Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007993.1 Hibiscus syriacus cultivar Beakdansim tig00110443_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: 2245901
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 5 of 12
Found at i:971378 original size:45 final size:45
Alignment explanation
Indices: 971324--971590 Score: 407
Period size: 45 Copynumber: 6.0 Consensus size: 45
971314 AGGAGCTTTT
971324 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCA
1 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCA
* * *
971369 TGTTGTTTTCAAAGCCTTCGGGTCATCTGTAATCCCTTCAGTGCA
1 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCA
* *
971414 TGATACTTTTCAAAACCTTCAGGTCATCTGTAAGCCCTTCAGTGCA
1 TGAT-GTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCA
*
971460 TGATG-TTT-ATAAACCTTTGGGTCATCTGTAAGCCCTTCAGTGCA
1 TGATGTTTTCA-AAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCA
971504 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCA
1 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCA
* *
971549 TGAT-TTTT-AAAATCCTTCGGGTCATCTGTAAGACCTACAGTG
1 TGATGTTTTCAAAA-CCTTCGGGTCATCTGTAAGCCCTTCAGTG
971591 AAAAATAATA
Statistics
Matches: 203, Mismatches: 14, Indels: 11
0.89 0.06 0.05
Matches are distributed among these distances:
43 5 0.02
44 71 0.35
45 85 0.42
46 42 0.21
ACGTcount: A:0.23, C:0.23, G:0.19, T:0.35
Consensus pattern (45 bp):
TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCA
Found at i:971762 original size:3 final size:3
Alignment explanation
Indices: 971754--971812 Score: 75
Period size: 3 Copynumber: 19.7 Consensus size: 3
971744 TCATTTCATT
** *
971754 TTA TTA TTA AAA TTA TTA TTA TTA TTA ATA TTA -TA TATA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA TTA
971799 TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TT
971813 TAATAAATAA
Statistics
Matches: 48, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
2 2 0.04
3 43 0.90
4 3 0.06
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (3 bp):
TTA
Found at i:972132 original size:31 final size:31
Alignment explanation
Indices: 972094--972160 Score: 116
Period size: 31 Copynumber: 2.2 Consensus size: 31
972084 GCTTCCGACA
972094 CTCCAGTGCCACGCCATCTTACCACCGAAGC
1 CTCCAGTGCCACGCCATCTTACCACCGAAGC
* *
972125 CTCCAGTGCCACGCCATCTTGCCGCCGAAGC
1 CTCCAGTGCCACGCCATCTTACCACCGAAGC
972156 CTCCA
1 CTCCA
972161 TAAGCTCTGC
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 34 1.00
ACGTcount: A:0.19, C:0.46, G:0.18, T:0.16
Consensus pattern (31 bp):
CTCCAGTGCCACGCCATCTTACCACCGAAGC
Found at i:972952 original size:2 final size:2
Alignment explanation
Indices: 972945--972985 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
972935 GACCGATTGT
972945 TA TA 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 TA TA T
972986 TAGGTTAAAT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:973650 original size:149 final size:148
Alignment explanation
Indices: 973357--973636 Score: 383
Period size: 149 Copynumber: 1.9 Consensus size: 148
973347 TAATCATATT
* * **
973357 TTAATATTTATTTATTTTTTAATATTAAGAAATGGGCTGTCTTAAAGCACCTAGAAGTTTTTTTC
1 TTAATATTTATTTATTTTTTAATATTAAGAAATGGACTATCTTAAAGCACCTAGAAGTCCTTTTC
* * * * *
973422 TGATATTCTTAAATAAATAAATATCATATTTTTATAAATTATATATATTATTTTATTTTAATTAT
66 TGATATTCTTAAATAAATAAATATCATATATTTATAAATGATATAAATTATTATATATTAATTAT
973487 TTTTATAAAAATATTTTA
131 TTTTATAAAAATATTTTA
973505 TTAATATTTATTTATTTTTTTAATATTAAGAAATGGACTATCTTAAAGCACCTAGAAGTCCTTTT
1 TTAATATTTATTTA-TTTTTTAATATTAAGAAATGGACTATCTTAAAGCACCTAGAAGTCCTTTT
*
973570 CTGATATT-TATAAGTAAATAAATAT-AT-TATTTATAAA-GATA-AAAGTGTA-TATATATTAA
65 CTGATATTCT-TAAATAAATAAATATCATATATTTATAAATGATATAAA-T-TATTATATATTAA
973629 TATATTTT
127 T-TATTTT
973637 CTTAAAATTA
Statistics
Matches: 117, Mismatches: 10, Indels: 11
0.85 0.07 0.08
Matches are distributed among these distances:
145 2 0.02
146 13 0.11
147 17 0.15
148 17 0.15
149 68 0.58
ACGTcount: A:0.39, C:0.06, G:0.07, T:0.49
Consensus pattern (148 bp):
TTAATATTTATTTATTTTTTAATATTAAGAAATGGACTATCTTAAAGCACCTAGAAGTCCTTTTC
TGATATTCTTAAATAAATAAATATCATATATTTATAAATGATATAAATTATTATATATTAATTAT
TTTTATAAAAATATTTTA
Found at i:978905 original size:20 final size:20
Alignment explanation
Indices: 978880--978943 Score: 82
Period size: 20 Copynumber: 3.4 Consensus size: 20
978870 TTTTTCAATG
978880 TTTCAATAGTTTGTATAATT
1 TTTCAATAGTTTGTATAATT
*
978900 TTTCAAT--TTT-T-TCAATG
1 TTTCAATAGTTTGTAT-AATT
978917 TTTCAATAGTTTGTATAATT
1 TTTCAATAGTTTGTATAATT
978937 TTTCAAT
1 TTTCAAT
978944 TTTACCCATC
Statistics
Matches: 37, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
16 1 0.03
17 11 0.30
18 3 0.08
19 3 0.08
20 18 0.49
21 1 0.03
ACGTcount: A:0.28, C:0.08, G:0.08, T:0.56
Consensus pattern (20 bp):
TTTCAATAGTTTGTATAATT
Found at i:978918 original size:37 final size:37
Alignment explanation
Indices: 978869--978946 Score: 156
Period size: 37 Copynumber: 2.1 Consensus size: 37
978859 ATTATTATTT
978869 TTTTTTCAATGTTTCAATAGTTTGTATAATTTTTCAA
1 TTTTTTCAATGTTTCAATAGTTTGTATAATTTTTCAA
978906 TTTTTTCAATGTTTCAATAGTTTGTATAATTTTTCAA
1 TTTTTTCAATGTTTCAATAGTTTGTATAATTTTTCAA
978943 TTTT
1 TTTT
978947 ACCCATCTTA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 41 1.00
ACGTcount: A:0.26, C:0.08, G:0.08, T:0.59
Consensus pattern (37 bp):
TTTTTTCAATGTTTCAATAGTTTGTATAATTTTTCAA
Found at i:980772 original size:17 final size:18
Alignment explanation
Indices: 980750--980783 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
980740 CCGAAAATAT
980750 TATTTAA-TAAAAATAAA
1 TATTTAATTAAAAATAAA
980767 TATTTAATTAAAAATAA
1 TATTTAATTAAAAATAA
980784 TAATATATAG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 7 0.44
18 9 0.56
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (18 bp):
TATTTAATTAAAAATAAA
Found at i:980785 original size:17 final size:16
Alignment explanation
Indices: 980743--980785 Score: 59
Period size: 17 Copynumber: 2.6 Consensus size: 16
980733 ATCTGACCCG
*
980743 AAAATATTATTTAATA
1 AAAATAATATTTAATA
980759 AAAATAAATATTTAATTA
1 AAAAT-AATATTTAA-TA
980777 AAAATAATA
1 AAAATAATA
980786 ATATATAGAG
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
16 5 0.21
17 12 0.50
18 7 0.29
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (16 bp):
AAAATAATATTTAATA
Found at i:982919 original size:10 final size:9
Alignment explanation
Indices: 982903--982933 Score: 55
Period size: 9 Copynumber: 3.6 Consensus size: 9
982893 ACACTTTAAA
982903 TAAAAAAAT
1 TAAAAAAAT
982912 TAAAAAAAT
1 TAAAAAAAT
982921 TAAAAAAA-
1 TAAAAAAAT
982929 TAAAA
1 TAAAA
982934 CTATAATGAC
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
8 5 0.23
9 17 0.77
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (9 bp):
TAAAAAAAT
Found at i:982925 original size:17 final size:17
Alignment explanation
Indices: 982900--982933 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
982890 ACTACACTTT
*
982900 AAATAAAAAAATTAAAA
1 AAATAAAAAAAATAAAA
*
982917 AAATTAAAAAAATAAAA
1 AAATAAAAAAAATAAAA
982934 CTATAATGAC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (17 bp):
AAATAAAAAAAATAAAA
Found at i:984348 original size:25 final size:26
Alignment explanation
Indices: 984315--984375 Score: 88
Period size: 25 Copynumber: 2.4 Consensus size: 26
984305 ATAGTTTTAT
984315 TTTTTTAAATTTTATTTAAAATG-CA
1 TTTTTTAAATTTTATTTAAAATGTCA
* * *
984340 TTTTTTAAAATTTATTTAAAGTGTCC
1 TTTTTTAAATTTTATTTAAAATGTCA
984366 TTTTTTAAAT
1 TTTTTTAAAT
984376 ATGTTTTCCA
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
25 21 0.68
26 10 0.32
ACGTcount: A:0.33, C:0.05, G:0.05, T:0.57
Consensus pattern (26 bp):
TTTTTTAAATTTTATTTAAAATGTCA
Found at i:987386 original size:2 final size:2
Alignment explanation
Indices: 987379--987426 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
987369 ACAGAAAATA
987379 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
987421 AT AT AT
1 AT AT AT
987427 TAAAACTATT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:990688 original size:60 final size:60
Alignment explanation
Indices: 990624--990798 Score: 178
Period size: 60 Copynumber: 2.9 Consensus size: 60
990614 AAACTATAAT
* * *
990624 TCTCATTTTAAATTGATCCTTAAACTTTTAAATATTATAATTTCATCCCCAAATTATG-CC
1 TCTCATTTTAAATTGATCCTTAAACTTTTGAATATT-TAATTTAATCCCTAAATTATGTCC
* * * * *
990684 TCTCATTCTCAATTGATCCTTAAACTTTTGAACATTTTAATTAAATCCCTAAACTATGTCC
1 TCTCATTTTAAATTGATCCTTAAACTTTTGAATA-TTTAATTTAATCCCTAAATTATGTCC
** *
990745 T-TC-TTTCTAAATT-AGTCCCCAAACTTTTGAATATTTCAATTTTATCCCTAAATT
1 TCTCATTT-TAAATTGA-TCCTTAAACTTTTGAATATTT-AATTTAATCCCTAAATT
990799 CATCCAAGTA
Statistics
Matches: 94, Mismatches: 16, Indels: 10
0.78 0.13 0.08
Matches are distributed among these distances:
59 6 0.06
60 83 0.88
61 5 0.05
ACGTcount: A:0.31, C:0.21, G:0.04, T:0.43
Consensus pattern (60 bp):
TCTCATTTTAAATTGATCCTTAAACTTTTGAATATTTAATTTAATCCCTAAATTATGTCC
Found at i:993445 original size:31 final size:31
Alignment explanation
Indices: 993410--993481 Score: 126
Period size: 31 Copynumber: 2.3 Consensus size: 31
993400 AAACTATACA
993410 TTTAGTACCTGAACTATCAACTTTGATCCAT
1 TTTAGTACCTGAACTATCAACTTTGATCCAT
**
993441 TTTAGTACCTGAACTATCAGTTTTGATCCAT
1 TTTAGTACCTGAACTATCAACTTTGATCCAT
993472 TTTAGTACCT
1 TTTAGTACCT
993482 AAATTTTCAA
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
31 39 1.00
ACGTcount: A:0.26, C:0.21, G:0.11, T:0.42
Consensus pattern (31 bp):
TTTAGTACCTGAACTATCAACTTTGATCCAT
Found at i:994064 original size:21 final size:21
Alignment explanation
Indices: 994038--994081 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
994028 ATGAAATTTA
**
994038 AAAATTAGAATTTTAAAGTTT
1 AAAATTAGAATACTAAAGTTT
*
994059 AAAATTAGAGTACTAAAGTTT
1 AAAATTAGAATACTAAAGTTT
994080 AA
1 AA
994082 TGTTAAAATT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.50, C:0.02, G:0.11, T:0.36
Consensus pattern (21 bp):
AAAATTAGAATACTAAAGTTT
Found at i:995288 original size:60 final size:58
Alignment explanation
Indices: 995221--995372 Score: 178
Period size: 60 Copynumber: 2.5 Consensus size: 58
995211 TTAAATTGAC
**
995221 CCCTAAACTTTTGAATGTTTCAATTTCATCCTCAAACTATGACTCGCATTCTAAATTAGT
1 CCCTAAACTTTTGAAT-TTTCAATTTCATCC-CAAACTACAACTCGCATTCTAAATTAGT
* ** * *
995281 CCTTAAACTTTTGAACATTCTAATTTCATCCCTAAACTACAACTCTCTTTCTAAATTAGT
1 CCCTAAACTTTTGAATTTTC-AATTTCATCCC-AAACTACAACTCGCATTCTAAATTAGT
* *
995341 CCCCAAACTTTTGAATTTCCCAATTTCATCCC
1 CCCTAAACTTTTGAATTT-TCAATTTCATCCC
995373 CAAATTCATC
Statistics
Matches: 77, Mismatches: 12, Indels: 6
0.81 0.13 0.06
Matches are distributed among these distances:
59 4 0.05
60 72 0.94
61 1 0.01
ACGTcount: A:0.30, C:0.27, G:0.05, T:0.38
Consensus pattern (58 bp):
CCCTAAACTTTTGAATTTTCAATTTCATCCCAAACTACAACTCGCATTCTAAATTAGT
Found at i:995668 original size:60 final size:60
Alignment explanation
