Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold285
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: 926752
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.34
File 3 of 6
Found at i:273640 original size:15 final size:15
Alignment explanation
Indices: 273615--273661 Score: 62
Period size: 15 Copynumber: 3.2 Consensus size: 15
273605 TTAAGTATTT
*
273615 TTATCATATAAAATA
1 TTATAATATAAAATA
273630 -TATATATATAAAATA
1 TTATA-ATATAAAATA
273645 TTATAATAT-AAATA
1 TTATAATATAAAATA
273659 TTA
1 TTA
273662 AAAATACGTT
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
14 11 0.38
15 14 0.48
16 4 0.14
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (15 bp):
TTATAATATAAAATA
Found at i:274491 original size:26 final size:26
Alignment explanation
Indices: 274444--274494 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
274434 AAATTATTTT
* *
274444 TTATTTTAAGTTACTTTCATTTTAAA
1 TTATTTTAAATTACATTCATTTTAAA
274470 TTATTTTAAATTCACATT-ATTTTAA
1 TTATTTTAAATT-ACATTCATTTTAA
274495 TTTTAAATTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
26 18 0.82
27 4 0.18
ACGTcount: A:0.33, C:0.08, G:0.02, T:0.57
Consensus pattern (26 bp):
TTATTTTAAATTACATTCATTTTAAA
Found at i:274515 original size:16 final size:16
Alignment explanation
Indices: 274424--274515 Score: 94
Period size: 16 Copynumber: 5.7 Consensus size: 16
274414 TTGAATTGTT
*
274424 TTTTATTTTTAAATTA
1 TTTTAATTTTAAATTA
* *
274440 TTTTTTATTTTAAGTTA
1 -TTTTAATTTTAAATTA
* *
274457 CTTTCATTTTAAATTA
1 TTTTAATTTTAAATTA
* * *
274473 TTTTAAATTCACATTA
1 TTTTAATTTTAAATTA
274489 TTTTAATTTTAAATTA
1 TTTTAATTTTAAATTA
*
274505 TTTTAAATTTA
1 TTTTAATTTTA
274516 TATCAATTAA
Statistics
Matches: 60, Mismatches: 15, Indels: 1
0.79 0.20 0.01
Matches are distributed among these distances:
16 47 0.78
17 13 0.22
ACGTcount: A:0.33, C:0.04, G:0.01, T:0.62
Consensus pattern (16 bp):
TTTTAATTTTAAATTA
Found at i:274914 original size:2 final size:2
Alignment explanation
Indices: 274907--274944 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
274897 CAAAAACATT
274907 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
274945 GAATACACTC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:275218 original size:34 final size:34
Alignment explanation
Indices: 275162--275379 Score: 278
Period size: 34 Copynumber: 6.4 Consensus size: 34
275152 TACGCTTCTT
*
275162 TTGTTGATTAAAT-GGTGATTTGGTAGTTTACCA
1 TTGTTGATTAAATGGGTGATTTGGTAGCTTACCA
* * * *
275195 TTATTGATTAAATGGGTGATTTGGTGGTTTGCCA
1 TTGTTGATTAAATGGGTGATTTGGTAGCTTACCA
* *
275229 TTGTTGACTAAATGGGAGATTTGGTAGCTTACCA
1 TTGTTGATTAAATGGGTGATTTGGTAGCTTACCA
* **
275263 TTGTTGATTAAATGAGAAATTTGGTAGCTTACCA
1 TTGTTGATTAAATGGGTGATTTGGTAGCTTACCA
* *
275297 TTATTGATTAAATGGGTGATTTGGTGGCTTACCA
1 TTGTTGATTAAATGGGTGATTTGGTAGCTTACCA
* * *
275331 TTGTTGACTAAAT-GGTAGATTTGGTAGGTTGCCA
1 TTGTTGATTAAATGGGT-GATTTGGTAGCTTACCA
275365 TTGTTGATTAAATGG
1 TTGTTGATTAAATGG
275380 TGGTTTTTAC
Statistics
Matches: 159, Mismatches: 23, Indels: 4
0.85 0.12 0.02
Matches are distributed among these distances:
33 15 0.09
34 143 0.90
35 1 0.01
ACGTcount: A:0.25, C:0.08, G:0.26, T:0.41
Consensus pattern (34 bp):
TTGTTGATTAAATGGGTGATTTGGTAGCTTACCA
Found at i:275295 original size:102 final size:101
Alignment explanation
Indices: 275162--275379 Score: 355
Period size: 102 Copynumber: 2.1 Consensus size: 101
275152 TACGCTTCTT
** * * *
275162 TTGTTGATTAAATGGTGATTTGGTAGTTTACCATTATTGATTAAATGGGTGATTTGGTGGTTTGC
1 TTGTTGATTAAATGGAAATTTGGTAGCTTACCATTATTGATTAAATGGGTGATTTGGTGGCTTAC
275227 CATTGTTGACTAAATGGGAGATTTGGTAGCTTACCA
66 CATTGTTGACTAAATGGGAGATTTGGTAGCTTACCA
275263 TTGTTGATTAAATGAGAAATTTGGTAGCTTACCATTATTGATTAAATGGGTGATTTGGTGGCTTA
1 TTGTTGATTAAATG-GAAATTTGGTAGCTTACCATTATTGATTAAATGGGTGATTTGGTGGCTTA
* * *
275328 CCATTGTTGACTAAATGGTAGATTTGGTAGGTTGCCA
65 CCATTGTTGACTAAATGGGAGATTTGGTAGCTTACCA
275365 TTGTTGATTAAATGG
1 TTGTTGATTAAATGG
275380 TGGTTTTTAC
Statistics
Matches: 108, Mismatches: 8, Indels: 2
0.92 0.07 0.02
Matches are distributed among these distances:
101 15 0.14
102 93 0.86
ACGTcount: A:0.25, C:0.08, G:0.26, T:0.41
Consensus pattern (101 bp):
TTGTTGATTAAATGGAAATTTGGTAGCTTACCATTATTGATTAAATGGGTGATTTGGTGGCTTAC
CATTGTTGACTAAATGGGAGATTTGGTAGCTTACCA
Found at i:275741 original size:19 final size:19
Alignment explanation
Indices: 275685--275747 Score: 90
Period size: 19 Copynumber: 3.3 Consensus size: 19
275675 TGGTTGTCGA
**
275685 GGTACTATTCACGTATATA
1 GGTACTATTCACGTATACG
275704 GGTACTATTCACGTATACG
1 GGTACTATTCACGTATACG
*
275723 GGTACTATTCAAGTATACG
1 GGTACTATTCACGTATACG
*
275742 GTTACT
1 GGTACT
275748 GTACACGTGA
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 40 1.00
ACGTcount: A:0.29, C:0.17, G:0.19, T:0.35
Consensus pattern (19 bp):
GGTACTATTCACGTATACG
Found at i:279870 original size:34 final size:34
Alignment explanation
Indices: 279813--280031 Score: 280
Period size: 34 Copynumber: 6.5 Consensus size: 34
279803 AAGTGGGAGA
*
279813 ATTGTTGATTAAAT-GGTGATTTGGTAGTTTACC
1 ATTGTTGATTAAATGGGTGATTTGGTAGCTTACC
* * * *
279846 ATTATTGATTAAATGGGTGATTTGGTGGTTTGCC
1 ATTGTTGATTAAATGGGTGATTTGGTAGCTTACC
* *
279880 ATTGTTGACTAAATGGGAGATTTGGTAGCTTACC
1 ATTGTTGATTAAATGGGTGATTTGGTAGCTTACC
* **
279914 ATTGTTGATTAAATGAGAAATTTGGTAGCTTACC
1 ATTGTTGATTAAATGGGTGATTTGGTAGCTTACC
* *
279948 ATTATTGATTAAATGGGTGATTTGGTGGCTTACC
1 ATTGTTGATTAAATGGGTGATTTGGTAGCTTACC
* * *
279982 ATTGTTGACTAAAT-GGTAGATTTGGTAGGTTGCC
1 ATTGTTGATTAAATGGGT-GATTTGGTAGCTTACC
280016 ATTGTTGATTAAATGG
1 ATTGTTGATTAAATGG
280032 TGGTTTTTAC
Statistics
Matches: 160, Mismatches: 23, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
33 16 0.10
34 143 0.89
35 1 0.01
ACGTcount: A:0.26, C:0.08, G:0.26, T:0.41
Consensus pattern (34 bp):
ATTGTTGATTAAATGGGTGATTTGGTAGCTTACC
Found at i:279953 original size:102 final size:101
Alignment explanation
Indices: 279813--280031 Score: 357
Period size: 102 Copynumber: 2.2 Consensus size: 101
279803 AAGTGGGAGA
** * * *
279813 ATTGTTGATTAAATGGTGATTTGGTAGTTTACCATTATTGATTAAATGGGTGATTTGGTGGTTTG
1 ATTGTTGATTAAATGGAAATTTGGTAGCTTACCATTATTGATTAAATGGGTGATTTGGTGGCTTA
279878 CCATTGTTGACTAAATGGGAGATTTGGTAGCTTACC
66 CCATTGTTGACTAAATGGGAGATTTGGTAGCTTACC
279914 ATTGTTGATTAAATGAGAAATTTGGTAGCTTACCATTATTGATTAAATGGGTGATTTGGTGGCTT
1 ATTGTTGATTAAATG-GAAATTTGGTAGCTTACCATTATTGATTAAATGGGTGATTTGGTGGCTT
* * *
279979 ACCATTGTTGACTAAATGGTAGATTTGGTAGGTTGCC
65 ACCATTGTTGACTAAATGGGAGATTTGGTAGCTTACC
280016 ATTGTTGATTAAATGG
1 ATTGTTGATTAAATGG
280032 TGGTTTTTAC
Statistics
Matches: 109, Mismatches: 8, Indels: 2
0.92 0.07 0.02
Matches are distributed among these distances:
101 16 0.15
102 93 0.85
ACGTcount: A:0.26, C:0.08, G:0.26, T:0.41
Consensus pattern (101 bp):
ATTGTTGATTAAATGGAAATTTGGTAGCTTACCATTATTGATTAAATGGGTGATTTGGTGGCTTA
CCATTGTTGACTAAATGGGAGATTTGGTAGCTTACC
Found at i:280438 original size:2 final size:2
Alignment explanation
Indices: 280426--280470 Score: 60
Period size: 2 Copynumber: 24.0 Consensus size: 2
280416 TTGTTTGTGT
*
280426 TA TA AA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -A T- TA T-
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
280465 TA TA TA
1 TA TA TA
280471 AACATGAGTT
Statistics
Matches: 38, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
1 3 0.08
2 35 0.92
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:283927 original size:35 final size:35
Alignment explanation
Indices: 283874--283942 Score: 104
Period size: 35 Copynumber: 2.0 Consensus size: 35
283864 TGTGGTTTGA
283874 TGATTCTTTCAAAAATAAGTACATCATAGTTTTCG
1 TGATTCTTTCAAAAATAAGTACATCATAGTTTTCG
* *
283909 TGATT-TTTGAAAAGATAAGTACATCATATTTTTC
1 TGATTCTTTCAAAA-ATAAGTACATCATAGTTTTC
283943 TATTGTGAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
34 7 0.23
35 24 0.77
ACGTcount: A:0.35, C:0.12, G:0.12, T:0.42
Consensus pattern (35 bp):
TGATTCTTTCAAAAATAAGTACATCATAGTTTTCG
Found at i:289698 original size:32 final size:32
Alignment explanation
Indices: 289643--289703 Score: 79
Period size: 31 Copynumber: 1.9 Consensus size: 32
289633 GAAAATTGAT
*
289643 AAAATAGTGAAATTTATTTTTTTA-ATTTTAA
1 AAAATAGTGAAATTTATTATTTTAGATTTTAA
* *
