Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: chr4
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: 31929104
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 1434590 characters in sequence are not A, C, G, or T
File 54 of 82
Found at i:19762244 original size:21 final size:20
Alignment explanation
Indices: 19762218--19762283 Score: 57
Period size: 21 Copynumber: 3.2 Consensus size: 20
19762208 ATCATATTTT
19762218 TTATTTTATTTCTAATTACTA
1 TTATTTTATTT-TAATTACTA
19762239 TTATTTT-TTTTATACCTTAC-A
1 TTATTTTATTTTA-A--TTACTA
*
19762260 TT-TTTTATTTTAAGTTACTC
1 TTATTTTATTTTAA-TTACTA
19762280 TTAT
1 TTAT
19762284 ATTTTCCTTT
Statistics
Matches: 37, Mismatches: 2, Indels: 12
0.73 0.04 0.24
Matches are distributed among these distances:
19 6 0.16
20 11 0.30
21 16 0.43
22 4 0.11
ACGTcount: A:0.24, C:0.11, G:0.02, T:0.64
Consensus pattern (20 bp):
TTATTTTATTTTAATTACTA
Found at i:19762365 original size:12 final size:12
Alignment explanation
Indices: 19762348--19762400 Score: 52
Period size: 14 Copynumber: 4.1 Consensus size: 12
19762338 AAAAATTTTA
19762348 TATTTTATATTT
1 TATTTTATATTT
19762360 TATTTTATATTTT
1 TATTTTATA-TTT
* *
19762373 TATATTTTTATATA
1 TAT-TTTATAT-TT
19762387 TATTTTTATATTT
1 TA-TTTTATATTT
19762400 T
1 T
19762401 TATATTTTTA
Statistics
Matches: 33, Mismatches: 4, Indels: 7
0.75 0.09 0.16
Matches are distributed among these distances:
12 9 0.27
13 9 0.27
14 14 0.42
15 1 0.03
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (12 bp):
TATTTTATATTT
Found at i:19762375 original size:8 final size:8
Alignment explanation
Indices: 19762343--19762426 Score: 87
Period size: 8 Copynumber: 11.5 Consensus size: 8
19762333 GTGACAAAAA
19762343 TTTTATA-
1 TTTTATAT
19762350 TTTTATA-
1 TTTTATAT
19762357 -TTT-TA-
1 TTTTATAT
19762362 TTTTATAT
1 TTTTATAT
19762370 TTTTATAT
1 TTTTATAT
19762378 TTTTATA-
1 TTTTATAT
19762385 ---TATAT
1 TTTTATAT
19762390 TTTTATAT
1 TTTTATAT
19762398 TTTTATAT
1 TTTTATAT
19762406 TTTTATCAT
1 TTTTAT-AT
*
19762415 TATTATAT
1 TTTTATAT
19762423 TTTT
1 TTTT
19762427 TCGTAAGCAA
Statistics
Matches: 67, Mismatches: 2, Indels: 15
0.80 0.02 0.18
Matches are distributed among these distances:
4 4 0.06
5 2 0.03
6 6 0.09
7 9 0.13
8 39 0.58
9 7 0.10
ACGTcount: A:0.26, C:0.01, G:0.00, T:0.73
Consensus pattern (8 bp):
TTTTATAT
Found at i:19762401 original size:20 final size:20
Alignment explanation
Indices: 19762346--19762405 Score: 88
Period size: 20 Copynumber: 3.0 Consensus size: 20
19762336 ACAAAAATTT
*
19762346 TATA-TTTTATA-TTTTATTT
1 TATATTTTTATATTTTTA-TA
19762365 TATATTTTTATATTTTTATA
1 TATATTTTTATATTTTTATA
19762385 TATATTTTTATATTTTTATA
1 TATATTTTTATATTTTTATA
19762405 T
1 T
19762406 TTTTATCATT
Statistics
Matches: 38, Mismatches: 1, Indels: 3
0.90 0.02 0.07
Matches are distributed among these distances:
19 4 0.11
20 29 0.76
21 5 0.13
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (20 bp):
TATATTTTTATATTTTTATA
Found at i:19762418 original size:20 final size:19
Alignment explanation
Indices: 19762343--19762418 Score: 79
Period size: 18 Copynumber: 4.1 Consensus size: 19
19762333 GTGACAAAAA
*
19762343 TTTTATA-TTTTATATTTT
1 TTTTATATTTTTATATTAT
19762361 ATTTTATATTTTTATATT-T
1 -TTTTATATTTTTATATTAT
*
19762380 TTATATATATTTT-TA-TAT
1 TTTTATAT-TTTTATATTAT
19762398 TTTTATATTTTTATCATTAT
1 TTTTATATTTTTAT-ATTAT
19762418 T
1 T
19762419 ATATTTTTTC
Statistics
Matches: 49, Mismatches: 2, Indels: 11
0.79 0.03 0.18
Matches are distributed among these distances:
17 5 0.10
18 18 0.37
19 13 0.27
20 13 0.27
ACGTcount: A:0.26, C:0.01, G:0.00, T:0.72
Consensus pattern (19 bp):
TTTTATATTTTTATATTAT
Found at i:19762418 original size:28 final size:27
Alignment explanation
Indices: 19762343--19762418 Score: 109
Period size: 28 Copynumber: 2.7 Consensus size: 27
19762333 GTGACAAAAA
*
19762343 TTTTATA-TTTTATATTTTATTTTATAT
1 TTTTATATTTTTATATTAT-TTTTATAT
19762370 TTTTATATTTTTATATATATTTTTATAT
1 TTTTATATTTTTATAT-TATTTTTATAT
19762398 TTTTATATTTTTATCATTATT
1 TTTTATATTTTTAT-ATTATT
19762419 ATATTTTTTC
Statistics
Matches: 45, Mismatches: 1, Indels: 5
0.88 0.02 0.10
Matches are distributed among these distances:
27 7 0.16
28 34 0.76
29 4 0.09
ACGTcount: A:0.26, C:0.01, G:0.00, T:0.72
Consensus pattern (27 bp):
TTTTATATTTTTATATTATTTTTATAT
Found at i:19762420 original size:17 final size:16
Alignment explanation
Indices: 19762343--19762426 Score: 79
Period size: 17 Copynumber: 5.2 Consensus size: 16
19762333 GTGACAAAAA
19762343 TTTTATATT-TTATA-
1 TTTTATATTATTATAT
19762357 -TTT-TATT-TTATAT
1 TTTTATATTATTATAT
19762370 TTTTATATTTTTATATATAT
1 TTTTATA---TTAT-TATAT
*
19762390 TTTTATATTTTTATAT
1 TTTTATATTATTATAT
19762406 TTTTATCATTATTATAT
1 TTTTAT-ATTATTATAT
19762423 TTTT
1 TTTT
19762427 TCGTAAGCAA
Statistics
Matches: 59, Mismatches: 2, Indels: 15
0.78 0.03 0.20
Matches are distributed among these distances:
12 9 0.15
13 3 0.05
14 3 0.05
15 2 0.03
16 11 0.19
17 16 0.27
18 2 0.03
19 1 0.02
20 12 0.20
ACGTcount: A:0.26, C:0.01, G:0.00, T:0.73
Consensus pattern (16 bp):
TTTTATATTATTATAT
Found at i:19762710 original size:11 final size:11
Alignment explanation
Indices: 19762682--19762728 Score: 69
Period size: 11 Copynumber: 4.2 Consensus size: 11
19762672 CGAATTATTA
19762682 ATATTATTTTT
1 ATATTATTTTT
19762693 ATCATTATTTTT
1 AT-ATTATTTTT
19762705 ATATTATTTTT
1 ATATTATTTTT
19762716 AT-TTATTTATT
1 ATATTATTT-TT
19762727 AT
1 AT
19762729 TTTTATTGAA
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
10 6 0.18
11 17 0.50
12 11 0.32
ACGTcount: A:0.28, C:0.02, G:0.00, T:0.70
Consensus pattern (11 bp):
ATATTATTTTT
Found at i:19762717 original size:17 final size:17
Alignment explanation
Indices: 19762697--19762735 Score: 62
Period size: 17 Copynumber: 2.3 Consensus size: 17
19762687 ATTTTTATCA
19762697 TTATTT-TTATATTATTT
1 TTATTTATT-TATTATTT
19762714 TTATTTATTTATTATTT
1 TTATTTATTTATTATTT
19762731 TTATT
1 TTATT
19762736 GAATAATTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
17 19 0.90
18 2 0.10
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (17 bp):
TTATTTATTTATTATTT
Found at i:19762735 original size:23 final size:23
Alignment explanation
Indices: 19762676--19762728 Score: 74
Period size: 23 Copynumber: 2.3 Consensus size: 23
19762666 TATATTCGAA
19762676 TTATTAATATTATTTTTATCATTAT
1 TTATT-ATATTATTTTTAT-ATTAT
19762701 TT-TTATATTATTTTTAT-TTAT
1 TTATTATATTATTTTTATATTAT
19762722 TTATTAT
1 TTATTAT
19762729 TTTTATTGAA
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
21 6 0.22
22 4 0.15
23 13 0.48
24 2 0.07
25 2 0.07
ACGTcount: A:0.28, C:0.02, G:0.00, T:0.70
Consensus pattern (23 bp):
TTATTATATTATTTTTATATTAT
Found at i:19763743 original size:36 final size:35
Alignment explanation
Indices: 19763693--19763814 Score: 136
Period size: 36 Copynumber: 3.3 Consensus size: 35
19763683 CTTTCTCACC
* * *
19763693 ATGCCCGTCGACGATCGGCTCTCTCCCTCTTTCTCT
1 ATGCCCGCCAACGATCAGCTCTCTCCCTCTTT-TCT
* *
19763729 ATGCCCGCCAACGATCAGCTCTCTCTCTCCCTTTCT
1 ATGCCCGCCAACGATCAGCTCTCTCCCT-CTTTTCT
* *
19763765 ATGCCCGCCAACTATCAACTCTCTCTCTCTCTCTTTCT
1 ATGCCCGCCAACGATCAGCTCTCTC-C-CTCT-TTTCT
19763803 ATGCCCGCCAAC
1 ATGCCCGCCAAC
19763815 CTCCTTCTCT
Statistics
Matches: 73, Mismatches: 9, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
36 50 0.68
37 4 0.05
38 19 0.26
ACGTcount: A:0.14, C:0.43, G:0.11, T:0.31
Consensus pattern (35 bp):
ATGCCCGCCAACGATCAGCTCTCTCCCTCTTTTCT
Found at i:19763753 original size:38 final size:37
Alignment explanation
Indices: 19763711--19763814 Score: 140
Period size: 36 Copynumber: 2.8 Consensus size: 37
19763701 CGACGATCGG
*
19763711 CTCTCTCCCTCTTTCTCTATGCCCGCCAACGATCAGCT
1 CTCTCTCCCTCTTT-TCTATGCCCGCCAACGATCAACT
*
19763749 CTCTCTCTCC-C-TTTCTATGCCCGCCAACTATCAACT
1 CTCTCTC-CCTCTTTTCTATGCCCGCCAACGATCAACT
*
19763785 CTCTCTCTCTCTCTTTCTATGCCCGCCAAC
1 CTCTCTCCCTCT-TTTCTATGCCCGCCAAC
19763815 CTCCTTCTCT
Statistics
Matches: 59, Mismatches: 3, Indels: 8
0.84 0.04 0.11
Matches are distributed among these distances:
35 1 0.02
36 29 0.49
37 2 0.03
38 25 0.42
39 2 0.03
ACGTcount: A:0.13, C:0.45, G:0.08, T:0.34
Consensus pattern (37 bp):
CTCTCTCCCTCTTTTCTATGCCCGCCAACGATCAACT
Found at i:19781332 original size:102 final size:102
Alignment explanation
Indices: 19781150--19781357 Score: 362
Period size: 102 Copynumber: 2.0 Consensus size: 102
19781140 AGATTGCTCC
* * *
19781150 TATTGACTCACATCAGCGATGTGACAAAGGATCGCATAGTTCTTATTGATGCCATTTTGATGCAT
1 TATTCACTCACATCAGCGATGTGACAAAAGATCACATAGTTCTTATTGATGCCATTTTGATGCAT
* *
19781215 AAATCCATTGCTATTGGGAAAGTTATCTTTCATGCCA
66 AAATCCATTGATATTGAGAAAGTTATCTTTCATGCCA
*
19781252 TATTCACTCACATCAGCTATGTGACAAAAGATCACATAGTTCTTATTGATGCCATTTTGATGCAT
1 TATTCACTCACATCAGCGATGTGACAAAAGATCACATAGTTCTTATTGATGCCATTTTGATGCAT
19781317 AAATCCATTGATATTGAGAAAGTTATCTTTCATGCCA
66 AAATCCATTGATATTGAGAAAGTTATCTTTCATGCCA
19781354 TATT
1 TATT
19781358 GCATACAGAC
Statistics
Matches: 100, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
102 100 1.00
ACGTcount: A:0.30, C:0.18, G:0.16, T:0.36
Consensus pattern (102 bp):
TATTCACTCACATCAGCGATGTGACAAAAGATCACATAGTTCTTATTGATGCCATTTTGATGCAT
AAATCCATTGATATTGAGAAAGTTATCTTTCATGCCA
Found at i:19783222 original size:35 final size:36
Alignment explanation
Indices: 19783162--19783230 Score: 104
Period size: 35 Copynumber: 1.9 Consensus size: 36
19783152 TGTGATAACT
* *
19783162 TTTACTTTTGCTTTTTTACGGGATCAAGCGATAATC
1 TTTACTTTAGCTTTTTTACGAGATCAAGCGATAATC
*
19783198 TTTACTTTAGC-TTTTTACGAGATCAAGTGATAA
1 TTTACTTTAGCTTTTTTACGAGATCAAGCGATAA
19783231 CCTTCACACT
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
35 20 0.67
36 10 0.33
ACGTcount: A:0.26, C:0.14, G:0.16, T:0.43
Consensus pattern (36 bp):
TTTACTTTAGCTTTTTTACGAGATCAAGCGATAATC
Found at i:19783247 original size:35 final size:35
Alignment explanation
Indices: 19783174--19783247 Score: 85
Period size: 35 Copynumber: 2.1 Consensus size: 35
19783164 TACTTTTGCT
* * * ** *
19783174 TTTTTACGGGATCAAGCGATAATCTTTACTTTAGC
1 TTTTTACGAGATCAAGCGATAACCTTCACACTAAC
*
19783209 TTTTTACGAGATCAAGTGATAACCTTCACACTAAC
