Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr13 ID=Chr13-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: 58321163
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 747533 characters in sequence are not A, C, G, or T
File 97 of 199
Found at i:29698677 original size:16 final size:16
Alignment explanation
Indices: 29698615--29698684 Score: 68
Period size: 16 Copynumber: 4.4 Consensus size: 16
29698605 TTCGGTTCGC
* *
29698615 TGTATTGGAATAGAGG
1 TGTAATGGAATAGAAG
* * *
29698631 CGTAATGGATTAGAGG
1 TGTAATGGAATAGAAG
* *
29698647 TGTAATAGATTAGAAG
1 TGTAATGGAATAGAAG
*
29698663 TGTAATGGAATAGAAT
1 TGTAATGGAATAGAAG
29698679 TGTAAT
1 TGTAAT
29698685 AGCAAATCAA
Statistics
Matches: 45, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
16 45 1.00
ACGTcount: A:0.37, C:0.01, G:0.30, T:0.31
Consensus pattern (16 bp):
TGTAATGGAATAGAAG
Found at i:29698729 original size:45 final size:44
Alignment explanation
Indices: 29698663--29698753 Score: 105
Period size: 44 Copynumber: 2.0 Consensus size: 44
29698653 AGATTAGAAG
**
29698663 TGTAATGGAATAGAATTGTAATAGCAAATCAAT-TGTTTGGTTGAA
1 TGTAATGGAATAGAAGCGTAATAG-AAATC-ATGTGTTTGGTTGAA
* *
29698708 TGTAATGGAATA-AAGGCGTAATAGTAATCTTGTGTTTGGTTGAA
1 TGTAATGGAATAGAA-GCGTAATAGAAATCATGTGTTTGGTTGAA
29698752 TG
1 TG
29698754 GAATAGAGGA
Statistics
Matches: 40, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
43 1 0.03
44 20 0.50
45 19 0.47
ACGTcount: A:0.34, C:0.04, G:0.25, T:0.36
Consensus pattern (44 bp):
TGTAATGGAATAGAAGCGTAATAGAAATCATGTGTTTGGTTGAA
Found at i:29698935 original size:16 final size:16
Alignment explanation
Indices: 29698898--29698939 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
29698888 TTAATCATAT
*
29698898 TTAAACATA-ATTATTA
1 TTAAA-ATATATTATAA
29698914 TT-AAATATATTATAA
1 TTAAAATATATTATAA
29698929 TTAAAATATAT
1 TTAAAATATAT
29698940 AATTTAATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 3 0.13
15 10 0.43
16 10 0.43
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (16 bp):
TTAAAATATATTATAA
Found at i:29698946 original size:14 final size:15
Alignment explanation
Indices: 29698907--29698948 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
29698897 TTTAAACATA
*
29698907 ATTATTATTAAATAT
1 ATTATAATTAAATAT
29698922 ATTATAATTAAA-AT
1 ATTATAATTAAATAT
*
29698936 A-TATAATTTAATA
1 ATTATAATTAAATA
29698949 AAATTCTTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 9 0.38
14 4 0.17
15 11 0.46
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
ATTATAATTAAATAT
Found at i:29699040 original size:120 final size:120
Alignment explanation
Indices: 29698896--29699247 Score: 582
Period size: 120 Copynumber: 2.9 Consensus size: 120
29698886 ATTTAATCAT
29698896 ATTTAAACATAATTATTATTAAATAT-ATTATAATTAAAATATATAATTTAATAAAATTCTTAAT
1 ATTT-AACATAATTATTATTAAATATAATT-TAATTAAAATATATAATTTAATAAAATTCTTAAT
* *
29698960 AATT-AATATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAAGATA
64 -ATTAAATATTCTTATATGAATTTACTAAAATCATAATATATAATACTATAAAAGATA
29699017 ATTTAACATAATTATTATTAAATATAATTTAATTAAAATATATAATTTAATAAAATTCTTAATAT
1 ATTTAACATAATTATTATTAAATATAATTTAATTAAAATATATAATTTAATAAAATTCTTAATAT
** * *
29699082 TAAATATTCTTAGGTGAATTTACTAAAATCATAATATATAATAATATAAAATATA
66 TAAATATTCTTATATGAATTTACTAAAATCATAATATATAATACTATAAAAGATA
* * *
29699137 ATTTAAAATGATTATTATTAAATATAATTTAATAAAAATATATAATTTAATAAAATTCTTAATAT
1 ATTTAACATAATTATTATTAAATATAATTTAATTAAAATATATAATTTAATAAAATTCTTAATAT
29699202 TAAATATTCTTATATGAATTTACTAAAATCATAATATATAATACTA
66 TAAATATTCTTATATGAATTTACTAAAATCATAATATATAATACTA
29699248 AAATCATAAT
Statistics
Matches: 217, Mismatches: 12, Indels: 5
0.93 0.05 0.02
Matches are distributed among these distances:
119 3 0.01
120 207 0.95
121 7 0.03
ACGTcount: A:0.50, C:0.05, G:0.02, T:0.43
Consensus pattern (120 bp):
ATTTAACATAATTATTATTAAATATAATTTAATTAAAATATATAATTTAATAAAATTCTTAATAT
TAAATATTCTTATATGAATTTACTAAAATCATAATATATAATACTATAAAAGATA
Found at i:29699059 original size:18 final size:17
Alignment explanation
Indices: 29699038--29699072 Score: 61
Period size: 18 Copynumber: 2.0 Consensus size: 17
29699028 TTATTATTAA
29699038 ATATAATTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
29699056 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
29699073 TCTTAATATT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 6 0.35
18 11 0.65
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:29704070 original size:6 final size:6
Alignment explanation
Indices: 29704059--29704087 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
29704049 CATCTTCGTC
29704059 AACACT AACACT AACACT AACACT -ACACT
1 AACACT AACACT AACACT AACACT AACACT
29704088 CTTTGCTTCC
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 5 0.22
6 18 0.78
ACGTcount: A:0.48, C:0.34, G:0.00, T:0.17
Consensus pattern (6 bp):
AACACT
Found at i:29704623 original size:3 final size:3
Alignment explanation
Indices: 29704615--29704670 Score: 112
Period size: 3 Copynumber: 18.7 Consensus size: 3
29704605 TAAGAAAGAT
29704615 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
29704663 TTA TTA TT
1 TTA TTA TT
29704671 CAAGTTGCTA
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 53 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:29705266 original size:17 final size:17
Alignment explanation
Indices: 29705235--29705267 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
29705225 TGTATAACAC
29705235 TTGTTTTATTGTTAAAT
1 TTGTTTTATTGTTAAAT
29705252 TTGTTATTATT-TTAAA
1 TTGTT-TTATTGTTAAA
29705268 GGCATTTGCT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.27, C:0.00, G:0.09, T:0.64
Consensus pattern (17 bp):
TTGTTTTATTGTTAAAT
Found at i:29705726 original size:7 final size:7
Alignment explanation
Indices: 29705694--29705861 Score: 83
Period size: 7 Copynumber: 24.0 Consensus size: 7
29705684 TTCTTTTTAA
*
29705694 CTCAATA
1 CTCAATT
29705701 CTCAATT
1 CTCAATT
* *
29705708 TTAAATT
1 CTCAATT
*
29705715 TTCAATT
1 CTCAATT
*
29705722 CTCAATC
1 CTCAATT
*
29705729 CTTAATT
1 CTCAATT
* * *
29705736 TTTAATC
1 CTCAATT
29705743 CTCAATT
1 CTCAATT
*
29705750 TTCAATT
1 CTCAATT
*
29705757 CTCAATC
1 CTCAATT
29705764 CTCAATT
1 CTCAATT
*
29705771 TTCAATT
1 CTCAATT
29705778 CTCAATT
1 CTCAATT
29705785 -TCCAATT
1 CT-CAATT
29705792 -TCCAATT
1 CT-CAATT
*
29705799 -TCCAGTT
1 CT-CAATT
*
29705806 TTCAATT
1 CTCAATT
*
29705813 CTCGA-T
1 CTCAATT
*
29705819 CGTCAATC
1 C-TCAATT
*
29705827 CTCAATC
1 CTCAATT
*
29705834 CTCAGTT
1 CTCAATT
*
29705841 CTAAATT
1 CTCAATT
*
29705848 CTAAATT
1 CTCAATT
*
29705855 CTAAATT
1 CTCAATT
29705862 ATTCTTTAAT
Statistics
Matches: 128, Mismatches: 29, Indels: 8
0.78 0.18 0.05
Matches are distributed among these distances:
6 3 0.02
7 123 0.96
8 2 0.02
ACGTcount: A:0.30, C:0.24, G:0.02, T:0.43
Consensus pattern (7 bp):
CTCAATT
Found at i:29705797 original size:21 final size:21
Alignment explanation
Indices: 29705694--29705783 Score: 101
Period size: 21 Copynumber: 4.3 Consensus size: 21
29705684 TTCTTTTTAA
* *
29705694 CTCAATACTCAATTTTAAATT
1 CTCAATCCTCAATTTTCAATT
* * *
29705715 TTCAATTCTCAATCCTT-AATT
1 CTCAATCCTCAAT-TTTCAATT
* *
29705736 TTTAATCCTCAATTTTCAATT
1 CTCAATCCTCAATTTTCAATT
29705757 CTCAATCCTCAATTTTCAATT
1 CTCAATCCTCAATTTTCAATT
29705778 CTCAAT
1 CTCAAT
29705784 TTCCAATTTC
Statistics
Matches: 59, Mismatches: 8, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
20 2 0.03
21 55 0.93
22 2 0.03
ACGTcount: A:0.31, C:0.23, G:0.00, T:0.46
Consensus pattern (21 bp):
CTCAATCCTCAATTTTCAATT
Found at i:29708160 original size:25 final size:25
Alignment explanation
Indices: 29708118--29708190 Score: 78
Period size: 25 Copynumber: 2.9 Consensus size: 25
29708108 TATTTGTAAT
*
29708118 TTTCCTAAATTGTATACTTTATTTT-
1 TTTCCCAAA-TGTATACTTTATTTTA
*
29708143 TCTTCCCAAATGTATACTTTGTTTTA
1 T-TTCCCAAATGTATACTTTATTTTA
* *
29708169 TATCCCAAATGTACAC-TTATTT
1 TTTCCCAAATGTATACTTTATTT
29708191 ACATTCTACG
Statistics
Matches: 41, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
24 5 0.12
25 28 0.68
26 8 0.20
ACGTcount: A:0.26, C:0.18, G:0.05, T:0.51
Consensus pattern (25 bp):
TTTCCCAAATGTATACTTTATTTTA
Found at i:29717146 original size:29 final size:29
Alignment explanation
Indices: 29717112--29717170 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
29717102 AAGTACTCCG
29717112 ATGATTGTACGATCATTAGATGTGAATAA
1 ATGATTGTACGATCATTAGATGTGAATAA
29717141 ATGATTGTACGATCATTAGATGTGAATAA
1 ATGATTGTACGATCATTAGATGTGAATAA
29717170 A
1 A
29717171 GATCAATTTC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.39, C:0.07, G:0.20, T:0.34
Consensus pattern (29 bp):
ATGATTGTACGATCATTAGATGTGAATAA
Found at i:29720074 original size:24 final size:24
Alignment explanation
Indices: 29720032--29720087 Score: 62
Period size: 24 Copynumber: 2.3 Consensus size: 24
29720022 ACATGCCATC
*
29720032 TTGATTCTGAAATTGAAATGTT-AGT
1 TTGATT-TGAAATTGAAAT-TTCACT
29720057 TTGATTTGATAA-TGAAATTTCACT
1 TTGATTTGA-AATTGAAATTTCACT
29720081 TTGATTT
1 TTGATTT
29720088 TGATTAATCG
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
23 2 0.07
24 18 0.64
25 8 0.29
ACGTcount: A:0.30, C:0.05, G:0.16, T:0.48
Consensus pattern (24 bp):
TTGATTTGAAATTGAAATTTCACT
Found at i:29720119 original size:27 final size:27
Alignment explanation
Indices: 29720086--29720147 Score: 97
Period size: 27 Copynumber: 2.3 Consensus size: 27
29720076 TCACTTTGAT
*
29720086 TTTGATTAATCGAATGCCATTTGAGAC
1 TTTGATTAATCGAATGCCATTTGACAC
* *
29720113 TTTGATTAATTGAATGCCATTTGACAT
1 TTTGATTAATCGAATGCCATTTGACAC
29720140 TTTGATTA
1 TTTGATTA
29720148 TGAAAGCTTA
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
27 32 1.00
ACGTcount: A:0.29, C:0.11, G:0.16, T:0.44
Consensus pattern (27 bp):
TTTGATTAATCGAATGCCATTTGACAC
Found at i:29721546 original size:28 final size:28
Alignment explanation
Indices: 29721514--29721573 Score: 84
Period size: 28 Copynumber: 2.1 Consensus size: 28
29721504 TCAATGGCCC
*
29721514 TATTGCAACGGTCAGATTCCAACAATCA
1 TATTGCAACGGTCAGATTCCAACAACCA
* * *
29721542 TATTGTAACGGTTAGATTCTAACAACCA
1 TATTGCAACGGTCAGATTCCAACAACCA
29721570 TATT
1 TATT
29721574 TGTAATACCC
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.35, C:0.20, G:0.13, T:0.32
Consensus pattern (28 bp):
TATTGCAACGGTCAGATTCCAACAACCA
Found at i:29738830 original size:18 final size:18
Alignment explanation
Indices: 29738807--29738868 Score: 70
Period size: 18 Copynumber: 3.4 Consensus size: 18
29738797 ATATGATAAA
*
29738807 AATTAAAATAATAAAAAC
1 AATTAAAATAAAAAAAAC
* *
29738825 AATTAAAATCAAAATAAC
1 AATTAAAATAAAAAAAAC
* *
29738843 AATAAAAATAAACAAAAAA
1 AATTAAAATAAA-AAAAAC
29738862 AATTAAA
1 AATTAAA
29738869 TTGAATAAAT
Statistics
Matches: 35, Mismatches: 8, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
18 25 0.71
19 10 0.29
ACGTcount: A:0.74, C:0.06, G:0.00, T:0.19
Consensus pattern (18 bp):
AATTAAAATAAAAAAAAC
Found at i:29742192 original size:30 final size:30
Alignment explanation
Indices: 29742136--29742192 Score: 71
Period size: 30 Copynumber: 1.9 Consensus size: 30
29742126 ATTGCATGAG
* *
29742136 AAATATTTAAATTTTATATTTCATATATCA
1 AAATATTAAAATATTATATTTCATATATCA
*
29742166 AAATATTAATAATATTAT-TTTTATATA
1 AAATATTAA-AATATTATATTTCATATA
29742193 GTTGCATTGA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
30 16 0.70
31 7 0.30
ACGTcount: A:0.46, C:0.04, G:0.00, T:0.51
Consensus pattern (30 bp):
AAATATTAAAATATTATATTTCATATATCA
Found at i:29746457 original size:6 final size:6
Alignment explanation
Indices: 29746448--29746476 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
29746438 TGTTTATAAG
29746448 TGTATA TGTATA TGTATA TGTATA TGTAT
1 TGTATA TGTATA TGTATA TGTATA TGTAT
29746477 GGGCATAATG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.31, C:0.00, G:0.17, T:0.52
Consensus pattern (6 bp):
TGTATA
Found at i:29748959 original size:83 final size:82
Alignment explanation
Indices: 29748820--29749023 Score: 329
Period size: 83 Copynumber: 2.5 Consensus size: 82
29748810 TGTATACATC
* *
29748820 TTTCAACAAAACATTTCAAAAAACAAACAAAAA-ATGTTATACTAACAAAATAATCCTATAGCAG
1 TTTCAACAAATCATTTCAAAAAACAAA-AAAAATATGTTATACTAACAAAATAATCCTATAGAAG
29748884 TAAGATGTTAACCAACCA
65 TAAGATGTTAACCAACCA
* *
29748902 TTTCAACAAATCATTTCAAAAAACAAAAAGAAATATGTTATGCTAACAAAATGATCCTATAGAAG
1 TTTCAACAAATCATTTCAAAAAACAAAAA-AAATATGTTATACTAACAAAATAATCCTATAGAAG
29748967 TAAGATGTTAACCAACCA
65 TAAGATGTTAACCAACCA
* *
29748985 TTTCAACAAATCATTTAAAAAAACAAACAAAATATGTTA
1 TTTCAACAAATCATTTCAAAAAACAAAAAAAATATGTTA
29749024 ACCATCTCAA
Statistics
Matches: 114, Mismatches: 6, Indels: 4
0.92 0.05 0.03
Matches are distributed among these distances:
81 2 0.02
82 39 0.34
83 73 0.64
ACGTcount: A:0.52, C:0.16, G:0.07, T:0.25
Consensus pattern (82 bp):
TTTCAACAAATCATTTCAAAAAACAAAAAAAATATGTTATACTAACAAAATAATCCTATAGAAGT
AAGATGTTAACCAACCA
Found at i:29749418 original size:158 final size:156
Alignment explanation
Indices: 29749100--29749556 Score: 551
Period size: 158 Copynumber: 2.9 Consensus size: 156
29749090 TATGCTGTCC
*** * * *
29749100 TTTTTTGGCTTCTAGTTCCCATACTTGTACCAGACT--GAGAACAAAAATCAGATCCCCAAATTA
1 TTTTTTGGCTTCTAGTTCTTGTACTTGTACCAGACTAAGACAAAAAAAATCAGAACCCCAAATTA
* *
29749163 GATTTAAATAATTTGGAATTGAAATTAAAAAAGTGTTACGATATACCTGTGATCCAGTTGTGTTA
