Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1396
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: 309291
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
File 3 of 3
Found at i:245402 original size:14 final size:14
Alignment explanation
Indices: 245337--245403 Score: 50
Period size: 14 Copynumber: 4.8 Consensus size: 14
245327 AATTTTTAAA
* *
245337 TAAATTTTATTTTT
1 TAAATTTAAATTTT
*
245351 TAAATTTAATAATTT
1 TAAATTTAA-ATTTT
245366 T--ATTTAAATTTTTT
1 TAAATTTAAA--TTTT
*
245380 TAAA-ATAAATTTT
1 TAAATTTAAATTTT
245393 TAAATTTAAAT
1 TAAATTTAAAT
245404 GAATAATCAG
Statistics
Matches: 41, Mismatches: 6, Indels: 12
0.69 0.10 0.20
Matches are distributed among these distances:
12 1 0.02
13 14 0.34
14 17 0.41
15 8 0.20
16 1 0.02
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (14 bp):
TAAATTTAAATTTT
Found at i:250280 original size:3 final size:3
Alignment explanation
Indices: 250274--250305 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
250264 TTGTTTTATT
250274 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
250306 CAAGTATTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:250771 original size:3 final size:3
Alignment explanation
Indices: 250763--250804 Score: 84
Period size: 3 Copynumber: 14.0 Consensus size: 3
250753 ATAAAACATG
250763 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
250805 TACATACCAG
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:251412 original size:10 final size:8
Alignment explanation
Indices: 251376--251408 Score: 57
Period size: 8 Copynumber: 4.1 Consensus size: 8
251366 CATATAAATA
*
251376 TAATTTTT
1 TAATATTT
251384 TAATATTT
1 TAATATTT
251392 TAATATTT
1 TAATATTT
251400 TAATATTT
1 TAATATTT
251408 T
1 T
251409 TTAAATAATG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
8 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (8 bp):
TAATATTT
Found at i:251804 original size:20 final size:23
Alignment explanation
Indices: 251779--251831 Score: 67
Period size: 25 Copynumber: 2.3 Consensus size: 23
251769 AGTTTGATTG
251779 ATTTAT-TT-TTTA-ATTATATA
1 ATTTATATTATTTATATTATATA
251799 ATTTATATTATTTATCTATTATATA
1 ATTTATATTATTTA--TATTATATA
251824 ATTTATAT
1 ATTTATAT
251832 CGTATAAAGA
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
20 6 0.21
21 2 0.07
22 4 0.14
25 16 0.57
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (23 bp):
ATTTATATTATTTATATTATATA
Found at i:252402 original size:12 final size:12
Alignment explanation
Indices: 252385--252409 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
252375 TATTTGTTTT
252385 GCCTTAGACGGC
1 GCCTTAGACGGC
252397 GCCTTAGACGGC
1 GCCTTAGACGGC
252409 G
1 G
252410 GTTATTGTTC
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:0.16, C:0.32, G:0.36, T:0.16
Consensus pattern (12 bp):
GCCTTAGACGGC
Found at i:252794 original size:20 final size:20
Alignment explanation
Indices: 252769--252807 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
252759 TAAGTATTAT
252769 ATATATTTATTCTTTATATG
1 ATATATTTATTCTTTATATG
*
252789 ATATATTTATTTTTTATAT
1 ATATATTTATTCTTTATAT
252808 AATAAAAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.31, C:0.03, G:0.03, T:0.64
Consensus pattern (20 bp):
ATATATTTATTCTTTATATG
Found at i:252842 original size:26 final size:26
Alignment explanation
Indices: 252809--252866 Score: 77
Period size: 26 Copynumber: 2.3 Consensus size: 26
252799 TTTTTATATA
252809 ATAAAAATTACATA-ATATATATA-AAT
1 ATAAAAATTA-ATATATAT-TATACAAT
252835 ATAAAAATTAATATATATTATACAAT
1 ATAAAAATTAATATATATTATACAAT
252861 -TAAAAA
1 ATAAAAA
252867 CGAGTCTAGT
Statistics
Matches: 30, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
25 13 0.43
26 17 0.57
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.34
Consensus pattern (26 bp):
ATAAAAATTAATATATATTATACAAT
Found at i:254582 original size:13 final size:13
Alignment explanation
Indices: 254564--254589 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
254554 CAATTTTTTG
254564 TGTATCGATACAT
1 TGTATCGATACAT
254577 TGTATCGATACAT
1 TGTATCGATACAT
254590 ACTTGCTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:257110 original size:13 final size:13
Alignment explanation
Indices: 257092--257130 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
257082 ATAATCACCC
*
257092 TGTATCGATACAG
1 TGTATCGATACAA
257105 TGTATCGATACAA
1 TGTATCGATACAA
257118 TGTATCGATACAA
1 TGTATCGATACAA
257131 AGAAAAATGT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.36, C:0.15, G:0.18, T:0.31
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:257141 original size:20 final size:20
Alignment explanation
