Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr09 ID=Chr09-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: 70713020
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1142373 characters in sequence are not A, C, G, or T
File 132 of 226
Found at i:44181826 original size:26 final size:26
Alignment explanation
Indices: 44181790--44181839 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
44181780 ATGATTTGTG
*
44181790 TTCAAAGTGATAATTGT-TGGCATGGT
1 TTCAAAATGATAATT-TATGGCATGGT
*
44181816 TTCAAAATGATCATTTATGGCATG
1 TTCAAAATGATAATTTATGGCATG
44181840 TATTGATATA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 1 0.05
26 20 0.95
ACGTcount: A:0.30, C:0.10, G:0.22, T:0.38
Consensus pattern (26 bp):
TTCAAAATGATAATTTATGGCATGGT
Found at i:44189905 original size:22 final size:22
Alignment explanation
Indices: 44189875--44189926 Score: 59
Period size: 22 Copynumber: 2.4 Consensus size: 22
44189865 AATGACTAAG
* * *
44189875 AGCCGTAAACAGGATAGCTATA
1 AGCCATAAACAGAATAGCTACA
* *
44189897 AGCTATAAACAGAATGGCTACA
1 AGCCATAAACAGAATAGCTACA
44189919 AGCCATAA
1 AGCCATAA
44189927 GTACAGTAAT
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.44, C:0.19, G:0.19, T:0.17
Consensus pattern (22 bp):
AGCCATAAACAGAATAGCTACA
Found at i:44189969 original size:32 final size:31
Alignment explanation
Indices: 44189931--44190117 Score: 169
Period size: 32 Copynumber: 5.8 Consensus size: 31
44189921 CCATAAGTAC
* *
44189931 AGTAATATGATTGGCACAAAACATTCAGTAGT
1 AGTAATATGATCGGCACAAACCA-TCAGTAGT
* *
44189963 AGTAATATGGTCGGCACACAGCCATCAGTAGT
1 AGTAATATGATCGGCACA-AACCATCAGTAGT
** *
44189995 AGTTGTATGATCGACACAAAGCCATCAGTAGT
1 AGTAATATGATCGGCACAAA-CCATCAGTAGT
* * *
44190027 AGTAATATGATCGGCATAAAGCCAGCAGTAAT
1 AGTAATATGATCGGCACAAA-CCATCAGTAGT
* * * *
44190059 GGTAATATGATTGACACACAACCATCAGTAAT
1 AGTAATATGATCGGCACA-AACCATCAGTAGT
*
44190091 GGTAATATGA-CTGGCACAAAGCCATCA
1 AGTAATATGATC-GGCACAAA-CCATCA
44190118 ATAGCATCGC
Statistics
Matches: 128, Mismatches: 22, Indels: 10
0.80 0.14 0.06
Matches are distributed among these distances:
31 3 0.02
32 120 0.94
33 5 0.04
ACGTcount: A:0.37, C:0.18, G:0.21, T:0.24
Consensus pattern (31 bp):
AGTAATATGATCGGCACAAACCATCAGTAGT
Found at i:44190013 original size:64 final size:63
Alignment explanation
Indices: 44189918--44190117 Score: 206
Period size: 64 Copynumber: 3.1 Consensus size: 63
44189908 GAATGGCTAC
* * * *
44189918 AAGCCATAAGT-ACAGTAATATGATTGGCACAAAACATTCAGTAGTAGTAATATGGTCGGCACA
1 AAGCCATCAGTAATAGTAATATGATTGACACAAACCA-TCAGTAGTAGTAATATGGTCGGCACA
* * ** * * *
44189981 CAGCCATCAGTAGTAGTTGTATGATCGACACAAAGCCATCAGTAGTAGTAATATGATCGGCATA
1 AAGCCATCAGTAATAGTAATATGATTGACACAAA-CCATCAGTAGTAGTAATATGGTCGGCACA
* * * * *
44190045 AAGCCAGCAGTAATGGTAATATGATTGACACACAACCATCAGTAATGGTAATAT-GACTGGCACA
1 AAGCCATCAGTAATAGTAATATGATTGACACA-AACCATCAGTAGTAGTAATATGGTC-GGCACA
44190109 AAGCCATCA
1 AAGCCATCA
44190118 ATAGCATCGC
Statistics
Matches: 109, Mismatches: 24, Indels: 7
0.78 0.17 0.05
Matches are distributed among these distances:
63 10 0.09
64 95 0.87
65 4 0.04
ACGTcount: A:0.38, C:0.18, G:0.20, T:0.23
Consensus pattern (63 bp):
AAGCCATCAGTAATAGTAATATGATTGACACAAACCATCAGTAGTAGTAATATGGTCGGCACA
Found at i:44190141 original size:23 final size:23
Alignment explanation
Indices: 44190115--44190169 Score: 56
Period size: 26 Copynumber: 2.3 Consensus size: 23
44190105 CACAAAGCCA
44190115 TCAATAGCATCGCAGCAAAGCTG
1 TCAATAGCATCGCAGCAAAGCTG
* *
44190138 TCAACAACAGTATCGCAGCAAAGCTG
1 T---CAATAGCATCGCAGCAAAGCTG
*
44190164 CCAATA
1 TCAATA
44190170 ACAGTATATG
Statistics
Matches: 25, Mismatches: 4, Indels: 6
0.71 0.11 0.17
Matches are distributed among these distances:
23 5 0.20
26 20 0.80
ACGTcount: A:0.38, C:0.27, G:0.18, T:0.16
Consensus pattern (23 bp):
TCAATAGCATCGCAGCAAAGCTG
Found at i:44190158 original size:26 final size:26
Alignment explanation
Indices: 44190123--44190176 Score: 90
Period size: 26 Copynumber: 2.1 Consensus size: 26
44190113 CATCAATAGC
*
44190123 ATCGCAGCAAAGCTGTCAACAACAGT
1 ATCGCAGCAAAGCTGCCAACAACAGT
*
44190149 ATCGCAGCAAAGCTGCCAATAACAGT
1 ATCGCAGCAAAGCTGCCAACAACAGT
44190175 AT
1 AT
44190177 ATGTGACCAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.39, C:0.26, G:0.19, T:0.17
Consensus pattern (26 bp):
ATCGCAGCAAAGCTGCCAACAACAGT
Found at i:44190350 original size:24 final size:24
Alignment explanation
Indices: 44190291--44190377 Score: 111
Period size: 24 Copynumber: 3.6 Consensus size: 24
44190281 GCCATGCACG
**
44190291 AAATCAGTCATACAAATCACAGAC
1 AAATCAGTCATTTAAATCACAGAC
44190315 AAATCAGTCATTTAAATCACAGAC
1 AAATCAGTCATTTAAATCACAGAC
* * *
44190339 AAATCAGTCATTTACATCTCGGAC
1 AAATCAGTCATTTAAATCACAGAC
* *
44190363 AAATCAATCGTTTAA
1 AAATCAGTCATTTAA
44190378 CCCCAAGGGG
Statistics
Matches: 55, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 55 1.00
ACGTcount: A:0.44, C:0.22, G:0.09, T:0.25
Consensus pattern (24 bp):
AAATCAGTCATTTAAATCACAGAC
Found at i:44190428 original size:27 final size:27
Alignment explanation
Indices: 44190398--44190623 Score: 229
Period size: 27 Copynumber: 8.4 Consensus size: 27
44190388 CAAAATAGTT
*
44190398 ATTTTACCCTACAAGGGTATTACGATC
1 ATTTTACCCTACAGGGGTATTACGATC
* *
44190425 ATTTTACCCTACAGGGGCATTACGGTC
1 ATTTTACCCTACAGGGGTATTACGATC
* * *
44190452 ATTTTACCCTAAAGGGGCATTACGGTC
1 ATTTTACCCTACAGGGGTATTACGATC
* * *
44190479 ATTTTACCCTACAGGGGCATTACGGTT
1 ATTTTACCCTACAGGGGTATTACGATC
* *
44190506 ATTTTACCTTACAGGGGCATTAC-AGTC
1 ATTTTACCCTACAGGGGTATTACGA-TC
*** *
44190533 ATTTTACCCTTTGGGGGTATTTCGATC
1 ATTTTACCCTACAGGGGTATTACGATC
*** *
44190560 ATTTTACCCTTTGGGGGTATTTCGATC
1 ATTTTACCCTACAGGGGTATTACGATC
* * * *
44190587 ATTTTACCTTTCAGGGGTATTTCGATA
1 ATTTTACCCTACAGGGGTATTACGATC
44190614 ATTTTACCCT
1 ATTTTACCCT
44190624 TCGAGGGTAT
Statistics
Matches: 177, Mismatches: 20, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
27 176 0.99
28 1 0.01
ACGTcount: A:0.22, C:0.21, G:0.19, T:0.37
Consensus pattern (27 bp):
ATTTTACCCTACAGGGGTATTACGATC
Found at i:44190624 original size:81 final size:81
Alignment explanation
Indices: 44190398--44190636 Score: 264
Period size: 81 Copynumber: 3.0 Consensus size: 81
44190388 CAAAATAGTT
* * * *
44190398 ATTTTACCCTACAAGGGTATTACGATCATTTTACCCTACAGGGGCATTACGGTCATTTTACCCTA
1 ATTTTACCCTACAGGGGTATTACGATCATTTTACCTTACAGGGGCATTACGATCATTTTACCCTT
* * * *
44190463 AAGGGGCATTACGGTC
66 AGGGGGTATTTCGATC
* * *
44190479 ATTTTACCCTACAGGGGCATTACGGTTATTTTACCTTACAGGGGCATTAC-AGTCATTTTACCCT
1 ATTTTACCCTACAGGGGTATTACGATCATTTTACCTTACAGGGGCATTACGA-TCATTTTACCCT
*
44190543 TTGGGGGTATTTCGATC
65 TAGGGGGTATTTCGATC
*** * * * * *
44190560 ATTTTACCCTTTGGGGGTATTTCGATCATTTTACCTTTCAGGGGTATTTCGATAATTTTACCCTT
1 ATTTTACCCTACAGGGGTATTACGATCATTTTACCTTACAGGGGCATTACGATCATTTTACCCTT
* *
44190625 CGAGGGTATTTC
66 AGGGGGTATTTC
44190637 ATTAATTTTA
Statistics
Matches: 131, Mismatches: 25, Indels: 4
0.82 0.16 0.03
Matches are distributed among these distances:
81 130 0.99
82 1 0.01
ACGTcount: A:0.22, C:0.21, G:0.20, T:0.37
Consensus pattern (81 bp):
ATTTTACCCTACAGGGGTATTACGATCATTTTACCTTACAGGGGCATTACGATCATTTTACCCTT
AGGGGGTATTTCGATC
Found at i:44190631 original size:27 final size:27
Alignment explanation
Indices: 44190533--44190646 Score: 133
Period size: 27 Copynumber: 4.2 Consensus size: 27
44190523 CATTACAGTC
* * *
44190533 ATTTTACCCTTTGGGGGTATTTCGATC
1 ATTTTACCCTTCGAGGGTATTTCGATA
* * *
44190560 ATTTTACCCTTTGGGGGTATTTCGATC
1 ATTTTACCCTTCGAGGGTATTTCGATA
*
44190587 ATTTTACCTTTC-AGGGGTATTTCGATA
1 ATTTTACCCTTCGA-GGGTATTTCGATA
44190614 ATTTTACCCTTCGAGGGTATTTC-ATTA
1 ATTTTACCCTTCGAGGGTATTTCGA-TA
44190641 ATTTTA
1 ATTTTA
44190647 TAACCTCTTT
Statistics
Matches: 79, Mismatches: 5, Indels: 6
0.88 0.06 0.07
Matches are distributed among these distances:
26 1 0.01
27 77 0.97
28 1 0.01
ACGTcount: A:0.19, C:0.17, G:0.18, T:0.46
Consensus pattern (27 bp):
ATTTTACCCTTCGAGGGTATTTCGATA
Found at i:44190645 original size:54 final size:54
Alignment explanation
Indices: 44190533--44190646 Score: 151
Period size: 54 Copynumber: 2.1 Consensus size: 54
44190523 CATTACAGTC
* * * * *
44190533 ATTTTACCCTTTGGGGGTATTTCGATCATTTTACCCTTTGGGGGTATTTCGATC
1 ATTTTACCCTTTAGGGGTATTTCGATAATTTTACCCTTCGAGGGTATTTCGATA
44190587 ATTTTA-CCTTTCAGGGGTATTTCGATAATTTTACCCTTCGAGGGTATTTC-ATTA
1 ATTTTACCCTTT-AGGGGTATTTCGATAATTTTACCCTTCGAGGGTATTTCGA-TA
44190641 ATTTTA
1 ATTTTA
44190647 TAACCTCTTT
Statistics
Matches: 53, Mismatches: 5, Indels: 4
0.85 0.08 0.06
Matches are distributed among these distances:
53 6 0.11
54 47 0.89
ACGTcount: A:0.19, C:0.17, G:0.18, T:0.46
Consensus pattern (54 bp):
ATTTTACCCTTTAGGGGTATTTCGATAATTTTACCCTTCGAGGGTATTTCGATA
Found at i:44199200 original size:50 final size:51
Alignment explanation
Indices: 44199029--44199275 Score: 184
Period size: 50 Copynumber: 4.8 Consensus size: 51
44199019 ATTTGGGTAA
* ** *
44199029 AGAAATCCCATGTAAGACCATGTCTGGGACATGGCATTGATATCATTGAGGTTATG
1 AGAACTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCA-T-A---TATG
** ** * *
44199085 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGTGTTGGCACC-GAGATG
1 AGAACTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCATATATG
* * *
44199135 ACAGA-TCTC-TCGTAAGACCATGTCTGGGACATGGCATGGGCACCA-ATATG
1 AGA-ACTCCCAT-GTAAGACCATGTCTGGGACATGGCATTGGCACCATATATG
* * * * * *
44199185 AGAACTCCCATGTAAGACCATATCTGGGATATGACATTGGCA--GTACAAG
1 AGAACTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCATATATG
* *
44199234 A-AACATCCCATGTAAGACCATGTTTGGGACATGGCTTTGGCA
1 AGAAC-TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA
44199276 TGTTATTATC
Statistics
Matches: 154, Mismatches: 30, Indels: 21
0.75 0.15 0.10
Matches are distributed among these distances:
48 3 0.02
49 38 0.25
50 74 0.48
51 1 0.01
53 1 0.01
56 37 0.24
ACGTcount: A:0.29, C:0.20, G:0.26, T:0.24
Consensus pattern (51 bp):
AGAACTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCATATATG
Found at i:44208792 original size:12 final size:12
Alignment explanation
Indices: 44208775--44208799 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
44208765 CTATAATTTA
44208775 TATATATTTTTT
1 TATATATTTTTT
44208787 TATATATTTTTT
1 TATATATTTTTT
44208799 T
1 T
44208800 GTTTTCATAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (12 bp):
TATATATTTTTT
Found at i:44210748 original size:12 final size:12
Alignment explanation
Indices: 44210731--44210758 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
44210721 GAGGGCAAGG
44210731 CCGTACATACAT
1 CCGTACATACAT
44210743 CCGTACATACAT
1 CCGTACATACAT
44210755 CCGT
1 CCGT
44210759 TTTATGTAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.29, C:0.36, G:0.11, T:0.25
Consensus pattern (12 bp):
CCGTACATACAT
Found at i:44212621 original size:42 final size:44
Alignment explanation
Indices: 44212524--44212622 Score: 109
Period size: 42 Copynumber: 2.3 Consensus size: 44
44212514 ATTATGTGTC
* *
44212524 TTATCCAATGGTAAACCAACCACTTGGAACAAATGTTTTGTCAA
1 TTATCCAATGGTAAAACAACCACTTGGAACAAATGTTTTGTAAA
* *
44212568 --ATCCAACGGTAAAACAACTGA-TTGGAACAAATG-TTT-TAAA
1 TTATCCAATGGTAAAACAAC-CACTTGGAACAAATGTTTTGTAAA
*
44212608 TTATCTAATGGTAAA
1 TTATCCAATGGTAAA
44212623 CCATCAAATT
Statistics
Matches: 46, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
40 3 0.07
41 3 0.07
42 39 0.85
43 1 0.02
ACGTcount: A:0.40, C:0.16, G:0.14, T:0.29
Consensus pattern (44 bp):
TTATCCAATGGTAAAACAACCACTTGGAACAAATGTTTTGTAAA
Found at i:44219347 original size:42 final size:43
Alignment explanation
Indices: 44219257--44219362 Score: 139
Period size: 42 Copynumber: 2.5 Consensus size: 43
44219247 ATTATGTGTC
*
44219257 TTATCCAATGGTAAACCAACCACTTGGAACAAATGTTTTGTCAA