66 GATTTAAATATTTTAGAATTGAAATT-AAAAAGTGTTACGATATACCTGTGATCCAGTTGTGTTA
* * *
29749228 GGCTGAATGGATGGTGTTCTGTTGTTC
130 GGCTGAATGCATGGTGTTATGTTGTTA
* * *
29749255 TTTTTTTGCTTCTAGTTCTTGTACTTGTACCGGACTAAGACAAAAAAAATTAGAACCCCAAATTA
1 TTTTTTGGCTTCTAGTTCTTGTACTTGTACCAGACTAAGACAAAAAAAATCAGAACCCCAAATTA
* * * * *
29749320 GATTAAAATATTTTTGAATTGAAATTAAAATAGTGTATAGGATATACCTATGATCCAGTTGTATT
66 GATTTAAATATTTTAGAATTGAAATTAAAA-AGTGT-TACGATATACCTGTGATCCAGTTGTGTT
29749385 AGGCTGAATGCATGGTGTTATGTTGTTA
129 AGGCTGAATGCATGGTGTTATGTTGTTA
** * *
29749413 TTTTTTAGGCTTCTAGTTCTTGTACTCATACCAGACAAAGACCAAAAAAATCAGAA-CCCAAATT
1 TTTTTT-GGCTTCTAGTTCTTGTACTTGTACCAGACTAAGACAAAAAAAATCAGAACCCCAAATT
* * * * * * * *
29749477 AGATTTTAATATTCTAGAATTGACAATGAAAAAGTGTTTATGATATACATGTGTTCCCGTTATGT
65 AGATTTAAATATTTTAGAATTGA-AATTAAAAAGTG-TTACGATATACCTGTGATCCAGTTGTGT
*
29749542 TAGGTTGAATGCATG
128 TAGGCTGAATGCATG
29749557 ATCTTTTGTT
Statistics
Matches: 257, Mismatches: 38, Indels: 11
0.84 0.12 0.04
Matches are distributed among these distances:
155 31 0.12
156 4 0.02
157 51 0.20
158 121 0.47
159 50 0.19
ACGTcount: A:0.33, C:0.14, G:0.18, T:0.36
Consensus pattern (156 bp):
TTTTTTGGCTTCTAGTTCTTGTACTTGTACCAGACTAAGACAAAAAAAATCAGAACCCCAAATTA
GATTTAAATATTTTAGAATTGAAATTAAAAAGTGTTACGATATACCTGTGATCCAGTTGTGTTAG
GCTGAATGCATGGTGTTATGTTGTTA
Found at i:29753639 original size:44 final size:44
Alignment explanation
Indices: 29753591--29753678 Score: 176
Period size: 44 Copynumber: 2.0 Consensus size: 44
29753581 ATCATCATTG
29753591 ATCTTTTACATTACATGTTTCTTTTAAAATTCTTACTTTTATCA
1 ATCTTTTACATTACATGTTTCTTTTAAAATTCTTACTTTTATCA
29753635 ATCTTTTACATTACATGTTTCTTTTAAAATTCTTACTTTTATCA
1 ATCTTTTACATTACATGTTTCTTTTAAAATTCTTACTTTTATCA
29753679 TTCTATTTCA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 44 1.00
ACGTcount: A:0.27, C:0.16, G:0.02, T:0.55
Consensus pattern (44 bp):
ATCTTTTACATTACATGTTTCTTTTAAAATTCTTACTTTTATCA
Found at i:29756547 original size:35 final size:35
Alignment explanation
Indices: 29756502--29756571 Score: 140
Period size: 35 Copynumber: 2.0 Consensus size: 35
29756492 GAGAGAGTAA
29756502 AAAAAATCAGTCTCAAGGAGAAAAGAAGATGAGAT
1 AAAAAATCAGTCTCAAGGAGAAAAGAAGATGAGAT
29756537 AAAAAATCAGTCTCAAGGAGAAAAGAAGATGAGAT
1 AAAAAATCAGTCTCAAGGAGAAAAGAAGATGAGAT
29756572 GAATAATATA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.54, C:0.09, G:0.23, T:0.14
Consensus pattern (35 bp):
AAAAAATCAGTCTCAAGGAGAAAAGAAGATGAGAT
Found at i:29758078 original size:6 final size:6
Alignment explanation
Indices: 29758029--29758103 Score: 50
Period size: 6 Copynumber: 12.8 Consensus size: 6
29758019 CAAAAAAAAA
* * * **
29758029 AAAAGC AAAAGC AAAATC AAGATC AAAAT- AAAA-- AAGAAGA AAAATC
1 AAAATC AAAATC AAAATC AAAATC AAAATC AAAATC AA-AATC AAAATC
*
29758075 AAAATC AAAATA AAAGATC AAAAT- AAAAT
1 AAAATC AAAATC AAA-ATC AAAATC AAAAT
29758104 GAGAGAAAAA
Statistics
Matches: 58, Mismatches: 7, Indels: 9
0.78 0.09 0.12
Matches are distributed among these distances:
4 2 0.03
5 11 0.19
6 38 0.66
7 7 0.12
ACGTcount: A:0.71, C:0.09, G:0.08, T:0.12
Consensus pattern (6 bp):
AAAATC
Found at i:29758078 original size:34 final size:33
Alignment explanation
Indices: 29758018--29758082 Score: 94
Period size: 34 Copynumber: 1.9 Consensus size: 33
29758008 AGATCCGATC
*
29758018 TCAAAAAAAAAAAAAGCAAAAGCAAAATCAAGA
1 TCAAAAAAAAAAAAAGAAAAAGCAAAATCAAGA
* *
29758051 TCAAAATAAAAAAGAAGAAAAATCAAAATCAA
1 TCAAAA-AAAAAAAAAGAAAAAGCAAAATCAA
29758083 AATAAAAGAT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
33 6 0.21
34 22 0.79
ACGTcount: A:0.72, C:0.11, G:0.08, T:0.09
Consensus pattern (33 bp):
TCAAAAAAAAAAAAAGAAAAAGCAAAATCAAGA
Found at i:29758094 original size:13 final size:12
Alignment explanation
Indices: 29758069--29758102 Score: 50
Period size: 13 Copynumber: 2.8 Consensus size: 12
29758059 AAAAAGAAGA
*
29758069 AAAATCAAAATC
1 AAAATAAAAATC
29758081 AAAATAAAAGATC
1 AAAATAAAA-ATC
29758094 AAAATAAAA
1 AAAATAAAA
29758103 TGAGAGAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
12 8 0.40
13 12 0.60
ACGTcount: A:0.74, C:0.09, G:0.03, T:0.15
Consensus pattern (12 bp):
AAAATAAAAATC
Found at i:29758113 original size:41 final size:40
Alignment explanation
Indices: 29758020--29758102 Score: 116
Period size: 40 Copynumber: 2.1 Consensus size: 40
29758010 ATCCGATCTC
*
29758020 AAAAAA-AA-AAAAAGCAAAAGCAAAATCAAGATCAAAAT
1 AAAAAAGAAGAAAAAGCAAAAGCAAAATAAAGATCAAAAT
* *
29758058 AAAAAAGAAGAAAAATCAAAATCAAAATAAAAGATCAAAAT
1 AAAAAAGAAGAAAAAGCAAAAGCAAAAT-AAAGATCAAAAT
29758099 AAAA
1 AAAA
29758103 TGAGAGAAAA
Statistics
Matches: 39, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
38 6 0.15
39 2 0.05
40 16 0.41
41 15 0.38
ACGTcount: A:0.75, C:0.08, G:0.07, T:0.10
Consensus pattern (40 bp):
AAAAAAGAAGAAAAAGCAAAAGCAAAATAAAGATCAAAAT
Found at i:29759016 original size:13 final size:13
Alignment explanation
Indices: 29758998--29759023 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
29758988 TTTGAGTAAA
29758998 AAAATGAAAAATG
1 AAAATGAAAAATG
29759011 AAAATGAAAAATG
1 AAAATGAAAAATG
29759024 GAAAGGCTAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.69, C:0.00, G:0.15, T:0.15
Consensus pattern (13 bp):
AAAATGAAAAATG
Found at i:29760310 original size:43 final size:43
Alignment explanation
Indices: 29760257--29760377 Score: 118
Period size: 44 Copynumber: 2.8 Consensus size: 43
29760247 AAAATTACAG
* * *
29760257 ATCTTGTCTCCCTAAGCA-ACAGTGGAGGAGATTGAAGCCAGAA
1 ATCTTATCTCCCTAAG-ATACAGCGGAGCAGATTGAAGCCAGAA
* *
29760300 ATCTTATCTCCCTAAGATTACAGCGGAGCAGATTGAAGCTAGTA
1 ATCTTATCTCCCTAAGA-TACAGCGGAGCAGATTGAAGCCAGAA
* * * * *
29760344 ATCCTACCTCCCTGAGATTACAGTGGAGCGGATT
1 ATCTTATCTCCCTAAGA-TACAGCGGAGCAGATT
29760378 AGAATAAAGG
Statistics
Matches: 66, Mismatches: 10, Indels: 3
0.84 0.13 0.04
Matches are distributed among these distances:
42 1 0.02
43 15 0.23
44 50 0.76
ACGTcount: A:0.30, C:0.22, G:0.23, T:0.25
Consensus pattern (43 bp):
ATCTTATCTCCCTAAGATACAGCGGAGCAGATTGAAGCCAGAA
Found at i:29760355 original size:44 final size:44
Alignment explanation
Indices: 29760275--29760377 Score: 134
Period size: 44 Copynumber: 2.3 Consensus size: 44
29760265 TCCCTAAGCA
* * *
29760275 ACAGTGGAGGAGATTGAAGCCAGAAATCTTATCTCCCTAAGATT
1 ACAGTGGAGCAGATTGAAGCCAGAAATCCTACCTCCCTAAGATT
* * * *
29760319 ACAGCGGAGCAGATTGAAGCTAGTAATCCTACCTCCCTGAGATT
1 ACAGTGGAGCAGATTGAAGCCAGAAATCCTACCTCCCTAAGATT
*
29760363 ACAGTGGAGCGGATT
1 ACAGTGGAGCAGATT
29760378 AGAATAAAGG
Statistics
Matches: 50, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
44 50 1.00
ACGTcount: A:0.31, C:0.20, G:0.25, T:0.23
Consensus pattern (44 bp):
ACAGTGGAGCAGATTGAAGCCAGAAATCCTACCTCCCTAAGATT
Found at i:29760501 original size:44 final size:44
Alignment explanation
Indices: 29760427--29760522 Score: 122
Period size: 44 Copynumber: 2.2 Consensus size: 44
29760417 AGATCGCATC
*
29760427 AGATTAAAGCCAGAAATCTTATCTCCCTGAGATTACAGCGGAGT
1 AGATTAAAGCCAGAAATCCTATCTCCCTGAGATTACAGCGGAGT
* * * * *
29760471 AGATTGAAGCTAGTAATCCTATCTCTCTGAGATTACAGTGGAGCT
1 AGATTAAAGCCAGAAATCCTATCTCCCTGAGATTACAGCGGAG-T
29760516 -GATTAAA
1 AGATTAAA
29760523 ATAAATGATC
Statistics
Matches: 44, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
44 43 0.98
45 1 0.02
ACGTcount: A:0.33, C:0.18, G:0.21, T:0.28
Consensus pattern (44 bp):
AGATTAAAGCCAGAAATCCTATCTCCCTGAGATTACAGCGGAGT
Found at i:29760538 original size:44 final size:44
Alignment explanation
Indices: 29760441--29760538 Score: 101
Period size: 44 Copynumber: 2.2 Consensus size: 44
29760431 TAAAGCCAGA
** *
29760441 AATCTTATCTCCCTGAGATTACAGCGGAGTAGATTGAAGCTAGT
1 AATCTTATCTCCCTGAGATTACAGCGGAGTAGATTGAAAATAAT
* * *
29760485 AATCCTATCTCTCTGAGATTACAGTGGAGCT-GATT-AAAATAAAT
1 AATCTTATCTCCCTGAGATTACAGCGGAG-TAGATTGAAAAT-AAT
*
29760529 GATCTTATCT
1 AATCTTATCT
29760539 TTTTGAAGTT
Statistics
Matches: 44, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
43 3 0.07
44 40 0.91
45 1 0.02
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Consensus pattern (44 bp):
AATCTTATCTCCCTGAGATTACAGCGGAGTAGATTGAAAATAAT
Found at i:29760546 original size:142 final size:142
Alignment explanation
Indices: 29760285--29760570 Score: 473
Period size: 142 Copynumber: 2.0 Consensus size: 142
29760275 ACAGTGGAGG
*
29760285 AGATTGAAGCCAGAAATCTTATCTCCCTAAGATTACAGCGGAGCAGATTGAAGCTAGTAATCCTA
1 AGATTAAAGCCAGAAATCTTATCTCCCTAAGATTACAGCGGAGCAGATTGAAGCTAGTAATCCTA
*
29760350 CCTCCCTGAGATTACAGTGGAGCGGATTAGAATAAAGGATCTTATCTCTCTGAAGTTACAGTAGA
66 CCTCCCTGAGATTACAGTGGAGCGGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGTAGA
*
29760415 GTAGATCGCATC
131 GTAGATCACATC
* *
29760427 AGATTAAAGCCAGAAATCTTATCTCCCTGAGATTACAGCGGAGTAGATTGAAGCTAGTAATCCTA
1 AGATTAAAGCCAGAAATCTTATCTCCCTAAGATTACAGCGGAGCAGATTGAAGCTAGTAATCCTA
* * * * * *
29760492 TCTCTCTGAGATTACAGTGGAGCTGATTAAAATAAATGATCTTATCTTTTTGAAGTTACAGTAGA
66 CCTCCCTGAGATTACAGTGGAGCGGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGTAGA
29760557 GTAGATCACATC
131 GTAGATCACATC
29760569 AG
1 AG
29760571 GTCTTATCTC
Statistics
Matches: 133, Mismatches: 11, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
142 133 1.00
ACGTcount: A:0.33, C:0.18, G:0.21, T:0.28
Consensus pattern (142 bp):
AGATTAAAGCCAGAAATCTTATCTCCCTAAGATTACAGCGGAGCAGATTGAAGCTAGTAATCCTA
CCTCCCTGAGATTACAGTGGAGCGGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGTAGA
GTAGATCACATC
Found at i:29760804 original size:49 final size:49
Alignment explanation
Indices: 29760647--29761226 Score: 210
Period size: 50 Copynumber: 11.6 Consensus size: 49
29760637 GCAGTGGAAC
* * *
29760647 AGATTAAAGCTACAACAGCGAATCATGCTTCCCCGACATTGCAGTTAAAA
1 AGATTAAAGCCAC-ACAGCGAATCTTACTTCCCCGACATTGCAGTTAAAA
* * *** *
29760697 AGATTAAAGCTACAACAGCGAATCTTAC-TCCCCAGGCGA-TGCAGCGGAAT
1 AGATTAAAGCCAC-ACAGCGAATCTTACTTCCCC-GAC-ATTGCAGTTAAAA
* * *
29760747 AGATTAAAGCCACACGGTGAATCTTTCTTCCCCGACATTGCAGTTAAAA
1 AGATTAAAGCCACACAGCGAATCTTACTTCCCCGACATTGCAGTTAAAA
* * * * * * * ** **
29760796 AGAGTAAAGCCACAGCGGCGAGTGTTACTTTCCTGGCGA-TGCAGTGGAGC
1 AGATTAAAGCCACA-CAGCGAATCTTACTTCCCCGAC-ATTGCAGTTAAAA
* * * ** *
29760846 AGATTAAAACCACA-ATGGCGTATC-CAGCTTCCTTGACATTGCGGTTAAAA
1 AGATTAAAGCCACACA--GCGAATCTTA-CTTCCCCGACATTGCAGTTAAAA
* * * * * * * **
29760896 AGATTAAAGCTACAACAGCGAATCTTACATTCTCTGGCAATGTAGTGAAGC
1 AGATTAAAGCCAC-ACAGCGAATCTTAC-TTCCCCGACATTGCAGTTAAAA
* * * *** *
29760947 AGATTAAAGCCACAACGGTGAATCTTGCTTTTTCGACA-TGCAGCTAAAA
1 AGATTAAAGCCAC-ACAGCGAATCTTACTTCCCCGACATTGCAGTTAAAA
* * * * * ** ** *
29760996 GGATTAAAGTCACA-ACGACGAATCTTACCTCCCAGGCGGTGCAGTGGAAC
1 AGATTAAAGCCACACA-G-CGAATCTTACTTCCCCGACATTGCAGTTAAAA
* * * * *
29761046 AGATTAAAGCCACAACGGTGAA--TAAGGTCTCCCTGACATTGC-GATTAAAA
1 AGATTAAAGCCAC-ACAGCGAATCTTA-CT-TCCCCGACATTGCAG-TTAAAA
* * * * * * * *
29761096 AGATTAAAGCTACAGCAGCGAATCTTACATTTCCAGGCAATACAGTGAAGCA
1 AGATTAAAGCCACA-CAGCGAATCTTAC-TTCCCCGACATTGCAGTTAA-AA
* * * *
29761148 A-ATTAAAGCCACAACGGTGAATCTTGCTTCCCCGACATTACAGTTAAAA
1 AGATTAAAGCCAC-ACAGCGAATCTTACTTCCCCGACATTGCAGTTAAAA
**
29761197 AGATTAAAGCCACGATGGCGAATCTTACTT
1 AGATTAAAGCCAC-ACAGCGAATCTTACTT
29761227 TCCAAAAGTT
Statistics
Matches: 375, Mismatches: 125, Indels: 60
0.67 0.22 0.11
Matches are distributed among these distances:
48 5 0.01
49 72 0.19
50 216 0.58
51 74 0.20
52 8 0.02
ACGTcount: A:0.34, C:0.23, G:0.20, T:0.23
Consensus pattern (49 bp):
AGATTAAAGCCACACAGCGAATCTTACTTCCCCGACATTGCAGTTAAAA
Found at i:29760904 original size:100 final size:100
Alignment explanation
Indices: 29760636--29761230 Score: 585
Period size: 100 Copynumber: 6.0 Consensus size: 100
29760626 TCCCAAACGG
* * *
29760636 TGCAGTGGAACAGATTAAAGCTACAACAGCGAATC-ATGCTTCCCCGACATTGCAGTTAAAAAGA
1 TGCAGTGGAACAGATTAAAGCCACAACGGTGAATCTA-GCTTCCCCGACATTGCAGTTAAAAAGA
* **
29760700 TTAAAGCTACAACAGCGAATCTTACTCCCCAGGCGA
65 TTAAAGCCACAACAGCGAATCTTACTTTCCAGGCGA
* * ** *
29760736 TGCAGCGGAATAGATTAAAGCCAC-ACGGTGAATCTTTCTTCCCCGACATTGCAGTTAAAAAGAG
1 TGCAGTGGAACAGATTAAAGCCACAACGGTGAATCTAGCTTCCCCGACATTGCAGTTAAAAAGAT
* * * * *
29760800 TAAAGCCACAGCGGCGAGTGTTACTTTCCTGGCGA
66 TAAAGCCACAACAGCGAATCTTACTTTCCAGGCGA
* * * * * * ** *
29760835 TGCAGTGGAGCAGATTAAAACCACAATGGCGTATCCAGCTTCCTTGACATTGCGGTTAAAAAGAT
1 TGCAGTGGAACAGATTAAAGCCACAACGGTGAATCTAGCTTCCCCGACATTGCAGTTAAAAAGAT
* * * *
29760900 TAAAGCTACAACAGCGAATCTTACATTCTCTGGCAA
66 TAAAGCCACAACAGCGAATCTTACTTTC-CAGGCGA
* * *** * *
29760936 TGTAGT-GAAGCAGATTAAAGCCACAACGGTGAATCTTGCTTTTTCGACA-TGCAGCTAAAAGGA
1 TGCAGTGGAA-CAGATTAAAGCCACAACGGTGAATCTAGCTTCCCCGACATTGCAGTTAAAAAGA
* * * *
29760999 TTAAAGTCACAAC-GACGAATCTTACCTCCCAGGCGG
65 TTAAAGCCACAACAG-CGAATCTTACTTTCCAGGCGA
* * *
29761035 TGCAGTGGAACAGATTAAAGCCACAACGGTGAAT-AAGGTCTCCCTGACATTGC-GATTAAAAAG
1 TGCAGTGGAACAGATTAAAGCCACAACGGTGAATCTAGCT-TCCCCGACATTGCAG-TTAAAAAG
* * *
29761098 ATTAAAGCTACAGCAGCGAATCTTACATTTCCAGGCAA
64 ATTAAAGCCACAACAGCGAATCTTAC-TTTCCAGGCGA
* * * *
29761136 TACAGT-GAAGCAAATTAAAGCCACAACGGTGAATCTTGCTTCCCCGACATTACAGTTAAAAAGA
1 TGCAGTGGAA-CAGATTAAAGCCACAACGGTGAATCTAGCTTCCCCGACATTGCAGTTAAAAAGA
* **
29761200 TTAAAGCCACGATGGCGAATCTTACTTTCCA
65 TTAAAGCCACAACAGCGAATCTTACTTTCCA
29761231 AAAGTTACGA
Statistics
Matches: 394, Mismatches: 87, Indels: 28
0.77 0.17 0.06
