Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr12 ID=Chr12-JGI_221_v2.0
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: 35429946
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 509281 characters in sequence are not A, C, G, or T
File 47 of 120
Found at i:12753700 original size:23 final size:23
Alignment explanation
Indices: 12753667--12753774 Score: 108
Period size: 23 Copynumber: 4.7 Consensus size: 23
12753657 AATTTAAAGA
*
12753667 AAACACTTCAATTTCCAACATTT
1 AAACACTTCAATTTACAACATTT
* * * **
12753690 AAACACCTCAAATTGCAACACCT
1 AAACACTTCAATTTACAACATTT
*
12753713 AAACACTTCAATTTACAAGATTT
1 AAACACTTCAATTTACAACATTT
* * * *
12753736 GAACACCTCCATTTACAACAATT
1 AAACACTTCAATTTACAACATTT
12753759 AAACACTTCAAATTTA
1 AAACACTTC-AATTTA
12753775 TAGCCTTTAA
Statistics
Matches: 65, Mismatches: 19, Indels: 1
0.76 0.22 0.01
Matches are distributed among these distances:
23 60 0.92
24 5 0.08
ACGTcount: A:0.43, C:0.26, G:0.03, T:0.29
Consensus pattern (23 bp):
AAACACTTCAATTTACAACATTT
Found at i:12753720 original size:46 final size:46
Alignment explanation
Indices: 12753667--12753774 Score: 135
Period size: 46 Copynumber: 2.3 Consensus size: 46
12753657 AATTTAAAGA
* * *
12753667 AAACACTTCAATTTCCAACATTTAAACACCTCAAATTGCAACACCT
1 AAACACTTCAATTTACAACATTTAAACACCTCAAATTACAACAACT
* * * * *
12753713 AAACACTTCAATTTACAAGATTTGAACACCTCCATTTACAACAATT
1 AAACACTTCAATTTACAACATTTAAACACCTCAAATTACAACAACT
12753759 AAACACTTCAAATTTA
1 AAACACTTC-AATTTA
12753775 TAGCCTTTAA
Statistics
Matches: 53, Mismatches: 8, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
46 47 0.89
47 6 0.11
ACGTcount: A:0.43, C:0.26, G:0.03, T:0.29
Consensus pattern (46 bp):
AAACACTTCAATTTACAACATTTAAACACCTCAAATTACAACAACT
Found at i:12757190 original size:66 final size:66
Alignment explanation
Indices: 12757084--12757243 Score: 248
Period size: 66 Copynumber: 2.4 Consensus size: 66
12757074 GAAATGGCCT
* *
12757084 CACACGCCCGTGTGTTAGGCCGTGTGAAAACTGGAGGGTATACTGACTTGTGCAACATGGCCAAG
1 CACACGCCCGTGTGCTAGGCCGTGTGAAAACTGGAGGGTATACTGACTTGTGCAACACGGCCAAG
12757149 A
66 A
* * *
12757150 CACACGCCCATATGCTAGGCCGTGTGAAAACTGGAGGGTATACTGACTTGTGCCACACGGCCAAG
1 CACACGCCCGTGTGCTAGGCCGTGTGAAAACTGGAGGGTATACTGACTTGTGCAACACGGCCAAG
*
12757215 C
66 A
* *
12757216 CACACGCCTGTGTGCTAGGCCATGTGAA
1 CACACGCCCGTGTGCTAGGCCGTGTGAA
12757244 GCTACTGACT
Statistics
Matches: 84, Mismatches: 10, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
66 84 1.00
ACGTcount: A:0.25, C:0.26, G:0.29, T:0.20
Consensus pattern (66 bp):
CACACGCCCGTGTGCTAGGCCGTGTGAAAACTGGAGGGTATACTGACTTGTGCAACACGGCCAAG
A
Found at i:12758382 original size:25 final size:25
Alignment explanation
Indices: 12758319--12758416 Score: 94
Period size: 25 Copynumber: 4.0 Consensus size: 25
12758309 GTATATGTAT
12758319 GCTCATACGAGC-G-ATAAACGGTAA
1 GCTCATACGAGCTGAAT-AACGGTAA
* * *
12758343 GCTCCTCCGAGCTGAATAACGATAA
1 GCTCATACGAGCTGAATAACGGTAA
* * *
12758368 GCTCATACGATCTGAGTATCGGTAA
1 GCTCATACGAGCTGAATAACGGTAA
* *
12758393 GCTCATAAGAGCTGAA-ATCGGTAA
1 GCTCATACGAGCTGAATAACGGTAA
12758417 CCCTAATGAC
Statistics
Matches: 60, Mismatches: 12, Indels: 4
0.79 0.16 0.05
Matches are distributed among these distances:
24 18 0.30
25 40 0.67
26 2 0.03
ACGTcount: A:0.34, C:0.21, G:0.23, T:0.21
Consensus pattern (25 bp):
GCTCATACGAGCTGAATAACGGTAA
Found at i:12759909 original size:53 final size:53
Alignment explanation
Indices: 12759840--12760115 Score: 201
Period size: 52 Copynumber: 5.1 Consensus size: 53
12759830 TAAAAAATTA
* *
12759840 GGGTGCTGGGACACTGATGGTTGACACTCCTTTATCTGA-TAGAAAT-TTTTTT
1 GGGTGCTGGGACACTGATGGTCGACACCCCTTTATCTGATTA-AAATATTTTTT
* ** *
12759892 AGGGTGCTGGGACACTGATAGTCGACACCCCTTTTAT-TAGATTTTAAAA-AAATTTG
1 -GGGTGCTGGGACACTGATGGTCGACACCCC-TTTATCT-GA--TTAAAATATTTTTT
* * *
12759948 GGGTGCT-GCACACTGATGGCCGACGCCCCCTTTATCTGATTAAAAAAAATATTTTTT
1 GGGTGCTGGGACACTGATGGTCGAC-ACCCCTTTATCTGATT----AAAATATTTTTT
* * * * * *
12760005 GGGTGTTGGGATACTGATGGTTGACATCCCTTTATTTGA-TAAAATGTTTTTT
1 GGGTGCTGGGACACTGATGGTCGACACCCCTTTATCTGATTAAAATATTTTTT
* * **
12760057 GGGTGCTGGGACATTAAT-GTCCGACACCCCTTTTATCTGA-TAATGT-TTTTTT
1 GGGTGCTGGGACACTGATGGT-CGACACCCC-TTTATCTGATTAAAATATTTTTT
12760109 GGGTGCT
1 GGGTGCT
12760116 AAGACATTGA
Statistics
Matches: 176, Mismatches: 31, Indels: 33
0.73 0.13 0.14
Matches are distributed among these distances:
51 2 0.01
52 47 0.27
53 40 0.23
54 28 0.16
55 12 0.07
56 11 0.06
57 23 0.13
58 13 0.07
ACGTcount: A:0.23, C:0.17, G:0.23, T:0.37
Consensus pattern (53 bp):
GGGTGCTGGGACACTGATGGTCGACACCCCTTTATCTGATTAAAATATTTTTT
Found at i:12759995 original size:54 final size:56
Alignment explanation
Indices: 12759893--12760001 Score: 125
Period size: 54 Copynumber: 2.0 Consensus size: 56
12759883 AATTTTTTTA
* * * **
12759893 GGGTGCTGGGACACTGATAGTCGACACCCCTTTTATTAGATTTTAAAAAA-ATTTG
1 GGGTGCTGGCACACTGATAGCCGACACCCCCTTTATTAGATTAAAAAAAATATTTG
* *
12759948 GGGTGCT-GCACACTGATGGCCGACGCCCCCTTTATCT-GATTAAAAAAAATATTT
1 GGGTGCTGGCACACTGATAGCCGACACCCCCTTTAT-TAGATTAAAAAAAATATTT
12760002 TTTGGGTGTT
Statistics
Matches: 45, Mismatches: 7, Indels: 4
0.80 0.12 0.07
Matches are distributed among these distances:
54 33 0.73
55 12 0.27
ACGTcount: A:0.28, C:0.20, G:0.21, T:0.30
Consensus pattern (56 bp):
GGGTGCTGGCACACTGATAGCCGACACCCCCTTTATTAGATTAAAAAAAATATTTG
Found at i:12766776 original size:13 final size:13
Alignment explanation
Indices: 12766760--12766784 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
12766750 TTACCTTTTA
12766760 ATTTTCTTAGTTG
1 ATTTTCTTAGTTG
12766773 ATTTTCTTAGTT
1 ATTTTCTTAGTT
12766785 AAAATCTAGT
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:0.16, C:0.08, G:0.12, T:0.64
Consensus pattern (13 bp):
ATTTTCTTAGTTG
Found at i:12773997 original size:30 final size:29
Alignment explanation
Indices: 12773948--12774006 Score: 91
Period size: 30 Copynumber: 2.0 Consensus size: 29
12773938 AATTATTTAA
* *
12773948 AAATTTTGGTTGTTCTTTTTGTAAATATT
1 AAATTTTAGATGTTCTTTTTGTAAATATT
12773977 AAATTTTAGATGTCTCTTTTTGTAAATATT
1 AAATTTTAGATGT-TCTTTTTGTAAATATT
12774007 TTCAAAGGTA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
29 11 0.41
30 16 0.59
ACGTcount: A:0.27, C:0.05, G:0.12, T:0.56
Consensus pattern (29 bp):
AAATTTTAGATGTTCTTTTTGTAAATATT
Found at i:12774838 original size:25 final size:26
Alignment explanation
Indices: 12774795--12774848 Score: 69
Period size: 25 Copynumber: 2.1 Consensus size: 26
12774785 TTCTCCTAAA
12774795 TTTCAATTTTATTTGATTATTTAAT-T
1 TTTCAATTTTATTTGATTA-TTAATAT
12774821 TTTCAA-TTTA-TTGAATTATTAATAT
1 TTTCAATTTTATTTG-ATTATTAATAT
12774846 TTT
1 TTT
12774849 ATGCAAATTA
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
24 8 0.31
25 12 0.46
26 6 0.23
ACGTcount: A:0.30, C:0.04, G:0.04, T:0.63
Consensus pattern (26 bp):
TTTCAATTTTATTTGATTATTAATAT
Found at i:12775748 original size:3 final size:3
Alignment explanation
Indices: 12775740--12775813 Score: 148
Period size: 3 Copynumber: 24.7 Consensus size: 3
12775730 TGAGGATCGC
12775740 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
12775788 GAA GAA GAA GAA GAA GAA GAA GAA GA
1 GAA GAA GAA GAA GAA GAA GAA GAA GA
12775814 TCCTATAGAG
Statistics
Matches: 71, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 71 1.00
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:12779136 original size:22 final size:21
Alignment explanation
Indices: 12779108--12779174 Score: 64
Period size: 22 Copynumber: 3.1 Consensus size: 21
12779098 CGCTACCAGT
12779108 TAACAGAACGGCTAAAAGCCA
1 TAACAGAACGGCTAAAAGCCA
* *
12779129 TAAGCAGAAAGGC-AGAAAGCCT
1 TAA-CAGAACGGCTA-AAAGCCA
* *
12779151 TGAACAGAACGGCTACAAGTCA
1 T-AACAGAACGGCTAAAAGCCA
12779173 TA
1 TA
12779175 CACTTCCTCC
Statistics
Matches: 36, Mismatches: 6, Indels: 8
0.72 0.12 0.16
Matches are distributed among these distances:
21 5 0.14
22 28 0.78
23 3 0.08
ACGTcount: A:0.45, C:0.21, G:0.22, T:0.12
Consensus pattern (21 bp):
TAACAGAACGGCTAAAAGCCA
Found at i:12779400 original size:27 final size:26
Alignment explanation
Indices: 12779344--12779400 Score: 60
Period size: 27 Copynumber: 2.2 Consensus size: 26
12779334 GAAAATGGTA
* * *
12779344 ATTTTACCCCTAGGGGTATTTTGGTT
1 ATTTTACCCCTAGGGGTAATTAGGTC
* *
12779370 ATTTTACCCTTCGAGGGTAATTAGGTC
1 ATTTTACCCCTAG-GGGTAATTAGGTC
12779397 ATTT
1 ATTT
12779401 AACAACCTTT
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
26 11 0.44
27 14 0.56
ACGTcount: A:0.19, C:0.16, G:0.21, T:0.44
Consensus pattern (26 bp):
ATTTTACCCCTAGGGGTAATTAGGTC
Found at i:12793019 original size:27 final size:27
Alignment explanation
Indices: 12792979--12793049 Score: 67
Period size: 27 Copynumber: 2.7 Consensus size: 27
12792969 GGCACAGGGT
* *
12792979 GCATAACATGACATTTTTTCA-ACTTC
1 GCATATCATTACATTTTTTCACACTTC
**
12793005 -CATATACCATTACATACTTTCACACTTC
1 GCATAT--CATTACATTTTTTCACACTTC
12793033 GCATATCATT-CATTTTT
1 GCATATCATTACATTTTT
12793050 ACAATTGACA
Statistics
Matches: 35, Mismatches: 6, Indels: 8
0.71 0.12 0.16
Matches are distributed among these distances:
25 4 0.11
26 5 0.14
27 16 0.46
28 5 0.14
29 5 0.14
ACGTcount: A:0.30, C:0.25, G:0.04, T:0.41
Consensus pattern (27 bp):
GCATATCATTACATTTTTTCACACTTC
Found at i:12793310 original size:5 final size:5
Alignment explanation
Indices: 12793302--12793328 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
12793292 CAAAACAAAA
12793302 CATTT CATTT CATTT CATTT CATTT CA
1 CATTT CATTT CATTT CATTT CATTT CA
12793329 AAAAAATTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.22, C:0.22, G:0.00, T:0.56
Consensus pattern (5 bp):
CATTT
Found at i:12793951 original size:60 final size:61
Alignment explanation
Indices: 12793839--12793959 Score: 149
Period size: 60 Copynumber: 2.0 Consensus size: 61
12793829 ACATCATAAA
* * * * *
12793839 TGCATAACAGAGGCACCAAAGTGCAGACAGGGGCATGAATATGCAATCAGAGGCACCGAAG
1 TGCATAACAGAGGCACCAAAGTGCAAACAGAGACACGAAGATGCAATCAGAGGCACCGAAG
*
12793900 TGCA-AACAGAGGCACCAAAGTGCAAACAGAGACACCGAAGA-GCAAAT-AGAGGCATCGAAG
1 TGCATAACAGAGGCACCAAAGTGCAAACAGAGACA-CGAAGATGC-AATCAGAGGCACCGAAG
12793960 CACACATTCT
Statistics
Matches: 52, Mismatches: 6, Indels: 5
