Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002039.1 Hibiscus syriacus cultivar Beakdansim tig00004159_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: 146967
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.34
Found at i:6387 original size:23 final size:23
Alignment explanation
Indices: 6359--6403 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
6349 CGAGATAATT
* *
6359 TTTGATCGATCTAGTTTTAAAAA
1 TTTGATCCATCTAATTTTAAAAA
*
6382 TTTGATCCATTTAATTTTAAAA
1 TTTGATCCATCTAATTTTAAAA
6404 TTGAAAATTA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.36, C:0.09, G:0.09, T:0.47
Consensus pattern (23 bp):
TTTGATCCATCTAATTTTAAAAA
Found at i:10212 original size:20 final size:20
Alignment explanation
Indices: 10187--10224 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
10177 AATTTAAGGA
10187 AAAGTGGAAAAAA-AATAACT
1 AAAGT-GAAAAAATAATAACT
10207 AAAGTGAAAAAATAATAA
1 AAAGTGAAAAAATAATAA
10225 AAATATAATG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 7 0.41
20 10 0.59
ACGTcount: A:0.68, C:0.03, G:0.13, T:0.16
Consensus pattern (20 bp):
AAAGTGAAAAAATAATAACT
Found at i:12769 original size:16 final size:15
Alignment explanation
Indices: 12750--12782 Score: 50
Period size: 14 Copynumber: 2.2 Consensus size: 15
12740 ATTTAAAATT
12750 TTAAAGAAAATATAAA
1 TTAAA-AAAATATAAA
12766 TT-AAAAAATATAAA
1 TTAAAAAAATATAAA
12780 TTA
1 TTA
12783 TATTTTCTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 3
0.84 0.00 0.16
Matches are distributed among these distances:
14 12 0.75
15 2 0.12
16 2 0.12
ACGTcount: A:0.67, C:0.00, G:0.03, T:0.30
Consensus pattern (15 bp):
TTAAAAAAATATAAA
Found at i:12775 original size:14 final size:14
Alignment explanation
Indices: 12756--12782 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
12746 AATTTTAAAG
12756 AAAATATAAATTAA
1 AAAATATAAATTAA
12770 AAAATATAAATTA
1 AAAATATAAATTA
12783 TATTTTCTAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (14 bp):
AAAATATAAATTAA
Found at i:14665 original size:2 final size:2
Alignment explanation
Indices: 14658--14700 Score: 59
Period size: 2 Copynumber: 21.0 Consensus size: 2
14648 AGGCTAAAGC
* *
14658 AT AT AT AT AT AT AT AA AGC AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT
14701 TAATAATGGC
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
2 36 0.97
3 1 0.03
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.44
Consensus pattern (2 bp):
AT
Found at i:14676 original size:19 final size:19
Alignment explanation
Indices: 14652--14691 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
14642 GGGAAAAGGC
14652 TAAAGCATATATATATATA
1 TAAAGCATATATATATATA
14671 TAAAGCATATATATATATA
1 TAAAGCATATATATATATA
14690 TA
1 TA
14692 TATATATATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.53, C:0.05, G:0.05, T:0.38
Consensus pattern (19 bp):
TAAAGCATATATATATATA
Found at i:17283 original size:2 final size:2
Alignment explanation
Indices: 17276--17328 Score: 106
Period size: 2 Copynumber: 26.5 Consensus size: 2
17266 CCAATCTAAC
17276 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
17318 TA TA TA TA TA T
1 TA TA TA TA TA T
17329 GAGAAAATAA
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 51 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:17480 original size:20 final size:20
Alignment explanation
Indices: 17455--17501 Score: 76
Period size: 20 Copynumber: 2.4 Consensus size: 20
17445 GTTTCCAAAT
17455 TCGCAACGCGAATCTGTAAA
1 TCGCAACGCGAATCTGTAAA
* *
17475 TCGCAACGCGAATTTGTAAT
1 TCGCAACGCGAATCTGTAAA
17495 TCGCAAC
1 TCGCAAC
17502 ACAAAAGTCA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.32, C:0.26, G:0.19, T:0.23
Consensus pattern (20 bp):
TCGCAACGCGAATCTGTAAA
Found at i:17515 original size:20 final size:20
Alignment explanation
Indices: 17492--17540 Score: 89
Period size: 20 Copynumber: 2.5 Consensus size: 20
17482 GCGAATTTGT
17492 AATTCGCAACACAAAAGTCA
1 AATTCGCAACACAAAAGTCA
*
17512 AATTCGCAACACATAAGTCA
1 AATTCGCAACACAAAAGTCA
17532 AATTCGCAA
1 AATTCGCAA
17541 AGCGCGTTTA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.47, C:0.24, G:0.10, T:0.18
Consensus pattern (20 bp):
AATTCGCAACACAAAAGTCA
Found at i:17728 original size:20 final size:21
Alignment explanation
Indices: 17688--17730 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 21
17678 TCACTCTCTA
*
17688 CGGCGACATCCGTCCCTATCTC
1 CGGCGAAATCCGT-CCTATCTC
17710 CGGCGAAATCCGT-CTATCTC
1 CGGCGAAATCCGTCCTATCTC
17730 C
1 C
17731 ATCTCTCAGA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 8 0.40
22 12 0.60
ACGTcount: A:0.16, C:0.42, G:0.19, T:0.23
Consensus pattern (21 bp):
CGGCGAAATCCGTCCTATCTC
Found at i:18590 original size:2 final size:2
Alignment explanation
Indices: 18585--18645 Score: 122
Period size: 2 Copynumber: 30.5 Consensus size: 2
18575 GATATATGTG
18585 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
18627 TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA T
18646 TTGTCTAGCA
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 59 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:27951 original size:20 final size:20
Alignment explanation
Indices: 27926--27963 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
27916 GAATGCTAGA
*
27926 GGGGAATCGATACCCCCAGG
1 GGGGAACCGATACCCCCAGG
*
27946 GGGGAACCGATTCCCCCA
1 GGGGAACCGATACCCCCA
27964 TGTATAAAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.24, C:0.34, G:0.32, T:0.11
Consensus pattern (20 bp):
GGGGAACCGATACCCCCAGG
Found at i:28637 original size:149 final size:150
Alignment explanation
Indices: 28449--28764 Score: 537
Period size: 150 Copynumber: 2.1 Consensus size: 150
28439 GGGTAGAGGG
* *
28449 TCTACGCGGTCCTTCGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTT-GAAAGACACA
