Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D02
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: 67659327
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 461372 characters in sequence are not A, C, G, or T
File 165 of 216
Found at i:51921911 original size:20 final size:20
Alignment explanation
Indices: 51921884--51921937 Score: 74
Period size: 20 Copynumber: 2.8 Consensus size: 20
51921874 AAAAATAGTT
51921884 TAAC-TGATTGAAAAAATTC
1 TAACTTGATTGAAAAAATTC
* *
51921903 TAACTTGATTGAAATAATTT
1 TAACTTGATTGAAAAAATTC
*
51921923 TAACTTGATTTAAAA
1 TAACTTGATTGAAAA
51921938 GTTTATTCAA
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
19 4 0.13
20 26 0.87
ACGTcount: A:0.44, C:0.07, G:0.09, T:0.39
Consensus pattern (20 bp):
TAACTTGATTGAAAAAATTC
Found at i:51924217 original size:12 final size:12
Alignment explanation
Indices: 51924200--51924237 Score: 58
Period size: 12 Copynumber: 3.2 Consensus size: 12
51924190 GGTACAAGCA
51924200 ATCATGGAGGAT
1 ATCATGGAGGAT
51924212 ATCATGGAGGAT
1 ATCATGGAGGAT
**
51924224 ATTGTGGAGGAT
1 ATCATGGAGGAT
51924236 AT
1 AT
51924238 AGAGGCAGAG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.32, C:0.05, G:0.34, T:0.29
Consensus pattern (12 bp):
ATCATGGAGGAT
Found at i:51938327 original size:3 final size:3
Alignment explanation
Indices: 51938319--51938360 Score: 75
Period size: 3 Copynumber: 14.0 Consensus size: 3
51938309 GCTCCTATTC
*
51938319 ATA ATA ATA ATG ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
51938361 GAAATGAAAT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:51956348 original size:15 final size:16
Alignment explanation
Indices: 51956318--51956350 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
51956308 CTCCTAAATC
*
51956318 ACATAATGTCTTTCCA
1 ACATAATGTATTTCCA
51956334 ACATAATG-ATTTCCA
1 ACATAATGTATTTCCA
51956349 AC
1 AC
51956351 TGAACAAAGG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 8 0.50
16 8 0.50
ACGTcount: A:0.36, C:0.24, G:0.06, T:0.33
Consensus pattern (16 bp):
ACATAATGTATTTCCA
Found at i:51959306 original size:36 final size:36
Alignment explanation
Indices: 51959266--51959341 Score: 134
Period size: 36 Copynumber: 2.1 Consensus size: 36
51959256 ATGTCCAAAG
* *
51959266 TCCATTTACAACGAAAACTAACTAATTCCTGGGAGT
1 TCCATTTACAACCAAAACCAACTAATTCCTGGGAGT
51959302 TCCATTTACAACCAAAACCAACTAATTCCTGGGAGT
1 TCCATTTACAACCAAAACCAACTAATTCCTGGGAGT
51959338 TCCA
1 TCCA
51959342 CAATGCCTAA
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
36 38 1.00
ACGTcount: A:0.36, C:0.26, G:0.12, T:0.26
Consensus pattern (36 bp):
TCCATTTACAACCAAAACCAACTAATTCCTGGGAGT
Found at i:51962482 original size:26 final size:26
Alignment explanation
Indices: 51962421--51962500 Score: 79
Period size: 26 Copynumber: 3.1 Consensus size: 26
51962411 GCCAACACAC
* **
51962421 CAATATCGCAGCTGAGCTGCCAGTAA
1 CAATAACGCAGCAAAGCTGCCAGTAA
* **
51962447 TAATGGCGCAGCAAAGCTGCCAGTAA
1 CAATAACGCAGCAAAGCTGCCAGTAA
* * *
51962473 CAATAACGCATCAAGGCTTCCAGTAA
1 CAATAACGCAGCAAAGCTGCCAGTAA
51962499 CA
1 CA
51962501 GTATATGTGG
Statistics
Matches: 43, Mismatches: 11, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
26 43 1.00
ACGTcount: A:0.35, C:0.26, G:0.21, T:0.17
Consensus pattern (26 bp):
CAATAACGCAGCAAAGCTGCCAGTAA
Found at i:51962716 original size:18 final size:18
Alignment explanation
Indices: 51962695--51962731 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
51962685 CACCCTTCGG
51962695 AGGTATTTCGATAATTTT
1 AGGTATTTCGATAATTTT
51962713 AGGTATTTCGATAATTTT
1 AGGTATTTCGATAATTTT
51962731 A
1 A
51962732 CCTTTCGAGG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.30, C:0.05, G:0.16, T:0.49
Consensus pattern (18 bp):
AGGTATTTCGATAATTTT
Found at i:51962852 original size:81 final size:81
Alignment explanation
Indices: 51962714--51962895 Score: 233
Period size: 81 Copynumber: 2.2 Consensus size: 81
51962704 GATAATTTTA
* * * ***
51962714 GGTATTTCGATAATTTTACCTTTCGAGGGTATTTCAATAATTTTACCCTTTGGGGGTATTTCAGT
1 GGTATTTCGGTAATTTTACCTTTCAAGAGTATTTCAATAATTTTACCCTTCAAGGGTATTTC-GT
*
51962779 GAA-TTTATCCATCAAG
65 GAATTTTACCCATCAAG
*
51962795 GGTATTTTGGTAATTTTACTCTTT-AAGAGTATTTCAATAATTTTACCCTTCAAGGGTATTTCGT
1 GGTATTTCGGTAATTTTAC-CTTTCAAGAGTATTTCAATAATTTTACCCTTCAAGGGTATTTCGT
* *
51962859 TAATTTTACCCATCGAG
65 GAATTTTACCCATCAAG
*
51962876 GGTATTTCGGCAATTTTACC
1 GGTATTTCGGTAATTTTACC
51962896 CATCGAGTCG
Statistics
Matches: 87, Mismatches: 12, Indels: 5
0.84 0.12 0.05
Matches are distributed among these distances:
80 5 0.06
81 78 0.90
82 4 0.05
ACGTcount: A:0.25, C:0.15, G:0.17, T:0.43
Consensus pattern (81 bp):
GGTATTTCGGTAATTTTACCTTTCAAGAGTATTTCAATAATTTTACCCTTCAAGGGTATTTCGTG
AATTTTACCCATCAAG
Found at i:51962896 original size:27 final size:27
Alignment explanation
Indices: 51962714--51962902 Score: 166
Period size: 27 Copynumber: 7.0 Consensus size: 27
51962704 GATAATTTTA
*
51962714 GGTATTTCGATAATTTTACCTTTCGAG
1 GGTATTTCGATAATTTTACCCTTCGAG
* * *
51962741 GGTATTTCAATAATTTTACCCTTTGGG
1 GGTATTTCGATAATTTTACCCTTCGAG
* * *
51962768 GGTATTTC-AGTGAA-TTTATCCATCAAG
1 GGTATTTCGA-T-AATTTTACCCTTCGAG
* * * **
51962795 GGTATTTTGGTAATTTTACTCTTTAAG
1 GGTATTTCGATAATTTTACCCTTCGAG
* * *
51962822 AGTATTTCAATAATTTTACCCTTCAAG
1 GGTATTTCGATAATTTTACCCTTCGAG
* *
51962849 GGTATTTCGTTAATTTTACCCATCGAG
1 GGTATTTCGATAATTTTACCCTTCGAG
** *
51962876 GGTATTTCGGCAATTTTACCCATCGAG
1 GGTATTTCGATAATTTTACCCTTCGAG
51962903 TCGCAAGTTG
Statistics
Matches: 130, Mismatches: 28, Indels: 8
0.78 0.17 0.05
Matches are distributed among these distances:
26 3 0.02
27 125 0.96
28 2 0.02
ACGTcount: A:0.25, C:0.16, G:0.17, T:0.42
Consensus pattern (27 bp):
GGTATTTCGATAATTTTACCCTTCGAG
Found at i:51967756 original size:15 final size:15
Alignment explanation
Indices: 51967736--51967764 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
51967726 TATTTTTTAA
51967736 ATTATTTTTATTTTC
1 ATTATTTTTATTTTC
51967751 ATTATTTTTATTTT
1 ATTATTTTTATTTT
51967765 TTTAGATTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.21, C:0.03, G:0.00, T:0.76
Consensus pattern (15 bp):
ATTATTTTTATTTTC
Found at i:51971073 original size:13 final size:12
Alignment explanation
Indices: 51971048--51971077 Score: 51
Period size: 13 Copynumber: 2.4 Consensus size: 12
51971038 AAATCCATTT
51971048 TTATTTTTTTAA
1 TTATTTTTTTAA
51971060 TTATTTTATTTAA
1 TTATTTT-TTTAA
51971073 TTATT
1 TTATT
51971078 CAATACACCA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 7 0.41
13 10 0.59
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (12 bp):
TTATTTTTTTAA
Found at i:51983790 original size:23 final size:24
Alignment explanation
Indices: 51983740--51983788 Score: 66
Period size: 22 Copynumber: 2.1 Consensus size: 24
51983730 TACTTATCAA
*
51983740 TTTGTTTGGATTTAATTCATTACT
1 TTTGTTTGGATTGAATTCATTACT
*
51983764 TTTGTTT-GATTGAA-TCTTTACT
1 TTTGTTTGGATTGAATTCATTACT
51983786 TTT
1 TTT
51983789 TGAATGACTC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
22 10 0.43
23 6 0.26
24 7 0.30
ACGTcount: A:0.18, C:0.08, G:0.12, T:0.61
Consensus pattern (24 bp):
TTTGTTTGGATTGAATTCATTACT
Found at i:51984492 original size:19 final size:19
Alignment explanation
Indices: 51984468--51984521 Score: 54
Period size: 19 Copynumber: 2.7 Consensus size: 19
51984458 ATATTCCTTT
51984468 TTCCCTTCCCAATCCCTAA
1 TTCCCTTCCCAATCCCTAA
* * * *
51984487 TTCCCTTTCCGATCTCTAT
1 TTCCCTTCCCAATCCCTAA
51984506 TTCCCCTTCCCTAATC
1 TT-CCCTTCCC-AATC
51984522 TTTAATGACT
Statistics
Matches: 27, Mismatches: 6, Indels: 2
0.77 0.17 0.06
Matches are distributed among these distances:
19 17 0.63
20 7 0.26
21 3 0.11
ACGTcount: A:0.15, C:0.44, G:0.02, T:0.39
Consensus pattern (19 bp):
TTCCCTTCCCAATCCCTAA
Found at i:51985755 original size:17 final size:17
Alignment explanation
Indices: 51985733--51985770 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
51985723 AATTTTCAAG
51985733 AATTCTAAAAAATTAAA
1 AATTCTAAAAAATTAAA
**
51985750 AATTCTTTAAAATTAAA
1 AATTCTAAAAAATTAAA
51985767 AATT
1 AATT
51985771 AGAAAAAATA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.58, C:0.05, G:0.00, T:0.37
Consensus pattern (17 bp):
AATTCTAAAAAATTAAA
Found at i:51990191 original size:41 final size:41
Alignment explanation
Indices: 51990134--51990367 Score: 387
Period size: 41 Copynumber: 5.7 Consensus size: 41
51990124 CAAGCTTAGT
*
51990134 GCCTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGCTATAA
1 GCCTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGTTATAA
* * *
51990175 GCCTAGCAGGCTAAGTGCTGGTGAACTGAATCAGGTTAAAA
1 GCCTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGTTATAA
* *
51990216 GCCTAGCAGGCTAAGTGCCGATGATCTGAATCAGGCTATAA
1 GCCTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGTTATAA
*
51990257 GCCTAGCAGGCTAAGTGCCGGTGAACTGAATCAGGTTATAA
1 GCCTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGTTATAA
*
51990298 GCCTAGCAGGCTAAGTGCCAGTGATCTGAATCAGGTTATAA
1 GCCTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGTTATAA
51990339 GCCTAGCAGGCTAAGTGCCGGTGAATCTG
1 GCCTAGCAGGCTAAGTGCCGGTG-ATCTG
51990368 TTTAAATTAA
Statistics
Matches: 177, Mismatches: 15, Indels: 1
0.92 0.08 0.01
Matches are distributed among these distances:
41 172 0.97
42 5 0.03
ACGTcount: A:0.28, C:0.21, G:0.29, T:0.22
Consensus pattern (41 bp):
GCCTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGTTATAA
Found at i:51992472 original size:43 final size:42
Alignment explanation
Indices: 51992378--51992541 Score: 190
Period size: 43 Copynumber: 3.9 Consensus size: 42
51992368 TAGGGTTACC
51992378 GAGATTACGTGTAAGACCATATCTGGGATATGGCATCGATAT
1 GAGATTACGTGTAAGACCATATCTGGGATATGGCATCGATAT
* *
51992420 GAGACTT-CGTGTAAGACCATTTCTGGGACATTGGCATCGATAT
1 GAGA-TTACGTGTAAGACCATATCTGGGATA-TGGCATCGATAT
* * * *
51992463 GTGATTTCGTGTAAGACCAT-TGCT-GGATTATTAGCATCGATAC
1 GAGATTACGTGTAAGACCATAT-CTGGGA-TA-TGGCATCGATAT
* *
51992506 AAGATTACATGTAAGACCATATCTGGGATATGGCAT
1 GAGATTACGTGTAAGACCATATCTGGGATATGGCAT
51992542 TGTTACGGTA
Statistics
Matches: 104, Mismatches: 11, Indels: 14
0.81 0.09 0.11
Matches are distributed among these distances:
42 36 0.35
43 64 0.62
44 4 0.04
ACGTcount: A:0.29, C:0.16, G:0.24, T:0.30
Consensus pattern (42 bp):
GAGATTACGTGTAAGACCATATCTGGGATATGGCATCGATAT
Found at i:52005376 original size:24 final size:24
Alignment explanation
Indices: 52005349--52005394 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
52005339 TAAATTTTTT
52005349 TATGATT-AAATTATTGTTATTAAG
1 TATGATTGAAATTATTG-TATTAAG
*
52005373 TATGCTTGAAATTATTGTATTA
1 TATGATTGAAATTATTGTATTA
52005395 TATCTTTTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
24 11 0.55
25 9 0.45
ACGTcount: A:0.35, C:0.02, G:0.13, T:0.50
Consensus pattern (24 bp):
TATGATTGAAATTATTGTATTAAG
Found at i:52020158 original size:30 final size:30
Alignment explanation
