Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002548.1 Hibiscus syriacus cultivar Beakdansim tig00005175_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: 122470
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.33
Found at i:353 original size:3 final size:3
Alignment explanation
Indices: 345--375 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
335 AATTCATCAG
345 TAT TAT TAT TAT TAT TAT TAT TAT TA- TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
376 AATTAATCAT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.07
3 25 0.93
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:669 original size:16 final size:16
Alignment explanation
Indices: 644--674 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
634 TTTAGGTGAG
*
644 GATGAGCATCATTAAC
1 GATGAACATCATTAAC
660 GATGAACATCATTAA
1 GATGAACATCATTAA
675 ATTAATTTAT
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:0.42, C:0.16, G:0.16, T:0.26
Consensus pattern (16 bp):
GATGAACATCATTAAC
Found at i:8085 original size:19 final size:19
Alignment explanation
Indices: 8049--8087 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
8039 TTAATTATTT
8049 AATTATTATTTTATTTAGA
1 AATTATTATTTTATTTAGA
8068 AATTAGTTATTTTA-TTAGA
1 AATTA-TTATTTTATTTAGA
8087 A
1 A
8088 CTCTTAATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 11 0.58
20 8 0.42
ACGTcount: A:0.38, C:0.00, G:0.08, T:0.54
Consensus pattern (19 bp):
AATTATTATTTTATTTAGA
Found at i:9407 original size:24 final size:23
Alignment explanation
Indices: 9374--9447 Score: 114
Period size: 24 Copynumber: 3.1 Consensus size: 23
9364 CCCCGCCCCG
9374 ATTATATATATATATAATATTTTT
1 ATTA-ATATATATATAATATTTTT
9398 ATTAATTATATATATAATATTTTAT
1 ATTAA-TATATATATAATATTTT-T
9423 ATTAAT-TATATATAATATTTTT
1 ATTAATATATATATAATATTTTT
9445 ATT
1 ATT
9448 TTTTTTATTT
Statistics
Matches: 48, Mismatches: 0, Indels: 6
0.89 0.00 0.11
Matches are distributed among these distances:
22 4 0.08
23 16 0.33
24 22 0.46
25 6 0.12
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (23 bp):
ATTAATATATATATAATATTTTT
Found at i:9455 original size:24 final size:24
Alignment explanation
Indices: 9382--9455 Score: 87
Period size: 24 Copynumber: 3.1 Consensus size: 24
9372 CGATTATATA
** *
9382 TATATATAATATTTTTATTAATTA
1 TATATATAATATTTTTATTTTTTT
* **
9406 TATATATAATA-TTTTATATTAAT
1 TATATATAATATTTTTATTTTTTT
9429 TATATATAATATTTTTATTTTTTT
1 TATATATAATATTTTTATTTTTTT
9453 TAT
1 TAT
9456 TTTTTTATGA
Statistics
Matches: 40, Mismatches: 9, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
23 17 0.43
24 23 0.57
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (24 bp):
TATATATAATATTTTTATTTTTTT
Found at i:24245 original size:18 final size:17
Alignment explanation
Indices: 24222--24259 Score: 67
Period size: 18 Copynumber: 2.2 Consensus size: 17
24212 CATTTTTATG
24222 TAATTATATTATAATGTT
1 TAATTATATTATAAT-TT
24240 TAATTATATTATAATTT
1 TAATTATATTATAATTT
24257 TAA
1 TAA
24260 GTTTGGAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 5 0.25
18 15 0.75
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (17 bp):
TAATTATATTATAATTT
Found at i:26592 original size:73 final size:73
Alignment explanation
Indices: 26473--26686 Score: 385
Period size: 73 Copynumber: 2.9 Consensus size: 73
26463 TGTGTATTTA
26473 GGGTGCGGATACCCTCTCCCCATCTCTATACCCATCTAATATTTTTCAATCCACCACCCGCCCAC
1 GGGTGCGGATACCCTCTCCCCATCTCTATACCCATCTAATATTTTTCAATCCACCACCCGCCCAC
26538 AACCTGTC
66 AACCTGTC
26546 GGGTGCGGATACCCTCTCCCCATCTCTATACCCATCTAATATTTTTCAATCCACCACCCGCCCAC
1 GGGTGCGGATACCCTCTCCCCATCTCTATACCCATCTAATATTTTTCAATCCACCACCCGCCCAC
26611 AACCTGTC
66 AACCTGTC
* * * *
26619 GGGTGCGGATACCCCCTCCCC-TCCCCATACCCACCTAATATTTTTCAATCCACCACCCGCCCAC
1 GGGTGCGGATACCCTCTCCCCATCTCTATACCCATCTAATATTTTTCAATCCACCACCCGCCCAC
26683 AACC
66 AACC
26687 CATAATAAGT
Statistics
Matches: 137, Mismatches: 4, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
72 44 0.32
73 93 0.68
ACGTcount: A:0.22, C:0.43, G:0.11, T:0.24
Consensus pattern (73 bp):
GGGTGCGGATACCCTCTCCCCATCTCTATACCCATCTAATATTTTTCAATCCACCACCCGCCCAC
