Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019666.1 Corchorus olitorius cultivar O-4 contig19699, 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: 88976
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.33
Found at i:1717 original size:334 final size:334
Alignment explanation
Indices: 1--4273 Score: 5209
Period size: 333 Copynumber: 12.9 Consensus size: 334
* * *
1 TCGGCGTCGAGACTCCTTCAAAAATCTATATTCATCTAGTCAAATCTCAGCCAAATTGCATTTAA
1 TCGGCGTCGAGACTCCTTCAAATATCTATATTCATCTAATCAAATCTCAGCCACATTGCATTTAA
** * * * *
66 GTTTTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTC-GATTAAATT
66 GAATTTGTTTTTACGAGCATCTAAATCTTGTTTCAATTTAATTAGAAATTAATTCGGA-AAAAGT
* * * * * * ** * * *
130 AATGAAAAACGATATGAAAAGTGTGAAAAGTCATCCAATCA-TTTTGGAG-TGAAATTATATATA
130 -AGGAAAAATGATATTAGAAGCGTAAAAAAACCTTCAAT-ATTTTTGGCGTTGAAA-TATATATA
* * * * * *
193 T-TAC-ACGAGTATATT-AGGC-AAAAATTGAGGAAAAATTTTTCGGATCATTTTTTGCAGAATT
192 TCT-CTATGAGTAT-TTCA-GCTAAAAATTGAGGAAATATCTTTCGGGTCAATTTTTGCAAAATT
* *
254 TTAGCCGAAATCGTGTACTAACCATCTCGA-TTTTTTGCTAAAAACGCTTTTCGGGGCCCCGACT
254 TTAGCCGAAATCGTGTACTAACCATCACGATTTTTTTGCTAAAAACGCGTTTCGGGGCCCCGACT
318 CAGTTCTGCATGATTT
319 CAGTTCTGCATGATTT
** * * * * *
334 TCGTTGTCGAGGCTACTTCAAATATCTATATTCATTTAATCAAATCTTAGTCACATTGCATTTAA
1 TCGGCGTCGAGACTCCTTCAAATATCTATATTCATCTAATCAAATCTCAGCCACATTGCATTTAA
* * * *
399 GAATTTGTTTTTACGAGCATCTATATCTTATTTCAACTTAATTAGAAATTTATTCGGAAAAAGTA
66 GAATTTGTTTTTACGAGCATCTAAATCTTGTTTCAATTTAATTAGAAATTAATTCGGAAAAAGTA
* *
464 GGAAAAATGATATTAGAAGCATAAAGAAACCTTCAATATTTTTGGCGTTGAAATATATATATCTC
131 GGAAAAATGATATTAGAAGCGTAAAAAAACCTTCAATATTTTTGGCGTTGAAATATATATATCTC
** * *
529 TATGAGTATTTCAGCTAAAAA-AAAAGAAATATCTTTCGGGTCAATTTTTGCTAAATTTTAGCCG
196 TATGAGTATTTCAGCTAAAAATTGAGGAAATATCTTTCGGGTCAATTTTTGCAAAATTTTAGCCG
* * * * *
593 AAATCATTTACTAACCATCACGATTTCTTTGCTAAAAATGCGTTTCGGGGCCCCGACTCAATTCT
261 AAATCGTGTACTAACCATCACGATTTTTTTGCTAAAAACGCGTTTCGGGGCCCCGACTCAGTTCT
658 GCATGATTT
326 GCATGATTT
* *
667 TCGGCGTCGAGACTCCTTCAAATATCTATATTTATCTAATCAAATCTCAGCCTCATTGCATTTAA
1 TCGGCGTCGAGACTCCTTCAAATATCTATATTCATCTAATCAAATCTCAGCCACATTGCATTTAA
* * * * * *
732 GAATTTATTTTTACGAGCATCTATATCTTATTTCAACTTAATTAGAAATTTATTCGGAAAAACTA
66 GAATTTGTTTTTACGAGCATCTAAATCTTGTTTCAATTTAATTAGAAATTAATTCGGAAAAAGTA
* *
797 GGAAAAATGATATTAGAAGCGTAAACAAACCTTAAATATTTTTGGCGTTGAAATATATATATCTC
131 GGAAAAATGATATTAGAAGCGTAAAAAAACCTTCAATATTTTTGGCGTTGAAATATATATATCTC
* *
862 TATGAGTATTTCAGCTAAAAATT-ATGGAAATATTTTTCGGGTCAACTTTTGCAAAATTTTAGCC
196 TATGAGTATTTCAGCTAAAAATTGA-GGAAATATCTTTCGGGTCAATTTTTGCAAAATTTTAGCC
* * * *
926 GAAATCGTGTACTAACCATCACGA-TTTATT-CTAAAAA-ACGTGTTCTGGGGCCTCGGCTCAGT
260 GAAATCGTGTACTAACCATCACGATTTTTTTGCTAAAAACGCGT-TTC-GGGGCCCCGACTCAGT
*
988 TCTGTATGATTT
323 TCTGCATGATTT
* * *
1000 TCGGCGTCGAGACTCCTTCAAAAATCTATATTCATCTAGTCAAATCTCAGCCAAATTGCATTTAA
1 TCGGCGTCGAGACTCCTTCAAATATCTATATTCATCTAATCAAATCTCAGCCACATTGCATTTAA
* * * * *
1065 G-TTTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTC-GATTAAATT
66 GAATTTGTTTTTACGAGCATCTAAATCTTGTTTCAATTTAATTAGAAATTAATTCGGA-AAAAGT
* * * * * * ** * *
1128 AATGAAAAACGATATGAAAAGTGTGAAAATTCCTCCAATCA-TTTTGGTG-TGAAATTATATATA
130 -AGGAAAAATGATATTAGAAGCGTAAAAAAACCTTCAAT-ATTTTTGGCGTTGAAA-TATATATA
* * * * * * *
1191 T-TAC-ACGAGTATATT-AGGC-AAAAATTGAGGAAAAATTTTTCGGATCATTTTTTGCATAAGT
192 TCT-CTATGAGTAT-TTCA-GCTAAAAATTGAGGAAATATCTTTCGGGTCAATTTTTGCAAAATT
* **
1252 TTA-CCTGAAATCGTGTACTAACCATCACGA-TTTTTTGCTAAAAACACGTTTCGGGGTTCCGAC
254 TTAGCC-GAAATCGTGTACTAACCATCACGATTTTTTTGCTAAAAACGCGTTTCGGGGCCCCGAC
*
1315 TCAGTTCAGCATGATTT
318 TCAGTTCTGCATGATTT
*
1332 TCGGCATCGAGACTCCTTCAAATATCTATATTCATCTAATCAAATCTCAGCCACATTGCATTTAA
1 TCGGCGTCGAGACTCCTTCAAATATCTATATTCATCTAATCAAATCTCAGCCACATTGCATTTAA
* * *
1397 GGATTTGTTTTTACGAGCATCTAAATCTTGTTTCAATTTAATTAGAAATTTATTAGGAAAAAGTA
66 GAATTTGTTTTTACGAGCATCTAAATCTTGTTTCAATTTAATTAGAAATTAATTCGGAAAAAGTA
* * *
1462 GGAAAAATGATATTAGAAGCGTAAAAAAATCTTAAATTTTTTTGGCGTTGAAATATATATATCTC
131 GGAAAAATGATATTAGAAGCGTAAAAAAACCTTCAATATTTTTGGCGTTGAAATATATATATCTC
* * * *
1527 TATGAGTATTTCAGCTAAAAATTGAGGAAATATCTTTCAGGTGAAGTTTTGCAAAATTTTAGCTG
196 TATGAGTATTTCAGCTAAAAATTGAGGAAATATCTTTCGGGTCAATTTTTGCAAAATTTTAGCCG
* * **
1592 AAATCGTGTACTAACCATCACGATTTTTTTGTTAAAAACGCGTTTCGGGGCCTCGACTCAAATCT
261 AAATCGTGTACTAACCATCACGATTTTTTTGCTAAAAACGCGTTTCGGGGCCCCGACTCAGTTCT
*
1657 ACATGATTT