Indices: 52020124--52020182 Score: 91
Period size: 30 Copynumber: 2.0 Consensus size: 30
52020114 CTTAACAAGT
*
52020124 AAATGCCTCTAAAATAATAATAAAATTAAA
1 AAATGCCTCTAAAATAATAACAAAATTAAA
* *
52020154 AAATGTCTTTAAAATAATAACAAAATTAA
1 AAATGCCTCTAAAATAATAACAAAATTAA
52020183 CAATAAAATA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.59, C:0.08, G:0.03, T:0.29
Consensus pattern (30 bp):
AAATGCCTCTAAAATAATAACAAAATTAAA
Found at i:52025051 original size:63 final size:63
Alignment explanation
Indices: 52024947--52025118 Score: 200
Period size: 63 Copynumber: 2.7 Consensus size: 63
52024937 TTTTTTTTGT
* * * * * ****
52024947 CACAAGCATCACAACACGCACACTTATTCCCTGCATTAACACATTCAGCTTTGGTTTATTTTA
1 CACAAGCACCACAACACACACAATCATTCCCTGCATCAACACATTCAGCACCAGTTTATTTTA
* * * *
52025010 CACAAGTACCACAACATACACAATCATTCCTTGCATCAACACACTCAGCACCAGTTTATTTTA
1 CACAAGCACCACAACACACACAATCATTCCCTGCATCAACACATTCAGCACCAGTTTATTTTA
* * *
52025073 CACAAGCACCACAGCACGCGCAATCATTCCCTGCATCAACACATTC
1 CACAAGCACCACAACACACACAATCATTCCCTGCATCAACACATTC
52025119 TTTAGTGATA
Statistics
Matches: 89, Mismatches: 20, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
63 89 1.00
ACGTcount: A:0.33, C:0.33, G:0.09, T:0.25
Consensus pattern (63 bp):
CACAAGCACCACAACACACACAATCATTCCCTGCATCAACACATTCAGCACCAGTTTATTTTA
Found at i:52028457 original size:6 final size:6
Alignment explanation
Indices: 52028448--52028473 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
52028438 TTAATATAAA
52028448 ATAATT ATAATT ATAATT ATAATT AT
1 ATAATT ATAATT ATAATT ATAATT AT
52028474 TATATATTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (6 bp):
ATAATT
Found at i:52028785 original size:26 final size:26
Alignment explanation
Indices: 52028735--52028786 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 26
52028725 GATGTTTAAT
*
52028735 TATTATTTGATATTCAATAGTTTTAC
1 TATTATTTGATATTCAATAATTTTAC
*
52028761 TATTATTTGAT-TTTAATAATATTTAC
1 TATTATTTGATATTCAATAAT-TTTAC
52028787 ATAATTGTGA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
25 7 0.30
26 16 0.70
ACGTcount: A:0.33, C:0.06, G:0.06, T:0.56
Consensus pattern (26 bp):
TATTATTTGATATTCAATAATTTTAC
Found at i:52035814 original size:39 final size:40
Alignment explanation
Indices: 52035762--52035849 Score: 160
Period size: 39 Copynumber: 2.2 Consensus size: 40
52035752 ATTAAAATAT
52035762 ATATTTAATATATTCATTAAAAATAT-TTTTTCAAAAAAA
1 ATATTTAATATATTCATTAAAAATATGTTTTTCAAAAAAA
52035801 ATATTTAATATATTCATTAAAAATATGTTTTTCAAAAAAA
1 ATATTTAATATATTCATTAAAAATATGTTTTTCAAAAAAA
52035841 ATTATTTAA
1 A-TATTTAA
52035850 AAATATATTT
Statistics
Matches: 47, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
39 26 0.55
40 14 0.30
41 7 0.15
ACGTcount: A:0.50, C:0.05, G:0.01, T:0.44
Consensus pattern (40 bp):
ATATTTAATATATTCATTAAAAATATGTTTTTCAAAAAAA
Found at i:52035862 original size:41 final size:38
Alignment explanation
Indices: 52035762--52035870 Score: 130
Period size: 39 Copynumber: 2.7 Consensus size: 38
52035752 ATTAAAATAT
*
52035762 ATATTTAATATATTCATTAAAAATATTTTTTCAAAAAAA
1 ATATTTAAAATATT-ATTAAAAATATTTTTTCAAAAAAA
*
52035801 ATATTTAATATATTCATTAAAAATATGTTTTTCAAAAAAA
1 ATATTTAAAATATT-ATTAAAAATAT-TTTTTCAAAAAAA
52035841 ATTATTTAAAA-ATATATTTAAAAATTATTT
1 A-TATTTAAAATAT-TA-TTAAAAA-TATTT
52035871 AAATATATAT
Statistics
Matches: 64, Mismatches: 1, Indels: 8
0.88 0.01 0.11
Matches are distributed among these distances:
39 26 0.41
40 17 0.27
41 18 0.28
42 3 0.05
ACGTcount: A:0.50, C:0.04, G:0.01, T:0.45
Consensus pattern (38 bp):
ATATTTAAAATATTATTAAAAATATTTTTTCAAAAAAA
Found at i:52035863 original size:23 final size:23
Alignment explanation
Indices: 52035837--52035882 Score: 83
Period size: 23 Copynumber: 2.0 Consensus size: 23
52035827 GTTTTTCAAA
52035837 AAAAATTATTTAAAAATATATTT
1 AAAAATTATTTAAAAATATATTT
*
52035860 AAAAATTATTTAAATATATATTT
1 AAAAATTATTTAAAAATATATTT
52035883 CTTTCCCAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (23 bp):
AAAAATTATTTAAAAATATATTT
Found at i:52035881 original size:12 final size:12
Alignment explanation
Indices: 52035837--52035882 Score: 69
Period size: 11 Copynumber: 4.0 Consensus size: 12
52035827 GTTTTTCAAA
52035837 AAAAAT-TATTT
1 AAAAATATATTT
52035848 AAAAATATATTT
1 AAAAATATATTT
52035860 AAAAAT-TATTT
1 AAAAATATATTT
*
52035871 AAATATATATTT
1 AAAAATATATTT
52035883 CTTTCCCAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
11 16 0.50
12 16 0.50
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (12 bp):
AAAAATATATTT
Found at i:52036200 original size:9 final size:10
Alignment explanation
Indices: 52036169--52036198 Score: 60
Period size: 10 Copynumber: 3.0 Consensus size: 10
52036159 GTTTTATTTC
52036169 TAAAAATATT
1 TAAAAATATT
52036179 TAAAAATATT
1 TAAAAATATT
52036189 TAAAAATATT
1 TAAAAATATT
52036199 AATATAAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (10 bp):
TAAAAATATT
Found at i:52036213 original size:21 final size:22
Alignment explanation
Indices: 52036169--52036228 Score: 56
Period size: 21 Copynumber: 2.9 Consensus size: 22
52036159 GTTTTATTTC
52036169 TAAAAATATT--TA-AAAATATT
1 TAAAAATATTAATATAAAATA-T
52036189 TAAAAATATTAATATAAAATA-
1 TAAAAATATTAATATAAAATAT
** *
52036210 TAAATTTATAAATATAAAA
1 TAAAAATATTAATATAAAA
52036229 AAATGTAAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
20 10 0.29
21 16 0.47
22 2 0.06
23 6 0.18
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (22 bp):
TAAAAATATTAATATAAAATAT
Found at i:52036241 original size:31 final size:32
Alignment explanation
Indices: 52036203--52036264 Score: 108
Period size: 31 Copynumber: 2.0 Consensus size: 32
52036193 AATATTAATA
52036203 TAAAATATAAATTTATAAATATAAAA-AAATG
1 TAAAATATAAATTTATAAATATAAAATAAATG
*
52036234 TAAAATATAAATTTATAGATATAAAATAAAT
1 TAAAATATAAATTTATAAATATAAAATAAAT
52036265 TCAATTAAAC
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
31 25 0.86
32 4 0.14
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.34
Consensus pattern (32 bp):
TAAAATATAAATTTATAAATATAAAATAAATG
Found at i:52041159 original size:10 final size:10
Alignment explanation
Indices: 52041144--52041175 Score: 57
Period size: 10 Copynumber: 3.3 Consensus size: 10
52041134 CAATTTAAAC
52041144 AAAAAAAA-A
1 AAAAAAAAGA
52041153 AAAAAAAAGA
1 AAAAAAAAGA
52041163 AAAAAAAAGA
1 AAAAAAAAGA
52041173 AAA
1 AAA
52041176 GAAGAAAAGG
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
9 8 0.36
10 14 0.64
ACGTcount: A:0.94, C:0.00, G:0.06, T:0.00
Consensus pattern (10 bp):
AAAAAAAAGA
Found at i:52041167 original size:15 final size:15
Alignment explanation
Indices: 52041147--52041183 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
52041137 TTTAAACAAA
52041147 AAAAAAAAAAAAAAG
1 AAAAAAAAAAAAAAG
*
52041162 AAAAAAAAAGAAAAG
1 AAAAAAAAAAAAAAG
*
52041177 AAGAAAA
1 AAAAAAA
52041184 GGCTGCTTGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.89, C:0.00, G:0.11, T:0.00
Consensus pattern (15 bp):
AAAAAAAAAAAAAAG
Found at i:52041167 original size:18 final size:18
Alignment explanation
Indices: 52041144--52041183 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
52041134 CAATTTAAAC
52041144 AAAAAAAAAAAAAAAAAG
1 AAAAAAAAAAAAAAAAAG
* *
52041162 AAAAAAAAAGAAAAGAAG
1 AAAAAAAAAAAAAAAAAG
52041180 AAAA
1 AAAA
52041184 GGCTGCTTGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.90, C:0.00, G:0.10, T:0.00
Consensus pattern (18 bp):
AAAAAAAAAAAAAAAAAG
Found at i:52042332 original size:16 final size:16
Alignment explanation
Indices: 52042313--52042355 Score: 68
Period size: 16 Copynumber: 2.7 Consensus size: 16
52042303 ATCTTTCTAG
52042313 TTTTCTATCCATTCAA
1 TTTTCTATCCATTCAA
*
52042329 TTTTCCATCCATTCAA
1 TTTTCTATCCATTCAA
*
52042345 TTTTCTTTCCA
1 TTTTCTATCCA
52042356 CCCTACCGAG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.21, C:0.28, G:0.00, T:0.51
Consensus pattern (16 bp):
TTTTCTATCCATTCAA
Found at i:52045729 original size:20 final size:20
Alignment explanation
Indices: 52045701--52045738 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
52045691 GGCTGTTACA
*
52045701 TCCAGTTCTACCAATACAAG
1 TCCACTTCTACCAATACAAG
*
52045721 TCCACTTCTACCCATACA
1 TCCACTTCTACCAATACA
52045739 TCTTGTGAGT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.32, C:0.37, G:0.05, T:0.26
Consensus pattern (20 bp):
TCCACTTCTACCAATACAAG
Found at i:52047694 original size:11 final size:10
Alignment explanation
Indices: 52047677--52047701 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
52047667 TTTAGTTTTG
52047677 TAAAAAAAAA
1 TAAAAAAAAA
52047687 TAAAAAAAAA
1 TAAAAAAAAA
52047697 TAAAA
1 TAAAA
52047702 TGGACTCTTT
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:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (10 bp):
TAAAAAAAAA
Found at i:52049576 original size:15 final size:15
Alignment explanation
Indices: 52049556--52049609 Score: 65
Period size: 15 Copynumber: 3.6 Consensus size: 15
52049546 GCAAAAAACT
52049556 GCTGGTTCTGCTACC
1 GCTGGTTCTGCTACC
* *
52049571 GCTGGTTTTGCTATC
1 GCTGGTTCTGCTACC
*
52049586 GCTGGTT-TAGCCACC
1 GCTGGTTCT-GCTACC
52049601 GCTGGTTCT
1 GCTGGTTCT
52049610 TCTAATGACC
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
14 1 0.03
15 31 0.94
16 1 0.03
ACGTcount: A:0.07, C:0.28, G:0.28, T:0.37
Consensus pattern (15 bp):
GCTGGTTCTGCTACC
Found at i:52058687 original size:25 final size:25
Alignment explanation
Indices: 52058659--52058711 Score: 61
Period size: 25 Copynumber: 2.1 Consensus size: 25
52058649 AACGCACATC
* **
52058659 TTCTACTCTGTTCTGTTTTACTATA
1 TTCTACTCTATTCTACTTTACTATA
* *
52058684 TTCTATTCTATTCTACTTTACTCTA
1 TTCTACTCTATTCTACTTTACTATA
52058709 TTC
1 TTC
52058712 AGTTCAGTTC
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.17, C:0.23, G:0.04, T:0.57
Consensus pattern (25 bp):
TTCTACTCTATTCTACTTTACTATA
Found at i:52064050 original size:69 final size:69
Alignment explanation
Indices: 52063972--52064311 Score: 360
Period size: 69 Copynumber: 4.9 Consensus size: 69
52063962 ATGCTCTCAA
* * * * *
52063972 CTATAATATTAAGGTTCGTAGGCAAAGAGCTGAAACCTTCAAAATAGTTAGCAAGAGCAAAGCTC
1 CTATCATATTAAGGTTCGCAGGCAAAGAGCTGCAACCTCCAAAATAATTAGCAAGAGCAAAGCTC
*
52064037 CCAA
66 CCAG
* * * * * *
52064041 CTATTATATTGAGGTTCGCAGGCAAAGAGTTGCAACCTCCAAAACAATTAGCAAGAGAAAATCTC
1 CTATCATATTAAGGTTCGCAGGCAAAGAGCTGCAACCTCCAAAATAATTAGCAAGAGCAAAGCTC
*
52064106 CTAG
66 CCAG
** * * * * * * *
52064110 CCGTCATATGAAGGTTCGCAGGCAAAGAGCCGCAATCTCCAAAACAATTAGCAAGAGTAAAGGTG
1 CTATCATATTAAGGTTCGCAGGCAAAGAGCTGCAACCTCCAAAATAATTAGCAAGAGCAAAGCTC
52064175 CCAG
66 CCAG
* *
52064179 CTTTCATATTAAGGTTCACAGGCAAAGAG-TCGCAACCTCCAAAATAATTAGCGAA-AGCAAAGC
1 CTATCATATTAAGGTTCGCAGGCAAAGAGCT-GCAACCTCCAAAATAATTAGC-AAGAGCAAAGC
52064242 TCCCAG
64 TCCCAG
* * ** ** * *
52064248 CTATCATATTAAGATTCACAGGTGAAGAGCCACAACCTCCAAAATAGTTAGCTAGAGCAAAGCT
