Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007925.1 Hibiscus syriacus cultivar Beakdansim tig00110331_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: 1316088
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 7
Found at i:225414 original size:2 final size:2
Alignment explanation
Indices: 225405--225439 Score: 54
Period size: 2 Copynumber: 18.0 Consensus size: 2
225395 ATACACACAC
*
225405 AT AT -T AT AT AT AT AT AT AT AT AT AT AT AC AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
225440 TTAAGAATTT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:226561 original size:13 final size:13
Alignment explanation
Indices: 226543--226589 Score: 60
Period size: 13 Copynumber: 3.6 Consensus size: 13
226533 ATTCCCTATC
*
226543 TTCTTCTTCACTT
1 TTCTTCTTCATTT
*
226556 TTCTTCTTCTTTCT
1 TTCTTCTTCATT-T
226570 TTC-TCTTCATTT
1 TTCTTCTTCATTT
226582 TTCTTCTT
1 TTCTTCTT
226590 TTCCTCTTAT
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
12 4 0.14
13 21 0.72
14 4 0.14
ACGTcount: A:0.04, C:0.28, G:0.00, T:0.68
Consensus pattern (13 bp):
TTCTTCTTCATTT
Found at i:226666 original size:3 final size:3
Alignment explanation
Indices: 226658--226694 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
226648 AACTTGCTTT
226658 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC A
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC A
226695 CCATTTCTTT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.35, C:0.32, G:0.00, T:0.32
Consensus pattern (3 bp):
ATC
Found at i:227984 original size:26 final size:27
Alignment explanation
Indices: 227947--228004 Score: 84
Period size: 26 Copynumber: 2.2 Consensus size: 27
227937 GGATAAGAGG
*
227947 AGAAGAAGAAAAGTGAAG-AGAA-AGAA
1 AGAAGAAAAAAAGTGAAGAAGAAGA-AA
227973 AGAAGAAAAAAAGTGAAGAAGAAGAAA
1 AGAAGAAAAAAAGTGAAGAAGAAGAAA
228000 AGAAG
1 AGAAG
228005 TAGAAGATGG
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
26 17 0.59
27 11 0.38
28 1 0.03
ACGTcount: A:0.67, C:0.00, G:0.29, T:0.03
Consensus pattern (27 bp):
AGAAGAAAAAAAGTGAAGAAGAAGAAA
Found at i:227996 original size:19 final size:20
Alignment explanation
Indices: 227972--228011 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 20
227962 AAGAGAAAGA
227972 AAGAAGAAAAAAAGT-GAAG
1 AAGAAGAAAAAAAGTAGAAG
*
227991 AAGAAGAAAAGAAGTAGAAG
1 AAGAAGAAAAAAAGTAGAAG
228011 A
1 A
228012 TGGGAACGAG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 14 0.74
20 5 0.26
ACGTcount: A:0.68, C:0.00, G:0.28, T:0.05
Consensus pattern (20 bp):
AAGAAGAAAAAAAGTAGAAG
Found at i:228041 original size:17 final size:17
Alignment explanation
Indices: 228019--228055 Score: 74
Period size: 17 Copynumber: 2.2 Consensus size: 17
228009 AGATGGGAAC
228019 GAGTTGAAAAAGAAGAA
1 GAGTTGAAAAAGAAGAA
228036 GAGTTGAAAAAGAAGAA
1 GAGTTGAAAAAGAAGAA
228053 GAG
1 GAG
228056 CCGAACAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.57, C:0.00, G:0.32, T:0.11
Consensus pattern (17 bp):
GAGTTGAAAAAGAAGAA
Found at i:228971 original size:20 final size:20
Alignment explanation
Indices: 228948--229007 Score: 55
Period size: 20 Copynumber: 3.4 Consensus size: 20
228938 ATTTATAAGA
228948 AAAATTTTGAGTCTAAATTT
1 AAAATTTTGAGTCTAAATTT
228968 AAAA-TTT-A---TAAGA---
1 AAAATTTTGAGTCTAA-ATTT
228981 AAAATTTTGAGTCTAAATTT
1 AAAATTTTGAGTCTAAATTT
229001 AAAATTT
1 AAAATTT
229008 GAAGGGTATA
Statistics
Matches: 31, Mismatches: 0, Indels: 18
0.63 0.00 0.37
Matches are distributed among these distances:
13 4 0.13
14 3 0.10
15 4 0.13
16 1 0.03
17 1 0.03
18 4 0.13
19 3 0.10
20 11 0.35
ACGTcount: A:0.47, C:0.03, G:0.08, T:0.42
Consensus pattern (20 bp):
AAAATTTTGAGTCTAAATTT
Found at i:228973 original size:33 final size:33
Alignment explanation
Indices: 228931--229007 Score: 154
Period size: 33 Copynumber: 2.3 Consensus size: 33
228921 CCCATATTGG
228931 ATTTAAAATTTATAAGAAAAATTTTGAGTCTAA
1 ATTTAAAATTTATAAGAAAAATTTTGAGTCTAA
228964 ATTTAAAATTTATAAGAAAAATTTTGAGTCTAA
1 ATTTAAAATTTATAAGAAAAATTTTGAGTCTAA
228997 ATTTAAAATTT
1 ATTTAAAATTT
229008 GAAGGGTATA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 44 1.00
ACGTcount: A:0.48, C:0.03, G:0.08, T:0.42
Consensus pattern (33 bp):
ATTTAAAATTTATAAGAAAAATTTTGAGTCTAA
Found at i:240557 original size:59 final size:59
Alignment explanation
Indices: 240474--240585 Score: 163
Period size: 59 Copynumber: 1.9 Consensus size: 59
240464 ATCTCTTGAT
*
240474 TATAGGGCACTGCTTTGGTGAGTCTCTCA-ACTATTAAAAGTTACAAAATGATCGTCAAC
1 TATAGGGCACTGCTTTGGTAAGTCT-TCACACTATTAAAAGTTACAAAATGATCGTCAAC
* * * *
240533 TATAGGGCGCTGTTTTGTTAAGTCTTTACACTATTAAAAGTTACAAAATGATC
1 TATAGGGCACTGCTTTGGTAAGTCTTCACACTATTAAAAGTTACAAAATGATC
240586 ATATGAGTAT
Statistics
Matches: 47, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
58 2 0.04
59 45 0.96
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.34
Consensus pattern (59 bp):
TATAGGGCACTGCTTTGGTAAGTCTTCACACTATTAAAAGTTACAAAATGATCGTCAAC
Found at i:244608 original size:77 final size:78
Alignment explanation
Indices: 244481--244635 Score: 303
Period size: 77 Copynumber: 2.0 Consensus size: 78
244471 TAAGATTTGG
244481 TCACTTTCGTTTCATTTTAATTAAGATGTGGCCACTGAATGTTAACGACTGTTAAACCTATAAC-
1 TCACTTTCGTTTCATTTTAATTAAGATGTGGCCACTGAATGTTAACGACTGTTAAACCTATAACG
244545 GTTTAGCTGACAT
66 GTTTAGCTGACAT
244558 TCACTTTCGTTTCATTTTAATTAAGATGTGGCCACTGAATGTTAACGACTGTTAAACCTATAACG
1 TCACTTTCGTTTCATTTTAATTAAGATGTGGCCACTGAATGTTAACGACTGTTAAACCTATAACG
244623 GTTTAGCTGACAT
66 GTTTAGCTGACAT
244636 GGCATGGTAA
Statistics
Matches: 77, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
77 64 0.83
78 13 0.17
ACGTcount: A:0.28, C:0.18, G:0.16, T:0.37
Consensus pattern (78 bp):
TCACTTTCGTTTCATTTTAATTAAGATGTGGCCACTGAATGTTAACGACTGTTAAACCTATAACG
GTTTAGCTGACAT
Found at i:244729 original size:31 final size:31
Alignment explanation
Indices: 244691--244772 Score: 119
Period size: 31 Copynumber: 2.6 Consensus size: 31
244681 ATAATACATG
* *
244691 TATTAAGTTTTGGTCATTTACATTATTATTT
1 TATTAAGTTTTGGTCACTTACATTATCATTT
* * *
244722 TATTAAGTTTTGGTCACTTACGTTGTCGTTT
1 TATTAAGTTTTGGTCACTTACATTATCATTT
244753 TATTAAGTTTTGGTCACTTA
1 TATTAAGTTTTGGTCACTTA
244773 GATGTTGAAT
Statistics
Matches: 46, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 46 1.00
ACGTcount: A:0.22, C:0.10, G:0.15, T:0.54
Consensus pattern (31 bp):
TATTAAGTTTTGGTCACTTACATTATCATTT
Found at i:245901 original size:31 final size:31
Alignment explanation
Indices: 245855--246022 Score: 202
Period size: 31 Copynumber: 5.5 Consensus size: 31
245845 CATCAAATCC
* * *
245855 AAGTGGCC-AAACTTAATAAAAAGATGACGT
1 AAGTGACCAAAACTTAATAAAAAGATAACAT
* * *
245885 ATGTGGCCAAAACTTAATAAATTA-ATAACAT
1 AAGTGACCAAAACTTAATAAA-AAGATAACAT
*
245916 AAGTGA-C-AAACTTAATAAAACGATAACAT
1 AAGTGACCAAAACTTAATAAAAAGATAACAT
*
245945 AAGTGACCAAAACTTAATAAAATGATAACAT
1 AAGTGACCAAAACTTAATAAAAAGATAACAT
*
245976 AAGTGACCAAAACTTAATAAAATA-ATAACGT
1 AAGTGACCAAAACTTAATAAAA-AGATAACAT
246007 AAGTGACCAAAACTTA
1 AAGTGACCAAAACTTA
246023 TGTTTTTTAA
Statistics
Matches: 121, Mismatches: 11, Indels: 11
0.85 0.08 0.08
Matches are distributed among these distances:
29 25 0.21
30 9 0.07
31 86 0.71
32 1 0.01
ACGTcount: A:0.52, C:0.14, G:0.12, T:0.23
Consensus pattern (31 bp):
AAGTGACCAAAACTTAATAAAAAGATAACAT
Found at i:245929 original size:60 final size:61
Alignment explanation
Indices: 245855--246022 Score: 232
Period size: 60 Copynumber: 2.8 Consensus size: 61
245845 CATCAAATCC
* * * * *
245855 AAGTGGCCAAACTTAATAAAAAGATGACGTATGTGGCCAAAACTTAATAAATTAATAACAT
1 AAGTGACCAAACTTAATAAAAAGATAACGTAAGTGACCAAAACTTAATAAAATAATAACAT
* * *
245916 AAGTGA-CAAACTTAATAAAACGATAACATAAGTGACCAAAACTTAATAAAATGATAACAT
1 AAGTGACCAAACTTAATAAAAAGATAACGTAAGTGACCAAAACTTAATAAAATAATAACAT
245976 AAGTGACCAAAACTTAATAAAATA-ATAACGTAAGTGACCAAAACTTA
1 AAGTGACC-AAACTTAATAAAA-AGATAACGTAAGTGACCAAAACTTA
246023 TGTTTTTTAA
Statistics
Matches: 94, Mismatches: 10, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
60 53 0.56
61 6 0.06
62 35 0.37
ACGTcount: A:0.52, C:0.14, G:0.12, T:0.23
Consensus pattern (61 bp):
AAGTGACCAAACTTAATAAAAAGATAACGTAAGTGACCAAAACTTAATAAAATAATAACAT
Found at i:245986 original size:91 final size:92
Alignment explanation
Indices: 245855--246022 Score: 241
Period size: 91 Copynumber: 1.8 Consensus size: 92
245845 CATCAAATCC
* * * * * *
245855 AAGTGGCCAAACTTAATAAAAAGATGACGTATGTGGCCAAAACTTAATAAATTAATAACATAAGT
1 AAGTGACCAAACTTAATAAAAAGATAACATAAGTGACCAAAACTTAATAAAATAATAACATAAGT
245920 GA-C-AAACTTAATAAAACGATAACAT
66 GACCAAAACTTAATAAAACGATAACAT
* *
245945 AAGTGACCAAAACTTAATAAAATGATAACATAAGTGACCAAAACTTAATAAAATAATAACGTAAG
1 AAGTGACC-AAACTTAATAAAAAGATAACATAAGTGACCAAAACTTAATAAAATAATAACATAAG
246010 TGACCAAAACTTA
65 TGACCAAAACTTA
246023 TGTTTTTTAA
Statistics
Matches: 67, Mismatches: 8, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
90 7 0.10
91 52 0.78
92 1 0.01
93 7 0.10
ACGTcount: A:0.52, C:0.14, G:0.12, T:0.23
Consensus pattern (92 bp):
AAGTGACCAAACTTAATAAAAAGATAACATAAGTGACCAAAACTTAATAAAATAATAACATAAGT
GACCAAAACTTAATAAAACGATAACAT
Found at i:246495 original size:104 final size:104
Alignment explanation
Indices: 246377--246584 Score: 400
Period size: 104 Copynumber: 2.0 Consensus size: 104
246367 AAACAAATAT
246377 ATTTATGACTATCATAAATTAAATATAATAATAATCGACTAATGATAGTCTGATAAGAAAAAAAA
1 ATTTATGACTATCATAAATTAAATATAATAATAATCGACTAATGATAGTCTGATAAGAAAAAAAA
246442 TGAACAATTGAGGCAATGACATG-ACAAAACGGATCACTC
66 TGAACAATTGAGGCAATGACATGCA-AAAACGGATCACTC
246481 ATTTATGACTATCATAAATTAAATATAATAATAATCGACTAATGATAGTCTGATAAGAAAAAAAA
1 ATTTATGACTATCATAAATTAAATATAATAATAATCGACTAATGATAGTCTGATAAGAAAAAAAA
246546 TGAACAATTGAGGCAATGACATGCAAAAACGGATCACTC
66 TGAACAATTGAGGCAATGACATGCAAAAACGGATCACTC
246585 TAACATCTCC
Statistics
Matches: 103, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
104 102 0.99
105 1 0.01
ACGTcount: A:0.48, C:0.12, G:0.13, T:0.26
Consensus pattern (104 bp):
ATTTATGACTATCATAAATTAAATATAATAATAATCGACTAATGATAGTCTGATAAGAAAAAAAA
TGAACAATTGAGGCAATGACATGCAAAAACGGATCACTC
Found at i:246878 original size:17 final size:17