1 TTATCCAATGGTAAACCAACCA-TTGGAACAAATGTTTTGTAAA
* *
44219301 --ATCCAATGATAAAACAACCGATTGGAACAAATG-TTT-TAAA
1 TTATCCAATGGTAAACCAACC-ATTGGAACAAATGTTTTGTAAA
44219341 TTATCCAATGGTAAACCAACCA
1 TTATCCAATGGTAAACCAACCA
44219363 ATTGAAACTT
Statistics
Matches: 54, Mismatches: 5, Indels: 9
0.79 0.07 0.13
Matches are distributed among these distances:
40 3 0.06
41 4 0.07
42 46 0.85
43 1 0.02
ACGTcount: A:0.42, C:0.20, G:0.12, T:0.26
Consensus pattern (43 bp):
TTATCCAATGGTAAACCAACCATTGGAACAAATGTTTTGTAAA
Found at i:44226080 original size:42 final size:43
Alignment explanation
Indices: 44226033--44226146 Score: 126
Period size: 42 Copynumber: 2.7 Consensus size: 43
44226023 TGAAAAAGAA
* * *
44226033 GTTCCAATTGGTTGGTTTACCATTAGATAATT-TAAAACATTT
1 GTTCCAACTGGTTGGTTTACCATTGGATAATTACAAAACATTT
** * *
44226075 GTTCCAACCAGTTGTTTTACCTTTGGAT--TTGACAAAACATTT
1 GTTCCAACTGGTTGGTTTACCATTGGATAATT-ACAAAACATTT
*
44226117 GTTCCAAGTGGTTGGTTTACCATTGGATAA
1 GTTCCAACTGGTTGGTTTACCATTGGATAA
44226147 GACACATAAT
Statistics
Matches: 56, Mismatches: 12, Indels: 6
0.76 0.16 0.08
Matches are distributed among these distances:
40 2 0.04
42 54 0.96
ACGTcount: A:0.27, C:0.15, G:0.18, T:0.40
Consensus pattern (43 bp):
GTTCCAACTGGTTGGTTTACCATTGGATAATTACAAAACATTT
Found at i:44235853 original size:23 final size:22
Alignment explanation
Indices: 44235810--44235853 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 22
44235800 TTCTAAGTCG
44235810 ATATTCAATTCAATTCCACACCT
1 ATATTCAATTCAATT-CACACCT
44235833 ATATTCATTATTCAATT-ACAC
1 ATATTCA--ATTCAATTCACAC
44235854 TTAGTCAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
23 11 0.58
25 8 0.42
ACGTcount: A:0.36, C:0.25, G:0.00, T:0.39
Consensus pattern (22 bp):
ATATTCAATTCAATTCACACCT
Found at i:44236091 original size:51 final size:49
Alignment explanation
Indices: 44235997--44236182 Score: 165
Period size: 51 Copynumber: 3.7 Consensus size: 49
44235987 TCGGTTCACA
* * ** * * *
44235997 TAGTAGCCTGCACATAGTATTATACATATAACCATTACCATCTGATACACG
1 TAGTAGCCTGCACATAGTACTACACACGTGACCA--AACATCTGGTACACG
* * * *
44236048 TAGTAGCTTGCACATAGTACTACACACGTGATCGAAACTATCTGGTACGCA
1 TAGTAGCCTGCACATAGTACTACACACGTGA-CCAAAC-ATCTGGTACACG
** * * * * *
44236099 TAGTAGCCTGTGCATAGTACTACACATGCGACCTATCATTCCGGTACACG
1 TAGTAGCCTGCACATAGTACTACACACGTGACCAAACA-TCTGGTACACG
44236149 TAGTAGCCTGCACATAGTACTACACACGTGACCA
1 TAGTAGCCTGCACATAGTACTACACACGTGACCA
44236183 TCACTTTCAC
Statistics
Matches: 105, Mismatches: 27, Indels: 7
0.76 0.19 0.05
Matches are distributed among these distances:
49 1 0.01
50 42 0.40
51 60 0.57
52 2 0.02
ACGTcount: A:0.31, C:0.26, G:0.17, T:0.26
Consensus pattern (49 bp):
TAGTAGCCTGCACATAGTACTACACACGTGACCAAACATCTGGTACACG
Found at i:44238137 original size:1 final size:1
Alignment explanation
Indices: 44238133--44238166 Score: 59
Period size: 1 Copynumber: 34.0 Consensus size: 1
44238123 CTCCAATCGC
*
44238133 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAGAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
44238167 CCAATCGGAT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
1 31 1.00
ACGTcount: A:0.97, C:0.00, G:0.03, T:0.00
Consensus pattern (1 bp):
A
Found at i:44240504 original size:17 final size:17
Alignment explanation
Indices: 44240482--44240514 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
44240472 TATGAATCAC
44240482 TAAGCTAAACCTTCAAT
1 TAAGCTAAACCTTCAAT
44240499 TAAGCTAAACCTTCAA
1 TAAGCTAAACCTTCAA
44240515 AGGGTACTCT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.42, C:0.24, G:0.06, T:0.27
Consensus pattern (17 bp):
TAAGCTAAACCTTCAAT
Found at i:44242470 original size:31 final size:29
Alignment explanation
Indices: 44242400--44242471 Score: 81
Period size: 29 Copynumber: 2.4 Consensus size: 29
44242390 ACTTCAGATT
*
44242400 ACATTTTAGTCACTTATGTTTGAAATGTT
1 ACATTTTAGTCACTTATGTTTGAAATGTA
* ***
44242429 ACGTTTTAGTCACTTATGTTATCGTGTTGTA
1 ACATTTTAGTCACTTATGTT-T-GAAATGTA
44242460 ACATTTTAGTCA
1 ACATTTTAGTCA
44242472 TTGAGCCATT
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
29 19 0.54
30 1 0.03
31 15 0.43
ACGTcount: A:0.25, C:0.12, G:0.15, T:0.47
Consensus pattern (29 bp):
ACATTTTAGTCACTTATGTTTGAAATGTA
Found at i:44243030 original size:31 final size:29
Alignment explanation
Indices: 44242995--44243071 Score: 82
Period size: 29 Copynumber: 2.6 Consensus size: 29
44242985 TTAATAGCTC
*
44242995 AGTGACTAAAATGTTACAACACGATAACATA
1 AGTGACTAAAATGTAACAACAC-A-AACATA
* * ***
44243026 AGTGACAAAAACGTAACATTTCAAACATA
1 AGTGACTAAAATGTAACAACACAAACATA
44243055 AGTGACTAAAATGTAAC
1 AGTGACTAAAATGTAAC
44243072 CTAAGGTAAA
Statistics
Matches: 38, Mismatches: 8, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
29 21 0.55
30 1 0.03
31 16 0.42
ACGTcount: A:0.49, C:0.16, G:0.13, T:0.22
Consensus pattern (29 bp):
AGTGACTAAAATGTAACAACACAAACATA
Found at i:44246247 original size:35 final size:35
Alignment explanation
Indices: 44246142--44246247 Score: 131
Period size: 35 Copynumber: 3.0 Consensus size: 35
44246132 TCTATGGAGT
* * * *
44246142 GACACCGTGTAAACGATATATAGGTCATTTGGGGC
1 GACAACGTGTAAACGGTACATAGGTCCTTTGGGGC
* * * *
44246177 AATAACATGTAAATGGTACATAGGTCCTTTGGGGC
1 GACAACGTGTAAACGGTACATAGGTCCTTTGGGGC
*
44246212 GACAACGTGTAAACGGTACATAGGTCCTTCGGGGC
1 GACAACGTGTAAACGGTACATAGGTCCTTTGGGGC
44246247 G
1 G
44246248 GCACCTCGAA
Statistics
Matches: 58, Mismatches: 13, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
35 58 1.00
ACGTcount: A:0.28, C:0.18, G:0.29, T:0.25
Consensus pattern (35 bp):
GACAACGTGTAAACGGTACATAGGTCCTTTGGGGC
Found at i:44248486 original size:9 final size:9
Alignment explanation
Indices: 44248472--44248496 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
44248462 ATAAAATATA
44248472 TTATTATTG
1 TTATTATTG
44248481 TTATTATTG
1 TTATTATTG
44248490 TTATTAT
1 TTATTAT
44248497 ATTATAAATT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.24, C:0.00, G:0.08, T:0.68
Consensus pattern (9 bp):
TTATTATTG
Found at i:44249069 original size:25 final size:26
Alignment explanation
Indices: 44248983--44249069 Score: 74
Period size: 26 Copynumber: 3.4 Consensus size: 26
44248973 ATGAAAGCAT
* **
44248983 AAAAAGAAACAAAA-AGAAATAGAAAG
1 AAAAAGAAAGAAAACA-AAATAGGGAG
*
44249009 AAACAGAATA-AAAACAAAATAGGGAG
1 AAAAAGAA-AGAAAACAAAATAGGGAG
*
44249035 AAAAAGAAAGAAAAGAAAA-AGGGA-
1 AAAAAGAAAGAAAACAAAATAGGGAG
44249059 AAGAAAGAAAG
1 AA-AAAGAAAG
44249070 GAGAAATAGG
Statistics
Matches: 52, Mismatches: 5, Indels: 9
0.79 0.08 0.14
Matches are distributed among these distances:
24 2 0.04
25 14 0.27
26 34 0.65
27 2 0.04
ACGTcount: A:0.72, C:0.03, G:0.21, T:0.03
Consensus pattern (26 bp):
AAAAAGAAAGAAAACAAAATAGGGAG
Found at i:44249734 original size:14 final size:14
Alignment explanation
Indices: 44249717--44249754 Score: 76
Period size: 14 Copynumber: 2.7 Consensus size: 14
44249707 TAACTTTATT
44249717 AAATTGAATTTAGA
1 AAATTGAATTTAGA
44249731 AAATTGAATTTAGA
1 AAATTGAATTTAGA
44249745 AAATTGAATT
1 AAATTGAATT
44249755 GAATGAGAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.13, T:0.37
Consensus pattern (14 bp):
AAATTGAATTTAGA
Found at i:44255936 original size:27 final size:27
Alignment explanation
Indices: 44255877--44255950 Score: 78
Period size: 27 Copynumber: 2.7 Consensus size: 27
44255867 CATAAATCGT
*
44255877 CACAAAGGCTTCAATTTCATAAACAGC
1 CACAAAGGCTTCAATTTCATAAACAGA
* * *
44255904 CACAAAGGCTTCCATTTCATAGATA-A
1 CACAAAGGCTTCAATTTCATAAACAGA
* *
44255930 CAGCAAAGGTTTCTATTTCAT
1 CA-CAAAGGCTTCAATTTCAT
44255951 GTCATGTTCA
Statistics
Matches: 40, Mismatches: 6, Indels: 2
0.83 0.12 0.04
Matches are distributed among these distances:
26 2 0.05
27 38 0.95
ACGTcount: A:0.36, C:0.23, G:0.12, T:0.28
Consensus pattern (27 bp):
CACAAAGGCTTCAATTTCATAAACAGA
Found at i:44259198 original size:21 final size:21
Alignment explanation
Indices: 44259174--44259213 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
44259164 TAACTTTGAT
*
44259174 AAATCATTATAAATTGTAAAA
1 AAATAATTATAAATTGTAAAA
* *
44259195 AAATAATTGTAATTTGTAA
1 AAATAATTATAAATTGTAA
44259214 TTTATATGAT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.53, C:0.03, G:0.07, T:0.38
Consensus pattern (21 bp):
AAATAATTATAAATTGTAAAA
Found at i:44260348 original size:43 final size:43
Alignment explanation
Indices: 44260287--44260434 Score: 176
Period size: 43 Copynumber: 3.5 Consensus size: 43
44260277 ACAGTAATTT
44260287 CGTGTAAGACCATGTCTGGGACATTGGCATCGATATGAGATTA
1 CGTGTAAGACCATGTCTGGGACATTGGCATCGATATGAGATTA
*
44260330 CGTGTAAGACCATGTCTGGGACATTGGCACCGTATAT-A-ATT-
1 CGTGTAAGACCATGTCTGGGACATTGGCATCG-ATATGAGATTA
* * ** * *
44260371 CGTGTAAGACCCTGTCTGAGACAGAGGCATCGATATGTGATAA
1 CGTGTAAGACCATGTCTGGGACATTGGCATCGATATGAGATTA
* * *
44260414 CATGTAAAACCATATCTGGGA
1 CGTGTAAGACCATGTCTGGGA
44260435 TATGACATTG
Statistics
Matches: 88, Mismatches: 13, Indels: 8
0.81 0.12 0.07
Matches are distributed among these distances:
40 4 0.05
41 27 0.31
42 5 0.06
43 48 0.55
44 4 0.05
ACGTcount: A:0.30, C:0.18, G:0.26, T:0.26
Consensus pattern (43 bp):
CGTGTAAGACCATGTCTGGGACATTGGCATCGATATGAGATTA
Found at i:44272497 original size:18 final size:18
Alignment explanation
Indices: 44272474--44272510 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
44272464 GGTGGCAATT
*
44272474 TGTTCTTCAAGAACGCAC
1 TGTTCTACAAGAACGCAC
44272492 TGTTCTACAAGAACGCAC
1 TGTTCTACAAGAACGCAC
44272510 T
1 T
44272511 ACACTCCTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.30, C:0.27, G:0.16, T:0.27
Consensus pattern (18 bp):
TGTTCTACAAGAACGCAC
Found at i:44275213 original size:27 final size:27
Alignment explanation
Indices: 44275175--44275480 Score: 449
Period size: 27 Copynumber: 11.4 Consensus size: 27
44275165 GGACCTTTCA
*
44275175 TAGGGTAAAATGATCGAATTACCCTCG
1 TAGGGTAAAATGACCGAATTACCCTCG
**
44275202 TAGGGTAAAATGACTAAATTACCCTCG
1 TAGGGTAAAATGACCGAATTACCCTCG
44275229 TAGGGTAAAATGACCGAATTAGCCCT-G
1 TAGGGTAAAATGACCGAATTA-CCCTCG
* *
44275256 TAGGGTAAAATGACCAAATTACCC-AG
1 TAGGGTAAAATGACCGAATTACCCTCG
*
44275282 TAGGGTAAAATGACCGAATTACCCTTG
1 TAGGGTAAAATGACCGAATTACCCTCG
*
44275309 TAGGGTAAAATTACCGAATTACCCTCG
1 TAGGGTAAAATGACCGAATTACCCTCG
44275336 TAGGGTAAAATGACCGAATTACCCTCG
1 TAGGGTAAAATGACCGAATTACCCTCG
*
44275363 TAGGGTAAAATGATCGAATTACCCTCG
1 TAGGGTAAAATGACCGAATTACCCTCG
* *
44275390 TAGGGTAAAATGACTGAATTACCCCCG
1 TAGGGTAAAATGACCGAATTACCCTCG
*
44275417 TAGGGTAAAATGACCGAATTACCTTC-
1 TAGGGTAAAATGACCGAATTACCCTCG
* *
44275443 TAGGGTAAAATGACTGAAATACCC-CG
1 TAGGGTAAAATGACCGAATTACCCTCG
44275469 ATAGGGTAAAAT
1 -TAGGGTAAAAT
44275481 AATGACTGTT
Statistics
Matches: 253, Mismatches: 21, Indels: 10
0.89 0.07 0.04
Matches are distributed among these distances:
25 1 0.00
26 48 0.19
27 200 0.79
28 4 0.02
ACGTcount: A:0.36, C:0.19, G:0.22, T:0.24
Consensus pattern (27 bp):
TAGGGTAAAATGACCGAATTACCCTCG
Found at i:44275366 original size:107 final size:108
Alignment explanation
Indices: 44275175--44275480 Score: 449
Period size: 107 Copynumber: 2.9 Consensus size: 108
44275165 GGACCTTTCA
* **
44275175 TAGGGTAAAATGATCGAATTACCCTCGTAGGGTAAAATGACTAAATTACCCTCGTAGGGTAAAAT
1 TAGGGTAAAATGACCGAATTACCCTCGTAGGGTAAAATGACCGAATTACCCTCGTAGGGTAAAAT
44275240 GACCGAATTAGCCCT-GTAGGGTAAAATGACCAAATTACCC-AG
66 GACCGAATTA-CCCTCGTAGGGTAAAATGACCAAATTACCCTAG
* *
44275282 TAGGGTAAAATGACCGAATTACCCTTGTAGGGTAAAATTACCGAATTACCCTCGTAGGGTAAAAT
1 TAGGGTAAAATGACCGAATTACCCTCGTAGGGTAAAATGACCGAATTACCCTCGTAGGGTAAAAT
* * *
44275347 GACCGAATTACCCTCGTAGGGTAAAATGATCGAATTACCCTCG
66 GACCGAATTACCCTCGTAGGGTAAAATGACCAAATTACCCTAG
* * *
44275390 TAGGGTAAAATGACTGAATTACCCCCGTAGGGTAAAATGACCGAATTACCTTC-TAGGGTAAAAT
