 468947--469094 Score: 278
Period size: 73 Copynumber: 2.0 Consensus size: 73
468937 TTATTCCAGG
*
468947 TTCGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTCGTTGCGATAGTCCAAGTTCA
1 TTCGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTACAAATTCGTTGCGATAGTCCAAGTTCA
469012 CGTTGCGA
66 CGTTGCGA
*
469020 TTCGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTACAAATTCGTTGCGATAGTCCAAGTTCT
1 TTCGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTACAAATTCGTTGCGATAGTCCAAGTTCA
469085 CGTTGCGA
66 CGTTGCGA
469093 TT
1 TT
469095 TATTCCAAGT
Statistics
Matches: 73, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
73 73 1.00
ACGTcount: A:0.20, C:0.20, G:0.24, T:0.36
Consensus pattern (73 bp):
TTCGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTACAAATTCGTTGCGATAGTCCAAGTTCA
CGTTGCGA
Found at i:469111 original size:115 final size:115
Alignment explanation
Indices: 468909--469121 Score: 345
Period size: 115 Copynumber: 1.9 Consensus size: 115
468899 CATATTCGCA
* * ** *
468909 TTGCGATATTCCAAGTTCACGTTGCGATTTATTCCAGGTTCGTTGCGATAGTCGAAGTTCGCGTT
1 TTGCGATAGTCCAAGTTCACGTTGCGATTTATTACAAATTCGTTGCGATAGTCCAAGTTCGCGTT
468974 GCGATTTATTCCAAATTCGTTGCGATAGTCCAAGTTCACGTTGCGATTCG
66 GCGATTTATTCCAAATTCGTTGCGATAGTCCAAGTTCACGTTGCGATTCG
* * *
469024 TTGCGATAGTCGAAGTTCGCGTTGCGATTTATTACAAATTCGTTGCGATAGTCCAAGTTCTCGTT
1 TTGCGATAGTCCAAGTTCACGTTGCGATTTATTACAAATTCGTTGCGATAGTCCAAGTTCGCGTT
*
469089 GCGATTTATTCCAAGTTCGTTGCGATAGTCCAA
66 GCGATTTATTCCAAATTCGTTGCGATAGTCCAA
469122 AATCGCAACG
Statistics
Matches: 89, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
115 89 1.00
ACGTcount: A:0.21, C:0.20, G:0.23, T:0.36
Consensus pattern (115 bp):
TTGCGATAGTCCAAGTTCACGTTGCGATTTATTACAAATTCGTTGCGATAGTCCAAGTTCGCGTT
GCGATTTATTCCAAATTCGTTGCGATAGTCCAAGTTCACGTTGCGATTCG
Found at i:469928 original size:20 final size:20
Alignment explanation
Indices: 469903--470013 Score: 120
Period size: 20 Copynumber: 5.5 Consensus size: 20
469893 ATCGCAACGT
469903 CATTGCGATTTACATATTCG
1 CATTGCGATTTACATATTCG
* *
469923 CATTGCGATAGTCCA-AGTTCG
1 CATTGCGAT-TTACATA-TTCG
*
469944 CATTGCGATAGT-CGACTA-TCG
1 CATTGCGAT-TTAC-A-TATTCG
469965 CATTGCGATTTACATATTCG
1 CATTGCGATTTACATATTCG
*
469985 CATTGCGATTTACATATTCA
1 CATTGCGATTTACATATTCG
470005 CATTGCGAT
1 CATTGCGAT
470014 AGTCCAAGTT
Statistics
Matches: 80, Mismatches: 4, Indels: 14
0.82 0.04 0.14
Matches are distributed among these distances:
19 2 0.03
20 44 0.55
21 33 0.41
23 1 0.01
ACGTcount: A:0.25, C:0.22, G:0.18, T:0.35
Consensus pattern (20 bp):
CATTGCGATTTACATATTCG
Found at i:469945 original size:21 final size:21
Alignment explanation
Indices: 469919--470096 Score: 177
Period size: 21 Copynumber: 8.6 Consensus size: 21
469909 GATTTACATA
469919 TTCGCATTGCGATAGTCCAAG
1 TTCGCATTGCGATAGTCCAAG
* *
469940 TTCGCATTGCGATAGT-CGAC
1 TTCGCATTGCGATAGTCCAAG
* *
469960 TATCGCATTGCGAT-TTACATA-
1 T-TCGCATTGCGATAGTCCA-AG
* *
469981 TTCGCATTGCGAT-TTACATA-
1 TTCGCATTGCGATAGTCCA-AG
*
470001 TTCACATTGCGATAGTCCAAG
1 TTCGCATTGCGATAGTCCAAG
* *
470022 TTTGCATTGCGATAGTCTAAG
1 TTCGCATTGCGATAGTCCAAG
* *
470043 TTCGTATTGCGATAGTCAAAG
1 TTCGCATTGCGATAGTCCAAG
*
470064 TTCGCATTGCGATAGTCGAAG
1 TTCGCATTGCGATAGTCCAAG
*
470085 TTCGCGTTGCGA
1 TTCGCATTGCGA
470097 ATCTGGAAAC
Statistics
Matches: 136, Mismatches: 16, Indels: 10
0.84 0.10 0.06
Matches are distributed among these distances:
20 36 0.26
21 99 0.73
22 1 0.01
ACGTcount: A:0.24, C:0.20, G:0.22, T:0.33
Consensus pattern (21 bp):
TTCGCATTGCGATAGTCCAAG
Found at i:470052 original size:82 final size:82
Alignment explanation
Indices: 469903--470055 Score: 245
Period size: 82 Copynumber: 1.9 Consensus size: 82
469893 ATCGCAACGT
* *
469903 CATTGCGATTTACATATTCGCATTGCGATAGTCCAAGTTCGCATTGCGATAGTCGACTATCGCAT
1 CATTGCGATTTACATATTCACATTGCGATAGTCCAAGTTCGCATTGCGATAGTCAACTATCGCAT
469968 TGCGATTTACATATTCG
66 TGCGATTTACATATTCG
* * *
469985 CATTGCGATTTACATATTCACATTGCGATAGTCCAAGTTTGCATTGCGATAGTCTAAGT-TCGTA
1 CATTGCGATTTACATATTCACATTGCGATAGTCCAAGTTCGCATTGCGATAGTC-AACTATCGCA
470049 TTGCGAT
65 TTGCGAT
470056 AGTCAAAGTT
Statistics
Matches: 65, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