AACCTGTC
Found at i:38954 original size:2 final size:2
Alignment explanation
Indices: 38949--38997 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
38939 TTCAGATACT
38949 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
38991 TC TC TC T
1 TC TC TC T
38998 ATATATATAT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:39002 original size:2 final size:2
Alignment explanation
Indices: 38997--39059 Score: 126
Period size: 2 Copynumber: 31.5 Consensus size: 2
38987 TCTCTCTCTC
38997 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
39039 TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA T
39060 GAGTCTATAA
Statistics
Matches: 61, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 61 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:39911 original size:18 final size:19
Alignment explanation
Indices: 39883--39923 Score: 66
Period size: 18 Copynumber: 2.2 Consensus size: 19
39873 AAAATAAGGA
39883 AAAACAGGAAAGAAAAAAG
1 AAAACAGGAAAGAAAAAAG
*
39902 AAAA-AGGAAAGAAAAATG
1 AAAACAGGAAAGAAAAAAG
39920 AAAA
1 AAAA
39924 TAAAAATAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
18 17 0.81
19 4 0.19
ACGTcount: A:0.76, C:0.02, G:0.20, T:0.02
Consensus pattern (19 bp):
AAAACAGGAAAGAAAAAAG
Found at i:39928 original size:23 final size:22
Alignment explanation
Indices: 39897--39947 Score: 57
Period size: 23 Copynumber: 2.3 Consensus size: 22
39887 CAGGAAAGAA
* *
39897 AAAAGAAAAAGGAAAGAAAAAT
1 AAAATAAAAAGAAAAGAAAAAT
* *
39919 GAAAATAAAAATAAAAGAAAGAT
1 -AAAATAAAAAGAAAAGAAAAAT
39942 AAAATA
1 AAAATA
39948 TTGGAAAAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
22 6 0.25
23 18 0.75
ACGTcount: A:0.76, C:0.00, G:0.14, T:0.10
Consensus pattern (22 bp):
AAAATAAAAAGAAAAGAAAAAT
Found at i:41250 original size:4 final size:4
Alignment explanation
Indices: 41241--41299 Score: 58
Period size: 4 Copynumber: 16.2 Consensus size: 4
41231 AGAAAAGAAA
* *
41241 AAAT AAAT AAAT AAAT AAAT AAAT -AA- AAAT AAGT -AAT AAAT TAA-
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT
41285 AAAT -AA- AAAT AAAT A
1 AAAT AAAT AAAT AAAT A
41300 GTAATAATAT
Statistics
Matches: 45, Mismatches: 4, Indels: 12
0.74 0.07 0.20
Matches are distributed among these distances:
3 12 0.27
4 33 0.73
ACGTcount: A:0.75, C:0.00, G:0.02, T:0.24
Consensus pattern (4 bp):
AAAT
Found at i:41258 original size:12 final size:12
Alignment explanation
Indices: 41241--41299 Score: 58
Period size: 10 Copynumber: 5.4 Consensus size: 12
41231 AGAAAAGAAA
41241 AAATAAATAAAT
1 AAATAAATAAAT
41253 AAATAAATAAAT
1 AAATAAATAAAT
*
41265 -AA-AAATAAGT
1 AAATAAATAAAT
*
41275 -AATAAATTAA-
1 AAATAAATAAAT
41285 AAAT-AA-AAAT
1 AAATAAATAAAT
41295 AAATA
1 AAATA
41300 GTAATAATAT
Statistics
Matches: 39, Mismatches: 4, Indels: 9
0.75 0.08 0.17
Matches are distributed among these distances:
9 2 0.05
10 15 0.38
11 10 0.26
12 12 0.31
ACGTcount: A:0.75, C:0.00, G:0.02, T:0.24
Consensus pattern (12 bp):
AAATAAATAAAT
Found at i:41280 original size:17 final size:16
Alignment explanation
Indices: 41239--41299 Score: 70
Period size: 16 Copynumber: 3.7 Consensus size: 16
41229 GAAGAAAAGA
41239 AAAAATAAATAAATAA-
1 AAAAATAAATAAA-AAT
*
41255 ATAAATAAATAAAAAT
1 AAAAATAAATAAAAAT
*
41271 AAGTAATAAATTAAAAAT
1 AA-AAATAAA-TAAAAAT
41289 AAAAATAAATA
1 AAAAATAAATA
41300 GTAATAATAT
Statistics
Matches: 38, Mismatches: 4, Indels: 6
0.79 0.08 0.12
Matches are distributed among these distances:
15 2 0.05
16 15 0.39
17 12 0.32
18 9 0.24
ACGTcount: A:0.75, C:0.00, G:0.02, T:0.23
Consensus pattern (16 bp):
AAAAATAAATAAAAAT
Found at i:41321 original size:30 final size:28
Alignment explanation
Indices: 41246--41311 Score: 82
Period size: 28 Copynumber: 2.3 Consensus size: 28
41236 AGAAAAAATA
*
41246 AATAAATAAATAAATAAATAAAAATAAGT
1 AATAAATTAA-AAATAAATAAAAATAAGT
41275 AATAAATTAAAAATAAA-AATAAAT-AGT
1 AATAAATTAAAAATAAATAA-AAATAAGT
41302 AATAATATTA
1 AATAA-ATTA
41312 TATATATAAA
Statistics
Matches: 34, Mismatches: 1, Indels: 5
0.85 0.03 0.12
Matches are distributed among these distances:
27 10 0.29
28 15 0.44
29 9 0.26