326 GCATGATTT
*
1666 TCGGCATCGAGACTCCTTCAAATATCTATATTCATCTAATCAAATCTCAGCCACATTGCATTTAA
1 TCGGCGTCGAGACTCCTTCAAATATCTATATTCATCTAATCAAATCTCAGCCACATTGCATTTAA
* *
1731 GGATTT-TTTTTACGAGCATCTAAATCTTGTTTCAATTTAATTAGAAATTAATTCGGAAAAAGCA
66 GAATTTGTTTTTACGAGCATCTAAATCTTGTTTCAATTTAATTAGAAATTAATTCGGAAAAAGTA
* * * * * *
1795 GGAAAGACGATATTAGAAACGTAAAAAACCCTTCAATATTTTTCGCGTTGAATTATATATATCTC
131 GGAAAAATGATATTAGAAGCGTAAAAAAACCTTCAATATTTTTGGCGTTGAAATATATATATCTC
* * * *
1860 TATGAGTATTTCATCTAAAATTTGAGGAAATACCTTTCGGGTCAATTTTTGCAAAATTTTAGCCA
196 TATGAGTATTTCAGCTAAAAATTGAGGAAATATCTTTCGGGTCAATTTTTGCAAAATTTTAGCCG
* *
1925 AAATCGTGTACTAACAATCACGATTTCTTTGCTAAAAACGCGTTTCGGGGCCCCGACTCAGTTCT
261 AAATCGTGTACTAACCATCACGATTTTTTTGCTAAAAACGCGTTTCGGGGCCCCGACTCAGTTCT
1990 GCATGATTT
326 GCATGATTT
* * * * * * *
1999 TCGGCGTCGAGACTTCTTAAAATATCAATATTCATCTAGTCAAATCTCAGTCAAATTTCATTTAA
1 TCGGCGTCGAGACTCCTTCAAATATCTATATTCATCTAATCAAATCTCAGCCACATTGCATTTAA
* * ** * * * **
2064 GTATTTGTTTTTACGGGCATCTGGATGTTTTTTCGATTTAATTAGAAATTAATTCGGAAAATTTA
66 GAATTTGTTTTTACGAGCATCTAAATCTTGTTTCAATTTAATTAGAAATTAATTCGGAAAAAGT-
* * * * * * ** * *
2129 ATGAAAAATGAAATGAAAAGTGTGAAAAGTCCTCCAATCA-TTTTGGTG-TGAAATTATATATAT
130 AGGAAAAATGATATTAGAAGCGTAAAAAAACCTTCAAT-ATTTTTGGCGTTGAAA-TATATATAT
* ** * * * * *
2192 -TAC-ACGAGTATATTTGGC-AAAAATTGAGGAAAAATTTTTCGGATCATTTTTTGCAGAATTTT
193 CT-CTATGAGTAT-TTCAGCTAAAAATTGAGGAAATATCTTTCGGGTCAATTTTTGCAAAATTTT
* * * * ** *
2254 AGTCGAAATTGTGTACTTACCATCACGA-TTTTTTGCTAAAAACACGTTTCGGGGTTCCAACTCA
256 AGCCGAAATCGTGTACTAACCATCACGATTTTTTTGCTAAAAACGCGTTTCGGGGCCCCGACTCA
2318 GTTCTGCATGATTT
321 GTTCTGCATGATTT
2332 TCGGCGTCGAGACTCCTTCAAATATCTATATTCATCTAATCAAATCTCAGCCACATTGCATTTAA
1 TCGGCGTCGAGACTCCTTCAAATATCTATATTCATCTAATCAAATCTCAGCCACATTGCATTTAA
* * *
2397 GAATTTGTTTTTACGAGCATCTAAATCTTATTTCAACTTAATTAGAAATTTATTCGGAAAAAGTA
66 GAATTTGTTTTTACGAGCATCTAAATCTTGTTTCAATTTAATTAGAAATTAATTCGGAAAAAGTA
*
2462 GGAAAAATGATATTAGAAGCGTAAAGAAACCTTCAATATTTTTGGCGTTGAAATATATATATCTC
131 GGAAAAATGATATTAGAAGCGTAAAAAAACCTTCAATATTTTTGGCGTTGAAATATATATATCTC
*
2527 TATGAGTATTTCAGCTAAAAATTGAGGAAATATCTTTCGGGTCAATTTTTGCTAAATTTTAGCCG
196 TATGAGTATTTCAGCTAAAAATTGAGGAAATATCTTTCGGGTCAATTTTTGCAAAATTTTAGCCG
* * * *
2592 AAATCATGTACTAACCATCACGATTTCTTTGCTAAAAATGCGTTTCGGGGCCCCGACTCAATTCT
261 AAATCGTGTACTAACCATCACGATTTTTTTGCTAAAAACGCGTTTCGGGGCCCCGACTCAGTTCT
2657 GCATGATTT
326 GCATGATTT
*
2666 TCGGTGTCGAGACTCCTTCAAATATCTATATTCATCTAATCAAATCTCAGCCACATTGCATTTAA
1 TCGGCGTCGAGACTCCTTCAAATATCTATATTCATCTAATCAAATCTCAGCCACATTGCATTTAA
* * * *
2731 GAATTTGTTTTTACGAGCATCTATATCTTATTTCAACTTAATTAGAAATTTATTCGGAAAAAGTA
66 GAATTTGTTTTTACGAGCATCTAAATCTTGTTTCAATTTAATTAGAAATTAATTCGGAAAAAGTA
* * *
2796 GGGAAAATGATATTAGAAGCGTAAAAAAACCTTCAATATTTTTGACGTTGAATTATATATATCTC
131 GGAAAAATGATATTAGAAGCGTAAAAAAACCTTCAATATTTTTGGCGTTGAAATATATATATCTC
*
2861 TATGAGTATTTCAGCTAAAAATTGTGGAAATATCTTTCGGGTCAATTTTTGCAAAATTTTAGCCG
196 TATGAGTATTTCAGCTAAAAATTGAGGAAATATCTTTCGGGTCAATTTTTGCAAAATTTTAGCCG
*
2926 -AA------A-T---CATCACGATTTTTTTGCTAAGAACGCGTTTC-GGGCCCCGACTCAGTTCT
261 AAATCGTGTACTAACCATCACGATTTTTTTGCTAAAAACGCGTTTCGGGGCCCCGACTCAGTTCT
2979 GCATGATTT
326 GCATGATTT
*
2988 TCGGCGTCGAGACTCCTTCAAATATCTATATTCATCTAATCAAATATCAGCCACATTGCATTTAA
1 TCGGCGTCGAGACTCCTTCAAATATCTATATTCATCTAATCAAATCTCAGCCACATTGCATTTAA
* * * *
3053 GAATTTGTTTTTACGAGCATCTATATCTTATTTCAACTTAATTAGAAATTTATTCGGAAAAAGTA
66 GAATTTGTTTTTACGAGCATCTAAATCTTGTTTCAATTTAATTAGAAATTAATTCGGAAAAAGTA
* * *
3118 GGAAAAATGATATTAGAAGCGTGAAAAAACCTTCAATATTTTTGGCATTGAATTATATATATCTC
131 GGAAAAATGATATTAGAAGCGTAAAAAAACCTTCAATATTTTTGGCGTTGAAATATATATATCTC
3183 TATGAGTATTTCAGCTAAAAATTGAGGAAATATCTTTCGGGTCAATTTTTGCAAAATTTTAGCCG
196 TATGAGTATTTCAGCTAAAAATTGAGGAAATATCTTTCGGGTCAATTTTTGCAAAATTTTAGCCG
3248 AAATCGTGTACTAACCATCACGATTTTTTTGCTAAAAACGCGTTTCGGGGCCCCGACTCAGTTCT
261 AAATCGTGTACTAACCATCACGATTTTTTTGCTAAAAACGCGTTTCGGGGCCCCGACTCAGTTCT
3313 GCATGATTT
326 GCATGATTT
* *
3322 TCGGAC-TCGAAACTCCTTCAAATATCTATATTCATCTAATCAAATCTCAGCCACATTACATTTA
1 TCGG-CGTCGAGACTCCTTCAAATATCTATATTCATCTAATCAAATCTCAGCCACATTGCATTTA
* *
3386 AGGATTTTTTTTTACGAGCATCTAAATCTTGTTTCAATTTAATTAGAAATTAATTCGGAAAAAGT
65 AGAATTTGTTTTTACGAGCATCTAAATCTTGTTTCAATTTAATTAGAAATTAATTCGGAAAAAGT
* * * ** *
3451 AGGAAAAACGATATTAGAAGCGTAAAAAACCCTT-AAGTGTTTTTCACGTTGAATTATATATATC
130 AGGAAAAATGATATTAGAAGCGTAAAAAAACCTTCAA-TATTTTTGGCGTTGAAATATATATATC
