Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009174.1 Hibiscus syriacus cultivar Beakdansim tig00112737_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: 1358226
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 5 of 7
Found at i:879572 original size:19 final size:19
Alignment explanation
Indices: 879550--879596 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 19
879540 TTGCGATTTT
879550 CATTTCGCATTACGATAGC
1 CATTTCGCATTACGATAGC
* * *
879569 CATTTCCGCGTTGCGATAGT
1 CATTT-CGCATTACGATAGC
879589 CATTTCGC
1 CATTTCGC
879597 GTTGCGATTT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
19 8 0.33
20 16 0.67
ACGTcount: A:0.19, C:0.28, G:0.19, T:0.34
Consensus pattern (19 bp):
CATTTCGCATTACGATAGC
Found at i:879599 original size:19 final size:19
Alignment explanation
Indices: 879538--879604 Score: 80
Period size: 19 Copynumber: 3.5 Consensus size: 19
879528 GCGATTTTGT
**
879538 CGTTGCGATTTTCATTTCG
1 CGTTGCGATAGTCATTTCG
* * *
879557 CATTACGATAGCCATTTCCG
1 CGTTGCGATAGTCATTT-CG
879577 CGTTGCGATAGTCATTTCG
1 CGTTGCGATAGTCATTTCG
879596 CGTTGCGAT
1 CGTTGCGAT
879605 TTTAAGTTTC
Statistics
Matches: 39, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
19 23 0.59
20 16 0.41
ACGTcount: A:0.16, C:0.24, G:0.22, T:0.37
Consensus pattern (19 bp):
CGTTGCGATAGTCATTTCG
Found at i:881492 original size:14 final size:14
Alignment explanation
Indices: 881473--881508 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
881463 ATTGTTTAAT
881473 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
* *
881487 TGATTTGTAAATGT
1 TGATTTGTAAAAGA
881501 TGATTTGT
1 TGATTTGT
881509 TTAATTGATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.22, T:0.47
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:881641 original size:33 final size:33
Alignment explanation
Indices: 881596--881711 Score: 142
Period size: 33 Copynumber: 3.4 Consensus size: 33
881586 AAAACAGACT
* ***
881596 ATCGCAACGCGAAATGGCTATCGCAACGAGAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAAA
*
881629 ATCGCAATGCGAAATGAAAATCACAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAAATCGCAA--CG--A-GAAA
881667 ATCGCAATGCGAAATGAAAATCGCAACGAGAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAAA
881700 ATCGCAATGCGA
1 ATCGCAATGCGA
881712 TTTTCATTTC
Statistics
Matches: 72, Mismatches: 6, Indels: 10
0.82 0.07 0.11
Matches are distributed among these distances:
33 37 0.51
34 1 0.01
35 2 0.03
36 2 0.03
37 1 0.01
38 29 0.40
ACGTcount: A:0.45, C:0.20, G:0.22, T:0.14
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAAA
Found at i:881647 original size:19 final size:19
Alignment explanation
Indices: 881625--881711 Score: 130
Period size: 19 Copynumber: 4.8 Consensus size: 19
881615 ATCGCAACGA
881625 GAAAATCGCAATGCGAAAT
1 GAAAATCGCAATGCGAAAT
*
881644 GAAAATCACAATGCGAAAT
1 GAAAATCGCAATGCGAAAT
881663 GAAAATCGCAATGCGAAAT
1 GAAAATCGCAATGCGAAAT
881682 GAAAATCGCAA--CG--A-
1 GAAAATCGCAATGCGAAAT
881696 GAAAATCGCAATGCGA
1 GAAAATCGCAATGCGA
881712 TTTTCATTTC
Statistics
Matches: 63, Mismatches: 2, Indels: 8
0.86 0.03 0.11
Matches are distributed among these distances:
14 11 0.17
15 1 0.02
16 2 0.03
17 2 0.03
19 47 0.75
ACGTcount: A:0.48, C:0.17, G:0.21, T:0.14
Consensus pattern (19 bp):
GAAAATCGCAATGCGAAAT
Found at i:881755 original size:20 final size:20
Alignment explanation
Indices: 881730--881780 Score: 93
Period size: 20 Copynumber: 2.5 Consensus size: 20
881720 TCGCATTGCG
*
881730 ATTTTCTCGTTGCGATAGCC
1 ATTTTCGCGTTGCGATAGCC
881750 ATTTTCGCGTTGCGATAGCC
1 ATTTTCGCGTTGCGATAGCC
881770 ATTTTCGCGTT
1 ATTTTCGCGTT
881781 ATGATAGTCA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.14, C:0.24, G:0.22, T:0.41
Consensus pattern (20 bp):
ATTTTCGCGTTGCGATAGCC
Found at i:881786 original size:20 final size:20
Alignment explanation
Indices: 881730--881787 Score: 80
Period size: 20 Copynumber: 2.9 Consensus size: 20
881720 TCGCATTGCG
* *
881730 ATTTTCTCGTTGCGATAGCC
1 ATTTTCGCGTTACGATAGCC
*
881750 ATTTTCGCGTTGCGATAGCC
1 ATTTTCGCGTTACGATAGCC
*
881770 ATTTTCGCGTTATGATAG
1 ATTTTCGCGTTACGATAG
881788 TCAAATGAAT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 35 1.00
ACGTcount: A:0.17, C:0.21, G:0.22, T:0.40
Consensus pattern (20 bp):
ATTTTCGCGTTACGATAGCC
Found at i:885395 original size:19 final size:19
Alignment explanation
Indices: 885373--885464 Score: 78
Period size: 19 Copynumber: 5.4 Consensus size: 19
885363 GGAAATTACT
885373 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
885392 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
885406 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
* *
885425 ATCGCAA--CG--CT-AAT
1 ATCGCAATGCGAAATGAAA
*
885439 TTCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
885458 ATCGCAA
1 ATCGCAA
885465 CGAGATAATC
Statistics
Matches: 55, Mismatches: 8, Indels: 20
0.66 0.10 0.24
Matches are distributed among these distances:
14 18 0.33
15 2 0.04
16 4 0.07
17 4 0.07
18 2 0.04
19 25 0.45
ACGTcount: A:0.43, C:0.20, G:0.21, T:0.16
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:885415 original size:33 final size:32
Alignment explanation
Indices: 885373--885485 Score: 163
Period size: 33 Copynumber: 3.4 Consensus size: 32
885363 GGAAATTACT
885373 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGA-A
**
885406 ATCGCAATGCGAAATGAAAATCGCAACGCTAA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAA
*
885438 TTTCGCAATGCGAAATGAAAATCGCAACGAGATA
1 -ATCGCAATGCGAAATGAAAATCGCAACGAGA-A
*
885472 ATCGCAACGCGAAA
1 ATCGCAATGCGAAA
885486 GGCTACCTGG
Statistics
Matches: 71, Mismatches: 7, Indels: 4
0.87 0.09 0.05
Matches are distributed among these distances:
32 1 0.01
33 69 0.97
34 1 0.01
ACGTcount: A:0.43, C:0.20, G:0.21, T:0.15
Consensus pattern (32 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAA
Found at i:885968 original size:33 final size:33
Alignment explanation
Indices: 885924--886050 Score: 175
Period size: 33 Copynumber: 3.8 Consensus size: 33
885914 GGAAATTACT
885924 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
* **
885957 ATCGCATTGCGAAATGAAAATCGCAACGCTA-A
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
* * *
885989 TTTCGCAATACGAAATGAAAATCGCAACGAGGGA
1 -ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
*
886023 ATCGCAACGCGAAATGAAAATCGCAACG
1 ATCGCAATGCGAAATGAAAATCGCAACG
886051 CGAATTTAAT
Statistics
Matches: 80, Mismatches: 12, Indels: 4
0.83 0.12 0.04
Matches are distributed among these distances:
32 1 0.01
33 78 0.98
34 1 0.01
ACGTcount: A:0.43, C:0.20, G:0.22, T:0.15
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:885974 original size:551 final size:551
Alignment explanation
Indices: 884933--886036 Score: 2154
Period size: 551 Copynumber: 2.0 Consensus size: 551
884923 CCATTGATAG
884933 AAGGCTACCTGGCCGACCAAAAAGTCACGATCGTATACCGTCTAAGGGTGAAGAGAAGAAGAGAT
1 AAGGCTACCTGGCCGACCAAAAAGTCACGATCGTATACCGTCTAAGGGTGAAGAGAAGAAGAGAT
884998 CGACATGTAGTCGGTGCAAGGAAAGTGGTCATACAAGGTTGACATGTGGATCACCAGTGCCATCA
66 CGACATGTAGTCGGTGCAAGGAAAGTGGTCATACAAGGTTGACATGTGGATCACCAGTGCCATCA
885063 CAATCATCTTTTCCTCTACCAAAATATGGATCATCATCAAAATCCAAAGCTCATATGGTGTCAAG
131 CAATCATCTTTTCCTCTACCAAAATATGGATCATCATCAAAATCCAAAGCTCATATGGTGTCAAG
*
885128 AAAAAGGCAATCAAAATCGCAATCATCTTTAAAATCCCAATCACAATTGGCTTCACCTTTTGGGA
196 AAAAAGGCAATCAAAATCGCAATCATCTTTAAAATCCCAATCACAACTGGCTTCACCTTTTGGGA
885193 CTGTTAACTTAGGTGATTTTTAAATGCAAACGTTGTATTATGTAGATTTTATGTGTGAACTTTTA
261 CTGTTAACTTAGGTGATTTTTAAATGCAAACGTTGTATTATGTAGATTTTATGTGTGAACTTTTA
885258 ACATTTTCAGTTAGGCATGTATTAGTAACTTGAGTTTGAAAATTGCTATGATCTGTTCAGTTGTT
326 ACATTTTCAGTTAGGCATGTATTAGTAACTTGAGTTTGAAAATTGCTATGATCTGTTCAGTTGTT
885323 ATCACTTAATAGGCAATCATCTTAATGTCTATCGCAACACGGAAATTACTATCGCAATGCGAAAT
391 ATCACTTAATAGGCAATCATCTTAATGTCTATCGCAACACGGAAATTACTATCGCAATGCGAAAT
*
885388 GAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCTAATTTCGCAATGCGAAA
456 GAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCTAATTTCGCAATACGAAA
*
885453 TGAAAATCGCAACGAGATAATCGCAACGCGA
521 TGAAAATCGCAACGAGAGAATCGCAACGCGA
885484 AAGGCTACCTGGCCGACCAAAAAGTCACGATCGTATACCGTCTAAGGGTGAAGAGAAGAAGAGAT
1 AAGGCTACCTGGCCGACCAAAAAGTCACGATCGTATACCGTCTAAGGGTGAAGAGAAGAAGAGAT
885549 CGACATGTAGTCGGTGCAAGGAAAGTGGTCATACAAGGTTGACATGTGGATCACCAGTGCCATCA
66 CGACATGTAGTCGGTGCAAGGAAAGTGGTCATACAAGGTTGACATGTGGATCACCAGTGCCATCA
885614 CAATCATCTTTTCCTCTACCAAAATATGGATCATCATCAAAATCCAAAGCTCATATGGTGTCAAG
131 CAATCATCTTTTCCTCTACCAAAATATGGATCATCATCAAAATCCAAAGCTCATATGGTGTCAAG
885679 AAAAAGGCAATCAAAATCGCAATCATCTTTAAAATCCCAATCACAACTGGCTTCACCTTTTGGGA
196 AAAAAGGCAATCAAAATCGCAATCATCTTTAAAATCCCAATCACAACTGGCTTCACCTTTTGGGA
885744 CTGTTAACTTAGGTGATTTTTAAATGCAAACGTTGTATTATGTAGATTTTATGTGTGAACTTTTA
261 CTGTTAACTTAGGTGATTTTTAAATGCAAACGTTGTATTATGTAGATTTTATGTGTGAACTTTTA
885809 ACATTTTCAGTTAGGCATGTATTAGTAACTTGAGTTTGAAAATTGCTATGATCTGTTCAGTTGTT
326 ACATTTTCAGTTAGGCATGTATTAGTAACTTGAGTTTGAAAATTGCTATGATCTGTTCAGTTGTT
*
885874 ATCACTTAATAGGCAATCATCTTAATGTCTATCGCAACGCGGAAATTACTATCGCAATGCGAAAT
391 ATCACTTAATAGGCAATCATCTTAATGTCTATCGCAACACGGAAATTACTATCGCAATGCGAAAT
*
885939 GAAAATCGCAACGAGAGAATCGCATTGCGAAATGAAAATCGCAACGCTAATTTCGCAATACGAAA
456 GAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCTAATTTCGCAATACGAAA
*
886004 TGAAAATCGCAACGAGGGAATCGCAACGCGA
521 TGAAAATCGCAACGAGAGAATCGCAACGCGA
886035 AA
1 AA
886037 TGAAAATCGC
Statistics
Matches: 547, Mismatches: 6, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
551 547 1.00
ACGTcount: A:0.35, C:0.19, G:0.20, T:0.27
Consensus pattern (551 bp):
AAGGCTACCTGGCCGACCAAAAAGTCACGATCGTATACCGTCTAAGGGTGAAGAGAAGAAGAGAT
CGACATGTAGTCGGTGCAAGGAAAGTGGTCATACAAGGTTGACATGTGGATCACCAGTGCCATCA
CAATCATCTTTTCCTCTACCAAAATATGGATCATCATCAAAATCCAAAGCTCATATGGTGTCAAG
AAAAAGGCAATCAAAATCGCAATCATCTTTAAAATCCCAATCACAACTGGCTTCACCTTTTGGGA
CTGTTAACTTAGGTGATTTTTAAATGCAAACGTTGTATTATGTAGATTTTATGTGTGAACTTTTA
ACATTTTCAGTTAGGCATGTATTAGTAACTTGAGTTTGAAAATTGCTATGATCTGTTCAGTTGTT
ATCACTTAATAGGCAATCATCTTAATGTCTATCGCAACACGGAAATTACTATCGCAATGCGAAAT
GAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCTAATTTCGCAATACGAAA
TGAAAATCGCAACGAGAGAATCGCAACGCGA
Found at i:886035 original size:66 final size:66
Alignment explanation
Indices: 885925--886057 Score: 221
Period size: 66 Copynumber: 2.0 Consensus size: 66
885915 GAAATTACTA
* ** *
885925 TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCATTGCGAAATGAAAATCGCAACGCTAAT
1 TCGCAATACGAAATGAAAATCGCAACGAGAGAATCGCAACGCGAAATGAAAATCGCAACGCGAAT
885990 T
66 T
*
885991 TCGCAATACGAAATGAAAATCGCAACGAGGGAATCGCAACGCGAAATGAAAATCGCAACGCGAAT
1 TCGCAATACGAAATGAAAATCGCAACGAGAGAATCGCAACGCGAAATGAAAATCGCAACGCGAAT
886056 T
66 T
886057 T
1 T
886058 AATTTCGCGT
Statistics
Matches: 62, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
66 62 1.00
ACGTcount: A:0.41, C:0.20, G:0.22, T:0.17
Consensus pattern (66 bp):
TCGCAATACGAAATGAAAATCGCAACGAGAGAATCGCAACGCGAAATGAAAATCGCAACGCGAAT
T
Found at i:886065 original size:19 final size:19
