Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D12
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: 58873029
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.33
Warning! 639818 characters in sequence are not A, C, G, or T
File 139 of 196
Found at i:41195399 original size:25 final size:25
Alignment explanation
Indices: 41195371--41195436 Score: 73
Period size: 25 Copynumber: 2.7 Consensus size: 25
41195361 AAGCTCCTCT
* *
41195371 GAGCTGAATAAT-GGTAAGCTCATAC
1 GAGCTGAAT-ATCAGTAAGCTCATAA
*
41195396 GAGCTGAGTATCAGTAAGCTCATAA
1 GAGCTGAATATCAGTAAGCTCATAA
*
41195421 GAGCTGGA-ATCAGTAA
1 GAGCTGAATATCAGTAA
41195437 CCCTAATGAC
Statistics
Matches: 35, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
24 10 0.29
25 25 0.71
ACGTcount: A:0.36, C:0.15, G:0.26, T:0.23
Consensus pattern (25 bp):
GAGCTGAATATCAGTAAGCTCATAA
Found at i:41202335 original size:25 final size:25
Alignment explanation
Indices: 41202307--41202355 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 25
41202297 AAGCTCCTTT
41202307 GAGCTGAATAACGGTAAACTCATAC
1 GAGCTGAATAACGGTAAACTCATAC
* * *
41202332 GAGCTGAGTATCGGTAAGCTCATA
1 GAGCTGAATAACGGTAAACTCATA
41202356 AGAGATGGAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.35, C:0.18, G:0.24, T:0.22
Consensus pattern (25 bp):
GAGCTGAATAACGGTAAACTCATAC
Found at i:41204695 original size:28 final size:28
Alignment explanation
Indices: 41204642--41204695 Score: 72
Period size: 28 Copynumber: 1.9 Consensus size: 28
41204632 TGAGTAGCCT
* *
41204642 AAATATCATAGCTTGTATCAGCAAATTC
1 AAATATCATAACTTGTATCAGAAAATTC
* *
41204670 AAATATCATAACTTGTGTGAGAAAAT
1 AAATATCATAACTTGTATCAGAAAAT
41204696 CGAATTATTC
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 22 1.00
ACGTcount: A:0.43, C:0.13, G:0.13, T:0.31
Consensus pattern (28 bp):
AAATATCATAACTTGTATCAGAAAATTC
Found at i:41208693 original size:13 final size:13
Alignment explanation
Indices: 41208675--41208699 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
41208665 ATAGTTAGTT
41208675 GTTTTATTATTTA
1 GTTTTATTATTTA
41208688 GTTTTATTATTT
1 GTTTTATTATTT
41208700 TATTTATTTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.20, C:0.00, G:0.08, T:0.72
Consensus pattern (13 bp):
GTTTTATTATTTA
Found at i:41208714 original size:21 final size:21
Alignment explanation
Indices: 41208676--41208719 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
41208666 TAGTTAGTTG
* *
41208676 TTTTATTATTTAGTTTTATTA
1 TTTTATTATTTAGCTTTAGTA
41208697 TTTTATTTATTTA-CTTTAGTA
1 TTTTA-TTATTTAGCTTTAGTA
41208718 TT
1 TT
41208720 AGTTTTGGTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 13 0.65
22 7 0.35
ACGTcount: A:0.23, C:0.02, G:0.05, T:0.70
Consensus pattern (21 bp):
TTTTATTATTTAGCTTTAGTA
Found at i:41212073 original size:47 final size:47
Alignment explanation
Indices: 41212004--41212098 Score: 190
Period size: 47 Copynumber: 2.0 Consensus size: 47
41211994 ATCGTCATAG
41212004 AATATTGAAGAAAAAACTCAAAAAAACACCATTGAAGCTGACTCTGA
1 AATATTGAAGAAAAAACTCAAAAAAACACCATTGAAGCTGACTCTGA
41212051 AATATTGAAGAAAAAACTCAAAAAAACACCATTGAAGCTGACTCTGA
1 AATATTGAAGAAAAAACTCAAAAAAACACCATTGAAGCTGACTCTGA
41212098 A
1 A
41212099 GCAAATTTCC
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
47 48 1.00
ACGTcount: A:0.52, C:0.17, G:0.13, T:0.19
Consensus pattern (47 bp):
AATATTGAAGAAAAAACTCAAAAAAACACCATTGAAGCTGACTCTGA
Found at i:41228022 original size:12 final size:12
Alignment explanation
Indices: 41228005--41228029 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
41227995 ACATACTTAA
41228005 AATAAGAATAAT
1 AATAAGAATAAT
41228017 AATAAGAATAAT
1 AATAAGAATAAT
41228029 A
1 A
41228030 TGAAAAGTAA
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:0.68, C:0.00, G:0.08, T:0.24
Consensus pattern (12 bp):
AATAAGAATAAT
Found at i:41230040 original size:23 final size:23
Alignment explanation
Indices: 41229999--41230404 Score: 263
Period size: 23 Copynumber: 17.4 Consensus size: 23
41229989 TATACATCAG
*
41229999 AAATT-GAGCAGCATGTATATACC
1 AAATTGGA-CAGCATATATATACC
* * *
41230022 AATTTGGACAGCACT-TATACACA
1 AAATTGGACAGCA-TATATATACC
* * *
41230045 AAATTTGACAGCATGTATATACA
1 AAATTGGACAGCATATATATACC
*
41230068 AAATTGGACAGCATTTAT-TCACCC
1 AAATTGGACAGCATATATAT-A-CC
*
41230092 AAATTGGGCAGCATATATATACC
1 AAATTGGACAGCATATATATACC
* * **
41230115 AATTTGGACAGCACT-TATACAAA
1 AAATTGGACAGCA-TATATATACC
* * *
41230138 AAATTTGACAGCATGTATATACA
1 AAATTGGACAGCATATATATACC
* * *
41230161 AAATTGGACAACATTTCT-TCACC
1 AAATTGGACAGCATATATAT-ACC
*
41230184 AAAATTGGGCAGCATATATATATACC
1 -AAATTGGACAGC--ATATATATACC
* *
41230210 AAATTGGACAGCACT-TATACACA
1 AAATTGGACAGCA-TATATATACC
* * *
41230233 AAATTTGACAGCATGTATATACA
1 AAATTGGACAGCATATATATACC
*
41230256 AAATTGGACAGCATTTAT-TCACC
1 AAATTGGACAGCATATATAT-ACC
*
41230279 AAAATTGGGCAGCATATATATACC
1 -AAATTGGACAGCATATATATACC
* * *
41230303 AATTTGGACAGCACT-TATACACA
1 AAATTGGACAGCA-TATATATACC
* * * *
41230326 AAATTTGACAGGATGTATATACA
1 AAATTGGACAGCATATATATACC
* * *
41230349 AAACTGGACAACATTTAT-TCACC
1 AAATTGGACAGCATATATAT-ACC
*
41230372 AAAATTGGGCAGCATATATATACC
1 -AAATTGGACAGCATATATATACC
*
41230396 AATTTGGAC
1 AAATTGGAC
41230405 CATTAAAGCA
Statistics
Matches: 301, Mismatches: 59, Indels: 46
0.74 0.15 0.11
Matches are distributed among these distances:
22 8 0.03
23 201 0.67
24 70 0.23
25 14 0.05
26 7 0.02
27 1 0.00
ACGTcount: A:0.40, C:0.18, G:0.14, T:0.28
Consensus pattern (23 bp):
AAATTGGACAGCATATATATACC
Found at i:41230103 original size:93 final size:93
Alignment explanation
Indices: 41229999--41230404 Score: 704
Period size: 93 Copynumber: 4.3 Consensus size: 93
41229989 TATACATCAG
* *
41229999 AAATTGAGCAGCATGTATATACCAATTTGGACAGCACTTATACACAAAATTTGACAGCATGTATA
1 AAATTGGGCAGCATATATATACCAATTTGGACAGCACTTATACACAAAATTTGACAGCATGTATA
* *
41230064 TACAAAATTGGACAGCATTTATTCACCC
66 TACAAAATTGGACAACATTTATTCACCA
*
41230092 AAATTGGGCAGCATATATATACCAATTTGGACAGCACTTATACAAAAAATTTGACAGCATGTATA
1 AAATTGGGCAGCATATATATACCAATTTGGACAGCACTTATACACAAAATTTGACAGCATGTATA
*
41230157 TACAAAATTGGACAACATTTCTTCACCA
66 TACAAAATTGGACAACATTTATTCACCA
*
41230185 AAATTGGGCAGCATATATATATACCAAATTGGACAGCACTTATACACAAAATTTGACAGCATGTA
1 AAATTGGGCAGC--ATATATATACCAATTTGGACAGCACTTATACACAAAATTTGACAGCATGTA
*
41230250 TATACAAAATTGGACAGCATTTATTCACCA
64 TATACAAAATTGGACAACATTTATTCACCA
*
41230280 AAATTGGGCAGCATATATATACCAATTTGGACAGCACTTATACACAAAATTTGACAGGATGTATA
1 AAATTGGGCAGCATATATATACCAATTTGGACAGCACTTATACACAAAATTTGACAGCATGTATA
*
41230345 TACAAAACTGGACAACATTTATTCACCA
66 TACAAAATTGGACAACATTTATTCACCA
41230373 AAATTGGGCAGCATATATATACCAATTTGGAC
1 AAATTGGGCAGCATATATATACCAATTTGGAC
41230405 CATTAAAGCA
Statistics
Matches: 297, Mismatches: 14, Indels: 4
0.94 0.04 0.01
Matches are distributed among these distances:
93 208 0.70
95 89 0.30
ACGTcount: A:0.40, C:0.18, G:0.14, T:0.28
Consensus pattern (93 bp):
AAATTGGGCAGCATATATATACCAATTTGGACAGCACTTATACACAAAATTTGACAGCATGTATA
TACAAAATTGGACAACATTTATTCACCA
Found at i:41230234 original size:188 final size:188
Alignment explanation
Indices: 41230014--41230393 Score: 706
Period size: 188 Copynumber: 2.0 Consensus size: 188
41230004 GAGCAGCATG
*
41230014 TATATACCAATTTGGACAGCACTTATACACAAAATTTGACAGCATGTATATACAAAATTGGACAG
1 TATATACCAAATTGGACAGCACTTATACACAAAATTTGACAGCATGTATATACAAAATTGGACAG
*
41230079 CATTTATTCACCCAAATTGGGCAGCATATATATACCAATTTGGACAGCACTTATACAAAAAATTT
66 CATTTATTCACCAAAATTGGGCAGCATATATATACCAATTTGGACAGCACTTATACAAAAAATTT
* *
41230144 GACAGCATGTATATACAAAATTGGACAACATTTCTTCACCAAAATTGGGCAGCATATA
131 GACAGCATGTATATACAAAACTGGACAACATTTATTCACCAAAATTGGGCAGCATATA
41230202 TATATACCAAATTGGACAGCACTTATACACAAAATTTGACAGCATGTATATACAAAATTGGACAG
1 TATATACCAAATTGGACAGCACTTATACACAAAATTTGACAGCATGTATATACAAAATTGGACAG
*
41230267 CATTTATTCACCAAAATTGGGCAGCATATATATACCAATTTGGACAGCACTTATACACAAAATTT
66 CATTTATTCACCAAAATTGGGCAGCATATATATACCAATTTGGACAGCACTTATACAAAAAATTT
*
41230332 GACAGGATGTATATACAAAACTGGACAACATTTATTCACCAAAATTGGGCAGCATATA
131 GACAGCATGTATATACAAAACTGGACAACATTTATTCACCAAAATTGGGCAGCATATA
41230390 TATA
1 TATA
41230394 CCAATTTGGA
Statistics
Matches: 186, Mismatches: 6, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
188 186 1.00
ACGTcount: A:0.41, C:0.18, G:0.13, T:0.28
Consensus pattern (188 bp):
TATATACCAAATTGGACAGCACTTATACACAAAATTTGACAGCATGTATATACAAAATTGGACAG
CATTTATTCACCAAAATTGGGCAGCATATATATACCAATTTGGACAGCACTTATACAAAAAATTT
GACAGCATGTATATACAAAACTGGACAACATTTATTCACCAAAATTGGGCAGCATATA
Found at i:41231133 original size:28 final size:28
Alignment explanation
Indices: 41231094--41231189 Score: 156
Period size: 28 Copynumber: 3.4 Consensus size: 28
41231084 TAATACGTTT
* *
41231094 GCACACTTAGTGCTTTGCCATTAAACTC
1 GCACACTTAGTGCTTTACAATTAAACTC
*
41231122 ACACACTTAGTGCTTTACAATTAAACTC
1 GCACACTTAGTGCTTTACAATTAAACTC
*
41231150 GCACACTTAGTGCTTTACAATTAAATTC
1 GCACACTTAGTGCTTTACAATTAAACTC
41231178 GCACACTTAGTG
1 GCACACTTAGTG
41231190 TCGAAAGTTA
Statistics
Matches: 63, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 63 1.00
ACGTcount: A:0.30, C:0.25, G:0.12, T:0.32
Consensus pattern (28 bp):
GCACACTTAGTGCTTTACAATTAAACTC
Found at i:41232795 original size:21 final size:20
Alignment explanation
Indices: 41232770--41232821 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 20
41232760 TTTTTCCTAG
41232770 GATGTAAATTGTA-TATAATT
1 GATGTAAATTGTATTA-AATT
*
41232790 GAATGTGAATTGTATTAAATT
1 G-ATGTAAATTGTATTAAATT
41232811 GATGTTAAATT
1 GATG-TAAATT
41232822 CATTCATATA
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
20 4 0.15
21 21 0.78
22 2 0.07
ACGTcount: A:0.38, C:0.00, G:0.17, T:0.44
Consensus pattern (20 bp):
GATGTAAATTGTATTAAATT
Found at i:41233432 original size:24 final size:25
Alignment explanation
Indices: 41233379--41233434 Score: 78
Period size: 25 Copynumber: 2.3 Consensus size: 25
41233369 TTCCCGATAT
* *
41233379 ATGGCTATTTGGAGCTTCCCAATTA
1 ATGGCTCTTTGGAGCTACCCAATTA
41233404 ATGGCTCTTTGGAGCTACCC-ATTA
1 ATGGCTCTTTGGAGCTACCCAATTA
*
41233428 TTGGCTC
1 ATGGCTC
41233435 GCATGAGCTT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
24 10 0.36
25 18 0.64
ACGTcount: A:0.20, C:0.23, G:0.21, T:0.36
Consensus pattern (25 bp):
ATGGCTCTTTGGAGCTACCCAATTA
Found at i:41233456 original size:24 final size:25
Alignment explanation
Indices: 41233429--41233484 Score: 78
Period size: 24 Copynumber: 2.3 Consensus size: 25
41233419 TACCCATTAT
*
41233429 TGGCTCGCATGAGCTTCTTG-AATA
1 TGGCTCGCATGAGCTTCCTGTAATA
* *
41233453 TGGCTCACATGAGCTTCCTGTTATA
1 TGGCTCGCATGAGCTTCCTGTAATA
41233478 TGGCTCG
1 TGGCTCG
41233485 AGAGAGGGCT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
24 18 0.67
25 9 0.33
ACGTcount: A:0.18, C:0.23, G:0.25, T:0.34
Consensus pattern (25 bp):
TGGCTCGCATGAGCTTCCTGTAATA
Found at i:41239679 original size:41 final size:41
Alignment explanation
Indices: 41239619--41239727 Score: 157
Period size: 41 Copynumber: 2.7 Consensus size: 41
41239609 TTTAACATAT