289674 AAAATATTTAAATATTATTATTTTAGATTT
1 AAAATAGTGAAAT-TTATTATTTTAGATTT
289704 ATCTCAGAGT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
31 11 0.44
32 10 0.40
33 4 0.16
ACGTcount: A:0.43, C:0.00, G:0.05, T:0.52
Consensus pattern (32 bp):
AAAATAGTGAAATTTATTATTTTAGATTTTAA
Found at i:291882 original size:38 final size:38
Alignment explanation
Indices: 291812--291980 Score: 160
Period size: 38 Copynumber: 4.5 Consensus size: 38
291802 ACAAGTTATG
* * * *
291812 AACAAAACCCACTATTTTAAATCGATGGCATGGTTCAA
1 AACAAAAACCACTATTCTAAATCGGTGACATGGTTCAA
* * **
291850 AACGAAAACCACTATTCTAAACCGGTGACATGGTTTGA
1 AACAAAAACCACTATTCTAAATCGGTGACATGGTTCAA
* * *
291888 AACAAAAATCACTATTTTAAA-CGGTGGCATGGTTCAA
1 AACAAAAACCACTATTCTAAATCGGTGACATGGTTCAA
* * * * * *
291925 TACAAAAACAACTATTCTTATTCGGTGACACGGTTCAT
1 AACAAAAACCACTATTCTAAATCGGTGACATGGTTCAA
* *
291963 TACAAAAACTACTATTCT
1 AACAAAAACCACTATTCT
291981 TATCTGGTGG
Statistics
Matches: 106, Mismatches: 24, Indels: 2
0.80 0.18 0.02
Matches are distributed among these distances:
37 28 0.26
38 78 0.74
ACGTcount: A:0.38, C:0.20, G:0.14, T:0.28
Consensus pattern (38 bp):
AACAAAAACCACTATTCTAAATCGGTGACATGGTTCAA
Found at i:292017 original size:76 final size:76
Alignment explanation
Indices: 291889--292073 Score: 230
Period size: 76 Copynumber: 2.4 Consensus size: 76
291879 ATGGTTTGAA
* * * * **
291889 ACAAAAATCACTATT-TTAAACGGTGGCATGGTTCAATACAAAAACAACTATTCTTATTCGGTGA
1 ACAAAAATCACTATTCTTAACCGGTGGTACGGTTCAATACAAAAACAACTATTCTTATCCAATGA
*
291953 CACGGTTCATT
66 CACGGTTCAAT
* * * * *
291964 ACAAAAA-CTACTATTCTTATCTGGTGGTACGGTTCATTACAAAAACCATTATTCTTATCCAATG
1 ACAAAAATC-ACTATTCTTAACCGGTGGTACGGTTCAATACAAAAACAACTATTCTTATCCAATG
292028 ACACGGTTCAAT
65 ACACGGTTCAAT
*
292040 ACAAAAATCACTATTTTTAACCGGTGGTACGGTT
1 ACAAAAATCACTATTCTTAACCGGTGGTACGGTT
292074 TGAAACCGAT
Statistics
Matches: 92, Mismatches: 15, Indels: 5
0.82 0.13 0.04
Matches are distributed among these distances:
74 1 0.01
75 13 0.14
76 77 0.84
77 1 0.01
ACGTcount: A:0.35, C:0.19, G:0.14, T:0.32
Consensus pattern (76 bp):
ACAAAAATCACTATTCTTAACCGGTGGTACGGTTCAATACAAAAACAACTATTCTTATCCAATGA
CACGGTTCAAT
Found at i:292072 original size:38 final size:37
Alignment explanation
Indices: 291837--292073 Score: 181
Period size: 38 Copynumber: 6.3 Consensus size: 37
291827 TTTAAATCGA
* * * * *
291837 TGGCATGGTTCAAAACGAAAACCACTATTCTAAACCGG
1 TGGCACGGTTCAATAC-AAAAACACTATTCTTATCCGG
* * * **
291875 TGACATGGTTTGAA-ACAAAAATCACTATT-TTAAACGG
1 TGGCACGG-TTCAATACAAAAA-CACTATTCTTATCCGG
* *
291912 TGGCATGGTTCAATACAAAAACAACTATTCTTATTCGG
1 TGGCACGGTTCAATACAAAAAC-ACTATTCTTATCCGG
* * *
291950 TGACACGGTTCATTACAAAAACTACTATTCTTATCTGG
1 TGGCACGGTTCAATACAAAAAC-ACTATTCTTATCCGG
* * * **
291988 TGGTACGGTTCATTACAAAAACCATTATTCTTATCCAA
1 TGGCACGGTTCAATACAAAAA-CACTATTCTTATCCGG
* * *
292026 TGACACGGTTCAATACAAAAATCACTATTTTTAACCGG
1 TGGCACGGTTCAATACAAAAA-CACTATTCTTATCCGG
*
292064 TGGTACGGTT
1 TGGCACGGTT
292074 TGAAACCGAT
Statistics
Matches: 161, Mismatches: 32, Indels: 12
0.79 0.16 0.06
Matches are distributed among these distances:
36 5 0.03
37 30 0.19
38 121 0.75
39 5 0.03
ACGTcount: A:0.35, C:0.19, G:0.16, T:0.30
Consensus pattern (37 bp):
TGGCACGGTTCAATACAAAAACACTATTCTTATCCGG
Found at i:297781 original size:36 final size:36
Alignment explanation
Indices: 297722--297810 Score: 110
Period size: 36 Copynumber: 2.5 Consensus size: 36
297712 ATTATAATGT
* *
297722 ATATATTAAAAATATATTAAATTATTTAAATTTTAAA
1 ATATAATAAAAATATATTAAATTA-TTAAATATTAAA
297759 ATATAATAAAAA-ATATTAAATTATTAAATATTAAA
1 ATATAATAAAAATATATTAAATTATTAAATATTAAA
* *
297794 TTTTTAA-AAAAATATAT
1 -ATATAATAAAAATATAT
297811 ATTTAAAAAA
Statistics
Matches: 46, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
35 16 0.35
36 19 0.41
37 11 0.24
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (36 bp):
ATATAATAAAAATATATTAAATTATTAAATATTAAA
Found at i:297789 original size:15 final size:15
Alignment explanation
Indices: 297769--297801 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
297759 ATATAATAAA
297769 AAATATTAAATTATT
1 AAATATTAAATTATT
*
297784 AAATATTAAATTTTT
1 AAATATTAAATTATT
297799 AAA
1 AAA
297802 AAAATATATA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (15 bp):
AAATATTAAATTATT
Found at i:297831 original size:13 final size:14
Alignment explanation
Indices: 297797--297842 Score: 58
Period size: 13 Copynumber: 3.3 Consensus size: 14
297787 TATTAAATTT
297797 TTAAAAAAATATATA
1 TTAAAAAAATA-ATA
*
297812 TTTAAAAAATAA-A
1 TTAAAAAAATAATA
*
297825 TTAAAAAATTAATA
1 TTAAAAAAATAATA
297839 TTAA
1 TTAA
297843 CGAGTCTGAA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
13 11 0.41
14 6 0.22
15 10 0.37
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (14 bp):
TTAAAAAAATAATA
Found at i:300880 original size:2 final size:2
Alignment explanation
Indices: 300873--300911 Score: 60
Period size: 2 Copynumber: 19.5 Consensus size: 2
300863 TTTTCATTGT
* *
300873 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TG TA TA AA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
300912 TGAGACAATG
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (2 bp):
TA
Found at i:303241 original size:25 final size:24
Alignment explanation
Indices: 303197--303244 Score: 78
Period size: 25 Copynumber: 2.0 Consensus size: 24
303187 TTCGGTTCCC
*
303197 ATTATATTTAATAATTTATATTTT
1 ATTATATTTAATAATATATATTTT
303221 ATTATATTATAATAATATATATTT
1 ATTATATT-TAATAATATATATTT
303245 ATAAAAATTT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
24 8 0.36
25 14 0.64
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (24 bp):
ATTATATTTAATAATATATATTTT
Found at i:303258 original size:25 final size:25
Alignment explanation
Indices: 303203--303259 Score: 62
Period size: 25 Copynumber: 2.3 Consensus size: 25
303193 TCCCATTATA
* * *
303203 TTTAATAATTTATATTTTATTATAT
1 TTTAATAATATATATTTTATAAAAT
*
303228 TATAATAATATATA-TTTATAAAAAT
1 TTTAATAATATATATTTTAT-AAAAT
303253 TTTAATA
1 TTTAATA
303260 TATTAATAAT
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
24 5 0.19
25 21 0.81
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (25 bp):
TTTAATAATATATATTTTATAAAAT
Found at i:303286 original size:32 final size:33
Alignment explanation
Indices: 303216--303283 Score: 82
Period size: 33 Copynumber: 2.0 Consensus size: 33
303206 AATAATTTAT
*
303216 ATTTTATTATATTATAATAATATATATTTATAAAA
1 ATTTTAATATA-T-TAATAATATATATTTATAAAA
* *
303251 ATTTTAATATATTAATAATTTTTATTATATAAA
1 ATTTTAATATATTAATAATATATATT-TATAAA
303284 TTTAAAAATA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
33 12 0.41
34 7 0.24
35 10 0.34
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (33 bp):
ATTTTAATATATTAATAATATATATTTATAAAA
Found at i:304472 original size:22 final size:21
Alignment explanation
Indices: 304422--304472 Score: 52
Period size: 22 Copynumber: 2.3 Consensus size: 21
304412 TTATGTAAAT
304422 AAATTAATATATTAATAATAA
1 AAATTAATATATTAATAATAA
304443 AAATTTAATGATA-TAATTTAAT-A
1 AAA-TTAAT-ATATTAA--TAATAA
304466 AAATTAA
1 AAATTAA
304473 AATTTTATGA
Statistics
Matches: 26, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
21 3 0.12
22 12 0.46
23 7 0.27
24 4 0.15
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (21 bp):
AAATTAATATATTAATAATAA
Found at i:308810 original size:36 final size:37
Alignment explanation
Indices: 308766--308845 Score: 96
Period size: 36 Copynumber: 2.2 Consensus size: 37
308756 ATTATATATA
* *
308766 AATT-TAATA-ATTTTAA-ATATGATATAATAAAAAAT
1 AATTATAATATATTATAATATATAATATAAT-AAAAAT
*
308801 AATTATAATATATTATAATATATAATTTAATAAAAAT
1 AATTATAATATATTATAATATATAATATAATAAAAAT
308838 -ATTATAAT
1 AATTATAAT
308846 TTATACATAT
Statistics
Matches: 39, Mismatches: 3, Indels: 5
0.83 0.06 0.11
Matches are distributed among these distances:
35 4 0.10
36 13 0.33
37 12 0.31
38 10 0.26
ACGTcount: A:0.56, C:0.00, G:0.01, T:0.42
Consensus pattern (37 bp):
AATTATAATATATTATAATATATAATATAATAAAAAT
Found at i:308818 original size:23 final size:22
Alignment explanation
Indices: 308787--308832 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 22
308777 TTTAAATATG
308787 ATATAATAAAAAATAATTATAAT