0.83 0.10 0.08
Matches are distributed among these distances:
60 41 0.79
61 11 0.21
ACGTcount: A:0.41, C:0.21, G:0.28, T:0.09
Consensus pattern (61 bp):
TGCATAACAGAGGCACCAAAGTGCAAACAGAGACACGAAGATGCAATCAGAGGCACCGAAG
Found at i:12793958 original size:20 final size:20
Alignment explanation
Indices: 12793839--12793959 Score: 118
Period size: 20 Copynumber: 6.0 Consensus size: 20
12793829 ACATCATAAA
*
12793839 TGCATAACAGAGGCACCAAAG
1 TGCA-AACAGAGGCACCGAAG
* * * *
12793860 TGCAGACAGGGGCA-TGAATA
1 TGCAAACAGAGGCACCGAA-G
*
12793880 TGCAATCAGAGGCACCGAAG
1 TGCAAACAGAGGCACCGAAG
*
12793900 TGCAAACAGAGGCACCAAAG
1 TGCAAACAGAGGCACCGAAG
*
12793920 TGCAAACAGAGACACCGAAG
1 TGCAAACAGAGGCACCGAAG
* * *
12793940 AGCAAATAGAGGCATCGAAG
1 TGCAAACAGAGGCACCGAAG
12793960 CACACATTCT
Statistics
Matches: 80, Mismatches: 18, Indels: 5
0.78 0.17 0.05
Matches are distributed among these distances:
19 2 0.03
20 71 0.89
21 7 0.09
ACGTcount: A:0.41, C:0.21, G:0.28, T:0.09
Consensus pattern (20 bp):
TGCAAACAGAGGCACCGAAG
Found at i:12801283 original size:51 final size:52
Alignment explanation
Indices: 12801200--12801314 Score: 144
Period size: 51 Copynumber: 2.2 Consensus size: 52
12801190 TTAGATATGG
*
12801200 TGAAAATGAAAAAATGGGAAACATTTGGAAATGATTATGGTTTTCTCCT-AAA
1 TGAAAATGAAAAAATGGGAAACATTTGGAAATGAATATGGTTTTCT-CTAAAA
* * * * * *
12801252 TGAAAATGAAGAGAT-GGAATCATTTGTAAATGAATGTGGTTTTCTTTAAAA
1 TGAAAATGAAAAAATGGGAAACATTTGGAAATGAATATGGTTTTCTCTAAAA
12801303 TGAAAATGAAAA
1 TGAAAATGAAAA
12801315 TGAATTGGAA
Statistics
Matches: 54, Mismatches: 8, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
50 1 0.02
51 40 0.74
52 13 0.24
ACGTcount: A:0.43, C:0.05, G:0.20, T:0.31
Consensus pattern (52 bp):
TGAAAATGAAAAAATGGGAAACATTTGGAAATGAATATGGTTTTCTCTAAAA
Found at i:12805733 original size:20 final size:20
Alignment explanation
Indices: 12805705--12805742 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
12805695 TAGTTAACTT
*
12805705 TAATTTAATCATCATTAAAC
1 TAATCTAATCATCATTAAAC
12805725 TAATCTAATCATCATTAA
1 TAATCTAATCATCATTAA
12805743 GCCAAACTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.45, C:0.16, G:0.00, T:0.39
Consensus pattern (20 bp):
TAATCTAATCATCATTAAAC
Found at i:12805752 original size:20 final size:20
Alignment explanation
Indices: 12805710--12805752 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
12805700 AACTTTAATT
* *
12805710 TAATCATCATTAAACTAATC
1 TAATCATCATTAAACCAAAC
*
12805730 TAATCATCATTAAGCCAAAC
1 TAATCATCATTAAACCAAAC
12805750 TAA
1 TAA
12805753 GTGGATAATG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.47, C:0.21, G:0.02, T:0.30
Consensus pattern (20 bp):
TAATCATCATTAAACCAAAC
Found at i:12822758 original size:28 final size:28
Alignment explanation
Indices: 12822727--12822784 Score: 107
Period size: 28 Copynumber: 2.1 Consensus size: 28
12822717 ATTTTTAGGC
*
12822727 TTAATTTTTATTATATATTAACTCGATA
1 TTAATTTTTATTATATATTAACTCAATA
12822755 TTAATTTTTATTATATATTAACTCAATA
1 TTAATTTTTATTATATATTAACTCAATA
12822783 TT
1 TT
12822785 GTATTTATTA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.36, C:0.07, G:0.02, T:0.55
Consensus pattern (28 bp):
TTAATTTTTATTATATATTAACTCAATA
Found at i:12829049 original size:7 final size:7
Alignment explanation
Indices: 12829037--12829080 Score: 52
Period size: 7 Copynumber: 6.3 Consensus size: 7
12829027 TTGTATGAAT
12829037 TTTAGGA
1 TTTAGGA
*
12829044 TTTAGGG
1 TTTAGGA
*
12829051 TTTAGGG
1 TTTAGGA
*
12829058 TTTAAGA
1 TTTAGGA
*
12829065 TTTAAGA
1 TTTAGGA
12829072 TTTAGGA
1 TTTAGGA
12829079 TT
1 TT
12829081 GTATAGGGTT
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
7 33 1.00
ACGTcount: A:0.27, C:0.00, G:0.27, T:0.45
Consensus pattern (7 bp):
TTTAGGA
Found at i:12829113 original size:21 final size:19
Alignment explanation
Indices: 12829098--12829153 Score: 78
Period size: 21 Copynumber: 2.8 Consensus size: 19
12829088 GTTTTGAGTC
12829098 TTTTTTATATATTTTTAAGT
1 TTTTTTATATATTTTT-AGT
12829118 GTTTTTTATATATTCTTTAGT
1 -TTTTTTATATATT-TTTAGT
12829139 TTTTTTATA-ATTTTT
1 TTTTTTATATATTTTT
12829154 TGAGATGTAA
Statistics
Matches: 34, Mismatches: 0, Indels: 5
0.87 0.00 0.13
Matches are distributed among these distances:
18 3 0.09
19 3 0.09
20 9 0.26
21 16 0.47
22 3 0.09
ACGTcount: A:0.21, C:0.02, G:0.05, T:0.71
Consensus pattern (19 bp):
TTTTTTATATATTTTTAGT
Found at i:12829127 original size:19 final size:18
Alignment explanation
Indices: 12829098--12829153 Score: 58
Period size: 20 Copynumber: 2.8 Consensus size: 18
12829088 GTTTTGAGTC
12829098 TTTTTTATATATTTTTAAG
1 TTTTTT-TATATTTTTAAG
*
12829117 TGTTTTTTATATATTCTTTAG
1 T-TTTTTTATAT-TT-TTAAG
12829138 TTTTTTTATAATTTTT
1 TTTTTTTAT-ATTTTT
12829154 TGAGATGTAA
Statistics
Matches: 32, Mismatches: 1, Indels: 8
0.78 0.02 0.20
Matches are distributed among these distances:
19 8 0.25
20 17 0.53
21 7 0.22
ACGTcount: A:0.21, C:0.02, G:0.05, T:0.71
Consensus pattern (18 bp):
TTTTTTTATATTTTTAAG
Found at i:12833048 original size:13 final size:15
Alignment explanation
Indices: 12833015--12833047 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
12833005 ATTCATGTCT
12833015 TTTTTAAAATATTTA
1 TTTTTAAAATATTTA
*
12833030 TTTTTAATAT-TTTA
1 TTTTTAAAATATTTA
12833044 TTTT
1 TTTT
12833048 ATGTAATAGG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 8 0.47
15 9 0.53
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (15 bp):
TTTTTAAAATATTTA
Found at i:12833944 original size:13 final size:13
Alignment explanation
Indices: 12833926--12833950 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
12833916 CATTCTTTCT
12833926 TCCCTCTAAACGA
1 TCCCTCTAAACGA
12833939 TCCCTCTAAACG
1 TCCCTCTAAACG
12833951 CTTCCTTCCC
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:0.28, C:0.40, G:0.08, T:0.24
Consensus pattern (13 bp):
TCCCTCTAAACGA
Found at i:12834841 original size:14 final size:14
Alignment explanation
Indices: 12834805--12834843 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
12834795 GCTTAATAAA
12834805 TTATGACATATGCT
1 TTATGACATATGCT
* * *
12834819 TAATAACATATGGT
1 TTATGACATATGCT
12834833 TTATGACATAT
1 TTATGACATAT
12834844 AAACTAATGA
Statistics
Matches: 20, Mismatches: 5, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.36, C:0.10, G:0.13, T:0.41
Consensus pattern (14 bp):
TTATGACATATGCT
Found at i:12835075 original size:21 final size:23
Alignment explanation
Indices: 12835032--12835076 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
12835022 AATAAAGTAG
**
12835032 ATTATATATATATTTTTTATAGT
1 ATTATATATATATGATTTATAGT
12835055 ATTATATAT-TATGATTT-TAGT
1 ATTATATATATATGATTTATAGT
12835076 A
1 A
12835077 AATTCATATA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 5 0.25
22 6 0.30
23 9 0.45
ACGTcount: A:0.36, C:0.00, G:0.07, T:0.58
Consensus pattern (23 bp):
ATTATATATATATGATTTATAGT
Found at i:12835127 original size:38 final size:36
Alignment explanation
Indices: 12835059--12835132 Score: 96
Period size: 37 Copynumber: 2.0 Consensus size: 36
12835049 TATAGTATTA
*
12835059 TATATTATGATTTTAGTAAATTCATATAATAATAAT
1 TATATTAAGATTTTAGTAAATTCATATAATAATAAT
*
12835095 TATATTAAGAATTTTATTAAATT-ATATTTAATAATAAT
1 TATATTAAG-ATTTTAGTAAATTCATA--TAATAATAAT
12835133 GTTAAAATGT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
36 11 0.33
37 12 0.36
38 10 0.30
ACGTcount: A:0.46, C:0.01, G:0.04, T:0.49
Consensus pattern (36 bp):
TATATTAAGATTTTAGTAAATTCATATAATAATAAT
Found at i:12836194 original size:15 final size:17
Alignment explanation
Indices: 12836173--12836213 Score: 59
Period size: 15 Copynumber: 2.5 Consensus size: 17
12836163 TAATCTTTTA
12836173 AAAATTATAAAAAT-AT
1 AAAATTATAAAAATAAT
*
12836189 -AAATTATTAAAATAAT
1 AAAATTATAAAAATAAT
12836205 AAAATTATA
1 AAAATTATA
12836214 TTTTTAATAT
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
15 12 0.57
16 2 0.10
17 7 0.33
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (17 bp):
AAAATTATAAAAATAAT
Found at i:12836235 original size:22 final size:22
Alignment explanation
Indices: 12836179--12836235 Score: 55
Period size: 22 Copynumber: 2.6 Consensus size: 22
12836169 TTTAAAAATT
*
12836179 ATAA-AAATATAAATTATTAAA
1 ATAATAAATATATATTATTAAA
* *
12836200 ATAATAAA-ATTATATTTTTAAT
1 ATAATAAATA-TATATTATTAAA
*
12836222 ATCATAAATATATA
1 ATAATAAATATATA
12836236 ATTTAATTTC
Statistics
Matches: 29, Mismatches: 4, Indels: 5
0.76 0.11 0.13
Matches are distributed among these distances:
21 5 0.17
22 23 0.79
23 1 0.03
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (22 bp):
ATAATAAATATATATTATTAAA
Found at i:12839100 original size:22 final size:22
Alignment explanation
Indices: 12839054--12839100 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 22
12839044 GTAATATAGA
* *
12839054 TTTAATAAATGTAGAAAAATCT
1 TTTAATAAATGAAAAAAAATCT
12839076 TTTAATAAATGAAAAGAAAAT-T
1 TTTAATAAATGAAAA-AAAATCT
12839098 TTT
1 TTT
12839101 GAACTGTTAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
22 17 0.77
23 5 0.23
ACGTcount: A:0.51, C:0.02, G:0.09, T:0.38
Consensus pattern (22 bp):
TTTAATAAATGAAAAAAAATCT
Found at i:12842431 original size:16 final size:16
Alignment explanation
Indices: 12842401--12842446 Score: 51
Period size: 16 Copynumber: 2.9 Consensus size: 16
12842391 TTAACATTAT
*
12842401 TATA-AAAACTAAAAA
1 TATAGAAAATTAAAAA
12842416 TA-AGAAGAATTAAAAA
1 TATAGAA-AATTAAAAA
*
12842432 TATATAAAATTAAAA
1 TATAGAAAATTAAAA
12842447 TTAAAAAATC
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
14 1 0.04
15 4 0.15
16 18 0.69
17 3 0.12
ACGTcount: A:0.70, C:0.02, G:0.04, T:0.24
Consensus pattern (16 bp):
TATAGAAAATTAAAAA
Found at i:12843836 original size:19 final size:19
Alignment explanation
Indices: 12843812--12843922 Score: 177
Period size: 19 Copynumber: 5.8 Consensus size: 19
12843802 AATTTTTGAG
12843812 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
* *
12843831 GATATGCAATCCTAGATTT
1 GATATGCAATCTTAGATAT
12843850 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
12843869 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
**
12843888 GATATATAATCTTAGATAT
1 GATATGCAATCTTAGATAT
*
12843907 GACATGCAATCTTAGA
1 GATATGCAATCTTAGA
