Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr1
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 106989029
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 3754247 characters in sequence are not A, C, G, or T
File 41 of 322
Found at i:12259276 original size:31 final size:31
Alignment explanation
Indices: 12259240--12259350 Score: 168
Period size: 31 Copynumber: 3.5 Consensus size: 31
12259230 TATCAGAACT
* * * *
12259240 AGAATCAGAATCAGAATCAGAATTAGGTGAC
1 AGAATCAAAATCAGAATCAGTATCAGGTAAC
*
12259271 AGAATCAGAATCAGAATCAGTATCAGGTAAC
1 AGAATCAAAATCAGAATCAGTATCAGGTAAC
12259302 AGAATCAAAATCAGAATCAGTATCAGGTAAC
1 AGAATCAAAATCAGAATCAGTATCAGGTAAC
12259333 AGAATCAAAAATCAGAAT
1 AGAATC-AAAATCAGAAT
12259351 GTGAATGCAA
Statistics
Matches: 75, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
31 64 0.85
32 11 0.15
ACGTcount: A:0.49, C:0.14, G:0.18, T:0.19
Consensus pattern (31 bp):
AGAATCAAAATCAGAATCAGTATCAGGTAAC
Found at i:12259306 original size:19 final size:19
Alignment explanation
Indices: 12259282--12259339 Score: 58
Period size: 19 Copynumber: 3.4 Consensus size: 19
12259272 GAATCAGAAT
12259282 CAGAATCAGTATCAGGTAA
1 CAGAATCAGTATCAGGTAA
*
12259301 CAGAATCA--A--A---AT
1 CAGAATCAGTATCAGGTAA
12259313 CAGAATCAGTATCAGGTAA
1 CAGAATCAGTATCAGGTAA
12259332 CAGAATCA
1 CAGAATCA
12259340 AAAATCAGAA
Statistics
Matches: 30, Mismatches: 2, Indels: 14
0.65 0.04 0.30
Matches are distributed among these distances:
12 9 0.30
14 1 0.03
15 1 0.03
16 1 0.03
17 1 0.03
19 17 0.57
ACGTcount: A:0.47, C:0.17, G:0.17, T:0.19
Consensus pattern (19 bp):
CAGAATCAGTATCAGGTAA
Found at i:12259529 original size:27 final size:26
Alignment explanation
Indices: 12259487--12259588 Score: 132
Period size: 27 Copynumber: 3.8 Consensus size: 26
12259477 GCTCAGTTAT
* *
12259487 CAGATATTGTGACAGAGTCACCAGATA
1 CAGATATTGTGGCAGAGCCACCAGA-A
12259514 CAGATATTGTGGCAGAGCCACCAGAA
1 CAGATATTGTGGCAGAGCCACCAGAA
*
12259540 CAGATATTTGTGGCATAGCCACCAGAAA
1 CAGATA-TTGTGGCAGAGCCACCAG-AA
* *
12259568 CAGATAATGTGGCAAAGCCAC
1 CAGATATTGTGGCAGAGCCAC
12259589 TTAACAGAAT
Statistics
Matches: 68, Mismatches: 5, Indels: 4
0.88 0.06 0.05
Matches are distributed among these distances:
26 7 0.10
27 53 0.78
28 8 0.12
ACGTcount: A:0.36, C:0.22, G:0.24, T:0.19
Consensus pattern (26 bp):
CAGATATTGTGGCAGAGCCACCAGAA
Found at i:12259775 original size:22 final size:22
Alignment explanation
Indices: 12259747--12259811 Score: 78
Period size: 22 Copynumber: 3.0 Consensus size: 22
12259737 GCAAATACGT
*
12259747 TTGGCACACAGCCATAATCAGG
1 TTGGCACAAAGCCATAATCAGG
* *
12259769 TTGGCACAGAGCCAT-ATGTAGG
1 TTGGCACAAAGCCATAAT-CAGG
*
12259791 TTGACACAAAGCCATAATCAG
1 TTGGCACAAAGCCATAATCAG
12259812 AAGGCTTTAA
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
21 2 0.06
22 32 0.89
23 2 0.06
ACGTcount: A:0.34, C:0.23, G:0.23, T:0.20
Consensus pattern (22 bp):
TTGGCACAAAGCCATAATCAGG
Found at i:12261000 original size:48 final size:48
Alignment explanation
Indices: 12260938--12261058 Score: 233
Period size: 48 Copynumber: 2.5 Consensus size: 48
12260928 AATTACAAAC
12260938 ATCAATTATTTACCCTATTAACAAATAATCTCATTTTCAAAATTTCAT
1 ATCAATTATTTACCCTATTAACAAATAATCTCATTTTCAAAATTTCAT
12260986 ATCAATTATTTACCCTATTAACAAATAATCTCATTTTCAAAATTTCAT
1 ATCAATTATTTACCCTATTAACAAATAATCTCATTTTCAAAATTTCAT
*
12261034 TTCAATTATTTACCCTATTAACAAA
1 ATCAATTATTTACCCTATTAACAAA
12261059 GCTCGGACTA
Statistics
Matches: 72, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
48 72 1.00
ACGTcount: A:0.40, C:0.19, G:0.00, T:0.41
Consensus pattern (48 bp):
ATCAATTATTTACCCTATTAACAAATAATCTCATTTTCAAAATTTCAT
Found at i:12262673 original size:5 final size:5
Alignment explanation
Indices: 12262663--12262700 Score: 67
Period size: 5 Copynumber: 7.6 Consensus size: 5
12262653 TATATATATA
*
12262663 ATAAT ATAAT ATAAA ATAAT ATAAT ATAAT ATAAT ATA
1 ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATA
12262701 CTTAATTATT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
5 31 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (5 bp):
ATAAT
Found at i:12262680 original size:15 final size:15
Alignment explanation
Indices: 12262656--12262700 Score: 72
Period size: 15 Copynumber: 3.0 Consensus size: 15
12262646 TTTCTTTTAT
*
12262656 ATATATAATAATATA
1 ATATAAAATAATATA
12262671 ATATAAAATAATATA
1 ATATAAAATAATATA
*
12262686 ATATAATATAATATA
1 ATATAAAATAATATA
12262701 CTTAATTATT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 28 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (15 bp):
ATATAAAATAATATA
Found at i:12263084 original size:27 final size:27
Alignment explanation
Indices: 12263054--12263194 Score: 219
Period size: 27 Copynumber: 5.2 Consensus size: 27
12263044 AGGTATCTTA
12263054 GTAATTCTACCCTACAGGGGTATTTCG
1 GTAATTCTACCCTACAGGGGTATTTCG
12263081 GTAATTCTACCCTACAGGGGTATTTCG
1 GTAATTCTACCCTACAGGGGTATTTCG
*
12263108 GTAATTCTACCCTACAGGGGTATTTCA
1 GTAATTCTACCCTACAGGGGTATTTCG
* * *
12263135 ATAATTCTACCCTACAGGGGTAGTTCA
1 GTAATTCTACCCTACAGGGGTATTTCG
* *
12263162 GTAATTTTACCCTACGGGGGTATTTCG
1 GTAATTCTACCCTACAGGGGTATTTCG
*
12263189 ATAATT
1 GTAATT
12263195 TCACAAACCA
Statistics
Matches: 105, Mismatches: 9, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 105 1.00
ACGTcount: A:0.25, C:0.21, G:0.21, T:0.34
Consensus pattern (27 bp):
GTAATTCTACCCTACAGGGGTATTTCG
Found at i:12263210 original size:27 final size:26
Alignment explanation
Indices: 12263179--12263348 Score: 180
Period size: 27 Copynumber: 6.3 Consensus size: 26
12263169 TACCCTACGG
* * *
12263179 GGGTATTTCGATAATTTCACAAACCA
1 GGGTATTTTGGTAATTTTACAAACCA
** *
12263205 GTGGTATTTTAATAATTTTACAGACCA
1 G-GGTATTTTGGTAATTTTACAAACCA
12263232 GGAGTATTTTGGTAATTTTACAAACCAA
1 GG-GTATTTTGGTAATTTTACAAACC-A
*
12263260 GGGTATTTTGGTAATTTTATAAACCA
1 GGGTATTTTGGTAATTTTACAAACCA
**
12263286 GGGGTATTTTGGTAATTTTGTA-AAATAA
1 -GGGTATTTTGGTAA-TTT-TACAAACCA
*
12263314 GGGTATTCTGGTAATTTTACAAACCA
1 GGGTATTTTGGTAATTTTACAAACCA
12263340 GGGGTATTT
1 -GGGTATTT
12263349 ATTGGTAAAC
Statistics
Matches: 122, Mismatches: 14, Indels: 15
0.81 0.09 0.10
Matches are distributed among these distances:
25 2 0.02
26 10 0.08
27 98 0.80
28 10 0.08
29 2 0.02
ACGTcount: A:0.32, C:0.10, G:0.20, T:0.38
Consensus pattern (26 bp):
GGGTATTTTGGTAATTTTACAAACCA
Found at i:12263211 original size:81 final size:81
Alignment explanation
Indices: 12263055--12263221 Score: 221
Period size: 81 Copynumber: 2.1 Consensus size: 81
12263045 GGTATCTTAG
* * * *
12263055 TAATTCTACCCTACAGGGGTATTTCGGTAATTCTACCCTACAGGGGTATTTCGGTAATTCTACCC
1 TAATTCTACCCTACAGGGGTAGTTCAGTAATTCTACCCTACAGGGGTATTTCGATAATTCTACCA
*
12263120 TACAGGGGTATTTCAA
66 AACAGGGGTATTTCAA
* *
12263136 TAATTCTACCCTACAGGGGTAGTTCAGTAATTTTACCCTACGGGGGTATTTCGATAATT-T-CAC
1 TAATTCTACCCTACAGGGGTAGTTCAGTAATTCTACCCTACAGGGGTATTTCGATAATTCTAC-C
* *
12263199 AAACCAGTGGTATTTTAA
65 AAA-CAGGGGTATTTCAA
12263217 TAATT
1 TAATT
12263222 TTACAGACCA
Statistics
Matches: 75, Mismatches: 9, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
79 1 0.01
80 3 0.04
81 71 0.95
ACGTcount: A:0.27, C:0.20, G:0.19, T:0.35
Consensus pattern (81 bp):
TAATTCTACCCTACAGGGGTAGTTCAGTAATTCTACCCTACAGGGGTATTTCGATAATTCTACCA
AACAGGGGTATTTCAA
Found at i:12263264 original size:81 final size:81
Alignment explanation
Indices: 12263179--12263348 Score: 200
Period size: 81 Copynumber: 2.1 Consensus size: 81
12263169 TACCCTACGG
* * * *
12263179 GGGTATTTCGATAATTTCACAAACCAGTGGTATTTTAATAA-TTT-TACAGACCAGGAGTATTTT
1 GGGTATTTCGATAATTTCACAAACCAGGGGTATTTTAATAATTTTGTA-AAACAAGG-GTATTCT
12263242 GGTAATTTTACAAACCAA
64 GGTAATTTTACAAACCAA
* * * * ** *
12263260 GGGTATTTTGGTAATTTTATAAACCAGGGGTATTTTGGTAATTTTGTAAAATAAGGGTATTCTGG
1 GGGTATTTCGATAATTTCACAAACCAGGGGTATTTTAATAATTTTGTAAAACAAGGGTATTCTGG
*
12263325 TAATTTTACAAACCAG
66 TAATTTTACAAACCAA
12263341 GGGTATTT
1 GGGTATTT
12263349 ATTGGTAAAC
Statistics
Matches: 75, Mismatches: 12, Indels: 4
0.82 0.13 0.04
Matches are distributed among these distances:
81 65 0.87
82 8 0.11
83 2 0.03
ACGTcount: A:0.32, C:0.10, G:0.20, T:0.38
Consensus pattern (81 bp):
GGGTATTTCGATAATTTCACAAACCAGGGGTATTTTAATAATTTTGTAAAACAAGGGTATTCTGG
TAATTTTACAAACCAA
Found at i:12266173 original size:26 final size:25
Alignment explanation
Indices: 12266144--12266192 Score: 71
Period size: 25 Copynumber: 1.9 Consensus size: 25
12266134 GAACTTTACA
12266144 ATGTTGTCCTAAACAAAATAGCATAT
1 ATGTT-TCCTAAACAAAATAGCATAT
* *
12266170 ATGTTTCTTATACAAAATAGCAT
1 ATGTTTCCTAAACAAAATAGCAT
12266193 GTAATAGAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 16 0.76
26 5 0.24
ACGTcount: A:0.41, C:0.14, G:0.10, T:0.35
Consensus pattern (25 bp):
ATGTTTCCTAAACAAAATAGCATAT
Found at i:12267119 original size:41 final size:41
Alignment explanation
Indices: 12267073--12267154 Score: 164
Period size: 41 Copynumber: 2.0 Consensus size: 41
12267063 AGTGGGAGAT
12267073 AAGAAAAATTTAGCTTTTTAATGTTTAAAACTTAAACTTAA
1 AAGAAAAATTTAGCTTTTTAATGTTTAAAACTTAAACTTAA
12267114 AAGAAAAATTTAGCTTTTTAATGTTTAAAACTTAAACTTAA
1 AAGAAAAATTTAGCTTTTTAATGTTTAAAACTTAAACTTAA
12267155 GCCTAATGCA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 41 1.00
ACGTcount: A:0.46, C:0.07, G:0.07, T:0.39
Consensus pattern (41 bp):
AAGAAAAATTTAGCTTTTTAATGTTTAAAACTTAAACTTAA
Found at i:12272395 original size:16 final size:15
Alignment explanation
Indices: 12272372--12272401 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
12272362 TTGATATGTT
12272372 TATTTATTCATATCA
1 TATTTATTCATATCA
12272387 TATTGTATTCATATC
1 TATT-TATTCATATC
12272402 GCATTTTTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.29
16 10 0.71
ACGTcount: A:0.30, C:0.13, G:0.03, T:0.53
Consensus pattern (15 bp):
TATTTATTCATATCA
Found at i:12274690 original size:69 final size:69
Alignment explanation
Indices: 12274589--12274748 Score: 200
Period size: 69 Copynumber: 2.3 Consensus size: 69
12274579 CTTTTAAAGT
* * * * *
12274589 ATTAAAATT--ATTTTTAATGAAATTAGTAAAGAATTGAGCTATAAGAGTATTCTTTGGTCAATG
1 ATTAAAATTAAATTTTTAATGAAAATAGTAAAGAAGTGAACTATAAGAGTATTCTCTAGTCAAT-
12274652 A-AGG
65 ATAGG
**
12274656 ATTAAAATTAAATTTTTAATGAAAATAGTAAAGAAGTGAACTATGTGAGTATTCTCTAGTCAATA
