Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D05
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: 64368997
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1610000 characters in sequence are not A, C, G, or T
File 82 of 208
Found at i:28805388 original size:23 final size:23
Alignment explanation
Indices: 28805362--28805449 Score: 97
Period size: 23 Copynumber: 3.8 Consensus size: 23
28805352 TTAATGTTTA
*
28805362 CGAACATGTTCATTTAAC-TTAAT
1 CGAACATGTTCA-TGAACATTAAT
* * *
28805385 CGAACATATTCACGAACATTAAA
1 CGAACATGTTCATGAACATTAAT
28805408 CGAACATGTTCATGAACATATAAT
1 CGAACATGTTCATGAACAT-TAAT
* *
28805432 TGAACATGTTCACGAACA
1 CGAACATGTTCATGAACA
28805450 ATGTTAATAA
Statistics
Matches: 54, Mismatches: 9, Indels: 3
0.82 0.14 0.05
Matches are distributed among these distances:
22 3 0.06
23 32 0.59
24 19 0.35
ACGTcount: A:0.41, C:0.19, G:0.11, T:0.28
Consensus pattern (23 bp):
CGAACATGTTCATGAACATTAAT
Found at i:28806567 original size:16 final size:17
Alignment explanation
Indices: 28806531--28806565 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
28806521 ATGATTCTCA
28806531 TTAAACCCCTAAAATTT
1 TTAAACCCCTAAAATTT
* *
28806548 TTAAACCTCTCAAATTT
1 TTAAACCCCTAAAATTT
28806565 T
1 T
28806566 AATCTTCCGG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.37, C:0.23, G:0.00, T:0.40
Consensus pattern (17 bp):
TTAAACCCCTAAAATTT
Found at i:28814504 original size:43 final size:43
Alignment explanation
Indices: 28814348--28814505 Score: 139
Period size: 43 Copynumber: 3.7 Consensus size: 43
28814338 TATGAGTTAT
*
28814348 CATGTAAGACCACGTCTGGGACGTTGGCATCGAT-TTGAGATTTA
1 CATGTAAGACCACGTCTGAGACGTTGGCATCGATATT-AGA-TTA
* ** * * *
28814392 CGTGTAAGACCATTTTTGAGACATCGGCATCG-TA-TACGATT-
1 CATGTAAGACCACGTCTGAGACGTTGGCATCGATATTA-GATTA
* *
28814433 CGTGTAAGACC-CTGTCTGAGACAG-TGGCATCGATATTTGATTA
1 CATGTAAGACCAC-GTCTGAGAC-GTTGGCATCGATATTAGATTA
*
28814476 CATGTAAGACCACGTCTGGGACGTTGGCAT
1 CATGTAAGACCACGTCTGAGACGTTGGCAT
28814506 TGTAAGAGCT
Statistics
Matches: 90, Mismatches: 15, Indels: 19
0.73 0.12 0.15
Matches are distributed among these distances:
41 25 0.28
42 10 0.11
43 29 0.32
44 26 0.29
ACGTcount: A:0.25, C:0.20, G:0.26, T:0.29
Consensus pattern (43 bp):
CATGTAAGACCACGTCTGAGACGTTGGCATCGATATTAGATTA
Found at i:28821645 original size:37 final size:37
Alignment explanation
Indices: 28821598--28821672 Score: 132
Period size: 37 Copynumber: 2.0 Consensus size: 37
28821588 TTGTATTAAT
* *
28821598 AGTTAGATTATATTTTGTCGTTTTTATTTAAAAATAG
1 AGTTAAATTATATTTTATCGTTTTTATTTAAAAATAG
28821635 AGTTAAATTATATTTTATCGTTTTTATTTAAAAATAG
1 AGTTAAATTATATTTTATCGTTTTTATTTAAAAATAG
28821672 A
1 A
28821673 CAAATTAATC
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 36 1.00
ACGTcount: A:0.36, C:0.03, G:0.11, T:0.51
Consensus pattern (37 bp):
AGTTAAATTATATTTTATCGTTTTTATTTAAAAATAG
Found at i:28821687 original size:35 final size:36
Alignment explanation
Indices: 28821604--28821687 Score: 118
Period size: 37 Copynumber: 2.3 Consensus size: 36
28821594 TAATAGTTAG
* *
28821604 ATTATATTTTGTCGTTTTTATTTAAAAATAGAGTTAA
1 ATTATATTTTATCGTTTTTATTTAAAAATAGAG-CAA
28821641 ATTATATTTTATCGTTTTTATTTAAAAATAGA-CAA
1 ATTATATTTTATCGTTTTTATTTAAAAATAGAGCAA
28821676 ATTA-ATCTTTAT
1 ATTATAT-TTTAT
28821688 ATATTAAAAG
Statistics
Matches: 44, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
34 2 0.05
35 11 0.25
37 31 0.70
ACGTcount: A:0.37, C:0.05, G:0.07, T:0.51
Consensus pattern (36 bp):
ATTATATTTTATCGTTTTTATTTAAAAATAGAGCAA
Found at i:28829477 original size:16 final size:18
Alignment explanation
Indices: 28829456--28829488 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
28829446 GAAACAAAAA
28829456 TATCAT-TT-TTATTTTT
1 TATCATATTATTATTTTT
28829472 TATCATATTATTATTTT
1 TATCATATTATTATTTT
28829489 GGTGTCGTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.40
17 2 0.13
18 7 0.47
ACGTcount: A:0.24, C:0.06, G:0.00, T:0.70
Consensus pattern (18 bp):
TATCATATTATTATTTTT
Found at i:28831961 original size:24 final size:22
Alignment explanation
Indices: 28831905--28831963 Score: 64
Period size: 24 Copynumber: 2.5 Consensus size: 22
28831895 AATAAATAAT
*
28831905 TTAAAATAATTATAAAAAATTTAA
1 TTAAAAT-ATT-TAAAAAATTCAA
28831929 TTAAAATATTTAAAAAATTACAA
1 TTAAAATATTTAAAAAATT-CAA
*
28831952 TCTAACATATTT
1 T-TAAAATATTT
28831964 TAATAATTTC
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
22 9 0.29
23 6 0.19
24 16 0.52
ACGTcount: A:0.56, C:0.05, G:0.00, T:0.39
Consensus pattern (22 bp):
TTAAAATATTTAAAAAATTCAA
Found at i:28837094 original size:20 final size:20
Alignment explanation
Indices: 28837069--28837113 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
28837059 CAATTTTTTT
* *
28837069 AAAAAATTCATTAAGAATCC
1 AAAAAATTAATTAAAAATCC
*
28837089 AAAAAATTAATTAAAAATCT
1 AAAAAATTAATTAAAAATCC
28837109 AAAAA
1 AAAAA
28837114 GCCCCCTCCC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.64, C:0.09, G:0.02, T:0.24
Consensus pattern (20 bp):
AAAAAATTAATTAAAAATCC
Found at i:28837254 original size:19 final size:18
Alignment explanation
Indices: 28837222--28837257 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
28837212 ATAAGTATGT
28837222 AAAACTTCAAAAATTTTA
1 AAAACTTCAAAAATTTTA
*
28837240 AAAACTTTCATAAATTTT
1 AAAAC-TTCAAAAATTTT
28837258 TTTAAAAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.50, C:0.11, G:0.00, T:0.39
Consensus pattern (18 bp):
AAAACTTCAAAAATTTTA
Found at i:28837409 original size:24 final size:24
Alignment explanation
Indices: 28837365--28837411 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
28837355 TTAGGGGTTT
*
28837365 TTTTGCATTTTTAAATGATTTTTA
1 TTTTGCATTTTTAAAGGATTTTTA
*
28837389 TTTTGTATTTTT-AAGGAATTTTT
1 TTTTGCATTTTTAAAGG-ATTTTT
28837412 TTAGTAAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 3 0.15
24 17 0.85
ACGTcount: A:0.23, C:0.02, G:0.11, T:0.64
Consensus pattern (24 bp):
TTTTGCATTTTTAAAGGATTTTTA
Found at i:28839482 original size:49 final size:49
Alignment explanation
Indices: 28839422--28839579 Score: 201
Period size: 49 Copynumber: 3.2 Consensus size: 49
28839412 CATATCGGAC
* *
28839422 ATGGTCTTACATGGGATGTTTCCTGCACTGCCAATGCCATATCCTAGAT
1 ATGGTCTTACATGGGATGTTTCCTGCACTGCCAAAGCCATATCCCAGAT
28839471 ATGGTCTTACATGGGATGTTTCCTGCACTGCCAAAGCCATATCCCAGAT
1 ATGGTCTTACATGGGATGTTTCCTGCACTGCCAAAGCCATATCCCAGAT
* * * ** * * *
28839520 ATAGTCTTACATGGGA-GTTCTCATATCGGTGCCCAAGCCATGTCCCAGAC
1 ATGGTCTTACATGGGATGTT-TCCT-GCACTGCCAAAGCCATATCCCAGAT
28839570 ATGGTCTTAC
1 ATGGTCTTAC
28839580 GGGGGACCTC
Statistics
Matches: 96, Mismatches: 11, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
48 3 0.03
49 65 0.68
50 28 0.29
ACGTcount: A:0.23, C:0.26, G:0.21, T:0.30
Consensus pattern (49 bp):
ATGGTCTTACATGGGATGTTTCCTGCACTGCCAAAGCCATATCCCAGAT
Found at i:28839577 original size:50 final size:50
Alignment explanation
Indices: 28839499--28839644 Score: 170
Period size: 50 Copynumber: 2.9 Consensus size: 50
28839489 TTTCCTGCAC
* * * * **
28839499 TGCCAAAGCCATATCCCAGATATAGTCTTACATGGGAGTTCTCATATCGG
1 TGCCCAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGG
** *
28839549 TGCCCAAGCCATGTCCCAGACATGGTCTTACGGGGGACCTCTCATCTCGG
1 TGCCCAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGG
*
28839599 TG-CCAA-CACTATGTCCTAGACATGGTCTTACATGGGACCTCTCATA
1 TGCCCAAGC-C-ATGTCCCAGACATGGTCTTACATGGGACCTCTCATA
28839645 ATCTCAATGA
Statistics
Matches: 81, Mismatches: 13, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
48 1 0.01
49 5 0.06
50 75 0.93
ACGTcount: A:0.24, C:0.29, G:0.21, T:0.26
Consensus pattern (50 bp):
TGCCCAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGG
Found at i:28840723 original size:24 final size:24
Alignment explanation
Indices: 28840690--28840784 Score: 136
Period size: 25 Copynumber: 3.9 Consensus size: 24
28840680 ATTGGACACC
28840690 AACGTGCTAAAATCAGAGAGCACT
1 AACGTGCTAAAATCAGAGAGCACT
* *
28840714 GACGTGCTAAAATCAGAGAGCACC
1 AACGTGCTAAAATCAGAGAGCACT
* *
28840738 AACGTGCTAGTATTCAGAGAGCACT
1 AACGTGCTA-AAATCAGAGAGCACT
28840763 AACGTGCTAATAATCAGAGAGC
1 AACGTGCTAA-AATCAGAGAGC
28840785 GCGCTAAAGT
Statistics
Matches: 61, Mismatches: 8, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
24 30 0.49
25 31 0.51
ACGTcount: A:0.38, C:0.21, G:0.23, T:0.18
Consensus pattern (24 bp):
AACGTGCTAAAATCAGAGAGCACT
Found at i:28840760 original size:25 final size:24
Alignment explanation
Indices: 28840686--28840784 Score: 135
Period size: 24 Copynumber: 4.0 Consensus size: 24
28840676 AACAATTGGA
28840686 CACCAACGTGCTAAAATCAGAGAG
1 CACCAACGTGCTAAAATCAGAGAG
**
28840710 CACTGACGTGCTAAAATCAGAGAG
1 CACCAACGTGCTAAAATCAGAGAG
* *
28840734 CACCAACGTGCTAGTATTCAGAGAG
1 CACCAACGTGCTA-AAATCAGAGAG
*
28840759 CACTAACGTGCTAATAATCAGAGAG
1 CACCAACGTGCTAA-AATCAGAGAG
28840784 C
1 C
28840785 GCGCTAAAGT
Statistics
Matches: 64, Mismatches: 9, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
24 33 0.52
25 31 0.48
ACGTcount: A:0.37, C:0.23, G:0.22, T:0.17
Consensus pattern (24 bp):
CACCAACGTGCTAAAATCAGAGAG
Found at i:28840768 original size:49 final size:49
Alignment explanation
Indices: 28840686--28840784 Score: 155
Period size: 49 Copynumber: 2.0 Consensus size: 49
28840676 AACAATTGGA
*
28840686 CACCAACGTGCTAAAATCAGAGAGCACTGACGTGCTAA-AATCAGAGAG
1 CACCAACGTGCTAAAATCAGAGAGCACTAACGTGCTAATAATCAGAGAG
* *
28840734 CACCAACGTGCTAGTATTCAGAGAGCACTAACGTGCTAATAATCAGAGAG
1 CACCAACGTGCTA-AAATCAGAGAGCACTAACGTGCTAATAATCAGAGAG
28840784 C
1 C
28840785 GCGCTAAAGT
Statistics
Matches: 46, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
48 13 0.28
49 22 0.48
50 11 0.24
ACGTcount: A:0.37, C:0.23, G:0.22, T:0.17
Consensus pattern (49 bp):
CACCAACGTGCTAAAATCAGAGAGCACTAACGTGCTAATAATCAGAGAG
Found at i:28841869 original size:5 final size:5
Alignment explanation
Indices: 28841851--28841890 Score: 53
Period size: 5 Copynumber: 7.6 Consensus size: 5
28841841 TGTTTTATGT
*
28841851 ATATA ATAATA ATATA ATATT ATAATA ATATA ATATA ATA
1 ATATA AT-ATA ATATA ATATA AT-ATA ATATA ATATA ATA
28841891 ACTTACTTAT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
5 22 0.71
6 9 0.29
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (5 bp):
ATATA
Found at i:28841875 original size:16 final size:16
Alignment explanation
Indices: 28841851--28841891 Score: 73
Period size: 16 Copynumber: 2.6 Consensus size: 16
28841841 TGTTTTATGT
28841851 ATATAATAATAATATA
1 ATATAATAATAATATA
*
28841867 ATATTATAATAATATA
1 ATATAATAATAATATA
28841883 ATATAATAA
1 ATATAATAA
28841892 CTTACTTATT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (16 bp):
ATATAATAATAATATA
Found at i:28841891 original size:8 final size:8
Alignment explanation
Indices: 28841856--28841885 Score: 51
Period size: 8 Copynumber: 3.8 Consensus size: 8
