Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: chr1
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: 37323695
ACGTcount: A:0.32, C:0.17, G:0.16, T:0.32
Warning! 1370832 characters in sequence are not A, C, G, or T
File 50 of 93
Found at i:19191449 original size:16 final size:17
Alignment explanation
Indices: 19191428--19191466 Score: 55
Period size: 16 Copynumber: 2.4 Consensus size: 17
19191418 ACCCCATTCT
*
19191428 TTTTATTTCTTTA-TTA
1 TTTTATTTATTTATTTA
19191444 TTTTA-TTATTTATTTA
1 TTTTATTTATTTATTTA
19191460 TTTTATT
1 TTTTATT
19191467 CTCTCCAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
15 6 0.30
16 13 0.65
17 1 0.05
ACGTcount: A:0.21, C:0.03, G:0.00, T:0.77
Consensus pattern (17 bp):
TTTTATTTATTTATTTA
Found at i:19192078 original size:34 final size:34
Alignment explanation
Indices: 19192040--19192155 Score: 126
Period size: 34 Copynumber: 3.4 Consensus size: 34
19192030 GCTTAAGCCC
* *
19192040 GTAAAAAGGCATTGTGAGTGTTGTGCTTGAGGTT
1 GTAAAAAGGCATTGTGAGTGTTGTGCTTGAGCTA
* * **
19192074 GTAAAAAGACATTGTGAATGTTGTGCTTGCTCTA
1 GTAAAAAGGCATTGTGAGTGTTGTGCTTGAGCTA
* * * *
19192108 GTAAAAAGGCACTGTGAGGGTTGTTCTTGAGCTC
1 GTAAAAAGGCATTGTGAGTGTTGTGCTTGAGCTA
*
19192142 G-AAAAAAGCATTGT
1 GTAAAAAGGCATTGT
19192156 AAAGGCTTGC
Statistics
Matches: 66, Mismatches: 16, Indels: 1
0.80 0.19 0.01
Matches are distributed among these distances:
33 11 0.17
34 55 0.83
ACGTcount: A:0.28, C:0.10, G:0.29, T:0.32
Consensus pattern (34 bp):
GTAAAAAGGCATTGTGAGTGTTGTGCTTGAGCTA
Found at i:19192182 original size:68 final size:68
Alignment explanation
Indices: 19192040--19192181 Score: 162
Period size: 68 Copynumber: 2.1 Consensus size: 68
19192030 GCTTAAGCCC
* * * * * * * * *
19192040 GTAAAAAGGCATTGTGAGTGTTGTGCTTGAGGTTGTAAAAAGACATTGTGAATGTTGTGCTTGCT
1 GTAAAAAGGCACTGTGAGGGTTGTGCTTGAGCTCGAAAAAAGACATTGTAAAGGCTGTGCTTGAT
19192105 CTA
66 CTA
*
19192108 GTAAAAAGGCACTGTGAGGGTTGTTCTTGAGCTCGAAAAAAG-CATTGTAAAGGCT-TGCTTGAT
1 GTAAAAAGGCACTGTGAGGGTTGTGCTTGAGCTCGAAAAAAGACATTGTAAAGGCTGTGCTTGAT
19192171 CCTA
66 -CTA
*
19192175 TTAAAAA
1 GTAAAAA
19192182 ACATTTTCCA
Statistics
Matches: 62, Mismatches: 11, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
66 7 0.11
67 19 0.31
68 36 0.58
ACGTcount: A:0.30, C:0.11, G:0.27, T:0.32
Consensus pattern (68 bp):
GTAAAAAGGCACTGTGAGGGTTGTGCTTGAGCTCGAAAAAAGACATTGTAAAGGCTGTGCTTGAT
CTA
Found at i:19194559 original size:54 final size:54
Alignment explanation
Indices: 19194501--19194605 Score: 158
Period size: 54 Copynumber: 1.9 Consensus size: 54
19194491 ATAGTTTCGG
* * *
19194501 TTATCCTTTTGTTGAGTAAGACGAGTGAGCTA-GATGCCATTAGTAAGGTTTTGA
1 TTATCCTTTTATTGAGTAAGACGAGTGAGC-ACGATGCCATCAGCAAGGTTTTGA
*
19194555 TTATCCTTTTATTGAGTAAGAGGAGTGAGCACGATGCCATCAGCAAGGTTT
1 TTATCCTTTTATTGAGTAAGACGAGTGAGCACGATGCCATCAGCAAGGTTT
19194606 CCATTTTGAT
Statistics
Matches: 46, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
53 1 0.02
54 45 0.98
ACGTcount: A:0.27, C:0.13, G:0.26, T:0.34
Consensus pattern (54 bp):
TTATCCTTTTATTGAGTAAGACGAGTGAGCACGATGCCATCAGCAAGGTTTTGA
Found at i:19194672 original size:60 final size:60
Alignment explanation
Indices: 19194549--19194662 Score: 140
Period size: 60 Copynumber: 1.9 Consensus size: 60
19194539 ATTAGTAAGG
* * * *
19194549 TTTTGATTATCCTTTTATTGAGTAAGAGGAGTGAGCACGATGCCATCAGCAAGGTTTCCA
1 TTTTGATTATCCTTTTATTAAGCAAGAGGAGTCAGCACGATACCATCAGCAAGGTTTCCA
* * * *
19194609 TTTTGATTATTCTTTTGTTAAGCAAGAGGAG-CACGCATGATACCATTAGCAAGG
1 TTTTGATTATCCTTTTATTAAGCAAGAGGAGTCA-GCACGATACCATCAGCAAGG
19194663 GTTTGATTTT
Statistics
Matches: 45, Mismatches: 8, Indels: 2
0.82 0.15 0.04
Matches are distributed among these distances:
59 1 0.02
60 44 0.98
ACGTcount: A:0.28, C:0.16, G:0.23, T:0.33
Consensus pattern (60 bp):
TTTTGATTATCCTTTTATTAAGCAAGAGGAGTCAGCACGATACCATCAGCAAGGTTTCCA
Found at i:19200674 original size:43 final size:43
Alignment explanation
Indices: 19200604--19200722 Score: 177
Period size: 43 Copynumber: 2.8 Consensus size: 43
19200594 GTAATTATGT
* *
19200604 TGACTCGGCTATGTGCGAGTAGGGAGTGCGCATAAGCCGAG-GA
1 TGACCCGGCTATGTGCGAGTAGGGAGTGCGCATAACCCG-GTGA
*
19200647 TGACCCGGTTATGTGCGAGTAGGGAGTGCGCATAACCCGGTGA
1 TGACCCGGCTATGTGCGAGTAGGGAGTGCGCATAACCCGGTGA
* *
19200690 TGACCCAGCCATGTGCGAGTAGGGAGTGCGCAT
1 TGACCCGGCTATGTGCGAGTAGGGAGTGCGCAT
19200723 GAGCTGGTGA
Statistics
Matches: 69, Mismatches: 6, Indels: 2
0.90 0.08 0.03
Matches are distributed among these distances:
42 1 0.01
43 68 0.99
ACGTcount: A:0.22, C:0.21, G:0.38, T:0.19
Consensus pattern (43 bp):
TGACCCGGCTATGTGCGAGTAGGGAGTGCGCATAACCCGGTGA
Found at i:19200732 original size:43 final size:43
Alignment explanation
Indices: 19200614--19200735 Score: 174
Period size: 43 Copynumber: 2.8 Consensus size: 43
19200604 TGACTCGGCT
* **
19200614 ATGTGCGAGTAGGGAGTGCGCATAAGCCGAG-GATGACCCGGTT
1 ATGTGCGAGTAGGGAGTGCGCATAAGCCG-GTGATGACCCAGCC
*
19200657 ATGTGCGAGTAGGGAGTGCGCATAACCCGGTGATGACCCAGCC
1 ATGTGCGAGTAGGGAGTGCGCATAAGCCGGTGATGACCCAGCC
* *
19200700 ATGTGCGAGTAGGGAGTGCGCATGAGCTGGTGATGA
1 ATGTGCGAGTAGGGAGTGCGCATAAGCCGGTGATGA
19200736 TGATGATGAG
Statistics
Matches: 71, Mismatches: 7, Indels: 2
0.89 0.09 0.03
Matches are distributed among these distances:
42 1 0.01
43 70 0.99
ACGTcount: A:0.23, C:0.19, G:0.39, T:0.19
Consensus pattern (43 bp):
ATGTGCGAGTAGGGAGTGCGCATAAGCCGGTGATGACCCAGCC
Found at i:19200746 original size:20 final size:20
Alignment explanation
Indices: 19200721--19200783 Score: 101
Period size: 20 Copynumber: 3.2 Consensus size: 20
19200711 GGGAGTGCGC
19200721 ATGAGCTGGTGATGATGATG
1 ATGAGCTGGTGATGATGATG
19200741 ATGAGCTGGTGATGATGATG
1 ATGAGCTGGTGATGATGATG
* *
19200761 ATGGGTTGGTGA-GATGATG
1 ATGAGCTGGTGATGATGATG
19200780 ATGA
1 ATGA
19200784 TGGGTATATA
Statistics
Matches: 40, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
19 10 0.25
20 30 0.75
ACGTcount: A:0.25, C:0.03, G:0.41, T:0.30
Consensus pattern (20 bp):
ATGAGCTGGTGATGATGATG
Found at i:19214550 original size:66 final size:65
Alignment explanation
Indices: 19214480--19214666 Score: 200
Period size: 66 Copynumber: 2.8 Consensus size: 65
19214470 GGCTTTTCGC
*
19214480 AGGCTCAGCCACAACCATTAGCAATGGTTTTTCACGGGATCAACCAAAACCCAAAGTGGTTTTTC
1 AGGCTCAACCACAACC-TTA-CAATGGTTTTTCACGGGATCAACCAAAACCCAAAGTGGTTTTTC
19214545 -A
64 AA
* * * * * *
19214546 AGGCTCAATCACAACCTTTTACACTAGTTTTTCACGGGCTAAACTAAAACCCAAAGTGGTTTTTC
1 AGGCTCAACCACAACC--TTACAATGGTTTTTCACGGGATCAACCAAAACCCAAAGTGGTTTTTC
19214611 AA
64 AA
* *
19214613 AGGCACAACCACAACC-TACAATAATGGTTTTT-ACCGAGATCAACCAAAACCCAA
1 AGGCTCAACCACAACCTTAC---AATGGTTTTTCA-CGGGATCAACCAAAACCCAA
19214667 CAACCAACTT
Statistics
Matches: 99, Mismatches: 16, Indels: 11
0.79 0.13 0.09
Matches are distributed among these distances:
64 3 0.03
66 54 0.55
67 42 0.42
ACGTcount: A:0.35, C:0.26, G:0.14, T:0.24
Consensus pattern (65 bp):
AGGCTCAACCACAACCTTACAATGGTTTTTCACGGGATCAACCAAAACCCAAAGTGGTTTTTCAA
Found at i:19214662 original size:67 final size:66
Alignment explanation
Indices: 19214501--19214666 Score: 199
Period size: 67 Copynumber: 2.5 Consensus size: 66
19214491 CAACCATTAG
* * ***
19214501 CAATGGTTTTTCACGGGATCAACCAAAACCCAAAGTGGTTTTTCAAGGCTCAATCACAACCTTTT
1 CAATGGTTTTTCACGGGATCAACCAAAACCCAAAGTGGTTTTTCAAGGCACAACCACAACCTACA
19214566 A
66 A
* * * * *
19214567 CACTAGTTTTTCACGGGCTAAACTAAAACCCAAAGTGGTTTTTCAAAGGCACAACCACAACCTAC
1 CAATGGTTTTTCACGGGATCAACCAAAACCCAAAGTGGTTTTTC-AAGGCACAACCACAACCTAC
19214632 AA
65 AA
* *
19214634 TAATGGTTTTT-ACCGAGATCAACCAAAACCCAA
1 CAATGGTTTTTCA-CGGGATCAACCAAAACCCAA
19214667 CAACCAACTT
Statistics
Matches: 81, Mismatches: 17, Indels: 3
0.80 0.17 0.03
Matches are distributed among these distances:
66 40 0.49
67 41 0.51
ACGTcount: A:0.36, C:0.25, G:0.14, T:0.25
Consensus pattern (66 bp):
CAATGGTTTTTCACGGGATCAACCAAAACCCAAAGTGGTTTTTCAAGGCACAACCACAACCTACA
A
Found at i:19225452 original size:13 final size:13
Alignment explanation
Indices: 19225434--19225458 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
19225424 AGAGAAATTG
19225434 TGATTTTATAAAA
1 TGATTTTATAAAA
19225447 TGATTTTATAAA
1 TGATTTTATAAA
19225459 TTTTCTGAAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.44, C:0.00, G:0.08, T:0.48
Consensus pattern (13 bp):
TGATTTTATAAAA
Found at i:19227212 original size:28 final size:27
Alignment explanation
Indices: 19227166--19227220 Score: 76
Period size: 28 Copynumber: 2.0 Consensus size: 27
19227156 AGACCTAAGG
*
19227166 AATAAATGAATGATGCATATAATAATGA
1 AATAAATGAATAATGCATA-AATAATGA
19227194 AATAAATGAATAAAT-CATAAATAATGA
1 AATAAATGAAT-AATGCATAAATAATGA
19227221 TAATTTTCAT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
27 8 0.32
28 15 0.60
29 2 0.08
ACGTcount: A:0.58, C:0.04, G:0.11, T:0.27
Consensus pattern (27 bp):
AATAAATGAATAATGCATAAATAATGA
Found at i:19228362 original size:52 final size:52
Alignment explanation
Indices: 19228281--19228436 Score: 231
Period size: 54 Copynumber: 3.0 Consensus size: 52
19228271 CACATGACGG
* *
19228281 TGATAGTGGTGTGTTGTGTGAGTGTACACACTAATGATATATGCCATGTGCA
1 TGATAGTGGTGTGCTGTGTGAGTGCACACACTAATGATATATGCCATGTGCA
* *
19228333 TGATAGTGGTGTGCTGTGTGAGTGCACACACACTGATGATATATGCCATGTGCG
1 TGATAGTGGTGTGCTGTGTGAGTG--CACACACTAATGATATATGCCATGTGCA
* * *
19228387 TGATTGTGGTGTGCTGTGTGAGTGCACACATTAATGATTTATGCCATGTG
1 TGATAGTGGTGTGCTGTGTGAGTGCACACACTAATGATATATGCCATGTG
19228437 TGATGTGAGA
Statistics
Matches: 94, Mismatches: 8, Indels: 4
0.89 0.08 0.04
Matches are distributed among these distances:
52 46 0.49
54 48 0.51
ACGTcount: A:0.22, C:0.13, G:0.30, T:0.34
Consensus pattern (52 bp):
TGATAGTGGTGTGCTGTGTGAGTGCACACACTAATGATATATGCCATGTGCA
Found at i:19235685 original size:18 final size:19
Alignment explanation
Indices: 19235662--19235701 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
19235652 CAAGTGAAAA
19235662 ATTTTA-GAATAAAATAAT
1 ATTTTATGAATAAAATAAT
* *
19235680 ATTTTATTAATAAAATATT
1 ATTTTATGAATAAAATAAT
19235699 ATT
1 ATT
19235702 AAAATATTAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 6 0.32
19 13 0.68
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (19 bp):
ATTTTATGAATAAAATAAT
Found at i:19235698 original size:11 final size:11
Alignment explanation
Indices: 19235684--19235718 Score: 61
Period size: 11 Copynumber: 3.2 Consensus size: 11
19235674 AATAATATTT
*
19235684 TATTAATAAAA
1 TATTATTAAAA
19235695 TATTATTAAAA
1 TATTATTAAAA
19235706 TATTATTAAAA
1 TATTATTAAAA
19235717 TA
1 TA
19235719 ATTTTTACGT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
