Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005777.1 Hibiscus syriacus cultivar Beakdansim tig00013524_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 147189
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:5370 original size:30 final size:30
Alignment explanation
Indices: 5326--5405 Score: 115
Period size: 30 Copynumber: 2.7 Consensus size: 30
5316 TATCACTATC
** *
5326 ATCTTCACTGACTTCAACATCCTCGCCACT
1 ATCTTCACCCACTTCAACATCCTCACCACT
*
5356 ATCTTTACCCACTTCAACATCCTCACCACT
1 ATCTTCACCCACTTCAACATCCTCACCACT
*
5386 ATCTTCACTCACTTCAACAT
1 ATCTTCACCCACTTCAACAT
5406 GTTTCTTTTC
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
30 44 1.00
ACGTcount: A:0.26, C:0.40, G:0.03, T:0.31
Consensus pattern (30 bp):
ATCTTCACCCACTTCAACATCCTCACCACT
Found at i:7486 original size:18 final size:18
Alignment explanation
Indices: 7463--7497 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
7453 TATATTTCTT
7463 TATATTATTTT-TAATTTA
1 TATATT-TTTTATAATTTA
7481 TATATTTTTTATAATTT
1 TATATTTTTTATAATTT
7498 TTTTATAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 4 0.25
18 12 0.75
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (18 bp):
TATATTTTTTATAATTTA
Found at i:8666 original size:21 final size:21
Alignment explanation
Indices: 8626--8675 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
8616 GATTCTTGAA
8626 AATCGCAATGCGATAGTACA-
1 AATCGCAATGCGATAGTACAG
* **
8646 AATTCGCATTGCGATTTTACAG
1 AA-TCGCAATGCGATAGTACAG
8668 AATCGCAA
1 AATCGCAA
8676 CGAGAATATG
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
20 2 0.08
21 20 0.83
22 2 0.08
ACGTcount: A:0.36, C:0.20, G:0.18, T:0.26
Consensus pattern (21 bp):
AATCGCAATGCGATAGTACAG
Found at i:8710 original size:20 final size:20
Alignment explanation
Indices: 8687--8896 Score: 237
Period size: 20 Copynumber: 10.5 Consensus size: 20
8677 GAGAATATGA
* *
8687 AAATCGCAACGCG-AACACAT
1 AAATCGCAACGCGTATC-CGT
8707 AAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
8727 AAATCGCAACGTGTATCCGT
1 AAATCGCAACGCGTATCCGT
8747 AAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
8767 AAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
8787 ATATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
8807 AAATCGCAACG-ATAATCCGT
1 AAATCGCAACGCGT-ATCCGT
* * *
8827 AAATCGCAACGAGAATCTGT
1 AAATCGCAACGCGTATCCGT
* *
8847 AAATCGCAACG-ATAATCTGT
1 AAATCGCAACGCGT-ATCCGT
* * *
8867 AAATCGCAACGAGAATCTGT
1 AAATCGCAACGCGTATCCGT
*
8887 AAATCACAAC
1 AAATCGCAAC
8897 ACTGAAATTT
Statistics
Matches: 168, Mismatches: 17, Indels: 10
0.86 0.09 0.05
Matches are distributed among these distances:
19 1 0.01
20 165 0.98
21 2 0.01
ACGTcount: A:0.36, C:0.26, G:0.18, T:0.20
Consensus pattern (20 bp):
AAATCGCAACGCGTATCCGT
Found at i:9627 original size:24 final size:24
Alignment explanation
Indices: 9588--9634 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
9578 AAATTTGGTC
9588 TTGGTCAATATCCGGACTTTGATA
1 TTGGTCAATATCCGGACTTTGATA
*
9612 TTGGTCAATA-CACGGATTTTGAT
1 TTGGTCAATATC-CGGACTTTGAT
9635 GATGTTTCAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.26, C:0.15, G:0.21, T:0.38
Consensus pattern (24 bp):
TTGGTCAATATCCGGACTTTGATA
Found at i:9826 original size:12 final size:12
Alignment explanation
Indices: 9809--9833 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
9799 ATATAATCCT
9809 GAAGAAGAAAAA
1 GAAGAAGAAAAA
9821 GAAGAAGAAAAA
1 GAAGAAGAAAAA
9833 G
1 G
9834 TCCCCGAAGA
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:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:12196 original size:53 final size:52
Alignment explanation
Indices: 12128--12350 Score: 358
Period size: 53 Copynumber: 4.2 Consensus size: 52
12118 GCAACGAGAG
* *
12128 AATCGCAATGCGAAATGAAAATCCCAAC-ATGAAAATCGCAATGCGGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAACGA-GAGAATCGCAATGC-GAAATGAA
*
12181 AATCGCAATGTGAAATGAAAATCGCAACGAGAGAATCGCAATGCGGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGC-GAAATGAA
12234 AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAA
* *
12286 AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCACAATGCGAAATTAA
1 AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAA
*
12338 AATCGCATTGCGA
1 AATCGCAATGCGA
12351 TTCTCTCGTT
Statistics
Matches: 162, Mismatches: 7, Indels: 3
0.94 0.04 0.02
Matches are distributed among these distances:
52 70 0.43
53 91 0.56
54 1 0.01
ACGTcount: A:0.46, C:0.17, G:0.22, T:0.15
Consensus pattern (52 bp):
AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAA
Found at i:12197 original size:19 final size:19
Alignment explanation
Indices: 12128--12350 Score: 216
Period size: 19 Copynumber: 12.7 Consensus size: 19
12118 GCAACGAGAG
12128 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
12147 AATCCCAA--C---ATGAA
1 AATCGCAATGCGAAATGAA
12161 AATCGCAATGCGGAAATGAA
1 AATCGCAATGC-GAAATGAA
*
12181 AATCGCAATGTGAAATGAA
1 AATCGCAATGCGAAATGAA
*
12200 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
12214 AATCGCAATGCGGAAATGAA
1 AATCGCAATGC-GAAATGAA
12234 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
12253 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
12267 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
12286 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
12305 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
* *
12319 AATCACAATGCGAAATTAA
1 AATCGCAATGCGAAATGAA
*
12338 AATCGCATTGCGA
1 AATCGCAATGCGA
12351 TTCTCTCGTT
Statistics
Matches: 168, Mismatches: 14, Indels: 44
0.74 0.06 0.19
Matches are distributed among these distances:
14 41 0.24
15 3 0.02
16 6 0.04
17 7 0.04
18 2 0.01
19 81 0.48
20 28 0.17
ACGTcount: A:0.46, C:0.17, G:0.22, T:0.15
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:12271 original size:86 final size:84
Alignment explanation
Indices: 12114--12293 Score: 233
Period size: 86 Copynumber: 2.1 Consensus size: 84
12104 CGGAAATTAC
