Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008950.1 Hibiscus syriacus cultivar Beakdansim tig00112276_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: 471712
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.32
File 2 of 2
Found at i:377025 original size:23 final size:22
Alignment explanation
Indices: 376922--377027 Score: 80
Period size: 23 Copynumber: 4.9 Consensus size: 22
376912 TTATCACTTC
* *
376922 ACATTTATTCAATTTATCCATA
1 ACATTTATCCAATTTATTCATA
*
376944 ACATTTTATCCAATATATTCA-A
1 ACA-TTTATCCAATTTATTCATA
*
376966 ACA---A-CCAATTGA-TCACTTA
1 ACATTTATCCAATTTATTCA--TA
*
376985 ACATTTATTCAATTTATTCATA
1 ACATTTATCCAATTTATTCATA
*
377007 ACATTTTATCCATTTTATTCA
1 ACA-TTTATCCAATTTATTCA
377028 AACTTCACAT
Statistics
Matches: 65, Mismatches: 9, Indels: 19
0.70 0.10 0.20
Matches are distributed among these distances:
16 3 0.05
17 6 0.09
18 1 0.02
19 4 0.06
22 13 0.20
23 35 0.54
24 3 0.05
ACGTcount: A:0.37, C:0.19, G:0.01, T:0.43
Consensus pattern (22 bp):
ACATTTATCCAATTTATTCATA
Found at i:377607 original size:138 final size:138
Alignment explanation
Indices: 377162--377664 Score: 918
Period size: 138 Copynumber: 3.7 Consensus size: 138
377152 CCATTCATCT
*
377162 ATAGTTCCCCGGGGGACATGAGTGATATAATAGGGCAATGATAACATATTCTCTGACAAAATAAT
1 ATAGTTCCCCGGGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAAT
*
377227 CGAAGGCGCGCGCCCGGGAACGCGCTTTCACCACTTTGCCAAGTCCCCTCAGAAATAATAGGTAC
66 CGAAGGCGCGCCCCCGGGAACGCGCTTTCACCACTTTGCCAAGTCCCCTCAGAAATAATAGGTAC
377292 TGACATGA
131 TGACATGA
*
377300 ATAGTTCCCCGGGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTTACAAAATAAT
1 ATAGTTCCCCGGGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAAT
377365 CGAAGGCGCG-CCCCGGGAACGCGCTTTCACCACTTTGCCAAGTCCCCTCAGAAATAATAGGTAC
66 CGAAGGCGCGCCCCCGGGAACGCGCTTTCACCACTTTGCCAAGTCCCCTCAGAAATAATAGGTAC
377429 TGACATGA
131 TGACATGA
*
377437 ATAGTTCCCCGGGGGACATGAGTGACACAATAGGGCAATGATAACATATTCTCTGACAAAATAAT
1 ATAGTTCCCCGGGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAAT
* *
377502 CGAAGGCGCACCCCCGGGAACGCGCTTTCACCACTTTGCCAAGTCCCCTCAGAAATAATAGATAC
66 CGAAGGCGCGCCCCCGGGAACGCGCTTTCACCACTTTGCCAAGTCCCCTCAGAAATAATAGGTAC
*
377567 TGATATGA
131 TGACATGA
* *
377575 ATAGTTCCCCGAGGGACATGAGTGATATAATAGGGCAATGATAACATATTCTCTGACAAAATAAT
1 ATAGTTCCCCGGGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAAT
377640 CGAAGGCGCGCCCCCGGGAACGCGC
66 CGAAGGCGCGCCCCCGGGAACGCGC
377665 CTTTACGTGA
Statistics
Matches: 352, Mismatches: 12, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
137 133 0.38
138 219 0.62
ACGTcount: A:0.32, C:0.24, G:0.23, T:0.21
Consensus pattern (138 bp):
ATAGTTCCCCGGGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAAT
CGAAGGCGCGCCCCCGGGAACGCGCTTTCACCACTTTGCCAAGTCCCCTCAGAAATAATAGGTAC
TGACATGA
Found at i:377653 original size:275 final size:276
Alignment explanation
Indices: 377162--377664 Score: 918
Period size: 275 Copynumber: 1.8 Consensus size: 276
377152 CCATTCATCT
* *
377162 ATAGTTCCCCGGGGGACATGAGTGATATAATAGGGCAATGATAACATATTCTCTGACAAAATAAT
1 ATAGTTCCCCGGGGGACATGAGTGACACAATAGGGCAATGATAACATATTCTCTGACAAAATAAT
* * *
377227 CGAAGGCGCGCGCCCGGGAACGCGCTTTCACCACTTTGCCAAGTCCCCTCAGAAATAATAGGTAC
66 CGAAGGCGCACCCCCGGGAACGCGCTTTCACCACTTTGCCAAGTCCCCTCAGAAATAATAGATAC
* *
377292 TGACATGAATAGTTCCCCGGGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTTAC
131 TGACATGAATAGTTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGAC
377357 AAAATAATCGAAGGCGCG-CCCCGGGAACGCGCTTTCACCACTTTGCCAAGTCCCCTCAGAAATA
196 AAAATAATCGAAGGCGCGCCCCCGGGAACGCGCTTTCACCACTTTGCCAAGTCCCCTCAGAAATA
377421 ATAGGTACTGACATGA
261 ATAGGTACTGACATGA
377437 ATAGTTCCCCGGGGGACATGAGTGACACAATAGGGCAATGATAACATATTCTCTGACAAAATAAT
1 ATAGTTCCCCGGGGGACATGAGTGACACAATAGGGCAATGATAACATATTCTCTGACAAAATAAT
377502 CGAAGGCGCACCCCCGGGAACGCGCTTTCACCACTTTGCCAAGTCCCCTCAGAAATAATAGATAC
66 CGAAGGCGCACCCCCGGGAACGCGCTTTCACCACTTTGCCAAGTCCCCTCAGAAATAATAGATAC
* *
377567 TGATATGAATAGTTCCCCGAGGGACATGAGTGATATAATAGGGCAATGATAACATATTCTCTGAC
131 TGACATGAATAGTTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGAC
377632 AAAATAATCGAAGGCGCGCCCCCGGGAACGCGC
196 AAAATAATCGAAGGCGCGCCCCCGGGAACGCGC
377665 CTTTACGTGA
Statistics
Matches: 218, Mismatches: 9, Indels: 1
0.96 0.04 0.00
Matches are distributed among these distances:
275 204 0.94
276 14 0.06
ACGTcount: A:0.32, C:0.24, G:0.23, T:0.21
Consensus pattern (276 bp):
ATAGTTCCCCGGGGGACATGAGTGACACAATAGGGCAATGATAACATATTCTCTGACAAAATAAT
CGAAGGCGCACCCCCGGGAACGCGCTTTCACCACTTTGCCAAGTCCCCTCAGAAATAATAGATAC
TGACATGAATAGTTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGAC
AAAATAATCGAAGGCGCGCCCCCGGGAACGCGCTTTCACCACTTTGCCAAGTCCCCTCAGAAATA
ATAGGTACTGACATGA
Found at i:380846 original size:21 final size:21
Alignment explanation
Indices: 380820--380861 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
380810 AATAATTAAT
*
380820 ATTATTTATTATAAAAAATTA
1 ATTATTAATTATAAAAAATTA
* *
380841 ATTATTAATTTTAAAATATTA
1 ATTATTAATTATAAAAAATTA
380862 TAATAATTCC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (21 bp):
ATTATTAATTATAAAAAATTA
Found at i:386541 original size:2 final size:2
Alignment explanation
Indices: 386529--386559 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
386519 ATCTTGTATT
*
386529 TA TA AA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
386560 GAACCAATAT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 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):
TA
Found at i:391816 original size:2 final size:2
Alignment explanation
Indices: 391811--391854 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
391801 TAGTGTAATC
391811 AT AT 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 AT AT
391853 AT
1 AT
391855 TCCAATAAAA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:392241 original size:14 final size:14
Alignment explanation
Indices: 392224--392269 Score: 56
Period size: 14 Copynumber: 3.1 Consensus size: 14
392214 TAAAAAATTT
*
392224 ATTTAAAATTTAAA
1 ATTTAAAAATTAAA
392238 ATTTAAAAATTAAA
1 ATTTAAAAATTAAA
392252 ATTATATAAAAATTAAA
1 A-T-T-TAAAAATTAAA
392269 A
1 A
392270 AGAAAATAGA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
14 14 0.50
15 1 0.04
16 1 0.04
17 12 0.43
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (14 bp):
ATTTAAAAATTAAA
Found at i:392248 original size:8 final size:7
Alignment explanation
Indices: 392224--392254 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
392214 TAAAAAATTT
392224 ATTTAAA
1 ATTTAAA
392231 ATTTAAA
1 ATTTAAA
392238 ATTTAAA
1 ATTTAAA
*
392245 AATTAAA
1 ATTTAAA
392252 ATT
1 ATT
392255 ATATAAAAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (7 bp):
ATTTAAA
Found at i:398258 original size:3 final size:3
Alignment explanation
Indices: 398252--398324 Score: 116
Period size: 3 Copynumber: 25.3 Consensus size: 3
398242 AATTTTTTTC
*
398252 ATT ATT ATT ATT ATT ATT ATT A-A ATT A-T ATT ATT A-T ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
398297 ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT A
