Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008360.1 Hibiscus syriacus cultivar Beakdansim tig00111099_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: 1563863
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 5 of 7
Found at i:927979 original size:33 final size:33
Alignment explanation
Indices: 927938--928031 Score: 143
Period size: 33 Copynumber: 2.8 Consensus size: 33
927928 GCGACCTACC
*
927938 CTCGCTCGGTTGCCCTCGGATTCCCTCGCATAG
1 CTCGCTCGGTTGCCCTCGGATGCCCTCGCATAG
927971 CTCGCTCGGTTGCCCTCGGATGCCCTCGCATAG
1 CTCGCTCGGTTGCCCTCGGATGCCCTCGCATAG
* * * *
928004 CTCGTTCGGATGGCCTCGGATGCTCTCG
1 CTCGCTCGGTTGCCCTCGGATGCCCTCG
928032 GATGGCCTCG
Statistics
Matches: 56, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 56 1.00
ACGTcount: A:0.09, C:0.37, G:0.28, T:0.27
Consensus pattern (33 bp):
CTCGCTCGGTTGCCCTCGGATGCCCTCGCATAG
Found at i:927994 original size:10 final size:10
Alignment explanation
Indices: 927942--928062 Score: 80
Period size: 10 Copynumber: 11.5 Consensus size: 10
927932 CCTACCCTCG
*
927942 CTCGGTTGCC
1 CTCGGATGCC
*
927952 CTCGGATTCC
1 CTCGGATGCC
*
927962 CTCGCATAGCTC
1 CTCGGAT-GC-C
*
927974 GCTCGGTTGCC
1 -CTCGGATGCC
927985 CTCGGATGCC
1 CTCGGATGCC
*
927995 CTCGCATAGCTC
1 CTCGGAT-GC-C
* *
928007 GTTCGGATGGC
1 -CTCGGATGCC
*
928018 CTCGGATGCT
1 CTCGGATGCC
*
928028 CTCGGATGGC
1 CTCGGATGCC
*
928038 CTCGGATGCT
1 CTCGGATGCC
* *
928048 TTCGGATGGC
1 CTCGGATGCC
928058 CTCGG
1 CTCGG
928063 TCGAATGGCC
Statistics
Matches: 83, Mismatches: 22, Indels: 12
0.71 0.19 0.10
Matches are distributed among these distances:
10 63 0.76
11 5 0.06
12 5 0.06
13 10 0.12
ACGTcount: A:0.09, C:0.34, G:0.31, T:0.26
Consensus pattern (10 bp):
CTCGGATGCC
Found at i:928034 original size:20 final size:20
Alignment explanation
Indices: 927975--928062 Score: 104
Period size: 20 Copynumber: 4.2 Consensus size: 20
927965 GCATAGCTCG
* * *
927975 CTCGGTTGCCCTCGGATGCC
1 CTCGGATGCTCTCGGATGGC
*
927995 CTCGCATAGCTCGTTCGGATGGC
1 CTCGGAT-GCTC--TCGGATGGC
928018 CTCGGATGCTCTCGGATGGC
1 CTCGGATGCTCTCGGATGGC
*
928038 CTCGGATGCTTTCGGATGGC
1 CTCGGATGCTCTCGGATGGC
928058 CTCGG
1 CTCGG
928063 TCGAATGGCC
Statistics
Matches: 59, Mismatches: 6, Indels: 6
0.83 0.08 0.08
Matches are distributed among these distances:
20 38 0.64
21 3 0.05
22 4 0.07
23 14 0.24
ACGTcount: A:0.09, C:0.32, G:0.33, T:0.26
Consensus pattern (20 bp):
CTCGGATGCTCTCGGATGGC
Found at i:928185 original size:29 final size:29
Alignment explanation
Indices: 928127--928227 Score: 139
Period size: 29 Copynumber: 3.4 Consensus size: 29
928117 CTGCATGGAT
** * *
928127 TGCATGGCGACCTACCTAGGTTGTTGGGCG
1 TGCATGGCGACCT-GGTAGGTCGATGGGCG
928157 TGCATGGCGACCTGGTAGGTCGATGGGCG
1 TGCATGGCGACCTGGTAGGTCGATGGGCG
*
928186 TGCATGGCGACCTGGTAGGTCGCTGGGCG
1 TGCATGGCGACCTGGTAGGTCGATGGGCG
*
928215 TGCATGGTGACCT
1 TGCATGGCGACCT
928228 ATATGAGGAC
Statistics
Matches: 65, Mismatches: 6, Indels: 1
0.90 0.08 0.01
Matches are distributed among these distances:
29 52 0.80
30 13 0.20
ACGTcount: A:0.13, C:0.23, G:0.41, T:0.24
Consensus pattern (29 bp):
TGCATGGCGACCTGGTAGGTCGATGGGCG
Found at i:930381 original size:64 final size:64
Alignment explanation
Indices: 930235--930382 Score: 144
Period size: 64 Copynumber: 2.3 Consensus size: 64
930225 GAAGGTGTAT
* ** * *
930235 CGATGAACAAGTAGTGCATCGATGCACTCTTTTAAAATAAAAAGATCGAATGCCATTAGTGCAT
1 CGATGCACAAGTAGTGCATCGATGCACTCCGTTAAAATAAAAACATCGAATGCCATTAGTGCAC
* * *
930299 CGATGCATAAGGCA-TGCATCGATGTA-TCCCGTTAATAAT-AAAACATCGAATG-CATTTCA-T
1 CGATGCACAA-GTAGTGCATCGATGCACT-CCGTTAA-AATAAAAACATCGAATGCCA-TT-AGT
930359 GCAC
61 GCAC
930363 CGATGCACAAGTAGTGCATC
1 CGATGCACAAGTAGTGCATC
930383 AGTGCATACC
Statistics
Matches: 68, Mismatches: 10, Indels: 12
0.76 0.11 0.13
Matches are distributed among these distances:
63 5 0.07
64 57 0.84
65 6 0.09
ACGTcount: A:0.35, C:0.20, G:0.19, T:0.26
Consensus pattern (64 bp):
CGATGCACAAGTAGTGCATCGATGCACTCCGTTAAAATAAAAACATCGAATGCCATTAGTGCAC
Found at i:930807 original size:29 final size:29
Alignment explanation
Indices: 930768--930848 Score: 146
Period size: 29 Copynumber: 2.8 Consensus size: 29
930758 TATGTGATAT
930768 GAGAACATGACATGAGCTACATGATCACAA
1 GAGAA-ATGACATGAGCTACATGATCACAA
930798 GAGAAATGACATGAGCTACATGATCACAA
1 GAGAAATGACATGAGCTACATGATCACAA
930827 GAGAAATGACATGAG-TACATGA
1 GAGAAATGACATGAGCTACATGA
930849 ACATATGGAA
Statistics
Matches: 51, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
28 7 0.14
29 39 0.76
30 5 0.10
ACGTcount: A:0.44, C:0.16, G:0.22, T:0.17
Consensus pattern (29 bp):
GAGAAATGACATGAGCTACATGATCACAA
Found at i:930951 original size:15 final size:15
Alignment explanation
Indices: 930933--930966 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
930923 GAGGGTATAA
930933 TAGTCATTCGGGACG
1 TAGTCATTCGGGACG
* *
930948 TAGTCCTTCGGGATG
1 TAGTCATTCGGGACG
930963 TAGT
1 TAGT
930967 GGTCCTACGG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.18, C:0.18, G:0.32, T:0.32
Consensus pattern (15 bp):
TAGTCATTCGGGACG
Found at i:931847 original size:26 final size:26
Alignment explanation
Indices: 931818--931872 Score: 101
Period size: 26 Copynumber: 2.1 Consensus size: 26
931808 ACCCGATTAT
*
931818 CCGAACTGATTTACCAGACCCAATAC
1 CCGAACCGATTTACCAGACCCAATAC
931844 CCGAACCGATTTACCAGACCCAATAC
1 CCGAACCGATTTACCAGACCCAATAC
931870 CCG
1 CCG
931873 TTATTAACCT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.33, C:0.38, G:0.13, T:0.16
Consensus pattern (26 bp):
CCGAACCGATTTACCAGACCCAATAC
Found at i:933204 original size:2 final size:2
Alignment explanation
Indices: 933199--933251 Score: 92
Period size: 2 Copynumber: 27.5 Consensus size: 2
933189 ATAGGAAGAA
933199 AT AT AT AT AT AT AT AT AT AT AT A- AT AT AT A- 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
933239 AT AT AT AT AT AT A
1 AT AT AT AT AT AT A
933252 ACCACTAATT
Statistics
Matches: 49, Mismatches: 0, Indels: 4
0.92 0.00 0.08
Matches are distributed among these distances:
1 2 0.04
2 47 0.96
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:933392 original size:3 final size:3
Alignment explanation
Indices: 933384--933419 Score: 63
Period size: 3 Copynumber: 12.0 Consensus size: 3
933374 ATCCAAATTT
*
933384 TAA TAA TAA TAA TAA TAA TAG TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
933420 ATTGAGCGGA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:936159 original size:2 final size:2
Alignment explanation
Indices: 936152--936176 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
936142 AAAGTTTTAC
936152 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
936177 GAGAGAGAGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:936181 original size:2 final size:2
Alignment explanation
Indices: 936176--936203 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
936166 ATATATATAT
936176 AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG
936204 GGTGGGTTAG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:938411 original size:29 final size:29
Alignment explanation
Indices: 938352--938461 Score: 197
Period size: 29 Copynumber: 3.9 Consensus size: 29
938342 AGTACCGGGT
938352 AGGTCGCCATGCAC-CCC-GCGACCAACC
1 AGGTCGCCATGCACGCCCGGCGACCAACC
938379 AGGTCGCCATGCACGCCCGGCGACCAACC
1 AGGTCGCCATGCACGCCCGGCGACCAACC
938408 AGGTCGCCATGCACGCCCGGCGACCAACC
1 AGGTCGCCATGCACGCCCGGCGACCAACC
*
938437 AGGTCGCCATGCACGCCCTGCGACC
1 AGGTCGCCATGCACGCCCGGCGACC
938462 TACCCCACGA
Statistics
Matches: 80, Mismatches: 1, Indels: 2
0.96 0.01 0.02
Matches are distributed among these distances:
27 14 0.17
28 3 0.04
29 63 0.79
ACGTcount: A:0.20, C:0.45, G:0.26, T:0.08
Consensus pattern (29 bp):
AGGTCGCCATGCACGCCCGGCGACCAACC
Found at i:938483 original size:32 final size:32
Alignment explanation
Indices: 938443--938575 Score: 104
Period size: 32 Copynumber: 4.4 Consensus size: 32
938433 AACCAGGTCG
* * *
938443 CCATGCACGCCCT-GCGACCTACCCCACGACCT
1 CCATGCACGCCCTACCG-CCCACCCAACGACCT
938475 CCATGCACGCCCTACCGCCCACCCAACGACCT
1 CCATGCACGCCCTACCGCCCACCCAACGACCT
* *
938507 CC-TGCATGCCC-A--G-GCACTCCAACGA-CT
1 CCATGCACGCCCTACCGCCCAC-CCAACGACCT
* * * *
938534 CCATGCACGGCC-A-TGCACGCCCAACGACCT
1 CCATGCACGCCCTACCGCCCACCCAACGACCT
938564 CCATGCACGCCC
1 CCATGCACGCCC
938576 AGCTCGCCAA
Statistics
Matches: 85, Mismatches: 10, Indels: 14
0.78 0.09 0.13
Matches are distributed among these distances:
27 7 0.08
28 16 0.19
29 8 0.09
30 16 0.19
31 8 0.09
32 28 0.33
33 2 0.02
ACGTcount: A:0.21, C:0.51, G:0.17, T:0.11
Consensus pattern (32 bp):
CCATGCACGCCCTACCGCCCACCCAACGACCT
Found at i:938540 original size:28 final size:30
Alignment explanation
Indices: 938468--938577 Score: 118
Period size: 28 Copynumber: 3.7 Consensus size: 30
938458 GACCTACCCC
* * *
938468 ACGACCTCCATGCACGCCCTACCGCCCACCCA
1 ACGACCTCCATGCACGCCC-A-GGCACGCCCA
* *
938500 ACGACCTCC-TGCATGCCCAGGCAC-TCCA
1 ACGACCTCCATGCACGCCCAGGCACGCCCA
* *
938528 ACGA-CTCCATGCACGGCCATGCACGCCCA
1 ACGACCTCCATGCACGCCCAGGCACGCCCA
938557 ACGACCTCCATGCACGCCCAG
1 ACGACCTCCATGCACGCCCAG
938578 CTCGCCAAAG
Statistics
Matches: 65, Mismatches: 10, Indels: 8
0.78 0.12 0.10
Matches are distributed among these distances:
27 4 0.06
28 19 0.29
29 10 0.15
30 15 0.23
31 8 0.12
32 9 0.14
ACGTcount: A:0.23, C:0.49, G:0.17, T:0.11
Consensus pattern (30 bp):
ACGACCTCCATGCACGCCCAGGCACGCCCA
Found at i:939226 original size:20 final size:21
Alignment explanation
Indices: 939179--939226 Score: 62
Period size: 20 Copynumber: 2.3 Consensus size: 21
939169 ACAGAAATTT
939179 AGTTAATTAGTTTGTTAGTATA
1 AGTT-ATTAGTTTGTTAGTATA
* *
939201 AATTATTAG-TTGTTAGTTTA
1 AGTTATTAGTTTGTTAGTATA
939221 AGTTAT
1 AGTTAT
939227 ATTATATTAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
20 15 0.65
21 5 0.22
22 3 0.13
ACGTcount: A:0.31, C:0.00, G:0.17, T:0.52
Consensus pattern (21 bp):
AGTTATTAGTTTGTTAGTATA
Found at i:939260 original size:30 final size:28
Alignment explanation
Indices: 939210--939265 Score: 85
Period size: 28 Copynumber: 1.9 Consensus size: 28
939200 AAATTATTAG
*
939210 TTGTTAGTTTAAGTTATATTATATTAAT
1 TTGTTAGTTTAAGTTATATTAGATTAAT
939238 TTGTTAGTTTAAGTTATATATTAGATTA
1 TTGTTAGTTTAAG-T-TATATTAGATTA
939266 TATAAAAAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
28 13 0.52
29 1 0.04
30 11 0.44
ACGTcount: A:0.32, C:0.00, G:0.12, T:0.55
Consensus pattern (28 bp):
TTGTTAGTTTAAGTTATATTAGATTAAT
Found at i:942364 original size:60 final size:59
Alignment explanation
Indices: 942291--943057 Score: 1173
Period size: 60 Copynumber: 13.2 Consensus size: 59
942281 GTATTTATAA
*
942291 GATTTAGTAATGATTAGTAATGATGAAATTATTATTAATTTTTAATGATTTGATAGTAAT
1 GATTTAGTAATGATTAGTAATAATGAAATTATTATTAATTTTT-ATGATTTGATAGTAAT
*
942351 GATTTAGTAATGATTAGTAATAATGAAATTATTATTAATTATGTATGATTTGATAGTAAT
1 GATTTAGTAATGATTAGTAATAATGAAATTATTATTAATT-TTTATGATTTGATAGTAAT
*
942411 GATTTAGTAATGATTAGTAATAATG-AATTATTATTAATTTTAATGA-TTGATAGTAAT
1 GATTTAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTATGATTTGATAGTAAT
* *
942468 GATTTAGTAATGATTAGTAATAATGAAATTATTATTAATTATGTATGATTTGTTAGTAAT
1 GATTTAGTAATGATTAGTAATAATGAAATTATTATTAATT-TTTATGATTTGATAGTAAT
*