1 TTTTTACGAGATCAAGCGATAACCTTCACACTAAC
19783244 TTTT
1 TTTT
19783248 CAAAATTAAG
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
35 32 1.00
ACGTcount: A:0.28, C:0.19, G:0.14, T:0.39
Consensus pattern (35 bp):
TTTTTACGAGATCAAGCGATAACCTTCACACTAAC
Found at i:19788406 original size:15 final size:15
Alignment explanation
Indices: 19788386--19788418 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
19788376 ATGCAATCAC
19788386 ATTGTA-AGAAATGTG
1 ATTGTAGAG-AATGTG
19788401 ATTGTAGAGAATGTG
1 ATTGTAGAGAATGTG
19788416 ATT
1 ATT
19788419 ACAAAGAGTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 15 0.88
16 2 0.12
ACGTcount: A:0.36, C:0.00, G:0.27, T:0.36
Consensus pattern (15 bp):
ATTGTAGAGAATGTG
Found at i:19789091 original size:158 final size:158
Alignment explanation
Indices: 19788803--19789102 Score: 503
Period size: 158 Copynumber: 1.9 Consensus size: 158
19788793 ATGAGTAAAT
* *
19788803 TATATGAGTTTGGAAACTTAAATCTGGTTAGGGGTAGCGAAATCAATCAGTTTATAGGTGATGCG
1 TATATGAGTTTGGAAACTTAAATCTGGCTAGGGGTAGCGAAATCAATCAGTTTATAGGCGATGCG
* * * * *
19788868 TGAATATTTGTTAGGCATTGAGTCAGTGGATATTAGGGTGTGTGATTGGATATTAGGAATCGTTA
66 TGAATATTTGTTAAGCATTGAGTCACTGAATATTAAGGTGTGTGACTGGATATTAGGAATCGTTA
*
19788933 CCTGTTTATTTGGCATTTGGTGCCTGAA
131 CCTATTTATTTGGCATTTGGTGCCTGAA
*
19788961 TATATGAGTTTGGAAACTTAAATCTGGCT-GGAGGTAGCGAAATCAATTAGTTTATAGGCGATGC
1 TATATGAGTTTGGAAACTTAAATCTGGCTAGG-GGTAGCGAAATCAATCAGTTTATAGGCGATGC
19789025 GTGAATATTTGTTAAGCATTGAGTCACTGAATATTAAGGTGTGTGACTGGATATTAGGAATCGTT
65 GTGAATATTTGTTAAGCATTGAGTCACTGAATATTAAGGTGTGTGACTGGATATTAGGAATCGTT
19789090 ACCTATTTATTTG
130 ACCTATTTATTTG
19789103 AAATTAGGTG
Statistics
Matches: 132, Mismatches: 9, Indels: 2
0.92 0.06 0.01
Matches are distributed among these distances:
157 2 0.02
158 130 0.98
ACGTcount: A:0.28, C:0.09, G:0.27, T:0.36
Consensus pattern (158 bp):
TATATGAGTTTGGAAACTTAAATCTGGCTAGGGGTAGCGAAATCAATCAGTTTATAGGCGATGCG
TGAATATTTGTTAAGCATTGAGTCACTGAATATTAAGGTGTGTGACTGGATATTAGGAATCGTTA
CCTATTTATTTGGCATTTGGTGCCTGAA
Found at i:19789191 original size:48 final size:46
Alignment explanation
Indices: 19789120--19789290 Score: 219
Period size: 48 Copynumber: 3.8 Consensus size: 46
19789110 GTGCTTAAAT
* *
19789120 ATTACGTGATTGAATATTTGTTGAGCATTGTGTGAGTTCTTTATTGGC
1 ATTACGTGACTGAATATTTGTTGAGCATTGCGTGAGTT-TTTA-TGGC
* *
19789168 ATTACGTGAATGAATATTTGTTGAGCGTTGCGTGA-----TA-GGC
1 ATTACGTGACTGAATATTTGTTGAGCATTGCGTGAGTTTTTATGGC
19789208 ATTACGTGACTGAATATTTGTTGAGCATTGCGTGAGTTTTTTATAGGC
1 ATTACGTGACTGAATATTTGTTGAGCATTGCGTGAG-TTTTTAT-GGC
*
19789256 ATTACGTGACTGAATATTTGTTGAGCGTTGCGTGA
1 ATTACGTGACTGAATATTTGTTGAGCATTGCGTGA
19789291 CAAGCATTAC
Statistics
Matches: 109, Mismatches: 6, Indels: 16
0.83 0.05 0.12
Matches are distributed among these distances:
40 36 0.33
42 2 0.02
46 2 0.02
48 69 0.63
ACGTcount: A:0.23, C:0.10, G:0.27, T:0.40
Consensus pattern (46 bp):
ATTACGTGACTGAATATTTGTTGAGCATTGCGTGAGTTTTTATGGC
Found at i:19789209 original size:40 final size:40
Alignment explanation
Indices: 19789165--19789313 Score: 172
Period size: 40 Copynumber: 3.5 Consensus size: 40
19789155 GTTCTTTATT
*
19789165 GGCATTACGTGAATGAATATTTGTTGAGCGTTGCGTGATA
1 GGCATTACGTGACTGAATATTTGTTGAGCGTTGCGTGATA
*
19789205 GGCATTACGTGACTGAATATTTGTTGAGCATTGCGTGAGTTTTTTATA
1 GGCATTACGTGACTGAATATTTGTTGAGCGTTGCGT--G------ATA
*
19789253 GGCATTACGTGACTGAATATTTGTTGAGCGTTGCGTGACA
1 GGCATTACGTGACTGAATATTTGTTGAGCGTTGCGTGATA
* * *
19789293 AGCATTACATGATTGAATATT
1 GGCATTACGTGACTGAATATT
19789314 ATATGACTGA
Statistics
Matches: 94, Mismatches: 7, Indels: 16
0.80 0.06 0.14
Matches are distributed among these distances:
40 54 0.57
42 1 0.01
46 1 0.01
48 38 0.40
ACGTcount: A:0.26, C:0.11, G:0.26, T:0.37
Consensus pattern (40 bp):
GGCATTACGTGACTGAATATTTGTTGAGCGTTGCGTGATA
Found at i:19789222 original size:88 final size:88
Alignment explanation
Indices: 19789120--19789313 Score: 316
Period size: 88 Copynumber: 2.2 Consensus size: 88
19789110 GTGCTTAAAT
* *
19789120 ATTACGTGATTGAATATTTGTTGAGCATTGTGTGAGTTCTTTATTGGCATTACGTGAATGAATAT
1 ATTACGTGATTGAATATTTGTTGAGCATTGCGTGAGTTCTTTATAGGCATTACGTGAATGAATAT
* *
19789185 TTGTTGAGCGTTGCGTGATAGGC
66 TTGTTGAGCGTTGCGTGACAAGC
* * *
19789208 ATTACGTGACTGAATATTTGTTGAGCATTGCGTGAGTTTTTTATAGGCATTACGTGACTGAATAT
1 ATTACGTGATTGAATATTTGTTGAGCATTGCGTGAGTTCTTTATAGGCATTACGTGAATGAATAT
19789273 TTGTTGAGCGTTGCGTGACAAGC
66 TTGTTGAGCGTTGCGTGACAAGC
*
19789296 ATTACATGATTGAATATT
1 ATTACGTGATTGAATATT
19789314 ATATGACTGA
Statistics
Matches: 97, Mismatches: 9, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
88 97 1.00
ACGTcount: A:0.25, C:0.10, G:0.25, T:0.40
Consensus pattern (88 bp):
ATTACGTGATTGAATATTTGTTGAGCATTGCGTGAGTTCTTTATAGGCATTACGTGAATGAATAT
TTGTTGAGCGTTGCGTGACAAGC
Found at i:19789242 original size:26 final size:26
Alignment explanation
Indices: 19789206--19789291 Score: 81
Period size: 26 Copynumber: 3.5 Consensus size: 26
19789196 TGCGTGATAG
19789206 GCATTACGTGACTGAATATTTGTTGA
1 GCATTACGTGACTGAATATTTGTTGA
* * * * *
19789232 GCATTGCGTGA--G-TTTTTTATAG-
1 GCATTACGTGACTGAATATTTGTTGA
19789254 GCATTACGTGACTGAATATTTGTTGA
1 GCATTACGTGACTGAATATTTGTTGA
* *
19789280 GCGTTGCGTGAC
1 GCATTACGTGAC
19789292 AAGCATTACA
Statistics
Matches: 44, Mismatches: 12, Indels: 8
0.69 0.19 0.12
Matches are distributed among these distances:
22 10 0.23
23 6 0.14
24 2 0.05
25 6 0.14
26 20 0.45
ACGTcount: A:0.22, C:0.13, G:0.27, T:0.38
Consensus pattern (26 bp):
GCATTACGTGACTGAATATTTGTTGA
Found at i:19790529 original size:213 final size:213
Alignment explanation
Indices: 19790160--19790562 Score: 682
Period size: 213 Copynumber: 1.9 Consensus size: 213
19790150 CGTTTCACGG
* * *
19790160 TCTGGTTGGGGAACAGAATATGTCATTCCTACGAAAACCTTAGATGATTCATCCAAATCTACTGG
1 TCTGGTTAGGGAACAGAAGATGTCATTCCTACGAAAACCTTAGATGATTCATCCAAATATACTGG
* *
19790225 CTGGGAACAACAAAAGTCACCTGAATGTTATGAAGGTTGGGGCTCTCTTGATGAGTCAAATCAAC
66 CTGGGAACAACAAAAGTCACCAGAATGTTATGAAGGTTGGGACTCTCTTGATGAGTCAAATCAAC
*
19790290 TAGCAAGTTCAAATGGCTAGGATACACCAAATGGTTTGGGTAGCACTCAAAGTGAAAAACCTTAT
131 TAACAAGTTCAAATGGCTAGGATACACCAAATGGTTTGGGTAGCACTCAAAGTGAAAAACCTTAT
19790355 AGTGATGCACTGCCATAA
196 AGTGATGCACTGCCATAA
* * *
19790373 TCTGGTTAGGGAACAGAAGATGTCATTCCTACGAAAACCTTGGATGATTCTTCCAAATATATTGG
1 TCTGGTTAGGGAACAGAAGATGTCATTCCTACGAAAACCTTAGATGATTCATCCAAATATACTGG
* *
19790438 CTGGGAAGAACAAAAGTCACCAGAATGTTATGAAGGTTTGGACTCTCTTGATGAGTCAAATCAAC
66 CTGGGAACAACAAAAGTCACCAGAATGTTATGAAGGTTGGGACTCTCTTGATGAGTCAAATCAAC
*
19790503 TAACAAGTTCAATTGGCT-GAGATACACCAAATGGTTTGGGTAGCACTCAAAGTGAAAAAC
131 TAACAAGTTCAAATGGCTAG-GATACACCAAATGGTTTGGGTAGCACTCAAAGTGAAAAAC
19790563 AGCATCAGTC
Statistics
Matches: 177, Mismatches: 12, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
212 1 0.01
213 176 0.99
ACGTcount: A:0.34, C:0.18, G:0.22, T:0.26
Consensus pattern (213 bp):
TCTGGTTAGGGAACAGAAGATGTCATTCCTACGAAAACCTTAGATGATTCATCCAAATATACTGG
CTGGGAACAACAAAAGTCACCAGAATGTTATGAAGGTTGGGACTCTCTTGATGAGTCAAATCAAC
TAACAAGTTCAAATGGCTAGGATACACCAAATGGTTTGGGTAGCACTCAAAGTGAAAAACCTTAT
AGTGATGCACTGCCATAA
Found at i:19791969 original size:46 final size:46
Alignment explanation
Indices: 19791916--19792058 Score: 135
Period size: 46 Copynumber: 3.1 Consensus size: 46
19791906 TAGAATAAAC
*
19791916 ACTCACGCCATTCCATAATAACTAGTAACGCCACTCCACATATATT
1 ACTCACGCGATTCCATAATAACTAGTAACGCCACTCCACATATATT
* * * * * * *
19791962 ACTCACGCGAGTCAAT-ATAAACTAGTGACGCGATTCCACAAAAATT
1 ACTCACGCGATTCCATAAT-AACTAGTAACGCCACTCCACATATATT
* * * * *
19792008 CATGTCACGCGTTTCCATATTAACTAGTAACGCCACTCCATATTTATT
1 -A-CTCACGCGATTCCATAATAACTAGTAACGCCACTCCACATATATT
19792056 ACT
1 ACT
19792059 AAAGGGAGTC
Statistics
Matches: 72, Mismatches: 21, Indels: 8
0.71 0.21 0.08
Matches are distributed among these distances:
45 2 0.03
46 36 0.50
47 2 0.03
48 31 0.43
49 1 0.01
ACGTcount: A:0.34, C:0.28, G:0.10, T:0.28
Consensus pattern (46 bp):
ACTCACGCGATTCCATAATAACTAGTAACGCCACTCCACATATATT
Found at i:19795623 original size:26 final size:26
Alignment explanation
Indices: 19795591--19795640 Score: 91
Period size: 26 Copynumber: 1.9 Consensus size: 26
19795581 ATAAATGAAT
*
19795591 ACAAAGAATAATATGTAAATGATACA
1 ACAAAGAATAATATGGAAATGATACA
19795617 ACAAAGAATAATATGGAAATGATA
1 ACAAAGAATAATATGGAAATGATA
19795641 TAGAATAATG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.58, C:0.06, G:0.14, T:0.22
Consensus pattern (26 bp):
ACAAAGAATAATATGGAAATGATACA
Found at i:19795626 original size:23 final size:24
Alignment explanation
Indices: 19795582--19795638 Score: 60
Period size: 26 Copynumber: 2.3 Consensus size: 24
19795572 GCTTATCACA
*
19795582 TAAATGAATACAAAGAATAATATG
1 TAAATGAATACAAAGAAGAATATG
* *
19795606 TAAATGATACAACAAAGAATAATATG
1 TAAATGA-A-TACAAAGAAGAATATG
*
19795632 GAAATGA
1 TAAATGA
19795639 TATAGAATAA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
24 7 0.24
25 1 0.03
26 21 0.72
ACGTcount: A:0.58, C:0.05, G:0.14, T:0.23
Consensus pattern (24 bp):
TAAATGAATACAAAGAAGAATATG
Found at i:19797244 original size:24 final size:24
Alignment explanation
Indices: 19797212--19797281 Score: 113
Period size: 24 Copynumber: 2.9 Consensus size: 24
19797202 TCGCCCTCTA
*
19797212 GATCTCCAACTACATTGACTGCTG
1 GATCTCCAACTGCATTGACTGCTG
*
19797236 GATCTCCAACTGCATTGACTGTTG
1 GATCTCCAACTGCATTGACTGCTG
*
19797260 GATCTCTAACTGCATTGACTGC
1 GATCTCCAACTGCATTGACTGC
19797282 ATCTGCATCT
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 42 1.00
ACGTcount: A:0.23, C:0.27, G:0.19, T:0.31
Consensus pattern (24 bp):
GATCTCCAACTGCATTGACTGCTG
Found at i:19797450 original size:24 final size:24
Alignment explanation
Indices: 19797409--19797458 Score: 64
Period size: 24 Copynumber: 2.1 Consensus size: 24
19797399 AACTCAGCAT
* *
19797409 GAGGGGCAGCACCTGAAGTAGGAG
1 GAGGGGCAGCACCAGAAGCAGGAG
* *
19797433 GAGGGGCAGTAGCAGAAGCAGGAG
1 GAGGGGCAGCACCAGAAGCAGGAG
19797457 GA
1 GA
19797459 AGAACAGCGA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.32, C:0.14, G:0.48, T:0.06
Consensus pattern (24 bp):
GAGGGGCAGCACCAGAAGCAGGAG
Found at i:19828407 original size:24 final size:24