1 ATTAAAATTAAATTTTTAATGAAAATAGTAAAGAAGTGAACTATAAGAGTATTCTCTAGTCAATA
*
12274721 TGGG
66 TAGG
* *
12274725 ATTAAAATTAACTTTTTTATGAAA
1 ATTAAAATTAAATTTTTAATGAAA
12274749 GCAGGGAAGA
Statistics
Matches: 80, Mismatches: 10, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
67 9 0.11
68 1 0.01
69 70 0.88
ACGTcount: A:0.42, C:0.05, G:0.16, T:0.38
Consensus pattern (69 bp):
ATTAAAATTAAATTTTTAATGAAAATAGTAAAGAAGTGAACTATAAGAGTATTCTCTAGTCAATA
TAGG
Found at i:12275177 original size:9 final size:9
Alignment explanation
Indices: 12275163--12275191 Score: 58
Period size: 9 Copynumber: 3.2 Consensus size: 9
12275153 TATATATGCT
12275163 AATACTTGC
1 AATACTTGC
12275172 AATACTTGC
1 AATACTTGC
12275181 AATACTTGC
1 AATACTTGC
12275190 AA
1 AA
12275192 CTGTTGGATA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.38, C:0.21, G:0.10, T:0.31
Consensus pattern (9 bp):
AATACTTGC
Found at i:12276808 original size:12 final size:12
Alignment explanation
Indices: 12276791--12276816 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
12276781 GAAAACGGAC
12276791 TTTTAGCGGCGT
1 TTTTAGCGGCGT
12276803 TTTTAGCGGCGT
1 TTTTAGCGGCGT
12276815 TT
1 TT
12276817 GGATAAAAAA
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:0.08, C:0.15, G:0.31, T:0.46
Consensus pattern (12 bp):
TTTTAGCGGCGT
Found at i:12277208 original size:102 final size:105
Alignment explanation
Indices: 12277029--12277215 Score: 299
Period size: 102 Copynumber: 1.8 Consensus size: 105
12277019 TATGTTAATG
*
12277029 AGCTATACAGGCATTAGTGGCGTTTTACTTAAAACACCGCAATATATCAGAATTAGCGGCGCTTC
1 AGCTATACAGGCATTAGTGGCGTTTTACTTAAAACACCGCAATATATAAGAATTAGCGGCGCTTC
*
12277094 TTTAAAAACGCCGCAAAAGTCTTGAGAGAAACGACGATGT
66 TATAAAAACGCCGCAAAAGTCTTGAGAGAAACGACGATGT
* * * *
12277134 AGCTATAGAGGCATTAGTGGTGTTTTAC-TAAAA-A-CTCAATATATAAGAATTAGTGGCGCTTC
1 AGCTATACAGGCATTAGTGGCGTTTTACTTAAAACACCGCAATATATAAGAATTAGCGGCGCTTC
12277196 TATAAAAACGCCGCAAAAGT
66 TATAAAAACGCCGCAAAAGT
12277216 GGCTATAGAG
Statistics
Matches: 76, Mismatches: 6, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
102 44 0.58
103 1 0.01
104 5 0.07
105 26 0.34
ACGTcount: A:0.36, C:0.18, G:0.20, T:0.26
Consensus pattern (105 bp):
AGCTATACAGGCATTAGTGGCGTTTTACTTAAAACACCGCAATATATAAGAATTAGCGGCGCTTC
TATAAAAACGCCGCAAAAGTCTTGAGAGAAACGACGATGT
Found at i:12278096 original size:7 final size:7
Alignment explanation
Indices: 12278086--12278155 Score: 52
Period size: 7 Copynumber: 10.0 Consensus size: 7
12278076 GGGGTTTAAA
12278086 GTTTAGG
1 GTTTAGG
12278093 GTTTAGG
1 GTTTAGG
12278100 GTTT-GG
1 GTTTAGG
* *
12278106 TGTTCATG
1 -GTTTAGG
*
12278114 GTTTAGT
1 GTTTAGG
*
12278121 GTTTATG
1 GTTTAGG
* *
12278128 ATTTTGG
1 GTTTAGG
12278135 GTTTAGG
1 GTTTAGG
* *
12278142 GTTTCGA
1 GTTTAGG
12278149 GTTTAGG
1 GTTTAGG
12278156 CTATATTTTT
Statistics
Matches: 45, Mismatches: 16, Indels: 4
0.69 0.25 0.06
Matches are distributed among these distances:
6 2 0.04
7 42 0.93
8 1 0.02
ACGTcount: A:0.13, C:0.03, G:0.36, T:0.49
Consensus pattern (7 bp):
GTTTAGG
Found at i:12279085 original size:37 final size:37
Alignment explanation
Indices: 12279028--12279149 Score: 138
Period size: 37 Copynumber: 3.3 Consensus size: 37
12279018 CCCCAAATCG
** * **
12279028 CCCCGTGCATTACAACCCATCTACTCTGTCGCCTTCT
1 CCCCGTGCATCGCAACCCATCTCCTCCATCGCCTTCT
* *
12279065 CCCCGTGCATCGCAAACCATCCCCTCCATCGCCTT-T
1 CCCCGTGCATCGCAACCCATCTCCTCCATCGCCTTCT
* * *
12279101 GCCCTGTGCATCGTAACCCATCTCCTCCATCGCCTTCG
1 -CCCCGTGCATCGCAACCCATCTCCTCCATCGCCTTCT
12279139 CCCCGTGCATC
1 CCCCGTGCATC
12279150 TACTACATAG
Statistics
Matches: 70, Mismatches: 13, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
36 1 0.01
37 69 0.99
ACGTcount: A:0.15, C:0.47, G:0.13, T:0.25
Consensus pattern (37 bp):
CCCCGTGCATCGCAACCCATCTCCTCCATCGCCTTCT
Found at i:12280745 original size:14 final size:15
Alignment explanation
Indices: 12280723--12280759 Score: 58
Period size: 14 Copynumber: 2.5 Consensus size: 15
12280713 TTAGTATAAT
12280723 AATTATATGAAGTAA
1 AATTATATGAAGTAA
*
12280738 AA-TATATGATGTAA
1 AATTATATGAAGTAA
12280752 AATTATAT
1 AATTATAT
12280760 TGTATACTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
14 13 0.65
15 7 0.35
ACGTcount: A:0.51, C:0.00, G:0.11, T:0.38
Consensus pattern (15 bp):
AATTATATGAAGTAA
Found at i:12281096 original size:19 final size:19
Alignment explanation
Indices: 12281072--12281162 Score: 152
Period size: 19 Copynumber: 4.9 Consensus size: 19
12281062 ATAATCTTCA
12281072 ATGATATGCAATCTTAGAT
1 ATGATATGCAATCTTAGAT
12281091 ATGATATGCAATCTTAGAT
1 ATGATATGCAATCTTAGAT
*
12281110 ATGATA--CAATCTTAAAT
1 ATGATATGCAATCTTAGAT
12281127 ATGAT-TGCAATCTTAGAT
1 ATGATATGCAATCTTAGAT
12281145 ATGATATGCAATCTTAGA
1 ATGATATGCAATCTTAGA
12281163 ATATATGATT
Statistics
Matches: 67, Mismatches: 2, Indels: 6
0.89 0.03 0.08
Matches are distributed among these distances:
17 15 0.22
18 15 0.22
19 37 0.55
ACGTcount: A:0.38, C:0.11, G:0.14, T:0.36
Consensus pattern (19 bp):
ATGATATGCAATCTTAGAT
Found at i:12281143 original size:35 final size:37
Alignment explanation
Indices: 12281072--12281166 Score: 140
Period size: 35 Copynumber: 2.5 Consensus size: 37
12281062 ATAATCTTCA
*
12281072 ATGATATGCAATCTTAGATATGATATGCAATCTTAGAT
1 ATGATA-GCAATCTTAAATATGATATGCAATCTTAGAT
12281110 ATGATA-CAATCTTAAATATGAT-TGCAATCTTAGAT
1 ATGATAGCAATCTTAAATATGATATGCAATCTTAGAT
12281145 ATGATATGCAATCTTAGAATAT
1 ATGATA-GCAATCTTA-AATAT
12281167 ATGATTTTAT
Statistics
Matches: 53, Mismatches: 1, Indels: 6
0.88 0.02 0.10
Matches are distributed among these distances:
35 19 0.36
36 15 0.28
37 8 0.15
38 11 0.21
ACGTcount: A:0.39, C:0.11, G:0.14, T:0.37
Consensus pattern (37 bp):
ATGATAGCAATCTTAAATATGATATGCAATCTTAGAT
Found at i:12281476 original size:18 final size:17
Alignment explanation
Indices: 12281453--12281486 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
12281443 TTTCCCGGAT
*
12281453 TTTTTTTATATATTTTAA
1 TTTTTTAATA-ATTTTAA
12281471 TTTTTTAATAATTTTA
1 TTTTTTAATAATTTTA
12281487 GTATCATATC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (17 bp):
TTTTTTAATAATTTTAA
Found at i:12283901 original size:19 final size:19
Alignment explanation
Indices: 12283877--12283967 Score: 161
Period size: 19 Copynumber: 4.9 Consensus size: 19
12283867 ATAATCTTCA
12283877 ATGATATGCAATCTTAGAT
1 ATGATATGCAATCTTAGAT
12283896 ATGATATGCAATCTTAGAT
1 ATGATATGCAATCTTAGAT
12283915 ATGATA--CAATCTTAGAT
1 ATGATATGCAATCTTAGAT
12283932 ATGAT-TGCAATCTTAGAT
1 ATGATATGCAATCTTAGAT
12283950 ATGATATGCAATCTTAGA
1 ATGATATGCAATCTTAGA
12283968 ATATATGATT
Statistics
Matches: 69, Mismatches: 0, Indels: 6
0.92 0.00 0.08
Matches are distributed among these distances:
17 16 0.23
18 16 0.23
19 37 0.54
ACGTcount: A:0.37, C:0.11, G:0.15, T:0.36
Consensus pattern (19 bp):
ATGATATGCAATCTTAGAT
Found at i:12283948 original size:35 final size:37
Alignment explanation
Indices: 12283877--12283974 Score: 150
Period size: 35 Copynumber: 2.7 Consensus size: 37
12283867 ATAATCTTCA
12283877 ATGATATGCAATCTTAGATATGATATGCAATCTTAGAT
1 ATGATA-GCAATCTTAGATATGATATGCAATCTTAGAT
12283915 ATGATA-CAATCTTAGATATGAT-TGCAATCTTAGAT
1 ATGATAGCAATCTTAGATATGATATGCAATCTTAGAT
12283950 ATGATATGCAATCTTAGA-AT-ATATG
1 ATGATA-GCAATCTTAGATATGATATG
12283975 ATTTTATAAT
Statistics
Matches: 57, Mismatches: 0, Indels: 8
0.88 0.00 0.12
Matches are distributed among these distances:
35 21 0.37
36 20 0.35
37 10 0.18
38 6 0.11
ACGTcount: A:0.38, C:0.10, G:0.15, T:0.37
Consensus pattern (37 bp):
ATGATAGCAATCTTAGATATGATATGCAATCTTAGAT
Found at i:12284282 original size:18 final size:17
Alignment explanation
Indices: 12284259--12284292 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
12284249 TTTCCCGGAT
*
12284259 TTTTTTTATATATTTTAA
1 TTTTTTAATA-ATTTTAA
12284277 TTTTTTAATAATTTTA
1 TTTTTTAATAATTTTA
12284293 GTATCATATC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (17 bp):
TTTTTTAATAATTTTAA
Found at i:12287760 original size:31 final size:31
Alignment explanation
Indices: 12287722--12287780 Score: 100
Period size: 31 Copynumber: 1.9 Consensus size: 31
12287712 TTTATGTTAA
*
12287722 ATTTGCTGTTTTTGGTTGCATTTCATGCTAT
1 ATTTGCTGTTTTTGGTTGCATTTAATGCTAT
*
12287753 ATTTGCTGTTTTTGGTTGGATTTAATGC
1 ATTTGCTGTTTTTGGTTGCATTTAATGC
12287781 ATGAAGGGTT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.14, C:0.10, G:0.22, T:0.54
Consensus pattern (31 bp):
ATTTGCTGTTTTTGGTTGCATTTAATGCTAT
Found at i:12290109 original size:22 final size:22
Alignment explanation
Indices: 12290084--12290133 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 22
12290074 TAATTGAGAA
12290084 TGAATTGATTC-TTTATTATTTT
1 TGAATTGATTCATTT-TTATTTT
*
12290106 TGAATTGATTCATTTTTCTTTT
1 TGAATTGATTCATTTTTATTTT
*
12290128 TTAATT
1 TGAATT
12290134 TTATGGACTT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 22 0.88
23 3 0.12
ACGTcount: A:0.22, C:0.06, G:0.08, T:0.64
Consensus pattern (22 bp):
TGAATTGATTCATTTTTATTTT
Found at i:12295738 original size:41 final size:41
Alignment explanation
Indices: 12295693--12295775 Score: 157
Period size: 41 Copynumber: 2.0 Consensus size: 41
12295683 CTATAATCCC
12295693 ATTATTTTGGGATAGTTTTAAAGTATGGGTATAGATTAGGT
1 ATTATTTTGGGATAGTTTTAAAGTATGGGTATAGATTAGGT
*
12295734 ATTATTTTGGGATATTTTTAAAGTATGGGTATAGATTAGGT
1 ATTATTTTGGGATAGTTTTAAAGTATGGGTATAGATTAGGT
12295775 A
1 A
12295776 ACGAAATTGA
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 41 1.00
ACGTcount: A:0.30, C:0.00, G:0.25, T:0.45
Consensus pattern (41 bp):
ATTATTTTGGGATAGTTTTAAAGTATGGGTATAGATTAGGT
Found at i:12299482 original size:16 final size:16
Alignment explanation
Indices: 12299461--12299531 Score: 74
Period size: 16 Copynumber: 4.4 Consensus size: 16
12299451 GTTTGGTTCA
12299461 CTGTAATGGAATA-AGG
1 CTGTAATGGAATAGA-G
*
12299477 CTGTAATTGAATAGAG
1 CTGTAATGGAATAGAG
* *
12299493 TTGTAATTGAATAGAG
1 CTGTAATGGAATAGAG
*
12299509 CTGTAATGAAATA-AGG
1 CTGTAATGGAATAGA-G
12299525 CTGTAAT
1 CTGTAAT
12299532 CAGTAATTCA
Statistics
Matches: 48, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
15 1 0.02
16 46 0.96
17 1 0.02
ACGTcount: A:0.38, C:0.06, G:0.25, T:0.31
Consensus pattern (16 bp):
CTGTAATGGAATAGAG
Found at i:12299781 original size:35 final size:37