1 CTATCATATTAAGGTTCGCAGGCAAAGAGCTGCAACCTCCAAAATAATTAGCAAGAGCAAAGCT
52064312 GTCAATTGTA
Statistics
Matches: 224, Mismatches: 43, Indels: 8
0.81 0.16 0.03
Matches are distributed among these distances:
68 1 0.00
69 221 0.99
70 2 0.01
ACGTcount: A:0.38, C:0.22, G:0.19, T:0.21
Consensus pattern (69 bp):
CTATCATATTAAGGTTCGCAGGCAAAGAGCTGCAACCTCCAAAATAATTAGCAAGAGCAAAGCTC
CCAG
Found at i:52078583 original size:12 final size:11
Alignment explanation
Indices: 52078553--52078604 Score: 54
Period size: 11 Copynumber: 4.8 Consensus size: 11
52078543 AATTTTCAAA
52078553 AAAAAAAAATC
1 AAAAAAAAATC
*
52078564 AATCAAAAAATC
1 AA-AAAAAAATC
* *
52078576 CAAAAAAATTC
1 AAAAAAAAATC
52078587 --AAAAAAATC
1 AAAAAAAAATC
52078596 AAAAAAAAA
1 AAAAAAAAA
52078605 AGAAAAAAGA
Statistics
Matches: 33, Mismatches: 5, Indels: 6
0.75 0.11 0.14
Matches are distributed among these distances:
9 8 0.24
11 16 0.48
12 9 0.27
ACGTcount: A:0.77, C:0.12, G:0.00, T:0.12
Consensus pattern (11 bp):
AAAAAAAAATC
Found at i:52078603 original size:10 final size:10
Alignment explanation
Indices: 52078554--52078603 Score: 57
Period size: 10 Copynumber: 4.8 Consensus size: 10
52078544 ATTTTCAAAA
52078554 AAAAAAAATC
1 AAAAAAAATC
52078564 AATCAAAAAATCC
1 AA--AAAAAAT-C
*
52078577 AAAAAAATTC
1 AAAAAAAATC
52078587 -AAAAAAATC
1 AAAAAAAATC
52078596 AAAAAAAA
1 AAAAAAAA
52078604 AAGAAAAAAG
Statistics
Matches: 34, Mismatches: 2, Indels: 8
0.77 0.05 0.18
Matches are distributed among these distances:
9 8 0.24
10 10 0.29
11 6 0.18
12 7 0.21
13 3 0.09
ACGTcount: A:0.76, C:0.12, G:0.00, T:0.12
Consensus pattern (10 bp):
AAAAAAAATC
Found at i:52078610 original size:20 final size:20
Alignment explanation
Indices: 52078568--52078612 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
52078558 AAAATCAATC
* **
52078568 AAAAAATCCAAAAAAATTCA
1 AAAAAATCAAAAAAAAAACA
*
52078588 AAAAAATCAAAAAAAAAAGA
1 AAAAAATCAAAAAAAAAACA
52078608 AAAAA
1 AAAAA
52078613 GAAAAAAAGA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.80, C:0.09, G:0.02, T:0.09
Consensus pattern (20 bp):
AAAAAATCAAAAAAAAAACA
Found at i:52079558 original size:15 final size:15
Alignment explanation
Indices: 52079531--52079568 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
52079521 TTGAGTCAGA
52079531 AAAAATATGAAAAA-T
1 AAAAA-ATGAAAAAGT
*
52079546 GAAAAATGAAAAAGT
1 AAAAAATGAAAAAGT
52079561 AAAAAATG
1 AAAAAATG
52079569 GATAGGCTAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
14 8 0.40
15 12 0.60
ACGTcount: A:0.71, C:0.00, G:0.13, T:0.16
Consensus pattern (15 bp):
AAAAAATGAAAAAGT
Found at i:52080844 original size:44 final size:44
Alignment explanation
Indices: 52080777--52081023 Score: 284
Period size: 44 Copynumber: 5.7 Consensus size: 44
52080767 GATGAAACTA
*
52080777 TAAGTCCTAGCTCCCTGTACAGCAGTGGAATAGGCGGAAGATTG
1 TAAGTCCTAGCTCCCTGAACAGCAGTGGAATAGGCGGAAGATTG
* * * * * *
52080821 TAAATCCTAGCTTCCTGACCAGCAGCGGAATAGGTGGAAGA--C
1 TAAGTCCTAGCTCCCTGAACAGCAGTGGAATAGGCGGAAGATTG
* * * * *
52080863 TATGTCCTAACTCCCTAAACAGCAGTGGAATATGCAGAAGATTG
1 TAAGTCCTAGCTCCCTGAACAGCAGTGGAATAGGCGGAAGATTG
* * * ** * *
52080907 TAAATCCTAGCTCTCTGACCAGCAGCAGAATAGGTGGAAGACTG
1 TAAGTCCTAGCTCCCTGAACAGCAGTGGAATAGGCGGAAGATTG
52080951 TAAGTCCTAGCTCCCTGAACAGCAGTGGAATAGG-GAGAAGATTG
1 TAAGTCCTAGCTCCCTGAACAGCAGTGGAATAGGCG-GAAGATTG
*
52080995 TAAGTCCTAGCTCCCTGAGCAGCAGTGGA
1 TAAGTCCTAGCTCCCTGAACAGCAGTGGA
52081024 GCAGGCTGAA
Statistics
Matches: 163, Mismatches: 37, Indels: 6
0.79 0.18 0.03
Matches are distributed among these distances:
42 31 0.19
43 1 0.01
44 131 0.80
ACGTcount: A:0.30, C:0.22, G:0.26, T:0.21
Consensus pattern (44 bp):
TAAGTCCTAGCTCCCTGAACAGCAGTGGAATAGGCGGAAGATTG
Found at i:52080925 original size:86 final size:87
Alignment explanation
Indices: 52080777--52081019 Score: 355
Period size: 86 Copynumber: 2.8 Consensus size: 87
52080767 GATGAAACTA
* *
52080777 TAAGTCCTAGCTCCCTGTACAGCAGTGGAATAGGCGGAAGATTGTAAATCCTAGCT-TCCTGACC
1 TAAGTCCTAGCTCCCTGAACAGCAGTGGAATAGGCAGAAGATTGTAAATCCTAGCTCT-CTGACC
*
52080841 AGCAGCGGAATAGGTGGAAGAC-
65 AGCAGCAGAATAGGTGGAAGACG
* * * *
52080863 TATGTCCTAACTCCCTAAACAGCAGTGGAATATGCAGAAGATTGTAAATCCTAGCTCTCTGACCA
1 TAAGTCCTAGCTCCCTGAACAGCAGTGGAATAGGCAGAAGATTGTAAATCCTAGCTCTCTGACCA
52080928 GCAGCAGAATAGGTGGAAGACTG
66 GCAGCAGAATAGGTGGAAGAC-G
* * * *
52080951 TAAGTCCTAGCTCCCTGAACAGCAGTGGAATAGGGAGAAGATTGTAAGTCCTAGCTCCCTGAGCA
1 TAAGTCCTAGCTCCCTGAACAGCAGTGGAATAGGCAGAAGATTGTAAATCCTAGCTCTCTGACCA
52081016 GCAG
66 GCAG
52081020 TGGAGCAGGC
Statistics
Matches: 139, Mismatches: 15, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
86 77 0.55
87 1 0.01
88 61 0.44
ACGTcount: A:0.30, C:0.22, G:0.26, T:0.21
Consensus pattern (87 bp):
TAAGTCCTAGCTCCCTGAACAGCAGTGGAATAGGCAGAAGATTGTAAATCCTAGCTCTCTGACCA
GCAGCAGAATAGGTGGAAGACG
Found at i:52081136 original size:44 final size:44
Alignment explanation
Indices: 52081088--52081226 Score: 126
Period size: 44 Copynumber: 3.2 Consensus size: 44
52081078 AGACACAAGC
*
52081088 CTTGCCTCCCTCGGTTGTAATGGAGCAGGTTGAAGATAGCAGAT
1 CTTGCCTCCCTCGATTGTAATGGAGCAGGTTGAAGATAGCAGAT
* * * * *
52081132 CTTGCCTTCCT-GCATTG-ACA-GCGAAGCAGATCGAAGACA-CA-AGC
1 CTTGCCTCCCTCG-ATTGTA-ATG-G-AGCAGGTTGAAGATAGCAGA-T
* *
52081176 CTTGTCTCCCTCGATTGTAGTGGAGCAGGTTGAAGATAGCAGAT
1 CTTGCCTCCCTCGATTGTAATGGAGCAGGTTGAAGATAGCAGAT
52081220 CTTGCCT
1 CTTGCCT
52081227 TCCTACATCA
Statistics
Matches: 71, Mismatches: 14, Indels: 20
0.68 0.13 0.19
Matches are distributed among these distances:
43 16 0.23
44 39 0.55
45 16 0.23
ACGTcount: A:0.24, C:0.24, G:0.27, T:0.26
Consensus pattern (44 bp):
CTTGCCTCCCTCGATTGTAATGGAGCAGGTTGAAGATAGCAGAT
Found at i:52081159 original size:88 final size:88
Alignment explanation
Indices: 52081018--52081343 Score: 467
Period size: 88 Copynumber: 3.7 Consensus size: 88
52081008 CCTGAGCAGC
* * * *
52081018 AGTGGAGCAGGCTGAAGATAACAGATCTTGCCTTCCTAG-ATCGACAACAAAGCAGATCGAAGAC
1 AGTGGAGCAGGTTGAAGATAGCAGATCTTGCCTTCCT-GCATCGACAGCGAAGCAGATCGAAGAC
52081082 ACAAGCCTTGCCTCCCTCGGTTGT
65 ACAAGCCTTGCCTCCCTCGGTTGT
* *
52081106 AATGGAGCAGGTTGAAGATAGCAGATCTTGCCTTCCTGCATTGACAGCGAAGCAGATCGAAGACA
1 AGTGGAGCAGGTTGAAGATAGCAGATCTTGCCTTCCTGCATCGACAGCGAAGCAGATCGAAGACA
* *
52081171 CAAGCCTTGTCTCCCTCGATTGT
66 CAAGCCTTGCCTCCCTCGGTTGT
* * * * *
52081194 AGTGGAGCAGGTTGAAGATAGCAGATCTTGCCTTCCTACATCAACGGCGAAGCAAATCTAAGACA
1 AGTGGAGCAGGTTGAAGATAGCAGATCTTGCCTTCCTGCATCGACAGCGAAGCAGATCGAAGACA
52081259 CAAGCCTTGCCTCCCTCGGTTGT
66 CAAGCCTTGCCTCCCTCGGTTGT
* * * *
52081282 AGTGGAGCTGGTTGAAGATAGCATG-TCTTACCTTCCTGCATCGACAGTGAAGTAGATCGAAG
1 AGTGGAGCAGGTTGAAGATAGCA-GATCTTGCCTTCCTGCATCGACAGCGAAGCAGATCGAAG
52081344 CCAATGGTCC
Statistics
Matches: 210, Mismatches: 26, Indels: 4
0.88 0.11 0.02
Matches are distributed among these distances:
87 1 0.00
88 208 0.99
89 1 0.00
ACGTcount: A:0.28, C:0.24, G:0.25, T:0.23
Consensus pattern (88 bp):
AGTGGAGCAGGTTGAAGATAGCAGATCTTGCCTTCCTGCATCGACAGCGAAGCAGATCGAAGACA
CAAGCCTTGCCTCCCTCGGTTGT
Found at i:52086656 original size:20 final size:20
Alignment explanation
Indices: 52086633--52086673 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
52086623 TTTGAATTGT
* *
52086633 TGCTAAACTATTTCATTGCA
1 TGCTAAACCATCTCATTGCA
52086653 TGCTAAACCATCTCATTGCA
1 TGCTAAACCATCTCATTGCA
52086673 T
1 T
52086674 TTTTCATTGC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.29, C:0.24, G:0.10, T:0.37
Consensus pattern (20 bp):
TGCTAAACCATCTCATTGCA
Found at i:52088104 original size:56 final size:60
Alignment explanation
Indices: 52088042--52088164 Score: 173
Period size: 65 Copynumber: 2.0 Consensus size: 60
52088032 GTTTGAGAAT
52088042 TGTCCATC-AAA-TCTT-GAG-TTTGTTTATTATGTAGAAAATCAGAACCAGAATATAAA
1 TGTCCATCAAAATTCTTAGAGTTTTGTTTATTATGTAGAAAATCAGAACCAGAATATAAA
52088098 TGTCCATCAAAAATCTTTTCTTAGAGTTTTGTTTATTATGTAGAAAATCAGAACCAGAATATAAA
1 TGTCCATC-AAAA----TTCTTAGAGTTTTGTTTATTATGTAGAAAATCAGAACCAGAATATAAA
52088163 TG
1 TG
52088165 GACAAGGACC
Statistics
Matches: 58, Mismatches: 0, Indels: 9
0.87 0.00 0.13
Matches are distributed among these distances:
56 8 0.14
58 3 0.05
63 4 0.07
64 3 0.05
65 40 0.69
ACGTcount: A:0.38, C:0.12, G:0.14, T:0.36
Consensus pattern (60 bp):
TGTCCATCAAAATTCTTAGAGTTTTGTTTATTATGTAGAAAATCAGAACCAGAATATAAA
Found at i:52093905 original size:11 final size:13
Alignment explanation
Indices: 52093885--52093916 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
52093875 AATAAATTAA
52093885 TAAAATATCAT-T
1 TAAAATATCATAT
52093897 TAAAA-ATCATAT
1 TAAAATATCATAT
52093909 TAAAATAT
1 TAAAATAT
52093917 TAATAAACTA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
11 5 0.28
12 11 0.61
13 2 0.11
ACGTcount: A:0.56, C:0.06, G:0.00, T:0.38
Consensus pattern (13 bp):
TAAAATATCATAT
Found at i:52102298 original size:285 final size:285
Alignment explanation
Indices: 52101778--52102313 Score: 952
Period size: 285 Copynumber: 1.9 Consensus size: 285
52101768 TCCCATTCAC
*
52101778 CACATTAACTCTCCTTCTCTCACCTTCCTTGTTTCTCCATATGGCAAGTCACAGTGTAATAATAG
1 CACATTAACTCTCCTTCTCTCACCTTCCTTATTTCTCCATATGGCAAGTCACAGTGTAATAATAG
52101843 CAATTATGGTCAACTTATGAGTTTTTGTGCACTAATGATCAAGTGTTTCTATTTTTGTGACCTTA
66 CAATTATGGTCAACTTATGAGTTTTTGTGCACTAATGATCAAGTGTTTCTATTTTTGTGACCTTA
52101908 TTTTTGGATCACTTTGACTTTTTCAACATTTTCTCACTCATAATGCTTTTTTATTGATTTTGTAC
131 TTTTTGGATCACTTTGACTTTTTCAACATTTTCTCACTCATAATGCTTTTTTATTGATTTTGTAC
*
52101973 TTTTCCACTCATTTTGACTTTTTCTAAAAATTTTTTTATTCGCATATTTGTAGCTTTAGCTATAA
196 TTTTCCACTCATTTTGACTTTTTCTAAAAATTTTTTTATTCACATATTTGTAGCTTTAGCTATAA
52102038 TTAATATATCACACTTTTTTATTCG
261 TTAATATATCACACTTTTTTATTCG
* *
52102063 CACATTAACTCTTCTTCTCTCACCTTTCTTATTTCTCCATATGAG-AAGTCACAGTGTAATAATA
1 CACATTAACTCTCCTTCTCTCACCTTCCTTATTTCTCCATATG-GCAAGTCACAGTGTAATAATA
52102127 GCAATTATGGTCAACTTATGAGTTTTTGTGCACTAATGATCAAGTGTTTCTATTTTTGTGACCTT
65 GCAATTATGGTCAACTTATGAGTTTTTGTGCACTAATGATCAAGTGTTTCTATTTTTGTGACCTT
* *
52102192 ATTTTTGGATCACTTTGATTTTTTCAACCTTTTCTCACTCATAATG-TTTTTCTATTGATTTTGT
130 ATTTTTGGATCACTTTGACTTTTTCAACATTTTCTCACTCATAATGCTTTTT-TATTGATTTTGT
* *
52102256 ACTTTTCCACTCGTTTTGACTTTTTCT-AAAATTTTCTTTATTCACATATTTTTAGCTT
194 ACTTTTCCACTCATTTTGACTTTTTCTAAAAATTTT-TTTATTCACATATTTGTAGCTT
52102314 AACCATTATC
Statistics
Matches: 240, Mismatches: 8, Indels: 6
0.94 0.03 0.02
Matches are distributed among these distances:
284 13 0.05
285 226 0.94
286 1 0.00
ACGTcount: A:0.23, C:0.18, G:0.10, T:0.48
Consensus pattern (285 bp):
CACATTAACTCTCCTTCTCTCACCTTCCTTATTTCTCCATATGGCAAGTCACAGTGTAATAATAG
CAATTATGGTCAACTTATGAGTTTTTGTGCACTAATGATCAAGTGTTTCTATTTTTGTGACCTTA
TTTTTGGATCACTTTGACTTTTTCAACATTTTCTCACTCATAATGCTTTTTTATTGATTTTGTAC
TTTTCCACTCATTTTGACTTTTTCTAAAAATTTTTTTATTCACATATTTGTAGCTTTAGCTATAA
TTAATATATCACACTTTTTTATTCG
Found at i:52112980 original size:20 final size:20
Alignment explanation
Indices: 52112955--52112994 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