Alignment explanation
Indices: 885904--886054 Score: 71
Period size: 19 Copynumber: 8.7 Consensus size: 19
885894 CTTAATGTCT
* **
885904 ATCGCAACGCGGAAATTACT
1 ATCGCAACGC-GAAATGAAA
*
885924 ATCGCAATGCGAAATGAAA
1 ATCGCAACGCGAAATGAAA
*
885943 ATCGCAA--CG--A-GAGA
1 ATCGCAACGCGAAATGAAA
**
885957 ATCGCATTGCGAAATGAAA
1 ATCGCAACGCGAAATGAAA
*
885976 ATCGCAACGC----T-AAT
1 ATCGCAACGCGAAATGAAA
* **
885990 TTCGCAATACGAAATGAAA
1 ATCGCAACGCGAAATGAAA
**
886009 ATCGCAA--CG--A-GGGA
1 ATCGCAACGCGAAATGAAA
886023 ATCGCAACGCGAAATGAAA
1 ATCGCAACGCGAAATGAAA
886042 ATCGCAACGCGAA
1 ATCGCAACGCGAA
886055 TTTAATTTCG
Statistics
Matches: 97, Mismatches: 19, Indels: 31
0.66 0.13 0.21
Matches are distributed among these distances:
14 27 0.28
15 3 0.03
16 4 0.04
17 4 0.04
18 3 0.03
19 47 0.48
20 9 0.09
ACGTcount: A:0.42, C:0.21, G:0.22, T:0.15
Consensus pattern (19 bp):
ATCGCAACGCGAAATGAAA
Found at i:886072 original size:19 final size:20
Alignment explanation
Indices: 886050--886092 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 20
886040 AAATCGCAAC
*
886050 GCGAATTT-AATTTCGCGTT
1 GCGAATTTCAATTTCGCATT
* *
886069 GCGATTTTCATTTTCGCATT
1 GCGAATTTCAATTTCGCATT
886089 GCGA
1 GCGA
886093 TTATCTCGTT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
19 7 0.35
20 13 0.65
ACGTcount: A:0.19, C:0.19, G:0.21, T:0.42
Consensus pattern (20 bp):
GCGAATTTCAATTTCGCATT
Found at i:886252 original size:14 final size:14
Alignment explanation
Indices: 886233--886269 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
886223 CATCAATTAA
886233 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
886247 ACAAATCACCTTTT
1 ACAAATCAACTTTT
886261 ACAAATCAA
1 ACAAATCAA
886270 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.24, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:889813 original size:14 final size:14
Alignment explanation
Indices: 889794--889830 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
889784 GGAAATGACT
*
889794 ATCGCAACGATAGA
1 ATCGCAACGAGAGA
*
889808 ATCGCAATGAGAGA
1 ATCGCAACGAGAGA
889822 ATCGCAACG
1 ATCGCAACG
889831 CGAAATGACT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.41, C:0.22, G:0.24, T:0.14
Consensus pattern (14 bp):
ATCGCAACGAGAGA
Found at i:889858 original size:47 final size:48
Alignment explanation
Indices: 889770--889861 Score: 141
Period size: 47 Copynumber: 1.9 Consensus size: 48
889760 ACGAGATAAT
* * *
889770 GAGAATCGCAACGCGGAAATGACTATCGCAACGATAGAATCGCAATGA
1 GAGAATCGCAACGCGGAAATGACTATCGCAACCAGACAATCGCAATGA
*
889818 GAGAATCGCAACGC-GAAATGACTATCGCGACCAGACAATCGCAA
1 GAGAATCGCAACGCGGAAATGACTATCGCAACCAGACAATCGCAA
889862 CGCGAAATGA
Statistics
Matches: 40, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
47 26 0.65
48 14 0.35
ACGTcount: A:0.39, C:0.24, G:0.24, T:0.13
Consensus pattern (48 bp):
GAGAATCGCAACGCGGAAATGACTATCGCAACCAGACAATCGCAATGA
Found at i:889876 original size:19 final size:19
Alignment explanation
Indices: 889854--889924 Score: 115
Period size: 19 Copynumber: 3.7 Consensus size: 19
889844 GCGACCAGAC
889854 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAA
*
889873 AATCGCAACCGCGAAATAAA
1 AATCGCAA-CGCGAAATGAA
889893 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAA
*
889912 AATCGCAATGCGA
1 AATCGCAACGCGA
889925 TTTTTGTTTC
Statistics
Matches: 48, Mismatches: 3, Indels: 2
0.91 0.06 0.04
Matches are distributed among these distances:
19 30 0.62
20 18 0.38
ACGTcount: A:0.46, C:0.23, G:0.20, T:0.11
Consensus pattern (19 bp):
AATCGCAACGCGAAATGAA
Found at i:889887 original size:20 final size:19
Alignment explanation
Indices: 889745--889924 Score: 118
Period size: 20 Copynumber: 9.1 Consensus size: 19
889735 TCTTTTGGTT
*
889745 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGC
*
889764 GATAATGAGAATCGCAACGC
1 GA-AATGAAAATCGCAACGC
**
889784 GGAAATGACTATCGCAACGATAGAATC
1 -GAAATGAAAATCGCAAC----G---C
*
889811 GCAATGAGAGAATCGCAACGC
1 GAAATGA-A-AATCGCAACGC
** *
889832 GAAATGACTATCGCGAC-C
1 GAAATGAAAATCGCAACGC
*
889850 ---A-GACAATCGCAACGC
1 GAAATGAAAATCGCAACGC
889865 GAAATGAAAATCGCAACCGC
1 GAAATGAAAATCGCAA-CGC
*
889885 GAAATAAAAATCGCAACGC
1 GAAATGAAAATCGCAACGC
*
889904 GAAATGAAAATCGCAATGC
1 GAAATGAAAATCGCAACGC
889923 GA
1 GA
889925 TTTTTGTTTC
Statistics
Matches: 127, Mismatches: 17, Indels: 34
0.71 0.10 0.19
Matches are distributed among these distances:
14 10 0.08
15 2 0.02
18 2 0.02
19 41 0.32
20 46 0.36
21 9 0.07
24 2 0.02
26 6 0.05
27 1 0.01
28 8 0.06
ACGTcount: A:0.43, C:0.22, G:0.22, T:0.13
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGC
Found at i:889956 original size:19 final size:19
Alignment explanation
Indices: 889920--889964 Score: 72
Period size: 19 Copynumber: 2.4 Consensus size: 19
889910 AAAATCGCAA
*
889920 TGCGATTTTTGTTTCGCGT
1 TGCGATTTTTATTTCGCGT
*
889939 TGCGTTTTTTATTTCGCGT
1 TGCGATTTTTATTTCGCGT
889958 TGCGATT
1 TGCGATT
889965 CTCTCGTTGC
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.07, C:0.16, G:0.24, T:0.53
Consensus pattern (19 bp):
TGCGATTTTTATTTCGCGT
Found at i:890583 original size:20 final size:20
Alignment explanation
Indices: 890558--890611 Score: 90
Period size: 20 Copynumber: 2.7 Consensus size: 20
890548 GATTTTGTAT
890558 TATCGCATTGCGATAGTAAG
1 TATCGCATTGCGATAGTAAG
*
890578 TATCGCATTGCGATAGTCAG
1 TATCGCATTGCGATAGTAAG
*
890598 TATCACATTGCGAT
1 TATCGCATTGCGAT
890612 TTTCCCAATT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.28, C:0.19, G:0.22, T:0.31
Consensus pattern (20 bp):
TATCGCATTGCGATAGTAAG
Found at i:890722 original size:21 final size:21
Alignment explanation
Indices: 890682--890722 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
890672 ACTGTATACC
**
890682 ATCGCAACGCGATTTCCAACT
1 ATCGCAACGCGAAATCCAACT
*
890703 ATCGCAACGCGAAATGCAAC
1 ATCGCAACGCGAAATCCAAC
890723 GCGAATTTGC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.34, C:0.32, G:0.17, T:0.17
Consensus pattern (21 bp):
ATCGCAACGCGAAATCCAACT
Found at i:891243 original size:32 final size:32
Alignment explanation
Indices: 891206--891278 Score: 112
Period size: 32 Copynumber: 2.3 Consensus size: 32
891196 TTTCGGGTCA
*
891206 AGTCGGGTTAGGTGGAGGGTATATATTTTTC-
1 AGTCGGGTTAGGTGAAGGGTATATATTTTTCG
*
891237 AGGTCGGGTTTGGTGAAGGGTATATATTTTTCG
1 A-GTCGGGTTAGGTGAAGGGTATATATTTTTCG
891270 AGTCGGGTT
1 AGTCGGGTT
891279 GGTCGAAACC
Statistics
Matches: 38, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
31 1 0.03
32 36 0.95
33 1 0.03
ACGTcount: A:0.18, C:0.07, G:0.37, T:0.38
Consensus pattern (32 bp):
AGTCGGGTTAGGTGAAGGGTATATATTTTTCG
Found at i:891993 original size:2 final size:2
Alignment explanation
Indices: 891986--892013 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
891976 ATTTCAAAAG
891986 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
892014 TGAAAAAAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:892757 original size:37 final size:38
Alignment explanation
Indices: 892707--892780 Score: 114
Period size: 37 Copynumber: 2.0 Consensus size: 38
892697 AAAACCGATC
* *
892707 CGACCCTACCCGATTTAATTTTTTATTT-ATTAAAAAT
1 CGACCCGACCCGATTTAATTTTTTATTTGATAAAAAAT
*
892744 CGACCCGATCCGATTTAATTTTTTATTTGATAAAAAA
1 CGACCCGACCCGATTTAATTTTTTATTTGATAAAAAA
892781 CTAACCCGAC
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
37 26 0.79
38 7 0.21
ACGTcount: A:0.34, C:0.18, G:0.08, T:0.41
Consensus pattern (38 bp):
CGACCCGACCCGATTTAATTTTTTATTTGATAAAAAAT
Found at i:892788 original size:38 final size:37
Alignment explanation
Indices: 892716--892789 Score: 105
Period size: 37 Copynumber: 2.0 Consensus size: 37
892706 CCGACCCTAC
* *
892716 CCGATTTAATTTTTTATTTATTAAAAATCGACCCGAT
1 CCGATTTAATTTTTTATTTATAAAAAATCAACCCGAT
892753 CCGATTTAATTTTTTATTTGATAAAAAA-CTAACCCGA
1 CCGATTTAATTTTTTATTT-ATAAAAAATC-AACCCGA
892790 CTAGCATAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
37 20 0.61
38 13 0.39
ACGTcount: A:0.35, C:0.16, G:0.08, T:0.41
Consensus pattern (37 bp):
CCGATTTAATTTTTTATTTATAAAAAATCAACCCGAT
Found at i:895384 original size:530 final size:518
Alignment explanation
Indices: 894395--895444 Score: 1920
Period size: 530 Copynumber: 2.0 Consensus size: 518
894385 AGATAAAGTT
894395 GTTTGGAGCATCAAGAATGTAGAATTCCATCGTGTTCTAACATCAGAACATAGCTTTTTTGTAGT
1 GTTTGGAGCATCAAGAATGTAGAATTCCATCGTGTTCTAACATCAGAACATAGCTTTTTTGTAGT
894460 TGAAATAAGCAACCACCTCATCAAATCGTTCCGACCTTTTTGGAGTAGCACTCCAAAAAAGAACA
66 TGAAATAAGCAACCACCTCATCAAATCGTTCCGACCTTTTTGGAGTAGCACTCCAAAAAAGAACA
894525 CTATGACGGATTCTTCCAATCACATTTAATCCATCTTTAACAATCAAATGCAATATATGTGCACA
131 CTATGACGGATTCTTCCAATCACATTTAATCCATCTTTAACAATCAAATGCAATATATGTGCACA
894590 ACGCATGTGGAAAAAAGTTACGTTAAGCAACAACATATTACTTCTCATTCTATCAACCAACAACT
196 ACGCATGTGGAAAAAAGTTACGTTAAGCAACAACATATTACTTCTCATTCTATCAACCAACAACT
*
894655 TAATGACATCATCATTCACACTACAGTTATCAACTGTAATAGATGTGAGTTTCCTATCAATATTA
261 TAATGACACCATCATTCACACTACAGTTATCAACTGTAATAGATGTGAGTTTCCTATCAATATTA
* * *
894720 CAATCTAGGAAACATTTTATCAAACTAGAAGCAATGGCATCAGTGGTATGTGGAGCTGGTATATA
326 CAATCTAGGAAACATTTTATCAAACTAGAAGCAATGACATCAATGGTATGTGGAGCTGGTACATA
894785 TTCGAACCTAATTAAACAACAAATAAAATGAATTAGTTTTAAACATATCGAAACATAACTAAATA
391 TTCGAACCTAATTAAACAACAAATAAAATGAATTAGTTTTAAACATATCGAAACATAACTAAATA
*
894850 TATGTAAACAAATACCTTAAAACGTGTTTTTGAAAACTCCAAGAGTTATCAATGTAATGAGTA
456 TATGTAAACAAATACCTTAAAACATGTTTTTGAAAACTCCAAGAGTTATCAATGTAATGAGTA
894913 GTTTGGAGCATCAAGAATGTAGAATTCCATCGTGTTCTAACATCAGAACATAGCTTTTTTGTAGT
1 GTTTGGAGCATCAAGAATGTAGAATTCCATCGTGTTCTAACATCAGAACATAGCTTTTTTGTAGT
*
894978 TGAAATAAGCAACCGCCTCATCAAATCGTTCCGACCTTTTTGGAGTAGCACTCCAAAAAAGAACA
66 TGAAATAAGCAACCACCTCATCAAATCGTTCCGACCTTTTTGGAGTAGCACTCCAAAAAAGAACA
895043 CTATGACGGATTCTTCCTATACCATCTCCAATCACATTTAATCCATCTTTAACAATCAAATGCAA
131 CTATGACGGA-------T-T--C-T-TCCAATCACATTTAATCCATCTTTAACAATCAAATGCAA
895108 TATATGTGCACAACGCATGTGGAAAAAAGTTACGTTAAGCAACAACATATTACTTCTCATTCTAT
184 TATATGTGCACAACGCATGTGGAAAAAAGTTACGTTAAGCAACAACATATTACTTCTCATTCTAT
895173 CAACCAACAACTTAATGACACCATCATTCACACTACAGTTATCAACTGTAATAGATGTGAGTTTC
249 CAACCAACAACTTAATGACACCATCATTCACACTACAGTTATCAACTGTAATAGATGTGAGTTTC
*
895238 CTATCAATATTCCAATCTAGGAAACATTTTATCAAACTAGAAGCAATGACATCAATGGTATGTGG
314 CTATCAATATTACAATCTAGGAAACATTTTATCAAACTAGAAGCAATGACATCAATGGTATGTGG
*
895303 AGCTGGTACATATTCGAACCTAATTAAACAACAAATAAAATGAATTAGTTTTAACCATATCGAAA
379 AGCTGGTACATATTCGAACCTAATTAAACAACAAATAAAATGAATTAGTTTTAAACATATCGAAA
895368 CATAACTAAATATATGTAAACAAATACCTTAAAACATGTTTTTGAAAACTCCAAGAGTTATCAAT
444 CATAACTAAATATATGTAAACAAATACCTTAAAACATGTTTTTGAAAACTCCAAGAGTTATCAAT
895433 GTAATGAGTA
509 GTAATGAGTA
895443 GT
1 GT
895445 AACAACCATA
Statistics
Matches: 512, Mismatches: 8, Indels: 12
0.96 0.02 0.02
Matches are distributed among these distances:
518 139 0.27
525 1 0.00
526 1 0.00
528 1 0.00
529 1 0.00
530 369 0.72
ACGTcount: A:0.38, C:0.19, G:0.13, T:0.30
Consensus pattern (518 bp):
GTTTGGAGCATCAAGAATGTAGAATTCCATCGTGTTCTAACATCAGAACATAGCTTTTTTGTAGT
TGAAATAAGCAACCACCTCATCAAATCGTTCCGACCTTTTTGGAGTAGCACTCCAAAAAAGAACA