1 TAGGGTAAAATGACCGAATTACCCTCGTAGGGTAAAATGACCGAATTACCCTCGTAGGGTAAAAT
* *
44275454 GACTGAAATACCC-CGATAGGGTAAAAT
66 GACCGAATTACCCTCG-TAGGGTAAAAT
44275481 AATGACTGTT
Statistics
Matches: 181, Mismatches: 15, Indels: 6
0.90 0.07 0.03
Matches are distributed among these distances:
106 6 0.03
107 126 0.70
108 49 0.27
ACGTcount: A:0.36, C:0.19, G:0.22, T:0.24
Consensus pattern (108 bp):
TAGGGTAAAATGACCGAATTACCCTCGTAGGGTAAAATGACCGAATTACCCTCGTAGGGTAAAAT
GACCGAATTACCCTCGTAGGGTAAAATGACCAAATTACCCTAG
Found at i:44277604 original size:45 final size:45
Alignment explanation
Indices: 44277540--44277727 Score: 202
Period size: 45 Copynumber: 4.2 Consensus size: 45
44277530 TACTACGTGT
* * *
44277540 ACCGGGTACCATTGATTATAAAGGTGGTTGTTGTGTGTTAATTCC
1 ACCGGGTATCATTGATTATAAAGGTGGTTGCTGTGTGTTGATTCC
* * *
44277585 ACCGGGTATCATTGATTATAAAGGTGGTTGTTGTGTGCTGATTAC
1 ACCGGGTATCATTGATTATAAAGGTGGTTGCTGTGTGTTGATTCC
* * * *
44277630 ACCGGGTA-CTATTGATTATGATGGTGGTTGCTATGTGATGATTCC
1 ACCGGGTATC-ATTGATTATAAAGGTGGTTGCTGTGTGTTGATTCC
** * * *
44277675 ACCTAGTATCATTGACTATAAGGGTGG-TACTGTGTGTTGA-TCC
1 ACCGGGTATCATTGATTATAAAGGTGGTTGCTGTGTGTTGATTCC
*
44277718 ACCGTGTATC
1 ACCGGGTATC
44277728 TGTTATTATT
Statistics
Matches: 121, Mismatches: 20, Indels: 6
0.82 0.14 0.04
Matches are distributed among these distances:
43 11 0.09
44 11 0.09
45 98 0.81
46 1 0.01
ACGTcount: A:0.22, C:0.14, G:0.27, T:0.37
Consensus pattern (45 bp):
ACCGGGTATCATTGATTATAAAGGTGGTTGCTGTGTGTTGATTCC
Found at i:44282163 original size:81 final size:79
Alignment explanation
Indices: 44282020--44282248 Score: 287
Period size: 81 Copynumber: 2.8 Consensus size: 79
44282010 AGGTAAAATG
* * * *
44282020 ACCAAAATACCACCATAAGGTAAAATGACTGAAATACCCTCATAAGGTAAAATGACTGAAATACC
1 ACCAAAATACC-CCATAAGGTAGAATGACT-AAATACCCCCATAGGGTAAAATGACCGAAATACC
44282085 CCCATAAAGTAGAATA
64 CCCATAAAGTAGAATA
** *
44282101 ACTGAAATACCCCTATAAGGTAGAATGACCTAAATACCCCCATAGGGTAAAATGACCAAAATACC
1 ACCAAAATACCCC-ATAAGGTAGAATGA-CTAAATACCCCCATAGGGTAAAATGACCGAAATACC
* *
44282166 CCCATAAGGTAGAATG
64 CCCATAAAGTAGAATA
* * * *
44282182 ACCAAAATAACCCCATAGGGTAGAATGATCAAAATACCCCCATAGGGTAGAATGATCGAAATACC
1 ACCAAAAT-ACCCCATAAGGTAGAATGA-CTAAATACCCCCATAGGGTAAAATGACCGAAATACC
44282247 CC
64 CC
44282249 TATAGGGTAA
Statistics
Matches: 128, Mismatches: 17, Indels: 6
0.85 0.11 0.04
Matches are distributed among these distances:
80 2 0.02
81 119 0.93
82 7 0.05
ACGTcount: A:0.44, C:0.23, G:0.15, T:0.18
Consensus pattern (79 bp):
ACCAAAATACCCCATAAGGTAGAATGACTAAATACCCCCATAGGGTAAAATGACCGAAATACCCC
CATAAAGTAGAATA
Found at i:44282263 original size:81 final size:78
Alignment explanation
Indices: 44282010--44282264 Score: 285
Period size: 81 Copynumber: 3.2 Consensus size: 78
44282000 ACCCTAAAAT
* * * *
44282010 AGGTAAAATGACCAAAATACCACCATAAGGTAAAATGACTGAAATACCCTCATAAGGTAAAATGA
1 AGGTAAAATGACCAAAATACC-CCATAAGGTAGAATGAC-AAAATACCCCCATAGGGTAAAATGA
44282075 CTGAAATACCCCCATA
64 C-GAAATACCCCCATA
* * * ** *
44282091 AAGTAGAATAACTGAAATACCCCTATAAGGTAGAATGACCTAAATACCCCCATAGGGTAAAATGA
1 AGGTAAAATGACCAAAATACCCC-ATAAGGTAGAATGA-CAAAATACCCCCATAGGGTAAAATGA
*
44282156 CCAAAATACCCCCATA
64 -CGAAATACCCCCATA
* * *
44282172 AGGTAGAATGACCAAAATAACCCCATAGGGTAGAATGATCAAAATACCCCCATAGGGTAGAATGA
1 AGGTAAAATGACCAAAAT-ACCCCATAAGGTAGAATGA-CAAAATACCCCCATAGGGTAAAATGA
*
44282237 TCGAAATACCCCTATA
64 -CGAAATACCCCCATA
*
44282253 GGGTAAAATGAC
1 AGGTAAAATGAC
44282265 TGTTATACCC
Statistics
Matches: 147, Mismatches: 23, Indels: 8
0.83 0.13 0.04
Matches are distributed among these distances:
80 2 0.01
81 138 0.94
82 7 0.05
ACGTcount: A:0.44, C:0.21, G:0.16, T:0.18
Consensus pattern (78 bp):
AGGTAAAATGACCAAAATACCCCATAAGGTAGAATGACAAAATACCCCCATAGGGTAAAATGACG
AAATACCCCCATA
Found at i:44282277 original size:27 final size:27
Alignment explanation
Indices: 44282010--44282275 Score: 259
Period size: 27 Copynumber: 9.9 Consensus size: 27
44282000 ACCCTAAAAT
* ** *
44282010 AGGTAAAATGACCAAAATACCACCATA
1 AGGTAGAATGACTGAAATACCCCCATA
* *
44282037 AGGTAAAATGACTGAAATACCCTCATA
1 AGGTAGAATGACTGAAATACCCCCATA
*
44282064 AGGTAAAATGACTGAAATACCCCCATA
1 AGGTAGAATGACTGAAATACCCCCATA
* * *
44282091 AAGTAGAATAACTGAAATACCCCTATA
1 AGGTAGAATGACTGAAATACCCCCATA
44282118 AGGTAGAATGACCT-AAATACCCCCATA
1 AGGTAGAATGA-CTGAAATACCCCCATA
* * **
44282145 GGGTAAAATGACCAAAATACCCCCATA
1 AGGTAGAATGACTGAAATACCCCCATA
** *
44282172 AGGTAGAATGACCAAAATAACCCCATA
1 AGGTAGAATGACTGAAATACCCCCATA
* *
44282199 GGGTAGAATGA-TCAAAATACCCCCATA
1 AGGTAGAATGACT-GAAATACCCCCATA
* *
44282226 GGGTAGAATGA-TCGAAATACCCCTATA
1 AGGTAGAATGACT-GAAATACCCCCATA
* * **
44282253 GGGTAAAATGACTGTTATACCCC
1 AGGTAGAATGACTGAAATACCCC
44282276 TAGGAGATGA
Statistics
Matches: 209, Mismatches: 26, Indels: 8
0.86 0.11 0.03
Matches are distributed among these distances:
26 1 0.00
27 205 0.98
28 3 0.01
ACGTcount: A:0.43, C:0.22, G:0.16, T:0.19
Consensus pattern (27 bp):
AGGTAGAATGACTGAAATACCCCCATA
Found at i:44282699 original size:29 final size:31
Alignment explanation
Indices: 44282657--44282723 Score: 93
Period size: 29 Copynumber: 2.2 Consensus size: 31
44282647 AACTGCATAT
* *
44282657 CTGCATTGATTAATGATATT-GTACTGTT-A
1 CTGCATCGATTAATGATATTAATACTGTTCA
44282686 CTGCATCGATTAATGATATTACATACTGTTCA
1 CTGCATCGATTAATGATATTA-ATACTGTTCA
44282718 CTGCAT
1 CTGCAT
44282724 GACTGATATC
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
29 19 0.58
31 7 0.21
32 7 0.21
ACGTcount: A:0.28, C:0.16, G:0.15, T:0.40
Consensus pattern (31 bp):
CTGCATCGATTAATGATATTAATACTGTTCA
Found at i:44294865 original size:42 final size:40
Alignment explanation
Indices: 44294809--44295095 Score: 315
Period size: 42 Copynumber: 6.8 Consensus size: 40
44294799 GCGTTTATAG
44294809 AAAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGTTT
1 AAAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGTTT
* *
44294849 GAAAAAAGACGACGCTAAAGATCATGTTCTTTAGCGGCGCTTA
1 -AAAAAA-ACGCCGCTAAAGATCATGTTCTTTAGCGGCG-TTT
* * *
44294892 ACAAAAAACGCCGCTAAAGAACATGCTCTTTAGCGGCGCTTAA
1 A-AAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCG-TT-T
*
44294935 AAAAAAGACGCCGCTAAAGATCATGTTCTTTAGCGGCGGTT
1 AAAAAA-ACGCCGCTAAAGATCATGTTCTTTAGCGGCGTTT
* * * * *
44294976 ACAAAAAATCGCCACTAAAGATAATGTTCTTTAGCTGCACTTA
1 A-AAAAAA-CGCCGCTAAAGATCATGTTCTTTAGCGGC-GTTT
* *
44295019 AAGAAAAATGCCGCTAAAGATAATGTTCTTTAGCGGCGCTTGGT
1 AA-AAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCG-TT--T
44295063 AAAAAAACGCCGCTATAA-ATCATGTTCTTTAGC
1 AAAAAAACGCCGCTA-AAGATCATGTTCTTTAGC
44295096 CGCGCTTTCA
Statistics
Matches: 211, Mismatches: 22, Indels: 24
0.82 0.09 0.09
Matches are distributed among these distances:
41 8 0.04
42 128 0.61
43 71 0.34
44 4 0.02
ACGTcount: A:0.35, C:0.20, G:0.20, T:0.25
Consensus pattern (40 bp):
AAAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGTTT
Found at i:44294954 original size:127 final size:127
Alignment explanation
Indices: 44294809--44295095 Score: 388
Period size: 127 Copynumber: 2.3 Consensus size: 127
44294799 GCGTTTATAG
* * *
44294809 AAAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGTTTGA-AAAAAGA-CGACGCTAAAGATC
1 AAAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGGTT-ACAAAAA-ATCGACACTAAAGATA
*
44294872 ATGTTCTTTAGCGGCGCTTAACA-AAAAACGCCGCTAAAGA-ACATGCTCTTTAGCGGCGCTT-A
64 ATGTTCTTTAGCGGCACTTAA-AGAAAAACGCCGCTAAAGATA-ATGCTCTTTAGCGGCGCTTGA
44294934 A
127 A
*
44294935 AAAAAAGACGCCGCTAAAGATCATGTTCTTTAGCGGCGGTTACAAAAAATCGCCACTAAAGATAA
1 AAAAAA-ACGCCGCTAAAGATCATGTTCTTTAGCGGCGGTTACAAAAAATCGACACTAAAGATAA
* * * **
44295000 TGTTCTTTAGCTGCACTTAAAGAAAAATGCCGCTAAAGATAATGTTCTTTAGCGGCGCTTGGT
65 TGTTCTTTAGCGGCACTTAAAGAAAAACGCCGCTAAAGATAATGCTCTTTAGCGGCGCTTGAA
44295063 AAAAAAACGCCGCTATAA-ATCATGTTCTTTAGC
1 AAAAAAACGCCGCTA-AAGATCATGTTCTTTAGC
44295096 CGCGCTTTCA
Statistics
Matches: 144, Mismatches: 10, Indels: 13
0.86 0.06 0.08
Matches are distributed among these distances:
126 9 0.06
127 126 0.88
128 9 0.06
ACGTcount: A:0.35, C:0.20, G:0.20, T:0.25
Consensus pattern (127 bp):
AAAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGGTTACAAAAAATCGACACTAAAGATAAT
GTTCTTTAGCGGCACTTAAAGAAAAACGCCGCTAAAGATAATGCTCTTTAGCGGCGCTTGAA
Found at i:44294960 original size:85 final size:84
Alignment explanation
Indices: 44294810--44295102 Score: 362
Period size: 85 Copynumber: 3.5 Consensus size: 84
44294800 CGTTTATAGA
* ** *
44294810 AAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCG-TTTGAAAAAAGACGACGCTAAAGATCAT
1 AAAAAACGCCGCTAAAGAACATGTTCTTTAGCGGCGCTTAAAAAAAAGACGCCGCTAAAGATCAT
44294874 GTTCTTTAGCGGCGCTTAAC
66 GTTCTTTAGCGGCGCTT-AC
*
44294894 AAAAAACGCCGCTAAAGAACATGCTCTTTAGCGGCGCTTAAAAAAAAGACGCCGCTAAAGATCAT
1 AAAAAACGCCGCTAAAGAACATGTTCTTTAGCGGCGCTTAAAAAAAAGACGCCGCTAAAGATCAT
*
44294959 GTTCTTTAGCGGCGGTTAC
66 GTTCTTTAGCGGCGCTTAC
* * * * * *
44294978 AAAAAATCGCCACTAAAGATA-ATGTTCTTTAGCTGCACTTAAAGAAAA-ATGCCGCTAAAGATA
1 AAAAAA-CGCCGCTAAAGA-ACATGTTCTTTAGCGGCGCTTAAAAAAAAGACGCCGCTAAAGATC
44295041 ATGTTCTTTAGCGGCGCTTGGTA-
64 ATGTTCTTTAGCGGCGC-T--TAC
* *
44295064 AAAAAACGCCGCTATAA-ATCATGTTCTTTAGCCGCGCTT
1 AAAAAACGCCGCTA-AAGAACATGTTCTTTAGCGGCGCTT
44295103 TCATCGCGAA
Statistics
Matches: 183, Mismatches: 18, Indels: 15
0.85 0.08 0.07
Matches are distributed among these distances:
84 71 0.39
85 101 0.55
86 9 0.05
87 2 0.01
ACGTcount: A:0.34, C:0.21, G:0.20, T:0.25
Consensus pattern (84 bp):
AAAAAACGCCGCTAAAGAACATGTTCTTTAGCGGCGCTTAAAAAAAAGACGCCGCTAAAGATCAT
GTTCTTTAGCGGCGCTTAC
Found at i:44295574 original size:21 final size:21
Alignment explanation
Indices: 44295563--44295618 Score: 85
Period size: 21 Copynumber: 2.7 Consensus size: 21
44295553 CTTCTCGCGC
*
44295563 TGCAGCCTCTGCTTCACTTGT
1 TGCAGCCTCTGCTTCACTCGT
*
44295584 TGCAGCCTCTGCTTCCCTCGT
1 TGCAGCCTCTGCTTCACTCGT
*
44295605 TGCCGCCTCTGCTT
1 TGCAGCCTCTGCTT
44295619 TAAGTTGTAC
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.05, C:0.39, G:0.20, T:0.36
Consensus pattern (21 bp):
TGCAGCCTCTGCTTCACTCGT
Found at i:44301059 original size:9 final size:9
Alignment explanation
Indices: 44301042--44301297 Score: 204
Period size: 9 Copynumber: 29.8 Consensus size: 9
44301032 TATGTATTAA
*
44301042 GTAAATTAT
1 GTAAGTTAT
44301051 GTAAGTTAT
1 GTAAGTTAT
*
44301060 GTATGTGTA-
1 GTAAGT-TAT
44301069 -TAAGTTAT
1 GTAAGTTAT
44301077 GTAAGTTAT
1 GTAAGTTAT
*
44301086 GT-A-TTAA
1 GTAAGTTAT
*
44301093 GTAAGCTAT
1 GTAAGTTAT
*
44301102 GTAAGTTGT
1 GTAAGTTAT
44301111 GT-A-TTAT
1 GTAAGTTAT
44301118 GTAAGTTAT
1 GTAAGTTAT
44301127 GTAAGTTAT
1 GTAAGTTAT
** *
44301136 CAAAGTAAT
1 GTAAGTTAT
*
44301145 GTATGTTAT
1 GTAAGTTAT
*
44301154 TTAAG-T-T
1 GTAAGTTAT
44301161 GTAAGTTAT
1 GTAAGTTAT
*
44301170 -TATGTATTAT
1 GTAAG--TTAT
44301180 GTAAGTTAT
1 GTAAGTTAT
44301189 GTAAGTTAAAT
1 GTAAGTT--AT
44301200 GT-A-TTAT
1 GTAAGTTAT
*
44301207 GTAGGTTAT
1 GTAAGTTAT
44301216 GTAAGTTAT
1 GTAAGTTAT
*
44301225 GTAAGTTTT
1 GTAAGTTAT
44301234 GT-A-TTAT
1 GTAAGTTAT
44301241 GTAAGTTAT
1 GTAAGTTAT
*
44301250 GTAAGTTTT
1 GTAAGTTAT
44301259 GT-A-TTAT
1 GTAAGTTAT
44301266 GTAAGTTAT
1 GTAAGTTAT
* *
44301275 GTATGCTAT
1 GTAAGTTAT
44301284 GT-A-TTAT
1 GTAAGTTAT
44301291 GTAAGTT
1 GTAAGTT
44301298 GTTATGTTAT
Statistics
Matches: 194, Mismatches: 31, Indels: 44
0.72 0.12 0.16
Matches are distributed among these distances:
7 36 0.19
8 18 0.09
9 126 0.65
10 7 0.04
11 7 0.04
ACGTcount: A:0.32, C:0.01, G:0.20, T:0.47
Consensus pattern (9 bp):
GTAAGTTAT
Found at i:44301062 original size:25 final size:25
Alignment explanation
Indices: 44301031--44301293 Score: 150
Period size: 25 Copynumber: 10.3 Consensus size: 25
44301021 TGATATATAT
* *
44301031 TTATGTATTAAGTAAATTATGTAAG
1 TTATGTATTATGTAAGTTATGTAAG
* *