11 23 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (11 bp):
TATTATTAAAA
Found at i:19235712 original size:14 final size:15
Alignment explanation
Indices: 19235674--19235713 Score: 50
Period size: 14 Copynumber: 2.9 Consensus size: 15
19235664 TTTAGAATAA
19235674 AATAATATT-TTATT
1 AATAATATTATTATT
*
19235688 AATAA-AATATTATT
1 AATAATATTATTATT
19235702 AA-AATATTATTA
1 AATAATATTATTA
19235714 AAATAATTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
13 4 0.18
14 18 0.82
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (15 bp):
AATAATATTATTATT
Found at i:19237376 original size:2 final size:2
Alignment explanation
Indices: 19237371--19237405 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
19237361 AAGCTCCATA
19237371 AT AT AT 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 A
19237406 ATGTTGTTTC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:19237934 original size:28 final size:28
Alignment explanation
Indices: 19237902--19237962 Score: 104
Period size: 28 Copynumber: 2.2 Consensus size: 28
19237892 GGTTGCCTAC
*
19237902 GGGCTGTGAATATACGTGGCAAGGCCAT
1 GGGCTATGAATATACGTGGCAAGGCCAT
*
19237930 GGGCTATGATTATACGTGGCAAGGCCAT
1 GGGCTATGAATATACGTGGCAAGGCCAT
19237958 GGGCT
1 GGGCT
19237963 TTTATACATG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
28 31 1.00
ACGTcount: A:0.23, C:0.18, G:0.36, T:0.23
Consensus pattern (28 bp):
GGGCTATGAATATACGTGGCAAGGCCAT
Found at i:19239272 original size:38 final size:37
Alignment explanation
Indices: 19239192--19239273 Score: 101
Period size: 38 Copynumber: 2.2 Consensus size: 37
19239182 ATAGCCAGAG
* ** *
19239192 TCATCGTGTGCATCCCCCATATCGTGCACAGCTAATG
1 TCATCGTGTGCATCCCCCACATCACGCACAGCTAATA
* *
19239229 CCATCGTGTGCATCCCCCCACATCACGCACAGGTAATA
1 TCATCGTGTGCAT-CCCCCACATCACGCACAGCTAATA
19239267 TCATCGT
1 TCATCGT
19239274 CCACACTCTT
Statistics
Matches: 37, Mismatches: 7, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
37 12 0.32
38 25 0.68
ACGTcount: A:0.23, C:0.35, G:0.17, T:0.24
Consensus pattern (37 bp):
TCATCGTGTGCATCCCCCACATCACGCACAGCTAATA
Found at i:19247112 original size:32 final size:32
Alignment explanation
Indices: 19247032--19247176 Score: 123
Period size: 35 Copynumber: 4.3 Consensus size: 32
19247022 TAGTTATTGC
* *
19247032 GTTTTGGTTGA-TCTTATGAAAAACCATTATTGTAG
1 GTTTTGGTTGAGCCTT-TGAAAAACCACT-TTG--G
* *
19247067 GTTATGGTTGAGCCTTTGAAAAATCACTTTGG
1 GTTTTGGTTGAGCCTTTGAAAAACCACTTTGG
**
19247099 GTTTTGGTTGAGCCCGTGAAAAACCA-TTGTGAAAG
1 GTTTTGGTTGAGCCTTTGAAAAACCACTT-TG---G
* *
19247134 GTTGTGGTTAAGCCTTTGAAAAACCACTTTGG
1 GTTTTGGTTGAGCCTTTGAAAAACCACTTTGG
*
19247166 GTTTTTGTTGA
1 GTTTTGGTTGA
19247177 TCCCGGTAAA
Statistics
Matches: 89, Mismatches: 15, Indels: 15
0.75 0.13 0.13
Matches are distributed among these distances:
31 2 0.02
32 34 0.38
34 3 0.03
35 45 0.51
36 5 0.06
ACGTcount: A:0.26, C:0.12, G:0.25, T:0.38
Consensus pattern (32 bp):
GTTTTGGTTGAGCCTTTGAAAAACCACTTTGG
Found at i:19247119 original size:67 final size:67
Alignment explanation
Indices: 19247048--19247195 Score: 192
Period size: 67 Copynumber: 2.2 Consensus size: 67
19247038 GTTGATCTTA
* * * *
19247048 TGAAAAACCATTATTG-TAGGTTATGGTTGAGCCTTTGAAAAATCACTTTGGGTTTTGGTTGAGC
1 TGAAAAACCATT-GTGAAAGGTTATGGTTAAGCCTTTGAAAAACCACTTTGGGTTTTGGTTGAGC
19247112 CCG
65 CCG
* * *
19247115 TGAAAAACCATTGTGAAAGGTTGTGGTTAAGCCTTTGAAAAACCACTTTGGGTTTTTGTTGATCC
1 TGAAAAACCATTGTGAAAGGTTATGGTTAAGCCTTTGAAAAACCACTTTGGGTTTTGGTTGAGCC
19247180 CG
66 CG
*
19247182 -GTAAAAACTATTGT
1 TG-AAAAACCATTGT
19247196 AAAAAGTTTT
Statistics
Matches: 71, Mismatches: 8, Indels: 4
0.86 0.10 0.05
Matches are distributed among these distances:
66 3 0.04
67 68 0.96
ACGTcount: A:0.28, C:0.14, G:0.24, T:0.35
Consensus pattern (67 bp):
TGAAAAACCATTGTGAAAGGTTATGGTTAAGCCTTTGAAAAACCACTTTGGGTTTTGGTTGAGCC
CG
Found at i:19247215 original size:67 final size:67
Alignment explanation
Indices: 19247075--19247215 Score: 176
Period size: 67 Copynumber: 2.1 Consensus size: 67
19247065 AGGTTATGGT
* * *
19247075 TGAGCCTTTGAAAAATCACTTTGGGTTTTGGTTGAGCCCGTGAAAAACCATTGTGAAAGGTTGTG
1 TGAGCCTTTGAAAAACCACTTTGGGTTTTGGTTGAGCCCGTGAAAAACCATTGTAAAAAGTTGTG
**
19247140 GT
66 AC
* * * * *
19247142 TAAGCCTTTGAAAAACCACTTTGGGTTTTTGTTGATCCCG-GTAAAAACTATTGTAAAAAGTTTT
1 TGAGCCTTTGAAAAACCACTTTGGGTTTTGGTTGAGCCCGTG-AAAAACCATTGTAAAAAGTTGT
19247206 GAC
65 GAC
19247209 TGAGCCT
1 TGAGCCT
19247216 GGTAAAAGCC
Statistics
Matches: 62, Mismatches: 11, Indels: 2
0.83 0.15 0.03
Matches are distributed among these distances:
66 1 0.02
67 61 0.98
ACGTcount: A:0.28, C:0.15, G:0.23, T:0.34
Consensus pattern (67 bp):
TGAGCCTTTGAAAAACCACTTTGGGTTTTGGTTGAGCCCGTGAAAAACCATTGTAAAAAGTTGTG
AC
Found at i:19256522 original size:12 final size:12
Alignment explanation
Indices: 19256501--19256562 Score: 72
Period size: 12 Copynumber: 5.2 Consensus size: 12
19256491 GAGAAATTAT
*
19256501 GGAAATATTAAG
1 GGAAAGATTAAG
*
19256513 GGAAAGATTAGG
1 GGAAAGATTAAG
* *
19256525 GGAAA-ATTTAT
1 GGAAAGATTAAG
19256536 GGAAAGATTAAG
1 GGAAAGATTAAG
*
19256548 GGAAAGATTAGG
1 GGAAAGATTAAG
19256560 GGA
1 GGA
19256563 GATAGGAAGT
Statistics
Matches: 41, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
11 8 0.20
12 33 0.80
ACGTcount: A:0.45, C:0.00, G:0.34, T:0.21
Consensus pattern (12 bp):
GGAAAGATTAAG
Found at i:19256522 original size:23 final size:23
Alignment explanation
Indices: 19256501--19256562 Score: 70
Period size: 23 Copynumber: 2.6 Consensus size: 23
19256491 GAGAAATTAT
19256501 GGAAATATTAAGGGAAAGATTAGG
1 GGAAA-ATTAAGGGAAAGATTAGG
* * *
19256525 GGAAAATTTATGGAAAGATTAAG
1 GGAAAATTAAGGGAAAGATTAGG
*
19256548 GGAAAGATTAGGGGA
1 GGAAA-ATTAAGGGA
19256563 GATAGGAAGT
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
23 20 0.65
24 11 0.35
ACGTcount: A:0.45, C:0.00, G:0.34, T:0.21
Consensus pattern (23 bp):
GGAAAATTAAGGGAAAGATTAGG
Found at i:19256524 original size:35 final size:36
Alignment explanation
Indices: 19256485--19256564 Score: 137
Period size: 35 Copynumber: 2.3 Consensus size: 36
19256475 GGTAGGGACC
*
19256485 TTAGGGGAGAAA-TTATGGAAATATTAAGGGAAAGA
1 TTAGGGGAGAAATTTATGGAAAGATTAAGGGAAAGA
19256520 TTAGGGGA-AAATTTATGGAAAGATTAAGGGAAAGA
1 TTAGGGGAGAAATTTATGGAAAGATTAAGGGAAAGA
19256555 TTAGGGGAGA
1 TTAGGGGAGA
19256565 TAGGAAGTAG
Statistics
Matches: 42, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
34 3 0.07
35 38 0.90
36 1 0.02
ACGTcount: A:0.44, C:0.00, G:0.34, T:0.23
Consensus pattern (36 bp):
TTAGGGGAGAAATTTATGGAAAGATTAAGGGAAAGA
Found at i:19257148 original size:17 final size:17
Alignment explanation
Indices: 19257126--19257161 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
19257116 AAGTAAAATA
19257126 AGCACACACTAAGGGGG
1 AGCACACACTAAGGGGG
*
19257143 AGCACACACTTAGGGGG
1 AGCACACACTAAGGGGG
19257160 AG
1 AG
19257162 TAATCCTCCA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.33, C:0.22, G:0.36, T:0.08
Consensus pattern (17 bp):
AGCACACACTAAGGGGG
Found at i:19259841 original size:63 final size:63
Alignment explanation
Indices: 19259722--19259842 Score: 154
Period size: 63 Copynumber: 1.9 Consensus size: 63
19259712 ACCTAGTTGT
* * * * *
19259722 AGAAGAACCGACATCTCAAAATAAAAGAATTGATTCTTCAGAGATAGAAAGCTCTAGACTTTA
1 AGAAGAACCAACATCTCAAAATAAAAGAATCGATTCTTCAAAGACAAAAAGCTCTAGACTTTA
* * *
19259785 AGAAGAACTAACATCTCAAAATATAAGAATCGATTC-TCTAAAGACAAAAAGTTCTAGA
1 AGAAGAACCAACATCTCAAAATAAAAGAATCGATTCTTC-AAAGACAAAAAGCTCTAGA
19259843 TTTTGTGAAG
Statistics
Matches: 49, Mismatches: 8, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
62 2 0.04
63 47 0.96
ACGTcount: A:0.47, C:0.16, G:0.14, T:0.23
Consensus pattern (63 bp):
AGAAGAACCAACATCTCAAAATAAAAGAATCGATTCTTCAAAGACAAAAAGCTCTAGACTTTA
Found at i:19259853 original size:63 final size:63
Alignment explanation
Indices: 19259718--19259853 Score: 148
Period size: 63 Copynumber: 2.1 Consensus size: 63
19259708 TTGAACCTAG
* * * * *
19259718 TTGTAGAAGAACCGACATCTCAAAATAAAAGAATTGATTCTTCAGAGATAGAAAGCTCTAGACT
1 TTGT-GAAGAACCAACATCTCAAAATAAAAGAATCGATTCTTCAAAGACAAAAAGCTCTAGACT
** * * * *
19259782 TTAAGAAGAACTAACATCTCAAAATATAAGAATCGATTC-TCTAAAGACAAAAAGTTCTAGATT
1 TTGTGAAGAACCAACATCTCAAAATAAAAGAATCGATTCTTC-AAAGACAAAAAGCTCTAGACT
19259845 TTGTGAAGA
1 TTGTGAAGA
19259854 GTCGATTACT
Statistics
Matches: 58, Mismatches: 13, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
62 2 0.03
63 54 0.93
64 2 0.03
ACGTcount: A:0.44, C:0.14, G:0.15, T:0.26
Consensus pattern (63 bp):
TTGTGAAGAACCAACATCTCAAAATAAAAGAATCGATTCTTCAAAGACAAAAAGCTCTAGACT
Found at i:19260407 original size:36 final size:36
Alignment explanation
Indices: 19260357--19260441 Score: 109
Period size: 36 Copynumber: 2.4 Consensus size: 36
19260347 AGTTAGGCCA
*
19260357 GATCTTG-TAAAAGGCATGTTGCGAAGGGTACACTT
1 GATCTTGTTAAAAGGCATGTTGCAAAGGGTACACTT
* * **
19260392 GATCTTGTTAAAAGGCATGTTGTAAAGGTTATGCTT
1 GATCTTGTTAAAAGGCATGTTGCAAAGGGTACACTT
19260428 GATCTTGTTGAAAA
1 GATCTTGTT-AAAA
19260442 AGCAAGCTGA
Statistics
Matches: 43, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
35 7 0.16
36 32 0.74
37 4 0.09
ACGTcount: A:0.29, C:0.11, G:0.26, T:0.34
Consensus pattern (36 bp):
GATCTTGTTAAAAGGCATGTTGCAAAGGGTACACTT
Found at i:19261613 original size:67 final size:67
Alignment explanation
Indices: 19261540--19261782 Score: 246
Period size: 67 Copynumber: 3.6 Consensus size: 67
19261530 TAAAGGGAAC
* * *
19261540 ATGGGTACTTTTCCCAATTCAA-CATTGTGGTAATCTTACCC-ACACC-AGACTTTAGAAAGGGG
1 ATGGGTACATTTGCCAACTCAACCA-TGTGGTAATCTTACCCTACACCGAG-CTTTAGAAA-GGG
19261602 AAAAT
63 AAAAT
* *
19261607 ATGGGTACATTTGCCTACTCAACCATGTGGTATTCTTACCCTTACACCGAGCTTTAGAAAGGGAA
1 ATGGGTACATTTGCCAACTCAACCATGTGGTAATCTTACCC-TACACCGAGCTTTAGAAAGGGAA
19261672 AAT
65 AAT
* * * * * * *
19261675 ATGGGTACATTTGCCAACTGAACCCTATGGTATTCTTACCC-CCAAACTAGGCTTTAG-AAGGGA
1 ATGGGTACATTTGCCAACTCAACCATGTGGTAATCTTACCCTAC-ACCGA-GCTTTAGAAAGGGA
*
19261738 AAAA
64 AAAT
** *
19261742 ATGGGTACATTTG-CAACTTGACCATGTGGTATTCTTACCCT
1 ATGGGTACATTTGCCAACTCAACCATGTGGTAATCTTACCCT
19261783 TAAACAAGGG
Statistics
Matches: 152, Mismatches: 17, Indels: 14
0.83 0.09 0.08
Matches are distributed among these distances:
66 24 0.16
67 58 0.38
68 54 0.36
69 14 0.09
70 2 0.01
ACGTcount: A:0.30, C:0.22, G:0.19, T:0.29
Consensus pattern (67 bp):
ATGGGTACATTTGCCAACTCAACCATGTGGTAATCTTACCCTACACCGAGCTTTAGAAAGGGAAA
AT
Found at i:19261686 original size:68 final size:67
Alignment explanation
Indices: 19261540--19261784 Score: 275
Period size: 68 Copynumber: 3.7 Consensus size: 67
