Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015590.1 Corchorus olitorius cultivar O-4 contig15623, 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: 117546
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:2680 original size:12 final size:12
Alignment explanation
Indices: 2663--2702 Score: 53
Period size: 12 Copynumber: 3.1 Consensus size: 12
2653 CAACAAGTAG
2663 TTCAGATGATGA
1 TTCAGATGATGA
2675 TTCAGATGATGATGA
1 TTC--A-GATGATGA
2690 TTCAGATGATGA
1 TTCAGATGATGA
2702 T
1 T
2703 GATTATTAAG
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
12 12 0.48
13 1 0.04
14 1 0.04
15 11 0.44
ACGTcount: A:0.33, C:0.07, G:0.25, T:0.35
Consensus pattern (12 bp):
TTCAGATGATGA
Found at i:2687 original size:15 final size:15
Alignment explanation
Indices: 2667--2706 Score: 80
Period size: 15 Copynumber: 2.7 Consensus size: 15
2657 AAGTAGTTCA
2667 GATGATGATTCAGAT
1 GATGATGATTCAGAT
2682 GATGATGATTCAGAT
1 GATGATGATTCAGAT
2697 GATGATGATT
1 GATGATGATT
2707 ATTAAGTAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 25 1.00
ACGTcount: A:0.33, C:0.05, G:0.28, T:0.35
Consensus pattern (15 bp):
GATGATGATTCAGAT
Found at i:11838 original size:161 final size:155
Alignment explanation
Indices: 11569--12016 Score: 518
Period size: 151 Copynumber: 2.9 Consensus size: 155
11559 GAGGATCGAA
* * *
11569 ACGCCACTGATTCGCGGCGTCTGGTGGGTAAACGCCGCTATATATTATAGGTGTAGAGTTGGAAA
1 ACGCCACTGATTAGCGGCGTCTGGTGGGAAAACGCCGCTATATATTATAGGCGTAGAGTTGGAAA
* *
11634 GTTTCTATGTTTTA-GGGGGAGGGAATTTTTCCCTCCAAAAAAAAGGGGAAAAAAATCTCT-CTC
66 CTTTCTTTGTTTTAGGGGGGAGGGAATTTTTCCCTCC-AAAAAAA-GGGAAAAAAATCTCTCCTC
11697 CATATATTAAAATAGCAGCGTTTCCTT
129 CATATATTAAAATAGCAGCGTTTCCTT
*
11724 CCCAAGACGCCACTGATTAGCGGCGTCTGGTGGGAAAACGCCGCTATATATTATTGGCGTAGAGT
1 ------ACGCCACTGATTAGCGGCGTCTGGTGGGAAAACGCCGCTATATATTATAGGCGTAGAGT
* * *
11789 TAGCAAA-ATTCTTTGTTTTAGGGGGGAGGGAATTTTTCCCTCCAAAAAAAAAGGAAAAAAATCT
60 T-GGAAACTTTCTTTGTTTTAGGGGGGAGGGAATTTTTCCCTCC-AAAAAAAGGGAAAAAAATCT
* * * *
11853 CTCCCTCCATATATTAAGATAGCGGTGTTTTCTT
123 CT-CCTCCATATATTAAAATAGCAGCGTTTCCTT
** * **
11887 ---TTAC--A-TAGCGGCGTCTGATGCAAAAACGCCGCTATATATTATAGGCGTAGAGTTGGAAA
1 ACGCCACTGATTAGCGGCGTCTGGTGGGAAAACGCCGCTATATATTATAGGCGTAGAGTTGGAAA
* * * *
11946 CTTTCTTTGTTTTAGGGGCGAGGGAATTTTTCCCTCCAAAAATAGAGAAAAAAATTATCTCCTCC
66 CTTTCTTTGTTTTAGGGGGGAGGGAATTTTTCCCTCCAAAAAAAGGGAAAAAAA-TCTCTCCTCC
*
12011 GTATAT
130 ATATAT
12017 CAATATGGCG
Statistics
Matches: 255, Mismatches: 26, Indels: 23
0.84 0.09 0.08
Matches are distributed among these distances:
150 28 0.11
151 83 0.33
152 1 0.00
154 2 0.01
161 81 0.32
162 34 0.13
163 26 0.10
ACGTcount: A:0.30, C:0.18, G:0.23, T:0.30
Consensus pattern (155 bp):
ACGCCACTGATTAGCGGCGTCTGGTGGGAAAACGCCGCTATATATTATAGGCGTAGAGTTGGAAA
CTTTCTTTGTTTTAGGGGGGAGGGAATTTTTCCCTCCAAAAAAAGGGAAAAAAATCTCTCCTCCA
TATATTAAAATAGCAGCGTTTCCTT
Found at i:13862 original size:15 final size:15
Alignment explanation
Indices: 13842--13880 Score: 78
Period size: 15 Copynumber: 2.6 Consensus size: 15
13832 ACCGTTTGAA
13842 ATAGAAATTTCATAT
1 ATAGAAATTTCATAT
13857 ATAGAAATTTCATAT
1 ATAGAAATTTCATAT
13872 ATAGAAATT
1 ATAGAAATT
13881 ATGGAGTACA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.49, C:0.05, G:0.08, T:0.38
Consensus pattern (15 bp):
ATAGAAATTTCATAT
Found at i:17211 original size:14 final size:14
Alignment explanation
Indices: 17192--18077 Score: 219
Period size: 14 Copynumber: 62.0 Consensus size: 14
17182 AAATTGAAAC
17192 ATTGAAGAATTGAA
1 ATTGAAGAATTGAA
*
17206 ATTGAAGCATTGAAGA
1 ATTGAAGAATTG-A-A
17222 ATTG-A-AATTGAAA
1 ATTGAAGAATTG-AA
* **
17235 CATTGAATAATTGGC
1 -ATTGAAGAATTGAA
17250 ATTGAAGAATTGAA
1 ATTGAAGAATTGAA
*
17264 ATT---GAA--G-C
1 ATTGAAGAATTGAA
17272 ATTGAAGAATTGAA
1 ATTGAAGAATTGAA
* *
17286 ATTGAAGCATTGGGGA
1 ATTGAAGAATT--GAA
17302 ATTG-A-AATTGAAA
1 ATTGAAGAATTG-AA
17315 CATTGAAGAATTGAA
1 -ATTGAAGAATTGAA
* *
17330 ATTGAAGCATTAGGGA
1 ATTGAAGAATT--GAA
17346 ATTG-A-AATTGAAA
1 ATTGAAGAATTG-AA
*
17359 CATT-AGGGAATTGAA
1 -ATTGA-AGAATTGAA
17374 ATTGAA-ACATTGAAGA
1 ATTGAAGA-ATTG-A-A
17390 ATTG-A-AATTGAA
1 ATTGAAGAATTGAA
17402 GCATTGAAGAATTGAA
1 --ATTGAAGAATTGAA
*
17418 ATTGAAGCATTGAA
1 ATTGAAGAATTGAA
17432 ATTG-A-AATTGAAA
1 ATTGAAGAATTG-AA
17445 CATTGAAGAATTGAA
1 -ATTGAAGAATTGAA
17460 ATTGAA-ACATTGAAA
1 ATTGAAGA-ATTG-AA
17475 TATTG-A-AATTGAAA
1 -ATTGAAGAATTG-AA
*
17489 CATTGAAGCATTGACA
1 -ATTGAAGAATTGA-A
*
17505 TATTG-A-AACTGAAA
1 -ATTGAAGAATTG-AA
17519 CATTGAAGAATTGAA
1 -ATTGAAGAATTGAA
*
17534 ATTGAAGCATTGAAA
1 ATTGAAGAATTG-AA
17549 TATTG-A-AATTGAAA
1 -ATTGAAGAATTG-AA
* *
17563 CATTAAAGGATTGAA
1 -ATTGAAGAATTGAA
*
17578 TTTGAAGAATTGAA
1 ATTGAAGAATTGAA
*
17592 ATTGAA-ACACTG-A
1 ATTGAAGA-ATTGAA
17605 A--G--G-ATTGAA
1 ATTGAAGAATTGAA
* * *
17614 TTTGAATAACTGAA
1 ATTGAAGAATTGAA
17628 ATTG-A-AATTGAA
1 ATTGAAGAATTGAA
17640 GCATTGGAAGAATTGAA
1 --ATT-GAAGAATTGAA
* *
17657 ATTAAAGTATTGAA
1 ATTGAAGAATTGAA
17671 GTATTGAA-ATATTGAA
1 --ATTGAAGA-ATTGAA
* *
17687 GCATTCG--CATTTGGAA
1 --ATT-GAAGAATT-GAA
*
17703 TTTGAAGAATTGAA
1 ATTGAAGAATTGAA
* *
17717 ATTCAAGCATTGAAA
1 ATTGAAGAATTG-AA
17732 TATTG-A-AATTGAA
1 -ATTGAAGAATTGAA
* *
17745 GCATTGAAAAATGGAA
1 --ATTGAAGAATTGAA
*
17761 ATTGAAGTATTGAAAA
1 ATTGAAGAATTG--AA
* *
17777 ATAGAA-ATATTAAA
1 ATTGAAGA-ATTGAA
* *
17791 GCATTG-ATATTTGGAA
1 --ATTGAAGAATT-GAA
*
17807 TTTGAAGAATTGAA
1 ATTGAAGAATTGAA
*
17821 ATTGAAGCATTGACA
1 ATTGAAGAATTGA-A
* *
17836 AATGGA-AATT-AA
1 ATTGAAGAATTGAA
* **
17848 AGT-ATTAATTGAA
1 ATTGAAGAATTGAA
17861 GCATTGAAGAATTGAA
1 --ATTGAAGAATTGAA
*
17877 ATTGAAGCATTG--
1 ATTGAAGAATTGAA
17889 ---GAAGAATTGAA
1 ATTGAAGAATTGAA
* *
17900 ATTAAAGTATTGAAA
1 ATTGAAGAATTG-AA
17915 TATTGAA-ATATTGAA
1 -ATTGAAGA-ATTGAA
* *
17930 GCATTG-ACATTTGGAA
1 --ATTGAAGAATT-GAA
*
17946 TTTGAAGAATTGAA
1 ATTGAAGAATTGAA
*
17960 ATTGAAGCATTGAAA
1 ATTGAAGAATTG-AA
17975 TATTG-A-AATTGAA
1 -ATTGAAGAATTGAA
*
17988 GCATTGGAA-AATGGAA
1 --ATT-GAAGAATTGAA
* *
18004 ATTGAGGTATTGAAGA
1 ATTGAAGAATTG-A-A
18020 ATTGAA-ATATTGAA
1 ATTGAAGA-ATTGAA
* *
18034 GCATTG-ACATTTGGAA
1 --ATTGAAGAATT-GAA
18050 ATTGAAGAATTGAA
1 ATTGAAGAATTGAA
*
18064 ATTGAAGCATTGAA
1 ATTGAAGAATTGAA
18078 GAAAGAGATC
Statistics
Matches: 649, Mismatches: 108, Indels: 230
0.66 0.11 0.23
Matches are distributed among these distances:
8 6 0.01
9 10 0.02
11 8 0.01
12 20 0.03
13 24 0.04
14 314 0.48
15 86 0.13
16 173 0.27
17 8 0.01
ACGTcount: A:0.45, C:0.05, G:0.21, T:0.30
Consensus pattern (14 bp):
ATTGAAGAATTGAA
Found at i:17247 original size:44 final size:44
Alignment explanation
Indices: 17182--18080 Score: 623
Period size: 44 Copynumber: 20.9 Consensus size: 44
17172 AATCAAACTT
17182 AAATTGAAACATTGAAGAATTGAAATTGAAGCATTGAAGAATTG
1 AAATTGAAACATTGAAGAATTGAAATTGAAGCATTGAAGAATTG
17226 AAATTGAAACATT---GAA-T--AATTG--GCATTGAAGAATTG
1 AAATTGAAACATTGAAGAATTGAAATTGAAGCATTGAAGAATTG
* **
17262 AAATTGAAGCATTGAAGAATTGAAATTGAAGCATTGGGGAATTG
1 AAATTGAAACATTGAAGAATTGAAATTGAAGCATTGAAGAATTG
*
17306 AAATTGAAACATTGAAGAATTGAAATTGAAGCATT-AGGGAATTG
1 AAATTGAAACATTGAAGAATTGAAATTGAAGCATTGA-AGAATTG
* *
17350 AAATTGAAACATT-AGGGAATTGAAATTGAAACATTGAAGAATTG
1 AAATTGAAACATTGA-AGAATTGAAATTGAAGCATTGAAGAATTG
*
17394 AAATTGAAGCATTGAAGAATTGAAATTGAAGCATTG-A-AATTG
1 AAATTGAAACATTGAAGAATTGAAATTGAAGCATTGAAGAATTG
*
17436 AAATTGAAACATTGAAGAATTGAAATTGAAACATTGAA-ATATTG
1 AAATTGAAACATTGAAGAATTGAAATTGAAGCATTGAAGA-ATTG
*
17480 AAATTGAAACATTGAAGCATTGACATATTGAAACTGAAACATTGAAGAATTG
1 AAATTGAAACATTGAAGAATTGA-A-ATTG-AA--G---CATTGAAGAATTG
* *
17532 AAATTGAAGCATTGAA-ATATTGAAATTGAAACATT--A-AA--G
1 AAATTGAAACATTGAAGA-ATTGAAATTGAAGCATTGAAGAATTG
* * * * *
17571 -GATTG-AA-TTTGAAGAATTGAAATTGAAACACTGAAGGATTG
