Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009066.1 Hibiscus syriacus cultivar Beakdansim tig00112490_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: 821833
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 5
Found at i:156461 original size:42 final size:42
Alignment explanation
Indices: 156415--156535 Score: 100
Period size: 42 Copynumber: 3.1 Consensus size: 42
156405 AATACAGACG
156415 TTCAAAATGCGCCAATATTCCAATTTCTGATTGAAATGGGCT
1 TTCAAAATGCGCCAATATTCCAATTTCTGATTGAAATGGGCT
* * * * * * *
156457 TTCAACATGC-CC--CA--GC-ATTTGCT-AAT-ACA--GACG
1 TTCAAAATGCGCCAATATTCCAATTT-CTGATTGAAATGGGCT
156490 TTCAAAATGCGCCAATATTCCAATTTCTGATTGAAATGGGCT
1 TTCAAAATGCGCCAATATTCCAATTTCTGATTGAAATGGGCT
156532 TTCA
1 TTCA
156536 GCATGCCCCA
Statistics
Matches: 54, Mismatches: 14, Indels: 22
0.60 0.16 0.24
Matches are distributed among these distances:
33 11 0.20
34 2 0.04
35 2 0.04
36 7 0.13
37 3 0.06
38 3 0.06
39 7 0.13
40 2 0.04
41 2 0.04
42 15 0.28
ACGTcount: A:0.31, C:0.22, G:0.16, T:0.31
Consensus pattern (42 bp):
TTCAAAATGCGCCAATATTCCAATTTCTGATTGAAATGGGCT
Found at i:158067 original size:19 final size:19
Alignment explanation
Indices: 158011--158073 Score: 54
Period size: 19 Copynumber: 3.2 Consensus size: 19
158001 CTATTTAAAC
**
158011 TAAAATACCTAAAAAATAAT
1 TAAAATA-CTAAAACCTAAT
* * *
158031 ATAATATTCTAAATCCTAAT
1 -TAAAATACTAAAACCTAAT
*
158051 TAAAATACTAAAACCTATT
1 TAAAATACTAAAACCTAAT
158070 TAAA
1 TAAA
158074 CTAAAATACA
Statistics
Matches: 33, Mismatches: 9, Indels: 2
0.75 0.20 0.05
Matches are distributed among these distances:
19 19 0.58
20 9 0.27
21 5 0.15
ACGTcount: A:0.56, C:0.13, G:0.00, T:0.32
Consensus pattern (19 bp):
TAAAATACTAAAACCTAAT
Found at i:158101 original size:64 final size:68
Alignment explanation
Indices: 157972--158173 Score: 209
Period size: 64 Copynumber: 2.9 Consensus size: 68
157962 AAGCTAAAAC
* ** *
157972 ATCTTAAATCCTAATTAAAACACTTAAAA-CTATTTAAACTAAAATAC--CTA-AAAAAT-AATA
1 ATCTTAAATCCTAATTAAAATAC-TAAAACCTATTTAAACTAAAATACAAAGATAAAAATAAAAA
158032 TAAT
65 TAAT
158036 AT-TCTAAATCCTAATTAAAATACTAAAACCTATTTAAACTAAAATACAAAGATAAAGATAAAAT
1 ATCT-TAAATCCTAATTAAAATACTAAAACCTATTTAAACTAAAATAC------AAAGATAAAA-
158100 ATAAAAATAAT
58 ATAAAAATAAT
* *
158111 ATCTTAAAACTTAATTAAAATACTAAAAACCTATTTAAACTAAAATACAAAGATAAAATATAA
1 ATCTTAAATCCTAATTAAAATACT-AAAACCTATTTAAACTAAAATACAAAGATAAAA-ATAA
158174 TGTTTAAAAT
Statistics
Matches: 117, Mismatches: 6, Indels: 24
0.80 0.04 0.16
Matches are distributed among these distances:
63 6 0.05
64 38 0.32
70 15 0.13
72 1 0.01
73 4 0.03
74 2 0.02
75 27 0.23
76 24 0.21
ACGTcount: A:0.57, C:0.12, G:0.01, T:0.29
Consensus pattern (68 bp):
ATCTTAAATCCTAATTAAAATACTAAAACCTATTTAAACTAAAATACAAAGATAAAAATAAAAAT
AAT
Found at i:158183 original size:76 final size:75
Alignment explanation
Indices: 158031--158194 Score: 231
Period size: 76 Copynumber: 2.2 Consensus size: 75
158021 AAAAAATAAT
* * *
158031 ATAATATTCTAAATCCTAATTAAAATACTAAAACCTATTTAAACTAAAATACAAAGATAAAGATA
1 ATAATATCCTAAAACTTAATTAAAATACTAAAACCTATTTAAACTAAAATACAAAGATAAAGATA
158096 AAATATAAAA
66 AAATATAAAA
*
158106 ATAATATCTTAAAACTTAATTAAAATACTAAAAACCTATTTAAACTAAAATACAAAGATAAA-AT
1 ATAATATCCTAAAACTTAATTAAAATACT-AAAACCTATTTAAACTAAAATACAAAGATAAAGAT
* * *
158170 ATAATGTTTAAA
65 AAAAT-ATAAAA
*
158182 ATATTATCCTAAA
1 ATAATATCCTAAA
158195 TTTGAGTTTA
Statistics
Matches: 78, Mismatches: 9, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
75 31 0.40
76 47 0.60
ACGTcount: A:0.57, C:0.10, G:0.02, T:0.30
Consensus pattern (75 bp):
ATAATATCCTAAAACTTAATTAAAATACTAAAACCTATTTAAACTAAAATACAAAGATAAAGATA
AAATATAAAA
Found at i:158869 original size:28 final size:28
Alignment explanation
Indices: 158827--158921 Score: 74
Period size: 28 Copynumber: 3.5 Consensus size: 28
158817 CTGCTGTGTA
* *
158827 TTTTTCTACATTGTTCGAACCAAATCAG
1 TTTTTCTGCACTGTTCGAACCAAATCAG
** *
158855 TTTTTCTGCACTGTTCTG-TTC-GA--A-
1 TTTTTCTGCACTGTTC-GAACCAAATCAG
** *
158879 TTTTTCTGCACAATTCGAACCAAGTCAG
1 TTTTTCTGCACTGTTCGAACCAAATCAG
158907 TTTTTCTGCACTGTT
1 TTTTTCTGCACTGTT
158922 TTTTTCGTTA
Statistics
Matches: 48, Mismatches: 13, Indels: 12
0.66 0.18 0.16
Matches are distributed among these distances:
23 1 0.02
24 15 0.31
25 1 0.02
27 2 0.04
28 28 0.58
29 1 0.02
ACGTcount: A:0.21, C:0.22, G:0.14, T:0.43
Consensus pattern (28 bp):
TTTTTCTGCACTGTTCGAACCAAATCAG
Found at i:158982 original size:15 final size:15
Alignment explanation
Indices: 158964--159003 Score: 80
Period size: 15 Copynumber: 2.7 Consensus size: 15
158954 TTGTTCAGAA
158964 AAAATAAAATTAATC
1 AAAATAAAATTAATC
158979 AAAATAAAATTAATC
1 AAAATAAAATTAATC
158994 AAAATAAAAT
1 AAAATAAAAT
159004 AAATAGAATG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 25 1.00
ACGTcount: A:0.70, C:0.05, G:0.00, T:0.25
Consensus pattern (15 bp):
AAAATAAAATTAATC
Found at i:159069 original size:20 final size:19
Alignment explanation
Indices: 159038--159077 Score: 62
Period size: 20 Copynumber: 2.1 Consensus size: 19
159028 AAAAATATAA
*
159038 AAAAAAATAAAACGAAAAT
1 AAAAAAATAAAACAAAAAT
159057 AAAAAAATAAAAACAAAAAT
1 AAAAAAAT-AAAACAAAAAT
159077 A
1 A
159078 TAACGAAATG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 8 0.42
20 11 0.58
ACGTcount: A:0.82, C:0.05, G:0.03, T:0.10
Consensus pattern (19 bp):
AAAAAAATAAAACAAAAAT
Found at i:164640 original size:58 final size:58
Alignment explanation
Indices: 164550--164663 Score: 228
Period size: 58 Copynumber: 2.0 Consensus size: 58
164540 AGGGTCGATC
164550 CATAAAGACTGTGGTGTTTCTGATTTAATAAAACTCTTTCTTGATTTTAGAAAAAGGT
1 CATAAAGACTGTGGTGTTTCTGATTTAATAAAACTCTTTCTTGATTTTAGAAAAAGGT
164608 CATAAAGACTGTGGTGTTTCTGATTTAATAAAACTCTTTCTTGATTTTAGAAAAAG
1 CATAAAGACTGTGGTGTTTCTGATTTAATAAAACTCTTTCTTGATTTTAGAAAAAG
164664 ATAGAATTCC
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
58 56 1.00
ACGTcount: A:0.33, C:0.11, G:0.17, T:0.39
Consensus pattern (58 bp):
CATAAAGACTGTGGTGTTTCTGATTTAATAAAACTCTTTCTTGATTTTAGAAAAAGGT
Found at i:164817 original size:21 final size:21
Alignment explanation
Indices: 164792--164833 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
164782 TGGTTAAAAT
*
164792 GAAAAATAAGAATTAAATAAA
1 GAAAAATAAGAATGAAATAAA
*
164813 GAAAAATAATAATGAAATAAA
1 GAAAAATAAGAATGAAATAAA
164834 CAAATTAAAG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.71, C:0.00, G:0.10, T:0.19
Consensus pattern (21 bp):
GAAAAATAAGAATGAAATAAA
Found at i:165517 original size:19 final size:19
Alignment explanation
Indices: 165461--165523 Score: 63
Period size: 19 Copynumber: 3.2 Consensus size: 19
165451 CTATTTAAAC
*
165461 TAAAATACCTAAAACATAAT
1 TAAAATA-CTAAAACCTAAT
* * *
165481 ATAATATTCTAAATCCTAAT
1 -TAAAATACTAAAACCTAAT
*
165501 TAAAATACTAAAACCTATT
1 TAAAATACTAAAACCTAAT
165520 TAAA
1 TAAA
165524 CTAAAATACA
Statistics
Matches: 34, Mismatches: 8, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
19 19 0.56
20 10 0.29
21 5 0.15
ACGTcount: A:0.54, C:0.14, G:0.00, T:0.32
Consensus pattern (19 bp):
TAAAATACTAAAACCTAAT
Found at i:165551 original size:64 final size:68
Alignment explanation
Indices: 165426--165623 Score: 201
Period size: 64 Copynumber: 2.8 Consensus size: 68
165416 TAAAACATCT
* * *
165426 TAAATCCTAATTAAAACACTTAAAA-CTATTTAAACTAAAATAC----CTAAAACAT-AATATAA
1 TAAATCCTAATTAAAATAC-TAAAACCTATTTAAACTAAAATACAAAGATAAAA-ATAAAAATAA
*
165485 TATTC
64 TATCC
165490 TAAATCCTAATTAAAATACTAAAACCTATTTAAACTAAAATACAAAGATAAAGATAAAATATAAA
1 TAAATCCTAATTAAAATACTAAAACCTATTTAAACTAAAATAC------AAAGATAAAA-ATAAA
165555 AATAATATCC
59 AATAATATCC
* *
165565 TAAAACATAATTAAAATACTAAAAACCTATTTAAACTAAAATACAAAGATAAAATATAA
1 TAAATCCTAATTAAAATACT-AAAACCTATTTAAACTAAAATACAAAGATAAAA-ATAA
165624 TGTTTAAAAT
Statistics
Matches: 114, Mismatches: 7, Indels: 20
0.81 0.05 0.14
Matches are distributed among these distances:
63 5 0.04
64 36 0.32
70 15 0.13
74 7 0.06
75 28 0.25
76 23 0.20
ACGTcount: A:0.58, C:0.13, G:0.02, T:0.28
Consensus pattern (68 bp):
TAAATCCTAATTAAAATACTAAAACCTATTTAAACTAAAATACAAAGATAAAAATAAAAATAATA
TCC
Found at i:165568 original size:75 final size:76
Alignment explanation
Indices: 165481--165645 Score: 244
Period size: 76 Copynumber: 2.2 Consensus size: 76
165471 AAAACATAAT
* *
165481 ATAATATTCTAAATCCTAATTAAAATACT-AAAACCTATTTAAACTAAAATACAAAGATAAAGAT
1 ATAATATCCTAAATCATAATTAAAATACTAAAAACCTATTTAAACTAAAATACAAAGATAAA-AT
165545 AAAAT-ATAAAA
65 AAAATGATAAAA
*
165556 ATAATATCCTAAAACATAATTAAAATACTAAAAACCTATTTAAACTAAAATACAAAGATAAAATA
1 ATAATATCCTAAATCATAATTAAAATACTAAAAACCTATTTAAACTAAAATACAAAGATAAAATA
* * *
165621 TAATGTTTAAA
66 AAATGATAAAA
*
165632 ATATTATCCTAAAT
1 ATAATATCCTAAAT
165646 TTGAGTTTAA
Statistics
Matches: 80, Mismatches: 8, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
75 32 0.40
76 48 0.60
ACGTcount: A:0.57, C:0.11, G:0.02, T:0.30
Consensus pattern (76 bp):
ATAATATCCTAAATCATAATTAAAATACTAAAAACCTATTTAAACTAAAATACAAAGATAAAATA
AAATGATAAAA
Found at i:167535 original size:20 final size:19
Alignment explanation
Indices: 167498--167543 Score: 65
Period size: 19 Copynumber: 2.4 Consensus size: 19
167488 AGTTCACTAA
*
167498 AAAAATTAAAAAATAAAAC
1 AAAAATAAAAAAATAAAAC
*
167517 GAAAATAAAAAAATAAAAAC
1 AAAAATAAAAAAAT-AAAAC
167537 AAAAATA
1 AAAAATA
167544 TAACGAAATG
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
19 12 0.52
20 11 0.48
ACGTcount: A:0.80, C:0.04, G:0.02, T:0.13
Consensus pattern (19 bp):
AAAAATAAAAAAATAAAAC
Found at i:177306 original size:3 final size:3
Alignment explanation
Indices: 177300--177352 Score: 79
Period size: 3 Copynumber: 17.0 Consensus size: 3
177290 TATTTATTAT
*
177300 TAA TAA TAA TAA TATA TAA TAA TAA TAA TAA TAA TAA TATT TAA TAA
1 TAA TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA TAA TA-A TAA TAA
177347 TAA TAA
1 TAA TAA
177353 AAATGAAAAT
Statistics
Matches: 46, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
3 41 0.89
4 5 0.11
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (3 bp):
TAA
Found at i:177334 original size:25 final size:25
Alignment explanation
Indices: 177300--177352 Score: 97
Period size: 25 Copynumber: 2.1 Consensus size: 25
177290 TATTTATTAT
177300 TAATAATAATAATATATAATAATAA
1 TAATAATAATAATATATAATAATAA
*
177325 TAATAATAATAATATTTAATAATAA
1 TAATAATAATAATATATAATAATAA
177350 TAA
1 TAA
177353 AAATGAAAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (25 bp):
TAATAATAATAATATATAATAATAA
Found at i:181004 original size:29 final size:31
Alignment explanation
Indices: 180936--181001 Score: 80
Period size: 33 Copynumber: 2.1 Consensus size: 31
180926 TGTTCAAAGT
* * *
180936 TTGGCAACCAACCAAGATGAAATTTCTAATAAG
1 TTGGCCACCAACCAAGATGAAATTTC--ACAAC
180969 TTGGCCACCAACCAAGATGAAATTTC-CAAC
1 TTGGCCACCAACCAAGATGAAATTTCACAAC
180999 TTG
1 TTG
181002 CCAACTTAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
30 5 0.17
33 25 0.83
ACGTcount: A:0.38, C:0.23, G:0.15, T:0.24