Indices: 995542--995673 Score: 133
Period size: 60 Copynumber: 2.2 Consensus size: 60
995532 TTAGAATAAA
* * * * * * *
995542 AGTCATAGTTTGAGGATGAAATTGAAATGCTCAAAATTTTGAGGATTATTTTACAATCATG
1 AGTCATAGTTT-AGGATGAAATTGAAATACTCAAAAGTCTAAGGATCAATTTAAAATCATG
* * *
995603 A-TCATAGTTTATGGATGAAATTGAAATATTTAAAAGTCTAAGGATCAATTTAAAATGA-G
1 AGTCATAGTTTA-GGATGAAATTGAAATACTCAAAAGTCTAAGGATCAATTTAAAATCATG
*
995662 AGTCATATTTTA
1 AGTCATAGTTTA
995674 AGACATGATG
Statistics
Matches: 58, Mismatches: 11, Indels: 5
0.78 0.15 0.07
Matches are distributed among these distances:
59 3 0.05
60 54 0.93
61 1 0.02
ACGTcount: A:0.39, C:0.07, G:0.17, T:0.36
Consensus pattern (60 bp):
AGTCATAGTTTAGGATGAAATTGAAATACTCAAAAGTCTAAGGATCAATTTAAAATCATG
Found at i:996253 original size:20 final size:20
Alignment explanation
Indices: 996228--996265 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
996218 AATGTTAAAT
996228 AATAAGATAAA-ATAAAATAA
1 AATAAGA-AAACATAAAATAA
996248 AATAAGAAAACATAAAAT
1 AATAAGAAAACATAAAAT
996266 TTTAAATTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 3 0.18
20 14 0.82
ACGTcount: A:0.74, C:0.03, G:0.05, T:0.18
Consensus pattern (20 bp):
AATAAGAAAACATAAAATAA
Found at i:997560 original size:3 final size:3
Alignment explanation
Indices: 997549--997620 Score: 78
Period size: 3 Copynumber: 23.7 Consensus size: 3
997539 TGTTTAAAAA
997549 AAT AA- AAT AAT -AT AAAT AAT AAT -AT AAAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT -AAT AAT AAT AAT -AAT AAT AAT AAT AAT AAT
*
997593 AAAT AAT AAT AAA AAT AAT ATAT AAT AA
1 -AAT AAT AAT AAT AAT AAT A-AT AAT AA
997621 AATTTATATA
Statistics
Matches: 60, Mismatches: 2, Indels: 14
0.79 0.03 0.18
Matches are distributed among these distances:
2 6 0.10
3 44 0.73
4 10 0.17
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:997571 original size:12 final size:12
Alignment explanation
Indices: 997554--997638 Score: 78
Period size: 12 Copynumber: 7.8 Consensus size: 12
997544 AAAAAAATAA
997554 AATAATATAAAT
1 AATAATATAAAT
997566 AATAATATAAAT
1 AATAATATAAAT
997578 AAT-A-AT-AAT
1 AATAATATAAAT
997587 AAT-A-ATAAAT
1 AATAATATAAAT
*
997597 AATAATAAAAAT
1 AATAATATAAAT
997609 AAT-ATAT-AAT
1 AATAATATAAAT
* *
997619 AA-AATTTATAT
1 AATAATATAAAT
*
997630 AATATTATA
1 AATAATATA
997639 TTTTTCAAAA
Statistics
Matches: 61, Mismatches: 6, Indels: 12
0.77 0.08 0.15
Matches are distributed among these distances:
9 9 0.15
10 16 0.26
11 9 0.15
12 27 0.44
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (12 bp):
AATAATATAAAT
Found at i:997594 original size:19 final size:19
Alignment explanation
Indices: 997563--997620 Score: 91
Period size: 19 Copynumber: 3.1 Consensus size: 19
997553 AAATAATATA
997563 AATAATAAT-ATAAATAAT
1 AATAATAATAATAAATAAT
997581 AATAATAATAATAAATAAT
1 AATAATAATAATAAATAAT
* *
997600 AATAAAAATAATATATAAT
1 AATAATAATAATAAATAAT
997619 AA
1 AA
997621 AATTTATATA
Statistics
Matches: 37, Mismatches: 2, Indels: 1
0.93 0.05 0.03
Matches are distributed among these distances:
18 9 0.24
19 28 0.76
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (19 bp):
AATAATAATAATAAATAAT
Found at i:997621 original size:16 final size:15
Alignment explanation
Indices: 997546--997622 Score: 90
Period size: 16 Copynumber: 5.3 Consensus size: 15
997536 ACTTGTTTAA
997546 AAAAATAA-AATAAT
1 AAAAATAATAATAAT
*
997560 ATAAATAATAAT-AT
1 AAAAATAATAATAAT
997574 --AAATAATAATAAT
1 AAAAATAATAATAAT
*
997587 AATAATAAATAATAAT
1 AAAAAT-AATAATAAT
997603 AAAAATAATATATAAT
1 AAAAATAATA-ATAAT
997619 AAAA
1 AAAA
997623 TTTATATAAT
Statistics
Matches: 54, Mismatches: 3, Indels: 10
0.81 0.04 0.15
Matches are distributed among these distances:
12 10 0.19
13 2 0.04
14 9 0.17
15 10 0.19
16 23 0.43
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (15 bp):
AAAAATAATAATAAT
Found at i:997662 original size:17 final size:16
Alignment explanation
Indices: 997636--997672 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 16
997626 ATATAATATT
997636 ATATTTTTCAAAAATA
1 ATATTTTTCAAAAATA
*
997652 ATATGTTTTCAAAAATT
1 ATAT-TTTTCAAAAATA
997669 ATAT
1 ATAT
997673 ATTATATATG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 4 0.21
17 15 0.79
ACGTcount: A:0.46, C:0.05, G:0.03, T:0.46
Consensus pattern (16 bp):
ATATTTTTCAAAAATA
Found at i:997716 original size:42 final size:43
Alignment explanation
Indices: 997619--997714 Score: 119
Period size: 43 Copynumber: 2.3 Consensus size: 43
997609 AATATATAAT
* * *
997619 AAAATTTATATAATATTATATTTTTCAAAAATAATATGTTTTC
1 AAAAATTATATATTATTATATTTTTCAAAAATAATACGTTTTC
997662 AAAAATTATATATTA-TATATGTTTTCAAAAA-AAT-CGTTTT-
1 AAAAATTATATATTATTATAT-TTTTCAAAAATAATACGTTTTC
*
997702 AAAAACTATATAT
1 AAAAATTATATAT
997715 ATGTTTTCAA
Statistics
Matches: 48, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
40 12 0.25
41 5 0.10
42 8 0.17
43 23 0.48
ACGTcount: A:0.47, C:0.05, G:0.03, T:0.45
Consensus pattern (43 bp):
AAAAATTATATATTATTATATTTTTCAAAAATAATACGTTTTC
Found at i:997731 original size:13 final size:13
Alignment explanation
Indices: 997713--997739 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
997703 AAAACTATAT
997713 ATATGTTTTCAAA
1 ATATGTTTTCAAA
997726 ATATGTTTTCAAA
1 ATATGTTTTCAAA
997739 A
1 A
997740 CTATATTATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.07, G:0.07, T:0.44
Consensus pattern (13 bp):
ATATGTTTTCAAA
Found at i:997791 original size:37 final size:37
Alignment explanation
Indices: 997651--997960 Score: 202
Period size: 37 Copynumber: 8.4 Consensus size: 37
997641 TTTCAAAAAT
* *
997651 AATATGTTTTCAAAAATTATATATTATATATGTTTTCAAA
1 AATATGTTTTC-AAAACTATATA-TATATACGTTTT-AAA
* * *
997691 AAAATCGTTTTAAAAAC--TATATATAT--GTTTTCAA
1 AATAT-GTTTTCAAAACTATATATATATACGTTTTAAA
997725 AATATGTTTTCAAAACTATAT-TATATACGTTTTAAA
1 AATATGTTTTCAAAACTATATATATATACGTTTTAAA
*
997761 AATTTGTTTT-AAAACTATATATATTATACGTTTTCAAA
1 AATATGTTTTCAAAACTATATATA-TATACGTTTT-AAA
* * * *
997799 AATGTGTTTTCAAAATTATATA-ATATATGTTTTCGAA
1 AATATGTTTTCAAAACTATATATATATACGTTTT-AAA
** *
997836 AAGGTATTTTCAAAATCT-TAT-TATATA--TTTTCAAA
1 AATATGTTTTCAAAA-CTATATATATATACGTTTT-AAA
* * *
997871 AAT-TGGTTTTTAAAAACTATATAT-TATATGCTTTCAAA
1 AATAT-G-TTTTCAAAACTATATATATATACG-TTTTAAA
* *
997909 AA-ACGTTTTCTAAAAACTATATAT-TATATGTTTTCAAA
1 AATATGTTTTC--AAAACTATATATATATACGTTTT-AAA
*
997947 AAT-TATTTTCAAAA
1 AATATGTTTTCAAAA
997961 ACTACATTAT
Statistics
Matches: 222, Mismatches: 25, Indels: 50
0.75 0.08 0.17
Matches are distributed among these distances:
33 10 0.05
34 12 0.05
35 29 0.13
36 41 0.18
37 53 0.24
38 51 0.23
39 13 0.06
40 8 0.04
41 5 0.02
ACGTcount: A:0.41, C:0.08, G:0.06, T:0.45
Consensus pattern (37 bp):
AATATGTTTTCAAAACTATATATATATACGTTTTAAA
Found at i:997961 original size:37 final size:37
Alignment explanation
Indices: 997631--997964 Score: 230
Period size: 38 Copynumber: 9.0 Consensus size: 37
997621 AATTTATATA
*
997631 ATATTATAT-TTTTCAAAAATAATATGTTTTCAAAAATTAT
1 ATATTATATGTTTTCAAAAAT--TA--TTTTCAAAAACTAT
* *
997671 ATATTATATATGTTTTCAAAAA-AATCGTTTTAAAAAC--T
1 ATA-T-TATATGTTTTCAAAAATTAT--TTTCAAAAACTAT
*
997709 ATA-TATATGTTTTC-AAAATATGTTTTC-AAAACTAT
1 ATATTATATGTTTTCAAAAAT-TATTTTCAAAAACTAT
* *
997744 AT-TATATACGTTTT-AAAAATT-TGTTT-TAAAACTATAT
1 ATAT-TATATGTTTTCAAAAATTAT-TTTCAAAAAC--TAT
* * *
997781 ATATTATACGTTTTCAAAAATGTGTTTTC-AAAATTAT
1 ATATTATATGTTTTCAAAAAT-TATTTTCAAAAACTAT
* ** *
997818 ATAATATATGTTTTCGAAAAGGTATTTTC-AAAA-TCT
1 ATATTATATGTTTTC-AAAAATTATTTTCAAAAACTAT
* * *
997854 -TATTATATATTTTCAAAAATTGGTTTTTAAAAACTAT
1 ATATTATATGTTTTCAAAAATT-ATTTTCAAAAACTAT
* ***
997891 ATATTATATGCTTTCAAAAAACGTTTTCTAAAAACTAT
1 ATATTATATGTTTTCAAAAATTATTTTC-AAAAACTAT
997929 ATATTATATGTTTTCAAAAATTATTTTCAAAAACTA
1 ATATTATATGTTTTCAAAAATTATTTTCAAAAACTA
997965 CATTATATTA
Statistics
Matches: 237, Mismatches: 30, Indels: 57
0.73 0.09 0.18
Matches are distributed among these distances:
33 5 0.02
34 13 0.05
35 39 0.16
36 21 0.09
37 56 0.24
38 66 0.28
39 8 0.03
40 13 0.05
41 1 0.00
42 5 0.02
43 10 0.04
ACGTcount: A:0.42, C:0.08, G:0.06, T:0.45
Consensus pattern (37 bp):
ATATTATATGTTTTCAAAAATTATTTTCAAAAACTAT
Found at i:999075 original size:201 final size:201
Alignment explanation
Indices: 998719--999083 Score: 453
Period size: 201 Copynumber: 1.8 Consensus size: 201
998709 AAATCGTAGT
* * * * *
998719 CAACCTTGGTCTTCTTCTTGGCTTACAGACCTCGGTTTGAAATTCAACCAAAAACTAGTTCATCG
1 CAACCTAGGTCTTCTTCTTGGCTTAAAGACCTCGATTTAAAATTCAACCAAAAACTAGTTAATCG
* * * *
998784 CTGCTACTATACGGTTGATACACCATCGAATTGAATGGATTCGAACTCGAAAATATTTGTTGACA
66 CTGCTACTATACGGTTGATACACCATCGAACTGAATAGAATCAAACTCGAAAATATTTGTTGACA
* ** *
998849 TACAACTTTTCTTGACTTAAGCTATGTTGTAAATTAGACTGGGAGATAGTTTCTTGTTGCTAAAT
131 GACAACCATTCTTGACTTAAGCTATGCTGTAAATTAGACTGGGAGATAGTTTCTTGTTGCTAAAT
998914 CGCAAC
196 CGCAAC
* * * * *
998920 CAACCTAGGTCTTCTTTTTGGCTTAAAGACCTCTATTTAAAATTCGACCGAAAAGTAGTTAATCG
1 CAACCTAGGTCTTCTTCTTGGCTTAAAGACCTCGATTTAAAATTCAACCAAAAACTAGTTAATCG
* * * * * * *
998985 CTGCTACTATGCGGTTGATACGCCCTTGAGCTGAATAGAATCAAATTCGAAAGT-TTTCGTTGAC
66 CTGCTACTATACGGTTGATACACCATCGAACTGAATAGAATCAAACTCGAAAATATTT-GTTGAC
* * * *
999049 AGATATCCATTCTTGCCTTGAGCTATGCTGTAAAT
130 AGACAACCATTCTTGACTTAAGCTATGCTGTAAAT
999084 GGTTCCTCTA
Statistics
Matches: 134, Mismatches: 29, Indels: 2
0.81 0.18 0.01
Matches are distributed among these distances:
200 3 0.02
201 131 0.98
ACGTcount: A:0.28, C:0.20, G:0.18, T:0.34
Consensus pattern (201 bp):
CAACCTAGGTCTTCTTCTTGGCTTAAAGACCTCGATTTAAAATTCAACCAAAAACTAGTTAATCG
CTGCTACTATACGGTTGATACACCATCGAACTGAATAGAATCAAACTCGAAAATATTTGTTGACA
GACAACCATTCTTGACTTAAGCTATGCTGTAAATTAGACTGGGAGATAGTTTCTTGTTGCTAAAT
CGCAAC
Found at i:999507 original size:22 final size:22
Alignment explanation
Indices: 999479--999521 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
999469 CTGAATTCGT
999479 TCTGAATTGA-CTCTCGAACCCA
1 TCTGAATT-ATCTCTCGAACCCA
999501 TCTGAATTATCTCTCGAACCC
1 TCTGAATTATCTCTCGAACCC
999522 GATTTGAAGT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 1 0.05
22 19 0.95
ACGTcount: A:0.26, C:0.33, G:0.12, T:0.30
Consensus pattern (22 bp):
TCTGAATTATCTCTCGAACCCA
Found at i:1003512 original size:23 final size:23
Alignment explanation
Indices: 1003478--1003538 Score: 86
Period size: 23 Copynumber: 2.7 Consensus size: 23
1003468 CTCATATAAT
1003478 TGCACCGAAGTGCCACGTAGAAA
1 TGCACCGAAGTGCCACGTAGAAA
* * *
1003501 TGCACCGTAGTGCCACGTAGGAT
1 TGCACCGAAGTGCCACGTAGAAA
*
1003524 TGTACCGAAGTGCCA
1 TGCACCGAAGTGCCA
1003539 TATAAAATGT
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.28, C:0.26, G:0.28, T:0.18
Consensus pattern (23 bp):
TGCACCGAAGTGCCACGTAGAAA
Found at i:1005086 original size:21 final size:21
Alignment explanation
Indices: 1005060--1005104 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
1005050 GATTTCTGGG
* *
