Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009137.1 Hibiscus syriacus cultivar Beakdansim tig00112637_pilon, whole genome shotgun sequence
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: 390993
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
File 2 of 2
Found at i:205651 original size:165 final size:164
Alignment explanation
Indices: 205377--205830 Score: 556
Period size: 165 Copynumber: 2.7 Consensus size: 164
205367 TAAACAAACT
*
205377 ATTTGCAGCATAACTTAAGTCTAGAAGGGCTATCTGCCGAAGACCCCTGAGTTCGATTACACTCA
1 ATTTGCAGCATAACTTAAGTCTAGAAGGGCTATCTGCCAAAGACCCCTGAGTTCGATTACACTCA
* * * * **
205442 GCTTCGAGGGCACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTG-TGACCAAAAGAC
66 GCTTCGA-GGCACATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACC-AAAGAC
* *
205506 CTTTGAGTTCGACTACGATCAG-TTCAACGGCACATC
129 CTTCGAGTTCGACTACGATCAGCTCCAA-GGCACATC
* * * * *
205542 ATTTGCAGTATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCCCGAGTTTGATTACACTCA
1 ATTTGCAGCATAACTTAAGTCTAGAAGGGCTATCTGCCAAAGACCCCTGAGTTCGATTACACTCA
205607 GCTTCGAGGACACATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACC
66 GCTTCGAGG-CACATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACC
* *
205672 TTCGAGTTCGACTACGCTCAGCTCCAAGGCATATC
130 TTCGAGTTCGACTACGATCAGCTCCAAGGCACATC
* * * * ** *
205707 ATTTGCAGCACAACTTAAGTCTACAAGGGTTGTCTGCCAACAAAAGACCTTTGAGTTCGACTACG
1 ATTTGCAGCATAACTTAAGTCTAGAAGGGCTATCTG-C--C-AAAGACCCCTGAGTTCGATTAC-
* * *
205772 A-TCAGC-TCAACGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAA
61 ACTCAGCTTCGA-GGCACATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAA
205831 AGACCCCCGA
Statistics
Matches: 249, Mismatches: 31, Indels: 15
0.84 0.11 0.05
Matches are distributed among these distances:
164 2 0.01
165 166 0.67
166 8 0.03
168 48 0.19
169 24 0.10
170 1 0.00
ACGTcount: A:0.30, C:0.25, G:0.21, T:0.24
Consensus pattern (164 bp):
ATTTGCAGCATAACTTAAGTCTAGAAGGGCTATCTGCCAAAGACCCCTGAGTTCGATTACACTCA
GCTTCGAGGCACATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCT
TCGAGTTCGACTACGATCAGCTCCAAGGCACATC
Found at i:205812 original size:249 final size:246
Alignment explanation
Indices: 205377--205875 Score: 723
Period size: 249 Copynumber: 2.0 Consensus size: 246
205367 TAAACAAACT
* * *
205377 ATTTGCAGCATAACTTAAGTCTAGAAGGGCTATCTGCCGAAGACCCCTGAGTTCGATTACACTCA
1 ATTTGCAGCATAACTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCCTGAGTTCGACTACACTCA
* * * * ** *
205442 GCTTCGAGGGCACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTGACCAAAAGACC
66 GCTTCCAAGGCACATCATTTACAGCACAACTCAAGGCTACAAGGGTTATCTGCCAACAAAAGACC
* *
205507 TTTGAGTTCGACTACGATCAGTTCAACGGCACATCATTTGCAGTATAGCTTAAGTCGAGAAGGGC
131 TTTGAGTTCGACTACGATCAGCTCAACGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGC
* *
205572 TATCTGCCAAAGACCCCCGAGTTTGATTACACTCAGCTTCGAGGACACATC
196 TATCTGCCAAAGACCCCCGAGTTCGATTACACTCAACTTCGAGGACACATC
* *
205623 ATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGA-CCTTCGAGTTCGACTAC
1 ATTTGCAGCATAACTTAAGTCGAGAAGGGCTATCTG----CCAAAGACCCCT-GAGTTCGACTAC
* * * * * *
205687 GCTCAGC-TCCAAGGCATATCATTTGCAGCACAACTTAAGTCTACAAGGGTTGTCTGCCAACAAA
61 ACTCAGCTTCCAAGGCACATCATTTACAGCACAACTCAAGGCTACAAGGGTTATCTGCCAACAAA
205751 AGACCTTTGAGTTCGACTACGATCAGCTCAACGGCACATCATTTGCAGCATAGCTTAAGTCGAGA
126 AGACCTTTGAGTTCGACTACGATCAGCTCAACGGCACATCATTTGCAGCATAGCTTAAGTCGAGA
* *
205816 AGGGCTATCTGCCAAAGACCCCCGAGTTCGATTACACTCAACTTCGAGGTCATATC
191 AGGGCTATCTGCCAAAGACCCCCGAGTTCGATTACACTCAACTTCGAGGACACATC
205872 ATTT
1 ATTT
205876 ACAACATAGC
Statistics
Matches: 224, Mismatches: 24, Indels: 7
0.88 0.09 0.03
Matches are distributed among these distances:
246 34 0.15
249 167 0.75
250 23 0.10
ACGTcount: A:0.29, C:0.25, G:0.21, T:0.25
Consensus pattern (246 bp):
ATTTGCAGCATAACTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCCTGAGTTCGACTACACTCA
GCTTCCAAGGCACATCATTTACAGCACAACTCAAGGCTACAAGGGTTATCTGCCAACAAAAGACC
TTTGAGTTCGACTACGATCAGCTCAACGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGC
TATCTGCCAAAGACCCCCGAGTTCGATTACACTCAACTTCGAGGACACATC
Found at i:205827 original size:84 final size:82
Alignment explanation
Indices: 205377--205830 Score: 447
Period size: 84 Copynumber: 5.5 Consensus size: 82
205367 TAAACAAACT
* * ** *
205377 ATTTGCAGCATAACTTAAGTCTAGAAGGGCTATCTG-C--CGAAGACCCCTGAGTTCGATTAC-A
1 ATTTGCAGCATAACTTAAGTCGAGAAGGGCTATCTGCCAACAAAGACCTTTGAGTTCGACTACGA
*
205438 CTCAGCTTCGAGGGCACATC
66 -TCAGC-TC-AAGGCACATC
* * * * * ** *
205458 ATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTGACCAAAAGACCTTTGAGTTCGACTACG
1 ATTTGCAGCATAACTTAAGTCGAGAAGGGCTATCTGCCAAC-AAAGACCTTTGAGTTCGACTACG
*
205523 ATCAGTTCAACGGCACATC
65 ATCAGCTCAA-GGCACATC
* * *** * *
205542 ATTTGCAGTATAGCTTAAGTCGAGAAGGGCTATCTG-C--CAAAGACCCCCGAGTTTGATTAC-A
1 ATTTGCAGCATAACTTAAGTCGAGAAGGGCTATCTGCCAACAAAGACCTTTGAGTTCGACTACGA
*
205603 CTCAGCTTCGAGGACACATC
66 -TCAGC-TCAAGG-CACATC
* *
205623 ATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACG
1 ATTTGCAGCATAACTTAAGTCGAGAAGGGCTATCTGCCAA-CAAAGACCTTTGAGTTCGACTACG
* *
205688 CTCAGCTCCAAGGCATATC
65 ATCAGCT-CAAGGCACATC
* * * * *
205707 ATTTGCAGCACAACTTAAGTCTACAAGGGTTGTCTGCCAACAAAAGACCTTTGAGTTCGACTACG
1 ATTTGCAGCATAACTTAAGTCGAGAAGGGCTATCTGCCAAC-AAAGACCTTTGAGTTCGACTACG
205772 ATCAGCTCAACGGCACATC
65 ATCAGCTCAA-GGCACATC
*
205791 ATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAA
1 ATTTGCAGCATAACTTAAGTCGAGAAGGGCTATCTGCCAA
205831 AGACCCCCGA
Statistics
Matches: 307, Mismatches: 49, Indels: 31
0.79 0.13 0.08
Matches are distributed among these distances:
79 1 0.00
80 23 0.07
81 75 0.24
82 1 0.00
83 5 0.02
84 151 0.49
85 50 0.16
86 1 0.00
ACGTcount: A:0.30, C:0.25, G:0.21, T:0.24
Consensus pattern (82 bp):
ATTTGCAGCATAACTTAAGTCGAGAAGGGCTATCTGCCAACAAAGACCTTTGAGTTCGACTACGA
TCAGCTCAAGGCACATC
Found at i:206609 original size:34 final size:34
Alignment explanation
Indices: 206473--206812 Score: 192
Period size: 34 Copynumber: 9.9 Consensus size: 34
206463 CATATATATG
* *
206473 TATATAATATATAGTTTTGAAAACATATTTGAAACA
1 TATATATTATATAGTTTTAAAAACAT-TTTGAAA-A
* *
206509 TTTATATATTATATAGTTTTTAAAACACTTTGAAAA
1 --TATATATTATATAGTTTTAAAAACATTTTGAAAA
* *
206545 TA-A-A-TATA-A-TTTTTAAAACGTTTTTGAAAA
1 TATATATTATATAGTTTTAAAAAC-ATTTTGAAAA
* *
206575 TATATATTATATGGTTTTAAAAACATTTTTAAAA
1 TATATATTATATAGTTTTAAAAACATTTTGAAAA
*
206609 TA-A-A-TATA-ATTTTTAAAAAGAAACATTTTGAAAACATA
1 TATATATTATATAGTTTT---AA-AAACATTTTG--AA-A-A
* *
206647 TATATATTATATAGTTTTGAAATCATTTTGAAAA
1 TATATATTATATAGTTTTAAAAACATTTTGAAAA
* *
206681 CT-TATAATATATAGTTTTAAAAAATATTTTTG-AAA
1 -TATATATTATATAGTTTT-AAAAACA-TTTTGAAAA
* * *
206716 -A-CTA-TATA-A-TTTTGAAAACGTTTTAGAAAAA
1 TATATATTATATAGTTTTAAAAACATTTT-G-AAAA
* *
206747 TATATAATATATAATTTTAAAATAC-TTTTGAAAA
1 TATATATTATATAGTTTTAAAA-ACATTTTGAAAA
*
206781 TATATATTTATATAGTTTGTAGAAAATATTTT
1 TATATA-TTATATAGTTT-TA-AAAACATTTT
206813 ATATTATTAT
Statistics
Matches: 239, Mismatches: 28, Indels: 71
0.71 0.08 0.21
Matches are distributed among these distances:
28 4 0.02
29 15 0.06
30 19 0.08
31 13 0.05
32 8 0.03
33 12 0.05
34 51 0.21
35 29 0.12
36 24 0.10
37 17 0.07
38 35 0.15
39 2 0.01
40 1 0.00
41 4 0.02
42 5 0.02
ACGTcount: A:0.46, C:0.04, G:0.07, T:0.44
Consensus pattern (34 bp):
TATATATTATATAGTTTTAAAAACATTTTGAAAA
Found at i:206757 original size:64 final size:62
Alignment explanation
Indices: 206654--206786 Score: 144
Period size: 64 Copynumber: 2.1 Consensus size: 62
206644 ATATATATAT
* * * *
206654 TATATAGTTTTGAAATCATTTTGAAAACTTATAATATATAGT-TTTAAAAAATATTTTTGAAAA
1 TATATAATTTTGAAAACATTTTGAAAACATATAATATATA-TATTT-AAAAATACTTTTGAAAA
* * *
206717 CTATATAATTTTGAAAACGTTTTAGAAAAATATATAATATATA-ATTTTAAAATACTTTTGAAAA
1 -TATATAATTTTGAAAACATTTT-G-AAAACATATAATATATATATTTAAAAATACTTTTGAAAA
206781 TATATA
1 TATATA
206787 TTTATATAGT
Statistics
Matches: 59, Mismatches: 7, Indels: 7
0.81 0.10 0.10
Matches are distributed among these distances:
63 6 0.10
64 34 0.58
65 4 0.07
66 15 0.25
ACGTcount: A:0.47, C:0.04, G:0.07, T:0.43
Consensus pattern (62 bp):
TATATAATTTTGAAAACATTTTGAAAACATATAATATATATATTTAAAAATACTTTTGAAAA
Found at i:206759 original size:36 final size:36
Alignment explanation
Indices: 206718--206787 Score: 99
Period size: 36 Copynumber: 1.9 Consensus size: 36
206708 TTTTGAAAAC
*
206718 TATATAATTTTGAAA-ACGTTTTAGAAAA-ATATATAA
1 TATATAATTTTAAAATAC-TTTT-GAAAATATATATAA
206754 TATATAATTTTAAAATACTTTTGAAAATATATAT
1 TATATAATTTTAAAATACTTTTGAAAATATATAT
206788 TTATATAGTT
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
35 5 0.16
36 24 0.77
37 2 0.06
ACGTcount: A:0.49, C:0.03, G:0.06, T:0.43
Consensus pattern (36 bp):
TATATAATTTTAAAATACTTTTGAAAATATATATAA
Found at i:208763 original size:18 final size:20
Alignment explanation
Indices: 208723--208764 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 20
208713 TAGACCGTAT
*
208723 AATAAAAAATTACCAGTAGG
1 AATAAAAAATTACCAGGAGG
*
208743 AATAAAAGATTACC-GGA-G
1 AATAAAAAATTACCAGGAGG
208761 AATA
1 AATA
208765 GGATTACTGA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
18 5 0.25
19 2 0.10
20 13 0.65
ACGTcount: A:0.55, C:0.10, G:0.17, T:0.19
Consensus pattern (20 bp):
AATAAAAAATTACCAGGAGG
Found at i:213009 original size:2 final size:2
Alignment explanation
Indices: 213002--213034 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
212992 TGTAAGGTGA
213002 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
213035 GTCATTCTCA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:219368 original size:15 final size:15
Alignment explanation
Indices: 219326--219374 Score: 80
Period size: 15 Copynumber: 3.3 Consensus size: 15
219316 TGCACCTGCT
* *
219326 CCATCAACTAGTGCT
1 CCATCAACTAGTACC
219341 CCATCAACTAGTACC
1 CCATCAACTAGTACC
219356 CCATCAACTAGTACC
1 CCATCAACTAGTACC
219371 CCAT
1 CCAT
219375 TCTCCATAAC
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 32 1.00
ACGTcount: A:0.31, C:0.39, G:0.08, T:0.22
Consensus pattern (15 bp):
CCATCAACTAGTACC
Found at i:222784 original size:11 final size:11
Alignment explanation
Indices: 222768--222794 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
222758 TACTACTCTC
222768 CCTTCTCTATT
1 CCTTCTCTATT
222779 CCTTCTCTATT
1 CCTTCTCTATT
222790 CCTTC
1 CCTTC
222795 AATGACTTCG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.07, C:0.41, G:0.00, T:0.52
Consensus pattern (11 bp):
CCTTCTCTATT
Found at i:225891 original size:91 final size:91
Alignment explanation
Indices: 225736--225920 Score: 370
Period size: 91 Copynumber: 2.0 Consensus size: 91
225726 ATTGATTGGA
225736 GCATATGCTCCTTTTTCATCCAAGGCTGGAAAGGTATGGCTGTTTTGAAGGTAGGTTAGTCTTAT
1 GCATATGCTCCTTTTTCATCCAAGGCTGGAAAGGTATGGCTGTTTTGAAGGTAGGTTAGTCTTAT
225801 CTTGCTGCGTTTTAATGTCTCACCAT
66 CTTGCTGCGTTTTAATGTCTCACCAT
225827 GCATATGCTCCTTTTTCATCCAAGGCTGGAAAGGTATGGCTGTTTTGAAGGTAGGTTAGTCTTAT
1 GCATATGCTCCTTTTTCATCCAAGGCTGGAAAGGTATGGCTGTTTTGAAGGTAGGTTAGTCTTAT
225892 CTTGCTGCGTTTTAATGTCTCACCAT
66 CTTGCTGCGTTTTAATGTCTCACCAT
225918 GCA
1 GCA
225921 GGGACCTGGA
Statistics
Matches: 94, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
91 94 1.00
ACGTcount: A:0.20, C:0.19, G:0.23, T:0.38
Consensus pattern (91 bp):
GCATATGCTCCTTTTTCATCCAAGGCTGGAAAGGTATGGCTGTTTTGAAGGTAGGTTAGTCTTAT
CTTGCTGCGTTTTAATGTCTCACCAT
Found at i:227106 original size:7 final size:7
Alignment explanation
Indices: 227079--227109 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
227069 TAGTCTTTGG
*
227079 TCCACCG
1 TCCACCT
227086 TCCACCT
1 TCCACCT
227093 TCCACCT
1 TCCACCT
227100 TCCACCT
1 TCCACCT
227107 TCC
1 TCC
227110 CTCGTTATCC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.13, C:0.58, G:0.03, T:0.26
Consensus pattern (7 bp):
TCCACCT
Found at i:231366 original size:21 final size:20
Alignment explanation
Indices: 231327--231364 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
231317 AGATTATGCA
231327 GGGGGTACAGATTCCCCCTG
1 GGGGGTACAGATTCCCCCTG
231347 GGGGGTATC-GATTCCCCC
1 GGGGGTA-CAGATTCCCCC
231365 CTAAAGAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
20 16 0.94
21 1 0.06
ACGTcount: A:0.13, C:0.32, G:0.34, T:0.21
Consensus pattern (20 bp):
GGGGGTACAGATTCCCCCTG
Found at i:231555 original size:23 final size:23
Alignment explanation
Indices: 231496--231542 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