1 ATATAATAAAAAATAATT-TAAT
* * *
308810 ATATTATAATATATAATTTAAT
1 ATATAATAAAAAATAATTTAAT
308832 A
1 A
308833 AAAATATTAT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
22 5 0.25
23 15 0.75
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (22 bp):
ATATAATAAAAAATAATTTAAT
Found at i:309871 original size:17 final size:18
Alignment explanation
Indices: 309836--309875 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
309826 ACTTAGATTT
*
309836 TTTATATTTTATAAAATA
1 TTTATATTTAATAAAATA
*
309854 TTTATATTTAAT-ATATA
1 TTTATATTTAATAAAATA
309871 TTTAT
1 TTTAT
309876 TATACATTAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 9 0.45
18 11 0.55
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (18 bp):
TTTATATTTAATAAAATA
Found at i:310858 original size:5 final size:5
Alignment explanation
Indices: 310850--310886 Score: 56
Period size: 5 Copynumber: 7.4 Consensus size: 5
310840 TTTTAAACAC
* *
310850 AATTT AATTT AATTT AAATT AATTT AATTA AATTT AA
1 AATTT AATTT AATTT AATTT AATTT AATTT AATTT AA
310887 ATTATTATTT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
5 28 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (5 bp):
AATTT
Found at i:310875 original size:20 final size:20
Alignment explanation
Indices: 310850--310890 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
310840 TTTTAAACAC
*
310850 AATTTAATTTAATTTAAATT
1 AATTTAATTAAATTTAAATT
310870 AATTTAATTAAATTTAAATT
1 AATTTAATTAAATTTAAATT
310890 A
1 A
310891 TTATTTAATA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (20 bp):
AATTTAATTAAATTTAAATT
Found at i:311997 original size:5 final size:5
Alignment explanation
Indices: 311987--312050 Score: 55
Period size: 5 Copynumber: 13.2 Consensus size: 5
311977 CATATTTAAA
* *
311987 TATAT TATAT TATAC T-TAT TATAT TAT-T TAATAT T-TAT TA-AA TATAT
1 TATAT TATAT TATAT TATAT TATAT TATAT T-ATAT TATAT TATAT TATAT
*
312034 TATATT TAAAT TATAT T
1 TATA-T TATAT TATAT T
312051 TTATATCATA
Statistics
Matches: 47, Mismatches: 6, Indels: 12
0.72 0.09 0.18
Matches are distributed among these distances:
4 12 0.26
5 29 0.62
6 6 0.13
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.58
Consensus pattern (5 bp):
TATAT
Found at i:312011 original size:19 final size:19
Alignment explanation
Indices: 311987--312037 Score: 61
Period size: 19 Copynumber: 2.7 Consensus size: 19
311977 CATATTTAAA
311987 TATATTATATTATACTTAT
1 TATATTATATTATACTTAT
*
312006 TATATTAT-TTAATATTTAT
1 TATATTATATT-ATACTTAT
*
312025 TA-AATATATTATA
1 TATATTATATTATA
312038 TTTAAATTAT
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
18 9 0.32
19 19 0.68
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (19 bp):
TATATTATATTATACTTAT
Found at i:312039 original size:14 final size:14
Alignment explanation
Indices: 311982--312050 Score: 61
Period size: 14 Copynumber: 4.8 Consensus size: 14
311972 TAAATCATAT
311982 TTAAATATATTATA
1 TTAAATATATTATA
*
311996 TTATACT-TATTATA
1 TTA-AATATATTATA
**
312010 TTATTTAATATT-TA
1 TTAAAT-ATATTATA
312024 TTAAATATATTATA
1 TTAAATATATTATA
312038 TTTAAATTATATT
1 -TTAAA-TATATT
312051 TTATATCATA
Statistics
Matches: 44, Mismatches: 5, Indels: 10
0.75 0.08 0.17
Matches are distributed among these distances:
13 6 0.14
14 21 0.48
15 11 0.25
16 6 0.14
ACGTcount: A:0.42, C:0.01, G:0.00, T:0.57
Consensus pattern (14 bp):
TTAAATATATTATA
Found at i:312967 original size:2 final size:2
Alignment explanation
Indices: 312960--312985 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
312950 AAGAGCCACA
312960 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
312986 TGTAAATTTC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:313484 original size:2 final size:2
Alignment explanation
Indices: 313477--313510 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
313467 GTATGACTTC
313477 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
313511 ATCTATATAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:316020 original size:20 final size:20
Alignment explanation
Indices: 315985--316037 Score: 61
Period size: 20 Copynumber: 2.5 Consensus size: 20
315975 ACATAAAAGC
*
315985 TAAATATATATAAAAATTATAA
1 TAAA-ATAT-TAAAAAATATAA
*
316007 TAAAATATTAAAAAATATAT
1 TAAAATATTAAAAAATATAA
*
316027 TAAACTATTAA
1 TAAAATATTAA
316038 TATTTTAAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
20 20 0.71
21 4 0.14
22 4 0.14
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (20 bp):
TAAAATATTAAAAAATATAA
Found at i:316030 original size:12 final size:11
Alignment explanation
Indices: 315986--316026 Score: 50
Period size: 11 Copynumber: 3.7 Consensus size: 11
315976 CATAAAAGCT
315986 AAATATATATAA
1 AAATATATA-AA
315998 AAAT-TATAATA
1 AAATATATAA-A
316009 AAATAT-TAAA
1 AAATATATAAA
316019 AAATATAT
1 AAATATAT
316027 TAAACTATTA
Statistics
Matches: 26, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
10 8 0.31
11 13 0.50
12 5 0.19
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (11 bp):
AAATATATAAA
Found at i:318127 original size:13 final size:14
Alignment explanation
Indices: 318105--318136 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
318095 TTGCTTGACC
318105 AAAT-TAAAATTA-
1 AAATATAAAATTAT
318117 AAATATAAAATTAT
1 AAATATAAAATTAT
318131 AAATAT
1 AAATAT
318137 TTTTAAGAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 4 0.22
13 8 0.44
14 6 0.33
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (14 bp):
AAATATAAAATTAT
Found at i:318225 original size:11 final size:12
Alignment explanation
Indices: 318208--318248 Score: 50
Period size: 11 Copynumber: 3.5 Consensus size: 12
318198 AGAGATTTTC
318208 ATATATTTTATTT
1 ATAT-TTTTATTT
*
318221 ATATTTTTAATT
1 ATATTTTTATTT
318233 A-ATTTTTATTT
1 ATATTTTTATTT
318244 -TATTT
1 ATATTT
318249 AAAAATATCT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
11 13 0.52
12 8 0.32
13 4 0.16
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (12 bp):
ATATTTTTATTT
Found at i:319349 original size:13 final size:12
Alignment explanation
Indices: 319293--319380 Score: 58
Period size: 11 Copynumber: 7.5 Consensus size: 12
319283 AATTTATTTT
319293 AAAT-TTATT-A
1 AAATATTATTAA
* *
319303 AAATTTTGTTAA
1 AAATATTATTAA
*
319315 TAATATT-TTAA
1 AAATATTATTAA
* *
319326 ATATAGT-TTAA
1 AAATATTATTAA
*
319337 ATATATTAGTTAA
1 AAATATTA-TTAA
*
319350 AAATATTATTAC
1 AAATATTATTAA
*
319362 ATATAATTATTAA
1 AAAT-ATTATTAA
319375 AAATAT
1 AAATAT
319381 ATTTTTAGAT
Statistics
Matches: 61, Mismatches: 12, Indels: 8
0.75 0.15 0.10
Matches are distributed among these distances:
10 4 0.07
11 22 0.36
12 14 0.23
13 21 0.34
ACGTcount: A:0.49, C:0.01, G:0.03, T:0.47
Consensus pattern (12 bp):
AAATATTATTAA
Found at i:319354 original size:26 final size:26
Alignment explanation
Indices: 319324--319382 Score: 70
Period size: 25 Copynumber: 2.3 Consensus size: 26
319314 ATAATATTTT
319324 AAATATAGT-TTAAATAT-ATTAGTTAA
1 AAATATA-TATTAAATATAATTA-TTAA
*
319350 AAATAT-TATTACATATAATTATTAA
1 AAATATATATTAAATATAATTATTAA
319375 AAATATAT
1 AAATATAT
319383 TTTTAGATTA
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
24 1 0.03
25 17 0.59
26 11 0.38
ACGTcount: A:0.53, C:0.02, G:0.03, T:0.42
Consensus pattern (26 bp):
AAATATATATTAAATATAATTATTAA
Found at i:320345 original size:16 final size:16
Alignment explanation
Indices: 320292--320385 Score: 107
Period size: 16 Copynumber: 5.7 Consensus size: 16
320282 TGAATTCGAG
320292 TTAAATTATTTTAAATTT
1 TTAAATTATTTT-AA-TT
*
320310 TTAAATTATTTTTATGT
1 TTAAATTATTTTAAT-T
* * *
320327 TTATATTGTTTTGATT
1 TTAAATTATTTTAATT
*
320343 TTAAATTATTTTAAAT
1 TTAAATTATTTTAATT
320359 TTAAATTATTTTAATT
1 TTAAATTATTTTAATT
*
320375 TTAAATAATTT
1 TTAAATTATTT
320386 AAAATTTTTT
Statistics
Matches: 65, Mismatches: 10, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
16 39 0.60
17 14 0.22
18 12 0.18
ACGTcount: A:0.35, C:0.00, G:0.03, T:0.62
Consensus pattern (16 bp):
TTAAATTATTTTAATT
Found at i:320405 original size:25 final size:25
Alignment explanation
Indices: 320356--320405 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
320346 AATTATTTTA
* *
320356 AATTTAAATTATTTTAATTTTAAAT
1 AATTTAAATTATTTTAAATTAAAAT
320381 AATTTAAAATT-TTTTAAATTAAAAT