12114 AATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCCCAACATGAAAATCGCAATGCGGAAATG
1 AATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCCCAACATGAAAATCGCAA-GCGG-AATG
*
12179 AAAATCGCAATGTGAAATGAA
64 AAAATCGCAATGCGAAATGAA
*
12200 AATCGCAACGAGAGAATCGCAATGCGGAAATGAAAATCGCAATGCGAAATGAAAATCGCAA-C-G
1 AATCGCAACGAGAGAATCGCAATGC-GAAATGAAAATCCCAA--C---ATGAAAATCGCAAGCGG
*
12263 -A-GAGAATCGCAATGCGAAATGAA
60 AATGAAAATCGCAATGCGAAATGAA
12286 AATCGCAA
1 AATCGCAA
12294 TGCGAAATGA
Statistics
Matches: 85, Mismatches: 3, Indels: 12
0.85 0.03 0.12
Matches are distributed among these distances:
86 53 0.62
87 16 0.19
89 2 0.02
90 1 0.01
92 13 0.15
ACGTcount: A:0.46, C:0.18, G:0.22, T:0.14
Consensus pattern (84 bp):
AATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCCCAACATGAAAATCGCAAGCGGAATGAA
AATCGCAATGCGAAATGAA
Found at i:12290 original size:33 final size:33
Alignment explanation
Indices: 12114--12293 Score: 161
Period size: 33 Copynumber: 5.2 Consensus size: 33
12104 CGGAAATTAC
*
12114 AATCGCAACGAGAGAATCGCAATGCGAAATGAA
1 AATCGCAACGAGAAAATCGCAATGCGAAATGAA
*
12147 AATCCCAAC-ATGAAAATCGCAATGCGGAAATGAA
1 AATCGCAACGA-GAAAATCGCAATGC-GAAATGAA
* * * * *
12181 AATCGCAATGTG-AAAT-GAAAAT-CGCAACGAGA
1 AATCGCAACGAGAAAATCG-CAATGCGAAATGA-A
12213 GAATCGCAATGCGGAAATGAAAATCGCAATGCGAAATGAA
1 -AATCGCAA--C-G--A-GAAAATCGCAATGCGAAATGAA
*
12253 AATCGCAACGAGAGAATCGCAATGCGAAATGAA
1 AATCGCAACGAGAAAATCGCAATGCGAAATGAA
12286 AATCGCAA
1 AATCGCAA
12294 TGCGAAATGA
Statistics
Matches: 118, Mismatches: 14, Indels: 30
0.73 0.09 0.19
Matches are distributed among these distances:
31 5 0.04
32 4 0.03
33 65 0.55
34 17 0.14
36 2 0.02
37 1 0.01
39 9 0.08
40 8 0.07
41 7 0.06
ACGTcount: A:0.46, C:0.18, G:0.22, T:0.14
Consensus pattern (33 bp):
AATCGCAACGAGAAAATCGCAATGCGAAATGAA
Found at i:12333 original size:33 final size:33
Alignment explanation
Indices: 12181--12344 Score: 145
Period size: 33 Copynumber: 4.8 Consensus size: 33
12171 CGGAAATGAA
*
12181 AATCGCAATGTGAAATGAAAATCGCAACGAGAG
1 AATCGCAATGCGAAATGAAAATCGCAACGAGAG
* *
12214 AATCGCAATGCGGAAATGAAAATCGCAATGCGA-
1 AATCGCAATGC-GAAATGAAAATCGCAACGAGAG
* * * *
12247 AAT-GAAAAT-CGCAACGAGAGAATCGCAATGCGAAATGAA
1 AATCG-CAATGCGAAATGA-A-AATCGCAA--CG--A-GAG
12286 AATCGCAATGCGAAATGAAAATCGCAACGAGAG
1 AATCGCAATGCGAAATGAAAATCGCAACGAGAG
* *
12319 AATCACAATGCGAAATTAAAATCGCA
1 AATCGCAATGCGAAATGAAAATCGCA
12345 TTGCGATTCT
Statistics
Matches: 105, Mismatches: 14, Indels: 24
0.73 0.10 0.17
Matches are distributed among these distances:
31 5 0.05
32 3 0.03
33 50 0.48
34 20 0.19
35 1 0.01
36 2 0.02
38 10 0.10
39 7 0.07
40 7 0.07
ACGTcount: A:0.46, C:0.17, G:0.22, T:0.15
Consensus pattern (33 bp):
AATCGCAATGCGAAATGAAAATCGCAACGAGAG
Found at i:12510 original size:14 final size:14
Alignment explanation
Indices: 12491--12527 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
12481 CATCAATTAC
12491 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
12505 ACAAATCATCTTTT
1 ACAAATCAACTTTT
12519 ACAAATCAA
1 ACAAATCAA
12528 TTAAACAATA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:14486 original size:19 final size:19
Alignment explanation
Indices: 14444--14547 Score: 127
Period size: 19 Copynumber: 5.4 Consensus size: 19
14434 TAGTTTACTT
* *
14444 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAAC-CAAAA
** *
14464 TCGCAACGCGAAATGAGAA
1 TCGCAACGCGAAACCAAAA
*
14483 TCGCAACGAGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
14502 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
**
14521 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAACCAAAA
14540 TCGCAACG
1 TCGCAACG
14548 ACAGAATCGC
Statistics
Matches: 73, Mismatches: 11, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
19 61 0.84
20 12 0.16
ACGTcount: A:0.46, C:0.26, G:0.18, T:0.10
Consensus pattern (19 bp):
TCGCAACGCGAAACCAAAA
Found at i:16276 original size:41 final size:38
Alignment explanation
Indices: 16231--16332 Score: 140
Period size: 35 Copynumber: 2.7 Consensus size: 38
16221 TCTTTTGGTT
16231 GAAATGAAAATCGCAACGAGAGAATGACTGTCGCAACGAGA
1 GAAATGAAAATCGCAACGAGAGAATGA---TCGCAACGAGA
16272 GAAATGAAAATCGCAACGAGAG-A--ATCGCAACGAGA
1 GAAATGAAAATCGCAACGAGAGAATGATCGCAACGAGA
*
16307 AAAATGAAAATCGCAACGAGA-AATGA
1 GAAATGAAAATCGCAACGAGAGAATGA
16333 AAATCGCAAT
Statistics
Matches: 57, Mismatches: 1, Indels: 10
0.84 0.01 0.15
Matches are distributed among these distances:
35 32 0.56
37 1 0.02
38 1 0.02
40 1 0.02
41 22 0.39
ACGTcount: A:0.49, C:0.16, G:0.25, T:0.11
Consensus pattern (38 bp):
GAAATGAAAATCGCAACGAGAGAATGATCGCAACGAGA
Found at i:16285 original size:21 final size:21
Alignment explanation
Indices: 16231--16341 Score: 116
Period size: 21 Copynumber: 5.8 Consensus size: 21
16221 TCTTTTGGTT
16231 GAAATGAAAATCGCAACGAGA
1 GAAATGAAAATCGCAACGAGA
***
16252 G-AATGACTGTCGCAACGAGA
1 GAAATGAAAATCGCAACGAGA
16272 GAAATGAAAATCGCAAC--GA
1 GAAATGAAAATCGCAACGAGA
16291 G--A-G--AATCGCAACGAGA
1 GAAATGAAAATCGCAACGAGA
*
16307 AAAATGAAAATCGCAAC--GA
1 GAAATGAAAATCGCAACGAGA
16326 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
16342 TGCGATTTTG
Statistics
Matches: 74, Mismatches: 8, Indels: 18
0.74 0.08 0.18
Matches are distributed among these distances:
14 9 0.12
16 3 0.04
17 1 0.01
18 1 0.01
19 21 0.28
20 17 0.23
21 22 0.30
ACGTcount: A:0.50, C:0.16, G:0.23, T:0.11
Consensus pattern (21 bp):
GAAATGAAAATCGCAACGAGA
Found at i:16299 original size:14 final size:14
Alignment explanation
Indices: 16280--16306 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
16270 GAGAAATGAA
16280 AATCGCAACGAGAG
1 AATCGCAACGAGAG
16294 AATCGCAACGAGA
1 AATCGCAACGAGA
16307 AAAATGAAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.44, C:0.22, G:0.26, T:0.07
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:16390 original size:33 final size:33
Alignment explanation
Indices: 16342--16421 Score: 133
Period size: 33 Copynumber: 2.4 Consensus size: 33