28841846 TATGTATATA
28841856 ATAATAAT
1 ATAATAAT
*
28841864 ATAATATT
1 ATAATAAT
28841872 ATAATAAT
1 ATAATAAT
28841880 ATAATA
1 ATAATA
28841886 TAATAACTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (8 bp):
ATAATAAT
Found at i:28843947 original size:16 final size:16
Alignment explanation
Indices: 28843928--28843962 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
28843918 ATATGTAGGT
*
28843928 ATATAAAAATTATAAA
1 ATATAAAAATAATAAA
*
28843944 ATATGAAAATAATAAA
1 ATATAAAAATAATAAA
28843960 ATA
1 ATA
28843963 CATATAAAAG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.69, C:0.00, G:0.03, T:0.29
Consensus pattern (16 bp):
ATATAAAAATAATAAA
Found at i:28844171 original size:16 final size:16
Alignment explanation
Indices: 28844150--28844184 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
28844140 ATATATATGC
* *
28844150 ATATATATAATAATAT
1 ATATATAAAATAAGAT
28844166 ATATATAAAATAAGAT
1 ATATATAAAATAAGAT
28844182 ATA
1 ATA
28844185 AAGATATATA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.60, C:0.00, G:0.03, T:0.37
Consensus pattern (16 bp):
ATATATAAAATAAGAT
Found at i:28844281 original size:17 final size:17
Alignment explanation
Indices: 28844259--28844305 Score: 62
Period size: 17 Copynumber: 2.8 Consensus size: 17
28844249 TAAATATGAA
28844259 ATAATAATATAACAATG
1 ATAATAATATAACAATG
*
28844276 ATAAT-ATAAAACTAATG
1 ATAATAATATAAC-AATG
28844293 AT-ATAATATAACA
1 ATAATAATATAACA
28844306 GTAGTAACAA
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
16 9 0.35
17 17 0.65
ACGTcount: A:0.60, C:0.06, G:0.04, T:0.30
Consensus pattern (17 bp):
ATAATAATATAACAATG
Found at i:28869552 original size:21 final size:21
Alignment explanation
Indices: 28869523--28869575 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
28869513 TACGGTGGTA
*
28869523 TTAAAGTTTCGTTAAAAAATT
1 TTAACGTTTCGTTAAAAAATT
* *
28869544 TTAACGTTTCGTTGAAAATTT
1 TTAACGTTTCGTTAAAAAATT
*
28869565 TTAACATTTCG
1 TTAACGTTTCG
28869576 ATAGTTAAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.34, C:0.09, G:0.11, T:0.45
Consensus pattern (21 bp):
TTAACGTTTCGTTAAAAAATT
Found at i:28895584 original size:6 final size:6
Alignment explanation
Indices: 28895575--28895608 Score: 68
Period size: 6 Copynumber: 5.7 Consensus size: 6
28895565 AAACATGGCA
28895575 ATGGTG ATGGTG ATGGTG ATGGTG ATGGTG ATGG
1 ATGGTG ATGGTG ATGGTG ATGGTG ATGGTG ATGG
28895609 ATCAAACTAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.18, C:0.00, G:0.50, T:0.32
Consensus pattern (6 bp):
ATGGTG
Found at i:28907376 original size:25 final size:26
Alignment explanation
Indices: 28907340--28907393 Score: 76
Period size: 26 Copynumber: 2.1 Consensus size: 26
28907330 AAATTCTAAA
*
28907340 TATTATAGAAT-ATTTTTATAATTTT
1 TATTATAGAATAATTTTTATAATCTT
28907365 TATTATTA-AATAATTTTTATAATCTT
1 TATTA-TAGAATAATTTTTATAATCTT
28907391 TAT
1 TAT
28907394 GCTTTTTTAA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
25 8 0.31
26 18 0.69
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.59
Consensus pattern (26 bp):
TATTATAGAATAATTTTTATAATCTT
Found at i:28908881 original size:21 final size:20
Alignment explanation
Indices: 28908854--28908909 Score: 87
Period size: 21 Copynumber: 2.8 Consensus size: 20
28908844 TGGATCAACT
28908854 TTTACGAGCTTCTGTTCAGC
1 TTTACGAGCTTCTGTTCAGC
28908874 TCTTACGAGCTTCTGTTCAGC
1 T-TTACGAGCTTCTGTTCAGC
*
28908895 TTT-CAAGCTTCTGTT
1 TTTACGAGCTTCTGTT
28908910 GGCGTATTTG
Statistics
Matches: 34, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
19 11 0.32
20 3 0.09
21 20 0.59
ACGTcount: A:0.14, C:0.25, G:0.18, T:0.43
Consensus pattern (20 bp):
TTTACGAGCTTCTGTTCAGC
Found at i:28910468 original size:7 final size:7
Alignment explanation
Indices: 28910456--28910480 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
28910446 TAAAATGTTT
28910456 CAAAAAA
1 CAAAAAA
28910463 CAAAAAA
1 CAAAAAA
28910470 CAAAAAA
1 CAAAAAA
28910477 CAAA
1 CAAA
28910481 TAGAGGGATC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.84, C:0.16, G:0.00, T:0.00
Consensus pattern (7 bp):
CAAAAAA
Found at i:28934041 original size:13 final size:14
Alignment explanation
Indices: 28934018--28934046 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
28934008 ACAAGCATCC
28934018 AAGTCCCTTTGAAT
1 AAGTCCCTTTGAAT
28934032 AAGT-CCTTTGAAT
1 AAGTCCCTTTGAAT
28934045 AA
1 AA
28934047 CCTGGAGCTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.73
14 4 0.27
ACGTcount: A:0.34, C:0.17, G:0.14, T:0.34
Consensus pattern (14 bp):
AAGTCCCTTTGAAT
Found at i:28936660 original size:25 final size:25
Alignment explanation
Indices: 28936629--28936683 Score: 83
Period size: 25 Copynumber: 2.1 Consensus size: 25
28936619 TTATGTATAT
*
28936629 AATATAAAAATTTATAACTTAAATTTG
1 AATA-AAAAATTT-TAAATTAAATTTG
28936656 AATAAAAAATTTTAAATTAAATTTG
1 AATAAAAAATTTTAAATTAAATTTG
28936681 AAT
1 AAT
28936684 GTAATTAACT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
25 15 0.56
26 8 0.30
27 4 0.15
ACGTcount: A:0.55, C:0.02, G:0.04, T:0.40
Consensus pattern (25 bp):
AATAAAAAATTTTAAATTAAATTTG
Found at i:28937273 original size:11 final size:11
Alignment explanation
Indices: 28937257--28937286 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
28937247 TTCTTCTTTT
*
28937257 ATTTTTTTATA
1 ATTTTTTAATA
28937268 ATTTTTTAATA
1 ATTTTTTAATA
28937279 ATTTTTTA
1 ATTTTTTA
28937287 TGGAATCAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (11 bp):
ATTTTTTAATA
Found at i:28938798 original size:54 final size:54
Alignment explanation
Indices: 28938696--28938798 Score: 118
Period size: 54 Copynumber: 1.9 Consensus size: 54
28938686 TTTTTTAAAA
* * * * * *
28938696 TTTTAGAATTACAACTAAATTAATAAATTTTGTAAATTTTAAATGTTAATTTTT
1 TTTTAGAATTACAACTAAAATAAAAAATGTTATAAATATTAAAGGTTAATTTTT
* *
28938750 TTTTAGAATT-CAAATTAAAATAAAAAATGTTATAAATATTAAGGGTTAA
1 TTTTAGAATTAC-AACTAAAATAAAAAATGTTATAAATATTAAAGGTTAA
28938799 ATATTTTATA
Statistics
Matches: 40, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
53 1 0.03
54 39 0.98
ACGTcount: A:0.46, C:0.03, G:0.08, T:0.44
Consensus pattern (54 bp):
TTTTAGAATTACAACTAAAATAAAAAATGTTATAAATATTAAAGGTTAATTTTT
Found at i:28941284 original size:19 final size:19
Alignment explanation
Indices: 28941260--28941305 Score: 65
Period size: 19 Copynumber: 2.4 Consensus size: 19
28941250 GCCTCTATTA
*
28941260 ATGTAAATATGATTCTAGC
1 ATGTAAATATAATTCTAGC
*
28941279 ATGTAAATTTAATTCTAGC
1 ATGTAAATATAATTCTAGC
*
28941298 ATGCAAAT
1 ATGTAAAT
28941306 TAGGATTTTG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.39, C:0.11, G:0.13, T:0.37
Consensus pattern (19 bp):
ATGTAAATATAATTCTAGC
Found at i:28964584 original size:30 final size:30
Alignment explanation
Indices: 28964550--28964674 Score: 159
Period size: 29 Copynumber: 4.2 Consensus size: 30
28964540 TTTATTTTTG
28964550 CATTTTGACCCCTAAACTTTTCTAAAATTA
1 CATTTTGACCCCTAAACTTTTCTAAAATTA
28964580 CATTTT-ACCCCTAAACTTTATC-AAAATTA
1 CATTTTGACCCCTAAACTTT-TCTAAAATTA
* *
28964609 CATTTTTACCCTTAAACTTTTCT-AAATTA
1 CATTTTGACCCCTAAACTTTTCTAAAATTA
* * *
28964638 CATTTGGGCCCTTAAAC-TTTCTATAAATTA
1 CATTTTGACCCCTAAACTTTTCTA-AAATTA
28964668 CATTTTG
1 CATTTTG
28964675 GCCATTTATT
Statistics
Matches: 85, Mismatches: 5, Indels: 10
0.85 0.05 0.10
Matches are distributed among these distances:
28 5 0.06
29 48 0.56
30 32 0.38
ACGTcount: A:0.32, C:0.22, G:0.04, T:0.42
Consensus pattern (30 bp):
CATTTTGACCCCTAAACTTTTCTAAAATTA
Found at i:28964613 original size:59 final size:59
Alignment explanation
Indices: 28964550--28964674 Score: 164
Period size: 59 Copynumber: 2.1 Consensus size: 59
28964540 TTTATTTTTG
*
28964550 CATTTTGACCCCTAAACTTTTCTAAAATTACATTT-TACCCCTAAACTTTATCA-AAATTA
1 CATTTTGACCCCTAAACTTTTCT-AAATTACATTTGGACCCCTAAACTTTAT-ATAAATTA
* * * * *
28964609 CATTTTTACCCTTAAACTTTTCTAAATTACATTTGGGCCCTTAAACTTTCTATAAATTA
1 CATTTTGACCCCTAAACTTTTCTAAATTACATTTGGACCCCTAAACTTTATATAAATTA
28964668 CATTTTG
1 CATTTTG
28964675 GCCATTTATT
Statistics
Matches: 57, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
58 12 0.21
59 45 0.79
ACGTcount: A:0.32, C:0.22, G:0.04, T:0.42
Consensus pattern (59 bp):
CATTTTGACCCCTAAACTTTTCTAAATTACATTTGGACCCCTAAACTTTATATAAATTA
Found at i:28965069 original size:34 final size:32
Alignment explanation
Indices: 28965025--28965087 Score: 90
Period size: 32 Copynumber: 1.9 Consensus size: 32
28965015 CAACTAGCAA
28965025 AACAACCAAAAAGCAAAAAAAAAGAGAAAGAAAC
1 AACAACC-AAAAG-AAAAAAAAAGAGAAAGAAAC
* *
28965059 AACAAGCAAAAGAGAAAAAAAGAGAAAGA
1 AACAACCAAAAGAAAAAAAAAGAGAAAGA
28965088 GAAAAGAAGA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
32 16 0.59
33 5 0.19
34 6 0.22
ACGTcount: A:0.73, C:0.11, G:0.16, T:0.00
Consensus pattern (32 bp):
AACAACCAAAAGAAAAAAAAAGAGAAAGAAAC
Found at i:28965086 original size:16 final size:16
Alignment explanation
Indices: 28965041--28965097 Score: 64
Period size: 16 Copynumber: 3.6 Consensus size: 16
28965031 CAAAAAGCAA
28965041 AAAAAAAGAGAAAGA-
1 AAAAAAAGAGAAAGAG
*
28965056 AACAACAAGCA-AAAGAG
1 AA-AAAAAG-AGAAAGAG
28965073 AAAAAAAGAGAAAGAG
1 AAAAAAAGAGAAAGAG
*
28965089 AAAAGAAGA
1 AAAAAAAGA
28965098 AAGATGGGGG
Statistics
Matches: 35, Mismatches: 3, Indels: 7
0.78 0.07 0.16
Matches are distributed among these distances:
15 3 0.09
16 29 0.83
17 3 0.09
ACGTcount: A:0.74, C:0.05, G:0.21, T:0.00
Consensus pattern (16 bp):
AAAAAAAGAGAAAGAG
Found at i:28965211 original size:4 final size:4
Alignment explanation
Indices: 28965202--28965281 Score: 72
Period size: 4 Copynumber: 19.0 Consensus size: 4
28965192 GGCTGATTGG
*
28965202 GAAA GAAA GAAA AAAGA GAAA GAAAA GATAA GAAA GAAA GAAA GAAA G-AA
1 GAAA GAAA GAAA GAA-A GAAA G-AAA GA-AA GAAA GAAA GAAA GAAA GAAA
* * *
28965252 GAAA AAGAA GGAA GAAGA AAAA GAAA GAAA
1 GAAA GA-AA GAAA GAA-A GAAA GAAA GAAA
28965282 AAAATAAAAA
Statistics
Matches: 62, Mismatches: 8, Indels: 12
0.76 0.10 0.15
Matches are distributed among these distances:
3 3 0.05
4 43 0.69
5 16 0.26
ACGTcount: A:0.74, C:0.00, G:0.25, T:0.01
Consensus pattern (4 bp):
GAAA
Found at i:28965223 original size:13 final size:12
Alignment explanation
Indices: 28965203--28965285 Score: 85
Period size: 13 Copynumber: 6.2 Consensus size: 12
28965193 GCTGATTGGG
28965203 AAAGAAAGAAAA
1 AAAGAAAGAAAA
28965215 AAGAGAAAGAAAA
1 AA-AGAAAGAAAA
*
28965228 GATAAGAAAGAAAG
1 -A-AAGAAAGAAAA
28965242 AAAGAAAGAAGAA
1 AAAGAAAGAA-AA
28965255 AAAGAAGGAAGAAGAA
1 AAAG-A--AAGAA-AA
28965271 AAAGAAAGAAAA
1 AAAGAAAGAAAA
28965283 AAA
1 AAA
28965286 TAAAAAATTT
Statistics
Matches: 62, Mismatches: 2, Indels: 14
0.79 0.03 0.18
Matches are distributed among these distances:
12 16 0.26
13 21 0.34
14 11 0.18
15 2 0.03
16 12 0.19
ACGTcount: A:0.76, C:0.00, G:0.23, T:0.01
Consensus pattern (12 bp):