Alignment explanation
Indices: 12299744--12299823 Score: 92
Period size: 37 Copynumber: 2.2 Consensus size: 37
12299734 AAAATAATAA
* *
12299744 ATAATTTAATCATATT-TTAAAATAATAATTATTAAAT
1 ATAATTTAATAACATTCTTAAAATAATAATTATT-AAT
* *
12299781 ATAATTTAATAACATTCTTAATATAATTATTATT-AT
1 ATAATTTAATAACATTCTTAAAATAATAATTATTAAT
12299817 ATGAATT
1 AT-AATT
12299824 AAAAAATTCA
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
36 4 0.11
37 18 0.49
38 15 0.41
ACGTcount: A:0.47, C:0.04, G:0.01, T:0.47
Consensus pattern (37 bp):
ATAATTTAATAACATTCTTAAAATAATAATTATTAAT
Found at i:12303465 original size:27 final size:27
Alignment explanation
Indices: 12303435--12303612 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
12303425 ATATTGAGTC
* * * *
12303435 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAAAT
* *
12303462 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
12303489 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAAA-T
** * *
12303517 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAAAT
* **
12303544 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAGTCAAAT
*
12303571 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
12303598 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
12303613 GTACAATTTA
Statistics
Matches: 130, Mismatches: 18, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 24 0.18
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAAAT
Found at i:12303574 original size:82 final size:81
Alignment explanation
Indices: 12303456--12303611 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
12303446 TGCTATATAA
* *
12303456 TCAACTCGCACACTTAGTGCTACGTAATCAAATCGCACACTTAGTGCTACATAGTCAAACTCGCA
1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAA-TCGCA
12303521 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * **
12303538 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAATCGCA
1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCA
12303602 CACTTAGTGC
65 CACTTAGTGC
12303612 TGTACAATTT
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 16 0.24
82 51 0.76
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.27
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCAC
ACTTAGTGCCGCATGG
Found at i:12311869 original size:28 final size:28
Alignment explanation
Indices: 12311829--12312099 Score: 418
Period size: 28 Copynumber: 9.6 Consensus size: 28
12311819 NNNNNNNNNN
*
12311829 AACTCGCACACTTAGTGCTATATAATCA
1 AACTCGCACACTTAGTGCTACATAATCA
12311857 AACTCGCACACTTAGTGCTACATAATCA
1 AACTCGCACACTTAGTGCTACATAATCA
* *
12311885 AACTTGCACACTTAGTGCTATATAATCA
1 AACTCGCACACTTAGTGCTACATAATCA
12311913 AACTCGCACACTTAGTGCTACATAATCA
1 AACTCGCACACTTAGTGCTACATAATCA
* *
12311941 AGCTCGCACACTTAGTGCTACATAGTCA
1 AACTCGCACACTTAGTGCTACATAATCA
12311969 AACTCGCACACTTAGTGCTACATAATCA
1 AACTCGCACACTTAGTGCTACATAATCA
* *
12311997 AGCTCGCACACTTAGTGCTACATAGTCA
1 AACTCGCACACTTAGTGCTACATAATCA
12312025 AACTCGCACACTTAGTGCTACATAATCA
1 AACTCGCACACTTAGTGCTACATAATCA
* * *
12312053 AGCTCGCACACTTAGTGCTGTACA-ATTTA
1 AACTCGCACACTTAGTGC--TACATAATCA
*
12312082 AACCCGCACACTTAGTGC
1 AACTCGCACACTTAGTGC
12312100 CAATCTCATG
Statistics
Matches: 223, Mismatches: 18, Indels: 3
0.91 0.07 0.01
Matches are distributed among these distances:
28 200 0.90
29 19 0.09
30 4 0.02
ACGTcount: A:0.33, C:0.28, G:0.13, T:0.26
Consensus pattern (28 bp):
AACTCGCACACTTAGTGCTACATAATCA
Found at i:12315269 original size:78 final size:78
Alignment explanation
Indices: 12315154--12315308 Score: 283
Period size: 78 Copynumber: 2.0 Consensus size: 78
12315144 TCTCCTTAAA
*
12315154 GAAATTTCGTCCTTGACATTTACCTGCTGACAAATCAATTGCTTAATCATAAAATCTTTTCCTCT
1 GAAATTTCGTCCTTGACATTTACCTGCTGACAAATCAATTGCTTAATCACAAAATCTTTTCCTCT
12315219 TTTTAAACCAACT
66 TTTTAAACCAACT
* *
12315232 GAAATTTTGTCCTTGACATTTACCTGCTGACACATCAATTGCTTAATCACAAAATCTTTTCCTCT
1 GAAATTTCGTCCTTGACATTTACCTGCTGACAAATCAATTGCTTAATCACAAAATCTTTTCCTCT
12315297 TTTTAAACCAAC
66 TTTTAAACCAAC
12315309 CACTACGCTT
Statistics
Matches: 74, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
78 74 1.00
ACGTcount: A:0.30, C:0.24, G:0.08, T:0.38
Consensus pattern (78 bp):
GAAATTTCGTCCTTGACATTTACCTGCTGACAAATCAATTGCTTAATCACAAAATCTTTTCCTCT
TTTTAAACCAACT
Found at i:12321480 original size:90 final size:90
Alignment explanation
Indices: 12321314--12321488 Score: 199
Period size: 90 Copynumber: 1.9 Consensus size: 90
12321304 TGCAATTCTG
* * * * *
12321314 GTGGTTCATCCACATATTATTTGACAACTTTTATCTGCAATTAAGTTGTGCATTCACAACCACCT
1 GTGGTTCACCCACATATTATCTGACAACTCTCATATGCAATTAAGTTGTGCATTCACAACCACCT
*** *
12321379 GGCAGTGTATTAAGCTGCAACACTA
66 GGCAACATATTAACCTGCAACACTA
* * * * **
12321404 GTGGTTCGCCCACCTATTATCTGACAACTCTCATATGCATTTATA-TTGTGTATTCACAACCATT
1 GTGGTTCACCCACATATTATCTGACAACTCTCATATGCAATTA-AGTTGTGCATTCACAACCACC
12321468 TGGCAACATATTAACCTGCAA
65 TGGCAACATATTAACCTGCAA
12321489 ATTTGTGGCT
Statistics
Matches: 69, Mismatches: 15, Indels: 2
0.80 0.17 0.02
Matches are distributed among these distances:
90 68 0.99
91 1 0.01
ACGTcount: A:0.29, C:0.23, G:0.14, T:0.34
Consensus pattern (90 bp):
GTGGTTCACCCACATATTATCTGACAACTCTCATATGCAATTAAGTTGTGCATTCACAACCACCT
GGCAACATATTAACCTGCAACACTA
Found at i:12324216 original size:27 final size:28
Alignment explanation
Indices: 12324164--12324216 Score: 72
Period size: 28 Copynumber: 1.9 Consensus size: 28
12324154 TATTGTAATA
* * *
12324164 GGGCTATGGCCTAGATTAATACTGATAT
1 GGGCTAAGGCCCAGATTAACACTGATAT
12324192 GGGCTAAGGCCCAG-TTAACACTGAT
1 GGGCTAAGGCCCAGATTAACACTGAT
12324217 TTCTGAATAG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
27 10 0.45
28 12 0.55
ACGTcount: A:0.28, C:0.19, G:0.26, T:0.26
Consensus pattern (28 bp):
GGGCTAAGGCCCAGATTAACACTGATAT
Found at i:12325194 original size:41 final size:41
Alignment explanation
Indices: 12325137--12325215 Score: 140
Period size: 41 Copynumber: 1.9 Consensus size: 41
12325127 TTTAATTTGA
*
12325137 ATTTTAGGATATCAAGTGACATTTAATAATTCTATTCTCAT
1 ATTTTAAGATATCAAGTGACATTTAATAATTCTATTCTCAT
*
12325178 ATTTTAAGATATCAAGTGACGTTTAATAATTCTATTCT
1 ATTTTAAGATATCAAGTGACATTTAATAATTCTATTCT
12325216 TATGCTTCAA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 36 1.00
ACGTcount: A:0.34, C:0.11, G:0.10, T:0.44
Consensus pattern (41 bp):
ATTTTAAGATATCAAGTGACATTTAATAATTCTATTCTCAT
Found at i:12328902 original size:36 final size:36
Alignment explanation
Indices: 12328855--12328928 Score: 139
Period size: 36 Copynumber: 2.1 Consensus size: 36
12328845 ACGAATAGGG
*
12328855 AAGAAAGGATATATGGCAGTAAAGCTTGACATGAGT
1 AAGAAAAGATATATGGCAGTAAAGCTTGACATGAGT
12328891 AAGAAAAGATATATGGCAGTAAAGCTTGACATGAGT
1 AAGAAAAGATATATGGCAGTAAAGCTTGACATGAGT
12328927 AA
1 AA
12328929 AGCTTACGAC
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 37 1.00
ACGTcount: A:0.45, C:0.08, G:0.26, T:0.22
Consensus pattern (36 bp):
AAGAAAAGATATATGGCAGTAAAGCTTGACATGAGT
Found at i:12329878 original size:5 final size:5
Alignment explanation
Indices: 12329870--12329894 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
12329860 AATACAGTGG
12329870 TAAAA TAAAA TAAAA TAAAA TAAAA
1 TAAAA TAAAA TAAAA TAAAA TAAAA
12329895 ATCCATATAG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (5 bp):
TAAAA
Found at i:12342936 original size:13 final size:14
Alignment explanation
Indices: 12342918--12342946 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
12342908 TAATTAAATG
12342918 AATAAAGAAA-TAA
1 AATAAAGAAAGTAA
12342931 AATAAAGAAAGTAA
1 AATAAAGAAAGTAA
12342945 AA
1 AA
12342947 GAAATGAAGA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 10 0.67
14 5 0.33
ACGTcount: A:0.76, C:0.00, G:0.10, T:0.14
Consensus pattern (14 bp):
AATAAAGAAAGTAA
Found at i:12350765 original size:11 final size:11
Alignment explanation
Indices: 12350749--12350775 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
12350739 CTATTTTGTC
12350749 CGTTTTTGGCT
1 CGTTTTTGGCT
12350760 CGTTTTTGGCT
1 CGTTTTTGGCT
12350771 CGTTT
1 CGTTT
12350776 CTTACTCTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.00, C:0.19, G:0.26, T:0.56
Consensus pattern (11 bp):
CGTTTTTGGCT
Found at i:12359665 original size:142 final size:142
Alignment explanation
Indices: 12359416--12359692 Score: 441
Period size: 142 Copynumber: 2.0 Consensus size: 142
12359406 TCGATCTCTT
* *
12359416 GGGATTAGGTTCGTAACACCCCGAACCCGTCTCTGTCGCCTGATTAGGGTTACGGAATGCTACGA
1 GGGATTAGGTTCATAACACCCCGAACCCATCTCTGTCGCCTGATTAGGGTTACGGAATGCTACGA
* *
12359481 TAATTAACAATTCAAATAATATATCATTAAAATTTAGAATTTAATTTAATCATCAATTATAAATA
66 CAATTAACAATTCAAATAATATATCATTAAAATTTAAAATTTAATTTAATCATCAATTATAAATA
12359546 GTCATATCTCCG
131 GTCATATCTCCG
* ** *
12359558 GGGATTGGGTTCATAACACCTTGAACCCATCTCTGTTG-CTGAATTAGGGTTACAGG-ATGCTAC
1 GGGATTAGGTTCATAACACCCCGAACCCATCTCTGTCGCCTG-ATTAGGGTTAC-GGAATGCTAC
*
12359621 GACAATTAACAGTTCAAATAATATATCATTAAAATTTAAAATTTAATTTAATCATCAATTATAAA
64 GACAATTAACAATTCAAATAATATATCATTAAAATTTAAAATTTAATTTAATCATCAATTATAAA
12359686 TAGTCAT
129 TAGTCAT
12359693 TCATTATTCA
Statistics
Matches: 124, Mismatches: 9, Indels: 4
0.91 0.07 0.03
Matches are distributed among these distances:
141 3 0.02
142 119 0.96
143 2 0.02
ACGTcount: A:0.36, C:0.17, G:0.14, T:0.33
Consensus pattern (142 bp):
GGGATTAGGTTCATAACACCCCGAACCCATCTCTGTCGCCTGATTAGGGTTACGGAATGCTACGA
CAATTAACAATTCAAATAATATATCATTAAAATTTAAAATTTAATTTAATCATCAATTATAAATA
GTCATATCTCCG
Found at i:12362333 original size:25 final size:25
Alignment explanation
Indices: 12362286--12362350 Score: 67
Period size: 25 Copynumber: 2.6 Consensus size: 25
12362276 ACGAGTTATA
* *
12362286 AACGGTAAGCTCATCCAAGCTGAAT
1 AACGGGAAGCTCATCCAACCTGAAT
* * *
12362311 AACGGGAAGCTCATGCGACCTGAGT
1 AACGGGAAGCTCATCCAACCTGAAT
*
12362336 ATCGGGGAAGCTCAT
1 AAC-GGGAAGCTCAT
12362351 AAGAGCTGGA
Statistics
Matches: 33, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
25 22 0.67
26 11 0.33
ACGTcount: A:0.31, C:0.23, G:0.28, T:0.18
Consensus pattern (25 bp):
AACGGGAAGCTCATCCAACCTGAAT
Found at i:12363348 original size:18 final size:17
Alignment explanation
Indices: 12363325--12363366 Score: 50
Period size: 18 Copynumber: 2.5 Consensus size: 17
12363315 AAGACCTCCA
12363325 ATTTAAAATTCTATAGCT
1 ATTTAAAATT-TATAGCT
* *