Alignment explanation
Indices: 19828361--19828407 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 24
19828351 AATTTGGATG
* * * *
19828361 AACATGGTATGTAATATTTTTTTC
1 AACATGGCATGTAACAATATTTTC
19828385 AACATGGCATGTAACAATATTTT
1 AACATGGCATGTAACAATATTTT
19828408 TCGATATGAC
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.34, C:0.11, G:0.13, T:0.43
Consensus pattern (24 bp):
AACATGGCATGTAACAATATTTTC
Found at i:19836694 original size:108 final size:105
Alignment explanation
Indices: 19836547--19836753 Score: 326
Period size: 108 Copynumber: 1.9 Consensus size: 105
19836537 TATGAGAAAT
* *
19836547 TTTGAGTAAATTTAAATAAAAAGGTAAATTTGGTAAGAGTTGAATAATTGCAAAAGAATGTGTAT
1 TTTGAGTAAATTTAAATAAAAAGGTAAATTGGGTAAGAGTTGAATAATTGCAAAAAAATGTGTAT
19836612 TTGTAAATCGTGAAAGTTGTAACTAAATCAACATATTTTGCTAA
66 TTGT--AT--TGAAAGTTGTAACTAAATCAACATATTTTGCTAA
*
19836656 TTTGAGTAAATTTAAAT-AAAAGGTAAATTGGGTAAGAGTTGAATAATTTCAAAAAAATGTGTAT
1 TTTGAGTAAATTTAAATAAAAAGGTAAATTGGGTAAGAGTTGAATAATTGCAAAAAAATGTGTAT
* *
19836720 TTGTATTTAAAGTTGTAATTAAATCAACATATTT
66 TTGTATTGAAAGTTGTAACTAAATCAACATATTT
19836754 AGTCATTTTA
Statistics
Matches: 93, Mismatches: 5, Indels: 5
0.90 0.05 0.05
Matches are distributed among these distances:
104 26 0.28
106 2 0.02
108 48 0.52
109 17 0.18
ACGTcount: A:0.43, C:0.04, G:0.16, T:0.37
Consensus pattern (105 bp):
TTTGAGTAAATTTAAATAAAAAGGTAAATTGGGTAAGAGTTGAATAATTGCAAAAAAATGTGTAT
TTGTATTGAAAGTTGTAACTAAATCAACATATTTTGCTAA
Found at i:19839368 original size:43 final size:43
Alignment explanation
Indices: 19839305--19839559 Score: 290
Period size: 43 Copynumber: 5.9 Consensus size: 43
19839295 TTGTGTGATA
* *
19839305 ATGATGACCCAGCTATGTGCGGTGTGGGAGTGCACATGAGCTG
1 ATGATGACCAAGCAATGTGCGGTGTGGGAGTGCACATGAGCTG
* *
19839348 AAGATGACCAAGCTATGTGCGGTGTGGGAGTGCACATGAGCTG
1 ATGATGACCAAGCAATGTGCGGTGTGGGAGTGCACATGAGCTG
*
19839391 ATGATGACCCAA-CAATGTGCGGTGTGGGAGTGCACATGAGCTT
1 ATGATGA-CCAAGCAATGTGCGGTGTGGGAGTGCACATGAGCTG
* *
19839434 ATGATGA-TATTGC-ATGGTGC-GTGTAGGGAGTGCACATGAGCTG
1 ATGATGACCA-AGCAAT-GTGCGGTGT-GGGAGTGCACATGAGCTG
* * *
19839477 ATGATGACCCAGCAATATGCGGTGTGGGAGTGCACATGAGCTT
1 ATGATGACCAAGCAATGTGCGGTGTGGGAGTGCACATGAGCTG
* *
19839520 ATGATGA-TATTGC-ATGGTGC-GTGTAGGGAGTGCACATGAG
1 ATGATGACCA-AGCAAT-GTGCGGTGT-GGGAGTGCACATGAG
19839560 TTGAGTGTGG
Statistics
Matches: 184, Mismatches: 17, Indels: 22
0.83 0.08 0.10
Matches are distributed among these distances:
41 1 0.01
42 12 0.07
43 161 0.88
44 10 0.05
ACGTcount: A:0.24, C:0.16, G:0.36, T:0.24
Consensus pattern (43 bp):
ATGATGACCAAGCAATGTGCGGTGTGGGAGTGCACATGAGCTG
Found at i:19839540 original size:129 final size:129
Alignment explanation
Indices: 19839321--19839559 Score: 340
Period size: 129 Copynumber: 1.9 Consensus size: 129
19839311 ACCCAGCTAT
* *
19839321 GTGCGGTGTGGGAGTGCACATGAGCTGAAGATGACCAAGCTATGTGCGGTGTGGGAGTGCACATG
1 GTGCGGTGTGGGAGTGCACATGAGCTGAAGATGACCAAGCAATATGCGGTGTGGGAGTGCACATG
*
19839386 AGCTGATGATGACCCAACAATGTGCGGTGT-GGGAGTGCACATGAGCTTATGATGATATTGCATG
66 AGCTGATGATGACACAACAATGTGC-GTGTAGGGAGTGCACATGAGCTTATGATGATATTGCATG
* *
19839450 GTGC-GTGTAGGGAGTGCACATGAGCTGATGATGACCCAGCAATATGCGGTGTGGGAGTGCACAT
1 GTGCGGTGT-GGGAGTGCACATGAGCTGAAGATGACCAAGCAATATGCGGTGTGGGAGTGCACAT
* * ***
19839514 GAGCTTATGATGATATTGC-ATGGTGCGTGTAGGGAGTGCACATGAG
65 GAGCTGATGATGACACAACAAT-GTGCGTGTAGGGAGTGCACATGAG
19839560 TTGAGTGTGG
Statistics
Matches: 97, Mismatches: 10, Indels: 6
0.86 0.09 0.05
Matches are distributed among these distances:
128 10 0.10
129 87 0.90
ACGTcount: A:0.24, C:0.15, G:0.37, T:0.24
Consensus pattern (129 bp):
GTGCGGTGTGGGAGTGCACATGAGCTGAAGATGACCAAGCAATATGCGGTGTGGGAGTGCACATG
AGCTGATGATGACACAACAATGTGCGTGTAGGGAGTGCACATGAGCTTATGATGATATTGCATG
Found at i:19839582 original size:86 final size:85
Alignment explanation
Indices: 19839305--19839559 Score: 363
Period size: 86 Copynumber: 3.0 Consensus size: 85
19839295 TTGTGTGATA
* * * * * *
19839305 ATGATGACCCAGCTATGTGCGGTGTGGGAGTGCACATGAGCTGAAGATGACCA-AGCTAT-GTGC
1 ATGATGACCCAG-AATATGCGGTGTGGGAGTGCACATGAGCTTATGATGA-TATTGC-ATGGTGC
19839368 GGTGT-GGGAGTGCACATGAGCTG
63 -GTGTAGGGAGTGCACATGAGCTG
* *
19839391 ATGATGACCCAACAATGTGCGGTGTGGGAGTGCACATGAGCTTATGATGATATTGCATGGTGCGT
1 ATGATGACCC-AGAATATGCGGTGTGGGAGTGCACATGAGCTTATGATGATATTGCATGGTGCGT
19839456 GTAGGGAGTGCACATGAGCTG
65 GTAGGGAGTGCACATGAGCTG
19839477 ATGATGACCCAGCAATATGCGGTGTGGGAGTGCACATGAGCTTATGATGATATTGCATGGTGCGT
1 ATGATGACCCAG-AATATGCGGTGTGGGAGTGCACATGAGCTTATGATGATATTGCATGGTGCGT
19839542 GTAGGGAGTGCACATGAG
65 GTAGGGAGTGCACATGAG
19839560 TTGAGTGTGG
Statistics
Matches: 156, Mismatches: 8, Indels: 10
0.90 0.05 0.06
Matches are distributed among these distances:
85 8 0.05
86 147 0.94
87 1 0.01
ACGTcount: A:0.24, C:0.16, G:0.36, T:0.24
Consensus pattern (85 bp):
ATGATGACCCAGAATATGCGGTGTGGGAGTGCACATGAGCTTATGATGATATTGCATGGTGCGTG
TAGGGAGTGCACATGAGCTG
Found at i:19846547 original size:43 final size:43
Alignment explanation
Indices: 19846486--19846570 Score: 125
Period size: 43 Copynumber: 2.0 Consensus size: 43
19846476 TGTGATAATT
* *
19846486 ATGACCCAACTATGTGCGGTATGGGAGTACACATGAGCTGATG
1 ATGACCCAACTATGTGCGGTATAGGAGTACACATAAGCTGATG
* * *
19846529 ATGACCCAGCTATGTGCGGTATAGGAGTGCATATAAGCTGAT
1 ATGACCCAACTATGTGCGGTATAGGAGTACACATAAGCTGAT
19846571 TATTATATTG
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
43 37 1.00
ACGTcount: A:0.28, C:0.18, G:0.29, T:0.25
Consensus pattern (43 bp):
ATGACCCAACTATGTGCGGTATAGGAGTACACATAAGCTGATG
Found at i:19849130 original size:66 final size:66
Alignment explanation
Indices: 19849013--19849161 Score: 174
Period size: 66 Copynumber: 2.3 Consensus size: 66
19849003 CCATTGTTGT
* * * *
19849013 AGGTTGTGGTTGAGCCTTGAAAAACCACCTTCGGTTTTAGTTTAGCCCGTGAAAAACTAGTG-TA
1 AGGTTGTGGTTGAGCTTTGAAAAACCACCTTCGGCTTTAGTTGAGCCCGTGAAAAACCAGTGCT-
19849077 AA
65 AA
* * * * * *
19849079 AGGTTGTGGTTGAGCTTTGAAAAACCACTTTGGGCTTTGGTTGATCTCGTGAAAAACCATTGCTA
1 AGGTTGTGGTTGAGCTTTGAAAAACCACCTTCGGCTTTAGTTGAGCCCGTGAAAAACCAGTGCTA
19849144 A
66 A
**
19849145 AGGTTGTGACTGAGCTT
1 AGGTTGTGGTTGAGCTT
19849162 GCGAAAAGTC
Statistics
Matches: 70, Mismatches: 12, Indels: 2
0.83 0.14 0.02
Matches are distributed among these distances:
66 69 0.99
67 1 0.01
ACGTcount: A:0.26, C:0.15, G:0.26, T:0.32
Consensus pattern (66 bp):
AGGTTGTGGTTGAGCTTTGAAAAACCACCTTCGGCTTTAGTTGAGCCCGTGAAAAACCAGTGCTA
A
Found at i:19852394 original size:26 final size:26
Alignment explanation
Indices: 19852358--19852419 Score: 106
Period size: 26 Copynumber: 2.4 Consensus size: 26
19852348 NNNNNTATGA
19852358 GATGATGATGATGGGATGATGTGCAT
1 GATGATGATGATGGGATGATGTGCAT
*
19852384 GATGATGATGATGGGATGGTGTGCAT
1 GATGATGATGATGGGATGATGTGCAT
*
19852410 GTTGATGATG
1 GATGATGATG
19852420 GGTATATGGT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 34 1.00
ACGTcount: A:0.24, C:0.03, G:0.40, T:0.32
Consensus pattern (26 bp):
GATGATGATGATGGGATGATGTGCAT
Found at i:19853411 original size:13 final size:13
Alignment explanation
Indices: 19853393--19853431 Score: 60
Period size: 13 Copynumber: 3.0 Consensus size: 13
19853383 AGCTTAAGTT
*
19853393 AGACAAGGGTGTA
1 AGACAAGGGTATA
*
19853406 AGACAAGTGTATA
1 AGACAAGGGTATA
19853419 AGACAAGGGTATA
1 AGACAAGGGTATA
19853432 GTAACCTAAG
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.44, C:0.08, G:0.31, T:0.18
Consensus pattern (13 bp):
AGACAAGGGTATA
Found at i:19855267 original size:36 final size:37
Alignment explanation
Indices: 19855209--19855280 Score: 101
Period size: 36 Copynumber: 2.0 Consensus size: 37
19855199 ATGACAAAAG
* * *
19855209 TGTAATCTTTTGTTAGTGCATACAATCTTTTTTTAAA
1 TGTAATCTTTTGTTAATCCATACAATCTTCTTTTAAA
*
19855246 TGTAATC-TTTGTTAATCCATACGATCTTCTTTTAA
1 TGTAATCTTTTGTTAATCCATACAATCTTCTTTTAA
19855281 GTCCAATATT
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
36 24 0.77
37 7 0.23
ACGTcount: A:0.26, C:0.14, G:0.10, T:0.50
Consensus pattern (37 bp):
TGTAATCTTTTGTTAATCCATACAATCTTCTTTTAAA
Found at i:19857365 original size:44 final size:44
Alignment explanation
Indices: 19857311--19857430 Score: 204
Period size: 44 Copynumber: 2.7 Consensus size: 44
19857301 CACATAACAC
* *
19857311 CATCATAAAACATATAAACAACACAACCATTGTTCAACATTATT
1 CATCACAAAACATATAAACCACACAACCATTGTTCAACATTATT
*
19857355 CATCACAAAACATATAAACCACACAACCATTGTTCAACATTGTT
1 CATCACAAAACATATAAACCACACAACCATTGTTCAACATTATT
*
19857399 CATCAGAAAACATATAAACCACACAACCATTG
1 CATCACAAAACATATAAACCACACAACCATTG
19857431 AAAACAAAGA
Statistics
Matches: 72, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
44 72 1.00
ACGTcount: A:0.47, C:0.26, G:0.04, T:0.23
Consensus pattern (44 bp):
CATCACAAAACATATAAACCACACAACCATTGTTCAACATTATT
Found at i:19859925 original size:2 final size:2
Alignment explanation
Indices: 19859913--19859944 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
19859903 TAATCATGCA
*
19859913 AT AT CT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
19859945 CATACAAAAC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:19860072 original size:20 final size:20
Alignment explanation
Indices: 19860042--19860091 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
19860032 CATTTGATTT
*
19860042 AAATAATAAAAGAAT-AAATA
1 AAAT-ATAAAAAAATAAAATA
* *
19860062 AAATATAAAAATATAAAATG
1 AAATATAAAAAAATAAAATA
19860082 AAATATAAAA
1 AAATATAAAA
19860092 TAAAGGCCTA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
19 8 0.31
20 18 0.69
ACGTcount: A:0.74, C:0.00, G:0.04, T:0.22
Consensus pattern (20 bp):
AAATATAAAAAAATAAAATA
Found at i:19860544 original size:2 final size:2
Alignment explanation
Indices: 19860537--19860561 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
19860527 TGGTGTCATT
19860537 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
19860562 GATTGAATGG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:19861021 original size:19 final size:19
Alignment explanation
Indices: 19860993--19861040 Score: 53
Period size: 20 Copynumber: 2.5 Consensus size: 19
19860983 TGAGAGCCAT
*
19860993 TAAAAATATA-TATAAGAAA
1 TAAAATTATATTA-AAGAAA
19861012 TAAAATTATATTGAAAGAAA