Indices: 257116--257154 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
257106 GTATCGATAC
257116 AATGTATCGATACAAAGAAA
1 AATGTATCGATACAAAGAAA
*
257136 AATGTATCGATACATAGAA
1 AATGTATCGATACAAAGAA
257155 TTTCCAGATG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.51, C:0.10, G:0.15, T:0.23
Consensus pattern (20 bp):
AATGTATCGATACAAAGAAA
Found at i:261066 original size:21 final size:21
Alignment explanation
Indices: 261037--261081 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
261027 AAGTTTTCAT
*
261037 TTTTCTTAGCTAAC-TCATTA
1 TTTTCTTAGCCAACTTCATTA
*
261057 TTTTCATTAGCCAACTTCTTTA
1 TTTTC-TTAGCCAACTTCATTA
261079 TTT
1 TTT
261082 CAACTTGCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 8 0.38
22 8 0.38
ACGTcount: A:0.22, C:0.20, G:0.04, T:0.53
Consensus pattern (21 bp):
TTTTCTTAGCCAACTTCATTA
Found at i:263313 original size:13 final size:13
Alignment explanation
Indices: 263295--263320 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
263285 CAATTTTTTG
263295 TGTATCGATACAT
1 TGTATCGATACAT
263308 TGTATCGATACAT
1 TGTATCGATACAT
263321 ACTTGCTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:265409 original size:20 final size:20
Alignment explanation
Indices: 265381--265455 Score: 87
Period size: 20 Copynumber: 3.8 Consensus size: 20
265371 TCATACCCTG
265381 ATGTATCGATACATTTTTCA
1 ATGTATCGATACATTTTTCA
* * * *
265401 ATATATCGATACATGTATGA
1 ATGTATCGATACATTTTTCA
* * *
265421 ATGTATCGATATATTCTACA
1 ATGTATCGATACATTTTTCA
265441 ATGTATCGATACATT
1 ATGTATCGATACATT
265456 ATGTCTTTTT
Statistics
Matches: 43, Mismatches: 12, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
20 43 1.00
ACGTcount: A:0.35, C:0.13, G:0.12, T:0.40
Consensus pattern (20 bp):
ATGTATCGATACATTTTTCA
Found at i:265448 original size:40 final size:39
Alignment explanation
Indices: 265381--265458 Score: 111
Period size: 40 Copynumber: 2.0 Consensus size: 39
265371 TCATACCCTG
* *
265381 ATGTATCGATACATTTTTCAATATATCGATACATGTATGA
1 ATGTATCGATACATTCTACAATATATCGATACAT-TATGA
* *
265421 ATGTATCGATATATTCTACAATGTATCGATACATTATG
1 ATGTATCGATACATTCTACAATATATCGATACATTATG
265459 TCTTTTTACC
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
39 4 0.12
40 30 0.88
ACGTcount: A:0.35, C:0.13, G:0.13, T:0.40
Consensus pattern (39 bp):
ATGTATCGATACATTCTACAATATATCGATACATTATGA
Found at i:266392 original size:23 final size:23
Alignment explanation
Indices: 266365--266420 Score: 96
Period size: 22 Copynumber: 2.5 Consensus size: 23
266355 AGCCTTTGAC
266365 CATGCATTTTTTTTATTATGTTT
1 CATGCATTTTTTTTATTATGTTT
266388 CATGCA-TTTTTTTATTATGTTT
1 CATGCATTTTTTTTATTATGTTT
*
266410 CATGTATTTTT
1 CATGCATTTTT
266421 AACATGTCCA
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
22 21 0.68
23 10 0.32
ACGTcount: A:0.18, C:0.09, G:0.09, T:0.64
Consensus pattern (23 bp):
CATGCATTTTTTTTATTATGTTT
Found at i:269611 original size:20 final size:20
Alignment explanation
Indices: 269583--269657 Score: 87
Period size: 20 Copynumber: 3.8 Consensus size: 20
269573 TTTTACCTTG
269583 ATGTATCGATACATTTTTCA
1 ATGTATCGATACATTTTTCA
* * * *
269603 ATATATCGATACATGTATGA
1 ATGTATCGATACATTTTTCA
* * *
269623 ATGTATCGATATATTCTACA
1 ATGTATCGATACATTTTTCA
269643 ATGTATCGATACATT
1 ATGTATCGATACATT
269658 ATGTCTTTTT
Statistics
Matches: 43, Mismatches: 12, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
20 43 1.00
ACGTcount: A:0.35, C:0.13, G:0.12, T:0.40
Consensus pattern (20 bp):
ATGTATCGATACATTTTTCA
Found at i:269650 original size:40 final size:39
Alignment explanation
Indices: 269583--269660 Score: 111
Period size: 40 Copynumber: 2.0 Consensus size: 39
269573 TTTTACCTTG
* *
269583 ATGTATCGATACATTTTTCAATATATCGATACATGTATGA
1 ATGTATCGATACATTCTACAATATATCGATACAT-TATGA
* *
269623 ATGTATCGATATATTCTACAATGTATCGATACATTATG
1 ATGTATCGATACATTCTACAATATATCGATACATTATG
269661 TCTTTTTACC
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
39 4 0.12
40 30 0.88
ACGTcount: A:0.35, C:0.13, G:0.13, T:0.40
Consensus pattern (39 bp):
ATGTATCGATACATTCTACAATATATCGATACATTATGA
Found at i:280283 original size:456 final size:456
Alignment explanation
Indices: 279430--280344 Score: 1767
Period size: 456 Copynumber: 2.0 Consensus size: 456
279420 GACATTTGTG
279430 GGAGAAGGGTTGCCAATAATTGAACCTTGCTTGTCAGGAAGCACCCATTTGGGTTTAAAAATGAC
1 GGAGAAGGGTTGCCAATAATTGAACCTTGCTTGTCAGGAAGCACCCATTTGGGTTTAAAAATGAC
**
279495 CGTGGGCAAAGGGTGTCGTGCTGGAAAAGGGCTCGGCAAGGATCTACAAGGGATAACACAAGCTT
66 CGTGGGCAAAGGGTGTCACGCTGGAAAAGGGCTCGGCAAGGATCTACAAGGGATAACACAAGCTT
279560 TGCAAGTAGCCACTCAAGTGGATAAAAGAGGCTTAAGATATAAAGCTAATGCACAGTCAAGGAAG
