Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008923.1 Hibiscus syriacus cultivar Beakdansim tig00112227_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: 468757
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
File 2 of 3
Found at i:264917 original size:13 final size:14
Alignment explanation
Indices: 264893--264927 Score: 54
Period size: 13 Copynumber: 2.6 Consensus size: 14
264883 GAATGCACAA
*
264893 ATAGTTCAAAATAT
1 ATAGTGCAAAATAT
264907 AT-GTGCAAAATAT
1 ATAGTGCAAAATAT
264920 ATAGTGCA
1 ATAGTGCA
264928 TGGTAATAGG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
13 12 0.63
14 7 0.37
ACGTcount: A:0.46, C:0.09, G:0.14, T:0.31
Consensus pattern (14 bp):
ATAGTGCAAAATAT
Found at i:266449 original size:39 final size:39
Alignment explanation
Indices: 266384--266461 Score: 111
Period size: 39 Copynumber: 2.0 Consensus size: 39
266374 TCAATAGTCC
* *
266384 TGTTTTAATCTATATTATCTATATTATTGCTGTTTTAAT
1 TGTTTTAATCTATATTATCTAGATTATTGCTGCTTTAAT
* * *
266423 TGTTTTAATCTATGTTATGTAGATTATTGTTGCTTTAAT
1 TGTTTTAATCTATATTATCTAGATTATTGCTGCTTTAAT
266462 CTATGTTATC
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
39 34 1.00
ACGTcount: A:0.24, C:0.06, G:0.12, T:0.58
Consensus pattern (39 bp):
TGTTTTAATCTATATTATCTAGATTATTGCTGCTTTAAT
Found at i:276498 original size:24 final size:24
Alignment explanation
Indices: 276466--276516 Score: 102
Period size: 24 Copynumber: 2.1 Consensus size: 24
276456 GTATTACCTT
276466 ATTTCTGTGCCATACTAATCGACC
1 ATTTCTGTGCCATACTAATCGACC
276490 ATTTCTGTGCCATACTAATCGACC
1 ATTTCTGTGCCATACTAATCGACC
276514 ATT
1 ATT
276517 AAATTCCATT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.25, C:0.27, G:0.12, T:0.35
Consensus pattern (24 bp):
ATTTCTGTGCCATACTAATCGACC
Found at i:278622 original size:16 final size:16
Alignment explanation
Indices: 278603--278641 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
278593 TAAAATGTTT
*
278603 ATTATTTAAGTAATTA
1 ATTATTTAAGTAAGTA
*
278619 ATTATTTAATTAAGTA
1 ATTATTTAAGTAAGTA
*
278635 TTTATTT
1 ATTATTT
278642 TATTTGATTA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.38, C:0.00, G:0.05, T:0.56
Consensus pattern (16 bp):
ATTATTTAAGTAAGTA
Found at i:278849 original size:14 final size:14
Alignment explanation
Indices: 278826--278856 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
278816 ATTATTTAAA
278826 TTATTAGAATTTAT
1 TTATTAGAATTTAT
*
278840 TTATTTGAATTTAT
1 TTATTAGAATTTAT
278854 TTA
1 TTA
278857 AATAATTTTG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.32, C:0.00, G:0.06, T:0.61
Consensus pattern (14 bp):
TTATTAGAATTTAT
Found at i:279676 original size:2 final size:2
Alignment explanation
Indices: 279669--279705 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
279659 ATAGAATGAC
279669 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
279706 TAAATAGGTG
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 33 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:282113 original size:49 final size:50
Alignment explanation
Indices: 282053--282161 Score: 148
Period size: 49 Copynumber: 2.2 Consensus size: 50
282043 TAAGTATATA
* * *
282053 TTTATTGTTAGGCTGGGAGATGTACATACTTATACC-ATGTAAGCATGTG
1 TTTATTGTTAGGCTGAGAGATGTACATACTTACACCGATATAAGCATGTG
* * *
282102 TTTATTTTTAGGCTGAGAGATGTATATACTTACACCGATATAAGTATGTG
1 TTTATTGTTAGGCTGAGAGATGTACATACTTACACCGATATAAGCATGTG
*
282152 TTAATTGTTA
1 TTTATTGTTA
282162 CAATTTTTTA
Statistics
Matches: 51, Mismatches: 8, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
49 32 0.63
50 19 0.37
ACGTcount: A:0.28, C:0.10, G:0.21, T:0.40
Consensus pattern (50 bp):
TTTATTGTTAGGCTGAGAGATGTACATACTTACACCGATATAAGCATGTG
Found at i:282134 original size:790 final size:802
Alignment explanation
Indices: 280752--282356 Score: 2894
Period size: 790 Copynumber: 2.0 Consensus size: 802
280742 CACATGAGAA
280752 AAATAACATAAACACAACGAATGCATCACCATGAAGATGATTAATCCCAAAACACAATATTGTTA
1 AAATAACATAAACACAACGAATGCATCACCATGAAGATGATTAATCCCAAAACACAATATTGTTA
280817 GAACTCAGCACAAAGAAGAATCCTTGGGGAAGATTAACATGGAGTGGTATTGTTGCTTATATCAT
66 GAACTCAGCAC-AAGAAGAATCCTTGGGGAAGATTAACATGGAGTGGTATTGTTGCTTATATCAT
280882 CTTTCAGAAACCAATTTATAAATGATAAAGAAAAAAATAGCACCAGTCAGGGACGTATTATGTTT
130 CTTTCAGAAACCAATTTATAAATGATAAAGAAAAAAATAGCACCAGTCAGGGACGTATTATGTTT
*
280947 CATTTTGGAGTCCTTAATTTTTTTATTTTGATTTTAGTCTTTTATTTTATTTGGTTAATTATATT
195 CATTTTGGAGTCCTTAATTTTTTTATTTTGATTTTAGTCTTTTATTTTATGTGGTTAATTATATT
281012 TTGTCTACCTCCTATATTTCTATTATTAAAAAATACATATGATTGAAATCTTGGCTCAACACCCT
260 TTGTCTACCTCCTATATTTCTATTATTAAAAAATACATATGATTGAAATCTTGGCTCAACACCCT
281077 ATCTTTTAAAAAGTATATTTAATAGACTATTTTTTCTACCTAACATTTTAGTCAATAAAAGTTTT
325 ATCTTTTAAAAAG-ATATTTAATAGACTATTTTTTCTACCTAACATTTTAGTCAATAAAAGTTTT
281142 GATTTATATGAAAATACACTGATCGAAAGCTCATAGAAATATAATTTTTTATTATTTTTTAATAA
389 GATTTATATGAAAATACACTGATCGAAAGCTCATAGAAATATAATTTTTTATTATTTTTTAATAA
281207 AATTATACAAAAATAAAAATATATATTTTATGAAAGATGCACGTAGTAAGTATATATTATTTGTT
454 AATTATACAAAAATAAAAATATATATTTTATGAAAGATGCACGTAGTAAGTATATATTATTTGTT
281272 AGGCTGGGAGATGTACATACTTATACCATGTAAGCATGTGTTTATTTTTAGGCTGAGAGATGTAT
519 AGGCTGGGAGATGTACATACTTATACCATGTAAGCATGTGTTTATTTTTAGGCTGAGAGATGTAT
281337 ATACTTACACCGATAT-AG-ATGTGTTAATTG-T-TTTTTTATTTATGCTATAAGTATAAGTTGT
584 ATACTTACACCGATATAAGTATGTGTTAATTGTTATTTTTTATTTATGCTATAAGTATAAGTTGT
281398 ACAATAAAATATTAAATC-A-A-ATAGTAAAATTAATTGAAAATATTAAAAAATAT-A-ATAATA
649 ACAATAAAATATTAAATCAATATATAGTAAAATTAATTGAAAATATTAAAAAATATAATATAATA
281458 TCCTTTTATGAAAATTAATTCTAAAT-A-ACACGTAATAAAACATATACAAAAATAAAATTTGAA
714 TCCTTTTATGAAAATTAATTCTAAATAACACACGTAATAAAACATATACAAAAATAAAATTTGAA
281521 TAGAACGCATACGTAAAAATAAT-
779 TAGAACGCATACGTAAAAATAATC
281544 AAATAACATAAACACAACGAATGCATCACCATGAAGATGATTAATCCCAAAACACAATATTGTTA
1 AAATAACATAAACACAACGAATGCATCACCATGAAGATGATTAATCCCAAAACACAATATTGTTA
281609 GAAACTCAGCAC-A-AAGAATCCTT-GGGAAGATTAACATGGAGTGGTATTGTTGCTTATATCAT
66 G-AACTCAGCACAAGAAGAATCCTTGGGGAAGATTAACATGGAGTGGTATTGTTGCTTATATCAT
281671 CTTTCAGAAACCAATTTATAAATGATAAAGAAAAAAAATAGCACCAGTCAGGGACGTAATTATGT
130 CTTTCAGAAACCAATTTATAAATGATAAAG-AAAAAAATAGCACCAGTCAGGGACGT-ATTATGT
281736 TTCATTTTGGAGTCCTTAATTTTTTTATTTTGATTTTAGTCTTTTATTTTATGTGGTTAATTATA
193 TTCATTTTGGAGTCCTTAATTTTTTTATTTTGATTTTAGTCTTTTATTTTATGTGGTTAATTATA
281801 TTTTGTCTACCTCCTATATTTCTATTATT-AAAAA-ACATATG-TTGAAATCTTGGCTCAAC-CT
258 TTTTGTCTACCTCCTATATTTCTATTATTAAAAAATACATATGATTGAAATCTTGGCTCAACAC-
281862 CCTATCTTTT-AAAA-ATATTTAATAGACTATTTTTTCTACCTAACATTTTAGTCAATAAAAGTT
322 CCTATCTTTTAAAAAGATATTTAATAGACTATTTTTTCTACCTAACATTTTAGTCAATAAAAGTT
281925 TTGATTTATATGAAAAATACACTGATCGAAAGCTCATAGAAAATATAATTTTTTATTATTTTTTA
387 TTGATTTATATG-AAAATACACTGATCGAAAGCTCATAG-AAATATAATTTTTTATTATTTTTTA
281990 ATAAAATTTATACAAAAATAAAAATATATATTTTTATGAAAGATGCACGTATGTAAGTATATATT
450 ATAAAA-TTATACAAAAATAAAAATATATA-TTTTATGAAAGATGCACGTA-GTAAGTATATATT
282055 -TATTGTTAGGCTGGGAGATGTACATACTTATACCATGTAAGCATGTGTTTATTTTTAGGCTGAG
512 AT-TTGTTAGGCTGGGAGATGTACATACTTATACCATGTAAGCATGTGTTTATTTTTAGGCTGAG
282119 AGATGTATATACTTACACCGATATAAGTATGTGTTAATTGTTACAATTTTTTATTTATGCTATAA
576 AGATGTATATACTTACACCGATATAAGTATGTGTTAATTGTT---ATTTTTTATTTATGCTATAA
282184 GTATAAGTTGTACAATAAAATATTAAATCAAATTATATAGTAAAATTAATTGAAAATATTAAAAA
638 GTATAAGTTGTACAATAAAATATTAAATC-AA-TATATAGTAAAATTAATTGAAAATATTAAAAA
282249 ATATAATATAATATCCTTTTATGAAAATTAATTCTAAATAACACACGTAATAAAACATATACAAA
701 ATATAATATAATATCCTTTTATGAAAATTAATTCTAAATAACACACGTAATAAAACATATACAAA
282314 AATAAAATTTGAATAGAACGCATACGTAAAAATAATC
766 AATAAAATTTGAATAGAACGCATACGTAAAAATAATC
282351 AAATAA
1 AAATAA
282357 ATTAAAATTT
Statistics
Matches: 785, Mismatches: 1, Indels: 39
0.95 0.00 0.05
Matches are distributed among these distances:
785 61 0.08
786 26 0.03
787 36 0.05
788 51 0.06
789 97 0.12
790 140 0.18
791 103 0.13
792 78 0.10
793 11 0.01
797 48 0.06
799 1 0.00
801 1 0.00
802 33 0.04
803 1 0.00
804 32 0.04
805 1 0.00
806 59 0.08
807 6 0.01
ACGTcount: A:0.40, C:0.11, G:0.12, T:0.37
Consensus pattern (802 bp):
AAATAACATAAACACAACGAATGCATCACCATGAAGATGATTAATCCCAAAACACAATATTGTTA
GAACTCAGCACAAGAAGAATCCTTGGGGAAGATTAACATGGAGTGGTATTGTTGCTTATATCATC
TTTCAGAAACCAATTTATAAATGATAAAGAAAAAAATAGCACCAGTCAGGGACGTATTATGTTTC
ATTTTGGAGTCCTTAATTTTTTTATTTTGATTTTAGTCTTTTATTTTATGTGGTTAATTATATTT
TGTCTACCTCCTATATTTCTATTATTAAAAAATACATATGATTGAAATCTTGGCTCAACACCCTA
TCTTTTAAAAAGATATTTAATAGACTATTTTTTCTACCTAACATTTTAGTCAATAAAAGTTTTGA
TTTATATGAAAATACACTGATCGAAAGCTCATAGAAATATAATTTTTTATTATTTTTTAATAAAA
TTATACAAAAATAAAAATATATATTTTATGAAAGATGCACGTAGTAAGTATATATTATTTGTTAG
GCTGGGAGATGTACATACTTATACCATGTAAGCATGTGTTTATTTTTAGGCTGAGAGATGTATAT
ACTTACACCGATATAAGTATGTGTTAATTGTTATTTTTTATTTATGCTATAAGTATAAGTTGTAC
AATAAAATATTAAATCAATATATAGTAAAATTAATTGAAAATATTAAAAAATATAATATAATATC
CTTTTATGAAAATTAATTCTAAATAACACACGTAATAAAACATATACAAAAATAAAATTTGAATA
GAACGCATACGTAAAAATAATC
Found at i:282480 original size:14 final size:15
Alignment explanation
Indices: 282461--282490 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
282451 CACGTGTAAT
282461 TATATAC-AAAGGAA
1 TATATACAAAAGGAA
282475 TATATACAAAAGGAA
1 TATATACAAAAGGAA
282490 T
1 T
282491 GATTATTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 7 0.47
15 8 0.53
ACGTcount: A:0.57, C:0.07, G:0.13, T:0.23
Consensus pattern (15 bp):
TATATACAAAAGGAA
Found at i:286620 original size:29 final size:29
Alignment explanation
Indices: 286586--286644 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
286576 CCTAAATTAA
286586 TTTGATGTCATTGCTTACATCAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
286615 TTTGATGTCATTGCTTACATCAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
286644 T
1 T
286645 AGGTGAAAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.24, C:0.14, G:0.14, T:0.49
Consensus pattern (29 bp):