1 TCTACGCGGTCCTTCGGGACATATATATATTCTGTGGAACATGTGTGAAGTCTTGGAAAGACACA
* *
28513 TATTTGATCCCTAGTATATGTATATAATTCTTAAGGAATAATATGTGGTCCTTATGGACATTATT
66 TACTTGATCCCTAGTATATGTATATAATTCTTAAGGAATAATATGTGGTCCTTATGGACATCATT
28578 ATATGGCACTACGGTGCAAT
131 ATATGGCACTACGGTGCAAT
*
28598 TCTACGCGGTCCTTCGGGATATATATATATTCTGTGGAACATGTGTGAAGTCTTGGAAAGACACA
1 TCTACGCGGTCCTTCGGGACATATATATATTCTGTGGAACATGTGTGAAGTCTTGGAAAGACACA
* **
28663 TACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATCATT
66 TACTTGATCCCTAGTATATGTATATAATTCTTAAGGAATAATATGTGGTCCTTATGGACATCATT
28728 ATATGGCACTACGGTGCAAT
131 ATATGGCACTACGGTGCAAT
28748 TCTACGCGG-CACTTCGG
1 TCTACGCGGTC-CTTCGG
28765 TGCATTTATA
Statistics
Matches: 157, Mismatches: 8, Indels: 3
0.93 0.05 0.02
Matches are distributed among these distances:
149 52 0.33
150 105 0.67
ACGTcount: A:0.27, C:0.17, G:0.21, T:0.34
Consensus pattern (150 bp):
TCTACGCGGTCCTTCGGGACATATATATATTCTGTGGAACATGTGTGAAGTCTTGGAAAGACACA
TACTTGATCCCTAGTATATGTATATAATTCTTAAGGAATAATATGTGGTCCTTATGGACATCATT
ATATGGCACTACGGTGCAAT
Found at i:28776 original size:23 final size:23
Alignment explanation
Indices: 28732--28776 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
28722 ATCATTATAT
*
28732 GGCACTACGGTGCAATTCTACGC
1 GGCACTACGGTGCAATTATACGC
* *
28755 GGCACTTCGGTGCATTTATACG
1 GGCACTACGGTGCAATTATACG
28777 AGCTGTGGTG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.20, C:0.27, G:0.27, T:0.27
Consensus pattern (23 bp):
GGCACTACGGTGCAATTATACGC
Found at i:31884 original size:14 final size:13
Alignment explanation
Indices: 31863--31930 Score: 57
Period size: 13 Copynumber: 4.9 Consensus size: 13
31853 TTTTTCGTCC
31863 TTATTTTATTTTA
1 TTATTTTATTTTA
*
31876 TTTTATTTA-TTTA
1 TTAT-TTTATTTTA
* *
31889 GGTTAATTTATTTCA
1 --TTATTTTATTTTA
31904 CTTATTTTTATTTTA
1 -TTA-TTTTATTTTA
31919 TTATTTTATTTT
1 TTATTTTATTTT
31931 TAAAATTAAC
Statistics
Matches: 43, Mismatches: 7, Indels: 10
0.72 0.12 0.17
Matches are distributed among these distances:
13 16 0.37
14 14 0.33
15 13 0.30
ACGTcount: A:0.22, C:0.03, G:0.03, T:0.72
Consensus pattern (13 bp):
TTATTTTATTTTA
Found at i:33556 original size:2 final size:2
Alignment explanation
Indices: 33549--33582 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
33539 TGATGTTTGG
33549 TC TC TC TC TC TC TC TC TC TC TC TC -C TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
33583 TGGACTTTTA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:35106 original size:14 final size:13
Alignment explanation
Indices: 35086--35120 Score: 52
Period size: 14 Copynumber: 2.6 Consensus size: 13
35076 ATAAAAAATA
*
35086 TTTTTAAATATTT
1 TTTTTAAATATAT
35099 TATTTTAAATATAT
1 T-TTTTAAATATAT
35113 TTTTTAAA
1 TTTTTAAA
35121 AAATAAAGTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
13 8 0.40
14 12 0.60
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (13 bp):
TTTTTAAATATAT
Found at i:36398 original size:17 final size:17
Alignment explanation
Indices: 36376--36408 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
36366 TCATACTATA
*
36376 ATATTATTTTTTATATT
1 ATATTAATTTTTATATT
36393 ATATTAATTTTTATAT
1 ATATTAATTTTTATAT
36409 AAATAAATAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (17 bp):
ATATTAATTTTTATATT
Found at i:36820 original size:14 final size:16
Alignment explanation
Indices: 36793--36824 Score: 50
Period size: 14 Copynumber: 2.1 Consensus size: 16
36783 ATATTATTAG
36793 AATAATATTATATTTT
1 AATAATATTATATTTT
36809 AATAAT-TT-TATTTT
1 AATAATATTATATTTT
36823 AA
1 AA
36825 AAAGAATTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 8 0.50
15 2 0.12
16 6 0.38
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (16 bp):
AATAATATTATATTTT
Found at i:36834 original size:17 final size:17
Alignment explanation
Indices: 36812--36867 Score: 57
Period size: 17 Copynumber: 3.5 Consensus size: 17
36802 ATATTTTAAT
36812 AATTTTATTTTAAAAAG
1 AATTTTATTTTAAAAAG
36829 AATTTTA---TAAAAAG
1 AATTTTATTTTAAAAAG
* *
36843 AA-TTTATTTTCAAAAT
1 AATTTTATTTTAAAAAG
*
36859 AATCTTATT
1 AATTTTATT
36868 ATGTTATGTG
Statistics
Matches: 32, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
13 4 0.12
14 9 0.28
16 7 0.22
17 12 0.38
ACGTcount: A:0.46, C:0.04, G:0.04, T:0.46
Consensus pattern (17 bp):
AATTTTATTTTAAAAAG
Found at i:38410 original size:24 final size:25
Alignment explanation
Indices: 38378--38426 Score: 91
Period size: 24 Copynumber: 2.0 Consensus size: 25
38368 TTTTTGTTTT
38378 TAACCAGCTAAAATTATAT-GATTA
1 TAACCAGCTAAAATTATATAGATTA
38402 TAACCAGCTAAAATTATATAGATTA
1 TAACCAGCTAAAATTATATAGATTA
38427 CCAGCTAGGG
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
24 19 0.79
25 5 0.21
ACGTcount: A:0.47, C:0.12, G:0.08, T:0.33
Consensus pattern (25 bp):
TAACCAGCTAAAATTATATAGATTA
Found at i:44480 original size:32 final size:32
Alignment explanation
Indices: 44444--44540 Score: 158
Period size: 32 Copynumber: 3.0 Consensus size: 32
44434 GTTACCTCCT
*
44444 TTAGTTTTTGCTGACATGGCAACTAACTCTCG
1 TTAGTTTTTGCTGACATGGCAACTAACTCCCG
*
44476 TTAGTTTTTGCTAACATGGCAACTAACTCCCG
1 TTAGTTTTTGCTGACATGGCAACTAACTCCCG
* *
44508 TTAGTTTTTGCTGACATGGCACCCAACTCCCG
1 TTAGTTTTTGCTGACATGGCAACTAACTCCCG
44540 T
1 T
44541 ACAATCATCG
Statistics
Matches: 60, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
32 60 1.00
ACGTcount: A:0.22, C:0.26, G:0.18, T:0.35
Consensus pattern (32 bp):
TTAGTTTTTGCTGACATGGCAACTAACTCCCG
Found at i:44929 original size:28 final size:29
Alignment explanation
Indices: 44869--44940 Score: 89
Period size: 29 Copynumber: 2.5 Consensus size: 29
44859 CTATATTATT
44869 AAAT-TAAGATTAAAATTTAAAAATTTAG
1 AAATATAAGATTAAAATTTAAAAATTTAG
44897 AAATATAAGATTAAAA-TTAATCAAA-TTA-
1 AAATATAAGATTAAAATTTAA--AAATTTAG
44925 AAATATAAAGATTAAA
1 AAATAT-AAGATTAAA