16332 AAAATCGCAA
**
16342 TGCGATTTTGGTTTCGCGTTGCGATTCTCTCAT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCAT
*
16375 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCAT
16408 TGCGATTTTCATTT
1 TGCGATTTTCATTT
16422 TTCTCGTTGC
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 44 1.00
ACGTcount: A:0.10, C:0.21, G:0.21, T:0.47
Consensus pattern (33 bp):
TGCGATTTTCATTTCGCGTTGCGATTCTCTCAT
Found at i:16410 original size:14 final size:14
Alignment explanation
Indices: 16358--16414 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 14
16348 TTTGGTTTCG
16358 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
* *
16372 CATTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
16391 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
16405 CGTTGCGATT
1 CGTTGCGATT
16415 TTCATTTTTC
Statistics
Matches: 34, Mismatches: 4, Indels: 10
0.71 0.08 0.21
Matches are distributed among these distances:
14 19 0.56
16 3 0.09
17 3 0.09
19 9 0.26
ACGTcount: A:0.11, C:0.25, G:0.21, T:0.44
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:16427 original size:21 final size:21
Alignment explanation
Indices: 16402--16474 Score: 87
Period size: 21 Copynumber: 3.5 Consensus size: 21
16392 GTTGCGATTC
16402 TCTCGTTGCGATTTTCATTTT
1 TCTCGTTGCGATTTTCATTTT
**
16423 TCTCGTTGCAGATAGTCA-TTT
1 TCTCGTTGC-GATTTTCATTTT
* *
16444 TCACGTTGCGA-TTTCATTTA
1 TCTCGTTGCGATTTTCATTTT
16464 TCTCGTTGCGA
1 TCTCGTTGCGA
16475 CTCTTCTGCA
Statistics
Matches: 43, Mismatches: 7, Indels: 5
0.78 0.13 0.09
Matches are distributed among these distances:
19 3 0.07
20 14 0.33
21 20 0.47
22 6 0.14
ACGTcount: A:0.15, C:0.21, G:0.18, T:0.47
Consensus pattern (21 bp):
TCTCGTTGCGATTTTCATTTT
Found at i:16596 original size:33 final size:33
Alignment explanation
Indices: 16554--16624 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
16544 AATACTAACT
*
16554 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
1 TGAAAATCGCAACAAGAGAATAGCAACGCGAAA
* *
16587 TGAAAATCGCAACAAGAGAATCGTAACGCGAAA
1 TGAAAATCGCAACAAGAGAATAGCAACGCGAAA
16620 TGAAA
1 TGAAA
16625 TCTAAGTGAA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.49, C:0.17, G:0.23, T:0.11
Consensus pattern (33 bp):
TGAAAATCGCAACAAGAGAATAGCAACGCGAAA
Found at i:17029 original size:20 final size:20
Alignment explanation
Indices: 17004--17196 Score: 228
Period size: 20 Copynumber: 9.6 Consensus size: 20
16994 CTTTAAAAAT
17004 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
17024 CGCGTTGCGATTTTACGTAT-
1 CGCGTTGCGA-TTTACGGATA
*
17044 TGTCGTTGCGATTTACGGATA
1 CG-CGTTGCGATTTACGGATA
*
17065 CGCGTTGCGATATACGGATA
1 CGCGTTGCGATTTACGGATA
* *
17085 CGCATTGCGATTTATGGATA
1 CGCGTTGCGATTTACGGATA
17105 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
17125 CACGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* * *
17145 TGCGTTGCGATTTATGTG-TT
1 CGCGTTGCGATTTACG-GATA
* ** *
17165 CGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATA
17185 CGCGTTGCGATT
1 CGCGTTGCGATT
17197 CTGTAAAATC
Statistics
Matches: 148, Mismatches: 20, Indels: 10
0.83 0.11 0.06
Matches are distributed among these distances:
20 130 0.88
21 18 0.12
ACGTcount: A:0.19, C:0.18, G:0.27, T:0.36
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:17214 original size:21 final size:20
Alignment explanation
Indices: 17190--17239 Score: 55
Period size: 21 Copynumber: 2.4 Consensus size: 20
17180 ATATTCGCGT
17190 TGCGATTCTGTAAAATCGCAA
1 TGCGATT-TGTAAAATCGCAA
** *
17211 TGCGAATTTGTACTATCGCAT
1 TGCG-ATTTGTAAAATCGCAA
17232 TGCGATTT
1 TGCGATTT
17240 TCAAGAATCG
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
20 4 0.16
21 18 0.72
22 3 0.12
ACGTcount: A:0.26, C:0.18, G:0.20, T:0.36
Consensus pattern (20 bp):
TGCGATTTGTAAAATCGCAA
Found at i:21397 original size:38 final size:38
Alignment explanation
Indices: 21355--21436 Score: 137
Period size: 38 Copynumber: 2.2 Consensus size: 38
21345 AAAATTCAGT
*
21355 AAATAATAAACTCATTCGCTTCAATTAAGTAATAAACA
1 AAATAATAAAATCATTCGCTTCAATTAAGTAATAAACA
* *
21393 AAATACTAAAATCATTCGCTTGAATTAAGTAATAAACA
1 AAATAATAAAATCATTCGCTTCAATTAAGTAATAAACA
21431 AAATAA
1 AAATAA
21437 ACAAAATAAA
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
38 40 1.00
ACGTcount: A:0.52, C:0.13, G:0.06, T:0.28
Consensus pattern (38 bp):
AAATAATAAAATCATTCGCTTCAATTAAGTAATAAACA
Found at i:21751 original size:15 final size:15
Alignment explanation
Indices: 21731--21783 Score: 70
Period size: 15 Copynumber: 3.5 Consensus size: 15
21721 CCTAACTCTC
*
21731 ATCATCATCATCATT
1 ATCATCATCATCAAT
**
21746 ATCATCATCATCACC
1 ATCATCATCATCAAT
21761 ATCATCATCATCAAT
1 ATCATCATCATCAAT
*
21776 GTCATCAT
1 ATCATCAT
21784 TGTCATCATT
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
15 33 1.00
ACGTcount: A:0.34, C:0.30, G:0.02, T:0.34
Consensus pattern (15 bp):
ATCATCATCATCAAT
Found at i:21792 original size:3 final size:3
Alignment explanation
Indices: 21729--21773 Score: 72
Period size: 3 Copynumber: 15.0 Consensus size: 3
21719 CTCCTAACTC
* *
21729 TCA TCA TCA TCA TCA TTA TCA TCA TCA TCA CCA TCA TCA TCA TCA
1 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA
21774 ATGTCATCAT
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.33, C:0.33, G:0.00, T:0.33
Consensus pattern (3 bp):
TCA
Found at i:24347 original size:2 final size:2
Alignment explanation
Indices: 24340--24396 Score: 114
Period size: 2 Copynumber: 28.5 Consensus size: 2
24330 TTAAGTACAT
24340 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
24382 TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA T
24397 TTTGTAAGGC
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 55 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:25429 original size:30 final size:30
Alignment explanation
Indices: 25359--25431 Score: 85
Period size: 30 Copynumber: 2.4 Consensus size: 30
25349 ATAAAAAGTT
*
25359 AAGGGCCAAATTGTAGATAAATCCAAATTC