ACGTcount: A:0.70, C:0.00, G:0.03, T:0.27
Consensus pattern (28 bp):
AATAAATTAAAAATAAATAAAAATAAGT
Found at i:42216 original size:84 final size:83
Alignment explanation
Indices: 42116--42829 Score: 726
Period size: 84 Copynumber: 8.6 Consensus size: 83
42106 CCAGGGGTCT
* *
42116 TTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCGTTGAGCTGAGCGTAGT
1 TTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCC-TTGAGCTGAGCGTAGT
42181 CGAACTCAAAGGTCTTTTG
65 CGAACTCAAAGGTCTTTTG
* * * * * *
42200 TTGGCAGACAACCCTTCTAGACTTAAGTTGTACTGCAAATGATATGCCTTGGAGCTGAGCATAGT
1 TTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCTT-GAGCTGAGCGTAGT
*
42265 CGAACTCGAAGGTCTTTTG
65 CGAACTCAAAGGTCTTTTG
* * * ** *
42284 TTGGCATATAGCCCTTCTCGACTTAAGCTACACTGGAAATGATGTGCCGTTGAGCTGAGCGTAGT
1 TTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCC-TTGAGCTGAGCGTAGT
42349 CGAACTCAAAGGTCTTTTG
65 CGAACTCAAAGGTCTTTTG
* ** * * * * * * * * *
42368 ATCACAGCTAACCCTTCTAGCCTTGAGTTATGCTGTAAATGTTATGCCCTTGAAGCTGAGTGTAA
1 TTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTG-CCTTG-AGCTGAGCGTAG
* *
42433 TCGAACTTAAGGGTC---T-
64 TCGAACTCAAAGGTCTTTTG
* * ** *
42449 TTGGCAGATAGCCCTTCTCGACTTAAGCTACACTAG-AAATGATGTGACGTTGAGCTGAGCGTAG
1 TTGGCAGATAACCCTTCTCGACTTAAGTTATGCT-GCAAATGATGTG-CCTTGAGCTGAGCGTAG
42513 TCGAACTCAAAGGTCTTTTG
64 TCGAACTCAAAGGTCTTTTG
* ** * * * * * * * * *
42533 ATCACAGCTAACCCTTCTAGCCTTGAGTTATGCTGTAAATGTTATGCCCTTGAAGCTGAGTGTAA
1 TTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTG-CCTTG-AGCTGAGCGTAG
* *
42598 TCGAACTTAAGGGTC---T-
64 TCGAACTCAAAGGTCTTTTG
* * *
42614 TTGGCAGATAGCCCTTCTCGACTTAAGCTATTCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGT
1 TTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCTT-GAGCTGAGCGTAGT
* *
42679 CGAACTCGAAGGTCTTGTG
65 CGAACTCAAAGGTCTTTTG
* * * * **
42698 TTGGCAGACAACCCTTCTAGACTTAAGTTGTGCTGCAAATGATATGCCTTGGAGCTGAGCACAGT
1 TTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCTT-GAGCTGAGCGTAGT
*
42763 CGAACTCGAAGGTCTTTTG
65 CGAACTCAAAGGTCTTTTG
42782 TTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCC
1 TTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCC
42830 CTCAAAGCTG
Statistics
Matches: 505, Mismatches: 109, Indels: 32
0.78 0.17 0.05
Matches are distributed among these distances:
80 49 0.10
81 69 0.14
82 3 0.01
83 5 0.01
84 329 0.65
85 50 0.10
ACGTcount: A:0.25, C:0.21, G:0.24, T:0.30
Consensus pattern (83 bp):
TTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCTTGAGCTGAGCGTAGTC
GAACTCAAAGGTCTTTTG
Found at i:42466 original size:249 final size:247
Alignment explanation
Indices: 42086--42902 Score: 829
Period size: 249 Copynumber: 3.3 Consensus size: 247
42076 ATATGACCCC
* * * ** * * *
42086 GAAGTTGAGTGTAATCGAACCCAGGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTG
1 GAAGCTGAGCGTAATCGAACTCAAAGGTCTTTGACAGATAACCCTTCTAGACTTAAGCTATGCTG
* * *
42151 CAAATGATGTGCCGTTG-AGCTGAGCGTAGTCGAACTCAAAGGTCTTTTGTTGGCAGACAACCCT
66 CAAATGATATGCC-TTGAAGCTGAGCGTAATCGAACTCGAAGGTC--TTGTTGGCAGACAACCCT
42215 TCTAGACTTAAGTTGTACTGCAAATGATATGCCTTGGAGCTGAGCATAGTCGAACTCGAAGGTCT
128 TCTAGACTTAAGTTGTACTGCAAATGATATGCCTTGGAGCTGAGCATAGTCGAACTCGAAGGTCT
* * * ** * *
42280 TTTGTTGGCATATAGCCCTTCTCGACTTAAGCTACACTGGAAATGATGTGCCGTT
193 TTTGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCCTT
* * * * *
42335 G-AGCTGAGCGTAGTCGAACTCAAAGGTCTTTTGATCACAGCTAACCCTTCTAGCCTTGAGTTAT
1 GAAGCTGAGCGTAATCGAACTCAAAGGTC-TTTG---ACAGATAACCCTTCTAGACTTAAGCTAT
* * * * * *
42399 GCTGTAAATGTTATGCCCTTGAAGCTGAGTGTAATCGAACT-TAAGGGTC-T-TTGGCAGATAGC
62 GCTGCAAATGATATG-CCTTGAAGCTGAGCGTAATCGAACTCGAA-GGTCTTGTTGGCAGACAAC
* * ** * * * *
42461 CCTTCTCGACTTAAGCTACACTAG-AAATGATGTGACGTT-GAGCTGAGCGTAGTCGAACTCAAA
125 CCTTCTAGACTTAAGTTGTACT-GCAAATGATATG-CCTTGGAGCTGAGCATAGTCGAACTCGAA
* ** * * * * * * *
42524 GGTCTTTTGATCACAGCTAACCCTTCTAGCCTTGAGTTATGCTGTAAATGTTATGCCCTT
188 GGTCTTTTGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCCTT
* * * * * * *
42584 GAAGCTGAGTGTAATCGAACTTAAGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATTCTG
1 GAAGCTGAGCGTAATCGAACTCAAAGGTCTTTGACAGATAACCCTTCTAGACTTAAGCTATGCTG
* * *
42649 CAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTGTGTTGGCAGACAACCCTT
66 CAAATGATATGCCTTGAAGCTGAGCGTAATCGAACTCGAAGGTC-T-TGTTGGCAGACAACCCTT
* *
42714 CTAGACTTAAGTTGTGCTGCAAATGATATGCCTTGGAGCTGAGCACAGTCGAACTCGAAGGTCTT
129 CTAGACTTAAGTTGTACTGCAAATGATATGCCTTGGAGCTGAGCATAGTCGAACTCGAAGGTCTT
*
42779 TTGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCCTC
194 TTGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCCTT
* * *** * * * * * *
42833 AAAGCTGAGTGTAATCGAACTCGGGGGTCTTTGGCAGATAGCCCTTCTGGCCTTGAGCTAAGCTG
1 GAAGCTGAGCGTAATCGAACTCAAAGGTCTTTGACAGATAACCCTTCTAGACTTAAGCTATGCTG
42898 CAAAT
66 CAAAT
42903 AGTTTGTTTA
Statistics
Matches: 455, Mismatches: 96, Indels: 34
0.78 0.16 0.06
Matches are distributed among these distances:
245 26 0.06
246 34 0.07
248 26 0.06
249 280 0.62
250 28 0.06
252 38 0.08
253 23 0.05
ACGTcount: A:0.25, C:0.21, G:0.25, T:0.29
Consensus pattern (247 bp):
GAAGCTGAGCGTAATCGAACTCAAAGGTCTTTGACAGATAACCCTTCTAGACTTAAGCTATGCTG
CAAATGATATGCCTTGAAGCTGAGCGTAATCGAACTCGAAGGTCTTGTTGGCAGACAACCCTTCT
AGACTTAAGTTGTACTGCAAATGATATGCCTTGGAGCTGAGCATAGTCGAACTCGAAGGTCTTTT
GTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCCTT
Found at i:42516 original size:165 final size:165
Alignment explanation
Indices: 42048--42829 Score: 925
Period size: 165 Copynumber: 4.7 Consensus size: 165
42038 ACAAATAGCT
* * * * * ** *
42048 CTTCTTGCCTTGAGCTATGTTGTAAATGATATGACCC-CGAAGTTGAGTGTAATCGAACCCAGGG
1 CTTCTAGCCTTGAGTTATGCTGTAAATGATATG-CCCTTGAAGCTGAGTGTAATCGAACTTAAGG
**
42112 GTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCGTTGAGCTGAGCG
65 GTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTACACTGCAAATGATGTGCCGTTGAGCTGAGCG
* **
42177 TAGTCGAACTCAAAGGTCTTTTGTTGGCAGACAACC
130 TAGTCGAACTCAAAGGTCTTTTGATCACAGACAACC
* * * * * * ** * *
42213 CTTCTAGACTTAAGTTGTACTGCAAATGATATG-CCTTGGAGCTGAGCATAGTCGAACTCGAA-G
1 CTTCTAGCCTTGAGTTATGCTGTAAATGATATGCCCTTGAAGCTGAGTGTAATCGAACT-TAAGG
* *
42276 GTCTTTTGTTGGCATATAGCCCTTCTCGACTTAAGCTACACTGGAAATGATGTGCCGTTGAGCTG
65 GTC---T-TTGGCAGATAGCCCTTCTCGACTTAAGCTACACTGCAAATGATGTGCCGTTGAGCTG
42341 AGCGTAGTCGAACTCAAAGGTCTTTTGATCACAG-CTAACC
126 AGCGTAGTCGAACTCAAAGGTCTTTTGATCACAGAC-AACC
*
42381 CTTCTAGCCTTGAGTTATGCTGTAAATGTTATGCCCTTGAAGCTGAGTGTAATCGAACTTAAGGG
1 CTTCTAGCCTTGAGTTATGCTGTAAATGATATGCCCTTGAAGCTGAGTGTAATCGAACTTAAGGG
*
42446 TCTTTGGCAGATAGCCCTTCTCGACTTAAGCTACACTAG-AAATGATGTGACGTTGAGCTGAGCG
66 TCTTTGGCAGATAGCCCTTCTCGACTTAAGCTACACT-GCAAATGATGTGCCGTTGAGCTGAGCG
42510 TAGTCGAACTCAAAGGTCTTTTGATCACAG-CTAACC
130 TAGTCGAACTCAAAGGTCTTTTGATCACAGAC-AACC
*
42546 CTTCTAGCCTTGAGTTATGCTGTAAATGTTATGCCCTTGAAGCTGAGTGTAATCGAACTTAAGGG
1 CTTCTAGCCTTGAGTTATGCTGTAAATGATATGCCCTTGAAGCTGAGTGTAATCGAACTTAAGGG
**
42611 TCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATTCTGCAAATGATGTGCC-TTGGAGCTGAGCG
66 TCTTTGGCAGATAGCCCTTCTCGACTTAAGCTACACTGCAAATGATGTGCCGTT-GAGCTGAGCG
* * * **
42675 TAGTCGAACTCGAAGGTCTTGTGTTGGCAGACAACC
130 TAGTCGAACTCAAAGGTCTTTTGATCACAGACAACC
* * * * * *** * *
42711 CTTCTAGACTTAAGTTGTGCTGCAAATGATATG-CCTTGGAGCTGAGCACAGTCGAACTCGAA-G
1 CTTCTAGCCTTGAGTTATGCTGTAAATGATATGCCCTTGAAGCTGAGTGTAATCGAACT-TAAGG
* * **
42774 GTCTTTTGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCC
65 GTC---T-TTGGCAGATAGCCCTTCTCGACTTAAGCTACACTGCAAATGATGTGCC
42830 CTCAAAGCTG
Statistics
Matches: 540, Mismatches: 59, Indels: 33
0.85 0.09 0.05
Matches are distributed among these distances:
163 2 0.00
164 46 0.09
165 299 0.55
166 3 0.01
167 3 0.01
168 162 0.30
169 25 0.05
ACGTcount: A:0.25, C:0.21, G:0.24, T:0.30
Consensus pattern (165 bp):
CTTCTAGCCTTGAGTTATGCTGTAAATGATATGCCCTTGAAGCTGAGTGTAATCGAACTTAAGGG
TCTTTGGCAGATAGCCCTTCTCGACTTAAGCTACACTGCAAATGATGTGCCGTTGAGCTGAGCGT
AGTCGAACTCAAAGGTCTTTTGATCACAGACAACC
Found at i:46269 original size:18 final size:19
Alignment explanation
Indices: 46228--46272 Score: 74
Period size: 19 Copynumber: 2.4 Consensus size: 19
46218 AGTTAATGTG
46228 AATGCAAAGAAAATAACAA
1 AATGCAAAGAAAATAACAA
*
46247 AATGCAAAGAAAATAA-GA