Matches are distributed among these distances:
98 2 0.01
99 121 0.31
100 151 0.38
101 117 0.30
102 3 0.01
ACGTcount: A:0.34, C:0.23, G:0.21, T:0.23
Consensus pattern (100 bp):
TGCAGTGGAACAGATTAAAGCCACAACGGTGAATCTAGCTTCCCCGACATTGCAGTTAAAAAGAT
TAAAGCCACAACAGCGAATCTTACTTTCCAGGCGA
Found at i:29761086 original size:200 final size:201
Alignment explanation
Indices: 29760633--29761224 Score: 685
Period size: 200 Copynumber: 3.0 Consensus size: 201
29760623 TCTTCCCAAA
* * * * *
29760633 CGGTGCAGTGGAACAGATTAAAGCTACAACAGCGAATCATG-CTTCCCCGACATTGCAGTTAAAA
1 CGGTGCAGTGGAACAGATTAAAGCCACAACGGCGAATCAGGTC-TCCCTGACATTGCGGTTAAAA
* * * * *
29760697 AGATTAAAGCTACAACAGCGAATCTTAC-TCCCCAGGCGATGCAGCGGAA-TAGATTAAAGCCAC
65 AGATTAAAGCTACAACAGCGAATCTTACATTCTCAGGCAATGCAG-TGAAGCAGATTAAAGCCAC
* * * * * *
29760760 -ACGGTGAATCTTTCTTCCCCGACATTGCAGTTAAAAAGAGTAAAGCCACAGCGGCGAGTGTTAC
129 AACGGTGAATCTTGCTTCCCCGACATTGCAGCTAAAAAGAGTAAAGCCACAACGACGAATCTTAC
* * *
29760824 TTTCCTGG
194 CTCCCAGG
* * * * * * *
29760832 CGATGCAGTGGAGCAGATTAAAACCACAATGGCGTATCCAGCT-TCCTTGACATTGCGGTTAAAA
1 CGGTGCAGTGGAACAGATTAAAGCCACAACGGCGAAT-CAGGTCTCCCTGACATTGCGGTTAAAA
* *
29760896 AGATTAAAGCTACAACAGCGAATCTTACATTCTCTGGCAATGTAGTGAAGCAGATTAAAGCCACA
65 AGATTAAAGCTACAACAGCGAATCTTACATTCTCAGGCAATGCAGTGAAGCAGATTAAAGCCACA
*** * * *
29760961 ACGGTGAATCTTGCTTTTTCGACA-TGCAGCTAAAAGGATTAAAGTCACAACGACGAATCTTACC
130 ACGGTGAATCTTGCTTCCCCGACATTGCAGCTAAAAAGAGTAAAGCCACAACGACGAATCTTACC
29761025 TCCCAGG
195 TCCCAGG
* * *
29761032 CGGTGCAGTGGAACAGATTAAAGCCACAACGGTGAATAAGGTCTCCCTGACATTGCGATTAAAAA
1 CGGTGCAGTGGAACAGATTAAAGCCACAACGGCGAATCAGGTCTCCCTGACATTGCGGTTAAAAA
* * *
29761097 GATTAAAGCTACAGCAGCGAATCTTACATT-TCCAGGCAATACAGTGAAGCAAATTAAAGCCACA
66 GATTAAAGCTACAACAGCGAATCTTACATTCT-CAGGCAATGCAGTGAAGCAGATTAAAGCCACA
* * * * * *
29761161 ACGGTGAATCTTGCTTCCCCGACATTACAGTTAAAAAGATTAAAGCCACGATGGCGAATCTTAC
130 ACGGTGAATCTTGCTTCCCCGACATTGCAGCTAAAAAGAGTAAAGCCACAACGACGAATCTTAC
29761225 TTTCCAAAAG
Statistics
Matches: 326, Mismatches: 59, Indels: 14
0.82 0.15 0.04
Matches are distributed among these distances:
199 83 0.25
200 191 0.59
201 52 0.16
ACGTcount: A:0.34, C:0.23, G:0.21, T:0.22
Consensus pattern (201 bp):
CGGTGCAGTGGAACAGATTAAAGCCACAACGGCGAATCAGGTCTCCCTGACATTGCGGTTAAAAA
GATTAAAGCTACAACAGCGAATCTTACATTCTCAGGCAATGCAGTGAAGCAGATTAAAGCCACAA
CGGTGAATCTTGCTTCCCCGACATTGCAGCTAAAAAGAGTAAAGCCACAACGACGAATCTTACCT
CCCAGG
Found at i:29776265 original size:5 final size:5
Alignment explanation
Indices: 29776255--29776283 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
29776245 CAAATCGGTC
29776255 TAAAA TAAAA TAAAA TAAAA TAAAA TAAA
1 TAAAA TAAAA TAAAA TAAAA TAAAA TAAA
29776284 TTAACATTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (5 bp):
TAAAA
Found at i:29777280 original size:34 final size:34
Alignment explanation
Indices: 29777237--29777304 Score: 118
Period size: 34 Copynumber: 2.0 Consensus size: 34
29777227 CTACTCTCTG
29777237 TTATTCGAGATGAATTTACTTAGTTGTTAAGAAC
1 TTATTCGAGATGAATTTACTTAGTTGTTAAGAAC
* *
29777271 TTATTCGAGATTAATTTACTTGGTTGTTAAGAAC
1 TTATTCGAGATGAATTTACTTAGTTGTTAAGAAC
29777305 ACATAGGCAA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 32 1.00
ACGTcount: A:0.31, C:0.09, G:0.18, T:0.43
Consensus pattern (34 bp):
TTATTCGAGATGAATTTACTTAGTTGTTAAGAAC
Found at i:29777797 original size:127 final size:124
Alignment explanation
Indices: 29777534--29777762 Score: 332
Period size: 126 Copynumber: 1.8 Consensus size: 124
29777524 GTTCTTATAT
* **
29777534 AAAAGCTTTAACTATTTTAGATTTTTTTTTTAAATCATCTTTCTTACCAAACAAGTCTAAGCAGT
1 AAAAACTTTAACTATTTTAGATTTTTTTTAAAAATCATCTTTCTTACCAAACAAGTCTAAGCAGT
* * * ** * *
29777599 CGTCAATGAGTGGATTGAAAGAAGGAATTATTTTTGCAACTTTCAGTTCATGTTCTTATAT
66 CGTCAATGAGTGGATTAAAAGAAGGAATTATTTTTGCAACTATAAG-TCAAATTC-TAAAG
*
29777660 AAAAGCTTTAACTATTTTAGATTTTTTTTAAAAATCATCTTTCTTACCAAACAAGTCTAAAGCAG
1 AAAAACTTTAACTATTTTAGATTTTTTTTAAAAATCATCTTTCTTACCAAACAAGTCT-AAGCAG
29777725 TCGTCAATGAGTGGATTAAAAGAAGGAATTATTTTTGC
65 TCGTCAATGAGTGGATTAAAAGAAGGAATTATTTTTGC
29777763 TCATAAGGAA
Statistics
Matches: 99, Mismatches: 3, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
126 56 0.57
127 43 0.43
ACGTcount: A:0.34, C:0.13, G:0.14, T:0.39
Consensus pattern (124 bp):
AAAAACTTTAACTATTTTAGATTTTTTTTAAAAATCATCTTTCTTACCAAACAAGTCTAAGCAGT
CGTCAATGAGTGGATTAAAAGAAGGAATTATTTTTGCAACTATAAGTCAAATTCTAAAG
Found at i:29781931 original size:17 final size:18
Alignment explanation
Indices: 29781900--29781941 Score: 50
Period size: 17 Copynumber: 2.4 Consensus size: 18
29781890 CAACTTAAGT
29781900 TGAGCTCACAGCTTT-GA
1 TGAGCTCACAGCTTTAGA
* * *
29781917 TGAGCTCATATCTTTAGG
1 TGAGCTCACAGCTTTAGA
29781935 TGAGCTC
1 TGAGCTC
29781942 CCAAGTGTAG
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
17 13 0.62
18 8 0.38
ACGTcount: A:0.21, C:0.21, G:0.24, T:0.33
Consensus pattern (18 bp):
TGAGCTCACAGCTTTAGA
Found at i:29783004 original size:29 final size:29
Alignment explanation
Indices: 29782962--29783023 Score: 97
Period size: 29 Copynumber: 2.1 Consensus size: 29
29782952 CTATTAACGA
*
29782962 TGCTCCTTTCAAATCCCAAGCTTGCTAGG
1 TGCTCCTTTCAAATCCCAAGCTCGCTAGG
* *
29782991 TGCTCTTTTTAAATCCCAAGCTCGCTAGG
1 TGCTCCTTTCAAATCCCAAGCTCGCTAGG
29783020 TGCT
1 TGCT
29783024 TGGCAACTTT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.19, C:0.29, G:0.18, T:0.34
Consensus pattern (29 bp):
TGCTCCTTTCAAATCCCAAGCTCGCTAGG
Found at i:29785898 original size:18 final size:18
Alignment explanation
Indices: 29785875--29785918 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
29785865 ACTTTAATAT
*
29785875 GCTCGCAACTTGAGTTGA
1 GCTCGCAACTTGAGGTGA
* *
29785893 GCTCGCATCTTTAGGTGA
1 GCTCGCAACTTGAGGTGA
*
29785911 GCTTGCAA
1 GCTCGCAA
29785919 GTGCAGAGCT
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.20, C:0.23, G:0.27, T:0.30
Consensus pattern (18 bp):
GCTCGCAACTTGAGGTGA
Found at i:29787469 original size:71 final size:74
Alignment explanation
Indices: 29787384--29787524 Score: 216
Period size: 75 Copynumber: 1.9 Consensus size: 74
29787374 AAAACTGTCA
* *
29787384 AGTTTCAAAACTAG-T-G-TAAATAAAAAAAAGCTTCAAAAAGTAAGTTAAGAACAATTGTCAAG
1 AGTTTCAAAACTAGATAGATAAATAAAAAAAAGCTTCAAAAAATAAGTTAAGAACAATTATCAAG
29787446 TTCAGTAAC
66 TTCAGTAAC
* *
29787455 AGTTTCGAAACTAGTATAGATATATAAAAAAAAGCTTCAAAAAATAAGTTAAGAACAATTATCAA
1 AGTTTCAAAACTAG-ATAGATAAATAAAAAAAAGCTTCAAAAAATAAGTTAAGAACAATTATCAA
29787520 GTTCA
65 GTTCA
29787525 ATAATTAAAT
Statistics
Matches: 62, Mismatches: 4, Indels: 4
0.89 0.06 0.06
Matches are distributed among these distances:
71 13 0.21
73 1 0.02
74 1 0.02
75 47 0.76
ACGTcount: A:0.50, C:0.11, G:0.13, T:0.26
Consensus pattern (74 bp):
AGTTTCAAAACTAGATAGATAAATAAAAAAAAGCTTCAAAAAATAAGTTAAGAACAATTATCAAG
TTCAGTAAC
Found at i:29790562 original size:20 final size:18
Alignment explanation
Indices: 29790519--29790553 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
29790509 AAATATGTTT
29790519 TTATT-TTTTTAAATAGA
1 TTATTATTTTTAAATAGA
*
29790536 TTTTTATTTTTAAATAGA
1 TTATTATTTTTAAATAGA
29790554 ATATATTATG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 4 0.25
18 12 0.75
ACGTcount: A:0.34, C:0.00, G:0.06, T:0.60
Consensus pattern (18 bp):
TTATTATTTTTAAATAGA
Found at i:29794459 original size:48 final size:48
Alignment explanation
Indices: 29794372--29794480 Score: 141
Period size: 48 Copynumber: 2.3 Consensus size: 48
29794362 TATGTAACCC
* * *
29794372 AATGTACCTAATTTATATTACAAAGTTTAATCATCGTTTTAATGTTGT
1 AATGTATCTAATTTATATTACAAAGTTTAATCATAGTTTTAATGTTGG
**
29794420 AATGTATCTAATTTATATTACAAAGTTTGTTCCA-AGTTTTAATGTTGG
1 AATGTATCTAATTTATATTACAAAGTTTAAT-CATAGTTTTAATGTTGG
29794468 AAT-TGATCTAATT
1 AATGT-ATCTAATT
29794481 AAATAAATAC
Statistics
Matches: 54, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
47 1 0.02
48 51 0.94
49 2 0.04
ACGTcount: A:0.33, C:0.09, G:0.12, T:0.46
Consensus pattern (48 bp):
AATGTATCTAATTTATATTACAAAGTTTAATCATAGTTTTAATGTTGG
Found at i:29794888 original size:6 final size:6
Alignment explanation
Indices: 29794877--29794917 Score: 55
Period size: 6 Copynumber: 6.8 Consensus size: 6
29794867 CAACCGCTTA
* * *
29794877 GGCTCT GGCTCT GGCTTT GGCTCT AGCTCA GGCTCT GGCTC
1 GGCTCT GGCTCT GGCTCT GGCTCT GGCTCT GGCTCT GGCTC
29794918 GTATGCCCCA
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.05, C:0.32, G:0.32, T:0.32
Consensus pattern (6 bp):
GGCTCT
Found at i:29794898 original size:18 final size:18
Alignment explanation
Indices: 29794872--29794917 Score: 56
Period size: 18 Copynumber: 2.6 Consensus size: 18
29794862 GTATGCAACC
* * *
29794872 GCTTAGGCTCTGGCTCTG
1 GCTTTGGCTCTAGCTCAG
29794890 GCTTTGGCTCTAGCTCAG
1 GCTTTGGCTCTAGCTCAG
*
29794908 GCTCTGGCTC
1 GCTTTGGCTC
29794918 GTATGCCCCA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.07, C:0.30, G:0.30, T:0.33
Consensus pattern (18 bp):
GCTTTGGCTCTAGCTCAG
Found at i:29806444 original size:18 final size:18
Alignment explanation
Indices: 29806418--29806491 Score: 80
Period size: 18 Copynumber: 4.1 Consensus size: 18
29806408 AACACGTGAG
* *
29806418 TTTTGAAACACAACTTTT
1 TTTTAAAACACAAATTTT
*
29806436 TTTTAAAACACGAATTTT
1 TTTTAAAACACAAATTTT
29806454 TTTT-AAACACAAAATTTT
1 TTTTAAAACAC-AAATTTT
29806472 TTTT-AAACACGAGAATTTT
1 TTTTAAAACAC-A-AATTTT
29806491 T
1 T
29806492 GAAAACACGA
Statistics
Matches: 49, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
17 6 0.12
18 36 0.73
19 7 0.14
ACGTcount: A:0.38, C:0.12, G:0.05, T:0.45
Consensus pattern (18 bp):
TTTTAAAACACAAATTTT
Found at i:29806488 original size:19 final size:19
Alignment explanation
Indices: 29806432--29806528 Score: 94
Period size: 18 Copynumber: 5.3 Consensus size: 19
29806422 GAAACACAAC
29806432 TTTTTTTTAAAACACG--AA
1 TTTTTTTT-AAACACGAAAA
29806450 TTTTTTTTAAACAC-AAAA
1 TTTTTTTTAAACACGAAAA
*
29806468 TTTTTTTTAAACACGAGAA
1 TTTTTTTTAAACACGAAAA
** *
29806487 -TTTTTGAAAACACGACAA
1 TTTTTTTTAAACACGAAAA
* **
29806505 TTTCTTGAAAACACGAAAA
1 TTTTTTTTAAACACGAAAA
29806524 TTTTT
1 TTTTT
29806529 GAATCACAGA
Statistics
Matches: 68, Mismatches: 7, Indels: 7
0.83 0.09 0.09
Matches are distributed among these distances:
17 6 0.09
18 39 0.57
19 23 0.34
ACGTcount: A:0.40, C:0.12, G:0.07, T:0.40
Consensus pattern (19 bp):
TTTTTTTTAAACACGAAAA
Found at i:29806491 original size:35 final size:36
Alignment explanation
Indices: 29806418--29806620 Score: 145
Period size: 35 Copynumber: 5.8 Consensus size: 36
29806408 AACACGTGAG
* *
29806418 TTTTGAAACAC--AACTTTTTTTTAAAACACGA-ATTT
1 TTTTGAAACACGAAAATTTTTTTT-AAACACGAGA-AT
*
29806453 TTTTTAAACAC-AAAATTTTTTTTAAACACGAGAAT
1 TTTTGAAACACGAAAATTTTTTTTAAACACGAGAAT
* * ** *
29806488 TTTTGAAAACACGACAATTTCTTGAAAACACGAAAAT
1 TTTTG-AAACACGAAAATTTTTTTTAAACACGAGAAT
* * *
29806525 TTTTGAATCAC-AGAAA--TTTGTGAAACACGAGAAT
1 TTTTGAAACACGA-AAATTTTTTTTAAACACGAGAAT
* * * *
29806559 TATTGAAAACACGAAAA--ATTTTAAAACACGACAAT
1 TTTTG-AAACACGAAAATTTTTTTTAAACACGAGAAT
* *
29806594 TTTTGAAATACGAGAATTTTTTTTAAA
1 TTTTGAAACACGAAAATTTTTTTTAAA
29806621 AAAACACGAA
Statistics
Matches: 132, Mismatches: 27, Indels: 17
0.75 0.15 0.10
Matches are distributed among these distances:
34 26 0.20
35 50 0.38
36 32 0.24
37 24 0.18
ACGTcount: A:0.43, C:0.12, G:0.10, T:0.34
Consensus pattern (36 bp):
TTTTGAAACACGAAAATTTTTTTTAAACACGAGAAT
Found at i:29806497 original size:18 final size:18
Alignment explanation
Indices: 29806476--29806614 Score: 144
Period size: 17 Copynumber: 7.9 Consensus size: 18
29806466 AATTTTTTTT
29806476 AAACACGAGAATTTTTGA
1 AAACACGAGAATTTTTGA
*
29806494 AAACACGACAATTTCTTGA
1 AAACACGAGAATTT-TTGA
*
29806513 AAACACGAAAATTTTTG-
1 AAACACGAGAATTTTTGA
* *
29806530 AATCAC-AGAAATTTGTG-
1 AAACACGAG-AATTTTTGA
*
29806547 AAACACGAGAATTATTGA
1 AAACACGAGAATTTTTGA
* *
29806565 AAACACGAAAAATTTT-A
1 AAACACGAGAATTTTTGA
*
29806582 AAACACGACAATTTTTG-
1 AAACACGAGAATTTTTGA
*
29806599 AAATACGAGAATTTTT
1 AAACACGAGAATTTTT
29806615 TTTAAAAAAA
Statistics
Matches: 101, Mismatches: 15, Indels: 11
0.80 0.12 0.09
Matches are distributed among these distances:
16 1 0.01
17 52 0.51
18 31 0.31
19 17 0.17
ACGTcount: A:0.46, C:0.13, G:0.13, T:0.28
Consensus pattern (18 bp):
AAACACGAGAATTTTTGA
Found at i:29806575 original size:52 final size:52
Alignment explanation
Indices: 29806471--29806611 Score: 167
Period size: 52 Copynumber: 2.7 Consensus size: 52
29806461 CACAAAATTT
* * * * *
29806471 TTTTTAAACACGAGAATTTTTGAAAACACGACAATTTCTTGAAAACACGAAAAT
1 TTTTAAAACACGACAATTTTTG-AAACACGAGAA-TTATTGAAAACACGAAAAA
* * *
29806525 TTTTGAATCACAGA-AATTTGTGAAACACGAGAATTATTGAAAACACGAAAAA
1 TTTTAAAACAC-GACAATTTTTGAAACACGAGAATTATTGAAAACACGAAAAA
*
29806577 TTTTAAAACACGACAATTTTTGAAATACGAGAATT
1 TTTTAAAACACGACAATTTTTGAAACACGAGAATT
29806612 TTTTTTAAAA
Statistics
Matches: 75, Mismatches: 10, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
51 2 0.03
52 45 0.60
53 10 0.13
54 16 0.21
55 2 0.03
ACGTcount: A:0.45, C:0.13, G:0.13, T:0.29
Consensus pattern (52 bp):
TTTTAAAACACGACAATTTTTGAAACACGAGAATTATTGAAAACACGAAAAA
Found at i:29806687 original size:16 final size:16
Alignment explanation
Indices: 29806668--29806731 Score: 60
Period size: 16 Copynumber: 3.9 Consensus size: 16
29806658 GAAAATGCGA
*
29806668 AAATTCGAAAATTTTG