52112945 CGTAAAATGA
*
52112955 TTTCTGGAAAATGCTTTACT
1 TTTCTGGAAAATGATTTACT
*
52112975 TTTCTGTAAAATGATTTACT
1 TTTCTGGAAAATGATTTACT
52112995 GAAAAATATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.28, C:0.12, G:0.12, T:0.47
Consensus pattern (20 bp):
TTTCTGGAAAATGATTTACT
Found at i:52113445 original size:13 final size:13
Alignment explanation
Indices: 52113427--52113454 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
52113417 ATTCTTTCTC
52113427 TATTTATGAAGTT
1 TATTTATGAAGTT
52113440 TATTTATGAAGTT
1 TATTTATGAAGTT
52113453 TA
1 TA
52113455 CTTGTACAAG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.32, C:0.00, G:0.14, T:0.54
Consensus pattern (13 bp):
TATTTATGAAGTT
Found at i:52114850 original size:12 final size:12
Alignment explanation
Indices: 52114833--52114858 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
52114823 TTTTCCAGAA
52114833 AACATTATATCG
1 AACATTATATCG
52114845 AACATTATATCG
1 AACATTATATCG
52114857 AA
1 AA
52114859 TACACAAACG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.46, C:0.15, G:0.08, T:0.31
Consensus pattern (12 bp):
AACATTATATCG
Found at i:52115587 original size:18 final size:18
Alignment explanation
Indices: 52115564--52115615 Score: 59
Period size: 18 Copynumber: 2.9 Consensus size: 18
52115554 ATTTGAAGGA
52115564 ATGAAGGGAGAAGAATGG
1 ATGAAGGGAGAAGAATGG
* *** *
52115582 ATGAAGGAAGCTTACTGG
1 ATGAAGGGAGAAGAATGG
52115600 ATGAAGGGAGAAGAAT
1 ATGAAGGGAGAAGAAT
52115616 ACATGAGAGC
Statistics
Matches: 24, Mismatches: 10, Indels: 0
0.71 0.29 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.42, C:0.04, G:0.38, T:0.15
Consensus pattern (18 bp):
ATGAAGGGAGAAGAATGG
Found at i:52129906 original size:30 final size:30
Alignment explanation
Indices: 52129872--52129928 Score: 114
Period size: 30 Copynumber: 1.9 Consensus size: 30
52129862 ATTAAGAGAG
52129872 AAGTGATGGCTAAATATTGCAAGGGTTCAA
1 AAGTGATGGCTAAATATTGCAAGGGTTCAA
52129902 AAGTGATGGCTAAATATTGCAAGGGTT
1 AAGTGATGGCTAAATATTGCAAGGGTT
52129929 TAAATAAAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.35, C:0.09, G:0.28, T:0.28
Consensus pattern (30 bp):
AAGTGATGGCTAAATATTGCAAGGGTTCAA
Found at i:52132539 original size:30 final size:30
Alignment explanation
Indices: 52132505--52132566 Score: 90
Period size: 30 Copynumber: 2.1 Consensus size: 30
52132495 GCTTTTTGAA
*
52132505 AATATTTACAAAAAGAGGC-ATCTAATTTTT
1 AATATTTACAAAAAGA-GCAATCAAATTTTT
*
52132535 AATATTTATAAAAAGAGCAATCAAATTTTT
1 AATATTTACAAAAAGAGCAATCAAATTTTT
52132565 AA
1 AA
52132567 AAATAATTCA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
29 2 0.07
30 27 0.93
ACGTcount: A:0.48, C:0.08, G:0.08, T:0.35
Consensus pattern (30 bp):
AATATTTACAAAAAGAGCAATCAAATTTTT
Found at i:52143666 original size:22 final size:22
Alignment explanation
Indices: 52143622--52143672 Score: 59
Period size: 22 Copynumber: 2.3 Consensus size: 22
52143612 AATAGAAAAT
*
52143622 TGAAAGAAAAACTAAATACAAA
1 TGAAAGCAAAACTAAATACAAA
*
52143644 TGAAAGCAAAATTAAA-ACTAAA
1 TGAAAGCAAAACTAAATAC-AAA
*
52143666 TAAAAGC
1 TGAAAGC
52143673 TAAGTAAAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
21 2 0.08
22 23 0.92
ACGTcount: A:0.65, C:0.10, G:0.10, T:0.16
Consensus pattern (22 bp):
TGAAAGCAAAACTAAATACAAA
Found at i:52152734 original size:62 final size:61
Alignment explanation
Indices: 52152606--52152782 Score: 162
Period size: 62 Copynumber: 2.9 Consensus size: 61
52152596 TTTATATGTT
* * * * * * * * *
52152606 TTGAATTTTATAAGTTAAAATAAAATGTATGAATTGTATATATGTGTTAGTC-AATGTATGTT
1 TTGAGTTTTATAAGTTGAAATAAATTGAATGAATTATATATAT-T-TTAGCCGAATATATATG
* *
52152668 TTGAGTTTTATAAGTTGAAATAAATTGCATAAATTATATATATATTTAGCCGAATATATATG
1 TTGAGTTTTATAAGTTGAAATAAATTGAATGAATTATATATAT-TTTAGCCGAATATATATG
* * * *
52152730 TTGAG-TTTGTAAGTTG-AATGAAATTTAATGAATTACATATATGTTAGCCGAAT
1 TTGAGTTTTATAAGTTGAAAT-AAATTGAATGAATTATATATATTTTAGCCGAAT
52152783 GTATGTATTG
Statistics
Matches: 96, Mismatches: 17, Indels: 6
0.81 0.14 0.05
Matches are distributed among these distances:
60 13 0.14
61 33 0.34
62 50 0.52
ACGTcount: A:0.38, C:0.04, G:0.16, T:0.42
Consensus pattern (61 bp):
TTGAGTTTTATAAGTTGAAATAAATTGAATGAATTATATATATTTTAGCCGAATATATATG
Found at i:52157796 original size:2 final size:2
Alignment explanation
Indices: 52157789--52157828 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
52157779 TCCACTCGCT
52157789 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
52157829 CTTATACTCA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:52179840 original size:23 final size:24
Alignment explanation
Indices: 52179795--52179841 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 24
52179785 TATTGTAAGT
* *
52179795 TTAATCTTAATTAAATTTGATTAA
1 TTAATCTTAATCAAATTTAATTAA
*
52179819 TTAAT-TTAATCAAGTTTAATTAA
1 TTAATCTTAATCAAATTTAATTAA
52179842 GCTTTAATCC
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
23 15 0.75
24 5 0.25
ACGTcount: A:0.43, C:0.04, G:0.04, T:0.49
Consensus pattern (24 bp):
TTAATCTTAATCAAATTTAATTAA
Found at i:52184051 original size:68 final size:68
Alignment explanation
Indices: 52183934--52184105 Score: 218
Period size: 68 Copynumber: 2.5 Consensus size: 68
52183924 TATAAGACTA
* * * *
52183934 TAAGACCATAGTTAGGCTATAGCAACATATGAAGTCCGCCAGGACAGTAAACATGTCATCATATA
1 TAAGACCATAGTTGGGCTATGGCAACATATGAAGTCCGACAGGACAGTAAACATGGCATCATATA
52183999 GTG
66 GTG
* * * * * * *
52184002 TAAGACCATAGCTGGGTTATGGAAACATATGAATTCTGACATGATAGTAAACATGGCATCATATA
1 TAAGACCATAGTTGGGCTATGGCAACATATGAAGTCCGACAGGACAGTAAACATGGCATCATATA
52184067 GTG
66 GTG
* * *
52184070 TAAGACTATAGTTGGGCTATGGCAATATATGTAGTC
1 TAAGACCATAGTTGGGCTATGGCAACATATGAAGTC
52184106 TGCCAAGACA
Statistics
Matches: 86, Mismatches: 18, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
68 86 1.00
ACGTcount: A:0.35, C:0.15, G:0.22, T:0.27
Consensus pattern (68 bp):
TAAGACCATAGTTGGGCTATGGCAACATATGAAGTCCGACAGGACAGTAAACATGGCATCATATA
GTG
Found at i:52191161 original size:22 final size:23
Alignment explanation
Indices: 52191128--52191180 Score: 65
Period size: 23 Copynumber: 2.3 Consensus size: 23
52191118 ACCCCTTAAC
* *
52191128 TAACATTACCAAT-TCATAATT-
1 TAACATTCCCAATCTCAAAATTA
52191149 TAGACATTCCCAATCTCAAAATTA
1 TA-ACATTCCCAATCTCAAAATTA
52191173 TAACATTC
1 TAACATTC
52191181 AATCCAAATT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
21 2 0.07
22 10 0.37
23 13 0.48
24 2 0.07
ACGTcount: A:0.42, C:0.23, G:0.02, T:0.34
Consensus pattern (23 bp):
TAACATTCCCAATCTCAAAATTA
Found at i:52228890 original size:20 final size:20
Alignment explanation
Indices: 52228865--52228905 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
52228855 GGGACGTGTT
*
52228865 AGGTTTTAAACAATTTAATC
1 AGGTTTGAAACAATTTAATC
52228885 AGGTTTGAAACAATTTAATC
1 AGGTTTGAAACAATTTAATC
52228905 A
1 A
52228906 CACAAATCTA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.41, C:0.10, G:0.12, T:0.37
Consensus pattern (20 bp):
AGGTTTGAAACAATTTAATC
Found at i:52234770 original size:30 final size:30
Alignment explanation
Indices: 52234735--52234801 Score: 91
Period size: 30 Copynumber: 2.2 Consensus size: 30
52234725 GTTGCAGGGG
*
52234735 ACACAC-AGCCGTGTTGCCTGGCCATGTGTC
1 ACACACGA-CCGTGTTGCCCGGCCATGTGTC
* *
52234765 ACACACGACCGTGTTGCCCGGTCGTGTGTC
1 ACACACGACCGTGTTGCCCGGCCATGTGTC
52234795 ACACACG
1 ACACACG
52234802 GCTGAGACAC
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
30 32 0.97
31 1 0.03
ACGTcount: A:0.18, C:0.34, G:0.27, T:0.21
Consensus pattern (30 bp):
ACACACGACCGTGTTGCCCGGCCATGTGTC
Found at i:52241963 original size:7 final size:7
Alignment explanation
Indices: 52241953--52241983 Score: 55
Period size: 7 Copynumber: 4.6 Consensus size: 7
52241943 GAAAACTAAA
52241953 AAAAATG
1 AAAAATG
52241960 AAAAATG
1 AAAAATG
52241967 -AAAATG
1 AAAAATG
52241973 AAAAATG
1 AAAAATG
52241980 AAAA
1 AAAA
52241984 GCAATGACGA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
6 6 0.26
7 17 0.74
ACGTcount: A:0.74, C:0.00, G:0.13, T:0.13
Consensus pattern (7 bp):
AAAAATG
Found at i:52241972 original size:13 final size:13
Alignment explanation
Indices: 52241954--52241983 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
52241944 AAAACTAAAA
52241954 AAAATGAAAAATG
1 AAAATGAAAAATG
52241967 AAAATGAAAAATG
1 AAAATGAAAAATG
52241980 AAAA
1 AAAA
52241984 GCAATGACGA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.73, C:0.00, G:0.13, T:0.13
Consensus pattern (13 bp):
AAAATGAAAAATG
Found at i:52243462 original size:128 final size:128
Alignment explanation
Indices: 52243234--52243979 Score: 1225
Period size: 128 Copynumber: 5.9 Consensus size: 128
52243224 GTGAAATCAT
* *
52243234 AAGTCCTATGTCCCTGACCAGCAGTGGAATAGGTTGGAAATTGCAGATCTTGTCTCCTTAAGTAG
1 AAGTCCTATGTCCCTGACCAGCAGTGGAATAGGTTGGAAATTGCAGATCTTGTCTCCCTAAGCAG
*
52243299 TAACGGAGCAGATCGAAGACGGCGAATCTTATCTTCAAGTGTAAGGAAGCAGATTTAAGCCAC
66 TAGCGGAGCAGATCGAAGACGGCGAATCTTATCTTCAAGTGTAAGGAAGCAGATTTAAGCCAC
* *
52243362 AAGTCCTATGTCCCTGACCAGCAGTGGAATAGGTTAGAAATTACAGATCTTGTCTCCCTAAGCAG
1 AAGTCCTATGTCCCTGACCAGCAGTGGAATAGGTTGGAAATTGCAGATCTTGTCTCCCTAAGCAG
*
52243427 TAGTGGAGCAGATCGAAGACGGCGAATCTTATCTTCAAGTGTAAGGAAGCA-AGTTTAAGCCAC
66 TAGCGGAGCAGATCGAAGACGGCGAATCTTATCTTCAAGTGTAAGGAAGCAGA-TTTAAGCCAC
* *
52243490 AAGTCTTATGTCCCTGACCAGCAGTGGAATAGGTTGGAAATTGCAGATCTTGTCTCCCTAAGTAG
1 AAGTCCTATGTCCCTGACCAGCAGTGGAATAGGTTGGAAATTGCAGATCTTGTCTCCCTAAGCAG
*
52243555 TA-CAGAGCAGATCGAAGACGGCGAATCTTATCTTCAAGTGTAAGGAAGCAGATTTAAGCCAC
66 TAGCGGAGCAGATCGAAGACGGCGAATCTTATCTTCAAGTGTAAGGAAGCAGATTTAAGCCAC
* * *
52243617 AAGTCCTATGTCCCTTACCAGCAGTGGAATAGGCTGGAAATTGCA-A------AT--CT----AG
1 AAGTCCTATGTCCCTGACCAGCAGTGGAATAGGTTGGAAATTGCAGATCTTGTCTCCCTAAGCAG
*
52243669 TAGCGGAGCAGATCGAAGTCGGCGAATCTTATCTTCAAGTGTAAGGAAGCAGATTTAAGCCAC
66 TAGCGGAGCAGATCGAAGACGGCGAATCTTATCTTCAAGTGTAAGGAAGCAGATTTAAGCCAC
52243732 AAGTCCTATGTCCCTGACCAGCAGTGGAATAGGTTGGAAATTGCAGATCTTGTCTCCCTAAGCAG
1 AAGTCCTATGTCCCTGACCAGCAGTGGAATAGGTTGGAAATTGCAGATCTTGTCTCCCTAAGCAG
*
52243797 TAGCAGAGCAGATCGAAGACGGCGAATCTTATCTTCAAGTGTAAGGAAGCAGATTTAAGCCAC
66 TAGCGGAGCAGATCGAAGACGGCGAATCTTATCTTCAAGTGTAAGGAAGCAGATTTAAGCCAC
*
52243860 AAGTCCTATGTCCTTGACCAGCAGTGGAATAGGTTGGAAATTGCAGATCTTGTCTCCCTAAGCAG
1 AAGTCCTATGTCCCTGACCAGCAGTGGAATAGGTTGGAAATTGCAGATCTTGTCTCCCTAAGCAG
* *
52243925 TAGCGGAGCAGATGGAAGACGGCAAATCTTATCTTCAAGTGTAAGGAAGCAGATT
66 TAGCGGAGCAGATCGAAGACGGCGAATCTTATCTTCAAGTGTAAGGAAGCAGATT
52243980 GAAGTCGATA
Statistics
Matches: 575, Mismatches: 27, Indels: 32
0.91 0.04 0.05
Matches are distributed among these distances:
114 4 0.01
115 101 0.18
116 1 0.00
118 2 0.00
120 1 0.00
122 1 0.00
124 2 0.00
126 1 0.00
127 99 0.17
128 363 0.63
ACGTcount: A:0.31, C:0.20, G:0.25, T:0.24
Consensus pattern (128 bp):
AAGTCCTATGTCCCTGACCAGCAGTGGAATAGGTTGGAAATTGCAGATCTTGTCTCCCTAAGCAG