1 AAATTGAAACATTGAAGAATTGAAATTGAAGCATTGAAGAATTG
* *
17612 AATTTGAATA-ACTG-A-AATTGAAATTGAAGCATTGGAAGAATTG
1 AAATTGAA-ACATTGAAGAATTGAAATTGAAGCATT-GAAGAATTG
* * *
17655 AAATT-AAAGTATTGAAGTATTGAAA-T-----ATTGAAGCATTCG
1 AAATTGAAA-CATTGAAGAATTGAAATTGAAGCATTGAAGAATT-G
* * * * *
17694 CATTTGGAA-TTTGAAGAATTGAAATTCAAGCATTGAA-ATATTG
1 AAATTGAAACATTGAAGAATTGAAATTGAAGCATTGAAGA-ATTG
* * * * * *
17737 AAATTGAAGCATTGAAAAATGGAAATTGAAGTATTGAAAAATAG
1 AAATTGAAACATTGAAGAATTGAAATTGAAGCATTGAAGAATTG
* *
17781 AAATATTAAAGCATTGATATTTGGAATTTGAAGAATTGAA--ATTGAAGCATTG
1 AAAT-TGAAA-CATTGA-A----GAA-TTG-A-AATTGAAGCATTGAAGAATTG
* * * *
17833 ACAAATGGAA-ATTAAAGTATT--AATTGAAGCATTGAAGAATTG
1 A-AATTGAAACATTGAAGAATTGAAATTGAAGCATTGAAGAATTG
* * *
17875 AAATTGAAGCATTGGAAGAATTGAAATTAAAGTATTG-A-AA-T-
1 AAATTGAAACATT-GAAGAATTGAAATTGAAGCATTGAAGAATTG
* * * *
17916 --ATTGAAATATTGAAGCATTGACATTTGGAA--TTTGAAGAATTG
1 AAATTGAAACATTGAAGAATTGA-AATT-GAAGCATTGAAGAATTG
* *
17958 AAATTGAAGCATTGAA-ATATTGAAATTGAAGCATTGGAA-AATGG
1 AAATTGAAACATTGAAGA-ATTGAAATTGAAGCATT-GAAGAATTG
*** *
18002 AAATTGAGGTATTGAAGAATTGAAA-T-----ATTGAAGCATTG
1 AAATTGAAACATTGAAGAATTGAAATTGAAGCATTGAAGAATTG
* *
18040 ACATTTGGAA-ATTGAAGAATTGAAATTGAAGCATTGAAGAA
1 A-AATTGAAACATTGAAGAATTGAAATTGAAGCATTGAAGAA
18081 AGAGATCATT
Statistics
Matches: 677, Mismatches: 91, Indels: 174
0.72 0.10 0.18
Matches are distributed among these distances:
36 47 0.07
37 5 0.01
38 64 0.09
39 31 0.05
40 15 0.02
41 13 0.02
42 85 0.13
43 39 0.06
44 263 0.39
45 31 0.05
46 10 0.01
47 3 0.00
49 3 0.00
50 8 0.01
51 3 0.00
52 46 0.07
53 4 0.01
54 7 0.01
ACGTcount: A:0.45, C:0.05, G:0.20, T:0.29
Consensus pattern (44 bp):
AAATTGAAACATTGAAGAATTGAAATTGAAGCATTGAAGAATTG
Found at i:17261 original size:22 final size:22
Alignment explanation
Indices: 17182--17598 Score: 175
Period size: 22 Copynumber: 19.1 Consensus size: 22
17172 AATCAAACTT
17182 AAATTGAA-ACATTGAAGAATTG
1 AAATTGAAGA-ATTGAAGAATTG
*
17204 AAATTGAAGCATTGAAGAATTG
1 AAATTGAAGAATTGAAGAATTG
*
17226 AAATTGAA-ACATTGAATAATTG
1 AAATTGAAGA-ATTGAAGAATTG
**
17248 GCATTGAAGAATTG-A-AATTG
1 AAATTGAAGAATTGAAGAATTG
17268 AAGCATTGAAGAATTG-A-AATTG
1 AA--ATTGAAGAATTGAAGAATTG
**
17290 AAGCATTGGGGAATTG-A-AATTG
1 AA--ATTGAAGAATTGAAGAATTG
17312 AAACATTGAAGAATTG-A-AATTG
1 -AA-ATTGAAGAATTGAAGAATTG
*
17334 AAGCATT-AGGGAATTG-A-AATTG
1 AA--ATTGA-AGAATTGAAGAATTG
*
17356 AAACATT-AGGGAATTG-A-AATTG
1 -AA-ATTGA-AGAATTGAAGAATTG
17378 AAACATTGAAGAATTG-A-AATTG
1 -AA-ATTGAAGAATTGAAGAATTG
17400 AAGCATTGAAGAATTG-A-AATTG
1 AA--ATTGAAGAATTGAAGAATTG
17422 AAGCATTG-A-AATTG-A-AATTG
1 AA--ATTGAAGAATTGAAGAATTG
17442 AAACATTGAAGAATTG-A-AATTG
1 -AA-ATTGAAGAATTGAAGAATTG
17464 AAACATTGAA-ATATTG-A-AATTG
1 -AA-ATTGAAGA-ATTGAAGAATTG
* *
17486 AAACATTGAAGCATTGACA-TATTG
1 -AA-ATTGAAGAATTGA-AGAATTG
*
17510 AAACTGAA-ACATTGAAGAATTG
1 AAATTGAAGA-ATTGAAGAATTG
*
17532 AAATTGAAGCATTGAA-ATATTG
1 AAATTGAAGAATTGAAGA-ATTG
* *
17554 AAATTGAA-ACATTAAAGGATTG
1 AAATTGAAGA-ATTGAAGAATTG
*
17576 AATTTGAAGAATTG-A-AATTG
1 AAATTGAAGAATTGAAGAATTG
17596 AAA
1 AAA
17599 CACTGAAGGA
Statistics
Matches: 343, Mismatches: 27, Indels: 52
0.81 0.06 0.12
Matches are distributed among these distances:
20 27 0.08
21 14 0.04
22 288 0.84
23 9 0.03
24 5 0.01
ACGTcount: A:0.47, C:0.05, G:0.20, T:0.28
Consensus pattern (22 bp):
AAATTGAAGAATTGAAGAATTG
Found at i:17676 original size:22 final size:23
Alignment explanation
Indices: 17627--17680 Score: 74
Period size: 23 Copynumber: 2.4 Consensus size: 23
17617 GAATAACTGA
*
17627 AATTGAAATTGAAGCATTGGAAG
1 AATTGAAATTAAAGCATTGGAAG
*
17650 AATTGAAATTAAAGTATT-GAAG
1 AATTGAAATTAAAGCATTGGAAG
*
17672 TATTGAAAT
1 AATTGAAAT
17681 ATTGAAGCAT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
22 12 0.43
23 16 0.57
ACGTcount: A:0.46, C:0.02, G:0.20, T:0.31
Consensus pattern (23 bp):
AATTGAAATTAAAGCATTGGAAG
Found at i:17729 original size:22 final size:22
Alignment explanation
Indices: 17704--17936 Score: 134
Period size: 22 Copynumber: 10.2 Consensus size: 22
17694 CATTTGGAAT
* *
17704 TTGAAGAATTGAAATTCAAGCA
1 TTGAAAAATTGAAATTGAAGCA
*
17726 TTGAAATATTGAAATTGAAGCA
1 TTGAAAAATTGAAATTGAAGCA
* *
17748 TTGAAAAATGGAAATTGAAGTA
1 TTGAAAAATTGAAATTGAAGCA
* *
17770 TTGAAAAATAGAAATATTAAAGCA
1 TTGAAAAATTG-AA-ATTGAAGCA
* * * *
17794 TTG-ATATTTGGAATTTGAAGAA
1 TTGAAAAATT-GAAATTGAAGCA
*
17816 TTG--AAATTGAAGCATTGACA-AA
1 TTGAAAAATTGAA--ATTGA-AGCA
* *
17838 TGGAAATTAAAGTAT-TAATTGAAGCA
1 TTG-AA--AAA-T-TGAAATTGAAGCA
*
17864 TTGAAGAATTGAAATTGAAGCA
1 TTGAAAAATTGAAATTGAAGCA
* * *
17886 TTGGAAGAATTGAAATTAAAGTA
1 TT-GAAAAATTGAAATTGAAGCA
*
17909 TTGAAATATTGAAATATTGAAGCA
1 TTGAAAAATTG-AA-ATTGAAGCA
17933 TTGA
1 TTGA
17937 CATTTGGAAT
Statistics
Matches: 163, Mismatches: 30, Indels: 34
0.72 0.13 0.15
Matches are distributed among these distances:
20 3 0.02
21 4 0.02
22 85 0.52
23 32 0.20
24 22 0.13
25 3 0.02
26 8 0.05
27 3 0.02
28 2 0.01
29 1 0.01
ACGTcount: A:0.46, C:0.04, G:0.19, T:0.30
Consensus pattern (22 bp):
TTGAAAAATTGAAATTGAAGCA
Found at i:17844 original size:104 final size:104
Alignment explanation
Indices: 17626--17845 Score: 309
Period size: 104 Copynumber: 2.1 Consensus size: 104
17616 TGAATAACTG
* * ** * *
17626 AAATTGAAATTGAAGCATTGGAAGAATTGAAATTAAAGTATTGAAGTATTGAAATATTGAAGCAT
1 AAATTGAAATTGAAGCATTGGAAAAATGGAAATTAAAGTATTGAAAAATAGAAATATTAAAGCAT
17691 TCGCATTTGGAATTTGAAGAATTGAAATTCAAGCATTGA
66 TCGCATTTGGAATTTGAAGAATTGAAATTCAAGCATTGA
*
17730 AATATTGAAATTGAAGCATT-GAAAAATGGAAATTGAAGTATTGAAAAATAGAAATATTAAAGCA
1 AA-ATTGAAATTGAAGCATTGGAAAAATGGAAATTAAAGTATTGAAAAATAGAAATATTAAAGCA
* *
17794 TT-GATATTTGGAATTTGAAGAATTGAAATTGAAGCATTGA
65 TTCG-CATTTGGAATTTGAAGAATTGAAATTCAAGCATTGA
*
17834 CAAATGGAAATT
1 -AAATTGAAATT
17846 AAAGTATTAA
Statistics
Matches: 103, Mismatches: 10, Indels: 6
0.87 0.08 0.05
Matches are distributed among these distances:
103 1 0.01
104 83 0.81
105 19 0.18
ACGTcount: A:0.45, C:0.05, G:0.20, T:0.31
Consensus pattern (104 bp):
AAATTGAAATTGAAGCATTGGAAAAATGGAAATTAAAGTATTGAAAAATAGAAATATTAAAGCAT
TCGCATTTGGAATTTGAAGAATTGAAATTCAAGCATTGA
Found at i:17866 original size:8 final size:8
Alignment explanation
Indices: 17855--18078 Score: 67
Period size: 8 Copynumber: 29.9 Consensus size: 8
17845 TAAAGTATTA
17855 ATTGAAGC
1 ATTGAAGC
*
17863 ATTGAAGA
1 ATTGAAGC
17871 ATTGAA--
1 ATTGAAGC
17877 ATTGAAGC
1 ATTGAAGC
*
17885 ATTGGAAGA
1 ATT-GAAGC
17894 ATTGAA--
1 ATTGAAGC
* *
17900 ATTAAAGT
1 ATTGAAGC
**
17908 ATTGAAAT
1 ATTGAAGC
**
17916 ATTGAAAT
1 ATTGAAGC
17924 ATTGAAGC
1 ATTGAAGC
17932 ATTG-A-C
1 ATTGAAGC
17938 ATTTGGAA--
1 A-TT-GAAGC
* *
17946 TTTGAAGA
1 ATTGAAGC
17954 ATTGAA--
1 ATTGAAGC
17960 ATTGAAGC
1 ATTGAAGC
**
17968 ATTGAAAT
1 ATTGAAGC
17976 ATTGAA--
1 ATTGAAGC
17982 ATTGAAGC
1 ATTGAAGC
*
17990 ATTGGAA-A
1 ATT-GAAGC
*
17998 ATGGAA--
1 ATTGAAGC
* *
18004 ATTGAGGT
1 ATTGAAGC
*
18012 ATTGAAGA
1 ATTGAAGC
**
18020 ATTGAAAT
1 ATTGAAGC
18028 ATTGAAGC
1 ATTGAAGC
18036 ATTG-A-C
1 ATTGAAGC
18042 ATTTGGAA--
1 A-TT-GAAGC
*
18050 ATTGAAGA
1 ATTGAAGC
18058 ATTGAA--
1 ATTGAAGC
18064 ATTGAAGC
1 ATTGAAGC
18072 ATTGAAG
1 ATTGAAG
18079 AAAGAGATCA
Statistics
Matches: 171, Mismatches: 21, Indels: 48
0.71 0.09 0.20
Matches are distributed among these distances:
6 43 0.25
7 13 0.08
8 103 0.60
9 12 0.07
ACGTcount: A:0.43, C:0.04, G:0.22, T:0.30
Consensus pattern (8 bp):
ATTGAAGC
Found at i:17899 original size:243 final size:243
Alignment explanation
Indices: 17627--18076 Score: 803
Period size: 243 Copynumber: 1.9 Consensus size: 243
17617 GAATAACTGA
*
17627 AATTGAAATTGAAGCATTGGAAGAATTGAAATTAAAGTATTGAAGTATTGAAATATTGAAGCATT
1 AATTGAAATTGAAGCATTGGAAGAATTGAAATTAAAGTATTGAAATATTGAAATATTGAAGCATT
17692 CG-CATTTGGAATTTGAAGAATTGAAATTCAAGCATTGAAATATTGAAATTGAAGCATTGAAAAA