131 TGCAAGTAGCCACTCAAGTGGATAAAAGAGGCTTAAGATATAAAGCTAATGCACAGTCAAGGAAG
279625 CAGCAGGCAAGAATGATCCATAGCCAGAAGATGAGGCAATCTTTGGGTCAAGAAGAGGAATTAAA
196 CAGCAGGCAAGAATGATCCATAGCCAGAAGATGAGGCAATCTTTGGGTCAAGAAGAGGAATTAAA
279690 ATCAACAATGTTCCCACCACTCCATAAGACATTCTGCTTAGGAGGACAAACCGATTCACCCCAAC
261 ATCAACAATGTTCCCACCACTCCATAAGACATTCTGCTTAGGAGGACAAACCGATTCACCCCAAC
279755 CAGAAAAGCAAAAGACTGCAGATGTCTTAGTCATCTTAAATAAAGCAATCCATAACCTCTATCTC
326 CAGAAAAGCAAAAGACTGCAGATGTCTTAGTCATCTTAAATAAAGCAATCCATAACCTCTATCTC
*
279820 CAGGATATCGAGCCATAAAACTTGTGTCTTTCCTGTAAAACCTAATCTTGACAATGGGATCATGG
391 CAGGATATCGAGCCATAAAACTTGTGTCTTTCCTGTAAAACCTAATCTTAACAATGGGATCATGG
279885 C
456 C
279886 GGAGAAGGGTTGCCAATAATTGAACCTTGCTTGTCAGGAAGCACCCATTTGGGTTTAAAAATGAC
1 GGAGAAGGGTTGCCAATAATTGAACCTTGCTTGTCAGGAAGCACCCATTTGGGTTTAAAAATGAC
279951 CGTGGGCAAAGGGTGTCACGCTGGAAAAGGGCTCGGCAAGGATCTACAAGGGATAACACAAGCTT
66 CGTGGGCAAAGGGTGTCACGCTGGAAAAGGGCTCGGCAAGGATCTACAAGGGATAACACAAGCTT
* *
280016 TGCAAGTAGCCACTTAAGTGGATAAAAGAGGCTTAGGATATAAAGCTAATGCACAGTCAAGGAAG
131 TGCAAGTAGCCACTCAAGTGGATAAAAGAGGCTTAAGATATAAAGCTAATGCACAGTCAAGGAAG
280081 CAGCAGGCAAGAATGATCCATAGCCAGAAGATGAGGCAATCTTTGGGTCAAGAAGAGGAATTAAA
196 CAGCAGGCAAGAATGATCCATAGCCAGAAGATGAGGCAATCTTTGGGTCAAGAAGAGGAATTAAA
280146 ATCAACAATGTTCCCACCACTCCATAAGACATTCTGCTTAGGAGGACAAACCGATTCACCCCAAC
261 ATCAACAATGTTCCCACCACTCCATAAGACATTCTGCTTAGGAGGACAAACCGATTCACCCCAAC
* *
280211 CAGAAAAGCAGAAGGCTGCAGATGTCTTAGTCATCTTAAATAAAGCAATCCATAACCTCTATCTC
326 CAGAAAAGCAAAAGACTGCAGATGTCTTAGTCATCTTAAATAAAGCAATCCATAACCTCTATCTC
280276 CAGGATATCGAGCCATAAAACTTGTGTCTTTCCTGTAAAACCTAATCTTAACAATGGGATCATGG
391 CAGGATATCGAGCCATAAAACTTGTGTCTTTCCTGTAAAACCTAATCTTAACAATGGGATCATGG
280341 C
456 C
280342 GGA
1 GGA
280345 AACCCCTGCA
Statistics
Matches: 452, Mismatches: 7, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
456 452 1.00
ACGTcount: A:0.35, C:0.21, G:0.23, T:0.22
Consensus pattern (456 bp):
GGAGAAGGGTTGCCAATAATTGAACCTTGCTTGTCAGGAAGCACCCATTTGGGTTTAAAAATGAC
CGTGGGCAAAGGGTGTCACGCTGGAAAAGGGCTCGGCAAGGATCTACAAGGGATAACACAAGCTT
TGCAAGTAGCCACTCAAGTGGATAAAAGAGGCTTAAGATATAAAGCTAATGCACAGTCAAGGAAG
CAGCAGGCAAGAATGATCCATAGCCAGAAGATGAGGCAATCTTTGGGTCAAGAAGAGGAATTAAA
ATCAACAATGTTCCCACCACTCCATAAGACATTCTGCTTAGGAGGACAAACCGATTCACCCCAAC
CAGAAAAGCAAAAGACTGCAGATGTCTTAGTCATCTTAAATAAAGCAATCCATAACCTCTATCTC
CAGGATATCGAGCCATAAAACTTGTGTCTTTCCTGTAAAACCTAATCTTAACAATGGGATCATGG
C
Found at i:284119 original size:11 final size:10
Alignment explanation
Indices: 284103--284148 Score: 65
Period size: 10 Copynumber: 4.5 Consensus size: 10
284093 TTTACACCCC
284103 AAAAAAAACA
1 AAAAAAAACA
284113 AAAAAAAACA
1 AAAAAAAACA
*
284123 AAAAAAAAGA
1 AAAAAAAACA
*
284133 AAAAAATAGCA
1 AAAAAA-AACA
284144 AAAAA
1 AAAAA
284149 TAGAAGGGTC
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
10 25 0.78
11 7 0.22
ACGTcount: A:0.87, C:0.07, G:0.04, T:0.02
Consensus pattern (10 bp):
AAAAAAAACA
Found at i:285392 original size:29 final size:29
Alignment explanation
Indices: 285350--286265 Score: 1283
Period size: 28 Copynumber: 31.9 Consensus size: 29
285340 AATGTTCATC
285350 CCTTTCAAAGCCCACAAGTCAGTGGCACT
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
*
285379 CCTTTCAAAGCCCACAAATCAGTGGCACT
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
** *
285408 ATTTTTAAAGCCCACAAGTCAGTGGCAC-
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
*
285436 CTTTTCAAAGCCCACAAGTCAGTGGCAC-
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
285464 CCTTTCAAAGCCCACAAGTCAGTGGCACT
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
*
285493 CTTTTCAAAGCCCACAAGTCAGTGGCAC-
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
285521 CCTTTCAAAGCCCACAAGTCAGTGGCACT
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
* * *
285550 CTTTTCAAAGCCCACAAGTTAATGGCAC-
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
285578 CCTTTCAAAGCCCACAAGTCAGTGGCACT
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
285607 CCTTTCAAAGCCCACAAGTCAGTGGCACT
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
*
285636 CTTTTCAAAGCCCACAAGTCAGTGGCAC-
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
* *
285664 CCTTTCAAAGCCCACAACTCAGTGACAC-
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
*
285692 CCTTTCAAAGCCCACAAGTTAGTGGCACT
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
* *
285721 TCTTTCAAAGCCCACAAGTCAATGGCACT
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
* *
285750 CTTTTCAAAGCCCACAAATCAGTGGCACT
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
* * *
285779 CTTTTCAAAGCCCACAAGTTAGTGACAC-
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
*