1 AATGCAAAGAAAATAACAA
46265 AATGCAAA
1 AATGCAAA
46273 ATGTCTAAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
18 9 0.36
19 16 0.64
ACGTcount: A:0.67, C:0.09, G:0.13, T:0.11
Consensus pattern (19 bp):
AATGCAAAGAAAATAACAA
Found at i:48059 original size:18 final size:19
Alignment explanation
Indices: 48031--48071 Score: 66
Period size: 18 Copynumber: 2.2 Consensus size: 19
48021 AAAATAAGGA
48031 AAAACAGGAAAGAAAAAAG
1 AAAACAGGAAAGAAAAAAG
*
48050 AAAA-AGGAAAGAAAAATG
1 AAAACAGGAAAGAAAAAAG
48068 AAAA
1 AAAA
48072 TAAAAATAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
18 17 0.81
19 4 0.19
ACGTcount: A:0.76, C:0.02, G:0.20, T:0.02
Consensus pattern (19 bp):
AAAACAGGAAAGAAAAAAG
Found at i:48076 original size:23 final size:22
Alignment explanation
Indices: 48045--48095 Score: 57
Period size: 23 Copynumber: 2.3 Consensus size: 22
48035 CAGGAAAGAA
* *
48045 AAAAGAAAAAGGAAAGAAAAAT
1 AAAATAAAAAGAAAAGAAAAAT
* *
48067 GAAAATAAAAATAAAAGAAAGAT
1 -AAAATAAAAAGAAAAGAAAAAT
48090 AAAATA
1 AAAATA
48096 TTGGAAAAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
22 6 0.25
23 18 0.75
ACGTcount: A:0.76, C:0.00, G:0.14, T:0.10
Consensus pattern (22 bp):
AAAATAAAAAGAAAAGAAAAAT
Found at i:49398 original size:4 final size:4
Alignment explanation
Indices: 49389--49459 Score: 82
Period size: 4 Copynumber: 19.2 Consensus size: 4
49379 AAGAAAAAGA
*
49389 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT -AA- AAAT AAGT
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT
*
49435 -AAT AAAT TAA- AAAT -AA- AAAT AAAT A
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT A
49460 GTAATAATAT
Statistics
Matches: 57, Mismatches: 4, Indels: 12
0.78 0.05 0.16
Matches are distributed among these distances:
3 12 0.21
4 45 0.79
ACGTcount: A:0.75, C:0.00, G:0.01, T:0.24
Consensus pattern (4 bp):
AAAT
Found at i:49481 original size:30 final size:28
Alignment explanation
Indices: 49388--49471 Score: 86
Period size: 28 Copynumber: 3.0 Consensus size: 28
49378 GAAGAAAAAG
* *
49388 AAAATAAAT--AAATAAATAAATAAATAA
1 AAAATAAATAAAAATAAGT-AATAAATTA
49415 ATAAATAAATAAAAATAAGTAATAAATTA
1 A-AAATAAATAAAAATAAGTAATAAATTA
49444 AAAATAAA-AATAAAT-AGTAATAATATTA
1 AAAATAAATAA-AAATAAGTAATAA-ATTA
49472 TATATATAAA
Statistics
Matches: 50, Mismatches: 2, Indels: 9
0.82 0.03 0.15
Matches are distributed among these distances:
27 11 0.22
28 23 0.46
29 9 0.18
30 7 0.14
ACGTcount: A:0.71, C:0.00, G:0.02, T:0.26
Consensus pattern (28 bp):
AAAATAAATAAAAATAAGTAATAAATTA
Found at i:49519 original size:17 final size:19
Alignment explanation
Indices: 49499--49540 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 19
49489 AAAAACATAT
49499 AATATAT-AAAAATT-TAA
1 AATATATGAAAAATTATAA
* *
49516 AATATTTGAAAAATTATAT
1 AATATATGAAAAATTATAA
49535 AATATA
1 AATATA
49541 CATATTTTCA
Statistics
Matches: 20, Mismatches: 3, Indels: 2
0.80 0.12 0.08
Matches are distributed among these distances:
17 6 0.30
18 7 0.35
19 7 0.35
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (19 bp):
AATATATGAAAAATTATAA
Found at i:52524 original size:25 final size:26
Alignment explanation
Indices: 52489--52539 Score: 77
Period size: 25 Copynumber: 2.0 Consensus size: 26
52479 TAATATTTCG
*
52489 GTCACAACCTAAAATGTTATGAAGAA
1 GTCACAACCTAAAATGTTATAAAGAA
*
52515 GTCA-AACCTAAAATTTTATAAAGAA
1 GTCACAACCTAAAATGTTATAAAGAA
52540 TATAACATTT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 19 0.83
26 4 0.17
ACGTcount: A:0.49, C:0.14, G:0.12, T:0.25
Consensus pattern (26 bp):
GTCACAACCTAAAATGTTATAAAGAA
Found at i:54490 original size:338 final size:338
Alignment explanation
Indices: 53874--54552 Score: 1304
Period size: 338 Copynumber: 2.0 Consensus size: 338
53864 AGAGTGTTGA
53874 TGCCTTTATACCAAATCATTAATGGCAGAAACTTAAAACATCAGCATTTCAGCATGGGATATTCA
1 TGCCTTTATACCAAATCATTAATGGCAGAAACTTAAAACATCAGCATTTCAGCATGGGATATTCA
* *
53939 GATTCACTTTCTGCAAATCAAGTTCACAACAGATTATCGAGGTGAATTTATGTCCTTTTCACTGA
66 GATTCACTTTCTGCAAATAAAGTTCACAACAGATTATCGAGGTGAATTTATGTCCTTTTCACCGA
54004 AGTTTTCATTCAAACACCTTAAATGTTGAACGGTAACCGACCGCCAAATATGATTGTGCACACAG