1 AAATACGAAAATTTTG
*
29806684 AAATACGAGTAATATTTG
1 AAATACGA-AAAT-TTTG
29806702 AAAATACGAAAA-TTTG
1 -AAATACGAAAATTTTG
*
29806718 AAACAC-AAAATTTT
1 AAATACGAAAATTTT
29806732 TTTAAAAAAA
Statistics
Matches: 40, Mismatches: 4, Indels: 9
0.75 0.08 0.17
Matches are distributed among these distances:
14 4 0.10
15 8 0.20
16 11 0.28
17 3 0.08
18 6 0.15
19 8 0.20
ACGTcount: A:0.50, C:0.08, G:0.11, T:0.31
Consensus pattern (16 bp):
AAATACGAAAATTTTG
Found at i:29807208 original size:15 final size:15
Alignment explanation
Indices: 29807188--29807219 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
29807178 CAATTCGGGC
*
29807188 CTTTTTTGTTTTTTT
1 CTTTTTTCTTTTTTT
29807203 CTTTTTTCTTTTTTT
1 CTTTTTTCTTTTTTT
29807218 CT
1 CT
29807220 GCAGATTGGG
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:0.00, C:0.12, G:0.03, T:0.84
Consensus pattern (15 bp):
CTTTTTTCTTTTTTT
Found at i:29807635 original size:19 final size:18
Alignment explanation
Indices: 29807604--29807647 Score: 61
Period size: 19 Copynumber: 2.4 Consensus size: 18
29807594 TCTCTCTACT
* *
29807604 TTTTCTTTTTTTTCTTTC
1 TTTTCTTTGTTTTCTCTC
29807622 TTTTCTTTCGTTTTCTCTC
1 TTTTCTTT-GTTTTCTCTC
29807641 TTTTCTT
1 TTTTCTT
29807648 CTCTTCTCTT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 8 0.35
19 15 0.65
ACGTcount: A:0.00, C:0.20, G:0.02, T:0.77
Consensus pattern (18 bp):
TTTTCTTTGTTTTCTCTC
Found at i:29807650 original size:10 final size:9
Alignment explanation
Indices: 29807604--29807657 Score: 63
Period size: 9 Copynumber: 5.8 Consensus size: 9
29807594 TCTCTCTACT
*
29807604 TTTTCTTTT
1 TTTTCTTTC
29807613 TTTTCTTTC
1 TTTTCTTTC
29807622 TTTTCTTTC
1 TTTTCTTTC
*
29807631 GTTTTCTCTC
1 -TTTTCTTTC
29807641 TTTTCTTCTC
1 TTTTCTT-TC
*
29807651 TTCTCTT
1 TTTTCTT
29807658 CTCCCCTTTC
Statistics
Matches: 39, Mismatches: 4, Indels: 3
0.85 0.09 0.07
Matches are distributed among these distances:
9 23 0.59
10 16 0.41
ACGTcount: A:0.00, C:0.24, G:0.02, T:0.74
Consensus pattern (9 bp):
TTTTCTTTC
Found at i:29807675 original size:23 final size:24
Alignment explanation
Indices: 29807640--29807685 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 24
29807630 CGTTTTCTCT
*
29807640 CTTTTCTTCTCTTCTC-TTCTCCC
1 CTTTCCTTCTCTTCTCTTTCTCCC
* *
29807663 CTTTCCTTTTCTTTTCTTTCTCC
1 CTTTCCTTCTCTTCTCTTTCTCC
29807686 TTCGAAACCT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
23 13 0.68
24 6 0.32
ACGTcount: A:0.00, C:0.39, G:0.00, T:0.61
Consensus pattern (24 bp):
CTTTCCTTCTCTTCTCTTTCTCCC
Found at i:29808302 original size:30 final size:29
Alignment explanation
Indices: 29808246--29808345 Score: 103
Period size: 30 Copynumber: 3.4 Consensus size: 29
29808236 TAGAGGCCCG
*
29808246 AATGTAATTTACAAAATA-TTAGGGGTCAA
1 AATGTAATTTACAAAA-AGTTAAGGGTCAA
* *
29808275 GATGTAAATTTAGAAAAAGTTAAGGGTCAA
1 AATGT-AATTTACAAAAAGTTAAGGGTCAA
** * *
29808305 AATGTAATTTTTAAAAAGTTCAGTGGCCAA
1 AATGTAATTTACAAAAAGTTAAG-GGTCAA
29808335 AATGTAATTTA
1 AATGTAATTTA
29808346 TATTTTTTGT
Statistics
Matches: 59, Mismatches: 9, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
29 20 0.34
30 39 0.66
ACGTcount: A:0.44, C:0.06, G:0.18, T:0.32
Consensus pattern (29 bp):
AATGTAATTTACAAAAAGTTAAGGGTCAA
Found at i:29808553 original size:5 final size:5
Alignment explanation
Indices: 29808543--29808573 Score: 62
Period size: 5 Copynumber: 6.2 Consensus size: 5
29808533 TTAAATATAT
29808543 ATAAA ATAAA ATAAA ATAAA ATAAA ATAAA A
1 ATAAA ATAAA ATAAA ATAAA ATAAA ATAAA A
29808574 ACACGAAGAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 26 1.00
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (5 bp):
ATAAA
Found at i:29808841 original size:76 final size:76
Alignment explanation
Indices: 29808741--29809650 Score: 884
Period size: 76 Copynumber: 11.7 Consensus size: 76
29808731 CTATCCGAAA
* * * * * *
29808741 CTCAACTCACCTCTCGGATTATGAGTTGA-TCTTTGGAAAACAGAAATTAAAAAATATCTCGGCG
1 CTCAACTCACCTCTCGCAATATGAGTTGATTTTTTGAAAAACAGAAATT-AAAAATACCTCAGCG
29808805 TGTGACCCGAGAG
65 TGTGACCCGAG-G
* * ** *
29808818 -TCAACTCACCTCTCACAACATGAGTTGATTTTTT-AGAAAGTAGAAATTAAAATATACGTCAGC
1 CTCAACTCACCTCTCGCAATATGAGTTGATTTTTTGA-AAAACAGAAATTAAAA-ATACCTCAGC
* *
29808881 ATGTGACCTGAGG
64 GTGTGACCCGAGG
* * *
29808894 CTCAACTCACTTCTCGCAATATGGGTTGATTTTTTTGAAAAACAGAAATTGAAAATACCTCAG-G
1 CTCAACTCACCTCTCGCAATATGAGTTGA-TTTTTTGAAAAACAGAAATTAAAAATACCTCAGCG
* *
29808958 -ATGACCTGAGG
65 TGTGACCCGAGG
* *
29808969 CTCAACTCACCTTTCGCAATATGAGTTGATTTTTTGAAAAACAGAAATTGAAAATACCTCAG-GA
1 CTCAACTCACCTCTCGCAATATGAGTTGATTTTTTGAAAAACAGAAATTAAAAATACCTCAGCG-
*
29809033 TGTGACCCAAGG
65 TGTGACCCGAGG
* * *
29809045 CTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTTTTTGAAAACATAGAAATTAAAGATACTT
1 CTCAACTCACCTCTCGCAATATGAGTTGA-----TTTTTTGAAAA-ACAGAAATTAAAAATACCT
* * *
29809110 CGGCATGTGACCCGAGA
60 CAGCGTGTGACCCGAGG
*
29809127 CTCAACTCACCTCTCGCATTATGAGTTGATTCTTGATTTGATTTTTTTAAAA-AGAAATTAAAAA
1 CTCAACTCACCTCTCGCAATATGAGTTGA-T-TT--TTTGA-------AAAACAGAAATT-AAAA
29809191 ATACCTCAGC-T-TGCAGCCCGAGG
54 ATACCTCAGCGTGTG-A-CCCGAGG
* *
29809214 CTCAACTCACTTCTCGCAATATGAGTTGA-TTTTTGAAAAACAGAAATTGAAAATACCTCAGCGT
1 CTCAACTCACCTCTCGCAATATGAGTTGATTTTTTGAAAAACAGAAATTAAAAATACCTCAGCGT
*
29809278 G-G-CTCGAGG
66 GTGACCCGAGG
** * ** *
29809287 CTCAACTCAGTTCTCGCAATATGAGTTGATTATTTGAAAAGTAGAAATTGAAAATACCTCAGC--
1 CTCAACTCACCTCTCGCAATATGAGTTGATTTTTTGAAAAACAGAAATTAAAAATACCTCAGCGT
29809350 GTGACCCGAGG
66 GTGACCCGAGG
*
29809361 CTCAACTCACCTCTCGCAATATGAGTTAATTTTTTTTTGAAAAACAGAAATTGAAAAATACCTCA
1 CTCAACTCACCTCTCGCAATATGAGTTGA---TTTTTTGAAAAACAGAAATT-AAAAATACCTCA
* *
29809426 G-G-ATGACTCGAGG
62 GCGTGTGACCCGAGG
* ** *
29809439 CTCAACTCACCTCTCGCATTATGAGTTTCTTTTTTTGAAAAATAGAAATTGAAAAATACCTCAG-
1 CTCAACTCACCTCTCGCAATATGAG-TTGATTTTTTGAAAAACAGAAATT-AAAAATACCTCAGC
*
29809503 G-ATGACCCGAGG
64 GTGTGACCCGAGG
* * * * * *
29809515 CTCAACTCAGCTCTCGCAATATAAGTTGATTTTTTAAAAAAAATAGAAATTAAAGATACCTCGGC
1 CTCAACTCACCTCTCGCAATATGAGTTGATTTTTT--GAAAAACAGAAATTAAAAATACCTCAGC
*
29809580 ATGTGACCCGAGG
64 GTGTGACCCGAGG
* *
29809593 CTCAACTCACCTCTCGCAATATGAGTTGATTTTTTGGAAAAATAAAAATTGAAAAATA
1 CTCAACTCACCTCTCGCAATATGAGTTGATTTTTT-GAAAAACAGAAATT-AAAAATA
29809651 ATTCTTAAAA
Statistics
Matches: 706, Mismatches: 82, Indels: 89
0.81 0.09 0.10
Matches are distributed among these distances:
72 1 0.00
73 35 0.05
74 96 0.14
75 61 0.09
76 151 0.21
77 105 0.15
78 115 0.16
79 5 0.01
81 16 0.02
82 60 0.08
84 2 0.00
85 2 0.00
86 9 0.01
87 45 0.06
88 3 0.00
ACGTcount: A:0.34, C:0.19, G:0.17, T:0.29
Consensus pattern (76 bp):
CTCAACTCACCTCTCGCAATATGAGTTGATTTTTTGAAAAACAGAAATTAAAAATACCTCAGCGT
GTGACCCGAGG
Found at i:29809443 original size:470 final size:468
Alignment explanation
Indices: 29808741--29809623 Score: 1273
Period size: 470 Copynumber: 1.9 Consensus size: 468
29808731 CTATCCGAAA
* * * * *
29808741 CTCAACTCACCTCTCGGATTATGAGTTGATCTTTGGAAAACAGAAATTAAAAAATATCTCGGCGT
1 CTCAACTCACCTCTCGCAATATGAGTTGATCTTTGAAAAACAGAAATTAAAAAATACCTCAGCGT
*
29808806 GTGACCCGAGAGTCAACTCACCTCTCACAACATGAGTTGATTTTTTAGAAAGTAGAAATTAAAAT
66 GTGACCCGAGAGTCAACTCACCTCTCACAACATGAGTTGATTTTTGAGAAAGTAGAAATTAAAAT
* * * * *
29808871 ATACGTCAGCATGTGACCTGAGGCTCAACTCACTTCTCGCAATATGGGTTGATTTTTTTGAAAAA
131 ATACCTCAGCA-GTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTAATTTTTTTGAAAAA
* *
29808936 CAGAAATTGAAAATACCTCAGGATGACCTGAGGCTCAACTCACCTTTCGCAATATGAG-TTGATT
195 CAGAAATTGAAAATACCTCAGGATGACCTGAGGCTCAACTCACCTCTCGCAATATGAGTTTCATT
29809000 TTTTGAAAAACAGAAATTG-AAAATACCTCAGGATGTGACCCAAGGCTCAACTCACCTCTCGCAA
260 TTTTGAAAAACAGAAATTGAAAAATACCTCAGGA--TGACCCAAGGCTCAACTCACCTCTCGCAA
* ** * *
29809064 TATGAGTTGATTTTTTTTTTTGAAAACATAGAAATTAAAGATACTTCGGCATGTGACCCGAGACT
323 TATAAGTTGA----TTTTTTAAAAAAAATAGAAATTAAAGATACCTCGGCATGTGACCCGAGACT
*
29809129 CAACTCACCTCTCGCATTATGAGTTGATTCTTGATTTGATTTTTTTAAAAAGAAATTAAAAAATA
384 CAACTCACCTCTCGCAATATGAGTTGATTCTTGATTTGATTTTTTTAAAAAGAAATTAAAAAATA
29809194 CCTCAGCTTGCAGCCCGAGG
449 CCTCAGCTTGCAGCCCGAGG
* * *
29809214 CTCAACTCACTTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATT-GAAAATACCTCAGCGT
1 CTCAACTCACCTCTCGCAATATGAGTTGATCTTTGAAAAACAGAAATTAAAAAATACCTCAGCGT
* ** * * *
29809278 G-G-CTCGAG-GCTCAACTCAGTTCTCGCAATATGAGTTGATTATTTGA-AAAGTAGAAATTGAA
66 GTGACCCGAGAG-TCAACTCACCTCTCACAACATGAGTTGATT-TTTGAGAAAGTAGAAATTAAA
29809339 A-ATACCTCAGC-GTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTAATTTTTTTTTGAA
129 ATATACCTCAGCAGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTAA--TTTTTTTGAA
*
29809402 AAACAGAAATTGAAAAATACCTCAGGATGA-CTCGAGGCTCAACTCACCTCTCGCATTATGAGTT
192 AAACAGAAATTG-AAAATACCTCAGGATGACCT-GAGGCTCAACTCACCTCTCGCAATATGAGTT
* * * *
29809466 TCTTTTTTTGAAAAATAGAAATTGAAAAATACCTCAGGATGACCCGAGGCTCAACTCAGCTCTCG
255 TCATTTTTTGAAAAACAGAAATTGAAAAATACCTCAGGATGACCCAAGGCTCAACTCACCTCTCG
*
29809531 CAATATAAGTTGATTTTTTAAAAAAAATAGAAATTAAAGATACCTCGGCATGTGACCCGAGGCTC
320 CAATATAAGTTGATTTTTTAAAAAAAATAGAAATTAAAGATACCTCGGCATGTGACCCGAGACTC
29809596 AACTCACCTCTCGCAATATGAGTTGATT
385 AACTCACCTCTCGCAATATGAGTTGATT
29809624 TTTTGGAAAA
Statistics
Matches: 368, Mismatches: 34, Indels: 23
0.87 0.08 0.05
Matches are distributed among these distances:
466 74 0.20
467 36 0.10
469 34 0.09
470 126 0.34
471 27 0.07
472 28 0.08
473 43 0.12
ACGTcount: A:0.34, C:0.20, G:0.17, T:0.29
Consensus pattern (468 bp):
CTCAACTCACCTCTCGCAATATGAGTTGATCTTTGAAAAACAGAAATTAAAAAATACCTCAGCGT
GTGACCCGAGAGTCAACTCACCTCTCACAACATGAGTTGATTTTTGAGAAAGTAGAAATTAAAAT
ATACCTCAGCAGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTAATTTTTTTGAAAAAC
AGAAATTGAAAATACCTCAGGATGACCTGAGGCTCAACTCACCTCTCGCAATATGAGTTTCATTT
TTTGAAAAACAGAAATTGAAAAATACCTCAGGATGACCCAAGGCTCAACTCACCTCTCGCAATAT
AAGTTGATTTTTTAAAAAAAATAGAAATTAAAGATACCTCGGCATGTGACCCGAGACTCAACTCA
CCTCTCGCAATATGAGTTGATTCTTGATTTGATTTTTTTAAAAAGAAATTAAAAAATACCTCAGC
TTGCAGCCCGAGG
Found at i:29809517 original size:154 final size:154
Alignment explanation
Indices: 29808741--29809650 Score: 882
Period size: 154 Copynumber: 5.9 Consensus size: 154
29808731 CTATCCGAAA
* * * * * *
29808741 CTCAACTCACCTCTCGGATTATGAGTTGA---TCTTTGGAAAACAGAAATTAAAAAATATCTC-G
1 CTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTTGAAAAACAGAAATTGAAAAATACCTCAG
* * * * * *
29808802 GCGTGTGACCCGAGAG-TCAACTCACCTCTCACAACATGAGTTGATTTTTTAG-AAAGTAGAAAT
66 GC--ATGACCCGAG-GCTCAACTCACCTCTCGCAATATGAGTTTATTTTTTTGAAAAATAGAAAT
* * *
29808865 T-AAAATATACGTCAGCATGTGACCTGAGG
128 TGAAAA-ATACCTCAGGA--TGACCCGAGG
* *
29808894 CTCAACTCACTTCTCGCAATATGGGTTGA-TTTTTTTGAAAAACAGAAATTG-AAAATACCTCAG
1 CTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTTGAAAAACAGAAATTGAAAAATACCTCAG
* * * *
29808957 G-ATGACCTGAGGCTCAACTCACCTTTCGCAATATGAGTTGA-TTTTTTGAAAAACAGAAATTG-
66 GCATGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTTATTTTTTTGAAAAATAGAAATTGA
*
29809019 AAAATACCTCAGGATGTGACCCAAGG
131 AAAATACCTCAGGA--TGACCCGAGG
* * *
29809045 CTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTTTTTGAAAACATAGAAATT-AAAGATACT
1 CTCAACTCACCTCTCGCAATATGAGTTGA---TTTTTTTTGAAAA-ACAGAAATTGAAAAATACC
* * *
29809109 TC-GGCATGTGACCCGAGACTCAACTCACCTCTCGCATTATGAGTTGATTCTTGATTTGATTTTT
62 TCAGGCA--TGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTTATT-TT--TTTGA-----
* **
29809173 TTAAAA-AGAAATTAAAAAATACCTCAGCTTGCAGCCCGAGG
117 --AAAATAGAAATTGAAAAATACCTCAGGATG-A-CCCGAGG
*
29809214 CTCAACTCACTTCTCGCAATATGAGTTGA---TTTTTGAAAAACAGAAATTG-AAAATACCTCA-
1 CTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTTGAAAAACAGAAATTGAAAAATACCTCAG
* * * ** * * *
29809274 GCGTGGCTCGAGGCTCAACTCAGTTCTCGCAATATGAGTTGA-TTATTTGAAAAGTAGAAATTG-
66 GCATGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTTATTTTTTTGAAAAATAGAAATTGA
29809337 AAAATACCTCAGCG-TGACCCGAGG
131 AAAATACCTCAG-GATGACCCGAGG
*
29809361 CTCAACTCACCTCTCGCAATATGAGTTAATTTTTTTTTGAAAAACAGAAATTGAAAAATACCTCA
1 CTCAACTCACCTCTCGCAATATGAGTTGA-TTTTTTTTGAAAAACAGAAATTGAAAAATACCTCA
* * *
29809426 GG-ATGACTCGAGGCTCAACTCACCTCTCGCATTATGAGTTTCTTTTTTTGAAAAATAGAAATTG
65 GGCATGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTTATTTTTTTGAAAAATAGAAATTG
29809490 AAAAATACCTCAGGATGACCCGAGG
130 AAAAATACCTCAGGATGACCCGAGG
* * *** * *
29809515 CTCAACTCAGCTCTCGCAATATAAGTTGATTTTTTAAAAAAAATAGAAATT-AAAGATACCTC-G
1 CTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTTGAAAAACAGAAATTGAAAAATACCTCAG
* * *
29809578 GCATGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTGGAAAAATAAAAATT
66 GCA--TGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTTATTTTTTTGAAAAATAGAAATT
29809643 GAAAAATA
129 GAAAAATA
29809651 ATTCTTAAAA
Statistics
Matches: 639, Mismatches: 73, Indels: 89
0.80 0.09 0.11
Matches are distributed among these distances:
147 34 0.05
148 1 0.00
149 17 0.03
150 7 0.01
151 75 0.12
152 101 0.16
153 64 0.10
154 119 0.19
155 33 0.05
156 22 0.03
158 36 0.06
159 2 0.00
160 35 0.05
162 23 0.04
163 10 0.02
167 2 0.00
168 8 0.01
169 50 0.08
ACGTcount: A:0.34, C:0.19, G:0.17, T:0.29
Consensus pattern (154 bp):
CTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTTGAAAAACAGAAATTGAAAAATACCTCAG
GCATGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTTATTTTTTTGAAAAATAGAAATTGA
AAAATACCTCAGGATGACCCGAGG
Found at i:29809544 original size:228 final size:224