285807 CCTTTCAAAGCCCACAAGTTAGTGGCACT
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
285836 CCTTTCAAAGCCCACAAGTCAGTGGCACT
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
285865 CCTTTCAAAGCCCACAAGTCAGTGGCACT
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
*
285894 CTTTTCAAAGCCCACAAGTCAGTGGCAC-
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
*
285922 CCTTTCAAAGCCCACAAGTTAGTGGCAC-
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
*
285950 CCTTTCAGAGCCCACAAGTCAGTGGCA-T
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
*
285978 CCTTTCGAAGCCCACAAGTCAGTGGCAC-
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
* * * * *
286006 CATTGCGAAGCCCACAATTCGGTGGCACT
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
286035 -CTTTCAAAGCCCACAAGTCAGTGGCAC-
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
*
286062 CCTTTTAAAGCCCACACAAGTCAGTGGCACT
1 CCTTTCAAAG-CC-CACAAGTCAGTGGCACT
* *
286093 CCTTTTAAAGCTCACACAAGTCAGTGGTAC-
1 CCTTTCAAAGC-C-CACAAGTCAGTGGCACT
*
286123 CTTTTCAAAGCCCACAAGTCAGTGGCACT
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
286152 -CTTTCAAAGCCCACAAGTCAGTGGCA-T
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
* *
286179 CCTTTCAAAGCCCACGAGTTAGTGGCA-T
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
*
286207 TCTTTCAAAGCCCACGCAAGTCAGTGGCAC-
1 CCTTTCAAAGCCCA--CAAGTCAGTGGCACT
* *
286237 CCTTTTAAAGCCCATGCAAGTCAATGGCA
1 CCTTTCAAAGCCCA--CAAGTCAGTGGCA
286266 ACCCTTTTCA
Statistics
Matches: 802, Mismatches: 67, Indels: 35
0.89 0.07 0.04
Matches are distributed among these distances:
27 1 0.00
28 389 0.49
29 323 0.40
30 62 0.08
31 27 0.03
ACGTcount: A:0.29, C:0.32, G:0.17, T:0.22
Consensus pattern (29 bp):
CCTTTCAAAGCCCACAAGTCAGTGGCACT
Found at i:285460 original size:57 final size:57
Alignment explanation
Indices: 285350--286265 Score: 1246
Period size: 57 Copynumber: 16.0 Consensus size: 57
285340 AATGTTCATC
* *
285350 CCTTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCCCACAAATCAGTGGCACT
1 CCTTTCAAAGCCCACAAGTCAGTGGCAC-CTTTTCAAAGCCCACAAGTCAGTGGCACT
** *
285408 ATTTTTAAAGCCCACAAGTCAGTGGCACCTTTTCAAAGCCCACAAGTCAGTGGCAC-
1 CCTTTCAAAGCCCACAAGTCAGTGGCACCTTTTCAAAGCCCACAAGTCAGTGGCACT
285464 CCTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCAC-
1 CCTTTCAAAGCCCACAAGTCAGTGGCAC-CTTTTCAAAGCCCACAAGTCAGTGGCACT
* *
285521 CCTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACAAGTTAATGGCAC-
1 CCTTTCAAAGCCCACAAGTCAGTGGCAC-CTTTTCAAAGCCCACAAGTCAGTGGCACT
*
285578 CCTTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCCCACAAGTCAGTGGCACT
1 CCTTTCAAAGCCCACAAGTCAGTGGCAC-CTTTTCAAAGCCCACAAGTCAGTGGCACT
* * * *
285636 CTTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAACTCAGTGACAC-
1 CCTTTCAAAGCCCACAAGTCAGTGGCACCTTTTCAAAGCCCACAAGTCAGTGGCACT
* * *
285692 CCTTTCAAAGCCCACAAGTTAGTGGCACTTCTTTCAAAGCCCACAAGTCAATGGCACT
1 CCTTTCAAAGCCCACAAGTCAGTGGCACCT-TTTCAAAGCCCACAAGTCAGTGGCACT
* * * *
285750 CTTTTCAAAGCCCACAAATCAGTGGCACTCTTTTCAAAGCCCACAAGTTAGTGACAC-
1 CCTTTCAAAGCCCACAAGTCAGTGGCAC-CTTTTCAAAGCCCACAAGTCAGTGGCACT
* *
285807 CCTTTCAAAGCCCACAAGTTAGTGGCACTCCTTTCAAAGCCCACAAGTCAGTGGCACT
1 CCTTTCAAAGCCCACAAGTCAGTGGCAC-CTTTTCAAAGCCCACAAGTCAGTGGCACT
285865 CCTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCAC-
1 CCTTTCAAAGCCCACAAGTCAGTGGCAC-CTTTTCAAAGCCCACAAGTCAGTGGCACT
* * *
285922 CCTTTCAAAGCCCACAAGTTAGTGGCACCCTTTCAGAGCCCACAAGTCAGTGGCA-T
1 CCTTTCAAAGCCCACAAGTCAGTGGCACCTTTTCAAAGCCCACAAGTCAGTGGCACT
* * * * * *
285978 CCTTTCGAAGCCCACAAGTCAGTGGCACCATTGCGAAGCCCACAATTCGGTGGCACT
1 CCTTTCAAAGCCCACAAGTCAGTGGCACCTTTTCAAAGCCCACAAGTCAGTGGCACT
286035 -CTTTCAAAGCCCACAAGTCAGTGGCACCCTTTT-AAAGCCCACACAAGTCAGTGGCACT
1 CCTTTCAAAGCCCACAAGTCAGTGGCA-CCTTTTCAAAG-CC-CACAAGTCAGTGGCACT
* *
286093 CCTTTTAAAGCTCACACAAGTCAGTGGTACCTTTTCAAAGCCCACAAGTCAGTGGCACT
1 CCTTTCAAAGC-C-CACAAGTCAGTGGCACCTTTTCAAAGCCCACAAGTCAGTGGCACT
* *
286152 -CTTTCAAAGCCCACAAGTCAGTGGCATCC-TTTCAAAGCCCACGAGTTAGTGGCA-T
1 CCTTTCAAAGCCCACAAGTCAGTGGCA-CCTTTTCAAAGCCCACAAGTCAGTGGCACT
* *
286207 TCTTTCAAAGCCCACGCAAGTCAGTGGCACCCTTTT-AAAGCCCATGCAAGTCAATGGCA
1 CCTTTCAAAGCCCA--CAAGTCAGTGGCA-CCTTTTCAAAGCCCA--CAAGTCAGTGGCA
286266 ACCCTTTTCA
Statistics
Matches: 771, Mismatches: 65, Indels: 42
0.88 0.07 0.05
Matches are distributed among these distances:
55 1 0.00
56 201 0.26
57 300 0.39
58 202 0.26
59 30 0.04
60 19 0.02
61 18 0.02
ACGTcount: A:0.29, C:0.32, G:0.17, T:0.22
Consensus pattern (57 bp):
CCTTTCAAAGCCCACAAGTCAGTGGCACCTTTTCAAAGCCCACAAGTCAGTGGCACT
Found at i:286781 original size:20 final size:20
Alignment explanation
Indices: 286753--286827 Score: 87