12363343 ATTTAATATTTTTAGCT
1 ATTTAAAATTTATAGCT
12363360 A-TTAAAA
1 ATTTAAAA
12363367 CTCAACATTT
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
16 5 0.24
17 7 0.33
18 9 0.43
ACGTcount: A:0.40, C:0.07, G:0.05, T:0.48
Consensus pattern (17 bp):
ATTTAAAATTTATAGCT
Found at i:12379691 original size:24 final size:24
Alignment explanation
Indices: 12379663--12379709 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
12379653 CTATGGATTT
*
12379663 TGTGACAGGGTTGCCGTTAACACC
1 TGTGACAGGATTGCCGTTAACACC
12379687 TGTGACAGGATTGCCGTTAACAC
1 TGTGACAGGATTGCCGTTAACAC
12379710 TGAAAAAGAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.23, C:0.23, G:0.28, T:0.26
Consensus pattern (24 bp):
TGTGACAGGATTGCCGTTAACACC
Found at i:12382022 original size:46 final size:44
Alignment explanation
Indices: 12381963--12382077 Score: 149
Period size: 44 Copynumber: 2.6 Consensus size: 44
12381953 ACAGGACAGA
* *
12381963 ACAGAAATGAGCCATGTAAGTCCATATTAGAAATATGGCTTTGGAG
1 ACAGGAATGAGCCATGTAAGTCCATATT--AAATATGGCATTGGAG
* *
12382009 ACAGGATTGAGCCATGTAAGTCCATATTATATATGGCATTGGAG
1 ACAGGAATGAGCCATGTAAGTCCATATTAAATATGGCATTGGAG
* **
12382053 ACAGGAATAATTCATGTAAGTCCAT
1 ACAGGAATGAGCCATGTAAGTCCAT
12382078 GTCAAAGACA
Statistics
Matches: 61, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
44 35 0.57
46 26 0.43
ACGTcount: A:0.36, C:0.14, G:0.23, T:0.28
Consensus pattern (44 bp):
ACAGGAATGAGCCATGTAAGTCCATATTAAATATGGCATTGGAG
Found at i:12382058 original size:44 final size:45
Alignment explanation
Indices: 12381963--12382096 Score: 153
Period size: 46 Copynumber: 3.0 Consensus size: 45
12381953 ACAGGACAGA
* *
12381963 ACAGAAATGAGCCATGTAAGTCCATATTAGAAATATGGCTTTGGAG
1 ACAGGAATGAGCCATGTAAGTCCATATTA-AAATATGGCATTGGAG
* *
12382009 ACAGGATTGAGCCATGTAAGTCCATATT-ATATATGGCATTGGAG
1 ACAGGAATGAGCCATGTAAGTCCATATTAAAATATGGCATTGGAG
* ** * * *
12382053 ACAGGAATAATTCATGTAAGTCCATGTCAAAGACATGGCATTGG
1 ACAGGAATGAGCCATGTAAGTCCATATTAAA-ATATGGCATTGG
12382097 CAGGGTATTG
Statistics
Matches: 74, Mismatches: 12, Indels: 4
0.82 0.13 0.04
Matches are distributed among these distances:
44 36 0.49
45 1 0.01
46 37 0.50
ACGTcount: A:0.35, C:0.14, G:0.24, T:0.27
Consensus pattern (45 bp):
ACAGGAATGAGCCATGTAAGTCCATATTAAAATATGGCATTGGAG
Found at i:12392323 original size:13 final size:13
Alignment explanation
Indices: 12392305--12392344 Score: 53
Period size: 13 Copynumber: 3.0 Consensus size: 13
12392295 ATCTTCTTAT
12392305 AAAATATATTTTA
1 AAAATATATTTTA
* *
12392318 ATAATAAATTTTA
1 AAAATATATTTTA
12392331 AAAATAATATTTTA
1 AAAAT-ATATTTTA
12392345 TTAAAAAATA
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
13 15 0.68
14 7 0.32
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (13 bp):
AAAATATATTTTA
Found at i:12392384 original size:15 final size:15
Alignment explanation
Indices: 12392310--12392420 Score: 70
Period size: 15 Copynumber: 7.5 Consensus size: 15
12392300 CTTATAAAAT
12392310 ATATTTTAATAAT-A
1 ATATTTTAATAATAA
*
12392324 A-ATTTTAAAAAT-A
1 ATATTTTAATAATAA
* *
12392337 ATATTTTATTAAAAA
1 ATATTTTAATAATAA
** *
12392352 ATA-TTCCAT-ATTA
1 ATATTTTAATAATAA
12392365 ATATTTTAATAATAA
1 ATATTTTAATAATAA
*
12392380 ATATTTATTACAATTATAA
1 ATA-TT-TT--AATAATAA
* *
12392399 ATATATTAATAGTAA
1 ATATTTTAATAATAA
12392414 ATATTTT
1 ATATTTT
12392421 GTAGTATAAA
Statistics
Matches: 72, Mismatches: 17, Indels: 15
0.69 0.16 0.14
Matches are distributed among these distances:
13 17 0.24
14 16 0.22
15 22 0.31
16 2 0.03
17 4 0.06
18 1 0.01
19 10 0.14
ACGTcount: A:0.50, C:0.03, G:0.01, T:0.47
Consensus pattern (15 bp):
ATATTTTAATAATAA
Found at i:12392813 original size:27 final size:26
Alignment explanation
Indices: 12392774--12392824 Score: 77
Period size: 27 Copynumber: 1.9 Consensus size: 26
12392764 TATAAGGACT
12392774 TATGACATATTTTAATCTAGTATAAAAA
1 TATGACATATTTTAAT-TA-TATAAAAA
12392802 TATGA-ATATTTTAATTATATAAA
1 TATGACATATTTTAATTATATAAA
12392825 TATAAGTATT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
25 6 0.26
26 2 0.09
27 10 0.43
28 5 0.22
ACGTcount: A:0.47, C:0.04, G:0.06, T:0.43
Consensus pattern (26 bp):
TATGACATATTTTAATTATATAAAAA
Found at i:12400963 original size:27 final size:27
Alignment explanation
Indices: 12400919--12400972 Score: 65
Period size: 27 Copynumber: 2.0 Consensus size: 27
12400909 GGATTAATTC
*
12400919 AAATATTTGTTAATAATAAATATTAAT
1 AAATATTTATTAATAATAAATATTAAT
**
12400946 AAATATTTAATTAA-AATATTTATTAAT
1 AAATATTT-ATTAATAATAAATATTAAT
12400973 TATAAAAATT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
27 19 0.83
28 4 0.17
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (27 bp):
AAATATTTATTAATAATAAATATTAAT
Found at i:12401014 original size:19 final size:19
Alignment explanation
Indices: 12400955--12401014 Score: 52
Period size: 19 Copynumber: 3.2 Consensus size: 19
12400945 TAAATATTTA
*
12400955 ATTAAAATAT-TTATTAATT
1 ATTAAAATATATTAAT-ATT
* * *
12400974 ATAAAAAT-TATTGAAAAAT
1 ATTAAAATATATT-AATATT
12400993 ATTAAAATATATTAATATT
1 ATTAAAATATATTAATATT
12401012 ATT
1 ATT
12401015 TTTATTTAAT
Statistics
Matches: 31, Mismatches: 7, Indels: 6
0.70 0.16 0.14
Matches are distributed among these distances:
18 1 0.03
19 25 0.81
20 5 0.16
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (19 bp):
ATTAAAATATATTAATATT
Found at i:12405964 original size:11 final size:11
Alignment explanation
Indices: 12405948--12405978 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
12405938 AAGTATGGGT
12405948 AGGTATGGGAA
1 AGGTATGGGAA
*
12405959 AGGTATGGGCA
1 AGGTATGGGAA
12405970 AGGTATGGG
1 AGGTATGGG
12405979 GTATGGGTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.29, C:0.03, G:0.48, T:0.19
Consensus pattern (11 bp):
AGGTATGGGAA
Found at i:12414329 original size:18 final size:18
Alignment explanation
Indices: 12414296--12414354 Score: 64
Period size: 18 Copynumber: 3.2 Consensus size: 18
12414286 TTCCACTTAC
*
12414296 AATTTCATAATTATTTTAT
1 AATTTCAT-ATAATTTTAT
*
12414315 ATTTTCATATAATTTTAT
1 AATTTCATATAATTTTAT
* *
12414333 AATTTAAAATACATTTTAT
1 AATTTCATATA-ATTTTAT
12414352 AAT
1 AAT
12414355 ATTTTAATAA
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
18 17 0.50
19 17 0.50
ACGTcount: A:0.41, C:0.05, G:0.00, T:0.54
Consensus pattern (18 bp):
AATTTCATATAATTTTAT
Found at i:12414929 original size:28 final size:30
Alignment explanation
Indices: 12414897--12414952 Score: 98
Period size: 28 Copynumber: 1.9 Consensus size: 30
12414887 GTTTTGGAAG
12414897 AATAAATTAGGGTTTA-TGTTT-TTTTTAA
1 AATAAATTAGGGTTTATTGTTTATTTTTAA
12414925 AATAAATTAGGGTTTATTGTTTATTTTT
1 AATAAATTAGGGTTTATTGTTTATTTTT
12414953 TCAAAAACCT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
28 16 0.62
29 5 0.19
30 5 0.19
ACGTcount: A:0.30, C:0.00, G:0.14, T:0.55
Consensus pattern (30 bp):
AATAAATTAGGGTTTATTGTTTATTTTTAA
Found at i:12422006 original size:11 final size:11
Alignment explanation
Indices: 12421979--12422021 Score: 61
Period size: 11 Copynumber: 4.0 Consensus size: 11
12421969 TGACCTTTCC
12421979 AAGGTATGGG-
1 AAGGTATGGGA
*
12421989 TAGGTATGGGA
1 AAGGTATGGGA
*
12422000 AAGGTATGGGC
1 AAGGTATGGGA
12422011 AAGGTATGGGA
1 AAGGTATGGGA
12422022 TATATTCTAA
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
10 9 0.32
11 19 0.68
ACGTcount: A:0.30, C:0.02, G:0.47, T:0.21
Consensus pattern (11 bp):
AAGGTATGGGA
Found at i:12422018 original size:22 final size:21
Alignment explanation
Indices: 12421979--12422021 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
12421969 TGACCTTTCC
*
12421979 AAGGTATGGGTAGGTATGGGA
1 AAGGTATGGGAAGGTATGGGA
12422000 AAGGTATGGGCAAGGTATGGGA
1 AAGGTATGGG-AAGGTATGGGA
12422022 TATATTCTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 10 0.50
22 10 0.50
ACGTcount: A:0.30, C:0.02, G:0.47, T:0.21
Consensus pattern (21 bp):
AAGGTATGGGAAGGTATGGGA
Found at i:12424553 original size:3 final size:3
Alignment explanation
Indices: 12424547--12424578 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
12424537 GAATTCCTCC
12424547 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
12424579 CAAAAAAAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:12427270 original size:33 final size:33
Alignment explanation
Indices: 12427233--12427301 Score: 138
Period size: 33 Copynumber: 2.1 Consensus size: 33
12427223 CAAACATACG
12427233 AAGTAATAATTAAATAATGCATGATATACAAAA
1 AAGTAATAATTAAATAATGCATGATATACAAAA
12427266 AAGTAATAATTAAATAATGCATGATATACAAAA
1 AAGTAATAATTAAATAATGCATGATATACAAAA
12427299 AAG
1 AAG
12427302 AGTAATACAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.58, C:0.06, G:0.10, T:0.26
Consensus pattern (33 bp):
AAGTAATAATTAAATAATGCATGATATACAAAA
Found at i:12427650 original size:19 final size:19
Alignment explanation
Indices: 12427591--12427654 Score: 55
Period size: 18 Copynumber: 3.5 Consensus size: 19
12427581 AAAAGAATTT
* *
12427591 ATAAAATAACACATAATAT
1 ATAAAATAATACATAATAA
**
12427610 A-AAAAT-AT-CATTTTAA
1 ATAAAATAATACATAATAA
12427626 AGTAAAATAATACATAATAA
1 A-TAAAATAATACATAATAA
12427646 AT-AAATAAT
1 ATAAAATAAT
12427655 TAATAATTTA
Statistics
Matches: 35, Mismatches: 6, Indels: 9
0.70 0.12 0.18
Matches are distributed among these distances:
16 6 0.17
17 1 0.03
18 17 0.49
19 4 0.11
20 7 0.20
ACGTcount: A:0.62, C:0.06, G:0.02, T:0.30
Consensus pattern (19 bp):
ATAAAATAATACATAATAA
Found at i:12427848 original size:53 final size:53
Alignment explanation
Indices: 12427783--12427897 Score: 128
Period size: 53 Copynumber: 2.2 Consensus size: 53
12427773 ATACATAACA
12427783 TATATAAAAAAATGATAA-GTAATATAGAATA-AAAATAA-AAATATAATAAATGT
1 TATATAAAAAAAT-ATAATGTAA-ATA-AATAGAAAATAAGAAATATAATAAATGT
* * * * *
12427836 TATATAATAAAATATAATTTAAATATATAGAAAATAAGAAATATAATAGATAT
1 TATATAAAAAAATATAATGTAAATAAATAGAAAATAAGAAATATAATAAATGT
*
12427889 AATATAAAA
1 TATATAAAA
12427898 TAATTAAGTT
Statistics
Matches: 52, Mismatches: 7, Indels: 6
0.80 0.11 0.09
Matches are distributed among these distances:
51 3 0.06
52 14 0.27
53 35 0.67
ACGTcount: A:0.63, C:0.00, G:0.06, T:0.30
Consensus pattern (53 bp):
TATATAAAAAAATATAATGTAAATAAATAGAAAATAAGAAATATAATAAATGT
Found at i:12428068 original size:25 final size:23
Alignment explanation
Indices: 12428025--12428075 Score: 70