CTATGACGGATTCTTCCAATCACATTTAATCCATCTTTAACAATCAAATGCAATATATGTGCACA
ACGCATGTGGAAAAAAGTTACGTTAAGCAACAACATATTACTTCTCATTCTATCAACCAACAACT
TAATGACACCATCATTCACACTACAGTTATCAACTGTAATAGATGTGAGTTTCCTATCAATATTA
CAATCTAGGAAACATTTTATCAAACTAGAAGCAATGACATCAATGGTATGTGGAGCTGGTACATA
TTCGAACCTAATTAAACAACAAATAAAATGAATTAGTTTTAAACATATCGAAACATAACTAAATA
TATGTAAACAAATACCTTAAAACATGTTTTTGAAAACTCCAAGAGTTATCAATGTAATGAGTA
Found at i:906072 original size:29 final size:29
Alignment explanation
Indices: 906030--906088 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
906020 CCTAAATAAA
906030 TTTGATGTCATTGCTTACATCAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
906059 TTTGATGTCATTGCTTACATCAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
906088 T
1 T
906089 AGGTGAAAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.24, C:0.14, G:0.14, T:0.49
Consensus pattern (29 bp):
TTTGATGTCATTGCTTACATCAATTTAGT
Found at i:910757 original size:29 final size:29
Alignment explanation
Indices: 910721--910779 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
910711 CATAAATTAA
910721 TTTGATGTCATTGCTTACATCAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
910750 TTTGATGTCATTGCTTACATCAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
910779 T
1 T
910780 AGGTGAAAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.24, C:0.14, G:0.14, T:0.49
Consensus pattern (29 bp):
TTTGATGTCATTGCTTACATCAATTTAGT
Found at i:916974 original size:12 final size:13
Alignment explanation
Indices: 916864--916966 Score: 71
Period size: 14 Copynumber: 7.1 Consensus size: 13
916854 AGTTTGGATT
* *
916864 AATATCATTTATTT
1 AATATTATTTA-TA
916878 AATATTATTTTTATA
1 AATATTA--TTTATA
916893 ATTATATTAATTTATA
1 A--ATATT-ATTTATA
*
916909 AACATTATTTATA
1 AATATTATTTATA
*
916922 AGTGATATTATTTATTT
1 A---ATATTATTTA-TA
916939 AATATTATTTTATA
1 AATATTA-TTTATA
916953 AATATTATTTATA
1 AATATTATTTATA
916966 A
1 A
916967 TTTTATTTCT
Statistics
Matches: 73, Mismatches: 6, Indels: 21
0.73 0.06 0.21
Matches are distributed among these distances:
13 15 0.21
14 24 0.33
15 6 0.08
16 20 0.27
17 7 0.10
18 1 0.01
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.55
Consensus pattern (13 bp):
AATATTATTTATA
Found at i:916980 original size:26 final size:27
Alignment explanation
Indices: 916864--916974 Score: 91
Period size: 31 Copynumber: 3.9 Consensus size: 27
916854 AGTTTGGATT
*
916864 AATATCATTTATTTAATATTATTTTTATA
1 AATATTATTTA-TTAATATTA-TTTTATA
* *
916893 ATTATATTAATTTATAAACATTA-TTTATA
1 A--ATATT-ATTTATTAATATTATTTTATA
916922 AGTGATATTATTTATTTAATATTATTTTATA
1 A---ATATTATTTA-TTAATATTATTTTATA
*
916953 AATATTATTTA-TAATTTTATTT
1 AATATTATTTATTAATATTATTT
916975 CTTAAAAAAT
Statistics
Matches: 69, Mismatches: 7, Indels: 15
0.76 0.08 0.16
Matches are distributed among these distances:
26 10 0.14
28 10 0.14
29 13 0.19
30 13 0.19
31 18 0.26
32 5 0.07
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.58
Consensus pattern (27 bp):
AATATTATTTATTAATATTATTTTATA
Found at i:919796 original size:20 final size:20
Alignment explanation
Indices: 919771--919808 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
919761 ATTCATCTCA
*
919771 GTTCATCCAGTATCGATAAT
1 GTTCATCCAATATCGATAAT
919791 GTTCATCCAATATCGATA
1 GTTCATCCAATATCGATA
919809 TTCGAACCCA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.32, C:0.21, G:0.13, T:0.34
Consensus pattern (20 bp):
GTTCATCCAATATCGATAAT
Found at i:929019 original size:14 final size:14
Alignment explanation
Indices: 929000--929029 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
928990 GATAATTCTC
929000 CTATAGTATCGATA
1 CTATAGTATCGATA
929014 CTATAGTATCGATA
1 CTATAGTATCGATA
929028 CT
1 CT
929030 CAGGGTGTCT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.33, C:0.17, G:0.13, T:0.37
Consensus pattern (14 bp):
CTATAGTATCGATA
Found at i:939558 original size:6 final size:6
Alignment explanation
Indices: 939547--939617 Score: 70
Period size: 6 Copynumber: 11.5 Consensus size: 6
939537 GCCAAAGTAG
* * * *
939547 AAAGTC AAAGTC AAAGTC AAAGCC AAAGTAG AAAGTC AAAGCC AAAGCC
1 AAAGTC AAAGTC AAAGTC AAAGTC AAAGT-C AAAGTC AAAGTC AAAGTC
* *
939596 AAAGTAG AAAGTC AAAGCC AAA
1 AAAGT-C AAAGTC AAAGTC AAA
939618 TTGGTTCATC
Statistics
Matches: 54, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
6 44 0.81
7 10 0.19
ACGTcount: A:0.54, C:0.18, G:0.18, T:0.10
Consensus pattern (6 bp):
AAAGTC
Found at i:939563 original size:19 final size:18
Alignment explanation
Indices: 939537--939617 Score: 72
Period size: 19 Copynumber: 4.3 Consensus size: 18
939527 AAATTGCATG
* *
939537 GCCAAAGTAGAAAGTCAAA
1 GCCAAAGT-CAAAGCCAAA
*
939556 GTCAAAGTCAAAGCCAAA
1 GCCAAAGTCAAAGCCAAA
**
939574 GTAGAAAGTCAAAGCCAAA
1 G-CCAAAGTCAAAGCCAAA
* *
939593 GCCAAAGTAGAAAGTCAAA
1 GCCAAAGT-CAAAGCCAAA
939612 GCCAAA
1 GCCAAA
939618 TTGGTTCATC
Statistics
Matches: 51, Mismatches: 9, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
18 14 0.27
19 37 0.73
ACGTcount: A:0.52, C:0.19, G:0.20, T:0.10
Consensus pattern (18 bp):
GCCAAAGTCAAAGCCAAA
Found at i:939575 original size:31 final size:28
Alignment explanation
Indices: 939537--939613 Score: 106
Period size: 25 Copynumber: 2.8 Consensus size: 28
939527 AAATTGCATG
939537 GCCAAAGTAGAAAGTCAAAGTCAAAGTCAAA
1 GCCAAAGTAGAAAGTCAAAG-CAAA--CAAA
939568 GCCAAAGTAGAAAGTCAAAGC---CAAA
1 GCCAAAGTAGAAAGTCAAAGCAAACAAA
939593 GCCAAAGTAGAAAGTCAAAGC
1 GCCAAAGTAGAAAGTCAAAGC
939614 CAAATTGGTT
Statistics
Matches: 46, Mismatches: 0, Indels: 6
0.88 0.00 0.12
Matches are distributed among these distances:
25 25 0.54
30 1 0.02
31 20 0.43
ACGTcount: A:0.51, C:0.18, G:0.21, T:0.10
Consensus pattern (28 bp):
GCCAAAGTAGAAAGTCAAAGCAAACAAA
Found at i:939581 original size:25 final size:25
Alignment explanation
Indices: 939553--939617 Score: 121
Period size: 25 Copynumber: 2.6 Consensus size: 25
939543 GTAGAAAGTC
*
939553 AAAGTCAAAGTCAAAGCCAAAGTAG
1 AAAGTCAAAGCCAAAGCCAAAGTAG
939578 AAAGTCAAAGCCAAAGCCAAAGTAG
1 AAAGTCAAAGCCAAAGCCAAAGTAG
939603 AAAGTCAAAGCCAAA
1 AAAGTCAAAGCCAAA
939618 TTGGTTCATC
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
25 39 1.00
ACGTcount: A:0.54, C:0.18, G:0.18, T:0.09
Consensus pattern (25 bp):
AAAGTCAAAGCCAAAGCCAAAGTAG
Found at i:939653 original size:13 final size:14
Alignment explanation
Indices: 939635--939671 Score: 51
Period size: 13 Copynumber: 2.7 Consensus size: 14
939625 ATCTTTGACT
939635 ATGGGAAATTTT-A
1 ATGGGAAATTTTCA
939648 ATGGGAAATATTTCA
1 ATGGGAAAT-TTTCA
939663 AT-GGAAATT
1 ATGGGAAATT
939672 GGTAATTATC
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
13 10 0.45
14 9 0.41
15 3 0.14
ACGTcount: A:0.41, C:0.03, G:0.22, T:0.35
Consensus pattern (14 bp):
ATGGGAAATTTTCA
Found at i:942508 original size:29 final size:29
Alignment explanation
Indices: 942463--942521 Score: 109
Period size: 29 Copynumber: 2.0 Consensus size: 29
942453 ATTTTCACCT
942463 AACTAAATTGATATAAGCAATGACATCAA
1 AACTAAATTGATATAAGCAATGACATCAA
*
942492 AACTAAATTGATGTAAGCAATGACATCAA
1 AACTAAATTGATATAAGCAATGACATCAA
942521 A
1 A
942522 TTAATTTAGG
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.51, C:0.14, G:0.12, T:0.24
Consensus pattern (29 bp):
AACTAAATTGATATAAGCAATGACATCAA
Found at i:947159 original size:29 final size:29
Alignment explanation
Indices: 947116--947171 Score: 103
Period size: 29 Copynumber: 1.9 Consensus size: 29
947106 TTAACCTAAT
947116 TAAATTGATGCAAGCAATGACATCAAAAC
1 TAAATTGATGCAAGCAATGACATCAAAAC
*
947145 TAAATTGATGTAAGCAATGACATCAAA
1 TAAATTGATGCAAGCAATGACATCAAA
947172 TCAATTTAGG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.48, C:0.14, G:0.14, T:0.23
Consensus pattern (29 bp):
TAAATTGATGCAAGCAATGACATCAAAAC
Found at i:948359 original size:10 final size:10
Alignment explanation
Indices: 948337--948389 Score: 65
Period size: 10 Copynumber: 5.5 Consensus size: 10
948327 TCCTATTAAA
*
948337 TTTTATATAT
1 TTTTTTATAT
*
948347 TTTTTTATCT
1 TTTTTTATAT
*
948357 TTTATTA-AT
1 TTTTTTATAT
948366 TTTTTTATA-
1 TTTTTTATAT
948375 TTTTTTATAT
1 TTTTTTATAT
948385 TTTTT
1 TTTTT
948390 CTTCTGTCTT
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
9 16 0.44
10 20 0.56
ACGTcount: A:0.21, C:0.02, G:0.00, T:0.77
Consensus pattern (10 bp):
TTTTTTATAT
Found at i:948359 original size:19 final size:19
Alignment explanation
Indices: 948336--948389 Score: 74
Period size: 19 Copynumber: 2.8 Consensus size: 19
948326 ATCCTATTAA
948336 ATTTTATATATTTTTTTAT
1 ATTTTATATATTTTTTTAT
*
948355 CTTTTAT-TAATTTTTTTAT
1 ATTTTATAT-ATTTTTTTAT
*
948374 ATTTTTTATATTTTTT
1 ATTTTATATATTTTTT
948390 CTTCTGTCTT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
18 1 0.03
19 28 0.93
20 1 0.03
ACGTcount: A:0.22, C:0.02, G:0.00, T:0.76
Consensus pattern (19 bp):
ATTTTATATATTTTTTTAT
Found at i:948369 original size:29 final size:30
Alignment explanation
Indices: 948330--948389 Score: 86
Period size: 29 Copynumber: 2.0 Consensus size: 30
948320 TATCATATCC
948330 TATTAAATTTTATATATTTTTT-TATCTTT
1 TATTAAATTTTATATATTTTTTATATCTTT
* * *
948359 TATTAATTTTTTTATATTTTTTATATTTTT
1 TATTAAATTTTATATATTTTTTATATCTTT
948389 T
1 T
948390 CTTCTGTCTT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
29 20 0.74
30 7 0.26
ACGTcount: A:0.25, C:0.02, G:0.00, T:0.73
Consensus pattern (30 bp):
TATTAAATTTTATATATTTTTTATATCTTT
Found at i:948378 original size:8 final size:9
Alignment explanation
Indices: 948336--948389 Score: 56
Period size: 9 Copynumber: 5.8 Consensus size: 9
948326 ATCCTATTAA
*
948336 ATTTTATAT
1 ATTTTTTAT
948345 ATTTTTT-T
1 ATTTTTTAT
*
948353 ATCTTTTATT
1 ATTTTTTA-T
948363 AATTTTTTTAT
1 -A-TTTTTTAT
948374 ATTTTTTAT
1 ATTTTTTAT
948383 ATTTTTT
1 ATTTTTT
948390 CTTCTGTCTT
Statistics
Matches: 38, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
8 7 0.18
9 21 0.55
10 2 0.05
11 2 0.05
12 6 0.16
ACGTcount: A:0.22, C:0.02, G:0.00, T:0.76
Consensus pattern (9 bp):
ATTTTTTAT
Found at i:952629 original size:31 final size:31
Alignment explanation
Indices: 952559--952631 Score: 101
Period size: 31 Copynumber: 2.4 Consensus size: 31
952549 TGAAATATCA
* * *
952559 CTTCTCTCTCTGCTTCTATCGCTGCTTTTTG
1 CTTCTCTCACTGCTTCTATCGCTGCTCTCTG
*
952590 GTTCTCTCACTGCTTCTATCGCTGCTCTCTG
1 CTTCTCTCACTGCTTCTATCGCTGCTCTCTG
*
952621 CTTGTCTCACT
1 CTTCTCTCACT
952632 TCTCTCTCTT
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 36 1.00
ACGTcount: A:0.05, C:0.34, G:0.14, T:0.47
Consensus pattern (31 bp):
CTTCTCTCACTGCTTCTATCGCTGCTCTCTG
Found at i:953287 original size:16 final size:17
Alignment explanation
Indices: 953262--953295 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
953252 CTGAGGTGTC
953262 ACATTGACTTTT-CAAA
1 ACATTGACTTTTACAAA
*
953278 ACATTTACTTTTACAAA
1 ACATTGACTTTTACAAA
953295 A
1 A
953296 GAATAAAGGA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 11 0.69
17 5 0.31
ACGTcount: A:0.41, C:0.18, G:0.03, T:0.38
Consensus pattern (17 bp):
ACATTGACTTTTACAAA
Found at i:960341 original size:103 final size:103
