Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr03 ID=Chr03-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 45765648
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 655849 characters in sequence are not A, C, G, or T
File 90 of 150
Found at i:28081543 original size:87 final size:86
Alignment explanation
Indices: 28081365--28081550 Score: 273
Period size: 87 Copynumber: 2.2 Consensus size: 86
28081355 AAGATATATT
* * * *
28081365 TTTAGCGGCGTTTGTGTGAAAAGCGTCTCTAAAGGTCTTGGTCTTTAGCGGTGCTTGTGGGAAAA
1 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCTTGGTCTTTAGCGGCGCTTGTGGGAAAA
* * **
28081430 GCGCCGTTAAAGGTCTTGGTC
66 GCGCCGCTAAAGGTCATGACC
* *
28081451 TTTAGCGGCGTTTGTGGGAAAAGTGCCGCTAAAGGTCTTGGTCTTTTAGCGGCGTTTGTGGGAAA
1 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCTTGGTC-TTTAGCGGCGCTTGTGGGAAA
28081516 AGCGCCGCTAAAGGTCATGACC
65 AGCGCCGCTAAAGGTCATGACC
28081538 TTTAGCGGCGTTT
1 TTTAGCGGCGTTT
28081551 ATTTCTAAAA
Statistics
Matches: 89, Mismatches: 10, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
86 39 0.44
87 50 0.56
ACGTcount: A:0.19, C:0.17, G:0.33, T:0.31
Consensus pattern (86 bp):
TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCTTGGTCTTTAGCGGCGCTTGTGGGAAAA
GCGCCGCTAAAGGTCATGACC
Found at i:28081758 original size:43 final size:42
Alignment explanation
Indices: 28081711--28081797 Score: 106
Period size: 42 Copynumber: 2.0 Consensus size: 42
28081701 AGTAAGCATG
28081711 ATAATA-TATTTTAATAAAATATTAAATT-TGTTTAATAAAAAAT
1 ATAATATTATTTTAA-AAAAT-TTAAATTAT-TTTAATAAAAAAT
* * *
28081754 ATAATATTATTTTTAAAAATTTTAATTATTTTAATTAAAAAT
1 ATAATATTATTTTAAAAAATTTAAATTATTTTAATAAAAAAT
28081796 AT
1 AT
28081798 TTTAATATAT
Statistics
Matches: 39, Mismatches: 3, Indels: 5
0.83 0.06 0.11
Matches are distributed among these distances:
42 20 0.51
43 12 0.31
44 7 0.18
ACGTcount: A:0.51, C:0.00, G:0.01, T:0.48
Consensus pattern (42 bp):
ATAATATTATTTTAAAAAATTTAAATTATTTTAATAAAAAAT
Found at i:28081905 original size:12 final size:12
Alignment explanation
Indices: 28081888--28081922 Score: 70
Period size: 12 Copynumber: 2.9 Consensus size: 12
28081878 TTAAAAGAAT
28081888 ATTAAATAAATC
1 ATTAAATAAATC
28081900 ATTAAATAAATC
1 ATTAAATAAATC
28081912 ATTAAATAAAT
1 ATTAAATAAAT
28081923 AAAATATAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.60, C:0.06, G:0.00, T:0.34
Consensus pattern (12 bp):
ATTAAATAAATC
Found at i:28089564 original size:16 final size:16
Alignment explanation
Indices: 28089540--28089582 Score: 52
Period size: 16 Copynumber: 2.7 Consensus size: 16
28089530 TATTATAAGT
*
28089540 TAAATAATAA-TAAAG
1 TAAAAAATAAGTAAAG
28089555 TAATAAAATAAGTAAAG
1 TAA-AAAATAAGTAAAG
*
28089572 TTAAAAATAAG
1 TAAAAAATAAG
28089583 AAAACATAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
15 3 0.12
16 14 0.58
17 7 0.29
ACGTcount: A:0.65, C:0.00, G:0.09, T:0.26
Consensus pattern (16 bp):
TAAAAAATAAGTAAAG
Found at i:28093718 original size:27 final size:27
Alignment explanation
Indices: 28093688--28093744 Score: 114
Period size: 27 Copynumber: 2.1 Consensus size: 27
28093678 AAGTTGTTTC
28093688 ACAGATATTCGTCTCTCAAGGAGGTAG
1 ACAGATATTCGTCTCTCAAGGAGGTAG
28093715 ACAGATATTCGTCTCTCAAGGAGGTAG
1 ACAGATATTCGTCTCTCAAGGAGGTAG
28093742 ACA
1 ACA
28093745 ACTAAGATAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.32, C:0.19, G:0.25, T:0.25
Consensus pattern (27 bp):
ACAGATATTCGTCTCTCAAGGAGGTAG
Found at i:28113521 original size:26 final size:26
Alignment explanation
Indices: 28113485--28113534 Score: 100
Period size: 26 Copynumber: 1.9 Consensus size: 26
28113475 TGACATCTCA
28113485 TGGTTCTTCCCTCTAGGTTATACTCC
1 TGGTTCTTCCCTCTAGGTTATACTCC
28113511 TGGTTCTTCCCTCTAGGTTATACT
1 TGGTTCTTCCCTCTAGGTTATACT
28113535 AACTCTACAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.12, C:0.28, G:0.16, T:0.44
Consensus pattern (26 bp):
TGGTTCTTCCCTCTAGGTTATACTCC
Found at i:28115229 original size:24 final size:24
Alignment explanation
Indices: 28115175--28115251 Score: 72
Period size: 24 Copynumber: 3.3 Consensus size: 24
28115165 ACATGTGGAT
*
28115175 ATCACTTTGCACCAAAGT---ACC
1 ATCACTTTGCACCATAGTGCCACC
**
28115196 ATTCAC-TTGCACTGTAGTGCCACC
1 A-TCACTTTGCACCATAGTGCCACC
* *
28115220 ATCACTTTGCACCATAGTGCCTCT
1 ATCACTTTGCACCATAGTGCCACC
28115244 ATCACTTT
1 ATCACTTT
28115252 AATATTGGCA
Statistics
Matches: 44, Mismatches: 7, Indels: 7
0.76 0.12 0.12
Matches are distributed among these distances:
21 10 0.23
22 4 0.09
23 4 0.09
24 26 0.59
ACGTcount: A:0.25, C:0.32, G:0.12, T:0.31
Consensus pattern (24 bp):
ATCACTTTGCACCATAGTGCCACC
Found at i:28119972 original size:39 final size:40
Alignment explanation
Indices: 28119842--28119978 Score: 156
Period size: 40 Copynumber: 3.5 Consensus size: 40
28119832 GGCGTTTGGA
* *
28119842 TAAAAAACGCCGCTAAAAATCAATCATTAGCGGCG-CTTC
1 TAAAAAACGCCGCTAAAAATCAAGCATTAGCGGCGTTTTC
* * * *
28119881 TAGAAAAACGCCGCTACAGATCAAGTATTCGCGGCGCTTTTC
1 TA-AAAAACGCCGCTAAAAATCAAGCATTAGCGGCG-TTTTC
28119923 T-AAAAACGCCGCTAAAAATC-AGCATTAGCGGCGTTTTC
1 TAAAAAACGCCGCTAAAAATCAAGCATTAGCGGCGTTTTC
* *
28119961 CAAAAAGCGCCGC-AAAAA
1 TAAAAAACGCCGCTAAAAA
28119979 CCTAAGCCCA
Statistics
Matches: 82, Mismatches: 12, Indels: 9
0.80 0.12 0.09
Matches are distributed among these distances:
38 10 0.12
39 23 0.28
40 45 0.55
42 4 0.05
ACGTcount: A:0.36, C:0.26, G:0.18, T:0.20
Consensus pattern (40 bp):
TAAAAAACGCCGCTAAAAATCAAGCATTAGCGGCGTTTTC
Found at i:28120068 original size:41 final size:41
Alignment explanation
Indices: 28120011--28120115 Score: 174
Period size: 41 Copynumber: 2.6 Consensus size: 41
28120001 TTGTTAGTTT
*
28120011 TTGGGACTTTAGCGGCATTTTTGAAGAAGCGCCGCTAATGC
1 TTGGGTCTTTAGCGGCATTTTTGAAGAAGCGCCGCTAATGC
* *
28120052 TTGGGTCTTTAGCGGCACTTTTGAAGAAGCGCTGCTAATGC
1 TTGGGTCTTTAGCGGCATTTTTGAAGAAGCGCCGCTAATGC
*
28120093 TTGGGTCTTTAGCGGCGTTTTTG
1 TTGGGTCTTTAGCGGCATTTTTG
28120116 GAAAAGTGCC
Statistics
Matches: 59, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
41 59 1.00
ACGTcount: A:0.17, C:0.18, G:0.30, T:0.34
Consensus pattern (41 bp):
TTGGGTCTTTAGCGGCATTTTTGAAGAAGCGCCGCTAATGC
Found at i:28120502 original size:7 final size:7
Alignment explanation
Indices: 28120487--28120620 Score: 76
Period size: 7 Copynumber: 18.9 Consensus size: 7
28120477 ATTATAATAA
28120487 GGTTTAT
1 GGTTTAT
*
28120494 GGATTAT
1 GGTTTAT
*
28120501 GGGTTTAG
1 -GGTTTAT
*
28120509 GGGTTAT
1 GGTTTAT
*
28120516 GATTTAT
1 GGTTTAT
28120523 GGTTTAT
1 GGTTTAT
28120530 GGTTTAT
1 GGTTTAT
*
28120537 GGTTTAAA
1 GGTTT-AT
**
28120545 GG-TTGG
1 GGTTTAT
*
28120551 GGTTTAA
1 GGTTTAT
28120558 GGTTTA-
1 GGTTTAT
*
28120564 GAGGTTAT
1 G-GTTTAT
* *
28120572 GTGTTAAG
1 G-GTTTAT
*
28120580 GGTTTAA
1 GGTTTAT
*
28120587 GGTTTTAG
1 GG-TTTAT
28120595 GGTTTA-
1 GGTTTAT
28120601 GGTTTAT
1 GGTTTAT
*
28120608 GGTTTAG
1 GGTTTAT
28120615 GGTTTA
1 GGTTTA
28120621 GATTAACTAG
Statistics
Matches: 98, Mismatches: 22, Indels: 14
0.73 0.16 0.10
Matches are distributed among these distances:
6 9 0.09
7 70 0.71
8 19 0.19
ACGTcount: A:0.19, C:0.00, G:0.34, T:0.46
Consensus pattern (7 bp):
GGTTTAT
Found at i:28121243 original size:13 final size:15
Alignment explanation
Indices: 28121215--28121246 Score: 50
Period size: 13 Copynumber: 2.3 Consensus size: 15
28121205 CTCGTATTAT
28121215 TATTAATTTAATATA
1 TATTAATTTAATATA
28121230 TATTAA-TT-ATATA
1 TATTAATTTAATATA
28121243 TATT
1 TATT
28121247 TTTCATTTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
13 9 0.53
14 2 0.12
15 6 0.35
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (15 bp):
TATTAATTTAATATA
Found at i:28125950 original size:43 final size:43
Alignment explanation
Indices: 28125894--28126101 Score: 267
Period size: 43 Copynumber: 4.8 Consensus size: 43
28125884 AAAGGTTTGT
* * * *
28125894 TCTTTAGCGGCGTTTGTAAGAAAAGTGCCGTTAAAGGTCGTGG
1 TCTTTAGCGGCGTTTGTAGGAAAAGCGCCGCTAAAGATCGTGG
* *
28125937 TCTTTAGCGGCGTTTGT-GGAATAAGGGCCGCTATAGATCGTGG
1 TCTTTAGCGGCGTTTGTAGGAA-AAGCGCCGCTAAAGATCGTGG
* * *
28125980 TCTTTAGCGGCGTTTGTTGGAAAAGCGTCGCTATAGATCGTGG
1 TCTTTAGCGGCGTTTGTAGGAAAAGCGCCGCTAAAGATCGTGG
* * *
28126023 TCTTTAGCGGCGTTTGTGGGAAAAGCGCCACTAAAGGTCGTGG
1 TCTTTAGCGGCGTTTGTAGGAAAAGCGCCGCTAAAGATCGTGG
*
28126066 TCTTTAGCGGCGTTTGT-GAAAAAAGCGCCGCTAAAG
1 TCTTTAGCGGCGTTTGTAG-GAAAAGCGCCGCTAAAG
28126102 TTAGCGACGC
Statistics
Matches: 148, Mismatches: 14, Indels: 6
0.88 0.08 0.04
Matches are distributed among these distances:
42 4 0.03
43 140 0.95
44 4 0.03
ACGTcount: A:0.22, C:0.17, G:0.33, T:0.29
Consensus pattern (43 bp):
TCTTTAGCGGCGTTTGTAGGAAAAGCGCCGCTAAAGATCGTGG
Found at i:28127872 original size:15 final size:16
Alignment explanation
Indices: 28127818--28127889 Score: 65
Period size: 16 Copynumber: 4.4 Consensus size: 16
28127808 ACATTACCAT
* *
28127818 AGAACAACTCTTATTC
1 AGAACAACTCATATTG
* *
28127834 AGAACAACCTCTACATTA
1 AGAACAA-CTC-ATATTG
28127852 AGAACAACT-ATATTG
1 AGAACAACTCATATTG
* *
28127867 AGAACAACTCATGTTT
1 AGAACAACTCATATTG
28127883 AGAACAA
1 AGAACAA
28127890 GTCAAAGTAA
Statistics
Matches: 46, Mismatches: 7, Indels: 6
0.78 0.12 0.10
Matches are distributed among these distances:
15 13 0.28
16 18 0.39
17 5 0.11
18 10 0.22
ACGTcount: A:0.44, C:0.21, G:0.10, T:0.25
Consensus pattern (16 bp):
AGAACAACTCATATTG
Found at i:28128856 original size:18 final size:17
Alignment explanation
Indices: 28128816--28128856 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 17
28128806 TAATATGAAC
*
28128816 TAAAAAAAATGAACTAT
1 TAAAAAAAATGAACTAA
28128833 TCAAAAAAAATGAACTCAA
1 T-AAAAAAAATGAACT-AA
28128852 TAAAA
1 TAAAA
28128857 TAATTAATGG
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
17 1 0.05
18 18 0.86
19 2 0.10
ACGTcount: A:0.66, C:0.10, G:0.05, T:0.20
Consensus pattern (17 bp):
TAAAAAAAATGAACTAA
Found at i:28138404 original size:24 final size:26
Alignment explanation
Indices: 28138359--28138423 Score: 75
Period size: 25 Copynumber: 2.6 Consensus size: 26
28138349 TGATTTGTAC
28138359 ATAA-TATAAAAAATGTATAAACAT-
1 ATAATTATAAAAAATGTATAAACATA
*
28138383 ATGAATTATAAAACATG-A-AAACATAA
1 AT-AATTATAAAAAATGTATAAACAT-A
28138409 ATAATTATAAAAAAT
1 ATAATTATAAAAAAT
28138424 ATGAATGTAT
Statistics
Matches: 35, Mismatches: 2, Indels: 7
0.80 0.05 0.16
Matches are distributed among these distances:
24 8 0.23
25 15 0.43
26 12 0.34
ACGTcount: A:0.63, C:0.05, G:0.05, T:0.28
Consensus pattern (26 bp):
ATAATTATAAAAAATGTATAAACATA
Found at i:28138474 original size:15 final size:15
Alignment explanation
Indices: 28138431--28138490 Score: 68
Period size: 15 Copynumber: 4.0 Consensus size: 15
28138421 AATATGAATG
*
28138431 TATATAATATATATA
1 TATATAAAATATATA
*
28138446 TATATAAACTATATA
1 TATATAAAATATATA
* *
28138461 TATATAAAAAATATGG
1 TATATAAAATATAT-A
28138477 TA-ATAAAATATATA
1 TATATAAAATATATA
28138491 CGCACTATAT
Statistics
Matches: 37, Mismatches: 7, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
15 35 0.95
16 2 0.05
ACGTcount: A:0.57, C:0.02, G:0.03, T:0.38
Consensus pattern (15 bp):
TATATAAAATATATA
Found at i:28138508 original size:49 final size:48
Alignment explanation
Indices: 28138414--28138552 Score: 120
Period size: 49 Copynumber: 2.9 Consensus size: 48
28138404 CATAAATAAT
* * * * * *
28138414 TATAAAAAATAT-GAATGTATATAATATATATATATATAAACTATATATA
1 TATAAAAAATATAGAA-ATAAAAAATATACACATATATATA-TATATATA
* * * *
28138463 TATAAAAAATATGGTAATAAAATATATACGCACTATATATATATATATA
1 TATAAAAAATATAGAAATAAAAAATATACACA-TATATATATATATATA
* * *
28138512 TTTAAAACATTTAGAAATAAAAAATATACACATATAT-TATA
1 TATAAAAAATATAGAAATAAAAAATATACACATATATATATA
28138553 AAGTACACAT
Statistics
Matches: 72, Mismatches: 16, Indels: 6
0.77 0.17 0.06
Matches are distributed among these distances:
47 4 0.06
48 5 0.07
49 54 0.75
50 9 0.12
ACGTcount: A:0.55, C:0.05, G:0.04, T:0.36
Consensus pattern (48 bp):
TATAAAAAATATAGAAATAAAAAATATACACATATATATATATATATA
Found at i:28138596 original size:12 final size:12
Alignment explanation
