Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019105.1 Corchorus olitorius cultivar O-4 contig19138, 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: 31464
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.34
Found at i:3822 original size:18 final size:18
Alignment explanation
Indices: 3799--3833 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
3789 ACAAAAAATT
3799 AAATTGTTCATAAACAAA
1 AAATTGTTCATAAACAAA
*
3817 AAATTGTTCATGAACAA
1 AAATTGTTCATAAACAA
3834 TGTAATAATT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.51, C:0.11, G:0.09, T:0.29
Consensus pattern (18 bp):
AAATTGTTCATAAACAAA
Found at i:3896 original size:9 final size:9
Alignment explanation
Indices: 3872--3900 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
3862 AACAAACAAA
3872 ATATTATAT
1 ATATTATAT
3881 A-ATTATAT
1 ATATTATAT
3889 ATATTATAT
1 ATATTATAT
3898 ATA
1 ATA
3901 ATAATTAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
8 8 0.42
9 11 0.58
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (9 bp):
ATATTATAT
Found at i:4083 original size:35 final size:35
Alignment explanation
Indices: 4032--4106 Score: 118
Period size: 35 Copynumber: 2.1 Consensus size: 35
4022 TTATATAAAC
4032 GAACACTTAATCGAACAATAAACGAGTC-TGTTCGT
1 GAACACTTAATCGAACAATAAACGAG-CATGTTCGT
4067 GAACACTTAAAT-GAACAATAAACGAGCATGTTCGT
1 GAACACTT-AATCGAACAATAAACGAGCATGTTCGT
4102 GAACA
1 GAACA
4107 TAAACGAACT
Statistics
Matches: 38, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
34 1 0.03
35 34 0.89
36 3 0.08
ACGTcount: A:0.41, C:0.19, G:0.17, T:0.23
Consensus pattern (35 bp):
GAACACTTAATCGAACAATAAACGAGCATGTTCGT
Found at i:5698 original size:5 final size:5
Alignment explanation
Indices: 5688--5712 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
5678 TCAATAGTTT
5688 TCTTA TCTTA TCTTA TCTTA TCTTA
1 TCTTA TCTTA TCTTA TCTTA TCTTA
5713 CTACTATGTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.20, C:0.20, G:0.00, T:0.60
Consensus pattern (5 bp):
TCTTA
Found at i:5837 original size:26 final size:27
Alignment explanation
Indices: 5801--5857 Score: 80
Period size: 27 Copynumber: 2.1 Consensus size: 27
5791 TTTTAATAAG
*
5801 TATTCTTTTTA-ATCATTTAACTTTTT
1 TATTCTTTTTAGATCATTCAACTTTTT
* *
5827 TATTTTTTTTAGATGATTCAACTTTTT
1 TATTCTTTTTAGATCATTCAACTTTTT
5854 TATT
1 TATT
5858 AATTATGGAA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
26 10 0.37
27 17 0.63
ACGTcount: A:0.23, C:0.09, G:0.04, T:0.65
Consensus pattern (27 bp):
TATTCTTTTTAGATCATTCAACTTTTT
Found at i:5989 original size:15 final size:16
Alignment explanation
Indices: 5964--5993 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
5954 AATAATTATT
5964 TTTAGATTATAATATA
1 TTTAGATTATAATATA
5980 TTTA-ATTATAATAT
1 TTTAGATTATAATAT
5994 TATTATTTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.53
Consensus pattern (16 bp):
TTTAGATTATAATATA
Found at i:7662 original size:667 final size:662
Alignment explanation
Indices: 6345--9531 Score: 3267
Period size: 654 Copynumber: 4.8 Consensus size: 662
6335 ATACTTTACA
* * * *
6345 TCATCTAACCAAATCTCAGCAACATTGGATTGAAGAATTTGATTTTACGAGCATCTGAATTTTGT
1 TCATCTAACCAAATCTCAAC-ACATTGGATTTAAGAATTTGTTTTTACGAGCATCTGAATCTTGT
* * * * * * *
6410 TTCGGTTTAATTAAAAATTAATTTAG-AAAAATAAGAAATACGAAATTAAAAACGTGAAAAG-CC
65 TTCGATTTAATTAGAAATTAATTCAGAAAAAATATGAAAAACGATATTAAAAGCGTGAAAAGTCC
* * * *
6473 CTCGAATCTTTATGGCGTTTAA-T-TATATATTTTTATG-GTTATTTTAGCCAAAAATTGAGGAG
130 TTC-AATCTTTTTGGCGTTAAATTATATATATTTTTATGAG-TATTTTAGCCAAAAATTGAGGAA
*
6535 AAATCTTTCGGGTCAATTTTTGCAAAATTTTAGCTGAAATCGTGTACTTAACTAACCATCACAG-
193 AAATATTTCGGGTCAATTTTTGCAAAATTTTAGC-GAAATCGTGTAC-TAA-T---CATCACAGT
* * * * * * *
6599 -TTTTTGGCTAAAAACGTGTTCCGGAGACCCGGCTCAATTTTGCATGATTTTTGACTCGGAGACT
252 TTTTTTAGCTAAAAACGCGTTCCGGGGACCCGGCTCAGTTTTGCATGATTTTTGGCGCCGAGACT