1 AATTT-AAATTATTTTAAATTAAAAT
320406 CAAAATTAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
25 17 0.77
26 5 0.23
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (25 bp):
AATTTAAATTATTTTAAATTAAAAT
Found at i:323640 original size:2 final size:2
Alignment explanation
Indices: 323635--323662 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
323625 ACACACACAC
323635 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
323663 CTCTCTCTCT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:323667 original size:2 final size:2
Alignment explanation
Indices: 323662--323686 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
323652 TATATATATA
323662 TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC T
323687 TTTCTGGTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:327866 original size:2 final size:2
Alignment explanation
Indices: 327859--327885 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
327849 TCTTTTACTT
327859 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
327886 GATCAACATC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:328327 original size:17 final size:16
Alignment explanation
Indices: 328295--328331 Score: 58
Period size: 15 Copynumber: 2.4 Consensus size: 16
328285 ATGATATAAG
328295 AAAATAATATAAATAT
1 AAAATAATATAAATAT
328311 AAAATAA-ATAAATAT
1 AAAATAATATAAATAT
*
328326 ATAATA
1 AAAATA
328332 TTTTTTACAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
15 13 0.65
16 7 0.35
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (16 bp):
AAAATAATATAAATAT
Found at i:328676 original size:3 final size:3
Alignment explanation
Indices: 328668--328697 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
328658 AAAATAAAAA
328668 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
328698 TGTTTCTAGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:338325 original size:3 final size:3
Alignment explanation
Indices: 338319--338359 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
338309 TTTCTATCTT
338319 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
338360 TTGCAATGAT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:360065 original size:2 final size:2
Alignment explanation
Indices: 360058--360087 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
360048 AGGGAAACAA
360058 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
360088 CATTGTACTC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:360287 original size:2 final size:2
Alignment explanation
Indices: 360280--360307 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
360270 GGTGGATTGG
360280 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
360308 TGGTATGAGG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:362015 original size:21 final size:21
Alignment explanation
Indices: 361989--362029 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
361979 TATTGTTAAA
361989 TTTTATAAATAATAATTATAT
1 TTTTATAAATAATAATTATAT
362010 TTTTATAAATAATAATTATA
1 TTTTATAAATAATAATTATA
362030 AATAATAATT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (21 bp):
TTTTATAAATAATAATTATAT
Found at i:362030 original size:13 final size:13
Alignment explanation
Indices: 362012--362040 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
362002 AATTATATTT
362012 TTATAAATAATAA
1 TTATAAATAATAA
362025 TTATAAATAATAA
1 TTATAAATAATAA
362038 TTA
1 TTA
362041 AAGAGGATTG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (13 bp):
TTATAAATAATAA
Found at i:362485 original size:19 final size:18
Alignment explanation
Indices: 362463--362503 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
362453 TATTTAAATA
362463 TTAATATTAAATTAATTTT
1 TTAATATTAAA-TAATTTT
**
362482 TTAATATTTTATAATTTT
1 TTAATATTAAATAATTTT
362500 TTAA
1 TTAA
362504 ACAATGATCC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 11 0.55
19 9 0.45
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (18 bp):
TTAATATTAAATAATTTT
Found at i:363230 original size:5 final size:5
Alignment explanation
Indices: 363220--363246 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
363210 TATTAATAAA
363220 TAATT TAATT TAATT TAATT TAATT TA
1 TAATT TAATT TAATT TAATT TAATT TA
363247 TTTGATCTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (5 bp):
TAATT
Found at i:363737 original size:13 final size:12
Alignment explanation
Indices: 363721--363761 Score: 57
Period size: 11 Copynumber: 3.4 Consensus size: 12
363711 AAATGTGCAT
363721 AATAAATTTGAAA
1 AATAAATTT-AAA
*
363734 AATAAATTTTAA
1 AATAAATTTAAA
363746 AA-AAATTTAAA
1 AATAAATTTAAA
363757 AATAA
1 AATAA
363762 TAAAATTTTA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
11 10 0.40
12 6 0.24
13 9 0.36
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.32
Consensus pattern (12 bp):
AATAAATTTAAA
Found at i:363808 original size:34 final size:36
Alignment explanation
Indices: 363741--363811 Score: 92
Period size: 37 Copynumber: 2.0 Consensus size: 36
363731 AAAAATAAAT
*
363741 TTTAAAAAAATTTAAAAATAATAAAATTTTAATTTTA
1 TTTAAAAAAATTTAAAAAT-ATAAAATTATAATTTTA
* *
363778 TTTAAAAATATTTATAAAT-T-AAATTATAATTTTA
1 TTTAAAAAAATTTAAAAATATAAAATTATAATTTTA
363812 AATTTTAAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
34 13 0.42
35 1 0.03
37 17 0.55
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (36 bp):
TTTAAAAAAATTTAAAAATATAAAATTATAATTTTA
Found at i:363913 original size:22 final size:21
Alignment explanation
Indices: 363886--363927 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
363876 AAAATAAAAA
363886 ATAT-TTTTAT-ATTAATATTT
1 ATATATTTTATAATTAA-ATTT
363906 ATATATTTTATAATTAAATTT
1 ATATATTTTATAATTAAATTT
363927 A
1 A
363928 AATAAAAATT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
20 4 0.20
21 11 0.55
22 5 0.25
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (21 bp):
ATATATTTTATAATTAAATTT
Found at i:363948 original size:13 final size:14
Alignment explanation
Indices: 363930--363961 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
363920 TAAATTTAAA
*
363930 TAAAAATTTTATTT
1 TAAAAATATTATTT
363944 TAAAAATATTATTT
1 TAAAAATATTATTT
363958 TAAA
1 TAAA
363962 CTTAACTAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (14 bp):
TAAAAATATTATTT
Found at i:365610 original size:24 final size:24
Alignment explanation
Indices: 365574--365637 Score: 67
Period size: 24 Copynumber: 2.6 Consensus size: 24
365564 GTGGTTATTT
* *
365574 TTGTTTGTAAAAATAGGTGGCTTA
1 TTGTTTATAAAAATAGGTGGCTAA
* *
365598 TTGTTTATCAAAATTGGTGGCTAA
1 TTGTTTATAAAAATAGGTGGCTAA
365622 TT-TTTATTAGAAAATA
1 TTGTTTA-TA-AAAATA
365638 TGAGAGGATA
Statistics
Matches: 32, Mismatches: 6, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
23 4 0.12
24 23 0.72
25 5 0.16
ACGTcount: A:0.33, C:0.05, G:0.19, T:0.44
Consensus pattern (24 bp):
TTGTTTATAAAAATAGGTGGCTAA
Found at i:368275 original size:21 final size:22
Alignment explanation
Indices: 368246--368291 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 22
368236 TGTTCAGATA
** *
368246 AGTAGTACTCCGCAGCAGGTGG
1 AGTAGTACTCCAAAACAGGTGG
368268 AGTA-TACTCCAAAACAGGTGG
1 AGTAGTACTCCAAAACAGGTGG
368289 AGT
1 AGT
368292 TTCAATAGAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 17 0.81
22 4 0.19
ACGTcount: A:0.30, C:0.20, G:0.30, T:0.20
Consensus pattern (22 bp):
AGTAGTACTCCAAAACAGGTGG
Found at i:386769 original size:26 final size:26
Alignment explanation
Indices: 386731--386797 Score: 91
Period size: 26 Copynumber: 2.6 Consensus size: 26
386721 GTCAAAGATG
*
386731 AAGATTCAATGTTGTGTGTAA-TATGA
1 AAGATTCAATGTTGTGTCTAAGT-TGA
* *
386757 AAGTTTCGATGTTGTGTCTAAGTTGA
1 AAGATTCAATGTTGTGTCTAAGTTGA
386783 AAGATTCAATGTTGT
1 AAGATTCAATGTTGT
386798 ACTTTAAATA
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
26 34 0.97
27 1 0.03
ACGTcount: A:0.30, C:0.06, G:0.24, T:0.40
Consensus pattern (26 bp):
AAGATTCAATGTTGTGTCTAAGTTGA
Found at i:389835 original size:2 final size:2
Alignment explanation
Indices: 389828--389874 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
389818 TGAAATAGAT
389828 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
389870 TA TA T
1 TA TA T
389875 TTGAGAATAG
