Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007959.1 Hibiscus syriacus cultivar Beakdansim tig00110386_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: 1044826
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
File 1 of 5
Found at i:5598 original size:131 final size:132
Alignment explanation
Indices: 5355--5625 Score: 517
Period size: 131 Copynumber: 2.1 Consensus size: 132
5345 TAAACAAAGG
*
5355 AGTTGCTAGGAACCCTTGTTCCATGTTCAATTGAGGTATTGTGTTCCTATTTTTAGAGTTCTGGA
1 AGTTGCTAGGAACCCTTGTTCCATGTTCAATTGAGGTATTGTGTTCCTATTTTTAGAGTTCTGAA
*
5420 AAATAGAGTTGGCATGTAACGAATATCTTCTTGTGTCACTTTCACCTGAAACTGATTGTCATTTG
66 AAATAGAGTTGGCATGTAACGAATATCTTCTTGTGTCACTTTCACCTGAAACTGATTATCATTTG
5485 TC
131 TC
5487 AGTTGCTA-GAACCCTTGTTCCATGTTCAATTGAGGTATTGTGTTCCTATTTTTAGAGTTCTGAA
1 AGTTGCTAGGAACCCTTGTTCCATGTTCAATTGAGGTATTGTGTTCCTATTTTTAGAGTTCTGAA
5551 AAATAGAGTTGGCATGTAACGAATATCTTCTTGTGTCACTTTCACCTGAAACTGATTATCATTTG
66 AAATAGAGTTGGCATGTAACGAATATCTTCTTGTGTCACTTTCACCTGAAACTGATTATCATTTG
5616 TC
131 TC
5618 AGTTGCTA
1 AGTTGCTA
5626 TTTATGTTGA
Statistics
Matches: 137, Mismatches: 2, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
131 129 0.94
132 8 0.06
ACGTcount: A:0.24, C:0.17, G:0.20, T:0.39
Consensus pattern (132 bp):
AGTTGCTAGGAACCCTTGTTCCATGTTCAATTGAGGTATTGTGTTCCTATTTTTAGAGTTCTGAA
AAATAGAGTTGGCATGTAACGAATATCTTCTTGTGTCACTTTCACCTGAAACTGATTATCATTTG
TC
Found at i:15938 original size:14 final size:15
Alignment explanation
Indices: 15896--15940 Score: 56
Period size: 14 Copynumber: 3.0 Consensus size: 15
15886 ATAAAATATT
15896 TAAAAATATAAACAAG
1 TAAAAATA-AAACAAG
*
15912 TAAAATTAAAACAA-
1 TAAAAATAAAACAAG
*
15926 TAAAAATACAACAAG
1 TAAAAATAAAACAAG
15941 AACGATATAT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
14 12 0.48
15 6 0.24
16 7 0.28
ACGTcount: A:0.69, C:0.09, G:0.04, T:0.18
Consensus pattern (15 bp):
TAAAAATAAAACAAG
Found at i:16757 original size:21 final size:21
Alignment explanation
Indices: 16733--16773 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
16723 CTCTGTAAGT
16733 TTTTCTTCTTCT-TCTTTTTTC
1 TTTTCTT-TTCTGTCTTTTTTC
*
16754 TTTTCTTTTCTGTTTTTTTT
1 TTTTCTTTTCTGTCTTTTTT
16774 TCTGCGTTGT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.00, C:0.17, G:0.02, T:0.80
Consensus pattern (21 bp):
TTTTCTTTTCTGTCTTTTTTC
Found at i:16764 original size:17 final size:18
Alignment explanation
Indices: 16732--16776 Score: 58
Period size: 17 Copynumber: 2.6 Consensus size: 18
16722 CCTCTGTAAG
*
16732 TTTTTCTTCTTCTTCT-T
1 TTTTTTTTCTTCTTCTGT
16749 TTTTCTTTTCTT-TTCTGT
1 TTTT-TTTTCTTCTTCTGT
16767 TTTTTTTTCT
1 TTTTTTTTCT
16777 GCGTTGTTGT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
17 14 0.56
18 11 0.44
ACGTcount: A:0.00, C:0.18, G:0.02, T:0.80
Consensus pattern (18 bp):
TTTTTTTTCTTCTTCTGT
Found at i:17300 original size:11 final size:10
Alignment explanation
Indices: 17267--17305 Score: 53
Period size: 11 Copynumber: 3.8 Consensus size: 10
17257 GCTTTGTGTA
17267 ATTTAATATT
1 ATTTAATATT
17277 ATTT-ATATGT
1 ATTTAATAT-T
17287 ATTTAATATAT
1 ATTTAATAT-T
17298 ATTTAATA
1 ATTTAATA
17306 ATAATAATAA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
9 4 0.15
10 9 0.35
11 13 0.50
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (10 bp):
ATTTAATATT
Found at i:17309 original size:3 final size:3
Alignment explanation
Indices: 17301--17387 Score: 115
Period size: 3 Copynumber: 29.7 Consensus size: 3
17291 AATATATATT
*
17301 TAA TAA TAA TAA TAA TAA TGA TAA T-A TAA TAA TAA T-A TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* * * *
17347 TTA TAG TAA TAA TAA TAA TTA TAA TAA CAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
17388 TTTATAATAT
Statistics
Matches: 72, Mismatches: 10, Indels: 4
0.84 0.12 0.05
Matches are distributed among these distances:
2 4 0.06
3 68 0.94
ACGTcount: A:0.61, C:0.01, G:0.02, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:18060 original size:110 final size:110
Alignment explanation
Indices: 17694--18563 Score: 1044
Period size: 110 Copynumber: 7.8 Consensus size: 110
17684 TCTTTCTGTG
* * * * *
17694 ATAGAATTATGCAAAAAGTTGAACAAGTTCTTCTTATTATGAACTTCTTCTTCCTTCTTCAGATG
1 ATAGATTTAAGCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATG
* *
17759 AGTTCTTCTCATTATGAAC-TTCTCTGGAAAAGCTGCCCCAT-CAAGTG
66 AGTTCTTCTCATTATGAACTTTCTCTGGAAAAGATG----ATCCAAGTA
* *
17806 ATAGATTTGAGCAAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATG
1 ATAGATTTAAGCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGAT-
* * * * ***
17871 ACGAGTTCTTCTCATTATGAAC-TAC-CTGGCAATGTTGATCCATCAA
65 --GAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGATGATCCAAGTA
* * * *
17917 ATGATGATTCAAACAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGA
1 AT-A-GATTTAAGCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGA
*
17982 TGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGCTGATCCAAGTA
64 TGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGATGATCCAAGTA
* *
18029 ATAGATTTGAGCAAAAGGTTGAACAAATTCTTCTCATTACGAACTTCTTCTTCCTTCTTCAGATG
1 ATAGATTTAAGCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATG
* * * *
18094 AGTTCTTCTCATTATGAACTTTCTCTGGAAAAGATAATTCATCATTG
66 AGTTCTTCTCATTATGAACTTTCTCTGGAAAAGATGATCCA--AGTA
* * *
18141 AT-GAATTCAAACAAAA-GTTGAACAAGTTCTTCTCATTATGAACTTCTTCTT-CTTCTTCAGAT
1 ATAG-ATTTAAGCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGAT
*
18203 GAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGCTGATCCATCAAGTA
65 GAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGATGAT-C--CAAGTA
* *
18252 ATAGATTT-AGTAAAAGGTTGAACAAATTCTTC-CATTACGAACTTCTTCTTCCTTCTTCAGATG
1 ATAGATTTAAGCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATG
*
18315 AGTTCTTCTCATTATGAACTTTCTCTGGAAAAGATAATCC-A-TCA
66 AGTTCTTCTCATTATGAACTTTCTCTGGAAAAGATGATCCAAGT-A
* * * *
18359 ATTGATGAATTCAGGTAAAAGGTTGAAC-AATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCA
1 A-T-A-G-ATTTAAGCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCA
* * *
18423 GATGAGTTCTTCTCATTATGAACTTTCTCTGGAAATGATGATCCATCAAATG
62 GATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGATGAT-C--CAAGTA
* * * *
18475 ATGGATTCAAGTAAAAGGTTGAACAAATTCTTCTCATTACGAACTTCTTCTTCCTTCTTCAGATG
1 ATAGATTTAAGCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATG
18540 AGTTCTTCTCATTATGAACTTTCT
66 AGTTCTTCTCATTATGAACTTTCT
18564 GGAAATGTCA
Statistics
Matches: 661, Mismatches: 67, Indels: 59
0.84 0.09 0.07
Matches are distributed among these distances:
106 1 0.00
107 3 0.00
108 2 0.00
109 1 0.00
110 188 0.28
111 122 0.18
112 187 0.28
113 121 0.18
114 9 0.01
115 24 0.04
116 2 0.00
117 1 0.00
ACGTcount: A:0.29, C:0.19, G:0.13, T:0.38
Consensus pattern (110 bp):
ATAGATTTAAGCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATG
AGTTCTTCTCATTATGAACTTTCTCTGGAAAAGATGATCCAAGTA
Found at i:18498 original size:446 final size:444
Alignment explanation
Indices: 17707--18563 Score: 1364
Period size: 446 Copynumber: 1.9 Consensus size: 444
17697 GAATTATGCA
*
17707 AAAAGTTGAACAAGTTCTTCTTATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
1 AAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
* *
17772 ATGAACTTCTCTGGAAAAGCTGCCCCATCAAGTGATAGATTTGAGCAAAAGGTTGAACAAATTCT
66 ATGAACTTCTCTGGAAAAGCTGACCCATCAAGTAATAGATTTGAGCAAAAGGTTGAACAAATTCT
* * *
17837 TCTCATTATGAATTTCTTCTTCCTTCTTCAGATGACGAGTTCTTCTCATTATGAACTACCTGGCA
131 TCTCATTACGAACTTCTTCTTCCTTCTTCAGAT-A-GAGTTCTTCTCATTATGAACTACCTGGAA
* * *
17902 ATGTTGATCCATCAAATGATGATTCAAACAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCT
194 AAGATAATCCATCAAATGATGATTCAAACAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCT
* *
17967 TCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGCTGATCCAAGTAATA
259 TCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGATGATCCAAATAATA
**
18032 GATTTGAGCAAAAGGTTGAACAAATTCTTCTCATTACGAACTTCTTCTTCCTTCTTCAGATGAGT
324 GATTCAAGCAAAAGGTTGAACAAATTCTTCTCATTACGAACTTCTTCTTCCTTCTTCAGATGAGT
18097 TCTTCTCATTATGAACTTTCTCTGGAAAAGATAATTCATCATTGATGAATTCAAAC
389 TCTTCTCATTATGAACTTTCTCTGGAAAAGATAATTCATCATTGATGAATTCAAAC
18153 AAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTT-CTTCTTCAGATGAGTTCTTCTCATT
1 AAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
* *
18217 ATGAACTTTCTCTGGAAAAGCTGATCCATCAAGTAATAGATTT-AGTAAAAGGTTGAACAAATTC
66 ATGAAC-TTCTCTGGAAAAGCTGACCCATCAAGTAATAGATTTGAGCAAAAGGTTGAACAAATTC
*
18281 TTC-CATTACGAACTTCTTCTTCCTTCTTCAGAT-GAGTTCTTCTCATTATGAACTTTCTCTGGA
130 TTCTCATTACGAACTTCTTCTTCCTTCTTCAGATAGAGTTCTTCTCATTATGAAC-TAC-CTGGA
* *** * *
18344 AAAGATAATCCATCAATTGATGAATTCAGGTAAAAGGTTGAACAA-TTCTTCTCATTATGAATTT
193 AAAGATAATCCATCAAATGATG-ATTCAAACAAAAAGTTGAACAAGTTCTTCTCATTATGAACTT
*
18408 CTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAATGATGATCCATCAAA
257 CTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGATGAT-C--CAAA
* * *
18473 TGATGGATTCAAGTAAAAGGTTGAACAAATTCTTCTCATTACGAACTTCTTCTTCCTTCTTCAGA
319 TAATAGATTCAAGCAAAAGGTTGAACAAATTCTTCTCATTACGAACTTCTTCTTCCTTCTTCAGA
18538 TGAGTTCTTCTCATTATGAACTTTCT
384 TGAGTTCTTCTCATTATGAACTTTCT
18564 GGAAATGTCA
Statistics
Matches: 378, Mismatches: 26, Indels: 14
0.90 0.06 0.03
Matches are distributed among these distances:
441 20 0.05
442 2 0.01
443 95 0.25
444 47 0.12
445 54 0.14
446 160 0.42
ACGTcount: A:0.29, C:0.20, G:0.13, T:0.38
Consensus pattern (444 bp):
AAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
ATGAACTTCTCTGGAAAAGCTGACCCATCAAGTAATAGATTTGAGCAAAAGGTTGAACAAATTCT
TCTCATTACGAACTTCTTCTTCCTTCTTCAGATAGAGTTCTTCTCATTATGAACTACCTGGAAAA
GATAATCCATCAAATGATGATTCAAACAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTC
TTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGATGATCCAAATAATAGA
TTCAAGCAAAAGGTTGAACAAATTCTTCTCATTACGAACTTCTTCTTCCTTCTTCAGATGAGTTC
TTCTCATTATGAACTTTCTCTGGAAAAGATAATTCATCATTGATGAATTCAAAC
Found at i:19645 original size:165 final size:165
Alignment explanation
Indices: 19371--19736 Score: 619
Period size: 165 Copynumber: 2.2 Consensus size: 165
19361 CTCCTTATTT
* * *
19371 CTATGAGCAAATTCATCTTCCAAATTCAATGATTGGTTTTACCAAACCAGATCAGATAATTCAAA
1 CTATGAGCACATTTATCTTCCAAATTCAATGATTGGTTTTACCAAACCAGATCAGATAACTCAAA
* * *
19436 GACCACTTTCAGAAAATGCTATGAACACATTATCTTCTCAATTCAATGATTGGTTTTATCAAACC
66 GAACACTTTCAGAAAATGCTATGAACACATTATCTTCCCAATTCAATGATTGGTTTTACCAAACC
*
19501 AGATCGGATAACTCAAAGAACACTTCCAGAAGATG
131 AGATCAGATAACTCAAAGAACACTTCCAGAAGATG
19536 CTATGAGCACATTTATCTTCCAAATTCAATGATTGG-TTTACCAAACCAGATCAGATAACTCAAA
1 CTATGAGCACATTTATCTTCCAAATTCAATGATTGGTTTTACCAAACCAGATCAGATAACTCAAA
* *
19600 GAACA-TTTCCAGAAGATGCTATGAGCACATTTATCTTCCCAATTCAATGATTGGTTTTACCAAA
66 GAACACTTT-CAGAAAATGCTATGAACACA-TTATCTTCCCAATTCAATGATTGGTTTTACCAAA
19664 CCAGATCAGATAACTCAAAGAACACTTCCAGAAGATG
129 CCAGATCAGATAACTCAAAGAACACTTCCAGAAGATG
19701 CTATGAGCACATTTATCTTCCAAATTCAATGATTGG
1 CTATGAGCACATTTATCTTCCAAATTCAATGATTGG
19737 ACTAGGATAT
Statistics
Matches: 190, Mismatches: 9, Indels: 4
0.94 0.04 0.02
Matches are distributed among these distances:
163 3 0.02
164 49 0.26
165 138 0.73
ACGTcount: A:0.37, C:0.21, G:0.13, T:0.29
Consensus pattern (165 bp):
CTATGAGCACATTTATCTTCCAAATTCAATGATTGGTTTTACCAAACCAGATCAGATAACTCAAA
GAACACTTTCAGAAAATGCTATGAACACATTATCTTCCCAATTCAATGATTGGTTTTACCAAACC
AGATCAGATAACTCAAAGAACACTTCCAGAAGATG
Found at i:19705 original size:83 final size:83
Alignment explanation
Indices: 19371--19736 Score: 603
Period size: 82 Copynumber: 4.4 Consensus size: 83
19361 CTCCTTATTT
* * *
