Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014066.1 Corchorus capsularis cultivar CVL-1 contig14087, 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: 178136
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:2219 original size:3 final size:3
Alignment explanation
Indices: 2211--2236 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
2201 ATCACATCAC
2211 ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA AT
2237 TTTATTAATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
ATA
Found at i:10728 original size:338 final size:332
Alignment explanation
Indices: 9828--10915 Score: 1119
Period size: 337 Copynumber: 3.3 Consensus size: 332
9818 AAAGCGATAT
* * * * *
9828 TAGAAGCATGAGAAGCTCTTC-ATTCTTTTTGGCGTAT-AGTTATATATTTTTTATTAGTATTGT
1 TAGAAGCGTGAGAAGCCCTTCAATT-TTTTTGGCGT-TGAATTATATATTTTTTA-TAATATCGT
* * * *
9891 GGCCCAAAATGGAGGAGAAA-TTTCTCGGATCAATTTTTGCAAAATTTTAGCTGAAATCGTATAC
63 GGCCAAAAATTGAGGAGAAATTTTCTCGGGTCAATTTTTGCAAAATTTTAACTGAAATCGTATAC
* * * * * * *
9955 TAACCATCATGGTTTTTGATTAAAAACGTGTTCTGGAGCCCTGACTCAGTTTTGCACAATTTTTG
128 TAACTATCACGATTTTTGACTAAAAACGCGTTCTGGAGTCCTGGCTCAGTTTTGCACAATTTTTG
* * **
10020 GCGCCAAGTCTCAATGAAA-ATCTGTATCCAT-TAACCAAATCTTACCCACATTGGATTTAAACA
193 GCGCCAAGTCTCATTGAAATATCTATATCCATCTAACCAAATCTTACCCACATTGGATTTAAGGA
* * * ** * *
10083 TTTATTTTTACGAGCATATGAATCATGTTTCGATTCAATTAGAAATTAATTCGGTAAAAATAGGA
258 TTTGTTTTTACGAGCATATCAATCACGAATCGATTCAATTAGAAATTAATTCGGAAAAAATAGAA
*
10148 AAAACAATAT
323 AAAACAATAC
* * **
10158 TAGAAGCGTGA-ATAGCCTTTCAATATTTTTGGTATTGAATTATATATATTCTTTATAAGTATCG
1 TAGAAGCGTGAGA-AGCCCTTCAATTTTTTTGGCGTTGAATTATATAT-TT-TTTATAA-TATCG
* * *
10222 TGGTCAAAAATTGAGGA-AAATTCTT-TCGGGTCAATTTTTACAAAA-TTTAAGCCGAAATCGTA
62 TGGCCAAAAATTGAGGAGAAATT-TTCTCGGGTCAATTTTTGCAAAATTTTAA-CTGAAATCGTA
* * * * * * *
10284 TACTAATTATCACGGTTTTTTTTG-CTAAAAACGCGTTCCGGGGCTCC-AGCTCAGTTTTGTATA
125 TACTAACTATCAC-G--ATTTTTGACTAAAAACGCGTTCTGGAG-TCCTGGCTCAGTTTTGCACA
* ** * * * *
10347 ATTTTTGGCGCCAAGACTCATTGAAATATCTATATTTATCTAACGAAATCTCAGCCAGATTGGAT
186 ATTTTTGGCGCCAAGTCTCATTGAAATATCTATATCCATCTAACCAAATCTTACCCACATTGGAT
* *
10412 TTAAGGATTTTGTTTTTACGAGCATCTCAATC-CGAAATCGATTTAATTAGAAATTAATTCGGAA
251 TTAAGGA-TTTGTTTTTACGAGCATATCAATCACG-AATCGATTCAATTAGAAATTAATTCGGAA
10476 AAAATAGAAAAAAAAACAATAC
314 AAAATAG---AAAAAACAATAC
*
10498 TAGAAGCGTGAGAAGCCCTTCAACTTTTTTTGGCGTTGAATTATATATTTTTTATGAATATGGTG
1 TAGAAGCGTGAGAAGCCCTTCAA-TTTTTTTGGCGTTGAATTATATATTTTTTAT-AATATCGTG
** * *
10563 GCCGGAAATTGAGGAGAAATTTTCTCGGGTCAATTTTTGCAAAATTTTAACTGAAACCGTGTACT
64 GCCAAAAATTGAGGAGAAATTTTCTCGGGTCAATTTTTGCAAAATTTTAACTGAAATCGTATACT
* *
10628 AACTATCACGATTTTTGACTAAAAACGCGTTCTAGAGTCCTGGCTCAGTTTTGCACAATTTTAGG
129 AACTATCACGATTTTTGACTAAAAACGCGTTCTGGAGTCCTGGCTCAGTTTTGCACAATTTTTGG
* *
10693 CGTCAAGTCTCATTGAAATATCTATATCCATCTAACCAAACCTTACCCACATTGGATTTAAGGAT
194 CGCCAAGTCTCATTGAAATATCTATATCCATCTAACCAAATCTTACCCACATTGGATTTAAGGAT
* * ** * * * * *
10758 TTGTTTTTACGAGCATATTAATCATGTTTCAATTC-ATTAAGGAACTAATTTGGAAAAAATAGGA
259 TTGTTTTTACGAGCATATCAATCACGAATCGATTCAATT-AGAAATTAATTCGGAAAAAATAGAA
* *
10822 AAAACGATAT
323 AAAACAATAC
* * * * * * *
10832 TAGAAG-G-AAGAATAGCCTTTCAATCTTTTTGGTGTTGAATTATATAATTTCTATGATTATCGT
1 TAGAAGCGTGAG-A-AGCCCTTCAATTTTTTTGGCGTTGAATTATATATTTTTTAT-AATATCGT
* * *
10895 AGCCAAATATTTAGGA-AAATT
63 GGCCAAAAATTGAGGAGAAATT
10916 CTTTTGAGTC
Statistics
Matches: 620, Mismatches: 106, Indels: 62
0.79 0.13 0.08
Matches are distributed among these distances:
329 2 0.00
330 33 0.05
331 13 0.02
332 68 0.11
333 50 0.08
334 75 0.12
335 17 0.03
336 30 0.05
337 109 0.18
338 92 0.15
339 26 0.04
340 78 0.13
341 27 0.04
ACGTcount: A:0.33, C:0.15, G:0.16, T:0.36
Consensus pattern (332 bp):
TAGAAGCGTGAGAAGCCCTTCAATTTTTTTGGCGTTGAATTATATATTTTTTATAATATCGTGGC
CAAAAATTGAGGAGAAATTTTCTCGGGTCAATTTTTGCAAAATTTTAACTGAAATCGTATACTAA
CTATCACGATTTTTGACTAAAAACGCGTTCTGGAGTCCTGGCTCAGTTTTGCACAATTTTTGGCG
CCAAGTCTCATTGAAATATCTATATCCATCTAACCAAATCTTACCCACATTGGATTTAAGGATTT
GTTTTTACGAGCATATCAATCACGAATCGATTCAATTAGAAATTAATTCGGAAAAAATAGAAAAA
ACAATAC
Found at i:11547 original size:335 final size:330
Alignment explanation