Consensus pattern (31 bp):
TTGGCCACCAACCAAGATGAAATTTCACAAC
Found at i:185600 original size:29 final size:31
Alignment explanation
Indices: 185532--185597 Score: 89
Period size: 33 Copynumber: 2.1 Consensus size: 31
185522 TGTTCAAAGT
* *
185532 TTGGCCACCAACCAAGATGAAATTTCTAATAAG
1 TTGGCCACCAACCAAGATGAAATTTC--ACAAC
185565 TTGGCCACCAACCAAGATGAAATTTC-CAAC
1 TTGGCCACCAACCAAGATGAAATTTCACAAC
185595 TTG
1 TTG
185598 CCAACTTAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
30 5 0.16
33 26 0.84
ACGTcount: A:0.36, C:0.24, G:0.15, T:0.24
Consensus pattern (31 bp):
TTGGCCACCAACCAAGATGAAATTTCACAAC
Found at i:185833 original size:81 final size:81
Alignment explanation
Indices: 185698--185858 Score: 322
Period size: 81 Copynumber: 2.0 Consensus size: 81
185688 AAACTTTTCT
185698 TCCTAATAGATTTAAAGGCAATCCCCCAAATCTACTCAATGATTTCAATCATCATACAAAAATGT
1 TCCTAATAGATTTAAAGGCAATCCCCCAAATCTACTCAATGATTTCAATCATCATACAAAAATGT
185763 AAAGAGAGGAACAAAA
66 AAAGAGAGGAACAAAA
185779 TCCTAATAGATTTAAAGGCAATCCCCCAAATCTACTCAATGATTTCAATCATCATACAAAAATGT
1 TCCTAATAGATTTAAAGGCAATCCCCCAAATCTACTCAATGATTTCAATCATCATACAAAAATGT
185844 AAAGAGAGGAACAAA
66 AAAGAGAGGAACAAA
185859 TAAAAGTGAG
Statistics
Matches: 80, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
81 80 1.00
ACGTcount: A:0.45, C:0.20, G:0.11, T:0.24
Consensus pattern (81 bp):
TCCTAATAGATTTAAAGGCAATCCCCCAAATCTACTCAATGATTTCAATCATCATACAAAAATGT
AAAGAGAGGAACAAAA
Found at i:186872 original size:15 final size:15
Alignment explanation
Indices: 186854--186882 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
186844 ATCTTTTAAT
186854 AATAGAAAATTTGGG
1 AATAGAAAATTTGGG
186869 AATAGAAAATTTGG
1 AATAGAAAATTTGG
186883 AGGCAGCCCC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.48, C:0.00, G:0.24, T:0.28
Consensus pattern (15 bp):
AATAGAAAATTTGGG
Found at i:188822 original size:13 final size:12
Alignment explanation
Indices: 188806--188848 Score: 50
Period size: 13 Copynumber: 3.3 Consensus size: 12
188796 TTTTTTTTTA
188806 TAATAATTTATAT
1 TAATAA-TTATAT
*
188819 TAATTATTATATT
1 TAATAATTATA-T
188832 TAATAATTATAAT
1 TAATAATTAT-AT
188845 TAAT
1 TAAT
188849 CATTTTAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
12 5 0.19
13 20 0.77
14 1 0.04
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (12 bp):
TAATAATTATAT
Found at i:188846 original size:26 final size:26
Alignment explanation
Indices: 188772--188848 Score: 72
Period size: 26 Copynumber: 3.0 Consensus size: 26
188762 AGGTTGAATT
* *
188772 TTATAATATTTTA-AATTATAA-TAA
1 TTATTATATTTAATAATTATAATTAA
* *
188796 TT-TTTTTTTATAATAATT-TATATTAA
1 TTATTATATT-TAATAATTATA-ATTAA
188822 TTATTATATTTAATAATTATAATTAA
1 TTATTATATTTAATAATTATAATTAA
188848 T
1 T
188849 CATTTTAAAA
Statistics
Matches: 41, Mismatches: 6, Indels: 10
0.72 0.11 0.18
Matches are distributed among these distances:
23 4 0.10
24 6 0.15
25 5 0.12
26 19 0.46
27 7 0.17
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (26 bp):
TTATTATATTTAATAATTATAATTAA
Found at i:192972 original size:14 final size:14
Alignment explanation
Indices: 192953--192980 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
192943 TAACACGTGG
192953 GTTTTAATGTATAT
1 GTTTTAATGTATAT
192967 GTTTTAATGTATAT
1 GTTTTAATGTATAT
192981 ATTAAGGATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.29, C:0.00, G:0.14, T:0.57
Consensus pattern (14 bp):
GTTTTAATGTATAT
Found at i:193082 original size:18 final size:19
Alignment explanation
Indices: 193040--193082 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 19
193030 GTATAAACTA
*
193040 TAATTT-GAATATAACTTT
1 TAATTTCGAATACAACTTT
*
193058 TACTTTCGAATACAA-TTT
1 TAATTTCGAATACAACTTT
193076 TAATTTC
1 TAATTTC
193083 AATTGGAATA
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
18 14 0.67
19 7 0.33
ACGTcount: A:0.35, C:0.12, G:0.05, T:0.49
Consensus pattern (19 bp):
TAATTTCGAATACAACTTT
Found at i:193147 original size:33 final size:34
Alignment explanation
Indices: 193103--193174 Score: 128
Period size: 33 Copynumber: 2.1 Consensus size: 34
193093 TTAAGTTGAA
193103 TTTAATGTTAAATTTCGAATACTATAATTTGTAT
1 TTTAATGTTAAATTTCGAATACTATAATTTGTAT
*
193137 TTTAA-GTTAAATTTTGAATACTATAATTTGTAT
1 TTTAATGTTAAATTTCGAATACTATAATTTGTAT
193170 TTTAA
1 TTTAA
193175 AAACATTAAC
Statistics
Matches: 37, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
33 32 0.86
34 5 0.14
ACGTcount: A:0.36, C:0.04, G:0.08, T:0.51
Consensus pattern (34 bp):
TTTAATGTTAAATTTCGAATACTATAATTTGTAT
Found at i:195517 original size:12 final size:12
Alignment explanation
Indices: 195488--195520 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
195478 TAATTAGCAC
195488 AAATAATAA-TT
1 AAATAATAATTT
*
195499 AAGTAATAATTT
1 AAATAATAATTT
195511 AAATAATAAT
1 AAATAATAAT
195521 AATTATAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
11 8 0.42
12 11 0.58
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.36
Consensus pattern (12 bp):
AAATAATAATTT
Found at i:195552 original size:33 final size:33
Alignment explanation
Indices: 195505--195568 Score: 94
Period size: 33 Copynumber: 1.9 Consensus size: 33
195495 AATTAAGTAA
*
195505 TAATTTAAATAATAATAATTATAA-ATATTATTT
1 TAATATAAATAATAATAA-TATAATATATTATTT
*
195538 TAATATAAATAATAATTATATAATATATTAT
1 TAATATAAATAATAATAATATAATATATTAT
195569 ACCAAATATA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
32 5 0.18
33 23 0.82
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (33 bp):
TAATATAAATAATAATAATATAATATATTATTT
Found at i:195910 original size:59 final size:56
Alignment explanation
Indices: 195781--195917 Score: 152
Period size: 59 Copynumber: 2.3 Consensus size: 56
195771 ATGGAAGGCG
* *
195781 CGTCCCCGGGATGCTCCTTACCTCCGTGGCATCCGACTCAGCAAAACCCCGTGAAA
1 CGTCCCCGGGATGCGCCTTACCTCCGTGGCATCCCACTCAGCAAAACCCCGTGAAA
* *
195837 GCGCGTCCCCGGGATGCGCCTTACC-CGCGTGGCATCCCAGTCAGCTAAAACCCAGGTAGAAA
1 ---CGTCCCCGGGATGCGCCTTACCTC-CGTGGCATCCCACTCAGC-AAAACCC-CGT-GAAA
195899 -GTCCCCAGGGATGCGCCTT
1 CGTCCCC-GGGATGCGCCTT
195918 TGTACCAAAT
Statistics
Matches: 69, Mismatches: 4, Indels: 10
0.83 0.05 0.12
Matches are distributed among these distances:
58 7 0.10
59 49 0.71
60 7 0.10
61 2 0.03
62 4 0.06
ACGTcount: A:0.20, C:0.37, G:0.26, T:0.17
Consensus pattern (56 bp):
CGTCCCCGGGATGCGCCTTACCTCCGTGGCATCCCACTCAGCAAAACCCCGTGAAA
Found at i:197436 original size:21 final size:21
Alignment explanation
Indices: 197410--197452 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
197400 TGATGTCTGG
197410 GGAATTGTTTGGACCTTGTAT
1 GGAATTGTTTGGACCTTGTAT
197431 GGAATTGTTTGGACCTTGTAT
1 GGAATTGTTTGGACCTTGTAT
197452 G
1 G
197453 ATCATGGAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.19, C:0.09, G:0.30, T:0.42
Consensus pattern (21 bp):
GGAATTGTTTGGACCTTGTAT
Found at i:200345 original size:3 final size:3
Alignment explanation
Indices: 200337--200393 Score: 84
Period size: 3 Copynumber: 19.7 Consensus size: 3
200327 AATTGTAAAT
200337 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA -AA T-A TAA T-A
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
200382 TAA TAA CTAA TA
1 TAA TAA -TAA TA
200394 TTTTAATAGA
Statistics
Matches: 50, Mismatches: 0, Indels: 8
0.86 0.00 0.14
Matches are distributed among these distances:
2 6 0.12
3 41 0.82
4 3 0.06
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:204264 original size:21 final size:21
Alignment explanation
Indices: 204062--204267 Score: 191
Period size: 21 Copynumber: 9.7 Consensus size: 21
204052 AGGGTTCTAC
*
204062 GTGGTCATTCGGGGCATATAT
1 GTGGTCATTCGGGACATATAT
* * * *
204083 GTGATCCTTTGGAACATATAT
1 GTGGTCATTCGGGACATATAT
* * *
204104 GAGGCCCTTCGGGACATATAT
1 GTGGTCATTCGGGACATATAT
* * * *
204125 TTGGTCCTTTGGAACATATAT
1 GTGGTCATTCGGGACATATAT
204146 GTGGTCA-TCGGGACA-ATAT
1 GTGGTCATTCGGGACATATAT
*
204165 GTGGTCATTTGGGACAATATAT
1 GTGGTCATTCGGGAC-ATATAT
* * *
204187 GTAGTCGTTCGGGACAATTCTAT
1 GTGGTCATTCGGGAC-A-TATAT
*
204210 GTGGTCATTCGGGACAATTTTAT
1 GTGGTCATTCGGGAC-A-TATAT
*
204233 GTGGTCCTTCGGGACATATAT
1 GTGGTCATTCGGGACATATAT
204254 GTGGTCATTCGGGA
1 GTGGTCATTCGGGA
204268 TACGAGGTCC
Statistics
Matches: 151, Mismatches: 30, Indels: 8
0.80 0.16 0.04
Matches are distributed among these distances:
19 11 0.07
20 12 0.08
21 71 0.47
22 19 0.13
23 38 0.25
ACGTcount: A:0.23, C:0.16, G:0.28, T:0.34
Consensus pattern (21 bp):
GTGGTCATTCGGGACATATAT
Found at i:204712 original size:15 final size:16
Alignment explanation
Indices: 204694--204724 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
204684 AAACCGTATA
204694 TATTTTGTT-ACATAT
1 TATTTTGTTGACATAT
204709 TATTTTGTTGACATAT
1 TATTTTGTTGACATAT
204725 AAAGGAACGT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 9 0.60
16 6 0.40
ACGTcount: A:0.26, C:0.06, G:0.10, T:0.58
Consensus pattern (16 bp):
TATTTTGTTGACATAT
Found at i:206106 original size:18 final size:18
Alignment explanation
Indices: 206083--206117 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
206073 AGGGAATATC
206083 AGTGGTCCTTCGGGACAT
1 AGTGGTCCTTCGGGACAT
*
206101 AGTGGTCTTTCGGGACA
1 AGTGGTCCTTCGGGACA
206118 AATATTCAGT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.17, C:0.20, G:0.34, T:0.29
Consensus pattern (18 bp):
AGTGGTCCTTCGGGACAT
Found at i:216979 original size:71 final size:72
Alignment explanation
Indices: 216862--216994 Score: 232
Period size: 71 Copynumber: 1.9 Consensus size: 72
216852 AAAAATTTAA
*
216862 AATTACAGAATAGGAAAAAAAGAGGGGGGTTAGATCTGAAAAATACCTTTAATGGTTTGATACTG
1 AATTACAGAATAGGAAAAAAAGAGGGGGCTTAGATCTGAAAAATACCTTTAATGGTTTGATACTG
216927 GAATCGT
66 GAATCGT
* *
216934 AATTACAGAATAGG-AAAAAAGAGTGGGCTTAGATCTGAAAAATACCTTTACTGGTTTGATA
1 AATTACAGAATAGGAAAAAAAGAGGGGGCTTAGATCTGAAAAATACCTTTAATGGTTTGATA
216995 ATGCACTCGT
Statistics
Matches: 58, Mismatches: 3, Indels: 1
0.94 0.05 0.02
Matches are distributed among these distances:
71 44 0.76
72 14 0.24
ACGTcount: A:0.41, C:0.09, G:0.23, T:0.27
Consensus pattern (72 bp):
AATTACAGAATAGGAAAAAAAGAGGGGGCTTAGATCTGAAAAATACCTTTAATGGTTTGATACTG
GAATCGT
Found at i:217543 original size:20 final size:20
Alignment explanation
Indices: 217506--217545 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
217496 ATATTAAATT
* * *
217506 TTCATTTTATTGATTTATAA
1 TTCATTTTAATAAATTATAA
217526 TTCATTTTAATAAATTATAA
1 TTCATTTTAATAAATTATAA
217546 AAATCATGCT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.38, C:0.05, G:0.03, T:0.55
Consensus pattern (20 bp):
TTCATTTTAATAAATTATAA
Found at i:217915 original size:32 final size:33
Alignment explanation
Indices: 217863--217981 Score: 134
Period size: 32 Copynumber: 3.5 Consensus size: 33
217853 CCTAAACCTG
*
217863 AACCCGACTCGACCCAAATATCACACTTAAAAA
1 AACCCGACTCGACCCGAATATCACACTTAAAAA
* *
217896 AACCCGAC-CGACCTGAATATCACACTGAAAAAAA
1 AACCCGACTCGACCCGAATATCACACT--TAAAAA
*
217930 CCCAACCCGACTTGACCCGAATATCACACTT-AAAA
1 ---AACCCGACTCGACCCGAATATCACACTTAAAAA
*
217965 AACCCGACCCGACCCGA