Alignment explanation
Indices: 960014--960334 Score: 624
Period size: 103 Copynumber: 3.1 Consensus size: 103
960004 GTCGAGGGTC
960014 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
*
960079 TTGATCCCTAGTATATGTATATGATTATTAAGGAATGA
66 TTGATCCCTAGTATATGTATATGATTCTTAAGGAATGA
*
960117 TATGTGGTCCTTCGGGATATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
960182 TTGATCCCTAGTATATGTATATGATTCTTAAGGAATGA
66 TTGATCCCTAGTATATGTATATGATTCTTAAGGAATGA
960220 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
960285 TTGATCCCTAGTATATGTATATGATTCTTAAGGAATGA
66 TTGATCCCTAGTATATGTATATGATTCTTAAGGAATGA
960323 TATGTGGTCCTT
1 TATGTGGTCCTT
960335 ATGGACAGTA
Statistics
Matches: 215, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
103 215 1.00
ACGTcount: A:0.27, C:0.13, G:0.23, T:0.37
Consensus pattern (103 bp):
TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
TTGATCCCTAGTATATGTATATGATTCTTAAGGAATGA
Found at i:960417 original size:23 final size:23
Alignment explanation
Indices: 960350--960418 Score: 93
Period size: 23 Copynumber: 3.0 Consensus size: 23
960340 CAGTATTATA
* * *
960350 TGGCACTACGGTGCAATTCTACG
1 TGGCACTTCGGTGCAATTATATG
*
960373 CGGCACTTCGGTGCAATTATATG
1 TGGCACTTCGGTGCAATTATATG
*
960396 TGGCACTTCGGTGTAATTATATG
1 TGGCACTTCGGTGCAATTATATG
960419 AGTTGTGGTG
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 40 1.00
ACGTcount: A:0.22, C:0.20, G:0.26, T:0.32
Consensus pattern (23 bp):
TGGCACTTCGGTGCAATTATATG
Found at i:966395 original size:103 final size:103
Alignment explanation
Indices: 966068--966388 Score: 633
Period size: 103 Copynumber: 3.1 Consensus size: 103
966058 GTCGAGGGTC
966068 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
*
966133 TTGATCCCTAGTATATGTATATGATTATTAAGGAATGA
66 TTGATCCCTAGTATATGTATATGATTCTTAAGGAATGA
966171 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
966236 TTGATCCCTAGTATATGTATATGATTCTTAAGGAATGA
66 TTGATCCCTAGTATATGTATATGATTCTTAAGGAATGA
966274 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
966339 TTGATCCCTAGTATATGTATATGATTCTTAAGGAATGA
66 TTGATCCCTAGTATATGTATATGATTCTTAAGGAATGA
966377 TATGTGGTCCTT
1 TATGTGGTCCTT
966389 ATGGACAGTA
Statistics
Matches: 217, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
103 217 1.00
ACGTcount: A:0.27, C:0.13, G:0.23, T:0.36
Consensus pattern (103 bp):
TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
TTGATCCCTAGTATATGTATATGATTCTTAAGGAATGA
Found at i:966471 original size:23 final size:23
Alignment explanation
Indices: 966404--966472 Score: 93
Period size: 23 Copynumber: 3.0 Consensus size: 23
966394 CAGTATTATA
* * *
966404 TGGCACTACGGTGCAATTCTACG
1 TGGCACTTCGGTGCAATTATATG
*
966427 CGGCACTTCGGTGCAATTATATG
1 TGGCACTTCGGTGCAATTATATG
*
966450 TGGCACTTCGGTGTAATTATATG
1 TGGCACTTCGGTGCAATTATATG
966473 AGTTGTGGTG
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 40 1.00
ACGTcount: A:0.22, C:0.20, G:0.26, T:0.32
Consensus pattern (23 bp):
TGGCACTTCGGTGCAATTATATG
Found at i:967638 original size:83 final size:82
Alignment explanation
Indices: 967526--967797 Score: 282
Period size: 83 Copynumber: 3.3 Consensus size: 82
967516 TTGCGTTGAG
* * * *
967526 TTTGTAAAAAAAGCGCAGCTAAAGTACTACTCTATTGCGGTGTTCT-TCGAAAAAGCGCCACTAT
1 TTTGTATAAAAA-CGCCGCTAAAGTACTACTCTATTGCGGTGTT-TGTTGAAAAAACGCCACTAT
* *
967590 AAATGAACCCTATTACGATA
64 AGATGAACCCTATT-CGACA
* * * *
967610 TTTGTATAAAAACGACGCTAAAGTACTACTCTATTAC-GTCATTTGTTGAAAAAACTCCACTATA
1 TTTGTATAAAAACGCCGCTAAAGTACTACTCTATTGCGGT-GTTTGTTGAAAAAACGCCACTATA
*
967674 GATGAACCCTATCGCGACA
65 GATGAACCCTAT-TCGACA
* * * * * *
967693 TTTATATGAAAAA-GCCTCTAAAGTATTACTCTATTGCGGCGTTTGTTGAAAAAATGTCACTATA
1 TTTGTAT-AAAAACGCCGCTAAAGTACTACTCTATTGCGGTGTTTGTTGAAAAAACGCCACTATA
*
967757 GATAAACCCTATT-GTAGCA
65 GATGAACCCTATTCG-A-CA
967776 TTTGTATAAAAACGCCGCTAAA
1 TTTGTATAAAAACGCCGCTAAA
967798 ATTACCATTT
Statistics
Matches: 155, Mismatches: 25, Indels: 17
0.79 0.13 0.09
Matches are distributed among these distances:
81 1 0.01
82 9 0.06
83 128 0.83
84 17 0.11
ACGTcount: A:0.36, C:0.19, G:0.15, T:0.30
Consensus pattern (82 bp):
TTTGTATAAAAACGCCGCTAAAGTACTACTCTATTGCGGTGTTTGTTGAAAAAACGCCACTATAG
ATGAACCCTATTCGACA
Found at i:970302 original size:2 final size:2
Alignment explanation
Indices: 970295--970325 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
970285 TCGCCCTGAT
970295 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
970326 TTTATATTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:970333 original size:7 final size:7
Alignment explanation
Indices: 970321--970410 Score: 76
Period size: 7 Copynumber: 13.1 Consensus size: 7
970311 TATATATATA
970321 TATATTT
1 TATATTT
970328 TATATTT
1 TATATTT
* *
970335 TTTATAT
1 TATATTT
*
970342 TA-ATTA
1 TATATTT
*
970348 TATATAT
1 TATATTT
*
970355 AATATTT
1 TATATTT
970362 TATATTT
1 TATATTT
* *
970369 TTTATAT
1 TATATTT
*
970376 TA-ATTA
1 TATATTT
*
970382 TATATAT
1 TATATTT
*
970389 AATATTT
1 TATATTT
970396 TATATTT
1 TATATTT
970403 TATATTT
1 TATATTT
970410 T
1 T
970411 TTATATTAAT
Statistics
Matches: 61, Mismatches: 20, Indels: 4
0.72 0.24 0.05
Matches are distributed among these distances:
6 8 0.13
7 53 0.87
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (7 bp):
TATATTT
Found at i:970337 original size:9 final size:9
Alignment explanation
Indices: 970319--970417 Score: 57
Period size: 9 Copynumber: 11.7 Consensus size: 9
970309 TATATATATA
*
970319 TATATATTT
1 TATATTTTT
970328 TATATTTTT
1 TATATTTTT
**
970337 TATATTAAT
1 TATATTTTT
* *
970346 TATA-TATA
1 TATATTTTT
*
970354 TA-ATATTT
1 TATATTTTT
970362 TATATTTTT
1 TATATTTTT
**
970371 TATATTAAT
1 TATATTTTT
* *
970380 TATA-TATA
1 TATATTTTT
*
970388 TA-ATATTT
1 TATATTTTT
970396 TATA--TTT
1 TATATTTTT
970403 TATATTTTT
1 TATATTTTT
970412 TATATT
1 TATATT
970418 AATTATATAT
Statistics
Matches: 68, Mismatches: 16, Indels: 12
0.71 0.17 0.12
Matches are distributed among these distances:
7 9 0.13
8 14 0.21
9 45 0.66
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (9 bp):
TATATTTTT
Found at i:970352 original size:41 final size:41
Alignment explanation
Indices: 970305--970428 Score: 174
Period size: 41 Copynumber: 3.2 Consensus size: 41
970295 TATATATATA
970305 TATATATATATATATATATATTTTATA-TTTTT-TA-T-AT
1 TATATATATATATATATATATTTTATATTTTTTATATTAAT
970342 TA-AT-TATATATATA-ATATTTTATATTTTTTATATTAAT
1 TATATATATATATATATATATTTTATATTTTTTATATTAAT
*
970380 TATATATATA-ATATTTTATATTTTATATTTTTTATATTAAT
1 TATATATATATATA-TATATATTTTATATTTTTTATATTAAT
970421 TATATATA
1 TATATATA
970429 AAATATTTTC
Statistics
Matches: 78, Mismatches: 1, Indels: 12
0.86 0.01 0.13
Matches are distributed among these distances:
34 10 0.13
35 15 0.19
36 4 0.05
37 3 0.04
38 4 0.05
39 5 0.06
40 5 0.06
41 32 0.41
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (41 bp):
TATATATATATATATATATATTTTATATTTTTTATATTAAT
Found at i:970360 original size:34 final size:34
Alignment explanation
Indices: 970311--970403 Score: 177
Period size: 34 Copynumber: 2.7 Consensus size: 34
970301 TATATATATA
970311 TATATATATATATATTTTATATTTTTTATATTAAT
1 TATATATATA-ATATTTTATATTTTTTATATTAAT
970346 TATATATATAATATTTTATATTTTTTATATTAAT
1 TATATATATAATATTTTATATTTTTTATATTAAT
970380 TATATATATAATATTTTATATTTT
1 TATATATATAATATTTTATATTTT
970404 ATATTTTTTA
Statistics
Matches: 58, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
34 48 0.83
35 10 0.17
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (34 bp):
TATATATATAATATTTTATATTTTTTATATTAAT
Found at i:970434 original size:41 final size:41
Alignment explanation
Indices: 970356--970437 Score: 155
Period size: 41 Copynumber: 2.0 Consensus size: 41
970346 TATATATATA
*
970356 ATATTTTATATTTTTTATATTAATTATATATATAATATTTT
1 ATATTTTATATTTTTTATATTAATTATATATAAAATATTTT
970397 ATATTTTATATTTTTTATATTAATTATATATAAAATATTTT
1 ATATTTTATATTTTTTATATTAATTATATATAAAATATTTT
970438 CGGGTTCGGG
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 40 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (41 bp):
ATATTTTATATTTTTTATATTAATTATATATAAAATATTTT
Found at i:970460 original size:20 final size:20
Alignment explanation
Indices: 970430--970467 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
970420 TTATATATAA
970430 AATATTTTCGGGTTCGGGTAT
1 AATATTTTCGGG-TCGGGTAT
970451 AATA-TTTCGGGTCGGGT
1 AATATTTTCGGGTCGGGT
970468 TCGGAGACGG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 6 0.35
20 7 0.41
21 4 0.24
ACGTcount: A:0.18, C:0.11, G:0.32, T:0.39
Consensus pattern (20 bp):
AATATTTTCGGGTCGGGTAT
Found at i:970941 original size:35 final size:35
Alignment explanation
Indices: 970895--970963 Score: 120
Period size: 35 Copynumber: 2.0 Consensus size: 35
970885 TTAAATAAAA
*
970895 AAACACAAATATTTTTATAAATAAATAAACAAATC
1 AAACACAAATATTTTTAAAAATAAATAAACAAATC
*
970930 AAACATAAATATTTTTAAAAATAAATAAACAAAT
1 AAACACAAATATTTTTAAAAATAAATAAACAAAT
970964 TTGAATATAA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 32 1.00
ACGTcount: A:0.62, C:0.09, G:0.00, T:0.29
Consensus pattern (35 bp):
AAACACAAATATTTTTAAAAATAAATAAACAAATC
Found at i:974774 original size:36 final size:36
Alignment explanation
Indices: 974718--974786 Score: 95
Period size: 36 Copynumber: 1.9 Consensus size: 36
974708 TGTTTGAAAA
*
974718 TATTTTTTAGAAAACAGTTTTTGAAAACATATAATT
1 TATTTTTTAGAAAACAGTTTTCGAAAACATATAATT
* *
974754 TATTTTTTA-AAAATCGGTTTTCGAAAATATATA
1 TATTTTTTAGAAAA-CAGTTTTCGAAAACATATA
974787 TAATATATAG
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
35 4 0.14
36 25 0.86
ACGTcount: A:0.41, C:0.06, G:0.09, T:0.45
Consensus pattern (36 bp):
TATTTTTTAGAAAACAGTTTTCGAAAACATATAATT
Found at i:974823 original size:37 final size:37
Alignment explanation
Indices: 974771--975123 Score: 262
Period size: 37 Copynumber: 9.8 Consensus size: 37
974761 TAAAAATCGG
974771 TTTTCGAAAATATATATAATATATAGTTTTTGAAAACA
1 TTTT-GAAAATATATATAATATATAGTTTTTGAAAACA
* * * ** *
974809 TCTTGAAAACATATATAGTATATAAATTTTGAAAATA
1 TTTTGAAAATATATATAATATATAGTTTTTGAAAACA
* *
974846 TTTCGAAAATATATATATTATATAG-TTTTGAAAACA
1 TTTTGAAAATATATATAATATATAGTTTTTGAAAACA
974882 TTTTGAATATATATATATATATAATATAGTTTTTGAAAACGA
1 TTTTGAA-A-ATATATATA-AT-ATATAGTTTTTGAAAAC-A
** * *
974924 TTTTTGAAAATGCATATATTATACAGTTTTTGAAAAC-
1 -TTTTGAAAATATATATAATATATAGTTTTTGAAAACA
* * *
974961 --TT----ATAT-GAT-ATAT-GA-TTTTT-AAAAAA
1 TTTTGAAAATATATATAATATATAGTTTTTGAAAACA
974987 TATTTGAAAATATATATAATATATAGTTTTT-AAAACA
1 T-TTTGAAAATATATATAATATATAGTTTTTGAAAACA
* * *
975024 TTTTGAAGA-CTATAT-A-A-ATAG-TTTTGAAAACTT
1 TTTTGAAAATATATATAATATATAGTTTTTGAAAAC-A
* *
975057 TTTTAAAAATATATATATAATATATAG-TTTT-AAAATA
1 TTTT-GAAA-ATATATATAATATATAGTTTTTGAAAACA
*
975094 TTTTTGAAAATATATATATTATATAGTTTT
1 -TTTTGAAAATATATATAATATATAGTTTT
975124 GGGAAATATT
Statistics
Matches: 249, Mismatches: 37, Indels: 59
0.72 0.11 0.17
Matches are distributed among these distances:
25 4 0.02
26 5 0.02
27 1 0.00
28 3 0.01
29 4 0.02
30 2 0.01
31 4 0.02
32 9 0.04
33 9 0.04
34 7 0.03