19371 CTATGAGCAAATTCATCTTCCAAATTCAATGATTGGTTTTACCAAACCAGATCAGATAATTCAAA
1 CTATGAGCACATTTATCTTCCAAATTCAATGATTGGTTTTACCAAACCAGATCAGATAACTCAAA
* * *
19436 GACCACTTTCAGAAAATG
66 GAACACTTCCAGAAGATG
* * *
19454 CTATGAACACA-TTATCTTCTC-AATTCAATGATTGGTTTTATCAAACCAGATCGGATAACTCAA
1 CTATGAGCACATTTATCTTC-CAAATTCAATGATTGGTTTTACCAAACCAGATCAGATAACTCAA
19517 AGAACACTTCCAGAAGATG
65 AGAACACTTCCAGAAGATG
19536 CTATGAGCACATTTATCTTCCAAATTCAATGATTGG-TTTACCAAACCAGATCAGATAACTCAAA
1 CTATGAGCACATTTATCTTCCAAATTCAATGATTGGTTTTACCAAACCAGATCAGATAACTCAAA
*
19600 GAACATTTCCAGAAGATG
66 GAACACTTCCAGAAGATG
*
19618 CTATGAGCACATTTATCTTCCCAATTCAATGATTGGTTTTACCAAACCAGATCAGATAACTCAAA
1 CTATGAGCACATTTATCTTCCAAATTCAATGATTGGTTTTACCAAACCAGATCAGATAACTCAAA
19683 GAACACTTCCAGAAGATG
66 GAACACTTCCAGAAGATG
19701 CTATGAGCACATTTATCTTCCAAATTCAATGATTGG
1 CTATGAGCACATTTATCTTCCAAATTCAATGATTGG
19737 ACTAGGATAT
Statistics
Matches: 263, Mismatches: 16, Indels: 8
0.92 0.06 0.03
Matches are distributed among these distances:
82 151 0.57
83 112 0.43
ACGTcount: A:0.37, C:0.21, G:0.13, T:0.29
Consensus pattern (83 bp):
CTATGAGCACATTTATCTTCCAAATTCAATGATTGGTTTTACCAAACCAGATCAGATAACTCAAA
GAACACTTCCAGAAGATG
Found at i:20509 original size:16 final size:18
Alignment explanation
Indices: 20469--20515 Score: 71
Period size: 18 Copynumber: 2.7 Consensus size: 18
20459 AATTCAATAG
*
20469 AAAATAAATTGAATTTCC
1 AAAATAAATTGAATCTCC
20487 AAAATAAATTGAATCT-C
1 AAAATAAATTGAATCTCC
20504 -AAATAAATTGAA
1 AAAATAAATTGAA
20516 CTTGAAATAG
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
16 12 0.43
17 1 0.04
18 15 0.54
ACGTcount: A:0.55, C:0.09, G:0.06, T:0.30
Consensus pattern (18 bp):
AAAATAAATTGAATCTCC
Found at i:20858 original size:9 final size:8
Alignment explanation
Indices: 20839--20908 Score: 61
Period size: 9 Copynumber: 8.4 Consensus size: 8
20829 CTTGACCCCC
20839 CTTTTTTT
1 CTTTTTTT
20847 CTTTTTTCT
1 CTTTTTT-T
20856 CTTTTTTT
1 CTTTTTTT
*
20864 TTTCTTTTT
1 CTT-TTTTT
*
20873 TTTTTTTT
1 CTTTTTTT
20881 CTTTTCTTT
1 CTTTT-TTT
**
20890 -TTTCCTT
1 CTTTTTTT
20897 CATTTTTTT
1 C-TTTTTTT
20906 CTT
1 CTT
20909 CAAGCATAAT
Statistics
Matches: 51, Mismatches: 6, Indels: 10
0.76 0.09 0.15
Matches are distributed among these distances:
7 2 0.04
8 24 0.47
9 25 0.49
ACGTcount: A:0.01, C:0.16, G:0.00, T:0.83
Consensus pattern (8 bp):
CTTTTTTT
Found at i:20863 original size:20 final size:20
Alignment explanation
Indices: 20840--20908 Score: 90
Period size: 20 Copynumber: 3.5 Consensus size: 20
20830 TTGACCCCCC
20840 TTTTTTTCTTTTTTCTCTTT
1 TTTTTTTCTTTTTTCTCTTT
20860 TTTTTTTCTTTTTT-T-TTT
1 TTTTTTTCTTTTTTCTCTTT
*
20878 TTTCTTTTCTTTTTTC-CTTCA
1 TTT-TTTTCTTTTTTCTCTT-T
20899 TTTTTTTCTT
1 TTTTTTTCTT
20909 CAAGCATAAT
Statistics
Matches: 44, Mismatches: 1, Indels: 8
0.83 0.02 0.15
Matches are distributed among these distances:
18 6 0.14
19 12 0.27
20 23 0.52
21 3 0.07
ACGTcount: A:0.01, C:0.14, G:0.00, T:0.84
Consensus pattern (20 bp):
TTTTTTTCTTTTTTCTCTTT
Found at i:20864 original size:11 final size:10
Alignment explanation
Indices: 20840--20892 Score: 65
Period size: 9 Copynumber: 5.4 Consensus size: 10
20830 TTGACCCCCC
20840 TTTTTTTC-T
1 TTTTTTTCTT
*
20849 TTTTTCTCTTT
1 TTTTTTTC-TT
20860 TTTTTTTCTT
1 TTTTTTTCTT
20870 TTTTTTT-TT
1 TTTTTTTCTT
*
20879 TTCTTTTCTT
1 TTTTTTTCTT
20889 TTTT
1 TTTT
20893 CCTTCATTTT
Statistics
Matches: 37, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
9 15 0.41
10 14 0.38
11 8 0.22
ACGTcount: A:0.00, C:0.11, G:0.00, T:0.89
Consensus pattern (10 bp):
TTTTTTTCTT
Found at i:20866 original size:13 final size:13
Alignment explanation
Indices: 20843--20907 Score: 71
Period size: 13 Copynumber: 4.9 Consensus size: 13
20833 ACCCCCCTTT
20843 TTTTCTTTTTTCTC
1 TTTT-TTTTTTCTC
20857 TTTTTTTTTTCT-
1 TTTTTTTTTTCTC
*
20869 TTTTTTTTTTTTC
1 TTTTTTTTTTCTC
20882 TTTTCTTTTTTC-C
1 TTTT-TTTTTTCTC
*
20895 TTCATTTTTTTCT
1 TT-TTTTTTTTCT
20908 TCAAGCATAA
Statistics
Matches: 44, Mismatches: 3, Indels: 8
0.80 0.05 0.15
Matches are distributed among these distances:
12 11 0.25
13 22 0.50
14 11 0.25
ACGTcount: A:0.02, C:0.15, G:0.00, T:0.83
Consensus pattern (13 bp):
TTTTTTTTTTCTC
Found at i:20902 original size:27 final size:25
Alignment explanation
Indices: 20848--20907 Score: 75
Period size: 25 Copynumber: 2.3 Consensus size: 25
20838 CCTTTTTTTC
**
20848 TTTTTTCTCTTTTTTTTTTCTTTTT
1 TTTTTTCTCTTTTTTTTTTCTTCAT
*
20873 TTTTTTTTCTTTTCTTTTTTCCTTCAT
1 TTTTTTCTCTTTT-TTTTTT-CTTCAT
20900 TTTTTTCT
1 TTTTTTCT
20908 TCAAGCATAA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
25 12 0.41
26 6 0.21
27 11 0.38
ACGTcount: A:0.02, C:0.15, G:0.00, T:0.83
Consensus pattern (25 bp):
TTTTTTCTCTTTTTTTTTTCTTCAT
Found at i:20903 original size:30 final size:27
Alignment explanation
Indices: 20841--20905 Score: 76
Period size: 28 Copynumber: 2.3 Consensus size: 27
20831 TGACCCCCCT
*
20841 TTTTTTCTTTTTTCTCTTTTTTTTTTCT
1 TTTTTT-TTTTTTCTCTTTTTTTTTTCA
*
20869 TTTTTTTTTTTTCTTTTCTTTTTTCCTTCA
1 TTTTTTTTTTTTCTCTT-TTTTTT--TTCA
20899 TTTTTTT
1 TTTTTTT
20906 CTTCAAGCAT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
27 10 0.31
28 12 0.38
30 10 0.31
ACGTcount: A:0.02, C:0.14, G:0.00, T:0.85
Consensus pattern (27 bp):
TTTTTTTTTTTTCTCTTTTTTTTTTCA
Found at i:20905 original size:1 final size:1
Alignment explanation
Indices: 20840--20892 Score: 52
Period size: 1 Copynumber: 53.0 Consensus size: 1
20830 TTGACCCCCC
* * * * * *
20840 TTTTTTTCTTTTTTCTCTTTTTTTTTTCTTTTTTTTTTTTTCTTTTCTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
20893 CCTTCATTTT
Statistics
Matches: 40, Mismatches: 12, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
1 40 1.00
ACGTcount: A:0.00, C:0.11, G:0.00, T:0.89
Consensus pattern (1 bp):
T
Found at i:33575 original size:11 final size:10
Alignment explanation
Indices: 33545--33585 Score: 55
Period size: 11 Copynumber: 3.8 Consensus size: 10
33535 GGGCTTTGTA
33545 ATTTAATATT
1 ATTTAATATT
33555 ATTTATATATGT
1 ATTTA-ATAT-T
33567 ATTTAATATAT
1 ATTTAATAT-T
33578 ATTTAATA
1 ATTTAATA
33586 ATAATAATAA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
10 5 0.18
11 17 0.61
12 6 0.21
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.56
Consensus pattern (10 bp):
ATTTAATATT
Found at i:33589 original size:3 final size:3
Alignment explanation
Indices: 33581--33714 Score: 223
Period size: 3 Copynumber: 44.7 Consensus size: 3
33571 AATATATATT
* *
33581 TAA TAA TAA TAA TAA TAA TGA TAA TAA TAA TAA TAA TAA TAA TGA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* *
33629 TAA TAA TAA TAA TAA TAA TAA TAA TAA TGA TAA TGA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
33677 TAA TGA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
33715 TGGGTAAAAA
Statistics
Matches: 121, Mismatches: 10, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
3 121 1.00
ACGTcount: A:0.63, C:0.00, G:0.04, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:35505 original size:18 final size:18
Alignment explanation
Indices: 35484--35520 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
35474 TAACCACTGT
35484 AGACCT-ATTAAATTGTTA
1 AGACCTAATTAAATT-TTA
35502 AGACCTAATTAAATTTTA
1 AGACCTAATTAAATTTTA
35520 A
1 A
35521 CCCAAATAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 10 0.56
19 8 0.44
ACGTcount: A:0.43, C:0.11, G:0.08, T:0.38
Consensus pattern (18 bp):
AGACCTAATTAAATTTTA
Found at i:36132 original size:19 final size:18
Alignment explanation
Indices: 36110--36149 Score: 62
Period size: 19 Copynumber: 2.2 Consensus size: 18
36100 TAAAAACCTT
36110 AAAAATATAATTTCTTTTA
1 AAAAATATAATTTC-TTTA
*
36129 AAAAATCTAATTTCTTTA
1 AAAAATATAATTTCTTTA
36147 AAA
1 AAA
36150 TTACAAAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
18 7 0.35
19 13 0.65
ACGTcount: A:0.50, C:0.07, G:0.00, T:0.42
Consensus pattern (18 bp):
AAAAATATAATTTCTTTA
Found at i:39187 original size:31 final size:31
Alignment explanation
Indices: 39149--39215 Score: 116
Period size: 31 Copynumber: 2.2 Consensus size: 31
39139 AAGCGTGATA
39149 ACATGACTTATTTTATTAACATTTTGCTATG
1 ACATGACTTATTTTATTAACATTTTGCTATG
**
39180 ACATGACTTATTTTATTAATTTTTTGCTATG
1 ACATGACTTATTTTATTAACATTTTGCTATG
39211 ACATG
1 ACATG
39216 TAGGATTTAC
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 34 1.00
ACGTcount: A:0.28, C:0.12, G:0.10, T:0.49
Consensus pattern (31 bp):
ACATGACTTATTTTATTAACATTTTGCTATG
Found at i:49186 original size:85 final size:84
Alignment explanation
Indices: 49043--49209 Score: 262
Period size: 85 Copynumber: 2.0 Consensus size: 84
49033 TTATGATGCG
* * * *
49043 AATTTATGACACGCATTTATGACGCGCATTGTGTGTCATTGAAGCCCTTGTCATAAATGAAGATG
1 AATTTATGACACGCATGTATGACGCACATTGCGTGTCATTGAAGCCCTTGTCATAAATGAAGACG
49108 ACACACATTTGTGTGTCATA
66 ACACACA-TTGTGTGTCATA
* **
49128 AATTTATGACATGCATGTATGACTTACATTGCGTGTCATTGAAGCCCTTGTCATAAATGAAGACG
1 AATTTATGACACGCATGTATGACGCACATTGCGTGTCATTGAAGCCCTTGTCATAAATGAAGACG
49193 ACACACATTGTGTGTCA
66 ACACACATTGTGTGTCA
49210 GAGAGTATAT
Statistics
Matches: 75, Mismatches: 7, Indels: 1
0.90 0.08 0.01
Matches are distributed among these distances:
84 10 0.13
85 65 0.87
ACGTcount: A:0.30, C:0.18, G:0.20, T:0.32
Consensus pattern (84 bp):
AATTTATGACACGCATGTATGACGCACATTGCGTGTCATTGAAGCCCTTGTCATAAATGAAGACG
ACACACATTGTGTGTCATA
Found at i:53619 original size:27 final size:27
Alignment explanation
Indices: 53571--53641 Score: 108
Period size: 27 Copynumber: 2.7 Consensus size: 27
53561 CCCCTTACTC
* *
53571 TAACACTTCT-CCCCTTTAAAACATTT
1 TAACATTTCTCCCCCTTTAAAACACTT
53597 TAACATTTCTCCCCCTTTAAAACACTT
1 TAACATTTCTCCCCCTTTAAAACACTT
*
53624 TATCATTTCTCCCCCTTT
1 TAACATTTCTCCCCCTTT
53642 TTGTTAAATC
Statistics
Matches: 41, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
26 9 0.22
27 32 0.78
ACGTcount: A:0.25, C:0.34, G:0.00, T:0.41
Consensus pattern (27 bp):
TAACATTTCTCCCCCTTTAAAACACTT
Found at i:60559 original size:23 final size:23
Alignment explanation
Indices: 60496--60615 Score: 122
Period size: 23 Copynumber: 5.3 Consensus size: 23
60486 CACCACAGCT
*
60496 CACATA-ATTTGTACCGAAGTG-C
1 CACATAGATTTGTCCCGAAG-GAC
* *
60518 CACAT--ATTTATCTCGAAGGAC
1 CACATAGATTTGTCCCGAAGGAC
* * **
60539 TACATAGGTTTGTCTTGAAGGAC
1 CACATAGATTTGTCCCGAAGGAC
*
60562 CACATATATTTGTCCCGAAGGAC
1 CACATAGATTTGTCCCGAAGGAC
*
60585 CATATAGATTTGTCCCGAAGGAC
1 CACATAGATTTGTCCCGAAGGAC
60608 CACATAGA
1 CACATAGA
60616 ACCCTCGACT
Statistics
Matches: 80, Mismatches: 15, Indels: 5
0.80 0.15 0.05
Matches are distributed among these distances:
20 1 0.01
21 15 0.19
22 5 0.06
23 59 0.74
ACGTcount: A:0.32, C:0.22, G:0.19, T:0.28
Consensus pattern (23 bp):
CACATAGATTTGTCCCGAAGGAC
Found at i:61310 original size:46 final size:46
Alignment explanation
Indices: 61252--61346 Score: 190
Period size: 46 Copynumber: 2.1 Consensus size: 46
61242 AAAAGGTTTC
61252 AAAAATAATTCAAAGTCCATTAAAATCGGATTTGAGCAAAAATGCT
1 AAAAATAATTCAAAGTCCATTAAAATCGGATTTGAGCAAAAATGCT
61298 AAAAATAATTCAAAGTCCATTAAAATCGGATTTGAGCAAAAATGCT
1 AAAAATAATTCAAAGTCCATTAAAATCGGATTTGAGCAAAAATGCT
61344 AAA
1 AAA
61347 GGGTGTCAAA
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 49 1.00
ACGTcount: A:0.49, C:0.13, G:0.13, T:0.25
Consensus pattern (46 bp):
AAAAATAATTCAAAGTCCATTAAAATCGGATTTGAGCAAAAATGCT
Found at i:61382 original size:21 final size:20
Alignment explanation
Indices: 61356--61455 Score: 121
Period size: 21 Copynumber: 4.8 Consensus size: 20
61346 AGGGTGTCAA
61356 AGTGCATCCATGCATCCCTGC
1 AGTGCATCCATGCA-CCCTGC
61377 AGTGCATCCATGCACCCCTGC