TTTGATGTCATTGCTTACATCAATTTAGT
Found at i:287164 original size:18 final size:20
Alignment explanation
Indices: 287133--287169 Score: 60
Period size: 18 Copynumber: 1.9 Consensus size: 20
287123 GCTTTATAAT
287133 ATATATTTTCATATATCATC
1 ATATATTTTCATATATCATC
287153 ATATA-TTT-ATATATCAT
1 ATATATTTTCATATATCAT
287170 TCTCTCTTCA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 9 0.53
19 3 0.18
20 5 0.29
ACGTcount: A:0.38, C:0.11, G:0.00, T:0.51
Consensus pattern (20 bp):
ATATATTTTCATATATCATC
Found at i:288456 original size:13 final size:14
Alignment explanation
Indices: 288432--288466 Score: 54
Period size: 13 Copynumber: 2.6 Consensus size: 14
288422 GAATGCACAA
*
288432 ATAGTTCAAAATAT
1 ATAGTGCAAAATAT
288446 AT-GTGCAAAATAT
1 ATAGTGCAAAATAT
288459 ATAGTGCA
1 ATAGTGCA
288467 TGGTAATAGG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
13 12 0.63
14 7 0.37
ACGTcount: A:0.46, C:0.09, G:0.14, T:0.31
Consensus pattern (14 bp):
ATAGTGCAAAATAT
Found at i:289978 original size:39 final size:39
Alignment explanation
Indices: 289913--289990 Score: 111
Period size: 39 Copynumber: 2.0 Consensus size: 39
289903 TCAGTAGTCC
* *
289913 TGTTTTAATCTATATTATCTATATTATTGCTGTTTTAAT
1 TGTTTTAATCTATATTATCTAGATTATTGCTGCTTTAAT
* * *
289952 TGTTTTAATCTATGTTATGTAGATTATTGTTGCTTTAAT
1 TGTTTTAATCTATATTATCTAGATTATTGCTGCTTTAAT
289991 CTATGTTATC
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
39 34 1.00
ACGTcount: A:0.24, C:0.06, G:0.12, T:0.58
Consensus pattern (39 bp):
TGTTTTAATCTATATTATCTAGATTATTGCTGCTTTAAT
Found at i:292222 original size:14 final size:14
Alignment explanation
Indices: 292199--292229 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
292189 ATTATTTAAA
292199 TTATTAGAATTTAT
1 TTATTAGAATTTAT
*
292213 TTATTTGAATTTAT
1 TTATTAGAATTTAT
292227 TTA
1 TTA
292230 ATTAATTTTG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.32, C:0.00, G:0.06, T:0.61
Consensus pattern (14 bp):
TTATTAGAATTTAT
Found at i:295597 original size:49 final size:50
Alignment explanation
Indices: 295525--295645 Score: 174
Period size: 49 Copynumber: 2.5 Consensus size: 50
295515 AAGATGCACT
* *
295525 ATGTAAGTATAT-ATTATTGTTAGGCTGAGAGATGTACATACTTACACC-
1 ATGTAAGTATGTGTTTATTGTTAGGCTGAGAGATGTACATACTTACACCG
* *
295573 ATGTAAGTATGTGTTTATTTTTAGGCTGAGAGATGTATATACTTACACCG
1 ATGTAAGTATGTGTTTATTGTTAGGCTGAGAGATGTACATACTTACACCG
* *
295623 ATATAAGTATGTGTTAATTGTTA
1 ATGTAAGTATGTGTTTATTGTTA
295646 CACTTTTTTT
Statistics
Matches: 64, Mismatches: 7, Indels: 2
0.88 0.10 0.03
Matches are distributed among these distances:
48 11 0.17
49 33 0.52
50 20 0.31
ACGTcount: A:0.31, C:0.09, G:0.20, T:0.40
Consensus pattern (50 bp):
ATGTAAGTATGTGTTTATTGTTAGGCTGAGAGATGTACATACTTACACCG
Found at i:295973 original size:15 final size:15
Alignment explanation
Indices: 295953--295983 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
295943 CACGTGTAAT
295953 TATATACAAAAGGAA
1 TATATACAAAAGGAA
295968 TATATACAAAAGGAA
1 TATATACAAAAGGAA
295983 T
1 T
295984 GATTATTTGG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.58, C:0.06, G:0.13, T:0.23
Consensus pattern (15 bp):
TATATACAAAAGGAA
Found at i:296696 original size:18 final size:20
Alignment explanation
Indices: 296665--296701 Score: 60
Period size: 18 Copynumber: 1.9 Consensus size: 20
296655 GAGCTTTATA
296665 ATATATTTTCATATATCATC
1 ATATATTTTCATATATCATC
296685 ATATA-TTT-ATATATCAT
1 ATATATTTTCATATATCAT
296702 TCTCTCTTCA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 9 0.53
19 3 0.18
20 5 0.29
ACGTcount: A:0.38, C:0.11, G:0.00, T:0.51
Consensus pattern (20 bp):
ATATATTTTCATATATCATC
Found at i:298001 original size:13 final size:14
Alignment explanation
Indices: 297977--298011 Score: 54
Period size: 13 Copynumber: 2.6 Consensus size: 14
297967 GAATGCACAA
*
297977 ATAGTTCAAAATAT
1 ATAGTGCAAAATAT
297991 AT-GTGCAAAATAT
1 ATAGTGCAAAATAT
298004 ATAGTGCA
1 ATAGTGCA
298012 TGGTAATAGG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
13 12 0.63
14 7 0.37
ACGTcount: A:0.46, C:0.09, G:0.14, T:0.31
Consensus pattern (14 bp):
ATAGTGCAAAATAT
Found at i:310880 original size:49 final size:50
Alignment explanation
Indices: 310809--310922 Score: 176
Period size: 49 Copynumber: 2.3 Consensus size: 50
310799 AGATGCATGT
* * *
310809 ATGTAAGTATATATTTATTTTTAGGCTGGGAGATGTACATACTTACACC-
1 ATGTAAGTATGTGTTTATTTTTAGGCTGAGAGATGTACATACTTACACCG
*
310858 ATGTAAGTATGTGTTTATTTTTAGGCTGAGAGATGTATATACTTACACCG
1 ATGTAAGTATGTGTTTATTTTTAGGCTGAGAGATGTACATACTTACACCG
*
310908 ATATAAGTATGTGTT
1 ATGTAAGTATGTGTT
310923 AATTGTTACA
Statistics
Matches: 59, Mismatches: 5, Indels: 1
0.91 0.08 0.02
Matches are distributed among these distances:
49 45 0.76
50 14 0.24
ACGTcount: A:0.30, C:0.10, G:0.20, T:0.40
Consensus pattern (50 bp):
ATGTAAGTATGTGTTTATTTTTAGGCTGAGAGATGTACATACTTACACCG
Found at i:311341 original size:18 final size:20
Alignment explanation
Indices: 311310--311346 Score: 60
Period size: 18 Copynumber: 1.9 Consensus size: 20
311300 GCTTTATAAT
311310 ATATATTTTCATATATCATC
1 ATATATTTTCATATATCATC
311330 ATATA-TTT-ATATATCAT
1 ATATATTTTCATATATCAT
311347 TCTCTCTTCA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 9 0.53
19 3 0.18
20 5 0.29
ACGTcount: A:0.38, C:0.11, G:0.00, T:0.51
Consensus pattern (20 bp):
ATATATTTTCATATATCATC
Found at i:313654 original size:30 final size:30
Alignment explanation
Indices: 313620--313678 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 30
313610 CTTTTTCTGG
313620 ATTTTAAT-TTTA-ATTATATTTTTATATTAC
1 ATTTTAATATTTATA-TAT-TTTTTATATTAC
313650 ATTTTAATATTTATATATTTTTTATATTA
1 ATTTTAATATTTATATATTTTTTATATTA
313679 TTATTAGTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
30 19 0.70
31 7 0.26
32 1 0.04
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (30 bp):
ATTTTAATATTTATATATTTTTTATATTAC
Found at i:313824 original size:19 final size:18
Alignment explanation
Indices: 313787--313860 Score: 55
Period size: 19 Copynumber: 4.1 Consensus size: 18
313777 GTATTTTATC
*
313787 TTATTATTTCTTTACTTTT
1 TTATTATTTATTTA-TTTT
313806 TTATTATTATATTTA-TTT
1 TTATTATT-TATTTATTTT
* *
313824 TCATTATTTA-GT-TTTT
1 TTATTATTTATTTATTTT
* *
313840 CTATTATTATATATATTTT
1 TTATTATT-TATTTATTTT
313859 TT
1 TT
313861 CCTCTCTCTC
Statistics
Matches: 43, Mismatches: 7, Indels: 10
0.72 0.12 0.17
Matches are distributed among these distances:
16 10 0.23
17 4 0.09
18 11 0.26
19 13 0.30
20 5 0.12
ACGTcount: A:0.23, C:0.05, G:0.01, T:0.70
Consensus pattern (18 bp):
TTATTATTTATTTATTTT
Found at i:324653 original size:46 final size:46
Alignment explanation
Indices: 324585--324672 Score: 158
Period size: 46 Copynumber: 1.9 Consensus size: 46
324575 AATATTTCGC
*
324585 TTAGGATGAAAACCCGAGAGGGCGCCCTAAATTGAAAAAAAAATGT
1 TTAGGATGAAAACCCGAAAGGGCGCCCTAAATTGAAAAAAAAATGT
*
324631 TTAGGGTGAAAACCCGAAAGGGCGCCCTAAATTGAAAAAAAA
1 TTAGGATGAAAACCCGAAAGGGCGCCCTAAATTGAAAAAAAA
324673 TAGAAAAACA
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
46 40 1.00
ACGTcount: A:0.44, C:0.16, G:0.24, T:0.16
Consensus pattern (46 bp):
TTAGGATGAAAACCCGAAAGGGCGCCCTAAATTGAAAAAAAAATGT
Found at i:325842 original size:106 final size:103
Alignment explanation
Indices: 325451--325894 Score: 585
Period size: 106 Copynumber: 4.3 Consensus size: 103
325441 AGGTTTTACC
* *
325451 CAGAGTCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCAAGACAACGCAAGTTCAACTTCACG
* * *
325516 GCGAAGGGACCGCTGGTTGTCAACAGACATTTCTCAATTT
66 ACGAAGGGACCGCTGGTTGTCAACA-AAAATTC-CAATTT
* *
325556 CAGAGCCAATTTCAACTTCACAACAAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCAAGACAACGCAAGTTCAACTTCACG
* * *
325621 ACGAAGGTACCGCTGGTTGTC--GATAAA---CAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAAAATTCCAATTT
* *
325654 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGAC-GACAGACAATGCAAGTTCAACTTCAC
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCA-AGACAACGCAAGTTCAACTTCAC
325718 GACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTT
65 GACGAAGGGACCGCTGGTTGTCAACAAA-AA-TTC-CAATTT
* * *
325760 CAGAGCCAAATTCAACTTCACAACGAAGGATATTGGACTCAAGACAACACAAGTTCAACTTCACA
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCAAGACAACGCAAGTTCAACTTCACG
* * *
325825 ACGAAGGGGCCGTTGGTTGTCAACAAAAATTCCAGTTT
66 ACGAAGGGACCGCTGGTTGTCAACAAAAATTCCAATTT
* *
325863 CAGACAACACAAGTTCAACTTCACAACGAAGG
1 CAG--AGC-CAATTTCAACTTCACAACGAAGG
325895 GGCCGCTGGT
Statistics
Matches: 301, Mismatches: 25, Indels: 25
0.86 0.07 0.07
Matches are distributed among these distances:
98 86 0.29
100 2 0.01
101 2 0.01
102 1 0.00
103 9 0.03
104 3 0.01
105 86 0.29
106 111 0.37
107 1 0.00
ACGTcount: A:0.35, C:0.25, G:0.19, T:0.22
Consensus pattern (103 bp):
CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCAAGACAACGCAAGTTCAACTTCACG
ACGAAGGGACCGCTGGTTGTCAACAAAAATTCCAATTT
Found at i:325905 original size:63 final size:64
Alignment explanation
Indices: 325801--325996 Score: 313
Period size: 64 Copynumber: 3.0 Consensus size: 64
325791 ATTGGACTCA
*
325801 AGACAACACAAGTTCAACTTCACAACGAAGGGGCCGTTGGTTGTCAACAAAAATT-CCAGTTTC
1 AGACAACACAAGTTCAACTTCACAACGAAGGGGCCGCTGGTTGTCAACAAAAATTCCCAGTTTC
* *
325864 AGACAACACAAGTTCAACTTCACAACGAAGGGGCCGCTGGTTGTCAACAAAATTTCCCAGTTTA
1 AGACAACACAAGTTCAACTTCACAACGAAGGGGCCGCTGGTTGTCAACAAAAATTCCCAGTTTC
* * *
325928 AGACAGCACAAGTTCAACTTCACAACGAAGGGGCCGCTGGCTGTCAACAAACAACTTCCCAATTT
1 AGACAACACAAGTTCAACTTCACAACGAAGGGGCCGCTGGTTGTCAACAAA-AA-TTCCCAGTTT
325993 C
64 C
325994 AGA
1 AGA
325997 GCCAATTTCA
Statistics
Matches: 122, Mismatches: 8, Indels: 3
0.92 0.06 0.02
Matches are distributed among these distances:
63 53 0.43
64 56 0.46
65 1 0.01
66 12 0.10
ACGTcount: A:0.35, C:0.26, G:0.19, T:0.20
Consensus pattern (64 bp):
AGACAACACAAGTTCAACTTCACAACGAAGGGGCCGCTGGTTGTCAACAAAAATTCCCAGTTTC