231486 AACAAGTTTT
231496 GGAATAATCAAAGGATTAGGATC
1 GGAATAATCAAAGGATTAGGATC
231519 GGAATAATCAAAGGATTAGGATC
1 GGAATAATCAAAGGATTAGGATC
231542 G
1 G
231543 AATCAAATCA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.43, C:0.09, G:0.28, T:0.21
Consensus pattern (23 bp):
GGAATAATCAAAGGATTAGGATC
Found at i:232176 original size:2 final size:2
Alignment explanation
Indices: 232169--232219 Score: 102
Period size: 2 Copynumber: 25.5 Consensus size: 2
232159 AACATAGATG
232169 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
232211 AT AT AT AT A
1 AT AT AT AT A
232220 ATAAGACATG
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:233408 original size:21 final size:22
Alignment explanation
Indices: 233382--233424 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
233372 GTAGTAGTAG
*
233382 TGTAGC-AGGGTATCGGTTCCC
1 TGTAGCAAGGGAATCGGTTCCC
233403 TGTAGCAAGGGAATCGGTTCCC
1 TGTAGCAAGGGAATCGGTTCCC
233425 CTATTACAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 6 0.30
22 14 0.70
ACGTcount: A:0.19, C:0.23, G:0.33, T:0.26
Consensus pattern (22 bp):
TGTAGCAAGGGAATCGGTTCCC
Found at i:237745 original size:23 final size:22
Alignment explanation
Indices: 237711--237755 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 22
237701 AAACATAAAT
* *
237711 AAAAAGATATAGTTATAGTACA
1 AAAAAGACATAGTTAAAGTACA
237733 AAAAAGTACATAGTTAAAGTACA
1 AAAAAG-ACATAGTTAAAGTACA
237756 TAATATTTTG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 6 0.30
23 14 0.70
ACGTcount: A:0.56, C:0.07, G:0.13, T:0.24
Consensus pattern (22 bp):
AAAAAGACATAGTTAAAGTACA
Found at i:238934 original size:28 final size:29
Alignment explanation
Indices: 238902--238961 Score: 77
Period size: 28 Copynumber: 2.1 Consensus size: 29
238892 AACATACTCT
* * *
238902 TATTTTTTTAATATTTGTTATTAAGGA-C
1 TATTTTTTAAATACTAGTTATTAAGGAGC
*
238930 TATTTTTTAAATACTAGTTATTATGGAGC
1 TATTTTTTAAATACTAGTTATTAAGGAGC
238959 TAT
1 TAT
238962 CCTTAAAAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
28 23 0.85
29 4 0.15
ACGTcount: A:0.30, C:0.05, G:0.12, T:0.53
Consensus pattern (29 bp):
TATTTTTTAAATACTAGTTATTAAGGAGC
Found at i:239716 original size:26 final size:26
Alignment explanation
Indices: 239670--239724 Score: 60
Period size: 26 Copynumber: 2.1 Consensus size: 26
239660 TTTATAATTT
* *
239670 TTATTATAATTTTTTATTTAATAAA-A
1 TTATTATAATTTATTAATTAA-AAATA
239696 TTATATATAA-TTATTAATTAAAAATA
1 TTAT-TATAATTTATTAATTAAAAATA
239722 TTA
1 TTA
239725 AAAAAATAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
25 3 0.12
26 17 0.68
27 5 0.20
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (26 bp):
TTATTATAATTTATTAATTAAAAATA
Found at i:242094 original size:73 final size:73
Alignment explanation
Indices: 242010--242155 Score: 211
Period size: 73 Copynumber: 2.0 Consensus size: 73
242000 GCGTAAAAAT
** * * * *
242010 TTTAGACTTGTTTTAAATATTGGTCGGGTTTGGATTTCATAATTGTTCATATTTATAATTATAAT
1 TTTAGACTTGTTTTAAATATTAATCGAGTTTGGACTTCATAATAGTCCATATTTATAATTATAAT
*
242075 AAATGAAA
66 AAACGAAA
* *
242083 TTTAGGCTTGTTTTAAATATTAATCGAGTTTGGGCTTCATAATAGTCCATATTTATAATTATAAT
1 TTTAGACTTGTTTTAAATATTAATCGAGTTTGGACTTCATAATAGTCCATATTTATAATTATAAT
242148 AAACGAAA
66 AAACGAAA
242156 AATATTAAAA
Statistics
Matches: 64, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
73 64 1.00
ACGTcount: A:0.34, C:0.08, G:0.14, T:0.44
Consensus pattern (73 bp):
TTTAGACTTGTTTTAAATATTAATCGAGTTTGGACTTCATAATAGTCCATATTTATAATTATAAT
AAACGAAA
Found at i:242194 original size:2 final size:2
Alignment explanation
Indices: 242187--242226 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
242177 TTGAGAATCA
242187 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
242227 TTTGGACTCC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:255304 original size:2 final size:2
Alignment explanation
Indices: 255297--255322 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
255287 GCTTTATGGT
255297 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
255323 CACACACACA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:267764 original size:40 final size:40
Alignment explanation
Indices: 267709--267830 Score: 226
Period size: 40 Copynumber: 3.0 Consensus size: 40
267699 TGCAAGTTTA
267709 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
1 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
*
267749 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATATG
1 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
*
267789 TAGTACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
1 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
267829 TA
1 TA
267831 GCACTACGGT
Statistics
Matches: 79, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
40 79 1.00
ACGTcount: A:0.23, C:0.17, G:0.27, T:0.33
Consensus pattern (40 bp):
TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
Found at i:268037 original size:48 final size:45
Alignment explanation
Indices: 267934--268060 Score: 148
Period size: 48 Copynumber: 2.8 Consensus size: 45
267924 GTAACCATGC
* * * *
267934 AAATAAGTTTATGAGCTTACGGAAT-AATGGCAAGTATATTGGAA
1 AAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTGGAA
* *
267978 AAATAAGCTTACGAGCTTATGGAATTTAAATGGTAAGTATTTTGGGTA
1 AAATAAGCTTACGAGCTTATGGAA--TAAATGGTAAGTATATT-GGAA
* *
268026 AAATAATCTTACGAGCTTATGGGATAAATGGTAAG
1 AAATAAGCTTACGAGCTTATGGAATAAATGGTAAG
268061 AGATTTTATA
Statistics
Matches: 71, Mismatches: 8, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
44 21 0.30
46 12 0.17
47 13 0.18
48 25 0.35
ACGTcount: A:0.39, C:0.07, G:0.23, T:0.31
Consensus pattern (45 bp):
AAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTGGAA
Found at i:268839 original size:21 final size:21
Alignment explanation
Indices: 268814--268853 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
268804 TTTATTTTCA
268814 TAATAAATTATATACTAAAAG
1 TAATAAATTATATACTAAAAG
*
268835 TAATAATTTATATACTAAA
1 TAATAAATTATATACTAAA
268854 CGGGTAGTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.55, C:0.05, G:0.03, T:0.38
Consensus pattern (21 bp):
TAATAAATTATATACTAAAAG
Found at i:277118 original size:7 final size:7
Alignment explanation
Indices: 277106--277148 Score: 50
Period size: 7 Copynumber: 6.0 Consensus size: 7
277096 TTATGGGGTC
277106 GGGTTTA
1 GGGTTTA
277113 GGGTTTA
1 GGGTTTA
**
277120 AAGTTTA
1 GGGTTTA
277127 GGGGTTTA
1 -GGGTTTA
*
277135 AGGTTTA
1 GGGTTTA
277142 GGGTTTA
1 GGGTTTA
277149 ACAAAAAAAG
Statistics
Matches: 29, Mismatches: 6, Indels: 2
0.78 0.16 0.05
Matches are distributed among these distances:
7 24 0.83
8 5 0.17
ACGTcount: A:0.21, C:0.00, G:0.37, T:0.42
Consensus pattern (7 bp):
GGGTTTA
Found at i:277133 original size:15 final size:14
Alignment explanation
Indices: 277108--277149 Score: 66
Period size: 14 Copynumber: 2.9 Consensus size: 14
277098 ATGGGGTCGG
277108 GTTTAGGGTTTAAA
1 GTTTAGGGTTTAAA
*
277122 GTTTAGGGGTTTAAG
1 GTTTA-GGGTTTAAA
277137 GTTTAGGGTTTAA
1 GTTTAGGGTTTAA
277150 CAAAAAAAGT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
14 13 0.50
15 13 0.50
ACGTcount: A:0.24, C:0.00, G:0.33, T:0.43
Consensus pattern (14 bp):
GTTTAGGGTTTAAA
Found at i:281404 original size:16 final size:17
Alignment explanation
Indices: 281370--281409 Score: 55
Period size: 16 Copynumber: 2.4 Consensus size: 17
281360 TTATATGAAC
*
281370 TGATATGTGCTTATATG
1 TGATATGTGATTATATG
*
281387 TGCTATGTGATT-TATG
1 TGATATGTGATTATATG
281403 TGATATG
1 TGATATG
281410 CCATATGTGA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
16 10 0.50
17 10 0.50
ACGTcount: A:0.23, C:0.05, G:0.25, T:0.47
Consensus pattern (17 bp):
TGATATGTGATTATATG
Found at i:281837 original size:21 final size:21
Alignment explanation
Indices: 281811--281864 Score: 90
Period size: 21 Copynumber: 2.6 Consensus size: 21
281801 GAGTTTTATA
281811 GGTCCTTCGGGACAATACAAT
1 GGTCCTTCGGGACAATACAAT
*
281832 GGTCCTTCGGGACAATACAGT
1 GGTCCTTCGGGACAATACAAT
*
281853 GGTCATTCGGGA
1 GGTCCTTCGGGA
281865 TAAATTTCAT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.24, C:0.22, G:0.30, T:0.24
Consensus pattern (21 bp):
GGTCCTTCGGGACAATACAAT
Found at i:282173 original size:18 final size:17
Alignment explanation
Indices: 282135--282176 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 17
282125 TATGCTTATA
*
282135 TGATAAAAATGAATTAG
1 TGATAAAAATGAATTAC
282152 TGATAACAATATG-ATTAC
1 TGATAA-AA-ATGAATTAC
282170 TGATAAA
1 TGATAAA
282177 TACGTTCATG
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
17 7 0.32
18 12 0.55
19 3 0.14
ACGTcount: A:0.50, C:0.05, G:0.14, T:0.31
Consensus pattern (17 bp):
TGATAAAAATGAATTAC
Found at i:286490 original size:14 final size:14
Alignment explanation
Indices: 286471--286502 Score: 64
Period size: 14 Copynumber: 2.3 Consensus size: 14
286461 TGCGTGCACG
286471 CGTGCGCACATACA
1 CGTGCGCACATACA
286485 CGTGCGCACATACA
1 CGTGCGCACATACA
286499 CGTG
1 CGTG
286503 TTGAGTCGGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.25, C:0.34, G:0.25, T:0.16
Consensus pattern (14 bp):
CGTGCGCACATACA
Found at i:292598 original size:31 final size:31
Alignment explanation
Indices: 292562--292620 Score: 100
Period size: 31 Copynumber: 1.9 Consensus size: 31
292552 AACTTAAAAG
*
292562 AGTTTTGCAATACTGAAATTTAAATAATTTT
1 AGTTTTACAATACTGAAATTTAAATAATTTT
*
292593 AGTTTTATAATACTGAAATTTAAATAAT
1 AGTTTTACAATACTGAAATTTAAATAAT
292621 CCATGCAACA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.42, C:0.05, G:0.08, T:0.44
Consensus pattern (31 bp):
AGTTTTACAATACTGAAATTTAAATAATTTT
Found at i:292674 original size:22 final size:22
Alignment explanation
Indices: 292644--292788 Score: 202
Period size: 22 Copynumber: 6.6 Consensus size: 22
292634 ATAATAATTT
*
292644 TTTTTAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATCCATA
***
292666 TTTTAAAATAAATTTTTCCATA
1 TTTTAAAATAAATCAATCCATA
*
292688 TTTTAAAATAAATCAATCTATA
1 TTTTAAAATAAATCAATCCATA
** *
292710 TTTTAAAATAAAAT-TTTTCATA
1 TTTTAAAAT-AAATCAATCCATA
292732 TTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATCCATA
292754 TTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATCCATA
292776 TTTTAAAATAAAT
1 TTTTAAAATAAAT
292789 TTTAAAATAG
Statistics
Matches: 106, Mismatches: 15, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
21 4 0.04
22 98 0.92
23 4 0.04
ACGTcount: A:0.48, C:0.10, G:0.00, T:0.43
Consensus pattern (22 bp):
TTTTAAAATAAATCAATCCATA
Found at i:292699 original size:44 final size:44
Alignment explanation
Indices: 292644--292788 Score: 229
Period size: 44 Copynumber: 3.3 Consensus size: 44
292634 ATAATAATTT
*
292644 TTTTTAAATAAATCAATCCATATTTTAAAATAAATTTTTCCATA
1 TTTTAAAATAAATCAATCCATATTTTAAAATAAATTTTTCCATA
*
292688 TTTTAAAATAAATCAATCTATATTTTAAAATAAAATTTTT-CATA
1 TTTTAAAATAAATCAATCCATATTTTAAAAT-AAATTTTTCCATA
***
292732 TTTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATCCATATTTTAAAATAAATTTTTCCATA
292776 TTTTAAAATAAAT
1 TTTTAAAATAAAT
292789 TTTAAAATAG
Statistics
Matches: 93, Mismatches: 6, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
43 5 0.05
44 80 0.86
45 8 0.09
ACGTcount: A:0.48, C:0.10, G:0.00, T:0.43
Consensus pattern (44 bp):
TTTTAAAATAAATCAATCCATATTTTAAAATAAATTTTTCCATA
Found at i:292805 original size:11 final size:12
Alignment explanation
Indices: 292775--292814 Score: 50
Period size: 12 Copynumber: 3.6 Consensus size: 12
292765 ATCAATCCAT
292775 ATTTTAAAATAA
1 ATTTTAAAATAA
*
292787 ATTTTAAAATAG
1 ATTTTAAAATAA
292799 A-TTT-AAAT-A
1 ATTTTAAAATAA
292808 ATTTTAA
1 ATTTTAA
292815 TATTCTTTGA
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
9 1 0.04
10 7 0.29
11 4 0.17
12 12 0.50
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.45
Consensus pattern (12 bp):
ATTTTAAAATAA
Found at i:292808 original size:66 final size:66
Alignment explanation
Indices: 292667--292805 Score: 190
Period size: 66 Copynumber: 2.1 Consensus size: 66
292657 CAATCCATAT
*** * **
292667 TTTAAAATAAATTTTTCCATATTTTAAAATAAATCAATCTATATTTTAAAATAAAATTTTTCATA
1 TTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATATTTTAAAATAAAATTTTAAATA
*
292732 T
66 A
292733 TTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATATTTTAAAAT-AAATTTTAAAAT
1 TTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATATTTTAAAATAAAATTTT-AAAT
292797 AGA
65 A-A
292800 TTTAAA
1 TTTAAA
292806 TAATTTTAAT
Statistics