Alignment explanation
Indices: 246851--246899 Score: 64
Period size: 17 Copynumber: 2.9 Consensus size: 17
246841 ATAATTATAT
*
246851 ATAAATAAAATTTTGAAA
1 ATAATTAAAATTTT-AAA
*
246869 A-GATTAAAATTTTAAA
1 ATAATTAAAATTTTAAA
246885 ATAATTAAAATTTTA
1 ATAATTAAAATTTTA
246900 CTGGAAAAGT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
16 4 0.15
17 22 0.81
18 1 0.04
ACGTcount: A:0.57, C:0.00, G:0.04, T:0.39
Consensus pattern (17 bp):
ATAATTAAAATTTTAAA
Found at i:248472 original size:14 final size:14
Alignment explanation
Indices: 248453--248482 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
248443 GAACTCAACT
*
248453 TTTCCAGCTTACCA
1 TTTCCAGATTACCA
248467 TTTCCAGATTACCA
1 TTTCCAGATTACCA
248481 TT
1 TT
248483 CGTCGGATTC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.23, C:0.30, G:0.07, T:0.40
Consensus pattern (14 bp):
TTTCCAGATTACCA
Found at i:249635 original size:34 final size:34
Alignment explanation
Indices: 249592--249670 Score: 149
Period size: 34 Copynumber: 2.3 Consensus size: 34
249582 TTCCGCAAAA
249592 ATTAATATTTCATATTCTCAATTTGTTCTCATCG
1 ATTAATATTTCATATTCTCAATTTGTTCTCATCG
*
249626 ATTAATATTTCATATTGTCAATTTGTTCTCATCG
1 ATTAATATTTCATATTCTCAATTTGTTCTCATCG
249660 ATTAATATTTC
1 ATTAATATTTC
249671 TGTTATATGA
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
34 44 1.00
ACGTcount: A:0.28, C:0.15, G:0.06, T:0.51
Consensus pattern (34 bp):
ATTAATATTTCATATTCTCAATTTGTTCTCATCG
Found at i:250455 original size:36 final size:37
Alignment explanation
Indices: 250415--250504 Score: 157
Period size: 36 Copynumber: 2.5 Consensus size: 37
250405 CATTTACGCC
250415 TAGGTAAAAGCTTAA-ACGTAATATGAACCTTAGCTT
1 TAGGTAAAAGCTTAATACGTAATATGAACCTTAGCTT
*
250451 TAGGTAAAAGC-TAATACGTAATATGAACTTTAGCTT
1 TAGGTAAAAGCTTAATACGTAATATGAACCTTAGCTT
250487 TAGGTAAAAGCTTAATAC
1 TAGGTAAAAGCTTAATAC
250505 TTATGAAATA
Statistics
Matches: 51, Mismatches: 1, Indels: 3
0.93 0.02 0.05
Matches are distributed among these distances:
35 3 0.06
36 42 0.82
37 6 0.12
ACGTcount: A:0.40, C:0.12, G:0.17, T:0.31
Consensus pattern (37 bp):
TAGGTAAAAGCTTAATACGTAATATGAACCTTAGCTT
Found at i:263940 original size:31 final size:30
Alignment explanation
Indices: 263873--264036 Score: 166
Period size: 31 Copynumber: 5.3 Consensus size: 30
263863 CCTGAGAGCT
* * * *
263873 TACCTAAGAAAGTTCTCAGGGCCACGGGTC
1 TACCCAAGAAAGATCTCAGGGCCGCGGGCC
263903 TACCCAAGAAAGATCTCAGGGCCGCAGGGCC
1 TACCCAAGAAAGATCTCAGGGCCGC-GGGCC
* * *
263934 TACCCAAGAATGATATCAGGGCCACGGAGCC
1 TACCCAAGAAAGATCTCAGGGCCGCGG-GCC
* *
263965 TACCCAAGAAAAAAATCCCAGGGCCGCGGGCC
1 TACCCAAG--AAAGATCTCAGGGCCGCGGGCC
* * * *
263997 TACCCAAGAATGATCTCAAGGCTGCAGAGCC
1 TACCCAAGAAAGATCTCAGGGCCGC-GGGCC
264028 TACCCAAGA
1 TACCCAAGA
264037 GTCACATTAT
Statistics
Matches: 111, Mismatches: 18, Indels: 9
0.80 0.13 0.07
Matches are distributed among these distances:
30 36 0.32
31 50 0.45
32 11 0.10
33 14 0.13
ACGTcount: A:0.32, C:0.30, G:0.25, T:0.13
Consensus pattern (30 bp):
TACCCAAGAAAGATCTCAGGGCCGCGGGCC
Found at i:264004 original size:63 final size:63
Alignment explanation
Indices: 263888--264036 Score: 196
Period size: 63 Copynumber: 2.4 Consensus size: 63
263878 AAGAAAGTTC
* * *
263888 TCAGGGCCACGG-GTCTACCCAAG-AAAGATCTCAGGGCCGCAGGGCCTACCCAAGAATGATA
1 TCAGGGCCACGGAGCCTACCCAAGAAAAAATCCCAGGGCCGCAGGGCCTACCCAAGAATGATA
*
263949 TCAGGGCCACGGAGCCTACCCAAGAAAAAAATCCCAGGGCCGC-GGGCCTACCCAAGAATGATC
1 TCAGGGCCACGGAGCCTACCCAAG-AAAAAATCCCAGGGCCGCAGGGCCTACCCAAGAATGATA
* ** *
264012 TCAAGGCTGCAGAGCCTACCCAAGA
1 TCAGGGCCACGGAGCCTACCCAAGA
264037 GTCACATTAT
Statistics
Matches: 77, Mismatches: 8, Indels: 5
0.86 0.09 0.06
Matches are distributed among these distances:
61 12 0.16
62 11 0.14
63 39 0.51
64 15 0.19
ACGTcount: A:0.31, C:0.32, G:0.26, T:0.11
Consensus pattern (63 bp):
TCAGGGCCACGGAGCCTACCCAAGAAAAAATCCCAGGGCCGCAGGGCCTACCCAAGAATGATA
Found at i:265518 original size:20 final size:20
Alignment explanation
Indices: 265493--265534 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
265483 AAATTGGCAT
* * *
265493 GGGGGTATCGGTACTATCTG
1 GGGGGTACCAGTACCATCTG
265513 GGGGGTACCAGTACCATCTG
1 GGGGGTACCAGTACCATCTG
265533 GG
1 GG
265535 CAATCTAGTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.17, C:0.19, G:0.40, T:0.24
Consensus pattern (20 bp):
GGGGGTACCAGTACCATCTG
Found at i:268164 original size:23 final size:23
Alignment explanation
Indices: 268134--268194 Score: 97
Period size: 23 Copynumber: 2.7 Consensus size: 23
268124 TACCCTCATG
268134 GGGGGTATCGATACCCATTC-AA
1 GGGGGTATCGATACCCATTCAAA
*
268156 GGATGGTATCGATACCCATTCAAA
1 GG-GGGTATCGATACCCATTCAAA
268180 GGGGGTATCGATACC
1 GGGGGTATCGATACC
268195 TAGCACGCAG
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
22 2 0.06
23 29 0.83
24 4 0.11
ACGTcount: A:0.28, C:0.21, G:0.28, T:0.23
Consensus pattern (23 bp):
GGGGGTATCGATACCCATTCAAA
Found at i:274179 original size:19 final size:19
Alignment explanation
Indices: 274155--274191 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
274145 TAAGTGACTA
* *
274155 GGGGGTATCAGTACCATCT
1 GGGGGTACCAATACCATCT
274174 GGGGGTACCAATACCATC
1 GGGGGTACCAATACCATC
274192 CGAGCATTAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.24, C:0.24, G:0.30, T:0.22
Consensus pattern (19 bp):
GGGGGTACCAATACCATCT
Found at i:274251 original size:19 final size:19
Alignment explanation
Indices: 274227--274268 Score: 75
Period size: 19 Copynumber: 2.2 Consensus size: 19
274217 AAAATTGGCA
*
274227 TGGGGGTATCGGTACCATC
1 TGGGGGTACCGGTACCATC
274246 TGGGGGTACCGGTACCATC
1 TGGGGGTACCGGTACCATC
274265 TGGG
1 TGGG
274269 CAATCTGGTT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.14, C:0.21, G:0.40, T:0.24
Consensus pattern (19 bp):
TGGGGGTACCGGTACCATC
Found at i:275859 original size:18 final size:18
Alignment explanation
Indices: 275829--275882 Score: 72
Period size: 18 Copynumber: 2.9 Consensus size: 18
275819 ACGGTCAACG
275829 GCTCAGTCGGCTTGGCTCA
1 GCTCAG-CGGCTTGGCTCA
*
275848 GCTCAGCGGCTTGGCTCG
1 GCTCAGCGGCTTGGCTCA
* *
275866 GCTTAGCGGCTCGGCTC
1 GCTCAGCGGCTTGGCTC
275883 GGTTTAGCGG
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
18 26 0.81
19 6 0.19
ACGTcount: A:0.07, C:0.33, G:0.35, T:0.24
Consensus pattern (18 bp):
GCTCAGCGGCTTGGCTCA
Found at i:275883 original size:18 final size:18
Alignment explanation
Indices: 275836--275899 Score: 83
Period size: 18 Copynumber: 3.6 Consensus size: 18
275826 ACGGCTCAGT
* * *
275836 CGGCTTGGCTCAGCTCAG
1 CGGCTCGGCTCGGCTTAG
*
275854 CGGCTTGGCTCGGCTTAG
1 CGGCTCGGCTCGGCTTAG
*
275872 CGGCTCGGCTCGGTTTAG
1 CGGCTCGGCTCGGCTTAG
275890 CGGCTCGGCT
1 CGGCTCGGCT
275900 AAGTGGCTCA
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 42 1.00
ACGTcount: A:0.06, C:0.31, G:0.38, T:0.25
Consensus pattern (18 bp):
CGGCTCGGCTCGGCTTAG
Found at i:279015 original size:231 final size:228
Alignment explanation
Indices: 278696--279197 Score: 693
Period size: 231 Copynumber: 2.2 Consensus size: 228
278686 AAAGTAGTTG
*
278696 TAAAGTTTATGTTCAAATTTAATTATAAATATTTATTATATTAAAGATATCTAAAAATAAAATTT
1 TAAAGTTTATGTTCAAATTTAATTATAAATATTTATAATATTAAAGATATCTAAAAATAAAATTT
* * *
278761 TAAAATCATAATATAATTTGAAGTGAAAAATATATAATTTAAACTATATATTCTTATTAGGATGA
66 TAAAATCATAATAAAATTTGAAGTGAAAAATATATAATTTAAACTATATATTCTTAATAAGATGA
** * * * * *
278826 GTATTTGATGGATTCGAATCAAAATGTTTTGAGTTGGTTGAGTCGATAACTCTTATTCTAGGATT
131 GTATTTGATCAATTCGAATAAAAAGGTTTTGAGTTAGTTGAGTCAATAACTCCTATTCTAGGATT
* * * *
278891 CAAATTTTATTTGAAACTCTTTTGATTCTAATTT
196 CAAA-TTTAATCGAAACTCTTTAGACTCTAATTT
* *
278925 TAAAGTTTTTGTTCAAAAATTTAATTATAAATATTTATAATATTAAGGATATCT-AAAATGAAAA
1 TAAAGTTTATGTTC--AAATTTAATTATAAATATTTATAATATTAAAGATATCTAAAAAT-AAAA
278989 -TTTAAAATCATAAATAAAATTTGAAGTGAAAAATATATAATTTAAACTATATATTCTTAATAAG
63 TTTTAAAATCAT-AATAAAATTTGAAGTGAAAAATATATAATTTAAACTATATATTCTTAATAAG
* * * *
279053 ATTAGTATTTGATCAATTTGAATAAAAAGGTTTTGAGTTAGTTGAGTTAATAAGTCCTATTCTAG
127 ATGAGTATTTGATCAATTCGAATAAAAAGGTTTTGAGTTAGTTGAGTCAATAACTCCTATTCTAG
* * *
279118 GATTTAAATTTAATCGAAATTCTTTAGACTCTAGTTT
192 GATTCAAATTTAATCGAAACTCTTTAGACTCTAATTT
* * * *
279155 TAAAATTTCTGTTTAAATTTAATTATAAATATTTATAGTATTA
1 TAAAGTTTATGTTCAAATTTAATTATAAATATTTATAATATTA
279198 TATTGTATCT
Statistics
Matches: 241, Mismatches: 28, Indels: 9
0.87 0.10 0.03
Matches are distributed among these distances:
228 28 0.12
229 13 0.05
230 50 0.21
231 150 0.62
ACGTcount: A:0.41, C:0.06, G:0.11, T:0.43
Consensus pattern (228 bp):
TAAAGTTTATGTTCAAATTTAATTATAAATATTTATAATATTAAAGATATCTAAAAATAAAATTT
TAAAATCATAATAAAATTTGAAGTGAAAAATATATAATTTAAACTATATATTCTTAATAAGATGA
GTATTTGATCAATTCGAATAAAAAGGTTTTGAGTTAGTTGAGTCAATAACTCCTATTCTAGGATT
CAAATTTAATCGAAACTCTTTAGACTCTAATTT
Found at i:280306 original size:20 final size:19
Alignment explanation
Indices: 280283--280326 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
280273 ATTTTTAAAA
280283 TATTTAAATAATTTATTTAT
1 TATTTAAAT-ATTTATTTAT
* *
280303 TATTAAAATATTTTTTTAT
1 TATTTAAATATTTATTTAT
*
280322 AATTT
1 TATTT
280327 TATTAATAAA
Statistics
Matches: 20, Mismatches: 4, Indels: 1
0.80 0.16 0.04
Matches are distributed among these distances:
19 12 0.60
20 8 0.40
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (19 bp):
TATTTAAATATTTATTTAT
Found at i:280315 original size:19 final size:20
Alignment explanation
Indices: 280283--280321 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 20
280273 ATTTTTAAAA
*
280283 TATTTAAATAATTTATTTAT
1 TATTAAAATAATTTATTTAT
*
280303 TATTAAAAT-ATTTTTTTAT
1 TATTAAAATAATTTATTTAT
280322 AATTTTATTA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (20 bp):
TATTAAAATAATTTATTTAT
Found at i:280511 original size:19 final size:19
Alignment explanation
Indices: 280443--280523 Score: 64
Period size: 19 Copynumber: 4.3 Consensus size: 19
280433 TTAAATATCT
280443 TTATTAA-AATATTATTAGA
1 TTATTAATAATATTATTA-A
280462 TTATTATATTAATATTA--AA
1 TTATTA-A-TAATATTATTAA
* *
280481 TATATAAATAATATTATTCA
1 T-TATTAATAATATTATTAA
*
280501 TTATTAATAAT-TTAATAA
1 TTATTAATAATATTATTAA
280519 -TATTA
1 TTATTA