Period size: 23 Copynumber: 2.3 Consensus size: 23
12428015 AAAATAATAG
12428025 ATAAT-AAATAATATTAATATAT
1 ATAATAAAATAATATTAATATAT
*
12428047 ATAATAAAATAATCTTACA-ATAT
1 ATAATAAAATAATATTA-ATATAT
12428070 ATAATA
1 ATAATA
12428076 TAAAAGCAAG
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
22 5 0.19
23 20 0.77
24 1 0.04
ACGTcount: A:0.59, C:0.04, G:0.00, T:0.37
Consensus pattern (23 bp):
ATAATAAAATAATATTAATATAT
Found at i:12432386 original size:128 final size:128
Alignment explanation
Indices: 12432149--12432384 Score: 282
Period size: 128 Copynumber: 1.8 Consensus size: 128
12432139 TTTAATTTTA
*
12432149 AAAGGATATTCGGTCATTTGGGTCAAACAAGAAAAATCGAAACCCAGTACGTTAGGGCACGATCT
1 AAAGGATATTCGGTCATTTGGGTCAAACAAGAAAAATCGAAACCCAGTAAGTTAGGGCACGATCT
* *
12432214 CTCGAATTCCTAAACACGGAATATTGCCTTTTTTATTTAAAAATTCATATATTTTGAAATTTG
66 CTCGAATTCCTAAACACGAAATATTGCCTTTATTATTTAAAAATTCATATATTTTGAAATTTG
* * * * * *
12432277 AAAGGATATTTGGTTATTTAGGTTC-AACGAGAAAAATCGAAACTCC-GTAAGTTAGGGTATGAT
1 AAAGGATATTCGGTCATTT-GGGTCAAACAAGAAAAATCGAAAC-CCAGTAAGTTAGGGCACGA-
* * * *
12432340 TTTCTCGAGTTTCCTAAATC-CGAAATATTGTC-TTATTATTGAAAA
63 TCTCTCGA-ATTCCTAAA-CACGAAATATTGCCTTTATTATTTAAAA
12432385 TTTTCCCTTT
Statistics
Matches: 90, Mismatches: 13, Indels: 9
0.80 0.12 0.08
Matches are distributed among these distances:
128 47 0.52
129 24 0.27
130 18 0.20
131 1 0.01
ACGTcount: A:0.35, C:0.14, G:0.17, T:0.33
Consensus pattern (128 bp):
AAAGGATATTCGGTCATTTGGGTCAAACAAGAAAAATCGAAACCCAGTAAGTTAGGGCACGATCT
CTCGAATTCCTAAACACGAAATATTGCCTTTATTATTTAAAAATTCATATATTTTGAAATTTG
Found at i:12432957 original size:3 final size:3
Alignment explanation
Indices: 12432928--12433221 Score: 137
Period size: 3 Copynumber: 98.7 Consensus size: 3
12432918 TTAATTAGTT
* * * * *
12432928 TAA TAA T-A TGA TGA TAA CAA TAG TAA TAA T-A TAA TAA TAA -AG TAGA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA-A
* * * *
12432974 AAA TAA TAA TAA TAA TAA TAA TACA TTAA TCA GAA TAA TAA TAG T-A
1 TAA TAA TAA TAA TAA TAA TAA TA-A -TAA TAA TAA TAA TAA TAA TAA
* * * *
12433020 TAT TAA TAA TAA CAA TAA TAGA AAA TAA TAA TAA TAA -AA TAA GGAA
1 TAA TAA TAA TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA TAA -TAA
* * * *
12433066 TAA TAA TAA TAA TAA CAA TAA T-A TAAA TAA TAA TAA AAA CAA CAA
1 TAA TAA TAA TAA TAA TAA TAA TAA T-AA TAA TAA TAA TAA TAA TAA
* ** * * *
12433111 GAGA -AA TCG TAA CAA TAA TAG TAA TAA -AA GAA TAA -AA GTAA TAA
1 TA-A TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA -TAA TAA
** * *
12433155 TAA TAA TAA TGG CAA TAA TAA TAA -AA TTAA CAA TAA -AA TAA -AA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA -TAA TAA TAA TAA TAA TAA
**
12433198 TTAA TCAA TTT TAA TAA TAA -AA TA
1 -TAA T-AA TAA TAA TAA TAA TAA TA
12433222 GCAAAATAAC
Statistics
Matches: 218, Mismatches: 49, Indels: 48
0.69 0.16 0.15
Matches are distributed among these distances:
2 23 0.11
3 174 0.80
4 19 0.09
5 2 0.01
ACGTcount: A:0.62, C:0.04, G:0.06, T:0.28
Consensus pattern (3 bp):
TAA
Found at i:12435071 original size:140 final size:140
Alignment explanation
Indices: 12434876--12435377 Score: 708
Period size: 140 Copynumber: 3.6 Consensus size: 140
12434866 ATAGCTTTAA
* * * ***
12434876 TCTGCTCTACTGCAACTTCAGAGAGATAAGA-TTCGCTATCTTCAGTTTGCTCCACTGCAACTTC
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGACTT-G-TAACTTCAACCTGCTCCACTGCAACTTC
*
12434940 AAGGAGATAAGATTTGTGATTTGTAGCTTCAATCTACTTCACTGTAACTTCAGAGAGATAAGATT
64 AAGGAGATAAGGTTTGTGATTTGTAGCTTCAATCTACTTCACTGTAACTTCAGAGAGATAAGATT
*
12435005 CGCTCTCTTCAG
129 CGCTATCTTCAG
12435017 TCTGCTCCACTGCAACTTCAGGGAGATAAGACTTGTAACTTCAACCTGCTCCACTGCAACTTCAA
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGACTTGTAACTTCAACCTGCTCCACTGCAACTTCAA
* *
12435082 GGAGATAAGGTTTGTGATTTGTAGCTTCAATCTACTCCACTGCAACTTCATG-GAGATAAGATTC
66 GGAGATAAGGTTTGTGATTTGTAGCTTCAATCTACTTCACTGTAACTTCA-GAGAGATAAGATTC
12435146 GCTATCTTCAG
130 GCTATCTTCAG
* * * *
12435157 TCTGTTCCACTGCAACTTCAGGGAGATAAAACTTGTAACTTCAACCTGCTCCACTGCAACTTTAG
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGACTTGTAACTTCAACCTGCTCCACTGCAACTTCAA
*
12435222 GGAGATAAGGTTTGTGATTTGTAGCTTCAATCT-GTTCCACTGTAACTTCAGAGAGATAAGATTC
66 GGAGATAAGGTTTGTGATTTGTAGCTTCAATCTACTT-CACTGTAACTTCAGAGAGATAAGATTC
*
12435286 GCTATCTTTAG
130 GCTATCTTCAG
* * * * * *
12435297 -CTTGCTCCACTACAACTTTAGGGAGATAAGACTTATAACTTCAACTTACCCCACTGCAACTTC-
1 TC-TGCTCCACTGCAACTTCAGGGAGATAAGACTTGTAACTTCAACCTGCTCCACTGCAACTTCA
*
12435360 AGAAAGATAAGGTTTGTG
65 AG-GAGATAAGGTTTGTG
12435378 GCTTCAATCT
Statistics
Matches: 326, Mismatches: 29, Indels: 13
0.89 0.08 0.04
Matches are distributed among these distances:
139 4 0.01
140 289 0.89
141 31 0.10
142 2 0.01
ACGTcount: A:0.28, C:0.23, G:0.18, T:0.31
Consensus pattern (140 bp):
TCTGCTCCACTGCAACTTCAGGGAGATAAGACTTGTAACTTCAACCTGCTCCACTGCAACTTCAA
GGAGATAAGGTTTGTGATTTGTAGCTTCAATCTACTTCACTGTAACTTCAGAGAGATAAGATTCG
CTATCTTCAG
Found at i:12435073 original size:44 final size:44
Alignment explanation
Indices: 12434861--12435512 Score: 453
Period size: 44 Copynumber: 14.1 Consensus size: 44
12434851 AGAGGTATAG
* * * *
12434861 GATTTATAGCTTTAATCTGCTCTACTGCAACTTCAGAGAGATAA
1 GATTTGTAGCTTCAATCTGCTCCACTGCAACTTCAGGGAGATAA
* * * * *
12434905 GATTCGCTATCTTCAGTTTGCTCCACTGCAACTTCAAGGAGATAAGA
1 GATTTG-TAGCTTCAATCTGCTCCACTGCAACTTCAGGGAGAT-A-A
* * * *
12434952 TTTGTGATTTGTAGCTTCAATCTACTTCACTGTAACTTCAGAGAGATAA
1 -----GATTTGTAGCTTCAATCTGCTCCACTGCAACTTCAGGGAGATAA
* ** *
12435001 GATTCGCTCTCTTCAGTCTGCTCCACTGCAACTTCAGGGAGATAA
1 GATTTG-TAGCTTCAATCTGCTCCACTGCAACTTCAGGGAGATAA
* * * *
12435046 GACTTGTAACTTCAACCTGCTCCACTGCAACTTCAAGGAGATAA
1 GATTTGTAGCTTCAATCTGCTCCACTGCAACTTCAGGGAGATAA
* *
12435090 GGTTTGTGATTTGTAGCTTCAATCTACTCCACTGCAACTTCATGGAGATAA
1 -------GATTTGTAGCTTCAATCTGCTCCACTGCAACTTCAGGGAGATAA
* * * *
12435141 GATTCGCTATCTTCAGTCTGTTCCACTGCAACTTCAGGGAGATAA
1 GATTTG-TAGCTTCAATCTGCTCCACTGCAACTTCAGGGAGATAA
* * * * *
12435186 AACTTGTAACTTCAACCTGCTCCACTGCAACTTTAGGGAGATAA
1 GATTTGTAGCTTCAATCTGCTCCACTGCAACTTCAGGGAGATAA
* * *
12435230 GGTTTGTGATTTGTAGCTTCAATCTGTTCCACTGTAACTTCAGAGAGATAA
1 -------GATTTGTAGCTTCAATCTGCTCCACTGCAACTTCAGGGAGATAA
* * * * * *
12435281 GATTCGCTATCTT-TAGCTTGCTCCACTACAACTTTAGGGAGATAA
1 GATTTG-TAGCTTCAATC-TGCTCCACTGCAACTTCAGGGAGATAA
* * * * * **
12435326 GACTTATAACTTCAA-CTTACCCCACTGCAACTTCAGAAAGATAA
1 GATTTGTAGCTTCAATC-TGCTCCACTGCAACTTCAGGGAGATAA
* * *
12435370 GGTTTGTGGCTTCAATCTGCTCCATTGCAACTTCAGGGAGATAA
1 GATTTGTAGCTTCAATCTGCTCCACTGCAACTTCAGGGAGATAA
* *
12435414 GGTTTGTAATTTGTAGCTTCAATCTACTCCACTACAACTTCAGGGAGATAA
1 -----G--ATTTGTAGCTTCAATCTGCTCCACTGCAACTTCAGGGAGATAA
* * * * **
12435465 GGTTCGTGGCTTTAATCTAATCCACTGCAACTTCAGGGAGATAA
1 GATTTGTAGCTTCAATCTGCTCCACTGCAACTTCAGGGAGATAA
12435509 GATT
1 GATT
12435513 CACCGTCTTC
Statistics
Matches: 471, Mismatches: 102, Indels: 70
0.73 0.16 0.11
Matches are distributed among these distances:
44 187 0.40
45 132 0.28
46 2 0.00
47 1 0.00
49 2 0.00
50 1 0.00
51 141 0.30
52 5 0.01
ACGTcount: A:0.28, C:0.22, G:0.18, T:0.32
Consensus pattern (44 bp):
GATTTGTAGCTTCAATCTGCTCCACTGCAACTTCAGGGAGATAA
Found at i:12441069 original size:32 final size:32
Alignment explanation
Indices: 12441033--12441093 Score: 122
Period size: 32 Copynumber: 1.9 Consensus size: 32
12441023 TGTATGCATT
12441033 TTAGCATTTTAATAGTTAATGGATGATGGACA
1 TTAGCATTTTAATAGTTAATGGATGATGGACA
12441065 TTAGCATTTTAATAGTTAATGGATGATGG
1 TTAGCATTTTAATAGTTAATGGATGATGG
12441094 GCATGGTAAG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.33, C:0.05, G:0.23, T:0.39
Consensus pattern (32 bp):
TTAGCATTTTAATAGTTAATGGATGATGGACA
Found at i:12447358 original size:23 final size:23
Alignment explanation
Indices: 12447272--12447419 Score: 90
Period size: 23 Copynumber: 6.5 Consensus size: 23
12447262 ATAACAATAG
* * *
12447272 TAATAAT-ATAATAATAATGAAG
1 TAATAATAATAATAATAGTAAAT
* * *
12447294 TAGAAAATAATAATAATAATACAT
1 TA-ATAATAATAATAATAGTAAAT
* *
12447318 TAATAAGAATAATAATAGTATAT
1 TAATAATAATAATAATAGTAAAT
* *
12447341 TAATAATAACAATAATAG-AAAA
1 TAATAATAATAATAATAGTAAAT
* *
12447363 TAATAATAA-AAT-A-AGGAATAA
1 TAATAATAATAATAATAGTAA-AT
* * *
12447384 TAATAATAATACTAACAATAATAT
1 TAATAATAATAATAATAGTAA-AT
*
12447408 AAATAATAATAA
1 TAATAATAATAA
12447420 AAACAACAAG
Statistics
Matches: 101, Mismatches: 18, Indels: 12
0.77 0.14 0.09
Matches are distributed among these distances:
19 2 0.02
20 3 0.03
21 14 0.14
22 15 0.15
23 38 0.38
24 29 0.29
ACGTcount: A:0.63, C:0.03, G:0.05, T:0.29
Consensus pattern (23 bp):
TAATAATAATAATAATAGTAAAT
Found at i:12447532 original size:3 final size:3
Alignment explanation
Indices: 12447249--12447515 Score: 135
Period size: 3 Copynumber: 89.0 Consensus size: 3
12447239 TTAATTAGTT
* * * *
12447249 TAA TAA T-A TGA TGA TAA CAA TAG TAA TAA T-A TAA TAA TAA TGAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T-AA
* * * *
12447293 GTAGA AAA TAA TAA TAA TAA TACA TTAA TAA GAA TAA TAA TAG T-A TAT
1 -TA-A TAA TAA TAA TAA TAA TA-A -TAA TAA TAA TAA TAA TAA TAA TAA
* * *
12447341 TAA TAA TAA CAA TAA TAGA AAA TAA TAA TAA -AA TAA GGAA TAA TAA
1 TAA TAA TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA -TAA TAA TAA
* * * * * *
12447387 TAA TAA TAC TAA CAA TAA T-A TAAA TAA TAA TAA AAA CAA CAA GAGA
1 TAA TAA TAA TAA TAA TAA TAA T-AA TAA TAA TAA TAA TAA TAA TA-A
** * * *
12447433 -AA TCG TAA CAA TAA TAG TAA TAA -AA GAA TAA -AA GTAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA -TAA TAA TAA
*
12447476 TAA TAGA -AA TAA TAA TAA -AA TTAA AAA TAA -AA TAA -AA TAA
1 TAA TA-A TAA TAA TAA TAA TAA -TAA TAA TAA TAA TAA TAA TAA
12447516 ATCAATTTTA
Statistics
Matches: 203, Mismatches: 37, Indels: 48
0.70 0.13 0.17
Matches are distributed among these distances:
2 21 0.10
3 160 0.79
4 18 0.09
5 4 0.02
ACGTcount: A:0.64, C:0.03, G:0.07, T:0.26
Consensus pattern (3 bp):
TAA
Found at i:12449503 original size:7 final size:7
Alignment explanation
Indices: 12449481--12449515 Score: 54
Period size: 7 Copynumber: 5.1 Consensus size: 7
12449471 ACAATTTAAG
12449481 ATAAAA-
1 ATAAAAT
*
12449487 ATAAATT
1 ATAAAAT
12449494 ATAAAAT
1 ATAAAAT
12449501 ATAAAAT
1 ATAAAAT
12449508 ATAAAAT