Matches: 64, Mismatches: 7, Indels: 3
0.86 0.09 0.04
Matches are distributed among these distances:
65 7 0.11
66 51 0.80
67 6 0.09
ACGTcount: A:0.49, C:0.08, G:0.01, T:0.42
Consensus pattern (66 bp):
TTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATATTTTAAAATAAAATTTTAAATA
A
Found at i:294136 original size:17 final size:17
Alignment explanation
Indices: 294114--294169 Score: 62
Period size: 17 Copynumber: 3.4 Consensus size: 17
294104 TATTTTTTAT
294114 TATTATATTTATATAAA
1 TATTATATTTATATAAA
*
294131 TATTAT-TTTTTATTAAA
1 TATTATATTTATA-TAAA
* *
294148 -ATAATATTTATATAAT
1 TATTATATTTATATAAA
294164 TATTAT
1 TATTAT
294170 TTATTTAAAT
Statistics
Matches: 31, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
16 12 0.39
17 19 0.61
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (17 bp):
TATTATATTTATATAAA
Found at i:294138 original size:30 final size:31
Alignment explanation
Indices: 294104--294176 Score: 94
Period size: 33 Copynumber: 2.3 Consensus size: 31
294094 ATAGTTGTTA
*
294104 TATTTTTTATT-ATTATATTTATATAAATAT
1 TATTTTTTATTAATAATATTTATATAAATAT
*
294134 TATTTTTTATTAAAATAATATTTATATAATTAT
1 TATTTTTTATT--AATAATATTTATATAAATAT
294167 TATTTATTTA
1 TATTT-TTTA
294177 AATTAGTTAA
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
30 11 0.30
33 22 0.59
34 4 0.11
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (31 bp):
TATTTTTTATTAATAATATTTATATAAATAT
Found at i:294170 original size:15 final size:15
Alignment explanation
Indices: 294119--294179 Score: 59
Period size: 15 Copynumber: 3.9 Consensus size: 15
294109 TTTATTATTA
294119 TATTTATATAAATAT
1 TATTTATATAAATAT
* *
294134 TATTTTTTATTAAAATAA
1 TA-TTTATA-T-AAATAT
*
294152 TATTTATATAATTAT
1 TATTTATATAAATAT
*
294167 TATTTATTTAAAT
1 TATTTATATAAAT
294180 TAGTTAATTA
Statistics
Matches: 36, Mismatches: 7, Indels: 6
0.73 0.14 0.12
Matches are distributed among these distances:
15 17 0.47
16 6 0.17
17 6 0.17
18 7 0.19
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (15 bp):
TATTTATATAAATAT
Found at i:295958 original size:42 final size:42
Alignment explanation
Indices: 295899--295978 Score: 106
Period size: 42 Copynumber: 1.9 Consensus size: 42
295889 ACCGATGATG
* * * *
295899 ATGCCCAGCCCTCCAGTTCAGATGTCATCTCCTCAGGGGTAT
1 ATGCCAAGCCCACCAGTTCAGATGCCATCTCCGCAGGGGTAT
* *
295941 ATGCCAAGCCCACCAGTTTATATGCCATCTCCGCAGGG
1 ATGCCAAGCCCACCAGTTCAGATGCCATCTCCGCAGGG
295979 TTTCATTCCT
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
42 32 1.00
ACGTcount: A:0.21, C:0.34, G:0.21, T:0.24
Consensus pattern (42 bp):
ATGCCAAGCCCACCAGTTCAGATGCCATCTCCGCAGGGGTAT
Found at i:295998 original size:21 final size:21
Alignment explanation
Indices: 295974--296044 Score: 74
Period size: 21 Copynumber: 3.4 Consensus size: 21
295964 GCCATCTCCG
*
295974 CAGGGTTTCATTCCTAGCCCT
1 CAGGGTTTCATTCCTAGCCCC
295995 CAGGGTTAT-ATTCCTAGCCCGC
1 CAGGGTT-TCATTCCTAGCCC-C
* * *
296017 CA-GGTTACATACCTAGCCCG
1 CAGGGTTTCATTCCTAGCCCC
296037 CAGGGTTT
1 CAGGGTTT
296045 TATGACACCA
Statistics
Matches: 41, Mismatches: 5, Indels: 8
0.76 0.09 0.15
Matches are distributed among these distances:
20 2 0.05
21 36 0.88
22 3 0.07
ACGTcount: A:0.18, C:0.31, G:0.23, T:0.28
Consensus pattern (21 bp):
CAGGGTTTCATTCCTAGCCCC
Found at i:296423 original size:117 final size:117
Alignment explanation
Indices: 296156--297403 Score: 1852
Period size: 117 Copynumber: 10.7 Consensus size: 117
296146 AGAAATAATA
* ** * * *
296156 GGTACTGACATGAATAGTTCTTCGGGGGGACATGAGTGACATAATAGGGCAATGATAACATATTA
1 GGTACTGACATGAATAGTGCCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTC
* *
296221 TCTGACAAAATAATGGAA-G-GCGCCCTCGAGAACGCGCTTTCACCACTTTG
66 TCTGACAAAATAATGGAAGGCGCGCCCCCGGGAACGCGCTTTCACCACTTTG
* *
296271 GGTACTGACATGAATAGTGCCCCCGATGGACATGAGTGACATAATAGGGCAATGATAACATATTA
1 GGTACTGACATGAATAGTGCCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTC
* * * *
296336 TCTGAAAAAATAATGGAAGACACGCCCCCGGTAACGCGCTTTCACCACTTTG
66 TCTGACAAAATAATGGAAGGCGCGCCCCCGGGAACGCGCTTTCACCACTTTG
* **
296388 GGTACTGACATGAATAGTGCCCCTGAATGACATGAGTGACATAATAGGGCAATGATAACATATTC
1 GGTACTGACATGAATAGTGCCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTC
* * * *
296453 TCTAACAAAATAATGAAAGGTGC-CCCCTC-AGAACGCGCTTTCACCACTTTG
66 TCTGACAAAATAATGGAAGGCGCGCCCC-CGGGAACGCGCTTTCACCACTTTG
*
296504 GGTACTGACATAAATAGTGCCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTC
1 GGTACTGACATGAATAGTGCCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTC
* * * *
296569 TCTGAAAAAATAATGGAAGGTGCTCCACCGGGAACGCGCTTTCACCACTTTG
66 TCTGACAAAATAATGGAAGGCGCGCCCCCGGGAACGCGCTTTCACCACTTTG
*
296621 GGTACTGATATGAATAGTGCCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTC
1 GGTACTGACATGAATAGTGCCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTC
*
296686 TCTGACAAAATAATGGAAGGCGTC-CCCCCGGGAATGCGCTTTCACCACTTTG
66 TCTGACAAAATAATGGAAGGCG-CGCCCCCGGGAACGCGCTTTCACCACTTTG
* *
296738 GGTACTGACATGAATAGTG-CCCCGATGGACATGAGTGGCATAATAGGGCAATGATAACATATTC
1 GGTACTGACATGAATAGTGCCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTC
* * * *
296802 TCTAAAAAAATAATGGAAGGCGCGCCCCCGGGAACGCGTTTTCACCACTTTC
66 TCTGACAAAATAATGGAAGGCGCGCCCCCGGGAACGCGCTTTCACCACTTTG
* * * *
296854 GGTACTGACATGAATAATGCCCCCGAGGGACATGAGAGACATAATAGGGCAATGATCATATATTC
1 GGTACTGACATGAATAGTGCCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTC
*
296919 TCTGACAAAATAATGGAAGGCGC-CCCCC-GGAACGCACTTTCACCACTTTG
66 TCTGACAAAATAATGGAAGGCGCGCCCCCGGGAACGCGCTTTCACCACTTTG
* * * *
296969 GGTACTGATATGAATAGTGCCCTCGTGGGACATGAGTGATATAATAGGGCAATGATAACATATTC
1 GGTACTGACATGAATAGTGCCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTC
* * *
297034 TCTGACAAAATAATGGAAGGTGC-CCCCTGGGAACGCACTTTCACCACTTTG
66 TCTGACAAAATAATGGAAGGCGCGCCCCCGGGAACGCGCTTTCACCACTTTG
* *
297085 GGTACTGACATAAATAGTGCCCCCGAGGGACATGAGTGACATAATAAGGCAATGATAACATATTC
1 GGTACTGACATGAATAGTGCCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTC
*
297150 TCTGACAAAATAATGGAAGGCG-TCCCCCGGGAACGCGCTTTCACCACTTTG
66 TCTGACAAAATAATGGAAGGCGCGCCCCCGGGAACGCGCTTTCACCACTTTG
* * *
297201 GGTATTGATATGAATAGTGCCCCCGAGGGACATGAGTGACATAATAGGGTAATGATAACATATTC
1 GGTACTGACATGAATAGTGCCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTC
* * * * * *
297266 TCTGAAAAAATAATAGAATGC-CTCCCCCCGGGAACACGCTTTTACCACTTTG
66 TCTGACAAAATAATGGAAGGCGC-GCCCCCGGGAACGCGCTTTCACCACTTTG
*
297318 GGTACTGACATGAATAGTGCCCCCGAGGGACATGAGTGACAAAATAGGGCAATGATAACATATTC
1 GGTACTGACATGAATAGTGCCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTC
*
297383 TCTGACAAAATAATAGAAGGC
66 TCTGACAAAATAATGGAAGGC
297404 CCCCCAAAAA
Statistics
Matches: 1027, Mismatches: 94, Indels: 22
0.90 0.08 0.02
Matches are distributed among these distances:
115 179 0.17
116 423 0.41
117 424 0.41
118 1 0.00
ACGTcount: A:0.32, C:0.21, G:0.23, T:0.23
Consensus pattern (117 bp):
GGTACTGACATGAATAGTGCCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTC
TCTGACAAAATAATGGAAGGCGCGCCCCCGGGAACGCGCTTTCACCACTTTG
Found at i:296536 original size:116 final size:115
Alignment explanation
Indices: 296156--297408 Score: 1846
Period size: 116 Copynumber: 10.8 Consensus size: 115
296146 AGAAATAATA
* ** * * *
296156 GGTACTGACATGAATAGTTCTTCGGGGGGACATGAGTGACATAATAGGGCAATGATAACATATTA
1 GGTACTGACATGAATAGTGCCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTC
*
296221 TCTGACAAAATAATGGAAGGCG-CCCTCGAGAACGCGCTTTCACCACTTTG
66 TCTGACAAAATAATGGAAGGCGCCCCCCG-GAACGCGCTTTCACCACTTTG
* *
296271 GGTACTGACATGAATAGTGCCCCCGATGGACATGAGTGACATAATAGGGCAATGATAACATATTA
1 GGTACTGACATGAATAGTGCCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTC
* * *
296336 TCTGAAAAAATAATGGAAGACACGCCCCCGGTAACGCGCTTTCACCACTTTG
66 TCTGACAAAATAATGGAAGGCGC-CCCCCGG-AACGCGCTTTCACCACTTTG
* **
296388 GGTACTGACATGAATAGTGCCCCTGAATGACATGAGTGACATAATAGGGCAATGATAACATATTC
1 GGTACTGACATGAATAGTGCCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTC
* * * *
296453 TCTAACAAAATAATGAAAGGTGCCCCCTCAGAACGCGCTTTCACCACTTTG
66 TCTGACAAAATAATGGAAGGCGCCCCC-CGGAACGCGCTTTCACCACTTTG
*
296504 GGTACTGACATAAATAGTGCCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTC
1 GGTACTGACATGAATAGTGCCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTC
* * *
296569 TCTGAAAAAATAATGGAAGGTGCTCCACCGGGAACGCGCTTTCACCACTTTG
66 TCTGACAAAATAATGGAAGGCGC-CC-CCCGGAACGCGCTTTCACCACTTTG
*
296621 GGTACTGATATGAATAGTGCCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTC
1 GGTACTGACATGAATAGTGCCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTC
*
296686 TCTGACAAAATAATGGAAGGCGTCCCCCCGGGAATGCGCTTTCACCACTTTG
66 TCTGACAAAATAATGGAAGGCG-CCCCCC-GGAACGCGCTTTCACCACTTTG
* *
296738 GGTACTGACATGAATAGTG-CCCCGATGGACATGAGTGGCATAATAGGGCAATGATAACATATTC
1 GGTACTGACATGAATAGTGCCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTC
* * * *
296802 TCTAAAAAAATAATGGAAGGCGCGCCCCCGGGAACGCGTTTTCACCACTTTC
66 TCTGACAAAATAATGGAAGGCGC-CCCCC-GGAACGCGCTTTCACCACTTTG
* * * *
296854 GGTACTGACATGAATAATGCCCCCGAGGGACATGAGAGACATAATAGGGCAATGATCATATATTC
1 GGTACTGACATGAATAGTGCCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTC
*
296919 TCTGACAAAATAATGGAAGGCGCCCCCCGGAACGCACTTTCACCACTTTG
66 TCTGACAAAATAATGGAAGGCGCCCCCCGGAACGCGCTTTCACCACTTTG
* * * *
296969 GGTACTGATATGAATAGTGCCCTCGTGGGACATGAGTGATATAATAGGGCAATGATAACATATTC
1 GGTACTGACATGAATAGTGCCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTC
* * *
297034 TCTGACAAAATAATGGAAGGTGCCCCCTGGGAACGCACTTTCACCACTTTG
66 TCTGACAAAATAATGGAAGGCGCCCCC-CGGAACGCGCTTTCACCACTTTG
* *
297085 GGTACTGACATAAATAGTGCCCCCGAGGGACATGAGTGACATAATAAGGCAATGATAACATATTC
1 GGTACTGACATGAATAGTGCCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTC
*
297150 TCTGACAAAATAATGGAAGGCGTCCCCCGGGAACGCGCTTTCACCACTTTG
66 TCTGACAAAATAATGGAAGGCG-CCCCCCGGAACGCGCTTTCACCACTTTG
* * *
297201 GGTATTGATATGAATAGTGCCCCCGAGGGACATGAGTGACATAATAGGGTAATGATAACATATTC
1 GGTACTGACATGAATAGTGCCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTC
* * * * * *
297266 TCTGAAAAAATAATAGAATGCCTCCCCCCGGGAACACGCTTTTACCACTTTG
66 TCTGACAAAATAATGGAA-GGCGCCCCCC-GGAACGCGCTTTCACCACTTTG
*
297318 GGTACTGACATGAATAGTGCCCCCGAGGGACATGAGTGACAAAATAGGGCAATGATAACATATTC
1 GGTACTGACATGAATAGTGCCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTC
*
297383 TCTGACAAAATAATAGAAGGC-CCCCC
66 TCTGACAAAATAATGGAAGGCGCCCCC
297409 AAAAACGTGT
Statistics
Matches: 1033, Mismatches: 91, Indels: 28
0.90 0.08 0.02
Matches are distributed among these distances:
115 186 0.18
116 426 0.41
117 418 0.40
118 3 0.00
ACGTcount: A:0.32, C:0.22, G:0.23, T:0.23
Consensus pattern (115 bp):
GGTACTGACATGAATAGTGCCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTC
TCTGACAAAATAATGGAAGGCGCCCCCCGGAACGCGCTTTCACCACTTTG
Found at i:296562 original size:233 final size:232
Alignment explanation
Indices: 296156--297408 Score: 1913
Period size: 233 Copynumber: 5.4 Consensus size: 232
296146 AGAAATAATA
* ** * * *
296156 GGTACTGACATGAATAGTTCTTCGGGGGGACATGAGTGACATAATAGGGCAATGATAACATATTA
1 GGTACTGACATGAATAGTGCCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTC
*
296221 TCTGACAAAATAATGGAAGGCG-CCCTCGAGAACGCGCTTTCACCACTTTGGGTACTGACATGAA
66 TCTGACAAAATAATGGAAGGCGCCCCCCG-GAACGCGCTTTCACCACTTTGGGTACTGACATGAA
* *
296285 TAGTGCCCCCGATGGACATGAGTGACATAATAGGGCAATGATAACATATTATCTGAAAAAATAAT
130 TAGTGCCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGAAAAAATAAT
* * *
296350 GGAAGACACGCCCCCGGTAACGCGCTTTCACCACTTTG
195 GGAAGGCGCGCCCCCGGGAACGCGCTTTCACCACTTTG
* **
296388 GGTACTGACATGAATAGTGCCCCTGAATGACATGAGTGACATAATAGGGCAATGATAACATATTC
1 GGTACTGACATGAATAGTGCCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTC
* * * * *
296453 TCTAACAAAATAATGAAAGGTGCCCCCTCAGAACGCGCTTTCACCACTTTGGGTACTGACATAAA
66 TCTGACAAAATAATGGAAGGCGCCCCC-CGGAACGCGCTTTCACCACTTTGGGTACTGACATGAA
296518 TAGTGCCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGAAAAAATAAT
130 TAGTGCCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGAAAAAATAAT
* * *
296583 GGAAGGTGCTCCACCGGGAACGCGCTTTCACCACTTTG
195 GGAAGGCGCGCCCCCGGGAACGCGCTTTCACCACTTTG
*
296621 GGTACTGATATGAATAGTGCCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTC
1 GGTACTGACATGAATAGTGCCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTC
*
296686 TCTGACAAAATAATGGAAGGCGTCCCCCCGGGAATGCGCTTTCACCACTTTGGGTACTGACATGA
66 TCTGACAAAATAATGGAAGGCG-CCCCCC-GGAACGCGCTTTCACCACTTTGGGTACTGACATGA
* * *