280524 TTTCTATGAA
Statistics
Matches: 51, Mismatches: 5, Indels: 14
0.73 0.07 0.20
Matches are distributed among these distances:
17 5 0.10
18 13 0.25
19 18 0.35
20 8 0.16
22 7 0.14
ACGTcount: A:0.48, C:0.01, G:0.01, T:0.49
Consensus pattern (19 bp):
TTATTAATAATATTATTAA
Found at i:280822 original size:13 final size:13
Alignment explanation
Indices: 280804--280836 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
280794 TACCAAAGAT
280804 GTGTCGGATTCGG
1 GTGTCGGATTCGG
280817 GTGTCGGATTCGG
1 GTGTCGGATTCGG
*
280830 GAGTCGG
1 GTGTCGG
280837 TTACCAAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.09, C:0.15, G:0.48, T:0.27
Consensus pattern (13 bp):
GTGTCGGATTCGG
Found at i:280882 original size:2 final size:2
Alignment explanation
Indices: 280877--280903 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
280867 AACGAAAATA
280877 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
280904 AAGTTATAAG
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:281090 original size:2 final size:2
Alignment explanation
Indices: 281083--281107 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
281073 TTAAAGAAAC
281083 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 A
281108 ATAAAATATA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:281178 original size:18 final size:17
Alignment explanation
Indices: 281155--281224 Score: 62
Period size: 18 Copynumber: 4.4 Consensus size: 17
281145 ATATATACGT
281155 ATAATAATAATAACATGA
1 ATAATAATAATAA-ATGA
*
281173 ATAATAAAAATAAATGA
1 ATAATAATAATAAATGA
*
281190 ATAA-AAT-ATACAT--
1 ATAATAATAATAAATGA
281203 ATAAT-A-AATAAATGA
1 ATAATAATAATAAATGA
281218 ACTAATA
1 A-TAATA
281225 TAGATTTTTA
Statistics
Matches: 42, Mismatches: 4, Indels: 13
0.71 0.07 0.22
Matches are distributed among these distances:
13 10 0.24
15 6 0.14
16 6 0.14
17 8 0.19
18 12 0.29
ACGTcount: A:0.64, C:0.04, G:0.04, T:0.27
Consensus pattern (17 bp):
ATAATAATAATAAATGA
Found at i:281618 original size:35 final size:35
Alignment explanation
Indices: 281574--281645 Score: 135
Period size: 35 Copynumber: 2.1 Consensus size: 35
281564 CTATAAAACC
281574 CTATGTTAGACTAGTATTTGAGTCCTAATCCAACT
1 CTATGTTAGACTAGTATTTGAGTCCTAATCCAACT
*
281609 CTATTTTAGACTAGTATTTGAGTCCTAATCCAACT
1 CTATGTTAGACTAGTATTTGAGTCCTAATCCAACT
281644 CT
1 CT
281646 TCTTTTTTGG
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.28, C:0.21, G:0.12, T:0.39
Consensus pattern (35 bp):
CTATGTTAGACTAGTATTTGAGTCCTAATCCAACT
Found at i:282592 original size:106 final size:106
Alignment explanation
Indices: 282352--282787 Score: 696
Period size: 106 Copynumber: 4.1 Consensus size: 106
282342 TCCAAGTAGG
* * * * * * *
282352 TTGTATTGTTTCGAGTCCAATATCC-TCTGCCGTGAAGTTGAAATTGGTTTTGGAACTGGGAAAT
1 TTGTGTTGTCTCGAGTCCAATATCCTTC-GCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAAT
282416 TGTTTGTTGACAACCAGTCGT-CCTTCGTTGTGAAGTTGAAC
65 TGTTTGTTGACAACCAGTCGTCCCTTCGTTGTGAAGTTGAAC
*
282457 TTGTGTTGTCTCGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGTTCTGAAATTGGGAAATT
1 TTGTGTTGTCTCGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATT
* *
282522 GTTTGTTAACAACCAGCCGTCCCTTCGTTGTGAAGTTGAAC
66 GTTTGTTGACAACCAGTCGTCCCTTCGTTGTGAAGTTGAAC
* ** *
282563 TTGTGCTGTCTCGAGTCCAATGCCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTAGGAAATT
1 TTGTGTTGTCTCGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATT
282628 GTTTGTTGACAACCAGTCGTCCCTTCGTTGTGAAGTTGAAC
66 GTTTGTTGACAACCAGTCGTCCCTTCGTTGTGAAGTTGAAC
* * *
282669 TTGTGTTGTCTTGAGTCCAATATCATTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTT
1 TTGTGTTGTCTCGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATT
282734 GTTTGTTGACAACCAGTCGTCCCTTCGTTGTGAAGTTGAAC
66 GTTTGTTGACAACCAGTCGTCCCTTCGTTGTGAAGTTGAAC
282775 TTGTGTTGTCTCG
1 TTGTGTTGTCTCG
282788 GGTGGCGCGA
Statistics
Matches: 306, Mismatches: 23, Indels: 3
0.92 0.07 0.01
Matches are distributed among these distances:
105 74 0.24
106 232 0.76
ACGTcount: A:0.21, C:0.17, G:0.25, T:0.36
Consensus pattern (106 bp):
TTGTGTTGTCTCGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATT
GTTTGTTGACAACCAGTCGTCCCTTCGTTGTGAAGTTGAAC
Found at i:283733 original size:32 final size:32
Alignment explanation
Indices: 283689--283805 Score: 110
Period size: 32 Copynumber: 3.6 Consensus size: 32
283679 GAGCACGATT
*
283689 CCCTTCGTCGTGAAGTTGAAACCGTGGGTGGC
1 CCCTTCGCCGTGAAGTTGAAACCGTGGGTGGC
* * **** *
283721 CCCTTCACCGTGAAGTTG-AGCCAGAAATTGGATA
1 CCCTTCGCCGTGAAGTTGAAACC-GTGGGTGG--C
* *
283755 TCCTTCGTCGTGAAGTTGAAACCGTGGGTGGC
1 CCCTTCGCCGTGAAGTTGAAACCGTGGGTGGC
283787 CCCTTCGCCGTGAAGTTGA
1 CCCTTCGCCGTGAAGTTGA
283806 GCTAGAAATT
Statistics
Matches: 62, Mismatches: 19, Indels: 8
0.70 0.21 0.09
Matches are distributed among these distances:
31 3 0.05
32 37 0.60
34 19 0.31
35 3 0.05
ACGTcount: A:0.20, C:0.25, G:0.30, T:0.26
Consensus pattern (32 bp):
CCCTTCGCCGTGAAGTTGAAACCGTGGGTGGC
Found at i:283767 original size:34 final size:34
Alignment explanation
Indices: 283729--283839 Score: 111
Period size: 34 Copynumber: 3.3 Consensus size: 34
283719 GCCCCTTCAC
283729 CGTGAAGTTGAGCCAGAAATTGGATATCCTTCGT
1 CGTGAAGTTGAGCCAGAAATTGGATATCCTTCGT
* **** ** *
283763 CGTGAAGTTGAAACC-GTGGGTGG--CCCCTTCGC
1 CGTGAAGTTG-AGCCAGAAATTGGATATCCTTCGT
*
283795 CGTGAAGTTGAGCTAGAAATTGGATATCCTTCGT
1 CGTGAAGTTGAGCCAGAAATTGGATATCCTTCGT
283829 CGTGAAGTTGA
1 CGTGAAGTTGA
283840 AATCCAACTT
Statistics
Matches: 56, Mismatches: 17, Indels: 8
0.69 0.21 0.10
Matches are distributed among these distances:
31 2 0.04
32 20 0.36
34 31 0.55
35 3 0.05
ACGTcount: A:0.23, C:0.19, G:0.30, T:0.28
Consensus pattern (34 bp):
CGTGAAGTTGAGCCAGAAATTGGATATCCTTCGT
Found at i:283798 original size:66 final size:66
Alignment explanation
Indices: 283690--283841 Score: 286
Period size: 66 Copynumber: 2.3 Consensus size: 66
283680 AGCACGATTC
283690 CCTTCGTCGTGAAGTTGAAACCGTGGGTGGCCCCTTCACCGTGAAGTTGAGCCAGAAATTGGATA
1 CCTTCGTCGTGAAGTTGAAACCGTGGGTGGCCCCTTCACCGTGAAGTTGAGCCAGAAATTGGATA
283755 T
66 T
* *
283756 CCTTCGTCGTGAAGTTGAAACCGTGGGTGGCCCCTTCGCCGTGAAGTTGAGCTAGAAATTGGATA
1 CCTTCGTCGTGAAGTTGAAACCGTGGGTGGCCCCTTCACCGTGAAGTTGAGCCAGAAATTGGATA
283821 T
66 T
283822 CCTTCGTCGTGAAGTTGAAA
1 CCTTCGTCGTGAAGTTGAAA
283842 TCCAACTTGA
Statistics
Matches: 84, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
66 84 1.00
ACGTcount: A:0.22, C:0.22, G:0.29, T:0.27
Consensus pattern (66 bp):
CCTTCGTCGTGAAGTTGAAACCGTGGGTGGCCCCTTCACCGTGAAGTTGAGCCAGAAATTGGATA
T
Found at i:284252 original size:18 final size:18
Alignment explanation
Indices: 284225--284260 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
284215 GATTGAATCC
*
284225 CCAAAGATGCCCCAATAT
1 CCAAAAATGCCCCAATAT
284243 CCAAAAATGCCCCAATAT
1 CCAAAAATGCCCCAATAT
284261 TTGATGTTGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.42, C:0.33, G:0.08, T:0.17
Consensus pattern (18 bp):
CCAAAAATGCCCCAATAT
Found at i:288815 original size:10 final size:9
Alignment explanation
Indices: 288796--288849 Score: 65
Period size: 10 Copynumber: 5.8 Consensus size: 9
288786 ACAATTAGTA
288796 AAATAAAAAT
1 AAAT-AAAAT
288806 AAATAGAAAT
1 AAATA-AAAT
288816 AAATAAAAAT
1 AAAT-AAAAT
288826 AAATAAAA-
1 AAATAAAAT
*
288834 AAATAAAAA
1 AAATAAAAT
288843 AAATAAA
1 AAATAAA
288850 TGTCAAGAAA
Statistics
Matches: 41, Mismatches: 0, Indels: 7
0.85 0.00 0.15
Matches are distributed among these distances:
8 8 0.20
9 12 0.29
10 20 0.49
11 1 0.02
ACGTcount: A:0.81, C:0.00, G:0.02, T:0.17
Consensus pattern (9 bp):
AAATAAAAT
Found at i:288821 original size:14 final size:13
Alignment explanation
Indices: 288802--288850 Score: 53
Period size: 14 Copynumber: 3.6 Consensus size: 13
288792 AGTAAAATAA
288802 AAATAAATAGAAAT
1 AAATAAATA-AAAT
*
288816 AAATAAAAATAAAT
1 AAATAAATA-AAAT
* *
288830 AAAAAAATAAAAA
1 AAATAAATAAAAT
288843 AAATAAAT
1 AAATAAAT
288851 GTCAAGAAAA
Statistics
Matches: 29, Mismatches: 6, Indels: 1
0.81 0.17 0.03
Matches are distributed among these distances:
13 10 0.34
14 19 0.66
ACGTcount: A:0.80, C:0.00, G:0.02, T:0.18
Consensus pattern (13 bp):
AAATAAATAAAAT
Found at i:288821 original size:20 final size:18
Alignment explanation
Indices: 288795--288849 Score: 85
Period size: 20 Copynumber: 3.0 Consensus size: 18
288785 AACAATTAGT
288795 AAAATAAAAATAAATAGAA
1 AAAATAAAAATAAATA-AA
288814 ATAAATAAAAATAAATAAA
1 A-AAATAAAAATAAATAAA
288833 AAAATAAAAA-AAATAAA
1 AAAATAAAAATAAATAAA
288850 TGTCAAGAAA
Statistics
Matches: 35, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
17 7 0.20
18 9 0.26
19 4 0.11
20 15 0.43
ACGTcount: A:0.82, C:0.00, G:0.02, T:0.16
Consensus pattern (18 bp):
AAAATAAAAATAAATAAA
Found at i:289966 original size:38 final size:40
Alignment explanation
Indices: 289897--289976 Score: 112
Period size: 40 Copynumber: 2.0 Consensus size: 40
289887 ATGAAATATA
*
289897 TATATATATATACATCAAAGTATTAATAAAATA-AATAAGC
1 TATATATATATACAACAAAGTATTAATAAAATAGAA-AAGC
*
289937 TATATATATATACAACAAA-TATTTA-AAAATAGAAAAGC
1 TATATATATATACAACAAAGTATTAATAAAATAGAAAAGC
289975 TA
1 TA
289977 CCCTCTCACT
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
38 12 0.32
39 7 0.19
40 18 0.49
ACGTcount: A:0.56, C:0.07, G:0.05, T:0.31
Consensus pattern (40 bp):
TATATATATATACAACAAAGTATTAATAAAATAGAAAAGC
Found at i:290221 original size:2 final size:2
Alignment explanation
Indices: 290175--290204 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
290165 AAACAAAATA
290175 AT AT AT AT AT AT AT AT AT AT A- AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
290205 AAGTTATAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:290384 original size:2 final size:2
Alignment explanation
Indices: 290377--290409 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
290367 TTAAAGAAAC
290377 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
290410 ATAAAATATA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:290483 original size:18 final size:17
Alignment explanation
Indices: 290460--290529 Score: 62
Period size: 18 Copynumber: 4.4 Consensus size: 17
290450 ATATATGCGT