Period size: 20 Copynumber: 3.8 Consensus size: 20
286743 TTTTACCTTG
286753 ATGTATCGATACATTTTTCA
1 ATGTATCGATACATTTTTCA
* * * *
286773 ATATATCGATACATGTATGA
1 ATGTATCGATACATTTTTCA
* * *
286793 ATGTATCGATATATTCTACA
1 ATGTATCGATACATTTTTCA
286813 ATGTATCGATACATT
1 ATGTATCGATACATT
286828 ATGTCTTTTT
Statistics
Matches: 43, Mismatches: 12, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
20 43 1.00
ACGTcount: A:0.35, C:0.13, G:0.12, T:0.40
Consensus pattern (20 bp):
ATGTATCGATACATTTTTCA
Found at i:286820 original size:40 final size:39
Alignment explanation
Indices: 286753--286830 Score: 111
Period size: 40 Copynumber: 2.0 Consensus size: 39
286743 TTTTACCTTG
* *
286753 ATGTATCGATACATTTTTCAATATATCGATACATGTATGA
1 ATGTATCGATACATTCTACAATATATCGATACAT-TATGA
* *
286793 ATGTATCGATATATTCTACAATGTATCGATACATTATG
1 ATGTATCGATACATTCTACAATATATCGATACATTATG
286831 TCTTTTTACC
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
39 4 0.12
40 30 0.88
ACGTcount: A:0.35, C:0.13, G:0.13, T:0.40
Consensus pattern (39 bp):
ATGTATCGATACATTCTACAATATATCGATACATTATGA
Found at i:291642 original size:20 final size:20
Alignment explanation
Indices: 291619--291657 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
291609 TTATAATTAC
291619 ATTTAAATAAA-AATAATTTT
1 ATTT-AATAAATAATAATTTT
*
291639 ATTTATTAAATAATAATTT
1 ATTTAATAAATAATAATTT
291658 AAACTAACCT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (20 bp):
ATTTAATAAATAATAATTTT
Found at i:292840 original size:13 final size:14
Alignment explanation
Indices: 292822--292855 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
292812 GATATTGATT
292822 TTATTAAA-TTATA
1 TTATTAAATTTATA
*
292835 TTATTAAATTTTTA
1 TTATTAAATTTATA
292849 TTATTAA
1 TTATTAA
292856 TAGATTAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 8 0.42
14 11 0.58
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (14 bp):
TTATTAAATTTATA
Found at i:292854 original size:22 final size:23
Alignment explanation
Indices: 292820--292872 Score: 56
Period size: 22 Copynumber: 2.3 Consensus size: 23
292810 ATGATATTGA
*
292820 TTTTATTAAATT-ATATTATTAAAT
1 TTTTATT-AATTAATA-GATTAAAT
292844 TTTTATT-ATTAATAGATTAAAT
1 TTTTATTAATTAATAGATTAAAT
292866 TATTTAT
1 T-TTTAT
292873 ACTACTTTGT
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
22 11 0.42
23 8 0.31
24 7 0.27
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (23 bp):
TTTTATTAATTAATAGATTAAAT
Found at i:293362 original size:16 final size:19
Alignment explanation
Indices: 293317--293366 Score: 61
Period size: 20 Copynumber: 2.7 Consensus size: 19
293307 AATACATAAT
*
293317 TTTACTAATTATTTATTATA
1 TTTAATAATTATTTA-TATA
293337 TTTAATAATTATTTA-ATA
1 TTTAATAATTATTTATATA
293355 -TTAA-AATTATTT
1 TTTAATAATTATTT
293367 TTAAAATATT
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
16 8 0.28
17 4 0.14
18 3 0.10
20 14 0.48
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (19 bp):
TTTAATAATTATTTATATA
Found at i:293376 original size:20 final size:21
Alignment explanation
Indices: 293351--293392 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
293341 ATAATTATTT
293351 AATA-TTAAAATTATT-TTTAA
1 AATATTTAAAATT-TTATTTAA
293371 AATATTTAAAATTTTATTTAA
1 AATATTTAAAATTTTATTTAA
293392 A
1 A
293393 TAAATTAATA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
20 6 0.30
21 14 0.70
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (21 bp):
AATATTTAAAATTTTATTTAA
Found at i:293393 original size:20 final size:20
Alignment explanation
Indices: 293344--293394 Score: 63
Period size: 20 Copynumber: 2.6 Consensus size: 20
293334 ATATTTAATA
293344 ATTATTT-AATATTAAAATT
1 ATTATTTAAATATTAAAATT
293363 ATT-TTTAAAATATTTAAAATT
1 ATTATTT-AAATA-TTAAAATT
293384 -TTATTTAAATA
1 ATTATTTAAATA
293395 AATTAATAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 7
0.80 0.00 0.20
Matches are distributed among these distances:
18 3 0.11
19 3 0.11
20 11 0.39
21 11 0.39
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (20 bp):
ATTATTTAAATATTAAAATT
Found at i:293400 original size:21 final size:21
Alignment explanation
Indices: 293354--293400 Score: 53
Period size: 21 Copynumber: 2.2 Consensus size: 21
293344 ATTATTTAAT
293354 ATTAAAATTATTTTTAAAATA
1 ATTAAAATTATTTTTAAAATA
*
293375 TTTAAAATT-TTATTT-AAATAA
1 ATTAAAATTATT-TTTAAAAT-A
293396 ATTAA
1 ATTAA
293401 TAAATTCAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
20 6 0.27
21 16 0.73
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (21 bp):
ATTAAAATTATTTTTAAAATA
Found at i:293532 original size:16 final size:16
Alignment explanation
Indices: 293513--293557 Score: 72
