Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008670.1 Hibiscus syriacus cultivar Beakdansim tig00111678_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: 969061
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
File 3 of 5
Found at i:481473 original size:20 final size:20
Alignment explanation
Indices: 481448--481495 Score: 96
Period size: 20 Copynumber: 2.4 Consensus size: 20
481438 CTGATAGGTT
481448 TGGGCTTGGTCTCTTGTAAC
1 TGGGCTTGGTCTCTTGTAAC
481468 TGGGCTTGGTCTCTTGTAAC
1 TGGGCTTGGTCTCTTGTAAC
481488 TGGGCTTG
1 TGGGCTTG
481496 TCTGGGTTGG
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:0.08, C:0.19, G:0.33, T:0.40
Consensus pattern (20 bp):
TGGGCTTGGTCTCTTGTAAC
Found at i:481533 original size:3 final size:3
Alignment explanation
Indices: 481525--481602 Score: 115
Period size: 3 Copynumber: 25.7 Consensus size: 3
481515 GGCCTGTTTG
481525 TAA TAA TAA TAA TAA TAAA TAA -AA TAA TAA TAA TAA TAA TAA TATA
1 TAA TAA TAA TAA TAA T-AA TAA TAA TAA TAA TAA TAA TAA TAA TA-A
481571 TAA -AA TAA TAA TAA TAA TAAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA T-AA TAA TAA TAA TA
481603 GAAAATGGAG
Statistics
Matches: 70, Mismatches: 0, Indels: 10
0.88 0.00 0.12
Matches are distributed among these distances:
2 4 0.06
3 57 0.81
4 9 0.13
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
TAA
Found at i:481563 original size:27 final size:27
Alignment explanation
Indices: 481525--481597 Score: 128
Period size: 27 Copynumber: 2.7 Consensus size: 27
481515 GGCCTGTTTG
481525 TAATAATAATAATAATAAATAAAATAA
1 TAATAATAATAATAATAAATAAAATAA
*
481552 TAATAATAATAATAATATATAAAATAA
1 TAATAATAATAATAATAAATAAAATAA
481579 TAATAATAATAAATAATAA
1 TAATAATAAT-AATAATAA
481598 TAATAGAAAA
Statistics
Matches: 43, Mismatches: 2, Indels: 1
0.93 0.04 0.02
Matches are distributed among these distances:
27 36 0.84
28 7 0.16
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (27 bp):
TAATAATAATAATAATAAATAAAATAA
Found at i:484234 original size:12 final size:12
Alignment explanation
Indices: 484193--484269 Score: 72
Period size: 12 Copynumber: 6.5 Consensus size: 12
484183 ACTCAAACGT
*
484193 TATTATATTATA
1 TATTATATAATA
* *
484205 TAATATATATTGA
1 TATTATATAAT-A
484218 TATTATA-AATCA
1 TATTATATAAT-A
484230 TATTATATAATA
1 TATTATATAATA
484242 TATTCATAT-ATA
1 TATT-ATATAATA
484254 TA-TATATAATA
1 TATTATATAATA
484265 T-TTAT
1 TATTAT
484270 TTACATTCTT
Statistics
Matches: 54, Mismatches: 6, Indels: 11
0.76 0.08 0.15
Matches are distributed among these distances:
10 4 0.07
11 8 0.15
12 28 0.52
13 14 0.26
ACGTcount: A:0.45, C:0.03, G:0.01, T:0.51
Consensus pattern (12 bp):
TATTATATAATA
Found at i:485463 original size:2 final size:2
Alignment explanation
Indices: 485456--485495 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
485446 TTATCATTAT
485456 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
485496 ATTATATTTT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:485637 original size:15 final size:15
Alignment explanation
Indices: 485598--485718 Score: 51
Period size: 15 Copynumber: 8.1 Consensus size: 15
485588 ATTATATATA
485598 TTTAGTTATATTTT-T
1 TTTA-TTATATTTTAT
* *
485613 TTCA-TGTATTTTAT
1 TTTATTATATTTTAT
485627 TTTATTATATTTT-T
1 TTTATTATATTTTAT
** *
485641 CCTA-TGTATTTT-T
1 TTTATTATATTTTAT
*
485654 TTTATTATA-TATATT
1 TTTATTATATTTTA-T
485669 TTTACTTATTATTTTAT
1 TTTA-TTA-TATTTTAT
* *
485686 TATT-CTATATTTGAT
1 T-TTATTATATTTTAT
485701 TATTA-TATATATTTAT
1 T-TTATTATAT-TTTAT
485717 TT
1 TT
485719 GTTTTTTTAT
Statistics
Matches: 80, Mismatches: 15, Indels: 22
0.68 0.13 0.19
Matches are distributed among these distances:
13 19 0.24
14 10 0.12
15 32 0.40
16 10 0.12
17 4 0.05
18 5 0.06
ACGTcount: A:0.25, C:0.04, G:0.03, T:0.68
Consensus pattern (15 bp):
TTTATTATATTTTAT
Found at i:485656 original size:27 final size:28
Alignment explanation
Indices: 485581--485663 Score: 93
Period size: 28 Copynumber: 3.0 Consensus size: 28
485571 TTTATTGTTA
*
485581 TTTTCTCAT-TA-TATATATTTAGTTATAT
1 TTTTCTCATGTATTTTAT-TTTA-TTATAT
*
485609 TTTTTTCATGTATTTTATTTTATTATAT
1 TTTTCTCATGTATTTTATTTTATTATAT
485637 TTTTC-CTATGTATTTT-TTTTATTATAT
1 TTTTCTC-ATGTATTTTATTTTATTATAT
485664 ATATTTTTAC
Statistics
Matches: 49, Mismatches: 3, Indels: 7
0.83 0.05 0.12
Matches are distributed among these distances:
27 12 0.24
28 27 0.55
29 6 0.12
30 4 0.08
ACGTcount: A:0.23, C:0.06, G:0.04, T:0.67
Consensus pattern (28 bp):
TTTTCTCATGTATTTTATTTTATTATAT
Found at i:485695 original size:30 final size:30
Alignment explanation
Indices: 485604--485695 Score: 95
Period size: 30 Copynumber: 3.2 Consensus size: 30
485594 TATATTTAGT
*
485604 TATAT-TTTTTTC-ATGTATTTTATT-TTA
1 TATATATTTTTCCTATGTATTTTATTATTA
*
485631 T-TATATTTTTCCTATGTATTTTTTTTATTA
1 TATATATTTTTCCTATGTA-TTTTATTATTA
* *
485661 TATATATTTTTACTTAT-TATTTTATTATTC
1 TATATATTTTT-CCTATGTATTTTATTATTA
485691 TATAT
1 TATAT
485696 TTGATTATTA
Statistics
Matches: 54, Mismatches: 5, Indels: 9
0.79 0.07 0.13
Matches are distributed among these distances:
26 3 0.06
27 7 0.13
28 5 0.09
29 6 0.11
30 18 0.33
31 11 0.20
32 4 0.07
ACGTcount: A:0.24, C:0.05, G:0.02, T:0.68
Consensus pattern (30 bp):
TATATATTTTTCCTATGTATTTTATTATTA
Found at i:485753 original size:21 final size:20
Alignment explanation
Indices: 485728--485770 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 20
485718 TGTTTTTTTA
485728 TTTATT-GTTACTTTCATCTTT
1 TTTATTAGTTA-TTTCA-CTTT
*
485749 TTTATTATTTATTTCACTTT
1 TTTATTAGTTATTTCACTTT
485769 TT
1 TT
485771 GTTATTTATT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
20 6 0.30
21 11 0.55
22 3 0.15
ACGTcount: A:0.16, C:0.12, G:0.02, T:0.70
Consensus pattern (20 bp):
TTTATTAGTTATTTCACTTT
Found at i:485937 original size:15 final size:13
Alignment explanation
Indices: 485910--486011 Score: 57
Period size: 14 Copynumber: 7.5 Consensus size: 13
485900 CCTTGTTTCA
485910 TTTATTTTTTTAT
1 TTTATTTTTTTAT
485923 TTTACTTTTTGTTATT
1 TTTA-TTTTT-TTA-T
* *
485939 TTTGTTATTTGTTTT
1 TTTATT-TTT-TTAT
*
485954 TTTA-TTTTCTAT
1 TTTATTTTTTTAT
*
485966 TTTA--TTTTCAT
1 TTTATTTTTTTAT
*
485977 TCTTATTTCCTTTAT
1 T-TTATTT-TTTTAT
*
485992 TTTATTATTTTTAC
1 TTTATT-TTTTTAT
486006 TTTATT
1 TTTATT
486012 CATTTTCGTT
Statistics
Matches: 69, Mismatches: 11, Indels: 17
0.71 0.11 0.18
Matches are distributed among these distances:
11 6 0.09
12 9 0.13
13 7 0.10
14 22 0.32
15 15 0.22
16 10 0.14
ACGTcount: A:0.15, C:0.07, G:0.03, T:0.75
Consensus pattern (13 bp):
TTTATTTTTTTAT
Found at i:485954 original size:23 final size:22
Alignment explanation
Indices: 485911--485973 Score: 69
Period size: 20 Copynumber: 2.9 Consensus size: 22
485901 CTTGTTTCAT
485911 TTATTTTTTTATTTTACTTTTTG
1 TTATTTTTTTATTTTA-TTTTTG
*
485934 TTATTTTTGTTA-TTTGTTTTT-
1 TTATTTTT-TTATTTTATTTTTG
*
485955 TTA-TTTTCTATTTTATTTT
1 TTATTTTTTTATTTTATTTT
485974 CATTCTTATT
Statistics
Matches: 35, Mismatches: 3, Indels: 7
0.78 0.07 0.16
Matches are distributed among these distances:
19 2 0.06
20 11 0.31
21 3 0.09
22 5 0.14
23 11 0.31
24 3 0.09
ACGTcount: A:0.13, C:0.03, G:0.05, T:0.79
Consensus pattern (22 bp):
TTATTTTTTTATTTTATTTTTG
Found at i:485983 original size:36 final size:36
Alignment explanation
Indices: 485909--485984 Score: 84
Period size: 36 Copynumber: 2.1 Consensus size: 36
485899 TCCTTGTTTC
* * *
485909 ATTTATTTTTTTATTTTACTTTTTGTTATTTTTGTT
1 ATTTATTTTTTTATTTTACTTTTTATTATTATTCTT
*
485945 ATTTGTTTTTTTATTTT-CTATTTTATT-TTCATTCTT
1 ATTTATTTTTTTATTTTACT-TTTTATTATT-ATTCTT
485981 ATTT
1 ATTT
485985 CCTTTATTTT
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
35 4 0.12
36 30 0.88
ACGTcount: A:0.14, C:0.05, G:0.04, T:0.76
Consensus pattern (36 bp):
ATTTATTTTTTTATTTTACTTTTTATTATTATTCTT
Found at i:489756 original size:21 final size:21
Alignment explanation
Indices: 489730--489769 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
489720 GCGAAAAGGA
*
489730 TGGAAGATAAGATTAAGATAC
1 TGGAAGATAAGATGAAGATAC
*
489751 TGGAAGATCAGATGAAGAT
1 TGGAAGATAAGATGAAGAT
489770 GATCAAAGGG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.45, C:0.05, G:0.28, T:0.23
Consensus pattern (21 bp):
TGGAAGATAAGATGAAGATAC
Found at i:497396 original size:110 final size:110
Alignment explanation
Indices: 497190--497535 Score: 423
Period size: 110 Copynumber: 3.2 Consensus size: 110
497180 GGTTTTTGCT
* * *
497190 AGAGCCAATTTCAACTTCACAATGAAGGATATTGGAATCAAGACAACAAAAGCTCAACTTCACAG
1 AGAGCCAATTTCAACTTCACAACGAAGGATATTGGAATCGAGACAACACAAGCTCAACTTCACAG
* *
497255 TGAAGGGGCGACTGACTGTTAATAAAAAACTTTTCAGTTTCATTC
66 TGAAGGGGCGACTGACTGTCAACAAAAAACTTTTCAGTTTCATTC
* * * *
497300 AGAGTCAATTTCAACTTCACAGCGAAGGATATTAGACTCGAGACAACACAAGCTCAACTTCACAG
1 AGAGCCAATTTCAACTTCACAACGAAGGATATTGGAATCGAGACAACACAAGCTCAACTTCACAG
* * *
497365 TGAAGGGGCGACTGACTGTCAACAAACAACTTTTCAATTTCATTT
66 TGAAGGGGCGACTGACTGTCAACAAAAAACTTTTCAGTTTCATTC
** * * * * *
497410 AGAGTTAATTTCAACTTCATAACAAAGGATATTGGAATCGAGATAACACAAGCTCAACTTTACAA
1 AGAGCCAATTTCAACTTCACAACGAAGGATATTGGAATCGAGACAACACAAGCTCAACTTCACAG
* ** * * *
497475 CGAAGGGGCGGTTGGCTGTCAACAAATAA-TTTCCCAG--T--TTC
66 TGAAGGGGCGACTGACTGTCAACAAAAAACTTT-TCAGTTTCATTC
497516 AGAGCCAATTTCAACTTCAC
1 AGAGCCAATTTCAACTTCAC
497536 GGCGGAGGAT
Statistics
Matches: 203, Mismatches: 32, Indels: 6
0.84 0.13 0.02
Matches are distributed among these distances:
106 19 0.09
108 1 0.00
109 3 0.01
110 180 0.89
ACGTcount: A:0.36, C:0.21, G:0.17, T:0.25
Consensus pattern (110 bp):
AGAGCCAATTTCAACTTCACAACGAAGGATATTGGAATCGAGACAACACAAGCTCAACTTCACAG
TGAAGGGGCGACTGACTGTCAACAAAAAACTTTTCAGTTTCATTC
Found at i:497955 original size:254 final size:254
Alignment explanation
Indices: 497502--498161 Score: 909
Period size: 253 Copynumber: 2.6 Consensus size: 254
497492 GTCAACAAAT
* * * *
497502 AATTTCCCAGTTTCAGAGCCAATTTCAACTTCACGGCGGAGGATATTTGACTCGAAACAATA-CA
1 AATTT-CCAGTTTCAGAGTCAATTTCAACTTCACGGCGAAGGATATTGGCCTCGAAACAA-AGCA
* * *
497566 ACCTAC-TTGGATTTCAACTTCACGACGAAGGATATCCAATT--TCAGGCTCAACTTAACGAAGA
64 ACTTACATTGGATTTCAACTTCACGATGAAGGATATCCAATTCCTCAGGCTCAACTTCACGAAGA
**** * * * * *
497628 ATGGGCCACCCGCGGTTTTAACTTCACGACAAAGGGAATCGTGTACACAAGCAGCATCCATCTCT
129 ATGGGCCATATACGATTTCAACTTCACGACAAAGGGAATCATGCACACAAGCAACATCCATCTCT
* * * * *
497693 ATATTGGATTTCAACTTCACGACAAAGGATATCCAACTCATAGAAGGAGTGTCTGCCAATA
194 AGATTGGATTTCAACTTCACGACAAAAGATATCCAACTCAAAGAAGGAGTGTATGCCAACA
*
497754 AACTTTCCAGTTTCAGAGTCAATTTCAACTTAACGGCGAAGGATATTGGCCTCGAAACAAAGCAA
1 AA-TTTCCAGTTTCAGAGTCAATTTCAACTTCACGGCGAAGGATATTGGCCTCGAAACAAAGCAA
* * *
497819 CTTACATTGGATTTCAACTTCACGATGAAGGATTTCCAATTCCTC-GGCTCAACTTCATGACGAA
65 CTTACATTGGATTTCAACTTCACGATGAAGGATATCCAATTCCTCAGGCTCAACTTCACGAAGAA
* * * *
497883 GGGGCCATATATGATTCCAACTTCACGACGAAGGGAATCATGCACACAAGCAACATCCATCTCTA
130 TGGGCCATATACGATTTCAACTTCACGACAAAGGGAATCATGCACACAAGCAACATCCATCTCTA
* *
497948 GATTGGATTTCAACTTCACGACAAAAGATATCCAACTCAAAGAATGAGTGTATGTCAACA
195 GATTGGATTTCAACTTCACGACAAAAGATATCCAACTCAAAGAAGGAGTGTATGCCAACA
* * **
498008 AATTTTCAGTTTCAGAGTCAATTTCAACTTCACAGCGAAGGATATTGGCCTCGAAACAGCGCAAC
1 AATTTCCAGTTTCAGAGTCAATTTCAACTTCACGGCGAAGGATATTGGCCTCGAAACAAAGCAAC
*
498073 TTACATTGGATTTCAACTTCACGATGAAGGACATCCAATTCC-CAGGCTCAACTTCACGAAGAAT
66 TTACATTGGATTTCAACTTCACGATGAAGGATATCCAATTCCTCAGGCTCAACTTCACGAAGAAT
* *
498137 GGGCCCTATACGATTTCAACCTCAC
131 GGGCCATATACGATTTCAACTTCAC
498162 AAACAGATTG
Statistics
Matches: 357, Mismatches: 45, Indels: 11
0.86 0.11 0.03
Matches are distributed among these distances:
251 1 0.00
252 59 0.17
253 172 0.48
254 123 0.34
255 2 0.01
ACGTcount: A:0.33, C:0.24, G:0.18, T:0.25
Consensus pattern (254 bp):
AATTTCCAGTTTCAGAGTCAATTTCAACTTCACGGCGAAGGATATTGGCCTCGAAACAAAGCAAC