82 63 0.97
83 2 0.03
ACGTcount: A:0.25, C:0.20, G:0.20, T:0.35
Consensus pattern (82 bp):
CATTGCGATTTACATATTCACATTGCGATAGTCCAAGTTCGCATTGCGATAGTCAACTATCGCAT
TGCGATTTACATATTCG
Found at i:473685 original size:12 final size:12
Alignment explanation
Indices: 473668--473692 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
473658 TAGAGTTGAT
473668 AAGTTAAATTTG
1 AAGTTAAATTTG
473680 AAGTTAAATTTG
1 AAGTTAAATTTG
473692 A
1 A
473693 CTTGTCATCA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.44, C:0.00, G:0.16, T:0.40
Consensus pattern (12 bp):
AAGTTAAATTTG
Found at i:475268 original size:32 final size:31
Alignment explanation
Indices: 475227--475349 Score: 108
Period size: 31 Copynumber: 4.0 Consensus size: 31
475217 AGTTGAGGGT
*
475227 TTACCTATGTTCTACGGAACATATGGATAGAA
1 TTACCTATGTTCTACGGAACATATGGACAG-A
* * *
475259 TTACCTATG-TCTTTCAGAACATATGGACATA
1 TTACCTATGTTC-TACGGAACATATGGACAGA
* * * *
475290 -TACTTATGTTCTAAGGAACATATGAACAGT
1 TTACCTATGTTCTACGGAACATATGGACAGA
* *
475320 TTACCTAGGTTCTAC-GAGACCTATGGACAG
1 TTACCTATGTTCTACGGA-ACATATGGACAG
475350 GTGCCGAGGT
Statistics
Matches: 71, Mismatches: 16, Indels: 9
0.74 0.17 0.09
Matches are distributed among these distances:
30 22 0.31
31 26 0.37
32 23 0.32
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.32
Consensus pattern (31 bp):
TTACCTATGTTCTACGGAACATATGGACAGA
Found at i:476196 original size:22 final size:22
Alignment explanation
Indices: 476146--476211 Score: 60
Period size: 22 Copynumber: 3.0 Consensus size: 22
476136 TAACATTCGG
* * * *
476146 TACTGTTCACGGCATTGTTCAC
1 TACTGTTAACGGTACTGTTCAT
*
476168 TACTGTTAATGGTACTGTTCAT
1 TACTGTTAACGGTACTGTTCAT
* * *
476190 TATTGTTTACGGTACTATTCAT
1 TACTGTTAACGGTACTGTTCAT
476212 ACCGTATAGT
Statistics
Matches: 35, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
22 35 1.00
ACGTcount: A:0.21, C:0.18, G:0.17, T:0.44
Consensus pattern (22 bp):
TACTGTTAACGGTACTGTTCAT
Found at i:496015 original size:12 final size:12
Alignment explanation
Indices: 495998--496022 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
495988 GTCAAATAAT
495998 TTAGGCACCAAA
1 TTAGGCACCAAA
496010 TTAGGCACCAAA
1 TTAGGCACCAAA
496022 T
1 T
496023 GGTATTTTGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.40, C:0.24, G:0.16, T:0.20
Consensus pattern (12 bp):
TTAGGCACCAAA
Found at i:501340 original size:14 final size:14
Alignment explanation
Indices: 501318--501374 Score: 59
Period size: 14 Copynumber: 4.4 Consensus size: 14
501308 CGTTCATGAA
*
501318 CGTTCGGTTATGTT
1 CGTTTGGTTATGTT
501332 CGTTTGGTTATGTT
1 CGTTTGGTTATGTT
501346 CG--T--TTATGTT
1 CGTTTGGTTATGTT
* *
501356 CGTTCGATTATGTT
1 CGTTTGGTTATGTT
501370 CGTTT
1 CGTTT
501375 ATGTTCATTC
Statistics
Matches: 36, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
10 9 0.25
12 1 0.03
14 26 0.72
ACGTcount: A:0.09, C:0.12, G:0.25, T:0.54
Consensus pattern (14 bp):
CGTTTGGTTATGTT
Found at i:501346 original size:24 final size:24
Alignment explanation
Indices: 501319--501393 Score: 98
Period size: 24 Copynumber: 3.1 Consensus size: 24
501309 GTTCATGAAC
* * *
501319 GTTCGGTTATGTTCGTTTGGTTAT
1 GTTCGTTTATGTTCGTTCGATTAT
501343 GTTCGTTTATGTTCGTTCGATTAT
1 GTTCGTTTATGTTCGTTCGATTAT
*
501367 GTTCGTTTATGTTCATTC-ATTTAT
1 GTTCGTTTATGTTCGTTCGA-TTAT
501391 GTT
1 GTT
501394 TAACACAATC
Statistics
Matches: 46, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
23 1 0.02
24 45 0.98
ACGTcount: A:0.12, C:0.11, G:0.21, T:0.56
Consensus pattern (24 bp):
GTTCGTTTATGTTCGTTCGATTAT
Found at i:502142 original size:16 final size:16
Alignment explanation
Indices: 502121--502186 Score: 100
Period size: 16 Copynumber: 4.2 Consensus size: 16
502111 CCTCCAACGC
502121 TTATGTTCGTGTTCAT
1 TTATGTTCGTGTTCAT
*
502137 TTATGTTCGTGTTCGT
1 TTATGTTCGTGTTCAT
*
502153 TTATGTTCGTGTTCGT
1 TTATGTTCGTGTTCAT
502169 TTATGTTCGT-TT-AT
1 TTATGTTCGTGTTCAT
502183 TTAT
1 TTAT
502187 TAAATAAACG
Statistics
Matches: 48, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
14 5 0.10
15 2 0.04
16 41 0.85
ACGTcount: A:0.11, C:0.11, G:0.20, T:0.59
Consensus pattern (16 bp):
TTATGTTCGTGTTCAT