Period size: 16 Copynumber: 2.8 Consensus size: 16
293503 TTTAAATTTT
*
293513 TTTACATTATTTTTAA
1 TTTAAATTATTTTTAA
*
293529 TTTAAATCATTTTTAA
1 TTTAAATTATTTTTAA
293545 TTTAAATTATTTT
1 TTTAAATTATTTT
293558 AGTTTTGAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 26 1.00
ACGTcount: A:0.33, C:0.04, G:0.00, T:0.62
Consensus pattern (16 bp):
TTTAAATTATTTTTAA
Found at i:293638 original size:16 final size:16
Alignment explanation
Indices: 293617--293672 Score: 69
Period size: 16 Copynumber: 3.6 Consensus size: 16
293607 ATCGAGTTTT
293617 ATTATTTTAGATTCGA
1 ATTATTTTAGATTCGA
*
293633 ATTATTTTA-ATTCAA
1 ATTATTTTAGATTCGA
* *
293648 ATAATTTTAGATTCGT
1 ATTATTTTAGATTCGA
*
293664 AGTATTTTA
1 ATTATTTTA
293673 AATTTATTGA
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
15 13 0.39
16 20 0.61
ACGTcount: A:0.34, C:0.05, G:0.09, T:0.52
Consensus pattern (16 bp):
ATTATTTTAGATTCGA
Found at i:293654 original size:15 final size:16
Alignment explanation
Indices: 293620--293661 Score: 59
Period size: 15 Copynumber: 2.7 Consensus size: 16
293610 GAGTTTTATT
* *
293620 ATTTTAGATTCGAATT
1 ATTTTAGATTCAAATA
293636 ATTTTA-ATTCAAATA
1 ATTTTAGATTCAAATA
293651 ATTTTAGATTC
1 ATTTTAGATTC
293662 GTAGTATTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
15 13 0.57
16 10 0.43
ACGTcount: A:0.36, C:0.07, G:0.07, T:0.50
Consensus pattern (16 bp):
ATTTTAGATTCAAATA
Found at i:295795 original size:13 final size:13
Alignment explanation
Indices: 295777--295820 Score: 54
Period size: 13 Copynumber: 3.5 Consensus size: 13
295767 TTTTTTAAAA
295777 AAATATTTATATT
1 AAATATTTATATT
295790 AAATATTTATATT
1 AAATATTTATATT
** *
295803 CGATATATAT-TT
1 AAATATTTATATT
295815 AAATAT
1 AAATAT
295821 AAATAAATTT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
12 6 0.23
13 20 0.77
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.50
Consensus pattern (13 bp):
AAATATTTATATT
Found at i:295835 original size:18 final size:17
Alignment explanation
Indices: 295809--295852 Score: 61
Period size: 18 Copynumber: 2.5 Consensus size: 17
295799 TATTCGATAT
295809 ATATTTAAATATAAATAA
1 ATATTTAAATATAAA-AA
* *
295827 ATTTTTAAATATATAAA
1 ATATTTAAATATAAAAA
295844 ATATTTAAA
1 ATATTTAAA
295853 AATTTTAAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
17 10 0.43
18 13 0.57
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (17 bp):
ATATTTAAATATAAAAA
Found at i:295843 original size:26 final size:26
Alignment explanation
Indices: 295815--295866 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 26
295805 ATATATATTT
295815 AAATA-TAAATAAATTTTTAAATATATA
1 AAATATTAAA-AAA-TTTTAAATATATA
*
295842 AAATATTTAAAAATTTTAAATATAT
1 AAATATTAAAAAATTTTAAATATAT
295867 TCATATTAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
26 12 0.52
27 8 0.35
28 3 0.13
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (26 bp):
AAATATTAAAAAATTTTAAATATATA
Found at i:297325 original size:14 final size:15
Alignment explanation
Indices: 297299--297327 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
297289 ATATATATAT
297299 ATATAATAAATATGA
1 ATATAATAAATATGA
297314 ATATAA-AAATATGA
1 ATATAATAAATATGA
297328 TTCTCGAATA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 8 0.57
15 6 0.43
ACGTcount: A:0.62, C:0.00, G:0.07, T:0.31
Consensus pattern (15 bp):
ATATAATAAATATGA
Found at i:297642 original size:20 final size:19
Alignment explanation
Indices: 297615--297676 Score: 59
Period size: 17 Copynumber: 3.7 Consensus size: 19
297605 TATTTAAAAT
297615 ATTTT-ATAT-TTATATAA
1 ATTTTAATATATTATATAA
297632 ATTTTAATATATTA-AT-A
1 ATTTTAATATATTATATAA
297649 A--TT--TATATTATATAA
1 ATTTTAATATATTATATAA
*
297664 ATTTTAAAATATT
1 ATTTTAATATATT
297677 TGTATATATA
Statistics
Matches: 36, Mismatches: 1, Indels: 14
0.71 0.02 0.27
Matches are distributed among these distances:
13 7 0.19
14 2 0.06
15 4 0.11
17 9 0.25
18 6 0.17
19 8 0.22
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (19 bp):
ATTTTAATATATTATATAA
Found at i:297663 original size:32 final size:33
Alignment explanation
Indices: 297612--297676 Score: 105
Period size: 32 Copynumber: 2.0 Consensus size: 33
297602 TTATATTTAA
* *
297612 AATATTTTATATTTATATAAATTTTAATATATT
1 AATAATTTATATTTATATAAATTTTAAAATATT
297645 AATAATTTATA-TTATATAAATTTTAAAATATT
1 AATAATTTATATTTATATAAATTTTAAAATATT
297677 TGTATATATA
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 20 0.67
33 10 0.33
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (33 bp):
AATAATTTATATTTATATAAATTTTAAAATATT
Found at i:297669 original size:16 final size:17
Alignment explanation
Indices: 297602--297669 Score: 65
Period size: 16 Copynumber: 4.2 Consensus size: 17