1 TAAAATTATATT-AAAGAAA
*
19861032 TACAATTAT
1 TAAAATTAT
19861041 TTCATTTTAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 9 0.36
20 15 0.60
21 1 0.04
ACGTcount: A:0.60, C:0.02, G:0.06, T:0.31
Consensus pattern (19 bp):
TAAAATTATATTAAAGAAA
Found at i:19861393 original size:19 final size:19
Alignment explanation
Indices: 19861369--19861411 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
19861359 AACATATAAG
19861369 TAAATAGAATAGAAACAA-A
1 TAAATA-AATAGAAACAATA
* *
19861388 TAAATAAATATAAATAATA
1 TAAATAAATAGAAACAATA
19861407 TAAAT
1 TAAAT
19861412 TGAAAAAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 9 0.43
19 12 0.57
ACGTcount: A:0.67, C:0.02, G:0.05, T:0.26
Consensus pattern (19 bp):
TAAATAAATAGAAACAATA
Found at i:19865374 original size:36 final size:36
Alignment explanation
Indices: 19865327--19865475 Score: 198
Period size: 36 Copynumber: 4.2 Consensus size: 36
19865317 AATTGTTTAA
*
19865327 TTTAATCAATTAGGCCTAATAACTTAATTAAACAAT
1 TTTAATCAATTAGGCCCAATAACTTAATTAAACAAT
*
19865363 TTTAATCAATTAGGCCCAATGACTTAATTAAACAAT
1 TTTAATCAATTAGGCCCAATAACTTAATTAAACAAT
* * * *
19865399 TTTAATCAACTAGACCCAATGACTTAATTAAGCAA-
1 TTTAATCAATTAGGCCCAATAACTTAATTAAACAAT
* *
19865434 TTTAATTAATTAGG--C-ACAACTTAATTAAACAAT
1 TTTAATCAATTAGGCCCAATAACTTAATTAAACAAT
19865467 TTTAATCAA
1 TTTAATCAA
19865476 GTACTTGAGA
Statistics
Matches: 100, Mismatches: 12, Indels: 5
0.85 0.10 0.04
Matches are distributed among these distances:
32 14 0.14
33 9 0.09
35 11 0.11
36 66 0.66
ACGTcount: A:0.44, C:0.15, G:0.07, T:0.34
Consensus pattern (36 bp):
TTTAATCAATTAGGCCCAATAACTTAATTAAACAAT
Found at i:19874093 original size:34 final size:34
Alignment explanation
Indices: 19874034--19874184 Score: 169
Period size: 34 Copynumber: 4.4 Consensus size: 34
19874024 GTGGGCAGGG
* * * *
19874034 TTCATTTTTCCTTTCGCGATAGTCATGAAGGAAT
1 TTCATTTTTCCATTAGCAATTGTCATGAAGGAAT
*
19874068 TTCATTTTTTCATTAGCAATTGTCATGAAGGAAT
1 TTCATTTTTCCATTAGCAATTGTCATGAAGGAAT
* * *
19874102 TTCATTTTTCCATTCA-CGATGGTCATCAAGGAAT
1 TTCATTTTTCCATT-AGCAATTGTCATGAAGGAAT
* * * *
19874136 TTCGTTTTTTTCATTTGCAATTGTCGTGAAGGAAT
1 TTC-ATTTTTCCATTAGCAATTGTCATGAAGGAAT
19874171 TTCATTTTTCCATT
1 TTCATTTTTCCATT
19874185 CGCTATGATA
Statistics
Matches: 96, Mismatches: 18, Indels: 6
0.80 0.15 0.05
Matches are distributed among these distances:
34 69 0.72
35 27 0.28
ACGTcount: A:0.24, C:0.16, G:0.15, T:0.45
Consensus pattern (34 bp):
TTCATTTTTCCATTAGCAATTGTCATGAAGGAAT
Found at i:19874127 original size:68 final size:69
Alignment explanation
Indices: 19874034--19874185 Score: 234
Period size: 69 Copynumber: 2.2 Consensus size: 69
19874024 GTGGGCAGGG
* * *
19874034 TTCATTTTTCCTTTCGCGATAGTCATGAAGGAATTTC-ATTTTTTCATTAGCAATTGTCATGAAG
1 TTCATTTTTCCATTCACGATAGTCATCAAGGAATTTCGATTTTTTCATTAGCAATTGTCATGAAG
19874098 GAAT
66 GAAT
* * * *
19874102 TTCATTTTTCCATTCACGATGGTCATCAAGGAATTTCGTTTTTTTCATTTGCAATTGTCGTGAAG
1 TTCATTTTTCCATTCACGATAGTCATCAAGGAATTTCGATTTTTTCATTAGCAATTGTCATGAAG
19874167 GAAT
66 GAAT
19874171 TTCATTTTTCCATTC
1 TTCATTTTTCCATTC
19874186 GCTATGATAC
Statistics
Matches: 76, Mismatches: 7, Indels: 1
0.90 0.08 0.01
Matches are distributed among these distances:
68 33 0.43
69 43 0.57
ACGTcount: A:0.24, C:0.16, G:0.15, T:0.45
Consensus pattern (69 bp):
TTCATTTTTCCATTCACGATAGTCATCAAGGAATTTCGATTTTTTCATTAGCAATTGTCATGAAG
GAAT
Found at i:19877179 original size:17 final size:18
Alignment explanation
Indices: 19877140--19877188 Score: 66
Period size: 17 Copynumber: 2.7 Consensus size: 18
19877130 AAATTAAAAT
19877140 AAATAAATAATCAAAACTA
1 AAATAAATAAT-AAAACTA
19877159 AAATTAAA-AATAAAA-TA
1 AAA-TAAATAATAAAACTA
19877176 AAATAAATAATAA
1 AAATAAATAATAA
19877189 TAAGAAAAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
16 4 0.14
17 10 0.36
18 4 0.14
19 6 0.21
20 4 0.14
ACGTcount: A:0.73, C:0.04, G:0.00, T:0.22
Consensus pattern (18 bp):
AAATAAATAATAAAACTA
Found at i:19877198 original size:36 final size:36
Alignment explanation
Indices: 19877134--19877207 Score: 98
Period size: 36 Copynumber: 2.1 Consensus size: 36
19877124 ATCATCAAAT
*
19877134 TAAAATAAATAAATAATCAAAACTAAAAT-TAAAAA
1 TAAAATAAATAAATAATCAAAACAAAAATATAAAAA
*
19877169 TAAAATAAAATAAATAAT-AATAAGAAAAATATAAAAA
1 TAAAAT-AAATAAATAATCAA-AACAAAAATATAAAAA
19877206 TA
1 TA
19877208 GTGTCTGCAG
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
35 8 0.24
36 18 0.53
37 8 0.24
ACGTcount: A:0.73, C:0.03, G:0.01, T:0.23
Consensus pattern (36 bp):
TAAAATAAATAAATAATCAAAACAAAAATATAAAAA
Found at i:19877575 original size:51 final size:52
Alignment explanation
Indices: 19877312--19877560 Score: 292
Period size: 51 Copynumber: 4.9 Consensus size: 52
19877302 CAAGGTTTTA
* * * * ***
19877312 CACTTCAAAAATCAACTT-AAAAGATAAACAACTCCTTATTCGAAG-TTTCTC
1 CACTTTAAAAATCAATTTGAAAA-ATAAACAACTCCTCATTCGAGGCTTAAAC
* * * *
19877363 AACTTT-AAAATTAGTTTGAAAAATAAACAACTCCTCATCCGAGGCTTAAAC
1 CACTTTAAAAATCAATTTGAAAAATAAACAACTCCTCATTCGAGGCTTAAAC
**
19877414 CACTTTAAAAA-CAATTTGAAAAATAAACAACTCCTCATTTAAGGCTTAAAC
1 CACTTTAAAAATCAATTTGAAAAATAAACAACTCCTCATTCGAGGCTTAAAC
** *
19877465 CACTTTAAAAA-CAATTTGAAAAATAAACAACTCCTCATTTAAGGCTTAGAC
1 CACTTTAAAAATCAATTTGAAAAATAAACAACTCCTCATTCGAGGCTTAAAC
* *
19877516 CACTTTAAAAATCAATTTGAAAAATAAACAACTCCTTATCCGAGG
1 CACTTTAAAAATCAATTTGAAAAATAAACAACTCCTCATTCGAGG
19877561 TTCCATAACT
Statistics
Matches: 172, Mismatches: 22, Indels: 7
0.86 0.11 0.03
Matches are distributed among these distances:
50 27 0.16
51 112 0.65
52 33 0.19
ACGTcount: A:0.44, C:0.20, G:0.08, T:0.28
Consensus pattern (52 bp):
CACTTTAAAAATCAATTTGAAAAATAAACAACTCCTCATTCGAGGCTTAAAC
Found at i:19877660 original size:44 final size:42
Alignment explanation
Indices: 19877596--19877716 Score: 127
Period size: 44 Copynumber: 2.8 Consensus size: 42
19877586 GAGTACCTGA
* * *
19877596 AGGTTTTGGAGAATGCACCTGGAGGTTTTAAAAAGCACACTCGG
1 AGGTTTTGAAGAATGTACCTGAAGGTTTTAAAAAG--CACTCGG
* * * *
19877640 AGGTTTTGAAGAATGTACCTGAAGGTTTTGGAGATGTACTCGG
1 AGGTTTTGAAGAATGTACCTGAAGGTTTT-AAAAAGCACTCGG
*
19877683 AGGTTTTGAA-AATGTACCCGAAGGTTTTATAAAA
1 AGGTTTTGAAGAATGTACCTGAAGGTTTTA-AAAA
19877717 AAATGTTGTT
Statistics
Matches: 64, Mismatches: 11, Indels: 6
0.79 0.14 0.07
Matches are distributed among these distances:
42 19 0.30
43 16 0.25
44 26 0.41
45 3 0.05
ACGTcount: A:0.31, C:0.12, G:0.28, T:0.30
Consensus pattern (42 bp):
AGGTTTTGAAGAATGTACCTGAAGGTTTTAAAAAGCACTCGG
Found at i:19877678 original size:21 final size:21
Alignment explanation
Indices: 19877588--19877710 Score: 88
Period size: 22 Copynumber: 5.7 Consensus size: 21
19877578 AAATAAATGA
*
19877588 GTACCTGAAGGTTTTGGAGAAT
1 GTACCTGAAGGTTTTGAAG-AT
* * * *
19877610 GCACCTGGAGGTTTT-AAAAA
1 GTACCTGAAGGTTTTGAAGAT
* *
19877630 GCACACTCGGAGGTTTTGAAGAAT
1 GTAC-CT-GAAGGTTTTGAAG-AT
*
19877654 GTACCTGAAGGTTTTGGAGAT
1 GTACCTGAAGGTTTTGAAGAT
* *
19877675 GTA-CTCGGAGGTTTTGAAAAT
1 GTACCT-GAAGGTTTTGAAGAT
*
19877696 GTACCCGAAGGTTTT
1 GTACCTGAAGGTTTT
19877711 ATAAAAAAAT
Statistics
Matches: 80, Mismatches: 15, Indels: 13
0.74 0.14 0.12
Matches are distributed among these distances:
20 7 0.09
21 31 0.39
22 34 0.43
23 4 0.05
24 4 0.05
ACGTcount: A:0.28, C:0.13, G:0.29, T:0.30
Consensus pattern (21 bp):
GTACCTGAAGGTTTTGAAGAT
Found at i:19877952 original size:22 final size:21
Alignment explanation
Indices: 19877881--19877959 Score: 97
Period size: 21 Copynumber: 3.7 Consensus size: 21
19877871 TAATGCTAAT
*
19877881 TACCCGGAGGTTTTGAGAATG
1 TACCCGAAGGTTTTGAGAATG
* *
19877902 TATCCAAAGGTTTTGAGAATG
1 TACCCGAAGGTTTTGAGAATG
*
19877923 TACTCGAAGGTTTT-AGAACATG
1 TACCCGAAGGTTTTGAG-A-ATG
19877945 TACCCGAAGGTTTTG
1 TACCCGAAGGTTTTG
19877960 GAGATATACC
Statistics
Matches: 48, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
20 2 0.04
21 30 0.62
22 16 0.33
ACGTcount: A:0.28, C:0.14, G:0.27, T:0.32
Consensus pattern (21 bp):
TACCCGAAGGTTTTGAGAATG
Found at i:19878169 original size:144 final size:143
Alignment explanation
Indices: 19877909--19878336 Score: 552
Period size: 144 Copynumber: 3.0 Consensus size: 143
19877899 ATGTATCCAA
* * * *
19877909 AGGTTTTGAGAATGTACTCGAAGGTTTTAGAACATGTACCCGAAGGTTTTGGAGATATACCCAGA
1 AGGTTTTAAGAATGTACCCGAAGGTTTTAGAAAATGTACCC-AAGATTTTGGAGATATACCCAGA
* *
19877974 GGTTTTAAAAGAAAAAGTTGCTCCCCATCTCAAAATGAGGCTACATAACTTTAAAGAAATATTAA
65 GGTTTTAAAAGAAAAAGTTGCTTCCCATCTCAAAATGAGGCTATATAACTTTAAAGAAATATTAA
19878039 TGCTAATTACTCAG
130 TGCTAATTACTCAG
* * * * *
19878053 AGGTTTTAAGAATGTACCCAAAGCTTTTAGAAAATGTACCCATAAATTTTGGAGATCTACCTAGA
1 AGGTTTTAAGAATGTACCCGAAGGTTTTAGAAAATGTACCCA-AGATTTTGGAGATATACCCAGA
* * * *
19878118 GATTTTAAAAGAAAATGTTGCTTCCCATCTCAAAATGAGGCTATGTAACTTTAAAAAAATATTAA
65 GGTTTTAAAAGAAAAAGTTGCTTCCCATCTCAAAATGAGGCTATATAACTTTAAAGAAATATTAA
*
19878183 TGCTAATTACCCAG
130 TGCTAATTACTCAG
* * * * * * *
19878197 AGGTTTTGAA-AATGTACCTGGAGGTTTTAGAAAATGTACCGAAGCTTTTGAAGATGTACCCGGA
1 AGGTTTT-AAGAATGTACCCGAAGGTTTTAGAAAATGTACCCAAGATTTTGGAGATATACCCAGA
* * * * * *
19878261 GGTTTTAAAAGAAAAGGTTGTTTTCCACCTTAAAATGAAGCTATATAACTTTAAAGAAATATTAA
65 GGTTTTAAAAGAAAAAGTTGCTTCCCATCTCAAAATGAGGCTATATAACTTTAAAGAAATATTAA
*
19878326 TACTAATTACT
130 TGCTAATTACT
19878337 TGGAATCTTT
Statistics
Matches: 244, Mismatches: 38, Indels: 5
0.85 0.13 0.02
Matches are distributed among these distances:
143 82 0.34
144 160 0.66
145 2 0.01
ACGTcount: A:0.37, C:0.14, G:0.18, T:0.31
Consensus pattern (143 bp):
AGGTTTTAAGAATGTACCCGAAGGTTTTAGAAAATGTACCCAAGATTTTGGAGATATACCCAGAG
GTTTTAAAAGAAAAAGTTGCTTCCCATCTCAAAATGAGGCTATATAACTTTAAAGAAATATTAAT
GCTAATTACTCAG
Found at i:19878232 original size:22 final size:20
Alignment explanation
Indices: 19878196--19878270 Score: 89
Period size: 21 Copynumber: 3.6 Consensus size: 20
19878186 TAATTACCCA
19878196 GAGGTTTTGAAAATGTACCTG
1 GAGGTTTTGAAAATGTACC-G
19878217 GAGGTTTTAGAAAATGTACCG
1 GAGGTTTT-GAAAATGTACCG
* * *
19878238 AAGCTTTTGAAGATGTACCCG
1 GAGGTTTTGAAAATGTA-CCG
19878259 GAGGTTTT-AAAA
1 GAGGTTTTGAAAA
19878271 GAAAAGGTTG
Statistics
Matches: 46, Mismatches: 6, Indels: 5
0.81 0.11 0.09
Matches are distributed among these distances:
20 11 0.24
21 24 0.52
22 11 0.24
ACGTcount: A:0.32, C:0.11, G:0.27, T:0.31
Consensus pattern (20 bp):
GAGGTTTTGAAAATGTACCG
Found at i:19883022 original size:19 final size:19
Alignment explanation
Indices: 19882998--19883034 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
19882988 CTTATATGTC
*
19882998 TTTTTTCTT-TTTTTCTTT
1 TTTTTTTTTGTTTTTCTTT
19883016 TTTTTTTTTGTTTTTCTTT
1 TTTTTTTTTGTTTTTCTTT
19883035 CATTGCAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 8 0.47
19 9 0.53
ACGTcount: A:0.00, C:0.08, G:0.03, T:0.89
Consensus pattern (19 bp):
TTTTTTTTTGTTTTTCTTT
Found at i:19883495 original size:16 final size:17
Alignment explanation
Indices: 19883469--19883516 Score: 64
Period size: 16 Copynumber: 2.9 Consensus size: 17
19883459 TTTTAATTTC
19883469 TTTCTTTCTTTTCTTTT
1 TTTCTTTCTTTTCTTTT
19883486 TTTC-TTCTTTT-TATTT
1 TTTCTTTCTTTTCT-TTT
*
19883502 GTTCTTTCTTTTCTT
1 TTTCTTTCTTTTCTT
19883517 CACAACTCAA
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
15 1 0.04
16 13 0.48
17 12 0.44
18 1 0.04
ACGTcount: A:0.02, C:0.17, G:0.02, T:0.79
Consensus pattern (17 bp):
TTTCTTTCTTTTCTTTT
Found at i:19891725 original size:13 final size:13
Alignment explanation
Indices: 19891707--19891731 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
19891697 GGAAAATGGG
19891707 ATTTTATAAAATA
1 ATTTTATAAAATA
19891720 ATTTTATAAAAT
1 ATTTTATAAAAT
19891732 TTTTGAAAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (13 bp):
ATTTTATAAAATA
Found at i:19893638 original size:16 final size:18
Alignment explanation
Indices: 19893617--19893654 Score: 62
Period size: 16 Copynumber: 2.2 Consensus size: 18
19893607 TGAATAAATC
19893617 TTTTATTTTTA-TATA-A
1 TTTTATTTTTATTATATA
19893633 TTTTATTTTTATTATATA
1 TTTTATTTTTATTATATA
19893651 TTTT
1 TTTT
19893655 TATATATCTA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
16 11 0.55
17 4 0.20
18 5 0.25
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (18 bp):
TTTTATTTTTATTATATA
Found at i:19893661 original size:10 final size:10
Alignment explanation
Indices: 19893620--19893661 Score: 52
Period size: 10 Copynumber: 4.3 Consensus size: 10
19893610 ATAAATCTTT
19893620 TATTTTTATA
1 TATTTTTATA
*
19893630 TAATTTTAT-
1 TATTTTTATA
19893639 T-TTTATTATA
1 TATTT-TTATA
19893649 TATTTTTATA
1 TATTTTTATA
19893659 TAT
1 TAT
19893662 CTAAGTATTT
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
8 2 0.07
9 5 0.19
10 17 0.63
11 3 0.11
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (10 bp):
TATTTTTATA
Found at i:19894031 original size:3 final size:3
Alignment explanation
Indices: 19894023--19894069 Score: 76
Period size: 3 Copynumber: 15.7 Consensus size: 3
19894013 CCTCTCACAT
* *
19894023 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTC TTG TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
19894070 TCTTTTTTTA
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.28, C:0.02, G:0.02, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:19894080 original size:15 final size:16
Alignment explanation
Indices: 19894029--19894086 Score: 59
Period size: 15 Copynumber: 3.8 Consensus size: 16
19894019 ACATTTATTA
* *
19894029 TTATTATTA-TTATTA
1 TTATTATTATTTCTTG
19894044 TTATTATTA-TTCTTG
1 TTATTATTATTTCTTG
19894059 TTATTATTATTTCTT-
1 TTATTATTATTTCTTG
*
19894074 TTTTTATATATTT
1 TTATTAT-TATTT
19894087 TGTTTGATTA
Statistics
Matches: 38, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
15 28 0.74
16 10 0.26
ACGTcount: A:0.24, C:0.03, G:0.02, T:0.71
Consensus pattern (16 bp):
TTATTATTATTTCTTG
Found at i:19895533 original size:17 final size:17
Alignment explanation
Indices: 19895511--19895545 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
19895501 TCATTGTGCA
*
19895511 TTTTTTGTTTTG-TATT
1 TTTTTTTTTTTGCTATT
19895527 TTTTTTTTTTTGCTATT
1 TTTTTTTTTTTGCTATT
19895544 TT
1 TT
19895546 CTATGATTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 11 0.65
17 6 0.35
ACGTcount: A:0.06, C:0.03, G:0.09, T:0.83
Consensus pattern (17 bp):
TTTTTTTTTTTGCTATT
Found at i:19896858 original size:19 final size:19
Alignment explanation
Indices: 19896836--19896873 Score: 60
Period size: 19 Copynumber: 2.0 Consensus size: 19
19896826 ATACTCCCCC
19896836 TGGAG-ATGAATATTCATGA
1 TGGAGCATGAATA-TCATGA
19896855 TGGAGCATGAATATCATGA
1 TGGAGCATGAATATCATGA
19896874 ATATTCATCT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 11 0.61
20 7 0.39
ACGTcount: A:0.37, C:0.08, G:0.26, T:0.29
Consensus pattern (19 bp):
TGGAGCATGAATATCATGA
Found at i:19902533 original size:25 final size:23
Alignment explanation
Indices: 19902477--19902534 Score: 62
Period size: 25 Copynumber: 2.4 Consensus size: 23
19902467 TATTTTATAT
**
19902477 TTTAAAATTAAATTAAAATTGTA
1 TTTAAAATTAAAAAAAAATTGTA
*
19902500 ATTATAAATTATAAAAAAAATTGATA
1 TTTA-AAATTA-AAAAAAAATTG-TA
19902526 TTTAAAATT
1 TTTAAAATT
19902535 TTATTGTTAA
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
23 3 0.11
24 6 0.21
25 14 0.50
26 5 0.18
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.41
Consensus pattern (23 bp):
TTTAAAATTAAAAAAAAATTGTA
Found at i:19904006 original size:27 final size:28
Alignment explanation
Indices: 19903952--19904005 Score: 74
Period size: 28 Copynumber: 1.9 Consensus size: 28
19903942 TTTAATTTAA
19903952 AATAAAAATATAAAAACTTGATTAAAAT
1 AATAAAAATATAAAAACTTGATTAAAAT
* *
19903980 AATAAAAGA-ATAAAAATTTGTTTAAA
1 AATAAAA-ATATAAAAACTTGATTAAA
19904006 TTTTTTAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
28 22 0.96
29 1 0.04
ACGTcount: A:0.63, C:0.02, G:0.06, T:0.30
Consensus pattern (28 bp):
AATAAAAATATAAAAACTTGATTAAAAT
Found at i:19909159 original size:83 final size:84
Alignment explanation
Indices: 19909020--19909176 Score: 228
Period size: 83 Copynumber: 1.9 Consensus size: 84
19909010 CAAATATTAA
* * *
19909020 ATAATTGGAAAAATTATACAATTAGTCTCTGTATTTTATCAAAGTGGTAGATTTAAT-CCTTATA
1 ATAATTGGAAAAATTATACAATTAGTCTCTATACTTTATCAAAGTAGTAGATTTAATCCCTTATA
*
19909084 CAATGATTTCTAAAAATTG
66 AAATGATTTCTAAAAATTG
** *
19909103 ATAATT-GATAAAATTATGTAATTAGTCTCTATACTTTATCAAAGTAGTAGATTTAATCCCTTGT
1 ATAATTGGA-AAAATTATACAATTAGTCTCTATACTTTATCAAAGTAGTAGATTTAATCCCTTAT
19909167 AAAATGATTT
65 AAAATGATTT
19909177 ATATAACTTG
Statistics
Matches: 65, Mismatches: 7, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
82 2 0.03
83 49 0.75
84 14 0.22
ACGTcount: A:0.38, C:0.10, G:0.11, T:0.41
Consensus pattern (84 bp):
ATAATTGGAAAAATTATACAATTAGTCTCTATACTTTATCAAAGTAGTAGATTTAATCCCTTATA
AAATGATTTCTAAAAATTG
Found at i:19910293 original size:30 final size:30
Alignment explanation
Indices: 19910259--19910318 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 30
19910249 GTTGTCTTGC
19910259 ATAATTGATAAATGTCGACATTTTTATAGT
1 ATAATTGATAAATGTCGACATTTTTATAGT
* * *
19910289 ATAATTGATGAATGTTGGCATTTTTATAGT
1 ATAATTGATAAATGTCGACATTTTTATAGT
19910319 GTTATGGTAA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.33, C:0.05, G:0.17, T:0.45
Consensus pattern (30 bp):
ATAATTGATAAATGTCGACATTTTTATAGT
Found at i:19911559 original size:25 final size:25
Alignment explanation
Indices: 19911531--19911587 Score: 78
Period size: 25 Copynumber: 2.3 Consensus size: 25
19911521 AATAAACGTG
19911531 ATTATAGGAATTAGAAATCACCATA
1 ATTATAGGAATTAGAAATCACCATA
* * * *
19911556 ATTATAGGGATTGGGAATCATCATA
1 ATTATAGGAATTAGAAATCACCATA
19911581 ATTATAG
1 ATTATAG
19911588 AGATTTTATT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.42, C:0.09, G:0.18, T:0.32
Consensus pattern (25 bp):
ATTATAGGAATTAGAAATCACCATA
Found at i:19912148 original size:33 final size:33
Alignment explanation
Indices: 19912054--19912141 Score: 158
Period size: 33 Copynumber: 2.7 Consensus size: 33
19912044 TCAAATTAAT
*
19912054 ATATCACATTATCATCAATTATGTTATATCAAG
1 ATATTACATTATCATCAATTATGTTATATCAAG
19912087 ATATTACATTATCATCAATTATGTTATATCAAG
1 ATATTACATTATCATCAATTATGTTATATCAAG
*
19912120 ATATTACATCATCATCAATTAT
1 ATATTACATTATCATCAATTAT
19912142 AATATATTCG
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 53 1.00
ACGTcount: A:0.40, C:0.15, G:0.05, T:0.41
Consensus pattern (33 bp):
ATATTACATTATCATCAATTATGTTATATCAAG
Found at i:19912889 original size:33 final size:33
Alignment explanation
Indices: 19912852--19912930 Score: 95
Period size: 33 Copynumber: 2.4 Consensus size: 33
19912842 ATTATGTCAA
* * *
19912852 ATTAACATGTCATATCATCATCAATTATGATAC
1 ATTAACATGCCACATCATAATCAATTATGATAC
* *
19912885 ATTAATATGCCACATCATAATCAATTATGATAT
1 ATTAACATGCCACATCATAATCAATTATGATAC
* *
19912918 TTTAACATACCAC
1 ATTAACATGCCAC
19912931 GTCAACATCA
Statistics
Matches: 38, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
33 38 1.00
ACGTcount: A:0.41, C:0.19, G:0.05, T:0.35
Consensus pattern (33 bp):
ATTAACATGCCACATCATAATCAATTATGATAC
Found at i:19913063 original size:31 final size:31
Alignment explanation
Indices: 19912988--19913053 Score: 100
Period size: 31 Copynumber: 2.2 Consensus size: 31
19912978 AATCATTAGT
*
19912988 TATAAAAACTTATTTGACTCAAAATAAAAAA
1 TATAAAAGCTTATTTGACTCAAAATAAAAAA
19913019 TATAAAAGCTTATTT-ATCTCAAAAT-AAAAA
1 TATAAAAGCTTATTTGA-CTCAAAATAAAAAA
19913049 TATAA
1 TATAA
19913054 GGGTTTTATT
Statistics
Matches: 33, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
30 11 0.33
31 22 0.67
ACGTcount: A:0.56, C:0.09, G:0.03, T:0.32
Consensus pattern (31 bp):
TATAAAAGCTTATTTGACTCAAAATAAAAAA
Found at i:19913191 original size:28 final size:28
Alignment explanation
Indices: 19913138--19913192 Score: 76
Period size: 28 Copynumber: 2.0 Consensus size: 28
19913128 TATGCCTTTA
*
19913138 TTTTAAGTCAAATAAGCCATTGTAATTT
1 TTTTAAGTCAAATAAGCCATTATAATTT
*
19913166 TTTTTAGTCAAATAAGCTC-TTATAATT
1 TTTTAAGTCAAATAAGC-CATTATAATT
19913193 AATGATTGAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 23 0.96
29 1 0.04
ACGTcount: A:0.35, C:0.11, G:0.09, T:0.45
Consensus pattern (28 bp):
TTTTAAGTCAAATAAGCCATTATAATTT
Found at i:19914746 original size:2 final size:2
Alignment explanation
Indices: 19914739--19914763 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
19914729 TTCATTTGAT