Indices: 28138581--28138640 Score: 70
Period size: 12 Copynumber: 5.1 Consensus size: 12
28138571 ATATGTAAGT
28138581 ATAATAAATATA
1 ATAATAAATATA
28138593 ATAAT-AATAGTA
1 ATAATAAATA-TA
*
28138605 ATAATAAAAATA
1 ATAATAAATATA
*
28138617 ATAATAACTATA
1 ATAATAAATATA
*
28138629 TTAATAAA-ATA
1 ATAATAAATATA
28138640 A
1 A
28138641 ACTAAAAAAA
Statistics
Matches: 40, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
11 7 0.17
12 30 0.75
13 3 0.08
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.32
Consensus pattern (12 bp):
ATAATAAATATA
Found at i:28138617 original size:24 final size:24
Alignment explanation
Indices: 28138581--28138637 Score: 80
Period size: 24 Copynumber: 2.4 Consensus size: 24
28138571 ATATGTAAGT
*
28138581 ATAATAAATATAATAATAA-TAGTA
1 ATAATAAAAATAATAATAACTA-TA
28138605 ATAATAAAAATAATAATAACTATA
1 ATAATAAAAATAATAATAACTATA
*
28138629 TTAATAAAA
1 ATAATAAAA
28138638 TAAACTAAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
24 28 0.93
25 2 0.07
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.32
Consensus pattern (24 bp):
ATAATAAAAATAATAATAACTATA
Found at i:28150676 original size:46 final size:44
Alignment explanation
Indices: 28150599--28150698 Score: 114
Period size: 46 Copynumber: 2.2 Consensus size: 44
28150589 AATAGTAACA
*
28150599 GATACACGG-TGGATTCAGCACACAACAACCACCCATTGTAATCAAT
1 GATAC-CGGTTGGATTCAGCACACAACAACCA-CC-TTATAATCAAT
* * *
28150645 GATATCCGGTTGGA-TCAGCACATAGCAACCACCTTATAATTAAT
1 GATA-CCGGTTGGATTCAGCACACAACAACCACCTTATAATCAAT
28150689 GATACCGGTT
1 GATACCGGTT
28150699 CACATAGTAG
Statistics
Matches: 48, Mismatches: 4, Indels: 7
0.81 0.07 0.12
Matches are distributed among these distances:
43 6 0.12
44 13 0.27
45 2 0.04
46 22 0.46
47 5 0.10
ACGTcount: A:0.34, C:0.25, G:0.17, T:0.24
Consensus pattern (44 bp):
GATACCGGTTGGATTCAGCACACAACAACCACCTTATAATCAAT
Found at i:28150825 original size:50 final size:50
Alignment explanation
Indices: 28150704--28150887 Score: 192
Period size: 50 Copynumber: 3.7 Consensus size: 50
28150694 CGGTTCACAT
* * * * * *
28150704 AGTAGCCTACACATAGTACTACACATGTGACCATCA-CTATCCGATACATGT
1 AGTAGCCTGCACATAGTACTACACACGTGACCA--AGCTATCTGGTACACGA
* *
28150755 AGTAGCCTGCACATAGTACTACACACGTGATCGAAGCTATCTGGTACGC-A
1 AGTAGCCTGCACATAGTACTACACACGTGA-CCAAGCTATCTGGTACACGA
* * * * * *
28150805 AGTAGCCTGCACATAGTACTACACATGCGACCTATCTTTCTGGTACACGT
1 AGTAGCCTGCACATAGTACTACACACGTGACCAAGCTATCTGGTACACGA
*
28150855 AGTAGCCTGTACATAGTACTACACACGTGACCA
1 AGTAGCCTGCACATAGTACTACACACGTGACCA
28150888 TCACTTTCAC
Statistics
Matches: 110, Mismatches: 20, Indels: 7
0.80 0.15 0.05
Matches are distributed among these distances:
49 13 0.12
50 58 0.53
51 37 0.34
52 2 0.02
ACGTcount: A:0.30, C:0.27, G:0.18, T:0.24
Consensus pattern (50 bp):
AGTAGCCTGCACATAGTACTACACACGTGACCAAGCTATCTGGTACACGA
Found at i:28150879 original size:100 final size:100
Alignment explanation
Indices: 28150704--28150884 Score: 274
Period size: 100 Copynumber: 1.8 Consensus size: 100
28150694 CGGTTCACAT
* *
28150704 AGTAGCCTACACATAGTACTACACATGTGACCATCACTATCCGATACATGTAGTAGCCTGCACAT
1 AGTAGCCTACACATAGTACTACACATGCGACCAT-ACTATCCGATACACGTAGTAGCCTGCACAT
28150769 AGTACTACACACGTGATCGAAGCTATCTGGTACGCA
65 AGTACTACACACGTGATCGAAGCTATCTGGTACGCA
* * * * *
28150805 AGTAGCCTGCACATAGTACTACACATGCGACC-TATCTTTCTGGTACACGTAGTAGCCTGTACAT
1 AGTAGCCTACACATAGTACTACACATGCGACCATA-CTATCCGATACACGTAGTAGCCTGCACAT
28150869 AGTACTACACACGTGA
65 AGTACTACACACGTGA
28150885 CCATCACTTT
Statistics
Matches: 72, Mismatches: 7, Indels: 3
0.88 0.09 0.04
Matches are distributed among these distances:
99 1 0.01
100 41 0.57
101 30 0.42
ACGTcount: A:0.30, C:0.27, G:0.18, T:0.25
Consensus pattern (100 bp):
AGTAGCCTACACATAGTACTACACATGCGACCATACTATCCGATACACGTAGTAGCCTGCACATA
GTACTACACACGTGATCGAAGCTATCTGGTACGCA
Found at i:28154507 original size:33 final size:33
Alignment explanation
Indices: 28154470--28154576 Score: 169
Period size: 33 Copynumber: 3.2 Consensus size: 33
28154460 ATCCCTCCAG
*
28154470 CACACCAATGCTCAGAAGAGCTAATCCAACCAA
1 CACACCAATGCTCATAAGAGCTAATCCAACCAA
*
28154503 CACACCAATGCTCATAAGAGCTAATCCAACCAT
1 CACACCAATGCTCATAAGAGCTAATCCAACCAA
* * *
28154536 CACACCAGTGCTCATAAGAGCTAGTCCAACCAG
1 CACACCAATGCTCATAAGAGCTAATCCAACCAA
28154569 CACACCAA
1 CACACCAA
28154577 CAGATAATAT
Statistics
Matches: 68, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 68 1.00
ACGTcount: A:0.39, C:0.35, G:0.12, T:0.14
Consensus pattern (33 bp):
CACACCAATGCTCATAAGAGCTAATCCAACCAA
Found at i:28156563 original size:53 final size:54
Alignment explanation
Indices: 28156481--28156590 Score: 150
Period size: 53 Copynumber: 2.1 Consensus size: 54
28156471 TTTCTTAAAT
* * * *
28156481 TTTCCTATATTATGCCATAACCCACCAGTTACTATCTTACATGATATGGTCTTC
1 TTTCCTATATGATGCCATAACCCACCAGTTACGATCTTACACGATATGGTATTC
* * *
28156535 TTTCC-ATATGATGCCATAACTCATCAGTTACGGTCTTACACGATATGGTATTC
1 TTTCCTATATGATGCCATAACCCACCAGTTACGATCTTACACGATATGGTATTC
28156588 TTT
1 TTT
28156591 AGTGCCACGA
Statistics
Matches: 49, Mismatches: 7, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
53 44 0.90
54 5 0.10
ACGTcount: A:0.25, C:0.24, G:0.12, T:0.39
Consensus pattern (54 bp):
TTTCCTATATGATGCCATAACCCACCAGTTACGATCTTACACGATATGGTATTC
Found at i:28157582 original size:2 final size:2
Alignment explanation
Indices: 28157575--28157613 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
28157565 TTATAACCGA
28157575 AT AT AT 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 AT AT AT A
28157614 CACATCAAAT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:28157732 original size:2 final size:2
Alignment explanation
Indices: 28157725--28157764 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
28157715 ATAAAATTGA
28157725 AT AT AT AT A- 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 AT AT AT AT A
28157765 AATTCATACT
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 36 0.97
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:28158005 original size:41 final size:41
Alignment explanation
Indices: 28157960--28158119 Score: 275
Period size: 41 Copynumber: 3.9 Consensus size: 41
28157950 ACTGGCACTT
*
28157960 AGCCTGCTAGACATAAAGTCTGAAATGTTTCACCGGCGTCA
1 AGCCTGCTAGACTTAAAGTCTGAAATGTTTCACCGGCGTCA
* *
28158001 AGCCTGCTAGACTTAAAGTCTGAAATGTTTCATCAGCGTCA
1 AGCCTGCTAGACTTAAAGTCTGAAATGTTTCACCGGCGTCA
* *
28158042 AGCCTGCTAGACTTAAAGTCTGAAATGTTTCATCGGCATCA
1 AGCCTGCTAGACTTAAAGTCTGAAATGTTTCACCGGCGTCA
28158083 AGCCTGCTAGACTTAAAGTCTGAAATGTTTCACCGGC
1 AGCCTGCTAGACTTAAAGTCTGAAATGTTTCACCGGC
28158120 AATAAACCTG
Statistics
Matches: 113, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 113 1.00
ACGTcount: A:0.29, C:0.23, G:0.21, T:0.28
Consensus pattern (41 bp):
AGCCTGCTAGACTTAAAGTCTGAAATGTTTCACCGGCGTCA
Found at i:28158639 original size:2 final size:2
Alignment explanation
Indices: 28158632--28158688 Score: 114
Period size: 2 Copynumber: 28.5 Consensus size: 2
28158622 AATCTTAAGT
28158632 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
28158674 AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC A
28158689 TATATACCTT
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 55 1.00
ACGTcount: A:0.51, C:0.49, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:28167736 original size:46 final size:46
Alignment explanation
Indices: 28167669--28167853 Score: 307
Period size: 46 Copynumber: 4.0 Consensus size: 46
28167659 ACATTGCTAT
* * **
28167669 AACTCAGTATGGCTTTCTTCACGGAATTACCATACCTACTTTTCAC
1 AACTCAGTATGGTTTTCTTCACCGAAACACCATACCTACTTTTCAC
* *
28167715 AACTCAGTATAGTTTTCTTCACCGAAACACCATACCTACTTTTCAT
1 AACTCAGTATGGTTTTCTTCACCGAAACACCATACCTACTTTTCAC
*
28167761 AACTCAGTATGGTTTTCTTCACCAAAACACCATACCTACTTTTCAC
1 AACTCAGTATGGTTTTCTTCACCGAAACACCATACCTACTTTTCAC
28167807 AACTCAGTATGGTTTTCTTCACCGAAACACCATACCTACTTTTCAC
1 AACTCAGTATGGTTTTCTTCACCGAAACACCATACCTACTTTTCAC
28167853 A
1 A
28167854 CTTCGCCATG
Statistics
Matches: 129, Mismatches: 10, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
46 129 1.00
ACGTcount: A:0.29, C:0.29, G:0.08, T:0.34
Consensus pattern (46 bp):
AACTCAGTATGGTTTTCTTCACCGAAACACCATACCTACTTTTCAC
Found at i:28169124 original size:16 final size:16
Alignment explanation
Indices: 28169084--28169125 Score: 57
Period size: 17 Copynumber: 2.6 Consensus size: 16
28169074 TTTTAAATCG
*
28169084 CAAAAATTCACTAAAT
1 CAAAAATTCACCAAAT
*
28169100 CACAAAATTCACCAATT
1 CA-AAAATTCACCAAAT
28169117 CAAAAATTC
1 CAAAAATTC
28169126 TTCTAAATTC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
16 9 0.39
17 14 0.61
ACGTcount: A:0.52, C:0.24, G:0.00, T:0.24
Consensus pattern (16 bp):
CAAAAATTCACCAAAT
Found at i:28170188 original size:17 final size:17
Alignment explanation
Indices: 28170166--28170199 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
28170156 TGGAGCCAAT
*
28170166 CTCCTCCACGTGCGCCA
1 CTCCTCCACGCGCGCCA
28170183 CTCCTCCACGCGCGCCA
1 CTCCTCCACGCGCGCCA
28170200 TGGCTTGCGC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.12, C:0.56, G:0.18, T:0.15
Consensus pattern (17 bp):
CTCCTCCACGCGCGCCA
Found at i:28171194 original size:38 final size:39
Alignment explanation
Indices: 28171147--28171238 Score: 116
Period size: 40 Copynumber: 2.3 Consensus size: 39
28171137 TATATATATA
28171147 TATTCTAATTTCAAAAAACGTTTT-AC-TTTTGTAAATGT
1 TATTCTAATTTC-AAAAACGTTTTCACTTTTTGTAAATGT
*
28171185 TATTTTAATTTCAAAAACGTTTTCCACTTTTTGTAAATGT
1 TATTCTAATTTCAAAAACGTTTT-CACTTTTTGTAAATGT
28171225 ATAATTCTATATTT
1 -T-ATTCTA-ATTT
28171239 TATTATAAAT
Statistics
Matches: 46, Mismatches: 2, Indels: 7
0.84 0.04 0.13
Matches are distributed among these distances:
37 11 0.24
38 11 0.24
39 2 0.04
40 12 0.26
41 1 0.02
42 5 0.11
43 4 0.09
ACGTcount: A:0.33, C:0.11, G:0.07, T:0.50
Consensus pattern (39 bp):
TATTCTAATTTCAAAAACGTTTTCACTTTTTGTAAATGT
Found at i:28180888 original size:7 final size:7
Alignment explanation
Indices: 28180876--28180902 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
28180866 TTGCCACTTT
28180876 ATTCTTC
1 ATTCTTC
28180883 ATTCTTC
1 ATTCTTC
28180890 ATTCTTC
1 ATTCTTC
28180897 ATTCTT
1 ATTCTT
28180903 TTGCCATATA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.15, C:0.26, G:0.00, T:0.59
Consensus pattern (7 bp):
ATTCTTC
Found at i:28181024 original size:10 final size:9
Alignment explanation
Indices: 28181004--28181028 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
28180994 TCATTTGTAG
28181004 TTTTATTTT
1 TTTTATTTT
28181013 TTTTATTTT
1 TTTTATTTT
28181022 TTTTATT
1 TTTTATT
28181029 ACTGATAGAG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.12, C:0.00, G:0.00, T:0.88
Consensus pattern (9 bp):
TTTTATTTT
Found at i:28182163 original size:44 final size:45
Alignment explanation
Indices: 28182077--28182167 Score: 121
Period size: 45 Copynumber: 2.0 Consensus size: 45
28182067 TTTGGTTCGC
* * *
28182077 TGTATTGGATTAGAGGTGTAATAGCTAATCCACTGTTTGGTTGAA
1 TGTAATGGAATAGAGGCGTAATAGCTAATCCACTGTTTGGTTGAA
***
28182122 TGTAATGGAATAGAGGCGTAATAG-TAATCTTGTGTTTGGTTGAA
1 TGTAATGGAATAGAGGCGTAATAGCTAATCCACTGTTTGGTTGAA
28182166 TG
1 TG
28182168 GAATAGAGGT
Statistics
Matches: 40, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
44 19 0.47
45 21 0.52
ACGTcount: A:0.27, C:0.07, G:0.29, T:0.37
Consensus pattern (45 bp):
TGTAATGGAATAGAGGCGTAATAGCTAATCCACTGTTTGGTTGAA
Found at i:28182349 original size:16 final size:16
Alignment explanation
Indices: 28182312--28182366 Score: 53
Period size: 15 Copynumber: 3.4 Consensus size: 16
28182302 TTAATCATAT
*
28182312 TTAAACATA-ATTATAA
1 TTAAA-ATATATTTTAA
28182328 TT-AAATATATTTTAA
1 TTAAAATATATTTTAA
28182343 TTAAAATATATAATTTAA
1 TTAAAATATAT--TTTAA
28182361 -TAAAAT
1 TTAAAAT
28182367 TCTTATAATT
Statistics
Matches: 34, Mismatches: 1, Indels: 7
0.81 0.02 0.17
Matches are distributed among these distances:
14 3 0.09
15 10 0.29
16 10 0.29
17 6 0.18
18 5 0.15
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.44
Consensus pattern (16 bp):