* *
3515 TCTATGAGTATTTCATCTAAAAATTGAGGAAATATCTTTCGGGTCAA-TTTTGCAAAATTTTAAC
194 TCTATGAGTATTTCAGCTAAAAATTGAGGAAATATCTTTCGGGTCAATTTTTGCAAAATTTTAGC
* *
3579 CGAAATCGTGTACTAACCATCACGATTTTTTTGCTAAAAACGTGTTTCAGGGCCCCGACTCAGTT
259 CGAAATCGTGTACTAACCATCACGATTTTTTTGCTAAAAACGCGTTTCGGGGCCCCGACTCAGTT
3644 CTGCATGATTT
324 CTGCATGATTT
* * * * * * * *
3655 TCGGCGTCGAGACTCGTTAAAACATCAATATTCATCTAGTCAAAATCTCAGTCAAATTTCATTTA
1 TCGGCGTCGAGACTCCTTCAAATATCTATATTCATCTAATC-AAATCTCAGCCACATTGCATTTA
* * * * * * * *
3720 AGTATTTGTTTTTACGATCATCTGAATGTTTTTTCGATTTAATTAGAAATTAATTTGGAAAAATT
65 AGAATTTGTTTTTACGAGCATCTAAATCTTGTTTCAATTTAATTAGAAATTAATTCGGAAAAAGT
* * * * * ** *
3785 AATGAAAAATGATATGAAAAGTGTGAAAAGTCCTTCAAT-TATTTTGGTG-TGAAATTATATATA
130 -AGGAAAAATGATATTAGAAGCGTAAAAAAACCTTCAATAT-TTTTGGCGTTGAAA-TATATATA
* * * * * * *
3848 T-TAC-ACGAGTATATT-AGCCAAAAATTGAGCAAAAATTTTTCGGAT-AATTTTTTGCAGAATT
192 TCT-CTATGAGTAT-TTCAGCTAAAAATTGAGGAAATATCTTTCGGGTCAA-TTTTTGCAAAATT
* * *
3909 TTAACCGAAATC--G----------CA--A-TTTTTTGCTAAAAACACATTTCGGGGCCCCGACT
254 TTAGCCGAAATCGTGTACTAACCATCACGATTTTTTTGCTAAAAACGCGTTTCGGGGCCCCGACT
3959 CAGTTCTGCATGATTT
319 CAGTTCTGCATGATTT
*
3975 TCGGCGTCGAGACTCCTTCAAATATCTATATTCATCTAATCAAATCTTAGCCACATTGCATTTAA
1 TCGGCGTCGAGACTCCTTCAAATATCTATATTCATCTAATCAAATCTCAGCCACATTGCATTTAA
* ** * * * *
4040 GTATTTGTTTTTACGAATATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCAGAAAAATTA
66 GAATTTGTTTTTACGAGCATCTAAATCTTGTTTCAATTTAATTAGAAATTAATTCGGAAAAAGT-
* * * * * * *** * * *
4105 ATGAAAAACGATATGAAAAGTGTGAAAAGTTCTCCAATCA-TTTTGGAG-TGAAAT-TATATATG
130 AGGAAAAATGATATTAGAAGCGTAAAAAAACCTTCAAT-ATTTTTGGCGTTGAAATATATATATC
* * ** ** * *
4167 T-TACATGAGTATATT-AGGC-AAAAATTGAGGAAAAATTTTTCGAATCCTTTTTTGTAGAATTT
194 TCT--ATGAGTAT-TTCA-GCTAAAAATTGAGGAAATATCTTTCGGGTCAATTTTTGCAAAATTT
* *
4229 TAGCCGAAATCATGTACTACTAACCATCATGA-TTTTTTGCTAAAA
255 TAGCCGAAATC--GT-GTACTAACCATCACGATTTTTTTGCTAAAA
4274 TGCTTAAGTT
Statistics
Matches: 3444, Mismatches: 402, Indels: 185
0.85 0.10 0.05
Matches are distributed among these distances:
317 7 0.00
318 2 0.00
319 184 0.05
320 84 0.02
321 1 0.00
322 279 0.08
323 32 0.01
326 1 0.00
327 1 0.00
329 1 0.00
330 1 0.00
331 9 0.00
332 422 0.12
333 1336 0.39
334 954 0.28
335 113 0.03
336 17 0.00
ACGTcount: A:0.33, C:0.16, G:0.15, T:0.36
Consensus pattern (334 bp):
TCGGCGTCGAGACTCCTTCAAATATCTATATTCATCTAATCAAATCTCAGCCACATTGCATTTAA
GAATTTGTTTTTACGAGCATCTAAATCTTGTTTCAATTTAATTAGAAATTAATTCGGAAAAAGTA
GGAAAAATGATATTAGAAGCGTAAAAAAACCTTCAATATTTTTGGCGTTGAAATATATATATCTC
TATGAGTATTTCAGCTAAAAATTGAGGAAATATCTTTCGGGTCAATTTTTGCAAAATTTTAGCCG
AAATCGTGTACTAACCATCACGATTTTTTTGCTAAAAACGCGTTTCGGGGCCCCGACTCAGTTCT
GCATGATTT
Found at i:4864 original size:7 final size:7
Alignment explanation
Indices: 4852--4885 Score: 68
Period size: 7 Copynumber: 4.9 Consensus size: 7
4842 TTGTTAAAAG
4852 CTTTTTT
1 CTTTTTT
4859 CTTTTTT
1 CTTTTTT
4866 CTTTTTT
1 CTTTTTT
4873 CTTTTTT
1 CTTTTTT
4880 CTTTTT
1 CTTTTT
4886 AAATATCAAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 27 1.00
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (7 bp):
CTTTTTT
Found at i:6384 original size:32 final size:32
Alignment explanation
Indices: 6343--6841 Score: 782
Period size: 32 Copynumber: 15.0 Consensus size: 32
6333 ATTAACTTTC
6343 CCAAATGACATTGAACTTGCCTTAATTCACAT
1 CCAAATGACATTGAACTTGCCTTAATTCACAT
6375 CCAAATGACATTGAACTTGCCTTAATTCACAT
1 CCAAATGACATTGAACTTGCCTTAATTCACAT
6407 CCAAATGACATTGAACTTGCCTTAATTCACATCCAACTTT
1 CCAAATGACATTGAACTTGCCTTAATT--CA--C-A---T
6447 CCCAAATGACATTGAACTTGCCTTAATTCACAT
1 -CCAAATGACATTGAACTTGCCTTAATTCACAT
6480 CCAAATGACATTGAACTTGCCTTAATTCACAT
1 CCAAATGACATTGAACTTGCCTTAATTCACAT
6512 CCAAATGACATTGAACTTGCCTTAATTCACAT
1 CCAAATGACATTGAACTTGCCTTAATTCACAT
*
6544 CCAAAAGACATTGAACTTGCCATTAATTCACAT
1 CCAAATGACATTGAACTTGCC-TTAATTCACAT
*
6577 CCAAATTACATTGAACTTGCCTTAATTCACAT
1 CCAAATGACATTGAACTTGCCTTAATTCACAT
6609 CCAAATGACATTGAACTTGCCTTAATTCACATCCAACTTT
1 CCAAATGACATTGAACTTGCCTTAATT--CA--C-A---T
6649 CCCAAATGACATTGAACTTGCCTTAATTCACAT
1 -CCAAATGACATTGAACTTGCCTTAATTCACAT
6682 CCAAATGACATTGAACTTGCCTTAATTCACAT
1 CCAAATGACATTGAACTTGCCTTAATTCACAT
6714 CCAAATGACATTGAACTTGCCTTAATTCACAT
1 CCAAATGACATTGAACTTGCCTTAATTCACAT
*
6746 CCAAAAGACATTGAACTTGCCTTAATTCACAT
1 CCAAATGACATTGAACTTGCCTTAATTCACAT
*
6778 CCAAATTACATTGAACTTGCCTTAATTCACAT