942528 GATTTAGTAATGATTAGTAATAATGAAATTATTATTAATTTTAATGATTTGATAGTAAT
1 GATTTAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTATGATTTGATAGTAAT
*
942587 GATTTAGTAATGATTAGTAATAATGAAATTATTA-TAATTATGTATGATTTGATAGTAAT
1 GATTTAGTAATGATTAGTAATAATGAAATTATTATTAATT-TTTATGATTTGATAGTAAT
942646 GATTTAGTAATGA-TAGTAATAATGAAATTATT-TTAA-TTTT-T-A--TGATAGTAAT
1 GATTTAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTATGATTTGATAGTAAT
*
942698 GATTTAGTAATGATTAGTAATAATG-AA--ATTATTAATTATGTATGATTTGATAGTAAT
1 GATTTAGTAATGATTAGTAATAATGAAATTATTATTAATT-TTTATGATTTGATAGTAAT
942755 GGATTTAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGATAGTAAT
1 -GATTTAGTAATGATTAGTAATAATGAAATTATTATTAATTTTT-ATGATTTGATAGTAAT
*
942816 GATTTAGTAATGATTAGTAATAATGAAATTATTATTAATTATGTATGATTTGATAGTAAT
1 GATTTAGTAATGATTAGTAATAATGAAATTATTATTAATT-TTTATGATTTGATAGTAAT
*
942876 GATTTA--AATGATTAGT-ATAAT-AAATGATTATTAATTTTTAATGATTTGATAGTAAT
1 GATTTAGTAATGATTAGTAATAATGAAATTATTATTAATTTTT-ATGATTTGATAGTAAT
* *
942932 GATTTAGTAATGATTAG---TAATGAAATTATTATTAATTATGTATGATTTAATAGTAAT
1 GATTTAGTAATGATTAGTAATAATGAAATTATTATTAATT-TTTATGATTTGATAGTAAT
942989 GATTTAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGA-TTGATAGTAAT
1 GATTTAGTAATGATTAGTAATAATGAAATTATTATTAATTTTT-ATGATTTGATAGTAAT
943048 GA-TTAGTAAT
1 GATTTAGTAAT
943058 AATAATTTAT
Statistics
Matches: 655, Mismatches: 23, Indels: 60
0.89 0.03 0.08
Matches are distributed among these distances:
50 3 0.00
51 4 0.01
52 26 0.04
53 13 0.02
54 2 0.00
55 4 0.01
56 42 0.06
57 98 0.15
58 100 0.15
59 115 0.18
60 218 0.33
61 30 0.05
ACGTcount: A:0.40, C:0.00, G:0.14, T:0.46
Consensus pattern (59 bp):
GATTTAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTATGATTTGATAGTAAT
Found at i:942544 original size:21 final size:20
Alignment explanation
Indices: 942520--942608 Score: 60
Period size: 21 Copynumber: 4.5 Consensus size: 20
942510 GTATGATTTG
942520 TTAGTAATGATTTAGTAATGA
1 TTAGTAAT-ATTTAGTAATGA
* * *
942541 TTAGTAATA-AT-GAAATTA
1 TTAGTAATATTTAGTAATGA
* * *
942559 TTATTAAT-TTTAATGATTTGA
1 TTAGTAATATTTAGT-A-ATGA
942580 -TAGTAATGATTTAGTAATGA
1 TTAGTAAT-ATTTAGTAATGA
942600 TTAGTAATA
1 TTAGTAATA
942609 ATGAAATTAT
Statistics
Matches: 49, Mismatches: 12, Indels: 15
0.64 0.16 0.20
Matches are distributed among these distances:
18 13 0.27
19 1 0.02
20 12 0.24
21 18 0.37
22 5 0.10
ACGTcount: A:0.40, C:0.00, G:0.15, T:0.45
Consensus pattern (20 bp):
TTAGTAATATTTAGTAATGA
Found at i:942561 original size:177 final size:178
Alignment explanation
Indices: 942291--943108 Score: 1190
Period size: 177 Copynumber: 4.7 Consensus size: 178
942281 GTATTTATAA
*
942291 GATTTAGTAATGATTAGTAATGATGAAATTATTATTAATTTTTAATGATTTGATAGTAATGATTT
1 GATTTAGTAATGATTAGTAATAATGAAATTATTATTAA-TTTT-ATGATTTGATAGTAATGATTT
942356 AGTAATGATTAGTAATAATGAAATTATTATTAATTATGT-ATGATTTGATAGTAATGATTTAGTA
64 AGTAATGATTAGTAATAATGAAATTATTATTAATTAT-TAATGATTTGATAGTAATGATTTAGTA
942420 ATGATTAGTAATAATG-AATTATTATTAATT-T-TAATGA-TTGATAGTAAT
128 ATGATTAGTAATAATGAAATTATTATTAATTATGT-ATGATTTGATAGTAAT
*
942468 GATTTAGTAATGATTAGTAATAATGAAATTATTATTAATTATGTATGATTTGTTAGTAATGATTT
1 GATTTAGTAATGATTAGTAATAATGAAATTATTATTAATT-T-TATGATTTGATAGTAATGATTT
942533 AGTAATGATTAGTAATAATGAAATTATTATTAATT-TTAATGATTTGATAGTAATGATTTAGTAA
64 AGTAATGATTAGTAATAATGAAATTATTATTAATTATTAATGATTTGATAGTAATGATTTAGTAA
942597 TGATTAGTAATAATGAAATTATTA-TAATTATGTATGATTTGATAGTAAT
129 TGATTAGTAATAATGAAATTATTATTAATTATGTATGATTTGATAGTAAT
942646 GATTTAGTAATGA-TAGTAATAATGAAATTATT-TTAATTTT-T-A--TGATAGTAATGATTTAG
1 GATTTAGTAATGATTAGTAATAATGAAATTATTATTAATTTTATGATTTGATAGTAATGATTTAG
942705 TAATGATTAGTAATAATG-AA--ATTATTAATTATGT-ATGATTTGATAGTAATGGATTTAGTAA
66 TAATGATTAGTAATAATGAAATTATTATTAATTAT-TAATGATTTGATAGTAAT-GATTTAGTAA
*
942766 TGATTAGTAATAATGAAATTATTATTAATT-TTTAATGATTTGATAGTAAT
129 TGATTAGTAATAATGAAATTATTATTAATTATGT-ATGATTTGATAGTAAT
942816 GATTTAGTAATGATTAGTAATAATGAAATTATTATTAATTATGTATGATTTGATAGTAATGATTT
1 GATTTAGTAATGATTAGTAATAATGAAATTATTATTAATT-T-TATGATTTGATAGTAATGATTT
* *
942881 A--AATGATTAGT-ATAAT-AAATGATTATTAATTTTTAATGATTTGATAGTAATGATTTAGTAA
64 AGTAATGATTAGTAATAATGAAATTATTATTAATTATTAATGATTTGATAGTAATGATTTAGTAA
*
942942 TGATTAG---TAATGAAATTATTATTAATTATGTATGATTTAATAGTAAT
129 TGATTAGTAATAATGAAATTATTATTAATTATGTATGATTTGATAGTAAT
*
942989 GATTTAGTAATGATTAGTAATAATGAAATTATTATTAATTTT-T-A----AT-G-ATTGA--TAG
1 GATTTAGTAATGATTAGTAATAATGAAATTATTATTAATTTTATGATTTGATAGTAATGATTTAG
* *
943044 TAATGATTAGTAATAAT-AATTTATTATTAA-TATTAATGATTTGATA-TTATGATTTAGTAATG
66 TAATGATTAGTAATAATGAAATTATTATTAATTATTAATGATTTGATAGTAATGATTTAGTAATG
943106 ATT
131 ATT
943109 TGATAGTAAT
Statistics
Matches: 601, Mismatches: 12, Indels: 71
0.88 0.02 0.10
Matches are distributed among these distances:
161 2 0.00
162 18 0.03
163 29 0.05
164 17 0.03
165 2 0.00
167 10 0.02
168 17 0.03
169 40 0.07
170 69 0.11
171 20 0.03
172 8 0.01
173 77 0.13
174 4 0.01
175 10 0.02
176 84 0.14
177 152 0.25
178 42 0.07
ACGTcount: A:0.40, C:0.00, G:0.14, T:0.46
Consensus pattern (178 bp):
GATTTAGTAATGATTAGTAATAATGAAATTATTATTAATTTTATGATTTGATAGTAATGATTTAG
TAATGATTAGTAATAATGAAATTATTATTAATTATTAATGATTTGATAGTAATGATTTAGTAATG
ATTAGTAATAATGAAATTATTATTAATTATGTATGATTTGATAGTAAT
Found at i:942605 original size:10 final size:11
Alignment explanation
Indices: 942404--942607 Score: 71
Period size: 11 Copynumber: 17.6 Consensus size: 11
942394 TATGATTTGA
942404 TAGTAATGATT
1 TAGTAATGATT
942415 TAGTAATGATT
1 TAGTAATGATT
* *
942426 AGTAATAATGAAT
1 --TAGTAATGATT
* * *
942439 TATTATTAATT
1 TAGTAATGATT
942450 T--TAATGATT
1 TAGTAATGATT
942459 GATAGTAATGATT
1 --TAGTAATGATT
942472 TAGTAATGATT
1 TAGTAATGATT
* *
942483 AGTAATAATGAAAT
1 --TAGTAATG-ATT
* * *
942497 TA-TTATTAAT
1 TAGTAATGATT
942507 TATGT-ATGATTTGT
1 TA-GTAATGA--T-T
942521 TAGTAATGATT
1 TAGTAATGATT
942532 TAGTAATGATT
1 TAGTAATGATT
* *
942543 AGTAATAATGAAAT
1 --TAGTAATG-ATT
* * *
942557 TATTATTAATT
1 TAGTAATGATT
942568 T--TAATGATTT
1 TAGTAATGA-TT
942578 GATAGTAATGATT
1 --TAGTAATGATT
942591 TAGTAATGA-T
1 TAGTAATGATT
942601 TAGTAAT
1 TAGTAAT
942608 AATGAAATTA
Statistics
Matches: 148, Mismatches: 22, Indels: 47
0.68 0.10 0.22
Matches are distributed among these distances:
9 10 0.07
10 15 0.10
11 61 0.41
12 10 0.07
13 35 0.24
14 17 0.11
ACGTcount: A:0.40, C:0.00, G:0.15, T:0.46
Consensus pattern (11 bp):
TAGTAATGATT
Found at i:942941 original size:11 final size:11
Alignment explanation
Indices: 942925--943009 Score: 61
Period size: 11 Copynumber: 7.6 Consensus size: 11
942915 AATGATTTGA
942925 TAGTAATGATT
1 TAGTAATGATT
942936 TAGTAATGA-T
1 TAGTAATGATT
*
942946 TAGTAATGAAAT
1 TAGTAATG-ATT
* * *
942958 TA-TTATTAAT
1 TAGTAATGATT
942968 TATGT-ATGATTT
1 TA-GTAATGA-TT
942980 AATAGTAATGATT
1 --TAGTAATGATT
942993 TAGTAATGA-T
1 TAGTAATGATT
943003 TAGTAAT
1 TAGTAAT
943010 AATGAAATTA
Statistics
Matches: 62, Mismatches: 4, Indels: 17
0.75 0.05 0.20
Matches are distributed among these distances:
10 22 0.35
11 25 0.40
12 5 0.08
13 4 0.06
14 6 0.10
ACGTcount: A:0.40, C:0.00, G:0.15, T:0.45
Consensus pattern (11 bp):
TAGTAATGATT
Found at i:942949 original size:21 final size:21
Alignment explanation
Indices: 942925--943009 Score: 66
Period size: 21 Copynumber: 3.9 Consensus size: 21
942915 AATGATTTGA
942925 TAGTAATGATTTAGTAATGAT
1 TAGTAATGATTTAGTAATGAT
* * * *
942946 TAGTAATGAAATTATTATTAAT
1 TAGTAATG-ATTTAGTAATGAT
942968 TATGT-ATGATTTAATAGTAATGATT
1 TA-GTAATGA-TT--TAGTAATGA-T
942993 TAGTAATGA-TTAGTAAT
1 TAGTAATGATTTAGTAAT
943010 AATGAAATTA
Statistics
Matches: 49, Mismatches: 8, Indels: 14
0.69 0.11 0.20
Matches are distributed among these distances:
21 16 0.33
22 15 0.31
23 3 0.06
24 8 0.16
25 7 0.14
ACGTcount: A:0.40, C:0.00, G:0.15, T:0.45
Consensus pattern (21 bp):
TAGTAATGATTTAGTAATGAT
Found at i:943090 original size:14 final size:14
Alignment explanation
Indices: 943077--943123 Score: 57
Period size: 14 Copynumber: 3.6 Consensus size: 14
943067 TTATTAATAT
943077 TAATGATTTGATA-
1 TAATGATTTGATAG
*
943090 TTATGA-TT--TAG
1 TAATGATTTGATAG
943101 TAATGATTTGATAG
1 TAATGATTTGATAG
943115 TAATGATTT
1 TAATGATTT
943124 ACGACTTGAA
Statistics
Matches: 28, Mismatches: 2, Indels: 7
0.76 0.05 0.19
Matches are distributed among these distances:
10 2 0.07
11 5 0.18
12 4 0.14
13 5 0.18
14 12 0.43
ACGTcount: A:0.34, C:0.00, G:0.17, T:0.49
Consensus pattern (14 bp):
TAATGATTTGATAG
Found at i:943106 original size:24 final size:25
Alignment explanation
Indices: 943077--943124 Score: 80
Period size: 24 Copynumber: 2.0 Consensus size: 25
943067 TTATTAATAT
*
943077 TAATGATTTGATA-TTATGATTTAG
1 TAATGATTTGATAGTAATGATTTAG
943101 TAATGATTTGATAGTAATGATTTA
1 TAATGATTTGATAGTAATGATTTA
943125 CGACTTGAAC
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
24 13 0.59
25 9 0.41
ACGTcount: A:0.35, C:0.00, G:0.17, T:0.48
Consensus pattern (25 bp):
TAATGATTTGATAGTAATGATTTAG
Found at i:943208 original size:7 final size:7
Alignment explanation
Indices: 943196--943222 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
943186 ATTTTTGGTT
943196 CAATGAA
1 CAATGAA
943203 CAATGAA
1 CAATGAA
943210 CAATGAA
1 CAATGAA
943217 CAATGA
1 CAATGA
943223 TTTAGTAATA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.56, C:0.15, G:0.15, T:0.15
Consensus pattern (7 bp):
CAATGAA
Found at i:943259 original size:11 final size:11
Alignment explanation
Indices: 943228--943469 Score: 52
Period size: 11 Copynumber: 20.5 Consensus size: 11
943218 AATGATTTAG
*
943228 TAATAATCATT
1 TAATAATGATT
943239 ATAA-AATGATT
1 -TAATAATGATT
943250 TAATAATGATT
1 TAATAATGATT
943261 T-A-AAT-ATT
1 TAATAATGATT
943269 TAATGATTTGATGATT
1 TAAT-A----ATGATT
*
943285 TAGTAATGATTT
1 TAATAATGA-TT
*
943297 GATAATAATCATT
1 --TAATAATGATT
*
943310 ATAGTAATGATTT
1 -TAATAATGA-TT
*
943323 AGTAATAATCATT
1 --TAATAATGATT
*
943336 ATAAAAATGATT
1 -TAATAATGATT
943348 T--TAATGATT
1 TAATAATGATT
943357 T-A-AAT-ATT
1 TAATAATGATT
943365 TAATGATTTGATGATT
1 TAAT-A----ATGATT
*
943381 TAGTAATGATTT
1 TAATAATGA-TT
*
943393 GATAATAATCATT
1 --TAATAATGATT
943406 ATAATAATGATT
1 -TAATAATGATT
* *
943418 TTATAATAATTAT
1 TAATAATGA-T-T
* * *
943431 TATGTTATTATT
1 TA-ATAATGATT
* *
943443 TAGTAATTATT
1 TAATAATGATT
943454 TAATAATGATT
1 TAATAATGATT
943465 TAATA
1 TAATA
943470 TTATTACTAA
Statistics
Matches: 175, Mismatches: 26, Indels: 59
0.67 0.10 0.23
Matches are distributed among these distances:
8 8 0.05
9 16 0.09
10 4 0.02
11 54 0.31
12 39 0.22
13 11 0.06
14 25 0.14
15 6 0.03
16 12 0.07
ACGTcount: A:0.42, C:0.02, G:0.10, T:0.47
Consensus pattern (11 bp):
TAATAATGATT
Found at i:943269 original size:19 final size:22
Alignment explanation
Indices: 943228--943272 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 22
943218 AATGATTTAG
943228 TAATAATCATTATAAAATGATT
1 TAATAATCATTATAAAATGATT
*
943250 TAATAATGATT-T-AAAT-ATT
1 TAATAATCATTATAAAATGATT
943269 TAAT
1 TAAT
943273 GATTTGATGA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
19 7 0.32
20 4 0.18
21 1 0.05
22 10 0.45
ACGTcount: A:0.49, C:0.02, G:0.04, T:0.44
Consensus pattern (22 bp):
TAATAATCATTATAAAATGATT
Found at i:943314 original size:26 final size:26