1 AGTGCATCCATGCA-CCCTGC
61398 AGTGCATCCATGCA-CCTGCCAC
1 AGTGCATCCATGCACCCTG---C
* *
61420 TAGTGCATCAATGCACCATGC
1 -AGTGCATCCATGCACCCTGC
61441 AGTGCATCCATGCAC
1 AGTGCATCCATGCAC
61456 TCAAACATCA
Statistics
Matches: 70, Mismatches: 4, Indels: 11
0.82 0.05 0.13
Matches are distributed among these distances:
19 4 0.06
20 14 0.20
21 35 0.50
22 1 0.01
23 13 0.19
24 3 0.04
ACGTcount: A:0.23, C:0.37, G:0.19, T:0.21
Consensus pattern (20 bp):
AGTGCATCCATGCACCCTGC
Found at i:63875 original size:21 final size:20
Alignment explanation
Indices: 63850--63897 Score: 69
Period size: 20 Copynumber: 2.4 Consensus size: 20
63840 AAGTTTGGTT
*
63850 TGAAAAATTCATTTTTCTTAA
1 TGAAAAATTCA-ATTTCTTAA
*
63871 TGAAAAATTGAATTTCTTAA
1 TGAAAAATTCAATTTCTTAA
63891 TGAAAAA
1 TGAAAAA
63898 GGGGGAGCTT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
20 15 0.60
21 10 0.40
ACGTcount: A:0.46, C:0.06, G:0.08, T:0.40
Consensus pattern (20 bp):
TGAAAAATTCAATTTCTTAA
Found at i:63976 original size:21 final size:21
Alignment explanation
Indices: 63937--63975 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
63927 CAACAATTGG
63937 TAACAATTGATATCATTTTGT
1 TAACAATTGATATCATTTTGT
*
63958 TAACAATTGGTAT-ATTTT
1 TAACAATTGATATCATTTT
63976 TCATTAAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.33, C:0.08, G:0.10, T:0.49
Consensus pattern (21 bp):
TAACAATTGATATCATTTTGT
Found at i:64224 original size:21 final size:21
Alignment explanation
Indices: 64198--64273 Score: 116
Period size: 21 Copynumber: 3.6 Consensus size: 21
64188 AGGGTGTCAA
* *
64198 AGTGCATCCATGTATCCCTGC
1 AGTGCATCCATGCACCCCTGC
64219 AGTGCATCCATGCACCCCTGC
1 AGTGCATCCATGCACCCCTGC
* *
64240 AGTGCATTCATGCACCCCTGT
1 AGTGCATCCATGCACCCCTGC
64261 AGTGCATCCATGC
1 AGTGCATCCATGC
64274 CCCTTCCACT
Statistics
Matches: 50, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 50 1.00
ACGTcount: A:0.20, C:0.36, G:0.20, T:0.25
Consensus pattern (21 bp):
AGTGCATCCATGCACCCCTGC
Found at i:66369 original size:23 final size:21
Alignment explanation
Indices: 66311--66369 Score: 57
Period size: 23 Copynumber: 2.7 Consensus size: 21
66301 ATCACATATA
*
66311 TCATGTAACAT-TCTCATATGT
1 TCATGT-ACATATATCATATGT
*
66332 TCATGTAGATCATATCATATAGT
1 TCATGTACAT-ATATCATAT-GT
66355 TCATGTATCATATAT
1 TCATGTA-CATATAT
66370 ATCTTGTCAC
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
20 3 0.10
21 6 0.19
22 7 0.23
23 13 0.42
24 2 0.06
ACGTcount: A:0.32, C:0.15, G:0.10, T:0.42
Consensus pattern (21 bp):
TCATGTACATATATCATATGT
Found at i:67859 original size:95 final size:95
Alignment explanation
Indices: 67691--67913 Score: 266
Period size: 95 Copynumber: 2.3 Consensus size: 95
67681 CAAGCAATGT
* * *
67691 GGTATCAATACCATGGTAAGGGTATCGATACCAGTAAACATCAAATCTAATTTGGGTATTGATAC
1 GGTATCGATACCATGGTAAGGGTATCGATACCAGGAAACATCAAAGCTAATTTGGGTATTGATAC
* * *
67756 CTAGAGGGGGTATCGATACCATAACATAGG
66 ATAAAGGGGGTATCGATACCATAACAGAGG
* * * * * *
67786 GGTATCGATACCATGGTGATGGTATCGATACCAGGATACATCGAAGCTAATTTTGGTATTGATAT
1 GGTATCGATACCATGGTAAGGGTATCGATACCAGGAAACATCAAAGCTAATTTGGGTATTGATAC
* * *
67851 ATAAAGGGGGTATCGATACCCTAATAGAGT
66 ATAAAGGGGGTATCGATACCATAACAGAGG
* * * *
67881 AGTATCGATACCATAAGCAGGGGTATCGATACC
1 GGTATCGATACCAT-GGTAAGGGTATCGATACC
67914 TAAGGGCTGG
Statistics
Matches: 106, Mismatches: 21, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
95 93 0.88
96 13 0.12
ACGTcount: A:0.33, C:0.16, G:0.24, T:0.27
Consensus pattern (95 bp):
GGTATCGATACCATGGTAAGGGTATCGATACCAGGAAACATCAAAGCTAATTTGGGTATTGATAC
ATAAAGGGGGTATCGATACCATAACAGAGG
Found at i:68428 original size:45 final size:44
Alignment explanation
Indices: 68350--68655 Score: 276
Period size: 45 Copynumber: 6.8 Consensus size: 44
68340 AGGATGCCTA
* * * * *
68350 GTTGAAATGTATATGGGTACATTATCAATAGAAAAGCATAATTTG
1 GTTGAAATGCATATGGGTGCATTATCAACAGAAAAGTAT-CTTTG
* *
68395 GTTGGAATGCATATGGGTGCATTATTAACAGAAAAGTATGC-TTG
1 GTTGAAATGCATATGGGTGCATTATCAACAGAAAAGTAT-CTTTG
* *
68439 AGTTGAAATGCATATGGATGCATTATCAACAGAAAAGTATGC-TAG
1 -GTTGAAATGCATATGGGTGCATTATCAACAGAAAAGTAT-CTTTG
* * * * ***
68484 AGTTTAAATGCATATGGGTGCATTATCAACATAATAGAATGCTAAA
1 -GTTGAAATGCATATGGGTGCATTATCAACAGAAAAGTAT-CTTTG
* * * *
68530 GTTGAAATGTATATGGGTACATTATCAACATAAAAGTGTACTATT-
1 GTTGAAATGCATATGGGTGCATTATCAACAGAAAAGTAT-CT-TTG
* * * * * *
68575 GTTGAAATGTATATAGGTACATTATCAATAGAAAAGTATGCTATA
1 GTTGAAATGCATATGGGTGCATTATCAACAGAAAAGTAT-CTTTG
68620 GTTGAAATGCATATGGGTGCATTATCAACAGAAAAG
1 GTTGAAATGCATATGGGTGCATTATCAACAGAAAAG
68656 ATGTTATAGC
Statistics
Matches: 219, Mismatches: 38, Indels: 8
0.83 0.14 0.03
Matches are distributed among these distances:
44 4 0.02
45 214 0.98
46 1 0.00
ACGTcount: A:0.39, C:0.09, G:0.21, T:0.31
Consensus pattern (44 bp):
GTTGAAATGCATATGGGTGCATTATCAACAGAAAAGTATCTTTG
Found at i:68464 original size:90 final size:89
Alignment explanation
Indices: 68312--68655 Score: 343
Period size: 90 Copynumber: 3.8 Consensus size: 89
68302 AAAAATAAAT
* *** * * *
68312 ATGCATATGGGTGCATTGTTGGCATG-AAAGGATGCCTAGTTGAAATGTATATGGGTACATTATC
1 ATGCATATGGGTGCATTATCAACA-GAAAAGTATGCTTAGTTGAAATGCATATGGGTACATTATC
* * *
68376 AATAGAAAAGCATAATTTGGTTGGA
65 AACAGAAAAGTATAATTTGGTTGAA
* * *
68401 ATGCATATGGGTGCATTATTAACAGAAAAGTATGCTTGAGTTGAAATGCATATGGATGCATTATC
1 ATGCATATGGGTGCATTATCAACAGAAAAGTATGCTT-AGTTGAAATGCATATGGGTACATTATC
** * *
68466 AACAGAAAAGTAT-GCTAGAGTTTAA
65 AACAGAAAAGTATAATTTG-GTTGAA
* * * * *
68491 ATGCATATGGGTGCATTATCAACATAATAGAATGCTAAAGTTGAAATGTATATGGGTACATTATC
1 ATGCATATGGGTGCATTATCAACAGAAAAGTATGCT-TAGTTGAAATGCATATGGGTACATTATC
* * *
68556 AACATAAAAGTGTACTATT-GTTGAA
65 AACAGAAAAGTATAAT-TTGGTTGAA
* * * * *
68581 ATGTATATAGGTACATTATCAATAGAAAAGTATGCTATAGTTGAAATGCATATGGGTGCATTATC
1 ATGCATATGGGTGCATTATCAACAGAAAAGTATGCT-TAGTTGAAATGCATATGGGTACATTATC
68646 AACAGAAAAG
65 AACAGAAAAG
68656 ATGTTATAGC
Statistics
Matches: 209, Mismatches: 40, Indels: 11
0.80 0.15 0.04
Matches are distributed among these distances:
88 1 0.00
89 32 0.15
90 175 0.84
92 1 0.00
ACGTcount: A:0.38, C:0.10, G:0.22, T:0.31
Consensus pattern (89 bp):
ATGCATATGGGTGCATTATCAACAGAAAAGTATGCTTAGTTGAAATGCATATGGGTACATTATCA
ACAGAAAAGTATAATTTGGTTGAA
Found at i:68553 original size:135 final size:135
Alignment explanation
Indices: 68395--68649 Score: 361
Period size: 135 Copynumber: 1.9 Consensus size: 135
68385 GCATAATTTG
* * * *
68395 GTTGGAATGCATATGGGTGCATTATTAACAGAAAAGTATGCT-TGAGTTGAAATGCATAT-GGAT
1 GTTGAAATGCATATGGGTACATTATCAACAGAAAAGTATACTAT-AGTTGAAATGCATATAGG-T
* *
68458 GCATTATCAACAGAAAAGTATGCTAGAGTTTAAATGCATATGGGTGCATTATCAACATAATAGAA
64 ACATTATCAACAGAAAAGTATGCTAGAGTTGAAATGCATATGGGTGCATTATCAACATAATAGAA
68523 TGCTAAA
129 TGCTAAA
* * * * *
68530 GTTGAAATGTATATGGGTACATTATCAACATAAAAGTGTACTATTGTTGAAATGTATATAGGTAC
1 GTTGAAATGCATATGGGTACATTATCAACAGAAAAGTATACTATAGTTGAAATGCATATAGGTAC
* *
68595 ATTATCAATAGAAAAGTATGCTATAGTTGAAATGCATATGGGTGCATTATCAACA
66 ATTATCAACAGAAAAGTATGCTAGAGTTGAAATGCATATGGGTGCATTATCAACA
68650 GAAAAGATGT
Statistics
Matches: 105, Mismatches: 13, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
135 102 0.97
136 3 0.03
ACGTcount: A:0.38, C:0.10, G:0.21, T:0.31
Consensus pattern (135 bp):
GTTGAAATGCATATGGGTACATTATCAACAGAAAAGTATACTATAGTTGAAATGCATATAGGTAC
ATTATCAACAGAAAAGTATGCTAGAGTTGAAATGCATATGGGTGCATTATCAACATAATAGAATG
CTAAA
Found at i:68698 original size:135 final size:134
Alignment explanation
Indices: 68349--68656 Score: 341
Period size: 135 Copynumber: 2.3 Consensus size: 134
68339 AAGGATGCCT
* * * * ** *** * *
68349 AGTTGAAATGTATATGGGTACATTATCAATAGAAAAGCATAATTTGGTTGGAATGCATATGGGTG
1 AGTTGAAATGCATATGGGTGCATTATCAACAGAAAAGAATGCTAAAGTTGAAATGTATATGGGT-
* * * * * * *
68414 CATTATTAACAGAAAAGTATGCT-TGAGTTGAAATGCATATGGATGCATTATCAACAGAAAAGTA
65 AATTATAAACATAAAAGTGTACTAT-TGTTGAAATGCATATGGATACATTATCAACAGAAAAGTA
68478 TGCTAG
129 TGCTAG
* * *
68484 AGTTTAAATGCATATGGGTGCATTATCAACATAATAGAATGCTAAAGTTGAAATGTATATGGGTA
1 AGTTGAAATGCATATGGGTGCATTATCAACAGAAAAGAATGCTAAAGTTGAAATGTATATGGGTA
* * *
68549 CATTATCAACATAAAAGTGTACTATTGTTGAAATGTATATAGG-TACATTATCAATAGAAAAGTA
66 -ATTATAAACATAAAAGTGTACTATTGTTGAAATGCATAT-GGATACATTATCAACAGAAAAGTA
*
68613 TGCTAT
129 TGCTAG
68619 AGTTGAAATGCATATGGGTGCATTATCAACAGAAAAGA
1 AGTTGAAATGCATATGGGTGCATTATCAACAGAAAAGA
68657 TGTTATAGCT
Statistics
Matches: 143, Mismatches: 27, Indels: 6
0.81 0.15 0.03
Matches are distributed among these distances:
135 140 0.98
136 3 0.02
ACGTcount: A:0.39, C:0.09, G:0.21, T:0.31
Consensus pattern (134 bp):
AGTTGAAATGCATATGGGTGCATTATCAACAGAAAAGAATGCTAAAGTTGAAATGTATATGGGTA
ATTATAAACATAAAAGTGTACTATTGTTGAAATGCATATGGATACATTATCAACAGAAAAGTATG
CTAG
Found at i:75194 original size:45 final size:46
Alignment explanation
Indices: 75115--75376 Score: 293
Period size: 45 Copynumber: 5.8 Consensus size: 46
75105 TAGGATGCCT
* * * ** *
75115 AGTTGAAATGTATATGGGTACATTATCAATAGAAAAACATAATTTG
1 AGTTGAAATGCATATGGGTGCATTATCAACAGAAAAGTATACTTTG
* *
75161 A-TTGGAATGCATATGGGTGCATTATCAACAGAAAAGTATGC-TTG
1 AGTTGAAATGCATATGGGTGCATTATCAACAGAAAAGTATACTTTG
* * *
75205 AGTTGAAATGCATCTGGGTGCATTATCAACAGAAAAGTATGC-TAG
1 AGTTGAAATGCATATGGGTGCATTATCAACAGAAAAGTATACTTTG
* *
75250 AGTTGAAATGCATATGGGTGTATTATCAACATAAAAGTATACTATT-
1 AGTTGAAATGCATATGGGTGCATTATCAACAGAAAAGTATACT-TTG
* * ** * * *
75296 -GTTGAAATGTATATGAGTATATTATCAATAGAAAATTATACTAT-
1 AGTTGAAATGCATATGGGTGCATTATCAACAGAAAAGTATACTTTG
75340 AGTTGAAATGCATATGGGTGCATTATCAACAGAAAAG
1 AGTTGAAATGCATATGGGTGCATTATCAACAGAAAAG
75377 ATGTTATACT
Statistics
Matches: 183, Mismatches: 29, Indels: 9
0.83 0.13 0.04
Matches are distributed among these distances:
44 5 0.03
45 176 0.96
46 1 0.01
47 1 0.01
ACGTcount: A:0.39, C:0.09, G:0.20, T:0.31
Consensus pattern (46 bp):
AGTTGAAATGCATATGGGTGCATTATCAACAGAAAAGTATACTTTG
Found at i:79838 original size:18 final size:18
Alignment explanation
Indices: 79815--79855 Score: 64
Period size: 18 Copynumber: 2.3 Consensus size: 18
79805 AGGCATTTGA
* *
79815 TCCTCTGGTTGTGCTTGT
1 TCCTCTGCTCGTGCTTGT
79833 TCCTCTGCTCGTGCTTGT
1 TCCTCTGCTCGTGCTTGT
79851 TCCTC
1 TCCTC
79856 GTGTTGTTCT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.00, C:0.32, G:0.22, T:0.46
Consensus pattern (18 bp):
TCCTCTGCTCGTGCTTGT
Found at i:81435 original size:22 final size:22
Alignment explanation
Indices: 81407--81489 Score: 96
Period size: 22 Copynumber: 3.7 Consensus size: 22
81397 AGAACCCTCA
*
81407 GGGGGTATCGATTCCCCTATGG
1 GGGGGTATCGATTCCCCTATAG
*
81429 GGGGGTATGGATTCCCCTATAG
1 GGGGGTATCGATTCCCCTATAG
* * *
81451 GGGGGAATCGGTTCCCCT-TCAAA
1 GGGGGTATCGATTCCCCTAT--AG
81474 GGGGGTATCGATTCCC
1 GGGGGTATCGATTCCC
81490 TCTGCACCAA
Statistics
Matches: 51, Mismatches: 8, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
21 1 0.02
22 35 0.69
23 15 0.29
ACGTcount: A:0.17, C:0.23, G:0.35, T:0.25
Consensus pattern (22 bp):
GGGGGTATCGATTCCCCTATAG
Found at i:93207 original size:54 final size:54
Alignment explanation
Indices: 92707--93199 Score: 776
Period size: 54 Copynumber: 9.1 Consensus size: 54
92697 GCACCCGTAT
* * *
92707 TGCCAATATGGAAATTCATAAAC-CTATTATGAATTTCTTAAGTTGCACACATAG
1 TGCCAATACGAAAATTCATAAACTC-ATTATGAATTTCTTAGGTTGCACACATAG
* *
92761 TGCCAATACGAAAATTCATAAACTCATTATAAACTTCTTAGGTTGCACACATAG
1 TGCCAATACGAAAATTCATAAACTCATTATGAATTTCTTAGGTTGCACACATAG
*
92815 TGTCAATAC-AGAAATTCATAAACTCATTATGAATTTCTTAGGTTGC-CACATAG
1 TGCCAATACGA-AAATTCATAAACTCATTATGAATTTCTTAGGTTGCACACATAG
*
92868 TGCCAATACGAAAATTCATAAACTCATTATGAATTTCTTAGGTTGTACACATAG
1 TGCCAATACGAAAATTCATAAACTCATTATGAATTTCTTAGGTTGCACACATAG