35 10 0.04
36 45 0.18
37 67 0.27
38 21 0.08
39 25 0.10
40 7 0.03
41 17 0.07
42 2 0.01
43 7 0.03
ACGTcount: A:0.44, C:0.04, G:0.08, T:0.44
Consensus pattern (37 bp):
TTTTGAAAATATATATAATATATAGTTTTTGAAAACA
Found at i:974972 original size:63 final size:62
Alignment explanation
Indices: 974899--975022 Score: 144
Period size: 63 Copynumber: 2.0 Consensus size: 62
974889 TATATATATA
* * * *
974899 TATATAATATA-G-TTTTTGAAAACGATTTTTGAAAATGCATATATTATACAGTTTTTGAAAACT
1 TATATAATATATGATTTTT-AAAA-AATATTTGAAAATACATATAATATACAGTTTTT-AAAACT
* * *
974962 TATATGATATATGATTTTTAAAAAATATTTGAAAATATATATAATATATAGTTTTTAAAAC
1 TATATAATATATGATTTTTAAAAAATATTTGAAAATACATATAATATACAGTTTTTAAAAC
975023 ATTTTGAAGA
Statistics
Matches: 52, Mismatches: 7, Indels: 5
0.81 0.11 0.08
Matches are distributed among these distances:
62 5 0.10
63 37 0.71
64 5 0.10
65 5 0.10
ACGTcount: A:0.44, C:0.04, G:0.09, T:0.44
Consensus pattern (62 bp):
TATATAATATATGATTTTTAAAAAATATTTGAAAATACATATAATATACAGTTTTTAAAACT
Found at i:975070 original size:32 final size:32
Alignment explanation
Indices: 974989--975071 Score: 85
Period size: 32 Copynumber: 2.5 Consensus size: 32
974979 TTAAAAAATA
*
974989 TTTGAAAATATATATAATATATAGTTTTTAAAACAT
1 TTTGAAAA-ATATAT-A-A-ATAGTTTTGAAAACAT
* * *
975025 TTTGAAGACTATATAAATAGTTTTGAAAACTT
1 TTTGAAAAATATATAAATAGTTTTGAAAACAT
*
975057 TTTTAAAAATATATA
1 TTTGAAAAATATATA
975072 TATAATATAT
Statistics
Matches: 40, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
32 26 0.65
33 1 0.03
34 1 0.03
35 5 0.12
36 7 0.17
ACGTcount: A:0.46, C:0.04, G:0.07, T:0.43
Consensus pattern (32 bp):
TTTGAAAAATATATAAATAGTTTTGAAAACAT
Found at i:975098 original size:38 final size:37
Alignment explanation
Indices: 974993--975124 Score: 125
Period size: 38 Copynumber: 3.7 Consensus size: 37
974983 AAAATATTTG
* * * *
974993 AAAATATATATAATATATAGTTTTTAAAAC-ATTTTG
1 AAAATATATATATTATATAGTTTTGAAAACTTTTTTA
* *
975029 AAGA-CTATATA--A-ATAGTTTTGAAAACTTTTTTA
1 AAAATATATATATTATATAGTTTTGAAAACTTTTTTA
*
975062 AAAATATATATATAATATATAGTTTT-AAAA-TATTTTTG
1 AAAATATATATAT--TATATAGTTTTGAAAACT-TTTTTA
975100 AAAATATATATATTATATAGTTTTG
1 AAAATATATATATTATATAGTTTTG
975125 GGAAATATTT
Statistics
Matches: 79, Mismatches: 8, Indels: 17
0.76 0.08 0.16
Matches are distributed among these distances:
32 13 0.16
33 8 0.10
34 6 0.08
35 6 0.08
36 14 0.18
37 1 0.01
38 23 0.29
39 8 0.10
ACGTcount: A:0.45, C:0.02, G:0.07, T:0.45
Consensus pattern (37 bp):
AAAATATATATATTATATAGTTTTGAAAACTTTTTTA
Found at i:976713 original size:6 final size:6
Alignment explanation
Indices: 976699--976733 Score: 61
Period size: 6 Copynumber: 5.7 Consensus size: 6
976689 CGAATTGAAT
976699 TTTTAAA TTTTAA TTTTAA TTTTAA TTTTAA TTTT
1 TTTT-AA TTTTAA TTTTAA TTTTAA TTTTAA TTTT
976734 CGTGATTAAG
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
6 24 0.86
7 4 0.14
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (6 bp):
TTTTAA
Found at i:982114 original size:169 final size:169
Alignment explanation
Indices: 981834--982491 Score: 820
Period size: 169 Copynumber: 3.9 Consensus size: 169
981824 CTATTCGCAA
** * * * * * *
981834 CATAGCTCAAGGTAATAAGGGCTATATGTCAGCAAAAATCCTTCGAGTTCGATTACATTCAGCTT
1 CATAGCTCAAGGCGAGAAGGGCTATCTGTCAACAAAAA-CCTTCGAGTTCGATTCCAGTCAGCTC
* * * * * *
981899 AAGGACATATCAAATTTTCAGCATAGCTCAAGGCGAGAAAGGCTATCTATCAAAAAAAACCTTCA
65 AAGGCCATATCAAATTTACAGCATAGCTCAAGGCAAGAAGGGCTATCTGTCAACAAAAACCTTCA
981964 AGTTCGATTTCATTCAGCTCAAGGGCA-ACTAAATTTACAG
130 AGTTCGATTTCATTCAGCTCAAGGGCATA-TAAATTTACAG
* *
982004 CATAGCTCAAGGCGAGAAGGGCTATCTATAAACAAAAACCTTCGAGTTCGATTCCAGTCAGCTCA
1 CATAGCTCAAGGCGAGAAGGGCTATCTGTCAACAAAAACCTTCGAGTTCGATTCCAGTCAGCTCA
* * *
982069 AGGGCATATCAAATTTACAGCATAACTCAAGGCAAGAAGGGCTATCTGTCAACAAAAACCTTCGA
66 AGGCCATATCAAATTTACAGCATAGCTCAAGGCAAGAAGGGCTATCTGTCAACAAAAACCTTCAA
* *
982134 GTTCGA-TTCTAGTCAGCTCAAGGGCATATCAAATTTACAA
131 GTTCGATTTC-ATTCAGCTCAAGGGCATAT-AAATTTACAG
* * * *
982174 CATAGCTCAAGACGAGAATGGATATCTGTCAACAAAAATCTTCGAGTTCGATTCCAGTCAGCTCA
1 CATAGCTCAAGGCGAGAAGGGCTATCTGTCAACAAAAACCTTCGAGTTCGATTCCAGTCAGCTCA
* * * * **
982239 AGGCCAAATCAAATTTACAGTATAGCTCAAGGCAAGAAGGGTTATCTGTTAACAAAAACCTTTGA
66 AGGCCATATCAAATTTACAGCATAGCTCAAGGCAAGAAGGGCTATCTGTCAACAAAAACCTTCAA
* * * * * * *
982304 GTTTGATTCCAATCAACTCAAGGCCATATCAATTTATAG
131 GTTCGATTTCATTCAGCTCAAGGGCATATAAATTTACAG
* * * *
982343 TATAGCTCAAGGCGAGAAAGGCTATCTGTCAACAAAAACCTTCGGGTTCGATTTCAGTCAGCTCA
1 CATAGCTCAAGGCGAGAAGGGCTATCTGTCAACAAAAACCTTCGAGTTCGATTCCAGTCAGCTCA
* * *
982408 AGGCCATATCAAATTTACAGTATAGCTCAAGGCGAGAAGAGCTATCTGTCAACAAAAACCTTCGA
66 AGGCCATATCAAATTTACAGCATAGCTCAAGGCAAGAAGGGCTATCTGTCAACAAAAACCTTC-A
*
982473 A-TTAGATTAT-ATTCAGCTC
130 AGTTCGATT-TCATTCAGCTC
982492 GATGACAGCG
Statistics
Matches: 423, Mismatches: 59, Indels: 13
0.85 0.12 0.03
Matches are distributed among these distances:
168 3 0.01
169 238 0.56
170 180 0.43
171 2 0.00
ACGTcount: A:0.36, C:0.21, G:0.18, T:0.25
Consensus pattern (169 bp):
CATAGCTCAAGGCGAGAAGGGCTATCTGTCAACAAAAACCTTCGAGTTCGATTCCAGTCAGCTCA
AGGCCATATCAAATTTACAGCATAGCTCAAGGCAAGAAGGGCTATCTGTCAACAAAAACCTTCAA
GTTCGATTTCATTCAGCTCAAGGGCATATAAATTTACAG
Found at i:982368 original size:254 final size:253
Alignment explanation
Indices: 981834--982472 Score: 861
Period size: 254 Copynumber: 2.5 Consensus size: 253
981824 CTATTCGCAA
* * * * *
981834 CATAGCTCAAGGTAATAAGGGCTATATGTCAGCAAAAATCCTTCGAGTTCGATTAC-ATTCAGCT
1 CATAGCTCAAGGCAAGAAGGGCTATCTGTCAACAAAAA-CCTTCGAGTTCGATT-CTAGTCAGCT
* * * *
981898 TAAGGACATATCAAATTTTCAGCATAGCTCAAGGCGAGAAAGGCTATCTATCAAAAAAAACCTTC
64 CAAGGACATATCAAATTTACAGCATAGCTCAAGGCGAG-AAGGCTATCTGTCAACAAAAACCTTC
* * * * * *
981963 AAGTTCGATTTCATTCAGCTCAAGGGCAACTAAATTTACAGCATAGCTCAAGGCGAGAAGGGCTA
128 GAGTTCGATTCCAGTCAGCTCAAGGCCAAATAAATTTACAGCATAGCTCAAGGCAAGAAGGGCTA
* * *
982028 TCTATAAACAAAAACCTTCGAGTTCGATTCCAGTCAGCTCAAGGGCATATCAAATTTACAG
193 TCTATAAACAAAAACCTTCGAGTTCGATTCCAATCAACTCAAGGCCATATCAAATTTACAG
*
982089 CATAACTCAAGGCAAGAAGGGCTATCTGTCAACAAAAACCTTCGAGTTCGATTCTAGTCAGCTCA
1 CATAGCTCAAGGCAAGAAGGGCTATCTGTCAACAAAAACCTTCGAGTTCGATTCTAGTCAGCTCA
* * * * *
982154 AGGGCATATCAAATTTACAACATAGCTCAAGACGAGAATGGATATCTGTCAACAAAAATCTTCGA
66 AGGACATATCAAATTTACAGCATAGCTCAAGGCGAGAA-GGCTATCTGTCAACAAAAACCTTCGA
* *
982219 GTTCGATTCCAGTCAGCTCAAGGCCAAATCAAATTTACAGTATAGCTCAAGGCAAGAAGGGTTAT
130 GTTCGATTCCAGTCAGCTCAAGGCCAAAT-AAATTTACAGCATAGCTCAAGGCAAGAAGGGCTAT
* * * * *
982284 CTGTTAACAAAAACCTTTGAGTTTGATTCCAATCAACTCAAGGCCATATC-AATTTATAG
194 CTATAAACAAAAACCTTCGAGTTCGATTCCAATCAACTCAAGGCCATATCAAATTTACAG
* * * *
982343 TATAGCTCAAGGCGAGAAAGGCTATCTGTCAACAAAAACCTTCGGGTTCGATT-TCAGTCAGCTC
1 CATAGCTCAAGGCAAGAAGGGCTATCTGTCAACAAAAACCTTCGAGTTCGATTCT-AGTCAGCTC
* *
982407 AAGGCCATATCAAATTTACAGTATAGCTCAAGGCGAGAAGAGCTATCTGTCAACAAAAACCTTCG
65 AAGGACATATCAAATTTACAGCATAGCTCAAGGCGAGAAG-GCTATCTGTCAACAAAAACCTTCG
982472 A
129 A
982473 ATTAGATTAT
Statistics
Matches: 337, Mismatches: 42, Indels: 11
0.86 0.11 0.03
Matches are distributed among these distances:
253 5 0.01
254 224 0.66
255 108 0.32
ACGTcount: A:0.36, C:0.21, G:0.18, T:0.25
Consensus pattern (253 bp):
CATAGCTCAAGGCAAGAAGGGCTATCTGTCAACAAAAACCTTCGAGTTCGATTCTAGTCAGCTCA
AGGACATATCAAATTTACAGCATAGCTCAAGGCGAGAAGGCTATCTGTCAACAAAAACCTTCGAG
TTCGATTCCAGTCAGCTCAAGGCCAAATAAATTTACAGCATAGCTCAAGGCAAGAAGGGCTATCT
ATAAACAAAAACCTTCGAGTTCGATTCCAATCAACTCAAGGCCATATCAAATTTACAG
Found at i:982491 original size:85 final size:85
Alignment explanation
Indices: 981834--982472 Score: 834
Period size: 85 Copynumber: 7.5 Consensus size: 85
981824 CTATTCGCAA
** * * * * * *
981834 CATAGCTCAAGGTAATAAGGGCTATATGTCAGCAAAAATCCTTCGAGTTCGATTACATTCAGCTT
1 CATAGCTCAAGGCGAGAAGGGCTATCTGTCAACAAAAA-CCTTCGAGTTCGATTCCAGTCAGCTC
* *
981899 AAGGACATATCAAATTTTCAG
65 AAGGCCATATCAAATTTACAG
* * * * * *
981920 CATAGCTCAAGGCGAGAAAGGCTATCTATCAAAAAAAACCTTCAAGTTCGATTTCATTCAGCTCA
1 CATAGCTCAAGGCGAGAAGGGCTATCTGTCAACAAAAACCTTCGAGTTCGATTCCAGTCAGCTCA
*
981985 AGGGCA-A-CTAAATTTACAG
66 AGGCCATATC-AAATTTACAG
* *
982004 CATAGCTCAAGGCGAGAAGGGCTATCTATAAACAAAAACCTTCGAGTTCGATTCCAGTCAGCTCA
1 CATAGCTCAAGGCGAGAAGGGCTATCTGTCAACAAAAACCTTCGAGTTCGATTCCAGTCAGCTCA
*
982069 AGGGCATATCAAATTTACAG
66 AGGCCATATCAAATTTACAG
* * *
982089 CATAACTCAAGGCAAGAAGGGCTATCTGTCAACAAAAACCTTCGAGTTCGATTCTAGTCAGCTCA
1 CATAGCTCAAGGCGAGAAGGGCTATCTGTCAACAAAAACCTTCGAGTTCGATTCCAGTCAGCTCA
* *
982154 AGGGCATATCAAATTTACAA
66 AGGCCATATCAAATTTACAG
* * * *
982174 CATAGCTCAAGACGAGAATGGATATCTGTCAACAAAAATCTTCGAGTTCGATTCCAGTCAGCTCA
1 CATAGCTCAAGGCGAGAAGGGCTATCTGTCAACAAAAACCTTCGAGTTCGATTCCAGTCAGCTCA
*
982239 AGGCCAAATCAAATTTACAG
66 AGGCCATATCAAATTTACAG
* * * * * * * *
982259 TATAGCTCAAGGCAAGAAGGGTTATCTGTTAACAAAAACCTTTGAGTTTGATTCCAATCAACTCA
1 CATAGCTCAAGGCGAGAAGGGCTATCTGTCAACAAAAACCTTCGAGTTCGATTCCAGTCAGCTCA
*
982324 AGGCCATATC-AATTTATAG
66 AGGCCATATCAAATTTACAG
* * * *
982343 TATAGCTCAAGGCGAGAAAGGCTATCTGTCAACAAAAACCTTCGGGTTCGATTTCAGTCAGCTCA
1 CATAGCTCAAGGCGAGAAGGGCTATCTGTCAACAAAAACCTTCGAGTTCGATTCCAGTCAGCTCA
982408 AGGCCATATCAAATTTACAG
66 AGGCCATATCAAATTTACAG
* *
982428 TATAGCTCAAGGCGAGAAGAGCTATCTGTCAACAAAAACCTTCGA
1 CATAGCTCAAGGCGAGAAGGGCTATCTGTCAACAAAAACCTTCGA
982473 ATTAGATTAT
Statistics
Matches: 487, Mismatches: 62, Indels: 9
0.87 0.11 0.02
Matches are distributed among these distances:
83 1 0.00
84 148 0.30
85 307 0.63
86 31 0.06
ACGTcount: A:0.36, C:0.21, G:0.18, T:0.25
Consensus pattern (85 bp):
CATAGCTCAAGGCGAGAAGGGCTATCTGTCAACAAAAACCTTCGAGTTCGATTCCAGTCAGCTCA
AGGCCATATCAAATTTACAG
Found at i:983149 original size:36 final size:34
Alignment explanation
Indices: 983104--983438 Score: 135
Period size: 35 Copynumber: 9.2 Consensus size: 34
983094 AATGTTTGAA
*
983104 AATAT-TTTTTAGAAAATGACTTTTGAAAACATAT
1 AATATATTTTTAGAAAATCA-TTTTGAAAACATAT
*
983138 AATATACTTTTTA-AAAATCAGTTTTCGAAAATATTTAT
1 AATATA-TTTTTAGAAAATCA-TTTT-GAAAACA--TAT
983176 AATATATAGTTTT-GAAAA-CATTTTGAAAACATAT
1 AATATAT--TTTTAGAAAATCATTTTGAAAACATAT
*
983210 ATAGTAAATAGTTTTT-GAAAA-CATTTTGAAAATATAT
1 A-A-T--ATA-TTTTTAGAAAATCATTTTGAAAACATAT
*
983247 ATATTATATAGTTTT-GAAAA-CATTTTGAATATATATATATAT
1 A-A-TATAT--TTTTAGAAAATCATTTTG---A-A-A-ACATAT
* *
983289 AATATAGTTTTTA-AACA-CGATTTTTGAAAATGTATAT
1 AATATA-TTTTTAGAAAATC-A-TTTTGAAAA--CATAT
*
983326 ATTATATAGTTTTT-GAAAA-CATTTTGAAAATATATT
1 A--ATATA-TTTTTAGAAAATCATTTTGAAAACATA-T
*
983362 AATATATAGTTTT-TAAAA-CATTTTGAAAACTATAT
1 AATATAT--TTTTAGAAAATCATTTTGAAAAC-ATAT
*
983397 AATATATAGTTTT-GAAAAT-ATTTTTAAAACATAT
1 AATATAT--TTTTAGAAAATCATTTTGAAAACATAT
983431 ATATATAT
1 A-ATATAT
983439 ATAGTTTTAA
Statistics
Matches: 253, Mismatches: 12, Indels: 71
0.75 0.04 0.21
Matches are distributed among these distances:
33 1 0.00
34 20 0.08
35 72 0.28
36 41 0.16
37 49 0.19
38 16 0.06
39 33 0.13
40 6 0.02
41 8 0.03
42 7 0.03
ACGTcount: A:0.44, C:0.04, G:0.08, T:0.44
Consensus pattern (34 bp):
AATATATTTTTAGAAAATCATTTTGAAAACATAT
Found at i:983199 original size:11 final size:11
Alignment explanation
Indices: 983185--983241 Score: 51