Found at i:502269 original size:16 final size:16
Alignment explanation
Indices: 502248--502280 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
502238 AAAAATATTT
502248 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
502264 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
502280 T
1 T
502281 TTATTTATTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.06, C:0.12, G:0.24, T:0.58
Consensus pattern (16 bp):
TGTTCGTTTATGTTCG
Found at i:514021 original size:35 final size:35
Alignment explanation
Indices: 513974--514087 Score: 138
Period size: 35 Copynumber: 3.3 Consensus size: 35
513964 AAAACAATCC
* * *
513974 TCAATTTCATTCTAAACCCCAATTTCCAAAGTAAT
1 TCAATTTAATTCTAAACCCCAAATTCCAAAATAAT
* *
514009 TCAATTTTATTCTAAACCCTAAATTCCAAAATAAT
1 TCAATTTAATTCTAAACCCCAAATTCCAAAATAAT
* * * **
514044 TCAATTAAATTTTAAACCCCAAATTCTAAAATTCT
1 TCAATTTAATTCTAAACCCCAAATTCCAAAATAAT
514079 TCAATTTAA
1 TCAATTTAA
514088 GGTTTAGAAT
Statistics
Matches: 67, Mismatches: 12, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
35 67 1.00
ACGTcount: A:0.41, C:0.21, G:0.01, T:0.37
Consensus pattern (35 bp):
TCAATTTAATTCTAAACCCCAAATTCCAAAATAAT
Found at i:514149 original size:35 final size:35
Alignment explanation
Indices: 514081--514155 Score: 89
Period size: 35 Copynumber: 2.1 Consensus size: 35
514071 AAAATTCTTC
* * * *
514081 AATTTAAGGTTTAGAATGTAATTGAATTATTTTGG
1 AATTTAAGATTTAGAATGAAATTGAAGTATTTTGA
*
514116 AATTTAAGATTTAGAATGAAATT-AAGGTGTTTTGA
1 AATTTAAGATTTAGAATGAAATTGAA-GTATTTTGA
514151 AATTT
1 AATTT
514156 TGAACATGAA
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
34 2 0.06
35 32 0.94
ACGTcount: A:0.37, C:0.00, G:0.19, T:0.44
Consensus pattern (35 bp):
AATTTAAGATTTAGAATGAAATTGAAGTATTTTGA
Found at i:516838 original size:13 final size:13
Alignment explanation
Indices: 516820--516850 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
516810 ATAACCGATG
*
516820 TTAAAAAACTCTA
1 TTAAAAAACTCCA
516833 TTAAAAAACTCCA
1 TTAAAAAACTCCA
516846 TTAAA
1 TTAAA
516851 TAACACAAGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.55, C:0.16, G:0.00, T:0.29
Consensus pattern (13 bp):
TTAAAAAACTCCA
Found at i:518365 original size:18 final size:18
Alignment explanation
Indices: 518342--518383 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
518332 AATTTTTGTT
518342 AGATGAAAAAATAGAAGA
1 AGATGAAAAAATAGAAGA
**
518360 AGATGATGAAATAGAAGA
1 AGATGAAAAAATAGAAGA
518378 AGATGA
1 AGATGA
518384 TGATTTCTCA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.60, C:0.00, G:0.26, T:0.14
Consensus pattern (18 bp):
AGATGAAAAAATAGAAGA
Found at i:518384 original size:18 final size:18
Alignment explanation
Indices: 518350--518386 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
518340 TTAGATGAAA
518350 AAATAGAAGAAGATGATG
1 AAATAGAAGAAGATGATG
518368 AAATAGAAGAAGATGATG
1 AAATAGAAGAAGATGATG
518386 A
1 A
518387 TTTCTCATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.57, C:0.00, G:0.27, T:0.16
Consensus pattern (18 bp):
AAATAGAAGAAGATGATG
Found at i:524034 original size:44 final size:45
Alignment explanation
Indices: 523940--524041 Score: 127
Period size: 44 Copynumber: 2.3 Consensus size: 45
523930 ATTGTTCAAG
* * *
523940 GTGTATCGATGCACTCCTTTAAAATAAAAACATCGAATGCCATCA
1 GTGTATCGATGCACCCCCTTAAAATAAAAACATCGAATGACATCA
* * *
523985 GTGTATCGATGCACCCCCTT-AAATACAAACATCGAATGAGATTTA
1 GTGTATCGATGCACCCCCTTAAAATAAAAACATCGAATGACA-TCA
524030 -TGTATCGATGCA
1 GTGTATCGATGCA
524042 TAGATAGTGC
Statistics
Matches: 50, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
44 30 0.60
45 20 0.40
ACGTcount: A:0.35, C:0.22, G:0.16, T:0.27
Consensus pattern (45 bp):
GTGTATCGATGCACCCCCTTAAAATAAAAACATCGAATGACATCA
Found at i:524733 original size:23 final size:23
Alignment explanation
Indices: 524699--524758 Score: 70
Period size: 23 Copynumber: 2.6 Consensus size: 23
524689 AATCTTATAT
*
524699 GGCACTAT-GGTGTAATTCTACA-C
1 GGCACT-TCGGTGCAATTCTA-AGC
*
524722 GGCACTTCGGTGCAATTCTAAGT
1 GGCACTTCGGTGCAATTCTAAGC
524745 GGCACTTCGGTGCA
1 GGCACTTCGGTGCA
524759 TTTATCAATT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
22 2 0.06
23 31 0.94