Found at i:326113 original size:106 final size:106
Alignment explanation
Indices: 325936--326146 Score: 334
Period size: 106 Copynumber: 2.0 Consensus size: 106
325926 TAAGACAGCA
325936 CAAGTTCAACTTCACAACGAAGGGGCCGCTGGCTGTCAACAAACAACTTCCCAATTTCAGAGCCA
1 CAAGTTCAACTTCACAACGAAGGGGCCGCTGGCTGTCAACAAACAACTTCCCAATTTCAGAGCCA
* * *
326001 ATTTCAACTTCACATCAAAGGATATTGGACTCGAGACAACG
66 ATTTCAACTTCACAACAAAGGATATCGGACTCGAAACAACG
* * *
326042 CAAGTTCAACTTCACAACGAAGGGGCCGCTGGTTGTCAACAAAC-ACTTTCCAAGTTTCAGAGTC
1 CAAGTTCAACTTCACAACGAAGGGGCCGCTGGCTGTCAACAAACAACTTCCCAA-TTTCAGAGCC
* *
326106 AATTTCAACTTCACAACGAAGGATATCGGCCTCGAAACAAC
65 AATTTCAACTTCACAACAAAGGATATCGGACTCGAAACAAC
326147 ACAGCTTGCA
Statistics
Matches: 96, Mismatches: 8, Indels: 2
0.91 0.08 0.02
Matches are distributed among these distances:
105 8 0.08
106 88 0.92
ACGTcount: A:0.34, C:0.27, G:0.18, T:0.21
Consensus pattern (106 bp):
CAAGTTCAACTTCACAACGAAGGGGCCGCTGGCTGTCAACAAACAACTTCCCAATTTCAGAGCCA
ATTTCAACTTCACAACAAAGGATATCGGACTCGAAACAACG
Found at i:326115 original size:233 final size:231
Alignment explanation
Indices: 325703--326127 Score: 672
Period size: 233 Copynumber: 1.8 Consensus size: 231
325693 ACAGACAATG
* * *
325703 CAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTTCAGAGCCA
1 CAAGTTCAACTTCACAACGAAGGGACCGCTGGCTGTCAACAAACAACTTCCCAATTTCAGAGCCA
*
325768 AATTCAACTTCACAACGAAGGATATTGGACTCAAGACAACACAAGTTCAACTTCACAACGAAGGG
66 AATTCAACTTCACAACAAAGGATATTGGACTCAAGACAACACAAGTTCAACTTCACAACGAAGGG
*
325833 GCCGTTGGTTGTCAACAAAAATTCCAGTTTCAGACAACACAAGTTCAACTTCACAACGAAGGGGC
131 GCCGCTGGTTGTCAACAAAAATTCCAGTTTCAG--AACACAAGTTCAACTTCACAACGAAGGGGC
325898 CGCTGGTTGTCAACAAAATTTCCCAGTTTAAGACAGCA
194 CGCTGGTTGTCAACAAAATTTCCCAGTTTAAGACAGCA
*
325936 CAAGTTCAACTTCACAACGAAGGGGCCGCTGGCTGTCAACAAACAACTTCCCAATTTCAGAGCCA
1 CAAGTTCAACTTCACAACGAAGGGACCGCTGGCTGTCAACAAACAACTTCCCAATTTCAGAGCCA
* * * *
326001 ATTTCAACTTCACATCAAAGGATATTGGACTCGAGACAACGCAAGTTCAACTTCACAACGAAGGG
66 AATTCAACTTCACAACAAAGGATATTGGACTCAAGACAACACAAGTTCAACTTCACAACGAAGGG
* ** *
326066 GCCGCTGGTTGTCAACAAACACTTTCCAAGTTTCAG-AGTCAATTTCAACTTCACAACGAAGG
131 GCCGCTGGTTGTCAACAAA-A-ATTCC-AGTTTCAGAACACAAGTTCAACTTCACAACGAAGG
326128 ATATCGGCCT
Statistics
Matches: 175, Mismatches: 14, Indels: 6
0.90 0.07 0.03
Matches are distributed among these distances:
233 162 0.93
234 1 0.01
235 4 0.02
236 8 0.05
ACGTcount: A:0.34, C:0.26, G:0.18, T:0.22
Consensus pattern (231 bp):
CAAGTTCAACTTCACAACGAAGGGACCGCTGGCTGTCAACAAACAACTTCCCAATTTCAGAGCCA
AATTCAACTTCACAACAAAGGATATTGGACTCAAGACAACACAAGTTCAACTTCACAACGAAGGG
GCCGCTGGTTGTCAACAAAAATTCCAGTTTCAGAACACAAGTTCAACTTCACAACGAAGGGGCCG
CTGGTTGTCAACAAAATTTCCCAGTTTAAGACAGCA
Found at i:327692 original size:37 final size:40
Alignment explanation
Indices: 327651--327733 Score: 93
Period size: 40 Copynumber: 2.1 Consensus size: 40
327641 ATATATTTTG
*
327651 TATTTTATCTT-ATTATTT-CTTTACT-TTTTTATTATTA
1 TATTTTATCTTCATTATTTACTTTACTATTATTATTATTA
* * *
327688 TA-TTTATTTTCATTATTTAGTTTTTCTATTATTATTATTA
1 TATTTTATCTTCATTATTTA-CTTTACTATTATTATTATTA
327728 TATTTT
1 TATTTT
327734 TTTTCCTCTC
Statistics
Matches: 37, Mismatches: 4, Indels: 6
0.79 0.09 0.13
Matches are distributed among these distances:
36 7 0.19
37 9 0.24
39 5 0.14
40 13 0.35
41 3 0.08
ACGTcount: A:0.23, C:0.06, G:0.01, T:0.70
Consensus pattern (40 bp):
TATTTTATCTTCATTATTTACTTTACTATTATTATTATTA
Found at i:331077 original size:14 final size:14
Alignment explanation
Indices: 331054--331084 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
331044 ATTATTTAAA
331054 TTATTAGAATTTAT
1 TTATTAGAATTTAT
*
331068 TTATTTGAATTTAT
1 TTATTAGAATTTAT
331082 TTA
1 TTA
331085 AATAATTTTG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.32, C:0.00, G:0.06, T:0.61
Consensus pattern (14 bp):
TTATTAGAATTTAT
Found at i:331904 original size:2 final size:2
Alignment explanation
Indices: 331897--331926 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
331887 ATAGAATGAC
331897 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
331927 TAAATAGGTG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:334808 original size:49 final size:50
Alignment explanation
Indices: 334735--334856 Score: 174
Period size: 49 Copynumber: 2.5 Consensus size: 50
334725 AGATGCACGT
* * *
334735 ATGTAAGTATATATTTATTGTTAGGCTGGGAGATGTACATACTTACACC-
1 ATGTAAGTATGTGTTTATTGTTAGGCTGAGAGATGTACATACTTACACCG
* *
334784 ATGTAAGTATGTGTTTATTTTTAGGCTGAGAGATGTATATACTTACACCG
1 ATGTAAGTATGTGTTTATTGTTAGGCTGAGAGATGTACATACTTACACCG
* *
334834 ATATAAGTATGTGTTAATTGTTA
1 ATGTAAGTATGTGTTTATTGTTA
334857 CACTTTTTTA
Statistics
Matches: 64, Mismatches: 8, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
49 44 0.69
50 20 0.31
ACGTcount: A:0.30, C:0.09, G:0.20, T:0.40
Consensus pattern (50 bp):
ATGTAAGTATGTGTTTATTGTTAGGCTGAGAGATGTACATACTTACACCG
Found at i:335185 original size:15 final size:15
Alignment explanation
Indices: 335165--335195 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
335155 CACGTGTAAT
335165 TATATACAAAAGGAA
1 TATATACAAAAGGAA
335180 TATATACAAAAGGAA
1 TATATACAAAAGGAA
335195 T
1 T
335196 GATTATTTTG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.58, C:0.06, G:0.13, T:0.23
Consensus pattern (15 bp):
TATATACAAAAGGAA
Found at i:335915 original size:18 final size:20
Alignment explanation
Indices: 335884--335920 Score: 60
Period size: 18 Copynumber: 1.9 Consensus size: 20
335874 GCTTTATAAT
335884 ATATATTTTCATATATCATC
1 ATATATTTTCATATATCATC
335904 ATATA-TTT-ATATATCAT
1 ATATATTTTCATATATCAT
335921 TCTCTCTTCA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 9 0.53
19 3 0.18
20 5 0.29
ACGTcount: A:0.38, C:0.11, G:0.00, T:0.51
Consensus pattern (20 bp):
ATATATTTTCATATATCATC
Found at i:337007 original size:26 final size:26
Alignment explanation
Indices: 336974--337029 Score: 112
Period size: 26 Copynumber: 2.2 Consensus size: 26
336964 TGAATAATTC
336974 ATTTAGGTAATTAATAATATAAAGGA
1 ATTTAGGTAATTAATAATATAAAGGA
337000 ATTTAGGTAATTAATAATATAAAGGA
1 ATTTAGGTAATTAATAATATAAAGGA
337026 ATTT
1 ATTT
337030 CAAACCTCAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 30 1.00
ACGTcount: A:0.48, C:0.00, G:0.14, T:0.38
Consensus pattern (26 bp):
ATTTAGGTAATTAATAATATAAAGGA
Found at i:337942 original size:39 final size:39
Alignment explanation
Indices: 337877--337954 Score: 111
Period size: 39 Copynumber: 2.0 Consensus size: 39
337867 TCAGTAGTCC
* *
337877 TGTTTTAATCTATATTATCTATATTATTGCTGTTTTAAT
1 TGTTTTAATCTATATTATCTAGATTATTGCTGCTTTAAT
* * *
337916 TGTTTTAATCTATGTTATGTAGATTATTGTTGCTTTAAT
1 TGTTTTAATCTATATTATCTAGATTATTGCTGCTTTAAT
337955 CTATGTTATC
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
39 34 1.00
ACGTcount: A:0.24, C:0.06, G:0.12, T:0.58
Consensus pattern (39 bp):
TGTTTTAATCTATATTATCTAGATTATTGCTGCTTTAAT
Found at i:351746 original size:49 final size:50
Alignment explanation
Indices: 351676--351794 Score: 159
Period size: 49 Copynumber: 2.4 Consensus size: 50
351666 TGCACGTATG
* * * *
351676 TAAGTATATATTTATTGTTAGGCTGGGAGATGTACATACTTACACC-ATG
1 TAAGTATGTGTTTATTGTTAGGCTGAGAGATGTACATACTTACACCGATA
* * *
351725 TATGTATGTGTTTATTTTTAGGCTGAGAGATGTATATACTTACACCGATA
1 TAAGTATGTGTTTATTGTTAGGCTGAGAGATGTACATACTTACACCGATA
*
351775 TAAGTATGTGTTAATTGTTA
1 TAAGTATGTGTTTATTGTTA
351795 CACTTTTTTA
Statistics
Matches: 59, Mismatches: 10, Indels: 1
0.84 0.14 0.01
Matches are distributed among these distances:
49 40 0.68
50 19 0.32
ACGTcount: A:0.29, C:0.09, G:0.20, T:0.41
Consensus pattern (50 bp):
TAAGTATGTGTTTATTGTTAGGCTGAGAGATGTACATACTTACACCGATA
Found at i:352840 original size:18 final size:20
Alignment explanation
Indices: 352809--352845 Score: 60
Period size: 18 Copynumber: 1.9 Consensus size: 20
352799 GCTTTATAAT
352809 ATATATTTTCATATATCATC
1 ATATATTTTCATATATCATC
352829 ATATA-TTT-ATATATCAT
1 ATATATTTTCATATATCAT
352846 TCTCTCTTCA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 9 0.53
19 3 0.18
20 5 0.29
ACGTcount: A:0.38, C:0.11, G:0.00, T:0.51
Consensus pattern (20 bp):
ATATATTTTCATATATCATC
Found at i:354140 original size:13 final size:14
Alignment explanation
Indices: 354116--354150 Score: 54
Period size: 13 Copynumber: 2.6 Consensus size: 14
354106 GAATGCACAA
*
354116 ATAGTTCAAAATAT
1 ATAGTGCAAAATAT
354130 AT-GTGCAAAATAT
1 ATAGTGCAAAATAT
354143 ATAGTGCA
1 ATAGTGCA
354151 TGGTAATAGG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
13 12 0.63
14 7 0.37
ACGTcount: A:0.46, C:0.09, G:0.14, T:0.31
Consensus pattern (14 bp):
ATAGTGCAAAATAT
Found at i:355683 original size:39 final size:39
Alignment explanation
Indices: 355607--355684 Score: 104
Period size: 39 Copynumber: 2.0 Consensus size: 39
355597 TCAGTAGTCC
* *
355607 TGTTTTAATCTATATTATCTATATTATTGATGTTTTAAT
1 TGTTTTAATCTATATTATCTAGATTATTGATGCTTTAAT
* *
355646 TGTTTTAATCTATGTTATGTAGATTATTG-TGGCTTTAAT
1 TGTTTTAATCTATATTATCTAGATTATTGAT-GCTTTAAT
355685 CTATGTTATC
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
38 1 0.03
39 33 0.97
ACGTcount: A:0.26, C:0.05, G:0.13, T:0.56
Consensus pattern (39 bp):
TGTTTTAATCTATATTATCTAGATTATTGATGCTTTAAT
Found at i:357108 original size:29 final size:29
Alignment explanation
Indices: 357066--357124 Score: 100
Period size: 29 Copynumber: 2.0 Consensus size: 29
357056 ATTTTCACCT
357066 AACTAAATTGATGTAAGAAATGACATCAA
1 AACTAAATTGATGTAAGAAATGACATCAA
**
357095 AACTAAATTGATGTAATCAATGACATCAA
1 AACTAAATTGATGTAAGAAATGACATCAA
357124 A
1 A
357125 TTAATTTAGG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.51, C:0.12, G:0.12, T:0.25
Consensus pattern (29 bp):
AACTAAATTGATGTAAGAAATGACATCAA
Found at i:362997 original size:19 final size:19
Alignment explanation
Indices: 362939--362997 Score: 50
Period size: 19 Copynumber: 3.0 Consensus size: 19