Period size: 11 Copynumber: 4.8 Consensus size: 11
983175 TAATATATAG
983185 TTTTGAAAACA
1 TTTTGAAAACA
983196 TTTTGAAAACA
1 TTTTGAAAACA
* **
983207 TATATAGTAAATAGT
1 T-T-TTG-AAA-ACA
983222 TTTTGAAAACA
1 TTTTGAAAACA
983233 TTTTGAAAA
1 TTTTGAAAA
983242 TATATATATT
Statistics
Matches: 36, Mismatches: 6, Indels: 8
0.72 0.12 0.16
Matches are distributed among these distances:
11 22 0.61
12 4 0.11
13 4 0.11
14 4 0.11
15 2 0.06
ACGTcount: A:0.46, C:0.05, G:0.11, T:0.39
Consensus pattern (11 bp):
TTTTGAAAACA
Found at i:983451 original size:36 final size:38
Alignment explanation
Indices: 983134--983472 Score: 372
Period size: 36 Copynumber: 9.2 Consensus size: 38
983124 TTTTGAAAAC
* * *
983134 ATATA-ATATACTTTTTAAAAATCAGTTTTCGAAAATATTT
1 ATATATATATAGTTTTTGAAAA-CA-TTTT-GAAAATATAT
*
983174 ATA-ATATATAG-TTTTGAAAACATTTTGAAAACATAT
1 ATATATATATAGTTTTTGAAAACATTTTGAAAATATAT
983210 ATAGTA-A-ATAGTTTTTGAAAACATTTTGAAAATATAT
1 ATA-TATATATAGTTTTTGAAAACATTTTGAAAATATAT
*
983247 ATAT-TATATAG-TTTTGAAAACATTTTGAATATATAT
1 ATATATATATAGTTTTTGAAAACATTTTGAAAATATAT
*
983283 ATATATAATATAGTTTTT-AAACACGATTTTTGAAAATGTAT
1 ATATAT-ATATAGTTTTTGAAA-AC-A-TTTTGAAAATATAT
983324 ATAT-TATATAGTTTTTGAAAACATTTTGAAAATATAT
1 ATATATATATAGTTTTTGAAAACATTTTGAAAATATAT
*
983361 -TA-ATATATAGTTTTT-AAAACATTTTGAAAA-CTAT
1 ATATATATATAGTTTTTGAAAACATTTTGAAAATATAT
* * *
983395 ATA-ATATATAG-TTTTGAAAATATTTTTAAAACATAT
1 ATATATATATAGTTTTTGAAAACATTTTGAAAATATAT
* *
983431 ATATATATATAG-TTTT-AAAATATTTT-TAAATATAT
1 ATATATATATAGTTTTTGAAAACATTTTGAAAATATAT
983466 ATATATA
1 ATATATA
983473 GTTTTGCGAA
Statistics
Matches: 266, Mismatches: 15, Indels: 41
0.83 0.05 0.13
Matches are distributed among these distances:
34 7 0.03
35 52 0.20
36 75 0.28
37 62 0.23
38 13 0.05
39 28 0.11
40 13 0.05
41 16 0.06
ACGTcount: A:0.45, C:0.04, G:0.07, T:0.45
Consensus pattern (38 bp):
ATATATATATAGTTTTTGAAAACATTTTGAAAATATAT
Found at i:983488 original size:31 final size:31
Alignment explanation
Indices: 983321--983477 Score: 134
Period size: 35 Copynumber: 4.5 Consensus size: 31
983311 TTTGAAAATG
* *
983321 TATATATTATATAGTTTTTGAAAACATTTTGAAAA
1 TATATA-TATATAG-TTTT-AAAATATTTT-TAAA
* *
983356 TATATTAATATATAGTTTTTAAAACATTTTGAAAA
1 TATA-T-ATATATAG-TTTTAAAATATTTT-TAAA
983391 CTATATAATATATAGTTTTGAAAATATTTTTAAAACATA
1 -TATAT-ATATATAGTTTT-AAAATATTTTT---A-A-A
983430 TATATATATATAGTTTTAAAATATTTTTAAA
1 TATATATATATAGTTTTAAAATATTTTTAAA
983461 TATATATATATAGTTTT
1 TATATATATATAGTTTT
983478 GCGAATTTTT
Statistics
Matches: 111, Mismatches: 2, Indels: 22
0.82 0.01 0.16
Matches are distributed among these distances:
31 18 0.16
32 1 0.01
33 1 0.01
34 4 0.04
35 38 0.34
36 28 0.25
37 14 0.13
38 6 0.05
39 1 0.01
ACGTcount: A:0.44, C:0.03, G:0.06, T:0.48
Consensus pattern (31 bp):
TATATATATATAGTTTTAAAATATTTTTAAA
Found at i:983506 original size:5 final size:5
Alignment explanation
Indices: 983496--983527 Score: 57
Period size: 5 Copynumber: 6.6 Consensus size: 5
983486 TTTTATATGA
983496 TTTAT TTTAT TTTA- TTTAT TTTAT TTTAT TTT
1 TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT TTT
983528 GGTCTAGGTC
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
4 4 0.15
5 22 0.85
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (5 bp):
TTTAT
Found at i:983510 original size:19 final size:19
Alignment explanation
Indices: 983486--983527 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
983476 TTGCGAATTT
983486 TTTTATATGA-TTTATTTTA
1 TTTTAT-TGATTTTATTTTA
*
983505 TTTTATTTATTTTATTTTA
1 TTTTATTGATTTTATTTTA
983524 TTTT
1 TTTT
983528 GGTCTAGGTC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 2 0.10
19 19 0.90
ACGTcount: A:0.21, C:0.00, G:0.02, T:0.76
Consensus pattern (19 bp):
TTTTATTGATTTTATTTTA
Found at i:983520 original size:14 final size:14
Alignment explanation
Indices: 983482--983526 Score: 65
Period size: 14 Copynumber: 3.3 Consensus size: 14
983472 AGTTTTGCGA
* *
983482 ATTT-TTTTATATG
1 ATTTATTTTATTTT
983495 ATTTATTTTATTTT
1 ATTTATTTTATTTT
983509 ATTTATTTTATTTT
1 ATTTATTTTATTTT
983523 ATTT
1 ATTT
983527 TGGTCTAGGT
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
13 4 0.14
14 25 0.86
ACGTcount: A:0.22, C:0.00, G:0.02, T:0.76
Consensus pattern (14 bp):
ATTTATTTTATTTT
Found at i:984858 original size:16 final size:16
Alignment explanation
Indices: 984839--984872 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
984829 ATTTTATTAC
984839 TTTTAAAATTTAATTT
1 TTTTAAAATTTAATTT
**
984855 TTTTAATTTTTAATTT
1 TTTTAAAATTTAATTT
984871 TT
1 TT
984873 AATTTATTTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (16 bp):
TTTTAAAATTTAATTT
Found at i:986426 original size:13 final size:12
Alignment explanation
Indices: 986399--986436 Score: 53
Period size: 12 Copynumber: 3.2 Consensus size: 12
986389 AATTTAATTC
986399 TTAATTCTT--T
1 TTAATTCTTAAT
986409 TTAATTCTTTAAT
1 TTAATTC-TTAAT
986422 TTAATTCTTAAT
1 TTAATTCTTAAT
986434 TTA
1 TTA
986437 GATAGTGAAG
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
10 7 0.28
11 2 0.08
12 8 0.32
13 8 0.32
ACGTcount: A:0.29, C:0.08, G:0.00, T:0.63
Consensus pattern (12 bp):
TTAATTCTTAAT
Found at i:989851 original size:26 final size:26
Alignment explanation
Indices: 989795--989855 Score: 61
Period size: 26 Copynumber: 2.4 Consensus size: 26
989785 GCATTCAAAT
* *
989795 TTATGATTATCACTATTTGATTCGAA
1 TTATGATTATCAATAATTGATTCGAA
* * * *
989821 CTATGATTATTAATAATTGATTTGGA
1 TTATGATTATCAATAATTGATTCGAA
989847 TTATG-TTAT
1 TTATGATTAT
989856 GACTTGTGTT
Statistics
Matches: 28, Mismatches: 7, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
25 4 0.14
26 24 0.86
ACGTcount: A:0.31, C:0.07, G:0.13, T:0.49
Consensus pattern (26 bp):
TTATGATTATCAATAATTGATTCGAA
Found at i:998201 original size:57 final size:57
Alignment explanation
Indices: 998123--998293 Score: 236
Period size: 57 Copynumber: 3.0 Consensus size: 57
998113 CATAACCATA
* * * * * *
998123 CAACCCCATCACGAACAGTAAGACCCTGACCACAAAGCCAAGGAACCTACAAGTATT
1 CAACCCCGTCACGAACAGTAAGACTCTCAGCACAAAGCCGAGGAACCTGCAAGTATT
* * *
998180 CAACCCCGTCACAAATAGTAAGACTCTCAGCACAAAGCCGAGTAACCTGCAAGTATT
1 CAACCCCGTCACGAACAGTAAGACTCTCAGCACAAAGCCGAGGAACCTGCAAGTATT
* *
998237 CAA-CCCGTCACGAACAATAAGGCTCTCAGCACAAAGCCGAGGAACCTGCAAGTATT
1 CAACCCCGTCACGAACAGTAAGACTCTCAGCACAAAGCCGAGGAACCTGCAAGTATT
998293 C
1 C
998294 TTCCTCCAAC
Statistics
Matches: 100, Mismatches: 14, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
56 49 0.49
57 51 0.51
ACGTcount: A:0.37, C:0.32, G:0.16, T:0.15
Consensus pattern (57 bp):
CAACCCCGTCACGAACAGTAAGACTCTCAGCACAAAGCCGAGGAACCTGCAAGTATT
Found at i:1003229 original size:21 final size:20
Alignment explanation
Indices: 1003205--1003243 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
1003195 ACCAATGAAA
1003205 ATATACAGATCTTTTTAAAAC
1 ATATACAGAT-TTTTTAAAAC
* *
1003226 ATATATATATTTTTTAAA
1 ATATACAGATTTTTTAAA
1003244 TTTGAAAACC
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 8 0.50
21 8 0.50
ACGTcount: A:0.44, C:0.08, G:0.03, T:0.46
Consensus pattern (20 bp):
ATATACAGATTTTTTAAAAC
Found at i:1003507 original size:56 final size:57
Alignment explanation
Indices: 1003308--1003535 Score: 314
Period size: 57 Copynumber: 4.0 Consensus size: 57
1003298 CATAACCATA
* * * * * * *
1003308 CAACCCCGTAACAAACAGTAAGACCCTGAGCACAAAGCCAAGGAACCTACAAGTATT
1 CAACCCCGTCACGAACAGTAAGGCTCTCAGCACAAAGCCGAGGAACCTGCAAGTATT
* * * * *
1003365 CAACCCCGTCACGAACAGTAAGACTCTCAACACAAAGTCGAGAAACTTGCAAGTATT
1 CAACCCCGTCACGAACAGTAAGGCTCTCAGCACAAAGCCGAGGAACCTGCAAGTATT
* *
1003422 CAACCCCGTCACGAACAGTAAGGCTCTCAGTACAAAGCCGAGTAACCTGCAAGTATT
1 CAACCCCGTCACGAACAGTAAGGCTCTCAGCACAAAGCCGAGGAACCTGCAAGTATT
*
1003479 CAA-CCCGTCACGAACAATAAGGCTCTCAGCACAAAGCCGAGGAACCTGCAAGTATT
1 CAACCCCGTCACGAACAGTAAGGCTCTCAGCACAAAGCCGAGGAACCTGCAAGTATT
1003535 C
1 C
1003536 TTCCTCCAAC
Statistics
Matches: 152, Mismatches: 19, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
56 51 0.34
57 101 0.66
ACGTcount: A:0.37, C:0.30, G:0.18, T:0.15
Consensus pattern (57 bp):
CAACCCCGTCACGAACAGTAAGGCTCTCAGCACAAAGCCGAGGAACCTGCAAGTATT
Found at i:1010633 original size:34 final size:34
Alignment explanation
Indices: 1010538--1010633 Score: 101
Period size: 34 Copynumber: 2.8 Consensus size: 34
1010528 ATACAATTAG
* *
1010538 ATATCTTTTAATATTCAAATGTAAATAGATAATA
1 ATATCTTTTAATATTCAAATATAAAAAGATAATA
*
1010572 ATATCTTTTAAT-TTAAAATATACAAAAGTATAA-A
1 ATATCTTTTAATATTCAAATATA-AAAAG-ATAATA
1010606 ATTATC-TTTAATATTCAAAGT-TAAAAAG
1 A-TATCTTTTAATATTCAAA-TATAAAAAG
1010634 GTAACACACA
Statistics
Matches: 53, Mismatches: 4, Indels: 10
0.79 0.06 0.15
Matches are distributed among these distances:
33 8 0.15
34 29 0.55
35 15 0.28
36 1 0.02
ACGTcount: A:0.49, C:0.06, G:0.05, T:0.40
Consensus pattern (34 bp):
ATATCTTTTAATATTCAAATATAAAAAGATAATA
Found at i:1015195 original size:18 final size:18
Alignment explanation
Indices: 1015172--1015210 Score: 69
Period size: 18 Copynumber: 2.2 Consensus size: 18
1015162 ATCAATCAAG
*
1015172 TAATAAATTTAATATTAA
1 TAATAAATTGAATATTAA
1015190 TAATAAATTGAATATTAA
1 TAATAAATTGAATATTAA
1015208 TAA
1 TAA
1015211 ACTTGGATTC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.41
Consensus pattern (18 bp):
TAATAAATTGAATATTAA
Found at i:1018293 original size:31 final size:30
Alignment explanation
Indices: 1018258--1018336 Score: 79
Period size: 31 Copynumber: 2.5 Consensus size: 30
1018248 GTCCTTATTG
*
1018258 TTTAAAATATATATTAATTATTTTATAATAA
1 TTTAAAATATATAATAATTATTTT-TAATAA
* *
1018289 TTTAATAA-ATTTAATGATTATTTTTAATAA
1 TTTAA-AATATATAATAATTATTTTTAATAA
*
1018319 CTTAAAATAATTATAATA
1 TTTAAAAT-A-TATAATA
1018337 TAATATATAT
Statistics
Matches: 38, Mismatches: 6, Indels: 7
0.75 0.12 0.14
Matches are distributed among these distances:
29 2 0.05
30 10 0.26
31 19 0.50
32 7 0.18
ACGTcount: A:0.48, C:0.01, G:0.01, T:0.49
Consensus pattern (30 bp):
TTTAAAATATATAATAATTATTTTTAATAA
Found at i:1018373 original size:34 final size:35
Alignment explanation
Indices: 1018325--1018393 Score: 131
Period size: 34 Copynumber: 2.0 Consensus size: 35
1018315 ATAACTTAAA
1018325 ATAATTATAATATAATATATATTTAAAAAATAATT
1 ATAATTATAATATAATATATATTTAAAAAATAATT
1018360 ATAA-TATAATATAATATATATTTAAAAAATAATT
1 ATAATTATAATATAATATATATTTAAAAAATAATT
1018394 TATTAACAAT
Statistics
Matches: 34, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
34 30 0.88
35 4 0.12
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (35 bp):
ATAATTATAATATAATATATATTTAAAAAATAATT
Found at i:1018405 original size:34 final size:34
Alignment explanation
Indices: 1018333--1018406 Score: 114
Period size: 34 Copynumber: 2.2 Consensus size: 34
1018323 AAATAATTAT
*
1018333 AATATAATATATATTTAAAAAATAATTATAATAT
1 AATATAATATATATTTAAAAAATAATTATAATAC
*
1018367 AATATAATATATATTTAAAAAATAATT-TATTAAC
1 AATATAATATATATTTAAAAAATAATTATAAT-AC
1018401 AATATA
1 AATATA
1018407 TAAATAGTTT
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
33 3 0.08
34 34 0.92
ACGTcount: A:0.58, C:0.01, G:0.00, T:0.41