Indices: 10935--11960 Score: 1162
Period size: 335 Copynumber: 3.1 Consensus size: 330
10925 CAATTCTCAG
** * *
10935 CCACATTAAATTTAAGGATTTGTTTGTACGAGCATCTCAATCCGATTTCGATTTAATTACAAATT
1 CCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTCAATCCG-TTTCGATTTAATTAGAAATT
*
11000 AATTCGGAAAAATAGAAAAAAAAAACAATATTAGAAGCATGAGA-AGCCCTTCAATCTTTTTGGC
65 AATTCGGAAAAATAG-AAAAAAAAACAATATTAGAAGC--GAGACAGCCCTTCAATCTTTTTGGT
* * * **
11064 ATTGAATTATATATTTTTTATGAATATGGTGGCAAGAAATTGAGGAGAAATTTTCTCGGGTCAAT
127 GTTGAATTATATATTTTTTATGAATATAGTGCCAA-AAATTGAGGAGAAATTTT-TCAAGTCAAT
* * *
11129 TTTTGCAAAATTTTAGCTGAAATTGTGTACTAACCATCACAGTTTTTTACTAAAAACGCGTT-TT
190 TTTTGCAAAATTTTAGCTGAAATCGTGTACT-ACCATCACAGTTTTTGACTAAAAACGCGTTCGT
* * * *
11193 AGAGCCTCGGCTCAGTTTTGCACGATTTTTTTGTGCCAAGTCTCACTGAAATATCTATATCCTTC
254 -GAGCCCCGGCTCAGTTTTGCACGA-TTTTTTGCGCCAAGTCTCATTGAAATATCTATATCCATC
*
11258 TAACCAAATTTTAC
317 TAACCAAATCTTAC
* * * * * *
11272 CCACATTGGATTTAAGGATTTGTTTTTACGAGAATATGAATCATGTTTCGATTCAATTAGGAATT
1 CCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTCAATC-CGTTTCGATTTAATTAGAAATT
* * **
11337 AATTC-GAAAAA-A-AATAGGAAAAACGATATTAGAAGCGAGACTAGCATTTCAATCTTTTTGGT
65 AATTCGGAAAAATAGAA-A-AAAAAACAATATTAGAAGCGAGAC-AGCCCTTCAATCTTTTTGGT
* * * * *
11399 GTTGAATTATATATTTTCTATGAGTTTCGTAGCCAAAAATTGAGGA-AAATTCTTTCAATTCAAT
127 GTTGAATTATATATTTTTTATGAATATAGT-GCCAAAAATTGAGGAGAAATT-TTTCAAGTCAAT
* * * **
11463 TTTTACAAAATTTTAGCCGAAATCGGTGTACTAGCCATCACAGTTTTTGGCTAAAAGTGCGTTCC
190 TTTTGCAAAATTTTAGCTGAAATC-GTGTACTA-CCATCACAGTTTTTGACTAAAAACGCGTT-C
* * * ** **
11528 GTG-GCCCCTGTTCAGTTTTGCATGATTTTTTGCGCCAAAACTCATTGAAATATCTATATTAATC
252 GTGAGCCCCGGCTCAGTTTTGCACGATTTTTTGCGCCAAGTCTCATTGAAATATCTATATCCATC
** * *
11592 TAAAGAAATCTCAG
317 TAACCAAATCTTAC
*
11606 CCACATTGGATTTAAGGATTTGTTTTTGCGAGCATCTCAATCCGGTTTCGATTTAATTAGAAATT
1 CCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTCAATCC-GTTTCGATTTAATTAGAAATT
* *
11671 AATTCGGAAAAATAGAAAAAAAAATAATATTAGAAGCGTG-CGAAGCCCTTCAATCTTTTTGGTG
65 AATTCGGAAAAATAGAAAAAAAAACAATATTAGAAGCGAGAC--AGCCCTTCAATCTTTTTGGTG
**
11735 TTGAATTATATATTTTTTATGAATATAGTGGCCGGAAATTGAGGAGAAATTTTTCAAGTCAATTT
128 TTGAATTATATATTTTTTATGAATATAGT-GCCAAAAATTGAGGAGAAATTTTTCAAGTCAATTT
* * *
11800 TTGCAAAATTTTAGCTGAAATC--GTA-TA-CTTTACGGTTTTTGACTAAAAACGCGTTC-TGGA
192 TTGCAAAATTTTAGCTGAAATCGTGTACTACCATCACAGTTTTTGACTAAAAACGCGTTCGT-GA
* * * * * *
11860 GTCCCGGCTCAATTTTGCACAATTTTTGGCGCCAAGTCTGATTGAAATATTTATATCCATCTAAC
256 GCCCCGGCTCAGTTTTGCACGATTTTTTGCGCCAAGTCTCATTGAAATATCTATATCCATCTAAC
11925 CAAATCTTAC
321 CAAATCTTAC
**
11935 TTACATTGGATTTAAGGATTT-TTTTT
1 CCACATTGGATTTAAGGATTTGTTTTT
11961 GTATCGTGGC
Statistics
Matches: 573, Mismatches: 97, Indels: 47
0.80 0.14 0.07
Matches are distributed among these distances:
327 1 0.00
328 7 0.01
329 99 0.17
331 2 0.00
332 3 0.01
333 6 0.01
334 139 0.24
335 236 0.41
336 18 0.03
337 61 0.11
338 1 0.00
ACGTcount: A:0.33, C:0.15, G:0.16, T:0.36
Consensus pattern (330 bp):
CCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTCAATCCGTTTCGATTTAATTAGAAATTA
ATTCGGAAAAATAGAAAAAAAAACAATATTAGAAGCGAGACAGCCCTTCAATCTTTTTGGTGTTG
AATTATATATTTTTTATGAATATAGTGCCAAAAATTGAGGAGAAATTTTTCAAGTCAATTTTTGC
AAAATTTTAGCTGAAATCGTGTACTACCATCACAGTTTTTGACTAAAAACGCGTTCGTGAGCCCC
GGCTCAGTTTTGCACGATTTTTTGCGCCAAGTCTCATTGAAATATCTATATCCATCTAACCAAAT
CTTAC
Found at i:16614 original size:41 final size:41
Alignment explanation
Indices: 16569--16656 Score: 158
Period size: 41 Copynumber: 2.1 Consensus size: 41
16559 TTATATCCGT
*
16569 ATCCGCCAACTATATGCCTATTTTTTAAAAGCAATATCCAA
1 ATCCGCCAACTATATGCCTATTTTTTAAAAACAATATCCAA
*
16610 ATCCGCCAGCTATATGCCTATTTTTTAAAAACAATATCCAA
1 ATCCGCCAACTATATGCCTATTTTTTAAAAACAATATCCAA
16651 ATCCGC
1 ATCCGC
16657 TCCGCCACTG
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 45 1.00
ACGTcount: A:0.35, C:0.26, G:0.08, T:0.31
Consensus pattern (41 bp):
ATCCGCCAACTATATGCCTATTTTTTAAAAACAATATCCAA
Found at i:28168 original size:19 final size:19
Alignment explanation
Indices: 28136--28182 Score: 64
Period size: 19 Copynumber: 2.6 Consensus size: 19
28126 TCTATCGGGT
28136 TCAG-TCAG-TTTTTTGAG