362929 AATACAAAAC
*
362939 TATATTATTTTGAATT-TTA
1 TATATTA-TTTAAATTATTA
*
362958 TGAATATTA-TGAAATTGATTA
1 T--ATATTATTTAAATT-ATTA
362979 TATATTATTTAAATTATTA
1 TATATTATTTAAATTATTA
362998 GAATTTATTT
Statistics
Matches: 32, Mismatches: 3, Indels: 10
0.71 0.07 0.22
Matches are distributed among these distances:
19 16 0.50
20 6 0.19
21 10 0.31
ACGTcount: A:0.39, C:0.00, G:0.07, T:0.54
Consensus pattern (19 bp):
TATATTATTTAAATTATTA
Found at i:363015 original size:14 final size:14
Alignment explanation
Indices: 362992--363022 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
362982 ATTATTTAAA
362992 TTATTAGAATTTAT
1 TTATTAGAATTTAT
*
363006 TTATTTGAATTTAT
1 TTATTAGAATTTAT
363020 TTA
1 TTA
363023 AATAATTTTG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.32, C:0.00, G:0.06, T:0.61
Consensus pattern (14 bp):
TTATTAGAATTTAT
Found at i:363978 original size:20 final size:20
Alignment explanation
Indices: 363953--364084 Score: 106
Period size: 20 Copynumber: 6.5 Consensus size: 20
363943 TGGGAAAATT
363953 GCAATGCGATACTGACTATC
1 GCAATGCGATACTGACTATC
*
363973 GCAATGCGATACTTACTATC
1 GCAATGCGATACTGACTATC
* *
363993 GCAATGCGATAAT-ACAAAATC
1 GCAATGCGATACTGAC--TATC
* * *
364014 GCAACGAGATACTGACTTTC
1 GCAATGCGATACTGACTATC
* ** *
364034 GCAACGCGATTTTGACTTTC
1 GCAATGCGATACTGACTATC
* *
364054 GCAACGCGATAAT-ACATAATC
1 GCAATGCGATACTGAC-T-ATC
364075 GCAATGCGAT
1 GCAATGCGAT
364085 TTTCAAAGCG
Statistics
Matches: 92, Mismatches: 15, Indels: 9
0.79 0.13 0.08
Matches are distributed among these distances:
19 4 0.04
20 62 0.67
21 24 0.26
22 2 0.02
ACGTcount: A:0.33, C:0.23, G:0.18, T:0.25
Consensus pattern (20 bp):
GCAATGCGATACTGACTATC
Found at i:363994 original size:61 final size:61
Alignment explanation
Indices: 363960--364078 Score: 168
Period size: 61 Copynumber: 2.0 Consensus size: 61
363950 ATTGCAATGC
* *
363960 GATACTGACTATCGCAATGCGATACTT-ACTATCGCAATGCGATAATACAAAATCGCAACGA
1 GATACTGACTATCGCAACGCGAT-CTTGACTATCGCAACGCGATAATACAAAATCGCAACGA
* * * *
364021 GATACTGACTTTCGCAACGCGATTTTGACTTTCGCAACGCGATAATACATAATCGCAA
1 GATACTGACTATCGCAACGCGATCTTGACTATCGCAACGCGATAATACAAAATCGCAA
364079 TGCGATTTTC
Statistics
Matches: 51, Mismatches: 6, Indels: 2
0.86 0.10 0.03
Matches are distributed among these distances:
60 2 0.04
61 49 0.96
ACGTcount: A:0.34, C:0.24, G:0.17, T:0.25
Consensus pattern (61 bp):
GATACTGACTATCGCAACGCGATCTTGACTATCGCAACGCGATAATACAAAATCGCAACGA
Found at i:364280 original size:22 final size:22
Alignment explanation
Indices: 364252--364295 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
364242 CACTCTCTCA
364252 CCCATCTCC-GACGAAATCCGTC
1 CCCATCTCCAG-CGAAATCCGTC
364274 CCCATCTCCAGCGAAATCCGTC
1 CCCATCTCCAGCGAAATCCGTC
364296 TATCTCCATC
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 20 0.95
23 1 0.05
ACGTcount: A:0.23, C:0.45, G:0.14, T:0.18
Consensus pattern (22 bp):
CCCATCTCCAGCGAAATCCGTC
Found at i:364302 original size:20 final size:21
Alignment explanation
Indices: 364252--364303 Score: 63
Period size: 22 Copynumber: 2.5 Consensus size: 21
364242 CACTCTCTCA
364252 CCCATCTCC-GACGAAATCCGT
1 CCCATCTCCAG-CGAAATCCGT
364273 CCCCATCTCCAGCGAAATCCGT
1 -CCCATCTCCAGCGAAATCCGT
*
364295 -CTATCTCCA
1 CCCATCTCCA
364304 TCTCTCAGAG
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
20 8 0.29
22 19 0.68
23 1 0.04
ACGTcount: A:0.23, C:0.44, G:0.12, T:0.21
Consensus pattern (21 bp):
CCCATCTCCAGCGAAATCCGT
Found at i:364612 original size:20 final size:20
Alignment explanation
Indices: 364559--364616 Score: 80
Period size: 20 Copynumber: 2.9 Consensus size: 20
364549 CGATTCTCTC
**
364559 GTTGCGATAGTCAAATTCGT
1 GTTGCGATAGTCATTTTCGT
364579 GTTGCGATAGTCATTTTCGT
1 GTTGCGATAGTCATTTTCGT
**
364599 GTTGCGATTTTCATTTTC
1 GTTGCGATAGTCATTTTC
364617 AGAAACTATT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.17, C:0.16, G:0.22, T:0.45
Consensus pattern (20 bp):
GTTGCGATAGTCATTTTCGT
Found at i:365956 original size:18 final size:18
Alignment explanation
Indices: 365935--365979 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
365925 TCCACTTTGG
*
365935 GAGCCATCACCTCGCCCA
1 GAGCCATCACCTCACCCA
*
365953 GAGCTATCACCTCACCCA
1 GAGCCATCACCTCACCCA
365971 GAGCCATCA
1 GAGCCATCA
365980 TCTGATCGAC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.27, C:0.44, G:0.16, T:0.13
Consensus pattern (18 bp):
GAGCCATCACCTCACCCA
Found at i:366515 original size:19 final size:20
Alignment explanation
Indices: 366461--366516 Score: 69
Period size: 20 Copynumber: 2.9 Consensus size: 20
366451 TAGTTTACTT
* *
366461 TCGCAACACGAAAATGACTA
1 TCGCAACGCGGAAATGACTA
*
366481 TCGCAACGCGGAAATGGCTA
1 TCGCAACGCGGAAATGACTA
*
366501 TCGCAATGC-GAAATGA
1 TCGCAACGCGGAAATGA
366517 AAATCACAAC
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
19 6 0.19
20 25 0.81
ACGTcount: A:0.38, C:0.23, G:0.23, T:0.16
Consensus pattern (20 bp):
TCGCAACGCGGAAATGACTA
Found at i:366563 original size:32 final size:33
Alignment explanation
Indices: 366500--366590 Score: 139
Period size: 32 Copynumber: 2.8 Consensus size: 33
366490 GGAAATGGCT
*
366500 ATCGCAATGCGAAATGAAAATCACAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
*
366533 ATCGCAATGCGAAATG-AAATCGCAAGGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
* *
366565 ATTGCAACGCGAAATGAAAATCGCAA
1 ATCGCAATGCGAAATGAAAATCGCAA
366591 TGCGATTTGT
Statistics
Matches: 53, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
32 28 0.53
33 25 0.47
ACGTcount: A:0.48, C:0.20, G:0.19, T:0.13
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGACAAA
Found at i:366626 original size:14 final size:14
Alignment explanation
Indices: 366607--366664 Score: 62
Period size: 14 Copynumber: 3.9 Consensus size: 14
366597 TTGTGTTTCG
366607 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
366621 CGTTGCGATTTCATTT
1 CGTTGCGATTT--TGT
366637 CGCGTTGCGATTTTGT
1 --CGTTGCGATTTTGT
*
366653 CATTGCGATTTT
1 CGTTGCGATTTT
366665 CATTTCGCAT
Statistics
Matches: 37, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
14 22 0.59
16 4 0.11
18 11 0.30
ACGTcount: A:0.10, C:0.17, G:0.24, T:0.48
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:366641 original size:32 final size:33
Alignment explanation
Indices: 366602--366680 Score: 133
Period size: 32 Copynumber: 2.4 Consensus size: 33
366592 GCGATTTGTG
*
366602 TTTCGCGTTGCGATTTTGTCGTTGCGA-TTTCA
1 TTTCGCGTTGCGATTTTGTCATTGCGATTTTCA
366634 TTTCGCGTTGCGATTTTGTCATTGCGATTTTCA
1 TTTCGCGTTGCGATTTTGTCATTGCGATTTTCA
*
366667 TTTCGCATTGCGAT
1 TTTCGCGTTGCGAT
366681 AGCCATTTCT
Statistics
Matches: 44, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
32 26 0.59
33 18 0.41
ACGTcount: A:0.11, C:0.19, G:0.23, T:0.47
Consensus pattern (33 bp):
TTTCGCGTTGCGATTTTGTCATTGCGATTTTCA
Found at i:366644 original size:18 final size:16
Alignment explanation
Indices: 366602--366650 Score: 57
Period size: 14 Copynumber: 3.1 Consensus size: 16
366592 GCGATTTGTG
366602 TTTCGCGTTGCGATTT
1 TTTCGCGTTGCGATTT
*
366618 TGT--CGTTGCGATTT
1 TTTCGCGTTGCGATTT
366632 CATTTCGCGTTGCGATTT
1 --TTTCGCGTTGCGATTT
366650 T
1 T
366651 GTCATTGCGA
Statistics
Matches: 27, Mismatches: 2, Indels: 8
0.73 0.05 0.22
Matches are distributed among these distances:
14 11 0.41
16 5 0.19
18 11 0.41
ACGTcount: A:0.08, C:0.18, G:0.24, T:0.49
Consensus pattern (16 bp):
TTTCGCGTTGCGATTT
Found at i:366687 original size:19 final size:20
Alignment explanation
Indices: 366665--366708 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
366655 TTGCGATTTT
*
366665 CATTTC-GCATTGCGATAGC
1 CATTTCTGCATTGAGATAGC
* *
366684 CATTTCTGCGTTGAGATAGT
1 CATTTCTGCATTGAGATAGC
366704 CATTT
1 CATTT
366709 TCGTGTTGTG
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
19 6 0.29
20 15 0.71
ACGTcount: A:0.20, C:0.20, G:0.20, T:0.39
Consensus pattern (20 bp):
CATTTCTGCATTGAGATAGC
Found at i:368635 original size:13 final size:13
Alignment explanation
Indices: 368588--368640 Score: 52
Period size: 14 Copynumber: 3.9 Consensus size: 13
368578 TTGATTGTTT
368588 AATTGATTTGTAA
1 AATTGATTTGTAA
*
368601 AAGATGATTTGTAA
1 AA-TTGATTTGTAA
**
368615 ATATTGATTTGTTT
1 A-ATTGATTTGTAA
*
368629 AATTGATGTGTA
1 AATTGATTTGTA
368641 CATAATTCTT
Statistics
Matches: 32, Mismatches: 6, Indels: 4
0.76 0.14 0.10
Matches are distributed among these distances:
13 11 0.34
14 20 0.62
15 1 0.03
ACGTcount: A:0.34, C:0.00, G:0.19, T:0.47
Consensus pattern (13 bp):
AATTGATTTGTAA
Found at i:368734 original size:20 final size:20
Alignment explanation
Indices: 368709--368747 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
368699 ATGTTGAAGG
368709 CAAAACAGACTATCGCAACA
1 CAAAACAGACTATCGCAACA
*
368729 CAAAACTGACTATCGCAAC
1 CAAAACAGACTATCGCAAC
368748 GAGAGAATCG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.46, C:0.31, G:0.10, T:0.13
Consensus pattern (20 bp):
CAAAACAGACTATCGCAACA
Found at i:368777 original size:19 final size:19
Alignment explanation
Indices: 368753--368817 Score: 86
Period size: 19 Copynumber: 3.7 Consensus size: 19
368743 GCAACGAGAG
368753 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
368772 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
368791 AATCACAA--CG--A-GAA
1 AATCGCAATGCGAAATGAA
368805 AATCGCAATGCGA
1 AATCGCAATGCGA
368818 TTTTCATTTC
Statistics
Matches: 41, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
14 10 0.24
15 1 0.02
16 2 0.05
17 2 0.05
19 26 0.63
ACGTcount: A:0.48, C:0.18, G:0.20, T:0.14
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:368867 original size:19 final size:20
Alignment explanation
Indices: 368843--368892 Score: 84
Period size: 20 Copynumber: 2.5 Consensus size: 20
368833 GCGATTTTGT
368843 CGTTGCGATAGCCA-TTTCA
1 CGTTGCGATAGCCATTTTCA
*
368862 CGTTGCGATAGCCATTTTCG
1 CGTTGCGATAGCCATTTTCA