1 AAGGGCCAAATTGTAGATAAAGCCAAATTC
* * *
25389 AAGTGCCAAATTGTATATCAAAGCTAAATTC
1 AAGGGCCAAATTGTAGAT-AAAGCCAAATTC
*
25420 -AGGGTCAAATTG
1 AAGGGCCAAATTG
25432 CAGGGGGAAA
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
30 26 0.72
31 10 0.28
ACGTcount: A:0.41, C:0.15, G:0.18, T:0.26
Consensus pattern (30 bp):
AAGGGCCAAATTGTAGATAAAGCCAAATTC
Found at i:25448 original size:25 final size:26
Alignment explanation
Indices: 25414--25466 Score: 81
Period size: 26 Copynumber: 2.1 Consensus size: 26
25404 TATCAAAGCT
25414 AAATTCA-GGGTCAAATTGCAGGGGG
1 AAATTCAGGGGTCAAATTGCAGGGGG
* *
25439 AAATTCAGGGGTCAATTTGCAGGTGG
1 AAATTCAGGGGTCAAATTGCAGGGGG
25465 AA
1 AA
25467 GCCGATGTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
25 7 0.28
26 18 0.72
ACGTcount: A:0.32, C:0.11, G:0.34, T:0.23
Consensus pattern (26 bp):
AAATTCAGGGGTCAAATTGCAGGGGG
Found at i:31663 original size:16 final size:16
Alignment explanation
Indices: 31642--31675 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
31632 TTACTATTCA
*
31642 CGTGAATAGTGAATTT
1 CGTGAATAGTGAAATT
31658 CGTGAATAGTGAAATT
1 CGTGAATAGTGAAATT
31674 CG
1 CG
31676 GTCGGTGATA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.32, C:0.09, G:0.26, T:0.32
Consensus pattern (16 bp):
CGTGAATAGTGAAATT
Found at i:32446 original size:15 final size:16
Alignment explanation
Indices: 32426--32457 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
32416 TGGCAGATCC
32426 AAATCCAG-ACGGGAA
1 AAATCCAGAACGGGAA
32441 AAATCCAGAACGGGAA
1 AAATCCAGAACGGGAA
32457 A
1 A
32458 GAAAGATTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 8 0.50
16 8 0.50
ACGTcount: A:0.50, C:0.19, G:0.25, T:0.06
Consensus pattern (16 bp):
AAATCCAGAACGGGAA
Found at i:44150 original size:34 final size:34
Alignment explanation
Indices: 44097--44173 Score: 118
Period size: 34 Copynumber: 2.3 Consensus size: 34
44087 TCATGATCAA
* * *
44097 CCACGCATAAGGACAGTGAGATAACTTCACTTGT
1 CCACACATAAGGACAGTGAGATAACTCCACTCGT
*
44131 CCACACATAAGGACTGTGAGATAACTCCACTCGT
1 CCACACATAAGGACAGTGAGATAACTCCACTCGT
44165 CCACACATA
1 CCACACATA
44174 TTCACACTTA
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
34 39 1.00
ACGTcount: A:0.34, C:0.29, G:0.17, T:0.21
Consensus pattern (34 bp):
CCACACATAAGGACAGTGAGATAACTCCACTCGT
Found at i:45551 original size:64 final size:64
Alignment explanation
Indices: 45477--45640 Score: 204
Period size: 65 Copynumber: 2.5 Consensus size: 64
45467 CGGTGCACCA
*
45477 AGTGTGCATCGATGCATGAAATGCATTCGATGTTTGAAAAATAGCCTG-GTGCATCGATGCATGG
1 AGTGTGCATCGATGCATGAAATGCATTCGATGTTTG-AAAATAGCCAGAGTGCATCGATGCATGG
** * * **
45541 CTTGTGCATCGATGCATCAAATGCATTCAATGTTTTGAAAATATTCAGAGTGCATCGATGCATGG
1 AGTGTGCATCGATGCATGAAATGCATTCGATG-TTTGAAAATAGCCAGAGTGCATCGATGCATGG
** * *
45606 AGAATGCATCGGTGCATGGAATGCATTCGATGTTT
1 AGTGTGCATCGATGCATGAAATGCATTCGATGTTT
45641 CAATTAATTC
Statistics
Matches: 83, Mismatches: 15, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
64 39 0.47
65 44 0.53
ACGTcount: A:0.28, C:0.16, G:0.26, T:0.30
Consensus pattern (64 bp):
AGTGTGCATCGATGCATGAAATGCATTCGATGTTTGAAAATAGCCAGAGTGCATCGATGCATGG
Found at i:45629 original size:17 final size:19
Alignment explanation
Indices: 45591--45637 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 19
45581 ATATTCAGAG
45591 TGCATCGATGCATGGAGAA
1 TGCATCGATGCATGGAGAA
*
45610 TGCATCGGTGCAT-G-GAA
1 TGCATCGATGCATGGAGAA
45627 TGCATTCGATG
1 TGCA-TCGATG
45638 TTTCAATTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
17 7 0.28
18 6 0.24
19 12 0.48
ACGTcount: A:0.26, C:0.17, G:0.32, T:0.26
Consensus pattern (19 bp):
TGCATCGATGCATGGAGAA
Found at i:52155 original size:22 final size:21
Alignment explanation
Indices: 52113--52152 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
52103 GAGTTTGTTT
*
52113 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
52134 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
52153 ACAGTTTTTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:54231 original size:19 final size:17
Alignment explanation
Indices: 54207--54253 Score: 51
Period size: 19 Copynumber: 2.6 Consensus size: 17
54197 ATATTCAGAG
54207 TGCATCGATGCATGGAGAA
1 TGCATCGATGCAT-G-GAA
54226 TGCATCGGA-GCATGGAA
1 TGCATC-GATGCATGGAA
54243 TGCATTCGATG
1 TGCA-TCGATG
54254 TTTCAATTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 7
0.78 0.00 0.22
Matches are distributed among these distances:
17 9 0.36
18 4 0.16
19 10 0.40
20 2 0.08
ACGTcount: A:0.28, C:0.17, G:0.32, T:0.23
Consensus pattern (17 bp):
TGCATCGATGCATGGAA
Found at i:54276 original size:65 final size:62
Alignment explanation
Indices: 54097--54305 Score: 217
Period size: 65 Copynumber: 3.2 Consensus size: 62
54087 GCACCAAGTG
* * *
54097 TGCATCGATGCATGAAATGCATTCGATGTTTGAAAAATAGCATGGTGCATCGATGCATGGCTTG-
1 TGCATCGATGCATGAAATGCATTCGATGTTTGAAAAAT-TCATGATGCATCGATGCATGG--AGA
*
54161 TGCATCGATGCATCAAATGCATTCGATGTTTTGAAAATATTCA-GAGTGCATCGATGCATGGAGA
1 TGCATCGATGCATGAAATGCATTCGATG-TTTGAAAA-ATTCATGA-TGCATCGATGCATGGAG-
54225 A
62 A
* * *
54226 TGCATCGGA-GCATGGAATGCATTCGATGTTTCAATTAATTCATCGATGCATCGATGCATGGACT
1 TGCATC-GATGCATGAAATGCATTCGATGTTTGAA-AAATTCAT-GATGCATCGATGCATGGA--
54290 GA
61 GA
*
54292 TGCATCGGTGCATG
1 TGCATCGATGCATG
54306 CCTTTGAATA
Statistics
Matches: 124, Mismatches: 9, Indels: 22
0.80 0.06 0.14
Matches are distributed among these distances:
63 1 0.01
64 38 0.31
65 66 0.53
66 18 0.15
67 1 0.01
ACGTcount: A:0.28, C:0.17, G:0.25, T:0.30
Consensus pattern (62 bp):
TGCATCGATGCATGAAATGCATTCGATGTTTGAAAAATTCATGATGCATCGATGCATGGAGA
Found at i:57856 original size:64 final size:64
Alignment explanation
Indices: 57777--57916 Score: 165
Period size: 64 Copynumber: 2.2 Consensus size: 64
57767 CGGATCCTGG
* * * *
57777 CAGGTCGGGTAAAATCGGATACAGGTCA-AGTCAGGTAAATTTGACACCAGATCCAGGTCGGGTT
1 CAGGTCAGGTCAAATCAG-TACAGGTCATAGTCAGGTAAATTTGACACCAGATCCAGATCGGGTT
* * * ** **
57841 CAGGTCAGGTCAAATCAGTTCGGGTTATTTTCAGGTTGATTTGACACCAGATCCAGATCGGGTT
