Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008822.1 Hibiscus syriacus cultivar Beakdansim tig00111990_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: 699754
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
File 2 of 4
Found at i:181974 original size:20 final size:20
Alignment explanation
Indices: 181835--181979 Score: 116
Period size: 20 Copynumber: 7.3 Consensus size: 20
181825 AAGGTACACT
* *
181835 TTCGCAACGCGAAAATCAAA
1 TTCGCAACGCTAAAGTCAAA
*
181855 TTCGTAACG-TGAAAGTCAAA
1 TTCGCAACGCT-AAAGTCAAA
*
181875 CTCGCAACG-TGAAAGTCAAA
1 TTCGCAACGCT-AAAGTCAAA
* * *
181895 CTCACAACGCAAAAGTCAAA
1 TTCGCAACGCTAAAGTCAAA
*
181915 CTCGCAACGC-AAAGTCAAA
1 TTCGCAACGCTAAAGTCAAA
*** * *
181934 TTCGCGTTGCAAAAGTAAAA
1 TTCGCAACGCTAAAGTCAAA
*
181954 TTCGCAACGCTAAATTCAAA
1 TTCGCAACGCTAAAGTCAAA
*
181974 TGCGCA
1 TTCGCA
181980 TTGCGATTTT
Statistics
Matches: 102, Mismatches: 20, Indels: 6
0.80 0.16 0.05
Matches are distributed among these distances:
19 15 0.15
20 87 0.85
ACGTcount: A:0.41, C:0.24, G:0.17, T:0.18
Consensus pattern (20 bp):
TTCGCAACGCTAAAGTCAAA
Found at i:182001 original size:20 final size:20
Alignment explanation
Indices: 181976--182019 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
181966 AATTCAAATG
*
181976 CGCATTGCGATTTTCG-CTTT
1 CGCATTGCGAATTT-GACTTT
*
181996 CGCATTTCGAATTTGACTTT
1 CGCATTGCGAATTTGACTTT
182016 CGCA
1 CGCA
182020 ACAATCACAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 1 0.05
20 20 0.95
ACGTcount: A:0.16, C:0.25, G:0.18, T:0.41
Consensus pattern (20 bp):
CGCATTGCGAATTTGACTTT
Found at i:182282 original size:18 final size:18
Alignment explanation
Indices: 182259--182294 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
182249 AAGCTGGTTG
*
182259 TGATTGGGATTTTGATTT
1 TGATTGGAATTTTGATTT
*
182277 TGATTGTAATTTTGATTT
1 TGATTGGAATTTTGATTT
182295 CCTTTTGCTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.19, C:0.00, G:0.22, T:0.58
Consensus pattern (18 bp):
TGATTGGAATTTTGATTT
Found at i:185589 original size:20 final size:20
Alignment explanation
Indices: 185543--185631 Score: 69
Period size: 20 Copynumber: 4.5 Consensus size: 20
185533 CAAAACATTT
*
185543 GTGTTGCGAAAATAAAA--C
1 GTGTTGCGAAATTAAAATTC
* *
185561 CTTTTGCGAAATTAAAATTC
1 GTGTTGCGAAATTAAAATTC
*
185581 GTGTTGCG-AATTCAAAAATC
1 GTGTTGCGAAATT-AAAATTC
* *
185601 GAGTTGC-AAATTTGAAATTC
1 GTGTTGCGAAA-TTAAAATTC
185621 AGTGTTGCGAA
1 -GTGTTGCGAA
185632 TTTGACTTCT
Statistics
Matches: 54, Mismatches: 10, Indels: 10
0.73 0.14 0.14
Matches are distributed among these distances:
18 14 0.26
19 4 0.07
20 26 0.48
21 8 0.15
22 2 0.04
ACGTcount: A:0.36, C:0.12, G:0.20, T:0.31
Consensus pattern (20 bp):
GTGTTGCGAAATTAAAATTC
Found at i:185669 original size:20 final size:20
Alignment explanation
Indices: 185646--185688 Score: 77
Period size: 20 Copynumber: 2.1 Consensus size: 20
185636 ACTTCTGCGA
185646 TGCGATTTACAGATTCGCGT
1 TGCGATTTACAGATTCGCGT
*
185666 TGCGATTTACATATTCGCGT
1 TGCGATTTACAGATTCGCGT
185686 TGC
1 TGC
185689 AAAATTAGAG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.19, C:0.21, G:0.23, T:0.37
Consensus pattern (20 bp):
TGCGATTTACAGATTCGCGT
Found at i:186952 original size:2 final size:2
Alignment explanation
Indices: 186945--186981 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
186935 CCCGGTTTAT
186945 TA 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 TA T
186982 TATTTTTATA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:186998 original size:20 final size:19
Alignment explanation
Indices: 186977--187013 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
186967 TATATATATA
186977 TATATT-ATTTTTATATTT
1 TATATTAATTTTTATATTT
*
186995 TATATTAATTTTTTTATTT
1 TATATTAATTTTTATATTT
187014 ATAATTCTCA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 6 0.35
19 11 0.65
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (19 bp):
TATATTAATTTTTATATTT
Found at i:187103 original size:39 final size:39
Alignment explanation
Indices: 187018--187128 Score: 104
Period size: 39 Copynumber: 2.8 Consensus size: 39
187008 TTATTTATAA
* * *
187018 TTCTCAAATCATTTCAC-TCTAACATTCAAAATTCCTAAT
1 TTCTTAAATTATTTCACAT-TAACATTCTAAATTCCTAAT
* *
187057 TTCTTAAATT-TTATCACCA-TAACATTCTAAATTCTTAGT
1 TTCTTAAATTATT-TCA-CATTAACATTCTAAATTCCTAAT
*
187096 ATT-TTAAATTATTTCATATTAACATTCTAAATT
1 -TTCTTAAATTATTTCACATTAACATTCTAAATT
187129 ATTTTTTAAA
Statistics
Matches: 60, Mismatches: 6, Indels: 12
0.77 0.08 0.15
Matches are distributed among these distances:
38 3 0.05
39 52 0.87
40 5 0.08
ACGTcount: A:0.36, C:0.18, G:0.01, T:0.45
Consensus pattern (39 bp):
TTCTTAAATTATTTCACATTAACATTCTAAATTCCTAAT
Found at i:199614 original size:18 final size:18
Alignment explanation
Indices: 199591--199626 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
199581 TGTTGCTTAC
199591 GTCTCTGACAAGCCACAA
1 GTCTCTGACAAGCCACAA
199609 GTCTCTGACAAGCCACAA
1 GTCTCTGACAAGCCACAA
199627 CAGGATCGAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.33, C:0.33, G:0.17, T:0.17
Consensus pattern (18 bp):
GTCTCTGACAAGCCACAA
Found at i:202156 original size:34 final size:34
Alignment explanation
Indices: 202111--202177 Score: 84
Period size: 34 Copynumber: 1.9 Consensus size: 34
202101 AATATGAATT
*
202111 ACAATTTCTCTC-GATCTAACAAGGAGAAAACAATA
1 ACAATTTCTCTCTGA--TAAAAAGGAGAAAACAATA
202146 ACAA-TTCTCTCTTGATAAAAAGGAGAAAACAA
1 ACAATTTCTCTC-TGATAAAAAGGAGAAAACAA
202178 CTCTCAAGAA
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
34 23 0.79
35 4 0.14
36 2 0.07
ACGTcount: A:0.48, C:0.18, G:0.12, T:0.22
Consensus pattern (34 bp):
ACAATTTCTCTCTGATAAAAAGGAGAAAACAATA
Found at i:206724 original size:57 final size:57
Alignment explanation
Indices: 206455--206783 Score: 164
Period size: 57 Copynumber: 5.7 Consensus size: 57
206445 TAACACTGAA
* * * *
206455 AAAAGAGAAATAAATTGTTGAATTTATTTCATCTTAGAATCTTGCGT-TGATTCTAACTT-T
1 AAAA-AGAAATAAATTGTTGACTTTATTTC-T-TGAGAATC-T-AGTATGATTCTATCTTGT
* * * * * *
206515 GAAAAGGAATTAATTGTTGAATTTATTTTCCT-ATGAATCTTA-TATGATTCTGT-TTGAT
1 AAAAAGAAATAAATTGTTGACTTTA-TTTCTTGA-GAATC-TAGTATGATTCTATCTTG-T
* * ** * * *
206573 AAAAGGAAATAAAATGTCAAATATATTTGCTTGAAAATCTAG-ATCGATT-TCATCTTGT
1 AAAAAGAAATAAATTGTTGACTTTATTT-CTTGAGAATCTAGTAT-GATTCT-ATCTTGT
* * * * * *
206631 -AGAAGAAAATAAATTGTTAAATTTAATTT-TAT-AGAATCTTGTATGA-TCATGTTTTGT
1 AAAAAG-AAATAAATTGTTGACTTT-ATTTCT-TGAGAATCTAGTATGATTC-TATCTTGT
*
206688 -AAAAGAAATTAAATCAT-TTGA-TTTATTTCTTGAGAATCAAGTATGATTCTATCTTGT
1 AAAAAGAAA-TAAAT--TGTTGACTTTATTTCTTGAGAATCTAGTATGATTCTATCTTGT
*
206745 AAAAAGAAATAAATTGTTGACTTTATTTCTTGAAAATCT
1 AAAAAGAAATAAATTGTTGACTTTATTTCTTGAGAATCT
206784 CGAATCAAAG
Statistics
Matches: 208, Mismatches: 35, Indels: 55
0.70 0.12 0.18
Matches are distributed among these distances:
55 1 0.00
56 16 0.08
57 86 0.41
58 70 0.34
59 28 0.13
60 7 0.03
ACGTcount: A:0.37, C:0.08, G:0.13, T:0.41
Consensus pattern (57 bp):
AAAAAGAAATAAATTGTTGACTTTATTTCTTGAGAATCTAGTATGATTCTATCTTGT
Found at i:212710 original size:24 final size:24
Alignment explanation
Indices: 212678--212732 Score: 101
Period size: 24 Copynumber: 2.3 Consensus size: 24
212668 ATGATTTAAA
*
212678 TTGATTTATTCGGTTTAATTCAGT
1 TTGAATTATTCGGTTTAATTCAGT
212702 TTGAATTATTCGGTTTAATTCAGT
1 TTGAATTATTCGGTTTAATTCAGT
212726 TTGAATT
1 TTGAATT
212733 TTTTTAATTT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.24, C:0.07, G:0.16, T:0.53
Consensus pattern (24 bp):
TTGAATTATTCGGTTTAATTCAGT
Found at i:213545 original size:39 final size:39
Alignment explanation
Indices: 213481--213555 Score: 100
Period size: 40 Copynumber: 1.9 Consensus size: 39
213471 CTCGAAAATA
* *
213481 TAATATATTAAGATTTTATT-TTTTTTAAAATAAATTAT
1 TAATATATTAACATTTTATTGTTTTTTAAAAAAAATTAT
213519 TAATAATATTAACA-TTTATGTGTTTTTTAAAAAAAAT
1 TAAT-ATATTAACATTTTAT-TGTTTTTTAAAAAAAAT
213556 ACAGTAAGGT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
38 9 0.28
39 9 0.28
40 14 0.44
ACGTcount: A:0.44, C:0.01, G:0.04, T:0.51
Consensus pattern (39 bp):
TAATATATTAACATTTTATTGTTTTTTAAAAAAAATTAT
Found at i:214514 original size:20 final size:20
Alignment explanation
Indices: 214489--214535 Score: 94
Period size: 20 Copynumber: 2.4 Consensus size: 20
214479 TGTTCCCTAA
214489 TAATCTTTTATTCCCACTGG
1 TAATCTTTTATTCCCACTGG
214509 TAATCTTTTATTCCCACTGG
1 TAATCTTTTATTCCCACTGG
214529 TAATCTT
1 TAATCTT
214536 ACATTCAGTG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.21, C:0.23, G:0.09, T:0.47
Consensus pattern (20 bp):
TAATCTTTTATTCCCACTGG
Found at i:214541 original size:20 final size:20
Alignment explanation
Indices: 214498--214541 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
214488 ATAATCTTTT
**
214498 ATTCCCACTGGTAATCTTTT
1 ATTCCCACTGGTAATCTTAC
214518 ATTCCCACTGGTAATCTTAC
1 ATTCCCACTGGTAATCTTAC
214538 ATTC
1 ATTC
214542 AGTGAACCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.23, C:0.27, G:0.09, T:0.41
Consensus pattern (20 bp):
ATTCCCACTGGTAATCTTAC
Found at i:214994 original size:2 final size:2
Alignment explanation
Indices: 214987--215024 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
214977 TATTTGTAAG
214987 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
215025 CATCAATGAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:216543 original size:16 final size:17
Alignment explanation
Indices: 216516--216551 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
216506 GATATGAGAA
216516 AAATTCAATTTAAATTT
1 AAATTCAATTTAAATTT
*
216533 AAATT-AATTTAATTTT
1 AAATTCAATTTAAATTT
216549 AAA
1 AAA
216552 ATAACCTTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 13 0.72
17 5 0.28
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (17 bp):
AAATTCAATTTAAATTT
Found at i:217633 original size:2 final size:2
Alignment explanation
Indices: 217626--217665 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
217616 GCTGGTAGGA
217626 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
217666 TGACAAGAAT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:218455 original size:27 final size:23
Alignment explanation
Indices: 218425--218480 Score: 67
Period size: 26 Copynumber: 2.3 Consensus size: 23
218415 TTTCGAATGT
218425 TTTATTTATTTAATTTGTTAGTATTA
1 TTTATTT-TTTAATTTG-TA-TATTA
*
218451 GTTTATATTTTAATTTGTATATTA
1 -TTTATTTTTTAATTTGTATATTA
218475 TTTATT
1 TTTATT