398325 AATAAAAAAT
Statistics
Matches: 65, Mismatches: 2, Indels: 6
0.89 0.03 0.08
Matches are distributed among these distances:
2 5 0.08
3 60 0.92
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (3 bp):
ATT
Found at i:402064 original size:8 final size:7
Alignment explanation
Indices: 402040--402081 Score: 50
Period size: 7 Copynumber: 6.0 Consensus size: 7
402030 TTTTCATACA
402040 TGCA-TT
1 TGCATTT
402046 TGCATTT
1 TGCATTT
402053 TGCATCTT
1 TGCAT-TT
402061 TGCATTT
1 TGCATTT
* *
402068 TTCATTG
1 TGCATTT
402075 TGCATTT
1 TGCATTT
402082 ATACTTTTAT
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
6 4 0.13
7 19 0.63
8 7 0.23
ACGTcount: A:0.14, C:0.17, G:0.14, T:0.55
Consensus pattern (7 bp):
TGCATTT
Found at i:402064 original size:15 final size:14
Alignment explanation
Indices: 402040--402081 Score: 50
Period size: 15 Copynumber: 3.0 Consensus size: 14
402030 TTTTCATACA
402040 TGCA-TTTGCATTT
1 TGCATTTTGCATTT
402053 TGCATCTTTGCATTT
1 TGCAT-TTTGCATTT
* *
402068 TTCATTGTGCATTT
1 TGCATTTTGCATTT
402082 ATACTTTTAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 4 0.16
14 8 0.32
15 13 0.52
ACGTcount: A:0.14, C:0.17, G:0.14, T:0.55
Consensus pattern (14 bp):
TGCATTTTGCATTT
Found at i:408483 original size:76 final size:76
Alignment explanation
Indices: 408395--408569 Score: 235
Period size: 76 Copynumber: 2.3 Consensus size: 76
408385 ATTAACAAGA
* *
408395 AGCAAATGTTGGGGCATACTGAAAACCCTTTTCAATCAGAATCATGAATATTGAAGTA-TTCTGA
1 AGCAAATGTTGGGGCATGCTGAAAACCCTTTTCAATCAGAATCAGGAATATTGAAGTATTTCTGA
408459 ATATTTATATC
66 ATATTTATATC
* * * * * *
408470 AGCAAAATGTTGGGGCATGCTGAAAGCTCTTTTCAATCAGAATCAGGACTGTTGATGTATTTTTG
1 AGC-AAATGTTGGGGCATGCTGAAAACCCTTTTCAATCAGAATCAGGAATATTGAAGTATTTCTG
* *
408535 AATATTTGTATT
65 AATATTTATATC
*
408547 AGCAAATGATGGGGCATGCTGAA
1 AGCAAATGTTGGGGCATGCTGAA
408570 GGCCCACATC
Statistics
Matches: 87, Mismatches: 11, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
75 3 0.03
76 67 0.77
77 17 0.20
ACGTcount: A:0.33, C:0.13, G:0.21, T:0.33
Consensus pattern (76 bp):
AGCAAATGTTGGGGCATGCTGAAAACCCTTTTCAATCAGAATCAGGAATATTGAAGTATTTCTGA
ATATTTATATC
Found at i:409781 original size:22 final size:23
Alignment explanation
Indices: 409728--409783 Score: 64
Period size: 22 Copynumber: 2.5 Consensus size: 23
409718 TACATCTACA
*
409728 TTTTTCAAAGATGATAGACTATC
1 TTTTTCAAAGATAATAGACTATC
*
409751 TCTTT-AAAGATAATAGA-T-TC
1 TTTTTCAAAGATAATAGACTATC
409771 TTTTTTCAAAGAT
1 -TTTTTCAAAGAT
409784 GAAAGCTTTA
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
20 2 0.07
21 5 0.18
22 17 0.61
23 4 0.14
ACGTcount: A:0.36, C:0.11, G:0.11, T:0.43
Consensus pattern (23 bp):
TTTTTCAAAGATAATAGACTATC
Found at i:410532 original size:45 final size:45
Alignment explanation
Indices: 410440--411103 Score: 984
Period size: 45 Copynumber: 14.8 Consensus size: 45
410430 CTATTTCCCA
* *
410440 CATCTGTAAG-CTCTTTAGTGCATGATATTTTTCAAAACCTTCGGGT
1 CATCTGTAAGTC-CTTCAGTGCATGAT-GTTTTCAAAACCTTCGGGT
*
410486 CATCTGTAAGTGCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
* *
410531 CATCTGTAAG-CC--C--TTC--GATGTTATCAAAAACCTTCGGGT
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTTC-AAAACCTTCGGGT
410570 CATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
* *
410615 CATCTGTAAGCCCTTCAGTGCTTGATGTTTTCAAAACCTTCGGGGT
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAACCTTC-GGGT
* * *
410661 CATCTGTAAGCCCTTCAGTGCTTGATGTTATCAAAAACCTTCGGGT
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTTC-AAAACCTTCGGGT
*
410707 CATCTGTAAGTCCTTCAGTGCTTGATGTTTTCAAAACCTTCGGGT
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
*
410752 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAAACCTTCGGGT
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTTC-AAAACCTTCGGGT
* *
410798 CATCTGTAAGTCCTTCAGTGCTTGATGTTCTCAAAACCTTCGGGT
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
*
410843 CATCTGTAAGTCCTTCAGTGCATGATGTTCTCAAAACCTTCGGGT
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
410888 CATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
* *
410933 CATCTGTAAGCCCTTCATTGCATGATGTTTTCAAAACCTTCGGGT
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
410978 CATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAAACCTTCGGGT
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTTC-AAAACCTTCGGGT
* * * * *
411024 CGTCTATAAGCCCTTCAGTACATGATATTTTCAAAACCTTCGGGT
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
* * *
411069 CATTTATAAGCCCTTCAGTGCATGATGTTTTCAAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAA
411104 CATTTCCATC
Statistics
Matches: 572, Mismatches: 33, Indels: 27
0.91 0.05 0.04
Matches are distributed among these distances:
38 8 0.01
39 23 0.04
40 4 0.01
42 2 0.00
44 3 0.01
45 341 0.60
46 182 0.32
47 9 0.02
ACGTcount: A:0.23, C:0.23, G:0.19, T:0.35
Consensus pattern (45 bp):
CATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
Found at i:410661 original size:91 final size:90
Alignment explanation
Indices: 410547--411103 Score: 898
Period size: 91 Copynumber: 6.1 Consensus size: 90
410537 TAAGCCCTTC
* *
410547 GATGTTATCAAAAACCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAACCTTCG
1 GATGTTTTC-AAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCG
* *
410612 GGTCATCTGTAAGCCCTTCAGTGCTT
65 GGTCATCTGTAAGTCCTTCAGTGCAT
* *
410638 GATGTTTTCAAAACCTTCGGGGTCATCTGTAAGCCCTTCAGTGCTTGATGTTATCAAAAACCTTC
1 GATGTTTTCAAAACCTTC-GGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTC-AAAACCTTC
*
410703 GGGTCATCTGTAAGTCCTTCAGTGCTT
64 GGGTCATCTGTAAGTCCTTCAGTGCAT
410730 GATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAAACCTTCG
1 GATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTC-AAAACCTTCG
*
410795 GGTCATCTGTAAGTCCTTCAGTGCTT
65 GGTCATCTGTAAGTCCTTCAGTGCAT
* * *
410821 GATGTTCTCAAAACCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTCTCAAAACCTTCGG
1 GATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGG
410886 GTCATCTGTAAGTCCTTCAGTGCAT
66 GTCATCTGTAAGTCCTTCAGTGCAT
*
410911 GATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCATTGCATGATGTTTTCAAAACCTTCGG
1 GATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGG
410976 GTCATCTGTAAGTCCTTCAGTGCAT
66 GTCATCTGTAAGTCCTTCAGTGCAT
* * * *
411001 GATGTTTTCAAAAACCTTCGGGTCGTCTATAAGCCCTTCAGTACATGATATTTTCAAAACCTTCG
1 GATGTTTTC-AAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCG
* * *
411066 GGTCATTTATAAGCCCTTCAGTGCAT
65 GGTCATCTGTAAGTCCTTCAGTGCAT
411092 GATGTTTTCAAA
1 GATGTTTTCAAA
411104 CATTTCCATC
Statistics
Matches: 440, Mismatches: 23, Indels: 7
0.94 0.05 0.01
Matches are distributed among these distances:
90 142 0.32
91 245 0.56
92 53 0.12
ACGTcount: A:0.23, C:0.23, G:0.19, T:0.35
Consensus pattern (90 bp):
GATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGG
GTCATCTGTAAGTCCTTCAGTGCAT
Found at i:411228 original size:3 final size:3
Alignment explanation
Indices: 411222--411314 Score: 158
Period size: 3 Copynumber: 32.3 Consensus size: 3
411212 AATTTTTTTC
411222 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