ACGTcount: A:0.22, C:0.23, G:0.27, T:0.28
Consensus pattern (23 bp):
GGCACTTCGGTGCAATTCTAAGC
Found at i:529245 original size:239 final size:241
Alignment explanation
Indices: 528825--529305 Score: 903
Period size: 239 Copynumber: 2.0 Consensus size: 241
528815 TGCACTCGGG
*
528825 TGGAACCAAGATGTATATGGATTTAAAAGATCGGTATTGGTGGCCAGGGATGAAACGAAGCATTA
1 TGGAACCAAGATGTATATGGATTTAAAAGATCGGTATTGGTGGCCAGGGATGAAACAAAGCATTA
*
528890 CTGAATTTGTGTCAAAGTGCTTAATATGTCAGCAAGTCAAAGCCGAACATCAAGTTCCGTCTAGA
66 CTGAATTTGTGTCAAAGTGCTTAATATGTCAGCAAGTCAAAACCGAACATCAAGTTCCGTCTAGA
528955 TTATTGTAAACACTTTCCATTCCACAATGGAAGTGGGAAAATGTAATGATGATTTTTTTCGGGGT
131 TTATTGTAAACACTTTCCATTCCACAATGGAAGTGGGAAAATGTAATGATGATTTTTTTCGGGGT
*
529020 TACCCCTGACTCCAAAC-AAAGAGATTCGATTTGGGTAATTGTTGA
196 TACCCCTGACTCCAAACAAAAGAGATTCAATTTGGGTAATTGTTGA
*
529065 TGGAACCAAGATGTATATGGATTTAAAAGATCGGTATTGGTGGCCAGGGATGAAATAAAGCATTA
1 TGGAACCAAGATGTATATGGATTTAAAAGATCGGTATTGGTGGCCAGGGATGAAACAAAGCATTA
*
529130 CTGAATTTGTGTC-AAGTGTTTAATATGTCAGCAAGTCAAAACCGAACATCAAGTTCCGTCTAGA
66 CTGAATTTGTGTCAAAGTGCTTAATATGTCAGCAAGTCAAAACCGAACATCAAGTTCCGTCTAGA
529194 TTATTGTAAACACTTTCCATTCCACAATGGAAGTGGGAAAATGTAATGATGATTTTTTTCGGGGT
131 TTATTGTAAACACTTTCCATTCCACAATGGAAGTGGGAAAATGTAATGATGATTTTTTTCGGGGT
529259 TACCCCTGACTCCAAACAAAAGAGATTCAATTTGGGTAATTGTTGA
196 TACCCCTGACTCCAAACAAAAGAGATTCAATTTGGGTAATTGTTGA
529305 T
1 T
529306 CGATTGACTA
Statistics
Matches: 235, Mismatches: 5, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
239 131 0.56
240 104 0.44
ACGTcount: A:0.33, C:0.15, G:0.22, T:0.30
Consensus pattern (241 bp):
TGGAACCAAGATGTATATGGATTTAAAAGATCGGTATTGGTGGCCAGGGATGAAACAAAGCATTA
CTGAATTTGTGTCAAAGTGCTTAATATGTCAGCAAGTCAAAACCGAACATCAAGTTCCGTCTAGA
TTATTGTAAACACTTTCCATTCCACAATGGAAGTGGGAAAATGTAATGATGATTTTTTTCGGGGT
TACCCCTGACTCCAAACAAAAGAGATTCAATTTGGGTAATTGTTGA
Found at i:531172 original size:64 final size:63
Alignment explanation
Indices: 531104--531265 Score: 175
Period size: 63 Copynumber: 2.5 Consensus size: 63
531094 ATTGTTCAAG
* * * *
531104 GTGTATCGATGCACATGAAGTGCATCGATGCACTCCTTTAAAATAAAAACATTGAATGCCA-TCA
1 GTGTATCGATGCACA-GAAGTGCATCGATGCACCCCCTT-AAATAAAAACATCGAATGACATTCA
* * * * * *
531168 GTGTATCTATGAACAAGTAGTGCATCGATGCACCCCCTTAAATACAAACATCGAATGAGATTTA
1 GTGTATCGATGCAC-AGAAGTGCATCGATGCACCCCCTTAAATAAAAACATCGAATGACATTCA
*
531232 -TGTATCGATGCATAGATAGTGCATCGATGCACCC
1 GTGTATCGATGCACAGA-AGTGCATCGATGCACCC
531266 GTCAAGGGAT
Statistics
Matches: 81, Mismatches: 14, Indels: 7
0.79 0.14 0.07
Matches are distributed among these distances:
62 2 0.02
63 44 0.54
64 34 0.42
65 1 0.01
ACGTcount: A:0.34, C:0.21, G:0.19, T:0.27
Consensus pattern (63 bp):
GTGTATCGATGCACAGAAGTGCATCGATGCACCCCCTTAAATAAAAACATCGAATGACATTCA
Found at i:537854 original size:21 final size:20
Alignment explanation
Indices: 537796--537857 Score: 60
Period size: 20 Copynumber: 3.2 Consensus size: 20
537786 TGATTGTAAA
537796 ATTTTATTGTAATTTGAGAT
1 ATTTTATTGTAATTTGAGAT
* * *
537816 ATTTT-TT-CAA--TAAAAT
1 ATTTTATTGTAATTTGAGAT
537832 ATCTTTATTGTAATTTGAGAT
1 AT-TTTATTGTAATTTGAGAT
537853 ATTTT
1 ATTTT
537858 TATTTTCAAT
Statistics
Matches: 31, Mismatches: 6, Indels: 10
0.66 0.13 0.21
Matches are distributed among these distances:
16 6 0.19
17 3 0.10
18 4 0.13
19 4 0.13
20 8 0.26
21 6 0.19
ACGTcount: A:0.32, C:0.03, G:0.10, T:0.55
Consensus pattern (20 bp):
ATTTTATTGTAATTTGAGAT
Found at i:537859 original size:21 final size:21
Alignment explanation
Indices: 537797--537861 Score: 59
Period size: 21 Copynumber: 3.3 Consensus size: 21
537787 GATTGTAAAA
537797 TTTTATTGTAATTTGAGATA-
1 TTTTATTGTAATTTGAGATAT
* * *
537817 TTTT-TT-CAA--TAAAATAT
1 TTTTATTGTAATTTGAGATAT
*
537834 CTTTATTGTAATTTGAGATAT
1 TTTTATTGTAATTTGAGATAT
537855 TTTTATT
1 TTTTATT
537862 TTCAATAAAA
Statistics
Matches: 32, Mismatches: 8, Indels: 9
0.65 0.16 0.18
Matches are distributed among these distances:
16 5 0.16
17 3 0.09
18 4 0.12
19 4 0.12
20 4 0.12
21 12 0.38
ACGTcount: A:0.31, C:0.03, G:0.09, T:0.57
Consensus pattern (21 bp):
TTTTATTGTAATTTGAGATAT
Found at i:540943 original size:21 final size:21
Alignment explanation