* * * * * ** *
6663 ACTTGAAATATCTATATTCATCAAATAAAATCTCAGTCACGTTGGATTTAATAATTT-ATTTTAC
317 CCTTGAAATATCTATATTCATCTAATAAAATCTCAGCCACATTGGATTAAAGGATTTGTTTTTAC
* * * * *
6727 GAGTATCTGATTATTGTTTCGATTTAATTAGAAATTAATTCGGAAAAATAGGAAAAACGATATTA
382 GAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCAGAAAAATATGAAAAACGATATTA
* * *
6792 GAAACGTGAAAAGCCCTTCAATCTTTTTGGCGTTGAATTCTATATTTTTTATGAGTATTTTAGCC
447 AAAACGTGAAAAGCCCTTCAATCTTTTTGGCGTTGAATTATATATTTTTTATGAGTATTTTGGCC
*
6857 AAAAATTGA-GAAAATATCTTTTGGGTCAATTTTTACAAAATTTTAGCCGAAATCGTGTAATAAC
512 AAAAATTGAGGAAAA-ATCTTTCGGGTCAATTTTTACAAAATTTTAGCCGAAATCGTGTAATAAC
* * * * * *
6921 CATCACAGTTTTTTGCTTAAAAGGCGTTCCAGGGCCCGGCTCAATTTTGCATGATTTTTGGTGCC
576 CATCACGGTTTTTGGCTAAAAACGCGTTCC-GGGCCCAGTTCAATTTTGCATGATTTTTGGTGCC
* *
6986 -AAGACTCCTTGAGATATCCATAT
640 GAA-ACTCCTTGAAATATCTATAT
* *
7009 TCATCTAATCAAATCTCAACCACATTGGATTTAAGAATTTGTTTTTACGAGCATCTAAATCTTGT
1 TCATCTAACCAAATCTCAA-CACATTGGATTTAAGAATTTGTTTTTACGAGCATCTGAATCTTGT
*
7074 TTCGATTTAATTAGAAATTAATTCAGAAAAAATATGAAAAACGATATTAAAAGTGTGAAAAGTCC
65 TTCGATTTAATTAGAAATTAATTCAGAAAAAATATGAAAAACGATATTAAAAGCGTGAAAAGTCC
* * * * * *
7139 TCCAATATTTTAGGCGTTAAATTATATATATATTTTACGAGTATTTTATCCAAAGATTGAGGAAA
130 TTCAATCTTTTTGGCGTTAAATTATATATAT-TTTTATGAGTATTTTAGCCAAAAATTGAGGAAA
* * * * * *
7204 AATTTTTTGGGTC-ATTATTTGCAAAATTGTAGTCAAAATCGTGTACTAATGATCACGGTTTTTT
194 AATATTTCGGGTCAATT-TTTGCAAAATTTTAG-CGAAATCGTGTACTAATCATCACAG-TTTTT
* * * * * *
7268 TTAACTAAAAAACTCGTTTCGGGGCCCCGGCTTAGTTTT-AACTGATTTTTGGCGCCGAGACTCC
256 TTAGCT-AAAAACGCGTTCCGGGGACCCGGCTCAGTTTTGCA-TGATTTTTGGCGCCGAGACTCC
* * * * *
7332 TTGAAATATCTATATTCATCTTATAAAATCTTAGCCACATTGCATTAAAGGATTTG-ATTTATGA
319 TTGAAATATCTATATTCATCTAATAAAATCTCAGCCACATTGGATTAAAGGATTTGTTTTTACGA
* * * *
7396 GCATCTGAATCGTGTTTCGATTTTATTAGAAATTAATTCAGAAAACTATGAAAAACAATATTAAA
384 GCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCAGAAAAATATGAAAAACGATATTAAA
* * * * * *
7461 AACGTGAAAAACCCTTCAATCTTTTTGGAGTTAAATTATATATTTTTCTATGAGTGTTGTGGCTA
449 AACGTGAAAAGCCCTTCAATCTTTTTGGCGTTGAATTATATATTTTT-TATGAGTATTTTGGCCA
* * * *
7526 AAAATTTAGGAAATATCTTTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTAATAATCA
513 AAAATTGAGGAAAAATCTTTCGGGTCAATTTTTACAAAATTTTAGCCGAAATCGTGTAATAACCA
* * * **
7591 TCACGGTTTTTGGCTAAAAACGCGTTCCGGTGACCAGTTCAGTTTTGCATTA-TTTTGGCACCGA
578 TCACGGTTTTTGGCTAAAAACGCGTTCCGG-GCCCAGTTCAATTTTGCATGATTTTTGGTGCCGA
7655 AACTCCTTGAAATATCTATAT
642 AACTCCTTGAAATATCTATAT
* * * * * *
7676 TCATCT-----AA-C-CAA-A-A-TGCA--TCAGCCA-TTGTTTTTACAAGCATCTGAATCATAT
1 TCATCTAACCAAATCTCAACACATTGGATTTAAG-AATTTGTTTTTACGAGCATCTGAATCTTGT
* *
7728 TTCGATTTAATTGGAAATTAATTC-GGAAAAATATGAAAAACGATATTAAAAGCGTGAAAAGTCC
65 TTCGATTTAATTAGAAATTAATTCAGAAAAAATATGAAAAACGATATTAAAAGCGTGAAAAGTCC
* * * *
7792 TTCAATCTTTTTGGCGTTGAATTATATAT-TTTTTATGAGTATTGTGGCTAAAAATTGAGGAAAA
130 TTCAATCTTTTTGGCGTTAAATTATATATATTTTTATGAGTATTTTAGCCAAAAATTGAGGAAAA
* * * *
7856 ATATTTCGGGTCAATTTTTGCAAAATATTAGCCGAAATAGTGTAATGATCATCACAGTTTTTTTC
195 ATATTTCGGGTCAATTTTTGCAAAATTTTAG-CGAAATCGTGTACTAATCATCACAG---TTTT-
* * * * * * * * *
7921 TTCTTGCTAAAAACGGGTTCCGGGAACCTGGGTCATTTTTGCATGATTTTTGACGCCAAGACTCT
255 TT-TAGCTAAAAACGCGTTCCGGGGACCCGGCTCAGTTTTGCATGATTTTTGGCGCCGAGACTCC
* * * * * * *
7986 TTGAGATATCCATATTCACCTAATCAAATCTCAGCTACATTGGATTCAAGAATTTGTTTTTACGA
319 TTGAAATATCTATATTCATCTAATAAAATCTCAGCCACATTGGATTAAAGGATTTGTTTTTACGA
* * * * *
8051 CCATTTGATTCTTGTTTCGTTTTAATTAGAAATTAATTCAGAAAAATATGAAAAATGATATTAAA
384 GCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCAGAAAAATATGAAAAACGATATTAAA
* * * * * ** * *
8116 AGCGTGAAAAGTCCTCCAATCTTTTTGGCTTTAAATTATATATACTTTATGAGTATTTTAGACAA
449 AACGTGAAAAGCCCTTCAATCTTTTTGGCGTTGAATTATATATTTTTTATGAGTATTTTGGCCAA
* * * *
8181 AAATTGAGGAAAAAAT-TTTCGGGTCATTTTTTGCAAAATTATAGCCGAAATCGTGT-ACAACCA