218481 AAATTATGAG
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
23 5 0.19
24 5 0.19
25 2 0.07
26 9 0.33
27 6 0.22
ACGTcount: A:0.27, C:0.00, G:0.07, T:0.66
Consensus pattern (23 bp):
TTTATTTTTTAATTTGTATATTA
Found at i:219986 original size:21 final size:21
Alignment explanation
Indices: 219962--220034 Score: 87
Period size: 21 Copynumber: 3.5 Consensus size: 21
219952 CACTCCCATA
*
219962 TCAGATGTCACCGCAGTCGA-G
1 TCAGATGCCACCGCAG-CGAGG
*
219983 TCAGATGCCACCGCAGCTAGG
1 TCAGATGCCACCGCAGCGAGG
*
220004 TCAGATGCCACCGCAGCTG-GC
1 TCAGATGCCACCGCAGC-GAGG
220025 TCAGATGCCA
1 TCAGATGCCA
220035 ACGCCGGAGG
Statistics
Matches: 46, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
20 2 0.04
21 44 0.96
ACGTcount: A:0.23, C:0.33, G:0.27, T:0.16
Consensus pattern (21 bp):
TCAGATGCCACCGCAGCGAGG
Found at i:223038 original size:36 final size:36
Alignment explanation
Indices: 222978--223147 Score: 229
Period size: 36 Copynumber: 4.6 Consensus size: 36
222968 TGCAAACGAT
222978 TTTTGAAAATACATATATAATATATAGTTTTTAAAACA
1 TTTTG-AAA-ACATATATAATATATAGTTTTTAAAACA
223016 CTTTTGAAAAC-TATATAATATATAGTTTTTAAAACA
1 -TTTTGAAAACATATATAATATATAGTTTTTAAAACA
*
223052 TTTT-AGAAA-ATATATAATATATAATTTTTAAAATCA
1 TTTTGA-AAACATATATAATATATAGTTTTTAAAA-CA
* *
223088 TTTTGAAAACTTATATAATATATAGGTTTTGAAAACA
1 TTTTGAAAACATATATAATATATA-GTTTTTAAAACA
223125 TTTTTGAAAACATATATAATATA
1 -TTTTGAAAACATATATAATATA
223148 ATATTTTAAA
Statistics
Matches: 119, Mismatches: 5, Indels: 15
0.86 0.04 0.11
Matches are distributed among these distances:
34 1 0.01
35 29 0.24
36 34 0.29
37 18 0.15
38 32 0.27
39 5 0.04
ACGTcount: A:0.46, C:0.05, G:0.06, T:0.42
Consensus pattern (36 bp):
TTTTGAAAACATATATAATATATAGTTTTTAAAACA
Found at i:223203 original size:28 final size:30
Alignment explanation
Indices: 223160--223215 Score: 82
Period size: 28 Copynumber: 1.9 Consensus size: 30
223150 ATTTTAAATT
223160 TTTTAAAAATTATATAGTA-TTTAAAAAACA
1 TTTTAAAAATTATATA-TAGTTTAAAAAACA
223190 TTTTAAAAA-T-TATATAGTTTAAAAAA
1 TTTTAAAAATTATATATAGTTTAAAAAA
223216 AACAAATTTG
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
27 2 0.08
28 13 0.52
29 1 0.04
30 9 0.36
ACGTcount: A:0.54, C:0.02, G:0.04, T:0.41
Consensus pattern (30 bp):
TTTTAAAAATTATATATAGTTTAAAAAACA
Found at i:223219 original size:30 final size:30
Alignment explanation
Indices: 223160--223216 Score: 98
Period size: 30 Copynumber: 1.9 Consensus size: 30
223150 ATTTTAAATT
*
223160 TTTTAAAAATTATATAGTATTTAAAAAACA
1 TTTTAAAAATTATATAGTATTAAAAAAACA
223190 TTTTAAAAATTATATAGT-TTAAAAAAA
1 TTTTAAAAATTATATAGTATTAAAAAAA
223217 ACAAATTTGA
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
29 8 0.31
30 18 0.69
ACGTcount: A:0.54, C:0.02, G:0.04, T:0.40
Consensus pattern (30 bp):
TTTTAAAAATTATATAGTATTAAAAAAACA
Found at i:223310 original size:22 final size:23
Alignment explanation
Indices: 223265--223318 Score: 65
Period size: 23 Copynumber: 2.3 Consensus size: 23
223255 ATGAAAAAAC
* *
223265 ATTTTTAAAAATTTATATTATAT
1 ATTTTTAAAAAATAATATTATAT
*
223288 ATTTTTAAAAAATAAT-TTTTAT
1 ATTTTTAAAAAATAATATTATAT
223310 ATTTATTAA
1 ATTT-TTAA
223319 TATTATTATT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
22 9 0.33
23 18 0.67
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (23 bp):
ATTTTTAAAAAATAATATTATAT
Found at i:228752 original size:36 final size:36
Alignment explanation
Indices: 228668--228781 Score: 178
Period size: 34 Copynumber: 3.2 Consensus size: 36
228658 AATTTACTCA
*
228668 AAACAAATTTTTGTCTCTCTTGAGATAGTTTCTCTTG
1 AAACAAA-TTTTGTCTCTCTTGAGATAGTTTCACTTG
228705 AAACAAA--TTGTCTCTCTTGAGATAGTTTCACTTG
1 AAACAAATTTTGTCTCTCTTGAGATAGTTTCACTTG
* *
228739 AAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTG
1 AAACAAATTTTGTCTCTCTTGAGATAGTTTCACTTG
228775 AAACAAA
1 AAACAAA
228782 ATTGAATATG
Statistics
Matches: 72, Mismatches: 3, Indels: 5
0.90 0.04 0.06
Matches are distributed among these distances:
34 33 0.46
36 32 0.44
37 7 0.10
ACGTcount: A:0.30, C:0.18, G:0.13, T:0.39
Consensus pattern (36 bp):
AAACAAATTTTGTCTCTCTTGAGATAGTTTCACTTG
Found at i:228919 original size:73 final size:71
Alignment explanation
Indices: 228800--228951 Score: 216
Period size: 73 Copynumber: 2.1 Consensus size: 71
228790 TGTGTTCCTT
*
228800 GAAACAAATTTTGTCTCCCTTGAGACAGATTTTTCCCTGAACAAGTTTTGTCTCTCTTGAGACAT
1 GAAACAAATTTTGTCTCCCTTGAGACAG--TTTTCCCTGAACAAGTTTTGTCTCTCTTGAGACAG
228865 TTTCTCTC
64 TTTCTCTC
* *
228873 GAAACAAATTTTGTCTCTCTTTAGACAG-TTTCCCTTGAAACAAAGTTTTGTCTCTCTTGAGACA
1 GAAACAAATTTTGTCTCCCTTGAGACAGTTTTCCC-TG-AAC-AAGTTTTGTCTCTCTTGAGACA
*
228937 GTTTCTCTT
63 GTTTCTCTC
228946 GAAACA
1 GAAACA
228952 CCAACCTTTG
Statistics
Matches: 72, Mismatches: 4, Indels: 6
0.88 0.05 0.07
Matches are distributed among these distances:
70 6 0.08
71 2 0.03
72 3 0.04
73 61 0.85
ACGTcount: A:0.26, C:0.22, G:0.14, T:0.39
Consensus pattern (71 bp):
GAAACAAATTTTGTCTCCCTTGAGACAGTTTTCCCTGAACAAGTTTTGTCTCTCTTGAGACAGTT
TCTCTC
Found at i:228938 original size:37 final size:36
Alignment explanation
Indices: 228796--228951 Score: 199
Period size: 37 Copynumber: 4.3 Consensus size: 36
228786 AATATGTGTT
*
228796 CCTTGAAACAAATTTTGTCTCCCTTGAGACAGATTTTTC
1 CCTTGAAACAAATTTTGTCTCTCTTGAGACAG---TTTC
* *
228835 CC-TG-AACAAGTTTTGTCTCTCTTGAGACATTTTC
1 CCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTC
* * *
228869 TCTCGAAACAAATTTTGTCTCTCTTTAGACAGTTTC
1 CCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTC
228905 CCTTGAAACAAAGTTTTGTCTCTCTTGAGACAGTTTC
1 CCTTGAAACAAA-TTTTGTCTCTCTTGAGACAGTTTC
*
228942 TCTTGAAACA
1 CCTTGAAACA
228952 CCAACCTTTG
Statistics
Matches: 102, Mismatches: 12, Indels: 8
0.84 0.10 0.07
Matches are distributed among these distances:
34 5 0.05
35 1 0.01
36 37 0.36
37 55 0.54
38 2 0.02
39 2 0.02
ACGTcount: A:0.25, C:0.22, G:0.13, T:0.39
Consensus pattern (36 bp):
CCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTC
Found at i:229077 original size:37 final size:35
Alignment explanation
Indices: 229003--229090 Score: 130
Period size: 36 Copynumber: 2.6 Consensus size: 35
228993 CCCTGGAGAC
229003 AGTTTCTCTTGAAACAC---AAAAAACCTTTGAAA
1 AGTTTCTCTTGAAACACAAAAAAAAACCTTTGAAA
229035 AGTTTCTCTTGAAACACAAAAAAAAAACCTTTGAAA
1 AGTTTCTCTTGAAACAC-AAAAAAAAACCTTTGAAA
229071 ATGTTTCTCTTG-AACACAAA
1 A-GTTTCTCTTGAAACACAAA
229091 GACCTTTGAG
Statistics
Matches: 51, Mismatches: 0, Indels: 7
0.88 0.00 0.12
Matches are distributed among these distances:
32 17 0.33
35 3 0.06
36 21 0.41
37 10 0.20
ACGTcount: A:0.44, C:0.18, G:0.09, T:0.28
Consensus pattern (35 bp):
AGTTTCTCTTGAAACACAAAAAAAAACCTTTGAAA
Found at i:229239 original size:83 final size:84
Alignment explanation
Indices: 229087--229272 Score: 225
Period size: 83 Copynumber: 2.2 Consensus size: 84
229077 CTCTTGAACA
* * * ** *
229087 CAAAGACCTTTGAGTTCGACTACACTCGCTTCGAGGGCACAACATTTGCAGTATAACTCAAGGCT
1 CAAAGACCTTCGAGTTCGACTACACTCGCTTCAAAGGCACAACATTTGCAACATAACTCAAGGCG
229152 AGAAGGG-TATCTG-CTAAC
66 AGAAGGGCTATCTGTC-AAC
* * * * * *
229170 CAAATACCTTCGAGTTCGACTACGCTCAGC-TCAAAGGCACATCATTTGCAACATAGCTTAAGTC
1 CAAAGACCTTCGAGTTCGACTACACTC-GCTTCAAAGGCACAACATTTGCAACATAACTCAAGGC
229234 GAGAAGGGCTATCTGTCAAC
65 GAGAAGGGCTATCTGTCAAC
229254 CAAAGACCTTCGAGTTCGA
1 CAAAGACCTTCGAGTTCGA
229273 TTATATTCAA
Statistics
Matches: 87, Mismatches: 13, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
83 57 0.66
84 29 0.33
85 1 0.01
ACGTcount: A:0.31, C:0.25, G:0.20, T:0.24
Consensus pattern (84 bp):
CAAAGACCTTCGAGTTCGACTACACTCGCTTCAAAGGCACAACATTTGCAACATAACTCAAGGCG
AGAAGGGCTATCTGTCAAC
Found at i:229625 original size:35 final size:35
Alignment explanation
Indices: 229563--229650 Score: 153
Period size: 35 Copynumber: 2.5 Consensus size: 35
229553 CCTAGAGACA
229563 GTTTCTCTTGAAACAC-AAAAAAACCTTTG-AAAT
1 GTTTCTCTTGAAACACAAAAAAAACCTTTGAAAAT
229596 CGTTTCTCTTGAAACACAAAAAAAACCTTTGAAAAT
1 -GTTTCTCTTGAAACACAAAAAAAACCTTTGAAAAT
229632 GTTTCTCTTGAAACACAAA
1 GTTTCTCTTGAAACACAAA
229651 GACCTTTGAG
Statistics
Matches: 52, Mismatches: 0, Indels: 3
0.95 0.00 0.05
Matches are distributed among these distances:
34 16 0.31
35 32 0.62
36 4 0.08
ACGTcount: A:0.42, C:0.19, G:0.09, T:0.30
Consensus pattern (35 bp):
GTTTCTCTTGAAACACAAAAAAAACCTTTGAAAAT
Found at i:229801 original size:84 final size:85
Alignment explanation
Indices: 229647--229834 Score: 227
Period size: 84 Copynumber: 2.2 Consensus size: 85
229637 TCTTGAAACA
* * * **
229647 CAAAGACCTTTGAGTTCGACTACACTCAGCTTCGAGGGCACAACATTTGCAGTATAACTCAAGGC
1 CAAAGACCTTCGAGTTCGACTACACTCAGCTTCAAAGGCACAACATTTGCAACATAACTCAAGGC
* *
229712 TAGAAGGGTTATCTG-CTAAC
66 GAGAAGGGCTATCTGTC-AAC
* * * * * * *
229732 CAAATACGTTCGAGTTCGACTACGCTCAGC-TCAAAGGCACATCATTTGCAACATAGCTTAAGTC
1 CAAAGACCTTCGAGTTCGACTACACTCAGCTTCAAAGGCACAACATTTGCAACATAACTCAAGGC
229796 GAGAAGGGCTATCTGTCAAC
66 GAGAAGGGCTATCTGTCAAC
229816 CAAAGACCTTCGAGTTCGA
1 CAAAGACCTTCGAGTTCGA
229835 TATATTCAAT
Statistics
Matches: 86, Mismatches: 16, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
84 59 0.69
85 27 0.31
ACGTcount: A:0.31, C:0.24, G:0.21, T:0.24
Consensus pattern (85 bp):
CAAAGACCTTCGAGTTCGACTACACTCAGCTTCAAAGGCACAACATTTGCAACATAACTCAAGGC
GAGAAGGGCTATCTGTCAAC
Found at i:229993 original size:560 final size:558
Alignment explanation
Indices: 228913--230033 Score: 2079
Period size: 560 Copynumber: 2.0 Consensus size: 558
228903 TCCCTTGAAA
228913 CAAAGTTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACACCAACCTTTGAGTATGTTTCCCTTGA
1 CAAAGTTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACACCAACCTTTGAGTATGTTTCCCTTGA
*
228978 GACAAAATTTTGCCTCCCTGGAGACAGTTTCTCTTGAAACACAAAAAACCTTTGAAAAGTTTCTC
66 GACAAAATTTTGCCTCCCTAGAGACAGTTTCTCTTGAAACACAAAAAACCTTTGAAAAGTTTCTC
229043 TTGAAACACAAAAAAAAAACCTTTGAAAATGTTTCTCTTGAACACAAAGACCTTTGAGTTCGACT
131 TTGAAACAC-AAAAAAAAACCTTTGAAAATGTTTCTCTTGAACACAAAGACCTTTGAGTTCGACT
229108 ACACTCGCTTCGAGGGCACAACATTTGCAGTATAACTCAAGGCTAGAAGGGTATCTGCTAACCAA
195 ACACTCGCTTCGAGGGCACAACATTTGCAGTATAACTCAAGGCTAGAAGGGTATCTGCTAACCAA
229173 ATACCTTCGAGTTCGACTACGCTCAGCTCAAAGGCACATCATTTGCAACATAGCTTAAGTCGAGA
260 ATACCTTCGAGTTCGACTACGCTCAGCTCAAAGGCACATCATTTGCAACATAGCTTAAGTCGAGA
229238 AGGGCTATCTGTCAACCAAAGACCTTCGAGTTCGATTATATTCAACTCAGAGGAAAATCAAATTT
325 AGGGCTATCTGTCAACCAAAGACCTTCGAGTTCGATTATATTCAACTCAGAGGAAAATCAAATTT
*
229303 ATAGCATAGCTCAAGGCAATAAGGGCTATCTATTAATTAAATGTCGAGTTCGATTCCATTCAGCT