1 ATAAAAT
12449515 A
1 A
12449516 AATTTACCTA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
6 5 0.19
7 21 0.81
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (7 bp):
ATAAAAT
Found at i:12449515 original size:26 final size:27
Alignment explanation
Indices: 12449484--12449542 Score: 77
Period size: 26 Copynumber: 2.2 Consensus size: 27
12449474 ATTTAAGATA
12449484 AAAATAAATTATA-AAATATAAAA-TAT
1 AAAATAAATT-TACAAATATAAAATTAT
**
12449510 AAAATAAATTTACCTATATAAAATTAT
1 AAAATAAATTTACAAATATAAAATTAT
12449537 AAAATA
1 AAAATA
12449543 GAAAATTATA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
25 2 0.07
26 18 0.62
27 9 0.31
ACGTcount: A:0.64, C:0.03, G:0.00, T:0.32
Consensus pattern (27 bp):
AAAATAAATTTACAAATATAAAATTAT
Found at i:12449559 original size:17 final size:16
Alignment explanation
Indices: 12449529--12449575 Score: 60
Period size: 17 Copynumber: 2.9 Consensus size: 16
12449519 TTACCTATAT
12449529 AAAATTAT-AAAATAG
1 AAAATTATAAAAATAG
12449544 AAAATTATAAAAAATAG
1 AAAATTAT-AAAAATAG
*
12449561 AAAATCATATAAAAT
1 AAAATTATA-AAAAT
12449576 CTAGTCATGT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
15 8 0.29
16 1 0.04
17 19 0.68
ACGTcount: A:0.68, C:0.02, G:0.04, T:0.26
Consensus pattern (16 bp):
AAAATTATAAAAATAG
Found at i:12460760 original size:23 final size:23
Alignment explanation
Indices: 12460716--12460760 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
12460706 ACCAATTCAA
*
12460716 CATATTTTCAAGATAAATTCATG
1 CATATTTTCAAGATAAAGTCATG
*
12460739 CATATTTAT-AAGATAACGTCAT
1 CATATTT-TCAAGATAAAGTCAT
12460761 CACATACCCA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 18 0.95
24 1 0.05
ACGTcount: A:0.40, C:0.13, G:0.09, T:0.38
Consensus pattern (23 bp):
CATATTTTCAAGATAAAGTCATG
Found at i:12465276 original size:181 final size:181
Alignment explanation
Indices: 12464972--12465335 Score: 728
Period size: 181 Copynumber: 2.0 Consensus size: 181
12464962 CTTGGCATCC
12464972 ACGAAGCAATCGGTCGTTGTAATATGCAGTGTCGTTTCAAGGTCTGTTATGCAACCTGGGACATA
1 ACGAAGCAATCGGTCGTTGTAATATGCAGTGTCGTTTCAAGGTCTGTTATGCAACCTGGGACATA
12465037 TCTCTCCAGCACCTGACACCACTGCCACACTTCATTATATGAAGCGTCCCACCGACCATGCATAT
66 TCTCTCCAGCACCTGACACCACTGCCACACTTCATTATATGAAGCGTCCCACCGACCATGCATAT
12465102 TTTCCAACGCCTTCTGCTTAGCTATCCAAACCTTGCGGTAAGAGGGCGTGT
131 TTTCCAACGCCTTCTGCTTAGCTATCCAAACCTTGCGGTAAGAGGGCGTGT
12465153 ACGAAGCAATCGGTCGTTGTAATATGCAGTGTCGTTTCAAGGTCTGTTATGCAACCTGGGACATA
1 ACGAAGCAATCGGTCGTTGTAATATGCAGTGTCGTTTCAAGGTCTGTTATGCAACCTGGGACATA
12465218 TCTCTCCAGCACCTGACACCACTGCCACACTTCATTATATGAAGCGTCCCACCGACCATGCATAT
66 TCTCTCCAGCACCTGACACCACTGCCACACTTCATTATATGAAGCGTCCCACCGACCATGCATAT
12465283 TTTCCAACGCCTTCTGCTTAGCTATCCAAACCTTGCGGTAAGAGGGCGTGT
131 TTTCCAACGCCTTCTGCTTAGCTATCCAAACCTTGCGGTAAGAGGGCGTGT
12465334 AC
1 AC
12465336 TTCAATTGGC
Statistics
Matches: 183, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
181 183 1.00
ACGTcount: A:0.24, C:0.28, G:0.20, T:0.27
Consensus pattern (181 bp):
ACGAAGCAATCGGTCGTTGTAATATGCAGTGTCGTTTCAAGGTCTGTTATGCAACCTGGGACATA
TCTCTCCAGCACCTGACACCACTGCCACACTTCATTATATGAAGCGTCCCACCGACCATGCATAT
TTTCCAACGCCTTCTGCTTAGCTATCCAAACCTTGCGGTAAGAGGGCGTGT
Found at i:12467017 original size:126 final size:126
Alignment explanation
Indices: 12466781--12467240 Score: 653
Period size: 126 Copynumber: 3.7 Consensus size: 126
12466771 AGTTTAAGGC
* * * *
12466781 TTTT-TCAGATACCACTGTAGCAAAAGAGCGTCCACGTGGGAGCTTTTTTTC-AAAATTTTGTTG
1 TTTTATCATATACCACTGTAGCAAAAGAGCGTCCACGTAGGAG-TTTTTTTCTGAAATTTTGCTG
* * *
12466844 AAAGTGCATCCTTTTTGAAGCGTTTTTGACACTATTTGTTCAGAAACATCTTCTCAAAATTA
65 AAAGTGCATCATTCTTGAAGCGTTTTTGACACTATTTGTTCAAAAACATCTTCTCAAAATTA
* **
12466906 TTTTATCATAGACCACTGTAGCAAAAGAGCGTCCACGTAGGAGTTTTTTTCTGAAATTTTAATGA
1 TTTTATCATATACCACTGTAGCAAAAGAGCGTCCACGTAGGAGTTTTTTTCTGAAATTTTGCTGA
*
12466971 AAGTGCATCCTTCTTGAAGCGTTTTTGACACTATTTGTTCAAAAACATCTTCTCAAAATTA
66 AAGTGCATCATTCTTGAAGCGTTTTTGACACTATTTGTTCAAAAACATCTTCTCAAAATTA
* * * *
12467032 TTTTCTCAGATACCACTGTAGCAAAAGAGCGTTCACGT-GGAATCTTTTTTCTGAAATTTTGCTG
1 TTTTATCATATACCACTGTAGCAAAAGAGCGTCCACGTAGGAGT-TTTTTTCTGAAATTTTGCTG
* * *
12467096 AAAGTACATCATTCTTGAAGCGTTTTTAACACTATTTGTTCATAAACATCTTCTCAAAATTA
65 AAAGTGCATCATTCTTGAAGCGTTTTTGACACTATTTGTTCAAAAACATCTTCTCAAAATTA
* *
12467158 TTTTATC-TGATACCACTGTAGCAAAAGAGCGTCCA--TATGGAAGCTTTTTTCCGAAATTTTGC
1 TTTTATCAT-ATACCACTGTAGCAAAAGAGCGTCCACGTA-GG-AGTTTTTTTCTGAAATTTTGC
12467220 TGAAAGTGCATCATTCTTGAA
63 TGAAAGTGCATCATTCTTGAA
12467241 TGTGTTCATT
Statistics
Matches: 302, Mismatches: 26, Indels: 13
0.89 0.08 0.04
Matches are distributed among these distances:
124 1 0.00
125 16 0.05
126 284 0.94
127 1 0.00
ACGTcount: A:0.30, C:0.18, G:0.16, T:0.37
Consensus pattern (126 bp):
TTTTATCATATACCACTGTAGCAAAAGAGCGTCCACGTAGGAGTTTTTTTCTGAAATTTTGCTGA
AAGTGCATCATTCTTGAAGCGTTTTTGACACTATTTGTTCAAAAACATCTTCTCAAAATTA
Found at i:12467313 original size:16 final size:16
Alignment explanation
Indices: 12467283--12467326 Score: 65
Period size: 16 Copynumber: 2.8 Consensus size: 16
12467273 TCTCCCTTAA
12467283 AAACCACTAAAAACCCT
1 AAACCACT-AAAACCCT
12467300 AAACCACTAAAACCCT
1 AAACCACTAAAACCCT
12467316 -AACC-CTAAAAC
1 AAACCACTAAAAC
12467327 AATCAAAACC
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
14 7 0.26
15 4 0.15
16 8 0.30
17 8 0.30
ACGTcount: A:0.52, C:0.36, G:0.00, T:0.11
Consensus pattern (16 bp):
AAACCACTAAAACCCT
Found at i:12467334 original size:23 final size:23
Alignment explanation
Indices: 12467294--12467364 Score: 83
Period size: 24 Copynumber: 3.1 Consensus size: 23
12467284 AACCACTAAA
* *
12467294 AACCCTAAACCACT-AAAACCCT
1 AACCCTAAAACAATCAAAACCCT
12467316 AACCCTAAAACAATCAAAACCCCT
1 AACCCTAAAACAATCAAAA-CCCT
*
12467340 AACCTTAAAA-AATTCAAAACCCT
1 AACCCTAAAACAA-TCAAAACCCT
12467363 AA
1 AA
12467365 TTTAATTGAT
Statistics
Matches: 43, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
22 12 0.28
23 12 0.28
24 19 0.44
ACGTcount: A:0.51, C:0.34, G:0.00, T:0.15
Consensus pattern (23 bp):
AACCCTAAAACAATCAAAACCCT
Found at i:12467474 original size:16 final size:16
Alignment explanation
Indices: 12467444--12467486 Score: 63
Period size: 16 Copynumber: 2.8 Consensus size: 16
12467434 TCTCCCTTAA
12467444 AAACCACTAAAAACCCT
1 AAACCACT-AAAACCCT
12467461 AAACCACTAAAACCCT
1 AAACCACTAAAACCCT
12467477 -AACC-CTAAAA
1 AAACCACTAAAA
12467487 AACTTGAAAC
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
14 6 0.23
15 4 0.15
16 8 0.31
17 8 0.31
ACGTcount: A:0.53, C:0.35, G:0.00, T:0.12
Consensus pattern (16 bp):
AAACCACTAAAACCCT
Found at i:12467479 original size:137 final size:136
Alignment explanation
Indices: 12467308--12467623 Score: 435
Period size: 137 Copynumber: 2.3 Consensus size: 136
12467298 CTAAACCACT
* *
12467308 AAAACCCT--AACCCTAAAACAATCAAAACCCCTAACCTTAAAAAA-TTCAAAACCCTAATTTAA
1 AAAACCCTAAAACCCTAAACCAAT-AAAACCCCTAACCCTAAAAAACTT-AAAACCCTAATTTAA
*
12467370 TTGATTTTTTTATTCTCATAGTTAATTTAATTAATT-AACTCTCAACTCTAAATGTTCATTAATT
64 TTAATTTTTTTATTCTCATAGTTAATTTAATTAATTAAAC-CTCAACTCTAAATGTTCATTAATT
12467434 TCTCCCTTA
128 TCTCCCTTA
* *
12467443 AAAACCACTAAAAACCCTAAACCACTAAAA-CCCTAACCCTAAAAAACTTGAAACCCTAATTTAA
1 AAAACC-CT-AAAACCCTAAACCAATAAAACCCCTAACCCTAAAAAACTTAAAACCCTAATTTAA
* *
12467507 TTAATTTTTTTATTCTCATAGTTAATTTAATTAATTAAACCTCAACTTTAAGTGTTCATTAATTT
64 TTAATTTTTTTATTCTCATAGTTAATTTAATTAATTAAACCTCAACTCTAAATGTTCATTAATTT
*
12467572 TTCCCTTA
129 CTCCCTTA
* * * *
12467580 AAAACCCTAAAACTCTAAACCATTAAAAACCTTAAACCCTAAAA
1 AAAACCCTAAAACCCTAAACCAATAAAACCCCT-AACCCTAAAA
12467624 CCCACCAAAA
Statistics
Matches: 162, Mismatches: 11, Indels: 14
0.87 0.06 0.07
Matches are distributed among these distances:
135 24 0.15
136 7 0.04
137 110 0.68
138 9 0.06
139 12 0.07
ACGTcount: A:0.42, C:0.22, G:0.02, T:0.34
Consensus pattern (136 bp):
AAAACCCTAAAACCCTAAACCAATAAAACCCCTAACCCTAAAAAACTTAAAACCCTAATTTAATT
AATTTTTTTATTCTCATAGTTAATTTAATTAATTAAACCTCAACTCTAAATGTTCATTAATTTCT
CCCTTA
Found at i:12467489 original size:16 final size:17
Alignment explanation
Indices: 12467444--12467487 Score: 67
Period size: 15 Copynumber: 2.8 Consensus size: 17
12467434 TCTCCCTTAA
12467444 AAACCACTAAAAACCCT
1 AAACCACTAAAAACCCT
12467461 AAACCACT-AAAACCCT
1 AAACCACTAAAAACCCT
12467477 -AACC-CTAAAAA
1 AAACCACTAAAAA
12467488 ACTTGAAACC
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
14 2 0.08
15 8 0.31
16 8 0.31
17 8 0.31
ACGTcount: A:0.55, C:0.34, G:0.00, T:0.11
Consensus pattern (17 bp):
AAACCACTAAAAACCCT
Found at i:12467656 original size:17 final size:18
Alignment explanation
Indices: 12467630--12467668 Score: 62
Period size: 17 Copynumber: 2.2 Consensus size: 18
12467620 AAAACCCACC
*
12467630 AAAAATCCTAAACC-TAA
1 AAAAACCCTAAACCTTAA
12467647 AAAAACCCTAAACCTTAA
1 AAAAACCCTAAACCTTAA
12467665 AAAA
1 AAAA
12467669 GGGGGGCAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
17 13 0.65
18 7 0.35
ACGTcount: A:0.62, C:0.23, G:0.00, T:0.15
Consensus pattern (18 bp):
AAAAACCCTAAACCTTAA
Found at i:12467949 original size:19 final size:19
Alignment explanation
Indices: 12467925--12467962 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
12467915 ATTAATATAT
12467925 CATATTTAATTTTTATTAA
1 CATATTTAATTTTTATTAA
12467944 CATATTTAATTTTTATTAA
1 CATATTTAATTTTTATTAA
12467963 TTTTGAAGTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.37, C:0.05, G:0.00, T:0.58
Consensus pattern (19 bp):
CATATTTAATTTTTATTAA
Found at i:12469027 original size:49 final size:50
Alignment explanation
Indices: 12468925--12469021 Score: 133
Period size: 52 Copynumber: 1.9 Consensus size: 50
12468915 TCTAAACAAT
*
12468925 ATAATAATTAACTATTTAAAATAAAATAATTTTATAATATTTTCTGAACACC
1 ATAATAATTAACTATTTAAAATAAAATAATTTAATAATATTTTCT--ACACC
* *
12468977 ATAATAATTAACTGA-TTAAAATTAAATAATTTAATAATTTTTTCT
1 ATAATAATTAACT-ATTTAAAATAAAATAATTTAATAATATTTTCT
12469022 TACCATTTGT
Statistics
Matches: 41, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
52 40 0.98
53 1 0.02
ACGTcount: A:0.47, C:0.07, G:0.02, T:0.43
Consensus pattern (50 bp):
ATAATAATTAACTATTTAAAATAAAATAATTTAATAATATTTTCTACACC
Found at i:12469104 original size:5 final size:5
Alignment explanation
Indices: 12469094--12469125 Score: 64