368882 CGTTGCGATAG
1 CGTTGCGATAG
368893 TCAAATGAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
19 14 0.48
20 15 0.52
ACGTcount: A:0.18, C:0.24, G:0.26, T:0.32
Consensus pattern (20 bp):
CGTTGCGATAGCCATTTTCA
Found at i:369130 original size:20 final size:20
Alignment explanation
Indices: 369105--369155 Score: 93
Period size: 20 Copynumber: 2.5 Consensus size: 20
369095 AAATGATTGC
*
369105 CTTTCGCAACGCGATTTTGA
1 CTTTCGCAACGCGATTCTGA
369125 CTTTCGCAACGCGATTCTGA
1 CTTTCGCAACGCGATTCTGA
369145 CTTTCGCAACG
1 CTTTCGCAACG
369156 AGATAATACA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.20, C:0.29, G:0.20, T:0.31
Consensus pattern (20 bp):
CTTTCGCAACGCGATTCTGA
Found at i:370146 original size:12 final size:12
Alignment explanation
Indices: 370129--370153 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
370119 ATATAATCTT
370129 GAAGAAGAAAAA
1 GAAGAAGAAAAA
370141 GAAGAAGAAAAA
1 GAAGAAGAAAAA
370153 G
1 G
370154 TCCCCGAAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:372487 original size:33 final size:33
Alignment explanation
Indices: 372445--372571 Score: 202
Period size: 33 Copynumber: 3.8 Consensus size: 33
372435 GGAAATTACT
372445 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
**
372478 ATCGCAATGCGAAATGAAAATCGCAACGCTA-A
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
* *
372510 TTTCGCAATGCGAAATGAAAATCGCAACGAGGGA
1 -ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
372544 ATCGCAATGCGAAATGAAAATCGCAACG
1 ATCGCAATGCGAAATGAAAATCGCAACG
372572 CAAATTTAAT
Statistics
Matches: 85, Mismatches: 7, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
32 1 0.01
33 83 0.98
34 1 0.01
ACGTcount: A:0.43, C:0.20, G:0.23, T:0.15
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:372552 original size:66 final size:66
Alignment explanation
Indices: 372446--372578 Score: 248
Period size: 66 Copynumber: 2.0 Consensus size: 66
372436 GAAATTACTA
*
372446 TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCTAAT
1 TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCAAAT
372511 T
66 T
*
372512 TCGCAATGCGAAATGAAAATCGCAACGAGGGAATCGCAATGCGAAATGAAAATCGCAACGCAAAT
1 TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCAAAT
372577 T
66 T
372578 T
1 T
372579 AATTTCGCGT
Statistics
Matches: 65, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
66 65 1.00
ACGTcount: A:0.42, C:0.20, G:0.22, T:0.17
Consensus pattern (66 bp):
TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCAAAT
T
Found at i:372602 original size:19 final size:19
Alignment explanation
Indices: 372580--372632 Score: 88
Period size: 19 Copynumber: 2.8 Consensus size: 19
372570 CGCAAATTTA
372580 ATTTCGCGTTGCGATTTTC
1 ATTTCGCGTTGCGATTTTC
372599 ATTTCGCGTTGCGATTTTC
1 ATTTCGCGTTGCGATTTTC
* *
372618 ATTACGCATTGCGAT
1 ATTTCGCGTTGCGAT
372633 AGTACTTTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 32 1.00
ACGTcount: A:0.15, C:0.21, G:0.21, T:0.43
Consensus pattern (19 bp):
ATTTCGCGTTGCGATTTTC
Found at i:372758 original size:14 final size:14
Alignment explanation
Indices: 372739--372775 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
372729 CATCAATTAA
372739 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
372753 ACAAATCACCTTTT
1 ACAAATCAACTTTT
372767 ACAAATCAA
1 ACAAATCAA
372776 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.24, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:374191 original size:42 final size:41
Alignment explanation
Indices: 374132--374337 Score: 155
Period size: 42 Copynumber: 4.9 Consensus size: 41
374122 GTGAATCGGG
* *
374132 CTCTTGAATGGTGGGAGGGACCTCTTCAACGATGACAGTGGC
1 CTCTTGAACGGTGGGAGGGA-CTCTTCAAGGATGACAGTGGC
* * *
374174 CTCTTGAACGGTGGGAGGGGACTC-TCGAGGAATGATAGGGGC
1 CTCTTGAACGGTGGGA-GGGACTCTTCAAGG-ATGACAGTGGC
* * * * * *
374216 CTCTTCAATGATAGGAGTGGACTCTTGAGGGATGACAGTGGC
1 CTCTTGAACGGTGGGAG-GGACTCTTCAAGGATGACAGTGGC
* * *
374258 CTCTTGAACGGTGGGAGGGGACTC-TCGAGGAATGATAGGGGC
1 CTCTTGAACGGTGGGA-GGGACTCTTCAAGG-ATGACAGTGGC
* ** * * *
374300 CTCTTCAACAATAGGAGTGGACTCTTGAGGGATGACAG
1 CTCTTGAACGGTGGGAG-GGACTCTTCAAGGATGACAG
374338 GCGAGTCGGG
Statistics
Matches: 125, Mismatches: 31, Indels: 16
0.73 0.18 0.09
Matches are distributed among these distances:
41 9 0.07
42 105 0.84
43 11 0.09
ACGTcount: A:0.23, C:0.18, G:0.36, T:0.22
Consensus pattern (41 bp):
CTCTTGAACGGTGGGAGGGACTCTTCAAGGATGACAGTGGC
Found at i:374198 original size:21 final size:21
Alignment explanation
Indices: 374132--374198 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
374122 GTGAATCGGG
*
374132 CTCTTGAATGGTGGGA-GGGA
1 CTCTTGAACGGTGGGAGGGGA
* * ** * *
374152 CCTCTTCAACGATGACAGTGGC
1 -CTCTTGAACGGTGGGAGGGGA
374174 CTCTTGAACGGTGGGAGGGGA
1 CTCTTGAACGGTGGGAGGGGA
374195 CTCT
1 CTCT
374199 CGAGGAATGA
Statistics
Matches: 32, Mismatches: 13, Indels: 2
0.68 0.28 0.04
Matches are distributed among these distances:
21 30 0.94
22 2 0.06
ACGTcount: A:0.19, C:0.21, G:0.36, T:0.24
Consensus pattern (21 bp):
CTCTTGAACGGTGGGAGGGGA
Found at i:374273 original size:84 final size:84
Alignment explanation
Indices: 374162--374337 Score: 334
Period size: 84 Copynumber: 2.1 Consensus size: 84
374152 CCTCTTCAAC
**
374162 GATGACAGTGGCCTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGGGGCCTCTTCAATGA
1 GATGACAGTGGCCTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGGGGCCTCTTCAACAA
374227 TAGGAGTGGACTCTTGAGG
66 TAGGAGTGGACTCTTGAGG
374246 GATGACAGTGGCCTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGGGGCCTCTTCAACAA
1 GATGACAGTGGCCTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGGGGCCTCTTCAACAA
374311 TAGGAGTGGACTCTTGAGG
66 TAGGAGTGGACTCTTGAGG
374330 GATGACAG
1 GATGACAG
374338 GCGAGTCGGG
Statistics
Matches: 90, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
84 90 1.00
ACGTcount: A:0.24, C:0.17, G:0.38, T:0.22
Consensus pattern (84 bp):
GATGACAGTGGCCTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGGGGCCTCTTCAACAA
TAGGAGTGGACTCTTGAGG
Found at i:374727 original size:91 final size:90
Alignment explanation
Indices: 374554--374740 Score: 295
Period size: 91 Copynumber: 2.0 Consensus size: 90
374544 ATATTTCAAA
* *
374554 ACTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGTTTA
1 ACTTCAACCAAAAGACAAAACAAAAACAAATACTAACTTCACAGTGTT--A-AATAAACAGTTTA
374619 GCAGAATTGGCAGCAACCGAATAAATTT
63 GCAGAATTGGCAGCAACCGAATAAATTT
374647 ACTTCAACCAAAAGACAAAACAAAAAAACAAATACTAACTTCACAGTGTT-AATAAACAGTTTAG
1 ACTTCAACCAAAAGACAAAAC--AAAAACAAATACTAACTTCACAGTGTTAAATAAACAGTTTAG
*
374711 CAGTATTGGCAGCAACCGAATAAATTT
64 CAGAATTGGCAGCAACCGAATAAATTT
374738 ACT
1 ACT
374741 AAGCAATCTA
Statistics
Matches: 89, Mismatches: 3, Indels: 6
0.91 0.03 0.06
Matches are distributed among these distances:
91 42 0.47
93 21 0.24
95 26 0.29
ACGTcount: A:0.48, C:0.19, G:0.12, T:0.21
Consensus pattern (90 bp):
ACTTCAACCAAAAGACAAAACAAAAACAAATACTAACTTCACAGTGTTAAATAAACAGTTTAGCA
GAATTGGCAGCAACCGAATAAATTT
Found at i:374980 original size:63 final size:63
Alignment explanation
Indices: 374907--375037 Score: 244
Period size: 63 Copynumber: 2.1 Consensus size: 63
374897 TAAAGTAGAC
*
374907 ACCTCCACACGCCATGCACCATCGTTATCGCGTAGAGTACCGATCTCCTCACGCAAGGCATTG
1 ACCTCCACACGCCATGCACCATCGTTATCCCGTAGAGTACCGATCTCCTCACGCAAGGCATTG
*
374970 ACCTCTACACGCCATGCACCATCGTTATCCCGTAGAGTACCGATCTCCTCACGCAAGGCATTG
1 ACCTCCACACGCCATGCACCATCGTTATCCCGTAGAGTACCGATCTCCTCACGCAAGGCATTG
375033 ACCTC
1 ACCTC
375038 ATCACGTAAC
Statistics
Matches: 66, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
63 66 1.00
ACGTcount: A:0.24, C:0.37, G:0.18, T:0.21
Consensus pattern (63 bp):
ACCTCCACACGCCATGCACCATCGTTATCCCGTAGAGTACCGATCTCCTCACGCAAGGCATTG
Found at i:376543 original size:19 final size:19
Alignment explanation
Indices: 376492--376636 Score: 139
Period size: 19 Copynumber: 8.1 Consensus size: 19
376482 TCTTTTGGTT
**
376492 GAAATGAAAATCGCAACAA
1 GAAATGAAAATCGCAACGC
*
376511 GATAATGAGAATCGCAACGC
1 GA-AATGAAAATCGCAACGC
**
376531 GAAATGACTATCGCAA--C
1 GAAATGAAAATCGCAACGC
*
376548 G--A-GAGAATCGCAACGC
1 GAAATGAAAATCGCAACGC
376564 GAAATGAAAATCGCAACGC
1 GAAATGAAAATCGCAACGC
376583 GAAATGAAAATCGCAA--C
1 GAAATGAAAATCGCAACGC
*
376600 G--A-GAGAATCGCAACGC
1 GAAATGAAAATCGCAACGC
*
376616 GAAATGAAAATCGCAATGC
1 GAAATGAAAATCGCAACGC
376635 GA
1 GA
376637 TTTTGGTTTC
Statistics
Matches: 104, Mismatches: 11, Indels: 22
0.76 0.08 0.16
Matches are distributed among these distances:
14 19 0.18
15 2 0.02
16 4 0.04
17 4 0.04
18 2 0.02
19 57 0.55
20 16 0.15
ACGTcount: A:0.46, C:0.20, G:0.23, T:0.12
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGC
Found at i:376559 original size:33 final size:33
Alignment explanation
Indices: 376517--376581 Score: 112
Period size: 33 Copynumber: 2.0 Consensus size: 33
376507 ACAAGATAAT
**
376517 GAGAATCGCAACGCGAAATGACTATCGCAACGA
1 GAGAATCGCAACGCGAAATGAAAATCGCAACGA
376550 GAGAATCGCAACGCGAAATGAAAATCGCAACG
1 GAGAATCGCAACGCGAAATGAAAATCGCAACG
376582 CGAAATGAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.42, C:0.23, G:0.25, T:0.11
Consensus pattern (33 bp):
GAGAATCGCAACGCGAAATGAAAATCGCAACGA
Found at i:376576 original size:52 final size:52
Alignment explanation
Indices: 376500--376636 Score: 211
Period size: 52 Copynumber: 2.6 Consensus size: 52
376490 TTGAAATGAA
** * **
376500 AATCGCAACAAGATAATGAGAATCGCAACGCGAAATGACTATCGCAACGAGAG
1 AATCGCAACGCGA-AATGAAAATCGCAACGCGAAATGAAAATCGCAACGAGAG
376553 AATCGCAACGCGAAATGAAAATCGCAACGCGAAATGAAAATCGCAACGAGAG
1 AATCGCAACGCGAAATGAAAATCGCAACGCGAAATGAAAATCGCAACGAGAG
*
376605 AATCGCAACGCGAAATGAAAATCGCAATGCGA
1 AATCGCAACGCGAAATGAAAATCGCAACGCGA
376637 TTTTGGTTTC
Statistics
Matches: 78, Mismatches: 6, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
52 67 0.86
53 11 0.14