1005060 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
1005081 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
1005102 CAA
1 CAA
1005105 ACGAACAAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:1005572 original size:20 final size:22
Alignment explanation
Indices: 1005532--1005588 Score: 66
Period size: 20 Copynumber: 2.7 Consensus size: 22
1005522 TGAATGTGTG
*
1005532 ATATGTTATGATGATATAAACC
1 ATATGATATGATGATATAAACC
*
1005554 ATATGATATGAT-A-ATAAACT
1 ATATGATATGATGATATAAACC
1005574 ATATGAATAT-ATGAT
1 ATATG-ATATGATGAT
1005589 TATGAATAGG
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
20 13 0.43
21 6 0.20
22 11 0.37
ACGTcount: A:0.46, C:0.05, G:0.12, T:0.37
Consensus pattern (22 bp):
ATATGATATGATGATATAAACC
Found at i:1006156 original size:31 final size:31
Alignment explanation
Indices: 1006118--1006304 Score: 340
Period size: 31 Copynumber: 6.0 Consensus size: 31
1006108 AGGGTCGAGG
1006118 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
1006149 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
1006180 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
1006211 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
1006242 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
* *
1006273 GTTTACCTAGGTTCTTCGGAATC-TATGGACT
1 GTTTACCTATGTTCTTCGGGA-CATATGGACT
1006304 G
1 G
1006305 GTCCTTCAGG
Statistics
Matches: 153, Mismatches: 2, Indels: 2
0.97 0.01 0.01
Matches are distributed among these distances:
31 152 0.99
32 1 0.01
ACGTcount: A:0.19, C:0.19, G:0.23, T:0.39
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGGGACATATGGACT
Found at i:1007243 original size:20 final size:22
Alignment explanation
Indices: 1007218--1007275 Score: 75
Period size: 20 Copynumber: 2.6 Consensus size: 22
1007208 TTCCCCTTGA
1007218 AGTGCATCGATGCATTC-T-AC
1 AGTGCATCGATGCATTCTTAAC
*
1007238 AGTGCATCGATGTATTCTTTAAC
1 AGTGCATCGATGCATTC-TTAAC
1007261 ATGTGCATCGATGCA
1 A-GTGCATCGATGCA
1007276 CTACCCATGC
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
20 16 0.50
22 1 0.03
23 3 0.09
24 12 0.38
ACGTcount: A:0.26, C:0.21, G:0.21, T:0.33
Consensus pattern (22 bp):
AGTGCATCGATGCATTCTTAAC
Found at i:1010541 original size:23 final size:23
Alignment explanation
Indices: 1010515--1010575 Score: 61
Period size: 23 Copynumber: 2.7 Consensus size: 23
1010505 CTCGTATAAT
*
1010515 TACACCGAAGTGCCGCGTAGAAA
1 TACACCGAAGTGCCACGTAGAAA
* * *
1010538 TACACTGTAA-TGCCACGTAGGAT
1 TACACCG-AAGTGCCACGTAGAAA
*
1010561 TGCACCGAAGTGCCA
1 TACACCGAAGTGCCA
1010576 TATAAAATGT
Statistics
Matches: 30, Mismatches: 6, Indels: 4
0.75 0.15 0.10
Matches are distributed among these distances:
22 2 0.07
23 26 0.87
24 2 0.07
ACGTcount: A:0.31, C:0.26, G:0.25, T:0.18
Consensus pattern (23 bp):
TACACCGAAGTGCCACGTAGAAA
Found at i:1011743 original size:20 final size:20
Alignment explanation
Indices: 1011715--1011752 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
1011705 TTTCCCTTGA
*
1011715 AGTGCATCGATGCATTCTAC
1 AGTGAATCGATGCATTCTAC
*
1011735 AGTGAATCGATGTATTCT
1 AGTGAATCGATGCATTCT
1011753 TTAACATGTG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.26, C:0.18, G:0.21, T:0.34
Consensus pattern (20 bp):
AGTGAATCGATGCATTCTAC
Found at i:1011852 original size:19 final size:19
Alignment explanation
Indices: 1011828--1011877 Score: 100
Period size: 19 Copynumber: 2.6 Consensus size: 19
1011818 AAGGGGGGTA
1011828 CATCGATGCACTCCTAATG
1 CATCGATGCACTCCTAATG
1011847 CATCGATGCACTCCTAATG
1 CATCGATGCACTCCTAATG
1011866 CATCGATGCACT
1 CATCGATGCACT
1011878 AACTGCATTC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 31 1.00
ACGTcount: A:0.26, C:0.32, G:0.16, T:0.26
Consensus pattern (19 bp):
CATCGATGCACTCCTAATG
Found at i:1011942 original size:83 final size:81
Alignment explanation
Indices: 1011757--1011942 Score: 196
Period size: 84 Copynumber: 2.2 Consensus size: 81
1011747 TATTCTTTAA
* * * *
1011757 CATGTGCATCGATGCACTACTCATGCATCGATACACCAATCACCTTCATTGTTTTCATTTAAAGG
1 CATGTGCATCGATGCACTCCTAATGCATCGATACACCAATCA-CTTCAATGTTTCCATTTAAA-G
1011822 GGGGTACATCGATGCACT
64 GGGGTACATCGATGCACT
* * * * *
1011840 CCTAATGCATCGATGCACTCCTAATGCATCGATGCACTAACTGCA-TTCAATGTTTCCATTTTTA
1 CAT-GTGCATCGATGCACTCCTAATGCATCGATACACCAA-T-CACTTCAATGTTTCCA-TTTAA
*
1011904 A-GGGGTGCATCGATGCACTT
62 AGGGGGTACATCGATGCAC-T
*
1011924 CATGTGCATCGATACACTC
1 CATGTGCATCGATGCACTC
1011943 TGAAAAATTC
Statistics
Matches: 85, Mismatches: 13, Indels: 10
0.79 0.12 0.09
Matches are distributed among these distances:
83 32 0.38
84 45 0.53
85 6 0.07
86 2 0.02
ACGTcount: A:0.26, C:0.26, G:0.18, T:0.31
Consensus pattern (81 bp):
CATGTGCATCGATGCACTCCTAATGCATCGATACACCAATCACTTCAATGTTTCCATTTAAAGGG
GGTACATCGATGCACT
Found at i:1016332 original size:6 final size:6
Alignment explanation
Indices: 1016308--1016345 Score: 58
Period size: 6 Copynumber: 6.3 Consensus size: 6
1016298 AGTTAGTATG
* *
1016308 ATAAAA ATAATA ATCAAA ATAAAA ATAAAA ATAAAA AT
1 ATAAAA ATAAAA ATAAAA ATAAAA ATAAAA ATAAAA AT
1016346 TCCTACCCCA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.76, C:0.03, G:0.00, T:0.21
Consensus pattern (6 bp):
ATAAAA
Found at i:1018680 original size:14 final size:14
Alignment explanation
Indices: 1018663--1018727 Score: 57
Period size: 14 Copynumber: 4.7 Consensus size: 14
1018653 AATTAATTAA
1018663 ATAATAATATAAAT
1 ATAATAATATAAAT
*
1018677 AT-A-AATA-ATAT
1 ATAATAATATAAAT
1018688 ATAATAATATAAAT
1 ATAATAATATAAAT
*
1018702 AATATATAATAAAAACT
1 -ATA-ATAATATAAA-T
1018719 AT-ATAATAT
1 ATAATAATAT
1018728 TATATTTTCA
Statistics
Matches: 41, Mismatches: 4, Indels: 12
0.72 0.07 0.21
Matches are distributed among these distances:
11 5 0.12
12 5 0.12
13 5 0.12
14 11 0.27
15 3 0.07
16 11 0.27
17 1 0.02
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (14 bp):
ATAATAATATAAAT
Found at i:1018691 original size:25 final size:26
Alignment explanation
Indices: 1018663--1018712 Score: 84
Period size: 25 Copynumber: 2.0 Consensus size: 26
1018653 AATTAATTAA
1018663 ATAATAATATAAAT-ATAAATAATAT
1 ATAATAATATAAATAATAAATAATAT
*
1018688 ATAATAATATAAATAATATATAATA
1 ATAATAATATAAATAATAAATAATA
1018713 AAAACTATAT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
25 14 0.61
26 9 0.39
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (26 bp):
ATAATAATATAAATAATAAATAATAT
Found at i:1018698 original size:19 final size:19
Alignment explanation
Indices: 1018643--1018713 Score: 87
Period size: 19 Copynumber: 3.8 Consensus size: 19
1018633 ATGTTTAAAA
*
1018643 AAATAAAAT-TAATTAAT-T
1 AAATAATATATAA-TAATAT
1018661 AAATAATA-AT-ATAAATAT
1 AAATAATATATAAT-AATAT
1018679 AAATAATATATAATAATAT
1 AAATAATATATAATAATAT
1018698 AAATAATATATAATAA
1 AAATAATATATAATAA
1018714 AAACTATATA
Statistics
Matches: 47, Mismatches: 1, Indels: 9
0.82 0.02 0.16
Matches are distributed among these distances:
16 1 0.02
17 4 0.09
18 17 0.36
19 23 0.49
20 2 0.04
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (19 bp):
AAATAATATATAATAATAT
Found at i:1018722 original size:33 final size:37
Alignment explanation
Indices: 1018660--1018731 Score: 98
Period size: 33 Copynumber: 2.1 Consensus size: 37
1018650 ATTAATTAAT
1018660 TAAATAATAATATAAATATAAATAATATATAATAATA
1 TAAATAATAATATAAATATAAATAATATATAATAATA
* *
1018697 TAAATAAT-ATAT-AATA-AAA-ACTATATAATATTA
1 TAAATAATAATATAAATATAAATAATATATAATAATA
1018730 TA
1 TA
1018732 TTTTCAAAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
33 14 0.42
34 3 0.09
35 4 0.12
36 4 0.12
37 8 0.24
ACGTcount: A:0.62, C:0.01, G:0.00, T:0.36
Consensus pattern (37 bp):
TAAATAATAATATAAATATAAATAATATATAATAATA
Found at i:1018743 original size:41 final size:43
Alignment explanation
Indices: 1018698--1018784 Score: 108
Period size: 42 Copynumber: 2.1 Consensus size: 43
1018688 ATAATAATAT
1018698 AAATAATATA-TAATAAAAACTATATAATATTATAT-TTT-CAA
1 AAATAATATATTAATAAAAACTATATAATA-TATATGTTTCCAA
** * *
1018739 AAATAATATATTTTTAAAAATTATATATTATATATGTTTCCAA
1 AAATAATATATTAATAAAAACTATATAATATATATGTTTCCAA
1018782 AAA
1 AAA
1018785 ATCGTTTTAA
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
41 15 0.38
42 18 0.46
43 6 0.15
ACGTcount: A:0.53, C:0.05, G:0.01, T:0.41
Consensus pattern (43 bp):
AAATAATATATTAATAAAAACTATATAATATATATGTTTCCAA
Found at i:1018748 original size:17 final size:17
Alignment explanation
Indices: 1018723--1018767 Score: 63
Period size: 17 Copynumber: 2.6 Consensus size: 17
1018713 AAAACTATAT
*
1018723 AATATTATATTTTCAAA
1 AATAATATATTTTCAAA
*
1018740 AATAATATATTTTTAAA
1 AATAATATATTTTCAAA
*
1018757 AATTATATATT
1 AATAATATATT
1018768 ATATATGTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 25 1.00
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (17 bp):
AATAATATATTTTCAAA
Found at i:1018817 original size:20 final size:21
Alignment explanation
Indices: 1018788--1018828 Score: 66
Period size: 20 Copynumber: 2.0 Consensus size: 21
1018778 CCAAAAAATC
1018788 GTTTTAAAAACTATA-TATAT
1 GTTTTAAAAACTATATTATAT
*
1018808 GTTTTCAAAACTATATTATAT
1 GTTTTAAAAACTATATTATAT
1018829 ATTATATATG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 14 0.74
21 5 0.26
ACGTcount: A:0.41, C:0.07, G:0.05, T:0.46
Consensus pattern (21 bp):
GTTTTAAAAACTATATTATAT
Found at i:1018845 original size:28 final size:29
Alignment explanation
Indices: 1018801--1018870 Score: 89
Period size: 25 Copynumber: 2.6 Consensus size: 29
1018791 TTAAAAACTA
1018801 TATATATGTTTTCAAAACTATATTATATAT
1 TATATATGTTTTCAAAACTATA-TATATAT
1018831 TATATATG-TTT-AAAAC--TATATATAT
1 TATATATGTTTTCAAAACTATATATATAT
1018856 TATA-A-GTTTTCAAAA
1 TATATATGTTTTCAAAA
1018871 ATGTGTTTTC
Statistics
Matches: 38, Mismatches: 0, Indels: 9
0.81 0.00 0.19
Matches are distributed among these distances:
23 1 0.03
24 4 0.11
25 15 0.39
26 2 0.05
28 5 0.13
29 3 0.08
30 8 0.21
ACGTcount: A:0.43, C:0.06, G:0.04, T:0.47
Consensus pattern (29 bp):
TATATATGTTTTCAAAACTATATATATAT
Found at i:1018885 original size:87 final size:90
Alignment explanation
Indices: 1018744--1018907 Score: 221
Period size: 90 Copynumber: 1.8 Consensus size: 90
1018734 TTCAAAAATA
*
1018744 ATATATTTTTAAAAATTATATATTATATATGTTTCCAAAAAATCGTTTTAAAAAC-TAT-ATATA
1 ATATATGTTTAAAAATTATATATTATATATGTTTCCAAAAAATCGTTTTAAAAACATATAATATA
1018807 TGTTTTCAAAACTATATTATATATT
66 TGTTTTCAAAACTATATTATATATT
* * * *
1018832 ATATATGTTTAAAACTATATATATTATA-A-GTTTTC-AAAAATGTGTTTTCAAAACTATATAAT
1 ATATATGTTTAAAAAT-TATATATTATATATGTTTCCAAAAAAT-CGTTTTAAAAAC-ATATAAT
1018894 ATATGTTTTCAAAA
63 ATATGTTTTCAAAA
1018908 ATGTATTTTC
Statistics
Matches: 66, Mismatches: 5, Indels: 8
0.84 0.06 0.10
Matches are distributed among these distances:
86 6 0.09
87 15 0.23
88 15 0.23
89 14 0.21
90 16 0.24
ACGTcount: A:0.43, C:0.07, G:0.05, T:0.45
Consensus pattern (90 bp):
ATATATGTTTAAAAATTATATATTATATATGTTTCCAAAAAATCGTTTTAAAAACATATAATATA
TGTTTTCAAAACTATATTATATATT