1 CCAAATGACATTGAACTTGCCTTAATTCACAT
*
6810 CCAAATGACATTGAACTTGCCTTAACTCACAT
1 CCAAATGACATTGAACTTGCCTTAATTCACAT
6842 TGGCCCTCAA
Statistics
Matches: 439, Mismatches: 9, Indels: 38
0.90 0.02 0.08
Matches are distributed among these distances:
32 335 0.76
33 32 0.07
34 4 0.01
36 4 0.01
37 4 0.01
39 4 0.01
40 2 0.00
41 54 0.12
ACGTcount: A:0.34, C:0.26, G:0.09, T:0.31
Consensus pattern (32 bp):
CCAAATGACATTGAACTTGCCTTAATTCACAT
Found at i:6444 original size:21 final size:21
Alignment explanation
Indices: 6420--6483 Score: 67
Period size: 21 Copynumber: 3.1 Consensus size: 21
6410 AATGACATTG
6420 AACTTGCCTTAATTCACATCC
1 AACTTGCCTTAATTCACATCC
* * * * **
6441 AACTTTCC-CAAATGACATTG
1 AACTTGCCTTAATTCACATCC
6461 AACTTGCCTTAATTCACATCC
1 AACTTGCCTTAATTCACATCC
6482 AA
1 AA
6484 ATGACATTGA
Statistics
Matches: 30, Mismatches: 12, Indels: 2
0.68 0.27 0.05
Matches are distributed among these distances:
20 14 0.47
21 16 0.53
ACGTcount: A:0.33, C:0.30, G:0.06, T:0.31
Consensus pattern (21 bp):
AACTTGCCTTAATTCACATCC
Found at i:6464 original size:20 final size:20
Alignment explanation
Indices: 6407--6468 Score: 61
Period size: 20 Copynumber: 3.0 Consensus size: 20
6397 TAATTCACAT
6407 CCAAATGACATTGAACTTGC
1 CCAAATGACATTGAACTTGC
* * * ** *
6427 CTTAATTCACATCCAACTTTC
1 C-CAAATGACATTGAACTTGC
6448 CCAAATGACATTGAACTTGC
1 CCAAATGACATTGAACTTGC
6468 C
1 C
6469 TTAATTCACA
Statistics
Matches: 29, Mismatches: 12, Indels: 2
0.67 0.28 0.05
Matches are distributed among these distances:
20 15 0.52
21 14 0.48
ACGTcount: A:0.32, C:0.29, G:0.10, T:0.29
Consensus pattern (20 bp):
CCAAATGACATTGAACTTGC
Found at i:6646 original size:21 final size:21
Alignment explanation
Indices: 6622--6685 Score: 67
Period size: 21 Copynumber: 3.1 Consensus size: 21
6612 AATGACATTG
6622 AACTTGCCTTAATTCACATCC
1 AACTTGCCTTAATTCACATCC
* * * * **
6643 AACTTTCC-CAAATGACATTG
1 AACTTGCCTTAATTCACATCC
6663 AACTTGCCTTAATTCACATCC
1 AACTTGCCTTAATTCACATCC
6684 AA
1 AA
6686 ATGACATTGA
Statistics
Matches: 30, Mismatches: 12, Indels: 2
0.68 0.27 0.05
Matches are distributed among these distances:
20 14 0.47
21 16 0.53
ACGTcount: A:0.33, C:0.30, G:0.06, T:0.31
Consensus pattern (21 bp):
AACTTGCCTTAATTCACATCC
Found at i:6666 original size:20 final size:20
Alignment explanation
Indices: 6609--6670 Score: 61
Period size: 20 Copynumber: 3.0 Consensus size: 20
6599 TAATTCACAT
6609 CCAAATGACATTGAACTTGC
1 CCAAATGACATTGAACTTGC
* * * ** *
6629 CTTAATTCACATCCAACTTTC
1 C-CAAATGACATTGAACTTGC
6650 CCAAATGACATTGAACTTGC
1 CCAAATGACATTGAACTTGC
6670 C
1 C
6671 TTAATTCACA
Statistics
Matches: 29, Mismatches: 12, Indels: 2
0.67 0.28 0.05
Matches are distributed among these distances:
20 15 0.52
21 14 0.48
ACGTcount: A:0.32, C:0.29, G:0.10, T:0.29
Consensus pattern (20 bp):
CCAAATGACATTGAACTTGC
Found at i:6710 original size:202 final size:201
Alignment explanation
Indices: 6343--6841 Score: 962
Period size: 202 Copynumber: 2.5 Consensus size: 201
6333 ATTAACTTTC
* *
6343 CCAAATGACATTGAACTTGCCTTAATTCACATCCAAATGACATTGAACTTGCCTTAATTCACATC
1 CCAAAAGACATTGAACTTGCCTTAATTCACATCCAAATTACATTGAACTTGCCTTAATTCACATC
6408 CAAATGACATTGAACTTGCCTTAATTCACATCCAACTTTCCCAAATGACATTGAACTTGCCTTAA
66 CAAATGACATTGAACTTGCCTTAATTCACATCCAACTTTCCCAAATGACATTGAACTTGCCTTAA
6473 TTCACATCCAAATGACATTGAACTTGCCTTAATTCACATCCAAATGACATTGAACTTGCCTTAAT
131 TTCACATCCAAATGACATTGAACTTGCCTTAATTCACATCCAAATGACATTGAACTTGCCTTAAT
6538 TCACAT
196 TCACAT
6544 CCAAAAGACATTGAACTTGCCATTAATTCACATCCAAATTACATTGAACTTGCCTTAATTCACAT
1 CCAAAAGACATTGAACTTGCC-TTAATTCACATCCAAATTACATTGAACTTGCCTTAATTCACAT
6609 CCAAATGACATTGAACTTGCCTTAATTCACATCCAACTTTCCCAAATGACATTGAACTTGCCTTA
65 CCAAATGACATTGAACTTGCCTTAATTCACATCCAACTTTCCCAAATGACATTGAACTTGCCTTA
6674 ATTCACATCCAAATGACATTGAACTTGCCTTAATTCACATCCAAATGACATTGAACTTGCCTTAA
130 ATTCACATCCAAATGACATTGAACTTGCCTTAATTCACATCCAAATGACATTGAACTTGCCTTAA
6739 TTCACAT
195 TTCACAT
6746 CCAAAAGACATTGAACTTGCCTTAATTCACATCCAAATTACATTGAACTTGCCTTAATTCACATC
1 CCAAAAGACATTGAACTTGCCTTAATTCACATCCAAATTACATTGAACTTGCCTTAATTCACATC
*
6811 CAAATGACATTGAACTTGCCTTAACTCACAT
66 CAAATGACATTGAACTTGCCTTAATTCACAT
6842 TGGCCCTCAA
Statistics
Matches: 294, Mismatches: 3, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
201 94 0.32
202 200 0.68
ACGTcount: A:0.34, C:0.26, G:0.09, T:0.31
Consensus pattern (201 bp):
CCAAAAGACATTGAACTTGCCTTAATTCACATCCAAATTACATTGAACTTGCCTTAATTCACATC