44301056 TTATGTATGTGTATAAGTTATGTAAG
1 TTATGTAT-TATGTAAGTTATGTAAG
* *
44301082 TTATGTATTAAGTAAGCTATGTAAG
1 TTATGTATTATGTAAGTTATGTAAG
*
44301107 TTGTGTATTATGTAAGTTATGTAAG
1 TTATGTATTATGTAAGTTATGTAAG
** * * *
44301132 TTATCAAAGTAATGTATGTTATTTAAG
1 TTAT-GTA-TTATGTAAGTTATGTAAG
*
44301159 TTGTAAGTTATTATGT-A-TTATGTAAG
1 -T-TATG-TATTATGTAAGTTATGTAAG
*
44301185 TTATGTAAGTTAAATGT-A-TTATGTAGG
1 TTATGT-A-TT--ATGTAAGTTATGTAAG
*
44301212 TTATGTAAGTTATGTAAGTTTTGT-A-
1 TTATGT-A-TTATGTAAGTTATGTAAG
*
44301237 TTATGTAAGTTATGTAAGTTTTGT-A-
1 TTATGT-A-TTATGTAAGTTATGTAAG
* *
44301262 TTATGTAAGTTATGTATGCTATGT-A-
1 TTATGT-A-TTATGTAAGTTATGTAAG
44301287 TTATGTA
1 TTATGTA
44301294 AGTTGTTATG
Statistics
Matches: 196, Mismatches: 30, Indels: 25
0.78 0.12 0.10
Matches are distributed among these distances:
23 1 0.01
24 5 0.03
25 106 0.54
26 31 0.16
27 44 0.22
28 6 0.03
29 3 0.02
ACGTcount: A:0.32, C:0.01, G:0.20, T:0.47
Consensus pattern (25 bp):
TTATGTATTATGTAAGTTATGTAAG
Found at i:44301131 original size:34 final size:32
Alignment explanation
Indices: 44301046--44301255 Score: 149
Period size: 34 Copynumber: 6.6 Consensus size: 32
44301036 TATTAAGTAA
* *
44301046 ATTATGTAAGTTATGTATGTGTATAAGTTATGT
1 ATTATGTAAGTTATGTAAGTAT-TAAGTTATGT
* *
44301079 AAGTTATGT-A-TTAAGTAAGCTATGTAAGTTGTGT
1 -A-TTATGTAAGTTATGTAAG-TAT-TAAGTTATGT
* *
44301113 ATTATGTAAGTTATGTAAGTTATCAAAGTAATGT
1 ATTATGTAAGTTATGTAAG-TAT-TAAGTTATGT
*
44301147 ATGTTATTTAAG-T-TGTAAG--TT-A-TTATGT
1 A--TTATGTAAGTTATGTAAGTATTAAGTTATGT
44301175 ATTATGTAAGTTATGTAAG--TTAA---ATGT
1 ATTATGTAAGTTATGTAAGTATTAAGTTATGT
* *
44301202 ATTATGTAGGTTATGTAAGTTATGTAAGTTTTGT
1 ATTATGTAAGTTATGTAAG-TAT-TAAGTTATGT
44301236 ATTATGTAAGTTATGTAAGT
1 ATTATGTAAGTTATGTAAGT
44301256 TTTGTATTAT
Statistics
Matches: 142, Mismatches: 18, Indels: 33
0.74 0.09 0.17
Matches are distributed among these distances:
26 8 0.06
27 23 0.16
28 14 0.10
29 2 0.01
30 1 0.01
31 4 0.03
32 6 0.04
33 10 0.07
34 59 0.42
35 7 0.05
36 8 0.06
ACGTcount: A:0.32, C:0.01, G:0.20, T:0.46
Consensus pattern (32 bp):
ATTATGTAAGTTATGTAAGTATTAAGTTATGT
Found at i:44301426 original size:16 final size:16
Alignment explanation
Indices: 44301405--44301454 Score: 63
Period size: 16 Copynumber: 3.4 Consensus size: 16
44301395 AAAATTTTTA
44301405 TAAGTTATGTATTATG
1 TAAGTTATGTATTATG
*
44301421 TAAGTTA---A-CATG
1 TAAGTTATGTATTATG
44301433 TAAGTTATGTATTATG
1 TAAGTTATGTATTATG
44301449 TAAGTT
1 TAAGTT
44301455 TACATATAAG
Statistics
Matches: 28, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
12 10 0.36
13 1 0.04
15 1 0.04
16 16 0.57
ACGTcount: A:0.34, C:0.02, G:0.18, T:0.46
Consensus pattern (16 bp):
TAAGTTATGTATTATG
Found at i:44301437 original size:28 final size:28
Alignment explanation
Indices: 44301403--44301590 Score: 121
Period size: 28 Copynumber: 6.4 Consensus size: 28
44301393 AAAAAATTTT
44301403 TATAAGTTATGTATTATGTAAGTTAACA
1 TATAAGTTATGTATTATGTAAGTTAACA
* *
44301431 TGTAAGTTATGTATTATGTAAGTTTACA
1 TATAAGTTATGTATTATGTAAGTTAACA
* *
44301459 TATAAGTTTATGTGATAATTATGTAAGTTTATA
1 TATAAG-TTA--TG-T-ATTATGTAAGTTAACA
* ** * *
44301492 TA-AATATTAATAAATTATGTAAGTTTATA
1 TATAA-GTT-ATGTATTATGTAAGTTAACA
* * *
44301521 TA-AATATTAAT-AAGTTATGTAAGTTAATA
1 TATAA-GTT-ATGTA-TTATGTAAGTTAACA
* * *
44301550 TGTAAGTAATGTATTATGTAAGTTTACA
1 TATAAGTTATGTATTATGTAAGTTAACA
44301578 TATAAGTTTATGT
1 TATAAG-TTATGT
44301591 GATAGGTTAT
Statistics
Matches: 133, Mismatches: 16, Indels: 21
0.78 0.09 0.12
Matches are distributed among these distances:
28 53 0.40
29 52 0.39
30 2 0.02
31 3 0.02
32 5 0.04
33 18 0.14
ACGTcount: A:0.39, C:0.02, G:0.14, T:0.45
Consensus pattern (28 bp):
TATAAGTTATGTATTATGTAAGTTAACA
Found at i:44301491 original size:29 final size:28
Alignment explanation
Indices: 44301467--44301697 Score: 132
Period size: 29 Copynumber: 7.9 Consensus size: 28
44301457 CATATAAGTT
* *
44301467 TATGTGATAATTATGTAAGTTTATATAAA
1 TATGTAATAATTATGTAAGTTTATA-ATA
*
44301496 TAT-TAATAAATTATGTAAGTTTATATAAA
1 TATGTAAT-AATTATGTAAGTTTATA-ATA
* *
44301525 TAT-TAATAAGTTATGTAAGTTAAT-ATG
1 TATGTAATAA-TTATGTAAGTTTATAATA
* * *
44301552 TAAGTAATGTATTATGTAAGTTTACATATAAGTT
1 TATGTAAT-AATTATGTAAG-TT---TATAA-TA
* * *
44301586 TATGTGATAGGTTATGTAAGTTTATATAAA
1 TATGTAATA-ATTATGTAAGTTTATA-ATA
*
44301616 TAT-TAATAAGTTATGTAAGTTTATATAAA
1 TATGTAATAA-TTATGTAAGTTTATA-ATA
* *
44301645 TAT-TAATAAGTTATGTAAGTTAAT-ATG
1 TATGTAATAA-TTATGTAAGTTTATAATA
* *
44301672 TAAGTAATGTATTATGTAAGTTTATA
1 TATGTAAT-AATTATGTAAGTTTATA
44301698 TAAAAAAATT
Statistics
Matches: 164, Mismatches: 22, Indels: 32
0.75 0.10 0.15
Matches are distributed among these distances:
27 6 0.04
28 35 0.21
29 94 0.57
30 7 0.04
31 1 0.01
32 2 0.01
33 3 0.02
34 16 0.10
ACGTcount: A:0.41, C:0.00, G:0.14, T:0.45
Consensus pattern (28 bp):
TATGTAATAATTATGTAAGTTTATAATA
Found at i:44301655 original size:120 final size:119
Alignment explanation
Indices: 44301416--44301695 Score: 515
Period size: 120 Copynumber: 2.3 Consensus size: 119
44301406 AAGTTATGTA
* *
44301416 TTATGTAAGTTAACATGTAAGTTATGTATTATGTAAGTTTACATATAAGTTTATGTGATAATTAT
1 TTATGTAAGTTAATATGTAAGTAATGTATTATGTAAGTTTACATATAAGTTTATGTGATAATTAT
44301481 GTAAGTTTATATAAATATTAATAAATTATGTAAGTTTATATAAATATTAATAAG
66 GTAAGTTTATATAAATATTAATAAATTATGTAAGTTTATATAAATATTAATAAG
*
44301535 TTATGTAAGTTAATATGTAAGTAATGTATTATGTAAGTTTACATATAAGTTTATGTGATAGGTTA
1 TTATGTAAGTTAATATGTAAGTAATGTATTATGTAAGTTTACATATAAGTTTATGTGATA-ATTA
*
44301600 TGTAAGTTTATATAAATATTAATAAGTTATGTAAGTTTATATAAATATTAATAAG
65 TGTAAGTTTATATAAATATTAATAAATTATGTAAGTTTATATAAATATTAATAAG
44301655 TTATGTAAGTTAATATGTAAGTAATGTATTATGTAAGTTTA
1 TTATGTAAGTTAATATGTAAGTAATGTATTATGTAAGTTTA
44301696 TATAAAAAAA
Statistics
Matches: 156, Mismatches: 4, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
119 58 0.37
120 98 0.63
ACGTcount: A:0.40, C:0.01, G:0.14, T:0.45
Consensus pattern (119 bp):
TTATGTAAGTTAATATGTAAGTAATGTATTATGTAAGTTTACATATAAGTTTATGTGATAATTAT
GTAAGTTTATATAAATATTAATAAATTATGTAAGTTTATATAAATATTAATAAG
Found at i:44301728 original size:57 final size:57
Alignment explanation
Indices: 44301416--44301733 Score: 250
Period size: 57 Copynumber: 5.4 Consensus size: 57
44301406 AAGTTATGTA
* * ** *
44301416 TTATGTAAGTTAACATGTAAGTTATGTATTATGTAAGTTTACATATAAGTTTATGTGATAA-
1 TTATGTAAGTTAATATGTAAGTAATGTATTATGTAAGTTT--ATATAA--AAAT-TAATAAG
* ** * ** *
44301477 TTATGTAAGTTTATATAAATATTAATAAATTATGTAAGTTTATATAAATATTAATAAG
1 TTATGTAAGTTAATATGTA-AGTAATGTATTATGTAAGTTTATATAAAAATTAATAAG
** * *
44301535 TTATGTAAGTTAATATGTAAGTAATGTATTATGTAAGTTTACATATAAGTTTATGTGATAGG
1 TTATGTAAGTTAATATGTAAGTAATGTATTATGTAAGTTT--ATATAA--AAAT-TAATAAG
* ** * * *
44301597 TTATGTAAGTTTATATAAATATTAAT-AAGTTATGTAAGTTTATATAAATATTAATAAG
1 TTATGTAAGTTAATATGTA-AGTAATGTA-TTATGTAAGTTTATATAAAAATTAATAAG
*
44301655 TTATGTAAGTTAATATGTAAGTAATGTATTATGTAAGTTTATATAAAAAAATTTTATAAG
1 TTATGTAAGTTAATATGTAAGTAATGTATTATGTAAGTTTATAT--AAAAA-TTAATAAG
44301715 TTATGT-A-TT-ATATGTAAGT
1 TTATGTAAGTTAATATGTAAGT
44301734 TTAAATATAA
Statistics
Matches: 210, Mismatches: 34, Indels: 30
0.77 0.12 0.11
Matches are distributed among these distances:
57 54 0.26
58 43 0.20
59 14 0.07
60 19 0.09
61 24 0.11
62 39 0.19
63 17 0.08
ACGTcount: A:0.41, C:0.01, G:0.14, T:0.45
Consensus pattern (57 bp):
TTATGTAAGTTAATATGTAAGTAATGTATTATGTAAGTTTATATAAAAATTAATAAG
Found at i:44301769 original size:28 final size:29
Alignment explanation
Indices: 44301709--44301797 Score: 108
Period size: 28 Copynumber: 2.9 Consensus size: 29
44301699 AAAAAAATTT
*
44301709 TATAAGTTATGTATTATATGTAAGTTTAAA
1 TATAAGTTATGTAGT-TATGTAAGTTTAAA
*
44301739 TATAAGTTATGTA-TTATGTAAGTTTACA
1 TATAAGTTATGTAGTTATGTAAGTTTAAA
44301767 TATAAGTTTATGTGATAGTTATGTAAGTTTA
1 TATAAG-TTA--TG-TAGTTATGTAAGTTTA
44301798 TATAAATATT
Statistics
Matches: 53, Mismatches: 1, Indels: 7
0.87 0.02 0.11
Matches are distributed among these distances:
28 19 0.36
29 4 0.08
30 13 0.25
31 2 0.04
32 2 0.04
33 13 0.25
ACGTcount: A:0.36, C:0.01, G:0.16, T:0.47
Consensus pattern (29 bp):
TATAAGTTATGTAGTTATGTAAGTTTAAA
Found at i:44301984 original size:13 final size:13
Alignment explanation
Indices: 44301966--44302176 Score: 140
Period size: 13 Copynumber: 16.0 Consensus size: 13
44301956 TAAATTTTAG
*
44301966 TAAGTAATGTATT
1 TAAGTAATATATT
*
44301979 TAAGTAACATATT
1 TAAGTAATATATT
*
44301992 TAAGTAATAAATT
1 TAAGTAATATATT
** *
44302005 TAACCAA-ATTTT
1 TAAGTAATATATT
*
44302017 AGTAAGTAATGTATT
1 --TAAGTAATATATT
*
44302032 TAAGTAACATATT
1 TAAGTAATATATT
*
44302045 TAAGTAATAAATT
1 TAAGTAATATATT
** *
44302058 TAAACAA-ATTTT
1 TAAGTAATATATT
*
44302070 AGTAAGTAATGTATT
1 --TAAGTAATATATT
*
44302085 TAAGTAACATATT
1 TAAGTAATATATT
* *
44302098 TAAGTAAGAAATT
1 TAAGTAATATATT
** *
44302111 TAACCAA-ATTTT
1 TAAGTAATATATT
* *
44302123 AGTAAGTAATGTGTT
1 --TAAGTAATATATT
*
44302138 TAAGTAATTTATT
1 TAAGTAATATATT
44302151 TAAGTAATATATT
1 TAAGTAATATATT
*
44302164 CAAGTAATATATT
1 TAAGTAATATATT
44302177 AAAGCAAATT
Statistics
Matches: 149, Mismatches: 40, Indels: 18
0.72 0.19 0.09
Matches are distributed among these distances:
12 9 0.06
13 116 0.78
14 15 0.10
15 9 0.06
ACGTcount: A:0.45, C:0.04, G:0.10, T:0.41
Consensus pattern (13 bp):
TAAGTAATATATT
Found at i:44302022 original size:53 final size:53
Alignment explanation
Indices: 44301957--44302159 Score: 361
Period size: 53 Copynumber: 3.8 Consensus size: 53
44301947 ATATATACTT
44301957 AAATTTTAGTAAGTAATGTATTTAAGTAACATATTTAAGTAATAAATTTAACC
1 AAATTTTAGTAAGTAATGTATTTAAGTAACATATTTAAGTAATAAATTTAACC
*
44302010 AAATTTTAGTAAGTAATGTATTTAAGTAACATATTTAAGTAATAAATTTAAAC
1 AAATTTTAGTAAGTAATGTATTTAAGTAACATATTTAAGTAATAAATTTAACC
*
44302063 AAATTTTAGTAAGTAATGTATTTAAGTAACATATTTAAGTAAGAAATTTAACC
1 AAATTTTAGTAAGTAATGTATTTAAGTAACATATTTAAGTAATAAATTTAACC
* **
44302116 AAATTTTAGTAAGTAATGTGTTTAAGTAATTTATTTAAGTAATA
1 AAATTTTAGTAAGTAATGTATTTAAGTAACATATTTAAGTAATA
44302160 TATTCAAGTA
Statistics
Matches: 143, Mismatches: 7, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
53 143 1.00
ACGTcount: A:0.45, C:0.04, G:0.11, T:0.40
Consensus pattern (53 bp):
AAATTTTAGTAAGTAATGTATTTAAGTAACATATTTAAGTAATAAATTTAACC
Found at i:44302204 original size:66 final size:66
Alignment explanation
Indices: 44302072--44302213 Score: 178
Period size: 66 Copynumber: 2.2 Consensus size: 66
44302062 CAAATTTTAG
* * ** *
44302072 TAAGTAATGTATTTAAGTAACATATTTAAGTAAGAAATTTAACCAAATTTTAGTAAGTAATGTGT
1 TAAGTAATGTATTTAAGTAACATATTCAAGTAAGAAATTAAACCAAATTTTAGTAAAAAATATGT
44302137 T
66 T
* * * * *
44302138 TAAGTAATTTATTTAAGTAATATATTCAAGTAATATATTAAAGCAAATTTTAGTAAAAAATATGT
1 TAAGTAATGTATTTAAGTAACATATTCAAGTAAGAAATTAAACCAAATTTTAGTAAAAAATATGT
44302203 T
66 T
*
44302204 TTAGT-ATGTA
1 TAAGTAATGTA
44302214 ATGTAAGTCA
Statistics
Matches: 64, Mismatches: 12, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
65 4 0.06
66 60 0.94
ACGTcount: A:0.44, C:0.04, G:0.12, T:0.41
Consensus pattern (66 bp):
TAAGTAATGTATTTAAGTAACATATTCAAGTAAGAAATTAAACCAAATTTTAGTAAAAAATATGT
T
Found at i:44304017 original size:19 final size:19
Alignment explanation
Indices: 44303993--44304034 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
44303983 GGTCGGGTTT
*
44303993 GGGGAGCTGTTAGGGATTA
1 GGGGAGATGTTAGGGATTA
* *
44304012 GGGGAGATTTTAGGGATTT
1 GGGGAGATGTTAGGGATTA
44304031 GGGG
1 GGGG
44304035 GAGAATGAGT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.19, C:0.02, G:0.50, T:0.29
Consensus pattern (19 bp):
GGGGAGATGTTAGGGATTA
Found at i:44305475 original size:7 final size:7
Alignment explanation
Indices: 44305465--44305505 Score: 64
Period size: 7 Copynumber: 5.9 Consensus size: 7
44305455 ACCCCAAAAT
44305465 CAAACCC