290460 ATAATAATAATAACATGA
1 ATAATAATAATAA-ATGA
*
290478 ATAATAAAAATAAATGA
1 ATAATAATAATAAATGA
*
290495 ATAA-AAT-ATACAT--
1 ATAATAATAATAAATGA
290508 ATAAT-A-AATAAATGA
1 ATAATAATAATAAATGA
290523 ACTAATA
1 A-TAATA
290530 TAGATTTTTA
Statistics
Matches: 42, Mismatches: 4, Indels: 13
0.71 0.07 0.22
Matches are distributed among these distances:
13 10 0.24
15 6 0.14
16 6 0.14
17 8 0.19
18 12 0.29
ACGTcount: A:0.64, C:0.04, G:0.04, T:0.27
Consensus pattern (17 bp):
ATAATAATAATAAATGA
Found at i:290920 original size:35 final size:35
Alignment explanation
Indices: 290876--290952 Score: 136
Period size: 35 Copynumber: 2.2 Consensus size: 35
290866 CTATAAAACC
*
290876 CTATGTTAGACTAGTATTTGAGTCCTAATCCAACT
1 CTATTTTAGACTAGTATTTGAGTCCTAATCCAACT
290911 CTATTTTAGACTAGTATTTGAGTCCTAATCCAACT
1 CTATTTTAGACTAGTATTTGAGTCCTAATCCAACT
*
290946 CTTTTTT
1 CTATTTT
290953 TTGGTTACAT
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
35 40 1.00
ACGTcount: A:0.26, C:0.19, G:0.12, T:0.43
Consensus pattern (35 bp):
CTATTTTAGACTAGTATTTGAGTCCTAATCCAACT
Found at i:299013 original size:19 final size:20
Alignment explanation
Indices: 298989--299036 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 20
298979 AACGATTTTC
*
298989 TTTTGAAAACAAAAAT-AGA
1 TTTTGAAAACAAAAATGAAA
* *
299008 TTTTGAAAGCCAAAATGAAA
1 TTTTGAAAACAAAAATGAAA
299028 TTTTGAAAA
1 TTTTGAAAA
299037 AGGATTTAGA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 14 0.58
20 10 0.42
ACGTcount: A:0.52, C:0.06, G:0.12, T:0.29
Consensus pattern (20 bp):
TTTTGAAAACAAAAATGAAA
Found at i:299337 original size:37 final size:37
Alignment explanation
Indices: 299291--299402 Score: 170
Period size: 37 Copynumber: 3.0 Consensus size: 37
299281 AACACAGCGT
299291 TAGAGTTTTACTAGGATTCAAACTCCTAAAAATAGGA
1 TAGAGTTTTACTAGGATTCAAACTCCTAAAAATAGGA
* * *
299328 TAGAATTTTAATAGGATTCAAACTTCTAAAAATAGGA
1 TAGAGTTTTACTAGGATTCAAACTCCTAAAAATAGGA
* * *
299365 TAGAGTTCTACTATGAGTCAAACTCCTAAAAATAGGA
1 TAGAGTTTTACTAGGATTCAAACTCCTAAAAATAGGA
299402 T
1 T
299403 CCATAAGCAT
Statistics
Matches: 66, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
37 66 1.00
ACGTcount: A:0.42, C:0.12, G:0.15, T:0.30
Consensus pattern (37 bp):
TAGAGTTTTACTAGGATTCAAACTCCTAAAAATAGGA
Found at i:299363 original size:21 final size:21
Alignment explanation
Indices: 299302--299365 Score: 59
Period size: 21 Copynumber: 3.3 Consensus size: 21
299292 AGAGTTTTAC
*
299302 TAGGATTCAAACTCCTAAAAA
1 TAGGATTCAAACTTCTAAAAA
*
299323 TAGGA-T-AGAA-TT-T--TAA
1 TAGGATTCA-AACTTCTAAAAA
299339 TAGGATTCAAACTTCTAAAAA
1 TAGGATTCAAACTTCTAAAAA
299360 TAGGAT
1 TAGGAT
299366 AGAGTTCTAC
Statistics
Matches: 33, Mismatches: 3, Indels: 14
0.66 0.06 0.28
Matches are distributed among these distances:
16 7 0.21
17 3 0.09
18 4 0.12
19 3 0.09
20 3 0.09
21 13 0.39
ACGTcount: A:0.45, C:0.11, G:0.14, T:0.30
Consensus pattern (21 bp):
TAGGATTCAAACTTCTAAAAA
Found at i:300014 original size:43 final size:43
Alignment explanation
Indices: 299937--300071 Score: 121
Period size: 43 Copynumber: 3.3 Consensus size: 43
299927 TTTACTTTAG
* *
299937 TATA-TATTTTTATT-TTT-TTTAGATTACATATATATATATATA
1 TATATTATTTTTATTATTTGTTT-TATTA-ATTTATATATATATA
* *
299979 TATGTTATTTTTATTATTTGTTTTATTAATTTATATACATAT-
1 TATATTATTTTTATTATTTGTTTTATTAATTTATATATATATA
* *
300021 T-TACTATTGTT-TTA--TG-TTT-TT-ATTTATATATATATA
1 TATATTATTTTTATTATTTGTTTTATTAATTTATATATATATA
300057 TATATTATTTTTATT
1 TATATTATTTTTATT
300072 TGTTATTATT
Statistics
Matches: 77, Mismatches: 10, Indels: 16
0.75 0.10 0.16
Matches are distributed among these distances:
35 13 0.17
36 3 0.04
37 11 0.14
38 4 0.05
40 3 0.04
41 7 0.09
42 4 0.05
43 22 0.29
44 7 0.09
45 3 0.04
ACGTcount: A:0.30, C:0.02, G:0.04, T:0.64
Consensus pattern (43 bp):
TATATTATTTTTATTATTTGTTTTATTAATTTATATATATATA
Found at i:300094 original size:16 final size:16
Alignment explanation
Indices: 300055--300098 Score: 56
Period size: 15 Copynumber: 2.8 Consensus size: 16
300045 TATATATATA
300055 TATATATTATTTTTATT
1 TATATATTA-TTTTATT
*
300072 TGT-TATTATTTTATT
1 TATATATTATTTTATT
300087 TATATATT-TTTT
1 TATATATTATTTT
300099 TCTTCTTTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
15 13 0.54
16 9 0.38
17 2 0.08
ACGTcount: A:0.25, C:0.00, G:0.02, T:0.73
Consensus pattern (16 bp):
TATATATTATTTTATT
Found at i:300099 original size:16 final size:16
Alignment explanation
Indices: 300055--300099 Score: 56
Period size: 16 Copynumber: 2.8 Consensus size: 16
300045 TATATATATA
300055 TATATATTATTTTTATT
1 TATATATT-TTTTTATT
* *
300072 TGT-TATTATTTTATT
1 TATATATTTTTTTATT
300087 TATATATTTTTTT
1 TATATATTTTTTT
300100 CTTCTTTTTA
Statistics
Matches: 23, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
15 9 0.39
16 12 0.52
17 2 0.09
ACGTcount: A:0.24, C:0.00, G:0.02, T:0.73
Consensus pattern (16 bp):
TATATATTTTTTTATT
Found at i:300139 original size:21 final size:21
Alignment explanation
Indices: 300038--300139 Score: 93
Period size: 21 Copynumber: 4.8 Consensus size: 21
300028 TGTTTTATGT
* *
300038 TTTTATTTATATATATATATA
1 TTTTATTTATATATTTTTATA
*
300059 TATTATTT-T-TATTTGTTATTA
1 TTTTATTTATATATTT-TTA-TA
* *
300080 TTTTATTTATATATTTTTTTC
1 TTTTATTTATATATTTTTATA
300101 TTCTT-TTTATATATTTTTTATA
1 TT-TTATTTATATA-TTTTTATA
*
300123 TTTTATTTATTTATTTT
1 TTTTATTTATATATTTT
300140 ACTTACTATT
Statistics
Matches: 65, Mismatches: 9, Indels: 14
0.74 0.10 0.16
Matches are distributed among these distances:
19 4 0.06
20 3 0.05
21 33 0.51
22 20 0.31
23 5 0.08
ACGTcount: A:0.25, C:0.02, G:0.01, T:0.73
Consensus pattern (21 bp):
TTTTATTTATATATTTTTATA
Found at i:300152 original size:43 final size:44
Alignment explanation
Indices: 300068--300153 Score: 106
Period size: 43 Copynumber: 2.0 Consensus size: 44
300058 ATATTATTTT
* *
300068 TATTTGTTATTATTTTATTTATATATTTTTTTCTTCTTTTTATA
1 TATTTGTTATTATTTTATTTATATATATTTTACTTCTTTTTATA
*
300112 TATTTTTTA-TATTTTATTTAT-T-TATTTTACTTACTATTTTAT
1 TATTTGTTATTATTTTATTTATATATATTTTACTT-CT-TTTTAT
300154 CTTTTCTTTC
Statistics
Matches: 37, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
41 8 0.22
42 3 0.08
43 18 0.49
44 8 0.22
ACGTcount: A:0.22, C:0.05, G:0.01, T:0.72
Consensus pattern (44 bp):
TATTTGTTATTATTTTATTTATATATATTTTACTTCTTTTTATA
Found at i:303315 original size:69 final size:69
Alignment explanation
Indices: 303197--303334 Score: 213
Period size: 69 Copynumber: 2.0 Consensus size: 69
303187 GATTCAAACT
* * *
303197 ATGAGATTGATCAAGCACATTCATTTTTGAATCACTGAACCACTTCACTCAAAGATCATAGAGCA
1 ATGAGATTGATCAAGCACAATCATTTCTGAATCACTGAACCACTCCACTCAAAGATCATAGAGCA
303262 TCAA
66 TCAA
* * * *
303266 ATGAGATTGATCAAGTACAATCATTTCTGAATCATTGAATCACTCCACTCGAAGATCATAGAGCA
1 ATGAGATTGATCAAGCACAATCATTTCTGAATCACTGAACCACTCCACTCAAAGATCATAGAGCA
303331 TCAA
66 TCAA
303335 GAGAGAGACA
Statistics
Matches: 62, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
69 62 1.00
ACGTcount: A:0.38, C:0.21, G:0.14, T:0.28
Consensus pattern (69 bp):
ATGAGATTGATCAAGCACAATCATTTCTGAATCACTGAACCACTCCACTCAAAGATCATAGAGCA
TCAA
Found at i:304239 original size:32 final size:32
Alignment explanation
Indices: 304214--304296 Score: 121
Period size: 32 Copynumber: 2.6 Consensus size: 32
304204 GCATCTTTGA
* *
304214 AGATTCAACATCAGATGTTGGGGCATTTTTTT
1 AGATTCAACATCAAATATTGGGGCATTTTTTT
* *
304246 AGATTTAACATCAAATATTGGGGTATTTTTTT
1 AGATTCAACATCAAATATTGGGGCATTTTTTT
*
304278 AGATTCAACATCGAATATT
1 AGATTCAACATCAAATATT
304297 AGGGTATCTT
Statistics
Matches: 45, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
32 45 1.00
ACGTcount: A:0.31, C:0.11, G:0.17, T:0.41
Consensus pattern (32 bp):
AGATTCAACATCAAATATTGGGGCATTTTTTT
Found at i:305309 original size:28 final size:28
Alignment explanation
Indices: 305260--305338 Score: 122
Period size: 28 Copynumber: 2.8 Consensus size: 28
305250 GTGCTCACCA
* *
305260 TTGTCTTTCTTGAGACAATTTCCAAGTT
1 TTGTCTCTCTTGAGACAGTTTCCAAGTT
* *
305288 TTGTCTCTCTTAAGATAGTTTCCAAGTT
1 TTGTCTCTCTTGAGACAGTTTCCAAGTT
305316 TTGTCTCTCTTGAGACAGTTTCC
1 TTGTCTCTCTTGAGACAGTTTCC
305339 CTTGAAACAA
Statistics
Matches: 45, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 45 1.00
ACGTcount: A:0.19, C:0.20, G:0.15, T:0.46
Consensus pattern (28 bp):
TTGTCTCTCTTGAGACAGTTTCCAAGTT
Found at i:305366 original size:37 final size:37
Alignment explanation
Indices: 305316--305427 Score: 199
Period size: 37 Copynumber: 3.1 Consensus size: 37
305306 TTTCCAAGTT
305316 TTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATC
1 TTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATC
*
305353 TTGTCTCTCTTGAGACAGTTTCCCTTGAAAC-AAATT
1 TTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATC
*
305389 TTGTCTCTCTTGGGACAGTTTCCCTTGAAACAAAATC
1 TTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATC
305426 TT
1 TT
305428 TGAATATATT
Statistics
Matches: 71, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
36 34 0.48
37 37 0.52
ACGTcount: A:0.25, C:0.23, G:0.14, T:0.38
Consensus pattern (37 bp):
TTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATC
Found at i:305400 original size:36 final size:36
Alignment explanation
Indices: 305314--305558 Score: 227
Period size: 36 Copynumber: 6.9 Consensus size: 36
305304 AGTTTCCAAG
305314 TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAA
1 TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAAC-AAA
*
305351 TCTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAA
1 TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAA
*
305387 TTTTGTCTCTCTTGGGACAGTTTCCCTTGAAACAAA
1 TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAA
* * * * * *
305423 ------ATCT-TTGA-ATATATTTTCCATGAAATAAA
1 TTTTGTCTCTCTTGAGACA-GTTTCCCTTGAAACAAA
** * ** ** *
305452 TTTCATCTCCCTTGAGACAGTTTCTTTTAGAATTAAG
1 TTTTGTCTCTCTTGAGACAGTTTCCCTT-GAAACAAA
**
305489 TTTTGTCTCTCTTGAGACAGTTTCTTTTGAAACAAA
1 TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAA
* *
305525 TTTTGTCCCTCTTGAGACAGTTTCTCTTGAAACA
1 TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACA
305559 CAAAAAAACC
Statistics
Matches: 170, Mismatches: 28, Indels: 21