Consensus pattern (34 bp):
AATATAATATATATTTAAAAAATAATTATAATAC
Found at i:1021477 original size:22 final size:22
Alignment explanation
Indices: 1021449--1021520 Score: 78
Period size: 22 Copynumber: 3.4 Consensus size: 22
1021439 TTCCATTTCG
*
1021449 CGTTGCGATAGTCTGCAGTTGT
1 CGTTGCGATAGTCTACAGTTGT
* * **
1021471 CGTTGCGAT--TTTCCAAAT-T
1 CGTTGCGATAGTCTACAGTTGT
1021490 CGTTGCGATAGTCTACAGTTGT
1 CGTTGCGATAGTCTACAGTTGT
1021512 CGTTGCGAT
1 CGTTGCGAT
1021521 TTTCCAAATT
Statistics
Matches: 39, Mismatches: 8, Indels: 6
0.74 0.15 0.11
Matches are distributed among these distances:
19 10 0.26
20 5 0.13
21 5 0.13
22 19 0.49
ACGTcount: A:0.17, C:0.19, G:0.26, T:0.38
Consensus pattern (22 bp):
CGTTGCGATAGTCTACAGTTGT
Found at i:1021494 original size:19 final size:19
Alignment explanation
Indices: 1021470--1021535 Score: 69
Period size: 19 Copynumber: 3.3 Consensus size: 19
1021460 TCTGCAGTTG
1021470 TCGTTGCGATTTTCCAAAT
1 TCGTTGCGATTTTCCAAAT
* * **
1021489 TCGTTGCGATAGTCTACAGTT
1 TCGTTGCGAT--TTTCCAAAT
1021510 GTCGTTGCGATTTTCCAAAT
1 -TCGTTGCGATTTTCCAAAT
1021530 TCGTTG
1 TCGTTG
1021536 AAAAAAAAGA
Statistics
Matches: 36, Mismatches: 8, Indels: 6
0.72 0.16 0.12
Matches are distributed among these distances:
19 16 0.44
20 5 0.14
21 5 0.14
22 10 0.28
ACGTcount: A:0.18, C:0.20, G:0.21, T:0.41
Consensus pattern (19 bp):
TCGTTGCGATTTTCCAAAT
Found at i:1021494 original size:41 final size:41
Alignment explanation
Indices: 1021429--1021535 Score: 171
Period size: 41 Copynumber: 2.6 Consensus size: 41
1021419 TTGAAAATCG
* *
1021429 CGTTGCGATTTTCC-ATTTCGCGTTGCGATAGTCTGCAGTTGT
1 CGTTGCGATTTTCCAAATT--CGTTGCGATAGTCTACAGTTGT
1021471 CGTTGCGATTTTCCAAATTCGTTGCGATAGTCTACAGTTGT
1 CGTTGCGATTTTCCAAATTCGTTGCGATAGTCTACAGTTGT
1021512 CGTTGCGATTTTCCAAATTCGTTG
1 CGTTGCGATTTTCCAAATTCGTTG
1021536 AAAAAAAAGA
Statistics
Matches: 62, Mismatches: 2, Indels: 3
0.93 0.03 0.04
Matches are distributed among these distances:
41 45 0.73
42 14 0.23
43 3 0.05
ACGTcount: A:0.16, C:0.21, G:0.23, T:0.40
Consensus pattern (41 bp):
CGTTGCGATTTTCCAAATTCGTTGCGATAGTCTACAGTTGT
Found at i:1021650 original size:5 final size:6
Alignment explanation
Indices: 1021611--1021647 Score: 60
Period size: 6 Copynumber: 6.5 Consensus size: 6
1021601 GACACGTATT
1021611 ACCACG ACCACG ACCACG ACCACG ACC-CG ACC-CG ACC
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACC
1021648 CGAGACGAGA
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 10 0.32
6 21 0.68
ACGTcount: A:0.30, C:0.54, G:0.16, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:1022051 original size:39 final size:39
Alignment explanation
Indices: 1021977--1022055 Score: 115
Period size: 40 Copynumber: 2.0 Consensus size: 39
1021967 ACTATTTAAG
* * *
1021977 GCTCAATCCCACATAGTATTGGGAACAAGTGTTGGTAAT
1 GCTCAATCCCACATAGTATTGGAAACAACTATTGGTAAT
1022016 GCTCAAATCCCACATAGTATTGGAAAC-ACTATTGGTAAT
1 GCTC-AATCCCACATAGTATTGGAAACAACTATTGGTAAT
1022055 G
1 G
1022056 GTATTTAAGG
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
39 15 0.42
40 21 0.58
ACGTcount: A:0.33, C:0.19, G:0.20, T:0.28
Consensus pattern (39 bp):
GCTCAATCCCACATAGTATTGGAAACAACTATTGGTAAT
Found at i:1022173 original size:6 final size:6
Alignment explanation
Indices: 1022157--1022194 Score: 69
Period size: 6 Copynumber: 6.5 Consensus size: 6
1022147 TCTCGTCTCG
1022157 GGTCG- GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGT
1022195 AATACGTGTC
Statistics
Matches: 32, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 5 0.16
6 27 0.84
ACGTcount: A:0.00, C:0.16, G:0.53, T:0.32
Consensus pattern (6 bp):
GGTCGT
Found at i:1022303 original size:19 final size:19
Alignment explanation
Indices: 1022279--1022344 Score: 69
Period size: 19 Copynumber: 3.3 Consensus size: 19
1022269 TTAACTATCA
1022279 CAACGAATTTGGAAAATCG
1 CAACGAATTTGGAAAATCG
* * **
1022298 CAACGACAACTGTAGACTATCG
1 CAACG--AA-TTTGGAAAATCG
1022320 CAACGAATTTGGAAAATCG
1 CAACGAATTTGGAAAATCG
1022339 CAACGA
1 CAACGA
1022345 CAACTGTAGA
Statistics
Matches: 36, Mismatches: 8, Indels: 6
0.72 0.16 0.12
Matches are distributed among these distances:
19 19 0.53
20 2 0.06
21 2 0.06
22 13 0.36
ACGTcount: A:0.41, C:0.21, G:0.20, T:0.18
Consensus pattern (19 bp):
CAACGAATTTGGAAAATCG
Found at i:1022321 original size:22 final size:22
Alignment explanation
Indices: 1022294--1022365 Score: 87
Period size: 22 Copynumber: 3.4 Consensus size: 22
1022284 AATTTGGAAA
1022294 ATCGCAACGACAACTGTAGACT
1 ATCGCAACGACAACTGTAGACT
* * **
1022316 ATCGCAACG--AA-TTTGGAAA
1 ATCGCAACGACAACTGTAGACT
1022335 ATCGCAACGACAACTGTAGACT
1 ATCGCAACGACAACTGTAGACT
1022357 ATCGCAACG
1 ATCGCAACG
1022366 CGAAATGGAA
Statistics
Matches: 39, Mismatches: 8, Indels: 6
0.74 0.15 0.11
Matches are distributed among these distances:
19 13 0.33
20 2 0.05
21 2 0.05
22 22 0.56
ACGTcount: A:0.38, C:0.25, G:0.19, T:0.18
Consensus pattern (22 bp):
ATCGCAACGACAACTGTAGACT
Found at i:1022329 original size:41 final size:41
Alignment explanation
Indices: 1022272--1022385 Score: 185
Period size: 41 Copynumber: 2.8 Consensus size: 41
1022262 TTTTTTTTTA
*
1022272 ACTATCACAACGAATTTGGAAAATCGCAACGACAACTGTAG
1 ACTATCGCAACGAATTTGGAAAATCGCAACGACAACTGTAG
1022313 ACTATCGCAACGAATTTGGAAAATCGCAACGACAACTGTAG
1 ACTATCGCAACGAATTTGGAAAATCGCAACGACAACTGTAG
*
1022354 ACTATCGCAACGCGAA-ATGGAAAATCGCAACG
1 ACTATCGCAA--CGAATTTGGAAAATCGCAACG
1022386 CGATTTTCAA
Statistics
Matches: 69, Mismatches: 2, Indels: 3
0.93 0.03 0.04
Matches are distributed among these distances:
41 50 0.72
42 15 0.22
43 4 0.06
ACGTcount: A:0.40, C:0.23, G:0.19, T:0.18
Consensus pattern (41 bp):
ACTATCGCAACGAATTTGGAAAATCGCAACGACAACTGTAG
Found at i:1022382 original size:20 final size:20
Alignment explanation
Indices: 1022357--1022425 Score: 84
Period size: 20 Copynumber: 3.4 Consensus size: 20
1022347 ACTGTAGACT
1022357 ATCGCAACGCGAAATGGAAA
1 ATCGCAACGCGAAATGGAAA
** ** *
1022377 ATCGCAACGCGATTTTCAACT
1 ATCGCAACGCGAAATGGAA-A
1022398 ATCGCAACGCGAAATGGAAA
1 ATCGCAACGCGAAATGGAAA
1022418 ATCGCAAC
1 ATCGCAAC
1022426 ACGATTTTCA
Statistics
Matches: 38, Mismatches: 10, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
20 23 0.61
21 15 0.39
ACGTcount: A:0.39, C:0.25, G:0.20, T:0.16
Consensus pattern (20 bp):
ATCGCAACGCGAAATGGAAA
Found at i:1022399 original size:41 final size:41
Alignment explanation
Indices: 1022354--1022454 Score: 184
Period size: 41 Copynumber: 2.5 Consensus size: 41
1022344 ACAACTGTAG
*
1022354 ACTATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCA
1 ACTATCGCAACGCGAAATGGAAAATCGCAACACGATTTTCA
1022395 ACTATCGCAACGCGAAATGGAAAATCGCAACACGATTTTCA
1 ACTATCGCAACGCGAAATGGAAAATCGCAACACGATTTTCA
*
1022436 ACTATCTCAACGCGAAATG
1 ACTATCGCAACGCGAAATG
1022455 CAACGCGAAT
Statistics
Matches: 58, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
41 58 1.00
ACGTcount: A:0.38, C:0.25, G:0.18, T:0.20
Consensus pattern (41 bp):
ACTATCGCAACGCGAAATGGAAAATCGCAACACGATTTTCA
Found at i:1022458 original size:21 final size:21
Alignment explanation
Indices: 1022354--1022458 Score: 88
Period size: 21 Copynumber: 5.1 Consensus size: 21
1022344 ACAACTGTAG
*
1022354 ACTATCGCAACGCGAAATGGA
1 ACTATCGCAACGCGAAATGCA
* ** *
1022375 A-AATCGCAACGCGATTTTCA
1 ACTATCGCAACGCGAAATGCA
*
1022395 ACTATCGCAACGCGAAATGGA
1 ACTATCGCAACGCGAAATGCA
* * ** *
1022416 A-AATCGCAACACGATTTTCA
1 ACTATCGCAACGCGAAATGCA
*
1022436 ACTATCTCAACGCGAAATGCA
1 ACTATCGCAACGCGAAATGCA
1022457 AC
1 AC
1022459 GCGAATTTGC
Statistics
Matches: 60, Mismatches: 22, Indels: 4
0.70 0.26 0.05
Matches are distributed among these distances:
20 29 0.48
21 31 0.52
ACGTcount: A:0.38, C:0.26, G:0.17, T:0.19
Consensus pattern (21 bp):
ACTATCGCAACGCGAAATGCA
Found at i:1038425 original size:54 final size:54
Alignment explanation
Indices: 1038367--1038754 Score: 446
Period size: 54 Copynumber: 7.4 Consensus size: 54
1038357 TTCTTTAGGG
** * *
1038367 TGCACACTTAGTGCCGATACGATCATTCATAAGCTCATTATGAATTCTGTGGGT
1 TGCACACTTAGTGCCGATACGATTGTTCATAAACTTATTATGAATTCTGTGGGT
*
1038421 TGCACACTTAGTGCCGATACGATCGTTCA-AAACTTATTATGAATTCTGTGGGTT
1 TGCACACTTAGTGCCGATACGATTGTTCATAAACTTATTATGAATTCTGTGGG-T
* * * *
1038475 TG--CACTTAGTGCTGATACGGTTGTTCATAAACTTATTGTGAATT-TCATGGGT
1 TGCACACTTAGTGCCGATACGATTGTTCATAAACTTATTATGAATTCT-GTGGGT
*
1038527 TGCACACTTAGTG-C--TACGGTTGTTCATAAACTTATTATGAATT-TCGTGGGT
1 TGCACACTTAGTGCCGATACGATTGTTCATAAACTTATTATGAATTCT-GTGGGT
*
1038578 T--ACACTTAGTGCCAATAC-AGTTGTTCATAAACTTATTATGAATTCTGT-GG-
1 TGCACACTTAGTGCCGATACGA-TTGTTCATAAACTTATTATGAATTCTGTGGGT
* * *
1038628 -GCACACTTAGTGTCAATACAATTGTTCATAAACTTATTATGAATTCTGTGGGT
1 TGCACACTTAGTGCCGATACGATTGTTCATAAACTTATTATGAATTCTGTGGGT
* * * ** *
1038681 TGCACACTTAGTGCCAATACGGGTT-TTCATAAACTTATTATGAATTCCGTACGC
1 TGCACACTTAGTGCCGATAC-GATTGTTCATAAACTTATTATGAATTCTGTGGGT
1038735 TGCACACTTAGTGCCGATAC
1 TGCACACTTAGTGCCGATAC
1038755 ATAAAAATGC
Statistics
Matches: 296, Mismatches: 21, Indels: 34
0.84 0.06 0.10
Matches are distributed among these distances:
49 10 0.03
50 1 0.00
51 82 0.28
52 58 0.20
53 41 0.14
54 102 0.34
55 2 0.01
ACGTcount: A:0.27, C:0.18, G:0.19, T:0.36
Consensus pattern (54 bp):
TGCACACTTAGTGCCGATACGATTGTTCATAAACTTATTATGAATTCTGTGGGT
Found at i:1038610 original size:103 final size:104
Alignment explanation
Indices: 1038370--1038754 Score: 426
Period size: 103 Copynumber: 3.7 Consensus size: 104
1038360 TTTAGGGTGC
* * ** * * *
1038370 ACACTTAGTGCCGATACGATCATTCATAAGCTCATTATGAATTCTGTGGGTTGCACACTTAGTGC
1 ACACTTAGTGCCAATACGGTTGTTCATAAACTTATTATGAATT-TCTGGGTTGCACACTTAGTGC
*
1038435 CGATACGATCGTTCA-AAACTTATTATGAATTCTGTGGGTTT
65 C-ATACGATTGTTCATAAACTTATTATGAATTCTGTGGG-TT
* ** *
1038476 GCACTTAGTGCTGATACGGTTGTTCATAAACTTATTGTGAATTTCATGGGTTGCACACTTAGTG-
1 ACACTTAGTGCCAATACGGTTGTTCATAAACTTATTATGAATTTC-TGGGTTGCACACTTAGTGC
*
1038540 C-TACGGTTGTTCATAAACTTATTATGAATT-TCGTGGGTT
65 CATACGATTGTTCATAAACTTATTATGAATTCT-GTGGGTT
*
1038579 ACACTTAGTGCCAATACAGTTGTTCATAAACTTATTATGAA-TTCTGTGG--GCACACTTAGTGT
1 ACACTTAGTGCCAATACGGTTGTTCATAAACTTATTATGAATTTCTG-GGTTGCACACTTAGTG-
* *
1038641 CAATACAATTGTTCATAAACTTATTATGAATTCTGTGGGTT
64 CCATACGATTGTTCATAAACTTATTATGAATTCTGTGGGTT
* ** *
1038682 GCACACTTAGTGCCAATACGGGTT-TTCATAAACTTATTATGAATTCCGTACGCTGCACACTTAG
1 --ACACTTAGTGCCAATAC-GGTTGTTCATAAACTTATTATGAATTTC-TGGGTTGCACACTTAG
1038746 TGCCGATAC
62 TGCC-ATAC
1038755 ATAAAAATGC
Statistics
Matches: 239, Mismatches: 24, Indels: 30
0.82 0.08 0.10
Matches are distributed among these distances:
100 12 0.05
101 2 0.01
102 5 0.02
103 83 0.35
104 22 0.09
105 38 0.16
106 59 0.25
107 2 0.01
108 16 0.07
ACGTcount: A:0.27, C:0.18, G:0.19, T:0.36
Consensus pattern (104 bp):
ACACTTAGTGCCAATACGGTTGTTCATAAACTTATTATGAATTTCTGGGTTGCACACTTAGTGCC
ATACGATTGTTCATAAACTTATTATGAATTCTGTGGGTT
Found at i:1040140 original size:27 final size:28
Alignment explanation
Indices: 1040110--1040163 Score: 74
Period size: 28 Copynumber: 2.0 Consensus size: 28
1040100 AATAAAAAAG
*