* *
92922 TGCCAATATGAAAATTCATAAACTCATTATGAACTTCTTAGGTTGCACACATAG
1 TGCCAATACGAAAATTCATAAACTCATTATGAATTTCTTAGGTTGCACACATAG
* *
92976 TGCAAATACGAAAATTCATAAACTCATTATGAACTTCTTAGGTTGCACACATAG
1 TGCCAATACGAAAATTCATAAACTCATTATGAATTTCTTAGGTTGCACACATAG
* * *
93030 TGCCAATATGAAAATTCATAAACTCATTATGAACTTCTTAGGTTGAACACATAG
1 TGCCAATACGAAAATTCATAAACTCATTATGAATTTCTTAGGTTGCACACATAG
* * *
93084 TGCCAACACGAAAATTTATAAACTCATTATGAATTTCTTAGGTTGCACACATAA
1 TGCCAATACGAAAATTCATAAACTCATTATGAATTTCTTAGGTTGCACACATAG
*
93138 TGCCAATACGTAAATTCATAAACTCATTATGAATTTCTTAGGTTGCACACATAG
1 TGCCAATACGAAAATTCATAAACTCATTATGAATTTCTTAGGTTGCACACATAG
*
93192 TGCTAATA
1 TGCCAATA
93200 TGGAAATTGT
Statistics
Matches: 406, Mismatches: 29, Indels: 8
0.92 0.07 0.02
Matches are distributed among these distances:
53 50 0.12
54 355 0.87
55 1 0.00
ACGTcount: A:0.38, C:0.18, G:0.13, T:0.32
Consensus pattern (54 bp):
TGCCAATACGAAAATTCATAAACTCATTATGAATTTCTTAGGTTGCACACATAG
Found at i:97386 original size:815 final size:815
Alignment explanation
Indices: 95790--97395 Score: 1877
Period size: 815 Copynumber: 2.0 Consensus size: 815
95780 TGAGTCAGTC
* *
95790 ATATGCTAAAACATAAATTTACTTAGTGATACAAGCATCATCAGGTTTTAGCAGTGAGTTCAATT
1 ATATGCTAAAACATAAATTTACTTAATGATACAAGCATCATCAGATTTTAGCAGTGAGTTCAATT
* * *** * * *
95855 TGTTAATTAATTTTTTCAGGTAATAGTCGGGAAACTTACATTCCGAAAGAAACATTTAGAGAGAC
66 TGTTAATTAAGTTTTTCAGGTAACAGTCAAAAAAATTACATTCCGAAAGAAACACTCAGAGAGAC
* * * * * * *
95920 AGATTTAGAAGATTGAGTTGAGGAATCTAGTGTGTTCTAACTAAACTAGATAAAAGTGTACAAAT
131 AGATTTAGAAGATTGAGTTGAAGAATCTAGTGTGTTCCAACAAAACCAGAGAAAAATATACAAAT
* *
95985 CTTAAAAACAGTAGTAGTTTAAAAACATGTTTTAAAACCATAGTAATACCCTCTAATCGAACACA
196 CTTAAAAACAGTAGTAGTTTAAAAACATATTTTAAAACCATAGTAATACCCTCTAACCGAACACA
* ** * * * *
96050 ATATGAAGTTCCCCATAACTGTATCCATAAGGACTTATCCTAGGCCATTGGGTAGGAACCATCCT
261 ATATGAAGTTCCCCAGAACTACATCCATAAGGACTTACCCTAGGCCATTGGATAGGAACCAACCG
* * * * * *
96115 AAGGGAGCATATTGGCCCAGGCAGATTTCCCTATGTACAAAGCAACGGAGAATAAAGTAAAGTTT
326 AAGGAAGCACATTAGCCCAGACAGATTTCCCTATGCACAAAGCAAAGGAGAATAAAGTAAAGTTT
* * *
96180 TCCCCTATACACGAAGTAAAAGGGGCATACGGTAAGGACTTACCCTGTACACAAAGCAAATGAGC
391 TCCCCTATACACAAAGCAAAAGGGGCATA--GTAAGGACTTACCCTGTACACAAAGCAAAGGAGC
** * * * * * *
96245 ATGTGGTAGGACTTACCTTAGCCAATGTGTCTGAGCCTACCCAAGGGTCACCTTAGGTCCATAAG
454 ATAAGGTAGGACTTACCCTAGCCAATGCGTATAAGCCTACCCAAAGGTCACCTTAAGTCCATAAG
* * * * *
96310 GATTTGTCAGCTTGATCAGAGCTGCACCTCAGAGACTCCATATCAGATCACAATAAACCCTAGTA
519 GATTTCTCACCTTAATCAAAGCTACACCTCAGAGACTCCATATCAGATCACAATAAACCCTAGTA
* *
96375 AAAAGAAATTTTCAAATAGTAAACGGTAATCTCAAAAATCATAAATCAAGAACTAGGAATCAAAT
584 AAAAGAAATTTTCAAATAGTAAACGGTAATATCAAAAATCATAAATCAAGAACTAAGAATCAAAT
* * *
96440 ATACTGGATCAGATAAAAAATCAGAGATCATACTTTCATTTCAGATAACATAGTCATACTATTAA
649 ATACT-GATCAGATAAAAAATCAAAGATCATACTTTCATTTCAGATAACAAAGTCACACTATTAA
* * * *
96505 AAACTAGAGAAAATATCCATGTCCATAGGGAACAAACTAGAGGATCCATATATTTTTCGGAGGTA
713 AAACAAGAGAAAATATCCATGTCCATAGGGAACAAACTAGAGGATCAATATATTTTCCAGAGGTA
96570 CTTG-TATTTACCAAATGAATACAATAGGTCATCAGGT
778 CTTGTTATTTACCAAATGAATACAATAGGTCATCAGGT
* * * * * *
96607 ATATGTTAAAGCATAAA-TTCCTTAATGATACAAGCATCATTAGATTTTAGCGGTGATTTCAGAT
1 ATATGCTAAAACATAAATTTACTTAATGATACAAGCATCATCAGATTTTAGCAGTGAGTTCA-AT
96671 TTGTTAATT-AGTTTTT-AGGTAACAGTCAAAAAAATTACAGTT-CGAAAGAAACACTCAGAGAG
65 TTGTTAATTAAGTTTTTCAGGTAACAGTCAAAAAAATTACA-TTCCGAAAGAAACACTCAGAGAG
** *
96733 GTAGATTTAGGAGATTGAGTT-AAGAAGTCTAGTGTGTTCCAACAAAACCAGAGAAAAATATACA
129 ACAGATTTAGAAGATTGAGTTGAAGAA-TCTAGTGTGTTCCAACAAAACCAGAGAAAAATATACA
* * * *
96797 TATCTTTAAAAGCAGTAGTAGTTTAAAAATATATTTTAAAACTCATAGTAATACGCT-TCAACCG
193 AATC-TTAAAAACAGTAGTAGTTTAAAAACATATTTTAAAAC-CATAGTAATACCCTCT-AACCG
* * *
96861 AACACTGATATGCAGTTCCCTAGAACTACATCCATAAGGACTTACCCTAGGACCATTGGACATAG
255 AACAC-AATATGAAGTTCCCCAGAACTACATCCATAAGGACTTACCCTAGG-CCATTGG--ATAG
* * * * * * * * *
96926 GAGCTAACCGAATGAAGCACCTTCAGTCCAGATAGATTTCCCCTATGCACAAAGGAAATGAGCAT
316 GAACCAACCGAAGGAAGCACATT-AGCCCAGACAGATTT-CCCTATGCACAAAGCAAAGGAGAAT
* * * *
96991 -ACGATAAATTTTTCCCCTATACACAAAGCAAAAGGGGCATA-TAAAGGACTTATCCTGTA-ATA
379 AAAG-TAAAGTTTTCCCCTATACACAAAGCAAAAGGGGCATAGT-AAGGACTTACCCTGTACACA
* * **
97053 AAGTAAAGGAGCTTAAGGTAAGGACTTACCCTAGTTGAA-GCGTATAAGCCTACCCAAAGGTCAC
442 AAGCAAAGGAGCATAAGGT-AGGACTTACCCTAG-CCAATGCGTATAAGCCTACCCAAAGGTCAC
* * *
97117 CTTAATTCCATAAGGATTTACT-ACCTTAATCAAAGCTACACCTCAGAGACTCCATGTCGGATC-
505 CTTAAGTCCATAAGGATTT-CTCACCTTAATCAAAGCTACACCTCAGAGACTCCATATCAGATCA
* * * ** * * *
97180 CAGATAAACCCTAGTAAAAAGAAATTTTTAATTAGTAAATGGTAATATCAGGAATCATGAATTAG
569 CA-ATAAACCCTAGTAAAAAGAAATTTTCAAATAGTAAACGGTAATATCAAAAATCATAAATCAA
* * * * * *
97245 GTA-TAAG-AT-ATAT-TA-T-ATCGGATACATAAATTAAAGATCATACTTTCATTTTAGATAAC
633 GAACTAAGAATCAAATATACTGATCAGATA-AAAAATCAAAGATCATACTTTCATTTCAGATAAC
*
97304 AAAGTCACACTTTTAAAAATCAAG-GAAAATATCCATGTCCATAGGGAACAAACTAGAGGATTCA
697 AAAGTCACACTATTAAAAA-CAAGAGAAAATATCCATGTCCATAGGGAACAAACTAGAGGA-TCA
97368 AT-TATTTTCCAGAGGTACTTGTTATTTA
760 ATATATTTTCCAGAGGTACTTGTTATTTA
97396 TCAGGTAAGA
Statistics
Matches: 659, Mismatches: 108, Indels: 45
0.81 0.13 0.06
Matches are distributed among these distances:
814 11 0.02
815 187 0.28
816 95 0.14
817 50 0.08
818 41 0.06
819 9 0.01
820 22 0.03
821 174 0.26
822 16 0.02
823 54 0.08
ACGTcount: A:0.38, C:0.17, G:0.17, T:0.28
Consensus pattern (815 bp):
ATATGCTAAAACATAAATTTACTTAATGATACAAGCATCATCAGATTTTAGCAGTGAGTTCAATT
TGTTAATTAAGTTTTTCAGGTAACAGTCAAAAAAATTACATTCCGAAAGAAACACTCAGAGAGAC
AGATTTAGAAGATTGAGTTGAAGAATCTAGTGTGTTCCAACAAAACCAGAGAAAAATATACAAAT
CTTAAAAACAGTAGTAGTTTAAAAACATATTTTAAAACCATAGTAATACCCTCTAACCGAACACA
ATATGAAGTTCCCCAGAACTACATCCATAAGGACTTACCCTAGGCCATTGGATAGGAACCAACCG
AAGGAAGCACATTAGCCCAGACAGATTTCCCTATGCACAAAGCAAAGGAGAATAAAGTAAAGTTT
TCCCCTATACACAAAGCAAAAGGGGCATAGTAAGGACTTACCCTGTACACAAAGCAAAGGAGCAT
AAGGTAGGACTTACCCTAGCCAATGCGTATAAGCCTACCCAAAGGTCACCTTAAGTCCATAAGGA
TTTCTCACCTTAATCAAAGCTACACCTCAGAGACTCCATATCAGATCACAATAAACCCTAGTAAA
AAGAAATTTTCAAATAGTAAACGGTAATATCAAAAATCATAAATCAAGAACTAAGAATCAAATAT
ACTGATCAGATAAAAAATCAAAGATCATACTTTCATTTCAGATAACAAAGTCACACTATTAAAAA
CAAGAGAAAATATCCATGTCCATAGGGAACAAACTAGAGGATCAATATATTTTCCAGAGGTACTT
GTTATTTACCAAATGAATACAATAGGTCATCAGGT
Found at i:106744 original size:3 final size:3
Alignment explanation
Indices: 106736--106774 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
106726 AACATTGCCA
106736 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
106775 GGTGTGAATT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:107768 original size:24 final size:24
Alignment explanation
Indices: 107736--107788 Score: 88
Period size: 24 Copynumber: 2.2 Consensus size: 24
107726 GCGACTTGCG
* *
107736 CTTAGGTTATAGGACTCTTATAGC
1 CTTAGGTTATAGCACTCTTACAGC
107760 CTTAGGTTATAGCACTCTTACAGC
1 CTTAGGTTATAGCACTCTTACAGC
107784 CTTAG
1 CTTAG
107789 TGTGCCTTGT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.25, C:0.21, G:0.19, T:0.36
Consensus pattern (24 bp):
CTTAGGTTATAGCACTCTTACAGC
Found at i:113193 original size:13 final size:13
Alignment explanation
Indices: 113172--113223 Score: 77
Period size: 13 Copynumber: 4.0 Consensus size: 13
113162 AATGGCGCTC
113172 AATGCGCGTCATA
1 AATGCGCGTCATA
*
113185 AATGAGCGTCATA
1 AATGCGCGTCATA
* *
113198 AATGTGTGTCATA
1 AATGCGCGTCATA
113211 AATGCGCGTCATA
1 AATGCGCGTCATA
113224 GATTTATGAC
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
13 34 1.00
ACGTcount: A:0.33, C:0.17, G:0.23, T:0.27
Consensus pattern (13 bp):
AATGCGCGTCATA
Found at i:116330 original size:23 final size:23
Alignment explanation
Indices: 116304--116349 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
116294 TAATTGCATC
116304 ATATGTCCGTAAATTATGATCTT
1 ATATGTCCGTAAATTATGATCTT
* *
116327 ATATGTCTGTAAATTATTATCTT
1 ATATGTCCGTAAATTATGATCTT
116350 CATTTTAAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.30, C:0.11, G:0.11, T:0.48
Consensus pattern (23 bp):
ATATGTCCGTAAATTATGATCTT
Found at i:116492 original size:60 final size:59
Alignment explanation
Indices: 116345--116496 Score: 142
Period size: 60 Copynumber: 2.5 Consensus size: 59
116335 GTAAATTATT
*
116345 ATCTTCATTTTAAATTGATCCTTTAAACTTTTAAACATTCTAATTTAATACATAAACTGTGA
1 ATCTT-ATTTTAAATTGAT-C-TTAAACTTTTAAACATTCTAATTTAATACATAAACTATGA
* * * * * * * * **
116407 ATCTCATTCTAGATTAGTTCTTAAACTTTTAAACCTTCTAATTTCATCCCTGTACTATGA
1 ATCTTATTTTAAATT-GATCTTAAACTTTTAAACATTCTAATTTAATACATAAACTATGA
* *
116467 TTCTTATTTTAAATTGGTCTATAAACTTTT
1 ATCTTATTTTAAATTGATCT-TAAACTTTT
116497 GAATCTTTCA
Statistics
Matches: 72, Mismatches: 16, Indels: 6
0.77 0.17 0.06
Matches are distributed among these distances:
59 4 0.06
60 53 0.74
61 9 0.12
62 6 0.08
ACGTcount: A:0.32, C:0.16, G:0.06, T:0.46
Consensus pattern (59 bp):
ATCTTATTTTAAATTGATCTTAAACTTTTAAACATTCTAATTTAATACATAAACTATGA
Found at i:126061 original size:92 final size:92
Alignment explanation
Indices: 125956--126148 Score: 341
Period size: 92 Copynumber: 2.1 Consensus size: 92
125946 TTAGTTTTAA
* * * *
125956 AATAATATCATGTACATGAAGTGCTAATCAATCATAAATGTAATGTTTAAATAAAAGTCTTATAA
1 AATAATATTATGTACATGAAATGCTAATCAATCATAAATGTAATGTTAAAATAAAAATCTTATAA
126021 TAAAATTTATGCAGTAGAAAATTAAAT
66 TAAAATTTATGCAGTAGAAAATTAAAT
*
126048 AATAATATTATGTACATGAAATGCTAATTAATCATAAATGTAATGTTAAAATAAAAATCTTATAA
1 AATAATATTATGTACATGAAATGCTAATCAATCATAAATGTAATGTTAAAATAAAAATCTTATAA
126113 TAAAATTTATGCAGTAGAAAATTAAAT
66 TAAAATTTATGCAGTAGAAAATTAAAT
126140 AATAATATT
1 AATAATATT
126149 GAATGAGAAG
Statistics
Matches: 96, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
92 96 1.00
ACGTcount: A:0.50, C:0.06, G:0.09, T:0.35
Consensus pattern (92 bp):
AATAATATTATGTACATGAAATGCTAATCAATCATAAATGTAATGTTAAAATAAAAATCTTATAA
TAAAATTTATGCAGTAGAAAATTAAAT
Found at i:130452 original size:44 final size:44
Alignment explanation
Indices: 130381--130464 Score: 107
Period size: 44 Copynumber: 1.9 Consensus size: 44
130371 CACCAATAAT
* * **
130381 TAATTATCCATTAATAACTCAGGTAGGTTGGTGGTTGGTGGTTA
1 TAATTATCCATGAATAACTCAGATAGGTTCCTGGTTGGTGGTTA
*
130425 TAATTATCCATGAATAA-TCCGAATAGGTTCCTGGTTGGTG
1 TAATTATCCATGAATAACTCAG-ATAGGTTCCTGGTTGGTG
130465 TTTGAATGGG
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
43 3 0.09
44 31 0.91
ACGTcount: A:0.26, C:0.12, G:0.25, T:0.37
Consensus pattern (44 bp):
TAATTATCCATGAATAACTCAGATAGGTTCCTGGTTGGTGGTTA
Found at i:130665 original size:45 final size:45
Alignment explanation
Indices: 130605--130708 Score: 120
Period size: 45 Copynumber: 2.3 Consensus size: 45
130595 ATTGCAACAT
* * *
130605 TAATTATCCGTTAATAATATC-AATAGGTTGGTGGTTGGTGGTTAA
1 TAATTATCCATTAATAA-ATCGAATAGATTGGTGGTTAGTGGTTAA
* * ** *
130650 TAATTATCCTTTAATAACTCGGGTAGATTGGTGGTTAGTGGTTAT
1 TAATTATCCATTAATAAATCGAATAGATTGGTGGTTAGTGGTTAA
130695 TAATTATCCATTAA
1 TAATTATCCATTAA
130709 CATCCCGGGT
Statistics
Matches: 50, Mismatches: 8, Indels: 2
0.83 0.13 0.03
Matches are distributed among these distances:
44 2 0.04
45 48 0.96
ACGTcount: A:0.29, C:0.09, G:0.21, T:0.41
Consensus pattern (45 bp):
TAATTATCCATTAATAAATCGAATAGATTGGTGGTTAGTGGTTAA
Found at i:130718 original size:45 final size:45
Alignment explanation
Indices: 130632--130730 Score: 135
Period size: 45 Copynumber: 2.2 Consensus size: 45
130622 TATCAATAGG
* * * *
130632 TTGGTGGTTGGTGGTTAATAATTATCCTTTAATAACTCGGGTAGA
1 TTGGTGGTTAGTGGTTAATAATTATCCATTAACAACCCGGGTAGA
* * *
130677 TTGGTGGTTAGTGGTTATTAATTATCCATTAACATCCCGGGTAGG
1 TTGGTGGTTAGTGGTTAATAATTATCCATTAACAACCCGGGTAGA
130722 TTGGTGGTT
1 TTGGTGGTT
130731 GCACAGGAAA
Statistics