296751 ATAGTG-CCCCGATGGACATGAGTGGCATAATAGGGCAATGATAACATATTCTCTAAAAAAATAA
129 ATAGTGCCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGAAAAAATAA
* *
296815 TGGAAGGCGCGCCCCCGGGAACGCGTTTTCACCACTTTC
194 TGGAAGGCGCGCCCCCGGGAACGCGCTTTCACCACTTTG
* * * *
296854 GGTACTGACATGAATAATGCCCCCGAGGGACATGAGAGACATAATAGGGCAATGATCATATATTC
1 GGTACTGACATGAATAGTGCCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTC
* *
296919 TCTGACAAAATAATGGAAGGCGCCCCCCGGAACGCACTTTCACCACTTTGGGTACTGATATGAAT
66 TCTGACAAAATAATGGAAGGCGCCCCCCGGAACGCGCTTTCACCACTTTGGGTACTGACATGAAT
* * * *
296984 AGTGCCCTCGTGGGACATGAGTGATATAATAGGGCAATGATAACATATTCTCTGACAAAATAATG
131 AGTGCCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGAAAAAATAATG
* * *
297049 GAAGGTGC-CCCCTGGGAACGCACTTTCACCACTTTG
196 GAAGGCGCGCCCCCGGGAACGCGCTTTCACCACTTTG
* *
297085 GGTACTGACATAAATAGTGCCCCCGAGGGACATGAGTGACATAATAAGGCAATGATAACATATTC
1 GGTACTGACATGAATAGTGCCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTC
* * *
297150 TCTGACAAAATAATGGAAGGCGTCCCCCGGGAACGCGCTTTCACCACTTTGGGTATTGATATGAA
66 TCTGACAAAATAATGGAAGGCG-CCCCCCGGAACGCGCTTTCACCACTTTGGGTACTGACATGAA
*
297215 TAGTGCCCCCGAGGGACATGAGTGACATAATAGGGTAATGATAACATATTCTCTGAAAAAATAAT
130 TAGTGCCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGAAAAAATAAT
* * * * *
297280 AGAATGC-CTCCCCCCGGGAACACGCTTTTACCACTTTG
195 GGAAGGCGC-GCCCCCGGGAACGCGCTTTCACCACTTTG
*
297318 GGTACTGACATGAATAGTGCCCCCGAGGGACATGAGTGACAAAATAGGGCAATGATAACATATTC
1 GGTACTGACATGAATAGTGCCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTC
*
297383 TCTGACAAAATAATAGAAGGC-CCCCC
66 TCTGACAAAATAATGGAAGGCGCCCCC
297409 AAAAACGTGT
Statistics
Matches: 928, Mismatches: 85, Indels: 17
0.90 0.08 0.02
Matches are distributed among these distances:
231 149 0.16
232 245 0.26
233 490 0.53
234 44 0.05
ACGTcount: A:0.32, C:0.22, G:0.23, T:0.23
Consensus pattern (232 bp):
GGTACTGACATGAATAGTGCCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTC
TCTGACAAAATAATGGAAGGCGCCCCCCGGAACGCGCTTTCACCACTTTGGGTACTGACATGAAT
AGTGCCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGAAAAAATAATG
GAAGGCGCGCCCCCGGGAACGCGCTTTCACCACTTTG
Found at i:300546 original size:16 final size:16
Alignment explanation
Indices: 300502--300546 Score: 51
Period size: 16 Copynumber: 2.9 Consensus size: 16
300492 TACATCTAAA
*
300502 TAAATTTTATTTT-TT
1 TAAAATTTATTTTATT
300517 TAAAAATTTA--TTATT
1 T-AAAATTTATTTTATT
300532 TAAAATTTATTTTAT
1 TAAAATTTATTTTAT
300547 GATATTTGAT
Statistics
Matches: 25, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
14 10 0.40
15 4 0.16
16 11 0.44
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (16 bp):
TAAAATTTATTTTATT
Found at i:300627 original size:26 final size:28
Alignment explanation
Indices: 300570--300627 Score: 66
Period size: 26 Copynumber: 2.1 Consensus size: 28
300560 TATTGTATAA
* * *
300570 ATTATTTATATTGTAATTTTATAAAATG
1 ATTAATTATATTGTAATTTAATAAAATC
*
300598 ATTAATTATATT-T-ATTTAATATAATC
1 ATTAATTATATTGTAATTTAATAAAATC
300624 ATTA
1 ATTA
300628 GTATTATTTA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
26 14 0.54
27 1 0.04
28 11 0.42
ACGTcount: A:0.41, C:0.02, G:0.03, T:0.53
Consensus pattern (28 bp):
ATTAATTATATTGTAATTTAATAAAATC
Found at i:300654 original size:20 final size:20
Alignment explanation
Indices: 300629--300670 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
300619 TAATCATTAG
*
300629 TATTATTTATTATAAAAAAT
1 TATTATTAATTATAAAAAAT
* *
300649 TATTATTAATTTTAAAATAT
1 TATTATTAATTATAAAAAAT
300669 TA
1 TA
300671 AAATAATTCT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (20 bp):
TATTATTAATTATAAAAAAT
Found at i:300908 original size:28 final size:29
Alignment explanation
Indices: 300855--300910 Score: 78
Period size: 28 Copynumber: 2.0 Consensus size: 29
300845 TTAAATAATT
* *
300855 AAATAATAAAATTAATAGATCGATAATCA
1 AAATAAAAAAATTAATAGATAGATAATCA
*
300884 AAATAAAAAAATT-ATAGATATATAATC
1 AAATAAAAAAATTAATAGATAGATAATC
300911 GTACAATTAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
28 12 0.50
29 12 0.50
ACGTcount: A:0.61, C:0.05, G:0.05, T:0.29
Consensus pattern (29 bp):
AAATAAAAAAATTAATAGATAGATAATCA
Found at i:301005 original size:28 final size:28
Alignment explanation
Indices: 300950--301007 Score: 82
Period size: 28 Copynumber: 2.1 Consensus size: 28
300940 AAATCTTTAT
* *
300950 TATTAATAATTTATACTGATACATAATA
1 TATTAATAATTTATAATAATACATAATA
300978 TATTAATAATTTATAATAATA-ATAAATA
1 TATTAATAATTTATAATAATACAT-AATA
301006 TA
1 TA
301008 AAATCTTTAT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
27 2 0.07
28 25 0.93
ACGTcount: A:0.52, C:0.03, G:0.02, T:0.43
Consensus pattern (28 bp):
TATTAATAATTTATAATAATACATAATA
Found at i:310841 original size:2 final size:2
Alignment explanation
Indices: 310834--310865 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
310824 TTCTTCCTTC
310834 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
310866 ATATATATAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:310870 original size:2 final size:2
Alignment explanation
Indices: 310865--310899 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
310855 TCTCTCTCTC
310865 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
310900 TTAATTGGAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:315628 original size:22 final size:22
Alignment explanation
Indices: 315598--315645 Score: 53
Period size: 22 Copynumber: 2.2 Consensus size: 22
315588 GGCAATCGCG
* *
315598 TAAATATCCGACTAGT-ATTAAT
1 TAAAAATCCGA-TAGTCATTAAA
*
315620 TAAAAATCCTATAGTCATTAAA
1 TAAAAATCCGATAGTCATTAAA
315642 TAAA
1 TAAA
315646 TAATAAATAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
21 4 0.18
22 18 0.82
ACGTcount: A:0.48, C:0.12, G:0.06, T:0.33
Consensus pattern (22 bp):
TAAAAATCCGATAGTCATTAAA
Found at i:317991 original size:15 final size:15
Alignment explanation
Indices: 317971--318000 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
317961 CCGGAAAGCC
317971 TAAAATACCCTACCT
1 TAAAATACCCTACCT
*
317986 TAAAATACCGTACCT
1 TAAAATACCCTACCT
318001 GAATTCAACT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.40, C:0.30, G:0.03, T:0.27
Consensus pattern (15 bp):
TAAAATACCCTACCT
Found at i:322513 original size:2 final size:2
Alignment explanation
Indices: 322506--322530 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
322496 ACCATATAAA
322506 TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC T
322531 GTATATATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:322573 original size:2 final size:2
Alignment explanation
Indices: 322532--322556 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
322522 TCTCTCTCTG
322532 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
322557 GTTTTTTTAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:322662 original size:3 final size:3
Alignment explanation
Indices: 322644--322732 Score: 142
Period size: 3 Copynumber: 29.7 Consensus size: 3
322634 AGTTTCTGTG
* *
322644 TCT TCT TCA TCA TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
* *
322692 TCT TCT TCT TCT ACT TCT TCT TCT TCT ACT TCT TCT TCT TC
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TC
322733 ATGGTCATTA
Statistics
Matches: 80, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 80 1.00
ACGTcount: A:0.04, C:0.34, G:0.00, T:0.62
Consensus pattern (3 bp):
TCT
Found at i:323220 original size:6 final size:6
Alignment explanation
Indices: 323189--323222 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
323179 ATATCAGGGA
* *
323189 AGGCTG AAGCTG AAGCTG AGGCTG AGGCTG AGGC
1 AGGCTG AGGCTG AGGCTG AGGCTG AGGCTG AGGC
323223 AGATGAGATG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.24, C:0.18, G:0.44, T:0.15
Consensus pattern (6 bp):
AGGCTG
Found at i:325341 original size:16 final size:16
Alignment explanation
Indices: 325320--325358 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
325310 GGTATTACCC
* *
325320 GACCTGTTTTCAACCT
1 GACCTGTTATAAACCT
*
325336 GACCTGCTATAAACCT
1 GACCTGTTATAAACCT
325352 GACCTGT
1 GACCTGT
325359 AATTGACTCA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.23, C:0.31, G:0.15, T:0.31
Consensus pattern (16 bp):
GACCTGTTATAAACCT
Found at i:325475 original size:27 final size:26
Alignment explanation
Indices: 325437--325489 Score: 63
Period size: 27 Copynumber: 2.0 Consensus size: 26
325427 AAGTTACCAT
* *
325437 TAATATAATTATGTTATTTTAAATTTA
1 TAATATAATTATGATA-ATTAAATTTA
325464 TAATA-AACTTATGATAATTAAATTTA
1 TAATATAA-TTATGATAATTAAATTTA
325490 GTTTTTATAT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
26 11 0.48
27 12 0.52
ACGTcount: A:0.45, C:0.02, G:0.04, T:0.49
Consensus pattern (26 bp):
TAATATAATTATGATAATTAAATTTA
Found at i:325517 original size:19 final size:19
Alignment explanation
Indices: 325493--325538 Score: 58
Period size: 19 Copynumber: 2.5 Consensus size: 19
325483 AAATTTAGTT
325493 TTTATATTAATTACAATTC
1 TTTATATTAATTACAATTC
** *
325512 TTTATATTTTTTATAATTC
1 TTTATATTAATTACAATTC
325531 -TTATATTA
1 TTTATATTA
325539 TAATTTGTAT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
18 7 0.30
19 16 0.70
ACGTcount: A:0.33, C:0.07, G:0.00, T:0.61
Consensus pattern (19 bp):
TTTATATTAATTACAATTC
Found at i:325560 original size:15 final size:14
Alignment explanation
Indices: 325522--325560 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 14
325512 TTTATATTTT
325522 TTATAATTCT-TATA
1 TTATAATT-TGTATA
325536 TTATAATTTGTATA
1 TTATAATTTGTATA
325550 TTATAAATTTG
1 TTAT-AATTTG
325561 AGTTTTATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 1 0.04
14 16 0.70
15 6 0.26
ACGTcount: A:0.36, C:0.03, G:0.05, T:0.56
Consensus pattern (14 bp):
TTATAATTTGTATA
Found at i:325567 original size:71 final size:70
Alignment explanation
Indices: 325482--325625 Score: 222
Period size: 71 Copynumber: 2.0 Consensus size: 70
325472 TTATGATAAT
*
325482 TAAATTTAGTTTTTATATTAATT-ACAATTCTTTATATTTTTTATAATTCTTATATTAT-AATTT
1 TAAATTTAGTTTTTATATTAATTCA-AATTCTTTATATTATTTATAATTCTTATATTATAAATTT
325545 GTATATTA
65 -TAT-TTA
325553 TAAATTTGAG-TTTTATATTAATTCAAATTCTTTATATTATTTATAATTCTTATATTATAAATTT
1 TAAATTT-AGTTTTTATATTAATTCAAATTCTTTATATTATTTATAATTCTTATATTATAAATTT
325617 TATTTA
65 TATTTA
325623 TAA
1 TAA
325626 TCACTAAATT
Statistics
Matches: 69, Mismatches: 1, Indels: 7
0.90 0.01 0.09
Matches are distributed among these distances:
70 6 0.09
71 55 0.80
72 8 0.12
ACGTcount: A:0.35, C:0.04, G:0.03, T:0.58
Consensus pattern (70 bp):
TAAATTTAGTTTTTATATTAATTCAAATTCTTTATATTATTTATAATTCTTATATTATAAATTTT
ATTTA
Found at i:325588 original size:19 final size:20
Alignment explanation
Indices: 325564--325609 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 20
325554 AAATTTGAGT
325564 TTTATATTAATTCA-AATTC
1 TTTATATTAATTCATAATTC
*
325583 TTTATATT-ATTTATAATTC
1 TTTATATTAATTCATAATTC
325602 -TTATATTA
1 TTTATATTA
325610 TAAATTTTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
18 11 0.46
19 13 0.54
ACGTcount: A:0.35, C:0.07, G:0.00, T:0.59
Consensus pattern (20 bp):
TTTATATTAATTCATAATTC
Found at i:325609 original size:37 final size:36
Alignment explanation
Indices: 325494--325609 Score: 109
Period size: 37 Copynumber: 3.2 Consensus size: 36
325484 AATTTAGTTT
*
325494 TTATATTAATTACAATTCTTTATATTTTTTATAATTC
1 TTATATTAATTA-AATTCTTTATATTATTTATAATTC
* *
325531 TTATATT-A-T-AATT-TGTATATTATAAATT-TGAGTT-
1 TTATATTAATTAAATTCTTTATATTAT---TTAT-AATTC
325565 TTATATTAATTCAAATTCTTTATATTATTTATAATTC
1 TTATATTAATT-AAATTCTTTATATTATTTATAATTC
325602 TTATATTA
1 TTATATTA
325610 TAAATTTTAT
Statistics
Matches: 63, Mismatches: 5, Indels: 22
0.70 0.06 0.24
Matches are distributed among these distances:
32 8 0.13
33 4 0.06
34 8 0.13
35 7 0.11
36 7 0.11
37 16 0.25
38 4 0.06
39 9 0.14
ACGTcount: A:0.34, C:0.05, G:0.03, T:0.58
Consensus pattern (36 bp):
TTATATTAATTAAATTCTTTATATTATTTATAATTC
Found at i:325623 original size:13 final size:14
Alignment explanation
Indices: 325589--325625 Score: 51
Period size: 13 Copynumber: 2.7 Consensus size: 14
325579 ATTCTTTATA
325589 TTATTTAT-AATTC
1 TTATTTATAAATTC
325602 TTATATTATAAATT-
1 TTAT-TTATAAATTC
325616 TTATTTATAA
1 TTATTTATAA
325626 TCACTAAATT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
13 10 0.45
14 8 0.36
15 4 0.18
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (14 bp):
TTATTTATAAATTC
Found at i:325969 original size:15 final size:15