297592 CATAATATAA
*
297602 TTATATT-TAAAATATT
1 TTATATTATATAATATT
297618 TTATATTTATATAA-ATT
1 TTATA-TTATATAATATT
*
297635 TTA-A-TATATTAATAAT
1 TTATATTATA-TAATATT
297651 TTATATTATATAA-ATT
1 TTATATTATATAATATT
297667 TTA
1 TTA
297670 AAATATTTGT
Statistics
Matches: 43, Mismatches: 3, Indels: 12
0.74 0.05 0.21
Matches are distributed among these distances:
14 4 0.09
15 3 0.07
16 16 0.37
17 12 0.28
18 8 0.19
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (17 bp):
TTATATTATATAATATT
Found at i:297686 original size:2 final size:2
Alignment explanation
Indices: 297679--297709 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
297669 AAAATATTTG
297679 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
297710 CTTGTTATTT
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:297693 original size:32 final size:31
Alignment explanation
Indices: 297619--297694 Score: 89
Period size: 32 Copynumber: 2.4 Consensus size: 31
297609 TAAAATATTT
* *
297619 TATATTTATATAAATTTTAATATATTAATAA
1 TATATATATATAAATTTTAAAATATTAATAA
* **
297650 TTTATATTATATAAATTTTAAAATATTTGTATA
1 TATATA-TATATAAATTTTAAAATATTAATA-A
297683 TATATATATATA
1 TATATATATATA
297695 TATATATATA
Statistics
Matches: 37, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
31 4 0.11
32 27 0.73
33 6 0.16
ACGTcount: A:0.46, C:0.00, G:0.01, T:0.53
Consensus pattern (31 bp):
TATATATATATAAATTTTAAAATATTAATAA
Found at i:301866 original size:6 final size:6
Alignment explanation
Indices: 301855--301888 Score: 54
Period size: 6 Copynumber: 6.0 Consensus size: 6
301845 ATCAACATTC
301855 CAAAAA CAAAAA CAAAAA C-AAAA -AAAAA CAAAAA
1 CAAAAA CAAAAA CAAAAA CAAAAA CAAAAA CAAAAA
301889 AATCCAAATT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
5 8 0.31
6 18 0.69
ACGTcount: A:0.85, C:0.15, G:0.00, T:0.00
Consensus pattern (6 bp):
CAAAAA
Found at i:301872 original size:12 final size:12
Alignment explanation
Indices: 301855--301888 Score: 54
Period size: 11 Copynumber: 3.0 Consensus size: 12
301845 ATCAACATTC
301855 CAAAAACAAAAA
1 CAAAAACAAAAA
301867 CAAAAAC-AAAA
1 CAAAAACAAAAA
301878 -AAAAACAAAAA
1 CAAAAACAAAAA
301889 AATCCAAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
10 6 0.29
11 8 0.38
12 7 0.33
ACGTcount: A:0.85, C:0.15, G:0.00, T:0.00
Consensus pattern (12 bp):
CAAAAACAAAAA
Found at i:301883 original size:16 final size:17
Alignment explanation
Indices: 301857--301888 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
301847 CAACATTCCA
301857 AAAACAAAAACAAAAAC
1 AAAACAAAAACAAAAAC
301874 AAAA-AAAAACAAAAA
1 AAAACAAAAACAAAAA
301889 AATCCAAATT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.88, C:0.12, G:0.00, T:0.00
Consensus pattern (17 bp):
AAAACAAAAACAAAAAC
Found at i:301896 original size:10 final size:10
Alignment explanation
Indices: 301856--301890 Score: 52
Period size: 10 Copynumber: 3.3 Consensus size: 10
301846 TCAACATTCC
301856 AAAAACAAAAA
1 AAAAAC-AAAA
301867 CAAAAACAAAA
1 -AAAAACAAAA
301878 AAAAACAAAA
1 AAAAACAAAA
301888 AAA
1 AAA
301891 TCCAAATTTC
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
10 13 0.57
11 4 0.17
12 6 0.26
ACGTcount: A:0.89, C:0.11, G:0.00, T:0.00
Consensus pattern (10 bp):
AAAAACAAAA
Found at i:303285 original size:24 final size:23
Alignment explanation
Indices: 303253--303307 Score: 67
Period size: 24 Copynumber: 2.3 Consensus size: 23
303243 ATATATATAT
*
303253 ATATATATATATATATATATGTTAAA
1 ATAT-TATATAAATATA-AT-TTAAA
303279 AT-TTATATAAATATAATTTAAA
1 ATATTATATAAATATAATTTAAA
303301 ATATTAT
1 ATATTAT
303308 TATGATAAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
22 7 0.26
23 6 0.22
24 11 0.41
25 1 0.04
26 2 0.07
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (23 bp):
ATATTATATAAATATAATTTAAA
Found at i:303287 original size:2 final size:2
Alignment explanation
Indices: 303242--303272 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
303232 AAAGTGTGTG
303242 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
303273 GTTAAAATTT
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:303700 original size:22 final size:22
Alignment explanation
Indices: 303667--303708 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
303657 AATTTTTATT
303667 TAAATTTAATTATAAAAATATA
1 TAAATTTAATTATAAAAATATA
303689 TAAATATT-ATTATAAAAATA
1 TAAAT-TTAATTATAAAAATA
303709 ATATTTTAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
22 17 0.89
23 2 0.11
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (22 bp):
TAAATTTAATTATAAAAATATA
Found at i:304604 original size:16 final size:16
Alignment explanation
Indices: 304583--304619 Score: 51