1 TCAGTTCAGTTTTTTTGAG
*
28153 TTAGTTCAGTTTTTTTGAG
1 TCAGTTCAGTTTTTTTGAG
28172 TCAGTT-AGTTT
1 TCAGTTCAGTTT
28183 GAGTCTGAGT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
17 3 0.12
18 9 0.35
19 14 0.54
ACGTcount: A:0.17, C:0.09, G:0.21, T:0.53
Consensus pattern (19 bp):
TCAGTTCAGTTTTTTTGAG
Found at i:29672 original size:35 final size:35
Alignment explanation
Indices: 29632--29701 Score: 113
Period size: 35 Copynumber: 2.0 Consensus size: 35
29622 ATCTTTTACT
29632 TTTCATCACCCTTGTTTTTACAAGGGGTAATCTTG
1 TTTCATCACCCTTGTTTTTACAAGGGGTAATCTTG
* * *
29667 TTTCATCACCCTTGTTTTTATAAGGTGTACTCTTG
1 TTTCATCACCCTTGTTTTTACAAGGGGTAATCTTG
29702 CTTCGGCAAT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
35 32 1.00
ACGTcount: A:0.19, C:0.20, G:0.16, T:0.46
Consensus pattern (35 bp):
TTTCATCACCCTTGTTTTTACAAGGGGTAATCTTG
Found at i:30565 original size:17 final size:17
Alignment explanation
Indices: 30537--30577 Score: 75
Period size: 17 Copynumber: 2.5 Consensus size: 17
30527 CATTGTGCTG
30537 CTATTT-TATTTACTTT
1 CTATTTCTATTTACTTT
30553 CTATTTCTATTTACTTT
1 CTATTTCTATTTACTTT
30570 CTATTTCT
1 CTATTTCT
30578 CCAGTGTGAT
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
16 6 0.25
17 18 0.75
ACGTcount: A:0.17, C:0.17, G:0.00, T:0.66
Consensus pattern (17 bp):
CTATTTCTATTTACTTT
Found at i:37735 original size:12 final size:12
Alignment explanation
Indices: 37720--37744 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
37710 CCATTGTCGA
37720 TAGCTAAAAAGT
1 TAGCTAAAAAGT
37732 TAGCTAAAAAGT
1 TAGCTAAAAAGT
37744 T
1 T
37745 GAAGCTTGTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.48, C:0.08, G:0.16, T:0.28
Consensus pattern (12 bp):
TAGCTAAAAAGT
Found at i:43650 original size:34 final size:34
Alignment explanation
Indices: 43591--43971 Score: 471
Period size: 34 Copynumber: 10.9 Consensus size: 34
43581 GTTTTATCGG
*
43591 CCCTGCCCAGTCGG-T-T-ATAATAACTGGAAGA
1 CCCTGCCCAGTGGGTTGTGATAATAACTGGAAGA
*
43622 TCCTGCCCAGTGGGTTGTGATAATAACTGGAAGA
1 CCCTGCCCAGTGGGTTGTGATAATAACTGGAAGA
* *
43656 CCCTGCCCAGTGGGTTGTGAAAATAACTAGAAGA
1 CCCTGCCCAGTGGGTTGTGATAATAACTGGAAGA
43690 CCCTGCCCAGTGGGTTGTGATTTGTGATAATAACTGGAAGA
1 CCCTGCCCAGT--G--G-G--TTGTGATAATAACTGGAAGA
* *
43731 CCTTGCCCAGTGGGTTGTGAAAATAACTGGAAGA
1 CCCTGCCCAGTGGGTTGTGATAATAACTGGAAGA
43765 CCCTGCCCAGTGGGTTGTGATAATAACTGGAAGA
1 CCCTGCCCAGTGGGTTGTGATAATAACTGGAAGA
* * * *
43799 CCCTGCACAGTGGGTTGAGATGATAACTAGAAGA
1 CCCTGCCCAGTGGGTTGTGATAATAACTGGAAGA
*
43833 CCCTGCCCAGTGGGTTGTGATAGTAACTGGAAGA
1 CCCTGCCCAGTGGGTTGTGATAATAACTGGAAGA
**
43867 CCCTGACCTTGCCCAGTGGGTTGTGATAGCAACTGGAAGA
1 --C---CC-TGCCCAGTGGGTTGTGATAATAACTGGAAGA
*
43907 CCCTGCCCAGTGGGTTGAGATAATAACTGGAAGA
1 CCCTGCCCAGTGGGTTGTGATAATAACTGGAAGA
* **
43941 CCATATCCAGTGGGTTGTGATAATAACTGGA
1 CCCTGCCCAGTGGGTTGTGATAATAACTGGA
43972 GGGCAGCCCT
Statistics
Matches: 306, Mismatches: 28, Indels: 29
0.84 0.08 0.08
Matches are distributed among these distances:
31 12 0.04
32 1 0.00
33 1 0.00
34 222 0.73
35 2 0.01
36 3 0.01
37 1 0.00
38 2 0.01
39 4 0.01
40 30 0.10
41 28 0.09
ACGTcount: A:0.28, C:0.20, G:0.29, T:0.24
Consensus pattern (34 bp):
CCCTGCCCAGTGGGTTGTGATAATAACTGGAAGA
Found at i:44006 original size:108 final size:105
Alignment explanation
Indices: 43607--43983 Score: 426
Period size: 108 Copynumber: 3.6 Consensus size: 105
43597 CCAGTCGGTT
43607 ATAATAACTGGAAGATCC-TGCCCAGTGGGTTGTGATAATAACTGGA-AG-A-CCCTGCCCAGTG
1 ATAATAACTGGAAGA-CCATGCCCAGTGGGTTGTGATAATAACTGGAGAGCAGCCCTGCCCAGTG
* ** * *
43668 GGTTGTGAAAATAACTAGAAGACCCTGCCCAGTGGGTTGTGATTTGTG
65 GGTTGTGATAGCAACTGGAAGACCCTGCACAGTGGG-T-TGA-----G
* *
43716 ATAATAACTGGAAGACCTTGCCCAGTGGGTTGTGAAAATAACTGGA-AG-A-CCCTGCCCAGTGG
1 ATAATAACTGGAAGACCATGCCCAGTGGGTTGTGATAATAACTGGAGAGCAGCCCTGCCCAGTGG
**
43778 GTTGTGATAATAACTGGAAGACCCTGCACAGTGGGTTGAG
66 GTTGTGATAGCAACTGGAAGACCCTGCACAGTGGGTTGAG
* * * * * * *
43818 ATGATAACTAGAAGACCCTGCCCAGTGGGTTGTGATAGTAACTGGAAGACCCTGACCTTGCCCAG
1 ATAATAACTGGAAGACCATGCCCAGTGGGTTGTGATAATAACTGG-AGA-GCAG-CCCTGCCCAG
*
43883 TGGGTTGTGATAGCAACTGGAAGACCCTGCCCAGTGGGTTGAG
63 TGGGTTGTGATAGCAACTGGAAGACCCTGCACAGTGGGTTGAG