TAGCGGAGCAGATCGAAGACGGCGAATCTTATCTTCAAGTGTAAGGAAGCAGATTTAAGCCAC
Found at i:52244052 original size:44 final size:44
Alignment explanation
Indices: 52243972--52244182 Score: 164
Period size: 44 Copynumber: 4.9 Consensus size: 44
52243962 AGTGTAAGGA
* * * * *
52243972 AGCAGATTGAAGTCGATA-ATCCTATTTCCCTGAAGTTGTAGTGG
1 AGCAGATTAAAGT-AATAGATCTTATCTCCCTAAAGTTGTAGTGG
* * *
52244016 AGCAGATTAAAGTAATAGATCTTATCTCTCTAAAGTTGCAGTAG
1 AGCAGATTAAAGTAATAGATCTTATCTCCCTAAAGTTGTAGTGG
** * * * * * *
52244060 AGTGGA-T--CGCAATAAATCTTATCTCCCTGAGGTTGAAGTGG
1 AGCAGATTAAAGTAATAGATCTTATCTCCCTAAAGTTGTAGTGG
* * * *
52244101 AGCAGATTGAAGTCGATA-ATCCTATCTCCCTGAAGTTGTAGTGG
1 AGCAGATTAAAGT-AATAGATCTTATCTCCCTAAAGTTGTAGTGG
*
52244145 AG-AGGATTAAAGTAATAGATCTTATCTCTCTAAAGTTG
1 AGCA-GATTAAAGTAATAGATCTTATCTCCCTAAAGTTG
52244183 CAGCAGAGTG
Statistics
Matches: 129, Mismatches: 31, Indels: 14
0.74 0.18 0.08
Matches are distributed among these distances:
41 30 0.23
42 1 0.01
43 8 0.06
44 87 0.67
45 3 0.02
ACGTcount: A:0.31, C:0.15, G:0.23, T:0.31
Consensus pattern (44 bp):
AGCAGATTAAAGTAATAGATCTTATCTCCCTAAAGTTGTAGTGG
Found at i:52244080 original size:41 final size:41
Alignment explanation
Indices: 52244029--52244227 Score: 136
Period size: 41 Copynumber: 4.7 Consensus size: 41
52244019 AGATTAAAGT
* *
52244029 AATAGATCTTATCTCTCTAAAGTTGCAGTAGAGTGGATCGC
1 AATAGATCTTATCTCCCTGAAGTTGCAGTAGAGTGGATCGC
* * * *
52244070 AATAAATCTTATCTCCCTGAGGTTGAAGTGGAGCAGATTGAAGTCG-
1 AATAGATCTTATCTCCCTGAAGTTGCAGT--AG-AG--TGGA-TCGC
* * * * * *
52244116 -ATA-ATCCTATCTCCCTGAAGTTGTAGTGGAGAGGATTAAAGT
1 AATAGATCTTATCTCCCTGAAGTTGCAGTAGAGTGGA-T--CGC
* * *
52244158 AATAGATCTTATCTCTCTAAAGTTGCAGCAGAGTGGATCGC
1 AATAGATCTTATCTCCCTGAAGTTGCAGTAGAGTGGATCGC
*
52244199 -ATCAGGTCTTATCTCCCTGAAGTTGCAGT
1 AAT-AGATCTTATCTCCCTGAAGTTGCAGT
52244228 GGAGCAGACT
Statistics
Matches: 119, Mismatches: 27, Indels: 24
0.70 0.16 0.14
Matches are distributed among these distances:
39 3 0.03
40 2 0.02
41 50 0.42
42 1 0.01
43 6 0.05
44 48 0.40
45 3 0.03
46 3 0.03
47 3 0.03
ACGTcount: A:0.29, C:0.18, G:0.23, T:0.31
Consensus pattern (41 bp):
AATAGATCTTATCTCCCTGAAGTTGCAGTAGAGTGGATCGC
Found at i:52244116 original size:129 final size:129
Alignment explanation
Indices: 52243972--52244235 Score: 442
Period size: 129 Copynumber: 2.0 Consensus size: 129
52243962 AGTGTAAGGA
*
52243972 AGCAGATTGAAGTCGATAATCCTATTTCCCTGAAGTTGTAGTGGAGCA-GATTAAAGTAATAGAT
1 AGCAGATTGAAGTCGATAATCCTATCTCCCTGAAGTTGTAGTGGAG-AGGATTAAAGTAATAGAT
* *
52244036 CTTATCTCTCTAAAGTTGCAGTAGAGTGGATCGCAAT-AAATCTTATCTCCCTGAGGTTGAAGTG
65 CTTATCTCTCTAAAGTTGCAGCAGAGTGGATCGC-ATCAAATCTTATCTCCCTGAAGTTGAAGTG
52244100 G
129 G
52244101 AGCAGATTGAAGTCGATAATCCTATCTCCCTGAAGTTGTAGTGGAGAGGATTAAAGTAATAGATC
1 AGCAGATTGAAGTCGATAATCCTATCTCCCTGAAGTTGTAGTGGAGAGGATTAAAGTAATAGATC
** *
52244166 TTATCTCTCTAAAGTTGCAGCAGAGTGGATCGCATCAGGTCTTATCTCCCTGAAGTTGCAGTGG
66 TTATCTCTCTAAAGTTGCAGCAGAGTGGATCGCATCAAATCTTATCTCCCTGAAGTTGAAGTGG
52244230 AGCAGA
1 AGCAGA
52244236 CTGAGAAAAC
Statistics
Matches: 127, Mismatches: 6, Indels: 4
0.93 0.04 0.03
Matches are distributed among these distances:
128 3 0.02
129 124 0.98
ACGTcount: A:0.30, C:0.17, G:0.24, T:0.30
Consensus pattern (129 bp):
AGCAGATTGAAGTCGATAATCCTATCTCCCTGAAGTTGTAGTGGAGAGGATTAAAGTAATAGATC
TTATCTCTCTAAAGTTGCAGCAGAGTGGATCGCATCAAATCTTATCTCCCTGAAGTTGAAGTGG
Found at i:52244273 original size:129 final size:128
Alignment explanation
Indices: 52243989--52244273 Score: 335
Period size: 129 Copynumber: 2.2 Consensus size: 128
52243979 TGAAGTCGAT
* ***
52243989 AATCCTATTTCCCTGAAGTTGTAGTGGAGCAGATTAAAGTAATAGATCTTATCTCTCTAAAGTTG
1 AATCCTATCTCCCTGAAGTCACAGTGGAGCAGATTAAAGTAATAGATCTTATCTCTCTAAAGTTG
* * * **
52244054 CAGTAGAGTGGATCGCAATAAATCTTATCTCCCTGAGGTTGAAGTGGAGCAGATTGAAGTCGA
66 CAGCAGAGTGGATCGCAATAAATCTTATCTCCCTGAAGTTGAAGTGGAGCAGATAGAAAACGA
***
52244117 TAATCCTATCTCCCTGAAGTTGTAGTGGAG-AGGATTAAAGTAATAGATCTTATCTCTCTAAAGT
1 -AATCCTATCTCCCTGAAGTCACAGTGGAGCA-GATTAAAGTAATAGATCTTATCTCTCTAAAGT
** *
52244181 TGCAGCAGAGTGGATCGC-ATCAGGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAGAAAA
64 TGCAGCAGAGTGGATCGCAAT-AAATCTTATCTCCCTGAAGTTGAAGTGGAGCAGA-T-AGAAAA
52244245 CG-
126 CGA
* *
52244247 AGTCTTATC-CCCTTGAAGTCACAGTGG
1 AATCCTATCTCCC-TGAAGTCACAGTGG
52244274 GATAGACTGA
Statistics
Matches: 137, Mismatches: 14, Indels: 10
0.85 0.09 0.06
Matches are distributed among these distances:
128 6 0.04
129 125 0.91
130 1 0.01
131 5 0.04
ACGTcount: A:0.29, C:0.18, G:0.24, T:0.29
Consensus pattern (128 bp):
AATCCTATCTCCCTGAAGTCACAGTGGAGCAGATTAAAGTAATAGATCTTATCTCTCTAAAGTTG
CAGCAGAGTGGATCGCAATAAATCTTATCTCCCTGAAGTTGAAGTGGAGCAGATAGAAAACGA
Found at i:52245412 original size:22 final size:24
Alignment explanation
Indices: 52245387--52245430 Score: 56
Period size: 22 Copynumber: 1.9 Consensus size: 24
52245377 GGCCGCCGCA
52245387 TGCGGCAAAGCC-ATGG-CGGAGG
1 TGCGGCAAAGCCTATGGTCGGAGG
* *
52245409 TGCGTCAGAGCCTATGGTCGGA
1 TGCGGCAAAGCCTATGGTCGGA
52245431 CTCGGGAGAG
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 10 0.56
23 4 0.22
24 4 0.22
ACGTcount: A:0.20, C:0.23, G:0.41, T:0.16
Consensus pattern (24 bp):
TGCGGCAAAGCCTATGGTCGGAGG
Found at i:52263404 original size:18 final size:18
Alignment explanation
Indices: 52263371--52263423 Score: 61
Period size: 18 Copynumber: 2.9 Consensus size: 18
52263361 ATTCACCTAA
*
52263371 ACCCAATCCAAACCCAAGT
1 ACCCAA-CCCAACCCAAGT
* *
52263390 ATCCAACCCAACCCAATT
1 ACCCAACCCAACCCAAGT
*
52263408 ACCCAACCTAACCCAA
1 ACCCAACCCAACCCAA
52263424 CCCAATCATA
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
18 24 0.83
19 5 0.17
ACGTcount: A:0.42, C:0.45, G:0.02, T:0.11
Consensus pattern (18 bp):
ACCCAACCCAACCCAAGT
Found at i:52263504 original size:25 final size:25
Alignment explanation
Indices: 52263476--52263530 Score: 67
Period size: 26 Copynumber: 2.2 Consensus size: 25
52263466 AATTTCAATT
*
52263476 ATGTGTTAATTTCAAA-ACTTATGTA
1 ATGTGGTAA-TTCAAAGACTTATGTA
*
52263501 ATGTTGGTGATTCAAAGACTTATGTA
1 ATG-TGGTAATTCAAAGACTTATGTA
52263527 ATGT
1 ATGT
52263531 TTTTAATTAT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
25 10 0.38
26 16 0.62
ACGTcount: A:0.33, C:0.07, G:0.18, T:0.42
Consensus pattern (25 bp):
ATGTGGTAATTCAAAGACTTATGTA
Found at i:52263565 original size:9 final size:9
Alignment explanation
Indices: 52263551--52263644 Score: 109
Period size: 9 Copynumber: 10.4 Consensus size: 9
52263541 GTAGTGATTC
52263551 AATTCGGTT
1 AATTCGGTT
*
52263560 AATTCGGGT
1 AATTCGGTT
*
52263569 AATTCGGGT
1 AATTCGGTT
*
52263578 AATTCGGGT
1 AATTCGGTT
*
52263587 AATTCTGTT
1 AATTCGGTT
52263596 AATTCGGTT
1 AATTCGGTT
*
52263605 ACTTCAGG-T
1 AATTC-GGTT
*
52263614 AATTCAGTT
1 AATTCGGTT
*
52263623 AATTCGGAT
1 AATTCGGTT
52263632 AATTCGGTT
1 AATTCGGTT
52263641 AATT
1 AATT
52263645 TTTAACCAAA
Statistics
Matches: 73, Mismatches: 10, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
8 1 0.01
9 70 0.96
10 2 0.03
ACGTcount: A:0.26, C:0.12, G:0.22, T:0.40
Consensus pattern (9 bp):
AATTCGGTT
Found at i:52265611 original size:13 final size:13
Alignment explanation
Indices: 52265593--52265645 Score: 54
Period size: 13 Copynumber: 4.1 Consensus size: 13
52265583 AAGAGTTTTT
52265593 TATAATTTTTAAA
1 TATAATTTTTAAA
**
52265606 TATAATTTTTATT
1 TATAATTTTTAAA
**
52265619 TATCAATTTTT-TT
1 TAT-AATTTTTAAA
52265632 TATAATTTTTAAA
1 TATAATTTTTAAA
52265645 T
1 T
52265646 TATTTATTAA
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
12 7 0.21
13 20 0.59
14 7 0.21
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (13 bp):
TATAATTTTTAAA
Found at i:52265628 original size:26 final size:26
Alignment explanation
Indices: 52265591--52265642 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 26
52265581 TGAAGAGTTT
52265591 TTTATAATTTTTAAATATAATTTTTA
1 TTTATAATTTTTAAATATAATTTTTA
**
52265617 TTTATCAATTTTT-TTTATAATTTTTA
1 TTTAT-AATTTTTAAATATAATTTTTA
52265643 AATTATTTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
26 16 0.70
27 7 0.30
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (26 bp):
TTTATAATTTTTAAATATAATTTTTA
Found at i:52277487 original size:26 final size:24
Alignment explanation
Indices: 52277458--52277529 Score: 83
Period size: 24 Copynumber: 2.9 Consensus size: 24
52277448 CTAAACCAAA
*
52277458 AAACTATAAAAATATTTAAAAATCCT
1 AAACT-TAAAAATA-TTAAAAACCCT
*
52277484 AAACCTTAATAATATT-AAAACCCT
1 AAA-CTTAAAAATATTAAAAACCCT
*
52277508 AAACCTAAAAATATTAAAAACC
1 AAACTTAAAAATATTAAAAACC
52277530 TTAACCCTAG
Statistics
Matches: 40, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
23 10 0.25
24 16 0.40
25 2 0.05
26 10 0.25
27 2 0.05
ACGTcount: A:0.57, C:0.17, G:0.00, T:0.26
Consensus pattern (24 bp):
AAACTTAAAAATATTAAAAACCCT
Found at i:52277524 original size:23 final size:24
Alignment explanation
Indices: 52277464--52277535 Score: 92
Period size: 23 Copynumber: 3.0 Consensus size: 24
52277454 CAAAAAACTA
52277464 TAAAAATATTTAAAAATCCTAAACCT
1 TAAAAATA-TTAAAAA-CCTAAACCT
* *
52277490 TAATAATATTAAAACCCTAAACC-
1 TAAAAATATTAAAAACCTAAACCT
*
52277513 TAAAAATATTAAAAACCTTAACC
1 TAAAAATATTAAAAACCTAAACC
52277536 CTAGGAGAGA
Statistics
Matches: 41, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
23 20 0.49
24 8 0.20
25 6 0.15
26 7 0.17
ACGTcount: A:0.54, C:0.18, G:0.00, T:0.28
Consensus pattern (24 bp):
TAAAAATATTAAAAACCTAAACCT
Found at i:52277538 original size:24 final size:24
Alignment explanation
Indices: 52277464--52277538 Score: 80
Period size: 24 Copynumber: 3.1 Consensus size: 24
52277454 CAAAAAACTA
* *
52277464 TAAAAATATTTAAAAATCCTAAACCT
1 TAAAAATA-TTAAAAA-CCTTAACCC
* * *
52277490 TAATAATATT-AAAACCCTAAACC
1 TAAAAATATTAAAAACCTTAACCC
52277513 TAAAAATATTAAAAACCTTAACCC
1 TAAAAATATTAAAAACCTTAACCC
52277537 TA
1 TA
52277539 GGAGAGAGAA
Statistics
Matches: 40, Mismatches: 8, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
23 14 0.35
24 17 0.43
25 2 0.05
26 7 0.17
ACGTcount: A:0.53, C:0.19, G:0.00, T:0.28
Consensus pattern (24 bp):
TAAAAATATTAAAAACCTTAACCC
Found at i:52285324 original size:18 final size:18
Alignment explanation
Indices: 52285301--52285348 Score: 62
Period size: 18 Copynumber: 2.7 Consensus size: 18
52285291 ATTCAATACT
52285301 TTAATTCGGTTAATTCAG
1 TTAATTCGGTTAATTCAG
* *
52285319 TTAATTAGGTTAATTTAG
1 TTAATTCGGTTAATTCAG
52285337 TT-ATTCCGGTTA
1 TTAATT-CGGTTA
52285349 TTTTTTTATG
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
17 3 0.12
18 23 0.88
ACGTcount: A:0.27, C:0.08, G:0.17, T:0.48
Consensus pattern (18 bp):
TTAATTCGGTTAATTCAG
Found at i:52295456 original size:103 final size:104
Alignment explanation
Indices: 52295275--52295540 Score: 401
Period size: 104 Copynumber: 2.5 Consensus size: 104
52295265 ACCGTTATTC
* * * *
52295275 GTGGATCTCGCACTTCAGCACCACCACTTAATCGGGGAATCAGCACTTTAGCAACCCCTTGGGGG