12843923 ATATATGATT
Statistics
Matches: 83, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 83 1.00
ACGTcount: A:0.37, C:0.12, G:0.15, T:0.36
Consensus pattern (19 bp):
GATATGCAATCTTAGATAT
Found at i:12844493 original size:3 final size:3
Alignment explanation
Indices: 12844485--12844542 Score: 75
Period size: 3 Copynumber: 19.0 Consensus size: 3
12844475 TGTTAATGTA
12844485 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT -TT CA-T ATGT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT -ATT AT-T
12844530 AATT ATT ATT ATT
1 -ATT ATT ATT ATT
12844543 TTAGCTATAT
Statistics
Matches: 50, Mismatches: 0, Indels: 10
0.83 0.00 0.17
Matches are distributed among these distances:
2 3 0.06
3 43 0.86
4 2 0.04
5 2 0.04
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:12844690 original size:24 final size:24
Alignment explanation
Indices: 12844646--12844718 Score: 67
Period size: 24 Copynumber: 2.9 Consensus size: 24
12844636 GTAATTATTT
*
12844646 TTATTTTATTTTATTTATATATAA
1 TTATTTTATTTTATATATATATAA
* *
12844670 TTATTTT-TTTTATAATCTATATATG
1 TTATTTTATTTTAT-ATATATATA-A
*
12844695 TTATATTTATCTTTGTATATATAT
1 TTAT-TTTAT-TTTATATATATAT
12844719 GTATGTATAC
Statistics
Matches: 39, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
23 6 0.15
24 14 0.36
25 4 0.10
26 3 0.08
27 8 0.21
28 4 0.10
ACGTcount: A:0.30, C:0.03, G:0.03, T:0.64
Consensus pattern (24 bp):
TTATTTTATTTTATATATATATAA
Found at i:12845103 original size:98 final size:98
Alignment explanation
Indices: 12844950--12845139 Score: 344
Period size: 98 Copynumber: 1.9 Consensus size: 98
12844940 CTAAACATAA
* *
12844950 GAAATATTCCGAGTTTGGGATTTTAAAGGAATTGTGCCCTAACGTATTGGGTGTGATTTCTTAAA
1 GAAATATTCCGAGTTTGGGATTCTAAAGGAATCGTGCCCTAACGTATTGGGTGTGATTTCTTAAA
*
12845015 TCTTGGATAAGTGGATGTTTTTTTAAAGTAAAG
66 TCTTGGATAAGTGGATGTTCTTTTAAAGTAAAG
*
12845048 GAAATATTCCGAGTTTGGGATTCTAGAGGAATCGTGCCCTAACGTATTGGGTGTGATTTCTTAAA
1 GAAATATTCCGAGTTTGGGATTCTAAAGGAATCGTGCCCTAACGTATTGGGTGTGATTTCTTAAA
12845113 TCTTGGATAAGTGGATGTTCTTTTAAA
66 TCTTGGATAAGTGGATGTTCTTTTAAA
12845140 ATTTTATTGT
Statistics
Matches: 88, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
98 88 1.00
ACGTcount: A:0.27, C:0.10, G:0.25, T:0.38
Consensus pattern (98 bp):
GAAATATTCCGAGTTTGGGATTCTAAAGGAATCGTGCCCTAACGTATTGGGTGTGATTTCTTAAA
TCTTGGATAAGTGGATGTTCTTTTAAAGTAAAG
Found at i:12846956 original size:2 final size:2
Alignment explanation
Indices: 12846949--12846973 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
12846939 AATTAGCTCA
12846949 AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC A
12846974 AATGGTATCA
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:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:12848464 original size:20 final size:19
Alignment explanation
Indices: 12848384--12848451 Score: 61
Period size: 19 Copynumber: 3.6 Consensus size: 19
12848374 TATTTCTTTG
12848384 AATATTTTTA--AAATT-A
1 AATATTTTTATTAAATTAA
* *
12848400 AATATTTTAATCATAATTAA
1 AATATTTTTATTA-AATTAA
**
12848420 TTTTATTTTTATTAAATTAA
1 -AATATTTTTATTAAATTAA
12848440 AATATTTTTATT
1 AATATTTTTATT
12848452 GGATGTAAGA
Statistics
Matches: 40, Mismatches: 7, Indels: 7
0.74 0.13 0.13
Matches are distributed among these distances:
16 9 0.22
18 1 0.03
19 14 0.35
20 7 0.17
21 9 0.22
ACGTcount: A:0.43, C:0.01, G:0.00, T:0.56
Consensus pattern (19 bp):
AATATTTTTATTAAATTAA
Found at i:12848723 original size:29 final size:30
Alignment explanation
Indices: 12848642--12848706 Score: 96
Period size: 30 Copynumber: 2.2 Consensus size: 30
12848632 ATTTTAAATT
* *
12848642 TTAAA-AGTACAAGAACTAAAATTAATTAA
1 TTAAATAGTACAAAAATTAAAATTAATTAA
12848671 TTAAATAGTACAAAAATTAAAATTAATTAAA
1 TTAAATAGTACAAAAATTAAAATTAATT-AA
12848702 TTAAA
1 TTAAA
12848707 GTATATGAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
29 5 0.16
30 20 0.62
31 7 0.22
ACGTcount: A:0.60, C:0.05, G:0.05, T:0.31
Consensus pattern (30 bp):
TTAAATAGTACAAAAATTAAAATTAATTAA
Found at i:12850138 original size:15 final size:15
Alignment explanation
Indices: 12850118--12850149 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
12850108 CATTTCACTA
*
12850118 TTATGTCTTTTGTAT
1 TTATGTCTTTTATAT
12850133 TTATGTCTTTTATAT
1 TTATGTCTTTTATAT
12850148 TT
1 TT
12850150 TGCATGCATA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.16, C:0.06, G:0.09, T:0.69
Consensus pattern (15 bp):
TTATGTCTTTTATAT
Found at i:12854300 original size:2 final size:2
Alignment explanation
Indices: 12854293--12854331 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
12854283 AATCTTAAGT
12854293 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
12854332 TATATACCTT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.49, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:12856446 original size:19 final size:17
Alignment explanation
Indices: 12856431--12856522 Score: 50
Period size: 17 Copynumber: 5.4 Consensus size: 17
12856421 ATTTTAATAG
12856431 TTTAATATTAAATTAAA
1 TTTAATATTAAATTAAA
12856448 TTTAATACTT--ATCTAAA
1 TTTAATA-TTAAAT-TAAA
* **
12856465 --TAGTATTTGATT-AA
1 TTTAATATTAAATTAAA
* *
12856479 TTTAATATTAAAGTGATTA
1 TTTAATATTAAA-TTA-AA
*
12856498 TCTTAATATTAAGTTAAA
1 T-TTAATATTAAATTAAA
12856516 TTTAATA
1 TTTAATA
12856523 GTTATCTTGT
Statistics
Matches: 56, Mismatches: 9, Indels: 20
0.66 0.11 0.24
Matches are distributed among these distances:
14 4 0.07
15 5 0.09
16 11 0.20
17 18 0.32
18 4 0.07
19 4 0.07
20 10 0.18
ACGTcount: A:0.43, C:0.03, G:0.05, T:0.48
Consensus pattern (17 bp):
TTTAATATTAAATTAAA
Found at i:12858509 original size:37 final size:37
Alignment explanation
Indices: 12858467--12858542 Score: 152
Period size: 37 Copynumber: 2.1 Consensus size: 37
12858457 TATTATTTTA
12858467 ATTGTTTAAGTAATTATAATAATAAAACAAAAAAATT
1 ATTGTTTAAGTAATTATAATAATAAAACAAAAAAATT
12858504 ATTGTTTAAGTAATTATAATAATAAAACAAAAAAATT
1 ATTGTTTAAGTAATTATAATAATAAAACAAAAAAATT
12858541 AT
1 AT
12858543 ATTCTTTTCA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 39 1.00
ACGTcount: A:0.57, C:0.03, G:0.05, T:0.36
Consensus pattern (37 bp):
ATTGTTTAAGTAATTATAATAATAAAACAAAAAAATT
Found at i:12866395 original size:2 final size:2
Alignment explanation
Indices: 12866390--12866420 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
12866380 AAATATATGA
12866390 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 A
12866421 GTAGATGAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:12869671 original size:29 final size:29
Alignment explanation
Indices: 12869639--12869775 Score: 123
Period size: 29 Copynumber: 4.8 Consensus size: 29
12869629 GTGATTACAG
*
12869639 TATCAGAAACTCTGTACCGGTGTTATATT
1 TATCAGATACTCTGTACCGGTGTTATATT
* * * * *
12869668 TATCAGGTGCTTTGTACTGGTATTATATT
1 TATCAGATACTCTGTACCGGTGTTATATT
* * *
12869697 TATCAGGTACTTTGTACCGGTGTTATA-G
1 TATCAGATACTCTGTACCGGTGTTATATT
* * * *
12869725 TATCAGACATTCTATATCGGTGTTATATT
1 TATCAGATACTCTGTACCGGTGTTATATT
* * *
12869754 TATCAGGTGCTATGTACCGGTG
1 TATCAGATACTCTGTACCGGTG
12869776 ATGGATACCA
Statistics
Matches: 83, Mismatches: 24, Indels: 2
0.76 0.22 0.02
Matches are distributed among these distances:
28 21 0.25
29 62 0.75
ACGTcount: A:0.23, C:0.15, G:0.21, T:0.41
Consensus pattern (29 bp):
TATCAGATACTCTGTACCGGTGTTATATT
Found at i:12869965 original size:5 final size:5
Alignment explanation
Indices: 12869957--12870011 Score: 110
Period size: 5 Copynumber: 11.0 Consensus size: 5
12869947 TGAAATGGAA
12869957 ATGAT ATGAT ATGAT ATGAT ATGAT ATGAT ATGAT ATGAT ATGAT ATGAT
1 ATGAT ATGAT ATGAT ATGAT ATGAT ATGAT ATGAT ATGAT ATGAT ATGAT
12870007 ATGAT
1 ATGAT
12870012 GAATTATAAG
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 50 1.00
ACGTcount: A:0.40, C:0.00, G:0.20, T:0.40
Consensus pattern (5 bp):
ATGAT
Found at i:12873937 original size:31 final size:31
Alignment explanation
Indices: 12873899--12873960 Score: 124
Period size: 31 Copynumber: 2.0 Consensus size: 31
12873889 CTTTAGTATA
12873899 TTGTTAAATAAGGTAATGTAATTCATGATTT
1 TTGTTAAATAAGGTAATGTAATTCATGATTT
12873930 TTGTTAAATAAGGTAATGTAATTCATGATTT
1 TTGTTAAATAAGGTAATGTAATTCATGATTT
12873961 GTGTGTTGAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.35, C:0.03, G:0.16, T:0.45
Consensus pattern (31 bp):
TTGTTAAATAAGGTAATGTAATTCATGATTT
Found at i:12880273 original size:16 final size:16
Alignment explanation
Indices: 12880254--12880305 Score: 86
Period size: 16 Copynumber: 3.2 Consensus size: 16
12880244 GATTTGCTAT
* *
12880254 TACACCTCTATTCCAT
1 TACACCTCTAATCCAA
12880270 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
12880286 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
12880302 TACA
1 TACA
12880306 GCGAACCAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 34 1.00
ACGTcount: A:0.35, C:0.37, G:0.00, T:0.29
Consensus pattern (16 bp):
TACACCTCTAATCCAA
Found at i:12880929 original size:22 final size:22
Alignment explanation
Indices: 12880894--12880951 Score: 64
Period size: 22 Copynumber: 2.6 Consensus size: 22
12880884 AAAGGATATC
* *
12880894 TACAAATTAAATCTT-TAAGAT
1 TACAAATCATATCTTCTAAGAT
12880915 TACAAAATCATATCTTCTAAGAT
1 TAC-AAATCATATCTTCTAAGAT
* *
12880938 TGCATATCATATCT
1 TACAAATCATATCT
12880952 AAGATTGCAT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
21 3 0.10
22 20 0.65
23 8 0.26
ACGTcount: A:0.41, C:0.16, G:0.05, T:0.38
Consensus pattern (22 bp):
TACAAATCATATCTTCTAAGAT
Found at i:12881763 original size:51 final size:51
Alignment explanation
Indices: 12881677--12881779 Score: 118
Period size: 51 Copynumber: 2.0 Consensus size: 51
12881667 TCCAAGTCTT
** * * * *
12881677 AACGCTAGGGGGATAAGATTCGCTGCCCTATGCTTTATTCTGCTCCGCTAC
1 AACGCTAGGGAAACAAGATTCGCTACCCTATGCTTTAATCTGCTCCACTAC
* *
12881728 AACGCTAGGGAAACAAGATTCGCTA-CCTTTAGCTTTAATCTGTTCCACTAC
1 AACGCTAGGGAAACAAGATTCGCTACCCTAT-GCTTTAATCTGCTCCACTAC
12881779 A
1 A
12881780 CTGCCAGGGA
Statistics
Matches: 43, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
50 4 0.09
51 39 0.91
ACGTcount: A:0.25, C:0.26, G:0.19, T:0.29
Consensus pattern (51 bp):
AACGCTAGGGAAACAAGATTCGCTACCCTATGCTTTAATCTGCTCCACTAC
Found at i:12881789 original size:51 final size:51