Alignment explanation
Indices: 29808741--29809650 Score: 983
Period size: 228 Copynumber: 3.9 Consensus size: 224
29808731 CTATCCGAAA
* * * * * * *
29808741 CTCAACTCACCTCTCGGATTATGAGTTGATCTTTGGAAAACAGAAATTAAAAAATATCTCGGCGT
1 CTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATT-GAAAATACCTCAGCG-
* * * *
29808806 GTGACCCGAGAG-TCAACTCACCTCTCACAACATGAGTTGATTTTTT-AGAAAGTAGAAATTAAA
64 ATGACCCGAG-GCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTGA-AAAATAGAAATT-AA
* * * * * *
29808869 ATATACGTCAGCATGTGACCTGAGGCTCAACTCACTTCTCGCAATATGGGTTGATTTTTTTGAAA
126 AGATACCTCAGCA-GTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTAATTTTTTTGAAA
29808934 AACAGAAATTG-AAAATACCTCAGGATGACCTGAGG
190 AACAGAAATTGAAAAATACCTCAGGATGACC-GAGG
*
29808969 CTCAACTCACCTTTCGCAATATGAGTTGATTTTTTGAAAAACAGAAATTGAAAATACCTCAG-GA
1 CTCAACTCACCTCTCGCAATATGAGTTGA-TTTTTGAAAAACAGAAATTGAAAATACCTCAGCGA
*
29809033 TGTGACCCAAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTTTTTGAAAACATAGAAA
65 --TGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGA-----TTTTTTGAAAA-ATAGAAA
* * * * *
29809098 TTAAAGATACTTCGGCATGTGACCCGAGACTCAACTCACCTCTCGCATTATGAGTTGATTCTTGA
122 TTAAAGATACCTCAGCA-GTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTAATT-TT--
* **
29809163 TTTGATTTTTTTAAAA-AGAAATTAAAAAATACCTCAGCTTGCAGCCCGAGG
183 TTTGA-------AAAACAGAAATTGAAAAATACCTCAGGATG-A--CCGAGG
*
29809214 CTCAACTCACTTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTGAAAATACCTCAGCG-T
1 CTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTGAAAATACCTCAGCGAT
* * ** * *
29809278 GGCTCGAGGCTCAACTCAGTTCTCGCAATATGAGTTGATTATTTGAAAAGTAGAAATTGAAA-AT
66 GACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTGAAAAATAGAAATT-AAAGAT
29809342 ACCTCAGC-GTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTAATTTTTTTTTGAAAAAC
130 ACCTCAGCAGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTAA--TTTTTTTGAAAAAC
29809406 AGAAATTGAAAAATACCTCAGGATGACTCGAGG
193 AGAAATTGAAAAATACCTCAGGATGAC-CGAGG
* ** *
29809439 CTCAACTCACCTCTCGCATTATGAGTTTCTTTTTTTGAAAAATAGAAATTGAAAAATACCTCAG-
1 CTCAACTCACCTCTCGCAATATGAG-TT-GATTTTTGAAAAACAGAAATTG-AAAATACCTCAGC
* * *
29809503 GATGACCCGAGGCTCAACTCAGCTCTCGCAATATAAGTTGATTTTTTAAAAAAAATAGAAATTAA
63 GATGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTT--GAAAAATAGAAATTAA
* * *
29809568 AGATACCTCGGCATGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTGGAAA
126 AGATACCTCAGCA-GTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTAATTTTTTTGAAA
* *
29809633 AATAAAAATTGAAAAATA
190 AACAGAAATTGAAAAATA
29809651 ATTCTTAAAA
Statistics
Matches: 584, Mismatches: 58, Indels: 78
0.81 0.08 0.11
Matches are distributed among these distances:
224 1 0.00
225 28 0.05
226 7 0.01
227 44 0.08
228 122 0.21
229 20 0.03
230 47 0.08
232 39 0.07
233 64 0.11
234 48 0.08
235 2 0.00
236 23 0.04
237 13 0.02
242 41 0.07
243 18 0.03
244 33 0.06
245 32 0.05
246 2 0.00
ACGTcount: A:0.34, C:0.19, G:0.17, T:0.29
Consensus pattern (224 bp):
CTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTGAAAATACCTCAGCGAT
GACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTGAAAAATAGAAATTAAAGATA
CCTCAGCAGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTAATTTTTTTGAAAAACAGA
AATTGAAAAATACCTCAGGATGACCGAGG
Found at i:29818034 original size:18 final size:17
Alignment explanation
Indices: 29818011--29818074 Score: 85
Period size: 18 Copynumber: 3.6 Consensus size: 17
29818001 AACACGTGAA
29818011 TTTTAAAACACAACTTTT
1 TTTTAAAACACAA-TTTT
29818029 TTTTAAAACACGAATTTT
1 TTTTAAAACAC-AATTTT
29818047 TTTT-AAACACAAATTTT
1 TTTTAAAACAC-AATTTT
*
29818064 TTTTTAAACAC
1 TTTTAAAACAC
29818075 GAGAATTTTT
Statistics
Matches: 43, Mismatches: 1, Indels: 4
0.90 0.02 0.08
Matches are distributed among these distances:
17 16 0.37
18 25 0.58
19 2 0.05
ACGTcount: A:0.39, C:0.14, G:0.02, T:0.45
Consensus pattern (17 bp):
TTTTAAAACACAATTTT
Found at i:29818083 original size:18 final size:17
Alignment explanation
Indices: 29818027--29818214 Score: 128
Period size: 17 Copynumber: 10.6 Consensus size: 17
29818017 AACACAACTT
*
29818027 TTTTTTAAAACACGAAT
1 TTTTTTAAAACACGAAA
*
29818044 TTTTTTTAAACAC-AAA
1 TTTTTTAAAACACGAAA
*
29818060 TTTTTTTTTAAACACGAGAA
1 --TTTTTTAAAACACGA-AA
*
29818080 TTTTTGAAAACACGAAAAA
1 TTTTTTAAAACACG--AAA
* *
29818099 TTCTTGAAAACACGAAA
1 TTTTTTAAAACACGAAA
* *
29818116 ATTTTTGAAACACGAAA
1 TTTTTTAAAACACGAAA
* * *
29818133 ATTTGTGAAACACGAGAA
1 TTTTTTAAAACACGA-AA
* *
29818151 TTATTGAAAACACGAAA
1 TTTTTTAAAACACGAAA
* *
29818168 ATTTTTAAAACATGACAA
1 TTTTTTAAAACACGA-AA
*
29818186 TTTTTGAAATACGA-GAAA
1 TTTTTTAAA-AC-ACGAAA
29818204 TTTTTTTAAAA
1 -TTTTTTAAAA
29818215 AAACGCGGAA
Statistics
Matches: 138, Mismatches: 22, Indels: 21
0.76 0.12 0.12
Matches are distributed among these distances:
16 2 0.01
17 55 0.40
18 49 0.36
19 28 0.20
20 4 0.03
ACGTcount: A:0.45, C:0.11, G:0.10, T:0.34
Consensus pattern (17 bp):
TTTTTTAAAACACGAAA
Found at i:29818084 original size:35 final size:35
Alignment explanation
Indices: 29818000--29818215 Score: 129
Period size: 35 Copynumber: 6.1 Consensus size: 35
29817990 GATCCGATTG
* *
29818000 AAACACGTGAA-TTTTAAAACACAACTTTTTTTTA
1 AAACACGAGAATTTTTAAAACACAAATTTTTTTTA
* * *
29818034 AAACACGA-ATTTTTTTTAAACACAAATTTTTTTTT
1 AAACACGAGA-ATTTTTAAAACACAAATTTTTTTTA
** * *
29818069 AAACACGAGAATTTTTGAAAACACGAAAAATTCTTGA
1 AAACACGAGAATTTTT-AAAACAC-AAATTTTTTTTA
* * * * *
29818106 AAACACGAAAATTTTTGAAACACGAAA--ATTTGTG
1 AAACACGAGAATTTTTAAAACAC-AAATTTTTTTTA
* *
29818140 AAACACGAGAATTATTGAAAACACGAAA--ATTTTTA
1 AAACACGAGAATT-TTTAAAACAC-AAATTTTTTTTA
* * * *
29818175 AAACATGACAATTTTTGAAATACGAGAAATTTTTTTAA
1 AAACACGAGAATTTTT-AAA-AC-ACAAATTTTTTTTA
29818213 AAA
1 AAA
29818216 AACGCGGAAA
Statistics
Matches: 141, Mismatches: 30, Indels: 18
0.75 0.16 0.10
Matches are distributed among these distances:
33 1 0.01
34 23 0.16
35 64 0.45
36 22 0.16
37 23 0.16
38 8 0.06
ACGTcount: A:0.46, C:0.12, G:0.10, T:0.33
Consensus pattern (35 bp):
AAACACGAGAATTTTTAAAACACAAATTTTTTTTA
Found at i:29818179 original size:52 final size:52
Alignment explanation
Indices: 29818063--29818202 Score: 181
Period size: 52 Copynumber: 2.7 Consensus size: 52
29818053 ACACAAATTT
* * * *
29818063 TTTTTTAAACACGAGAATTTTTGAAAACACGAAAAATTCTTGAAAACACGAAAA
1 TTTTTAAAACACGAAAATTTTTG-AAACACG-AGAATTATTGAAAACACGAAAA
* *
29818117 TTTTTGAAACACGAAAATTTGTGAAACACGAGAATTATTGAAAACACGAAAA
1 TTTTTAAAACACGAAAATTTTTGAAACACGAGAATTATTGAAAACACGAAAA
* * *
29818169 TTTTTAAAACATGACAATTTTTGAAATACGAGAA
1 TTTTTAAAACACGAAAATTTTTGAAACACGAGAA
29818203 ATTTTTTTAA
Statistics
Matches: 76, Mismatches: 10, Indels: 2
0.86 0.11 0.02
Matches are distributed among these distances:
52 49 0.64
53 7 0.09
54 20 0.26
ACGTcount: A:0.47, C:0.11, G:0.13, T:0.29
Consensus pattern (52 bp):
TTTTTAAAACACGAAAATTTTTGAAACACGAGAATTATTGAAAACACGAAAA
Found at i:29819158 original size:9 final size:9
Alignment explanation
Indices: 29819128--29819177 Score: 55
Period size: 10 Copynumber: 5.2 Consensus size: 9
29819118 TATTTTTTTA
29819128 TTTTTCTTC
1 TTTTTCTTC
29819137 TTTTTTCTCTC
1 -TTTTTCT-TC
29819148 TTTTTCTTC
1 TTTTTCTTC
*
29819157 TTTCTTTTTC
1 TTT-TTCTTC
*
29819167 TTCTTCTTC
1 TTTTTCTTC
29819176 TT
1 TT
29819178 CAGGCCGAAC
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
9 12 0.34
10 21 0.60
11 2 0.06
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (9 bp):
TTTTTCTTC
Found at i:29819162 original size:13 final size:13
Alignment explanation
Indices: 29819130--29819171 Score: 57
Period size: 13 Copynumber: 3.2 Consensus size: 13
29819120 TTTTTTTATT
*
29819130 TTTCTTCTTTTTTC
1 TTTCTT-TTTCTTC
*
29819144 TCTCTTTTTCTTC
1 TTTCTTTTTCTTC
29819157 TTTCTTTTTCTTC
1 TTTCTTTTTCTTC
29819170 TT
1 TT
29819172 CTTCTTCAGG
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
13 20 0.80
14 5 0.20
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (13 bp):
TTTCTTTTTCTTC
Found at i:29819977 original size:30 final size:28
Alignment explanation
Indices: 29819925--29820024 Score: 119
Period size: 30 Copynumber: 3.4 Consensus size: 28
29819915 TAGGGGCCCG
*
29819925 AATGTAATTTACAAAATATTAGGGGTCAA
1 AATGTAATTTAGAAAA-ATTAGGGGTCAA
*
29819954 GATGTAAATTTAGAAAAAGTTAGGGGTCAA
1 AATGT-AATTTAGAAAAA-TTAGGGGTCAA
* *
29819984 AATGTAATTGTTGAAAAATTTAGGGGCCAA
1 AATGTAATT-TAGAAAAA-TTAGGGGTCAA
29820014 AATGTAATTTA
1 AATGTAATTTA
29820025 TATTTTTTGT
Statistics
Matches: 61, Mismatches: 7, Indels: 6
0.82 0.09 0.08
Matches are distributed among these distances:
29 10 0.16
30 51 0.84
ACGTcount: A:0.43, C:0.05, G:0.21, T:0.31
Consensus pattern (28 bp):
AATGTAATTTAGAAAAATTAGGGGTCAA
Found at i:29820223 original size:5 final size:5
Alignment explanation
Indices: 29820213--29820242 Score: 60
Period size: 5 Copynumber: 6.0 Consensus size: 5
29820203 TCATAATTTT
29820213 TAAAA TAAAA TAAAA TAAAA TAAAA TAAAA
1 TAAAA TAAAA TAAAA TAAAA TAAAA TAAAA
29820243 ACACGAAGAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 25 1.00
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (5 bp):
TAAAA
Found at i:29822475 original size:41 final size:40
Alignment explanation
Indices: 29822419--29822564 Score: 138
Period size: 41 Copynumber: 3.6 Consensus size: 40
29822409 TGATTCGATA
29822419 CACCGGC-TTATAGCCTGCTAGACCTATAGTCCGAAATGTAT
1 CACCGGCATTA-AGCCTGCTAGACCTATAGTCCGAAAT-TAT
* * *
29822460 CACCGGCATTAAGCCTGCTAGACGTAAAGT-CTAAATTAATT
1 CACCGGCATTAAGCCTGCTAGACCTATAGTCCGAAATT-A-T
* *
29822501 CACCGGCATTAAGCCTGCTAGGCAC-ATAG-CCTGAATTATAT
1 CACCGGCATTAAGCCTGCTAGAC-CTATAGTCC-GAAAT-TAT
**
29822542 CACCGGCATCCAGCCTGCTAGAC
1 CACCGGCATTAAGCCTGCTAGAC
29822565 AATAAGTCTG
Statistics
Matches: 87, Mismatches: 11, Indels: 14
0.78 0.10 0.12
Matches are distributed among these distances:
39 1 0.01
40 6 0.07
41 72 0.83
42 7 0.08
43 1 0.01
ACGTcount: A:0.29, C:0.28, G:0.19, T:0.24
Consensus pattern (40 bp):
CACCGGCATTAAGCCTGCTAGACCTATAGTCCGAAATTAT
Found at i:29822572 original size:82 final size:82
Alignment explanation
Indices: 29822419--29822573 Score: 192
Period size: 82 Copynumber: 1.9 Consensus size: 82
29822409 TGATTCGATA
* * *
29822419 CACCGGCTTATAGCCTGCTAGACCTATAGTCCGAAATGTATCACCGGCATTAAGCCTGCTAGACG
1 CACCGGCTTATAGCCTGCTAGACCTATAGTCCGAAATATATCACCGGCATCAAGCCTGCTAGACA
29822484 TAAAGTCTAAATTAATT
66 TAAAGTCTAAATTAATT
* * *
29822501 CACCGGCATTA-AGCCTGCTAGGCAC-ATAG-CCTGAATTATATCACCGGCATCCAGCCTGCTAG
1 CACCGGC-TTATAGCCTGCTAGAC-CTATAGTCC-GAAATATATCACCGGCATCAAGCCTGCTAG
29822563 ACA-ATAAGTCT
63 ACATA-AAGTCT
29822574 GATTTACATT
Statistics
Matches: 63, Mismatches: 6, Indels: 8
0.82 0.08 0.10
Matches are distributed among these distances:
81 3 0.05
82 56 0.89
83 4 0.06
ACGTcount: A:0.30, C:0.27, G:0.19, T:0.25
Consensus pattern (82 bp):
CACCGGCTTATAGCCTGCTAGACCTATAGTCCGAAATATATCACCGGCATCAAGCCTGCTAGACA
TAAAGTCTAAATTAATT
Found at i:29830248 original size:41 final size:41
Alignment explanation
Indices: 29830158--29830260 Score: 122
Period size: 41 Copynumber: 2.5 Consensus size: 41
29830148 TGATTCGATA
*
29830158 CACCGGC-TTATAGCCTGCTAGACCTATAGTCCGAAATGTAT
1 CACCGGCATTA-AGCCTGCTAGACCTAAAGTCCGAAATGTAT
* * *
29830199 CACTGGCATTAAGCCTGCTAGACGTAAAGT-CTAAAT-TAATT
1 CACCGGCATTAAGCCTGCTAGACCTAAAGTCCGAAATGT-A-T
29830240 CACCGGCATTAAGCCTGCTAG
1 CACCGGCATTAAGCCTGCTAG
29830261 GCACATAGCC
Statistics
Matches: 54, Mismatches: 5, Indels: 6
0.83 0.08 0.09
Matches are distributed among these distances:
39 1 0.02
40 6 0.11
41 44 0.81
42 3 0.06
ACGTcount: A:0.29, C:0.25, G:0.19, T:0.26
Consensus pattern (41 bp):
CACCGGCATTAAGCCTGCTAGACCTAAAGTCCGAAATGTAT
Found at i:29830277 original size:41 final size:41
Alignment explanation
Indices: 29830158--29830304 Score: 113
Period size: 41 Copynumber: 3.6 Consensus size: 41
29830148 TGATTCGATA
* * *
29830158 CACCGGC-TTATAGCCTGCTAGAC-CTATAGTCCGAAA-TGTAT
1 CACCGGCATTA-AGCCTGCTAGACAC-AAAG-CCTAAATTATAT
* ** *
29830199 CACTGGCATTAAGCCTGCTAGACGTAAAGTCTAAATTA-ATT
1 CACCGGCATTAAGCCTGCTAGACACAAAGCCTAAATTATA-T
* * *
29830240 CACCGGCATTAAGCCTGCTAGGCACATAGCCTGAATTATAT
1 CACCGGCATTAAGCCTGCTAGACACAAAGCCTAAATTATAT
** *
29830281 CACCGGCATCCAGCCTACTAGACA
1 CACCGGCATTAAGCCTGCTAGACA
29830305 ATAAGTCTGA
Statistics
Matches: 84, Mismatches: 17, Indels: 10
0.76 0.15 0.09
Matches are distributed among these distances:
40 5 0.06
41 75 0.89
42 4 0.05
ACGTcount: A:0.30, C:0.27, G:0.18, T:0.24
Consensus pattern (41 bp):
CACCGGCATTAAGCCTGCTAGACACAAAGCCTAAATTATAT
Found at i:29833371 original size:85 final size:85
Alignment explanation
Indices: 29833229--29833440 Score: 372
Period size: 85 Copynumber: 2.5 Consensus size: 85
29833219 TAACCGTTAC
* *
29833229 ACGGTGGAATCAGCACTTAGCAACCACC-TTATAATCAATGATACGGGGAATCAGCACATAGTAA
1 ACGGTGGAATCAGCACTTAGCAACCACCTTTATATTCAATGATACGGGGAATCAGCACATAGCAA
29833293 CCCCTTTCACAGTCAAGGAT
66 CCCCTTTCACAGTCAAGGAT
*
29833313 ACGGTGGAATCTGCACTTAGCAACCACCTTTATATTCAATGATACGGGGAATCAGCACATAGCAA
1 ACGGTGGAATCAGCACTTAGCAACCACCTTTATATTCAATGATACGGGGAATCAGCACATAGCAA
*
29833378 CCCCTTTCACTGTCAAGGAT
66 CCCCTTTCACAGTCAAGGAT
*
29833398 ACGGTGGAATCAGCACTTAGCAACCACATTTATATTCAATGAT
1 ACGGTGGAATCAGCACTTAGCAACCACCTTTATATTCAATGAT
29833441 GCGGATTCAC
Statistics
Matches: 121, Mismatches: 6, Indels: 1