411270 ATT ATT A-T ATT A-T ATT ATT ATT A-T ATT A-T ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
411314 A
1 A
411315 AATAAAAAAT
Statistics
Matches: 86, Mismatches: 0, Indels: 8
0.91 0.00 0.09
Matches are distributed among these distances:
2 8 0.09
3 78 0.91
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:415221 original size:2 final size:2
Alignment explanation
Indices: 415214--415244 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
415204 AAAAAGATAC
415214 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 A
415245 GTAATAAATA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:415417 original size:28 final size:28
Alignment explanation
Indices: 415376--415429 Score: 74
Period size: 28 Copynumber: 1.9 Consensus size: 28
415366 AAATAAAACG
*
415376 AATAAATGAAAATAAATATACATACAAT
1 AATAAATGAAAATAAACATACATACAAT
*
415404 AATAAAT-AATAATAAACATATATACA
1 AATAAATGAA-AATAAACATACATACA
415430 TGCGCACATA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
27 2 0.09
28 21 0.91
ACGTcount: A:0.65, C:0.07, G:0.02, T:0.26
Consensus pattern (28 bp):
AATAAATGAAAATAAACATACATACAAT
Found at i:417484 original size:106 final size:106
Alignment explanation
Indices: 417299--417667 Score: 632
Period size: 106 Copynumber: 3.5 Consensus size: 106
417289 TGTATTGCTC
* * * *
417299 TGAGTCCAATATCCTCCGCCGTGAAGTTGAAATTGGTTCTAGAA-CTGGGAAATTATTTGTTGAC
1 TGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCT-GAAGTTGGGAAATTATTTGTTGAC
* *
417363 AGTCAGGCGCCCCTTCACCGTGAAGTTGAGCTTGTGCTGTCT
65 AGTCAGCCGCCCCTTCGCCGTGAAGTTGAGCTTGTGCTGTCT
*
417405 TGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAGTTGGGAAATTATTTGTTGACA
1 TGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAGTTGGGAAATTATTTGTTGACA
*
417470 GTCAGCCGCCCCTTCGCCGTGAAGTTGATCTTGTGCTGTCT
66 GTCAGCCGCCCCTTCGCCGTGAAGTTGAGCTTGTGCTGTCT
*
417511 TGAGTCCAATATCCTTCGCTATGAAGTTGAAATTGGCTCTGAAGTTGGGAAATTATTTGTTGACA
1 TGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAGTTGGGAAATTATTTGTTGACA
*
417576 GTCAGCTGCCCCTTCGCCGTGAAGTTGAGCTTGTGCTGTCT
66 GTCAGCCGCCCCTTCGCCGTGAAGTTGAGCTTGTGCTGTCT
417617 TGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAGTTGGGAA
1 TGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAGTTGGGAA
417668 GCCCCTTCTT
Statistics
Matches: 249, Mismatches: 13, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
105 3 0.01
106 246 0.99
ACGTcount: A:0.21, C:0.20, G:0.26, T:0.33
Consensus pattern (106 bp):
TGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAGTTGGGAAATTATTTGTTGACA
GTCAGCCGCCCCTTCGCCGTGAAGTTGAGCTTGTGCTGTCT
Found at i:418849 original size:11 final size:11
Alignment explanation
Indices: 418828--418857 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
418818 CTCTTTTTTG
418828 TTTTTTC-CTT
1 TTTTTTCTCTT
418838 TTTTTTCTCTT
1 TTTTTTCTCTT
418849 TTTTTTCTC
1 TTTTTTCTC
418858 GGGTTTTCAT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 7 0.37
11 12 0.63
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (11 bp):
TTTTTTCTCTT
Found at i:420220 original size:17 final size:17
Alignment explanation
Indices: 420198--420233 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
420188 CATCATTTCA
420198 GACTCCCCGCTAGCCTT
1 GACTCCCCGCTAGCCTT
*
420215 GACTCCCTGCTAGCCTT
1 GACTCCCCGCTAGCCTT
420232 GA
1 GA
420234 ATACGGCTGT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.14, C:0.42, G:0.19, T:0.25
Consensus pattern (17 bp):
GACTCCCCGCTAGCCTT
Found at i:426014 original size:23 final size:23
Alignment explanation
Indices: 425961--426014 Score: 65
Period size: 23 Copynumber: 2.3 Consensus size: 23
425951 ATACGAATGT
425961 AAAAACATGAAAAATATAAAATAA
1 AAAAACATG-AAAATATAAAATAA
*
425985 AACAAACATG-AAATATAAAATGCA
1 AA-AAACATGAAAATATAAAAT-AA
426009 AAAAAC
1 AAAAAC
426015 GCAATGCATG
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
23 15 0.56
24 5 0.19
25 7 0.26
ACGTcount: A:0.70, C:0.09, G:0.06, T:0.15
Consensus pattern (23 bp):
AAAAACATGAAAATATAAAATAA
Found at i:428056 original size:28 final size:28
Alignment explanation
Indices: 428015--428068 Score: 74
Period size: 28 Copynumber: 1.9 Consensus size: 28
428005 AAATAAAACG
*
428015 AATAAATGAAAATAAATATACATACAAT
1 AATAAATGAAAATAAACATACATACAAT
*
428043 AATAAAT-AATAATAAACATATATACA
1 AATAAATGAA-AATAAACATACATACA
428069 TGCGCACATA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
27 2 0.09
28 21 0.91
ACGTcount: A:0.65, C:0.07, G:0.02, T:0.26
Consensus pattern (28 bp):
AATAAATGAAAATAAACATACATACAAT
Found at i:428533 original size:17 final size:17
Alignment explanation
Indices: 428511--428546 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
428501 CTCGTTGGCC
428511 GCCGTTGAACGATGCCG
1 GCCGTTGAACGATGCCG
428528 GCCGTTGAACGATGCCG
1 GCCGTTGAACGATGCCG
428545 GC
1 GC
428547 GAAAATCCTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.17, C:0.31, G:0.36, T:0.17
Consensus pattern (17 bp):
GCCGTTGAACGATGCCG
Found at i:434564 original size:14 final size:14
Alignment explanation
Indices: 434545--434574 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
434535 GATAAGTTGA
*
434545 TTTTAATGTATATG
1 TTTTAATATATATG
434559 TTTTAATATATATG
1 TTTTAATATATATG
434573 TT
1 TT
434575 AATGATAAAA
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:0.30, C:0.00, G:0.10, T:0.60
Consensus pattern (14 bp):
TTTTAATATATATG
Found at i:434728 original size:34 final size:34
Alignment explanation
Indices: 434690--434790 Score: 157
Period size: 34 Copynumber: 3.0 Consensus size: 34
434680 GAATTTAATG
* *
434690 TTAAATTTTGAATACTATAATTTATATTTTAAAT
1 TTAAATTTCGAATACTATAATTTGTATTTTAAAT
* * *
434724 TTAAATTTCGAATAATATTATTTGTATTTTAATT
1 TTAAATTTCGAATACTATAATTTGTATTTTAAAT
434758 TTAAATTTCGAATACTATAATTTGTATTTTAAA
1 TTAAATTTCGAATACTATAATTTGTATTTTAAA
434791 AACATTAATT
Statistics
Matches: 59, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
34 59 1.00
ACGTcount: A:0.39, C:0.04, G:0.05, T:0.52
Consensus pattern (34 bp):
TTAAATTTCGAATACTATAATTTGTATTTTAAAT
Found at i:435332 original size:21 final size:21
Alignment explanation
Indices: 435308--435347 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
435298 ATAAAACCCT
* *
435308 GCGGGCTAGGCATGTAACCTG
1 GCGGACTAGGAATGTAACCTG
435329 GCGGACTAGGAATGTAACC
1 GCGGACTAGGAATGTAACC
435348 CTGCGAAGAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.25, C:0.23, G:0.35, T:0.17
Consensus pattern (21 bp):
GCGGACTAGGAATGTAACCTG
Found at i:435392 original size:42 final size:42
Alignment explanation
Indices: 435346--435430 Score: 98
Period size: 42 Copynumber: 2.0 Consensus size: 42
435336 AGGAATGTAA
* * *
435346 CCCTGCGAAGATGACATATGAACTGGTGGGCTTGGCATATAC
1 CCCTGAGAAGATGACATATGAACTGGAGGGCTGGGCATATAC
* * * * *
435388 CCCTGAGGAGATGGCATCTGAAGTGGAGGGCTGGGCATGTAC
1 CCCTGAGAAGATGACATATGAACTGGAGGGCTGGGCATATAC
435430 C
1 C
435431 ATTGTGGCAT
Statistics
Matches: 35, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
42 35 1.00
ACGTcount: A:0.24, C:0.21, G:0.34, T:0.21
Consensus pattern (42 bp):