514 AAATTGAGG-AAAAATCTTTCGGGTCAATTTTTACAAAATTTTAGCCGAAATCGTGTAATAACCA
* * *
8244 TCACGGTTTTTTGGCTAAAAACGCGTTCCGGGGCCCCGGGTCAATTTTGCATGATTTTTGGTGGC
578 TCACGG-TTTTTGGCTAAAAACGCGTTCC-GGG-CCCAGTTCAATTTTGCATGATTTTTGGTGCC
*
8309 GAAATTCCTTGAAATATCTATAT
640 GAAACTCCTTGAAATATCTATAT
* * * * * * *
8332 TCATCTAACCAAATCTTAGCCACATTGGATTTAGGGATTTGTTTTTACAAGCATTTGAATCATGT
1 TCATCTAACCAAATCTCA-ACACATTGGATTTAAGAATTTGTTTTTACGAGCATCTGAATCTTGT
* * * *
8397 TTCGATTTAATTAGAAATTAATT-TGAAAAAA-ATGATAAAACGATATTAGAAGCGCGAGAAG-C
65 TTCGATTTAATTAGAAATTAATTCAGAAAAAATATGA-AAAACGATATTAAAAGCGTGAAAAGTC
* * * * **
8459 CTTTTAATCTTTTTGGCGTTGAA-T-TATATATTTTTATGAGTATTATGGCTTAAAATTGA-G-A
129 C-TTCAATCTTTTTGGCGTTAAATTATATATATTTTTATGAGTATTTTAGCCAAAAATTGAGGAA
* * * *
8520 AAATATTTCGGATCACTTTTTGTAAAATTTTAGCTGAAATCGTGTAC----CATCAC-GGTTTTT
193 AAATATTTCGGGTCAATTTTTGCAAAATTTTAGC-GAAATCGTGTACTAATCATCACAGTTTTTT
* * * * *
8580 TAGCTAGAAACGCGTTTCGGGG-CCCGTG-TCAGTTTTGTATGATTTTTGGCGCCTAGACTACTT
257 TAGCTAAAAACGCGTTCCGGGGACCCG-GCTCAGTTTTGCATGATTTTTGGCGCCGAGACTCCTT
* * * * * * * * * *
8643 AAAAAATATATATTCATCTAATTAAATATCAACCATATTGTATTTAAGGATTTGTTTTTACGAGT
321 GAAATATCTATATTCATCTAATAAAATCTCAGCCACATTGGATTAAAGGATTTGTTTTTACGAGC
* * * * * *
8708 ATCTAAATCTTGTTTCGATTTAATCAGAAATTAATTTCGAAATAAAATAGGGAAAACGATATTAG
386 ATCTGAATCTTGTTTCGATTTAATTAGAAATTAA-TTC-AGA-AAAATATGAAAAACGATATTAA
** *** * * *
8773 AAGTGTGAAGAAGGATTTCAATATTTTTGGCGTTGAATTATATATTTTTTATGAGTATTTTCGCT
448 AAACGTGAA-AAGCCCTTCAATCTTTTTGGCGTTGAATTATATATTTTTTATGAGTATTTTGGCC
* * *
8838 AAAAATTGAGAAAAAATCTTTCGGGTCAATTTTTACAAAA-TTTAGCCGAAACCGTGTATTAACC
512 AAAAATTGAGGAAAAATCTTTCGGGTCAATTTTTACAAAATTTTAGCCGAAATCGTGTAATAACC
* * * * *
8902 ATCACGGTTTTCGGCTAAAAACGCGTTCTGGGTCCTA-TCTCAGTTTTGCATGATTTTTGGTGTC
577 ATCACGGTTTTTGGCTAAAAACGCGTTCCGGG-CCCAGT-TCAATTTTGCATGATTTTTGGTGCC
* *
8966 GAGACTCCTTGAAATATTTATAT
640 GAAACTCCTTGAAATATCTATAT
* * * * *
8989 TTATCTAACCAAATCT-----CA--GAATTTAAGGATTTGTTTTTACGAGTATCTGAATCTTATT
1 TCATCTAACCAAATCTCAACACATTGGATTTAAGAATTTGTTTTTACGAGCATCTGAATCTTGTT
* * * * ** *
9047 TCAATTTAATTAGAAATTAATTCAGAAAAAAATAGGAAAAACAATATTAGAAGTTTTAAAA-TCC
66 TCGATTTAATTAGAAATTAATTCAG-AAAAAATATGAAAAACGATATTAAAAGCGTGAAAAGTCC
** * *
9111 TTTCAATCTTTTTGATGTCAAATTATATAT-TTTTTATGAGTATTTTAGCCAAAAATTAAGGAAA
130 -TTCAATCTTTTTGGCGTTAAATTATATATATTTTTATGAGTATTTTAGCCAAAAATTGAGGAAA
* * * *
9175 TATCTTTCGGATCAATTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACCATCAC-GTTTTTTT
194 AATATTTCGGGTCAATTTTTGCAAAATTTTAG-CGAAATCGTGTACTAATCATCACAGTTTTTTT
* * ** ** * *
9239 GGCTAAAAACGCGTTCC-AGGATCATGGCTTTGTATTGCATGATTTTTGGCGCCGAAACTCCTTG
258 AGCTAAAAACGCGTTCCGGGGA-CCCGGCTCAGTTTTGCATGATTTTTGGCGCCGAGACTCCTTG
* * **
9303 AAATATCTTTATTCATCTAATCAAATCTCAGCCACATTGGA-TATAAGGATTTGTTTTTACCTGC
322 AAATATCTATATTCATCTAATAAAATCTCAGCCACATTGGATTA-AAGGATTTGTTTTTACGAGC
9367 ATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCAGAAAAAATTATGAAAAACGATATT-AA
386 ATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCAG-AAAAA-TATGAAAAACGATATTAAA
* * *
9431 AACGTGAAAAGTCC-TCTAATCTTTTTGGCGTTGAATTATATATATATATATTATAAGTATTTTT
449 AACGTGAAAAGCCCTTC-AATCTTTTTGGCGTTGAATTATATAT-T-T-T-TTATGAGTATTTTG
9495 GCCAAAAATTGAGGAAAAATCTTTCGGGTC-ATTTTTA
509 GCCAAAAATTGAGGAAAAATCTTTCGGGTCAATTTTTA
9532 TCATCATGGG
Statistics
Matches: 2088, Mismatches: 352, Indels: 171
0.80 0.13 0.07
Matches are distributed among these distances:
649 54 0.03
650 1 0.00
651 115 0.06
652 32 0.02
653 85 0.04
654 263 0.13
655 241 0.12
656 87 0.04
657 83 0.04
658 119 0.06
659 204 0.10
660 43 0.02
661 4 0.00
662 9 0.00
663 7 0.00
664 80 0.04
665 47 0.02
666 54 0.03
667 249 0.12
668 208 0.10
669 103 0.05
ACGTcount: A:0.33, C:0.14, G:0.16, T:0.37
Consensus pattern (662 bp):
TCATCTAACCAAATCTCAACACATTGGATTTAAGAATTTGTTTTTACGAGCATCTGAATCTTGTT