1 CAAACCC
44305472 CAAACCC
1 CAAACCC
44305479 CAAACCC
1 CAAACCC
*
44305486 TAAACCC
1 CAAACCC
*
44305493 CAAATCC
1 CAAACCC
44305500 CAAACC
1 CAAACC
44305506 ATAATATTCC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
7 30 1.00
ACGTcount: A:0.44, C:0.51, G:0.00, T:0.05
Consensus pattern (7 bp):
CAAACCC
Found at i:44305872 original size:14 final size:14
Alignment explanation
Indices: 44305861--44305900 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
44305851 TTCTAACCCT
44305861 TAACCCCAAACCAC
1 TAACCCCAAACCAC
* *
44305875 TAACCCCTAACTAC
1 TAACCCCAAACCAC
*
44305889 TAACCCTAAACC
1 TAACCCCAAACC
44305901 TTATTTAATA
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.40, C:0.45, G:0.00, T:0.15
Consensus pattern (14 bp):
TAACCCCAAACCAC
Found at i:44306014 original size:81 final size:81
Alignment explanation
Indices: 44305879--44306035 Score: 210
Period size: 81 Copynumber: 1.9 Consensus size: 81
44305869 AACCACTAAC
* * * *
44305879 CCCTAACTACTAACCCTAAACCTTATTTAATATACAAATTAAAAATATTGATTAATCAAAACCCT
1 CCCTAACCACTAACCCTAAACCTTATTTAATATACAAATTAAAAACACTAATTAATCAAAACCCT
44305944 AAATCCTAACCCGAAT
66 AAATCCTAACCCGAAT
* * *
44305960 CCCTAACCCCTAACCCTTAAACCTTATTTCATA-A-AAATTAAAACACACTAATTAATCTAAACC
1 CCCTAACCACTAACCC-TAAACCTTATTTAATATACAAATTAAAA-ACACTAATTAATCAAAACC
*
44306023 CTAAATTCTAACC
64 CTAAATCCTAACC
44306036 TGACACCGAA
Statistics
Matches: 66, Mismatches: 8, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
80 9 0.14
81 42 0.64
82 15 0.23
ACGTcount: A:0.43, C:0.27, G:0.01, T:0.28
Consensus pattern (81 bp):
CCCTAACCACTAACCCTAAACCTTATTTAATATACAAATTAAAAACACTAATTAATCAAAACCCT
AAATCCTAACCCGAAT
Found at i:44306834 original size:113 final size:114
Alignment explanation
Indices: 44306476--44307130 Score: 562
Period size: 114 Copynumber: 5.8 Consensus size: 114
44306466 CGGCGCTTTT
* * * * * * * * * *
44306476 TAAAAATGCCGCTAAAGCCCTAAAAGTTTAGAAAACGACGCCGTTGGGCTTAGG-TTTTTTGCGA
1 TAAAAACGCCACTAAATCCCTGAAAGCTCAGAAAACGGCGTCGTTGGGCTTTGGTTTTTTTGCGG
* * * * *
44306540 CGC-TTCAACAAAAACGCCGCTAAAGCCCTAAACATTAGCAGCGCATT--C
66 CGCTTTC-TCGAAAACGCCGCTAAAGCCCTGAGCATTAGCGGCGC-TTACC
* ** * * * * * * *
44306588 TTAAAACGCCGGTAAAGCCCACGAATTG-TCAGAAAACGGTGTAGTTTGGC-TTAGTTTTTGTTG
1 TAAAAACGCCACTAAATCCC-TGAA-AGCTCAGAAAACGGCGTCGTTGGGCTTTGGTTTTT-TTG
* * * * * * *
44306651 CGGCGCTTTCTCAAAAACGCCGCTGAAGGCCTGAACATTAGCAGCACTTACT
63 CGGCGCTTTCTCGAAAACGCCGCTAAAGCCCTGAGCATTAGCGGCGCTTACC
* * * * *
44306703 TATAAATGCCACTGAATCCCTGAAAGCTCAAAAAACGGCGTCGTTGGGCTTTGGTTTTTTTGTGG
1 TAAAAACGCCACTAAATCCCTGAAAGCTCAGAAAACGGCGTCGTTGGGCTTTGGTTTTTTTGCGG
* *
44306768 CGCTTTCTC-AAAAGTGCTGCTAAAG-CCTGAGCATTAGCGGCGCTTACC
66 CGCTTTCTCGAAAA-CGCCGCTAAAGCCCTGAGCATTAGCGGCGCTTACC
* * *
44306816 TAAAAACGCCACTAAATCCCTGAATGCTCAGAAAACAGCGTCGTTGGGCTTAGGTATTTTTT-CG
1 TAAAAACGCCACTAAATCCCTGAAAGCTCAGAAAACGGCGTCGTTGGGCTTTGGT-TTTTTTGCG
* * *
44306880 GCGCTTTCCCGAAAACGCCGCTAAAGCCCTGAGCATTAGCGGCGTTTACG
65 GCGCTTTCTCGAAAACGCCGCTAAAGCCCTGAGCATTAGCGGCGCTTACC
* * * * *
44306930 AAAAAATGCCACTAAATCCCCGAAAGCTCAGAAAACGGCGTCGTTGGGCTTTAGTTTTTTTGTGG
1 TAAAAACGCCACTAAATCCCTGAAAGCTCAGAAAACGGCGTCGTTGGGCTTTGGTTTTTTTGCGG
* * * * *
44306995 CGCTTTCTCGAAAACGCCGCAAAAGCCCAGGGCATTAGCGACGCTTTCC
66 CGCTTTCTCGAAAACGCCGCTAAAGCCCTGAGCATTAGCGGCGCTTACC
* * * * *
44307044 TAAAAACGCCGCTAAAT-CCTCGAAAAGCTTAGAAAACGGTGTCGTTGTG-TTTAGG-TATTTTG
1 TAAAAACGCCACTAAATCCCT-G-AAAGCTCAGAAAACGGCGTCGTTGGGCTTT-GGTTTTTTTG
* * *
44307106 CGGTGCTTTAT-GGAAACGCCGCTAA
63 CGGCGCTTTCTCGAAAACGCCGCTAA
44307131 TGCTTATTTT
Statistics
Matches: 440, Mismatches: 86, Indels: 33
0.79 0.15 0.06
Matches are distributed among these distances:
112 19 0.04
113 135 0.31
114 238 0.54
115 48 0.11
ACGTcount: A:0.28, C:0.24, G:0.23, T:0.26
Consensus pattern (114 bp):
TAAAAACGCCACTAAATCCCTGAAAGCTCAGAAAACGGCGTCGTTGGGCTTTGGTTTTTTTGCGG
CGCTTTCTCGAAAACGCCGCTAAAGCCCTGAGCATTAGCGGCGCTTACC
Found at i:44306884 original size:227 final size:231
Alignment explanation
Indices: 44306616--44307105 Score: 627
Period size: 227 Copynumber: 2.1 Consensus size: 231
44306606 CCACGAATTG
* * * *
44306616 TCAGAAAACGGTGTAGTTTGGCTTA-GT-TTTTGTTGCGGCGCTTTCTCAAAAACGCCGCTGAAG
1 TCAGAAAACGGTGTCGTTGGGCTTAGGTATTTTGTTGCGGCGCTTTCCCAAAAACGCCGCTAAAG
* ** * * *
44306679 GCCTGAACATTAGCAGCACTTACTTATAAATGCCACTGAATCCCTGAAAGCTCAAAAAACGGCGT
66 CCCTGAACATTAGCAGCACTTACGAAAAAATGCCACTAAATCCCCGAAAGCTCAAAAAACGGCGT
* * * * *
44306744 CGTTGGGCTTTGGTTTTTTTGTGGCGCTTTCTC-AAAAGTGCTGCTAAAG-CCTGAGCATTAGCG
131 CGTTGGGCTTTAGTTTTTTTGTGGCGCTTTCTCGAAAA-CGCCGCAAAAGCCCAGAGCATTAGCG
* *
44306807 GCGCTTACCTAAAAACGCCACTAAATCC-CTG-AATGC
195 ACGCTTACCTAAAAACGCCACTAAATCCTC-GAAAAGC
* * *
44306843 TCAGAAAACAGCGTCGTTGGGCTTAGGTATTTT-TT-CGGCGCTTTCCCGAAAACGCCGCTAAAG
1 TCAGAAAACGGTGTCGTTGGGCTTAGGTATTTTGTTGCGGCGCTTTCCCAAAAACGCCGCTAAAG
* * ** *
44306906 CCCTGAGCATTAGCGGCGTTTACGAAAAAATGCCACTAAATCCCCGAAAGCTCAGAAAACGGCGT
66 CCCTGAACATTAGCAGCACTTACGAAAAAATGCCACTAAATCCCCGAAAGCTCAAAAAACGGCGT
*
44306971 CGTTGGGCTTTAGTTTTTTTGTGGCGCTTTCTCGAAAACGCCGCAAAAGCCCAGGGCATTAGCGA
131 CGTTGGGCTTTAGTTTTTTTGTGGCGCTTTCTCGAAAACGCCGCAAAAGCCCAGAGCATTAGCGA
* *
44307036 CGCTTTCCTAAAAACGCCGCTAAATCCTCGAAAAGC
196 CGCTTACCTAAAAACGCCACTAAATCCTCGAAAAGC
* * *
44307072 TTAGAAAACGGTGTCGTTGTGTTTAGGTATTTTG
1 TCAGAAAACGGTGTCGTTGGGCTTAGGTATTTTG
44307106 CGGTGCTTTA
Statistics
Matches: 223, Mismatches: 33, Indels: 11
0.84 0.12 0.04
Matches are distributed among these distances:
227 140 0.63
228 46 0.21
229 37 0.17
ACGTcount: A:0.26, C:0.23, G:0.23, T:0.27
Consensus pattern (231 bp):
TCAGAAAACGGTGTCGTTGGGCTTAGGTATTTTGTTGCGGCGCTTTCCCAAAAACGCCGCTAAAG
CCCTGAACATTAGCAGCACTTACGAAAAAATGCCACTAAATCCCCGAAAGCTCAAAAAACGGCGT
CGTTGGGCTTTAGTTTTTTTGTGGCGCTTTCTCGAAAACGCCGCAAAAGCCCAGAGCATTAGCGA
CGCTTACCTAAAAACGCCACTAAATCCTCGAAAAGC
Found at i:44309709 original size:27 final size:27
Alignment explanation
Indices: 44309679--44309837 Score: 210
Period size: 27 Copynumber: 5.9 Consensus size: 27
44309669 GCAGACCTTT
44309679 CGTAGGGTAAAATGACCGAATTACCCC
1 CGTAGGGTAAAATGACCGAATTACCCC
* *
44309706 CGTAGGGTAAAATCATCGAATTACCCC
1 CGTAGGGTAAAATGACCGAATTACCCC
* **
44309733 TGTAGGGTAAAATGACCGAATTACCGT
1 CGTAGGGTAAAATGACCGAATTACCCC
* * *
44309760 CGTACGGTAAAATGACTGAATTACCCT
1 CGTAGGGTAAAATGACCGAATTACCCC
* * *
44309787 CATAGGGTAAAATGACCAAATTAGCCC
1 CGTAGGGTAAAATGACCGAATTACCCC
*
44309814 CGTAGGGTAAAATGACCAAATTAC
1 CGTAGGGTAAAATGACCGAATTAC
44309838 ACGTGAGCAG
Statistics
Matches: 113, Mismatches: 19, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 113 1.00
ACGTcount: A:0.36, C:0.21, G:0.21, T:0.22
Consensus pattern (27 bp):
CGTAGGGTAAAATGACCGAATTACCCC
Found at i:44309784 original size:81 final size:81
Alignment explanation
Indices: 44309678--44309837 Score: 232
Period size: 81 Copynumber: 2.0 Consensus size: 81
44309668 TGCAGACCTT
* * * *
44309678 TCGTAGGGTAAAATGACCGAATTACCCCCGTAGGGTAAAATCATCGAATTA-CCCCTGTAGGGTA
1 TCGTACGGTAAAATGACCGAATTACCCCCATAGGGTAAAATCACCAAATTAGCCCC-GTAGGGTA
*
44309742 AAATGACCGAATTACCG
65 AAATGACCAAATTACCG
* * *
44309759 TCGTACGGTAAAATGACTGAATTACCCTCATAGGGTAAAATGACCAAATTAGCCCCGTAGGGTAA
1 TCGTACGGTAAAATGACCGAATTACCCCCATAGGGTAAAATCACCAAATTAGCCCCGTAGGGTAA
44309824 AATGACCAAATTAC
66 AATGACCAAATTAC
44309838 ACGTGAGCAG
Statistics
Matches: 70, Mismatches: 8, Indels: 2
0.88 0.10 0.03
Matches are distributed among these distances:
81 66 0.94
82 4 0.06
ACGTcount: A:0.36, C:0.21, G:0.21, T:0.23
Consensus pattern (81 bp):
TCGTACGGTAAAATGACCGAATTACCCCCATAGGGTAAAATCACCAAATTAGCCCCGTAGGGTAA
AATGACCAAATTACCG
Found at i:44310087 original size:26 final size:26
Alignment explanation
Indices: 44310007--44310087 Score: 110
Period size: 26 Copynumber: 3.1 Consensus size: 26
44309997 TGGAGGAAGT
* *
44310007 ATACTATTACTAGCAGCTTT-TCTACG
1 ATACTATTACTGGCAGCTTTGT-TGCG
* *
44310033 ATACTATTACTGGCAGCTTTGCTGTG
1 ATACTATTACTGGCAGCTTTGTTGCG
44310059 ATACTATTACTGGCAGCTTTGTTGCG
1 ATACTATTACTGGCAGCTTTGTTGCG
44310085 ATA
1 ATA
44310088 TTGGTGTGTT
Statistics
Matches: 48, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
26 48 1.00
ACGTcount: A:0.23, C:0.20, G:0.19, T:0.38
Consensus pattern (26 bp):
ATACTATTACTGGCAGCTTTGTTGCG
Found at i:44310256 original size:27 final size:28
Alignment explanation
Indices: 44310199--44310282 Score: 109
Period size: 27 Copynumber: 3.1 Consensus size: 28
44310189 TACCAATATC
* * *
44310199 GTATTGGGTTAAGGCCCACATTATTACT
1 GTATTGGGCTAAGGCCCACATTGTTATT
*
44310227 GTATTGTGCTAAGG-CCACATTGTTATT
1 GTATTGGGCTAAGGCCCACATTGTTATT
*
44310254 GTATTGGGCTAAGGCCCACACTG-TATT
1 GTATTGGGCTAAGGCCCACATTGTTATT
44310281 GT
1 GT
44310283 TTCTAAAAAG
Statistics
Matches: 49, Mismatches: 6, Indels: 3
0.84 0.10 0.05
Matches are distributed among these distances:
27 30 0.61
28 19 0.39
ACGTcount: A:0.23, C:0.18, G:0.24, T:0.36
Consensus pattern (28 bp):
GTATTGGGCTAAGGCCCACATTGTTATT
Found at i:44310572 original size:17 final size:17
Alignment explanation
Indices: 44310550--44310591 Score: 84
Period size: 17 Copynumber: 2.5 Consensus size: 17
44310540 TTAATTGGGC
44310550 TTTTCAAAAGGTAACTA
1 TTTTCAAAAGGTAACTA
44310567 TTTTCAAAAGGTAACTA
1 TTTTCAAAAGGTAACTA
44310584 TTTTCAAA
1 TTTTCAAA
44310592 GACACCACGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 25 1.00
ACGTcount: A:0.40, C:0.12, G:0.10, T:0.38
Consensus pattern (17 bp):
TTTTCAAAAGGTAACTA
Found at i:44315689 original size:3 final size:3
Alignment explanation
Indices: 44315683--44315721 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
44315673 TATATGTTTT
44315683 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
44315722 GAAAGTAAAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:44316891 original size:17 final size:17
Alignment explanation
Indices: 44316862--44316894 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
44316852 AAGTTCTATA
44316862 ATTGATATAGAAATGAC
1 ATTGATATAGAAATGAC
44316879 ATTG-TATATGAAATGA
1 ATTGATATA-GAAATGA
44316895 AAATGAGATA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.45, C:0.03, G:0.18, T:0.33
Consensus pattern (17 bp):
ATTGATATAGAAATGAC
Found at i:44317944 original size:252 final size:251
Alignment explanation
Indices: 44317494--44317993 Score: 788
Period size: 252 Copynumber: 2.0 Consensus size: 251
44317484 TTGATAGGTG
* * *
44317494 TATGTGAACTTAAGCTTAATGTTTTAGGTAGATATATGTTAGGCTATACTGAGTGGTTTGGTATG
1 TATGTAAACTTAAGCTTAATGTTTTAGGTAGATATATGTTAGGCTAAACTGAGTGATTTGGTATG
* *
44317559 CTTGAAATTTTGATTTGAATGTTGTATTGATGATATGTTTTGATGATATAAATTGTGGTACCAAT
66 CTTGAAATCTTGATTTGAATGTTGCATTGATGATATGTTTTGATGATATAAATTGTGGTACCAAT
* * *
44317624 AAGGGTACATTGGTGACACACCTAAGATGATTGTTTCAGCATGTTTTGAGTATGTTTGATCGTAT
131 AAGGGTACATTAGTGACACACCTAAGATGATTGTTTCAGCATGTTCTGAGTATGTTTGACCGTAT
* *
44317689 TTTGAATAGGTTAAATGTTTGGTTTTTGAGTTGCTTAATGCCCAAGAAAGTAGATA
196 TTTGAATAGGTTAAATATTTGGTTTTTGAGTTGCATAATGCCCAAGAAAGTAGATA
* *
44317745 TATGTAAACTTAAGCTTGATGTTTTAGGTAGATATATGTTAGGCTAAATTGAGTGATTTGGTATG
1 TATGTAAACTTAAGCTTAATGTTTTAGGTAGATATATGTTAGGCTAAACTGAGTGATTTGGTATG
*
44317810 CTTGAAATCTTGATTTGAATGTTGCATTGGTGATATGTTTTTGATGATATAAATTGTGGTACCAA
66 CTTGAAATCTTGATTTGAATGTTGCATTGATGATATG-TTTTGATGATATAAATTGTGGTACCAA
* * **
44317875 TGAGGGTACATTAGT-TCAGCACCTAAGATGATTGTTTTGGCATGTTCTGAGTATGTTTCG-CCG
130 TAAGGGTACATTAGTGACA-CACCTAAGATGATTGTTTCAGCATGTTCTGAGTATGTTT-GACCG
* *
44317938 TATTTTGAATAGGTTAAATATTTGGTTTTTGAGTTTCATAATGCCCAAGCAAGTAG
193 TATTTTGAATAGGTTAAATATTTGGTTTTTGAGTTGCATAATGCCCAAGAAAGTAG
44317994 GAATTTGTAG
Statistics
Matches: 227, Mismatches: 19, Indels: 5
0.90 0.08 0.02
Matches are distributed among these distances:
251 96 0.42
252 130 0.57
253 1 0.00