CCCTGAGAAGATGACATATGAACTGGAGGGCTGGGCATATAC
Found at i:437517 original size:21 final size:21
Alignment explanation
Indices: 437499--437597 Score: 103
Period size: 21 Copynumber: 4.6 Consensus size: 21
437489 ATGAAGCAAG
437499 GGAAACAGAGAGAGCAGCAGC
1 GGAAACAGAGAGAGCAGCAGC
* **
437520 GGAAGCAGCTAGAGCAGCAGC
1 GGAAACAGAGAGAGCAGCAGC
* *
437541 GGAAGCAGAGAGAGAAGCAGC
1 GGAAACAGAGAGAGCAGCAGC
437562 GGCAACACAGAGAGAG--GCAGC
1 GG-AA-ACAGAGAGAGCAGCAGC
437583 GGCAGAACAGAGAGA
1 GG-A-AACAGAGAGA
437598 AGTAATATAT
Statistics
Matches: 68, Mismatches: 7, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
21 56 0.82
22 3 0.04
23 9 0.13
ACGTcount: A:0.40, C:0.19, G:0.39, T:0.01
Consensus pattern (21 bp):
GGAAACAGAGAGAGCAGCAGC
Found at i:438075 original size:43 final size:44
Alignment explanation
Indices: 437988--438101 Score: 108
Period size: 43 Copynumber: 2.6 Consensus size: 44
437978 TTCTGCGGCG
* *
437988 TTTGTAAGAAAACGCCGGTAAAAAT-AAAAATCTACTGCGGCGTT
1 TTTGT-AGAAAACGCCGCTAAAAATCAAAAATCTACTGCGACGTT
* ** *
438032 TTTGTAGAAAACGCCGCTAAACATCAACGA-CTATTGCGACGTT
1 TTTGTAGAAAACGCCGCTAAAAATCAAAAATCTACTGCGACGTT
** *
438075 TTAAT-GATAAACGCCGCTAAATATCAA
1 TTTGTAGA-AAACGCCGCTAAAAATCAA
438102 TACCTTTTGC
Statistics
Matches: 59, Mismatches: 9, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
42 2 0.03
43 49 0.83
44 8 0.14
ACGTcount: A:0.38, C:0.19, G:0.18, T:0.25
Consensus pattern (44 bp):
TTTGTAGAAAACGCCGCTAAAAATCAAAAATCTACTGCGACGTT
Found at i:438215 original size:15 final size:15
Alignment explanation
Indices: 438184--438242 Score: 50
Period size: 15 Copynumber: 3.9 Consensus size: 15
438174 CGCCGCAAAC
* *
438184 TTTAGCGGCGCTATT
1 TTTAGCGGCGTTTTT
438199 TTTAGCGGCG-TTTT
1 TTTAGCGGCGTTTTT
*
438213 TTTA-CGCCGTATGTGTT
1 TTTAGCGGCGT-T-T-TT
438230 TTTAGCGGCGTTT
1 TTTAGCGGCGTTT
438243 AAAAACGCCG
Statistics
Matches: 36, Mismatches: 3, Indels: 9
0.75 0.06 0.19
Matches are distributed among these distances:
13 4 0.11
14 7 0.19
15 11 0.31
16 2 0.06
17 7 0.19
18 5 0.14
ACGTcount: A:0.10, C:0.17, G:0.27, T:0.46
Consensus pattern (15 bp):
TTTAGCGGCGTTTTT
Found at i:438419 original size:30 final size:30
Alignment explanation
Indices: 438353--438447 Score: 88
Period size: 30 Copynumber: 3.2 Consensus size: 30
438343 TAATTAGCAC
* * *
438353 AAAAAATAATTA-ATTAAT-TAATTTAAAT
1 AAAAAATAATTATATAAATATTATTTTAAT
*
438381 AAATAATAATTATATAAATATTATTTTAAT
1 AAAAAATAATTATATAAATATTATTTTAAT
* * *
438411 AAAAAATAA-TATTTATATAATTATATTAAT
1 AAAAAATAATTATATAAAT-ATTATTTTAAT
*
438441 ATAAAAT
1 AAAAAAT
438448 GTAATAACTA
Statistics
Matches: 55, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
28 11 0.20
29 12 0.22
30 32 0.58
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (30 bp):
AAAAAATAATTATATAAATATTATTTTAAT
Found at i:443945 original size:18 final size:18
Alignment explanation
Indices: 443924--443964 Score: 73
Period size: 18 Copynumber: 2.3 Consensus size: 18
443914 GAGGTCGATC
443924 GATGCTAGTTTTTAGAAA
1 GATGCTAGTTTTTAGAAA
*
443942 GATGCTAGTTTTTGGAAA
1 GATGCTAGTTTTTAGAAA
443960 GATGC
1 GATGC
443965 GATTAAAGAC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.29, C:0.07, G:0.27, T:0.37
Consensus pattern (18 bp):
GATGCTAGTTTTTAGAAA
Found at i:450810 original size:18 final size:18
Alignment explanation
Indices: 450783--450817 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
450773 TCATATTTAT
*
450783 ATATTTTTTAAAAATAAA
1 ATATTATTTAAAAATAAA
450801 ATATTATTTAAAAATAA
1 ATATTATTTAAAAATAA
450818 TTTTTTAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (18 bp):
ATATTATTTAAAAATAAA
Found at i:455132 original size:8 final size:7
Alignment explanation
Indices: 455102--455133 Score: 55
Period size: 7 Copynumber: 4.6 Consensus size: 7
455092 ATTATAGACC
455102 TTTAAAT
1 TTTAAAT
455109 TTTAAAT
1 TTTAAAT
455116 TTTAAAT
1 TTTAAAT
*
455123 TTTAAAA
1 TTTAAAT
455130 TTTA
1 TTTA
455134 TATATATATA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (7 bp):
TTTAAAT
Found at i:455160 original size:16 final size:17
Alignment explanation
Indices: 455141--455174 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
455131 TTATATATAT
*
455141 ATATATTTTAAA-AATA
1 ATATAATTTAAAGAATA
455157 ATATAATTTAAAGAATA
1 ATATAATTTAAAGAATA
455174 A
1 A
455175 AAAAATATGA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 11 0.69
17 5 0.31
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (17 bp):
ATATAATTTAAAGAATA
Found at i:457135 original size:18 final size:19
Alignment explanation
Indices: 457090--457136 Score: 51
Period size: 18 Copynumber: 2.5 Consensus size: 19
457080 TAAATCAAAG
*
457090 GAGGAAAAAATGAGAATGAA
1 GAGGAAAAAAT-AGAATAAA
**
457110 GAAAAAAAAAT-GAATAAA
1 GAGGAAAAAATAGAATAAA
457128 GAGGAAAAA
1 GAGGAAAAA
457137 TATTAAATAA
Statistics
Matches: 22, Mismatches: 5, Indels: 2
0.76 0.17 0.07
Matches are distributed among these distances:
18 13 0.59
20 9 0.41
ACGTcount: A:0.68, C:0.00, G:0.23, T:0.09
Consensus pattern (19 bp):
GAGGAAAAAATAGAATAAA
Found at i:458467 original size:5 final size:5
Alignment explanation
Indices: 458453--458504 Score: 54
Period size: 5 Copynumber: 10.4 Consensus size: 5
458443 AAAAATAAGG
* *
458453 AATAA AATAA CATAA AATAA AATAA TAATAA TAAT-A AATAA TA-AA AATAA
1 AATAA AATAA AATAA AATAA AATAA -AATAA -AATAA AATAA AATAA AATAA
458503 AA
1 AA
458505 ATATTTTCAA
Statistics
Matches: 40, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
4 6 0.15
5 25 0.62
6 9 0.22
ACGTcount: A:0.75, C:0.02, G:0.00, T:0.23
Consensus pattern (5 bp):
AATAA
Found at i:458491 original size:16 final size:15
Alignment explanation
Indices: 458456--458507 Score: 61
Period size: 15 Copynumber: 3.4 Consensus size: 15
458446 AATAAGGAAT
*
458456 AAAATAACATAAAAT-
1 AAAATAATA-AAAATA
*
458471 AAAATAATAATAATA
1 AAAATAATAAAAATA
458486 ATAAATAATAAAAATA
1 A-AAATAATAAAAATA
458502 AAAATA
1 AAAATA
458508 TTTTCAAAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
14 4 0.12
15 14 0.44
16 14 0.44
ACGTcount: A:0.75, C:0.02, G:0.00, T:0.23
Consensus pattern (15 bp):
AAAATAATAAAAATA
Found at i:458561 original size:37 final size:36
Alignment explanation
Indices: 458509--458842 Score: 220
Period size: 37 Copynumber: 9.1 Consensus size: 36
458499 ATAAAAATAT
* *
458509 TTTCAAAAACATATATAATATATAAATTTCTTATATAT-
1 TTTCAAAAAC-TATATAATATATAAATTT-TCA-AAATG
**
458547 TTTCAAAAACTATATAATATATATGTTTTCAAAAATG
1 TTTCAAAAACTATATAATATATAAATTTTC-AAAATG
* * **
458584 TTTTAAAAACTATATATTATATTTATTTTCAAAATG
1 TTTCAAAAACTATATAATATATAAATTTTCAAAATG
*
458620 TTTTAAAAACTATATAATATATAAATGTTTTCAAACATG
1 TTTCAAAAACTATATAATATATAAA--TTTTCAAA-ATG
* *
458659 TTTTC-AAAA--ATAT--TATATAAGTTTTCAGAAACG
1 -TTTCAAAAACTATATAATATATAAATTTTCA-AAATG
* *
458692 TTTTAAAAACTATATAATATATAAATGTTTTCAAAAATAT
1 TTTCAAAAACTATATAATATATAAA--TTTTC-AAAAT-G
****
458732 TTTC-AAAAC--TATAATATATGTGCTTTCAAAAATG
1 TTTCAAAAACTATATAATATATAAATTTTC-AAAATG
* *
458766 TTTTCAAAAATTATAT-ATATATAAGTTTTCAAAATG
1 -TTTCAAAAACTATATAATATATAAATTTTCAAAATG
* * * * * *
458802 ATTTTAAAAATTATACATTATATATATTTTTTAAAATG
1 -TTTCAAAAACTATATAATATATA-AATTTTCAAAATG