** *
43926 ATAATAACTGGAAGACCATATCCAGTGGGTTGTGATAATAACTGGAGGGCAGCCCTGC
1 ATAATAACTGGAAGACCATGCCCAGTGGGTTGTGATAATAACTGGAGAGCAGCCCTGC
43984 TAATGGGTTA
Statistics
Matches: 236, Mismatches: 25, Indels: 18
0.85 0.09 0.06
Matches are distributed among these distances:
102 41 0.17
103 1 0.00
104 1 0.00
105 5 0.02
106 2 0.01
107 5 0.02
108 91 0.39
109 90 0.38
ACGTcount: A:0.28, C:0.20, G:0.29, T:0.23
Consensus pattern (105 bp):
ATAATAACTGGAAGACCATGCCCAGTGGGTTGTGATAATAACTGGAGAGCAGCCCTGCCCAGTGG
GTTGTGATAGCAACTGGAAGACCCTGCACAGTGGGTTGAG
Found at i:51928 original size:15 final size:15
Alignment explanation
Indices: 51905--51934 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
51895 ATCGGTTGAA
*
51905 ATATTGTGTATCGTG
1 ATATCGTGTATCGTG
51920 ATATCGTGTATCGTG
1 ATATCGTGTATCGTG
51935 GCAGCCTGAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.20, C:0.10, G:0.27, T:0.43
Consensus pattern (15 bp):
ATATCGTGTATCGTG
Found at i:67482 original size:17 final size:17
Alignment explanation
Indices: 67442--67482 Score: 50
Period size: 15 Copynumber: 2.5 Consensus size: 17
67432 TGTCATTCAT
* *
67442 AATACAGAAGGAAAAAA
1 AATACACAAAGAAAAAA
67459 AA-A-ACAAAGAAAAAA
1 AATACACAAAGAAAAAA
67474 AATACACAA
1 AATACACAA
67483 CAACAACAAC
Statistics
Matches: 20, Mismatches: 2, Indels: 4
0.77 0.08 0.15
Matches are distributed among these distances:
15 12 0.60
16 2 0.10
17 6 0.30
ACGTcount: A:0.76, C:0.10, G:0.10, T:0.05
Consensus pattern (17 bp):
AATACACAAAGAAAAAA
Found at i:73141 original size:2 final size:2
Alignment explanation
Indices: 73134--73159 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
73124 TAGGGTTAAT
73134 GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA
73160 TACGACGTCG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:74554 original size:24 final size:23
Alignment explanation
Indices: 74511--74555 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
74501 TATGTTACTT
*
74511 TTTTTTTTTACCAAATCAAATGG
1 TTTTTTTTTACCAAACCAAATGG
*
74534 TTTTTTTTTGCCATAACCAAAT
1 TTTTTTTTTACCA-AACCAAAT
74556 CAAATGGTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 12 0.63
24 7 0.37
ACGTcount: A:0.29, C:0.16, G:0.07, T:0.49
Consensus pattern (23 bp):
TTTTTTTTTACCAAACCAAATGG
Found at i:74684 original size:47 final size:49
Alignment explanation
Indices: 74549--74696 Score: 174
Period size: 49 Copynumber: 2.9 Consensus size: 49
74539 TTTTGCCATA
* *
74549 ACCAAATCAAATGGTTATCCCTAATATTTTATATTTTATATGTTACTTCTTTTTTT
1 ACCAAATCAAATGGTTATCACT-A-A-TTT-T-TTTTATATGTTAC-T-TTTTGTT
* *
74605 ACCCAATCAAATGGTTGTCACTAATTTTTTTTATATGTTACTTTTTGTT
1 ACCAAATCAAATGGTTATCACTAATTTTTTTTATATGTTACTTTTTGTT
*
74654 ACCAAATCAAATGGTTATCTCT-A-TTTTTTTATATGTTACTTTT
1 ACCAAATCAAATGGTTATCACTAATTTTTTTTATATGTTACTTTT
74697 AGAGAATATA
Statistics
Matches: 85, Mismatches: 7, Indels: 9
0.84 0.07 0.09
Matches are distributed among these distances:
47 20 0.24
48 1 0.01
49 25 0.29
50 1 0.01
51 13 0.15
52 1 0.01
53 3 0.04
54 1 0.01
55 1 0.01
56 19 0.22
ACGTcount: A:0.27, C:0.14, G:0.07, T:0.51
Consensus pattern (49 bp):
ACCAAATCAAATGGTTATCACTAATTTTTTTTATATGTTACTTTTTGTT
Found at i:75380 original size:78 final size:78
Alignment explanation
Indices: 75288--75534 Score: 397
Period size: 78 Copynumber: 3.2 Consensus size: 78
75278 GTTTTTTAAT
*
75288 TAAAATAGTAAAATGGTAAAATATAATAGTAATAAAGATATTAGATTTAATTATATAAAAATAGA
1 TAAAATAGTAAAATGGTAAAATATAATAGTTATAAAGATATTAGATTTAATTATATAAAAATAGA
*
75353 GTTTTTAGTTGAG
66 GTTTTTAGTTGAA
* * *
75366 TAAGATAGTAAAATGGTAAAATATAATAGTTATAAGGATATTAGATTCAATTATATAAAAATAGA
1 TAAAATAGTAAAATGGTAAAATATAATAGTTATAAAGATATTAGATTTAATTATATAAAAATAGA
75431 GTTTTTAGTTGAA
66 GTTTTTAGTTGAA
* ** *
75444 TAAAATAGTAAAATGGTAAAATAAAATAGTTATAAAGATATTATTTTTAATTAAATAAAAATAGA
1 TAAAATAGTAAAATGGTAAAATATAATAGTTATAAAGATATTAGATTTAATTATATAAAAATAGA
75509 GTTTTTAGTTGAA
66 GTTTTTAGTTGAA
75522 TAAAACTA-TAAAA
1 TAAAA-TAGTAAAA
75535 ACATTTAATG
Statistics
Matches: 156, Mismatches: 12, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
78 154 0.99
79 2 0.01
ACGTcount: A:0.51, C:0.01, G:0.13, T:0.36
Consensus pattern (78 bp):
TAAAATAGTAAAATGGTAAAATATAATAGTTATAAAGATATTAGATTTAATTATATAAAAATAGA