Alignment explanation
Indices: 12881691--12881799 Score: 114
Period size: 51 Copynumber: 2.1 Consensus size: 51
12881681 CTAGGGGGAT
* * * *
12881691 AAGATTCGCTGCCCTATGCTTTATTCTGCTCCGCTACAACGCTAGGGAAAC
1 AAGATTCGCTACCCTATGCTTTAATCTGCTCCACTACAACGCCAGGGAAAC
* * **
12881742 AAGATTCGCTA-CCTTTAGCTTTAATCTGTTCCACTAC-ACTGCCAGGGAAGT
1 AAGATTCGCTACCCTAT-GCTTTAATCTGCTCCACTACAAC-GCCAGGGAAAC
12881793 AAGATTC
1 AAGATTC
12881800 ACCGTTGTGG
Statistics
Matches: 48, Mismatches: 8, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
50 6 0.12
51 42 0.88
ACGTcount: A:0.26, C:0.27, G:0.18, T:0.29
Consensus pattern (51 bp):
AAGATTCGCTACCCTATGCTTTAATCTGCTCCACTACAACGCCAGGGAAAC
Found at i:12881871 original size:100 final size:100
Alignment explanation
Indices: 12881757--12882021 Score: 458
Period size: 100 Copynumber: 2.6 Consensus size: 100
12881747 TCGCTACCTT
* *
12881757 TAGCTTTAATCTGTTCCACTACACTGCCAGGGAAGTAAGATTCACCGTTGTGGCTTCAATCTATT
1 TAGCTTCAATCTGTTCCACTACACCGCCAGGGAAGTAAGATTCACCGTTGTGGCTTCAATCTATT
* *
12881822 TAACTGCAATGTTGGGGAAACAAGATTCACTGTCG
66 TAACTGCAATGTTGGAGAAACAAGATTCACCGTCG
*
12881857 TAGCTTCAATCTGTTCCACTGCACCGCCAGGGAAGTAAGATTCACCGTTGTGGCTTCAATCTATT
1 TAGCTTCAATCTGTTCCACTACACCGCCAGGGAAGTAAGATTCACCGTTGTGGCTTCAATCTATT
**
12881922 TAACTGCAATGTTGGAGAAACAAGATTTGCCGTCG
66 TAACTGCAATGTTGGAGAAACAAGATTCACCGTCG
*
12881957 TAGCTTCAATCTGTTCCACTACACCACCAGGGAAGTAAGATTCACCGTTGTGGCTTCAATCTATT
1 TAGCTTCAATCTGTTCCACTACACCGCCAGGGAAGTAAGATTCACCGTTGTGGCTTCAATCTATT
12882022 CCACTGTAAT
Statistics
Matches: 156, Mismatches: 9, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
100 156 1.00
ACGTcount: A:0.26, C:0.23, G:0.20, T:0.30
Consensus pattern (100 bp):
TAGCTTCAATCTGTTCCACTACACCGCCAGGGAAGTAAGATTCACCGTTGTGGCTTCAATCTATT
TAACTGCAATGTTGGAGAAACAAGATTCACCGTCG
Found at i:12881997 original size:50 final size:50
Alignment explanation
Indices: 12881757--12882027 Score: 195
Period size: 50 Copynumber: 5.4 Consensus size: 50
12881747 TCGCTACCTT
* * * ** *
12881757 TAGCTTTAATCTGTTCCACTACACTGCCAGGGAAGTAAGATTCACCGTTG
1 TAGCTTCAATCTATTCCACTGCACCACCAGGGAAGTAAGATTCACCGTCG
* ** ****** ** *
12881807 TGGCTTCAATCTATTTAACTGCAATGTTGGGGAAACAAGATTCACTGTCG
1 TAGCTTCAATCTATTCCACTGCACCACCAGGGAAGTAAGATTCACCGTCG
* * *
12881857 TAGCTTCAATCTGTTCCACTGCACCGCCAGGGAAGTAAGATTCACCGTTG
1 TAGCTTCAATCTATTCCACTGCACCACCAGGGAAGTAAGATTCACCGTCG
* ** *** ** **
12881907 TGGCTTCAATCTATTTAACTGCA--ATGTTGGAGAAACAAGATTTGCCGTCG
1 TAGCTTCAATCTATTCCACTGCACCA-CCAGG-GAAGTAAGATTCACCGTCG
* * *
12881957 TAGCTTCAATCTGTTCCACTACACCACCAGGGAAGTAAGATTCACCGTTG
1 TAGCTTCAATCTATTCCACTGCACCACCAGGGAAGTAAGATTCACCGTCG
*
12882007 TGGCTTCAATCTATTCCACTG
1 TAGCTTCAATCTATTCCACTG
12882028 TAATGCCAAA
Statistics
Matches: 161, Mismatches: 56, Indels: 8
0.72 0.25 0.04
Matches are distributed among these distances:
49 2 0.01
50 156 0.97
51 2 0.01
52 1 0.01
ACGTcount: A:0.26, C:0.24, G:0.20, T:0.30
Consensus pattern (50 bp):
TAGCTTCAATCTATTCCACTGCACCACCAGGGAAGTAAGATTCACCGTCG
Found at i:12882208 original size:44 final size:44
Alignment explanation
Indices: 12882160--12882274 Score: 151
Period size: 44 Copynumber: 2.6 Consensus size: 44
12882150 CATCGATCTG
* * * *
12882160 CTCCACTACTGCTTAGGGAGATAAGATCTATAATTTTCAACCTA
1 CTCCACTGCTGCTCAGGGAGATAAGATCTACAATCTTCAACCTA
* *
12882204 CTCCACTGCTGCTCAGGGAGATAGGATTTACAATCTTCAACCTA
1 CTCCACTGCTGCTCAGGGAGATAAGATCTACAATCTTCAACCTA
*
12882248 TTCCACTGCTGAC-CAGGGAGATAAGAT
1 CTCCACTGCTG-CTCAGGGAGATAAGAT
12882275 TCACCTATTC
Statistics
Matches: 62, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
44 61 0.98
45 1 0.02
ACGTcount: A:0.30, C:0.24, G:0.18, T:0.28
Consensus pattern (44 bp):
CTCCACTGCTGCTCAGGGAGATAAGATCTACAATCTTCAACCTA
Found at i:12882286 original size:34 final size:34
Alignment explanation
Indices: 12882243--12882382 Score: 147
Period size: 34 Copynumber: 3.8 Consensus size: 34
12882233 ACAATCTTCA
12882243 ACCTATTCCACTGCTGACCAGGGAGATAAGATTC
1 ACCTATTCCACTGCTGACCAGGGAGATAAGATTC
12882277 ACCTATTCCACTGCTGACCAGGAAGATAGGACTTACA-ATCTTC
1 ACCTATTCCACTGCTGACCAGG--G--A-GA--TA-AGA--TTC
*
12882320 AACCTATTCCACTGCTGACCAGGGAGATAGGATTC
1 -ACCTATTCCACTGCTGACCAGGGAGATAAGATTC
* *
12882355 ACTTATTCCACTGCTGGCCAGGGAGATA
1 ACCTATTCCACTGCTGACCAGGGAGATA
12882383 GGACTTACAA
Statistics
Matches: 91, Mismatches: 3, Indels: 24
0.77 0.03 0.20
Matches are distributed among these distances:
34 48 0.53
35 3 0.03
36 1 0.01
37 3 0.03
38 1 0.01
39 4 0.04
40 1 0.01
41 3 0.03
42 2 0.02
43 3 0.03
44 22 0.24
ACGTcount: A:0.29, C:0.26, G:0.21, T:0.24
Consensus pattern (34 bp):
ACCTATTCCACTGCTGACCAGGGAGATAAGATTC
Found at i:12882340 original size:44 final size:44
Alignment explanation
Indices: 12882277--12882410 Score: 180
Period size: 44 Copynumber: 3.3 Consensus size: 44
12882267 GATAAGATTC
*
12882277 ACCTATTCCACTGCTGACCAGGAAGATAGGACTTACAATCTTCA
1 ACCTATTCCACTGCTGACCAGGGAGATAGGACTTACAATCTTCA
12882321 ACCTATTCCACTGCTGACCAGGGAGATAGGA-TT-C-A-C-T--
1 ACCTATTCCACTGCTGACCAGGGAGATAGGACTTACAATCTTCA
*
12882358 ---TATTCCACTGCTGGCCAGGGAGATAGGACTTACAATCTTCA
1 ACCTATTCCACTGCTGACCAGGGAGATAGGACTTACAATCTTCA
12882399 ACCTATTCCACT
1 ACCTATTCCACT
12882411 ACTTTCCAAG
Statistics
Matches: 78, Mismatches: 2, Indels: 20
0.78 0.02 0.20
Matches are distributed among these distances:
34 27 0.35
35 2 0.03
36 1 0.01
37 1 0.01
38 1 0.01
39 2 0.03
40 1 0.01
41 1 0.01
42 1 0.01
43 2 0.03
44 39 0.50
ACGTcount: A:0.28, C:0.28, G:0.18, T:0.26
Consensus pattern (44 bp):
ACCTATTCCACTGCTGACCAGGGAGATAGGACTTACAATCTTCA
Found at i:12882424 original size:78 final size:78
Alignment explanation
Indices: 12882199--12882410 Score: 354
Period size: 78 Copynumber: 2.7 Consensus size: 78
12882189 ATAATTTTCA
* *
12882199 ACCTACTCCACTGCT-GCTCAGGGAGATAGGATTTACAATCTTCAACCTATTCCACTGCTGACCA
1 ACCTATTCCACTGCTGGC-CAGGGAGATAGGACTTACAATCTTCAACCTATTCCACTGCTGACCA
12882263 GGGAGATAAGATTC
65 GGGAGATAAGATTC
* *
12882277 ACCTATTCCACTGCTGACCAGGAAGATAGGACTTACAATCTTCAACCTATTCCACTGCTGACCAG
1 ACCTATTCCACTGCTGGCCAGGGAGATAGGACTTACAATCTTCAACCTATTCCACTGCTGACCAG
*
12882342 GGAGATAGGATTC
66 GGAGATAAGATTC
*
12882355 ACTTATTCCACTGCTGGCCAGGGAGATAGGACTTACAATCTTCAACCTATTCCACT
1 ACCTATTCCACTGCTGGCCAGGGAGATAGGACTTACAATCTTCAACCTATTCCACT
12882411 ACTTTCCAAG
Statistics
Matches: 125, Mismatches: 8, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
78 124 0.99
79 1 0.01
ACGTcount: A:0.28, C:0.27, G:0.18, T:0.26
Consensus pattern (78 bp):
ACCTATTCCACTGCTGGCCAGGGAGATAGGACTTACAATCTTCAACCTATTCCACTGCTGACCAG
GGAGATAAGATTC
Found at i:12889838 original size:22 final size:22
Alignment explanation
Indices: 12889816--12889882 Score: 107
Period size: 22 Copynumber: 3.0 Consensus size: 22
12889806 AAATTAAATC
* *
12889816 TCTAAGATTACAAAATCATATCT
1 TCTAAGATTGC-ATATCATATCT
12889839 TCTAAGATTGCATATCATATCT
1 TCTAAGATTGCATATCATATCT
12889861 TCTAAGATTGCATATCATATCT
1 TCTAAGATTGCATATCATATCT
12889883 AAGATTGTAT
Statistics
Matches: 42, Mismatches: 2, Indels: 1
0.93 0.04 0.02
Matches are distributed among these distances:
22 32 0.76
23 10 0.24
ACGTcount: A:0.36, C:0.18, G:0.07, T:0.39
Consensus pattern (22 bp):
TCTAAGATTGCATATCATATCT
Found at i:12889885 original size:19 final size:20
Alignment explanation
Indices: 12889838--12889895 Score: 82
Period size: 22 Copynumber: 2.9 Consensus size: 20
12889828 AAATCATATC
12889838 TTCTAAGATTGCATATCATA
1 TTCTAAGATTGCATATCATA
12889858 TCTTCTAAGATTGCATATCATA
1 --TTCTAAGATTGCATATCATA
*
12889880 -TCTAAGATTGTATATC
1 TTCTAAGATTGCATATC
12889896 CTTGAAGATT
Statistics
Matches: 35, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
19 15 0.43
22 20 0.57
ACGTcount: A:0.33, C:0.16, G:0.10, T:0.41
Consensus pattern (20 bp):
TTCTAAGATTGCATATCATA
Found at i:12890733 original size:125 final size:124
Alignment explanation
Indices: 12890562--12890801 Score: 367
Period size: 125 Copynumber: 1.9 Consensus size: 124
12890552 CTTCTACTAG
* *
12890562 GATGCTATTTGAGAAGAAATTGTGAAATCATGGCCTCGTGGACGCGATTTCGGTACAG-TGGTCA
1 GATGCTATTTGAGAAGAAATTGTGAAATCATGCCCTCGTGGACGCGATTTCGCTACAGTTGGTCA
*
12890626 TGTA-AGAAATAATTTTTTTTGACGTTTTCTGAGTAAATAGTATAAAATCGCTGATACAAT
66 TGTAGA-AAATAATTTTTTTTGACG-TTTCTGAGCAAATAGTATAAAATCGCTGATACAAT
* * *
12890686 GATGCTATATTGGGCAGAAATTGTGAAATCGTGCCCTCGTGGACGCGATTTCGCTACAGTTGGTC
1 GATGCTAT-TTGAGAAGAAATTGTGAAATCATGCCCTCGTGGACGCGATTTCGCTACAGTTGGTC
* *
12890751 ATGTAGAAAATAATTTTTTTTGACGTTTCTGAGCAAATAGTGTCAAATCGC
65 ATGTAGAAAATAATTTTTTTTGACGTTTCTGAGCAAATAGTATAAAATCGC
12890802 GCCCTCGTGG
Statistics
Matches: 105, Mismatches: 8, Indels: 5
0.89 0.07 0.04
Matches are distributed among these distances:
124 8 0.08
125 68 0.65
126 28 0.27
127 1 0.01
ACGTcount: A:0.29, C:0.14, G:0.23, T:0.33
Consensus pattern (124 bp):
GATGCTATTTGAGAAGAAATTGTGAAATCATGCCCTCGTGGACGCGATTTCGCTACAGTTGGTCA
TGTAGAAAATAATTTTTTTTGACGTTTCTGAGCAAATAGTATAAAATCGCTGATACAAT
Found at i:12894166 original size:23 final size:22
Alignment explanation
Indices: 12894136--12894602 Score: 363
Period size: 23 Copynumber: 20.3 Consensus size: 22
12894126 ATTAGCTTAG
12894136 GGTTAGGGTTTTACATTAAGTTA
1 GGTTAGGGTTTTA-ATTAAGTTA
12894159 GGTTAGGGTTTTTAATTAA---A
1 GGTTAGGG-TTTTAATTAAGTTA
*
12894179 --TTAGGTTTTTAATTCAA-TTA
1 GGTTAGGGTTTTAATT-AAGTTA
12894199 GGTTAGGGTTTTACATTAAGTTA
1 GGTTAGGGTTTTA-ATTAAGTTA
*
12894222 GGTTAGGATTTTTAATTAAGTTA
1 GGTTAGG-GTTTTAATTAAGTTA
12894245 GGTTAGGGTTTTTAATTAAGTTA
1 GGTTAGGG-TTTTAATTAAGTTA
*
12894268 AGTTAGGGTTTTTAATTAAATTAAGTTA
1 GGTTAGGG---TT--TT-AATTAAGTTA
12894296 GG-TAGGGTTTTACATTAAGTTA
1 GGTTAGGGTTTTA-ATTAAGTTA
*
12894318 GGTTAGGGTTTTTATTAAGTTA
1 GGTTAGGGTTTTAATTAAGTTA
* *
12894340 GGGTAGGGTTTTAAATACAGTTA
1 GGTTAGGGTTTTAATTA-AGTTA
*
12894363 GCTTAGGGTTTTTAATTAAATTAAGTTA
1 GGTTAGGG---TT--TT-AATTAAGTTA
*
12894391 GGTTAGGGTTTTTAATTAAATTA
1 GGTTAGGG-TTTTAATTAAGTTA
*
12894414 AGTTA-GGTTTTAAGTTAAGTTA
1 GGTTAGGGTTTTAA-TTAAGTTA
*
12894436 GGTTAAGGTTTTACATTAAGTTA
1 GGTTAGGGTTTTA-ATTAAGTTA
**
12894459 GGTTAGAATTTTTAATTAA---A
1 GGTTAG-GGTTTTAATTAAGTTA
*
12894479 --TTAGGTTTTTAATTCAA-TTA
1 GGTTAGGGTTTTAATT-AAGTTA
12894499 GGTTAGGGTTTTTAATTCAA-TTA
1 GGTTAGGG-TTTTAATT-AAGTTA