Indices: 540917--540964 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
540907 TTATTCAAAT
*
540917 TAAAAAAAAAAATAATAAAAAA
1 TAAAAGAAAAAAT-ATAAAAAA
* *
540939 TAAAAGACATAATATAAAAAA
1 TAAAAGAAAAAATATAAAAAA
540960 TAAAA
1 TAAAA
540965 TAATAATAGT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
21 13 0.57
22 10 0.43
ACGTcount: A:0.79, C:0.02, G:0.02, T:0.17
Consensus pattern (21 bp):
TAAAAGAAAAAATATAAAAAA
Found at i:540970 original size:20 final size:21
Alignment explanation
Indices: 540931--540972 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
540921 AAAAAAAATA
540931 ATAAAAAATAAAAGACATAAT
1 ATAAAAAATAAAAGACATAAT
*
540952 ATAAAAAATAAAATA-ATAAT
1 ATAAAAAATAAAAGACATAAT
540972 A
1 A
540973 GTCTCCGACT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
20 6 0.30
21 14 0.70
ACGTcount: A:0.74, C:0.02, G:0.02, T:0.21
Consensus pattern (21 bp):
ATAAAAAATAAAAGACATAAT
Found at i:548087 original size:90 final size:90
Alignment explanation
Indices: 547934--548109 Score: 316
Period size: 90 Copynumber: 2.0 Consensus size: 90
547924 TAACACACCA
*
547934 TTTTATAGCCAAGTTACCCTAATCATATTAGGGTTTTTATTATTTCAAATTAATTAAATCTATAT
1 TTTTATAGCCAAGTTACCCTAATCATATTAGGGATTTTATTATTTCAAATTAATTAAATCTATAT
* *
547999 TTAATTAATTGGAATTTAATAATCC
66 TTAATTAATTGAAATTAAATAATCC
*
548024 TTTTATATCCAAGTTACCCTAATCATATTAGGGATTTTATTATTTCAAATTAATTAAATCTATAT
1 TTTTATAGCCAAGTTACCCTAATCATATTAGGGATTTTATTATTTCAAATTAATTAAATCTATAT
548089 TTAATTAATTGAAATTAAATA
66 TTAATTAATTGAAATTAAATA
548110 TTCGGGATTA
Statistics
Matches: 82, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
90 82 1.00
ACGTcount: A:0.38, C:0.10, G:0.07, T:0.45
Consensus pattern (90 bp):
TTTTATAGCCAAGTTACCCTAATCATATTAGGGATTTTATTATTTCAAATTAATTAAATCTATAT
TTAATTAATTGAAATTAAATAATCC
Found at i:553218 original size:12 final size:12
Alignment explanation
Indices: 553203--553232 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
553193 GTTCGTTTAT
553203 ATGTTCATGAAC
1 ATGTTCATGAAC
*
553215 ATGTTCATGAAT
1 ATGTTCATGAAC
553227 ATGTTC
1 ATGTTC
553233 GTTTAGTGTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.30, C:0.13, G:0.17, T:0.40
Consensus pattern (12 bp):
ATGTTCATGAAC
Found at i:553248 original size:11 final size:11
Alignment explanation
Indices: 553228--553258 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
553218 TTCATGAATA
*
553228 TGTTCGTTTAG
1 TGTTCATTTAG
553239 TGTTCATTTAG
1 TGTTCATTTAG
553250 TGTTCATTT
1 TGTTCATTT
553259 TAGCGTTGCT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.13, C:0.10, G:0.19, T:0.58
Consensus pattern (11 bp):
TGTTCATTTAG
Found at i:553656 original size:10 final size:10
Alignment explanation
Indices: 553641--553688 Score: 60
Period size: 10 Copynumber: 4.7 Consensus size: 10
553631 TTAGCATAAC
553641 AAACGAACAT
1 AAACGAACAT
*
553651 AAACGAATATT
1 AAACGAACA-T
*
553662 ATACGAACAT
1 AAACGAACAT
*
553672 AAATGAACAT
1 AAACGAACAT
553682 AAACGAA
1 AAACGAA
553689 GATTATACAA
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
10 23 0.74
11 8 0.26
ACGTcount: A:0.58, C:0.15, G:0.10, T:0.17
Consensus pattern (10 bp):
AAACGAACAT
Found at i:555186 original size:16 final size:16
Alignment explanation
Indices: 555165--555202 Score: 76
Period size: 16 Copynumber: 2.4 Consensus size: 16
555155 TGTCACGTTG
555165 ACTTTTCTAAATGTTC
1 ACTTTTCTAAATGTTC
555181 ACTTTTCTAAATGTTC
1 ACTTTTCTAAATGTTC
555197 ACTTTT
1 ACTTTT
555203 ACAAAAGAAC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.24, C:0.18, G:0.05, T:0.53
Consensus pattern (16 bp):
ACTTTTCTAAATGTTC
Found at i:556989 original size:16 final size:17
Alignment explanation
Indices: 556963--557001 Score: 71
Period size: 16 Copynumber: 2.4 Consensus size: 17
556953 ATAACATATA
556963 TATATATATATATACAT
1 TATATATATATATACAT
556980 TATA-ATATATATACAT
1 TATATATATATATACAT
556996 TATATA
1 TATATA
557002 ATCACAAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
16 16 0.76
17 5 0.24
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.46
Consensus pattern (17 bp):
TATATATATATATACAT
Found at i:558034 original size:106 final size:106
Alignment explanation
Indices: 557859--558945 Score: 1499