Matches: 47, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
45 47 1.00
ACGTcount: A:0.21, C:0.10, G:0.28, T:0.40
Consensus pattern (45 bp):
TTGGTGGTTAGTGGTTAATAATTATCCATTAACAACCCGGGTAGA
Found at i:133704 original size:27 final size:27
Alignment explanation
Indices: 133626--133710 Score: 107
Period size: 27 Copynumber: 3.1 Consensus size: 27
133616 TCAAACATAT
* *
133626 TATGGATAATATCAATAGTTGAATGAA
1 TATGAATAATATCAATAGTTGAATTAA
*
133653 TGTGAATAATATCAATAGTTGAATTAA
1 TATGAATAATATCAATAGTTGAATTAA
* * * *
133680 TATGATTAATATCAACAATTAAATTAA
1 TATGAATAATATCAATAGTTGAATTAA
133707 TATG
1 TATG
133711 TTGGATATTT
Statistics
Matches: 50, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 50 1.00
ACGTcount: A:0.46, C:0.05, G:0.13, T:0.36
Consensus pattern (27 bp):
TATGAATAATATCAATAGTTGAATTAA
Found at i:136766 original size:35 final size:35
Alignment explanation
Indices: 136720--136795 Score: 118
Period size: 35 Copynumber: 2.2 Consensus size: 35
136710 TTCAATTCGA
* *
136720 TGCCCATTATTGCTGCATAATGGCACCATT-TTAGG
1 TGCCCATTATTGATGCACAATGGCACCATTATT-GG
136755 TGCCCATTATTGATGCACAATGGCACCATTATTGG
1 TGCCCATTATTGATGCACAATGGCACCATTATTGG
136790 TGCCCA
1 TGCCCA
136796 ATAATTACAC
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
35 36 0.95
36 2 0.05
ACGTcount: A:0.24, C:0.25, G:0.20, T:0.32
Consensus pattern (35 bp):
TGCCCATTATTGATGCACAATGGCACCATTATTGG
Found at i:137195 original size:15 final size:15
Alignment explanation
Indices: 137175--137203 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
137165 AATTACATAA
137175 TTTGGATGATGCAAC
1 TTTGGATGATGCAAC
137190 TTTGGATGATGCAA
1 TTTGGATGATGCAA
137204 TAATTTCTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.28, C:0.10, G:0.28, T:0.34
Consensus pattern (15 bp):
TTTGGATGATGCAAC
Found at i:144215 original size:16 final size:16
Alignment explanation
Indices: 144187--144219 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
144177 GTTAAGTGTA
144187 ATAAAAAATATAATTT
1 ATAAAAAATATAATTT
144203 ATAAATAAA-ATAATTT
1 ATAAA-AAATATAATTT
144219 A
1 A
144220 CTTTTATCTA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 13 0.81
17 3 0.19
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (16 bp):
ATAAAAAATATAATTT
Found at i:147241 original size:3 final size:3
Alignment explanation
Indices: 147226--147276 Score: 84
Period size: 3 Copynumber: 17.0 Consensus size: 3
147216 CCTACTATCT
* *
147226 TTA TTA GTA TTA TTA TTA TTG TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
147274 TTA
1 TTA
147277 AATACATTTA
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
3 44 1.00
ACGTcount: A:0.31, C:0.00, G:0.04, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:149510 original size:129 final size:129
Alignment explanation
Indices: 149337--149643 Score: 314
Period size: 129 Copynumber: 2.4 Consensus size: 129
149327 AAGGCATAAG
** * * * *** * *
149337 AGGTCATTTATTCTTGATTGAAAATAATTTGATATTACCGTTTTCTCTCGAATTAATATCG-ATT
1 AGGTCATTTATTCTCAATTGGAAATAATTAGATGTTATTATTTTCACTCGAATCAATATCGAATT
* * * * *
149401 TTTAGAGGGAATATTAATATCTCTTTATTTCAGTTGGGGTAATAAATGAC-AGTTTTAATACACG
66 TTAAGAGGAAATAGT-A-ATCTCTTTATTTCAATTGGAGTAATAAATGACTA-TTTTAATACACG
149465 -A
128 AA
* * * * * * *
149466 AGGTCGTTTATTCTCGATTGGAAATCATTAGATGTTATTATTTTCACTTGAGTCGATATTGAATT
1 AGGTCATTTATTCTCAATTGGAAATAATTAGATGTTATTATTTTCACTCGAATCAATATCGAATT
* *
149531 TTAAGATGAAATAGTAATCTCTTTATTTCAATTGGAGTAATAAATGACTATTTTAATGCACGAA
66 TTAAGAGGAAATAGTAATCTCTTTATTTCAATTGGAGTAATAAATGACTATTTTAATACACGAA
* * **
149595 AGGTCATTTATTCTCAATTGGAAATAATTAAATATTATCGTTTTCACTC
1 AGGTCATTTATTCTCAATTGGAAATAATTAGATGTTATTATTTTCACTC
149644 TTAAAATTAT
Statistics
Matches: 145, Mismatches: 30, Indels: 6
0.80 0.17 0.03
Matches are distributed among these distances:
128 41 0.28
129 90 0.62
130 14 0.10
ACGTcount: A:0.32, C:0.11, G:0.15, T:0.42
Consensus pattern (129 bp):
AGGTCATTTATTCTCAATTGGAAATAATTAGATGTTATTATTTTCACTCGAATCAATATCGAATT
TTAAGAGGAAATAGTAATCTCTTTATTTCAATTGGAGTAATAAATGACTATTTTAATACACGAA
Found at i:153413 original size:99 final size:99
Alignment explanation
Indices: 153288--153487 Score: 303
Period size: 99 Copynumber: 2.0 Consensus size: 99
153278 GTATACCCAG
* *
153288 AATGTAATTATATATGTATACAAATAAAGCTTGAGTTGTCCCTCTAGAGTAATTGGTTAAACGCC
1 AATGTAATTATATATATATACAAATAAAGCTTGAGTTGTCCCTCTAGAGCAATTGGTTAAACGCC
* ** *
153353 TCAGCTTTATGGATAAGATTCAGCTAGTCTGATA
66 CCAGCTTTATAAATAAGATTCAGCTACTCTGATA
* *
153387 AATGTGATTATAATATATATAC-AATAAAGCTTGAGTTGTCCCTCTAGAGCAATTGGTTAAATGC
1 AATGTAATTAT-ATATATATACAAATAAAGCTTGAGTTGTCCCTCTAGAGCAATTGGTTAAACGC
*
153451 CCCAGTTTTATAAATAAGATTCAGCTACTCTGATA
65 CCCAGCTTTATAAATAAGATTCAGCTACTCTGATA
153486 AA
1 AA
153488 GGCAAACTAC
Statistics
Matches: 91, Mismatches: 9, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
99 82 0.90
100 9 0.10
ACGTcount: A:0.35, C:0.14, G:0.17, T:0.34
Consensus pattern (99 bp):
AATGTAATTATATATATATACAAATAAAGCTTGAGTTGTCCCTCTAGAGCAATTGGTTAAACGCC
CCAGCTTTATAAATAAGATTCAGCTACTCTGATA
Found at i:156065 original size:20 final size:20
Alignment explanation
Indices: 156040--156156 Score: 58
Period size: 20 Copynumber: 5.7 Consensus size: 20
156030 CTGAATATGA
156040 TAAGTCCTTCGGGCCATCAG
1 TAAGTCCTTCGGGCCATCAG
* * * *
156060 TAAGTCTTTCGAGCAATACGAT
1 TAAGTCCTTCGGGCCAT-C-AG
* * *
156082 TAAATCCTTCGGGTCATCTG
1 TAAGTCCTTCGGGCCATCAG
* ** **
156102 TAAGTCTTTCAAG-CAAGATG
1 TAAGTCCTTCGGGCCATCA-G
156122 ATAAGTCCTTCGGGCCATCCA-
1 -TAAGTCCTTCGGGCCAT-CAG
*
156143 TAAGACCTTCGGGC
1 TAAGTCCTTCGGGC
156157 AGGATGTTTT
Statistics
Matches: 67, Mismatches: 24, Indels: 12
0.65 0.23 0.12
Matches are distributed among these distances:
19 2 0.03
20 37 0.55
21 12 0.18
22 15 0.22
23 1 0.01
ACGTcount: A:0.26, C:0.25, G:0.21, T:0.28
Consensus pattern (20 bp):
TAAGTCCTTCGGGCCATCAG
Found at i:156105 original size:42 final size:41
Alignment explanation
Indices: 156038--156140 Score: 134
Period size: 42 Copynumber: 2.5 Consensus size: 41
156028 TTCTGAATAT
* * *
156038 GATAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCAATAC
1 GATAAATCCTTCGGGCCATCAGTAAGTCTTTCAAGCAAGAC
* * *
156079 GATTAAATCCTTCGGGTCATCTGTAAGTCTTTCAAGCAAGAT
1 GA-TAAATCCTTCGGGCCATCAGTAAGTCTTTCAAGCAAGAC
*
156121 GATAAGTCCTTCGGGCCATC
1 GATAAATCCTTCGGGCCATC
156141 CATAAGACCT
Statistics
Matches: 53, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
41 18 0.34
42 35 0.66
ACGTcount: A:0.26, C:0.23, G:0.21, T:0.29
Consensus pattern (41 bp):
GATAAATCCTTCGGGCCATCAGTAAGTCTTTCAAGCAAGAC
Found at i:163065 original size:40 final size:42
Alignment explanation
Indices: 162971--163070 Score: 123
Period size: 42 Copynumber: 2.4 Consensus size: 42
162961 GGATATTACA
* * * *
162971 CTTCAGGCCATCAGTAAGTCTTTCGAGCATGATGATTAAATC
1 CTTCGGGCCATCTGTAAGCCTTTCGAGCAAGATGATTAAATC
* *
163013 CTTCGAGTCATCTGTAAGCCTTTCGAGCAAGATGA-T-AATC
1 CTTCGGGCCATCTGTAAGCCTTTCGAGCAAGATGATTAAATC
*
163053 CTTCGGGCCATCTATAAG
1 CTTCGGGCCATCTGTAAG
163071 ATCTTCGGGC
Statistics
Matches: 49, Mismatches: 9, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
40 19 0.39
41 1 0.02
42 29 0.59
ACGTcount: A:0.27, C:0.23, G:0.20, T:0.30
Consensus pattern (42 bp):
CTTCGGGCCATCTGTAAGCCTTTCGAGCAAGATGATTAAATC
Found at i:163272 original size:41 final size:42
Alignment explanation
Indices: 163206--163343 Score: 181
Period size: 41 Copynumber: 3.3 Consensus size: 42
163196 ACTTAGTAAG
*
163206 TCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATGCTTAAA
1 TCCTTCAGGCCATCAGTAAGTCTTTCGAGCATGATGCTTAAA
** * * * *
163248 TCCTTCAGG-CATTTGTAAGCCTTTCGAGCAAGATG-ATAAG
1 TCCTTCAGGCCATCAGTAAGTCTTTCGAGCATGATGCTTAAA
*
163288 TCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATGCTTAAA
1 TCCTTCAGGCCATCAGTAAGTCTTTCGAGCATGATGCTTAAA
*
163330 TCCTTCAGGTCATC
1 TCCTTCAGGCCATC
163344 TGCAAGTCGA
Statistics
Matches: 78, Mismatches: 16, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
40 11 0.14
41 44 0.56
42 23 0.29
ACGTcount: A:0.24, C:0.24, G:0.21, T:0.31
Consensus pattern (42 bp):
TCCTTCAGGCCATCAGTAAGTCTTTCGAGCATGATGCTTAAA
Found at i:163873 original size:3 final size:3
Alignment explanation
Indices: 163865--163939 Score: 141
Period size: 3 Copynumber: 24.7 Consensus size: 3
163855 TTCGTCCTAC
163865 TAT TAT TAT TATT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TA-T TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
163911 TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
163940 AATACATTTT
Statistics
Matches: 71, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
3 68 0.96
4 3 0.04
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:164546 original size:55 final size:55
Alignment explanation
Indices: 164457--164625 Score: 302
Period size: 55 Copynumber: 3.1 Consensus size: 55
164447 ATAAAATCAG
*
164457 ATAACATTCGAATCGACAATGAGAATAGTAATATCCTTTCATTTCGTTCGGAGTA
1 ATAACATTCGAATCGACAATGAGAATAGTAATATCCTTTCATTTCGATCGGAGTA
*
164512 ATAATATTCGAATCGACAATGAGAATAGTAATATCCTTTCATTTCGATCGGAGTA
1 ATAACATTCGAATCGACAATGAGAATAGTAATATCCTTTCATTTCGATCGGAGTA
* *
164567 ATAACATTCGAATCGACAATGAGAATATTAATATCCTTTCATTTCGGTCGGAGTA
1 ATAACATTCGAATCGACAATGAGAATAGTAATATCCTTTCATTTCGATCGGAGTA
164622 ATAA
1 ATAA
164626 ATGACTACTT
Statistics
Matches: 109, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
55 109 1.00
ACGTcount: A:0.36, C:0.15, G:0.16, T:0.33
Consensus pattern (55 bp):
ATAACATTCGAATCGACAATGAGAATAGTAATATCCTTTCATTTCGATCGGAGTA
Found at i:164896 original size:130 final size:130
Alignment explanation
Indices: 164647--164955 Score: 375
Period size: 130 Copynumber: 2.4 Consensus size: 130
164637 AAGGCATAAG
** * * * * * * ** * *
164647 AGGTCATTTATTCTCGCTTGGAAATAATTTGATATTGTCGTTTTCTCTCGAATTAATATCGATTT
1 AGGTCATTTATTCTCAATTGGAAATAATTAGATATTATCATTTTCACTTGAGTCGATATTGA-AT
* * *
164712 TTTAGAGGGAATATTAATATCTCTTTATTTCAATTGGGGGGATAAATGAATGTTTTAATGCACGA
65 TTTAGAGGAAATAGTAATATCTCTTTATTTCAATTGGAGGGATAAATGAATGTTTTAATGCACGA
164777 A
130 A
* * * * *
164778 AGGTCGTTTATTCTCGATTGGAAATCATTAGATGTTATTATTTTCACTTGAGTCGATATTGAATT
1 AGGTCATTTATTCTCAATTGGAAATAATTAGATATTATCATTTTCACTTGAGTCGATATTGAATT
* * * *
164843 TTAGATGAAATAGTAATATCTCTTTATTTCAATTGGAGTGATAAATTATTGTTTTAATGCACGAA
66 TTAGAGGAAATAGTAATATCTCTTTATTTCAATTGGAGGGATAAATGAATGTTTTAATGCACGAA
* *
164908 AGGTTATTTATTCTCAATTGGAAATAATTAGATATTATCGTTTTCACT
1 AGGTCATTTATTCTCAATTGGAAATAATTAGATATTATCATTTTCACT
164956 CTTAAAATTA
Statistics
Matches: 149, Mismatches: 29, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
130 101 0.68
131 48 0.32
ACGTcount: A:0.30, C:0.10, G:0.17, T:0.43
Consensus pattern (130 bp):
AGGTCATTTATTCTCAATTGGAAATAATTAGATATTATCATTTTCACTTGAGTCGATATTGAATT
TTAGAGGAAATAGTAATATCTCTTTATTTCAATTGGAGGGATAAATGAATGTTTTAATGCACGAA
Found at i:173920 original size:18 final size:19
Alignment explanation
Indices: 173879--173929 Score: 86
Period size: 19 Copynumber: 2.7 Consensus size: 19
173869 ACTACTATAT
173879 TACTTGCATCGATTGTGTA
1 TACTTGCATCGATTGTGTA
173898 TACTTGCATCGATTGTG-A
1 TACTTGCATCGATTGTGTA
*
173916 TACTTGCATAGATT
1 TACTTGCATCGATT
173930 TTTGTGCCAT
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
18 14 0.45
19 17 0.55
ACGTcount: A:0.24, C:0.16, G:0.20, T:0.41
Consensus pattern (19 bp):
TACTTGCATCGATTGTGTA
Found at i:174616 original size:24 final size:23
Alignment explanation
Indices: 174568--174626 Score: 75
Period size: 24 Copynumber: 2.5 Consensus size: 23
174558 TATTTAAATT
* *
174568 TAAAATATAAAATATTCAAAAAA
1 TAAAAAATAAAATATCCAAAAAA
174591 TAAATATAATAAAATA-CCAAAAAA
1 TAAA-A-AATAAAATATCCAAAAAA