*
41239619 TCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGATTCCA-A
1 TCACCGGCACTTAGCCTGCTAGGCTTATAACCTGATT-CAGA
* * *
41239660 TCACCGACACTTAGTCTGCTAGGTTTATAACCTGATTCAGA
1 TCACCGGCACTTAGCCTGCTAGGCTTATAACCTGATTCAGA
*
41239701 TCACCGGCACTTAGCCTGCTAGACTTA
1 TCACCGGCACTTAGCCTGCTAGGCTTA
41239728 AAGTCCGAAT
Statistics
Matches: 59, Mismatches: 8, Indels: 2
0.86 0.12 0.03
Matches are distributed among these distances:
40 2 0.03
41 57 0.97
ACGTcount: A:0.24, C:0.29, G:0.18, T:0.28
Consensus pattern (41 bp):
TCACCGGCACTTAGCCTGCTAGGCTTATAACCTGATTCAGA
Found at i:41239764 original size:82 final size:82
Alignment explanation
Indices: 41239619--41239776 Score: 182
Period size: 82 Copynumber: 1.9 Consensus size: 82
41239609 TTTAACATAT
* * * * *
41239619 TCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGATTCCAATCACCGACACTTAGTCTGCTAGG-
1 TCACCGGCACTTAGCCTGCTAGACTTAAAGCCTGAATCCAATCACCGACACTTAGCCTACTAGGT
41239683 TTTATAACCTGATTCAGA
66 TTTA-AACCTGATTCAGA
*
41239701 TCACCGGCACTTAGCCTGCTAGACTTAAAGTCC-GAAT-CATTTCACC-AGC-CTTAAGCCTACT
1 TCACCGGCACTTAGCCTGCTAGACTTAAAG-CCTGAATCCA-ATCACCGA-CACTT-AGCCTACT
41239762 AGGTTTTAAACCTGA
62 AGGTTTTAAACCTGA
41239777 AAATTTCAAT
Statistics
Matches: 65, Mismatches: 6, Indels: 10
0.80 0.07 0.12
Matches are distributed among these distances:
81 6 0.09
82 53 0.82
83 6 0.09
ACGTcount: A:0.26, C:0.28, G:0.17, T:0.28
Consensus pattern (82 bp):
TCACCGGCACTTAGCCTGCTAGACTTAAAGCCTGAATCCAATCACCGACACTTAGCCTACTAGGT
TTTAAACCTGATTCAGA
Found at i:41251112 original size:26 final size:26
Alignment explanation
Indices: 41251083--41251150 Score: 75
Period size: 26 Copynumber: 2.7 Consensus size: 26
41251073 CCGATATATA
* *
41251083 GCTCTTCGTGAGCTTTCTGATTAAAG
1 GCTCTTCGTGAGCTTTCTAATTAAAC
* * *
41251109 GCTCTTTGTGAGCTTCCTAATTAATC
1 GCTCTTCGTGAGCTTTCTAATTAAAC
*
41251135 GCTCTCCG-GAGCTTTC
1 GCTCTTCGTGAGCTTTC
41251151 CGATATAGCT
Statistics
Matches: 34, Mismatches: 8, Indels: 1
0.79 0.19 0.02
Matches are distributed among these distances:
25 7 0.21
26 27 0.79
ACGTcount: A:0.16, C:0.25, G:0.21, T:0.38
Consensus pattern (26 bp):
GCTCTTCGTGAGCTTTCTAATTAAAC
Found at i:41251220 original size:25 final size:25
Alignment explanation
Indices: 41251083--41251220 Score: 63
Period size: 26 Copynumber: 5.5 Consensus size: 25
41251073 CCGATATATA
* *
41251083 GCTCTTCGTGAGCTTTCTGATTAAAG
1 GCTCTTCG-GAGCTTCCTGATTAATG
* * *
41251109 GCTCTTTGTGAGCTTCCTAATTAATC
1 GCTCTTCG-GAGCTTCCTGATTAATG
* *
41251135 GCTCTCCGGAGCTTTCC-GA-T-ATA
1 GCTCTTCGGAGC-TTCCTGATTAATG
* *
41251158 GCTCGCTT--GAACTTCCCGA-TATATG
1 GCT--CTTCGGAGCTTCCTGATTA-ATG
* * *
41251183 GCTATCCGAAGCTTCCTGATTAATG
1 GCTCTTCGGAGCTTCCTGATTAATG
*
41251208 GCTCTTTGGAGCT
1 GCTCTTCGGAGCT
41251221 ACCCATTATT
Statistics
Matches: 82, Mismatches: 21, Indels: 19
0.67 0.17 0.16
Matches are distributed among these distances:
22 4 0.05
23 12 0.15
24 1 0.01
25 32 0.39
26 33 0.40
ACGTcount: A:0.19, C:0.25, G:0.21, T:0.36
Consensus pattern (25 bp):
GCTCTTCGGAGCTTCCTGATTAATG
Found at i:41254025 original size:26 final size:26
Alignment explanation
Indices: 41253957--41254035 Score: 97
Period size: 26 Copynumber: 3.0 Consensus size: 26
41253947 TTCTATTGCT
* * * *
41253957 ATACCAATATTTTTAAAGATATACCA
1 ATACTAATATTTCTAACGACATACCA
*
41253983 ATACTAAAATTTCTAACGACATACCA
1 ATACTAATATTTCTAACGACATACCA
41254009 ATACTAATATTTCTAAC-ACTATACCA
1 ATACTAATATTTCTAACGAC-ATACCA
41254035 A
1 A
41254036 AATTTTTATC
Statistics
Matches: 46, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
25 2 0.04
26 44 0.96
ACGTcount: A:0.46, C:0.20, G:0.03, T:0.32
Consensus pattern (26 bp):
ATACTAATATTTCTAACGACATACCA
Found at i:41254789 original size:4 final size:4
Alignment explanation
Indices: 41254780--41254806 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
41254770 ACTAGTCTTA
41254780 AAAT AAAT AAAT AAAT AAAT AAAT AAA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAA
41254807 AGTTCTTCAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (4 bp):
AAAT
Found at i:41260075 original size:25 final size:25
Alignment explanation
Indices: 41260046--41260180 Score: 125
Period size: 25 Copynumber: 5.5 Consensus size: 25
41260036 AGCATCAATT
41260046 TGGACAGCATTAATATGCTCAAAAA
1 TGGACAGCATTAATATGCTCAAAAA
* * * **
41260071 TGGACAGCATT--TAAGCACTAATT
1 TGGACAGCATTAATATGCTCAAAAA
*
41260094 TGGACAGCATTAATATGCTAAAAAA
1 TGGACAGCATTAATATGCTCAAAAA
* * * * **
41260119 TAGACAGCATT--TAAGCACTAATT
1 TGGACAGCATTAATATGCTCAAAAA
41260142 TGGACAGCATTAATATGCTCAAAAA
1 TGGACAGCATTAATATGCTCAAAAA
41260167 TGGACAGCAATTAA
1 TGGACAGC-ATTAA
41260181 GCACTAATTT
Statistics
Matches: 81, Mismatches: 24, Indels: 9
0.71 0.21 0.08
Matches are distributed among these distances:
23 34 0.42
25 42 0.52
26 5 0.06
ACGTcount: A:0.42, C:0.16, G:0.16, T:0.26
Consensus pattern (25 bp):
TGGACAGCATTAATATGCTCAAAAA
Found at i:41260094 original size:48 final size:48
Alignment explanation
Indices: 41260021--41260199 Score: 297
Period size: 48 Copynumber: 3.7 Consensus size: 48
41260011 TTTGTACAAC
*
41260021 AATGGATAGCAATTAAGCA-TCAATTTGGACAGCATTAATATGCTCAAA
1 AATGGACAGCAATTAAGCACT-AATTTGGACAGCATTAATATGCTCAAA
* *
41260069 AATGGACAGCATTTAAGCACTAATTTGGACAGCATTAATATGCTAAAA
1 AATGGACAGCAATTAAGCACTAATTTGGACAGCATTAATATGCTCAAA
* *
41260117 AATAGACAGCATTTAAGCACTAATTTGGACAGCATTAATATGCTCAAA
1 AATGGACAGCAATTAAGCACTAATTTGGACAGCATTAATATGCTCAAA
41260165 AATGGACAGCAATTAAGCACTAATTTGGACAGCAT
1 AATGGACAGCAATTAAGCACTAATTTGGACAGCAT
41260200 CTTATCATCA
Statistics
Matches: 123, Mismatches: 7, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
48 122 0.99
49 1 0.01
ACGTcount: A:0.41, C:0.16, G:0.17, T:0.26
Consensus pattern (48 bp):
AATGGACAGCAATTAAGCACTAATTTGGACAGCATTAATATGCTCAAA
Found at i:41260101 original size:23 final size:23
Alignment explanation
Indices: 41260071--41260199 Score: 107
Period size: 23 Copynumber: 5.4 Consensus size: 23
41260061 TGCTCAAAAA
41260071 TGGACAGCATTTAAGCACTAATT
1 TGGACAGCATTTAAGCACTAATT
* * **
41260094 TGGACAGCATTAATATGCTA-AAAAA
1 TGGACAGCATT--TAAGC-ACTAATT
*
41260119 TAGACAGCATTTAAGCACTAATT
1 TGGACAGCATTTAAGCACTAATT
* * * **
41260142 TGGACAGCATTAATATGCTCAAAAA
1 TGGACAGCATT--TAAGCACTAATT
*
41260167 TGGACAGCAATTAAGCACTAATT
1 TGGACAGCATTTAAGCACTAATT
41260190 TGGACAGCAT
1 TGGACAGCAT
41260200 CTTATCATCA
Statistics
Matches: 78, Mismatches: 22, Indels: 12
0.70 0.20 0.11
Matches are distributed among these distances:
22 1 0.01
23 43 0.55
25 33 0.42
26 1 0.01
ACGTcount: A:0.40, C:0.16, G:0.17, T:0.26
Consensus pattern (23 bp):
TGGACAGCATTTAAGCACTAATT
Found at i:41267461 original size:48 final size:48
Alignment explanation
Indices: 41267405--41267605 Score: 298
Period size: 48 Copynumber: 4.2 Consensus size: 48
41267395 AACAACATTC
* * *
41267405 GGACAGCATTGATTTG-TACAAAAATGGACAGCAACTAAGCA-TCAATTT
1 GGACAGCATTAATATGCT-CAAAAATGGACAGCAATTAAGCACT-AATTT
*
41267453 GGACAGCATTAATATGCTCAAAAATGGACAGCATTTAAGCACTAATTT
1 GGACAGCATTAATATGCTCAAAAATGGACAGCAATTAAGCACTAATTT
* * *
41267501 GGACAGCATTAATATGCTTAAAAATAGACAGCATTTAAGCACTAATTT
1 GGACAGCATTAATATGCTCAAAAATGGACAGCAATTAAGCACTAATTT
*
41267549 GGACAGCATTAATATGTTCAAAAATGGACAGCAATTAAGCACTAATTT
1 GGACAGCATTAATATGCTCAAAAATGGACAGCAATTAAGCACTAATTT
41267597 GGACAGCAT
1 GGACAGCAT
41267606 CTTATCATCA
Statistics
Matches: 141, Mismatches: 10, Indels: 4
0.91 0.06 0.03
Matches are distributed among these distances:
48 139 0.99
49 2 0.01
ACGTcount: A:0.40, C:0.16, G:0.17, T:0.26
Consensus pattern (48 bp):
GGACAGCATTAATATGCTCAAAAATGGACAGCAATTAAGCACTAATTT
Found at i:41267483 original size:25 final size:25
Alignment explanation
Indices: 41267452--41267586 Score: 116
Period size: 25 Copynumber: 5.5 Consensus size: 25
41267442 AGCATCAATT
41267452 TGGACAGCATTAATATGCTCAAAAA
1 TGGACAGCATTAATATGCTCAAAAA
* * * **
41267477 TGGACAGCATT--TAAGCACTAATT
1 TGGACAGCATTAATATGCTCAAAAA
*
41267500 TGGACAGCATTAATATGCTTAAAAA
1 TGGACAGCATTAATATGCTCAAAAA
* * * * **
41267525 TAGACAGCATT--TAAGCACTAATT
1 TGGACAGCATTAATATGCTCAAAAA
*
41267548 TGGACAGCATTAATATGTTCAAAAA
1 TGGACAGCATTAATATGCTCAAAAA
41267573 TGGACAGCAATTAA
1 TGGACAGC-ATTAA
41267587 GCACTAATTT
Statistics
Matches: 80, Mismatches: 25, Indels: 9
0.70 0.22 0.08
Matches are distributed among these distances:
23 34 0.43
25 41 0.51
26 5 0.06
ACGTcount: A:0.41, C:0.15, G:0.16, T:0.27
Consensus pattern (25 bp):
TGGACAGCATTAATATGCTCAAAAA
Found at i:41267507 original size:23 final size:23
Alignment explanation
Indices: 41267477--41267605 Score: 98
Period size: 23 Copynumber: 5.4 Consensus size: 23
41267467 TGCTCAAAAA
41267477 TGGACAGCATTTAAGCACTAATT
1 TGGACAGCATTTAAGCACTAATT
* * **
41267500 TGGACAGCATTAATATGC-TTAAAAA
1 TGGACAGCATT--TAAGCACT-AATT
*
41267525 TAGACAGCATTTAAGCACTAATT
1 TGGACAGCATTTAAGCACTAATT
* ** * **
41267548 TGGACAGCATTAATATGTTCAAAAA
1 TGGACAGCATT--TAAGCACTAATT
*
41267573 TGGACAGCAATTAAGCACTAATT
1 TGGACAGCATTTAAGCACTAATT
41267596 TGGACAGCAT
1 TGGACAGCAT
41267606 CTTATCATCA
Statistics
Matches: 76, Mismatches: 24, Indels: 12
0.68 0.21 0.11
Matches are distributed among these distances:
23 42 0.55
24 2 0.03
25 32 0.42
ACGTcount: A:0.40, C:0.16, G:0.17, T:0.28
Consensus pattern (23 bp):
TGGACAGCATTTAAGCACTAATT
Found at i:41268274 original size:43 final size:43
Alignment explanation
Indices: 41268209--41268362 Score: 133
Period size: 43 Copynumber: 3.7 Consensus size: 43
41268199 AGCTCATACA
* * *
41268209 ATGCCA-TATCCCAGATATGGTCTTACATGTTAACATATTTCG
1 ATGCCACTGTCCCAGACATGGTCTTACATGTTATCATATTTCG
* * * *
41268251 ATGCCACTGTCCCAGACAGGGTCTTATACG--ACTCATA-TACG
1 ATGCCACTGTCCCAGACATGGTCTTACATGTTA-TCATATTTCG
* *
41268292 ATGCCAAC-GTCCCAGACATGGCCTTACATGTTCTC-TCACTTT-G
1 ATGCC-ACTGTCCCAGACATGGTCTTACATGTTATCAT-A-TTTCG
*
41268335 ATGCCAATGTCCCAGACATGGTCTTACA
1 ATGCCACTGTCCCAGACATGGTCTTACA
41268363 CAAAATCACA
Statistics
Matches: 88, Mismatches: 15, Indels: 17
0.73 0.12 0.14
Matches are distributed among these distances:
41 28 0.32
42 16 0.18
43 43 0.49
44 1 0.01
ACGTcount: A:0.26, C:0.28, G:0.17, T:0.29
Consensus pattern (43 bp):
ATGCCACTGTCCCAGACATGGTCTTACATGTTATCATATTTCG
Found at i:41273570 original size:20 final size:22
Alignment explanation
Indices: 41273545--41273598 Score: 67
Period size: 20 Copynumber: 2.5 Consensus size: 22
41273535 TTATATGGTC
* *
41273545 CTTTTCTTTTTA-TT-TTTTTT
1 CTTTTCTTTCTAGTTCTTTGTT
41273565 CTTTTCTTTCTAGTTCTTTGTT
1 CTTTTCTTTCTAGTTCTTTGTT
41273587 CTTCTTCTTTCT
1 CTT-TTCTTTCT
41273599 TTTATCTTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
20 11 0.38
21 2 0.07
22 8 0.28
23 8 0.28
ACGTcount: A:0.04, C:0.19, G:0.04, T:0.74
Consensus pattern (22 bp):
CTTTTCTTTCTAGTTCTTTGTT
Found at i:41274873 original size:22 final size:24
Alignment explanation
Indices: 41274830--41274894 Score: 73
Period size: 22 Copynumber: 2.8 Consensus size: 24
41274820 ATCTTTTTGT
41274830 ATATGAAACTGAAATTGCTTCTGC
1 ATATGAAACTGAAATTGCTTCTGC