TTACATTGGATTTCAACTTCACGATGAAGGATATCCAATTCCTCAGGCTCAACTTCACGAAGAAT
GGGCCATATACGATTTCAACTTCACGACAAAGGGAATCATGCACACAAGCAACATCCATCTCTAG
ATTGGATTTCAACTTCACGACAAAAGATATCCAACTCAAAGAAGGAGTGTATGCCAACA
Found at i:498556 original size:2 final size:2
Alignment explanation
Indices: 498540--498624 Score: 108
Period size: 2 Copynumber: 44.5 Consensus size: 2
498530 CAAACGTTAT
* *
498540 TA TA T- TA TA TA -A TA TA TA TT TA TA T- TA TA AA TCA TA T- TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T-A TA TA TA
498579 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
498621 -A TA T
1 TA TA T
498625 TTATTTACAT
Statistics
Matches: 73, Mismatches: 4, Indels: 12
0.82 0.04 0.13
Matches are distributed among these distances:
1 5 0.07
2 66 0.90
3 2 0.03
ACGTcount: A:0.48, C:0.01, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:499989 original size:28 final size:27
Alignment explanation
Indices: 499937--500011 Score: 66
Period size: 28 Copynumber: 2.7 Consensus size: 27
499927 TATATTATAT
*
499937 TATATTTTTATTATTATTTTCTCATTA
1 TATATATTTATTATTATTTTCTCATTA
*
499964 TATATATTTAGTTA-TACTTTTTTCATGTA
1 TATATATTTA-TTATTA-TTTTCTCAT-TA
*
499993 T-TTTATTTTATTA-TATTTT
1 TATATA-TTTATTATTATTTT
500012 TCCTATGTAC
Statistics
Matches: 41, Mismatches: 3, Indels: 8
0.79 0.06 0.15
Matches are distributed among these distances:
27 15 0.37
28 19 0.46
29 7 0.17
ACGTcount: A:0.25, C:0.05, G:0.03, T:0.67
Consensus pattern (27 bp):
TATATATTTATTATTATTTTCTCATTA
Found at i:499995 original size:40 final size:40
Alignment explanation
Indices: 499921--499996 Score: 95
Period size: 40 Copynumber: 1.9 Consensus size: 40
499911 TTCATTTGTG
*
499921 TTATATTATATTATATTATATTTTTATTATTATTTTCTCA
1 TTATATTATATTATATTATATTTTTATCATTATTTTCTCA
499961 TTATA-TATATT-TAGTTATACTTTTT-TCATGTATTTT
1 TTATATTATATTATA-TTATA-TTTTTATCAT-TATTTT
499997 ATTTTATTAT
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
38 2 0.06
39 14 0.44
40 16 0.50
ACGTcount: A:0.28, C:0.05, G:0.03, T:0.64
Consensus pattern (40 bp):
TTATATTATATTATATTATATTTTTATCATTATTTTCTCA
Found at i:500019 original size:28 final size:26
Alignment explanation
Indices: 499970--500035 Score: 69
Period size: 27 Copynumber: 2.4 Consensus size: 26
499960 ATTATATATA
* **
499970 TTTAGTTATACTTTTTTCATGTATTTTAT
1 TTTA-TTATA-TTTTTCCATGTACATT-T
499999 TTTATTATATTTTTCCTATGTACATTT
1 TTTATTATATTTTTCC-ATGTACATTT
500026 TTTATTATAT
1 TTTATTATAT
500036 ATATTTTTAC
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
27 17 0.52
28 12 0.36
29 4 0.12
ACGTcount: A:0.23, C:0.08, G:0.05, T:0.65
Consensus pattern (26 bp):
TTTATTATATTTTTCCATGTACATTT
Found at i:500042 original size:15 final size:15
Alignment explanation
Indices: 500024--500086 Score: 67
Period size: 15 Copynumber: 4.2 Consensus size: 15
500014 CTATGTACAT
500024 TTTTTATTATATATA
1 TTTTTATTATATATA
*
500039 TTTTTACTTAT-TATT
1 TTTTTA-TTATATATA
*
500054 TTTTTATTCTATAT-
1 TTTTTATTATATATA
*
500068 TTGATTATTATATATA
1 TT-TTTATTATATATA
500084 TTT
1 TTT
500087 ATTTTTTTTA
Statistics
Matches: 39, Mismatches: 5, Indels: 8
0.75 0.10 0.15
Matches are distributed among these distances:
14 5 0.13
15 28 0.72
16 6 0.15
ACGTcount: A:0.27, C:0.03, G:0.02, T:0.68
Consensus pattern (15 bp):
TTTTTATTATATATA
Found at i:500155 original size:67 final size:69
Alignment explanation
Indices: 500023--500164 Score: 152
Period size: 65 Copynumber: 2.1 Consensus size: 69
500013 CCTATGTACA
* * * *
500023 TTTTTTATTATATATATTTTTACTTATTATTTTTTTATTCTATATTTGATTATTATATATATTTA
1 TTTTTTATTATATATATTGTTACTTATCATTTTTTTATTATATATTTCATTATTATATATATTTA
500088 T-T-
66 TCTC
* *
500090 TTTTTTATTAT-T-TATTGTTACTT-TCATCTTTTTTATTATTTATTTCACTT-TTAGTTATTTA
1 TTTTTTATTATATATATTGTTACTTATCAT-TTTTTTATTATATATTTCA-TTATTA--TATATA
500151 TTTATCTC
62 TTTATCTC
500159 TTTTTT
1 TTTTTT
500165 TTACATTTCA
Statistics
Matches: 63, Mismatches: 6, Indels: 10
0.80 0.08 0.13
Matches are distributed among these distances:
64 3 0.05
65 29 0.46
66 3 0.05
67 21 0.33
68 1 0.02
69 6 0.10
ACGTcount: A:0.22, C:0.06, G:0.02, T:0.70
Consensus pattern (69 bp):
TTTTTTATTATATATATTGTTACTTATCATTTTTTTATTATATATTTCATTATTATATATATTTA
TCTC
Found at i:500164 original size:23 final size:20
Alignment explanation
Indices: 500111--500167 Score: 51
Period size: 23 Copynumber: 2.6 Consensus size: 20
500101 TTATTGTTAC
500111 TTTCATCTTTTTTATTATTTA
1 TTTC-TCTTTTTTATTATTTA
*
500132 TTTCACTTTTAGTTATTTATTTA
1 TTTCTCTTTT--TTA-TTATTTA
* *
500155 TCTCTTTTTTTTA
1 TTTCTCTTTTTTA
500168 CATTTCATTT
Statistics
Matches: 29, Mismatches: 4, Indels: 6
0.74 0.10 0.15
Matches are distributed among these distances:
20 5 0.17
21 7 0.24
22 3 0.10
23 14 0.48
ACGTcount: A:0.18, C:0.11, G:0.02, T:0.70
Consensus pattern (20 bp):
TTTCTCTTTTTTATTATTTA
Found at i:500239 original size:34 final size:34
Alignment explanation
Indices: 500171--500260 Score: 85
Period size: 34 Copynumber: 2.5 Consensus size: 34
500161 TTTTTTACAT
*
500171 TTCATTTTTTATGTATATTTATTTCCTTTATTTA
1 TTCATTTTTTATGTATATTTATTACCTTTATTTA
* *
500205 TTCATTTTTT-TGGTAT-TTTATTACTTATTCTTTATA
1 TTCATTTTTTAT-GTATATTTATTACCT-TT-ATT-TA
500241 TTGCATTGTTTTATGTATAT
1 TT-CATT-TTTTATGTATAT
500261 GATACCTTTA
Statistics
Matches: 45, Mismatches: 3, Indels: 11
0.76 0.05 0.19
Matches are distributed among these distances:
33 9 0.20
34 16 0.36
35 2 0.04
36 4 0.09
37 4 0.09
38 8 0.18
39 2 0.04
ACGTcount: A:0.20, C:0.08, G:0.07, T:0.66
Consensus pattern (34 bp):
TTCATTTTTTATGTATATTTATTACCTTTATTTA
Found at i:500346 original size:19 final size:20
Alignment explanation
Indices: 500303--500340 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
500293 TTTATTTTAC
*
500303 TTTTTGTTATTTTTTATTTG
1 TTTTTGTTATTTTCTATTTG
500323 TTTTT-TTATTTTCTATTT
1 TTTTTGTTATTTTCTATTT
500341 TATTTTCATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 12 0.71
20 5 0.29
ACGTcount: A:0.11, C:0.03, G:0.05, T:0.82
Consensus pattern (20 bp):
TTTTTGTTATTTTCTATTTG
Found at i:500922 original size:24 final size:24
Alignment explanation
Indices: 500888--500947 Score: 111
Period size: 24 Copynumber: 2.5 Consensus size: 24
500878 ATGCCTGTTA
*
500888 TTATTCTAGGCAATCAATCTGCTT
1 TTATTCAAGGCAATCAATCTGCTT
500912 TTATTCAAGGCAATCAATCTGCTT
1 TTATTCAAGGCAATCAATCTGCTT
500936 TTATTCAAGGCA
1 TTATTCAAGGCA
500948 GTAGTATTTC
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 35 1.00
ACGTcount: A:0.28, C:0.20, G:0.13, T:0.38
Consensus pattern (24 bp):
TTATTCAAGGCAATCAATCTGCTT
Found at i:510021 original size:3 final size:3
Alignment explanation
Indices: 510013--510079 Score: 104
Period size: 3 Copynumber: 23.0 Consensus size: 3
510003 AATTTTATTT
510013 TAA TAA TAA -AA TAA TAA TAA TAA TAA -AA TAA TAA TAA -AA GTAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA -TAA
510056 TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA
510080 ATTAAGACAT
Statistics
Matches: 60, Mismatches: 0, Indels: 8
0.88 0.00 0.12
Matches are distributed among these distances:
2 6 0.10
3 52 0.87
4 2 0.03
ACGTcount: A:0.69, C:0.00, G:0.01, T:0.30
Consensus pattern (3 bp):
TAA
Found at i:515123 original size:57 final size:57
Alignment explanation
Indices: 515035--515149 Score: 221
Period size: 57 Copynumber: 2.0 Consensus size: 57
515025 ATGGAACCTT
515035 CAGCACCTCTGCAGCAAAACCAAGAATCTGATCCTAGTCCAAGATCTTGTGAAGATC
1 CAGCACCTCTGCAGCAAAACCAAGAATCTGATCCTAGTCCAAGATCTTGTGAAGATC
*
515092 CAGCACCTCTGCAGCAAAACCAAGAATCTGATCCTGGTCCAAGATCTTGTGAAGATC
1 CAGCACCTCTGCAGCAAAACCAAGAATCTGATCCTAGTCCAAGATCTTGTGAAGATC
515149 C
1 C
515150 TTTAGGTAAT
Statistics
Matches: 57, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
57 57 1.00
ACGTcount: A:0.32, C:0.29, G:0.18, T:0.21
Consensus pattern (57 bp):
CAGCACCTCTGCAGCAAAACCAAGAATCTGATCCTAGTCCAAGATCTTGTGAAGATC
Found at i:531888 original size:2 final size:2
Alignment explanation
Indices: 531821--531871 Score: 102
Period size: 2 Copynumber: 25.5 Consensus size: 2
531811 GTATGTATTA
531821 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
531863 AT AT AT AT A
1 AT AT AT AT A
531872 CACACACACA
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:533358 original size:2 final size:2
Alignment explanation
Indices: 533351--533377 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
533341 CATGAATTGA
533351 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
533378 AGTTAAGCTG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:540888 original size:28 final size:28
Alignment explanation
Indices: 540848--540902 Score: 101
Period size: 28 Copynumber: 2.0 Consensus size: 28
540838 TAACGTCAGC
540848 ACACATATGTTAACAACATAAAATTTTA
1 ACACATATGTTAACAACATAAAATTTTA
*
540876 ACACATATGTTAATAACATAAAATTTT
1 ACACATATGTTAACAACATAAAATTTT
540903 TAAAAAGGAT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.49, C:0.13, G:0.04, T:0.35
Consensus pattern (28 bp):
ACACATATGTTAACAACATAAAATTTTA
Found at i:540914 original size:29 final size:28
Alignment explanation
Indices: 540854--540929 Score: 77
Period size: 28 Copynumber: 2.7 Consensus size: 28
540844 CAGCACACAT
* *
540854 ATGTTAACAACATAAAATTTTAACACAT
1 ATGTTAACAACATAAAATTTTAACAAAG
*
540882 ATGTTAATAACATAAAATTTTTAA-AAAGG
1 ATGTTAACAACATAAAA-TTTTAACAAA-G
540911 ATGTGT-ACAA-ATAAAATTT
1 ATGT-TAACAACATAAAATTT
540930 AGGGTGGATA
Statistics
Matches: 41, Mismatches: 4, Indels: 7
0.79 0.08 0.13
Matches are distributed among these distances:
27 3 0.07
28 24 0.59
29 13 0.32
30 1 0.02
ACGTcount: A:0.50, C:0.08, G:0.08, T:0.34
Consensus pattern (28 bp):
ATGTTAACAACATAAAATTTTAACAAAG
Found at i:541722 original size:17 final size:17
Alignment explanation
Indices: 541702--541740 Score: 78
Period size: 17 Copynumber: 2.3 Consensus size: 17
541692 TTTTCAAGTT
541702 TTGCTAAATTTCCAGTC
1 TTGCTAAATTTCCAGTC
541719 TTGCTAAATTTCCAGTC
1 TTGCTAAATTTCCAGTC
541736 TTGCT
1 TTGCT
541741 GGTTTTGTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.21, C:0.23, G:0.13, T:0.44
Consensus pattern (17 bp):
TTGCTAAATTTCCAGTC
Found at i:543304 original size:3 final size:3
Alignment explanation
Indices: 543296--543327 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
543286 TGAGGCAATG
543296 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
543328 GCAAGGAACT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:543603 original size:24 final size:25
Alignment explanation
Indices: 543565--543614 Score: 84
Period size: 24 Copynumber: 2.0 Consensus size: 25
543555 CGAAGTGCCG
*
543565 CGTAGAAATTTGTCCCGAATGACCA
1 CGTAGAAATTTGTCCCGAAGGACCA
543590 CGTAG-AATTTGTCCCGAAGGACCA
1 CGTAGAAATTTGTCCCGAAGGACCA
543614 C
1 C
543615 ATATAAACTC
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
24 19 0.79
25 5 0.21
ACGTcount: A:0.30, C:0.26, G:0.22, T:0.22
Consensus pattern (25 bp):
CGTAGAAATTTGTCCCGAAGGACCA
Found at i:543850 original size:30 final size:31
Alignment explanation
Indices: 543801--543871 Score: 108
Period size: 31 Copynumber: 2.3 Consensus size: 31
543791 ACATAATTTA
* *
543801 TATCGCATAGACATATCA-TTTCCATACCTT
1 TATCACATAAACATATCATTTTCCATACCTT
*
543831 TATCACATAAACATTTCATTTTCCATACCTT
1 TATCACATAAACATATCATTTTCCATACCTT
543862 TATCACATAA
1 TATCACATAA
543872 TTCATATAAT
Statistics
Matches: 37, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
30 15 0.41
31 22 0.59
ACGTcount: A:0.34, C:0.25, G:0.03, T:0.38
Consensus pattern (31 bp):
TATCACATAAACATATCATTTTCCATACCTT
Found at i:544223 original size:24 final size:22
Alignment explanation
Indices: 544173--544230 Score: 68
Period size: 20 Copynumber: 2.6 Consensus size: 22
544163 AATAAGGGTA
544173 TGCATCGATGCACTCTACAGTG
1 TGCATCGATGCACTCTACAGTG
544195 T--ATCGATGCACTCCTTA-ATGTG