1 CAGGTCAGGTCAAATCAGTACAGGTCATAGTCAGGTAAATTTGACACCAGATCCAGATCGGGTT
57905 CAGGTCAGGTCA
1 CAGGTCAGGTCA
57917 TTTTCAGTTC
Statistics
Matches: 64, Mismatches: 11, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
63 6 0.09
64 58 0.91
ACGTcount: A:0.26, C:0.19, G:0.29, T:0.26
Consensus pattern (64 bp):
CAGGTCAGGTCAAATCAGTACAGGTCATAGTCAGGTAAATTTGACACCAGATCCAGATCGGGTT
Found at i:58478 original size:14 final size:14
Alignment explanation
Indices: 58459--58487 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
58449 ACTAAATTGA
58459 ACAAATAAAAAATT
1 ACAAATAAAAAATT
58473 ACAAATAAAAAATT
1 ACAAATAAAAAATT
58487 A
1 A
58488 AATAAACTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.72, C:0.07, G:0.00, T:0.21
Consensus pattern (14 bp):
ACAAATAAAAAATT
Found at i:58609 original size:210 final size:211
Alignment explanation
Indices: 58235--58729 Score: 755
Period size: 211 Copynumber: 2.3 Consensus size: 211
58225 ATTTAAGAAT
58235 TAAATTGAACAAATATGAAATTGA-AAATAAAAATTTAAATAAATTAAACAACACACATTTATGA
1 TAAATTGAACAAATATGAAATT-ACAAATAAAAATTTAAATAAATTAAACAACACA-A---A--A
*
58299 GGGATCAAATCGAAATAATTTTAAATTGTGATGTTGAAATTAATACAAAAAAGTACTAAATTATA
59 GGGATCAAATCGAAATAATTTTAAATTGTGAGGTTGAAATTAATACAAAAAAGTACTAAATTATA
58364 CCCATTTAAAAAGTTATGGGCCAATTTAAAAATAG-AAATAAGTAATAAGTATGGGTCAATTTCA
124 CCCATTTAAAAAGTTATGGGCCAATTTAAAAATAGAAAATAAGTAATAAGTATGGGTCAATTTCA
* *
58428 GATGCAAA-AAACATTTGGAGGAC
189 GATGCAAATAAA-ATGTAGAGGAC
** * *
58451 TAAATTGAACAAATAAAAAATTACAAATAAAAAATTAAATAAACTAAACAACACAAAAGGGATCA
1 TAAATTGAACAAATATGAAATTACAAATAAAAATTTAAATAAATTAAACAACACAAAAGGGATCA
* * * *
58516 AATCGAAATAATTTTAAATTTTGAGGTTGAAATTAATACAAACATGTACTAAATTATACTCATTT
66 AATCGAAATAATTTTAAATTGTGAGGTTGAAATTAATACAAAAAAGTACTAAATTATACCCATTT
*
58581 AAAAAGTTATGGGCCAA-TTAATAAATAGAAAATAAGTAATAAGTATGGGTCAATTTCATATGCA
131 AAAAAGTTATGGGCCAATTTAA-AAATAGAAAATAAGTAATAAGTATGGGTCAATTTCAGATGCA
58645 AATAAAATGTAGAGGAC
195 AATAAAATGTAGAGGAC
* *
58662 TAAATTGAACAAATATGAAATGACAAATAAAAATTTAAATAAATTAAACAACACAAAATGGATCA
1 TAAATTGAACAAATATGAAATTACAAATAAAAATTTAAATAAATTAAACAACACAAAAGGGATCA
58727 AAT
66 AAT
58730 ATGAAAAATA
Statistics
Matches: 257, Mismatches: 18, Indels: 13
0.89 0.06 0.05
Matches are distributed among these distances:
209 4 0.02
210 91 0.35
211 107 0.42
212 4 0.02
215 2 0.01
216 49 0.19
ACGTcount: A:0.52, C:0.09, G:0.12, T:0.27
Consensus pattern (211 bp):
TAAATTGAACAAATATGAAATTACAAATAAAAATTTAAATAAATTAAACAACACAAAAGGGATCA
AATCGAAATAATTTTAAATTGTGAGGTTGAAATTAATACAAAAAAGTACTAAATTATACCCATTT
AAAAAGTTATGGGCCAATTTAAAAATAGAAAATAAGTAATAAGTATGGGTCAATTTCAGATGCAA
ATAAAATGTAGAGGAC
Found at i:58776 original size:2 final size:2
Alignment explanation
Indices: 58769--58859 Score: 60
Period size: 2 Copynumber: 44.0 Consensus size: 2
58759 GCATTCATTT
* * * *
58769 TA TA TA TA TG TA -A TA TA AA CTA TA TA GTT TA TA TA TA AA CTA
1 TA TA TA TA TA TA TA TA TA TA -TA TA TA -TA TA TA TA TA TA -TA
* * *
58811 TA TA GTT TA TA TA TA TA TA TA TA TA TA TA T- TA TG TA TA AA CTA
1 TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA
58854 TA TA TA
1 TA TA TA
58860 CCATGTATAA
Statistics
Matches: 68, Mismatches: 14, Indels: 14
0.71 0.15 0.15
Matches are distributed among these distances:
1 2 0.03
2 61 0.90
3 5 0.07
ACGTcount: A:0.46, C:0.03, G:0.04, T:0.46
Consensus pattern (2 bp):
TA
Found at i:58794 original size:20 final size:20
Alignment explanation
Indices: 58769--58885 Score: 98
Period size: 20 Copynumber: 5.8 Consensus size: 20
58759 GCATTCATTT
58769 TATATATATGTA-ATATAAAC
1 TATATATAT-TATATATAAAC
58789 TATATAGT-TTATATATAAAC
1 TATATA-TATTATATATAAAC
*
58809 TATATAGT-TTATATATATATATA
1 TATATA-TATTATATATA-A-A-C
*
58832 TATATATATTATGTATAAAC
1 TATATATATTATATATAAAC
** *
58852 TATATATACCATGTATAAAC
1 TATATATATTATATATAAAC
*
58872 TATA-ATACTATATA
1 TATATATATTATATA
58886 GTTTATATAT
Statistics
Matches: 84, Mismatches: 7, Indels: 13
0.81 0.07 0.12
Matches are distributed among these distances:
19 10 0.12
20 54 0.64
21 3 0.04
22 3 0.04
23 14 0.17
ACGTcount: A:0.46, C:0.06, G:0.04, T:0.44
Consensus pattern (20 bp):
TATATATATTATATATAAAC
Found at i:58990 original size:17 final size:17
Alignment explanation
Indices: 58970--59023 Score: 72
Period size: 17 Copynumber: 3.1 Consensus size: 17
58960 CTATACAATT
* *
58970 TATATTTATATATTATG
1 TATATTTATAAATTATA
*
58987 TATAATTATAAATTATA
1 TATATTTATAAATTATA
59004 TATATTGTATAAATTATA
1 TATATT-TATAAATTATA
59022 TA
1 TA
59024 GTTTATTAAT
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
17 19 0.59
18 13 0.41
ACGTcount: A:0.44, C:0.00, G:0.04, T:0.52
Consensus pattern (17 bp):
TATATTTATAAATTATA
Found at i:59002 original size:24 final size:25
Alignment explanation
Indices: 58975--59021 Score: 71
Period size: 24 Copynumber: 1.9 Consensus size: 25
58965 CAATTTATAT
58975 TTATATAT-TATGTAT-AATTATAAA
1 TTATATATAT-TGTATAAATTATAAA
58999 TTATATATATTGTATAAATTATA
1 TTATATATATTGTATAAATTATA
59022 TAGTTTATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
24 13 0.62
25 8 0.38
ACGTcount: A:0.45, C:0.00, G:0.04, T:0.51
Consensus pattern (25 bp):
TTATATATATTGTATAAATTATAAA
Found at i:59059 original size:24 final size:22
Alignment explanation
Indices: 59011--59067 Score: 71
Period size: 22 Copynumber: 2.6 Consensus size: 22
59001 ATATATATTG
*
59011 TATAAATTATATAGTTTATTAA
1 TATAAACTATATAGTTTATTAA
59033 TATAAACTATATAGTTT-TTATA
1 TATAAACTATATAGTTTATTA-A
* *
59055 TATATAGTATATA
1 TATAAACTATATA
59068 TGGTTTAAGG
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
21 3 0.10
22 28 0.90
ACGTcount: A:0.44, C:0.02, G:0.05, T:0.49
Consensus pattern (22 bp):
TATAAACTATATAGTTTATTAA
Found at i:59095 original size:21 final size:21
Alignment explanation
Indices: 59060--59113 Score: 65
Period size: 21 Copynumber: 2.5 Consensus size: 21
59050 TTATATATAT
*
59060 AGTATATATGGTTTAAGGTTTA
1 AGTAT-TAGGGTTTAAGGTTTA
*