* * *
41274854 ATATGTAACT-AATTTG-TTCTGA
1 ATATGAAACTGAAATTGCTTCTGC
*
41274876 ATCTG-AACTGAAATTGCTT
1 ATATGAAACTGAAATTGCTT
41274895 TTGTTACCAA
Statistics
Matches: 34, Mismatches: 5, Indels: 5
0.77 0.11 0.11
Matches are distributed among these distances:
21 4 0.12
22 14 0.41
23 7 0.21
24 9 0.26
ACGTcount: A:0.32, C:0.14, G:0.15, T:0.38
Consensus pattern (24 bp):
ATATGAAACTGAAATTGCTTCTGC
Found at i:41275880 original size:15 final size:15
Alignment explanation
Indices: 41275860--41275898 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
41275850 TACTGATTTC
*
41275860 TTAAATTTTTAGATA
1 TTAAATTTATAGATA
*
41275875 TTAAATTTATAGATT
1 TTAAATTTATAGATA
*
41275890 TTAAGTTTA
1 TTAAATTTA
41275899 AAGGTAAAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.38, C:0.00, G:0.08, T:0.54
Consensus pattern (15 bp):
TTAAATTTATAGATA
Found at i:41276504 original size:15 final size:17
Alignment explanation
Indices: 41276465--41276505 Score: 50
Period size: 16 Copynumber: 2.5 Consensus size: 17
41276455 ATTGGAATGG
41276465 TGAATTGATGATGAAAT
1 TGAATTGATGATGAAAT
*
41276482 TGATATTGAT-A-GAATT
1 TGA-ATTGATGATGAAAT
41276498 TGAATTGA
1 TGAATTGA
41276506 ACTGATAATA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
15 5 0.23
16 7 0.32
17 4 0.18
18 6 0.27
ACGTcount: A:0.39, C:0.00, G:0.22, T:0.39
Consensus pattern (17 bp):
TGAATTGATGATGAAAT
Found at i:41281203 original size:28 final size:28
Alignment explanation
Indices: 41281163--41281219 Score: 114
Period size: 28 Copynumber: 2.0 Consensus size: 28
41281153 ACTATCTCCC
41281163 ACTTACTCTTTGCAGATGATTGCATCTT
1 ACTTACTCTTTGCAGATGATTGCATCTT
41281191 ACTTACTCTTTGCAGATGATTGCATCTT
1 ACTTACTCTTTGCAGATGATTGCATCTT
41281219 A
1 A
41281220 TTTGCAGAAG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.23, C:0.21, G:0.14, T:0.42
Consensus pattern (28 bp):
ACTTACTCTTTGCAGATGATTGCATCTT
Found at i:41283814 original size:19 final size:19
Alignment explanation
Indices: 41283783--41283829 Score: 55
Period size: 19 Copynumber: 2.6 Consensus size: 19
41283773 TTATTTTAGT
*
41283783 AATTA-TTTT-TAAATTTA
1 AATTATTTTTGTAAATATA
41283800 AATTATTTTTGTAAATATA
1 AATTATTTTTGTAAATATA
41283819 ATATT-TTTTTG
1 A-ATTATTTTTG
41283830 AACTAATTTA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
17 5 0.19
18 4 0.15
19 14 0.54
20 3 0.12
ACGTcount: A:0.36, C:0.00, G:0.04, T:0.60
Consensus pattern (19 bp):
AATTATTTTTGTAAATATA
Found at i:41293611 original size:6 final size:6
Alignment explanation
Indices: 41293600--41293631 Score: 64
Period size: 6 Copynumber: 5.3 Consensus size: 6
41293590 GAGGGTAAGC
41293600 TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT TT
1 TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT TT
41293632 GTTAATTTCG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (6 bp):
TTTCTT
Found at i:41297388 original size:19 final size:20
Alignment explanation
Indices: 41297345--41297388 Score: 63
Period size: 19 Copynumber: 2.2 Consensus size: 20
41297335 TATGACCCCT
41297345 ATTTTCTAAAATTTTTAAGA
1 ATTTTCTAAAATTTTTAAGA
* *
41297365 TTTTTCTAAAA-TTTTATGA
1 ATTTTCTAAAATTTTTAAGA
41297384 ATTTT
1 ATTTT
41297389 TTCGTTTTAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
19 11 0.52
20 10 0.48
ACGTcount: A:0.34, C:0.05, G:0.05, T:0.57
Consensus pattern (20 bp):
ATTTTCTAAAATTTTTAAGA
Found at i:41298619 original size:23 final size:23
Alignment explanation
Indices: 41298589--41298655 Score: 91
Period size: 23 Copynumber: 2.9 Consensus size: 23
41298579 AGACACAATG
*
41298589 CACAAAGTCTCGAGACATGAACC
1 CACAAAGTCTCGAGACAAGAACC
41298612 CACAAAGTCTCGAGACAAGAACC
1 CACAAAGTCTCGAGACAAGAACC
* *
41298635 C-CTAATGTCTCAAGACAAGAA
1 CAC-AAAGTCTCGAGACAAGAA
41298656 AACATCGAAG
Statistics
Matches: 40, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
22 1 0.03
23 39 0.98
ACGTcount: A:0.42, C:0.28, G:0.16, T:0.13
Consensus pattern (23 bp):
CACAAAGTCTCGAGACAAGAACC
Found at i:41304258 original size:56 final size:56
Alignment explanation
Indices: 41304191--41304302 Score: 224
Period size: 56 Copynumber: 2.0 Consensus size: 56
41304181 CAAGTGCCAA
41304191 GCTATTGGTTGAATGGTAATATGATTATTTATAAGATGCATTGAATTGGTTAGTAT
1 GCTATTGGTTGAATGGTAATATGATTATTTATAAGATGCATTGAATTGGTTAGTAT
41304247 GCTATTGGTTGAATGGTAATATGATTATTTATAAGATGCATTGAATTGGTTAGTAT
1 GCTATTGGTTGAATGGTAATATGATTATTTATAAGATGCATTGAATTGGTTAGTAT
41304303 TTAAGTGAAA
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
56 56 1.00
ACGTcount: A:0.30, C:0.04, G:0.23, T:0.43
Consensus pattern (56 bp):
GCTATTGGTTGAATGGTAATATGATTATTTATAAGATGCATTGAATTGGTTAGTAT
Found at i:41307762 original size:9 final size:8
Alignment explanation
Indices: 41307734--41307761 Score: 56
Period size: 8 Copynumber: 3.5 Consensus size: 8
41307724 ATATATTTAT
41307734 TTTTAAAA
1 TTTTAAAA
41307742 TTTTAAAA
1 TTTTAAAA
41307750 TTTTAAAA
1 TTTTAAAA
41307758 TTTT
1 TTTT
41307762 TTTAAAATAC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (8 bp):
TTTTAAAA
Found at i:41307777 original size:14 final size:14
Alignment explanation
Indices: 41307756--41307804 Score: 57
Period size: 14 Copynumber: 3.6 Consensus size: 14
41307746 AAAATTTTAA
41307756 AATTTTTTTAAAAT
1 AATTTTTTTAAAAT
*
41307770 ACTTTTTTT-AAAT
1 AATTTTTTTAAAAT
*
41307783 -TTTTTTTTAAAAAT
1 AATTTTTTT-AAAAT
41307797 AATTTTTT
1 AATTTTTT
41307805 AGTGTTTTAT
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
12 7 0.24
13 4 0.14
14 12 0.41
15 6 0.21
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (14 bp):
AATTTTTTTAAAAT
Found at i:41307778 original size:25 final size:27
Alignment explanation
Indices: 41307750--41307804 Score: 78
Period size: 27 Copynumber: 2.1 Consensus size: 27
41307740 AATTTTAAAA
*
41307750 TTTTAAA-ATTTTTTT-AAAATACTTT
1 TTTTAAATATTTTTTTAAAAATAATTT
*
41307775 TTTTAAATTTTTTTTTAAAAATAATTT
1 TTTTAAATATTTTTTTAAAAATAATTT
41307802 TTT
1 TTT
41307805 AGTGTTTTAT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
25 7 0.27
26 7 0.27
27 12 0.46
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.64
Consensus pattern (27 bp):
TTTTAAATATTTTTTTAAAAATAATTT
Found at i:41307787 original size:12 final size:12
Alignment explanation
Indices: 41307750--41307793 Score: 52
Period size: 12 Copynumber: 3.6 Consensus size: 12
41307740 AATTTTAAAA
*
41307750 TTTTAAAATTTT
1 TTTTAAATTTTT
* *
41307762 TTTAAAATACTTT
1 TTTTAAAT-TTTT
41307775 TTTTAAATTTTT
1 TTTTAAATTTTT
41307787 TTTTAAA
1 TTTTAAA
41307794 AATAATTTTT
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
12 16 0.62
13 10 0.38
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (12 bp):
TTTTAAATTTTT
Found at i:41307789 original size:11 final size:11
Alignment explanation
Indices: 41307750--41307788 Score: 51
Period size: 11 Copynumber: 3.4 Consensus size: 11
41307740 AATTTTAAAA
41307750 TTTTAAAATTT
1 TTTTAAAATTT
41307761 TTTTAAAATACTT
1 TTTTAAAAT--TT
*
41307774 TTTTTAAATTT
1 TTTTAAAATTT
41307785 TTTT
1 TTTT
41307789 TTAAAAATAA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
11 15 0.60
13 10 0.40
ACGTcount: A:0.31, C:0.03, G:0.00, T:0.67
Consensus pattern (11 bp):
TTTTAAAATTT
Found at i:41307812 original size:26 final size:27
Alignment explanation
Indices: 41307750--41307805 Score: 73
Period size: 26 Copynumber: 2.2 Consensus size: 27
41307740 AATTTTAAAA
* *
41307750 TTTTAAA-ATTTTTTT-AAAATACTTT
1 TTTTAAATTTTTTTTTAAAAATACATT
41307775 TTTTAAATTTTTTTTTAAAAATA-ATT
1 TTTTAAATTTTTTTTTAAAAATACATT
41307801 TTTTA
1 TTTTA
41307806 GTGTTTTATT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
25 7 0.26
26 14 0.52
27 6 0.22
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (27 bp):
TTTTAAATTTTTTTTTAAAAATACATT
Found at i:41308951 original size:16 final size:16
Alignment explanation
Indices: 41308926--41308960 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
41308916 GTTTTACTCT
*
41308926 TAAAAGTATTTTTAAA
1 TAAAAGTATTATTAAA
*
41308942 TAAAATTATTATTAAA
1 TAAAAGTATTATTAAA
41308958 TAA
1 TAA
41308961 GATGTTTTTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.43
Consensus pattern (16 bp):
TAAAAGTATTATTAAA
Found at i:41315764 original size:21 final size:21
Alignment explanation
Indices: 41315739--41315809 Score: 88
Period size: 21 Copynumber: 3.1 Consensus size: 21
41315729 TGGATAAGTA
41315739 TTTTGTATGAATATTGTAATT
1 TTTTGTATGAATATTGTAATT
41315760 TTTTGTATGAATATTGTAATATTAT
1 TTTTGTATGAATATTGT-A-A-T-T
41315785 AATTTTGTATGAATATTGTAATT
1 --TTTTGTATGAATATTGTAATT
41315808 TT
1 TT
41315810 GTAATTTTGT
Statistics
Matches: 44, Mismatches: 0, Indels: 12
0.79 0.00 0.21
Matches are distributed among these distances:
21 19 0.43
22 1 0.02
23 2 0.05
24 2 0.05
25 2 0.05
26 1 0.02
27 17 0.39
ACGTcount: A:0.31, C:0.00, G:0.13, T:0.56
Consensus pattern (21 bp):
TTTTGTATGAATATTGTAATT
Found at i:41315765 original size:48 final size:47
Alignment explanation
Indices: 41315738--41316016 Score: 144
Period size: 48 Copynumber: 5.4 Consensus size: 47
41315728 TTGGATAAGT
41315738 ATTTTGTATGAATATTGTAATTTTTTGTATGAATATTGTAATATTATA
1 ATTTTGTATGAATATTGTAATTTTTTGTATGAATATTGTAATA-TATA
*
41315786 ATTTTGTATGAATATTGTAATTTTGTAATTTTGTATGAATATTGTAATGTCGGGAT-
1 ATTTTGTATGAATATTGTAA---T-T--TTTTGTATGAATATTGTAATAT----ATA
*
41315842 ATATTG--T-AATATTGTAATTTTTTGTATGAATATTGTAATTATTTTATA
1 ATTTTGTATGAATATTGTAATTTTTTGTATGAATATTGTAA-TA---TATA
* * * *
41315890 ATTAAATTTGTATTTATAGTTTTGGATTAGTATTTTGTATGAATATTGT-A-AT-T-
1 A-T---TTTGTA-TGA-A-TATT-G--TAATTTTTTGTATGAATATTGTAATATATA
*
41315943 -TTTTGTATGAATATTGTAATATTATAATTTTGTATGAATATTGTAATATTGTA
1 ATTTTGTATGAATATTGT-A-A-T-T--TTTTGTATGAATATTGTAATA-TATA
41315996 ATTTTGTATGAATATTGTAAT
1 ATTTTGTATGAATATTGTAAT
41316017 GTCGGGATAT
Statistics
Matches: 180, Mismatches: 11, Indels: 77
0.67 0.04 0.29
Matches are distributed among these distances:
42 1 0.01
43 1 0.01
44 1 0.01
45 4 0.02
46 1 0.01
47 23 0.13
48 45 0.25
49 3 0.02
50 2 0.01
51 5 0.03
52 6 0.03
53 12 0.07
54 39 0.22
55 2 0.01
56 6 0.03
57 3 0.02
58 4 0.02
59 1 0.01
60 1 0.01
61 20 0.11
ACGTcount: A:0.32, C:0.00, G:0.14, T:0.53
Consensus pattern (47 bp):
ATTTTGTATGAATATTGTAATTTTTTGTATGAATATTGTAATATATA
Found at i:41315798 original size:27 final size:27
Alignment explanation
Indices: 41315760--41316016 Score: 181
Period size: 27 Copynumber: 9.7 Consensus size: 27
41315750 TATTGTAATT
41315760 TTTTGTATGAATATTGTAATATTATAA
1 TTTTGTATGAATATTGTAATATTATAA
* *
41315787 TTTTGTATGAATATTGTAATTTTGTAA
1 TTTTGTATGAATATTGTAATATTATAA
* *
41315814 TTTTGTATGAATATTGTAATGTCGGGAT-A
1 TTTTGTATGAATATTGTAATAT---TATAA
*
41315843 TATTG--T-AATATTGT-A-A-T-T--
1 TTTTGTATGAATATTGTAATATTATAA
41315861 TTTTGTATGAATATTGTAATTATTTTATAA
1 TTTTGTATGAATATTGTAA-TA--TTATAA
** ***
41315891 TTAAATTTGTATTTATAGTT-TTGGATTAGT-A
1 -T---TTTGTATGAATA-TTGTAATATTA-TAA
41315922 TTTTGTATGAATATTGT-A-A-T-T--
1 TTTTGTATGAATATTGTAATATTATAA
41315943 TTTTGTATGAATATTGTAATATTATAA
1 TTTTGTATGAATATTGTAATATTATAA
*