1 TGCATCGATGCACT-C-TACA-GTG
544217 TGCATCGATGCACT
1 TGCATCGATGCACT
544231 ACCTGTGCAT
Statistics
Matches: 31, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
20 11 0.35
21 2 0.06
22 7 0.23
24 11 0.35
ACGTcount: A:0.22, C:0.26, G:0.21, T:0.31
Consensus pattern (22 bp):
TGCATCGATGCACTCTACAGTG
Found at i:544322 original size:63 final size:63
Alignment explanation
Indices: 544211--544374 Score: 186
Period size: 63 Copynumber: 2.6 Consensus size: 63
544201 TGCACTCCTT
* * **
544211 AATGTGTGCATCGATGCACTACCTGTGCATCGGTACACAAATGTCATTCGACGTTTGT-ATTTA
1 AATGAGTGCATCGATGCACTACCTGTGCATCGATACACAAATAACATTCGACGTTT-TCATTTA
* * ** * *
544274 AGTGGGTGCATCGATGCACTACCTGTGCATCGATACACGGATAACATTCGATGTTTTCTTTTA
1 AATGAGTGCATCGATGCACTACCTGTGCATCGATACACAAATAACATTCGACGTTTTCATTTA
* * * *
544337 AATTAATGCATCGATGCACTTCATGTGCATCGATACAC
1 AATGAGTGCATCGATGCACTACCTGTGCATCGATACAC
544375 CTAGCACTAA
Statistics
Matches: 85, Mismatches: 15, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
62 1 0.01
63 84 0.99
ACGTcount: A:0.26, C:0.21, G:0.20, T:0.32
Consensus pattern (63 bp):
AATGAGTGCATCGATGCACTACCTGTGCATCGATACACAAATAACATTCGACGTTTTCATTTA
Found at i:548219 original size:172 final size:172
Alignment explanation
Indices: 547933--548276 Score: 688
Period size: 172 Copynumber: 2.0 Consensus size: 172
547923 TTACTTGTTC
547933 AATTCTTTTCAAACACATTTCATCCTTAATTTGCAATTCTCCTATTTGTTCCAACCATGTTGGTT
1 AATTCTTTTCAAACACATTTCATCCTTAATTTGCAATTCTCCTATTTGTTCCAACCATGTTGGTT
547998 TAAGTTTTAACACTGCACATAGACCACCATCTCCAGTTAAAGATAATCTTGCATCCATAGCTCGT
66 TAAGTTTTAACACTGCACATAGACCACCATCTCCAGTTAAAGATAATCTTGCATCCATAGCTCGT
548063 AAGGCTGCAAACGTCTTTCTACTCAAAGCATCTGCTACCACG
131 AAGGCTGCAAACGTCTTTCTACTCAAAGCATCTGCTACCACG
548105 AATTCTTTTCAAACACATTTCATCCTTAATTTGCAATTCTCCTATTTGTTCCAACCATGTTGGTT
1 AATTCTTTTCAAACACATTTCATCCTTAATTTGCAATTCTCCTATTTGTTCCAACCATGTTGGTT
548170 TAAGTTTTAACACTGCACATAGACCACCATCTCCAGTTAAAGATAATCTTGCATCCATAGCTCGT
66 TAAGTTTTAACACTGCACATAGACCACCATCTCCAGTTAAAGATAATCTTGCATCCATAGCTCGT
548235 AAGGCTGCAAACGTCTTTCTACTCAAAGCATCTGCTACCACG
131 AAGGCTGCAAACGTCTTTCTACTCAAAGCATCTGCTACCACG
548277 TTAGCCTTTC
Statistics
Matches: 172, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
172 172 1.00
ACGTcount: A:0.28, C:0.26, G:0.12, T:0.34
Consensus pattern (172 bp):
AATTCTTTTCAAACACATTTCATCCTTAATTTGCAATTCTCCTATTTGTTCCAACCATGTTGGTT
TAAGTTTTAACACTGCACATAGACCACCATCTCCAGTTAAAGATAATCTTGCATCCATAGCTCGT
AAGGCTGCAAACGTCTTTCTACTCAAAGCATCTGCTACCACG
Found at i:550498 original size:3 final size:3
Alignment explanation
Indices: 550485--550556 Score: 60
Period size: 3 Copynumber: 24.3 Consensus size: 3
550475 TATTTATTAA
* * *
550485 AAT ATAT AAT AAT AAT AATT AA- AAT TAT AAT AAT -TT AAT TAT AAT
1 AAT A-AT AAT AAT AAT AA-T AAT AAT AAT AAT AAT AAT AAT AAT AAT
* *
550530 AAT TAT AAT AAT AAT AAT TAT AA- AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT A
550557 TAAATATTCA
Statistics
Matches: 54, Mismatches: 10, Indels: 10
0.73 0.14 0.14
Matches are distributed among these distances:
2 5 0.09
3 43 0.80
4 6 0.11
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (3 bp):
AAT
Found at i:551157 original size:241 final size:236
Alignment explanation
Indices: 550863--551298 Score: 732
Period size: 241 Copynumber: 1.8 Consensus size: 236
550853 AAAAAAATTA
* *
550863 AACAAGTTCTTCTCATTTTGAACTTCTTCTTCCTTCTTCAATGAGTTCTTCTCATTATGAACTTC
1 AACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAATGAGTTCTTCTCATTATGAACTTC
*
550928 TCTGGAAAAGTTGATGTTGA-TATCTCCTTATGTGATAGAGTCATGCAAAAGGTTGAACAAGCTC
66 TCTGGAAAAGTTGATGTTGACTAT-TCATTATGTGAT--AGTCATG--AAAGGTTGAACAAGCTC
*
550992 TTCTCATTATGAACTCTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTCTATGGAAAAG
126 TTCTCATTATGAACT-TCTTCCTTCTTCAGATGAGTTATTCTCATTATGAACTTCTATGGAAAAG
551057 TTGATGTTGATCTATCTCCTTCTGTGATAGAGTAATACAAAAGGTTG
190 TTGATGTTGATCTATCTCCTTCTGTGATAGAGTAATACAAAAGGTTG
551104 AACAAGCTCTTCTCA-TATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTT
1 AACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCA-ATGAGTTCTTCTCATTATGAACTT
*
551168 CTCTGGAAAAGTTGATGTTGATCTATTCATTCTGTGATAGTCATGAAAGGTTGAACAAGCTCTTC
65 CTCTGGAAAAGTTGATGTTGA-CTATTCATTATGTGATAGTCATGAAAGGTTGAACAAGCTCTTC
*
551233 TCATTATGAACTTCTTCTTTCTTCAGATGAGTTATTCTCATTATGAACTTCTATGGAAAAGTTGA
129 TCATTATGAACTTCTTCCTTCTTCAGATGAGTTATTCTCATTATGAACTTCTATGGAAAAGTTGA
551298 T
194 T
551299 CCATCGAATG
Statistics
Matches: 186, Mismatches: 6, Indels: 10
0.92 0.03 0.05
Matches are distributed among these distances:
237 52 0.28
238 32 0.17
240 30 0.16
241 59 0.32
242 10 0.05
243 3 0.02
ACGTcount: A:0.26, C:0.19, G:0.15, T:0.40
Consensus pattern (236 bp):
AACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAATGAGTTCTTCTCATTATGAACTTC
TCTGGAAAAGTTGATGTTGACTATTCATTATGTGATAGTCATGAAAGGTTGAACAAGCTCTTCTC
ATTATGAACTTCTTCCTTCTTCAGATGAGTTATTCTCATTATGAACTTCTATGGAAAAGTTGATG
TTGATCTATCTCCTTCTGTGATAGAGTAATACAAAAGGTTG
Found at i:551176 original size:122 final size:122
Alignment explanation
Indices: 550863--551298 Score: 682
Period size: 122 Copynumber: 3.7 Consensus size: 122
550853 AAAAAAATTA
* *
550863 AACAAGTTCTTCTCATTTTGAACTTCTTCTTCCTTCTTCA-ATGAGTTCTTCTCATTATGAACTT
1 AACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTT
* *
550927 CTCTGGAAAAGTTGATGTTGA--TATCTCCTTATGTGATAGAGTCATGCAAAAGGTTG
66 CTATGGAAAAGTTGATGTTGATCTATCTCCTTCTGTGATAGAGTCAT-CAAAAGGTTG
550983 AACAAGCTCTTCTCATTATGAAC-TC-TCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTT
1 AACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTT
*
551046 CTATGGAAAAGTTGATGTTGATCTATCTCCTTCTGTGATAGAGTAATACAAAAGGTTG
66 CTATGGAAAAGTTGATGTTGATCTATCTCCTTCTGTGATAGAGTCAT-CAAAAGGTTG
551104 AACAAGCTCTTCTCA-TATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTT
1 AACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTT
* * *
551168 CTCTGGAAAAGTTGATGTTGATCTAT-TCATTCTGTGAT--AGTCAT-GAAAGGTTG
66 CTATGGAAAAGTTGATGTTGATCTATCTCCTTCTGTGATAGAGTCATCAAAAGGTTG
*
551221 AACAAGCTCTTCTCATTATGAACTTCTTC-T--TTCTTCAGATGAGTTATTCTCATTATGAACTT
1 AACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTT
551283 CTATGGAAAAGTTGAT
66 CTATGGAAAAGTTGAT
551299 CCATCGAATG
Statistics
Matches: 298, Mismatches: 12, Indels: 17
0.91 0.04 0.05
Matches are distributed among these distances:
115 46 0.15
117 24 0.08
118 26 0.09
119 51 0.17
120 28 0.09
121 60 0.20
122 63 0.21
ACGTcount: A:0.26, C:0.19, G:0.15, T:0.40
Consensus pattern (122 bp):
AACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTT
CTATGGAAAAGTTGATGTTGATCTATCTCCTTCTGTGATAGAGTCATCAAAAGGTTG
Found at i:551425 original size:112 final size:111
Alignment explanation
Indices: 550863--551539 Score: 569
Period size: 112 Copynumber: 5.9 Consensus size: 111
550853 AAAAAAATTA
* *
550863 AACAAGTTCTTCTCATTTTGAACTTCTTCTTCCTTCTTCA-ATGAGTTCTTCTCATTATGAACTT
1 AACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTT
* ** * *
550927 CTCTGGAAAAGTTGATGTTGATATC-TCCTTATG-TGATAGAGTCATGCAAAAGGTTG
66 CTCTGG--AA----ATGTTGAT-CCAT-CGAATGATG--A-ATTCA-ACAAAAGGTTG
550983 AACAAGCTCTTCTCATTATGAAC-TC-TCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTT
1 AACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTT
* * *** * *
551046 CTATGGAAAAGTTGATGTTGATCTATCTCCTTCTG-TGATAGAGTAATACAAAAGGTTG
66 CTCTGG--AA----ATGTTGATCCA--T-CGAATGATG--A-ATTCA-ACAAAAGGTTG
551104 AACAAGCTCTTCTCA-TATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTT
1 AACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTT
* * * **
551168 CTCTGGAAAAGTTGATGTTGATCTATTC-ATTCTG-TGATAGTC-ATGAAAGGTTG
66 CTCTGG--AA----ATGTTGATCCA-TCGA--ATGATGA-ATTCAACAAAAGGTTG
*
551221 AACAAGCTCTTCTCATTATGAACTTCTTC-T--TTCTTCAGATGAGTTATTCTCATTATGAACTT
1 AACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTT
* *
551283 CTATGGAAAAGTTGATCCATCGAATGATGAATTCAAACAAAAGGTTTG
66 CTCTGGAAATGTTGATCCATCGAATGATGAATTC-AACAAAAGG-TTG
** *
551331 AACAAATTCTT-TCATTATGAATTTCTTCTTCC-TCTTCAGATGAGTTCTTCTCATTATGAACTC
1 AACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACT-
* * * *
551394 TCTCTGGAAATGCTGATCCATC-AAGTGATGAATTTGAGCAAAAGGTTA
65 TCTCTGGAAATGTTGATCCATCGAA-TGATGAA-TTCAACAAAAGGTTG
* * *
551442 AACAAGTTCTTCACATTATGAACTTCTTTTTCCTTCTTCAGATGAG-TCTTCTCATTATGAACTT
1 AACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTT
* *
551506 TTCTGGAAATGTTGATCCATCGAATGATGGATTC
66 CTCTGGAAATGTTGATCCATCGAATGATGAATTC
551540 GAATCTTTGC
Statistics
Matches: 493, Mismatches: 41, Indels: 56
0.84 0.07 0.09
Matches are distributed among these distances:
107 5 0.01
108 5 0.01
109 32 0.06
110 15 0.03
111 69 0.14
112 71 0.14
113 16 0.03
115 36 0.07
117 25 0.05
118 26 0.05
119 51 0.10
120 29 0.06
121 51 0.10
122 62 0.13
ACGTcount: A:0.27, C:0.19, G:0.15, T:0.39
Consensus pattern (111 bp):
AACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTT
CTCTGGAAATGTTGATCCATCGAATGATGAATTCAACAAAAGGTTG
Found at i:552707 original size:18 final size:18
Alignment explanation
Indices: 552684--552718 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
552674 TATATGAAAC
552684 AAATTGAATTTCAAAAAT
1 AAATTGAATTTCAAAAAT
552702 AAATTGAATTTCAAAAA
1 AAATTGAATTTCAAAAA
552719 GATAAACTTG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.57, C:0.06, G:0.06, T:0.31
Consensus pattern (18 bp):
AAATTGAATTTCAAAAAT
Found at i:553085 original size:27 final size:26
Alignment explanation
Indices: 553055--553130 Score: 80
Period size: 28 Copynumber: 2.8 Consensus size: 26
553045 CTGACCCTCC
553055 TTTTCTATTTTTTCTTTTTTCAACATT
1 TTTTCT-TTTTTTCTTTTTTCAACATT
* **
553082 TTTTCTCTTTCTTTTTTTTTTCTTCATT
1 TTTTCT-TTT-TTTCTTTTTTCAACATT
*
553110 TTTTCTTTTCTTCATTTTTTC
1 TTTTCTTTTTTTC-TTTTTTC
553131 TTCAAGCATA
Statistics
Matches: 41, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
26 2 0.05
27 19 0.46
28 20 0.49
ACGTcount: A:0.08, C:0.17, G:0.00, T:0.75
Consensus pattern (26 bp):
TTTTCTTTTTTTCTTTTTTCAACATT
Found at i:553112 original size:16 final size:16
Alignment explanation
Indices: 553093--553132 Score: 73
Period size: 16 Copynumber: 2.6 Consensus size: 16
553083 TTTCTCTTTC
553093 TTTTTT-TTTTCTTCA
1 TTTTTTCTTTTCTTCA
553108 TTTTTTCTTTTCTTCA
1 TTTTTTCTTTTCTTCA
553124 TTTTTTCTT
1 TTTTTTCTT
553133 CAAGCATAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
15 6 0.25
16 18 0.75
ACGTcount: A:0.05, C:0.15, G:0.00, T:0.80
Consensus pattern (16 bp):
TTTTTTCTTTTCTTCA
Found at i:553131 original size:27 final size:27
Alignment explanation
Indices: 553055--553134 Score: 90
Period size: 27 Copynumber: 2.9 Consensus size: 27
553045 CTGACCCTCC
* **
553055 TTTTCTATTTTTTCTTTTTTCAACATT
1 TTTTCTATTTCTTCTTTTTTCTTCATT
* *
553082 TTTTCTCTTTCTTTTTTTTTTCTTCATT
1 TTTTCTATTTC-TTCTTTTTTCTTCATT
553110 TTTTCT-TTTCTTCATTTTTTCTTCA
1 TTTTCTATTTCTTC-TTTTTTCTTCA
553135 AGCATAATAT
Statistics
Matches: 45, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
26 2 0.04
27 24 0.53
28 19 0.42
ACGTcount: A:0.09, C:0.17, G:0.00, T:0.74
Consensus pattern (27 bp):
TTTTCTATTTCTTCTTTTTTCTTCATT
Found at i:561883 original size:14 final size:15
Alignment explanation
Indices: 561864--561893 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
561854 TTCGAGCAGC
561864 ATCACC-CATTTGTA
1 ATCACCACATTTGTA
561878 ATCACCACATTTGTA
1 ATCACCACATTTGTA
561893 A
1 A
561894 AAGAATTCCC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 6 0.40
15 9 0.60
ACGTcount: A:0.33, C:0.27, G:0.07, T:0.33
Consensus pattern (15 bp):
ATCACCACATTTGTA
Found at i:563538 original size:2 final size:2
Alignment explanation
Indices: 563531--563561 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
563521 TAATAAAATA
563531 AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