1040110 AATT-TTTAAAATTGTTGTTTAAAATTT
1 AATTGTTTAAAATTGTTGTTAAAAATTT
* *
1040137 AATTGTTTGATATTGTTGTTAAAAATT
1 AATTGTTTAAAATTGTTGTTAAAAATT
1040164 GAGTTTGAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
27 4 0.17
28 19 0.83
ACGTcount: A:0.35, C:0.00, G:0.11, T:0.54
Consensus pattern (28 bp):
AATTGTTTAAAATTGTTGTTAAAAATTT
Found at i:1040601 original size:21 final size:22
Alignment explanation
Indices: 1040550--1040601 Score: 54
Period size: 21 Copynumber: 2.4 Consensus size: 22
1040540 AATATGAATT
*
1040550 TTATTTATTTTTAAGTAATTAAA
1 TTATTT-TTATTAAGTAATTAAA
* *
1040573 ATA-ATTTATTAAGTAA-TAAA
1 TTATTTTTATTAAGTAATTAAA
1040593 TTATTTTTA
1 TTATTTTTA
1040602 AGGATGTTAA
Statistics
Matches: 23, Mismatches: 5, Indels: 4
0.72 0.16 0.12
Matches are distributed among these distances:
20 6 0.26
21 14 0.61
22 1 0.04
23 2 0.09
ACGTcount: A:0.42, C:0.00, G:0.04, T:0.54
Consensus pattern (22 bp):
TTATTTTTATTAAGTAATTAAA
Found at i:1041658 original size:15 final size:15
Alignment explanation
Indices: 1041638--1041678 Score: 73
Period size: 15 Copynumber: 2.7 Consensus size: 15
1041628 ACCCAAAGCT
1041638 GAGAAGAAGCCGGCG
1 GAGAAGAAGCCGGCG
*
1041653 GAGAAGAAACCGGCG
1 GAGAAGAAGCCGGCG
1041668 GAGAAGAAGCC
1 GAGAAGAAGCC
1041679 AGCTGAGGAG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.39, C:0.20, G:0.41, T:0.00
Consensus pattern (15 bp):
GAGAAGAAGCCGGCG
Found at i:1041690 original size:15 final size:15
Alignment explanation
Indices: 1041638--1041691 Score: 63
Period size: 15 Copynumber: 3.6 Consensus size: 15
1041628 ACCCAAAGCT
*
1041638 GAGAAGAAGCCGGCG
1 GAGAAGAAGCCAGCG
* *
1041653 GAGAAGAAACCGGCG
1 GAGAAGAAGCCAGCG
*
1041668 GAGAAGAAGCCAGCT
1 GAGAAGAAGCCAGCG
*
1041683 GAGGAGAAG
1 GAGAAGAAG
1041692 AAAACCGTCG
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
15 34 1.00
ACGTcount: A:0.39, C:0.17, G:0.43, T:0.02
Consensus pattern (15 bp):
GAGAAGAAGCCAGCG
Found at i:1042116 original size:6 final size:6
Alignment explanation
Indices: 1042105--1042129 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
1042095 GCTGTTCTAT
1042105 GGTTAG GGTTAG GGTTAG GGTTAG G
1 GGTTAG GGTTAG GGTTAG GGTTAG G
1042130 ATTTCCCCCT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.16, C:0.00, G:0.52, T:0.32
Consensus pattern (6 bp):
GGTTAG
Found at i:1052466 original size:89 final size:89
Alignment explanation
Indices: 1052315--1052496 Score: 355
Period size: 89 Copynumber: 2.0 Consensus size: 89
1052305 GGTGTTCGTG
*
1052315 GGAGTTTCTAAGTCGTTTAAAAAACGATGGAGGATTAGGTTTCAGATATATGGCTAAATTCAATG
1 GGAGTTTCTAAGTCGTTTAAAAAACGATGGAGGATTAGGTTTCAGAGATATGGCTAAATTCAATG
1052380 TTGCTCTGTTGGCAAAACAGGGAT
66 TTGCTCTGTTGGCAAAACAGGGAT
1052404 GGAGTTTCTAAGTCGTTTAAAAAACGATGGAGGATTAGGTTTCAGAGATATGGCTAAATTCAATG
1 GGAGTTTCTAAGTCGTTTAAAAAACGATGGAGGATTAGGTTTCAGAGATATGGCTAAATTCAATG
1052469 TTGCTCTGTTGGCAAAACAGGGAT
66 TTGCTCTGTTGGCAAAACAGGGAT
1052493 GGAG
1 GGAG
1052497 ATTGATTGTA
Statistics
Matches: 92, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
89 92 1.00
ACGTcount: A:0.31, C:0.11, G:0.27, T:0.30
Consensus pattern (89 bp):
GGAGTTTCTAAGTCGTTTAAAAAACGATGGAGGATTAGGTTTCAGAGATATGGCTAAATTCAATG
TTGCTCTGTTGGCAAAACAGGGAT
Found at i:1058193 original size:36 final size:36
Alignment explanation
Indices: 1058146--1058219 Score: 148
Period size: 36 Copynumber: 2.1 Consensus size: 36
1058136 TTTCATCTGG
1058146 ATCGTTAAATAATTATGTCATATGCTTCCAATATAT
1 ATCGTTAAATAATTATGTCATATGCTTCCAATATAT
1058182 ATCGTTAAATAATTATGTCATATGCTTCCAATATAT
1 ATCGTTAAATAATTATGTCATATGCTTCCAATATAT
1058218 AT
1 AT
1058220 ATATAACATG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 38 1.00
ACGTcount: A:0.36, C:0.14, G:0.08, T:0.42
Consensus pattern (36 bp):
ATCGTTAAATAATTATGTCATATGCTTCCAATATAT
Found at i:1058279 original size:25 final size:25
Alignment explanation
Indices: 1058211--1058279 Score: 68
Period size: 25 Copynumber: 2.7 Consensus size: 25
1058201 ATATGCTTCC
* *
1058211 AATATATATATATAACATGGTTTTGAA
1 AATATA-ATATAT-ATATAGTTTTGAA
* *
1058238 AATAT-ATGACATTTATAGTTTTGAA
1 AATATAAT-ATATATATAGTTTTGAA
1058263 AATATAATATATATATA
1 AATATAATATATATATA
1058280 TTTATATTCT
Statistics
Matches: 34, Mismatches: 6, Indels: 6
0.74 0.13 0.13
Matches are distributed among these distances:
25 24 0.71
26 5 0.15
27 5 0.15
ACGTcount: A:0.46, C:0.03, G:0.09, T:0.42
Consensus pattern (25 bp):
AATATAATATATATATAGTTTTGAA
Found at i:1058350 original size:28 final size:28
Alignment explanation
Indices: 1058298--1058351 Score: 72
Period size: 28 Copynumber: 1.9 Consensus size: 28
1058288 CTAAGTTGTA
*
1058298 ATATATAACTTTGAAAACGTGTATATAT
1 ATATATAACTTTGAAAACGTATATATAT
* * *
1058326 ATATATAATTTTGAAAGCTTATATAT
1 ATATATAACTTTGAAAACGTATATAT
1058352 TTTTAAAAAT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 22 1.00
ACGTcount: A:0.43, C:0.06, G:0.09, T:0.43
Consensus pattern (28 bp):
ATATATAACTTTGAAAACGTATATATAT
Found at i:1058677 original size:2 final size:2
Alignment explanation
Indices: 1058670--1058712 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
1058660 AAACATTGTT
1058670 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
1058712 T
1 T
1058713 TTTAATGGTA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1058915 original size:27 final size:27
Alignment explanation
Indices: 1058882--1058958 Score: 136
Period size: 27 Copynumber: 2.9 Consensus size: 27
1058872 ATTTTTACAT
1058882 ACATAACACACTCTTTTCATCTTTTAC
1 ACATAACACACTCTTTTCATCTTTTAC
*
1058909 ACATAACACACTCATTTCATCTTTTAC
1 ACATAACACACTCTTTTCATCTTTTAC
*
1058936 ACACAACACACTCTTTTCATCTT
1 ACATAACACACTCTTTTCATCTT
1058959 CAATCTCTTA
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 47 1.00
ACGTcount: A:0.31, C:0.31, G:0.00, T:0.38
Consensus pattern (27 bp):
ACATAACACACTCTTTTCATCTTTTAC
Found at i:1059846 original size:17 final size:17
Alignment explanation
Indices: 1059824--1059857 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
1059814 GCATAACTAG
1059824 CAATCAAGGAGTACTGC
1 CAATCAAGGAGTACTGC
*
1059841 CAATCAATGAGTACTGC
1 CAATCAAGGAGTACTGC
1059858 ATCAAAGCTC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.35, C:0.24, G:0.21, T:0.21
Consensus pattern (17 bp):
CAATCAAGGAGTACTGC
Found at i:1061784 original size:21 final size:21
Alignment explanation
Indices: 1061733--1061785 Score: 67
Period size: 20 Copynumber: 2.6 Consensus size: 21
1061723 TAAATAGGTA
*
1061733 TTTTTAACTTGT-ATTATGTT
1 TTTTTAACTTGTAACTATGTT
1061753 TTTTGT-A-TTGTAACTATGTT
1 TTTT-TAACTTGTAACTATGTT
1061773 TTTTTAACTTGTA
1 TTTTTAACTTGTA
1061786 TTATATTGAA
Statistics
Matches: 28, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
19 5 0.18
20 17 0.61
21 6 0.21
ACGTcount: A:0.21, C:0.06, G:0.11, T:0.62
Consensus pattern (21 bp):
TTTTTAACTTGTAACTATGTT
Found at i:1062299 original size:16 final size:16
Alignment explanation
Indices: 1062276--1062329 Score: 67
Period size: 18 Copynumber: 3.3 Consensus size: 16
1062266 TATGAATGAT
1062276 TTTTTTAATTAAATT-
1 TTTTTTAATTAAATTA
1062291 TTATTTTAATTAAAAGTTA
1 TT-TTTTAATT-AAA-TTA
1062310 TTTTTTAATTAAA-TA
1 TTTTTTAATTAAATTA
1062325 TTTTT
1 TTTTT
1062330 CATTTTTATT
Statistics
Matches: 35, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
15 9 0.26
16 8 0.23
17 6 0.17
18 10 0.29
19 2 0.06
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (16 bp):
TTTTTTAATTAAATTA
Found at i:1062797 original size:19 final size:19
Alignment explanation
Indices: 1062773--1062811 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
1062763 TCGAATGCAT
1062773 TCCATGCAGCGATGCACTC
1 TCCATGCAGCGATGCACTC
*
1062792 TCCATGCATCGATGCACTC
1 TCCATGCAGCGATGCACTC
1062811 T
1 T
1062812 GAATATTTTC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.21, C:0.36, G:0.18, T:0.26
Consensus pattern (19 bp):
TCCATGCAGCGATGCACTC
Found at i:1062912 original size:64 final size:65
Alignment explanation
Indices: 1062759--1062919 Score: 218
Period size: 65 Copynumber: 2.5 Consensus size: 65
1062749 GAATTAATTG
* * *** *
1062759 AACATCGAATGCATTCCATGCAGCGATGCACTCTCCATGCATCGATGCACTCTGAATATTTTCAA
1 AACATCGAATGCATTTCATGCATCGATGCACAAGCCATGCATCGATGCACTCAGAATATTTTCAA
* **
1062824 AACATCGAATGCATTTGATGCATCGATGCACAAGCCATGCATCGATGCA-TCAGGCTATTTTTC-
1 AACATCGAATGCATTTCATGCATCGATGCACAAGCCATGCATCGATGCACTCAGAATA-TTTTCA
1062887 A
65 A
1062888 AACATCGAATGCATTTCATGCATCGATGCACA
1 AACATCGAATGCATTTCATGCATCGATGCACA
1062920 CTTGGTGCAC
Statistics
Matches: 85, Mismatches: 10, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
64 37 0.44
65 48 0.56
ACGTcount: A:0.30, C:0.25, G:0.17, T:0.27
Consensus pattern (65 bp):
AACATCGAATGCATTTCATGCATCGATGCACAAGCCATGCATCGATGCACTCAGAATATTTTCAA
Found at i:1062934 original size:64 final size:64
Alignment explanation
Indices: 1062759--1062939 Score: 220
Period size: 64 Copynumber: 2.8 Consensus size: 64
1062749 GAATTAATTG
* * * *
1062759 AACATCGAATGCATTCCATGCAGCGATGCACTCTCCATGCATCGATGCACTCTGAATATTTTCAA
1 AACATCGAATGCATTTCATGCATCGATGCACACTCCATGCATCGATGCA-TCAGAATATTTTCAA
* ** **
1062824 AACATCGAATGCATTTGATGCATCGATGCACAAGCCATGCATCGATGCATCAGGCTATTTTTC-A
1 AACATCGAATGCATTTCATGCATCGATGCACACTCCATGCATCGATGCATCAGAATA-TTTTCAA
*** *
1062888 AACATCGAATGCATTTCATGCATCGATGCACACTTGGTGCACCGATGCATCA
1 AACATCGAATGCATTTCATGCATCGATGCACACTCCATGCATCGATGCATCA
1062940 AGTGTTCCAA
Statistics
Matches: 99, Mismatches: 16, Indels: 3
0.84 0.14 0.03
Matches are distributed among these distances:
64 51 0.52
65 48 0.48
ACGTcount: A:0.29, C:0.26, G:0.18, T:0.27
Consensus pattern (64 bp):
AACATCGAATGCATTTCATGCATCGATGCACACTCCATGCATCGATGCATCAGAATATTTTCAA
Found at i:1069192 original size:21 final size:21
Alignment explanation
Indices: 1069150--1069193 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
1069140 ACCCCGGGAG
*
1069150 CTAGTTCTTCACGAGCTGCTC
1 CTAGTTCTTCACGAGCTCCTC
* *
1069171 CTAGTTCTTCTCGTGCTCCTC
1 CTAGTTCTTCACGAGCTCCTC
1069192 CT
1 CT
1069194 CCTCCTCTAG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.09, C:0.36, G:0.16, T:0.39
Consensus pattern (21 bp):
CTAGTTCTTCACGAGCTCCTC
Found at i:1069572 original size:8 final size:8
Alignment explanation
Indices: 1069533--1069570 Score: 58
Period size: 8 Copynumber: 4.8 Consensus size: 8
1069523 TGTTTATGTT
1069533 TGTTTGGA
1 TGTTTGGA
1069541 TGTTTGGA
1 TGTTTGGA
1069549 TGTTTGGA
1 TGTTTGGA
* *
1069557 TGCTTGAA
1 TGTTTGGA
1069565 TGTTTG
1 TGTTTG
1069571 AACTTAATTT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
8 27 1.00
ACGTcount: A:0.13, C:0.03, G:0.34, T:0.50
Consensus pattern (8 bp):
TGTTTGGA
Found at i:1070267 original size:19 final size:19
Alignment explanation
Indices: 1070243--1070281 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
1070233 TCGAATGCAT
1070243 TCCATGCAGCGATGCACTC
1 TCCATGCAGCGATGCACTC
*
1070262 TCCATGCATCGATGCACTC
1 TCCATGCAGCGATGCACTC
1070281 T
1 T
1070282 GAATATTTTC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.21, C:0.36, G:0.18, T:0.26
Consensus pattern (19 bp):
TCCATGCAGCGATGCACTC
Done.