ACGTcount: A:0.27, C:0.08, G:0.23, T:0.41
Consensus pattern (251 bp):
TATGTAAACTTAAGCTTAATGTTTTAGGTAGATATATGTTAGGCTAAACTGAGTGATTTGGTATG
CTTGAAATCTTGATTTGAATGTTGCATTGATGATATGTTTTGATGATATAAATTGTGGTACCAAT
AAGGGTACATTAGTGACACACCTAAGATGATTGTTTCAGCATGTTCTGAGTATGTTTGACCGTAT
TTTGAATAGGTTAAATATTTGGTTTTTGAGTTGCATAATGCCCAAGAAAGTAGATA
Found at i:44337416 original size:27 final size:27
Alignment explanation
Indices: 44337380--44337548 Score: 230
Period size: 27 Copynumber: 6.3 Consensus size: 27
44337370 AGAGGTCAAT
*
44337380 AAATGACCAAAATACCCCCATATGGTA
1 AAATGACCAAAATACCCCCATAGGGTA
* *
44337407 AAATGACCAAAATACCCTCATAGGGTG
1 AAATGACCAAAATACCCCCATAGGGTA
* * * *
44337434 AAATGGCCGAAATACCCCTATACGGTA
1 AAATGACCAAAATACCCCCATAGGGTA
*
44337461 AAATGACCAAAATACCCCCATAAGGTA
1 AAATGACCAAAATACCCCCATAGGGTA
* * *
44337488 AAATGACCTAAATACCCCAATTGGGTA
1 AAATGACCAAAATACCCCCATAGGGTA
*
44337515 AAATGACCAAAATACACCCATAGGGTA
1 AAATGACCAAAATACCCCCATAGGGTA
44337542 AAATGAC
1 AAATGAC
44337549 TGTTATACCC
Statistics
Matches: 121, Mismatches: 21, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 121 1.00
ACGTcount: A:0.44, C:0.24, G:0.15, T:0.18
Consensus pattern (27 bp):
AAATGACCAAAATACCCCCATAGGGTA
Found at i:44337573 original size:54 final size:52
Alignment explanation
Indices: 44337404--44337575 Score: 161
Period size: 54 Copynumber: 3.2 Consensus size: 52
44337394 CCCCCATATG
* * * *
44337404 GTAAAATGACCAAAATACCCTCATAGGGTGAAATGGCCGAAATACCCCTA-TA
1 GTAAAATGACCAAAATACCC-CATAGGGTAAAATGACTGAAATACCCCTAGGA
* *
44337456 CGGTAAAATGACCAAAATACCCCCATAAGGTAAAATGACCT-AAATACCCCAATTGG-
1 --GTAAAATGACCAAAATA-CCCCATAGGGTAAAATGA-CTGAAATACCCC--TAGGA
**
44337512 GTAAAATGACCAAAATACACCCATAGGGTAAAATGACTGTTATACCCCTAGGA
1 GTAAAATGACCAAAATAC-CCCATAGGGTAAAATGACTGAAATACCCCTAGGA
*
44337565 GATGAAATGAC
1 G-TAAAATGAC
44337576 TGATATGGTC
Statistics
Matches: 98, Mismatches: 11, Indels: 18
0.77 0.09 0.14
Matches are distributed among these distances:
52 3 0.03
53 4 0.04
54 86 0.88
55 4 0.04
56 1 0.01
ACGTcount: A:0.42, C:0.22, G:0.17, T:0.19
Consensus pattern (52 bp):
GTAAAATGACCAAAATACCCCATAGGGTAAAATGACTGAAATACCCCTAGGA
Found at i:44337804 original size:26 final size:26
Alignment explanation
Indices: 44337696--44337802 Score: 142
Period size: 26 Copynumber: 4.1 Consensus size: 26
44337686 TGGAGGAAGT
* * *
44337696 ATACTGATACTGGCAGCTTTGCTACG
1 ATACTGTTACTGGCAGCTTTACTGCG
*
44337722 ATACTGTTACTGGCAGCTTTACCGCG
1 ATACTGTTACTGGCAGCTTTACTGCG
44337748 ATACTGTTACTGGCAGCTTTACTGCG
1 ATACTGTTACTGGCAGCTTTACTGCG
* * * *
44337774 ATATTATAACTGGCAGCTTTGCTGCG
1 ATACTGTTACTGGCAGCTTTACTGCG
44337800 ATA
1 ATA
44337803 TTGGTGTGTT
Statistics
Matches: 72, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 72 1.00
ACGTcount: A:0.22, C:0.22, G:0.22, T:0.33
Consensus pattern (26 bp):
ATACTGTTACTGGCAGCTTTACTGCG
Found at i:44344939 original size:23 final size:19
Alignment explanation
Indices: 44344882--44344941 Score: 59
Period size: 20 Copynumber: 2.9 Consensus size: 19
44344872 GTCAATTATT
*
44344882 TAAATCAAAAGAAGAGAAAA
1 TAAATGAAAAGAA-AGAAAA
44344902 TAAATGAAAAG-AAGAAAA
1 TAAATGAAAAGAAAGAAAA
44344920 GTAATGATAGAAAAGAAAGAAA
1 -TAA--AT-GAAAAGAAAGAAA
44344942 TAATAGATAA
Statistics
Matches: 34, Mismatches: 1, Indels: 7
0.81 0.02 0.17
Matches are distributed among these distances:
18 6 0.18
19 4 0.12
20 10 0.29
21 2 0.06
22 6 0.18
23 6 0.18
ACGTcount: A:0.68, C:0.02, G:0.18, T:0.12
Consensus pattern (19 bp):
TAAATGAAAAGAAAGAAAA
Found at i:44352739 original size:3 final size:3
Alignment explanation
Indices: 44352731--44352763 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
44352721 ATATTGTTAA
44352731 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
44352764 CTCTTAACTA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:44352855 original size:20 final size:20
Alignment explanation
Indices: 44352813--44352854 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
44352803 GTTAACAATT
*
44352813 AAATAATTTTTTAAATATAA
1 AAATAATTTTTAAAATATAA
*
44352833 AAATTATTTTTAAAAT-TAA
1 AAATAATTTTTAAAATATAA
44352852 AAA
1 AAA
44352855 AGTATAAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 6 0.30
20 14 0.70
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (20 bp):
AAATAATTTTTAAAATATAA
Found at i:44353376 original size:18 final size:17
Alignment explanation
Indices: 44353326--44353376 Score: 50
Period size: 18 Copynumber: 2.9 Consensus size: 17
44353316 GATTTTTAAA
*
44353326 ATTTAAAAATTAGAAAATT
1 ATTTAAAAA-TA-TAAATT
*
44353345 -TTTAAAAATTTAAATT
1 ATTTAAAAATATAAATT
44353361 ATTTAAAAAGTATAAA
1 ATTTAAAAA-TATAAA
44353377 AAAATATTAA
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
16 5 0.19
17 9 0.33
18 13 0.48
ACGTcount: A:0.57, C:0.00, G:0.04, T:0.39
Consensus pattern (17 bp):
ATTTAAAAATATAAATT
Found at i:44353781 original size:30 final size:30
Alignment explanation
Indices: 44353747--44353811 Score: 121
Period size: 30 Copynumber: 2.2 Consensus size: 30
44353737 ACTTATTTTA
44353747 TTGTTAATTTTGTTATTATTTTAAAGGCAT
1 TTGTTAATTTTGTTATTATTTTAAAGGCAT
*
44353777 TTGTTAATTTTGTTATTATTTTAGAGGCAT
1 TTGTTAATTTTGTTATTATTTTAAAGGCAT
44353807 TTGTT
1 TTGTT
44353812 TGTTAAGTTG
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 34 1.00
ACGTcount: A:0.23, C:0.03, G:0.15, T:0.58
Consensus pattern (30 bp):
TTGTTAATTTTGTTATTATTTTAAAGGCAT
Found at i:44353947 original size:11 final size:11
Alignment explanation
Indices: 44353931--44353961 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
44353921 TATATATATT
44353931 TAAAAATTATA
1 TAAAAATTATA
*
44353942 TAAAAATAATA
1 TAAAAATTATA
44353953 TAAAAATTA
1 TAAAAATTA
44353962 ATACGGGCGG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (11 bp):
TAAAAATTATA
Found at i:44354224 original size:13 final size:13
Alignment explanation
Indices: 44354190--44354222 Score: 50
Period size: 12 Copynumber: 2.5 Consensus size: 13
44354180 TTTAACAAAC
44354190 AATTCAAATAGAAA
1 AATT-AAATAGAAA
44354204 AATTAAAT-GAAA
1 AATTAAATAGAAA
44354216 AATTAAA
1 AATTAAA
44354223 ATATTTTTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 11 0.58
13 4 0.21
14 4 0.21
ACGTcount: A:0.67, C:0.03, G:0.06, T:0.24
Consensus pattern (13 bp):
AATTAAATAGAAA
Found at i:44367540 original size:107 final size:107
Alignment explanation
Indices: 44367354--44367567 Score: 419
Period size: 107 Copynumber: 2.0 Consensus size: 107
44367344 TTTCATTGTT
44367354 TGTTCAATTTCCAGCAAGTTGTTTTTCTATGTTGTAGTCACTAAATTATTTTTATCTGGAGCTAC
1 TGTTCAATTTCCAGCAAGTTGTTTTTCTATGTTGTAGTCACTAAATTATTTTTATCTGGAGCTAC
44367419 AGGGCTCCAAATTAAGTTCTGTTATTTTTTCCTAAAACTAGA
66 AGGGCTCCAAATTAAGTTCTGTTATTTTTTCCTAAAACTAGA
44367461 TGTTCAATTTCCAGCAAGTTGTTTTTCTATGTTGTAGTCACTAAATTATTTTTATCTGGAGCTAC
1 TGTTCAATTTCCAGCAAGTTGTTTTTCTATGTTGTAGTCACTAAATTATTTTTATCTGGAGCTAC
*
44367526 AGGGTTCCAAATTAAGTTCTGTTATTTTTTCCTAAAACTAGA
66 AGGGCTCCAAATTAAGTTCTGTTATTTTTTCCTAAAACTAGA
44367568 CTCACATATA
Statistics
Matches: 106, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
107 106 1.00
ACGTcount: A:0.26, C:0.15, G:0.15, T:0.43
Consensus pattern (107 bp):
TGTTCAATTTCCAGCAAGTTGTTTTTCTATGTTGTAGTCACTAAATTATTTTTATCTGGAGCTAC
AGGGCTCCAAATTAAGTTCTGTTATTTTTTCCTAAAACTAGA
Found at i:44373860 original size:19 final size:19
Alignment explanation
Indices: 44373825--44373892 Score: 57
Period size: 20 Copynumber: 3.4 Consensus size: 19
44373815 TCAATTTCTT
44373825 TTTC-TTTTTCATTCTCTCA
1 TTTCTTTTTTC-TTCTCTCA
* *
44373844 TTTCTTTTTTCTCCTCTTGA
1 TTTCTTTTTTCTTCTC-TCA
* *
44373864 ATTCTTTTATTTTTCTCTCA
1 TTTCTTTT-TTCTTCTCTCA
44373884 TTTTCTTTT
1 -TTTCTTTT
44373893 ATCAACAACT
Statistics
Matches: 38, Mismatches: 7, Indels: 6
0.75 0.14 0.12
Matches are distributed among these distances:
19 8 0.21
20 17 0.45
21 13 0.34
ACGTcount: A:0.09, C:0.22, G:0.01, T:0.68
Consensus pattern (19 bp):
TTTCTTTTTTCTTCTCTCA
Found at i:44377054 original size:14 final size:14
Alignment explanation
Indices: 44377029--44377064 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
44377019 TTTCTCCTCG
44377029 TTCTTTTCCTTTTCT
1 TTCTTTT-CTTTTCT
44377044 TTCTTTTCTTTTCT
1 TTCTTTTCTTTTCT
44377058 TT-TTTTC
1 TTCTTTTC
44377065 ATGAATTTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
13 5 0.24
14 9 0.43
15 7 0.33
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (14 bp):
TTCTTTTCTTTTCT
Found at i:44379694 original size:21 final size:20
Alignment explanation
Indices: 44379659--44379703 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
44379649 AATAGAAATC
44379659 AATAGAATTGTTATTTTAAAA
1 AATAGAATTGTTA-TTTAAAA
*
44379680 AATAGAATT-TATATTTAGAA
1 AATAGAATTGT-TATTTAAAA
44379700 AATA
1 AATA
44379704 AAATCTCACT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
20 11 0.50
21 11 0.50
ACGTcount: A:0.51, C:0.00, G:0.09, T:0.40
Consensus pattern (20 bp):
AATAGAATTGTTATTTAAAA
Found at i:44381911 original size:50 final size:50
Alignment explanation
Indices: 44381856--44381953 Score: 187
Period size: 50 Copynumber: 2.0 Consensus size: 50
44381846 AACATACCTC
44381856 ATATGCATATTCAACTACTATTTTACCTTTCATCCTCCAACCACAAATCA
1 ATATGCATATTCAACTACTATTTTACCTTTCATCCTCCAACCACAAATCA
*
44381906 ATATGCATATTCAACTACTATTTTACCTTTCATCCTTCAACCACAAAT
1 ATATGCATATTCAACTACTATTTTACCTTTCATCCTCCAACCACAAAT
44381954 TAATCCACAC
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
50 47 1.00
ACGTcount: A:0.34, C:0.29, G:0.02, T:0.36
Consensus pattern (50 bp):
ATATGCATATTCAACTACTATTTTACCTTTCATCCTCCAACCACAAATCA
Found at i:44384235 original size:22 final size:22
Alignment explanation
Indices: 44384207--44384252 Score: 83
Period size: 22 Copynumber: 2.1 Consensus size: 22
44384197 AATTGGTTAG
44384207 TGGAACAAGCGTTGTTCCGGCA
1 TGGAACAAGCGTTGTTCCGGCA
*
44384229 TGGAACAAGGGTTGTTCCGGCA
1 TGGAACAAGCGTTGTTCCGGCA
44384251 TG
1 TG
44384253 AAACCCCAGG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.22, C:0.20, G:0.35, T:0.24
Consensus pattern (22 bp):
TGGAACAAGCGTTGTTCCGGCA
Found at i:44395711 original size:26 final size:26
Alignment explanation
Indices: 44395673--44395724 Score: 77
Period size: 26 Copynumber: 2.0 Consensus size: 26
44395663 TTCTAAAATG
44395673 GATACATGCTATGATATTGTGAAACT
1 GATACATGCTATGATATTGTGAAACT
* * *
44395699 GATATATGTTATGATATTTTGAAACT
1 GATACATGCTATGATATTGTGAAACT
44395725 ACTGTAGGTA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.35, C:0.08, G:0.17, T:0.40
Consensus pattern (26 bp):
GATACATGCTATGATATTGTGAAACT
Found at i:44402328 original size:33 final size:35
Alignment explanation
Indices: 44402291--44402358 Score: 86
Period size: 34 Copynumber: 2.0 Consensus size: 35
44402281 GCATTTTTGA
* *
44402291 CACTG-TACTGAGATGGGCTAAGGCCCAA-ACTGT
1 CACTGATACTGAAAAGGGCTAAGGCCCAAGACTGT
* *
44402324 CACTGATACTGAAAAGGGCTTAGGCCTAAGACTGT
1 CACTGATACTGAAAAGGGCTAAGGCCCAAGACTGT
44402359 TCAACTGTGC
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
33 5 0.17
34 19 0.66
35 5 0.17
ACGTcount: A:0.29, C:0.22, G:0.26, T:0.22
Consensus pattern (35 bp):
CACTGATACTGAAAAGGGCTAAGGCCCAAGACTGT
Found at i:44408026 original size:16 final size:17
Alignment explanation
Indices: 44408005--44408039 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
44407995 ATTTTAAACA
*
44408005 AATTAATTAA-TTTCTC
1 AATTAAATAATTTTCTC
44408021 AATTAAATAATTTTCTC
1 AATTAAATAATTTTCTC
44408038 AA
1 AA
44408040 CCCAATTTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 9 0.53
17 8 0.47
ACGTcount: A:0.43, C:0.11, G:0.00, T:0.46
Consensus pattern (17 bp):
AATTAAATAATTTTCTC
Found at i:44409209 original size:20 final size:20
Alignment explanation
Indices: 44409184--44409267 Score: 100
Period size: 20 Copynumber: 4.2 Consensus size: 20