59082 AGTATTAGGGTTTAGGGTTTA
1 AGTATTAGGGTTTAAGGTTTA
59103 AGGT-TTAGGGT
1 A-GTATTAGGGT
59114 GTATATTTAT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
21 22 0.76
22 7 0.24
ACGTcount: A:0.26, C:0.00, G:0.31, T:0.43
Consensus pattern (21 bp):
AGTATTAGGGTTTAAGGTTTA
Found at i:59107 original size:14 final size:14
Alignment explanation
Indices: 59069--59113 Score: 56
Period size: 14 Copynumber: 3.2 Consensus size: 14
59059 TAGTATATAT
59069 GGTTTAAGGTTTA-
1 GGTTTAAGGTTTAG
* *
59082 AGTATTAGGGTTTAG
1 GGT-TTAAGGTTTAG
59097 GGTTTAAGGTTTAG
1 GGTTTAAGGTTTAG
59111 GGT
1 GGT
59114 GTATATTTAT
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
13 2 0.08
14 22 0.85
15 2 0.08
ACGTcount: A:0.22, C:0.00, G:0.36, T:0.42
Consensus pattern (14 bp):
GGTTTAAGGTTTAG
Found at i:59164 original size:20 final size:20
Alignment explanation
Indices: 59139--59199 Score: 64
Period size: 20 Copynumber: 3.4 Consensus size: 20
59129 TATAAACTAC
59139 ATACTATAATTTATATTTAT
1 ATACTATAATTTATATTTAT
59159 ATAC--T-ATTTATA--TA-
1 ATACTATAATTTATATTTAT
*
59173 A-ACTATAGTTTATATTTAT
1 ATACTATAATTTATATTTAT
59192 ATACTATA
1 ATACTATA
59200 TATATGAACT
Statistics
Matches: 33, Mismatches: 1, Indels: 14
0.69 0.02 0.29
Matches are distributed among these distances:
13 2 0.06
14 1 0.03
15 3 0.09
16 6 0.18
17 7 0.21
18 3 0.09
19 1 0.03
20 10 0.30
ACGTcount: A:0.41, C:0.07, G:0.02, T:0.51
Consensus pattern (20 bp):
ATACTATAATTTATATTTAT
Found at i:59185 original size:33 final size:33
Alignment explanation
Indices: 59115--59406 Score: 156
Period size: 33 Copynumber: 8.6 Consensus size: 33
59105 GTTTAGGGTG
* * *
59115 TATATTTATAT-TTATATAAACTACATACTATAATT
1 TATATTTATATACTATATATA-TA-A-ACTATAGTT
*
59150 TATATTTATATACTATTTATATAAACTATAGTT
1 TATATTTATATACTATATATATAAACTATAGTT
*
59183 TATATTTATATACTATATATATGAACTATAGTT
1 TATATTTATATACTATATATATAAACTATAGTT
*
59216 TACA--TATGA-ACTATATATATAAACTATATAGTT
1 TATATTTAT-ATACTATATATATAAAC--TATAGTT
* * * * *
59249 TACA-TAAGA-ACTATATATATATACTAAAGTT
1 TATATTTATATACTATATATATAAACTATAGTT
*
59280 GATATTTATATATGAACTATAGTTTACATATAAACTATAGTT
1 TATA-TT-TATAT--ACTATA---T--ATATAAACTATAGTT
* *
59322 TACATATGA-ACTA-TATATATATAAACTATATAGTT
1 TATAT-TTATA-TACTATATATATAAAC--TATAGTT
* * *
59357 TACA--TATGA-CCTATATATATATACTATAGTT
1 TATATTTAT-ATACTATATATATAAACTATAGTT
* *
59388 GATATTTATACACTATATA
1 TATATTTATATACTATATA
59407 GTTTACATAT
Statistics
Matches: 204, Mismatches: 27, Indels: 54
0.72 0.09 0.19
Matches are distributed among these distances:
31 34 0.17
32 3 0.01
33 99 0.49
34 5 0.02
35 25 0.12
36 6 0.03
37 6 0.03
38 4 0.02
39 1 0.00
40 2 0.01
41 3 0.01
42 16 0.08
ACGTcount: A:0.42, C:0.09, G:0.05, T:0.43
Consensus pattern (33 bp):
TATATTTATATACTATATATATAAACTATAGTT
Found at i:59210 original size:13 final size:13
Alignment explanation
Indices: 59194--59245 Score: 50
Period size: 13 Copynumber: 3.6 Consensus size: 13
59184 ATATTTATAT
59194 ACTATATATATGA
1 ACTATATATATGA
59207 ACTATAGTTTACATATGA
1 ACTATA---T--ATATGA
*
59225 ACTATATATATAA
1 ACTATATATATGA
59238 ACTATATA
1 ACTATATA
59246 GTTTACATAA
Statistics
Matches: 33, Mismatches: 1, Indels: 10
0.75 0.02 0.23
Matches are distributed among these distances:
13 19 0.58
15 1 0.03
16 1 0.03
18 12 0.36
ACGTcount: A:0.46, C:0.10, G:0.06, T:0.38
Consensus pattern (13 bp):
ACTATATATATGA
Found at i:59222 original size:18 final size:18
Alignment explanation
Indices: 59201--59371 Score: 110
Period size: 18 Copynumber: 9.7 Consensus size: 18
59191 TATACTATAT
59201 ATATGAACTATAGTTTAC
1 ATATGAACTATAGTTTAC
59219 ATATGAACTATA---T--
1 ATATGAACTATAGTTTAC
*
59232 ATATAAACTATATAGTTTAC
1 ATATGAAC--TATAGTTTAC
* * *
59252 ATAAGAACTATA-TATAT
1 ATATGAACTATAGTTTAC
* * *
59269 ATACTAAAGTTGATA-TTTAT
1 ATA-TGAA-CT-ATAGTTTAC
59289 ATATGAACTATAGTTTAC
1 ATATGAACTATAGTTTAC
*
59307 ATATAAACTATAGTTTAC
1 ATATGAACTATAGTTTAC
*
59325 ATATGAACTATA---TAT
1 ATATGAACTATAGTTTAC
*
59340 ATATAAACTATATAGTTTAC
1 ATATGAAC--TATAGTTTAC
*
59360 ATATGACCTATA
1 ATATGAACTATA
59372 TATATATACT
Statistics
Matches: 118, Mismatches: 19, Indels: 32
0.70 0.11 0.19
Matches are distributed among these distances:
13 7 0.06
15 14 0.12
17 13 0.11
18 56 0.47
19 4 0.03
20 24 0.20
ACGTcount: A:0.44, C:0.09, G:0.08, T:0.39
Consensus pattern (18 bp):
ATATGAACTATAGTTTAC
Found at i:59311 original size:108 final size:107
Alignment explanation
Indices: 59201--59397 Score: 342
Period size: 108 Copynumber: 1.8 Consensus size: 107
59191 TATACTATAT
*
59201 ATATGAACTATAGTTTACATATGAAC-TATATATATAAACTATATAGTTTACATAAGAACTATAT
1 ATATAAACTATAGTTTACATATGAACATATATATATAAACTATATAGTTTACATAAGAACTATAT
59265 ATATATACTAAAGTTGATATTTATATATGAACTATAGTTTAC
66 ATATATACTAAAGTTGATATTTATATATGAACTATAGTTTAC
* *
59307 ATATAAACTATAGTTTACATATGAACTATATATATATAAACTATATAGTTTACATATGACCTATA
1 ATATAAACTATAGTTTACATATGAAC-ATATATATATAAACTATATAGTTTACATAAGAACTATA
*
59372 TATATATACTATAGTTGATATTTATA
65 TATATATACTAAAGTTGATATTTATA
59398 CACTATATAG
Statistics
Matches: 85, Mismatches: 4, Indels: 2
0.93 0.04 0.02
Matches are distributed among these distances:
106 25 0.29
108 60 0.71
ACGTcount: A:0.43, C:0.09, G:0.08, T:0.41
Consensus pattern (107 bp):
ATATAAACTATAGTTTACATATGAACATATATATATAAACTATATAGTTTACATAAGAACTATAT
ATATATACTAAAGTTGATATTTATATATGAACTATAGTTTAC
Found at i:59392 original size:20 final size:18
Alignment explanation
Indices: 59368--59537 Score: 81
Period size: 20 Copynumber: 9.3 Consensus size: 18
59358 ACATATGACC
59368 TATATATATATACTATAGT
1 TATATATATATACTATA-T
* *
59387 TGATATTTATACACTATA-
1 T-ATATATATATACTATAT
* *
59405 TAGTTTACATATGAC-ATA-
1 TA-TATATATAT-ACTATAT
*
59423 TATATATATATGCTATAGCT
1 TATATATATATACTATA--T
*
59443 TATATTTATATACTATATAT
1 TATATATATATAC--TATAT
*
59463 TATATATATAAACTATA-
1 TATATATATATACTATAT
59480 TATACTATATAGTA-TA-AT
1 TATA-TATATA-TACTATAT
*
59498 T-TACATATGA-ACTATA-
1 TATATATAT-ATACTATAT
*
59514 TAGTTTATATAT-CTATAT
1 TA-TATATATATACTATAT
59532 TATATA
1 TATATA