TTAAAATATATTTTAA
Found at i:28182359 original size:18 final size:18
Alignment explanation
Indices: 28182318--28182366 Score: 61
Period size: 16 Copynumber: 2.9 Consensus size: 18
28182308 ATATTTAAAC
28182318 ATAATTATAATT-AAATAT
1 ATAATT-TAATTAAAATAT
28182336 AT--TTTAATTAAAATAT
1 ATAATTTAATTAAAATAT
28182352 ATAATTTAA-TAAAAT
1 ATAATTTAATTAAAAT
28182367 TCTTATAATT
Statistics
Matches: 28, Mismatches: 0, Indels: 7
0.80 0.00 0.20
Matches are distributed among these distances:
15 5 0.18
16 10 0.36
17 6 0.21
18 7 0.25
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (18 bp):
ATAATTTAATTAAAATAT
Found at i:28182503 original size:156 final size:156
Alignment explanation
Indices: 28182219--28182702 Score: 914
Period size: 156 Copynumber: 3.1 Consensus size: 156
28182209 TAGAATACCC
* *
28182219 TTAGCATAAAATTGTTTTGGTAAATGATTATTGTTATTGTTATTTAAATTTTAATAAGATTATTA
1 TTAGCAGAAAATTGTTTTGGTAAATGATTATTGTTAATGTTATTTAAATTTTAATAAGATTATTA
*
28182284 TTATCAGTAATAAATATTTTAATCATATTTAAACATAATTATAATTAAATATATTTTAATTAAAA
66 TTATCAGTAATAAATATTTTAATCATATTTAAACATAATTATTATTAAATATATTTTAATTAAAA
28182349 TATATAATTTAATAAAATTCTTATAA
131 TATATAATTTAATAAAATTCTTATAA
28182375 TTAGCAGAAAATTGTTTTGGTAAATGATTATTGTTAATGTTATTTAAATTTTAATAAGATTATTA
1 TTAGCAGAAAATTGTTTTGGTAAATGATTATTGTTAATGTTATTTAAATTTTAATAAGATTATTA
28182440 TTATCAGTAATAAATATTTTAATCATATTTAAACATAATTATTATTAAATATATTTTAATTAAAA
66 TTATCAGTAATAAATATTTTAATCATATTTAAACATAATTATTATTAAATATATTTTAATTAAAA
28182505 TATATAATTTAATAAAATTCTTATAA
131 TATATAATTTAATAAAATTCTTATAA
* *
28182531 TTAGCAAAAAATTGTGTTGGTAAATGATTATTGTTAATGTTATTTAAATTTTAATAAGATTATTA
1 TTAGCAGAAAATTGTTTTGGTAAATGATTATTGTTAATGTTATTTAAATTTTAATAAGATTATTA
28182596 TTATCAGTAATAAATATTTTAATCATATTTAAACATAATTATTATTAAATATATTTTAATTAAAA
66 TTATCAGTAATAAATATTTTAATCATATTTAAACATAATTATTATTAAATATATTTTAATTAAAA
28182661 TATATAATTTAATAAAATTCTTATAA
131 TATATAATTTAATAAAATTCTTATAA
*
28182687 TTAGCAGAAATTTGTT
1 TTAGCAGAAAATTGTT
28182703 ATTGTTATTT
Statistics
Matches: 320, Mismatches: 8, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
156 320 1.00
ACGTcount: A:0.43, C:0.03, G:0.07, T:0.47
Consensus pattern (156 bp):
TTAGCAGAAAATTGTTTTGGTAAATGATTATTGTTAATGTTATTTAAATTTTAATAAGATTATTA
TTATCAGTAATAAATATTTTAATCATATTTAAACATAATTATTATTAAATATATTTTAATTAAAA
TATATAATTTAATAAAATTCTTATAA
Found at i:28182509 original size:18 final size:17
Alignment explanation
Indices: 28182488--28182522 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
28182478 TTATTATTAA
*
28182488 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
28182506 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
28182523 TCTTATAATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:28182513 original size:137 final size:147
Alignment explanation
Indices: 28182256--28182820 Score: 749
Period size: 156 Copynumber: 3.8 Consensus size: 147
28182246 TTATTGTTAT
28182256 TGTTATTTAAATTTTAATAAGATTATTATTATCAGTAATAAATATTTTAATCATATTTAAACATA
1 TGTTATTTAAATTTTAATAAGATTATTATTATCAGTAATAAATATTTTAATCATATTTAAACATA
*
28182321 ATTATAATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTATAATTAGCAGAAAA
66 ATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAT-ATTAG-AGAAAA
*
28182386 TTGTTTTGGTAAATGATTATTGTTAA
129 TTG--AT-GTAAATGA-TA---TTAA
28182412 TGTTATTTAAATTTTAATAAGATTATTATTATCAGTAATAAATATTTTAATCATATTTAAACATA
1 TGTTATTTAAATTTTAATAAGATTATTATTATCAGTAATAAATATTTTAATCATATTTAAACATA
*
28182477 ATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTATAATTAGCAAAAAA
66 ATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAT-ATTAG-AGAAAA
*
28182542 TTGTGTTGGTAAATGATTATTGTTAA
129 -T-TGAT-GTAAATGA-TA---TTAA
28182568 TGTTATTTAAATTTTAATAAGATTATTATTATCAGTAATAAATATTTTAATCATATTTAAACATA
1 TGTTATTTAAATTTTAATAAGATTATTATTATCAGTAATAAATATTTTAATCATATTTAAACATA
28182633 ATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTATAATTAGCAG-AAA
66 ATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAT-ATTAG-AGAAAA
28182697 TT--TG----T--TA-T--
129 TTGATGTAAATGATATTAA
* * *
28182705 TGTTATTTAAATTTTAATAAGATTATTAATATCAATAATAAATAATTTAATCATATTTAAACATA
1 TGTTATTTAAATTTTAATAAGATTATTATTATCAGTAATAAATATTTTAATCATATTTAAACATA
* * ****
28182770 ATTATTATTAAATACATTATAATTTTGGTATATAATTTAATAAAATTCTTA
66 ATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTA
28182821 ATAATTCATA
Statistics
Matches: 395, Mismatches: 12, Indels: 23
0.92 0.03 0.05
Matches are distributed among these distances:
137 107 0.27
139 1 0.00
143 2 0.01
146 1 0.00
150 1 0.00
151 1 0.00
153 1 0.00
154 1 0.00
155 3 0.01
156 274 0.69
157 1 0.00
158 2 0.01
ACGTcount: A:0.45, C:0.04, G:0.05, T:0.47
Consensus pattern (147 bp):
TGTTATTTAAATTTTAATAAGATTATTATTATCAGTAATAAATATTTTAATCATATTTAAACATA
ATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTATATTAGAGAAAATT
GATGTAAATGATATTAA
Found at i:28182641 original size:67 final size:67
Alignment explanation
Indices: 28182570--28182782 Score: 168
Period size: 67 Copynumber: 3.1 Consensus size: 67
28182560 ATTGTTAATG
*
28182570 TTATTTAAATTTTAATAAGATTATTATTATCAGTAATAAATATTTTAATCATATTTAAACATAAT
1 TTATTTAAATTTTAATAAGATTATTATTATCAATAATAAATATTTTAATCATATTTAAACATAAT
28182635 TA
66 TA
* * * * * * ***
28182637 TTATTAAATATATTTTAATTAAAATATATAATT-T-AATAA-AATTCTTATAAT--TAGCAGAAA
1 TTATT---TAAATTTTAA-TAAGAT-TATTATTATCAATAATAAATATTTTAATCATA-TTTAAA
** * *
28182697 TTTGTTATTG
60 --CATAATTA
* *
28182707 TTATTTAAATTTTAATAAGATTATTAATATCAATAATAAATAATTTAATCATATTTAAACATAAT
1 TTATTTAAATTTTAATAAGATTATTATTATCAATAATAAATATTTTAATCATATTTAAACATAAT
28182772 TA
66 TA
28182774 TTA-TTAAAT
1 TTATTTAAAT
28182783 ACATTATAAT
Statistics
Matches: 104, Mismatches: 29, Indels: 27
0.65 0.18 0.17
Matches are distributed among these distances:
65 5 0.05
66 12 0.12
67 28 0.27
68 11 0.11
69 12 0.12
70 24 0.23
71 6 0.06
72 6 0.06
ACGTcount: A:0.46, C:0.04, G:0.03, T:0.47
Consensus pattern (67 bp):
TTATTTAAATTTTAATAAGATTATTATTATCAATAATAAATATTTTAATCATATTTAAACATAAT
TA
Found at i:28182665 original size:18 final size:17
Alignment explanation
Indices: 28182644--28182678 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
28182634 TTATTATTAA
*
28182644 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
28182662 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
28182679 TCTTATAATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:28182860 original size:137 final size:135
Alignment explanation
Indices: 28182582--28182860 Score: 339
Period size: 137 Copynumber: 2.0 Consensus size: 135
28182572 ATTTAAATTT
* * *
28182582 TAATAAGATTATTATTATCAGTAATAAATATTTTAATCATATTTAAACATAATTATTATTAAATA
1 TAATAAGATTATTAATATCAATAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATA
* * * *
28182647 TATTTTAATTAAAATATATAATTTAATAAAATTCTTATAATTAGCAGAAATTTGTTATTGTTATT
66 CATTATAATTAAAATATATAATTTAATAAAATTCTTATAATTA-CA-AAATTTCTTATTGTTACT
* **
28182712 TAAATTT
129 CAAATCA
28182719 TAATAAGATTATTAATATCAATAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATA
1 TAATAAGATTATTAATATCAATAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATA
**** *
28182784 CATTATAATTTTGGTATATAATTTAATAAAATTCTTAATAATT-C-ATA-TTCTTATATGAATTT
66 CATTATAATTAAAATATATAATTTAATAAAATTCTT-ATAATTACAAAATTTCTTAT-TG---TT
28182846 ACTCAAATCA
126 ACTCAAATCA
28182856 TAATA
1 TAATA
28182861 TATGATACTA
Statistics
Matches: 122, Mismatches: 15, Indels: 10
0.83 0.10 0.07
Matches are distributed among these distances:
133 6 0.05
134 4 0.03
136 1 0.01
137 105 0.86
138 6 0.05
ACGTcount: A:0.46, C:0.05, G:0.04, T:0.46
Consensus pattern (135 bp):
TAATAAGATTATTAATATCAATAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATA
CATTATAATTAAAATATATAATTTAATAAAATTCTTATAATTACAAAATTTCTTATTGTTACTCA
AATCA
Found at i:28185767 original size:57 final size:57
Alignment explanation
Indices: 28185679--28185800 Score: 235
Period size: 57 Copynumber: 2.1 Consensus size: 57
28185669 AAGGCGTAGG
28185679 ACCTAATCCTTGGTTGATAAGTCTGTAGGCTAAGGCTGTCACCCATTCTAAACAAGA
1 ACCTAATCCTTGGTTGATAAGTCTGTAGGCTAAGGCTGTCACCCATTCTAAACAAGA
28185736 ACCTAATCCTTGGTTGATAAGTCTGTAGGCTAAGGCTGTCACCCATTCTAAACAAGA
1 ACCTAATCCTTGGTTGATAAGTCTGTAGGCTAAGGCTGTCACCCATTCTAAACAAGA
*
28185793 ACCAAATC
1 ACCTAATC
28185801 GCAATTCTAC
Statistics
Matches: 64, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
57 64 1.00
ACGTcount: A:0.31, C:0.24, G:0.18, T:0.27
Consensus pattern (57 bp):
ACCTAATCCTTGGTTGATAAGTCTGTAGGCTAAGGCTGTCACCCATTCTAAACAAGA
Found at i:28189503 original size:27 final size:27
Alignment explanation
Indices: 28189462--28189527 Score: 105
Period size: 27 Copynumber: 2.4 Consensus size: 27
28189452 TTGTTTACTG
* *
28189462 ACATATAAGATAAAATAGTATCACATTA
1 ACATTTAA-ATAAAATAGTACCACATTA
28189490 ACATTTAAATAAAATAGTACCACATTA
1 ACATTTAAATAAAATAGTACCACATTA
28189517 ACATTTAAATA
1 ACATTTAAATA
28189528 CATTTGGATG
Statistics
Matches: 36, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
27 29 0.81
28 7 0.19
ACGTcount: A:0.53, C:0.12, G:0.05, T:0.30
Consensus pattern (27 bp):
ACATTTAAATAAAATAGTACCACATTA
Found at i:28211037 original size:36 final size:36
Alignment explanation
Indices: 28210991--28211250 Score: 221
Period size: 36 Copynumber: 7.4 Consensus size: 36
28210981 ATATTGTCGG
* * *
28210991 TTATCCGACTAGAGCTGGGTGCAATTATTTGTCGAT
1 TTATTCGACTAGTGCTGGGTACAATTATTTGTCGAT
* * *
28211027 TTATTCGACTAGTGC-AGGTCACAACTA-TTGTCG-G
1 TTATTCGACTAGTGCTGGGT-ACAATTATTTGTCGAT
* *
28211061 TTATTCGTCTAGTGCTGGGTGCAATTATTTGTCGAT
1 TTATTCGACTAGTGCTGGGTACAATTATTTGTCGAT
* * *
28211097 TTACTCGACTAGTGC-AGGTCACAACTA-TTGTCGA-
1 TTATTCGACTAGTGCTGGGT-ACAATTATTTGTCGAT
* ** **
28211131 TTATCCGACTAGCACTGGGCGCAATTATTTGTCGAT
1 TTATTCGACTAGTGCTGGGTACAATTATTTGTCGAT
* * * * *
28211167 TTATTCGACTAGTGCAGGGCACAACTA-TTGTTG-G
1 TTATTCGACTAGTGCTGGGTACAATTATTTGTCGAT
* * *
28211201 TTATTCGACTAGCGCTAGGCACAATTATTTGTCGAT
1 TTATTCGACTAGTGCTGGGTACAATTATTTGTCGAT
*
28211237 TTATTCAACTAGTG
1 TTATTCGACTAGTG
28211251 TAAGGCACAA
Statistics
Matches: 174, Mismatches: 40, Indels: 20
0.74 0.17 0.09
Matches are distributed among these distances:
34 58 0.33
35 47 0.27
36 69 0.40
ACGTcount: A:0.23, C:0.19, G:0.23, T:0.35
Consensus pattern (36 bp):
TTATTCGACTAGTGCTGGGTACAATTATTTGTCGAT
Found at i:28211078 original size:70 final size:70
Alignment explanation
Indices: 28210982--28211291 Score: 442
Period size: 70 Copynumber: 4.4 Consensus size: 70
28210972 GTGTAATTGA
* *
28210982 TATTGTCGGTTATCCGACTAGAGCTGGGTGCAATTATTTGTCGATTTATTCGACTAGTGCAGGTC
1 TATTGTCGGTTATCCGACTAGCGCTGGGCGCAATTATTTGTCGATTTATTCGACTAGTGCAGGTC
28211047 ACAAC
66 ACAAC
* * * * *
28211052 TATTGTCGGTTATTCGTCTAGTGCTGGGTGCAATTATTTGTCGATTTACTCGACTAGTGCAGGTC
1 TATTGTCGGTTATCCGACTAGCGCTGGGCGCAATTATTTGTCGATTTATTCGACTAGTGCAGGTC
28211117 ACAAC
66 ACAAC
* * *
28211122 TATTGTCGATTATCCGACTAGCACTGGGCGCAATTATTTGTCGATTTATTCGACTAGTGCAGGGC
1 TATTGTCGGTTATCCGACTAGCGCTGGGCGCAATTATTTGTCGATTTATTCGACTAGTGCAGGTC
28211187 ACAAC
66 ACAAC
* * * * * *
28211192 TATTGTTGGTTATTCGACTAGCGCTAGGCACAATTATTTGTCGATTTATTCAACTAGTGTAAGG-
1 TATTGTCGGTTATCCGACTAGCGCTGGGCGCAATTATTTGTCGATTTATTCGACTAGTG-CAGGT
28211256 CACAAC
65 CACAAC
* *
28211262 TATTATCGGTTATCCAACTAGCGCTGGGCG
1 TATTGTCGGTTATCCGACTAGCGCTGGGCG
28211292 TAAAACTTTA
Statistics
Matches: 213, Mismatches: 26, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
70 210 0.99
71 3 0.01
ACGTcount: A:0.23, C:0.19, G:0.23, T:0.34
Consensus pattern (70 bp):
TATTGTCGGTTATCCGACTAGCGCTGGGCGCAATTATTTGTCGATTTATTCGACTAGTGCAGGTC
ACAAC
Found at i:28217186 original size:13 final size:13
Alignment explanation
Indices: 28217168--28217198 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
28217158 TTATTTATAT
*
28217168 TTTATTTTATTTA
1 TTTATTTTAATTA
28217181 TTTATTTTAATTA
1 TTTATTTTAATTA
28217194 TTTAT
1 TTTAT
28217199 CCATCTTCCA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (13 bp):
TTTATTTTAATTA
Found at i:28219977 original size:11 final size:11
Alignment explanation
Indices: 28219961--28220056 Score: 76