19914739 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
19914764 GACATCATCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:19915468 original size:297 final size:300
Alignment explanation
Indices: 19914955--19915536 Score: 1059
Period size: 297 Copynumber: 1.9 Consensus size: 300
19914945 AATGACTCTC
19914955 AAAATAATTAATTTTATTCTTCAAATTGTTTGATAAAATTAAAATCATTATGATTAGCATATTGC
1 AAAATAATTAATTTTATTCTTCAAATTGTTTGATAAAATTAAAATCATTATGATTAGCATATTGC
19915020 TAGTTAAGCCTAGCAAATAAATTCTAAACTAATATGTTAACTCTATCAAATTTTAAAAAATAAAA
66 TAGTTAAGCCTAGCAAATAAATTCTAAACTAATATGTTAACTCTATCAAA-TTTAAAAAATAAAA
*
19915085 GTGAATCTACTAATCCAAACTCATTAAATTTTAATATAAATTTAAATCTATCATAATATATTATA
130 ATGAATCTACTAATCCAAACTCATTAAATTTTAATATAAATTTAAATCTATCATAATATATTATA
19915150 TCTTAACAGCTCAATCTAATAGTATATCCTAACATATTATATCTCAATAATTAAACTCAATAACC
195 TCTTAACAGCTCAATCTAATAGTATATCCTAACATATTATATCTCAATAATTAAACTCAATAACC
19915215 TAATATGTTAATTAACAA-TTAAGAGTCAAATAAAAAAATA
260 TAATATGTTAATTAACAATTTAAGAGTCAAATAAAAAAATA
19915255 NAAAATAA-TAATTTTATTCTTC-AATTGTTTGATAAAATTAAAATCATTATGATTAGCATATTG
1 -AAAATAATTAATTTTATTCTTCAAATTGTTTGATAAAATTAAAATCATTATGATTAGCATATTG
19915318 CTAGTTAAGCCTAGCAAATAAATTCTAAACTAATATGTTAACTCTATCAAA-TTAAAAAA-AAAA
65 CTAGTTAAGCCTAGCAAATAAATTCTAAACTAATATGTTAACTCTATCAAATTTAAAAAATAAAA
* *
19915381 CATGAGTCTACTAATCCAAACTCATTAAATTTTAATATAAATTT-AAGCTTATCATAATATATTA
130 -ATGAATCTACTAATCCAAACTCATTAAATTTTAATATAAATTTAAATC-TATCATAATATATTA
19915445 TATCTTAACAGCTCAATCTAATAGTATATCCTAACATATTATATCTCAATAATTAAACTCAATAA
193 TATCTTAACAGCTCAATCTAATAGTATATCCTAACATATTATATCTCAATAATTAAACTCAATAA
19915510 CCTAATATGTTAATTAACAATTTAAGA
258 CCTAATATGTTAATTAACAATTTAAGA
19915537 AATAAATAGA
Statistics
Matches: 275, Mismatches: 3, Indels: 9
0.96 0.01 0.03
Matches are distributed among these distances:
296 7 0.03
297 149 0.54
298 6 0.02
299 92 0.33
300 14 0.05
301 7 0.03
ACGTcount: A:0.45, C:0.13, G:0.05, T:0.36
Consensus pattern (300 bp):
AAAATAATTAATTTTATTCTTCAAATTGTTTGATAAAATTAAAATCATTATGATTAGCATATTGC
TAGTTAAGCCTAGCAAATAAATTCTAAACTAATATGTTAACTCTATCAAATTTAAAAAATAAAAA
TGAATCTACTAATCCAAACTCATTAAATTTTAATATAAATTTAAATCTATCATAATATATTATAT
CTTAACAGCTCAATCTAATAGTATATCCTAACATATTATATCTCAATAATTAAACTCAATAACCT
AATATGTTAATTAACAATTTAAGAGTCAAATAAAAAAATA
Found at i:19926845 original size:108 final size:109
Alignment explanation
Indices: 19926682--19926897 Score: 321
Period size: 108 Copynumber: 2.0 Consensus size: 109
19926672 TATAAGAAAT
19926682 TTTGAGTAAATTTAAATAAAAAGGTAAAGTGAGTAAGAGTTGAATAATTGTAAAAGAATGTATAT
1 TTTGAGTAAATTTAAATAAAAAGGTAAAGTGAGTAAGAGTTGAATAATTGTAAAAGAATGTATAT
* *
19926747 CTGTAAATTGTGAAAGTTGAAACTAAATTAACATATTTTATTAA
66 CTGTAAATTGTGAAAGTTGAAACTAAATCAACATATTTAATTAA
* *
19926791 TTTGAGTAAATTTAAATAAAAA-GTAAATTG-GATAAGAGTTGAATAATT-TCAAAAGAATGTGT
1 TTTGAGTAAATTTAAATAAAAAGGTAAAGTGAG-TAAGAGTTGAATAATTGT-AAAAGAATGTAT
* * * *
19926853 ATTTGTAAATTGTTAAAGTTGTAATTAAATCAACATATTTAATTA
64 ATCTGTAAATTGTGAAAGTTGAAACTAAATCAACATATTTAATTA
19926898 TTTTATATTA
Statistics
Matches: 97, Mismatches: 8, Indels: 5
0.88 0.07 0.05
Matches are distributed among these distances:
107 2 0.02
108 73 0.75
109 22 0.23
ACGTcount: A:0.45, C:0.03, G:0.15, T:0.37
Consensus pattern (109 bp):
TTTGAGTAAATTTAAATAAAAAGGTAAAGTGAGTAAGAGTTGAATAATTGTAAAAGAATGTATAT
CTGTAAATTGTGAAAGTTGAAACTAAATCAACATATTTAATTAA
Found at i:19927378 original size:30 final size:31
Alignment explanation
Indices: 19927323--19927380 Score: 91
Period size: 31 Copynumber: 1.9 Consensus size: 31
19927313 GGTATCGTAT
* *
19927323 AGTGCCACGTGGCATTGCCATGTCATCACTC
1 AGTGCCACATGGCATTGCCACGTCATCACTC
19927354 AGTGCCACATGGCA-TGCCACGTCATCA
1 AGTGCCACATGGCATTGCCACGTCATCA
19927381 TCTTAAAATG
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
30 12 0.48
31 13 0.52
ACGTcount: A:0.22, C:0.33, G:0.22, T:0.22
Consensus pattern (31 bp):
AGTGCCACATGGCATTGCCACGTCATCACTC
Found at i:19934347 original size:1 final size:1
Alignment explanation
Indices: 19934341--19934381 Score: 73
Period size: 1 Copynumber: 41.0 Consensus size: 1
19934331 CCCACCCCAA
*
19934341 CCCCCCCCCCCCCCCCCCNCCCCCCCCCCCCCCCCCCCCCC
1 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
19934382 ACCCAAGGTC
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
1 38 1.00
ACGTcount: A:0.00, C:0.98, G:0.00, T:0.00
Consensus pattern (1 bp):
C
Found at i:19934358 original size:20 final size:19
Alignment explanation
Indices: 19934330--19934381 Score: 70
Period size: 19 Copynumber: 2.8 Consensus size: 19
19934320 CAACACCAAA
* *
19934330 CCCCACCCCAACCCCCCCC
1 CCCCCCCCCCACCCCCCCC
*
19934349 CCCCCCCCCCNCCCCCCCC
1 CCCCCCCCCCACCCCCCCC
19934368 CCCCCCCCCC-CCCC
1 CCCCCCCCCCACCCC
19934382 ACCCAAGGTC
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
18 4 0.13
19 26 0.87
ACGTcount: A:0.06, C:0.92, G:0.00, T:0.00
Consensus pattern (19 bp):
CCCCCCCCCCACCCCCCCC
Found at i:19948245 original size:8 final size:9
Alignment explanation
Indices: 19948221--19948260 Score: 53
Period size: 9 Copynumber: 4.3 Consensus size: 9
19948211 ATATAATATT
19948221 TTTAAAAAA
1 TTTAAAAAA
19948230 TTTAAAAAA
1 TTTAAAAAA
**
19948239 TTTAAAATT
1 TTTAAAAAA
19948248 TTTAAATAAA
1 TTTAAA-AAA
19948258 TTT
1 TTT
19948261 TTATTATTTT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
9 22 0.85
10 4 0.15
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (9 bp):
TTTAAAAAA
Found at i:19949396 original size:2 final size:2
Alignment explanation
Indices: 19949389--19949422 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
19949379 GTTATTCTTT
19949389 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
19949423 CATCTAGGTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:19951864 original size:31 final size:31
Alignment explanation
Indices: 19951823--19951939 Score: 153
Period size: 31 Copynumber: 3.8 Consensus size: 31
19951813 ATTGTTATAA
* * * * *
19951823 AACGTCAAATGTTGTAACACGTCATGTATAG
1 AACGTAAAATGTGGTAACACGCCATGCATAT
19951854 AACGTAAAATGTGGTAACACGCCATGCATAT
1 AACGTAAAATGTGGTAACACGCCATGCATAT
*
19951885 AACGTTAAATGTGGTAACACGCCATGCATAT
1 AACGTAAAATGTGGTAACACGCCATGCATAT
* * *
19951916 AATGTAAACTGTGATAACACGCCA
1 AACGTAAAATGTGGTAACACGCCA
19951940 ATGCTGACAC
Statistics
Matches: 76, Mismatches: 10, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 76 1.00
ACGTcount: A:0.38, C:0.19, G:0.19, T:0.25
Consensus pattern (31 bp):
AACGTAAAATGTGGTAACACGCCATGCATAT
Found at i:19957440 original size:44 final size:44
Alignment explanation
Indices: 19957368--19957457 Score: 126
Period size: 44 Copynumber: 2.0 Consensus size: 44
19957358 GTTTTGGTGG
** * * *
19957368 TTTTTAGTTATTACGTAATTGATTTTTAAGTATTGTTTGACTGA
1 TTTTTAGGCATTACGTAATTAATATTTAAGTATTGTGTGACTGA
*
19957412 TTTTTAGGCATTACGTTATTAATATTTAAGTATTGTGTGACTGA
1 TTTTTAGGCATTACGTAATTAATATTTAAGTATTGTGTGACTGA
19957456 TT
1 TT
19957458 GATAGAACAT
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
44 40 1.00
ACGTcount: A:0.26, C:0.06, G:0.17, T:0.52
Consensus pattern (44 bp):
TTTTTAGGCATTACGTAATTAATATTTAAGTATTGTGTGACTGA
Found at i:19957479 original size:23 final size:22
Alignment explanation
Indices: 19957449--19957498 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 22
19957439 AAGTATTGTG
19957449 TGACTGATTGATAGAACATTACA
1 TGACTGATTGATAG-ACATTACA
** *
19957472 TGACTGATTTTTAGATATTACA
1 TGACTGATTGATAGACATTACA
19957494 TGACT
1 TGACT
19957499 AGTTAATAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
22 12 0.50
23 12 0.50
ACGTcount: A:0.34, C:0.12, G:0.16, T:0.38
Consensus pattern (22 bp):
TGACTGATTGATAGACATTACA
Found at i:19958063 original size:69 final size:70
Alignment explanation
Indices: 19957988--19958129 Score: 223
Period size: 70 Copynumber: 2.0 Consensus size: 70
19957978 TTTTGTCTGG
**
19957988 ATGGCGAGATAGAGAAACTGAAA-CATTTGAATCTGTCTAAAATTGTTTAAAAGGCATTATTGTC
1 ATGGCGAGATAGAGAAACCAAAATCATTTGAATCTGTCTAAAATTGTTTAAAAGGCATTATTGTC
19958052 AAGTC
66 AAGTC
* * * *
19958057 ATGGCGAGATAGAGAAACCAAAATCATTTTAATTTGTTTAAAATTGTTTAAAAGGTATTATTGTC
1 ATGGCGAGATAGAGAAACCAAAATCATTTGAATCTGTCTAAAATTGTTTAAAAGGCATTATTGTC
19958122 AAGTC
66 AAGTC
19958127 ATG
1 ATG
19958130 TTAAAAATAG
Statistics
Matches: 66, Mismatches: 6, Indels: 1
0.90 0.08 0.01
Matches are distributed among these distances:
69 21 0.32
70 45 0.68
ACGTcount: A:0.38, C:0.10, G:0.19, T:0.33
Consensus pattern (70 bp):
ATGGCGAGATAGAGAAACCAAAATCATTTGAATCTGTCTAAAATTGTTTAAAAGGCATTATTGTC
AAGTC
Found at i:19960193 original size:17 final size:18
Alignment explanation
Indices: 19960168--19960201 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
19960158 TTTTTGTTTC
19960168 TTTTCACC-TAACATTTT
1 TTTTCACCTTAACATTTT
*
19960185 TTTTTACCTTAACATTT
1 TTTTCACCTTAACATTT
19960202 GATAATTCTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.24, C:0.21, G:0.00, T:0.56
Consensus pattern (18 bp):
TTTTCACCTTAACATTTT
Found at i:19961773 original size:18 final size:19
Alignment explanation
Indices: 19961752--19961804 Score: 67
Period size: 18 Copynumber: 2.9 Consensus size: 19
19961742 TTTTTAAAAA
19961752 AATAT-TTAAATATTATTT
1 AATATATTAAATATTATTT
19961770 AATATATT-AATATT-TTT
1 AATATATTAAATATTATTT
*
19961787 AACTATAATAAATATTAT
1 AA-TATATTAAATATTAT
19961805 AAAGAATATT
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
17 5 0.17
18 16 0.53
19 8 0.27
20 1 0.03
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (19 bp):
AATATATTAAATATTATTT
Found at i:19961831 original size:32 final size:32
Alignment explanation
Indices: 19961778--19961849 Score: 89
Period size: 32 Copynumber: 2.3 Consensus size: 32
19961768 TTAATATATT
19961778 AATATT-TTTAACTATAATAAATATT-ATAAAG
1 AATATTATTTAACTATAATAAAT-TTAATAAAG
*
19961809 AATATTATTTAA-TAATATTAAATTTAATAAAG
1 AATATTATTTAACT-ATAATAAATTTAATAAAG
19961841 AATA-TATTT
1 AATATTATTT
19961850 TATCTTTAAT
Statistics
Matches: 37, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
31 14 0.38
32 23 0.62
ACGTcount: A:0.51, C:0.01, G:0.03, T:0.44
Consensus pattern (32 bp):
AATATTATTTAACTATAATAAATTTAATAAAG
Found at i:19961944 original size:47 final size:44
Alignment explanation
Indices: 19961819--19961944 Score: 128