Found at i:1018981 original size:38 final size:37
Alignment explanation
Indices: 1018839--1019032 Score: 166
Period size: 37 Copynumber: 5.2 Consensus size: 37
1018829 ATTATATATG
* * *
1018839 TTTAAAACTATATATATTATAAGTTTTCAAAAATGTGT
1 TTTAAAAAT-TATATATTATATGTTTTCAAAAATGTAT
* * *
1018877 TTTCAAAACTATATAATATATGTTTTCAAAAATGTAT
1 TTTAAAAATTATATATTATATGTTTTCAAAAATGTAT
* * *
1018914 TTTCAAAATCATAT-TATATAT-TTTT-AAAAACCG-ATT
1 TTTAAAAATTATATAT-TATATGTTTTCAAAAA-TGTA-T
*
1018950 TTTAAAAATTATATATTATATGCTTTCAAAAAATGT-T
1 TTTAAAAATTATATATTATATGTTTTC-AAAAATGTAT
* * *
1018987 TTCTAAAAAATATATATTATATATTTTC-AAAATTTAT
1 TT-TAAAAATTATATATTATATGTTTTCAAAAATGTAT
1019024 TTTCAAAAA
1 TTT-AAAAA
1019033 CTACATTATA
Statistics
Matches: 127, Mismatches: 18, Indels: 23
0.76 0.11 0.14
Matches are distributed among these distances:
35 6 0.05
36 30 0.24
37 57 0.45
38 29 0.23
39 5 0.04
ACGTcount: A:0.44, C:0.07, G:0.04, T:0.45
Consensus pattern (37 bp):
TTTAAAAATTATATATTATATGTTTTCAAAAATGTAT
Found at i:1020197 original size:34 final size:38
Alignment explanation
Indices: 1020129--1020197 Score: 92
Period size: 34 Copynumber: 1.9 Consensus size: 38
1020119 ATGTACCAGC
**
1020129 TCTGGGATTATTTTTTTCTTCTCTTTTTTTTGATGTTT
1 TCTGGGATTATTTTTTTCTTCTCTTTTTGGTGATGTTT
1020167 TCTGGG-TT-TTTTTTT-TTC-CTTTTTGGTGATG
1 TCTGGGATTATTTTTTTCTTCTCTTTTTGGTGATG
1020198 GAGCAGGCAT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
34 11 0.38
35 3 0.10
36 7 0.24
37 2 0.07
38 6 0.21
ACGTcount: A:0.06, C:0.10, G:0.17, T:0.67
Consensus pattern (38 bp):
TCTGGGATTATTTTTTTCTTCTCTTTTTGGTGATGTTT
Found at i:1028503 original size:19 final size:19
Alignment explanation
Indices: 1028481--1028533 Score: 52
Period size: 19 Copynumber: 2.7 Consensus size: 19
1028471 GTCGACACGT
* *
1028481 TTTTTTATCTTTTGATACG
1 TTTTTAATCTTTTGATAAG
*
1028500 TTTTTAATCTTCTTTATAAG
1 TTTTTAATCTT-TTGATAAG
*
1028520 TTGTTTGATCTTTT
1 TT-TTTAATCTTTT
1028534 ATTTTGTTTA
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
19 10 0.36
20 10 0.36
21 8 0.29
ACGTcount: A:0.17, C:0.09, G:0.09, T:0.64
Consensus pattern (19 bp):
TTTTTAATCTTTTGATAAG
Found at i:1034370 original size:345 final size:345
Alignment explanation
Indices: 1033739--1034432 Score: 1361
Period size: 345 Copynumber: 2.0 Consensus size: 345
1033729 TCGATATGCA
*
1033739 AGTGTTAACACTCACCTTGGAGTTGGTGAGTGAACTGACAGCAATGAATGTTCATTTGTGTTTTA
1 AGTGTTAACACTCACCTTGGAGTTGGTGAGTGAACTGACAGCAACGAATGTTCATTTGTGTTTTA
1033804 CTTTCAGCAACACCCCTTGCCATTGATTTTTTTTGGCTTAATATGTGATCCAACTATGCTCCATG
66 CTTTCAGCAACACCCCTTGCCATTGATTTTTTTTGGCTTAATATGTGATCCAACTATGCTCCATG
1033869 GAACTTGCAGAGCAAAGCAGGAGAGATGATCTGGAATCTCTTGGTTACGTGCTTATGTACTTCCT
131 GAACTTGCAGAGCAAAGCAGGAGAGATGATCTGGAATCTCTTGGTTACGTGCTTATGTACTTCCT
1033934 GCGGGGAAGGTTGGTTGAACCATTTACTTTGTTGCCTACTTCACAACCCGGTTTAAATGTTGAGT
196 GCGGGGAAGGTTGGTTGAACCATTTACTTTGTTGCCTACTTCACAACCCGGTTTAAATGTTGAGT
*
1033999 CACATTATTAACTTTCTTGTTCCCTGTCAGCCTTCCATGGCAGGGCCTGAAAGCTGGCACCAAAA
261 CACATTATTAACTTTCTTGTTCCCTGTCAGCCTTCCATGGCAGGGCCTGAAAGCCGGCACCAAAA
1034064 AGCAGAAGTATGACAAGATT
326 AGCAGAAGTATGACAAGATT
1034084 AGTGTTAACACTCACCTTGGAGTTGGTGAGTGAACTGACAGCAACGAATGTTCATTTGTGTTTTA
1 AGTGTTAACACTCACCTTGGAGTTGGTGAGTGAACTGACAGCAACGAATGTTCATTTGTGTTTTA
1034149 CTTTCAGCAACACCCCTTGCCATTGATTTTTTTTGGCTTAATATGTGATCCAACTATGCTCCATG
66 CTTTCAGCAACACCCCTTGCCATTGATTTTTTTTGGCTTAATATGTGATCCAACTATGCTCCATG
1034214 GAACTTGCAGAGCAAAGCAGGAGAGATGATCTGGAATCTCTTGGTTACGTGCTTATGTACTTCCT
131 GAACTTGCAGAGCAAAGCAGGAGAGATGATCTGGAATCTCTTGGTTACGTGCTTATGTACTTCCT
*
1034279 GCGGGGAAGGTTGGTTGAACCATTTACTTTGTTGCTTACTTCACAACCCGGTTTAAATGTTGAGT
196 GCGGGGAAGGTTGGTTGAACCATTTACTTTGTTGCCTACTTCACAACCCGGTTTAAATGTTGAGT
1034344 CACATTATTAACTTTCTTGTTCCCTGTCAGCCTTCCATGGCAGGGCCTGAAAGCCGGCACCAAAA
261 CACATTATTAACTTTCTTGTTCCCTGTCAGCCTTCCATGGCAGGGCCTGAAAGCCGGCACCAAAA
1034409 AGCAGAAGTATGACAAGATT
326 AGCAGAAGTATGACAAGATT
1034429 AGTG
1 AGTG
1034433 AAAAGAAGAT
Statistics
Matches: 346, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
345 346 1.00
ACGTcount: A:0.25, C:0.21, G:0.22, T:0.32
Consensus pattern (345 bp):
AGTGTTAACACTCACCTTGGAGTTGGTGAGTGAACTGACAGCAACGAATGTTCATTTGTGTTTTA
CTTTCAGCAACACCCCTTGCCATTGATTTTTTTTGGCTTAATATGTGATCCAACTATGCTCCATG
GAACTTGCAGAGCAAAGCAGGAGAGATGATCTGGAATCTCTTGGTTACGTGCTTATGTACTTCCT
GCGGGGAAGGTTGGTTGAACCATTTACTTTGTTGCCTACTTCACAACCCGGTTTAAATGTTGAGT
CACATTATTAACTTTCTTGTTCCCTGTCAGCCTTCCATGGCAGGGCCTGAAAGCCGGCACCAAAA
AGCAGAAGTATGACAAGATT
Found at i:1037470 original size:31 final size:31
Alignment explanation
Indices: 1037432--1037507 Score: 152
Period size: 31 Copynumber: 2.5 Consensus size: 31
1037422 ATTTTAAATT
1037432 AAATAATAATAAAAAATGTCACATCATTAAG
1 AAATAATAATAAAAAATGTCACATCATTAAG
1037463 AAATAATAATAAAAAATGTCACATCATTAAG
1 AAATAATAATAAAAAATGTCACATCATTAAG
1037494 AAATAATAATAAAA
1 AAATAATAATAAAA
1037508 TAGATCAAAG
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 45 1.00
ACGTcount: A:0.62, C:0.08, G:0.05, T:0.25
Consensus pattern (31 bp):
AAATAATAATAAAAAATGTCACATCATTAAG
Found at i:1039307 original size:2 final size:2
Alignment explanation
Indices: 1039291--1039340 Score: 86
Period size: 2 Copynumber: 26.0 Consensus size: 2
1039281 TTGCATTACC
1039291 AT AT AT -T AT AT -T 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
1039331 AT AT AT AT AT
1 AT AT AT AT AT
1039341 TCCATATTTT
Statistics
Matches: 46, Mismatches: 0, Indels: 4
0.92 0.00 0.08
Matches are distributed among these distances:
1 2 0.04
2 44 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:1040251 original size:55 final size:55
Alignment explanation
Indices: 1040185--1040295 Score: 195
Period size: 55 Copynumber: 2.0 Consensus size: 55
1040175 TTGGAAATTG
* * *
1040185 AGAATTTAGTTTTATTTAATTCACGATTCTTTTGATTTCTTTCAATTCTTTTATT
1 AGAATTCAGTTTTATTTAATTAACGATTATTTTGATTTCTTTCAATTCTTTTATT
1040240 AGAATTCAGTTTTATTTAATTAACGATTATTTTGATTTCTTTCAATTCTTTTATT
1 AGAATTCAGTTTTATTTAATTAACGATTATTTTGATTTCTTTCAATTCTTTTATT
1040295 A
1 A
1040296 TTTTATATTC
Statistics
Matches: 53, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
55 53 1.00
ACGTcount: A:0.26, C:0.10, G:0.07, T:0.57
Consensus pattern (55 bp):
AGAATTCAGTTTTATTTAATTAACGATTATTTTGATTTCTTTCAATTCTTTTATT
Found at i:1044947 original size:26 final size:26
Alignment explanation
Indices: 1044918--1044977 Score: 63
Period size: 25 Copynumber: 2.3 Consensus size: 26
1044908 TGATATGAAC
1044918 ATATAATATAAGGTATATGT-TTATA-A
1 ATATAATAT-AGGT-TATGTGTTATATA
* *
1044944 ATATGACATAGGTTATGTGTTATATA
1 ATATAATATAGGTTATGTGTTATATA
1044970 ATA-AATAT
1 ATATAATAT
1044978 GAACATATGA
Statistics
Matches: 28, Mismatches: 4, Indels: 5
0.76 0.11 0.14
Matches are distributed among these distances:
24 5 0.18
25 12 0.43
26 11 0.39
ACGTcount: A:0.43, C:0.02, G:0.13, T:0.42
Consensus pattern (26 bp):
ATATAATATAGGTTATGTGTTATATA
Found at i:1046519 original size:24 final size:23
Alignment explanation
Indices: 1046492--1046566 Score: 84
Period size: 22 Copynumber: 3.3 Consensus size: 23
1046482 TAACACAAAT
1046492 AGAAAAAGAAAAGATATAGTAAAA
1 AGAAAAAGAAAAGA-ATAGTAAAA
*
1046516 AGAAAAAGAAAAAAATA-TAAAA
1 AGAAAAAGAAAAGAATAGTAAAA
* *
1046538 A-AATAGAGAAAAGAA-AGAAAAA
1 AGAA-AAAGAAAAGAATAGTAAAA
1046560 AGAAAAA
1 AGAAAAA
1046567 AAAGCAAAAA
Statistics
Matches: 43, Mismatches: 5, Indels: 8
0.77 0.09 0.14
Matches are distributed among these distances:
21 3 0.07
22 22 0.51
23 5 0.12
24 13 0.30
ACGTcount: A:0.77, C:0.00, G:0.15, T:0.08
Consensus pattern (23 bp):
AGAAAAAGAAAAGAATAGTAAAA
Found at i:1046565 original size:16 final size:17
Alignment explanation
Indices: 1046544--1046585 Score: 61
Period size: 16 Copynumber: 2.6 Consensus size: 17
1046534 AAAAAAATAG
1046544 AGAAAAGAAAG-AAAAA
1 AGAAAAGAAAGCAAAAA
*
1046560 AGAAAAAAAAGCAAAAA
1 AGAAAAGAAAGCAAAAA
1046577 AG-AAAGAAA
1 AGAAAAGAAA
1046586 AAGTGGAAGA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
16 16 0.70
17 7 0.30
ACGTcount: A:0.81, C:0.02, G:0.17, T:0.00
Consensus pattern (17 bp):
AGAAAAGAAAGCAAAAA
Found at i:1046575 original size:17 final size:16
Alignment explanation
Indices: 1046512--1046588 Score: 66
Period size: 17 Copynumber: 4.4 Consensus size: 16
1046502 AAGATATAGT
1046512 AAAAAG-AAAAAGAAAA
1 AAAAAGAAAAAAG-AAA
*
1046528 AAATATAAAAAAATAGAGAA
1 AAA-A-AGAAAAA-AGA-AA
1046548 AAGAAAGAAAAAAGAAA
1 AA-AAAGAAAAAAGAAA
1046565 AAAAAGCAAAAAAGAAA
1 AAAAAG-AAAAAAGAAA
1046582 GAAAAAG
1 -AAAAAG
1046589 TGGAAGAAAA
Statistics
Matches: 51, Mismatches: 2, Indels: 14
0.76 0.03 0.21
Matches are distributed among these distances:
16 7 0.14
17 15 0.29
18 10 0.20
19 11 0.22
20 7 0.14
21 1 0.02
ACGTcount: A:0.81, C:0.01, G:0.14, T:0.04
Consensus pattern (16 bp):
AAAAAGAAAAAAGAAA
Found at i:1046576 original size:37 final size:37
Alignment explanation
Indices: 1046514--1046586 Score: 94
Period size: 37 Copynumber: 2.0 Consensus size: 37
1046504 GATATAGTAA
* * *
1046514 AAAGAAAAAGAAAAAAATATAAAAAAATAGAGAAAAG
1 AAAGAAAAAGAAAAAAATAGAAAAAAAGAAAGAAAAG
*
1046551 AAAGAAAAAAGAAAAAAA-AGCAAAAAAGAAAGAAAA
1 AAAG-AAAAAGAAAAAAATAGAAAAAAAGAAAGAAAA
1046587 AGTGGAAGAA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
37 18 0.58
38 13 0.42
ACGTcount: A:0.81, C:0.01, G:0.14, T:0.04
Consensus pattern (37 bp):
AAAGAAAAAGAAAAAAATAGAAAAAAAGAAAGAAAAG
Found at i:1046582 original size:12 final size:10
Alignment explanation
Indices: 1046546--1046587 Score: 50
Period size: 11 Copynumber: 4.0 Consensus size: 10
1046536 AAAAATAGAG
1046546 AAAAGAAAGAA
1 AAAAGAAA-AA
1046557 AAAAG-AAAA
1 AAAAGAAAAA
1046566 AAAAGCAAAAA
1 AAAAG-AAAAA
1046577 AGAAAGAAAAA
1 A-AAAGAAAAA
1046588 GTGGAAGAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
9 7 0.25
10 2 0.07
11 15 0.54
12 4 0.14
ACGTcount: A:0.83, C:0.02, G:0.14, T:0.00
Consensus pattern (10 bp):
AAAAGAAAAA
Found at i:1046587 original size:28 final size:28
Alignment explanation
Indices: 1046518--1046587 Score: 90
Period size: 28 Copynumber: 2.5 Consensus size: 28
1046508 TAGTAAAAAG
* *
1046518 AAAAAGAAA-AAAATATAAAAAAATAGA
1 AAAAAGAAAGAAAAAAGAAAAAAATAGA
*
1046545 GAAAAGAAAGAAAAAAGAAAAAAA-AGCA
1 AAAAAGAAAGAAAAAAGAAAAAAATAG-A
1046573 AAAAAGAAAGAAAAA
1 AAAAAGAAAGAAAAA
1046588 GTGGAAGAAA
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
27 10 0.27
28 27 0.73
ACGTcount: A:0.81, C:0.01, G:0.13, T:0.04
Consensus pattern (28 bp):
AAAAAGAAAGAAAAAAGAAAAAAATAGA
Found at i:1046588 original size:38 final size:37
Alignment explanation
Indices: 1046514--1046588 Score: 91
Period size: 38 Copynumber: 2.0 Consensus size: 37
1046504 GATATAGTAA
* *
1046514 AAAGAAAAAGAAAAAAATATAAAAAAATAGAGAAAAG
1 AAAGAAAAAGAAAAAAATACAAAAAAAAAGAGAAAAG
1046551 AAAGAAAAAAGAAAAAAA-AGCAAAAAAGAAAGA-AAAAG
1 AAAG-AAAAAGAAAAAAATA-CAAAAAA-AAAGAGAAAAG
1046589 TGGAAGAAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