Period size: 11 Copynumber: 9.0 Consensus size: 11
28219951 CTCTATTATT
*
28219961 CTCTCAATGTC
1 CTCTCAATTTC
*
28219972 CTCTCAATTTG
1 CTCTCAATTTC
28219983 CTCTCAATTTC
1 CTCTCAATTTC
*
28219994 CTTCTAAATTT-
1 C-TCTCAATTTC
*
28220005 CTCTCAA-ATC
1 CTCTCAATTTC
*
28220015 C-CT--ATTTA
1 CTCTCAATTTC
* *
28220023 ATCTCAATTTA
1 CTCTCAATTTC
28220034 CTCTCAATTTC
1 CTCTCAATTTC
28220045 CTCTCAAATTTC
1 CTCTC-AATTTC
28220057 TCTTAAATCC
Statistics
Matches: 67, Mismatches: 11, Indels: 13
0.74 0.12 0.14
Matches are distributed among these distances:
7 1 0.01
8 1 0.01
9 5 0.07
10 6 0.09
11 40 0.60
12 14 0.21
ACGTcount: A:0.24, C:0.30, G:0.02, T:0.44
Consensus pattern (11 bp):
CTCTCAATTTC
Found at i:28220031 original size:51 final size:51
Alignment explanation
Indices: 28219973--28220072 Score: 157
Period size: 51 Copynumber: 2.0 Consensus size: 51
28219963 CTCAATGTCC
* *
28219973 TCTCAATTTGCTCTCAATTTCCT-TCTAAATTTCTCTCAAATCCCTATTTAA
1 TCTCAATTTACTCTCAATTTCCTCTC-AAATTTCTCTCAAATCCATATTTAA
*
28220024 TCTCAATTTACTCTCAATTTCCTCTCAAATTTCTCTTAAATCCATATTT
1 TCTCAATTTACTCTCAATTTCCTCTCAAATTTCTCTCAAATCCATATTT
28220073 TTTAATTATT
Statistics
Matches: 45, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
51 43 0.96
52 2 0.04
ACGTcount: A:0.26, C:0.27, G:0.01, T:0.46
Consensus pattern (51 bp):
TCTCAATTTACTCTCAATTTCCTCTCAAATTTCTCTCAAATCCATATTTAA
Found at i:28220130 original size:29 final size:30
Alignment explanation
Indices: 28220070--28220126 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 30
28220060 TAAATCCATA
**
28220070 TTTTTTAATTATTTTTTAAAAAGATTTAAT
1 TTTTTTAATTATTTTTTAAAAAGATAAAAT
*
28220100 TTTTTTAATT-TTTTTTAAATAG-TAAAA
1 TTTTTTAATTATTTTTTAAAAAGATAAAA
28220127 ATTTGTACGA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
28 3 0.12
29 11 0.46
30 10 0.42
ACGTcount: A:0.37, C:0.00, G:0.04, T:0.60
Consensus pattern (30 bp):
TTTTTTAATTATTTTTTAAAAAGATAAAAT
Found at i:28221247 original size:14 final size:14
Alignment explanation
Indices: 28221216--28221261 Score: 51
Period size: 14 Copynumber: 3.3 Consensus size: 14
28221206 TAGCTGATTG
*
28221216 GTATTTAGTATT-T
1 GTATTTATTATTAT
28221229 AGTATTTATTATTAT
1 -GTATTTATTATTAT
28221244 GTA-TTATGTATTAT
1 GTATTTAT-TATTAT
28221258 GTAT
1 GTAT
28221262 ATAACTAATA
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
13 4 0.14
14 23 0.82
15 1 0.04
ACGTcount: A:0.28, C:0.00, G:0.13, T:0.59
Consensus pattern (14 bp):
GTATTTATTATTAT
Found at i:28221939 original size:18 final size:18
Alignment explanation
Indices: 28221903--28221945 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 18
28221893 TGCCAGGTGC
* *
28221903 GTATCCTAACCTTTTTAT
1 GTATCCTAACCCTTATAT
*
28221921 GTATCTTAACCCTTATAT
1 GTATCCTAACCCTTATAT
*
28221939 GTTTCCT
1 GTATCCT
28221946 TTTCTGAGTC
Statistics
Matches: 20, Mismatches: 5, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.21, C:0.23, G:0.07, T:0.49
Consensus pattern (18 bp):
GTATCCTAACCCTTATAT
Found at i:28222245 original size:21 final size:21
Alignment explanation
Indices: 28222201--28222245 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
28222191 AGATACCCTA
* * * *
28222201 CCGGAGGAACCAGAATCCCCG
1 CCGGAGCAACCACAAGCCCAG
28222222 CCGGAGCAACCACAAGCCCAG
1 CCGGAGCAACCACAAGCCCAG
28222243 CCG
1 CCG
28222246 AAAGCTGGAC
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.29, C:0.42, G:0.27, T:0.02
Consensus pattern (21 bp):
CCGGAGCAACCACAAGCCCAG
Found at i:28223698 original size:230 final size:228
Alignment explanation
Indices: 28223295--28223963 Score: 1006
Period size: 230 Copynumber: 3.0 Consensus size: 228
28223285 ATTTGGAAAT
**
28223295 AACTCTAAACCCTAACTTATTTAATTTTTCCTTAAAAATCCTTAACTTAAAAACACCAAAACCCT
1 AACTCTAAACCCTAACTTATTTAATTTTTCCTTAAAAA-CCTTAACTTAAAAACATTAAAACCCT
28223360 AACAAAAACCCTAACCCTAACCCTAATCTAATTTTTAAATTTTTTTAATTAAATTACTCAAGTAA
65 AACAAAAACCCTAACCCTAACCCTAATCTAATTTTTAAATTTTTTTAATTAAATTACTCAAGTAA
* *
28223425 CCCTAAACCCTAATATAATTGATTTTTTCTTAAAAAATAATAAACACGAAAACTAATCCAATTTT
130 CCTTAAA-CCTAATTTAATTGATTTTTTCTTAAAAAATAATAAACACGAAAACTAATCCAATTTT
* * *
28223490 GAAAAATTTATAAATAATTTAATTGACAAATCCTA
194 GAAAATTTTTTAAATAATTTAATTGACAAACCCTA
*
28223525 AACTCTAAACCCTAACTTATTTGATTTTTCCTTAAAAACCCTTAACTTAAAAACATTAAAACCCT
1 AACTCTAAACCCTAACTTATTTAATTTTTCCTTAAAAA-CCTTAACTTAAAAACATTAAAACCCT
* *
28223590 AACAAAAACCCTAACCCTAACCCTAATCTAATTTTTAAAATTTTTTAATTAAATTACACAAGTAA
65 AACAAAAACCCTAACCCTAACCCTAATCTAATTTTTAAATTTTTTTAATTAAATTACTCAAGTAA
28223655 CCTTAAACACTAATTTAATTGATTTTTTCTTAAAAAATAATAAACACGAAAACTAATCCAATTTT
130 CCTTAAAC-CTAATTTAATTGATTTTTTCTTAAAAAATAATAAACACGAAAACTAATCCAATTTT
28223720 GAAAATTTTTTAAATAATTTAATTGACAAACCCTA
194 GAAAATTTTTTAAATAATTTAATTGACAAACCCTA
28223755 AACTCTAAACCCTAACTTATTTAATTTTTCCTTAAAAA-C----C-------C-TT--AACCCTA
1 AACTCTAAACCCTAACTTATTTAATTTTTCCTTAAAAACCTTAACTTAAAAACATTAAAACCCTA
28223805 ACAAAAACCCTAA------CCCTAATCTAATTTTTAAATTTTTTTAATTAAATTACTCAAGTAA-
66 ACAAAAACCCTAACCCTAACCCTAATCTAATTTTTAAATTTTTTTAATTAAATTACTCAAGTAAC
28223863 CTCTAAACCTTAATTTAATTGA-TTTTTCTTAAAAAATAATAAACACGAAAACTAATCCAATTTT
131 CT-TAAACC-TAATTTAATTGATTTTTTCTTAAAAAATAATAAACACGAAAACTAATCCAATTTT
** *
28223927 GAATTTTTTTTAAATAATTTAATTGACAAACCTTA
194 GAAAATTTTTTAAATAATTTAATTGACAAACCCTA
28223962 AA
1 AA
28223964 GTAGAGGTGT
Statistics
Matches: 419, Mismatches: 17, Indels: 29
0.90 0.04 0.06
Matches are distributed among these distances:
207 79 0.19
208 60 0.14
214 20 0.05
216 2 0.00
217 1 0.00
224 1 0.00
228 1 0.00
229 1 0.00
230 254 0.61
ACGTcount: A:0.43, C:0.19, G:0.02, T:0.36
Consensus pattern (228 bp):
AACTCTAAACCCTAACTTATTTAATTTTTCCTTAAAAACCTTAACTTAAAAACATTAAAACCCTA
ACAAAAACCCTAACCCTAACCCTAATCTAATTTTTAAATTTTTTTAATTAAATTACTCAAGTAAC
CTTAAACCTAATTTAATTGATTTTTTCTTAAAAAATAATAAACACGAAAACTAATCCAATTTTGA
AAATTTTTTAAATAATTTAATTGACAAACCCTA
Found at i:28223725 original size:95 final size:94
Alignment explanation
Indices: 28223612--28223939 Score: 259
Period size: 102 Copynumber: 3.3 Consensus size: 94
28223602 AACCCTAACC
* *
28223612 CTAATCTAATTTTTAAAATTTTTTAATTAAATTACACAAGTAAC-CTTAAACACTAATTTAATTG
1 CTAATCCAATTTTGAAAATTTTTTAATTAAATTACACAAGTAACTC-TAAAC-CTAATTTAATTG
28223676 ATTTTTTCTTAAAAAATAATAAACACGAAAA
64 ATTTTTTCTTAAAAAATAATAAACACGAAAA
* * *
28223707 CTAATCCAATTTTGAAAATTTTTTAAATAATTTAATTGACA-AACCCTAAACTCTAAACCCTAAC
1 CTAATCCAATTTTGAAAA-TTTTT---TAATTAAATT-ACACAA--GT-AACTCTAAA-CCTAAT
* * * * **
28223771 TTATTTAATTTTTCCTTAAAAACCCTTAACCCT-AACAAAAACCCTAA
57 TTAATTGATTTTTTCTTAAAAA---ATAA---TAAACACGAA----AA
* * * *
28223818 CCCTAATCTAATTTTTAAATTTTTTTAATTAAATTACTCAAGTAACTCTAAACCTTAATTTAATT
1 --CTAATCCAATTTTGAAAATTTTTTAATTAAATTACACAAGTAACTCTAAACC-TAATTTAATT
28223883 GA-TTTTTCTTAAAAAATAATAAACACGAAAA
63 GATTTTTTCTTAAAAAATAATAAACACGAAAA
**
28223914 CTAATCCAATTTTGAATTTTTTTTAA
1 CTAATCCAATTTTGAAAATTTTTTAA
28223940 ATAATTTAAT
Statistics
Matches: 181, Mismatches: 27, Indels: 51
0.70 0.10 0.20
Matches are distributed among these distances:
94 23 0.13
95 16 0.09
96 7 0.04
99 12 0.07
100 9 0.05
101 1 0.01
102 33 0.18
103 2 0.01
105 17 0.09
106 18 0.10
107 7 0.04
108 3 0.02
109 11 0.06
111 2 0.01
112 5 0.03
113 15 0.08
ACGTcount: A:0.42, C:0.16, G:0.03, T:0.39
Consensus pattern (94 bp):
CTAATCCAATTTTGAAAATTTTTTAATTAAATTACACAAGTAACTCTAAACCTAATTTAATTGAT
TTTTTCTTAAAAAATAATAAACACGAAAA
Found at i:28223818 original size:18 final size:19
Alignment explanation
Indices: 28223788--28223823 Score: 65
Period size: 18 Copynumber: 1.9 Consensus size: 19
28223778 ATTTTTCCTT
28223788 AAAAACCCTTAACCCTAAC
1 AAAAACCCTTAACCCTAAC
28223807 AAAAACCC-TAACCCTAA
1 AAAAACCCTTAACCCTAA
28223824 TCTAATTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 9 0.53
19 8 0.47
ACGTcount: A:0.50, C:0.36, G:0.00, T:0.14
Consensus pattern (19 bp):
AAAAACCCTTAACCCTAAC
Found at i:28227414 original size:18 final size:17
Alignment explanation
Indices: 28227393--28227426 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
28227383 AAAAAATAAA
28227393 AAAAATAATTACATTATT
1 AAAAATAATTA-ATTATT
*
28227411 AAAATTAATTAATTAT
1 AAAAATAATTAATTAT
28227427 AAGAAAAATG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.41
Consensus pattern (17 bp):
AAAAATAATTAATTATT
Found at i:28229454 original size:9 final size:9
Alignment explanation
Indices: 28229437--28229467 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
28229427 TCGAGTTGAT
28229437 TCGAATAAC
1 TCGAATAAC
*
28229446 TCGATTAAC
1 TCGAATAAC
28229455 TCGAATAAC
1 TCGAATAAC
28229464 TCGA
1 TCGA
28229468 TTCGTTTAAC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.39, C:0.23, G:0.13, T:0.26
Consensus pattern (9 bp):
TCGAATAAC
Found at i:28235759 original size:17 final size:17
Alignment explanation
Indices: 28235737--28235771 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
28235727 CTTCAAAAGA
28235737 AAACTCAAGTTTCTTTC
1 AAACTCAAGTTTCTTTC
28235754 AAACTCAAGTTTCTTTC
1 AAACTCAAGTTTCTTTC
28235771 A
1 A
28235772 TTAAATCTTG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.31, C:0.23, G:0.06, T:0.40
Consensus pattern (17 bp):
AAACTCAAGTTTCTTTC
Found at i:28240032 original size:75 final size:74
Alignment explanation
Indices: 28239921--28240068 Score: 215
Period size: 75 Copynumber: 2.0 Consensus size: 74
28239911 TGTTTTAGAG
*
28239921 TTTCTTCTATGAAAAAAATGTTGTACTTCTTAATGTTCTACAATAATAAGGCATGGGCATGCCTT
1 TTTCTTCTATGAAAAAAATGTTGTACTTCCTAATGTTCTACAATAATAAGGCATGGGCATGCCTT
28239986 ATTCTTGAA
66 ATTCTTGAA
* * * * * **
28239995 TTTCTTTTGTGAACAAAAATTTTGTACTTCCTGATGTTCTGCAATAATAAGGTGTGGGCATGCCT
1 TTTCTTCTATGAA-AAAAATGTTGTACTTCCTAATGTTCTACAATAATAAGGCATGGGCATGCCT
28240060 TATTCTTGA
65 TATTCTTGA
28240069 TTCGCCCAAA
Statistics
Matches: 65, Mismatches: 8, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
74 11 0.17
75 54 0.83
ACGTcount: A:0.28, C:0.15, G:0.17, T:0.41
Consensus pattern (74 bp):
TTTCTTCTATGAAAAAAATGTTGTACTTCCTAATGTTCTACAATAATAAGGCATGGGCATGCCTT
ATTCTTGAA
Found at i:28242666 original size:78 final size:78
Alignment explanation
Indices: 28242529--28242685 Score: 244
Period size: 78 Copynumber: 2.0 Consensus size: 78
28242519 TGATGCGTTG
* *
28242529 CTAGATGCCGCTCATTTCTTATAACATTAAAAATGTTCTAGTATTACTACAAACATTACAAGAAC
1 CTAGATGCCACTCATTGCTTATAACATTAAAAATGTTCTAGTATTACTACAAACATTACAAGAAC
28242594 CTACAGGGTCACA
66 CTACAGGGTCACA
* * *
28242607 CTAGATGCCACTTATTGCTTGTAACATTAAAAATGTTCTAGTATTACTA-ACAACGTTACAAGAA
1 CTAGATGCCACTCATTGCTTATAACATTAAAAATGTTCTAGTATTACTACA-AACATTACAAGAA
*
28242671 TCTACAGGGTCACA
65 CCTACAGGGTCACA
28242685 C
1 C
28242686 CTTATGATTA
Statistics
Matches: 72, Mismatches: 6, Indels: 2
0.90 0.08 0.03
Matches are distributed among these distances:
77 1 0.01
78 71 0.99
ACGTcount: A:0.36, C:0.21, G:0.13, T:0.30
Consensus pattern (78 bp):
CTAGATGCCACTCATTGCTTATAACATTAAAAATGTTCTAGTATTACTACAAACATTACAAGAAC
CTACAGGGTCACA
Found at i:28249925 original size:124 final size:127
Alignment explanation
Indices: 28249707--28249958 Score: 368
Period size: 124 Copynumber: 2.0 Consensus size: 127
28249697 AAAATGCATT
* * *
28249707 TACTATGGATAATGATACATGTGATCTATTTATCTTACTTCATTGTTTTCATTCATTTCTCTCTA
1 TACTATGAATAATGATACATGTGATCTATTTATCTTACTTCATTGTTTTCATTCAATTCTATCTA
* *
28249772 TTTGTTCTACATGCAATTCTAGTTATCTCAAGCTAGCAG-AGGAACCGATTGGACATATTTAA
66 TTTGTTCTACATGCAATTCTAGTTATCTCAAGCTAGCAGAAGG-ACCGATTGAACATATATAA
* *
28249834 TACTATGAATAATGATACGTGTGATCTATTTCTCTTACTTCA-T-TTTT-ATTCAATTCTATCTA
1 TACTATGAATAATGATACATGTGATCTATTTATCTTACTTCATTGTTTTCATTCAATTCTATCTA
* * * *
28249896 TTTGTTCTACATGCAATTTTGGTTATCTCAAGTTAGCAGAAGGATCGATTGAACATATATAA
66 TTTGTTCTACATGCAATTCTAGTTATCTCAAGCTAGCAGAAGGACCGATTGAACATATATAA
28249958 T
1 T
28249959 TAGGACTTAA
Statistics
Matches: 113, Mismatches: 11, Indels: 5
0.88 0.09 0.04
Matches are distributed among these distances:
124 66 0.58
125 7 0.06
126 1 0.01
127 39 0.35
ACGTcount: A:0.29, C:0.16, G:0.13, T:0.42
Consensus pattern (127 bp):