ACGTcount: A:0.45, C:0.21, G:0.23, T:0.12
Consensus pattern (52 bp):
AATCGCAACGCGAAATGAAAATCGCAACGCGAAATGAAAATCGCAACGAGAG
Found at i:376654 original size:19 final size:18
Alignment explanation
Indices: 376632--376698 Score: 71
Period size: 19 Copynumber: 3.5 Consensus size: 18
376622 AAAATCGCAA
*
376632 TGCGATTTTGGTTTCGCGT
1 TGCGATTTT-ATTTCGCGT
*
376651 TGCGTTTTTTATTTCGCGT
1 TGCG-ATTTTATTTCGCGT
*
376670 TGCGATAGTTATTTCCGCGT
1 TGCGAT-TTTATTT-CGCGT
376690 TGCGATTTT
1 TGCGATTTT
376699 CATTCTCGAA
Statistics
Matches: 40, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
18 1 0.03
19 24 0.60
20 15 0.38
ACGTcount: A:0.09, C:0.16, G:0.25, T:0.49
Consensus pattern (18 bp):
TGCGATTTTATTTCGCGT
Found at i:377241 original size:20 final size:20
Alignment explanation
Indices: 377216--377268 Score: 88
Period size: 20 Copynumber: 2.6 Consensus size: 20
377206 GCGCTATGTA
377216 AATCGCGTTGCGAAAGTCAG
1 AATCGCGTTGCGAAAGTCAG
377236 AATCGCGTTGCGAAAGTCAG
1 AATCGCGTTGCGAAAGTCAG
* *
377256 TATCTCGTTGCGA
1 AATCGCGTTGCGA
377269 TTTTGTATTA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.26, C:0.21, G:0.28, T:0.25
Consensus pattern (20 bp):
AATCGCGTTGCGAAAGTCAG
Found at i:377288 original size:41 final size:40
Alignment explanation
Indices: 377217--377370 Score: 166
Period size: 40 Copynumber: 3.8 Consensus size: 40
377207 CGCTATGTAA
* * * * * *
377217 ATCGCGTTGCGAAAGTCAGAATCGCGTTGCGAAAGTCAGT
1 ATCGCATTGCGATAGTAAGTATCGCATTGCGATAGTCAGT
* * * * *
377257 ATCTCGTTGCGATTTTGT-ATTATCGCATTGCGATAGTAAGT
1 ATCGCATTGCGA--TAGTAAGTATCGCATTGCGATAGTCAGT
377298 ATCGCATTGCGATAGTAAGTATCGCATTGCGATAGTCAGT
1 ATCGCATTGCGATAGTAAGTATCGCATTGCGATAGTCAGT
* *
377338 ATCGCATTGCAATAGTCAGTATCGCATTGCGAT
1 ATCGCATTGCGATAGTAAGTATCGCATTGCGAT
377371 TTTCCCAATT
Statistics
Matches: 96, Mismatches: 15, Indels: 6
0.82 0.13 0.05
Matches are distributed among these distances:
39 3 0.03
40 63 0.66
41 28 0.29
42 2 0.02
ACGTcount: A:0.26, C:0.18, G:0.25, T:0.31
Consensus pattern (40 bp):
ATCGCATTGCGATAGTAAGTATCGCATTGCGATAGTCAGT
Found at i:377302 original size:20 final size:20
Alignment explanation
Indices: 377277--377370 Score: 161
Period size: 20 Copynumber: 4.7 Consensus size: 20
377267 GATTTTGTAT
377277 TATCGCATTGCGATAGTAAG
1 TATCGCATTGCGATAGTAAG
377297 TATCGCATTGCGATAGTAAG
1 TATCGCATTGCGATAGTAAG
*
377317 TATCGCATTGCGATAGTCAG
1 TATCGCATTGCGATAGTAAG
* *
377337 TATCGCATTGCAATAGTCAG
1 TATCGCATTGCGATAGTAAG
377357 TATCGCATTGCGAT
1 TATCGCATTGCGAT
377371 TTTCCCAATT
Statistics
Matches: 71, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 71 1.00
ACGTcount: A:0.28, C:0.18, G:0.23, T:0.31
Consensus pattern (20 bp):
TATCGCATTGCGATAGTAAG
Found at i:382084 original size:6 final size:5
Alignment explanation
Indices: 382070--382109 Score: 55
Period size: 5 Copynumber: 8.0 Consensus size: 5
382060 AAGTAATTAA
*
382070 TTATT TTATTT TTATT TTATT TTATT TTAGT TT-TT TTATT
1 TTATT TTA-TT TTATT TTATT TTATT TTATT TTATT TTATT
382110 ATTTAATTGT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
4 3 0.10
5 23 0.74
6 5 0.16
ACGTcount: A:0.17, C:0.00, G:0.03, T:0.80
Consensus pattern (5 bp):
TTATT
Found at i:382086 original size:11 final size:11
Alignment explanation
Indices: 382070--382113 Score: 56
Period size: 11 Copynumber: 4.0 Consensus size: 11
382060 AAGTAATTAA
382070 TTATTTTATTT
1 TTATTTTATTT
382081 TTATTTTA-TT
1 TTATTTTATTT
382091 TTATTTTAGTTT
1 TTATTTTA-TTT
382103 TT-TTATTATTT
1 TTATT-TTATTT
382114 AATTGTAAAC
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
10 10 0.33
11 13 0.43
12 7 0.23
ACGTcount: A:0.18, C:0.00, G:0.02, T:0.80
Consensus pattern (11 bp):
TTATTTTATTT
Found at i:382089 original size:16 final size:16
Alignment explanation
Indices: 382070--382114 Score: 58
Period size: 16 Copynumber: 2.9 Consensus size: 16
382060 AAGTAATTAA
*
382070 TTATTTTATTTTTATT
1 TTATTTTATTTTTAGT
382086 TTATTTTA-TTTTAGT
1 TTATTTTATTTTTAGT
382101 TT-TTTTATTATTTA
1 TTATTTTATT-TTTA
382115 ATTGTAAACT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
14 5 0.19
15 9 0.35
16 12 0.46
ACGTcount: A:0.20, C:0.00, G:0.02, T:0.78
Consensus pattern (16 bp):
TTATTTTATTTTTAGT
Found at i:385781 original size:17 final size:17
Alignment explanation
Indices: 385748--385780 Score: 52
Period size: 15 Copynumber: 2.1 Consensus size: 17
385738 ATAGAAAATA
385748 TAATTTTTTATTATTTT
1 TAATTTTTTATTATTTT
385765 TAA--TTTTATTATTTT
1 TAATTTTTTATTATTTT
385780 T
1 T
385781 TAATAAAATT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 13 0.81
17 3 0.19
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (17 bp):
TAATTTTTTATTATTTT
Found at i:385906 original size:49 final size:50
Alignment explanation
Indices: 385833--385954 Score: 165
Period size: 49 Copynumber: 2.5 Consensus size: 50
385823 AGATGCACGT
* * * *
385833 ATGTAAGTATATATTTATTGTTAGGTTGGGAGATGTACATACTTACACC-
1 ATGTAAGTATGTGTTTATTGTTAGGCTGAGAGATGTACATACTTACACCG
* *
385882 ATGTAAGTATGTGTTTATTTTTAGGCTGAGAGATGTATATACTTACACCG
1 ATGTAAGTATGTGTTTATTGTTAGGCTGAGAGATGTACATACTTACACCG
* *
385932 ATATAAGTATGTGTTAATTGTTA
1 ATGTAAGTATGTGTTTATTGTTA
385955 CACTTTTTTA
Statistics
Matches: 63, Mismatches: 9, Indels: 1
0.86 0.12 0.01
Matches are distributed among these distances:
49 43 0.68
50 20 0.32
ACGTcount: A:0.30, C:0.08, G:0.20, T:0.41
Consensus pattern (50 bp):
ATGTAAGTATGTGTTTATTGTTAGGCTGAGAGATGTACATACTTACACCG
Found at i:386276 original size:15 final size:15
Alignment explanation
Indices: 386253--386283 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
386243 CACGTGTAAT
386253 TATAAACAAAAGGAA
1 TATAAACAAAAGGAA
*
386268 TATATACAAAAGGAA
1 TATAAACAAAAGGAA
386283 T
1 T
386284 GATTATTTTG
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:0.61, C:0.06, G:0.13, T:0.19
Consensus pattern (15 bp):
TATAAACAAAAGGAA
Found at i:387131 original size:2 final size:2
Alignment explanation
Indices: 387126--387160 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
387116 TATTAAATAA
387126 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
387161 GGGTTTTGTA
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:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:389053 original size:3 final size:3
Alignment explanation
Indices: 389040--389121 Score: 107
Period size: 3 Copynumber: 28.0 Consensus size: 3
389030 GGCCTGTTTG
* * *
389040 TAA TGA TAA TAA TAT TAA TAA TAA AAA TAAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA T-AA TAA TAA TAA TAA TAA
389086 TAA T-A TAA TAA TAA T-A TAA TAA -AA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
389122 AGATAAAAAA
Statistics
Matches: 69, Mismatches: 6, Indels: 8
0.83 0.07 0.10
Matches are distributed among these distances:
2 6 0.09
3 60 0.87
4 3 0.04
ACGTcount: A:0.66, C:0.00, G:0.01, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:389072 original size:22 final size:22
Alignment explanation
Indices: 389047--389136 Score: 109
Period size: 22 Copynumber: 4.2 Consensus size: 22
389037 TTGTAATGAT
*
389047 AATAATATTAATAATAAAAATA
1 AATAATAATAATAATAAAAATA
*
389069 AATAATAATAATAATAATAATA
1 AATAATAATAATAATAAAAATA
389091 TAATAATAAT-ATAAT-AAAAT-
1 -AATAATAATAATAATAAAAATA
389111 AATAATAATAA-AGATAAAAA-A
1 AATAATAATAATA-ATAAAAATA
389132 AATAA
1 AATAA
389137 AATGAAAAAA
Statistics
Matches: 60, Mismatches: 3, Indels: 11
0.81 0.04 0.15
Matches are distributed among these distances:
19 10 0.17
20 3 0.05
21 13 0.22
22 25 0.42
23 9 0.15
ACGTcount: A:0.70, C:0.00, G:0.01, T:0.29
Consensus pattern (22 bp):
AATAATAATAATAATAAAAATA
Found at i:389077 original size:19 final size:19
Alignment explanation
Indices: 389050--389128 Score: 97
Period size: 19 Copynumber: 4.1 Consensus size: 19
389040 TAATGATAAT
*
389050 AATATTAATAATAAAAATA
1 AATAATAATAATAAAAATA
*
389069 AATAATAATAATAATAATA
1 AATAATAATAATAAAAATA
*
389088 ATATAATAATAAT-ATAATAA
1 A-ATAATAATAATAAAAAT-A
*
389108 AATAATAATAATAAAGATA
1 AATAATAATAATAAAAATA
389127 AA
1 AA
389129 AAAAATAAAA
Statistics
Matches: 53, Mismatches: 4, Indels: 6
0.84 0.06 0.10
Matches are distributed among these distances:
19 37 0.70
20 16 0.30
ACGTcount: A:0.68, C:0.00, G:0.01, T:0.30
Consensus pattern (19 bp):
AATAATAATAATAAAAATA
Found at i:389135 original size:15 final size:14
Alignment explanation
Indices: 389059--389146 Score: 59
Period size: 15 Copynumber: 5.6 Consensus size: 14
389049 TAATATTAAT
389059 AATAAAAATAAATAA
1 AATAAAAA-AAATAA
*
389074 TAATAATAATAATAATAT
1 -AATAA-AA-AA-AATAA
*
389092 AATAATAATATAATAA
1 AATAA-AA-AAAATAA
* *
389108 AATAATAATAATAA
1 AATAAAAAAAATAA
389122 AGATAAAAAAAATAA
1 A-ATAAAAAAAATAA
389137 AATGAAAAAA
1 AAT-AAAAAA
389147 CTAGTGTCTT
Statistics
Matches: 61, Mismatches: 6, Indels: 11
0.78 0.08 0.14
Matches are distributed among these distances:
14 10 0.16
15 19 0.31
16 14 0.23
17 13 0.21
18 5 0.08
ACGTcount: A:0.73, C:0.00, G:0.02, T:0.25
Consensus pattern (14 bp):
AATAAAAAAAATAA
Found at i:389144 original size:6 final size:5
Alignment explanation
Indices: 389063--389144 Score: 55
Period size: 6 Copynumber: 15.8 Consensus size: 5
389053 ATTAATAATA
* *
389063 AAAAT -AAAT AATAAT AATAAT AATAAT ATAAT AATAAT ATAAT AAAAT
1 AAAAT AAAAT AA-AAT AA-AAT AA-AAT AAAAT AA-AAT AAAAT AAAAT
389111 --AAT AATAAT AAAGAT AAAA- AAAAT AAAAT GAAAA
1 AAAAT AA-AAT AAA-AT AAAAT AAAAT AAAAT -AAAA
389145 AACTAGTGTC
Statistics
Matches: 64, Mismatches: 4, Indels: 17
0.75 0.05 0.20
Matches are distributed among these distances:
3 3 0.05
4 8 0.12
5 19 0.30
6 34 0.53
ACGTcount: A:0.72, C:0.00, G:0.02, T:0.26
Consensus pattern (5 bp):
AAAAT
Found at i:389461 original size:18 final size:20
Alignment explanation
Indices: 389430--389466 Score: 60
Period size: 18 Copynumber: 1.9 Consensus size: 20
389420 GCTTTATAAT
389430 ATATATTTTCATATATCATC
1 ATATATTTTCATATATCATC