1 GTGGATATCGCACTT-AGCACCACCAATGAATCGGGGAATCAGCAC-TTAGCAACCCCTCGGGGG
** *
52295340 AATCAGCACATAGCAACCCCCTTT-TTATTTCAGAGATACG
64 AATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATACG
52295380 GTGGATATCGCACTTAGCACCACCAATGAA-CTGGGGAATCAGCACTTAGCAACCCCTCGGGGGA
1 GTGGATATCGCACTTAGCACCACCAATGAATC-GGGGAATCAGCACTTAGCAACCCCTCGGGGGA
52295444 ATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATACG
65 ATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATACG
* **
52295484 GTGGATATCGCACATAGCACCACCAATGAATCGGGGAATCAGCACACAGCAACCCCT
1 GTGGATATCGCACTTAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCT
52295541 TTATGTACAA
Statistics
Matches: 148, Mismatches: 10, Indels: 7
0.90 0.06 0.04
Matches are distributed among these distances:
103 42 0.28
104 91 0.61
105 15 0.10
ACGTcount: A:0.30, C:0.30, G:0.20, T:0.20
Consensus pattern (104 bp):
GTGGATATCGCACTTAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCTCGGGGGAA
TCAGCACATAGCAACCCCCTTTCACATTTCAAAGATACG
Found at i:52295902 original size:30 final size:29
Alignment explanation
Indices: 52295868--52295932 Score: 76
Period size: 30 Copynumber: 2.2 Consensus size: 29
52295858 TAATCCACCA
52295868 CCCAACTTTTTGAAAAATTACAATTTTGCC
1 CCCAAC-TTTTGAAAAATTACAATTTTGCC
* * * *
52295898 CCCAAACTTTTGCATAATTACACTTTTGTC
1 CCC-AACTTTTGAAAAATTACAATTTTGCC
52295928 CCCAA
1 CCCAA
52295933 GCTCGGAAAT
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
29 2 0.07
30 25 0.83
31 3 0.10
ACGTcount: A:0.31, C:0.28, G:0.06, T:0.35
Consensus pattern (29 bp):
CCCAACTTTTGAAAAATTACAATTTTGCC
Found at i:52295906 original size:31 final size:30
Alignment explanation
Indices: 52295875--52295932 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
52295865 CCACCCAACT
52295875 TTTTGAAAAATTACAATTTTGCCCCCAAAC
1 TTTTGAAAAATTACAATTTTGCCCCCAAAC
* * * *
52295905 TTTTGCATAATTACACTTTTGTCCCCAA
1 TTTTGAAAAATTACAATTTTGCCCCCAA
52295933 GCTCGGAAAT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.31, C:0.24, G:0.07, T:0.38
Consensus pattern (30 bp):
TTTTGAAAAATTACAATTTTGCCCCCAAAC
Found at i:52302918 original size:103 final size:104
Alignment explanation
Indices: 52302739--52303003 Score: 417
Period size: 103 Copynumber: 2.6 Consensus size: 104
52302729 AACCGTTATT
* * * *
52302739 GGTGGATCTCGCACTTAGCACCACCACTTAATCGGGGAATCAGCACTTAGCAACCCCTTGGGGGA
1 GGTGGATATCGCACTTAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCTCGGGGGA
** *
52302804 ATCAGCACATAGCAACCCCCTTT-TTATTTCAGAGATAC
66 ATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATAC
52302842 GGTGGATATCGCACTTAGCACCACCAATGAA-CTGGGGAATCAGCACTTAGCAACCCCTCGGGGG
1 GGTGGATATCGCACTTAGCACCACCAATGAATC-GGGGAATCAGCACTTAGCAACCCCTCGGGGG
52302906 AATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATAC
65 AATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATAC
* **
52302946 GGTGGATATCGCACATAGCACCACCAATGAATCGGGGAATCAGCACACAGCAACCCCT
1 GGTGGATATCGCACTTAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCT
52303004 TTATGTACAA
Statistics
Matches: 149, Mismatches: 10, Indels: 5
0.91 0.06 0.03
Matches are distributed among these distances:
102 1 0.01
103 82 0.55
104 65 0.44
105 1 0.01
ACGTcount: A:0.30, C:0.30, G:0.21, T:0.20
Consensus pattern (104 bp):
GGTGGATATCGCACTTAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCTCGGGGGA
ATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATAC
Found at i:52303365 original size:30 final size:29
Alignment explanation
Indices: 52303331--52303395 Score: 76
Period size: 30 Copynumber: 2.2 Consensus size: 29
52303321 TAATCCACCA
52303331 CCCAACTTTTTGAAAAATTACAATTTTGCC
1 CCCAAC-TTTTGAAAAATTACAATTTTGCC
* * * *
52303361 CCCAAACTTTTGCATAATTACACTTTTGTC
1 CCC-AACTTTTGAAAAATTACAATTTTGCC
52303391 CCCAA
1 CCCAA
52303396 GCTCGGAAAT
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
29 2 0.07
30 25 0.83
31 3 0.10
ACGTcount: A:0.31, C:0.28, G:0.06, T:0.35
Consensus pattern (29 bp):
CCCAACTTTTGAAAAATTACAATTTTGCC
Found at i:52303369 original size:31 final size:30
Alignment explanation
Indices: 52303338--52303395 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
52303328 CCACCCAACT
52303338 TTTTGAAAAATTACAATTTTGCCCCCAAAC
1 TTTTGAAAAATTACAATTTTGCCCCCAAAC
* * * *
52303368 TTTTGCATAATTACACTTTTGTCCCCAA
1 TTTTGAAAAATTACAATTTTGCCCCCAA
52303396 GCTCGGAAAT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.31, C:0.24, G:0.07, T:0.38
Consensus pattern (30 bp):
TTTTGAAAAATTACAATTTTGCCCCCAAAC
Found at i:52310423 original size:25 final size:25
Alignment explanation
Indices: 52310389--52310440 Score: 86
Period size: 25 Copynumber: 2.1 Consensus size: 25
52310379 GATACTTGTC
*
52310389 CACCTAAGTATCAATGGAAGTTATT
1 CACCTAAGTATCAATAGAAGTTATT
*
52310414 CACCTAAGTATCGATAGAAGTTATT
1 CACCTAAGTATCAATAGAAGTTATT
52310439 CA
1 CA
52310441 GACTTCAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.37, C:0.17, G:0.15, T:0.31
Consensus pattern (25 bp):
CACCTAAGTATCAATAGAAGTTATT
Found at i:52311180 original size:19 final size:19
Alignment explanation
Indices: 52311142--52311180 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
52311132 TTTAATTGGG
* *
52311142 AAATTAATTTTTTTTATTT
1 AAATTAATTTATTATATTT
*
52311161 AAATTAATTTATTATGTTT
1 AAATTAATTTATTATATTT
52311180 A
1 A
52311181 TTTTGAGAAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.36, C:0.00, G:0.03, T:0.62
Consensus pattern (19 bp):
AAATTAATTTATTATATTT
Found at i:52315121 original size:18 final size:18
Alignment explanation
Indices: 52315087--52315125 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
52315077 TACAAGCCAA
52315087 TATTTTTTAATGATTTTT
1 TATTTTTTAATGATTTTT
*
52315105 TATTTGTTT-ATGTTTTTT
1 TATTT-TTTAATGATTTTT
52315123 TAT
1 TAT
52315126 CGTAATAGAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 16 0.84
19 3 0.16
ACGTcount: A:0.18, C:0.00, G:0.08, T:0.74
Consensus pattern (18 bp):
TATTTTTTAATGATTTTT
Found at i:52317057 original size:30 final size:31
Alignment explanation
Indices: 52317023--52317087 Score: 80
Period size: 31 Copynumber: 2.1 Consensus size: 31
52317013 TTTCGTTAAA
52317023 AAAAGTTATAATTT-AATCACTT-AATTATTC
1 AAAAGTTATAATTTAAATCA-TTGAATTATTC
* * *
52317053 AAAAGTTTTCATTTAAATTATTGAATTATTC
1 AAAAGTTATAATTTAAATCATTGAATTATTC
52317084 AAAA
1 AAAA
52317088 ATTTTTATTT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
30 14 0.47
31 16 0.53
ACGTcount: A:0.45, C:0.08, G:0.05, T:0.43
Consensus pattern (31 bp):
AAAAGTTATAATTTAAATCATTGAATTATTC
Found at i:52318500 original size:27 final size:27
Alignment explanation
Indices: 52318470--52318594 Score: 133
Period size: 27 Copynumber: 4.6 Consensus size: 27
52318460 AGGAAGGGTA
52318470 TCTCATAGGCGGCACCAAAGGTGCCTT
1 TCTCATAGGCGGCACCAAAGGTGCCTT
* * * *
52318497 TCTCATGGGCGGCACCGATGGTGCCAT
1 TCTCATAGGCGGCACCAAAGGTGCCTT
* * * *
52318524 TCCCATGGGCGGCACCAAAAGTGCATT
1 TCTCATAGGCGGCACCAAAGGTGCCTT
* * *
52318551 TTTCATAGGCGGCACCGAATGTGCCTT
1 TCTCATAGGCGGCACCAAAGGTGCCTT
* *
52318578 TCCCATAAGCGGCACCA
1 TCTCATAGGCGGCACCA
52318595 CTTATGTCAT
Statistics
Matches: 78, Mismatches: 20, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
27 78 1.00
ACGTcount: A:0.22, C:0.30, G:0.26, T:0.22
Consensus pattern (27 bp):
TCTCATAGGCGGCACCAAAGGTGCCTT
Found at i:52318562 original size:54 final size:54
Alignment explanation
Indices: 52318473--52318594 Score: 165
Period size: 54 Copynumber: 2.3 Consensus size: 54
52318463 AAGGGTATCT
* * *
52318473 CATAGGCGGCACCAAAGGTGCCTTTCTCATGGGCGGCACCG-ATGGTGCCATTCC
1 CATAGGCGGCACCAAAAGTGCATTTCTCATAGGCGGCACCGAAT-GTGCCATTCC
* * *
52318527 CATGGGCGGCACCAAAAGTGCATTTTTCATAGGCGGCACCGAATGTGCCTTTCC
1 CATAGGCGGCACCAAAAGTGCATTTCTCATAGGCGGCACCGAATGTGCCATTCC
*
52318581 CATAAGCGGCACCA
1 CATAGGCGGCACCA
52318595 CTTATGTCAT
Statistics
Matches: 59, Mismatches: 8, Indels: 2
0.86 0.12 0.03
Matches are distributed among these distances:
54 57 0.97
55 2 0.03
ACGTcount: A:0.22, C:0.30, G:0.27, T:0.20
Consensus pattern (54 bp):
CATAGGCGGCACCAAAAGTGCATTTCTCATAGGCGGCACCGAATGTGCCATTCC
Found at i:52318844 original size:3 final size:3
Alignment explanation
Indices: 52318838--52318869 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
52318828 TAGTTAGTAG
52318838 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
52318870 GTTTTTAGAG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:52319076 original size:45 final size:44
Alignment explanation
Indices: 52319011--52319114 Score: 163
Period size: 45 Copynumber: 2.3 Consensus size: 44
52319001 TTATTACAGC
**
52319011 ATGTTTGGTTGGCTGTAATGGAATAGAGGCGTAATAGGTAATCTT
1 ATGTTTGGTTGAATGTAATGGAATAGAGGCGTAAT-GGTAATCTT
* *
52319056 TTGTTTGGTTGAATGTAATGGAATAGAGGCGTAATGGTATTCTT
1 ATGTTTGGTTGAATGTAATGGAATAGAGGCGTAATGGTAATCTT
52319100 ATGTTTGGTTGAATG
1 ATGTTTGGTTGAATG
52319115 GAATAGAGGT
Statistics
Matches: 54, Mismatches: 5, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
44 22 0.41
45 32 0.59
ACGTcount: A:0.25, C:0.05, G:0.31, T:0.39
Consensus pattern (44 bp):
ATGTTTGGTTGAATGTAATGGAATAGAGGCGTAATGGTAATCTT
Found at i:52319115 original size:39 final size:43
Alignment explanation
Indices: 52319024--52319131 Score: 143
Period size: 45 Copynumber: 2.6 Consensus size: 43
52319014 TTTGGTTGGC
*
52319024 TGTAATGGAATAGAGGCGTAATAGGTAATCTTTTGTTTGGTTGAA
1 TGTAATGGAATAGAGGCGTAATAGGTAATCTTATGTTTGGTT--A
*
52319069 TGTAATGGAATAGAGGCGTAAT-GGTATTCTTATGTTTGG-T-
1 TGTAATGGAATAGAGGCGTAATAGGTAATCTTATGTTTGGTTA
*
52319109 TG-AATGGAATAGAGGTGTAATAG
1 TGTAATGGAATAGAGGCGTAATAG
52319132 CATAAGGAAA
Statistics
Matches: 59, Mismatches: 3, Indels: 7
0.86 0.04 0.10
Matches are distributed among these distances:
39 18 0.31
40 3 0.05
43 1 0.02
44 15 0.25
45 22 0.37
ACGTcount: A:0.30, C:0.04, G:0.31, T:0.36
Consensus pattern (43 bp):
TGTAATGGAATAGAGGCGTAATAGGTAATCTTATGTTTGGTTA
Found at i:52319259 original size:18 final size:19
Alignment explanation
Indices: 52319230--52319273 Score: 63
Period size: 19 Copynumber: 2.3 Consensus size: 19
52319220 GCTTATTAAT
52319230 ATAAATAATATAT-AATTTA
1 ATAAA-AATATATGAATTTA
52319249 ATAAAAATATATGAATTTA
1 ATAAAAATATATGAATTTA
*
52319268 CTAAAA
1 ATAAAA
52319274 TCATAATATA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 7 0.30
19 16 0.70
ACGTcount: A:0.59, C:0.02, G:0.02, T:0.36
Consensus pattern (19 bp):
ATAAAAATATATGAATTTA
Found at i:52326942 original size:317 final size:316
Alignment explanation
Indices: 52326360--52327764 Score: 2402
Period size: 317 Copynumber: 4.4 Consensus size: 316
52326350 GCATGTTGAA
* *
52326360 AAAAAAGTTAGTAAAATACTCTTACTTCGGCCATTTGTTCGTATTTTTTTCTCCGTATTTTATTA
1 AAAAAATTTAGTAAAACACTCTTACTTCGGCCATTTGTTCGTATTTTTTTCTCCGTATTTTATTA
* *
52326425 CTTTAAAAAATATCATAATTTCTAATATTATAATTTTACATTATCTCAGTGCATTATGTTTGAAA
66 CTTTAAAAAATATCATAATTTCTAATTTTATAATTTTACATTATTTCAGTGCATTATGTTTGAAA
* * *