131 AGTTTTCATTCAAACACCTTAAATGTTGAACGGTAACCGACCGCCAAATATGATTGTGCACACAG
54069 AAAATCCATCAAATGGCGTGGAGAAGAGAAATATATTAAAAAAGGGTAAAGTATAGTAATGGTCA
196 AAAATCCATCAAATGGCGTGGAGAAGAGAAATATATTAAAAAAGGGTAAAGTATAGTAATGGTCA
*
54134 CTGAACTTTTCTAAAGCTTTCATTTAGGTCCCTTAACTTTTAAAACTTGCAATACAGTCCTCCAA
261 CTGAACTTTTCTAAAGCTTTCATTTAGGTCCCTCAACTTTTAAAACTTGCAATACAGTCCTCCAA
*
54199 TATTTATTCCGTT
326 CATTTATTCCGTT
54212 TGCCTTTATACCAAATCATTAATGGCAGAAACTTAAAACATCAGCATTTCAGCATGGGATATTCA
1 TGCCTTTATACCAAATCATTAATGGCAGAAACTTAAAACATCAGCATTTCAGCATGGGATATTCA
54277 GATTCACTTTCTGCAAATAAAGTTCACAACAGATTATCGAGGTGAATTTATGTCCTTTTCACCGA
66 GATTCACTTTCTGCAAATAAAGTTCACAACAGATTATCGAGGTGAATTTATGTCCTTTTCACCGA
*
54342 AGTTTTCATTCAAACACCTTAAATGTTGAACGGTAACCGACCGCCAAATATGATTGTGCATACAG
131 AGTTTTCATTCAAACACCTTAAATGTTGAACGGTAACCGACCGCCAAATATGATTGTGCACACAG
54407 AAAATCCATCAAATGGCGTGGAGAAGAGAAATATATTAAAAAAGGGTAAAGTATAGTAATGGTCA
196 AAAATCCATCAAATGGCGTGGAGAAGAGAAATATATTAAAAAAGGGTAAAGTATAGTAATGGTCA
54472 CTGAACTTTTCTAAAGCTTTCATTTAGGTCCCTCAACTTTTAAAACTTGCAATACAGTCCTCCAA
261 CTGAACTTTTCTAAAGCTTTCATTTAGGTCCCTCAACTTTTAAAACTTGCAATACAGTCCTCCAA
*
54537 CATTTATTCTGTT
326 CATTTATTCCGTT
54550 TGC
1 TGC
54553 AATATGGTCC
Statistics
Matches: 335, Mismatches: 6, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
338 335 1.00
ACGTcount: A:0.35, C:0.19, G:0.15, T:0.31
Consensus pattern (338 bp):
TGCCTTTATACCAAATCATTAATGGCAGAAACTTAAAACATCAGCATTTCAGCATGGGATATTCA
GATTCACTTTCTGCAAATAAAGTTCACAACAGATTATCGAGGTGAATTTATGTCCTTTTCACCGA
AGTTTTCATTCAAACACCTTAAATGTTGAACGGTAACCGACCGCCAAATATGATTGTGCACACAG
AAAATCCATCAAATGGCGTGGAGAAGAGAAATATATTAAAAAAGGGTAAAGTATAGTAATGGTCA
CTGAACTTTTCTAAAGCTTTCATTTAGGTCCCTCAACTTTTAAAACTTGCAATACAGTCCTCCAA
CATTTATTCCGTT
Found at i:61019 original size:10 final size:10
Alignment explanation
Indices: 61006--61038 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
60996 AAAGATTAAG
61006 AAAGTAAATC
1 AAAGTAAATC
61016 AAAGTAAATC
1 AAAGTAAATC
*
61026 AAAG-AAATA
1 AAAGTAAATC
61035 AAAG
1 AAAG
61039 AAAAAATGAA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
9 8 0.36
10 14 0.64
ACGTcount: A:0.67, C:0.06, G:0.12, T:0.15
Consensus pattern (10 bp):
AAAGTAAATC
Found at i:62322 original size:24 final size:24
Alignment explanation
Indices: 62276--62323 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
62266 AAAACTAATG
* * * *
62276 AATGAAATTAAATTAGATTAATAA
1 AATGAAATGAAATAAAATAAATAA
62300 AATGAAATGAAATAAAATAAATAA
1 AATGAAATGAAATAAAATAAATAA
62324 TAATAATATA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.65, C:0.00, G:0.08, T:0.27
Consensus pattern (24 bp):
AATGAAATGAAATAAAATAAATAA
Found at i:62466 original size:69 final size:68
Alignment explanation
Indices: 62369--62586 Score: 202
Period size: 71 Copynumber: 3.2 Consensus size: 68
62359 AATATTTTTT
* * * * *
62369 AAACTATATATTTTA-TTTAAAAACGTTTTCAAAACTAAATATCATATAGTTTTCAAAAATGATT
1 AAACTATATATTATATTTTCAAAATGTTTTCAAAACTATATATCATATAATTTTCAAAAATG-TT
62433 TTAA
65 TTAA
**
62437 AAA-TAT-TA-TATAAGTTTTCCAAAATGTTTTTTTTAAACTATATAT-ATA-AATTTTCAAAAA
1 AAACTATATATTAT-A-TTTT-CAAAATG--TTTTCAAAACTATATATCATATAATTTTC-AAAA
62497 ATGTTTTTTAA
60 ATG--TTTTAA
*
62508 AAACTATATATTATATTTTCAAAATGATTTCAAAACTATATA-CTATATAATTTTC-AAAATGTT
1 AAACTATATATTATATTTTCAAAATGTTTTCAAAACTATATATC-ATATAATTTTCAAAAATGTT
62571 TT-A
65 TTAA
62574 AAACTTATATATT
1 AAAC-TATATATT
62587 GTACATAAGT
Statistics
Matches: 124, Mismatches: 11, Indels: 31
0.75 0.07 0.19
Matches are distributed among these distances:
65 2 0.02
66 8 0.06
67 15 0.12
68 6 0.05
69 30 0.24
70 13 0.10
71 37 0.30
72 7 0.06
73 3 0.02
74 3 0.02
ACGTcount: A:0.44, C:0.08, G:0.04, T:0.44
Consensus pattern (68 bp):
AAACTATATATTATATTTTCAAAATGTTTTCAAAACTATATATCATATAATTTTCAAAAATGTTT
TAA
Found at i:62504 original size:35 final size:34
Alignment explanation
Indices: 62356--62585 Score: 172
Period size: 36 Copynumber: 6.8 Consensus size: 34
62346 TATGTTTCAA
* * **
62356 AAAAATATTTTTTAAACTATATAT-TTTA-TTT-
1 AAAAATGTTTTTAAAACTATATATATAAATTTTC
* * * *
62387 AAAAACGTTTTCAAAACTAAATATCATATAGTTTTC