Period size: 47 Copynumber: 2.8 Consensus size: 44
19961809 AATATTATTT
* * **
19961819 AATAATATTAAATT-TAATAAAGAATATATTTTATCTTTAATATTA
1 AATATTATTAAATTATAAT-AA-AATATTTTTTATCTTTAATAAAA
* * *
19961864 AATATTATTTAATTAGAATAAAATGTTTATTTATCTTCTAATACAAA
1 AATATTATTAAATTATAATAAAATATTT-TTTATCTT-TAATA-AAA
19961911 AATATTATTAAATTATAATAAAATATGTTTTTAT
1 AATATTATTAAATTATAATAAAATAT-TTTTTAT
19961945 TTTGGTGAAA
Statistics
Matches: 66, Mismatches: 10, Indels: 8
0.79 0.12 0.10
Matches are distributed among these distances:
44 5 0.08
45 22 0.33
46 8 0.12
47 29 0.44
48 2 0.03
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (44 bp):
AATATTATTAAATTATAATAAAATATTTTTTATCTTTAATAAAA
Found at i:19976936 original size:2 final size:2
Alignment explanation
Indices: 19976924--19976958 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
19976914 ATACATACAT
*
19976924 TA TA CA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
19976959 CATGTAAAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:19980354 original size:21 final size:20
Alignment explanation
Indices: 19980316--19980357 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
19980306 AATGCTTTGC
* *
19980316 AAAACATTTAAATTATTTTT
1 AAAAAATTTAAATAATTTTT
19980336 AAAAAATTTAAATAAATTTTT
1 AAAAAATTTAAAT-AATTTTT
19980357 A
1 A
19980358 TTCTTCTATT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 12 0.63
21 7 0.37
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (20 bp):
AAAAAATTTAAATAATTTTT
Found at i:19980870 original size:42 final size:42
Alignment explanation
Indices: 19980809--19980935 Score: 139
Period size: 42 Copynumber: 3.0 Consensus size: 42
19980799 ATTAGAAAGG
*
19980809 TTAAAAGGTGAACAGTAATCAAAACACTTAAATTAATCA-CAT
1 TTAAAAGGTGAATAGTAATCAAAACACTTAAATTAAT-AGCAT
* * * * * *
19980851 TTAAAAGGTGAATAATAATCTAAATAGTTAAGTTTATAGCAT
1 TTAAAAGGTGAATAGTAATCAAAACACTTAAATTAATAGCAT
* * * *
19980893 TTAAAGGGTGAATAGTAATCCAACCACTTAAATTAATTGCAT
1 TTAAAAGGTGAATAGTAATCAAAACACTTAAATTAATAGCAT
19980935 T
1 T
19980936 CATTCAATTA
Statistics
Matches: 68, Mismatches: 16, Indels: 2
0.79 0.19 0.02
Matches are distributed among these distances:
41 1 0.01
42 67 0.99
ACGTcount: A:0.45, C:0.11, G:0.13, T:0.31
Consensus pattern (42 bp):
TTAAAAGGTGAATAGTAATCAAAACACTTAAATTAATAGCAT
Found at i:19983800 original size:22 final size:24
Alignment explanation
Indices: 19983775--19983820 Score: 60
Period size: 22 Copynumber: 2.0 Consensus size: 24
19983765 TGTAGAAATT
19983775 GAAAGAAAAAAG-AAAT-GAAAAA
1 GAAAGAAAAAAGAAAATAGAAAAA
* *
19983797 GAAATAAAATAGAAAATAGAAAAA
1 GAAAGAAAAAAGAAAATAGAAAAA
19983821 CAAGCTGTCA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 10 0.50
23 4 0.20
24 6 0.30
ACGTcount: A:0.76, C:0.00, G:0.15, T:0.09
Consensus pattern (24 bp):
GAAAGAAAAAAGAAAATAGAAAAA
Found at i:19995398 original size:127 final size:127
Alignment explanation
Indices: 19995253--19995506 Score: 508
Period size: 127 Copynumber: 2.0 Consensus size: 127
19995243 AAGAGCTTAT
19995253 GGGCATCTTTAATTCTTTATATCCAGTAAGAGTAAATAGTAAATTCATGGGTTCTTTTTTTCTTT
1 GGGCATCTTTAATTCTTTATATCCAGTAAGAGTAAATAGTAAATTCATGGGTTCTTTTTTTCTTT
19995318 AAATTTTTTGGAAGTAGTTAGACACTTTAGTGTTTTCCACATAATATACACAAAATTTATGA
66 AAATTTTTTGGAAGTAGTTAGACACTTTAGTGTTTTCCACATAATATACACAAAATTTATGA
19995380 GGGCATCTTTAATTCTTTATATCCAGTAAGAGTAAATAGTAAATTCATGGGTTCTTTTTTTCTTT
1 GGGCATCTTTAATTCTTTATATCCAGTAAGAGTAAATAGTAAATTCATGGGTTCTTTTTTTCTTT
19995445 AAATTTTTTGGAAGTAGTTAGACACTTTAGTGTTTTCCACATAATATACACAAAATTTATGA
66 AAATTTTTTGGAAGTAGTTAGACACTTTAGTGTTTTCCACATAATATACACAAAATTTATGA
19995507 AATAGACTCT
Statistics
Matches: 127, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
127 127 1.00
ACGTcount: A:0.31, C:0.12, G:0.14, T:0.43
Consensus pattern (127 bp):
GGGCATCTTTAATTCTTTATATCCAGTAAGAGTAAATAGTAAATTCATGGGTTCTTTTTTTCTTT
AAATTTTTTGGAAGTAGTTAGACACTTTAGTGTTTTCCACATAATATACACAAAATTTATGA
Found at i:19995588 original size:24 final size:25
Alignment explanation
Indices: 19995539--19995593 Score: 85
Period size: 26 Copynumber: 2.2 Consensus size: 25
19995529 TTTAGCCGGT
*
19995539 AAGAAGGATGGAAATGGGGAGGGGAA
1 AAGAAGGATGGAAAT-GGGAGAGGAA
19995565 AAGAAGGATGGAAAT-GGAGAGGAA
1 AAGAAGGATGGAAATGGGAGAGGAA
19995589 AAGAA
1 AAGAA
19995594 ATTTTTTTTA
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
24 13 0.46
26 15 0.54
ACGTcount: A:0.49, C:0.00, G:0.44, T:0.07
Consensus pattern (25 bp):
AAGAAGGATGGAAATGGGAGAGGAA
Found at i:19996665 original size:2 final size:2
Alignment explanation
Indices: 19996658--19996696 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
19996648 TCCTAATGCA
*
19996658 AT AT AT AT AG AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
19996697 GTGATAATTT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (2 bp):
AT
Found at i:20004660 original size:20 final size:22
Alignment explanation
Indices: 20004635--20004679 Score: 67
Period size: 20 Copynumber: 2.1 Consensus size: 22
20004625 CGGCTAGATT
*
20004635 TGGCCGTTGG-AGCACC-AATC
1 TGGCCGTGGGAAGCACCAAATC
20004655 TGGCCGTGGGAAGCACCAAATC
1 TGGCCGTGGGAAGCACCAAATC
20004677 TGG
1 TGG
20004680 TAATGCCATT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 9 0.41
21 6 0.27
22 7 0.32
ACGTcount: A:0.22, C:0.27, G:0.33, T:0.18
Consensus pattern (22 bp):
TGGCCGTGGGAAGCACCAAATC
Found at i:20005013 original size:14 final size:14
Alignment explanation
Indices: 20004990--20005019 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
20004980 TAAAAAATTG
*
20004990 TATAACTAATTTAA
1 TATAAATAATTTAA
20005004 TATAAATAATTTAA
1 TATAAATAATTTAA
20005018 TA
1 TA
20005020 ATTTAATAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.43
Consensus pattern (14 bp):
TATAAATAATTTAA
Found at i:20005023 original size:22 final size:21
Alignment explanation
Indices: 20004996--20005054 Score: 66
Period size: 22 Copynumber: 2.8 Consensus size: 21
20004986 ATTGTATAAC
20004996 TAATTTAATATAAATAATTTAA
1 TAATTTAATATAAATAA-TTAA
* *
20005018 TAATTTAATAATAAATTATTGA
1 TAATTTAAT-ATAAATAATTAA
*
20005040 T-ATTTAATAAAAATA
1 TAATTTAATATAAATA
20005055 GAAATTAAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
20 5 0.16
21 7 0.22
22 13 0.41
23 7 0.22
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (21 bp):
TAATTTAATATAAATAATTAA
Found at i:20005097 original size:135 final size:136
Alignment explanation
Indices: 20004891--20005172 Score: 349
Period size: 135 Copynumber: 2.1 Consensus size: 136
20004881 TTATATTAGT
* * *
20004891 TAATAAATTATTGATATTTAATGAAAATAAAAATTAAAAGATAAAAATATGAAAAATACAATTGG
1 TAATAAATTATTGATATTTAATAAAAATAAAAATTAAAAGATAAAAATATGAAAAATACAAATAG
* * **
20004956 AAAAAAAT-TATTCAAACAATT-TATTAAAAAATTGTATAACTAATTTAAT-ATAAATAATT-TA
66 AAAAAAATAAATTC-AACAATTAAATT-AAAAATAATATAACTAATTTAATAATAAATAATTCT-
20005017 ATAATTTAA
128 ATAATTTAA
* *
20005026 TAATAAATTATTGATATTTAATAAAAATAGAAATTAAAAGATTAAGAA-ATGAAAAATACAAATA
1 TAATAAATTATTGATATTTAATAAAAATAAAAATTAAAAGA-TAAAAATATGAAAAATACAAATA
* * * *
20005090 GAGAAAAATAAATTCAATAATTAAAATTAAAAATAATATAACTAATTTAGTAATAAATTATTCTA
65 GAAAAAAATAAATTCAACAATT-AAATTAAAAATAATATAACTAATTTAATAATAAATAATTCTA
*
20005155 TAGTTTAA
129 TAATTTAA
*
20005163 TAAAAAATTA
1 TAATAAATTA
20005173 AAAATTTATA
Statistics
Matches: 126, Mismatches: 15, Indels: 10
0.83 0.10 0.07
Matches are distributed among these distances:
135 67 0.53
136 29 0.23
137 29 0.23
138 1 0.01
ACGTcount: A:0.58, C:0.03, G:0.06, T:0.34
Consensus pattern (136 bp):
TAATAAATTATTGATATTTAATAAAAATAAAAATTAAAAGATAAAAATATGAAAAATACAAATAG
AAAAAAATAAATTCAACAATTAAATTAAAAATAATATAACTAATTTAATAATAAATAATTCTATA
ATTTAA
Found at i:20006064 original size:22 final size:23
Alignment explanation
Indices: 20006020--20006064 Score: 58
Period size: 22 Copynumber: 2.0 Consensus size: 23
20006010 TTGTTATTTG
*
20006020 GATTGGAAGAACTCATAGGGAAA
1 GATTGGAAGAACTCATAGAGAAA
20006043 GATT-GAAGAACTC-TAGAAGAAA
1 GATTGGAAGAACTCATAG-AGAAA
20006065 AGGCTTGGAT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
21 3 0.15
22 13 0.65
23 4 0.20
ACGTcount: A:0.47, C:0.09, G:0.27, T:0.18
Consensus pattern (23 bp):
GATTGGAAGAACTCATAGAGAAA
Found at i:20010861 original size:34 final size:34
Alignment explanation
Indices: 20010818--20010886 Score: 138
Period size: 34 Copynumber: 2.0 Consensus size: 34
20010808 TTTAGGTGAT
20010818 TTATAATCCACTCAATTATGTGTTTAATAATATC
1 TTATAATCCACTCAATTATGTGTTTAATAATATC
20010852 TTATAATCCACTCAATTATGTGTTTAATAATATC
1 TTATAATCCACTCAATTATGTGTTTAATAATATC
20010886 T
1 T
20010887 ATCACTTTGT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.35, C:0.14, G:0.06, T:0.45
Consensus pattern (34 bp):
TTATAATCCACTCAATTATGTGTTTAATAATATC
Found at i:20011342 original size:3 final size:3
Alignment explanation
Indices: 20011334--20011376 Score: 52
Period size: 3 Copynumber: 14.7 Consensus size: 3
20011324 TTTTTTACTT
* * *
20011334 TTA TTA TTA TTA TTA TT- TTA TTA TTT TTA CTA TCA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
20011377 TTCTGATTTT
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
2 2 0.06
3 31 0.94
ACGTcount: A:0.28, C:0.05, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:20012338 original size:13 final size:13
Alignment explanation
Indices: 20012321--20012409 Score: 58
Period size: 14 Copynumber: 6.6 Consensus size: 13
20012311 TATTATTTTC
20012321 TTTATTTAT-TAT
1 TTTATTTATATAT
20012333 TATTATTTTATATAT
1 T-TTA-TTTATATAT
*
20012348 TTTATTTTACTTTAT
1 TTTA-TTTA-TATAT
* * *
20012363 TATAATTTAAATTT
1 T-TTATTTATATAT
*
20012377 TTTATTT-TTTAT
1 TTTATTTATATAT
20012389 TTATATTTATATAT
1 TT-TATTTATATAT
20012403 TTT-TTTA
1 TTTATTTA
20012410 AGTGTCTACA
Statistics
Matches: 60, Mismatches: 10, Indels: 14
0.71 0.12 0.17
Matches are distributed among these distances:
12 9 0.15
13 14 0.23
14 22 0.37
15 13 0.22
16 2 0.03
ACGTcount: A:0.28, C:0.01, G:0.00, T:0.71
Consensus pattern (13 bp):
TTTATTTATATAT
Found at i:20012351 original size:27 final size:27
Alignment explanation
Indices: 20012321--20012409 Score: 78
Period size: 26 Copynumber: 3.3 Consensus size: 27
20012311 TATTATTTTC
20012321 TTTATTTATTATTATTATTTTATATAT