AAAGAAAGAAAA
Found at i:28965248 original size:35 final size:33
Alignment explanation
Indices: 28965202--28965284 Score: 98
Period size: 35 Copynumber: 2.5 Consensus size: 33
28965192 GGCTGATTGG
*
28965202 GAAAGAAAGAAAAAAGAGAAAGAA-AAGATAAGAAA
1 GAAAGAAAGAAAAAAGAAAAAGAAGAAG--AAG-AA
*
28965237 GAAAGAAAGAAAGAAGAAAAAGAAGGAAGAAGAA
1 GAAAGAAAGAAAAAAGAAAAAGAA-GAAGAAGAA
28965271 -AAAGAAAGAAAAAA
1 GAAAGAAAGAAAAAA
28965285 ATAAAAAATT
Statistics
Matches: 43, Mismatches: 3, Indels: 6
0.83 0.06 0.12
Matches are distributed among these distances:
33 13 0.30
34 2 0.05
35 25 0.58
37 3 0.07
ACGTcount: A:0.75, C:0.00, G:0.24, T:0.01
Consensus pattern (33 bp):
GAAAGAAAGAAAAAAGAAAAAGAAGAAGAAGAA
Found at i:28965574 original size:11 final size:10
Alignment explanation
Indices: 28965560--28965616 Score: 57
Period size: 9 Copynumber: 5.8 Consensus size: 10
28965550 GGCCAGAAAA
28965560 AAAAAGAGAAG
1 AAAAA-AGAAG
28965571 AAAAACAG-AG
1 AAAAA-AGAAG
28965581 AAAAAA-AAG
1 AAAAAAGAAG
28965590 AAAAAAGAA-
1 AAAAAAGAAG
* *
28965599 AAAAGAGAAA
1 AAAAAAGAAG
28965609 AAAAAAGA
1 AAAAAAGA
28965617 GGTTCAATTT
Statistics
Matches: 40, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
9 17 0.43
10 16 0.40
11 7 0.17
ACGTcount: A:0.81, C:0.02, G:0.18, T:0.00
Consensus pattern (10 bp):
AAAAAAGAAG
Found at i:28965588 original size:25 final size:24
Alignment explanation
Indices: 28965554--28965617 Score: 92
Period size: 25 Copynumber: 2.6 Consensus size: 24
28965544 GAAGCAGGCC
28965554 AGAAAAAAAAAGAGAAGAAAAACAG
1 AGAAAAAAAAAGAGAAGAAAAA-AG
* *
28965579 AGAAAAAAAAGAAAAAAGAAAAAAG
1 AGAAAAAAAA-AGAGAAGAAAAAAG
28965604 AGAAAAAAAAAGAG
1 AGAAAAAAAAAGAG
28965618 GTTCAATTTG
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
24 2 0.06
25 22 0.65
26 10 0.29
ACGTcount: A:0.80, C:0.02, G:0.19, T:0.00
Consensus pattern (24 bp):
AGAAAAAAAAAGAGAAGAAAAAAG
Found at i:28965615 original size:26 final size:26
Alignment explanation
Indices: 28965554--28965616 Score: 87
Period size: 26 Copynumber: 2.5 Consensus size: 26
28965544 GAAGCAGGCC
*
28965554 AGAAAAAAAAAG-AGAAGAAAAACAG
1 AGAAAAAAAAAGAAAAAGAAAAACAG
28965579 AG-AAAAAAAAGAAAAAAGAAAAA-AG
1 AGAAAAAAAAAG-AAAAAGAAAAACAG
28965604 AGAAAAAAAAAGA
1 AGAAAAAAAAAGA
28965617 GGTTCAATTT
Statistics
Matches: 34, Mismatches: 1, Indels: 6
0.83 0.02 0.15
Matches are distributed among these distances:
24 9 0.26
25 7 0.21
26 18 0.53
ACGTcount: A:0.81, C:0.02, G:0.17, T:0.00
Consensus pattern (26 bp):
AGAAAAAAAAAGAAAAAGAAAAACAG
Found at i:28965805 original size:16 final size:16
Alignment explanation
Indices: 28965769--28965808 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
28965759 TTTGTATCTA
28965769 TATTTTAATTTAATTC
1 TATTTTAATTTAATTC
* * *
28965785 AATTTTAATTTTATTT
1 TATTTTAATTTAATTC
28965801 TATTTTAA
1 TATTTTAA
28965809 ATAATTTTAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.65
Consensus pattern (16 bp):
TATTTTAATTTAATTC
Found at i:28965967 original size:15 final size:16
Alignment explanation
Indices: 28965934--28965965 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
28965924 AAATATTCTA
28965934 AAATTCTCGTGTTTTTT
1 AAATTCTCGTG-TTTTT
28965951 AAATTCTCGTGTTTT
1 AAATTCTCGTGTTTT
28965966 AATAGAATCA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.19, C:0.12, G:0.12, T:0.56
Consensus pattern (16 bp):
AAATTCTCGTGTTTTT
Found at i:28966157 original size:23 final size:23
Alignment explanation
Indices: 28966130--28966174 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
28966120 CTCGTATTTC
* *
28966130 AAAAATTCCTTGTTTTCAAAAAA
1 AAAAATTCCGTGTCTTCAAAAAA
*
28966153 AAAAATTTCGTGTCTTCAAAAA
1 AAAAATTCCGTGTCTTCAAAAA
28966175 TCTTCGTGTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.47, C:0.13, G:0.07, T:0.33
Consensus pattern (23 bp):
AAAAATTCCGTGTCTTCAAAAAA
Found at i:28966204 original size:57 final size:59
Alignment explanation
Indices: 28966091--28966208 Score: 138
Period size: 60 Copynumber: 2.0 Consensus size: 59
28966081 ATCGTGTTTC
* * *
28966091 AAAAAATTTTCGTGTTTTCAAAAAAATTTCTCGTATTTCAAAAATTCCTTGTTTTCAAAA
1 AAAAAAATTTCGTGTCTTC-AAAAAATTTCTCGTATTTCAAAAATTCCGTGTTTTCAAAA
28966151 AAAAAAATTTCGTGTCTTC-AAAAATCTTCGT-GT-TTTC-AAAATTCCAGTG-TTTCAAAA
1 AAAAAAATTTCGTGTCTTCAAAAAAT-TTC-TCGTATTTCAAAAATTCC-GTGTTTTCAAAA
28966208 A
1 A
28966209 TTTTGTGTTT
Statistics
Matches: 52, Mismatches: 3, Indels: 9
0.81 0.05 0.14
Matches are distributed among these distances:
57 17 0.33
58 12 0.23
59 5 0.10
60 18 0.35
ACGTcount: A:0.38, C:0.14, G:0.08, T:0.39
Consensus pattern (59 bp):
AAAAAAATTTCGTGTCTTCAAAAAATTTCTCGTATTTCAAAAATTCCGTGTTTTCAAAA
Found at i:28966216 original size:16 final size:16
Alignment explanation
Indices: 28966153--28966218 Score: 71
Period size: 17 Copynumber: 3.9 Consensus size: 16
28966143 TTTCAAAAAA
28966153 AAAAATTTCGTGTCTTC
1 AAAAATTTCGTGT-TTC
28966170 AAAAATCTTCGTGTTTTC
1 AAAAAT-TTCGTG-TTTC
*
28966188 -AAAATTCCAGTGTTTC
1 AAAAATTTC-GTGTTTC
*
28966204 AAAAATTTTGTGTTT
1 AAAAATTTCGTGTTT
28966219 TTTAAAAAAA
Statistics
Matches: 42, Mismatches: 3, Indels: 9
0.78 0.06 0.17
Matches are distributed among these distances:
16 12 0.29
17 20 0.48
18 9 0.21
19 1 0.02
ACGTcount: A:0.30, C:0.14, G:0.12, T:0.44
Consensus pattern (16 bp):
AAAAATTTCGTGTTTC
Found at i:28966296 original size:35 final size:33
Alignment explanation
Indices: 28966257--28966414 Score: 138
Period size: 34 Copynumber: 4.5 Consensus size: 33
28966247 TCAAAAATCC
28966257 TCATGTTTTCAAAAATTCAGGTGTTTTAAAAACTT
1 TCATGTTTTCAAAAATTC-GGTGTTTTAAAAA-TT
* ***
28966292 TCATGTTTTCAAAAATTTCGATGATCAAAAAAAATT
1 TCATGTTTTCAAAAA-TTCGGTG-T-TTTAAAAATT
* *
28966328 TCGTGTTTTTCAAAAAATTTC-GTGTTTCAAAAATTT
1 TCATG-TTTTC-AAAAA-TTCGGTGTTTTAAAAA-TT
**
28966364 TCATGTTTTCAAAAATTCCCTGTTTTAAAAATT
1 TCATGTTTTCAAAAATTCGGTGTTTTAAAAATT
*
28966397 TCCGTGTTTTCAAAAATT
1 T-CATGTTTTCAAAAATT
28966415 TTCGTGTTTT
Statistics
Matches: 102, Mismatches: 13, Indels: 17
0.77 0.10 0.13
Matches are distributed among these distances:
33 6 0.06
34 30 0.29
35 28 0.27
36 17 0.17
37 12 0.12
38 9 0.09
ACGTcount: A:0.35, C:0.13, G:0.09, T:0.43
Consensus pattern (33 bp):
TCATGTTTTCAAAAATTCGGTGTTTTAAAAATT
Found at i:28966306 original size:79 final size:74
Alignment explanation
Indices: 28966126--28966306 Score: 193
Period size: 79 Copynumber: 2.4 Consensus size: 74
28966116 ATTTCTCGTA
* * * * *
28966126 TTTCAAAAATTCCTTGTTTTCAAAAAAAAAAATTTCGTGTCTTCAAAAATCTTCGTGTTTTCAAA
1 TTTCAAAAATTTCATGTTTTCAAAAAAAAAAATTTCGTATCTTCAAAAATCCTCATGTTTTCAAA
28966191 ATTCCAGTG
66 ATTCCAGTG
** * *
28966200 TTTCAAAAATTTTGTGTTTTTTAAAAAAAAGAAAATTTTTCGTATTTTCAAAAATCCTCATGTTT
1 TTTCAAAAATTTCATG--TTTTCAAAAAAA-AAAA--TTTCGTATCTTCAAAAATCCTCATGTTT
28966265 TCAAAAATT-CAGGTG
61 TC-AAAATTCCA-GTG
*
28966280 TTTTAAAAACTTTCATGTTTTCAAAAA
1 TTTCAAAAA-TTTCATGTTTTCAAAAA
28966307 TTTCGATGAT
Statistics
Matches: 87, Mismatches: 12, Indels: 11
0.79 0.11 0.10
Matches are distributed among these distances:
74 13 0.15
76 11 0.13
77 4 0.05
79 37 0.43
80 17 0.20
81 5 0.06
ACGTcount: A:0.37, C:0.13, G:0.09, T:0.41
Consensus pattern (74 bp):
TTTCAAAAATTTCATGTTTTCAAAAAAAAAAATTTCGTATCTTCAAAAATCCTCATGTTTTCAAA
ATTCCAGTG
Found at i:28966414 original size:18 final size:17
Alignment explanation
Indices: 28966082--28966482 Score: 167
Period size: 18 Copynumber: 21.9 Consensus size: 17
28966072 CTTAAAAAAA
28966082 TCGTG-TTTCAAAAAATTT
1 TCGTGTTTTC-AAAAA-TT
28966100 TCGTGTTTTCAAAAAAATT
1 TCGTGTTTTC--AAAAATT
28966119 TC-TCGTATTTCAAAAATT
1 TCGT-GT-TTTCAAAAATT
* *
28966137 CCTTGTTTTCAAAAAAAAAAATT
1 TCGTGTTTTC------AAAAATT
*
28966160 TCGTGTCTTCAAAAATCT
1 TCGTGTTTTCAAAAAT-T
28966178 TCGTGTTTTC-AAAATT
1 TCGTGTTTTCAAAAATT
*
28966194 CCAGTG-TTTCAAAAATT
1 TC-GTGTTTTCAAAAATT
* *
28966211 TTGTGTTTTTTAAAAAAAAGAAAATTTT
1 TCGTG--TTTT------CA-AAAA--TT
* *
28966239 TCGTATTTTCAAAAATCC
1 TCGTGTTTTCAAAAAT-T
*
28966257 TCATGTTTTCAAAAA-T
1 TCGTGTTTTCAAAAATT
28966273 TCAGGTGTTTT-AAAAACTT
1 TC--GTGTTTTCAAAAA-TT
*
28966292 TCATGTTTTCAAAAATT
1 TCGTGTTTTCAAAAATT
****
28966309 TCGATGATCAAAAAAAATT
1 TCG-TG-TTTTCAAAAATT
28966328 TCGTGTTTTTCAAAAAATT
1 TCGTG-TTTTC-AAAAATT
28966347 TCGTG-TTTCAAAAATTT
1 TCGTGTTTTCAAAAA-TT
*
28966364 TCATGTTTTCAAAAATT
1 TCGTGTTTTCAAAAATT
* *
28966381 CCCTGTTTT-AAAAATT
1 TCGTGTTTTCAAAAATT
28966397 TCCGTGTTTTCAAAAATTT
1 T-CGTGTTTTCAAAAA-TT
* *
28966416 TCGTGTTTT-ATGAATTT
1 TCGTGTTTTCA-AAAATT
* *
28966433 TCGTG-TCTCTAAAATT
1 TCGTGTTTTCAAAAATT
*
28966449 CTCGTGTTTT-AAAATTTTT
1 -TCGTGTTTTCAAAA--ATT
28966468 TCGTGTTTTCAAAAA
1 TCGTGTTTTCAAAAA
28966483 AATAATTATT
Statistics
Matches: 293, Mismatches: 43, Indels: 95
0.68 0.10 0.22
Matches are distributed among these distances:
16 29 0.10
17 82 0.28
18 90 0.31
19 53 0.18
20 11 0.04
23 14 0.05
25 1 0.00
26 8 0.03
28 5 0.02
ACGTcount: A:0.33, C:0.13, G:0.10, T:0.44
Consensus pattern (17 bp):
TCGTGTTTTCAAAAATT
Found at i:28966447 original size:52 final size:52
Alignment explanation
Indices: 28966340--28966482 Score: 145
Period size: 52 Copynumber: 2.8 Consensus size: 52
28966330 GTGTTTTTCA
* *
28966340 AAAAATTT-CGTG-TTTCAAAAATTTTCATGTTTTCAAAAATTCCCTGTTTT
1 AAAAATTTCCGTGTTTTCAAAAATTTTCGTGTTTTCAAAAATTCCCTGTTCT
* * * *
28966390 AAAAATTTCCGTGTTTTCAAAAATTTTCGTGTTTT-ATGAATTTTCGTGTCTCT
1 AAAAATTTCCGTGTTTTCAAAAATTTTCGTGTTTTCA-AAAATTCCCTGT-TCT
*
28966443 -AAAA-TTCTCGTGTTTT-AAAATTTTTTCGTGTTTTCAAAAA
1 AAAAATTTC-CGTGTTTTCAAAA-ATTTTCGTGTTTTCAAAAA
28966483 AATAATTATT
Statistics
Matches: 77, Mismatches: 9, Indels: 12
0.79 0.09 0.12
Matches are distributed among these distances:
50 8 0.10
51 12 0.16
52 54 0.70
53 3 0.04
ACGTcount: A:0.29, C:0.13, G:0.10, T:0.48
Consensus pattern (52 bp):
AAAAATTTCCGTGTTTTCAAAAATTTTCGTGTTTTCAAAAATTCCCTGTTCT
Found at i:28966448 original size:17 final size:16
Alignment explanation
Indices: 28966321--28966481 Score: 106
Period size: 17 Copynumber: 9.2 Consensus size: 16
28966311 GATGATCAAA
*
28966321 AAAAATTTCGTGTTTTT
1 AAAATTTTCGTG-TTTT
* *
28966338 CAAAAAATTTCGTGTTTCA
1 --AAAATTTTCGTGTTT-T
*
28966357 AAAATTTTCATGTTTT
1 AAAATTTTCGTGTTTT
* * *
28966373 CAAAAATTCCCTGTTTT
1 -AAAATTTTCGTGTTTT
*
28966390 AAAAATTTCCGTGTTTT
1 -AAAATTTTCGTGTTTT
28966407 CAAAAATTTTCGTGTTTT
1 --AAAATTTTCGTGTTTT
* *
28966425 ATGAATTTTCGTGTCTCT
1 A-AAATTTTCGTGT-TTT
*
28966443 AAAATTCTCGTGTTTT
1 AAAATTTTCGTGTTTT
28966459 AAAATTTTTTCGTGTTTT
1 AAAA--TTTTCGTGTTTT
28966477 CAAAA
1 -AAAA
28966482 AAATAATTAT
Statistics
Matches: 117, Mismatches: 17, Indels: 16
0.78 0.11 0.11
Matches are distributed among these distances:
16 7 0.06
17 61 0.52
18 33 0.28
19 16 0.14
ACGTcount: A:0.29, C:0.12, G:0.11, T:0.48
Consensus pattern (16 bp):
AAAATTTTCGTGTTTT
Found at i:28979963 original size:48 final size:46
Alignment explanation