390 ACAGCATAGCTCAAGGCAATAAGGGCTATCTATTAATTAAATGTCGAGTTCGATTCCATTCAGCT
*
229368 CGATAACACATCAATCACACTACTTTCCAGTTGCAGTCAAGGTTTTCAAGTTGAGAAGAAGACAT
455 CGATAACACATCAATCACACTACTTTCCAATTGCAGTCAAGGTTTTCAAGTTGAGAAGAAGACAT
229433 GGGTTAGTCGTGCCCTAGTGACAAGAAACCGTTTTTCGG
520 GGGTTAGTCGTGCCCTAGTGACAAGAAACCGTTTTTCGG
229472 CAAAGTTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACACCAACCTTTGAGTATGTTTCCCTTGA
1 CAAAGTTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACACCAACCTTTGAGTATGTTTCCCTTGA
*
229537 GACAAAATTTTGCCTCCCTAGAGACAGTTTCTCTTGAAACACAAAAAAACCTTTGAAATCGTTTC
66 GACAAAATTTTGCCTCCCTAGAGACAGTTTCTCTTGAAACAC-AAAAAACCTTTGAAA-AGTTTC
229602 TCTTGAAACAC-AAAAAAAACCTTTGAAAATGTTTCTCTTGAAACACAAAGACCTTTGAGTTCGA
129 TCTTGAAACACAAAAAAAAACCTTTGAAAATGTTTCTCTTG-AACACAAAGACCTTTGAGTTCGA
229666 CTACACTCAGCTTCGAGGGCACAACATTTGCAGTATAACTCAAGGCTAGAAGGGTTATCTGCTAA
193 CTACACTC-GCTTCGAGGGCACAACATTTGCAGTATAACTCAAGGCTAGAAGGG-TATCTGCTAA
*
229731 CCAAATACGTTCGAGTTCGACTACGCTCAGCTCAAAGGCACATCATTTGCAACATAGCTTAAGTC
256 CCAAATACCTTCGAGTTCGACTACGCTCAGCTCAAAGGCACATCATTTGCAACATAGCTTAAGTC
*
229796 GAGAAGGGCTATCTGTCAACCAAAGACCTTCGAGTTCGA-TATATTCAA-TCAGAGGCAAATCAA
321 GAGAAGGGCTATCTGTCAACCAAAGACCTTCGAGTTCGATTATATTCAACTCAGAGGAAAATCAA
*
229859 ATTTACAGCATAGCTC-AGGCAATAAGGGCTATCTATTAATTAAATTGTCGAGTTCGATTCTATT
386 ATTTACAGCATAGCTCAAGGCAATAAGGGCTATCTATTAATTAAA-TGTCGAGTTCGATTCCATT
229923 CAGCTCGATAACACATCAATCACACTACTTTCCAATTGCAGTCAAGGTTTTCAAGTTGAGAAGAA
450 CAGCTCGATAACACATCAATCACACTACTTTCCAATTGCAGTCAAGGTTTTCAAGTTGAGAAGAA
*
229988 GACATGGGTTAGTCGTGCCCTAGTGACAAGAAACCGTTTTTTGG
515 GACATGGGTTAGTCGTGCCCTAGTGACAAGAAACCGTTTTTCGG
230032 CA
1 CA
230034 GCACAACTTA
Statistics
Matches: 548, Mismatches: 8, Indels: 11
0.97 0.01 0.02
Matches are distributed among these distances:
559 163 0.30
560 202 0.37
561 70 0.13
562 113 0.21
ACGTcount: A:0.32, C:0.22, G:0.18, T:0.28
Consensus pattern (558 bp):
CAAAGTTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACACCAACCTTTGAGTATGTTTCCCTTGA
GACAAAATTTTGCCTCCCTAGAGACAGTTTCTCTTGAAACACAAAAAACCTTTGAAAAGTTTCTC
TTGAAACACAAAAAAAAACCTTTGAAAATGTTTCTCTTGAACACAAAGACCTTTGAGTTCGACTA
CACTCGCTTCGAGGGCACAACATTTGCAGTATAACTCAAGGCTAGAAGGGTATCTGCTAACCAAA
TACCTTCGAGTTCGACTACGCTCAGCTCAAAGGCACATCATTTGCAACATAGCTTAAGTCGAGAA
GGGCTATCTGTCAACCAAAGACCTTCGAGTTCGATTATATTCAACTCAGAGGAAAATCAAATTTA
CAGCATAGCTCAAGGCAATAAGGGCTATCTATTAATTAAATGTCGAGTTCGATTCCATTCAGCTC
GATAACACATCAATCACACTACTTTCCAATTGCAGTCAAGGTTTTCAAGTTGAGAAGAAGACATG
GGTTAGTCGTGCCCTAGTGACAAGAAACCGTTTTTCGG
Found at i:230553 original size:36 final size:35
Alignment explanation
Indices: 230469--230629 Score: 176
Period size: 36 Copynumber: 4.6 Consensus size: 35
230459 GAAAATACGT
*
230469 ATATAATATATAGTTTTT-AAACACTTTG---AATA
1 ATAT-ATATATAGTTTTTAAAACATTTTGAAAAATA
230501 CATATATAT-TAG-TTTTAAAATCATTTTGAAAAATA
1 -ATATATATATAGTTTTTAAAA-CATTTTGAAAAATA
230536 ATATATATATAGTTTTTAAAATCATTTTGAAAAAATA
1 ATATATATATAGTTTTTAAAA-CATTTTG-AAAAATA
*
230573 ATATA-ATATAGTTTTTGAAAAC-TTTTGAAAAATT
1 ATATATATATAGTTTTT-AAAACATTTTGAAAAATA
*
230607 ATATAATATATAGTTTTGAAAAC
1 ATAT-ATATATAGTTTTTAAAAC
230630 TTATATAATA
Statistics
Matches: 114, Mismatches: 3, Indels: 20
0.83 0.02 0.15
Matches are distributed among these distances:
30 4 0.04
31 6 0.05
32 10 0.09
33 4 0.04
34 18 0.16
35 18 0.16
36 38 0.33
37 16 0.14
ACGTcount: A:0.46, C:0.04, G:0.07, T:0.43
Consensus pattern (35 bp):
ATATATATATAGTTTTTAAAACATTTTGAAAAATA
Found at i:230654 original size:25 final size:25
Alignment explanation
Indices: 230595--230654 Score: 93
Period size: 25 Copynumber: 2.4 Consensus size: 25
230585 TTTTGAAAAC
* *
230595 TTTTGAAAAATTATATAATATATAG
1 TTTTGAAAACTTATATAATATATAA
230620 TTTTGAAAACTTATATAATATATAA
1 TTTTGAAAACTTATATAATATATAA
*
230645 TTTTTAAAAC
1 TTTTGAAAAC
230655 ATTTTTGAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 32 1.00
ACGTcount: A:0.47, C:0.03, G:0.05, T:0.45
Consensus pattern (25 bp):
TTTTGAAAACTTATATAATATATAA
Found at i:230680 original size:29 final size:30
Alignment explanation
Indices: 230638--230714 Score: 97
Period size: 31 Copynumber: 2.6 Consensus size: 30
230628 ACTTATATAA
*
230638 TATATAATTTTT-AAAACATTTTTGAAAAT
1 TATATAATTTTTAAAAACATTTTTAAAAAT
*
230667 TATATAGTTTTTAAAAAACATTTTTAAAAAT
1 TATATAATTTTT-AAAAACATTTTTAAAAAT
230698 TATAGT--TTTTTAAAAAC
1 TATA-TAATTTTTAAAAAC
230715 CAATTTGAAA
Statistics
Matches: 43, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
29 17 0.40
30 5 0.12
31 20 0.47
32 1 0.02
ACGTcount: A:0.45, C:0.04, G:0.04, T:0.47
Consensus pattern (30 bp):
TATATAATTTTTAAAAACATTTTTAAAAAT
Found at i:230685 original size:31 final size:30
Alignment explanation
Indices: 230650--230731 Score: 105
Period size: 30 Copynumber: 2.7 Consensus size: 30
230640 TATAATTTTT
230650 AAAACATTTTTGAAAATTATATAGTTTTTAA
1 AAAACATTTTTGAAAATT-TATAGTTTTTAA
*
230681 AAAACATTTTT-AAAAATTATAGTTTTTTAA
1 AAAACATTTTTGAAAATTTATAG-TTTTTAA
* *
230711 AAACCA-ATTTGAAAATTTATA
1 AAAACATTTTTGAAAATTTATA
230732 AATAATATAT
Statistics
Matches: 45, Mismatches: 4, Indels: 5
0.83 0.07 0.09
Matches are distributed among these distances:
29 8 0.18
30 26 0.58
31 11 0.24
ACGTcount: A:0.48, C:0.05, G:0.05, T:0.43
Consensus pattern (30 bp):
AAAACATTTTTGAAAATTTATAGTTTTTAA
Found at i:230710 original size:30 final size:30
Alignment explanation
Indices: 230638--230731 Score: 95
Period size: 30 Copynumber: 3.1 Consensus size: 30
230628 ACTTATATAA
*
230638 TATATAATTTTT--AAAACATTTTTGAAAAT
1 TATAT-ATTTTTAAAAAACATTTTTAAAAAT
230667 TATATAGTTTTTAAAAAACATTTTTAAAAAT
1 TATATA-TTTTTAAAAAACATTTTTAAAAAT
* * * *
230698 TATAGT-TTTTTAAAAACCAATTTGAAAATT
1 TATA-TATTTTTAAAAAACATTTTTAAAAAT
230728 TATA
1 TATA
230732 AATAATATAT
Statistics
Matches: 56, Mismatches: 5, Indels: 7
0.82 0.07 0.10
Matches are distributed among these distances:
28 1 0.02
29 10 0.18
30 24 0.43
31 20 0.36
32 1 0.02
ACGTcount: A:0.46, C:0.04, G:0.04, T:0.46
Consensus pattern (30 bp):
TATATATTTTTAAAAAACATTTTTAAAAAT
Found at i:230725 original size:29 final size:30
Alignment explanation
Indices: 230638--230731 Score: 90
Period size: 31 Copynumber: 3.2 Consensus size: 30
230628 ACTTATATAA
*
230638 TATATAATTTTT--AAAACATTTTTGAAAAT
1 TATAT-ATTTTTAAAAAACATATTTGAAAAT
* *
230667 TATATAGTTTTTAAAAAACATTTTTAAAAAT
1 TATATA-TTTTTAAAAAACATATTTGAAAAT
*
230698 TATAGT-TTTTTAAAAACCA-ATTTGAAAAT
1 TATA-TATTTTTAAAAAACATATTTGAAAAT
230727 T-TATA
1 TATATA
230732 AATAATATAT
Statistics
Matches: 56, Mismatches: 4, Indels: 11
0.79 0.06 0.15
Matches are distributed among these distances:
27 1 0.02
28 3 0.05
29 19 0.34
30 12 0.21
31 20 0.36
32 1 0.02
ACGTcount: A:0.46, C:0.04, G:0.04, T:0.46
Consensus pattern (30 bp):
TATATATTTTTAAAAAACATATTTGAAAAT
Found at i:230826 original size:20 final size:21
Alignment explanation
Indices: 230791--230839 Score: 68
Period size: 20 Copynumber: 2.4 Consensus size: 21
230781 GTTTTAAAAA
230791 TTTT-TTATATTTATTA-TTC
1 TTTTATTATATTTATTATTTC
230810 TTATTATTATA-TTATTATTTC
1 TT-TTATTATATTTATTATTTC
230831 TTTTATTAT
1 TTTTATTAT
230840 TCTTATTGTT
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
19 2 0.07
20 15 0.56
21 10 0.37
ACGTcount: A:0.24, C:0.04, G:0.00, T:0.71
Consensus pattern (21 bp):
TTTTATTATATTTATTATTTC
Found at i:234437 original size:4 final size:4
Alignment explanation
Indices: 234428--234453 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
234418 TTATTGTGAA
234428 TATT TATT TATT TATT TATT TATT TA
1 TATT TATT TATT TATT TATT TATT TA
234454 GTATTAATTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (4 bp):
TATT
Found at i:236853 original size:21 final size:21
Alignment explanation
Indices: 236829--236874 Score: 92
Period size: 21 Copynumber: 2.2 Consensus size: 21
236819 AAGCGACGTT
236829 GCCATATGGATTGTTCGTGGA
1 GCCATATGGATTGTTCGTGGA
236850 GCCATATGGATTGTTCGTGGA
1 GCCATATGGATTGTTCGTGGA
236871 GCCA
1 GCCA
236875 CATTGATATA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.20, C:0.17, G:0.33, T:0.30
Consensus pattern (21 bp):
GCCATATGGATTGTTCGTGGA
Found at i:237740 original size:19 final size:19
Alignment explanation
Indices: 237711--237761 Score: 84
Period size: 19 Copynumber: 2.7 Consensus size: 19
237701 ATGTAATTAG
*
237711 TGTACCAATACACCTGGGA
1 TGTACCGATACACCTGGGA
*
237730 TGTACTGATACACCTGGGA
1 TGTACCGATACACCTGGGA
237749 TGTACCGATACAC
1 TGTACCGATACAC
237762 TTGGTCAACT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.29, C:0.25, G:0.22, T:0.24
Consensus pattern (19 bp):
TGTACCGATACACCTGGGA
Found at i:239196 original size:21 final size:21
Alignment explanation
Indices: 239172--239213 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
239162 CGAGATAAAG
239172 AAGGAGACGGAGAAAAAAAAA
1 AAGGAGACGGAGAAAAAAAAA
239193 AAGGAGACGGAGAAAAAAAAA
1 AAGGAGACGGAGAAAAAAAAA
239214 GAACGTTGGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.67, C:0.05, G:0.29, T:0.00
Consensus pattern (21 bp):
AAGGAGACGGAGAAAAAAAAA
Found at i:241497 original size:12 final size:12
Alignment explanation
Indices: 241480--241504 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
241470 TTGTAAACAC
241480 ACATGACGTTGG
1 ACATGACGTTGG
241492 ACATGACGTTGG
1 ACATGACGTTGG
241504 A
1 A
241505 GAACCATCAT
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:0.28, C:0.16, G:0.32, T:0.24
Consensus pattern (12 bp):
ACATGACGTTGG
Found at i:243577 original size:23 final size:21
Alignment explanation
Indices: 243523--243580 Score: 57
Period size: 23 Copynumber: 2.7 Consensus size: 21
243513 ATCCTCGGTA
243523 TGTATCGATACACTATGAATG
1 TGTATCGATACACTATGAATG
*
243544 TGTA-CTAATACATTCCT-TGAATG
1 TGTATC-GATACA---CTATGAATG
243567 TGTATCGATACACT
1 TGTATCGATACACT
243581 CAGGAGTGTA
Statistics
Matches: 30, Mismatches: 2, Indels: 11
0.70 0.05 0.26
Matches are distributed among these distances:
20 3 0.10
21 9 0.30
23 15 0.50
24 3 0.10
ACGTcount: A:0.31, C:0.17, G:0.16, T:0.36
Consensus pattern (21 bp):
TGTATCGATACACTATGAATG
Found at i:250651 original size:3 final size:3
Alignment explanation
Indices: 250643--250667 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
250633 AATCAGGGTT
250643 TTG TTG TTG TTG TTG TTG TTG TTG T
1 TTG TTG TTG TTG TTG TTG TTG TTG T
250668 AATAACTATA
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:0.00, C:0.00, G:0.32, T:0.68