Period size: 106 Copynumber: 10.3 Consensus size: 106
557849 GCATTGTTCC
* * ** *
557859 GAGTCCAATATCCTCCG-TCGTGAAGTTGAAATTGGCT-TGGAACCGAGAAATTGTTTGTTGACC
1 GAGTCCAATATCCTTCGCT-GTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGA-C
* * * * *
557922 AGCCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTC
64 AACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
557965 AAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTTTGAAATTGGGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAA
* * * * *
558030 CCAGCCGTCCCTTTGTTTGTGAAGTTGAACTTGTGTTGTCTC
66 CCAGCGGTCCCTTCG-TCGTGAAGTTGAACTTGCGTTGTCTG
** * *
558072 GAGTATAATATCCTTCGCTGTGAAGTTGAAATTGACTCTG-AA-T---AAAAT-TTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAA
* * * * *
558131 TCAGCCGCCCCTTCGTCGTGAAGTTGAGCTTGTGTTGTCTTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTC-TG
* * * * *
558173 G-GTCCAAGATCCTTCGCTGAGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTAACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAA
* * * *
558237 TCAGCGGCCCCTTCGTTGTGAAGTTGAACTTGCGTTGTCTT
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
*
558278 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAA
* *
558343 CCAGCGGTCCCTTCGTTGTGATGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * * * *
558384 GAGTCCAATATCTTTCGTTGTGAAGTTGAAATTGGCTCCGAAATTGAGAAGTTATTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAA
558449 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
558490 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAA
558555 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * *
558596 GAGTCCAGTATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAA
558661 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * *
558702 GAGTCCAATATCCCTCGATGTGAAGTTAAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAA
* *
558767 CCAGCAGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTA
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
558808 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGATAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAA
* * *
558873 CCAGCGGTCCCTTCATCGTGAAGTTGAACTTGCGTTGTATC
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
** *
558914 GAGTCTGATATCCTTCGATGTGAAGTTGAAAT
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAAT
558946 CGCGGATGCC
Statistics
Matches: 885, Mismatches: 85, Indels: 22
0.89 0.09 0.02
Matches are distributed among these distances:
100 55 0.06
101 27 0.03
102 4 0.00
105 6 0.01
106 712 0.80
107 81 0.09
ACGTcount: A:0.23, C:0.18, G:0.25, T:0.34
Consensus pattern (106 bp):
GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAA
CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
Found at i:559453 original size:18 final size:18
Alignment explanation
Indices: 559427--559461 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
559417 GTTGAATCTT
* *
559427 CAAAGATGCCTCAATATC
1 CAAAAATGCCCCAATATC
559445 CAAAAATGCCCCAATAT
1 CAAAAATGCCCCAATAT
559462 TTGATGTTGA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.43, C:0.29, G:0.09, T:0.20
Consensus pattern (18 bp):
CAAAAATGCCCCAATATC
Found at i:559923 original size:22 final size:22
Alignment explanation
Indices: 559898--559940 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
559888 CATTTTTGTT
*
559898 CATTTGATGCTCAAAGGTTTGG
1 CATTGGATGCTCAAAGGTTTGG
*
559920 CATTGGATGTTCAAAGGTTTG
1 CATTGGATGCTCAAAGGTTTG
559941 ATGGGGTAGC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.23, C:0.12, G:0.28, T:0.37
Consensus pattern (22 bp):
CATTGGATGCTCAAAGGTTTGG
Found at i:564648 original size:2 final size:2
Alignment explanation
Indices: 564641--564698 Score: 77
Period size: 2 Copynumber: 30.5 Consensus size: 2
564631 TGTAAATAAC
*
564641 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AC AT -T AT A-
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
564681 AT AT AT AT AC AT -T AT AT A
1 AT AT AT AT AT AT AT AT AT A
564699 ATCACATATT
Statistics
Matches: 49, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
1 3 0.06
2 46 0.94
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:565260 original size:21 final size:21