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:393480 original size:2 final size:2
Alignment explanation
Indices: 393418--393461 Score: 79
Period size: 2 Copynumber: 22.0 Consensus size: 2
393408 TTGAGAGACG
*
393418 GA GA GA GT GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
393460 GA
1 GA
393462 ATTTGAGAAT
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.48, C:0.00, G:0.50, T:0.02
Consensus pattern (2 bp):
GA
Found at i:393770 original size:12 final size:13
Alignment explanation
Indices: 393738--393770 Score: 52
Period size: 12 Copynumber: 2.7 Consensus size: 13
393728 AATTAAAATA
393738 TTATTAT-ATATT
1 TTATTATAATATT
393750 TTATTATAATATT
1 TTATTATAATATT
393763 TT-TTATAA
1 TTATTATAA
393771 AAAATTTATA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
12 13 0.65
13 7 0.35
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (13 bp):
TTATTATAATATT
Found at i:395431 original size:21 final size:21
Alignment explanation
Indices: 395407--395460 Score: 74
Period size: 21 Copynumber: 2.6 Consensus size: 21
395397 TAATGTGTGA
395407 AATTAATTTAATTATATGTTG
1 AATTAATTTAATTATATGTTG
* * *
395428 AATTTATTTAGTTATATTTTG
1 AATTAATTTAATTATATGTTG
395449 -ATTAATTTAATT
1 AATTAATTTAATT
395461 TGAGTAATTA
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
20 10 0.36
21 18 0.64
ACGTcount: A:0.35, C:0.00, G:0.07, T:0.57
Consensus pattern (21 bp):
AATTAATTTAATTATATGTTG
Found at i:395651 original size:3 final size:3
Alignment explanation
Indices: 395645--395676 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
395635 AAAAAAAAAA
*
395645 AAT AAT AAT AAT AAT AAT AAC AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
395677 ATAGAAAGGA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.69, C:0.03, G:0.00, T:0.28
Consensus pattern (3 bp):
AAT
Found at i:396262 original size:13 final size:13
Alignment explanation
Indices: 396246--396270 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
396236 AGCCAACTTC
396246 AATAGTTTGAACA
1 AATAGTTTGAACA
396259 AATAGTTTGAAC
1 AATAGTTTGAAC
396271 GAATTGCAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.44, C:0.08, G:0.16, T:0.32
Consensus pattern (13 bp):
AATAGTTTGAACA
Found at i:396331 original size:13 final size:13
Alignment explanation
Indices: 396313--396337 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
396303 TACAGCTGGA
396313 ATTATTATAATTT
1 ATTATTATAATTT
396326 ATTATTATAATT
1 ATTATTATAATT
396338 ATCAAAAATT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (13 bp):
ATTATTATAATTT
Found at i:396941 original size:3 final size:3
Alignment explanation
Indices: 396935--396982 Score: 87
Period size: 3 Copynumber: 16.0 Consensus size: 3
396925 ATTAAGAGAC
*
396935 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAG TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
396983 AGGGAAAAAA
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 43 1.00
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:397815 original size:10 final size:10
Alignment explanation
Indices: 397786--397819 Score: 52
Period size: 10 Copynumber: 3.5 Consensus size: 10
397776 ATAGATGAAC
397786 ATAAATTAAT
1 ATAAATTAAT
*
397796 AT-AATCAAT
1 ATAAATTAAT
397805 ATAAATTAAT
1 ATAAATTAAT
397815 ATAAA
1 ATAAA
397820 AATTAATATT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
9 8 0.38
10 13 0.62
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.35
Consensus pattern (10 bp):
ATAAATTAAT
Found at i:397818 original size:29 final size:29
Alignment explanation
Indices: 397744--397828 Score: 71
Period size: 30 Copynumber: 2.8 Consensus size: 29
397734 ATGTAGATTG
* * * * *
397744 ATATATATTGATATTAATTAATAATGATCT
1 ATATAAATTAATATAAATTAAT-ATAATCA
* * *
397774 ATATAGATGAACATAAATTAATATAATCA
1 ATATAAATTAATATAAATTAATATAATCA
397803 ATATAAATTAATATAAAAATTAATAT
1 ATATAAATTAATAT--AAATTAATAT
397829 TATACGATAT
Statistics
Matches: 43, Mismatches: 10, Indels: 3
0.77 0.18 0.05
Matches are distributed among these distances:
29 16 0.37
30 17 0.40
31 10 0.23
ACGTcount: A:0.53, C:0.04, G:0.05, T:0.39
Consensus pattern (29 bp):
ATATAAATTAATATAAATTAATATAATCA
Found at i:402510 original size:109 final size:109
Alignment explanation
Indices: 402319--402536 Score: 391
Period size: 109 Copynumber: 2.0 Consensus size: 109
402309 TGAGAGCAAG
* *
402319 TGTTTTTTTTTTTTTTTTCCTTTCGCAGGATGGATAGCGAGTTTATTTACATATTAACAAATATC
1 TGTTTTTTTTTTTTTTTTCCTTGCGCAGGATGGATAGCAAGTTTATTTACATATTAACAAATATC
402384 ATGAAAAGGTGATATACCTCACACCGTAGAGCTTCATCAAGCTC
66 ATGAAAAGGTGATATACCTCACACCGTAGAGCTTCATCAAGCTC
402428 TGTTTTTTTTTTTTTTTTCCTTGCGCAGGATGGATAGCAAGTTTATTTACATATTAACAAATATC
1 TGTTTTTTTTTTTTTTTTCCTTGCGCAGGATGGATAGCAAGTTTATTTACATATTAACAAATATC
* * *
402493 ATGACAAGGTGATATACCTCACGCTGTAGAGCTTCATCAAGCTC
66 ATGAAAAGGTGATATACCTCACACCGTAGAGCTTCATCAAGCTC
402537 CTGCTTATCG
Statistics
Matches: 104, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
109 104 1.00
ACGTcount: A:0.27, C:0.17, G:0.16, T:0.39
Consensus pattern (109 bp):
TGTTTTTTTTTTTTTTTTCCTTGCGCAGGATGGATAGCAAGTTTATTTACATATTAACAAATATC
ATGAAAAGGTGATATACCTCACACCGTAGAGCTTCATCAAGCTC
Found at i:405566 original size:14 final size:14
Alignment explanation
Indices: 405549--405575 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
405539 ATTATTATTT
405549 TTAAAAAATATATC
1 TTAAAAAATATATC
405563 TTAAAAAATATAT
1 TTAAAAAATATAT
405576 ACCTACTACT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.59, C:0.04, G:0.00, T:0.37
Consensus pattern (14 bp):
TTAAAAAATATATC
Found at i:406241 original size:30 final size:30
Alignment explanation
Indices: 406207--406266 Score: 111
Period size: 30 Copynumber: 2.0 Consensus size: 30
406197 TGTCGGTGAG
*
406207 TTAATTATGATAAATATTTATGGACATTGT
1 TTAATTATGACAAATATTTATGGACATTGT
406237 TTAATTATGACAAATATTTATGGACATTGT
1 TTAATTATGACAAATATTTATGGACATTGT
406267 CATGTAAGGT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.37, C:0.05, G:0.13, T:0.45
Consensus pattern (30 bp):
TTAATTATGACAAATATTTATGGACATTGT
Found at i:406369 original size:32 final size:32
Alignment explanation
Indices: 406308--406369 Score: 79
Period size: 32 Copynumber: 1.9 Consensus size: 32
406298 TGGTTCAATT
* ** * *
406308 AAAATAATTTTAATGATTTTTTTATTATTTAA
1 AAAATAATTTTAATAATTAATTAAGTATTTAA
406340 AAAATAATTTTAATAATTAATTAAGTATTT
1 AAAATAATTTTAATAATTAATTAAGTATTT
406370 TTTATTTTTT
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
32 25 1.00
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (32 bp):
AAAATAATTTTAATAATTAATTAAGTATTTAA
Found at i:406386 original size:3 final size:3
Alignment explanation
Indices: 406378--406423 Score: 92
Period size: 3 Copynumber: 15.3 Consensus size: 3
406368 TTTTTATTTT
406378 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
406424 GCTTGAATTA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 43 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:406799 original size:18 final size:18
Alignment explanation
Indices: 406776--406824 Score: 64
Period size: 18 Copynumber: 2.8 Consensus size: 18
406766 CGATTAATCG
406776 ATTAAATTAATTAAATTT
1 ATTAAATTAATTAAATTT
* *
406794 ATTAAATTTATTTAATTT
1 ATTAAATTAATTAAATTT
*
406812 -TAAAATTAATTAA
1 ATTAAATTAATTAA
406825 TTATAAAAAT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
17 10 0.38
18 16 0.62
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (18 bp):
ATTAAATTAATTAAATTT
Found at i:406813 original size:10 final size:9
Alignment explanation
Indices: 406776--406824 Score: 55
Period size: 9 Copynumber: 5.6 Consensus size: 9
406766 CGATTAATCG
*
406776 ATTAAATTA
1 ATTAAATTT
406785 ATTAAATTT
1 ATTAAATTT
406794 ATTAAATTT
1 ATTAAATTT
*
406803 ATTTAATTT
1 ATTAAATTT
* *
406812 -TAAAATTA
1 ATTAAATTT
406820 ATTAA
1 ATTAA
406825 TTATAAAAAT
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
8 5 0.15
9 28 0.85
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (9 bp):
ATTAAATTT
Found at i:406824 original size:16 final size:16
Alignment explanation
Indices: 406779--406838 Score: 57
Period size: 16 Copynumber: 3.6 Consensus size: 16
406769 TTAATCGATT
406779 AAATTAATTAAATTTATTA
1 AAATTAATT-AA-TT-TTA
* *
406798 AATTTATTTAATTTTA
1 AAATTAATTAATTTTA