1 AACCCGACTCGACCCGA
217982 CCCGAACAAA
Statistics
Matches: 72, Mismatches: 8, Indels: 13
0.77 0.09 0.14
Matches are distributed among these distances:
32 31 0.43
33 8 0.11
34 5 0.07
35 4 0.06
37 8 0.11
38 16 0.22
ACGTcount: A:0.41, C:0.36, G:0.10, T:0.13
Consensus pattern (33 bp):
AACCCGACTCGACCCGAATATCACACTTAAAAA
Found at i:217937 original size:37 final size:36
Alignment explanation
Indices: 217863--217987 Score: 132
Period size: 37 Copynumber: 3.5 Consensus size: 36
217853 CCTAAACCTG
* *
217863 AACCCGACTCGACCCAAATATCACACT-TAAAAA---
1 AACCCGAC-CGACCCGAATATCACACTAAAAAAACCC
*
217896 AACCCGACCGACCTGAATATCACACTGAAAAAAACCC
1 AACCCGACCGACCCGAATATCACACT-AAAAAAACCC
* *
217933 AACCCGACTTGACCCGAATATCACACTTAAAAAACCC
1 AACCCGAC-CGACCCGAATATCACACTAAAAAAACCC
*
217970 GACCCGACCCGACCCGAA
1 AACCCGA-CCGACCCGAA
217988 CAAAATAAAG
Statistics
Matches: 77, Mismatches: 8, Indels: 10
0.81 0.08 0.11
Matches are distributed among these distances:
32 16 0.21
33 8 0.10
34 5 0.06
37 31 0.40
38 17 0.22
ACGTcount: A:0.41, C:0.37, G:0.10, T:0.12
Consensus pattern (36 bp):
AACCCGACCGACCCGAATATCACACTAAAAAAACCC
Found at i:218588 original size:16 final size:16
Alignment explanation
Indices: 218567--218624 Score: 53
Period size: 16 Copynumber: 3.6 Consensus size: 16
218557 ATATAATAAA
*
218567 TAAAAATAAATTTTCC
1 TAAAAATAAATTTCCC
* *
218583 TAAAAATTAGTTTCCC
1 TAAAAATAAATTTCCC
* * *
218599 TAAAACTCAATTTCCT
1 TAAAAATAAATTTCCC
*
218615 TTAAAATAAA
1 TAAAAATAAA
218625 ATAGAATGAA
Statistics
Matches: 32, Mismatches: 10, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
16 32 1.00
ACGTcount: A:0.47, C:0.16, G:0.02, T:0.36
Consensus pattern (16 bp):
TAAAAATAAATTTCCC
Found at i:218850 original size:3 final size:3
Alignment explanation
Indices: 218844--218882 Score: 55
Period size: 3 Copynumber: 13.7 Consensus size: 3
218834 TTCTTGAGAA
*
218844 AAT AAT AAA AAT AAT -AT AAT AAT -AT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
218883 GTAAGCATAG
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
2 4 0.12
3 28 0.88
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:218864 original size:14 final size:17
Alignment explanation
Indices: 218844--218882 Score: 57
Period size: 14 Copynumber: 2.5 Consensus size: 17
218834 TTCTTGAGAA
218844 AATAATAA-A-AATAAT
1 AATAATAATATAATAAT
218859 -ATAATAATATAATAAT
1 AATAATAATATAATAAT
218875 AATAATAA
1 AATAATAA
218883 GTAAGCATAG
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
14 7 0.33
15 1 0.05
16 6 0.29
17 7 0.33
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (17 bp):
AATAATAATATAATAAT
Found at i:219281 original size:12 final size:12
Alignment explanation
Indices: 219264--219327 Score: 50
Period size: 12 Copynumber: 5.7 Consensus size: 12
219254 TGAATAGTGA
219264 TGAACAGTACCG
1 TGAACAGTACCG
*
219276 TGAACA--A-TG
1 TGAACAGTACCG
219285 ATGAACAGTACCG
1 -TGAACAGTACCG
*
219298 TGAACA--A-TG
1 TGAACAGTACCG
219307 ATGAACAGTACCG
1 -TGAACAGTACCG
219320 TGAACAGT
1 TGAACAGT
219328 GAACAGTGCA
Statistics
Matches: 40, Mismatches: 4, Indels: 16
0.67 0.07 0.27
Matches are distributed among these distances:
9 2 0.05
10 14 0.35
12 22 0.55
13 2 0.05
ACGTcount: A:0.39, C:0.19, G:0.23, T:0.19
Consensus pattern (12 bp):
TGAACAGTACCG
Found at i:219286 original size:22 final size:22
Alignment explanation
Indices: 219261--219325 Score: 130
Period size: 22 Copynumber: 3.0 Consensus size: 22
219251 TTATGAATAG
219261 TGATGAACAGTACCGTGAACAA
1 TGATGAACAGTACCGTGAACAA
219283 TGATGAACAGTACCGTGAACAA
1 TGATGAACAGTACCGTGAACAA
219305 TGATGAACAGTACCGTGAACA
1 TGATGAACAGTACCGTGAACA
219326 GTGAACAGTG
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 43 1.00
ACGTcount: A:0.40, C:0.18, G:0.23, T:0.18
Consensus pattern (22 bp):
TGATGAACAGTACCGTGAACAA
Found at i:219993 original size:33 final size:33
Alignment explanation
Indices: 219956--220022 Score: 134
Period size: 33 Copynumber: 2.0 Consensus size: 33
219946 ACCGTAGTGC
219956 TAATCCGTATGACACATAAGGTCGTGTCCACCA
1 TAATCCGTATGACACATAAGGTCGTGTCCACCA
219989 TAATCCGTATGACACATAAGGTCGTGTCCACCA
1 TAATCCGTATGACACATAAGGTCGTGTCCACCA
220022 T
1 T
220023 CTGTACTAGG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.30, C:0.27, G:0.18, T:0.25
Consensus pattern (33 bp):
TAATCCGTATGACACATAAGGTCGTGTCCACCA
Found at i:222419 original size:20 final size:20
Alignment explanation
Indices: 222386--222440 Score: 69
Period size: 20 Copynumber: 2.9 Consensus size: 20
222376 CAAAACAATG
222386 AAGT-AGTA-CGATACTGCT
1 AAGTCAGTACCGATACTGCT
222404 AAGTCAGTACCGATACTGCT
1 AAGTCAGTACCGATACTGCT
** *
222424 ACTTCAGTACCGGTACT
1 AAGTCAGTACCGATACT
222441 ATCAAAACAA
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
18 4 0.12
19 4 0.12
20 24 0.75
ACGTcount: A:0.29, C:0.24, G:0.20, T:0.27
Consensus pattern (20 bp):
AAGTCAGTACCGATACTGCT
Found at i:222538 original size:74 final size:75
Alignment explanation
Indices: 222437--222589 Score: 218
Period size: 75 Copynumber: 2.1 Consensus size: 75
222427 TCAGTACCGG
* * *
222437 TACTATCAAAACAAAATGTTAAAATGGTA-CTATACTATTTACGGTATCGATACTACTTAGTATA
1 TACTATCAAAACAAAATGCTAAAATGGTATCAATACTATATACGGTATCGATACTACTTAGTATA
222501 GTAATATCGA
66 GTAATATCGA
* * * * *
222511 TACTGTCAAAGCATAATGCTAAAATGGTATCAATACTATATACGGTATTGATACTACTTAGTGTA
1 TACTATCAAAACAAAATGCTAAAATGGTATCAATACTATATACGGTATCGATACTACTTAGTATA
*
222576 GTAGTATCGA
66 GTAATATCGA
222586 TACT
1 TACT
222590 CTTTGTGGTG
Statistics
Matches: 69, Mismatches: 9, Indels: 1
0.87 0.11 0.01
Matches are distributed among these distances:
74 25 0.36
75 44 0.64
ACGTcount: A:0.38, C:0.14, G:0.14, T:0.34
Consensus pattern (75 bp):
TACTATCAAAACAAAATGCTAAAATGGTATCAATACTATATACGGTATCGATACTACTTAGTATA
GTAATATCGA
Found at i:223200 original size:18 final size:17
Alignment explanation
Indices: 223163--223202 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
223153 TTAAACAATT
*
223163 AATTTTAAAAGTAAATA
1 AATTTTAAAAATAAATA
*
223180 AATTTTAAAAATATATGA
1 AATTTTAAAAATAAAT-A
223198 AATTT
1 AATTT
223203 ATAATTTTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 14 0.70
18 6 0.30
ACGTcount: A:0.55, C:0.00, G:0.05, T:0.40
Consensus pattern (17 bp):
AATTTTAAAAATAAATA
Found at i:224442 original size:29 final size:29
Alignment explanation
Indices: 224400--224458 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
224390 TAGTCTCTGG
224400 AGCATGTTTTCGATGTGGGGACACATGAC
1 AGCATGTTTTCGATGTGGGGACACATGAC
224429 AGCATGTTTTCGATGTGGGGACACATGAC
1 AGCATGTTTTCGATGTGGGGACACATGAC
224458 A
1 A
224459 TTTTATCCGT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.25, C:0.17, G:0.31, T:0.27
Consensus pattern (29 bp):
AGCATGTTTTCGATGTGGGGACACATGAC
Found at i:228768 original size:32 final size:32
Alignment explanation
Indices: 228673--228773 Score: 120
Period size: 31 Copynumber: 3.2 Consensus size: 32
228663 CCAAATAACC
*
228673 TAGGTAA-ACTGTCCATATGTTCCTTAGAACA
1 TAGGTAATACTGTCCATATGTTCCGTAGAACA
*
228704 TAGGT-ATACTGTCCATATG-TCTCG-AAAGACA
1 TAGGTAATACTGTCCATATGTTC-CGTAGA-ACA
**
228735 TAGGTAATTTTGTCCATATGTTCCGTAGAACA
1 TAGGTAATACTGTCCATATGTTCCGTAGAACA
228767 TAGGTAA
1 TAGGTAA
228774 ACCCTCGACT
Statistics
Matches: 59, Mismatches: 5, Indels: 11
0.79 0.07 0.15
Matches are distributed among these distances:
30 5 0.08
31 26 0.44
32 24 0.41
33 4 0.07
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.33
Consensus pattern (32 bp):
TAGGTAATACTGTCCATATGTTCCGTAGAACA
Found at i:231840 original size:17 final size:18
Alignment explanation
Indices: 231818--231856 Score: 55
Period size: 17 Copynumber: 2.3 Consensus size: 18
231808 CCATGTACAC
231818 ATGTGAGAAC-TTAAGGT
1 ATGTGAGAACATTAAGGT
*
231835 ATGTGAGTACATTAAGGT
1 ATGTGAGAACATTAAGGT
231853 -TGTG
1 ATGTG
231857 CACCACTATG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 13 0.65
18 7 0.35
ACGTcount: A:0.31, C:0.05, G:0.31, T:0.33
Consensus pattern (18 bp):
ATGTGAGAACATTAAGGT
Found at i:232054 original size:32 final size:33
Alignment explanation
Indices: 231978--232054 Score: 79
Period size: 32 Copynumber: 2.4 Consensus size: 33
231968 ATATGTTTGT
*
231978 TAGAACATAGGT-ATACTATCCATATGTCCCGA
1 TAGAACATAGGTAATACTATCCATATATCCCGA
* * * * *
232010 AAG-ACATTGGTAATTCTGTCCATATATTCC-A
1 TAGAACATAGGTAATACTATCCATATATCCCGA
232041 TAGAACATAGGTAA
1 TAGAACATAGGTAA
232055 ACCCTCGACT
Statistics
Matches: 35, Mismatches: 8, Indels: 4
0.74 0.17 0.09
Matches are distributed among these distances:
31 10 0.29
32 25 0.71
ACGTcount: A:0.36, C:0.18, G:0.16, T:0.30
Consensus pattern (33 bp):
TAGAACATAGGTAATACTATCCATATATCCCGA
Found at i:237979 original size:45 final size:45
Alignment explanation
Indices: 237924--238025 Score: 195
Period size: 45 Copynumber: 2.3 Consensus size: 45
237914 CAAAATAAAA
*
237924 ACATATAAAATTCTTTAATAAGATAATTATTTCACATACATTTTT
1 ACATAAAAAATTCTTTAATAAGATAATTATTTCACATACATTTTT
237969 ACATAAAAAATTCTTTAATAAGATAATTATTTCACATACATTTTT
1 ACATAAAAAATTCTTTAATAAGATAATTATTTCACATACATTTTT
238014 ACATAAAAAATT
1 ACATAAAAAATT
238026 AATAATTTAA
Statistics
Matches: 56, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
45 56 1.00
ACGTcount: A:0.46, C:0.11, G:0.02, T:0.41
Consensus pattern (45 bp):
ACATAAAAAATTCTTTAATAAGATAATTATTTCACATACATTTTT
Found at i:243228 original size:14 final size:14
Alignment explanation
Indices: 243205--243250 Score: 65
Period size: 14 Copynumber: 3.3 Consensus size: 14
243195 TATTTTTTAA
* *
243205 TGGACCCCGATACG
1 TGGACTCCGATAAG
243219 TGGACTCCGATAAG
1 TGGACTCCGATAAG
*
243233 TGAACTCCGATAAG
1 TGGACTCCGATAAG
243247 TGGA
1 TGGA
243251 TCCCATGTAA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 28 1.00
ACGTcount: A:0.28, C:0.24, G:0.28, T:0.20
Consensus pattern (14 bp):
TGGACTCCGATAAG
Found at i:245078 original size:23 final size:25
Alignment explanation
Indices: 245052--245097 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
245042 AATATAATTG
245052 AATTT-AAAATT-CAATTAATGAGA
1 AATTTCAAAATTACAATTAATGAGA
*
245075 AATTTCAAAATTACCATTAATGA
1 AATTTCAAAATTACAATTAATGA
245098 ATCATGATAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 5 0.25
24 6 0.30
25 9 0.45
ACGTcount: A:0.50, C:0.09, G:0.07, T:0.35
Consensus pattern (25 bp):
AATTTCAAAATTACAATTAATGAGA
Found at i:251901 original size:21 final size:22
Alignment explanation
Indices: 251859--251902 Score: 54
Period size: 21 Copynumber: 2.0 Consensus size: 22
251849 GGATGAATAT
**
251859 TCTAGATTATTTTGGGGATGAA
1 TCTAGATTATTTTGAAGATGAA
*
251881 TCTAGA-TATTTTGAAGCTGAA
1 TCTAGATTATTTTGAAGATGAA
251902 T
1 T
251903 ATGGCCTTAT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
21 13 0.68
22 6 0.32
ACGTcount: A:0.30, C:0.07, G:0.23, T:0.41
Consensus pattern (22 bp):
TCTAGATTATTTTGAAGATGAA
Found at i:252661 original size:17 final size:17
Alignment explanation
Indices: 252636--252680 Score: 63
Period size: 17 Copynumber: 2.6 Consensus size: 17
252626 ATGAAAACAT
*
252636 TTAAAGAACTAGTTTAA