12894522 GGTTAGGGTTTTTAATTCAATTAAGTTA
1 GGTTAGGG---TT--TT-AATTAAGTTA
12894550 GGTTAGGGTTTTTAATTCAA-TTA
1 GGTTAGGG-TTTTAATT-AAGTTA
*
12894573 GGTTAGGGTTTTTAATTAAATTA
1 GGTTAGGG-TTTTAATTAAGTTA
*
12894596 AGTTAGG
1 GGTTAGG
12894603 TTAGGGTTTT
Statistics
Matches: 378, Mismatches: 24, Indels: 84
0.78 0.05 0.17
Matches are distributed among these distances:
17 17 0.04
18 13 0.03
20 4 0.01
21 7 0.02
22 68 0.18
23 176 0.47
24 24 0.06
25 6 0.02
26 8 0.02
27 11 0.03
28 40 0.11
29 4 0.01
ACGTcount: A:0.30, C:0.02, G:0.22, T:0.46
Consensus pattern (22 bp):
GGTTAGGGTTTTAATTAAGTTA
Found at i:12894187 original size:17 final size:17
Alignment explanation
Indices: 12894165--12894202 Score: 67
Period size: 17 Copynumber: 2.2 Consensus size: 17
12894155 GTTAGGTTAG
12894165 GGTTTTTAATTAAATTA
1 GGTTTTTAATTAAATTA
*
12894182 GGTTTTTAATTCAATTA
1 GGTTTTTAATTAAATTA
12894199 GGTT
1 GGTT
12894203 AGGGTTTTAC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.29, C:0.03, G:0.16, T:0.53
Consensus pattern (17 bp):
GGTTTTTAATTAAATTA
Found at i:12894274 original size:51 final size:49
Alignment explanation
Indices: 12894179--12894616 Score: 305
Period size: 51 Copynumber: 9.3 Consensus size: 49
12894169 TTTAATTAAA
*
12894179 TTAGG-TTTTTAATTCAA-TTAGGTTAGGG-TTTT-A-CATTAAGTTAGG
1 TTAGGATTTTTAATT-AAGTTAGGTTAGGGTTTTTAATAATTAAGTTAGG
*
12894224 TTAGGATTTTTAATTAAGTTAGGTTAGGG-TTTT--TAATTAAGTTAAG
1 TTAGGATTTTTAATTAAGTTAGGTTAGGGTTTTTAATAATTAAGTTAGG
* * * * *
12894270 TTAGGGTTTTTAATTAAATTAAGTTAGGTAGGGTTTT-A-CATTAAGTTAGG
1 TTAGGATTTTTAATTAAGTTAGGTTA-G--GGTTTTTAATAATTAAGTTAGG
* * *
12894320 TTAGGGTTTTT-ATTAAGTTAGGGTAGGG-TTTT-A-AA-TACAGTTAGC
1 TTAGGATTTTTAATTAAGTTAGGTTAGGGTTTTTAATAATTA-AGTTAGG
* * *
12894365 TTAGGGTTTTTAATTAAATTAAGTTAGGTTAGGG-TTTT--TAATTAAATTAAG
1 TTA-GG-ATTT--TT-AATTAAGTTAGGTTAGGGTTTTTAATAATTAAGTTAGG
* *
12894416 TTAGG--TTTTAAGTTAAGTTAGGTTAAGG-TTTT-A-CATTAAGTTAGG
1 TTAGGATTTTTAA-TTAAGTTAGGTTAGGGTTTTTAATAATTAAGTTAGG
* *
12894461 TTAGAATTTTTAATTAA---A--TTA-GGTTTTTAAT--TCAA-TTAGG
1 TTAGGATTTTTAATTAAGTTAGGTTAGGGTTTTTAATAATTAAGTTAGG
*
12894501 TTAGGGTTTTTAATTCAA-TTAGGTTAGGGTTTTTAATTCAATTAAGTTAGG
1 TTAGGATTTTTAATT-AAGTTAGGTTAGGGTTTTTAA-T-AATTAAGTTAGG
*
12894552 TTAGGGTTTTTAATTCAA-TTAGGTTAGGGTTTTTAATTAAATTAAGTTAGG
1 TTAGGATTTTTAATT-AAGTTAGGTTAGGGTTTTTAA-T-AATTAAGTTAGG
*
12894603 TTAGGGTTTTTAAT
1 TTAGGATTTTTAAT
12894617 CAAATAATGT
Statistics
Matches: 331, Mismatches: 27, Indels: 64
0.78 0.06 0.15
Matches are distributed among these distances:
40 20 0.06
41 12 0.04
42 1 0.00
43 2 0.01
44 4 0.01
45 59 0.18
46 74 0.22
47 13 0.04
48 1 0.00
49 15 0.05
50 30 0.09
51 98 0.30
52 2 0.01
ACGTcount: A:0.29, C:0.02, G:0.22, T:0.47
Consensus pattern (49 bp):
TTAGGATTTTTAATTAAGTTAGGTTAGGGTTTTTAATAATTAAGTTAGG
Found at i:12894320 original size:96 final size:95
Alignment explanation
Indices: 12894136--12894616 Score: 424
Period size: 96 Copynumber: 5.2 Consensus size: 95
12894126 ATTAGCTTAG
*
12894136 GGTTAGGG-TTTTACATTAAGTTAGGTTAGGG-TTT--TTAA-TTAAATTA-GGTTTTTAA-T--
1 GGTTAGGGTTTTTA-ATTAAGTTAGGTTAGGGTTTTAATTAAGTTAAGTTAGGGTTTTTAATTAA
*
12894192 -TCAA-TTAGGTTAGGGTTTTACATTAAGTTA
65 ATTAAGTTAGGTTAGGGTTTTA-ATTAAGTTA
*
12894222 GGTTAGGATTTTTAATTAAGTTAGGTTAGGGTTTTTAATTAAGTTAAGTTAGGGTTTTTAATTAA
1 GGTTAGGGTTTTTAATTAAGTTAGGTTAGGG-TTTTAATTAAGTTAAGTTAGGGTTTTTAATTAA
12894287 ATTAAGTTAGG-TAGGGTTTTACATTAAGTTA
65 ATTAAGTTAGGTTAGGGTTTTA-ATTAAGTTA
* *
12894318 GGTTAGGGTTTTT-ATTAAGTTAGGGTAGGGTTTTAAATACAGTT-AGCTTAGGGTTTTTAATTA
1 GGTTAGGGTTTTTAATTAAGTTAGGTTAGGGTTTTAATTA-AGTTAAG-TTAGGGTTTTTAATTA
*
12894381 AATTAAGTTAGGTTAGGGTTTTTAATTAAATTA
64 AATTAAGTTAGGTTAGGG-TTTTAATTAAGTTA
* * * **
12894414 AGTTA-GG-TTTTAAGTTAAGTTAGGTTAAGGTTTTACATTAAGTTAGGTTAGAATTTTTAATT-
1 GGTTAGGGTTTTTAA-TTAAGTTAGGTTAGGGTTTTA-ATTAAGTTAAGTTAGGGTTTTTAATTA
12894476 -A--AA-TTAGG-T----TTTTAATTCAA-TTA
64 AATTAAGTTAGGTTAGGGTTTTAATT-AAGTTA
*
12894499 GGTTAGGGTTTTTAATTCAA-TTAGGTTAGGGTTTTTAATTCAATTAAGTTAGGTTAGGGTTTTT
1 GGTTAGGGTTTTTAATT-AAGTTAGGTTAGGG---TT--TT-AATTAAGTTAAGTTAGGGTTTTT
* * ***** *
12894563 AATTCAATTAGGTTAGGGTTTTTAATTAAATTAAGTTA
59 AATTAAATTAAGTTA-GGTTAGGGTTTTAATTAAGTTA
12894601 GGTTAGGGTTTTTAAT
1 GGTTAGGGTTTTTAAT
12894617 CAAATAATGT
Statistics
Matches: 332, Mismatches: 21, Indels: 68
0.79 0.05 0.16
Matches are distributed among these distances:
85 15 0.05
86 40 0.12
87 13 0.04
88 3 0.01
89 2 0.01
90 5 0.02
91 38 0.11
92 12 0.04
93 2 0.01
94 15 0.05
95 52 0.16
96 91 0.27
97 16 0.05
98 1 0.00
101 2 0.01
102 25 0.08
ACGTcount: A:0.29, C:0.02, G:0.22, T:0.46
Consensus pattern (95 bp):
GGTTAGGGTTTTTAATTAAGTTAGGTTAGGGTTTTAATTAAGTTAAGTTAGGGTTTTTAATTAAA
TTAAGTTAGGTTAGGGTTTTAATTAAGTTA
Found at i:12894381 original size:28 final size:28
Alignment explanation
Indices: 12894350--12894419 Score: 115
Period size: 28 Copynumber: 2.5 Consensus size: 28
12894340 GGGTAGGGTT
12894350 TTAAA-TACAGTTAGCTTAGGGTTTTTAA
1 TTAAATTA-AGTTAGCTTAGGGTTTTTAA
*
12894378 TTAAATTAAGTTAGGTTAGGGTTTTTAA
1 TTAAATTAAGTTAGCTTAGGGTTTTTAA
12894406 TTAAATTAAGTTAG
1 TTAAATTAAGTTAG
12894420 GTTTTAAGTT
Statistics
Matches: 40, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
28 38 0.95
29 2 0.05
ACGTcount: A:0.34, C:0.03, G:0.19, T:0.44
Consensus pattern (28 bp):
TTAAATTAAGTTAGCTTAGGGTTTTTAA
Found at i:12894431 original size:17 final size:17
Alignment explanation
Indices: 12894406--12894439 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
12894396 GGGTTTTTAA
12894406 TTAAATTAAGTTAGGTT
1 TTAAATTAAGTTAGGTT
*
12894423 TTAAGTTAAGTTAGGTT
1 TTAAATTAAGTTAGGTT
12894440 AAGGTTTTAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.32, C:0.00, G:0.21, T:0.47
Consensus pattern (17 bp):
TTAAATTAAGTTAGGTT
Found at i:12894489 original size:17 final size:17
Alignment explanation
Indices: 12894467--12894502 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
12894457 TAGGTTAGAA
12894467 TTTTTAATTAAATTAGG
1 TTTTTAATTAAATTAGG
*
12894484 TTTTTAATTCAATTAGG
1 TTTTTAATTAAATTAGG
12894501 TT
1 TT
12894503 AGGGTTTTTA
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:0.31, C:0.03, G:0.11, T:0.56
Consensus pattern (17 bp):
TTTTTAATTAAATTAGG
Found at i:12894543 original size:28 final size:27
Alignment explanation
Indices: 12894487--12894616 Score: 154
Period size: 28 Copynumber: 5.0 Consensus size: 27
12894477 AATTAGGTTT
12894487 TTAATTCAATTAGGTTAGGG--TTT--
1 TTAATTCAATTAGGTTAGGGTTTTTAA
12894510 TTAATTCAATTAGGTTAGGGTTTTTAA
1 TTAATTCAATTAGGTTAGGGTTTTTAA
12894537 TTCAATT-AAGTTAGGTTAGGG--TTT--
1 TT-AATTCAA-TTAGGTTAGGGTTTTTAA
12894561 TTAATTCAATTAGGTTAGGGTTTTTAA
1 TTAATTCAATTAGGTTAGGGTTTTTAA
12894588 TTAAATT-AAGTTAGGTTAGGGTTTTTAA
1 TT-AATTCAA-TTAGGTTAGGGTTTTTAA
12894616 T
1 T
12894617 CAAATAATGT
Statistics
Matches: 94, Mismatches: 0, Indels: 21
0.82 0.00 0.18
Matches are distributed among these distances:
23 35 0.37
24 4 0.04
25 6 0.06
26 3 0.03
27 8 0.09
28 38 0.40
ACGTcount: A:0.28, C:0.03, G:0.21, T:0.48
Consensus pattern (27 bp):
TTAATTCAATTAGGTTAGGGTTTTTAA
Found at i:12894621 original size:28 final size:25
Alignment explanation
Indices: 12894482--12894616 Score: 156
Period size: 23 Copynumber: 5.4 Consensus size: 25
12894472 AATTAAATTA
12894482 GGTTTTTAAT--TCAATTAGGTTAG
1 GGTTTTTAATAATCAATTAGGTTAG
12894505 GGTTTTTAAT--TCAATTAGGTTAG
1 GGTTTTTAATAATCAATTAGGTTAG
*
12894528 GGTTTTTAATTCAATTAAGTTAGGTTAG
1 GGTTTTTAA-T-AATCAA-TTAGGTTAG
12894556 GGTTTTTAAT--TCAATTAGGTTAG
1 GGTTTTTAATAATCAATTAGGTTAG
*
12894579 GGTTTTTAATTAAATTAAGTTAGGTTAG
1 GGTTTTTAA-T-AATCAA-TTAGGTTAG
12894607 GGTTTTTAAT
1 GGTTTTTAAT
12894617 CAAATAATGT
Statistics
Matches: 99, Mismatches: 3, Indels: 16
0.84 0.03 0.14
Matches are distributed among these distances:
23 50 0.51
24 5 0.05
27 8 0.08
28 36 0.36
ACGTcount: A:0.27, C:0.03, G:0.21, T:0.48
Consensus pattern (25 bp):
GGTTTTTAATAATCAATTAGGTTAG
Found at i:12896812 original size:14 final size:15
Alignment explanation
Indices: 12896795--12896828 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
12896785 AATAAATATC
12896795 TAAAAATA-CATAAA
1 TAAAAATATCATAAA
*
12896809 TAAAAATATCTTAAA
1 TAAAAATATCATAAA
12896824 TAAAA
1 TAAAA
12896829 TATAAAATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 8 0.44
15 10 0.56
ACGTcount: A:0.68, C:0.06, G:0.00, T:0.26
Consensus pattern (15 bp):
TAAAAATATCATAAA
Found at i:12913083 original size:30 final size:30
Alignment explanation
Indices: 12913049--12913240 Score: 205
Period size: 30 Copynumber: 6.5 Consensus size: 30
12913039 TCATCGACGA
12913049 ATGAAAAGGGATGGCTTCGGCTATCGATAT
1 ATGAAAAGGGATGGCTTCGGCTATCGATAT
** *
12913079 ATGAAAAGGGATAACTTCGGCTATCAAT-T
1 ATGAAAAGGGATGGCTTCGGCTATCGATAT
* * * * *
12913108 ACGAAAAGGGATGG-TGACGACCATC-AAATT
1 ATGAAAAGGGATGGCT-TCGGCTATCGATA-T
12913138 ATGAAAAGGGATGGCTTCGGCTATCG-TAT
1 ATGAAAAGGGATGGCTTCGGCTATCGATAT
*
12913167 AATGAAAAGGGATGGCTTCGGCTATCGATCT
1 -ATGAAAAGGGATGGCTTCGGCTATCGATAT
* * *
12913198 ATGAAAAAGGATAGCTTCGGCTATCAAT-T
1 ATGAAAAGGGATGGCTTCGGCTATCGATAT
*
12913227 ATGAAAAAGGATGG
1 ATGAAAAGGGATGG
12913241 TGACAACCAC
Statistics
Matches: 135, Mismatches: 20, Indels: 15
0.79 0.12 0.09
Matches are distributed among these distances:
28 2 0.01
29 33 0.24
30 97 0.72
31 3 0.02
ACGTcount: A:0.35, C:0.14, G:0.27, T:0.24
Consensus pattern (30 bp):
ATGAAAAGGGATGGCTTCGGCTATCGATAT
Found at i:12913227 original size:89 final size:88
Alignment explanation
Indices: 12913049--12913324 Score: 272
Period size: 89 Copynumber: 3.1 Consensus size: 88
12913039 TCATCGACGA
** *
12913049 ATGAAAAGGGATGGCTTCGGCTATCGATATATGAAAAGGGATAACTTCGGCTATCAATTACGAAA
1 ATGAAAAGGGATGGCTTCGGCTATCGATA-ATGAAAAGGGATGGCTTCGGCTATCAATTATGAAA
* * * * *
12913114 AGGGAT-GGTGACGACCATCAAATT
65 AAGGATAGCT-TCGGCTATCAAATT
*
12913138 ATGAAAAGGGATGGCTTCGGCTATCGTATAATGAAAAGGGATGGCTTCGGCTATCGATCTATGAA
1 ATGAAAAGGGATGGCTTCGGCTATCG-ATAATGAAAAGGGATGGCTTCGGCTATCAAT-TATGAA
12913203 AAAGGATAGCTTCGGCTATC-AATT
64 AAAGGATAGCTTCGGCTATCAAATT
* * ** * * * * *
12913227 ATGAAAAAGGATGG-TGACAACCACCGAATAATGAAAAGGGATGG-TAACGACCATCAAATTATG
1 ATGAAAAGGGATGGCT-TCGGCTATCG-ATAATGAAAAGGGATGGCT-TCGGCTATC-AATTATG
* *
12913290 AAAAAGGATAGCTTCGGCTATCGAACT