0.95 0.05 0.01
Matches are distributed among these distances:
84 27 0.22
85 94 0.78
ACGTcount: A:0.33, C:0.25, G:0.18, T:0.24
Consensus pattern (85 bp):
ACGGTGGAATCAGCACTTAGCAACCACCTTTATATTCAATGATACGGGGAATCAGCACATAGCAA
CCCCTTTCACAGTCAAGGAT
Found at i:29833376 original size:42 final size:43
Alignment explanation
Indices: 29833229--29833440 Score: 256
Period size: 43 Copynumber: 5.0 Consensus size: 43
29833219 TAACCGTTAC
*
29833229 ACGGTGGAATCAGCACTTAGCAACCACC-TTATAATCAATGAT
1 ACGGTGGAATCAGCACTTAGCAACCACCTTTATAGTCAATGAT
* * * *
29833271 ACGG-GGAATCAGCACATAGTAACC-CCTTTCACAGTCAAGGAT
1 ACGGTGGAATCAGCACTTAGCAACCACCTTT-ATAGTCAATGAT
* *
29833313 ACGGTGGAATCTGCACTTAGCAACCACCTTTATATTCAATGAT
1 ACGGTGGAATCAGCACTTAGCAACCACCTTTATAGTCAATGAT
* *
29833356 ACGG-GGAATCAGCACATAGCAACC-CCTTTCACT-GTCAAGGAT
1 ACGGTGGAATCAGCACTTAGCAACCACCTTT-A-TAGTCAATGAT
* *
29833398 ACGGTGGAATCAGCACTTAGCAACCACATTTATATTCAATGAT
1 ACGGTGGAATCAGCACTTAGCAACCACCTTTATAGTCAATGAT
29833441 GCGGATTCAC
Statistics
Matches: 142, Mismatches: 19, Indels: 17
0.80 0.11 0.10
Matches are distributed among these distances:
40 2 0.01
41 25 0.18
42 48 0.34
43 58 0.41
44 9 0.06
ACGTcount: A:0.33, C:0.25, G:0.18, T:0.24
Consensus pattern (43 bp):
ACGGTGGAATCAGCACTTAGCAACCACCTTTATAGTCAATGAT
Found at i:29833477 original size:26 final size:26
Alignment explanation
Indices: 29833448--29833528 Score: 71
Period size: 26 Copynumber: 3.2 Consensus size: 26
29833438 GATGCGGATT
29833448 CACATAGTAGCATGCACATAGTACTA
1 CACATAGTAGCATGCACATAGTACTA
* *
29833474 CACAT-GTGACCAT-CAC-TA-TCCGATA
1 CACATAGT-AGCATGCACATAGTAC--TA
* *
29833499 CACGTAGTAGCCTGCACATAGTACTA
1 CACATAGTAGCATGCACATAGTACTA
29833525 CACA
1 CACA
29833529 CGTGATCGAA
Statistics
Matches: 41, Mismatches: 7, Indels: 14
0.66 0.11 0.23
Matches are distributed among these distances:
23 2 0.05
24 2 0.05
25 14 0.34
26 19 0.46
27 2 0.05
28 2 0.05
ACGTcount: A:0.35, C:0.28, G:0.15, T:0.22
Consensus pattern (26 bp):
CACATAGTAGCATGCACATAGTACTA
Found at i:29833515 original size:51 final size:51
Alignment explanation
Indices: 29833452--29833743 Score: 312
Period size: 51 Copynumber: 5.8 Consensus size: 51
29833442 CGGATTCACA
* * *
29833452 TAGTAGCATGCACATAGTACTACACATGTGACCATCACTATCCGATACACG
1 TAGTAGCCTGCACATAGTACTACACACGTGACCATCACTATCCGGTACACG
* * *
29833503 TAGTAGCCTGCACATAGTACTACACACGTGATCGA--AGCTATCCGGTACGCA
1 TAGTAGCCTGCACATAGTACTACACACGTGA-CCATCA-CTATCCGGTACACG
*** *
29833554 TAGTAGCCTGCACATAGTACTACACATACGACCTATCA-T-TCTGGTACACG
1 TAGTAGCCTGCACATAGTACTACACACGTGACC-ATCACTATCCGGTACACG
* * * *
29833604 TAGTAGCCTACACATAGTACTACACACGTGATCGA--AGCTATCCGGTACGCA
1 TAGTAGCCTGCACATAGTACTACACACGTGA-CCATCA-CTATCCGGTACACG
* * *
29833655 TAGTAGCCTGCACATAGTACTACACATGCGACCTATCA-T-TCTGGTACACG
1 TAGTAGCCTGCACATAGTACTACACACGTGACC-ATCACTATCCGGTACACG
*
29833705 TAGTAGCCTACACATAGTACTACACACGTGACCATCACT
1 TAGTAGCCTGCACATAGTACTACACACGTGACCATCACT
29833744 TTCACTTTCA
Statistics
Matches: 197, Mismatches: 31, Indels: 27
0.77 0.12 0.11
Matches are distributed among these distances:
48 1 0.01
49 4 0.02
50 79 0.40
51 109 0.55
52 2 0.01
53 2 0.01
ACGTcount: A:0.31, C:0.28, G:0.17, T:0.24
Consensus pattern (51 bp):
TAGTAGCCTGCACATAGTACTACACACGTGACCATCACTATCCGGTACACG
Found at i:29833626 original size:101 final size:101
Alignment explanation
Indices: 29833450--29833735 Score: 493
Period size: 101 Copynumber: 2.8 Consensus size: 101
29833440 TGCGGATTCA
* * * * *
29833450 CATAGTAGCATGCACATAGTACTACACATGTGACC-ATCACTATCCGATACACGTAGTAGCCTGC
1 CATAGTAGCCTGCACATAGTACTACACATGCGACCTATCA-T-TCTGGTACACGTAGTAGCCTAC
29833514 ACATAGTACTACACACGTGATCGAAGCTATCCGGTACG
64 ACATAGTACTACACACGTGATCGAAGCTATCCGGTACG
*
29833552 CATAGTAGCCTGCACATAGTACTACACATACGACCTATCATTCTGGTACACGTAGTAGCCTACAC
1 CATAGTAGCCTGCACATAGTACTACACATGCGACCTATCATTCTGGTACACGTAGTAGCCTACAC
29833617 ATAGTACTACACACGTGATCGAAGCTATCCGGTACG
66 ATAGTACTACACACGTGATCGAAGCTATCCGGTACG
29833653 CATAGTAGCCTGCACATAGTACTACACATGCGACCTATCATTCTGGTACACGTAGTAGCCTACAC
1 CATAGTAGCCTGCACATAGTACTACACATGCGACCTATCATTCTGGTACACGTAGTAGCCTACAC
29833718 ATAGTACTACACACGTGA
66 ATAGTACTACACACGTGA
29833736 CCATCACTTT
Statistics
Matches: 176, Mismatches: 7, Indels: 3
0.95 0.04 0.02
Matches are distributed among these distances:
101 139 0.79
102 33 0.19
103 4 0.02
ACGTcount: A:0.31, C:0.28, G:0.18, T:0.23
Consensus pattern (101 bp):
CATAGTAGCCTGCACATAGTACTACACATGCGACCTATCATTCTGGTACACGTAGTAGCCTACAC
ATAGTACTACACACGTGATCGAAGCTATCCGGTACG
Found at i:29833765 original size:152 final size:151
Alignment explanation
Indices: 29833446--29833769 Score: 341
Period size: 152 Copynumber: 2.1 Consensus size: 151
29833436 ATGATGCGGA
* * * *
29833446 TTCACATAGTAGCATGCACATAGTACTACACATGTGACCATCACTATCCGATACACGTAGTAGCC
1 TTCACATAGTAGCCTACACATAGTACTACACACGTGACCA-CACTATCCGATACACATAGTAGCC
* * * *
29833511 TGCACATAGTACTACACACGTGATCGAAGCTATCCGGTACGCATAGTAGCCTGCACATAGTACTA
65 TGCACATAGTACTACACACGCGATCCAAGCTATCCGGTACACATAGTAGCCTACACATAGTACTA
* **
29833576 CACATACGACCTATCATTCTGG
130 CACACACGACCTATCATTCACG
* * * * *
29833598 TACACGTAGTAGCCTACACATAGTACTACACACGTGATCGA-AGCTATCCGGTACGCATAGTAGC
1 TTCACATAGTAGCCTACACATAGTACTACACACGTGA-CCACA-CTATCCGATACACATAGTAGC
* * * * *
29833662 CTGCACATAGTACTACACATGCGA-CCTATC-ATTCTGGTACACGTAGTAGCCTACACATAGTAC
64 CTGCACATAGTACTACACACGCGATCCAAGCTA-TCCGGTACACATAGTAGCCTACACATAGTAC
** *
29833725 TACACACGTGACC-ATCACTTTCACT
128 TACACACACGACCTATCA--TTCACG
*
29833750 TTCACATAGTGGCCTACACA
1 TTCACATAGTAGCCTACACA
29833770 CAGTCCATGC
Statistics
Matches: 140, Mismatches: 27, Indels: 10
0.79 0.15 0.06
Matches are distributed among these distances:
150 5 0.04
151 41 0.29
152 92 0.66
153 2 0.01
ACGTcount: A:0.31, C:0.28, G:0.17, T:0.24
Consensus pattern (151 bp):
TTCACATAGTAGCCTACACATAGTACTACACACGTGACCACACTATCCGATACACATAGTAGCCT
GCACATAGTACTACACACGCGATCCAAGCTATCCGGTACACATAGTAGCCTACACATAGTACTAC
ACACACGACCTATCATTCACG
Found at i:29852543 original size:55 final size:56
Alignment explanation
Indices: 29852459--29852571 Score: 219
Period size: 55 Copynumber: 2.0 Consensus size: 56
29852449 TATAGATAAT
29852459 AATGCAATAAAATATTTCTTTTTTTTGTTCTTTCTTATTTTGTTTAGAATATAAAG
1 AATGCAATAAAATATTTCTTTTTTTTGTTCTTTCTTATTTTGTTTAGAATATAAAG
29852515 AATGCAATAAAATATTTC-TTTTTTTGTTCTTTCTTATTTTGTTTAGAATATAAAG
1 AATGCAATAAAATATTTCTTTTTTTTGTTCTTTCTTATTTTGTTTAGAATATAAAG
29852570 AA
1 AA
29852572 GAAAAAACAA
Statistics
Matches: 57, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
55 39 0.68
56 18 0.32
ACGTcount: A:0.32, C:0.07, G:0.09, T:0.52
Consensus pattern (56 bp):
AATGCAATAAAATATTTCTTTTTTTTGTTCTTTCTTATTTTGTTTAGAATATAAAG
Found at i:29852658 original size:7 final size:7
Alignment explanation
Indices: 29852648--29852672 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
29852638 ATAGTCAATA
29852648 ATAAATT
1 ATAAATT
29852655 ATAAATT
1 ATAAATT
29852662 ATAAATT
1 ATAAATT
29852669 ATAA
1 ATAA
29852673 TACCAACAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (7 bp):
ATAAATT
Found at i:29853277 original size:28 final size:29
Alignment explanation
Indices: 29853228--29853283 Score: 71
Period size: 28 Copynumber: 2.0 Consensus size: 29
29853218 TTTTAATTGT
*
29853228 AAAATCGAATAAATTGATTTCTT-TTAAA
1 AAAATCGAATAAATTGAATTCTTGTTAAA
*
29853256 AAAATCGAAGT-AATTTAATTCTTGTTAA
1 AAAATCGAA-TAAATTGAATTCTTGTTAA
29853284 TTTTAGAAGT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
28 19 0.79
29 5 0.21
ACGTcount: A:0.45, C:0.07, G:0.09, T:0.39
Consensus pattern (29 bp):
AAAATCGAATAAATTGAATTCTTGTTAAA
Found at i:29856738 original size:16 final size:16
Alignment explanation
Indices: 29856714--29856751 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
29856704 TTTGGTTCGC
* *
29856714 TGTATTGGATTAGAGG
1 TGTAATGGAATAGAGG
29856730 TGTAATGGAATAGAGG
1 TGTAATGGAATAGAGG
29856746 TGTAAT
1 TGTAAT
29856752 AGCAAATCAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.32, C:0.00, G:0.34, T:0.34
Consensus pattern (16 bp):
TGTAATGGAATAGAGG
Found at i:29857155 original size:26 final size:28
Alignment explanation
Indices: 29857126--29857186 Score: 81
Period size: 28 Copynumber: 2.2 Consensus size: 28
29857116 TATGAATTTG
*
29857126 TATAATTTAA-AATAAT-TATTATTACA
1 TATAATTTAATAATAATATATAATTACA
*
29857152 TATAATTTAATAATAATATATAATTTCA
1 TATAATTTAATAATAATATATAATTACA
*
29857180 TAAAATT
1 TATAATT
29857187 ATTGATAATA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
26 10 0.33
27 6 0.20
28 14 0.47
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (28 bp):
TATAATTTAATAATAATATATAATTACA
Found at i:29857188 original size:91 final size:89
Alignment explanation
Indices: 29857092--29857308 Score: 299
Period size: 91 Copynumber: 2.4 Consensus size: 89
29857082 AATTTAAAAT
* * * *
29857092 AATTATAACTAATAAATTATCTTATATGAATTTGTATAATTTAAAATAATTATTATTACATATAA
1 AATTATAA-TAATAAATT-TCTTATATGAATTTATACAATTTAAAATAATTAATATTAAATATAA
29857157 TTTAATAATAATATATAATTTCATAA
64 TTTAATAATAATATATAATTTCATAA
* *
29857183 AATTATTGATAATAATTTTTCTTATATGAATTTATACAATTTAAAATAATTAATATTAAATATAA
1 AATTA-TAATAATAA-ATTTCTTATATGAATTTATACAATTTAAAATAATTAATATTAAATATAA
*
29857248 TTTAATAATGATATATAATTTCATAA
64 TTTAATAATAATATATAATTTCATAA
*
29857274 AATTCTTAATAATAAAATGTTCTTATATGAATTTA
1 AATT-ATAATAAT-AAAT-TTCTTATATGAATTTA
29857309 CTAAAATCAA
Statistics
Matches: 111, Mismatches: 10, Indels: 9
0.85 0.08 0.07
Matches are distributed among these distances:
91 89 0.80
92 22 0.20
ACGTcount: A:0.47, C:0.04, G:0.03, T:0.46
Consensus pattern (89 bp):
AATTATAATAATAAATTTCTTATATGAATTTATACAATTTAAAATAATTAATATTAAATATAATT
TAATAATAATATATAATTTCATAA
Found at i:29857189 original size:44 final size:42
Alignment explanation
Indices: 29857126--29857268 Score: 119
Period size: 44 Copynumber: 3.2 Consensus size: 42
29857116 TATGAATTTG
29857126 TATAATTTAAAATAATTATTATTACATATAATTTAATAATAATA
1 TATAATTTAAAATAATTATTATTA-ATATAATTTAATAAT-ATA
* ** *
29857170 TATAATTTCATAA-AATTATTGA-TAATAATTTTTCTTATATGAATTTA
1 TATAATTT-AAAATAATTATT-ATTAAT-A-TAAT-TTA-AT-AATATA
* *
29857217 TACAATTTAAAATAATTAATATTAAATATAATTTAATAATGATA
1 TATAATTTAAAATAATTATTATT-AATATAATTTAATAAT-ATA
29857261 TATAATTT
1 TATAATTT
29857269 CATAAAATTC
Statistics
Matches: 77, Mismatches: 11, Indels: 22
0.70 0.10 0.20
Matches are distributed among these distances:
43 5 0.06
44 29 0.38
45 9 0.12
46 9 0.12
47 19 0.25
48 6 0.08
ACGTcount: A:0.48, C:0.03, G:0.02, T:0.47
Consensus pattern (42 bp):
TATAATTTAAAATAATTATTATTAATATAATTTAATAATATA
Found at i:29857283 original size:47 final size:47
Alignment explanation
Indices: 29857133--29857289 Score: 128
Period size: 47 Copynumber: 3.4 Consensus size: 47
29857123 TTGTATAATT
* * * * *
29857133 TAAAATAATTATTATTACATATAATTTAATAATAATATATAATTTCA
1 TAAAATTATTAATAATAAATATAATTTAATAATGATATATAATTTCA
* ** * *
29857180 TAAAATTATTGATAAT-AAT-T--TTTCTTATATGAATTTATACAATT--
1 TAAAATTATTAATAATAAATATAATTTAATA-ATG-ATATATA-ATTTCA
* *
29857224 TAAAATAATTAATATTAAATATAATTTAATAATGATATATAATTTCA
1 TAAAATTATTAATAATAAATATAATTTAATAATGATATATAATTTCA
*
29857271 TAAAATTCTTAATAATAAA
1 TAAAATTATTAATAATAAA
29857290 ATGTTCTTAT
Statistics
Matches: 81, Mismatches: 20, Indels: 18
0.68 0.17 0.15
Matches are distributed among these distances:
43 5 0.06
44 15 0.19
45 13 0.16
46 12 0.15
47 31 0.38
48 5 0.06
ACGTcount: A:0.50, C:0.04, G:0.02, T:0.45
Consensus pattern (47 bp):
TAAAATTATTAATAATAAATATAATTTAATAATGATATATAATTTCA
Found at i:29868398 original size:33 final size:33
Alignment explanation
Indices: 29868356--29868422 Score: 125
Period size: 33 Copynumber: 2.0 Consensus size: 33
29868346 GCAATGGTAA
29868356 TGCCCATAGCACTCCCAAAAGGAAAACATAAGT
1 TGCCCATAGCACTCCCAAAAGGAAAACATAAGT
*
29868389 TGCCCATAGCACTTCCAAAAGGAAAACATAAGT
1 TGCCCATAGCACTCCCAAAAGGAAAACATAAGT
29868422 T
1 T
29868423 TGAACCTTCG
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.42, C:0.25, G:0.15, T:0.18
Consensus pattern (33 bp):
TGCCCATAGCACTCCCAAAAGGAAAACATAAGT
Found at i:29879742 original size:56 final size:56
Alignment explanation
Indices: 29879682--29879806 Score: 189
Period size: 56 Copynumber: 2.2 Consensus size: 56
29879672 TATGTAAAAC
* *
29879682 TATGTAAAATTATTAAG-CCCAAAAACTTTTGTTAATGATTAGTAAAATTATCAAAT
1 TATGTAAAATTATTAAGCCCCAAAAA-ATGTGTTAATGATTAGTAAAATTATCAAAT
* *
29879738 TATGTAAAATTATTAAGCCCCAAAAAATGTGTTAATGGTTAGTAAGATTATCAAAT
1 TATGTAAAATTATTAAGCCCCAAAAAATGTGTTAATGATTAGTAAAATTATCAAAT
*
29879794 TAGGTAAAATTAT
1 TATGTAAAATTAT
29879807 GTTAGGATTT
Statistics
Matches: 63, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
56 55 0.87
57 8 0.13
ACGTcount: A:0.44, C:0.08, G:0.12, T:0.36
Consensus pattern (56 bp):
TATGTAAAATTATTAAGCCCCAAAAAATGTGTTAATGATTAGTAAAATTATCAAAT
Found at i:29879879 original size:29 final size:29
Alignment explanation
Indices: 29879829--29880092 Score: 366
Period size: 29 Copynumber: 8.6 Consensus size: 29
29879819 ACATAAATTA
*
29879829 GGTTAGGGTTTTTAATTAAAATAGGTTAG
1 GGTTAGGGTTTTTAATTAAATTAGGTTAG
29879858 GGTTTAGGGTTTTTAATTAAATTAGGTTAG
1 GG-TTAGGGTTTTTAATTAAATTAGGTTAG
29879888 GGTTAGGGTTTTTAATTAAATTAAATTAGGTTAG
1 GGTTAGGG--TTT--TT-AATTAAATTAGGTTAG
* *
29879922 GGTTAGGGTTTTTAATTAAAATAGGTTAA
1 GGTTAGGGTTTTTAATTAAATTAGGTTAG
29879951 GGTTAGGGTTTTTAATTAAATTAAATTAGGTTAG
1 GGTTAGGG--TTT--TT-AATTAAATTAGGTTAG