44941 TACAAAATTT
Statistics
Matches: 40, Mismatches: 0, Indels: 7
0.85 0.00 0.15
Matches are distributed among these distances:
28 14 0.35
29 23 0.57
30 3 0.08
ACGTcount: A:0.61, C:0.01, G:0.06, T:0.32
Consensus pattern (29 bp):
AAATATAAGATTAAAATTTAAAAATTTAG
Found at i:48797 original size:4 final size:4
Alignment explanation
Indices: 48788--49127 Score: 621
Period size: 4 Copynumber: 85.5 Consensus size: 4
48778 ATCATTATAC
* * * *
48788 ATGT ATGT ATGT ATGT ATGT GTGT GTGT GTGT GTGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
48836 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
48884 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
48932 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATG- -TGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
48978 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
49026 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
*
49074 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ACGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
49122 ATGT AT
1 ATGT AT
49128 TGCAGATACT
Statistics
Matches: 330, Mismatches: 4, Indels: 4
0.98 0.01 0.01
Matches are distributed among these distances:
2 2 0.01
4 328 0.99
ACGTcount: A:0.24, C:0.00, G:0.26, T:0.50
Consensus pattern (4 bp):
ATGT
Found at i:49371 original size:2 final size:2
Alignment explanation
Indices: 49352--49386 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
49342 ACCTCAAAAG
* *
49352 TA TA TA TG TA TA TG TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
49387 TCTCTGATGG
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.43, C:0.00, G:0.06, T:0.51
Consensus pattern (2 bp):
TA
Found at i:58917 original size:2 final size:2
Alignment explanation
Indices: 58875--58909 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
58865 TGAAAAAGAA
* *
58875 AG AG AA AG AG AG GG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
58910 ATGAGAGACA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:63206 original size:2 final size:2
Alignment explanation
Indices: 63199--63228 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
63189 CATGTTATTG
63199 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
63229 GATGAAAGAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:68540 original size:170 final size:169
Alignment explanation
Indices: 68249--68567 Score: 613
Period size: 170 Copynumber: 1.9 Consensus size: 169
68239 TTTCTATGTA
68249 ATGCAGAATTGTGAGATGGATGCAGCATTTAGTATTGTCCAATTTCTTTCAGGTTATGTTGCTAC
1 ATGCAGAATTGTGAGATGGATGCAGCATTTAGTATTGTCCAATTTCTTTCAGGTTATGTTGCTAC
68314 CATGAAAAACCCTTTCCCCTTTGCAAGAGAATAAAATGCTTCACATAAATCAGATACTGGAAGTA
66 CATGAAAAACCCTTTCCCCTTTGCAAGAGAATAAAATGCTTCACATAAATCAGATACTGGAAGTA
68379 ATTCGTATTCAGATTCGTTCCAAAGGGTGAACTCAGAAG
131 ATTCGTATTCAGATTCGTTCCAAAGGGTGAACTCAGAAG
68418 ATGCAGAATGTGTGAGATGGATGGCAGCATTTAGTATTGTCCAATTTCTTTCAGGTTATGTTGCT
1 ATGCAGAAT-TGTGAGATGGAT-GCAGCATTTAGTATTGTCCAATTTCTTTCAGGTTATGTTGCT
68483 ACCATG-AAAACCCTTTCCCCTTTGCAAGAGAATAAAATGCTTCACATAAATCAGATACTGGAAG
64 ACCATGAAAAACCCTTTCCCCTTTGCAAGAGAATAAAATGCTTCACATAAATCAGATACTGGAAG
68547 TAATTCGTATTCAGATTCGTT
129 TAATTCGTATTCAGATTCGTT
68568 ATGATCCCAT
Statistics
Matches: 148, Mismatches: 0, Indels: 3
0.98 0.00 0.02
Matches are distributed among these distances:
169 9 0.06
170 91 0.61
171 48 0.32
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.32
Consensus pattern (169 bp):
ATGCAGAATTGTGAGATGGATGCAGCATTTAGTATTGTCCAATTTCTTTCAGGTTATGTTGCTAC
CATGAAAAACCCTTTCCCCTTTGCAAGAGAATAAAATGCTTCACATAAATCAGATACTGGAAGTA
ATTCGTATTCAGATTCGTTCCAAAGGGTGAACTCAGAAG
Found at i:71840 original size:36 final size:37
Alignment explanation
Indices: 71767--71840 Score: 141
Period size: 37 Copynumber: 2.0 Consensus size: 37
71757 CTTTGTTGTT
71767 TTATCATTACCTAAACATTTGGACATTTTTGAAGTTC
1 TTATCATTACCTAAACATTTGGACATTTTTGAAGTTC
71804 TTATCATTACCTAAACATTTGGACA-TTTTGAAGTTC
1 TTATCATTACCTAAACATTTGGACATTTTTGAAGTTC
71840 T
1 T
71841 ACTATAATCA
Statistics
Matches: 37, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
36 12 0.32
37 25 0.68
ACGTcount: A:0.30, C:0.16, G:0.11, T:0.43
Consensus pattern (37 bp):
TTATCATTACCTAAACATTTGGACATTTTTGAAGTTC
Found at i:80486 original size:128 final size:128
Alignment explanation
Indices: 80258--80574 Score: 634
Period size: 128 Copynumber: 2.5 Consensus size: 128
80248 CTCATCAAAT
80258 AATTAATTAAGAAAAAGGTTTTATGGTGTCTAAAATTAATAAAGGAATAGCTAATATTATTATGT
1 AATTAATTAAGAAAAAGGTTTTATGGTGTCTAAAATTAATAAAGGAATAGCTAATATTATTATGT
80323 TCGAGGCGAAATTAAAATTCTATGTTGAGAGATGTATATAAGATTATAAAGTTTTGAGACTAA
66 TCGAGGCGAAATTAAAATTCTATGTTGAGAGATGTATATAAGATTATAAAGTTTTGAGACTAA
80386 AATTAATTAAGAAAAAGGTTTTATGGTGTCTAAAATTAATAAAGGAATAGCTAATATTATTATGT
1 AATTAATTAAGAAAAAGGTTTTATGGTGTCTAAAATTAATAAAGGAATAGCTAATATTATTATGT
80451 TCGAGGCGAAATTAAAATTCTATGTTGAGAGATGTATATAAGATTATAAAGTTTTGAGACTAA
66 TCGAGGCGAAATTAAAATTCTATGTTGAGAGATGTATATAAGATTATAAAGTTTTGAGACTAA
80514 AATTAATTAAGAAAAAGGTTTTATGGTGTCTAAAATTAATAAAGGAATAGCTAATATTATT
1 AATTAATTAAGAAAAAGGTTTTATGGTGTCTAAAATTAATAAAGGAATAGCTAATATTATT
80575 TGAGAAAATC
Statistics
Matches: 189, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
128 189 1.00
ACGTcount: A:0.43, C:0.04, G:0.17, T:0.35
Consensus pattern (128 bp):
AATTAATTAAGAAAAAGGTTTTATGGTGTCTAAAATTAATAAAGGAATAGCTAATATTATTATGT
TCGAGGCGAAATTAAAATTCTATGTTGAGAGATGTATATAAGATTATAAAGTTTTGAGACTAA
Found at i:80705 original size:20 final size:19
Alignment explanation
Indices: 80658--80957 Score: 262
Period size: 20 Copynumber: 14.9 Consensus size: 19
80648 AATGACCAAC
80658 AAAATCGCAACGCGATATC-
1 AAAATCGCAACGCGAT-TCA
* *
80677 AAAACCGCAACGCGATTTA
1 AAAATCGCAACGCGATTCA
* * **
80696 GAAAAGCGCAACGTTGA-AAA
1 -AAAATCGCAACG-CGATTCA