19261530 TAAAGGGAAC
* * * *
19261540 ATGGGTACTTTTCCCAATTCAA-CATTGTGGTAATCTTACCC--ACACCAGACTTTAGAAAGGGG
1 ATGGGTACATTTGCCAACTCAACCA-TGTGGTATTCTTACCCTTACACCAG-CTTTAGAAA-GGG
19261602 AAAAT
63 AAAAT
*
19261607 ATGGGTACATTTGCCTACTCAACCATGTGGTATTCTTACCCTTACACCGAGCTTTAGAAAGGGAA
1 ATGGGTACATTTGCCAACTCAACCATGTGGTATTCTTACCCTTACACC-AGCTTTAGAAAGGGAA
19261672 AAT
65 AAT
* * * ** * *
19261675 ATGGGTACATTTGCCAACTGAACCCTATGGTATTCTTACCCCCAAACTAGGCTTTAG-AAGGGAA
1 ATGGGTACATTTGCCAACTCAACCATGTGGTATTCTTACCCTTACACCA-GCTTTAGAAAGGGAA
*
19261739 AAA
65 AAT
**
19261742 ATGGGTACATTTG-CAACTTGACCATGTGGTATTCTTACCCTTA
1 ATGGGTACATTTGCCAACTCAACCATGTGGTATTCTTACCCTTA
19261785 AACAAGGGTT
Statistics
Matches: 153, Mismatches: 20, Indels: 11
0.83 0.11 0.06
Matches are distributed among these distances:
66 24 0.16
67 56 0.37
68 57 0.37
69 14 0.09
70 2 0.01
ACGTcount: A:0.30, C:0.22, G:0.19, T:0.29
Consensus pattern (67 bp):
ATGGGTACATTTGCCAACTCAACCATGTGGTATTCTTACCCTTACACCAGCTTTAGAAAGGGAAA
AT
Found at i:19265401 original size:2 final size:2
Alignment explanation
Indices: 19265394--19265424 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
19265384 TGGACATTCT
*
19265394 AG AG AG AG AA AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
19265425 TTTTCCATAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.55, C:0.00, G:0.45, T:0.00
Consensus pattern (2 bp):
AG
Found at i:19266177 original size:35 final size:34
Alignment explanation
Indices: 19266078--19266183 Score: 113
Period size: 35 Copynumber: 3.1 Consensus size: 34
19266068 GAAAGTGTGG
*
19266078 ATGATGATATTGCTTGTGCGAGTAGGGAGTGAAC
1 ATGATGATATTGCTTGTGCGAGTAGGGAGTGCAC
* * ** * *
19266112 ACGATTATATTGAAATGTGCGAGTAAGGAGTGCAT
1 ATGATGATATTG-CTTGTGCGAGTAGGGAGTGCAC
**
19266147 ATGATGATATTGCCTTGTGCGTTTAGGGAGTGCAC
1 ATGATGATATTG-CTTGTGCGAGTAGGGAGTGCAC
19266182 AT
1 AT
19266184 TGGCTGAGTG
Statistics
Matches: 55, Mismatches: 16, Indels: 1
0.76 0.22 0.01
Matches are distributed among these distances:
34 10 0.18
35 45 0.82
ACGTcount: A:0.27, C:0.10, G:0.31, T:0.31
Consensus pattern (34 bp):
ATGATGATATTGCTTGTGCGAGTAGGGAGTGCAC
Found at i:19268211 original size:35 final size:35
Alignment explanation
Indices: 19268172--19268254 Score: 148
Period size: 35 Copynumber: 2.4 Consensus size: 35
19268162 GTGTGGATAG
* *
19268172 TGATGTTGATGTGTGTGAGTTGGGAGTGCACACGA
1 TGATGTTGATGTGTGTGAGTAGGGAGTGCACAAGA
19268207 TGATGTTGATGTGTGTGAGTAGGGAGTGCACAAGA
1 TGATGTTGATGTGTGTGAGTAGGGAGTGCACAAGA
19268242 TGATGTTGATGTG
1 TGATGTTGATGTG
19268255 CGCGATGTGG
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
35 46 1.00
ACGTcount: A:0.22, C:0.06, G:0.40, T:0.33
Consensus pattern (35 bp):
TGATGTTGATGTGTGTGAGTAGGGAGTGCACAAGA
Found at i:19268279 original size:35 final size:34
Alignment explanation
Indices: 19268172--19268279 Score: 144
Period size: 35 Copynumber: 3.1 Consensus size: 34
19268162 GTGTGGATAG
19268172 TGATGTTGATGTGTGTGAGTTGGGAGTGCACACGA
1 TGATGTTGATGTGTGTGAG-TGGGAGTGCACACGA
*
19268207 TGATGTTGATGTGTGTGAGTAGGGAGTGCACAAGA
1 TGATGTTGATGTGTGTGAGT-GGGAGTGCACACGA
* * * *
19268242 TGATGTTGATGTGCGCGATGTGGGGGTGTACACGA
1 TGATGTTGATGTGTGTGA-GTGGGAGTGCACACGA
19268277 TGA
1 TGA
19268280 CTCCGGCTAT
Statistics
Matches: 65, Mismatches: 6, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
34 1 0.02
35 62 0.95
36 2 0.03
ACGTcount: A:0.21, C:0.08, G:0.41, T:0.30
Consensus pattern (34 bp):
TGATGTTGATGTGTGTGAGTGGGAGTGCACACGA
Found at i:19289095 original size:33 final size:33
Alignment explanation
Indices: 19289046--19289111 Score: 91
Period size: 33 Copynumber: 2.0 Consensus size: 33
19289036 TCTCGCAAAC
*
19289046 ATCTCCAAATATAGGGCATTTCAAT-ATCCTTAA
1 ATCTCCAAATATAGGGCATATC-ATCATCCTTAA
19289079 ATCTCC-AATATGAGGGCATATCATCATCCTTAA
1 ATCTCCAAATAT-AGGGCATATCATCATCCTTAA
19289112 TGTCTCTAAC
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
32 7 0.23
33 23 0.77
ACGTcount: A:0.35, C:0.23, G:0.11, T:0.32
Consensus pattern (33 bp):
ATCTCCAAATATAGGGCATATCATCATCCTTAA
Found at i:19292331 original size:25 final size:25
Alignment explanation
Indices: 19292298--19292512 Score: 99
Period size: 25 Copynumber: 8.6 Consensus size: 25
19292288 ACAATTAAAT
* * *
19292298 AGTTAAATTTATATAAAGTGTAAGCC
1 AGTTCAATTTCTATAAAATGTAAG-C
*
19292324 A-TTCAATTTCTATAAAATGTTAGC
1 AGTTCAATTTCTATAAAATGTAAGC
* * *
19292348 AGTTCAATTTCTATAATATGCAAAC
1 AGTTCAATTTCTATAAAATGTAAGC
*** * * **
19292373 AACACAATTTTTGTAAAATAAAAGC
1 AGTTCAATTTCTATAAAATGTAAGC
* * *
19292398 ATTTCAATTTCTATAAGATGCAAGC
1 AGTTCAATTTCTATAAAATGTAAGC
** * * * * *
19292423 AACTCCATTTTTATAATATGGAAAC
1 AGTTCAATTTCTATAAAATGTAAGC
** * * *
19292448 AACTCAATTTCTATAAGAGGTAAAC
1 AGTTCAATTTCTATAAAATGTAAGC
** * *
19292473 AACTCAATTACTATAAAATGCAAGC
1 AGTTCAATTTCTATAAAATGTAAGC
**
19292498 AACTCAATTTCTATA
1 AGTTCAATTTCTATA
19292513 TGATGTAAAC
Statistics
Matches: 145, Mismatches: 43, Indels: 3
0.76 0.23 0.02
Matches are distributed among these distances:
24 2 0.01
25 142 0.98
26 1 0.01
ACGTcount: A:0.42, C:0.15, G:0.09, T:0.33
Consensus pattern (25 bp):
AGTTCAATTTCTATAAAATGTAAGC
Found at i:19292381 original size:50 final size:50
Alignment explanation
Indices: 19292326--19292522 Score: 189
Period size: 50 Copynumber: 3.9 Consensus size: 50
19292316 TGTAAGCCAT
** ** *
19292326 TCAATTTCTATAAAATGTTAGCAGTTCAATTTCTATAATATGCAAACAAC
1 TCAATTTCTATAAAATGAAAGCAACTCAATTTCTATAAGATGCAAACAAC
* * * * ** *
19292376 ACAATTTTTGTAAAATAAAAGCATTTCAATTTCTATAAGATGCAAGCAAC
1 TCAATTTCTATAAAATGAAAGCAACTCAATTTCTATAAGATGCAAACAAC
* * * * *
19292426 TCCATTTTTATAATATGGAAA-CAACTCAATTTCTATAAGAGGTAAACAAC
1 TCAATTTCTATAAAAT-GAAAGCAACTCAATTTCTATAAGATGCAAACAAC
* * * *
19292476 TCAATTACTATAAAATGCAAGCAACTCAATTTCTATATGATGTAAAC
1 TCAATTTCTATAAAATGAAAGCAACTCAATTTCTATAAGATGCAAAC
19292523 CTAGTGCAAA
Statistics
Matches: 119, Mismatches: 26, Indels: 4
0.80 0.17 0.03
Matches are distributed among these distances:
49 3 0.03
50 113 0.95
51 3 0.03
ACGTcount: A:0.42, C:0.16, G:0.09, T:0.33
Consensus pattern (50 bp):
TCAATTTCTATAAAATGAAAGCAACTCAATTTCTATAAGATGCAAACAAC
Found at i:19293362 original size:27 final size:27
Alignment explanation
Indices: 19293331--19293428 Score: 117
Period size: 27 Copynumber: 3.6 Consensus size: 27
19293321 TGGTAGAACT
*
19293331 TGCCTTGGCATGTAACAAAGTGATTCA
1 TGCCTTGGCGTGTAACAAAGTGATTCA
*
19293358 TGCCTTGGTGTGTAA-AATAGTGATTCA
1 TGCCTTGGCGTGTAACAA-AGTGATTCA
**
19293385 TGCCTTCACGTGTAACAAAGTGATTCA
1 TGCCTTGGCGTGTAACAAAGTGATTCA
* **
19293412 TGCTTTTACGTGTAACA
1 TGCCTTGGCGTGTAACA
19293429 TCAATAAGAA
Statistics
Matches: 62, Mismatches: 7, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
26 2 0.03
27 58 0.94
28 2 0.03
ACGTcount: A:0.28, C:0.17, G:0.21, T:0.34
Consensus pattern (27 bp):
TGCCTTGGCGTGTAACAAAGTGATTCA
Found at i:19293633 original size:34 final size:33
Alignment explanation
Indices: 19293564--19293636 Score: 92
Period size: 34 Copynumber: 2.2 Consensus size: 33
19293554 AACATCTTTT
* *
19293564 GCTTTGGCTTTGCATATAACTTCTAGTGCTAAA
1 GCTTTGGCCTTGCATATAACATCTAGTGCTAAA
* * *
19293597 GCTTTGGCCTTGACATGTAACATCTGGTGCTGAA
1 GCTTTGGCCTTG-CATATAACATCTAGTGCTAAA
19293631 GCTTTG
1 GCTTTG
19293637 ACATTGGTGT
Statistics
Matches: 34, Mismatches: 5, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
33 11 0.32
34 23 0.68
ACGTcount: A:0.21, C:0.19, G:0.23, T:0.37
Consensus pattern (33 bp):
GCTTTGGCCTTGCATATAACATCTAGTGCTAAA
Found at i:19293855 original size:19 final size:20
Alignment explanation
Indices: 19293814--19293856 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
19293804 TTAAAACATG
19293814 TAACAAATTTTTTTCAACTA
1 TAACAAATTTTTTTCAACTA
* *
19293834 TAACAATTTTTTTTGAAC-A
1 TAACAAATTTTTTTCAACTA
19293853 TAAC
1 TAAC
19293857 TTGTAATAAC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 5 0.24
20 16 0.76
ACGTcount: A:0.40, C:0.14, G:0.02, T:0.44
Consensus pattern (20 bp):
TAACAAATTTTTTTCAACTA
Found at i:19293890 original size:29 final size:29
Alignment explanation
Indices: 19293833--19293891 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 29
19293823 TTTTTCAACT
** * *
19293833 ATAACAATTTTTTTTGAACATAACTTGTA
1 ATAACAACATTTTTTAAACATAACGTGTA
*
19293862 ATAACAACATTTTTTAAACATAGCGTGTA
1 ATAACAACATTTTTTAAACATAACGTGTA
19293891 A
1 A
19293892 CTTGTTTTCT
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.41, C:0.12, G:0.08, T:0.39
Consensus pattern (29 bp):
ATAACAACATTTTTTAAACATAACGTGTA
Found at i:19298257 original size:22 final size:22
Alignment explanation
Indices: 19298232--19298277 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 22
19298222 TACTTTTAGC
19298232 TTAACAATAAAAAATTAAA-TAT
1 TTAA-AATAAAAAATTAAATTAT
**
19298254 TTAATTTAAAAAATTAAATTAT
1 TTAAAATAAAAAATTAAATTAT
19298276 TT
1 TT
19298278 TTGCTTAATT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 12 0.57
22 9 0.43
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (22 bp):
TTAAAATAAAAAATTAAATTAT
Found at i:19299221 original size:16 final size:16
Alignment explanation
Indices: 19299197--19299239 Score: 52
Period size: 16 Copynumber: 2.7 Consensus size: 16
19299187 ATATAAAATT
*
19299197 AAAATAACTCATT-TA
1 AAAATAACTAATTATA
19299212 AAAATAAACTAATTATA
1 AAAAT-AACTAATTATA
*
19299229 AAAACAACTAA
1 AAAATAACTAA
19299240 AAATAACTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
15 5 0.21
16 13 0.54
17 6 0.25
ACGTcount: A:0.63, C:0.12, G:0.00, T:0.26
Consensus pattern (16 bp):
AAAATAACTAATTATA
Found at i:19300409 original size:31 final size:31
Alignment explanation
Indices: 19300356--19300415 Score: 77
Period size: 31 Copynumber: 1.9 Consensus size: 31
19300346 ATTACAATTT
* *
19300356 ATGAAATGTTTGGGGGACCAAATTGTAAAGG
1 ATGAAAAGTTTGGGGGACCAAATGGTAAAGG
*
19300387 ATGAAAAGTTTGGAGGG-TCAAATGGTAAA
1 ATGAAAAGTTTGG-GGGACCAAATGGTAAA
19300416 TAAGGAGAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
31 22 0.88
32 3 0.12
ACGTcount: A:0.38, C:0.05, G:0.32, T:0.25
Consensus pattern (31 bp):
ATGAAAAGTTTGGGGGACCAAATGGTAAAGG
Found at i:19305933 original size:25 final size:26
Alignment explanation
Indices: 19305854--19305943 Score: 76
Period size: 25 Copynumber: 3.5 Consensus size: 26
19305844 ATCGACAGGC
* * **
19305854 TGTTAGACGTGGCTAAGCCACGATCT
1 TGTTATACGTGGCTAGGCCACGAGGT
* *
19305880 GTGATTATACGTGGCAAGGCCA-TAGGT
1 -TG-TTATACGTGGCTAGGCCACGAGGT
19305907 TGTTATACGTGGCTAGGCCACGA-GT
1 TGTTATACGTGGCTAGGCCACGAGGT
* *
19305932 TGATATATGTGG
1 TGTTATACGTGG
19305944 TTGCGACCAC
Statistics
Matches: 51, Mismatches: 10, Indels: 6