44409174 GCGCTTGTAC
*
44409184 CTGTTTGCACTTTGGTGCCT
1 CTGTTTGCACTTCGGTGCCT
*
44409204 CTGTTTGGACTTCGGTGCCT
1 CTGTTTGCACTTCGGTGCCT
*
44409224 CTGATTGCACATT--GTGCCT
1 CTGTTTGCAC-TTCGGTGCCT
* *
44409243 CTGTCTGCACCTCGGTGCCT
1 CTGTTTGCACTTCGGTGCCT
44409263 CTGTT
1 CTGTT
44409268 ACACATTTTT
Statistics
Matches: 53, Mismatches: 8, Indels: 6
0.79 0.12 0.09
Matches are distributed among these distances:
18 1 0.02
19 14 0.26
20 36 0.68
21 2 0.04
ACGTcount: A:0.07, C:0.29, G:0.25, T:0.39
Consensus pattern (20 bp):
CTGTTTGCACTTCGGTGCCT
Found at i:44409243 original size:39 final size:39
Alignment explanation
Indices: 44409188--44409274 Score: 113
Period size: 39 Copynumber: 2.2 Consensus size: 39
44409178 TTGTACCTGT
* * * *
44409188 TTGCACTTTGGTGCCTCTGTTTGGACTTCGGTGCCTCTG
1 TTGCACATTGGTGCCTCTGTCTGCACCTCGGTGCCTCTG
44409227 ATTGCACATT-GTGCCTCTGTCTGCACCTCGGTGCCTCTG
1 -TTGCACATTGGTGCCTCTGTCTGCACCTCGGTGCCTCTG
*
44409266 TTACACATT
1 TTGCACATT
44409275 TTTGATGCCT
Statistics
Matches: 42, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
38 8 0.19
39 26 0.62
40 8 0.19
ACGTcount: A:0.10, C:0.29, G:0.23, T:0.38
Consensus pattern (39 bp):
TTGCACATTGGTGCCTCTGTCTGCACCTCGGTGCCTCTG
Found at i:44413355 original size:20 final size:20
Alignment explanation
Indices: 44413321--44413362 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
44413311 AACTATTTAA
** *
44413321 ATAATATTATTTGAATAGTT
1 ATAATATTAAATGAATAATT
44413341 ATAATATTAAATGAATAATT
1 ATAATATTAAATGAATAATT
44413361 AT
1 AT
44413363 GTGTTTATTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.48, C:0.00, G:0.07, T:0.45
Consensus pattern (20 bp):
ATAATATTAAATGAATAATT
Found at i:44416397 original size:15 final size:16
Alignment explanation
Indices: 44416377--44416412 Score: 56
Period size: 15 Copynumber: 2.3 Consensus size: 16
44416367 GTTAATTAAA
*
44416377 TTTTAAATATA-ATAT
1 TTTTAAACATATATAT
44416392 TTTTAAACATATATAT
1 TTTTAAACATATATAT
44416408 TTTTA
1 TTTTA
44416413 TAAATTTAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 10 0.53
16 9 0.47
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.56
Consensus pattern (16 bp):
TTTTAAACATATATAT
Found at i:44417015 original size:3 final size:3
Alignment explanation
Indices: 44417007--44417054 Score: 96
Period size: 3 Copynumber: 16.0 Consensus size: 3
44416997 TTCCAATGCC
44417007 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
44417055 TTTAGAAAGT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 45 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:44417242 original size:23 final size:23
Alignment explanation
Indices: 44417216--44417260 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
44417206 CTCCTTTGCA
* *
44417216 TTATTAAAATTTAGTTAATAAAT
1 TTATCAAAATTTAATTAATAAAT
*
44417239 TTATCAATATTTAATTAATAAA
1 TTATCAAAATTTAATTAATAAA
44417261 AAATAATAGA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (23 bp):
TTATCAAAATTTAATTAATAAAT
Found at i:44421851 original size:21 final size:21
Alignment explanation
Indices: 44421826--44421866 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
44421816 GGTAACTGGT
44421826 AAAAGGTATCGATACTTTTTG
1 AAAAGGTATCGATACTTTTTG
*
44421847 AAAAGGTGTCGATACTTTTT
1 AAAAGGTATCGATACTTTTT
44421867 TATAATTGAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.32, C:0.10, G:0.20, T:0.39
Consensus pattern (21 bp):
AAAAGGTATCGATACTTTTTG
Found at i:44439609 original size:52 final size:51
Alignment explanation
Indices: 44439526--44439625 Score: 164
Period size: 52 Copynumber: 1.9 Consensus size: 51
44439516 TATTAATCTG
* *
44439526 AACAGCATAATAATTAACTGTTTAAAATTAAATAATTTGATAATATTTTATT
1 AACAGCATAATAATTAACGGTTTAAAATTAAATAA-TTAATAATATTTTATT
*
44439578 AACATCATAATAATTAACGGTTTAAAATTAAATAATTAATAATATTTT
1 AACAGCATAATAATTAACGGTTTAAAATTAAATAATTAATAATATTTT
44439626 CTTACCATTT
Statistics
Matches: 45, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
51 12 0.27
52 33 0.73
ACGTcount: A:0.48, C:0.06, G:0.05, T:0.41
Consensus pattern (51 bp):
AACAGCATAATAATTAACGGTTTAAAATTAAATAATTAATAATATTTTATT
Found at i:44446476 original size:24 final size:20
Alignment explanation
Indices: 44446421--44446478 Score: 62
Period size: 20 Copynumber: 2.7 Consensus size: 20
44446411 TTTTTAAAAG
*
44446421 TTATATACTTTAAATTATAT
1 TTATATATTTTAAATTATAT
*
44446441 TTATTTATTTTAATATTATAT
1 TTATATATTTTAA-ATTATAT
44446462 AATTAATATATTTTAAA
1 --TT-ATATATTTTAAA
44446479 AATATTATTT
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
20 11 0.35
21 7 0.23
23 3 0.10
24 10 0.32
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (20 bp):
TTATATATTTTAAATTATAT
Found at i:44450697 original size:20 final size:21
Alignment explanation
Indices: 44450672--44450723 Score: 72
Period size: 21 Copynumber: 2.5 Consensus size: 21
44450662 GTATCGATCC
*
44450672 GGTATCGATACT-TTT-CTTAA
1 GGTATCGATA-TATTTCCTAAA
44450692 GGTATCGATATATTTCCTAAA
1 GGTATCGATATATTTCCTAAA
44450713 GGTATCGATAT
1 GGTATCGATAT
44450724 TCCTGCTCCA
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
19 1 0.03
20 13 0.45
21 15 0.52
ACGTcount: A:0.29, C:0.13, G:0.17, T:0.40
Consensus pattern (21 bp):
GGTATCGATATATTTCCTAAA
Found at i:44453294 original size:21 final size:21
Alignment explanation
Indices: 44453245--44453294 Score: 64
Period size: 21 Copynumber: 2.4 Consensus size: 21
44453235 GTCCAACGAC
* *
44453245 GGTGGTCAATGATGGCCCAAT
1 GGTGGTCGATGATGACCCAAT
* *
44453266 GGTGGTCGATGATGACTCGAT
1 GGTGGTCGATGATGACCCAAT
44453287 GGTGGTCG
1 GGTGGTCG
44453295 GTAATGACGG
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.18, C:0.16, G:0.40, T:0.26
Consensus pattern (21 bp):
GGTGGTCGATGATGACCCAAT
Found at i:44455049 original size:248 final size:249
Alignment explanation
Indices: 44454675--44455149 Score: 684
Period size: 248 Copynumber: 1.9 Consensus size: 249
44454665 TCTTATGTTG
* * * * * *
44454675 GTATACCAAAGGATTGTGAGCGCTCACTTCTCAGTTTTTGTGATTTTGGGCGTTGAGGCCCTAGA
1 GTATACCAAAGGATTGTGAGCACTAACCTATCAGTTTTTGTGATTTTGAGCATTGAGGCCCTAGA
* * * *
44454740 ACATGTGGAGAGATAAGGGAATGTCGAGCTATACTCTATTTATCGGGACATGTTACTATACAAGA
66 ACATGTGGAGAGATAAGGGAATGTCAAGCTATACTCTATTCACCAGGACATGTTACTATACAAGA
*
44454805 GAGTGTATTGCTTTGCGCTGCACTTATGGGACATGTTATAAGGACTCTTCAAGTCACTCTGAGGC
131 GAGTGTATTGCTTTGCGCTGCACTTATGGAACATGTTATAAGGACTCTTCAAGTCACTCTGAGGC
* *
44454870 GTTATAAGGAGATCTGCATATCCAACGAGACTTAAGTTATTTTATTATTTATTT
196 ATTATAAGGAGATCTACATATCCAACGAGACTTAAGTTATTTTATTATTTATTT
* * *
44454924 GTATACCAAAGGATTGTGAGTACTAACCTATCAG-TTTTGTGATTTTGAGCATTGATGCTCT-GT
1 GTATACCAAAGGATTGTGAGCACTAACCTATCAGTTTTTGTGATTTTGAGCATTGAGGCCCTAG-
* * * * *
44454987 GACATGTGGAGAGATAAGGGAATGTCAAGCTTTGCTCTATTCACCAGGACATGTTTCTATACATG
65 AACATGTGGAGAGATAAGGGAATGTCAAGCTATACTCTATTCACCAGGACATGTTACTATACAAG
* ** *
44455052 AGAGTGTATTGCTTTGTGCTGCACTTATGGAACATGTTATAAGGACTCTTTGAGTCACTTTGAGG
130 AGAGTGTATTGCTTTGCGCTGCACTTATGGAACATGTTATAAGGACTCTTCAAGTCACTCTGAGG
* *
44455117 CATTGTAAGGAGATTTACATATCCAACGAGACT
195 CATTATAAGGAGATCTACATATCCAACGAGACT
44455150 GATAAAATAA
Statistics
Matches: 198, Mismatches: 27, Indels: 3
0.87 0.12 0.01
Matches are distributed among these distances:
247 1 0.01
248 168 0.85
249 29 0.15
ACGTcount: A:0.27, C:0.16, G:0.24, T:0.34
Consensus pattern (249 bp):
GTATACCAAAGGATTGTGAGCACTAACCTATCAGTTTTTGTGATTTTGAGCATTGAGGCCCTAGA
ACATGTGGAGAGATAAGGGAATGTCAAGCTATACTCTATTCACCAGGACATGTTACTATACAAGA
GAGTGTATTGCTTTGCGCTGCACTTATGGAACATGTTATAAGGACTCTTCAAGTCACTCTGAGGC
ATTATAAGGAGATCTACATATCCAACGAGACTTAAGTTATTTTATTATTTATTT
Found at i:44455677 original size:43 final size:43
Alignment explanation
Indices: 44455573--44455715 Score: 225
Period size: 43 Copynumber: 3.3 Consensus size: 43
44455563 TTATGTGAAA
* * *
44455573 AAACGCCGCTAAAGATCATGACCTGTAGCGGCACTTTTATCAC
1 AAACGCCGCTAAAGATCTTGACCTTTAGCGGCGCTTTTATCAC
44455616 -AACGCCGCTAAAGATCTTGACCTTTAGCGGCGCTTTTATCAC
1 AAACGCCGCTAAAGATCTTGACCTTTAGCGGCGCTTTTATCAC
** *
44455658 AAACGCAACTAAAGATCTTGACCTTTAGCGGCGTTTTTATCAC
1 AAACGCCGCTAAAGATCTTGACCTTTAGCGGCGCTTTTATCAC
44455701 AAACGCCGCTAAAGA
1 AAACGCCGCTAAAGA
44455716 ACAAACCTTT
Statistics
Matches: 91, Mismatches: 8, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
42 39 0.43
43 52 0.57
ACGTcount: A:0.30, C:0.27, G:0.18, T:0.25
Consensus pattern (43 bp):
AAACGCCGCTAAAGATCTTGACCTTTAGCGGCGCTTTTATCAC
Found at i:44455755 original size:85 final size:85
Alignment explanation
Indices: 44455571--44455755 Score: 219
Period size: 85 Copynumber: 2.2 Consensus size: 85
44455561 GTTTATGTGA
* **
44455571 AAAAACGCCGCTAAAGATCATGACCTGTAGCGGCACTTTTATCACAACGCCGCTAAAGATCTTGA
1 AAAAACGCCGCTAAAGATCATGACCTGTAGCGGCACTTTTATCACAACGCCGCTAAAGAACTAAA
* * *
44455636 CCTTTAGCGGCGCTTTTATC
66 CCTTTAGCGACGCTTCTAGC
* ** * * **
44455656 ACAAACGCAACTAAAGATCTTGACCTTTAGCGGCGTTTTTATCACAAACGCCGCTAAAGAAC-AA
1 AAAAACGCCGCTAAAGATCATGACCTGTAGCGGCACTTTTATCAC-AACGCCGCTAAAGAACTAA
*
44455720 ACCTTTAGCGACGCTTCTCGC
65 ACCTTTAGCGACGCTTCTAGC
*
44455741 AAAAACACCGCTAAA
1 AAAAACGCCGCTAAA
44455756 AACATAACCT
Statistics
Matches: 81, Mismatches: 18, Indels: 2
0.80 0.18 0.02
Matches are distributed among these distances:
85 66 0.81
86 15 0.19
ACGTcount: A:0.32, C:0.28, G:0.17, T:0.23
Consensus pattern (85 bp):
AAAAACGCCGCTAAAGATCATGACCTGTAGCGGCACTTTTATCACAACGCCGCTAAAGAACTAAA
CCTTTAGCGACGCTTCTAGC
Found at i:44461963 original size:7 final size:7
Alignment explanation
Indices: 44461951--44462133 Score: 72
Period size: 7 Copynumber: 25.7 Consensus size: 7
44461941 CTTAATCTTT
44461951 TAAACCC
1 TAAACCC
44461958 TAAACCC
1 TAAACCC
* *
44461965 TAAAACA
1 TAAACCC
44461972 TAAACCC
1 TAAACCC
44461979 TAAACCC
1 TAAACCC
44461986 -ATAACCC
1 TA-AACCC
44461993 -ATAACCC
1 TA-AACCC
*
44462000 ATAACCCC
1 -TAAACCC
*
44462008 TAAACCT
1 TAAACCC
44462015 TAAACACC
1 TAAAC-CC
44462023 --AACCC
1 TAAACCC
*
44462028 TTAAACCA
1 -TAAACCC
*
44462036 TAAACCA
1 TAAACCC
* *
44462043 TAATCCA
1 TAAACCC
* *
44462050 TAATCCA
1 TAAACCC
*
44462057 TAATCCC
1 TAAACCC
*
44462064 TAAACACA
1 TAAAC-CC
* *
44462072 TAATCCT
1 TAAACCC
*
44462079 TAAACCT
1 TAAACCC
*
44462086 TAAA--A
1 TAAACCC
44462091 TAGTAACTCC
1 TA--AAC-CC
* *
44462101 TAAATCT
1 TAAACCC
44462108 TAAACCC
1 TAAACCC
*
44462115 TAAACCA
1 TAAACCC
44462122 TAAACCC
1 TAAACCC
44462129 TAAAC
1 TAAAC
44462134 TATAATGATA
Statistics
Matches: 139, Mismatches: 24, Indels: 26
0.74 0.13 0.14
Matches are distributed among these distances:
5 4 0.03
6 4 0.03
7 112 0.81
8 16 0.12
9 1 0.01
10 2 0.01
ACGTcount: A:0.46, C:0.33, G:0.01, T:0.20
Consensus pattern (7 bp):
TAAACCC
Found at i:44461975 original size:21 final size:21
Alignment explanation
Indices: 44461951--44462133 Score: 106
Period size: 21 Copynumber: 8.6 Consensus size: 21
44461941 CTTAATCTTT
*
44461951 TAAACCCTAAACCCTAAAACA
1 TAAACCCTAAACCCTAAACCA
*
44461972 TAAACCCTAAACCCATAACCCA
1 TAAACCCTAAACCC-TAAACCA
* *
44461994 T-AACCCATAACCCCTAAACCT
1 TAAACCC-TAAACCCTAAACCA
44462015 TAAACACC--AACCCTTAAACCA
1 TAAAC-CCTAAACCC-TAAACCA
* * * *
44462036 TAAACCATAATCCATAATCCA
1 TAAACCCTAAACCCTAAACCA
* * * *
44462057 TAATCCCTAAACACATAATCCT
1 TAAACCCTAAAC-CCTAAACCA
* * *
44462079 TAAACCTTAAA--ATAGTAACTCC
1 TAAACCCTAAACCCTA--AAC-CA
* *
44462101 TAAATCTTAAACCCTAAACCA
1 TAAACCCTAAACCCTAAACCA
44462122 TAAACCCTAAAC
1 TAAACCCTAAAC
44462134 TATAATGATA
Statistics
Matches: 125, Mismatches: 24, Indels: 26
0.71 0.14 0.15
Matches are distributed among these distances:
19 3 0.02
20 5 0.04
21 64 0.51
22 49 0.39
23 2 0.02
24 2 0.02
ACGTcount: A:0.46, C:0.33, G:0.01, T:0.20
Consensus pattern (21 bp):
TAAACCCTAAACCCTAAACCA
Found at i:44462116 original size:14 final size:14
Alignment explanation