458840 TTT
1 TTT
458843 TTTTTTAAAA
Statistics
Matches: 240, Mismatches: 34, Indels: 45
0.75 0.11 0.14
Matches are distributed among these distances:
32 3 0.01
33 12 0.05
34 2 0.01
35 25 0.10
36 55 0.23
37 84 0.35
38 32 0.13
39 20 0.08
40 7 0.03
ACGTcount: A:0.45, C:0.07, G:0.04, T:0.44
Consensus pattern (36 bp):
TTTCAAAAACTATATAATATATAAATTTTCAAAATG
Found at i:458713 original size:72 final size:70
Alignment explanation
Indices: 458546--458812 Score: 287
Period size: 72 Copynumber: 3.7 Consensus size: 70
458536 TTCTTATATA
458546 TTTTCAAAAACTATATAATATAT-ATGTTTTCAAAAATGTTTTAAAAACTATATATTATATTTA-
1 TTTTCAAAAACTATATAATATATAATGTTTTCAAAAATGTTTTAAAAA-TAT-TA-TATA---AG
458609 TTTTCAAAATG
60 TTTTCAAAATG
*
458620 TTTT-AAAAACTATATAATATATAAATGTTTTCAAACATGTTTTCAAAAATATTATATAAGTTTT
1 TTTTCAAAAACTATATAATATAT-AATGTTTTCAAAAATGTTTT-AAAAATATTATATAAGTTTT
*
458684 CAGAAACG
64 CA-AAATG
* * * *
458692 TTTT-AAAAACTATATAATATATAAATGTTTTCAAAAATATTTTCAAAACTATAATATATGTGCT
1 TTTTCAAAAACTATATAATATAT-AATGTTTTCAAAAATGTTTT-AAAAATATTATATAAGT--T
458756 TTCAAAAATG
62 TTC-AAAATG
*
458766 TTTTCAAAAATTATAT-ATATATAA-GTTTTC-AAAATGATTTTAAAAAT
1 TTTTCAAAAACTATATAATATATAATGTTTTCAAAAATG-TTTTAAAAAT
458813 TATACATTAT
Statistics
Matches: 172, Mismatches: 11, Indels: 23
0.83 0.05 0.11
Matches are distributed among these distances:
70 1 0.01
71 16 0.09
72 70 0.41
73 24 0.14
74 24 0.14
75 32 0.19
76 5 0.03
ACGTcount: A:0.45, C:0.07, G:0.05, T:0.43
Consensus pattern (70 bp):
TTTTCAAAAACTATATAATATATAATGTTTTCAAAAATGTTTTAAAAATATTATATAAGTTTTCA
AAATG
Found at i:459731 original size:165 final size:161
Alignment explanation
Indices: 459562--460267 Score: 707
Period size: 165 Copynumber: 4.3 Consensus size: 161
459552 CGAACCCAGG
* *
459562 GGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCGTTGAGCTGAGC
1 GGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATATGCCCTTGAGCTGAGC
* * * * *
459627 GTAGTCGAACTCAAAGGTCTTTTGGTCACAGATAACCCTTCTAGCCTTGAGTTACGCTGCAAATG
66 GTAATCGAACTCAAAGGTC-TTTGG---CAGATAACCCTTCTAGACTTAAGCTATGCTGCAAATG
* * * **
459692 ATGTGCCCTAGAAGCTGAGTGTAATCGAACTCGGG
127 ATGTGCCCTTGAAGCTGAGCGTAGTCGAACTCGAA
* * *
459727 GGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATACTGGAAATGATATGCCGTTGAGCTGAGC
1 GGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATATGCCCTTGAGCTGAGC
* * * *
459792 GTAGTCGAACTCAAAGGTCTTTTGTTGGCAGACAACCCTTCTAGACTTAAGTTGTGCTGCAAATG
66 GTAATCGAACTCAAAGGTC---T-TTGGCAGATAACCCTTCTAGACTTAAGCTATGCTGCAAATG
* * *
459857 ATATG-CCTTGGAGCTGAGCATAGTCGAACTCGAA
127 ATGTGCCCTTGAAGCTGAGCGTAGTCGAACTCGAA
* * * * **
459891 GGTCTTTTGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTACAAATGATGTGCCCTCAAAGC
1 GGTC---T-TTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATATGCCCT-TGAGC
* *** * * * *
459956 TGAGTGTAATCGAACTCGGGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATACTGGAAAT
61 TGAGCGTAATCGAACTCAAAGGTCTTTGGCAGATAACCCTTCTAGACTTAAGCTATGCTGCAAAT
* *
460021 GATGTGCCGTTG-AGCTGAGCGTAGTCGAACTCAAA
126 GATGTGCCCTTGAAGCTGAGCGTAGTCGAACTCGAA
* * * * * * *
460056 GGTCTTTTGGTCACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGTTATGCCCTTGAAGC
1 GGTC-TTTGG---CAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATATGCCCTTG-AGC
* * * * *
460121 TGAGTGTAATCGAACTTAAGGGTCTTTGGCAGATAACCCTTCTCGACTTAAGCTATTCTGCAAAT
61 TGAGCGTAATCGAACTCAAAGGTCTTTGGCAGATAACCCTTCTAGACTTAAGCTATGCTGCAAAT
*
460186 GATGTG-CCTTGGAGCTGAGCGTAGTCGAACTCGAA
126 GATGTGCCCTTGAAGCTGAGCGTAGTCGAACTCGAA
* * * * *
460221 GGTCTTGGTGGCAGGTAGCCCTTCTGGCCTTGAGCTAAGCTGCAAAT
1 GGTCTT--TGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAAT
460268 AGTTTGTTTA
Statistics
Matches: 461, Mismatches: 64, Indels: 34
0.82 0.11 0.06
Matches are distributed among these distances:
162 4 0.01
163 32 0.07
164 32 0.07
165 313 0.68
166 8 0.02
167 3 0.01
168 47 0.10
169 22 0.05
ACGTcount: A:0.24, C:0.21, G:0.25, T:0.29
Consensus pattern (161 bp):
GGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATATGCCCTTGAGCTGAGC
GTAATCGAACTCAAAGGTCTTTGGCAGATAACCCTTCTAGACTTAAGCTATGCTGCAAATGATGT
GCCCTTGAAGCTGAGCGTAGTCGAACTCGAA
Found at i:459842 original size:249 final size:246
Alignment explanation
Indices: 459567--460245 Score: 916
Period size: 249 Copynumber: 2.7 Consensus size: 246
459557 CCAGGGGTCT
* * * *
459567 TTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCGTTGAGCTGAGCGTAGT
1 TTGGCAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATATGCC-TTGAGCTGAGCGTAGT
* * * *
459632 CGAACTCAAAGGTCTTTTGGTCACAGATAACCCTTCTAGCCTTGAGTTACGCTGCAAATGATGTG
65 CGAACTCAAAGGTCTTTTGGT--CAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTG
459697 CCCTAGAAGCTGAGTGTAATCGAACTCGGGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTA
128 CCCTAGAAGCTGAGTGTAATCGAACTCGGGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTA
459762 TACTGGAAATGATATGCCGTTGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTTG
193 TACTGGAAATGATATGCCGTTGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTTG
* * *
459816 TTGGCAGACAACCCTTCTAGACTTAAGTTGTGCTGCAAATGATATGCCTTGGAGCTGAGCATAGT
1 TTGGCAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATATGCCTT-GAGCTGAGCGTAGT
* * *
459881 CGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTACAAATGATGTG
65 CGAACTCAAAGGTCTTTTG--GTCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTG
459946 CCCTCA-AAGCTGAGTGTAATCGAACTCGGGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCT
128 CCCT-AGAAGCTGAGTGTAATCGAACTCGGGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCT
*
460010 ATACTGGAAATGATGTGCCGTTGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTTG
192 ATACTGGAAATGATATGCCGTTGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTTG
* ** * * * * * *
460065 GTCACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGTTATGCCCTTGAAGCTGAGTGTAA
1 TTGGCAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATATG-CCTTG-AGCTGAGCGTAG
* * * *
460130 TCGAACTTAAGGGTC-TTTGG-CAGATAACCCTTCTCGACTTAAGCTATTCTGCAAATGATGTG-
64 TCGAACTCAAAGGTCTTTTGGTCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGC
* * * * ** *
460192 CCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTGGTGGCAGGTAGCCCTTCT
129 CCTAGAAGCTGAGTGTAATCGAACTCGGGGGTCTT--TGGCAGATAGCCCTTCT
460246 GGCCTTGAGC
Statistics
Matches: 381, Mismatches: 40, Indels: 20
0.86 0.09 0.05
Matches are distributed among these distances:
245 28 0.07
246 39 0.10
247 17 0.04
248 2 0.01
249 268 0.70
250 26 0.07
251 1 0.00
ACGTcount: A:0.24, C:0.21, G:0.25, T:0.29
Consensus pattern (246 bp):
TTGGCAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATATGCCTTGAGCTGAGCGTAGTC
GAACTCAAAGGTCTTTTGGTCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCC
TAGAAGCTGAGTGTAATCGAACTCGGGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATAC
TGGAAATGATATGCCGTTGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTTG
Found at i:463633 original size:18 final size:19
Alignment explanation
Indices: 463592--463636 Score: 65
Period size: 19 Copynumber: 2.4 Consensus size: 19
463582 AGTTAATGTG