Alignment explanation
Indices: 325949--325979 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
325939 TTCTCTCAGA
325949 TCTTATAATTAAGGT
1 TCTTATAATTAAGGT
*
325964 TCTTATAGTTAAGGT
1 TCTTATAATTAAGGT
325979 T
1 T
325980 TTACAAGGTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.29, C:0.06, G:0.16, T:0.48
Consensus pattern (15 bp):
TCTTATAATTAAGGT
Found at i:328133 original size:27 final size:26
Alignment explanation
Indices: 328103--328201 Score: 78
Period size: 27 Copynumber: 3.7 Consensus size: 26
328093 ATTAATAAAC
*
328103 TATTTTAATTAATATTAAAATATTATA
1 TATTATAATTAATATTAAAAT-TTATA
*
328130 TATTATAATT-ATATTAATTAACTTATA
1 TATTATAATTAATATTAA--AATTTATA
* *
328157 TTACTATAATATAAT-TTATAATTTATA
1 -TATTATAAT-TAATATTAAAATTTATA
*
328184 -ATTTGTAATTAATATTAA
1 TA-TTATAATTAATATTAA
328202 TATAAAATAT
Statistics
Matches: 57, Mismatches: 8, Indels: 15
0.71 0.10 0.19
Matches are distributed among these distances:
25 5 0.09
26 15 0.26
27 21 0.37
28 10 0.18
29 4 0.07
30 2 0.04
ACGTcount: A:0.45, C:0.02, G:0.01, T:0.52
Consensus pattern (26 bp):
TATTATAATTAATATTAAAATTTATA
Found at i:328227 original size:22 final size:21
Alignment explanation
Indices: 328202--328257 Score: 67
Period size: 22 Copynumber: 2.6 Consensus size: 21
328192 TTAATATTAA
328202 TATAAAATATAGTCTATAAAGT
1 TATAAAATATAGTCTAT-AAGT
** *
328224 TATAAAATATAAACTATATGT
1 TATAAAATATAGTCTATAAGT
*
328245 TATAAATTATAGT
1 TATAAAATATAGT
328258 ATAGTTTATA
Statistics
Matches: 28, Mismatches: 6, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
21 13 0.46
22 15 0.54
ACGTcount: A:0.50, C:0.04, G:0.07, T:0.39
Consensus pattern (21 bp):
TATAAAATATAGTCTATAAGT
Found at i:328232 original size:29 final size:28
Alignment explanation
Indices: 328200--328255 Score: 78
Period size: 29 Copynumber: 2.0 Consensus size: 28
328190 AATTAATATT
328200 AATATAAAATATA-GTCTATAAAGTTATAA
1 AATATAAAATATATGT-TATAAA-TTATAA
*
328229 AATATAAACTATATGTTATAAATTATA
1 AATATAAAATATATGTTATAAATTATA
328256 GTATAGTTTA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
28 5 0.20
29 18 0.72
30 2 0.08
ACGTcount: A:0.54, C:0.04, G:0.05, T:0.38
Consensus pattern (28 bp):
AATATAAAATATATGTTATAAATTATAA
Found at i:328266 original size:19 final size:19
Alignment explanation
Indices: 328244--328312 Score: 63
Period size: 19 Copynumber: 3.6 Consensus size: 19
328234 AAACTATATG
328244 TTATAAATTATAGTATAGT
1 TTATAAATTATAGTATAGT
* *
328263 TTATAAACTATAGT-TAAT
1 TTATAAATTATAGTATAGT
*
328281 ATAATTAATATTA-A-TATAGT
1 -TTA-TAA-ATTATAGTATAGT
328301 TTATAAATTATA
1 TTATAAATTATA
328313 TACTATATTA
Statistics
Matches: 39, Mismatches: 6, Indels: 11
0.70 0.11 0.20
Matches are distributed among these distances:
17 4 0.10
18 7 0.18
19 18 0.46
20 7 0.18
21 3 0.08
ACGTcount: A:0.46, C:0.01, G:0.06, T:0.46
Consensus pattern (19 bp):
TTATAAATTATAGTATAGT
Found at i:328298 original size:24 final size:22
Alignment explanation
Indices: 328263--328334 Score: 69
Period size: 22 Copynumber: 3.2 Consensus size: 22
328253 ATAGTATAGT
328263 TTATA-AACTATAGTTAATATAA
1 TTATATAA-TATAGTTAATATAA
*
328285 TTAATATTAATATAGTTTATA-AA
1 TT-ATA-TAATATAGTTAATATAA
*
328308 TTATATACTATA-TTAATATAAA
1 TTATATAATATAGTTAATAT-AA
328330 TTATA
1 TTATA
328335 GTTAAGATAA
Statistics
Matches: 42, Mismatches: 3, Indels: 10
0.76 0.05 0.18
Matches are distributed among these distances:
20 5 0.12
21 6 0.14
22 12 0.29
23 7 0.17
24 10 0.24
25 2 0.05
ACGTcount: A:0.49, C:0.03, G:0.03, T:0.46
Consensus pattern (22 bp):
TTATATAATATAGTTAATATAA
Found at i:328301 original size:38 final size:36
Alignment explanation
Indices: 328257--328337 Score: 101
Period size: 38 Copynumber: 2.2 Consensus size: 36
328247 TAAATTATAG
*
328257 TATAGTTTATAAACTATAGTTAATATAATTAATATTAA-
1 TATAGTTTATAAACTATA--TAATAT-ATTAATATAAAT
* *
328295 TATAGTTTATAAATTATATACTATATTAATATAAAT
1 TATAGTTTATAAACTATATAATATATTAATATAAAT
328331 TATAGTT
1 TATAGTT
328338 AAGATAATTA
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
35 10 0.26
36 12 0.31
38 17 0.44
ACGTcount: A:0.46, C:0.02, G:0.05, T:0.47
Consensus pattern (36 bp):
TATAGTTTATAAACTATATAATATATTAATATAAAT
Found at i:328367 original size:22 final size:22
Alignment explanation
Indices: 328341--328425 Score: 145
Period size: 22 Copynumber: 3.9 Consensus size: 22
328331 TATAGTTAAG
328341 ATAATTAACATTAATATAAACT
1 ATAATTAACATTAATATAAACT
328363 ATAATTAACATTAATATAAACT
1 ATAATTAACATTAATATAAACT
328385 ATAATTAACATTAATATAAACT
1 ATAATTAACATTAATATAAACT
*
328407 ATATAGT-ACATTAATATAA
1 ATA-ATTAACATTAATATAA
328426 TTATAGTTTA
Statistics
Matches: 61, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
22 59 0.97
23 2 0.03
ACGTcount: A:0.54, C:0.08, G:0.01, T:0.36
Consensus pattern (22 bp):
ATAATTAACATTAATATAAACT
Found at i:328388 original size:60 final size:60
Alignment explanation
Indices: 328264--328388 Score: 137
Period size: 60 Copynumber: 2.1 Consensus size: 60
328254 TAGTATAGTT
* * *** * *
328264 TATAAACTATAGTTAATATAATTAATATTAATATAGTTTATAAATTATATACTATATTAA
1 TATAAACTATAGTTAAGATAATTAACATTAATATAAACTATAAATTATACACTATATAAA
* *
328324 TATAAATTATAGTTAAGATAATTAACATTAATATAAACTAT-AATTA-ACATTAATATAAA
1 TATAAACTATAGTTAAGATAATTAACATTAATATAAACTATAAATTATACACT-ATATAAA
328383 CTATAA
1 -TATAA
328389 TTAACATTAA
Statistics
Matches: 54, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
58 3 0.06
59 11 0.20
60 40 0.74
ACGTcount: A:0.51, C:0.05, G:0.03, T:0.41
Consensus pattern (60 bp):
TATAAACTATAGTTAAGATAATTAACATTAATATAAACTATAAATTATACACTATATAAA
Found at i:328471 original size:21 final size:20
Alignment explanation
Indices: 328427--328471 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
328417 TTAATATAAT
* * *
328427 TATAGTTTATAAATTTATAC
1 TATAGGTTATAAATATAAAC
328447 TATAGGTTATAAAGTATAAAC
1 TATAGGTTATAAA-TATAAAC
328468 TATA
1 TATA
328472 AAGTACACTA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
20 12 0.57
21 9 0.43
ACGTcount: A:0.44, C:0.04, G:0.09, T:0.42
Consensus pattern (20 bp):
TATAGGTTATAAATATAAAC
Found at i:328534 original size:33 final size:32
Alignment explanation
Indices: 328497--328652 Score: 160
Period size: 33 Copynumber: 4.8 Consensus size: 32
328487 GTTTACATAT
* *
328497 ACTATATAGTTTATACTTTATATATACTAATGA
1 ACTATATA-TATATAGTTTATATATACTAATGA
328530 ACTATATAATATATAGTTTATATATACTAATGA
1 ACTATAT-ATATATAGTTTATATATACTAATGA
* * *
328563 AATATATATAATGTATAGTTTATATATACCATATAGTT
1 ACTATATAT-A--TATAGTTTATATATACTA-AT-G-A
328601 A-TATATATATATAG-TT-TATATACTAATGA
1 ACTATATATATATAGTTTATATATACTAATGA
328630 AC--TATATATATAGTTTATATATA
1 ACTATATATATATAGTTTATATATA
328653 TATAGTTTTA
Statistics
Matches: 106, Mismatches: 7, Indels: 23
0.78 0.05 0.17
Matches are distributed among these distances:
28 11 0.10
29 3 0.03
30 7 0.07
31 2 0.02
32 10 0.09
33 38 0.36
34 6 0.06
35 17 0.16
36 3 0.03
37 8 0.08
38 1 0.01
ACGTcount: A:0.43, C:0.06, G:0.06, T:0.45
Consensus pattern (32 bp):
ACTATATATATATAGTTTATATATACTAATGA
Found at i:328537 original size:17 final size:17
Alignment explanation
Indices: 328515--328572 Score: 50
Period size: 17 Copynumber: 3.5 Consensus size: 17
328505 GTTTATACTT
*
328515 TATATATACTAATGAAC
1 TATATATACTAATGAAA
**
328532 TATATA-A-TATAT-AGT
1 TATATATACTA-ATGAAA
328547 TTATATATACTAATGAAA
1 T-ATATATACTAATGAAA
328565 TATATATA
1 TATATATA
328573 ATGTATAGTT
Statistics
Matches: 32, Mismatches: 4, Indels: 10
0.70 0.09 0.22
Matches are distributed among these distances:
15 4 0.12
16 8 0.25
17 16 0.50
18 4 0.12
ACGTcount: A:0.48, C:0.05, G:0.05, T:0.41
Consensus pattern (17 bp):
TATATATACTAATGAAA
Found at i:328571 original size:35 final size:35
Alignment explanation
Indices: 328499--328639 Score: 150
Period size: 35 Copynumber: 4.2 Consensus size: 35
328489 TTACATATAC
* * * *
328499 TATATAGTTTATACTTTATATATACTAATG-AA-C
1 TATATAATATATAGTTTATATATACTAATGAAATA
328532 TATATAATATATAGTTTATATATACTAATGAAATA
1 TATATAATATATAGTTTATATATACTAATGAAATA
* * **
328567 TATATAATGTATAGTTTATATATACCATAT-AGTTA
1 TATATAATATATAGTTTATATATACTA-ATGAAATA
*
328602 TATAT-ATATATAG-TT-TATATACTAATGAACTA
1 TATATAATATATAGTTTATATATACTAATGAAATA
328634 TATATA
1 TATATA
328640 TAGTTTATAT
Statistics
Matches: 91, Mismatches: 12, Indels: 10
0.81 0.11 0.09
Matches are distributed among these distances:
31 2 0.02
32 16 0.18
33 29 0.32
34 9 0.10
35 33 0.36
36 2 0.02
ACGTcount: A:0.43, C:0.06, G:0.06, T:0.45
Consensus pattern (35 bp):
TATATAATATATAGTTTATATATACTAATGAAATA
Found at i:328604 original size:17 final size:17
Alignment explanation
Indices: 328576--328623 Score: 64
Period size: 17 Copynumber: 2.9 Consensus size: 17
328566 ATATATAATG
328576 TATAGTTTATATATACCA
1 TATAG-TTATATATACCA
*
328594 TATAGTTATATATA-TA
1 TATAGTTATATATACCA
328610 TATAGTT-TATATAC
1 TATAGTTATATATAC
328624 TAATGAACTA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
15 6 0.21
16 8 0.29
17 9 0.32
18 5 0.18
ACGTcount: A:0.40, C:0.06, G:0.06, T:0.48
Consensus pattern (17 bp):
TATAGTTATATATACCA
Found at i:328620 original size:15 final size:15
Alignment explanation
Indices: 328532--328673 Score: 96
Period size: 15 Copynumber: 8.9 Consensus size: 15
328522 ACTAATGAAC
328532 TATATAATATATAGTT
1 TATAT-ATATATAGTT
* *
328548 TATATATACTAATGAAATA
1 TATATATA-T-AT--AGTT
*
328567 TATATAATGTATAGTT
1 TATAT-ATATATAGTT
328583 TATATATACCATATAGTT
1 TATATAT---ATATAGTT
328601 ATATATATATATAGTT
1 -TATATATATATAGTT
328617 TATATACTA-AT-G--
1 TATATA-TATATAGTT
*
328629 AACTATATATATAGTT
1 TA-TATATATATAGTT
328645 TATATATATATAGTT
1 TATATATATATAGTT
328660 T-TATATACTATAGT
1 TATATATA-TATAGT
328674 ATAAATTATT
Statistics
Matches: 102, Mismatches: 8, Indels: 33
0.71 0.06 0.23
Matches are distributed among these distances:
12 3 0.03
13 6 0.06
14 8 0.08
15 33 0.32
16 24 0.24
17 2 0.02
18 9 0.09
19 15 0.15
20 2 0.02
ACGTcount: A:0.42, C:0.04, G:0.07, T:0.46
Consensus pattern (15 bp):
TATATATATATAGTT
Found at i:328671 original size:23 final size:24
Alignment explanation
Indices: 328645--328701 Score: 57
Period size: 23 Copynumber: 2.5 Consensus size: 24
328635 ATATATAGTT
328645 TATATATATATAGT-TTTATATAC
1 TATATATATATAGTATTTATATAC
* *
328668 TATAGTATA-A-ATTATTTATATAG
1 TATA-TATATATAGTATTTATATAC
*
328691 TATATAAATAT
1 TATATATATAT
328702 CAACTATAGT
Statistics
Matches: 27, Mismatches: 3, Indels: 7
0.73 0.08 0.19
Matches are distributed among these distances:
22 5 0.19
23 18 0.67
24 4 0.15
ACGTcount: A:0.44, C:0.02, G:0.05, T:0.49
Consensus pattern (24 bp):
TATATATATATAGTATTTATATAC
Found at i:328771 original size:9 final size:9
Alignment explanation
Indices: 328757--328816 Score: 52
Period size: 9 Copynumber: 6.7 Consensus size: 9
328747 TAAATTATAC
328757 TATATAGTA
1 TATATAGTA
*
328766 TATATAGTT
1 TATATAGTA
328775 TATATA-TA
1 TATATAGTA
328783 TAATATAGTA
1 T-ATATAGTA
* *
328793 TGTA-ACATA
1 TATATA-GTA
*
328802 AATATAGTA
1 TATATAGTA
328811 TATATA
1 TATATA
328817 TAGGTCATAT
Statistics
Matches: 39, Mismatches: 8, Indels: 8
0.71 0.15 0.15
Matches are distributed among these distances:
8 3 0.08
9 32 0.82
10 4 0.10
ACGTcount: A:0.47, C:0.02, G:0.08, T:0.43
Consensus pattern (9 bp):
TATATAGTA
Found at i:328819 original size:11 final size:11
Alignment explanation
Indices: 328538--328867 Score: 56
Period size: 11 Copynumber: 28.7 Consensus size: 11
328528 GAACTATATA
*
328538 ATATATAGTTT
1 ATATATAGTAT
*
328549 ATATATACTAAT
1 ATATATAGT-AT
*
328561 GAAATATA-TAT
1 -ATATATAGTAT
* *
328572 AATGTATAGTTT
1 -ATATATAGTAT
**
328584 ATATATACCAT
1 ATATATAGTAT
328595 ATAGTTATA-TAT
1 ATA--TATAGTAT
328607 ATATATAGT-T
1 ATATATAGTAT
*
328617 -TATATACTA-
1 ATATATAGTAT
328626 ATGAACTATA-TAT
1 AT--A-TATAGTAT
*
328639 ATAGTTTA-TAT
1 ATA-TATAGTAT
328650 ATATATAGT-T
1 ATATATAGTAT
* *
328660 TTATATACTAT
1 ATATATAGTAT
* *
328671 AGTATAAATTAT
1 A-TATATAGTAT
*
328683 TTATATAGTAT
1 ATATATAGTAT
*
328694 ATAAATATCAACTAT
1 AT--ATAT--AGTAT
328709 AGTATATAGT-T
1 A-TATATAGTAT
* *
328720 -TATATGATTTT
1 ATATAT-AGTAT
*
328731 ATATAGAGTTCAT
1 ATATATAG-T-AT
* * *
328744 ATGTAAATTAT
1 ATATATAGTAT
328755 ACTATATAGTAT
1 A-TATATAGTAT
*
328767 ATATAGT-TTAT
1 ATATA-TAGTAT
*
328778 ATATATAATAT
1 ATATATAGTAT
* **
328789 AGTATGTAACAT
1 A-TATATAGTAT
*
328801 AAATATAGTAT
1 ATATATAGTAT
328812 ATATATAGGTCAT
1 ATATATA-GT-AT
* *
328825 ATGTA-ACTAT
1 ATATATAGTAT
*
328835 ATAATATA-AAT
1 AT-ATATAGTAT
328846 ATCAACTATAGTAT