41315970 TTTTGTATGAATATTGTAATATTGTAA
1 TTTTGTATGAATATTGTAATATTATAA
41315997 TTTTGTATGAATATTGTAAT
1 TTTTGTATGAATATTGTAAT
41316017 GTCGGGATAT
Statistics
Matches: 184, Mismatches: 18, Indels: 56
0.71 0.07 0.22
Matches are distributed among these distances:
18 4 0.02
19 1 0.01
20 1 0.01
21 25 0.14
22 3 0.02
23 1 0.01
24 3 0.02
25 3 0.02
26 10 0.05
27 105 0.57
28 1 0.01
29 5 0.03
30 2 0.01
31 5 0.03
32 1 0.01
33 1 0.01
34 11 0.06
35 2 0.01
ACGTcount: A:0.32, C:0.00, G:0.14, T:0.53
Consensus pattern (27 bp):
TTTTGTATGAATATTGTAATATTATAA
Found at i:41315965 original size:8 final size:8
Alignment explanation
Indices: 41315952--41316042 Score: 56
Period size: 8 Copynumber: 10.4 Consensus size: 8
41315942 TTTTTGTATG
41315952 AATATTGT
1 AATATTGT
*
41315960 AATATTAT
1 AATATTGT
*
41315968 AATTTTGTAT
1 AATATTG--T
41315978 GAATATTGT
1 -AATATTGT
41315987 AATATTGT
1 AATATTGT
*
41315995 AATTTTGTAT
1 AATATTG--T
41316005 GAATATTGT
1 -AATATTGT
* * *
41316014 AATGTCGGG
1 AATAT-TGT
41316023 ATATATTGT
1 A-ATATTGT
41316032 AATATTGT
1 AATATTGT
41316040 AAT
1 AAT
41316043 TTTTTTGTAT
Statistics
Matches: 63, Mismatches: 12, Indels: 16
0.69 0.13 0.18
Matches are distributed among these distances:
8 40 0.63
9 6 0.10
10 5 0.08
11 12 0.19
ACGTcount: A:0.35, C:0.01, G:0.15, T:0.48
Consensus pattern (8 bp):
AATATTGT
Found at i:41315986 original size:183 final size:183
Alignment explanation
Indices: 41315668--41316083 Score: 784
Period size: 183 Copynumber: 2.3 Consensus size: 183
41315658 GGCGCCAATG
41315668 AATATTGTAA--TTTTGTATGAATATTGTAATTATTTTATAATTAAATTTGTATTTATAGTTTTG
1 AATATTGTAATTTTTTGTATGAATATTGTAATTATTTTATAATTAAATTTGTATTTATAGTTTTG
41315731 GATAAGTATTTTGTATGAATATTGTAATTTTTTGTATGAATATTGTAATATTATAATTTTGTATG
66 GATAAGTATTTTGTATGAATATTGTAATTTTTTGTATGAATATTGTAATATTATAATTTTGTATG
*
41315796 AATATTGTAATTTTGTAATTTTGTATGAATATTGTAATGTCGGGATATATTGT
131 AATATTGTAATATTGTAATTTTGTATGAATATTGTAATGTCGGGATATATTGT
41315849 AATATTGTAATTTTTTGTATGAATATTGTAATTATTTTATAATTAAATTTGTATTTATAGTTTTG
1 AATATTGTAATTTTTTGTATGAATATTGTAATTATTTTATAATTAAATTTGTATTTATAGTTTTG
*
41315914 GATTAGTATTTTGTATGAATATTGTAATTTTTTGTATGAATATTGTAATATTATAATTTTGTATG
66 GATAAGTATTTTGTATGAATATTGTAATTTTTTGTATGAATATTGTAATATTATAATTTTGTATG
41315979 AATATTGTAATATTGTAATTTTGTATGAATATTGTAATGTCGGGATATATTGT
131 AATATTGTAATATTGTAATTTTGTATGAATATTGTAATGTCGGGATATATTGT
41316032 AATATTGTAATTTTTTTGTATGAATATTGTAATTATTTTATAATT-AATTTGT
1 AATATTGTAA-TTTTTTGTATGAATATTGTAATTATTTTATAATTAAATTTGT
41316084 TAGTAATTTA
Statistics
Matches: 230, Mismatches: 2, Indels: 4
0.97 0.01 0.02
Matches are distributed among these distances:
181 10 0.04
183 186 0.81
184 34 0.15
ACGTcount: A:0.32, C:0.00, G:0.14, T:0.53
Consensus pattern (183 bp):
AATATTGTAATTTTTTGTATGAATATTGTAATTATTTTATAATTAAATTTGTATTTATAGTTTTG
GATAAGTATTTTGTATGAATATTGTAATTTTTTGTATGAATATTGTAATATTATAATTTTGTATG
AATATTGTAATATTGTAATTTTGTATGAATATTGTAATGTCGGGATATATTGT
Found at i:41316001 original size:75 final size:73
Alignment explanation
Indices: 41315921--41316064 Score: 191
Period size: 75 Copynumber: 1.9 Consensus size: 73
41315911 TTGGATTAGT
* ** *
41315921 ATTTTGTATGAATATTGTAATTTTTTGTATGAATATTGTAATATTATAA-TTTTGTATGAATATT
1 ATTTTGTATGAATATTGTAA-TGTCGGGAT--ATATTGTAATATTATAATTTTTGTATGAATATT
41315985 GTAATATTGTA
63 GTAATATTGTA
*
41315996 ATTTTGTATGAATATTGTAATGTCGGGATATATTGTAATATTGTAATTTTTTTGTATGAATATTG
1 ATTTTGTATGAATATTGTAATGTCGGGATATATTGTAATATTATAA--TTTTTGTATGAATATTG
41316061 TAAT
64 TAAT
41316065 TATTTTATAA
Statistics
Matches: 61, Mismatches: 5, Indels: 6
0.85 0.07 0.08
Matches are distributed among these distances:
72 16 0.26
74 5 0.08
75 40 0.66
ACGTcount: A:0.32, C:0.01, G:0.15, T:0.52
Consensus pattern (73 bp):
ATTTTGTATGAATATTGTAATGTCGGGATATATTGTAATATTATAATTTTTGTATGAATATTGTA
ATATTGTA
Found at i:41316083 original size:22 final size:22
Alignment explanation
Indices: 41316031--41316083 Score: 63
Period size: 22 Copynumber: 2.4 Consensus size: 22
41316021 GGATATATTG
* *
41316031 TAATATTGTAATTTTTTTGTAT
1 TAATATTGTAATTATTTTATAT
*
41316053 GAATATTGTAATTATTTTATAAT
1 TAATATTGTAATTATTTTAT-AT
41316076 TAAT-TTGT
1 TAATATTGT
41316084 TAGTAATTTA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
22 21 0.81
23 5 0.19
ACGTcount: A:0.32, C:0.00, G:0.09, T:0.58
Consensus pattern (22 bp):
TAATATTGTAATTATTTTATAT
Found at i:41316139 original size:60 final size:60
Alignment explanation
Indices: 41316058--41316179 Score: 174
Period size: 60 Copynumber: 2.0 Consensus size: 60
41316048 TGTATGAATA
* * * * *
41316058 TTGTAATTATTTTATAATTAATTTGTTAGTAATTTAGGATTATGTTATAAATTTTTGTGT
1 TTGTAATTATTTTAAAATTAATTTATTAGTAATTTAGGATTAAGCTATAAATTGTTGTGT
*
41316118 TTGTAATTA-TTTAAAATTTAATTTATTAGTAATTTAGGATTAAGCTATAAGTTGTTGTGT
1 TTGTAATTATTTTAAAA-TTAATTTATTAGTAATTTAGGATTAAGCTATAAATTGTTGTGT
41316178 TT
1 TT
41316180 AGTTTAATAT
Statistics
Matches: 55, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
59 6 0.11
60 49 0.89
ACGTcount: A:0.31, C:0.01, G:0.14, T:0.54
Consensus pattern (60 bp):
TTGTAATTATTTTAAAATTAATTTATTAGTAATTTAGGATTAAGCTATAAATTGTTGTGT
Found at i:41316257 original size:38 final size:38
Alignment explanation
Indices: 41316212--41316293 Score: 155
Period size: 38 Copynumber: 2.2 Consensus size: 38
41316202 CATATAAAGT
41316212 TTATAAAAAAATTAAAAATCATCTTATTAAAAGTTTAA
1 TTATAAAAAAATTAAAAATCATCTTATTAAAAGTTTAA
*
41316250 TTATAAAAAAATTAAAAATCATTTTATTAAAAGTTTAA
1 TTATAAAAAAATTAAAAATCATCTTATTAAAAGTTTAA
41316288 TTATAA
1 TTATAA
41316294 CTGACTTTTT
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
38 43 1.00
ACGTcount: A:0.55, C:0.04, G:0.02, T:0.39
Consensus pattern (38 bp):
TTATAAAAAAATTAAAAATCATCTTATTAAAAGTTTAA
Found at i:41316371 original size:15 final size:15
Alignment explanation
Indices: 41316330--41316371 Score: 57
Period size: 16 Copynumber: 2.7 Consensus size: 15
41316320 GTTAACTAAT
*
41316330 TTAATTTTTATATAA
1 TTAAATTTTATATAA
*
41316345 TGTAACTTTTATATAA
1 T-TAAATTTTATATAA
41316361 TTAAATTTTAT
1 TTAAATTTTAT
41316372 TTGATTTTGT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
15 10 0.42
16 14 0.58
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.57
Consensus pattern (15 bp):
TTAAATTTTATATAA
Found at i:41316532 original size:21 final size:21
Alignment explanation
Indices: 41316501--41316685 Score: 119
Period size: 21 Copynumber: 8.2 Consensus size: 21
41316491 AATTAATTAT
41316501 AAAATAATTACAATATTCATAC
1 AAAA-AATTACAATATTCATAC
41316523 AAAAAATTACAATATTACAATATATC
1 AAAAAATTACAATATT-C---ATA-C
*** *
41316549 CCGACATTACAATATTCATAC
1 AAAAAATTACAATATTCATAC
41316570 ---AAATTACAATATTACAATATTC
1 AAAAAATTACAATATT-C-ATA--C
*
41316592 ATACAAAATTATAATATTACAATATTC
1 A-A-AAAATTACAATATT-C-ATA--C
41316619 ATAAAAAATTACAATATTCAT--
1 --AAAAAATTACAATATTCATAC
*
41316640 ATAAAATTACAATATTCATAC
1 AAAAAATTACAATATTCATAC
41316661 AAAAAATTACAATATTCATAC
1 AAAAAATTACAATATTCATAC
41316682 AAAA
1 AAAA
41316686 TACTAATCCA
Statistics
Matches: 136, Mismatches: 9, Indels: 37
0.75 0.05 0.20
Matches are distributed among these distances:
18 12 0.09
19 19 0.14
20 3 0.02
21 37 0.27
22 9 0.07
25 6 0.04
26 14 0.10
27 34 0.25
28 1 0.01
29 1 0.01
ACGTcount: A:0.54, C:0.14, G:0.01, T:0.32
Consensus pattern (21 bp):
AAAAAATTACAATATTCATAC
Found at i:41316541 original size:8 final size:8
Alignment explanation
Indices: 41316528--41316617 Score: 56
Period size: 8 Copynumber: 10.4 Consensus size: 8
41316518 CATACAAAAA
41316528 ATTACAAT
1 ATTACAAT
41316536 ATTACAAT
1 ATTACAAT
* * *
41316544 ATATCCCGAC
1 AT-T-ACAAT
41316554 ATTACAAT
1 ATTACAAT
41316562 ATTCATACAA-
1 A-T--TACAAT
41316572 ATTACAAT
1 ATTACAAT
41316580 ATTACAAT
1 ATTACAAT
*
41316588 ATTCATACAAA
1 A-T--TACAAT
*
41316599 ATTATAAT
1 ATTACAAT
41316607 ATTACAAT
1 ATTACAAT
41316615 ATT
1 ATT
41316618 CATAAAAAAT
Statistics
Matches: 63, Mismatches: 10, Indels: 18
0.69 0.11 0.20
Matches are distributed among these distances:
7 5 0.08
8 36 0.57
9 5 0.08
10 6 0.10
11 11 0.17
ACGTcount: A:0.48, C:0.16, G:0.01, T:0.36
Consensus pattern (8 bp):
ATTACAAT
Found at i:41316575 original size:65 final size:66
Alignment explanation
Indices: 41316506--41316676 Score: 202
Period size: 71 Copynumber: 2.5 Consensus size: 66
41316496 ATTATAAAAT
*** *
41316506 AATTACAATATTCATACAAAAAATTACAATATTACAATATATC-CCGACATTACAATATTCATA-
1 AATTACAATATTCATACAAAAAATTACAATATTACAATAT-TCAAAAAAATTACAATATTCATAT
*
41316569 CA
65 AA
*
41316571 AATTACAATATTACAATATTCATACAAAATTATAATATTACAATATTCATAAAAAATTACAATAT
1 AATTACAATATT-C-ATA--CA-A-AAAATTACAATATTACAATATTCA-AAAAAATTACAATAT
41316636 TCATATAA
59 TCATATAA
41316644 AATTACAATATTCATACAAAAAATTACAATATT
1 AATTACAATATTCATACAAAAAATTACAATATT
41316677 CATACAAAAT
Statistics
Matches: 90, Mismatches: 7, Indels: 16
0.80 0.06 0.14
Matches are distributed among these distances:
65 12 0.13
66 1 0.01
67 16 0.18
68 1 0.01
69 4 0.04
70 3 0.03
71 23 0.26
72 17 0.19
73 13 0.14
ACGTcount: A:0.52, C:0.14, G:0.01, T:0.33
Consensus pattern (66 bp):
AATTACAATATTCATACAAAAAATTACAATATTACAATATTCAAAAAAATTACAATATTCATATA
A
Found at i:41316602 original size:19 final size:19
Alignment explanation
Indices: 41316554--41316759 Score: 128
Period size: 19 Copynumber: 10.7 Consensus size: 19
41316544 ATATCCCGAC
41316554 ATTACAATATTCATAC-AA
1 ATTACAATATTCATACAAA
41316572 ATTACAATA-T--TACAATA
1 ATTACAATATTCATACAA-A
* * *
41316589 TTCATACAAAATT-AT--AAT
1 AT--TACAATATTCATACAAA
*
41316607 ATTACAATATTCATAAAAA
1 ATTACAATATTCATACAAA
*
41316626 ATTACAATATTCATATAAA
1 ATTACAATATTCATACAAA
41316645 ATTACAATATTCATACAAAAA
1 ATTACAATATTCATAC--AAA
41316666 ATTACAATATTCATACAAA
1 ATTACAATATTCATACAAA
* * *
41316685 A-TACTA-ATCCAAAACTATAA
1 ATTACAATATTC-ATAC-A-AA
*
41316705 A-TACAAATTTAATT-ATAAAATA
1 ATTAC-AA--T-ATTCATACAA-A
*
41316727 ATTACAATATTAATACAAA
1 ATTACAATATTCATACAAA
41316746 ATTACAATATTCAT
1 ATTACAATATTCAT
41316760 TGGCGCCTCT
Statistics
Matches: 149, Mismatches: 17, Indels: 43
0.71 0.08 0.21
Matches are distributed among these distances:
15 3 0.02
16 9 0.06
17 8 0.05
18 17 0.11
19 65 0.44
20 13 0.09
21 22 0.15
22 5 0.03
23 5 0.03
25 2 0.01
ACGTcount: A:0.54, C:0.13, G:0.00, T:0.33
Consensus pattern (19 bp):
ATTACAATATTCATACAAA
Found at i:41316608 original size:27 final size:27
Alignment explanation
Indices: 41316554--41316636 Score: 141
Period size: 27 Copynumber: 3.1 Consensus size: 27
41316544 ATATCCCGAC
41316554 ATTACAATATTCATAC-AAATTACAAT
1 ATTACAATATTCATACAAAATTACAAT
*
41316580 ATTACAATATTCATACAAAATTATAAT
1 ATTACAATATTCATACAAAATTACAAT
*
41316607 ATTACAATATTCATAAAAAATTACAAT
1 ATTACAATATTCATACAAAATTACAAT
41316634 ATT
1 ATT
41316637 CATATAAAAT
Statistics
Matches: 53, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
26 16 0.30
27 37 0.70
ACGTcount: A:0.52, C:0.12, G:0.00, T:0.36
Consensus pattern (27 bp):
ATTACAATATTCATACAAAATTACAAT
Found at i:41316676 original size:40 final size:38
Alignment explanation
Indices: 41316601--41316686 Score: 136