*
463592 AATGCAAAGAAAATAACAA
1 AATGCAAAGAAAACAACAA
*
463611 AATGCAAAGAAAACAA-GA
1 AATGCAAAGAAAACAACAA
463629 AATGCAAA
1 AATGCAAA
463637 TGTCTAAATA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
18 9 0.38
19 15 0.62
ACGTcount: A:0.67, C:0.11, G:0.13, T:0.09
Consensus pattern (19 bp):
AATGCAAAGAAAACAACAA
Found at i:464283 original size:17 final size:17
Alignment explanation
Indices: 464257--464289 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
464247 TGCAAACAAT
*
464257 GAACACAAAATAAAAGA
1 GAACAAAAAATAAAAGA
464274 GAACAAAAAATAAAAG
1 GAACAAAAAATAAAAG
464290 GGTTAGTGAG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.73, C:0.09, G:0.12, T:0.06
Consensus pattern (17 bp):
GAACAAAAAATAAAAGA
Found at i:465255 original size:12 final size:12
Alignment explanation
Indices: 465238--465262 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
465228 CGAAAATTGA
465238 AAAATTTAAATT
1 AAAATTTAAATT
465250 AAAATTTAAATT
1 AAAATTTAAATT
465262 A
1 A
465263 CCCGATTCGA
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:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (12 bp):
AAAATTTAAATT
Found at i:465423 original size:18 final size:19
Alignment explanation
Indices: 465378--465424 Score: 51
Period size: 18 Copynumber: 2.5 Consensus size: 19
465368 TAAATCAAAG
*
465378 GAGGAAAAAATGAGAATGAA
1 GAGGAAAAAAT-AGAATAAA
**
465398 GAAAAAAAAAT-GAATAAA
1 GAGGAAAAAATAGAATAAA
465416 GAGGAAAAA
1 GAGGAAAAA
465425 TATTAAATAA
Statistics
Matches: 22, Mismatches: 5, Indels: 2
0.76 0.17 0.07
Matches are distributed among these distances:
18 13 0.59
20 9 0.41
ACGTcount: A:0.68, C:0.00, G:0.23, T:0.09
Consensus pattern (19 bp):
GAGGAAAAAATAGAATAAA
Found at i:466733 original size:5 final size:5
Alignment explanation
Indices: 466719--466777 Score: 50
Period size: 5 Copynumber: 11.4 Consensus size: 5
466709 AAAAATAAGG
* *
466719 AATAA AATAA CATAA AATAA TAATAA TAATAA TAAT-A AATAA TA-AA
1 AATAA AATAA AATAA AATAA -AATAA -AATAA -AATAA AATAA AATAA
466765 AATAAA AATAA AA
1 AAT-AA AATAA AA
466778 ATATTTTCAA
Statistics
Matches: 46, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
4 6 0.13
5 20 0.43
6 20 0.43
ACGTcount: A:0.75, C:0.02, G:0.00, T:0.24
Consensus pattern (5 bp):
AATAA
Found at i:466742 original size:3 final size:3
Alignment explanation
Indices: 466730--466780 Score: 59
Period size: 3 Copynumber: 17.0 Consensus size: 3
466720 ATAAAATAAC
* *
466730 ATA A-A ATA ATA ATA ATA ATA ATA ATAA ATA ATA AAA ATA AAA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA AT-A ATA ATA ATA ATA ATA ATA
*
466775 AAA ATA
1 ATA ATA
466781 TTTTCAAAAA
Statistics
Matches: 40, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
2 2 0.05
3 35 0.88
4 3 0.08
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (3 bp):
ATA
Found at i:466749 original size:22 final size:22
Alignment explanation
Indices: 466704--466777 Score: 66
Period size: 22 Copynumber: 3.4 Consensus size: 22
466694 CAACAAACAA
*
466704 AACATAAAAATAAGGAATAA-AAT
1 AACAT-AAAATAA-TAATAATAAT
466727 AACATAAAATAATAATAATAAT
1 AACATAAAATAATAATAATAAT
* *
466749 AATA-ATAAATAATAAAAATAA-
1 AACATA-AAATAATAATAATAAT
466770 AA-ATAAAA
1 AACATAAAA
466778 ATATTTTCAA
Statistics
Matches: 45, Mismatches: 3, Indels: 9
0.79 0.05 0.16
Matches are distributed among these distances:
20 4 0.09
21 9 0.20
22 27 0.60
23 5 0.11
ACGTcount: A:0.73, C:0.03, G:0.03, T:0.22
Consensus pattern (22 bp):
AACATAAAATAATAATAATAAT
Found at i:466751 original size:12 final size:12
Alignment explanation
Indices: 466707--466780 Score: 64
Period size: 12 Copynumber: 6.2 Consensus size: 12
466697 CAAACAAAAC
*
466707 ATAAAAATAAGGA
1 ATAAAAATAA-TA
*
466720 AT-AAAATAA-C
1 ATAAAAATAATA
466730 AT-AAAATAATA
1 ATAAAAATAATA
*
466741 ATAATAATAATA
1 ATAAAAATAATA
*
466753 ATAAATAATAAAA
1 ATAAA-AATAATA
*
466766 ATAAAAATAAAA
1 ATAAAAATAATA
466778 ATA
1 ATA
466781 TTTTCAAAAA
Statistics
Matches: 53, Mismatches: 5, Indels: 7
0.82 0.08 0.11
Matches are distributed among these distances:
10 9 0.17
11 2 0.04
12 29 0.55
13 13 0.25
ACGTcount: A:0.73, C:0.01, G:0.03, T:0.23
Consensus pattern (12 bp):
ATAAAAATAATA
Found at i:466759 original size:19 final size:19
Alignment explanation
Indices: 466732--466780 Score: 66
Period size: 19 Copynumber: 2.7 Consensus size: 19
466722 AAAATAACAT
*
466732 AAAAT-AATAATAATAATA
1 AAAATAAATAATAAAAATA
*
466750 ATAATAAATAATAAAAATA
1 AAAATAAATAATAAAAATA
466769 AAAATAAA-AATA
1 AAAATAAATAATA
466781 TTTTCAAAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
18 8 0.30
19 19 0.70
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (19 bp):
AAAATAAATAATAAAAATA
Found at i:466807 original size:37 final size:37
Alignment explanation
Indices: 466766--466914 Score: 94
Period size: 36 Copynumber: 4.1 Consensus size: 37
466756 AATAATAAAA
466766 ATAAAAAT-AAAAATATTTTCAAAAACATATATAATAT
1 ATAAAAATCAAAAATATTTTCAAAAAC-TATATAATAT
** ** *
466803 ATAAATTTCTTATATATTTTCAAAAACTATATAATAT
1 ATAAAAATCAAAAATATTTTCAAAAACTATATAATAT
**** * *
466840 AT-GTTTTCAAAAATGTTTT--AAAACTATATATTAT
1 ATAAAAATCAAAAATATTTTCAAAAACTATATAATAT
* *** *
466874 ATTTATTTTC-AAAATGTTTT-AAAAACTATATAATAT
1 A-TAAAAATCAAAAATATTTTCAAAAACTATATAATAT
466910 ATAAA
1 ATAAA
466915 TGTTTTCAAA
Statistics
Matches: 92, Mismatches: 16, Indels: 10
0.78 0.14 0.08
Matches are distributed among these distances:
34 15 0.16
35 13 0.14
36 31 0.34
37 18 0.20
38 15 0.16
ACGTcount: A:0.50, C:0.06, G:0.02, T:0.42
Consensus pattern (37 bp):
ATAAAAATCAAAAATATTTTCAAAAACTATATAATAT
Found at i:466869 original size:71 final size:70
Alignment explanation
Indices: 466787--467079 Score: 219
Period size: 71 Copynumber: 4.1 Consensus size: 70
466777 AATATTTTCA
* *
466787 AAAACATATATAATATATAAATTTCTTATATATTTTCAAAAACTATAT-A-ATAT-ATGTTTTCA
1 AAAAC-TATAT-ATATATAAATTT-TCA-AAATTTT-AAAAACTATATAATATATAATGTTTTCA
466849 AAAATGTTTT
61 AAAATGTTTT
**
466859 AAAACTATATATTATATTTATTTTCAAAATGTTTTAAAAACTATATAATATATAAATGTTTTCAA
1 AAAACTATATA-TATATAAATTTTCAAAA--TTTTAAAAACTATATAATATAT-AATGTTTTCAA
*
466924 ACATGTTTT
62 AAATGTTTT
* *
466933 CAAA--ATAT-TATATAAGTTTTCAGAAACGTTTTAAAAACTATATAATATATAAATGTTTTCAA
1 AAAACTATATATATATAAATTTTCA-AAA--TTTTAAAAACTATATAATATAT-AATGTTTTCAA
*
466995 AAATATTTT
62 AAATGTTTT
* **** *
467004 CAAAACTATA-ATATTTGTGCTTTCAAAAATGTTTTCAAAAATTATAT-ATATATAA-GTTTTC-
1 -AAAACTATATATATATAAATTTTC-AAAA--TTTT-AAAAACTATATAATATATAATGTTTTCA
467065 AAAATGATTTT
61 AAAATG-TTTT
467076 AAAA
1 AAAA
467080 ATTATACATT
Statistics
Matches: 186, Mismatches: 20, Indels: 31
0.78 0.08 0.13
Matches are distributed among these distances:
69 2 0.01
70 25 0.13
71 73 0.39
72 26 0.14
73 2 0.01
74 47 0.25
75 11 0.06
ACGTcount: A:0.45, C:0.07, G:0.05, T:0.43
Consensus pattern (70 bp):
AAAACTATATATATATAAATTTTCAAAATTTTAAAAACTATATAATATATAATGTTTTCAAAAAT
GTTTT
Found at i:466883 original size:36 final size:36
Alignment explanation
Indices: 466819--467112 Score: 184
Period size: 36 Copynumber: 8.1 Consensus size: 36
466809 TTCTTATATA
* *
466819 TTTTCAAAAACTATATA-ATATATGTTTTCAAAAATG