66 -GACATTTGGAATTTGAAGAATTGAAATTCAAGCATTGAAATATTGAAATTGAAGCATTGAAAAA
* *
17756 TGGAAATTGAAGTATTGAAAAATAGAAATATTAAAGCATTGATATTTGGAATTTGAAGAATTGAA
130 TGGAAATTGAAGTATTGAAAAATAGAAATATTAAAGCATTGACATTTGGAAATTGAAGAATTGAA
17821 ATTGAAGCATTGACAAATGGAAATTAAAGTATTAATTGAAGCATTGAAG
195 ATTGAAGCATTGACAAATGGAAATTAAAGTATTAATTGAAGCATTGAAG
17870 AATTGAAATTGAAGCATTGGAAGAATTGAAATTAAAGTATTGAAATATTGAAATATTGAAGCATT
1 AATTGAAATTGAAGCATTGGAAGAATTGAAATTAAAGTATTGAAATATTGAAATATTGAAGCATT
* *
17935 GACATTTGGAATTTGAAGAATTGAAATTGAAGCATTGAAATATTGAAATTGAAGCATTGGAAAAT
66 GACATTTGGAATTTGAAGAATTGAAATTCAAGCATTGAAATATTGAAATTGAAGCATTGAAAAAT
* * * *
18000 GGAAATTGAGGTATTGAAGAATTGAAATATTGAAGCATTGACATTTGGAAATTGAAGAATTGAAA
131 GGAAATTGAAGTATTGAAAAATAGAAATATTAAAGCATTGACATTTGGAAATTGAAGAATTGAAA
18065 TTGAAGCATTGA
196 TTGAAGCATTGA
18077 AGAAAGAGAT
Statistics
Matches: 197, Mismatches: 9, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
242 1 0.01
243 196 0.99
ACGTcount: A:0.44, C:0.04, G:0.21, T:0.31
Consensus pattern (243 bp):
AATTGAAATTGAAGCATTGGAAGAATTGAAATTAAAGTATTGAAATATTGAAATATTGAAGCATT
GACATTTGGAATTTGAAGAATTGAAATTCAAGCATTGAAATATTGAAATTGAAGCATTGAAAAAT
GGAAATTGAAGTATTGAAAAATAGAAATATTAAAGCATTGACATTTGGAAATTGAAGAATTGAAA
TTGAAGCATTGACAAATGGAAATTAAAGTATTAATTGAAGCATTGAAG
Found at i:17932 original size:139 final size:138
Alignment explanation
Indices: 17716--17972 Score: 417
Period size: 139 Copynumber: 1.9 Consensus size: 138
17706 GAAGAATTGA
*
17716 AATTCAAGCATTGAAATATTGAAATTGAAGCATTGAAAAATGGAAATTGAAGTATTGAAAAATAG
1 AATTCAAGCATTGAAATATTGAAATTGAAGCATTGAAAAATGGAAATTAAAGTATTGAAAAATAG
*
17781 AAATATTAAAGCATTGATATTTGGAATTTGAAGAATTGAAATTGAAGCATTGACAAATGGAAATT
66 AAATATTAAAGCATTGACATTTGGAATTTGAAGAATTGAAATTGAAGCATTGACAAATGGAAATT
17846 AAAGTATT
131 AAAGTATT
* * * *
17854 AATTGAAGCATTGAAGA-ATTGAAATTGAAGCATTGGAAGAATTGAAATTAAAGTATTGAAATAT
1 AATTCAAGCATTGAA-ATATTGAAATTGAAGCATT-GAAAAATGGAAATTAAAGTATTGAAAAAT
* *
17918 TGAAATATTGAAGCATTGACATTTGGAATTTGAAGAATTGAAATTGAAGCATTGA
64 AGAAATATTAAAGCATTGACATTTGGAATTTGAAGAATTGAAATTGAAGCATTGA
17973 AATATTGAAA
Statistics
Matches: 109, Mismatches: 8, Indels: 3
0.91 0.07 0.03
Matches are distributed among these distances:
138 31 0.28
139 78 0.72
ACGTcount: A:0.46, C:0.04, G:0.19, T:0.31
Consensus pattern (138 bp):
AATTCAAGCATTGAAATATTGAAATTGAAGCATTGAAAAATGGAAATTAAAGTATTGAAAAATAG
AAATATTAAAGCATTGACATTTGGAATTTGAAGAATTGAAATTGAAGCATTGACAAATGGAAATT
AAAGTATT
Found at i:17972 original size:22 final size:21
Alignment explanation
Indices: 17947--18078 Score: 122
Period size: 22 Copynumber: 5.9 Consensus size: 21
17937 CATTTGGAAT
17947 TTGAAGAATTGAAATTGAAGCA
1 TTGAA-AATTGAAATTGAAGCA
17969 TTGAAATATTGAAATTGAAGCA
1 TTGAAA-ATTGAAATTGAAGCA
* * *
17991 TTGGAAAATGGAAATTGAGGTA
1 TT-GAAAATTGAAATTGAAGCA
18013 TTGAAGAATTGAAATATTGAAGCA
1 TTGAA-AATTG-AA-ATTGAAGCA
* * *
18037 TTGACATTTGGAAATTGAAGAA
1 TTGAAAATT-GAAATTGAAGCA
18059 TTG-AAATTGAAGCATTGAAG
1 TTGAAAATTGAA--ATTGAAG
18079 AAAGAGATCA
Statistics
Matches: 91, Mismatches: 11, Indels: 16
0.77 0.09 0.14
Matches are distributed among these distances:
20 3 0.03
21 7 0.08
22 58 0.64
23 11 0.12
24 12 0.13
ACGTcount: A:0.43, C:0.04, G:0.23, T:0.30
Consensus pattern (21 bp):
TTGAAAATTGAAATTGAAGCA
Found at i:18080 original size:22 final size:22
Alignment explanation
Indices: 17248--17691 Score: 400
Period size: 22 Copynumber: 20.2 Consensus size: 22
17238 TGAATAATTG
17248 GCATTGAAGAATTGAAATTGAA
1 GCATTGAAGAATTGAAATTGAA
17270 GCATTGAAGAATTGAAATTGAA
1 GCATTGAAGAATTGAAATTGAA
**
17292 GCATTGGGGAATTGAAATTGAA
1 GCATTGAAGAATTGAAATTGAA
*
17314 ACATTGAAGAATTGAAATTGAA
1 GCATTGAAGAATTGAAATTGAA
*
17336 GCATT-AGGGAATTGAAATTGAA
1 GCATTGA-AGAATTGAAATTGAA
* *
17358 ACATT-AGGGAATTGAAATTGAA
1 GCATTGA-AGAATTGAAATTGAA
*
17380 ACATTGAAGAATTGAAATTGAA
1 GCATTGAAGAATTGAAATTGAA
17402 GCATTGAAGAATTGAAATTGAA
1 GCATTGAAGAATTGAAATTGAA
17424 GCATTG-A-AATTGAAATTGAA
1 GCATTGAAGAATTGAAATTGAA
*
17444 ACATTGAAGAATTGAAATTGAA
1 GCATTGAAGAATTGAAATTGAA
*
17466 ACATTGAA-ATATTGAAATTGAA
1 GCATTGAAGA-ATTGAAATTGAA
* *
17488 ACATTGAAGCATTGACATATTGAA
1 GCATTGAAGAATTGA-A-ATTGAA
*
17512 --ACTGAA-ACATTGAAGAATTGAA
1 GCATTGAAGA-ATTG-A-AATTGAA
*
17534 --ATTGAAGCATTGAAATATTGAA
1 GCATTGAAGAATTG-AA-ATTGAA
*
17556 --ATTGAA-ACATTAAAGGATTGAA
1 GCATTGAAGA-ATTGAA--ATTGAA
*
17578 --TTTGAAGAATTGAAATTGAA
1 GCATTGAAGAATTGAAATTGAA
* * * *
17598 ACACTGAAGGATTGAATTTGAA
1 GCATTGAAGAATTGAAATTGAA
** *
17620 TAACTG-A-AATTGAAATTGAA
1 GCATTGAAGAATTGAAATTGAA
*
17640 GCATTGGAAGAATTGAAATTAAA
1 GCATT-GAAGAATTGAAATTGAA
* *
17663 GTATTGAAGTATTGAAATATTGAA
1 GCATTGAAGAATTG-AA-ATTGAA
17687 GCATT
1 GCATT
17692 CGCATTTGGA
Statistics
Matches: 362, Mismatches: 38, Indels: 42
0.82 0.09 0.10
Matches are distributed among these distances:
20 37 0.10
21 9 0.02
22 278 0.77
23 23 0.06
24 15 0.04
ACGTcount: A:0.45, C:0.05, G:0.20, T:0.29
Consensus pattern (22 bp):
GCATTGAAGAATTGAAATTGAA
Found at i:19768 original size:7 final size:7
Alignment explanation
Indices: 19756--19789 Score: 50
Period size: 7 Copynumber: 4.9 Consensus size: 7
19746 TTCCAAGTGC
19756 TTTTTCT
1 TTTTTCT
19763 TTTTTCT
1 TTTTTCT
*
19770 TTTTTCA
1 TTTTTCT
*
19777 TTTATCT
1 TTTTTCT
19784 TTTTTC
1 TTTTTC
19790 ATGGGGGAAT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.06, C:0.15, G:0.00, T:0.79
Consensus pattern (7 bp):
TTTTTCT
Found at i:22660 original size:48 final size:48
Alignment explanation
Indices: 22589--22685 Score: 167
Period size: 48 Copynumber: 2.0 Consensus size: 48
22579 AGGACTTGTT
* *
22589 TTACTATACATCATTGTTTCTCTTATTCAATTGCATGTAAAGATAGTA
1 TTACTATACAACATTGTTTCTCTTATTCAATTGCATGTAAACATAGTA
*
22637 TTACTATACAACATTGTTTCTCTTATTCAATTGCATGTATACATAGTA
1 TTACTATACAACATTGTTTCTCTTATTCAATTGCATGTAAACATAGTA
22685 T
1 T
22686 AGTGATTTAA
Statistics
Matches: 46, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
48 46 1.00
ACGTcount: A:0.31, C:0.15, G:0.09, T:0.44
Consensus pattern (48 bp):
TTACTATACAACATTGTTTCTCTTATTCAATTGCATGTAAACATAGTA
Found at i:25743 original size:35 final size:35
Alignment explanation
Indices: 25697--25882 Score: 169
Period size: 35 Copynumber: 4.9 Consensus size: 35
25687 AATGGTAATG
*
25697 GTAATGGTAAAGAGTAAAAAGTAATCAGTAAAATC
1 GTAATGGTAAAGAGTAAAAAGTAATCAGTAAAATA
25732 GTAATGGTAAAGAGTAAAGAA-TAATCAGTAAAAT-
1 GTAATGGTAAAGAGTAAA-AAGTAATCAGTAAAATA
* *
25766 GATAATGGTAAAGAGTAAAGAGTAATGAGTAAATTGGTAATA
1 G-TAATGGTAAAGAGTAAAAAGTAATCAGT-AA-----AATA
* *
25808 GTAATGATAAAGAGTAAATAGTAATCAGTAAATTGGTAATA
1 GTAATGGTAAAGAGTAAAAAGTAATCAGT-AA-----AATA
*
25849 GTAATTGGTAAAGAGTAAAGAGTAATCAGTAAAA
1 GTAA-TGGTAAAGAGTAAAAAGTAATCAGTAAAA
25883 ATGATACTTG
Statistics
Matches: 133, Mismatches: 7, Indels: 21
0.83 0.04 0.13
Matches are distributed among these distances:
34 2 0.02
35 55 0.41
36 6 0.05
41 46 0.35
42 24 0.18
ACGTcount: A:0.50, C:0.03, G:0.22, T:0.25
Consensus pattern (35 bp):
GTAATGGTAAAGAGTAAAAAGTAATCAGTAAAATA
Found at i:25820 original size:76 final size:71
Alignment explanation
Indices: 25693--25873 Score: 195
Period size: 76 Copynumber: 2.5 Consensus size: 71
25683 AAAAAATGGT
* * * *
25693 AATGGTAATGGTAAAGAGTAAAAAGTAATCAGT-AAAATCGTAATGGTAAAGAGTAAAGAATAAT
1 AATGGTAATGGTAAAGAGTAAAGAGTAATGAGTAAAAATAGTAATGATAAAGAGTAAAGAATAAT
25757 CAGTAA
66 CAGTAA
* *
25763 AATGATAATGGTAAAGAGTAAAGAGTAATGAGTAAATTGGTAATAGTAATGATAAAGAGTAAATA
1 AATGGTAATGGTAAAGAGTAAAGAGTAATGAGTAAA-----AATAGTAATGATAAAGAGTAAAGA
*
25828 GTAATCAGTAA
61 ATAATCAGTAA
* * * *
25839 ATTGGTAATAGTAATTG-GTAAAGAGTAAAGAGTAA
1 AATGGTAATGGTAA-AGAGTAAAGAGTAATGAGTAA
25874 TCAGTAAAAA
Statistics
Matches: 92, Mismatches: 12, Indels: 8
0.82 0.11 0.07
Matches are distributed among these distances:
70 30 0.33
71 2 0.02
76 59 0.64
77 1 0.01
ACGTcount: A:0.50, C:0.02, G:0.23, T:0.25
Consensus pattern (71 bp):
AATGGTAATGGTAAAGAGTAAAGAGTAATGAGTAAAAATAGTAATGATAAAGAGTAAAGAATAAT
CAGTAA
Found at i:25879 original size:14 final size:14
Alignment explanation
Indices: 25665--25881 Score: 71
Period size: 14 Copynumber: 15.5 Consensus size: 14
25655 TCAATTCAAA
*
25665 GAGTAAAGAATAAT
1 GAGTAAAGAGTAAT
*
25679 GAGTAAAAAATGGTAAT
1 GAGT-AAAGA--GTAAT
* *
25696 G-GTAATG-GTAAA
1 GAGTAAAGAGTAAT
*
25708 GAGTAAAAAGTAAT
1 GAGTAAAGAGTAAT
*
25722 CAGTAAA-ATCGTAAT
1 GAGTAAAGA--GTAAT
*
25737 G-GTAAAGAGTAAA
1 GAGTAAAGAGTAAT
* **
25750 GAATAATCAGTAAAAT
1 GAGTAAAGAGT--AAT
* *
25766 GA-TAATG-GTAAA
1 GAGTAAAGAGTAAT
25778 GAGTAAAGAGTAAT
1 GAGTAAAGAGTAAT
25792 GAGTAAATTG-GTAAT
1 GAGTAAA--GAGTAAT
* *
25807 -AGTAATGA-TAAA
1 GAGTAAAGAGTAAT
*
25819 GAGTAAATAGTAAT
1 GAGTAAAGAGTAAT
*
25833 CAGTAAATTG-GTAAT
1 GAGTAAA--GAGTAAT
* *
25848 -AGTAATTG-GTAAA
1 GAGTAA-AGAGTAAT
25861 GAGTAAAGAGTAAT
1 GAGTAAAGAGTAAT
*
25875 CAGTAAA
1 GAGTAAA
25882 AATGATACTT
Statistics
Matches: 149, Mismatches: 31, Indels: 46
0.66 0.14 0.20
Matches are distributed among these distances:
12 13 0.09
13 26 0.17
14 72 0.48
15 26 0.17
16 7 0.05
17 5 0.03
ACGTcount: A:0.50, C:0.02, G:0.23, T:0.25
Consensus pattern (14 bp):
GAGTAAAGAGTAAT
Found at i:25954 original size:36 final size:35
Alignment explanation
Indices: 25893--26080 Score: 115
Period size: 36 Copynumber: 5.3 Consensus size: 35
25883 ATGATACTTG
* *
25893 GTAATTAAAGTTTAAAAAAAAAGTAAAGATGGTATTTA
1 GTAATTTAAG-TT-AAAAAAGAGTAAA-ATGGTATTTA
* *
25931 GTAATTTAAGTTAAAAAAGAGTAAAAATGGTATCTG
1 GTAATTTAAGTTAAAAAAGAGT-AAAATGGTATTTA
25967 GTAA-TTAA---AAAAAA-AGTAAAGATGGTATTTA
1 GTAATTTAAGTTAAAAAAGAGTAAA-ATGGTATTTA
* * * *
25998 GTAA-TTAAGTTTAAAAAGGGGTAAAATTGATATTCA
1 GTAATTTAAG-TTAAAAAAGAGTAAAA-TGGTATTTA
* * * *
26034 GTAA--TCAG-TAAAGAAGAGTAAGAAAAGGGTAATTA
1 GTAATTTAAGTTAAAAAAGAGT---AAAATGGTATTTA
26069 GTAATTTAAGTT
1 GTAATTTAAGTT
26081 TAGAAAGTAA
Statistics
Matches: 117, Mismatches: 19, Indels: 28
0.71 0.12 0.17
Matches are distributed among these distances:
30 3 0.03
31 19 0.16
32 6 0.05
33 8 0.07
35 22 0.19
36 41 0.35
37 8 0.07
38 10 0.09
ACGTcount: A:0.49, C:0.02, G:0.19, T:0.30
Consensus pattern (35 bp):
GTAATTTAAGTTAAAAAAGAGTAAAATGGTATTTA
Found at i:25985 original size:31 final size:31
Alignment explanation
Indices: 25904--26005 Score: 132
Period size: 31 Copynumber: 3.1 Consensus size: 31
25894 TAATTAAAGT
25904 TTAAAAAAAAAGTAAAGATGGTATTTAGTAA
1 TTAAAAAAAAAGTAAAGATGGTATTTAGTAA
* * *
25935 TTTAAGTTAAAAAAGAGTAAAAATGGTATCTGGTAA
1 -TTAA---AAAAAA-AGTAAAGATGGTATTTAGTAA
25971 TTAAAAAAAAAGTAAAGATGGTATTTAGTAA
1 TTAAAAAAAAAGTAAAGATGGTATTTAGTAA
26002 TTAA
1 TTAA
26006 GTTTAAAAAG
Statistics
Matches: 60, Mismatches: 6, Indels: 9
0.80 0.08 0.12
Matches are distributed among these distances:
31 22 0.37
32 10 0.17
35 10 0.17
36 18 0.30
ACGTcount: A:0.52, C:0.01, G:0.17, T:0.30
Consensus pattern (31 bp):
TTAAAAAAAAAGTAAAGATGGTATTTAGTAA
Found at i:26038 original size:67 final size:67
Alignment explanation
Indices: 25904--26038 Score: 193
Period size: 67 Copynumber: 2.0 Consensus size: 67
25894 TAATTAAAGT
* *
25904 TTAAAAAAAAAGTAAAGATGGTATTTAGTAATTTAAGTTAAAAAAGAGTAAAAATGGTATCTGGT
1 TTAAAAAAAAAGTAAAGATGGTATTTAGTAATTTAAGTTAAAAAAGAGTAAAAATGATATCTAGT
25969 AA
66 AA
* * *
25971 TTAAAAAAAAAGTAAAGATGGTATTTAGTAA-TTAAGTTTAAAAAGGGGTAAAATTGATAT-TCA
1 TTAAAAAAAAAGTAAAGATGGTATTTAGTAATTTAAG-TTAAAAAAGAGTAAAAATGATATCT-A
26034 GTAA
64 GTAA
26038 T
1 T
26039 CAGTAAAGAA
Statistics
Matches: 61, Mismatches: 5, Indels: 4
0.87 0.07 0.06
Matches are distributed among these distances:
66 6 0.10
67 55 0.90
ACGTcount: A:0.50, C:0.01, G:0.18, T:0.31
Consensus pattern (67 bp):
TTAAAAAAAAAGTAAAGATGGTATTTAGTAATTTAAGTTAAAAAAGAGTAAAAATGATATCTAGT
AA
Found at i:26153 original size:33 final size:34
Alignment explanation
Indices: 26097--26398 Score: 159
Period size: 35 Copynumber: 8.5 Consensus size: 34
26087 GTAAAAAGGT
26097 AAAAAG-AAAATATGGTATTTAGTAATTTAAGTT-
1 AAAAAGTAAAA-ATGGTATTTAGTAATTTAAGTTA
* *
26130 AAACAGTAAAAATGGTATCTAGTAATTTAAGTTAA
1 AAAAAGTAAAAATGGTATTTAGTAATTTAAGTT-A
* * *
26165 AAAAAG-AGAAAACGGTATTTGGTAATTAAAGTTTA
1 AAAAAGTA-AAAATGGTATTTAGTAATTTAAG-TTA
* * *
26200 AAAGAGTAAAATTGGTATTTGGTAATTTAAGTTAA
1 AAAAAGTAAAAATGGTATTTAGTAATTTAAGTT-A
* *
26235 AAAAGAGTAAAATTCGTAAAAAGATATTTATTAA-TTAAGTTTA
1 AAAA-AGTAAAAAT-G------G-TATTTAGTAATTTAAG-TTA
* *
26278 AAAAGAGTAAAAATGGTATTTAGTAATTAAAG-GA
1 AAAA-AGTAAAAATGGTATTTAGTAATTTAAGTTA
* * * * *
26312 AAAATGGCAAAATTGGTATTCAGTAA--TCAGTTA
1 AAAA-AGTAAAAATGGTATTTAGTAATTTAAGTTA
* * * * *
26345 AAAGGAGTAAGAAAAGGGTAATTAATAACTTAAGTTA
1 AAA-AAGT-A-AAAATGGTATTTAGTAATTTAAGTTA
* *
26382 AAAAGGGAAAAATGGTA
1 AAAAAGTAAAAATGGTA
26399 ATCAGTAAGG
Statistics
Matches: 206, Mismatches: 39, Indels: 47
0.71 0.13 0.16
Matches are distributed among these distances:
32 2 0.01
33 31 0.15
34 38 0.18
35 76 0.37
36 18 0.09
37 10 0.05
42 1 0.00
43 20 0.10
44 10 0.05
ACGTcount: A:0.49, C:0.03, G:0.18, T:0.30
Consensus pattern (34 bp):
AAAAAGTAAAAATGGTATTTAGTAATTTAAGTTA
Found at i:26168 original size:28 final size:30
Alignment explanation
Indices: 26103--26169 Score: 82
Period size: 33 Copynumber: 2.2 Consensus size: 30
26093 AGGTAAAAAG
* *
26103 AAAATATGGTATTTAGTAATTTAAGTTAAAC
1 AAAAAATGGTATCTAGTAATTTAAGTT-AAC
26134 AGTAAAAATGGTATCTAGTAATTTAAGTTAA-
1 A--AAAAATGGTATCTAGTAATTTAAGTTAAC
26165 AAAAA
1 AAAAA
26170 GAGAAAACGG
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
29 4 0.12
31 2 0.06
32 2 0.06
33 24 0.75
ACGTcount: A:0.49, C:0.03, G:0.13, T:0.34
Consensus pattern (30 bp):
AAAAAATGGTATCTAGTAATTTAAGTTAAC
Found at i:26225 original size:70 final size:67
Alignment explanation
Indices: 26097--26246 Score: 185
Period size: 70 Copynumber: 2.2 Consensus size: 67
26087 GTAAAAAGGT
* *
26097 AAAAAGA-AAATATGGTATTTAGTAATTTAAGTTAAACAGTAAAAATGGTATCTAGTAATTTAAG
1 AAAAAGAGAAA-ACGGTATTTAGTAATTAAAGTTAAACAGTAAAAATGGTATCTAGTAATTTAAG
26161 TTAA
65 TT-A
* * * * *
26165 AAAAAGAGAAAACGGTATTTGGTAATTAAAGTTTAAAAGAGTAAAATTGGTATTTGGTAATTTAA
1 AAAAAGAGAAAACGGTATTTAGTAATTAAAG-TT-AAACAGTAAAAATGGTATCTAGTAATTTAA
26230 GTTA
64 GTTA
26234 AAAAAGAGTAAAA
1 AAAAAGAG-AAAA
26247 TTCGTAAAAA
Statistics
Matches: 71, Mismatches: 7, Indels: 6
0.85 0.08 0.07
Matches are distributed among these distances:
68 24 0.34
69 14 0.20
70 33 0.46
ACGTcount: A:0.49, C:0.02, G:0.17, T:0.31
Consensus pattern (67 bp):
AAAAAGAGAAAACGGTATTTAGTAATTAAAGTTAAACAGTAAAAATGGTATCTAGTAATTTAAGT
TA
Found at i:26246 original size:44 final size:43
Alignment explanation
Indices: 26198--26289 Score: 96
Period size: 43 Copynumber: 2.1 Consensus size: 43
26188 AATTAAAGTT
* * *
26198 TAAAA-GAGTAAAATTGGTATTTGGTAATTTAAGTTAAAAAAGAG
1 TAAAATGAGTAAAA-AGATATTTAGTAA-TTAAGTTAAAAAAGAG
** * *
26242 TAAAATTCGTAAAAAGATATTTATTAATTAAGTTTAAAAAGAG
1 TAAAATGAGTAAAAAGATATTTAGTAATTAAGTTAAAAAAGAG
26285 TAAAA
1 TAAAA
26290 ATGGTATTTA
Statistics
Matches: 40, Mismatches: 7, Indels: 3
0.80 0.14 0.06
Matches are distributed among these distances:
43 20 0.50
44 14 0.35
45 6 0.15
ACGTcount: A:0.51, C:0.01, G:0.15, T:0.33
Consensus pattern (43 bp):
TAAAATGAGTAAAAAGATATTTAGTAATTAAGTTAAAAAAGAG
Found at i:29043 original size:2 final size:2
Alignment explanation
Indices: 29038--29070 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
29028 CTTTCTTTGG
29038 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 T
29071 TGTTGCCTTA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:29861 original size:38 final size:39
Alignment explanation
Indices: 29772--29874 Score: 147
Period size: 39 Copynumber: 2.7 Consensus size: 39