1 AT--A-TATAGTAT
328860 ATATATAG
1 ATATATAG
328868 GTCATATGTA
Statistics
Matches: 232, Mismatches: 51, Indels: 72
0.65 0.14 0.20
Matches are distributed among these distances:
9 12 0.05
10 24 0.10
11 93 0.40
12 53 0.23
13 36 0.16
14 8 0.03
15 5 0.02
16 1 0.00
ACGTcount: A:0.43, C:0.05, G:0.08, T:0.44
Consensus pattern (11 bp):
ATATATAGTAT
Found at i:328837 original size:2 final size:2
Alignment explanation
Indices: 328532--328818 Score: 53
Period size: 2 Copynumber: 137.0 Consensus size: 2
328522 ACTAATGAAC
* *
328532 TA TA TA -A TA TA TA GTT TA TA TA TA CTA -A TGA AA TA TA TA TA
1 TA TA TA TA TA TA TA -TA TA TA TA TA -TA TA T-A TA TA TA TA TA
* * *
328573 -A TG TA TA GTT TA TA TA TA CCA TA TA GT- TA TA TA TA TA TA TA
1 TA TA TA TA -TA TA TA TA TA -TA TA TA -TA TA TA TA TA TA TA TA
* *
328614 GTT TA TA TA CTA -A TGA -A CTA TA TA TA TA GTT TA TA TA TA TA TA
1 -TA TA TA TA -TA TA T-A TA -TA TA TA TA TA -TA TA TA TA TA TA TA
* * * *
328657 GT- TT TA TA TA CTA TA GTA TA AA T- TA TT TA TA TA GTA TA TA AA
1 -TA TA TA TA TA -TA TA -TA TA TA TA TA TA TA TA TA -TA TA TA TA
* * *
328699 TA TCA -A CTA TA GTA TA TA GTT TA TA TGA T- TT TA TA TA GA GT-
1 TA T-A TA -TA TA -TA TA TA -TA TA TA T-A TA TA TA TA TA TA -TA
* * *
328740 TCA TA TG TA AA T- TA TA CTA TA TA GTA TA TA TA GTT TA TA TA TA
1 T-A TA TA TA TA TA TA TA -TA TA TA -TA TA TA TA -TA TA TA TA TA
* * *
328783 TA -A TA TA GTA TG TA -A CA TA AA TA TA GTA TA TA TA TA
1 TA TA TA TA -TA TA TA TA TA TA TA TA TA -TA TA TA TA TA
328819 GGTCATATGT
Statistics
Matches: 207, Mismatches: 37, Indels: 82
0.63 0.11 0.25
Matches are distributed among these distances:
1 14 0.07
2 156 0.75
3 37 0.18
ACGTcount: A:0.43, C:0.04, G:0.08, T:0.45
Consensus pattern (2 bp):
TA
Found at i:328937 original size:35 final size:37
Alignment explanation
Indices: 328889--328957 Score: 99
Period size: 36 Copynumber: 1.9 Consensus size: 37
328879 ACTATCATAC
328889 TATAGTTCATATGTAAACTAT-GTT-AGTATAATACTA
1 TATAGTTCATATGTAAACTATAGTTCA-TATAATACTA
*
328925 TATAGTT-TTATGTAAACTATAGTTCATATAATA
1 TATAGTTCATATGTAAACTATAGTTCATATAATA
328958 TCACTTTATT
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
35 12 0.40
36 17 0.57
37 1 0.03
ACGTcount: A:0.39, C:0.07, G:0.10, T:0.43
Consensus pattern (37 bp):
TATAGTTCATATGTAAACTATAGTTCATATAATACTA
Found at i:329038 original size:30 final size:32
Alignment explanation
Indices: 328983--329046 Score: 105
Period size: 32 Copynumber: 2.1 Consensus size: 32
328973 TATTCATATG
*
328983 TAAACTATAGTTTATATATATAGTATATAATA
1 TAAACTATAGTTTATATATATAGTATAGAATA
329015 TAAACTATAGTTTATA-A-ATAGTATAGAATA
1 TAAACTATAGTTTATATATATAGTATAGAATA
329045 TA
1 TA
329047 GTATATAAAT
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
30 14 0.45
31 1 0.03
32 16 0.52
ACGTcount: A:0.48, C:0.03, G:0.08, T:0.41
Consensus pattern (32 bp):
TAAACTATAGTTTATATATATAGTATAGAATA
Found at i:329046 original size:42 final size:43
Alignment explanation
Indices: 329000--329106 Score: 177
Period size: 42 Copynumber: 2.6 Consensus size: 43
328990 TAGTTTATAT
329000 ATATAGTATATAATATAAACTATAGTTTATA-AATAGTATAGA
1 ATATAGTATATAATATAAACTATAGTTTATATAATAGTATAGA
329042 ATATAGTATATAA-ATATAACTATAGTTTATATAATAGTATAGA
1 ATATAGTATATAATATA-AACTATAGTTTATATAATAGTATAGA
329085 ATATAGTATA-AATATAAA-TATA
1 ATATAGTATATAATATAAACTATA
329107 AATTATAGTA
Statistics
Matches: 62, Mismatches: 0, Indels: 7
0.90 0.00 0.10
Matches are distributed among these distances:
41 7 0.11
42 31 0.50
43 24 0.39
ACGTcount: A:0.51, C:0.02, G:0.08, T:0.38
Consensus pattern (43 bp):
ATATAGTATATAATATAAACTATAGTTTATATAATAGTATAGA
Found at i:329113 original size:24 final size:22
Alignment explanation
Indices: 328996--329117 Score: 69
Period size: 24 Copynumber: 5.4 Consensus size: 22
328986 ACTATAGTTT
*
328996 ATATA-TATAGTATATAATATAA
1 ATATAGTATAATATA-AATATAA
*
329018 ACTATAGTTTATAA-AT-AGTATAGA
1 A-TATAG--TATAATATAAATATA-A
329042 ATATAG--T-ATATAAATATAA
1 ATATAGTATAATATAAATATAA
* *
329061 CTATAGT-TTATATAATAGTATAGA
1 ATATAGTATAATATAA-A-TATA-A
329085 ATATAGTATAAATATAAATATAA
1 ATATAGTAT-AATATAAATATAA
329108 ATTATAGTAT
1 A-TATAGTAT
329118 GTAGTTTATA
Statistics
Matches: 79, Mismatches: 6, Indels: 28
0.70 0.05 0.25
Matches are distributed among these distances:
18 1 0.01
19 9 0.11
20 6 0.08
21 6 0.08
22 2 0.03
23 20 0.25
24 21 0.27
25 4 0.05
26 10 0.13
ACGTcount: A:0.51, C:0.02, G:0.08, T:0.39
Consensus pattern (22 bp):
ATATAGTATAATATAAATATAA
Found at i:329425 original size:2 final size:2
Alignment explanation
Indices: 329418--329509 Score: 51
Period size: 2 Copynumber: 43.5 Consensus size: 2
329408 TTTTACATGG
* * * *
329418 TA TA TA TA GTT TA TA CA TA TA TA TA TA AA CTA TA TA GTT TA TA
1 TA TA TA TA -TA TA TA TA TA TA TA TA TA TA -TA TA TA -TA TA TA
* * * *
329461 TA TA -A TA CA TA TA CTT TA TA TA TA AA CTA TA TA GTT TA TA TA
1 TA TA TA TA TA TA TA -TA TA TA TA TA TA -TA TA TA -TA TA TA TA
329503 TA TA TA T
1 TA TA TA T
329510 TAGTTGTTTT
Statistics
Matches: 67, Mismatches: 16, Indels: 14
0.69 0.16 0.14
Matches are distributed among these distances:
1 1 0.01
2 60 0.90
3 6 0.09
ACGTcount: A:0.45, C:0.05, G:0.03, T:0.47
Consensus pattern (2 bp):
TA
Found at i:329427 original size:19 final size:19
Alignment explanation
Indices: 329399--329444 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 19
329389 TAACTATATA
329399 GTAT-TATAGTTT-TACAT
1 GTATATATAGTTTATACAT
329416 GGTATATATAGTTTATACAT
1 -GTATATATAGTTTATACAT
*
329436 ATATATATA
1 GTATATATA
329445 AACTATATAG
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
18 4 0.16
19 16 0.64
20 5 0.20
ACGTcount: A:0.37, C:0.04, G:0.11, T:0.48
Consensus pattern (19 bp):
GTATATATAGTTTATACAT
Found at i:329462 original size:20 final size:20
Alignment explanation
Indices: 329437--329504 Score: 111
Period size: 20 Copynumber: 3.4 Consensus size: 20
329427 TTTATACATA
329437 TATATATAAACTATATAGTT
1 TATATATAAACTATATAGTT
*
329457 TATATATAATAC-ATATACTT
1 TATATATAA-ACTATATAGTT
329477 TATATATAAACTATATAGTT
1 TATATATAAACTATATAGTT
329497 TATATATA
1 TATATATA
329505 TATATTAGTT
Statistics
Matches: 44, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
19 2 0.05
20 40 0.91
21 2 0.05
ACGTcount: A:0.46, C:0.06, G:0.03, T:0.46
Consensus pattern (20 bp):
TATATATAAACTATATAGTT
Found at i:330241 original size:217 final size:215
Alignment explanation
Indices: 329591--330289 Score: 1111
Period size: 210 Copynumber: 3.3 Consensus size: 215
329581 TTGATCCCTT
* *
329591 TTGTGTTGTTTAATTTATTTAAATTTTTATTTGTAATTTCATATTTGTTCAATCTAGTCCTCCAC
1 TTGTGTTGTTTAATTTATTTAAATTTTTATTTGTAATTTCATATTTGTTCAATTTAGTCCTCCAA
* * *
329656 ATTTTATTTGCATCTAAAATTGACCCATACTTATTACTTATTTCTATTTATTAATTGGCCCATAA
66 ATTTTATTTGCATATGAAATTGACCCATACTTATTACTTATTTCTATTTTTTAATTGGCCCATAA
* ** ** *
329721 CATTTTAAATGATTATAATTTAGTACACTTTTGTATTAATTTCAACCTCAAAATTTAAAATTATT
131 CTTTTTAAATGGGTATAATTTAGTACTTTTTTGTATTAATTTCAACCTCACAATTTAAAATTATT
**
329786 TCGATCGGATCCCT--T---
196 TCGATTTGATCCCTCATCAA
* *
329801 TTGTGTTGTTTAGTTTATTTAAATTTTTATTTGTAATTTTATATTTGTTCAATTTAGTCCTCCAA
1 TTGTGTTGTTTAATTTATTTAAATTTTTATTTGTAATTTCATATTTGTTCAATTTAGTCCTCCAA
* *
329866 ATTTTATTTGCATATGAAATTAACCCATACTTATTACTTATTTCTATTTTTAAATTGGCCCATAA
66 ATTTTATTTGCATATGAAATTGACCCATACTTATTACTTATTTCTATTTTTTAATTGGCCCATAA
*
329931 CTTTTTAAATGGGTATAATTTAGTACTTTTTTGTATTAATTTCAACATCACAATTTAAAATTATT
131 CTTTTTAAATGGGTATAATTTAGTACTTTTTTGTATTAATTTCAACCTCACAATTTAAAATTATT
329996 TCGATTTGATCCCTCATCAA
196 TCGATTTGATCCCTCATCAA
* *
330016 TATGTGTTGTTTAATTAATTTAAATTTTTATTTGTAATTTCATATTTGTTCAATTTAGTCCTCTA
1 T-TGTGTTGTTTAATTTATTTAAATTTTTATTTGTAATTTCATATTTGTTCAATTTAGTCCTCCA
* * *
330081 AATTTTATTTGCATATGAAATTGATCCATACTTTTTACTTAATTCTATTTTTTTAATTGGCCCAT
65 AATTTTATTTGCATATGAAATTGACCCATACTTATTACTTATTTCTA-TTTTTTAATTGGCCCAT
*
330146 AACTTTTTAAATGGGTATAATTTAGTATTTTTTTGTATTAATTTCAACCTCACAATTTAAAATTA
129 AACTTTTTAAATGGGTATAATTTAGTACTTTTTTGTATTAATTTCAACCTCACAATTTAAAATTA
330211 TTTCGATTTGATCCCTCATCAA
194 TTTCGATTTGATCCCTCATCAA
*
330233 TGTGTGTTGTTTAATTTATTTAAATTTTTATTTGCAATTTCATATTTGTTCAATTTA
1 T-TGTGTTGTTTAATTTATTTAAATTTTTATTTGTAATTTCATATTTGTTCAATTTA
330290 ATTCTTAAAT
Statistics
Matches: 450, Mismatches: 32, Indels: 7
0.92 0.07 0.01
Matches are distributed among these distances:
210 191 0.42
212 1 0.00
215 1 0.00
216 102 0.23
217 155 0.34
ACGTcount: A:0.29, C:0.12, G:0.08, T:0.50
Consensus pattern (215 bp):
TTGTGTTGTTTAATTTATTTAAATTTTTATTTGTAATTTCATATTTGTTCAATTTAGTCCTCCAA
ATTTTATTTGCATATGAAATTGACCCATACTTATTACTTATTTCTATTTTTTAATTGGCCCATAA
CTTTTTAAATGGGTATAATTTAGTACTTTTTTGTATTAATTTCAACCTCACAATTTAAAATTATT
TCGATTTGATCCCTCATCAA
Found at i:345952 original size:21 final size:20
Alignment explanation
Indices: 345913--345963 Score: 59
Period size: 21 Copynumber: 2.5 Consensus size: 20
345903 CTTCGGATTA
* *
345913 TGAAAAATTATTTTTAAAAT
1 TGAAAAATGATTTTCAAAAT
345933 AT-AAAAATGATGTTTCAAAAT
1 -TGAAAAATGAT-TTTCAAAAT
345954 TGAAAAATGA
1 TGAAAAATGA
345964 AAATAAACTC
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
20 9 0.35
21 17 0.65
ACGTcount: A:0.53, C:0.02, G:0.10, T:0.35
Consensus pattern (20 bp):
TGAAAAATGATTTTCAAAAT
Found at i:349794 original size:20 final size:21
Alignment explanation
Indices: 349769--349807 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
349759 TTTTGGTGCA
*
349769 GAGGGAATCGA-TCCCCCCAT
1 GAGGGAACCGATTCCCCCCAT
349789 GAGGGAACCGATTCCCCCC
1 GAGGGAACCGATTCCCCCC
349808 CACAGGGGAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 10 0.59
21 7 0.41
ACGTcount: A:0.23, C:0.38, G:0.26, T:0.13
Consensus pattern (21 bp):
GAGGGAACCGATTCCCCCCAT
Found at i:349814 original size:21 final size:23
Alignment explanation
Indices: 349781--349828 Score: 55
Period size: 22 Copynumber: 2.2 Consensus size: 23
349771 GGGAATCGAT
* *
349781 CCCCCCATGA-GGGAACCGATTC
1 CCCCCCATCAGGGGAACCGATAC
*
349803 CCCCCCA-CAGGGGAATCGATAC
1 CCCCCCATCAGGGGAACCGATAC
349825 CCCC
1 CCCC
349829 TTGGGGTTCT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
21 1 0.05
22 21 0.95
ACGTcount: A:0.23, C:0.46, G:0.21, T:0.10
Consensus pattern (23 bp):
CCCCCCATCAGGGGAACCGATAC
Found at i:367304 original size:23 final size:23
Alignment explanation
Indices: 367278--367321 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
367268 GTGTCTGTAG
*
367278 AAACAGAGTTTTCCGGTTCTGGT
1 AAACAGAGTTTTCCGATTCTGGT
* *
367301 AAACAGGGTTTTTCGATTCTG
1 AAACAGAGTTTTCCGATTCTG
367322 AATTTTTTTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.23, C:0.16, G:0.25, T:0.36
Consensus pattern (23 bp):
AAACAGAGTTTTCCGATTCTGGT
Found at i:368198 original size:15 final size:15
Alignment explanation
Indices: 368178--368207 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
368168 TCCTGTTGAA
368178 CTTCTAAGCTTTTTC
1 CTTCTAAGCTTTTTC
368193 CTTCTAAGCTTTTTC
1 CTTCTAAGCTTTTTC
368208 TCAAAGCACG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.27, G:0.07, T:0.53
Consensus pattern (15 bp):
CTTCTAAGCTTTTTC
Found at i:372945 original size:2 final size:2
Alignment explanation
Indices: 372938--372971 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
372928 TTTGCCTGAC
372938 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
372972 TTGTTTAAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:375829 original size:15 final size:15
Alignment explanation
Indices: 375809--375838 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
375799 TGGATGCTGC
375809 TTATTTTCTCAGATT
1 TTATTTTCTCAGATT
375824 TTATTTTCTCAGATT
1 TTATTTTCTCAGATT
375839 GAAGGGGAGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.20, C:0.13, G:0.07, T:0.60
Consensus pattern (15 bp):
TTATTTTCTCAGATT
Found at i:376602 original size:10 final size:10
Alignment explanation
Indices: 376589--377499 Score: 457
Period size: 10 Copynumber: 92.9 Consensus size: 10
376579 TTTATAATGA
*
376589 TTTACTATGG
1 TTTACTAGGG
376599 TTTAC--GGG
1 TTTACTAGGG
376607 TTTACTAGGG
1 TTTACTAGGG
376617 TTTAC--GGG
1 TTTACTAGGG
376625 TTTACTAGGG
1 TTTACTAGGG
376635 TTTAC--GGG
1 TTTACTAGGG
*
376643 TTTACGAGGG
1 TTTACTAGGG
*
376653 TTTACTAGGA
1 TTTACTAGGG
** *
376663 TTTGTTAGGA
1 TTTACTAGGG
376673 TTTA-TAAGGG
1 TTTACT-AGGG
* * *
376683 TTTATTATGA
1 TTTACTAGGG
376693 TTTACTAGGG
1 TTTACTAGGG
376703 TTTACTAGGG
1 TTTACTAGGG
* *
376713 TTTGCTAGGA
1 TTTACTAGGG