*
406814 AAATTAATTAATTATA
1 AAATTAATTAATTTTA
*
406830 AAAATAATT
1 AAATTAATT
406839 TATTCAATTA
Statistics
Matches: 35, Mismatches: 6, Indels: 3
0.80 0.14 0.07
Matches are distributed among these distances:
16 24 0.69
17 2 0.06
18 2 0.06
19 7 0.20
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (16 bp):
AAATTAATTAATTTTA
Found at i:409695 original size:17 final size:18
Alignment explanation
Indices: 409669--409715 Score: 55
Period size: 17 Copynumber: 2.8 Consensus size: 18
409659 GTATTTCAAT
409669 TTTAAA-TTTATATT-CA
1 TTTAAATTTTATATTACA
*
409685 TTTAAATTTTATGTTACA
1 TTTAAATTTTATATTACA
*
409703 TTT-ATTTTTATAT
1 TTTAAATTTTATAT
409716 GATTAATATA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
16 6 0.23
17 15 0.58
18 5 0.19
ACGTcount: A:0.32, C:0.04, G:0.02, T:0.62
Consensus pattern (18 bp):
TTTAAATTTTATATTACA
Found at i:412649 original size:2 final size:2
Alignment explanation
Indices: 412642--412673 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
412632 GAAAACATCT
412642 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
412674 ACATTGATAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:413155 original size:19 final size:20
Alignment explanation
Indices: 413131--413171 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
413121 ATAAGAATCT
413131 TTTTAAA-TTTTT-TTTATTA
1 TTTTAAAGTTTTTATTT-TTA
413150 TTTTAAAGTTTTTATTTTTA
1 TTTTAAAGTTTTTATTTTTA
413170 TT
1 TT
413172 AAATTTAATT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
19 7 0.35
20 10 0.50
21 3 0.15
ACGTcount: A:0.24, C:0.00, G:0.02, T:0.73
Consensus pattern (20 bp):
TTTTAAAGTTTTTATTTTTA
Found at i:420188 original size:15 final size:14
Alignment explanation
Indices: 420162--420210 Score: 55
Period size: 15 Copynumber: 3.4 Consensus size: 14
420152 TTATTATTAT
420162 TATTTGTTAATATAAA
1 TATTT-TTAATAT-AA
420178 TATTTTTAATATTAA
1 TATTTTTAATA-TAA
*
420193 TATTTATAAT-TAA
1 TATTTTTAATATAA
420206 TATTT
1 TATTT
420211 ATTATAATTA
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
13 8 0.26
15 17 0.55
16 6 0.19
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (14 bp):
TATTTTTAATATAA
Found at i:420204 original size:13 final size:13
Alignment explanation
Indices: 420139--420212 Score: 51
Period size: 13 Copynumber: 5.3 Consensus size: 13
420129 TAAATAGTAA
420139 TTATAATGTAATA-
1 TTATAAT-TAATAT
* *
420152 TTATTATTATTAT
1 TTATAATTAATAT
*
420165 TTGTTAATATAAATAT
1 TT-ATAAT-T-AATAT
*
420181 TTTTAATATTAATAT
1 TTAT-A-ATTAATAT
420196 TTATAATTAATAT
1 TTATAATTAATAT
420209 TTAT
1 TTAT
420213 TATAATTAAT
Statistics
Matches: 49, Mismatches: 6, Indels: 12
0.73 0.09 0.18
Matches are distributed among these distances:
12 4 0.08
13 20 0.41
14 4 0.08
15 11 0.22
16 8 0.16
17 2 0.04
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.57
Consensus pattern (13 bp):
TTATAATTAATAT
Found at i:420218 original size:25 final size:25
Alignment explanation
Indices: 420196--420272 Score: 75
Period size: 25 Copynumber: 3.0 Consensus size: 25
420186 ATATTAATAT
420196 TTATAATTAATATTTATTATAATTAA
1 TTATAA-TAATATTTATTATAATTAA
* *
420222 TTATTATAATATTTATTATATTTGTAA
1 TTATAATAATATTTATTATA-AT-TAA
* * *
420249 TTATACTAA-ATATAATATAATTAA
1 TTATAATAATATTTATTATAATTAA
420273 AAATATAGTT
Statistics
Matches: 42, Mismatches: 7, Indels: 6
0.76 0.13 0.11
Matches are distributed among these distances:
24 3 0.07
25 15 0.36
26 14 0.33
27 10 0.24
ACGTcount: A:0.45, C:0.01, G:0.01, T:0.52
Consensus pattern (25 bp):
TTATAATAATATTTATTATAATTAA
Found at i:423137 original size:14 final size:14
Alignment explanation
Indices: 423120--423162 Score: 50
Period size: 14 Copynumber: 3.0 Consensus size: 14
423110 TTATAATTTT
423120 TTTATTTTTTAATA
1 TTTATTTTTTAATA
* *
423134 TTTATATTTTAAAAA
1 TTTAT-TTTTTAATA
*
423149 TTTAATTTTTAATA
1 TTTATTTTTTAATA
423163 ATTTTTAATT
Statistics
Matches: 23, Mismatches: 5, Indels: 2
0.77 0.17 0.07
Matches are distributed among these distances:
14 12 0.52
15 11 0.48
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (14 bp):
TTTATTTTTTAATA
Found at i:423315 original size:15 final size:13
Alignment explanation
Indices: 423289--423317 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
423279 AATATCAATT
423289 ATATAATTAAATA
1 ATATAATTAAATA
423302 ATATAATTAAA-A
1 ATATAATTAAATA
423314 ATAT
1 ATAT
423318 TTTATAATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 5 0.31
13 11 0.69
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (13 bp):
ATATAATTAAATA
Found at i:423384 original size:31 final size:31
Alignment explanation
Indices: 423349--423413 Score: 78
Period size: 31 Copynumber: 2.1 Consensus size: 31
423339 GTTTGGTCCG
*
423349 TTTATAAAT-AAGTTTAATTTTTTTATCTAAA
1 TTTATAAATGAA-TTTAATTATTTTATCTAAA
***
423380 TTTATTTTTGAATTTAATTATTTTATCTAAA
1 TTTATAAATGAATTTAATTATTTTATCTAAA
423411 TTT
1 TTT
423414 TTTAAAATAT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
31 27 0.93
32 2 0.07
ACGTcount: A:0.34, C:0.03, G:0.03, T:0.60
Consensus pattern (31 bp):
TTTATAAATGAATTTAATTATTTTATCTAAA
Found at i:423434 original size:31 final size:31
Alignment explanation
Indices: 423369--423434 Score: 73
Period size: 31 Copynumber: 2.1 Consensus size: 31
423359 AGTTTAATTT
** *
423369 TTTTATCTAAATTTATTTTTGAATTTAATTA
1 TTTTATCTAAATTTATTTTAAAATTTAATAA
423400 TTTTATCTAAA-TT-TTTTAAAATATTAAATAA
1 TTTTATCTAAATTTATTTTAAAAT-TT-AATAA
423431 TTTT
1 TTTT
423435 TAAATTTAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
29 7 0.23
30 4 0.13
31 19 0.63
ACGTcount: A:0.36, C:0.03, G:0.02, T:0.59
Consensus pattern (31 bp):
TTTTATCTAAATTTATTTTAAAATTTAATAA
Found at i:423443 original size:17 final size:19
Alignment explanation
Indices: 423412--423447 Score: 58
Period size: 17 Copynumber: 2.0 Consensus size: 19
423402 TTATCTAAAT
423412 TTTTTAAAATATTAAATAA
1 TTTTTAAAATATTAAATAA
423431 TTTTT-AAAT-TTAAATAA
1 TTTTTAAAATATTAAATAA
423448 ATAACTCGAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 8 0.47
18 4 0.24
19 5 0.29
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (19 bp):
TTTTTAAAATATTAAATAA
Found at i:424163 original size:13 final size:13
Alignment explanation
Indices: 424145--424170 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
424135 TACTATTTTT
424145 AATTTTTTTTAAA
1 AATTTTTTTTAAA
424158 AATTTTTTTTAAA
1 AATTTTTTTTAAA
424171 GTTAGATAAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (13 bp):
AATTTTTTTTAAA
Found at i:424868 original size:9 final size:10
Alignment explanation
Indices: 424848--424882 Score: 54
Period size: 10 Copynumber: 3.6 Consensus size: 10
424838 AAATATAAAA
*
424848 TTAAATTAAT
1 TTAAATTATT
424858 TTAAATTATT
1 TTAAATTATT
424868 TTAAA-TATT
1 TTAAATTATT
424877 TTAAAT
1 TTAAAT
424883 AATCAAATTT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
9 9 0.39
10 14 0.61
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (10 bp):
TTAAATTATT
Found at i:428063 original size:2 final size:2
Alignment explanation
Indices: 428056--428086 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
428046 TTAATAAATC
428056 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
428087 CACCAATAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:430978 original size:2 final size:2
Alignment explanation
Indices: 430971--431015 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
430961 AGAATATGCA
430971 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
431013 AT A
1 AT A
431016 AAAGGAGAGA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:431220 original size:2 final size:2
Alignment explanation
Indices: 431215--431267 Score: 83
Period size: 2 Copynumber: 27.0 Consensus size: 2
431205 CACACATCTT
431215 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TCA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T-A TA
431257 TA T- TA TA TA TA
1 TA TA TA TA TA TA
431268 AAATATTTAT
Statistics
Matches: 48, Mismatches: 0, Indels: 6
0.89 0.00 0.11
Matches are distributed among these distances:
1 2 0.04
2 45 0.94
3 1 0.02
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:433000 original size:28 final size:27
Alignment explanation
Indices: 432959--433012 Score: 72