0.76 0.15 0.09
Matches are distributed among these distances:
25 29 0.57
26 3 0.06
27 4 0.08
28 15 0.29
ACGTcount: A:0.23, C:0.17, G:0.31, T:0.29
Consensus pattern (26 bp):
TGTTATACGTGGCTAGGCCACGAGGT
Found at i:19308926 original size:15 final size:16
Alignment explanation
Indices: 19308906--19308936 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
19308896 CTCCAAGACC
19308906 TTCTTTCTTT-TCTTT
1 TTCTTTCTTTCTCTTT
19308921 TTCTTTCTTTCTCTTT
1 TTCTTTCTTTCTCTTT
19308937 CTTCCAAGCT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 10 0.67
16 5 0.33
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (16 bp):
TTCTTTCTTTCTCTTT
Found at i:19316296 original size:21 final size:21
Alignment explanation
Indices: 19316259--19316298 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
19316249 CCACCTTTAC
*
19316259 CTCTTCATCTTCATCCTCTAA
1 CTCTTCATCTGCATCCTCTAA
19316280 CTCTTCATCTAGC-TCCTCT
1 CTCTTCATCT-GCATCCTCT
19316299 CGTAAGCCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 16 0.94
22 1 0.06
ACGTcount: A:0.15, C:0.40, G:0.03, T:0.42
Consensus pattern (21 bp):
CTCTTCATCTGCATCCTCTAA
Found at i:19318241 original size:2 final size:2
Alignment explanation
Indices: 19318234--19318259 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
19318224 CTATAATGTG
19318234 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
19318260 CTAGGTTTAA
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:19320739 original size:39 final size:40
Alignment explanation
Indices: 19320696--19320788 Score: 98
Period size: 40 Copynumber: 2.4 Consensus size: 40
19320686 CGAGATTCAA
* *** *
19320696 TCTCGCTGCAGTGAATTTTTTACCCAG-AAACAGAATGTT
1 TCTCGCTGCAGTGAAATTGCAACCCAGAAAACAGAAAGTT
* **
19320735 TCTCGCTGTAGCAAAATTGCAACCCAGAAAACAGAAAGTT
1 TCTCGCTGCAGTGAAATTGCAACCCAGAAAACAGAAAGTT
*
19320775 TTTCGCTGCAGTGA
1 TCTCGCTGCAGTGA
19320789 GAATGCATTT
Statistics
Matches: 41, Mismatches: 12, Indels: 1
0.76 0.22 0.02
Matches are distributed among these distances:
39 20 0.49
40 21 0.51
ACGTcount: A:0.31, C:0.22, G:0.19, T:0.28
Consensus pattern (40 bp):
TCTCGCTGCAGTGAAATTGCAACCCAGAAAACAGAAAGTT
Found at i:19328423 original size:60 final size:62
Alignment explanation
Indices: 19328329--19328478 Score: 227
Period size: 60 Copynumber: 2.5 Consensus size: 62
19328319 ATAAGATACC
* * *
19328329 AAAACAGAAATTTTTCT-GCTGCAGCGAGATTCAATCTCGCTACAGCGAAATTTCTACCCAG
1 AAAACAGAAATGTTTCTCGCTGCAGCGAGATTCAATCTCGCTACAGCGAAATTGCAACCCAG
*
19328390 -AAACA-AAATGTTTCTCACTGCAGCGAGATTCAATCTCGCTACAGCGAAATTGCAACCCAG
1 AAAACAGAAATGTTTCTCGCTGCAGCGAGATTCAATCTCGCTACAGCGAAATTGCAACCCAG
*
19328450 AAAACAGAAA-GTTTCTCGCTACAGCGAGA
1 AAAACAGAAATGTTTCTCGCTGCAGCGAGA
19328479 ATGCATTTCG
Statistics
Matches: 80, Mismatches: 6, Indels: 6
0.87 0.07 0.07
Matches are distributed among these distances:
59 9 0.11
60 46 0.57
61 22 0.28
62 3 0.04
ACGTcount: A:0.35, C:0.25, G:0.17, T:0.23
Consensus pattern (62 bp):
AAAACAGAAATGTTTCTCGCTGCAGCGAGATTCAATCTCGCTACAGCGAAATTGCAACCCAG
Found at i:19328911 original size:43 final size:43
Alignment explanation
Indices: 19328863--19328981 Score: 141
Period size: 43 Copynumber: 2.8 Consensus size: 43
19328853 TCACCAGCTC
**** *
19328863 ATGCGCACTCCCTACTCGCACATGGTTGGGTCATCAC-CGGGTT
1 ATGCGCACTCCCTACTCGCACATAACCGGGTCATC-CTCGGCTT
*
19328906 ATGCGCACTCCCTACTCACACATAACCGGGTCATCCTCGGCTT
1 ATGCGCACTCCCTACTCGCACATAACCGGGTCATCCTCGGCTT
* * *
19328949 ATGCGCACTCCCTACTTGCACATAGCCGAGTCA
1 ATGCGCACTCCCTACTCGCACATAACCGGGTCA
19328982 ATATAATTAC
Statistics
Matches: 65, Mismatches: 10, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
42 1 0.02
43 64 0.98
ACGTcount: A:0.20, C:0.36, G:0.20, T:0.24
Consensus pattern (43 bp):
ATGCGCACTCCCTACTCGCACATAACCGGGTCATCCTCGGCTT
Found at i:19329802 original size:19 final size:20
Alignment explanation
Indices: 19329768--19329805 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
19329758 GAAGAAGACC
19329768 AGCTGCTGAAAAATTCAAGA
1 AGCTGCTGAAAAATTCAAGA
*
19329788 AGCTGCTG-GAAATTCAAG
1 AGCTGCTGAAAAATTCAAG
19329806 GTATTTATAG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.39, C:0.16, G:0.24, T:0.21
Consensus pattern (20 bp):
AGCTGCTGAAAAATTCAAGA
Found at i:19338407 original size:2 final size:2
Alignment explanation
Indices: 19338400--19338449 Score: 73
Period size: 2 Copynumber: 25.0 Consensus size: 2
19338390 GGATGATTGA
* *
19338400 AT AT AT AT AT AT AT AC AT AT CT 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
*
19338442 TT AT AT AT
1 AT AT AT AT
19338450 TCTCATGTTG
Statistics
Matches: 42, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.46, C:0.04, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:19339765 original size:30 final size:30
Alignment explanation
Indices: 19339729--19339792 Score: 112
Period size: 30 Copynumber: 2.2 Consensus size: 30
19339719 TTACTTTGTG
19339729 TCTTTTAACTATAACAAGCTATAAATCTTC
1 TCTTTTAACTATAACAAGCTATAAATCTTC
*
19339759 TCTTTTAACTATAACAAGCTTTAAATCTTC
1 TCTTTTAACTATAACAAGCTATAAATCTTC
19339789 -CTTT
1 TCTTT
19339793 CTCTAATTGA
Statistics
Matches: 33, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
29 4 0.12
30 29 0.88
ACGTcount: A:0.33, C:0.20, G:0.03, T:0.44
Consensus pattern (30 bp):
TCTTTTAACTATAACAAGCTATAAATCTTC
Found at i:19340450 original size:252 final size:248
Alignment explanation
Indices: 19339886--19340637 Score: 892
Period size: 251 Copynumber: 3.0 Consensus size: 248
19339876 CGGAACCAAC
* * * *
19339886 ATGTCAAATAAACATAATTTTTTAAAAAAATTAAATATTTAAATTTTTATTCTTGAGTTTAAATT
1 ATGTCAAATAAACATAATTTTTT-AAGAAATTAAATATTTAAATTTTTATTATCGAGTTTAAAGT
* *
19339951 ATTTTACGGCTTACAAATTTTAATTTACGAATGAATAATAGTGAAGATAAAAAGAATTAAAG-TG
65 ATTTTACGGCTTACAAATTTTAATCTATGAATGAATAATAGT-AAGATAAAAAGAATT--AGTTG
* *
19340015 AAAATTAGTAGTTGAAAAACTTTGACGTAAAGAAGTAAAAATTAATGTAAAAAAATTA-AAGGTG
127 AAAATTAGTAGTTGAAAAACTTTGACGTAAA-AAGTAAGAATTAACGT-AAAAAATTATAAGGTG
* * *
19340079 CAAAAAAAAATT-TCAAAATATTGACGTAAATGTATAAGATTTAATGTAACAAGTCAATT
190 -AAAAAAGAATTGTCAAAATATTGACATAAATGTATAAGATTTAATATAACAAGTCAATT
* *
19340138 ATGTCAAATAAACATAA-TTTTCATGAAACTTAAATATTTAAATTTTTATTATCGAGTTTAAAGT
1 ATGTCAAATAAACATAATTTTTTAAGAAA-TTAAATATTTAAATTTTTATTATCGAGTTTAAAGT
* * * *
19340202 GTATTAGGGCTTACAAATTTTAATCTATGCATGAATAATAGTAACGATATAAAA-AATTATGTTG
65 ATTTTACGGCTTACAAATTTTAATCTATGAATGAATAATAGTAA-GATA-AAAAGAATTA-GTTG
* * *
19340266 AAAATTAGTAGTAGAAAAGCCTTT-ATGTAAAATAGTAAGAATTAACGTAAAAAATTATGAAGGT
127 AAAATTAGTAGTTGAAAA-ACTTTGACGTAAAA-AGTAAGAATTAACGTAAAAAATTAT-AAGGT
* * * * * * * *
19340330 GGAATAAGCATTGTCAAAAGATTGACATAAATGTTTGAGATTTAATTTAACAAGTCAGTT
189 GAAAAAAGAATTGTCAAAATATTGACATAAATGTATAAGATTTAATATAACAAGTCAATT
* * *
19340390 ATGTCAAATAAACATAATTTTTTAAGAAATTAAACATTCT-AATTTTTATTGTCAAGTTTAAAGT
1 ATGTCAAATAAACATAATTTTTTAAGAAATTAAATATT-TAAATTTTTATTATCGAGTTTAAAGT
* * * * *
19340454 ATTTTATGGTTTACAAGTTTTAATCTATGAATAAATAATAGTAAGGATAAAAATAATTA-TTGTA
65 ATTTTACGGCTTACAAATTTTAATCTATGAATGAATAATAGTAA-GATAAAAAGAATTAGTTG-A
*
19340518 AAAGTTAGTAGTTGAAAAACTTTGACG-AAAACAGTAAGAATTAACGTAAAAAATTATAAAAGTG
128 AAA-TTAGTAGTTGAAAAACTTTGACGTAAAA-AGTAAGAATTAACGTAAAAAATTAT-AAGGTG
* * * *
19340582 AAACAAGTATTGTTAAAATATTGACATAAATATATAAGATTTAATATAACAAGTCA
190 AAAAAAGAATTGTCAAAATATTGACATAAATGTATAAGATTTAATATAACAAGTCA
19340638 TAATAATAAT
Statistics
Matches: 429, Mismatches: 55, Indels: 33
0.83 0.11 0.06
Matches are distributed among these distances:
249 1 0.00
250 20 0.05
251 218 0.51
252 180 0.42
253 10 0.02
ACGTcount: A:0.46, C:0.06, G:0.13, T:0.35
Consensus pattern (248 bp):
ATGTCAAATAAACATAATTTTTTAAGAAATTAAATATTTAAATTTTTATTATCGAGTTTAAAGTA
TTTTACGGCTTACAAATTTTAATCTATGAATGAATAATAGTAAGATAAAAAGAATTAGTTGAAAA
TTAGTAGTTGAAAAACTTTGACGTAAAAAGTAAGAATTAACGTAAAAAATTATAAGGTGAAAAAA
GAATTGTCAAAATATTGACATAAATGTATAAGATTTAATATAACAAGTCAATT
Found at i:19344893 original size:20 final size:20
Alignment explanation
Indices: 19344865--19344912 Score: 53
Period size: 20 Copynumber: 2.4 Consensus size: 20
19344855 TTATAATTTG
*
19344865 TTTATTTTTAAGTGAGTTA-T
1 TTTAATTTTAAGTGA-TTATT
* *
19344885 TTTAATTTTATGTTATTATT
1 TTTAATTTTAAGTGATTATT
19344905 TTTAATTT
1 TTTAATTT
19344913 GATTATTATT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
19 3 0.12
20 21 0.88
ACGTcount: A:0.25, C:0.00, G:0.08, T:0.67
Consensus pattern (20 bp):
TTTAATTTTAAGTGATTATT
Found at i:19347139 original size:20 final size:20
Alignment explanation
Indices: 19347114--19347152 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
19347104 ATTTTGAAAA
**
19347114 GAATCTATTGATAGATTTTG
1 GAATCTATCAATAGATTTTG
19347134 GAATCTATCAATAGATTTT
1 GAATCTATCAATAGATTTT
19347153 ACATAGTATG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.33, C:0.08, G:0.15, T:0.44
Consensus pattern (20 bp):
GAATCTATCAATAGATTTTG
Found at i:19350599 original size:22 final size:22
Alignment explanation
Indices: 19350557--19350600 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
19350547 TTAGATTGGT
*
19350557 ATCAAAGCTTTTGGTTTTAAAG
1 ATCAAAGCTTTTGGTTCTAAAG
*
19350579 ATCAGAGCTTTTGAG-TCTAAAG
1 ATCAAAGCTTTTG-GTTCTAAAG
19350601 TTGTATTAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 18 0.95
23 1 0.05
ACGTcount: A:0.32, C:0.11, G:0.20, T:0.36
Consensus pattern (22 bp):
ATCAAAGCTTTTGGTTCTAAAG
Found at i:19350693 original size:5 final size:5
Alignment explanation
Indices: 19350634--19350689 Score: 94
Period size: 5 Copynumber: 11.2 Consensus size: 5
19350624 ATGTAGCCCC
*
19350634 AAGTT AAGTT AAGTT AAGTT AAGTT AAGTT AAGAT AAGTT AAGTT AAGTT
1 AAGTT AAGTT AAGTT AAGTT AAGTT AAGTT AAGTT AAGTT AAGTT AAGTT
*
19350684 AGGTT A
1 AAGTT A
19350690 GGTTGAATAG
Statistics
Matches: 48, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
5 48 1.00
ACGTcount: A:0.41, C:0.00, G:0.21, T:0.38
Consensus pattern (5 bp):
AAGTT
Found at i:19360789 original size:60 final size:60
Alignment explanation
Indices: 19360648--19361011 Score: 358
Period size: 60 Copynumber: 6.0 Consensus size: 60
19360638 AGACATCATC
* * * *
19360648 ACCTACTCATGGGAAACTGCCCATGCCACCATATATAAATCAAGGCTTCAGATCTCCCTTTTT
1 ACCTACTCGTGGG-AACTGCCCATGCCACCATATATAAATCGAGGCTTCAGGTC-CCC-CTTT
** *
19360711 GTCTACTCGTGGGATCTGCCCATGCCACCATATATAAATCGAGGCTTCAGGTCCCCCTTT
1 ACCTACTCGTGGGAACTGCCCATGCCACCATATATAAATCGAGGCTTCAGGTCCCCCTTT
* * * * * * *
19360771 ACCTACTCATAGGATCTGCCCATGCCACTATATATAAATCGGGGCTTTAAGTCCCCCTTT
1 ACCTACTCGTGGGAACTGCCCATGCCACCATATATAAATCGAGGCTTCAGGTCCCCCTTT
* * * * * * *
19360831 GCCTACTCGTGGAAACTGCCCACGTCATCCA-ATATGAATCG-GGACTTTAGGTCCCCTTTTT