1 TTTT-AAAAACTATATATATATTTATTTTCAAAAATG
466855 TTTT-AAAACTATATATTATATTTATTTTC-AAAATG
1 TTTTAAAAACTATATA-TATATTTATTTTCAAAAATG
* * *
466890 TTTTAAAAACTATATAATATATAAATGTTTTCAAACATG
1 TTTTAAAAACTATAT-ATATAT--TTATTTTCAAAAATG
* * *
466929 TTTTCAAAA-TAT-TATATA---AGTTTTCAGAAACG
1 TTTTAAAAACTATATATATATTTA-TTTTCAAAAATG
* * *
466961 TTTTAAAAACTATATAATATATAAATGTTTTCAAAAATA
1 TTTTAAAAACTATAT-ATATAT--TTATTTTCAAAAATG
* **
467000 TTTTCAAAACTATA-ATAT-TTGTGCTTTCAAAAATG
1 TTTTAAAAACTATATATATATT-TATTTTCAAAAATG
* *
467035 TTTTCAAAAATTATATATATA-TAAGTTTTC-AAAATG
1 TTTT-AAAAACTATATATATATTTA-TTTTCAAAAATG
* *
467071 ATTTTAAAAATTATACATTATATATATATTTT--AAAATG
1 -TTTTAAAAACTAT--A-TATATATTTATTTTCAAAAATG
467109 TTTT
1 TTTT
467113 TTTTAAAAAC
Statistics
Matches: 206, Mismatches: 26, Indels: 51
0.73 0.09 0.18
Matches are distributed among these distances:
32 17 0.08
33 3 0.01
34 12 0.06
35 31 0.15
36 58 0.28
37 23 0.11
38 16 0.08
39 45 0.22
40 1 0.00
ACGTcount: A:0.44, C:0.07, G:0.05, T:0.45
Consensus pattern (36 bp):
TTTTAAAAACTATATATATATTTATTTTCAAAAATG
Found at i:467066 original size:72 final size:72
Alignment explanation
Indices: 466819--467085 Score: 268
Period size: 71 Copynumber: 3.7 Consensus size: 72
466809 TTCTTATATA
* *
466819 TTTTCAAAAACTATAT-A-ATAT--ATGTTTTCAAAAATGTTTT-AAAACTATATATTATATTTA
1 TTTT-AAAAACTATATAATATATAAATGTTTTCAAAAATATTTTCAAAAC--TATA--ATATTTG
466879 TTTTC-AAAATG
61 TTTTCAAAAATG
* * * **
466890 TTTTAAAAACTATATAATATATAAATGTTTTCAAACATGTTTTCAAAA-TATTATATAAGTTTTC
1 TTTTAAAAACTATATAATATATAAATGTTTTCAAAAATATTTTCAAAACTATAATATTTGTTTTC
* *
466954 AGAAACG
66 AAAAATG
466961 TTTTAAAAACTATATAATATATAAATGTTTTCAAAAATATTTTCAAAACTATAATATTTGTGCTT
1 TTTTAAAAACTATATAATATATAAATGTTTTCAAAAATATTTTCAAAACTATAATATTTGT--TT
467026 TCAAAAATG
64 TCAAAAATG
* * *
467035 TTTTCAAAAATTATAT-ATATAT-AA-GTTTTC-AAAATGATTTTAAAAATTATA
1 TTTT-AAAAACTATATAATATATAAATGTTTTCAAAAAT-ATTTTCAAAACTATA
467086 CATTATATAT
Statistics
Matches: 168, Mismatches: 17, Indels: 21
0.82 0.08 0.10
Matches are distributed among these distances:
70 20 0.12
71 60 0.36
72 35 0.21
73 2 0.01
74 37 0.22
75 14 0.08
ACGTcount: A:0.44, C:0.07, G:0.05, T:0.43
Consensus pattern (72 bp):
TTTTAAAAACTATATAATATATAAATGTTTTCAAAAATATTTTCAAAACTATAATATTTGTTTTC
AAAAATG
Found at i:467112 original size:180 final size:179
Alignment explanation
Indices: 466781--467112 Score: 421
Period size: 180 Copynumber: 1.8 Consensus size: 179
466771 AATAAAAATA
*
466781 TTTTCAAAAACATATATAATATATAAATTTCTTATATATTTTCAAAAACTATATAATATATGTTT
1 TTTTCAAAAACATATATAATATATAAATTTCTTAAATATTTTCAAAAAC-ATATAATATATGTTT
* *
466846 TCAAAAATGTTTTAAAACTATATATTATATTTATTTTCAAAATGTTTTAAAAACTATATAATATA
65 TCAAAAATGTTTTAAAACTATATATTATATTAATTTTCAAAATGTTTTAAAAACTATACAATATA
*
466911 TAAATGTTTTCAAACATGTTTTCAAAATATTATATAAGTTTTCAGAAACG
130 TAAATATTTTCAAACATGTTTTCAAAATATTATATAAGTTTTCAGAAACG
*
466961 TTTT-AAAAAC-TATATAATATATAAATGTT-TTCAAAAATATTTTC-AAAAC-TATAATATTTG
1 TTTTCAAAAACATATATAATATATAAAT-TTCTT---AAATATTTTCAAAAACATATAATATATG
* *
467021 TGCTTTCAAAAATGTTTTCAAAAAT-TATA-TATATATAAGTTTTCAAAATGATTTTAAAAATTA
62 T--TTTCAAAAATGTTTT-AAAACTATATATTATAT-TAA-TTTTCAAAATG-TTTTAAAAACTA
* *
467084 TACATTATATATATATTTT-AAA-ATGTTTT
121 TACAATATATAAATATTTTCAAACATGTTTT
467113 TTTTAAAAAC
Statistics
Matches: 133, Mismatches: 9, Indels: 20
0.82 0.06 0.12
Matches are distributed among these distances:
178 29 0.22
179 13 0.10
180 37 0.28
181 28 0.21
182 26 0.20
ACGTcount: A:0.44, C:0.07, G:0.05, T:0.45
Consensus pattern (179 bp):
TTTTCAAAAACATATATAATATATAAATTTCTTAAATATTTTCAAAAACATATAATATATGTTTT
CAAAAATGTTTTAAAACTATATATTATATTAATTTTCAAAATGTTTTAAAAACTATACAATATAT
AAATATTTTCAAACATGTTTTCAAAATATTATATAAGTTTTCAGAAACG
Found at i:467145 original size:24 final size:24
Alignment explanation
Indices: 467113--467159 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
467103 AAAATGTTTT
467113 TTTTAAAAACTATACATTATATAG
1 TTTTAAAAACTATACATTATATAG
*
467137 TTTTAAAAACTATATATTATATA
1 TTTTAAAAACTATACATTATATA
467160 CGTAGTTTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.47, C:0.06, G:0.02, T:0.45
Consensus pattern (24 bp):
TTTTAAAAACTATACATTATATAG
Found at i:467180 original size:28 final size:27
Alignment explanation
Indices: 467113--467186 Score: 84
Period size: 28 Copynumber: 2.8 Consensus size: 27
467103 AAAATGTTTT
*
467113 TTTTAAAAACTATACAT-TATA--TAG
1 TTTTAAAAACTATATATATATACGTAG
467137 TTTTAAAAACTATATATTATATACGTAG
1 TTTTAAAAACTATATA-TATATACGTAG
*
467165 TTTTAAAATA-TGTATATATATA
1 TTTTAAAA-ACTATATATATATA
467187 AATATGTATG
Statistics
Matches: 43, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
24 15 0.35
25 1 0.02
26 4 0.09
27 6 0.14
28 16 0.37
29 1 0.02
ACGTcount: A:0.45, C:0.05, G:0.05, T:0.45
Consensus pattern (27 bp):
TTTTAAAAACTATATATATATACGTAG
Found at i:467186 original size:27 final size:28
Alignment explanation
Indices: 467113--467172 Score: 83
Period size: 24 Copynumber: 2.3 Consensus size: 28
467103 AAAATGTTTT
*
467113 TTTTAAAAACTATACA-T-TATA--TAG
1 TTTTAAAAACTATATATTATATACGTAG
467137 TTTTAAAAACTATATATTATATACGTAG
1 TTTTAAAAACTATATATTATATACGTAG
467165 TTTTAAAA
1 TTTTAAAA
467173 TATGTATATA
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
24 15 0.48
25 1 0.03
26 4 0.13
28 11 0.35
ACGTcount: A:0.45, C:0.07, G:0.05, T:0.43
Consensus pattern (28 bp):
TTTTAAAAACTATATATTATATACGTAG
Found at i:468481 original size:21 final size:22
Alignment explanation
Indices: 468452--468493 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
468442 TCTTTTCTTT
* *
468452 GATATAAT-AAATATTAATTTA
1 GATAAAATAAAATAATAATTTA
468473 GATAAAATAAAATAATAATTT
1 GATAAAATAAAATAATAATTT
468494 TTTATAGCAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 7 0.39
22 11 0.61
ACGTcount: A:0.57, C:0.00, G:0.05, T:0.38
Consensus pattern (22 bp):
GATAAAATAAAATAATAATTTA
Found at i:468597 original size:14 final size:14
Alignment explanation
Indices: 468561--468603 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
468551 CTTTTCTTTG
468561 ATATTGAAAAATAA
1 ATATTGAAAAATAA
* *
468575 ATATT-AAAATTAT
1 ATATTGAAAAATAA
*
468588 TTATTGAAAAATAA
1 ATATTGAAAAATAA
468602 AT
1 AT
468604 TATTATTATT
Statistics
Matches: 22, Mismatches: 6, Indels: 2
0.73 0.20 0.07
Matches are distributed among these distances:
13 10 0.45
14 12 0.55
ACGTcount: A:0.58, C:0.00, G:0.05, T:0.37
Consensus pattern (14 bp):
ATATTGAAAAATAA
Found at i:468606 original size:15 final size:15
Alignment explanation
Indices: 468562--468607 Score: 53
Period size: 15 Copynumber: 3.3 Consensus size: 15
468552 TTTTCTTTGA
468562 TATTGAAAAATAAA-
1 TATTGAAAAATAAAT
* *
468576 TATT--AAAATTATT
1 TATTGAAAAATAAAT
468589 TATTGAAAAATAAAT
1 TATTGAAAAATAAAT
468604 TATT
1 TATT
468608 ATTATTATAT
Statistics
Matches: 25, Mismatches: 4, Indels: 5
0.74 0.12 0.15
Matches are distributed among these distances:
12 6 0.24
13 4 0.16
14 4 0.16
15 11 0.44
ACGTcount: A:0.54, C:0.00, G:0.04, T:0.41
Consensus pattern (15 bp):
TATTGAAAAATAAAT
Found at i:470006 original size:3 final size:3
Alignment explanation