Period size: 40 Copynumber: 2.2 Consensus size: 38
41316591 CATACAAAAT
*
41316601 TATAATATTACAATATTCATAAAAAATTACAATATTCA
1 TATAAAATTACAATATTCATAAAAAATTACAATATTCA
41316639 TATAAAATTACAATATTCATACAAAAAATTACAATATTCA
1 TATAAAATTACAATATTCAT--AAAAAATTACAATATTCA
*
41316679 TACAAAAT
1 TATAAAAT
41316687 ACTAATCCAA
Statistics
Matches: 44, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
38 19 0.43
40 25 0.57
ACGTcount: A:0.55, C:0.12, G:0.00, T:0.34
Consensus pattern (38 bp):
TATAAAATTACAATATTCATAAAAAATTACAATATTCA
Found at i:41317509 original size:20 final size:20
Alignment explanation
Indices: 41317484--41317529 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
41317474 GTTGTTGCTA
*
41317484 TGTTTTGCTATTGTTTCCAC
1 TGTTTTGCTACTGTTTCCAC
* *
41317504 TGTTTTGTTACTGTTTCTAC
1 TGTTTTGCTACTGTTTCCAC
41317524 TGTTTT
1 TGTTTT
41317530 ATTGTTATCT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.09, C:0.15, G:0.15, T:0.61
Consensus pattern (20 bp):
TGTTTTGCTACTGTTTCCAC
Found at i:41317787 original size:21 final size:21
Alignment explanation
Indices: 41317742--41317838 Score: 96
Period size: 19 Copynumber: 4.7 Consensus size: 21
41317732 ATATTCAAGG
41317742 ATATGCAATCTTAGATATG--
1 ATATGCAATCTTAGATATGAT
*
41317761 ATATGCAACCTTAGATATGAT
1 ATATGCAATCTTAGATATGAT
*
41317782 ATATGCAATCTTGGATATG--
1 ATATGCAATCTTAGATATGAT
41317801 ATATGCAATCTTGGAAGATATGAT
1 ATATGCAATCTT---AGATATGAT
* *
41317825 -TTTGTAATCTTAGA
1 ATATGCAATCTTAGA
41317839 GATTTAATTT
Statistics
Matches: 65, Mismatches: 6, Indels: 13
0.77 0.07 0.15
Matches are distributed among these distances:
19 30 0.46
20 3 0.05
21 17 0.26
22 6 0.09
23 9 0.14
ACGTcount: A:0.35, C:0.10, G:0.18, T:0.37
Consensus pattern (21 bp):
ATATGCAATCTTAGATATGAT
Found at i:41317815 original size:19 final size:19
Alignment explanation
Indices: 41317741--41317812 Score: 108
Period size: 19 Copynumber: 3.7 Consensus size: 19
41317731 AATATTCAAG
41317741 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
*
41317760 GATATGCAACCTTAGATAT
1 GATATGCAATCTTAGATAT
*
41317779 GATATATGCAATCTTGGATAT
1 G--ATATGCAATCTTAGATAT
41317800 GATATGCAATCTT
1 GATATGCAATCTT
41317813 GGAAGATATG
Statistics
Matches: 48, Mismatches: 3, Indels: 4
0.87 0.05 0.07
Matches are distributed among these distances:
19 31 0.65
21 17 0.35
ACGTcount: A:0.35, C:0.12, G:0.17, T:0.36
Consensus pattern (19 bp):
GATATGCAATCTTAGATAT
Found at i:41321620 original size:12 final size:12
Alignment explanation
Indices: 41321605--41321634 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
41321595 AGTATAGCCT
41321605 TATATATATATG
1 TATATATATATG
*
41321617 TATATATATATT
1 TATATATATATG
41321629 TATATA
1 TATATA
41321635 AAGGTTAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.53
Consensus pattern (12 bp):
TATATATATATG
Found at i:41322715 original size:43 final size:43
Alignment explanation
Indices: 41322557--41322714 Score: 205
Period size: 43 Copynumber: 3.7 Consensus size: 43
41322547 TTTCTGATAA
*
41322557 GTGTTTTCGTGTAAGACCACGTCTGGGACGTTGGCATCGACTT
1 GTGTTTTCGTGTAAGACCACGTCTAGGACGTTGGCATCGACTT
41322600 GTGTTTTCGTGTAAGACCACGTCT-GAGACGTTGGCATCGACTT
1 GTGTTTTCGTGTAAGACCACGTCTAG-GACGTTGGCATCGACTT
** *
41322643 GTGTTTTCGTGTAAGACCTTGTCTAGGACAG-TGGCATTGA-TCT
1 GTGTTTTCGTGTAAGACCACGTCTAGGAC-GTTGGCATCGACT-T
* * *
41322686 GTGATTACATGTAAGACCACGTCTAGGAC
1 GTGTTTTCGTGTAAGACCACGTCTAGGAC
41322715 ATTGATATTG
Statistics
Matches: 103, Mismatches: 8, Indels: 8
0.87 0.07 0.07
Matches are distributed among these distances:
42 2 0.02
43 99 0.96
44 2 0.02
ACGTcount: A:0.20, C:0.20, G:0.28, T:0.32
Consensus pattern (43 bp):
GTGTTTTCGTGTAAGACCACGTCTAGGACGTTGGCATCGACTT
Found at i:41323809 original size:22 final size:24
Alignment explanation
Indices: 41323783--41323826 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
41323773 AAAAAATATT
41323783 AAATAT-ATA-TTTTTTATTTTTA
1 AAATATAATAGTTTTTTATTTTTA
41323805 AAATATAATAGTTTTTTATTTT
1 AAATATAATAGTTTTTTATTTT
41323827 AAGTTTATCT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 6 0.30
23 3 0.15
24 11 0.55
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.61
Consensus pattern (24 bp):
AAATATAATAGTTTTTTATTTTTA
Found at i:41323937 original size:9 final size:9
Alignment explanation
Indices: 41323923--41323950 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
41323913 TTTTGTTACA
41323923 ACAATTAAT
1 ACAATTAAT
41323932 ACAATTAAT
1 ACAATTAAT
41323941 ACAATTAAT
1 ACAATTAAT
41323950 A
1 A
41323951 ATTTGATAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.57, C:0.11, G:0.00, T:0.32
Consensus pattern (9 bp):
ACAATTAAT
Found at i:41323972 original size:68 final size:68
Alignment explanation
Indices: 41323893--41324102 Score: 388
Period size: 68 Copynumber: 3.1 Consensus size: 68
41323883 TTAAGTTTGT
*
41323893 TTTACTAATCAAATGTTAGATTTTGTTACAACAATTAATACAATTAATACAATTAATAATTTGAT
1 TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATTAATACAATTAATAATTTGAT
41323958 AAA
66 AAA
41323961 TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATTAATACAATTAATAATTTGAT
1 TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATTAATACAATTAATAATTTGAT
41324026 AAA
66 AAA
41324029 TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATTAAT--AATTAATAATTTGAT
1 TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATTAATACAATTAATAATTTGAT
*
41324092 AAT
66 AAA
41324095 TTTACTAA
1 TTTACTAA
41324103 CAATTAATTT
Statistics
Matches: 140, Mismatches: 2, Indels: 2
0.97 0.01 0.01
Matches are distributed among these distances:
66 25 0.18
68 115 0.82
ACGTcount: A:0.46, C:0.09, G:0.05, T:0.41
Consensus pattern (68 bp):
TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATTAATACAATTAATAATTTGAT
AAA
Found at i:41324003 original size:9 final size:9
Alignment explanation
Indices: 41323991--41324018 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
41323981 TTTTATTACA
41323991 ACAATTAAT
1 ACAATTAAT
41324000 ACAATTAAT
1 ACAATTAAT
41324009 ACAATTAAT
1 ACAATTAAT
41324018 A
1 A
41324019 ATTTGATAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.57, C:0.11, G:0.00, T:0.32
Consensus pattern (9 bp):
ACAATTAAT
Found at i:41324112 original size:16 final size:16
Alignment explanation
Indices: 41324091--41324132 Score: 66
Period size: 16 Copynumber: 2.6 Consensus size: 16
41324081 AATAATTTGA
*
41324091 TAATTTTACTAACAAT
1 TAATTTTAATAACAAT
41324107 TAATTTTAATAACAAT
1 TAATTTTAATAACAAT
*
41324123 TAGTTTTAAT
1 TAATTTTAAT
41324133 TTTATTTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.43, C:0.07, G:0.02, T:0.48
Consensus pattern (16 bp):
TAATTTTAATAACAAT
Found at i:41324116 original size:22 final size:23
Alignment explanation
Indices: 41324106--41324159 Score: 65
Period size: 23 Copynumber: 2.4 Consensus size: 23
41324096 TTACTAACAA
* * *
41324106 TTAATTTTA-ATAACAATTAGTT
1 TTAATTTTATATAAAAAATAATT
*
41324128 TTAATTTTATTTAAAAAATAATT
1 TTAATTTTATATAAAAAATAATT
41324151 TTAATTTTA
1 TTAATTTTA
41324160 ATTAAGAACG
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
22 9 0.33
23 18 0.67
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.54
Consensus pattern (23 bp):
TTAATTTTATATAAAAAATAATT
Found at i:41325732 original size:63 final size:63
Alignment explanation
Indices: 41325597--41325717 Score: 161
Period size: 63 Copynumber: 1.9 Consensus size: 63
41325587 GAGGGAAGCA
* ** * * **
41325597 TGCTTGAAAACGCATTTCAGAATATGCATTTTGATCGAATAATAATAATGAAAGCTTCAGAGG
1 TGCTTGAAAACGCATTTCAGAAGACACATTTTCATCAAATAATAATAATGAAAGAGTCAGAGG
* *
41325660 TGCTTGAAAATGCATTTCAGCAGACACATTTTCATCAAATAATAATAATGAAAGAGTC
1 TGCTTGAAAACGCATTTCAGAAGACACATTTTCATCAAATAATAATAATGAAAGAGTC
41325718 TTTTGTGCTT
Statistics
Matches: 49, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
63 49 1.00
ACGTcount: A:0.40, C:0.14, G:0.17, T:0.30
Consensus pattern (63 bp):
TGCTTGAAAACGCATTTCAGAAGACACATTTTCATCAAATAATAATAATGAAAGAGTCAGAGG
Found at i:41327523 original size:51 final size:51
Alignment explanation
Indices: 41327440--41327556 Score: 207
Period size: 51 Copynumber: 2.3 Consensus size: 51
41327430 CGGATCACAT
*
41327440 TTATCACTTGTCACTTGTCACTGATCAAATAAGTGTAGCTAAAGCTACCAC
1 TTATCACTTGTCACTTGTCACTAATCAAATAAGTGTAGCTAAAGCTACCAC
* *
41327491 TTATCACTTGTCACTTGTCACTAATCAGATAAGTGTAGCTAAAGTTACCAC
1 TTATCACTTGTCACTTGTCACTAATCAAATAAGTGTAGCTAAAGCTACCAC
41327542 TTATCACTTGTCACT
1 TTATCACTTGTCACT
41327557 GATCAGAAGT
Statistics
Matches: 63, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
51 63 1.00
ACGTcount: A:0.30, C:0.23, G:0.13, T:0.34
Consensus pattern (51 bp):
TTATCACTTGTCACTTGTCACTAATCAAATAAGTGTAGCTAAAGCTACCAC
Found at i:41334480 original size:21 final size:20
Alignment explanation
Indices: 41334438--41334480 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
41334428 TGAAATCATT
*
41334438 AAAAACTTTGGTAAAGTGAC
1 AAAAACTTTGGTAAAGTAAC
*
41334458 AAAAATTTTGGTAAAGGTAAC
1 AAAAACTTTGGTAAA-GTAAC
41334479 AA
1 AA
41334481 TTTTAGTAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 14 0.70
21 6 0.30
ACGTcount: A:0.49, C:0.07, G:0.19, T:0.26
Consensus pattern (20 bp):
AAAAACTTTGGTAAAGTAAC
Found at i:41334554 original size:20 final size:20
Alignment explanation
Indices: 41334501--41334558 Score: 64
Period size: 20 Copynumber: 2.9 Consensus size: 20
41334491 TGTTAAGATA
** *
41334501 TGGTAAAGGGTTAGAAATTT
1 TGGTAAAGTCTTATAAATTT
41334521 TGGTAATA-TCTTATAAATTT
1 TGGTAA-AGTCTTATAAATTT
*
41334541 TGGTAAAGTTTTATAAAT
1 TGGTAAAGTCTTATAAAT
41334559 ATTGATAATC
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
19 1 0.03
20 30 0.94
21 1 0.03
ACGTcount: A:0.36, C:0.02, G:0.19, T:0.43
Consensus pattern (20 bp):
TGGTAAAGTCTTATAAATTT
Found at i:41334694 original size:40 final size:39
Alignment explanation
Indices: 41334511--41335166 Score: 198
Period size: 40 Copynumber: 16.3 Consensus size: 39
41334501 TGGTAAAGGG
* * * *
41334511 TTAGAAATTTTGGTAATATC-TTATAAATTTTGGTAAAGTT
1 TTAGAAATTTTGATAA-ATCGTTAGATATTTTGGTAAA-TC
* * ** *
41334551 TTATAAATATTGAT-AATCAATAGAAATTTTGGTAAATC
1 TTAGAAATTTTGATAAATCGTTAGATATTTTGGTAAATC
* ** **
41334589 TTTAAAAAAATTG-TAAAT-GTTAGATATAATGGTAAATC
1 -TTAGAAATTTTGATAAATCGTTAGATATTTTGGTAAATC
* * * *
41334627 TTTGGAAATATTGA-ATAACCGTAAGATATTTTGGTAAATTC
1 -TTAGAAATTTTGATA-AATCGTTAGATATTTTGGTAAA-TC
* * **
41334668 TTAAAAATTTTGATAAATCGTTAGATATATTAATAAATC
1 TTAGAAATTTTGATAAATCGTTAGATATTTTGGTAAATC
* * * *
41334707 GTTA-AATATATT-AGTAAGTCCTTAGATATTTTGGTAAAGTG
1 -TTAGAA-ATTTTGA-TAAATCGTTAGATATTTTGGTAAA-TC
* * ** * *
41334748 ATAGAAATTTTGGT-AATTTTTAAGACTTGGTATAAGGTTTAGAAAAT-
1 TTAGAAATTTTGATAAATCGTT-AGA-----TAT----TTTGGTAAATC
* * *
41334795 TTAGAAATATTTG-TAAAAAC-TTGGAAATTTTGGTAAAGTC
1 TTAGAAAT-TTTGAT-AAATCGTTAGATATTTTGGTAAA-TC
* * * * * * * * *
41334835 TCATAAATATTGGTAAATTGATAGAAATTTTAGTAAAAC
1 TTAGAAATTTTGATAAATCGTTAGATATTTTGGTAAATC
* * *
41334874 ATTAGAAATTTTGATAAATTGTTAGATATCTTGATAAATTC