1 TTAATGAACTAGTTTAA
*
252653 TTAATGAACCAGTTTAA
1 TTAATGAACTAGTTTAA
*
252670 TTAGTGAACTA
1 TTAATGAACTA
252681 TCTTTATTGA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.42, C:0.09, G:0.13, T:0.36
Consensus pattern (17 bp):
TTAATGAACTAGTTTAA
Found at i:252833 original size:20 final size:20
Alignment explanation
Indices: 252795--252833 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
252785 CAACTTAATG
* *
252795 TCATGCAAATTTATTAACAC
1 TCATGCAAATTCATGAACAC
*
252815 TCATGGAAATTCATGAACA
1 TCATGCAAATTCATGAACA
252834 AGTAAAAGAT
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:0.41, C:0.18, G:0.10, T:0.31
Consensus pattern (20 bp):
TCATGCAAATTCATGAACAC
Found at i:257643 original size:243 final size:242
Alignment explanation
Indices: 257171--257657 Score: 949
Period size: 243 Copynumber: 2.0 Consensus size: 242
257161 ATTCCTTTCG
257171 GAACAAATCAGATCAAATAATAAATCATGCAACGAGAAATCAACCATGGGAACCAGATCCACCCT
1 GAACAAATCAGATCAAATAATAAATCATGCAACGAGAAATCAACCATGGGAACCAGATCCACCCT
257236 CTTTTCTGAGACACCAAACCCAAAAACAAAAGGAAGGGAAGATTTACAGGAAGAAAAACCTGGGG
66 CTTTTCTGAGACACCAAACCCAAAAACAAAAGGAAGGGAAGATTTACAGGAAGAAAAACCTGGGG
257301 GGAATTGGAGCTCTGGGCCCAAACGCTGCCGTCTTGGCCGATGATTGCAGCGGAAGTTAGATGGT
131 GGAATTGGAGCTCTGGGCCCAAACGCTGCCGTCTTGGCCGATGATTGCAGCGGAAGTTAGATGGT
257366 TGCCTTCAATATCACACAACAAGTGATCGTCGACAT-AGCTTGCCAC
196 TGCCTTCAATATCACACAACAAGTGATCGTCGACATAAGCTTGCCAC
257412 GAACAAATCAGATCAAATAATAAATCATGCAACGAGAAATCAACCATGGGAACCAGATCCACCCT
1 GAACAAATCAGATCAAATAATAAATCATGCAACGAGAAATCAACCATGGGAACCAGATCCACCCT
257477 CTTTTCTGAGACACCAAACCCAAAAACAAAAGGAAGGGAAGATTTACAGGAGAAGAAAAACCTGG
66 CTTTTCTGAGACACCAAACCCAAAAACAAAAGGAAGGGAAGATTTACA-G-GAAGAAAAACCTGG
257542 GGGGAATTGGAGCTCTGGGCCCAAACGCTGCCGTCTTGGCCGATGATTGCAGCGGAAGTTAGATG
129 GGGGAATTGGAGCTCTGGGCCCAAACGCTGCCGTCTTGGCCGATGATTGCAGCGGAAGTTAGATG
257607 GTTGCCTTCAATATCACACAACAAGTGATCGTCGACATAAGCTTGCCAC
194 GTTGCCTTCAATATCACACAACAAGTGATCGTCGACATAAGCTTGCCAC
257656 GA
1 GA
257658 CATCTTCTTC
Statistics
Matches: 243, Mismatches: 0, Indels: 3
0.99 0.00 0.01
Matches are distributed among these distances:
241 113 0.47
242 1 0.00
243 117 0.48
244 12 0.05
ACGTcount: A:0.36, C:0.23, G:0.23, T:0.18
Consensus pattern (242 bp):
GAACAAATCAGATCAAATAATAAATCATGCAACGAGAAATCAACCATGGGAACCAGATCCACCCT
CTTTTCTGAGACACCAAACCCAAAAACAAAAGGAAGGGAAGATTTACAGGAAGAAAAACCTGGGG
GGAATTGGAGCTCTGGGCCCAAACGCTGCCGTCTTGGCCGATGATTGCAGCGGAAGTTAGATGGT
TGCCTTCAATATCACACAACAAGTGATCGTCGACATAAGCTTGCCAC
Found at i:260562 original size:24 final size:24
Alignment explanation
Indices: 260535--260600 Score: 89
Period size: 24 Copynumber: 2.8 Consensus size: 24
260525 CATAATTCAA
260535 GTCAAGTATCATATCAGAATCCAG
1 GTCAAGTATCATATCAGAATCCAG
* * *
260559 GTCATGTATCATATCATAATCCAT
1 GTCAAGTATCATATCAGAATCCAG
*
260583 GTCAA-TATCAGATCAGAA
1 GTCAAGTATCATATCAGAA
260601 ATCAGATAAA
Statistics
Matches: 36, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
23 11 0.31
24 25 0.69
ACGTcount: A:0.38, C:0.20, G:0.14, T:0.29
Consensus pattern (24 bp):
GTCAAGTATCATATCAGAATCCAG
Found at i:265946 original size:20 final size:20
Alignment explanation
Indices: 265921--265970 Score: 75
Period size: 19 Copynumber: 2.5 Consensus size: 20
265911 TGAAAAGTTT
* *
265921 TAATAAAATAAAATAGATAA
1 TAATAAAATAAAAAAGAAAA
265941 TAAT-AAATAAAAAAGAAAA
1 TAATAAAATAAAAAAGAAAA
265960 TAATAAAATAA
1 TAATAAAATAA
265971 TAAATATTAA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
19 17 0.63
20 10 0.37
ACGTcount: A:0.74, C:0.00, G:0.04, T:0.22
Consensus pattern (20 bp):
TAATAAAATAAAAAAGAAAA
Found at i:266040 original size:28 final size:27
Alignment explanation
Indices: 266008--266060 Score: 70
Period size: 28 Copynumber: 1.9 Consensus size: 27
265998 AATGAGTTTT
*
266008 AAATTATTTAAAAAAATATAATAAAATA
1 AAATTAATTAAAAAAATA-AATAAAATA
**
266036 AAATTAATTAATTAAATAAATAAAA
1 AAATTAATTAAAAAAATAAATAAAA
266061 ATAACTGATT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
27 7 0.32
28 15 0.68
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (27 bp):
AAATTAATTAAAAAAATAAATAAAATA
Found at i:266822 original size:72 final size:73
Alignment explanation
Indices: 266711--266875 Score: 215
Period size: 72 Copynumber: 2.2 Consensus size: 73
266701 TAAAATACCT
* * * *
266711 AAAAATAATAATATTTAAAATAATATTCTAAATCATAATTAAAATACTAAAACCTATTTAAAC-A
1 AAAAATAA-AATA-TAAAAATAATATCCTAAAACATAATTAAAATACTAAAACCTATTCAAACAA
266775 TACATAAAAC
64 TACATAAAAC
* *
266785 AAAGATAAAATATAAAAATAATATCCTAAAACTTAATTAAAATACTAAAACCTATTCAAACTAAA
1 AAAAATAAAATATAAAAATAATATCCTAAAACATAATTAAAATACTAAAACCTATTCAAAC---A
*
266850 ATACCTAAAAC
63 ATACATAAAAC
266861 AAAAATAAAATATAA
1 AAAAATAAAATATAA
266876 TGTTTAAAAT
Statistics
Matches: 79, Mismatches: 8, Indels: 6
0.85 0.09 0.06
Matches are distributed among these distances:
72 44 0.56
73 4 0.05
74 7 0.09
76 24 0.30
ACGTcount: A:0.61, C:0.12, G:0.01, T:0.27
Consensus pattern (73 bp):
AAAAATAAAATATAAAAATAATATCCTAAAACATAATTAAAATACTAAAACCTATTCAAACAATA
CATAAAAC
Found at i:267652 original size:19 final size:20
Alignment explanation
Indices: 267614--267653 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
267604 AAGAAAAAAG
*
267614 AATACCTAAAACTTAATTAA
1 AATACCTAAAACATAATTAA
*
267634 AATA-CTAAAACATATTTAA
1 AATACCTAAAACATAATTAA
267653 A
1 A
267654 CTAAAATACC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 14 0.78
20 4 0.22
ACGTcount: A:0.57, C:0.12, G:0.00, T:0.30
Consensus pattern (20 bp):
AATACCTAAAACATAATTAA
Found at i:267678 original size:25 final size:24
Alignment explanation
Indices: 267631--267678 Score: 60
Period size: 25 Copynumber: 2.0 Consensus size: 24
267621 AAAACTTAAT
* **
267631 TAAAATACTAAAACATATTTAAAC
1 TAAAATACTAAAACAAAGATAAAC
267655 TAAAATACCTAAAACAAAGATAAA
1 TAAAATA-CTAAAACAAAGATAAA
267679 ATATAATATT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
24 7 0.35
25 13 0.65
ACGTcount: A:0.62, C:0.12, G:0.02, T:0.23
Consensus pattern (24 bp):
TAAAATACTAAAACAAAGATAAAC
Found at i:269455 original size:26 final size:25
Alignment explanation
Indices: 269399--269464 Score: 78
Period size: 25 Copynumber: 2.6 Consensus size: 25
269389 TGTTTAGAGA
* *
269399 AAAATAAAATAAAATTACTTAAAAT
1 AAAATGAAATAAAATTACTAAAAAT
* *
269424 AGAATGAAATAAAGTTCACTAAAAAT
1 AAAATGAAATAAAATT-ACTAAAAAT
269450 AAAATGAAAATAAAA
1 AAAATG-AAATAAAA
269465 CTAAAATATA
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
25 13 0.39
26 13 0.39
27 7 0.21
ACGTcount: A:0.67, C:0.05, G:0.06, T:0.23
Consensus pattern (25 bp):
AAAATGAAATAAAATTACTAAAAAT
Found at i:272389 original size:19 final size:19
Alignment explanation
Indices: 272360--272405 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
272350 TGAAAAGTTT
* *
272360 TAATAAAATAAAATAGATAA
1 TAAT-AAATAAAAGAGAAAA
*
272380 TAATAAATAAAAGCGAAAA
1 TAATAAATAAAAGAGAAAA
272399 TAATAAA
1 TAATAAA
272406 AACGGCGCCA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
19 19 0.83
20 4 0.17
ACGTcount: A:0.70, C:0.02, G:0.07, T:0.22
Consensus pattern (19 bp):
TAATAAATAAAAGAGAAAA
Found at i:272588 original size:230 final size:230
Alignment explanation
Indices: 272180--272636 Score: 799
Period size: 230 Copynumber: 2.0 Consensus size: 230
272170 CCCCGACAAC
* * * *
272180 GCGCCAATATGATGACCGTCGTTTTGCTATTAAAATAATTACGACTTCTATAATGAATATAAAGG
1 GCGCCAATATGATAACCGTCGTTTTGCTATCAAAATAATTACGACTTATATAATGAATAGAAAGG
*
272245 GAAAGGTAGTATAGAGAAGCAGAGTCGATCCACAGGGACTATGGTTTTTGTGATTTAGTAAAATT
66 GAAAGGTAGTATAGAGAAGCAGAGTCGATCCACAGAGACTATGGTTTTTGTGATTTAGTAAAATT
*
272310 GTTTCTTGATTTTAGGAAAAGATAGAATTCCAGGTAAAGTTGAAAAGTTTTAATAAAATAAAATA
131 GTTTCTTGATTTTAGGAAAAGATAGAATTCCAGGTAAAGTTAAAAAGTTTTAATAAAATAAAATA
*
272375 GATAATAATAAATAAAAGCGAAAATAATAAAAACG
196 GATAATAATAAATAAAAGAGAAAATAATAAAAACG
* * *
272410 GCGCCAATATTATAATCGTCGTTTTGCTATCAAAATAATTATGACTTATATAATGAATAGAAAGG
1 GCGCCAATATGATAACCGTCGTTTTGCTATCAAAATAATTACGACTTATATAATGAATAGAAAGG
*
272475 GAATGGTAGTATAGAGAAGCATG-GTCGATCCACAGAGACTATGGTTTTTGTGATTTAGTAAAAT
66 GAAAGGTAGTATAGAGAAGCA-GAGTCGATCCACAGAGACTATGGTTTTTGTGATTTAGTAAAAT
272539 TGTTTCTTGATTTTAGGAAAAGATAGAATTCCAGGTAAAGTTAAAAAGTTTTAATAAAATAAAAT
130 TGTTTCTTGATTTTAGGAAAAGATAGAATTCCAGGTAAAGTTAAAAAGTTTTAATAAAATAAAAT
272604 AGATAATAATAAATAAAAGAGAAAATAATAAAA
195 AGATAATAATAAATAAAAGAGAAAATAATAAAA
272637 TAATAAATAT
Statistics
Matches: 215, Mismatches: 11, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
230 214 1.00
231 1 0.00
ACGTcount: A:0.43, C:0.08, G:0.18, T:0.30
Consensus pattern (230 bp):
GCGCCAATATGATAACCGTCGTTTTGCTATCAAAATAATTACGACTTATATAATGAATAGAAAGG
GAAAGGTAGTATAGAGAAGCAGAGTCGATCCACAGAGACTATGGTTTTTGTGATTTAGTAAAATT
GTTTCTTGATTTTAGGAAAAGATAGAATTCCAGGTAAAGTTAAAAAGTTTTAATAAAATAAAATA
GATAATAATAAATAAAAGAGAAAATAATAAAAACG
Found at i:272615 original size:20 final size:20
Alignment explanation
Indices: 272590--272639 Score: 75
Period size: 19 Copynumber: 2.5 Consensus size: 20
272580 TAAAAAGTTT
* *
272590 TAATAAAATAAAATAGATAA
1 TAATAAAATAAAAGAGAAAA
272610 TAAT-AAATAAAAGAGAAAA
1 TAATAAAATAAAAGAGAAAA
272629 TAATAAAATAA
1 TAATAAAATAA
272640 TAAATATTAA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
19 17 0.63
20 10 0.37
ACGTcount: A:0.72, C:0.00, G:0.06, T:0.22
Consensus pattern (20 bp):
TAATAAAATAAAAGAGAAAA
Found at i:272705 original size:27 final size:25
Alignment explanation
Indices: 272675--272731 Score: 60
Period size: 29 Copynumber: 2.1 Consensus size: 25
272665 AAAGGGGTTT
**
272675 TAAATTATTTAAAAAAGTATAATAAAA
1 TAAATTAAATAAAAAA-TA-AATAAAA
272702 TAAAAATTAAATAAAAAATAAATAAAA
1 T--AAATTAAATAAAAAATAAATAAAA
272729 TAA
1 TAA
272732 TTGAATTGGG
Statistics
Matches: 26, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
25 2 0.08
27 9 0.35
28 2 0.08
29 13 0.50
ACGTcount: A:0.70, C:0.00, G:0.02, T:0.28
Consensus pattern (25 bp):
TAAATTAAATAAAAAATAAATAAAA
Found at i:272713 original size:11 final size:11
Alignment explanation
Indices: 272699--272728 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
272689 AAGTATAATA
*
272699 AAATAAAAATT
1 AAATAAAAAAT
272710 AAATAAAAAAT
1 AAATAAAAAAT
272721 AAATAAAA
1 AAATAAAA
272729 TAATTGAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (11 bp):
AAATAAAAAAT
Found at i:273497 original size:76 final size:76
Alignment explanation
Indices: 273334--273547 Score: 292
Period size: 76 Copynumber: 2.9 Consensus size: 76
273324 TAAAACATCT
* * * * * * *
273334 TAAATCCTAATTAAAAAACTTAAAA-TTATTTAAACTAAAATACCTAAAA-ATA-ACAATAT-TT
1 TAAAACCTAATTAAAATAC-TAAAACCTATTTAAACTAAAATACCTAAAACAAAGATAAAATATA
273395 AAAATAATATAC
65 AAAATAATATAC
* *
273407 TAAATCCTAATTAAAATAGTAAAACCTATTTAAACTAAAATACCTAAAACAAAGATAAAATATAA
1 TAAAACCTAATTAAAATACTAAAACCTATTTAAACTAAAATACCTAAAACAAAGATAAAATATAA
*
273472 AAATAATATCC
66 AAATAATATAC
*
273483 TAAAACTTAATTAAAATACTAAAACCTATTTAAACTAAAATACCTAAAACAAAGATAAAATATAA
1 TAAAACCTAATTAAAATACTAAAACCTATTTAAACTAAAATACCTAAAACAAAGATAAAATATAA