GTTTTTAGTTGAA
Found at i:77055 original size:21 final size:21
Alignment explanation
Indices: 77029--77071 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
77019 ATTAGCTGGA
77029 TTGCTAAACACCGCCCCATTT
1 TTGCTAAACACCGCCCCATTT
** *
77050 TTGCTATTCACTGCCCCATTT
1 TTGCTAAACACCGCCCCATTT
77071 T
1 T
77072 GACGCTTTTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.19, C:0.35, G:0.09, T:0.37
Consensus pattern (21 bp):
TTGCTAAACACCGCCCCATTT
Found at i:77474 original size:33 final size:33
Alignment explanation
Indices: 77427--77519 Score: 116
Period size: 33 Copynumber: 2.8 Consensus size: 33
77417 GACGGCTGAG
*
77427 CCATGGCCAAGCCGCCCTCCTGGGGCGGCACTA
1 CCATGGCCAGGCCGCCCTCCTGGGGCGGCACTA
*
77460 CCATGGCCAGGCCG-CCTCCCTGGGGCGGCCCTA
1 CCATGGCCAGGCCGCCCT-CCTGGGGCGGCACTA
** * *
77493 CCATGGATAGACCGCCCCCCTGGGGCG
1 CCATGGCCAGGCCGCCCTCCTGGGGCG
77520 ACACCAGTAC
Statistics
Matches: 52, Mismatches: 6, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
32 3 0.06
33 47 0.90
34 2 0.04
ACGTcount: A:0.13, C:0.43, G:0.32, T:0.12
Consensus pattern (33 bp):
CCATGGCCAGGCCGCCCTCCTGGGGCGGCACTA
Found at i:77617 original size:32 final size:32
Alignment explanation
Indices: 77567--77677 Score: 168
Period size: 32 Copynumber: 3.5 Consensus size: 32
77557 GCCTTGCCGC
77567 CCTAGTGGGGCGGCTAGCCGTGGCAGAGCCAT
1 CCTAGTGGGGCGGCTAGCCGTGGCAGAGCCAT
* * *
77599 CCTAGTGGGACGGTTAGCCGTGGCAGAGCCGT
1 CCTAGTGGGGCGGCTAGCCGTGGCAGAGCCAT
* *
77631 CCTAGTGGGGCGGCTAGCCATGGCAAAGCCAT
1 CCTAGTGGGGCGGCTAGCCGTGGCAGAGCCAT
*
77663 CCTAGTGGGGAGGCT
1 CCTAGTGGGGCGGCT
77678 CCGCGTGGCT
Statistics
Matches: 70, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
32 70 1.00
ACGTcount: A:0.17, C:0.26, G:0.40, T:0.17
Consensus pattern (32 bp):
CCTAGTGGGGCGGCTAGCCGTGGCAGAGCCAT
Found at i:88172 original size:31 final size:31
Alignment explanation
Indices: 88134--88197 Score: 110
Period size: 31 Copynumber: 2.1 Consensus size: 31
88124 GTGTCATTAG
*
88134 AAAACTTACCATAATTTCTAAAATCATATTC
1 AAAACTTACCATAATTTCTAAAACCATATTC
*
88165 AAAACTTACCATAATTTCTAAAACCCTATTC
1 AAAACTTACCATAATTTCTAAAACCATATTC
88196 AA
1 AA
88198 TAATAGCCTA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.45, C:0.22, G:0.00, T:0.33
Consensus pattern (31 bp):
AAAACTTACCATAATTTCTAAAACCATATTC
Found at i:96004 original size:13 final size:13
Alignment explanation
Indices: 95986--96028 Score: 56
Period size: 11 Copynumber: 3.5 Consensus size: 13
95976 ATTTTTAAAA
95986 TAAAAATAATAAT
1 TAAAAATAATAAT
*
95999 TAAAAAT--TATT
1 TAAAAATAATAAT
96010 TAAAAATAA-AAT
1 TAAAAATAATAAT
96022 TAAAAAT
1 TAAAAAT
96029 TAAAACACAC
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
11 10 0.38
12 9 0.35
13 7 0.27
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (13 bp):
TAAAAATAATAAT
Found at i:96018 original size:30 final size:28
Alignment explanation
Indices: 95975--96033 Score: 82
Period size: 30 Copynumber: 2.0 Consensus size: 28
95965 ATCTATATTT
*
95975 AATTTTTAAAATAAAAATAATAATTAAA
1 AATTTTTAAAATAAAAATAAAAATTAAA
*
96003 AATTATTTAAAAATAAAATTAAAAATTAAA
1 AATT-TTT-AAAATAAAAATAAAAATTAAA
96033 A
1 A
96034 CACACATAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
28 4 0.15
29 3 0.11
30 20 0.74
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (28 bp):
AATTTTTAAAATAAAAATAAAAATTAAA
Found at i:96022 original size:23 final size:24
Alignment explanation
Indices: 95986--96030 Score: 83
Period size: 23 Copynumber: 1.9 Consensus size: 24
95976 ATTTTTAAAA
95986 TAAAAATAATAATTAAAAATTATT
1 TAAAAATAATAATTAAAAATTATT
96010 TAAAAATAA-AATTAAAAATTA
1 TAAAAATAATAATTAAAAATTA
96031 AAACACACAT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
23 12 0.57
24 9 0.43
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (24 bp):
TAAAAATAATAATTAAAAATTATT
Found at i:96032 original size:13 final size:13
Alignment explanation
Indices: 95980--96033 Score: 55
Period size: 11 Copynumber: 4.5 Consensus size: 13
95970 TATTTAATTT
95980 TTAAAA-TAAAAA
1 TTAAAATTAAAAA
95992 -TAATAATTAAAAA
1 TTAA-AATTAAAAA
*
96005 TT--ATTTAAAAA
1 TTAAAATTAAAAA
96016 -TAAAATTAAAAA
1 TTAAAATTAAAAA
96028 TTAAAA