Period size: 5 Copynumber: 6.4 Consensus size: 5
12469084 TCGAAGAATG
12469094 AATAA AATAA AATAA AATAA AATAA AATAA AA
1 AATAA AATAA AATAA AATAA AATAA AATAA AA
12469126 AGATTTAAAC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 27 1.00
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (5 bp):
AATAA
Found at i:12471816 original size:17 final size:17
Alignment explanation
Indices: 12471781--12471815 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
12471771 GACATATCTT
12471781 AACAGGAAAAGATTAAA
1 AACAGGAAAAGATTAAA
*
12471798 AACA-GAAAGGATTAAA
1 AACAGGAAAAGATTAAA
12471814 AA
1 AA
12471816 ATTACCCAGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 13 0.76
17 4 0.24
ACGTcount: A:0.66, C:0.06, G:0.17, T:0.11
Consensus pattern (17 bp):
AACAGGAAAAGATTAAA
Found at i:12500995 original size:27 final size:26
Alignment explanation
Indices: 12500939--12501049 Score: 150
Period size: 27 Copynumber: 4.2 Consensus size: 26
12500929 AGCATGGCTG
* * *
12500939 CCAGAACAAATAATGTGACAGAGTCA
1 CCAGAACAGATAATGTGGCAGAGCCA
12500965 CCAGAACAGATAATCGTGGCAGAGCCA
1 CCAGAACAGATAAT-GTGGCAGAGCCA
12500992 CCAGAACAGATATATGTGGCAGAGCCA
1 CCAGAACAGATA-ATGTGGCAGAGCCA
* *
12501019 CCAGATCAGATAATTGTGGCATAGCCA
1 CCAGAACAGATAA-TGTGGCAGAGCCA
12501046 CCAG
1 CCAG
12501050 GATGCTTCCT
Statistics
Matches: 77, Mismatches: 5, Indels: 5
0.89 0.06 0.06
Matches are distributed among these distances:
26 14 0.18
27 61 0.79
28 2 0.03
ACGTcount: A:0.38, C:0.23, G:0.23, T:0.15
Consensus pattern (26 bp):
CCAGAACAGATAATGTGGCAGAGCCA
Found at i:12502497 original size:24 final size:24
Alignment explanation
Indices: 12502462--12502514 Score: 97
Period size: 24 Copynumber: 2.2 Consensus size: 24
12502452 CCAACACTGT
12502462 TCTCCCTAATCAGCTCCTAAATCC
1 TCTCCCTAATCAGCTCCTAAATCC
*
12502486 TCTCCCTTATCAGCTCCTAAATCC
1 TCTCCCTAATCAGCTCCTAAATCC
12502510 TCTCC
1 TCTCC
12502515 TGACAGACTT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.21, C:0.43, G:0.04, T:0.32
Consensus pattern (24 bp):
TCTCCCTAATCAGCTCCTAAATCC
Found at i:12521995 original size:22 final size:22
Alignment explanation
Indices: 12521967--12522011 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
12521957 CATGTTTATT
12521967 CCCTCTTCAAGCTACTAAAGAA
1 CCCTCTTCAAGCTACTAAAGAA
12521989 CCCTCTTCAAGCTACTAAAGAA
1 CCCTCTTCAAGCTACTAAAGAA
12522011 C
1 C
12522012 ATTAAGAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.36, C:0.33, G:0.09, T:0.22
Consensus pattern (22 bp):
CCCTCTTCAAGCTACTAAAGAA
Found at i:12527464 original size:31 final size:31
Alignment explanation
Indices: 12527405--12527470 Score: 78
Period size: 31 Copynumber: 2.1 Consensus size: 31
12527395 CTTGTCACTT
*
12527405 GTAGCCGAAGCTACCACTATTCACTGATCAG
1 GTAGCCGAAGCTACCACTATTCACTGATCAA
* * * * *
12527436 GTAGCCGGAGCTACCATTTTTGATTGATCAA
1 GTAGCCGAAGCTACCACTATTCACTGATCAA
12527467 GTAG
1 GTAG
12527471 TCGATGATCA
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.27, C:0.23, G:0.23, T:0.27
Consensus pattern (31 bp):
GTAGCCGAAGCTACCACTATTCACTGATCAA
Found at i:12527509 original size:45 final size:46
Alignment explanation
Indices: 12527429--12527515 Score: 122
Period size: 45 Copynumber: 1.9 Consensus size: 46
12527419 CACTATTCAC
* * * *
12527429 TGATCAGGTAGCCGGAGCTACCATTTTTGATTGATCAAGTAGTCGA
1 TGATCAGGTAGCCGAAGCTACCACTTTTCACTGATCAAGTAGTCGA
*
12527475 TGATCAGGTA-CCGAAGCTACCACTTTTCACTGATCAGGTAG
1 TGATCAGGTAGCCGAAGCTACCACTTTTCACTGATCAAGTAG
12527516 CCGAAGCTAC
Statistics
Matches: 36, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
45 26 0.72
46 10 0.28
ACGTcount: A:0.26, C:0.21, G:0.24, T:0.29
Consensus pattern (46 bp):
TGATCAGGTAGCCGAAGCTACCACTTTTCACTGATCAAGTAGTCGA
Found at i:12527511 original size:30 final size:31
Alignment explanation
Indices: 12527475--12527532 Score: 109
Period size: 31 Copynumber: 1.9 Consensus size: 31
12527465 AAGTAGTCGA
12527475 TGATCAGGTA-CCGAAGCTACCACTTTTCAC
1 TGATCAGGTAGCCGAAGCTACCACTTTTCAC
12527505 TGATCAGGTAGCCGAAGCTACCACTTTT
1 TGATCAGGTAGCCGAAGCTACCACTTTT
12527533 TACTTGTCAT
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
30 10 0.37
31 17 0.63
ACGTcount: A:0.26, C:0.28, G:0.19, T:0.28
Consensus pattern (31 bp):
TGATCAGGTAGCCGAAGCTACCACTTTTCAC
Found at i:12527602 original size:50 final size:50
Alignment explanation
Indices: 12527512--12527688 Score: 273
Period size: 50 Copynumber: 3.5 Consensus size: 50
12527502 CACTGATCAG
* * * *
12527512 GTAGCCGAAGCTACCACTTTTTACTTGTCATTTGTCCTTGATCAGATAAGT
1 GTAGCCGAAGCTATCACTTATCACTT-TCATTTATCCTTGATCAGATAAGT
* *
12527563 GTAGCCGAAGCTATCTCTTATCACTTTCATTTTTCCTTGATCAGATAAGT
1 GTAGCCGAAGCTATCACTTATCACTTTCATTTATCCTTGATCAGATAAGT
* *
12527613 GTAGCCGAAGCTATCACTTATCACTTTCACTTATCTTTGATCAGATAAGT
1 GTAGCCGAAGCTATCACTTATCACTTTCATTTATCCTTGATCAGATAAGT
12527663 GTAGCCGAAGCTATCACTTATCACTT
1 GTAGCCGAAGCTATCACTTATCACTT
12527689 GTTGCCATGG
Statistics
Matches: 117, Mismatches: 9, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
50 95 0.81
51 22 0.19
ACGTcount: A:0.25, C:0.23, G:0.15, T:0.37
Consensus pattern (50 bp):
GTAGCCGAAGCTATCACTTATCACTTTCATTTATCCTTGATCAGATAAGT
Found at i:12531385 original size:23 final size:23
Alignment explanation
Indices: 12531354--12531412 Score: 109
Period size: 23 Copynumber: 2.5 Consensus size: 23
12531344 ATTTGTTTTG
12531354 TTTTGCACATTTTATACATCATCA
1 TTTT-CACATTTTATACATCATCA
12531378 TTTTCACATTTTATACATCATCA
1 TTTTCACATTTTATACATCATCA
12531401 TTTTCACATTTT
1 TTTTCACATTTT
12531413 GCCACTGCAT
Statistics
Matches: 35, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
23 31 0.89
24 4 0.11
ACGTcount: A:0.27, C:0.20, G:0.02, T:0.51
Consensus pattern (23 bp):
TTTTCACATTTTATACATCATCA
Found at i:12535791 original size:27 final size:27
Alignment explanation
Indices: 12535753--12535806 Score: 81
Period size: 27 Copynumber: 2.0 Consensus size: 27
12535743 GGTGAGAAGT
* * *
12535753 GTACTATCTACATAGGTTACAAGAGTC
1 GTACTATCTACACAGATCACAAGAGTC
12535780 GTACTATCTACACAGATCACAAGAGTC
1 GTACTATCTACACAGATCACAAGAGTC
12535807 TCAAATATCT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.35, C:0.22, G:0.17, T:0.26
Consensus pattern (27 bp):
GTACTATCTACACAGATCACAAGAGTC
Found at i:12541358 original size:13 final size:13
Alignment explanation
Indices: 12541342--12541373 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
12541332 ATAAGGGACA
12541342 CATGGCCGTGTCG
1 CATGGCCGTGTCG
12541355 CATGGCCGTGTCG
1 CATGGCCGTGTCG
*
12541368 TATGGC
1 CATGGC
12541374 TGGGTGTCAC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.09, C:0.28, G:0.38, T:0.25
Consensus pattern (13 bp):
CATGGCCGTGTCG
Found at i:12542960 original size:40 final size:39
Alignment explanation
Indices: 12542906--12543009 Score: 113
Period size: 39 Copynumber: 2.6 Consensus size: 39
12542896 CACACCAGAA
* * *
12542906 AGAAGCTCATAAGAGCTGATCCGACTGAAATA-TGC-CAAAC
1 AGAAACTCATAAGAGCTGATCC-AC-CAAAAACT-CTCAAAC
* *
12542946 AGAAACTCATAAGAGCTGGTCCACCAAAAACTCTCTAAC
1 AGAAACTCATAAGAGCTGATCCACCAAAAACTCTCAAAC
*
12542985 AGAAACTCATAAGAGTTGATCCACC
1 AGAAACTCATAAGAGCTGATCCACC
12543010 CGAAACACGC
Statistics
Matches: 55, Mismatches: 7, Indels: 5
0.82 0.10 0.07
Matches are distributed among these distances:
38 5 0.09
39 30 0.55
40 20 0.36
ACGTcount: A:0.40, C:0.25, G:0.16, T:0.18
Consensus pattern (39 bp):
AGAAACTCATAAGAGCTGATCCACCAAAAACTCTCAAAC
Found at i:12560977 original size:23 final size:23
Alignment explanation
Indices: 12560921--12560967 Score: 85
Period size: 23 Copynumber: 2.0 Consensus size: 23
12560911 TCGCTGAAAC
12560921 CACATGACCAAGAAATCCGACTT
1 CACATGACCAAGAAATCCGACTT
*
12560944 CACATGACCAAGAAATCTGACTT
1 CACATGACCAAGAAATCCGACTT
12560967 C
1 C
12560968 TTTGAGCCAA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.38, C:0.30, G:0.13, T:0.19
Consensus pattern (23 bp):
CACATGACCAAGAAATCCGACTT
Found at i:12564747 original size:154 final size:154
Alignment explanation
Indices: 12564549--12564859 Score: 622
Period size: 154 Copynumber: 2.0 Consensus size: 154
12564539 GGGATCGCTC
12564549 TAAATGCTAAACCGAAACCTTAATTTCCACTAACCTGCGCACGGAAACAACCGTACACTGAGTAT
1 TAAATGCTAAACCGAAACCTTAATTTCCACTAACCTGCGCACGGAAACAACCGTACACTGAGTAT
12564614 TTCATACTCAGTGGTATTACTATAATTCAAATTATTAACCAAGTAAATTAAATCATTTAACTTTA
66 TTCATACTCAGTGGTATTACTATAATTCAAATTATTAACCAAGTAAATTAAATCATTTAACTTTA
12564679 AAATTTACCAGACTAATTCATATA
131 AAATTTACCAGACTAATTCATATA
12564703 TAAATGCTAAACCGAAACCTTAATTTCCACTAACCTGCGCACGGAAACAACCGTACACTGAGTAT
1 TAAATGCTAAACCGAAACCTTAATTTCCACTAACCTGCGCACGGAAACAACCGTACACTGAGTAT
12564768 TTCATACTCAGTGGTATTACTATAATTCAAATTATTAACCAAGTAAATTAAATCATTTAACTTTA
66 TTCATACTCAGTGGTATTACTATAATTCAAATTATTAACCAAGTAAATTAAATCATTTAACTTTA
12564833 AAATTTACCAGACTAATTCATATA
131 AAATTTACCAGACTAATTCATATA
12564857 TAA
1 TAA
12564860 CTTCCATTTC
Statistics
Matches: 157, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
154 157 1.00
ACGTcount: A:0.40, C:0.20, G:0.09, T:0.31
Consensus pattern (154 bp):
TAAATGCTAAACCGAAACCTTAATTTCCACTAACCTGCGCACGGAAACAACCGTACACTGAGTAT
TTCATACTCAGTGGTATTACTATAATTCAAATTATTAACCAAGTAAATTAAATCATTTAACTTTA
AAATTTACCAGACTAATTCATATA
Found at i:12565009 original size:19 final size:20
Alignment explanation
Indices: 12564967--12565009 Score: 54
Period size: 19 Copynumber: 2.2 Consensus size: 20
12564957 TCATGCTTTC
* *
12564967 TATTCACATTTTCATATTCA
1 TATTCAAATTTTCATAATCA
12564987 -ATTCAAATTTTCA-AATCA
1 TATTCAAATTTTCATAATCA
12565005 TATTC
1 TATTC
12565010 CACATTCACG
Statistics
Matches: 20, Mismatches: 2, Indels: 3
0.80 0.08 0.12
Matches are distributed among these distances:
18 4 0.20
19 16 0.80
ACGTcount: A:0.35, C:0.19, G:0.00, T:0.47
Consensus pattern (20 bp):
TATTCAAATTTTCATAATCA
Found at i:12565435 original size:31 final size:32
Alignment explanation
Indices: 12565370--12565438 Score: 88
Period size: 33 Copynumber: 2.2 Consensus size: 32
12565360 ATCCATTTTC
*
12565370 TCAATTCAATATCACTTTCAATTCATTTACAAA
1 TCAATTCAATATCACTTT-AATTCATATACAAA
*
12565403 TCAATTCAATTTCACTTT-A-TCAATATACAAA
1 TCAATTCAATATCACTTTAATTC-ATATACAAA
12565434 TCAAT
1 TCAAT
12565439 ATTAATACTT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
30 2 0.06
31 14 0.42
33 17 0.52
ACGTcount: A:0.41, C:0.20, G:0.00, T:0.39