TCGATTTAATTAGAAATTAATTCAGAAAAAATATGAAAAACGATATTAAAAGCGTGAAAAGTCCT
TCAATCTTTTTGGCGTTAAATTATATATATTTTTATGAGTATTTTAGCCAAAAATTGAGGAAAAA
TATTTCGGGTCAATTTTTGCAAAATTTTAGCGAAATCGTGTACTAATCATCACAGTTTTTTTAGC
TAAAAACGCGTTCCGGGGACCCGGCTCAGTTTTGCATGATTTTTGGCGCCGAGACTCCTTGAAAT
ATCTATATTCATCTAATAAAATCTCAGCCACATTGGATTAAAGGATTTGTTTTTACGAGCATCTG
AATCTTGTTTCGATTTAATTAGAAATTAATTCAGAAAAATATGAAAAACGATATTAAAAACGTGA
AAAGCCCTTCAATCTTTTTGGCGTTGAATTATATATTTTTTATGAGTATTTTGGCCAAAAATTGA
GGAAAAATCTTTCGGGTCAATTTTTACAAAATTTTAGCCGAAATCGTGTAATAACCATCACGGTT
TTTGGCTAAAAACGCGTTCCGGGCCCAGTTCAATTTTGCATGATTTTTGGTGCCGAAACTCCTTG
AAATATCTATAT
Found at i:13091 original size:31 final size:30
Alignment explanation
Indices: 13051--13310 Score: 423
Period size: 30 Copynumber: 8.5 Consensus size: 30
13041 AGCCCAGTAT
13051 AATAATACAGGTCAGAGGGTAGCAAAAAAA
1 AATAATACAGGTCAGAGGGTAGCAAAAAAA
*
13081 AACTAATACAGGTCAGAGGGTAGCAAAAAAT
1 AA-TAATACAGGTCAGAGGGTAGCAAAAAAA
*
13112 AATAATACAGGTCAGAGGGTAGCAAAAAAT
1 AATAATACAGGTCAGAGGGTAGCAAAAAAA
13142 AATAATACAGGTCAGAGGGTAGCAAAAAAA
1 AATAATACAGGTCAGAGGGTAGCAAAAAAA
* *
13172 TAATAATACATGTTAGAGGGTAGCAAAAAAA
1 -AATAATACAGGTCAGAGGGTAGCAAAAAAA
13203 AATAATACAGGTCAGAGGGTAGCAAAAAAA
1 AATAATACAGGTCAGAGGGTAGCAAAAAAA
13233 TAATAATACAGGTCAGAGGGTAGCAAAAAAAA
1 -AATAATACAGGTCAGAGGGTAGC-AAAAAAA
*
13265 TAATAATACATGTCAGAGGGTAG-AAAAAAA
1 -AATAATACAGGTCAGAGGGTAGCAAAAAAA
13295 AATAATACAGGTCAGA
1 AATAATACAGGTCAGA
13311 TTTCATTCTT
Statistics
Matches: 218, Mismatches: 8, Indels: 9
0.93 0.03 0.04
Matches are distributed among these distances:
29 15 0.07
30 94 0.43
31 80 0.37
32 29 0.13
ACGTcount: A:0.52, C:0.10, G:0.22, T:0.17
Consensus pattern (30 bp):
AATAATACAGGTCAGAGGGTAGCAAAAAAA
Found at i:13116 original size:61 final size:61
Alignment explanation
Indices: 13049--13310 Score: 440
Period size: 61 Copynumber: 4.3 Consensus size: 61
13039 AGAGCCCAGT
13049 ATAATAATACAGGTCAGAGGGTAGCAAAAAAAAACTAATACAGGTCAGAGGGTAGC-AAAAA
1 ATAATAATACAGGTCAGAGGGTAGCAAAAAAAAA-TAATACAGGTCAGAGGGTAGCAAAAAA
*
13110 ATAATAATACAGGTCAGAGGGTAGCAAAAAATAATAATACAGGTCAGAGGGTAGCAAAAAA
1 ATAATAATACAGGTCAGAGGGTAGCAAAAAAAAATAATACAGGTCAGAGGGTAGCAAAAAA
* *
13171 ATAATAATACATGTTAGAGGGTAGCAAAAAAAAATAATACAGGTCAGAGGGTAGCAAAAAA
1 ATAATAATACAGGTCAGAGGGTAGCAAAAAAAAATAATACAGGTCAGAGGGTAGCAAAAAA
*
13232 ATAATAATACAGGTCAGAGGGTAGCAAAAAAAATAATAATACATGTCAGAGGGTAG-AAAAAA
1 ATAATAATACAGGTCAGAGGGTAGC-AAAAAAA-AATAATACAGGTCAGAGGGTAGCAAAAAA
13294 A-AATAATACAGGTCAGA
1 ATAATAATACAGGTCAGA
13311 TTTCATTCTT
Statistics
Matches: 191, Mismatches: 7, Indels: 6
0.94 0.03 0.03
Matches are distributed among these distances:
60 21 0.11
61 135 0.71
62 14 0.07
63 21 0.11
ACGTcount: A:0.52, C:0.10, G:0.22, T:0.17
Consensus pattern (61 bp):
ATAATAATACAGGTCAGAGGGTAGCAAAAAAAAATAATACAGGTCAGAGGGTAGCAAAAAA
Found at i:13118 original size:30 final size:30
Alignment explanation
Indices: 13049--13310 Score: 418
Period size: 31 Copynumber: 8.6 Consensus size: 30
13039 AGAGCCCAGT
13049 ATAATAATACAGGTCAGAGGGTAGCAAAAA
1 ATAATAATACAGGTCAGAGGGTAGCAAAAA
*
13079 AAAACTAATACAGGTCAGAGGGTAGCAAAAA
1 ATAA-TAATACAGGTCAGAGGGTAGCAAAAA
13110 ATAATAATACAGGTCAGAGGGTAGCAAAAA
1 ATAATAATACAGGTCAGAGGGTAGCAAAAA
13140 ATAATAATACAGGTCAGAGGGTAGCAAAAAA
1 ATAATAATACAGGTCAGAGGGTAGC-AAAAA
* *
13171 ATAATAATACATGTTAGAGGGTAGCAAAAA
1 ATAATAATACAGGTCAGAGGGTAGCAAAAA
*
13201 AAAATAATACAGGTCAGAGGGTAGCAAAAAA
1 ATAATAATACAGGTCAGAGGGTAGC-AAAAA
13232 ATAATAATACAGGTCAGAGGGTAGCAAAAAAA
1 ATAATAATACAGGTCAGAGGGTAGC--AAAAA
*
13264 ATAATAATACATGTCAGAGGGTAG-AAAAA
1 ATAATAATACAGGTCAGAGGGTAGCAAAAA
*
13293 AAAATAATACAGGTCAGA
1 ATAATAATACAGGTCAGA
13311 TTTCATTCTT
Statistics
Matches: 217, Mismatches: 11, Indels: 9
0.92 0.05 0.04
Matches are distributed among these distances:
29 21 0.10
30 81 0.37
31 86 0.40
32 29 0.13