80716 GAAAATCGCAACGCGATCTTCCA
1 -AAAATCGCAACGCGA--TT-CA
* *
80739 AGAATCGCAATGCGATTCA
1 AAAATCGCAACGCGATTCA
80758 TAAAATCGCAACGCGATTCCA
1 -AAAATCGCAACGCGATT-CA
* *
80779 AGAATCGCAACGCGATTTA
1 AAAATCGCAACGCGATTCA
80798 GAAAATCGCAACGCGATTCCA
1 -AAAATCGCAACGCGATT-CA
*
80819 AGAATCGCAACGCGATTCCA
1 AAAATCGCAACGCGATT-CA
*
80839 AGAATCGCAACGCGATTCCA
1 AAAATCGCAACGCGATT-CA
*
80859 AGAATCGCAACGCGATTCCA
1 AAAATCGCAACGCGATT-CA
*
80879 AGAATCGCAACGCGATCTTCCA
1 AAAATCGCAACGCGA--TT-CA
* *
80901 AGAATCGCAACGCGATTAA
1 AAAATCGCAACGCGATTCA
80920 GAAAATCGCAACGCGATTCCA
1 -AAAATCGCAACGCGATT-CA
*
80941 AGAATCGCAACGCGATT
1 AAAATCGCAACGCGATT
80958 AAGAAAATGA
Statistics
Matches: 243, Mismatches: 23, Indels: 29
0.82 0.08 0.10
Matches are distributed among these distances:
18 1 0.00
19 21 0.09
20 181 0.74
21 6 0.02
22 33 0.14
23 1 0.00
ACGTcount: A:0.38, C:0.26, G:0.19, T:0.16
Consensus pattern (19 bp):
AAAATCGCAACGCGATTCA
Found at i:80826 original size:60 final size:60
Alignment explanation
Indices: 80719--80957 Score: 347
Period size: 60 Copynumber: 3.9 Consensus size: 60
80709 TTGAAAAGAA
** * *
80719 AATCGCAACGCGATCTTCCAAGAATCGCAATGCGATT-CATAAAATCGCAACGCGATTCCAAG
1 AATCGCAACGCGAT-TTAGAA-AATCGCAACGCGATTCCA-AGAATCGCAACGCGATTCCAAG
80781 AATCGCAACGCGATTTAGAAAATCGCAACGCGATTCCAAGAATCGCAACGCGATTCCAAG
1 AATCGCAACGCGATTTAGAAAATCGCAACGCGATTCCAAGAATCGCAACGCGATTCCAAG
* *
80841 AATCGCAACGCGATTCCA-AGAATCGCAACGCGATTCCAAGAATCGCAACGCGATCTTCCAAG
1 AATCGCAACGCGATT-TAGAAAATCGCAACGCGATTCCAAGAATCGCAACGCGA--TTCCAAG
*
80903 AATCGCAACGCGATTAAGAAAATCGCAACGCGATTCCAAGAATCGCAACGCGATT
1 AATCGCAACGCGATTTAGAAAATCGCAACGCGATTCCAAGAATCGCAACGCGATT
80958 AAGAAAATGA
Statistics
Matches: 164, Mismatches: 8, Indels: 12
0.89 0.04 0.07
Matches are distributed among these distances:
60 86 0.52
61 8 0.05
62 70 0.43
ACGTcount: A:0.36, C:0.28, G:0.19, T:0.17
Consensus pattern (60 bp):
AATCGCAACGCGATTTAGAAAATCGCAACGCGATTCCAAGAATCGCAACGCGATTCCAAG
Found at i:80958 original size:40 final size:40
Alignment explanation
Indices: 80714--80965 Score: 368
Period size: 40 Copynumber: 6.2 Consensus size: 40
80704 CAACGTTGAA
*
80714 AAGAAAATCGCAACGCGATCTTCCAAGAATCGCAATGCGATT
1 AAGAAAATCGCAACGCGA--TTCCAAGAATCGCAACGCGATT
* *
80756 CATAAAATCGCAACGCGATTCCAAGAATCGCAACGCGATT
1 AAGAAAATCGCAACGCGATTCCAAGAATCGCAACGCGATT
*
80796 TAGAAAATCGCAACGCGATTCCAAGAATCGCAACGCGATT
1 AAGAAAATCGCAACGCGATTCCAAGAATCGCAACGCGATT
80836 CCAAG--AATCGCAACGCGATTCCAAGAATCGCAACGCGATT
1 --AAGAAAATCGCAACGCGATTCCAAGAATCGCAACGCGATT
80876 CCAAG--AATCGCAACGCGATCTTCCAAGAATCGCAACGCGATT
1 --AAGAAAATCGCAACGCGA--TTCCAAGAATCGCAACGCGATT
80918 AAGAAAATCGCAACGCGATTCCAAGAATCGCAACGCGATT
1 AAGAAAATCGCAACGCGATTCCAAGAATCGCAACGCGATT
80958 AAGAAAAT
1 AAGAAAAT
80966 GAGTAAATTC
Statistics
Matches: 198, Mismatches: 6, Indels: 14
0.91 0.03 0.06
Matches are distributed among these distances:
40 145 0.73
42 53 0.27
ACGTcount: A:0.38, C:0.26, G:0.19, T:0.17
Consensus pattern (40 bp):
AAGAAAATCGCAACGCGATTCCAAGAATCGCAACGCGATT
Found at i:81072 original size:6 final size:6
Alignment explanation
Indices: 81061--81193 Score: 252
Period size: 6 Copynumber: 22.5 Consensus size: 6
81051 GACACGTATT
81061 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
81109 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
81157 ACCACG ACCACG ACCACG ACCACG ACC-CG ACC-CG ACC
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACC
81194 CGAGACGAGA
Statistics
Matches: 127, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
5 10 0.08
6 117 0.92
ACGTcount: A:0.32, C:0.51, G:0.17, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:81701 original size:6 final size:6
Alignment explanation
Indices: 81690--81752 Score: 126
Period size: 6 Copynumber: 10.5 Consensus size: 6
81680 TCTCGTCTCG
81690 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
81738 GGTCGT GGTCGT GGT
1 GGTCGT GGTCGT GGT
81753 AATACGTGTC
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 57 1.00
ACGTcount: A:0.00, C:0.16, G:0.51, T:0.33
Consensus pattern (6 bp):
GGTCGT
Found at i:81874 original size:20 final size:20
Alignment explanation
Indices: 81849--82182 Score: 287
Period size: 20 Copynumber: 16.2 Consensus size: 20
81839 GAATTTACTC
*
81849 ATTTTCTTAATCGCGTTGCG
1 ATTTTCTAAATCGCGTTGCG
*
81869 ATTTTCTTAATCGCGTTGCG
1 ATTTTCTAAATCGCGTTGCG
**
81889 ATTCTTGGAAGATCGCGTTGCG
1 ATT-TTCTAA-ATCGCGTTGCG
*
81911 ATATTCTAAATCGCGTTGCG
1 ATTTTCTAAATCGCGTTGCG
**
81931 ATTCTTGGAAGATCGCGTTGCG
1 ATT-TTCTAA-ATCGCGTTGCG
*
81953 ATTTTCTGAATCGCGTTGCG
1 ATTTTCTAAATCGCGTTGCG
** *
81973 ATTCTTGGAAGATCGTGTTGCG
1 ATT-TTCTAA-ATCGCGTTGCG
**
81995 ATTCTT-GGAATCGCGTTGCG
1 ATT-TTCTAAATCGCGTTGCG
**
82015 ATTTTCTGGATCGCGTTGCG
1 ATTTTCTAAATCGCGTTGCG
82035 ATTTTCTAAATCGCGTTGCG
1 ATTTTCTAAATCGCGTTGCG
**
82055 ATTCTTGGAAGATCGCGTTGCG
1 ATT-TTCTAA-ATCGCGTTGCG
**
82077 ATTCTTGGAAGATCGCGTTGCG
1 ATT-TTCTAA-ATCGCGTTGCG
*
82099 ATTTTCTGAATCGCGTTGCG
1 ATTTTCTAAATCGCGTTGCG
* ** *
82119 ATCTTCT-TTTCAACGTTGCG
1 ATTTTCTAAATC-GCGTTGCG
*
82139 CTTTTCTAAATCGCGTTGCG
1 ATTTTCTAAATCGCGTTGCG
* * *
82159 GTTTT-GATATCGCGTTGCG
1 ATTTTCTAAATCGCGTTGCG
82178 ATTTT
1 ATTTT
82183 GTTGGTCATT
Statistics
Matches: 263, Mismatches: 40, Indels: 23
0.81 0.12 0.07
Matches are distributed among these distances:
19 20 0.08
20 136 0.52
21 28 0.11
22 79 0.30
ACGTcount: A:0.16, C:0.19, G:0.26, T:0.39
Consensus pattern (20 bp):
ATTTTCTAAATCGCGTTGCG
Found at i:81906 original size:22 final size:22
Alignment explanation
Indices: 81878--82101 Score: 274
Period size: 22 Copynumber: 10.6 Consensus size: 22
81868 GATTTTCTTA
81878 ATCGCGTTGCGATTCTTGGAAG
1 ATCGCGTTGCGATTCTTGGAAG
* **
81900 ATCGCGTTGCGA-TATTCTAA-
1 ATCGCGTTGCGATTCTTGGAAG
81920 ATCGCGTTGCGATTCTTGGAAG
1 ATCGCGTTGCGATTCTTGGAAG
*