273548 TGTTTAAAAT
Statistics
Matches: 126, Mismatches: 11, Indels: 5
0.89 0.08 0.04
Matches are distributed among these distances:
72 5 0.04
73 40 0.32
74 2 0.02
75 5 0.04
76 74 0.59
ACGTcount: A:0.58, C:0.12, G:0.01, T:0.28
Consensus pattern (76 bp):
TAAAACCTAATTAAAATACTAAAACCTATTTAAACTAAAATACCTAAAACAAAGATAAAATATAA
AAATAATATAC
Found at i:274562 original size:20 final size:20
Alignment explanation
Indices: 274537--274574 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
274527 CTTTATATTG
274537 GAGGATTGGTATCCATACTA
1 GAGGATTGGTATCCATACTA
*
274557 GAGGATTGGTATCTATAC
1 GAGGATTGGTATCCATAC
274575 CAGATGAACT
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:0.29, C:0.13, G:0.26, T:0.32
Consensus pattern (20 bp):
GAGGATTGGTATCCATACTA
Found at i:279759 original size:3 final size:3
Alignment explanation
Indices: 279751--279826 Score: 145
Period size: 3 Copynumber: 25.7 Consensus size: 3
279741 AAAGAGAAAC
279751 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT- ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
279798 ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
279827 GGAGCTTGAA
Statistics
Matches: 72, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
2 2 0.03
3 70 0.97
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:287374 original size:150 final size:149
Alignment explanation
Indices: 287168--287483 Score: 571
Period size: 150 Copynumber: 2.1 Consensus size: 149
287158 TATAAATGTA
*
287168 CCGAAGTG-CCGCGTAGAATTGCACTGTAGTGCCATATAATGATGTCCATAAGGACCACATAGAA
1 CCGAAG-GACCGCGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACATAGAA
287232 TTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTTTCCAAGACTTCACACATGT
65 TTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTTT-CAAGACTTCACACATGT
* *
287297 TCCACAGAATATATATATATC
129 TCCAAAGAATATACATATATC
287318 CCGAAGGACCGCGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACATAGAAT
1 CCGAAGGACCGCGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACATAGAAT
287383 TCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTTC
66 TCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTTC
*
287448 CAAAGAATATACATATGTC
131 CAAAGAATATACATATATC
287467 CCGAAGGACCGCGTAGA
1 CCGAAGGACCGCGTAGA
287484 CCCTCTACCC
Statistics
Matches: 161, Mismatches: 4, Indels: 3
0.96 0.02 0.02
Matches are distributed among these distances:
149 53 0.33
150 108 0.67
ACGTcount: A:0.34, C:0.21, G:0.18, T:0.27
Consensus pattern (149 bp):
CCGAAGGACCGCGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACATAGAAT
TCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTTC
CAAAGAATATACATATATC
Found at i:288559 original size:19 final size:17
Alignment explanation
Indices: 288527--288561 Score: 52
Period size: 19 Copynumber: 1.9 Consensus size: 17
288517 ACGTTTGGAG
288527 AAGGAAGAGAAGAAGAT
1 AAGGAAGAGAAGAAGAT
288544 AAGGAAGAAGGAAGAAGA
1 AAGGAAG-A-GAAGAAGA
288562 AATGAGAGGA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 7 0.44
18 1 0.06
19 8 0.50
ACGTcount: A:0.60, C:0.00, G:0.37, T:0.03
Consensus pattern (17 bp):
AAGGAAGAGAAGAAGAT
Found at i:294074 original size:23 final size:23
Alignment explanation
Indices: 294048--294092 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
294038 CACCACAACT
*
294048 CGTATAAATGCACCGAAGTGCCG
1 CGTAGAAATGCACCGAAGTGCCG
* *
294071 CGTAGAATTGCACCGTAGTGCC
1 CGTAGAAATGCACCGAAGTGCC
294093 ATATAATGAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.27, C:0.27, G:0.27, T:0.20
Consensus pattern (23 bp):
CGTAGAAATGCACCGAAGTGCCG
Found at i:294260 original size:150 final size:149
Alignment explanation
Indices: 294060--294375 Score: 571
Period size: 150 Copynumber: 2.1 Consensus size: 149
294050 TATAAATGCA
294060 CCGAAGTG-CCGCGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACATAGAA
1 CCGAAG-GACCGCGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACATAGAA
294124 TTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTTTCCAAGACTTCACACATGT
65 TTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTTT-CAAGACTTCACACATGT
* *
294189 TCCACAGAATATATATATATC
129 TCCAAAGAATATACATATATC
294210 CCGAAGGACCGCGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACATAGAAT
1 CCGAAGGACCGCGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACATAGAAT
294275 TCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTTC
66 TCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTTC
* *
294340 TAAAGAATATACATATGTC
131 CAAAGAATATACATATATC
294359 CCGAAGGACCGCGTAGA
1 CCGAAGGACCGCGTAGA
294376 CCCTCTACCC
Statistics
Matches: 161, Mismatches: 4, Indels: 3
0.96 0.02 0.02
Matches are distributed among these distances:
149 52 0.32
150 109 0.68
ACGTcount: A:0.34, C:0.21, G:0.18, T:0.27
Consensus pattern (149 bp):
CCGAAGGACCGCGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACATAGAAT
TCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTTC
CAAAGAATATACATATATC
Found at i:295449 original size:19 final size:17
Alignment explanation
Indices: 295417--295451 Score: 52
Period size: 19 Copynumber: 1.9 Consensus size: 17
295407 ACGTTTGGAG
295417 AAGGAAGAGAAGAAGAT
1 AAGGAAGAGAAGAAGAT
295434 AAGGAAGAAGGAAGAAGA
1 AAGGAAG-A-GAAGAAGA
295452 AATGAGAGGA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 7 0.44
18 1 0.06
19 8 0.50
ACGTcount: A:0.60, C:0.00, G:0.37, T:0.03
Consensus pattern (17 bp):
AAGGAAGAGAAGAAGAT
Found at i:309474 original size:3 final size:3
Alignment explanation
Indices: 309466--309500 Score: 56
Period size: 3 Copynumber: 12.3 Consensus size: 3
309456 AAGAAGTTGT
309466 TTA TTA TTA TTA TTA -TA TTA TTA TTA TTA TT- TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
309501 GATATTTATA
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
2 4 0.13
3 26 0.87
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:309486 original size:14 final size:14
Alignment explanation
Indices: 309467--309500 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
309457 AGAAGTTGTT
309467 TATTATTATTATTA
1 TATTATTATTATTA
309481 TATTATTATTATTA
1 TATTATTATTATTA
*
309495 TTTTAT
1 TATTAT
309501 GATATTTATA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (14 bp):
TATTATTATTATTA
Found at i:309509 original size:20 final size:18
Alignment explanation
Indices: 309465--309519 Score: 56
Period size: 20 Copynumber: 2.8 Consensus size: 18
309455 AAAGAAGTTG
309465 TTTATTATTATTATTATAT
1 TTTATTATTATT-TTATAT
309484 TATTATTATTATTTTATGAT
1 T-TTATTATTATTTTAT-AT
* *
309504 ATTTATAATTTTTTTA
1 -TTTATTATTATTTTA
309520 CTGTAGAGAC
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
19 5 0.16
20 25 0.81
21 1 0.03
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (18 bp):
TTTATTATTATTTTATAT
Found at i:311254 original size:12 final size:11
Alignment explanation
Indices: 311212--311256 Score: 56
Period size: 11 Copynumber: 4.0 Consensus size: 11
311202 TGGAGGTACC
311212 TCATTTTGCACT
1 TCATTTTGCA-T
*
311224 T-ATTCTGCAT
1 TCATTTTGCAT
311234 TCATTTTGCAT
1 TCATTTTGCAT
311245 TCATTTTTGCAT
1 TCA-TTTTGCAT
311257 AACATAACAT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
10 2 0.07
11 18 0.62
12 9 0.31
ACGTcount: A:0.18, C:0.20, G:0.09, T:0.53
Consensus pattern (11 bp):
TCATTTTGCAT
Found at i:322988 original size:20 final size:20
Alignment explanation
Indices: 322948--322986 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
322938 CATTGCAGGA
322948 ATTTATGGCATCGACAAAAG
1 ATTTATGGCATCGACAAAAG
*
322968 ATTTCATGGCCTCGACAAA
1 ATTT-ATGGCATCGACAAA
322987 GACCTTGATG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.36, C:0.21, G:0.18, T:0.26
Consensus pattern (20 bp):
ATTTATGGCATCGACAAAAG
Found at i:332665 original size:90 final size:90
Alignment explanation
Indices: 332544--332721 Score: 293
Period size: 90 Copynumber: 2.0 Consensus size: 90
332534 TAATCCCGAA
* * * * * *
332544 TATTTAATTTCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAATCCCTGATATGAT
1 TATTAAATTCCAATTAATTAAATATAGATTTAATTAATTTAAAATAATAAAAACCCTAATATGAC
332609 TAGGGTAACTTGGATATAAAAGGAT
66 TAGGGTAACTTGGATATAAAAGGAT
332634 TATTAAATTCCAATTAATTAAATATAGATTTAATTAATTTAAAATAATAAAAACCCTAATATGAC
1 TATTAAATTCCAATTAATTAAATATAGATTTAATTAATTTAAAATAATAAAAACCCTAATATGAC
*
332699 TAGGGTAACTTGGCTATAAAAGG
66 TAGGGTAACTTGGATATAAAAGG
332722 GTGTGTTAGG
Statistics
Matches: 81, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
90 81 1.00
ACGTcount: A:0.45, C:0.07, G:0.11, T:0.37
Consensus pattern (90 bp):
TATTAAATTCCAATTAATTAAATATAGATTTAATTAATTTAAAATAATAAAAACCCTAATATGAC
TAGGGTAACTTGGATATAAAAGGAT
Found at i:339776 original size:90 final size:90
Alignment explanation
Indices: 339667--339833 Score: 280
Period size: 90 Copynumber: 1.9 Consensus size: 90
339657 ATTTAATTTT
* * * *
339667 AATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAATCGATGATATGATTAGGGTAACTT
1 AATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAAACCATAATATGACTAGGGTAACTT
339732 GGATATAAAAGGATTATTAAATTCC
66 GGATATAAAAGGATTATTAAATTCC
*
339757 AATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAAACCCTAATATGACTAGGGTAACTT
1 AATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAAACCATAATATGACTAGGGTAACTT
*
339822 GGCTATAAAAGG
66 GGATATAAAAGG
339834 GTGTGTTAGG
Statistics
Matches: 71, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
90 71 1.00
ACGTcount: A:0.46, C:0.06, G:0.13, T:0.35
Consensus pattern (90 bp):
AATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAAACCATAATATGACTAGGGTAACTT
GGATATAAAAGGATTATTAAATTCC
Found at i:349173 original size:95 final size:95
Alignment explanation
Indices: 349037--349217 Score: 283
Period size: 95 Copynumber: 1.9 Consensus size: 95
349027 GACCAGGTTA
* * *
349037 TATCGATACCATGGAAAGGGTATCGATACAAGGCAACATCGAATCTAAAATTGGTATCGATACCG
1 TATCAATACCATGGAAAGGGTATCGATACAAGGCAAAATCGAATCTAAAATTGATATCGATACCG
349102 GAAGGGGGTATCGGTACCATAGTATGGTAG
66 GAAGGGGGTATCGGTACCATAGTATGGTAG
* * * *
349132 TATCAATATCATGGTAAGGGTATCGATACCA-GCTAAAATCGAATCTAAAATTTATATCGATACC
1 TATCAATACCATGGAAAGGGTATCGATACAAGGC-AAAATCGAATCTAAAATTGATATCGATACC
349196 GGAAGGGGGTATCGGTACCATA
65 GGAAGGGGGTATCGGTACCATA
349218 TTATAAAAGT
Statistics
Matches: 78, Mismatches: 7, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
94 2 0.03
95 76 0.97
ACGTcount: A:0.35, C:0.16, G:0.24, T:0.25
Consensus pattern (95 bp):
TATCAATACCATGGAAAGGGTATCGATACAAGGCAAAATCGAATCTAAAATTGATATCGATACCG
GAAGGGGGTATCGGTACCATAGTATGGTAG
Found at i:349250 original size:95 final size:95
Alignment explanation
Indices: 349056--349255 Score: 253
Period size: 95 Copynumber: 2.1 Consensus size: 95
349046 CATGGAAAGG
* *
349056 GTATCGATACAAGGCAACATCGAATCTAAAATTGGTATCGATACCGGAAGGGGGTATCGGTACCA
1 GTATCGATACAAGGCAAAATCGAATCTAAAATTGATATCGATACCGGAAGGGGGTATCGGTACCA
*** * *
349121 TAGTATGGTAGTATCAATATCATGGTAAGG
66 TAGTATAAAAGTATCAATATCAGGGTAAGA
* *
349151 GTATCGATACCA-GCTAAAATCGAATCTAAAATTTATATCGATACCGGAAGGGGGTATCGGTACC