ACGTcount: A:0.52, C:0.10, G:0.22, T:0.17
Consensus pattern (30 bp):
ATAATAATACAGGTCAGAGGGTAGCAAAAA
Found at i:20153 original size:16 final size:15
Alignment explanation
Indices: 20127--20162 Score: 54
Period size: 16 Copynumber: 2.3 Consensus size: 15
20117 TTATTTGTTG
20127 ATATATAAATATAAT
1 ATATATAAATATAAT
20142 ATATATTAAATATAAT
1 ATATA-TAAATATAAT
*
20158 TTATA
1 ATATA
20163 CGTACACCGT
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:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (15 bp):
ATATATAAATATAAT
Found at i:20287 original size:14 final size:15
Alignment explanation
Indices: 20268--20331 Score: 84
Period size: 14 Copynumber: 4.6 Consensus size: 15
20258 ATTTTATATT
*
20268 TATAATTAT-ATTTA
1 TATAATTATAATTAA
20282 TATAA-T-TAATTAA
1 TATAATTATAATTAA
20295 TATAA-TATAATTAA
1 TATAATTATAATTAA
20309 TATAA-TATAATTAA
1 TATAATTATAATTAA
20323 TATAATTAT
1 TATAATTAT
20332 TAAAAAAATA
Statistics
Matches: 46, Mismatches: 1, Indels: 5
0.88 0.02 0.10
Matches are distributed among these distances:
12 1 0.02
13 11 0.24
14 31 0.67
15 3 0.07
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
TATAATTATAATTAA
Found at i:20291 original size:18 final size:18
Alignment explanation
Indices: 20281--20330 Score: 75
Period size: 18 Copynumber: 2.7 Consensus size: 18
20271 AATTATATTT
20281 ATATAATTAATTAATATA
1 ATATAATTAATTAATATA
20299 ATATAATTAATATAATATA
1 ATATAATTAAT-TAATATA
20318 AT-TAATATAATTA
1 ATATAAT-TAATTA
20331 TTAAAAAAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
18 17 0.57
19 13 0.43
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (18 bp):
ATATAATTAATTAATATA
Found at i:20302 original size:5 final size:5
Alignment explanation
Indices: 20281--20328 Score: 68
Period size: 5 Copynumber: 10.4 Consensus size: 5
20271 AATTATATTT
20281 ATATA AT-TA AT-TA ATATA ATATA AT-TA ATATA ATATA AT-TA ATATA
1 ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA
20327 AT
1 AT
20329 TATTAAAAAA
Statistics
Matches: 40, Mismatches: 0, Indels: 6
0.87 0.00 0.13
Matches are distributed among these distances:
4 16 0.40
5 24 0.60
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (5 bp):
ATATA
Found at i:20309 original size:9 final size:9
Alignment explanation
Indices: 20284--20330 Score: 62
Period size: 9 Copynumber: 5.2 Consensus size: 9
20274 TATATTTATA
20284 TAAT-TAAT
1 TAATATAAT
20292 TAATATAAT
1 TAATATAAT
20301 ATAAT-TAAT
1 -TAATATAAT
20310 ATAATATAAT
1 -TAATATAAT
20320 TAATATAAT
1 TAATATAAT
20329 TA
1 TA
20331 TTAAAAAAAT
Statistics
Matches: 36, Mismatches: 0, Indels: 5
0.88 0.00 0.12
Matches are distributed among these distances:
8 4 0.11
9 24 0.67
10 8 0.22
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (9 bp):
TAATATAAT
Found at i:21011 original size:17 final size:17
Alignment explanation
Indices: 20989--21023 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
20979 TATACGGAAT
20989 AAGAAGATAACTAAGAG
1 AAGAAGATAACTAAGAG
21006 AAGAAGATAACTAAGAG
1 AAGAAGATAACTAAGAG
21023 A
1 A
21024 TGAATGAATA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.60, C:0.06, G:0.23, T:0.11
Consensus pattern (17 bp):
AAGAAGATAACTAAGAG
Found at i:25181 original size:344 final size:331
Alignment explanation
Indices: 23422--26364 Score: 2350
Period size: 334 Copynumber: 8.9 Consensus size: 331
23412 CCATAATGGT
*
23422 AAAAA-TGACCCGAAAGATTTTTCCTCAATTTTTGACAAAAATACTCAT--AAAATATATATA-A
1 AAAAATTGACCCGAAATATTTTT-CTCAATTTTTGAC-AAAATACTCATAAAAAATATATATATA
* * * *
23483 TTAAACGCCAAAAATATTGGAGGACTTTTCACGCTTTTAATATCGTTTTTTCATTTTTTTCAGAA
64 TTAAA-ACCAAAAAGATTGGAGGACTTTTCACGCTTTTAATATCG-TTTTTCATATTTTTCTGAA
* * * * * *
23548 TTAATTTCTAATTAAATCGATACAAGATTCAGATACACATAAAAACAAATCCTTAAATCCAATGT
127 TTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAGATTCAATGT
* * * *