CAAATGACATTGAACTTGCCTTAATTCACATCCAACTTTCCCAAATGACATTGAACTTGCCTTAA
TTCACATCCAAATGACATTGAACTTGCCTTAATTCACATCCAAATGACATTGAACTTGCCTTAAT
TCACAT
Found at i:7125 original size:122 final size:122
Alignment explanation
Indices: 6908--7132 Score: 380
Period size: 122 Copynumber: 1.8 Consensus size: 122
6898 TCGAGACAAT
* * * *
6908 AAGGCAATCCTTGCTGCCACAAGGATATGCTCAGCTCCAATGGGGAGACAACTGCAGAGGAGAAG
1 AAGGCAATCCTAGCTGCCACAAGGATACGCTCAGATCCAATGGGGAGACAACTGCAGAAGAGAAG
**
6973 AAACGTTATCCAAAAACCATCAGAGCAGAAAAAGGAAACTTACAACAAACAAATCTG
66 AAACACTATCCAAAAACCATCAGAGCAGAAAAAGGAAACTTACAACAAACAAATCTG
7030 AAGGCAATCCTAGCTGCCACAAGGATACGCTCAGATCCAATGGGGAGACAACTGCAGAAGAGAAG
1 AAGGCAATCCTAGCTGCCACAAGGATACGCTCAGATCCAATGGGGAGACAACTGCAGAAGAGAAG
7095 AAACACTAT-CAAGAAACCATCAGAGCAGAAAAAGGAAA
66 AAACACTATCCAA-AAACCATCAGAGCAGAAAAAGGAAA
7133 ATCAGAGCAA
Statistics
Matches: 96, Mismatches: 6, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
121 3 0.03
122 93 0.97
ACGTcount: A:0.43, C:0.22, G:0.22, T:0.13
Consensus pattern (122 bp):
AAGGCAATCCTAGCTGCCACAAGGATACGCTCAGATCCAATGGGGAGACAACTGCAGAAGAGAAG
AAACACTATCCAAAAACCATCAGAGCAGAAAAAGGAAACTTACAACAAACAAATCTG
Found at i:14499 original size:27 final size:27
Alignment explanation
Indices: 14455--14507 Score: 81
Period size: 27 Copynumber: 2.0 Consensus size: 27
14445 GTCTCATGTT
14455 TATATGATGTAACGATAAGCCTGAATC
1 TATATGATGTAACGATAAGCCTGAATC
*
14482 TATATGATGT-ACTTATAAGCCTGAAT
1 TATATGATGTAAC-GATAAGCCTGAAT
14508 AGGCCTGAAC
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
26 2 0.08
27 22 0.92
ACGTcount: A:0.36, C:0.13, G:0.17, T:0.34
Consensus pattern (27 bp):
TATATGATGTAACGATAAGCCTGAATC
Found at i:14514 original size:37 final size:37
Alignment explanation
Indices: 14473--14544 Score: 99
Period size: 37 Copynumber: 1.9 Consensus size: 37
14463 GTAACGATAA
* * * *
14473 GCCTGAATCTATATGATGTACTTATAAGCCTGAATAG
1 GCCTGAACCTATATGATGTAATGATAAGCCCGAATAG
*
14510 GCCTGAACCTATATGCTGTAATGATAAGCCCGAAT
1 GCCTGAACCTATATGATGTAATGATAAGCCCGAAT
14545 TTATATGATG
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
37 30 1.00
ACGTcount: A:0.32, C:0.19, G:0.19, T:0.29
Consensus pattern (37 bp):
GCCTGAACCTATATGATGTAATGATAAGCCCGAATAG
Found at i:14588 original size:32 final size:32
Alignment explanation
Indices: 14546--14688 Score: 154
Period size: 32 Copynumber: 4.6 Consensus size: 32
14536 AGCCCGAATT
* *
14546 TATATGATGTAACGATAATCTTGAAAATGAAG
1 TATATGATGTAACGATAAACTTGAAAATGAAC
* * *
14578 TATATAATGTAACAATAAACCTG--AAT---C
1 TATATGATGTAACGATAAACTTGAAAATGAAC
*
14605 TATGTGATGTAACGATAAACTTGAAAATGAAC
1 TATATGATGTAACGATAAACTTGAAAATGAAC
* *
14637 TATATGATGTAACGATAAACCT-AGAAATGAGC
1 TATATGATGTAACGATAAACTTGA-AAATGAAC
*
14669 TATATGATGTGACGATAAAC
1 TATATGATGTAACGATAAAC
14689 CTAAAACCAA
Statistics
Matches: 92, Mismatches: 13, Indels: 12
0.79 0.11 0.10
Matches are distributed among these distances:
27 19 0.21
29 3 0.03
30 3 0.03
31 1 0.01
32 66 0.72
ACGTcount: A:0.44, C:0.10, G:0.17, T:0.29
Consensus pattern (32 bp):
TATATGATGTAACGATAAACTTGAAAATGAAC
Found at i:14613 original size:59 final size:59
Alignment explanation
Indices: 14541--14688 Score: 188
Period size: 59 Copynumber: 2.4 Consensus size: 59
14531 TGATAAGCCC
* * *
14541 GAATTTATATGATGTAACGATAATCTTGAAAATGAAGTATATAATGTAACAATAAACCT
1 GAATCTATATGATGTAACGATAAACTTGAAAATGAACTATATAATGTAACAATAAACCT
* * *
14600 GAATCTATGTGATGTAACGATAAACTTGAAAATGAACTATATGATGTAACGATAAACCT
1 GAATCTATATGATGTAACGATAAACTTGAAAATGAACTATATAATGTAACAATAAACCT
*
14659 AGAAATGAGCTATATGATGTGACGATAAAC
1 -G-AAT---CTATATGATGTAACGATAAAC
14689 CTAAAACCAA
Statistics
Matches: 76, Mismatches: 8, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
59 53 0.70
60 1 0.01
61 3 0.04
64 19 0.25
ACGTcount: A:0.44, C:0.10, G:0.17, T:0.29
Consensus pattern (59 bp):
GAATCTATATGATGTAACGATAAACTTGAAAATGAACTATATAATGTAACAATAAACCT
Found at i:20578 original size:30 final size:29
Alignment explanation
Indices: 20502--20579 Score: 102
Period size: 29 Copynumber: 2.7 Consensus size: 29
20492 ACTTGTAGTG
* *
20502 TTTGGACATTTTACCCCTTGAGTTTCAAT
1 TTTGGACATTTTACCCCCTGAATTTCAAT
*
20531 TTTTGACATTTTACCCCCTGAATTTCAAT
1 TTTGGACATTTTACCCCCTGAATTTCAAT
* *
20560 TTTGGGACGTTTTGCCCCCT
1 TTT-GGACATTTTACCCCCT
20580 CATACTAACG
Statistics
Matches: 42, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