Period size: 28 Copynumber: 2.0 Consensus size: 27
432949 TATATTATTA
*
432959 TTTTGATTTTATTTAATATTGTAATAAT
1 TTTTGATTTAATTTAA-ATTGTAATAAT
* *
432987 TTTTTATTTAATTTAAATTTTAATAA
1 TTTTGATTTAATTTAAATTGTAATAA
433013 ATGTAAAATG
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
27 9 0.39
28 14 0.61
ACGTcount: A:0.35, C:0.00, G:0.04, T:0.61
Consensus pattern (27 bp):
TTTTGATTTAATTTAAATTGTAATAAT
Found at i:434318 original size:2 final size:2
Alignment explanation
Indices: 434313--434341 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
434303 TAAGTGTGTG
434313 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
434342 CACTTTTAGT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:436096 original size:23 final size:24
Alignment explanation
Indices: 436065--436109 Score: 58
Period size: 23 Copynumber: 1.9 Consensus size: 24
436055 ATAAAAAGCT
*
436065 CTTCATCTC-CTTCCTTCCTTCCTC
1 CTTCATCTCGC-TCCCTCCTTCCTC
436089 CTTC-TCTCGCTCCCTCCTTCC
1 CTTCATCTCGCTCCCTCCTTCC
436110 CTTCATTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
23 14 0.74
24 5 0.26
ACGTcount: A:0.02, C:0.53, G:0.02, T:0.42
Consensus pattern (24 bp):
CTTCATCTCGCTCCCTCCTTCCTC
Found at i:438061 original size:21 final size:20
Alignment explanation
Indices: 438020--438063 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 20
438010 CATTATTAAA
* *
438020 ATTTTTAAAGATGATTTTTT
1 ATTTTTAAAGATAATTATTT
*
438040 ATTTTGTAGAGATAATTATTT
1 ATTTT-TAAAGATAATTATTT
438061 ATT
1 ATT
438064 ATCTTTAATT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
20 5 0.25
21 15 0.75
ACGTcount: A:0.32, C:0.00, G:0.11, T:0.57
Consensus pattern (20 bp):
ATTTTTAAAGATAATTATTT
Found at i:454659 original size:22 final size:22
Alignment explanation
Indices: 454629--454670 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
454619 AATTTATTAA
* *
454629 ATATTAATTTATAAAATTAATT
1 ATATAAATTAATAAAATTAATT
*
454651 ATATAAATTAATTAAATTAA
1 ATATAAATTAATAAAATTAA
454671 AATTAAAATT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (22 bp):
ATATAAATTAATAAAATTAATT
Found at i:454664 original size:13 final size:14
Alignment explanation
Indices: 454622--454676 Score: 62
Period size: 13 Copynumber: 4.0 Consensus size: 14
454612 AAATTAAAAT
454622 TTAT-TAAATATTAA
1 TTATATAAA-ATTAA
454636 TT-TATAAAATTAA
1 TTATATAAAATTAA
454649 TTATAT-AAATTAA
1 TTATATAAAATTAA
*
454662 TTAAATTAAAATTAA
1 TTATA-TAAAATTAA
454677 AATTTATTTT
Statistics
Matches: 36, Mismatches: 1, Indels: 7
0.82 0.02 0.16
Matches are distributed among these distances:
13 19 0.53
14 10 0.28
15 7 0.19
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (14 bp):
TTATATAAAATTAA
Found at i:454671 original size:28 final size:26
Alignment explanation
Indices: 454612--454676 Score: 71
Period size: 24 Copynumber: 2.5 Consensus size: 26
454602 AGATACTTTA
* *
454612 AAATTAAAATTTATTAAATATTAATT
1 AAATTAAAATTAATTAAAAATTAATT
*
454638 -TA-TAAAATTAATTATATAAATTAATT
1 AAATTAAAATTAATTA-A-AAATTAATT
454664 AAATTAAAATTAA
1 AAATTAAAATTAA
454677 AATTTATTTT
Statistics
Matches: 31, Mismatches: 4, Indels: 6
0.76 0.10 0.15
Matches are distributed among these distances:
24 11 0.35
25 2 0.06
26 8 0.26
27 1 0.03
28 9 0.29
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (26 bp):
AAATTAAAATTAATTAAAAATTAATT
Found at i:459224 original size:21 final size:21
Alignment explanation
Indices: 459198--459238 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
459188 GTGTTGGTTG
459198 TTAAAATCATATCGTAATTTA
1 TTAAAATCATATCGTAATTTA
459219 TTAAAATCATATCGTAATTT
1 TTAAAATCATATCGTAATTT
459239 TAAATTTTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.41, C:0.10, G:0.05, T:0.44
Consensus pattern (21 bp):
TTAAAATCATATCGTAATTTA
Found at i:459299 original size:23 final size:23
Alignment explanation
Indices: 459255--459303 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 23
459245 TTTTATTTAG
459255 ATTTAAATTTTAATTAATATAAA
1 ATTTAAATTTTAATTAATATAAA
* *
459278 ATTTATATTATTATTTAA-ATAAA
1 ATTTAAATT-TTAATTAATATAAA
459301 ATT
1 ATT
459304 AAAAATTATT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
23 16 0.70
24 7 0.30
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (23 bp):
ATTTAAATTTTAATTAATATAAA
Found at i:461047 original size:13 final size:12
Alignment explanation
Indices: 460998--461043 Score: 56
Period size: 12 Copynumber: 3.6 Consensus size: 12
460988 ACCTTCACTG
460998 TTTCAAATTGAA
1 TTTCAAATTGAA
*
461010 TTTCAACATTTACTA
1 TTTCAA-ATTGA--A
461025 TTTCAAATTGAA
1 TTTCAAATTGAA
461037 TTTCAAA
1 TTTCAAA
461044 ATTGGCGGCA
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
12 14 0.48
13 4 0.14
14 4 0.14
15 7 0.24
ACGTcount: A:0.39, C:0.13, G:0.04, T:0.43
Consensus pattern (12 bp):
TTTCAAATTGAA
Found at i:465067 original size:79 final size:79
Alignment explanation
Indices: 464956--465162 Score: 245
Period size: 79 Copynumber: 2.6 Consensus size: 79
464946 GAGATAATAA
* * * * * * *
464956 CGGGGTTGGAGTGTTCCCTTGAAAATAACGGGGCTGGAGTATCCCCGGTTGTGAGAAATCGATGA
1 CGGGGTTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCGATTATGAGAAATCAAT-A
*
465021 -TTAGAAAAAAAAAT
65 TTTAGAAAAAAAAAC
* *
465035 CGGGATTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCAATTATGAGAAATCAATAT
1 CGGGGTTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCGATTATGAGAAATCAATAT
* ** * *
465100 TTTGGGAATAAAGC
66 TTAGAAAAAAAAAC
* *
465114 CGGGGTTGGAGTATCCCCTCGGAAGTAACGGGGTTGGAGTATCCCCGAT
1 CGGGGTTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCGAT
465163 GAAATAACAA
Statistics
Matches: 108, Mismatches: 19, Indels: 2
0.84 0.15 0.02
Matches are distributed among these distances:
78 1 0.01
79 107 0.99
ACGTcount: A:0.29, C:0.17, G:0.30, T:0.24
Consensus pattern (79 bp):
CGGGGTTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCGATTATGAGAAATCAATAT
TTAGAAAAAAAAAC
Found at i:465170 original size:28 final size:28
Alignment explanation
Indices: 465114--465185 Score: 90
Period size: 28 Copynumber: 2.6 Consensus size: 28
465104 GGAATAAAGC
** *
465114 CGGGGTTGGAGTATCCCCTCGGAAGTAA
1 CGGGGTTGGAGTATCCCCGAGGAAATAA
*
465142 CGGGGTTGGAGTATCCCCGATGAAATAA
1 CGGGGTTGGAGTATCCCCGAGGAAATAA
**
465170 CAAGGTTGGAGTATCC
1 CGGGGTTGGAGTATCC
465186 TCGACTGTGA
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 38 1.00
ACGTcount: A:0.25, C:0.19, G:0.33, T:0.22
Consensus pattern (28 bp):
CGGGGTTGGAGTATCCCCGAGGAAATAA
Found at i:465303 original size:52 final size:51
Alignment explanation
Indices: 465173--465561 Score: 234
Period size: 52 Copynumber: 7.4 Consensus size: 51
465163 GAAATAACAA
* * * * *
465173 GGTTGGAGTATCCTCGACTGTGAAAAATTGGTATTTTTGGAAATAAAATCGA
1 GGTTGGAGTATCCCCGATTGTGAAAAATTGGT-GTTTTGAAAATAAAATCGG
* ** * *
465225 AGTTGGAGTATCCCCGATTAAAGAAAAATTGGTGTTTCGAAAATAAAACCGG
1 GGTTGGAGTATCCCCGATT-GTGAAAAATTGGTGTTTTGAAAATAAAATCGG
* * * *
465277 GGTTGGAGTATCCCCGATTGTGGAAAATTTAGTGTTTT-AGCAATAAAACCGG
1 GGTTGGAGTATCCCCGATTGT-GAAAAATTGGTGTTTTGA-AAATAAAATCGG
* * * *** * ** *
465329 GATTGGAATATCCCCGATTATGAAAAATCAATATTTTGGGAATAAAGTCGG
1 GGTTGGAGTATCCCCGATTGTGAAAAATTGGTGTTTTGAAAATAAAATCGG
* * ** ** *
465380 GGTTGGAGTATCCCC--TCG-GAAATAACGGGGTTGGAGTATCCCCGATGAT-CAA-CGG
1 GGTTGGAGTATCCCCGATTGTGAAA-AA-----TTGGTGT-T--TTGAAAATAAAATCGG
*
465435 GGTTGGAGTATCCCCGATTGTGAAGAAATTGGTGTTTTTTGGAAATAAAATCGG
1 GGTTGGAGTATCCCCGATTGTGAA-AAATTGGTG--TTTTGAAAATAAAATCGG
* * * *
465489 AGTTGGAGTATCCCCGATTAT-AGAAAATTAGTGTCTTGAAAATAAAATCGG
1 GGTTGGAGTATCCCCGATTGTGA-AAAATTGGTGTTTTGAAAATAAAATCGG
* *
465540 AGTTGGAATATCCCCGATTGTG
1 GGTTGGAGTATCCCCGATTGTG
465562 GAGAATTGAG
Statistics
Matches: 255, Mismatches: 59, Indels: 46
0.71 0.16 0.13
Matches are distributed among these distances:
48 4 0.02
49 3 0.01
51 70 0.27
52 93 0.36
53 27 0.11
54 26 0.10
55 20 0.08
56 1 0.00
57 5 0.02
58 5 0.02
59 1 0.00
ACGTcount: A:0.32, C:0.13, G:0.26, T:0.29
Consensus pattern (51 bp):
GGTTGGAGTATCCCCGATTGTGAAAAATTGGTGTTTTGAAAATAAAATCGG
Found at i:465386 original size:51 final size:52
Alignment explanation
Indices: 465266--465394 Score: 152
Period size: 51 Copynumber: 2.5 Consensus size: 52
465256 GTGTTTCGAA
* * * * *
465266 AATAAAACCGGGGTTGGAGTATCCCCGATTGTGGAAAATTTAGTGTTTTAGC