Period size: 14 Copynumber: 2.4 Consensus size: 16
304573 CTTCCAACTC
304583 AATTTAATAATTATT-A
1 AATTTAA-AATTATTAA
304599 AATTT-AAATTATTAA
1 AATTTAAAATTATTAA
304614 AATTTA
1 AATTTA
304620 TTTTTTAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
14 7 0.37
15 7 0.37
16 5 0.26
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (16 bp):
AATTTAAAATTATTAA
Found at i:304671 original size:33 final size:32
Alignment explanation
Indices: 304620--304681 Score: 97
Period size: 33 Copynumber: 1.9 Consensus size: 32
304610 TTAAAATTTA
* *
304620 TTTTTTAAATATATATTTTAATTTTAATTAGT
1 TTTTTTAAAAAAATATTTTAATTTTAATTAGT
304652 TTTTTTAAAAAAATAATTTTAATTTTAATT
1 TTTTTTAAAAAAAT-ATTTTAATTTTAATT
304682 TAAATATAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
32 12 0.44
33 15 0.56
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.60
Consensus pattern (32 bp):
TTTTTTAAAAAAATATTTTAATTTTAATTAGT
Found at i:304898 original size:6 final size:6
Alignment explanation
Indices: 304887--304952 Score: 59
Period size: 6 Copynumber: 11.3 Consensus size: 6
304877 TTATATAATT
*
304887 TTTATA TTTATA TTT-TA TTTATA --TAT- TTATATA TTTATA ATTATA
1 TTTATA TTTATA TTTATA TTTATA TTTATA TT-TATA TTTATA TTTATA
* *
304932 TTTAATA TATATA TATATA TT
1 TTT-ATA TTTATA TTTATA TT
304953 GATACATATT
Statistics
Matches: 50, Mismatches: 4, Indels: 12
0.76 0.06 0.18
Matches are distributed among these distances:
4 3 0.06
5 5 0.10
6 35 0.70
7 7 0.14
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (6 bp):
TTTATA
Found at i:304931 original size:33 final size:33
Alignment explanation
Indices: 304878--304951 Score: 96
Period size: 33 Copynumber: 2.3 Consensus size: 33
304868 TCAAGTAGAT
* * * *
304878 TATATA-ATTTTTATATTTATATTTTATTTATA
1 TATATATATATTTATAATTATATTTAATATATA
*
304910 TATTTATATATTTATAATTATATTTAATATATA
1 TATATATATATTTATAATTATATTTAATATATA
304943 TATATATAT
1 TATATATAT
304952 TGATACATAT
Statistics
Matches: 35, Mismatches: 6, Indels: 1
0.83 0.14 0.02
Matches are distributed among these distances:
32 5 0.14
33 30 0.86
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (33 bp):
TATATATATATTTATAATTATATTTAATATATA
Found at i:304944 original size:27 final size:27
Alignment explanation
Indices: 304889--304949 Score: 86
Period size: 29 Copynumber: 2.2 Consensus size: 27
304879 ATATAATTTT
* *
304889 TATATTTATATTTTATTTATATATTTA
1 TATATTTATATTATATTTATATATATA
304916 TATATTTATAATTATATTTAATATATATA
1 TATATTTAT-ATTATATTT-ATATATATA
304945 TATAT
1 TATAT
304950 ATTGATACAT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
27 9 0.30
28 8 0.27
29 13 0.43
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (27 bp):
TATATTTATATTATATTTATATATATA
Found at i:305265 original size:21 final size:21
Alignment explanation
Indices: 305228--305267 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
305218 TATTTTTATT
*
305228 TAAATTTAATTATAAAATATA
1 TAAATTTAATTAAAAAATATA
305249 TAAATATTAA-TAAAAAATA
1 TAAAT-TTAATTAAAAAATA
305268 ATTTTTTAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 13 0.76
22 4 0.24
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (21 bp):
TAAATTTAATTAAAAAATATA
Found at i:308103 original size:15 final size:14
Alignment explanation
Indices: 308079--308111 Score: 50
Period size: 15 Copynumber: 2.4 Consensus size: 14
308069 AATCACTCTA
308079 AATA-TATATATAT
1 AATAGTATATATAT
308092 ATATAGTATATATAT
1 A-ATAGTATATATAT
308107 AATAG
1 AATAG
308112 ACTTTGAACA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
13 1 0.06
14 7 0.39
15 10 0.56
ACGTcount: A:0.52, C:0.00, G:0.06, T:0.42
Consensus pattern (14 bp):
AATAGTATATATAT
Found at i:308624 original size:20 final size:20
Alignment explanation
Indices: 308578--308627 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
308568 TACGTGTATA
308578 TGTAATGTTTATATATAATC
1 TGTAATGTTTATATATAATC
* * * *
308598 GGCAATGTTTATATATACTT
1 TGTAATGTTTATATATAATC
308618 TGTAATGTTT
1 TGTAATGTTT
308628 TATGTAATTA
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.30, C:0.06, G:0.14, T:0.50
Consensus pattern (20 bp):
TGTAATGTTTATATATAATC
Found at i:308662 original size:18 final size:20
Alignment explanation
Indices: 308635--308681 Score: 55
Period size: 18 Copynumber: 2.5 Consensus size: 20
308625 TTTTATGTAA
*
308635 TTAT-TGTAAA-GATAATAT
1 TTATATGTAAATGATAACAT
*
308653 TT-TATGTAAATTATAACAT
1 TTATATGTAAATGATAACAT
308672 TTATATGTAA
1 TTATATGTAA
308682 TTAGTACTAT
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
17 1 0.04
18 8 0.33
19 8 0.33
20 7 0.29
ACGTcount: A:0.43, C:0.02, G:0.09, T:0.47
Consensus pattern (20 bp):
TTATATGTAAATGATAACAT
Done.