1 -TTAGAAATTTTGATAAATCGTTAGATATTTTGGTAAA-TC
* * * *
41334915 TTAGAAATTTTGATAAATTGTTAGATATATTCGTAAATTG
1 TTAGAAATTTTGATAAATCGTTAGATATTTTGGTAAA-TC
* * * ** *
41334955 TTAGATA-TTTGATAAATTCTTTA-AAATACTGGTAAACC
1 TTAGAAATTTTGATAAA-TCGTTAGATATTTTGGTAAATC
* * * *
41334993 ATTATATATATT-ATTAAATCGTTAGATATTTTGGTAAACC
1 -TTAGAAATTTTGA-TAAATCGTTAGATATTTTGGTAAATC
* * *
41335033 GATAG--ATTTCCTCGA-AAATCGATAGATATTTTTGATAAATCC
1 -TTAGAAATTT--T-GATAAATCGTTAGATA-TTTTGGTAAAT-C
* * * *
41335075 TTAGAAATATT-AGCAAGTCGTTAGATATATTGGTAAATCC
1 TTAGAAATTTTGA-TAAATCGTTAGATATTTTGGTAAAT-C
*
41335115 TTA-AATTTTTTGATAAATCGTTAGATATTTTGGTAAAGTC
1 TTAGAA-ATTTTGATAAATCGTTAGATATTTTGGTAAA-TC
*
41335155 ATAGAAATTTTG
1 TTAGAAATTTTG
41335167 GTAATTGTTA
Statistics
Matches: 457, Mismatches: 107, Indels: 104
0.68 0.16 0.16
Matches are distributed among these distances:
38 41 0.09
39 82 0.18
40 263 0.58
41 35 0.08
42 4 0.01
43 3 0.01
45 3 0.01
47 10 0.02
48 7 0.02
49 9 0.02
ACGTcount: A:0.39, C:0.06, G:0.14, T:0.41
Consensus pattern (39 bp):
TTAGAAATTTTGATAAATCGTTAGATATTTTGGTAAATC
Found at i:41334703 original size:20 final size:20
Alignment explanation
Indices: 41334680--41334735 Score: 76
Period size: 20 Copynumber: 2.8 Consensus size: 20
41334670 AAAAATTTTG
41334680 ATAAATCGTTAGATATATTA
1 ATAAATCGTTAGATATATTA
*
41334700 ATAAATCGTTAAATATATTA
1 ATAAATCGTTAGATATATTA
* * *
41334720 GTAAGTCCTTAGATAT
1 ATAAATCGTTAGATAT
41334736 TTTGGTAAAG
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.43, C:0.07, G:0.11, T:0.39
Consensus pattern (20 bp):
ATAAATCGTTAGATATATTA
Found at i:41334743 original size:20 final size:20
Alignment explanation
Indices: 41334650--41334744 Score: 73
Period size: 20 Copynumber: 4.8 Consensus size: 20
41334640 AATAACCGTA
*
41334650 AGATATTTTGGTAAATTCTT
1 AGATATTTTGGTAAATCCTT
* * * *
41334670 AAAAATTTTGATAAATCGTT
1 AGATATTTTGGTAAATCCTT
* ** *
41334690 AGATATATTAATAAATCGTT
1 AGATATTTTGGTAAATCCTT
* * * *
41334710 AAATATATTAGTAAGTCCTT
1 AGATATTTTGGTAAATCCTT
41334730 AGATATTTTGGTAAA
1 AGATATTTTGGTAAA
41334745 GTGATAGAAA
Statistics
Matches: 58, Mismatches: 17, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
20 58 1.00
ACGTcount: A:0.40, C:0.05, G:0.13, T:0.42
Consensus pattern (20 bp):
AGATATTTTGGTAAATCCTT
Found at i:41335002 original size:59 final size:59
Alignment explanation
Indices: 41334888--41335023 Score: 157
Period size: 59 Copynumber: 2.3 Consensus size: 59
41334878 GAAATTTTGA
** *** *
41334888 TAAATTGTTAGATATCTTGATAAATTCTTAGAAATTTTGATAAATTGTTAGATATATTCG
1 TAAATTGTTAGATAT-TTGATAAATTCTTAGAAATACTGATAAACCATTAGATATATTAG
* * *
41334948 TAAATTGTTAGATATTTGATAAATTCTTTA-AAATACTGGTAAACCATTATATATATTAT
1 TAAATTGTTAGATATTTGATAAATTC-TTAGAAATACTGATAAACCATTAGATATATTAG
*
41335007 TAAATCGTTAGATATTT
1 TAAATTGTTAGATATTT
41335024 TGGTAAACCG
Statistics
Matches: 65, Mismatches: 10, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
59 47 0.72
60 18 0.28
ACGTcount: A:0.38, C:0.06, G:0.11, T:0.45
Consensus pattern (59 bp):
TAAATTGTTAGATATTTGATAAATTCTTAGAAATACTGATAAACCATTAGATATATTAG
Found at i:41335030 original size:20 final size:20
Alignment explanation
Indices: 41334844--41335170 Score: 142
Period size: 20 Copynumber: 16.4 Consensus size: 20
41334834 CTCATAAATA
* * *
41334844 TTGGTAAATTGATAGAAATT
1 TTGGTAAATCGTTAGATATT
* * * *
41334864 TTAGTAAAACATTAGAAATT
1 TTGGTAAATCGTTAGATATT
* * *
41334884 TTGATAAATTGTTAGATATC
1 TTGGTAAATCGTTAGATATT
* *
41334904 TTGATAAATTC-TTAGAAATT
1 TTGGTAAA-TCGTTAGATATT
* * *
41334924 TTGATAAATTGTTAGATATA
1 TTGGTAAATCGTTAGATATT
* *
41334944 TTCGTAAATTGTTAGATA-T
1 TTGGTAAATCGTTAGATATT
* * * *
41334963 TTGATAAATTCTTTA-AAATA
1 TTGGTAAA-TCGTTAGATATT
* * * * *
41334983 CTGGTAAACCATTATATATA
1 TTGGTAAATCGTTAGATATT
**
41335003 TTATTAAATCGTTAGATATT
1 TTGGTAAATCGTTAGATATT
* *
41335023 TTGGTAAACCGATAGAT-TT
1 TTGGTAAATCGTTAGATATT
* * * *
41335042 CCTCGAAAATCGATAGATATTT
1 -TTGGTAAATCGTTAGATA-TT
* * * *
41335064 TTGATAAATCCTTAGAAATA
1 TTGGTAAATCGTTAGATATT
* * * *
41335084 TTAGCAAGTCGTTAGATATA
1 TTGGTAAATCGTTAGATATT
* * *
41335104 TTGGTAAATCCTTAAATTTT
1 TTGGTAAATCGTTAGATATT
*
41335124 TTGATAAATCGTTAGATATT
1 TTGGTAAATCGTTAGATATT
* *
41335144 TTGGTAAAGTC-ATAGAAATT
1 TTGGTAAA-TCGTTAGATATT
41335164 TTGGTAA
1 TTGGTAA
41335171 TTGTTAAAAC
Statistics
Matches: 223, Mismatches: 75, Indels: 18
0.71 0.24 0.06
Matches are distributed among these distances:
19 15 0.07
20 192 0.86
21 14 0.06
22 2 0.01
ACGTcount: A:0.38, C:0.07, G:0.14, T:0.41
Consensus pattern (20 bp):
TTGGTAAATCGTTAGATATT
Found at i:41335257 original size:20 final size:20
Alignment explanation
Indices: 41335234--41335335 Score: 75
Period size: 20 Copynumber: 5.1 Consensus size: 20
41335224 CTAAATATTA
*
41335234 GTAAAACGATAGAAATTTTG
1 GTAAATCGATAGAAATTTTG
* *
41335254 GTAACTC-ATTAGACATTTTG
1 GTAAATCGA-TAGAAATTTTG
*
41335274 GTAAATC-TTCAGAAATTTTG
1 GTAAATCGAT-AGAAATTTTG
* * * *
41335294 GTAAATTGTTAGATATATTG
1 GTAAATCGATAGAAATTTTG
*
41335314 GTAAGAT-GATAAAAATTTTG
1 GTAA-ATCGATAGAAATTTTG
41335334 GT
1 GT
41335336 GTTTGTCAAG
Statistics
Matches: 65, Mismatches: 13, Indels: 8
0.76 0.15 0.09
Matches are distributed among these distances:
19 2 0.03
20 59 0.91
21 4 0.06
ACGTcount: A:0.37, C:0.06, G:0.19, T:0.38
Consensus pattern (20 bp):
GTAAATCGATAGAAATTTTG
Found at i:41335278 original size:40 final size:40
Alignment explanation
Indices: 41335228--41335335 Score: 101
Period size: 40 Copynumber: 2.7 Consensus size: 40
41335218 AATCTCCTAA
* *
41335228 ATATTAGTAAAACGATAGAAATTTTGGTAACTCATTAGAC
1 ATATTGGTAAAACGATAGAAATTTTGGTAAATCATTAGAC
* * * ** *
41335268 ATTTTGGTAAATC-TTCAGAAATTTTGGTAAATTGTTAGAT
1 ATATTGGTAAAACGAT-AGAAATTTTGGTAAATCATTAGAC
* * *
41335308 ATATTGGTAAGATGATAAAAATTTTGGT
1 ATATTGGTAAAACGATAGAAATTTTGGT
41335336 GTTTGTCAAG
Statistics
Matches: 52, Mismatches: 14, Indels: 4
0.74 0.20 0.06
Matches are distributed among these distances:
39 1 0.02
40 50 0.96
41 1 0.02
ACGTcount: A:0.38, C:0.06, G:0.18, T:0.39
Consensus pattern (40 bp):
ATATTGGTAAAACGATAGAAATTTTGGTAAATCATTAGAC
Found at i:41335461 original size:40 final size:40
Alignment explanation
Indices: 41335414--41335545 Score: 113
Period size: 40 Copynumber: 3.3 Consensus size: 40
41335404 AGTTTCATAA
* * * *
41335414 ATATTGGTAAATAGATAGAAATTTTGGTAACTTATTAGAT
1 ATATTGGTAAATACATAGAAATATTGGTAAATCATTAGAT
* * * *
41335454 ATTTTGGTAAATCCTTAGAAATATTGGTAAATCGTTAGAT
1 ATATTGGTAAATACATAGAAATATTGGTAAATCATTAGAT
* * * * * * *
41335494 ATATTGGTAAATGCTTATAAATTTTGATAAAGTC-TTATAA
1 ATATTGGTAAATACATAGAAATATTGGTAAA-TCATTAGAT
41335534 ATATTGGTAAAT
1 ATATTGGTAAAT
41335546 TGATATATTT
Statistics
Matches: 76, Mismatches: 15, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
40 74 0.97
41 2 0.03
ACGTcount: A:0.39, C:0.05, G:0.16, T:0.41
Consensus pattern (40 bp):
ATATTGGTAAATACATAGAAATATTGGTAAATCATTAGAT
Found at i:41335464 original size:60 final size:60
Alignment explanation
Indices: 41335371--41335550 Score: 186
Period size: 60 Copynumber: 3.0 Consensus size: 60
41335361 TAGAAAATTT
* *
41335371 GAAATATCGGTAAAATCA-TAGAAATTTTGGTAAAGT-TTCATAAATATTGGTAAATAGATA
1 GAAATATTGGT-AAATGATTAGAAATTTTGGTAAAGTCTT-ATAAATATTGGTAAATAGATA
* * * * * * *
41335431 GAAATTTTGGTAACTTATTAGATATTTTGGTAAA-TCCTTAGAAATATTGGTAAATCGTTA
1 GAAATATTGGTAAATGATTAGAAATTTTGGTAAAGT-CTTATAAATATTGGTAAATAGATA
* * * * *
41335491 GATATATTGGTAAATGCTTATAAATTTTGATAAAGTCTTATAAATATTGGTAAATTGATA
1 GAAATATTGGTAAATGATTAGAAATTTTGGTAAAGTCTTATAAATATTGGTAAATAGATA
41335551 TATTTGTTAA
Statistics
Matches: 97, Mismatches: 19, Indels: 8
0.78 0.15 0.06
Matches are distributed among these distances:
59 5 0.05
60 89 0.92
61 3 0.03
ACGTcount: A:0.40, C:0.05, G:0.16, T:0.39
Consensus pattern (60 bp):
GAAATATTGGTAAATGATTAGAAATTTTGGTAAAGTCTTATAAATATTGGTAAATAGATA
Found at i:41335552 original size:20 final size:20
Alignment explanation
Indices: 41335392--41335552 Score: 92
Period size: 20 Copynumber: 8.1 Consensus size: 20
41335382 AAAATCATAG
* *
41335392 AAATTTTGGTAAAGTT-TCAT
1 AAATATTGGTAAA-TTGTTAT
* * *
41335412 AAATATTGGTAAATAGATAG
1 AAATATTGGTAAATTGTTAT
* * * *
41335432 AAATTTTGGTAACTTATTAG
1 AAATATTGGTAAATTGTTAT
* * ** *
41335452 ATATTTTGGTAAATCCTTAG
1 AAATATTGGTAAATTGTTAT
* *
41335472 AAATATTGGTAAATCGTTAG
1 AAATATTGGTAAATTGTTAT
*
41335492 ATATATTGGTAAA-TGCTTAT
1 AAATATTGGTAAATTG-TTAT
* * * *
41335512 AAATTTTGATAAAGTCTTAT
1 AAATATTGGTAAATTGTTAT
*
41335532 AAATATTGGTAAATTGATAT
1 AAATATTGGTAAATTGTTAT
41335552 A
1 A
41335553 TTTGTTAAAT
Statistics
Matches: 109, Mismatches: 29, Indels: 6
0.76 0.20 0.04
Matches are distributed among these distances:
19 2 0.02
20 106 0.97
21 1 0.01
ACGTcount: A:0.39, C:0.04, G:0.16, T:0.41
Consensus pattern (20 bp):
AAATATTGGTAAATTGTTAT
Found at i:41341883 original size:19 final size:19
Alignment explanation
Indices: 41341859--41341897 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
41341849 TTTCGTAAAT
41341859 TATATAATGTA-TGATGAAA
1 TATAT-ATGTATTGATGAAA
*
41341878 TATATATTTATTGATGAAA
1 TATATATGTATTGATGAAA
41341897 T
1 T
41341898 GAGAATAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 4 0.22
19 14 0.78
ACGTcount: A:0.44, C:0.00, G:0.13, T:0.44
Consensus pattern (19 bp):
TATATATGTATTGATGAAA
Found at i:41342163 original size:45 final size:46
Alignment explanation
Indices: 41341978--41342315 Score: 569
Period size: 46 Copynumber: 7.5 Consensus size: 46
41341968 TGATCAGTGA
41341978 CAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGAT
1 CAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGAT
*
41342024 CAAGTGACAAAGTGATAAATGGTAGCTTTAGCTACACTTATCTGAT
1 CAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGAT
* *
41342070 CAAGTGACAAAGTGATAGGTGGTAGCTTTAGCTACACTTATCTAAT
1 CAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGAT
*
41342116 CAAGTGACAAAGTGATAAGTGGTAGC-CTAGCTACACTTATCTGAT
1 CAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGAT
*
41342161 CAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACTCTTATCTGAT
1 CAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGAT
*
41342207 CAAGTGACAAAGTGATAAGTGGTAGC-CTAGCTACACTTATCTGAT
1 CAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGAT
*
41342252 CAAGTGACAAAGTGATAAGTGGTAGC-CTAGCTACACTTATCTGAT
1 CAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGAT
*
41342297 C-AGGGAC-AAGTGATAAGTG
1 CAAGTGACAAAGTGATAAGTG
41342316 ATCATACGTA
Statistics
Matches: 279, Mismatches: 12, Indels: 5
0.94 0.04 0.02
Matches are distributed among these distances:
43 12 0.04
44 5 0.02
45 106 0.38
46 156 0.56
ACGTcount: A:0.33, C:0.16, G:0.22, T:0.28
Consensus pattern (46 bp):
CAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGAT
Found at i:41342195 original size:91 final size:91
Alignment explanation
Indices: 41341978--41342315 Score: 583
Period size: 91 Copynumber: 3.7 Consensus size: 91
41341968 TGATCAGTGA
*
41341978 CAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGACAAAGTGATAAA
1 CAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGACAAAGTGATAAG
*
41342043 TGGTAGCTTTAGCTACACTTATCTGAT
66 TGGTAGC-CTAGCTACACTTATCTGAT
* *
41342070 CAAGTGACAAAGTGATAGGTGGTAGCTTTAGCTACACTTATCTAATCAAGTGACAAAGTGATAAG
1 CAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGACAAAGTGATAAG
41342135 TGGTAGCCTAGCTACACTTATCTGAT
66 TGGTAGCCTAGCTACACTTATCTGAT
*
41342161 CAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACTCTTATCTGATCAAGTGACAAAGTGATAAG
1 CAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGACAAAGTGATAAG
41342226 TGGTAGCCTAGCTACACTTATCTGAT
66 TGGTAGCCTAGCTACACTTATCTGAT
* *
41342252 CAAGTGACAAAGTGATAAGTGGTAGC-CTAGCTACACTTATCTGATC-AGGGAC-AAGTGATAAG
1 CAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGACAAAGTGATAAG
41342314 TG
66 TG
41342316 ATCATACGTA
Statistics
Matches: 236, Mismatches: 10, Indels: 4
0.94 0.04 0.02
Matches are distributed among these distances:
88 12 0.05
89 5 0.02
90 18 0.08
91 132 0.56
92 69 0.29
ACGTcount: A:0.33, C:0.16, G:0.22, T:0.28
Consensus pattern (91 bp):
CAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGACAAAGTGATAAG
TGGTAGCCTAGCTACACTTATCTGAT
Found at i:41345096 original size:91 final size:92
Alignment explanation
Indices: 41344941--41345156 Score: 254
Period size: 91 Copynumber: 2.3 Consensus size: 92
41344931 TGAACACTTC
* ** *
41344941 AGTTTATGGATGAACCACTAGTGTTTGTTGGTTAATACGCTGCTAGTAGGTTATGAATGCACAAC
1 AGTTTGTGGATGAACCACTAGTGTTTGCAGGTTAATACGCTGCCAGTAGGTTATGAATGCACAAC
* * *
41345006 -CTCTTTGCACATAAAAGTTGTCAGTA
66 ACTATTTGCACAAAAAAGCTGTCAGTA
* * * *
41345032 AGTTTGTGGATGAACCACTAGCGTTTGCAGGTTAATATGTTGCCAGTAGGTTGTGAATGCACAAC
1 AGTTTGTGGATGAACCACTAGTGTTTGCAGGTTAATACGCTGCCAGTAGGTTATGAATGCACAAC
* * *
41345097 ATATGTATTTGCAGAAAAAAGCTGTGAGTA
66 --A-CTATTTGCACAAAAAAGCTGTCAGTA
* *
41345127 AGTTTGTGGATAAACCACCAGTGTTTGCAG
1 AGTTTGTGGATGAACCACTAGTGTTTGCAG
41345157 ATTGTTAAAT
Statistics
Matches: 104, Mismatches: 17, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
91 57 0.55
95 47 0.45
ACGTcount: A:0.29, C:0.14, G:0.25, T:0.32
Consensus pattern (92 bp):
AGTTTGTGGATGAACCACTAGTGTTTGCAGGTTAATACGCTGCCAGTAGGTTATGAATGCACAAC
ACTATTTGCACAAAAAAGCTGTCAGTA
Found at i:41345325 original size:38 final size:39
Alignment explanation
Indices: 41345245--41345332 Score: 97
Period size: 38 Copynumber: 2.3 Consensus size: 39
41345235 TACATAAAAC
* * *
41345245 AGTAGACATGCTTTAATATGTATTATGTTCAACAATAGT
1 AGTAGACATGCTTTAACATGTATTAGGTTCAACAATAAT
* * **
41345284 AGTAGACATGC-TTAACATGTATTCGGTTCTACGGTAAT
1 AGTAGACATGCTTTAACATGTATTAGGTTCAACAATAAT
*
41345322 AGTAGGCATGC
1 AGTAGACATGC
41345333 AATCAATAAT
Statistics
Matches: 41, Mismatches: 8, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
38 30 0.73
39 11 0.27
ACGTcount: A:0.32, C:0.14, G:0.20, T:0.34
Consensus pattern (39 bp):
AGTAGACATGCTTTAACATGTATTAGGTTCAACAATAAT
Found at i:41348396 original size:24 final size:24
Alignment explanation
Indices: 41348364--41348412 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
41348354 GCAGACAGTT
41348364 AATACATTCTACTTATTAAACAAG
1 AATACATTCTACTTATTAAACAAG
41348388 AATACATTCTACTTATTAAACAAG
1 AATACATTCTACTTATTAAACAAG
41348412 A
1 A
41348413 TTTTATGGTC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.47, C:0.16, G:0.04, T:0.33
Consensus pattern (24 bp):
AATACATTCTACTTATTAAACAAG
Found at i:41353847 original size:31 final size:30
Alignment explanation
Indices: 41353808--41353871 Score: 85
Period size: 31 Copynumber: 2.1 Consensus size: 30
41353798 TTTTCATAAA
*
41353808 TTTAGAATTTAGT-CTTTGTACTTTTTTATT
1 TTTAGAATTTAGTCCTTT-TACTTTTTTAGT
*
41353838 TTTAGGAATTTTGTCCTTTTACTTTTTTAGT
1 TTTA-GAATTTAGTCCTTTTACTTTTTTAGT
41353869 TTT
1 TTT
41353872 CAAAATTCAA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
30 4 0.13
31 22 0.73
32 4 0.13
ACGTcount: A:0.17, C:0.08, G:0.11, T:0.64
Consensus pattern (30 bp):
TTTAGAATTTAGTCCTTTTACTTTTTTAGT
Found at i:41362143 original size:17 final size:18
Alignment explanation
Indices: 41362121--41362158 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 18
41362111 TTTTTGAATA
41362121 TTTGTA-TTTTGGAAC-TT
1 TTTGTACTTTT-GAACATT
41362138 TTTGTACTTTTGAACATT
1 TTTGTACTTTTGAACATT
41362156 TTT
1 TTT
41362159 CTGAATAAAG
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 10 0.53
18 9 0.47
ACGTcount: A:0.18, C:0.08, G:0.13, T:0.61
Consensus pattern (18 bp):
TTTGTACTTTTGAACATT
Found at i:41365693 original size:29 final size:30
Alignment explanation
Indices: 41365637--41365695 Score: 84
Period size: 29 Copynumber: 2.0 Consensus size: 30
41365627 CAAGAATTTG
*
41365637 ATAAAATAAAAATTTTATATATAAAATTAC
1 ATAAAATAAAAATTTTATATACAAAATTAC
* *
41365667 ATAAAATAAAAA-TTTATATGCACAATTAC
1 ATAAAATAAAAATTTTATATACAAAATTAC
41365696 GCGTTAAACC
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
29 14 0.54
30 12 0.46
ACGTcount: A:0.58, C:0.07, G:0.02, T:0.34
Consensus pattern (30 bp):
ATAAAATAAAAATTTTATATACAAAATTAC
Found at i:41368441 original size:24 final size:24
Alignment explanation
Indices: 41368394--41368442 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 24
41368384 GATCTTGAAA
* *
41368394 ACTTAGGTTTAAGGGTAAGTTTGG
1 ACTTAGGTTTAAGAGTAAGCTTGG
*
41368418 ACTTAGGTTTAAGAGTAGGCTTGG
1 ACTTAGGTTTAAGAGTAAGCTTGG
41368442 A
1 A
41368443 TGGATGACGT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.27, C:0.06, G:0.33, T:0.35
Consensus pattern (24 bp):
ACTTAGGTTTAAGAGTAAGCTTGG
Found at i:41373567 original size:124 final size:125
Alignment explanation
Indices: 41373439--41373694 Score: 356
Period size: 124 Copynumber: 2.1 Consensus size: 125
41373429 AAATAGTGGG
** * * * *
41373439 AAATCGCTTCTACTAAGATGCTATTTAAGAAGAAATTGTGAAATAGTGGCCTCGTGGACGCGATT
1 AAATCGCTGATACCAAGATGCTATATAAGAAGAAATTGTGAAATAGCGCCCTCGTGGACGCGATT
* *
41373504 TCGCTACAGT-GGTCATGT-GAGAAATAA-TTTTTTTTGACGTTTTCTGAGGAAATAGTATA
66 TCGCTACAGTCGGTCATGTAG-GAAATAATTTTTTTTTGACG-TTTCTGAGCAAACAGTATA
* * *
41373563 AAATCGCTGATACCAGGATGCTATATGAGAAGAAATTGTGAAATCGCGCCCTCGTGGACGCGATT
1 AAATCGCTGATACCAAGATGCTATATAAGAAGAAATTGTGAAATAGCGCCCTCGTGGACGCGATT
* *
41373628 TCGCTACAGTCGGTCATGTAGGAAATAATTTTTTTTTGACGTTTCTGAGCAAACAGTGTC
66 TCGCTACAGTCGGTCATGTAGGAAATAATTTTTTTTTGACGTTTCTGAGCAAACAGTATA
41373688 AAATCGC
1 AAATCGC
41373695 GCCCTCGTGG
Statistics
Matches: 116, Mismatches: 13, Indels: 5
0.87 0.10 0.04
Matches are distributed among these distances:
124 66 0.57
125 37 0.32
126 13 0.11
ACGTcount: A:0.30, C:0.16, G:0.23, T:0.31
Consensus pattern (125 bp):
AAATCGCTGATACCAAGATGCTATATAAGAAGAAATTGTGAAATAGCGCCCTCGTGGACGCGATT
TCGCTACAGTCGGTCATGTAGGAAATAATTTTTTTTTGACGTTTCTGAGCAAACAGTATA
Found at i:41374771 original size:17 final size:17
Alignment explanation
Indices: 41374749--41374788 Score: 71
Period size: 17 Copynumber: 2.4 Consensus size: 17
41374739 TTGGTGAACT
*
41374749 TGATGTACACGGCTCCG
1 TGATGTACACGGCCCCG
41374766 TGATGTACACGGCCCCG
1 TGATGTACACGGCCCCG
41374783 TGATGT
1 TGATGT
41374789 GTCGGCCATG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.17, C:0.28, G:0.30, T:0.25
Consensus pattern (17 bp):
TGATGTACACGGCCCCG
Found at i:41375547 original size:22 final size:22
Alignment explanation
Indices: 41375517--41375558 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
41375507 ATTTGGAGAT
*
41375517 TTTTTGAAGGAAATTGAGAGGA
1 TTTTGGAAGGAAATTGAGAGGA
*
41375539 TTTTGGAAGGAATTTGAGAG
1 TTTTGGAAGGAAATTGAGAG
41375559 TTTGAGAGAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.33, C:0.00, G:0.33, T:0.33
Consensus pattern (22 bp):
TTTTGGAAGGAAATTGAGAGGA
Found at i:41375566 original size:30 final size:30
Alignment explanation
Indices: 41375530--41375588 Score: 100
Period size: 30 Copynumber: 2.0 Consensus size: 30
41375520 TTGAAGGAAA
* *
41375530 TTGAGAGGATTTTGGAAGGAATTTGAGAGT
1 TTGAGAGAATTTTGGAAGGAAATTGAGAGT
41375560 TTGAGAGAATTTTGGAAGGAAATTGAGAG
1 TTGAGAGAATTTTGGAAGGAAATTGAGAG
41375589 AAATTTTGAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.34, C:0.00, G:0.36, T:0.31
Consensus pattern (30 bp):
TTGAGAGAATTTTGGAAGGAAATTGAGAGT
Found at i:41375579 original size:52 final size:51
Alignment explanation
Indices: 41375508--41375610 Score: 138
Period size: 52 Copynumber: 2.0 Consensus size: 51
41375498 TTAATATGGA
* * *
41375508 TTTGGAGATTTTTTGAAGGAAATTGAGAG-GATTTTGGAA-GGAATTTGAGAG
1 TTTGGAGAATTTTGGAAGGAAATTGAGAGAAATTTT-GAAGGGAA-TTGAGAG
41375559 TTTGAGAGAATTTTGGAAGGAAATTGAGAGAAATTTTGAAGGGAATTGAGAG
1 TTTG-GAGAATTTTGGAAGGAAATTGAGAGAAATTTTGAAGGGAATTGAGAG
41375611 AATTTTTGAA
Statistics
Matches: 46, Mismatches: 3, Indels: 5
0.85 0.06 0.09
Matches are distributed among these distances:
51 4 0.09
52 33 0.72
53 9 0.20
ACGTcount: A:0.35, C:0.00, G:0.33, T:0.32
Consensus pattern (51 bp):
TTTGGAGAATTTTGGAAGGAAATTGAGAGAAATTTTGAAGGGAATTGAGAG
Found at i:41375626 original size:22 final size:21
Alignment explanation
Indices: 41375560--41375627 Score: 91
Period size: 22 Copynumber: 3.1 Consensus size: 21
41375550 ATTTGAGAGT
*
41375560 TTGAGAGAATTTTGGAAGGAAA
1 TTGAGAGAATTTTGAAAGG-AA
*
41375582 TTGAGAGAAATTTTGAAGGGAA
1 TTGAGAG-AATTTTGAAAGGAA
41375604 TTGAGAGAATTTTTGAAAGGAA
1 TTGAGAGAA-TTTTGAAAGGAA
41375626 TT
1 TT
41375628 TGTTTGTGAA
Statistics
Matches: 41, Mismatches: 3, Indels: 4
0.85 0.06 0.08
Matches are distributed among these distances:
21 2 0.05
22 29 0.71
23 10 0.24
ACGTcount: A:0.40, C:0.00, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAGAGAATTTTGAAAGGAA
Found at i:41379562 original size:7 final size:7
Alignment explanation
Indices: 41379550--41379574 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
41379540 TCTAATAAAA
41379550 ACATGCC
1 ACATGCC
41379557 ACATGCC
1 ACATGCC
41379564 ACATGCC
1 ACATGCC
41379571 ACAT
1 ACAT
41379575 TTTCATTAAC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.32, C:0.40, G:0.12, T:0.16
Consensus pattern (7 bp):
ACATGCC
Found at i:41385836 original size:16 final size:17
Alignment explanation
Indices: 41385815--41385847 Score: 59
Period size: 16 Copynumber: 2.0 Consensus size: 17
41385805 TCATCATCAT
41385815 AAAAAAGAAAA-AAGAA
1 AAAAAAGAAAAGAAGAA
41385831 AAAAAAGAAAAGAAGAA
1 AAAAAAGAAAAGAAGAA
41385848 GATAACCTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 11 0.69
17 5 0.31
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (17 bp):
AAAAAAGAAAAGAAGAA
Found at i:41388023 original size:15 final size:17
Alignment explanation
Indices: 41388003--41388034 Score: 50
Period size: 15 Copynumber: 2.0 Consensus size: 17
41387993 ACTCTAAAAA
41388003 TTAAAAA-AT-ATTTTT
1 TTAAAAATATCATTTTT
41388018 TTAAAAATATCATTTTT
1 TTAAAAATATCATTTTT
41388035 AGCCCTTTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 7 0.47
16 2 0.13
17 6 0.40
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.53
Consensus pattern (17 bp):
TTAAAAATATCATTTTT
Found at i:41392195 original size:9 final size:9
Alignment explanation