0.78 0.13 0.10
Matches are distributed among these distances:
28 2 0.01
29 16 0.09
30 3 0.02
35 2 0.01
36 82 0.48
37 65 0.38
ACGTcount: A:0.26, C:0.20, G:0.13, T:0.40
Consensus pattern (36 bp):
TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAA
Found at i:305596 original size:30 final size:29
Alignment explanation
Indices: 305560--305619 Score: 84
Period size: 29 Copynumber: 2.1 Consensus size: 29
305550 CTTGAAACAC
* *
305560 AAAAAAACCCTCGAAATTGTTTCTCTTGA
1 AAAAAAAACCTCGAAAATGTTTCTCTTGA
* *
305589 AAAAAAAACTTTGAAAATGTTTCTCTTGA
1 AAAAAAAACCTCGAAAATGTTTCTCTTGA
305618 AA
1 AA
305620 CACAAAGCCT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.43, C:0.15, G:0.10, T:0.32
Consensus pattern (29 bp):
AAAAAAAACCTCGAAAATGTTTCTCTTGA
Found at i:305776 original size:83 final size:84
Alignment explanation
Indices: 305622--305811 Score: 251
Period size: 83 Copynumber: 2.3 Consensus size: 84
305612 TCTTGAAACA
* *
305622 CAAAG-CCTTCGAGTTCAAATACACTCAGCTTCAAGGGCACATCATTTGCAGCATAACTCAAGGC
1 CAAAGACCTTCGAGTTCGAATACACTCAGCTCCAAGGGCACATCATTTGCAGCATAACTCAAGGC
* *
305686 TAGAAGGGTTATCTGTCAAT
66 AAGAAGGGTTATCAGTC-AT
* * * *
305706 -AAAGACCTTCGAGTTCGACTACGCTCAGCTCCAA-GGCACATCATTTGTAGCATAACTCAATGC
1 CAAAGACCTTCGAGTTCGAATACACTCAGCTCCAAGGGCACATCATTTGCAGCATAACTCAAGGC
*
305769 AATAAGGGTTATCAGTCAT
66 AAGAAGGGTTATCAGTCAT
* *
305788 CAAATACCTTCGAGTTCGATTACA
1 CAAAGACCTTCGAGTTCGAATACA
305812 TTCAACTCAG
Statistics
Matches: 92, Mismatches: 12, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
82 2 0.02
83 65 0.71
84 25 0.27
ACGTcount: A:0.32, C:0.24, G:0.18, T:0.26
Consensus pattern (84 bp):
CAAAGACCTTCGAGTTCGAATACACTCAGCTCCAAGGGCACATCATTTGCAGCATAACTCAAGGC
AAGAAGGGTTATCAGTCAT
Found at i:306420 original size:37 final size:37
Alignment explanation
Indices: 306374--306485 Score: 188
Period size: 37 Copynumber: 3.0 Consensus size: 37
306364 AACATAGCGT
306374 TAGAGTTTTACTAGGATTCAAACTCCTAAAAATAGGA
1 TAGAGTTTTACTAGGATTCAAACTCCTAAAAATAGGA
*
306411 TAGAATTTTACTAGGATTCAAACTCCTAAAAATAGGA
1 TAGAGTTTTACTAGGATTCAAACTCCTAAAAATAGGA
* * *
306448 TAGAGTTCTACTATGATTCAAACTTCTAAAAATAGGA
1 TAGAGTTTTACTAGGATTCAAACTCCTAAAAATAGGA
306485 T
1 T
306486 CCATAAGCAT
Statistics
Matches: 70, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
37 70 1.00
ACGTcount: A:0.41, C:0.13, G:0.14, T:0.31
Consensus pattern (37 bp):
TAGAGTTTTACTAGGATTCAAACTCCTAAAAATAGGA
Found at i:307123 original size:54 final size:51
Alignment explanation
Indices: 307047--307176 Score: 143
Period size: 52 Copynumber: 2.7 Consensus size: 51
307037 TTTAGATTAC
*
307047 ATATATATATATATGT--TATTTTTTATTATTTGTGTTATTAATTTATATATAT
1 ATATATATATATATTTACTATTTTTTATTATTT-T-TTATTAA-TTATATATAT
* *
307099 ATATATATATATATTTACTATTTTTTA-T-GTTTTTATTTATTATATATAT
1 ATATATATATATATTTACTATTTTTTATTATTTTTTATTAATTATATATAT
307148 ATATAT-TAT-T-TTTAC--TTTTTTATTATTTT
1 ATATATATATATATTTACTATTTTTTATTATTTT
307177 ATTTATATAT
Statistics
Matches: 70, Mismatches: 4, Indels: 14
0.80 0.05 0.16
Matches are distributed among these distances:
44 7 0.10
45 1 0.01
46 8 0.11
47 1 0.01
48 3 0.04
49 16 0.23
50 6 0.09
51 1 0.01
52 17 0.24
53 1 0.01
54 9 0.13
ACGTcount: A:0.31, C:0.02, G:0.03, T:0.65
Consensus pattern (51 bp):
ATATATATATATATTTACTATTTTTTATTATTTTTTATTAATTATATATAT
Found at i:307139 original size:4 final size:4
Alignment explanation
Indices: 307062--307232 Score: 56
Period size: 4 Copynumber: 43.5 Consensus size: 4
307052 TATATATATG
* * * * * *
307062 TTAT TT-T TTA- TTAT TTGT GTTAT TAAT TTAT ATAT ATAT ATAT ATAT
1 TTAT TTAT TTAT TTAT TTAT -TTAT TTAT TTAT TTAT TTAT TTAT TTAT
* * * *
307109 ATAT TTA- CTAT TT-T TTAT GTT-T TTAT TTAT TATAT ATAT ATAT ATTA-
1 TTAT TTAT TTAT TTAT TTAT -TTAT TTAT TTAT T-TAT TTAT TTAT -TTAT
* * * * *
307156 TT-T TTACT TT-T TTA- TTATT TTAT TTAT ATAT TTTT TTCT TCTTT TTCT
1 TTAT TTA-T TTAT TTAT TTA-T TTAT TTAT TTAT TTAT TTAT T-TAT TTAT
* *
307204 TTAT TTTT TTAT AT-T TTAT TTAT TTAT TT
1 TTAT TTAT TTAT TTAT TTAT TTAT TTAT TT
307233 TACTTACTAT
Statistics
Matches: 129, Mismatches: 21, Indels: 34
0.70 0.11 0.18
Matches are distributed among these distances:
3 25 0.19
4 85 0.66
5 19 0.15
ACGTcount: A:0.25, C:0.03, G:0.02, T:0.70
Consensus pattern (4 bp):
TTAT
Found at i:307143 original size:37 final size:37
Alignment explanation
Indices: 307096--307188 Score: 109
Period size: 37 Copynumber: 2.5 Consensus size: 37
307086 AATTTATATA
307096 TATATATATATATATATTTACTATTTTTTA-TGTTTTTAT
1 TATAT-TATATATATATTTACTA-TTTTTACT-TTTTTAT
* *
307135 T-TATTATATATATATATATTATTTTTACTTTTTTAT
1 TATATTATATATATATTTACTATTTTTACTTTTTTAT
* *
307171 TATTTTATTTATATATTT
1 TATATTATATATATATTT
307189 TTTTCTTCTT
Statistics
Matches: 47, Mismatches: 5, Indels: 6
0.81 0.09 0.10
Matches are distributed among these distances:
36 14 0.30
37 29 0.62
38 3 0.06
39 1 0.02
ACGTcount: A:0.30, C:0.02, G:0.01, T:0.67
Consensus pattern (37 bp):
TATATTATATATATATTTACTATTTTTACTTTTTTAT
Found at i:307167 original size:35 final size:34
Alignment explanation
Indices: 307102--307208 Score: 92
Period size: 33 Copynumber: 3.0 Consensus size: 34
307092 TATATATATA
* * *
307102 TATATATATATTTACTATTTTTTATGTTTTTATTTAT
1 TATATATATATATATTA-TTTTTA-CTTTTT-TTTAT
307139 TATATATATATATATTATTTTTACTTTTTTATTAT
1 TATATATATATATATTATTTTTACTTTTTT-TTAT
* * *
307174 T-T-TATTTATATATTTTTTTCTTCTTTTTCTTTAT
1 TATATATATATATATTATTTT-TACTTTTT-TTTAT
307208 T
1 T
307209 TTTTTATATT
Statistics
Matches: 61, Mismatches: 6, Indels: 9
0.80 0.08 0.12
Matches are distributed among these distances:
33 15 0.25
34 14 0.23
35 11 0.18
36 6 0.10
37 15 0.25
ACGTcount: A:0.24, C:0.05, G:0.01, T:0.70
Consensus pattern (34 bp):
TATATATATATATATTATTTTTACTTTTTTTTAT
Found at i:307201 original size:33 final size:33
Alignment explanation
Indices: 307120--307224 Score: 99
Period size: 33 Copynumber: 3.1 Consensus size: 33
307110 TATTTACTAT
*
307120 TTTTTA-TGTTTTTATTTATTATATATATATATATTA
1 TTTTTACT-TTTTTA-TTATT-T-TATTTATATATTA
*
307156 TTTTTACTTTTTTATTATTTTATTTATATATTT
1 TTTTTACTTTTTTATTATTTTATTTATATATTA
* *
307189 TTTTCTTCTTTTTCT-TTATTTT-TTTATATTTTA
1 TTTT-TACTTTTT-TATTATTTTATTTATATATTA
307222 TTT
1 TTT
307225 ATTTATTTTA
Statistics
Matches: 61, Mismatches: 5, Indels: 9
0.81 0.07 0.12
Matches are distributed among these distances:
33 27 0.44
34 15 0.25
35 6 0.10
36 12 0.20
37 1 0.02
ACGTcount: A:0.21, C:0.04, G:0.01, T:0.74
Consensus pattern (33 bp):
TTTTTACTTTTTTATTATTTTATTTATATATTA
Found at i:307207 original size:29 final size:33
Alignment explanation
Indices: 307134--307209 Score: 81
Period size: 32 Copynumber: 2.5 Consensus size: 33
307124 TATGTTTTTA
* * *
307134 TTTATTA-TATATATATATATTATTTTTACTTT
1 TTTATTACTTTATTTATATATTATTTTTACTTC
*
307166 TTTATTATTTTATTTATATATT-TTTTT-CTTC
1 TTTATTACTTTATTTATATATTATTTTTACTTC
307197 TTT-TT-CTTTATTT
1 TTTATTACTTTATTT
307210 TTTTATATTT
Statistics
Matches: 39, Mismatches: 4, Indels: 5
0.81 0.08 0.10
Matches are distributed among these distances:
29 7 0.18
30 2 0.05
31 6 0.15
32 12 0.31
33 12 0.31
ACGTcount: A:0.22, C:0.05, G:0.00, T:0.72
Consensus pattern (33 bp):
TTTATTACTTTATTTATATATTATTTTTACTTC
Found at i:307212 original size:12 final size:11
Alignment explanation
Indices: 307163--307233 Score: 65
Period size: 10 Copynumber: 6.3 Consensus size: 11
307153 TTATTTTTAC
307163 TTTTTTATTAT
1 TTTTTTATTAT
307174 TTTATTTATATAT
1 TTT-TTTAT-TAT
* *
307187 TTTTTTCTTCT
1 TTTTTTATTAT
*
307198 TTTTCT-TTAT
1 TTTTTTATTAT
307208 TTTTTTA-TAT
1 TTTTTTATTAT
307218 TTTATTTATTTAT
1 TTT-TTTA-TTAT
307231 TTT
1 TTT
307234 ACTTACTATT
Statistics
Matches: 49, Mismatches: 5, Indels: 10
0.77 0.08 0.16
Matches are distributed among these distances:
10 14 0.29
11 14 0.29
12 9 0.18
13 12 0.24
ACGTcount: A:0.17, C:0.04, G:0.00, T:0.79
Consensus pattern (11 bp):
TTTTTTATTAT
Found at i:308533 original size:8 final size:8
Alignment explanation
Indices: 308520--308547 Score: 56
Period size: 8 Copynumber: 3.5 Consensus size: 8
308510 AAAGGGGGAG
308520 AAGTGTTA
1 AAGTGTTA
308528 AAGTGTTA
1 AAGTGTTA
308536 AAGTGTTA
1 AAGTGTTA
308544 AAGT
1 AAGT
308548 AAGGGGGAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.39, C:0.00, G:0.25, T:0.36
Consensus pattern (8 bp):
AAGTGTTA
Found at i:313419 original size:24 final size:24
Alignment explanation
Indices: 313361--313411 Score: 102
Period size: 24 Copynumber: 2.1 Consensus size: 24
313351 TTTTAGTTAG
313361 GTTTCGGTTATTTTGGTTGGGATT
1 GTTTCGGTTATTTTGGTTGGGATT
313385 GTTTCGGTTATTTTGGTTGGGATT
1 GTTTCGGTTATTTTGGTTGGGATT
313409 GTT
1 GTT
313412 GTTGTTATAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.08, C:0.04, G:0.33, T:0.55
Consensus pattern (24 bp):
GTTTCGGTTATTTTGGTTGGGATT
Found at i:318784 original size:4 final size:4
Alignment explanation
Indices: 318775--318822 Score: 71
Period size: 4 Copynumber: 12.2 Consensus size: 4
318765 AGAGCAAAGA
* *
318775 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAA ATAA ATA- ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
318822 A
1 A
318823 AATAAATATA
Statistics
Matches: 42, Mismatches: 1, Indels: 2
0.93 0.02 0.04
Matches are distributed among these distances:
3 3 0.07
4 39 0.93
ACGTcount: A:0.56, C:0.19, G:0.00, T:0.25
Consensus pattern (4 bp):
ATAC
Found at i:326041 original size:2 final size:2
Alignment explanation
Indices: 326034--326062 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
326024 AACTTGTATG
326034 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 T
326063 GTCAATGCCG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:331405 original size:16 final size:15
Alignment explanation
Indices: 331382--331439 Score: 57
Period size: 16 Copynumber: 3.7 Consensus size: 15
331372 GTAATAAGTA
331382 AATATAATAATTAAT
1 AATATAATAATTAAT
*
331397 AATATTAATTATTAA-
1 AATA-TAATAATTAAT
331412 ATATAGTAAATAATTAAT
1 A-ATA-T-AATAATTAAT
331430 -ATATAATAAT
1 AATATAATAAT
331440 ATATAAATAA
Statistics
Matches: 36, Mismatches: 3, Indels: 9
0.75 0.06 0.19
Matches are distributed among these distances:
14 6 0.17
15 6 0.17