37 5 0.15
38 24 0.73
39 4 0.12
ACGTcount: A:0.80, C:0.01, G:0.15, T:0.04
Consensus pattern (37 bp):
AAAGAAAAAGAAAAAAATACAAAAAAAAAGAGAAAAG
Found at i:1047391 original size:28 final size:28
Alignment explanation
Indices: 1047318--1047392 Score: 107
Period size: 28 Copynumber: 2.7 Consensus size: 28
1047308 AGCCAATCTA
*
1047318 AAACACATTACCTCCCCAAATTAACCTG
1 AAACACATTACCTTCCCAAATTAACCTG
* *
1047346 AAAGACAATA-CTTCCCCAAATTAACCTG
1 AAACACATTACCTT-CCCAAATTAACCTG
1047374 AAACACATTACCTTCCCAA
1 AAACACATTACCTTCCCAA
1047393 GGCATCATAA
Statistics
Matches: 40, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
27 2 0.05
28 35 0.88
29 3 0.08
ACGTcount: A:0.41, C:0.33, G:0.04, T:0.21
Consensus pattern (28 bp):
AAACACATTACCTTCCCAAATTAACCTG
Found at i:1047920 original size:18 final size:18
Alignment explanation
Indices: 1047897--1047996 Score: 96
Period size: 18 Copynumber: 5.6 Consensus size: 18
1047887 TACATATATA
1047897 ATCATTATCAACATCAAT
1 ATCATTATCAACATCAAT
**
1047915 ATCATTATC-ACGATCTTT
1 ATCATTATCAAC-ATCAAT
* *
1047933 ATCATTCTCAACATAAAT
1 ATCATTATCAACATCAAT
**
1047951 ATCATTATC-ACGATCTCT
1 ATCATTATCAAC-ATCAAT
*
1047969 ATAATTATCAACATCAAT
1 ATCATTATCAACATCAAT
*
1047987 ATAATTATCA
1 ATCATTATCA
1047997 TGAGCCCATT
Statistics
Matches: 65, Mismatches: 13, Indels: 8
0.76 0.15 0.09
Matches are distributed among these distances:
17 4 0.06
18 57 0.88
19 4 0.06
ACGTcount: A:0.40, C:0.21, G:0.02, T:0.37
Consensus pattern (18 bp):
ATCATTATCAACATCAAT
Found at i:1047937 original size:36 final size:36
Alignment explanation
Indices: 1047897--1047996 Score: 155
Period size: 36 Copynumber: 2.8 Consensus size: 36
1047887 TACATATATA
*
1047897 ATCATTATCAACATCAATATCATTATCACGATCTTT
1 ATCATTATCAACATCAATATCATTATCACGATCTCT
* *
1047933 ATCATTCTCAACATAAATATCATTATCACGATCTCT
1 ATCATTATCAACATCAATATCATTATCACGATCTCT
* *
1047969 ATAATTATCAACATCAATATAATTATCA
1 ATCATTATCAACATCAATATCATTATCA
1047997 TGAGCCCATT
Statistics
Matches: 57, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
36 57 1.00
ACGTcount: A:0.40, C:0.21, G:0.02, T:0.37
Consensus pattern (36 bp):
ATCATTATCAACATCAATATCATTATCACGATCTCT
Found at i:1048333 original size:20 final size:20
Alignment explanation
Indices: 1048308--1048355 Score: 87
Period size: 20 Copynumber: 2.4 Consensus size: 20
1048298 CCACAACTCG
1048308 TATAAATTCCCGCTAAGGCA
1 TATAAATTCCCGCTAAGGCA
*
1048328 TATAAATTCTCGCTAAGGCA
1 TATAAATTCCCGCTAAGGCA
1048348 TATAAATT
1 TATAAATT
1048356 ATCCCGAAGG
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.38, C:0.19, G:0.12, T:0.31
Consensus pattern (20 bp):
TATAAATTCCCGCTAAGGCA
Found at i:1048365 original size:20 final size:20
Alignment explanation
Indices: 1048322--1048365 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
1048312 AATTCCCGCT
* * *
1048322 AAGGCATATAAATTCTCGCT
1 AAGGCATATAAATTATCCCG
1048342 AAGGCATATAAATTATCCCG
1 AAGGCATATAAATTATCCCG
1048362 AAGG
1 AAGG
1048366 ATCTCGTATA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.39, C:0.18, G:0.18, T:0.25
Consensus pattern (20 bp):
AAGGCATATAAATTATCCCG
Found at i:1048778 original size:26 final size:26
Alignment explanation
Indices: 1048740--1048790 Score: 75
Period size: 26 Copynumber: 2.0 Consensus size: 26
1048730 TATGTTCACA
* *
1048740 TCAATCATGTCACATAAAATAACATG
1 TCAAACATATCACATAAAATAACATG
*
1048766 TCAAACATATCACATATAATAACAT
1 TCAAACATATCACATAAAATAACAT
1048791 ATGACACATA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.49, C:0.20, G:0.04, T:0.27
Consensus pattern (26 bp):
TCAAACATATCACATAAAATAACATG
Found at i:1048799 original size:26 final size:26
Alignment explanation
Indices: 1048739--1048801 Score: 72
Period size: 26 Copynumber: 2.4 Consensus size: 26
1048729 ATATGTTCAC
* *
1048739 ATCAATCATGTCACATAAAATAACAT
1 ATCAAACATATCACATAAAATAACAT
* *
1048765 GTCAAACATATCACATATAATAACAT
1 ATCAAACATATCACATAAAATAACAT
* *
1048791 ATGACACATAT
1 ATCAAACATAT
1048802 ACCCATTTTC
Statistics
Matches: 30, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
26 30 1.00
ACGTcount: A:0.49, C:0.19, G:0.05, T:0.27
Consensus pattern (26 bp):
ATCAAACATATCACATAAAATAACAT
Found at i:1050645 original size:30 final size:31
Alignment explanation
Indices: 1050611--1050669 Score: 93
Period size: 30 Copynumber: 1.9 Consensus size: 31
1050601 TTTTTAAAGT
* *
1050611 TTATACTTTGGTCACTAAACTTTC-AAAATC
1 TTATAATTTGATCACTAAACTTTCGAAAATC
1050641 TTATAATTTGATCACTAAACTTTCGAAAA
1 TTATAATTTGATCACTAAACTTTCGAAAA
1050670 AAGCCATTTA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
30 22 0.85
31 4 0.15
ACGTcount: A:0.37, C:0.17, G:0.07, T:0.39
Consensus pattern (31 bp):
TTATAATTTGATCACTAAACTTTCGAAAATC
Found at i:1051473 original size:9 final size:9
Alignment explanation
Indices: 1051459--1051539 Score: 67
Period size: 9 Copynumber: 8.9 Consensus size: 9
1051449 GCATCTCTCA
1051459 TCTTTTTTT
1 TCTTTTTTT
1051468 TCTTTTCTTT
1 TCTTTT-TTT
* *
1051478 TCATTTTTC
1 TCTTTTTTT
*
1051487 TGTTTTTTCAT
1 TCTTTTTT--T
1051498 T-TTTTTTT
1 TCTTTTTTT
*
1051506 TCATTTTTT
1 TCTTTTTTT
*
1051515 TCATTTTTT
1 TCTTTTTTT
*
1051524 TC-TTTCTT
1 TCTTTTTTT
1051532 TCTTTTTT
1 TCTTTTTT
1051540 AGTTTTTATG
Statistics
Matches: 59, Mismatches: 8, Indels: 10
0.77 0.10 0.13
Matches are distributed among these distances:
8 9 0.15
9 35 0.59
10 14 0.24
11 1 0.02
ACGTcount: A:0.05, C:0.14, G:0.01, T:0.80
Consensus pattern (9 bp):
TCTTTTTTT
Found at i:1051485 original size:21 final size:20
Alignment explanation
Indices: 1051456--1051538 Score: 66
Period size: 21 Copynumber: 4.0 Consensus size: 20
1051446 TAAGCATCTC
1051456 TCATCTTTTTTTTCTTTTCTTT
1 TCAT-TTTTTTTTCTTTT-TTT
*
1051478 TCA----TTTTTCTGTTTTT
1 TCATTTTTTTTTCTTTTTTT
*
1051494 TCATTTTTTTTTTCATTTTTT
1 TCA-TTTTTTTTTCTTTTTTT
1051515 TCATTTTTTTCTTTCTTTCTTTT
1 TCA-TTTTTT-TTTCTTT-TTTT
1051538 T
1 T
1051539 TAGTTTTTAT
Statistics
Matches: 50, Mismatches: 4, Indels: 13
0.75 0.06 0.19
Matches are distributed among these distances:
16 6 0.12
17 9 0.18
21 21 0.42
22 9 0.18
23 5 0.10
ACGTcount: A:0.06, C:0.14, G:0.01, T:0.78
Consensus pattern (20 bp):
TCATTTTTTTTTCTTTTTTT
Found at i:1051492 original size:28 final size:28
Alignment explanation
Indices: 1051459--1051532 Score: 82
Period size: 28 Copynumber: 2.7 Consensus size: 28
1051449 GCATCTCTCA
1051459 TCTTTTTTTTCTTTTCTTTTCATTTTTC
1 TCTTTTTTTTCTTTTCTTTTCATTTTTC
* *
1051487 TGTTTTTTCATT-TTTT-TTTTCATTTTTT
1 TCTTTTTT--TTCTTTTCTTTTCATTTTTC
*
1051515 TCATTTTTTTC-TTTCTTT
1 TCTTTTTTTTCTTTTCTTT
1051533 CTTTTTTAGT
Statistics
Matches: 38, Mismatches: 4, Indels: 9
0.75 0.08 0.18
Matches are distributed among these distances:
26 5 0.13
27 3 0.08
28 24 0.63
29 4 0.11
30 2 0.05
ACGTcount: A:0.05, C:0.14, G:0.01, T:0.80
Consensus pattern (28 bp):
TCTTTTTTTTCTTTTCTTTTCATTTTTC
Found at i:1051494 original size:16 final size:17
Alignment explanation
Indices: 1051464--1051501 Score: 60
Period size: 16 Copynumber: 2.3 Consensus size: 17
1051454 TCTCATCTTT
*
1051464 TTTTTCTTTTCTTTTCA
1 TTTTTCTGTTCTTTTCA
1051481 TTTTTCTGTT-TTTTCA
1 TTTTTCTGTTCTTTTCA
1051497 TTTTT
1 TTTTT
1051502 TTTTTCATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
16 11 0.55
17 9 0.45
ACGTcount: A:0.05, C:0.13, G:0.03, T:0.79
Consensus pattern (17 bp):
TTTTTCTGTTCTTTTCA
Found at i:1051523 original size:38 final size:38
Alignment explanation
Indices: 1051456--1051539 Score: 102
Period size: 38 Copynumber: 2.2 Consensus size: 38
1051446 TAAGCATCTC
* * *
1051456 TCATCTTTTTTTTCTTTTCTTTTCA-TTTTTCTGTTTTT
1 TCATTTTTTTTTTCATTTCTTTTCATTTTTTCT-TTCTT
1051494 TCATTTTTTTTTTCATTT-TTTTCATTTTTTTCTTTCTT
1 TCATTTTTTTTTTCATTTCTTTTCA-TTTTTTCTTTCTT
1051532 TC-TTTTTT
1 TCATTTTTT
1051540 AGTTTTTATG
Statistics
Matches: 41, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
37 12 0.29
38 22 0.54
39 7 0.17
ACGTcount: A:0.06, C:0.14, G:0.01, T:0.79
Consensus pattern (38 bp):
TCATTTTTTTTTTCATTTCTTTTCATTTTTTCTTTCTT
Found at i:1054049 original size:36 final size:36
Alignment explanation
Indices: 1054002--1054104 Score: 170
Period size: 36 Copynumber: 2.9 Consensus size: 36
1053992 CACATATGCC
* *
1054002 ATCATTATCAACATCAATATCGTTATCGTGATCTCT
1 ATCATTATCAACATCAATATCATTATCATGATCTCT
* *
1054038 ATCATTCTCAACATCAATATCATTATCATGATCTTT
1 ATCATTATCAACATCAATATCATTATCATGATCTCT
1054074 ATCATTATCAACATCAATATCATTATCATGA
1 ATCATTATCAACATCAATATCATTATCATGA
1054105 ACCCATTTAA
Statistics
Matches: 62, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
36 62 1.00
ACGTcount: A:0.35, C:0.21, G:0.05, T:0.39
Consensus pattern (36 bp):
ATCATTATCAACATCAATATCATTATCATGATCTCT
Found at i:1054058 original size:18 final size:18
Alignment explanation
Indices: 1054002--1054101 Score: 101
Period size: 18 Copynumber: 5.6 Consensus size: 18
1053992 CACATATGCC
1054002 ATCATTATCAACATCAAT
1 ATCATTATCAACATCAAT
* *** **
1054020 ATCGTTATCGTGATCTCT
1 ATCATTATCAACATCAAT
*
1054038 ATCATTCTCAACATCAAT
1 ATCATTATCAACATCAAT
** **
1054056 ATCATTATCATGATCTTT
1 ATCATTATCAACATCAAT
1054074 ATCATTATCAACATCAAT
1 ATCATTATCAACATCAAT
1054092 ATCATTATCA
1 ATCATTATCA
1054102 TGAACCCATT
Statistics
Matches: 60, Mismatches: 22, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
18 60 1.00
ACGTcount: A:0.35, C:0.22, G:0.04, T:0.39
Consensus pattern (18 bp):
ATCATTATCAACATCAAT
Found at i:1054102 original size:6 final size:6
Alignment explanation
Indices: 1054050--1054102 Score: 52
Period size: 6 Copynumber: 8.8 Consensus size: 6
1054040 CATTCTCAAC
* * * ** *
1054050 ATCAAT ATCATT ATCATG ATCTTT ATCATT ATCAAC ATCAAT ATCATT
1 ATCATT ATCATT ATCATT ATCATT ATCATT ATCATT ATCATT ATCATT
1054098 ATCAT
1 ATCAT
1054103 GAACCCATTT
Statistics
Matches: 38, Mismatches: 9, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
6 38 1.00
ACGTcount: A:0.38, C:0.19, G:0.02, T:0.42
Consensus pattern (6 bp):
ATCATT
Found at i:1054438 original size:20 final size:20
Alignment explanation
Indices: 1054413--1054460 Score: 87
Period size: 20 Copynumber: 2.4 Consensus size: 20
1054403 CGACAGCTCG
*
1054413 TATAAATTCCCGCTAAGGCA
1 TATAAATTCCCACTAAGGCA
1054433 TATAAATTCCCACTAAGGCA
1 TATAAATTCCCACTAAGGCA
1054453 TATAAATT
1 TATAAATT
1054461 ATTCCGAAGG
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.40, C:0.21, G:0.10, T:0.29
Consensus pattern (20 bp):
TATAAATTCCCACTAAGGCA
Found at i:1054886 original size:26 final size:26
Alignment explanation
Indices: 1054848--1054898 Score: 75
Period size: 26 Copynumber: 2.0 Consensus size: 26
1054838 TATGTTCACA
* *
1054848 TCAATCATGTCACATAAAATAACATG
1 TCAAACATATCACATAAAATAACATG
*
1054874 TCAAACATATCACATATAATAACAT
1 TCAAACATATCACATAAAATAACAT
1054899 ATGACACATA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.49, C:0.20, G:0.04, T:0.27
Consensus pattern (26 bp):
TCAAACATATCACATAAAATAACATG