81942 ATCGCGTTGCGATT-TTCTG-A-
1 ATCGCGTTGCGATTCTT-GGAAG
81962 ATCGCGTTGCGATTCTTGGAAG
1 ATCGCGTTGCGATTCTTGGAAG
*
81984 ATCGTGTTGCGATTCTTGG-A-
1 ATCGCGTTGCGATTCTTGGAAG
*
82004 ATCGCGTTGCGATT-TTCTG--G
1 ATCGCGTTGCGATTCTT-GGAAG
**
82024 ATCGCGTTGCGATT-TTCTAA-
1 ATCGCGTTGCGATTCTTGGAAG
82044 ATCGCGTTGCGATTCTTGGAAG
1 ATCGCGTTGCGATTCTTGGAAG
82066 ATCGCGTTGCGATTCTTGGAAG
1 ATCGCGTTGCGATTCTTGGAAG
82088 ATCGCGTTGCGATT
1 ATCGCGTTGCGATT
82102 TTCTGAATCG
Statistics
Matches: 175, Mismatches: 15, Indels: 24
0.82 0.07 0.11
Matches are distributed among these distances:
19 2 0.01
20 71 0.41
21 21 0.12
22 81 0.46
ACGTcount: A:0.17, C:0.19, G:0.29, T:0.35
Consensus pattern (22 bp):
ATCGCGTTGCGATTCTTGGAAG
Found at i:81907 original size:42 final size:42
Alignment explanation
Indices: 81858--82125 Score: 343
Period size: 42 Copynumber: 6.4 Consensus size: 42
81848 CATTTTCTTA
*
81858 ATCGCGTTGCGATTTTCTTAATCGCGTTGCGATTCTTGGAAG
1 ATCGCGTTGCGATTTTCTAAATCGCGTTGCGATTCTTGGAAG
*
81900 ATCGCGTTGCGATATTCTAAATCGCGTTGCGATTCTTGGAAG
1 ATCGCGTTGCGATTTTCTAAATCGCGTTGCGATTCTTGGAAG
*
81942 ATCGCGTTGCGATTTTCTGAATCGCGTTGCGATTCTTGGAAG
1 ATCGCGTTGCGATTTTCTAAATCGCGTTGCGATTCTTGGAAG
* ** *
81984 ATCGTGTTGCGATTCTT-GGAATCGCGTTGCGATT-TTCTG--G
1 ATCGCGTTGCGATT-TTCTAAATCGCGTTGCGATTCTT-GGAAG
82024 ATCGCGTTGCGATTTTCTAAATCGCGTTGCGATTCTTGGAAG
1 ATCGCGTTGCGATTTTCTAAATCGCGTTGCGATTCTTGGAAG
** *
82066 ATCGCGTTGCGATTCTTGGAAGATCGCGTTGCGATT-TTCTG-A-
1 ATCGCGTTGCGATT-TTCTAA-ATCGCGTTGCGATTCTT-GGAAG
*
82108 ATCGCGTTGCGATCTTCT
1 ATCGCGTTGCGATTTTCT
82126 TTTCAACGTT
Statistics
Matches: 200, Mismatches: 17, Indels: 19
0.85 0.07 0.08
Matches are distributed among these distances:
39 2 0.01
40 30 0.15
41 6 0.03
42 138 0.69
43 9 0.05
44 15 0.08
ACGTcount: A:0.17, C:0.19, G:0.27, T:0.37
Consensus pattern (42 bp):
ATCGCGTTGCGATTTTCTAAATCGCGTTGCGATTCTTGGAAG
Found at i:82007 original size:84 final size:83
Alignment explanation
Indices: 81849--82125 Score: 395
Period size: 84 Copynumber: 3.3 Consensus size: 83
81839 GAATTTACTC
* *
81849 ATTTTCTTA-ATCGCGTTGCGATTTTCTTAATCGCGTTGCGATTCTTGGAAGATCGCGTTGCGAT
1 ATTTTCTGAGATCGCGTTGCGATTTTCTAAATCGCGTTGCGATTCTTGGAAGATCGCGTTGCGAT
*
81913 AT-TCT-AAATCGCGTTGCG
66 -TCT-TGGAATCGCGTTGCG
* * *
81931 ATTCTT-GGAAGATCGCGTTGCGATTTTCTGAATCGCGTTGCGATTCTTGGAAGATCGTGTTGCG
1 ATT-TTCTG-AGATCGCGTTGCGATTTTCTAAATCGCGTTGCGATTCTTGGAAGATCGCGTTGCG
81995 ATTCTTGGAATCGCGTTGCG
64 ATTCTTGGAATCGCGTTGCG
82015 ATTTTCTG-GATCGCGTTGCGATTTTCTAAATCGCGTTGCGATTCTTGGAAGATCGCGTTGCGAT
1 ATTTTCTGAGATCGCGTTGCGATTTTCTAAATCGCGTTGCGATTCTTGGAAGATCGCGTTGCGAT
82079 TCTTGGAAGATCGCGTTGCG
66 TCTTGG-A-ATCGCGTTGCG
*
82099 ATTTTCTGA-ATCGCGTTGCGATCTTCT
1 ATTTTCTGAGATCGCGTTGCGATTTTCT
82126 TTTCAACGTT
Statistics
Matches: 177, Mismatches: 9, Indels: 16
0.88 0.04 0.08
Matches are distributed among these distances:
82 63 0.36
83 8 0.05
84 106 0.60
ACGTcount: A:0.17, C:0.19, G:0.26, T:0.38
Consensus pattern (83 bp):
ATTTTCTGAGATCGCGTTGCGATTTTCTAAATCGCGTTGCGATTCTTGGAAGATCGCGTTGCGAT
TCTTGGAATCGCGTTGCG
Found at i:82029 original size:104 final size:102
Alignment explanation
Indices: 81849--82180 Score: 354
Period size: 104 Copynumber: 3.2 Consensus size: 102
81839 GAATTTACTC
* ***
81849 ATTTTCTTAATCGCGTTGCGATT-TTCTTA-ATCGCGTTGCGATTCTTGGAAGATCGCGTTGCGA
1 ATTTTCTGAATCGCGTTGCGATTCTTGGAAGATCGCGTTGCGATTCTTGG-A-ATCGCGTTGCGA
*
81912 TATTCTAAATCGCGTTGCGATTCTTGGAAGATCGCGTTGCG
64 TATTCTAAATCGCGTTGCGATT-TTCGAA-ATCGCGTTGCG
* *
81953 ATTTTCTGAATCGCGTTGCGATTCTTGGAAGATCGTGTTGCGATTCTTGGAATCGCGTTGCGATT
1 ATTTTCTGAATCGCGTTGCGATTCTTGGAAGATCGCGTTGCGATTCTTGGAATCGCGTTGCGATA
** *
82018 TTCTGGATCGCGTTGCGATTTTCTAAATCGCGTTGCG
66 TTCTAAATCGCGTTGCGATTTTCGAAATCGCGTTGCG
* *
82055 ATTCTT-GGAAGATCGCGTTGCGATTCTTGGAAGATCGCGTTGCGATT-TTCTGAATCGCGTTGC
1 ATT-TTCTG-A-ATCGCGTTGCGATTCTTGGAAGATCGCGTTGCGATTCTT-GGAATCGCGTTGC
* ** * * *
82118 GATCTTCT-TTTCAACGTTGCGCTTTTCTAAATCGCGTTGCG
62 GATATTCTAAATC-GCGTTGCGATTTTCGAAATCGCGTTGCG
*
82159 -GTTT-TGATATCGCGTTGCGATT
1 ATTTTCTGA-ATCGCGTTGCGATT
82181 TTGTTGGTCA
Statistics
Matches: 200, Mismatches: 21, Indels: 17
0.84 0.09 0.07
Matches are distributed among these distances:
101 15 0.08
102 18 0.09
103 12 0.06
104 133 0.67
105 4 0.02
106 18 0.09
ACGTcount: A:0.17, C:0.19, G:0.26, T:0.38
Consensus pattern (102 bp):
ATTTTCTGAATCGCGTTGCGATTCTTGGAAGATCGCGTTGCGATTCTTGGAATCGCGTTGCGATA
TTCTAAATCGCGTTGCGATTTTCGAAATCGCGTTGCG
Found at i:82772 original size:2 final size:2
Alignment explanation
Indices: 82761--82800 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
82751 ACGTATATTG
82761 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
82801 TATGCATTTT
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 36 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:86605 original size:21 final size:22
Alignment explanation
Indices: 86553--86605 Score: 56
Period size: 21 Copynumber: 2.5 Consensus size: 22
86543 TTCGGACGAA
86553 GAGGA-CAAATCAAAGAAGATG
1 GAGGAGCAAATCAAAGAAGATG
* * * *
86574 GATGAGAAAATC-AAGCAGTTG
1 GAGGAGCAAATCAAAGAAGATG
86595 GAGGAGCAAAT
1 GAGGAGCAAAT
86606 GAAGGTAGTC
Statistics
Matches: 25, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
21 20 0.80
22 5 0.20
ACGTcount: A:0.47, C:0.09, G:0.30, T:0.13
Consensus pattern (22 bp):
GAGGAGCAAATCAAAGAAGATG
Found at i:88378 original size:95 final size:95
Alignment explanation
Indices: 88268--88456 Score: 290
Period size: 95 Copynumber: 2.0 Consensus size: 95
88258 TATTATTTTA
* * *
88268 TATACAATAAAGCTTGAGTTGTCCCTCT-AGAGCAATTGGTTAAACGCCTCGGCTTTATGGATAA
1 TATACAATAAAGCTTGAGCTGTCCCTCTAAG-GCAATTGGTTAAACGCCCCGACTTTATGGATAA
* *
88332 TATTCAGCTAGCCTGATAAAGGTGATTATAC
65 GATTCAGCTAACCTGATAAAGGTGATTATAC
* *
88363 TATACAATAAAGCTTGAGCTGTCCCTCTAAGGTAATTGGTTAAACGCCCCGATTTTATGGATAAG