59538 AAAACTATAT
Statistics
Matches: 114, Mismatches: 18, Indels: 40
0.66 0.10 0.23
Matches are distributed among these distances:
15 1 0.01
16 8 0.07
17 29 0.25
18 31 0.27
19 4 0.04
20 37 0.32
22 4 0.04
ACGTcount: A:0.41, C:0.08, G:0.05, T:0.46
Consensus pattern (18 bp):
TATATATATATACTATAT
Found at i:59458 original size:55 final size:52
Alignment explanation
Indices: 59227--59525 Score: 218
Period size: 53 Copynumber: 5.6 Consensus size: 52
59217 ACATATGAAC
* * *
59227 TATATATATAAACTATATAGTTTACATAAGA-ACTATATATATATACTAAAGT
1 TATATTTATAAACTATATAGTTTACATATGACA-TATATATATATACTATAGT
* * * *
59279 TGATATTTATATA-TGAACTATAGTTTACATATAAACTATAGTTTACATATGAACTATA--
1 T-ATATTTATAAACT--A-TATAGTTTACATAT-GAC-ATA-TATATATAT--ACTATAGT
*
59337 TATA--TATAAACTATATAGTTTACATATGACCTATATATATATACTATAGT
1 TATATTTATAAACTATATAGTTTACATATGACATATATATATATACTATAGT
*
59387 TGATATTTATACACTATATAGTTTACATATGACATATATATATATATGCTATAGCT
1 T-ATATTTATAAACTATATAGTTTACATATGACATATATATATATA--CTATAG-T
* * * * *
59443 TATATTTATATACTATATA-TTATATATATAAACTATATATACTATATAGTATAAT
1 TATATTTATAAACTATATAGTT-TACATAT-GAC-ATATATA-TATATACTATAGT
** * *
59498 T-TACATATGAACTATATAGTTTATATAT
1 TATATTTATAAACTATATAGTTTACATAT
59526 CTATATTATA
Statistics
Matches: 200, Mismatches: 23, Indels: 46
0.74 0.09 0.17
Matches are distributed among these distances:
48 6 0.03
50 8 0.04
51 5 0.03
52 4 0.02
53 60 0.30
54 24 0.12
55 51 0.25
56 10 0.05
57 12 0.06
58 15 0.08
60 5 0.03
ACGTcount: A:0.42, C:0.08, G:0.06, T:0.43
Consensus pattern (52 bp):
TATATTTATAAACTATATAGTTTACATATGACATATATATATATACTATAGT
Found at i:59468 original size:9 final size:9
Alignment explanation
Indices: 59449--59576 Score: 60
Period size: 9 Copynumber: 14.4 Consensus size: 9
59439 AGCTTATATT
59449 TATATACTA
1 TATATACTA
59458 TATATTA-TA
1 TATA-TACTA
59467 TATATAAACTA
1 TATAT--ACTA
59478 TATATACTA
1 TATATACTA
59487 TATAGTA-TA
1 TATA-TACTA
*
59496 -ATTTAC-A
1 TATATACTA
59503 TATGA-ACTA
1 TAT-ATACTA
*
59512 TATAGT-TTA
1 TATA-TACTA
59521 TATAT-CTA
1 TATATACTA
59529 TAT-TA-TA
1 TATATACTA
* *
59536 TAAAAACTA
1 TATATACTA
*
59545 TATATACCATG
1 TATATA-C-TA
*
59556 TATAAACTA
1 TATATACTA
59565 TA-ATACTA
1 TATATACTA
59573 TATA
1 TATA
59577 GTTTATATAT
Statistics
Matches: 90, Mismatches: 12, Indels: 34
0.66 0.09 0.25
Matches are distributed among these distances:
7 8 0.09
8 22 0.24
9 40 0.44
10 7 0.08
11 13 0.14
ACGTcount: A:0.46, C:0.09, G:0.03, T:0.42
Consensus pattern (9 bp):
TATATACTA
Found at i:59479 original size:108 final size:107
Alignment explanation
Indices: 59201--59488 Score: 315
Period size: 108 Copynumber: 2.7 Consensus size: 107
59191 TATACTATAT
* *
59201 ATATGAACTATAGTTTACATATGAAC--TATATATATAAACTATATAGTTTACATA-AGAACTAT
1 ATATAAACTATAGTATACATATGAACTATATATATATAAACTATATAGTTTACATATA-AACTAT
*
59263 ATATATATACTAAAGTTGATATTTATATATGAACTATAGTTTAC
65 ATATATATACTAAAGTTGATATTTATACAT-AACTATAGTTTAC
* * *
59307 ATATAAACTATAGTTTACATATGAACTATATATATATAAACTATATAGTTTACATATGACCTATA
1 ATATAAACTATAGTATACATATGAACTATATATATATAAACTATATAGTTTACATATAAACTATA
*
59372 TATATATACTATAGTTGATATTTATACACT-A-TATAGTTTAC
66 TATATATACTAAAGTTGATATTTATACA-TAACTATAGTTTAC
* * * * *
59413 ATAT-GACATATA-TATATATATGCTATAGCT-TATATTTATATACTATATA-TTATATATATAA
1 ATATAAAC-TATAGTATACATATG--A-A-CTATATATATATAAACTATATAGTT-TACATATAA
59474 ACTATATATACTATA
60 ACTATATATA-TATA
59489 TAGTATAATT
Statistics
Matches: 158, Mismatches: 13, Indels: 19
0.83 0.07 0.10
Matches are distributed among these distances:
105 10 0.06
106 43 0.27
107 4 0.03
108 94 0.59
109 7 0.04
ACGTcount: A:0.43, C:0.09, G:0.07, T:0.42
Consensus pattern (107 bp):
ATATAAACTATAGTATACATATGAACTATATATATATAAACTATATAGTTTACATATAAACTATA
TATATATACTAAAGTTGATATTTATACATAACTATAGTTTAC
Found at i:59684 original size:17 final size:18
Alignment explanation
Indices: 59664--59706 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
59654 TATATTATGT
*
59664 ATAATGTATAAT-TATAA
1 ATAATATATAATGTATAA
*
59681 ATAATATATATTGTATAA
1 ATAATATATAATGTATAA
*
59699 ATTATATA
1 ATAATATA
59707 GTTTATTAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
17 10 0.45
18 12 0.55
ACGTcount: A:0.51, C:0.00, G:0.05, T:0.44
Consensus pattern (18 bp):
ATAATATATAATGTATAA
Found at i:59750 original size:22 final size:22
Alignment explanation
Indices: 59694--59743 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 22
59684 ATATATATTG
* *
59694 TATAAATTATATAGTTTATTAA
1 TATAAACTATATAGTGTATTAA
59716 TATAAACTATATAGTGTATATATA
1 TATAAACTATATAGTGTAT-TA-A
59740 TATA
1 TATA
59744 GTATATATGG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 17 0.71
23 2 0.08
24 5 0.21
ACGTcount: A:0.46, C:0.02, G:0.06, T:0.46
Consensus pattern (22 bp):
TATAAACTATATAGTGTATTAA
Found at i:59799 original size:42 final size:42
Alignment explanation
Indices: 59752--59848 Score: 176
Period size: 42 Copynumber: 2.3 Consensus size: 42
59742 TAGTATATAT
59752 GGTTTAGGGTTTAGGGATCATGATTTAGTAGGTTAGGTTTAG
1 GGTTTAGGGTTTAGGGATCATGATTTAGTAGGTTAGGTTTAG
* *
59794 GGTTTAGAGTTTAGGGATCATGATTTAGTAGGTTGGGTTTAG
1 GGTTTAGGGTTTAGGGATCATGATTTAGTAGGTTAGGTTTAG
59836 GGTTTAGGGTTTA
1 GGTTTAGGGTTTA
59849 TATTTATATT
Statistics
Matches: 52, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 52 1.00
ACGTcount: A:0.21, C:0.02, G:0.36, T:0.41
Consensus pattern (42 bp):
GGTTTAGGGTTTAGGGATCATGATTTAGTAGGTTAGGTTTAG
Found at i:59896 original size:20 final size:20
Alignment explanation
Indices: 59871--59986 Score: 92
Period size: 20 Copynumber: 5.4 Consensus size: 20
59861 TATAAACTAC
59871 ATACTATAATTTATATTTAT
1 ATACTATAATTTATATTTAT
*
59891 ATACTATATTTTATACTATTTAT
1 ATACTATA-ATT-TA-TATTTAT
*
59914 ATAAACTATAGTTTATATTTAT
1 AT--ACTATAATTTATATTTAT
* *
59936 ATAATATATTTTATACTATTTAT
1 ATACTATA-ATT-TA-TATTTAT
59959 ATAAACTATAA-TT-TATTTAT
1 AT--ACTATAATTTATATTTAT
59979 ATACTATA
1 ATACTATA
59987 TATATGAACT
Statistics
Matches: 80, Mismatches: 6, Indels: 22
0.74 0.06 0.20