Found at i:1054907 original size:26 final size:26
Alignment explanation
Indices: 1054847--1054909 Score: 72
Period size: 26 Copynumber: 2.4 Consensus size: 26
1054837 ATATGTTCAC
* *
1054847 ATCAATCATGTCACATAAAATAACAT
1 ATCAAACATATCACATAAAATAACAT
* *
1054873 GTCAAACATATCACATATAATAACAT
1 ATCAAACATATCACATAAAATAACAT
* *
1054899 ATGACACATAT
1 ATCAAACATAT
1054910 TCCCATTTTC
Statistics
Matches: 30, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
26 30 1.00
ACGTcount: A:0.49, C:0.19, G:0.05, T:0.27
Consensus pattern (26 bp):
ATCAAACATATCACATAAAATAACAT
Found at i:1058122 original size:56 final size:55
Alignment explanation
Indices: 1058060--1058203 Score: 173
Period size: 56 Copynumber: 2.6 Consensus size: 55
1058050 GTGATTTTTT
* ** * * *
1058060 AGAAACTAAATCTGATTTTTGGAAGTTTCTTGATTATTTTTAAATGAGTTTTTTAA
1 AGAAACTAAGTCTGATTTTAAGAAGTTTCTTGATGATTTTTAAATGAG-CTTTCAA
*
1058116 AGAAACTAAGTCTGATTTTCAA-AAGTTTCTTGGTGATTTTTAAATGAGCTTTCAA
1 AGAAACTAAGTCTGATTTT-AAGAAGTTTCTTGATGATTTTTAAATGAGCTTTCAA
* * *
1058171 AGAAATTAAGTTTGATTTTAAGAGGTTTCTTGA
1 AGAAACTAAGTCTGATTTTAAGAAGTTTCTTGA
1058204 CTTGATTAAT
Statistics
Matches: 75, Mismatches: 11, Indels: 5
0.82 0.12 0.05
Matches are distributed among these distances:
54 2 0.03
55 31 0.41
56 42 0.56
ACGTcount: A:0.33, C:0.07, G:0.17, T:0.44
Consensus pattern (55 bp):
AGAAACTAAGTCTGATTTTAAGAAGTTTCTTGATGATTTTTAAATGAGCTTTCAA
Found at i:1058279 original size:53 final size:53
Alignment explanation
Indices: 1058211--1058519 Score: 370
Period size: 53 Copynumber: 5.8 Consensus size: 53
1058201 TGACTTGATT
* *
1058211 AATTTAAAAGAAGCTAAGCCTAATTTTTAGGGGTTTCTTGATGTTTTAAAATA
1 AATTTGAAAGAAGCTAAGCCTAATTTTTAGGGGTTTCTTGATGTTTTCAAATA
* * * * *
1058264 AATTTGAAAGAAGCTAAGCCTGATTTTAAGGTGTTTCTTGATGTTCTCAAATG
1 AATTTGAAAGAAGCTAAGCCTAATTTTTAGGGGTTTCTTGATGTTTTCAAATA
* ** * *
1058317 AATTTGAAAGAAGCTAAGCTTGGTTTTCAAGGGTTTCTTGATGTTTTCAAA-A
1 AATTTGAAAGAAGCTAAGCCTAATTTTTAGGGGTTTCTTGATGTTTTCAAATA
* *
1058369 CAATTTGAAAGAAGCTAAGCCTACTTTTTAGGGGTTTCTTGATGTTTTCAAATG
1 -AATTTGAAAGAAGCTAAGCCTAATTTTTAGGGGTTTCTTGATGTTTTCAAATA
* * * *
1058423 AATTT-AAAGGAAGTTAAGCCTTATTTTCAAGGGTTTCTTGATGTTTTCAAATGA
1 AATTTGAAA-GAAGCTAAGCCTAATTTTTAGGGGTTTCTTGATGTTTTCAAAT-A
* * * * *
1058477 ATTTTTAAAGGAGCTAATCCGAATTTTTAGGGGTTTCTTGATG
1 AATTTGAAAGAAGCTAAGCCTAATTTTTAGGGGTTTCTTGATG
1058520 ATAATTGTAA
Statistics
Matches: 217, Mismatches: 34, Indels: 9
0.83 0.13 0.03
Matches are distributed among these distances:
52 3 0.01
53 180 0.83
54 31 0.14
55 3 0.01
ACGTcount: A:0.30, C:0.10, G:0.20, T:0.39
Consensus pattern (53 bp):
AATTTGAAAGAAGCTAAGCCTAATTTTTAGGGGTTTCTTGATGTTTTCAAATA
Found at i:1059282 original size:137 final size:139
Alignment explanation
Indices: 1059029--1059384 Score: 522
Period size: 137 Copynumber: 2.6 Consensus size: 139
1059019 GATAAACCAG
1059029 TCAACATTTCCAGTGGAGAGTTCATAATGAGAAGAACTCA-TCGGATGAGGGAGAAGAAGTTCAT
1 TCAACATTTCCAGTGGAGAGTTCATAATGAGAAGAACTCATTCGG-TGAGGGAGAAGAAGTTCAT
* **
1059093 AATGAGAAGAACTTGTTCAACCTTAGCTTGATTCATCACATATGGAGTTGAATCAACAACAACTC
65 AATGAGAAGAACTTGTTCAACCTTAACTCAATTCATCACATATGGAGTTGAATCAACAACAACTC
1059158 ACTCGAGAG-A
130 ACTCGAG-GTA
* * * *
1059168 TCAATATTTCTAGTGGAGAGTTCATATTGAGAAGAACTCATTCGGTGA-GGA-AAAAAGTTCATA
1 TCAACATTTCCAGTGGAGAGTTCATAATGAGAAGAACTCATTCGGTGAGGGAGAAGAAGTTCATA
* * *
1059231 ATGAGAAGAACTTGTTCAAGCTTAACTCAATTCATCACATATGGAGTTGAATCAACAACACCTTA
66 ATGAGAAGAACTTGTTCAACCTTAACTCAATTCATCACATATGGAGTTGAATCAACAACAACTCA
*
1059296 CTTGAGGTA
131 CTCGAGGTA
* * * * *
1059305 TCAACATGTCCAGGGGAGAGTTCATAATGAGAAGAACTCATTCGATAAGGGATAAGAAGTTCATA
1 TCAACATTTCCAGTGGAGAGTTCATAATGAGAAGAACTCATTCGGTGAGGGAGAAGAAGTTCATA
1059370 ATGAGAAGAACTTGT
66 ATGAGAAGAACTTGT
1059385 CAAATCTTAG
Statistics
Matches: 194, Mismatches: 19, Indels: 8
0.88 0.09 0.04
Matches are distributed among these distances:
136 1 0.01
137 117 0.60
138 6 0.03
139 66 0.34
140 4 0.02
ACGTcount: A:0.37, C:0.15, G:0.21, T:0.26
Consensus pattern (139 bp):
TCAACATTTCCAGTGGAGAGTTCATAATGAGAAGAACTCATTCGGTGAGGGAGAAGAAGTTCATA
ATGAGAAGAACTTGTTCAACCTTAACTCAATTCATCACATATGGAGTTGAATCAACAACAACTCA
CTCGAGGTA
Found at i:1059613 original size:44 final size:44
Alignment explanation
Indices: 1059433--1059629 Score: 103
Period size: 44 Copynumber: 4.5 Consensus size: 44
1059423 CAGTACCAAT
* *
1059433 ATTTCATTCAATTCCATCATAGAAAGAGGT-GAATCAACATTTTC
1 ATTTCATTCAATTCCATCACAGAAAGAGGTAG-ATCAACATTATC
* * * * * * * *
1059477 ATTTCACTT-AAATCCATCGCATAAAGAGTTGGATCAGCATCAAC
1 ATTTCA-TTCAATTCCATCACAGAAAGAGGTAGATCAACATTATC
* * * * * * * * * **
1059521 TTTTTACTCGATTCTATAATAGAAGGAGGTAGATCAGCACCGAT-
1 ATTTCATTCAATTCCATCACAGAAAGAGGTAGATCAACA-TTATC
* * *
1059565 ATTTCATTCGATTCCATCACAGAAGGAGGTAGATCAACATTTTC
1 ATTTCATTCAATTCCATCACAGAAAGAGGTAGATCAACATTATC
** *
1059609 ATTTCGCTCAAATCCATCACA
1 ATTTCATTCAATTCCATCACA
1059630 TAGGGAGTTG
Statistics
Matches: 109, Mismatches: 39, Indels: 10
0.69 0.25 0.06
Matches are distributed among these distances:
43 2 0.02
44 103 0.94
45 4 0.04
ACGTcount: A:0.34, C:0.21, G:0.14, T:0.31
Consensus pattern (44 bp):
ATTTCATTCAATTCCATCACAGAAAGAGGTAGATCAACATTATC
Found at i:1059650 original size:132 final size:132
Alignment explanation
Indices: 1059431--1059744 Score: 391
Period size: 132 Copynumber: 2.4 Consensus size: 132
1059421 AGCAGTACCA
* * * *
1059431 ATATTTCATTCAATTCCATCATAGAAAGAGGT-GAATCAACATTTTCATTTCACTTAAATCCATC
1 ATATTTCATTCGATTCCATCACAGAAGGAGGTAG-ATCAACATTTTCATTTCACTCAAATCCATC
* * * * * * *
1059495 GCATAAAGAGTTGGATCAGCATCAACTTTTTACTCGATTCTATAATAGAAGGAGGTAGATCAGCA
65 ACATAAAGAGTTGGATCAACATCAACTTTTTACTCGATTATATAACAAAAGGAGGTAGAACAACA
1059560 CCG
130 CCG
*
1059563 ATATTTCATTCGATTCCATCACAGAAGGAGGTAGATCAACATTTTCATTTCGCTCAAATCCATCA
1 ATATTTCATTCGATTCCATCACAGAAGGAGGTAGATCAACATTTTCATTTCACTCAAATCCATCA
** * *
1059628 CATAGGGAGTTGGATCAACATCAACTTTTTGCTCGATTATATCACAAAAGGAGGTAGAACAACAC
66 CATAAAGAGTTGGATCAACATCAACTTTTTACTCGATTATATAACAAAAGGAGGTAGAACAACAC
1059693 CG
131 CG
* * * * *
1059695 ACATTAT-GTTCGATTCCATCACAGAAGAAGGTCA-ATCAATATTGTCATTT
1 ATATT-TCATTCGATTCCATCACAGAAGGAGGT-AGATCAACATTTTCATTT
1059745 TTGCTAGATT
Statistics
Matches: 158, Mismatches: 21, Indels: 6
0.85 0.11 0.03
Matches are distributed among these distances:
132 155 0.98
133 3 0.02
ACGTcount: A:0.34, C:0.20, G:0.16, T:0.30
Consensus pattern (132 bp):
ATATTTCATTCGATTCCATCACAGAAGGAGGTAGATCAACATTTTCATTTCACTCAAATCCATCA
CATAAAGAGTTGGATCAACATCAACTTTTTACTCGATTATATAACAAAAGGAGGTAGAACAACAC
CG
Found at i:1064658 original size:13 final size:13
Alignment explanation
Indices: 1064636--1064665 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
1064626 ACTAAACACC
1064636 TTTC-ACATACCT
1 TTTCAACATACCT
1064648 TTTCAACATACCT
1 TTTCAACATACCT
1064661 TTTCA
1 TTTCA
1064666 TCTTTGGCCA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 4 0.24
13 13 0.76
ACGTcount: A:0.27, C:0.30, G:0.00, T:0.43
Consensus pattern (13 bp):
TTTCAACATACCT
Found at i:1068345 original size:55 final size:56
Alignment explanation
Indices: 1068261--1068372 Score: 190
Period size: 55 Copynumber: 2.0 Consensus size: 56
1068251 TTGGAAATTG
*
1068261 AGAATTCAATTTTATTTAATTCACAATTCTTTTGATTTCTTT-CAATTCTTTTATT
1 AGAATTCAATTTTATTTAATTCACAATTCTTTTGATTTCTTTACAATTATTTTATT
* *
1068316 AGAATTCAGTTTTATTTAATTCACGATTCTTTTGATTTCTTTACAATTATTTTATT
1 AGAATTCAATTTTATTTAATTCACAATTCTTTTGATTTCTTTACAATTATTTTATT
1068372 A
1 A
1068373 TTTATTTTTT
Statistics
Matches: 53, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
55 40 0.75
56 13 0.25
ACGTcount: A:0.28, C:0.12, G:0.05, T:0.55
Consensus pattern (56 bp):
AGAATTCAATTTTATTTAATTCACAATTCTTTTGATTTCTTTACAATTATTTTATT
Found at i:1071889 original size:28 final size:27
Alignment explanation
Indices: 1071827--1071906 Score: 106
Period size: 28 Copynumber: 2.9 Consensus size: 27
1071817 GCGAGAAGCC
*
1071827 AACCTGAAACACATTACCTCCCAAATT
1 AACCTGAAACACATTACTTCCCAAATT
**
1071854 AAAATGAAACACATTACTTTCCCAAATT
1 AACCTGAAACACATTAC-TTCCCAAATT
*
1071882 AACCTGAAATACATTACCTTCCCAA
1 AACCTGAAACACATTA-CTTCCCAA
1071907 GGCATCCTAA
Statistics
Matches: 45, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
27 15 0.33
28 29 0.64
29 1 0.02
ACGTcount: A:0.42, C:0.29, G:0.04, T:0.25
Consensus pattern (27 bp):
AACCTGAAACACATTACTTCCCAAATT
Found at i:1073206 original size:55 final size:55
Alignment explanation
Indices: 1073168--1073344 Score: 221
Period size: 55 Copynumber: 3.2 Consensus size: 55
1073158 TTAATTTTTG
*
1073168 GAAGTTTCTTGATTATTTTTAAATGAATTATGAAAGAAACTAAGTCCGATTTTCA
1 GAAGTTTCTTGATTATTTTTAAATGAATTATGAAAGAAACTAAGTCTGATTTTCA
* * *
1073223 GAAGTTTCTTGATTATTTTTAAATGAGTTTTTAAAGAAACTAAGTCTGATTTTCA
1 GAAGTTTCTTGATTATTTTTAAATGAATTATGAAAGAAACTAAGTCTGATTTTCA
* * * * * * * *
1073278 AAAGTTTCTTGGTGATTTTTAAATGAGCTT-TCAAATAAATTAAGTCTGGTTTTCA
1 GAAGTTTCTTGATTATTTTTAAATGA-ATTATGAAAGAAACTAAGTCTGATTTTCA
*
1073333 GAGGTTTCTTGA
1 GAAGTTTCTTGA
1073345 CATGATTAAT
Statistics
Matches: 106, Mismatches: 15, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
55 104 0.98
56 2 0.02
ACGTcount: A:0.32, C:0.08, G:0.16, T:0.43
Consensus pattern (55 bp):
GAAGTTTCTTGATTATTTTTAAATGAATTATGAAAGAAACTAAGTCTGATTTTCA
Found at i:1073418 original size:53 final size:52
Alignment explanation
Indices: 1073352--1073603 Score: 335
Period size: 53 Copynumber: 4.7 Consensus size: 52
1073342 TGACATGATT
*
1073352 AATTTCAAAGAAGCTAAGCCTAATTTTTAGCGGTTTCTTGATGTTTTCAAATG
1 AATTTGAAAGAAGCTAAGCCTAATTTTTAG-GGTTTCTTGATGTTTTCAAATG
* * * *
1073405 AATTTGAAGGAAGCTAAGCCTGATTTTAAGGTGTTTCTTGATGTTCTCAAATG
1 AATTTGAAAGAAGCTAAGCCTAATTTTTAGG-GTTTCTTGATGTTTTCAAATG
1073458 AATTTGAAAGAAGCTAAGCCTAATTTTTAGGGGTTTCTTGATGTTTTCAAATG
1 AATTTGAAAGAAGCTAAGCCTAATTTTTA-GGGTTTCTTGATGTTTTCAAATG
* ** *
1073511 AATTT-AAAGGAAGTTAAGCCTTGTTTTCAAGGGTTTCTTGATGTTTTCAAATG
1 AATTTGAAA-GAAGCTAAGCCTAATTTT-TAGGGTTTCTTGATGTTTTCAAATG
* *
1073564 AATTTTTAAAGAAGCTAATCCTAATTTTTAGGCGTTTCTT
1 AA-TTTGAAAGAAGCTAAGCCTAATTTTTAGG-GTTTCTT
1073604 TATGATAATT
Statistics
Matches: 174, Mismatches: 18, Indels: 13
0.85 0.09 0.06
Matches are distributed among these distances:
52 4 0.02
53 140 0.80
54 27 0.16
55 3 0.02
ACGTcount: A:0.29, C:0.11, G:0.19, T:0.40
Consensus pattern (52 bp):
AATTTGAAAGAAGCTAAGCCTAATTTTTAGGGTTTCTTGATGTTTTCAAATG
Found at i:1073472 original size:106 final size:105
Alignment explanation
Indices: 1073352--1073603 Score: 382
Period size: 106 Copynumber: 2.4 Consensus size: 105
1073342 TGACATGATT
*
1073352 AATTTCAAAGAAGCTAAGCCTAATTTTTAGCGGTTTCTTGATGTTTTCAAATGAATTTGAAGGAA
1 AATTTCAAAGAAGCTAAGCCTAATTTTTAG-GGTTTCTTGATGTTTTCAAATGAATTTAAAGGAA
1073417 GCTAAGCC-TGATTTT-AAGGTGTTTCTTGATGTTCTCAAATG
65 GCTAAGCCTTG-TTTTCAAGG-GTTTCTTGATGTTCTCAAATG
*
1073458 AATTTGAAAGAAGCTAAGCCTAATTTTTAGGGGTTTCTTGATGTTTTCAAATGAATTTAAAGGAA
1 AATTTCAAAGAAGCTAAGCCTAATTTTTA-GGGTTTCTTGATGTTTTCAAATGAATTTAAAGGAA