16 16 0.44
17 8 0.22
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (15 bp):
AATATAATAATTAAT
Found at i:339603 original size:11 final size:10
Alignment explanation
Indices: 339579--339608 Score: 51
Period size: 11 Copynumber: 2.9 Consensus size: 10
339569 ATAAGAAGAC
339579 TAATTTATTT
1 TAATTTATTT
339589 TAATTTATCTT
1 TAATTTAT-TT
339600 TAATTTATT
1 TAATTTATT
339609 GATTTACGTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
10 9 0.47
11 10 0.53
ACGTcount: A:0.30, C:0.03, G:0.00, T:0.67
Consensus pattern (10 bp):
TAATTTATTT
Found at i:339922 original size:30 final size:32
Alignment explanation
Indices: 339864--339922 Score: 79
Period size: 30 Copynumber: 1.9 Consensus size: 32
339854 TATATAAAAC
*
339864 ATATTAATTTTTTTCTTTAATTATATAATTTA
1 ATATTAATATTTTTCTTTAATTATATAATTTA
339896 ATATT-ATATTTTT-TTT-ATTAATATAAT
1 ATATTAATATTTTTCTTTAATT-ATATAAT
339923 ATTTTATATT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
29 3 0.12
30 10 0.40
31 7 0.28
32 5 0.20
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.63
Consensus pattern (32 bp):
ATATTAATATTTTTCTTTAATTATATAATTTA
Found at i:339932 original size:32 final size:32
Alignment explanation
Indices: 339864--339934 Score: 85
Period size: 32 Copynumber: 2.2 Consensus size: 32
339854 TATATAAAAC
339864 ATATTAATTTTTTTCTTTAATTATATAATTTA
1 ATATTAATTTTTTTCTTTAATTATATAATTTA
*
339896 ATATTATATTTTTTT-TATTAA-TATA-ATATTTT
1 ATATTA-ATTTTTTTCT-TTAATTATATA-ATTTA
339928 ATATTAA
1 ATATTAA
339935 CCAAAATATA
Statistics
Matches: 35, Mismatches: 1, Indels: 7
0.81 0.02 0.16
Matches are distributed among these distances:
31 2 0.06
32 21 0.60
33 12 0.34
ACGTcount: A:0.37, C:0.01, G:0.00, T:0.62
Consensus pattern (32 bp):
ATATTAATTTTTTTCTTTAATTATATAATTTA
Found at i:340045 original size:30 final size:29
Alignment explanation
Indices: 339985--340091 Score: 110
Period size: 30 Copynumber: 3.6 Consensus size: 29
339975 TAAATTTTAA
* * *
339985 AAATATTTTTTA-TTTCGTCTTAACTGATT
1 AAATATATTTTATTTTTGTATTAACT-ATT
340014 AAATATATTTTATTTTTGTATTAACCTATT
1 AAATATATTTTATTTTTGTATTAA-CTATT
* *
340044 AAATATATTTTATTTTTATTTTAA-TATT
1 AAATATATTTTATTTTTGTATTAACTATT
340072 AAAATATATAATTTATTTTT
1 -AAATATAT--TTTATTTTT
340092 ATCTTCACTT
Statistics
Matches: 68, Mismatches: 5, Indels: 8
0.84 0.06 0.10
Matches are distributed among these distances:
28 4 0.06
29 19 0.28
30 34 0.50
31 11 0.16
ACGTcount: A:0.35, C:0.05, G:0.03, T:0.58
Consensus pattern (29 bp):
AAATATATTTTATTTTTGTATTAACTATT
Found at i:340087 original size:61 final size:62
Alignment explanation
Indices: 340016--340142 Score: 159
Period size: 61 Copynumber: 2.1 Consensus size: 62
340006 AACTGATTAA
* * * *
340016 ATATATTTTATTTTTGTATTAACCTATTAAATATA-TTTTATTTTTATTTTAATATT-AAAAT
1 ATATAATTTATTTTTATATTAACCTA-AAAATATATTTTTATTTTTATCTTAATATTAAAAAT
* * * *
340077 ATATAATTTATTTTTATCTTCACTTAAAAATATATTTTTATTTTTATCTTAATTTTAAAAAT
1 ATATAATTTATTTTTATATTAACCTAAAAATATATTTTTATTTTTATCTTAATATTAAAAAT
340139 ATAT
1 ATAT
340143 TAACTTAAAA
Statistics
Matches: 56, Mismatches: 8, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
60 7 0.12
61 40 0.71
62 9 0.16
ACGTcount: A:0.37, C:0.05, G:0.01, T:0.57
Consensus pattern (62 bp):
ATATAATTTATTTTTATATTAACCTAAAAATATATTTTTATTTTTATCTTAATATTAAAAAT
Found at i:340092 original size:31 final size:31
Alignment explanation
Indices: 340016--340143 Score: 124
Period size: 30 Copynumber: 4.2 Consensus size: 31
340006 AACTGATTAA
* *
340016 ATATATTTTATTTTTGTATTAACCTATT--AA-
1 ATATATTTTATTTTTATCTTAA--TATTAAAAT
*
340046 ATATATTTTATTTTTATTTTAATATTAAAAT
1 ATATATTTTATTTTTATCTTAATATTAAAAT
* * *
340077 ATATAATTTATTTTTATCTTCA-CTTAAAA-
1 ATATATTTTATTTTTATCTTAATATTAAAAT
*
340106 ATATATTTTTATTTTTATCTTAATTTTAAAA-
1 ATATA-TTTTATTTTTATCTTAATATTAAAAT
340137 ATATATT
1 ATATATT
340144 AACTTAAAAT
Statistics
Matches: 84, Mismatches: 9, Indels: 10
0.82 0.09 0.10
Matches are distributed among these distances:
28 4 0.05
29 5 0.06
30 45 0.54
31 30 0.36
ACGTcount: A:0.37, C:0.05, G:0.01, T:0.58
Consensus pattern (31 bp):
ATATATTTTATTTTTATCTTAATATTAAAAT
Found at i:340117 original size:30 final size:30
Alignment explanation
Indices: 340044--340143 Score: 114
Period size: 31 Copynumber: 3.3 Consensus size: 30
340034 TTAACCTATT
*
340044 AAATATA-TTTTATTTTTATTTTAATATT-A
1 AAATATATTTTTATTTTTATCTTAA-ATTAA
* * *
340073 AAATATATAATTTATTTTTATCTTCACTTAA
1 AAATATAT-TTTTATTTTTATCTTAAATTAA
*
340104 AAATATATTTTTATTTTTATCTTAATTTTAA
1 AAATATATTTTTATTTTTATCTTAA-ATTAA
340135 AAATATATT
1 AAATATATT
340144 AACTTAAAAT
Statistics
Matches: 60, Mismatches: 7, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
29 7 0.12
30 17 0.28
31 36 0.60
ACGTcount: A:0.39, C:0.04, G:0.00, T:0.57
Consensus pattern (30 bp):
AAATATATTTTTATTTTTATCTTAAATTAA
Found at i:342280 original size:14 final size:14
Alignment explanation
Indices: 342263--342289 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
342253 ATTACATTGC
342263 TTTAATTTTAATTA
1 TTTAATTTTAATTA
342277 TTTAATTTTAATT
1 TTTAATTTTAATT
342290 TTAAAATTAT
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:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (14 bp):
TTTAATTTTAATTA
Found at i:342586 original size:29 final size:31
Alignment explanation
Indices: 342537--342606 Score: 101
Period size: 30 Copynumber: 2.3 Consensus size: 31
342527 TTATATTTGG
342537 TCCCTTAACTTTAGAGTTTCT-ACATTTTAA
1 TCCCTTAACTTTAGAGTTTCTCACATTTTAA
342567 TCCCTT-ACATTTAGA-TTTCTCACATTTTAA
1 TCCCTTAAC-TTTAGAGTTTCTCACATTTTAA
*
342597 TCCCTAAACT
1 TCCCTTAACT
342607 ACTAATTAGA
Statistics
Matches: 36, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
29 7 0.19
30 27 0.75
31 2 0.06
ACGTcount: A:0.27, C:0.24, G:0.04, T:0.44
Consensus pattern (31 bp):
TCCCTTAACTTTAGAGTTTCTCACATTTTAA
Found at i:343743 original size:30 final size:27
Alignment explanation
Indices: 343703--343763 Score: 77
Period size: 30 Copynumber: 2.1 Consensus size: 27
343693 CAACATGCAT
*
343703 ATTTTTATTCAAATCAACACAATTATCATC
1 ATTTTCATTCAAATCAACA-AA--ATCATC
*
343733 ATTTTCATTCAAATTAACAAAATCATC
1 ATTTTCATTCAAATCAACAAAATCATC
343760 ATTT
1 ATTT
343764 AAAATAATTT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
27 10 0.34
29 2 0.07
30 17 0.59
ACGTcount: A:0.41, C:0.18, G:0.00, T:0.41
Consensus pattern (27 bp):
ATTTTCATTCAAATCAACAAAATCATC
Found at i:344587 original size:23 final size:23
Alignment explanation
Indices: 344560--344608 Score: 98
Period size: 23 Copynumber: 2.1 Consensus size: 23
344550 TTAAACAATA
344560 TTATTCATAAGATGTATATATAT
1 TTATTCATAAGATGTATATATAT
344583 TTATTCATAAGATGTATATATAT
1 TTATTCATAAGATGTATATATAT
344606 TTA
1 TTA
344609 CTTAGAATTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.39, C:0.04, G:0.08, T:0.49
Consensus pattern (23 bp):
TTATTCATAAGATGTATATATAT
Found at i:345503 original size:17 final size:17
Alignment explanation
Indices: 345452--345515 Score: 58
Period size: 17 Copynumber: 3.6 Consensus size: 17
345442 ATTTCTTAAT
*
345452 ATTAAAAAATAAATATTA
1 ATTAAAAAATATATA-TA
* * *
345470 A-TAAAACATTTAAATA
1 ATTAAAAAATATATATA
345486 ATTAAAAAATATATATA
1 ATTAAAAAATATATATA
345503 ATTTATAAAAATA
1 A-TTA-AAAAATA
345516 AGATATTTAT
Statistics
Matches: 36, Mismatches: 7, Indels: 5
0.75 0.15 0.10
Matches are distributed among these distances:
16 3 0.08
17 22 0.61
18 4 0.11
19 7 0.19
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (17 bp):
ATTAAAAAATATATATA
Found at i:345523 original size:17 final size:16
Alignment explanation
Indices: 345456--345525 Score: 52
Period size: 19 Copynumber: 4.0 Consensus size: 16
345446 CTTAATATTA
*
345456 AAAAATAAATATTAAT
1 AAAAATAAATATTTAT
*
345472 AAAACATTTAAATAATTA-
1 AAAA-A--TAAATATTTAT
345490 AAAAATATATATAATTTAT
1 AAAAATA-A-AT-ATTTAT
345509 AAAAATAAGATATTTAT
1 AAAAATAA-ATATTTAT
345526 TTATTTAAAA
Statistics
Matches: 43, Mismatches: 4, Indels: 13
0.72 0.07 0.22
Matches are distributed among these distances:
15 2 0.05
16 5 0.12
17 10 0.23
18 11 0.26
19 15 0.35
ACGTcount: A:0.61, C:0.01, G:0.01, T:0.36
Consensus pattern (16 bp):
AAAAATAAATATTTAT
Found at i:345708 original size:3 final size:3
Alignment explanation
Indices: 345702--345742 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
345692 ATATATGTTT
345702 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
345743 TAAATATATT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:345871 original size:30 final size:30
Alignment explanation
Indices: 345795--345872 Score: 79
Period size: 29 Copynumber: 2.6 Consensus size: 30
345785 AACAGTGTCT
* *
345795 AAAATAAATAAAATTAAAACTATTTATTTAA
1 AAAATAAAGAAAA-TAAAACTATTTAATTAA
* *
345826 AATATAAA-AGCAATAAAACT-TTTAATTAA
1 AAAATAAAGA-AAATAAAACTATTTAATTAA
345855 AAAATAAACGAAAATAAA
1 AAAATAAA-GAAAATAAA
345873 GTTAATGACT
Statistics
Matches: 39, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
29 15 0.38
30 14 0.36
31 10 0.26
ACGTcount: A:0.64, C:0.05, G:0.03, T:0.28
Consensus pattern (30 bp):
AAAATAAAGAAAATAAAACTATTTAATTAA
Found at i:346543 original size:28 final size:28
Alignment explanation
Indices: 346497--346551 Score: 69
Period size: 28 Copynumber: 2.0 Consensus size: 28
346487 CCAAAACCCA
346497 CCAAATCGAAGCCTTGTTTAT-CTTAAAC
1 CCAAATCGAAGCCTTGTTT-TGCTTAAAC
*
346525 CCAAATCTAAG-CTTAGTTTTGCTTAAA
1 CCAAATCGAAGCCTT-GTTTTGCTTAAA
346552 AATCTACCAA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
27 4 0.17
28 20 0.83
ACGTcount: A:0.33, C:0.22, G:0.11, T:0.35
Consensus pattern (28 bp):
CCAAATCGAAGCCTTGTTTTGCTTAAAC
Found at i:347213 original size:3 final size:3
Alignment explanation
Indices: 347205--347279 Score: 71
Period size: 3 Copynumber: 25.0 Consensus size: 3
347195 CTGTAATATG
* * * *
347205 TAA TAA TAA TATT TAT TAT TAA TAA TAA AAA T-A TAA TAA TAA TAA
1 TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* * *
347250 TAA TAA CAA TTA TAA TAA TAA TAA AAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
347280 AACGGGCTAA
Statistics
Matches: 60, Mismatches: 10, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
2 2 0.03
3 56 0.93