389450 ATATA-TTT-ATATATCAT
1 ATATATTTTCATATATCAT
389467 TCTCTCTTCA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 9 0.53
19 3 0.18
20 5 0.29
ACGTcount: A:0.38, C:0.11, G:0.00, T:0.51
Consensus pattern (20 bp):
ATATATTTTCATATATCATC
Found at i:392814 original size:17 final size:17
Alignment explanation
Indices: 392781--392813 Score: 52
Period size: 15 Copynumber: 2.1 Consensus size: 17
392771 ATAGAAAATA
392781 TAATTTTTTATTATTTT
1 TAATTTTTTATTATTTT
392798 TAA--TTTTATTATTTT
1 TAATTTTTTATTATTTT
392813 T
1 T
392814 TAATAAAATT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 13 0.81
17 3 0.19
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (17 bp):
TAATTTTTTATTATTTT
Found at i:392939 original size:49 final size:50
Alignment explanation
Indices: 392866--392987 Score: 156
Period size: 49 Copynumber: 2.5 Consensus size: 50
392856 AGATGCACGT
* * * * *
392866 ATGTAAGTATATATTTATTGTTAGGTTGGGAGATGTGCATACTTACACC-
1 ATGTAAGTATGTGTTTATTGTTAGGCTGAGAGATGTACATACTTACACCG
* *
392915 ATGTAAGTATGTGTTTATTTTTAGGCTGAGAGATGTATATACTTACACCG
1 ATGTAAGTATGTGTTTATTGTTAGGCTGAGAGATGTACATACTTACACCG
* *
392965 ATATAAGTATGTGTTAATTGTTA
1 ATGTAAGTATGTGTTTATTGTTA
392988 CACTTTTTTA
Statistics
Matches: 62, Mismatches: 10, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
49 42 0.68
50 20 0.32
ACGTcount: A:0.30, C:0.08, G:0.21, T:0.41
Consensus pattern (50 bp):
ATGTAAGTATGTGTTTATTGTTAGGCTGAGAGATGTACATACTTACACCG
Found at i:393306 original size:15 final size:15
Alignment explanation
Indices: 393283--393314 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
393273 CACGTGTAAT
393283 TATAAACAAAAGGAA
1 TATAAACAAAAGGAA
*
393298 TATATACAAAAGGAA
1 TATAAACAAAAGGAA
393313 TA
1 TA
393315 ATTATTTTGA
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:0.62, C:0.06, G:0.12, T:0.19
Consensus pattern (15 bp):
TATAAACAAAAGGAA
Found at i:394024 original size:14 final size:14
Alignment explanation
Indices: 393989--394024 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
393979 CGAACAAACG
*
393989 AAACAATATAAAAA
1 AAACAATGTAAAAA
394003 AAACAATGTAAAAA
1 AAACAATGTAAAAA
*
394017 AAAGAATG
1 AAACAATG
394025 AAATATGACT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.72, C:0.06, G:0.08, T:0.14
Consensus pattern (14 bp):
AAACAATGTAAAAA
Found at i:394127 original size:19 final size:19
Alignment explanation
Indices: 394097--394152 Score: 60
Period size: 19 Copynumber: 2.9 Consensus size: 19
394087 AAAAGAAGAA
*
394097 AATATAATAAAATATAAAT
1 AATAAAATAAAATATAAAT
* * *
394116 GGATAAAA-AAAATACACAT
1 -AATAAAATAAAATATAAAT
394135 AATAAAATAAAATATAAA
1 AATAAAATAAAATATAAA
394153 GCAATGAAAA
Statistics
Matches: 28, Mismatches: 7, Indels: 3
0.74 0.18 0.08
Matches are distributed among these distances:
18 6 0.21
19 17 0.61
20 5 0.18
ACGTcount: A:0.70, C:0.04, G:0.04, T:0.23
Consensus pattern (19 bp):
AATAAAATAAAATATAAAT
Found at i:396211 original size:105 final size:105
Alignment explanation
Indices: 395977--397086 Score: 1909
Period size: 105 Copynumber: 10.6 Consensus size: 105
395967 CGTCATGAGA
395977 TTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGA
1 TTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGA
*
396042 GAAGTTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAG
66 GAA-ATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAG
* * *
396083 TTAAACTTTCGTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGA
1 TTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGA
*
396148 GAAATGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAG
66 GAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAG
* *
396188 TTGAACTTTCGTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGA
1 TTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGA
*
396253 GAAATGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAG
66 GAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAG
396293 TTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGA
1 TTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGA
396358 GAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAG
66 GAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAG
* *
396398 TTGAACTTTCGTTGTCTGGGGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGA
1 TTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGA
*
396463 GAAACGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAG
66 GAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAG
396503 TTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGA
1 TTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGA
396568 GAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAG
66 GAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAG
* *
396608 TTGAACTTTCGTTGTCTGGGGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGA
1 TTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGA
*
396673 GAAACGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAG
66 GAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAG
* *
396713 TTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTATGAGGTTGAAATTGGCTCTGAAATTGA
1 TTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGA
*
396778 GAAACGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAG
66 GAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAG
**
396818 TTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGTGATTGGCTCTG-AATTGG
1 TTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATT-G
* *
396882 AGAAATGTTTGGTGACAACCAGCGGTCCCTTCATCGTGAAG
65 AGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAG
* *
396923 TTGAACTTGCGTCGTCTGGGGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTG-AATTGG
1 TTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATT-G
* * *
396987 AGAAATGTTTGGTGACAATCAGCGGTCCCTTCGTCATGAAG
65 AGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAG
* **
397028 TTGAACTTTGCATTGTCTATAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTG
1 TTGAAC-TTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTG
397087 GGTAAAACCT
Statistics
Matches: 961, Mismatches: 41, Indels: 4
0.96 0.04 0.00
Matches are distributed among these distances:
104 4 0.00
105 845 0.88
106 112 0.12
ACGTcount: A:0.23, C:0.18, G:0.25, T:0.34
Consensus pattern (105 bp):
TTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGA
GAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAG
Found at i:397927 original size:55 final size:57
Alignment explanation
Indices: 397853--397961 Score: 159
Period size: 56 Copynumber: 1.9 Consensus size: 57
397843 TTTTCTCTTC
* * *
397853 TTTTTTCTTTTTCTTTTTTT-AATTTAGGGCGCCCTTTCGGGTTTTCACCCTAAACG
1 TTTTTTCTTTTTCTTTTTTTCAACTTAGGACGCCCTCTCGGGTTTTCACCCTAAACG
* *
397909 TTTTTT-TTTTTTTTTTTTTCAACTTAGGACGCCCTCTCGGGTTTTCATCCTAA
1 TTTTTTCTTTTTCTTTTTTTCAACTTAGGACGCCCTCTCGGGTTTTCACCCTAA
397962 GCGAAATATT
Statistics
Matches: 47, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
55 12 0.26
56 35 0.74
ACGTcount: A:0.13, C:0.21, G:0.13, T:0.53
Consensus pattern (57 bp):
TTTTTTCTTTTTCTTTTTTTCAACTTAGGACGCCCTCTCGGGTTTTCACCCTAAACG
Found at i:410649 original size:2 final size:2
Alignment explanation
Indices: 410642--410689 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
410632 AAATAAATAA
410642 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
410684 AT AT AT
1 AT AT AT
410690 TTAGGGTTTT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:412554 original size:3 final size:3
Alignment explanation
Indices: 412541--412622 Score: 107
Period size: 3 Copynumber: 28.0 Consensus size: 3
412531 GGCCTGTTTG
* * *
412541 TAA TGA TAA TAA TAT TAA TAA TAA AAA TAA T-A TAA TAA TAA TATA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA-A
412586 TAA TAA TAA TAA TAA -AA TAA TAA -AA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
412623 AGATAAAAAA
Statistics
Matches: 69, Mismatches: 6, Indels: 8
0.83 0.07 0.10
Matches are distributed among these distances:
2 6 0.09
3 60 0.87
4 3 0.04
ACGTcount: A:0.66, C:0.00, G:0.01, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:412638 original size:35 final size:35
Alignment explanation
Indices: 412564--412638 Score: 91
Period size: 35 Copynumber: 2.1 Consensus size: 35
412554 ATTAATAATA
* * *
412564 AAAATAATATAATAATAATATATAATAATAATAAT
1 AAAATAATAAAATAATAATATATAATAATAAAAAC
412599 AAAATAATAAAATAATAATA-ATAA-AGATAAAAAAC
1 AAAATAATAAAATAATAATATATAATA-AT-AAAAAC
412634 AAAAT
1 AAAAT
412639 GAAAAAACTA
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
33 1 0.03
34 6 0.17
35 28 0.80
ACGTcount: A:0.71, C:0.01, G:0.01, T:0.27
Consensus pattern (35 bp):
AAAATAATAAAATAATAATATATAATAATAAAAAC
Found at i:412954 original size:18 final size:20
Alignment explanation
Indices: 412923--412959 Score: 60
Period size: 18 Copynumber: 1.9 Consensus size: 20
412913 GCTTTATAAT
412923 ATATATTTTCATATATCATC
1 ATATATTTTCATATATCATC
412943 ATATA-TTT-ATATATCAT
1 ATATATTTTCATATATCAT
412960 TCTCTCTTCA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 9 0.53
19 3 0.18
20 5 0.29
ACGTcount: A:0.38, C:0.11, G:0.00, T:0.51
Consensus pattern (20 bp):
ATATATTTTCATATATCATC
Found at i:416292 original size:17 final size:17
Alignment explanation
Indices: 416259--416291 Score: 52
Period size: 15 Copynumber: 2.1 Consensus size: 17
416249 ATAGAAAATA
416259 TAATTTTTTATTATTTT
1 TAATTTTTTATTATTTT
416276 TAA--TTTTATTATTTT
1 TAATTTTTTATTATTTT
416291 T
1 T
416292 TAATAAAATT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 13 0.81
17 3 0.19
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (17 bp):
TAATTTTTTATTATTTT
Found at i:416424 original size:49 final size:49
Alignment explanation
Indices: 416344--416455 Score: 147
Period size: 49 Copynumber: 2.3 Consensus size: 49
416334 AGATGCACGT
* * *