Indices: 28979888--28980028 Score: 198
Period size: 48 Copynumber: 3.0 Consensus size: 46
28979878 CTTAGCCTCT
*
28979888 CCTTTTTTTTTACTC-AAGGCTCCCTTTGTAGGGTTTCACCCTGGTC
1 CCTTTTTTTTTACTCAAAGGC-CCCTTTGTAGGGTTTCACCTTGGTC
*
28979934 TCTTTTTTTTTGACTCAAAGAGCCCCTTTGTAGGGTTTCACCTTGG-C
1 CCTTTTTTTTT-ACTCAAAG-GCCCCTTTGTAGGGTTTCACCTTGGTC
*
28979981 CCTTTTTTTTTACTCAAA-GCGCCCTTTGTAGGCTTTCACCTTGGTC
1 CCTTTTTTTTTACTCAAAGGC-CCCTTTGTAGGGTTTCACCTTGGTC
28980027 CC
1 CC
28980029 ACCTTTTTTA
Statistics
Matches: 86, Mismatches: 4, Indels: 10
0.86 0.04 0.10
Matches are distributed among these distances:
44 2 0.02
45 22 0.26
46 20 0.23
47 15 0.17
48 25 0.29
49 2 0.02
ACGTcount: A:0.13, C:0.28, G:0.17, T:0.43
Consensus pattern (46 bp):
CCTTTTTTTTTACTCAAAGGCCCCTTTGTAGGGTTTCACCTTGGTC
Found at i:28979987 original size:45 final size:48
Alignment explanation
Indices: 28979872--28980026 Score: 187
Period size: 48 Copynumber: 3.3 Consensus size: 48
28979862 ATTTGCGAGT
* *
28979872 TTTCACCTTAGCCTCTCCTTTTTTTTTACTC-AAGGCTCCCTTTGTAGGG
1 TTTCACCTTGGTCTCT-CTTTTTTTTTACTCAAAGGC-CCCTTTGTAGGG
* *
28979921 TTTCACCCTGGTCTCT-TTTTTTTTGACTCAAAGAGCCCCTTTGTAGGG
1 TTTCACCTTGGTCTCTCTTTTTTTTTACTCAAAG-GCCCCTTTGTAGGG
*
28979969 TTTCACCTTGG-C-C-CTTTTTTTTTACTCAAA-GCGCCCTTTGTAGGC
1 TTTCACCTTGGTCTCTCTTTTTTTTTACTCAAAGGC-CCCTTTGTAGGG
28980014 TTTCACCTTGGTC
1 TTTCACCTTGGTC
28980027 CCACCTTTTT
Statistics
Matches: 94, Mismatches: 7, Indels: 13
0.82 0.06 0.11
Matches are distributed among these distances:
44 2 0.02
45 22 0.23
46 17 0.18
47 13 0.14
48 25 0.27
49 15 0.16
ACGTcount: A:0.13, C:0.28, G:0.16, T:0.43
Consensus pattern (48 bp):
TTTCACCTTGGTCTCTCTTTTTTTTTACTCAAAGGCCCCTTTGTAGGG
Found at i:28980037 original size:48 final size:46
Alignment explanation
Indices: 28979888--28980028 Score: 203
Period size: 45 Copynumber: 3.0 Consensus size: 46
28979878 CTTAGCCTCT
* * *
28979888 CCTTTTTTTTTACTCAAGGCTCCCTTTGTAGGGTTTCACCCTGGTC
1 CCTTTTTTTTTACTCAAAGCGCCCTTTGTAGGGTTTCACCTTGGTC
* *
28979934 TCTTTTTTTTTGACTCAAAGAGCCCCTTTGTAGGGTTTCACCTTGG-C
1 CCTTTTTTTTT-ACTCAAAGCG-CCCTTTGTAGGGTTTCACCTTGGTC
*
28979981 CCTTTTTTTTTACTCAAAGCGCCCTTTGTAGGCTTTCACCTTGGTC
1 CCTTTTTTTTTACTCAAAGCGCCCTTTGTAGGGTTTCACCTTGGTC
28980027 CC
1 CC
28980029 ACCTTTTTTA
Statistics
Matches: 84, Mismatches: 8, Indels: 6
0.86 0.08 0.06
Matches are distributed among these distances:
45 22 0.26
46 22 0.26
47 18 0.21
48 22 0.26
ACGTcount: A:0.13, C:0.28, G:0.17, T:0.43
Consensus pattern (46 bp):
CCTTTTTTTTTACTCAAAGCGCCCTTTGTAGGGTTTCACCTTGGTC
Found at i:28984915 original size:8 final size:8
Alignment explanation
Indices: 28984857--28984919 Score: 55
Period size: 8 Copynumber: 8.4 Consensus size: 8
28984847 ATATATCAAT
28984857 AAAATATA
1 AAAATATA
28984865 AAATATATA
1 AAA-ATATA
*
28984874 AAAGT-TA
1 AAAATATA
*
28984881 AAAAGATA
1 AAAATATA
*
28984889 AAAAAATA
1 AAAATATA
28984897 AAAATAT-
1 AAAATATA
28984904 ---ATATA
1 AAAATATA
28984909 AAAATATA
1 AAAATATA
28984917 AAA
1 AAA
28984920 CGTATGTAAA
Statistics
Matches: 44, Mismatches: 5, Indels: 12
0.72 0.08 0.20
Matches are distributed among these distances:
4 4 0.09
7 5 0.11
8 27 0.61
9 8 0.18
ACGTcount: A:0.73, C:0.00, G:0.03, T:0.24
Consensus pattern (8 bp):
AAAATATA
Found at i:28989908 original size:19 final size:19
Alignment explanation
Indices: 28989884--28989933 Score: 59
Period size: 19 Copynumber: 2.7 Consensus size: 19
28989874 TATTTAACAC
28989884 TAATATATATATATTATTT
1 TAATATATATATATTATTT
*
28989903 TAATATA-ATATTTTTATTT
1 TAATATATATA-TATTATTT
*
28989922 TATTAT-TATATA
1 TAATATATATATA
28989934 ATTTTTGAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
18 4 0.15
19 22 0.85
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (19 bp):
TAATATATATATATTATTT
Found at i:28989911 original size:24 final size:24
Alignment explanation
Indices: 28989884--28989935 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 24
28989874 TATTTAACAC
28989884 TAATATATATATATTATT-TTAATA
1 TAATATATATATATTATTATT-ATA
* * *
28989908 TAATATTTTTATTTTATTATTATA
1 TAATATATATATATTATTATTATA
28989932 TAAT
1 TAAT
28989936 TTTTGAAAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
24 22 0.92
25 2 0.08
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (24 bp):
TAATATATATATATTATTATTATA
Found at i:28990943 original size:15 final size:15
Alignment explanation
Indices: 28990897--28990945 Score: 55
Period size: 15 Copynumber: 3.2 Consensus size: 15
28990887 ATCATATTTA
28990897 CACTTTCATTTTGGT
1 CACTTTCATTTTGGT
* *
28990912 CAC-CTAACTTTTGGGT
1 CACTTTCA-TTTT-GGT
28990928 CACTTTCATTTTGGT
1 CACTTTCATTTTGGT
28990943 CAC
1 CAC
28990946 CCAAAAAATA
Statistics
Matches: 27, Mismatches: 4, Indels: 6
0.73 0.11 0.16
Matches are distributed among these distances:
14 2 0.07
15 13 0.48
16 10 0.37
17 2 0.07
ACGTcount: A:0.16, C:0.24, G:0.14, T:0.45
Consensus pattern (15 bp):
CACTTTCATTTTGGT
Found at i:28991643 original size:14 final size:14
Alignment explanation
Indices: 28991626--28991667 Score: 50
Period size: 14 Copynumber: 3.0 Consensus size: 14
28991616 TTGAATCTTA
28991626 ATATTTAAAATTTT
1 ATATTTAAAATTTT
*
28991640 ATATTTCAAAACTTT
1 ATATTT-AAAATTTT
*
28991655 A-ATTTAGAATTTT
1 ATATTTAAAATTTT
28991668 CAGCAATTGG
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
13 6 0.25
14 10 0.42
15 8 0.33
ACGTcount: A:0.40, C:0.05, G:0.02, T:0.52
Consensus pattern (14 bp):
ATATTTAAAATTTT
Found at i:28992159 original size:26 final size:25
Alignment explanation
Indices: 28992130--28992193 Score: 76
Period size: 26 Copynumber: 2.5 Consensus size: 25
28992120 TTAAAAATCA
28992130 AATAATAAAAGTATCAAACAT-CAAAT
1 AATAATAAAA--ATCAAACATACAAAT
*
28992156 AATAATAAAAATCAAACATAACAGAT
1 AATAATAAAAATCAAACAT-ACAAAT
*
28992182 AATAATGAAAAT
1 AATAATAAAAAT
28992194 TAGGAGCGCA
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
24 9 0.26
26 25 0.74
ACGTcount: A:0.64, C:0.09, G:0.05, T:0.22
Consensus pattern (25 bp):
AATAATAAAAATCAAACATACAAAT
Found at i:29003223 original size:7 final size:7
Alignment explanation
Indices: 29003208--29003250 Score: 68
Period size: 7 Copynumber: 6.1 Consensus size: 7
29003198 TTATATATAC
29003208 TACTAAA
1 TACTAAA
*
29003215 TATTAAA
1 TACTAAA
29003222 TACTAAA
1 TACTAAA
29003229 TACTAAA
1 TACTAAA
29003236 TACTAAA
1 TACTAAA
*
29003243 TACGAAA
1 TACTAAA
29003250 T
1 T
29003251 CGACTACGTT
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
7 33 1.00
ACGTcount: A:0.56, C:0.12, G:0.02, T:0.30
Consensus pattern (7 bp):
TACTAAA
Found at i:29005240 original size:35 final size:36
Alignment explanation
Indices: 29005200--29005275 Score: 145
Period size: 35 Copynumber: 2.1 Consensus size: 36
29005190 TAAAAGAATT
29005200 ATATTGAATAATTAAATTTCAAAGGTACT-AAAAAA
1 ATATTGAATAATTAAATTTCAAAGGTACTAAAAAAA
29005235 ATATTGAATAATTAAATTTCAAAGGTACTAAAAAAA
1 ATATTGAATAATTAAATTTCAAAGGTACTAAAAAAA
29005271 ATATT
1 ATATT
29005276 ATATCTTTTC
Statistics
Matches: 40, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
35 29 0.73
36 11 0.28
ACGTcount: A:0.54, C:0.05, G:0.08, T:0.33
Consensus pattern (36 bp):
ATATTGAATAATTAAATTTCAAAGGTACTAAAAAAA
Found at i:29008200 original size:11 final size:11
Alignment explanation
Indices: 29008178--29008221 Score: 52
Period size: 12 Copynumber: 3.7 Consensus size: 11
29008168 TAATATTAAT
29008178 TTAAAGAAAATA
1 TTAAA-AAAATA
29008190 TTAAAAAAATA
1 TTAAAAAAATA
*
29008201 TTAAGATAAATA
1 TTAA-AAAAATA
29008213 TATAAAAAA
1 T-TAAAAAA
29008222 TTATAAATTA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
11 10 0.36
12 15 0.54
13 3 0.11
ACGTcount: A:0.68, C:0.00, G:0.05, T:0.27
Consensus pattern (11 bp):
TTAAAAAAATA
Found at i:29008211 original size:12 final size:11
Alignment explanation
Indices: 29008181--29008222 Score: 50
Period size: 11 Copynumber: 3.7 Consensus size: 11
29008171 TATTAATTTA
29008181 AAGAAAATATT
1 AAGAAAATATT
*
29008192 AAAAAAATATT
1 AAGAAAATATT
29008203 AAGATAAATATAT
1 AAGA-AAATAT-T
29008216 AA-AAAAT
1 AAGAAAAT
29008223 TATAAATTAA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
11 17 0.63
12 7 0.26
13 3 0.11
ACGTcount: A:0.69, C:0.00, G:0.05, T:0.26
Consensus pattern (11 bp):
AAGAAAATATT
Found at i:29008231 original size:7 final size:7
Alignment explanation
Indices: 29008219--29008261 Score: 59
Period size: 7 Copynumber: 6.0 Consensus size: 7
29008209 AATATATAAA
29008219 AAATTAT
1 AAATTAT
29008226 AAATTAAT
1 AAATT-AT
* *
29008234 AAATAAA
1 AAATTAT
29008241 AAATTAT
1 AAATTAT
29008248 AAATTAT
1 AAATTAT
29008255 AAATTAT
1 AAATTAT
29008262 TAAAATAAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
7 25 0.81
8 6 0.19
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (7 bp):
AAATTAT
Found at i:29008234 original size:22 final size:22
Alignment explanation
Indices: 29008186--29008253 Score: 84
Period size: 22 Copynumber: 3.0 Consensus size: 22
29008176 ATTTAAAGAA
* *
29008186 AATAT-TAAAAAAATATTAAGATA
1 AATATATAAAAAATTA-TAA-ATT
29008209 AATATATAAAAAATTATAAATT
1 AATATATAAAAAATTATAAATT
*
29008231 AATAAATAAAAAATTATAAATT
1 AATATATAAAAAATTATAAATT
29008253 A
1 A
29008254 TAAATTATTA
Statistics
Matches: 41, Mismatches: 3, Indels: 3
0.87 0.06 0.06
Matches are distributed among these distances:
22 24 0.59
23 8 0.20
24 9 0.22
ACGTcount: A:0.66, C:0.00, G:0.01, T:0.32
Consensus pattern (22 bp):
AATATATAAAAAATTATAAATT
Found at i:29013670 original size:21 final size:21
Alignment explanation
Indices: 29013644--29013684 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
29013634 AGACGAGCAA
* *
29013644 TACTCCACAGCAGGTGGAGTG
1 TACTCCAAAACAGGTGGAGTG
29013665 TACTCCAAAACAGGTGGAGT
1 TACTCCAAAACAGGTGGAGT
29013685 TTGAGCAGAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.29, C:0.22, G:0.29, T:0.20
Consensus pattern (21 bp):
TACTCCAAAACAGGTGGAGTG
Found at i:29019335 original size:45 final size:46
Alignment explanation
Indices: 29019264--29019371 Score: 134
Period size: 45 Copynumber: 2.4 Consensus size: 46
29019254 GATTGAAAAC
*
29019264 CATCATTGTCGGGCAACCCAGAGTGGTAG-ATTGTAC-A-TCTAGAGT
1 CATCGTTGTCGGGCAACCCAGAGTGGTAGTA-TGTACAAGT-TAGAGT
*
29019309 CATCGTTGTCGGGCAACCC-GAGGTGGTAGTATGTACAAGTTAGCGT
1 CATCGTTGTCGGGCAACCCAGA-GTGGTAGTATGTACAAGTTAGAGT
*
29019355 CATCGTTGTCGAGCAAC
1 CATCGTTGTCGGGCAAC
29019372 ATAGGGTGAT
Statistics
Matches: 56, Mismatches: 3, Indels: 7
0.85 0.05 0.11
Matches are distributed among these distances:
44 2 0.04
45 30 0.54
46 23 0.41
47 1 0.02
ACGTcount: A:0.24, C:0.21, G:0.29, T:0.26
Consensus pattern (46 bp):
CATCGTTGTCGGGCAACCCAGAGTGGTAGTATGTACAAGTTAGAGT
Found at i:29020522 original size:25 final size:25
Alignment explanation
Indices: 29020465--29020525 Score: 70
Period size: 25 Copynumber: 2.4 Consensus size: 25
29020455 TATAAACAAT
29020465 GAAATAAAAAAGAATAAATTAAAAA