TACTATGAATAATGATACATGTGATCTATTTATCTTACTTCATTGTTTTCATTCAATTCTATCTA
TTTGTTCTACATGCAATTCTAGTTATCTCAAGCTAGCAGAAGGACCGATTGAACATATATAA
Found at i:28262459 original size:27 final size:27
Alignment explanation
Indices: 28262405--28262459 Score: 67
Period size: 27 Copynumber: 2.0 Consensus size: 27
28262395 AATATAATAT
*
28262405 AATTATAAAATAATTAAATTGTACTTA
1 AATTATAAAATAATTAAATTGTAATTA
* *
28262432 AATTATTAAAAT-ATTGAATTTTAATTA
1 AATTA-TAAAATAATTAAATTGTAATTA
28262459 A
1 A
28262460 TTTTATAATA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
27 18 0.75
28 6 0.25
ACGTcount: A:0.51, C:0.02, G:0.04, T:0.44
Consensus pattern (27 bp):
AATTATAAAATAATTAAATTGTAATTA
Found at i:28263354 original size:20 final size:18
Alignment explanation
Indices: 28263321--28263357 Score: 56
Period size: 20 Copynumber: 1.9 Consensus size: 18
28263311 TGTTTTGTTG
28263321 ATATGTTTAATTTAATTA
1 ATATGTTTAATTTAATTA
28263339 ATATGATTTAAATTTAATT
1 ATATG-TTT-AATTTAATT
28263358 TGTGTTAGGT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 5 0.29
19 3 0.18
20 9 0.53
ACGTcount: A:0.41, C:0.00, G:0.05, T:0.54
Consensus pattern (18 bp):
ATATGTTTAATTTAATTA
Found at i:28267933 original size:16 final size:15
Alignment explanation
Indices: 28267891--28267935 Score: 54
Period size: 15 Copynumber: 2.9 Consensus size: 15
28267881 TGTTAAGGTA
28267891 AACTAATGAGCTCGC
1 AACTAATGAGCTCGC
** *
28267906 AACTAACAAGCTTGC
1 AACTAATGAGCTCGC
28267921 AGACTAATGAGCTCG
1 A-ACTAATGAGCTCG
28267936 TAGACTGACG
Statistics
Matches: 23, Mismatches: 6, Indels: 1
0.77 0.20 0.03
Matches are distributed among these distances:
15 13 0.57
16 10 0.43
ACGTcount: A:0.36, C:0.24, G:0.20, T:0.20
Consensus pattern (15 bp):
AACTAATGAGCTCGC
Found at i:28267940 original size:16 final size:16
Alignment explanation
Indices: 28267892--28267941 Score: 57
Period size: 16 Copynumber: 3.2 Consensus size: 16
28267882 GTTAAGGTAA
28267892 ACTAATGAGCTCGCA-
1 ACTAATGAGCTCGCAG
** *
28267907 ACTAACAAGCTTGCAG
1 ACTAATGAGCTCGCAG
*
28267923 ACTAATGAGCTCGTAG
1 ACTAATGAGCTCGCAG
28267939 ACT
1 ACT
28267942 GACGAACTTG
Statistics
Matches: 27, Mismatches: 7, Indels: 1
0.77 0.20 0.03
Matches are distributed among these distances:
15 12 0.44
16 15 0.56
ACGTcount: A:0.34, C:0.24, G:0.20, T:0.22
Consensus pattern (16 bp):
ACTAATGAGCTCGCAG
Found at i:28270355 original size:27 final size:26
Alignment explanation
Indices: 28270334--28270533 Score: 202
Period size: 27 Copynumber: 7.4 Consensus size: 26
28270324 GGGTATAATA
28270334 GTCATTTTACCCTATAGAGGTATTTC
1 GTCATTTTACCCTATAGAGGTATTTC
* *
28270360 GGTCATTTTACCTTATAGGGGTATTTC
1 -GTCATTTTACCCTATAGAGGTATTTC
* *
28270387 GATCATTCTACCCTATAGGGGTATTTC
1 G-TCATTTTACCCTATAGAGGTATTTC
* *
28270414 GATCATTTTACCCCATAGGGGTATTTC
1 G-TCATTTTACCCTATAGAGGTATTTC
* * *
28270441 GGTCATTTTACCCTATGGAGCTATTTTG
1 -GTCATTTTACCCTATAGAGGTA-TTTC
* *
28270469 GTCATTCTACCCTATGGAGGTATTTC
1 GTCATTTTACCCTATAGAGGTATTTC
* * *
28270495 GATCATTTTACCCTGTGGGGGTATTTC
1 G-TCATTTTACCCTATAGAGGTATTTC
*
28270522 GGTTATTTTACC
1 -GTCATTTTACC
28270534 TATTTTAGGG
Statistics
Matches: 150, Mismatches: 18, Indels: 10
0.84 0.10 0.06
Matches are distributed among these distances:
26 5 0.03
27 140 0.93
28 5 0.03
ACGTcount: A:0.20, C:0.20, G:0.20, T:0.41
Consensus pattern (26 bp):
GTCATTTTACCCTATAGAGGTATTTC
Found at i:28270393 original size:54 final size:54
Alignment explanation
Indices: 28270335--28270533 Score: 256
Period size: 54 Copynumber: 3.7 Consensus size: 54
28270325 GGTATAATAG
*
28270335 TCATTTTACCCTATAGAGGTATTTCGGTCATTTTACCTTATAGGGGTATTTCGA
1 TCATTTTACCCTATAGAGGTATTTCGGTCATTTTACCCTATAGGGGTATTTCGA
* * * * *
28270389 TCATTCTACCCTATAGGGGTATTTCGATCATTTTACCCCATAGGGGTATTTCGG
1 TCATTTTACCCTATAGAGGTATTTCGGTCATTTTACCCTATAGGGGTATTTCGA
* * * *
28270443 TCATTTTACCCTATGGAGCTATTTTGGTCATTCTACCCTAT-GGAGGTATTTCGA
1 TCATTTTACCCTATAGAGGTATTTCGGTCATTTTACCCTATAGG-GGTATTTCGA
* * * *
28270497 TCATTTTACCCTGTGGGGGTATTTCGGTTATTTTACC
1 TCATTTTACCCTATAGAGGTATTTCGGTCATTTTACC
28270534 TATTTTAGGG
Statistics
Matches: 123, Mismatches: 21, Indels: 2
0.84 0.14 0.01
Matches are distributed among these distances:
53 2 0.02
54 121 0.98
ACGTcount: A:0.20, C:0.20, G:0.20, T:0.41
Consensus pattern (54 bp):
TCATTTTACCCTATAGAGGTATTTCGGTCATTTTACCCTATAGGGGTATTTCGA
Found at i:28270443 original size:81 final size:81
Alignment explanation
Indices: 28270335--28270534 Score: 287
Period size: 81 Copynumber: 2.5 Consensus size: 81
28270325 GGTATAATAG
* *
28270335 TCATTTTACCCTATAGAGGTATTTCGGTCATTTTACCTTATAGG-GGTATTTCGATCATTCTACC
1 TCATTTTACCCTATAGGGGTATTTCGGTCATTTTACCTTAT-GGAGCTATTTCGATCATTCTACC
28270399 CTATAGG-GGTATTTCGA
65 CTAT-GGAGGTATTTCGA
* * * *
28270416 TCATTTTACCCCATAGGGGTATTTCGGTCATTTTACCCTATGGAGCTATTTTGGTCATTCTACCC
1 TCATTTTACCCTATAGGGGTATTTCGGTCATTTTACCTTATGGAGCTATTTCGATCATTCTACCC
28270481 TATGGAGGTATTTCGA
66 TATGGAGGTATTTCGA
* * *
28270497 TCATTTTACCCTGTGGGGGTATTTCGGTTATTTTACCT
1 TCATTTTACCCTATAGGGGTATTTCGGTCATTTTACCT
28270535 ATTTTAGGGT
Statistics
Matches: 106, Mismatches: 11, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
80 4 0.04
81 102 0.96
ACGTcount: A:0.20, C:0.20, G:0.20, T:0.41
Consensus pattern (81 bp):
TCATTTTACCCTATAGGGGTATTTCGGTCATTTTACCTTATGGAGCTATTTCGATCATTCTACCC
TATGGAGGTATTTCGA
Found at i:28284488 original size:51 final size:51
Alignment explanation
Indices: 28284433--28284610 Score: 178
Period size: 51 Copynumber: 3.5 Consensus size: 51
28284423 CGATAAATAA
* *
28284433 TGGTCACATTTGTAGTACTATGTGCAGGCTACTATGTGTACCGGATGGCCT
1 TGGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGATGGCCT
** * * * **
28284484 TGGTCATGTGTGTAGTACTATGTGCAAGCTACTACGTGAACCAGAAAG-CT
1 TGGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGATGGCCT
* * * * * * **
28284534 TGATCACGTGTGTAGTACTATGTGTAGGCTACTACATGTATCGGATGACAA
1 TGGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGATGGCCT
* *
28284585 TGGTCACATGGGTGGTACTATGTGCA
1 TGGTCACATGTGTAGTACTATGTGCA
28284611 AACCACCGAA
Statistics
Matches: 99, Mismatches: 27, Indels: 2
0.77 0.21 0.02
Matches are distributed among these distances:
50 39 0.39
51 60 0.61
ACGTcount: A:0.24, C:0.17, G:0.28, T:0.31
Consensus pattern (51 bp):
TGGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGATGGCCT
Found at i:28284565 original size:50 final size:51
Alignment explanation
Indices: 28284443--28284568 Score: 164
Period size: 50 Copynumber: 2.5 Consensus size: 51
28284433 TGGTCACATT
* * * ** * *
28284443 TGTAGTACTATGTGCAGGCTACTATGTGTACCGGATGGCCTTGGTCATGTG
1 TGTAGTACTATGTGCAGGCTACTACGTGAACCAGAAAGCCTTGATCACGTG
*
28284494 TGTAGTACTATGTGCAAGCTACTACGTGAACCAGAAAG-CTTGATCACGTG
1 TGTAGTACTATGTGCAGGCTACTACGTGAACCAGAAAGCCTTGATCACGTG
*
28284544 TGTAGTACTATGTGTAGGCTACTAC
1 TGTAGTACTATGTGCAGGCTACTAC
28284569 ATGTATCGGA
Statistics
Matches: 65, Mismatches: 10, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
50 33 0.51
51 32 0.49
ACGTcount: A:0.24, C:0.18, G:0.27, T:0.31
Consensus pattern (51 bp):
TGTAGTACTATGTGCAGGCTACTACGTGAACCAGAAAGCCTTGATCACGTG
Found at i:28292664 original size:27 final size:27
Alignment explanation
Indices: 28292634--28292694 Score: 122
Period size: 27 Copynumber: 2.3 Consensus size: 27
28292624 TAAGTAGGTG
28292634 TTACATTTTAATGAAACCATAAGGTTT
1 TTACATTTTAATGAAACCATAAGGTTT
28292661 TTACATTTTAATGAAACCATAAGGTTT
1 TTACATTTTAATGAAACCATAAGGTTT
28292688 TTACATT
1 TTACATT
28292695 CGGATTTAGG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 34 1.00
ACGTcount: A:0.36, C:0.11, G:0.10, T:0.43
Consensus pattern (27 bp):
TTACATTTTAATGAAACCATAAGGTTT
Found at i:28293083 original size:3 final size:3
Alignment explanation
Indices: 28293075--28293108 Score: 61
Period size: 3 Copynumber: 11.7 Consensus size: 3
28293065 ATTAAATATT
28293075 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA -AA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
28293109 GTGAATAAGT
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.07
3 28 0.93
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
TAA
Found at i:28297064 original size:17 final size:17
Alignment explanation
Indices: 28297039--28297083 Score: 81
Period size: 17 Copynumber: 2.6 Consensus size: 17
28297029 CCATACCCGA
*
28297039 GCCCGATACCTCCACGC
1 GCCCAATACCTCCACGC
28297056 GCCCAATACCTCCACGC
1 GCCCAATACCTCCACGC
28297073 GCCCAATACCT
1 GCCCAATACCT
28297084 GACTGTTAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 27 1.00
ACGTcount: A:0.22, C:0.51, G:0.13, T:0.13
Consensus pattern (17 bp):
GCCCAATACCTCCACGC
Found at i:28303799 original size:27 final size:27
Alignment explanation
Indices: 28303733--28303908 Score: 194
Period size: 27 Copynumber: 6.5 Consensus size: 27
28303723 AGACCCCAAA
* * *
28303733 ATAGGGTAACATGATCAAAATACCCTC
1 ATAGGGTAAAATGACCGAAATACCCTC
**
28303760 ATAAAGTAAAATGACCGAAATACCCTC
1 ATAGGGTAAAATGACCGAAATACCCTC
* *
28303787 ACAGGGTAGAATGACCGAAATACCCTC
1 ATAGGGTAAAATGACCGAAATACCCTC
* * * * *
28303814 ACAGGGTAGAATGAACAAAATTTCCC-C
1 ATAGGGTAAAATGACCGAAA-TACCCTC
28303841 ATAGGGTAAAATGACCGAAATACCGC-C
1 ATAGGGTAAAATGACCGAAATACC-CTC
* *
28303868 ATAGGGTAAAATGACCAAAATACCCCC
1 ATAGGGTAAAATGACCGAAATACCCTC
28303895 ATAGGGTAAAATGA
1 ATAGGGTAAAATGA
28303909 TTATTATACC
Statistics
Matches: 128, Mismatches: 18, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
26 4 0.03
27 120 0.94
28 4 0.03
ACGTcount: A:0.43, C:0.22, G:0.18, T:0.18
Consensus pattern (27 bp):
ATAGGGTAAAATGACCGAAATACCCTC
Found at i:28310807 original size:50 final size:50
Alignment explanation
Indices: 28310706--28310896 Score: 168
Period size: 50 Copynumber: 3.7 Consensus size: 50
28310696 GAATGAGATC
*
28310706 CCATGTAAGACCATGTCTGGGACATGGCATTGGCATCATTGAGATTATGAGAGGTT
1 CCATGTAAGACCATGTCTGGGACATGGCATTGGCA-C--CGAG---ATGAGAGGTT
* * * *
28310762 CCATGTAAGACCATGTTTAGGACATGGCGTTGGCACCGAGATGAGAGGTC
1 CCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAGGTT
** * * * **
28310812 CCCCGTAAGACCATATCTGGGACATGGCATGGGCACCGATATGAGA-ACT
1 CCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAGGTT
* * * *
28310861 CTCATGTAAGACCATATCTAGGATATGGAATTGGCA
1 C-CATGTAAGACCATGTCTGGGACATGGCATTGGCA
28310897 GTACAGAAAA
Statistics
Matches: 112, Mismatches: 22, Indels: 8
0.79 0.15 0.06
Matches are distributed among these distances:
49 1 0.01
50 75 0.67
53 3 0.03
55 1 0.01
56 32 0.29
ACGTcount: A:0.28, C:0.20, G:0.28, T:0.24
Consensus pattern (50 bp):
CCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAGGTT
Found at i:28318267 original size:50 final size:50
Alignment explanation
Indices: 28318164--28318356 Score: 206
Period size: 50 Copynumber: 3.7 Consensus size: 50
28318154 GGGAATGAGA
*
28318164 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCATTGAGATTATGAGAGG
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA-C--CGAG---ATGAGAGG
* * *
28318220 TCTCATATAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATGAGAGG
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAGG
** * * * **
28318270 TCCCCCGTAAGACCATCTCTGGGACATGGCATGGGCACCGATATGAGAAC
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAGG
* * *
28318320 TCCCATGTAAGACCATATCTAGGATATGGCATTGGCA
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA
28318357 GTACAGAAAA
Statistics
Matches: 117, Mismatches: 20, Indels: 6
0.82 0.14 0.04
Matches are distributed among these distances:
50 79 0.68
53 3 0.03
55 1 0.01
56 34 0.29
ACGTcount: A:0.27, C:0.22, G:0.27, T:0.23
Consensus pattern (50 bp):
TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAGG
Found at i:28321888 original size:20 final size:20
Alignment explanation
Indices: 28321863--28321900 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
28321853 ACTTCTCAAT
28321863 TCAACTTTCTTTGATACTCC
1 TCAACTTTCTTTGATACTCC
28321883 TCAACTTTCTTTGATACT
1 TCAACTTTCTTTGATACT
28321901 TTAGGTGAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.21, C:0.26, G:0.05, T:0.47
Consensus pattern (20 bp):
TCAACTTTCTTTGATACTCC