Consensus pattern (3 bp):
TTG
Found at i:251131 original size:20 final size:19
Alignment explanation
Indices: 251106--251159 Score: 65
Period size: 20 Copynumber: 2.7 Consensus size: 19
251096 GCGAAATAAA
251106 AATCGCAATGCGATCTCCAG
1 AATCGCAATGCGATC-CCAG
*
251126 AATCGCAAAT-CAGTTCCCAG
1 AATCGC-AATGC-GATCCCAG
251146 AATCGCAATGCGAT
1 AATCGCAATGCGAT
251160 TATGAAGAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 7
0.76 0.05 0.18
Matches are distributed among these distances:
19 5 0.17
20 18 0.62
21 6 0.21
ACGTcount: A:0.33, C:0.28, G:0.19, T:0.20
Consensus pattern (19 bp):
AATCGCAATGCGATCCCAG
Found at i:251237 original size:20 final size:20
Alignment explanation
Indices: 251209--251261 Score: 61
Period size: 20 Copynumber: 2.6 Consensus size: 20
251199 GATTTTCCAG
* * *
251209 AATCGCAACGCGAATATGAA
1 AATCACAACGCGAACATCAA
*
251229 AATCACAACGCGAACATCTA
1 AATCACAACGCGAACATCAA
*
251249 AATCACAATGCGA
1 AATCACAACGCGA
251262 TTCTGACTAT
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.45, C:0.25, G:0.15, T:0.15
Consensus pattern (20 bp):
AATCACAACGCGAACATCAA
Found at i:251294 original size:21 final size:21
Alignment explanation
Indices: 251270--251372 Score: 111
Period size: 21 Copynumber: 5.0 Consensus size: 21
251260 GATTCTGACT
*
251270 ATCGCAACGAGTATTCGTAAA
1 ATCGCAACGAGTATCCGTAAA
*
251291 ATCGCAACGCGTATCCGT-AA
1 ATCGCAACGAGTATCCGTAAA
** **
251311 ATCGCAACGACAATATGTAAA
1 ATCGCAACGAGTATCCGTAAA
*
251332 ATCGCAACGCGTATCCGT-AA
1 ATCGCAACGAGTATCCGTAAA
* *
251352 ATCGCAACGAGAATACGTAAA
1 ATCGCAACGAGTATCCGTAAA
251373 TAATTTTAGC
Statistics
Matches: 65, Mismatches: 15, Indels: 4
0.77 0.18 0.05
Matches are distributed among these distances:
20 32 0.49
21 33 0.51
ACGTcount: A:0.39, C:0.23, G:0.18, T:0.19
Consensus pattern (21 bp):
ATCGCAACGAGTATCCGTAAA
Found at i:251315 original size:41 final size:41
Alignment explanation
Indices: 251270--251372 Score: 163
Period size: 41 Copynumber: 2.5 Consensus size: 41
251260 GATTCTGACT
*
251270 ATCGCAACGAGTATTCGTAAAATCGCAACGCGTATCCGTAA
1 ATCGCAACGAGAATTCGTAAAATCGCAACGCGTATCCGTAA
*
251311 ATCGCAACGACAATAT-GTAAAATCGCAACGCGTATCCGTAA
1 ATCGCAACGAGAAT-TCGTAAAATCGCAACGCGTATCCGTAA
*
251352 ATCGCAACGAGAATACGTAAA
1 ATCGCAACGAGAATTCGTAAA
251373 TAATTTTAGC
Statistics
Matches: 56, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
41 55 0.98
42 1 0.02
ACGTcount: A:0.39, C:0.23, G:0.18, T:0.19
Consensus pattern (41 bp):
ATCGCAACGAGAATTCGTAAAATCGCAACGCGTATCCGTAA
Found at i:251370 original size:20 final size:20
Alignment explanation
Indices: 251270--251373 Score: 109
Period size: 20 Copynumber: 5.1 Consensus size: 20
251260 GATTCTGACT
*
251270 ATCGCAACGAGTATTCGTAAA
1 ATCGCAACGAGTATACGT-AA
* *
251291 ATCGCAACGCGTATCCGTAA
1 ATCGCAACGAGTATACGTAA
** *
251311 ATCGCAACGACAATATGTAAA
1 ATCGCAACGAGTATACGT-AA
* *
251332 ATCGCAACGCGTATCCGTAA
1 ATCGCAACGAGTATACGTAA
*
251352 ATCGCAACGAGAATACGTAA
1 ATCGCAACGAGTATACGTAA
251372 AT
1 AT
251374 AATTTTAGCA
Statistics
Matches: 67, Mismatches: 15, Indels: 3
0.79 0.18 0.04
Matches are distributed among these distances:
20 36 0.54
21 31 0.46
ACGTcount: A:0.38, C:0.23, G:0.18, T:0.20
Consensus pattern (20 bp):
ATCGCAACGAGTATACGTAA
Found at i:251700 original size:23 final size:21
Alignment explanation
Indices: 251646--251703 Score: 57
Period size: 23 Copynumber: 2.7 Consensus size: 21
251636 ATCCTCGCTA
251646 TGTATCGATACACTATGAATG
1 TGTATCGATACACTATGAATG
*
251667 TGTA-CTAATACATTCCT-TGAATG
1 TGTATC-GATACA---CTATGAATG
251690 TGTATCGATACACT
1 TGTATCGATACACT
251704 CAGGAGTGTA
Statistics
Matches: 30, Mismatches: 2, Indels: 11
0.70 0.05 0.26
Matches are distributed among these distances:
20 3 0.10
21 9 0.30
23 15 0.50
24 3 0.10
ACGTcount: A:0.31, C:0.17, G:0.16, T:0.36
Consensus pattern (21 bp):
TGTATCGATACACTATGAATG
Found at i:252694 original size:15 final size:15
Alignment explanation
Indices: 252674--252718 Score: 72
Period size: 15 Copynumber: 3.0 Consensus size: 15
252664 GCTAGGACAT
252674 TTGGTTTAGATAACG
1 TTGGTTTAGATAACG
252689 TTGGTTTAGATAACG
1 TTGGTTTAGATAACG
* *
252704 TCGGTTTAGACAACG
1 TTGGTTTAGATAACG
252719 AAAAAATTGT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 28 1.00
ACGTcount: A:0.27, C:0.11, G:0.27, T:0.36
Consensus pattern (15 bp):
TTGGTTTAGATAACG
Found at i:257920 original size:3 final size:3
Alignment explanation
Indices: 257912--257936 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
257902 AATCAGGGTT
257912 TTG TTG TTG TTG TTG TTG TTG TTG T
1 TTG TTG TTG TTG TTG TTG TTG TTG T
257937 AATAACTATA
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:0.00, C:0.00, G:0.32, T:0.68
Consensus pattern (3 bp):
TTG
Found at i:258401 original size:20 final size:20
Alignment explanation
Indices: 258376--258450 Score: 64
Period size: 20 Copynumber: 3.7 Consensus size: 20
258366 GCGAAATAAA
258376 AATCGCAATGCGATCTCCAG
1 AATCGCAATGCGATCTCCAG
*
258396 AATCGCAAAT-CAGTTC-CCAG
1 AATCGC-AATGC-GATCTCCAG
* * **
258416 AATCGCAACGCGATTATGAAG
1 AATCGCAATGCGA-TCTCCAG
258437 AATCGCAATGCGAT
1 AATCGCAATGCGAT
258451 AGTACAAATT
Statistics
Matches: 43, Mismatches: 7, Indels: 10
0.72 0.12 0.17
Matches are distributed among these distances:
19 3 0.07
20 20 0.47
21 20 0.47
ACGTcount: A:0.35, C:0.25, G:0.20, T:0.20
Consensus pattern (20 bp):
AATCGCAATGCGATCTCCAG
Found at i:258508 original size:20 final size:20
Alignment explanation
Indices: 258485--258531 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
258475 CCAGAATCGA
*
258485 AACGCGAATATGA-AAATCAC
1 AACGCGAACAT-ATAAATCAC
258505 AACGCGAACATATAAATCAC
1 AACGCGAACATATAAATCAC
*
258525 AATGCGA
1 AACGCGA
258532 TTCTGACTAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 1 0.04
20 23 0.96
ACGTcount: A:0.49, C:0.21, G:0.15, T:0.15
Consensus pattern (20 bp):
AACGCGAACATATAAATCAC
Found at i:258584 original size:20 final size:20
Alignment explanation
Indices: 258540--258733 Score: 187
Period size: 20 Copynumber: 9.6 Consensus size: 20
258530 GATTCTGACT
* *
258540 ATCGCAACGAGTATTCGTAAA
1 ATCGCAACGCGTATACGT-AA
*
258561 ATCGCAACGCGTATCCGTAA
1 ATCGCAACGCGTATACGTAA
*
258581 ATCGCAACGAC-AATACGTAAA
1 ATCGCAACG-CGTATACGT-AA
*
258602 ATCGCAACGCGTATCCGTAA
1 ATCGCAACGCGTATACGTAA
* *
258622 ATCGCAACGAGAATACGTAA
1 ATCGCAACGCGTATACGTAA
* *
258642 ATCGCAAAGCGTAT-CTATAA
1 ATCGCAACGCGTATAC-GTAA
* *
258662 ATCGCAACGAGAATACGTAA
1 ATCGCAACGCGTATACGTAA
* *
258682 ATCGCAATGCGTATCCGTAA
1 ATCGCAACGCGTATACGTAA
*
258702 ATCGCAACGAC-AATACGTAAA
1 ATCGCAACG-CGTATACGT-AA
258723 ATCGCAACGCG
1 ATCGCAACGCG
258734 ATTTTTAAAG
Statistics
Matches: 141, Mismatches: 24, Indels: 16
0.78 0.13 0.09
Matches are distributed among these distances:
19 1 0.01
20 94 0.67
21 46 0.33
ACGTcount: A:0.39, C:0.24, G:0.19, T:0.19
Consensus pattern (20 bp):
ATCGCAACGCGTATACGTAA
Found at i:258655 original size:40 final size:41
Alignment explanation
Indices: 258540--258733 Score: 302
Period size: 40 Copynumber: 4.8 Consensus size: 41
258530 GATTCTGACT
* *
258540 ATCGCAACGAGTATTCGTAAAATCGCAACGCGTATCCGTAA
1 ATCGCAACGAGAATACGTAAAATCGCAACGCGTATCCGTAA
*
258581 ATCGCAACGACAATACGTAAAATCGCAACGCGTATCCGTAA
1 ATCGCAACGAGAATACGTAAAATCGCAACGCGTATCCGTAA
* **
258622 ATCGCAACGAGAATACGT-AAATCGCAAAGCGTATCTATAA
1 ATCGCAACGAGAATACGTAAAATCGCAACGCGTATCCGTAA
*
258662 ATCGCAACGAGAATACGT-AAATCGCAATGCGTATCCGTAA
1 ATCGCAACGAGAATACGTAAAATCGCAACGCGTATCCGTAA
*
258702 ATCGCAACGACAATACGTAAAATCGCAACGCG
1 ATCGCAACGAGAATACGTAAAATCGCAACGCG
258734 ATTTTTAAAG
Statistics
Matches: 140, Mismatches: 12, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
40 73 0.52
41 67 0.48
ACGTcount: A:0.39, C:0.24, G:0.19, T:0.19
Consensus pattern (41 bp):
ATCGCAACGAGAATACGTAAAATCGCAACGCGTATCCGTAA
Found at i:259362 original size:19 final size:19
Alignment explanation
Indices: 259292--259367 Score: 71
Period size: 20 Copynumber: 3.9 Consensus size: 19
259282 TTCTAAACTT
* *
259292 AAAATCGCAACATGAAAATA
1 AAAATCGCAACACG-AAATG
*
259312 AAAATCGCAACACAAAAATG
1 AAAATCGCAACAC-GAAATG
** *
259332 ACTATCGCAACGCGAAATG
1 AAAATCGCAACACGAAATG
*
259351 AAAATCGCAACGCGAAA
1 AAAATCGCAACACGAAA
259368 CCAAAATTGC
Statistics
Matches: 46, Mismatches: 9, Indels: 3
0.79 0.16 0.05
Matches are distributed among these distances:
19 20 0.43
20 26 0.57
ACGTcount: A:0.53, C:0.21, G:0.14, T:0.12
Consensus pattern (19 bp):
AAAATCGCAACACGAAATG
Found at i:259373 original size:19 final size:19
Alignment explanation
Indices: 259335--259374 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
259325 AAAAATGACT
**
259335 ATCGCAACGCGAAATGAAA
1 ATCGCAACGCGAAACCAAA
259354 ATCGCAACGCGAAACCAAA
1 ATCGCAACGCGAAACCAAA
259373 AT
1 AT
259375 TGCATTGCGA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.47, C:0.25, G:0.17, T:0.10
Consensus pattern (19 bp):
ATCGCAACGCGAAACCAAA
Found at i:259464 original size:20 final size:20
Alignment explanation
Indices: 259403--259465 Score: 67
Period size: 20 Copynumber: 3.1 Consensus size: 20
259393 TCGCGTTGCG
*
259403 ATTCTCTCGTTACGATTTTC
1 ATTCTCTCGTTGCGATTTTC
**
259423 ATT-TC-CGCATTGCGATAGTC
1 ATTCTCTCG--TTGCGATTTTC
259443 ATTCTCTCGTTGCGATTTTC
1 ATTCTCTCGTTGCGATTTTC
259463 ATT
1 ATT
259466 TCAACCAAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 8
0.72 0.11 0.17
Matches are distributed among these distances:
18 2 0.06
19 2 0.06
20 26 0.76
21 2 0.06
22 2 0.06
ACGTcount: A:0.16, C:0.24, G:0.14, T:0.46
Consensus pattern (20 bp):
ATTCTCTCGTTGCGATTTTC
Found at i:261513 original size:186 final size:187
Alignment explanation
Indices: 261156--261533 Score: 645
Period size: 186 Copynumber: 2.0 Consensus size: 187
261146 TAGATTGCTT
*
261156 AGTAAATTTATTCGGTTGCTGCCAATACTGCTAAACTGTTTATTCTTTAACACTGTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATACTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
261221 ATTTGTCTTTTGTTTTATCTTTTGGTTGAAGTAAATTTATTCGGTTGCTGCCAATTCTACTAAAC
66 ATTTGTCTTTTGTTTTATCTTTTGGTTGAAGTAAATTTATTCGGTTGCTGCCAATTCTACTAAAC
* * *
261286 TGTGTTTTCTTTAACACTGTGAAGTTAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
131 TGTGTATTCTTTAACACTCTAAAGTTAGTATTTGTCTTTGTTTTGTCTTTTGGTTG-A
* *
261344 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATACTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
*
261409 ATTTGTCTTTT-TTTT-TCTTTTGGTTGAAAGT-AATTTGTTCGGTTGCTGCCAATTCTACTAAA