62 AAAAAGGATAGCTTCGGCTATCAAATT
12913317 ATGAAAAG
1 ATGAAAAG
12913325 TTGATACGAG
Statistics
Matches: 158, Mismatches: 22, Indels: 13
0.82 0.11 0.07
Matches are distributed among these distances:
88 2 0.01
89 122 0.77
90 32 0.20
91 2 0.01
ACGTcount: A:0.37, C:0.14, G:0.25, T:0.23
Consensus pattern (88 bp):
ATGAAAAGGGATGGCTTCGGCTATCGATAATGAAAAGGGATGGCTTCGGCTATCAATTATGAAAA
AGGATAGCTTCGGCTATCAAATT
Found at i:12913261 original size:119 final size:119
Alignment explanation
Indices: 12913048--12913323 Score: 374
Period size: 119 Copynumber: 2.3 Consensus size: 119
12913038 ATCATCGACG
* *
12913048 AATGAAAAGGGATGGCTTCGGCTATCGATATATGAAAAGGGATAACTTCGGCTATCAATTACGAA
1 AATGAAAAGGGATGGCTTCGGCTATCGATCTATGAAAAAGGATAACTTCGGCTATCAATTACGAA
* * * * * * * **
12913113 AAGGGATGGTGACGACCATCAAATTATGAAAAGGGATGGCT-TCGGCTATCGTAT
66 AAAGGATGGTGACAACCACCAAATAATGAAAAGGGATGG-TAACGACCATCAAAT
* *
12913167 AATGAAAAGGGATGGCTTCGGCTATCGATCTATGAAAAAGGATAGCTTCGGCTATCAATTATGAA
1 AATGAAAAGGGATGGCTTCGGCTATCGATCTATGAAAAAGGATAACTTCGGCTATCAATTACGAA
*
12913232 AAAGGATGGTGACAACCACCGAATAATGAAAAGGGATGGTAACGACCATCAAAT
66 AAAGGATGGTGACAACCACCAAATAATGAAAAGGGATGGTAACGACCATCAAAT
* * * *
12913286 TATGAAAAAGGATAGCTTCGGCTATCGAACTATGAAAA
1 AATGAAAAGGGATGGCTTCGGCTATCGATCTATGAAAA
12913324 GTTGATACGA
Statistics
Matches: 138, Mismatches: 18, Indels: 2
0.87 0.11 0.01
Matches are distributed among these distances:
118 1 0.01
119 137 0.99
ACGTcount: A:0.38, C:0.14, G:0.25, T:0.23
Consensus pattern (119 bp):
AATGAAAAGGGATGGCTTCGGCTATCGATCTATGAAAAAGGATAACTTCGGCTATCAATTACGAA
AAAGGATGGTGACAACCACCAAATAATGAAAAGGGATGGTAACGACCATCAAAT
Found at i:12913263 original size:30 final size:30
Alignment explanation
Indices: 12913227--12913298 Score: 90
Period size: 30 Copynumber: 2.4 Consensus size: 30
12913217 GCTATCAATT
* *
12913227 ATGAAAAAGGATGGTGACAACCACCGAATA
1 ATGAAAAAGGATGGTAACAACCACCAAATA
* * * *
12913257 ATGAAAAGGGATGGTAACGACCATCAAATT
1 ATGAAAAAGGATGGTAACAACCACCAAATA
12913287 ATGAAAAAGGAT
1 ATGAAAAAGGAT
12913299 AGCTTCGGCT
Statistics
Matches: 35, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
30 35 1.00
ACGTcount: A:0.47, C:0.12, G:0.24, T:0.17
Consensus pattern (30 bp):
ATGAAAAAGGATGGTAACAACCACCAAATA
Found at i:12913799 original size:17 final size:17
Alignment explanation
Indices: 12913777--12913812 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
12913767 TCCAAATTTG
12913777 TTTAACTAATTTTATTA
1 TTTAACTAATTTTATTA
12913794 TTTAACTAATTTTATTA
1 TTTAACTAATTTTATTA
12913811 TT
1 TT
12913813 CTCGTTTTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.33, C:0.06, G:0.00, T:0.61
Consensus pattern (17 bp):
TTTAACTAATTTTATTA
Found at i:12915908 original size:18 final size:19
Alignment explanation
Indices: 12915887--12915928 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 19
12915877 ATTAATAGAA
* *
12915887 TAAAATATAAT-TATATTT
1 TAAAATAAAATATATATTC
12915905 TAAAAATAAAATATATATTC
1 T-AAAATAAAATATATATTC
12915925 TAAA
1 TAAA
12915929 CTCAAATACT
Statistics
Matches: 20, Mismatches: 2, Indels: 3
0.80 0.08 0.12
Matches are distributed among these distances:
18 1 0.05
19 12 0.60
20 7 0.35
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.40
Consensus pattern (19 bp):
TAAAATAAAATATATATTC
Found at i:12915923 original size:20 final size:19
Alignment explanation
Indices: 12915888--12915928 Score: 55
Period size: 20 Copynumber: 2.1 Consensus size: 19
12915878 TTAATAGAAT
* *
12915888 AAAATATAATTATATTTTA
1 AAAATAAAATTATATTCTA
12915907 AAAATAAAATATATATTCTA
1 AAAATAAAAT-TATATTCTA
12915927 AA
1 AA
12915929 CTCAAATACT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 9 0.47
20 10 0.53
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (19 bp):
AAAATAAAATTATATTCTA
Found at i:12919437 original size:41 final size:41
Alignment explanation
Indices: 12919345--12919450 Score: 108
Period size: 41 Copynumber: 2.6 Consensus size: 41
12919335 AGGTTTAAAA
*
12919345 CCTAGCAGGCTTAAG-GCCGGTGAAATAATTCAGACTTTAAG
1 CCTAGCAGGC-TAAGTGCCGGTGAAATAATTCAGACTATAAG
* * ** *
12919386 TCTAGTAGGCTAAGTGCCGGTGATCTGAA-TCAGGCTATAAG
1 CCTAGCAGGCTAAGTGCCGGTGAAAT-AATTCAGACTATAAG
* *
12919427 CCTAGCAGGCTAATTGTCGGTGAA
1 CCTAGCAGGCTAAGTGCCGGTGAA
12919451 TATGTTAAAT
Statistics
Matches: 52, Mismatches: 11, Indels: 4
0.78 0.16 0.06
Matches are distributed among these distances:
40 4 0.08
41 46 0.88
42 2 0.04
ACGTcount: A:0.28, C:0.19, G:0.27, T:0.25
Consensus pattern (41 bp):
CCTAGCAGGCTAAGTGCCGGTGAAATAATTCAGACTATAAG
Found at i:12927556 original size:42 final size:43
Alignment explanation
Indices: 12927502--12927611 Score: 143
Period size: 42 Copynumber: 2.6 Consensus size: 43
12927492 GATTTGAGAT
*
12927502 TTACGTGTAAGACCATGTCTGGGACATTGACATCG-T-ATATAA
1 TTACGTGTAAGACCATGTCTGGGACAGTGACATCGATAAT-TAA
* * *
12927544 TTACGTATAAGACCTTGTCTGGGACAGTGGCATCGATAATTAA
1 TTACGTGTAAGACCATGTCTGGGACAGTGACATCGATAATTAA
* *
12927587 TTACATGTAAGACCACGTCTGGGAC
1 TTACGTGTAAGACCATGTCTGGGAC
12927612 GTTGGCATTG
Statistics
Matches: 58, Mismatches: 8, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
42 31 0.53
43 25 0.43
44 2 0.03
ACGTcount: A:0.30, C:0.18, G:0.23, T:0.29
Consensus pattern (43 bp):
TTACGTGTAAGACCATGTCTGGGACAGTGACATCGATAATTAA
Found at i:12928270 original size:2 final size:2
Alignment explanation
Indices: 12928254--12928295 Score: 68
Period size: 2 Copynumber: 21.0 Consensus size: 2
12928244 TAAGTTTAGT
12928254 TA TA GTA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
12928296 GCCATGGGAA
Statistics
Matches: 38, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
1 1 0.03
2 35 0.92
3 2 0.05
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (2 bp):
TA
Found at i:12930809 original size:41 final size:41
Alignment explanation
Indices: 12930752--12930843 Score: 141
Period size: 41 Copynumber: 2.2 Consensus size: 41
12930742 GTTGTTTAAC
*
12930752 TAGTAAGGATTAATTATT-ATGTTGTTCTCGTAATTAATTTA
1 TAGTAAGGATTAATTATTGA-GTTATTCTCGTAATTAATTTA
*
12930793 TAGTAAGGATTAATTATTGAGTTATTTTCGTAATTAATTTA
1 TAGTAAGGATTAATTATTGAGTTATTCTCGTAATTAATTTA
12930834 TAGCTAAGGA
1 TAG-TAAGGA
12930844 AAGATCAGTG
Statistics
Matches: 47, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
41 40 0.85
42 7 0.15
ACGTcount: A:0.34, C:0.04, G:0.16, T:0.46
Consensus pattern (41 bp):
TAGTAAGGATTAATTATTGAGTTATTCTCGTAATTAATTTA
Found at i:12935295 original size:23 final size:23
Alignment explanation
Indices: 12935267--12935311 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
12935257 GTTCAAAATT
*
12935267 TTAAAATAAACAATATATATGAG
1 TTAAAACAAACAATATATATGAG
*
12935290 TTAAAACAAATAATATATATGA
1 TTAAAACAAACAATATATATGA
12935312 ATGTACAATT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.58, C:0.04, G:0.07, T:0.31
Consensus pattern (23 bp):
TTAAAACAAACAATATATATGAG
Found at i:12936179 original size:23 final size:22
Alignment explanation
Indices: 12936151--12936195 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 22
12936141 AAATTAAATC
12936151 TCTAAGATTACAAACTCTTATCT
1 TCTAAGATTACAAA-TCTTATCT
* *
12936174 TCTAAGATTGCATATCTTATCT
1 TCTAAGATTACAAATCTTATCT
12936196 AAGATTGTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 8 0.40
23 12 0.60
ACGTcount: A:0.31, C:0.20, G:0.07, T:0.42
Consensus pattern (22 bp):
TCTAAGATTACAAATCTTATCT
Found at i:12936198 original size:19 final size:20
Alignment explanation
Indices: 12936174--12936227 Score: 85
Period size: 19 Copynumber: 2.8 Consensus size: 20
12936164 ACTCTTATCT
12936174 TCTAAGATTGCATATCT-TA
1 TCTAAGATTGCATATCTATA
*
12936193 TCTAAGATTGTATAT-TATA
1 TCTAAGATTGCATATCTATA
12936212 TCTAAGATTGCATATC
1 TCTAAGATTGCATATC
12936228 CTTTTTCAAG
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
18 1 0.03
19 30 0.97
ACGTcount: A:0.33, C:0.13, G:0.11, T:0.43
Consensus pattern (20 bp):
TCTAAGATTGCATATCTATA
Found at i:12947085 original size:30 final size:30
Alignment explanation
Indices: 12947051--12947107 Score: 87
Period size: 30 Copynumber: 1.9 Consensus size: 30
12947041 GTCGCATGAT
12947051 CGTGTGTCACACACCATTGTTTGGCACGAC
1 CGTGTGTCACACACCATTGTTTGGCACGAC
* **
12947081 CGTGTGTTACACACGGTTGTTTGGCAC
1 CGTGTGTCACACACCATTGTTTGGCAC
12947108 AACCATGTAG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.18, C:0.26, G:0.26, T:0.30
Consensus pattern (30 bp):
CGTGTGTCACACACCATTGTTTGGCACGAC
Found at i:12948598 original size:23 final size:23
Alignment explanation
Indices: 12948572--12948623 Score: 68
Period size: 23 Copynumber: 2.3 Consensus size: 23
12948562 AGGCTGAAAA
* *
12948572 TGCTAAAAATCTATTTGTTACAG
1 TGCTAAAAATCTATTTGTTAAAC
* *
12948595 TGCTGAAAATGTATTTGTTAAAC
1 TGCTAAAAATCTATTTGTTAAAC
12948618 TGCTAA
1 TGCTAA
12948624 GAAGGAAGAT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.35, C:0.12, G:0.15, T:0.38
Consensus pattern (23 bp):
TGCTAAAAATCTATTTGTTAAAC
Found at i:12948760 original size:6 final size:6
Alignment explanation
Indices: 12948749--12948774 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
12948739 TAATAAAAAA
12948749 TTTTAT TTTTAT TTTTAT TTTTAT TT
1 TTTTAT TTTTAT TTTTAT TTTTAT TT
12948775 AATTTTTCAC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (6 bp):
TTTTAT
Found at i:12948769 original size:11 final size:11
Alignment explanation
Indices: 12948748--12948781 Score: 50
Period size: 12 Copynumber: 3.0 Consensus size: 11
12948738 TTAATAAAAA
12948748 ATTTTATTTTT
1 ATTTTATTTTT
12948759 ATTTTTATTTTT
1 A-TTTTATTTTT
*
12948771 ATTTAATTTTT
1 ATTTTATTTTT
12948782 CACAATTTCC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
11 10 0.48
12 11 0.52
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (11 bp):
ATTTTATTTTT
Found at i:12957060 original size:44 final size:44
Alignment explanation
Indices: 12957010--12957098 Score: 160
Period size: 44 Copynumber: 2.0 Consensus size: 44
12957000 ATATATCTGA
* *
12957010 CAAGTTCGCTAAATCTGACATCAATATATACATGTAGAAGGTCC
1 CAAGTTCGCTAAATCTGACATCAATAAATACATGTAGAAGATCC
12957054 CAAGTTCGCTAAATCTGACATCAATAAATACATGTAGAAGATCC
1 CAAGTTCGCTAAATCTGACATCAATAAATACATGTAGAAGATCC
12957098 C
1 C
12957099 GAAGCTTAAC
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