4 2 0.03
ACGTcount: A:0.63, C:0.01, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:348285 original size:225 final size:224
Alignment explanation
Indices: 347888--348450 Score: 898
Period size: 225 Copynumber: 2.5 Consensus size: 224
347878 TATGATAGAG
*
347888 TCGAGCAAAAAGTTGAACAAGTTCTTCTTATTATGAACTTCTTCTTCATCTTCAGATAAGTTCTT
1 TCGAGCAAAAGGTTGAACAAGTTCTTCTTATTATGAACTTCTTCTTCATCTTCAGATAAGTTCTT
*
347953 CTCATTATGAACTTTCTCTGGAAAAGTTGATTCATCGAGTGATGAATTCAAACAAAAGGTTGAAC
66 CTCATTATGAACTTTCTCTGGAAAAGTTGATCCATCGAGTGATGAATTCAAACAAAAGGTTGAAC
*
348018 AAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTAC
131 AAATTCTTCTCATTATGAATTTCTTCTTCATTCTTCAGATGAGTTCTTC-CATTATGAACTCTAC
348083 CTGGCAATGCTT-ATCCATCAAGTGATGAAT
195 CTGGCAATG-TTGATCCATCAAGTGATGAAT
*
348113 TCGAGCAAAAGGTTGAACAAGTTCTTCTTATTATGAACTTCTTCTTCCTCTTCAGATAAGTTCTT
1 TCGAGCAAAAGGTTGAACAAGTTCTTCTTATTATGAACTTCTTCTTCATCTTCAGATAAGTTCTT
*
348178 CTCATTATGAACTTTCTCT-GAAAAGGTTGATCCATCGAGTGATGAATTCAAACAAAATGTTGAA
66 CTCATTATGAACTTTCTCTGGAAAA-GTTGATCCATCGAGTGATGAATTCAAACAAAAGGTTGAA
*
348242 CAAATTCTTCTCATTATGAATTTCTTCTTCATTCTTTAGATGAGTTCTTCCATTATGAACTCTAC
130 CAAATTCTTCTCATTATGAATTTCTTCTTCATTCTTCAGATGAGTTCTTCCATTATGAACTCTAC
348307 CTGGCAATGTTGATCCATCAAGTGATGAAT
195 CTGGCAATGTTGATCCATCAAGTGATGAAT
* * * * *
348337 TCGAGCAAAAGGTTGAACAAGTTCTTCTCATTATGAGCTTATTATTCATTCTTCAGATGAGTTCT
1 TCGAGCAAAAGGTTGAACAAGTTCTTCTTATTATGAACTTCTTCTTCA-TCTTCAGATAAGTTCT
* * ** * * * *
348402 TCTCATTTTGAACTCTAACTGG-CATGTTGATCCATTGAGTGATGGATTC
65 TCTCATTATGAACTTTCTCTGGAAAAGTTGATCCATCGAGTGATGAATTC
348451 GAATTTTTGC
Statistics
Matches: 314, Mismatches: 20, Indels: 9
0.92 0.06 0.03
Matches are distributed among these distances:
223 2 0.01
224 112 0.36
225 199 0.63
226 1 0.00
ACGTcount: A:0.28, C:0.19, G:0.15, T:0.38
Consensus pattern (224 bp):
TCGAGCAAAAGGTTGAACAAGTTCTTCTTATTATGAACTTCTTCTTCATCTTCAGATAAGTTCTT
CTCATTATGAACTTTCTCTGGAAAAGTTGATCCATCGAGTGATGAATTCAAACAAAAGGTTGAAC
AAATTCTTCTCATTATGAATTTCTTCTTCATTCTTCAGATGAGTTCTTCCATTATGAACTCTACC
TGGCAATGTTGATCCATCAAGTGATGAAT
Found at i:348406 original size:337 final size:343
Alignment explanation
Indices: 347780--348452 Score: 873
Period size: 337 Copynumber: 2.0 Consensus size: 343
347770 GCTAAGGTCA
*
347780 AACAAGTTCTTCTTATTATGAACTTCTTCTCCTTCTTCAGATGAGTTCTTCGCATTATGAACTTT
1 AACAAGTTCTTCTTATTATGAACTTCTTCTCCTTCTTCAGATAAGTTCTTCGCATTATGAACTTT
* * ** * * * *
347845 ATCTGGAAATGTTGGTGCTGATCTATCTGCTTCTATGATAGAGTCGAGCAAAAAGTTGAACAAGT
66 ATCTGGAAA--TAGGT-CTGATCCATCTGAGTCGATGA-AGAGTCAAACAAAAAGTTGAACAAAT
* *
347910 TCTTCTTATTATGAACTTCTTCTTCATCTTCAGATAAGTTCTTCTCATTATGAACTTTCTCTGGA
127 TCTTCTCATTATGAACTTCTTCTTCATCTTCAGATAAGTTCTTCTCATTATGAACTTACTCTGGA
* * *
347975 AAAGTTGATTCATCGAGTGATGAATTCAAACAAAAGGTTGAACAAATTCTTCTCATTATGAATTT
192 AAAGTTGATCCATCAAGTGATGAATTCAAACAAAAGGTTGAACAAATTCTTCTCATTATGAACTT
* * * *
348040 CTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTACCTGGCAATGCTT-ATCCATCAA
257 ATTATTCATTCTTCAGATGAGTTCTTCTCATTATGAACTCTAACTGGC-ATG-TTGATCCATCAA
348104 GTGATGAATTCGAGCAAAAGGTTG
320 GTGATGAATTCGAGCAAAAGGTTG
*
348128 AACAAGTTCTTCTTATTATGAACTTCTTCTTCC-TCTTCAGATAAGTTCTTCTCATTATGAACTT
1 AACAAGTTCTTCTTATTATGAACTTCTTC-TCCTTCTTCAGATAAGTTCTTCGCATTATGAACTT
* * *
348192 TCTCT-GAAA-AGGT-TGATCCATC-GAGT-GATG-A-ATTCAAACAAAATGTTGAACAAATTCT
65 TATCTGGAAATAGGTCTGATCCATCTGAGTCGATGAAGAGTCAAACAAAAAGTTGAACAAATTCT
* * * *
348250 TCTCATTATGAATTTCTTCTTCATTCTTTAGATGAGTTCTTC-CATTATGAACTCTAC-CTGGCA
130 TCTCATTATGAACTTCTTCTTCA-TCTTCAGATAAGTTCTTCTCATTATGAACT-TACTCTGGAA
* * * * *
348313 ATGTTGATCCATCAAGTGATGAATTCGAGCAAAAGGTTGAACAAGTTCTTCTCATTATGAGCTTA
193 AAGTTGATCCATCAAGTGATGAATTCAAACAAAAGGTTGAACAAATTCTTCTCATTATGAACTTA
* **
348378 TTATTCATTCTTCAGATGAGTTCTTCTCATTTTGAACTCTAACTGGCATGTTGATCCATTGAGTG
258 TTATTCATTCTTCAGATGAGTTCTTCTCATTATGAACTCTAACTGGCATGTTGATCCATCAAGTG
*
348443 ATGGATTCGA
323 ATGAATTCGA
348453 ATTTTTGCTA
Statistics
Matches: 286, Mismatches: 35, Indels: 20
0.84 0.10 0.06
Matches are distributed among these distances:
335 2 0.01
336 22 0.08
337 158 0.55
338 19 0.07
340 3 0.01
341 2 0.01
342 8 0.03
344 3 0.01
347 4 0.01
348 62 0.22
349 3 0.01
ACGTcount: A:0.28, C:0.19, G:0.15, T:0.38
Consensus pattern (343 bp):
AACAAGTTCTTCTTATTATGAACTTCTTCTCCTTCTTCAGATAAGTTCTTCGCATTATGAACTTT
ATCTGGAAATAGGTCTGATCCATCTGAGTCGATGAAGAGTCAAACAAAAAGTTGAACAAATTCTT
CTCATTATGAACTTCTTCTTCATCTTCAGATAAGTTCTTCTCATTATGAACTTACTCTGGAAAAG
TTGATCCATCAAGTGATGAATTCAAACAAAAGGTTGAACAAATTCTTCTCATTATGAACTTATTA
TTCATTCTTCAGATGAGTTCTTCTCATTATGAACTCTAACTGGCATGTTGATCCATCAAGTGATG
AATTCGAGCAAAAGGTTG
Found at i:348451 original size:112 final size:112
Alignment explanation
Indices: 347888--348452 Score: 719
Period size: 112 Copynumber: 5.0 Consensus size: 112
347878 TATGATAGAG
* * *
347888 TCGAGCAAAAAGTTGAACAAGTTCTTCTTATTATGAACTTCTTCTTCA-TCTTCAGATAAGTTCT
1 TCGAGCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCATTCTTCAGATGAGTTCT
* * * *
347952 TCTCATTATGAACT-TTCTCTGGAAAAGTTGATTCATCGAGTGATGAAT
66 TCTCATTATGAACTCTAC-CTGG-CATGTTGATCCATCGAGTGATGAAT
* * * * *
348000 TCAAACAAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCT
1 TCGAGCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCATTCTTCAGATGAGTTCT
*
348065 TCTCATTATGAACTCTACCTGGCAATGCTT-ATCCATCAAGTGATGAAT
66 TCTCATTATGAACTCTACCTGGC-ATG-TTGATCCATCGAGTGATGAAT
* * *
348113 TCGAGCAAAAGGTTGAACAAGTTCTTCTTATTATGAACTTCTTCTTC-CTCTTCAGATAAGTTCT
1 TCGAGCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCATTCTTCAGATGAGTTCT
* ** *
348177 TCTCATTATGAACT-TTCTCTGAAAAGGTTGATCCATCGAGTGATGAAT
66 TCTCATTATGAACTCTAC-CTG-GCATGTTGATCCATCGAGTGATGAAT
* * * * * *
348225 TCAAACAAAATGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCATTCTTTAGATGAGTTCT
1 TCGAGCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCATTCTTCAGATGAGTTCT
*
348290 TC-CATTATGAACTCTACCTGGCAATGTTGATCCATCAAGTGATGAAT
66 TCTCATTATGAACTCTACCTGGC-ATGTTGATCCATCGAGTGATGAAT
* * *
348337 TCGAGCAAAAGGTTGAACAAGTTCTTCTCATTATGAGCTTATTATTCATTCTTCAGATGAGTTCT
1 TCGAGCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCATTCTTCAGATGAGTTCT
* * * *
348402 TCTCATTTTGAACTCTAACTGGCATGTTGATCCATTGAGTGATGGAT
66 TCTCATTATGAACTCTACCTGGCATGTTGATCCATCGAGTGATGAAT
348449 TCGA
1 TCGA
348453 ATTTTTGCTA
Statistics
Matches: 389, Mismatches: 53, Indels: 22
0.84 0.11 0.05
Matches are distributed among these distances:
111 4 0.01
112 252 0.65
113 129 0.33
114 4 0.01
ACGTcount: A:0.28, C:0.19, G:0.15, T:0.38
Consensus pattern (112 bp):
TCGAGCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCATTCTTCAGATGAGTTCT
TCTCATTATGAACTCTACCTGGCATGTTGATCCATCGAGTGATGAAT
Found at i:348842 original size:22 final size:22
Alignment explanation
Indices: 348806--348860 Score: 60
Period size: 22 Copynumber: 2.5 Consensus size: 22
348796 TAAAGCTTTT
*
348806 ATCTTTGAA-AGAG-AATCTATC
1 ATCTTTAAAGAGAGAAAT-TATC
* *
348827 ATTTTTTAAGAGAGAAATTATC
1 ATCTTTAAAGAGAGAAATTATC
348849 ATCTTTAAAGAG
1 ATCTTTAAAGAG
348861 TGTAGATGTA
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
21 7 0.25
22 18 0.64
23 3 0.11
ACGTcount: A:0.40, C:0.09, G:0.15, T:0.36
Consensus pattern (22 bp):
ATCTTTAAAGAGAGAAATTATC
Found at i:349330 original size:54 final size:54
Alignment explanation
Indices: 349224--349477 Score: 341
Period size: 54 Copynumber: 4.7 Consensus size: 54
349214 ATAATCACTG
* * * * * *
349224 GTTCGTAAAACATTTGAC-ACACATTCATAATCTCTTGTGGTTTCTTCTCAGAT
1 GTTCGTAAAACATTTGACAACACATTCATCATTTCCTGTGGCTTCTGCCCAGAT
* *
349277 GTTCATAAAACATTTGACAACACATTCATCATTTCCTATGGCTTCTGCCCAGAT
1 GTTCGTAAAACATTTGACAACACATTCATCATTTCCTGTGGCTTCTGCCCAGAT
* * *
349331 GTTCGTAAAACATTTGACAACACATTCATCCTTTCCTGTGACTTCTGCTCAGAT
1 GTTCGTAAAACATTTGACAACACATTCATCATTTCCTGTGGCTTCTGCCCAGAT
* *
349385 GTTCGTAAAGCATTTGACAACACATTCATCCTTTCCTGTGGCTTCTGCCCAGAT
1 GTTCGTAAAACATTTGACAACACATTCATCATTTCCTGTGGCTTCTGCCCAGAT
* * * *
349439 GTTCATAAAGCATTTGACAA-AAATTCATCATTTCTTGTG
1 GTTCGTAAAACATTTGACAACACATTCATCATTTCCTGTG
349478 TTTTCTGCAC
Statistics
Matches: 180, Mismatches: 20, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
53 33 0.18
54 147 0.82
ACGTcount: A:0.27, C:0.24, G:0.13, T:0.36
Consensus pattern (54 bp):
GTTCGTAAAACATTTGACAACACATTCATCATTTCCTGTGGCTTCTGCCCAGAT
Found at i:350502 original size:75 final size:75
Alignment explanation
Indices: 350363--350532 Score: 198
Period size: 75 Copynumber: 2.3 Consensus size: 75
350353 GATATAGGCC
* * * * * *
350363 TTCAACATGCCTCAACATTTGCTGATACAAGCGTTCAAAATATGTTAACATTCATCATTCTGATT
1 TTCAGCATGCCCCAACATTTACTGATACAAGCGTTCAAAATACGTCAACATTCATCATTATGATT
350428 AAAATGGGCT
66 AAAATGGGCT
* * * * *
350438 TTCAGCATGCCCCAGCATTTACTGATACAAAG-GTTCAAAATGCGTCAATATTCCTGATTATGAT
1 TTCAGCATGCCCCAACATTTACTGATAC-AAGCGTTCAAAATACGTCAACATTCATCATTATGAT
*
350502 TGAAATGGGCT
65 TAAAATGGGCT
* *
350513 TTCAGCATGCTCCATCATTT
1 TTCAGCATGCCCCAACATTT
350533 GCTTCTTGTT
Statistics
Matches: 80, Mismatches: 14, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
75 77 0.96
76 3 0.04
ACGTcount: A:0.31, C:0.21, G:0.15, T:0.33
Consensus pattern (75 bp):
TTCAGCATGCCCCAACATTTACTGATACAAGCGTTCAAAATACGTCAACATTCATCATTATGATT
AAAATGGGCT
Found at i:352927 original size:8 final size:9
Alignment explanation
Indices: 352908--352939 Score: 55
Period size: 9 Copynumber: 3.6 Consensus size: 9
352898 CTTGATTCAA
*
352908 TTTTTCTTT
1 TTTTTCCTT
352917 TTTTTCCTT
1 TTTTTCCTT
352926 TTTTTCCTT
1 TTTTTCCTT
352935 TTTTT
1 TTTTT
352940 GTATAGGACT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
9 22 1.00
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (9 bp):
TTTTTCCTT
Found at i:364568 original size:24 final size:25
Alignment explanation
Indices: 364522--364570 Score: 75
Period size: 25 Copynumber: 2.0 Consensus size: 25
364512 AGAATTTTTC
364522 AAAAAAATTTAAATTTTCGAAATTA
1 AAAAAAATTTAAATTTTCGAAATTA
364547 AAAAAAATGTT-AATTTTC-AAATTA
1 AAAAAAAT-TTAAATTTTCGAAATTA
364571 TTGTGTTTTG
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
24 6 0.26
25 15 0.65
26 2 0.09
ACGTcount: A:0.55, C:0.04, G:0.04, T:0.37