1 GAAATAAAAAAGAATAAATTAAAAA
* ** *
29020490 TATTTAAAAAA-AATAAATGTAAAAC
1 GAAATAAAAAAGAATAAAT-TAAAAA
29020515 GAAATAAAAAA
1 GAAATAAAAAA
29020526 TACCAAAAAT
Statistics
Matches: 28, Mismatches: 7, Indels: 2
0.76 0.19 0.05
Matches are distributed among these distances:
24 7 0.25
25 21 0.75
ACGTcount: A:0.72, C:0.02, G:0.07, T:0.20
Consensus pattern (25 bp):
GAAATAAAAAAGAATAAATTAAAAA
Found at i:29021106 original size:13 final size:13
Alignment explanation
Indices: 29021090--29021116 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
29021080 AGAAAAATAA
29021090 ATATTTATTATAT
1 ATATTTATTATAT
29021103 ATATTTATTATAT
1 ATATTTATTATAT
29021116 A
1 A
29021117 AATACTAAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (13 bp):
ATATTTATTATAT
Found at i:29023701 original size:3 final size:3
Alignment explanation
Indices: 29023688--29023801 Score: 62
Period size: 3 Copynumber: 38.7 Consensus size: 3
29023678 TTTAGTCCCG
* * *
29023688 TTA TCA TTA TTA TTA TT- TT- TTA TTA TTA -AA CTAA TTA GTT- TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA -TTA TTA
* * * *
29023731 TTA TTA CTA TTA TTA TTA TTA TCA TTA TTG TT- GTA TT- TT- TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
*
29023776 TTA CTTA CCTTA TTA TTA TTT TTA TT
1 TTA -TTA --TTA TTA TTA TTA TTA TT
29023802 TACCCGTTTA
Statistics
Matches: 89, Mismatches: 13, Indels: 18
0.74 0.11 0.15
Matches are distributed among these distances:
2 12 0.13
3 66 0.74
4 7 0.08
5 4 0.04
ACGTcount: A:0.28, C:0.06, G:0.03, T:0.63
Consensus pattern (3 bp):
TTA
Found at i:29032198 original size:17 final size:17
Alignment explanation
Indices: 29032176--29032249 Score: 80
Period size: 17 Copynumber: 4.3 Consensus size: 17
29032166 AAAAATGTTT
29032176 AAAAAAGAGAAAAAAAG
1 AAAAAAGAGAAAAAAAG
*
29032193 AAAAAAAAGAAAAAGAA-
1 AAAAAAGAGAAAAA-AAG
*
29032210 AAAAAAGATGAAGAAAAG
1 AAAAAAGA-GAAAAAAAG
*
29032228 -AAAAAGAAAAGAAAAAG
1 AAAAAAGAGAA-AAAAAG
29032245 AAAAA
1 AAAAA
29032250 GAAAAAGAAA
Statistics
Matches: 47, Mismatches: 5, Indels: 9
0.77 0.08 0.15
Matches are distributed among these distances:
16 2 0.04
17 34 0.72
18 11 0.23
ACGTcount: A:0.82, C:0.00, G:0.16, T:0.01
Consensus pattern (17 bp):
AAAAAAGAGAAAAAAAG
Found at i:29032205 original size:6 final size:6
Alignment explanation
Indices: 29032177--29032266 Score: 96
Period size: 6 Copynumber: 14.7 Consensus size: 6
29032167 AAAATGTTTA
* *
29032177 AAAAAG AGAAAA- AAAGAAA AAAAAG AAAAAG AAAAA- AAAGATG AAGAAAAG
1 AAAAAG A-AAAAG AAA-AAG AAAAAG AAAAAG AAAAAG AAA-AAG -A-AAAAG
29032228 AAAAAG -AAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAA
1 AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAA
29032267 GGAGAGGTCA
Statistics
Matches: 73, Mismatches: 3, Indels: 16
0.79 0.03 0.17
Matches are distributed among these distances:
5 10 0.14
6 50 0.68
7 8 0.11
8 3 0.04
9 2 0.03
ACGTcount: A:0.82, C:0.00, G:0.17, T:0.01
Consensus pattern (6 bp):
AAAAAG
Found at i:29032267 original size:11 final size:11
Alignment explanation
Indices: 29032177--29032266 Score: 91
Period size: 11 Copynumber: 8.4 Consensus size: 11
29032167 AAAATGTTTA
*
29032177 AAAAAGAGAA-
1 AAAAAGAAAAG
29032187 AAAAAG-AAA-
1 AAAAAGAAAAG
29032196 AAAAAGAAAA-
1 AAAAAGAAAAG
29032206 AGAAAA-AAAAG
1 A-AAAAGAAAAG
**
29032217 ATGAAGAAAAG
1 AAAAAGAAAAG
29032228 AAAAAGAAAAG
1 AAAAAGAAAAG
29032239 AAAAAGAAAAAG
1 AAAAAG-AAAAG
29032251 AAAAAGAAAAAG
1 AAAAAG-AAAAG
29032263 AAAA
1 AAAA
29032267 GGAGAGGTCA
Statistics
Matches: 70, Mismatches: 5, Indels: 8
0.84 0.06 0.10
Matches are distributed among these distances:
9 8 0.11
10 16 0.23
11 25 0.36
12 21 0.30
ACGTcount: A:0.82, C:0.00, G:0.17, T:0.01
Consensus pattern (11 bp):
AAAAAGAAAAG
Found at i:29033700 original size:89 final size:89
Alignment explanation
Indices: 29033514--29034222 Score: 920
Period size: 89 Copynumber: 8.0 Consensus size: 89
29033504 GATAGCAGAT
* * * * * * * *
29033514 CTTGCCTTCATGTACTGACAGTGAAGCAGATTAAAGACACCAG-CCTTGCCTTCCT-TACTGACA
1 CTTGCCTTCCTGTACTGACAGCGGAGCAGACTGAAGATAGCAGATCTTGCCTTCCTGTACTGACA
* * * *
29033577 GCGGAGCAGA-CTGAAGATAGCAGAT
66 GCGAAGCAGATC-GAAGACACCAG-C
* * * *
29033602 ATTGCCTTCCTGTACTGATAGCGGAGCAGACTGAAGATAGCAGATCTTGCATTCCTGTATTGACA
1 CTTGCCTTCCTGTACTGACAGCGGAGCAGACTGAAGATAGCAGATCTTGCCTTCCTGTACTGACA
* * *
29033667 ACGAAGAAGATCAAAGACACCAGC
66 GCGAAGCAGATCGAAGACACCAGC
* * *
29033691 CTTGTCTTCCTGTACTGACAGCGGAGTAGACTGAAGATAGCAGATCTTGCCTTCCTGTACTGACG
1 CTTGCCTTCCTGTACTGACAGCGGAGCAGACTGAAGATAGCAGATCTTGCCTTCCTGTACTGACA
*
29033756 GTGAAGCAGATCGAAGACACCAGC
66 GCGAAGCAGATCGAAGACACCAGC
* * *
29033780 CTTGCCTTCCTTTACTGACAGCGGAGCAGACTGAAGATAACAGATCTTGCCTTCCTGTACTGACG
1 CTTGCCTTCCTGTACTGACAGCGGAGCAGACTGAAGATAGCAGATCTTGCCTTCCTGTACTGACA
* * *
29033845 GCGAAGTAAATCGAAGACATCAGC
66 GCGAAGCAGATCGAAGACACCAGC
* * * *
29033869 CTTGCCTTCCTGTACTGACAGCGGAGTAGACTGAAGATAACAGATCTTGCCTTCCTATACTGACG
1 CTTGCCTTCCTGTACTGACAGCGGAGCAGACTGAAGATAGCAGATCTTGCCTTCCTGTACTGACA
29033934 GCGAAGCAGATCGAAGACACCAGC
66 GCGAAGCAGATCGAAGACACCAGC
* * *
29033958 CTTGCCTTCCTGTACTGATAGCGGAGCAGACTAAAGATAGCAGATATTGCCTTCCTGTACTGACA
1 CTTGCCTTCCTGTACTGACAGCGGAGCAGACTGAAGATAGCAGATCTTGCCTTCCTGTACTGACA
* * *
29034023 GTGAAGTAGATCGAATACACCAGC
66 GCGAAGCAGATCGAAGACACCAGC
* * * * * *
29034047 TTTGCCTTCCTGTACTGACAGCGGAGAAGACTGAAAATAGTAGATCTTGCCTTCTTATACTGACA
1 CTTGCCTTCCTGTACTGACAGCGGAGCAGACTGAAGATAGCAGATCTTGCCTTCCTGTACTGACA
*
29034112 GCGAAGTAGATCGAAGACACCAGC
66 GCGAAGCAGATCGAAGACACCAGC
* * * *
29034136 CTTGCCTTCCTGTACTGACAGCGAAACAGACTGAAAATAGCAGATCTTGCCTTCCTGTATTGACA
1 CTTGCCTTCCTGTACTGACAGCGGAGCAGACTGAAGATAGCAGATCTTGCCTTCCTGTACTGACA
*
29034201 GCGAAGCAGATTGAAGACACCA
66 GCGAAGCAGATCGAAGACACCA
29034223 TAGTCTGCAG
Statistics
Matches: 543, Mismatches: 75, Indels: 5
0.87 0.12 0.01
Matches are distributed among these distances:
88 34 0.06
89 486 0.90
90 22 0.04
91 1 0.00
ACGTcount: A:0.29, C:0.25, G:0.23, T:0.23
Consensus pattern (89 bp):
CTTGCCTTCCTGTACTGACAGCGGAGCAGACTGAAGATAGCAGATCTTGCCTTCCTGTACTGACA
GCGAAGCAGATCGAAGACACCAGC
Found at i:29035518 original size:13 final size:14
Alignment explanation
Indices: 29035493--29035521 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
29035483 TGCATTTCTA
29035493 TTTCTATTTTTGTT
1 TTTCTATTTTTGTT
29035507 TTTCTA-TTTTGTT
1 TTTCTATTTTTGTT
29035520 TT
1 TT
29035522 GTAATAGCAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 9 0.60
14 6 0.40
ACGTcount: A:0.07, C:0.07, G:0.07, T:0.79
Consensus pattern (14 bp):
TTTCTATTTTTGTT
Found at i:29036161 original size:3 final size:3
Alignment explanation
Indices: 29036147--29036251 Score: 72
Period size: 3 Copynumber: 34.0 Consensus size: 3
29036137 ATTTAGTCCC
* * *
29036147 ATT ATC ATT ATT ATT ATTT ATA ATT AGTT -TT ATT ATT ACT ATT ATT
1 ATT ATT ATT ATT ATT A-TT ATT ATT A-TT ATT ATT ATT ATT ATT ATT
* * *
29036193 ATT ATT ATT ATC ATT ATT -TT -TGT ATT TTT AGT ATT ACTT ACCTT ATT
1 ATT ATT ATT ATT ATT ATT ATT AT-T ATT ATT ATT ATT A-TT A--TT ATT
*
29036240 ATT ATT TTT ATT
1 ATT ATT ATT ATT
29036252 TACCCGTTTA
Statistics
Matches: 81, Mismatches: 14, Indels: 14
0.74 0.13 0.13
Matches are distributed among these distances:
2 5 0.06
3 63 0.78
4 9 0.11
5 4 0.05
ACGTcount: A:0.29, C:0.06, G:0.03, T:0.63
Consensus pattern (3 bp):
ATT
Found at i:29036339 original size:23 final size:24
Alignment explanation
Indices: 29036313--29036364 Score: 79
Period size: 23 Copynumber: 2.2 Consensus size: 24
29036303 TTTTTTGTAC
*
29036313 TTTATAATATATATA-TACATATT
1 TTTATAATATATATACAACATATT
29036336 TTTATAATATATATACGAACATATT
1 TTTATAATATATATAC-AACATATT
29036361 TTTA
1 TTTA
29036365 ACTTTTGTAA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
23 15 0.58
25 11 0.42
ACGTcount: A:0.42, C:0.06, G:0.02, T:0.50
Consensus pattern (24 bp):
TTTATAATATATATACAACATATT
Found at i:29036988 original size:73 final size:74
Alignment explanation
Indices: 29036869--29037014 Score: 258
Period size: 73 Copynumber: 2.0 Consensus size: 74
29036859 TCTTTTCAAG
* *
29036869 CTCAAGTTTTAAATGATCTCGGGAATTTAGAAGAGATCGTGTCCTAACTTACTGGGCATGATC-C
1 CTCAAGTTTTAAATGATCTCGGGAATTAAGAAAAGATCGTGTCCTAACTTACTGGGCATGATCTC
*
29036933 TTTTTTTTT
66 TTTCTTTTT
29036942 CTCAAGTTTTAAATGATCTCGGGAATTAAGAAAAGATCGTGTCCTAACTTACTGGGCATGATCTC
1 CTCAAGTTTTAAATGATCTCGGGAATTAAGAAAAGATCGTGTCCTAACTTACTGGGCATGATCTC
29037007 TTTCTTTT
66 TTTCTTTT
29037015 AAAATCCAAG
Statistics
Matches: 69, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
73 61 0.88
74 8 0.12
ACGTcount: A:0.26, C:0.17, G:0.18, T:0.38
Consensus pattern (74 bp):
CTCAAGTTTTAAATGATCTCGGGAATTAAGAAAAGATCGTGTCCTAACTTACTGGGCATGATCTC
TTTCTTTTT
Found at i:29037656 original size:34 final size:34
Alignment explanation
Indices: 29037613--29037680 Score: 127
Period size: 34 Copynumber: 2.0 Consensus size: 34
29037603 TGAAAAAAAA
*
29037613 ACCCTTTAAGCATTGCTCCATATAAATTTCAGTT
1 ACCCTTTAAGCATTGCTCCATACAAATTTCAGTT
29037647 ACCCTTTAAGCATTGCTCCATACAAATTTCAGTT
1 ACCCTTTAAGCATTGCTCCATACAAATTTCAGTT
29037681 TTTTTATTAC
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 33 1.00
ACGTcount: A:0.29, C:0.25, G:0.09, T:0.37
Consensus pattern (34 bp):
ACCCTTTAAGCATTGCTCCATACAAATTTCAGTT
Found at i:29040778 original size:9 final size:9
Alignment explanation
Indices: 29040751--29040787 Score: 56
Period size: 9 Copynumber: 4.1 Consensus size: 9
29040741 TGAGTTTTCG
29040751 AATTCGAAT
1 AATTCGAAT
* *
29040760 AACTCTAAT
1 AATTCGAAT
29040769 AATTCGAAT
1 AATTCGAAT
29040778 AATTCGAAT
1 AATTCGAAT
29040787 A
1 A
29040788 TCAAACTATA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
9 24 1.00
ACGTcount: A:0.46, C:0.14, G:0.08, T:0.32
Consensus pattern (9 bp):
AATTCGAAT
Found at i:29041815 original size:5 final size:5
Alignment explanation
Indices: 29041805--29041840 Score: 72
Period size: 5 Copynumber: 7.2 Consensus size: 5
29041795 CTCGAAAATT
29041805 TTCGA TTCGA TTCGA TTCGA TTCGA TTCGA TTCGA T
1 TTCGA TTCGA TTCGA TTCGA TTCGA TTCGA TTCGA T
29041841 CGAATGCTCA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 31 1.00
ACGTcount: A:0.19, C:0.19, G:0.19, T:0.42
Consensus pattern (5 bp):
TTCGA
Found at i:29043556 original size:28 final size:28
Alignment explanation
Indices: 29043524--29043581 Score: 116
Period size: 28 Copynumber: 2.1 Consensus size: 28
29043514 AGCTATAGTT
29043524 GTTGTCTCACTGGGAACCTACTGATGGA
1 GTTGTCTCACTGGGAACCTACTGATGGA
29043552 GTTGTCTCACTGGGAACCTACTGATGGA
1 GTTGTCTCACTGGGAACCTACTGATGGA
29043580 GT
1 GT
29043582 AGACACCGCC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.21, C:0.21, G:0.29, T:0.29
Consensus pattern (28 bp):
GTTGTCTCACTGGGAACCTACTGATGGA
Found at i:29046715 original size:107 final size:107
Alignment explanation
Indices: 29046524--29046846 Score: 547