1 TTAAAA
96034 CACACATAAT
Statistics
Matches: 34, Mismatches: 2, Indels: 11
0.72 0.04 0.23
Matches are distributed among these distances:
10 1 0.03
11 11 0.32
12 10 0.29
13 11 0.32
14 1 0.03
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (13 bp):
TTAAAATTAAAAA
Found at i:96821 original size:167 final size:166
Alignment explanation
Indices: 96433--96885 Score: 547
Period size: 167 Copynumber: 2.7 Consensus size: 166
96423 GAGTCCATTT
* *
96433 GTCAATTGAGAAATGACAAAAAAAAACTTTAGTTATTTAATCCCCTCAAGAATCAAAAGTTAGGA
1 GTCAATTGAGAAATGAC---CAAAAA-GTTAGTTATTTAATCCCCTCAAGAATCAAAAGTTAGGA
* * ** *
96498 CATTTAAGTAATCTGCTAAGTAGGTAAAGACGAAAAAGATTAGTT-T-TCAAGCT-CATCATCAA
62 CATTTAAGTAATCTGCTAAGTAGGAAAAGACGAAAAAAATTAGTTCTCTC-A-CTCCAAAAGCAA
** * * *
96560 TTCTTGATGGGGATCTTTTATTAATTCCACTACTCTATTCAA
125 GCCTTGATAGGGATCTTTTAGTAATTCCACTACTCTATTAAA
* * * *
96602 GCCCATTGAGAAATGATCAAAAAGATTACTTATTTAATCCCCTCAAGAATCAAAAGTTAGGACAT
1 GTCAATTGAGAAATGACCAAAAAG-TTAGTTATTTAATCCCCTCAAGAATCAAAAGTTAGGACAT
* * *
96667 TTAAGTAATTTGCCAAGTAGGAAAAGACGAAAAAAATAAGTTCTCTCACTCCAAAAGCAAGCCTT
65 TTAAGTAATCTGCTAAGTAGGAAAAGACGAAAAAAATTAGTTCTCTCACTCCAAAAGCAAGCCTT
* *
96732 GGTAGGGATCTTTTAGTAATTCCACTACTTTATTAAA
130 GATAGGGATCTTTTAGTAATTCCACTACTCTATTAAA
* * *
96769 GTCAATTGAGAAATGACCAAAAAGTCTAGTTATTTAATCACATCAAGAATCAAAAGTTAGGGCAT
1 GTCAATTGAGAAATGACCAAAAAGT-TAGTTATTTAATCCCCTCAAGAATCAAAAGTTAGGACAT
* *
96834 TTAAGTAATCGGTTAAGT-GGAAAA-ACATGAAAAAAATTAGTTCTCTCACTCC
65 TTAAGTAATCTGCTAAGTAGGAAAAGAC--GAAAAAAATTAGTTCTCTCACTCC
96886 TCATTAATCC
Statistics
Matches: 244, Mismatches: 33, Indels: 16
0.83 0.11 0.05
Matches are distributed among these distances:
165 2 0.01
166 90 0.37
167 136 0.56
168 2 0.01
169 14 0.06
ACGTcount: A:0.40, C:0.16, G:0.15, T:0.29
Consensus pattern (166 bp):
GTCAATTGAGAAATGACCAAAAAGTTAGTTATTTAATCCCCTCAAGAATCAAAAGTTAGGACATT
TAAGTAATCTGCTAAGTAGGAAAAGACGAAAAAAATTAGTTCTCTCACTCCAAAAGCAAGCCTTG
ATAGGGATCTTTTAGTAATTCCACTACTCTATTAAA
Found at i:106937 original size:13 final size:13
Alignment explanation
Indices: 106921--106954 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
106911 TTAATTAAAA
106921 ATTTTAAAAAATC
1 ATTTTAAAAAATC
**
106934 ATTTTAATTAATC
1 ATTTTAAAAAATC
106947 ATTTTAAA
1 ATTTTAAA
106955 GTTCGATACC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.47, C:0.06, G:0.00, T:0.47
Consensus pattern (13 bp):
ATTTTAAAAAATC
Found at i:107007 original size:19 final size:19
Alignment explanation
Indices: 106983--107022 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
106973 TCGACAGGTA
106983 TATAGCTAATTTTTTTAAT
1 TATAGCTAATTTTTTTAAT
107002 TATAGCTAATTTTTTTAAT
1 TATAGCTAATTTTTTTAAT
107021 TA
1 TA
107023 AACAAATAAT
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:0.33, C:0.05, G:0.05, T:0.57
Consensus pattern (19 bp):
TATAGCTAATTTTTTTAAT
Found at i:119017 original size:2 final size:2
Alignment explanation
Indices: 119010--119049 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
119000 TTTTAAATTT
119010 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
119050 AGGATACATG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:126693 original size:15 final size:15
Alignment explanation
Indices: 126673--126703 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
126663 AGATGTGTAC
126673 ACCTTCAATGCTTTA
1 ACCTTCAATGCTTTA
126688 ACCTTCAATGCTTTA
1 ACCTTCAATGCTTTA
126703 A
1 A
126704 TCAGCTCGCT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.29, C:0.26, G:0.06, T:0.39
Consensus pattern (15 bp):
ACCTTCAATGCTTTA
Found at i:140489 original size:18 final size:21
Alignment explanation
Indices: 140452--140493 Score: 63
Period size: 18 Copynumber: 2.1 Consensus size: 21
140442 TAGCCTTTTA
140452 TTTTATTTTTCTCTTGTTCCC
1 TTTTATTTTTCTCTTGTTCCC
140473 TTTTA-TTTTCT-TT-TTCCC
1 TTTTATTTTTCTCTTGTTCCC
140491 TTT
1 TTT
140494 CTGCTTCTAC
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 8 0.38
19 2 0.10
20 6 0.29
21 5 0.24
ACGTcount: A:0.05, C:0.21, G:0.02, T:0.71
Consensus pattern (21 bp):
TTTTATTTTTCTCTTGTTCCC
Found at i:149989 original size:215 final size:213
Alignment explanation