29 29 0.69
30 13 0.31
ACGTcount: A:0.18, C:0.24, G:0.14, T:0.44
Consensus pattern (29 bp):
TTTGGACATTTTACCCCCTGAATTTCAAT
Found at i:20823 original size:29 final size:31
Alignment explanation
Indices: 20762--20826 Score: 100
Period size: 31 Copynumber: 2.2 Consensus size: 31
20752 ACAAAACGTC
20762 CCAAAATTGAAATTCATGTGGGATAAAATGT
1 CCAAAATTGAAATTCATGTGGGATAAAATGT
20793 CCAAAATTGAAATTCA-G-GGGACT-AAATGT
1 CCAAAATTGAAATTCATGTGGGA-TAAAATGT
20822 CCAAA
1 CCAAA
20827 TGCTACAAGT
Statistics
Matches: 33, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
29 15 0.45
30 2 0.06
31 16 0.48
ACGTcount: A:0.43, C:0.14, G:0.18, T:0.25
Consensus pattern (31 bp):
CCAAAATTGAAATTCATGTGGGATAAAATGT
Found at i:24012 original size:113 final size:112
Alignment explanation
Indices: 23797--24021 Score: 258
Period size: 113 Copynumber: 2.0 Consensus size: 112
23787 AAAGTTTTTT
* * * * *
23797 TCTTAATTTCTTTGATATGTTTTTTTTCGCGCATGGGTATCCAGAATTTTGCTCTGATTAATCTG
1 TCTTAATTTCTTTGATATGTTTTTTTTCGCCCATCGATATCCAGAATTTTGCTCTGACTAATCCG
* * * * ** *
23862 GATCCGACCCGCGTCGCGTACTGGTTATGGTGGGTGAGTCTATCAAC
66 GATCCAACCAGCGTCGCATACTGATTATACTGGGTGAGTCTACCAAC
*
23909 TCTTAATTTCTTTGATATGTTTTTTTTTAC-CCCATCGATATCCAGAGTTTTGCTC-GACTAATC
1 TCTTAATTTCTTTGATATG-TTTTTTTT-CGCCCATCGATATCCAGAATTTTGCTCTGACTAATC
* *
23972 CGGATTCAACCAGCGTTTTGCAT-CTGATTATACTGGGTGAGTCTACCAAC
64 CGGATCCAACCAGCG--TCGCATACTGATTATACTGGGTGAGTCTACCAAC
24022 AAACACCTAC
Statistics
Matches: 94, Mismatches: 15, Indels: 7
0.81 0.13 0.06
Matches are distributed among these distances:
112 37 0.39
113 52 0.55
114 5 0.05
ACGTcount: A:0.20, C:0.21, G:0.20, T:0.40
Consensus pattern (112 bp):
TCTTAATTTCTTTGATATGTTTTTTTTCGCCCATCGATATCCAGAATTTTGCTCTGACTAATCCG
GATCCAACCAGCGTCGCATACTGATTATACTGGGTGAGTCTACCAAC
Found at i:25538 original size:13 final size:13
Alignment explanation
Indices: 25520--25548 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
25510 ATCAAGTCAA
25520 TCCCCCCTTCACT
1 TCCCCCCTTCACT
25533 TCCCCCCTTCACT
1 TCCCCCCTTCACT
25546 TCC
1 TCC
25549 ATGTTAGCGC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.07, C:0.62, G:0.00, T:0.31
Consensus pattern (13 bp):
TCCCCCCTTCACT
Found at i:32328 original size:91 final size:91
Alignment explanation
Indices: 32217--32388 Score: 281
Period size: 91 Copynumber: 1.9 Consensus size: 91
32207 TAGCTACTTA
* * * * *
32217 GGTAAATTGTTTAAAATAATATATTAGGATAATACTGAATTAATAATATTTTAGAATATTTTTAA
1 GGTAAATTGCTGAAAATAATATATTAAGATAATACTGAATTAATAATATTTTAAAATACTTTTAA
*
32282 TTTACTCACCCAAACTTATCTACTCG
66 TTCACTCACCCAAACTTATCTACTCG
*
32308 GGTAAATTGCTGAAAATAATATATTAAGATAATAGTGAATTAATAATATTTTAAAATACTTTTAA
1 GGTAAATTGCTGAAAATAATATATTAAGATAATACTGAATTAATAATATTTTAAAATACTTTTAA
32373 TTCACTCACCCAAACT
66 TTCACTCACCCAAACT
32389 AATATATTGG
Statistics
Matches: 74, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
91 74 1.00
ACGTcount: A:0.42, C:0.11, G:0.09, T:0.38
Consensus pattern (91 bp):
GGTAAATTGCTGAAAATAATATATTAAGATAATACTGAATTAATAATATTTTAAAATACTTTTAA
TTCACTCACCCAAACTTATCTACTCG
Found at i:32424 original size:44 final size:44
Alignment explanation
Indices: 32367--32456 Score: 153
Period size: 44 Copynumber: 2.0 Consensus size: 44
32357 TTTAAAATAC
*
32367 TTTTAATTCACTCACCCAAACTAATATATTGGAATAATACTGAA
1 TTTTAATTAACTCACCCAAACTAATATATTGGAATAATACTGAA
* *
32411 TTTTAATTAACTCACCCAAACTAATATATTGGGATAATATTGAA
1 TTTTAATTAACTCACCCAAACTAATATATTGGAATAATACTGAA
32455 TT
1 TT
32457 AATGACTCTC
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
44 43 1.00
ACGTcount: A:0.40, C:0.16, G:0.08, T:0.37
Consensus pattern (44 bp):
TTTTAATTAACTCACCCAAACTAATATATTGGAATAATACTGAA
Found at i:34314 original size:40 final size:41
Alignment explanation
Indices: 34253--34329 Score: 147
Period size: 40 Copynumber: 1.9 Consensus size: 41
34243 TGCTATCCTC
34253 ACTCACCTATTTTCTTCTCTTGTCCTCATATCAAATACATT
1 ACTCACCTATTTTCTTCTCTTGTCCTCATATCAAATACATT
34294 ACTCACCTA-TTTCTTCTCTTGTCCTCATATCAAATA
1 ACTCACCTATTTTCTTCTCTTGTCCTCATATCAAATA
34330 ATATCAAATA
Statistics
Matches: 36, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
40 27 0.75
41 9 0.25
ACGTcount: A:0.25, C:0.30, G:0.03, T:0.43
Consensus pattern (41 bp):
ACTCACCTATTTTCTTCTCTTGTCCTCATATCAAATACATT
Found at i:36696 original size:190 final size:189
Alignment explanation
Indices: 36373--36757 Score: 630
Period size: 190 Copynumber: 2.0 Consensus size: 189