Found at i:28326822 original size:108 final size:106
Alignment explanation
Indices: 28326467--28326892 Score: 599
Period size: 107 Copynumber: 4.0 Consensus size: 106
28326457 TGGATTAAGA
* * * * *
28326467 TTTAAGAGGATATTTGGCTATTTGGTCGAAC-GAGAAACCGAAACCCAGCACATTAGGGCACG-T
1 TTTAAAAGGATATTTTGCTATTTGGTCGAACAAAAAAATCGAAACCCAGCACATTAGGGCACGTT
*
28326530 TTCTCAAATTTTCAAACGCAAAATATAGT-CTTACTTTGAAAT
66 TTCTCAAATTTCCAAACGCAAAATAT--TCCTTACTTTGAAAT
* * *
28326572 TTTAAAAGGTTA-TTTGACTATTTGGTCAAACAAAAAAATCGAAACTCAGCACATTAGGGCACGT
1 TTTAAAAGGATATTTTG-CTATTTGGTCGAACAAAAAAATCGAAACCCAGCACATTAGGGCACGT
*
28326636 TTTCTCAAATTTGCAAACGCAAAATATTACCTTACTTTGAAAT
65 TTTCTCAAATTTCCAAACGCAAAATATT-CCTTACTTTGAAAT
* *
28326679 TTTAAAAGGATATTTAGCTATTTGGTCGAACAAAAAAAATCGAAACCCAGTACATTAGGGCACGT
1 TTTAAAAGGATATTTTGCTATTTGGTCGAAC-AAAAAAATCGAAACCCAGCACATTAGGGCACGT
* *
28326744 TTTCTCGAATTTCCAAACGCAAAACATTCCTTACTTTGAAAT
65 TTTCTCAAATTTCCAAACGCAAAATATTCCTTACTTTGAAAT
* * *
28326786 TTTAATAGGATATTTTGCTATTTGGTCGAACGAAAAAAATCGAAACCCAGCACATTAAGACACGT
1 TTTAAAAGGATATTTTGCTATTTGGTCGAAC-AAAAAAATCGAAACCCAGCACATTAGGGCACGT
*
28326851 TTTCTCAAATTTCCAAATGCAAAATATTTCCTTACTTTGAAA
65 TTTCTCAAATTTCCAAACGCAAAATA-TTCCTTACTTTGAAA
28326893 AATTTTCCTT
Statistics
Matches: 287, Mismatches: 26, Indels: 13
0.88 0.08 0.04
Matches are distributed among these distances:
104 3 0.01
105 24 0.08
106 27 0.09
107 159 0.55
108 74 0.26
ACGTcount: A:0.37, C:0.18, G:0.14, T:0.31
Consensus pattern (106 bp):
TTTAAAAGGATATTTTGCTATTTGGTCGAACAAAAAAATCGAAACCCAGCACATTAGGGCACGTT
TTCTCAAATTTCCAAACGCAAAATATTCCTTACTTTGAAAT
Found at i:28326875 original size:215 final size:211
Alignment explanation
Indices: 28326467--28326892 Score: 613
Period size: 215 Copynumber: 2.0 Consensus size: 211
28326457 TGGATTAAGA
* * * *
28326467 TTTAAGAGGATATTTGGCTATTTGGTCGAACGAGAAACCGAAACCCAGCACATTAGGGCACGTTT
1 TTTAAAAGGATATTTAGCTATTTGGTCGAACAAAAAACCGAAACCCAGCACATTAGGGCACGTTT
* * *
28326532 CTCAAATTTTCAAACGCAAAATATAGTCTTACTTTGAAATTTTAAAAGGTTATTTGACTATTTGG
66 CTCAAATTTCCAAACGCAAAACATA-TCTTACTTTGAAATTTTAAAAGGATATTTGACTATTTGG
* * * *
28326597 TCAAACAAAAAAATCGAAACTCAGCACATTAGGGCACGTTTTCTCAAATTTGCAAACGCAAAATA
130 TCAAACAAAAAAATCGAAACCCAGCACATTAAGACACGTTTTCTCAAATTTCCAAACGCAAAATA
28326662 TTACCTTACTTTGAAAT
195 TTACCTTACTTTGAAAT
* *
28326679 TTTAAAAGGATATTTAGCTATTTGGTCGAACAAAAAAAATCGAAACCCAGTACATTAGGGCACGT
1 TTTAAAAGGATATTTAGCTATTTGGTCGAAC--AAAAAACCGAAACCCAGCACATTAGGGCACG-
* *
28326744 TTTCTCGAATTTCCAAACGCAAAACAT-TCCTTACTTTGAAATTTTAATAGGATATTTTG-CTAT
63 TTTCTCAAATTTCCAAACGCAAAACATAT-CTTACTTTGAAATTTTAAAAGGATA-TTTGACTAT
* *
28326807 TTGGTCGAACGAAAAAAATCGAAACCCAGCACATTAAGACACGTTTTCTCAAATTTCCAAATGCA
126 TTGGTCAAAC-AAAAAAATCGAAACCCAGCACATTAAGACACGTTTTCTCAAATTTCCAAACGCA
*
28326872 AAATATTTCCTTACTTTGAAA
190 AAATATTACCTTACTTTGAAA
28326893 AATTTTCCTT
Statistics
Matches: 190, Mismatches: 18, Indels: 9
0.88 0.08 0.04
Matches are distributed among these distances:
212 29 0.15
213 1 0.01
214 63 0.33
215 97 0.51
ACGTcount: A:0.37, C:0.18, G:0.14, T:0.31
Consensus pattern (211 bp):
TTTAAAAGGATATTTAGCTATTTGGTCGAACAAAAAACCGAAACCCAGCACATTAGGGCACGTTT
CTCAAATTTCCAAACGCAAAACATATCTTACTTTGAAATTTTAAAAGGATATTTGACTATTTGGT
CAAACAAAAAAATCGAAACCCAGCACATTAAGACACGTTTTCTCAAATTTCCAAACGCAAAATAT
TACCTTACTTTGAAAT
Found at i:28326908 original size:17 final size:19
Alignment explanation
Indices: 28326871--28326908 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
28326861 TTCCAAATGC
28326871 AAAATATTTCCTTACTTTGA
1 AAAATATTTCCTTA-TTTGA
28326891 AAAAT-TTTCCTT-TTTGA
1 AAAATATTTCCTTATTTGA
28326908 A
1 A
28326909 GCATGGTGTT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 6 0.33
19 7 0.39
20 5 0.28
ACGTcount: A:0.34, C:0.13, G:0.05, T:0.47
Consensus pattern (19 bp):
AAAATATTTCCTTATTTGA
Found at i:28328963 original size:44 final size:44
Alignment explanation
Indices: 28328901--28329361 Score: 355
Period size: 44 Copynumber: 10.7 Consensus size: 44
28328891 GACTGGATAC
* *
28328901 GATCTGCTCTACTGCAACTTCAGAGAGATAAGATCTGTGGTTTT
1 GATCTGCTCCACTGCAACTTCAGGGAGATAAGATCTGTGGTTTT
* * **
28328945 GATCCGCTCCACTGCAACTTCAGGGAGATAGGAT-TGTTTTCTTCT
1 GATCTGCTCCACTGCAACTTCAGGGAGATAAGATCTGTGGT-TT-T
* * *
28328990 G-TCTGCTCCACTGCAACTTCAGGGAGATAAGA-CTAT--ATGT
1 GATCTGCTCCACTGCAACTTCAGGGAGATAAGATCTGTGGTTTT
* * *
28329030 GATCTGCTCTACTGGAACTTCAGAGAGATAAGATCTGTGGTTTT
1 GATCTGCTCCACTGCAACTTCAGGGAGATAAGATCTGTGGTTTT
* * * *
28329074 AATCCGCTCCACTGCAAC-TCTAGGGAGATAGGAT-TG-GTTTCTTCT
1 GATCTGCTCCACTGCAACTTC-AGGGAGATAAGATCTGTG-GT-TT-T
* * * * **
28329119 G-TCTCCTCCACTACTACTTCAGGGAGATAAGA-CTG-GATGCT
1 GATCTGCTCCACTGCAACTTCAGGGAGATAAGATCTGTGGTTTT
* * * *
28329160 -ATCTACTCTACTGCAACTTCAGAGAGATAAGATCTGTGATTTT
1 GATCTGCTCCACTGCAACTTCAGGGAGATAAGATCTGTGGTTTT
* * *
28329203 GATCCGCTCCACTGCAACTTCAGGGAGATAGGAT-TG-GTTTCTTCT
1 GATCTGCTCCACTGCAACTTCAGGGAGATAAGATCTGTG-GT-TT-T
* * **
28329248 G-TCTGCTCCACTGCAACTTCAGGGATATAAGA-C--TGGATGC
1 GATCTGCTCCACTGCAACTTCAGGGAGATAAGATCTGTGGTTTT
* * * *
28329288 GATTTGCTCTATTGCAACTTCAGAGAGATAAGATCTGTGGTTTT
1 GATCTGCTCCACTGCAACTTCAGGGAGATAAGATCTGTGGTTTT
* * *
28329332 AATCCGCTCCACTGCAACTTTAGGGAGATA
1 GATCTGCTCCACTGCAACTTCAGGGAGATA
28329362 GGATTTGCTA
Statistics
Matches: 323, Mismatches: 68, Indels: 52
0.73 0.15 0.12
Matches are distributed among these distances:
40 3 0.01
41 83 0.26
42 9 0.03
43 18 0.06
44 203 0.63
45 7 0.02
ACGTcount: A:0.25, C:0.22, G:0.22, T:0.31
Consensus pattern (44 bp):
GATCTGCTCCACTGCAACTTCAGGGAGATAAGATCTGTGGTTTT
Found at i:28329085 original size:85 final size:85
Alignment explanation
Indices: 28328906--28329361 Score: 318
Period size: 85 Copynumber: 5.3 Consensus size: 85
28328896 GATACGATCT
* * * * * * *
28328906 GCTCTACTGCAACTTCAGAGAGATAAGATCTGTGGTTTTGATCCGCTCCACTGCAACTTCAGGGA
1 GCTCCACTGCAACTTCAGGGAGATAAGA-CTGT-GATGTGATCTGCTCTACTGCAACTTCAGAGA
* ** ** *
28328971 GATAGGAT-TGTTTTCTTCTGTCT
64 GATAAGATCTGGGTT-TT-AATCC
* *
28328994 GCTCCACTGCAACTTCAGGGAGATAAGACTAT-ATGTGATCTGCTCTACTGGAACTTCAGAGAGA
1 GCTCCACTGCAACTTCAGGGAGATAAGACTGTGATGTGATCTGCTCTACTGCAACTTCAGAGAGA
28329058 TAAGATCTGTGGTTTTAATCC
66 TAAGATCTG-GGTTTTAATCC
* * * ** * *
28329079 GCTCCACTGCAAC-TCTAGGGAGATAGGA-T-TGGTTTCTTCTGTCTCCTCCACTACTACTTCAG
1 GCTCCACTGCAACTTC-AGGGAGATAAGACTGTGATGTGATCTG-CT-CT--ACTGCAACTTCAG
* * ** *
28329141 GGAGATAAGA-CTGGATGCT-ATCT
61 AGAGATAAGATCTGGGTTTTAATCC
* * * * * * *
28329164 ACTCTACTGCAACTTCAGAGAGATAAGATCTGTGATTTTGATCCGCTCCACTGCAACTTCAGGGA
1 GCTCCACTGCAACTTCAGGGAGATAAGA-CTGTGA-TGTGATCTGCTCTACTGCAACTTCAGAGA
* * ** *
28329229 GATAGGAT-TGGTTTCTTCTGTCT
64 GATAAGATCTGGGTT-TT-AATCC
* * * *
28329252 GCTCCACTGCAACTTCAGGGATATAAGACTG-GATGCGATTTGCTCTATTGCAACTTCAGAGAGA
1 GCTCCACTGCAACTTCAGGGAGATAAGACTGTGATGTGATCTGCTCTACTGCAACTTCAGAGAGA
28329316 TAAGATCTGTGGTTTTAATCC
66 TAAGATCTG-GGTTTTAATCC
*
28329337 GCTCCACTGCAACTTTAGGGAGATA
1 GCTCCACTGCAACTTCAGGGAGATA
28329362 GGATTTGCTA
Statistics
Matches: 287, Mismatches: 62, Indels: 41
0.74 0.16 0.11
Matches are distributed among these distances:
83 1 0.00
84 9 0.03
85 161 0.56
86 18 0.06
87 16 0.06
88 76 0.26
89 6 0.02
ACGTcount: A:0.25, C:0.22, G:0.22, T:0.31
Consensus pattern (85 bp):
GCTCCACTGCAACTTCAGGGAGATAAGACTGTGATGTGATCTGCTCTACTGCAACTTCAGAGAGA
TAAGATCTGGGTTTTAATCC
Found at i:28329085 original size:129 final size:129
Alignment explanation
Indices: 28328855--28329366 Score: 801
Period size: 129 Copynumber: 4.0 Consensus size: 129
28328845 ACACTTGCTA
* * * * * *
28328855 TCTTCAGTCTGTTACACTGCAACCTCAGTGAGATAAGACTGGATACGATCTGCTCTACTGCAACT
1 TCTTCTGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTGGATGCGATCTGCTCTACTGCAACT
* *
28328920 TCAGAGAGATAAGATCTGTGGTTTTGATCCGCTCCACTGCAACTTCAGGGAGATAGGATTGTTT
66 TCAGAGAGATAAGATCTGTGGTTTTAATCCGCTCCACTGCAACTTCAGGGAGATAGGATTGGTT
** * *
28328984 TCTTCTGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTATATGTGATCTGCTCTACTGGAACT
1 TCTTCTGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTGGATGCGATCTGCTCTACTGCAACT
28329049 TCAGAGAGATAAGATCTGTGGTTTTAATCCGCTCCACTGCAAC-TCTAGGGAGATAGGATTGGTT
66 TCAGAGAGATAAGATCTGTGGTTTTAATCCGCTCCACTGCAACTTC-AGGGAGATAGGATTGGTT
* * * * *
28329113 TCTTCTGTCTCCTCCACTACTACTTCAGGGAGATAAGACTGGATGCTATCTACTCTACTGCAACT
1 TCTTCTGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTGGATGCGATCTGCTCTACTGCAACT
* *
28329178 TCAGAGAGATAAGATCTGTGATTTTGATCCGCTCCACTGCAACTTCAGGGAGATAGGATTGGTT
66 TCAGAGAGATAAGATCTGTGGTTTTAATCCGCTCCACTGCAACTTCAGGGAGATAGGATTGGTT
* * *
28329242 TCTTCTGTCTGCTCCACTGCAACTTCAGGGATATAAGACTGGATGCGATTTGCTCTATTGCAACT
1 TCTTCTGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTGGATGCGATCTGCTCTACTGCAACT
*
28329307 TCAGAGAGATAAGATCTGTGGTTTTAATCCGCTCCACTGCAACTTTAGGGAGATAGGATT
66 TCAGAGAGATAAGATCTGTGGTTTTAATCCGCTCCACTGCAACTTCAGGGAGATAGGATT
28329367 TGCTAGCTTT
Statistics
Matches: 347, Mismatches: 34, Indels: 4
0.90 0.09 0.01
Matches are distributed among these distances:
128 2 0.01
129 343 0.99
130 2 0.01
ACGTcount: A:0.25, C:0.22, G:0.22, T:0.31
Consensus pattern (129 bp):
TCTTCTGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTGGATGCGATCTGCTCTACTGCAACT
TCAGAGAGATAAGATCTGTGGTTTTAATCCGCTCCACTGCAACTTCAGGGAGATAGGATTGGTT
Found at i:28329431 original size:45 final size:45
Alignment explanation
Indices: 28329367--28329556 Score: 263
Period size: 45 Copynumber: 4.2 Consensus size: 45
28329357 AGATAGGATT
* * * *
28329367 TGCTAGCTTTGATCTACTTCGCTGCCAATACAGGAATACAAGATC
1 TGCTATCTTCGATCTACTTCACTGCCAATACAGGAAGACAAGATC
* *
28329412 TGCTATCTTTGATCTACTTCGCTGCCAATACAGGAAGACAAGATC
1 TGCTATCTTCGATCTACTTCACTGCCAATACAGGAAGACAAGATC
*
28329457 TGCTATCTTCGATCTACTTCACTGCCAATACAGGAATACAAGATC
1 TGCTATCTTCGATCTACTTCACTGCCAATACAGGAAGACAAGATC
* * * * **
28329502 TGCTATCTTCGATCTGCTTCACTGTCAGTACAAGAAGGTAAGATC
1 TGCTATCTTCGATCTACTTCACTGCCAATACAGGAAGACAAGATC
28329547 TGCTATCTTC
1 TGCTATCTTC
28329557 ACTGATCTGT
Statistics
Matches: 133, Mismatches: 12, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
45 133 1.00
ACGTcount: A:0.28, C:0.25, G:0.17, T:0.31
Consensus pattern (45 bp):
TGCTATCTTCGATCTACTTCACTGCCAATACAGGAAGACAAGATC
Found at i:28341368 original size:107 final size:108
Alignment explanation
Indices: 28341134--28341563 Score: 611
Period size: 108 Copynumber: 4.0 Consensus size: 108
28341124 ATGGATTAAG
* * * * *
28341134 ATTTAAGATGATATTTGGCTATTTGGTCGAACG--AGAAATCAAAACCCATCACATTAGGGCACG
1 ATTTAAAAGGATATTTGGCTATTTGGTCGAACGAAAAAAATCGAAACCCAGCACATTAGGGCACG
* * *
28341197 -TTCCTCGAATTTCCAAACGCAAAATA--GTCTTACTTTGAAA
66 TTTTCTCAAATTTCCAAACGCAAAATATTGCCTTACTTTGAAA
* * * *
28341237 TTTTAAAAGGTTATTTGGCTATTTGGTCAAACG-AAAAAATCGAAACCCAGCACATTAGGACACG
1 ATTTAAAAGGATATTTGGCTATTTGGTCGAACGAAAAAAATCGAAACCCAGCACATTAGGGCACG
*
28341301 TTTTCTCAAATTTCCAAACGCAAAATATTACCTTACTTTGAAA
66 TTTTCTCAAATTTCCAAACGCAAAATATTGCCTTACTTTGAAA
* * *
28341344 ATTTAAAAGGATATTTAGCAATTTGGTCGAACGAAAAAAATCGAAACCCAGCACATTAGGGCACA
1 ATTTAAAAGGATATTTGGCTATTTGGTCGAACGAAAAAAATCGAAACCCAGCACATTAGGGCACG
* *
28341409 TTTTCTCAAATTTCCAAACGCAAAACATTGCCTGACTTTGAAA
66 TTTTCTCAAATTTCCAAACGCAAAATATTGCCTTACTTTGAAA
* * * *
28341452 TTTTAATAGGATATTTTGCTATTTGGTCGAACGAAAAAAATCGAAACCCAGCACATTAGGGCATG
1 ATTTAAAAGGATATTTGGCTATTTGGTCGAACGAAAAAAATCGAAACCCAGCACATTAGGGCACG
*
28341517 TTTTCTCGAATTTCCAAACGCAAAATATTGCCTTACTTTGAAA
66 TTTTCTCAAATTTCCAAACGCAAAATATTGCCTTACTTTGAAA
28341560 ATTT
1 ATTT
28341564 TCCCTTTTTA
Statistics
Matches: 289, Mismatches: 33, Indels: 5
0.88 0.10 0.02
Matches are distributed among these distances:
103 28 0.10
104 26 0.09
105 24 0.08
107 40 0.14
108 171 0.59
ACGTcount: A:0.37, C:0.19, G:0.15, T:0.30
Consensus pattern (108 bp):
ATTTAAAAGGATATTTGGCTATTTGGTCGAACGAAAAAAATCGAAACCCAGCACATTAGGGCACG
TTTTCTCAAATTTCCAAACGCAAAATATTGCCTTACTTTGAAA
Found at i:28341765 original size:24 final size:23
Alignment explanation
Indices: 28341690--28341767 Score: 63
Period size: 24 Copynumber: 3.3 Consensus size: 23
28341680 ATACAATAAC