Alignment explanation
Indices: 943288--943433 Score: 112
Period size: 26 Copynumber: 5.9 Consensus size: 26
943278 GATGATTTAG
*
943288 TAATGATTTGATAATAATCATTATAG
1 TAATGATTTGATAATAATCATTATAA
943314 TAATGATTT-AGTAATAATCATTATAA
1 TAATGATTTGA-TAATAATCATTATAA
* *
943340 AAATGATTT--TAATGAT--TTA-AA
1 TAATGATTTGATAATAATCATTATAA
* * * * * * *
943361 TATTTA-ATGAT-TTGATGATT-TAG
1 TAATGATTTGATAATAATCATTATAA
943384 TAATGATTTGATAATAATCATTATAA
1 TAATGATTTGATAATAATCATTATAA
* *
943410 TAATGATTTTATAATAATTATTAT
1 TAATGATTTGATAATAATCATTAT
943434 GTTATTATTT
Statistics
Matches: 93, Mismatches: 18, Indels: 18
0.72 0.14 0.14
Matches are distributed among these distances:
20 1 0.01
21 9 0.10
22 4 0.04
23 7 0.08
24 10 0.11
25 7 0.08
26 55 0.59
ACGTcount: A:0.42, C:0.02, G:0.10, T:0.46
Consensus pattern (26 bp):
TAATGATTTGATAATAATCATTATAA
Found at i:943368 original size:96 final size:96
Alignment explanation
Indices: 943218--943433 Score: 373
Period size: 96 Copynumber: 2.2 Consensus size: 96
943208 AACAATGAAC
943218 AATGATTTAGTAATAATCATTATAAAATGATTTAATAATGATTTAAATATTTAATGATTTGATGA
1 AATGATTTAGTAATAATCATTATAAAATGATTT-ATAATGATTTAAATATTTAATGATTTGATGA
*
943283 TTTAGTAATGATTTGATAATAATCATTATAGT
65 TTTAGTAATGATTTGATAATAATCATTATAAT
943315 AATGATTTAGTAATAATCATTATAAAAATGATTT-TAATGATTTAAATATTTAATGATTTGATGA
1 AATGATTTAGTAATAATCATTAT-AAAATGATTTATAATGATTTAAATATTTAATGATTTGATGA
943379 TTTAGTAATGATTTGATAATAATCATTATAAT
65 TTTAGTAATGATTTGATAATAATCATTATAAT
*
943411 AATGATTTTA-TAATAATTATTAT
1 AATGA-TTTAGTAATAATCATTAT
943434 GTTATTATTT
Statistics
Matches: 115, Mismatches: 2, Indels: 5
0.94 0.02 0.04
Matches are distributed among these distances:
96 78 0.68
97 27 0.23
98 10 0.09
ACGTcount: A:0.43, C:0.02, G:0.10, T:0.45
Consensus pattern (96 bp):
AATGATTTAGTAATAATCATTATAAAATGATTTATAATGATTTAAATATTTAATGATTTGATGAT
TTAGTAATGATTTGATAATAATCATTATAAT
Found at i:943381 original size:16 final size:17
Alignment explanation
Indices: 943340--943382 Score: 54
Period size: 16 Copynumber: 2.6 Consensus size: 17
943330 ATCATTATAA
943340 AAATGATTTTAATGATTT
1 AAATGA-TTTAATGATTT
943358 AAAT-ATTTAATGATTT
1 AAATGATTTAATGATTT
*
943374 -GATGATTTA
1 AAATGATTTA
943383 GTAATGATTT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
15 2 0.09
16 16 0.70
17 1 0.04
18 4 0.17
ACGTcount: A:0.40, C:0.00, G:0.12, T:0.49
Consensus pattern (17 bp):
AAATGATTTAATGATTT
Found at i:943401 original size:14 final size:13
Alignment explanation
Indices: 943384--943427 Score: 54
Period size: 14 Copynumber: 3.3 Consensus size: 13
943374 GATGATTTAG
943384 TAATGATTTGATAA
1 TAATGATTT-ATAA
*
943398 TAATCA-TTATAA
1 TAATGATTTATAA
943410 TAATGATTTTATAA
1 TAATGA-TTTATAA
943424 TAAT
1 TAAT
943428 TATTATGTTA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
12 9 0.35
13 2 0.08
14 15 0.58
ACGTcount: A:0.45, C:0.02, G:0.07, T:0.45
Consensus pattern (13 bp):
TAATGATTTATAA
Found at i:943590 original size:14 final size:13
Alignment explanation
Indices: 943571--943635 Score: 50
Period size: 14 Copynumber: 5.2 Consensus size: 13
943561 TTTAAATATT
943571 TAATGATTTGATAC
1 TAATGATTT-ATAC
943585 TAATGA-TT-TAC
1 TAATGATTTATAC
*
943596 TAAT--TAT-TAC
1 TAATGATTTATAC
943606 TAATGATTTAATAC
1 TAATGATTT-ATAC
*
943620 TAATTATTTGATAC
1 TAATGATTT-ATAC
943634 TA
1 TA
943636 GTAATTATTG
Statistics
Matches: 42, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
10 8 0.19
11 7 0.17
12 2 0.05
13 2 0.05
14 23 0.55
ACGTcount: A:0.38, C:0.08, G:0.08, T:0.46
Consensus pattern (13 bp):
TAATGATTTATAC
Found at i:943607 original size:10 final size:11
Alignment explanation
Indices: 943582--943615 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
943572 AATGATTTGA
943582 TACTAATGATT
1 TACTAATGATT
*
943593 TACTAATTA-T
1 TACTAATGATT
943603 TACTAATGATT
1 TACTAATGATT
943614 TA
1 TA
943616 ATACTAATTA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
10 9 0.45
11 11 0.55
ACGTcount: A:0.38, C:0.09, G:0.06, T:0.47
Consensus pattern (11 bp):
TACTAATGATT
Found at i:943625 original size:21 final size:21
Alignment explanation
Indices: 943582--943625 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
943572 AATGATTTGA
* *
943582 TACTAATGATTTACTAATTAT
1 TACTAATGATTTAATAATAAT
*
943603 TACTAATGATTTAATACTAAT
1 TACTAATGATTTAATAATAAT
943624 TA
1 TA
943626 TTTGATACTA
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:0.41, C:0.09, G:0.05, T:0.45
Consensus pattern (21 bp):
TACTAATGATTTAATAATAAT
Found at i:943648 original size:16 final size:17
Alignment explanation
Indices: 943620--943651 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
943610 GATTTAATAC
943620 TAATTATTTGATACTAG
1 TAATTATTTGATACTAG
943637 TAATTA-TTGATACTA
1 TAATTATTTGATACTA
943652 AACATCATTG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.38, C:0.06, G:0.09, T:0.47
Consensus pattern (17 bp):
TAATTATTTGATACTAG
Found at i:945794 original size:15 final size:14
Alignment explanation
Indices: 945771--945801 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 14
945761 TACAACACTA
945771 AACTTTAATATAAT
1 AACTTTAATATAAT
945785 AACTTATAATATAAT
1 AACTT-TAATATAAT
945800 AA
1 AA
945802 ACTAATAAAC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.31
15 11 0.69
ACGTcount: A:0.55, C:0.06, G:0.00, T:0.39
Consensus pattern (14 bp):
AACTTTAATATAAT
Found at i:945809 original size:16 final size:16
Alignment explanation
Indices: 945776--945822 Score: 53
Period size: 16 Copynumber: 3.0 Consensus size: 16
945766 CACTAAACTT
*
945776 TAATATAAT-AACTTA
1 TAATATAATAAACTAA
945791 TAATATAATAAACTAA
1 TAATATAATAAACTAA
*
945807 TAA-ACTAACAAACTAA
1 TAATA-TAATAAACTAA
945823 ACTTTTTAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
15 10 0.36
16 18 0.64
ACGTcount: A:0.60, C:0.11, G:0.00, T:0.30
Consensus pattern (16 bp):
TAATATAATAAACTAA
Found at i:945943 original size:12 final size:12
Alignment explanation
Indices: 945918--945970 Score: 63
Period size: 12 Copynumber: 4.3 Consensus size: 12
945908 TTTTTCATTA
*
945918 TAATATACT-AC
1 TAATAAACTAAC
*
945929 TAATAAACTTAC
1 TAATAAACTAAC
945941 TAACTAAAACTAAC
1 TAA-T-AAACTAAC
945955 TAATAAACTAAC
1 TAATAAACTAAC
945967 TAAT
1 TAAT
945971 TTTTATATAA
Statistics
Matches: 37, Mismatches: 2, Indels: 5
0.84 0.05 0.11
Matches are distributed among these distances:
11 8 0.22
12 17 0.46
13 2 0.05
14 10 0.27
ACGTcount: A:0.53, C:0.17, G:0.00, T:0.30
Consensus pattern (12 bp):
TAATAAACTAAC
Found at i:946069 original size:42 final size:42
Alignment explanation
Indices: 945999--946128 Score: 104
Period size: 42 Copynumber: 3.0 Consensus size: 42
945989 CAACAAACAA
945999 ATATAACTTAACTATTTAACTAACAAAACTAATTAAATAATTTTTTT
1 ATATAAC-TAACTA-TTAAC--A-AAAACTAATTAAATAATTTTTTT
* * *
946046 ATATAACTAACTATTAACAAAAACAAACT-ATTAATTATTTTT
1 ATATAACTAACTATTAACAAAAACTAATTAAATAATT-TTTTT
* * *
946088 A-ACTATA-TAACTATCAAACATATACTAATTAAATAATTTTT
1 ATA-TA-ACTAACTAT-TAACAAAAACTAATTAAATAATTTTT
946129 AATTTATGTA
Statistics
Matches: 69, Mismatches: 9, Indels: 14
0.75 0.10 0.15
Matches are distributed among these distances:
41 7 0.10
42 23 0.33
43 15 0.22
44 6 0.09
45 5 0.07
46 6 0.09
47 7 0.10
ACGTcount: A:0.48, C:0.12, G:0.00, T:0.40
Consensus pattern (42 bp):
ATATAACTAACTATTAACAAAAACTAATTAAATAATTTTTTT
Found at i:946221 original size:16 final size:18
Alignment explanation
Indices: 946192--946230 Score: 55
Period size: 16 Copynumber: 2.3 Consensus size: 18
946182 ACTAATTAAC
*
946192 ATTTATAATAATAAACTA
1 ATTTATAATAATAAACAA
946210 ATTTA-AAT-ATAAACAA
1 ATTTATAATAATAAACAA
946226 ATTTA
1 ATTTA
946231 CCTTATCTCC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 12 0.60
17 3 0.15
18 5 0.25
ACGTcount: A:0.56, C:0.05, G:0.00, T:0.38
Consensus pattern (18 bp):
ATTTATAATAATAAACAA
Found at i:946519 original size:49 final size:49
Alignment explanation
Indices: 946442--946548 Score: 175
Period size: 49 Copynumber: 2.2 Consensus size: 49
946432 TAGGATCACA
*
946442 TGGCATGC-TGTAGGCATGCAGCGGGGAGCAGGAGCACGTGAAGTTATCT
1 TGGCATGCATGCAGGCATGCAGCGGGGAGCAGGAGCACGTGAAGTTAT-T
946491 TGGCATGCATGCAGGCATGCAGC-GGGAGCAGGAGCACGTGAAGTTATT
1 TGGCATGCATGCAGGCATGCAGCGGGGAGCAGGAGCACGTGAAGTTATT
946539 TGGC-TGCATG
1 TGGCATGCATG
946549 TGCATGCATG
Statistics
Matches: 56, Mismatches: 1, Indels: 4
0.92 0.02 0.07
Matches are distributed among these distances:
47 6 0.11
48 5 0.09
49 32 0.57
50 13 0.23
ACGTcount: A:0.22, C:0.19, G:0.38, T:0.21
Consensus pattern (49 bp):
TGGCATGCATGCAGGCATGCAGCGGGGAGCAGGAGCACGTGAAGTTATT
Found at i:946616 original size:29 final size:29
Alignment explanation
Indices: 946583--946677 Score: 163
Period size: 29 Copynumber: 3.3 Consensus size: 29
946573 TGGACGCCGG
946583 GGCGACCTACAAGGTCGCCGGGACTACAT
1 GGCGACCTACAAGGTCGCCGGGACTACAT
946612 GGCGACCTACAAGGTCGCCGGGACTACAT
1 GGCGACCTACAAGGTCGCCGGGACTACAT
** *
946641 GGCGACCTACAAGGTCGCCCAGACTGCAT
1 GGCGACCTACAAGGTCGCCGGGACTACAT
946670 GGCGACCT
1 GGCGACCT
946678 CTCTATTGGC
Statistics
Matches: 63, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
29 63 1.00
ACGTcount: A:0.23, C:0.33, G:0.31, T:0.14
Consensus pattern (29 bp):
GGCGACCTACAAGGTCGCCGGGACTACAT
Found at i:946706 original size:32 final size:32
Alignment explanation
Indices: 946664--946735 Score: 117
Period size: 32 Copynumber: 2.2 Consensus size: 32
946654 GTCGCCCAGA
*
946664 CTGCATGGCGACCTCTCTATTGGCTGGCTCGT
1 CTGCATGGCGACCTCTCCATTGGCTGGCTCGT
* *
946696 TTGCATGGCGACCTCTCCGTTGGCTGGCTCGT
1 CTGCATGGCGACCTCTCCATTGGCTGGCTCGT
946728 CTGCATGG
1 CTGCATGG
946736 TGAGTATATG
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 36 1.00
ACGTcount: A:0.08, C:0.31, G:0.31, T:0.31
Consensus pattern (32 bp):
CTGCATGGCGACCTCTCCATTGGCTGGCTCGT
Found at i:947690 original size:60 final size:60
Alignment explanation
Indices: 947577--947691 Score: 142
Period size: 60 Copynumber: 1.9 Consensus size: 60
947567 AAAATTTGGG
** * *
947577 GACTAATTTAGAAAGAGAATCATAGTTTTTGGATGGAAATATAATGTTCAAAAGTGAAAA
1 GACTAATTTAGAAAGAGAATCATAGTTTGGGGATGGAAATAAAATATTCAAAAGTGAAAA
* * * *
947637 GACTAATTTAGAATGAGAGTCATGGTTTGGGGAT-GAAATTAAAATATTTAAAAGT
1 GACTAATTTAGAAAGAGAATCATAGTTTGGGGATGGAAA-TAAAATATTCAAAAGT
947692 TTAAGGATCA
Statistics
Matches: 46, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
59 4 0.09
60 42 0.91
ACGTcount: A:0.43, C:0.04, G:0.22, T:0.31
Consensus pattern (60 bp):
GACTAATTTAGAAAGAGAATCATAGTTTGGGGATGGAAATAAAATATTCAAAAGTGAAAA
Found at i:949916 original size:2 final size:2
Alignment explanation
Indices: 949909--949937 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
949899 CTTATCCGGT
949909 TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
949938 GATATTATTC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:950079 original size:3 final size:3
Alignment explanation
Indices: 950071--950108 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
950061 TCCTTTGATT
950071 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
950109 TCATTAGTGA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:963803 original size:30 final size:30
Alignment explanation
Indices: 963767--963833 Score: 134
Period size: 30 Copynumber: 2.2 Consensus size: 30