1 TATACAATAAAGCTTGAGCTGTCCCTCTAAGGCAATTGGTTAAACGCCCCGACTTTATGGATAAG
*
88428 ATTCAGCTAACCTGATAAAGGTGTTTATA
66 ATTCAGCTAACCTGATAAAGGTGATTATA
88457 TATTGAGCTG
Statistics
Matches: 85, Mismatches: 8, Indels: 2
0.89 0.08 0.02
Matches are distributed among these distances:
95 83 0.98
96 2 0.02
ACGTcount: A:0.31, C:0.17, G:0.20, T:0.32
Consensus pattern (95 bp):
TATACAATAAAGCTTGAGCTGTCCCTCTAAGGCAATTGGTTAAACGCCCCGACTTTATGGATAAG
ATTCAGCTAACCTGATAAAGGTGATTATAC
Found at i:89549 original size:2 final size:2
Alignment explanation
Indices: 89544--89620 Score: 58
Period size: 2 Copynumber: 41.5 Consensus size: 2
89534 TTTAAATTAA
* * * *
89544 AT AT AT AA AT AT -T AT AT AT AT AT AT AT AT AT TT A- AT TT AA
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* *
89584 AT -T AA AT TT AT -T A- AT AT -T AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
89621 AAATAATTAT
Statistics
Matches: 57, Mismatches: 12, Indels: 12
0.70 0.15 0.15
Matches are distributed among these distances:
1 6 0.11
2 51 0.89
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:89584 original size:45 final size:45
Alignment explanation
Indices: 89533--89619 Score: 156
Period size: 45 Copynumber: 1.9 Consensus size: 45
89523 GTATACATAT
89533 ATTTAAATTAAATATATAAATATTATATATATATATATATATTTA
1 ATTTAAATTAAATATATAAATATTATATATATATATATATATTTA
* *
89578 ATTTAAATTAAATTTATTAATATTATATATATATATATATAT
1 ATTTAAATTAAATATATAAATATTATATATATATATATATAT
89620 AAAATAATTA
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
45 40 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (45 bp):
ATTTAAATTAAATATATAAATATTATATATATATATATATATTTA
Found at i:90358 original size:36 final size:37
Alignment explanation
Indices: 90298--90378 Score: 110
Period size: 36 Copynumber: 2.2 Consensus size: 37
90288 TAATTTACTC
* * *
90298 AAAATAAAGTTTTGTCCCTGTTGAGACATTTTCTCTT
1 AAAACAAAGTTTTGTCCCTCTTGAGACAGTTTCTCTT
*
90335 AAAACAAA-TTTTGTCTCTCTTGAGACAGTTTCTCTT
1 AAAACAAAGTTTTGTCCCTCTTGAGACAGTTTCTCTT
*
90371 GAAACAAA
1 AAAACAAA
90379 ATCTTTTAAT
Statistics
Matches: 39, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
36 32 0.82
37 7 0.18
ACGTcount: A:0.32, C:0.17, G:0.12, T:0.38
Consensus pattern (37 bp):
AAAACAAAGTTTTGTCCCTCTTGAGACAGTTTCTCTT
Found at i:90471 original size:33 final size:34
Alignment explanation
Indices: 90405--90472 Score: 93
Period size: 34 Copynumber: 2.0 Consensus size: 34
90395 TCCTTTAAAC
*
90405 AAATTTCGTCTCTCTCGAGACAGTTTCTCTTGAA
1 AAATTTCGTCTCCCTCGAGACAGTTTCTCTTGAA
* * *
90439 AAATTTTGTCTCCCTTGAGAC-GTTTCTTTTGAA
1 AAATTTCGTCTCCCTCGAGACAGTTTCTCTTGAA
90472 A
1 A
90473 CACAAAATCT
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
33 12 0.40
34 18 0.60
ACGTcount: A:0.24, C:0.21, G:0.15, T:0.41
Consensus pattern (34 bp):
AAATTTCGTCTCCCTCGAGACAGTTTCTCTTGAA
Found at i:90600 original size:36 final size:37
Alignment explanation
Indices: 90546--90632 Score: 113
Period size: 36 Copynumber: 2.4 Consensus size: 37
90536 ATTGAAAACA
* ** * *
90546 TTTCCCTTAAAATGAATTTTGTCTCTCTTGAGATAG-
1 TTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAGT
90582 TTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAGT
1 TTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAGT
*
90619 TTTCTCTTGAAACA
1 TTTCCCTTGAAACA
90633 TAAACATTGA
Statistics
Matches: 44, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
36 31 0.70
37 13 0.30
ACGTcount: A:0.25, C:0.21, G:0.13, T:0.41
Consensus pattern (37 bp):
TTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAGT
Found at i:90620 original size:102 final size:102
Alignment explanation
Indices: 90507--90733 Score: 429
Period size: 102 Copynumber: 2.2 Consensus size: 102
90497 CTTGAAATAA
90507 TTGAGACAGTTTTCTCTTGAAACATAAACATTGAAAACATTTCCCTTAAAATGAATTTTGTCTCT
1 TTGAGACAGTTTTCTCTTGAAACATAAACATTGAAAACATTTCCCTTAAAATGAATTTTGTCTCT
*
90572 CTTGAGATAGTTTCCCTTGAAACAAATTTTGTCTCCC
66 CTTGAGATAGTTTCCCTTGAAACAAATTTTATCTCCC
*
90609 TTGAGACAGTTTTCTCTTGAAACATAAACATTGAAAACATTTCCCTTGAAATGAATTTTGTCTCT
1 TTGAGACAGTTTTCTCTTGAAACATAAACATTGAAAACATTTCCCTTAAAATGAATTTTGTCTCT
90674 CTTGAGATAGTTTCCCTTGAAACAAATTTTATCTCCC
66 CTTGAGATAGTTTCCCTTGAAACAAATTTTATCTCCC
90711 TTGAGACAG-TTTCTCTTGAAACA
1 TTGAGACAGTTTTCTCTTGAAACA
90734 AAATCTTTGA
Statistics
Matches: 123, Mismatches: 2, Indels: 1
0.98 0.02 0.01
Matches are distributed among these distances:
101 14 0.11
102 109 0.89
ACGTcount: A:0.30, C:0.19, G:0.12, T:0.38
Consensus pattern (102 bp):
TTGAGACAGTTTTCTCTTGAAACATAAACATTGAAAACATTTCCCTTAAAATGAATTTTGTCTCT
CTTGAGATAGTTTCCCTTGAAACAAATTTTATCTCCC
Found at i:90695 original size:36 final size:36
Alignment explanation
Indices: 90648--90735 Score: 122
Period size: 36 Copynumber: 2.4 Consensus size: 36
90638 ATTGAAAACA
** * * *
90648 TTTCCCTTGAAATGAATTTTGTCTCTCTTGAGATAG
1 TTTCCCTTGAAACAAATTTTATCTCCCTTGAGACAG
90684 TTTCCCTTGAAACAAATTTTATCTCCCTTGAGACAG
1 TTTCCCTTGAAACAAATTTTATCTCCCTTGAGACAG
*
90720 TTTCTCTTGAAACAAA
1 TTTCCCTTGAAACAAA
90736 ATCTTTGAAT
Statistics
Matches: 46, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
36 46 1.00
ACGTcount: A:0.27, C:0.20, G:0.12, T:0.40
Consensus pattern (36 bp):
TTTCCCTTGAAACAAATTTTATCTCCCTTGAGACAG
Found at i:90795 original size:101 final size:100
Alignment explanation
Indices: 90507--90851 Score: 302
Period size: 102 Copynumber: 3.4 Consensus size: 100
90497 CTTGAAATAA
* *** * * * ** **
90507 TTGAGACAGTTTTCTCTTGAAACATAAACATTGAAAACATTTCCCTTAAAATGAATTTTGTCTCT
1 TTGAGACAG-TTTCTCTTGAAACA-AAACTTTGAAATGTTTTACATTGAAACAAATTCCGTCTCT
*
90572 CTTGAGATAGTTTCCCTTGAAACAAATTTTGTCTCCC
64 CTTGAGATAGTTTCCCTTGAAACAAATTTTATCTCCC
* *** * * ** **
90609 TTGAGACAGTTTTCTCTTGAAACATAAACATTGAAAACATTTCCCTTGAAATGAATTTTGTCTCT
1 TTGAGACAG-TTTCTCTTGAAACA-AAACTTTGAAATGTTTTACATTGAAACAAATTCCGTCTCT