29879985 GGTTAGGGTTTTTAATTAAATTAGGTTAG
1 GGTTAGGGTTTTTAATTAAATTAGGTTAG
*
29880014 GATTAGGGTTTTTAATTAAATTAGGTTAG
1 GGTTAGGGTTTTTAATTAAATTAGGTTAG
29880043 GGTTAGGGTTTTTAATTAAATTAGGTTAG
1 GGTTAGGGTTTTTAATTAAATTAGGTTAG
29880072 GGTTTTAGGGTTTTTTAATTA
1 GG--TTAGGG-TTTTTAATTA
29880093 CGNNNNNNNN
Statistics
Matches: 214, Mismatches: 7, Indels: 25
0.87 0.03 0.10
Matches are distributed among these distances:
29 104 0.49
30 32 0.15
31 12 0.06
32 16 0.07
33 4 0.02
34 46 0.21
ACGTcount: A:0.30, C:0.00, G:0.25, T:0.45
Consensus pattern (29 bp):
GGTTAGGGTTTTTAATTAAATTAGGTTAG
Found at i:29879888 original size:23 final size:23
Alignment explanation
Indices: 29879800--29879891 Score: 87
Period size: 23 Copynumber: 3.7 Consensus size: 23
29879790 AAATTAGGTA
* *
29879800 AAATTATGTTAGGATTTTTACA-T
1 AAATTAGGTTAGGGTTTTTA-ATT
29879823 AAATTAGGTTAGGGTTTTTAATT
1 AAATTAGGTTAGGGTTTTTAATT
29879846 AAAATAGGTTAGGGTTTAGGGTTTTTAATT
1 --AA-A--TTA-GG-TTAGGGTTTTTAATT
29879876 AAATTAGGTTAGGGTT
1 AAATTAGGTTAGGGTT
29879892 AGGGTTTTTA
Statistics
Matches: 59, Mismatches: 2, Indels: 16
0.77 0.03 0.21
Matches are distributed among these distances:
22 1 0.02
23 27 0.46
24 2 0.03
25 5 0.08
26 1 0.02
27 1 0.02
28 5 0.08
29 2 0.03
30 15 0.25
ACGTcount: A:0.32, C:0.01, G:0.23, T:0.45
Consensus pattern (23 bp):
AAATTAGGTTAGGGTTTTTAATT
Found at i:29879949 original size:63 final size:63
Alignment explanation
Indices: 29879842--29880092 Score: 395
Period size: 63 Copynumber: 4.0 Consensus size: 63
29879832 TAGGGTTTTT
*
29879842 AATTAAAATAGGTTAGGGTTTAGGGTTTTTAATTAAATTAGGTTAGGGTTAGGGTTTTTAATTA
1 AATTAAATTAGGTTAGGG-TTAGGGTTTTTAATTAAATTAGGTTAGGGTTAGGGTTTTTAATTA
* *
29879906 AATTAAATTAGGTTAGGGTTAGGGTTTTTAATTAAAATAGGTTAAGGTTAGGGTTTTTAATTA
1 AATTAAATTAGGTTAGGGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTAGGGTTTTTAATTA
*
29879969 AATTAAATTAGGTTAGGGTTAGGGTTTTTAATTAAATTAGGTTAGGATTAGGG--TTT--TT-
1 AATTAAATTAGGTTAGGGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTAGGGTTTTTAATTA
29880027 AATTAAATTAGGTTAGGGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTTTAGGGTTTTTTAATT
1 AATTAAATTAGGTTAGGGTTAGGGTTTTTAATTAAATTAGGTTAGGG--TTAGGG-TTTTTAATT
29880092 A
63 A
29880093 CGNNNNNNNN
Statistics
Matches: 172, Mismatches: 7, Indels: 14
0.89 0.04 0.07
Matches are distributed among these distances:
58 46 0.27
59 2 0.01
60 6 0.03
61 3 0.02
63 96 0.56
64 17 0.10
65 2 0.01
ACGTcount: A:0.31, C:0.00, G:0.25, T:0.45
Consensus pattern (63 bp):
AATTAAATTAGGTTAGGGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTAGGGTTTTTAATTA
Found at i:29879980 original size:92 final size:92
Alignment explanation
Indices: 29879829--29880092 Score: 385
Period size: 92 Copynumber: 2.8 Consensus size: 92
29879819 ACATAAATTA
29879829 GGTTAGGGTTTTTAATTAAAATAGGTTAGGGTTTAGGGTTTTTAATTAAATTAGGTTAGGGTTAG
1 GGTTAGGGTTTTTAATTAAAATAGGTTAGGG-TTAGGGTTTTTAATTAAATTAGGTTAGGGTTAG
29879894 GGTTTTTAATTAAATTAAATTAGGTTAG
65 GGTTTTTAATTAAATTAAATTAGGTTAG
*
29879922 GGTTAGGGTTTTTAATTAAAATAGGTTAAGGTTAGGGTTTTTAATTAAATTAAATTAGGTTAGGG
1 GGTTAGGGTTTTTAATTAAAATAGGTTAGGGTTAGGG--TTT--TT-AATTAAATTAGGTTAGGG
29879987 TTAGGG--TTT--TT-AATTAAATTAGGTTAG
61 TTAGGGTTTTTAATTAAATTAAATTAGGTTAG
* *
29880014 GATTAGGGTTTTTAATTAAATTAGGTTAGGGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTTTA
1 GGTTAGGGTTTTTAATTAAAATAGGTTAGGGTTAGGGTTTTTAATTAAATTAGGTTAGGG--TTA
29880079 GGGTTTTTTAATTA
64 GGG-TTTTTAATTA
29880093 CGNNNNNNNN
Statistics
Matches: 154, Mismatches: 4, Indels: 24
0.85 0.02 0.13
Matches are distributed among these distances:
87 18 0.12
88 2 0.01
89 6 0.04
90 3 0.02
92 59 0.38
93 32 0.21
94 5 0.03
95 3 0.02
96 2 0.01
97 24 0.16
ACGTcount: A:0.30, C:0.00, G:0.25, T:0.45
Consensus pattern (92 bp):
GGTTAGGGTTTTTAATTAAAATAGGTTAGGGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTAGG
GTTTTTAATTAAATTAAATTAGGTTAG
Found at i:29880237 original size:29 final size:29
Alignment explanation
Indices: 29880195--29880929 Score: 1110
Period size: 29 Copynumber: 25.2 Consensus size: 29
29880185 NNNNNNNNNN
29880195 TTAGGGTTAGGGTTTTTAATTAAATTAGG
1 TTAGGGTTAGGGTTTTTAATTAAATTAGG
29880224 TTAGGGTTAGGGTTTTTAATTAAATTAGG
1 TTAGGGTTAGGGTTTTTAATTAAATTAGG
*
29880253 TTAAGGTTAGGGTTTTTAATTAAATTAGG
1 TTAGGGTTAGGGTTTTTAATTAAATTAGG
*
29880282 CTAGGGTTAGGGTTTTTAATTAAATTAGG
1 TTAGGGTTAGGGTTTTTAATTAAATTAGG
* **
29880311 TTAGGGTTAGGGTTTTTAAATAAATTAAA
1 TTAGGGTTAGGGTTTTTAATTAAATTAGG
*
29880340 TTA-GGTTAGGGTTTTTAATTAAAATAGG
1 TTAGGGTTAGGGTTTTTAATTAAATTAGG
29880368 TTAGGGTTAGGGTTTTTAATTAAATTAAATTAGG
1 TTAGGGTTAGGG--TTT--TT-AATTAAATTAGG
29880402 TTAGGGTTAGGGTTTTTAATTAAATTAGG
1 TTAGGGTTAGGGTTTTTAATTAAATTAGG
29880431 TTAGGGTTAGGGTTTTTAATTAAATTAGG
1 TTAGGGTTAGGGTTTTTAATTAAATTAGG
29880460 TTAGGGTTAGGGTTTTTAATTAAATTAGG
1 TTAGGGTTAGGGTTTTTAATTAAATTAGG
29880489 TTAGGGTTAGGGTTTTTAATTAAATTAGG
1 TTAGGGTTAGGGTTTTTAATTAAATTAGG
* **
29880518 TTAGGGTTAGGGTTTTTAAATAAATTAAA
1 TTAGGGTTAGGGTTTTTAATTAAATTAGG
*
29880547 TTA-GGTTAGGGTTTTTAATTAAAATAGG
1 TTAGGGTTAGGGTTTTTAATTAAATTAGG
29880575 TTAGGGTTAGGGTTTTTAATTAAATTAGG
1 TTAGGGTTAGGGTTTTTAATTAAATTAGG
*
29880604 CTAGGGTTAGGGTTTTTAATTAAATTAGG
1 TTAGGGTTAGGGTTTTTAATTAAATTAGG
29880633 TTAGGGTTAGGGTTTTTAATTAAATTAAATTAGG
1 TTAGGGTTAGGG--TTT--TT-AATTAAATTAGG
29880667 TTAGGGTTAGGGTTTTTAATTAAATTAGG
1 TTAGGGTTAGGGTTTTTAATTAAATTAGG
29880696 TTAGGGTTAGGGTTTTTAATTAAATTAGG
1 TTAGGGTTAGGGTTTTTAATTAAATTAGG
* *
29880725 CTAGGGTTAGGGTTTTTAAATAAATTAGG
1 TTAGGGTTAGGGTTTTTAATTAAATTAGG
* **
29880754 TTAGGGTTAGGGTTTTTAAATAAATTAAA
1 TTAGGGTTAGGGTTTTTAATTAAATTAGG
**
29880783 TT-GGGTTAGGGTTTTTAATTAAATTAAA
1 TTAGGGTTAGGGTTTTTAATTAAATTAGG
*
29880811 TTA-GGTTAGGATTTTTAATTAAATTAGG
1 TTAGGGTTAGGGTTTTTAATTAAATTAGG
29880839 TTAGGGTTTAGGG-TTTT--TT--ATTACGG
1 TTAGGG-TTAGGGTTTTTAATTAAATTA-GG
29880865 TTAGGGGTTAGGGTTTTTAATTAAATTAGG
1 TTA-GGGTTAGGGTTTTTAATTAAATTAGG
*
29880895 TTAGGGTTAGGGTTTTTAAATAAATTAGG
1 TTAGGGTTAGGGTTTTTAATTAAATTAGG
29880924 TTAGGG
1 TTAGGG
29880930 ATCAAATAAT
Statistics
Matches: 651, Mismatches: 33, Indels: 44
0.89 0.05 0.06
Matches are distributed among these distances:
25 4 0.01
26 11 0.02
27 9 0.01
28 100 0.15
29 446 0.69
30 14 0.02
31 10 0.02
32 6 0.01
33 4 0.01
34 47 0.07
ACGTcount: A:0.30, C:0.01, G:0.26, T:0.44
Consensus pattern (29 bp):
TTAGGGTTAGGGTTTTTAATTAAATTAGG
Found at i:29880459 original size:207 final size:207
Alignment explanation
Indices: 29880195--29880929 Score: 1171
Period size: 207 Copynumber: 3.6 Consensus size: 207
29880185 NNNNNNNNNN
*
29880195 TTAGGGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTAGGGTTTTTAATTAAATTAGGTTAAGGT
1 TTAGGGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTAGGGTTTTTAATTAAATTAGGTTAGGGT
*
29880260 TAGGGTTTTTAATTAAATTAGGCTAGGGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTAGGGTT
66 TAGGGTTTTTAATTAAATTAGGTTAGGGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTAGGGTT
29880325 TTTAAATAAATTAAATTAGGTTAGGGTTTTTAATTAAAATAGGTTAGGGTTAGGGTTTTTAATTA
131 TTTAAATAAATTAAATTAGGTTAGGGTTTTTAATTAAAATAGGTTAGGGTTAGGGTTTTTAATTA
29880390 AATTAAATTAGG
196 AATTAAATTAGG
29880402 TTAGGGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTAGGGTTTTTAATTAAATTAGGTTAGGGT
1 TTAGGGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTAGGGTTTTTAATTAAATTAGGTTAGGGT
29880467 TAGGGTTTTTAATTAAATTAGGTTAGGGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTAGGGTT
66 TAGGGTTTTTAATTAAATTAGGTTAGGGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTAGGGTT
29880532 TTTAAATAAATTAAATTAGGTTAGGGTTTTTAATTAAAATAGGTTAGGGTTAGGG--TTT--TT-
131 TTTAAATAAATTAAATTAGGTTAGGGTTTTTAATTAAAATAGGTTAGGGTTAGGGTTTTTAATTA
29880592 AATTAAATTAGG
196 AATTAAATTAGG
*
29880604 CTAGGGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTAGGGTTTTTAATTAAATTAAATTAGGTT
1 TTAGGGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTAGGG--TTT--TT-AATTAAATTAGGTT
*
29880669 AGGGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTAGGGTTTTTAATTAAATTAGGCTAGGGTTA
61 AGGGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTA
** * * **
29880734 GGGTTTTTAAATAAATTAGGTTAGGGTTAGGGTTTTTAAATAAATTAAATT-GGGTTAGGGTTTT
126 GGGTTTTTAAATAAATTAAATTA-GGTTAGGGTTTTTAATTAAAATAGGTTAGGGTTAGGGTTTT
29880798 TAATTAAATTAAATTAGG
190 TAATTAAATTAAATTAGG
29880816 TTA-GG--A---TTTTTAATTAAATTAGGTTAGGGTTTAGGG-TTTT--TT--ATTACGGTTAGG
1 TTAGGGTTAGGGTTTTTAATTAAATTAGGTTAGGG-TTAGGGTTTTTAATTAAATTA-GGTTA-G
*
29880870 GGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTAGGGTTTTTAAATAAATTAGGTTAGGG
63 GGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTAGGGTTTTTAATTAAATTAGGTTAGGG
29880930 ATCAAATAAT
Statistics
Matches: 501, Mismatches: 13, Indels: 36
0.91 0.02 0.07
Matches are distributed among these distances:
197 4 0.01
198 5 0.01
199 61 0.12
202 54 0.11
203 2 0.00
204 5 0.01
205 3 0.01
206 25 0.05
207 297 0.59
208 23 0.05
209 4 0.01
211 4 0.01
212 14 0.03
ACGTcount: A:0.30, C:0.01, G:0.26, T:0.44
Consensus pattern (207 bp):
TTAGGGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTAGGGTTTTTAATTAAATTAGGTTAGGGT
TAGGGTTTTTAATTAAATTAGGTTAGGGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTAGGGTT
TTTAAATAAATTAAATTAGGTTAGGGTTTTTAATTAAAATAGGTTAGGGTTAGGGTTTTTAATTA
AATTAAATTAGG
Found at i:29880499 original size:236 final size:232
Alignment explanation
Indices: 29880195--29880929 Score: 1162
Period size: 236 Copynumber: 3.2 Consensus size: 232
29880185 NNNNNNNNNN
*
29880195 TTAGGGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTAGGGTTTTTAATTAAATTAGGTTAAGGT
1 TTAGGGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTAGGGTTTTTAATTAAATTAGGTTAGGGT
* * **
29880260 TAGGGTTTTTAATTAAATTAGGCTAGGGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTAGGGTT
66 TAGGGTTTTTAATTAAATTAGGTTAGGGTTAGGGTTTTTAAATAAATTAAATTAGGGTTAGGGTT
* *
29880325 TTTAAATAAATTAAATTAGGTTAGGGTTTTTAATTAAAATAGGTTAGGGTTAGGGTTTTTAATTA
131 TTTAATTAAATTAAATTAGGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTAGGG-TTTT--TT-
29880390 AATTAAATTAGGTTAGGGTTAGGGTTTTTAATTAAATTAGG
192 AATTAAATTAGGTTAGGGTTAGGGTTTTTAATTAAATTAGG
29880431 TTAGGGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTAGGGTTTTTAATTAAATTAGGTTAGGGT
1 TTAGGGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTAGGGTTTTTAATTAAATTAGGTTAGGGT
29880496 TAGGGTTTTTAATTAAATTAGGTTAGGGTTAGGGTTTTTAAATAAATTAAATTA-GGTTAGGGTT
66 TAGGGTTTTTAATTAAATTAGGTTAGGGTTAGGGTTTTTAAATAAATTAAATTAGGGTTAGGGTT
* ** *
29880560 TTTAATTAAAATAGGTTAGGGTTAGGGTTTTTAATTAAATTAGGCTAGGGTTAGGG-TTTTTAAT
131 TTTAATTAAATTAAATTA-GGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTAGGGTTTTTTAAT
29880624 TAAATTAGGTTAGGGTTAGGGTTTTTAATTAAATTAAATTAGG
195 TAAATTAGGTTAGGGTTAGGG--TTT--TT-AATTAAATTAGG
*
29880667 TTAGGGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTAGGGTTTTTAATTAAATTAGGCTAGGGT
1 TTAGGGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTAGGGTTTTTAATTAAATTAGGTTAGGGT
*
29880732 TAGGGTTTTTAAATAAATTAGGTTAGGGTTAGGGTTTTTAAATAAATTAAATT-GGGTTAGGGTT
66 TAGGGTTTTTAATTAAATTAGGTTAGGGTTAGGGTTTTTAAATAAATTAAATTAGGGTTAGGGTT
*
29880796 TTTAATTAAATTAAATTAGGTTAGGATTTTTAATTAAATTAGGTTAGGGTTTAGGGTTTTTT-AT
131 TTTAATTAAATTAAATTAGGTTAGGGTTTTTAATTAAATTAGGTTAGGG-TTAGGGTTTTTTAAT
*
29880860 T--A--CGGTTAGGGGTTAGGGTTTTTAATTAAATTAGG
195 TAAATTAGGTTA-GGGTTAGGGTTTTTAATTAAATTAGG
*
29880895 TTAGGGTTAGGGTTTTTAAATAAATTAGGTTAGGG
1 TTAGGGTTAGGGTTTTTAATTAAATTAGGTTAGGG
29880930 ATCAAATAAT
Statistics
Matches: 469, Mismatches: 20, Indels: 28
0.91 0.04 0.05
Matches are distributed among these distances:
228 46 0.10
229 2 0.00
231 27 0.06
232 7 0.01
233 12 0.03
234 4 0.01
235 55 0.12
236 311 0.66
237 5 0.01
ACGTcount: A:0.30, C:0.01, G:0.26, T:0.44
Consensus pattern (232 bp):
TTAGGGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTAGGGTTTTTAATTAAATTAGGTTAGGGT
TAGGGTTTTTAATTAAATTAGGTTAGGGTTAGGGTTTTTAAATAAATTAAATTAGGGTTAGGGTT
TTTAATTAAATTAAATTAGGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTAGGGTTTTTTAATT
AAATTAGGTTAGGGTTAGGGTTTTTAATTAAATTAGG
Found at i:29880870 original size:26 final size:25
Alignment explanation
Indices: 29880832--29880913 Score: 85
Period size: 26 Copynumber: 3.1 Consensus size: 25
29880822 TTTTTAATTA
*
29880832 AATTAGGTTAGGGTTTAGGGTTTTT
1 AATTAGGTTAGGGGTTAGGGTTTTT
*
29880857 TATTACGGTTAGGGGTTAGGGTTTTTAATT
1 AATTA-GGTTAGGGGTTAGGG--TTT--TT
29880887 AAATTAGGTTA-GGGTTAGGGTTTTT
1 -AATTAGGTTAGGGGTTAGGGTTTTT
29880912 AA
1 AA
29880914 ATAAATTAGG
Statistics
Matches: 48, Mismatches: 3, Indels: 13
0.75 0.05 0.20
Matches are distributed among these distances:
24 2 0.04
25 6 0.12
26 14 0.29
27 3 0.06
28 3 0.06
29 9 0.19
30 7 0.15
31 4 0.08
ACGTcount: A:0.23, C:0.01, G:0.30, T:0.45
Consensus pattern (25 bp):
AATTAGGTTAGGGGTTAGGGTTTTT
Found at i:29880902 original size:23 final size:25
Alignment explanation
Indices: 29880775--29880848 Score: 89
Period size: 23 Copynumber: 2.9 Consensus size: 25
29880765 GTTTTTAAAT
*
29880775 AAATTAAATTGGGTTAGGGTTTTTAATT
1 AAATTAAATTAGGTTAGGG--TTT-ATT
*
29880803 AAATTAAATTAGGTTAGGATTT-TT
1 AAATTAAATTAGGTTAGGGTTTATT
29880827 -AATTAAATTAGGTTAGGGTTTA
1 AAATTAAATTAGGTTAGGGTTTA
29880849 GGGTTTTTTA
Statistics
Matches: 42, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
23 20 0.48