Period size: 107 Copynumber: 3.0 Consensus size: 107
29046514 ACTATTCAAA
* *
29046524 AAGATTTTCTAAATAAGGCAATATTTTGCGTTTGAAAATTCGAGAAAACGTGCCTTAACGTGCTG
1 AAGATTTTCTAAATAAGGCAATATTTTGCGTTTGGAAATTCGAGAAAACGTGCCCTAACGTGCTG
* *
29046589 GGTTTCTATTTCTCATTCGACCAAATAGCCAAATATCCTTTT
66 GGTTTCGATTTCTCGTTCGACCAAATAGCCAAATATCCTTTT
* *
29046631 AAGATTTTTTAAATAAGGCAATATTTTGCGTTTGGAAATTCGAGAAAACGTTCCCTAACGTGCTG
1 AAGATTTTCTAAATAAGGCAATATTTTGCGTTTGGAAATTCGAGAAAACGTGCCCTAACGTGCTG
* *
29046696 GGTTTCGATTTCTCGTTCGATCAAATAGCCAAAGATCCTTTT
66 GGTTTCGATTTCTCGTTCGACCAAATAGCCAAATATCCTTTT
*
29046738 AAGATTTTCTAAATAAGGCAATATTTTGCGTTTGGAAATTCGAGAAAACGTGCCCTAACGTCCTG
1 AAGATTTTCTAAATAAGGCAATATTTTGCGTTTGGAAATTCGAGAAAACGTGCCCTAACGTGCTG
* *
29046803 GGTTTCGATTTCTCGTTCGACTAAATAGCCAAATATCCTCTT
66 GGTTTCGATTTCTCGTTCGACCAAATAGCCAAATATCCTTTT
29046845 AA
1 AA
29046847 AACTTCGAAG
Statistics
Matches: 201, Mismatches: 15, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
107 201 1.00
ACGTcount: A:0.30, C:0.18, G:0.17, T:0.35
Consensus pattern (107 bp):
AAGATTTTCTAAATAAGGCAATATTTTGCGTTTGGAAATTCGAGAAAACGTGCCCTAACGTGCTG
GGTTTCGATTTCTCGTTCGACCAAATAGCCAAATATCCTTTT
Found at i:29059940 original size:108 final size:108
Alignment explanation
Indices: 29059768--29059964 Score: 265
Period size: 108 Copynumber: 1.8 Consensus size: 108
29059758 TTTTACATCT
* ** * *
29059768 TAGCAAAATTTTCCATCTTGATTAATTTGTTCATTCAGATCTTTGCTCTTAATAAATTTCCATCT
1 TAGCAAAATTTGCCATCTTGATTAATTCATTCATTCAGAGCTTTGCTCTGAATAAATTTCCATCT
29059833 TATCCATTGTGATAATCTTTTTCATCTTTTTCGTCTCGTATTC
66 TATCCATTGTGATAATCTTTTTCATCTTTTTCGTCTCGTATTC
* *
29059876 TAGCAAAATTTGCTATCTTGATTGATTCATTCATTTC-GAGCTTTGCTCTCGACA-AAATTT-CA
1 TAGCAAAATTTGCCATCTTGATTAATTCATTCA-TTCAGAGCTTTGCTCT-GA-ATAAATTTCCA
* *
29059938 TCTTGTCCATTTTGATAATCTTTTTCA
63 TCTTATCCATTGTGATAATCTTTTTCA
29059965 AGCATTTTTT
Statistics
Matches: 77, Mismatches: 9, Indels: 6
0.84 0.10 0.07
Matches are distributed among these distances:
108 66 0.86
109 10 0.13
110 1 0.01
ACGTcount: A:0.24, C:0.19, G:0.10, T:0.47
Consensus pattern (108 bp):
TAGCAAAATTTGCCATCTTGATTAATTCATTCATTCAGAGCTTTGCTCTGAATAAATTTCCATCT
TATCCATTGTGATAATCTTTTTCATCTTTTTCGTCTCGTATTC
Found at i:29060505 original size:45 final size:45
Alignment explanation
Indices: 29060438--29060893 Score: 613
Period size: 45 Copynumber: 10.1 Consensus size: 45
29060428 TGAAGTCATC
29060438 ATAGCA-AGTCTTGTCTTCCTGTATTGGCAGCGAAGTAGA-CTGAAG
1 ATAGCAGA-TCTTGTCTTCCTGTATTGGCAGCGAAGTAGATC-GAAG
* **
29060483 ATAGCAGATCTTGTCTTTCTGTATTGGCAATGAAGTAGATCGAAG
1 ATAGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATCGAAG
* *
29060528 ATAGCA-AGTCTTATCTTCCTGTATTGGCAGCAAAGTAGA-CTGAAG
1 ATAGCAGA-TCTTGTCTTCCTGTATTGGCAGCGAAGTAGATC-GAAG
* * *
29060573 ATAGCAGGTCTTGTCTTCCTGTATTCGCAGTGAAGTAGATCGAAG
1 ATAGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATCGAAG
* * * *
29060618 ATAGCA-AGTCTTGTCTTCCTGCATTGGCAACGAAATAGA-CTAAAG
1 ATAGCAGA-TCTTGTCTTCCTGTATTGGCAGCGAAGTAGATC-GAAG
*
29060663 ATAGCAGATATTGTCTTCCTGTATTGGCAGCGAAGTAGATCGAAG
1 ATAGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATCGAAG
** *
29060708 ATAGCAGATCTTAACTTCCTGTATTGGCAGTGAAGTAGATCGAAG
1 ATAGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATCGAAG
* *
29060753 ATAGCA-AGTCTTGTCTTCCTGTATTGGCAGTGAAGTA-AACTGAAG
1 ATAGCAGA-TCTTGTCTTCCTGTATTGGCAGCGAAGTAGATC-GAAG
*
29060798 ATAGTAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATCGAAG
1 ATAGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATCGAAG
29060843 ATAGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATCGAAG
1 ATAGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATCGAAG
29060888 ATAGCA
1 ATAGCA
29060894 AGTCTTATCT
Statistics
Matches: 361, Mismatches: 36, Indels: 28
0.85 0.08 0.07
Matches are distributed among these distances:
44 6 0.02
45 347 0.96
46 8 0.02
ACGTcount: A:0.29, C:0.17, G:0.25, T:0.30
Consensus pattern (45 bp):
ATAGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATCGAAG
Found at i:29060680 original size:135 final size:135
Alignment explanation
Indices: 29060438--29060899 Score: 675
Period size: 135 Copynumber: 3.4 Consensus size: 135
29060428 TGAAGTCATC
29060438 ATAGCA-AGTCTTGTCTTCCTGTATTGGCAGCGAAGTAGA-CTGAAGATAGC-AGATCTTGTCTT
1 ATAGCAGA-TCTTGTCTTCCTGTATTGGCAGCGAAGTAGATC-GAAGATAGCAAG-TCTTGTCTT
* * *
29060500 TCTGTATTGGCAATGAAGTAGA-TCGAAGATAGCA-AGTCTTATCTTCCTGTATTGGCAGCAAAG
63 CCTGTATTGGCAATGAAGTAGACT-GAAGATAGCAGA-TCTTGTCTTCCTGTATTGGCAGCGAAG
29060563 TAGA-CTGAAG
126 TAGATC-GAAG
* * *
29060573 ATAGCAGGTCTTGTCTTCCTGTATTCGCAGTGAAGTAGATCGAAGATAGCAAGTCTTGTCTTCCT
1 ATAGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATCGAAGATAGCAAGTCTTGTCTTCCT
* * * * *
29060638 GCATTGGCAACGAAATAGACTAAAGATAGCAGATATTGTCTTCCTGTATTGGCAGCGAAGTAGAT
66 GTATTGGCAATGAAGTAGACTGAAGATAGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGAT
29060703 CGAAG
131 CGAAG
** *
29060708 ATAGCAGATCTTAACTTCCTGTATTGGCAGTGAAGTAGATCGAAGATAGCAAGTCTTGTCTTCCT
1 ATAGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATCGAAGATAGCAAGTCTTGTCTTCCT
* * *
29060773 GTATTGGCAGTGAAGTAAACTGAAGATAGTAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGAT
66 GTATTGGCAATGAAGTAGACTGAAGATAGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGAT
29060838 CGAAG
131 CGAAG
29060843 ATAGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATCGAAGATAGCAAGTCTT
1 ATAGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATCGAAGATAGCAAGTCTT
29060900 ATCTCCCTAA
Statistics
Matches: 295, Mismatches: 26, Indels: 12
0.89 0.08 0.04
Matches are distributed among these distances:
135 289 0.98
136 6 0.02
ACGTcount: A:0.29, C:0.17, G:0.25, T:0.30
Consensus pattern (135 bp):
ATAGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATCGAAGATAGCAAGTCTTGTCTTCCT
GTATTGGCAATGAAGTAGACTGAAGATAGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGAT
CGAAG
Found at i:29063497 original size:107 final size:107
Alignment explanation
Indices: 29063311--29063526 Score: 369
Period size: 107 Copynumber: 2.0 Consensus size: 107
29063301 ACTATTCAAA
*
29063311 AAGATTTTCTAAATAAGGCAATACTTTGCGTTTGAAAATTCGAGAAAACGTGCCCTAACGTGTTG
1 AAGATTTTCTAAATAAGGCAATACTTTGCGTTTGAAAATTCGAGAAAACGTGCCCTAACGTGCTG
*
29063376 GGTTTCGATTTCTCGTTCGACCAAATAGCCAAATATCCTTTT
66 GGTTTCGATTTCTCGTTCGACCAAATAGCCAAATATCCTCTT
* * * *
29063418 AAGATTTTTTAAATAAGGTAATATTTTGCGTTTGGAAATTCGAGAAAACGTGCCCTAACGTGCTG
1 AAGATTTTCTAAATAAGGCAATACTTTGCGTTTGAAAATTCGAGAAAACGTGCCCTAACGTGCTG
*
29063483 GGTTTCGATTTCTCGTTCGACTAAATAGCCAAATATCCTCTT
66 GGTTTCGATTTCTCGTTCGACCAAATAGCCAAATATCCTCTT
29063525 AA
1 AA
29063527 AACTTCGAAG
Statistics
Matches: 102, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
107 102 1.00
ACGTcount: A:0.30, C:0.18, G:0.18, T:0.34
Consensus pattern (107 bp):
AAGATTTTCTAAATAAGGCAATACTTTGCGTTTGAAAATTCGAGAAAACGTGCCCTAACGTGCTG
GGTTTCGATTTCTCGTTCGACCAAATAGCCAAATATCCTCTT
Found at i:29065120 original size:7 final size:7
Alignment explanation
Indices: 29065108--29065147 Score: 62
Period size: 7 Copynumber: 5.7 Consensus size: 7
29065098 AAAGTATTTT
29065108 AAAATTA
1 AAAATTA
29065115 AAAATTA
1 AAAATTA
29065122 AAAATTA
1 AAAATTA
*
29065129 AAAAATA
1 AAAATTA
*
29065136 AAAATAA
1 AAAATTA
29065143 AAAAT
1 AAAAT
29065148 ATATATTTAT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
7 30 1.00
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.23
Consensus pattern (7 bp):
AAAATTA
Found at i:29065146 original size:13 final size:13
Alignment explanation
Indices: 29065107--29065148 Score: 57
Period size: 13 Copynumber: 3.2 Consensus size: 13
29065097 TAAAGTATTT
* *
29065107 TAAAATTAAAAAT
1 TAAAAATAAAAAA
29065120 TAAAAATTAAAAAA
1 TAAAAA-TAAAAAA
29065134 TAAAAATAAAAAA
1 TAAAAATAAAAAA
29065147 TA
1 TA
29065149 TATATTTATT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
13 14 0.54
14 12 0.46
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (13 bp):
TAAAAATAAAAAA
Found at i:29066208 original size:30 final size:29
Alignment explanation
Indices: 29066172--29066274 Score: 100
Period size: 30 Copynumber: 3.5 Consensus size: 29
29066162 TCCAAAAATA
* * * *
29066172 TAAAATTACATTTTAACCTTTTAATTTTCT
1 TAAAATTATATTTTAACCTCTAAAATTT-T
*
29066202 TAAAATTATATTTTGACCTCTAAAATTTT
1 TAAAATTATATTTTAACCTCTAAAATTTT
* *
29066231 TAAAATTATATTTTAATCC-CTCAACTTATT
1 TAAAATTATATTTTAA-CCTCTAAAATT-TT
*
29066261 TAAAATTACATTTT
1 TAAAATTATATTTT
29066275 GATCCTAAAA
Statistics
Matches: 62, Mismatches: 9, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
29 22 0.35
30 40 0.65
ACGTcount: A:0.37, C:0.13, G:0.01, T:0.50
Consensus pattern (29 bp):
TAAAATTATATTTTAACCTCTAAAATTTT
Found at i:29066239 original size:29 final size:28
Alignment explanation
Indices: 29066172--29066286 Score: 95
Period size: 30 Copynumber: 3.9 Consensus size: 28
29066162 TCCAAAAATA
* * *
29066172 TAAAATTACATTTTAACCTTTTAATTTTCT
1 TAAAATTACATTTTAACC-CTAAAATTT-T
* *
29066202 TAAAATTATATTTTGACCTCTAAAATTTT
1 TAAAATTACATTTTAACC-CTAAAATTTT
* * *
29066231 TAAAATTATATTTTAATCCCTCAACTTATT
1 TAAAATTACATTTTAA-CCCTAAAATT-TT
* *
29066261 TAAAATTACATTTTGATCCTAAAATT
1 TAAAATTACATTTTAACCCTAAAATT
29066287 CCCAAAAATT
Statistics
Matches: 70, Mismatches: 13, Indels: 5
0.80 0.15 0.06
Matches are distributed among these distances:
29 29 0.41
30 41 0.59
ACGTcount: A:0.37, C:0.13, G:0.02, T:0.48
Consensus pattern (28 bp):
TAAAATTACATTTTAACCCTAAAATTTT
Found at i:29066703 original size:9 final size:10
Alignment explanation
Indices: 29066680--29066704 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
29066670 AAAGAAAAAG
29066680 AAAAAGGAAT
1 AAAAAGGAAT
29066690 AAAAAGGAAT
1 AAAAAGGAAT
29066700 AAAAA
1 AAAAA
29066705 CAATCGGGTC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.76, C:0.00, G:0.16, T:0.08
Consensus pattern (10 bp):
AAAAAGGAAT
Found at i:29066836 original size:17 final size:18
Alignment explanation
Indices: 29066806--29066840 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
29066796 CAGGCAACCC
29066806 AAGAAAAGAGGCAAAAAA
1 AAGAAAAGAGGCAAAAAA
*
29066824 AAGAAAATA-GCAAAAAA
1 AAGAAAAGAGGCAAAAAA
29066841 GGCCTAACCC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.74, C:0.06, G:0.17, T:0.03
Consensus pattern (18 bp):
AAGAAAAGAGGCAAAAAA
Found at i:29066935 original size:21 final size:23
Alignment explanation
Indices: 29066895--29066939 Score: 67
Period size: 21 Copynumber: 2.0 Consensus size: 23
29066885 CCACCAGCAG
29066895 CAGGCCAGCAGGCTCCAGGCCCAA
1 CAGGCCAGCA-GCTCCAGGCCCAA
29066919 CAGGCCAGC-GC-CCAGGCCCAA
1 CAGGCCAGCAGCTCCAGGCCCAA
29066940 TCTACAGCAG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
21 10 0.48
22 2 0.10
24 9 0.43
ACGTcount: A:0.24, C:0.44, G:0.29, T:0.02
Consensus pattern (23 bp):
CAGGCCAGCAGCTCCAGGCCCAA