174615 TAAAAAATAAAA
1 TAAAAAATAAAA
174627 ATATATTTTA
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
22 7 0.22
23 5 0.16
24 12 0.38
25 8 0.25
ACGTcount: A:0.73, C:0.05, G:0.00, T:0.22
Consensus pattern (23 bp):
TAAAAAATAAAATATCCAAAAAA
Found at i:174842 original size:22 final size:23
Alignment explanation
Indices: 174790--174843 Score: 56
Period size: 22 Copynumber: 2.3 Consensus size: 23
174780 GAATTAAACA
*
174790 AATATTATAAAGTCTTATAAAAAT
1 AATATT-TAAAATCTTATAAAAAT
* * *
174814 AAAATTTAAAAT-TTATGAAATT
1 AATATTTAAAATCTTATAAAAAT
174836 AATATTTA
1 AATATTTA
174844 TTTATGCATT
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
22 15 0.60
23 5 0.20
24 5 0.20
ACGTcount: A:0.54, C:0.02, G:0.04, T:0.41
Consensus pattern (23 bp):
AATATTTAAAATCTTATAAAAAT
Found at i:175333 original size:9 final size:9
Alignment explanation
Indices: 175321--175351 Score: 53
Period size: 9 Copynumber: 3.3 Consensus size: 9
175311 TCTTTTAGGG
175321 TTTTTATATT
1 TTTTTATA-T
175331 TTTTTATAT
1 TTTTTATAT
175340 TTTTTATAT
1 TTTTTATAT
175349 TTT
1 TTT
175352 AAATTTAAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 13 0.62
10 8 0.38
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (9 bp):
TTTTTATAT
Found at i:175336 original size:10 final size:10
Alignment explanation
Indices: 175321--175351 Score: 55
Period size: 10 Copynumber: 3.2 Consensus size: 10
175311 TCTTTTAGGG
175321 TTTTTATATT
1 TTTTTATATT
175331 TTTTTATA-T
1 TTTTTATATT
175340 TTTTTATATT
1 TTTTTATATT
175350 TT
1 TT
175352 AAATTTAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
9 9 0.45
10 11 0.55
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (10 bp):
TTTTTATATT
Found at i:178971 original size:37 final size:37
Alignment explanation
Indices: 178898--178971 Score: 96
Period size: 37 Copynumber: 2.0 Consensus size: 37
178888 TATATTTTTA
*
178898 ATTTTGTAAAAAAAAATTATATAAATATTATGAATTT
1 ATTTTGTAAAAAAAAATTATATAAATATTATCAATTT
* * *
178935 ATTTTGTTAAAGAAAA-TATATAAATATTTTACAATTT
1 ATTTTGTAAAAAAAAATTATATAAATATTAT-CAATTT
178972 GTAATATTAT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
36 13 0.41
37 19 0.59
ACGTcount: A:0.49, C:0.01, G:0.05, T:0.45
Consensus pattern (37 bp):
ATTTTGTAAAAAAAAATTATATAAATATTATCAATTT
Found at i:192949 original size:16 final size:17
Alignment explanation
Indices: 192918--192950 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
192908 GCTGATTCGA
*
192918 GAATTGATGCGTTGGTG
1 GAATTGAAGCGTTGGTG
192935 GAATTGAAG-GTTGGTG
1 GAATTGAAGCGTTGGTG
192951 ACAACTTCTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.21, C:0.03, G:0.42, T:0.33
Consensus pattern (17 bp):
GAATTGAAGCGTTGGTG
Found at i:213880 original size:47 final size:47
Alignment explanation
Indices: 213826--213948 Score: 169
Period size: 47 Copynumber: 2.7 Consensus size: 47
213816 AAATTGACGT
* **
213826 AAATAAACACTGGCCTTGTGCCTTTAGTCAATGGTGTAACCTGAGTG
1 AAATAAACACTGGCCTTGTGCCTTTAGTAAATGAAGTAACCTGAGTG
* * *
213873 AAATAAACCCTAGCCTTGTGCCTTTAGTAAATGAAGTAACCTGGGTG
1 AAATAAACACTGGCCTTGTGCCTTTAGTAAATGAAGTAACCTGAGTG
*
213920 AAATAAA-ATTGGCCTTGTGCCTTTA-TAAA
1 AAATAAACACTGGCCTTGTGCCTTTAGTAAA
213949 GTTATGTATA
Statistics
Matches: 67, Mismatches: 9, Indels: 2
0.86 0.12 0.03
Matches are distributed among these distances:
45 4 0.06
46 15 0.22
47 48 0.72
ACGTcount: A:0.32, C:0.18, G:0.20, T:0.30
Consensus pattern (47 bp):
AAATAAACACTGGCCTTGTGCCTTTAGTAAATGAAGTAACCTGAGTG
Found at i:214447 original size:61 final size:60
Alignment explanation
Indices: 214314--214499 Score: 225
Period size: 61 Copynumber: 3.1 Consensus size: 60
214304 GCATCATATG
* * * * *
214314 TCCCCAAGCTATGA-TCCTCATTTTAAATTGGTCCTTAAACTTTTGAATA-TCCAATTTAA
1 TCCCCAAACTATGACT-CTCATTCTAAATTAGTCCTTAAACTTTTGAACATTCCAATTTCA
* *
214373 TCCCCAAATTATGACTTTCATTCTAAATTAGTCCTTGAAACTTTTGAACATTCCAATTTCA
1 TCCCCAAACTATGACTCTCATTCTAAATTAGTCCTT-AAACTTTTGAACATTCCAATTTCA
* * * *
214434 TCCCCAAACTATGACCCTCATTCTAAATTAGTCCTCATACTTTTGAATC-TTTCAATTTCA
1 TCCCCAAACTATGACTCTCATTCTAAATTAGTCCTTAAACTTTTGAA-CATTCCAATTTCA
214494 TCCCCA
1 TCCCCA
214500 TGGGCAGCCA
Statistics
Matches: 110, Mismatches: 13, Indels: 7
0.85 0.10 0.05
Matches are distributed among these distances:
59 29 0.26
60 39 0.35
61 42 0.38
ACGTcount: A:0.30, C:0.26, G:0.06, T:0.38
Consensus pattern (60 bp):
TCCCCAAACTATGACTCTCATTCTAAATTAGTCCTTAAACTTTTGAACATTCCAATTTCA
Found at i:215579 original size:16 final size:16
Alignment explanation
Indices: 215558--215591 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
215548 TCACTATTCA
*
215558 CGTGAATAGTGAATTT
1 CGTGAATAGTGAAATT
215574 CGTGAATAGTGAAATT
1 CGTGAATAGTGAAATT
215590 CG
1 CG
215592 GTCGGCGATA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.32, C:0.09, G:0.26, T:0.32
Consensus pattern (16 bp):
CGTGAATAGTGAAATT
Found at i:220164 original size:29 final size:29
Alignment explanation
Indices: 220129--220210 Score: 137
Period size: 29 Copynumber: 2.8 Consensus size: 29
220119 AAACTAAATT
*
220129 GATGTCATTACTTACATCATTTAATTAAA
1 GATGTCATTGCTTACATCATTTAATTAAA
*
220158 GATGTCATTGCTTACATCATTTAATTAAT
1 GATGTCATTGCTTACATCATTTAATTAAA
220187 GATGTCATTGCTTACATCAATTTA
1 GATGTCATTGCTTACATC-ATTTA
220211 GTTAGGTGAG
Statistics
Matches: 50, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
29 45 0.90
30 5 0.10
ACGTcount: A:0.33, C:0.15, G:0.10, T:0.43
Consensus pattern (29 bp):
GATGTCATTGCTTACATCATTTAATTAAA
Found at i:221909 original size:60 final size:60
Alignment explanation
Indices: 221836--221985 Score: 219
Period size: 60 Copynumber: 2.5 Consensus size: 60
221826 GACTAATTTA
* * * *
221836 TAATTTTTAATAGTCAGGAGACTCAATAAAATAATGTTATATAATTAGAAAATCATTTTG
1 TAATTTTTAATAGTCAGAAAACTCAACAAAATAATATTATATAATTAGAAAATCATTTTG
*
221896 TAATTTTTAATAGTCAGAAAACTCAACAAAATAATATTATATAATTAGAATATCATTTTG
1 TAATTTTTAATAGTCAGAAAACTCAACAAAATAATATTATATAATTAGAAAATCATTTTG
* * * *
221956 TAACTTTTAATAGTCGGGAAATTCAACAAA
1 TAATTTTTAATAGTCAGAAAACTCAACAAA
221986 GCAACACTCT
Statistics
Matches: 81, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
60 81 1.00
ACGTcount: A:0.45, C:0.09, G:0.10, T:0.37
Consensus pattern (60 bp):
TAATTTTTAATAGTCAGAAAACTCAACAAAATAATATTATATAATTAGAAAATCATTTTG
Found at i:222995 original size:60 final size:60
Alignment explanation
Indices: 222862--222974 Score: 154
Period size: 60 Copynumber: 1.9 Consensus size: 60
222852 TCGAGTGATC
* * * * *
222862 ATTTTGTAATTTTTAATAGTTGAGGGACTCAACAAAGCAACGCCTTATAGTTGGAGGACT
1 ATTTTATAACTTTTAATAGTTGAAGGACTCAACAAAGCAACACCATATAGTTGGAGGACT
* * *
222922 ATTTTATAACTTTTAATAGTTGAATGATTCAACAAAGCAACATCATATAGTTG
1 ATTTTATAACTTTTAATAGTTGAAGGACTCAACAAAGCAACACCATATAGTTG
222975 ATGGATCATT
Statistics
Matches: 45, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
60 45 1.00
ACGTcount: A:0.35, C:0.12, G:0.17, T:0.35
Consensus pattern (60 bp):
ATTTTATAACTTTTAATAGTTGAAGGACTCAACAAAGCAACACCATATAGTTGGAGGACT
Found at i:223713 original size:17 final size:16
Alignment explanation
Indices: 223693--223748 Score: 62
Period size: 16 Copynumber: 3.5 Consensus size: 16
223683 TTTTAAAACT
*
223693 AAAATATAAAAATATTC
1 AAAATATAAAAATA-TA
223710 AAAATAT-AAAATATA
1 AAAATATAAAAATATA
223725 AAAATACTAAAAATA-A
1 AAAATA-TAAAAATATA
*
223741 AAATTATA
1 AAAATATA
223749 TTTCTAAAAT
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
15 9 0.26
16 13 0.37
17 13 0.37
ACGTcount: A:0.70, C:0.04, G:0.00, T:0.27
Consensus pattern (16 bp):
AAAATATAAAAATATA
Found at i:223720 original size:7 final size:7
Alignment explanation
Indices: 223692--223742 Score: 50
Period size: 8 Copynumber: 6.7 Consensus size: 7
223682 GTTTTAAAAC
223692 TAAAATA
1 TAAAATA
223699 TAAAAATA
1 T-AAAATA
223707 TTCAAAATA
1 -T-AAAATA
223716 TAAAATA
1 TAAAATA
223723 TAAAAATA
1 T-AAAATA
223731 CTAAAA-A
1 -TAAAATA
223738 TAAAA
1 TAAAA
223743 ATTATATTTC
Statistics
Matches: 39, Mismatches: 1, Indels: 9
0.80 0.02 0.18
Matches are distributed among these distances:
6 5 0.13
7 9 0.23
8 17 0.44
9 8 0.21
ACGTcount: A:0.71, C:0.04, G:0.00, T:0.25
Consensus pattern (7 bp):
TAAAATA
Found at i:223730 original size:15 final size:15
Alignment explanation
Indices: 223693--223744 Score: 61
Period size: 15 Copynumber: 3.3 Consensus size: 15
223683 TTTTAAAACT
*
223693 AAAATATAAAAATATTC
1 AAAATAT-AAAATA-TA
223710 AAAATATAAAATATA
1 AAAATATAAAATATA
223725 AAAATACTAAAA-ATA
1 AAAATA-TAAAATATA
223740 AAAAT
1 AAAAT
223745 TATATTTCTA
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
15 15 0.45
16 11 0.33
17 7 0.21
ACGTcount: A:0.71, C:0.04, G:0.00, T:0.25
Consensus pattern (15 bp):
AAAATATAAAATATA
Found at i:223735 original size:9 final size:8
Alignment explanation
Indices: 223693--223748 Score: 62
Period size: 9 Copynumber: 7.0 Consensus size: 8
223683 TTTTAAAACT
223693 AAAATATA
1 AAAATATA
*
223701 AAAATATTC
1 AAAATA-TA
223710 AAAATAT-
1 AAAATATA
223717 AAAATATA
1 AAAATATA
223725 AAAATACTA
1 AAAATA-TA
223734 AAAATA-A
1 AAAATATA
*
223741 AAATTATA
1 AAAATATA
223749 TTTCTAAAAT
Statistics
Matches: 42, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
7 13 0.31
8 14 0.33
9 15 0.36
ACGTcount: A:0.70, C:0.04, G:0.00, T:0.27
Consensus pattern (8 bp):
AAAATATA
Found at i:223748 original size:24 final size:24
Alignment explanation
Indices: 223692--223744 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
223682 GTTTTAAAAC
* *
223692 TAAAATATAAAAATATTCAAAATA
1 TAAAATATAAAAATACTAAAAATA
223716 TAAAATATAAAAATACTAAAAATA
1 TAAAATATAAAAATACTAAAAATA
223740 -AAAAT
1 TAAAAT
223745 TATATTTCTA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
23 5 0.19
24 22 0.81
ACGTcount: A:0.70, C:0.04, G:0.00, T:0.26
Consensus pattern (24 bp):
TAAAATATAAAAATACTAAAAATA
Found at i:223757 original size:21 final size:23
Alignment explanation
Indices: 223731--223773 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
223721 TATAAAAATA
223731 CTAAAA-ATAAAAAT-TATATTT
1 CTAAAATATAAAAATATATATTT
*
223752 CTAAAATTTAAAAATATATATT
1 CTAAAATATAAAAATATATATT
223774 AATGAGAGTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 6 0.32
22 7 0.37
23 6 0.32
ACGTcount: A:0.56, C:0.05, G:0.00, T:0.40
Consensus pattern (23 bp):
CTAAAATATAAAAATATATATTT
Found at i:226044 original size:15 final size:15
Alignment explanation
Indices: 226026--226071 Score: 56
Period size: 18 Copynumber: 2.9 Consensus size: 15
226016 TAACCGGTTT
226026 CGGTTTTAAAAAAAC
1 CGGTTTTAAAAAAAC
226041 CGGTTTTTTAAAAAAAAC
1 CGG--TTTT-AAAAAAAC
*
226059 CGGTTATAAAAAA
1 CGGTTTTAAAAAA
226072 CCGATTATAA
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
15 9 0.33
16 3 0.11
17 4 0.15
18 11 0.41
ACGTcount: A:0.48, C:0.11, G:0.13, T:0.28
Consensus pattern (15 bp):
CGGTTTTAAAAAAAC
Found at i:226051 original size:17 final size:18
Alignment explanation
Indices: 226029--226063 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
226019 CCGGTTTCGG
226029 TTTT-AAAAAAACCGGTT
1 TTTTAAAAAAAACCGGTT
226046 TTTTAAAAAAAACCGGTT
1 TTTTAAAAAAAACCGGTT
226064 ATAAAAAACC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 4 0.24
18 13 0.76
ACGTcount: A:0.43, C:0.11, G:0.11, T:0.34
Consensus pattern (18 bp):
TTTTAAAAAAAACCGGTT
Found at i:226069 original size:14 final size:14
Alignment explanation
Indices: 226052--226081 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
226042 GGTTTTTTAA
*
226052 AAAAAACCGGTTAT
1 AAAAAACCGATTAT
226066 AAAAAACCGATTAT
1 AAAAAACCGATTAT
226080 AA
1 AA
226082 TATTATTAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.57, C:0.13, G:0.10, T:0.20