52326490 TTTATTAATTTAGTGTGTTTTTTTAAATTAATTTAGTGTAAAAAAATCCTTATTCCTACCATTTG
131 TTTATTAATTTAGTGTG-TTTTTTAAATTAATTTAGTGTAAAAAAACCCTTATTCCTGCCCTTTG
52326555 CTCGTATTATTTTCCCGAATTTTATTACGT-TCAATAAAAAATATTATTTTCGTATTTTATTATT
195 CTCGTATTATTTTCCCGAATTTTATTAC-TCTCAATAAAAAATATTATTTTCGTATTTTATTATT
*
52326619 TTATATTATTTCAGTACATTTTGTTTGAAATATTTGTATTATTTATTTCTGAATTTTT
259 TTATATTATTTCAGTACATTTTGTTTGAAATATTTGTATTATTTATTTCTAAATTTTT
*
52326677 AAAATATTTAGTAAAACACTCTTACTTCGGCCATTTGTTCGTATTTTTTTCTCCGTATTTTATTA
1 AAAAAATTTAGTAAAACACTCTTACTTCGGCCATTTGTTCGTATTTTTTTCTCCGTATTTTATTA
52326742 CTTTAAAAAATATCATAATTTCTAATTTTATAATTTTACATTATTTCAGTGCATTATGTTTGAAA
66 CTTTAAAAAATATCATAATTTCTAATTTTATAATTTTACATTATTTCAGTGCATTATGTTTGAAA
* *
52326807 TTTATTAATTTAGTGTGTTTTTTAAATAAATTTAGTGTAAAAAAACCCCTTATTCCTGCCCTGTG
131 TTTATTAATTTAGTGTGTTTTTTAAATTAATTTAGTGTAAAAAAA-CCCTTATTCCTGCCCTTTG
** *
52326872 CTCGTATTATTTTCTTGAATTTTATTACTTTCAATAAAAAATATTATTTTCGTATTTTATTATTT
195 CTCGTATTATTTTCCCGAATTTTATTACTCTCAATAAAAAATATTATTTTCGTATTTTATTATTT
52326937 TATATTATTTCAGTACATTTTGTTTGAAATATTTGTATTATTTATTTCTAAATTTTT
260 TATATTATTTCAGTACATTTTGTTTGAAATATTTGTATTATTTATTTCTAAATTTTT
* *
52326994 AAAAAATTTAGTAAAACACTCTTACTTCGGCCATTTGTTCATATTTTTTTCTCCGCATTTTATTA
1 AAAAAATTTAGTAAAACACTCTTACTTCGGCCATTTGTTCGTATTTTTTTCTCCGTATTTTATTA
* *
52327059 TTTTAGAAAATATCATAATTTCTAATTTTATAATTTTACATTATTTCAGTGCATTATGTTTGAAA
66 CTTTAAAAAATATCATAATTTCTAATTTTATAATTTTACATTATTTCAGTGCATTATGTTTGAAA
* * * *
52327124 TTTATTATTTTAGTGTGTTTTTTAAAATTAATTTAGTGTAGAAAAAACCTTTATTCATGCACTTT
131 TTTATTAATTTAGTGTGTTTTTT-AAATTAATTTAGTGTA-AAAAAACCCTTATTCCTGCCCTTT
* *
52327189 GCTCGTATTATTTTCTCGAATTTTATTAGTCTCAAT-AAAAATATTATTTTCGTATTTTATTATT
194 GCTCGTATTATTTTCCCGAATTTTATTACTCTCAATAAAAAATATTATTTTCGTATTTTATTATT
*
52327253 TTATATTATTTCAGTACATTTTGTTTGAAATATTTGTATTATTTATTTCTGAATTTTT
259 TTATATTATTTCAGTACATTTTGTTTGAAATATTTGTATTATTTATTTCTAAATTTTT
*
52327311 AAAATATTTAGTAAAACACTCTTACTTCGGCCATTTGTTCGTATTTTTTTCTCCGTATTTTATTA
1 AAAAAATTTAGTAAAACACTCTTACTTCGGCCATTTGTTCGTATTTTTTTCTCCGTATTTTATTA
*
52327376 CTTT-AAAAATATCATAATTTCTAATTTTATAATTTTACATTATTTCAGTACATTATGTTTGAAA
66 CTTTAAAAAATATCATAATTTCTAATTTTATAATTTTACATTATTTCAGTGCATTATGTTTGAAA
* **
52327440 TTTATTAATTTAGTGTATTTTTTAAATTAATTTAGTGTAAAAAAAACATTTATTCCTGCCCTTTG
131 TTTATTAATTTAGTGTGTTTTTTAAATTAATTTAGTGT-AAAAAAACCCTTATTCCTGCCCTTTG
*
52327505 CTCGTATTATTTTCCCGAATTTTATTAGTCTCAATAAAAAATATTATTTTCGTATTTTATTATTT
195 CTCGTATTATTTTCCCGAATTTTATTACTCTCAATAAAAAATATTATTTTCGTATTTTATTATTT
52327570 TATATTATTTCAGTACATTTTGTTTGAAATATTTGTATTATTTATTTCTAAATTTTT
260 TATATTATTTCAGTACATTTTGTTTGAAATATTTGTATTATTTATTTCTAAATTTTT
* * **
52327627 AAAAAATTTAGTAAAACACTCTTACTTCGGTCATTTGTTCGGATTTTTTTCTCCACATTTTATTA
1 AAAAAATTTAGTAAAACACTCTTACTTCGGCCATTTGTTCGTATTTTTTTCTCCGTATTTTATTA
* *
52327692 TTTTAAAAAATATCATAATTTCTAATTTTATAATTTTACTTTATTTCAGTGCATTATGTTTGAAA
66 CTTTAAAAAATATCATAATTTCTAATTTTATAATTTTACATTATTTCAGTGCATTATGTTTGAAA
52327757 TTTATTAA
131 TTTATTAA
52327765 ATATACCATT
Statistics
Matches: 1032, Mismatches: 49, Indels: 14
0.94 0.04 0.01
Matches are distributed among these distances:
315 71 0.07
316 256 0.25
317 637 0.62
318 62 0.06
319 6 0.01
ACGTcount: A:0.31, C:0.11, G:0.08, T:0.51
Consensus pattern (316 bp):
AAAAAATTTAGTAAAACACTCTTACTTCGGCCATTTGTTCGTATTTTTTTCTCCGTATTTTATTA
CTTTAAAAAATATCATAATTTCTAATTTTATAATTTTACATTATTTCAGTGCATTATGTTTGAAA
TTTATTAATTTAGTGTGTTTTTTAAATTAATTTAGTGTAAAAAAACCCTTATTCCTGCCCTTTGC
TCGTATTATTTTCCCGAATTTTATTACTCTCAATAAAAAATATTATTTTCGTATTTTATTATTTT
ATATTATTTCAGTACATTTTGTTTGAAATATTTGTATTATTTATTTCTAAATTTTT
Found at i:52327780 original size:633 final size:634
Alignment explanation
Indices: 52326360--52327764 Score: 2487
Period size: 633 Copynumber: 2.2 Consensus size: 634
52326350 GCATGTTGAA
* * *
52326360 AAAAAAGTTAGTAAAATACTCTTACTTCGGCCATTTGTTCGTATTTTTTTCTCCGTATTTTATTA
1 AAAAAATTTAGTAAAACACTCTTACTTCGGCCATTTGTTCGTATTTTTTTCTCCGCATTTTATTA
* * *
52326425 CTTTAAAAAATATCATAATTTCTAATATTATAATTTTACATTATCTCAGTGCATTATGTTTGAAA
66 TTTTAAAAAATATCATAATTTCTAATTTTATAATTTTACATTATTTCAGTGCATTATGTTTGAAA
* *
52326490 TTTATTAATTTAGTGTGTTTTTTTAAATTAATTTAGTGTAAAAAAATCCTTATTCCTACCATTTG
131 TTTATTAATTTAGTGTGTTTTTTAAAATTAATTTAGTGTAAAAAAATCCTTATTCATACCATTTG
52326555 CTCGTATTATTTTCCCGAATTTTATTACGTTCAATAAAAAATATTATTTTCGTATTTTATTATTT
196 CTCGTATTATTTTCCCGAATTTTATTACGTTCAATAAAAAATATTATTTTCGTATTTTATTATTT
52326620 TATATTATTTCAGTACATTTTGTTTGAAATATTTGTATTATTTATTTCTGAATTTTTAAAATATT
261 TATATTATTTCAGTACATTTTGTTTGAAATATTTGTATTATTTATTTCTGAATTTTTAAAATATT
52326685 TAGTAAAACACTCTTACTTCGGCCATTTGTTCGTATTTTTTTCTCCGTATTTTATTACTTTAAAA
326 TAGTAAAACACTCTTACTTCGGCCATTTGTTCGTATTTTTTTCTCCGTATTTTATTACTTTAAAA
*
52326750 AATATCATAATTTCTAATTTTATAATTTTACATTATTTCAGTGCATTATGTTTGAAATTTATTAA
391 AATATCATAATTTCTAATTTTATAATTTTACATTATTTCAGTACATTATGTTTGAAATTTATTAA
* * *
52326815 TTTAGTGTGTTTTTTAAATAAATTTAGTGTAAAAAAACCCCTTATTCCTGCCCTGTGCTCGTATT
456 TTTAGTGTATTTTTTAAATAAATTTAGTGTAAAAAAAACACTTATTCCTGCCCTGTGCTCGTATT
** *
52326880 ATTTTCTTGAATTTTATTACTTTCAATAAAAAATATTATTTTCGTATTTTATTATTTTATATTAT
521 ATTTTCCCGAATTTTATTACTCTCAATAAAAAATATTATTTTCGTATTTTATTATTTTATATTAT
52326945 TTCAGTACATTTTGTTTGAAATATTTGTATTATTTATTTCTAAATTTTT
586 TTCAGTACATTTTGTTTGAAATATTTGTATTATTTATTTCTAAATTTTT
*
52326994 AAAAAATTTAGTAAAACACTCTTACTTCGGCCATTTGTTCATATTTTTTTCTCCGCATTTTATTA
1 AAAAAATTTAGTAAAACACTCTTACTTCGGCCATTTGTTCGTATTTTTTTCTCCGCATTTTATTA
*
52327059 TTTTAGAAAATATCATAATTTCTAATTTTATAATTTTACATTATTTCAGTGCATTATGTTTGAAA
66 TTTTAAAAAATATCATAATTTCTAATTTTATAATTTTACATTATTTCAGTGCATTATGTTTGAAA
* *
52327124 TTTATTATTTTAGTGTGTTTTTTAAAATTAATTTAGTGTAGAAAAAA-CCTTTATTCAT-GCACT
131 TTTATTAATTTAGTGTGTTTTTTAAAATTAATTTAGTGTA-AAAAAATCC-TTATTCATACCA-T
*
52327187 TTGCTCGTATTATTTTCTCGAATTTTATTA-GTCTCAAT-AAAAATATTATTTTCGTATTTTATT
193 TTGCTCGTATTATTTTCCCGAATTTTATTACGT-TCAATAAAAAATATTATTTTCGTATTTTATT
52327250 ATTTTATATTATTTCAGTACATTTTGTTTGAAATATTTGTATTATTTATTTCTGAATTTTTAAAA
257 ATTTTATATTATTTCAGTACATTTTGTTTGAAATATTTGTATTATTTATTTCTGAATTTTTAAAA
52327315 TATTTAGTAAAACACTCTTACTTCGGCCATTTGTTCGTATTTTTTTCTCCGTATTTTATTACTTT
322 TATTTAGTAAAACACTCTTACTTCGGCCATTTGTTCGTATTTTTTTCTCCGTATTTTATTACTTT
52327380 -AAAAATATCATAATTTCTAATTTTATAATTTTACATTATTTCAGTACATTATGTTTGAAATTTA
387 AAAAAATATCATAATTTCTAATTTTATAATTTTACATTATTTCAGTACATTATGTTTGAAATTTA
* * *
52327444 TTAATTTAGTGTATTTTTTAAATTAATTTAGTGTAAAAAAAACATTTATTCCTGCCCTTTGCTCG
452 TTAATTTAGTGTATTTTTTAAATAAATTTAGTGTAAAAAAAACACTTATTCCTGCCCTGTGCTCG
*
52327509 TATTATTTTCCCGAATTTTATTAGTCTCAATAAAAAATATTATTTTCGTATTTTATTATTTTATA
517 TATTATTTTCCCGAATTTTATTACTCTCAATAAAAAATATTATTTTCGTATTTTATTATTTTATA
52327574 TTATTTCAGTACATTTTGTTTGAAATATTTGTATTATTTATTTCTAAATTTTT
582 TTATTTCAGTACATTTTGTTTGAAATATTTGTATTATTTATTTCTAAATTTTT
* * *
52327627 AAAAAATTTAGTAAAACACTCTTACTTCGGTCATTTGTTCGGATTTTTTTCTCCACATTTTATTA
1 AAAAAATTTAGTAAAACACTCTTACTTCGGCCATTTGTTCGTATTTTTTTCTCCGCATTTTATTA
*
52327692 TTTTAAAAAATATCATAATTTCTAATTTTATAATTTTACTTTATTTCAGTGCATTATGTTTGAAA
66 TTTTAAAAAATATCATAATTTCTAATTTTATAATTTTACATTATTTCAGTGCATTATGTTTGAAA
52327757 TTTATTAA
131 TTTATTAA
52327765 ATATACCATT
Statistics
Matches: 736, Mismatches: 31, Indels: 9
0.95 0.04 0.01
Matches are distributed among these distances:
633 367 0.50
634 321 0.44
635 48 0.07
ACGTcount: A:0.31, C:0.11, G:0.08, T:0.51
Consensus pattern (634 bp):
AAAAAATTTAGTAAAACACTCTTACTTCGGCCATTTGTTCGTATTTTTTTCTCCGCATTTTATTA
TTTTAAAAAATATCATAATTTCTAATTTTATAATTTTACATTATTTCAGTGCATTATGTTTGAAA
TTTATTAATTTAGTGTGTTTTTTAAAATTAATTTAGTGTAAAAAAATCCTTATTCATACCATTTG
CTCGTATTATTTTCCCGAATTTTATTACGTTCAATAAAAAATATTATTTTCGTATTTTATTATTT
TATATTATTTCAGTACATTTTGTTTGAAATATTTGTATTATTTATTTCTGAATTTTTAAAATATT
TAGTAAAACACTCTTACTTCGGCCATTTGTTCGTATTTTTTTCTCCGTATTTTATTACTTTAAAA
AATATCATAATTTCTAATTTTATAATTTTACATTATTTCAGTACATTATGTTTGAAATTTATTAA
TTTAGTGTATTTTTTAAATAAATTTAGTGTAAAAAAAACACTTATTCCTGCCCTGTGCTCGTATT
ATTTTCCCGAATTTTATTACTCTCAATAAAAAATATTATTTTCGTATTTTATTATTTTATATTAT
TTCAGTACATTTTGTTTGAAATATTTGTATTATTTATTTCTAAATTTTT
Found at i:52328139 original size:14 final size:14
Alignment explanation
Indices: 52328122--52328263 Score: 64
Period size: 14 Copynumber: 9.9 Consensus size: 14
52328112 TCCTCCCCTC
52328122 TTCTTCTTCTTTTT
1 TTCTTCTTCTTTTT
*
52328136 TTC-TCTTCTCCTTTCC
1 TTCTTCTTCT--TTT-T
52328152 TT-TTCTTTCATTCTTT
1 TTCTTC-TTC-TT-TTT
*
52328168 TTCATTCTT-TTTTC
1 TTC-TTCTTCTTTTT
*
52328182 TTCTTCTCCTTTCCTT
1 TTCTTCTTCTTT--TT
*
52328198 TTCTT-TCCTTCTTT
1 TTCTTCTTCTT-TTT
*
52328212 TTC-T-TTCTTTCT
1 TTCTTCTTCTTTTT
* * *
52328224 TTCCTCTCCTTTCT
1 TTCTTCTTCTTTTT
52328238 TT-TTCTTTCTTTTT
1 TTCTTC-TTCTTTTT
52328252 TTCTTCTTCTTT
1 TTCTTCTTCTTT
52328264 CCCTCTCCTT
Statistics
Matches: 100, Mismatches: 11, Indels: 34
0.69 0.08 0.23
Matches are distributed among these distances:
12 5 0.05
13 18 0.18
14 39 0.39
15 13 0.13
16 14 0.14
17 7 0.07
18 4 0.04
ACGTcount: A:0.01, C:0.28, G:0.00, T:0.70
Consensus pattern (14 bp):
TTCTTCTTCTTTTT
Found at i:52328144 original size:16 final size:16
Alignment explanation
Indices: 52328123--52328169 Score: 51
Period size: 16 Copynumber: 2.8 Consensus size: 16
52328113 CCTCCCCTCT
52328123 TCTTCTTCTTTTTTTC
1 TCTTCTTCTTTTTTTC
*
52328139 TCTTCTCCTTTCCTTTTC
1 TCTTCTTCTTT--TTTTC
52328157 T-TTCATTCTTTTT
1 TCTTC-TTCTTTTT
52328170 CATTCTTTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
16 12 0.46
17 3 0.12
18 11 0.42
ACGTcount: A:0.02, C:0.28, G:0.00, T:0.70
Consensus pattern (16 bp):
TCTTCTTCTTTTTTTC
Found at i:52328159 original size:10 final size:10
Alignment explanation
Indices: 52328146--52328265 Score: 52
Period size: 10 Copynumber: 11.6 Consensus size: 10
52328136 TTCTCTTCTC
52328146 CTTTCCTTTT
1 CTTTCCTTTT
*
52328156 CTTTCATTCTT
1 CTTTCCTT-TT
*
52328167 -TTTCATTCTT
1 CTTTCCTT-TT
* *
52328177 TTTTCTTCTTCT
1 CTTTC--CTTTT
52328189 CCTTTCCTTTT
1 C-TTTCCTTTT
52328200 CTTTCCTTCTT
1 CTTTCCTT-TT
*
52328211 -TTTCTTTCTTT
1 CTTTC-CT-TTT
* *
52328222 CTTTCCTCTC
1 CTTTCCTTTT
*
52328232 CTTTCTTTTT
1 CTTTCCTTTT
52328242 CTTT-CTTTT
1 CTTTCCTTTT
52328251 -TTT-CTTCTT
1 CTTTCCTT-TT
52328260 CTTTCC
1 CTTTCC
52328266 CTCTCCTTCT
Statistics
Matches: 85, Mismatches: 13, Indels: 23
0.70 0.11 0.19
Matches are distributed among these distances:
8 6 0.07
9 6 0.07
10 43 0.51
11 18 0.21
12 6 0.07
13 6 0.07
ACGTcount: A:0.02, C:0.29, G:0.00, T:0.69
Consensus pattern (10 bp):
CTTTCCTTTT
Found at i:52328170 original size:32 final size:31
Alignment explanation
Indices: 52328089--52328170 Score: 82
Period size: 29 Copynumber: 2.6 Consensus size: 31
52328079 TAAAAAATTA
52328089 CCTTTTCTTTCTTTCTTTTTCCTTCCTCCCCT
1 CCTTTTCTTTC-TTCTTTTTCCTTCCTCCCCT
**
52328121 -CTTCTTC-TTCTT-TTTTTCTCTT-CTCCTTT
1 CCTT-TTCTTTCTTCTTTTTC-CTTCCTCCCCT
52328150 CCTTTTCTTTCATTCTTTTTC
1 CCTTTTCTTTC-TTCTTTTTC
52328171 ATTCTTTTTT
Statistics
Matches: 42, Mismatches: 2, Indels: 12