29762 AATCAATTAA
* * * *
29772 TTTCCAAAATTTTTTTTTGGGA-TATCTTAAACTTTTATT
1 TTTCCAAAATCTTCTTTTGGAATTA-CCTAAACTTTTATT
29811 TTTCCAAAATCTTCTTTTGGAATTACCTAAACTTTTA-T
1 TTTCCAAAATCTTCTTTTGGAATTACCTAAACTTTTATT
29849 TTTCCAAAATCTTCTTTTGGAATTAC
1 TTTCCAAAATCTTCTTTTGGAATTAC
29875 TTAATTAAAA
Statistics
Matches: 59, Mismatches: 4, Indels: 3
0.89 0.06 0.05
Matches are distributed among these distances:
38 27 0.46
39 30 0.51
40 2 0.03
ACGTcount: A:0.27, C:0.16, G:0.07, T:0.50
Consensus pattern (39 bp):
TTTCCAAAATCTTCTTTTGGAATTACCTAAACTTTTATT
Found at i:36707 original size:13 final size:12
Alignment explanation
Indices: 36689--36733 Score: 54
Period size: 14 Copynumber: 3.5 Consensus size: 12
36679 ATTTTATTAC
36689 TGTTTTATTAAAT
1 TGTTTTA-TAAAT
36702 TGTTTTATAAAT
1 TGTTTTATAAAT
*
36714 GGTTTTAAATAAAT
1 TGTTTT--ATAAAT
36728 TGTTTT
1 TGTTTT
36734 GGGTGCATGA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
12 10 0.36
13 7 0.25
14 11 0.39
ACGTcount: A:0.31, C:0.00, G:0.11, T:0.58
Consensus pattern (12 bp):
TGTTTTATAAAT
Found at i:42131 original size:16 final size:15
Alignment explanation
Indices: 42093--42134 Score: 66
Period size: 15 Copynumber: 2.7 Consensus size: 15
42083 ACAGAGATTG
*
42093 ACAGAAAGCAATTAA
1 ACAGAAAACAATTAA
42108 ACAGAAAACAATTAA
1 ACAGAAAACAATTAA
42123 ACTAGAAAACAA
1 AC-AGAAAACAA
42135 AGCAAAGTAA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
15 16 0.64
16 9 0.36
ACGTcount: A:0.64, C:0.14, G:0.10, T:0.12
Consensus pattern (15 bp):
ACAGAAAACAATTAA
Found at i:42910 original size:11 final size:11
Alignment explanation
Indices: 42894--42919 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
42884 CCTTTGCCTA
42894 AAAACTAGAAG
1 AAAACTAGAAG
42905 AAAACTAGAAG
1 AAAACTAGAAG
42916 AAAA
1 AAAA
42920 GAAATTATCT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.69, C:0.08, G:0.15, T:0.08
Consensus pattern (11 bp):
AAAACTAGAAG
Found at i:44544 original size:22 final size:22
Alignment explanation
Indices: 44517--44558 Score: 84
Period size: 22 Copynumber: 1.9 Consensus size: 22
44507 TCAAGTTTCT
44517 GGGGGTACCCGGGGCTGGGTGG
1 GGGGGTACCCGGGGCTGGGTGG
44539 GGGGGTACCCGGGGCTGGGT
1 GGGGGTACCCGGGGCTGGGT
44559 AGCCTCAGAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.05, C:0.19, G:0.62, T:0.14
Consensus pattern (22 bp):
GGGGGTACCCGGGGCTGGGTGG
Found at i:46207 original size:6 final size:6
Alignment explanation
Indices: 46196--46240 Score: 63
Period size: 6 Copynumber: 7.0 Consensus size: 6
46186 AACAAAAGTC
46196 TAAAAA TAAAAA TAAAAA TAATAACAA TAAAAA TAAAAA TAAAAA
1 TAAAAA TAAAAA TAAAAA T-A-AA-AA TAAAAA TAAAAA TAAAAA
46241 ACTAAACTAA
Statistics
Matches: 36, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
6 27 0.75
7 3 0.08
8 3 0.08
9 3 0.08
ACGTcount: A:0.80, C:0.02, G:0.00, T:0.18
Consensus pattern (6 bp):
TAAAAA
Found at i:46218 original size:15 final size:15
Alignment explanation
Indices: 46200--46231 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
46190 AAAGTCTAAA
46200 AATAAAAATAAAAAT
1 AATAAAAATAAAAAT
*
46215 AATAACAATAAAAAT
1 AATAAAAATAAAAAT
46230 AA
1 AA
46232 AAATAAAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.78, C:0.03, G:0.00, T:0.19
Consensus pattern (15 bp):
AATAAAAATAAAAAT
Found at i:46478 original size:20 final size:20
Alignment explanation
Indices: 46453--46491 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
46443 ATAAACTATG
*
46453 AACTAAAATTAAAATAATTA
1 AACTAAAATGAAAATAATTA
*
46473 AACTAAAGTGAAAATAATT
1 AACTAAAATGAAAATAATT
46492 CAAATAAGAG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.62, C:0.05, G:0.05, T:0.28
Consensus pattern (20 bp):
AACTAAAATGAAAATAATTA
Found at i:53435 original size:14 final size:14
Alignment explanation
Indices: 53415--53446 Score: 55
Period size: 14 Copynumber: 2.2 Consensus size: 14
53405 ATTATGCTTA
53415 AAAAAAACACAAAAC
1 AAAAAAA-ACAAAAC
53430 AAAAAAAACAAAAC
1 AAAAAAAACAAAAC
53444 AAA
1 AAA
53447 CTCAGCCTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 10 0.59
15 7 0.41
ACGTcount: A:0.84, C:0.16, G:0.00, T:0.00
Consensus pattern (14 bp):
AAAAAAAACAAAAC
Found at i:53968 original size:83 final size:84
Alignment explanation
Indices: 53822--53987 Score: 289
Period size: 83 Copynumber: 2.0 Consensus size: 84
53812 ATCTCTTCAG
53822 CATCTTTTTGTTAGTATATATATATATATATATATATTAATTTCCCTGTTATATAAGTGTATCTC
1 CATCTTTTTGTTAG-ATATATATATATATATATATATTAATTTCCCTGTTATATAAGTGTATCTC
53887 TTTCCTATTTGTACATGCAA
65 TTTCCTATTTGTACATGCAA
* * *
53907 CATCTTTTTGTTAG-TGTATATATATATATATATATTAATTTCCTTGTTATATAAGTTTATCTCT
1 CATCTTTTTGTTAGATATATATATATATATATATATTAATTTCCCTGTTATATAAGTGTATCTCT
53971 TTCCTATTTGTACATGC
66 TTCCTATTTGTACATGC
53988 TTCTTTATTA
Statistics
Matches: 78, Mismatches: 3, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
83 64 0.82
85 14 0.18
ACGTcount: A:0.28, C:0.13, G:0.08, T:0.51
Consensus pattern (84 bp):
CATCTTTTTGTTAGATATATATATATATATATATATTAATTTCCCTGTTATATAAGTGTATCTCT
TTCCTATTTGTACATGCAA
Found at i:54933 original size:48 final size:48
Alignment explanation
Indices: 54862--54958 Score: 158
Period size: 48 Copynumber: 2.0 Consensus size: 48
54852 AGGACCTGTT
54862 TTACTATACAACATTGTTTCTCTTATTCAATTACATGTAAAGATAGTA
1 TTACTATACAACATTGTTTCTCTTATTCAATTACATGTAAAGATAGTA
* * * *
54910 TTACTATACATCATTGTTTCTCTTATTCGATTGCATGTAAAGGTAGTA
1 TTACTATACAACATTGTTTCTCTTATTCAATTACATGTAAAGATAGTA
54958 T
1 T
54959 AGTGATTTAA
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
48 45 1.00
ACGTcount: A:0.31, C:0.14, G:0.11, T:0.43
Consensus pattern (48 bp):
TTACTATACAACATTGTTTCTCTTATTCAATTACATGTAAAGATAGTA
Found at i:58330 original size:41 final size:40
Alignment explanation
Indices: 58286--58488 Score: 194
Period size: 41 Copynumber: 5.2 Consensus size: 40
58276 AATTCAATTC
* *
58286 AAAGAGTACAGAATAATGAGTAAAATGGTAATGGTAATGG
1 AAAGAGTAAAGAATAATCAGTAAAATGGTAATGGTAATGG
*
58326 CAAAGAGTAAA-AAGTAATCAGTAAAATGGTACTGG---T--
1 -AAAGAGTAAAGAA-TAATCAGTAAAATGGTAATGGTAATGG
*
58362 AAAGAGTAAAGAATAATCAGTAAAATGATAATGG---T-G
1 AAAGAGTAAAGAATAATCAGTAAAATGGTAATGGTAATGG
* * *
58398 -AAGAGTAAAGAGTAATCAGTAAATTGGTAATAGTAATGG
1 AAAGAGTAAAGAATAATCAGTAAAATGGTAATGGTAATGG
* * *
58437 TAAAGAGTAAAGAGTAATCAGTAAATTGGTAATAGTAATCGG
1 -AAAGAGTAAAGAATAATCAGTAAAATGGTAATGGTAAT-GG
58479 TAAAGAGTAA
1 -AAAGAGTAA
58489 TCAGTAAAAA
Statistics
Matches: 143, Mismatches: 9, Indels: 19
0.84 0.05 0.11
Matches are distributed among these distances:
35 59 0.41
36 2 0.01
38 2 0.01
39 1 0.01
40 2 0.01
41 65 0.45
42 12 0.08
ACGTcount: A:0.48, C:0.04, G:0.24, T:0.24
Consensus pattern (40 bp):
AAAGAGTAAAGAATAATCAGTAAAATGGTAATGGTAATGG
Found at i:58354 original size:35 final size:35
Alignment explanation
Indices: 58315--58497 Score: 206
Period size: 35 Copynumber: 5.1 Consensus size: 35
58305 GTAAAATGGT
* *
58315 AATGGTAATGGCAAAGAGTAAAAAGTAATCAGTAA
1 AATGGTAATGGTAAAGAGTAAAGAGTAATCAGTAA
* *
58350 AATGGTACTGGTAAAGAGTAAAGAATAATCAGTAA
1 AATGGTAATGGTAAAGAGTAAAGAGTAATCAGTAA
* *
58385 AATGATAATGGTGAAGAGTAAAGAGTAATCAGTAAA
1 AATGGTAATGGTAAAGAGTAAAGAGTAATCAGT-AA
*
58421 TTGGTAATAGTAATGGTAAAGAGTAAAGAGTAATCAGTAA
1 -----AATGGTAATGGTAAAGAGTAAAGAGTAATCAGTAA
* * *
58461 ATTGGTAATAGTAATCG-GTAAAGAGTAATCAGTAA
1 AATGGTAATGGTAA-AGAGTAAAGAGTAATCAGTAA
58496 AA
1 AA
58498 ATGATACTTG
Statistics
Matches: 125, Mismatches: 16, Indels: 14
0.81 0.10 0.09
Matches are distributed among these distances:
35 90 0.72
36 3 0.02
40 2 0.02
41 30 0.24
ACGTcount: A:0.48, C:0.04, G:0.23, T:0.24
Consensus pattern (35 bp):
AATGGTAATGGTAAAGAGTAAAGAGTAATCAGTAA
Found at i:58394 original size:76 final size:75
Alignment explanation
Indices: 58286--58488 Score: 230
Period size: 76 Copynumber: 2.7 Consensus size: 75