1 TTTATTTATTATTATTATTTTATATAT
* * *
20012348 TTTATTTTACTTTATTA-TAATTTAAATTT
1 TTTA-TTTA--TTATTATTATTTTATATAT
*
20012377 TTTATTTTTTA-T-TTATATTTATATAT
1 TTTATTTATTATTATTAT-TTTATATAT
20012403 TTT-TTTA
1 TTTATTTA
20012410 AGTGTCTACA
Statistics
Matches: 49, Mismatches: 8, Indels: 12
0.71 0.12 0.17
Matches are distributed among these distances:
25 6 0.12
26 13 0.27
27 4 0.08
28 7 0.14
29 13 0.27
30 6 0.12
ACGTcount: A:0.28, C:0.01, G:0.00, T:0.71
Consensus pattern (27 bp):
TTTATTTATTATTATTATTTTATATAT
Found at i:20012377 original size:36 final size:33
Alignment explanation
Indices: 20012304--20012398 Score: 97
Period size: 36 Copynumber: 2.8 Consensus size: 33
20012294 TTTTTTTTTT
* *
20012304 TTAATTTTAT-TATTTT-CTTTATTTATTATTA
1 TTAATTTTATATATTTTATTTTATTTATTATAA
20012335 TT-ATTTTATATATTTTATTTTACTTTATTATAA
1 TTAATTTTATATATTTTATTTTA-TTTATTATAA
* *
20012368 TTTAAATTTTTTATTTTTTATTTATATTTAT
1 -TT-AATTTTATATATTTTATTT-TATTTAT
20012399 ATATTTTTTT
Statistics
Matches: 53, Mismatches: 4, Indels: 9
0.80 0.06 0.14
Matches are distributed among these distances:
30 7 0.13
31 8 0.15
32 4 0.08
33 9 0.17
34 2 0.04
36 21 0.40
37 2 0.04
ACGTcount: A:0.27, C:0.02, G:0.00, T:0.71
Consensus pattern (33 bp):
TTAATTTTATATATTTTATTTTATTTATTATAA
Found at i:20012390 original size:20 final size:21
Alignment explanation
Indices: 20012367--20012407 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
20012357 CTTTATTATA
*
20012367 ATTTAAATTT-TTTATTTTTT
1 ATTTAAATTTATATATTTTTT
*
20012387 ATTTATATTTATATATTTTTT
1 ATTTAAATTTATATATTTTTT
20012408 TAAGTGTCTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 9 0.50
21 9 0.50
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (21 bp):
ATTTAAATTTATATATTTTTT
Found at i:20012409 original size:22 final size:21
Alignment explanation
Indices: 20012295--20012409 Score: 69
Period size: 22 Copynumber: 5.4 Consensus size: 21
20012285 AGCCATTCCT
*
20012295 TTTTTTTTTTTA-ATTTTATTA
1 TTTTTTTATTTATATTTTA-TA
20012316 TTTTCTTTATTTATTATTATTAT-
1 TTTT-TTTATTTA-TATT-TTATA
* *
20012339 TTTATATATTT-TATTTTACT-
1 TTTTTTTATTTATATTTTA-TA
* * * *
20012359 TTATTATAATTTAAATTTTTTA
1 TT-TTTTTATTTATATTTTATA
20012381 -TTTTTTATTTATATTTATATA
1 TTTTTTTATTTATATTT-TATA
20012402 TTTTTTTA
1 TTTTTTTA
20012410 AGTGTCTACA
Statistics
Matches: 71, Mismatches: 13, Indels: 19
0.69 0.13 0.18
Matches are distributed among these distances:
19 3 0.04
20 19 0.27
21 14 0.20
22 25 0.35
23 3 0.04
24 4 0.06
25 3 0.04
ACGTcount: A:0.25, C:0.02, G:0.00, T:0.73
Consensus pattern (21 bp):
TTTTTTTATTTATATTTTATA
Found at i:20014841 original size:15 final size:15
Alignment explanation
Indices: 20014821--20014850 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
20014811 AGTTATATAT
20014821 ATGTACATGCATACA
1 ATGTACATGCATACA
20014836 ATGTACATGCATACA
1 ATGTACATGCATACA
20014851 TTGTGGTCAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.40, C:0.20, G:0.13, T:0.27
Consensus pattern (15 bp):
ATGTACATGCATACA
Found at i:20016556 original size:2 final size:2
Alignment explanation
Indices: 20016551--20016576 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
20016541 AAAAAAAAAA
20016551 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
20016577 TTTTTTTTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:20022226 original size:25 final size:28
Alignment explanation
Indices: 20022198--20022253 Score: 73
Period size: 27 Copynumber: 2.1 Consensus size: 28
20022188 TGATTTATAG
*
20022198 ATTT-GTTAAGA-TAATTATATAA-ATT
1 ATTTAGTTAAGAGTAATTATACAATATT
*
20022223 ATTTAGTTAAGAGTTATTATACAATATT
1 ATTTAGTTAAGAGTAATTATACAATATT
20022251 ATT
1 ATT
20022254 ATCCAATGGG
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
25 4 0.15
26 7 0.27
27 9 0.35
28 6 0.23
ACGTcount: A:0.41, C:0.02, G:0.09, T:0.48
Consensus pattern (28 bp):
ATTTAGTTAAGAGTAATTATACAATATT
Found at i:20028049 original size:36 final size:37
Alignment explanation
Indices: 20027966--20028050 Score: 102
Period size: 38 Copynumber: 2.3 Consensus size: 37
20027956 CCTCACCAGC
20027966 TCATGTGCAACCCCCACATCGCACACATAGCTAGAGTCA
1 TCATGTGC-ACCCCCACATCGCACACATA-CTAGAGTCA
* * *
20028005 TCGTGTGCACCCCCACATCGCGCACACTA-TATA-TCA
1 TCATGTGCACCCCCACATCGCACACA-TACTAGAGTCA
20028041 TCATGTGCAC
1 TCATGTGCAC
20028051 TCCTTACTCG
Statistics
Matches: 41, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
36 12 0.29
37 3 0.07
38 17 0.41
39 9 0.22
ACGTcount: A:0.27, C:0.36, G:0.15, T:0.21
Consensus pattern (37 bp):
TCATGTGCACCCCCACATCGCACACATACTAGAGTCA
Found at i:20028083 original size:35 final size:35
Alignment explanation
Indices: 20028002--20028138 Score: 170
Period size: 35 Copynumber: 3.9 Consensus size: 35
20027992 ATAGCTAGAG
* *
20028002 TCATCGTGTGCAC-CCCCACATCGCGCACAC-TATATA
1 TCATCGTGTGCACTCCCTAC-T--CGCACACTTCTATA
* * *
20028038 TCATCATGTGCACTCCTTACTCGCACATTTCTATA
1 TCATCGTGTGCACTCCCTACTCGCACACTTCTATA
* *
20028073 TCATCGTGTGCACTCCCTACTCGCACACTTCAACA
1 TCATCGTGTGCACTCCCTACTCGCACACTTCTATA
20028108 TCATCGTGTGCACTCCCTACTCGCACACTTC
1 TCATCGTGTGCACTCCCTACTCGCACACTTC
20028139 AACATCATTA
Statistics
Matches: 89, Mismatches: 10, Indels: 5
0.86 0.10 0.05
Matches are distributed among these distances:
34 6 0.07
35 66 0.74
36 13 0.15
37 4 0.04
ACGTcount: A:0.22, C:0.38, G:0.12, T:0.28
Consensus pattern (35 bp):
TCATCGTGTGCACTCCCTACTCGCACACTTCTATA
Found at i:20028139 original size:35 final size:35
Alignment explanation
Indices: 20028037--20028146 Score: 175
Period size: 35 Copynumber: 3.1 Consensus size: 35
20028027 CACACTATAT
* * * * *
20028037 ATCATCATGTGCACTCCTTACTCGCACATTTCTAT
1 ATCATCGTGTGCACTCCCTACTCGCACACTTCAAC
20028072 ATCATCGTGTGCACTCCCTACTCGCACACTTCAAC
1 ATCATCGTGTGCACTCCCTACTCGCACACTTCAAC
20028107 ATCATCGTGTGCACTCCCTACTCGCACACTTCAAC
1 ATCATCGTGTGCACTCCCTACTCGCACACTTCAAC
20028142 ATCAT
1 ATCAT
20028147 TATCCACACT
Statistics
Matches: 70, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
35 70 1.00
ACGTcount: A:0.24, C:0.36, G:0.10, T:0.30
Consensus pattern (35 bp):
ATCATCGTGTGCACTCCCTACTCGCACACTTCAAC
Found at i:20053121 original size:28 final size:28
Alignment explanation
Indices: 20053058--20053146 Score: 106
Period size: 29 Copynumber: 3.1 Consensus size: 28
20053048 AAAAGTTAAT
* * *
20053058 ATGGATTTGTGGTGATCTCGTTAAAAACC
1 ATGGGTTTGTGGTGAACCCGTT-AAAACC
20053087 ATGGGTTTGTGGTGAACCCGTTAAAACC
1 ATGGGTTTGTGGTGAACCCGTTAAAACC
* *
20053115 ATGGGTTTGTGATTGAACCCTTTAAAAGCC
1 ATGGGTTTGTG-GTGAACCCGTTAAAA-CC
20053145 AT
1 AT
20053147 CGTAAGAGTT
Statistics
Matches: 53, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
28 17 0.32
29 32 0.60
30 4 0.08
ACGTcount: A:0.27, C:0.16, G:0.25, T:0.33
Consensus pattern (28 bp):
ATGGGTTTGTGGTGAACCCGTTAAAACC
Found at i:20077955 original size:15 final size:16
Alignment explanation
Indices: 20077935--20077968 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
20077925 TGTTATGTAG
*
20077935 ATTTT-ATTTTTAATA
1 ATTTTAATTTTTAAAA
20077950 ATTTTAATTTTTAAAA
1 ATTTTAATTTTTAAAA
20077966 ATT
1 ATT
20077969 AAAATATTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 5 0.29
16 12 0.71
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (16 bp):
ATTTTAATTTTTAAAA
Found at i:20086127 original size:21 final size:20
Alignment explanation
Indices: 20086102--20086148 Score: 58
Period size: 21 Copynumber: 2.3 Consensus size: 20
20086092 TGGAGGTCGA
* **
20086102 AAAAGAGAGGAATGAGGAGG
1 AAAAGAGAGAAAAAAGGAGG
20086122 AGAAAGAGAGAAAAAAGGAGG
1 A-AAAGAGAGAAAAAAGGAGG
20086143 AAAAGA
1 AAAAGA
20086149 ATAAGAAGAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
20 6 0.26
21 17 0.74
ACGTcount: A:0.60, C:0.00, G:0.38, T:0.02
Consensus pattern (20 bp):
AAAAGAGAGAAAAAAGGAGG
Found at i:20087199 original size:23 final size:23
Alignment explanation
Indices: 20087173--20087257 Score: 93
Period size: 23 Copynumber: 3.7 Consensus size: 23
20087163 GTAATGCCTA
*
20087173 AGTCATGCAATGCCTTACTAACT
1 AGTCACGCAATGCCTTACTAACT
* * *
20087196 AGTCACGGAATGCTTTACTAACA
1 AGTCACGCAATGCCTTACTAACT
*
20087219 AGTCATGCAATG-CTTA-TCAACT
1 AGTCACGCAATGCCTTACT-AACT
*
20087241 AGTCACACAATGCCTTA
1 AGTCACGCAATGCCTTA
20087258 TAAAAAACTA
Statistics
Matches: 50, Mismatches: 10, Indels: 4
0.78 0.16 0.06
Matches are distributed among these distances:
21 1 0.02
22 16 0.32
23 33 0.66
ACGTcount: A:0.33, C:0.25, G:0.14, T:0.28
Consensus pattern (23 bp):
AGTCACGCAATGCCTTACTAACT
Found at i:20087299 original size:21 final size:20
Alignment explanation
Indices: 20087275--20087322 Score: 69
Period size: 21 Copynumber: 2.3 Consensus size: 20
20087265 CTAGTCAGGC
*
20087275 AATGCCGAAAGTCAGTCACGT
1 AATGCC-AAAGTCAGTCACCT
20087296 AATGTCCAAAGTCAGTCACCT
1 AATG-CCAAAGTCAGTCACCT
20087317 AATGCC
1 AATGCC
20087323 TAAAAACTAG
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
20 2 0.08
21 21 0.84
22 2 0.08
ACGTcount: A:0.33, C:0.27, G:0.19, T:0.21
Consensus pattern (20 bp):
AATGCCAAAGTCAGTCACCT
Found at i:20091817 original size:2 final size:2
Alignment explanation
Indices: 20091810--20091853 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
20091800 TTGCATAAAC
20091810 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
20091852 AT
1 AT
20091854 TACATATGTA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:20094772 original size:39 final size:39
Alignment explanation
Indices: 20094718--20094868 Score: 212
Period size: 39 Copynumber: 3.9 Consensus size: 39
20094708 AAATTCATTC
* * * *
20094718 TCGCTGCAGCGAGAAACTTTTTGTTTCTGGATTATAATT
1 TCGCTGCAGCAAGAAACTTTCTGTTTCTGGGTTACAATT
*
20094757 TCGCTGCAGCGAGAAACTTTCTGTTTCTGGGTTACAATT
1 TCGCTGCAGCAAGAAACTTTCTGTTTCTGGGTTACAATT
* *
20094796 TCGTTGCAGCAAGAAACTTTCTATTTCTGGGTTACAATT
1 TCGCTGCAGCAAGAAACTTTCTGTTTCTGGGTTACAATT
* * *
20094835 TCACTACAGCAAGAAACTTTCTGTTTTTGGGTTA
1 TCGCTGCAGCAAGAAACTTTCTGTTTCTGGGTTA
20094869 ATCTCGCTAT
Statistics
Matches: 101, Mismatches: 11, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
39 101 1.00
ACGTcount: A:0.24, C:0.18, G:0.20, T:0.38
Consensus pattern (39 bp):
TCGCTGCAGCAAGAAACTTTCTGTTTCTGGGTTACAATT
Done.