Indices: 149587--150195 Score: 857
Period size: 215 Copynumber: 2.8 Consensus size: 213
149577 ATTGCTCACG
* * * * *
149587 CTTTTACGACATTTGTAAAGACATTTTTGTCAAACGTCGTTCAATCATGCGACA-TTTTTAACAA
1 CTTTTGCGACGTTTGTAGAGACGTTTTTCTCAAACGTCGTTCAATCATGCGACATTTTTTAAC-A
* * * *
149651 AACTCGTTTTAAGATAGACTTTTCCGACATTTATAACAACGTTTTAAGGAAACGTCG-TTTAATA
65 AACCCGCTTTAAGATGGACTTTTCCGACATTTATAACAACGTTTT-TGGAAACGTCGTTTTAATA
** * * ** * *
149715 AATGACATTTTAATAAACGTCGTAAAATCTTGTGACTCTTTTTTAAAATTGAGTGACGTTTTTTA
129 TGTGACATTTTAATATACGTCGCAGTATCTTGCGACTCTTTTTT-AAATTGAATGACGTTTTTTA
**
149780 ATTGCGTCGCTCTTGTTTATA
193 ATAACGTCGCTCTTGTTTATA
149801 CTTTTGCGACGCTTT-TAGAGACGTTTTTCTCAAACGTCGTTCAATCATGCGACATTTTTTAACA
1 CTTTTGCGACG-TTTGTAGAGACGTTTTTCTCAAACGTCGTTCAATCATGCGACATTTTTTAACA
149865 AACGCCGCTTTAAGATGGACTTTTCCGACATTTATAACAACGTTTTTCGGAAACGTCGTTTTAAT
65 AAC-CCGCTTTAAGATGGACTTTTCCGACATTTATAACAACGTTTTT-GGAAACGTCGTTTTAAT
* *
149930 ATGTGACATTTTAATATACGTCGCAGTACCTTGCAACTCTTTTTTAAATTGAATGACGTTTTTTA
128 ATGTGACATTTTAATATACGTCGCAGTATCTTGCGACTCTTTTTTAAATTGAATGACGTTTTTTA
*
149995 ATAACGTCGCTCTTGTTTATG
193 ATAACGTCGCTCTTGTTTATA
* * ** *
150016 TTTTTGCGACGTTTGTAGAAACGTTTTTCTCAAATATCGTTCAATCATGCGATATTTTTTAACAA
1 CTTTTGCGACGTTTGTAGAGACGTTTTTCTCAAACGTCGTTCAATCATGCGACATTTTTTAACAA
* * *
150081 ACACCGCTTTAAGATGAACTTTTCCAACATTTATAACAAC-ATTTTGGAAACGTCGTTTTAATAT
66 AC-CCGCTTTAAGATGGACTTTTCCGACATTTATAACAACGTTTTTGGAAACGTCGTTTTAATAT
150145 GTGACATTTTAATATACGTCGCAGTATCTTGCGACTCTTTTTTAAATTGAA
130 GTGACATTTTAATATACGTCGCAGTATCTTGCGACTCTTTTTTAAATTGAA
150196 GTTTCTTAAA
Statistics
Matches: 356, Mismatches: 33, Indels: 13
0.89 0.08 0.03
Matches are distributed among these distances:
213 68 0.19
214 56 0.16
215 190 0.53
216 42 0.12
ACGTcount: A:0.29, C:0.17, G:0.14, T:0.40
Consensus pattern (213 bp):
CTTTTGCGACGTTTGTAGAGACGTTTTTCTCAAACGTCGTTCAATCATGCGACATTTTTTAACAA
ACCCGCTTTAAGATGGACTTTTCCGACATTTATAACAACGTTTTTGGAAACGTCGTTTTAATATG
TGACATTTTAATATACGTCGCAGTATCTTGCGACTCTTTTTTAAATTGAATGACGTTTTTTAATA
ACGTCGCTCTTGTTTATA
Found at i:150487 original size:31 final size:31
Alignment explanation
Indices: 150449--150528 Score: 160
Period size: 31 Copynumber: 2.6 Consensus size: 31
150439 GAATTAATTG
150449 AGTAAACTTTACATATATTTTTTCGATACAT
1 AGTAAACTTTACATATATTTTTTCGATACAT
150480 AGTAAACTTTACATATATTTTTTCGATACAT
1 AGTAAACTTTACATATATTTTTTCGATACAT
150511 AGTAAACTTTACATATAT
1 AGTAAACTTTACATATAT
150529 ATATATATAC
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 49 1.00
ACGTcount: A:0.38, C:0.12, G:0.06, T:0.44
Consensus pattern (31 bp):
AGTAAACTTTACATATATTTTTTCGATACAT
Found at i:151975 original size:126 final size:126
Alignment explanation
Indices: 151619--152102 Score: 615
Period size: 126 Copynumber: 3.9 Consensus size: 126
151609 ATTTTAAAGA
* *
151619 GATGTTTAACAAATGTCACG----AATATCTATACCCACGCTTACAAATGTCGGAATACATCAAA
1 GATGTTTAACAAATGTCACGATATAATATCTATACCGACACTTACAAATGTCGGAATACATCAAA
* * ** *
151680 AACAAATGATGTGAAGAAA-TTGTTATGACATTTGCAAACGTCGGTATAATA-TTTTTTAGC
66 ATCAAATGATGTGAA-AAACTTATTCCGACATTTGCAAACGTCGGTATAGTATTTTTTTAGC
** * * * * * * * *
151740 GACATTTAATAAATGTCACAATATAATATCTATACCAACGCTTAC-AATATCGGATTACGTCGAA
1 GATGTTTAACAAATGTCACGATATAATATCTATACCGACACTTACAAATGTCGGAATACATCAAA
*
151804 ATCAAATGATGTG-AAAACTTATTCCGACATTTGCAAACGTCGGTATAGTATTTTTTTAAC
66 ATCAAATGATGTGAAAAACTTATTCCGACATTTGCAAACGTCGGTATAGTATTTTTTTAGC
* * * ** * * *
151864 GATGTTTAGCAAATGTCACGATACAATATCTATATCGACACTTACAAATGTCAAAATATAACGAA
1 GATGTTTAACAAATGTCACGATATAATATCTATACCGACACTTACAAATGTCGGAATACATCAAA
*
151929 ATCAAATGATATGAAAAACTTATTCCGACATTTGCAAACGTCGGTATAGTATTTTTTTAGC
66 ATCAAATGATGTGAAAAACTTATTCCGACATTTGCAAACGTCGGTATAGTATTTTTTTAGC
** *
151990 GATGTTTAGTAAATGTCACGATATAATATCTATACCGACACTTACAAATGTCGGAATACGTCAAA
1 GATGTTTAACAAATGTCACGATATAATATCTATACCGACACTTACAAATGTCGGAATACATCAAA
* *
152055 ATCAAATGATGTGAAAAACTTGTTCCGACATTTGTAAACGTCGGTATA
66 ATCAAATGATGTGAAAAACTTATTCCGACATTTGCAAACGTCGGTATA
152103 ATATATATAT
Statistics
Matches: 310, Mismatches: 45, Indels: 11
0.85 0.12 0.03
Matches are distributed among these distances:
121 16 0.05
122 3 0.01
123 29 0.09
124 71 0.23
125 44 0.14