Found at i:29067412 original size:18 final size:18
Alignment explanation
Indices: 29067389--29067433 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 18
29067379 ACTTTCAAAA
* * *
29067389 TATTATTATTATTACTAT
1 TATTATTATCAATACCAT
*
29067407 TATTATTGTCAATACCAT
1 TATTATTATCAATACCAT
29067425 TATTATTAT
1 TATTATTAT
29067434 ATTTCTCGTA
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.33, C:0.09, G:0.02, T:0.56
Consensus pattern (18 bp):
TATTATTATCAATACCAT
Found at i:29069008 original size:27 final size:29
Alignment explanation
Indices: 29068956--29069009 Score: 76
Period size: 27 Copynumber: 1.9 Consensus size: 29
29068946 ACATTTTTAA
29068956 ATTTTAGATTTAATTATATATACATACAT
1 ATTTTAGATTTAATTATATATACATACAT
* *
29068985 ATTTTTGATTT-A-TATATATGCATAC
1 ATTTTAGATTTAATTATATATACATAC
29069010 TTCTATACTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
27 12 0.52
28 1 0.04
29 10 0.43
ACGTcount: A:0.37, C:0.07, G:0.06, T:0.50
Consensus pattern (29 bp):
ATTTTAGATTTAATTATATATACATACAT
Found at i:29069032 original size:16 final size:17
Alignment explanation
Indices: 29069006--29069041 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
29068996 ATATATATGC
*
29069006 ATACTTCTATACTTTAT
1 ATACTTCTATAATTTAT
29069023 ATACTT-TATAATTTAT
1 ATACTTCTATAATTTAT
29069039 ATA
1 ATA
29069042 TATACGTTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 12 0.67
17 6 0.33
ACGTcount: A:0.36, C:0.11, G:0.00, T:0.53
Consensus pattern (17 bp):
ATACTTCTATAATTTAT
Found at i:29069051 original size:29 final size:30
Alignment explanation
Indices: 29069013--29069073 Score: 79
Period size: 32 Copynumber: 2.0 Consensus size: 30
29069003 TGCATACTTC
* *
29069013 TATACTTTATATAC-TTTATAATTTATATA
1 TATACGTTATATACTTTTATAATATATATA
29069042 TATACGTTATATACATTTTTATAATATATATA
1 TATACGTTATATAC--TTTTATAATATATATA
29069074 CATATATACA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
29 13 0.48
32 14 0.52
ACGTcount: A:0.39, C:0.07, G:0.02, T:0.52
Consensus pattern (30 bp):
TATACGTTATATACTTTTATAATATATATA
Found at i:29069555 original size:20 final size:20
Alignment explanation
Indices: 29069520--29069557 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
29069510 TTGCTCATAT
29069520 TGTTTTTATTCACATTATCA
1 TGTTTTTATTCACATTATCA
29069540 TGTTTATTATTC-CATTAT
1 TGTTT-TTATTCACATTAT
29069558 GCATATTAAC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.24, C:0.13, G:0.05, T:0.58
Consensus pattern (20 bp):
TGTTTTTATTCACATTATCA
Found at i:29069787 original size:109 final size:109
Alignment explanation
Indices: 29069585--29069913 Score: 482
Period size: 109 Copynumber: 3.0 Consensus size: 109
29069575 TTCAAAAAGG
* * * *
29069585 AAAATTTTTCTAAGTAAGGCAATATTTTGCGTTTGAAAATTCGAGAAAACGTGCCCTAATATGCT
1 AAAA-TTTTCAAAATAAGGCAATGTTTTGCGTTTGAAAATTCGAGAAAACGTGCCCTAATGTGCT
* * *
29069650 GGGTTTTGATTTCTCTCATTCGACCAAATAGCCAAATATCCTTTT
65 GGGTTTCGATTTTTCTCGTTCGACCAAATAGCCAAATATCCTTTT
* * *
29069695 AAAATTTTCAAAATAAGACAATGTTTTGCGTTTGGAAATTCGAGAAAATGTGCCCTAATGTGCTG
1 AAAATTTTCAAAATAAGGCAATGTTTTGCGTTTGAAAATTCGAGAAAACGTGCCCTAATGTGCTG
* * *
29069760 GGTTTCGATTTTTCTCGTCCGATCAAATTGCCAAATATCCTTTT
66 GGTTTCGATTTTTCTCGTTCGACCAAATAGCCAAATATCCTTTT
*
29069804 AAAAATTTCAAAATAAGGCAATGTTTTGCGTTTGAAAATTCGAGAAAACGTGCCCTAATGTGCTG
1 AAAATTTTCAAAATAAGGCAATGTTTTGCGTTTGAAAATTCGAGAAAACGTGCCCTAATGTGCTG
* * *
29069869 GGTTTCGA--TTTCTCGTTGGACCAAATAGCCGAATATCCTCTT
66 GGTTTCGATTTTTCTCGTTCGACCAAATAGCCAAATATCCTTTT
29069911 AAA
1 AAA
29069914 TCTTAATCCA
Statistics
Matches: 196, Mismatches: 23, Indels: 3
0.88 0.10 0.01
Matches are distributed among these distances:
107 31 0.16
109 161 0.82
110 4 0.02
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.35
Consensus pattern (109 bp):
AAAATTTTCAAAATAAGGCAATGTTTTGCGTTTGAAAATTCGAGAAAACGTGCCCTAATGTGCTG
GGTTTCGATTTTTCTCGTTCGACCAAATAGCCAAATATCCTTTT
Found at i:29075377 original size:16 final size:16
Alignment explanation
Indices: 29075353--29075406 Score: 90
Period size: 16 Copynumber: 3.4 Consensus size: 16
29075343 TTTGGTTCGC
* *
29075353 TGTATTGGATTAGAGG
1 TGTAATGGAATAGAGG
29075369 TGTAATGGAATAGAGG
1 TGTAATGGAATAGAGG
29075385 TGTAATGGAATAGAGG
1 TGTAATGGAATAGAGG
29075401 TGTAAT
1 TGTAAT
29075407 AGCAAATCAA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 36 1.00
ACGTcount: A:0.33, C:0.00, G:0.35, T:0.31
Consensus pattern (16 bp):
TGTAATGGAATAGAGG
Found at i:29075490 original size:39 final size:43
Alignment explanation
Indices: 29075385--29075494 Score: 129
Period size: 45 Copynumber: 2.6 Consensus size: 43
29075375 GGAATAGAGG
29075385 TGTAATGGAATAGAGGTGTAATAGCAAATCAACTGTTTGGTTGAA
1 TGTAATGGAATAGAGGTGTAATAGCAAATCAACTGTTTGGTT--A
* * ***
29075430 TGTAATGGAATAGAGGCGTAATAG-TAATCTTGTGTTTGG-T-
1 TGTAATGGAATAGAGGTGTAATAGCAAATCAACTGTTTGGTTA
29075470 TG-AATGGAATAGAGGTGTAATAGCA
1 TGTAATGGAATAGAGGTGTAATAGCA
29075495 TAATGGAAAA
Statistics
Matches: 57, Mismatches: 7, Indels: 7
0.80 0.10 0.10
Matches are distributed among these distances:
39 20 0.35
40 2 0.04
43 1 0.02
44 11 0.19
45 23 0.40
ACGTcount: A:0.34, C:0.05, G:0.29, T:0.32
Consensus pattern (43 bp):
TGTAATGGAATAGAGGTGTAATAGCAAATCAACTGTTTGGTTA
Found at i:29075648 original size:25 final size:25
Alignment explanation
Indices: 29075616--29075670 Score: 69
Period size: 25 Copynumber: 2.2 Consensus size: 25
29075606 TAATTTAATC
*
29075616 ATAT-TTAAACATAATTATTATT-AA
1 ATATATTAAACAT-ATTATAATTAAA
*
29075640 ATATATTAAATATATTATAATTAAA
1 ATATATTAAACATATTATAATTAAA
29075665 ATATAT
1 ATATAT
29075671 AATTTAATAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
24 12 0.44
25 15 0.56
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (25 bp):
ATATATTAAACATATTATAATTAAA
Found at i:29075989 original size:24 final size:27
Alignment explanation
Indices: 29075938--29075990 Score: 67
Period size: 27 Copynumber: 2.1 Consensus size: 27
29075928 TATATGTAAT
*
29075938 ATTATTAAAATAATATTTTTTATTTTA
1 ATTATTAAAATAATATTTTTTATATTA
*
29075965 ATTATTTAAA-AATA-TTTTTA-ATTA
1 ATTATTAAAATAATATTTTTTATATTA
29075989 AT
1 AT
29075991 GCGGTGTATA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
24 5 0.21
25 6 0.25
26 4 0.17
27 9 0.38
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (27 bp):
ATTATTAAAATAATATTTTTTATATTA
Found at i:29079384 original size:20 final size:20
Alignment explanation
Indices: 29079361--29079433 Score: 65
Period size: 20 Copynumber: 3.4 Consensus size: 20
29079351 TCATTTCGTT
29079361 TTTTTAATTTCAAGATTCTA
1 TTTTTAATTTCAAGATTCTA
* ** *
29079381 TTTTTAATCTCCAATTTTACCATTT
1 TTTTTAAT-TTCAAGATT--C--TA
29079406 TTTTTAATTTCAAGATTCTA
1 TTTTTAATTTCAAGATTCTA
29079426 TTTTTAAT
1 TTTTTAAT
29079434 CTCCAATTTT
Statistics
Matches: 40, Mismatches: 8, Indels: 10
0.69 0.14 0.17
Matches are distributed among these distances:
20 17 0.43
21 6 0.15
22 1 0.03
23 1 0.03
24 6 0.15
25 9 0.22
ACGTcount: A:0.27, C:0.12, G:0.03, T:0.58
Consensus pattern (20 bp):
TTTTTAATTTCAAGATTCTA
Found at i:29079405 original size:22 final size:22
Alignment explanation
Indices: 29079380--29079452 Score: 69
Period size: 20 Copynumber: 3.3 Consensus size: 22
29079370 TCAAGATTCT
29079380 ATTTTTAATCTCCAATTTTACC
1 ATTTTTAATCTCCAATTTTACC
* ** *
29079402 ATTTTTTTTAAT-TTCAAGATT-CT
1 A---TTTTTAATCTCCAATTTTACC
29079425 ATTTTTAATCTCCAATTTTACC
1 ATTTTTAATCTCCAATTTTACC
29079447 ATTTTT
1 ATTTTT
29079453 TTCTGATTCT
Statistics
Matches: 38, Mismatches: 8, Indels: 10
0.68 0.14 0.18
Matches are distributed among these distances:
20 8 0.21
21 6 0.16
22 8 0.21
23 2 0.05
24 6 0.16
25 8 0.21
ACGTcount: A:0.26, C:0.16, G:0.01, T:0.56
Consensus pattern (22 bp):
ATTTTTAATCTCCAATTTTACC
Found at i:29079419 original size:45 final size:45
Alignment explanation
Indices: 29079359--29079454 Score: 192
Period size: 45 Copynumber: 2.1 Consensus size: 45
29079349 TTTCATTTCG
29079359 TTTTTTTAATTTCAAGATTCTATTTTTAATCTCCAATTTTACCAT
1 TTTTTTTAATTTCAAGATTCTATTTTTAATCTCCAATTTTACCAT
29079404 TTTTTTTAATTTCAAGATTCTATTTTTAATCTCCAATTTTACCAT
1 TTTTTTTAATTTCAAGATTCTATTTTTAATCTCCAATTTTACCAT
29079449 TTTTTT
1 TTTTTT
29079455 CTGATTCTTT
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 51 1.00
ACGTcount: A:0.25, C:0.15, G:0.02, T:0.58
Consensus pattern (45 bp):
TTTTTTTAATTTCAAGATTCTATTTTTAATCTCCAATTTTACCAT
Found at i:29081309 original size:38 final size:38
Alignment explanation
Indices: 29081267--29081341 Score: 125
Period size: 38 Copynumber: 2.0 Consensus size: 38
29081257 TCTTGTATTA
*
29081267 GGATCCATTTTGGTAAAGTAGTTG-CTCTTTTTTCCCTG
1 GGATCCATTTTGGTAAAGTAATTGCCT-TTTTTTCCCTG
29081305 GGATCCATTTTGGTAAAGTAATTGCCTTTTTTTCCCT
1 GGATCCATTTTGGTAAAGTAATTGCCTTTTTTTCCCT
29081342 TTCCTCAACC
Statistics
Matches: 35, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
38 33 0.94
39 2 0.06
ACGTcount: A:0.17, C:0.19, G:0.19, T:0.45
Consensus pattern (38 bp):
GGATCCATTTTGGTAAAGTAATTGCCTTTTTTTCCCTG
Found at i:29082911 original size:45 final size:44
Alignment explanation
Indices: 29082823--29082915 Score: 152
Period size: 45 Copynumber: 2.1 Consensus size: 44
29082813 ATTACGACAT
29082823 CATTCCATTCAACCAAACACAAGAATACTATTACAGTTCTATTC
1 CATTCCATTCAACCAAACACAAGAATACTATTACAGTTCTATTC
*
29082867 CATTCCATTCAACCAAACA-ATTGAATTACTATTACAGTTCTATTC
1 CATTCCATTCAACCAAACACA-AGAA-TACTATTACAGTTCTATTC
29082912 CATT
1 CATT
29082916 ATAGCTCTAT
Statistics
Matches: 46, Mismatches: 1, Indels: 3
0.92 0.02 0.06
Matches are distributed among these distances:
43 1 0.02
44 22 0.48
45 23 0.50
ACGTcount: A:0.37, C:0.26, G:0.04, T:0.33
Consensus pattern (44 bp):
CATTCCATTCAACCAAACACAAGAATACTATTACAGTTCTATTC
Found at i:29089388 original size:9 final size:9
Alignment explanation
Indices: 29089374--29089404 Score: 55
Period size: 9 Copynumber: 3.6 Consensus size: 9
29089364 AAAAACAATG
29089374 AATAATAAC
1 AATAATAAC
29089383 AATAATAAC
1 AATAATAAC
29089392 AATAATAA-
1 AATAATAAC
29089400 AATAA
1 AATAA
29089405 ACACATAACA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
8 5 0.23
9 17 0.77
ACGTcount: A:0.71, C:0.06, G:0.00, T:0.23
Consensus pattern (9 bp):
AATAATAAC
Found at i:29095010 original size:9 final size:9
Alignment explanation
Indices: 29094998--29095052 Score: 51
Period size: 9 Copynumber: 6.3 Consensus size: 9
29094988 CAAATAAAAC
29094998 TAATAATGA
1 TAATAATGA
29095007 TAATAAT--
1 TAATAATGA
*
29095014 TAATAATAA
1 TAATAATGA
*
29095023 TAATAATAA
1 TAATAATGA
*
29095032 TAATGATGA
1 TAATAATGA
* *
29095041 TGATGATGA
1 TAATAATGA
29095050 TAA
1 TAA
29095053 ATGCTAATAC
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
7 7 0.17
9 33 0.82
ACGTcount: A:0.55, C:0.00, G:0.11, T:0.35
Consensus pattern (9 bp):
TAATAATGA
Found at i:29095012 original size:3 final size:3
Alignment explanation
Indices: 29094998--29095035 Score: 58