563562 TATGAAAATA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:564205 original size:18 final size:19
Alignment explanation
Indices: 564170--564205 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
564160 ATATTAAAGC
*
564170 ATTTATTAAAATAGATATA
1 ATTTATAAAAATAGATATA
564189 ATTTATAAAAATA-ATAT
1 ATTTATAAAAATAGATAT
564206 CTTATTTAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 4 0.25
19 12 0.75
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.42
Consensus pattern (19 bp):
ATTTATAAAAATAGATATA
Found at i:565753 original size:3 final size:3
Alignment explanation
Indices: 565747--565815 Score: 76
Period size: 3 Copynumber: 24.7 Consensus size: 3
565737 AATATATTAT
* * *
565747 TAA TAA TAA TAA AAA TAA TAA -AA TAA TTA TTA TAA TAA T-A TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
565793 TAA TAA T-A TAA -AA TAA -AA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TA
565816 TTCAAATGAA
Statistics
Matches: 57, Mismatches: 4, Indels: 10
0.80 0.06 0.14
Matches are distributed among these distances:
2 10 0.18
3 47 0.82
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:565771 original size:8 final size:8
Alignment explanation
Indices: 565751--565815 Score: 60
Period size: 8 Copynumber: 7.9 Consensus size: 8
565741 TATTATTAAT
565751 AATAATAAA
1 AATAAT-AA
565760 AATAATAA
1 AATAATAA
*
565768 AATAATTAT
1 AATAA-TAA
*
565777 TATAATAA
1 AATAATAA
*
565785 TATAATAA
1 AATAATAA
*
565793 TAATAATAT
1 -AATAATAA
565802 AA-AATAA
1 AATAATAA
565809 AATAATA
1 AATAATA
565816 TTCAAATGAA
Statistics
Matches: 47, Mismatches: 6, Indels: 7
0.78 0.10 0.12
Matches are distributed among these distances:
7 6 0.13
8 23 0.49
9 18 0.38
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (8 bp):
AATAATAA
Found at i:565771 original size:17 final size:17
Alignment explanation
Indices: 565751--565815 Score: 62
Period size: 17 Copynumber: 3.9 Consensus size: 17
565741 TATTATTAAT
565751 AATAATAAAAATAATAA
1 AATAATAAAAATAATAA
* **
565768 AATAATTATTATAATAA
1 AATAATAAAAATAATAA
* * *
565785 TATAATAATAATAATAT
1 AATAATAAAAATAATAA
565802 AA-AAT-AAAATAATA
1 AATAATAAAAATAATA
565816 TTCAAATGAA
Statistics
Matches: 39, Mismatches: 9, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
15 8 0.21
16 3 0.08
17 28 0.72
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (17 bp):
AATAATAAAAATAATAA
Found at i:565773 original size:20 final size:20
Alignment explanation
Indices: 565748--565815 Score: 75
Period size: 20 Copynumber: 3.4 Consensus size: 20
565738 ATATATTATT
565748 AATAATAATAAAAATAATAA
1 AATAATAATAAAAATAATAA
* * * *
565768 AATAATTATTATAATAATAT
1 AATAATAATAAAAATAATAA
565788 AATAATAATAATATAA-AATAA
1 AATAATAATAA-A-AATAATAA
565809 AATAATA
1 AATAATA
565816 TTCAAATGAA
Statistics
Matches: 38, Mismatches: 8, Indels: 3
0.78 0.16 0.06
Matches are distributed among these distances:
20 25 0.66
21 11 0.29
22 2 0.05
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (20 bp):
AATAATAATAAAAATAATAA
Found at i:569670 original size:29 final size:29
Alignment explanation
Indices: 569626--569695 Score: 106
Period size: 29 Copynumber: 2.4 Consensus size: 29
569616 ATTCACATAA
*
569626 TTTATCGCATAGACATATCATTTCCATACC
1 TTTATCACATA-ACATATCATTTCCATACC
*
569656 TTTATCACATAACATTTCATTTCCATACC
1 TTTATCACATAACATATCATTTCCATACC
569685 TTTA-CACATAA
1 TTTATCACATAA
569696 TTCATATAAT
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
28 7 0.18
29 21 0.55
30 10 0.26
ACGTcount: A:0.33, C:0.26, G:0.03, T:0.39
Consensus pattern (29 bp):
TTTATCACATAACATATCATTTCCATACC
Found at i:570106 original size:63 final size:63
Alignment explanation
Indices: 570037--570195 Score: 196
Period size: 63 Copynumber: 2.5 Consensus size: 63
570027 TCCTTAATGT
* *
570037 ATGCATCGATGCACTACCTGTGCATCGATACACAAAT-GTCATTCGATGTTTGT-ATTTAAGGGG
1 ATGCATCGATGCACTACCTGTGCATCGATACACAAATAG-CATTCGATGTTT-TCATTTAAAGGA
* ** * **
570100 GTGCATCGATGCACTACCTGTGCATCGATACACGGATAGCATTCGATGTTTTCTTTTAAATTA
1 ATGCATCGATGCACTACCTGTGCATCGATACACAAATAGCATTCGATGTTTTCATTTAAAGGA
* *
570163 ATGCATCGATGCACTTCATGTGCATCGATACAC
1 ATGCATCGATGCACTACCTGTGCATCGATACAC
570196 CTAGCACTAA
Statistics
Matches: 83, Mismatches: 11, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
62 1 0.01
63 81 0.98
64 1 0.01
ACGTcount: A:0.26, C:0.21, G:0.20, T:0.32
Consensus pattern (63 bp):
ATGCATCGATGCACTACCTGTGCATCGATACACAAATAGCATTCGATGTTTTCATTTAAAGGA
Found at i:571664 original size:22 final size:22
Alignment explanation
Indices: 571639--571691 Score: 88
Period size: 22 Copynumber: 2.4 Consensus size: 22
571629 GGGTATATTA
* *
571639 GTCCTTCGGGATGTATCTAGTG
1 GTCCTTCGGGATGTATCCAATG
571661 GTCCTTCGGGATGTATCCAATG
1 GTCCTTCGGGATGTATCCAATG
571683 GTCCTTCGG
1 GTCCTTCGG
571692 AACATAGTGG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.13, C:0.23, G:0.30, T:0.34
Consensus pattern (22 bp):
GTCCTTCGGGATGTATCCAATG
Found at i:578571 original size:18 final size:18
Alignment explanation
Indices: 578548--578582 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
578538 GGACGTATCC
* *
578548 AGTGGTCCTTTGGGACAT
1 AGTGGTCATTCGGGACAT
578566 AGTGGTCATTCGGGACA
1 AGTGGTCATTCGGGACA
578583 AATACTAAAC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.20, C:0.17, G:0.34, T:0.29
Consensus pattern (18 bp):
AGTGGTCATTCGGGACAT
Found at i:583106 original size:64 final size:64
Alignment explanation
Indices: 583015--583173 Score: 185
Period size: 64 Copynumber: 2.5 Consensus size: 64
583005 TTCAATGTGC
* * * * ** *
583015 ATCGATTCACATGAAGTGTATCGATGCACTTCTTTAAAATAAAAACATCGAAT-ATCATTAGTGT
1 ATCGATGCACAAGTAGTGCATCGATGCACCCCCTTAAAATAAAAACATCGAATGA-CATTAGTGT
* * * *
583079 ATCGATGCACAAGTAGTGCATCTATGCACCCCCTTAAAATATAAACATCGAATGAGATTTGTGT
1 ATCGATGCACAAGTAGTGCATCGATGCACCCCCTTAAAATAAAAACATCGAATGACATTAGTGT
* *
583143 ACCGATGCACAGGTAGTGCATCGATGCACCC
1 ATCGATGCACAAGTAGTGCATCGATGCACCC
583174 GTTAAGGAAT
Statistics
Matches: 80, Mismatches: 14, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
64 79 0.99
65 1 0.01
ACGTcount: A:0.34, C:0.21, G:0.18, T:0.28
Consensus pattern (64 bp):
ATCGATGCACAAGTAGTGCATCGATGCACCCCCTTAAAATAAAAACATCGAATGACATTAGTGT
Found at i:583770 original size:18 final size:18
Alignment explanation
Indices: 583747--583819 Score: 92
Period size: 18 Copynumber: 3.9 Consensus size: 18
583737 AGGGATTATC
583747 AGTGGTCATTCGGGACAT
1 AGTGGTCATTCGGGACAT
* *
583765 AGTGGTTATTCGGAACAAT
1 AGTGGTCATTCGGGAC-AT
* *
583784 CAGTGGTCCTTCGGGATAT
1 -AGTGGTCATTCGGGACAT
583803 AGTGGTCATTCGGGACA
1 AGTGGTCATTCGGGACA
583820 AATATTCAGT
Statistics
Matches: 45, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
18 29 0.64
19 4 0.09
20 12 0.27
ACGTcount: A:0.23, C:0.16, G:0.32, T:0.29
Consensus pattern (18 bp):
AGTGGTCATTCGGGACAT
Found at i:583797 original size:38 final size:38
Alignment explanation
Indices: 583744--583820 Score: 118
Period size: 38 Copynumber: 2.0 Consensus size: 38
583734 TCGAGGGATT
*
583744 ATCAGTGGTCATTCGGGACATAGTGGTTATTCGGAACA
1 ATCAGTGGTCATTCGGGACATAGTGGTCATTCGGAACA
* * *
583782 ATCAGTGGTCCTTCGGGATATAGTGGTCATTCGGGACA
1 ATCAGTGGTCATTCGGGACATAGTGGTCATTCGGAACA
583820 A
1 A
583821 ATATTCAGTG
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
38 35 1.00
ACGTcount: A:0.25, C:0.17, G:0.30, T:0.29
Consensus pattern (38 bp):
ATCAGTGGTCATTCGGGACATAGTGGTCATTCGGAACA
Found at i:587759 original size:21 final size:20
Alignment explanation
Indices: 587730--587773 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 20
587720 AAAATAAAAT
* *
587730 AATTCAAATGTTAGATGATCA
1 AATTAAAATGTTAG-TGACCA
*
587751 AATTAAAATTTTAGTGACCA
1 AATTAAAATGTTAGTGACCA
587771 AAT
1 AAT
587774 CAAGAATTAT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
20 8 0.40
21 12 0.60
ACGTcount: A:0.45, C:0.09, G:0.11, T:0.34
Consensus pattern (20 bp):
AATTAAAATGTTAGTGACCA
Found at i:587781 original size:21 final size:21
Alignment explanation
Indices: 587735--587781 Score: 51
Period size: 21 Copynumber: 2.2 Consensus size: 21
587725 AAAATAATTC
* * *
587735 AAATGTTAGATGATCAAATTA
1 AAATTTTAGATGACCAAATCA
587756 AAATTTTAG-TGACCAAATCA
1 AAATTTTAGATGACCAAATCA
587776 AGAATT
1 A-AATT
587782 ATGTAAAGCT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
20 10 0.45
21 12 0.55
ACGTcount: A:0.47, C:0.09, G:0.13, T:0.32
Consensus pattern (21 bp):
AAATTTTAGATGACCAAATCA
Found at i:589578 original size:2 final size:2
Alignment explanation
Indices: 589573--589636 Score: 128
Period size: 2 Copynumber: 32.0 Consensus size: 2
589563 ATACACACAC
589573 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
589615 AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG
589637 GAAAATATAC
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 62 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:596294 original size:15 final size:15
Alignment explanation
Indices: 596274--596305 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
596264 AGTACTTTTG
596274 ATCGATAATTCATCA
1 ATCGATAATTCATCA
596289 ATCGATAATTCATCA
1 ATCGATAATTCATCA
596304 AT
1 AT
596306 TCGACTATTG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.41, C:0.19, G:0.06, T:0.34
Consensus pattern (15 bp):
ATCGATAATTCATCA
Found at i:598541 original size:211 final size:209
Alignment explanation
Indices: 598025--598635 Score: 695
Period size: 211 Copynumber: 2.9 Consensus size: 209
598015 AGATGGTTTG
* * ** *
598025 GAGAAGTGGGAAATGTGGCATTTAATCCAGGATTGTGATCAAAATGTCAGATACCCATCTCCCTC
1 GAGAAGTGGGAAATGTGGCGTTTGATAAAGGATTGTGATCAAAATGTCAGATAACCATCTCCCTC
* * * * * ** *
598090 TTTTATCTTCTTCGGATAGTAAATCAGAAGTTAATTCTTGTGCTCTATTTCTCATGGAGTTCAAA
66 TTGTATCTTCTCCAGATATTAAATCAGAAGTTAATGCTTGTGCTCTGCTTCTCATGGAGTTCAAG
* * * * *** * * *
598155 TTTGGCTCTTATTTTACATAATCCTC-AATATGGAAAAGGCATTTGTTTTAAATTACTTAAGAGT
131 TTTGGCTCTTCTTTTACATAATTCTCAAATATGGAAAAAG-A-ATACCTTAATTTACTGAAGAGA
* *
598219 GATTAGAACGTGGATT
194 AATAAGAACGTGGATT
** * * * * * * *
598235 GAAGAAGTGGGAAATGTGGCGTCGGATAAAGAATTGTGGTTAAAATATCATATAGCCATCACCCT
1 G-AGAAGTGGGAAATGTGGCGTTTGATAAAGGATTGTGATCAAAATGTCAGATAACCATCTCCCT
* ** * *
598300 CTTTGTATCTTCTCCATATATTAAATCAGAAGTTAATGCCCGTGCACTGCTTCTCATGGAGTGCA
65 C-TTGTATCTTCTCCAGATATTAAATCAGAAGTTAATGCTTGTGCTCTGCTTCTCATGGAGTTCA
598365 AGTTTGGCTCTTCTTTTACATAATTCTCAAATATGGAAAAAGAATACCTTAATTTA-TGGAAGAG
129 AGTTTGGCTCTTCTTTTACATAATTCTCAAATATGGAAAAAGAATACCTTAATTTACT-GAAGAG
*
598429 AAATAAGAATGTGGATT
193 AAATAAGAACGTGGATT
* * * **
598446 AGAGAAGTGGGAAATGGGGTGTTTGATAGAGGATTGCAATCAAAATGTCAGATAACCATCTCCCT
1 -GAGAAGTGGGAAATGTGGCGTTTGATAAAGGATTGTGATCAAAATGTCAGATAACCATCTCCCT
* *
598511 CATTGTATCTTCTCCAGATATTAAATCAGAAGTTAATGATTGTGCTCTGCCTCTCATGGAGTTCA
65 C-TTGTATCTTCTCCAGATATTAAATCAGAAGTTAATGCTTGTGCTCTGCTTCTCATGGAGTTCA
*
598576 AGTTTGGCTCTTCTTTTACATAATTCTCAAATATGGAAAATGAATTGACCTTAATTTACT
129 AGTTTGGCTCTTCTTTTACATAATTCTCAAATATGGAAAAAGAA-T-ACCTTAATTTACT
598636 TACTAAATAG
Statistics
Matches: 331, Mismatches: 62, Indels: 12
0.82 0.15 0.03
Matches are distributed among these distances:
210 2 0.01
211 226 0.68
212 79 0.24
213 23 0.07
214 1 0.00
ACGTcount: A:0.31, C:0.16, G:0.19, T:0.34
Consensus pattern (209 bp):
GAGAAGTGGGAAATGTGGCGTTTGATAAAGGATTGTGATCAAAATGTCAGATAACCATCTCCCTC
TTGTATCTTCTCCAGATATTAAATCAGAAGTTAATGCTTGTGCTCTGCTTCTCATGGAGTTCAAG
TTTGGCTCTTCTTTTACATAATTCTCAAATATGGAAAAAGAATACCTTAATTTACTGAAGAGAAA
TAAGAACGTGGATT
Found at i:610634 original size:34 final size:32
Alignment explanation
Indices: 610572--610641 Score: 86
Period size: 34 Copynumber: 2.1 Consensus size: 32
610562 ACCTTACAAC
* * *
610572 TCCCTAGTTTTTCCGGGCTAAACTAGAACCTT
1 TCCCTAGTTTTACCGGGATAAACTAGAACATT
*
610604 TCCCTAGCTTTTACACGGGATAAGCTAGAACATT