Consensus pattern (25 bp):
AAAAAAATTTAAATTTTCGAAATTA
Found at i:366394 original size:16 final size:16
Alignment explanation
Indices: 366373--366432 Score: 85
Period size: 16 Copynumber: 4.1 Consensus size: 16
366363 GAAGTGGTTT
366373 TAAGTGTGTTTTAAAA
1 TAAGTGTGTTTTAAAA
366389 TAAGTGTG-TTT----
1 TAAGTGTGTTTTAAAA
366400 TAAGTGTGTTTTAAAA
1 TAAGTGTGTTTTAAAA
366416 TAAGTGTGTTTTAAAA
1 TAAGTGTGTTTTAAAA
366432 T
1 T
366433 GATAAATGGG
Statistics
Matches: 39, Mismatches: 0, Indels: 10
0.80 0.00 0.20
Matches are distributed among these distances:
11 8 0.21
12 3 0.08
15 3 0.08
16 25 0.64
ACGTcount: A:0.33, C:0.00, G:0.20, T:0.47
Consensus pattern (16 bp):
TAAGTGTGTTTTAAAA
Found at i:366401 original size:27 final size:27
Alignment explanation
Indices: 366364--366429 Score: 125
Period size: 27 Copynumber: 2.5 Consensus size: 27
366354 AAAGGGGGAG
366364 AAGTG-GTTTTAAGTGTGTTTTAAAAT
1 AAGTGTGTTTTAAGTGTGTTTTAAAAT
366390 AAGTGTGTTTTAAGTGTGTTTTAAAAT
1 AAGTGTGTTTTAAGTGTGTTTTAAAAT
366417 AAGTGTGTTTTAA
1 AAGTGTGTTTTAA
366430 AATGATAAAT
Statistics
Matches: 39, Mismatches: 0, Indels: 1
0.98 0.00 0.03
Matches are distributed among these distances:
26 5 0.13
27 34 0.87
ACGTcount: A:0.30, C:0.00, G:0.23, T:0.47
Consensus pattern (27 bp):
AAGTGTGTTTTAAGTGTGTTTTAAAAT
Found at i:370087 original size:20 final size:20
Alignment explanation
Indices: 370062--370099 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
370052 TTTTGGTGCA
*
370062 GAGGGAATCGATACCCCCAT
1 GAGGGAACCGATACCCCCAT
*
370082 GAGGGAACCGATTCCCCC
1 GAGGGAACCGATACCCCC
370100 TTTGAAGGGG
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:0.26, C:0.34, G:0.26, T:0.13
Consensus pattern (20 bp):
GAGGGAACCGATACCCCCAT
Found at i:370143 original size:21 final size:21
Alignment explanation
Indices: 370105--370144 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
370095 CCCCCTTTGA
**
370105 AGGGGAACCGATTTCCCCCAC
1 AGGGGAACCGATACCCCCCAC
*
370126 AGGGGAATCGATACCCCCC
1 AGGGGAACCGATACCCCCC
370145 TGGGGTTCTG
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.25, C:0.38, G:0.25, T:0.12
Consensus pattern (21 bp):
AGGGGAACCGATACCCCCCAC
Found at i:372117 original size:17 final size:18
Alignment explanation
Indices: 372084--372120 Score: 58
Period size: 17 Copynumber: 2.1 Consensus size: 18
372074 GTTTCAATAT
*
372084 TTTGAATATTTTGGATTG
1 TTTGAATATTGTGGATTG
372102 TTTGAAT-TTGTGGATTG
1 TTTGAATATTGTGGATTG
372119 TT
1 TT
372121 AGACTTTGAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 11 0.61
18 7 0.39
ACGTcount: A:0.19, C:0.00, G:0.24, T:0.57
Consensus pattern (18 bp):
TTTGAATATTGTGGATTG
Found at i:372128 original size:17 final size:17
Alignment explanation
Indices: 372091--372128 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
372081 TATTTTGAAT
*
372091 ATTT-TGGATTGTTTGA
1 ATTTGTGGATTGTTAGA
372107 ATTTGTGGATTGTTAGA
1 ATTTGTGGATTGTTAGA
*
372124 CTTTG
1 ATTTG
372129 AATTTATTTG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
16 4 0.21
17 15 0.79
ACGTcount: A:0.18, C:0.03, G:0.26, T:0.53
Consensus pattern (17 bp):
ATTTGTGGATTGTTAGA
Found at i:375098 original size:43 final size:43
Alignment explanation
Indices: 375018--375099 Score: 128
Period size: 43 Copynumber: 1.9 Consensus size: 43
375008 CCATGCATCA
* *
375018 AACAAAACTTTACATATAGGGGACATCTTTCAGTCCTAACTTC
1 AACAAAACTTTACATATAGGGGACAACTTTCACTCCTAACTTC
* *
375061 AACAAAACTTTACATATAGGGGATAACTTTCCCTCCTAA
1 AACAAAACTTTACATATAGGGGACAACTTTCACTCCTAA
375100 AGCCAAGTTA
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
43 35 1.00
ACGTcount: A:0.37, C:0.23, G:0.11, T:0.29
Consensus pattern (43 bp):
AACAAAACTTTACATATAGGGGACAACTTTCACTCCTAACTTC
Found at i:375919 original size:45 final size:45
Alignment explanation
Indices: 375770--375919 Score: 124
Period size: 45 Copynumber: 3.2 Consensus size: 45
375760 ATGAAAAATT
*
375770 CTAGCTCCATATTTTGTTTGGAAAAATTACCTAATCGCATGATTA
1 CTAGTTCCATATTTTGTTTGGAAAAATTACCTAATCGCATGATTA
* * * * * * *
375815 CTAGTTTGCATGCATTTCTATCTATCAAGGTATAAA-T-CCTAACCTCATGCTTT
1 CTAG-TTCCAT--ATTT-TGT-T-T---GG-AAAAATTACCTAATCGCATGATTA
375868 CTAGTTCCATATTTTGTTTGGAAAAATTACCTAATCGCATGATTA
1 CTAGTTCCATATTTTGTTTGGAAAAATTACCTAATCGCATGATTA
375913 CTAGTTC
1 CTAGTTC
375920 GCATGCATTT
Statistics
Matches: 78, Mismatches: 15, Indels: 24
0.67 0.13 0.21
Matches are distributed among these distances:
43 4 0.05
44 3 0.04
45 23 0.29
46 4 0.05
47 1 0.01
48 5 0.06
49 4 0.05
50 5 0.06
51 1 0.01
52 5 0.06
53 16 0.21
54 3 0.04
55 4 0.05
ACGTcount: A:0.29, C:0.19, G:0.13, T:0.39
Consensus pattern (45 bp):
CTAGTTCCATATTTTGTTTGGAAAAATTACCTAATCGCATGATTA
Found at i:376463 original size:24 final size:24
Alignment explanation
Indices: 376436--376487 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
376426 AAAAACATAA
*
376436 AAAATAATATA-TATAAATATTATG
1 AAAATAATA-AGTATAAAAATTATG
*
376460 AAAATAATAAGTATAAAAATTTTG
1 AAAATAATAAGTATAAAAATTATG
376484 AAAA
1 AAAA
376488 GAAAGAATTA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
23 1 0.04
24 24 0.96
ACGTcount: A:0.62, C:0.00, G:0.06, T:0.33
Consensus pattern (24 bp):
AAAATAATAAGTATAAAAATTATG
Found at i:377273 original size:38 final size:38
Alignment explanation
Indices: 377231--377324 Score: 88
Period size: 38 Copynumber: 2.4 Consensus size: 38
377221 AAAGTAATTT
377231 ATAAAATTAAATTTA-TAGATATGATTTAAAATA-AATAA
1 ATAAAATTAAATTTATTAGATATG-TTTAAAATACAAT-A
* *
377269 ATAAATATT--ATTTATTATATATGTTTATAATACTAATA
1 ATAAA-ATTAAATTTATTAGATATGTTTAAAATAC-AATA
*
377307 ATAATAATTAAATATATT
1 ATAA-AATTAAATTTATT
377325 GAAAATAAAC
Statistics
Matches: 46, Mismatches: 3, Indels: 12
0.75 0.05 0.20
Matches are distributed among these distances:
37 13 0.28
38 20 0.43
39 7 0.15
40 6 0.13
ACGTcount: A:0.52, C:0.01, G:0.03, T:0.44
Consensus pattern (38 bp):
ATAAAATTAAATTTATTAGATATGTTTAAAATACAATA
Found at i:377945 original size:27 final size:27
Alignment explanation
Indices: 377914--377976 Score: 126
Period size: 27 Copynumber: 2.3 Consensus size: 27
377904 TTCTCATTTC
377914 ATTTCTCTCTCTAAGAGAGAGAATGAA
1 ATTTCTCTCTCTAAGAGAGAGAATGAA
377941 ATTTCTCTCTCTAAGAGAGAGAATGAA
1 ATTTCTCTCTCTAAGAGAGAGAATGAA
377968 ATTTCTCTC
1 ATTTCTCTC
377977 ATCCTTCTCT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 36 1.00
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.33
Consensus pattern (27 bp):
ATTTCTCTCTCTAAGAGAGAGAATGAA
Found at i:378825 original size:3 final size:3
Alignment explanation
Indices: 378817--378891 Score: 53
Period size: 3 Copynumber: 25.0 Consensus size: 3
378807 CTGTAATATG
* * * * *
378817 TAA TAA TAA TATT TAT TAA TAA TAA AAA AAA T-A TAA TAA TAA TTA
1 TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* * * *
378862 TTA TAA CAA TTA TAA TAA TAA TAA AAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
378892 AATGGGCCAA
Statistics
Matches: 58, Mismatches: 12, Indels: 4
0.78 0.16 0.05
Matches are distributed among these distances:
2 2 0.03
3 54 0.93
4 2 0.03
ACGTcount: A:0.63, C:0.01, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:380839 original size:14 final size:14
Alignment explanation
Indices: 380820--380853 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
380810 ATCGAAATTC
*
380820 TTTTTTTTTTAATA
1 TTTTTTTATTAATA
380834 TTTTTTTATTAATA
1 TTTTTTTATTAATA
380848 TTTTTT
1 TTTTTT
380854 GAAATAACAC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (14 bp):
TTTTTTTATTAATA
Found at i:381301 original size:23 final size:24
Alignment explanation
Indices: 381243--381304 Score: 62
Period size: 20 Copynumber: 2.8 Consensus size: 24
381233 GTTATATTTT
*
381243 ATATTAATATAATTA-TATAAATA
1 ATATTTATATAATTATTATAAATA
* *
381266 TTA-TTAT-T-TTTATTA-AAATA
1 ATATTTATATAATTATTATAAATA
381286 ATATTTATATAATTATTAT
1 ATATTTATATAATTATTAT
381305 TATTTAAATT
Statistics
Matches: 29, Mismatches: 5, Indels: 9
0.67 0.12 0.21
Matches are distributed among these distances:
20 10 0.34
21 7 0.24
22 4 0.14
23 8 0.28
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (24 bp):
ATATTTATATAATTATTATAAATA
Found at i:381326 original size:35 final size:36
Alignment explanation
Indices: 381245--381326 Score: 96
Period size: 35 Copynumber: 2.3 Consensus size: 36
381235 TATATTTTAT
* **
381245 ATTAATATAATTATATAAATATTATTATTTTTATTAA
1 ATTAAT-TATTTATATAAATATTATTATTTAAATTAA
* *
381282 AATAA-TATTTATATAATTATTATTATTTAAATT-A
1 ATTAATTATTTATATAAATATTATTATTTAAATTAA
381316 ATTAATTATTT
1 ATTAATTATTT
381327 TTTGTGCTAA
Statistics
Matches: 38, Mismatches: 6, Indels: 4
0.79 0.12 0.08
Matches are distributed among these distances:
34 5 0.13
35 29 0.76
37 4 0.11
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (36 bp):
ATTAATTATTTATATAAATATTATTATTTAAATTAA
Found at i:381491 original size:17 final size:17
Alignment explanation
Indices: 381471--381509 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
381461 TATTATTTTT
*
381471 AATTTAAATTTATCATA
1 AATTTAAATTAATCATA
* *
381488 AATTTATATTAATTATA
1 AATTTAAATTAATCATA
381505 AATTT
1 AATTT
381510 TTATAATGCA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (17 bp):
AATTTAAATTAATCATA
Found at i:383149 original size:21 final size:21
Alignment explanation
Indices: 383123--383189 Score: 98
Period size: 21 Copynumber: 3.2 Consensus size: 21
383113 ATCTCCGTAG
* *
383123 GGTTACATTCTTAGCCCTCAA
1 GGTTACATTCCTAGCCCGCAA
*
383144 GGTTACATTCCTAGCCCGCCA
1 GGTTACATTCCTAGCCCGCAA
*
383165 GGTTACATGCCTAGCCCGCAA
1 GGTTACATTCCTAGCCCGCAA
383186 GGTT
1 GGTT
383190 TTATGACACC
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 41 1.00
ACGTcount: A:0.21, C:0.31, G:0.21, T:0.27
Consensus pattern (21 bp):
GGTTACATTCCTAGCCCGCAA
Found at i:383904 original size:14 final size:14
Alignment explanation
Indices: 383885--383915 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
383875 TTTTATCCTT
383885 AACATATACATTAA
1 AACATATACATTAA
383899 AACATATACATTAA
1 AACATATACATTAA
383913 AAC
1 AAC
383916 CAACTTATCA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.58, C:0.16, G:0.00, T:0.26
Consensus pattern (14 bp):
AACATATACATTAA
Done.