23613 GGCTGAGATTTTATTAGATGAACAAAGATATTTCAAGGAGTCTCGGCGCCAAAAATCATGCAAAA
192 GGCTGAGATTTGATTAGATGAATATAGATATTTCAAGGAGTCT-GGCGCAAAAAATCATGCAAAA
** * * ** *
23678 CAAAGTCGTGGCCTTGGAACGCGTTTTTAGCCAAAAAACTGTGATGGTTAGTACACGATTTTGGC
256 CTGAGCCGGGGCCCCGGAACGCGTTTTTAGCCAAAAAACTGTGATGGTTAGTACACGATTTCGGC
23743 TAAAATTTTGC
321 TAAAATTTTGC
* * *
23754 AAAAATTGACCCGAAATATATTTCCTCAATTTTTGGCTAAAATACTCA-AGAAAAATATAT-GAT
1 AAAAATTGACCCGAAATAT-TTTTCTCAATTTTTGAC-AAAATACTCATA-AAAAATATATATAT
** * * * * * * * * * *
23817 -TCGATATCAAAAAGATTGAAGGGCTTTTAACTCTTCTAATATTGTTTTTCCTATTTCTTTCCGA
63 ATTAAAACCAAAAAGATTGGAGGACTTTTCACGCTTTTAATATCGTTTTTCATA-TT-TTTCTGA
* * ** *
23881 ATTAATTTCTAATTAAATCGAACCAAGATTCAGATGCTCGTAAAAATAAATTTTTA-AATCTAAT
126 ATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAGATTC-AAT
* * * *
23945 GTGGCTAAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTTGGCACCAAAAATCATGCAA
190 GTGGCTGAGATTTGATTAGATGAATATAGATATTTCAAGGAGTC-TGGCGCAAAAAATCATGCAA
* * * * * *
24010 AACTGAGCC-AGACCCCGGAACGCGTTTTTAGTC-GAAAACTGTGATGGTTAGTACAAGATTTCA
254 AACTGAGCCGGGGCCCCGGAACGCGTTTTTAGCCAAAAAACTGTGATGGTTAGTACACGATTTCG
* *
24073 ACTAAAATTTTCC
319 GCTAAAATTTTGC
* * *
24086 AAAAATGGACCCGAAATATTTTTCCTCGATTTCT-AGCGAAAATACTCATAAAAAATATATA-AT
1 AAAAATTGACCCGAAATATTTTT-CTCAATTTTTGA-C-AAAATACTCATAAAAAATATATATAT
* * * * * * * * *
24149 -TCAACACCAAAAA-AATGAAAGCCTTTTTCACGCTTTTAATATCGTTTTCCCTATTTTATTTCC
63 ATTAAAACCAAAAAGATTGGAGGAC-TTTTCACGCTTTTAATATCGTTTT-TC-ATATT-TTTCT
* * * * *** *
24212 AAATTAATTTCTGATTAAATCAAAACAAGATTTAGAAATTCGTAAAAACAAATCCTT-GAATACA
124 GAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAG-ATTCA
* * * * *
24276 ATGTGGCTGAGATTTGGTTAAATGAATATAGATATATTTTAAGGAGTCTTGACGCCAAAAATCAT
188 ATGTGGCTGAGATTTGATTAGATGAATATAG--ATATTTCAAGGAGTC-TGGCGCAAAAAATCAT
* * * **
24341 GCAAAACTGACCCAGGACCCCGGAACGCGTTTTTAGCCAAAAAAACAATGAT-G---GTACACGA
250 GCAAAACTGAGCCGGGGCCCCGGAACGCGTTTTTAGCC-AAAAAACTGTGATGGTTAGTACACGA
*
24402 TTTCGTCTAAAATTTTGC
314 TTTCGGCTAAAATTTTGC
* * * *
24420 AAAAATTAACCC-AGAATATTTTTCTCAATTTTTAACCACAATACTCATTAAAAATATATA-AT-
1 AAAAATTGACCCGA-AATATTTTTCTCAATTTTTGA-CAAAATACTCATAAAAAATATATATATA
* ** * * * ** * * *
24482 TCAACGCCAAAAGGATT-G-GG-CTTCTCACGCTTCTAATATAATTTTTCCTATTTTTTTAAATT
64 TTAAAACCAAAAAGATTGGAGGACTTTTCACGCTTTTAATATCGTTTTTCATATTTTTCTGAATT
* * * * * *
24544 AATTTATAATTAAATTGAAACATGATTCAAATGCTCGCAAAAAAAAAATCCTTAGA-TCAAGTGT
129 AATTTCTAATTAAATCGAAACAAGATTCAGATGCTCG-TAAAAACAAATCCTTAGATTCAA-TGT
* * * * *
24608 GACTAAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTTTTGC-CACCAAAAATCATGCAAA
192 GGCTGAGATTTGATTAGATGAATATAGATATTTCAAGGAGTCTGGCGCA--AAAAATCATGCAAA
* *
24672 ACTGA-CCTGGGGCCCCGGAACGCCTTTTTGGCCAAAAAACTGTGAT-G---GTACACGATTTCG
255 ACTGAGCC-GGGGCCCCGGAACGCGTTTTTAGCCAAAAAACTGTGATGGTTAGTACACGATTTCG
24732 GCTAAAATTTTGC
319 GCTAAAATTTTGC
* * * * *
24745 AAAAATTGACCCGAAATATTTTGTCTCAATTTTAGGCCACAACACT-A-ATAAAATATATATA-A
1 AAAAATTGACCCGAAATATTTT-TCTCAATTTT-TGACAAAATACTCATAAAAAATATATATATA
* * *
24807 TTCAACACCAAAAAGACTGCAGGACTTTTCACGCTTTTAATATCGTTTTTCATATTTTTCTGAAT
64 TT-AAAACCAAAAAGATTGGAGGACTTTTCACGCTTTTAATATCGTTTTTCATATTTTTCTGAAT
*
24872 TAATTTCTAATTAAATCGAAACAAGATTCAGAGGCTCGTAAAAACAAATCCTTAGATTCAATGTG
128 TAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAGATTCAATGTG
* * * *
24937 GCTGAGATTTGATTAGATGAATGTAGATATTTCAAGAAGTCTCAGTGCAAAAAATCATGCAAAAC
193 GCTGAGATTTGATTAGATGAATATAGATATTTCAAGGAGTCT-GGCGCAAAAAATCATGCAAAAC
* * * *
25002 TAAGCCGGGGCCTCGAAACGCGTTTTTAGCC-AAAAACTGTGATGGTTAGTACATGATTTCGGCT
257 TGAGCCGGGGCCCCGGAACGCGTTTTTAGCCAAAAAACTGTGATGGTTAGTACACGATTTCGGCT
25066 AAAATTTTGC
322 AAAATTTTGC
* *
25076 AAAAATTGACCCGAAAAATTTTTCTGACAATTTTTGACTTAAATACTCATAATATATATATATAT
1 AAAAATTGACCCGAAATATTTTTCT--CAATTTTTGAC-AAAATACTCATAA-A-A-A-ATATAT
*
25141 ATATATATAATTTAATGCCAAAAAGATTGGAGAACTTTTCACGCTTTTAATATCGTTTTT-ATTA