1 TCCCTAG-TTTTAC-CGGGATAAACTAGAACATT
610638 TCCC
1 TCCC
610642 CTTTACAATA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
32 7 0.22
33 5 0.16
34 20 0.62
ACGTcount: A:0.24, C:0.29, G:0.16, T:0.31
Consensus pattern (32 bp):
TCCCTAGTTTTACCGGGATAAACTAGAACATT
Found at i:610950 original size:21 final size:21
Alignment explanation
Indices: 610924--610965 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
610914 CCAGAATGGG
*
610924 GGGAATCGGTACCCCTTCATA
1 GGGAATCGATACCCCTTCATA
*
610945 GGGAATTGATACCCCTTCATA
1 GGGAATCGATACCCCTTCATA
610966 ATATTCAAAT
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:0.26, C:0.26, G:0.21, T:0.26
Consensus pattern (21 bp):
GGGAATCGATACCCCTTCATA
Found at i:612643 original size:19 final size:20
Alignment explanation
Indices: 612600--612647 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 20
612590 TCTAAATCCT
*
612600 TTTTCAAAATTTCATTTTGG
1 TTTTCAAAATCTCATTTTGG
* *
612620 CTTTCAAAATCT-ATTTTTG
1 TTTTCAAAATCTCATTTTGG
612639 TTTTCAAAA
1 TTTTCAAAA
612648 GAAAATCGTT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 14 0.58
20 10 0.42
ACGTcount: A:0.29, C:0.12, G:0.06, T:0.52
Consensus pattern (20 bp):
TTTTCAAAATCTCATTTTGG
Found at i:613562 original size:34 final size:32
Alignment explanation
Indices: 613500--613569 Score: 86
Period size: 34 Copynumber: 2.1 Consensus size: 32
613490 ACCTTACAAC
* * *
613500 TCCCTAGTTTTTCCGGGCTAAACTAGAACCTT
1 TCCCTAGTTTTACCGGGATAAACTAGAACATT
*
613532 TCCCTAGCTTTTACACGGGATAAGCTAGAACATT
1 TCCCTAG-TTTTAC-CGGGATAAACTAGAACATT
613566 TCCC
1 TCCC
613570 CTTTACAATA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
32 7 0.22
33 5 0.16
34 20 0.62
ACGTcount: A:0.24, C:0.29, G:0.16, T:0.31
Consensus pattern (32 bp):
TCCCTAGTTTTACCGGGATAAACTAGAACATT
Found at i:613812 original size:21 final size:21
Alignment explanation
Indices: 613784--613823 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
613774 AGTCATGTCT
*
613784 AGCCTTTGGGGATG-TTTTGG
1 AGCCTTTGGGAATGATTTTGG
613804 AGCCGTTTGGGAATGATTTT
1 AGCC-TTTGGGAATGATTTT
613824 TCTACAAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 4 0.24
21 9 0.53
22 4 0.24
ACGTcount: A:0.15, C:0.10, G:0.35, T:0.40
Consensus pattern (21 bp):
AGCCTTTGGGAATGATTTTGG
Found at i:613877 original size:21 final size:21
Alignment explanation
Indices: 613852--613893 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
613842 CCAGAATGAG
*
613852 GGGAATCGGTACCCCTTCATA
1 GGGAATCGATACCCCTTCATA
613873 GGGAATCGATACCCCTTCATA
1 GGGAATCGATACCCCTTCATA
613894 ATATTCAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.26, C:0.29, G:0.21, T:0.24
Consensus pattern (21 bp):
GGGAATCGATACCCCTTCATA
Found at i:614030 original size:21 final size:21
Alignment explanation
Indices: 614006--614045 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
613996 AACCATGCAA
614006 GGGGAATCTGTACCCCCTGGG
1 GGGGAATCTGTACCCCCTGGG
614027 GGGGAATCTGTACCCCCTG
1 GGGGAATCTGTACCCCCTG
614046 AACAATCTGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.15, C:0.30, G:0.35, T:0.20
Consensus pattern (21 bp):
GGGGAATCTGTACCCCCTGGG
Found at i:623339 original size:47 final size:48
Alignment explanation
Indices: 623270--623399 Score: 156
Period size: 47 Copynumber: 2.8 Consensus size: 48
623260 TCCTATAAAT
* *
623270 AAATTTTCACTGTATAATTATTTTTTATTTATTTACTTTTC-TTTTAA
1 AAATTTTCACTGTATAATTATTTTGTATTTATTTACTTTCCTTTTTAA
* * * **
623317 AAATTTTCACTGCATAATTATTTCGTATTTATTT-GTTTCCTTTTTTT
1 AAATTTTCACTGTATAATTATTTTGTATTTATTTACTTTCCTTTTTAA
** *
623364 TTATTTTCACTGTTTAATTATTTTGTATTTATTTAC
1 AAATTTTCACTGTATAATTATTTTGTATTTATTTAC
623400 ATCTTTAAGT
Statistics
Matches: 68, Mismatches: 13, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
46 4 0.06
47 64 0.94
ACGTcount: A:0.24, C:0.10, G:0.05, T:0.62
Consensus pattern (48 bp):
AAATTTTCACTGTATAATTATTTTGTATTTATTTACTTTCCTTTTTAA
Found at i:625430 original size:31 final size:31
Alignment explanation
Indices: 625385--625455 Score: 106
Period size: 31 Copynumber: 2.3 Consensus size: 31
625375 TAACTCGGGA
* *
625385 TGACCACATCTTAATTAAATAAAAACGAAAG
1 TGACCATATTTTAATTAAATAAAAACGAAAG
* *
625416 TGATCATATTTTAATTAAATAAAAACGAAAT
1 TGACCATATTTTAATTAAATAAAAACGAAAG
625447 TGACCATAT
1 TGACCATAT
625456 ATGTTTTTTT
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 35 1.00
ACGTcount: A:0.49, C:0.13, G:0.08, T:0.30
Consensus pattern (31 bp):
TGACCATATTTTAATTAAATAAAAACGAAAG
Found at i:629395 original size:31 final size:31
Alignment explanation
Indices: 629357--629510 Score: 233
Period size: 31 Copynumber: 5.0 Consensus size: 31
629347 CCCGAAGGAC
* * *
629357 CAGTCCATA-GATTCCGAAGAACCTAGGTAAT
1 CAGTCCATATG-TCCCGAAGAACATAGGTAAA
629388 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
*
629419 CAGTCCATATGTCCCGAA-AA-ATAGATAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
*
629448 CAGTCCATATGTCCCAAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
629479 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
629510 C
1 C
629511 CCTCGACCCT
Statistics
Matches: 113, Mismatches: 7, Indels: 6
0.90 0.06 0.05
Matches are distributed among these distances:
29 25 0.22
30 4 0.04
31 83 0.73
32 1 0.01
ACGTcount: A:0.40, C:0.23, G:0.18, T:0.20
Consensus pattern (31 bp):
CAGTCCATATGTCCCGAAGAACATAGGTAAA
Found at i:629461 original size:60 final size:62
Alignment explanation
Indices: 629357--629510 Score: 224
Period size: 60 Copynumber: 2.5 Consensus size: 62
629347 CCCGAAGGAC
* * * * *
629357 CAGTCCATA-GATTCCGAAGAACCTAGGTAATCAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATG-TCCCGAAGAACATAGATAAACAGTCCATATGTCCCAAAGAACATAGGTAAA
629419 CAGTCCATATGTCCCGAA-AA-ATAGATAAACAGTCCATATGTCCCAAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGATAAACAGTCCATATGTCCCAAAGAACATAGGTAAA
*
629479 CAGTCCATATGTCCCGAAGAACATAGGTAAAC
1 CAGTCCATATGTCCCGAAGAACATAGATAAAC
629511 CCTCGACCCT
Statistics
Matches: 83, Mismatches: 6, Indels: 6
0.87 0.06 0.06
Matches are distributed among these distances:
60 54 0.65
61 4 0.05
62 24 0.29
63 1 0.01
ACGTcount: A:0.40, C:0.23, G:0.18, T:0.20
Consensus pattern (62 bp):
CAGTCCATATGTCCCGAAGAACATAGATAAACAGTCCATATGTCCCAAAGAACATAGGTAAA
Found at i:633574 original size:31 final size:31
Alignment explanation
Indices: 633536--633691 Score: 260
Period size: 31 Copynumber: 5.0 Consensus size: 31
633526 CCCGAAGGAC
* * *
633536 CAGTCCATA-GATTCCGAAGAACCTAGGTAAT
1 CAGTCCATATG-TCCCGAAGAACATAGGTAAA
633567 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
633598 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
*
633629 CAGCCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
633660 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
633691 C
1 C
633692 CCTCGACCCT
Statistics
Matches: 119, Mismatches: 5, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
31 118 0.99
32 1 0.01
ACGTcount: A:0.38, C:0.24, G:0.19, T:0.19
Consensus pattern (31 bp):
CAGTCCATATGTCCCGAAGAACATAGGTAAA
Found at i:639361 original size:17 final size:18
Alignment explanation
Indices: 639341--639383 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 18
639331 GTCCATTTCT
639341 TAATAAAAAAAATAA-AA
1 TAATAAAAAAAATAATAA
*
639358 TAATATTAATAAAATAATAA
1 TAATA--AAAAAAATAATAA
639378 TAATAA
1 TAATAA
639384 TAGTATATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 5
0.79 0.04 0.18
Matches are distributed among these distances:
17 5 0.23
18 1 0.05
19 9 0.41
20 7 0.32
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (18 bp):
TAATAAAAAAAATAATAA
Found at i:639368 original size:14 final size:14
Alignment explanation
Indices: 639351--639383 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
639341 TAATAAAAAA
*
639351 AATAAAATAATATT
1 AATAAAATAATAAT
639365 AATAAAATAATAAT
1 AATAAAATAATAAT
639379 AATAA
1 AATAA
639384 TAGTATATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (14 bp):
AATAAAATAATAAT
Found at i:639370 original size:23 final size:23
Alignment explanation
Indices: 639340--639385 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
639330 AGTCCATTTC
639340 TTAATAAAAAAAATAA-AATAATA
1 TTAAT-AAAAAAATAATAATAATA
*
639363 TTAATAAAATAATAATAATAATA
1 TTAATAAAAAAATAATAATAATA
639386 GTATATATAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 9 0.43
23 12 0.57
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (23 bp):
TTAATAAAAAAATAATAATAATA
Found at i:641263 original size:13 final size:13
Alignment explanation
Indices: 641245--641269 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
641235 TACAGACGCG
641245 CATATGAAGACTA
1 CATATGAAGACTA
641258 CATATGAAGACT
1 CATATGAAGACT
641270 GTTCAACTAT
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:0.44, C:0.16, G:0.16, T:0.24
Consensus pattern (13 bp):
CATATGAAGACTA
Found at i:642799 original size:27 final size:29
Alignment explanation
Indices: 642746--642800 Score: 69
Period size: 27 Copynumber: 2.0 Consensus size: 29
642736 CCGGAATTTA
**
642746 AAAAAATTATAATTTTGACCCTTATTTTT
1 AAAAAATTATAATTTTGACCCCAATTTTT
*
642775 AAAAAATT-TAA-TTTGGCCCCAATTTT
1 AAAAAATTATAATTTTGACCCCAATTTT
642801 GTTTAGGAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
27 12 0.52
28 3 0.13
29 8 0.35
ACGTcount: A:0.38, C:0.13, G:0.05, T:0.44
Consensus pattern (29 bp):
AAAAAATTATAATTTTGACCCCAATTTTT
Found at i:644518 original size:4 final size:4
Alignment explanation
Indices: 644482--644555 Score: 73
Period size: 4 Copynumber: 18.8 Consensus size: 4
644472 TTAGATGGAA
* *
644482 AAAT AAA- AAA- AAAT CAAAT GAA- AAAT AAAAT AAAT AAAT AAAT AGAT
1 AAAT AAAT AAAT AAAT -AAAT AAAT AAAT -AAAT AAAT AAAT AAAT AAAT
* *
644529 AAAT AAAT AAAA AAAT AAAA AAAT AAA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAA
644556 AAAAATGTGT
Statistics
Matches: 58, Mismatches: 8, Indels: 8
0.78 0.11 0.11
Matches are distributed among these distances:
3 8 0.14
4 42 0.72
5 8 0.14
ACGTcount: A:0.78, C:0.01, G:0.03, T:0.18
Consensus pattern (4 bp):
AAAT
Found at i:644605 original size:16 final size:15
Alignment explanation
Indices: 644482--644606 Score: 78
Period size: 16 Copynumber: 7.9 Consensus size: 15
644472 TTAGATGGAA
644482 AAATAAA-AAAAAAT
1 AAATAAATAAAAAAT
644496 CAAATGAAA-AATAAAAT
1 -AAAT-AAATAA-AAAAT
*
644513 AAATAAATAAATAGAT
1 AAATAAATAAA-AAAT
644529 AAATAAATAAAAAAAT
1 AAATAAAT-AAAAAAT
*
644545 AAAAAAATAAAAAA-
1 AAATAAATAAAAAAT
* * *
644559 AATGTGTAATAAAAAAG
1 AA-AT-AAATAAAAAAT
*
644576 GAA-AAATAAGAAAAAT
1 AAATAAAT-A-AAAAAT
644592 AAATAAATATAAAAA
1 AAATAAATA-AAAAA
644607 ATGTTAAAAG
Statistics
Matches: 87, Mismatches: 12, Indels: 21
0.73 0.10 0.17
Matches are distributed among these distances:
14 5 0.06
15 15 0.17
16 54 0.62
17 13 0.15
ACGTcount: A:0.76, C:0.01, G:0.06, T:0.18
Consensus pattern (15 bp):
AAATAAATAAAAAAT
Found at i:644621 original size:47 final size:46
Alignment explanation
Indices: 644533--644621 Score: 126
Period size: 47 Copynumber: 1.9 Consensus size: 46
644523 ATAGATAAAT
*
644533 AAATAAAAAAATAAAAAAATAAAAAAAATGTGTAATAAAAAAGGAA
1 AAATAAAAAAATAAAAAAATAAAAAAAATGTGTAAAAAAAAAGGAA
* *
644579 AAATAAGAAAAATAAATAAATATAAAAAATGT-TAAAAGAAAAA
1 AAATAA-AAAAATAAAAAAATAAAAAAAATGTGTAAAA-AAAAA
644622 CAGAACAAAA
Statistics
Matches: 38, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
46 10 0.26
47 28 0.74
ACGTcount: A:0.75, C:0.00, G:0.08, T:0.17
Consensus pattern (46 bp):
AAATAAAAAAATAAAAAAATAAAAAAAATGTGTAAAAAAAAAGGAA
Found at i:644634 original size:47 final size:47
Alignment explanation
Indices: 644533--644634 Score: 120
Period size: 47 Copynumber: 2.2 Consensus size: 47
644523 ATAGATAAAT
* *
644533 AAATAA-AAAAATAAAAAAATAAAAAAAATGTGTAATAAAAAAGGAA
1 AAATAAGAAAAATAAAAAAATAAAAAAAATGTGTAAAAAAAAAAGAA
* *