963757 GTCGCATCAG
963767 GAACCAATTTGTATGGAAGAATAGAAAATT
1 GAACCAATTTGTATGGAAGAATAGAAAATT
963797 GAACCAATTTGTATGGAAGAATAGAAAATT
1 GAACCAATTTGTATGGAAGAATAGAAAATT
963827 GAACCAA
1 GAACCAA
963834 CTTGACTTTC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 37 1.00
ACGTcount: A:0.48, C:0.09, G:0.19, T:0.24
Consensus pattern (30 bp):
GAACCAATTTGTATGGAAGAATAGAAAATT
Found at i:969808 original size:119 final size:119
Alignment explanation
Indices: 969597--969834 Score: 476
Period size: 119 Copynumber: 2.0 Consensus size: 119
969587 TTGTTGATTT
969597 CATCGCCAAGCATGATGTTCCTCCTTATGGTGCTCTTGCAGTCTTTGACTCTCCACCAGATCAAC
1 CATCGCCAAGCATGATGTTCCTCCTTATGGTGCTCTTGCAGTCTTTGACTCTCCACCAGATCAAC
969662 TTGCTGGTATCATGGCTAGAGATTTTTTCGGCCCTCCTTATAGCCGTGTAAATA
66 TTGCTGGTATCATGGCTAGAGATTTTTTCGGCCCTCCTTATAGCCGTGTAAATA
969716 CATCGCCAAGCATGATGTTCCTCCTTATGGTGCTCTTGCAGTCTTTGACTCTCCACCAGATCAAC
1 CATCGCCAAGCATGATGTTCCTCCTTATGGTGCTCTTGCAGTCTTTGACTCTCCACCAGATCAAC
969781 TTGCTGGTATCATGGCTAGAGATTTTTTCGGCCCTCCTTATAGCCGTGTAAATA
66 TTGCTGGTATCATGGCTAGAGATTTTTTCGGCCCTCCTTATAGCCGTGTAAATA
969835 AGTAATTTTC
Statistics
Matches: 119, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
119 119 1.00
ACGTcount: A:0.20, C:0.27, G:0.19, T:0.34
Consensus pattern (119 bp):
CATCGCCAAGCATGATGTTCCTCCTTATGGTGCTCTTGCAGTCTTTGACTCTCCACCAGATCAAC
TTGCTGGTATCATGGCTAGAGATTTTTTCGGCCCTCCTTATAGCCGTGTAAATA
Found at i:970760 original size:20 final size:20
Alignment explanation
Indices: 970666--971034 Score: 458
Period size: 20 Copynumber: 18.4 Consensus size: 20
970656 GATTTTCCAT
* ** *
970666 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGTATCCGTA
* *
970686 AATCGCAACGCG-AACACATA
1 AATCGCAACGCGTATC-CGTA
970706 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
970726 AATCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTA
**
970746 AATCGCAACGCGTATGGGTA
1 AATCGCAACGCGTATCCGTA
*
970766 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
970786 TATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
970806 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
* *
970826 AACCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTA
970846 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
970866 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
970886 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
970906 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
970926 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
970946 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
970966 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
970986 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
971006 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
971026 AATCACAAC
1 AATCGCAAC
971035 ACTGAAATTT
Statistics
Matches: 305, Mismatches: 36, Indels: 16
0.85 0.10 0.04
Matches are distributed among these distances:
19 3 0.01
20 299 0.98
21 3 0.01
ACGTcount: A:0.35, C:0.26, G:0.19, T:0.20
Consensus pattern (20 bp):
AATCGCAACGCGTATCCGTA
Found at i:971746 original size:24 final size:24
Alignment explanation
Indices: 971707--971753 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
971697 AAATTTGGTC
971707 TTGGTCAATATCCGGACTTTGATA
1 TTGGTCAATATCCGGACTTTGATA
*
971731 TTGGTCAATA-CACGGATTTTGAT
1 TTGGTCAATATC-CGGACTTTGAT
971754 GATGTTTCAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.26, C:0.15, G:0.21, T:0.38
Consensus pattern (24 bp):
TTGGTCAATATCCGGACTTTGATA
Found at i:971945 original size:12 final size:12
Alignment explanation
Indices: 971928--971952 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
971918 ATATAATCCT
971928 GAAGAAGAAAAA
1 GAAGAAGAAAAA
971940 GAAGAAGAAAAA
1 GAAGAAGAAAAA
971952 G
1 G
971953 TCCCCGAAGA
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:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:974271 original size:19 final size:19
Alignment explanation
Indices: 974249--974555 Score: 351
Period size: 19 Copynumber: 17.4 Consensus size: 19
974239 CGGAAAATAC
*
974249 AATCGCAACGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
974268 AATCCCAA--C---ATGAA
1 AATCGCAATGCGAAATGAA
974282 AATCGCAATGCGGAAATGAA
1 AATCGCAATGC-GAAATGAA
*
974302 AATCGCAA--CG---TGAG
1 AATCGCAATGCGAAATGAA
974316 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
974335 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
974354 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
974368 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
974387 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
974406 AATCG-AA--CAGACAT---
1 AATCGCAATGC-GAAATGAA
*
974420 AATCGCAATGCGAAATTAA
1 AATCGCAATGCGAAATGAA
*
974439 AATCGCAATACGAAATGAA
1 AATCGCAATGCGAAATGAA
974458 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
974477 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
974496 AATCGCAA--CGAAA-G--
1 AATCGCAATGCGAAATGAA
974510 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
974529 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
974548 AATCGCAA
1 AATCGCAA
974556 CGAGATAATC
Statistics
Matches: 249, Mismatches: 11, Indels: 56
0.79 0.03 0.18
Matches are distributed among these distances:
14 46 0.18
15 3 0.01
16 16 0.06
17 15 0.06
18 4 0.02
19 152 0.61
20 13 0.05
ACGTcount: A:0.47, C:0.18, G:0.20, T:0.15
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:974369 original size:52 final size:52
Alignment explanation
Indices: 974277--974555 Score: 347
Period size: 52 Copynumber: 5.2 Consensus size: 52
974267 AAATCCCAAC
* *
974277 ATGAAAATCGCAATGCGGAAATGAAAATCGCAACGTGAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGC-GAAATGAAAATCGCAACGAGAAAATCGCAATGCGAA
*
974330 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAAAATCGCAATGCGAA
974382 ATGAAAATCGCAATGCGAAATGAAAATCG-AAC-AGACATAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGA-A-AATCGCAATGCGAA
* *
974434 ATTAAAATCGCAATACGAAATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAA--CG--A-GAAAATCGCAATGCGAA
974491 ATGAAAATCGCAA--CGAAA-G--AATCGCAATGCGAAATGAAAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAA--CG--A-GAAAATCGCAATGCGAA
974543 ATGAAAATCGCAA
1 ATGAAAATCGCAA
974556 CGAGATAATC
Statistics
Matches: 212, Mismatches: 5, Indels: 19
0.90 0.02 0.08
Matches are distributed among these distances:
50 3 0.01
51 3 0.01
52 151 0.71
53 18 0.08
54 1 0.00
55 6 0.03
57 26 0.12
58 2 0.01
59 2 0.01
ACGTcount: A:0.47, C:0.17, G:0.21, T:0.15
Consensus pattern (52 bp):
ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAAAATCGCAATGCGAA
Found at i:974400 original size:71 final size:71
Alignment explanation
Indices: 974316--974555 Score: 348
Period size: 71 Copynumber: 3.4 Consensus size: 71
974306 GCAACGTGAG
*
974316 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGA
1 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGA
974381 AATGAA
66 AATGAA
* *
974387 AATCGCAATGCGAAATGAAAATCG-AA--CAGACAT---AATCGCAATGCGAAATTAAAATCGCA
1 AATCGCAATGCGAAATGAAAATCGCAATGC-GAAATGAAAATCGCAA--CG-AA--AGAATCGCA
*
974446 ATACGAAATGAA
60 ATGCGAAATGAA
974458 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGA
1 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGA
974523 AATGAA
66 AATGAA
974529 AATCGCAATGCGAAATGAAAATCGCAA
1 AATCGCAATGCGAAATGAAAATCGCAA
974556 CGAGATAATC
Statistics
Matches: 150, Mismatches: 7, Indels: 24
0.83 0.04 0.13
Matches are distributed among these distances:
66 8 0.05
68 3 0.02
69 5 0.03
70 2 0.01
71 113 0.75
72 2 0.01
73 6 0.04
74 3 0.02
76 8 0.05
ACGTcount: A:0.48, C:0.17, G:0.20, T:0.15
Consensus pattern (71 bp):
AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGA
AATGAA
Found at i:974501 original size:142 final size:137
Alignment explanation
Indices: 974249--974587 Score: 506
Period size: 142 Copynumber: 2.4 Consensus size: 137
974239 CGGAAAATAC
* * *
974249 AATCGCAACGCGAAATGAAAATCCCAACATGAA-AATCGCAATGCGGAAATGAAAATCGC-AACG
1 AATCGCAATGCGAAATGAAAAT-CGAACA-GAATAATCGCAATGC-GAAATTAAAATCGCAAACG
* *
974312 TGAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAAT
63 TGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCAAT
974377 GCGAAATGAA
128 GCGAAATGAA
974387 AATCGCAATGCGAAATGAAAATCGAACAGACATAATCGCAATGCGAAATTAAAATCGCAATACGA
1 AATCGCAATGCGAAATGAAAATCGAACAGA-ATAATCGCAATGCGAAATTAAAATCGCAA-ACG-
974452 AATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCA
63 --TGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCA
974517 ATGCGAAATGAA
126 ATGCGAAATGAA
974529 AATCGCAATGCGAAATGAAAATCGCAAC-GAGATAATCGCAATGCGAAATTATAAA-CGCA
1 AATCGCAATGCGAAATGAAAATCG-AACAGA-ATAATCGCAATGCGAAATTA-AAATCGCA
974588 TTGCGATTTT
Statistics
Matches: 186, Mismatches: 6, Indels: 14
0.90 0.03 0.07
Matches are distributed among these distances:
136 2 0.01
137 19 0.10
138 33 0.18
139 3 0.02
142 123 0.66
143 6 0.03
ACGTcount: A:0.47, C:0.18, G:0.20, T:0.15
Consensus pattern (137 bp):
AATCGCAATGCGAAATGAAAATCGAACAGAATAATCGCAATGCGAAATTAAAATCGCAAACGTGA
AAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCG
AAATGAA
Found at i:974693 original size:19 final size:19
Alignment explanation
Indices: 974584--974685 Score: 151
Period size: 19 Copynumber: 5.6 Consensus size: 19
974574 AAATTATAAA
974584 CGCATTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
974603 CCGCATTGCGATTTTCATTT
1 -CGCATTGCGATTTTCATTT
*
974623 CGCATTGCGA--TTC-TCT
1 CGCATTGCGATTTTCATTT
974639 CG--TTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
974656 CGCATTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
974675 CGCATTGCGAT
1 CGCATTGCGAT
974686 AGTCATTTTT
Statistics
Matches: 75, Mismatches: 2, Indels: 11
0.85 0.02 0.12
Matches are distributed among these distances:
14 6 0.08
16 7 0.09
17 7 0.09
19 36 0.48
20 19 0.25
ACGTcount: A:0.15, C:0.24, G:0.18, T:0.44
Consensus pattern (19 bp):
CGCATTGCGATTTTCATTT
Found at i:974816 original size:14 final size:14
Alignment explanation
Indices: 974797--974833 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
974787 CATCAATTAC
974797 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
974811 ACAAATCATCTTTT
1 ACAAATCAACTTTT
974825 ACAAATCAA
1 ACAAATCAA
974834 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:974845 original size:12 final size:12
Alignment explanation
Indices: 974828--974900 Score: 53
Period size: 12 Copynumber: 6.0 Consensus size: 12
974818 ATCTTTTACA
974828 AATCAATTAAAC
1 AATCAATTAAAC
*
974840 AATCAA--AAATTG
1 AATCAATTAAA--C
**
974852 AATCAACTTTTAC
1 AATCAA-TTAAAC
974865 AAATCAATTAAAC
1 A-ATCAATTAAAC
*
974878 AATCAA-AAAAC
1 AATCAATTAAAC
974889 AATCAATTAAAC
1 AATCAATTAAAC
974901 TATTGAATCA
Statistics
Matches: 46, Mismatches: 8, Indels: 14
0.68 0.12 0.21
Matches are distributed among these distances:
10 3 0.07
11 10 0.22
12 21 0.46
13 6 0.13
14 5 0.11
15 1 0.02
ACGTcount: A:0.58, C:0.16, G:0.01, T:0.25
Consensus pattern (12 bp):
AATCAATTAAAC
Found at i:974862 original size:38 final size:38
Alignment explanation
Indices: 974814--974886 Score: 137
Period size: 38 Copynumber: 1.9 Consensus size: 38
974804 AACTTTTACA
*
974814 AATCATCTTTTACAAATCAATTAAACAATCAAAAATTG