66 ATTTGTCTTTTGTTTTATCTTTTGGTTG-AAGTAAATTTATTCGGTTGCTGCCAATTCTACTAAA
*
261471 CTGTGTATTCTTTAATACTCTAAAGTTAGTATTTGTCTTTGTTTTGTCTTTTGGTTGA
130 CTGTGTATTCTTTAACACTCTAAAGTTAGTATTTGTCTTTGTTTTGTCTTTTGGTTGA
261529 AGTAA
1 AGTAA
261534 TGCAATCCGT
Statistics
Matches: 181, Mismatches: 8, Indels: 5
0.93 0.04 0.03
Matches are distributed among these distances:
185 6 0.03
186 94 0.52
187 8 0.04
188 73 0.40
ACGTcount: A:0.22, C:0.13, G:0.18, T:0.48
Consensus pattern (187 bp):
AGTAAATTTATTCGGTTGCTGCCAATACTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
ATTTGTCTTTTGTTTTATCTTTTGGTTGAAGTAAATTTATTCGGTTGCTGCCAATTCTACTAAAC
TGTGTATTCTTTAACACTCTAAAGTTAGTATTTGTCTTTGTTTTGTCTTTTGGTTGA
Found at i:261534 original size:92 final size:94
Alignment explanation
Indices: 261156--261533 Score: 611
Period size: 94 Copynumber: 4.1 Consensus size: 94
261146 TAGATTGCTT
* * *
261156 AGTAAATTTATTCGGTTGCTGCCAATACTGCTAAACTGTTTATTCTTTAACACTGTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTACTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
*
261221 ATTTGTCTTTTGTTTTATCTTTTGGTTG-A
66 ATTTGTC-TTTGTTTTGTCTTTTGGTTGAA
*
261250 AGTAAATTTATTCGGTTGCTGCCAATTCTACTAAACTGTGTTTTCTTTAACACTGTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTACTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
261315 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
* *
261344 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTACTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
*
261409 ATTTGTCTTT-TTTTTTCTTTTGGTTGAA
66 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
* * * *
261437 AGT-AATTTGTTCGGTTGCTGCCAATTCTACTAAACTGTGTATTCTTTAATACTCTAAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTACTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
261501 ATTTGTCTTTGTTTTGTCTTTTGGTTG-A
66 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
261529 AGTAA
1 AGTAA
261534 TGCAATCCGT
Statistics
Matches: 267, Mismatches: 14, Indels: 7
0.93 0.05 0.02
Matches are distributed among these distances:
92 71 0.27
93 55 0.21
94 141 0.53
ACGTcount: A:0.22, C:0.13, G:0.18, T:0.48
Consensus pattern (94 bp):
AGTAAATTTATTCGGTTGCTGCCAATTCTACTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:261637 original size:19 final size:19
Alignment explanation
Indices: 261621--261738 Score: 112
Period size: 19 Copynumber: 6.7 Consensus size: 19
261611 AAAAATGACT
261621 ATCGCAACGCGAAATGAAA
1 ATCGCAACGCGAAATGAAA
*
261640 ATCGCAA--CG--A-GAGA
1 ATCGCAACGCGAAATGAAA
261654 ATCGCAACGCGAAATGAAA
1 ATCGCAACGCGAAATGAAA
261673 ATCGCAACGCGAAATGAAA
1 ATCGCAACGCGAAATGAAA
* *
261692 AGCGCAA--CG--A-CAAA
1 ATCGCAACGCGAAATGAAA
**
261706 ATCGCAACGCGAAACCAAA
1 ATCGCAACGCGAAATGAAA
*
261725 ATCGCAACGTGAAA
1 ATCGCAACGCGAAA
261739 CTATAATCGC
Statistics
Matches: 83, Mismatches: 6, Indels: 20
0.76 0.06 0.18
Matches are distributed among these distances:
14 19 0.23
15 2 0.02
16 4 0.05
17 4 0.05
18 2 0.02
19 52 0.63
ACGTcount: A:0.47, C:0.24, G:0.21, T:0.08
Consensus pattern (19 bp):
ATCGCAACGCGAAATGAAA
Found at i:261679 original size:52 final size:52
Alignment explanation
Indices: 261621--261738 Score: 182
Period size: 52 Copynumber: 2.3 Consensus size: 52
261611 AAAAATGACT
* * * **
261621 ATCGCAACGCGAAATGAAAATCGCAACGAGAGAATCGCAACGCGAAATGAAA
1 ATCGCAACGCGAAATGAAAAGCGCAACGACAAAATCGCAACGCGAAACCAAA
261673 ATCGCAACGCGAAATGAAAAGCGCAACGACAAAATCGCAACGCGAAACCAAA
1 ATCGCAACGCGAAATGAAAAGCGCAACGACAAAATCGCAACGCGAAACCAAA
*
261725 ATCGCAACGTGAAA
1 ATCGCAACGCGAAA
261739 CTATAATCGC
Statistics
Matches: 60, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
52 60 1.00
ACGTcount: A:0.47, C:0.24, G:0.21, T:0.08
Consensus pattern (52 bp):
ATCGCAACGCGAAATGAAAAGCGCAACGACAAAATCGCAACGCGAAACCAAA
Found at i:261707 original size:33 final size:33
Alignment explanation
Indices: 261670--261733 Score: 101
Period size: 33 Copynumber: 1.9 Consensus size: 33
261660 ACGCGAAATG
**
261670 AAAATCGCAACGCGAAATGAAAAGCGCAACGAC
1 AAAATCGCAACGCGAAACCAAAAGCGCAACGAC
*
261703 AAAATCGCAACGCGAAACCAAAATCGCAACG
1 AAAATCGCAACGCGAAACCAAAAGCGCAACG
261734 TGAAACTATA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 28 1.00
ACGTcount: A:0.48, C:0.27, G:0.19, T:0.06
Consensus pattern (33 bp):
AAAATCGCAACGCGAAACCAAAAGCGCAACGAC
Found at i:261767 original size:19 final size:19
Alignment explanation
Indices: 261745--261865 Score: 100
Period size: 19 Copynumber: 6.8 Consensus size: 19
261735 GAAACTATAA
261745 TCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
261764 TCGCATTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
261778 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
261797 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
261811 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
**
261830 TCGCGTTGCGATAGTCATTTT
1 TCGCGTTGCGATTTTCA--TT
*
261851 TCACGTTGCGATTTT
1 TCGCGTTGCGATTTT
261866 AAGTTCCAGA
Statistics
Matches: 79, Mismatches: 11, Indels: 22
0.71 0.10 0.20
Matches are distributed among these distances:
14 19 0.24
16 6 0.08
17 6 0.08
19 34 0.43
21 14 0.18
ACGTcount: A:0.12, C:0.22, G:0.21, T:0.45
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:261788 original size:14 final size:14
Alignment explanation
Indices: 261769--261823 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
261759 TCATTTCGCA
261769 TTGCGATTCTCTCG
1 TTGCGATTCTCTCG
*
261783 TTGCGATTTTCATTTCGCG
1 TTGCGA--TTC---TCTCG
261802 TTGCGATTCTCTCG
1 TTGCGATTCTCTCG
261816 TTGCGATT
1 TTGCGATT
261824 TTCATTTCGC
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
14 18 0.53
16 3 0.09
17 3 0.09
19 10 0.29
ACGTcount: A:0.09, C:0.24, G:0.22, T:0.45
Consensus pattern (14 bp):
TTGCGATTCTCTCG
Found at i:261790 original size:33 final size:33
Alignment explanation
Indices: 261748--261841 Score: 179
Period size: 33 Copynumber: 2.8 Consensus size: 33
261738 ACTATAATCG
*
261748 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCGTTGCGATTCTCT
261781 CGTTGCGATTTTCATTTCGCGTTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCGTTGCGATTCTCT
261814 CGTTGCGATTTTCATTTCGCGTTGCGAT
1 CGTTGCGATTTTCATTTCGCGTTGCGAT
261842 AGTCATTTTT
Statistics
Matches: 60, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 60 1.00
ACGTcount: A:0.11, C:0.23, G:0.21, T:0.45
Consensus pattern (33 bp):
CGTTGCGATTTTCATTTCGCGTTGCGATTCTCT
Found at i:263747 original size:14 final size:14
Alignment explanation
Indices: 263728--263754 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
263718 ATTGTTTAAT
263728 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
263742 TGATTTGTAAAAG
1 TGATTTGTAAAAG
263755 TTAATTTGTT
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:0.00, G:0.22, T:0.37
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:263761 original size:14 final size:14
Alignment explanation
Indices: 263730--263763 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
263720 TGTTTAATTG
*
263730 ATTTGTAAAAGATG
1 ATTTGTAAAAGATA
*
263744 ATTTGTAAAAGTTA
1 ATTTGTAAAAGATA
263758 ATTTGT
1 ATTTGT
263764 TTAATTGATG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.38, C:0.00, G:0.18, T:0.44
Consensus pattern (14 bp):
ATTTGTAAAAGATA
Found at i:263891 original size:19 final size:19
Alignment explanation
Indices: 263869--263960 Score: 87
Period size: 19 Copynumber: 5.4 Consensus size: 19
263859 AAAAATGACT
263869 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
263888 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
*
263902 ATCACAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
263921 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
263935 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
263954 ATCGCAA
1 ATCGCAA
263961 CGACAAAATC
Statistics
Matches: 57, Mismatches: 6, Indels: 20
0.69 0.07 0.24
Matches are distributed among these distances:
14 19 0.33
15 2 0.04
16 4 0.07
17 4 0.07
18 2 0.04
19 26 0.46
ACGTcount: A:0.47, C:0.18, G:0.22, T:0.13
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:263915 original size:33 final size:33
Alignment explanation
Indices: 263869--263981 Score: 190
Period size: 33 Copynumber: 3.4 Consensus size: 33
263859 AAAAATGACT
263869 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
*
263902 ATCACAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
* *
263935 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
*
263968 ATCGCAACGCGAAA
1 ATCGCAATGCGAAA
263982 CTAAATTCGC
Statistics
Matches: 75, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 75 1.00
ACGTcount: A:0.47, C:0.20, G:0.21, T:0.12
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:264033 original size:33 final size:33
Alignment explanation
Indices: 263991--264190 Score: 229
Period size: 33 Copynumber: 5.8 Consensus size: 33
263981 ACTAAATTCG
* *
263991 CGTTGCGATTTTCATTTCGCTTTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCTCA
* * *
264024 CGTTGCGATTTTCATTTTGCTTTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCTCA
* *
264057 CATTGCGATTTTCATTTCGCATTGCGATAGTCATTTCCG
1 CGTTGCGATTTTCATTTCGCATTGCGAT--TC---T-CA
* * * *
264096 CGTTGCGATATTCTAATTCGCGTTGCGATTTTCA
1 CGTTGCGATTTTC-ATTTCGCATTGCGATTCTCA
*
264130 CGTTGCGATTTTCATTTCGCATTGCGATTTTCA
1 CGTTGCGATTTTCATTTCGCATTGCGATTCTCA
264163 CGTTGCGATTTTCATTTCGCATTGCGAT
1 CGTTGCGATTTTCATTTCGCATTGCGAT
264191 AGACATTAAG
Statistics
Matches: 146, Mismatches: 14, Indels: 14
0.84 0.08 0.08
Matches are distributed among these distances:
33 103 0.71
34 13 0.09
35 3 0.02
38 2 0.01
39 12 0.08
40 13 0.09
ACGTcount: A:0.14, C:0.22, G:0.19, T:0.45
Consensus pattern (33 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCTCA
Found at i:264103 original size:20 final size:19
Alignment explanation
Indices: 264068--264124 Score: 69
Period size: 20 Copynumber: 2.9 Consensus size: 19
264058 ATTGCGATTT
*
264068 TCATTTCGCATTGCGATAG
1 TCATTTCGCGTTGCGATAG
*
264087 TCATTTCCGCGTTGCGATAT
1 TCATTT-CGCGTTGCGATAG
*
264107 TCTAATTCGCGTTGCGAT
1 TC-ATTTCGCGTTGCGAT
264125 TTTCACGTTG
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
19 6 0.18
20 24 0.73
21 3 0.09
ACGTcount: A:0.18, C:0.23, G:0.21, T:0.39
Consensus pattern (19 bp):
TCATTTCGCGTTGCGATAG
Found at i:264135 original size:14 final size:14
Alignment explanation
Indices: 264116--264176 Score: 77
Period size: 14 Copynumber: 4.0 Consensus size: 14
264106 TTCTAATTCG