644579 AAATAAGAAAAATAAATAAATATAAAAAATGT-TAAAAGAAAAACAGAA
1 AAATAAGAAAAATAAAAAAATAAAAAAAATGTGTAAAA-AAAAA-AGAA
*
644627 CAA-AAGAA
1 AAATAAGAA
644635 GAAAATATTA
Statistics
Matches: 48, Mismatches: 5, Indels: 5
0.83 0.09 0.09
Matches are distributed among these distances:
46 10 0.21
47 33 0.69
48 5 0.10
ACGTcount: A:0.75, C:0.02, G:0.09, T:0.15
Consensus pattern (47 bp):
AAATAAGAAAAATAAAAAAATAAAAAAAATGTGTAAAAAAAAAAGAA
Found at i:644737 original size:41 final size:39
Alignment explanation
Indices: 644653--644739 Score: 97
Period size: 39 Copynumber: 2.2 Consensus size: 39
644643 TAAATTTTAG
* *
644653 AAAAAAATTAAAATAATAAAAAAATGTAAAAGAGAAAAT
1 AAAAAAATCAAAATAATAAAAAAATGGAAAAGAGAAAAT
*
644692 AAAAAAATCAAAATGAAATAAAAAAAATGGGAAAATA-AAAA-
1 AAAAAAATCAAAAT--AAT-AAAAAAAT-GGAAAAGAGAAAAT
644733 AAAAAAA
1 AAAAAAA
644740 GGAAAAATGT
Statistics
Matches: 41, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
39 13 0.32
41 10 0.24
42 12 0.29
43 6 0.15
ACGTcount: A:0.77, C:0.01, G:0.08, T:0.14
Consensus pattern (39 bp):
AAAAAAATCAAAATAATAAAAAAATGGAAAAGAGAAAAT
Found at i:644746 original size:20 final size:22
Alignment explanation
Indices: 644701--644748 Score: 64
Period size: 20 Copynumber: 2.3 Consensus size: 22
644691 TAAAAAAATC
* *
644701 AAAATGAAATAAAAAAAATGGG
1 AAAATGAAATAAAAAAAAAGGA
644723 AAAAT-AAA-AAAAAAAAAGGA
1 AAAATGAAATAAAAAAAAAGGA
644743 AAAATG
1 AAAATG
644749 TTAAATTTGA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
20 15 0.65
21 3 0.13
22 5 0.22
ACGTcount: A:0.75, C:0.00, G:0.15, T:0.10
Consensus pattern (22 bp):
AAAATGAAATAAAAAAAAAGGA
Found at i:646638 original size:14 final size:14
Alignment explanation
Indices: 646613--646648 Score: 54
Period size: 14 Copynumber: 2.5 Consensus size: 14
646603 ATCTTCTTAT
*
646613 TTTTACTTTAATTAC
1 TTTTA-TTTAATCAC
646628 TTTTATTTAATCAC
1 TTTTATTTAATCAC
646642 TTTTATT
1 TTTTATT
646649 ATCTTTTTAC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
14 15 0.75
15 5 0.25
ACGTcount: A:0.25, C:0.11, G:0.00, T:0.64
Consensus pattern (14 bp):
TTTTATTTAATCAC
Found at i:652774 original size:14 final size:14
Alignment explanation
Indices: 652749--652784 Score: 54
Period size: 14 Copynumber: 2.5 Consensus size: 14
652739 ATCTTCTTAT
*
652749 TTTTACTTTAATTAC
1 TTTTA-TTTAATCAC
652764 TTTTATTTAATCAC
1 TTTTATTTAATCAC
652778 TTTTATT
1 TTTTATT
652785 ATATTTTTAC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
14 15 0.75
15 5 0.25
ACGTcount: A:0.25, C:0.11, G:0.00, T:0.64
Consensus pattern (14 bp):
TTTTATTTAATCAC
Found at i:660066 original size:215 final size:216
Alignment explanation
Indices: 659182--660306 Score: 1903
Period size: 216 Copynumber: 5.3 Consensus size: 216
659172 ATTTAAGAAT
*
659182 TAAATTGAACAAATATGAAATTACAAATAAAAACTTAAATAAATTAAACAACACACATTGATGAG
1 TAAATTGAACAAATATGAAATTACAAATAAAAATTTAAATAAATTAAACAACACACATTGATGAG
659247 GGATCAAATCGAAATAATTTTAAATTGTGAGGTTGAAATTAATACAAAAAAGTACTAAATTATAC
66 GGATCAAATCGAAATAATTTTAAATTGTGAGGTTGAAATTAATACAAAAAAGTACTAAATTATAC
*
659312 CCATTTAAAAAGTTATGGGCCAATTAAAAAATAGAAATAAGTAATAAGTATGGATCAATTTCAGA
131 CCATTTAAAAAGTTATGGGCCAATTAAAAAATAGAAATAAGTAATAAGTATGGGTCAATTTCAGA
*
659377 TTCAAATAAAATTTGGAGGAC
196 TGCAAATAAAATTTGGAGGAC
**
659398 TAAATTGAACAAATACAAAATTACAAATAAAAATTTAAATAAATTTAAA-AA-ACACATTGATGA
1 TAAATTGAACAAATATGAAATTACAAATAAAAATTTAAATAAA-TTAAACAACACACATTGATGA
*
659461 GGGATCAATTCGAAATAATTTTAAATTGTGAGGTTGAAATTAATAC-AAAAAGTACTAAATTATA
65 GGGATCAAATCGAAATAATTTTAAATTGTGAGGTTGAAATTAATACAAAAAAGTACTAAATTATA
*
659525 CCCATTTAAAAAGTTATGGTCCAATTAAAAAATAG-----A--AATAAGTATGGGTCAATTTCAG
130 CCCATTTAAAAAGTTATGGGCCAATTAAAAAATAGAAATAAGTAATAAGTATGGGTCAATTTCAG
659583 ATGCAAATAAAATTTGGAGGAC
195 ATGCAAATAAAATTTGGAGGAC
*
659605 TAAATTGAACAAATATGAAATTATAAATAAAAATTTAAATAAATTAAACAACACACATTGATGAG
1 TAAATTGAACAAATATGAAATTACAAATAAAAATTTAAATAAATTAAACAACACACATTGATGAG
659670 GGATCAAATCGAAATAATTTTAAATTGTGAGGTTGAAATTAATACAAAAAAGTACTAAATTATAC
66 GGATCAAATCGAAATAATTTTAAATTGTGAGGTTGAAATTAATACAAAAAAGTACTAAATTATAC
* *
659735 CCATTTAAAAAGTTATGGGCCAATTAAAAAATAGAAATAATTAATAAGTATGGATCAATTTCAGA
131 CCATTTAAAAAGTTATGGGCCAATTAAAAAATAGAAATAAGTAATAAGTATGGGTCAATTTCAGA
659800 TGCAAATAAAATTTGGAGGAC
196 TGCAAATAAAATTTGGAGGAC
* * *
659821 TAAATTGAACAAATATGAAACTAAAAATAAAAATTTAAATAAATTAAACAACTCACATTGATGAG
1 TAAATTGAACAAATATGAAATTACAAATAAAAATTTAAATAAATTAAACAACACACATTGATGAG
* * *
659886 GGACCAAATCGAAATAATTTTAAATTTTGAGGTTGAAATTAATAC-AAAAAGTTCTAAATTATAC
66 GGATCAAATCGAAATAATTTTAAATTGTGAGGTTGAAATTAATACAAAAAAGTACTAAATTATAC
*** *
659950 ATTTTTAAAAAGTTATGTGCCAATTAAAAAATAGAAATAAGTAATAAGTATGGGTCAATTTCAGA
131 CCATTTAAAAAGTTATGGGCCAATTAAAAAATAGAAATAAGTAATAAGTATGGGTCAATTTCAGA
*
660015 TGCAAATAAACTTTGGAGGAC
196 TGCAAATAAAATTTGGAGGAC
*
660036 TAAATTGAACAAATATGAAATTACAAATAAAAAATTAAATAAATTAAACAACACACATTGATGAG
1 TAAATTGAACAAATATGAAATTACAAATAAAAATTTAAATAAATTAAACAACACACATTGATGAG
* * *
660101 GGATCAAATCAAAATAATTTTAAATTGTGAGGTTCAAATTAATACAAAAAAATACTAAATTATAC
66 GGATCAAATCGAAATAATTTTAAATTGTGAGGTTGAAATTAATACAAAAAAGTACTAAATTATAC
* *
660166 CCATTTAAAAAGTTATGGGCCAATTAAAAAATAGAAATAAGTAATAAGTTTGGGTCAATTTTAGA
131 CCATTTAAAAAGTTATGGGCCAATTAAAAAATAGAAATAAGTAATAAGTATGGGTCAATTTCAGA
660231 TGCAAATAAAATTTGGAGGAC
196 TGCAAATAAAATTTGGAGGAC
* *
660252 TAAATTGAATAAATATGAAATTACAAATAAAGATTTAAATAAATTAAACAACACA
1 TAAATTGAACAAATATGAAATTACAAATAAAAATTTAAATAAATTAAACAACACA
660307 AAGGGATCAA
Statistics
Matches: 851, Mismatches: 46, Indels: 24
0.92 0.05 0.03
Matches are distributed among these distances:
206 5 0.01
207 84 0.10
208 57 0.07
209 53 0.06
214 53 0.06
215 256 0.30
216 338 0.40
217 5 0.01
ACGTcount: A:0.50, C:0.09, G:0.13, T:0.29
Consensus pattern (216 bp):
TAAATTGAACAAATATGAAATTACAAATAAAAATTTAAATAAATTAAACAACACACATTGATGAG
GGATCAAATCGAAATAATTTTAAATTGTGAGGTTGAAATTAATACAAAAAAGTACTAAATTATAC
CCATTTAAAAAGTTATGGGCCAATTAAAAAATAGAAATAAGTAATAAGTATGGGTCAATTTCAGA
TGCAAATAAAATTTGGAGGAC
Found at i:660197 original size:431 final size:424
Alignment explanation
Indices: 659182--660306 Score: 1914
Period size: 431 Copynumber: 2.6 Consensus size: 424
659172 ATTTAAGAAT
*
659182 TAAATTGAACAAATATGAAATTACAAATAAAAACTTAAATAAATTAAACAACACACATTGATGAG
1 TAAATTGAACAAATATGAAATTACAAATAAAAAATTAAATAAATTAAACAACACACATTGATGAG
659247 GGATCAAATCGAAATAATTTTAAATTGTGAGGTTGAAATTAATACAAAAAAGTACTAAATTATAC
66 GGATCAAATCGAAATAATTTTAAATTGTGAGGTTGAAATTAATACAAAAAAGTACTAAATTATAC
659312 CCATTTAAAAAGTTATGGGCCAATTAAAAAATAGAAATAAGTAATAAGTATGGATCAATTTCAGA
131 CCATTTAAAAAGTTATGGGCCAATTAAAAAATAGAAATAAGTAATAAGTATGGATCAATTTCAGA
* **
659377 TTCAAATAAAATTTGGAGGACTAAATTGAACAAATACAAAATTACAAATAAAAATTTAAATAAAT
196 TGCAAATAAAATTTGGAGGACTAAATTGAACAAATATGAAATTACAAATAAAAATTTAAATAAA-
* *
659442 TTAAA-AA-ACACATTGATGAGGGATCAATTCGAAATAATTTTAAATTGTGAGGTTGAAATTAAT
260 TTAAACAACACACATTGATGAGGGACCAAATCGAAATAATTTTAAATTGTGAGGTTGAAATTAAT
*
659505 ACAAAAAGTACTAAATTATACCCATTTAAAAAGTTATGGTCCAATTAAAAAATAGAAATAAGTAT
325 ACAAAAAGTACTAAATTATACACATTTAAAAAGTTATGGTCCAATTAAAAAATAGAAATAAGTAT
659570 GGGTCAATTTCAGATGCAAATAAAATTTGGAGGAC
390 GGGTCAATTTCAGATGCAAATAAAATTTGGAGGAC
* *
659605 TAAATTGAACAAATATGAAATTATAAATAAAAATTTAAATAAATTAAACAACACACATTGATGAG
1 TAAATTGAACAAATATGAAATTACAAATAAAAAATTAAATAAATTAAACAACACACATTGATGAG
659670 GGATCAAATCGAAATAATTTTAAATTGTGAGGTTGAAATTAATACAAAAAAGTACTAAATTATAC
66 GGATCAAATCGAAATAATTTTAAATTGTGAGGTTGAAATTAATACAAAAAAGTACTAAATTATAC
*
659735 CCATTTAAAAAGTTATGGGCCAATTAAAAAATAGAAATAATTAATAAGTATGGATCAATTTCAGA
131 CCATTTAAAAAGTTATGGGCCAATTAAAAAATAGAAATAAGTAATAAGTATGGATCAATTTCAGA
* *
659800 TGCAAATAAAATTTGGAGGACTAAATTGAACAAATATGAAACTAAAAATAAAAATTTAAATAAAT
196 TGCAAATAAAATTTGGAGGACTAAATTGAACAAATATGAAATTACAAATAAAAATTTAAATAAAT
* *
659865 TAAACAACTCACATTGATGAGGGACCAAATCGAAATAATTTTAAATTTTGAGGTTGAAATTAATA
261 TAAACAACACACATTGATGAGGGACCAAATCGAAATAATTTTAAATTGTGAGGTTGAAATTAATA
* **
659930 CAAAAAGTTCTAAATTATACATTTTTAAAAAGTTAT-GTGCCAATTAAAAAATAGAAATAAGTAA
326 CAAAAAGTACTAAATTATACACATTTAAAAAGTTATGGT-CCAATTAAAAAATAG-----A--AA
*
659994 TAAGTATGGGTCAATTTCAGATGCAAATAAACTTTGGAGGAC
383 TAAGTATGGGTCAATTTCAGATGCAAATAAAATTTGGAGGAC
660036 TAAATTGAACAAATATGAAATTACAAATAAAAAATTAAATAAATTAAACAACACACATTGATGAG
1 TAAATTGAACAAATATGAAATTACAAATAAAAAATTAAATAAATTAAACAACACACATTGATGAG
* * *
660101 GGATCAAATCAAAATAATTTTAAATTGTGAGGTTCAAATTAATACAAAAAAATACTAAATTATAC
66 GGATCAAATCGAAATAATTTTAAATTGTGAGGTTGAAATTAATACAAAAAAGTACTAAATTATAC
* * *
660166 CCATTTAAAAAGTTATGGGCCAATTAAAAAATAGAAATAAGTAATAAGTTTGGGTCAATTTTAGA
131 CCATTTAAAAAGTTATGGGCCAATTAAAAAATAGAAATAAGTAATAAGTATGGATCAATTTCAGA
* *
660231 TGCAAATAAAATTTGGAGGACTAAATTGAATAAATATGAAATTACAAATAAAGATTTAAATAAAT
196 TGCAAATAAAATTTGGAGGACTAAATTGAACAAATATGAAATTACAAATAAAAATTTAAATAAAT
660296 TAAACAACACA
261 TAAACAACACA
660307 AAGGGATCAA
Statistics
Matches: 661, Mismatches: 31, Indels: 12
0.94 0.04 0.02
Matches are distributed among these distances:
422 5 0.01
423 255 0.39
424 100 0.15
429 1 0.00
431 300 0.45
ACGTcount: A:0.50, C:0.09, G:0.13, T:0.29
Consensus pattern (424 bp):
TAAATTGAACAAATATGAAATTACAAATAAAAAATTAAATAAATTAAACAACACACATTGATGAG
GGATCAAATCGAAATAATTTTAAATTGTGAGGTTGAAATTAATACAAAAAAGTACTAAATTATAC
CCATTTAAAAAGTTATGGGCCAATTAAAAAATAGAAATAAGTAATAAGTATGGATCAATTTCAGA
TGCAAATAAAATTTGGAGGACTAAATTGAACAAATATGAAATTACAAATAAAAATTTAAATAAAT
TAAACAACACACATTGATGAGGGACCAAATCGAAATAATTTTAAATTGTGAGGTTGAAATTAATA
CAAAAAGTACTAAATTATACACATTTAAAAAGTTATGGTCCAATTAAAAAATAGAAATAAGTATG
GGTCAATTTCAGATGCAAATAAAATTTGGAGGAC
Found at i:660393 original size:2 final size:2
Alignment explanation
Indices: 660388--660466 Score: 92
Period size: 2 Copynumber: 40.0 Consensus size: 2
660378 AAAACGACTA
* *
660388 AT AT AT AT AT AT AT AT AT AT AT A- AT AT AA ACT AT AT AGT TT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT A-T AT AT
*
660431 AT AT AT AT AT AT AT AT AT -T AT AT AA AT -T AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
660467 CATGTATAAA
Statistics
Matches: 66, Mismatches: 6, Indels: 10
0.80 0.07 0.12
Matches are distributed among these distances:
1 3 0.05
2 61 0.92
3 2 0.03
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.48
Consensus pattern (2 bp):
AT
Found at i:660443 original size:39 final size:39
Alignment explanation
Indices: 660389--660463 Score: 132
Period size: 39 Copynumber: 1.9 Consensus size: 39
660379 AAACGACTAA
660389 TATATATATATATATATATATAATATAAACTATATAGTT
1 TATATATATATATATATATATAATATAAACTATATAGTT
* *
660428 TATATATATATATATATATATTATATAAATTATATA
1 TATATATATATATATATATATAATATAAACTATATA
660464 TATCATGTAT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
39 34 1.00
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.48
Consensus pattern (39 bp):
TATATATATATATATATATATAATATAAACTATATAGTT
Found at i:660806 original size:11 final size:11
Alignment explanation
Indices: 660757--660810 Score: 53
Period size: 11 Copynumber: 5.2 Consensus size: 11
660747 TAGTAGTATT
660757 TAAACTATATA
1 TAAACTATATA
660768 TAAAC-A-ATA
1 TAAACTATATA
660777 TAAACTA-ACT-
1 TAAACTATA-TA
* *
660787 TATACTATATG
1 TAAACTATATA
660798 TAAACTATATA
1 TAAACTATATA
660809 TA
1 TA
660811 CTATATAGTT
Statistics
Matches: 36, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
9 8 0.22
10 10 0.28
11 18 0.50
ACGTcount: A:0.52, C:0.11, G:0.02, T:0.35
Consensus pattern (11 bp):
TAAACTATATA
Found at i:660849 original size:33 final size:32
Alignment explanation
Indices: 660804--660907 Score: 86
Period size: 33 Copynumber: 3.2 Consensus size: 32
660794 TATGTAAACT
*
660804 ATATATACTATATAGTTTACATATGAACTATA
1 ATATAAACTATATAGTTTACATATGAACTATA
* *** *
660836 GGTATAAACTATATAAACTATATAT-ATA-TATA
1 -ATATAAACTATATAGTTTACATATGA-ACTATA
*
660868 ATATGTAAACTATATAGTTTACATATGACCTATA