* *
1073523 GTTAAGCCTTGTTTTCAAGGGTTTCTTGATGTTTTCAAATG
65 GCTAAGCCTTGTTTTCAAGGGTTTCTTGATGTTCTCAAATG
* *
1073564 AATTTTTAAAGAAGCTAATCCTAATTTTTAGGCGTTTCTT
1 AA-TTTCAAAGAAGCTAAGCCTAATTTTTAGG-GTTTCTT
1073604 TATGATAATT
Statistics
Matches: 135, Mismatches: 6, Indels: 9
0.90 0.04 0.06
Matches are distributed among these distances:
106 96 0.71
107 39 0.29
ACGTcount: A:0.29, C:0.11, G:0.19, T:0.40
Consensus pattern (105 bp):
AATTTCAAAGAAGCTAAGCCTAATTTTTAGGGTTTCTTGATGTTTTCAAATGAATTTAAAGGAAG
CTAAGCCTTGTTTTCAAGGGTTTCTTGATGTTCTCAAATG
Found at i:1073691 original size:20 final size:20
Alignment explanation
Indices: 1073666--1073713 Score: 87
Period size: 20 Copynumber: 2.4 Consensus size: 20
1073656 TTTCTTGATG
*
1073666 AGTAAGTCCTTCGGGCCATC
1 AGTAAGTCCTTCGGGACATC
1073686 AGTAAGTCCTTCGGGACATC
1 AGTAAGTCCTTCGGGACATC
1073706 AGTAAGTC
1 AGTAAGTC
1073714 TTTCTAGCAT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.25, C:0.25, G:0.25, T:0.25
Consensus pattern (20 bp):
AGTAAGTCCTTCGGGACATC
Found at i:1073972 original size:31 final size:31
Alignment explanation
Indices: 1073874--1073964 Score: 168
Period size: 31 Copynumber: 3.0 Consensus size: 31
1073864 CAATTTAAGG
1073874 CAAAATGGTTTTTGGACTTGAATTGAATTTA
1 CAAAATGGTTTTTGGACTTGAATTGAATTTA
1073905 CAAAATGGTTTTTGGACTTGAATTGAATTTA
1 CAAAATGGTTTTTGGACTTGAATTGAATTTA
1073936 CAAAAT-GTTTTTGGACTT-AATTGAATTTA
1 CAAAATGGTTTTTGGACTTGAATTGAATTTA
1073965 TTCAAAATTT
Statistics
Matches: 60, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
29 11 0.18
30 12 0.20
31 37 0.62
ACGTcount: A:0.33, C:0.07, G:0.18, T:0.43
Consensus pattern (31 bp):
CAAAATGGTTTTTGGACTTGAATTGAATTTA
Found at i:1074053 original size:19 final size:19
Alignment explanation
Indices: 1074029--1074095 Score: 89
Period size: 19 Copynumber: 3.5 Consensus size: 19
1074019 AATGTTTTTA
* *
1074029 TGAATAGTAATTTACTATT
1 TGAACAGTAAATTACTATT
*
1074048 TGAATAGTAAATTACTATT
1 TGAACAGTAAATTACTATT
* *
1074067 TGAACAGTAAATCACTGTT
1 TGAACAGTAAATTACTATT
1074086 TGAACAGTAA
1 TGAACAGTAA
1074096 CCGAGGCTCA
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 44 1.00
ACGTcount: A:0.40, C:0.09, G:0.13, T:0.37
Consensus pattern (19 bp):
TGAACAGTAAATTACTATT
Found at i:1074303 original size:21 final size:21
Alignment explanation
Indices: 1074270--1074309 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 21
1074260 TTTGAGTAGA
*
1074270 AAAATCATTCCCAAACGGCTCC
1 AAAATCA-TCCCCAACGGCTCC
1074292 AAAA-CATCCCCAACGGCT
1 AAAATCATCCCCAACGGCT
1074310 AGATATGACT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 11 0.65
21 2 0.12
22 4 0.24
ACGTcount: A:0.38, C:0.38, G:0.10, T:0.15
Consensus pattern (21 bp):
AAAATCATCCCCAACGGCTCC
Found at i:1075196 original size:22 final size:22
Alignment explanation
Indices: 1075164--1075221 Score: 89
Period size: 22 Copynumber: 2.6 Consensus size: 22
1075154 AGGTCACTAG
*
1075164 TAAGCCTTTCGAGCATGATGAT
1 TAAGCCCTTCGAGCATGATGAT
*
1075186 TAAGCCCTTCGAGCATGGTGAT
1 TAAGCCCTTCGAGCATGATGAT
*
1075208 TAAGCCCTCCGAGC
1 TAAGCCCTTCGAGC
1075222 CGTCCATATG
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 33 1.00
ACGTcount: A:0.24, C:0.26, G:0.24, T:0.26
Consensus pattern (22 bp):
TAAGCCCTTCGAGCATGATGAT
Found at i:1075919 original size:139 final size:139
Alignment explanation
Indices: 1075577--1075921 Score: 438
Period size: 139 Copynumber: 2.5 Consensus size: 139
1075567 CATTTCCAAT
*
1075577 GGAGAGTTCATAATGAGAAGAACTCATCCGATGAGGGAGAAGAAGTTCATAATGAGAAGAACTTA
1 GGAGAGTTCATAATGAGAAGAACTCATCCGATGAGGGAGAAGAAGTTCATAATGAGAAGAACTTG
* * * *
1075642 TTCAACCTTAGCTCGATTCATCGCATATGGAGTTGAATCAACAACACCTCACTCGAGGGATCAAC
66 TTCAACCTTAACTCAATTCATCACATATGGAGTTGAATCAACAACACCTCACTAGAGGGATCAAC
* * *
1075707 ATTTCCAGT
131 ATGTACAGG
* * ** * *
1075716 GGAGAGTTCATATTAAGAAGAACTCATTGGGTGAGGAAGAAGAAGTTCATAATGAGAAGAACTTG
1 GGAGAGTTCATAATGAGAAGAACTCATCCGATGAGGGAGAAGAAGTTCATAATGAGAAGAACTTG
** * * * *
1075781 TTCAAGTTTAACTCAATTCATCACATATGGAGTTGAATCAACAACACTTTACTATATGGATCAAC
66 TTCAACCTTAACTCAATTCATCACATATGGAGTTGAATCAACAACACCTCACTAGAGGGATCAAC
1075846 ATGTACAGG
131 ATGTACAGG
* * * * * * * *
1075855 GGAGAGTTTACAATGAGGAGAACTCATCCAATAAGGGAGAATAAGTTAATAATGAGAAGTACTTG
1 GGAGAGTTCATAATGAGAAGAACTCATCCGATGAGGGAGAAGAAGTTCATAATGAGAAGAACTTG
1075920 TT
66 TT
1075922 AAATCTTAGC
Statistics
Matches: 172, Mismatches: 34, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
139 172 1.00
ACGTcount: A:0.37, C:0.15, G:0.22, T:0.26
Consensus pattern (139 bp):
GGAGAGTTCATAATGAGAAGAACTCATCCGATGAGGGAGAAGAAGTTCATAATGAGAAGAACTTG
TTCAACCTTAACTCAATTCATCACATATGGAGTTGAATCAACAACACCTCACTAGAGGGATCAAC
ATGTACAGG
Found at i:1076016 original size:44 final size:44
Alignment explanation
Indices: 1075967--1076312 Score: 137
Period size: 44 Copynumber: 7.9 Consensus size: 44
1075957 AACAGTACCA
*
1075967 ACATTTTATTCAATTCCATCACAGAAAGAGGTGGATCAACATTT
1 ACATTTTACTCAATTCCATCACAGAAAGAGGTGGATCAACATTT
* * * * * * ** **
1076011 TCATTTCACTCAAATCCATCGCATAAGGATTTGGATCAACATCA
1 ACATTTTACTCAATTCCATCACAGAAAGAGGTGGATCAACATTT
* * * * * * * * *
1076055 ACTTTTTGCTCGATTCTATAACA-AAAGGAGGTAGATCAGCACTG
1 ACATTTTACTCAATTCCATCACAGAAA-GAGGTGGATCAACATTT
** * *
1076099 ACATTTTGTTCGATTCCATCACAGAAGGAGGTGGATCAACATTT
1 ACATTTTACTCAATTCCATCACAGAAAGAGGTGGATCAACATTT
* * * * * * * * **
1076143 TCATTTCT-CTCAAATCTATCACATAATGAGTTCGATCAGCATCA
1 ACATTT-TACTCAATTCCATCACAGAAAGAGGTGGATCAACATTT
* * * ** * * * *
1076187 ACTTTTTGCTCGATTATATCATA-AAGGAGGTAGATCAACATTG
1 ACATTTTACTCAATTCCATCACAGAAAGAGGTGGATCAACATTT
* ** * *
1076230 ACATTATGTTCGATTCCATCACAG-AAGAATGTGGATCAACA-TT
1 ACATTTTACTCAATTCCATCACAGAAAG-AGGTGGATCAACATTT
* * *
1076273 ATCATTTTTGCT-AGATTTCATCACAGAAGGAGGTGGATCA
1 A-CA-TTTTACTCA-ATTCCATCACAGAAAGAGGTGGATCA
1076313 GCACAATTGA
Statistics
Matches: 215, Mismatches: 77, Indels: 19
0.69 0.25 0.06
Matches are distributed among these distances:
43 38 0.18
44 147 0.68
45 28 0.13
46 2 0.01
ACGTcount: A:0.33, C:0.19, G:0.16, T:0.32
Consensus pattern (44 bp):
ACATTTTACTCAATTCCATCACAGAAAGAGGTGGATCAACATTT
Found at i:1076161 original size:88 final size:87
Alignment explanation
Indices: 1076069--1076228 Score: 187
Period size: 88 Copynumber: 1.8 Consensus size: 87
1076059 TTTGCTCGAT
* * * *
1076069 TCTATAACAAAAGGAGGTAGATCAGCA-CTGACATTTTGTTCGATTCCATCACAGAAGGAGGTGG
1 TCTATAACAAAAGGAGGTAGATCAGCATC-AACATTTTGCTCGATTACATCACA-AAGGAGGTAG
1076133 ATCAACATTTTCATTTCTCTCAAA
64 ATCAACATTTTCATTTCTCTCAAA
* * * * * * * *
1076157 TCTATCACATAATGAGTTCGATCAGCATCAACTTTTTGCTCGATTATATCATAAAGGAGGTAGAT
1 TCTATAACAAAAGGAGGTAGATCAGCATCAACATTTTGCTCGATTACATCACAAAGGAGGTAGAT
1076222 CAACATT
66 CAACATT
1076229 GACATTATGT
Statistics
Matches: 59, Mismatches: 12, Indels: 3
0.80 0.16 0.04
Matches are distributed among these distances:
87 18 0.31
88 40 0.68
89 1 0.02
ACGTcount: A:0.33, C:0.19, G:0.17, T:0.31
Consensus pattern (87 bp):
TCTATAACAAAAGGAGGTAGATCAGCATCAACATTTTGCTCGATTACATCACAAAGGAGGTAGAT
CAACATTTTCATTTCTCTCAAA
Found at i:1078938 original size:55 final size:55
Alignment explanation
Indices: 1078854--1078959 Score: 194
Period size: 55 Copynumber: 1.9 Consensus size: 55
1078844 GGAAATTGAG
1078854 AATTCAGTTTTATTTAATTCACAATTCTTTTGATTTCTTTCAATTCTTTTATTAA
1 AATTCAGTTTTATTTAATTCACAATTCTTTTGATTTCTTTCAATTCTTTTATTAA
* *
1078909 AATTCAGTTTTATTTAATTCACGATTCTTTTGATTTCTTTTAATTCTTTTA
1 AATTCAGTTTTATTTAATTCACAATTCTTTTGATTTCTTTCAATTCTTTTA
1078960 ATATTTATTT
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
55 49 1.00
ACGTcount: A:0.25, C:0.12, G:0.05, T:0.58
Consensus pattern (55 bp):
AATTCAGTTTTATTTAATTCACAATTCTTTTGATTTCTTTCAATTCTTTTATTAA
Found at i:1080447 original size:20 final size:21
Alignment explanation
Indices: 1080422--1080471 Score: 59
Period size: 22 Copynumber: 2.4 Consensus size: 21
1080412 AATTCCTTTG
1080422 TTGCA-TTTATATTTTGCAT-T
1 TTGCATTTTAT-TTTTGCATCT
1080442 TTGCATTCTTATTTTTGCATCT
1 TTGCATT-TTATTTTTGCATCT
*
1080464 ATGCATTT
1 TTGCATTT
1080472 GCATATGCAT
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
20 5 0.19
21 10 0.38
22 11 0.42
ACGTcount: A:0.18, C:0.14, G:0.10, T:0.58
Consensus pattern (21 bp):
TTGCATTTTATTTTTGCATCT
Found at i:1080482 original size:20 final size:20
Alignment explanation
Indices: 1080457--1080495 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
1080447 TTCTTATTTT
*
1080457 TGCATCTATGCATTTGCATA
1 TGCATCTATGCATTAGCATA
*
1080477 TGCATCTTTGCATTAGCAT
1 TGCATCTATGCATTAGCAT
1080496 CTATACATCG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.23, C:0.21, G:0.15, T:0.41
Consensus pattern (20 bp):
TGCATCTATGCATTAGCATA
Found at i:1081873 original size:18 final size:16
Alignment explanation
Indices: 1081851--1081918 Score: 55
Period size: 17 Copynumber: 3.9 Consensus size: 16
1081841 AGATATAGAA
1081851 AAAAAAGAAGAGAAAAC
1 AAAAAAGAA-AGAAAAC
* *
1081868 ATAAAAAGGAGAAAAAAAG
1 A-AAAAA-GA-AAGAAAAC
* *
1081887 AAAGAAGAAAAAAAAGC
1 AAAAAAGAAAGAAAA-C
1081904 AAAAAAGAAAGAAAA
1 AAAAAAGAAAGAAAA
1081919 AGAGGAAGAA
Statistics
Matches: 41, Mismatches: 6, Indels: 8
0.75 0.11 0.15
Matches are distributed among these distances:
16 7 0.17
17 16 0.39
18 9 0.22
19 8 0.20
20 1 0.02
ACGTcount: A:0.78, C:0.03, G:0.18, T:0.01
Consensus pattern (16 bp):
AAAAAAGAAAGAAAAC
Found at i:1081897 original size:24 final size:23
Alignment explanation
Indices: 1081870--1081932 Score: 72
Period size: 24 Copynumber: 2.7 Consensus size: 23
1081860 GAGAAAACAT
1081870 AAAAAGGAGAAAAAAAGAAAGAA
1 AAAAAGGAGAAAAAAAGAAAGAA
** *
1081893 GAAAAAAAAGCAAAAAAGAAAGAA
1 -AAAAAGGAGAAAAAAAGAAAGAA
*
1081917 AAAGAGGAAGAAAAAA
1 AAAAAGG-AGAAAAAA
1081933 CACTTCAAGA
Statistics
Matches: 31, Mismatches: 7, Indels: 2
0.77 0.17 0.05
Matches are distributed among these distances:
23 4 0.13
24 27 0.87
ACGTcount: A:0.78, C:0.02, G:0.21, T:0.00
Consensus pattern (23 bp):
AAAAAGGAGAAAAAAAGAAAGAA
Found at i:1081919 original size:18 final size:17
Alignment explanation
Indices: 1081851--1081920 Score: 63
Period size: 18 Copynumber: 3.9 Consensus size: 17
1081841 AGATATAGAA
*
1081851 AAAAAAGAAGAGAAAA-C
1 AAAAAAGAA-AAAAAAGC
1081868 ATAAAAAGGAGAAAAAAAG-
1 A-AAAAA-GA-AAAAAAAGC
*
1081887 AAAGAAGAAAAAAAAGC
1 AAAAAAGAAAAAAAAGC
1081904 AAAAAAGAAAGAAAAAG
1 AAAAAAGAAA-AAAAAG
1081921 AGGAAGAAAA
Statistics
Matches: 44, Mismatches: 3, Indels: 11
0.76 0.05 0.19
Matches are distributed among these distances:
16 8 0.18
17 12 0.27
18 15 0.34
19 8 0.18
20 1 0.02
ACGTcount: A:0.77, C:0.03, G:0.19, T:0.01
Consensus pattern (17 bp):
AAAAAAGAAAAAAAAGC
Found at i:1082782 original size:56 final size:55
Alignment explanation
Indices: 1082624--1082828 Score: 232
Period size: 55 Copynumber: 3.7 Consensus size: 55
1082614 GACTAACGCT
* *
1082624 ATTTTTT-TAGAAACTAAGTCCGATTTTCTGAAGTTTCTTGATTATTTTTAAATG