1 ACCTACTCGTGGGAACTGCCCATGCCA-CCATATATAAATCGAGG-CTTCAGGTCCCC-CTTT
* * *
19360892 ACTTACTCGTGGGAACTGCCCATGCCACCATATATAAATCGGGGCTTCAGGTCTCCCTTT
1 ACCTACTCGTGGGAACTGCCCATGCCACCATATATAAATCGAGGCTTCAGGTCCCCCTTT
* * * * * *
19360952 GCTTACTCGTGAGAACTACCCACGCCACC-TAATATGAATC-AGGGCTTCAGGTCCCCCTTT
1 ACCTACTCGTGGGAACTGCCCATGCCACCAT-ATATAAATCGA-GGCTTCAGGTCCCCCTTT
19361012 TTAAATCAAA
Statistics
Matches: 252, Mismatches: 42, Indels: 17
0.81 0.14 0.05
Matches are distributed among these distances:
59 3 0.01
60 151 0.60
61 49 0.19
62 39 0.15
63 10 0.04
ACGTcount: A:0.23, C:0.31, G:0.18, T:0.28
Consensus pattern (60 bp):
ACCTACTCGTGGGAACTGCCCATGCCACCATATATAAATCGAGGCTTCAGGTCCCCCTTT
Found at i:19360927 original size:121 final size:119
Alignment explanation
Indices: 19360648--19361014 Score: 407
Period size: 121 Copynumber: 3.0 Consensus size: 119
19360638 AGACATCATC
** * *
19360648 ACCTACTCATGGGAAACTGCCCATGCCACCATATATAAATCAAGGC-TTCAGATCTCCCTTTTTG
1 ACCTACTCATGGG-AACTGCCCATGCCACCATATATAAATCGGGGCTTTAAG-TC-CCC-CTTTG
* * * * * *
19360712 TCTACTCGTGGGATCTGCCCATGCCACCATATATAAATCGAGGCTTCAGGTCCCC-CTTT
62 CCTACTCGTGGAAACTGCCCACGCCACCA-ATATGAATCG-GGCTTCAGGTCCCCTTTTT
* * *
19360771 ACCTACTCATAGGATCTGCCCATGCCACTATATATAAATCGGGGCTTTAAGTCCCCCTTTGCCTA
1 ACCTACTCATGGGAACTGCCCATGCCACCATATATAAATCGGGGCTTTAAGTCCCCCTTTGCCTA
* *
19360836 CTCGTGGAAACTGCCCACGTCATCCAATATGAATCGGGACTTTAGGTCCCCTTTTT
66 CTCGTGGAAACTGCCCACGCCA-CCAATATGAATCGGG-CTTCAGGTCCCCTTTTT
* * * * * *
19360892 ACTTACTCGTGGGAACTGCCCATGCCACCATATATAAATCGGGGCTTCAGGTCTCCCTTTGCTTA
1 ACCTACTCATGGGAACTGCCCATGCCACCATATATAAATCGGGGCTTTAAGTCCCCCTTTGCCTA
*
19360957 CTCGT-GAGAACTACCCACGCCACCTAATATGAATCAGGGCTTCAGGTCCCCCTTTTT
66 CTCGTGGA-AACTGCCCACGCCACC-AATATGAATC-GGGCTTCAGGT-CCCCTTTTT
19361014 A
1 A
19361015 AATCAAATAT
Statistics
Matches: 209, Mismatches: 27, Indels: 17
0.83 0.11 0.07
Matches are distributed among these distances:
119 2 0.01
120 49 0.23
121 99 0.47
122 43 0.21
123 16 0.08
ACGTcount: A:0.23, C:0.31, G:0.17, T:0.29
Consensus pattern (119 bp):
ACCTACTCATGGGAACTGCCCATGCCACCATATATAAATCGGGGCTTTAAGTCCCCCTTTGCCTA
CTCGTGGAAACTGCCCACGCCACCAATATGAATCGGGCTTCAGGTCCCCTTTTT
Found at i:19361604 original size:15 final size:14
Alignment explanation
Indices: 19361586--19361615 Score: 51
Period size: 15 Copynumber: 2.1 Consensus size: 14
19361576 GCTCCTTCTG
19361586 TTCTTTTTCTTCTTT
1 TTCTTTTTCTT-TTT
19361601 TTCTTTTTCTTTTT
1 TTCTTTTTCTTTTT
19361615 T
1 T
19361616 CTTCCCTCTC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 4 0.27
15 11 0.73
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (14 bp):
TTCTTTTTCTTTTT
Found at i:19361648 original size:69 final size:69
Alignment explanation
Indices: 19361535--19361691 Score: 219
Period size: 69 Copynumber: 2.3 Consensus size: 69
19361525 ATTCTCTCTT
* * * * *
19361535 TTTTTCTTCTTTCTTCCCTCTCTTTCTTCTTCTCTGCCGCTGCTCCTTCTGTTCTTTTTCTTCTT
1 TTTTTCTTCTTTCTTCCCTCTCTTTCTTATCCTCTGCCGCTGCTCCTTCTATCCTTCTTCTTCTT
19361600 TTTC
66 TTTC
* * * *
19361604 TTTTTCTTTTTTCTTCCCTCTCTTTCTTATCCTTTGCTGTTGCTCCTTCTATCCTTCTTCTTCTT
1 TTTTTCTTCTTTCTTCCCTCTCTTTCTTATCCTCTGCCGCTGCTCCTTCTATCCTTCTTCTTCTT
19361669 TTTC
66 TTTC
19361673 --TTTCTTCTTTCTTCCCTCT
1 TTTTTCTTCTTTCTTCCCTCT
19361692 TCTTCTTCTC
Statistics
Matches: 78, Mismatches: 10, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
67 18 0.23
69 60 0.77
ACGTcount: A:0.01, C:0.32, G:0.04, T:0.62
Consensus pattern (69 bp):
TTTTTCTTCTTTCTTCCCTCTCTTTCTTATCCTCTGCCGCTGCTCCTTCTATCCTTCTTCTTCTT
TTTC
Found at i:19361790 original size:13 final size:13
Alignment explanation
Indices: 19361772--19361807 Score: 54
Period size: 13 Copynumber: 2.8 Consensus size: 13
19361762 CCCCACTCTT
19361772 TTTCTTCTCTTTC
1 TTTCTTCTCTTTC
* *
19361785 TTTCTTTTTTTTC
1 TTTCTTCTCTTTC
19361798 TTTCTTCTCT
1 TTTCTTCTCT
19361808 CCTTTTTGGC
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.00, C:0.25, G:0.00, T:0.75
Consensus pattern (13 bp):
TTTCTTCTCTTTC
Found at i:19362892 original size:20 final size:20
Alignment explanation
Indices: 19362867--19362915 Score: 80
Period size: 20 Copynumber: 2.5 Consensus size: 20
19362857 CTAGTAAACT
* *
19362867 ATGGTCCCTTATCGGACACA
1 ATGGTCACTTAACGGACACA
19362887 ATGGTCACTTAACGGACACA
1 ATGGTCACTTAACGGACACA
19362907 ATGGTCACT
1 ATGGTCACT
19362916 GGTACGCCAT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.29, C:0.27, G:0.20, T:0.24
Consensus pattern (20 bp):
ATGGTCACTTAACGGACACA
Found at i:19367997 original size:60 final size:60
Alignment explanation
Indices: 19367915--19368155 Score: 252
Period size: 60 Copynumber: 4.0 Consensus size: 60
19367905 GACATCATCA
* * *
19367915 CCTACTTGTGGGAAACTGCCCACACCA-CCATATATAAATTGGGGCTTCAAGTCCCCCTTTG
1 CCTACTCGTGGG-AACTGCCCACACCACCCA-ATATAAATCGGGGCTTCAGGTCCCCCTTTG
* ** * * *
19367976 CTTACTCGTGGGAACTGCCCACGTCACCCAATATGAATCGGGGTTTCAGGTCCCCCTTTTA
1 CCTACTCGTGGGAACTGCCCACACCACCCAATATAAATCGGGGCTTCAGGTCCCCC-TTTG
* ** **
19368037 CCTACTTGTGGGAACTGCCCACGTCA-CCATATATAAATCGGGGCTTCAGGTCCCATTTTG
1 CCTACTCGTGGGAACTGCCCACACCACCCA-ATATAAATCGGGGCTTCAGGTCCCCCTTTG
* * * * * *
19368097 CCTACTCGTGGGAATTACTCACACCACCCAATATGAATCGGGACTTCAGGTCTCCCTTT
1 CCTACTCGTGGGAACTGCCCACACCACCCAATATAAATCGGGGCTTCAGGTCCCCCTTT
19368156 TTAAATCAAA
Statistics
Matches: 149, Mismatches: 27, Indels: 9
0.81 0.15 0.05
Matches are distributed among these distances:
60 84 0.56
61 65 0.44
ACGTcount: A:0.22, C:0.31, G:0.20, T:0.27
Consensus pattern (60 bp):
CCTACTCGTGGGAACTGCCCACACCACCCAATATAAATCGGGGCTTCAGGTCCCCCTTTG
Found at i:19368145 original size:121 final size:122
Alignment explanation
Indices: 19367914--19368156 Score: 344
Period size: 121 Copynumber: 2.0 Consensus size: 122
19367904 AGACATCATC
* * *
19367914 ACCTACTTGTGGGAAACTGCCCACACCACCATATATAAATTGGGGCTTCAAGTCCCCCTTTGCTT
1 ACCTACTTGTGGGAAACTGCCCACACCACCATATATAAATCGGGGCTTCAAGTCCCACTTTGCCT
* ** **
19367979 ACTCGTGGGAACTGCCCACGTCACCCAATATGAATCGGGGTTTCAGGTCCCCCTTTT
66 ACTCGTGGGAACTACCCACACCACCCAATATGAATCGGGACTTCAGGTCCCCCTTTT
** * *
19368036 ACCTACTTGTGGG-AACTGCCCACGTCACCATATATAAATCGGGGCTTCAGGTCCCATTTTGCCT
1 ACCTACTTGTGGGAAACTGCCCACACCACCATATATAAATCGGGGCTTCAAGTCCCACTTTGCCT
* * *
19368100 ACTCGTGGGAATTACTCACACCACCCAATATGAATCGGGACTTCAGGTCTCCCTTTT
66 ACTCGTGGGAACTACCCACACCACCCAATATGAATCGGGACTTCAGGTCCCCCTTTT
19368157 TAAATCAAAT
Statistics
Matches: 106, Mismatches: 15, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
121 93 0.88
122 13 0.12
ACGTcount: A:0.23, C:0.30, G:0.19, T:0.28
Consensus pattern (122 bp):
ACCTACTTGTGGGAAACTGCCCACACCACCATATATAAATCGGGGCTTCAAGTCCCACTTTGCCT
ACTCGTGGGAACTACCCACACCACCCAATATGAATCGGGACTTCAGGTCCCCCTTTT
Found at i:19368704 original size:16 final size:15
Alignment explanation
Indices: 19368667--19368698 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
19368657 TACTTAAATA
19368667 TTCTCTTTTTTTTCT
1 TTCTCTTTTTTTTCT
19368682 TTCTCTTTTTTTTCT
1 TTCTCTTTTTTTTCT
19368697 TT
1 TT
19368699 TTTCTTCCCT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (15 bp):
TTCTCTTTTTTTTCT
Found at i:19368711 original size:25 final size:24
Alignment explanation
Indices: 19368670--19368718 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 24
19368660 TTAAATATTC
**
19368670 TCTTTTTTTTCTTTCTCTTTTTTT
1 TCTTTTTTTTCCCTCTCTTTTTTT
19368694 TCTTTTTTCTTCCCTCTCTTTTTTT
1 TCTTTTTT-TTCCCTCTCTTTTTTT
19368719 CTCCTCTACC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 8 0.36
25 14 0.64
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (24 bp):
TCTTTTTTTTCCCTCTCTTTTTTT
Found at i:19368824 original size:68 final size:69
Alignment explanation
Indices: 19368667--19368928 Score: 329
Period size: 68 Copynumber: 3.8 Consensus size: 69
19368657 TACTTAAATA
* * * * * *
19368667 TTCTCTTTTTTTTCTTTCTCTTTTTTTTCTTTTTTCTTCCCTCTCTTTTTTTCTCCTCTACCGCT
1 TTCTCTTATTCTTCTTTTTC-TTTTTTTCTTCTTTCTTCCCTCTCTTTTTTTCTCCTTTGCCGCT
19368732 GCTCC
65 GCTCC
19368737 TTTTCTCTTATTCTTCTTTTTCTTTTTTT-TTCTTTCTTCCCTCTCTTTTTTTCTCCTTTGCCGC
1 --TTCTCTTATTCTTCTTTTTCTTTTTTTCTTCTTTCTTCCCTCTCTTTTTTTCTCCTTTGCCGC
19368801 TGCTCC
64 TGCTCC
* * **
19368807 TTCTCTTATTCTTCTTTTTC--TTTTTCTTCTTTCTTCCCTATC-TTTTTTCTCCTTTGTCATTG
1 TTCTCTTATTCTTCTTTTTCTTTTTTTCTTCTTTCTTCCCTCTCTTTTTTTCTCCTTTGCCGCTG
19368869 CTCC
66 CTCC
* * *
19368873 TTCTCTTCTTCTTCTTTTT-TTTTCTTTCTTCTTTCTTCCCTCT-TCTTCTTCTCCTT
1 TTCTCTTATTCTTCTTTTTCTTTT-TTTCTTCTTTCTTCCCTCTCTTTTTTTCTCCTT
19368929 GAGACGTCGC
Statistics
Matches: 171, Mismatches: 14, Indels: 14
0.86 0.07 0.07
Matches are distributed among these distances:
66 44 0.26
67 17 0.10
68 48 0.28
70 38 0.22
71 7 0.04
72 17 0.10
ACGTcount: A:0.02, C:0.31, G:0.03, T:0.65
Consensus pattern (69 bp):
TTCTCTTATTCTTCTTTTTCTTTTTTTCTTCTTTCTTCCCTCTCTTTTTTTCTCCTTTGCCGCTG
CTCC
Found at i:19369067 original size:16 final size:15
Alignment explanation
Indices: 19369046--19369090 Score: 56
Period size: 16 Copynumber: 2.9 Consensus size: 15
19369036 CCCCCCCCTT
19369046 TTTCTTCTTTTTCTTC
1 TTTCTTCTTTTTC-TC
19369062 TTTCTTCTCTTTTCTC
1 TTTCTTCT-TTTTCTC
19369078 TTT-TATCTTTTTC
1 TTTCT-TCTTTTTC
19369091 CTTCCCTTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
15 6 0.22
16 16 0.59
17 5 0.19
ACGTcount: A:0.02, C:0.24, G:0.00, T:0.73
Consensus pattern (15 bp):
TTTCTTCTTTTTCTC
Found at i:19369086 original size:26 final size:26
Alignment explanation
Indices: 19369045--19369100 Score: 71
Period size: 26 Copynumber: 2.2 Consensus size: 26
19369035 CCCCCCCCCT
*
19369045 TTTTCTTCTTTTTCTTCTTT-CTTCTC
1 TTTTCTTCTTTTTCTT-TTTCCTTCCC
19369071 TTTTC-TCTTTTATCTTTTTCCTTCCC
1 TTTTCTTCTTTT-TCTTTTTCCTTCCC
19369097 TTTT
1 TTTT
19369101 TCTGTTCCTT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
25 9 0.33
26 18 0.67
ACGTcount: A:0.02, C:0.27, G:0.00, T:0.71
Consensus pattern (26 bp):
TTTTCTTCTTTTTCTTTTTCCTTCCC
Found at i:19372342 original size:26 final size:27
Alignment explanation
Indices: 19372286--19372349 Score: 76
Period size: 27 Copynumber: 2.4 Consensus size: 27
19372276 GAGATCAAGT
* *
19372286 TACACGCCATGTTGAAAAAAAAGTTGC
1 TACACGTCATGTTGAAAAAAAAGTTAC
* * *
19372313 TACATGTCATGTTGAAAATAAA-TTAT
1 TACACGTCATGTTGAAAAAAAAGTTAC
19372339 TACACGTCATG
1 TACACGTCATG
19372350 CTTAAAGTGG
Statistics
Matches: 31, Mismatches: 6, Indels: 1
0.82 0.16 0.03
Matches are distributed among these distances:
26 12 0.39
27 19 0.61
ACGTcount: A:0.39, C:0.16, G:0.16, T:0.30
Consensus pattern (27 bp):
TACACGTCATGTTGAAAAAAAAGTTAC
Found at i:19372427 original size:28 final size:28