1 ATA--TAAACTATATAGTTTACATATGAACTATA
660902 TATATA
1 -ATATA
660908 GTTTATTAGT
Statistics
Matches: 53, Mismatches: 12, Indels: 12
0.69 0.16 0.16
Matches are distributed among these distances:
31 2 0.04
32 5 0.09
33 38 0.72
34 5 0.09
35 3 0.06
ACGTcount: A:0.45, C:0.09, G:0.07, T:0.39
Consensus pattern (32 bp):
ATATAAACTATATAGTTTACATATGAACTATA
Found at i:660852 original size:9 final size:9
Alignment explanation
Indices: 660838--660883 Score: 53
Period size: 9 Copynumber: 5.4 Consensus size: 9
660828 GAACTATAGG
660838 TATAAACTA
1 TATAAACTA
660847 TATAAACTA
1 TATAAACTA
*
660856 TATATA-TA
1 TATAAACTA
660864 TAT-AA-TA
1 TATAAACTA
*
660871 TGTAAACTA
1 TATAAACTA
660880 TATA
1 TATA
660884 GTTTACATAT
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
7 5 0.16
8 7 0.23
9 19 0.61
ACGTcount: A:0.52, C:0.07, G:0.02, T:0.39
Consensus pattern (9 bp):
TATAAACTA
Found at i:660924 original size:24 final size:24
Alignment explanation
Indices: 660807--660927 Score: 71
Period size: 24 Copynumber: 5.2 Consensus size: 24
660797 GTAAACTATA
660807 TATACTATATAGTTTACATATGAAC
1 TATA-TATATAGTTTACATATGAAC
** * *
660832 TATAGGTATA---AACTATATAAAC
1 TATATATATAGTTTAC-ATATGAAC
*
660854 TATATATATA-TATA-ATATGTAA-
1 TATATATATAGTTTACATATG-AAC
* *
660876 -A-CTATATAGTTTACATATGACC
1 TATATATATAGTTTACATATGAAC
*
660898 TATATATATAGTTTA-TTAGTGAAC
1 TATATATATAGTTTACATA-TGAAC
660922 TATATA
1 TATATA
660928 AACTATTTAT
Statistics
Matches: 72, Mismatches: 14, Indels: 21
0.67 0.13 0.20
Matches are distributed among these distances:
20 6 0.08
21 7 0.10
22 24 0.33
23 5 0.07
24 26 0.36
25 4 0.06
ACGTcount: A:0.43, C:0.08, G:0.08, T:0.40
Consensus pattern (24 bp):
TATATATATAGTTTACATATGAAC
Found at i:661022 original size:33 final size:33
Alignment explanation
Indices: 660968--661058 Score: 137
Period size: 33 Copynumber: 2.7 Consensus size: 33
660958 AATTATAGTT
660968 TATATATACTACATACTATAGTTTATATTTATATAC
1 TATATATA-TA-A-ACTATAGTTTATATTTATATAC
*
661004 TATTTATATAAACTATAGTTTATATTTATATAC
1 TATATATATAAACTATAGTTTATATTTATATAC
*
661037 TATATATATGAACTATAGTTTA
1 TATATATATAAACTATAGTTTA
661059 CATATAAACT
Statistics
Matches: 52, Mismatches: 3, Indels: 3
0.90 0.05 0.05
Matches are distributed among these distances:
33 42 0.81
34 1 0.02
35 2 0.04
36 7 0.13
ACGTcount: A:0.40, C:0.08, G:0.04, T:0.48
Consensus pattern (33 bp):
TATATATATAAACTATAGTTTATATTTATATAC
Found at i:661063 original size:18 final size:18
Alignment explanation
Indices: 661042--661189 Score: 102
Period size: 18 Copynumber: 7.7 Consensus size: 18
661032 TATACTATAT
*
661042 ATATGAACTATAGTTTAC
1 ATATAAACTATAGTTTAC
*
661060 ATATAAACTATATAGTTTAT
1 ATATAAAC--TATAGTTTAC
*
661080 ATACT-AGCTATAGTTTAC
1 ATA-TAAACTATAGTTTAC
*
661098 ATATAAACTATATAGTTTAT
1 ATATAAAC--TATAGTTTAC
*
661118 AT-TCTAACTATAGTTTAC
1 ATAT-AAACTATAGTTTAC
*
661136 ATATAAAATATAGTTGATATTTAC
1 ATATAAACTATA---G---TTTAC
*
661160 ATATGAACTATAGTTTAC
1 ATATAAACTATAGTTTAC
*
661178 ATATGAACTATA
1 ATATAAACTATA
661190 TATATAAACT
Statistics
Matches: 104, Mismatches: 12, Indels: 28
0.72 0.08 0.19
Matches are distributed among these distances:
17 1 0.01
18 55 0.53
19 2 0.02
20 28 0.27
21 3 0.03
24 15 0.14
ACGTcount: A:0.41, C:0.09, G:0.08, T:0.41
Consensus pattern (18 bp):
ATATAAACTATAGTTTAC
Found at i:661073 original size:38 final size:37
Alignment explanation
Indices: 661030--661195 Score: 165
Period size: 38 Copynumber: 4.3 Consensus size: 37
661020 AGTTTATATT
661030 TATATACTATATATATGAACTATAGTTTACATATAAAC
1 TATATA-TATATATATGAACTATAGTTTACATATAAAC
* *
661068 TATATAGTTTATATACT-AGCTATAGTTTACATATAAAC
1 TATATA-TATATATA-TGAACTATAGTTTACATATAAAC
* * *
661106 TATATAGTTTATAT-TCTAACTATAGTTTACATATAAAA
1 TATATA-TATATATAT-GAACTATAGTTTACATATAAAC
* *
661144 TATAGTTGATATTTACATATGAACTATAGTTTACATATGAAC
1 TATA--T-ATA--TATATATGAACTATAGTTTACATATAAAC
661186 TATATATATA
1 TATATATATA
661196 AACTATATAG
Statistics
Matches: 109, Mismatches: 10, Indels: 19
0.79 0.07 0.14
Matches are distributed among these distances:
36 1 0.01
37 2 0.02
38 70 0.64
39 4 0.04
40 3 0.03
41 1 0.01
42 27 0.25
43 1 0.01
ACGTcount: A:0.42, C:0.09, G:0.07, T:0.42
Consensus pattern (37 bp):
TATATATATATATATGAACTATAGTTTACATATAAAC
Found at i:661264 original size:7 final size:6
Alignment explanation
Indices: 661252--661614 Score: 58
Period size: 7 Copynumber: 57.7 Consensus size: 6
661242 ATAAACTATT
* * * *
661252 TATATA GTATATA T-TATA TATATA AACTATA GTTTATA TTTATA TACTACA
1 TATATA -TATATA TATATA TATATA TA-TATA -TATATA TATATA TA-TATA
* * * *
661303 TACTATA GTTTATA TTTATG TACTATA TAT-TA TATATA TAAACTA TATATA
1 TA-TATA -TATATA TATATA TA-TATA TATATA TATATA TATA-TA TATATA
* * * * * *
661354 CTATATA GTATA-A TTTACA TATGA-A CTATATA TAAAAA CCATATA AACTATA
1 -TATATA -TATATA TATATA TAT-ATA -TATATA TATATA -TATATA TA-TATA
* *
661406 TACTATA GT-TGATA TTTATA TACTATA TA-ATA TA-ATT TATACTA TAGTATA
1 TA-TATA -TAT-ATA TATATA TA-TATA TATATA TATATA TATA-TA TA-TATA
* * *
661457 TATAAA CTATATA T-TATA TAGT-TCA T-TAGTA TATATA -AAACTA TACAT-
1 TATATA -TATATA TATATA TA-TAT-A TATA-TA TATATA TATA-TA TATATA
* * * *
661505 TATATA GTTTAT- TAGTATA TATAAA CTATATA -ATATA TATAAA CTATATGG
1 TATATA -TATATA TA-TATA TATATA -TATATA TATATA TATATA -TATAT-A
* * * *
661556 TATATA TAAACTA TACAT- TATATA TATTTCA T-TAGTA TATATA AACTATA
1 TATATA TATA-TA TATATA TATATA TATAT-A TATA-TA TATATA TA-TATA
661606 TAT-TA TATA
1 TATATA TATA
661615 GTTCATTAGT
Statistics
Matches: 265, Mismatches: 45, Indels: 93
0.66 0.11 0.23
Matches are distributed among these distances:
5 49 0.18
6 82 0.31
7 130 0.49
8 4 0.02
ACGTcount: A:0.45, C:0.07, G:0.04, T:0.44
Consensus pattern (6 bp):
TATATA
Found at i:661264 original size:9 final size:8
Alignment explanation
Indices: 661252--661614 Score: 58
Period size: 9 Copynumber: 43.2 Consensus size: 8
661242 ATAAACTATT
661252 TATATAGTA
1 TATATA-TA
661261 TATAT-TA
1 TATATATA
661268 TATATATA
1 TATATATA
* *
661276 AACTATAGTT
1 TA-TATA-TA
*
661286 TATATTTA
1 TATATATA
*
661294 TATACTACA
1 TATA-TATA
*
661303 TACTATAGTT
1 TA-TATA-TA
*
661313 TATATTTA
1 TATATATA
*
661321 TGTACTATA
1 TATA-TATA
661330 TAT-TATA
1 TATATATA
*
661337 TATATAAA
1 TATATATA
661345 CTATATATA
1 -TATATATA
661354 CTATATAGTA
1 -TATATA-TA
*
661364 TA-ATTTA
1 TATATATA
*
661371 CATATGA-A
1 TATAT-ATA
661379 CTATATATA
1 -TATATATA
* * *
661388 AAAACCATA
1 TATA-TATA
*
661397 TAAACTATA
1 TATA-TATA
661406 TACTATAGT-
1 TA-TATA-TA
*
661415 TGATATTTA
1 T-ATATATA
661424 TATACTATA
1 TATA-TATA
661433 TA-ATATA
1 TATATATA
*
661440 -ATTTATA
1 TATATATA
661447 CTATAGTATA
1 -TATA-TATA
*
661457 TATAAACTA
1 TATATA-TA
661466 TATAT-TA
1 TATATATA
661473 TATAGT-TCA
1 TATA-TAT-A
661482 T-TAGTATA
1 TATA-TATA
*
661490 TATA-AAA
1 TATATATA
*
661497 CTATACAT-
1 -TATATATA
*
661505 TATATAGTT
1 TATATA-TA
661514 TAT-TAGTA
1 TATATA-TA
*
661522 TATATAAA
1 TATATATA
661530 CTATATA-A
1 -TATATATA
661538 TATATATA
1 TATATATA
* *
661546 AACTATATGG
1 TA-TATAT-A
661556 TATATATA
1 TATATATA
* *
661564 AACTATACA
1 TA-TATATA
661573 T-TATATA
1 TATATATA
*
661580 TATTTCAT-
1 TATAT-ATA
661588 TAGTATATA
1 TA-TATATA
*
661597 TAAACTATA
1 TATA-TATA
661606 TAT-TATA
1 TATATATA
661613 TA
1 TA
661615 GTTCATTAGT
Statistics
Matches: 261, Mismatches: 49, Indels: 90
0.65 0.12 0.22
Matches are distributed among these distances:
6 1 0.00
7 56 0.21
8 61 0.23
9 127 0.49
10 16 0.06
ACGTcount: A:0.45, C:0.07, G:0.04, T:0.44
Consensus pattern (8 bp):
TATATATA
Found at i:661275 original size:20 final size:20
Alignment explanation
Indices: 661252--661614 Score: 104
Period size: 20 Copynumber: 18.0 Consensus size: 20
661242 ATAAACTATT
*
661252 TATATAGTATATATTATATA
1 TATATACTATATATTATATA
*
661272 TATAAACTATAGT-TTATATTTA
1 TATATACTATA-TATTATA--TA
*
661294 TATACTACATACTATAGTTTATATT
1 TATA-TAC-TA-TATA--TTATATA
*
661319 TATGTACTATATATTATATA
1 TATATACTATATATTATATA
*
661339 TATAAACTATATATACTATATA
1 TATATACTATATAT--TATATA
*
661361 GTATAATTTAC-ATATGAACTATATA
1 -TAT-A--TACTATAT--ATTATATA
* * * *
661386 TAAAAACCATATA--A-A-C
1 TATATACTATATATTATATA
* *
661402 TATATACTATAGT-TGATATT
1 TATATACTATA-TATTATATA
*
661422 TATATACTATATAATATA-A
1 TATATACTATATATTATATA
* *
661441 TTTATACTATAGTATATATAAA
1 TATATACTATA-TAT-TATATA
*
661463 CTATATATTATATAGTTCAT-TA
1 -TATATACTATATA-TT-ATATA
* * *
661485 GTATATA-TA-AAACTATACA
1 -TATATACTATATATTATATA
*
661504 T-TATA-TAGTTTATTAGTATA
1 TATATACTA-TATATTA-TATA
*
661524 TATAAACTATATA--ATATA
1 TATATACTATATATTATATA
* **
661542 TATAAACTATATGGTATATA
1 TATATACTATATATTATATA
*
661562 TA-A-ACTATACATTATATA
1 TATATACTATATATTATATA
* *
661580 TAT-TTC-AT-TAGTATATA
1 TATATACTATATATTATATA
661597 TA-A-ACTATATATTATATA
1 TATATACTATATATTATATA
661615 GTTCATTAGT
Statistics
Matches: 256, Mismatches: 44, Indels: 88
0.66 0.11 0.23
Matches are distributed among these distances:
16 9 0.04
17 19 0.07
18 45 0.18
19 20 0.08
20 62 0.24
21 15 0.06
22 33 0.13
23 20 0.08
24 9 0.04
25 16 0.06
26 2 0.01
27 6 0.02
ACGTcount: A:0.45, C:0.07, G:0.04, T:0.44
Consensus pattern (20 bp):
TATATACTATATATTATATA
Found at i:661487 original size:33 final size:33
Alignment explanation
Indices: 661450--661763 Score: 311
Period size: 33 Copynumber: 9.8 Consensus size: 33
661440 ATTTATACTA
661450 TAGTATATATAAACTATATATTATATAGTTCAT
1 TAGTATATATAAACTATATATTATATAGTTCAT
* *
661483 TAGTATATATAAAACTATACATTATATAGTTTAT
1 TAGTATATAT-AAACTATATATTATATAGTTCAT
**
661517 TAGTATATATAAACTATATAATATATATA-AACTAT
1 TAGTATATATAAACTATAT-AT-TATATAGTTC-AT
* * *
661552 ATGGTATATATAAACTATACATTATATATATTTCAT
1 -TAGTATATATAAACTATATA-T-TATATAGTTCAT
661588 TAGTATATATAAACTATATATTATATAGTTCAT
1 TAGTATATATAAACTATATATTATATAGTTCAT
* *
661621 TAGTATATATAACCTATATAGTATAT-G-----
1 TAGTATATATAAACTATATATTATATAGTTCAT
* *
661648 --GTATATACAAACTATATATTATATAGTGCAT
1 TAGTATATATAAACTATATATTATATAGTTCAT
*
661679 TAGTATATAT-AAC-CTATA-TA-ATA--T-A-
1 TAGTATATATAAACTATATATTATATAGTTCAT
*
661704 TGGTATATATAAACTATATATTATATAGTTCAT
1 TAGTATATATAAACTATATATTATATAGTTCAT
* *
661737 TAATATATATAAACTATATAGTATATA
1 TAGTATATATAAACTATATATTATATA
661764 TAAACTATAT
Statistics
Matches: 232, Mismatches: 26, Indels: 46
0.76 0.09 0.15
Matches are distributed among these distances:
25 30 0.13
26 5 0.02
27 4 0.02
28 2 0.01
29 6 0.03
30 2 0.01
31 5 0.02
32 5 0.02
33 84 0.36
34 34 0.15
35 27 0.12
36 27 0.12
37 1 0.00
ACGTcount: A:0.44, C:0.07, G:0.06, T:0.43
Consensus pattern (33 bp):
TAGTATATATAAACTATATATTATATAGTTCAT
Found at i:661536 original size:138 final size:137
Alignment explanation
Indices: 661382--661632 Score: 341
Period size: 138 Copynumber: 1.8 Consensus size: 137
661372 ATATGAACTA
* * *
661382 TATATAAAAACCATATAA-ACTATAT-ACTATAGTTGATATTTATATACTATATAATATA-AT-T
1 TATATAAAAACCATATAATA-TATATAACTATA--TGATATATATAAACTATACAATATATATAT
661443 TAT-ACTATAGTATATATAAACTATATATTATATAGTTCATTAGTATATATAAAACTATACATTA
63 T-TCA-T-TAGTATATATAAACTATATATTATATAGTTCATTAGTATATATAAAACTATACATTA
661507 TATAGTTTATTAG
125 TATAGTTTATTAG
* * * *
661520 TATATATAAACTATATAATATATATAAACTATATGGTATATATAAACTATACATTATATATATTT
1 TATATAAAAACCATATAATATATAT-AACTATATGATATATATAAACTATACAATATATATATTT
661585 CATTAGTATATATAAACTATATATTATATAGTTCATTAGTATATATAA
65 CATTAGTATATATAAACTATATATTATATAGTTCATTAGTATATATAA
661633 CCTATATAGT
Statistics
Matches: 100, Mismatches: 7, Indels: 12
0.84 0.06 0.10
Matches are distributed among these distances:
138 86 0.86
139 5 0.05
140 9 0.09
ACGTcount: A:0.45, C:0.07, G:0.05, T:0.43
Consensus pattern (137 bp):
TATATAAAAACCATATAATATATATAACTATATGATATATATAAACTATACAATATATATATTTC
ATTAGTATATATAAACTATATATTATATAGTTCATTAGTATATATAAAACTATACATTATATAGT
TTATTAG
Found at i:661568 original size:69 final size:71
Alignment explanation