264116 CGTTGCGATTTTCA
1 CGTTGCGATTTTCA
264130 CGTTGCGATTTTCA
1 CGTTGCGATTTTCA
264144 TTTCGCATTGCGATTTTCA
1 ---CG--TTGCGATTTTCA
264163 CGTTGCGATTTTCA
1 CGTTGCGATTTTCA
264177 TTTCGCATTG
Statistics
Matches: 42, Mismatches: 0, Indels: 10
0.81 0.00 0.19
Matches are distributed among these distances:
14 26 0.62
16 2 0.05
17 2 0.05
19 12 0.29
ACGTcount: A:0.15, C:0.21, G:0.20, T:0.44
Consensus pattern (14 bp):
CGTTGCGATTTTCA
Found at i:264137 original size:106 final size:105
Alignment explanation
Indices: 263989--264197 Score: 310
Period size: 106 Copynumber: 2.0 Consensus size: 105
263979 AAACTAAATT
* * * * * *
263989 CGCGTTGCGATTTTCATTTCGCTTTGCGATTCTCTCGTTGCGATTTTCATTTTGCTTTGCGATTC
1 CGCGTTGCGATATTCAATTCGCGTTGCGATTCTCACGTTGCGATTTTCATTTCGCATTGCGATTC
* *
264054 TCTCATTGCGATTTTCATTTCGCATTGCGATAGTCATTTC
66 TCACATTGCGATTTTCATTTCGCATTGCGATAGACATTTC
*
264094 CGCGTTGCGATATTCTAATTCGCGTTGCGATTTTCACGTTGCGATTTTCATTTCGCATTGCGATT
1 CGCGTTGCGATATTC-AATTCGCGTTGCGATTCTCACGTTGCGATTTTCATTTCGCATTGCGATT
* *
264159 TTCACGTTGCGATTTTCATTTCGCATTGCGATAGACATT
65 CTCACATTGCGATTTTCATTTCGCATTGCGATAGACATT
264198 AAGATGATTG
Statistics
Matches: 92, Mismatches: 11, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
105 14 0.15
106 78 0.85
ACGTcount: A:0.15, C:0.22, G:0.19, T:0.44
Consensus pattern (105 bp):
CGCGTTGCGATATTCAATTCGCGTTGCGATTCTCACGTTGCGATTTTCATTTCGCATTGCGATTC
TCACATTGCGATTTTCATTTCGCATTGCGATAGACATTTC
Found at i:264142 original size:73 final size:66
Alignment explanation
Indices: 263991--264190 Score: 211
Period size: 73 Copynumber: 2.9 Consensus size: 66
263981 ACTAAATTCG
* * * * * *
263991 CGTTGCGATTTTCATTTCGCTTTGCGATTCTCTCGTTGCGATTTTCATTTTGCTTTGCGATTCTC
1 CGTTGCGATTTTCATTTCGCATTGCGATTCTCGCGTTGCGATATTCAATTCGCGTTGCGATTCTC
*
264056 T
66 A
*
264057 CATTGCGATTTTCATTTCGCATTGCGATAGTCATTTCCGCGTTGCGATATTCTAATTCGCGTTGC
1 CGTTGCGATTTTCATTTCGCATTGCGAT--TC---T-CGCGTTGCGATATTC-AATTCGCGTTGC
*
264122 GATTTTCA
59 GATTCTCA
* * * * *
264130 CGTTGCGATTTTCATTTCGCATTGCGATTTTCACGTTGCGATTTTCATTTCGCATTGCGAT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCTCGCGTTGCGATATTCAATTCGCGTTGCGAT
264191 AGACATTAAG
Statistics
Matches: 112, Mismatches: 15, Indels: 14
0.79 0.11 0.10
Matches are distributed among these distances:
66 39 0.35
67 13 0.12
68 3 0.03
71 2 0.02
72 13 0.12
73 42 0.38
ACGTcount: A:0.14, C:0.22, G:0.19, T:0.45
Consensus pattern (66 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCTCGCGTTGCGATATTCAATTCGCGTTGCGATTCTC
A
Found at i:266653 original size:24 final size:24
Alignment explanation
Indices: 266619--266672 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
266609 CTGAAAAATC
266619 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
* *
266643 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
266667 ATCAAA
1 ATCAAA
266673 TTTCGAATAC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.41, C:0.20, G:0.19, T:0.20
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:266686 original size:24 final size:24
Alignment explanation
Indices: 266619--266686 Score: 64
Period size: 24 Copynumber: 2.8 Consensus size: 24
266609 CTGAAAAATC
* * *
266619 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAGTCCGAATACTGACCAAG
** *
266643 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAGTCCGAATACTGACCAAG
* *
266667 ATCAAATTTCGAATACTGAC
1 ATCAAAGTCCGAATACTGAC
266687 TAGTACTCAC
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 37 1.00
ACGTcount: A:0.38, C:0.21, G:0.18, T:0.24
Consensus pattern (24 bp):
ATCAAAGTCCGAATACTGACCAAG
Found at i:267557 original size:20 final size:20
Alignment explanation
Indices: 267532--267662 Score: 147
Period size: 20 Copynumber: 6.5 Consensus size: 20
267522 GTCAGAATCT
* *
267532 CGTTGCGATTTACGTATTCG
1 CGTTGCGATTTACGGATACG
*
267552 CATTGCGATTTACGGATACG
1 CGTTGCGATTTACGGATACG
267572 CGTTGCGATTTACGGATACG
1 CGTTGCGATTTACGGATACG
* *
267592 CGTTGCGATTTTACGTAT-TG
1 CGTTGCGA-TTTACGGATACG
* * *
267612 TCGTTGTGATTTACGAATATG
1 -CGTTGCGATTTACGGATACG
*
267633 CGTTGCGATTTTACGGATACT
1 CGTTGCGA-TTTACGGATACG
267654 CGTTGCGAT
1 CGTTGCGAT
267663 AGTCAGAATC
Statistics
Matches: 95, Mismatches: 12, Indels: 8
0.83 0.10 0.07
Matches are distributed among these distances:
20 61 0.64
21 34 0.36
ACGTcount: A:0.19, C:0.18, G:0.26, T:0.37
Consensus pattern (20 bp):
CGTTGCGATTTACGGATACG
Found at i:267617 original size:41 final size:41
Alignment explanation
Indices: 267531--267684 Score: 163
Period size: 41 Copynumber: 3.8 Consensus size: 41
267521 AGTCAGAATC
* * *
267531 TCGTTGCGATTTACGTATTCGCATTGCGA-TTTACGGATACG
1 TCGTTGCGATTTACGAATACGCGTTGCGATTTTACGGATA-G
* * *
267572 -CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTG
1 TCGTTGCGATTTACGAATACGCGTTGCGATTTTACGGATAG
* * *
267612 TCGTTGTGATTTACGAATATGCGTTGCGATTTTACGGATAC
1 TCGTTGCGATTTACGAATACGCGTTGCGATTTTACGGATAG
*
267653 TCGTTGCGATAGT-CAGAAT-CGCGTTGCGATTT
1 TCGTTGCGAT-TTAC-GAATACGCGTTGCGATTT
267685 ATATGTTCGC
Statistics
Matches: 95, Mismatches: 14, Indels: 8
0.81 0.12 0.07
Matches are distributed among these distances:
40 26 0.27
41 64 0.67
42 5 0.05
ACGTcount: A:0.19, C:0.18, G:0.26, T:0.37
Consensus pattern (41 bp):
TCGTTGCGATTTACGAATACGCGTTGCGATTTTACGGATAG
Found at i:267636 original size:61 final size:62
Alignment explanation
Indices: 267532--267662 Score: 187
Period size: 61 Copynumber: 2.1 Consensus size: 62
267522 GTCAGAATCT
*
267532 CGTTGCGA-TTTACGTATTCGCATTGCGATTTACGGATACGCGTTGCGA-TTTACGGATACG
1 CGTTGCGATTTTACGTATTCGCATTGCGATTTACGAATACGCGTTGCGATTTTACGGATACG
* * * *
267592 CGTTGCGATTTTACGTATT-GTCGTTGTGATTTACGAATATGCGTTGCGATTTTACGGATACT
1 CGTTGCGATTTTACGTATTCG-CATTGCGATTTACGAATACGCGTTGCGATTTTACGGATACG
267654 CGTTGCGAT
1 CGTTGCGAT
267663 AGTCAGAATC
Statistics
Matches: 63, Mismatches: 5, Indels: 4
0.88 0.07 0.06
Matches are distributed among these distances:
60 9 0.14
61 34 0.54
62 20 0.32
ACGTcount: A:0.19, C:0.18, G:0.26, T:0.37
Consensus pattern (62 bp):
CGTTGCGATTTTACGTATTCGCATTGCGATTTACGAATACGCGTTGCGATTTTACGGATACG
Found at i:267694 original size:20 final size:20
Alignment explanation
Indices: 267671--267723 Score: 81
Period size: 20 Copynumber: 2.6 Consensus size: 20
267661 ATAGTCAGAA
*
267671 TCGCGTTGCGATTTAT-ATGT
1 TCGCGTTGCGATTT-TCATAT
267691 TCGCGTTGCGATTTTCATAT
1 TCGCGTTGCGATTTTCATAT
267711 TCGCGTTGCGATT
1 TCGCGTTGCGATT
267724 CTGGAAAATC
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 1 0.03
20 30 0.97
ACGTcount: A:0.13, C:0.19, G:0.25, T:0.43
Consensus pattern (20 bp):
TCGCGTTGCGATTTTCATAT
Found at i:267776 original size:21 final size:21
Alignment explanation
Indices: 267691--267788 Score: 76
Period size: 21 Copynumber: 4.7 Consensus size: 21
267681 ATTTATATGT
* *
267691 TCGCGTTGCGATT-TTCATAT
1 TCGCGTTGCGATTCTTCAAAA
**
267711 TCGCGTTGCGATTCTGGAAAA
1 TCGCGTTGCGATTCTTCAAAA
** * **
267732 TCGCAATGCTAATT-TGT-ACTA
1 TCGCGTTGC-GATTCT-TCAAAA
267753 TCGCGTTGCGATTCTTCAAAA
1 TCGCGTTGCGATTCTTCAAAA
267774 TCGCGTTGCGATTCT
1 TCGCGTTGCGATTCT
267789 GGGAACTGAT
Statistics
Matches: 58, Mismatches: 15, Indels: 9
0.71 0.18 0.11
Matches are distributed among these distances:
20 17 0.29
21 38 0.66
22 3 0.05
ACGTcount: A:0.20, C:0.21, G:0.21, T:0.37
Consensus pattern (21 bp):
TCGCGTTGCGATTCTTCAAAA
Found at i:270344 original size:29 final size:28
Alignment explanation
Indices: 270284--270423 Score: 115
Period size: 29 Copynumber: 4.8 Consensus size: 28
270274 TTTTTTTGAA
* **
270284 AAATATTTTTTATTGTCATCTTAACTTATT
1 AAATATATTTTATT-TTTTCTTAACTTA-T
*
270314 AAATATATTTTATTTTTTCTTAACCTATT
1 AAATATATTTTATTTTTTCTTAACTTA-T
270343 AAATATATTTTATTTTATT-TTAA-TGTAT
1 AAATATATTTTATTTT-TTCTTAACT-TAT
* * * *
270371 ATATATATATTTATCTTTATCTTCACTTAA
1 AAATATAT-TTTAT-TTTTTCTTAACTTAT
270401 AAATAT-TTTTATTTTTATCTTAA
1 AAATATATTTTATTTTT-TCTTAA
270424 TTTTTAAAAA
Statistics
Matches: 91, Mismatches: 12, Indels: 16
0.76 0.10 0.13
Matches are distributed among these distances:
27 3 0.03
28 18 0.20
29 41 0.45
30 28 0.31
31 1 0.01
ACGTcount: A:0.33, C:0.08, G:0.01, T:0.58
Consensus pattern (28 bp):
AAATATATTTTATTTTTTCTTAACTTAT
Found at i:270433 original size:30 final size:30
Alignment explanation
Indices: 270276--270436 Score: 100
Period size: 28 Copynumber: 5.4 Consensus size: 30
270266 ATTCTTAATT
* *
270276 TTTTTGAAAAATATTTTTTATTGTCATCTTAA
1 TTTTT-AAAAATA-TTTTTATTTTTATCTTAA
* *
270308 CTTATTAAATATA-TTTTATTTTT-TCTTAA
1 -TTTTTAAAAATATTTTTATTTTTATCTTAA
* * * *
270337 CCTATTAAATATA-TTTTA-TTTTATTTTAA
1 -TTTTTAAAAATATTTTTATTTTTATCTTAA
* * * * * * *
270366 TGTATATATATATATTTATCTTTATCTTCA
1 TTTTTAAAAATATTTTTATTTTTATCTTAA
*
270396 --CTTAAAAATATTTTTATTTTTATCTTAA
1 TTTTTAAAAATATTTTTATTTTTATCTTAA
270424 TTTTTAAAAATAT
1 TTTTTAAAAATAT
270437 ATATTTTTAA
Statistics
Matches: 100, Mismatches: 23, Indels: 13
0.74 0.17 0.10
Matches are distributed among these distances:
28 32 0.32
29 32 0.32
30 26 0.26
32 6 0.06
33 4 0.04
ACGTcount: A:0.34, C:0.07, G:0.02, T:0.58
Consensus pattern (30 bp):
TTTTTAAAAATATTTTTATTTTTATCTTAA
Found at i:270437 original size:58 final size:57
Alignment explanation
Indices: 270282--270438 Score: 147
Period size: 58 Copynumber: 2.7 Consensus size: 57
270272 AATTTTTTTG
* * * *
270282 AAAAATATTTTTTATTGTCATCTTAACTTATTAAATATAT-TTTATTTTTTCTTAACCT
1 AAAAATA-TTTTTATTTTTATCTTAA-TTTTTAAATATATATTTATTTTATCTTAACCT
* * * * * * *
270340 ATTAAATATATTTTA-TTTTATTTTAATGTATATATATATATTTATCTTTATCTTCACTT
1 A-AAAATAT-TTTTATTTTTATCTTAATTTTTAAATATATATTTAT-TTTATCTTAACCT
*
270399 AAAAATATTTTTATTTTTATCTTAATTTTTAAAAATATAT
1 AAAAATATTTTTATTTTTATCTTAATTTTTAAATATATAT
270439 ATTTTTAAAA
Statistics
Matches: 77, Mismatches: 17, Indels: 10
0.74 0.16 0.10
Matches are distributed among these distances:
57 14 0.18
58 42 0.55
59 21 0.27
ACGTcount: A:0.35, C:0.07, G:0.01, T:0.57
Consensus pattern (57 bp):
AAAAATATTTTTATTTTTATCTTAATTTTTAAATATATATTTATTTTATCTTAACCT
Found at i:270448 original size:15 final size:16
Alignment explanation
Indices: 270423--270453 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
270413 TTTTATCTTA
270423 ATTTTTAAAAATATAT
1 ATTTTTAAAAATATAT
270439 ATTTTT-AAAATATAT
1 ATTTTTAAAAATATAT
270454 TAACTTAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 9 0.60
16 6 0.40
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (16 bp):
ATTTTTAAAAATATAT