416344 ATGTAAGTATAT-TTTTTGTTAGGTTGGGAGATGTACATACTTACACC-
1 ATGTAAGTATGTGTTTTTGTTAGGCTGAGAGATGTACATACTTACACCG
* *
416391 ATGTAAGTATGTGTTTATTTTTAGGCTGAGAGATGTATATACTTACACCG
1 ATGTAAGTATGTGTTT-TTGTTAGGCTGAGAGATGTACATACTTACACCG
*
416441 ATATAAGTATGTGTT
1 ATGTAAGTATGTGTT
416456 AATTGTTACA
Statistics
Matches: 56, Mismatches: 6, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
47 11 0.20
48 3 0.05
49 28 0.50
50 14 0.25
ACGTcount: A:0.29, C:0.09, G:0.21, T:0.41
Consensus pattern (49 bp):
ATGTAAGTATGTGTTTTTGTTAGGCTGAGAGATGTACATACTTACACCG
Found at i:416776 original size:15 final size:15
Alignment explanation
Indices: 416753--416784 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
416743 CACGTGTAAT
416753 TATAAACAAAAGGAA
1 TATAAACAAAAGGAA
*
416768 TATATACAAAAGGAA
1 TATAAACAAAAGGAA
416783 TA
1 TA
416785 ATTATTTTGA
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:0.62, C:0.06, G:0.12, T:0.19
Consensus pattern (15 bp):
TATAAACAAAAGGAA
Found at i:417637 original size:2 final size:2
Alignment explanation
Indices: 417630--417655 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
417620 AAATAAATAA
417630 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
417656 TTAGGGTTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:418044 original size:18 final size:18
Alignment explanation
Indices: 418021--418057 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
418011 CCTTTCTTAA
418021 TATTTAAAAAATAAATAT
1 TATTTAAAAAATAAATAT
* *
418039 TATTTAAACAATATATAT
1 TATTTAAAAAATAAATAT
418057 T
1 T
418058 TATATGACTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.43
Consensus pattern (18 bp):
TATTTAAAAAATAAATAT
Found at i:419517 original size:3 final size:3
Alignment explanation
Indices: 419504--419591 Score: 119
Period size: 3 Copynumber: 30.0 Consensus size: 3
419494 GGCCTGTTTG
* * *
419504 TAA TGA TAA TAA TAT TAA TAA TAA AAA TAAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA T-AA TAA TAA TAA TAA TAA
419550 T-A TAA TAA TAA TAA TAA TAA -AA TAA TAA -AA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
419592 AGATAAAAAA
Statistics
Matches: 75, Mismatches: 6, Indels: 8
0.84 0.07 0.09
Matches are distributed among these distances:
2 6 0.08
3 66 0.88
4 3 0.04
ACGTcount: A:0.67, C:0.00, G:0.01, T:0.32
Consensus pattern (3 bp):
TAA
Found at i:419591 original size:42 final size:43
Alignment explanation
Indices: 419504--419597 Score: 138
Period size: 42 Copynumber: 2.2 Consensus size: 43
419494 GGCCTGTTTG
* *
419504 TAATGATAATAATATTAATAATAAAAATAAATAATAATAATAA
1 TAATGATAATAATAATAATAATAAAAATAAAAAATAATAATAA
419547 TAAT-ATAATAATAATAATAAT-AAAATAATAAAATAATAATAA
1 TAATGATAATAATAATAATAATAAAAATAA-AAAATAATAATAA
*
419589 TAAAGATAA
1 TAATGATAA
419598 AAAACAAAAT
Statistics
Matches: 46, Mismatches: 3, Indels: 4
0.87 0.06 0.08
Matches are distributed among these distances:
41 7 0.15
42 31 0.67
43 8 0.17
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (43 bp):
TAATGATAATAATAATAATAATAAAAATAAAAAATAATAATAA
Found at i:419597 original size:28 final size:27
Alignment explanation
Indices: 419511--419607 Score: 97
Period size: 28 Copynumber: 3.4 Consensus size: 27
419501 TTGTAATGAT
* *
419511 AATAATATTAATAATAAAAATAAATAATAA
1 AATAATA-AAATAATAATAAT-AA-AATAA
*
419541 TAATAATAATATAATAATAATAATAATAA
1 -AATAATAAAATAATAATAATAA-AATAA
419570 AATAATAAAATAATAATAATAAAGATAA
1 AATAATAAAATAATAATAATAAA-ATAA
*
419598 AA-AACAAAAT
1 AATAATAAAAT
419608 GAAAAAACTA
Statistics
Matches: 60, Mismatches: 5, Indels: 6
0.85 0.07 0.08
Matches are distributed among these distances:
27 8 0.13
28 27 0.45
29 8 0.13
30 10 0.17
31 7 0.12
ACGTcount: A:0.70, C:0.01, G:0.01, T:0.28
Consensus pattern (27 bp):
AATAATAAAATAATAATAATAAAATAA
Found at i:419929 original size:18 final size:20
Alignment explanation
Indices: 419898--419934 Score: 60
Period size: 18 Copynumber: 1.9 Consensus size: 20
419888 GCTTTATAAT
419898 ATATATTTTCATATATCATC
1 ATATATTTTCATATATCATC
419918 ATATA-TTT-ATATATCAT
1 ATATATTTTCATATATCAT
419935 TCTGTCTTCA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 9 0.53
19 3 0.18
20 5 0.29
ACGTcount: A:0.38, C:0.11, G:0.00, T:0.51
Consensus pattern (20 bp):
ATATATTTTCATATATCATC
Found at i:423334 original size:15 final size:15
Alignment explanation
Indices: 423314--423344 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
423304 AAATATAATT
423314 TTTTATTATTTTTAA
1 TTTTATTATTTTTAA
423329 TTTTATTATTTTTAA
1 TTTTATTATTTTTAA
423344 T
1 T
423345 AAAATTATAC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (15 bp):
TTTTATTATTTTTAA
Found at i:423462 original size:49 final size:50
Alignment explanation
Indices: 423389--423510 Score: 165
Period size: 49 Copynumber: 2.5 Consensus size: 50
423379 AGATGCACGT
* * * *
423389 ATGTAAGTATATATTTATTGTTAGGTTAGGAGATGTACATACTTACACC-
1 ATGTAAGTATGTGTTTATTGTTAGGCTAAGAGATGTACATACTTACACCG
* *
423438 ATGTAAGTATGTGTTTATTTTTAGGCTAAGAGATGTATATACTTACACCG
1 ATGTAAGTATGTGTTTATTGTTAGGCTAAGAGATGTACATACTTACACCG
* *
423488 ATATAAGTATGTGTTAATTGTTA
1 ATGTAAGTATGTGTTTATTGTTA
423511 CACTTTTTAT
Statistics
Matches: 63, Mismatches: 9, Indels: 1
0.86 0.12 0.01
Matches are distributed among these distances:
49 43 0.68
50 20 0.32
ACGTcount: A:0.32, C:0.08, G:0.19, T:0.41
Consensus pattern (50 bp):
ATGTAAGTATGTGTTTATTGTTAGGCTAAGAGATGTACATACTTACACCG
Found at i:423824 original size:15 final size:15
Alignment explanation
Indices: 423801--423831 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
423791 ACACGTGTAT
423801 TATAAACAAAAGGAA
1 TATAAACAAAAGGAA
*
423816 TATATACAAAAGGAA
1 TATAAACAAAAGGAA
423831 T
1 T
423832 GATTATTTTG
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:0.61, C:0.06, G:0.13, T:0.19
Consensus pattern (15 bp):
TATAAACAAAAGGAA
Found at i:428821 original size:49 final size:51
Alignment explanation
Indices: 428740--428860 Score: 164
Period size: 49 Copynumber: 2.5 Consensus size: 51
428730 AGATGCACGT
*
428740 ATGTAAGTATAT-TTT-ATTGTTAGGCTAGGAGATGTACATACTTACACC-
1 ATGTAAGTATGTGTTTAATTGTTAGGCTAGGAGATGTACATACTTACACCG
*
428788 ATGTAAGTATGTGTTTAATT-TTAGGCT-GAGAGATGTATATACTTACACCG
1 ATGTAAGTATGTGTTTAATTGTTAGGCTAG-GAGATGTACATACTTACACCG
*
428838 ATATAAGTATGTG-TTAATTGTTA
1 ATGTAAGTATGTGTTTAATTGTTA
428861 CACTTTTTTA
Statistics
Matches: 65, Mismatches: 3, Indels: 8
0.86 0.04 0.11
Matches are distributed among these distances:
48 12 0.18
49 35 0.54
50 18 0.28
ACGTcount: A:0.31, C:0.09, G:0.20, T:0.40
Consensus pattern (51 bp):
ATGTAAGTATGTGTTTAATTGTTAGGCTAGGAGATGTACATACTTACACCG
Found at i:429191 original size:17 final size:15
Alignment explanation
Indices: 429169--429199 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
429159 CACGTGTAAT
*
429169 TATATACAAAAGGAA
1 TATATATAAAAGGAA
429184 TATATATAAAAGGAA
1 TATATATAAAAGGAA
429199 T
1 T
429200 GATTATTTTG
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:0.58, C:0.03, G:0.13, T:0.26
Consensus pattern (15 bp):
TATATATAAAAGGAA
Found at i:431219 original size:13 final size:14
Alignment explanation
Indices: 431195--431229 Score: 54
Period size: 13 Copynumber: 2.6 Consensus size: 14
431185 GAATGCACAA
*
431195 ATAGTTCAAAATAT
1 ATAGTGCAAAATAT
431209 AT-GTGCAAAATAT
1 ATAGTGCAAAATAT
431222 ATAGTGCA
1 ATAGTGCA
431230 TGGTAATAGG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
13 12 0.63
14 7 0.37
ACGTcount: A:0.46, C:0.09, G:0.14, T:0.31
Consensus pattern (14 bp):
ATAGTGCAAAATAT
Found at i:432761 original size:39 final size:39
Alignment explanation
Indices: 432685--432762 Score: 104
Period size: 39 Copynumber: 2.0 Consensus size: 39
432675 TCAGTAGTCC
* *
432685 TGTTTTAATCTATATTATCTATATTATTGCTGTTTTAAT
1 TGTTTTAATCTATATTATCTAGATTATTGCTGCTTTAAT
* *
432724 TGTTTTAATCTATGTTATGTAGATTATTG-TGGCTTTAAT
1 TGTTTTAATCTATATTATCTAGATTATTGCT-GCTTTAAT
432763 CTATGTTATC
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
38 1 0.03
39 33 0.97
ACGTcount: A:0.24, C:0.06, G:0.13, T:0.56
Consensus pattern (39 bp):
TGTTTTAATCTATATTATCTAGATTATTGCTGCTTTAAT
Found at i:432790 original size:2 final size:2
Alignment explanation
Indices: 432783--432808 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
432773 TAGATTATTA
432783 AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG
432809 CACGTGAACA
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:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:434199 original size:29 final size:29
Alignment explanation
Indices: 434157--434215 Score: 100
Period size: 29 Copynumber: 2.0 Consensus size: 29
434147 ATTTTCACCT
434157 AACTAAATTGATGTAAGAAATGACATCAA
1 AACTAAATTGATGTAAGAAATGACATCAA
**
434186 AACTAAATTGATGTAATCAATGACATCAA
1 AACTAAATTGATGTAAGAAATGACATCAA
434215 A
1 A
434216 TTAATTTAGG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.51, C:0.12, G:0.12, T:0.25
Consensus pattern (29 bp):
AACTAAATTGATGTAAGAAATGACATCAA
Found at i:438886 original size:29 final size:29
Alignment explanation
Indices: 438844--438902 Score: 100
Period size: 29 Copynumber: 2.0 Consensus size: 29
438834 ATTTTCACCT
*
438844 AACTAAATTGATGTAAGAAATGACATCAA
1 AACTAAATTAATGTAAGAAATGACATCAA
*
438873 AACTAAATTAATGTAAGCAATGACATCAA
1 AACTAAATTAATGTAAGAAATGACATCAA
438902 A
1 A
438903 TTAATTTAGG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.53, C:0.12, G:0.12, T:0.24
Consensus pattern (29 bp):
AACTAAATTAATGTAAGAAATGACATCAA
Found at i:440097 original size:14 final size:14
Alignment explanation
Indices: 440080--440110 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
440070 ATTATTTAAA
440080 TTATTAGAATTTAT
1 TTATTAGAATTTAT
*
440094 TTATTTGAATTTAT
1 TTATTAGAATTTAT
440108 TTA
1 TTA
440111 AATAATTTTG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.32, C:0.00, G:0.06, T:0.61
Consensus pattern (14 bp):
TTATTAGAATTTAT
Done.