28341690 AAATAAATAAAT-AA-ATAAACTAA
1 AAATAAATAAATGAACATAAA-T-A
* *
28341713 AACATAAAAAAATGGACATATGAAT-
1 AA-ATAAATAAATGAACATA--AATA
28341738 AAATAAATAAATGAACATAAAGTA
1 AAATAAATAAATGAACATAAA-TA
28341762 AAATAA
1 AAATAA
28341768 TAATAATAAA
Statistics
Matches: 44, Mismatches: 4, Indels: 13
0.72 0.07 0.21
Matches are distributed among these distances:
22 2 0.05
23 3 0.07
24 30 0.68
25 3 0.07
26 3 0.07
27 1 0.02
28 2 0.05
ACGTcount: A:0.68, C:0.05, G:0.06, T:0.21
Consensus pattern (23 bp):
AAATAAATAAATGAACATAAATA
Found at i:28354348 original size:44 final size:43
Alignment explanation
Indices: 28354292--28354597 Score: 185
Period size: 44 Copynumber: 7.1 Consensus size: 43
28354282 AAACCAATCC
* * * *
28354292 TATCTCCCTGAAGTTGAAGTGGAGCGGATTAAAACCACAGATCT
1 TATCTCTCTGAAGTTGCAGTAGAGCAGA-TAAAACCACAGATCT
* * * * *
28354336 TATATCTCTGAAGTTGCAGTAGATCAGATCACATC-CAG-TCT
1 TATCTCTCTGAAGTTGCAGTAGAGCAGATAAAACCACAGATCT
* * * **
28354377 TATCTCTTTGAAATTGCAGTAGAGCAGACAAAAGAAACCA-ATCT
1 TATCTCTCTGAAGTTGCAGTAGAGCAGATAAAA-CCA-CAGATCT
* * * *
28354421 TATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAACCACAAATCT
1 TATCTCTCTGAAGTTGCAGTAGAGCAGA-TAAAACCACAGATCT
* *** * *
28354465 TATCTCTCTGAAGTTGCAGTAGAGTAGATCGCATC-CAG-TTT
1 TATCTCTCTGAAGTTGCAGTAGAGCAGATAAAACCACAGATCT
* * * *
28354506 TATCTCCCTGAAGTTGCAGCAGAGCAGACAGAAGA-AACCA-ATCT
1 TATCTCTCTGAAGTTGCAGTAGAGCAGATA-AA-ACCA-CAGATCT
* * * * * *
28354550 TATCTCCCTGAAGTTGTAATGGAGCGGATTAAAACCACATATCT
1 TATCTCTCTGAAGTTGCAGTAGAGCAGA-TAAAACCACAGATCT
28354594 TATC
1 TATC
28354598 CCCATTGAGT
Statistics
Matches: 196, Mismatches: 52, Indels: 28
0.71 0.19 0.10
Matches are distributed among these distances:
41 56 0.29
42 5 0.03
43 13 0.07
44 117 0.60
45 5 0.03
ACGTcount: A:0.32, C:0.21, G:0.19, T:0.27
Consensus pattern (43 bp):
TATCTCTCTGAAGTTGCAGTAGAGCAGATAAAACCACAGATCT
Found at i:28354510 original size:129 final size:129
Alignment explanation
Indices: 28354280--28354661 Score: 538
Period size: 129 Copynumber: 3.0 Consensus size: 129
28354270 AGAACAAATC
* * *
28354280 AGAAACCAATCCTATCTCCCTGAAGTTGAAGTGGAGCGGATTAAAACCACAGATCTTATATCTCT
1 AGAAACCAATCTTATCTCCCTGAAGTTGAAGTGGAGCGGATTAAAACCACAAATCTTATCTCTCT
* **
28354345 GAAGTTGCAGTAGA-TCAGATCACATCCAGTCTTATCTCTTTGAAATTGCAGTAGAGCAGACAAA
66 GAAGTTGCAGTAGAGT-AGATCGCATCCAGTCTTATCTCCCTGAAATTGCAGTAGAGCAGACAAA
*
28354409 AGAAACCAATCTTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAACCACAAATCTTATCTCTCT
1 AGAAACCAATCTTATCTCCCTGAAGTTGAAGTGGAGCGGATTAAAACCACAAATCTTATCTCTCT
* * * *
28354474 GAAGTTGCAGTAGAGTAGATCGCATCCAGTTTTATCTCCCTGAAGTTGCAGCAGAGCAGACAGA
66 GAAGTTGCAGTAGAGTAGATCGCATCCAGTCTTATCTCCCTGAAATTGCAGTAGAGCAGACAAA
* *
28354538 AGAAACCAATCTTATCTCCCTGAAGTTGTAA-TGGAGCGGATTAAAACCACATATCTTATC-CCC
1 AGAAACCAATCTTATCTCCCTGAAGTTG-AAGTGGAGCGGATTAAAACCACAAATCTTATCTCTC
* * * * *
28354601 ATTG-AGTTACAGTAGAGTAGATCGCATCAAGCCTTATCTCCCTGAATTTGCAGTGGAGCAG
65 --TGAAGTTGCAGTAGAGTAGATCGCATCCAGTCTTATCTCCCTGAAATTGCAGTAGAGCAG
28354662 GTTGAAGATA
Statistics
Matches: 228, Mismatches: 21, Indels: 8
0.89 0.08 0.03
Matches are distributed among these distances:
128 2 0.01
129 222 0.97
130 4 0.02
ACGTcount: A:0.32, C:0.22, G:0.20, T:0.26
Consensus pattern (129 bp):
AGAAACCAATCTTATCTCCCTGAAGTTGAAGTGGAGCGGATTAAAACCACAAATCTTATCTCTCT
GAAGTTGCAGTAGAGTAGATCGCATCCAGTCTTATCTCCCTGAAATTGCAGTAGAGCAGACAAA
Found at i:28354637 original size:85 final size:85
Alignment explanation
Indices: 28354548--28354707 Score: 211
Period size: 85 Copynumber: 1.9 Consensus size: 85
28354538 AGAAACCAAT
* * *
28354548 CTTATCTCCCTGAAGTTGTAATGGAGC-GGATT-AA-A-ACCACATATCTTATCCCCATTGAGTT
1 CTTATCTCCCTGAAGTTGCAATGGAGCAGG-TTGAAGATA-C-CA-ATCTCATCCCCATGGAGTT
28354609 ACAGTAGAGTAGATCGCATCAAGC
62 ACAGTAGAGTAGATCGCATCAAGC
* *
28354633 CTTATCTCCCTGAATTTGCAGTGGAGCAGGTTGAAGATACCAATCTCATCCCCATGGAGTTACAG
1 CTTATCTCCCTGAAGTTGCAATGGAGCAGGTTGAAGATACCAATCTCATCCCCATGGAGTTACAG
28354698 TAGAGTAGAT
66 TAGAGTAGAT
28354708 TGAAGTTACA
Statistics
Matches: 66, Mismatches: 5, Indels: 8
0.84 0.06 0.10
Matches are distributed among these distances:
85 57 0.86
86 6 0.09
87 2 0.03
88 1 0.02
ACGTcount: A:0.29, C:0.22, G:0.21, T:0.28
Consensus pattern (85 bp):
CTTATCTCCCTGAAGTTGCAATGGAGCAGGTTGAAGATACCAATCTCATCCCCATGGAGTTACAG
TAGAGTAGATCGCATCAAGC
Found at i:28360635 original size:25 final size:25
Alignment explanation
Indices: 28360580--28360652 Score: 96
Period size: 25 Copynumber: 2.9 Consensus size: 25
28360570 CCATAGTTCG
*
28360580 TATGATCTTACCGATTTCAGCTCGT
1 TATGAGCTTACCGATTTCAGCTCGT
*
28360605 TA-GAGCTTACCGATTCTCAGCT-TT
1 TATGAGCTTACCGATT-TCAGCTCGT
28360629 TATGAGCTTACCGTATTTCAGCTC
1 TATGAGCTTACCG-ATTTCAGCTC
28360653 AATGGAGCTT
Statistics
Matches: 42, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
24 15 0.36
25 24 0.57
26 3 0.07
ACGTcount: A:0.21, C:0.25, G:0.16, T:0.38
Consensus pattern (25 bp):
TATGAGCTTACCGATTTCAGCTCGT
Found at i:28360660 original size:25 final size:23
Alignment explanation
Indices: 28360581--28360665 Score: 80
Period size: 25 Copynumber: 3.5 Consensus size: 23
28360571 CATAGTTCGT
* *
28360581 ATGATCTTACCGATTTCAGCTCG
1 ATGAGCTTACCGATTTCAGCTCA
* **
28360604 TTAGAGCTTACCGATTCTCAGCTTTT
1 AT-GAGCTTACCGATT-TCAGC-TCA
28360630 ATGAGCTTACCGTATTTCAGCTCA
1 ATGAGCTTACCG-ATTTCAGCTCA
28360654 ATGGAGCTTACC
1 AT-GAGCTTACC
28360666 AATTATGGTT
Statistics
Matches: 50, Mismatches: 7, Indels: 8
0.77 0.11 0.12
Matches are distributed among these distances:
23 1 0.02
24 15 0.30
25 29 0.58
26 5 0.10
ACGTcount: A:0.22, C:0.25, G:0.18, T:0.35
Consensus pattern (23 bp):
ATGAGCTTACCGATTTCAGCTCA
Found at i:28360780 original size:50 final size:50
Alignment explanation
Indices: 28360705--28360804 Score: 191
Period size: 50 Copynumber: 2.0 Consensus size: 50
28360695 AAAAATTGAA
*
28360705 GGACTTACAGTTCAATACACCTCATATGTACTACCTGCGTATCTAACGAT
1 GGACTTACAGTTCAATACACCTCATATGTACTACCTGCCTATCTAACGAT
28360755 GGACTTACAGTTCAATACACCTCATATGTACTACCTGCCTATCTAACGAT
1 GGACTTACAGTTCAATACACCTCATATGTACTACCTGCCTATCTAACGAT
28360805 ATTCTAAGCG
Statistics
Matches: 49, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
50 49 1.00
ACGTcount: A:0.30, C:0.27, G:0.13, T:0.30
Consensus pattern (50 bp):
GGACTTACAGTTCAATACACCTCATATGTACTACCTGCCTATCTAACGAT
Found at i:28366571 original size:14 final size:15
Alignment explanation
Indices: 28366549--28366625 Score: 52
Period size: 14 Copynumber: 5.0 Consensus size: 15
28366539 CAATCAAACA
28366549 CCAGAAAAT-ATTTT
1 CCAGAAAATCATTTT
*
28366563 CCAGTAAATCATTTT
1 CCAGAAAATCATTTT
*
28366578 ACAGAAAAGTAAAACATTTT
1 CCAGAAAA-T----CATTTT
28366598 CCAG-AAATCATTTT
1 CCAGAAAATCATTTT
* *
28366612 ACGGAAAA-CATTTT
1 CCAGAAAATCATTTT
28366626 ACTGGCAATC
Statistics
Matches: 50, Mismatches: 6, Indels: 14
0.71 0.09 0.20
Matches are distributed among these distances:
14 22 0.44
15 14 0.28
16 1 0.02
18 1 0.02
19 3 0.06
20 9 0.18
ACGTcount: A:0.43, C:0.16, G:0.09, T:0.32
Consensus pattern (15 bp):
CCAGAAAATCATTTT
Found at i:28366590 original size:20 final size:20
Alignment explanation
Indices: 28366565--28366604 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
28366555 AATATTTTCC
*
28366565 AGTAAATCATTTTACAGAAA
1 AGTAAAACATTTTACAGAAA
*
28366585 AGTAAAACATTTTCCAGAAA
1 AGTAAAACATTTTACAGAAA
28366605 TCATTTTACG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.50, C:0.12, G:0.10, T:0.28
Consensus pattern (20 bp):
AGTAAAACATTTTACAGAAA
Found at i:28366610 original size:34 final size:35
Alignment explanation
Indices: 28366553--28366619 Score: 109
Period size: 34 Copynumber: 1.9 Consensus size: 35
28366543 CAAACACCAG
*
28366553 AAAATATTTTCCAGTAAATCATTTTACAGAAAAGT
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
*
28366588 AAAACATTTTCCAG-AAATCATTTTACGGAAAA
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAA
28366620 CATTTTACTG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 17 0.57
35 13 0.43
ACGTcount: A:0.46, C:0.13, G:0.09, T:0.31
Consensus pattern (35 bp):
AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
Found at i:28366626 original size:14 final size:14
Alignment explanation
Indices: 28366588--28366627 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
28366578 ACAGAAAAGT
*
28366588 AAAACATTTTCCAG
1 AAAACATTTTACAG
* *
28366602 AAATCATTTTACGG
1 AAAACATTTTACAG
28366616 AAAACATTTTAC
1 AAAACATTTTAC
28366628 TGGCAATCAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.42, C:0.17, G:0.07, T:0.33
Consensus pattern (14 bp):
AAAACATTTTACAG
Found at i:28372194 original size:21 final size:21
Alignment explanation
Indices: 28372170--28372228 Score: 55
Period size: 21 Copynumber: 2.8 Consensus size: 21
28372160 ATTTTAGAAT
* * *
28372170 TAAATATTATTAAAATATATA
1 TAAAAATTATAAAAAAATATA
*
28372191 TAAAAATTATAAAAAAATATTT
1 TAAAAATTATAAAAAAATA-TA
* *
28372213 TTAAAATTTTAAAAAA
1 TAAAAATTATAAAAAA
28372229 TTAATTAATT
Statistics
Matches: 31, Mismatches: 6, Indels: 1
0.82 0.16 0.03
Matches are distributed among these distances:
21 16 0.52
22 15 0.48
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (21 bp):
TAAAAATTATAAAAAAATATA
Found at i:28372207 original size:23 final size:22
Alignment explanation
Indices: 28372181--28372228 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 22
28372171 AAATATTATT
28372181 AAAATATATATAAAAATTATAAA
1 AAAATAT-TATAAAAATTATAAA
* * *
28372204 AAAATATTTTTAAAATTTTAAA
1 AAAATATTATAAAAATTATAAA
28372226 AAA
1 AAA
28372229 TTAATTAATT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
22 15 0.68
23 7 0.32
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (22 bp):
AAAATATTATAAAAATTATAAA
Found at i:28377956 original size:38 final size:39
Alignment explanation
Indices: 28377905--28377996 Score: 143
Period size: 38 Copynumber: 2.4 Consensus size: 39
28377895 AGTTTAAGTC
*
28377905 TTTAATTATGTCATAATTTGAACATCATTAAT-ATGAG-T
1 TTTAATTATGTCATAATCTGAACATCATTAATAATG-GTT
*
28377943 TTTAATTATGTCATAATCTGAACATCTTTAATAATGGTT
1 TTTAATTATGTCATAATCTGAACATCATTAATAATGGTT
28377982 TTTAATTATGTCATA
1 TTTAATTATGTCATA
28377997 GTTTAGGACA
Statistics
Matches: 50, Mismatches: 2, Indels: 3
0.91 0.04 0.05
Matches are distributed among these distances:
38 31 0.62
39 19 0.38
ACGTcount: A:0.35, C:0.09, G:0.10, T:0.47
Consensus pattern (39 bp):
TTTAATTATGTCATAATCTGAACATCATTAATAATGGTT
Found at i:28378011 original size:38 final size:36
Alignment explanation
Indices: 28377905--28378011 Score: 117
Period size: 38 Copynumber: 2.8 Consensus size: 36
28377895 AGTTTAAGTC
28377905 TTTAATTATGTCATAATTTGAACATCATTAATATGAGT
1 TTTAATTATGTCATAATTTGAACAT--TTAATATGAGT
*
28377943 TTTAATTATGTCATAATCTGAACATCTTTAATAATG-GTT
1 TTTAATTATGTCATAATTTGAACA--TTTAAT-ATGAG-T
* *
28377982 TTTAATTATGTCATAGTTTAGGACATTTAA
1 TTTAATTATGTCATAATTT-GAACATTTAA
28378012 AACATATTTT
Statistics
Matches: 60, Mismatches: 4, Indels: 10
0.81 0.05 0.14
Matches are distributed among these distances:
38 34 0.57
39 21 0.35
40 5 0.08
ACGTcount: A:0.35, C:0.08, G:0.11, T:0.46
Consensus pattern (36 bp):
TTTAATTATGTCATAATTTGAACATTTAATATGAGT
Found at i:28386079 original size:49 final size:49
Alignment explanation
Indices: 28386016--28386114 Score: 198
Period size: 49 Copynumber: 2.0 Consensus size: 49
28386006 AACAATTTGG
28386016 ACTAAACAAAAGCGATTGTGATCATTCAATGTTTTTTATAAACAATCAA
1 ACTAAACAAAAGCGATTGTGATCATTCAATGTTTTTTATAAACAATCAA
28386065 ACTAAACAAAAGCGATTGTGATCATTCAATGTTTTTTATAAACAATCAA
1 ACTAAACAAAAGCGATTGTGATCATTCAATGTTTTTTATAAACAATCAA
28386114 A
1 A
28386115 GGCTGAAGTT
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
49 50 1.00
ACGTcount: A:0.43, C:0.14, G:0.10, T:0.32
Consensus pattern (49 bp):
ACTAAACAAAAGCGATTGTGATCATTCAATGTTTTTTATAAACAATCAA
Found at i:28392950 original size:52 final size:52
Alignment explanation
Indices: 28392868--28392976 Score: 175
Period size: 52 Copynumber: 2.1 Consensus size: 52
28392858 AATCCAAATA
*
28392868 GTCACAAATTAACTAATCTTTTGAGCTTGAAAATTGACAGCTTGT-TTGAATT