58276 AATTCAATTC
* * *
58286 AAAGAGTACAGAATAATGAGTAAAATGGTAATGGTAATGGCAAAGAGTAAAAAGT-AATCAGTAA
1 AAAGAGTAAAGAATAATCAGTAAAATGGTAATGGTAATGGTAAAGAGTAAAAAGTAAATCAGT--
* *
58350 AATGGTACTGGT
64 AATAGTAATGGT
* ** **
58362 AAAGAGTAAAGAATAATCAGTAAAATGATAATGGTGAA-GAGTAAAGAGTAATCAGTAAATTGGT
1 AAAGAGTAAAGAATAATCAGTAAAATGGTAATGGT-AATG-GTAAAGAGTAAAAAGTAAATCAGT
58426 AATAGTAATGGT
64 AATAGTAATGGT
* * *
58438 AAAGAGTAAAGAGTAATCAGTAAATTGGTAATAGTAATCGGTAAAGAGTAA
1 AAAGAGTAAAGAATAATCAGTAAAATGGTAATGGTAAT-GGTAAAGAGTAA
58489 TCAGTAAAAA
Statistics
Matches: 108, Mismatches: 14, Indels: 10
0.82 0.11 0.08
Matches are distributed among these distances:
75 2 0.02
76 85 0.79
77 16 0.15
78 5 0.05
ACGTcount: A:0.48, C:0.04, G:0.24, T:0.24
Consensus pattern (75 bp):
AAAGAGTAAAGAATAATCAGTAAAATGGTAATGGTAATGGTAAAGAGTAAAAAGTAAATCAGTAA
TAGTAATGGT
Found at i:58420 original size:14 final size:13
Alignment explanation
Indices: 58401--58474 Score: 53
Period size: 14 Copynumber: 5.4 Consensus size: 13
58391 AATGGTGAAG
58401 AGTAAAGAGTAATC
1 AGTAAAG-GTAATC
58415 AGTAAATTGGTAAT-
1 AGTAAA--GGTAATC
* **
58429 AGTAATGGTAAAG
1 AGTAAAGGTAATC
58442 AGTAAAGAGTAATC
1 AGTAAAG-GTAATC
58456 AGTAAATTGGTAAT-
1 AGTAAA--GGTAATC
58470 AGTAA
1 AGTAA
58475 TCGGTAAAGA
Statistics
Matches: 49, Mismatches: 5, Indels: 12
0.74 0.08 0.18
Matches are distributed among these distances:
12 5 0.10
13 6 0.12
14 26 0.53
15 10 0.20
16 2 0.04
ACGTcount: A:0.47, C:0.03, G:0.23, T:0.27
Consensus pattern (13 bp):
AGTAAAGGTAATC
Found at i:58420 original size:111 final size:112
Alignment explanation
Indices: 58287--58503 Score: 303
Period size: 111 Copynumber: 1.9 Consensus size: 112
58277 ATTCAATTCA
* * *
58287 AAGAGTACAGAATAATGAGTAAAATGGTAATGGTAATGGCAAAGAGTAAAAAGTAATCAGTAAAA
1 AAGAGTAAAGAATAATCAGTAAAATGGTAATAGTAATGGCAAAGAGTAAAAAGTAATCAGTAAAA
* *
58352 TGGTACTGGTAA-AGAGTAAAGAATAATCAGT-AAAATGATAATGGTG
66 TGGTAATAGTAATAG-GTAAAGAATAATCAGTAAAAATGATAATGGTG
* * * * *
58398 AAGAGTAAAGAGTAATCAGTAAATTGGTAATAGTAATGGTAAAGAGTAAAGAGTAATCAGTAAAT
1 AAGAGTAAAGAATAATCAGTAAAATGGTAATAGTAATGGCAAAGAGTAAAAAGTAATCAGTAAAA
* *
58463 TGGTAATAGTAATCGGTAAAGAGTAATCAGTAAAAATGATA
66 TGGTAATAGTAATAGGTAAAGAATAATCAGTAAAAATGATA
58504 CTTGGTAACT
Statistics
Matches: 92, Mismatches: 12, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
111 82 0.89
112 10 0.11
ACGTcount: A:0.48, C:0.04, G:0.24, T:0.24
Consensus pattern (112 bp):
AAGAGTAAAGAATAATCAGTAAAATGGTAATAGTAATGGCAAAGAGTAAAAAGTAATCAGTAAAA
TGGTAATAGTAATAGGTAAAGAATAATCAGTAAAAATGATAATGGTG
Found at i:58473 original size:21 final size:21
Alignment explanation
Indices: 58408--58482 Score: 84
Period size: 21 Copynumber: 3.6 Consensus size: 21
58398 AAGAGTAAAG
58408 AGTAATCAGTAAATTGGTAAT
1 AGTAATCAGTAAATTGGTAAT
* *
58429 AGTAAT-GGTAAA--GAGTAAAG
1 AGTAATCAGTAAATTG-GT-AAT
58449 AGTAATCAGTAAATTGGTAAT
1 AGTAATCAGTAAATTGGTAAT
*
58470 AGTAATCGGTAAA
1 AGTAATCAGTAAA
58483 GAGTAATCAG
Statistics
Matches: 44, Mismatches: 5, Indels: 10
0.75 0.08 0.17
Matches are distributed among these distances:
18 1 0.02
19 2 0.05
20 13 0.30
21 25 0.57
22 2 0.05
23 1 0.02
ACGTcount: A:0.45, C:0.04, G:0.23, T:0.28
Consensus pattern (21 bp):
AGTAATCAGTAAATTGGTAAT
Found at i:58576 original size:36 final size:36
Alignment explanation
Indices: 58522--59024 Score: 256
Period size: 35 Copynumber: 13.8 Consensus size: 36
58512 CTAAAGTTAA
* * *
58522 AAAAAAAATTAAAGATGGTATTTAGTAATTTAAGTT
1 AAAAAAGAGTAAAAATGGTATTTAGTAATTTAAGTT
* *
58558 AAAAAAGAGTAAAAATGGTATCTGGTAA-TTAA---
1 AAAAAAGAGTAAAAATGGTATTTAGTAATTTAAGTT
* *
58590 AAAAAAAAGTAAAGATGGTATTTAGTAA-TTAAGTTT
1 AAAAAAGAGTAAAAATGGTATTTAGTAATTTAAG-TT
* * * * * *
58626 AAAAAGGGGTAAAATTGATATTCAGTAA--TCAG-T
1 AAAAAAGAGTAAAAATGGTATTTAGTAATTTAAGTT
* * *
58659 AAAGAAGAGTAAGAAAAGGGTAATTAGTAATTTAAGTTT
1 AAAAAAGAGT-A-AAAATGGTATTTAGTAATTTAAG-TT
* * *** * *
58698 AGAAAGTAAAAAGGTAAAAA--GAAAAAAGGTATTTAGTAATTT
1 --AAA--AAAGA-GTAAAAATGGTATTTA-GTAATT--TAAGTT
* * * * *
58740 AAGTTAAAAAGTAAAAATGGTATCTAGTAA-TAAAGGT
1 AA--AAAAGAGTAAAAATGGTATTTAGTAATTTAAGTT
*
58777 -AAAAAGA--AAAAATGGTATTTGGTAATTTAAGTT
1 AAAAAAGAGTAAAAATGGTATTTAGTAATTTAAGTT
*
58810 --AAAA-AGTAAAAATGGTATCTAGTAATTTAAGTT
1 AAAAAAGAGTAAAAATGGTATTTAGTAATTTAAGTT
* * *
58843 AAAAAAAAGAGTAAAAACGGTATTTTGGTAATTAAAGTT
1 --AAAAAAGAGTAAAAATGGTA-TTTAGTAATTTAAGTT
* * *
58882 -AAAAAGAGTAAAATTGGTATTTGGTAATTAAAGTT
1 AAAAAAGAGTAAAAATGGTATTTAGTAATTTAAGTT
* * *
58917 -AAAAAGAGTAAAATTGGTATTTGGCAATTTAAGTT
1 AAAAAAGAGTAAAAATGGTATTTAGTAATTTAAGTT
*
58952 AAAAAAGATTAGAATTGGTAAAAA-GATATTTAGTAA-TTAAGTT
1 --AAAA-A--AG-A---GTAAAAATGGTATTTAGTAATTTAAGTT
*
58995 TAAAAAGAGTAAAAATGGTATTTAGTAATT
1 AAAAAAGAGTAAAAATGGTATTTAGTAATT
59025 AAAGGAAAAA
Statistics
Matches: 360, Mismatches: 64, Indels: 86
0.71 0.13 0.17
Matches are distributed among these distances:
31 1 0.00
32 48 0.13
33 37 0.10
34 12 0.03
35 79 0.22
36 63 0.17
37 11 0.03
38 17 0.05
39 23 0.06
40 15 0.04
41 16 0.04
42 7 0.02
43 14 0.04
44 11 0.03
45 6 0.02
ACGTcount: A:0.50, C:0.01, G:0.18, T:0.31
Consensus pattern (36 bp):
AAAAAAGAGTAAAAATGGTATTTAGTAATTTAAGTT
Found at i:58601 original size:32 final size:32
Alignment explanation
Indices: 58518--58621 Score: 127
Period size: 32 Copynumber: 3.1 Consensus size: 32
58508 GTAACTAAAG
*
58518 TTAAAAAAAAAATTAAAGATGGTATTTAGTAA
1 TTAAAAAAAAAAGTAAAGATGGTATTTAGTAA
* * * *
58550 TTTAAGTTAAAAAAGAGTAAAAATGGTATCTGGTAA
1 -TTAA---AAAAAAAAGTAAAGATGGTATTTAGTAA
58586 TTAAAAAAAAAAGTAAAGATGGTATTTAGTAA
1 TTAAAAAAAAAAGTAAAGATGGTATTTAGTAA
58618 TTAA
1 TTAA
58622 GTTTAAAAAG
Statistics
Matches: 59, Mismatches: 9, Indels: 7
0.79 0.12 0.09
Matches are distributed among these distances:
32 28 0.47
33 4 0.07
35 4 0.07
36 23 0.39
ACGTcount: A:0.53, C:0.01, G:0.15, T:0.31
Consensus pattern (32 bp):
TTAAAAAAAAAAGTAAAGATGGTATTTAGTAA
Found at i:58654 original size:68 final size:68
Alignment explanation
Indices: 58518--58654 Score: 188
Period size: 68 Copynumber: 2.0 Consensus size: 68
58508 GTAACTAAAG
* * *
58518 TTAAAAAAAAAATTAAAGATGGTATTTAGTAATTTAAGTTAAAAAAGAGTAAAAATGGTATCTGG
1 TTAAAAAAAAAAGTAAAGATGGTATTTAGTAATTTAAGTTAAAAAAGAGTAAAAATGATATCTAG
58583 TAA
66 TAA
* * *
58586 TTAAAAAAAAAAGTAAAGATGGTATTTAGTAA-TTAAGTTTAAAAAGGGGTAAAATTGATAT-TC
1 TTAAAAAAAAAAGTAAAGATGGTATTTAGTAATTTAAG-TTAAAAAAGAGTAAAAATGATATCT-
58649 AGTAA
64 AGTAA
58654 T
1 T
58655 CAGTAAAGAA
Statistics
Matches: 61, Mismatches: 6, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
67 6 0.10
68 55 0.90
ACGTcount: A:0.50, C:0.01, G:0.17, T:0.31
Consensus pattern (68 bp):
TTAAAAAAAAAAGTAAAGATGGTATTTAGTAATTTAAGTTAAAAAAGAGTAAAAATGATATCTAG
TAA
Found at i:58762 original size:33 final size:33
Alignment explanation
Indices: 58712--58956 Score: 251
Period size: 33 Copynumber: 7.2 Consensus size: 33
58702 AGTAAAAAGG
* *
58712 TAAAAAG-AAAAAAGGTATTTAGTAATTTAAGT
1 TAAAAAGTAAAAATGGTATTTGGTAATTTAAGT
* * * *
58744 TAAAAAGTAAAAATGGTATCTAGTAA-TAAAGG
1 TAAAAAGTAAAAATGGTATTTGGTAATTTAAGT
*
58776 TAAAAAGAAAAAATGGTATTTGGTAATTTAAGT
1 TAAAAAGTAAAAATGGTATTTGGTAATTTAAGT
* *
58809 TAAAAAGTAAAAATGGTATCTAGTAATTTAAGT
1 TAAAAAGTAAAAATGGTATTTGGTAATTTAAGT
* *
58842 TAAAAAAAAGAGTAAAAACGGTATTTTGGTAATTAAAGT
1 T----AAAA-AGTAAAAATGGTA-TTTGGTAATTTAAGT
* *
58881 TAAAAAGAGTAAAATTGGTATTTGGTAATTAAAGT
1 T-AAAA-AGTAAAAATGGTATTTGGTAATTTAAGT
* *
58916 TAAAAAGAGTAAAATTGGTATTTGGCAATTTAAGT
1 T-AAAA-AGTAAAAATGGTATTTGGTAATTTAAGT
58951 TAAAAA
1 TAAAAA
58957 AGATTAGAAT
Statistics
Matches: 185, Mismatches: 20, Indels: 15
0.84 0.09 0.07
Matches are distributed among these distances:
32 34 0.18
33 52 0.28
34 4 0.02
35 49 0.26
36 17 0.09
37 4 0.02
38 12 0.06
39 13 0.07
ACGTcount: A:0.50, C:0.02, G:0.18, T:0.31