Found at i:270486 original size:19 final size:21
Alignment explanation
Indices: 270462--270501 Score: 66
Period size: 19 Copynumber: 2.0 Consensus size: 21
270452 ATTAACTTAA
270462 AATATTTTAT-TAT-TATTTT
1 AATATTTTATATATGTATTTT
270481 AATATTTTATATATGTATTTT
1 AATATTTTATATATGTATTTT
270502 TTGTTAATCT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 10 0.53
20 3 0.16
21 6 0.32
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.65
Consensus pattern (21 bp):
AATATTTTATATATGTATTTT
Found at i:272093 original size:2 final size:2
Alignment explanation
Indices: 272086--272113 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
272076 TTTTATAACC
272086 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
272114 TCATATGTGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:277910 original size:20 final size:20
Alignment explanation
Indices: 277881--277925 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
277871 AATTTGCAGA
* * *
277881 AAAATTATCCTCAATGGCTC
1 AAAATCATCCCCAACGGCTC
*
277901 CAAATCATCCCCAACGGCTC
1 AAAATCATCCCCAACGGCTC
277921 AAAAT
1 AAAAT
277926 GGCCACAAAC
Statistics
Matches: 20, Mismatches: 5, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.38, C:0.31, G:0.09, T:0.22
Consensus pattern (20 bp):
AAAATCATCCCCAACGGCTC
Found at i:278903 original size:141 final size:140
Alignment explanation
Indices: 278621--278891 Score: 341
Period size: 141 Copynumber: 1.9 Consensus size: 140
278611 TTAGTCCCTT
** *
278621 AATTTAGGGAATAATTTGAATTGGCTCCCGTATTTAACATGCCCAGAGGACCATTTTGATTATTC
1 AATTTAGGGAATAACCTGAATTGGCTCCCGCATTTAACATGCCCAGAGGACCATTTTGATTATTC
* * * *
278686 GACTAAATAATTGGTTAAAATAAACGAGGGTTAATTAGAGCCTCCACTTTTTGTTTAATTTTACC
66 GACTAAATAATTGGTTAAAATAAACGAGGGTAAATTAGAACCTCCACTTTTAGTTT-ATATTACC
*
278751 TCAGTCCTTTA
130 TCAATCCTTTA
** * *
278762 AATTTAGGGAATAACCTGAATTGGCTTTCGCATTTAACATGTCCAGAGGACTATTTTGATTATTC
1 AATTTAGGGAATAACCTGAATTGGCTCCCGCATTTAACATGCCCAGAGGACCATTTTGATTATTC
* * ** *
278827 GACTAAATAGTTGTTTAAAATAAATTAGGGATAATATTAGAACCTCTA-TTTTAGTTT-TATT-C
66 GACTAAATAATTGGTTAAAATAAACGAGGG-TAA-ATTAGAACCTCCACTTTTAGTTTATATTAC
278889 CTC
129 CTC
278892 TAAATTCTTT
Statistics
Matches: 112, Mismatches: 16, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
139 4 0.04
140 3 0.03
141 84 0.75
142 10 0.09
143 11 0.10
ACGTcount: A:0.31, C:0.15, G:0.16, T:0.38
Consensus pattern (140 bp):
AATTTAGGGAATAACCTGAATTGGCTCCCGCATTTAACATGCCCAGAGGACCATTTTGATTATTC
GACTAAATAATTGGTTAAAATAAACGAGGGTAAATTAGAACCTCCACTTTTAGTTTATATTACCT
CAATCCTTTA
Found at i:280312 original size:30 final size:31
Alignment explanation
Indices: 280255--280312 Score: 82
Period size: 31 Copynumber: 1.9 Consensus size: 31
280245 CAATGATTGG
*
280255 AAAAGTTTAAGTACCAAAAGGGTAATTTCCC
1 AAAAGTTTAAGGACCAAAAGGGTAATTTCCC
* *
280286 AAAAGTTTAGGGACC-AAAGTGTAATTT
1 AAAAGTTTAAGGACCAAAAGGGTAATTT
280313 TCAAAATTTA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
30 11 0.46
31 13 0.54
ACGTcount: A:0.41, C:0.12, G:0.19, T:0.28
Consensus pattern (31 bp):
AAAAGTTTAAGGACCAAAAGGGTAATTTCCC
Found at i:281535 original size:19 final size:20
Alignment explanation
Indices: 281492--281537 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
281482 TATTATGCTG
* *
281492 GAAATTTATGTTAGAGTGTT
1 GAAATTGATGTTAGAATGTT
281512 GAAATTGATGTTAGAATG-T
1 GAAATTGATGTTAGAATGTT
281531 GAAATTG
1 GAAATTG
281538 GGTTATTTTG
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
19 8 0.33
20 16 0.67
ACGTcount: A:0.35, C:0.00, G:0.26, T:0.39
Consensus pattern (20 bp):
GAAATTGATGTTAGAATGTT
Found at i:286094 original size:18 final size:18
Alignment explanation
Indices: 286068--286115 Score: 69
Period size: 18 Copynumber: 2.7 Consensus size: 18
286058 ATGTCAAAAT
*
286068 GGTAACGGTACCGAAGTG
1 GGTATCGGTACCGAAGTG
*
286086 GGTATCGGTATCGAAGTG
1 GGTATCGGTACCGAAGTG
*
286104 GGTATCGATACC
1 GGTATCGGTACC
286116 ATAGAAGGGA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.25, C:0.17, G:0.35, T:0.23
Consensus pattern (18 bp):
GGTATCGGTACCGAAGTG
Found at i:289741 original size:19 final size:19
Alignment explanation
Indices: 289717--289754 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
289707 ATTGATGTAC
289717 ATTGAGAGTCATAGGTGCA
1 ATTGAGAGTCATAGGTGCA
289736 ATTGAGAGTCATAGGTGCA
1 ATTGAGAGTCATAGGTGCA
289755 TTTCAACATA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.32, C:0.11, G:0.32, T:0.26
Consensus pattern (19 bp):
ATTGAGAGTCATAGGTGCA
Found at i:295445 original size:114 final size:114
Alignment explanation
Indices: 295244--295465 Score: 336
Period size: 114 Copynumber: 1.9 Consensus size: 114
295234 CACGTTCTCG
* * *
295244 TAGTAGAAATAAAGAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATTTGATCTGATTT
1 TAGTAGAAATAAAGAAACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTC
* *
295309 GGTATGAACCCCAAAACCAATCATTAGATTTAAAAGATGAATTTGTTCA
66 GGTAGGAACCCCAAAACCAATCATTAGAATTAAAAGATGAATTTGTTCA
* * *
295358 TAGTATAAATAAGGAAACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTC
1 TAGTAGAAATAAAGAAACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTC
* * * *
295423 GGTAGGAACCCCAGAACTAATCATTGGAATTGAAAGATGAATT
66 GGTAGGAACCCCAAAACCAATCATTAGAATTAAAAGATGAATT
295466 GCATGATCGT
Statistics
Matches: 96, Mismatches: 12, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
114 96 1.00
ACGTcount: A:0.34, C:0.14, G:0.19, T:0.32
Consensus pattern (114 bp):
TAGTAGAAATAAAGAAACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTC
GGTAGGAACCCCAAAACCAATCATTAGAATTAAAAGATGAATTTGTTCA
Found at i:298025 original size:22 final size:23
Alignment explanation
Indices: 297972--298029 Score: 82
Period size: 25 Copynumber: 2.5 Consensus size: 23
297962 ATCTACACTC
297972 TTCAAAGATGATAGATTCTCATTTT
1 TTCAAAGATGATAGATTCTC--TTT
*
297997 TTTAAAGATGATAGATTCTC-TT
1 TTCAAAGATGATAGATTCTCTTT
298019 TTCAAAGATGA
1 TTCAAAGATGA
298030 AAGCTTTATG
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
22 12 0.39
25 19 0.61
ACGTcount: A:0.34, C:0.10, G:0.14, T:0.41
Consensus pattern (23 bp):
TTCAAAGATGATAGATTCTCTTT
Found at i:298802 original size:76 final size:76
Alignment explanation
Indices: 298704--299489 Score: 1373
Period size: 76 Copynumber: 10.4 Consensus size: 76
298694 TATTTCCCAT
* *
298704 ATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTTGGGAGCTTTTTGATGTTTTCAAA
1 ATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAA
298769 ACCTTAGGGTC
66 ACCTTAGGGTC
* *
298780 ATCTGTAAGTACTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGTTTTTTGATGTTTTCAAA
1 ATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAA
298845 ACCTTAGGGTC
66 ACCTTAGGGTC
298856 ATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAA
1 ATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAA
*
298921 GCCTTAGGGTC
66 ACCTTAGGGTC
*
298932 ATCTGTAAGTCCTGCAGTTCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAA
1 ATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAA
298997 ACCTTAGGGTC
66 ACCTTAGGGTC
* *
299008 ATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCAGGAGCTTTTTGATATTTTCAAA
1 ATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAA
299073 ACCTTAGGGTC
66 ACCTTAGGGTC
*
299084 ATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGATTTTTGATGTTTTCAAA
1 ATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAA
299149 ACCTTAGGGTC
66 ACCTTAGGGTC
*
299160 ATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGGGCTTTTTGATGTTTTCAAA
1 ATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAA
299225 ACCTTAGGGTC
66 ACCTTAGGGTC
* * *
299236 ATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAATCCTTCAGAAGCTTTTTGATGTTTTCAAA
1 ATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAA
*
299301 GCCTTAGGGTC
66 ACCTTAGGGTC
299312 ATCTGTAAGTCCTGGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGC-TTTTGATG-TTTCAA
1 ATCTGTAAGTCCT-GCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
299375 AACCTTAGGGTC
65 AACCTTAGGGTC
* * *
299387 ATATATAAGTACTGCAGTGCATGATGTTTCC-AAAAGCCTTCGGGAGC-TTTTGATGTTTTCAAA
1 ATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAA
*
299450 GCCTTAGGGTC
66 ACCTTAGGGTC
299461 ATCTGTAAGTCCTGCAGTGCATGATGTTT
1 ATCTGTAAGTCCTGCAGTGCATGATGTTT
299490 TTAAGACCAC
Statistics
Matches: 675, Mismatches: 33, Indels: 6
0.95 0.05 0.01
Matches are distributed among these distances:
73 24 0.04
74 61 0.09
75 27 0.04
76 531 0.79
77 32 0.05
ACGTcount: A:0.24, C:0.19, G:0.22, T:0.35
Consensus pattern (76 bp):
ATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAA
ACCTTAGGGTC
Found at i:299656 original size:18 final size:18
Alignment explanation
Indices: 299635--299709 Score: 93
Period size: 18 Copynumber: 4.2 Consensus size: 18
299625 TTTTACTTAA
299635 ATTATTATTAAAATTATT
1 ATTATTATTAAAATTATT
299653 ATTATTATTAAATATTATT
1 ATTATTATTAAA-ATTATT
*
299672 ATTA-TATTATATATTA-T
1 ATTATTATTA-AAATTATT
*
299689 ATTATTATT-AAATAATT
1 ATTATTATTAAAATTATT
299706 ATTA
1 ATTA
299710 CAAGCCCAAA
Statistics
Matches: 50, Mismatches: 3, Indels: 9
0.81 0.05 0.15
Matches are distributed among these distances:
16 4 0.08
17 10 0.20
18 25 0.50
19 11 0.22
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (18 bp):
ATTATTATTAAAATTATT
Found at i:299673 original size:31 final size:37
Alignment explanation
Indices: 299635--299709 Score: 104
Period size: 36 Copynumber: 2.1 Consensus size: 37
299625 TTTTACTTAA
299635 ATTATTAT-TAA-A-ATTATTATTATTATTAAAT-ATT
1 ATTATTATATAATATATTA-TATTATTATTAAATAATT
*
299669 ATTATTATATTATATATTATATTATTATTAAATAATT
1 ATTATTATATAATATATTATATTATTATTAAATAATT
299706 ATTA
1 ATTA
299710 CAAGCCCAAA
Statistics
Matches: 36, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
34 8 0.22
35 2 0.06
36 15 0.42
37 11 0.31
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (37 bp):
ATTATTATATAATATATTATATTATTATTAAATAATT
Found at i:299709 original size:3 final size:3
Alignment explanation
Indices: 299635--299698 Score: 69
Period size: 3 Copynumber: 21.3 Consensus size: 3
299625 TTTTACTTAA
** *
299635 ATT ATT ATT AAA ATT ATT ATT ATT ATT AAAT ATT ATT ATT A-T ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT -ATT ATT ATT ATT ATT ATT
299680 ATAT ATT A-T ATT ATT ATT A
1 AT-T ATT ATT ATT ATT ATT A
299699 AATAATTATT
Statistics
Matches: 51, Mismatches: 6, Indels: 8
0.78 0.09 0.12
Matches are distributed among these distances:
2 4 0.08
3 42 0.82