1 AATCAACTTTTACAAATCAATTAAACAATCAAAAATTG
974852 AATCAACTTTTACAAATCAATTAAACAATCAAAAA
1 AATCAACTTTTACAAATCAATTAAACAATCAAAAA
974887 ACAATCAATT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 34 1.00
ACGTcount: A:0.53, C:0.16, G:0.01, T:0.29
Consensus pattern (38 bp):
AATCAACTTTTACAAATCAATTAAACAATCAAAAATTG
Found at i:976700 original size:20 final size:19
Alignment explanation
Indices: 976675--976739 Score: 89
Period size: 18 Copynumber: 3.4 Consensus size: 19
976665 TAGTTTACTT
*
976675 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAAC-TAAAA
976695 TCGCAACGCGAAAC-AAAA
1 TCGCAACGCGAAACTAAAA
976713 TCGCAACGCGAAA-TGAAAA
1 TCGCAACGCGAAACT-AAAA
976732 TCGCAACG
1 TCGCAACG
976740 ACAGAATCGC
Statistics
Matches: 42, Mismatches: 1, Indels: 5
0.88 0.02 0.10
Matches are distributed among these distances:
18 17 0.40
19 12 0.29
20 13 0.31
ACGTcount: A:0.46, C:0.26, G:0.17, T:0.11
Consensus pattern (19 bp):
TCGCAACGCGAAACTAAAA
Found at i:976733 original size:19 final size:19
Alignment explanation
Indices: 976675--976798 Score: 101
Period size: 19 Copynumber: 7.1 Consensus size: 19
976665 TAGTTTACTT
* *
976675 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAA-TGAAAA
*
976695 TCGCAACGCGAAA-CAAAA
1 TCGCAACGCGAAATGAAAA
976713 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
976732 TCGCAA--CGACA-G--AA
1 TCGCAACGCGAAATGAAAA
*
976746 TCGCAATGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
976765 TCGCAA--CGACAA-G---A
1 TCGCAACGCGA-AATGAAAA
976779 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
976798 T
1 T
976799 GGCAGCAACC
Statistics
Matches: 86, Mismatches: 5, Indels: 27
0.73 0.04 0.23
Matches are distributed among these distances:
14 15 0.17
15 2 0.02
16 9 0.10
17 9 0.10
18 19 0.22
19 20 0.23
20 12 0.14
ACGTcount: A:0.47, C:0.23, G:0.19, T:0.11
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:976757 original size:33 final size:32
Alignment explanation
Indices: 976710--976798 Score: 151
Period size: 33 Copynumber: 2.7 Consensus size: 32
976700 ACGCGAAACA
976710 AAATCGCAACGCGAAATGAAAATCGCAACGAC
1 AAATCGCAACGCGAAATGAAAATCGCAACGAC
*
976742 AGAATCGCAATGCGAAATGAAAATCGCAACGAC
1 A-AATCGCAACGCGAAATGAAAATCGCAACGAC
976775 AAGATCGCAACGCGAAATGAAAAT
1 AA-ATCGCAACGCGAAATGAAAAT
976799 GGCAGCAACC
Statistics
Matches: 53, Mismatches: 2, Indels: 3
0.91 0.03 0.05
Matches are distributed among these distances:
32 2 0.04
33 51 0.96
ACGTcount: A:0.47, C:0.21, G:0.20, T:0.11
Consensus pattern (32 bp):
AAATCGCAACGCGAAATGAAAATCGCAACGAC
Found at i:977087 original size:174 final size:172
Alignment explanation
Indices: 976798--977168 Score: 608
Period size: 174 Copynumber: 2.1 Consensus size: 172
976788 GAAATGAAAA
976798 TGGCAGCAACCG-CAAATTTACTTTCAACCAAAGCAAAAACAAAGACAAATACTTCACAGTGTTA
1 TGGCAGCAACCGACAAATTTACTTTCAACCAAAGCAAAAACAAAGACAAATACTTCACAGTGTTA
976862 AAGAATACACAGTTTAGCAGAATTGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAAC
66 AAGAATACACAGTTTA--AGAATTGCAGCAACCGAACAAATTTACTTTCAACC-AAAGAC-AAAC
*
976927 AAAGAC-AA-ACTATTTCACAGTGTTAAGAATACATTTAGCAGAAT
127 AAAGACAAATACTATTTCACAGTGTTAAAAATACATTTAGCAGAAT
*
976971 TGGCAGCAACCGACAAATTTACTTTCAACCAAAG-ACAAAACAAAGACAAATATATTTCACAGTG
1 TGGCAGCAACCGACAAATTTACTTTCAACCAAAGCA-AAAACAAAGAC-AA-ATACTTCACAGTG
977035 TTAAAGAATACACAGTTT-AGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAGACAAAC
63 TTAAAGAATACACAGTTTAAGAATT-GCAGCAACCGAACAAATTTACTTTCAACCAAAGACAAAC
977099 AAAGACAAATACTATTTCACAGTGTTAAAAATACATTTAGCAGAAT
127 AAAGACAAATACTATTTCACAGTGTTAAAAATACATTTAGCAGAAT
977145 TGGCAGCAACCGAACAAATTTACT
1 TGGCAGCAACCG-ACAAATTTACT
977169 AAGCAATCTA
Statistics
Matches: 188, Mismatches: 2, Indels: 14
0.92 0.01 0.07
Matches are distributed among these distances:
172 10 0.05
173 27 0.14
174 108 0.57
175 13 0.07
176 30 0.16
ACGTcount: A:0.45, C:0.20, G:0.13, T:0.22
Consensus pattern (172 bp):
TGGCAGCAACCGACAAATTTACTTTCAACCAAAGCAAAAACAAAGACAAATACTTCACAGTGTTA
AAGAATACACAGTTTAAGAATTGCAGCAACCGAACAAATTTACTTTCAACCAAAGACAAACAAAG
ACAAATACTATTTCACAGTGTTAAAAATACATTTAGCAGAAT
Found at i:977097 original size:88 final size:85
Alignment explanation
Indices: 976798--977168 Score: 501
Period size: 87 Copynumber: 4.3 Consensus size: 85
976788 GAAATGAAAA
*
976798 TGGCAGCAACCG--CAAATTTACTTTCAACCAAAG-CAAAAACAAAGAC-AAATACTTCACAGTG
1 TGGCAGCAACCGAACAAATTTACTTTCAACCAAAGAC-AAAACAAAGACAAAATATTTCACAGTG
976859 TTAAAGAATACACAGTTTAGCAGAAT
65 TTAAAGAAT--ACA-TTTA--AGAAT
*
976885 T-GCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAACTATTTCACAGTG
1 TGGCAGCAACCGAACAAATTTACTTTCAACC-AAAGACAAAACAAAGACAAAATATTTCACAGTG
976949 TT-AAGAATACATTTAGCAGAAT
65 TTAAAGAATACATTTA--AGAAT
976971 TGGCAGCAACCG-ACAAATTTACTTTCAACCAAAGACAAAACAAAGACAAATATATTTCACAGTG
1 TGGCAGCAACCGAACAAATTTACTTTCAACCAAAGACAAAACAAAGACAAA-ATATTTCACAGTG
977035 TTAAAGAATACACAGTTT-AGAAT
65 TTAAAGAAT--ACA-TTTAAGAAT
977058 TGGCAGCAACCGAACAAATTTACTTTCAACCAAAGAC-AAACAAAGACAAATACTATTTCACAGT
1 TGGCAGCAACCGAACAAATTTACTTTCAACCAAAGACAAAACAAAGACAAA-A-TATTTCACAGT
977122 GTTAAA-AATACATTTAGCAGAAT
64 GTTAAAGAATACATTTA--AGAAT
977145 TGGCAGCAACCGAACAAATTTACT
1 TGGCAGCAACCGAACAAATTTACT
977169 AAGCAATCTA
Statistics
Matches: 265, Mismatches: 3, Indels: 32
0.88 0.01 0.11
Matches are distributed among these distances:
84 3 0.01
85 23 0.09
86 54 0.20
87 84 0.32
88 58 0.22
89 24 0.09
90 19 0.07
ACGTcount: A:0.45, C:0.20, G:0.13, T:0.22
Consensus pattern (85 bp):
TGGCAGCAACCGAACAAATTTACTTTCAACCAAAGACAAAACAAAGACAAAATATTTCACAGTGT
TAAAGAATACATTTAAGAAT
Found at i:978813 original size:14 final size:14
Alignment explanation
Indices: 978794--978883 Score: 81
Period size: 14 Copynumber: 5.7 Consensus size: 14
978784 TTGAAATGAA
978794 AATCGCAACGAGAG
1 AATCGCAACGAGAG
978808 AATCGCAACGCGAGATG
1 AATCGCAA--CGAGA-G
978825 ACAATCGCAACGAGAG
1 --AATCGCAACGAGAG
*
978841 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
978860 AATCGCAACGAGAG
1 AATCGCAACGAGAG
978874 AATCGCAACG
1 AATCGCAACG
978884 CGAAATGAAA
Statistics
Matches: 64, Mismatches: 2, Indels: 20
0.74 0.02 0.23
Matches are distributed among these distances:
14 28 0.44
15 1 0.02
16 8 0.12
17 8 0.12
18 1 0.02
19 18 0.28
ACGTcount: A:0.42, C:0.23, G:0.26, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:978831 original size:33 final size:33
Alignment explanation
Indices: 978786--978900 Score: 212
Period size: 33 Copynumber: 3.5 Consensus size: 33
978776 TCTTTTGGTT
978786 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
* *
978819 GAGATGACAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
978852 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
978885 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
978901 TGCGATTTTG
Statistics
Matches: 78, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 78 1.00
ACGTcount: A:0.45, C:0.21, G:0.24, T:0.10
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:978832 original size:19 final size:18
Alignment explanation
Indices: 978793--978905 Score: 88
Period size: 19 Copynumber: 6.8 Consensus size: 18
978783 GTTGAAATGA
978793 AAATCGCAA--CGAGA-G
1 AAATCGCAACGCGAGATG
978808 -AATCGCAACGCGAGATG
1 AAATCGCAACGCGAGATG
978825 ACAATCGCAA--CGAGA-G
1 A-AATCGCAACGCGAGATG
*
978841 -AATCGCAACGCGAAATG
1 AAATCGCAACGCGAGATG
978858 AAAATCGCAA--CGAGA-G
1 -AAATCGCAACGCGAGATG
*
978874 -AATCGCAACGCGAAATG
1 AAATCGCAACGCGAGATG
*
978891 AAAATCGCAATGCGA
1 -AAATCGCAACGCGA
978906 TTTTGGTTTC
Statistics
Matches: 79, Mismatches: 4, Indels: 26
0.72 0.04 0.24
Matches are distributed among these distances:
14 24 0.30
16 15 0.19
17 12 0.15
19 28 0.35
ACGTcount: A:0.43, C:0.22, G:0.25, T:0.10
Consensus pattern (18 bp):
AAATCGCAACGCGAGATG
Found at i:978936 original size:14 final size:14
Alignment explanation
Indices: 978917--978971 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
978907 TTTGGTTTCG
978917 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
978931 CGTTGCGATTTCCATTTCG
1 CGTTGCGA-TT-C---TCT
978950 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
978964 CGTTGCGA
1 CGTTGCGA
978972 CAGTCATTCT
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
14 18 0.53
15 2 0.06
16 1 0.03
17 1 0.03
18 2 0.06
19 10 0.29
ACGTcount: A:0.09, C:0.27, G:0.24, T:0.40
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:979134 original size:33 final size:33
Alignment explanation
Indices: 979092--979162 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
979082 AATACTAACT
*
979092 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
* *
979125 TGAAAATCGCAACGACAGAATCGTAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
979158 TGAAA
1 TGAAA
979163 TCTAAGTGAA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.48, C:0.18, G:0.23, T:0.11
Consensus pattern (33 bp):
TGAAAATCGCAACGACAGAATAGCAACGCGAAA
Found at i:979395 original size:22 final size:22
Alignment explanation
Indices: 979343--979397 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
979333 TGGTTGTGAG
**
979343 GGATTTCGCCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
**
979365 GGAAATCTTCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
979387 GGATTTCTTCG
1 GGATTTCTTCG
979398 CCGTAGAGAG
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.20, C:0.16, G:0.40, T:0.24
Consensus pattern (22 bp):
GGATTTCTTCGGAGATGGGGAC
Found at i:979568 original size:20 final size:20
Alignment explanation
Indices: 979543--979736 Score: 221
Period size: 20 Copynumber: 9.7 Consensus size: 20
979533 CTTTAAATAT
979543 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
979563 CGCGTTGCGATTTTATGTATTA
1 CGCGTTGCGA-TTTACGGA-TA
*
979585 -TCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
979604 CGCGTTGCGATATACGGATA
1 CGCGTTGCGATTTACGGATA
* **
979624 CGCATTGCGATTTACCCATA
1 CGCGTTGCGATTTACGGATA
979644 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
979664 CACGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
979684 CGCGTTGCGATTTATGTG-TT
1 CGCGTTGCGATTTACG-GATA
* ** *
979704 CGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATA
979724 CGCGTTGCGATTT
1 CGCGTTGCGATTT
979737 TGGAAAATCG
Statistics
Matches: 147, Mismatches: 22, Indels: 10
0.82 0.12 0.06
Matches are distributed among these distances:
19 2 0.01
20 128 0.87
21 15 0.10
22 2 0.01
ACGTcount: A:0.19, C:0.20, G:0.26, T:0.36
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:979730 original size:60 final size:60
Alignment explanation
Indices: 979543--979736 Score: 253
Period size: 60 Copynumber: 3.2 Consensus size: 60
979533 CTTTAAATAT
**
979543 CGCGTTGCGATTTACGGATACGCGTTGCGATTTTATGTATTATCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGA-TTTATGTATTCGCGTTGCGATTTACGGATA
* * *** *
979604 CGCGTTGCGATATACGGATACGCATTGCGATTTACCCATACGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
* * * ** *
979664 CACGTTGCGATTTACGGATACGCGTTGCGATTTATGTGTTCGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
979724 CGCGTTGCGATTT
1 CGCGTTGCGATTT
979737 TGGAAAATCG
Statistics
Matches: 112, Mismatches: 21, Indels: 1
0.84 0.16 0.01
Matches are distributed among these distances:
60 84 0.75
61 28 0.25