1 AATAAAACCGGGGTTGGAGTATCCCCGATTATGGAAAAATCAATATTTTAGC
* * * *
465318 AATAAAACCGGGATTGGAATATCCCCGATTAT-GAAAAATCAATATTTTGGG
1 AATAAAACCGGGGTTGGAGTATCCCCGATTATGGAAAAATCAATATTTTAGC
**
465369 AATAAAGTCGGGGTTGGAGTATCCCC
1 AATAAAACCGGGGTTGGAGTATCCCC
465395 TCGGAAATAA
Statistics
Matches: 64, Mismatches: 13, Indels: 1
0.82 0.17 0.01
Matches are distributed among these distances:
51 35 0.55
52 29 0.45
ACGTcount: A:0.33, C:0.15, G:0.25, T:0.28
Consensus pattern (52 bp):
AATAAAACCGGGGTTGGAGTATCCCCGATTATGGAAAAATCAATATTTTAGC
Found at i:465441 original size:27 final size:26
Alignment explanation
Indices: 465377--465452 Score: 100
Period size: 27 Copynumber: 2.8 Consensus size: 26
465367 GGAATAAAGT
465377 CGGGGTTGGAGTATCCCCTCGGA-AATAA
1 CGGGGTTGGAGTAT-CCC-C-GATAATAA
*
465405 CGGGGTTGGAGTATCCCCGATGATCAA
1 CGGGGTTGGAGTATCCCCGATAAT-AA
465432 CGGGGTTGGAGTATCCCCGAT
1 CGGGGTTGGAGTATCCCCGAT
465453 TGTGAAGAAA
Statistics
Matches: 45, Mismatches: 1, Indels: 5
0.88 0.02 0.10
Matches are distributed among these distances:
25 2 0.04
26 3 0.07
27 26 0.58
28 14 0.31
ACGTcount: A:0.21, C:0.22, G:0.34, T:0.22
Consensus pattern (26 bp):
CGGGGTTGGAGTATCCCCGATAATAA
Found at i:465554 original size:263 final size:262
Alignment explanation
Indices: 465063--465568 Score: 784
Period size: 263 Copynumber: 1.9 Consensus size: 262
465053 TCGAAAATAA
* * *
465063 CGGGGTTGGAGTATCCCCAATTATGAGAAATCAATATTTTGGGAATAAAGCCGGGGTTGGAGTAT
1 CGGGATTGGAATATCCCCAATTATGAAAAATCAATATTTTGGGAATAAAGCCGGGGTTGGAGTAT
* *
465128 CCCCTCGGAAGTAACGGGGTTGGAGTATCCCCGATGAAATAACAAGGTTGGAGTATCCTCGACTG
66 CCCCTCGGAAATAACGGGGTTGGAGTATCCCCGATG-AATAACAAGGTTGGAGTATCCCCGACTG
*
465193 TGAAAAATTGGTATTTTTGGAAATAAAATCGAAGTTGGAGTATCCCCGATTAAAGAAAAATTGGT
130 TGAAAAATTGGTATTTTTGGAAATAAAATCGAAGTTGGAGTATCCCCGATTAAAGAAAAATTAGT
* *
465258 GTTTCGAAAATAAAACCGGGGTTGGAGTATCCCCGATTGTGGAAAATTTAGTGTTTTAGCAATAA
195 GTTTCGAAAATAAAACCGGAGTTGGAATATCCCCGATTGTGGAAAATTTAGTGTTTTAGCAATAA
465323 AAC
260 AAC
* *
465326 CGGGATTGGAATATCCCCGATTATGAAAAATCAATATTTTGGGAATAAAGTCGGGGTTGGAGTAT
1 CGGGATTGGAATATCCCCAATTATGAAAAATCAATATTTTGGGAATAAAGCCGGGGTTGGAGTAT
** *
465391 CCCCTCGGAAATAACGGGGTTGGAGTATCCCCGATG-ATCAACGGGGTTGGAGTATCCCCGATTG
66 CCCCTCGGAAATAACGGGGTTGGAGTATCCCCGATGAAT-AACAAGGTTGGAGTATCCCCGACTG
* * *
465455 TGAAGAAATTGGTGTTTTTTGGAAATAAAATCGGAGTTGGAGTATCCCCGATTATAG-AAAATTA
130 TGAA-AAATTGGT-ATTTTTGGAAATAAAATCGAAGTTGGAGTATCCCCGATTAAAGAAAAATTA
* *
465519 GTGTCTT-GAAAATAAAATCGGAGTTGGAATATCCCCGATTGTGGAGAATT
193 GTGT-TTCGAAAATAAAACCGGAGTTGGAATATCCCCGATTGTGGAAAATT
465569 GAGAAACTCA
Statistics
Matches: 221, Mismatches: 18, Indels: 8
0.89 0.07 0.03
Matches are distributed among these distances:
261 2 0.01
262 25 0.11
263 152 0.69
264 42 0.19
ACGTcount: A:0.31, C:0.14, G:0.27, T:0.28
Consensus pattern (262 bp):
CGGGATTGGAATATCCCCAATTATGAAAAATCAATATTTTGGGAATAAAGCCGGGGTTGGAGTAT
CCCCTCGGAAATAACGGGGTTGGAGTATCCCCGATGAATAACAAGGTTGGAGTATCCCCGACTGT
GAAAAATTGGTATTTTTGGAAATAAAATCGAAGTTGGAGTATCCCCGATTAAAGAAAAATTAGTG
TTTCGAAAATAAAACCGGAGTTGGAATATCCCCGATTGTGGAAAATTTAGTGTTTTAGCAATAAA
AC
Found at i:467942 original size:13 final size:13
Alignment explanation
Indices: 467924--467949 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
467914 ACAAAGATCC
467924 ATGTATCGATACA
1 ATGTATCGATACA
467937 ATGTATCGATACA
1 ATGTATCGATACA
467950 CAGAAAAATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:467945 original size:33 final size:33
Alignment explanation
Indices: 467903--467969 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
467893 AAAATTTCCA
***
467903 AATGTATCGATACAAAGATCCATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
*
467936 AATGTATCGATACACAGAAAAATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
467969 A
1 A
467970 TTTCCTTGGC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.43, C:0.16, G:0.15, T:0.25
Consensus pattern (33 bp):
AATGTATCGATACAAAGAAAAATGTATCGATAC
Found at i:468013 original size:19 final size:18
Alignment explanation
Indices: 467989--468088 Score: 103
Period size: 19 Copynumber: 5.9 Consensus size: 18
467979 CAGTAGCTAA
467989 TTATGTATCGATACAATAC
1 TTATGTATCGATACAA-AC
468008 TTATGTATCGATAC--A-
1 TTATGTATCGATACAAAC
468023 -T-TGTATCGATACAAAAC
1 TTATGTATCGATAC-AAAC
468040 TTATGTATCGATAC--A-
1 TTATGTATCGATACAAAC
468055 -T-TGTATCGATACAAAAC
1 TTATGTATCGATAC-AAAC
468072 TTATGTATCGATACAAA
1 TTATGTATCGATACAAA
468089 TTGTTGAATT
Statistics
Matches: 69, Mismatches: 0, Indels: 25
0.73 0.00 0.27
Matches are distributed among these distances:
13 22 0.32
14 2 0.03
16 4 0.06
18 5 0.07
19 36 0.52
ACGTcount: A:0.38, C:0.15, G:0.12, T:0.35
Consensus pattern (18 bp):
TTATGTATCGATACAAAC
Found at i:468029 original size:13 final size:13
Alignment explanation
Indices: 468011--468067 Score: 60
Period size: 13 Copynumber: 3.9 Consensus size: 13
468001 ACAATACTTA
468011 TGTATCGATACAT
1 TGTATCGATACAT
468024 TGTATCGATACAAAACTT
1 TGTATCGATAC---A--T
468042 ATGTATCGATACAT
1 -TGTATCGATACAT
468056 TGTATCGATACA
1 TGTATCGATACA
468068 AAACTTATGT
Statistics
Matches: 38, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
13 23 0.61
14 1 0.03
16 2 0.05
18 1 0.03
19 11 0.29
ACGTcount: A:0.35, C:0.16, G:0.14, T:0.35
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:468033 original size:32 final size:32
Alignment explanation
Indices: 467992--468086 Score: 181
Period size: 32 Copynumber: 3.0 Consensus size: 32
467982 TAGCTAATTA
*
467992 TGTATCGATACAATACTTATGTATCGATACAT
1 TGTATCGATACAAAACTTATGTATCGATACAT
468024 TGTATCGATACAAAACTTATGTATCGATACAT
1 TGTATCGATACAAAACTTATGTATCGATACAT
468056 TGTATCGATACAAAACTTATGTATCGATACA
1 TGTATCGATACAAAACTTATGTATCGATACA
468087 AATTGTTGAA
Statistics
Matches: 62, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
32 62 1.00
ACGTcount: A:0.37, C:0.16, G:0.13, T:0.35
Consensus pattern (32 bp):
TGTATCGATACAAAACTTATGTATCGATACAT
Found at i:474210 original size:19 final size:21
Alignment explanation
Indices: 474159--474211 Score: 58
Period size: 21 Copynumber: 2.6 Consensus size: 21
474149 AATTTTTGTT
474159 TAAA-TTTAATTATAAAATATA
1 TAAATTTTAA-TATAAAATATA
*
474180 TAAATATTAATATAAAA-ATA
1 TAAATTTTAATATAAAATATA
*
474200 -ATATTTTAATAT
1 TAAATTTTAATAT
474212 TTTTTAAATA
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
19 10 0.36
20 3 0.11
21 11 0.39
22 4 0.14
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (21 bp):
TAAATTTTAATATAAAATATA
Found at i:484000 original size:18 final size:18
Alignment explanation
Indices: 483977--484012 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
483967 TCTGATTTTA
483977 GTTTAGTGATCCCCAGTT
1 GTTTAGTGATCCCCAGTT
483995 GTTTAGTGATCCCCAGTT
1 GTTTAGTGATCCCCAGTT
484013 TTCTCAATCG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.17, C:0.22, G:0.22, T:0.39
Consensus pattern (18 bp):
GTTTAGTGATCCCCAGTT
Found at i:486326 original size:3 final size:3
Alignment explanation
Indices: 486318--486354 Score: 67
Period size: 3 Copynumber: 12.7 Consensus size: 3
486308 TATTTGTCTC
486318 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT -TT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
486355 AATGTTTAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.06
3 31 0.94
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
ATT
Found at i:487304 original size:2 final size:2
Alignment explanation
Indices: 487297--487329 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
487287 TCTTGGAATC
487297 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
487330 GTGAAGAGAC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:487815 original size:19 final size:19
Alignment explanation
Indices: 487768--487815 Score: 55
Period size: 19 Copynumber: 2.5 Consensus size: 19
487758 TTACATTATA
*
487768 AAATTTAACATAAATTTTT
1 AAATTTATCATAAATTTTT
487787 --ATTTAAATCATAAATTTTT
1 AAATTT--ATCATAAATTTTT
487806 AAATTTATCA
1 AAATTTATCA
487816 AATTATATTT
Statistics
Matches: 24, Mismatches: 1, Indels: 8
0.73 0.03 0.24
Matches are distributed among these distances:
17 4 0.17
19 16 0.67
21 4 0.17
ACGTcount: A:0.46, C:0.06, G:0.00, T:0.48
Consensus pattern (19 bp):
AAATTTATCATAAATTTTT
Done.