Consensus pattern (14 bp):
AAAAAACCGATTAT
Found at i:226170 original size:33 final size:33
Alignment explanation
Indices: 226123--226226 Score: 174
Period size: 33 Copynumber: 3.2 Consensus size: 33
226113 ACAAAGTTTA
* *
226123 CGAT-AATTGAAATACTTAAATACTTCCAAGTT
1 CGATAAATTCAAATACTTAAAAACTTCCAAGTT
226155 CGATAAATTCAAATACTTAAAAACTTCCAAGTT
1 CGATAAATTCAAATACTTAAAAACTTCCAAGTT
*
226188 CGATAAATTCAAATACTTAAAAACTTTCAAGTT
1 CGATAAATTCAAATACTTAAAAACTTCCAAGTT
226221 CGATAA
1 CGATAA
226227 TTGAAACAAA
Statistics
Matches: 68, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
32 4 0.06
33 64 0.94
ACGTcount: A:0.44, C:0.16, G:0.08, T:0.32
Consensus pattern (33 bp):
CGATAAATTCAAATACTTAAAAACTTCCAAGTT
Found at i:226246 original size:21 final size:21
Alignment explanation
Indices: 226221--226262 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
226211 CTTTCAAGTT
226221 CGATAATTGAAACAAAGTTTA
1 CGATAATTGAAACAAAGTTTA
*
226242 CGATAATTGAAATAAAGTTTA
1 CGATAATTGAAACAAAGTTTA
226263 AAAATAAACT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.48, C:0.07, G:0.14, T:0.31
Consensus pattern (21 bp):
CGATAATTGAAACAAAGTTTA
Found at i:228641 original size:13 final size:13
Alignment explanation
Indices: 228623--228647 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
228613 TTTTTTTCCA
228623 AACCGGTTAAAAT
1 AACCGGTTAAAAT
228636 AACCGGTTAAAA
1 AACCGGTTAAAA
228648 AAAATCCGAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.16, G:0.16, T:0.20
Consensus pattern (13 bp):
AACCGGTTAAAAT
Found at i:228714 original size:28 final size:29
Alignment explanation
Indices: 228684--228740 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 29
228674 GGTTTTCTTC
228684 AAATCCGAT-TTCAGATATTTTTT-TGCACA
1 AAATCCGATATTC-GA-ATTTTTTGTGCACA
*
228713 AAATCGGATATTCGAATTTTTTGTGCAC
1 AAATCCGATATTCGAATTTTTTGTGCAC
228741 CTCTACCCGC
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
28 7 0.28
29 15 0.60
30 3 0.12
ACGTcount: A:0.30, C:0.16, G:0.14, T:0.40
Consensus pattern (29 bp):
AAATCCGATATTCGAATTTTTTGTGCACA
Found at i:233074 original size:2 final size:2
Alignment explanation
Indices: 233067--233094 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
233057 TCCAACAACG
233067 CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT
233095 TAATTTCTGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:234261 original size:16 final size:16
Alignment explanation
Indices: 234240--234270 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
234230 AATTATTTTT
234240 ATTTAATAAAAAAATG
1 ATTTAATAAAAAAATG
*
234256 ATTTAATTAAAAAAT
1 ATTTAATAAAAAAAT
234271 AATATATAGA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.35
Consensus pattern (16 bp):
ATTTAATAAAAAAATG
Found at i:235844 original size:21 final size:21
Alignment explanation
Indices: 235794--235844 Score: 61
Period size: 20 Copynumber: 2.5 Consensus size: 21
235784 TTTTTATTCT
* *
235794 TTATCTTTTAGTTTTATTAAG
1 TTATATTTTACTTTTATTAAG
235815 TTA-ATTTTACTTTTATATAA-
1 TTATATTTTACTTTTAT-TAAG
235835 TTATATTTTA
1 TTATATTTTA
235845 TAAAACTTTG
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
20 14 0.54
21 12 0.46
ACGTcount: A:0.29, C:0.04, G:0.04, T:0.63
Consensus pattern (21 bp):
TTATATTTTACTTTTATTAAG
Found at i:236106 original size:24 final size:27
Alignment explanation
Indices: 236073--236135 Score: 78
Period size: 24 Copynumber: 2.4 Consensus size: 27
236063 ATCAAAGTTT
*
236073 ATAATTAATAGTACACCACA-T-TAA-A
1 ATAA-TAATAGTACACAACATTGTAATA
*
236098 ATAATAATAGTACATAACATTGTAATA
1 ATAATAATAGTACACAACATTGTAATA
236125 ATAATAATAGT
1 ATAATAATAGT
236136 GTCAAACTGT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
24 13 0.39
25 5 0.15
26 3 0.09
27 12 0.36
ACGTcount: A:0.52, C:0.10, G:0.06, T:0.32
Consensus pattern (27 bp):
ATAATAATAGTACACAACATTGTAATA
Found at i:236299 original size:46 final size:45
Alignment explanation
Indices: 236200--236324 Score: 128
Period size: 46 Copynumber: 2.8 Consensus size: 45
236190 ATAATACAAA
* * *
236200 GTCTAATTCATAATTAGTGCTACAACACATCAAACCAACAATACT
1 GTCTAAGTCATAATTAGTACTACAACACATTAAACCAACAATACT
* *
236245 GT-TGAAGTCTATAATTAGTACTACAACACATTAAAGCTAA-AATATT
1 GTCT-AAGTC-ATAATTAGTACTACAACACATTAAA-CCAACAATACT
* * * *
236291 GTCTAAGTCATAAATAATATTACACCACATTAAA
1 GTCTAAGTCATAATTAGTACTACAACACATTAAA
236325 AGTTCACATC
Statistics
Matches: 67, Mismatches: 9, Indels: 8
0.80 0.11 0.10
Matches are distributed among these distances:
44 1 0.01
45 27 0.40
46 35 0.52
47 4 0.06
ACGTcount: A:0.44, C:0.18, G:0.08, T:0.30
Consensus pattern (45 bp):
GTCTAAGTCATAATTAGTACTACAACACATTAAACCAACAATACT
Found at i:237937 original size:21 final size:21
Alignment explanation
Indices: 237895--237937 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
237885 TTTCTGGGTT
* * *
237895 AGGGGAATCGGTACCCATTCA
1 AGGGGAACCGATACCCACTCA
*
237916 AGGGGAACCGATACCCCCTCA
1 AGGGGAACCGATACCCACTCA
237937 A
1 A
237938 CGAATATGAT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.30, C:0.30, G:0.26, T:0.14
Consensus pattern (21 bp):
AGGGGAACCGATACCCACTCA
Found at i:237997 original size:66 final size:68
Alignment explanation
Indices: 237917--238067 Score: 234
Period size: 67 Copynumber: 2.2 Consensus size: 68
237907 ACCCATTCAA
*
237917 GGGGAACCGATACCCCCTCAACGAATATG-ATTTCCAGAATGCTAGAGGGGAATCGATACCCCCA
1 GGGGAACCGATACCCCCTCAACGAATATGAAATTCCAGAATGCTAGAGGGGAATCGATACCCCCA
237981 -GG
66 GGG
* * * *
237983 GGGGAACCGATACCCCCTCATCGTATATGAAATTCCAGATTGCTTGAGGGGAATCGATACCCCCA
1 GGGGAACCGATACCCCCTCAACGAATATGAAATTCCAGAATGCTAGAGGGGAATCGATACCCCCA
238048 GGG
66 GGG
*
238051 GGGGAACCGATTCCCCC
1 GGGGAACCGATACCCCC
238068 ATGAGAAAAA
Statistics
Matches: 77, Mismatches: 6, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
66 27 0.35
67 32 0.42
68 18 0.23
ACGTcount: A:0.27, C:0.28, G:0.26, T:0.18
Consensus pattern (68 bp):
GGGGAACCGATACCCCCTCAACGAATATGAAATTCCAGAATGCTAGAGGGGAATCGATACCCCCA
GGG
Found at i:238402 original size:29 final size:29
Alignment explanation
Indices: 238368--238439 Score: 99
Period size: 29 Copynumber: 2.5 Consensus size: 29
238358 CATATTATGA
* *
238368 TACATGACATGAATTTATATTAAATGTAT
1 TACATGACATGAATTCATATGAAATGTAT
*
238397 TACATGACATGAATTCATATGATATGTAT
1 TACATGACATGAATTCATATGAAATGTAT
* *
238426 TGCATGGCATGAAT
1 TACATGACATGAAT
238440 ATGCAGAAAA
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
29 38 1.00
ACGTcount: A:0.38, C:0.10, G:0.15, T:0.38
Consensus pattern (29 bp):
TACATGACATGAATTCATATGAAATGTAT
Found at i:238495 original size:30 final size:30
Alignment explanation
Indices: 238453--238529 Score: 118
Period size: 30 Copynumber: 2.5 Consensus size: 30
238443 CAGAAAAGTT
* *
238453 ATATGAGCTATGTGATAAAGGTATGTAAATG
1 ATATGA-CTATGTGATAAAGGTATGGAAATA
238484 ATATGACTATGTGATAAAGGTATGGAAATA
1 ATATGACTATGTGATAAAGGTATGGAAATA
*
238514 ATATGACTACGTGATA
1 ATATGACTATGTGATA
238530 TGAACTACGG
Statistics
Matches: 43, Mismatches: 3, Indels: 1
0.91 0.06 0.02
Matches are distributed among these distances:
30 37 0.86
31 6 0.14
ACGTcount: A:0.40, C:0.05, G:0.23, T:0.31
Consensus pattern (30 bp):
ATATGACTATGTGATAAAGGTATGGAAATA
Found at i:238806 original size:23 final size:23
Alignment explanation
Indices: 238740--238798 Score: 102
Period size: 22 Copynumber: 2.6 Consensus size: 23
238730 ATCATTATAT
*
238740 GGCACTACGGTGCAATTCTAC-G
1 GGCACTTCGGTGCAATTCTACGG
238762 GGCACTTCGGTGCAATTCTACGG
1 GGCACTTCGGTGCAATTCTACGG
238785 GGCACTTCGGTGCA
1 GGCACTTCGGTGCA
238799 TTTATACGAG
Statistics
Matches: 35, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
22 20 0.57
23 15 0.43
ACGTcount: A:0.19, C:0.27, G:0.31, T:0.24
Consensus pattern (23 bp):
GGCACTTCGGTGCAATTCTACGG
Found at i:242966 original size:44 final size:43
Alignment explanation
Indices: 242747--242963 Score: 177
Period size: 43 Copynumber: 5.0 Consensus size: 43
242737 ACGTCACAAT
** * * *
242747 AGGTCAAGATCTATTGCGACATTTTTGGA-GCAAACGCAGCAAA
1 AGGTC-AGATCTATAACGACGTTTTTGGATACAAACGCCGCAAA
* * * * * * * **
242790 AGGTTGATATCTAAAACGACATTTTTGGAAAAAAACTCTACAAA
1 AGG-TCAGATCTATAACGACGTTTTTGGATACAAACGCCGCAAA
* * * * * *
242834 AAGTCAGATCTATAGCGGCGTTTTCGGA-ATAAACGCCACAAA
1 AGGTCAGATCTATAACGACGTTTTTGGATACAAACGCCGCAAA
* *
242876 ATGTCAGATATATAACGACGTTTTTTGGATACAAACGCCGCAAA
1 AGGTCAGATCTATAACGACG-TTTTTGGATACAAACGCCGCAAA
* *
242920 AGGTTAGATCTATAACGACGTTTTTAGATACAAACGCCGCAAA
1 AGGTCAGATCTATAACGACGTTTTTGGATACAAACGCCGCAAA
242963 A
1 A
242964 AGGCTAATGA
Statistics
Matches: 138, Mismatches: 32, Indels: 8
0.78 0.18 0.04
Matches are distributed among these distances:
42 27 0.20
43 70 0.51
44 41 0.30
ACGTcount: A:0.38, C:0.18, G:0.19, T:0.25
Consensus pattern (43 bp):
AGGTCAGATCTATAACGACGTTTTTGGATACAAACGCCGCAAA
Found at i:244826 original size:140 final size:140
Alignment explanation
Indices: 244574--244850 Score: 464
Period size: 140 Copynumber: 2.0 Consensus size: 140
244564 AAACCAACCA
* * * * *
244574 GAAAAACATGATATAAGCATACCAGAGCTTGTCCCTGCAGAAGAAAAGCAGCTTCATTGTGAAAT
1 GAAAAACATGATATAAGCATACAAGAGCTTGTCCCTACAGAAGAAAAACAACTTCATGGTGAAAT
* *
244639 ATTTTAGTAAGATGATAAATTCAAAATTTAAACCTTTGTCCAATAAACATTCTAGTAAAAATGCA
66 ATTTAAGTAAGATGATAAATTCAAAATTTAAACCTTTATCCAATAAACATTCTAGTAAAAATGCA
244704 GATAAGTCCT
131 GATAAGTCCT
* *
244714 GAAAAACATGATATAAGCATATAAGAGCTTGTCTCTACAGAAGAAAAACAACTTCATGGTGAAAT
1 GAAAAACATGATATAAGCATACAAGAGCTTGTCCCTACAGAAGAAAAACAACTTCATGGTGAAAT
*
244779 ATTTAAGTAAGGTGATAAATTCAAAATTTAAACCTTTATCCAATAAACATTCTAGTAAAAATGCA
66 ATTTAAGTAAGATGATAAATTCAAAATTTAAACCTTTATCCAATAAACATTCTAGTAAAAATGCA
244844 GATAAGT
131 GATAAGT
244851 TCTCAAAGAA
Statistics
Matches: 127, Mismatches: 10, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
140 127 1.00
ACGTcount: A:0.44, C:0.14, G:0.14, T:0.28
Consensus pattern (140 bp):
GAAAAACATGATATAAGCATACAAGAGCTTGTCCCTACAGAAGAAAAACAACTTCATGGTGAAAT
ATTTAAGTAAGATGATAAATTCAAAATTTAAACCTTTATCCAATAAACATTCTAGTAAAAATGCA
GATAAGTCCT
Found at i:245854 original size:41 final size:41
Alignment explanation
Indices: 245783--246098 Score: 337
Period size: 41 Copynumber: 7.6 Consensus size: 41
245773 TAAACTTACG
* * *
245783 GCGGCGTTTGTAAAAACAAACACCACTAAAGTACGAGTCTATA
1 GCGGCGTTTGT-ATAA-AAACGCCACTAAAGTACAAGTCTATA
** * **
245826 GCGGCGTAAGTATATAAACGATACTAAAGTACAAG-CGTATA
1 GCGGCGTTTGTATAAAAACGCCACTAAAGTACAAGTC-TATA
*
245867 GCGGCGTTTGTATAAAAACGCCACTAAAGTACAAGTGTATA
1 GCGGCGTTTGTATAAAAACGCCACTAAAGTACAAGTCTATA
* * *
245908 GCAGCGTTTGTATATAAACGCCACTAAAGTACAAGTGTATA
1 GCGGCGTTTGTATAAAAACGCCACTAAAGTACAAGTCTATA
* *
245949 GCTGCATTTGTATAAAAACGCCACTAAAGTACAAGTCTATA
1 GCGGCGTTTGTATAAAAACGCCACTAAAGTACAAGTCTATA
* * * * *
245990 ACTGCATTTGTATAAAAACACCACTAAAGTACAAGTCTTTA
1 GCGGCGTTTGTATAAAAACGCCACTAAAGTACAAGTCTATA
** * * * * *
246031 GCAACGTTTGTATAAAAACGCCACTAAAATACTACTCTGTT
1 GCGGCGTTTGTATAAAAACGCCACTAAAGTACAAGTCTATA
* *
246072 GCGGCGTTTGTTTAAAAGACACCACTA
1 GCGGCGTTTGTATAAAA-ACGCCACTA
246099 TGGATGAACC
Statistics
Matches: 233, Mismatches: 37, Indels: 7
0.84 0.13 0.03
Matches are distributed among these distances:
40 1 0.00
41 213 0.91
42 10 0.04
43 9 0.04
ACGTcount: A:0.38, C:0.19, G:0.17, T:0.26
Consensus pattern (41 bp):
GCGGCGTTTGTATAAAAACGCCACTAAAGTACAAGTCTATA
Found at i:247342 original size:28 final size:28
Alignment explanation
Indices: 247284--247343 Score: 93
Period size: 28 Copynumber: 2.1 Consensus size: 28
247274 GAAGGATTTT
* **
247284 GGGTGTGGAGAGCTTTGAATGAGCGTTA
1 GGGTGTGGAGAGCTTTGAAGGAGCGAGA
247312 GGGTGTGGAGAGCTTTGAAGGAGCGAGA
1 GGGTGTGGAGAGCTTTGAAGGAGCGAGA
247340 GGGT