1 AAAAATGTTTTTAAAACTATATAT-ATA-AATTTTC
* * *
62423 AAAAATGATTTTAAAAATAT-TATATAAGTTTTC
1 AAAAATGTTTTTAAAACTATATATATAAATTTTC
* *
62456 CAAAATGTTTTTTTTAAACTATATATATAAATTTTC
1 AAAAATG--TTTTTAAAACTATATATATAAATTTTC
*
62492 AAAAAATGTTTTTTAAAAACTATATAT-TATATTTTC
1 -AAAAATG-TTTTT-AAAACTATATATATAAATTTTC
* *
62528 -AAAATGATTTCAAAACTATATACTATATAATTTTC
1 AAAAATGTTTTTAAAACTATATA-TATA-AATTTTC
62563 -AAAATG-TTTTAAAACT-TATATAT
1 AAAAATGTTTTTAAAACTATATATAT
62586 TGTACATAAG
Statistics
Matches: 161, Mismatches: 25, Indels: 25
0.76 0.12 0.12
Matches are distributed among these distances:
31 19 0.12
32 14 0.09
33 22 0.14
34 20 0.12
35 28 0.17
36 41 0.25
37 17 0.11
ACGTcount: A:0.44, C:0.07, G:0.03, T:0.45
Consensus pattern (34 bp):
AAAAATGTTTTTAAAACTATATATATAAATTTTC
Found at i:62510 original size:71 final size:69
Alignment explanation
Indices: 62337--62586 Score: 202
Period size: 69 Copynumber: 3.7 Consensus size: 69
62327 TAATATAGAT
** * * * *
62337 TATATA-ATAT-ATGTTTCAAAAAAAT-ATTTTTTAAACTATATATTTTA-TTTAAAAACGTTTT
1 TATATATATATAAT-TTTC-AAAAAATGATTTTAAAAACTATATATTATATTTTCAAAATGATTT
62398 CAAAAC
64 CAAAAC
* *
62404 TAAATATCATATAGTTTTC-AAAAATGATTTTAAAAA-TAT-TA-TATAAGTTTTCCAAAATGTT
1 TATATAT-ATATAATTTTCAAAAAATGATTTTAAAAACTATATATTAT-A-TTTT-CAAAATG--
* **
62465 TTTTTTAAAC
60 ATTTCAAAAC
*
62475 TATATATATA-AATTTTCAAAAAATGTTTTTTAAAAACTATATATTATATTTTCAAAATGATTTC
1 TATATATATATAATTTTCAAAAAATG-ATTTTAAAAACTATATATTATATTTTCAAAATGATTTC
62539 AAAAC
65 AAAAC
62544 TATATACTATATAATTTTC--AAAATG-TTTT-AAAACTTATATATT
1 TATATA-TATATAATTTTCAAAAAATGATTTTAAAAAC-TATATATT
62587 GTACATAAGT
Statistics
Matches: 150, Mismatches: 15, Indels: 36
0.75 0.07 0.18
Matches are distributed among these distances:
65 2 0.01
66 8 0.05
67 26 0.17
68 11 0.07
69 38 0.25
70 15 0.10
71 37 0.25
72 7 0.05
73 3 0.02
74 3 0.02
ACGTcount: A:0.44, C:0.07, G:0.04, T:0.45
Consensus pattern (69 bp):
TATATATATATAATTTTCAAAAAATGATTTTAAAAACTATATATTATATTTTCAAAATGATTTCA
AAAC
Found at i:62512 original size:37 final size:35
Alignment explanation
Indices: 62394--62585 Score: 159
Period size: 37 Copynumber: 5.5 Consensus size: 35
62384 TTTAAAAACG
* * * *
62394 TTTTCAAAACTAAATATCATATAGTTTTCAAAAATGA
1 TTTTAAAAACTATATAT-ATA-AATTTTCAAAAATGT
* *
62431 TTTTAAAAA-TAT-TATATAAGTTTTCCAAAATGTT
1 TTTTAAAAACTATATATATAAATTTTCAAAAATG-T
**
62465 TTTTTTAAACTATATATATAAATTTTCAAAAAATGTT
1 TTTTAAAAACTATATATATAAATTTTC-AAAAATG-T
*
62502 TTTTAAAAACTATATAT-TATATTTTC-AAAATG-
1 TTTTAAAAACTATATATATAAATTTTCAAAAATGT
* *
62534 ATTTCAAAACTATATACTATATAATTTTC-AAAATG-
1 TTTTAAAAACTATATA-TATA-AATTTTCAAAAATGT
62569 TTTT-AAAACT-TATATAT
1 TTTTAAAAACTATATATAT
62586 TGTACATAAG
Statistics
Matches: 133, Mismatches: 15, Indels: 19
0.80 0.09 0.11
Matches are distributed among these distances:
32 17 0.13
33 18 0.14
34 24 0.18
35 21 0.16
36 22 0.17
37 31 0.23
ACGTcount: A:0.44, C:0.08, G:0.04, T:0.45
Consensus pattern (35 bp):
TTTTAAAAACTATATATATAAATTTTCAAAAATGT
Found at i:71629 original size:31 final size:32
Alignment explanation
Indices: 71576--71656 Score: 80
Period size: 31 Copynumber: 2.6 Consensus size: 32
71566 TCAATTTTAG
*
71576 TTAAA-CTCTAACT-TTTTAGAAAAATGTAAA
1 TTAAACCTCTAAATATTTTAGAAAAATGTAAA
* * * *
71606 TTAAATCCTTTAAA-ATTTT-GAAAATTTTAAT
1 TTAAA-CCTCTAAATATTTTAGAAAAATGTAAA
71637 TTAAACCTCTAAATATTTTA
1 TTAAACCTCTAAATATTTTA
71657 AAGTTTTAAG
Statistics
Matches: 40, Mismatches: 6, Indels: 8
0.74 0.11 0.15
Matches are distributed among these distances:
30 12 0.30
31 19 0.47
32 9 0.22
ACGTcount: A:0.43, C:0.10, G:0.04, T:0.43
Consensus pattern (32 bp):
TTAAACCTCTAAATATTTTAGAAAAATGTAAA
Found at i:75914 original size:16 final size:17
Alignment explanation
Indices: 75864--75915 Score: 58
Period size: 16 Copynumber: 3.2 Consensus size: 17
75854 TAAAAAATTA
75864 AATTTGAAAGTTAGAGT
1 AATTTGAAAGTTAGAGT
*
75881 GA-TT-AAA-TTAGGAGT
1 AATTTGAAAGTTA-GAGT
75896 AATTTGAAAGTTA-AGT
1 AATTTGAAAGTTAGAGT
75912 AATT
1 AATT
75916 ATATTAAAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 9
0.73 0.05 0.22
Matches are distributed among these distances:
14 3 0.10
15 8 0.28
16 11 0.38
17 4 0.14
18 3 0.10
ACGTcount: A:0.42, C:0.00, G:0.21, T:0.37
Consensus pattern (17 bp):
AATTTGAAAGTTAGAGT
Found at i:81457 original size:2 final size:2
Alignment explanation
Indices: 81450--81487 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
81440 ACATCTTCTA
81450 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
81488 TAAGATTATG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:83437 original size:13 final size:13
Alignment explanation
Indices: 83419--83445 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
83409 CCCGGTTAGT
83419 TTTTATTTTTTTA
1 TTTTATTTTTTTA
83432 TTTTATTTTTTTA
1 TTTTATTTTTTTA
83445 T
1 T
83446 ATATAATTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (13 bp):
TTTTATTTTTTTA
Found at i:95266 original size:20 final size:20
Alignment explanation
Indices: 95243--95280 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
95233 ATGCAAAACG
95243 ACCCCGAAATGTTCAAATAA
1 ACCCCGAAATGTTCAAATAA
*
95263 ACCCCGAAATGTTGAAAT
1 ACCCCGAAATGTTCAAAT
95281 CAACATCTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.42, C:0.24, G:0.13, T:0.21
Consensus pattern (20 bp):
ACCCCGAAATGTTCAAATAA
Found at i:95538 original size:24 final size:24
Alignment explanation
Indices: 95504--95578 Score: 105
Period size: 24 Copynumber: 3.1 Consensus size: 24
95494 AAGAATTGAG
*
95504 TAAACGAGCTTATAAATGAGTCGA
1 TAAACGAGCTTATAAATGAGTCAA
* * *
95528 TCAACGAGCTTATAGATGAGCCAA
1 TAAACGAGCTTATAAATGAGTCAA
*
95552 TAAACGAGCTTGTAAATGAGTCAA
1 TAAACGAGCTTATAAATGAGTCAA
95576 TAA
1 TAA
95579 GCAAATTTGT
Statistics
Matches: 43, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 43 1.00
ACGTcount: A:0.41, C:0.15, G:0.20, T:0.24
Consensus pattern (24 bp):
TAAACGAGCTTATAAATGAGTCAA
Found at i:105090 original size:19 final size:16
Alignment explanation
Indices: 105051--105086 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
105041 TAAAATACAA
105051 AATAT-AATAATTCAT
1 AATATAAATAATTCAT
105066 AATATAAATAATTCAT
1 AATATAAATAATTCAT
*
105082 TATAT
1 AATAT
105087 TATATATATA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 5 0.26
16 14 0.74
ACGTcount: A:0.53, C:0.06, G:0.00, T:0.42
Consensus pattern (16 bp):
AATATAAATAATTCAT
Found at i:105506 original size:20 final size:20
Alignment explanation
Indices: 105481--105526 Score: 83
Period size: 20 Copynumber: 2.3 Consensus size: 20
105471 TAAAAAAAAT
105481 GACAATTAAGCAATTATTGA
1 GACAATTAAGCAATTATTGA
*
105501 GACAATTATGCAATTATTGA
1 GACAATTAAGCAATTATTGA
105521 GACAAT
1 GACAAT
105527 GAAAGCAGCA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.43, C:0.11, G:0.15, T:0.30
Consensus pattern (20 bp):
GACAATTAAGCAATTATTGA
Found at i:106837 original size:23 final size:23
Alignment explanation
Indices: 106811--106865 Score: 65
Period size: 23 Copynumber: 2.4 Consensus size: 23
106801 TACTTTTACG
*
106811 ACACATTTTATTATGTCATTATT
1 ACACATTTTATTATGTCATTATA
* * *
106834 ACACGTTTTTTTATGTCTTTATA
1 ACACATTTTATTATGTCATTATA
*
106857 ACATATTTT
1 ACACATTTT
106866 CAATCATTTA
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.27, C:0.13, G:0.05, T:0.55
Consensus pattern (23 bp):
ACACATTTTATTATGTCATTATA
Found at i:119377 original size:3 final size:3
Alignment explanation
Indices: 119369--119579 Score: 385
Period size: 3 Copynumber: 71.3 Consensus size: 3
119359 CTATGAACTG
119369 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA- TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
119416 TAT TAT TAT TAT TAT TAT TAT TAT TA- TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
119463 TA- TATT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TA-T TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
119508 TAT TAT TAT TA- TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
119555 TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT T
119580 CGACATAAAT
Statistics
Matches: 203, Mismatches: 0, Indels: 10
0.95 0.00 0.05
Matches are distributed among these distances:
2 8 0.04
3 193 0.95
4 2 0.01
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Done.