90674 CTTGAGATAGTTTCCCTTGAAACAAATTTTATCTCCC
64 CTTGAGATAGTTTCCCTTGAAACAAATTTTATCTCCC
*
90711 TTGAGACAGTTTCTCTTGAAACAAAATCTTTGAATATGTTTTACATT-AAACAAATTCCGTCTCC
1 TTGAGACAGTTTCTCTTGAAACAAAA-CTTTGAA-ATGTTTTACATTGAAACAAATTCCGTCTCT
* ** * *
90775 CTTGAGACAGTTTCTTTTG--A-AAGTTTTATCTCTC
64 CTTGAGATAGTTTCCCTTGAAACAAATTTTATCTCCC
* * *
90809 TTGAGATAATTTCTCTTGAAGCAAATACCTTTGAAATCGTTTT
1 TTGAGACAGTTTCTCTTGAAACAAA-A-CTTTGAAAT-GTTTT
90852 CTCTTAGAAC
Statistics
Matches: 217, Mismatches: 22, Indels: 11
0.87 0.09 0.04
Matches are distributed among these distances:
98 36 0.17
99 14 0.06
100 3 0.01
101 48 0.22
102 116 0.53
ACGTcount: A:0.30, C:0.19, G:0.12, T:0.39
Consensus pattern (100 bp):
TTGAGACAGTTTCTCTTGAAACAAAACTTTGAAATGTTTTACATTGAAACAAATTCCGTCTCTCT
TGAGATAGTTTCCCTTGAAACAAATTTTATCTCCC
Found at i:90902 original size:34 final size:34
Alignment explanation
Indices: 90835--90929 Score: 102
Period size: 35 Copynumber: 2.7 Consensus size: 34
90825 TGAAGCAAAT
*
90835 ACCTTTGAAATCGTTTTCTCTT-AGAACACAAAAAA
1 ACCTCTGAAATCG-TTTCTCTTGA-AACACAAAAAA
*
90870 ACCTCTGAAATCGTTTCTCTTGAAACATAAAAAA
1 ACCTCTGAAATCGTTTCTCTTGAAACACAAAAAA
** * *
90904 AAGTCTTGATATTGTTTCTCTTGAAA
1 ACCTC-TGAAATCGTTTCTCTTGAAA
90930 GAAACCTTTG
Statistics
Matches: 52, Mismatches: 6, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
34 21 0.40
35 31 0.60
ACGTcount: A:0.37, C:0.18, G:0.11, T:0.35
Consensus pattern (34 bp):
ACCTCTGAAATCGTTTCTCTTGAAACACAAAAAA
Found at i:91579 original size:2 final size:2
Alignment explanation
Indices: 91563--91614 Score: 69
Period size: 2 Copynumber: 28.5 Consensus size: 2
91553 ATATTAAGTG
91563 TA TA T- TA TA TA -A TA TA TA TA TA TA TA TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
91602 T- TA TA TA T- TA TA T
1 TA TA TA TA TA TA TA T
91615 GCATTTTTTG
Statistics
Matches: 45, Mismatches: 0, Indels: 10
0.82 0.00 0.18
Matches are distributed among these distances:
1 5 0.11
2 40 0.89
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (2 bp):
TA
Found at i:91589 original size:12 final size:12
Alignment explanation
Indices: 91563--91614 Score: 69
Period size: 11 Copynumber: 4.8 Consensus size: 12
91553 ATATTAAGTG
91563 TATAT-TATATA
1 TATATATATATA
91574 -ATATATATATA
1 TATATATATATA
91585 TATATATATATA
1 TATATATATATA
91597 T-TATAT-TATA
1 TATATATATATA
91607 TAT-TATAT
1 TATATATAT
91615 GCATTTTTTG
Statistics
Matches: 37, Mismatches: 0, Indels: 8
0.82 0.00 0.18
Matches are distributed among these distances:
10 12 0.32
11 13 0.35
12 12 0.32
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (12 bp):
TATATATATATA
Found at i:92673 original size:2 final size:2
Alignment explanation
Indices: 92666--92711 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
92656 CACTGTTATC
92666 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
92708 AT AT
1 AT AT
92712 TTATTTATTT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:107949 original size:18 final size:19
Alignment explanation
Indices: 107914--107951 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
107904 CTTCAAATTT
107914 AATCAAAATAAAACTTAAA
1 AATCAAAATAAAACTTAAA
*
107933 AATCAAAAT-ATACTTAAA
1 AATCAAAATAAAACTTAAA
107951 A
1 A
107952 TAAAGGAAGT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 9 0.50
19 9 0.50
ACGTcount: A:0.66, C:0.11, G:0.00, T:0.24
Consensus pattern (19 bp):
AATCAAAATAAAACTTAAA
Found at i:108163 original size:33 final size:34
Alignment explanation
Indices: 108118--108185 Score: 79
Period size: 33 Copynumber: 2.0 Consensus size: 34
108108 AATATGATAA
*
108118 AAATTTAGTTTAATC-CTTTTAAAA-TTATAATTT
1 AAATTTAGTTTAAACTC-TTTAAAACTTATAATTT
108151 AAATTATA-TTTAAACTCTTTAAAATCTTATAATTT
1 AAATT-TAGTTTAAACTCTTTAAAA-CTTATAATTT
108186 TATTCTTGCC
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
33 18 0.60
34 3 0.10
35 9 0.30
ACGTcount: A:0.41, C:0.07, G:0.01, T:0.50
Consensus pattern (34 bp):
AAATTTAGTTTAAACTCTTTAAAACTTATAATTT
Found at i:108716 original size:31 final size:30
Alignment explanation
Indices: 108665--108722 Score: 73
Period size: 30 Copynumber: 1.9 Consensus size: 30
108655 TATGGTTTTG
*
108665 GAAAAAAAATAAAGTCTAGGTA-TAAAAAC
1 GAAAAAAAATAAAATCTAGGTACTAAAAAC
*
108694 GAAATAAAAATAATAATTTAGGTACTAAA
1 GAAA-AAAAATAA-AATCTAGGTACTAAA
108723 TTGTGTAGTT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
29 4 0.17
30 8 0.33
31 8 0.33
32 4 0.17
ACGTcount: A:0.60, C:0.05, G:0.12, T:0.22
Consensus pattern (30 bp):
GAAAAAAAATAAAATCTAGGTACTAAAAAC
Found at i:110096 original size:3 final size:3
Alignment explanation
Indices: 110088--110123 Score: 63
Period size: 3 Copynumber: 12.0 Consensus size: 3
110078 TATTGGAGTT
*
110088 TTA TTA TTA TTA TTA TTA TTA GTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
110124 AATATTCAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:114538 original size:50 final size:50
Alignment explanation
Indices: 114435--114543 Score: 112
Period size: 50 Copynumber: 2.2 Consensus size: 50
114425 ATTAAAAATT
* * * * *
114435 TAAAAATTCAAAATATATTTAATTTATAATCCTATTATTTCAAAATTATA
1 TAAAAATTCAAAATATAATTAATTTATAATCATATAATTTCAAAATAAAA
* ** *
114485 TAAAAATATTAAAATATAATTCTTTTATAAT-ATATAATTTTAAAATAAAA
1 TAAAAAT-TCAAAATATAATTAATTTATAATCATATAATTTCAAAATAAAA
114535 TAAATAATT
1 TAAA-AATT
114544 TATTTTAAAT
Statistics
Matches: 48, Mismatches: 9, Indels: 4
0.79 0.15 0.07
Matches are distributed among these distances:
50 26 0.54
51 22 0.46
ACGTcount: A:0.52, C:0.05, G:0.00, T:0.43
Consensus pattern (50 bp):
TAAAAATTCAAAATATAATTAATTTATAATCATATAATTTCAAAATAAAA
Found at i:116004 original size:3 final size:3
Alignment explanation
Indices: 115996--116082 Score: 113
Period size: 3 Copynumber: 29.0 Consensus size: 3
115986 TTAATATATT
* * *