36363 CTTAAATAAT
*
36373 TACTATATTTATAACAATGCTTAATTTTAATGCATGTTTACTTCATGACCATATCTTTTGATATG
1 TACTATATTTATAACAATGCTTAATTTTAATGCATGTTTACTTCATGACCATATATTTTGATATG
*
36438 TGAAGTTGTCAATAATTGAATTTGAACGCTAATAATCAACATACAACACATATGTTCACATATAT
66 TGAAGTTGTCAATAATTAAATTTGAACGCTAATAATCAACATACAACACATATGTTCACATATAT
*
36503 TTTCTTCTTGCACACAAGACACTACTTGAGTAAAAGGTGATCTTCTGATCTAATTGCGAA
131 TTTCTTCTTG-ACACAAGACACTACTTGAGTAAAAGGTGATCTTCCGATCTAATTGCGAA
* *
36563 TACTATATTTATAACGATGCTTAATTTTAATGCAAT-TTTACTTCTTGACCATATATTTTGATAT
1 TACTATATTTATAACAATGCTTAATTTTAATGC-ATGTTTACTTCATGACCATATATTTTGATAT
* * *
36627 GTGAAGTTGTCAATAATTAAATTTGAACGCTCAA-AATCAACATACAACGCGTCTGTTCACATAT
65 GTGAAGTTGTCAATAATTAAATTTGAACGCT-AATAATCAACATACAACACATATGTTCACATAT
* *
36691 ATTTTCTTCTTGACACAAGACACTACTTGAGTAAAAGGTGGTCTTCCGGTCTAATTGCGAA
129 ATTTTCTTCTTGACACAAGACACTACTTGAGTAAAAGGTGATCTTCCGATCTAATTGCGAA
*
36752 TGCTAT
1 TACTAT
36758 TAGTAGCTAC
Statistics
Matches: 182, Mismatches: 11, Indels: 5
0.92 0.06 0.03
Matches are distributed among these distances:
189 51 0.28
190 127 0.70
191 4 0.02
ACGTcount: A:0.33, C:0.17, G:0.13, T:0.37
Consensus pattern (189 bp):
TACTATATTTATAACAATGCTTAATTTTAATGCATGTTTACTTCATGACCATATATTTTGATATG
TGAAGTTGTCAATAATTAAATTTGAACGCTAATAATCAACATACAACACATATGTTCACATATAT
TTTCTTCTTGACACAAGACACTACTTGAGTAAAAGGTGATCTTCCGATCTAATTGCGAA
Found at i:37170 original size:19 final size:20
Alignment explanation
Indices: 37138--37176 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 20
37128 TATTAAATTA
**
37138 ATTATAATTTAGAT-TTAAT
1 ATTATAATGAAGATCTTAAT
37157 ATTATAATGAAGATCTTAAT
1 ATTATAATGAAGATCTTAAT
37177 CCAATCATAC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 12 0.71
20 5 0.29
ACGTcount: A:0.44, C:0.03, G:0.08, T:0.46
Consensus pattern (20 bp):
ATTATAATGAAGATCTTAAT
Found at i:38867 original size:15 final size:14
Alignment explanation
Indices: 38842--38871 Score: 51
Period size: 15 Copynumber: 2.1 Consensus size: 14
38832 GTTCTTATAC
38842 TTTTATTTTTAATT
1 TTTTATTTTTAATT
38856 TTTTAGTTTTTAATT
1 TTTTA-TTTTTAATT
38871 T
1 T
38872 GATGGTACAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.33
15 10 0.67
ACGTcount: A:0.20, C:0.00, G:0.03, T:0.77
Consensus pattern (14 bp):
TTTTATTTTTAATT
Found at i:53625 original size:2 final size:2
Alignment explanation
Indices: 53618--53645 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
53608 ATTGATATGG
53618 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
53646 TCAGAGACAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:54542 original size:3 final size:3
Alignment explanation
Indices: 54534--54595 Score: 56
Period size: 3 Copynumber: 21.0 Consensus size: 3
54524 CCTTTCTCTC
* * * * *
54534 CTT CTT CTT CTT CTT CAT -TT CTT CTG CTT CTT CTC CTT TTT TTT CTT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
54581 CTT -TCT CTT CTT CTT
1 CTT CT-T CTT CTT CTT
54596 TATATCTGTC
Statistics
Matches: 48, Mismatches: 8, Indels: 6
0.77 0.13 0.10
Matches are distributed among these distances:
2 2 0.04
3 45 0.94
4 1 0.02
ACGTcount: A:0.02, C:0.31, G:0.02, T:0.66
Consensus pattern (3 bp):
CTT
Found at i:61305 original size:50 final size:49
Alignment explanation
Indices: 61250--61390 Score: 213
Period size: 43 Copynumber: 3.0 Consensus size: 49
61240 ATTATAGGAG
61250 TTTTTACATAGTAATCTCAATTCGTATAGAAAAACAAAAGGGTAACGGGT
1 TTTTTACATAGTAATCTCAATTCGTATAGAAAAA-AAAAGGGTAACGGGT
*
61300 TTTTTACATAGTAATCTCAATTCGTATAG-AAAAATAA----AA-GGGT
1 TTTTTACATAGTAATCTCAATTCGTATAGAAAAAAAAAGGGTAACGGGT
61343 TTTTTACATAGTAATCTCAATTCGTATAGAAAAATAAAAGGGTAACGG
1 TTTTTACATAGTAATCTCAATTCGTATAGAAAAA-AAAAGGGTAACGG
61391 ACCAACATTA
Statistics
Matches: 82, Mismatches: 2, Indels: 14
0.84 0.02 0.14
Matches are distributed among these distances:
43 33 0.40
44 6 0.07
45 3 0.04
48 3 0.04
49 6 0.07
50 31 0.38
ACGTcount: A:0.41, C:0.11, G:0.16, T:0.32
Consensus pattern (49 bp):
TTTTTACATAGTAATCTCAATTCGTATAGAAAAAAAAAGGGTAACGGGT
Found at i:64951 original size:31 final size:29
Alignment explanation
Indices: 64915--64984 Score: 86
Period size: 29 Copynumber: 2.3 Consensus size: 29
64905 ATCATTTTCG
*
64915 CCCCTGAACTTGTACGGTTTGGACGATTTGC
1 CCCCTGAACTT-TA-AGTTTGGACGATTTGC
* *
64946 CCCCTGAACTTTAATTTTGGACGTTTTGC
1 CCCCTGAACTTTAAGTTTGGACGATTTGC
*
64975 CCCCTAAACT
1 CCCCTGAACT
64985 CTCAATGCTG
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