Consensus pattern (32 bp):
TCAATTCAATATCACTTTAATTCATATACAAA
Found at i:12566176 original size:16 final size:15
Alignment explanation
Indices: 12566146--12566184 Score: 55
Period size: 16 Copynumber: 2.7 Consensus size: 15
12566136 CCCCTTTCCT
12566146 TTCTTTCT-T-TTTC
1 TTCTTTCTCTGTTTC
12566159 TTCTGTTCTCTGTTTC
1 TTCT-TTCTCTGTTTC
12566175 TTCTTTCTCT
1 TTCTTTCTCT
12566185 CTTTTGTTTC
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
13 4 0.17
14 4 0.17
15 7 0.30
16 8 0.35
ACGTcount: A:0.00, C:0.26, G:0.05, T:0.69
Consensus pattern (15 bp):
TTCTTTCTCTGTTTC
Found at i:12566484 original size:21 final size:21
Alignment explanation
Indices: 12566449--12566489 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
12566439 TATTTATCTC
* *
12566449 ATAAATATTTTTTTAATAATA
1 ATAAATATCTATTTAATAATA
*
12566470 ATAAATATCTATTTACTAAT
1 ATAAATATCTATTTAATAAT
12566490 TAAATAAAAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.46, C:0.05, G:0.00, T:0.49
Consensus pattern (21 bp):
ATAAATATCTATTTAATAATA
Found at i:12567290 original size:21 final size:21
Alignment explanation
Indices: 12567264--12567308 Score: 90
Period size: 21 Copynumber: 2.1 Consensus size: 21
12567254 GTAATGTCAA
12567264 CATATCACCTATTCAAACTAT
1 CATATCACCTATTCAAACTAT
12567285 CATATCACCTATTCAAACTAT
1 CATATCACCTATTCAAACTAT
12567306 CAT
1 CAT
12567309 GCTTTCATAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.38, C:0.29, G:0.00, T:0.33
Consensus pattern (21 bp):
CATATCACCTATTCAAACTAT
Found at i:12568286 original size:20 final size:20
Alignment explanation
Indices: 12568261--12568330 Score: 59
Period size: 20 Copynumber: 3.3 Consensus size: 20
12568251 GTAACATATA
12568261 TCATGAACTCAGACCACAAC
1 TCATGAACTCAGACCACAAC
** * *
12568281 TCATGAGTTCAGATGTCACATATA
1 TCATGAACTCAGA--CCACA-A-C
*
12568305 TTATGAACTCAGACCACAAC
1 TCATGAACTCAGACCACAAC
12568325 TCATGA
1 TCATGA
12568331 GTTCAGCTCA
Statistics
Matches: 36, Mismatches: 10, Indels: 8
0.67 0.19 0.15
Matches are distributed among these distances:
20 16 0.44
21 1 0.03
22 8 0.22
23 1 0.03
24 10 0.28
ACGTcount: A:0.37, C:0.26, G:0.13, T:0.24
Consensus pattern (20 bp):
TCATGAACTCAGACCACAAC
Found at i:12571219 original size:26 final size:26
Alignment explanation
Indices: 12571188--12571295 Score: 189
Period size: 26 Copynumber: 4.2 Consensus size: 26
12571178 TGAAATGCCC
*
12571188 ATCATGGAACATTTACCTAAACCATT
1 ATCATGGAACATTTACCTAACCCATT
12571214 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
* *
12571240 ATCATGGAATATTTACCTAATCCATT
1 ATCATGGAACATTTACCTAACCCATT
12571266 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
12571292 ATCA
1 ATCA
12571296 ATTTGTACCA
Statistics
Matches: 77, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 77 1.00
ACGTcount: A:0.36, C:0.24, G:0.07, T:0.32
Consensus pattern (26 bp):
ATCATGGAACATTTACCTAACCCATT
Found at i:12575939 original size:12 final size:12
Alignment explanation
Indices: 12575922--12575951 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
12575912 GTACTACTTT
12575922 GGCCTCAACCAC
1 GGCCTCAACCAC
*
12575934 GGCCTCGACCAC
1 GGCCTCAACCAC
12575946 GGCCTC
1 GGCCTC
12575952 TTCCCCGAGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.17, C:0.50, G:0.23, T:0.10
Consensus pattern (12 bp):
GGCCTCAACCAC
Found at i:12579122 original size:32 final size:32
Alignment explanation
Indices: 12579085--12579146 Score: 115
Period size: 32 Copynumber: 1.9 Consensus size: 32
12579075 GCTTACCATG
12579085 CCCATCATCCATTAACTATTAAAATGCTAATA
1 CCCATCATCCATTAACTATTAAAATGCTAATA
*
12579117 CCCATCATCCATTAACTATTAAATTGCTAA
1 CCCATCATCCATTAACTATTAAAATGCTAA
12579147 AATGCATACA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.39, C:0.26, G:0.03, T:0.32
Consensus pattern (32 bp):
CCCATCATCCATTAACTATTAAAATGCTAATA
Found at i:12580070 original size:27 final size:28
Alignment explanation
Indices: 12580032--12580086 Score: 94
Period size: 27 Copynumber: 2.0 Consensus size: 28
12580022 CGAAGTTTCC
12580032 AAACATCAAGCATTGCCTTTTAT-TTTT
1 AAACATCAAGCATTGCCTTTTATATTTT
*
12580059 AAACATTAAGCATTGCCTTTTATATTTT
1 AAACATCAAGCATTGCCTTTTATATTTT
12580087 TTTTAAAAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
27 22 0.85
28 4 0.15
ACGTcount: A:0.31, C:0.16, G:0.07, T:0.45
Consensus pattern (28 bp):
AAACATCAAGCATTGCCTTTTATATTTT
Found at i:12580915 original size:22 final size:21
Alignment explanation
Indices: 12580885--12580950 Score: 64
Period size: 19 Copynumber: 3.2 Consensus size: 21
12580875 TACAAATTAA
12580885 ATCTCCAAGATTACAAGATCAT
1 ATCTCCAAGATTAC-AGATCAT
* * *
12580907 ATCTTCAAGATTGCATATCAT
1 ATCTCCAAGATTACAGATCAT
* *
12580928 ATCT--AAGATTGCATATCAT
1 ATCTCCAAGATTACAGATCAT
12580947 ATCT
1 ATCT
12580951 AAGATTGTAT
Statistics
Matches: 41, Mismatches: 3, Indels: 3
0.87 0.06 0.06
Matches are distributed among these distances:
19 19 0.46
21 10 0.24
22 12 0.29
ACGTcount: A:0.36, C:0.20, G:0.09, T:0.35
Consensus pattern (21 bp):
ATCTCCAAGATTACAGATCAT
Found at i:12580937 original size:19 final size:19
Alignment explanation
Indices: 12580902--12580999 Score: 128
Period size: 19 Copynumber: 5.2 Consensus size: 19
12580892 AGATTACAAG
12580902 ATCATATCTTCAAGATTGCAT
1 ATCATATC-T-AAGATTGCAT
12580923 ATCATATCTAAGATTGCAT
1 ATCATATCTAAGATTGCAT
12580942 ATCATATCTAAGATTG--T
1 ATCATATCTAAGATTGCAT
* *
12580959 ATCATATCTAATATCGCAT
1 ATCATATCTAAGATTGCAT
* *
12580978 ATCATATTTAAGATTTCAT
1 ATCATATCTAAGATTGCAT
12580997 ATC
1 ATC
12581000 CTTAAAGATT
Statistics
Matches: 69, Mismatches: 6, Indels: 6
0.85 0.07 0.07
Matches are distributed among these distances:
17 15 0.22
19 45 0.65
20 1 0.01
21 8 0.12
ACGTcount: A:0.36, C:0.16, G:0.08, T:0.40
Consensus pattern (19 bp):
ATCATATCTAAGATTGCAT
Found at i:12580966 original size:36 final size:37
Alignment explanation
Indices: 12580902--12580992 Score: 121
Period size: 36 Copynumber: 2.4 Consensus size: 37
12580892 AGATTACAAG
*
12580902 ATCATATCTTCAAGATTGCATATCATATCTAAGATTGCAT
1 ATCATATC-T-AAGATTG-ATATCATATCTAAGATCGCAT
*
12580942 ATCATATCTAAGATTG-TATCATATCTAATATCGCAT
1 ATCATATCTAAGATTGATATCATATCTAAGATCGCAT
*
12580978 ATCATATTTAAGATT
1 ATCATATCTAAGATT
12580993 TCATATCCTT
Statistics
Matches: 48, Mismatches: 3, Indels: 4
0.87 0.05 0.07
Matches are distributed among these distances:
36 32 0.67
38 7 0.15
39 1 0.02
40 8 0.17
ACGTcount: A:0.36, C:0.15, G:0.09, T:0.40
Consensus pattern (37 bp):
ATCATATCTAAGATTGATATCATATCTAAGATCGCAT
Found at i:12582075 original size:27 final size:27
Alignment explanation
Indices: 12582037--12582098 Score: 115
Period size: 27 Copynumber: 2.3 Consensus size: 27
12582027 CACAAGTTTT
12582037 ACAAATTATTCAATTTAGTCCCTAAAG
1 ACAAATTATTCAATTTAGTCCCTAAAG
12582064 ACAAATTATTCAATTTAGTCCCTAAAG
1 ACAAATTATTCAATTTAGTCCCTAAAG
*
12582091 TCAAATTA
1 ACAAATTA
12582099 CTGTTCTGAC
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 34 1.00
ACGTcount: A:0.42, C:0.18, G:0.06, T:0.34
Consensus pattern (27 bp):
ACAAATTATTCAATTTAGTCCCTAAAG
Found at i:12590228 original size:15 final size:15
Alignment explanation
Indices: 12590208--12590236 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
12590198 TTTATCAAAC
12590208 ATAATTTAAAATAAT
1 ATAATTTAAAATAAT
12590223 ATAATTTAAAATAA
1 ATAATTTAAAATAA
12590237 AACGATAGCT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (15 bp):
ATAATTTAAAATAAT
Found at i:12591260 original size:16 final size:16
Alignment explanation
Indices: 12591228--12591261 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
12591218 TTCTATTAAT
*
12591228 ATTTTTATGAGATAAC
1 ATTTTTATGAGAAAAC
*
12591244 ATTTTTATGATAAAAC
1 ATTTTTATGAGAAAAC
12591260 AT
1 AT
12591262 GCAAAGGAGA
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:0.41, C:0.06, G:0.09, T:0.44
Consensus pattern (16 bp):
ATTTTTATGAGAAAAC
Found at i:12593303 original size:29 final size:30
Alignment explanation
Indices: 12593264--12593329 Score: 93
Period size: 30 Copynumber: 2.3 Consensus size: 30
12593254 GGTATCTTTA
12593264 ATAAAAT-TTATAAATATA-ATTTTATT-TT
1 ATAAAATATTATAAATATATATTTT-TTGTT
*
12593292 ATAAAATATTATTAATATATATTTTTTGTT
1 ATAAAATATTATAAATATATATTTTTTGTT
12593322 ATAAAATA
1 ATAAAATA
12593330 AAAGACTGAG
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
28 7 0.21
29 12 0.35
30 15 0.44
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.52
Consensus pattern (30 bp):
ATAAAATATTATAAATATATATTTTTTGTT
Found at i:12596012 original size:39 final size:39
Alignment explanation
Indices: 12595958--12596037 Score: 151
Period size: 39 Copynumber: 2.1 Consensus size: 39
12595948 GACAGGTTGT
*
12595958 AGTAGCTATGGTGTCTCAGTCCATTAGTAAATTAGCTAA
1 AGTAGCTATGATGTCTCAGTCCATTAGTAAATTAGCTAA
12595997 AGTAGCTATGATGTCTCAGTCCATTAGTAAATTAGCTAA
1 AGTAGCTATGATGTCTCAGTCCATTAGTAAATTAGCTAA
12596036 AG
1 AG
12596038 ATCATGACAG
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
39 40 1.00
ACGTcount: A:0.33, C:0.15, G:0.20, T:0.33
Consensus pattern (39 bp):
AGTAGCTATGATGTCTCAGTCCATTAGTAAATTAGCTAA
Found at i:12614150 original size:24 final size:24
Alignment explanation
Indices: 12614122--12614173 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
12614112 TTTGTAGGTC
* *
12614122 AAATAAATTATGCTAATAAATGCT
1 AAATAAATTATACTAATAAATACT
*
12614146 AAATATATTATACTAATAAATACT
1 AAATAAATTATACTAATAAATACT
12614170 AAAT
1 AAAT
12614174 CCTCTAGAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.54, C:0.08, G:0.04, T:0.35
Consensus pattern (24 bp):
AAATAAATTATACTAATAAATACT
Found at i:12618006 original size:55 final size:56
Alignment explanation
Indices: 12617901--12618007 Score: 128
Period size: 55 Copynumber: 1.9 Consensus size: 56
12617891 TTAATTTGTA
* * * * *
12617901 TTGTATTAAATTTTTTCATCCATAATGTACTTATTCCAATTATATCAAAAAAGTTG
1 TTGTATTAAATTTTTACATCAATAATGTACTCATTACAATTATAACAAAAAAGTTG
* *
12617957 TTGTATTATA-TTTTACATCAATAATGTACTCATTTACAA-TATAAGAAAAAA
1 TTGTATTAAATTTTTACATCAATAATGTACTCA-TTACAATTATAACAAAAAA
12618008 ATTAAAAAAT
Statistics
Matches: 43, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
55 29 0.67
56 14 0.33
ACGTcount: A:0.40, C:0.11, G:0.07, T:0.42
Consensus pattern (56 bp):
TTGTATTAAATTTTTACATCAATAATGTACTCATTACAATTATAACAAAAAAGTTG
Done.