Alignment explanation
Indices: 19372389--19372462 Score: 98
Period size: 28 Copynumber: 2.7 Consensus size: 28
19372379 TCCTAGTGAA
*
19372389 AAAAAAAAAGTTATTACACGGCATATTG
1 AAAAAAAAAGTTATTACACGCCATATTG
* * *
19372417 AAAAAAAAAGTTGTTACACACCGTATTG
1 AAAAAAAAAGTTATTACACGCCATATTG
19372445 --AAAAAAAGTTATTACACG
1 AAAAAAAAAGTTATTACACG
19372463 TCATGTTTAA
Statistics
Matches: 40, Mismatches: 6, Indels: 2
0.83 0.12 0.04
Matches are distributed among these distances:
26 16 0.40
28 24 0.60
ACGTcount: A:0.50, C:0.12, G:0.14, T:0.24
Consensus pattern (28 bp):
AAAAAAAAAGTTATTACACGCCATATTG
Found at i:19372501 original size:118 final size:125
Alignment explanation
Indices: 19372207--19372537 Score: 360
Period size: 118 Copynumber: 2.7 Consensus size: 125
19372197 TGAAGTACTT
* *
19372207 AAGTTATTACACATTATGTTTAAAGTGTTTAACTTAAAGAGTTCTATGTCCTAGTGAAATACAAA
1 AAGTTATTACACGTCATGTTTAAAGTGTTTAACTTAAAGAGTT-TATGTCCTAGTGAAATACAAA
* * *** *
19372272 GATAGAGATCAAGTTACACGCCATGTTGAAAAAAAAGTTGCTACATGTCATGTTGAAAATA
65 GATAAAGATCAAGTTACACGCCATATTGAAAAAAAAGTTGCTACACACCATATTGAAAATA
* * * * * *
19372333 AA-TTATTACACGTCATGCTTAAAGTGGTTAACTTAAACAATATATATCCTAGTGAAA-A-AAA-
1 AAGTTATTACACGTCATGTTTAAAGTGTTTAACTTAAAGAGTTTATGTCCTAGTGAAATACAAAG
* * * *
19372394 A-AAAG-T-TA-TTACACGGCATATTGAAAAAAAAAGTTGTTACACACCGTATTGAAAA-A
66 ATAAAGATCAAGTTACACGCCATATTG-AAAAAAAAGTTGCTACACACCATATTGAAAATA
19372450 AAGTTATTACACGTCATGTTTAAAGTGTTTAACTCT-AAGAGTTTATGTCCTAGTGAAATACAAA
1 AAGTTATTACACGTCATGTTTAAAGTGTTTAACT-TAAAGAGTTTATGTCCTAGTGAAATACAAA
* * *
19372514 GA-AAGCGATTAAGTTACATGCCAT
65 GATAA-AGATCAAGTTACACGCCAT
19372538 GTTTAAATCG
Statistics
Matches: 167, Mismatches: 28, Indels: 21
0.77 0.13 0.10
Matches are distributed among these distances:
117 16 0.10
118 73 0.44
119 3 0.02
120 6 0.04
121 4 0.02
122 4 0.02
123 2 0.01
124 15 0.09
125 42 0.25
126 2 0.01
ACGTcount: A:0.41, C:0.13, G:0.15, T:0.31
Consensus pattern (125 bp):
AAGTTATTACACGTCATGTTTAAAGTGTTTAACTTAAAGAGTTTATGTCCTAGTGAAATACAAAG
ATAAAGATCAAGTTACACGCCATATTGAAAAAAAAGTTGCTACACACCATATTGAAAATA
Found at i:19373422 original size:28 final size:29
Alignment explanation
Indices: 19373367--19373427 Score: 106
Period size: 28 Copynumber: 2.1 Consensus size: 29
19373357 TGCGTGTATG
19373367 ATATCCAATTTTATATTTTTTTTCTTATC
1 ATATCCAATTTTATATTTTTTTTCTTATC
*
19373396 ATATCCAGTTTTAT-TTTTTTTTCTTATC
1 ATATCCAATTTTATATTTTTTTTCTTATC
19373424 ATAT
1 ATAT
19373428 ATTTTGTACA
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
28 18 0.58
29 13 0.42
ACGTcount: A:0.23, C:0.13, G:0.02, T:0.62
Consensus pattern (29 bp):
ATATCCAATTTTATATTTTTTTTCTTATC
Found at i:19373710 original size:31 final size:31
Alignment explanation
Indices: 19373673--19373763 Score: 98
Period size: 31 Copynumber: 2.9 Consensus size: 31
19373663 TAACAGAAAA
19373673 AATCGTATGT-GCTTCCCCGTAACCCATTGCC
1 AATCGTATGTAGCTTCCCC-TAACCCATTGCC
* *
19373704 AGTCGTATGTGGGCTTCCGCC--ACCCATTGCC
1 AATCGTATGT-AGCTTCC-CCTAACCCATTGCC
*
19373735 AATCGTATGTAACCTTCCCCTAACCCATT
1 AATCGTATGT-AGCTTCCCCTAACCCATT
19373764 ACCACATACC
Statistics
Matches: 50, Mismatches: 5, Indels: 9
0.78 0.08 0.14
Matches are distributed among these distances:
30 2 0.04
31 33 0.66
32 7 0.14
33 6 0.12
34 2 0.04
ACGTcount: A:0.20, C:0.35, G:0.16, T:0.29
Consensus pattern (31 bp):
AATCGTATGTAGCTTCCCCTAACCCATTGCC
Found at i:19381239 original size:24 final size:24
Alignment explanation
Indices: 19381205--19381251 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
19381195 GGGAAAATCA
*
19381205 GAGATAGAATATAGAAATCTAGAG
1 GAGATAAAATATAGAAATCTAGAG
19381229 GAGATAAAATATAGAAATCTAGA
1 GAGATAAAATATAGAAATCTAGA
19381252 AGGAAAATCA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.53, C:0.04, G:0.21, T:0.21
Consensus pattern (24 bp):
GAGATAAAATATAGAAATCTAGAG
Found at i:19384853 original size:31 final size:31
Alignment explanation
Indices: 19384818--19384879 Score: 115
Period size: 31 Copynumber: 2.0 Consensus size: 31
19384808 AAACATCTAA
19384818 AAATGGTATATGTGTGTGCATTTTTAAAATT
1 AAATGGTATATGTGTGTGCATTTTTAAAATT
*
19384849 AAATGGTATATGTGTGTGCATTTTTATAATT
1 AAATGGTATATGTGTGTGCATTTTTAAAATT
19384880 CAACTTCACA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.31, C:0.03, G:0.19, T:0.47
Consensus pattern (31 bp):
AAATGGTATATGTGTGTGCATTTTTAAAATT
Found at i:19388799 original size:41 final size:41
Alignment explanation
Indices: 19388731--19388809 Score: 97
Period size: 41 Copynumber: 1.9 Consensus size: 41
19388721 TTCTATTTGA
* *
19388731 AATCTATCGATACAAGTGAGAACTGTATCGATAAATCAAAC
1 AATCTATCAATACAACTGAGAACTGTATCGATAAATCAAAC
* * *
19388772 AATCTATCAATACATCTGAGCAA-TGTATTGATAGATCA
1 AATCTATCAATACAACTGAG-AACTGTATCGATAAATCA
19388810 GGCTTATTTT
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
41 30 0.94
42 2 0.06
ACGTcount: A:0.42, C:0.16, G:0.14, T:0.28
Consensus pattern (41 bp):
AATCTATCAATACAACTGAGAACTGTATCGATAAATCAAAC
Found at i:19392333 original size:22 final size:22
Alignment explanation
Indices: 19392308--19392349 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
19392298 AAATGAAATC
19392308 TTAGAAACTT-AGACAAAATATA
1 TTAGAAA-TTAAGACAAAATATA
*
19392330 TTAGAAATTAAGACCAAATA
1 TTAGAAATTAAGACAAAATA
19392350 ACTCTATAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 2 0.11
22 16 0.89
ACGTcount: A:0.55, C:0.10, G:0.10, T:0.26
Consensus pattern (22 bp):
TTAGAAATTAAGACAAAATATA
Found at i:19394542 original size:20 final size:20
Alignment explanation
Indices: 19394517--19394562 Score: 83
Period size: 20 Copynumber: 2.3 Consensus size: 20
19394507 TTTTGATCCC
19394517 ATTTGACTTATTGGAGTATA
1 ATTTGACTTATTGGAGTATA
*
19394537 ATTTGACTTATTGGAGTATG
1 ATTTGACTTATTGGAGTATA
19394557 ATTTGA
1 ATTTGA
19394563 GGTTTAGAAG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.28, C:0.04, G:0.22, T:0.46
Consensus pattern (20 bp):
ATTTGACTTATTGGAGTATA
Found at i:19410342 original size:2 final size:2
Alignment explanation
Indices: 19410335--19410393 Score: 82
Period size: 2 Copynumber: 29.5 Consensus size: 2
19410325 TCTTCCGATT
* *
19410335 TA TA TA TA TA TA TA TA TA TA TA CA TA TC TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* *
19410377 TA CA TA TA TA CA TA TA T
1 TA TA TA TA TA TA TA TA T
19410394 GGTATATGGT
Statistics
Matches: 49, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.47, C:0.07, G:0.00, T:0.46
Consensus pattern (2 bp):
TA
Found at i:19420011 original size:13 final size:13
Alignment explanation
Indices: 19419989--19420018 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
19419979 ACTAATTCCA
19419989 TCACTAGTATTTG
1 TCACTAGTATTTG
*
19420002 TCACTGGTATTTG
1 TCACTAGTATTTG
19420015 TCAC
1 TCAC
19420019 AATGTGAGAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.20, C:0.20, G:0.17, T:0.43
Consensus pattern (13 bp):
TCACTAGTATTTG
Found at i:19422141 original size:35 final size:36
Alignment explanation
Indices: 19422078--19422147 Score: 97
Period size: 35 Copynumber: 2.0 Consensus size: 36
19422068 TAAAATGCGA
** *
19422078 TTGTAAAGGTTTGTGCTTGATCTTGTTAATAAGCAT
1 TTGTAAAGGTTTGTGCTTGATCCCGTTAAAAAGCAT
*
19422114 TTGTAAGGGTTT-TGCTTGATCCCGTTAAAAAGCA
1 TTGTAAAGGTTTGTGCTTGATCCCGTTAAAAAGCA
19422148 CTTTCCTTTA
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
35 19 0.63
36 11 0.37
ACGTcount: A:0.26, C:0.11, G:0.23, T:0.40
Consensus pattern (36 bp):
TTGTAAAGGTTTGTGCTTGATCCCGTTAAAAAGCAT
Found at i:19434317 original size:35 final size:34
Alignment explanation
Indices: 19434251--19434320 Score: 95
Period size: 35 Copynumber: 2.0 Consensus size: 34
19434241 TTTCACCAAG
* * *
19434251 CTTTACAATGGCTTTTACCAGGCTTAGCCAAAAC
1 CTTTACAATGGCTTTTACCAGGATCAACCAAAAC
*
19434285 CTTTCACAATGGCTTTTACCGGGATCAACCAAAAC
1 CTTT-ACAATGGCTTTTACCAGGATCAACCAAAAC
19434320 C
1 C
19434321 CAAAGTGGTT
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
34 4 0.13
35 27 0.87
ACGTcount: A:0.30, C:0.29, G:0.14, T:0.27
Consensus pattern (34 bp):
CTTTACAATGGCTTTTACCAGGATCAACCAAAAC
Found at i:19434356 original size:67 final size:67
Alignment explanation
Indices: 19434282--19434457 Score: 257
Period size: 67 Copynumber: 2.6 Consensus size: 67
19434272 GCTTAGCCAA
*
19434282 AACCTTTCACAATGGCTTTT-ACCGGGATCAACCAAAACCCAAAGTGGTTTTTCAAAGGCTCAAC
1 AACCTTTCACAATGGTTTTTCA-CGGGATCAACCAAAACCCAAAGTGGTTTTTCAAAGGCTCAAC
*
19434346 CAT
65 CAC
* *
19434349 AACCTTTCACAATGGTTTTTCATGGGCTCAACCAAAACCCAAAGTGGTTTTTCAAAGGCTCAACC
1 AACCTTTCACAATGGTTTTTCACGGGATCAACCAAAACCCAAAGTGGTTTTTCAAAGGCTCAACC
19434414 AC
66 AC
* * *
19434416 AACC-TACAACAATGGTTTTTCACAGGATTAACCAAAACCCAA
1 AACCTTTC-ACAATGGTTTTTCACGGGATCAACCAAAACCCAA
19434458 CAACTAACTT
Statistics
Matches: 98, Mismatches: 9, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
66 2 0.02
67 95 0.97
68 1 0.01
ACGTcount: A:0.35, C:0.27, G:0.14, T:0.25
Consensus pattern (67 bp):
AACCTTTCACAATGGTTTTTCACGGGATCAACCAAAACCCAAAGTGGTTTTTCAAAGGCTCAACC
AC
Found at i:19434402 original size:32 final size:32
Alignment explanation
Indices: 19434309--19434457 Score: 156
Period size: 35 Copynumber: 4.5 Consensus size: 32
19434299 TTTACCGGGA
19434309 TCAACCAAAACCCAAAGTGGTTTTTCAAAGGC
1 TCAACCAAAACCCAAAGTGGTTTTTCAAAGGC
* **
19434341 TCAACCATAACCTTTCACAA-TGGTTTTTCATGGGC
1 TCAACCAAAACC---CA-AAGTGGTTTTTCAAAGGC
19434376 TCAACCAAAACCCAAAGTGGTTTTTCAAAGGC
1 TCAACCAAAACCCAAAGTGGTTTTTCAAAGGC
* * * *
19434408 TCAACCACAACCTACAACAATGGTTTTTCACAGGA
1 TCAACCAAAACC--CAA-AGTGGTTTTTCAAAGGC
*
19434443 TTAACCAAAACCCAA
1 TCAACCAAAACCCAA
19434458 CAACTAACTT
Statistics
Matches: 97, Mismatches: 12, Indels: 15
0.78 0.10 0.12
Matches are distributed among these distances:
31 2 0.02
32 37 0.38
33 3 0.03
34 3 0.03
35 50 0.52
36 2 0.02
ACGTcount: A:0.36, C:0.27, G:0.13, T:0.24
Consensus pattern (32 bp):
TCAACCAAAACCCAAAGTGGTTTTTCAAAGGC
Found at i:19435006 original size:73 final size:73
Alignment explanation
Indices: 19434844--19434998 Score: 231
Period size: 73 Copynumber: 2.1 Consensus size: 73
19434834 CAAACAAAAT
* *
19434844 GCTCTTAGTCGACTAACATACTTCTTAGTCGATTAAGTCATCTCTGTCTTCTGATCCCAATTTTT
1 GCTCTTAGTCGACTAACATACTTCTTAGCCGATTAAGTCATCTCTGTCTTCTGAACCCAATTTTT
* * *
19434909 GGCAGTGA
66 AGCAATAA
* *
19434917 GCTCTTAGTCGACTAACAATTCTTCTTAGCCGATTAAGTCGTCTCTGTCTT-TGAACCCAATTTT
1 GCTCTTAGTCGACTAAC-ATACTTCTTAGCCGATTAAGTCATCTCTGTCTTCTGAACCCAATTTT
19434981 TAGCAATAA
65 TAGCAATAA
19434990 GCTCTTAGT
1 GCTCTTAGT
19434999 TGGCTAACCA
Statistics
Matches: 74, Mismatches: 7, Indels: 2
0.89 0.08 0.02
Matches are distributed among these distances:
73 44 0.59
74 30 0.41
ACGTcount: A:0.23, C:0.23, G:0.15, T:0.38
Consensus pattern (73 bp):
GCTCTTAGTCGACTAACATACTTCTTAGCCGATTAAGTCATCTCTGTCTTCTGAACCCAATTTTT
AGCAATAA
Found at i:19435028 original size:73 final size:73
Alignment explanation
Indices: 19434844--19435041 Score: 224
Period size: 73 Copynumber: 2.7 Consensus size: 73
19434834 CAAACAAAAT
*
19434844 GCTCTTAGTCGACTAA-CATAC-TTCTTAGTCGATTAAGTCATCTCTGTCTTCTGATCCCAATTT
1 GCTCTTAGTCGACTAACCAT-CTTTCTTAGTCGATTAAGTCATCTCTGTCTT-TGAACCCAATTT
* * *
19434907 TTGGCAGTGA
64 TTAGCAATAA
* * *
19434917 GCTCTTAGTCGACTAACAAT-TCTTCTTAGCCGATTAAGTCGTCTCTGTCTTTGAACCCAATTTT
1 GCTCTTAGTCGACTAACCATCT-TTCTTAGTCGATTAAGTCATCTCTGTCTTTGAACCCAATTTT
19434981 TAGCAATAA
65 TAGCAATAA
* * * * **
19434990 GCTCTTAGTTGGCTAACCATCTTTCTTGGTCGACTAAGTTTTCTCTGT-TTTG
1 GCTCTTAGTCGACTAACCATCTTTCTTAGTCGATTAAGTCATCTCTGTCTTTG
19435042 CAATATACTC
Statistics
Matches: 106, Mismatches: 15, Indels: 9
0.82 0.12 0.07
Matches are distributed among these distances:
72 4 0.04
73 72 0.68
74 30 0.28
ACGTcount: A:0.21, C:0.23, G:0.16, T:0.40
Consensus pattern (73 bp):
GCTCTTAGTCGACTAACCATCTTTCTTAGTCGATTAAGTCATCTCTGTCTTTGAACCCAATTTTT
AGCAATAA
Found at i:19445240 original size:43 final size:43
Alignment explanation
Indices: 19445177--19445288 Score: 154
Period size: 43 Copynumber: 2.6 Consensus size: 43
19445167 TATTGACTCG
*
19445177 GCTATGTGCGAGTAGGGAGTGCGCATAAGC-CGAGGATGACCTA
1 GCTATGTGCGAGTAGGGAGTGCGCATAA-CTCGAGGATGACCCA
* * *
19445220 GTTATGTGCGAGTAAGGAGTGCGCATAACTCGATGATGACCCA
1 GCTATGTGCGAGTAGGGAGTGCGCATAACTCGAGGATGACCCA
* *
19445263 GCCATGTGCGAGTAGGGAGTGTGCAT
1 GCTATGTGCGAGTAGGGAGTGCGCAT
19445289 GAGCTGTTGA
Statistics
Matches: 60, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
42 1 0.02
43 59 0.98
ACGTcount: A:0.25, C:0.18, G:0.36, T:0.21
Consensus pattern (43 bp):
GCTATGTGCGAGTAGGGAGTGCGCATAACTCGAGGATGACCCA
Found at i:19445678 original size:21 final size:21
Alignment explanation
Indices: 19445632--19445678 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
19445622 GACACTGTAG
19445632 CTTT-TCGCTGCAGCGAAATA
1 CTTTCTCGCTGCAGCGAAATA
*
19445652 CATTCTCGCTGCAGCGAGAA-A
1 CTTTCTCGCTGCAGCGA-AATA
19445673 CTTTCT
1 CTTTCT
19445679 GTTTTTGGGT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
20 3 0.13
21 18 0.78
22 2 0.09
ACGTcount: A:0.23, C:0.28, G:0.19, T:0.30
Consensus pattern (21 bp):
CTTTCTCGCTGCAGCGAAATA
Found at i:19445731 original size:60 final size:60
Alignment explanation
Indices: 19445634--19445769 Score: 195
Period size: 60 Copynumber: 2.3 Consensus size: 60
19445624 CACTGTAGCT
* *
19445634 TTTCGCTGCAGCGAAATACATTCTCGCTGCAGCGAGAAACTTTCTGTTTTTGGGTTGCAA
1 TTTCGCTGCAGCGAAATACATTCTCGCTGCAGCGAGAAACATTCTGTTTCTGGGTTGCAA
* * *
19445694 TTTCGCTGCAGCGAGATTGA-ATT-TGGCTGCAGTGAGAAACATTCTGTTTCTGGGTTGCAA
1 TTTCGCTGCAGCGA-AAT-ACATTCTCGCTGCAGCGAGAAACATTCTGTTTCTGGGTTGCAA
19445754 TTTCGCTGCAGCGAAA
1 TTTCGCTGCAGCGAAA
19445770 AACTTTCTGT
Statistics
Matches: 68, Mismatches: 6, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
59 1 0.01
60 61 0.90
61 5 0.07
62 1 0.01
ACGTcount: A:0.22, C:0.20, G:0.26, T:0.32
Consensus pattern (60 bp):
TTTCGCTGCAGCGAAATACATTCTCGCTGCAGCGAGAAACATTCTGTTTCTGGGTTGCAA
Found at i:19454524 original size:27 final size:27
Alignment explanation
Indices: 19454482--19454535 Score: 90
Period size: 27 Copynumber: 2.0 Consensus size: 27
19454472 TTGTTTTGGA
* *
19454482 CTGGGCAGTGGTGGAGCTATAGGTGGT
1 CTGGGCAGTGGAGGAGCAATAGGTGGT
19454509 CTGGGCAGTGGAGGAGCAATAGGTGGT
1 CTGGGCAGTGGAGGAGCAATAGGTGGT
19454536 GGGCATGTTG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.19, C:0.11, G:0.48, T:0.22
Consensus pattern (27 bp):
CTGGGCAGTGGAGGAGCAATAGGTGGT
Found at i:19457942 original size:22 final size:20
Alignment explanation
Indices: 19457917--19457956 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
19457907 CATCAATCAG
19457917 TAAAATTAAAGTCATATTGATT
1 TAAAA-TAAA-TCATATTGATT
*
19457939 TAAAATAAATTATATTGA
1 TAAAATAAATCATATTGA
19457957 CCTCTCAAGT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 8 0.47
21 4 0.24
22 5 0.29
ACGTcount: A:0.50, C:0.03, G:0.07, T:0.40
Consensus pattern (20 bp):
TAAAATAAATCATATTGATT
Found at i:19459499 original size:25 final size:25
Alignment explanation
Indices: 19459471--19459520 Score: 82
Period size: 25 Copynumber: 2.0 Consensus size: 25
19459461 AAGCTATCAG
*
19459471 TTATAAATGTGTCAGTAGATCACAA
1 TTATAAATGTGTCACTAGATCACAA
*
19459496 TTATAAATGTGTCACTTGATCACAA
1 TTATAAATGTGTCACTAGATCACAA
19459521 ACTAATCAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.38, C:0.14, G:0.14, T:0.34
Consensus pattern (25 bp):
TTATAAATGTGTCACTAGATCACAA
Found at i:19460639 original size:19 final size:19
Alignment explanation
Indices: 19460590--19460639 Score: 59
Period size: 19 Copynumber: 2.6 Consensus size: 19
19460580 GCTATAAATA
*
19460590 TCTTCTCCTTCCAGTAGCT
1 TCTTCTTCTTCCAGTAGCT
19460609 TCTT-TAAT-TTCCAGTAGCT
1 TCTTCT--TCTTCCAGTAGCT
19460628 TCTTCTTCTTCC
1 TCTTCTTCTTCC
19460640 TCCTTCTATC
Statistics
Matches: 26, Mismatches: 1, Indels: 8
0.74 0.03 0.23
Matches are distributed among these distances:
18 2 0.08
19 23 0.88
20 1 0.04
ACGTcount: A:0.12, C:0.32, G:0.08, T:0.48
Consensus pattern (19 bp):
TCTTCTTCTTCCAGTAGCT
Found at i:19468664 original size:2 final size:2
Alignment explanation
Indices: 19468619--19468656 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
19468609 CATTATGTTG
*
19468619 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AC AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
19468657 GAATATATTG
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:19468725 original size:42 final size:41
Alignment explanation
Indices: 19468678--19468769 Score: 103
Period size: 42 Copynumber: 2.2 Consensus size: 41
19468668 TGTGTAACGA
* *
19468678 TGATGACCCGGCTATGTACGAATAGGAATGTGCATACGCCGG
1 TGATGACCCGGCTATGTACGAATAGGAATGCGCATAAGCC-G
* * * * *
19468720 TGATGACCTGGTTATGTGCGAGTAGGAGTGCGCATAAGCCG
1 TGATGACCCGGCTATGTACGAATAGGAATGCGCATAAGCCG
*
19468761 TGCTGACCC
1 TGATGACCC
19468770 AGCCATGTGC
Statistics
Matches: 41, Mismatches: 9, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
41 8 0.20
42 33 0.80
ACGTcount: A:0.23, C:0.22, G:0.33, T:0.23
Consensus pattern (41 bp):
TGATGACCCGGCTATGTACGAATAGGAATGCGCATAAGCCG
Found at i:19476333 original size:38 final size:39
Alignment explanation
Indices: 19476247--19476349 Score: 140
Period size: 38 Copynumber: 2.6 Consensus size: 39
19476237 ACCCGGCTCA
19476247 TGTACATCCCCCCACATCGTGCAC-ATAGCCGGCACCATCG
1 TGTACATCCCCCCACATCGTGCACAATAG-CGG-ACCATCG
* *
19476287 TGTGCATCCCCCCACATCGTGCACAATTAG-TG-CCATCG
1 TGTACATCCCCCCACATCGTGCACAA-TAGCGGACCATCG
19476325 TGTACATCCCCCCACATCGTGCACA
1 TGTACATCCCCCCACATCGTGCACA
19476350 CGGGCACTAT
Statistics
Matches: 58, Mismatches: 3, Indels: 6
0.87 0.04 0.09
Matches are distributed among these distances:
38 30 0.52
40 24 0.41
41 1 0.02
42 3 0.05
ACGTcount: A:0.22, C:0.41, G:0.17, T:0.20
Consensus pattern (39 bp):
TGTACATCCCCCCACATCGTGCACAATAGCGGACCATCG
Found at i:19487349 original size:2 final size:2
Alignment explanation
Indices: 19487342--19487378 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
19487332 ATTATGTTGG
*
19487342 TA TA TA TA TA GA 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 TA T
19487379 GTTGTGCATG
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (2 bp):
TA
Found at i:19490906 original size:35 final size:35
Alignment explanation
Indices: 19490788--19490895 Score: 162
Period size: 35 Copynumber: 3.1 Consensus size: 35
19490778 CTTACTCAGC
* ** ***
19490788 TCATGTGCACTCCTTACGCGCACAAGGCAATATCA
1 TCATGTGCACTCCCTACAAGCACATTTCAATATCA
19490823 TCATGTGCACTCCCTACAAGCACATTTCAATATCA
1 TCATGTGCACTCCCTACAAGCACATTTCAATATCA
19490858 TCATGTGCACTCCCTACAAGCACATTTCAATATCA
1 TCATGTGCACTCCCTACAAGCACATTTCAATATCA
19490893 TCA
1 TCA
19490896 CACGCACTCC
Statistics
Matches: 67, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
35 67 1.00
ACGTcount: A:0.31, C:0.31, G:0.11, T:0.27
Consensus pattern (35 bp):
TCATGTGCACTCCCTACAAGCACATTTCAATATCA
Found at i:19492170 original size:19 final size:19
Alignment explanation
Indices: 19492146--19492183 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
19492136 GGTGGTAAGG
19492146 TGAAAATAGCATGGGAGCA
1 TGAAAATAGCATGGGAGCA
* *
19492165 TGAAAATGGCGTGGGAGCA
1 TGAAAATAGCATGGGAGCA
19492184 AGATGGAGAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.37, C:0.11, G:0.37, T:0.16
Consensus pattern (19 bp):
TGAAAATAGCATGGGAGCA
Found at i:19496997 original size:43 final size:42
Alignment explanation
Indices: 19496939--19497316 Score: 397
Period size: 43 Copynumber: 9.0 Consensus size: 42
19496929 TGTGATCATT
* *
19496939 ATGACCCAGCCATGTGCG-GTGCAGGAGTGCACATGAGCTGATC
1 ATGACCCAGCTATGTGCGAGT--AGGAGTGCACATGAGCTGATG
*
19496982 ATGACCCAGCTATGTGCGAGTAAAGAGTGCACATGAGCTGATG
1 ATGACCCAGCTATGTGCGAGT-AGGAGTGCACATGAGCTGATG
* * * * * *
19497025 ATGACCTAGCCATGTGTGTGGAGGAGTACACATGAGCTGATG
1 ATGACCCAGCTATGTGCGAGTAGGAGTGCACATGAGCTGATG
* *
19497067 ATGACCCAGTTATGTGCGAGTAGGGAGTGCACATGAACTGATG
1 ATGACCCAGCTATGTGCGAGTA-GGAGTGCACATGAGCTGATG
* * * *
19497110 ATGACCCAGCCATGTGTG-G-AGGAGTACACATGAGTTGATG
1 ATGACCCAGCTATGTGCGAGTAGGAGTGCACATGAGCTGATG
** * * *
19497150 ATGACCTTGCTATGTACGAATAGGGAGTGCACATGAGTTGATG
1 ATGACCCAGCTATGTGCGAGTA-GGAGTGCACATGAGCTGATG
* * *
19497193 ATGACCCAACCATGTGTG-G-AGGAGTGCACATGAGCTGATG
1 ATGACCCAGCTATGTGCGAGTAGGAGTGCACATGAGCTGATG
*
19497233 ATGACCCAGCTATGTGCGAGTAGGGAGTGCTCATGAGCTGATG
1 ATGACCCAGCTATGTGCGAGTA-GGAGTGCACATGAGCTGATG
* * * * *
19497276 ATGACCTAGCTATGTGCAATGTGGGAGCGCACATAAGCTGA
1 ATGACCCAGCTATGTGCGA-GTAGGAGTGCACATGAGCTGA
19497317 GAGAGAGTTA
Statistics
Matches: 276, Mismatches: 50, Indels: 18
0.80 0.15 0.05
Matches are distributed among these distances:
40 64 0.23
41 3 0.01
42 38 0.14
43 167 0.61
44 4 0.01
ACGTcount: A:0.27, C:0.19, G:0.32, T:0.22
Consensus pattern (42 bp):
ATGACCCAGCTATGTGCGAGTAGGAGTGCACATGAGCTGATG
Found at i:19497174 original size:83 final size:83
Alignment explanation
Indices: 19496939--19497291 Score: 490
Period size: 83 Copynumber: 4.2 Consensus size: 83
19496929 TGTGATCATT
* * *
19496939 ATGACCCAGCCATGTGCGGTGCAGGAGTGCACATGAGCTGATCATGACCCAGCTATGTGCGAGTA
1 ATGACCCAGCCATGT---GTGGAGGAGTACACATGAGCTGATGATGACCCAGCTATGTGCGAGTA
**
19497004 AAGAGTGCACATGAGCTGATG
63 GGGAGTGCACATGAGCTGATG
* *
19497025 ATGACCTAGCCATGTGTGTGGAGGAGTACACATGAGCTGATGATGACCCAGTTATGTGCGAGTAG