29 22 0.63
30 2 0.06
31 11 0.31
ACGTcount: A:0.19, C:0.29, G:0.19, T:0.34
Consensus pattern (29 bp):
CCCCTGAACTTTAAGTTTGGACGATTTGC
Found at i:68459 original size:204 final size:203
Alignment explanation
Indices: 67988--68397 Score: 603
Period size: 204 Copynumber: 2.0 Consensus size: 203
67978 TTCCTTAATA
* * * * *
67988 ATAAATAAATCGGATCTTTAATATCTTTTATAATTTTGAAAGT-TTGTTTGACATTGATCTAATT
1 ATAAATAAAGCGGAACGTTAATATCTTTTATAATTATGAAA-TATAGTTTGACATT-ATCTAATT
*
68052 TAATTTAATAAATCAACCACTAATATTCAACTAATTTTTTTTGGTATAGTTCTATATATATAATA
64 TAATTTAATAAATCAACCACTAATATTCAACTAATGTTTTTTGGTATAGTTCTATATATATAATA
* * *
68117 GTAATGTGTTGTATCTTATTCACTACAACTTTGATAGTAACCTTAGACTTAAAAAATTATTAACA
129 ATAATGTGTTGTATCTTATTCACTACAACTTTGATAGAAACCTTAGACTTAAAAAATTAATAACA
68182 TTCACCATTG
194 TTCACCATTG
* * * * * *
68192 ATAAATAAATCGGATCTTTAATATCTTTTATAATTTTGAAATTTTGTTTGACATTGATCTAATTT
1 ATAAATAAAGCGGAACGTTAATATCTTTTATAATTATGAAATATAGTTTGACATT-ATCTAATTT
*
68257 AATTTAATAAATCAACCACTAATGTTCAACTAATGTTTTTTGGTATAGTT-T-TATATATAATAA
65 AATTTAATAAATCAACCACTAATATTCAACTAATGTTTTTTGGTATAGTTCTATATATATAATAA
* *
68320 TAATGTGTTGTATCTTATTCACTACAACTTTGTTAGAAATCTTAGACTT-AAAAATTAATAACAT
130 TAATGTGTTGTATCTTATTCACTACAACTTTGATAGAAACCTTAGACTTAAAAAATTAATAACAT
68384 TCACCATTG
195 TCACCATTG
68393 ATAAA
1 ATAAA
68398 GTTATTAAGC
Statistics
Matches: 198, Mismatches: 7, Indels: 5
0.94 0.03 0.02
Matches are distributed among these distances:
201 28 0.14
202 57 0.29
203 2 0.01
204 111 0.56
ACGTcount: A:0.37, C:0.11, G:0.09, T:0.43
Consensus pattern (203 bp):
ATAAATAAAGCGGAACGTTAATATCTTTTATAATTATGAAATATAGTTTGACATTATCTAATTTA
ATTTAATAAATCAACCACTAATATTCAACTAATGTTTTTTGGTATAGTTCTATATATATAATAAT
AATGTGTTGTATCTTATTCACTACAACTTTGATAGAAACCTTAGACTTAAAAAATTAATAACATT
CACCATTG
Found at i:68958 original size:36 final size:36
Alignment explanation
Indices: 68911--68980 Score: 113
Period size: 36 Copynumber: 1.9 Consensus size: 36
68901 GAGATTTTGG
* *
68911 AGAAATATGATAATCAAAATTACAAAAAATGTAATA
1 AGAAATATGATAACCAAAATCACAAAAAATGTAATA
*
68947 AGAAATATGATAACCAAAATCACAAAAGATGTAA
1 AGAAATATGATAACCAAAATCACAAAAAATGTAA
68981 GGTTATCGAA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 31 1.00
ACGTcount: A:0.60, C:0.09, G:0.10, T:0.21
Consensus pattern (36 bp):
AGAAATATGATAACCAAAATCACAAAAAATGTAATA
Found at i:76907 original size:32 final size:32
Alignment explanation
Indices: 76866--76977 Score: 154
Period size: 32 Copynumber: 3.5 Consensus size: 32
76856 GGTATTGCTA
76866 ACGTGGCAATGCCACGTTGGACCAAAAATGTC
1 ACGTGGCAATGCCACGTTGGACCAAAAATGTC
* * **
76898 ACGTGGCAATGCCAAGTCGGATAAAAAATGTC
1 ACGTGGCAATGCCACGTTGGACCAAAAATGTC
* * *
76930 ACGTGGCATTGCCACATTGGACC-AAAATGCC
1 ACGTGGCAATGCCACGTTGGACCAAAAATGTC
76961 ACGTGGCAATGCCACGT
1 ACGTGGCAATGCCACGT
76978 CAGCAATATT
Statistics
Matches: 67, Mismatches: 13, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
31 22 0.33
32 45 0.67
ACGTcount: A:0.31, C:0.25, G:0.25, T:0.19
Consensus pattern (32 bp):
ACGTGGCAATGCCACGTTGGACCAAAAATGTC
Found at i:81364 original size:20 final size:20
Alignment explanation
Indices: 81339--81379 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
81329 TCCATAGTTT
*
81339 TAAATAAAGGATAATCGCAA
1 TAAATAAAGGACAATCGCAA
81359 TAAATAAAGGACAATCGCAA
1 TAAATAAAGGACAATCGCAA
81379 T
1 T
81380 CTCAGAAATG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.54, C:0.12, G:0.15, T:0.20
Consensus pattern (20 bp):
TAAATAAAGGACAATCGCAA
Found at i:88923 original size:13 final size:14
Alignment explanation
Indices: 88904--88937 Score: 52
Period size: 13 Copynumber: 2.5 Consensus size: 14
88894 GGTGTTTCAA
88904 ATAATATTTAA-AT
1 ATAATATTTAATAT
*
88917 TTAATATTTAATAT
1 ATAATATTTAATAT
88931 ATAATAT
1 ATAATAT
88938 ATATATAATT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
13 10 0.56
14 8 0.44
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (14 bp):
ATAATATTTAATAT
Found at i:88927 original size:7 final size:7
Alignment explanation
Indices: 88905--88937 Score: 50
Period size: 7 Copynumber: 4.9 Consensus size: 7
88895 GTGTTTCAAA
88905 TAATATT
1 TAATATT
88912 TAA-ATT
1 TAATATT
88918 TAATATT
1 TAATATT
*
88925 TAATATA
1 TAATATT
88932 TAATAT
1 TAATAT
88938 ATATATAATT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
6 6 0.25
7 18 0.75
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (7 bp):
TAATATT
Done.