115996 TAA TAA TAA TAA TAA TAT TTA TAA TAA TAA TAA TTA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* *
116044 TAA -AGA TAA TAA TAA TAA TTA TAG TAA TAA TAA TAA TAA
1 TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
116083 ATAAATCAAA
Statistics
Matches: 72, Mismatches: 10, Indels: 4
0.84 0.12 0.05
Matches are distributed among these distances:
2 1 0.01
3 70 0.97
4 1 0.01
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (3 bp):
TAA
Found at i:121870 original size:6 final size:6
Alignment explanation
Indices: 121859--122231 Score: 647
Period size: 6 Copynumber: 61.7 Consensus size: 6
121849 TGGCCAAAAC
* *
121859 ACATAT ACATAT ATATAT ACATAT ACATAT ATATAT ACATAT ACATAT
1 ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT
* * * * *
121907 ACATAT ACACATAC ACATAC ACATAC ACATAC ACATAT ACATAT ACATAC
1 ACATAT --ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT
121957 ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT
1 ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT
122005 ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT
1 ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT
122053 ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT
1 ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT
122101 ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT
1 ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT
122149 ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT
1 ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT
*
122197 ACATAT ACATAT ACATAT ACATAT GCATAT CACAT
1 ACATAT ACATAT ACATAT ACATAT ACATAT -ACAT
122232 GGTTTTTGAT
Statistics
Matches: 354, Mismatches: 10, Indels: 5
0.96 0.03 0.01
Matches are distributed among these distances:
6 346 0.98
7 3 0.01
8 5 0.01
ACGTcount: A:0.50, C:0.18, G:0.00, T:0.32
Consensus pattern (6 bp):
ACATAT
Found at i:123441 original size:29 final size:29
Alignment explanation
Indices: 123399--123457 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
123389 GATTCTAGCT
123399 GAATATGAACTTTGTTGATGGAACAAGGA
1 GAATATGAACTTTGTTGATGGAACAAGGA
123428 GAATATGAACTTTGTTGATGGAACAAGGA
1 GAATATGAACTTTGTTGATGGAACAAGGA
123457 G
1 G
123458 GGTTATGTCG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.37, C:0.07, G:0.29, T:0.27
Consensus pattern (29 bp):
GAATATGAACTTTGTTGATGGAACAAGGA
Found at i:131344 original size:26 final size:26
Alignment explanation
Indices: 131315--131365 Score: 93
Period size: 26 Copynumber: 2.0 Consensus size: 26
131305 GTATTCCTTA
*
131315 CTTATTTACTTACGTATCAACATGTC
1 CTTATTTACTTACATATCAACATGTC
131341 CTTATTTACTTACATATCAACATGT
1 CTTATTTACTTACATATCAACATGT
131366 TAAGTTAGGA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.29, C:0.22, G:0.06, T:0.43
Consensus pattern (26 bp):
CTTATTTACTTACATATCAACATGTC
Found at i:135030 original size:2 final size:2
Alignment explanation
Indices: 135025--135053 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
135015 AAAATTAAAT
135025 TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
135054 GATTTAATTT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:135376 original size:6 final size:6
Alignment explanation
Indices: 135361--135394 Score: 54
Period size: 6 Copynumber: 6.0 Consensus size: 6
135351 TAAAATAAAA
135361 TATT-T TATTGT TATTGT TATTGT TATT-T TATTGT
1 TATTGT TATTGT TATTGT TATTGT TATTGT TATTGT
135395 CATTTAATTA
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
5 9 0.33
6 18 0.67
ACGTcount: A:0.18, C:0.00, G:0.12, T:0.71
Consensus pattern (6 bp):
TATTGT
Found at i:135382 original size:12 final size:11
Alignment explanation
Indices: 135361--135399 Score: 60
Period size: 11 Copynumber: 3.5 Consensus size: 11
135351 TAAAATAAAA
135361 TATTTTATTGT
1 TATTTTATTGT
135372 TATTGTTATTGT
1 TATT-TTATTGT
135384 TATTTTATTGT
1 TATTTTATTGT
*
135395 CATTT
1 TATTT
135400 AATTAGGTTG
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
11 15 0.58
12 11 0.42
ACGTcount: A:0.18, C:0.03, G:0.10, T:0.69
Consensus pattern (11 bp):
TATTTTATTGT
Found at i:135391 original size:17 final size:16
Alignment explanation
Indices: 135361--135399 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 16
135351 TAAAATAAAA
135361 TATTTTATTGTTATTGT
1 TATTTTATT-TTATTGT
135378 TATTGTTATTTTATTGT
1 TATT-TTATTTTATTGT
*
135395 CATTT
1 TATTT
135400 AATTAGGTTG
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
16 1 0.05
17 14 0.70
18 5 0.25
ACGTcount: A:0.18, C:0.03, G:0.10, T:0.69
Consensus pattern (16 bp):
TATTTTATTTTATTGT
Found at i:141876 original size:27 final size:28
Alignment explanation
Indices: 141845--141917 Score: 132
Period size: 28 Copynumber: 2.7 Consensus size: 28
141835 TGCATGGTAT
141845 TTTTC-TTTGTTTCCTTTAGCCTTTTGA
1 TTTTCTTTTGTTTCCTTTAGCCTTTTGA
141872 TTTTCTTTTGTTTCCTTTAGCCTTTTGA
1 TTTTCTTTTGTTTCCTTTAGCCTTTTGA
141900 TTTTCTTTTGTTT-CTTTA
1 TTTTCTTTTGTTTCCTTTA
141918 CTCTACTTGA
Statistics
Matches: 45, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
27 10 0.22
28 35 0.78
ACGTcount: A:0.07, C:0.16, G:0.10, T:0.67
Consensus pattern (28 bp):
TTTTCTTTTGTTTCCTTTAGCCTTTTGA
Found at i:143277 original size:39 final size:40
Alignment explanation
Indices: 143187--143285 Score: 155
Period size: 40 Copynumber: 2.5 Consensus size: 40
143177 TTTTGTTGCA
*
143187 AATCATCATCTTTTATTCAAAAGAATCAAACATTTATGAT
1 AATCATAATCTTTTATTCAAAAGAATCAAACATTTATGAT
* *
143227 AATTATTATCTTTTATTCAAAAGAATCAAACA-TTATGAT
1 AATCATAATCTTTTATTCAAAAGAATCAAACATTTATGAT
*
143266 AATCATAATCTTTTGTTCAA
1 AATCATAATCTTTTATTCAA
143286 TGCAAACCCC
Statistics
Matches: 54, Mismatches: 5, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
39 24 0.44
40 30 0.56
ACGTcount: A:0.41, C:0.13, G:0.05, T:0.40
Consensus pattern (40 bp):
AATCATAATCTTTTATTCAAAAGAATCAAACATTTATGAT
Done.