4 5 0.10
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (3 bp):
ATT
Found at i:301280 original size:115 final size:115
Alignment explanation
Indices: 301119--301436 Score: 503
Period size: 115 Copynumber: 2.8 Consensus size: 115
301109 TATGTTTTAG
** * * * *
301119 TTATTTATTTATTTTTTAAATATTGAAGGAAAGAGCTGTCTGAAAACAACTAGAAGTTCTTTTCT
1 TTATTTATTTATTTTTT-AATATCAAAAGAAAAAGCTGTCTTAAAACAACTAGAAGTCCTTTTCT
*
301184 AATATTTTTAAATAAATAAATATCTTACTATATTAAAATATTTTTTTATTA
65 AATATTTTTAAATAAATAAATATCTTACTATATTAAAATAATTTTTTATTA
301235 TTATTTATTTATTTTTTAATATCAAAAGAAAAAGCTGTCTTAAAACAACTAGAAG-CCATTTTCT
1 TTATTTATTTATTTTTTAATATCAAAAGAAAAAGCTGTCTTAAAACAACTAGAAGTCC-TTTTCT
301299 AATATTTTTAAATAAATAAATATCTTACTATATTAAAATAATTTTTTATTA
65 AATATTTTTAAATAAATAAATATCTTACTATATTAAAATAATTTTTTATTA
* * * *
301350 TTATTTATTTATTTTTTAATATCAAAAGAAAAATCTGTCTTAAAGCACCTAGAAGTCCTTTTCTG
1 TTATTTATTTATTTTTTAATATCAAAAGAAAAAGCTGTCTTAAAACAACTAGAAGTCCTTTTCTA
*
301415 ATATTTCTAAATAAATAAATAT
66 ATATTTTTAAATAAATAAATAT
301437 TTTATTTATA
Statistics
Matches: 188, Mismatches: 12, Indels: 5
0.92 0.06 0.02
Matches are distributed among these distances:
114 1 0.01
115 168 0.89
116 19 0.10
ACGTcount: A:0.40, C:0.09, G:0.06, T:0.45
Consensus pattern (115 bp):
TTATTTATTTATTTTTTAATATCAAAAGAAAAAGCTGTCTTAAAACAACTAGAAGTCCTTTTCTA
ATATTTTTAAATAAATAAATATCTTACTATATTAAAATAATTTTTTATTA
Found at i:306936 original size:24 final size:25
Alignment explanation
Indices: 306901--306956 Score: 78
Period size: 24 Copynumber: 2.3 Consensus size: 25
306891 GAAAAAATAA
* *
306901 AAAAAAATTGTTCATTGTTTCGAAC
1 AAAAAAATTGTTCACTATTTCGAAC
*
306926 AAAAAAA-TGTTTACTATTTCGAAC
1 AAAAAAATTGTTCACTATTTCGAAC
306950 AAAAAAA
1 AAAAAAA
306957 GAAGGAAAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
24 21 0.75
25 7 0.25
ACGTcount: A:0.50, C:0.11, G:0.09, T:0.30
Consensus pattern (25 bp):
AAAAAAATTGTTCACTATTTCGAAC
Found at i:307882 original size:20 final size:22
Alignment explanation
Indices: 307859--307898 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
307849 TTTTAAGTAT
307859 TTTAAT-TAGGATT-TATTTTC
1 TTTAATCTAGGATTATATTTTC
*
307879 TTTATTCTAGGATTATATTT
1 TTTAATCTAGGATTATATTT
307899 ACCTTGTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 5 0.29
21 7 0.41
22 5 0.29
ACGTcount: A:0.25, C:0.05, G:0.10, T:0.60
Consensus pattern (22 bp):
TTTAATCTAGGATTATATTTTC
Found at i:309437 original size:26 final size:25
Alignment explanation
Indices: 309349--309446 Score: 96
Period size: 24 Copynumber: 3.8 Consensus size: 25
309339 ATATAAATAC
* *
309349 TTAACTTAAATTCATAATATTATATATA
1 TTAACTT-AATT-AAAATATT-TTTATA
309377 TTAACTTAA--AAAATATTTTTATA
1 TTAACTTAATTAAAATATTTTTATA
309400 TTAACTT-ATTAAATATATTTTT-TA
1 TTAACTTAATTAAA-ATATTTTTATA
309424 TTAACTTAATTTAAAATTATTTT
1 TTAACTTAA-TTAAAA-TATTTT
309447 ATTTTTACTT
Statistics
Matches: 62, Mismatches: 2, Indels: 14
0.79 0.03 0.18
Matches are distributed among these distances:
22 1 0.02
23 12 0.19
24 19 0.31
25 10 0.16
26 11 0.18
27 2 0.03
28 7 0.11
ACGTcount: A:0.43, C:0.05, G:0.00, T:0.52
Consensus pattern (25 bp):
TTAACTTAATTAAAATATTTTTATA
Found at i:309456 original size:26 final size:28
Alignment explanation
Indices: 309377--309466 Score: 77
Period size: 27 Copynumber: 3.4 Consensus size: 28
309367 ATTATATATA
* *
309377 TTAACTTAAAAAATATTTTTATATTAAC-
1 TTAATTTAAAATATATTTTT-TATTAACT
309405 TT-A-TT-AAATATATTTTTTATTAAC-
1 TTAATTTAAAATATATTTTTTATTAACT
*
309429 TTAATTTAAAAT-TATTTTATT-TTTACT
1 TTAATTTAAAATATATTTT-TTATTAACT
*
309456 TTTATTTAAAA
1 TTAATTTAAAA
309467 ATGTATATTT
Statistics
Matches: 54, Mismatches: 3, Indels: 11
0.79 0.04 0.16
Matches are distributed among these distances:
24 9 0.17
25 12 0.22
26 14 0.26
27 17 0.31
28 2 0.04
ACGTcount: A:0.40, C:0.04, G:0.00, T:0.56
Consensus pattern (28 bp):
TTAATTTAAAATATATTTTTTATTAACT
Found at i:309545 original size:25 final size:24
Alignment explanation
Indices: 309507--309568 Score: 79
Period size: 25 Copynumber: 2.5 Consensus size: 24
309497 TTAAGATAAG
**
309507 AATAAAATATATTTAATAATTTAA
1 AATAAAATATATTTAATAAAGTAA
*
309531 AATAATAATATATTTAGTAAAGTAA
1 AATAA-AATATATTTAATAAAGTAA
*
309556 GATAAAATATATT
1 AATAAAATATATT
309569 CTTTAAAAAG
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
24 13 0.39
25 20 0.61
ACGTcount: A:0.56, C:0.00, G:0.05, T:0.39
Consensus pattern (24 bp):
AATAAAATATATTTAATAAAGTAA
Found at i:309637 original size:33 final size:33
Alignment explanation
Indices: 309548--309640 Score: 104
Period size: 31 Copynumber: 2.9 Consensus size: 33
309538 ATATATTTAG
*
309548 TAAAGTAAG-ATAAAATATAT-TCTTTAAAAAGTT
1 TAAA-TAAGAATAAAATATATAT-TTTTAAAAGTT
* * *
309581 CAAATAATAA-CAAA-ATATATTTTTAAAAGTT
1 TAAATAAGAATAAAATATATATTTTTAAAAGTT
309612 TAAATAAGAATAAAATATATATTTTTAAA
1 TAAATAAGAATAAAATATATATTTTTAAA
309641 TCCAGCGGTA
Statistics
Matches: 49, Mismatches: 7, Indels: 8
0.77 0.11 0.12
Matches are distributed among these distances:
31 22 0.45
32 10 0.20
33 17 0.35
ACGTcount: A:0.55, C:0.03, G:0.05, T:0.37
Consensus pattern (33 bp):
TAAATAAGAATAAAATATATATTTTTAAAAGTT
Found at i:327351 original size:26 final size:26
Alignment explanation
Indices: 327284--327342 Score: 70
Period size: 25 Copynumber: 2.3 Consensus size: 26
327274 AAAAAAAGAT
327284 TAAGTTAA--TAACAAAATATATTTAA
1 TAAGTTAATGTAA-AAAATATATTTAA
* *
327309 TAAGTTAATGTAAAAAATATTTTTTA
1 TAAGTTAATGTAAAAAATATATTTAA
327335 -AAGTTAAT
1 TAAGTTAAT
327343 TTATTAAAAG
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
25 16 0.53
26 11 0.37
27 3 0.10
ACGTcount: A:0.51, C:0.02, G:0.07, T:0.41
Consensus pattern (26 bp):
TAAGTTAATGTAAAAAATATATTTAA
Found at i:329001 original size:7 final size:7
Alignment explanation
Indices: 328982--329068 Score: 99
Period size: 7 Copynumber: 12.4 Consensus size: 7
328972 AGTTGGTTGC
328982 AGGGGAG
1 AGGGGAG
328989 -GGGGAG
1 AGGGGAG
328995 AGGGGAG
1 AGGGGAG
329002 AGGGGAG
1 AGGGGAG
*
329009 GGGGGAGG
1 AGGGGA-G
329017 AGGGAGAAG
1 AGGG-G-AG
*
329026 ACGGG-G
1 AGGGGAG
*
329032 -TGGGAG
1 AGGGGAG
329038 AGGGGAG
1 AGGGGAG
329045 AGGGGAG
1 AGGGGAG
329052 AGGGGAG
1 AGGGGAG
329059 AGGGGAG
1 AGGGGAG
329066 AGG
1 AGG
329069 AGGGGAAACA
Statistics
Matches: 69, Mismatches: 5, Indels: 12
0.80 0.06 0.14
Matches are distributed among these distances:
5 3 0.04
6 8 0.12
7 47 0.68
8 5 0.07
9 5 0.07
10 1 0.01
ACGTcount: A:0.26, C:0.01, G:0.71, T:0.01
Consensus pattern (7 bp):
AGGGGAG
Found at i:329967 original size:28 final size:27
Alignment explanation
Indices: 329881--329967 Score: 79
Period size: 29 Copynumber: 3.1 Consensus size: 27
329871 AATAAGTTAT
* ** *
329881 TAAAGTAT-TTTTTATCAAAAAAAATA
1 TAAAGTATATTTTTATCAAAATAGGTC
*
329907 TAAAGT-TATTTTTTGTCAAAATAGGTAAC
1 TAAAGTATA-TTTTTATCAAAATAGGT--C
329936 TAAAGTATATTTTTATCAAAATAGGTCC
1 TAAAGTATATTTTTATCAAAATAGGT-C
329964 TAAA
1 TAAA
329968 TTATTCAAAT
Statistics
Matches: 49, Mismatches: 7, Indels: 8
0.77 0.11 0.12
Matches are distributed among these distances:
25 1 0.02
26 6 0.12
27 13 0.27
28 5 0.10
29 22 0.45
30 2 0.04
ACGTcount: A:0.45, C:0.07, G:0.09, T:0.39
Consensus pattern (27 bp):
TAAAGTATATTTTTATCAAAATAGGTC
Found at i:330387 original size:24 final size:24
Alignment explanation
Indices: 330353--330399 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
330343 TTATAACAAA
330353 CTATAAATGTTTA-ACAATCATCAG
1 CTATAAATGTTTATACAA-CATCAG
*
330377 CTATAACTGTTTATACAACATCA
1 CTATAAATGTTTATACAACATCA
330400 CACTACAGCT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 17 0.81
25 4 0.19
ACGTcount: A:0.40, C:0.19, G:0.06, T:0.34
Consensus pattern (24 bp):
CTATAAATGTTTATACAACATCAG
Found at i:335065 original size:21 final size:21
Alignment explanation
Indices: 335041--335080 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
335031 CAATGGGATT
335041 AGGATTAGGAAT-TGGATTTTG
1 AGGATTAGG-ATGTGGATTTTG
*
335062 AGGATTTGGATGTGGATTT
1 AGGATTAGGATGTGGATTT
335081 GGTTGATGGT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 2 0.12
21 15 0.88
ACGTcount: A:0.25, C:0.00, G:0.35, T:0.40
Consensus pattern (21 bp):
AGGATTAGGATGTGGATTTTG
Found at i:335838 original size:20 final size:20
Alignment explanation
Indices: 335809--335846 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
335799 CCCCTTCAAA
*
335809 GGGGGAATCGGTTCCCTCAT
1 GGGGGAATCGATTCCCTCAT
*
335829 GGGGGGATCGATTCCCTC
1 GGGGGAATCGATTCCCTC
335847 TGCACCAAAA
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:0.13, C:0.26, G:0.37, T:0.24
Consensus pattern (20 bp):
GGGGGAATCGATTCCCTCAT
Found at i:344538 original size:34 final size:33
Alignment explanation
Indices: 344491--344554 Score: 101
Period size: 34 Copynumber: 1.9 Consensus size: 33
344481 AACCACCTAG
*
344491 CTATAACGTCTAACAACCATCAGTTATAACAAA
1 CTATAACGTCTAACAACCATCAGCTATAACAAA
*
344524 CTATAACTGTCTAACAATCATCAGCTATAAC
1 CTATAAC-GTCTAACAACCATCAGCTATAAC
344555 TGTTTATACA
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
33 7 0.25
34 21 0.75
ACGTcount: A:0.42, C:0.25, G:0.06, T:0.27
Consensus pattern (33 bp):
CTATAACGTCTAACAACCATCAGCTATAACAAA
Found at i:344551 original size:24 final size:24
Alignment explanation
Indices: 344524--344570 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
344514 TTATAACAAA
344524 CTATAACTGTCTA-ACAATCATCAG
1 CTATAACTGTCTATACAA-CATCAG
*
344548 CTATAACTGTTTATACAACATCA
1 CTATAACTGTCTATACAACATCA
344571 CACTGCAGCT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 17 0.81
25 4 0.19
ACGTcount: A:0.38, C:0.23, G:0.06, T:0.32
Consensus pattern (24 bp):
CTATAACTGTCTATACAACATCAG
Found at i:345630 original size:2 final size:2
Alignment explanation
Indices: 345623--345651 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
345613 TGTTTATTAA
345623 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
345652 AACCTATTTC
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:346797 original size:17 final size:18
Alignment explanation
Indices: 346758--346804 Score: 69
Period size: 18 Copynumber: 2.7 Consensus size: 18
346748 TGTTTACGAG
*
346758 GGAATTAGAATCTGTGAA
1 GGAATTGGAATCTGTGAA
*
346776 GGAATTGGAATCTGT-TA
1 GGAATTGGAATCTGTGAA
346793 GGAATTGGAATC
1 GGAATTGGAATC
346805 CAATTCCATA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
17 13 0.48
18 14 0.52
ACGTcount: A:0.34, C:0.06, G:0.30, T:0.30
Consensus pattern (18 bp):
GGAATTGGAATCTGTGAA
Done.