0.75 0.04 0.21
Matches are distributed among these distances:
29 14 0.33
30 11 0.26
31 8 0.19
32 9 0.21
ACGTcount: A:0.01, C:0.34, G:0.00, T:0.65
Consensus pattern (31 bp):
CCTTTTCTTTCTTCTTTTTCCTTCCTCCCCT
Found at i:52328188 original size:44 final size:41
Alignment explanation
Indices: 52328120--52328273 Score: 181
Period size: 44 Copynumber: 3.7 Consensus size: 41
52328110 CTTCCTCCCC
*
52328120 TCTTCTTCTTCTTTTTTTCTCTTCTCCTTTCCTTTTCTTTCAT
1 TCTTTTTCTTC-TTTTTTCTCTTCTCCTTTCCTTTTCTTTC-T
52328163 TCTTTTTCATTCTTTTTTCTTCTTCTCCTTTCCTTTTCTTTCCT
1 TCTTTTTC-TTCTTTTTTC-TCTTCTCCTTTCCTTTTCTTT-CT
*
52328207 TCTTTTTCTTTCTTTCTTTC-C-TCTCCTTTCTTTTTCTTTCT
1 TCTTTTTC-TTCTTT-TTTCTCTTCTCCTTTCCTTTTCTTTCT
* *
52328248 T-TTTTTCTTCTTCTTTC-CCTCTCCTT
1 TCTTTTTCTTCTTTTTTCTCTTCTCCTT
52328274 CTCTTCCCCC
Statistics
Matches: 102, Mismatches: 4, Indels: 14
0.85 0.03 0.12
Matches are distributed among these distances:
38 5 0.05
39 12 0.12
40 6 0.06
41 3 0.03
42 17 0.17
43 15 0.15
44 39 0.38
45 5 0.05
ACGTcount: A:0.01, C:0.31, G:0.00, T:0.68
Consensus pattern (41 bp):
TCTTTTTCTTCTTTTTTCTCTTCTCCTTTCCTTTTCTTTCT
Found at i:52328235 original size:18 final size:18
Alignment explanation
Indices: 52328178--52328239 Score: 63
Period size: 18 Copynumber: 3.4 Consensus size: 18
52328168 TTCATTCTTT
52328178 TTTC-TTCTTCTCCTTTCC
1 TTTCTTTCTT-TCCTTTCC
* * *
52328196 TTTTCTTTCCTTCTTTTTC
1 -TTTCTTTCTTTCCTTTCC
*
52328215 TTTCTTTCTTTCCTCTCC
1 TTTCTTTCTTTCCTTTCC
52328233 TTTCTTT
1 TTTCTTT
52328240 TTCTTTCTTT
Statistics
Matches: 35, Mismatches: 7, Indels: 3
0.78 0.16 0.07
Matches are distributed among these distances:
18 21 0.60
19 10 0.29
20 4 0.11
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (18 bp):
TTTCTTTCTTTCCTTTCC
Found at i:52328254 original size:18 final size:19
Alignment explanation
Indices: 52328191--52328265 Score: 71
Period size: 22 Copynumber: 3.8 Consensus size: 19
52328181 CTTCTTCTCC
*
52328191 TTTCCTTTTCTTTCCTTCTT
1 TTTCTTTTTCTTTCCTT-TT
**
52328211 TTTCTTTCTTTCTTTCCTCTCC
1 TTTC-TT-TTTCTTTCCT-TTT
52328233 TTTCTTTTTCTTT-CTTTT
1 TTTCTTTTTCTTTCCTTTT
*
52328251 TTTCTTCTTCTTTCC
1 TTTCTTTTTCTTTCC
52328266 CTCTCCTTCT
Statistics
Matches: 45, Mismatches: 6, Indels: 9
0.75 0.10 0.15
Matches are distributed among these distances:
18 13 0.29
19 3 0.07
20 11 0.24
21 3 0.07
22 14 0.31
23 1 0.02
ACGTcount: A:0.00, C:0.29, G:0.00, T:0.71
Consensus pattern (19 bp):
TTTCTTTTTCTTTCCTTTT
Found at i:52328261 original size:24 final size:24
Alignment explanation
Indices: 52328152--52328263 Score: 83
Period size: 28 Copynumber: 4.6 Consensus size: 24
52328142 TCTCCTTTCC
*
52328152 TTTTCTTTCATTCTTTTTCATTC-TT
1 TTTTC-TTC-TTCTTTTTCTTTCTTT
*
52328177 TTTTCTTCTTC---TCCTTTCCTTT
1 TTTTCTTCTTCTTTTTCTTT-CTTT
52328199 TCTTTC--CTTCTTTTTCTTTCTTT
1 T-TTTCTTCTTCTTTTTCTTTCTTT
*
52328222 CTTTCCTCTCCTTTCTTTTTCTTTCTTT
1 -TTT--TCTTC-TTCTTTTTCTTTCTTT
52328250 TTTTCTTCTTCTTT
1 TTTTCTTCTTCTTT
52328264 CCCTCTCCTT
Statistics
Matches: 71, Mismatches: 4, Indels: 25
0.71 0.04 0.25
Matches are distributed among these distances:
20 4 0.06
21 5 0.07
22 3 0.04
23 13 0.18
24 15 0.21
25 11 0.15
27 4 0.06
28 16 0.23
ACGTcount: A:0.02, C:0.27, G:0.00, T:0.71
Consensus pattern (24 bp):
TTTTCTTCTTCTTTTTCTTTCTTT
Found at i:52332298 original size:69 final size:70
Alignment explanation
Indices: 52332151--52332289 Score: 237
Period size: 69 Copynumber: 2.0 Consensus size: 70
52332141 TCGGATTTTT
*
52332151 AAAAAAA-GATCATGCCCAGTAAGTTAGGACACGATCTTTTCTTAATTCCCGAGATCGTTTAAAA
1 AAAAAAAGGATCATGCCCAATAAGTTAGGACACGA--TTTTCTTAATTCCCGAGATCGTTTAAAA
52332215 CTTGAGA
64 CTTGAGA
52332222 AAAAAAAGGATCATGCCCAATAAGTTAGGACACGA-TTTCTTAATTCCCGAGATCGTTTAAAACT
1 AAAAAAAGGATCATGCCCAATAAGTTAGGACACGATTTTCTTAATTCCCGAGATCGTTTAAAACT
52332286 TGAG
66 TGAG
52332290 TTTAAAAAGA
Statistics
Matches: 66, Mismatches: 1, Indels: 4
0.93 0.01 0.06
Matches are distributed among these distances:
69 33 0.50
71 7 0.11
72 26 0.39
ACGTcount: A:0.37, C:0.18, G:0.17, T:0.27
Consensus pattern (70 bp):
AAAAAAAGGATCATGCCCAATAAGTTAGGACACGATTTTCTTAATTCCCGAGATCGTTTAAAACT
TGAGA
Found at i:52332695 original size:16 final size:16
Alignment explanation
Indices: 52332674--52332704 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
52332664 AAGTAAAAGA
52332674 TATATATATGTATATG
1 TATATATATGTATATG
52332690 TATATATATGTATAT
1 TATATATATGTATAT
52332705 AAAAATTGTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.39, C:0.00, G:0.10, T:0.52
Consensus pattern (16 bp):
TATATATATGTATATG
Found at i:52332829 original size:21 final size:23
Alignment explanation
Indices: 52332802--52332849 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 23
52332792 AAATTATACA
52332802 ATATATAAAAAAT-ATAAG-TATGT
1 ATATAT-AAAAATCA-AAGATATGT
52332825 ATATATAAAAATCAAAGATATGT
1 ATATATAAAAATCAAAGATATGT
52332848 AT
1 AT
52332850 GTAGAATAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
22 9 0.39
23 14 0.61
ACGTcount: A:0.56, C:0.02, G:0.08, T:0.33
Consensus pattern (23 bp):
ATATATAAAAATCAAAGATATGT
Found at i:52333143 original size:3 final size:3
Alignment explanation
Indices: 52333135--52333218 Score: 89
Period size: 3 Copynumber: 27.3 Consensus size: 3
52333125 AAACTAATAC
*
52333135 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AGT AAT AACCT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA--T
* * * *
52333185 AATT AGT -TT AAT AAT AAT AAA AAT AAC AAT AAT A
1 AA-T AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
52333219 GGACTAAATT
Statistics
Matches: 68, Mismatches: 10, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
2 1 0.01
3 62 0.91
4 2 0.03
5 3 0.04
ACGTcount: A:0.62, C:0.04, G:0.02, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:52335570 original size:9 final size:9
Alignment explanation
Indices: 52335553--52335590 Score: 58
Period size: 9 Copynumber: 4.2 Consensus size: 9
52335543 AAAAATGGTA
52335553 AGAATTGAG
1 AGAATTGAG
*
52335562 AGAACTGAG
1 AGAATTGAG
*
52335571 AGAGTTGAG
1 AGAATTGAG
52335580 AGAATTGAG
1 AGAATTGAG
52335589 AG
1 AG
52335591 TTTAGAGAGA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
9 25 1.00
ACGTcount: A:0.42, C:0.03, G:0.37, T:0.18
Consensus pattern (9 bp):
AGAATTGAG
Found at i:52336579 original size:16 final size:17
Alignment explanation
Indices: 52336558--52336591 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
52336548 AAGTCAATAC
52336558 ACATCTTGTC-ACTTCA
1 ACATCTTGTCTACTTCA
*
52336574 ACATCTTTTCTACTTCA
1 ACATCTTGTCTACTTCA
52336591 A
1 A
52336592 GACGTTTTGA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 9 0.56
17 7 0.44
ACGTcount: A:0.26, C:0.29, G:0.03, T:0.41
Consensus pattern (17 bp):
ACATCTTGTCTACTTCA
Found at i:52348879 original size:5 final size:5
Alignment explanation
Indices: 52348869--52348949 Score: 85
Period size: 5 Copynumber: 16.2 Consensus size: 5
52348859 AAAATGCATC
* **
52348869 ATAAA ATAAA ATAAA ATAAA ATAAA ATAAA ATAAA ATAAA AGAATAA ATCCA
1 ATAAA ATAAA ATAAA ATAAA ATAAA ATAAA ATAAA ATAAA A-TA-AA ATAAA
* *
52348921 A-AAA ATAAA AAAAA AT-AA AGAAA ATAAA A
1 ATAAA ATAAA ATAAA ATAAA ATAAA ATAAA A
52348950 ATAAGGCTTC
Statistics
Matches: 62, Mismatches: 10, Indels: 8
0.77 0.12 0.10
Matches are distributed among these distances:
4 5 0.08
5 53 0.85
6 1 0.02
7 3 0.05
ACGTcount: A:0.79, C:0.02, G:0.02, T:0.16
Consensus pattern (5 bp):
ATAAA
Found at i:52348999 original size:16 final size:16
Alignment explanation
Indices: 52348978--52349008 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
52348968 GTAGGGAGGA
*
52348978 ACAAAAGAATAAAACG
1 ACAAAAGAAAAAAACG
52348994 ACAAAAGAAAAAAAC
1 ACAAAAGAAAAAAAC
52349009 ATCTTTAAAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.74, C:0.13, G:0.10, T:0.03
Consensus pattern (16 bp):
ACAAAAGAAAAAAACG
Found at i:52351753 original size:34 final size:34
Alignment explanation
Indices: 52351710--52351775 Score: 132
Period size: 34 Copynumber: 1.9 Consensus size: 34
52351700 AACATGTTAC
52351710 TTTTAGCACTTATCATGAATAGAATAATTACCCA
1 TTTTAGCACTTATCATGAATAGAATAATTACCCA
52351744 TTTTAGCACTTATCATGAATAGAATAATTACC
1 TTTTAGCACTTATCATGAATAGAATAATTACC
52351776 TTACAAAAAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 32 1.00
ACGTcount: A:0.38, C:0.17, G:0.09, T:0.36
Consensus pattern (34 bp):
TTTTAGCACTTATCATGAATAGAATAATTACCCA
Found at i:52359983 original size:14 final size:14
Alignment explanation
Indices: 52359964--52360001 Score: 58
Period size: 15 Copynumber: 2.6 Consensus size: 14
52359954 GCTCAATGAA
52359964 TTTTTTTTCTTTCCT
1 TTTTTTTTCTTT-CT
52359979 TTTTTTTTCTTTCT
1 TTTTTTTTCTTTCT
52359993 TCTTTTTTT
1 T-TTTTTTT
52360002 AGAACAAGAA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
14 3 0.14
15 19 0.86
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (14 bp):
TTTTTTTTCTTTCT
Found at i:52363602 original size:31 final size:32
Alignment explanation
Indices: 52363559--52363619 Score: 97
Period size: 31 Copynumber: 1.9 Consensus size: 32
52363549 TCGTGTGGCC
52363559 TTTTTTATTTTTTAAGTAAAATAAACAAACCG
1 TTTTTTATTTTTTAAGTAAAATAAACAAACCG
**
52363591 TTTTTTA-TTTTTATTTAAAATAAACAAAC
1 TTTTTTATTTTTTAAGTAAAATAAACAAAC
52363620 TAAAAATAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
31 20 0.74
32 7 0.26
ACGTcount: A:0.41, C:0.08, G:0.03, T:0.48
Consensus pattern (32 bp):
TTTTTTATTTTTTAAGTAAAATAAACAAACCG
Found at i:52366658 original size:19 final size:18
Alignment explanation
Indices: 52366632--52366674 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 18
52366622 ATTAGAATGT
*
52366632 AAAAATTAAATTAAAAAC
1 AAAAATTAAAATAAAAAC
*
52366650 AAAATATTAAAATAAAAAT
1 AAAA-ATTAAAATAAAAAC
52366669 AAAAAT
1 AAAAAT
52366675 GGCTAAATTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
18 6 0.27
19 16 0.73
ACGTcount: A:0.74, C:0.02, G:0.00, T:0.23
Consensus pattern (18 bp):
AAAAATTAAAATAAAAAC
Found at i:52367493 original size:20 final size:21
Alignment explanation
Indices: 52367454--52367494 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
52367444 CTTGCATGGT
52367454 ATGATTTTGAATTATGTTTTTA
1 ATGATTTT-AATTATGTTTTTA
*
52367476 ATGATTTT-ATTTTGTTTTT
1 ATGATTTTAATTATGTTTTT
52367495 GAGGTTGTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 10 0.56
22 8 0.44
ACGTcount: A:0.22, C:0.00, G:0.12, T:0.66
Consensus pattern (21 bp):
ATGATTTTAATTATGTTTTTA
Found at i:52371186 original size:4 final size:4
Alignment explanation
Indices: 52371177--52371223 Score: 94
Period size: 4 Copynumber: 11.8 Consensus size: 4
52371167 TGAAGGATAA
52371177 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TAT
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TAT
52371224 ATCTACATCC
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 43 1.00
ACGTcount: A:0.26, C:0.00, G:0.23, T:0.51
Consensus pattern (4 bp):
TATG
Done.