44 43 1.00
ACGTcount: A:0.38, C:0.21, G:0.15, T:0.26
Consensus pattern (44 bp):
CAAGTTCGCTAAATCTGACATCAATAAATACATGTAGAAGATCC
Found at i:12960121 original size:74 final size:74
Alignment explanation
Indices: 12959973--12960141 Score: 214
Period size: 74 Copynumber: 2.3 Consensus size: 74
12959963 TGTAAGAGAG
* *
12959973 CCACAAACCCTGAAAACATTAATTTTCATAAACCGTAATTCAAACATGAAAGAGATTACATTGTT
1 CCACAAACCCTGAAAACATTAATTTTCATAAACCGTAATTCAAACATGAAAGAGATGACATTATT
*
12960038 GGTAGACAA
66 GGTACACAA
** * * ** * *
12960047 CCATGAACCCTGAAAACATTAATTTTCATATACTGTAATTCGGACGTGAAAGAGATGATATTATT
1 CCACAAACCCTGAAAACATTAATTTTCATAAACCGTAATTCAAACATGAAAGAGATGACATTATT
12960112 -GTGACACAA
66 GGT-ACACAA
*
12960121 CCACAAAACCTGAAAACATTA
1 CCACAAACCCTGAAAACATTA
12960142 GTTTCCATGG
Statistics
Matches: 80, Mismatches: 14, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
73 2 0.03
74 78 0.98
ACGTcount: A:0.42, C:0.19, G:0.13, T:0.26
Consensus pattern (74 bp):
CCACAAACCCTGAAAACATTAATTTTCATAAACCGTAATTCAAACATGAAAGAGATGACATTATT
GGTACACAA
Found at i:12971569 original size:41 final size:40
Alignment explanation
Indices: 12971481--12971573 Score: 98
Period size: 40 Copynumber: 2.2 Consensus size: 40
12971471 TCATCCATTT
* * *
12971481 AATTCAAACCCCCAAATCTATTCTTTTTCTTAAAAAAACTTA
1 AATT-AAA-CCCCAAATCTATTATTCTTCTTAAAAAAACCTA
*
12971523 AATTAAACCCCAAATAC-ATTATTCTTCTTAAAAAATCCCTA
1 AATTAAACCCCAAAT-CTATTATTCTTCTTAAAAAA-ACCTA
*
12971564 GATTAAACCC
1 AATTAAACCC
12971574 TCTATTCATC
Statistics
Matches: 44, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
40 24 0.55
41 16 0.36
42 4 0.09
ACGTcount: A:0.42, C:0.25, G:0.01, T:0.32
Consensus pattern (40 bp):
AATTAAACCCCAAATCTATTATTCTTCTTAAAAAAACCTA
Found at i:12983397 original size:27 final size:27
Alignment explanation
Indices: 12983357--12983409 Score: 79
Period size: 27 Copynumber: 2.0 Consensus size: 27
12983347 CCAGTGAGTC
* * *
12983357 GGGGAATTAGCACTTCGCAACCCCTTG
1 GGGGAATCAACACTTAGCAACCCCTTG
12983384 GGGGAATCAACACTTAGCAACCCCTT
1 GGGGAATCAACACTTAGCAACCCCTT
12983410 ATACAATCCG
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.26, C:0.30, G:0.23, T:0.21
Consensus pattern (27 bp):
GGGGAATCAACACTTAGCAACCCCTTG
Found at i:12983469 original size:33 final size:33
Alignment explanation
Indices: 12983427--12983631 Score: 115
Period size: 33 Copynumber: 5.6 Consensus size: 33
12983417 CCGTTACGGT
12983427 GGAATCAGCACTTAGCAACCACCGATGATTTGG
1 GGAATCAGCACTTAGCAACCACCGATGATTTGG
** *
12983460 GGAATCAGCACTTAGCAACC-CCTTTCATATTCGAAGACACGG
1 GGAATCAGCACTTAGCAACCACCGATGAT-TT---------GG
** *
12983502 TGGAATCAATATTTAGCAACCACCGATGATTTGG
1 -GGAATCAGCACTTAGCAACCACCGATGATTTGG
* * ***
12983536 GGAATCAGCACTTAGAAACCCCTTTCATATCCGAAGACACGG
1 GGAATCAGCACTTAGCAA---C---C--A-CCGATGATTTGG
12983578 TGGAATCAGCACTTAGCAACCACCGATGATTTGG
1 -GGAATCAGCACTTAGCAACCACCGATGATTTGG
12983612 GGAATCAGCACTTAGCAACC
1 GGAATCAGCACTTAGCAACC
12983632 CCTTTTTATG
Statistics
Matches: 128, Mismatches: 22, Indels: 44
0.66 0.11 0.23
Matches are distributed among these distances:
32 5 0.04
33 56 0.44
34 10 0.08
35 1 0.01
36 1 0.01
37 1 0.01
39 1 0.01
40 1 0.01
41 1 0.01
42 10 0.08
43 36 0.28
44 5 0.04
ACGTcount: A:0.32, C:0.25, G:0.21, T:0.22
Consensus pattern (33 bp):
GGAATCAGCACTTAGCAACCACCGATGATTTGG
Found at i:12983526 original size:76 final size:76
Alignment explanation
Indices: 12983384--12983636 Score: 388
Period size: 76 Copynumber: 3.4 Consensus size: 76
12983374 CAACCCCTTG
* **
12983384 GGGGAATCAACACTTAGCAACCCCTTATACA-ATCC---GTTACGGTGGAATCAGCACTTAGCAA
1 GGGGAATCAGCACTTAGCAACCCCTT-T-CATATCCGAAGACACGGTGGAATCAGCACTTAGCAA
12983445 CCACCGATGATTT
64 CCACCGATGATTT
* ** *
12983458 GGGGAATCAGCACTTAGCAACCCCTTTCATATTCGAAGACACGGTGGAATCAATATTTAGCAACC
1 GGGGAATCAGCACTTAGCAACCCCTTTCATATCCGAAGACACGGTGGAATCAGCACTTAGCAACC
12983523 ACCGATGATTT
66 ACCGATGATTT
*
12983534 GGGGAATCAGCACTTAGAAACCCCTTTCATATCCGAAGACACGGTGGAATCAGCACTTAGCAACC
1 GGGGAATCAGCACTTAGCAACCCCTTTCATATCCGAAGACACGGTGGAATCAGCACTTAGCAACC
12983599 ACCGATGATTT
66 ACCGATGATTT
12983610 GGGGAATCAGCACTTAGCAACCCCTTT
1 GGGGAATCAGCACTTAGCAACCCCTTT
12983637 TTATGTTCAA
Statistics
Matches: 162, Mismatches: 13, Indels: 6
0.90 0.07 0.03
Matches are distributed among these distances:
72 2 0.01
73 4 0.02
74 25 0.15
76 131 0.81
ACGTcount: A:0.31, C:0.26, G:0.20, T:0.23
Consensus pattern (76 bp):
GGGGAATCAGCACTTAGCAACCCCTTTCATATCCGAAGACACGGTGGAATCAGCACTTAGCAACC
ACCGATGATTT
Found at i:12991919 original size:29 final size:30
Alignment explanation
Indices: 12991877--12991933 Score: 89
Period size: 29 Copynumber: 1.9 Consensus size: 30
12991867 CACCTACGTC
*
12991877 ACCCTTTCAGTCTC-TTTCTAGGCACAAAT
1 ACCCTTTCAGTCTCATTGCTAGGCACAAAT
*
12991906 ACCCTTTCAGTCTCATTGCTTGGCACAA
1 ACCCTTTCAGTCTCATTGCTAGGCACAA
12991934 GTTATACTCA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
29 14 0.56
30 11 0.44
ACGTcount: A:0.23, C:0.32, G:0.12, T:0.33
Consensus pattern (30 bp):
ACCCTTTCAGTCTCATTGCTAGGCACAAAT
Found at i:13000470 original size:39 final size:39
Alignment explanation
Indices: 13000425--13000509 Score: 109
Period size: 39 Copynumber: 2.2 Consensus size: 39
13000415 CAATATTGTT
*
13000425 ATTTTTTAATAAAAATTCTATAAAACTTAAATTTTT-TATA
1 ATTTTTTAAT-AAAATTCTATAAAA-TTAAATTTTTAAATA
* * *
13000465 ATTTTTTAATAAAATTTTATAATATTATATTTTTAAATA
1 ATTTTTTAATAAAATTCTATAAAATTAAATTTTTAAATA
13000504 ATTTTT
1 ATTTTT
13000510 AAATTTTAAA
Statistics
Matches: 40, Mismatches: 4, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
38 9 0.22
39 21 0.52
40 10 0.25
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.55
Consensus pattern (39 bp):
ATTTTTTAATAAAATTCTATAAAATTAAATTTTTAAATA
Found at i:13012723 original size:31 final size:30
Alignment explanation
Indices: 13012678--13012737 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 30
13012668 TATTATCTAT
* *
13012678 CTAGATTATATATTTTATTTTAAGTTGGTAC
1 CTAGATTATATA-TTTATCTCAAGTTGGTAC
* *
13012709 CTAGATTTTTTATTTATCTCAAGTTGGTA
1 CTAGATTATATATTTATCTCAAGTTGGTA
13012738 TTTAAACATT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
30 15 0.60
31 10 0.40
ACGTcount: A:0.27, C:0.08, G:0.13, T:0.52
Consensus pattern (30 bp):
CTAGATTATATATTTATCTCAAGTTGGTAC
Found at i:13013927 original size:2 final size:2
Alignment explanation
Indices: 13013922--13013956 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
13013912 GACCACACAA
13013922 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
13013957 ATATATATAT
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:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:13013961 original size:2 final size:2
Alignment explanation
Indices: 13013956--13013997 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
13013946 TCTCTCTCTC
13013956 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
13013998 AAAGTTTCTA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:13032876 original size:27 final size:26
Alignment explanation
Indices: 13032844--13032894 Score: 77
Period size: 27 Copynumber: 1.9 Consensus size: 26
13032834 ACCGTAAGTA
13032844 GCGGAC-AGTCATGCAAACATACAAATG
1 GCGGACTA-TCATGCAAACA-ACAAATG
13032871 GCGGACTATCATGCAAACAACAAA
1 GCGGACTATCATGCAAACAACAAA
13032895 CTGTAGATTC
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
26 5 0.22
27 17 0.74
28 1 0.04
ACGTcount: A:0.43, C:0.24, G:0.20, T:0.14
Consensus pattern (26 bp):
GCGGACTATCATGCAAACAACAAATG
Found at i:13044167 original size:8 final size:8
Alignment explanation
Indices: 13044154--13044206 Score: 52
Period size: 8 Copynumber: 6.4 Consensus size: 8
13044144 CCGTAAAAAT
13044154 TAAAATAA
1 TAAAATAA
13044162 TAAAATAA
1 TAAAATAA
* *
13044170 TAATATAT
1 TAAAATAA
* *
13044178 TCGTAAATAT
1 T--AAAATAA
13044188 TAAAATAA
1 TAAAATAA
13044196 TAAAATAA
1 TAAAATAA
13044204 TAA
1 TAA
13044207 CTTACTCATC
Statistics
Matches: 37, Mismatches: 6, Indels: 4
0.79 0.13 0.09
Matches are distributed among these distances:
8 31 0.84
10 6 0.16
ACGTcount: A:0.64, C:0.02, G:0.02, T:0.32
Consensus pattern (8 bp):
TAAAATAA
Found at i:13044174 original size:34 final size:34
Alignment explanation
Indices: 13044136--13044206 Score: 124
Period size: 34 Copynumber: 2.1 Consensus size: 34
13044126 AATACGACCT
13044136 TAATATATCCGTAAAAATTAAAATAATAAAATAA
1 TAATATATCCGTAAAAATTAAAATAATAAAATAA
* *
13044170 TAATATATTCGTAAATATTAAAATAATAAAATAA
1 TAATATATCCGTAAAAATTAAAATAATAAAATAA
13044204 TAA
1 TAA
13044207 CTTACTCATC
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.61, C:0.04, G:0.03, T:0.32
Consensus pattern (34 bp):
TAATATATCCGTAAAAATTAAAATAATAAAATAA
Found at i:13048971 original size:45 final size:44
Alignment explanation
Indices: 13048897--13048999 Score: 145
Period size: 45 Copynumber: 2.3 Consensus size: 44
13048887 GCTATACGCC
* * *
13048897 TAAAAATGAGTAAGACCATAACTGAAAGATGCTATGACATCATGA
1 TAAAGATGAGTAAGAACATAACTGAAAGATGCTATGACATCA-CA
*
13048942 TAAAGATGAATAAGAACATAGA-TGAAAGATGCTATGACATCACA
1 TAAAGATGAGTAAGAACATA-ACTGAAAGATGCTATGACATCACA
13048986 TAAAGATGAGTAAG
1 TAAAGATGAGTAAG
13049000 TGATACGTCT
Statistics
Matches: 52, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
44 14 0.27
45 37 0.71
46 1 0.02
ACGTcount: A:0.49, C:0.11, G:0.19, T:0.21
Consensus pattern (44 bp):
TAAAGATGAGTAAGAACATAACTGAAAGATGCTATGACATCACA
Found at i:13048990 original size:21 final size:21
Alignment explanation
Indices: 13048921--13048993 Score: 76
Period size: 22 Copynumber: 3.3 Consensus size: 21
13048911 ACCATAACTG
13048921 AAAGATGCTATGACATCATGAT
1 AAAGATGCTATGACATCA-GAT
* *
13048943 AAAGATGAATAAGAACAT-AGAT
1 AAAGATG-CTATG-ACATCAGAT
*
13048965 GAAAGATGCTATGACATCACAT
1 -AAAGATGCTATGACATCAGAT
13048987 AAAGATG
1 AAAGATG
13048994 AGTAAGTGAT
Statistics
Matches: 42, Mismatches: 5, Indels: 9
0.75 0.09 0.16
Matches are distributed among these distances:
21 11 0.26
22 16 0.38
23 11 0.26
24 4 0.10
ACGTcount: A:0.48, C:0.11, G:0.19, T:0.22
Consensus pattern (21 bp):
AAAGATGCTATGACATCAGAT
Found at i:13050533 original size:15 final size:16
Alignment explanation
Indices: 13050513--13050542 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