59 ATATAT-TAA---AA--CCAAAAAGATTGGAGGACTTTTCACGCTTTTAATATCGTTTTTCA-TA
* * * * *
25205 TTTTTCTGAATTAATTTCTAATTAAATCGAGATAAGATTCATATGCTCATAAAAACAAATTCTTA
117 TTTTTCTGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTA
* * * * * * * * * *
25270 AATCCAATGTTGCTGATATTTGATTATATGGATATGGATATCTCAAAGAGTTTTGGCGCAAAAAA
182 GATTCAATGTGGCTGAGATTTGATTAGATGAATATAGATATTTCAAGGAG-TCTGGCGCAAAAAA
* * * * * *
25335 TCATGCAAAACTGAGCTGGGGTCCCGAAACGCGATTTTAGCCAAAAATC-GTGATGATTA-T-CA
246 TCATGCAAAACTGAGCCGGGGCCCCGGAACGCGTTTTTAGCCAAAAAACTGTGATGGTTAGTACA
*
25397 --A-AT--G-----ATTTT--
311 CGATTTCGGCTAAAATTTTGC
* * * *
25406 ----A--G--CC-AAAGT-TATTTCCTCAATTTTTAGCCACAATACTCAT-TAAAAT-TATATA-
1 AAAAATTGACCCGAAA-TAT-TTTTCTCAATTTTT-GACAAAATACTCATAAAAAATATATATAT
** * * ** * * *
25458 ATTCAACGCCAATAAGATTGAAGGGTTTTTCATGCTTCTCATATCGTTTTTCCTATTATTTTTC-
63 ATT-AAAACCAAAAAGATTGGAGGACTTTTCACGCTTTTAATATCGTTTTT-C-A-TATTTTTCT
* * * * *** * ** * *
25522 GAATTAATTTATGATTAAATCGAAACATGATTCAGATGCTTGT-TTTAGATTTCCTTAAATCCAA
124 GAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAGATTCAA
* * * * *
25586 TGTGGCCGAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTCAGTGCCAAAAATCATGCA
189 TGTGGCTGAGATTTGATTAGATGAATATAGATATTTCAAGGAGTCT-GGCGCAAAAAATCATGCA
* * ** * * * * *
25651 ACACTGTA-CCAGGATCCCGGAACGCATTTTTAGCAAAAAAAAAAAC-GTAATTTCGACTAACGT
253 AAACTG-AGCCGGGGCCCCGGAACGCGTTTTTAGC----CAAAAAACTGTGA--T-G-GTTA-GT
*
25714 ACACGATTTCGGCTAATATTTTGC
308 ACACGATTTCGGCTAAAATTTTGC
* * * * *
25738 AAAAATTTACCAGAATTATTTTTCCTCAATTTTTGTCTAAAATACTCATAAAAAATATATATTTC
1 AAAAATTGACCCGAAATATTTTT-CTCAATTTTTGAC-AAAATACTCATAAAAAATATATATAT-
* * * *
25803 ATT---GCCAAAAAGATTGCAGAACTTTTCACGCTTTTAATATCGTTTTTCATATTTTTCTTAAT
63 ATTAAAACCAAAAAGATTGGAGGACTTTTCACGCTTTTAATATCGTTTTTCATATTTTTCTGAAT
* * * * * * *
25865 TAATTTCAAATTAAATCAAAACAAGATTTAGATGCTCGTAAAAACACATCCTTAAATGCAATGTA
128 TAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAGATTCAATGTG
* * * *
25930 GCTGAGATTTGATTAGATAAATATAGGTATGTCAATGAGTCT--CGACTAAAAAATCATGCAAAA
193 GCTGAGATTTGATTAGATGAATATAGATATTTCAAGGAGTCTGGCG-C-AAAAAATCATGCAAAA
* * *
25993 CTGAGTCGGGGCCCCGAAACGCGTTTTTAGCAAAAAAAAAACTGTGATGGTTAGTACACGATTTC
256 CTGAGCCGGGGCCCCGGAACGCGTTTTTAGC---CAAAAAACTGTGATGGTTAGTACACGATTTC
26058 GGCTAAAATTTTGC
318 GGCTAAAATTTTGC
* ** * * * * *
26072 AAAAAATGACTAGAAAAATTTTTCCTTAATTTTTGTCTAAAATACTCATGAAATATATATA-AT-
1 AAAAATTGACCCGAAATATTTTT-CTCAATTTTTGAC-AAAATACTCATAAAAAATATATATATA
** * * * *
26135 TTAACGCCAAAAGGATTAGAGGACTTTTCGCGCTTTTCATATCGTTTTTCATATTTTTTCT-AAT
64 TTAAAACCAAAAAGATTGGAGGACTTTTCACGCTTTTAATATCGTTTTTCATA-TTTTTCTGAAT
* * * * * *
26199 TAATTTGTAATTAAATCGAAACAAGATACAGATGCTCGTAAAAACAAAACATTAAATGCAATGTG
128 TAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAGATTCAATGTG
* * * * * * * * * *
26264 GATGAGATTTGACTAGATTAAAATGGATATCTCAAGGATTCTTAGCCCCAAAAATCATGCAAAAC
193 GCTGAGATTTGATTAGATGAATATAGATATTTCAAGGAGTC-TGGCGCAAAAAATCATGCAAAAC
* * * * *
26329 TGATCTGGGGCCCTGGAATGTGTTTTTAGCCAAAAA
257 TGAGCCGGGGCCCCGGAACGCGTTTTTAGCCAAAAA
26365 TTGACCGAAA
Statistics
Matches: 2104, Mismatches: 377, Indels: 260
0.77 0.14 0.09
Matches are distributed among these distances:
308 37 0.02
309 88 0.04
310 36 0.02
311 10 0.00
312 1 0.00
313 13 0.01
314 6 0.00
315 3 0.00
316 2 0.00
317 3 0.00
318 1 0.00
319 1 0.00
320 19 0.01
321 6 0.00
322 8 0.00
323 1 0.00
324 12 0.01
325 64 0.03
326 85 0.04
327 50 0.02
328 142 0.07
329 76 0.04
330 30 0.01
331 61 0.03
332 151 0.07
333 217 0.10
334 386 0.18
335 101 0.05
336 26 0.01
337 6 0.00
338 39 0.02
339 81 0.04
340 63 0.03
341 59 0.03
342 8 0.00
343 7 0.00
344 195 0.09
345 10 0.00
ACGTcount: A:0.37, C:0.16, G:0.14, T:0.33
Consensus pattern (331 bp):
AAAAATTGACCCGAAATATTTTTCTCAATTTTTGACAAAATACTCATAAAAAATATATATATATT