Alignment explanation
Indices: 565207--565261 Score: 58
Period size: 21 Copynumber: 2.6 Consensus size: 21
565197 TAAGTGTACC
*
565207 AAAGTACCACATATATGTTCCA
1 AAAG-ACCACATATATGTCCCA
**
565229 AAAGATTACATATATGTCCCGA
1 AAAGACCACATATATGTCCC-A
565251 AAA-ACCACATA
1 AAAGACCACATA
565262 GAACCCTCGA
Statistics
Matches: 27, Mismatches: 5, Indels: 3
0.77 0.14 0.09
Matches are distributed among these distances:
21 19 0.70
22 8 0.30
ACGTcount: A:0.45, C:0.22, G:0.09, T:0.24
Consensus pattern (21 bp):
AAAGACCACATATATGTCCCA
Found at i:568049 original size:87 final size:87
Alignment explanation
Indices: 567947--568121 Score: 350
Period size: 87 Copynumber: 2.0 Consensus size: 87
567937 TAAACTCTGG
567947 TTTCCTTTATCTTATACACTTGTCACTGATGAACTTATTCTTGAACTCTTCTACAAATTCTAACC
1 TTTCCTTTATCTTATACACTTGTCACTGATGAACTTATTCTTGAACTCTTCTACAAATTCTAACC
568012 ACATCAGTTGATCTTTTAACGT
66 ACATCAGTTGATCTTTTAACGT
568034 TTTCCTTTATCTTATACACTTGTCACTGATGAACTTATTCTTGAACTCTTCTACAAATTCTAACC
1 TTTCCTTTATCTTATACACTTGTCACTGATGAACTTATTCTTGAACTCTTCTACAAATTCTAACC
568099 ACATCAGTTGATCTTTTAACGT
66 ACATCAGTTGATCTTTTAACGT
568121 T
1 T
568122 CTTATGGTGA
Statistics
Matches: 88, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
87 88 1.00
ACGTcount: A:0.26, C:0.23, G:0.08, T:0.43
Consensus pattern (87 bp):
TTTCCTTTATCTTATACACTTGTCACTGATGAACTTATTCTTGAACTCTTCTACAAATTCTAACC
ACATCAGTTGATCTTTTAACGT
Found at i:569622 original size:30 final size:32
Alignment explanation
Indices: 569587--569687 Score: 104
Period size: 30 Copynumber: 3.2 Consensus size: 32
569577 CATAGTACGT
569587 TGTCATATAAT-TCATAT-ATCACATATCTCA
1 TGTCATATAATCTCATATGATCACATATCTCA
* *
569617 TGTCATAT--TCTCATATGGTCACATAGCTCA
1 TGTCATATAATCTCATATGATCACATATCTCA
* * *
569647 TGTCACT-TAATCTCTTATGTTCACATATCACA
1 TGTCA-TATAATCTCATATGATCACATATCTCA
569679 TGATCATAT
1 TG-TCATAT
569688 CATTCCTTAT
Statistics
Matches: 58, Mismatches: 6, Indels: 11
0.77 0.08 0.15
Matches are distributed among these distances:
28 1 0.02
29 6 0.10
30 25 0.43
31 1 0.02
32 21 0.36
33 4 0.07
ACGTcount: A:0.31, C:0.22, G:0.08, T:0.40
Consensus pattern (32 bp):
TGTCATATAATCTCATATGATCACATATCTCA
Found at i:570863 original size:3 final size:3
Alignment explanation
Indices: 570855--570883 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
570845 ACTCATTGGC
570855 AGA AGA AGA AGA AGA AGA AGA AGA AGA AG
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AG
570884 CTACCTAAAC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:573503 original size:15 final size:15
Alignment explanation
Indices: 573483--573513 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
573473 GAAAGATGAG
*
573483 TTCATTTATATTCAC
1 TTCATTTACATTCAC
573498 TTCATTTACATTCAC
1 TTCATTTACATTCAC
573513 T
1 T
573514 AAGAAAATCT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.26, C:0.23, G:0.00, T:0.52
Consensus pattern (15 bp):
TTCATTTACATTCAC
Found at i:576913 original size:20 final size:21
Alignment explanation
Indices: 576877--576934 Score: 66
Period size: 20 Copynumber: 2.9 Consensus size: 21
576867 ATAGTCAGTG
*
576877 AGTATCGATAC-CAAGGGGTG
1 AGTATCGATACTCAAGGGGTC
* *
576897 GGTATCGATACTC-AGGGTTC
1 AGTATCGATACTCAAGGGGTC
*
576917 AGTATCGATACTGAAGGG
1 AGTATCGATACTCAAGGG
576935 CTAGTTCAGT
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
20 26 0.84
21 5 0.16
ACGTcount: A:0.28, C:0.16, G:0.33, T:0.24
Consensus pattern (21 bp):
AGTATCGATACTCAAGGGGTC
Found at i:577461 original size:22 final size:22
Alignment explanation
Indices: 577433--577483 Score: 93
Period size: 22 Copynumber: 2.3 Consensus size: 22
577423 CTAGTGAATG
577433 TGTGTAGTATAGTACAATTCTT
1 TGTGTAGTATAGTACAATTCTT
577455 TGTGTAGTATAGTACAATTCTT
1 TGTGTAGTATAGTACAATTCTT
*
577477 AGTGTAG
1 TGTGTAG
577484 CACTAAGCTC
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.27, C:0.08, G:0.22, T:0.43
Consensus pattern (22 bp):
TGTGTAGTATAGTACAATTCTT
Found at i:579474 original size:138 final size:138
Alignment explanation
Indices: 579224--579479 Score: 363
Period size: 138 Copynumber: 1.9 Consensus size: 138
579214 ACCAAAGTAC
* * * *