13050503 TTTTTTGCAT
13050513 TTCA-TTGCATTTAGG
1 TTCATTTGCATTTAGG
13050528 TTCATTTGCATTTAG
1 TTCATTTGCATTTAG
13050543 TTAATTAATT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.29
16 10 0.71
ACGTcount: A:0.20, C:0.13, G:0.17, T:0.50
Consensus pattern (16 bp):
TTCATTTGCATTTAGG
Found at i:13054890 original size:21 final size:21
Alignment explanation
Indices: 13054852--13054892 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
13054842 TTGATTGGTT
*
13054852 TATTTATTTTTATCATTTGTC
1 TATTTATTCTTATCATTTGTC
13054873 TATTT-TTCTTATCTATTTGT
1 TATTTATTCTTATC-ATTTGT
13054893 TTTTTGTTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 7 0.39
21 11 0.61
ACGTcount: A:0.17, C:0.10, G:0.05, T:0.68
Consensus pattern (21 bp):
TATTTATTCTTATCATTTGTC
Found at i:13060883 original size:25 final size:25
Alignment explanation
Indices: 13060851--13060934 Score: 159
Period size: 25 Copynumber: 3.4 Consensus size: 25
13060841 AGCTGTAAAT
13060851 GGTAAGCTCCTCCAAGCTGAATAAC
1 GGTAAGCTCCTCCAAGCTGAATAAC
13060876 GGTAAGCTCCTCCAAGCTGAATAAC
1 GGTAAGCTCCTCCAAGCTGAATAAC
*
13060901 GGTAAGCTCCTCTAAGCTGAATAAC
1 GGTAAGCTCCTCCAAGCTGAATAAC
13060926 GGTAAGCTC
1 GGTAAGCTC
13060935 ATGCGAGTTG
Statistics
Matches: 58, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
25 58 1.00
ACGTcount: A:0.31, C:0.26, G:0.21, T:0.21
Consensus pattern (25 bp):
GGTAAGCTCCTCCAAGCTGAATAAC
Found at i:13060955 original size:50 final size:50
Alignment explanation
Indices: 13060848--13060959 Score: 161
Period size: 50 Copynumber: 2.2 Consensus size: 50
13060838 ACGAGCTGTA
*
13060848 AATGGTAAGCTCCTCCAAGCTGAATAACGGTAAGCTCCTCCAAGCTGAAT
1 AATGGTAAGCTCCTCCAAGCTGAATAACGGTAAGCTCATCCAAGCTGAAT
* * * * * *
13060898 AACGGTAAGCTCCTCTAAGCTGAATAACGGTAAGCTCATGCGAGTTGAGT
1 AATGGTAAGCTCCTCCAAGCTGAATAACGGTAAGCTCATCCAAGCTGAAT
13060948 AATGGTAAGCTC
1 AATGGTAAGCTC
13060960 ATATGAGATG
Statistics
Matches: 54, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
50 54 1.00
ACGTcount: A:0.31, C:0.22, G:0.23, T:0.23
Consensus pattern (50 bp):
AATGGTAAGCTCCTCCAAGCTGAATAACGGTAAGCTCATCCAAGCTGAAT
Found at i:13069405 original size:25 final size:24
Alignment explanation
Indices: 13069377--13069445 Score: 75
Period size: 25 Copynumber: 2.8 Consensus size: 24
13069367 GTTACCAATG
*
13069377 TCAGCTCGTATGAGCTTACTGATA
1 TCAGCTCGCATGAGCTTACTGATA
* *
13069401 CTCAGCTCACATGAGCTTACTGTTA
1 -TCAGCTCGCATGAGCTTACTGATA
* *
13069426 TCCAGCTCGGAGGAGCTTAC
1 T-CAGCTCGCATGAGCTTAC
13069446 CGTTATTCAG
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
24 1 0.03
25 36 0.97
ACGTcount: A:0.23, C:0.26, G:0.22, T:0.29
Consensus pattern (24 bp):
TCAGCTCGCATGAGCTTACTGATA
Found at i:13069450 original size:25 final size:25
Alignment explanation
Indices: 13069403--13069471 Score: 93
Period size: 25 Copynumber: 2.8 Consensus size: 25
13069393 TACTGATACT
* * *
13069403 CAGCTCACATGAGCTTACTGTTATC
1 CAGCTCAGAGGAGCTTACCGTTATC
* *
13069428 CAGCTCGGAGGAGCTTACCGTTATT
1 CAGCTCAGAGGAGCTTACCGTTATC
13069453 CAGCTCAGAGGAGCTTACC
1 CAGCTCAGAGGAGCTTACC
13069472 ATTTACAGCT
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
25 38 1.00
ACGTcount: A:0.23, C:0.28, G:0.23, T:0.26
Consensus pattern (25 bp):
CAGCTCAGAGGAGCTTACCGTTATC
Found at i:13069495 original size:24 final size:25
Alignment explanation
Indices: 13069468--13069519 Score: 61
Period size: 25 Copynumber: 2.1 Consensus size: 25
13069458 CAGAGGAGCT
*
13069468 TACC-ATTTACAGCTCGTAAAAGCA
1 TACCGATTCACAGCTCGTAAAAGCA
* **
13069492 TACCGATTCAGAGCTCGTATGAGCA
1 TACCGATTCACAGCTCGTAAAAGCA
13069517 TAC
1 TAC
13069520 ATGTACAAGA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
24 4 0.17
25 19 0.83
ACGTcount: A:0.33, C:0.25, G:0.17, T:0.25
Consensus pattern (25 bp):
TACCGATTCACAGCTCGTAAAAGCA
Found at i:13075444 original size:25 final size:24
Alignment explanation
Indices: 13075396--13075479 Score: 116
Period size: 25 Copynumber: 3.4 Consensus size: 24
13075386 TCATTAGGGA
*
13075396 TTACCGATTTCAGCTTGTATGAGC
1 TTACCGATTTCAGCTCGTATGAGC
13075420 TTACCGATTTACAGCTCGTGA-GAGC
1 TTACCGATTT-CAGCTCGT-ATGAGC
*
13075445 TTATCGATTCTCAGCTCGTATGAGC
1 TTACCGATT-TCAGCTCGTATGAGC
13075470 TTACCGATTT
1 TTACCGATTT
13075480 ACATCTCATA
Statistics
Matches: 53, Mismatches: 3, Indels: 8
0.83 0.05 0.12
Matches are distributed among these distances:
24 12 0.23
25 39 0.74
26 2 0.04
ACGTcount: A:0.21, C:0.23, G:0.20, T:0.36
Consensus pattern (24 bp):
TTACCGATTTCAGCTCGTATGAGC
Found at i:13075503 original size:50 final size:50
Alignment explanation
Indices: 13075398--13075517 Score: 136
Period size: 50 Copynumber: 2.4 Consensus size: 50
13075388 ATTAGGGATT
* * * * **
13075398 ACCGATT-TCAGCTTGTATGAGCTTACCGATTTACAGCTCGTGAGAGCTT
1 ACCGATTCTCAGCTCGTATGAGCTTACCGATTTACAGCTCATAAAAGCAG
* *
13075447 ATCGATTCTCAGCTCGTATGAGCTTACCGATTTACATCTCATAAAAGCAG
1 ACCGATTCTCAGCTCGTATGAGCTTACCGATTTACAGCTCATAAAAGCAG
*
13075497 ACCGATTCAT-AGCTCGAATGA
1 ACCGATTC-TCAGCTCGTATGA
13075518 CCATACATGT
Statistics
Matches: 59, Mismatches: 10, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
49 6 0.10
50 52 0.88
51 1 0.02
ACGTcount: A:0.28, C:0.23, G:0.19, T:0.30
Consensus pattern (50 bp):
ACCGATTCTCAGCTCGTATGAGCTTACCGATTTACAGCTCATAAAAGCAG
Found at i:13076645 original size:15 final size:16
Alignment explanation
Indices: 13076625--13076654 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
13076615 TGGTACCTTG
13076625 TTGAT-ATGTGTTAAT
1 TTGATAATGTGTTAAT
13076640 TTGATAATGTGTTAA
1 TTGATAATGTGTTAA
13076655 AGCATGTTTG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.30, C:0.00, G:0.20, T:0.50
Consensus pattern (16 bp):
TTGATAATGTGTTAAT
Found at i:13076995 original size:16 final size:15
Alignment explanation
Indices: 13076968--13076997 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
13076958 ATGAGTTATG
13076968 GTTAATTATGTATAA
1 GTTAATTATGTATAA
13076983 GTTAATATATGTATA
1 GTTAAT-TATGTATA
13076998 TTTGAGATGC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.40, C:0.00, G:0.13, T:0.47
Consensus pattern (15 bp):
GTTAATTATGTATAA
Found at i:13093495 original size:14 final size:14
Alignment explanation
Indices: 13093476--13093508 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
13093466 GTAAACTCCT
13093476 TTAACCCTTAACTC
1 TTAACCCTTAACTC
13093490 TTAACCCTTAACTC
1 TTAACCCTTAACTC
*
13093504 CTAAC
1 TTAAC
13093509 TCCATGGACA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.30, C:0.36, G:0.00, T:0.33
Consensus pattern (14 bp):
TTAACCCTTAACTC
Found at i:13094706 original size:20 final size:20
Alignment explanation
Indices: 13094667--13094707 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
13094657 ATTCATGAAG
*
13094667 TTAAAAAAATAAATCTTAAT
1 TTAAAAAAATAAATCGTAAT
13094687 TTAAAGAAAATAAA-CGTAAT
1 TTAAA-AAAATAAATCGTAAT
13094707 T
1 T
13094708 ATCTACAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 11 0.58
21 8 0.42
ACGTcount: A:0.59, C:0.05, G:0.05, T:0.32
Consensus pattern (20 bp):
TTAAAAAAATAAATCGTAAT
Found at i:13096776 original size:127 final size:125
Alignment explanation
Indices: 13096550--13096830 Score: 302
Period size: 127 Copynumber: 2.2 Consensus size: 125
13096540 CAAGTTTAAT
* * * *
13096550 GAGAAAGATCGAAATCCCGTAAGTTAGGGTACGATTTCTCGAATTACCCAAAACGCGAAATGTTG
1 GAGAAA-ATTGAAACCCCGTAAGTTAGGGTACGATTTCTCGAATTACCCAAAACGCAAAATATTG
* * * * *
13096615 CCGTATATCGAAATTTCTTTGATTTTGAAGCTTAAAAAGGGTACTT-TGCTATTTAGGTTT-GAC
65 CCGTACATCGAAATTCCTTTGATTTTGAAGCTT-AAAAGGATACTTCTGCT-TTCA-ATTTAG-C
*
13096678 GAGAAAATTGAAACCCCGTAAGTTAGGGTACGATTTCTCGAAATTA-CCAAAATGCAAAATATTG
1 GAGAAAATTGAAACCCCGTAAGTTAGGGTACGATTTCTCG-AATTACCCAAAACGCAAAATATTG
* * * * * *
13096742 CC-T-CGTCGAGATTCCTTTCGTTTTTGAAATCTTAAAAGGATACTTCGTGGTTTCAATTTAGT
65 CCGTACATCGAAATTCCTTT-GATTTTG-AAGCTTAAAAGGATACTTC-TGCTTTCAATTTAGC
13096804 GAGAAAATTGAAACCCCGTAAGTTAGG
1 GAGAAAATTGAAACCCCGTAAGTTAGG
13096831 ATACTGTAGC
Statistics
Matches: 131, Mismatches: 16, Indels: 14
0.81 0.10 0.09
Matches are distributed among these distances:
125 11 0.08
126 48 0.37
127 58 0.44
128 14 0.11
ACGTcount: A:0.32, C:0.16, G:0.20, T:0.31
Consensus pattern (125 bp):
GAGAAAATTGAAACCCCGTAAGTTAGGGTACGATTTCTCGAATTACCCAAAACGCAAAATATTGC
CGTACATCGAAATTCCTTTGATTTTGAAGCTTAAAAGGATACTTCTGCTTTCAATTTAGC
Found at i:13099604 original size:29 final size:30
Alignment explanation
Indices: 13099557--13099637 Score: 92
Period size: 31 Copynumber: 2.7 Consensus size: 30
13099547 GAATTTGATC
* *
13099557 AAATCAAAATCTCATGTATAAAATTGT-GTA
1 AAATCAAAGT-TCATGTATAAAATTGTAATA
* *
13099587 AAATCAAAGTTCATGTATACAATTGTACATT
1 AAATCAAAGTTCATGTATAAAATTGTA-ATA
*
13099618 AAATCATAGTTCATGTATAA
1 AAATCAAAGTTCATGTATAA
13099638 TTTTGATATT
Statistics
Matches: 43, Mismatches: 6, Indels: 3
0.83 0.12 0.06
Matches are distributed among these distances:
29 15 0.35
30 9 0.21
31 19 0.44
ACGTcount: A:0.44, C:0.11, G:0.10, T:0.35
Consensus pattern (30 bp):
AAATCAAAGTTCATGTATAAAATTGTAATA
Found at i:13136492 original size:29 final size:29
Alignment explanation
Indices: 13136448--13136715 Score: 290
Period size: 29 Copynumber: 9.2 Consensus size: 29
13136438 GTGTGCTAAA
13136448 CGATGGTCGAAACCATCCCTTTTCATATT
1 CGATGGTCGAAACCATCCCTTTTCATATT
*
13136477 CAATGGTC-AAAGCCATCCCTTTTCATATT
1 CGATGGTCGAAA-CCATCCCTTTTCATATT
13136506 CGATGGTCGAAACCATCCCTTTTCATATT
1 CGATGGTCGAAACCATCCCTTTTCATATT
* * ** *
13136535 TGATAGTCGTCACCATCCCTTTACATATT
1 CGATGGTCGAAACCATCCCTTTTCATATT
*
13136564 CGATGGTC-ATCACCATCCCTTTTCATATT
1 CGATGGTCGA-AACCATCCCTTTTCATATT
* * * *
13136593 TGATAGTCGAAACCATCCATTTTCTTTAATT
1 CGATGGTCGAAACCATCCCTTTTC-AT-ATT
* *
13136624 -GATGGTCGAAGCCATCCTTTTTCATATT
1 CGATGGTCGAAACCATCCCTTTTCATATT
** ** * *
13136652 TAATGGTCGTCACCATCTCTTTTCATATC
1 CGATGGTCGAAACCATCCCTTTTCATATT
* *
13136681 CAATGGTCGAAACCATCCGTTTTCATATT
1 CGATGGTCGAAACCATCCCTTTTCATATT
13136710 CGATGG
1 CGATGG
13136716 GTGTCGATAC
Statistics
Matches: 198, Mismatches: 34, Indels: 14
0.80 0.14 0.06
Matches are distributed among these distances:
28 6 0.03
29 164 0.83
30 25 0.13
31 3 0.02
ACGTcount: A:0.24, C:0.26, G:0.13, T:0.37
Consensus pattern (29 bp):
CGATGGTCGAAACCATCCCTTTTCATATT
Done.