1 GTATCGATACAAGGC-AAAATCGAATCTAAAATTGATATCGATACCGGAAGGGGGTATCGGTACC
* *
349215 ATATTATAAAAGTATCGAT-TCCAGGGT-AGTA
65 ATAGTATAAAAGTATCAATAT-CAGGGTAAG-A
349246 GTATCGATAC
1 GTATCGATAC
349256 TATTGAGCTT
Statistics
Matches: 91, Mismatches: 11, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
94 5 0.05
95 86 0.95
ACGTcount: A:0.34, C:0.15, G:0.23, T:0.27
Consensus pattern (95 bp):
GTATCGATACAAGGCAAAATCGAATCTAAAATTGATATCGATACCGGAAGGGGGTATCGGTACCA
TAGTATAAAAGTATCAATATCAGGGTAAGA
Found at i:349692 original size:46 final size:46
Alignment explanation
Indices: 349639--350112 Score: 375
Period size: 46 Copynumber: 10.3 Consensus size: 46
349629 AAATTGAATT
* * *
349639 CATAATTAAAATGCATGAAAGGATTCATTAAGACATGAAATGATGC
1 CATAATTAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGC
* * * *
349685 CATAATTAAAATGTATGAAAGGATGCATTAAGGAATAAAAGGATAC
1 CATAATTAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGC
* * *
349731 CATAAACTAAAATGCATGAAATGATGCATTAAGGCATGAAATGATG-
1 CAT-AATTAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGC
* * * * *
349777 C---ATT--AAGGCATGAAAGAATGCCATAATTACAATGCA-AAAAAGATG-
1 CATAATTAAAATGCATGAAAGGATG-C---ATT--AAGGCATGAAAGGATGC
* * * *
349822 C---ATT--AAGGCATGAAAGGATATCATAATTAAAATGCATGAAAGGATAC
1 CATAATTAAAATGCATGAAAGGAT-GC---ATT--AAGGCATGAAAGGATGC
349869 CATAATTAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGC
1 CATAATTAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGC
* * * * * *
349915 CATAAACTAAAATGCGT-TAATGATGCATTTAGGCATCAAAGGATGC
1 CAT-AATTAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGC
* * *
349961 CATAATTACAATGTATGAAAGGATGCATTAAGGCATGAAAGGATGT
1 CATAATTAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGC
* *
350007 CATAATTAAAATGTATGAAATGATGCATTAAGGCATGAAAGGATGTC
1 CATAATTAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATG-C
* ** * *
350054 ACA-AACTAAAATGCATGAAATTATGCATTAAGGTATGAAAGGATAC
1 -CATAATTAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGC
*
350100 CATAATTTAAATG
1 CATAATTAAAATG
350113 AATAAATGGA
Statistics
Matches: 352, Mismatches: 56, Indels: 40
0.79 0.12 0.09
Matches are distributed among these distances:
40 13 0.04
41 1 0.00
42 2 0.01
44 3 0.01
45 50 0.14
46 176 0.50
47 84 0.24
48 5 0.01
50 3 0.01
51 1 0.00
52 14 0.04
ACGTcount: A:0.45, C:0.11, G:0.20, T:0.25
Consensus pattern (46 bp):
CATAATTAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGC
Found at i:349797 original size:20 final size:20
Alignment explanation
Indices: 349744--349791 Score: 96
Period size: 20 Copynumber: 2.4 Consensus size: 20
349734 AAACTAAAAT
349744 GCATGAAATGATGCATTAAG
1 GCATGAAATGATGCATTAAG
349764 GCATGAAATGATGCATTAAG
1 GCATGAAATGATGCATTAAG
349784 GCATGAAA
1 GCATGAAA
349792 GAATGCCATA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.42, C:0.10, G:0.25, T:0.23
Consensus pattern (20 bp):
GCATGAAATGATGCATTAAG
Found at i:349859 original size:26 final size:26
Alignment explanation
Indices: 349829--349892 Score: 119
Period size: 26 Copynumber: 2.5 Consensus size: 26
349819 ATGCATTAAG
*
349829 GCATGAAAGGATATCATAATTAAAAT
1 GCATGAAAGGATACCATAATTAAAAT
349855 GCATGAAAGGATACCATAATTAAAAT
1 GCATGAAAGGATACCATAATTAAAAT
349881 GCATGAAAGGAT
1 GCATGAAAGGAT
349893 GCATTAAGGC
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 37 1.00
ACGTcount: A:0.48, C:0.09, G:0.19, T:0.23
Consensus pattern (26 bp):
GCATGAAAGGATACCATAATTAAAAT
Found at i:350000 original size:20 final size:20
Alignment explanation
Indices: 349975--350051 Score: 73
Period size: 20 Copynumber: 3.5 Consensus size: 20
349965 ATTACAATGT
349975 ATGAAAGGATGCATTAAGGC
1 ATGAAAGGATGCATTAAGGC
* *
349995 ATGAAAGGATGTCATAATTAAAATGT
1 ATGAAAGGATG-C---ATT--AAGGC
*
350021 ATGAAATGATGCATTAAGGC
1 ATGAAAGGATGCATTAAGGC
350041 ATGAAAGGATG
1 ATGAAAGGATG
350052 TCACAAACTA
Statistics
Matches: 45, Mismatches: 6, Indels: 12
0.71 0.10 0.19
Matches are distributed among these distances:
20 24 0.53
21 1 0.02
22 3 0.07
24 3 0.07
25 1 0.02
26 13 0.29
ACGTcount: A:0.43, C:0.06, G:0.26, T:0.25
Consensus pattern (20 bp):
ATGAAAGGATGCATTAAGGC
Found at i:350025 original size:26 final size:24
Alignment explanation
Indices: 349952--350034 Score: 75
Period size: 26 Copynumber: 3.5 Consensus size: 24
349942 TTTAGGCATC
349952 AAAGGATGCCATAATTACAATGTATG
1 AAAGGATG-CATAATTA-AATGTATG
* *
349978 AAAGGATGC---ATT-AAGGCATG
1 AAAGGATGCATAATTAAATGTATG
349998 AAAGGATGTCATAATTAAAATGTATG
1 AAAGGATG-CATAATT-AAATGTATG
*
350024 AAATGATGCAT
1 AAAGGATGCAT
350035 TAAGGCATGA
Statistics
Matches: 46, Mismatches: 5, Indels: 13
0.72 0.08 0.20
Matches are distributed among these distances:
20 14 0.30
21 1 0.02
22 3 0.07
24 3 0.07
25 4 0.09
26 21 0.46
ACGTcount: A:0.43, C:0.08, G:0.22, T:0.27
Consensus pattern (24 bp):
AAAGGATGCATAATTAAATGTATG
Found at i:350163 original size:138 final size:138
Alignment explanation
Indices: 349869--350151 Score: 329
Period size: 138 Copynumber: 2.1 Consensus size: 138
349859 GAAAGGATAC
* * * *
349869 CATAATTAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGCCATAAACTAAAATGCGTTA
1 CATAATTAAAATGTATGAAAGGATGCATTAAGGCATGAAAGGATGCCACAAACTAAAATGCATAA
* * * *
349934 ATGATGCATTTAGGCATCAAAGGATGCCATAATTACAATGTATGAAAGGATGCATTAAGGCATGA
66 ATGATGCATTAAGGCATCAAAGGATACCATAATTACAATGAATGAAAGGATGCATTAAGACATGA
** * *
349999 AAGGATGT
131 AAAAAAGA
* *
350007 CATAATTAAAATGTATGAAATGATGCATTAAGGCATGAAAGGATGTCACAAACTAAAATGCATGA
1 CATAATTAAAATGTATGAAAGGATGCATTAAGGCATGAAAGGATGCCACAAACTAAAATGCAT-A
* * * ** * *
350072 AATTATGCATTAAGGTATGAAAGGATACCATAATTTA-AATGAAT-AAATGGATGTGTTAATACG
65 AATGATGCATTAAGGCATCAAAGGATACCATAA-TTACAATGAATGAAA-GGATGCATTAAGACA
350135 T-AAAAAAAGA
128 TGAAAAAAAGA
350145 CATAATT
1 CATAATT
350152 GAAGTTAATG
Statistics
Matches: 121, Mismatches: 21, Indels: 6
0.82 0.14 0.04
Matches are distributed among these distances:
138 73 0.60
139 45 0.37
140 3 0.02
ACGTcount: A:0.44, C:0.10, G:0.20, T:0.26
Consensus pattern (138 bp):
CATAATTAAAATGTATGAAAGGATGCATTAAGGCATGAAAGGATGCCACAAACTAAAATGCATAA
ATGATGCATTAAGGCATCAAAGGATACCATAATTACAATGAATGAAAGGATGCATTAAGACATGA
AAAAAAGA
Found at i:356488 original size:95 final size:96
Alignment explanation
Indices: 356286--356488 Score: 293
Period size: 95 Copynumber: 2.1 Consensus size: 96
356276 ATACGATGAG
* * * *
356286 GTAGCATCGATACCAGGCAATATCGAATCTAAAATTGGTATCAATACCAGAAGGGGGTATCGATA
1 GTAGTATCGATACCAGACAACATCAAATCTAAAATTGGTATCAATACCAGAAGGGGGTATCGATA
* * *
356351 CCATAGTATGGTAGTATCGATACCATGGTAA
66 CCATAGTATAGAAGTATCGATACCAGGGTAA
* * * *
356382 GGA-TATTGATACCAGACAACATCAAATCTAAAATTGGTATCGATACCAGAAGGGGGTATCGGTA
1 GTAGTATCGATACCAGACAACATCAAATCTAAAATTGGTATCAATACCAGAAGGGGGTATCGATA
356446 CCATAGTATAGAAGTATCGATACCAGGGT-A
66 CCATAGTATAGAAGTATCGATACCAGGGTAA
356476 GTAGTATCGATAC
1 GTAGTATCGATAC
356489 TATTGAGCTT
Statistics
Matches: 93, Mismatches: 13, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
94 3 0.03
95 88 0.95
96 2 0.02
ACGTcount: A:0.36, C:0.16, G:0.23, T:0.25
Consensus pattern (96 bp):
GTAGTATCGATACCAGACAACATCAAATCTAAAATTGGTATCAATACCAGAAGGGGGTATCGATA
CCATAGTATAGAAGTATCGATACCAGGGTAA
Found at i:356929 original size:46 final size:46
Alignment explanation
Indices: 356876--357336 Score: 607
Period size: 46 Copynumber: 10.0 Consensus size: 46
356866 ACATCGAATT
* *
356876 CATAATTAAAATGCATGAAATGATGCATTAAGGCATGAAAGGATTC
1 CATAATTAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGC
** * *
356922 CATAATTAAAATGCACAAAAGGTTGCATTAAGGCATGACAGGATGC
1 CATAATTAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGC
* *
356968 CATAAACTAAAATGCATGAAAGGATACATTAAGGCATGAAAGGATGC
1 CAT-AATTAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGC
* * *
357015 CATAATTACAATGCATGAAACGAAGCATTAAGGCATGAAAGGATGC
1 CATAATTAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGC
* * *
357061 CATAATTAAAATGCATGAAACGAAGCATTAAGGCATGAAATGATGC
1 CATAATTAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGC
* ** *
357107 CATAAACTAAAATGCATGAAAGGATTAATTAAGGCATGAAAGGATTC
1 CAT-AATTAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGC
*
357154 CATAATTAAAATGCATGAAAGGATGCATTAAGGCATGAAAGTATGC
1 CATAATTAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGC
* ** * *
357200 CATAAACTAAAATGCATGAAATAATGCATTAAGGCATAAAAAGATGC
1 CAT-AATTAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGC
** * **
357247 CATAATTTCAATGCATGGAATAATGCATTAAGGCATGAAAGGATGC
1 CATAATTAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGC
* **
357293 CATACTTAAAATGCATGAAAATATGCATTAAGGCATGAAAGGAT
1 CATAATTAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGAT
357337 ACATTGATGC
Statistics
Matches: 363, Mismatches: 49, Indels: 6
0.87 0.12 0.01
Matches are distributed among these distances:
46 244 0.67
47 119 0.33
ACGTcount: A:0.45, C:0.13, G:0.20, T:0.23
Consensus pattern (46 bp):
CATAATTAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGC
Found at i:356999 original size:93 final size:92
Alignment explanation
Indices: 356876--357336 Score: 584
Period size: 93 Copynumber: 5.0 Consensus size: 92
356866 ACATCGAATT
* * **
356876 CATAATTAAAATGCATGAAATGATGCATTAAGGCATGAAAGGATTCCATAATTAAAATGCACAAA
1 CATAATTAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGCCATAATTAAAATGCATGAA
*
356941 AGGTTGCATTAAGGCATGACAGGATGC
66 AGGTTGCATTAAGGCATGAAAGGATGC
* * *
356968 CATAAACTAAAATGCATGAAAGGATACATTAAGGCATGAAAGGATGCCATAATTACAATGCATGA
1 CAT-AATTAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGCCATAATTAAAATGCATGA
* **
357033 AACGAAGCATTAAGGCATGAAAGGATGC
65 AAGGTTGCATTAAGGCATGAAAGGATGC
* * * *
357061 CATAATTAAAATGCATGAAACGAAGCATTAAGGCATGAAATGATGCCATAAACTAAAATGCATGA
1 CATAATTAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGCCAT-AATTAAAATGCATGA
* *
357126 AAGGATT-AATTAAGGCATGAAAGGATTC
65 AAGG-TTGCATTAAGGCATGAAAGGATGC
* *
357154 CATAATTAAAATGCATGAAAGGATGCATTAAGGCATGAAAGTATGCCATAAACTAAAATGCATGA
1 CATAATTAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGCCAT-AATTAAAATGCATGA
*** * *
357219 AATAATGCATTAAGGCATAAAAAGATGC
65 AAGGTTGCATTAAGGCATGAAAGGATGC
** * ** *
357247 CATAATTTCAATGCATGGAATAATGCATTAAGGCATGAAAGGATGCCATACTTAAAATGCATGAA
1 CATAATTAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGCCATAATTAAAATGCATGAA
*
357312 A-ATATGCATTAAGGCATGAAAGGAT
66 AGGT-TGCATTAAGGCATGAAAGGAT
357337 ACATTGATGC
Statistics
Matches: 319, Mismatches: 45, Indels: 10
0.85 0.12 0.03
Matches are distributed among these distances:
91 1 0.00
92 79 0.25
93 239 0.75
ACGTcount: A:0.45, C:0.13, G:0.20, T:0.23
Consensus pattern (92 bp):
CATAATTAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGCCATAATTAAAATGCATGAA
AGGTTGCATTAAGGCATGAAAGGATGC
Found at i:357052 original size:20 final size:20
Alignment explanation
Indices: 357027--357100 Score: 67
Period size: 20 Copynumber: 3.4 Consensus size: 20
357017 TAATTACAAT
357027 GCATGAAACGAAGCATTAAG
1 GCATGAAACGAAGCATTAAG
* * *
357047 GCATGAAAGGATGCCATAATTAAAAT