376723 TTTACTAGGG
1 TTTACTAGGG
376733 TTT-CTAAGAGGG
1 TTTACT---AGGG
376745 TTT--TAGGG
1 TTTACTAGGG
* *
376753 TTT-TTAGGA
1 TTTACTAGGG
*
376762 TTTATTAGGG
1 TTTACTAGGG
* *
376772 TTTTCTAAGG
1 TTTACTAGGG
376782 TTT-CTTAGGG
1 TTTAC-TAGGG
376792 TTTACTAGGG
1 TTTACTAGGG
376802 TTT-CTAAGGG
1 TTTACT-AGGG
376812 TTTA-TAAGGG
1 TTTACT-AGGG
376822 ATTT-CTAGGG
1 -TTTACTAGGG
*
376832 TTTACTAGGA
1 TTTACTAGGG
376842 TTTA-TAAGGG
1 TTTACT-AGGG
376852 TTTACTAGGG
1 TTTACTAGGG
*
376862 TTTACAAGGG
1 TTTACTAGGG
376872 TTTA-TAAGGG
1 TTTACT-AGGG
* *
376882 TTTATTAGTG
1 TTTACTAGGG
**
376892 TTCGCTAGGG
1 TTTACTAGGG
*
376902 TTTATTAGGG
1 TTTACTAGGG
* *
376912 GTTA-TAAGGA
1 TTTACT-AGGG
**
376922 TTTGTTAGGG
1 TTTACTAGGG
*
376932 TTTGCTAGGG
1 TTTACTAGGG
** *
376942 TTTGTTGGGG
1 TTTACTAGGG
376952 TTTA-TCAGGG
1 TTTACT-AGGG
376962 TTTA-TCAGGG
1 TTTACT-AGGG
** *
376972 TTTGTTATGGC
1 TTTACTA-GGG
* *
376983 TTT-TTAAGG
1 TTTACTAGGG
*
376992 TTTCCTAGGG
1 TTTACTAGGG
377002 TTT-CATAGGG
1 TTTAC-TAGGG
*
377012 TTTCCTAGGG
1 TTTACTAGGG
** * *
377022 TTTGTTAAGA
1 TTTACTAGGG
*
377032 TTTA-TAAGGA
1 TTTACT-AGGG
*
377042 TTTATTAGGG
1 TTTACTAGGG
377052 TTTACTAGGG
1 TTTACTAGGG
377062 TTTA--A-GG
1 TTTACTAGGG
*
377069 TTTA-TAAGAG
1 TTTACT-AGGG
377079 -TT--TAGGG
1 TTTACTAGGG
*
377086 TTTGCTAGGG
1 TTTACTAGGG
*
377096 TATACTAGGG
1 TTTACTAGGG
* *
377106 TATACTAGGA
1 TTTACTAGGG
*
377116 TTTTCTAGGG
1 TTTACTAGGG
*
377126 TCTA-TAAGGG
1 TTTACT-AGGG
377136 TTTACTAGGG
1 TTTACTAGGG
377146 TTTA-TAAGGG
1 TTTACT-AGGG
*
377156 TTTATTAGGG
1 TTTACTAGGG
** *
377166 TTTGTTAGAG
1 TTTACTAGGG
*
377176 TTTGCTAGGG
1 TTTACTAGGG
*
377186 TTTAATTAGGG
1 TTT-ACTAGGG
* *
377197 TTTAATAGAG
1 TTTACTAGGG
*
377207 TGTT-CTAAGG
1 T-TTACTAGGG
*
377217 TTTGCTAGGG
1 TTTACTAGGG
377227 TTT-CTTAGGG
1 TTTAC-TAGGG
*
377237 TTTAATAGGG
1 TTTACTAGGG
** * *
377247 GCTGCTTGGG
1 TTTACTAGGG
*
377257 TTTATTAGGG
1 TTTACTAGGG
** *
377267 TTTGTTAGAG
1 TTTACTAGGG
* *
377277 TTTTCAAGGG
1 TTTACTAGGG
*
377287 TTTATTAGGG
1 TTTACTAGGG
*
377297 TTTACTAGTG
1 TTTACTAGGG
*
377307 TTTATTAGGG
1 TTTACTAGGG
* *
377317 TTTATTAGGA
1 TTTACTAGGG
*
377327 TTT-TTAGGG
1 TTTACTAGGG
* *
377336 TTTATTGGGG
1 TTTACTAGGG
*
377346 TTTACTAGAG
1 TTTACTAGGG
377356 --TACTAGGG
1 TTTACTAGGG
*
377364 TTTATTAGGG
1 TTTACTAGGG
377374 -TT--T--GG
1 TTTACTAGGG
* *
377379 TTTGCTAAGG
1 TTTACTAGGG
* *
377389 TTTACAAGGA
1 TTTACTAGGG
377399 TTTACTAGGG
1 TTTACTAGGG
*
377409 TTTACAAGGG
1 TTTACTAGGG
*
377419 TTTACAAGGG
1 TTTACTAGGG
*
377429 TTTACTAGTG
1 TTTACTAGGG
377439 TTTAGCTAGGG
1 TTTA-CTAGGG
* *
377450 TTTAACTAAGA
1 TTT-ACTAGGG
*
377461 TTTGCTAGGG
1 TTTACTAGGG
*
377471 TTTACAAGGG
1 TTTACTAGGG
* *
377481 TTTATTGGGG
1 TTTACTAGGG
377491 TTTACTAGG
1 TTTACTAGG
377500 CTTTGATAAG
Statistics
Matches: 707, Mismatches: 135, Indels: 118
0.74 0.14 0.12
Matches are distributed among these distances:
5 2 0.00
6 2 0.00
7 10 0.01
8 42 0.06
9 43 0.06
10 555 0.79
11 45 0.06
12 8 0.01
ACGTcount: A:0.21, C:0.07, G:0.30, T:0.42
Consensus pattern (10 bp):
TTTACTAGGG
Found at i:376610 original size:8 final size:8
Alignment explanation
Indices: 376597--376648 Score: 68
Period size: 8 Copynumber: 6.0 Consensus size: 8
376587 GATTTACTAT
376597 GGTTTACG
1 GGTTTACG
376605 GGTTTACTAG
1 GGTTTAC--G
376615 GGTTTACG
1 GGTTTACG
376623 GGTTTACTAG
1 GGTTTAC--G
376633 GGTTTACG
1 GGTTTACG
376641 GGTTTACG
1 GGTTTACG
376649 AGGGTTTACT
Statistics
Matches: 40, Mismatches: 0, Indels: 8
0.83 0.00 0.17
Matches are distributed among these distances:
8 24 0.60
10 16 0.40
ACGTcount: A:0.15, C:0.12, G:0.35, T:0.38
Consensus pattern (8 bp):
GGTTTACG
Found at i:376612 original size:18 final size:18
Alignment explanation
Indices: 376589--376657 Score: 120
Period size: 18 Copynumber: 3.8 Consensus size: 18
376579 TTTATAATGA
*
376589 TTTACTATGGTTTACGGG
1 TTTACTAGGGTTTACGGG
376607 TTTACTAGGGTTTACGGG
1 TTTACTAGGGTTTACGGG
376625 TTTACTAGGGTTTACGGG
1 TTTACTAGGGTTTACGGG
*
376643 TTTACGAGGGTTTAC
1 TTTACTAGGGTTTAC
376658 TAGGATTTGT
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 49 1.00
ACGTcount: A:0.17, C:0.12, G:0.30, T:0.41
Consensus pattern (18 bp):
TTTACTAGGGTTTACGGG
Found at i:377072 original size:17 final size:17
Alignment explanation
Indices: 377050--377096 Score: 51
Period size: 17 Copynumber: 2.8 Consensus size: 17
377040 GATTTATTAG
377050 GGTTTACTAGGGTTTAA
1 GGTTTACTAGGGTTTAA
* *
377067 GGTTTA-TAAGAGTTTAG
1 GGTTTACT-AGGGTTTAA
*
377084 GGTTTGCTAGGGT
1 GGTTTACTAGGGT
377097 ATACTAGGGT
Statistics
Matches: 24, Mismatches: 4, Indels: 4
0.75 0.12 0.12
Matches are distributed among these distances:
16 1 0.04
17 22 0.92
18 1 0.04
ACGTcount: A:0.21, C:0.04, G:0.34, T:0.40
Consensus pattern (17 bp):
GGTTTACTAGGGTTTAA
Found at i:377219 original size:31 final size:31
Alignment explanation
Indices: 377159--377219 Score: 79
Period size: 31 Copynumber: 2.0 Consensus size: 31
377149 ATAAGGGTTT
** *
377159 ATTAGGGTTTGTTAGAGTTTGCTAGGGTTTA
1 ATTAGGGTTTAATAGAGTTTGCTAAGGTTTA
377190 ATTAGGGTTTAATAGAGTGTT-CTAAGGTTT
1 ATTAGGGTTTAATAGAGT-TTGCTAAGGTTT
377220 GCTAGGGTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
31 24 0.92
32 2 0.08
ACGTcount: A:0.23, C:0.03, G:0.30, T:0.44
Consensus pattern (31 bp):
ATTAGGGTTTAATAGAGTTTGCTAAGGTTTA
Found at i:378222 original size:20 final size:20
Alignment explanation
Indices: 378178--378489 Score: 229
Period size: 20 Copynumber: 15.2 Consensus size: 20
378168 AATGACCAAC
* **
378178 AAAATCGCAATGCGA-TATC
1 AAAATCGCAACGCGATTAAG
*
378197 AAAATCGCAACGCGATTTAG
1 AAAATCGCAACGCGATTAAG
* *
378217 AAAATCGCAACGTTGA-AAAG
1 AAAATCGCAACG-CGATTAAG
* *
378237 AAAATCGCAA-G-GGTCAAAAG
1 AAAATCGCAACGCGAT--TAAG
***
378257 AAAATCGCAACGCGATATTCC
1 AAAATCGCAACGCGAT-TAAG
***
378278 AAGAATCGCAACGCGATATTCC
1 AA-AATCGCAACGCGAT-TAAG
*
378300 AAGAATCGCAATGCGATTAAG
1 AA-AATCGCAACGCGATTAAG
* ***
378321 AGAATCGCAACGCGATATTCC
1 AAAATCGCAACGCGAT-TAAG
*
378342 AAGAATCGCAATGCGATTAAG
1 AA-AATCGCAACGCGATTAAG
* ***
378363 AGAATCGCAACGCGATCTTCC
1 AAAATCGCAACGCGAT-TAAG
*
378384 AAGAATCGCAATGCGATTAAG
1 AA-AATCGCAACGCGATTAAG
378405 AAAATCGCAACGCGATTAAG
1 AAAATCGCAACGCGATTAAG
378425 AAAATCGCAACGCGATTCAA-
1 AAAATCGCAACGCGATT-AAG
*
378445 AGAATCGCAACGCGATTAAG
1 AAAATCGCAACGCGATTAAG
* *
378465 AAAATCGCAATGCGATTCAG
1 AAAATCGCAACGCGATTAAG
378485 AAAAT
1 AAAAT
378490 GAGTAAATTC
Statistics
Matches: 237, Mismatches: 42, Indels: 27
0.77 0.14 0.09
Matches are distributed among these distances:
17 1 0.00
19 17 0.07
20 137 0.58
21 19 0.08
22 63 0.27
ACGTcount: A:0.42, C:0.21, G:0.20, T:0.18
Consensus pattern (20 bp):
AAAATCGCAACGCGATTAAG
Found at i:378325 original size:42 final size:41
Alignment explanation
Indices: 378279--378481 Score: 277
Period size: 42 Copynumber: 4.9 Consensus size: 41
378269 CGATATTCCA
378279 AGAATCGCAACGCGATATTCCAAGAATCGCAATGCGATTAAG
1 AGAATCGCAACGCGAT-TTCCAAGAATCGCAATGCGATTAAG
378321 AGAATCGCAACGCGATATTCCAAGAATCGCAATGCGATTAAG
1 AGAATCGCAACGCGAT-TTCCAAGAATCGCAATGCGATTAAG
378363 AGAATCGCAACGCGATCTTCCAAGAATCGCAATGCGATTAAG
1 AGAATCGCAACGCGAT-TTCCAAGAATCGCAATGCGATTAAG
* *** *
378405 AAAATCGCAACGCGATTAAGAA-AATCGCAACGCGATTCAA-
1 AGAATCGCAACGCGATTTCCAAGAATCGCAATGCGATT-AAG
***
378445 AGAATCGCAACGCGATTAAGAA-AATCGCAATGCGATT
1 AGAATCGCAACGCGATTTCCAAGAATCGCAATGCGATT
378482 CAGAAAATGA
Statistics
Matches: 152, Mismatches: 8, Indels: 4
0.93 0.05 0.02
Matches are distributed among these distances:
40 49 0.32
41 5 0.03
42 98 0.64
ACGTcount: A:0.39, C:0.22, G:0.21, T:0.18
Consensus pattern (41 bp):
AGAATCGCAACGCGATTTCCAAGAATCGCAATGCGATTAAG
Found at i:378367 original size:84 final size:81
Alignment explanation
Indices: 378175--378489 Score: 304
Period size: 84 Copynumber: 3.9 Consensus size: 81
378165 GAAAATGACC
* ** * * *
378175 AACAAAATCGCAATGCGATATC-AA-AATCGCAACGCGATTTAGAA-AATCGCAACGTTGA-AAA
1 AACAAAATCGCAACGCGAT-TCAAAGAATCGCAACGCGATTTCCAAGAATCGCAATG-CGATTAA
* *
378236 GAAAATCGCAA-G-GGTCAA
64 GAAAATCGCAACGCGAT--T
* *
378254 AAGAAAATCGCAACGCGATATTCCAAGAATCGCAACGCGATATTCCAAGAATCGCAATGCGATTA
1 AACAAAATCGCAACGCG--ATTCAAAGAATCGCAACGCGAT-TTCCAAGAATCGCAATGCGATTA
*
378319 AGAGAATCGCAACGCGATAT
63 AGAAAATCGCAACGCGAT-T
** *
378339 TCCAAGAATCGCAATGCGATT-AAGAGAATCGCAACGCGATCTTCCAAGAATCGCAATGCGATTA
1 AACAA-AATCGCAACGCGATTCAA-AGAATCGCAACGCGAT-TTCCAAGAATCGCAATGCGATTA
378403 AGAAAATCGCAACGCGATT
63 AGAAAATCGCAACGCGATT
* *** *
378422 AAGAAAATCGCAACGCGATTCAAAGAATCGCAACGCGATTAAGAA-AATCGCAATGCGATTCAGA
1 AACAAAATCGCAACGCGATTCAAAGAATCGCAACGCGATTTCCAAGAATCGCAATGCGATTAAGA
378486 AAAT
66 AAAT
378490 GAGTAAATTC
Statistics
Matches: 199, Mismatches: 25, Indels: 23
0.81 0.10 0.09
Matches are distributed among these distances:
79 15 0.08
80 24 0.12
81 7 0.04
82 44 0.22
83 12 0.06
84 80 0.40
85 4 0.02
86 13 0.07
ACGTcount: A:0.42, C:0.21, G:0.20, T:0.17
Consensus pattern (81 bp):
AACAAAATCGCAACGCGATTCAAAGAATCGCAACGCGATTTCCAAGAATCGCAATGCGATTAAGA
AAATCGCAACGCGATT
Found at i:378596 original size:6 final size:6
Alignment explanation
Indices: 378585--378665 Score: 162
Period size: 6 Copynumber: 13.5 Consensus size: 6
378575 GACACGTATT
378585 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
378633 ACCACG ACCACG ACCACG ACCACG ACCACG ACC
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACC
378666 CGAGACGAGA
Statistics
Matches: 75, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 75 1.00
ACGTcount: A:0.33, C:0.51, G:0.16, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:379313 original size:20 final size:20
Alignment explanation
Indices: 379288--379508 Score: 193
Period size: 20 Copynumber: 10.8 Consensus size: 20
379278 CTCATTTTCT
*
379288 GAATCGCATTGCGATTCTTG
1 GAATCGCGTTGCGATTCTTG
***
379308 GAATCGCGTTGCGATTCCAA
1 GAATCGCGTTGCGATTCTTG
*
379328 GAATTGCGTTGCGATTTTCTT-
1 GAATCGCGTTGCGA--TTCTTG
*
379349 -AAACGCGTTGCGATTTTCTT-
1 GAATCGCGTTGCGA--TTCTTG
*
379369 -AATCCCGTTGCGATTCTTG
1 GAATCGCGTTGCGATTCTTG
379388 GAAGATCGCGTTGCGATTCTTG
1 G-A-ATCGCGTTGCGATTCTTG
*
379410 GAATCGCGTTGCGATT-TTCT
1 GAATCGCGTTGCGATTCTT-G
379430 GAATCGCGTTGCGATTCTTG
1 GAATCGCGTTGCGATTCTTG
*
379450 GAAGATCGCGTTGCGATT-TTAT
1 G-A-ATCGCGTTGCGATTCTT-G
* *
379472 GAATCGCATTACGATTCTTG
1 GAATCGCGTTGCGATTCTTG
379492 GAAGATCGCGTTGCGAT
1 G-A-ATCGCGTTGCGAT
379509 CTTCTTTTCA
Statistics
Matches: 167, Mismatches: 20, Indels: 26
0.78 0.09 0.12
Matches are distributed among these distances:
18 5 0.03
19 2 0.01
20 102 0.61
21 11 0.07
22 47 0.28
ACGTcount: A:0.19, C:0.19, G:0.26, T:0.35
Consensus pattern (20 bp):
GAATCGCGTTGCGATTCTTG
Found at i:379458 original size:42 final size:42
Alignment explanation
Indices: 379290--379513 Score: 205
Period size: 42 Copynumber: 5.4 Consensus size: 42
379280 CATTTTCTGA
* * *
379290 ATCGCATTGCGATTCTT-GGAATCGCGTTGCGATTC---CAAG
1 ATCGCGTTGCGATT-TTCTGAATCGCGTTGCGATTCTTGGAAG
* * * ***
379329 AATTGCGTTGCGATTTTCTTAAACGCGTTGCGATT-TTCTTA-
1 -ATCGCGTTGCGATTTTCTGAATCGCGTTGCGATTCTTGGAAG
* *
379370 ATCCCGTTGCGATTCTT-GGAAGATCGCGTTGCGATTCTTGG-A-
1 ATCGCGTTGCGATT-TTCTG-A-ATCGCGTTGCGATTCTTGGAAG
379412 ATCGCGTTGCGATTTTCTGAATCGCGTTGCGATTCTTGGAAG
1 ATCGCGTTGCGATTTTCTGAATCGCGTTGCGATTCTTGGAAG
* * *
379454 ATCGCGTTGCGATTTTATGAATCGCATTACGATTCTTGGAAG
1 ATCGCGTTGCGATTTTCTGAATCGCGTTGCGATTCTTGGAAG
*
379496 ATCGCGTTGCGATCTTCT
1 ATCGCGTTGCGATTTTCT
379514 TTTCAACGTT
Statistics
Matches: 152, Mismatches: 21, Indels: 20
0.79 0.11 0.10
Matches are distributed among these distances:
39 2 0.01
40 57 0.38
41 7 0.05
42 84 0.55
43 2 0.01
ACGTcount: A:0.19, C:0.20, G:0.25, T:0.36
Consensus pattern (42 bp):
ATCGCGTTGCGATTTTCTGAATCGCGTTGCGATTCTTGGAAG
Found at i:379476 original size:62 final size:62
Alignment explanation
Indices: 379281--379487 Score: 244
Period size: 62 Copynumber: 3.4 Consensus size: 62
379271 GAATTTACTC
* * *
379281 ATTTTCTGAATCGCATTGCGATTCTT-GGAATCGCGTTGCGATTC---CAAGAATTGCGTTGCG
1 ATTTTCTGAATCGCATTGCGATT-TTCTGAATCGCGTTGCGATTCTTGGAAG-ATCGCGTTGCG
* * * * *
379341 ATTTTCTTAAACGCGTTGCGATTTTCTTAATCCCGTTGCGATTCTTGGAAGATCGCGTTGCG
1 ATTTTCTGAATCGCATTGCGATTTTCTGAATCGCGTTGCGATTCTTGGAAGATCGCGTTGCG
* *
379403 ATTCTT-GGAATCGCGTTGCGATTTTCTGAATCGCGTTGCGATTCTTGGAAGATCGCGTTGCG
1 ATT-TTCTGAATCGCATTGCGATTTTCTGAATCGCGTTGCGATTCTTGGAAGATCGCGTTGCG
* *
379465 ATTTTATGAATCGCATTACGATT
1 ATTTTCTGAATCGCATTGCGATT
379488 CTTGGAAGAT
Statistics