Indices: 44462108--44462138 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
44462098 TCCTAAATCT
44462108 TAAACCCTAAACCA
1 TAAACCCTAAACCA
*
44462122 TAAACCCTAAACTA
1 TAAACCCTAAACCA
44462136 TAA
1 TAA
44462139 TGATAATTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.52, C:0.29, G:0.00, T:0.19
Consensus pattern (14 bp):
TAAACCCTAAACCA
Found at i:44462230 original size:21 final size:22
Alignment explanation
Indices: 44462201--44462243 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
44462191 TAGCGGCGCT
*
44462201 TCTTCAAAAA-CGCCGCTAAAG
1 TCTTCAAAAAGAGCCGCTAAAG
*
44462222 TCTTGAAAAAGAGCCGCTAAAG
1 TCTTCAAAAAGAGCCGCTAAAG
44462244 CCCCAAAAAC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 9 0.47
22 10 0.53
ACGTcount: A:0.40, C:0.23, G:0.19, T:0.19
Consensus pattern (22 bp):
TCTTCAAAAAGAGCCGCTAAAG
Found at i:44462340 original size:40 final size:40
Alignment explanation
Indices: 44462263--44462374 Score: 111
Period size: 40 Copynumber: 2.8 Consensus size: 40
44462253 CTCTAAAAAT
* * * ***
44462263 GCCGCTAATGCTC-ATTTTTAGCGGCATTTTCCAAAAAGC
1 GCCGCTAATGCTCGATCTTTAGCTGCGTTTTTTGAAAAGC
**
44462302 GGGGCTAATGCTCGATCTTTAGC-GACGTTTTTTGAAAAGC
1 GCCGCTAATGCTCGATCTTTAGCTG-CGTTTTTTGAAAAGC
* *
44462342 GCCGCTAATGCTTGATTTTTAGCTGCGTTTTTT
1 GCCGCTAATGCTCGATCTTTAGCTGCGTTTTTT
44462375 TATCCAAATG
Statistics
Matches: 59, Mismatches: 11, Indels: 5
0.79 0.15 0.07
Matches are distributed among these distances:
39 12 0.20
40 46 0.78
41 1 0.02
ACGTcount: A:0.21, C:0.21, G:0.22, T:0.37
Consensus pattern (40 bp):
GCCGCTAATGCTCGATCTTTAGCTGCGTTTTTTGAAAAGC
Found at i:44462397 original size:12 final size:12
Alignment explanation
Indices: 44462380--44462405 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
44462370 TTTTTTATCC
44462380 AAATGCCGCTAA
1 AAATGCCGCTAA
44462392 AAATGCCGCTAA
1 AAATGCCGCTAA
44462404 AA
1 AA
44462406 GCCTATTTTG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.46, C:0.23, G:0.15, T:0.15
Consensus pattern (12 bp):
AAATGCCGCTAA
Found at i:44467734 original size:18 final size:18
Alignment explanation
Indices: 44467713--44467759 Score: 51
Period size: 18 Copynumber: 2.6 Consensus size: 18
44467703 CTGCAATAAG
44467713 AAAATGTTTTG-AAATTGA
1 AAAATGTTTTGTAAA-TGA
* *
44467731 AAAACGATTTGTAAATGA
1 AAAATGTTTTGTAAATGA
*
44467749 ATAATGTTTTG
1 AAAATGTTTTG
44467760 GAAACGAACG
Statistics
Matches: 23, Mismatches: 5, Indels: 2
0.77 0.17 0.07
Matches are distributed among these distances:
18 20 0.87
19 3 0.13
ACGTcount: A:0.43, C:0.02, G:0.17, T:0.38
Consensus pattern (18 bp):
AAAATGTTTTGTAAATGA
Found at i:44468761 original size:20 final size:20
Alignment explanation
Indices: 44468736--44468840 Score: 65
Period size: 20 Copynumber: 5.3 Consensus size: 20
44468726 TGTACTTCGA
44468736 TGCCTCTGATTGCACAATTG
1 TGCCTCTGATTGCACAATTG
* *
44468756 TGCCTCTGTTTTCAC--TTCGG
1 TGCCTCTGATTGCACAATT--G
* *
44468776 TGCCTCTAATTGCAAAATTG
1 TGCCTCTGATTGCACAATTG
* *
44468796 TGCCTCCG-TTGCAC-TTTG
1 TGCCTCTGATTGCACAATTG
* * * *
44468814 ATGCCTCTAATTTCATAATCG
1 -TGCCTCTGATTGCACAATTG
44468835 TGCCTC
1 TGCCTC
44468841 AATTTGCACT
Statistics
Matches: 62, Mismatches: 16, Indels: 14
0.67 0.17 0.15
Matches are distributed among these distances:
18 5 0.08
19 11 0.18
20 42 0.68
21 2 0.03
22 2 0.03
ACGTcount: A:0.17, C:0.28, G:0.17, T:0.38
Consensus pattern (20 bp):
TGCCTCTGATTGCACAATTG
Found at i:44468822 original size:39 final size:40
Alignment explanation
Indices: 44468723--44468861 Score: 154
Period size: 40 Copynumber: 3.5 Consensus size: 40
44468713 GGTTGTATAG
* * * *
44468723 GTTTGTACTTCGATGCCTCTGATTGCACAATTGTGCCTCT
1 GTTTGCACTTCGATGCCTCTAATTGCAAAATTGTGCCTCC
* *
44468763 GTTTTCACTTCGGTGCCTCTAATTGCAAAATTGTGCCTCC
1 GTTTGCACTTCGATGCCTCTAATTGCAAAATTGTGCCTCC
* * * * *
44468803 G-TTGCACTTTGATGCCTCTAATTTCATAATCGTGCCTCA
1 GTTTGCACTTCGATGCCTCTAATTGCAAAATTGTGCCTCC
* *
44468842 ATTTGCACTTCGGTGCCTCT
1 GTTTGCACTTCGATGCCTCT
44468862 GATAGCACTA
Statistics
Matches: 82, Mismatches: 16, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
39 31 0.38
40 51 0.62
ACGTcount: A:0.17, C:0.27, G:0.18, T:0.39
Consensus pattern (40 bp):
GTTTGCACTTCGATGCCTCTAATTGCAAAATTGTGCCTCC
Found at i:44478079 original size:16 final size:16
Alignment explanation
Indices: 44478054--44478087 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
44478044 GTTTCCTGTA
44478054 CTGCCAATGCCATATC
1 CTGCCAATGCCATATC
* *
44478070 CTGCCCATGCCATGTC
1 CTGCCAATGCCATATC
44478086 CT
1 CT
44478088 AAACATGGTC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.18, C:0.41, G:0.15, T:0.26
Consensus pattern (16 bp):
CTGCCAATGCCATATC
Found at i:44478203 original size:50 final size:50
Alignment explanation
Indices: 44478078--44478213 Score: 200
Period size: 50 Copynumber: 2.7 Consensus size: 50
44478068 TCCTGCCCAT
* * ** *
44478078 GCCATGTCCTAAACATGGTCTTACGGGGGACCTCTCATCTCGGTGCCAAC
1 GCCATGTCCCAGACATGGTCTTACATGGGACCTCTTATCTCGGTGCCAAC
* *
44478128 GTCATGTCCCAGACATGGTCTTACATAGGACCTCTTATCTCGGTGCCAAC
1 GCCATGTCCCAGACATGGTCTTACATGGGACCTCTTATCTCGGTGCCAAC
*
44478178 GCCATGTCCCAGACATGGTCTTACATGGGATCTCTT
1 GCCATGTCCCAGACATGGTCTTACATGGGACCTCTT
44478214 TACCCAAATG
Statistics
Matches: 76, Mismatches: 10, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
50 76 1.00
ACGTcount: A:0.21, C:0.30, G:0.22, T:0.27
Consensus pattern (50 bp):
GCCATGTCCCAGACATGGTCTTACATGGGACCTCTTATCTCGGTGCCAAC
Found at i:44485796 original size:50 final size:50
Alignment explanation
Indices: 44485721--44485962 Score: 258
Period size: 50 Copynumber: 4.9 Consensus size: 50
44485711 CATTTGGGTA
* **
44485721 AAGAGATCCCATGTAAGACCATGTCTGGGACATGGTGTTGGCACCGAGAT
1 AAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGAT
*
44485771 AAGAGGTCCCATGTAAGATCATGTCTGGGACATGGCATTGGCACCGAGAT
1 AAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGAT
** * * *
44485821 AAGAGGTCCCCCGTAAGACCATGTCTGGGACATGGCATGGGCACCAATAT
1 AAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGAT
* ** * * * *
44485871 GAGAACTCCCATGTAAGACCATATCTAGGATATGGCATTGGCAGTAC-AGGA-
1 AAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA--CCGA-GAT
* * *
44485922 AACA--TCCCATGTAAGACCATGTTTGGGACATGGCTTTGGCA
1 AAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA
44485963 TGTTATTATC
Statistics
Matches: 161, Mismatches: 28, Indels: 7
0.82 0.14 0.04
Matches are distributed among these distances:
49 32 0.20
50 124 0.77
51 3 0.02
52 2 0.01
ACGTcount: A:0.29, C:0.21, G:0.28, T:0.22
Consensus pattern (50 bp):
AAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGAT
Found at i:44492698 original size:50 final size:48
Alignment explanation
Indices: 44492618--44492856 Score: 178
Period size: 50 Copynumber: 4.8 Consensus size: 48
44492608 TGGGTAAAGC
* *
44492618 GATCACATGTAAGACCATGTCTTGGACATGGCATTGGCATTGAGATAA
1 GATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATTGAGATAA
* * *
44492666 GAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACTGATATGAGA
1 GA--TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATTGAGAT-A-A
* * *** * *
44492718 TATCCC-TCGTAAGACCATGTCTGGGACATGGCATGGGCACCAATATGA
1 GATCCCAT-GTAAGACCATGTCTGGGACATGGCATTGGCATTGAGATAA
* * * * * *
44492766 GAACTCTCATGAAAGACCATATCTGGGATATGGTATTGGTAGTACTG-GA-AA
1 G-A-TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA-T--TGAGATAA
* * *
44492817 CATCCCATGTAAGACTATGTCTGGGACATGGCTTTGGCAT
1 GATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCAT
44492857 GTTATTATCA
Statistics
Matches: 147, Mismatches: 33, Indels: 22
0.73 0.16 0.11
Matches are distributed among these distances:
48 4 0.03
49 31 0.21
50 106 0.72
51 3 0.02
52 3 0.02
ACGTcount: A:0.28, C:0.19, G:0.27, T:0.26
Consensus pattern (48 bp):
GATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATTGAGATAA
Found at i:44495693 original size:9 final size:9
Alignment explanation
Indices: 44495675--44495717 Score: 59
Period size: 9 Copynumber: 4.6 Consensus size: 9
44495665 TTAATTTAGA
*
44495675 TAAAACTAT
1 TAAAATTAT
44495684 TAAAATTATT
1 TAAAATTA-T
44495694 TAAAATATAT
1 TAAAAT-TAT
44495704 TAAAATTAT
1 TAAAATTAT
44495713 TAAAA
1 TAAAA
44495718 ATATAAAAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
9 15 0.48
10 14 0.45
11 2 0.06
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (9 bp):
TAAAATTAT
Found at i:44495704 original size:20 final size:20
Alignment explanation
Indices: 44495681--44495722 Score: 75
Period size: 20 Copynumber: 2.1 Consensus size: 20
44495671 TAGATAAAAC
*
44495681 TATTAAAATTATTTAAAATA
1 TATTAAAATTATTAAAAATA
44495701 TATTAAAATTATTAAAAATA
1 TATTAAAATTATTAAAAATA
44495721 TA
1 TA
44495723 AAAAATTCAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (20 bp):
TATTAAAATTATTAAAAATA
Found at i:44496168 original size:30 final size:29
Alignment explanation
Indices: 44496097--44496187 Score: 93
Period size: 28 Copynumber: 3.2 Consensus size: 29
44496087 AAAAATCAAT
*
44496097 AAAAATA-TAAAAATAT-A-AAAATCTATA
1 AAAAATATTAAAATTATGATAAAAT-TATA
*
44496124 AAAAATATTTAAATTA-GATAAAATTATA
1 AAAAATATTAAAATTATGATAAAATTATA
*
44496152 AAAAATATATCAAAATTATTATAAAA-TATA
1 AAAAATAT-T-AAAATTATGATAAAATTATA
44496182 AAAAAT
1 AAAAAT
44496188 TCATAAAAGT
Statistics
Matches: 54, Mismatches: 4, Indels: 9
0.81 0.06 0.13
Matches are distributed among these distances:
27 7 0.13
28 19 0.35
29 6 0.11
30 16 0.30
31 6 0.11
ACGTcount: A:0.66, C:0.02, G:0.01, T:0.31
Consensus pattern (29 bp):
AAAAATATTAAAATTATGATAAAATTATA
Found at i:44496177 original size:11 final size:10
Alignment explanation
Indices: 44496101--44496188 Score: 60
Period size: 9 Copynumber: 9.0 Consensus size: 10
44496091 ATCAATAAAA
*
44496101 ATATAAAAAT
1 ATATAAAATT
44496111 ATA-AAAATCT
1 ATATAAAAT-T
*
44496121 ATA-AAAAAT
1 ATATAAAATT
*
44496130 AT-TTAAATT
1 ATATAAAATT
*
44496139 AGATAAAATT
1 ATATAAAATT
*
44496149 ATA-AAAAAT
1 ATATAAAATT
44496158 ATATCAAAATT
1 ATAT-AAAATT
44496169 ATTATAAAA-T
1 A-TATAAAATT
*
44496179 ATAAAAAATT
1 ATATAAAATT
44496189 CATAAAAGTT
Statistics
Matches: 61, Mismatches: 10, Indels: 14
0.72 0.12 0.16
Matches are distributed among these distances:
9 26 0.43
10 22 0.36
11 10 0.16
12 3 0.05
ACGTcount: A:0.64, C:0.02, G:0.01, T:0.33
Consensus pattern (10 bp):
ATATAAAATT
Found at i:44496185 original size:19 final size:18
Alignment explanation
Indices: 44496098--44496185 Score: 63
Period size: 19 Copynumber: 4.7 Consensus size: 18
44496088 AAAATCAATA
44496098 AAAATATAAAAA-TATA-
1 AAAATATAAAAATTATAT
* *
44496114 AAAATCTATAAAAAATATTT
1 AAAA--TATAAAAATTATAT
* * *
44496134 AAATTAGATAAAATTATAA
1 AAAATATA-AAAATTATAT
44496153 AAAATATATCAAAATTATTAT
1 AAAATATA--AAAATTA-TAT
44496174 AAAATATAAAAA
1 AAAATATAAAAA
44496186 ATTCATAAAA
Statistics
Matches: 55, Mismatches: 10, Indels: 11
0.72 0.13 0.14
Matches are distributed among these distances:
16 4 0.07
18 11 0.20
19 20 0.36
20 10 0.18
21 10 0.18
ACGTcount: A:0.66, C:0.02, G:0.01, T:0.31
Consensus pattern (18 bp):
AAAATATAAAAATTATAT
Found at i:44496186 original size:20 final size:20
Alignment explanation
Indices: 44496120--44496188 Score: 63
Period size: 20 Copynumber: 3.5 Consensus size: 20
44496110 TATAAAAATC
*
44496120 TATAAAAAA-TATT-TAAAT
1 TATAAAAAATTATTATAAAA
* * *
44496138 TAGATAAAATTA-TAAAAAA
1 TATAAAAAATTATTATAAAA
*
44496157 TATATCAAAATTATTATAAAA
1 TATA-AAAAATTATTATAAAA
44496178 TATAAAAAATT
1 TATAAAAAATT
44496189 CATAAAAGTT
Statistics
Matches: 39, Mismatches: 8, Indels: 6
0.74 0.15 0.11
Matches are distributed among these distances:
18 8 0.21
19 8 0.21
20 13 0.33
21 10 0.26
ACGTcount: A:0.62, C:0.01, G:0.01, T:0.35
Consensus pattern (20 bp):
TATAAAAAATTATTATAAAA
Done.