579224 CGAAATGGAAATTCACAAACTTATTATGAATTCCATGGATGCACACATAGTGTCGAAAGTACACA
1 CGAAATGGAAATTCACAAACTCATTATGAATACCATGGATGCACACATAGTGCCAAAAGTACACA
* *
579289 CAACACTAATACTAAAATGCACCGTTATGCATTAAACAAAATTGATCGATAACTTTTATGCATAA
66 CAACACTAATACAAAAATGCACCGTTATGCATTAAACAAAATCGATCGATAACTTTTATGCATAA
579354 TTGTATAA
131 TTGTATAA
** *
579362 CGAAATGGTGATTTACAAACTCATTATGAATACCAT-GATTGCACATC-TAGTGCCAAAAGTACA
1 CGAAATGGAAATTCACAAACTCATTATGAATACCATGGA-TGCACA-CATAGTGCCAAAAGTACA
* * * *
579425 TACAATACTGATACAAAAATGCACTGTTATGCATTAAACAAAATCGATCGATAAC
64 CACAACACTAATACAAAAATGCACCGTTATGCATTAAACAAAATCGATCGATAAC
579480 CATTACATAC
Statistics
Matches: 103, Mismatches: 13, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
137 2 0.02
138 100 0.97
139 1 0.01
ACGTcount: A:0.41, C:0.18, G:0.13, T:0.27
Consensus pattern (138 bp):
CGAAATGGAAATTCACAAACTCATTATGAATACCATGGATGCACACATAGTGCCAAAAGTACACA
CAACACTAATACAAAAATGCACCGTTATGCATTAAACAAAATCGATCGATAACTTTTATGCATAA
TTGTATAA
Found at i:599835 original size:23 final size:22
Alignment explanation
Indices: 599806--599878 Score: 87
Period size: 23 Copynumber: 3.3 Consensus size: 22
599796 TAAGGTACCA
*
599806 AAAGACAGAGAAAAACATGCCAC
1 AAAGACAGAG-AAAACATGTCAC
*
599829 AAAGACAGAGATAAACATGTCAT
1 AAAGACAGAGA-AAACATGTCAC
*
599852 AAAGGCAGAG--AACATGTCAC
1 AAAGACAGAGAAAACATGTCAC
599872 AAAGACA
1 AAAGACA
599879 TAATTATTCT
Statistics
Matches: 44, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
20 15 0.34
22 1 0.02
23 28 0.64
ACGTcount: A:0.53, C:0.18, G:0.19, T:0.10
Consensus pattern (22 bp):
AAAGACAGAGAAAACATGTCAC
Found at i:605189 original size:23 final size:21
Alignment explanation
Indices: 605163--605205 Score: 59
Period size: 23 Copynumber: 2.0 Consensus size: 21
605153 TACTATGTAT
*
605163 ATATTTTTTTAATATTATATTTA
1 ATATGTTTTT-ATA-TATATTTA
605186 ATATGTTTTTATATATATTT
1 ATATGTTTTTATATATATTT
605206 TCTTAATATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 7 0.37
22 3 0.16
23 9 0.47
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (21 bp):
ATATGTTTTTATATATATTTA
Found at i:605206 original size:37 final size:34
Alignment explanation
Indices: 605160--605254 Score: 106
Period size: 37 Copynumber: 2.8 Consensus size: 34
605150 ATTTACTATG
605160 TATATATTTTTTTAATATTATATTTAATATGTTTTTA
1 TATATATTTTTTTAATATTATATTT--T-TGTTTTTA
* *
605197 TATATATTTTCTTAATATTCTATTTTTGTTTTTA
1 TATATATTTTTTTAATATTATATTTTTGTTTTTA
* *
605231 T-T-TATTTATAT-ATATTATATTTTT
1 TATATATTTTTTTAATATTATATTTTT
605255 ACTTTATTTT
Statistics
Matches: 52, Mismatches: 6, Indels: 6
0.81 0.09 0.09
Matches are distributed among these distances:
31 12 0.23
32 6 0.12
33 1 0.02
34 9 0.17
35 1 0.02
37 23 0.44
ACGTcount: A:0.28, C:0.02, G:0.02, T:0.67
Consensus pattern (34 bp):
TATATATTTTTTTAATATTATATTTTTGTTTTTA
Found at i:605229 original size:59 final size:57
Alignment explanation
Indices: 605166--605293 Score: 127
Period size: 59 Copynumber: 2.2 Consensus size: 57
605156 TATGTATATA
* * *
605166 TTTTTTTAATATTATATTTAATATGTTTTTA-TATATATTTTCTTAATATTCTATT-TTTG
1 TTTTTTTAATATTATATATAATATATTTTTACT-T-TATTTTATT--TATTCTATTATTTG
* * *
605225 TTTTTATTTAT-TTATATATATTATATTTTTACTTTATTTTATTTTTTCTATTATTTG
1 TTTTT-TTAATATTATATATAATATATTTTTACTTTATTTTATTTATTCTATTATTTG
*
605282 TTTTCTTAATAT
1 TTTTTTTAATAT
605294 CATGTATATC
Statistics
Matches: 57, Mismatches: 8, Indels: 10
0.76 0.11 0.13
Matches are distributed among these distances:
56 12 0.21
57 9 0.16
58 8 0.14
59 23 0.40
60 5 0.09
ACGTcount: A:0.25, C:0.04, G:0.02, T:0.69
Consensus pattern (57 bp):
TTTTTTTAATATTATATATAATATATTTTTACTTTATTTTATTTATTCTATTATTTG
Found at i:605267 original size:16 final size:17
Alignment explanation
Indices: 605231--605280 Score: 52
Period size: 16 Copynumber: 3.1 Consensus size: 17
605221 TTTGTTTTTA
*
605231 TTTATTTATA-TA-TAT
1 TTTATTTTTACTATTAT
*
605246 TATATTTTTACT-TTAT
1 TTTATTTTTACTATTAT
*
605262 TTTATTTTTTCTATTAT
1 TTTATTTTTACTATTAT
605279 TT
1 TT
605281 GTTTTCTTAA
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
15 8 0.29
16 14 0.50
17 6 0.21
ACGTcount: A:0.24, C:0.04, G:0.00, T:0.72
Consensus pattern (17 bp):
TTTATTTTTACTATTAT
Done.