1 ATGACCCAGCCA--TGTGTGGAGGAGTACACATGAGCTGATGATGACCCAGCTATGTGCGAGTAG
*
19497090 GGAGTGCACATGAACTGATG
64 GGAGTGCACATGAGCTGATG
* ** * *
19497110 ATGACCCAGCCATGTGTGGAGGAGTACACATGAGTTGATGATGACCTTGCTATGTACGAATAGGG
1 ATGACCCAGCCATGTGTGGAGGAGTACACATGAGCTGATGATGACCCAGCTATGTGCGAGTAGGG
*
19497175 AGTGCACATGAGTTGATG
66 AGTGCACATGAGCTGATG
* *
19497193 ATGACCCAACCATGTGTGGAGGAGTGCACATGAGCTGATGATGACCCAGCTATGTGCGAGTAGGG
1 ATGACCCAGCCATGTGTGGAGGAGTACACATGAGCTGATGATGACCCAGCTATGTGCGAGTAGGG
*
19497258 AGTGCTCATGAGCTGATG
66 AGTGCACATGAGCTGATG
* *
19497276 ATGACCTAGCTATGTG
1 ATGACCCAGCCATGTG
19497292 CAATGTGGGA
Statistics
Matches: 236, Mismatches: 29, Indels: 7
0.87 0.11 0.03
Matches are distributed among these distances:
83 150 0.64
85 72 0.31
86 11 0.05
88 3 0.01
ACGTcount: A:0.27, C:0.18, G:0.32, T:0.23
Consensus pattern (83 bp):
ATGACCCAGCCATGTGTGGAGGAGTACACATGAGCTGATGATGACCCAGCTATGTGCGAGTAGGG
AGTGCACATGAGCTGATG
Found at i:19501334 original size:3 final size:3
Alignment explanation
Indices: 19501328--19501352 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
19501318 ACTTTTAATA
19501328 TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT T
19501353 TTTAAATGCA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:19517157 original size:21 final size:22
Alignment explanation
Indices: 19517133--19517179 Score: 69
Period size: 22 Copynumber: 2.2 Consensus size: 22
19517123 CTACCAAAAC
* *
19517133 AGAATG-TTTCTCGTTGCAGCG
1 AGAATGCTTTCTCGCTGCAGAG
19517154 AGAATGCTTTCTCGCTGCAGAG
1 AGAATGCTTTCTCGCTGCAGAG
19517176 AGAA
1 AGAA
19517180 GTAGAGCACC
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 6 0.26
22 17 0.74
ACGTcount: A:0.26, C:0.19, G:0.28, T:0.28
Consensus pattern (22 bp):
AGAATGCTTTCTCGCTGCAGAG
Found at i:19517419 original size:37 final size:36
Alignment explanation
Indices: 19517368--19517464 Score: 144
Period size: 34 Copynumber: 2.7 Consensus size: 36
19517358 ATACATCGTC
* *
19517368 ATCATGTGTTCACTCCTTACTCGCACACTCTATCATT
1 ATCATGTGTGCACTCC-TACTCGCACACTCCATCATT
19517405 ATCATGTGTGCACTCC--CTCGCACACTCCATCATT
1 ATCATGTGTGCACTCCTACTCGCACACTCCATCATT
19517439 ATCATGTGTGCACTCCCTACTCGCAC
1 ATCATGTGTGCACT-CCTACTCGCAC
19517465 CCTCAACATC
Statistics
Matches: 55, Mismatches: 2, Indels: 6
0.87 0.03 0.10
Matches are distributed among these distances:
34 31 0.56
35 2 0.04
37 22 0.40
ACGTcount: A:0.21, C:0.36, G:0.11, T:0.32
Consensus pattern (36 bp):
ATCATGTGTGCACTCCTACTCGCACACTCCATCATT
Found at i:19521464 original size:19 final size:20
Alignment explanation
Indices: 19521430--19521467 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
19521420 GAAGAAGACT
*
19521430 AGCTGCTGGAAAATTCAAGA
1 AGCTGCTAGAAAATTCAAGA
19521450 AGCTGCTAG-AAATTCAAG
1 AGCTGCTAGAAAATTCAAG
19521468 GTATTTATAG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.39, C:0.16, G:0.24, T:0.21
Consensus pattern (20 bp):
AGCTGCTAGAAAATTCAAGA
Found at i:19535044 original size:42 final size:42
Alignment explanation
Indices: 19534992--19535284 Score: 354
Period size: 42 Copynumber: 7.0 Consensus size: 42
19534982 CATCTCATAT
** * * *
19534992 GCAACGGCTTATACGTACTCCCACTCGCATATAGTCGGGTCA
1 GCAACGGCTTATGTGCACTCCCACTCACACATAGTCGGGTCA
*
19535034 GCAACGGCTTATGTGCACTCTCACTCACACATAGTCGGGTCA
1 GCAACGGCTTATGTGCACTCCCACTCACACATAGTCGGGTCA
* * * *
19535076 ACAACGGCTTATGTGCACTCCTACTCGCACATAGCCGGGTCA
1 GCAACGGCTTATGTGCACTCCCACTCACACATAGTCGGGTCA
* * **
19535118 GCAATGGCTTATGTGCACTCCTACTTGCACATAG-CTGGGTCA
1 GCAACGGCTTATGTGCACTCCCACTCACACATAGTC-GGGTCA
*
19535160 GCAACGGCTTATGTGCACTCCCACTCACACATAGCCGGGTCA
1 GCAACGGCTTATGTGCACTCCCACTCACACATAGTCGGGTCA
* * *
19535202 GCAACGACTTATGTGCACTCCCACTCACACATAGTCGAGTTA
1 GCAACGGCTTATGTGCACTCCCACTCACACATAGTCGGGTCA
* * ** * *
19535244 GCAATGACTTATGTGCACTCTTACTCGCACATAGCCGGGTC
1 GCAACGGCTTATGTGCACTCCCACTCACACATAGTCGGGTC
19535285 CACATCAACA
Statistics
Matches: 220, Mismatches: 29, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
41 1 0.00
42 218 0.99
43 1 0.00
ACGTcount: A:0.24, C:0.31, G:0.21, T:0.24
Consensus pattern (42 bp):
GCAACGGCTTATGTGCACTCCCACTCACACATAGTCGGGTCA
Found at i:19535222 original size:126 final size:126
Alignment explanation
Indices: 19535008--19535284 Score: 410
Period size: 126 Copynumber: 2.2 Consensus size: 126
19534998 GCTTATACGT
* * * * *
19535008 ACTCCCACTCGCATATAGTCGGGTCAGCAACGGCTTATGTGCACTCTCACTCACACATAGTCGGG
1 ACTCCTACTCGCACATAGCCGGGTCAGCAACGGCTTATGTGCACTCCCACTCACACATAGCCGGG
* * * * *
19535073 TCAACAACGGCTTATGTGCACTCCTACTCGCACATAGCCGGGTCAGCAATGGCTTATGTGC
66 TCAACAACGACTTATGTGCACTCCCACTCACACATAGCCGAGTCAGCAATGACTTATGTGC
* *
19535134 ACTCCTACTTGCACATAGCTGGGTCAGCAACGGCTTATGTGCACTCCCACTCACACATAGCCGGG
1 ACTCCTACTCGCACATAGCCGGGTCAGCAACGGCTTATGTGCACTCCCACTCACACATAGCCGGG
* * *
19535199 TCAGCAACGACTTATGTGCACTCCCACTCACACATAGTCGAGTTAGCAATGACTTATGTGC
66 TCAACAACGACTTATGTGCACTCCCACTCACACATAGCCGAGTCAGCAATGACTTATGTGC
*
19535260 ACTCTTACTCGCACATAGCCGGGTC
1 ACTCCTACTCGCACATAGCCGGGTC
19535285 CACATCAACA
Statistics
Matches: 133, Mismatches: 18, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
126 133 1.00
ACGTcount: A:0.24, C:0.31, G:0.21, T:0.24
Consensus pattern (126 bp):
ACTCCTACTCGCACATAGCCGGGTCAGCAACGGCTTATGTGCACTCCCACTCACACATAGCCGGG
TCAACAACGACTTATGTGCACTCCCACTCACACATAGCCGAGTCAGCAATGACTTATGTGC
Found at i:19537840 original size:35 final size:35
Alignment explanation
Indices: 19537657--19537832 Score: 221
Period size: 35 Copynumber: 5.0 Consensus size: 35
19537647 CAGTCAGCCA
* ***
19537657 ATGTGCACTCCCTACACGCACAAGGCAATATCATC
1 ATGTGCACTCCCTACTCGCACACTTCAATATCATC
* * *
19537692 ATGTGCACTCCCTACTCACACATTTCTATATCATC
1 ATGTGCACTCCCTACTCGCACACTTCAATATCATC
* *
19537727 ATGTGCACTCCCTATTTGCACACATT-AATATCATC
1 ATGTGCACTCCCTACTCGCACAC-TTCAATATCATC
*
19537762 ATGTGCATTCCCTACTCGCACACTTCAATATCATC
1 ATGTGCACTCCCTACTCGCACACTTCAATATCATC
*
19537797 -TGGTGCACTTCCTACTCGCACACTTCAATATCATC
1 AT-GTGCACTCCCTACTCGCACACTTCAATATCATC
19537832 A
1 A
19537833 CACGCACTCC
Statistics
Matches: 121, Mismatches: 16, Indels: 7
0.84 0.11 0.05
Matches are distributed among these distances:
34 3 0.02
35 116 0.96
36 2 0.02
ACGTcount: A:0.27, C:0.33, G:0.10, T:0.30
Consensus pattern (35 bp):
ATGTGCACTCCCTACTCGCACACTTCAATATCATC
Found at i:19541962 original size:36 final size:35
Alignment explanation
Indices: 19541901--19541982 Score: 130
Period size: 36 Copynumber: 2.3 Consensus size: 35
19541891 ATGTTGTGTG
* *
19541901 ATGATGTTGA-AGTGTGCGAGTAGGGAGTGCACAC
1 ATGATGATGATAGAGTGCGAGTAGGGAGTGCACAC
19541935 ATGATGATGATAGAGTGCGCAGTAGGGAGTGCACAC
1 ATGATGATGATAGAGTGCG-AGTAGGGAGTGCACAC
19541971 ATGATGATGATA
1 ATGATGATGATA
19541983 TTGCATTGAG
Statistics
Matches: 44, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
34 9 0.20
35 7 0.16
36 28 0.64
ACGTcount: A:0.30, C:0.11, G:0.35, T:0.23
Consensus pattern (35 bp):
ATGATGATGATAGAGTGCGAGTAGGGAGTGCACAC
Found at i:19547202 original size:35 final size:35
Alignment explanation
Indices: 19547137--19547311 Score: 194
Period size: 35 Copynumber: 5.0 Consensus size: 35
19547127 CACTCAGCCA
* ***
19547137 ATGTGCACT-CCTACACGCACAAGGCAATATCATC
1 ATGTGCACTCCCTACTCGCACACTTCAATATCATC
* * *
19547171 ATGTGCACTCCCTACTCGTACATTTCTATATCATC
1 ATGTGCACTCCCTACTCGCACACTTCAATATCATC
* *
19547206 GTGTGCACTCCCTACTCGCACACATT-AATATCATT
1 ATGTGCACTCCCTACTCGCACAC-TTCAATATCATC
* * *
19547241 GTGTGCATTCCCTACTCGCACACTTCAATATAATC
1 ATGTGCACTCCCTACTCGCACACTTCAATATCATC
*
19547276 -TAGTGCACTCCCTACTAGCACACTTCAATATCATC
1 AT-GTGCACTCCCTACTCGCACACTTCAATATCATC
19547311 A
1 A
19547312 CACACATTCC
Statistics
Matches: 119, Mismatches: 17, Indels: 8
0.83 0.12 0.06
Matches are distributed among these distances:
34 12 0.10
35 105 0.88
36 2 0.02
ACGTcount: A:0.27, C:0.32, G:0.11, T:0.30
Consensus pattern (35 bp):
ATGTGCACTCCCTACTCGCACACTTCAATATCATC
Found at i:19549394 original size:2 final size:2
Alignment explanation
Indices: 19549387--19549411 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
19549377 CATGTATAAT
19549387 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
19549412 TGCACTCTCA
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:19549877 original size:35 final size:35
Alignment explanation
Indices: 19549802--19549886 Score: 89
Period size: 35 Copynumber: 2.4 Consensus size: 35
19549792 AGCATTGAGT
* * * * *
19549802 GGAGAACAGATCACACGCATGCCGAAGCAATGGGT
1 GGAGAACAGATCATACACATGCCAAAGCAATAGGC
* *
19549837 TGAGAACAGATCATGCACATGCCAAAGCAATAGGC
1 GGAGAACAGATCATACACATGCCAAAGCAATAGGC
*
19549872 GGAGAATCAAATCAT
1 GGAGAA-CAGATCAT
19549887 CAATCGGAGT
Statistics
Matches: 40, Mismatches: 9, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
35 33 0.82
36 7 0.17
ACGTcount: A:0.39, C:0.21, G:0.26, T:0.14
Consensus pattern (35 bp):
GGAGAACAGATCATACACATGCCAAAGCAATAGGC
Found at i:19551094 original size:33 final size:33
Alignment explanation
Indices: 19551052--19551126 Score: 150
Period size: 33 Copynumber: 2.3 Consensus size: 33
19551042 TGATGTATCA
19551052 ATACATTTGGCAATGTATCGATACATTCCATCG
1 ATACATTTGGCAATGTATCGATACATTCCATCG
19551085 ATACATTTGGCAATGTATCGATACATTCCATCG
1 ATACATTTGGCAATGTATCGATACATTCCATCG
19551118 ATACATTTG
1 ATACATTTG
19551127 AAGCAGAAAG
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 42 1.00
ACGTcount: A:0.31, C:0.20, G:0.15, T:0.35
Consensus pattern (33 bp):
ATACATTTGGCAATGTATCGATACATTCCATCG
Found at i:19551106 original size:20 final size:20
Alignment explanation
Indices: 19551044--19551111 Score: 69
Period size: 20 Copynumber: 3.8 Consensus size: 20
19551034 TCTGTCTGTG
*
19551044 ATGTATCAATACATTTGGCA
1 ATGTATCGATACATTTGGCA
19551064 ATGTATCGATACA-TT--C-
1 ATGTATCGATACATTTGGCA
*
19551080 ---CATCGATACATTTGGCA
1 ATGTATCGATACATTTGGCA
19551097 ATGTATCGATACATT
1 ATGTATCGATACATT
19551112 CCATCGATAC
Statistics
Matches: 38, Mismatches: 3, Indels: 14
0.69 0.05 0.25
Matches are distributed among these distances:
13 9 0.24
14 2 0.05
16 1 0.03
17 1 0.03
19 2 0.05
20 23 0.61
ACGTcount: A:0.32, C:0.18, G:0.15, T:0.35
Consensus pattern (20 bp):
ATGTATCGATACATTTGGCA
Found at i:19552547 original size:19 final size:19
Alignment explanation
Indices: 19552523--19552560 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
19552513 CCATTTGACT
19552523 TATTGGAGTATGATTTGAG
1 TATTGGAGTATGATTTGAG
19552542 TATTGGAGTATGATTTGAG
1 TATTGGAGTATGATTTGAG
19552561 GTTTAGAAGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.26, C:0.00, G:0.32, T:0.42
Consensus pattern (19 bp):
TATTGGAGTATGATTTGAG
Done.