ACGTcount: A:0.19, C:0.20, G:0.26, T:0.36
Consensus pattern (60 bp):
CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
Found at i:979753 original size:21 final size:20
Alignment explanation
Indices: 979729--979805 Score: 57
Period size: 21 Copynumber: 3.7 Consensus size: 20
979719 ATATTCGCGT
979729 TGCGATTTTGGAAAATCGCAA
1 TGCGATTTTGGAAAATCGC-A
* * **
979750 TGCGAATTTGTACTATCGCA
1 TGCGATTTTGGAAAATCGCA
* *
979770 TCGCGATTTT-CAAGAATCGCGT
1 T-GCGATTTTGGAA-AATCGC-A
979792 TGCGATTTTGGAAA
1 TGCGATTTTGGAAA
979806 CTGATTTGCG
Statistics
Matches: 42, Mismatches: 10, Indels: 8
0.70 0.17 0.13
Matches are distributed among these distances:
20 3 0.07
21 36 0.86
22 3 0.07
ACGTcount: A:0.27, C:0.17, G:0.23, T:0.32
Consensus pattern (20 bp):
TGCGATTTTGGAAAATCGCA
Found at i:979816 original size:20 final size:20
Alignment explanation
Indices: 979791--979842 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
979781 AAGAATCGCG
*
979791 TTGCGATTTTGGAAACTGAT
1 TTGCGATTCTGGAAACTGAT
979811 TTGCGATTCTGGAAACTGAT
1 TTGCGATTCTGGAAACTGAT
979831 TTGCGATTCTGG
1 TTGCGATTCTGG
979843 GGATCGCGTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.21, C:0.13, G:0.27, T:0.38
Consensus pattern (20 bp):
TTGCGATTCTGGAAACTGAT
Found at i:986188 original size:2 final size:2
Alignment explanation
Indices: 986181--986208 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
986171 CAAATCGGAG
986181 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
986209 TTGAATTTTC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:988318 original size:20 final size:21
Alignment explanation
Indices: 988281--988320 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
988271 AAATTAAATT
988281 AAATGAATTTTAAGATTTTAC
1 AAATGAATTTTAAGATTTTAC
988302 AAATG-ATTTTACA-ATTTTA
1 AAATGAATTTTA-AGATTTTA
988321 TATTCGATTC
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 12 0.67
21 6 0.33
ACGTcount: A:0.42, C:0.05, G:0.07, T:0.45
Consensus pattern (21 bp):
AAATGAATTTTAAGATTTTAC
Found at i:988566 original size:17 final size:19
Alignment explanation
Indices: 988546--988586 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 19
988536 GAAACATCGA
988546 ATGCATT-T-CATGCACCG
1 ATGCATTCTCCATGCACCG
*
988563 ATGCATTCTCCATGCATCG
1 ATGCATTCTCCATGCACCG
988582 ATGCA
1 ATGCA
988587 CTCTGAATAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 7 0.33
18 1 0.05
19 13 0.62
ACGTcount: A:0.24, C:0.29, G:0.17, T:0.29
Consensus pattern (19 bp):
ATGCATTCTCCATGCACCG
Found at i:988606 original size:65 final size:63
Alignment explanation
Indices: 988490--988696 Score: 238
Period size: 65 Copynumber: 3.2 Consensus size: 63
988480 ATTTGAAGTG
* * * *
988490 ATGCACCGATGCATCAACCATGCATCGATGCATTAGTGAAT-TAATTGAAACATCGAATGCATTT
1 ATGCACCGATGCATC-ACCATGCATCGATGCACT-CTGAATAT-TTTCAAACATCGAATGCATTT
988554 C
63 C
* *
988555 ATGCACCGATGCATTCTCCATGCATCGATGCACTCTGAATATTTTCAAAACATCGAATGCATTTG
1 ATGCACCGATGCA-TCACCATGCATCGATGCACTCTGAATATTTTC-AAACATCGAATGCATTTC
* * **
988620 ATGCATCGATGCA-CAAACCATGCATCGATGCACTCAGGCTATTTTCAAACATCGAATGCATTTC
1 ATGCACCGATGCATC--ACCATGCATCGATGCACTCTGAATATTTTCAAACATCGAATGCATTTC
*
988684 ATGCATCGATGCA
1 ATGCACCGATGCA
988697 CACTTGGTGC
Statistics
Matches: 125, Mismatches: 12, Indels: 11
0.84 0.08 0.07
Matches are distributed among these distances:
63 1 0.01
64 37 0.30
65 85 0.68
66 2 0.02
ACGTcount: A:0.31, C:0.24, G:0.16, T:0.28
Consensus pattern (63 bp):
ATGCACCGATGCATCACCATGCATCGATGCACTCTGAATATTTTCAAACATCGAATGCATTTC
Found at i:988715 original size:64 final size:65
Alignment explanation
Indices: 988537--988700 Score: 240
Period size: 65 Copynumber: 2.5 Consensus size: 65
988527 GAATTAATTG
* ** *
988537 AAACATCGAATGCATTTCATGCACCGATGCATTCTCCATGCATCGATGCACTCTGAATATTTTCA
1 AAACATCGAATGCATTTCATGCATCGATGCACACTCCATGCATCGATGCACTCAGAATATTTTCA
* ** **
988602 AAACATCGAATGCATTTGATGCATCGATGCACAAACCATGCATCGATGCACTCAGGCTATTTTC-
1 AAACATCGAATGCATTTCATGCATCGATGCACACTCCATGCATCGATGCACTCAGAATATTTTCA
988666 AAACATCGAATGCATTTCATGCATCGATGCACACT
1 AAACATCGAATGCATTTCATGCATCGATGCACACT
988701 TGGTGCACCG
Statistics
Matches: 87, Mismatches: 12, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
64 32 0.37
65 55 0.63
ACGTcount: A:0.31, C:0.26, G:0.15, T:0.28
Consensus pattern (65 bp):
AAACATCGAATGCATTTCATGCATCGATGCACACTCCATGCATCGATGCACTCAGAATATTTTCA
Found at i:994576 original size:23 final size:23
Alignment explanation
Indices: 994499--994623 Score: 100
Period size: 23 Copynumber: 5.6 Consensus size: 23
994489 GCACTTAACA
*
994499 ATGCATCGATGCATCCCTTTGAAT
1 ATGCATCGATGCATTCC-TTGAAT
* * *
994523 ATGTATCGATGCATCACCATG---
1 ATGCATCGATGCAT-TCCTTGAAT
*
994544 ATGCACCGATGCATTCCTTGAAT
1 ATGCATCGATGCATTCCTTGAAT
** **
994567 ATGCATCGATGCA-T--AAGACC
1 ATGCATCGATGCATTCCTTGAAT
*
994587 ATGCACCGATGCATTCCTTGAAT
1 ATGCATCGATGCATTCCTTGAAT
994610 ATGCATCGATGCAT
1 ATGCATCGATGCAT
994624 AAGACCATGC
Statistics
Matches: 76, Mismatches: 18, Indels: 15
0.70 0.17 0.14
Matches are distributed among these distances:
20 18 0.24
21 13 0.17
22 1 0.01
23 27 0.36
24 15 0.20
25 2 0.03
ACGTcount: A:0.28, C:0.25, G:0.18, T:0.29
Consensus pattern (23 bp):
ATGCATCGATGCATTCCTTGAAT
Found at i:994596 original size:20 final size:20
Alignment explanation
Indices: 994567--994643 Score: 73
Period size: 20 Copynumber: 3.7 Consensus size: 20
994557 TTCCTTGAAT
*
994567 ATGCATCGATGCATAAGACC
1 ATGCACCGATGCATAAGACC
** **
994587 ATGCACCGATGCATTCCTTGAAT
1 ATGCACCGATGCA-T--AAGACC
*
994610 ATGCATCGATGCATAAGACC
1 ATGCACCGATGCATAAGACC
994630 ATGCACCGATGCAT
1 ATGCACCGATGCAT
994644 CCGTCGGGTT
Statistics
Matches: 43, Mismatches: 11, Indels: 6
0.72 0.18 0.10
Matches are distributed among these distances:
20 27 0.63
21 1 0.02
22 1 0.02
23 14 0.33
ACGTcount: A:0.31, C:0.26, G:0.19, T:0.23
Consensus pattern (20 bp):
ATGCACCGATGCATAAGACC
Found at i:994605 original size:43 final size:43
Alignment explanation
Indices: 994499--994643 Score: 209
Period size: 43 Copynumber: 3.3 Consensus size: 43
994489 GCACTTAACA
* * * ** **
994499 ATGCATCGATGCATCCCTTTGAATATGTATCGATGCATCACCATG
1 ATGCACCGATGCATTCC-TTGAATATGCATCGATGCAT-AAGACC
994544 ATGCACCGATGCATTCCTTGAATATGCATCGATGCATAAGACC
1 ATGCACCGATGCATTCCTTGAATATGCATCGATGCATAAGACC
994587 ATGCACCGATGCATTCCTTGAATATGCATCGATGCATAAGACC
1 ATGCACCGATGCATTCCTTGAATATGCATCGATGCATAAGACC
994630 ATGCACCGATGCAT
1 ATGCACCGATGCAT
994644 CCGTCGGGTT
Statistics
Matches: 93, Mismatches: 7, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
43 59 0.63
44 19 0.20
45 15 0.16
ACGTcount: A:0.29, C:0.26, G:0.19, T:0.27
Consensus pattern (43 bp):
ATGCACCGATGCATTCCTTGAATATGCATCGATGCATAAGACC
Found at i:995548 original size:20 final size:21
Alignment explanation
Indices: 995511--995550 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
995501 AAATTAAGTT
995511 AAATGAATTTTAAGATTTTAC
1 AAATGAATTTTAAGATTTTAC
995532 AAATG-ATTTTACA-ATTTTA
1 AAATGAATTTTA-AGATTTTA
995551 TATTCGATTC
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 12 0.67
21 6 0.33
ACGTcount: A:0.42, C:0.05, G:0.07, T:0.45
Consensus pattern (21 bp):
AAATGAATTTTAAGATTTTAC
Found at i:995796 original size:17 final size:19
Alignment explanation
Indices: 995776--995816 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 19
995766 GAAACATCGA
995776 ATGCATT-T-CATGCACCG
1 ATGCATTCTCCATGCACCG
*
995793 ATGCATTCTCCATGCATCG
1 ATGCATTCTCCATGCACCG
995812 ATGCA
1 ATGCA
995817 CTTTGAATAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 7 0.33
18 1 0.05
19 13 0.62
ACGTcount: A:0.24, C:0.29, G:0.17, T:0.29
Consensus pattern (19 bp):
ATGCATTCTCCATGCACCG
Found at i:995836 original size:65 final size:63
Alignment explanation
Indices: 995720--995926 Score: 231
Period size: 65 Copynumber: 3.2 Consensus size: 63
995710 ATTTGAAGTG
* *
995720 ATGCACCGATGCATCAACCATGCATCGATGCA-TTAGTGAAT-TAATTGAAACATCGAATGCATT
1 ATGCACCGATGCATC-ACCATGCATCGATGCACTT--TGAATAT-TTTCAAACATCGAATGCATT
995783 TC
62 TC
* *
995785 ATGCACCGATGCATTCTCCATGCATCGATGCACTTTGAATATTTTCAAAACATCGAATGCATTTG
1 ATGCACCGATGCA-TCACCATGCATCGATGCACTTTGAATATTTTC-AAACATCGAATGCATTTC
* ** **
995850 ATGCATCGATGCA-CAAGCCATGCATCGATGCACTCAGGCTATTTTCAAACATCGAATGCATTTC
1 ATGCACCGATGCATC-A-CCATGCATCGATGCACTTTGAATATTTTCAAACATCGAATGCATTTC
*
995914 ATGCATCGATGCA
1 ATGCACCGATGCA
995927 CACTTGGTGC
Statistics
Matches: 125, Mismatches: 11, Indels: 13
0.84 0.07 0.09
Matches are distributed among these distances:
63 1 0.01
64 37 0.30
65 83 0.66
66 4 0.03
ACGTcount: A:0.31, C:0.24, G:0.17, T:0.29
Consensus pattern (63 bp):
ATGCACCGATGCATCACCATGCATCGATGCACTTTGAATATTTTCAAACATCGAATGCATTTC
Found at i:997650 original size:35 final size:34
Alignment explanation
Indices: 997565--997651 Score: 90
Period size: 35 Copynumber: 2.5 Consensus size: 34
997555 AATATAATTT
*
997565 TAAATACAACAAACTTACAATAAGTATTAAATGG
1 TAAATACAACAAAATTACAATAAGTATTAAATGG
*
997599 TAAATGATAA-ACAAATTACAATAATTGATATTAAATGG
1 TAAAT-ACAACA-AAATTACAATAA--G-TATTAAATGG
997637 T-AATA-AACAAAATTA
1 TAAATACAACAAAATTA
997652 ACCAAAATAT
Statistics
Matches: 45, Mismatches: 2, Indels: 11
0.78 0.03 0.19
Matches are distributed among these distances:
34 6 0.13
35 22 0.49
36 2 0.04
37 4 0.09
38 11 0.24
ACGTcount: A:0.55, C:0.08, G:0.08, T:0.29
Consensus pattern (34 bp):
TAAATACAACAAAATTACAATAAGTATTAAATGG
Found at i:999984 original size:16 final size:18
Alignment explanation
Indices: 999965--1000006 Score: 52
Period size: 16 Copynumber: 2.4 Consensus size: 18
999955 AAAAATAATT
999965 AAATAAAATA-TTAAA-A
1 AAATAAAATACTTAAAGA
*
999981 AAATTAAATACTTAAAGA
1 AAATAAAATACTTAAAGA
*
999999 AATTAAAA
1 AAATAAAA
1000007 ATAAAATATT
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
16 9 0.43
17 5 0.24
18 7 0.33
ACGTcount: A:0.69, C:0.02, G:0.02, T:0.26
Consensus pattern (18 bp):
AAATAAAATACTTAAAGA
Found at i:999988 original size:17 final size:18
Alignment explanation
Indices: 999968--1000006 Score: 55
Period size: 17 Copynumber: 2.3 Consensus size: 18
999958 AATAATTAAA
999968 TAAAATA-TTAAAAAAAT
1 TAAAATACTTAAAAAAAT
*
999985 T-AAATACTTAAAGAAAT
1 TAAAATACTTAAAAAAAT
1000002 TAAAA
1 TAAAA
1000007 ATAAAATATT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
16 5 0.26
17 11 0.58
18 3 0.16
ACGTcount: A:0.67, C:0.03, G:0.03, T:0.28
Consensus pattern (18 bp):
TAAAATACTTAAAAAAAT
Found at i:1001426 original size:22 final size:22
Alignment explanation
Indices: 1001400--1001476 Score: 109
Period size: 22 Copynumber: 3.4 Consensus size: 22
1001390 TATAATGTAC
* *
1001400 ATAGTTTTTGAAGATATATAGT
1 ATAGTTTTTGAAAATATATAAT
1001422 ATAGTTTTTGAAAACATATATAAT
1 ATAGTTTTTG-AAA-ATATATAAT
*
1001446 ATAGTTTTTGAAAACATATAAT
1 ATAGTTTTTGAAAATATATAAT
1001468 ATAGTTTTT
1 ATAGTTTTT
1001477 AATACGGTTT
Statistics
Matches: 50, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
22 27 0.54
23 5 0.10
24 18 0.36
ACGTcount: A:0.40, C:0.03, G:0.12, T:0.45
Consensus pattern (22 bp):
ATAGTTTTTGAAAATATATAAT
Found at i:1001440 original size:24 final size:23
Alignment explanation
Indices: 1001400--1001476 Score: 106
Period size: 24 Copynumber: 3.4 Consensus size: 23
1001390 TATAATGTAC
*