Indices: 41392181--41392217 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
41392171 TATAGTTTGA
41392181 TATTCGAAT
1 TATTCGAAT
41392190 TATTCGAAT
1 TATTCGAAT
*
41392199 TATTCGAGT
1 TATTCGAAT
41392208 TATTCGAAT
1 TATTCGAAT
41392217 T
1 T
41392218 CAAAAACTTA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.30, C:0.11, G:0.14, T:0.46
Consensus pattern (9 bp):
TATTCGAAT
Found at i:41392289 original size:9 final size:9
Alignment explanation
Indices: 41392272--41392302 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
41392262 TCGAGTTGAT
41392272 TCGAATAAC
1 TCGAATAAC
*
41392281 TCGATTAAC
1 TCGAATAAC
41392290 TCGAATAAC
1 TCGAATAAC
41392299 TCGA
1 TCGA
41392303 TTCGTTTAAC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.39, C:0.23, G:0.13, T:0.26
Consensus pattern (9 bp):
TCGAATAAC
Found at i:41394008 original size:41 final size:41
Alignment explanation
Indices: 41393963--41394107 Score: 229
Period size: 41 Copynumber: 3.5 Consensus size: 41
41393953 GACTTTAAGT
41393963 CTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGTTATAAAC
1 CTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGTTATAAAC
* * *
41394004 CTAGCAGGTTAAGTGTCGATGATCTGAATCAGGTTATAAAC
1 CTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGTTATAAAC
* *
41394045 CTAGCAGGCTAAGTGCCGGTGAT-TGGAATCAGGCTATAAGC
1 CTAGCAGGCTAAGTGCCGGTGATCT-GAATCAGGTTATAAAC
41394086 CTAGCAGGCTAAGTGCCGGTGA
1 CTAGCAGGCTAAGTGCCGGTGA
41394108 ATATGTTAAA
Statistics
Matches: 95, Mismatches: 8, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
40 1 0.01
41 94 0.99
ACGTcount: A:0.28, C:0.19, G:0.29, T:0.24
Consensus pattern (41 bp):
CTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGTTATAAAC
Found at i:41401517 original size:41 final size:41
Alignment explanation
Indices: 41401472--41401575 Score: 174
Period size: 41 Copynumber: 2.5 Consensus size: 41
41401462 GACTTTAAGT
*
41401472 CTAGCAGGCTAAGTGCCGGTGATCT-GAATCAGGTTATAAAC
1 CTAGCAGGCTAAGTGCCGGTGAT-TGGAATCAGGCTATAAAC
*
41401513 CTAGCAGGCTAAGTGCCGGTGATTGGAATCAGGCTATAAGC
1 CTAGCAGGCTAAGTGCCGGTGATTGGAATCAGGCTATAAAC
41401554 CTAGCAGGCTAAGTGCCGGTGA
1 CTAGCAGGCTAAGTGCCGGTGA
41401576 ATATGTTAAA
Statistics
Matches: 60, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
40 1 0.02
41 59 0.98
ACGTcount: A:0.27, C:0.20, G:0.31, T:0.22
Consensus pattern (41 bp):
CTAGCAGGCTAAGTGCCGGTGATTGGAATCAGGCTATAAAC
Found at i:41406011 original size:59 final size:60
Alignment explanation
Indices: 41405897--41406022 Score: 150
Period size: 59 Copynumber: 2.1 Consensus size: 60
41405887 TATTTTTTAA
* * * *
41405897 TTTTTAGAGTTAGGACTAAATTGATAGATTTTGTAAATATTGAGGACCAAATTTATT-ACAT
1 TTTTTAGAATTAGAACTAAAATGA-ACATTTTGTAAATATTGAGGACCAAATTTATTGA-AT
* *
41405958 TTTTTAGAATTAGAACTAAAATG-ACATTTTGTAAATATTGAAGG-CTAATTTTATTGAAT
1 TTTTTAGAATTAGAACTAAAATGAACATTTTGTAAATATTG-AGGACCAAATTTATTGAAT
41406017 TTTTTA
1 TTTTTA
41406023 TATTTTATGA
Statistics
Matches: 57, Mismatches: 6, Indels: 6
0.83 0.09 0.09
Matches are distributed among these distances:
59 33 0.58
60 4 0.07
61 20 0.35
ACGTcount: A:0.37, C:0.06, G:0.14, T:0.44
Consensus pattern (60 bp):
TTTTTAGAATTAGAACTAAAATGAACATTTTGTAAATATTGAGGACCAAATTTATTGAAT
Found at i:41408077 original size:16 final size:17
Alignment explanation
Indices: 41408050--41408082 Score: 59
Period size: 16 Copynumber: 2.0 Consensus size: 17
41408040 TTAGGTTATC
41408050 TTCTTCTTTTCTTTTTT
1 TTCTTCTTTTCTTTTTT
41408067 TTCTT-TTTTCTTTTTT
1 TTCTTCTTTTCTTTTTT
41408083 ATGATGATGA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 11 0.69
17 5 0.31
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (17 bp):
TTCTTCTTTTCTTTTTT
Found at i:41413913 original size:32 final size:32
Alignment explanation
Indices: 41413872--41413945 Score: 130
Period size: 32 Copynumber: 2.3 Consensus size: 32
41413862 TGACGTTCAT
41413872 ATAGATGCTATCAGAACGATAAAGTGAAGTTG
1 ATAGATGCTATCAGAACGATAAAGTGAAGTTG
41413904 ATAGATGCTATCAGAACGATAAAGTGAAGTTG
1 ATAGATGCTATCAGAACGATAAAGTGAAGTTG
**
41413936 GCAGATGCTA
1 ATAGATGCTA
41413946 ACTCTGAAAG
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
32 40 1.00
ACGTcount: A:0.39, C:0.11, G:0.26, T:0.24
Consensus pattern (32 bp):
ATAGATGCTATCAGAACGATAAAGTGAAGTTG
Found at i:41416532 original size:196 final size:197
Alignment explanation
Indices: 41416161--41416540 Score: 475
Period size: 196 Copynumber: 1.9 Consensus size: 197
41416151 TTATATGCTC
* * * * * *
41416161 ATTTTTTTAACAACTTCATTATAGGTTCTGATCATATCTGCTTTTTTGACATAATGTCTAGAACT
1 ATTTTTTTAACAACTTCATTATAGATTCTAATCATATATGCTTTTTTGACACAATGCCTAAAACT
* * * * *
41416226 ACGCATAGCCCCTCTCCCCAACTCATAAATAGGAGGATAATGCGATTTAGTGCACTCGAACCGAC
66 ACCCATAGACCCTCTCCCCAACCCATAAATAGGAGGATAATGCGATTTAGCGCACTCGAACCCAC
* *
41416291 GTCTTCATGCATTCGCAACAATGCCTATATCAATTGAACTAAGACTCAATCAACACATATGCTAT
131 GTCTTCATGCATTCGCAACAATGCCTATACCAATTAAACTAAGACTCAATCAACACATATGCTAT
41416356 AA
196 AA
* *
41416358 ATTTTTTTGAACAA-TCTCATTATAGATTCTAATCATATATGTTTTTTTTACACAATGCCTAAAA
1 ATTTTTTT-AACAACT-TCATTATAGATTCTAATCATATATGCTTTTTTGACACAATGCCTAAAA
* * *
41416422 CTACCCATA-ACCC-CTCCCTAACCCATAAATAGGAGGATAATGC-ATTTCAGCGCATTTGAACC
64 CTACCCATAGACCCTCTCCCCAACCCATAAATAGGAGGATAATGCGATTT-AGCGCACTCGAACC
* * * *
41416484 CATGTCTTCCTGCATT-GATAACAATGTCC-ATACCAATTAAATTAAGACTCAATCAAC
128 CACGTCTTCATGCATTCG-CAACAATG-CCTATACCAATTAAACTAAGACTCAATCAAC
41416541 TATATACTAC
Statistics
Matches: 156, Mismatches: 22, Indels: 11
0.83 0.12 0.06
Matches are distributed among these distances:
195 5 0.03
196 84 0.54
197 14 0.09
198 53 0.34
ACGTcount: A:0.33, C:0.23, G:0.11, T:0.32
Consensus pattern (197 bp):
ATTTTTTTAACAACTTCATTATAGATTCTAATCATATATGCTTTTTTGACACAATGCCTAAAACT
ACCCATAGACCCTCTCCCCAACCCATAAATAGGAGGATAATGCGATTTAGCGCACTCGAACCCAC
GTCTTCATGCATTCGCAACAATGCCTATACCAATTAAACTAAGACTCAATCAACACATATGCTAT
AA
Found at i:41420294 original size:6 final size:7
Alignment explanation
Indices: 41420277--41420304 Score: 56
Period size: 7 Copynumber: 4.0 Consensus size: 7
41420267 TAAGTATGTC
41420277 TTTTTAA
1 TTTTTAA
41420284 TTTTTAA
1 TTTTTAA
41420291 TTTTTAA
1 TTTTTAA
41420298 TTTTTAA
1 TTTTTAA
41420305 AATTCATGGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (7 bp):
TTTTTAA
Found at i:41427528 original size:56 final size:56
Alignment explanation
Indices: 41427462--41427575 Score: 228
Period size: 56 Copynumber: 2.0 Consensus size: 56
41427452 TATGTACTAA
41427462 ACTTAATAATATGTCTTTACTATTAAAATGGATTGTATTTGATTGTAGTTGCCCAG
1 ACTTAATAATATGTCTTTACTATTAAAATGGATTGTATTTGATTGTAGTTGCCCAG
41427518 ACTTAATAATATGTCTTTACTATTAAAATGGATTGTATTTGATTGTAGTTGCCCAG
1 ACTTAATAATATGTCTTTACTATTAAAATGGATTGTATTTGATTGTAGTTGCCCAG
41427574 AC
1 AC
41427576 AACGAATGTG
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
56 58 1.00
ACGTcount: A:0.31, C:0.11, G:0.16, T:0.42
Consensus pattern (56 bp):
ACTTAATAATATGTCTTTACTATTAAAATGGATTGTATTTGATTGTAGTTGCCCAG
Found at i:41429454 original size:9 final size:9
Alignment explanation
Indices: 41429436--41429531 Score: 106
Period size: 9 Copynumber: 10.4 Consensus size: 9
41429426 TTTAGTTAAA
41429436 AATTACCCG
1 AATTACCCG
*
41429445 AATTATCCG
1 AATTACCCG
41429454 AATTACCC-
1 AATTACCCG
41429462 AACTTACCCG
1 AA-TTACCCG
*
41429472 AATTACTC-
1 AATTACCCG
41429480 AACTTACCCG
1 AA-TTACCCG
*
41429490 ACTTACCCG
1 AATTACCCG
*
41429499 AATTAACCG
1 AATTACCCG
41429508 AAAATTACCCG
1 --AATTACCCG
41429519 AATTACCCG
1 AATTACCCG
41429528 AATT
1 AATT
41429532 GACACTTTGA
Statistics
Matches: 73, Mismatches: 8, Indels: 12
0.78 0.09 0.13
Matches are distributed among these distances:
8 4 0.05
9 58 0.79
10 3 0.04
11 8 0.11
ACGTcount: A:0.35, C:0.31, G:0.08, T:0.25
Consensus pattern (9 bp):
AATTACCCG
Found at i:41429517 original size:20 final size:20
Alignment explanation
Indices: 41429492--41429529 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
41429482 CTTACCCGAC
41429492 TTACCCGAATTAACCGAAAA
1 TTACCCGAATTAACCGAAAA
*
41429512 TTACCCGAATTACCCGAA
1 TTACCCGAATTAACCGAA
41429530 TTGACACTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.39, C:0.29, G:0.11, T:0.21
Consensus pattern (20 bp):
TTACCCGAATTAACCGAAAA
Found at i:41430287 original size:16 final size:16
Alignment explanation
Indices: 41430266--41430305 Score: 71
Period size: 16 Copynumber: 2.5 Consensus size: 16
41430256 GCCTAAGAGA
41430266 AAATTGGGCTGGATTT
1 AAATTGGGCTGGATTT
*
41430282 AAATTGGGCTGGGTTT
1 AAATTGGGCTGGATTT
41430298 AAATTGGG
1 AAATTGGG
41430306 AGGGAGTAGG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.25, C:0.05, G:0.35, T:0.35
Consensus pattern (16 bp):
AAATTGGGCTGGATTT
Found at i:41437886 original size:20 final size:20
Alignment explanation
Indices: 41437848--41437886 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
41437838 TTGTTTGTAA
* * *
41437848 CTTTTATGTTTTATTTTTTT
1 CTTTTATATTATATATTTTT
41437868 CTTTTATATTATATATTTT
1 CTTTTATATTATATATTTT
41437887 GTAAATGAAA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.18, C:0.05, G:0.03, T:0.74
Consensus pattern (20 bp):
CTTTTATATTATATATTTTT
Found at i:41440174 original size:31 final size:29
Alignment explanation
Indices: 41440114--41440181 Score: 91
Period size: 29 Copynumber: 2.3 Consensus size: 29
41440104 GTGATAGTTT
*
41440114 AAGTACCACATTAGACATTTTCAAAGTAC
1 AAGTACCACATTAGACATTATCAAAGTAC
*
41440143 AAGTACCACATTAGACATGTAATGAAAGTAC
1 AAGTACCACATTAGACAT-T-ATCAAAGTAC
*
41440174 AGGTACCA
1 AAGTACCA
41440182 AATAATACAC
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
29 18 0.53
30 1 0.03
31 15 0.44
ACGTcount: A:0.43, C:0.19, G:0.15, T:0.24
Consensus pattern (29 bp):
AAGTACCACATTAGACATTATCAAAGTAC
Found at i:41440269 original size:91 final size:91
Alignment explanation
Indices: 41439994--41440275 Score: 266
Period size: 91 Copynumber: 3.1 Consensus size: 91
41439984 TAACTCCAAA
* * * * * *
41439994 TACCATAATAATACCCAGATTGATAGTTCAAGTACCACATT-GAATATTTTCAAAGTATAAGTAT
1 TACCA-AATAATACACAAAGTGATAGTTCAAGTACCACATTAG-ACATTTTCAAAGTACAAGTAC
** * * * *
41440058 CATGTTGGGCATTTCATGAAAGTACA--
64 CACATTAGACATGTAATGAAAGTACAGG
* *
41440084 AACCTTAAATAATACACAAAGTGATAGTTTAAGTACCACATTAGACATTTTCAAAGTACAAGTAC
1 TACC--AAATAATACACAAAGTGATAGTTCAAGTACCACATTAGACATTTTCAAAGTACAAGTAC
41440149 CACATTAGACATGTAATGAAAGTACAGG
64 CACATTAGACATGTAATGAAAGTACAGG
* * ** * *
41440177 TACCAAATAATACACAAATTGATGGTTCAAGTACGGCATTAGACATTTTTAAGGTACATA-TACC
1 TACCAAATAATACACAAAGTGATAGTTCAAGTACCACATTAGACATTTTCAAAGTACA-AGTACC
* * * * *
41440241 ACATTGGATATTTTATGAAAGTATAGG
65 ACATTAGACATGTAATGAAAGTACAGG
41440268 TACCAAAT
1 TACCAAAT
41440276 GTGACATTAT
Statistics
Matches: 159, Mismatches: 27, Indels: 11
0.81 0.14 0.06
Matches are distributed among these distances:
90 3 0.02
91 150 0.94
92 3 0.02
93 3 0.02
ACGTcount: A:0.40, C:0.15, G:0.15, T:0.30
Consensus pattern (91 bp):
TACCAAATAATACACAAAGTGATAGTTCAAGTACCACATTAGACATTTTCAAAGTACAAGTACCA
CATTAGACATGTAATGAAAGTACAGG
Done.