1 GGGT
247344 ACCCAAGGAA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.22, C:0.07, G:0.48, T:0.23
Consensus pattern (28 bp):
GGGTGTGGAGAGCTTTGAAGGAGCGAGA
Found at i:248554 original size:223 final size:222
Alignment explanation
Indices: 247831--248580 Score: 1010
Period size: 223 Copynumber: 3.3 Consensus size: 222
247821 TTTATTCATA
* * * * ** **
247831 TATTAAATAGAAATATTTTTTTATTATTTCGGGTCGGGTCGG-GTAAAATT--T-TATTTTGGTC
1 TATTGAATAAAAATAATTTTTTATTATTTCGGGTCGGGTCGGTTTCTAATTCATATATTCGGGTC
* * *** **
247892 GGGTCGGGTTAATTTTTTAAAGTGTGATATTCGGGTCGGG-TCGAGTTT-AGGTTTAGGGTGAAA
66 GGGTCGGG-T--TTTTTT-AAGTGTGATATTCGGGTCGGGTTCGGGTTTAAGG-TGAAAAT-ACC
* * * *
247955 AATATCCGACCTAAAAATATATATAATTTTACCTTATATATTTAGGAATAATTACAATAATATCT
125 AA-ACCCGACCCAAAAATATATATAATTTTACCTTATATATTTATGAATAATTATAATAATATC-
*
248020 CTCTATATATAATTTTTTTCAATTAAGTCATTGTTTT
188 CTCTCTATAT--TTTTTTTCAATTAAGTCATTGTTTT
* *
248057 TATTGAATAAAAATAATTTTTTTTATTATTTCAGGTCAGGTCGGATTTCTAATTCATATATTCGG
1 TATTGAATAAAAATAA--TTTTTTATTATTTCGGGTCGGGTCGG-TTTCTAATTCATATATTCGG
* * **
248122 GTCGGGTCGGTTTTTTTTAAGTGTGATATTCGGATCGGGTTCGGGTTTAAGGTGAAAAATACCCG
63 GTCGGGTCGGGTTTTTTTAAGTGTGATATTCGGGTCGGGTTCGGGTTTAAGGTG-AAAATACCAA
*
248187 ACTCGACCCAAAAATATATATAATTTTACCTTATATATTTATGAATAATTATAATAATACTCCTC
127 ACCCGACCCAAAAATATATATAATTTTACCTTATATATTTATGAATAATTATAATAATA-TCCTC
**
248252 TCTATATTTTTTTTCAATTAAGTCGCTGTTTT
191 TCTATATTTTTTTTCAATTAAGTCATTGTTTT
*
248284 TATTGAATAAAAATAATTTTTTATTATTTCGGGTCGGGTCGGTTTCTAATTCATATATTTGGGTC
1 TATTGAATAAAAATAATTTTTTATTATTTCGGGTCGGGTCGGTTTCTAATTCATATATTCGGGTC
*
248349 GGGTCGGGTTTTTTTAAGTGTGATATTTGGGTCGGGTTCGGGTTTAAGGTGAAAATACCAAACCC
66 GGGTCGGGTTTTTTTAAGTGTGATATTCGGGTCGGGTTCGGGTTTAAGGTGAAAATACCAAACCC
248414 GACCCAAAAA-ATATATAATTTTACCTTATATATTTATGAATAATTATAATAATATCACTCTCTA
131 GACCCAAAAATATATATAATTTTACCTTATATATTTATGAATAATTATAATAATATC-CTCTCTA
248478 TATTTTTTTTCCAATTAAGTCATTGTTTT
195 TATTTTTTTT-CAATTAAGTCATTGTTTT
*
248507 AATTGAATAAAAATAATTTTTTATTATTTCGGGTCGGGTCGGTTTCTAATTCATATATTCGGGTC
1 TATTGAATAAAAATAATTTTTTATTATTTCGGGTCGGGTCGGTTTCTAATTCATATATTCGGGTC
248572 GGGTCGGGT
66 GGGTCGGGT
248581 GAAACTTTAT
Statistics
Matches: 469, Mismatches: 42, Indels: 29
0.87 0.08 0.05
Matches are distributed among these distances:
221 2 0.00
222 61 0.13
223 109 0.23
224 70 0.15
225 24 0.05
226 13 0.03
227 39 0.08
228 24 0.05
229 83 0.18
230 22 0.05
231 5 0.01
232 2 0.00
233 15 0.03
ACGTcount: A:0.29, C:0.11, G:0.17, T:0.43
Consensus pattern (222 bp):
TATTGAATAAAAATAATTTTTTATTATTTCGGGTCGGGTCGGTTTCTAATTCATATATTCGGGTC
GGGTCGGGTTTTTTTAAGTGTGATATTCGGGTCGGGTTCGGGTTTAAGGTGAAAATACCAAACCC
GACCCAAAAATATATATAATTTTACCTTATATATTTATGAATAATTATAATAATATCCTCTCTAT
ATTTTTTTTCAATTAAGTCATTGTTTT
Found at i:249908 original size:16 final size:15
Alignment explanation
Indices: 249876--249923 Score: 57
Period size: 15 Copynumber: 3.3 Consensus size: 15
249866 ACGAGAGATT
249876 AGAGAAGTAGAGAGA
1 AGAGAAGTAGAGAGA
*
249891 AGAGAACGTAG-GAGG
1 AGAGAA-GTAGAGAGA
249906 A-AGAAGTAGAGA-A
1 AGAGAAGTAGAGAGA
249919 AGAGA
1 AGAGA
249924 TGAAGAAATC
Statistics
Matches: 28, Mismatches: 2, Indels: 7
0.76 0.05 0.19
Matches are distributed among these distances:
13 5 0.18
14 9 0.32
15 10 0.36
16 4 0.14
ACGTcount: A:0.52, C:0.02, G:0.40, T:0.06
Consensus pattern (15 bp):
AGAGAAGTAGAGAGA
Found at i:253451 original size:16 final size:15
Alignment explanation
Indices: 253419--253466 Score: 57
Period size: 15 Copynumber: 3.3 Consensus size: 15
253409 ACGAGAGATT
253419 AGAGAAGTAGAGAGA
1 AGAGAAGTAGAGAGA
*
253434 AGAGAACGTAG-GAGG
1 AGAGAA-GTAGAGAGA
253449 A-AGAAGTAGAGA-A
1 AGAGAAGTAGAGAGA
253462 AGAGA
1 AGAGA
253467 TGAAGAAATC
Statistics
Matches: 28, Mismatches: 2, Indels: 7
0.76 0.05 0.19
Matches are distributed among these distances:
13 5 0.18
14 9 0.32
15 10 0.36
16 4 0.14
ACGTcount: A:0.52, C:0.02, G:0.40, T:0.06
Consensus pattern (15 bp):
AGAGAAGTAGAGAGA
Found at i:253883 original size:67 final size:67
Alignment explanation
Indices: 253775--253909 Score: 270
Period size: 67 Copynumber: 2.0 Consensus size: 67
253765 CCTTAGTAAT
253775 TCCCAAATTCCTTTCTTCGAGTCTAACTTCTTCTTCTCTGCCTTTTCTCTTGTGCATGACAACTG
1 TCCCAAATTCCTTTCTTCGAGTCTAACTTCTTCTTCTCTGCCTTTTCTCTTGTGCATGACAACTG
253840 GG
66 GG
253842 TCCCAAATTCCTTTCTTCGAGTCTAACTTCTTCTTCTCTGCCTTTTCTCTTGTGCATGACAACTG
1 TCCCAAATTCCTTTCTTCGAGTCTAACTTCTTCTTCTCTGCCTTTTCTCTTGTGCATGACAACTG
253907 GG
66 GG
253909 T
1 T
253910 GGAGACGGTG
Statistics
Matches: 68, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
67 68 1.00
ACGTcount: A:0.15, C:0.30, G:0.13, T:0.42
Consensus pattern (67 bp):
TCCCAAATTCCTTTCTTCGAGTCTAACTTCTTCTTCTCTGCCTTTTCTCTTGTGCATGACAACTG
GG
Found at i:258801 original size:18 final size:18
Alignment explanation
Indices: 258774--258843 Score: 77
Period size: 18 Copynumber: 3.7 Consensus size: 18
258764 TTAAGGAGTA
*
258774 GTCCTTCGGGACATAGTG
1 GTCCTACGGGACATAGTG
*
258792 GTCCTACGGGATATATACAGTG
1 GTCCTACGGG--ACAT--AGTG
*
258814 GTCCTTCGGGACATAGTG
1 GTCCTACGGGACATAGTG
258832 GTCCTACGGGAC
1 GTCCTACGGGAC
258844 GAATACTGAA
Statistics
Matches: 43, Mismatches: 5, Indels: 8
0.77 0.09 0.14
Matches are distributed among these distances:
18 24 0.56
20 6 0.14
22 13 0.30
ACGTcount: A:0.20, C:0.23, G:0.31, T:0.26
Consensus pattern (18 bp):
GTCCTACGGGACATAGTG
Found at i:260453 original size:23 final size:23
Alignment explanation
Indices: 260395--260454 Score: 70
Period size: 23 Copynumber: 2.7 Consensus size: 23
260385 AATTTACATA
*
260395 TATAACACATTTTTCTCTGTCTT
1 TATAACACATTTTTCTCTATCTT
* *
260418 TATGACAC-GTTTTCTTCTATCTT
1 TATAACACATTTTTC-TCTATCTT
260441 T-TAACACATTTTTC
1 TATAACACATTTTTC
260455 AACCGTTTGG
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
22 10 0.33
23 20 0.67
ACGTcount: A:0.22, C:0.22, G:0.05, T:0.52
Consensus pattern (23 bp):
TATAACACATTTTTCTCTATCTT
Found at i:260952 original size:2 final size:2
Alignment explanation
Indices: 260940--260986 Score: 85
Period size: 2 Copynumber: 23.0 Consensus size: 2
260930 AATTATCATG
260940 AT AT GAT 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
260983 AT AT
1 AT AT
260987 TAATTAGATT
Statistics
Matches: 44, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 42 0.95
3 2 0.05
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (2 bp):
AT
Found at i:265024 original size:9 final size:9
Alignment explanation
Indices: 265010--265108 Score: 72
Period size: 10 Copynumber: 10.0 Consensus size: 9
265000 GGCTGCTGGA
265010 AACCGGTTT
1 AACCGGTTT
265019 AACCGGTTTT
1 AACCGG-TTT
265029 CAACCGGTTCT
1 -AACCGGTT-T
*
265040 GACCGGTTT
1 AACCGGTTT
*
265049 GACCGGTTT
1 AACCGGTTT
265058 CAACCGGTTTT
1 -AACCGG-TTT
265069 CAACCGGGTTCT
1 -AACC-GGTT-T
*
265081 GACCGGTTT
1 AACCGGTTT
* *
265090 GACCGGTCTG
1 AACCGGT-TT
265100 AACCGGTTT
1 AACCGGTTT
265109 GATCGGTCTG
Statistics
Matches: 76, Mismatches: 6, Indels: 16
0.78 0.06 0.16
Matches are distributed among these distances:
9 25 0.33
10 28 0.37
11 20 0.26
12 3 0.04
ACGTcount: A:0.16, C:0.26, G:0.26, T:0.31
Consensus pattern (9 bp):
AACCGGTTT
Found at i:265055 original size:19 final size:19
Alignment explanation
Indices: 265031--265121 Score: 89
Period size: 19 Copynumber: 4.7 Consensus size: 19
265021 CCGGTTTTCA
265031 ACCGGTTCTGACCGGTTTG
1 ACCGGTTCTGACCGGTTTG
* *
265050 ACCGGTT-TCAACCGGTTTTCA
1 ACCGGTTCT-GACCGG-TTT-G
265071 ACCGGGTTCTGACCGGTTTG
1 ACC-GGTTCTGACCGGTTTG
265091 ACCGG-TCTGAACCGGTTTG
1 ACCGGTTCTG-ACCGGTTTG
*
265110 ATCGG-TCTGACC
1 ACCGGTTCTGACC
265122 CGACCCGACC
Statistics
Matches: 61, Mismatches: 5, Indels: 13
0.77 0.06 0.16
Matches are distributed among these distances:
18 8 0.13
19 31 0.51
20 6 0.10
21 6 0.10
22 9 0.15
23 1 0.02
ACGTcount: A:0.14, C:0.27, G:0.29, T:0.30
Consensus pattern (19 bp):
ACCGGTTCTGACCGGTTTG
Found at i:265091 original size:41 final size:39
Alignment explanation
Indices: 265011--265108 Score: 160
Period size: 41 Copynumber: 2.4 Consensus size: 39
265001 GCTGCTGGAA
265011 ACCGGTTTAACCGGTTTTCAACCGGTTCTGACCGGTTTG
1 ACCGGTTTAACCGGTTTTCAACCGGTTCTGACCGGTTTG
265050 ACCGGTTTCAACCGGTTTTCAACCGGGTTCTGACCGGTTTG
1 ACCGGTTT-AACCGGTTTTCAACC-GGTTCTGACCGGTTTG
*
265091 ACCGGTCTGAACCGGTTT
1 ACCGGT-TTAACCGGTTT
265109 GATCGGTCTG
Statistics
Matches: 55, Mismatches: 1, Indels: 4
0.92 0.02 0.07
Matches are distributed among these distances:
39 8 0.15
40 15 0.27
41 31 0.56
42 1 0.02
ACGTcount: A:0.15, C:0.27, G:0.27, T:0.32
Consensus pattern (39 bp):
ACCGGTTTAACCGGTTTTCAACCGGTTCTGACCGGTTTG
Found at i:265115 original size:9 final size:9
Alignment explanation
Indices: 265011--265121 Score: 78
Period size: 9 Copynumber: 11.3 Consensus size: 9
265001 GCTGCTGGAA
*
265011 ACCGGTTTA
1 ACCGGTTTG
*
265020 ACCGGTTTTCA
1 ACCGG-TTT-G
265031 ACCGGTTCTG
1 ACCGGTT-TG
265041 ACCGGTTTG
1 ACCGGTTTG
*
265050 ACCGGTTTCA
1 ACCGGTTT-G
*
265060 ACCGGTTTTCA
1 ACCGG-TTT-G
265071 ACCGGGTTCTG
1 ACC-GGTT-TG
265082 ACCGGTTTG
1 ACCGGTTTG
*
265091 ACCGGTCTG
1 ACCGGTTTG
265100 AACCGGTTTG
1 -ACCGGTTTG
* *
265110 ATCGGTCTG
1 ACCGGTTTG
265119 ACC
1 ACC
265122 CGACCCGACC
Statistics
Matches: 86, Mismatches: 8, Indels: 16
0.78 0.07 0.15
Matches are distributed among these distances:
9 34 0.40
10 29 0.34
11 20 0.23
12 3 0.03
ACGTcount: A:0.15, C:0.27, G:0.27, T:0.31
Consensus pattern (9 bp):
ACCGGTTTG
Found at i:265139 original size:17 final size:17
Alignment explanation
Indices: 265117--265189 Score: 137
Period size: 17 Copynumber: 4.3 Consensus size: 17
265107 TTGATCGGTC
265117 TGACCCGACCCGACCGT
1 TGACCCGACCCGACCGT
265134 TGACCCGACCCGACCGT
1 TGACCCGACCCGACCGT
*
265151 TGACCCGATCCGACCGT
1 TGACCCGACCCGACCGT
265168 TGACCCGACCCGACCGT
1 TGACCCGACCCGACCGT
265185 TGACC
1 TGACC
265190 GTTGACCGTT
Statistics
Matches: 54, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 54 1.00
ACGTcount: A:0.18, C:0.45, G:0.23, T:0.14
Consensus pattern (17 bp):
TGACCCGACCCGACCGT
Found at i:267592 original size:11 final size:11
Alignment explanation
Indices: 267576--267604 Score: 58
Period size: 11 Copynumber: 2.6 Consensus size: 11
267566 AAGTTGCTGA
267576 AGTATGGATTC
1 AGTATGGATTC
267587 AGTATGGATTC
1 AGTATGGATTC
267598 AGTATGG
1 AGTATGG
267605 TACCTACGGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.28, C:0.07, G:0.31, T:0.34
Consensus pattern (11 bp):
AGTATGGATTC
Found at i:272387 original size:9 final size:9
Alignment explanation
Indices: 272373--272438 Score: 60
Period size: 10 Copynumber: 6.8 Consensus size: 9
272363 GGCTGCTGGA
272373 AACCGGTTT
1 AACCGGTTT
272382 AACCGGTTTT
1 AACCGG-TTT
272392 CAACCGGTTCT
1 -AACCGGTT-T
*
272403 GACCGGTTT
1 AACCGGTTT
*
272412 CAACCGGTTCG
1 -AACCGGTT-T
272423 AACCGGTTT
1 AACCGGTTT
*
272432 GACCGGT
1 AACCGGT
272439 CTGACCCGAC
Statistics
Matches: 47, Mismatches: 5, Indels: 10
0.76 0.08 0.16
Matches are distributed among these distances:
9 13 0.28
10 27 0.57
11 7 0.15
ACGTcount: A:0.18, C:0.27, G:0.26, T:0.29
Consensus pattern (9 bp):
AACCGGTTT
Found at i:272398 original size:20 final size:21
Alignment explanation
Indices: 272373--272431 Score: 86
Period size: 20 Copynumber: 2.9 Consensus size: 21
272363 GGCTGCTGGA
272373 AACCGGTT-TAACCGGTTTTC
1 AACCGGTTCTAACCGGTTTTC
*
272393 AACCGGTTCTGACCGG-TTTC
1 AACCGGTTCTAACCGGTTTTC
*
272413 AACCGGTTCGAACCGGTTT
1 AACCGGTTCTAACCGGTTT
272432 GACCGGTCTG
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
20 26 0.76
21 8 0.24
ACGTcount: A:0.19, C:0.27, G:0.24, T:0.31
Consensus pattern (21 bp):
AACCGGTTCTAACCGGTTTTC
Done.