1 GTCACAAATTAACTAATCTTTTGAGATTGAAAATTGACAGCTT-TATTGAATT
* *
28392920 GTCACAAATTGAGTAATCTTTTGAGATTGAAAATTGACAGCTTTATTGAATT
1 GTCACAAATTAACTAATCTTTTGAGATTGAAAATTGACAGCTTTATTGAATT
28392972 GTCAC
1 GTCAC
28392977 TAATAAATTT
Statistics
Matches: 53, Mismatches: 3, Indels: 2
0.91 0.05 0.03
Matches are distributed among these distances:
51 1 0.02
52 52 0.98
ACGTcount: A:0.33, C:0.13, G:0.17, T:0.38
Consensus pattern (52 bp):
GTCACAAATTAACTAATCTTTTGAGATTGAAAATTGACAGCTTTATTGAATT
Found at i:28410018 original size:23 final size:23
Alignment explanation
Indices: 28409969--28410020 Score: 59
Period size: 23 Copynumber: 2.3 Consensus size: 23
28409959 ACCTACTTTC
* * * * *
28409969 TTACTGTAGTGATTTTTGGGTTG
1 TTACAGTAGTAATTTTCGGGATA
28409992 TTACAGTAGTAATTTTCGGGATA
1 TTACAGTAGTAATTTTCGGGATA
28410015 TTACAG
1 TTACAG
28410021 GAAAGACGAA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.23, C:0.08, G:0.25, T:0.44
Consensus pattern (23 bp):
TTACAGTAGTAATTTTCGGGATA
Found at i:28438017 original size:25 final size:24
Alignment explanation
Indices: 28437984--28438038 Score: 69
Period size: 25 Copynumber: 2.2 Consensus size: 24
28437974 TTTCTCAAAA
28437984 AATTAATAAATAT-AAAATATTA-AT
1 AATTAATAAAT-TGAAAA-ATTAGAT
28438008 AATTCAATAAATTGAAAAATTAGAT
1 AATT-AATAAATTGAAAAATTAGAT
28438033 AATTAA
1 AATTAA
28438039 ATTAAAATTT
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
24 11 0.39
25 17 0.61
ACGTcount: A:0.60, C:0.02, G:0.04, T:0.35
Consensus pattern (24 bp):
AATTAATAAATTGAAAAATTAGAT
Found at i:28438749 original size:30 final size:32
Alignment explanation
Indices: 28438688--28438751 Score: 78
Period size: 30 Copynumber: 2.1 Consensus size: 32
28438678 GCTTTTTGAA
* * *
28438688 AATATTTACAAAAAAAAGGCATCTAATTTTTT
1 AATATTTACAAAAAAAAGGCAACCAAATTTTT
*
28438720 AATATTTAC-AAAAAGA-GCAACCAAATTTTT
1 AATATTTACAAAAAAAAGGCAACCAAATTTTT
28438750 AA
1 AA
28438752 AAATAATTCA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
30 13 0.46
31 6 0.21
32 9 0.32
ACGTcount: A:0.50, C:0.11, G:0.06, T:0.33
Consensus pattern (32 bp):
AATATTTACAAAAAAAAGGCAACCAAATTTTT
Found at i:28450608 original size:36 final size:37
Alignment explanation
Indices: 28450568--28450639 Score: 94
Period size: 38 Copynumber: 1.9 Consensus size: 37
28450558 TACTCTTTTT
28450568 TCTTTTCATTGTTC-TTT-TCTTTTTCACTCTCTTCAC
1 TCTTTTC-TTGTTCTTTTATCTTTTTCACTCTCTTCAC
* *
28450604 TCTTTTCTTTTTCTTTTGATTTTTTTCACTCTCTTC
1 TCTTTTCTTGTTCTTTT-ATCTTTTTCACTCTCTTC
28450640 TTTCAAACAA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
35 5 0.16
36 10 0.32
38 16 0.52
ACGTcount: A:0.07, C:0.25, G:0.03, T:0.65
Consensus pattern (37 bp):
TCTTTTCTTGTTCTTTTATCTTTTTCACTCTCTTCAC
Found at i:28452176 original size:21 final size:21
Alignment explanation
Indices: 28452152--28452195 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
28452142 TAGTCTTGAG
*
28452152 GTGGAGGTGAACGACCTCGTT
1 GTGGAGGTAAACGACCTCGTT
*
28452173 GTGGAGGTAAACGTCCTCGTT
1 GTGGAGGTAAACGACCTCGTT
28452194 GT
1 GT
28452196 AGTTGTAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.18, C:0.18, G:0.36, T:0.27
Consensus pattern (21 bp):
GTGGAGGTAAACGACCTCGTT
Found at i:28467607 original size:75 final size:75
Alignment explanation
Indices: 28467514--28467671 Score: 169
Period size: 75 Copynumber: 2.1 Consensus size: 75
28467504 TATGAAACAT
* * * *** *
28467514 ACATAATGCAAGTCTTAAAGGATGCT-AATGTATTAATGTAAAGTGTTAACTAAAGACGCATTCA
1 ACATAATGCAAGTCTTAAAAGATG-TAAATGTACTAATGCAAAACATTAAATAAAGACGCATTCA
*
28467578 ATAAACAAGAA-
65 ACAAACAA-AAC
* * *
28467589 ACATAATGCACA-TTTTAAAAGATGTAAATGTACTAATGCAAAACATTAAATAAAGATGCATTTA
1 ACATAATGCA-AGTCTTAAAAGATGTAAATGTACTAATGCAAAACATTAAATAAAGACGCATTCA
28467653 ACAAACAAAAC
65 ACAAACAAAAC
28467664 ACATAATG
1 ACATAATG
28467672 AAGCAGATCA
Statistics
Matches: 69, Mismatches: 11, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
74 3 0.04
75 65 0.94
76 1 0.01
ACGTcount: A:0.49, C:0.13, G:0.13, T:0.26
Consensus pattern (75 bp):
ACATAATGCAAGTCTTAAAAGATGTAAATGTACTAATGCAAAACATTAAATAAAGACGCATTCAA
CAAACAAAAC
Found at i:28480346 original size:27 final size:27
Alignment explanation
Indices: 28480244--28480474 Score: 239
Period size: 27 Copynumber: 8.6 Consensus size: 27
28480234 TAACCTTGAT
* * *
28480244 GGGTAAAATGACCATAATACCACTGCA
1 GGGTAAAATGACCGTAATACCCCTGTA
* **
28480271 GGATAAAATGACCGTAATACCCCTACA
1 GGGTAAAATGACCGTAATACCCCTGTA
* *
28480298 GGGTAAAATGACCGTAGTACCCCTATA
1 GGGTAAAATGACCGTAATACCCCTGTA
* *
28480325 GGGTAAAATGACTGTAATACCCTTGTA
1 GGGTAAAATGACCGTAATACCCCTGTA
** * * *
28480352 AAGTAAAATAACCGTAATGCCCTTGTA
1 GGGTAAAATGACCGTAATACCCCTGTA
* * *
28480379 GGGTAAAATGACTGTAATGCCCCTTTA
1 GGGTAAAATGACCGTAATACCCCTGTA
* *
28480406 GGGTAAAATGACTGTAATGCCCCTGTA
1 GGGTAAAATGACCGTAATACCCCTGTA
* * *
28480433 GGGTAAAATGACCGT-ATACTCTTATA
1 GGGTAAAATGACCGTAATACCCCTGTA
*
28480459 GGATAAAATGACCGTA
1 GGGTAAAATGACCGTA
28480475 TTGCCCTGGT
Statistics
Matches: 174, Mismatches: 29, Indels: 2
0.85 0.14 0.01
Matches are distributed among these distances:
26 21 0.12
27 153 0.88
ACGTcount: A:0.36, C:0.19, G:0.20, T:0.25
Consensus pattern (27 bp):
GGGTAAAATGACCGTAATACCCCTGTA
Found at i:28480763 original size:32 final size:32
Alignment explanation
Indices: 28480722--28480835 Score: 133
Period size: 32 Copynumber: 3.6 Consensus size: 32
28480712 GCTGCAATGC
* * *
28480722 TACTGATGGCTTTATGCCAATCATAGAACCGT
1 TACTGATGGCTTTGTGCCGATCATAGTACCGT
**
28480754 TACTGATGGCTTTGTGCCGATCATAGTACTAT
1 TACTGATGGCTTTGTGCCGATCATAGTACCGT
* *
28480786 TACTGATGGATTTGTGCCGATCATATTACCGT
1 TACTGATGGCTTTGTGCCGATCATAGTACCGT
28480818 TA-TCGATGG-TTGTGTGCC
1 TACT-GATGGCTT-TGTGCC
28480836 ATTCATTTCA
Statistics
Matches: 71, Mismatches: 9, Indels: 4
0.85 0.11 0.05
Matches are distributed among these distances:
31 3 0.04
32 68 0.96
ACGTcount: A:0.22, C:0.19, G:0.23, T:0.36
Consensus pattern (32 bp):
TACTGATGGCTTTGTGCCGATCATAGTACCGT
Found at i:28480939 original size:22 final size:21
Alignment explanation
Indices: 28480914--28480977 Score: 65
Period size: 22 Copynumber: 2.9 Consensus size: 21
28480904 ATTACTGTAC
28480914 TTATGGCTTGTAGCCATTCTCT
1 TTATGGCTT-TAGCCATTCTCT
* * * *
28480936 TTATAGCTTATAGCTATCCTGT
1 TTATGGCTT-TAGCCATTCTCT
28480958 TTATGGCTCTTAGCCATTCT
1 TTATGGCT-TTAGCCATTCT
28480978 GACTACTGGC
Statistics
Matches: 33, Mismatches: 8, Indels: 2
0.77 0.19 0.05
Matches are distributed among these distances:
22 32 0.97
23 1 0.03
ACGTcount: A:0.17, C:0.22, G:0.16, T:0.45
Consensus pattern (21 bp):
TTATGGCTTTAGCCATTCTCT
Found at i:28492824 original size:31 final size:29
Alignment explanation
Indices: 28492789--28492854 Score: 100
Period size: 27 Copynumber: 2.3 Consensus size: 29
28492779 AGAAATTGGC
28492789 AAGAGAGTAAGGGAATTTTGGAATGAAAAAG
1 AAGAGAG--AGGGAATTTTGGAATGAAAAAG
28492820 -A-AGAGAGGGAATTTTGGAATGAAAAAG
1 AAGAGAGAGGGAATTTTGGAATGAAAAAG
28492847 AAGAGAGA
1 AAGAGAGA
28492855 CAGTGGAGAG
Statistics
Matches: 33, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
27 22 0.67
28 1 0.03
29 9 0.27
30 1 0.03
ACGTcount: A:0.50, C:0.00, G:0.33, T:0.17
Consensus pattern (29 bp):
AAGAGAGAGGGAATTTTGGAATGAAAAAG
Found at i:28492828 original size:27 final size:27
Alignment explanation
Indices: 28492798--28492853 Score: 112
Period size: 27 Copynumber: 2.1 Consensus size: 27
28492788 CAAGAGAGTA
28492798 AGGGAATTTTGGAATGAAAAAGAAGAG
1 AGGGAATTTTGGAATGAAAAAGAAGAG
28492825 AGGGAATTTTGGAATGAAAAAGAAGAG
1 AGGGAATTTTGGAATGAAAAAGAAGAG
28492852 AG
1 AG
28492854 ACAGTGGAGA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.34, T:0.18
Consensus pattern (27 bp):
AGGGAATTTTGGAATGAAAAAGAAGAG
Found at i:28503099 original size:31 final size:30
Alignment explanation
Indices: 28503064--28503123 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 30
28503054 GGAGGTGGGA
*
28503064 TGGGAAGAGAATAAAAGTTTTAGGGGAAAAG
1 TGGG-AGAGAATAAAAATTTTAGGGGAAAAG
* * *
28503095 TGGGAGGGAGTAAAAATTTTGGGGGAAAA
1 TGGGAGAGAATAAAAATTTTAGGGGAAAA
28503124 TAAAAGGGTT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
30 21 0.84
31 4 0.16
ACGTcount: A:0.42, C:0.00, G:0.38, T:0.20
Consensus pattern (30 bp):
TGGGAGAGAATAAAAATTTTAGGGGAAAAG
Found at i:28507991 original size:22 final size:22
Alignment explanation
Indices: 28507964--28508008 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
28507954 AATTTAACCA
28507964 TAACATAAATAACTATTTACAT
1 TAACATAAATAACTATTTACAT
28507986 TAACATAAATAACTATTTACAT
1 TAACATAAATAACTATTTACAT
28508008 T
1 T
28508009 CATCCAAAAA
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:0.49, C:0.13, G:0.00, T:0.38
Consensus pattern (22 bp):
TAACATAAATAACTATTTACAT
Found at i:28509475 original size:22 final size:22
Alignment explanation
Indices: 28509450--28509491 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
28509440 AGCAAAAGAA
28509450 TGAGAGAAAAAAAAATGAAAAT
1 TGAGAGAAAAAAAAATGAAAAT
* *
28509472 TGAGAGAGAAAAGAATGAAA
1 TGAGAGAAAAAAAAATGAAA
28509492 CGATATCTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.64, C:0.00, G:0.24, T:0.12
Consensus pattern (22 bp):
TGAGAGAAAAAAAAATGAAAAT
Found at i:28512148 original size:41 final size:41
Alignment explanation
Indices: 28512065--28512420 Score: 323
Period size: 41 Copynumber: 8.7 Consensus size: 41
28512055 CTTTCGGGGA
*** * * * *
28512065 TTTAGCGGCGTTTTAAAAAAAAGCGTCGCTAGTTCCCAGATC
1 TTTAGCGGCGTTTT-TGTAAAAGCGCCGCTAATGCTCAGATC
*
28512107 TTTAGCGGCGTTTTTGTAAAATCGCCGCTAATGCTCAGATC
1 TTTAGCGGCGTTTTTGTAAAAGCGCCGCTAATGCTCAGATC
* * **
28512148 TTTAGCGACGTTTTT-TGAGAAGCATCGCTAATGCTCAGATC
1 TTTAGCGGCGTTTTTGT-AAAAGCGCCGCTAATGCTCAGATC
* * *
28512189 TTTAGCAGCGTTTTTGAAAAAGCGCCAG-TAATGCTCAGATA
1 TTTAGCGGCGTTTTTGTAAAAGCGCC-GCTAATGCTCAGATC
* * * *
28512230 TTTAGCGACGTTTCTGTAGAAGCGCCGCTAAAGCTCAGATC
1 TTTAGCGGCGTTTTTGTAAAAGCGCCGCTAATGCTCAGATC
* * * *
28512271 TTT-GTCAGCGTTTTT-TCAAAATCGCCGC-GATGCTCAAATC
1 TTTAG-CGGCGTTTTTGT-AAAAGCGCCGCTAATGCTCAGATC
*
28512311 TTTAGCGGCGTTTATAG-AAAAGCGCCGCTAATGCTCAGATC
1 TTTAGCGGCGTTT-TTGTAAAAGCGCCGCTAATGCTCAGATC
** * * *
28512352 TTTAGCGATGTTTTTGGT-AAAGCGTCGCTAATGCTCCGATA
1 TTTAGCGGCGTTTTT-GTAAAAGCGCCGCTAATGCTCAGATC
28512393 TTTAGCGGCGTTTTTG-AAAATGCGCCGC
1 TTTAGCGGCGTTTTTGTAAAA-GCGCCGC
28512421 AAAAACATTT
Statistics
Matches: 251, Mismatches: 49, Indels: 29
0.76 0.15 0.09
Matches are distributed among these distances:
40 38 0.15
41 198 0.79
42 15 0.06
ACGTcount: A:0.25, C:0.21, G:0.23, T:0.31
Consensus pattern (41 bp):
TTTAGCGGCGTTTTTGTAAAAGCGCCGCTAATGCTCAGATC
Found at i:28512356 original size:122 final size:122
Alignment explanation
Indices: 28512065--28512407 Score: 354
Period size: 122 Copynumber: 2.8 Consensus size: 122
28512055 CTTTCGGGGA
* * * * * * * *
28512065 TTTAGCGGCGTTTTAAAAAAAAGCGTCGCTAGTTCCCAGATCTTTAGCGGCGTTTTTGTAAAATC
1 TTTAGCGGCG-TTTATAGAAAAGCGCCGCTAATGCTCAGATCTTTAGCGACGTTTTTGT-AAAGC
* * * *
28512130 GCCGCTAATGCTCAGATCTTTAGCGACGTTTTTTGAGAAGCATCGCTAATGCTCAGATC
64 GCCGCTAATGCTCAGATCTTTAGCGACGTTTTTTCAAAAGCACCGCTAATGCTCAAATC
* * * *
28512189 TTTAGCAGCGTTT-TTGAAAAAGCGCCAG-TAATGCTCAGATATTTAGCGACGTTTCTGTAGAAG
1 TTTAGCGGCGTTTATAG-AAAAGCGCC-GCTAATGCTCAGATCTTTAGCGACGTTTTTGTA-AAG
* * * *
28512252 CGCCGCTAAAGCTCAGATCTTT-GTC-AGCGTTTTTTCAAAATCGCCGC-GATGCTCAAATC
63 CGCCGCTAATGCTCAGATCTTTAG-CGA-CGTTTTTTCAAAAGCACCGCTAATGCTCAAATC
*
28512311 TTTAGCGGCGTTTATAGAAAAGCGCCGCTAATGCTCAGATCTTTAGCGATGTTTTTGGTAAAGCG
1 TTTAGCGGCGTTTATAGAAAAGCGCCGCTAATGCTCAGATCTTTAGCGACGTTTTT-GTAAAGCG
* * * *
28512376 TCGCTAATGCTCCGATATTTAGCGGCGTTTTT
65 CCGCTAATGCTCAGATCTTTAGCGACGTTTTT
28512408 GAAAATGCGC
Statistics
Matches: 179, Mismatches: 30, Indels: 22
0.77 0.13 0.10
Matches are distributed among these distances:
121 1 0.01
122 88 0.49
123 80 0.45
124 10 0.06
ACGTcount: A:0.24, C:0.21, G:0.22, T:0.32
Consensus pattern (122 bp):
TTTAGCGGCGTTTATAGAAAAGCGCCGCTAATGCTCAGATCTTTAGCGACGTTTTTGTAAAGCGC
CGCTAATGCTCAGATCTTTAGCGACGTTTTTTCAAAAGCACCGCTAATGCTCAAATC
Done.