1001400 ATAGTTTTTG--AAGATATATAGT
1 ATAGTTTTTGAAAACATATATA-T
1001422 ATAGTTTTTGAAAACATATATAAT
1 ATAGTTTTTGAAAACATATAT-AT
1001446 ATAGTTTTTGAAAACATATA-AT
1 ATAGTTTTTGAAAACATATATAT
1001468 ATAGTTTTT
1 ATAGTTTTT
1001477 AATACGGTTT
Statistics
Matches: 51, Mismatches: 1, Indels: 6
0.88 0.02 0.10
Matches are distributed among these distances:
22 21 0.41
24 29 0.57
25 1 0.02
ACGTcount: A:0.40, C:0.03, G:0.12, T:0.45
Consensus pattern (23 bp):
ATAGTTTTTGAAAACATATATAT
Found at i:1001505 original size:52 final size:52
Alignment explanation
Indices: 1001444--1001543 Score: 157
Period size: 52 Copynumber: 1.9 Consensus size: 52
1001434 AACATATATA
*
1001444 ATATAGTTTTTGAAAACATATAATATAG-TTTTTAATACGGTTTTTGAATCAT
1 ATATAGTTTTTGAAAACATAT-ATATAGTTTTTTAAAACGGTTTTTGAATCAT
* *
1001496 ATATAGTTTTTGAATATATATATATAGTTTTTTAAAACGGTTTTTGAA
1 ATATAGTTTTTGAAAACATATATATAGTTTTTTAAAACGGTTTTTGAA
1001544 AACGTATATA
Statistics
Matches: 44, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
51 6 0.14
52 38 0.86
ACGTcount: A:0.36, C:0.04, G:0.12, T:0.48
Consensus pattern (52 bp):
ATATAGTTTTTGAAAACATATATATAGTTTTTTAAAACGGTTTTTGAATCAT
Found at i:1001519 original size:19 final size:18
Alignment explanation
Indices: 1001483--1001517 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
1001473 TTTTAATACG
1001483 GTTTTTGAATCATATATA
1 GTTTTTGAATCATATATA
1001501 GTTTTTGAAT-ATATATA
1 GTTTTTGAATCATATATA
1001518 TATAGTTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 7 0.41
18 10 0.59
ACGTcount: A:0.34, C:0.03, G:0.11, T:0.51
Consensus pattern (18 bp):
GTTTTTGAATCATATATA
Found at i:1003437 original size:20 final size:21
Alignment explanation
Indices: 1003408--1003446 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
1003398 AAAATTAAAA
1003408 ATATTATTA-TTAATATTTAT
1 ATATTATTATTTAATATTTAT
*
1003428 ATATTTTTATTTAATATTT
1 ATATTATTATTTAATATTT
1003447 TTATCCAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (21 bp):
ATATTATTATTTAATATTTAT
Found at i:1003444 original size:13 final size:14
Alignment explanation
Indices: 1003421--1003450 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
1003411 TTATTATTAA
1003421 TATTTATATATTTT
1 TATTTATATATTTT
1003435 TATTTA-ATATTTT
1 TATTTATATATTTT
1003448 TAT
1 TAT
1003451 CCAATAAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 10 0.62
14 6 0.38
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (14 bp):
TATTTATATATTTT
Found at i:1015796 original size:111 final size:115
Alignment explanation
Indices: 1015677--1015909 Score: 332
Period size: 116 Copynumber: 2.0 Consensus size: 115
1015667 TTGTCCAATC
* * * * *
1015677 ATGAATGAAATAATTTCAATTAACAATAA-T-AAAGTGATTCATTTATAC-AAATCATAAATTAA
1 ATGAATGAAATAATTTCAAATAAAAATAATTAAAAGTAATTAATTTATACAAAATCATAAATCAA
1015739 TCATTAACAAAATAAAACAAAGGATATAAGAATATTT-AA-AAATAAAAAA
66 TCATTAACAAAATAAAACAAAGGATATAAGAATATTTAAAGAAAT-AAAAA
1015788 ATGAATGAAATAATTTCAAATAAAAATAATTTTAAAAGTAATTAATTTATACAAAATCATAAATC
1 ATGAATGAAATAATTTCAAATAAAAATAA--TTAAAAGTAATTAATTTATACAAAATCATAAATC
* * *
1015853 AATTATTAACAAAATAAAATAGAGGATATAAGAATATTTAAAGAAATAAAAA
64 AATCATTAACAAAATAAAACAAAGGATATAAGAATATTTAAAGAAATAAAAA
1015905 ATGAA
1 ATGAA
1015910 ACTAAAGATA
Statistics
Matches: 107, Mismatches: 8, Indels: 8
0.87 0.07 0.07
Matches are distributed among these distances:
111 27 0.25
114 1 0.01
115 16 0.15
116 47 0.44
117 12 0.11
118 4 0.04
ACGTcount: A:0.58, C:0.06, G:0.07, T:0.29
Consensus pattern (115 bp):
ATGAATGAAATAATTTCAAATAAAAATAATTAAAAGTAATTAATTTATACAAAATCATAAATCAA
TCATTAACAAAATAAAACAAAGGATATAAGAATATTTAAAGAAATAAAAA
Found at i:1038104 original size:50 final size:50
Alignment explanation
Indices: 1038029--1038129 Score: 202
Period size: 50 Copynumber: 2.0 Consensus size: 50
1038019 TCATCAAGTG
1038029 TCATGTAAATACTCATACATATTATACATAATATATGCTGACATGAATGT
1 TCATGTAAATACTCATACATATTATACATAATATATGCTGACATGAATGT
1038079 TCATGTAAATACTCATACATATTATACATAATATATGCTGACATGAATGT
1 TCATGTAAATACTCATACATATTATACATAATATATGCTGACATGAATGT
1038129 T
1 T
1038130 AGAATAAACT
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
50 51 1.00
ACGTcount: A:0.40, C:0.14, G:0.10, T:0.37
Consensus pattern (50 bp):
TCATGTAAATACTCATACATATTATACATAATATATGCTGACATGAATGT
Found at i:1042513 original size:27 final size:29
Alignment explanation
Indices: 1042457--1042518 Score: 101
Period size: 27 Copynumber: 2.2 Consensus size: 29
1042447 AAGTGAATGG
1042457 CAACCTGTCAATTTAAAGTAGTATCAATAC
1 CAACCTGTCAATTT-AAGTAGTATCAATAC
1042487 CAACCTGTCAATTT-A-TAGTATCAATAC
1 CAACCTGTCAATTTAAGTAGTATCAATAC
1042514 CAACC
1 CAACC
1042519 ATTTGGGTAT
Statistics
Matches: 32, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
27 17 0.53
28 1 0.03
30 14 0.44
ACGTcount: A:0.39, C:0.24, G:0.08, T:0.29
Consensus pattern (29 bp):
CAACCTGTCAATTTAAGTAGTATCAATAC
Found at i:1050183 original size:18 final size:19
Alignment explanation
Indices: 1050148--1050184 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
1050138 CACGGAATGT
1050148 AAGATTACCAGTGGGAATAA
1 AAGATTACCAG-GGGAATAA
1050168 AAGATTACCA-GGGAATA
1 AAGATTACCAGGGGAATA
1050185 GGATTACTGG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 7 0.41
20 10 0.59
ACGTcount: A:0.46, C:0.11, G:0.24, T:0.19
Consensus pattern (19 bp):
AAGATTACCAGGGGAATAA
Found at i:1055071 original size:60 final size:59
Alignment explanation
Indices: 1054952--1055107 Score: 170
Period size: 60 Copynumber: 2.6 Consensus size: 59
1054942 TCATTTTAAG
* ** * *
1054952 TTAGTCCCTAAACTTTTAAACATTTTAATTTCATCCTTAAGCTATGACTATTATTCTAAA
1 TTAGT-CCTAAACTTTTAAACATTTCAATTTCATCCCCAAGCTATGACTATCATCCTAAA
*
1055012 TTAGTCCTTAAACTTTTAAACATTTCATTTTCATCCCCAAGCTATGATCT-TCATCCTAAA
1 TTAGTCC-TAAACTTTTAAACATTTCAATTTCATCCCCAAGCTATGA-CTATCATCCTAAA
* * * * *
1055072 TTGGTCCCAAACTTTTTGAATATTTCAATTTTATCC
1 TTAGTCCTAAAC-TTTTAAACATTTCAATTTCATCC
1055108 TAAATTATTT
Statistics
Matches: 81, Mismatches: 12, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
59 6 0.07
60 73 0.90
61 2 0.02
ACGTcount: A:0.30, C:0.21, G:0.06, T:0.43
Consensus pattern (59 bp):
TTAGTCCTAAACTTTTAAACATTTCAATTTCATCCCCAAGCTATGACTATCATCCTAAA
Found at i:1055823 original size:2 final size:2
Alignment explanation
Indices: 1055818--1055870 Score: 106
Period size: 2 Copynumber: 26.5 Consensus size: 2
1055808 TCCTTTTTTA
1055818 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
1055860 AT AT AT AT AT A
1 AT AT AT AT AT A
1055871 GGTTATTTTT
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 51 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1071407 original size:11 final size:11
Alignment explanation
Indices: 1071393--1071435 Score: 59
Period size: 11 Copynumber: 3.8 Consensus size: 11
1071383 GTCGAACAAA
1071393 GTTAAAACATT
1 GTTAAAACATT
1071404 GTTAAAACATT
1 GTTAAAACATT
**
1071415 GCCCAAAACATT
1 G-TTAAAACATT
1071427 GTTAAAACA
1 GTTAAAACA
1071436 AGTAATATTC
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
11 18 0.67
12 9 0.33
ACGTcount: A:0.47, C:0.16, G:0.09, T:0.28
Consensus pattern (11 bp):
GTTAAAACATT
Found at i:1071634 original size:34 final size:33
Alignment explanation
Indices: 1071549--1071694 Score: 93
Period size: 34 Copynumber: 4.4 Consensus size: 33
1071539 TATTTTGTCT
1071549 AAATAAAAAATTATGACAAAT-TTATTTAATCA
1 AAATAAAAAATTATGACAAATATTATTTAATCA
* * * *
1071581 AAATAACAATTTATAACAAATATTAATTT-CTCA
1 AAATAAAAAATTATGACAAATATT-ATTTAATCA
** * *
1071614 TTATAAAAAAATTATGACAAATAATATTCT-TTCA
1 AAAT-AAAAAATTATGACAAATATTATT-TAATCA
* * * *
1071648 CAATAAAAAAATTGTAACAAA-ATTATTTAGTCA
1 AAAT-AAAAAATTATGACAAATATTATTTAATCA
* * *
1071681 CAGTAAAAAGTTAT
1 AAATAAAAAATTAT
1071695 AAAAAAATAT
Statistics
Matches: 89, Mismatches: 20, Indels: 10
0.75 0.17 0.08
Matches are distributed among these distances:
32 27 0.30
33 21 0.24
34 41 0.46
ACGTcount: A:0.53, C:0.09, G:0.04, T:0.34
Consensus pattern (33 bp):
AAATAAAAAATTATGACAAATATTATTTAATCA
Found at i:1075659 original size:286 final size:281
Alignment explanation
Indices: 1075020--1076069 Score: 957
Period size: 284 Copynumber: 3.7 Consensus size: 281
1075010 GTGCCTAGAT
* * * *
1075020 CATCTTATTTCACCCAGCCTACTCCCCACATTAGGGCGCT-TGACGTAAGATCAGGTCATCCTGC
1 CATCTTATTTCACCCGGCCTACTCCACACGTTA-GGCGCTCAG-CGTAAGATCAGGTCATCCTGC
*
1075084 CTACTCCCCTCTGGAAGCGCTCGGCATGAACTCTGTCTATCCTGCCTA-CCCTACACGTTGGAGT
64 CTACTCCCCTCTGGAAGCGCTCGGCATGAACTCTGTCTA-CCTGCCTATCCC-ACACGTTGAAGT
* * * *
1075148 ACTCGGTGTAAATCAAGAACACCCTGTCTACTCCACACATTAGAGCGCTCGGCGTAAGATCAGGT
127 GCTCGGTGTGAATC-AGAACACCCTGCCTACTCCACACGTTAGAGCGCTCGGCGTAAGATCAGGT
* * * * *
1075213 CATCCTACTTACTCCCTTCAGAAAGCACTCGGCATGCATTGTCTCCCCTGCCTACTTTTAACGTT
191 CATCCTACATACTCCCTTCAGAAAGCACTCGACATGCACTGTCTCCCCTGCCTACTCTCAACGTT
*
1075278 GAAGCGCTCGGCGTGATATTAAAGCA
256 AAAGCGCTCGGCGTGATATTAAAGCA
* * *
1075304 CATCTTATTTCACTCGGCCTACTCCACACGTTAGGACGCTCGGCGTAAGATCAGGTCATCCTACC
1 CATCTTATTTCACCCGGCCTACTCCACACGTTAGG-CGCTCAGCGTAAGATCAGGTCATCCTGCC
* * *
1075369 TACTCCCCTCTGGAAGTGCTCGGCATAAACTCTGTCTACCTTGCATATCCCACACGTTGAAGTGC
65 TACTCCCCTCTGGAAGCGCTCGGCATGAACTCTGTCTACC-TGCCTATCCCACACGTTGAAGTGC
* * *
1075434 TCGGCGTGAATCAGGAACACCCTACCTACTCCACATGTTAGAGCGCTCGGCGTAAGATCAGGTCA
129 TCGGTGTGAATCA-GAACACCCTGCCTACTCCACACGTTAGAGCGCTCGGCGTAAGATCAGGTCA
* * * * *
1075499 TCATTA-ATACT-TCTCTCTGGAAA-CGCTCGACATGTACACTGTCTCCCGTGCCTACTCTCAAC
193 TC-CTACATACTCCCT-TC-AGAAAGCACTCGACATG--CACTGTCTCCCCTGCCTACTCTCAAC
*
1075561 GTTAAAGCGCTCGGCGTGATATTAATGCA
253 GTTAAAGCGCTCGGCGTGATATTAAAGCA
1075590 CATCTTATTTCACCCGGCCTACTCCACACGTTAGAGCGCTCAGCGTAAGATCAGGTCATCCTGCC
1 CATCTTATTTCACCCGGCCTACTCCACACGTTAG-GCGCTCAGCGTAAGATCAGGTCATCCTGCC
* * * ** *
1075655 TACTCCCCTCTGGAAACGCTCAGCATGTACTCTGTCCCCCTGCCTACTCTCA-ACGTTGAAGTGC
65 TACTCCCCTCTGGAAGCGCTCGGCATGAACTCTGTCTACCTGCCTA-TCCCACACGTTGAAGTGC
* * * * * *
1075719 TCAGTGTGACATTA-AAGCACCCTGCCTACTCCACACGTTAGAGCTCCCAGCGTAAGATCGGGTC
129 TCGGTGTGA-ATCAGAA-CACCCTGCCTACTCCACACGTTAGAGCGCTCGGCGTAAGATCAGGTC
* * * * ** * * * *
1075783 ATCCTGCCTACTACCC-ACTAG-AAGCGCTCGGTATGAACTCTGTC-CCCCTTCCAACTCTTAAC
192 ATCCTACATACT-CCCTTC-AGAAAGCACTCGACATG--CACTGTCTCCCCTGCCTACTCTCAAC
* * *
1075845 GGTAAAGCGCTCGGCGAGA-ATT-ATG--
253 GTTAAAGCGCTCGGCGTGATATTAAAGCA
* * * *
1075870 -A----A--T-GCCCTGCCTACTCCACACGTTA--CAGCATCCGGCGTAAGATCATGTCATCCTG
1 CATCTTATTTCACCCGGCCTACTCCACACGTTAGGC-GC-T-CAGCGTAAGATCAGGTCATCCTG
* * ** * ** * *
1075925 CCTACTCCCCACTGGAAGCGCTCGCCATGAACTCTGTCCCCCT-TCTAACTCTTA-ATGGTGAAG
63 CCTACTCCCCTCTGGAAGCGCTCGGCATGAACTCTGTCTACCTGCCT-A-TCCCACACGTTGAAG
* ** ** * * *
1075988 CGCTCGACGAAAAAT-AGGAATACCCTGCCTACTCCACACGTTAGAGCACCCGGCGTAAGATCAG
126 TGCTCGGTG-TGAATCA-GAACACCCTGCCTACTCCACACGTTAGAGCGCTCGGCGTAAGATCAG
* *
1076052 GTCATCCTGCCTACTCCC
189 GTCATCCTACATACTCCC
1076070 CACTAGAATC
Statistics
Matches: 652, Mismatches: 89, Indels: 63
0.81 0.11 0.08
Matches are distributed among these distances:
269 1 0.00
270 2 0.00
271 7 0.01
272 154 0.24
273 4 0.01
275 1 0.00
279 1 0.00
282 3 0.00
283 10 0.02
284 217 0.33
285 101 0.15
286 149 0.23
287 2 0.00
ACGTcount: A:0.23, C:0.33, G:0.19, T:0.25
Consensus pattern (281 bp):
CATCTTATTTCACCCGGCCTACTCCACACGTTAGGCGCTCAGCGTAAGATCAGGTCATCCTGCCT