Indices: 661450--661632 Score: 238
Period size: 69 Copynumber: 2.7 Consensus size: 71
661440 ATTTATACTA
** *
661450 TAGTATATATAAACTATAT-AT-TATATAGTTCATTAGTATATATAAAACTATACATTATATA-G
1 TAGTATATATAAACTATATAATATATATAACTCATTAGTATATATAAAACTATACATTATATATA
661512 TTT-AT
66 TTTCAT
*
661517 TAGTATATATAAACTATATAATATATATAAACT-ATATGGTATATAT-AAACTATACATTATATA
1 TAGTATATATAAACTATATAATATATAT-AACTCAT-TAGTATATATAAAACTATACATTATATA
661580 TATTTCAT
64 TATTTCAT
**
661588 TAGTATATATAAACTATAT-AT-TATATAGTTCATTAGTATATATAA
1 TAGTATATATAAACTATATAATATATATAACTCATTAGTATATATAA
661633 CCTATATAGT
Statistics
Matches: 101, Mismatches: 7, Indels: 14
0.83 0.06 0.11
Matches are distributed among these distances:
67 19 0.19
68 13 0.13
69 32 0.32
70 16 0.16
71 21 0.21
ACGTcount: A:0.45, C:0.06, G:0.05, T:0.44
Consensus pattern (71 bp):
TAGTATATATAAACTATATAATATATATAACTCATTAGTATATATAAAACTATACATTATATATA
TTTCAT
Found at i:661631 original size:2 final size:2
Alignment explanation
Indices: 661252--661614 Score: 58
Period size: 2 Copynumber: 173.0 Consensus size: 2
661242 ATAAACTATT
* * *
661252 TA TA TA GTA TA TA T- TA TA TA TA TA AA CTA TA GTT TA TA TT TA
1 TA TA TA -TA TA TA TA TA TA TA TA TA TA -TA TA -TA TA TA TA TA
* * * *
661294 TA TA CTA CA TA CTA TA GTT TA TA TT TA TG TA CTA TA TA T- TA TA
1 TA TA -TA TA TA -TA TA -TA TA TA TA TA TA TA -TA TA TA TA TA TA
* * *
661337 TA TA TA AA CTA TA TA TA CTA TA TA GTA TA -A TT TA CA TA TGA -A
1 TA TA TA TA -TA TA TA TA -TA TA TA -TA TA TA TA TA TA TA T-A TA
* * * * *
661379 CTA TA TA TA AA AA CCA TA TA AA CTA TA TA CTA TA GT- TGA TA TT
1 -TA TA TA TA TA TA -TA TA TA TA -TA TA TA -TA TA -TA T-A TA TA
* *
661422 TA TA TA CTA TA TA -A TA TA -A TT TA TA CTA TA GTA TA TA TA AA
1 TA TA TA -TA TA TA TA TA TA TA TA TA TA -TA TA -TA TA TA TA TA
* *
661463 CTA TA TA T- TA TA TA GT- TCA T- TA GTA TA TA TA -A AA CTA TA CA
1 -TA TA TA TA TA TA TA -TA T-A TA TA -TA TA TA TA TA TA -TA TA TA
* *
661504 T- TA TA TA GTT TA T- TA GTA TA TA TA AA CTA TA TA -A TA TA TA
1 TA TA TA TA -TA TA TA TA -TA TA TA TA TA -TA TA TA TA TA TA TA
* * * * *
661544 TA AA CTA TA TGG TA TA TA TA AA CTA TA CA T- TA TA TA TA TT TCA
1 TA TA -TA TA T-A TA TA TA TA TA -TA TA TA TA TA TA TA TA TA T-A
*
661587 T- TA GTA TA TA TA AA CTA TA TA T- TA TA TA
1 TA TA -TA TA TA TA TA -TA TA TA TA TA TA TA
661615 GTTCATTAGT
Statistics
Matches: 260, Mismatches: 50, Indels: 102
0.63 0.12 0.25
Matches are distributed among these distances:
1 17 0.07
2 196 0.75
3 47 0.18
ACGTcount: A:0.45, C:0.07, G:0.04, T:0.44
Consensus pattern (2 bp):
TA
Found at i:661660 original size:58 final size:58
Alignment explanation
Indices: 661590--661802 Score: 307
Period size: 58 Copynumber: 3.8 Consensus size: 58
661580 TATTTCATTA
661590 GTATATATAAACTATATATTATATAGTTCATTAGTATATATAACCTATATAGTATATG
1 GTATATATAAACTATATATTATATAGTTCATTAGTATATATAACCTATATAGTATATG
* * *
661648 GTATATACAAACTATATATTATATAGTGCATTAGTATATATAACCTATATAATATATG
1 GTATATATAAACTATATATTATATAGTTCATTAGTATATATAACCTATATAGTATATG
* *
661706 GTATATATAAACTATATATTATATAGTTCATTA--ATATAT-A--TA-A-ACTATATA
1 GTATATATAAACTATATATTATATAGTTCATTAGTATATATAACCTATATAGTATATG
*
661757 GTATATATAAACTATATATTGA-AAAGTTCATTAGTATATATAACCT
1 GTATATATAAACTATATATT-ATATAGTTCATTAGTATATATAACCT
661803 GAATTGCCCA
Statistics
Matches: 141, Mismatches: 8, Indels: 14
0.87 0.05 0.09
Matches are distributed among these distances:
51 36 0.26
52 2 0.01
53 8 0.06
54 1 0.01
55 1 0.01
56 7 0.05
58 86 0.61
ACGTcount: A:0.44, C:0.08, G:0.08, T:0.41
Consensus pattern (58 bp):
GTATATATAAACTATATATTATATAGTTCATTAGTATATATAACCTATATAGTATATG
Found at i:661662 original size:25 final size:25
Alignment explanation
Indices: 661623--661776 Score: 116
Period size: 25 Copynumber: 5.8 Consensus size: 25
661613 TAGTTCATTA
* *
661623 GTATATATAACCTATATAGTATATG
1 GTATATATAAACTATATATTATATG
*
661648 GTATATACAAACTATATATTATATAG
1 GTATATATAAACTATATATTATAT-G
*
661674 TGCATTAGTATATATAACCTATATAATATATG
1 -G---TA-TATATA-AA-CTATATATTATATG
*
661706 GTATATATAAACTATATATTATATA
1 GTATATATAAACTATATATTATATG
* *
661731 GT-TCAT-TAATA-TATATAAACTATATA
1 GTAT-ATATAA-ACTATAT--ATTATATG
661757 GTATATATAAACTATATATT
1 GTATATATAAACTATATATT
661777 GAAAAGTTCA
Statistics
Matches: 105, Mismatches: 9, Indels: 30
0.73 0.06 0.21
Matches are distributed among these distances:
24 9 0.09
25 40 0.38
26 15 0.14
27 16 0.15
28 2 0.02
30 2 0.02
31 6 0.06
32 3 0.03
33 12 0.11
ACGTcount: A:0.44, C:0.07, G:0.07, T:0.42
Consensus pattern (25 bp):
GTATATATAAACTATATATTATATG
Found at i:662149 original size:61 final size:60
Alignment explanation
Indices: 662068--662207 Score: 181
Period size: 61 Copynumber: 2.3 Consensus size: 60
662058 TATAAGGATC
* *
662068 AAATTGAAAAAAAATTAAATATTAAGCTTAAATTAATAAACTATAACATTAAATTTGGACT
1 AAATTG-AAAAAAATTAAATATGAAGCTTAAATTAATAAACTACAACATTAAATTTGGACT
* * * * *
662129 AAATTGAATAAAATTGAAATATGAAGCTTAAATTAATATATTACATCATTAACTTTGGACT
1 AAATTGAAAAAAATT-AAATATGAAGCTTAAATTAATAAACTACAACATTAAATTTGGACT
* *
662190 AAATTGAACAAATTTAAA
1 AAATTGAAAAAAATTAAA
662208 ACTAGGAGAC
Statistics
Matches: 69, Mismatches: 9, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
60 11 0.16
61 58 0.84
ACGTcount: A:0.51, C:0.07, G:0.08, T:0.34
Consensus pattern (60 bp):
AAATTGAAAAAAATTAAATATGAAGCTTAAATTAATAAACTACAACATTAAATTTGGACT
Found at i:662683 original size:100 final size:104
Alignment explanation
Indices: 662556--662769 Score: 321
Period size: 101 Copynumber: 2.1 Consensus size: 104
662546 TGTTCTTTAT
* *
662556 TTGTTCATCCCAGTTCTTCCCCAAAACCCTCCTTTGATCTTC-AAAACACCGAAACACAAACCAT
1 TTGTTCATCCCAATTCTTCCCCAAAACCCTCATTTGATCTTCAAAAACACCGAAACACAAACCAT
*
662620 TTCATG-TTTTTTCGATCAAACACCCA-AATATTCATCCG
66 TTCATGTTTTTTTCGATCAAACACACACAA-ATTCATCCG
*
662658 -TGTTCAT-CCAATTCTTCCCCAAAACCCTCATTTGATCTTCAAAAACACCGAAACCCAAACCAT
1 TTGTTCATCCCAATTCTTCCCCAAAACCCTCATTTGATCTTCAAAAACACCGAAACACAAACCAT
*
662721 TTCATGTTTTTTTTTCGATCAAACACACACAAATTCTTCCG
66 TTCATG--TTTTTTTCGATCAAACACACACAAATTCATCCG
662762 TTGTTCAT
1 TTGTTCAT
662770 TCGTGTTCTT
Statistics
Matches: 101, Mismatches: 5, Indels: 9
0.88 0.04 0.08
Matches are distributed among these distances:
100 31 0.31
101 34 0.34
104 27 0.27
105 9 0.09
ACGTcount: A:0.30, C:0.31, G:0.07, T:0.32
Consensus pattern (104 bp):
TTGTTCATCCCAATTCTTCCCCAAAACCCTCATTTGATCTTCAAAAACACCGAAACACAAACCAT
TTCATGTTTTTTTCGATCAAACACACACAAATTCATCCG
Found at i:662949 original size:6 final size:6
Alignment explanation
Indices: 662909--663103 Score: 160
Period size: 6 Copynumber: 32.8 Consensus size: 6
662899 ACCCCTAACT
* * * * * *
662909 CAAACC CTAACC CTAACC TAAATC CAATCC CAAACC TAAACC CAAACC
1 CAAACC CAAACC CAAACC CAAACC CAAACC CAAACC CAAACC CAAACC
* * ** *
662957 CAAA-C CGAACT CAAA-C TGAACC CAAACC CAAACC CAAACC CGAACC
1 CAAACC CAAACC CAAACC CAAACC CAAACC CAAACC CAAACC CAAACC
* * * * **
663003 CAAACC CAAGCC CAAACC CAAGCC CAAACC TAAACC TAAACC TTAACC
1 CAAACC CAAACC CAAACC CAAACC CAAACC CAAACC CAAACC CAAACC
* ** * * * *
663051 CAAACT TGAACC TAAACC CAAACC CGAACC CGAACC CGAACC CAAACC
1 CAAACC CAAACC CAAACC CAAACC CAAACC CAAACC CAAACC CAAACC
663099 CAAAC
1 CAAAC
663104 TATTCGAAAC
Statistics
Matches: 151, Mismatches: 36, Indels: 4
0.79 0.19 0.02
Matches are distributed among these distances:
5 6 0.04
6 145 0.96
ACGTcount: A:0.44, C:0.44, G:0.05, T:0.08
Consensus pattern (6 bp):
CAAACC
Found at i:663364 original size:31 final size:31
Alignment explanation
Indices: 663329--663490 Score: 279
Period size: 31 Copynumber: 5.2 Consensus size: 31
663319 CTTGATATAT
*
663329 ATATACTGGTTTATTTCTGTTGATGTAAATG
1 ATATACTGGTTTATTGCTGTTGATGTAAATG
663360 ATATACTGGTTTATTGCTGTTGATGTAAATG
1 ATATACTGGTTTATTGCTGTTGATGTAAATG
*
663391 ATATATTGGTTTATTGCTGTTGATGTAAATG
1 ATATACTGGTTTATTGCTGTTGATGTAAATG
**
663422 ATATACTGGTTTATTATTGTTGATGTAAATG
1 ATATACTGGTTTATTGCTGTTGATGTAAATG
*
663453 ATATACTAGTTTATTGCTGTTGATGTAAATG
1 ATATACTGGTTTATTGCTGTTGATGTAAATG
663484 ATATACT
1 ATATACT
663491 TTCAGAAGCA
Statistics
Matches: 123, Mismatches: 8, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 123 1.00
ACGTcount: A:0.28, C:0.06, G:0.20, T:0.47
Consensus pattern (31 bp):
ATATACTGGTTTATTGCTGTTGATGTAAATG
Found at i:663689 original size:64 final size:63
Alignment explanation
Indices: 663462--663690 Score: 323
Period size: 63 Copynumber: 3.6 Consensus size: 63
663452 GATATACTAG
* *
663462 TTTATTGCTGTTGATGTAAATGATATACTTTCAGAAGCATTTAATGTAAACTAACCCTGGTTT
1 TTTATTGTTGTTGATGTAAATGATATACTGTCAGAAGCATTTAATGTAAACTAACCCTGGTTT
*
663525 TTTATTGTTGTTGATGTAAATGATATACTGTCAGAAGTATTTAATGTAAACTAACCCTGGTTT
1 TTTATTGTTGTTGATGTAAATGATATACTGTCAGAAGCATTTAATGTAAACTAACCCTGGTTT
* * * *
663588 TTTATTGTTGTTGATATAAATGATATACTATCAGAAGCATTTAATGTAAACTAGCCATGGTTT
1 TTTATTGTTGTTGATGTAAATGATATACTGTCAGAAGCATTTAATGTAAACTAACCCTGGTTT
* ** ** * *
663651 TTTTTTGCAAGGGGATGTAAATGATATAATGTCTGAAGCA
1 TTTATTG-TTGTTGATGTAAATGATATACTGTCAGAAGCA
663691 ATTGATTTAA
Statistics
Matches: 148, Mismatches: 17, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
63 124 0.84
64 24 0.16
ACGTcount: A:0.31, C:0.10, G:0.18, T:0.41
Consensus pattern (63 bp):
TTTATTGTTGTTGATGTAAATGATATACTGTCAGAAGCATTTAATGTAAACTAACCCTGGTTT
Found at i:665058 original size:23 final size:23
Alignment explanation
Indices: 665031--665078 Score: 96
Period size: 23 Copynumber: 2.1 Consensus size: 23
665021 GCAGGATACG
665031 TGCTGAATCGATGCAACGATGCT
1 TGCTGAATCGATGCAACGATGCT
665054 TGCTGAATCGATGCAACGATGCT
1 TGCTGAATCGATGCAACGATGCT
665077 TG
1 TG
665079 TCGGTTGCTG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.25, C:0.21, G:0.27, T:0.27
Consensus pattern (23 bp):
TGCTGAATCGATGCAACGATGCT
Found at i:665595 original size:18 final size:17
Alignment explanation
Indices: 665572--665607 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 17
665562 ACCAAATTTA
665572 TAATATACAAACTATAAT
1 TAATATACAAACTA-AAT
*
665590 TAATATATAAACTAAAT
1 TAATATACAAACTAAAT
665607 T
1 T
665608 TCAAAAAGTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 4 0.24
18 13 0.76
ACGTcount: A:0.56, C:0.08, G:0.00, T:0.36
Consensus pattern (17 bp):
TAATATACAAACTAAAT
Found at i:665776 original size:16 final size:16
Alignment explanation
Indices: 665757--665795 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
665747 TGAGTCAATT
* *
665757 ACAGGTCAGGTTCATA
1 ACAGGTCAGGTTAAAA
*
665773 ACAGGTCTGGTTAAAA
1 ACAGGTCAGGTTAAAA
665789 ACAGGTC
1 ACAGGTC
665796 GGGTAATACC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.33, C:0.18, G:0.26, T:0.23
Consensus pattern (16 bp):
ACAGGTCAGGTTAAAA
Found at i:665882 original size:25 final size:26
Alignment explanation
Indices: 665820--665885 Score: 82
Period size: 25 Copynumber: 2.5 Consensus size: 26
665810 ATTTACCAAG
665820 TCAATCTCGGGTTCATATCAGTCGGAT
1 TCAAT-TCGGGTTCATATCAGTCGGAT
* *
665847 GCAATTCGGGTATCATAT-ATTCGG-T
1 TCAATTCGGGT-TCATATCAGTCGGAT
665872 TCAATTCGGGTTCA
1 TCAATTCGGGTTCA
665886 GGTTGTTCTC
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
24 3 0.09
25 11 0.31
26 11 0.31
27 10 0.29
ACGTcount: A:0.23, C:0.20, G:0.23, T:0.35
Consensus pattern (26 bp):
TCAATTCGGGTTCATATCAGTCGGAT
Found at i:680158 original size:21 final size:21
Alignment explanation
Indices: 680104--680151 Score: 64
Period size: 21 Copynumber: 2.3 Consensus size: 21
680094 GTACATAGAT
680104 ATAAAATCTA-AAAAATATAAA
1 ATAAAAT-TATAAAAATATAAA
*
680125 ATGAAATTATAAAAATAT-AA
1 ATAAAATTATAAAAATATAAA
680145 ATAAAAT
1 ATAAAAT
680152 ATTTAAATTA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
20 10 0.42
21 14 0.58
ACGTcount: A:0.69, C:0.02, G:0.02, T:0.27
Consensus pattern (21 bp):
ATAAAATTATAAAAATATAAA
Done.