Consensus pattern (33 bp):
TAAAAAGTAAAAATGGTATTTGGTAATTTAAGT
Found at i:58912 original size:35 final size:35
Alignment explanation
Indices: 58707--59028 Score: 272
Period size: 35 Copynumber: 9.1 Consensus size: 35
58697 TAGAAAGTAA
*
58707 AAAGGTAAAAAGA--AAAAA-GGTATTTAGTAATT
1 AAAGTTAAAAAGAGTAAAAATGGTATTTAGTAATT
* *
58739 TAAGTT-AAAA-AGTAAAAATGGTATCTAGTAA-T
1 AAAGTTAAAAAGAGTAAAAATGGTATTTAGTAATT
* *
58771 AAAGGTAAAAAGA--AAAAATGGTATTTGGTAATT
1 AAAGTTAAAAAGAGTAAAAATGGTATTTAGTAATT
* *
58804 TAAGTT-AAAA-AGTAAAAATGGTATCTAGTAATT
1 AAAGTTAAAAAGAGTAAAAATGGTATTTAGTAATT
* * *
58837 TAAGTTAAAAAAAAGAGTAAAAACGGTATTTTGGTAATT
1 AAAGTT---AAAAAGAGTAAAAATGGTA-TTTAGTAATT
* *
58876 AAAGTTAAAAAGAGTAAAATTGGTATTTGGTAATT
1 AAAGTTAAAAAGAGTAAAAATGGTATTTAGTAATT
* * *
58911 AAAGTTAAAAAGAGTAAAATTGGTATTTGGCAATT
1 AAAGTTAAAAAGAGTAAAAATGGTATTTAGTAATT
* *
58946 TAAGTTAAAAAAGATTAGAATTGGTAAAAA-GATATTTAGTAATT
1 AAAGTT---AAA-A--AG-A---GTAAAAATGGTATTTAGTAATT
58990 -AAGTTTAAAAAGAGTAAAAATGGTATTTAGTAATT
1 AAAG-TTAAAAAGAGTAAAAATGGTATTTAGTAATT
59025 AAAG
1 AAAG
59029 GAAAAATGGC
Statistics
Matches: 239, Mismatches: 24, Indels: 50
0.76 0.08 0.16
Matches are distributed among these distances:
30 1 0.00
31 5 0.02
32 34 0.14
33 44 0.18
34 8 0.03
35 62 0.26
36 20 0.08
37 5 0.02
38 17 0.07
39 14 0.06
40 1 0.00
41 5 0.02
42 1 0.00
43 3 0.01
44 13 0.05
45 6 0.03
ACGTcount: A:0.50, C:0.01, G:0.18, T:0.31
Consensus pattern (35 bp):
AAAGTTAAAAAGAGTAAAAATGGTATTTAGTAATT
Found at i:58971 original size:71 final size:68
Alignment explanation
Indices: 58707--58956 Score: 305
Period size: 65 Copynumber: 3.7 Consensus size: 68
58697 TAGAAAGTAA
* *
58707 AAAGGTAAAAAGA--AAAAA-GGTATTTAGTAATTTAAGTTAAAAAGTAAAAATGGTATCTAGTA
1 AAAGTTAAAAAGAGTAAAAATGGTATTTGGTAATTTAAGTTAAAAAGTAAAAATGGTATCTAGTA
58769 A-T
66 ATT
*
58771 AAAGGTAAAAAGA--AAAAATGGTATTTGGTAATTTAAGTTAAAAAGTAAAAATGGTATCTAGTA
1 AAAGTTAAAAAGAGTAAAAATGGTATTTGGTAATTTAAGTTAAAAAGTAAAAATGGTATCTAGTA
58834 ATT
66 ATT
* * * *
58837 TAAGTTAAAAAAAAGAGTAAAAACGGTATTTTGGTAATTAAAGTTAAAAAGAGTAAAATTGGTAT
1 AAAGTT---AAAAAGAGTAAAAATGGTA-TTTGGTAATTTAAGTT-AAAA-AGTAAAAATGGTAT
* *
58902 TTGGTAATT
60 CTAGTAATT
* *
58911 AAAGTTAAAAAGAGTAAAATTGGTATTTGGCAATTTAAGTTAAAAA
1 AAAGTTAAAAAGAGTAAAAATGGTATTTGGTAATTTAAGTTAAAAA
58957 AGATTAGAAT
Statistics
Matches: 163, Mismatches: 13, Indels: 16
0.85 0.07 0.08
Matches are distributed among these distances:
64 18 0.11
65 44 0.27
66 5 0.03
68 1 0.01
69 11 0.07
70 14 0.09
71 26 0.16
72 15 0.09
73 4 0.02
74 25 0.15
ACGTcount: A:0.50, C:0.02, G:0.18, T:0.30
Consensus pattern (68 bp):
AAAGTTAAAAAGAGTAAAAATGGTATTTGGTAATTTAAGTTAAAAAGTAAAAATGGTATCTAGTA
ATT
Found at i:59017 original size:114 final size:107
Alignment explanation
Indices: 58725--59050 Score: 325
Period size: 114 Copynumber: 3.1 Consensus size: 107
58715 AAAGAAAAAA
* * * * *
58725 GGTATTTAGTAATTTAAGTT----AAAA-AGTAAAAATGGTATCTAGTAATAAAGGTAAAAAGA-
1 GGTATTTAGCAATTTAAGTTAAAAAAAAGAGTAAAAACGGTATTTAGTAATTAAGTTAAAAAGAG
* *
58784 -AAAAATGGTATTTGGTAATTTAAGTT-AAAA-AGTAAAAAT
66 TAAAAATGGTATTTGGTAATTAAAGTTAAAAAGAGTAAAATT
* * *
58823 GGTATCTAGTAATTTAAGTTAAAAAAAAGAGTAAAAACGGTATTTTGGTAATTAAAGTTAAAAAG
1 GGTATTTAGCAATTTAAGTTAAAAAAAAGAGTAAAAACGGTA-TTTAGTAATT-AAGTTAAAAAG
*
58888 AGTAAAATTGGTATTTGGTAATTAAAGTTAAAAAGAGTAAAATT
64 AGTAAAAATGGTATTTGGTAATTAAAGTTAAAAAGAGTAAAATT
* *
58932 GGTATTTGGCAATTTAAGTTAAAAAAGATTAGAATTGGTAAAAA-GATATTTAGTAATTAAGTTT
1 GGTATTTAGCAATTTAAGTTAAAAAA-A--AG-A---GTAAAAACGGTATTTAGTAATTAAG-TT
* * *
58996 AAAAAGAGTAAAAATGGTATTTAGTAATTAAAG-GAAAAATG-GCAAAATT
58 AAAAAGAGTAAAAATGGTATTTGGTAATTAAAGTTAAAAA-GAGTAAAATT
59045 GGTATT
1 GGTATT
59051 CAGTAATCAG
Statistics
Matches: 190, Mismatches: 18, Indels: 25
0.82 0.08 0.11
Matches are distributed among these distances:
98 19 0.10
102 4 0.02
103 12 0.06
104 7 0.04
105 11 0.06
107 24 0.13
108 4 0.02
109 31 0.16
110 1 0.01
112 2 0.01
113 22 0.12
114 43 0.23
115 3 0.02
116 7 0.04
ACGTcount: A:0.48, C:0.02, G:0.18, T:0.32
Consensus pattern (107 bp):
GGTATTTAGCAATTTAAGTTAAAAAAAAGAGTAAAAACGGTATTTAGTAATTAAGTTAAAAAGAG
TAAAAATGGTATTTGGTAATTAAAGTTAAAAAGAGTAAAATT
Found at i:59034 original size:34 final size:34
Alignment explanation
Indices: 58967--59057 Score: 89
Period size: 34 Copynumber: 2.7 Consensus size: 34
58957 AGATTAGAAT
* *
58967 TGGTAAAAA-GATATTTAGTAATTAAGTTTAAAAA
1 TGGTAAAAATGGTATTTAGTAATTAAG-TGAAAAA
59001 -GAGTAAAAATGGTATTTAGTAATTAAAG-GAAAAA
1 TG-GTAAAAATGGTATTTAGTAATT-AAGTGAAAAA
* * *
59035 TGGCAAAATTGGTATTCAGTAAT
1 TGGTAAAAATGGTATTTAGTAAT
59058 CAGTAAAAAG
Statistics
Matches: 48, Mismatches: 5, Indels: 8
0.79 0.08 0.13
Matches are distributed among these distances:
33 1 0.02
34 30 0.62
35 14 0.29
36 3 0.06
ACGTcount: A:0.47, C:0.02, G:0.19, T:0.32
Consensus pattern (34 bp):
TGGTAAAAATGGTATTTAGTAATTAAGTGAAAAA
Found at i:59719 original size:1 final size:1
Alignment explanation
Indices: 59713--59739 Score: 54
Period size: 1 Copynumber: 27.0 Consensus size: 1
59703 GAAAACTTAT
59713 AAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAA
59740 CTGGATGGGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 26 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:59799 original size:40 final size:39
Alignment explanation
Indices: 59735--59822 Score: 140
Period size: 40 Copynumber: 2.2 Consensus size: 39
59725 AAAAAAAAAA
*
59735 AAAAACTGGATGGGATCTTACCCTAAATTGAAAACTTTG
1 AAAAACTTGATGGGATCTTACCCTAAATTGAAAACTTTG
* *
59774 CAAAATCTTGATGGGATCTTTCCCTAAATTGAAAACTTTG
1 -AAAAACTTGATGGGATCTTACCCTAAATTGAAAACTTTG
59814 AAAAACTTG
1 AAAAACTTG
59823 GATTGAATAC
Statistics
Matches: 44, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
39 8 0.18
40 36 0.82
ACGTcount: A:0.38, C:0.16, G:0.16, T:0.31
Consensus pattern (39 bp):
AAAAACTTGATGGGATCTTACCCTAAATTGAAAACTTTG
Found at i:59834 original size:23 final size:22
Alignment explanation
Indices: 59801--59844 Score: 70
Period size: 23 Copynumber: 2.0 Consensus size: 22
59791 CTTTCCCTAA
59801 ATTGAAAACTTTGAAAAACTTGG
1 ATTGAAAACTTTG-AAAACTTGG
*
59824 ATTGAATACTTTGAAAACTTG
1 ATTGAAAACTTTGAAAACTTG
59845 ACGGGATCTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
22 8 0.40
23 12 0.60
ACGTcount: A:0.41, C:0.09, G:0.16, T:0.34
Consensus pattern (22 bp):
ATTGAAAACTTTGAAAACTTGG
Found at i:62977 original size:14 final size:14
Alignment explanation
Indices: 62958--62986 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
62948 TTGCCACGCC
62958 ATTTACTTGTTGAA
1 ATTTACTTGTTGAA
62972 ATTTACTTGTTGAA
1 ATTTACTTGTTGAA
62986 A
1 A
62987 CATCTTCTTG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.31, C:0.07, G:0.14, T:0.48
Consensus pattern (14 bp):
ATTTACTTGTTGAA
Found at i:63954 original size:2 final size:2
Alignment explanation
Indices: 63941--63974 Score: 59
Period size: 2 Copynumber: 16.5 Consensus size: 2
63931 ACTAAAAATA
63941 AT AT AT AGT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT A
63975 AGCTTGAGAG
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 29 0.94
3 2 0.06
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (2 bp):
AT
Found at i:66626 original size:2 final size:2
Alignment explanation
Indices: 66619--66648 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
66609 TTGGCCCCTA
66619 AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
66649 ATTTATACAC
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:67437 original size:3 final size:3
Alignment explanation
Indices: 67429--67502 Score: 139
Period size: 3 Copynumber: 24.3 Consensus size: 3
67419 GCATCTCTAA
67429 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
67477 TAT TAT TAT TAT TAT TAT TAT ATAT T
1 TAT TAT TAT TAT TAT TAT TAT -TAT T
67503 TTTCTTCTTG