1 GCATGAAACGAAG-C---ATT--AAG
357073 GCATGAAACGAAGCATTAAG
1 GCATGAAACGAAGCATTAAG
357093 GCATGAAA
1 GCATGAAA
357101 TGATGCCATA
Statistics
Matches: 42, Mismatches: 6, Indels: 12
0.70 0.10 0.20
Matches are distributed among these distances:
20 21 0.50
21 1 0.02
22 3 0.07
24 3 0.07
25 1 0.02
26 13 0.31
ACGTcount: A:0.46, C:0.14, G:0.23, T:0.18
Consensus pattern (20 bp):
GCATGAAACGAAGCATTAAG
Found at i:357089 original size:139 final size:138
Alignment explanation
Indices: 356876--357336 Score: 620
Period size: 139 Copynumber: 3.3 Consensus size: 138
356866 ACATCGAATT
* * **
356876 CATAATTAAAATGCATGAAATGATGCATTAAGGCATGAAAGGATTCCATAATTAAAATGCACAAA
1 CATAATTAAAATGCATGAAAAGATGCATTAAGGCATGAAAGGATGCCATAATTAAAATGCATGAA
** * *
356941 AGGTTGCATTAAGGCATGACAGGATGCCATAAACTAAAATGCATGAAAGGATACATTAAGGCATG
66 A-GAAGCATTAAGGCATGAAAAGATGCCATAAACTAAAATGCATGAAAGGATACATTAAGGCATG
357006 AAAGGATGC
130 AAAGGATGC
* * *
357015 CATAATTACAATGCATGAAACGAAGCATTAAGGCATGAAAGGATGCCATAATTAAAATGCATGAA
1 CATAATTAAAATGCATGAAAAGATGCATTAAGGCATGAAAGGATGCCATAATTAAAATGCATGAA
*
357080 ACGAAGCATTAAGGCATGAAATGATGCCATAAACTAAAATGCATGAAAGGATTA-ATTAAGGCAT
66 A-GAAGCATTAAGGCATGAAAAGATGCCATAAACTAAAATGCATGAAAGGA-TACATTAAGGCAT
*
357144 GAAAGGATTC
129 GAAAGGATGC
* * *
357154 CATAATTAAAATGCATGAAAGGATGCATTAAGGCATGAAAGTATGCCATAAACTAAAATGCATGA
1 CATAATTAAAATGCATGAAAAGATGCATTAAGGCATGAAAGGATGCCAT-AATTAAAATGCATGA
* * * ** * ** *
357219 AATAATGCATTAAGGCATAAAAAGATGCCAT-AATTTCAATGCATGGAATAATGCATTAAGGCAT
65 AAGAA-GCATTAAGGCATGAAAAGATGCCATAAACTAAAATGCATGAAAGGATACATTAAGGCAT
357283 GAAAGGATGC
129 GAAAGGATGC
* *
357293 CATACTTAAAATGCATGAAAATATGCATTAAGGCATGAAAGGAT
1 CATAATTAAAATGCATGAAAAGATGCATTAAGGCATGAAAGGAT
357337 ACATTGATGC
Statistics
Matches: 286, Mismatches: 32, Indels: 8
0.88 0.10 0.02
Matches are distributed among these distances:
138 1 0.00
139 244 0.85
140 41 0.14
ACGTcount: A:0.45, C:0.13, G:0.20, T:0.23
Consensus pattern (138 bp):
CATAATTAAAATGCATGAAAAGATGCATTAAGGCATGAAAGGATGCCATAATTAAAATGCATGAA
AGAAGCATTAAGGCATGAAAAGATGCCATAAACTAAAATGCATGAAAGGATACATTAAGGCATGA
AAGGATGC
Found at i:357145 original size:20 final size:20
Alignment explanation
Indices: 357120--357194 Score: 69
Period size: 20 Copynumber: 3.5 Consensus size: 20
357110 AAACTAAAAT
357120 GCATGAAAGGATTAATTAAG
1 GCATGAAAGGATTAATTAAG
*
357140 GCATGAAAGGATTCCATAATTAAAAT
1 GCATGAAAGGA-T---TAATT--AAG
**
357166 GCATGAAAGGATGCATTAAG
1 GCATGAAAGGATTAATTAAG
357186 GCATGAAAG
1 GCATGAAAG
357195 TATGCCATAA
Statistics
Matches: 45, Mismatches: 4, Indels: 12
0.74 0.07 0.20
Matches are distributed among these distances:
20 22 0.49
21 1 0.02
22 3 0.07
24 5 0.11
25 1 0.02
26 13 0.29
ACGTcount: A:0.44, C:0.09, G:0.24, T:0.23
Consensus pattern (20 bp):
GCATGAAAGGATTAATTAAG
Found at i:357292 original size:20 final size:20
Alignment explanation
Indices: 357269--357341 Score: 56
Period size: 20 Copynumber: 3.4 Consensus size: 20
357259 GCATGGAATA
357269 ATGCATTAAGGCATGAAAGG
1 ATGCATTAAGGCATGAAAGG
* **
357289 ATGCCATACTTAAAATGCATGAAAAT
1 ATG-C--A-TT--AAGGCATGAAAGG
357315 ATGCATTAAGGCATGAAAGG
1 ATGCATTAAGGCATGAAAGG
*
357335 ATACATT
1 ATGCATT
357342 GATGCATTAA
Statistics
Matches: 40, Mismatches: 7, Indels: 12
0.68 0.12 0.20
Matches are distributed among these distances:
20 19 0.47
21 1 0.03
22 2 0.05
23 2 0.05
24 2 0.05
25 1 0.03
26 13 0.32
ACGTcount: A:0.42, C:0.12, G:0.21, T:0.25
Consensus pattern (20 bp):
ATGCATTAAGGCATGAAAGG
Found at i:364445 original size:34 final size:35
Alignment explanation
Indices: 364372--364461 Score: 101
Period size: 34 Copynumber: 2.6 Consensus size: 35
364362 CTTCTCCAGG
* ** * *
364372 GAAATTGTCTCAAGAGAGACAAAATTTGTTTCAAGA
1 GAAACTGTCTCAAGAGAGACAAAA-TACTTCCAAAA
364408 GAAACTGTCTCAAGAGAGACAAAA-ACTTCCAAAA
1 GAAACTGTCTCAAGAGAGACAAAATACTTCCAAAA
* *
364442 GAAACTATCTCAAGGGAGAC
1 GAAACTGTCTCAAGAGAGAC
364462 GAGATTTGTT
Statistics
Matches: 47, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
34 24 0.51
36 23 0.49
ACGTcount: A:0.44, C:0.17, G:0.19, T:0.20
Consensus pattern (35 bp):
GAAACTGTCTCAAGAGAGACAAAATACTTCCAAAA
Found at i:364584 original size:36 final size:35
Alignment explanation
Indices: 364530--364611 Score: 83
Period size: 36 Copynumber: 2.3 Consensus size: 35
364520 AATTTTATGC
* * * * * *
364530 TTCAAGAGAAATTGTCTCAAGGGAGACAAAATTTAT
1 TTCAAGGGAAACTATCTCAAGAGAGA-AAAAATCAT
* *
364566 TTCAAGGGAAACTATCTCATGAGTGAAAAAATCAT
1 TTCAAGGGAAACTATCTCAAGAGAGAAAAAATCAT
364601 TTCAAGGGAAA
1 TTCAAGGGAAA
364612 TGTTTTCAAT
Statistics
Matches: 38, Mismatches: 8, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
35 18 0.47
36 20 0.53
ACGTcount: A:0.43, C:0.12, G:0.20, T:0.26
Consensus pattern (35 bp):
TTCAAGGGAAACTATCTCAAGAGAGAAAAAATCAT
Found at i:364732 original size:102 final size:101
Alignment explanation
Indices: 364498--364880 Score: 441
Period size: 102 Copynumber: 3.8 Consensus size: 101
364488 CAAAGATTTT
* * * * *
364498 ATTTCAAAGGAAATTGTTTTCAAAT-TTTATGCTTCAAGAGAAATTGTCTCAAGGGAGACAAAAT
1 ATTTCAAGGGAAA-TGTTTTC-AATGTTTATGTTTCAAGAGAAACTATCTCAAGAGAGACAAAAT
* * *
364562 TTATTTCAAGGGAAACTATCTCATGAGTGA-AAAAATC
64 TTATTTCAAGGGAAACTATCTCAAGAGAGACAAAATTC
* * *
364599 ATTTCAAGGGAAATGTTTTCAATGTTTATGTTTCCAGAGAAACTGTCTCAAGGGAGACAAAATTT
1 ATTTCAAGGGAAATGTTTTCAATGTTTATGTTTCAAGAGAAACTATCTCAAGAGAGACAAAA-TT
* * *
364664 TGTTTCAAGGGAACCTATATCAAGAGAGACAAAATTC
65 TATTTCAAGGGAAACTATCTCAAGAGAGACAAAATTC
* *
364701 ATCTCAAGGGAAATGTTTTCAATGTTTATGTTTCAAGAGAAACTATCTCAAGAGAGACAAAACTT
1 ATTTCAAGGGAAATGTTTTCAATGTTTATGTTTCAAGAGAAACTATCTCAAGAGAGACAAAATTT
* ** * * * *
364766 AGTTCCAAAAGAAAATGTCTCAAGGGAGACAAAATTT
66 A-TTTCAAGGGAAACTATCTCAAGAGAGACAAAATTC
* * *
364803 GTTTCAAGGGAAATAG-ATTCAAAGATTT-TGTTTCAAGAGAAACTATCTCAAGAGAGACAAAAT
1 ATTTCAAGGGAAAT-GTTTTCAATG-TTTATGTTTCAAGAGAAACTATCTCAAGAGAGACAAAAT
*
364866 TCATTTCAAGGGAAA
64 TTATTTCAAGGGAAA
364881 TGTTTTCAAT
Statistics
Matches: 242, Mismatches: 34, Indels: 12
0.84 0.12 0.04
Matches are distributed among these distances:
99 3 0.01
100 42 0.17
101 49 0.20
102 144 0.60
103 4 0.02
ACGTcount: A:0.40, C:0.13, G:0.18, T:0.29
Consensus pattern (101 bp):
ATTTCAAGGGAAATGTTTTCAATGTTTATGTTTCAAGAGAAACTATCTCAAGAGAGACAAAATTT
ATTTCAAGGGAAACTATCTCAAGAGAGACAAAATTC
Found at i:364856 original size:167 final size:167
Alignment explanation
Indices: 364656--365179 Score: 908
Period size: 167 Copynumber: 3.1 Consensus size: 167
364646 TCAAGGGAGA
* * * *
364656 CAAA-ATTTTGTTTCAAGGGAACCTATATCAAGAGAGACAAAATTCATCTCAAGGGAAATGTTTT
1 CAAAGATTTTGTTTCAAGAGAAACTATCTCAAGAGAGACAAAATTCATTTCAAGGGAAATGTTTT
364720 CAATGTTTATGTTTCAAGAGAAACTATCTCAAGAGAGACAAAACTTAGTTCCAAAAGAAAATGTC
66 CAATGTTTATGTTTCAAGAGAAACTATCTCAAGAGAGACAAAACTTAGTTCCAAAAGAAAATGTC
*
364785 TCAAGGGAGACAAAATTTGTTTCAAGGGAAATAGATT
131 TCAAGGGAGACAAAATTTGTTTCAAGGGAAACAGATT
364822 CAAAGATTTTGTTTCAAGAGAAACTATCTCAAGAGAGACAAAATTCATTTCAAGGGAAATGTTTT
1 CAAAGATTTTGTTTCAAGAGAAACTATCTCAAGAGAGACAAAATTCATTTCAAGGGAAATGTTTT
364887 CAATGTTTATGTTTCAAGAGAAACTATCTCAAGAGAGACAAAACTTAGTTCCAAAAGAAAATGTC
66 CAATGTTTATGTTTCAAGAGAAACTATCTCAAGAGAGACAAAACTTAGTTCCAAAAGAAAATGTC
*
364952 TCAAGGGAGACGAAATTTGTTTCAAGGGAAACAGATT
131 TCAAGGGAGACAAAATTTGTTTCAAGGGAAACAGATT
364989 CAAAGATTTTGTTTCAAGAGAAACTATCTCAAGAGAGACAAAATTCATTTCAAGGGAAATGTTTT
1 CAAAGATTTTGTTTCAAGAGAAACTATCTCAAGAGAGACAAAATTCATTTCAAGGGAAATGTTTT
* * *
365054 CAATGTTTATGTTTCAAGAGAAACTATCTCAAGGGAGACAAAATTTAGTTCTAAAAGAAAATGTC
66 CAATGTTTATGTTTCAAGAGAAACTATCTCAAGAGAGACAAAACTTAGTTCCAAAAGAAAATGTC
* * *
365119 TCAAGGGAGACAAAATTAGTTTCAATGAAAACAGATT
131 TCAAGGGAGACAAAATTTGTTTCAAGGGAAACAGATT
* *
365156 TAAATATTTTGTTTCAAG-GAAACT
1 CAAAGATTTTGTTTCAAGAGAAACT
365180 TGGAAATTGT
Statistics
Matches: 342, Mismatches: 15, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
166 10 0.03
167 332 0.97
ACGTcount: A:0.41, C:0.13, G:0.18, T:0.29
Consensus pattern (167 bp):
CAAAGATTTTGTTTCAAGAGAAACTATCTCAAGAGAGACAAAATTCATTTCAAGGGAAATGTTTT
CAATGTTTATGTTTCAAGAGAAACTATCTCAAGAGAGACAAAACTTAGTTCCAAAAGAAAATGTC
TCAAGGGAGACAAAATTTGTTTCAAGGGAAACAGATT
Found at i:364879 original size:65 final size:65
Alignment explanation
Indices: 364783--364929 Score: 217
Period size: 65 Copynumber: 2.3 Consensus size: 65
364773 AAAGAAAATG
* **
364783 TCTCAAGGGAGACAAAATTTGTTTCAAGGGAAATAG-ATTCAAAGATTT-TGTTTCAAGAGAAAC
1 TCTCAAGAGAGACAAAATTCATTTCAAGGGAAAT-GTATTCAAAG-TTTATGTTTCAAGAGAAAC
364846 TA
64 TA
* *
364848 TCTCAAGAGAGACAAAATTCATTTCAAGGGAAATGTTTTCAATGTTTATGTTTCAAGAGAAACTA
1 TCTCAAGAGAGACAAAATTCATTTCAAGGGAAATGTATTCAAAGTTTATGTTTCAAGAGAAACTA
364913 TCTCAAGAGAGACAAAA
1 TCTCAAGAGAGACAAAA
364930 CTTAGTTCCA
Statistics
Matches: 75, Mismatches: 5, Indels: 4
0.89 0.06 0.05
Matches are distributed among these distances:
64 4 0.05
65 71 0.95
ACGTcount: A:0.41, C:0.12, G:0.18, T:0.29
Consensus pattern (65 bp):
TCTCAAGAGAGACAAAATTCATTTCAAGGGAAATGTATTCAAAGTTTATGTTTCAAGAGAAACTA
Found at i:364946 original size:102 final size:102
Alignment explanation
Indices: 364840--365031 Score: 271
Period size: 102 Copynumber: 1.9 Consensus size: 102
364830 TTGTTTCAAG
* * * *
364840 AGAAACTATCTCAAGAGAGACAAAATTCATTTCAAGGGAAA-TGTTTTCAATG-TTTATGTTTCA
1 AGAAAATATCTCAAGAGAGACAAAATTCATTTCAAGGGAAACAG-ATTCAAAGATTT-TGTTTCA
364903 AGAGAAACTATCTCAAGAGAGACAAAACTTAGTTCCAAA
64 AGAGAAACTATCTCAAGAGAGACAAAACTTAGTTCCAAA
* * * **
364942 AGAAAATGTCTCAAGGGAGACGAAATTTGTTTCAAGGGAAACAGATTCAAAGATTTTGTTTCAAG
1 AGAAAATATCTCAAGAGAGACAAAATTCATTTCAAGGGAAACAGATTCAAAGATTTTGTTTCAAG
365007 AGAAACTATCTCAAGAGAGACAAAA
66 AGAAACTATCTCAAGAGAGACAAAA
365032 TTCATTTCAA
Statistics
Matches: 79, Mismatches: 9, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
102 75 0.95
103 4 0.05
ACGTcount: A:0.43, C:0.14, G:0.18, T:0.26
Consensus pattern (102 bp):
AGAAAATATCTCAAGAGAGACAAAATTCATTTCAAGGGAAACAGATTCAAAGATTTTGTTTCAAG
AGAAACTATCTCAAGAGAGACAAAACTTAGTTCCAAA
Found at i:365046 original size:65 final size:65
Alignment explanation
Indices: 364950--365098 Score: 203
Period size: 65 Copynumber: 2.3 Consensus size: 65
364940 AAAGAAAATG
* **
364950 TCTCAAGGGAGACGAAATTTGTTTCAAGGGAAACAG-ATTCAAAGATTT-TGTTTCAAGAGAAAC
1 TCTCAAGGGAGACAAAATTCATTTCAAGGGAAA-AGTATTCAAAG-TTTATGTTTCAAGAGAAAC
365013 TA
64 TA
* * * *
365015 TCTCAAGAGAGACAAAATTCATTTCAAGGGAAATGTTTTCAATGTTTATGTTTCAAGAGAAACTA
1 TCTCAAGGGAGACAAAATTCATTTCAAGGGAAAAGTATTCAAAGTTTATGTTTCAAGAGAAACTA
365080 TCTCAAGGGAGACAAAATT
1 TCTCAAGGGAGACAAAATT
365099 TAGTTCTAAA
Statistics
Matches: 74, Mismatches: 8, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
64 4 0.05
65 70 0.95
ACGTcount: A:0.39, C:0.13, G:0.19, T:0.29
Consensus pattern (65 bp):
TCTCAAGGGAGACAAAATTCATTTCAAGGGAAAAGTATTCAAAGTTTATGTTTCAAGAGAAACTA
Found at i:365510 original size:106 final size:106
Alignment explanation
Indices: 365325--365524 Score: 256
Period size: 106 Copynumber: 1.9 Consensus size: 106
365315 TTGTATTGTT
* ** *