1 ATTTTTTAAAGAAACTAAGTCCGATTTTCAGAAGTTTCTTGATTATTTTTAAATG
* * * * * *
1082678 AATTCTGAAATAAACTAAGTCCGTTTTTCAAAAGTTTCTTGATTATTTTTAAATG
1 ATTTTTTAAAGAAACTAAGTCCGATTTTCAGAAGTTTCTTGATTATTTTTAAATG
* * * *
1082733 ATTTTTTTAAAGAAACTAAGTCTGATTTTCAGATGTTTCTTGGTGATTTTTAAATG
1 A-TTTTTTAAAGAAACTAAGTCCGATTTTCAGAAGTTTCTTGATTATTTTTAAATG
** * * * *
1082789 AGCTTTCAAAGAAATTAAGTCTGATTTTCAGAGGTTTCTT
1 ATTTTTTAAAGAAACTAAGTCCGATTTTCAGAAGTTTCTT
1082829 AACATGATTA
Statistics
Matches: 126, Mismatches: 23, Indels: 3
0.83 0.15 0.02
Matches are distributed among these distances:
54 4 0.03
55 77 0.61
56 45 0.36
ACGTcount: A:0.30, C:0.10, G:0.14, T:0.46
Consensus pattern (55 bp):
ATTTTTTAAAGAAACTAAGTCCGATTTTCAGAAGTTTCTTGATTATTTTTAAATG
Found at i:1082826 original size:111 final size:109
Alignment explanation
Indices: 1082624--1082828 Score: 259
Period size: 111 Copynumber: 1.9 Consensus size: 109
1082614 GACTAACGCT
* * * *
1082624 ATTTTTTTAGAAACTAAGTCCGATTTTCTGAAGTTTCTTGATTATTTTTAAATGAATTCTGAAAT
1 ATTTTTTTAGAAACTAAGTCCGATTTTCAGAAGTTTCTTGATGATTTTTAAATGAATTCTCAAAG
*
1082689 AAACTAAGTCCGTTTTTCAAAAGTTTCTTGATTATTTTTAAATG
66 AAACTAAGTCCGATTTTCAAAAGTTTCTTGATTATTTTTAAATG
* * * *
1082733 ATTTTTTTAAAGAAACTAAGTCTGATTTTCAGATGTTTCTTGGTGATTTTTAAATGAGCTT-TCA
1 ATTTTTTT--AGAAACTAAGTCCGATTTTCAGAAGTTTCTTGATGATTTTTAAATGA-ATTCTCA
* * * *
1082797 AAGAAATTAAGTCTGATTTTCAGAGGTTTCTT
63 AAGAAACTAAGTCCGATTTTCAAAAGTTTCTT
1082829 AACATGATTA
Statistics
Matches: 80, Mismatches: 13, Indels: 4
0.82 0.13 0.04
Matches are distributed among these distances:
109 8 0.10
111 70 0.88
112 2 0.03
ACGTcount: A:0.30, C:0.10, G:0.14, T:0.46
Consensus pattern (109 bp):
ATTTTTTTAGAAACTAAGTCCGATTTTCAGAAGTTTCTTGATGATTTTTAAATGAATTCTCAAAG
AAACTAAGTCCGATTTTCAAAAGTTTCTTGATTATTTTTAAATG
Found at i:1082901 original size:53 final size:53
Alignment explanation
Indices: 1082838--1083358 Score: 656
Period size: 53 Copynumber: 9.8 Consensus size: 53
1082828 TAACATGATT
* * *
1082838 AATTTAAAAGAAGCTAAGCCTAATTTTTATGGGTTTATTGATGTTTTCAAATG
1 AATTTGAAAGAAGCTAAGCCTAATTTTTAGGGGTTTCTTGATGTTTTCAAATG
* *
1082891 AATTTTAAAGAAGATAAGCCTAATTTTTAGGGGTTTCTTGATGTTTTCAAATG
1 AATTTGAAAGAAGCTAAGCCTAATTTTTAGGGGTTTCTTGATGTTTTCAAATG
* * *
1082944 AATTTGAAAGAAGCTATGCCTGATTTTAAGGGGTTTCTTGATGTTCTT-AAATG
1 AATTTGAAAGAAGCTAAGCCTAATTTTTAGGGGTTTCTTGATGTT-TTCAAATG
* *
1082997 AATTTGAAAGAAGCTAAGCCT-GTTTTTCAAGGGTTTCTTGATGTTTTCAAATG
1 AATTTGAAAGAAGCTAAGCCTAATTTTT-AGGGGTTTCTTGATGTTTTCAAATG
1083050 AATTTGAAAGAAGCTAAGCCTAATTTTTAGGGGTTTCTTGATGTTTGT-AAATG
1 AATTTGAAAGAAGCTAAGCCTAATTTTTAGGGGTTTCTTGATGTTT-TCAAATG
* * * * *
1083103 AATTTGAAAGAA-CATAAGCCTGATTTTCAAGAGTTTCTTGATGTGTTCAAATG
1 AATTTGAAAGAAGC-TAAGCCTAATTTTTAGGGGTTTCTTGATGTTTTCAAATG
* *
1083156 AATTTTAAAGAAGCTAAGCCTAATTTTTAGGGGATTCTTGATGTTTTCAAATG
1 AATTTGAAAGAAGCTAAGCCTAATTTTTAGGGGTTTCTTGATGTTTTCAAATG
* * * * * *
1083209 AATTTGAAAAAATCTAAGCCTAATTTTTAAGGGTTTCTTGACGTTTCCAAATT
1 AATTTGAAAGAAGCTAAGCCTAATTTTTAGGGGTTTCTTGATGTTTTCAAATG
* * * *
1083262 AATTT-AAAGGAAGTTAAACATGATTTTTAGGGGTTTCTTGATGTTTTCAAATG
1 AATTTGAAA-GAAGCTAAGCCTAATTTTTAGGGGTTTCTTGATGTTTTCAAATG
* ** * * *
1083315 AACTTTTAAAGAATATAATCCTAATTTTTAGGTGTTTATTGATG
1 AA-TTTGAAAGAAGCTAAGCCTAATTTTTAGGGGTTTCTTGATG
1083359 ATAATTGTAA
Statistics
Matches: 405, Mismatches: 52, Indels: 21
0.85 0.11 0.04
Matches are distributed among these distances:
52 11 0.03
53 352 0.87
54 39 0.10
55 3 0.01
ACGTcount: A:0.32, C:0.09, G:0.19, T:0.40
Consensus pattern (53 bp):
AATTTGAAAGAAGCTAAGCCTAATTTTTAGGGGTTTCTTGATGTTTTCAAATG
Found at i:1083490 original size:20 final size:20
Alignment explanation
Indices: 1083419--1083491 Score: 60
Period size: 20 Copynumber: 3.5 Consensus size: 20
1083409 TCTTGATGAA
* *
1083419 TAAGTCCTTT-GGGCCATCAG
1 TAAGT-CTTTCGGGTCATCTG
*
1083439 TAAGTCTTTCGAGCGTGATGCT-
1 TAAGTCTTTCG-G-GTCAT-CTG
*
1083461 TAAATCTTTCGGGTCATCTG
1 TAAGTCTTTCGGGTCATCTG
1083481 TAAGTCTTTCG
1 TAAGTCTTTCG
1083492 AACAATATGA
Statistics
Matches: 42, Mismatches: 6, Indels: 10
0.72 0.10 0.17
Matches are distributed among these distances:
19 6 0.14
20 20 0.48
21 2 0.05
22 13 0.31
23 1 0.02
ACGTcount: A:0.19, C:0.21, G:0.23, T:0.37
Consensus pattern (20 bp):
TAAGTCTTTCGGGTCATCTG
Found at i:1084424 original size:50 final size:50
Alignment explanation
Indices: 1084349--1084449 Score: 184
Period size: 50 Copynumber: 2.0 Consensus size: 50
1084339 CATAATGAGA
1084349 AGAACCTGTTCAACCTTAGCTCGATTCATCACATATGGAGTTGAATCAGC
1 AGAACCTGTTCAACCTTAGCTCGATTCATCACATATGGAGTTGAATCAGC
* *
1084399 AGAACTTGTTCAACCTTAGCTCGATTCATCGCATATGGAGTTGAATCAGC
1 AGAACCTGTTCAACCTTAGCTCGATTCATCACATATGGAGTTGAATCAGC
1084449 A
1 A
1084450 ACATCTCACT
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
50 49 1.00
ACGTcount: A:0.30, C:0.23, G:0.19, T:0.29
Consensus pattern (50 bp):
AGAACCTGTTCAACCTTAGCTCGATTCATCACATATGGAGTTGAATCAGC
Found at i:1084717 original size:139 final size:139
Alignment explanation
Indices: 1084399--1084719 Score: 439
Period size: 139 Copynumber: 2.3 Consensus size: 139
1084389 TTGAATCAGC
* * *
1084399 AGAACTTGTTCAACCTTAGCTCGATTCATCGCATATGGAGTTGAATCAGCAACATCTCACTCGAG
1 AGAACTTGTTCAACCTTAGCTAGTTTCATCGCATATGGAGTTGAATCAGCAACACCTCACTCGAG
* * * * * * *
1084464 GGATCAACATTTCCAGTGGAGATTTCATATTGAGAAGAACTCATTCGATGAGGAAGAATAAGTTC
66 GGATCAACATGTCCAGTAGAGAGTTCATAATGAGAAGAACTCATCCGATAAGGAAGAAGAAGTTC
1084529 ATAATGAGA
131 ATAATGAGA
* * *
1084538 AGAACTTGTTCAACCTTAACTCAATTT-ATCACATATGGAGTTGAATCAGCAACACCTCACTCGA
1 AGAACTTGTTCAACCTTAGCT-AGTTTCATCGCATATGGAGTTGAATCAGCAACACCTCACTCGA
*
1084602 GGGATCAACATGTCCAG-AGAGAGTTCATAATGAGAAGAACTCATCCGATAAGGGAGAAGAAGTT
65 GGGATCAACATGTCCAGTAGAGAGTTCATAATGAGAAGAACTCATCCGATAAGGAAGAAGAAGTT
1084666 CATAATGAGA
130 CATAATGAGA
* * * * *
1084676 AGAACTTGTTAAATCTTAGCTTGTTTCCATTGCATAAGGAGTTG
1 AGAACTTGTTCAACCTTAGCTAGTTT-CATCGCATATGGAGTTG
1084720 GAACAACACC
Statistics
Matches: 157, Mismatches: 22, Indels: 6
0.85 0.12 0.03
Matches are distributed among these distances:
137 3 0.02
138 68 0.43
139 84 0.54
140 2 0.01
ACGTcount: A:0.35, C:0.18, G:0.21, T:0.27
Consensus pattern (139 bp):
AGAACTTGTTCAACCTTAGCTAGTTTCATCGCATATGGAGTTGAATCAGCAACACCTCACTCGAG
GGATCAACATGTCCAGTAGAGAGTTCATAATGAGAAGAACTCATCCGATAAGGAAGAAGAAGTTC
ATAATGAGA
Found at i:1085020 original size:132 final size:132
Alignment explanation
Indices: 1084723--1085020 Score: 402
Period size: 132 Copynumber: 2.3 Consensus size: 132
1084713 GGAGTTGGAA
* * * *
1084723 CAACACCGCCATTTCTTTCGATTCCATCACAGAAAGAGGTGGATAAACATTTTCTTTTCACTCAA
1 CAACACCGACATTTCGTTCGATTCCATCACAGAAAGAGGTGGATAAACATTTACATTTCACTCAA
* * *
1084788 ATCCATCGCATAAGGAGTTGGATCAACATCAACTTTTTGCTCGATTCTATAACAGAAAGAGGAAT
66 ATCCATCACACAAGGAGTTGGATCAACATCAACTTTTTGCTCGATTCTATAACAGAAAGAGGAAG
1084853 AT
131 AT
* * * * *
1084855 CAGCACCGACATTTCGTTTGATTCCATAACAGAATGAGGTGGATAAACATTTACATTTCGCTCAA
1 CAACACCGACATTTCGTTCGATTCCATCACAGAAAGAGGTGGATAAACATTTACATTTCACTCAA
* * * * *
1084920 ATCCATCATACAAGGAGTTGGATCAGCATCAACTTTTTGCTTGATTCTATCACA-AAATGAGGTA
66 ATCCATCACACAAGGAGTTGGATCAACATCAACTTTTTGCTCGATTCTATAACAGAAA-GAGGAA
1084984 GAT
130 GAT
*
1084987 CAACACCGACATTAT-GTTCGATTCCATCGCAGAA
1 CAACACCGACATT-TCGTTCGATTCCATCACAGAA
1085021 GAATATGGAT
Statistics
Matches: 143, Mismatches: 21, Indels: 4
0.85 0.12 0.02
Matches are distributed among these distances:
131 3 0.02
132 139 0.97
133 1 0.01
ACGTcount: A:0.33, C:0.22, G:0.16, T:0.29
Consensus pattern (132 bp):
CAACACCGACATTTCGTTCGATTCCATCACAGAAAGAGGTGGATAAACATTTACATTTCACTCAA
ATCCATCACACAAGGAGTTGGATCAACATCAACTTTTTGCTCGATTCTATAACAGAAAGAGGAAG
AT
Found at i:1087637 original size:40 final size:40
Alignment explanation
Indices: 1087582--1087703 Score: 244
Period size: 40 Copynumber: 3.0 Consensus size: 40
1087572 TGCAGGTTTA
1087582 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
1 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
1087622 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
1 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
1087662 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
1 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
1087702 TA
1 TA
1087704 GCACTACGGT
Statistics
Matches: 82, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 82 1.00
ACGTcount: A:0.23, C:0.17, G:0.27, T:0.33
Consensus pattern (40 bp):
TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
Found at i:1087901 original size:47 final size:44
Alignment explanation
Indices: 1087807--1087924 Score: 146
Period size: 47 Copynumber: 2.6 Consensus size: 44
1087797 GTAACCATGC
* *
1087807 AAATAAGCTTATGAGCTTACGGAATAATGGCAAGTATATTGGAA
1 AAATAAGCTTACGAGCTTATGGAATAATGGCAAGTATATTGGAA
* * * *
1087851 AAATAAGCTTACGAGCTTATGTAATTTAAATGGTAAGTATTTTGGTA
1 AAATAAGCTTACGAGCTTATGGAA--T-AATGGCAAGTATATTGGAA
*
1087898 AAATAAGCTTACGAGCTTATGGGATAA
1 AAATAAGCTTACGAGCTTATGGAATAA
1087925 ATGGTAAGAG
Statistics
Matches: 63, Mismatches: 8, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
44 23 0.37
45 1 0.02
46 1 0.02
47 38 0.60
ACGTcount: A:0.39, C:0.08, G:0.21, T:0.31
Consensus pattern (44 bp):
AAATAAGCTTACGAGCTTATGGAATAATGGCAAGTATATTGGAA
Found at i:1090776 original size:16 final size:16
Alignment explanation
Indices: 1090748--1090790 Score: 61
Period size: 16 Copynumber: 2.8 Consensus size: 16
1090738 ATATATTATA
1090748 AGAAGAA-AAAAAAAC
1 AGAAGAAGAAAAAAAC
*
1090763 AGAAGAAGAAAAAAAT
1 AGAAGAAGAAAAAAAC
*
1090779 AGAAAAAGAAAA
1 AGAAGAAGAAAA
1090791 TATAGAAAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
15 7 0.28
16 18 0.72
ACGTcount: A:0.79, C:0.02, G:0.16, T:0.02
Consensus pattern (16 bp):
AGAAGAAGAAAAAAAC
Found at i:1090788 original size:6 final size:6
Alignment explanation
Indices: 1090750--1090858 Score: 50
Period size: 6 Copynumber: 18.3 Consensus size: 6
1090740 ATATTATAAG
* *
1090750 AAGAAA AA-AAA ACAGAAG AAG-AA AA-AAA TAGAAA AAGAAAA TATAGAAA
1 AAGAAA AAGAAA A-AGAAA AAGAAA AAGAAA AAGAAA AAG-AAA -A-AGAAA
* * * * * * *
1090799 ATGAAA ATGAAA ACGAAG AAG-AA AA-AAA ATGAAA ACGAGA AAG-AA
1 AAGAAA AAGAAA AAGAAA AAGAAA AAGAAA AAGAAA AAGAAA AAGAAA
1090844 AAGAAA AAGAGAA AA
1 AAGAAA AAGA-AA AA
1090859 AAATGAGAGA
Statistics
Matches: 78, Mismatches: 14, Indels: 21
0.69 0.12 0.19
Matches are distributed among these distances:
5 20 0.26
6 41 0.53
7 11 0.14
8 4 0.05
9 2 0.03
ACGTcount: A:0.74, C:0.03, G:0.17, T:0.06
Consensus pattern (6 bp):
AAGAAA
Found at i:1090795 original size:15 final size:15
Alignment explanation
Indices: 1090772--1090806 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
1090762 CAGAAGAAGA
*
1090772 AAAAAATAGAAAAAG
1 AAAATATAGAAAAAG
*
1090787 AAAATATAGAAAATG
1 AAAATATAGAAAAAG
1090802 AAAAT
1 AAAAT
1090807 GAAAACGAAG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.74, C:0.00, G:0.11, T:0.14
Consensus pattern (15 bp):
AAAATATAGAAAAAG
Done.