Statistics
Matches: 70, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
3 67 0.96
4 3 0.04
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:70205 original size:131 final size:123
Alignment explanation
Indices: 69954--70208 Score: 368
Period size: 131 Copynumber: 2.0 Consensus size: 123
69944 CATTGTTTAA
* * * *
69954 ACTTTTATAGTTTTACTCAACTAAAAATTCTATTTTTATTTAATTAAATCTAATATCTTTATAAT
1 ACTTTTACAGTTTTACTCAACTAAAAACTCTATTTCTATTTAATTAAATCCAATATCTTTATAAT
70019 TTTTACCATTTTACTATTTTAATTAAAAAACTTATATATATTAGAATTTTTTAAATAT
66 TTTTACCATTTTACTATTTTAATTAAAAAACTTATATATATTAGAATTTTTTAAATAT
* *
70077 ACTTTTACAGTTTTACTCAACT-AAAACTCTATTTCTATTTATTTAATTCCAATATCCTTATACC
1 ACTTTTACAGTTTTACTCAACTAAAAACTCTATTTCTATTTAATTAAATCCAATAT-CTT-TA--
70141 TATTTTATTTTTACCATTTTACTATTTTAATTAAAAAAACTTATATATATTAGAATTTTTTAAAT
62 TA----ATTTTTACCATTTTACTATTTTAATT-AAAAAACTTATATATATTAGAATTTTTTAAAT
70206 AT
122 AT
70208 A
1 A
70209 TTCACTACTA
Statistics
Matches: 117, Mismatches: 6, Indels: 10
0.88 0.05 0.08
Matches are distributed among these distances:
122 28 0.24
123 24 0.21
124 2 0.02
126 2 0.02
130 26 0.22
131 35 0.30
ACGTcount: A:0.37, C:0.11, G:0.02, T:0.50
Consensus pattern (123 bp):
ACTTTTACAGTTTTACTCAACTAAAAACTCTATTTCTATTTAATTAAATCCAATATCTTTATAAT
TTTTACCATTTTACTATTTTAATTAAAAAACTTATATATATTAGAATTTTTTAAATAT
Found at i:74052 original size:27 final size:27
Alignment explanation
Indices: 74022--74081 Score: 104
Period size: 27 Copynumber: 2.3 Consensus size: 27
74012 CTTATATTTC
*
74022 ATATGAATGTAATTTCTTTTGTAGTTA
1 ATATGAATGTAATTTCTTTTGTAATTA
74049 ATATGAATGTAATTTCTTTTGTAATTA
1 ATATGAATGTAATTTCTTTTGTAATTA
74076 A-ATGAA
1 ATATGAA
74082 ATTTTATGAA
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
26 5 0.16
27 27 0.84
ACGTcount: A:0.35, C:0.03, G:0.13, T:0.48
Consensus pattern (27 bp):
ATATGAATGTAATTTCTTTTGTAATTA
Found at i:74115 original size:12 final size:12
Alignment explanation
Indices: 74098--74132 Score: 61
Period size: 12 Copynumber: 2.9 Consensus size: 12
74088 TGAAAAAAGA
*
74098 AGCTTTGCTAGG
1 AGCTTTGCTACG
74110 AGCTTTGCTACG
1 AGCTTTGCTACG
74122 AGCTTTGCTAC
1 AGCTTTGCTAC
74133 AGACTCTGAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.17, C:0.23, G:0.26, T:0.34
Consensus pattern (12 bp):
AGCTTTGCTACG
Found at i:75107 original size:15 final size:16
Alignment explanation
Indices: 75067--75107 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
75057 TTTTCTCGGG
*
75067 TCATTCGGGTTTTGAC
1 TCATTCGGGTTTAGAC
75083 TCA-TCTGGGTTTAGA-
1 TCATTC-GGGTTTAGAC
75098 TCATTCGGGT
1 TCATTCGGGT
75108 ATGCTGGGTC
Statistics
Matches: 22, Mismatches: 1, Indels: 5
0.79 0.04 0.18
Matches are distributed among these distances:
15 9 0.41
16 13 0.59
ACGTcount: A:0.15, C:0.17, G:0.27, T:0.41
Consensus pattern (16 bp):
TCATTCGGGTTTAGAC
Found at i:96856 original size:21 final size:20
Alignment explanation
Indices: 96824--96864 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 20
96814 AATTCCACAT
*
96824 AAAAATACCAAAAAACATAG
1 AAAAATACCAAAAAAAATAG
*
96844 AAAAATGATCAAAAAAAATAG
1 AAAAAT-ACCAAAAAAAATAG
96865 GGTCTTTTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 6 0.33
21 12 0.67
ACGTcount: A:0.71, C:0.10, G:0.07, T:0.12
Consensus pattern (20 bp):
AAAAATACCAAAAAAAATAG
Found at i:100696 original size:12 final size:12
Alignment explanation
Indices: 100679--100711 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
100669 ATATGCGGGA
100679 ATTGGATATTTC
1 ATTGGATATTTC
100691 ATTGGATATTTC
1 ATTGGATATTTC
*
100703 CTTGGATAT
1 ATTGGATAT
100712 AGGAGGCGCA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.24, C:0.09, G:0.18, T:0.48
Consensus pattern (12 bp):
ATTGGATATTTC
Found at i:102526 original size:2 final size:2
Alignment explanation
Indices: 102519--102543 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
102509 CAAATAATAG
102519 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
102544 GTATGGGGAG
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:102923 original size:1 final size:1
Alignment explanation
Indices: 102919--102957 Score: 51
Period size: 1 Copynumber: 39.0 Consensus size: 1
102909 AAAATGAAAG
* * *
102919 AAAAAGAAAAAGAAAAAAAAAAAAAAAAAAAAAGAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
102958 GAGGCCAAAG
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
1 32 1.00
ACGTcount: A:0.92, C:0.00, G:0.08, T:0.00
Consensus pattern (1 bp):
A
Found at i:102926 original size:6 final size:6
Alignment explanation
Indices: 102915--102959 Score: 67
Period size: 6 Copynumber: 7.8 Consensus size: 6
102905 GTTAAAAATG
*
102915 AAAGAA AAAGAA AAAGAA AAA-AA AAA-AA AAAAAA AAAGAA AAAGA
1 AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGA
102960 GGCCAAAGGG
Statistics
Matches: 37, Mismatches: 1, Indels: 2
0.93 0.03 0.05
Matches are distributed among these distances:
5 10 0.27
6 27 0.73
ACGTcount: A:0.89, C:0.00, G:0.11, T:0.00
Consensus pattern (6 bp):
AAAGAA
Found at i:104669 original size:12 final size:13
Alignment explanation
Indices: 104640--104669 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
104630 TTTTTCTTTT
*
104640 TTTTTCTTTACAA
1 TTTTTCTATACAA
104653 TTTTTCTATACAA
1 TTTTTCTATACAA
104666 TTTT
1 TTTT
104670 AATTGGTGGC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.23, C:0.13, G:0.00, T:0.63
Consensus pattern (13 bp):
TTTTTCTATACAA
Found at i:105237 original size:1 final size:1
Alignment explanation
Indices: 105231--105256 Score: 52
Period size: 1 Copynumber: 26.0 Consensus size: 1
105221 GGCAATTAGC
105231 TTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTT
105257 AAGTAGGGGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 25 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:105500 original size:104 final size:104
Alignment explanation
Indices: 105320--105530 Score: 413
Period size: 104 Copynumber: 2.0 Consensus size: 104
105310 CCCTATTCTC
*
105320 TCAATTCCTTGGCTACCATTTACCATTGTTGAAGTTTAACTCTTGGGAGAAGTTCTCTACTCTTC
1 TCAATTCCTTGGCTACCATTTACCATTGTTGAAGTTTAACTCTCGGGAGAAGTTCTCTACTCTTC
105385 TTCTTCCCTGACTTACTTCTAATTCAAATTCATCCCCTA
66 TTCTTCCCTGACTTACTTCTAATTCAAATTCATCCCCTA
105424 TCAATTCCTTGGCTACCATTTACCATTGTTGAAGTTTAACTCTCGGGAGAAGTTCTCTACTCTTC
1 TCAATTCCTTGGCTACCATTTACCATTGTTGAAGTTTAACTCTCGGGAGAAGTTCTCTACTCTTC
105489 TTCTTCCCTGACTTACTTCTAATTCAAATTCATCCCCTA
66 TTCTTCCCTGACTTACTTCTAATTCAAATTCATCCCCTA
105528 TCA
1 TCA
105531 TTTGGTATCA
Statistics
Matches: 106, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
104 106 1.00
ACGTcount: A:0.22, C:0.27, G:0.10, T:0.40
Consensus pattern (104 bp):
TCAATTCCTTGGCTACCATTTACCATTGTTGAAGTTTAACTCTCGGGAGAAGTTCTCTACTCTTC
TTCTTCCCTGACTTACTTCTAATTCAAATTCATCCCCTA
Found at i:114581 original size:36 final size:36
Alignment explanation
Indices: 114541--114612 Score: 108
Period size: 36 Copynumber: 2.0 Consensus size: 36
114531 GACATTGAGC
* *
114541 AAAAGAGTAAGAAGGGAAATAGAAAATGTCGTGGAA
1 AAAAGAGGAAGAAGGAAAATAGAAAATGTCGTGGAA
* *
114577 AAAAGAGGAAGGAGGAAAATAGAAAATGTTGTGGAA
1 AAAAGAGGAAGAAGGAAAATAGAAAATGTCGTGGAA
114613 TGAAATTCAA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
36 32 1.00
ACGTcount: A:0.53, C:0.01, G:0.32, T:0.14
Consensus pattern (36 bp):
AAAAGAGGAAGAAGGAAAATAGAAAATGTCGTGGAA
Found at i:115672 original size:3 final size:3
Alignment explanation
Indices: 115666--115712 Score: 67
Period size: 3 Copynumber: 15.7 Consensus size: 3
115656 CGCACAACAA
* * *
115666 AAT AAT AAT AAT AAT AAT AAT AAT AAT CAT AAT AAT CAT AAT TAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
115713 AAAGTCTAAC
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.62, C:0.04, G:0.00, T:0.34
Consensus pattern (3 bp):
AAT
Done.