365325 TCGAGTCCAATATCCTCCGCCGTTAAGTTAAAATTGGCTTTGGAACTAAGAAATTGTTTGTTGAC
1 TCGAGTCCAATATCCTCCGCCGTGAAGTTAAAATTGGCTCCGAAACTAAGAAATTGTTTGTTGAC
* *
365390 AGCCAGCCGCCCCTTTGCTGTAAAGTTGAGCTTGTGCTATC
66 AACCAGCCGCCCCTTCGCTGTAAAGTTGAGCTTGTGCTATC
* * * * **
365431 TCGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCCGAAATTGGGAAATTGTTTGTTGAC
1 TCGAGTCCAATATCCTCCGCCGTGAAGTTAAAATTGGCTCCGAAACTAAGAAATTGTTTGTTGAC
* * * *
365496 AACCAGTCGTCCCTTCGTTGTGAAGTTGA
66 AACCAGCCGCCCCTTCGCTGTAAAGTTGA
365525 AATTGGCTCT
Statistics
Matches: 78, Mismatches: 16, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
106 78 1.00
ACGTcount: A:0.23, C:0.21, G:0.23, T:0.33
Consensus pattern (106 bp):
TCGAGTCCAATATCCTCCGCCGTGAAGTTAAAATTGGCTCCGAAACTAAGAAATTGTTTGTTGAC
AACCAGCCGCCCCTTCGCTGTAAAGTTGAGCTTGTGCTATC
Found at i:365543 original size:63 final size:63
Alignment explanation
Indices: 365444--365585 Score: 230
Period size: 63 Copynumber: 2.3 Consensus size: 63
365434 AGTCCAATAT
* * * *
365444 CCTTCGCTGTGAAGTTGAAATTGGCTCCGAAATTGGGAAATTGTTTGTTGACAACCAGTCGTC
1 CCTTCGTTGTGAAGTTGAAATTGGCTCCGAAATTGGGAAATTATTTGTTGAAAACCAGTCCTC
*
365507 CCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTATTTGTTGAAAACCAGTCCTC
1 CCTTCGTTGTGAAGTTGAAATTGGCTCCGAAATTGGGAAATTATTTGTTGAAAACCAGTCCTC
*
365570 CCTTCGTTGTGGAGTT
1 CCTTCGTTGTGAAGTT
365586 AAACTTGTGT
Statistics
Matches: 73, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
63 73 1.00
ACGTcount: A:0.23, C:0.18, G:0.25, T:0.35
Consensus pattern (63 bp):
CCTTCGTTGTGAAGTTGAAATTGGCTCCGAAATTGGGAAATTATTTGTTGAAAACCAGTCCTC
Found at i:366253 original size:32 final size:32
Alignment explanation
Indices: 366179--366290 Score: 147
Period size: 32 Copynumber: 3.5 Consensus size: 32
366169 TTTGCATCAG
* * *
366179 GATGTTGAAT-TCCCAAAGATGCCCCAA-ATTC
1 GATGTTGAATCT-CAAAAAATGCCCCAACATTT
366210 GATGTTGAATCTCAAAAAATGCCCCAACATTT
1 GATGTTGAATCTCAAAAAATGCCCCAACATTT
* *
366242 GATGTTAAATCTAAAAAAATGCCCCAACATTT
1 GATGTTGAATCTCAAAAAATGCCCCAACATTT
366274 GATGTTGAATCTTCAAA
1 GATGTTGAATC-TCAAA
366291 GATGCCCTAA
Statistics
Matches: 71, Mismatches: 7, Indels: 4
0.87 0.09 0.05
Matches are distributed among these distances:
31 23 0.32
32 44 0.62
33 4 0.06
ACGTcount: A:0.38, C:0.21, G:0.13, T:0.29
Consensus pattern (32 bp):
GATGTTGAATCTCAAAAAATGCCCCAACATTT
Found at i:367394 original size:20 final size:21
Alignment explanation
Indices: 367336--367395 Score: 72
Period size: 20 Copynumber: 3.0 Consensus size: 21
367326 TTGCATATGC
*
367336 ATCTTGTCTTT-TTTTTCTTCA
1 ATCTTCTCTTTGTTTTT-TTCA
*
367357 ATTTTC-CTTTGTTTTTTT-A
1 ATCTTCTCTTTGTTTTTTTCA
367376 ATCTTCTCTTTGTTTTTTTC
1 ATCTTCTCTTTGTTTTTTTC
367396 TCTTTTTTCT
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
19 6 0.18
20 18 0.55
21 9 0.27
ACGTcount: A:0.08, C:0.17, G:0.05, T:0.70
Consensus pattern (21 bp):
ATCTTCTCTTTGTTTTTTTCA
Found at i:370290 original size:25 final size:24
Alignment explanation
Indices: 370221--370299 Score: 70
Period size: 25 Copynumber: 3.2 Consensus size: 24
370211 AAAAGGTAAG
* *
370221 AAATAA-ATAAATAAATTAAATTA
1 AAATAAGATAAAAAAATTAAATAA
*
370244 AAATGAAGAAAAAAAAATTAAATAA
1 AAAT-AAGATAAAAAAATTAAATAA
* * *
370269 AAGATAAGATAAAGAAAGTAAAGATA
1 AA-ATAAGATAAAAAAATTAAATA-A
370295 AAATA
1 AAATA
370300 GTAAGTAAAA
Statistics
Matches: 45, Mismatches: 7, Indels: 6
0.78 0.12 0.10
Matches are distributed among these distances:
23 4 0.09
24 2 0.04
25 34 0.76
26 5 0.11
ACGTcount: A:0.71, C:0.00, G:0.09, T:0.20
Consensus pattern (24 bp):
AAATAAGATAAAAAAATTAAATAA
Found at i:370331 original size:17 final size:17
Alignment explanation
Indices: 370311--370372 Score: 52
Period size: 19 Copynumber: 3.3 Consensus size: 17
370301 TAAGTAAAAT
370311 AAATATAAAAAAAGAAA
1 AAATATAAAAAAAGAAA
*
370328 AAATAAAGAAAAAGAAGAAAA
1 AAAT--ATAAAAA-AAG-AAA
*
370349 AAATATAAATAAAACAAA
1 AAATATAAA-AAAAGAAA
370367 TAAATA
1 -AAATA
370373 AAATAACAAT
Statistics
Matches: 36, Mismatches: 3, Indels: 10
0.73 0.06 0.20
Matches are distributed among these distances:
17 4 0.11
18 3 0.08
19 17 0.47
20 5 0.14
21 7 0.19
ACGTcount: A:0.79, C:0.02, G:0.06, T:0.13
Consensus pattern (17 bp):
AAATATAAAAAAAGAAA
Found at i:370335 original size:44 final size:43
Alignment explanation
Indices: 370287--370383 Score: 107
Period size: 39 Copynumber: 2.3 Consensus size: 43
370277 ATAAAGAAAG
*
370287 TAAAGATAAAATAGTAAGTAAAATAAATATAAA-AAAAGAAA-AAA
1 TAAAGATAAAATAG-AAG-AAAA-AAATATAAATAAAACAAATAAA
370331 TAAAG--AAAA-AGAAGAAAAAAATATAAATAAAACAAATAAA
1 TAAAGATAAAATAGAAGAAAAAAATATAAATAAAACAAATAAA
370371 TAAA-ATAACAATA
1 TAAAGATAA-AATA
370384 AAAAAGTAAA
Statistics
Matches: 46, Mismatches: 1, Indels: 13
0.77 0.02 0.22
Matches are distributed among these distances:
38 9 0.20
39 11 0.24
40 10 0.22
41 4 0.09
42 6 0.13
43 1 0.02
44 5 0.11
ACGTcount: A:0.74, C:0.02, G:0.07, T:0.16
Consensus pattern (43 bp):
TAAAGATAAAATAGAAGAAAAAAATATAAATAAAACAAATAAA
Found at i:370340 original size:20 final size:21
Alignment explanation
Indices: 370306--370398 Score: 68
Period size: 21 Copynumber: 4.3 Consensus size: 21
370296 AATAGTAAGT
*
370306 AAAATAAATATAAAAAAAGAA
1 AAAATAAAGATAAAAAAAGAA
*
370327 AAAATAAAGA-AAAAGAAGAAA
1 AAAATAAAGATAAAAAAAG-AA
*
370348 AAAATATAA-ATAAAACAAATAAA
1 AAAATA-AAGATAAAA-AAA-GAA
*
370371 TAAAATAACA-AT-AAAAAAGTA
1 -AAAATAA-AGATAAAAAAAGAA
370392 AAAATAA
1 AAAATAA
370399 TATATATATA
Statistics
Matches: 59, Mismatches: 6, Indels: 15
0.74 0.08 0.19
Matches are distributed among these distances:
20 14 0.24
21 19 0.32
22 9 0.15
23 8 0.14
24 9 0.15
ACGTcount: A:0.78, C:0.02, G:0.05, T:0.14
Consensus pattern (21 bp):
AAAATAAAGATAAAAAAAGAA
Found at i:370378 original size:5 final size:5
Alignment explanation
Indices: 370221--370386 Score: 53
Period size: 5 Copynumber: 32.6 Consensus size: 5
370211 AAAAGGTAAG
* * * *
370221 AAAT- AAAT- AAATA AATTA AATTA AAATGA AGA-A AAA-A AAATT AAATAA
1 AAATA AAATA AAATA AAATA AAATA AAAT-A AAATA AAATA AAATA AAAT-A
* * * *
370269 AAGATA AGAT- AAAGA AAGTA AAGATA AAATA GTAAGTA AAATA AATATA
1 AA-ATA AAATA AAATA AAATA AA-ATA AAATA --AAATA AAATA AA-ATA
* * * *
370318 AAA-A AAGAAA AAATA AAGA-A AAAGA AGAAAA AAATA TAAATA AAA-C
1 AAATA AA-ATA AAATA AA-ATA AAATA A-AATA AAATA -AAATA AAATA
370364 AAAT- AAATA AAATA ACAATA AAA
1 AAATA AAATA AAATA A-AATA AAA
370387 AAGTAAAAAT
Statistics
Matches: 125, Mismatches: 18, Indels: 37
0.69 0.10 0.21
Matches are distributed among these distances:
4 28 0.22
5 57 0.46
6 34 0.27
7 6 0.05
ACGTcount: A:0.73, C:0.01, G:0.08, T:0.17
Consensus pattern (5 bp):
AAATA
Found at i:370387 original size:38 final size:39
Alignment explanation
Indices: 370305--370398 Score: 95
Period size: 38 Copynumber: 2.4 Consensus size: 39
370295 AAATAGTAAG
* *
370305 TAAAATAAATATAAA-AAAAGAAAAAATAAAGAAAAAGAA
1 TAAAA-AAATATAAATAAAACAAAAAATAAAGAAAAACAA
* *
370344 GAAAAAAATATAAATAAAACAAATAAAT-AA-AATAACAA
1 TAAAAAAATATAAATAAAACAAA-AAATAAAGAAAAACAA
* *
370382 TAAAAAAGTAAAAATAA
1 TAAAAAAATATAAATAA
370399 TATATATATA
Statistics
Matches: 46, Mismatches: 7, Indels: 5
0.79 0.12 0.09
Matches are distributed among these distances:
38 29 0.63
39 13 0.28
40 4 0.09
ACGTcount: A:0.78, C:0.02, G:0.05, T:0.15
Consensus pattern (39 bp):
TAAAAAAATATAAATAAAACAAAAAATAAAGAAAAACAA
Found at i:370420 original size:6 final size:7
Alignment explanation
Indices: 370318--370431 Score: 51
Period size: 7 Copynumber: 16.1 Consensus size: 7
370308 AATAAATATA
*
370318 AAAAAAG
1 AAAAAAT
370325 AAAAAAT
1 AAAAAAT
370332 AAAGAAA-
1 AAA-AAAT
370339 AAGAAGAA-
1 AA-AA-AAT
370347 AAAAATAT
1 AAAAA-AT
*
370355 AAATAA-
1 AAAAAAT
*
370361 AACAAAT
1 AAAAAAT
370368 AAATAAA-
1 AAA-AAAT
*
370375 ATAACAAT
1 A-AAAAAT
370383 AAAAAAGT
1 AAAAAA-T
370391 -AAAAAT
1 AAAAAAT
* *
370397 AATATAT
1 AAAAAAT
* *
370404 -ATATAT
1 AAAAAAT
370410 AAAAAAT
1 AAAAAAT
370417 AAAAAAT
1 AAAAAAT
370424 AAAAAAT
1 AAAAAAT
370431 A
1 A
370432 GTATATATAT
Statistics
Matches: 84, Mismatches: 11, Indels: 24
0.71 0.09 0.20
Matches are distributed among these distances:
6 12 0.14
7 53 0.63
8 19 0.23
ACGTcount: A:0.77, C:0.02, G:0.04, T:0.17
Consensus pattern (7 bp):
AAAAAAT
Found at i:370423 original size:47 final size:43
Alignment explanation
Indices: 370306--370426 Score: 124
Period size: 47 Copynumber: 2.7 Consensus size: 43
370296 AATAGTAAGT
*
370306 AAAATA-AATATAAAAAAAGAAAAAATAAAGAAAAAGAAGAAA
1 AAAATATAATATAAAAAAATAAAAAATAAAGAAAAAGAAGAAA
370348 AAAATATAA-ATAAAACAAATAAATAAAATAACA-ATAAAA-AAGTAAA
1 AAAATATAATATAAAA-AAAT-AA-AAAATAA-AGA-AAAAGAAG-AAA
370394 AATAATATATATATATAAAAAATAAAAAATAAA
1 AA-AATATA-ATATA-AAAAAATAAAAAATAAA
370427 AAATAGTATA
Statistics
Matches: 67, Mismatches: 1, Indels: 18
0.78 0.01 0.21
Matches are distributed among these distances:
42 12 0.18
43 5 0.07
44 2 0.03
45 11 0.16
46 11 0.16
47 13 0.19
48 3 0.04
49 7 0.10
50 3 0.04
ACGTcount: A:0.77, C:0.02, G:0.04, T:0.17
Consensus pattern (43 bp):
AAAATATAATATAAAAAAATAAAAAATAAAGAAAAAGAAGAAA
Found at i:370461 original size:34 final size:34
Alignment explanation
Indices: 370380--370444 Score: 105
Period size: 34 Copynumber: 1.9 Consensus size: 34
370370 ATAAAATAAC
370380 AATAAAAAAGT-AAAAATAATATATATATATAAAA
1 AATAAAAAA-TAAAAAATAATATATATATATAAAA
*
370414 AATAAAAAATAAAAAATAGTATATATATATA
1 AATAAAAAATAAAAAATAATATATATATATA
370445 TATATAAATT
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
33 1 0.03
34 28 0.97
ACGTcount: A:0.69, C:0.00, G:0.03, T:0.28
Consensus pattern (34 bp):
AATAAAAAATAAAAAATAATATATATATATAAAA
Found at i:370476 original size:8 final size:9
Alignment explanation
Indices: 370350--370499 Score: 50
Period size: 9 Copynumber: 16.8 Consensus size: 9
370340 AGAAGAAAAA
370350 AATATAAAT
1 AATATAAAT
* *
370359 AAAACAAAT
1 AATATAAAT
370368 AA-ATAAAAT
1 AATAT-AAAT
* *
370377 AACAATAAAA
1 AA-TATAAAT
*
370387 AAGTAAAAAT
1 AA-TATAAAT
*
370397 AATATATAT
1 AATATAAAT
370406 -ATATAAA-
1 AATATAAAT
370413 AA-ATAAA-
1 AATATAAAT
*
370420 AA-ATAAAA
1 AATATAAAT
*
370428 AATAGTATAT
1 AATA-TAAAT
*
370438 -ATATATAT
1 AATATAAAT
370446 -ATATAAATT
1 AATATAAA-T
370455 AATA-AAACT
1 AATATAAA-T
*
370464 GATAATAAAAT
1 AAT-AT-AAAT
370475 AATATAAAT
1 AATATAAAT
*
370484 -ATATATAT
1 AATATAAAT
370492 ATATATAA
1 A-ATATAA
370500 TCTAAAAAAA
Statistics
Matches: 108, Mismatches: 19, Indels: 27
0.70 0.12 0.18
Matches are distributed among these distances:
7 12 0.11
8 28 0.26
9 35 0.32
10 25 0.23
11 5 0.05
12 3 0.03
ACGTcount: A:0.67, C:0.02, G:0.02, T:0.29
Consensus pattern (9 bp):
AATATAAAT
Found at i:373573 original size:10 final size:10
Alignment explanation
Indices: 373558--373582 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
373548 ATGAAATGTC
373558 CTAAATGCAA
1 CTAAATGCAA
373568 CTAAATGCAA
1 CTAAATGCAA
373578 CTAAA
1 CTAAA
373583 ATGTTATGAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.52, C:0.20, G:0.08, T:0.20
Consensus pattern (10 bp):
CTAAATGCAA
Done.