Matches: 125, Mismatches: 16, Indels: 10
0.83 0.11 0.07
Matches are distributed among these distances:
59 2 0.02
60 35 0.28
61 2 0.02
62 81 0.65
63 5 0.04
ACGTcount: A:0.19, C:0.19, G:0.24, T:0.37
Consensus pattern (62 bp):
ATTTTCTGAATCGCATTGCGATTTTCTGAATCGCGTTGCGATTCTTGGAAGATCGCGTTGCG
Found at i:379543 original size:20 final size:20
Alignment explanation
Indices: 379281--379570 Score: 169
Period size: 20 Copynumber: 14.2 Consensus size: 20
379271 GAATTTACTC
* *
379281 ATTTTCTGAATCGCATTGCG
1 ATTTTCTAAATCGCGTTGCG
**
379301 ATTCTT-GGAATCGCGTTGCG
1 ATT-TTCTAAATCGCGTTGCG
* * *
379321 A-TTCCAAGAATTGCGTTGCG
1 ATTTTCTA-AATCGCGTTGCG
379341 ATTTTCTTAAA-CGCGTTGCG
1 ATTTTC-TAAATCGCGTTGCG
* *
379361 ATTTTCTTAATCCCGTTGCG
1 ATTTTCTAAATCGCGTTGCG
**
379381 ATTCTTGGAAGATCGCGTTGCG
1 ATT-TTCTAA-ATCGCGTTGCG
**
379403 ATTCTT-GGAATCGCGTTGCG
1 ATT-TTCTAAATCGCGTTGCG
*
379423 ATTTTCTGAATCGCGTTGCG
1 ATTTTCTAAATCGCGTTGCG
**
379443 ATTCTTGGAAGATCGCGTTGCG
1 ATT-TTCTAA-ATCGCGTTGCG
* * * *
379465 ATTTTATGAATCGCATTACG
1 ATTTTCTAAATCGCGTTGCG
**
379485 ATTCTTGGAAGATCGCGTTGCG
1 ATT-TTCTAA-ATCGCGTTGCG
* ** *
379507 ATCTTCT-TTTCAACGTTGCG
1 ATTTTCTAAATC-GCGTTGCG
*
379527 CTTTTCTAAATCGCGTTGCG
1 ATTTTCTAAATCGCGTTGCG
* * *
379547 GTTTT-GATATCGCGTTGCG
1 ATTTTCTAAATCGCGTTGCG
379566 ATTTT
1 ATTTT
379571 GTTGGTCATT
Statistics
Matches: 210, Mismatches: 45, Indels: 31
0.73 0.16 0.11
Matches are distributed among these distances:
18 1 0.00
19 24 0.11
20 118 0.56
21 25 0.12
22 42 0.20
ACGTcount: A:0.18, C:0.20, G:0.24, T:0.38
Consensus pattern (20 bp):
ATTTTCTAAATCGCGTTGCG
Found at i:382524 original size:49 final size:47
Alignment explanation
Indices: 382379--382524 Score: 133
Period size: 49 Copynumber: 3.1 Consensus size: 47
382369 GGTTTTTTGG
*
382379 GTTTTT-GGG-TTTACTAGGGTTTATAAGGGTTTATTAGGGTT-T-AA
1 GTTTTTAGGGATTTACTAGGGTTTAT-AGTGTTTATTAGGGTTATAAA
* * * **
382423 G-GTTTAGGGGTTTACTAGGGTTTATAGGTGTTTACTAGGGTTATTAGG
1 GTTTTTAGGGATTTACTAGGGTTTATA-GTGTTTATTAGGGTTA-TAAA
*
382471 GTTTTCTA-GGATTTCCTAGGGTTTATGAGTGTTTATTAGGGTTTATAAA
1 GTTTT-TAGGGATTTACTAGGGTTTAT-AGTGTTTATTAGGG-TTATAAA
382520 GTTTT
1 GTTTT
382525 ATTAGGGGTT
Statistics
Matches: 81, Mismatches: 11, Indels: 15
0.76 0.10 0.14
Matches are distributed among these distances:
43 3 0.04
44 5 0.06
45 28 0.35
47 1 0.01
48 1 0.01
49 37 0.46
50 6 0.07
ACGTcount: A:0.20, C:0.04, G:0.29, T:0.47
Consensus pattern (47 bp):
GTTTTTAGGGATTTACTAGGGTTTATAGTGTTTATTAGGGTTATAAA
Found at i:383755 original size:10 final size:10
Alignment explanation
Indices: 381510--383789 Score: 1086
Period size: 10 Copynumber: 230.8 Consensus size: 10
381500 TTCACGGGCA
381510 AGGGTTTACTT
1 AGGGTTTAC-T
381521 A-GGTTTACTT
1 AGGGTTTAC-T
381531 A-GGTTTACT
1 AGGGTTTACT
*
381540 AGGGTTTACA
1 AGGGTTTACT
*
381550 AGGGTTTATT
1 AGGGTTTACT
381560 AGGGTTTACT
1 AGGGTTTACT
*
381570 AGGGTTTATT
1 AGGGTTTACT
381580 AGGGTTTACT
1 AGGGTTTACT
381590 AGGGTTTA-T
1 AGGGTTTACT
381599 AAGGGTTTACT
1 -AGGGTTTACT
* *
381610 AGGATTTATT
1 AGGGTTTACT
381620 AGGGTTTACT
1 AGGGTTTACT
*
381630 AAGGTTTA-T
1 AGGGTTTACT
381639 AAGGGTTTA-T
1 -AGGGTTTACT
*
381649 AAAGGTTTACT
1 -AGGGTTTACT
381660 AGGGTTTACT
1 AGGGTTTACT
* **
381670 AGGATTTGTT
1 AGGGTTTACT
381680 AGGGTTTA-T
1 AGGGTTTACT
* *
381689 AAGGATTTTCT
1 -AGGGTTTACT
381700 AGGGTTTA-T
1 AGGGTTTACT
381709 AGGGGTTTACT
1 A-GGGTTTACT
381720 AGGGTTTA-T
1 AGGGTTTACT
*
381729 AAGGGTTTTCT
1 -AGGGTTTACT
*
381740 AGGGTTT-TT
1 AGGGTTTACT
* *
381749 AGAGTTTTCT
1 AGGGTTTACT
*
381759 AGGATTTACT
1 AGGGTTTACT
*
381769 AGGGTTTATT
1 AGGGTTTACT
*
381779 AGGGTTTATT
1 AGGGTTTACT
* *
381789 AGTGTTTACA
1 AGGGTTTACT
381799 AGGGTTTACT
1 AGGGTTTACT
*
381809 AGGATTTA-T
1 AGGGTTTACT
381818 AAGGGTTTTA-T
1 -AGGG-TTTACT
**
381829 AGGGTTTGTT
1 AGGGTTTACT
*
381839 AGGGTTT-TT
1 AGGGTTTACT
** *
381848 AAAGTTTGCT
1 AGGGTTTACT
381858 AGGGTTTACT
1 AGGGTTTACT
* *
381868 AGGATTTAAT
1 AGGGTTTACT
*
381878 ATGGTTTA-T
1 AGGGTTTACT
* *
381887 AATGGTTTGA-A
1 -AGGGTTT-ACT
*
381898 AGGGTTTGCT
1 AGGGTTTACT
381908 AGGGTTTAC-
1 AGGGTTTACT
*
381917 ATGGGTTTATT
1 A-GGGTTTACT
** *
381928 ATAGCTTACT
1 AGGGTTTACT
*
381938 AGGGTTTATT
1 AGGGTTTACT
381948 AGGGTTTA-T
1 AGGGTTTACT
*
381957 AAGGGTTTATT
1 -AGGGTTTACT
* *
381968 AGGATTTACA
1 AGGGTTTACT
**
381978 AGTATTTACT
1 AGGGTTTACT
*
381988 AGTGTTTACT
1 AGGGTTTACT
381998 AGGGTTTACT
1 AGGGTTTACT
382008 AGGGTTTA-T
1 AGGGTTTACT
*
382017 AAGGGTTTTCT
1 -AGGGTTTACT
*
382028 AGGGTTTATT
1 AGGGTTTACT
* **
382038 AGGGCTTGTT
1 AGGGTTTACT
382048 AGGGTTTACT
1 AGGGTTTACT
** *
382058 ATAGTTTATT
1 AGGGTTTACT
382068 AGGGTTTACTT
1 AGGGTTTAC-T
*
382079 AGGG-TTATT
1 AGGGTTTACT
382088 AGGGTTTA-T
1 AGGGTTTACT
*
382097 AAGGGTTTGTCT
1 -AGGGTTT-ACT
*
382109 AGGGTTTGCT
1 AGGGTTTACT
*
382119 AGGGTTTTGCT
1 AGGG-TTTACT
*
382130 AGGATTTA-T
1 AGGGTTTACT
**
382139 AGGGGTTTGTT
1 A-GGGTTTACT
382150 AGGG-TTACT
1 AGGGTTTACT
*
382159 AGGGTTTGCT
1 AGGGTTTACT
382169 AGGGTTTA-T
1 AGGGTTTACT
382178 AGGGGTTTACT
1 A-GGGTTTACT
*
382189 AGGGTTT-TT
1 AGGGTTTACT
382198 AGGGTTTACT
1 AGGGTTTACT
*
382208 AGGGTTTATT
1 AGGGTTTACT
**
382218 AAAGTTTA-T
1 AGGGTTTACT
382227 ATGGGTTTGA-T
1 A-GGGTTT-ACT
382238 AGGGTTT--T
1 AGGGTTTACT
382246 AGGGGTTT-CT
1 A-GGGTTTACT
382256 AGGGTTTGA-T
1 AGGGTTT-ACT
382266 AGGGTTTA-T
1 AGGGTTTACT
382275 AAGGGTTTACT
1 -AGGGTTTACT
*
382286 AGGGTTTACA
1 AGGGTTTACT
* *
382296 AGGTTTTGCT
1 AGGGTTTACT
*
382306 AGGGTTTATT
1 AGGGTTTACT
*
382316 AGGGTTTTCT
1 AGGGTTTACT
*
382326 AGGATTTA-T
1 AGGGTTTACT
*
382335 GAGGGTTTACA
1 -AGGGTTTACT
* *
382346 AAGTTTTACT
1 AGGGTTTACT
*
382356 AGGGGTTA-T
1 AGGGTTTACT
*
382365 AAGGGGTTT-TT
1 -A-GGGTTTACT
*
382376 TGGGTTT--T
1 AGGGTTTACT
*
382384 TGGGTTTACT
1 AGGGTTTACT
382394 AGGGTTTA-T
1 AGGGTTTACT
*
382403 AAGGGTTTATT
1 -AGGGTTTACT
382414 AGGGTTTA--
1 AGGGTTTACT
382422 A-GGTTTA--
1 AGGGTTTACT
*
382429 GGGGTTTACT
1 AGGGTTTACT
382439 AGGGTTTA-T
1 AGGGTTTACT
382448 AGGTGTTTACT
1 AGG-GTTTACT
*
382459 AGGG-TTATT
1 AGGGTTTACT
*
382468 AGGGTTTTCT
1 AGGGTTTACT
* *
382478 AGGATTTCCT
1 AGGGTTTACT
382488 AGGGTTTA-T
1 AGGGTTTACT
* *
382497 GAGTGTTTATT
1 -AGGGTTTACT
382508 AGGGTTTA-T
1 AGGGTTTACT
* * *
382517 AAAGTTTTATT
1 -AGGGTTTACT
*
382528 AGGGGTTA-T
1 AGGGTTTACT
*
382537 AAGGGTTTTCT
1 -AGGGTTTACT
382548 AGGGTTT--T
1 AGGGTTTACT
* * *
382556 TGGATTTATT
1 AGGGTTTACT
*
382566 AAGGTTTA-T
1 AGGGTTTACT
382575 AAGGGTTTACT
1 -AGGGTTTACT
**
382586 AGGGTTTGTT
1 AGGGTTTACT
**
382596 AGGGTTTAAA
1 AGGGTTTACT
*
382606 AGGGTTTACA
1 AGGGTTTACT
* *
382616 AGGATTTAAT
1 AGGGTTTACT
382626 AGGGTTTA-T
1 AGGGTTTACT
*
382635 AAGGGTTTATT
1 -AGGGTTTACT
**
382646 AATGTTTA-T
1 AGGGTTTACT
* *
382655 GAGAGTTTATT
1 -AGGGTTTACT
382666 AGGGTTTAC-
1 AGGGTTTACT
** *
382675 AAAGTTTAAT
1 AGGGTTTACT
* *
382685 AGTGTTT-TT
1 AGGGTTTACT
*
382694 AGGGTTT-TT
1 AGGGTTTACT
*
382703 AGGGGTTT-TT
1 A-GGGTTTACT
382713 AGGGTTTACT
1 AGGGTTTACT
*
382723 AAGGTTTA-T
1 AGGGTTTACT
382732 AGGGGTTTA-T
1 A-GGGTTTACT
* **
382742 AAGGATTTGTT
1 -AGGGTTTACT
**
382753 AGGGTTTGTT
1 AGGGTTTACT
* *
382763 AAGGTTTTCT
1 AGGGTTTACT
*
382773 AAGGTTTACT
1 AGGGTTTACT
**
382783 AGGGTTTTTT
1 AGGGTTTACT
382793 AGGGTTTA-T
1 AGGGTTTACT
*
382802 AGTGGTTTGCT
1 AG-GGTTTACT
* *
382813 AGGATTTACA
1 AGGGTTTACT
*
382823 AGGATTTACT
1 AGGGTTTACT
* * **
382833 ATGATTTGTT
1 AGGGTTTACT
382843 AGGGTTTACT
1 AGGGTTTACT
* *
382853 AAGATTTACT
1 AGGGTTTACT
*
382863 AGAGTTTACT
1 AGGGTTTACT
*
382873 A--ATATT--T
1 AGGGT-TTACT
*
382880 AGGGTTTAGT
1 AGGGTTTACT
*
382890 AAGGTTTACT
1 AGGGTTTACT
*
382900 AGGGTTTATT
1 AGGGTTTACT
* *
382910 AGGATTTGCT
1 AGGGTTTACT
* *
382920 AGGTTTTTCT
1 AGGGTTTACT
**
382930 ATAGTTTA-T
1 AGGGTTTACT
*
382939 AAGGGTTTATT
1 -AGGGTTTACT
*
382950 AGTGTTTACT
1 AGGGTTTACT
*
382960 AGGGGTTA-T
1 AGGGTTTACT
*
382969 AAGGGTTTGCT
1 -AGGGTTTACT
*
382980 AGGATTTA-T
1 AGGGTTTACT
382989 AAGGGTTTAC-
1 -AGGGTTTACT
382999 AGGGGTTTAC-
1 A-GGGTTTACT
383009 AGTGGTTTACT
1 AG-GGTTTACT
**
383020 AGGGTTTGTT
1 AGGGTTTACT
383030 AGGGTTT-CTT
1 AGGGTTTAC-T
* *
383040 AGAGTTTATT
1 AGGGTTTACT
383050 AGGGTTTA-T
1 AGGGTTTACT
* *
383059 AAAGTTTTACT
1 -AGGGTTTACT
383070 ACGGG-TTA-T
1 A-GGGTTTACT
* *
383079 AAGAGTTTTCT
1 -AGGGTTTACT
**
383090 AGGGTTTTTT
1 AGGGTTTACT
*
383100 A-GGTTTACA
1 AGGGTTTACT
**
383109 AGGGTTTGTT
1 AGGGTTTACT
* *
383119 AAGGTTTA-G
1 AGGGTTTACT
*
383128 GGGGTTTACT
1 AGGGTTTACT
*
383138 AGGGTTTA-A
1 AGGGTTTACT
*
383147 AGGTGTTTGCT
1 AGG-GTTTACT
*
383158 AGGGTTTATT
1 AGGGTTTACT
*
383168 AGGGTTT-GT
1 AGGGTTTACT
* *
383177 AAGGGTTGATT
1 -AGGGTTTACT
*
383188 AGGGTTTACA
1 AGGGTTTACT
* *
383198 AAGTTTTACT
1 AGGGTTTACT
*
383208 AGGGGTTA-T
1 AGGGTTTACT
*
383217 AAGGGTTTTCT
1 -AGGGTTTACT
*
383228 AGGGTTT-TT
1 AGGGTTTACT
*
383237 GGGGTTTACT
1 AGGGTTTACT
**
383247 AGGGTTTGTT
1 AGGGTTTACT
*
383257 AGGGTTTACA
1 AGGGTTTACT
*
383267 AGGGTTTGCT
1 AGGGTTTACT
*
383277 AGAGTTTACT
1 AGGGTTTACT
383287 AGGGTTTA-T
1 AGGGTTTACT
**
383296 AAGGGTTTGTT
1 -AGGGTTTACT
383307 AGGGTTTA-T
1 AGGGTTTACT
383316 AAGGGTTTA-T
1 -AGGGTTTACT
*
383326 GAGGGTTTATT
1 -AGGGTTTACT
*
383337 ATGGTTTA-T
1 AGGGTTTACT
* *
383346 AAAGTTTTA-T
1 -AGGGTTTACT
383356 AAGGGTTTA-T
1 -AGGGTTTACT
** *
383366 AAAGTTTAAT
1 AGGGTTTACT
* *
383376 AGGGTTCATT
1 AGGGTTTACT
*
383386 AGGGTTTTCT
1 AGGGTTTACT
*
383396 AGGGGTTT-TT
1 A-GGGTTTACT
*
383406 AGGATTTACT
1 AGGGTTTACT
383416 AGGGTTTA-T
1 AGGGTTTACT
383425 AGGGGTTTA-T
1 A-GGGTTTACT
* *
383435 AAGGATTTATT
1 -AGGGTTTACT
*
383446 AGGGTTTCCT
1 AGGGTTTACT
383456 AGGGGTTTAC-
1 A-GGGTTTACT
*
383466 AGGGGTTTGCT
1 A-GGGTTTACT
383477 AGGGTTTAC-
1 AGGGTTTACT
383486 AGGGATTTACT
1 AGGG-TTTACT
*
383497 AGGATTTACT
1 AGGGTTTACT
* **
383507 ATGGTTTGTT
1 AGGGTTTACT
*
383517 AGGGTTTATT
1 AGGGTTTACT
* *
383527 AAGATTTGA-T
1 AGGGTTT-ACT
* *
383537 AAGGTTTGCT
1 AGGGTTTACT
*
383547 AGGGTTTTCT
1 AGGGTTTACT
* *
383557 A-AGATT--T
1 AGGGTTTACT
*
383564 AGGGTTTAAT
1 AGGGTTTACT
*
383574 AAGGTTTACT
1 AGGGTTTACT
*
383584 AGGGTTTAAT
1 AGGGTTTACT
* * *
383594 AGGATTTGCA
1 AGGGTTTACT
383604 AGGGTTTGA-T
1 AGGGTTT-ACT
*
383614 AGGGTTTGCT
1 AGGGTTTACT
* *
383624 AGGTTTTCCT
1 AGGGTTTACT
*
383634 AGGGTTT-GT
1 AGGGTTTACT
*
383643 AAGGGTTTATT
1 -AGGGTTTACT
*
383654 AGTGTTTACT
1 AGGGTTTACT
*
383664 AGGGTTTACA
1 AGGGTTTACT
383674 AGGG-TTAGCT
1 AGGGTTTA-CT
383684 AGGGTTTA-T
1 AGGGTTTACT
383693 AAGGGTTTACT
1 -AGGGTTTACT
*
383704 AGGGTTTTCT
1 AGGGTTTACT
* **
383714 AGGATTTGTT
1 AGGGTTTACT
383724 AGGGTTTA-T
1 AGGGTTTACT
383733 AAGGGTTTACT
1 -AGGGTTTACT
*
383744 AGGGTTTGCT
1 AGGGTTTACT
* **
383754 AGGATTTGTT
1 AGGGTTTACT
383764 A-GG-TTACT
1 AGGGTTTACT
*
383772 AGGGTTTGCT
1 AGGGTTTACT
*
383782 AGGATTTA
1 AGGGTTTA
383790 GTGTTTTTGA
Statistics
Matches: 1753, Mismatches: 371, Indels: 291
0.73 0.15 0.12
Matches are distributed among these distances:
7 10 0.01
8 33 0.02
9 193 0.11
10 1409 0.80
11 107 0.06
12 1 0.00
ACGTcount: A:0.22, C:0.05, G:0.29, T:0.44
Consensus pattern (10 bp):
AGGGTTTACT
Found at i:385869 original size:18 final size:18
Alignment explanation
Indices: 385846--385902 Score: 87
Period size: 18 Copynumber: 3.2 Consensus size: 18
385836 TCAACATAAC
385846 GGTCAACGGGTCGGGTTG
1 GGTCAACGGGTCGGGTTG
*
385864 GGTCAACTGGTCGGGTTG
1 GGTCAACGGGTCGGGTTG
* *
385882 GGTAAACGGGTCGGGTCG
1 GGTCAACGGGTCGGGTTG
385900 GGT
1 GGT
385903 TGTAACCGGT
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 35 1.00
ACGTcount: A:0.12, C:0.16, G:0.49, T:0.23
Consensus pattern (18 bp):
GGTCAACGGGTCGGGTTG
Found at i:389101 original size:64 final size:65
Alignment explanation
Indices: 388969--389123 Score: 165
Period size: 64 Copynumber: 2.4 Consensus size: 65
388959 GAAGGTGTAT
* * ** * *
388969 CGATGCACAGGTAGTGCATCGATGCA-CTCTTTTAAAATAAAAACATCGAATGCAATTGGTGCAT
1 CGATGCACAAGCAGTGCATCGATGCATCTCCATTAAAATAAAAACATCGAATGCAATTGATGCAC
* * *
389033 CGATGCATAAGGCA-TGCATCGATGCATC-CCATTAATAAT-AAAACATCGAATGCATTTTATGC
1 CGATGCACAA-GCAGTGCATCGATGCATCTCCATTAA-AATAAAAACATCGAATGCAATTGATGC
389095 AC
64 AC
* *
389097 CGATGTACAAGTAGTGCATCGATGCAT
1 CGATGCACAAGCAGTGCATCGATGCAT
389124 ACCTTCATTA
Statistics
Matches: 75, Mismatches: 12, Indels: 8
0.79 0.13 0.08
Matches are distributed among these distances:
63 2 0.03
64 67 0.89
65 6 0.08
ACGTcount: A:0.34, C:0.20, G:0.19, T:0.26
Consensus pattern (65 bp):
CGATGCACAAGCAGTGCATCGATGCATCTCCATTAAAATAAAAACATCGAATGCAATTGATGCAC
Done.