ACTCCCCTCTGGAAGCGCTCGGCATGAACTCTGTCTACCTGCCTATCCCACACGTTGAAGTGCTC
GGTGTGAATCAGAACACCCTGCCTACTCCACACGTTAGAGCGCTCGGCGTAAGATCAGGTCATCC
TACATACTCCCTTCAGAAAGCACTCGACATGCACTGTCTCCCCTGCCTACTCTCAACGTTAAAGC
GCTCGGCGTGATATTAAAGCA
Found at i:1075878 original size:136 final size:135
Alignment explanation
Indices: 1075606--1076108 Score: 625
Period size: 136 Copynumber: 3.7 Consensus size: 135
1075596 ATTTCACCCG
* * * * *
1075606 GCCTACTCCACACGTTAGAGCGCTCAGCGTAAGATCAGGTCATCCTGCCTACTCCCCTCTGGAAA
1 GCCTACTCCACACGTTAGAGCTCCCAGCGTAAGATCAGGTCATCCTGCCTACTCCCCACTAGAAG
* * * * * * * * * *
1075671 CGCTCAGCATGTACTCTGTCCCCCTGCCTACTCTCAACGTTGAAGTGCTCAGTGTGACATTA-AA
66 CGCTCGGCATGAACTCTGTCCCCCTTCCAACTCTTAACGGTGAAGCGCTCGGCGAGA-ATTAGAA
1075735 -GCACCCT
130 TG--CCCT
* *
1075742 GCCTACTCCACACGTTAGAGCTCCCAGCGTAAGATCGGGTCATCCTGCCTACTACCCACTAGAAG
1 GCCTACTCCACACGTTAGAGCTCCCAGCGTAAGATCAGGTCATCCTGCCTACTCCCCACTAGAAG
* *
1075807 CGCTCGGTATGAACTCTGTCCCCCTTCCAACTCTTAACGGTAAAGCGCTCGGCGAGAATTATGAA
66 CGCTCGGCATGAACTCTGTCCCCCTTCCAACTCTTAACGGTGAAGCGCTCGGCGAGAATTA-GAA
1075872 TGCCCT
130 TGCCCT
* * * *
1075878 GCCTACTCCACACGTTACAGCAT-CCGGCGTAAGATCATGTCATCCTGCCTACTCCCCACTGGAA
1 GCCTACTCCACACGTTAGAGC-TCCCAGCGTAAGATCAGGTCATCCTGCCTACTCCCCACTAGAA
* * * * * *
1075942 GCGCTCGCCATGAACTCTGTCCCCCTTCTAACTCTTAATGGTGAAGCGCTCGACGAAAAATAGGA
65 GCGCTCGGCATGAACTCTGTCCCCCTTCCAACTCTTAACGGTGAAGCGCTCGGCGAGAATTA-GA
*
1076007 ATACCCT
129 ATGCCCT
* * *
1076014 GCCTACTCCACACGTTAGAGCACCCGGCGTAAGATCAGGTCATCCTGCCTACTCCCCACTAGAAT
1 GCCTACTCCACACGTTAGAGCTCCCAGCGTAAGATCAGGTCATCCTGCCTACTCCCCACTAGAAG
*
1076079 CGCTCGACATGAACTCTGTCCCCCTTCCAA
66 CGCTCGGCATGAACTCTGTCCCCCTTCCAA
1076109 TTAGGTTTGC
Statistics
Matches: 320, Mismatches: 42, Indels: 10
0.86 0.11 0.03
Matches are distributed among these distances:
135 4 0.01
136 312 0.98
137 3 0.01
138 1 0.00
ACGTcount: A:0.23, C:0.35, G:0.19, T:0.23
Consensus pattern (135 bp):
GCCTACTCCACACGTTAGAGCTCCCAGCGTAAGATCAGGTCATCCTGCCTACTCCCCACTAGAAG
CGCTCGGCATGAACTCTGTCCCCCTTCCAACTCTTAACGGTGAAGCGCTCGGCGAGAATTAGAAT
GCCCT
Found at i:1076093 original size:272 final size:272
Alignment explanation
Indices: 1075606--1076108 Score: 694
Period size: 272 Copynumber: 1.8 Consensus size: 272
1075596 ATTTCACCCG
* *
1075606 GCCTACTCCACACGTTAGAGCGCTCAGCGTAAGATCAGGTCATCCTGCCTACTCCCCTCTGGAAA
1 GCCTACTCCACACGTTACAGCGCTCAGCGTAAGATCAGGTCATCCTGCCTACTCCCCACTGGAAA
* * * * * * *
1075671 CGCTCAGCATGTACTCTGTCCCCCTGCCTACTCTCAACGTTGAAGTGCTCAGTGTGACATTAAAG
66 CGCTCAGCATGAACTCTGTCCCCCTGCCTACTCTCAACGGTGAAGCGCTCAGCGTAAAAATAAAG
* *
1075736 CACCCTGCCTACTCCACACGTTAGAGCTCCCAGCGTAAGATCGGGTCATCCTGCCTACTACCCAC
131 CACCCTGCCTACTCCACACGTTAGAGCACCCAGCGTAAGATCAGGTCATCCTGCCTACTACCCAC
**
1075801 TAGAAGCGCTCGGTATGAACTCTGTCCCCCTTCCAACTCTTAACGGTAAAGCGCTCGGCGAGAAT
196 TAGAAGCGCTCGACATGAACTCTGTCCCCCTTCCAACTCTTAACGGTAAAGCGCTCGGCGAGAAT
1075866 TATGAATGCCCT
261 TATGAATGCCCT
* * *
1075878 GCCTACTCCACACGTTACAGC-ATCCGGCGTAAGATCATGTCATCCTGCCTACTCCCCACTGGAA
1 GCCTACTCCACACGTTACAGCGCT-CAGCGTAAGATCAGGTCATCCTGCCTACTCCCCACTGGAA
* * * *
1075942 GCGCTC-GCCATGAACTCTGTCCCCCT-TCTAACTCTTAATGGTGAAGCGCTC-GACG-AAAAAT
65 ACGCTCAG-CATGAACTCTGTCCCCCTGCCT-ACTCTCAACGGTGAAGCGCTCAG-CGTAAAAAT
* *
1076003 AGGAA-TACCCTGCCTACTCCACACGTTAGAGCACCCGGCGTAAGATCAGGTCATCCTGCCTACT
127 A--AAGCACCCTGCCTACTCCACACGTTAGAGCACCCAGCGTAAGATCAGGTCATCCTGCCTACT
* *
1076067 CCCCACTAGAATCGCTCGACATGAACTCTGTCCCCCTTCCAA
190 ACCCACTAGAAGCGCTCGACATGAACTCTGTCCCCCTTCCAA
1076109 TTAGGTTTGC
Statistics
Matches: 201, Mismatches: 24, Indels: 12
0.85 0.10 0.05
Matches are distributed among these distances:
271 9 0.04
272 190 0.95
273 2 0.01
ACGTcount: A:0.23, C:0.35, G:0.19, T:0.23
Consensus pattern (272 bp):
GCCTACTCCACACGTTACAGCGCTCAGCGTAAGATCAGGTCATCCTGCCTACTCCCCACTGGAAA
CGCTCAGCATGAACTCTGTCCCCCTGCCTACTCTCAACGGTGAAGCGCTCAGCGTAAAAATAAAG
CACCCTGCCTACTCCACACGTTAGAGCACCCAGCGTAAGATCAGGTCATCCTGCCTACTACCCAC
TAGAAGCGCTCGACATGAACTCTGTCCCCCTTCCAACTCTTAACGGTAAAGCGCTCGGCGAGAAT
TATGAATGCCCT
Found at i:1078278 original size:16 final size:18
Alignment explanation
Indices: 1078257--1078291 Score: 56
Period size: 16 Copynumber: 2.1 Consensus size: 18
1078247 TTCGGTTGGA
1078257 TAAAATTA-AAAAA-AAT
1 TAAAATTACAAAAATAAT
1078273 TAAAATTACAAAAATAAT
1 TAAAATTACAAAAATAAT
1078291 T
1 T
1078292 TTAAAAAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 8 0.47
17 5 0.29
18 4 0.24
ACGTcount: A:0.69, C:0.03, G:0.00, T:0.29
Consensus pattern (18 bp):
TAAAATTACAAAAATAAT
Found at i:1089513 original size:44 final size:45
Alignment explanation
Indices: 1089428--1089516 Score: 126
Period size: 44 Copynumber: 2.0 Consensus size: 45
1089418 AAGTATAAAA
* *
1089428 AGTGTATTAAACCTTTGACGTACAAATGTTTTGTTAGTCCAATGTT
1 AGTGTATCAAACCTTTGAC-TACAAATCTTTTGTTAGTCCAATGTT
* *
1089474 AGTGTATCAAGCCTTTGA-TACACATCTTTTGTTAGTCCAATGT
1 AGTGTATCAAACCTTTGACTACAAATCTTTTGTTAGTCCAATGT
1089517 CTTAAGTTCT
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
44 23 0.59
46 16 0.41
ACGTcount: A:0.27, C:0.16, G:0.17, T:0.40
Consensus pattern (45 bp):
AGTGTATCAAACCTTTGACTACAAATCTTTTGTTAGTCCAATGTT
Found at i:1093111 original size:31 final size:28
Alignment explanation
Indices: 1093073--1093130 Score: 89
Period size: 31 Copynumber: 2.0 Consensus size: 28
1093063 GAGTATTGCT
1093073 GAGCTCGACTCGACTCGAAAACTCTGAAATG
1 GAGCTCGACTCGACTC--AAACTC-GAAATG
1093104 GAGCTCGACTCGACTCAAACTCGAAAT
1 GAGCTCGACTCGACTCAAACTCGAAAT
1093131 CCTGAACTGA
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
28 5 0.19
29 6 0.22
31 16 0.59
ACGTcount: A:0.33, C:0.28, G:0.21, T:0.19
Consensus pattern (28 bp):
GAGCTCGACTCGACTCAAACTCGAAATG
Found at i:1093136 original size:36 final size:36
Alignment explanation
Indices: 1093076--1093146 Score: 90
Period size: 36 Copynumber: 2.0 Consensus size: 36
1093066 TATTGCTGAG
* *
1093076 CTCGACTCGACTCGAAAACTCTGAAATGGAGCTCGA
1 CTCGACTCAACTCGAAAACTCTGAAATGAAGCTCGA
* *
1093112 CTCGACTCAAACTCGAAATC-CTGAACTGAAGCTCG
1 CTCGACTC-AACTCGAAAACTCTGAAATGAAGCTCG
1093147 TGAGCAGTTC
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
36 21 0.70
37 9 0.30
ACGTcount: A:0.31, C:0.30, G:0.20, T:0.20
Consensus pattern (36 bp):
CTCGACTCAACTCGAAAACTCTGAAATGAAGCTCGA
Found at i:1097552 original size:25 final size:25
Alignment explanation
Indices: 1097524--1097576 Score: 79
Period size: 25 Copynumber: 2.1 Consensus size: 25
1097514 ATAAAATATT
*
1097524 AAAACAATTAAGTGGTAATTCAGAA
1 AAAACAATTAAGAGGTAATTCAGAA
* *
1097549 AAAATAATTAAGAGGTAATTCAGTA
1 AAAACAATTAAGAGGTAATTCAGAA
1097574 AAA
1 AAA
1097577 GTGGCCAAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.55, C:0.06, G:0.15, T:0.25
Consensus pattern (25 bp):
AAAACAATTAAGAGGTAATTCAGAA
Found at i:1099008 original size:24 final size:24
Alignment explanation
Indices: 1098976--1099038 Score: 99
Period size: 24 Copynumber: 2.6 Consensus size: 24
1098966 AAAGACGATT
*
1098976 GGTGACAAGTAATGATTGACTATC
1 GGTGACAAGCAATGATTGACTATC
*
1099000 GGTGACAAGCGATGATTGACTATC
1 GGTGACAAGCAATGATTGACTATC
*
1099024 GGTGACAGGCAATGA
1 GGTGACAAGCAATGA
1099039 GTATTGATTA
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 35 1.00
ACGTcount: A:0.32, C:0.14, G:0.30, T:0.24
Consensus pattern (24 bp):
GGTGACAAGCAATGATTGACTATC
Found at i:1100063 original size:3 final size:3
Alignment explanation
Indices: 1100055--1100083 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
1100045 TCAATTTATG
1100055 ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1100084 CAAACTTGAG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:1107088 original size:17 final size:19
Alignment explanation
Indices: 1107052--1107088 Score: 51
Period size: 17 Copynumber: 2.1 Consensus size: 19
1107042 AAATAAAATT
*
1107052 TTCATATCATATTTGTATA
1 TTCATATCATATTAGTATA
1107071 TTCA-ATCA-ATTAGTATA
1 TTCATATCATATTAGTATA
1107088 T
1 T
1107089 GGTTTTATGA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
17 9 0.53
18 4 0.24
19 4 0.24
ACGTcount: A:0.35, C:0.11, G:0.05, T:0.49
Consensus pattern (19 bp):
TTCATATCATATTAGTATA
Found at i:1107864 original size:32 final size:29
Alignment explanation
Indices: 1107826--1107891 Score: 78
Period size: 29 Copynumber: 2.2 Consensus size: 29
1107816 TTAAATTAAC
*
1107826 ATCTTAACATTAAAAATATATATTTTATTTTT
1 ATCTTAA-ATTAAAAA-ATAT-TTTAATTTTT
**
1107858 ATCTTAAATTTTAAAATATTTTAATTTTT
1 ATCTTAAATTAAAAAATATTTTAATTTTT
1107887 ATCTT
1 ATCTT
1107892 CACCTATTTT
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
29 14 0.45
30 4 0.13
31 6 0.19
32 7 0.23
ACGTcount: A:0.38, C:0.06, G:0.00, T:0.56
Consensus pattern (29 bp):
ATCTTAAATTAAAAAATATTTTAATTTTT
Found at i:1112653 original size:27 final size:27
Alignment explanation
Indices: 1112623--1112712 Score: 162
Period size: 27 Copynumber: 3.3 Consensus size: 27
1112613 ATCAAAAAGC
1112623 AGACGGAAAGCTCTAAAGTTAAGTTAA
1 AGACGGAAAGCTCTAAAGTTAAGTTAA
1112650 AGACGGAAAGCTCTAAAGTTAAGTTAA
1 AGACGGAAAGCTCTAAAGTTAAGTTAA
*
1112677 AGACGGAAAACTCTAAAGTTAAGTTAA
1 AGACGGAAAGCTCTAAAGTTAAGTTAA
*
1112704 AGTCGGAAA
1 AGACGGAAA
1112713 CATAGGGGGG
Statistics
Matches: 61, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 61 1.00
ACGTcount: A:0.46, C:0.11, G:0.22, T:0.21
Consensus pattern (27 bp):
AGACGGAAAGCTCTAAAGTTAAGTTAA
Found at i:1114507 original size:24 final size:23
Alignment explanation
Indices: 1114479--1114524 Score: 83
Period size: 24 Copynumber: 2.0 Consensus size: 23
1114469 CATATATATG
1114479 TCTATTATATTATATTTTGATTTC
1 TCTATTATATTATATTTT-ATTTC
1114503 TCTATTATATTATATTTTATTT
1 TCTATTATATTATATTTTATTT
1114525 AGATTTTACT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
23 4 0.18
24 18 0.82
ACGTcount: A:0.26, C:0.07, G:0.02, T:0.65
Consensus pattern (23 bp):
TCTATTATATTATATTTTATTTC
Found at i:1121157 original size:2 final size:2
Alignment explanation
Indices: 1121150--1121183 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
1121140 TTTATAAATT
1121150 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1121184 TTAATATTTT
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:1123952 original size:6 final size:6
Alignment explanation
Indices: 1123917--1123951 Score: 61
Period size: 6 Copynumber: 5.8 Consensus size: 6
1123907 CTTCCATGGA
*
1123917 GCCACT GCCACT GCCACT GCCACT GCCACC GCCAC
1 GCCACT GCCACT GCCACT GCCACT GCCACT GCCAC
1123952 CACCTCCTCT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.17, C:0.54, G:0.17, T:0.11
Consensus pattern (6 bp):
GCCACT
Found at i:1130859 original size:15 final size:15
Alignment explanation
Indices: 1130831--1130908 Score: 106
Period size: 15 Copynumber: 5.3 Consensus size: 15
1130821 AAATAATTTT
1130831 AAATAATTTA--ATA
1 AAATAATTTATTATA
* *
1130844 AGATTATTTATTATA
1 AAATAATTTATTATA
1130859 AAATAATTTATTATA
1 AAATAATTTATTATA
*
1130874 AAATAATTTATTTTA
1 AAATAATTTATTATA
*
1130889 AAATAAATTATTATA
1 AAATAATTTATTATA
1130904 AAATA
1 AAATA
1130909 TATATTGATT
Statistics
Matches: 56, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
13 8 0.14
15 48 0.86
ACGTcount: A:0.54, C:0.00, G:0.01, T:0.45
Consensus pattern (15 bp):
AAATAATTTATTATA
Done.