Period size: 3 Copynumber: 12.3 Consensus size: 3
29094988 CAAATAAAAC
*
29094998 TAA TAA TGA TAA TAA TTAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA -TAA TAA TAA TAA TAA TAA TAA T
29095036 GATGATGATG
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
3 29 0.91
4 3 0.09
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.37
Consensus pattern (3 bp):
TAA
Found at i:29095796 original size:2 final size:2
Alignment explanation
Indices: 29095791--29095818 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
29095781 TCTTATATAT
29095791 TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG
29095819 CTTTAAAAAA
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:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:29096650 original size:44 final size:44
Alignment explanation
Indices: 29096587--29097172 Score: 336
Period size: 44 Copynumber: 13.7 Consensus size: 44
29096577 ATTGGATGCG
* *
29096587 ATCTGCTCTACTGCAACTTCAGAGAGATAAGATATGTGGTTTTA
1 ATCTGCTCCACTGCAACTTCAGGGAGATAAGATATGTGGTTTTA
** * * *
29096631 ATCCACTCCACTGCAACTTCAGGGAGATAGGAT-TG-GTTTCTTCT
1 ATCTGCTCCACTGCAACTTCAGGGAGATAAGATATGTGGTT-TT-A
* * ** * * ***
29096675 GTCTGCTCCACTACTGCTT-AGGGAGATAAGA-CT-T-GATGCG
1 ATCTGCTCCACTGCAACTTCAGGGAGATAAGATATGTGGTTTTA
* * * *
29096715 ATCTGTTCTACTGCAACTTCAGAGAGATAAGATCTGTGGTTTTA
1 ATCTGCTCCACTGCAACTTCAGGGAGATAAGATATGTGGTTTTA
* * * * *
29096759 ATCTGCTCCACTTCAATTTCAGGGAGATAGGAT-TAGT-TTATTTC
1 ATCTGCTCCACTGCAACTTCAGGGAGATAAGATAT-GTGGT-TTTA
* * * *
29096803 GTCTGCTCCACTGCAACTTCAGGGAGATAAG--AT-TGGATGTG
1 ATCTGCTCCACTGCAACTTCAGGGAGATAAGATATGTGGTTTTA
** * ** *
29096844 AT-T-CTTTACTGTAACTTCAAAGAGATAAGATCTGTGGTTTTA
1 ATCTGCTCCACTGCAACTTCAGGGAGATAAGATATGTGGTTTTA
* * * * *
29096886 ATCCGCTCCACTGCAACTTCAGAGAGATAGGAT-TAGT-TTCTTTT
1 ATCTGCTCCACTGCAACTTCAGGGAGATAAGATAT-GTGGT-TTTA
* * * ***
29096930 GTCTGCTCCACTGCAACTTCAGGGAGATAAG--A-CTGGATGCG
1 ATCTGCTCCACTGCAACTTCAGGGAGATAAGATATGTGGTTTTA
* * * *
29096971 ATCTCCTCTACTGCAACTTCAGAGAGATAAGATATGTTGTTTTA
1 ATCTGCTCCACTGCAACTTCAGGGAGATAAGATATGTGGTTTTA
* * * * *
29097015 ATCCGCTCCACTGCAACTTTAGGGAGATAGGAT-TGAT-TTCTTTC
1 ATCTGCTCCACTGCAACTTCAGGGAGATAAGATATG-TGGT-TTTA
* * * **
29097059 GTCTGCTCCACTGCAACTTCAGGGAGATAAG--A-CTGGATGCA
1 ATCTGCTCCACTGCAACTTCAGGGAGATAAGATATGTGGTTTTA
* * * *
29097100 ATCTGATCTACTGCAACTTCAGAGAGATAAGATCTGTGGTTTTA
1 ATCTGCTCCACTGCAACTTCAGGGAGATAAGATATGTGGTTTTA
** *
29097144 ATCCACTCCACTGCAAGTTCAGGGAGATA
1 ATCTGCTCCACTGCAACTTCAGGGAGATA
29097173 GGATTTACAA
Statistics
Matches: 394, Mismatches: 117, Indels: 62
0.69 0.20 0.11
Matches are distributed among these distances:
39 21 0.05
40 14 0.04
41 74 0.19
42 13 0.03
43 26 0.07
44 246 0.62
ACGTcount: A:0.26, C:0.20, G:0.22, T:0.32
Consensus pattern (44 bp):
ATCTGCTCCACTGCAACTTCAGGGAGATAAGATATGTGGTTTTA
Found at i:29097048 original size:129 final size:129
Alignment explanation
Indices: 29096564--29097177 Score: 905
Period size: 129 Copynumber: 4.8 Consensus size: 129
29096554 CACTACATCC
* * * *
29096564 TCAGAGAGATAGGATTGGATGCGATCTGCTCTACTGCAACTTCAGAGAGATAAGATATGTGGTTT
1 TCAGGGAGATAAGACTGGATGCGATCTGCTCTACTGCAACTTCAGAGAGATAAGATCTGTGGTTT
* * * **
29096629 TAATCCACTCCACTGCAACTTCAGGGAGATAGGATTGGTTTC-TTCTGTCTGCTCCACTACTGCT
66 TAATCCGCTCCACTGCAACTTCAGGGAGATAGGATTAGTTTCTTTC-GTCTGCTCCACTGCAACT
* *
29096693 T-AGGGAGATAAGACTTGATGCGATCTGTTCTACTGCAACTTCAGAGAGATAAGATCTGTGGTTT
1 TCAGGGAGATAAGACTGGATGCGATCTGCTCTACTGCAACTTCAGAGAGATAAGATCTGTGGTTT
* * * *
29096757 TAATCTGCTCCACTTCAATTTCAGGGAGATAGGATTAGTTTATTTCGTCTGCTCCACTGCAACT
66 TAATCCGCTCCACTGCAACTTCAGGGAGATAGGATTAGTTTCTTTCGTCTGCTCCACTGCAACT
* * * * *
29096821 TCAGGGAGATAAGATTGGATGTGAT-T-CTTTACTGTAACTTCAAAGAGATAAGATCTGTGGTTT
1 TCAGGGAGATAAGACTGGATGCGATCTGCTCTACTGCAACTTCAGAGAGATAAGATCTGTGGTTT
* *
29096884 TAATCCGCTCCACTGCAACTTCAGAGAGATAGGATTAGTTTCTTTTGTCTGCTCCACTGCAACT
66 TAATCCGCTCCACTGCAACTTCAGGGAGATAGGATTAGTTTCTTTCGTCTGCTCCACTGCAACT
* * *
29096948 TCAGGGAGATAAGACTGGATGCGATCTCCTCTACTGCAACTTCAGAGAGATAAGATATGTTGTTT
1 TCAGGGAGATAAGACTGGATGCGATCTGCTCTACTGCAACTTCAGAGAGATAAGATCTGTGGTTT
*
29097013 TAATCCGCTCCACTGCAACTTTAGGGAGATAGGATT-GATTTCTTTCGTCTGCTCCACTGCAACT
66 TAATCCGCTCCACTGCAACTTCAGGGAGATAGGATTAG-TTTCTTTCGTCTGCTCCACTGCAACT
* *
29097077 TCAGGGAGATAAGACTGGATGCAATCTGATCTACTGCAACTTCAGAGAGATAAGATCTGTGGTTT
1 TCAGGGAGATAAGACTGGATGCGATCTGCTCTACTGCAACTTCAGAGAGATAAGATCTGTGGTTT
* *
29097142 TAATCCACTCCACTGCAAGTTCAGGGAGATAGGATT
66 TAATCCGCTCCACTGCAACTTCAGGGAGATAGGATT
29097178 TACAATCTTC
Statistics
Matches: 434, Mismatches: 46, Indels: 10
0.89 0.09 0.02
Matches are distributed among these distances:
127 114 0.26
128 112 0.26
129 208 0.48
ACGTcount: A:0.27, C:0.20, G:0.22, T:0.31
Consensus pattern (129 bp):
TCAGGGAGATAAGACTGGATGCGATCTGCTCTACTGCAACTTCAGAGAGATAAGATCTGTGGTTT
TAATCCGCTCCACTGCAACTTCAGGGAGATAGGATTAGTTTCTTTCGTCTGCTCCACTGCAACT
Found at i:29097061 original size:256 final size:254
Alignment explanation
Indices: 29096564--29097177 Score: 899
Period size: 256 Copynumber: 2.4 Consensus size: 254
29096554 CACTACATCC
* * * *
29096564 TCAGAGAGATAGGATTGGATGCGATCTGCTCTACTGCAACTTCAGAGAGATAAGATATGTGGTTT
1 TCAGGGAGATAAGATTGGATG-GAT-T-CTTTACTGCAACTTCAGAGAGATAAGATCTGTGGTTT
* **
29096629 TAATCCACTCCACTGCAACTTCAGGGAGATAGGATTGGTTTCTTCTGTCTGCTCCACTACTGCTT
63 TAATCCACTCCACTGCAACTTCAGGGAGATAGGATTAGTTTCTTCTGTCTGCTCCACTACAACTT
* ** *
29096694 AGGGAGATAAGACTTGATGCGATCTGTTCTACTGCAACTTCAGAGAGATAAGATCTGTGGTTTTA
128 AGGGAGATAAGACTGGATGCGATCTCCTCTACTGCAACTTCAGAGAGATAAGATATGTGGTTTTA
* *
29096759 ATCTGCTCCACTTCAATTTCAGGGAGATAGGATTAGTTTATTTCGTCTGCTCCACTGCAACT
193 ATCCGCTCCACTGCAATTTCAGGGAGATAGGATTAGTTTATTTCGTCTGCTCCACTGCAACT
* *
29096821 TCAGGGAGATAAGATTGGATGTGATTCTTTACTGTAACTTCAAAGAGATAAGATCTGTGGTTTTA
1 TCAGGGAGATAAGATTGGATG-GATTCTTTACTGCAACTTCAGAGAGATAAGATCTGTGGTTTTA
* * * *
29096886 ATCCGCTCCACTGCAACTTCAGAGAGATAGGATTAGTTTCTTTTGTCTGCTCCACTGCAACTTCA
65 ATCCACTCCACTGCAACTTCAGGGAGATAGGATTAGTTTCTTCTGTCTGCTCCACTACAACTT-A
*
29096951 GGGAGATAAGACTGGATGCGATCTCCTCTACTGCAACTTCAGAGAGATAAGATATGTTGTTTTAA
129 GGGAGATAAGACTGGATGCGATCTCCTCTACTGCAACTTCAGAGAGATAAGATATGTGGTTTTAA
*
29097016 TCCGCTCCACTGCAACTTT-AGGGAGATAGGATT-GATTTCTTTCGTCTGCTCCACTGCAACT
194 TCCGCTCCACTGCAA-TTTCAGGGAGATAGGATTAG-TTTATTTCGTCTGCTCCACTGCAACT
* * *
29097077 TCAGGGAGATAAGACTGGATGCAATCTGATCTACTGCAACTTCAGAGAGATAAGATCTGTGGTTT
1 TCAGGGAGATAAGATTGGATGGATTCT--T-TACTGCAACTTCAGAGAGATAAGATCTGTGGTTT
*
29097142 TAATCCACTCCACTGCAAGTTCAGGGAGATAGGATT
63 TAATCCACTCCACTGCAACTTCAGGGAGATAGGATT
29097178 TACAATCTTC
Statistics
Matches: 321, Mismatches: 30, Indels: 11
0.89 0.08 0.03
Matches are distributed among these distances:
255 96 0.30
256 134 0.42
257 26 0.08
258 65 0.20
ACGTcount: A:0.27, C:0.20, G:0.22, T:0.31
Consensus pattern (254 bp):
TCAGGGAGATAAGATTGGATGGATTCTTTACTGCAACTTCAGAGAGATAAGATCTGTGGTTTTAA
TCCACTCCACTGCAACTTCAGGGAGATAGGATTAGTTTCTTCTGTCTGCTCCACTACAACTTAGG
GAGATAAGACTGGATGCGATCTCCTCTACTGCAACTTCAGAGAGATAAGATATGTGGTTTTAATC
CGCTCCACTGCAATTTCAGGGAGATAGGATTAGTTTATTTCGTCTGCTCCACTGCAACT
Found at i:29097154 original size:85 final size:85
Alignment explanation
Indices: 29096531--29097177 Score: 372
Period size: 85 Copynumber: 7.6 Consensus size: 85
29096521 TAGGAGGACG
* * * * * * * * * *
29096531 AGATTTGTGGTTTTAGTCCACTCCACTACATCCTCAGAGAGATAGGATTGGATGCGATCTGCTCT
1 AGATCTGTGGTTTTAATCCGCTCCACTGCAACTTCAGAGAGATAAGATTGGTTTCAATCTGCTCT
*
29096596 ACTGCAACTTCAGAGAGATA
66 ACTGCAACTTCAGGGAGATA
* * * * *
29096616 AGATATGTGGTTTTAATCCACTCCACTGCAACTTCAGGGAGATAGGATTGGTTTC-TTCTG-TCT
1 AGATCTGTGGTTTTAATCCGCTCCACTGCAACTTCAGAGAGATAAGATTGGTTTCAATCTGCTCT
* * *
29096679 GCTCCACTACTGCTTAGGGAGATA
66 ACTGCA--ACT--TCAGGGAGATA
* *** * * * *
29096703 AGA-CT-T-GATGCGATCTGTTCTACTGCAACTTCAGAGAGATAAGATCTGTGGTTTTAATCTGC
1 AGATCTGTGGTTTTAATCCGCTCCACTGCAACTTCAGAGAGATAAGA--T-TGGTTTCAATCTGC
* * *
29096765 TCCACTTCAATTTCAGGGAGATA
63 TCTACTGCAACTTCAGGGAGATA
* * ** * * * *
29096788 GGAT-TAGT-TTATTTCGTCTGCTCCACTGCAACTTCAGGGAGATAAGATTGGATGT-GAT-T-C
1 AGATCT-GTGGT-TTTAATCCGCTCCACTGCAACTTCAGAGAGATAAGATTGG-TTTCAATCTGC
* * **
29096848 TTTACTGTAACTTCAAAGAGATA
63 TCTACTGCAACTTCAGGGAGATA
* * **
29096871 AGATCTGTGGTTTTAATCCGCTCCACTGCAACTTCAGAGAGATAGGATTAGTTTCTTTTGTCTGC
1 AGATCTGTGGTTTTAATCCGCTCCACTGCAACTTCAGAGAGATAAGATTGGTTTC---AATCTGC
*
29096936 TCCACTGCAACTTCAGGGAGATA
63 TCTACTGCAACTTCAGGGAGATA
* *** * * *
29096959 AGA-C--TGGATGCGATCTC-CTCTACTGCAACTTCAGAGAGATAAGATATGTTGTTTTAATCCG
1 AGATCTGTGGTTTTAATC-CGCTCCACTGCAACTTCAGAGAGATAAGAT-TG--GTTTCAATCTG
* *
29097020 CTCCACTGCAACTTTAGGGAGATA
62 CTCTACTGCAACTTCAGGGAGATA
* * ** * * * * * *
29097044 GGAT-TGAT-TTCTTTCGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTGGATGCAATCTGAT
1 AGATCTG-TGGT-TTTAATCCGCTCCACTGCAACTTCAGAGAGATAAGATTGGTTTCAATCTGCT
*
29097107 CTACTGCAACTTCAGAGAGATA
64 CTACTGCAACTTCAGGGAGATA
* * * *
29097129 AGATCTGTGGTTTTAATCCACTCCACTGCAAGTTCAGGGAGATAGGATT
1 AGATCTGTGGTTTTAATCCGCTCCACTGCAACTTCAGAGAGATAAGATT
29097178 TACAATCTTC
Statistics
Matches: 422, Mismatches: 106, Indels: 68
0.71 0.18 0.11
Matches are distributed among these distances:
82 2 0.00
83 63 0.15
84 35 0.08
85 192 0.45
86 11 0.03
87 25 0.06
88 88 0.21
89 6 0.01
ACGTcount: A:0.26, C:0.20, G:0.22, T:0.32
Consensus pattern (85 bp):
AGATCTGTGGTTTTAATCCGCTCCACTGCAACTTCAGAGAGATAAGATTGGTTTCAATCTGCTCT
ACTGCAACTTCAGGGAGATA
Found at i:29097329 original size:44 final size:44
Alignment explanation
Indices: 29097281--29097375 Score: 120
Period size: 44 Copynumber: 2.2 Consensus size: 44
29097271 CTTCGATCTG
* * *
29097281 CTCCACTACTATTTAGGGAGATAAGATCTGTTATC-TCTAACCTA
1 CTCCACTACTACTTAAGGAGATAAGATCTGTAATCTTC-AACCTA
* *
29097325 CTCCACTACTGCTTAAGGAGATAGGATCTGTAATCTTCAACCTA
1 CTCCACTACTACTTAAGGAGATAAGATCTGTAATCTTCAACCTA
*
29097369 TTCCACT
1 CTCCACT
29097376 GCTGCTCAGG
Statistics
Matches: 44, Mismatches: 6, Indels: 2
0.85 0.12 0.04
Matches are distributed among these distances:
44 42 0.95
45 2 0.05
ACGTcount: A:0.28, C:0.25, G:0.14, T:0.33
Consensus pattern (44 bp):
CTCCACTACTACTTAAGGAGATAAGATCTGTAATCTTCAACCTA
Found at i:29097381 original size:44 final size:44
Alignment explanation
Indices: 29097297--29097394 Score: 126
Period size: 44 Copynumber: 2.2 Consensus size: 44
29097287 TACTATTTAG
* * *
29097297 GGAGATAAGATCTGTTATCTCTAACCTACTCCACTACTGCTTAA
1 GGAGATAGGATCTGTAATCTCTAACCTACTCCACTACTGCTCAA
* * *
29097341 GGAGATAGGATCTGTAATCT-TCAACCTATTCCACTGCTGCTCAG
1 GGAGATAGGATCTGTAATCTCT-AACCTACTCCACTACTGCTCAA
29097385 GGAGATAGGA
1 GGAGATAGGA
29097395 CTTGATATGA
Statistics
Matches: 47, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
43 1 0.02
44 46 0.98
ACGTcount: A:0.29, C:0.22, G:0.20, T:0.29
Consensus pattern (44 bp):
GGAGATAGGATCTGTAATCTCTAACCTACTCCACTACTGCTCAA
Done.