126 147 0.47
ACGTcount: A:0.38, C:0.16, G:0.15, T:0.31
Consensus pattern (126 bp):
GATGTTTAACAAATGTCACGATATAATATCTATACCGACACTTACAAATGTCGGAATACATCAAA
ATCAAATGATGTGAAAAACTTATTCCGACATTTGCAAACGTCGGTATAGTATTTTTTTAGC
Found at i:156584 original size:2 final size:2
Alignment explanation
Indices: 156577--156607 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
156567 AGATAAAGTG
156577 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 T
156608 TTGTAAAACA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:157851 original size:22 final size:23
Alignment explanation
Indices: 157826--157873 Score: 71
Period size: 24 Copynumber: 2.1 Consensus size: 23
157816 TTGGTGGCTG
157826 GTGAACAAAC-TTATTTTCTGGT
1 GTGAACAAACTTTATTTTCTGGT
*
157848 GTGAACAAACTTTTTTTTTCTGGT
1 GTGAACAAAC-TTTATTTTCTGGT
157872 GT
1 GT
157874 TGGTGTGAGG
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 10 0.43
24 13 0.57
ACGTcount: A:0.23, C:0.12, G:0.19, T:0.46
Consensus pattern (23 bp):
GTGAACAAACTTTATTTTCTGGT
Found at i:164037 original size:21 final size:20
Alignment explanation
Indices: 164013--164077 Score: 87
Period size: 21 Copynumber: 3.2 Consensus size: 20
164003 GGTATAGTAA
164013 AATGTAGTCACTATTTGGTGT
1 AATGTA-TCACTATTTGGTGT
*
164034 AATG-ATCACAATTTGGTGT
1 AATGTATCACTATTTGGTGT
*
164053 AATGGTATCACTTTTTGGTGT
1 AAT-GTATCACTATTTGGTGT
164074 AATG
1 AATG
164078 AAAATTATCA
Statistics
Matches: 39, Mismatches: 3, Indels: 5
0.83 0.06 0.11
Matches are distributed among these distances:
19 16 0.41
20 3 0.08
21 20 0.51
ACGTcount: A:0.26, C:0.09, G:0.23, T:0.42
Consensus pattern (20 bp):
AATGTATCACTATTTGGTGT
Found at i:164047 original size:19 final size:19
Alignment explanation
Indices: 164020--164078 Score: 82
Period size: 19 Copynumber: 3.0 Consensus size: 19
164010 TAAAATGTAG
164020 TCACTATTTGGTGTAATGA
1 TCACTATTTGGTGTAATGA
*
164039 TCACAATTTGGTGTAATGGTA
1 TCACTATTTGGTGTAAT-G-A
*
164060 TCACTTTTTGGTGTAATGA
1 TCACTATTTGGTGTAATGA
164079 AAATTATCAT
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
19 17 0.49
20 2 0.06
21 16 0.46
ACGTcount: A:0.25, C:0.10, G:0.22, T:0.42
Consensus pattern (19 bp):
TCACTATTTGGTGTAATGA
Found at i:165090 original size:3 final size:3
Alignment explanation
Indices: 165069--165108 Score: 57
Period size: 3 Copynumber: 14.0 Consensus size: 3
165059 TGAACTTTTA
*
165069 ATT ATT AGT A-T ATT A-T ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
165109 TACTTCTTCC
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
2 4 0.12
3 30 0.88
ACGTcount: A:0.35, C:0.00, G:0.03, T:0.62
Consensus pattern (3 bp):
ATT
Found at i:169372 original size:14 final size:15
Alignment explanation
Indices: 169355--169394 Score: 55
Period size: 14 Copynumber: 2.7 Consensus size: 15
169345 AAATTTCAAA
*
169355 TTCTTCTTCTC-TGT
1 TTCTTCTTCTCTTCT
169369 TTCTTCTTCTCTTCT
1 TTCTTCTTCTCTTCT
169384 TTCTCTCTTCT
1 TTCT-TCTTCT
169395 TTCCCTCTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 11 0.48
15 6 0.26
16 6 0.26
ACGTcount: A:0.00, C:0.33, G:0.03, T:0.65
Consensus pattern (15 bp):
TTCTTCTTCTCTTCT
Found at i:169396 original size:11 final size:11
Alignment explanation
Indices: 169376--169412 Score: 56
Period size: 11 Copynumber: 3.3 Consensus size: 11
169366 TGTTTCTTCT
169376 TCTCTTCTTTC
1 TCTCTTCTTTC
169387 TCTCTTCTTTC
1 TCTCTTCTTTC
*
169398 CCTCTTTCTTTC
1 TCTC-TTCTTTC
169410 TCT
1 TCT
169413 TGAAATTCAG
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
11 14 0.61
12 9 0.39
ACGTcount: A:0.00, C:0.38, G:0.00, T:0.62
Consensus pattern (11 bp):
TCTCTTCTTTC
Found at i:171673 original size:30 final size:30
Alignment explanation
Indices: 171596--171674 Score: 140
Period size: 30 Copynumber: 2.6 Consensus size: 30
171586 AGCTGGTTTG
*
171596 TGAGATGAGTGATATCTATGAATTGTGTGT
1 TGAGATGAGTGATATCTGTGAATTGTGTGT
171626 TGAGATGAGTGATATCTGTGAATTGTGTGT
1 TGAGATGAGTGATATCTGTGAATTGTGTGT
*
171656 TGAGATAAGTGATATCTGT
1 TGAGATGAGTGATATCTGT
171675 TTGAAACTCT
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 47 1.00
ACGTcount: A:0.27, C:0.04, G:0.30, T:0.39
Consensus pattern (30 bp):
TGAGATGAGTGATATCTGTGAATTGTGTGT
Done.