24 2 0.05
26 3 0.07
28 17 0.40
ACGTcount: A:0.35, C:0.00, G:0.20, T:0.45
Consensus pattern (25 bp):
AAATTAAATTAGGTTAGGGTTTATT
Found at i:29882106 original size:7 final size:7
Alignment explanation
Indices: 29882096--29882120 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
29882086 TTATATACAT
29882096 AATACTA
1 AATACTA
29882103 AATACTA
1 AATACTA
29882110 AATACTA
1 AATACTA
29882117 AATA
1 AATA
29882121 TCAATCCACT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.60, C:0.12, G:0.00, T:0.28
Consensus pattern (7 bp):
AATACTA
Found at i:29882859 original size:10 final size:10
Alignment explanation
Indices: 29882833--29882896 Score: 60
Period size: 10 Copynumber: 6.4 Consensus size: 10
29882823 GCCATTGTTG
29882833 AAAATA-TTA
1 AAAATATTTA
29882842 AAAA-ATTTA
1 AAAATATTTA
*
29882851 AAATTATTTTA
1 AAAATA-TTTA
* *
29882862 AAAAAATATA
1 AAAATATTTA
29882872 AAAATATTTA
1 AAAATATTTA
*
29882882 AAATTATCTTA
1 AAAATAT-TTA
29882893 AAAA
1 AAAA
29882897 ATGAAATTGA
Statistics
Matches: 43, Mismatches: 8, Indels: 6
0.75 0.14 0.11
Matches are distributed among these distances:
8 1 0.02
9 10 0.23
10 18 0.42
11 14 0.33
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (10 bp):
AAAATATTTA
Found at i:29882867 original size:21 final size:20
Alignment explanation
Indices: 29882833--29882884 Score: 63
Period size: 21 Copynumber: 2.6 Consensus size: 20
29882823 GCCATTGTTG
*
29882833 AAAATA-TT-AAAAAATTTA
1 AAAATATTTAAAAAAATATA
*
29882851 AAATTATTTTAAAAAAATATA
1 AAAATA-TTTAAAAAAATATA
29882872 AAAATATTTAAAA
1 AAAATATTTAAAA
29882885 TTATCTTAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
18 5 0.18
20 9 0.32
21 14 0.50
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (20 bp):
AAAATATTTAAAAAAATATA
Found at i:29882868 original size:31 final size:31
Alignment explanation
Indices: 29882833--29882897 Score: 105
Period size: 31 Copynumber: 2.1 Consensus size: 31
29882823 GCCATTGTTG
*
29882833 AAAATATTAAAAA-ATTTAAAATTATTTTAAA
1 AAAATA-TAAAAATATTTAAAATTATCTTAAA
29882864 AAAATATAAAAATATTTAAAATTATCTTAAA
1 AAAATATAAAAATATTTAAAATTATCTTAAA
29882895 AAA
1 AAA
29882898 TGAAATTGAA
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
30 6 0.19
31 26 0.81
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (31 bp):
AAAATATAAAAATATTTAAAATTATCTTAAA
Found at i:29882966 original size:22 final size:22
Alignment explanation
Indices: 29882941--29882982 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
29882931 TTTTAGAGAT
29882941 TTTTGGAAGGAAATTGAGAGGA
1 TTTTGGAAGGAAATTGAGAGGA
* *
29882963 TTTTTGAAGGAATTTGAGAG
1 TTTTGGAAGGAAATTGAGAG
29882983 TTTGAGAGAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.33, C:0.00, G:0.33, T:0.33
Consensus pattern (22 bp):
TTTTGGAAGGAAATTGAGAGGA
Found at i:29882990 original size:30 final size:30
Alignment explanation
Indices: 29882954--29883012 Score: 91
Period size: 30 Copynumber: 2.0 Consensus size: 30
29882944 TGGAAGGAAA
* * *
29882954 TTGAGAGGATTTTTGAAGGAATTTGAGAGT
1 TTGAGAGAATTTTGGAAGGAAATTGAGAGT
29882984 TTGAGAGAATTTTGGAAGGAAATTGAGAG
1 TTGAGAGAATTTTGGAAGGAAATTGAGAG
29883013 AATTTTGAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.34, C:0.00, G:0.34, T:0.32
Consensus pattern (30 bp):
TTGAGAGAATTTTGGAAGGAAATTGAGAGT
Found at i:29882997 original size:52 final size:52
Alignment explanation
Indices: 29882935--29883034 Score: 157
Period size: 52 Copynumber: 1.9 Consensus size: 52
29882925 TATGGATTTT
* * *
29882935 AGAGATTTTTGGAAGGAAATTGAGAGGATTTTTG-AAGGAATTTGAGAGTTTG
1 AGAGAATTTTGGAAGGAAATTGAGA-GAATTTTGAAAGGAAATTGAGAGTTTG
29882987 AGAGAATTTTGGAAGGAAATTGAGAGAATTTTGAAAGGAAATTGAGAG
1 AGAGAATTTTGGAAGGAAATTGAGAGAATTTTGAAAGGAAATTGAGAG
29883035 AATTTTGGAA
Statistics
Matches: 44, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
51 7 0.16
52 37 0.84
ACGTcount: A:0.38, C:0.00, G:0.32, T:0.30
Consensus pattern (52 bp):
AGAGAATTTTGGAAGGAAATTGAGAGAATTTTGAAAGGAAATTGAGAGTTTG
Found at i:29883009 original size:22 final size:22
Alignment explanation
Indices: 29882984--29883051 Score: 127
Period size: 22 Copynumber: 3.1 Consensus size: 22
29882974 ATTTGAGAGT
29882984 TTGAGAGAATTTTGGAAGGAAA
1 TTGAGAGAATTTTGGAAGGAAA
*
29883006 TTGAGAGAATTTTGAAAGGAAA
1 TTGAGAGAATTTTGGAAGGAAA
29883028 TTGAGAGAATTTTGGAAGGAAA
1 TTGAGAGAATTTTGGAAGGAAA
29883050 TT
1 TT
29883052 TAGATAGGAT
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 44 1.00
ACGTcount: A:0.41, C:0.00, G:0.29, T:0.29
Consensus pattern (22 bp):
TTGAGAGAATTTTGGAAGGAAA
Found at i:29885888 original size:22 final size:23
Alignment explanation
Indices: 29885862--29885907 Score: 69
Period size: 23 Copynumber: 2.0 Consensus size: 23
29885852 GGAAAATATT
29885862 AAATAT-ATA-TTTTTTAATTTTA
1 AAATATAATAGTTTTTT-ATTTTA
29885884 AAATATAATAGTTTTTTATTTTA
1 AAATATAATAGTTTTTTATTTTA
29885907 A
1 A
29885908 GTTTATTTAC
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
22 6 0.27
23 10 0.45
24 6 0.27
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (23 bp):
AAATATAATAGTTTTTTATTTTA
Found at i:29886011 original size:68 final size:66
Alignment explanation
Indices: 29885946--29886169 Score: 211
Period size: 59 Copynumber: 3.5 Consensus size: 66
29885936 TGTTACAAAA
*
29885946 TAATAATAAAACATCAAGTTTG-T-TTTACTAATCAAATGTTAGATTTTGTTACAACAATTAATA
1 TAATAATAAAA-AT-AA-TTTGATATTTACTAATCAAATGTTAGATTTTATTACAACAATTAATA
29886009 CAAT
63 CAAT
** *
29886013 TAATACA-ATTAATAATTTGATAAATTTACTAATCAAATGTTAGATTTTATTGCAACAATTAATA
1 TAATA-ATAAAAATAATTTGAT--ATTTACTAATCAAATGTTAGATTTTATTACAACAATTAATA
29886077 CAAT
63 CAAT
* * *
29886081 TAATAAT----TTGA--T-AAATTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAA
1 TAATAATAAAAATAATTTGATATTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAA
29886139 T
66 T
* *
29886140 TAACAAT--TAATAATTTGATAATTTTACTAA
1 TAATAATAAAAATAATTTGAT-A-TTTACTAA
29886170 CAATTAATTT
Statistics
Matches: 132, Mismatches: 12, Indels: 27
0.77 0.07 0.16
Matches are distributed among these distances:
59 50 0.38
61 3 0.02
62 1 0.01
63 1 0.01
64 7 0.05
65 4 0.03
66 10 0.08
67 8 0.06
68 48 0.36
ACGTcount: A:0.45, C:0.09, G:0.06, T:0.40
Consensus pattern (66 bp):
TAATAATAAAAATAATTTGATATTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAA
T
Found at i:29886013 original size:9 final size:9
Alignment explanation
Indices: 29885999--29886026 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
29885989 TTTTGTTACA
29885999 ACAATTAAT
1 ACAATTAAT
29886008 ACAATTAAT
1 ACAATTAAT
29886017 ACAATTAAT
1 ACAATTAAT
29886026 A
1 A
29886027 ATTTGATAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.57, C:0.11, G:0.00, T:0.32
Consensus pattern (9 bp):
ACAATTAAT
Found at i:29886080 original size:59 final size:59
Alignment explanation
Indices: 29886008--29886147 Score: 262
Period size: 59 Copynumber: 2.4 Consensus size: 59
29885998 AACAATTAAT
*
29886008 ACAATTAATACAATTAATAATTTGATAAATTTACTAATCAAATGTTAGATTTTATTGCA
1 ACAATTAATACAATTAATAATTTGATAAATTTACTAATCAAATGTTAGATTTTATTACA
29886067 ACAATTAATACAATTAATAATTTGATAAATTTACTAATCAAATGTTAGATTTTATTACA
1 ACAATTAATACAATTAATAATTTGATAAATTTACTAATCAAATGTTAGATTTTATTACA
*
29886126 ACAATTAATACAATTAACAATT
1 ACAATTAATACAATTAATAATT
29886148 AATAATTTGA
Statistics
Matches: 79, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
59 79 1.00
ACGTcount: A:0.46, C:0.09, G:0.05, T:0.39
Consensus pattern (59 bp):
ACAATTAATACAATTAATAATTTGATAAATTTACTAATCAAATGTTAGATTTTATTACA
Found at i:29886179 original size:16 final size:16
Alignment explanation
Indices: 29886158--29886196 Score: 69
Period size: 16 Copynumber: 2.4 Consensus size: 16
29886148 AATAATTTGA
*
29886158 TAATTTTACTAACAAT
1 TAATTTTAATAACAAT
29886174 TAATTTTAATAACAAT
1 TAATTTTAATAACAAT
29886190 TAATTTT
1 TAATTTT
29886197 TATTTTATTA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.44, C:0.08, G:0.00, T:0.49
Consensus pattern (16 bp):
TAATTTTAATAACAAT
Found at i:29886183 original size:22 final size:23
Alignment explanation
Indices: 29886173--29886228 Score: 69
Period size: 23 Copynumber: 2.5 Consensus size: 23
29886163 TTACTAACAA
* *
29886173 TTAATTTTAAT-AACAATTAATT
1 TTAATTTTAATAAAAAAATAATT
* *
29886195 TTTATTTTATTAAAAAAATAATT
1 TTAATTTTAATAAAAAAATAATT
29886218 TTAATTTTAAT
1 TTAATTTTAAT
29886229 TTTAATTAAA
Statistics
Matches: 27, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
22 9 0.33
23 18 0.67
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.54
Consensus pattern (23 bp):
TTAATTTTAATAAAAAAATAATT
Found at i:29887612 original size:17 final size:17
Alignment explanation
Indices: 29887592--29887656 Score: 60
Period size: 17 Copynumber: 3.6 Consensus size: 17
29887582 TTGTTTGTCC
29887592 TTTTCCTTTTTTATTTG
1 TTTTCCTTTTTTATTTG
*
29887609 TTTTTCTTTATTTCATTT-
1 TTTTCCTTT-TTT-ATTTG
**
29887627 TATTTGTTTTTTTATTTG
1 T-TTTCCTTTTTTATTTG
29887645 TTTGTCCTTTTT
1 TTT-TCCTTTTT
29887657 CTGTTTTTTA
Statistics
Matches: 38, Mismatches: 5, Indels: 9
0.73 0.10 0.17
Matches are distributed among these distances:
17 14 0.37
18 14 0.37
19 10 0.26
ACGTcount: A:0.08, C:0.09, G:0.06, T:0.77
Consensus pattern (17 bp):
TTTTCCTTTTTTATTTG
Found at i:29887613 original size:34 final size:33
Alignment explanation
Indices: 29887575--29887748 Score: 126
Period size: 34 Copynumber: 5.3 Consensus size: 33
29887565 TTTTTTTTAT
*
29887575 TTTTTATTTGTTTGTCCTTTTC-CTTTTTTATTTG
1 TTTTTATTT-ATT-TCCTTTTCTCTTTTTTATTTG
* * * *
29887609 TTTTTCTTTATTTCATTTTAT-TTGTTT-TTT-
1 TTTTTATTTATTTCCTTTTCTCTTTTTTATTTG
* * * *
29887639 TATTT-GTT-TGTCCTTTTTCTGTTTTTTATTTG
1 TTTTTATTTATTTCC-TTTTCTCTTTTTTATTTG
* *
29887671 TTTTTCTTTATTTCATTTTTCTCTTTTTTATTTG
1 TTTTTATTTATTTC-CTTTTCTCTTTTTTATTTG
* * *
29887705 TTTTTCTTTATTTCATTTTTCTATTTTTTATTTG
1 TTTTTATTTATTTC-CTTTTCTCTTTTTTATTTG
29887739 TTTATTATTT
1 TTT-TTATTT
29887749 TTATAATATT
Statistics
Matches: 113, Mismatches: 18, Indels: 17
0.76 0.12 0.11
Matches are distributed among these distances:
28 3 0.03
29 7 0.06
30 9 0.08
31 6 0.05
32 15 0.13
33 4 0.04
34 64 0.57
35 5 0.04
ACGTcount: A:0.09, C:0.09, G:0.06, T:0.76
Consensus pattern (33 bp):
TTTTTATTTATTTCCTTTTCTCTTTTTTATTTG
Found at i:29887654 original size:60 final size:60
Alignment explanation
Indices: 29887557--29887707 Score: 225
Period size: 60 Copynumber: 2.5 Consensus size: 60
29887547 TTCTACTACC
29887557 TATTGTCATTTTTTTTATTTTTTATTTGTTTGTCC-TTTTC-CTTTTTTATTTGTTTTTCTT
1 TATT-TCATTTTTTTT-TTTTTTATTTGTTTGTCCTTTTTCTCTTTTTTATTTGTTTTTCTT
*
29887617 TATTTCATTTTATTTGTTTTTTTATTTGTTTGTCCTTTTTCTGTTTTTTATTTGTTTTTCTT
1 TATTTCATTTT-TTT-TTTTTTTATTTGTTTGTCCTTTTTCTCTTTTTTATTTGTTTTTCTT
* *
29887679 TATTTCATTTTTCTCTTTTTTATTTGTTT
1 TATTTCATTTTTTTTTTTTTTATTTGTTT
29887708 TTCTTTATTT
Statistics
Matches: 84, Mismatches: 3, Indels: 8
0.88 0.03 0.08
Matches are distributed among these distances:
59 7 0.08
60 39 0.46
61 8 0.10
62 30 0.36
ACGTcount: A:0.09, C:0.09, G:0.07, T:0.75
Consensus pattern (60 bp):
TATTTCATTTTTTTTTTTTTTATTTGTTTGTCCTTTTTCTCTTTTTTATTTGTTTTTCTT
Found at i:29887674 original size:19 final size:18
Alignment explanation
Indices: 29887592--29887741 Score: 85
Period size: 19 Copynumber: 8.1 Consensus size: 18
29887582 TTGTTTGTCC
*
29887592 TTTTCCTTTTTTATTTGT
1 TTTTCTTTTTTTATTTGT
*
29887610 TTTTCTTTATTTCATTT-T
1 TTTTCTTT-TTTTATTTGT
* *
29887628 ATTTGTTTTTTTATTTGT
1 TTTTCTTTTTTTATTTGT
* * * *
29887646 TTGTCCTTTTTCTGTTTTT
1 TT-TTCTTTTTTTATTTGT
* *
29887665 TATTTGTTTTTCTTTATTTCAT
1 T-TTT-CTTTT-TTTATTT-GT
29887687 TTTTCTCTTTTTTATTTGT
1 TTTTCT-TTTTTTATTTGT
*
29887706 TTTTC----TTTATTTCAT
1 TTTTCTTTTTTTATTT-GT
29887721 TTTTCTATTTTTTATTTGT
1 TTTTCT-TTTTTTATTTGT
29887740 TT
1 TT
29887742 ATTATTTTTA
Statistics
Matches: 98, Mismatches: 20, Indels: 27
0.68 0.14 0.19
Matches are distributed among these distances:
14 7 0.07
15 6 0.06
17 7 0.07
18 16 0.16
19 29 0.30
20 20 0.20
21 11 0.11
22 2 0.02
ACGTcount: A:0.09, C:0.09, G:0.05, T:0.77
Consensus pattern (18 bp):
TTTTCTTTTTTTATTTGT
Found at i:29887684 original size:27 final size:26
Alignment explanation
Indices: 29887625--29887690 Score: 80
Period size: 26 Copynumber: 2.5 Consensus size: 26
29887615 TTTATTTCAT
*
29887625 TTTATTTGTTTTTTTATTTGTTTGTC
1 TTTATTTCTTTTTTTATTTGTTTGTC
* *
29887651 CTT-TTTCTGTTTTTTATTTGTTTTTC
1 TTTATTTCT-TTTTTTATTTGTTTGTC
*
29887677 TTTATTTCATTTTT
1 TTTATTTCTTTTTT
29887691 CTCTTTTTTA
Statistics
Matches: 33, Mismatches: 5, Indels: 4
0.79 0.12 0.10
Matches are distributed among these distances:
25 4 0.12
26 25 0.76
27 4 0.12
ACGTcount: A:0.08, C:0.08, G:0.08, T:0.77
Consensus pattern (26 bp):
TTTATTTCTTTTTTTATTTGTTTGTC
Found at i:29887691 original size:15 final size:15
Alignment explanation
Indices: 29887671--29887726 Score: 51
Period size: 14 Copynumber: 3.5 Consensus size: 15
29887661 TTTTTATTTG
29887671 TTTTTCTTTATTTCA
1 TTTTTCTTTATTTCA
*
29887686 TTTTTCTCTTTTTTATTT-G
1 -TTTT-TC---TTTATTTCA
29887705 TTTTTCTTTATTTCA
1 TTTTTCTTTATTTCA
29887720 TTTTTCT
1 TTTTTCT
29887727 ATTTTTTATT
Statistics
Matches: 33, Mismatches: 2, Indels: 11
0.72 0.04 0.24
Matches are distributed among these distances:
14 7 0.21
15 7 0.21
16 4 0.12
17 4 0.12
18 4 0.12
20 7 0.21
ACGTcount: A:0.09, C:0.12, G:0.02, T:0.77
Consensus pattern (15 bp):
TTTTTCTTTATTTCA
Done.