Indices: 470000--470056 Score: 73
Period size: 3 Copynumber: 19.3 Consensus size: 3
469990 ATAATATATT
* *
470000 TAA TAA TAA TATA TAA TAA T-A TTA TAA TAA TAA TAA TAA TAA T-T
1 TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
470044 TAA TAA TAA TAA T
1 TAA TAA TAA TAA T
470057 TTAAGTAAAA
Statistics
Matches: 48, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
2 3 0.06
3 42 0.88
4 3 0.06
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (3 bp):
TAA
Found at i:470026 original size:8 final size:10
Alignment explanation
Indices: 470002--470056 Score: 69
Period size: 11 Copynumber: 5.5 Consensus size: 10
469992 AATATATTTA
470002 ATAATAATAT
1 ATAATAATAT
470012 ATAATAATATT
1 ATAATAATA-T
470023 ATAATAATA-
1 ATAATAATAT
470032 ATAATAATAAT
1 ATAATAAT-AT
*
470043 TTAATAATA-
1 ATAATAATAT
470052 ATAAT
1 ATAAT
470057 TTAAGTAAAA
Statistics
Matches: 40, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
9 12 0.30
10 11 0.28
11 17 0.43
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (10 bp):
ATAATAATAT
Found at i:470032 original size:17 final size:17
Alignment explanation
Indices: 470000--470056 Score: 64
Period size: 17 Copynumber: 3.4 Consensus size: 17
469990 ATAATATATT
*
470000 TAATAATAATAT-ATAA
1 TAATAATATTATAATAA
* *
470016 TAATATTATAATAATAA
1 TAATAATATTATAATAA
470033 TAATAATAATT-TAATAA
1 TAATAAT-ATTATAATAA
470050 TAATAAT
1 TAATAAT
470057 TTAAGTAAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
16 9 0.26
17 23 0.68
18 2 0.06
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (17 bp):
TAATAATATTATAATAA
Found at i:470453 original size:75 final size:76
Alignment explanation
Indices: 470225--470960 Score: 1100
Period size: 74 Copynumber: 9.9 Consensus size: 76
470215 CATGTATTGA
* *
470225 AAGGTTTTGAAAACATC-AAAAGCTCCCGAAGGCTTTTTTGG-AACATCATGCACTGCAGGACTT
1 AAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGC-TTTTTGGAAACATCATGCACTGAAGGACTT
470288 ACAGATGA-CCG
65 ACAGATGACCCG
* * *
470299 AAGAC-TTGAAAA-ATCAAAAAGCTCCAGAAGGCTTTTTTTGGAAACATCATGCACTG-CGGACT
1 AAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGC--TTTTTGGAAACATCATGCACTGAAGGACT
*
470361 TACAGATGACCCT
64 TACAGATGACCCG
*
470374 AAGGCTTT-AAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGGCTTA
1 AAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTA
470438 CAGATGACCCG
66 CAGATGACCCG
470449 AAGGCTTTGAAAACATCAAAAAGCTCCCG-AGGCTTTTTGG-AACATCATGCACTGAAGGACTTA
1 AAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTA
*
470512 CAGATGA-CCT
66 CAGATGACCCG
* * *
470522 AAGGCTTT--AAACATAAAAAAGATCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGGCTTA
1 AAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTA
470585 CAGATGACCCG
66 CAGATGACCCG
* *
470596 AAGGCTTTG-AAACATC-AAAAGAT-CCGAAGGCTTTTTGGAAACATCATGCA-TGAAGGGCTTA
1 AAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTA
*
470657 CAGATTA-CCG
66 CAGATGACCCG
470667 AAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGAC-TA
1 AAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTA
*
470731 CAGATGACCCT
66 CAGATGACCCG
* *
470742 AAGGCTTT-AAAACATCAAAAAGATCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGGCTTA
1 AAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTA
470806 CAGATGA-CCG
66 CAGATGACCCG
470816 AAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTA
1 AAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTA
*
470881 CAGATGACCCT
66 CAGATGACCCG
* * *
470892 AAGGTTTTGAAAACATCAAAAAAACTCCCGAAGGC-TTTTGGAAACATCATGCACTGCAGGACTT
1 AAGGCTTTGAAAACATC-AAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTT
470956 ACAGA
65 ACAGA
470961 GTGGGGAAAT
Statistics
Matches: 610, Mismatches: 31, Indels: 40
0.90 0.05 0.06
Matches are distributed among these distances:
71 29 0.05
72 38 0.06
73 94 0.15
74 189 0.31
75 152 0.25
76 92 0.15
77 16 0.03
ACGTcount: A:0.36, C:0.21, G:0.21, T:0.23
Consensus pattern (76 bp):
AAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTA
CAGATGACCCG
Found at i:470509 original size:149 final size:151
Alignment explanation
Indices: 470225--470960 Score: 1112
Period size: 149 Copynumber: 5.0 Consensus size: 151
470215 CATGTATTGA
* *
470225 AAGGTTTTGAAAACATC-AAAAGCTCCCGAAGGCTTTTTTGG-AACATCATGCACTGCAGGACTT
1 AAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGC-TTTTTGGAAACATCATGCACTGAAGGACTT
* *
470288 ACAGATGA-CCGAAGAC-TTGAAAA-ATCAAAAAGCTCCAGAAGGCTTTTTTTGGAAACATCATG
65 ACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGC--TTTTTGGAAACATCATG
* *
470350 CACTG-CGGACTTACAGATGACCCT
128 CACTGAAGGACTTACAGATGA-CCG
*
470374 AAGGCTTT-AAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGGCTTA
1 AAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTA
470438 CAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCG-AGGCTTTTTGG-AACATCATGCAC
66 CAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCAC
*
470501 TGAAGGACTTACAGATGACCT
131 TGAAGGACTTACAGATGACCG
* * *
470522 AAGGCTTT--AAACATAAAAAAGATCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGGCTTA
1 AAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTA
*
470585 CAGATGACCCGAAGGCTTTG-AAACATC-AAAAGAT-CCGAAGGCTTTTTGGAAACATCATGCA-
66 CAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCAC
* *
470646 TGAAGGGCTTACAGATTACCG
131 TGAAGGACTTACAGATGACCG
470667 AAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGAC-TA
1 AAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTA
* *
470731 CAGATGACCCTAAGGCTTT-AAAACATCAAAAAGATCCCGAAGGCTTTTTGGAAACATCATGCAC
66 CAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCAC
*
470795 TGAAGGGCTTACAGATGACCG
131 TGAAGGACTTACAGATGACCG
470816 AAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTA
1 AAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTA
* * *
470881 CAGATGACCCTAAGGTTTTGAAAACATCAAAAAAACTCCCGAAGGC-TTTTGGAAACATCATGCA
66 CAGATGACCCGAAGGCTTTGAAAACATC-AAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCA
*
470945 CTGCAGGACTTACAGA
130 CTGAAGGACTTACAGA
470961 GTGGGGAAAT
Statistics
Matches: 548, Mismatches: 22, Indels: 32
0.91 0.04 0.05
Matches are distributed among these distances:
144 3 0.01
145 43 0.08
146 45 0.08
147 129 0.24
148 67 0.12
149 154 0.28
150 27 0.05
151 51 0.09
152 29 0.05
ACGTcount: A:0.36, C:0.21, G:0.21, T:0.23
Consensus pattern (151 bp):
AAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTA
CAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCAC
TGAAGGACTTACAGATGACCG
Found at i:471652 original size:21 final size:21
Alignment explanation
Indices: 471627--471699 Score: 103
Period size: 21 Copynumber: 3.5 Consensus size: 21
471617 CATAAATATT
471627 TCATCTTTGAAAAGAGAATCA
1 TCATCTTTGAAAAGAGAATCA
* *
471648 TCATCTTTAAAAAGAG-ATCT
1 TCATCTTTGAAAAGAGAATCA
* *
471668 TTATCTTTGAAAAGAGAATTA
1 TCATCTTTGAAAAGAGAATCA
471689 TCATCTTTGAA
1 TCATCTTTGAA
471700 GAATGTAGAT
Statistics
Matches: 44, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
20 17 0.39
21 27 0.61
ACGTcount: A:0.40, C:0.12, G:0.12, T:0.36
Consensus pattern (21 bp):
TCATCTTTGAAAAGAGAATCA
Done.