AAAACCAAAAAGATTGGAGGACTTTTCACGCTTTTAATATCGTTTTTCATATTTTTCTGAATTAA
TTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAGATTCAATGTGGCT
GAGATTTGATTAGATGAATATAGATATTTCAAGGAGTCTGGCGCAAAAAATCATGCAAAACTGAG
CCGGGGCCCCGGAACGCGTTTTTAGCCAAAAAACTGTGATGGTTAGTACACGATTTCGGCTAAAA
TTTTGC
Found at i:27948 original size:333 final size:329
Alignment explanation
Indices: 27186--28131 Score: 1068
Period size: 332 Copynumber: 2.9 Consensus size: 329
27176 GCAAAATTCA
* * * * *
27186 AAACAAGATTCAGATGCTCGT-AAAACAAATCTTTAATTGTAATGTGGCTAAGATTTTATTATAT
1 AAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCTAATGTGGCTGAGATTTGATTATAT
* * * * * **
27250 GAATATAAATATTCCAAGAAGTGTCT--ACGCCAAAAATCATGCAAAACTAAGCCGGGC-CCCGA
66 GAATATAGATATTTCAAGAAGTCT-TGGA-GCCAAAAATCATGCAAAACTGAG-CAGGCTCCTAA
** * * * * * *
27312 AACGCA-TTTTTAATCAAAAACCGTGATGGTTAGTACACGATTTTGGCTAAAGTTATGCAAAAAA
128 AACGCATTTTTTAGCCAAAAACCGTGATGATTATTAGACGATTTCGGCTAAAATTATGCAAAAAT
* * * *
27376 TGACCCGAAAAATTTTTCCTCAATTTTTGGATAAAACACTCATAAAAAATATATAATTTAACGCC
193 TGACCCGAAAGA-TTTTCCTCAATTTTTGGCTAAAATACTCATAAAAAATATATAATTCAACGCC
* * ** *
27441 AAAACAATTGGAGGACTTTTCACGCTTTTAATATCATTTTTCATATTTTTCTTAATTAATTTCTG
257 AAAA-AATTGGAGGGCTTTTTACGCTTTTAATATCATTTTTCATATTTTTCCAAATTAATTTCTA
27506 ATTAAATCG
321 ATTAAATCG
* * * * *
27515 AAACAAGATTCAGATGCTTGTAAAAACAAATTCTTAAATCCAATGTAGCTGAGATTTGATTAGAT
1 AAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCTAATGTGGCTGAGATTTGATTATAT
* * * * *
27580 GAATATGGATATCTCAAGGAGTCTTGGCA-CCAAAAATCAGGCATAACTGAGTCAGGCTCCTAAA
66 GAATATAGATATTTCAAGAAGTCTTGG-AGCCAAAAATCATGCAAAACTGAG-CAGGCTCCTAAA
* * *
27644 ACGCATTTTTTAGCCAAAAACTGTGATGATTATTAGACGATTTCGGCTAAAATTACGTAAAAATT
129 ACGCATTTTTTAGCCAAAAACCGTGATGATTATTAGACGATTTCGGCTAAAATTATGCAAAAATT
*
27709 GACCCGAAAGATATTTCCTCAATTTTTGGCTAAAATACTCATAAAAAATATATAATTCAACCCCA
194 GACCCGAAAGAT-TTTCCTCAATTTTTGGCTAAAATACTCATAAAAAATATATAATTCAACGCCA
* * *
27774 AAAATATTGAAGGGCTTTTTACG-TTTCTAATATCGTTTTTCCTATTTTTTCCAAATTAATTTCT
258 AAAA-ATTGGAGGGCTTTTTACGCTTT-TAATATCATTTTTCATA-TTTTTCCAAATTAATTTCT
27838 AATTAAATCG
320 AATTAAATCG
* * *
27848 AAACAAGATTTAGATGCTCGTAAAAACAAACCCTTAAGTCTAATGTGGCTGAGATTTGATTATAT
1 AAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCTAATGTGGCTGAGATTTGATTATAT
* * * *
27913 GAATATAGATATTTCAAGTAGTCTTGGAGCCAAAAATCATGCAAAATTGAGCCGG-TACCTAGAA
66 GAATATAGATATTTCAAGAAGTCTTGGAGCCAAAAATCATGCAAAACTGAGCAGGCT-CCTAAAA
* * * * * *
27977 CG--TGGTTTTAGCAAAAAACCGTGATGGTTTGTTAGTACACAATTTCGGCTAAAATTTTGCAAA
130 CGCAT-TTTTTAGCCAAAAACCGTGAT-GATTATTAG---ACGATTTCGGCTAAAATTATGCAAA
* * * * *
28040 AATTGACACGAAAGATTTCTTCTCTATTTTTGACTAAAATACTCAT-AAAAATATATAATTCAAT
190 AATTGACCCGAAAGATTT-TCCTCAATTTTTGGCTAAAATACTCATAAAAAATATATAATTCAAC
28104 GCCAAAAAAATTGGAGGGCTTTTTACGC
254 GCC-AAAAAATTGGAGGGCTTTTTACGC
28132 ATTTCTTATT
Statistics
Matches: 518, Mismatches: 79, Indels: 34
0.82 0.13 0.05
Matches are distributed among these distances:
329 21 0.04
330 76 0.15
331 33 0.06
332 159 0.31
333 126 0.24
334 38 0.07
335 65 0.13
ACGTcount: A:0.37, C:0.16, G:0.14, T:0.32
Consensus pattern (329 bp):
AAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCTAATGTGGCTGAGATTTGATTATAT
GAATATAGATATTTCAAGAAGTCTTGGAGCCAAAAATCATGCAAAACTGAGCAGGCTCCTAAAAC
GCATTTTTTAGCCAAAAACCGTGATGATTATTAGACGATTTCGGCTAAAATTATGCAAAAATTGA
CCCGAAAGATTTTCCTCAATTTTTGGCTAAAATACTCATAAAAAATATATAATTCAACGCCAAAA
AATTGGAGGGCTTTTTACGCTTTTAATATCATTTTTCATATTTTTCCAAATTAATTTCTAATTAA
ATCG
Found at i:28553 original size:15 final size:16
Alignment explanation
Indices: 28535--28564 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
28525 ATAAATAATA
28535 ATATTATAAT-TAAAT
1 ATATTATAATCTAAAT
28550 ATATTATAATCTAAA
1 ATATTATAATCTAAA
28565 AATAATTATT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.43
Consensus pattern (16 bp):
ATATTATAATCTAAAT
Done.