Matches are distributed among these distances:
18 6 0.08
20 22 0.28
21 4 0.05
22 14 0.17
23 21 0.26
24 2 0.03
25 11 0.14
ACGTcount: A:0.41, C:0.06, G:0.01, T:0.53
Consensus pattern (20 bp):
ATACTATAATTTATATTTAT
Found at i:59922 original size:25 final size:24
Alignment explanation
Indices: 59884--59974 Score: 111
Period size: 23 Copynumber: 3.9 Consensus size: 24
59874 CTATAATTTA
59884 TATTTATAT-ACTATATTTTATAC
1 TATTTATATAACTATATTTTATAC
*
59907 TATTTATATAAACTATA-GTT-TA-
1 TATTTATAT-AACTATATTTTATAC
59929 TATTTATATAA-TATATTTTATAC
1 TATTTATATAACTATATTTTATAC
*
59952 TATTTATATAAACTATAATTTAT
1 TATTTATAT-AACTATATTTTAT
59975 TTATATACTA
Statistics
Matches: 58, Mismatches: 3, Indels: 12
0.79 0.04 0.16
Matches are distributed among these distances:
20 4 0.07
21 4 0.07
22 11 0.19
23 20 0.34
24 4 0.07
25 15 0.26
ACGTcount: A:0.40, C:0.05, G:0.01, T:0.54
Consensus pattern (24 bp):
TATTTATATAACTATATTTTATAC
Found at i:59929 original size:45 final size:44
Alignment explanation
Indices: 59873--59987 Score: 187
Period size: 45 Copynumber: 2.6 Consensus size: 44
59863 TAAACTACAT
59873 ACTATAATTTATATTTATATACTATATTTTATACTATTTATATAA
1 ACTAT-ATTTATATTTATATACTATATTTTATACTATTTATATAA
*
59918 ACTATAGTTTATATTTATATAATATATTTTATACTATTTATATAA
1 ACTATA-TTTATATTTATATACTATATTTTATACTATTTATATAA
*
59963 ACTATAATT-TATTTATATACTATAT
1 ACTATATTTATATTTATATACTATAT
59988 ATATGAACTA
Statistics
Matches: 66, Mismatches: 3, Indels: 4
0.90 0.04 0.05
Matches are distributed among these distances:
43 15 0.23
44 3 0.05
45 48 0.73
ACGTcount: A:0.40, C:0.06, G:0.01, T:0.53
Consensus pattern (44 bp):
ACTATATTTATATTTATATACTATATTTTATACTATTTATATAA
Found at i:59985 original size:31 final size:31
Alignment explanation
Indices: 59935--60030 Score: 115
Period size: 31 Copynumber: 3.1 Consensus size: 31
59925 TTTATATTTA
* *
59935 TATAATATATTT-TATACTATTTATATAAAC
1 TATAATTTATTTATATACTATATATATAAAC
*
59965 TATAATTTATTTATATACTATATATATGAAC
1 TATAATTTATTTATATACTATATATATAAAC
* **
59996 TATAGTTTACATATGA-ACTATATATATAAAC
1 TATAATTTATTTAT-ATACTATATATATAAAC
60027 TATA
1 TATA
60031 TAAACTATAT
Statistics
Matches: 57, Mismatches: 7, Indels: 3
0.85 0.10 0.04
Matches are distributed among these distances:
30 11 0.19
31 45 0.79
32 1 0.02
ACGTcount: A:0.44, C:0.07, G:0.03, T:0.46
Consensus pattern (31 bp):
TATAATTTATTTATATACTATATATATAAAC
Found at i:59990 original size:52 final size:48
Alignment explanation
Indices: 59855--59980 Score: 159
Period size: 45 Copynumber: 2.6 Consensus size: 48
59845 TTTATATTTA
* *
59855 TATTTATATAAACTACATACTATAATTTATATTTATATACTATATTTTATAC
1 TATTTATATAAACT--ATA--ATTATTTATATTTATATAATATATTTTATAC
*
59907 TATTTATATAAACTAT-A--GTTTATATTTATATAATATATTTTATAC
1 TATTTATATAAACTATAATTATTTATATTTATATAATATATTTTATAC
59952 TATTTATATAAACTATAATTTATTTATAT
1 TATTTATATAAACTATAA-TTATTTATAT
59981 ACTATATATA
Statistics
Matches: 67, Mismatches: 3, Indels: 11
0.83 0.04 0.14
Matches are distributed among these distances:
45 42 0.63
46 1 0.01
47 1 0.01
49 7 0.10
50 2 0.03
52 14 0.21
ACGTcount: A:0.40, C:0.06, G:0.01, T:0.52
Consensus pattern (48 bp):
TATTTATATAAACTATAATTATTTATATTTATATAATATATTTTATAC
Found at i:59997 original size:13 final size:13
Alignment explanation
Indices: 59981--60032 Score: 50
Period size: 13 Copynumber: 3.6 Consensus size: 13
59971 TTATTTATAT
59981 ACTATATATATGA
1 ACTATATATATGA
59994 ACTATAGTTTACATATGA
1 ACTATA---T--ATATGA
*
60012 ACTATATATATAA
1 ACTATATATATGA
60025 ACTATATA
1 ACTATATA
60033 AACTATATAG
Statistics
Matches: 33, Mismatches: 1, Indels: 10
0.75 0.02 0.23
Matches are distributed among these distances:
13 19 0.58
15 1 0.03
16 1 0.03
18 12 0.36
ACGTcount: A:0.46, C:0.10, G:0.06, T:0.38
Consensus pattern (13 bp):
ACTATATATATGA
Found at i:59999 original size:18 final size:17
Alignment explanation
Indices: 59978--60023 Score: 56
Period size: 18 Copynumber: 2.6 Consensus size: 17
59968 AATTTATTTA
59978 TATACTATATATATGAAC
1 TATA-TATATATATGAAC
* *
59996 TATAGTTTACATATGAAC
1 TATA-TATATATATGAAC
60014 TATATATATA
1 TATATATATA
60024 AACTATATAA
Statistics
Matches: 23, Mismatches: 5, Indels: 1
0.79 0.17 0.03
Matches are distributed among these distances:
17 4 0.17
18 19 0.83
ACGTcount: A:0.43, C:0.09, G:0.07, T:0.41
Consensus pattern (17 bp):
TATATATATATATGAAC
Found at i:61525 original size:2 final size:2
Alignment explanation
Indices: 61518--61560 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
61508 ATTATTGTTA
61518 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
61560 A
1 A
61561 CTGGTTTATT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:63784 original size:23 final size:23
Alignment explanation
Indices: 63731--63784 Score: 54
Period size: 23 Copynumber: 2.3 Consensus size: 23
63721 CTTAATGCAG
* *
63731 GATGCTTGCTGAATTGATGCAAC
1 GATGCTTGCTAAATTGATACAAC
* * **
63754 GATACTTGCTAAATTGGTACATT
1 GATGCTTGCTAAATTGATACAAC
63777 GATGCTTG
1 GATGCTTG
63785 TCGGTTGCTG
Statistics
Matches: 24, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.26, C:0.15, G:0.24, T:0.35
Consensus pattern (23 bp):
GATGCTTGCTAAATTGATACAAC
Found at i:64298 original size:15 final size:15
Alignment explanation
Indices: 64278--64317 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 15
64268 TAACTTAATT
*
64278 AATAAAATTTATTAA
1 AATAAAATTTAATAA
64293 AATAAAATTTAATAA
1 AATAAAATTTAATAA
* *
64308 GATAATATTT
1 AATAAAATTT
64318 TAAATTTAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.40
Consensus pattern (15 bp):
AATAAAATTTAATAA
Found at i:67392 original size:9 final size:9
Alignment explanation
Indices: 67378--67425 Score: 51
Period size: 9 Copynumber: 5.0 Consensus size: 9
67368 GGCTGCTGGA
67378 AACCGGTTT
1 AACCGGTTT
67387 AACCGGTTTT
1 AACCGG-TTT
67397 CAACCGGTTCT
1 -AACCGGTT-T
*
67408 GACCGGTTT
1 AACCGGTTT
*
67417 GACCGGTTT
1 AACCGGTTT
67426 CGACCGGTCT
Statistics
Matches: 35, Mismatches: 1, Indels: 6
0.83 0.02 0.14
Matches are distributed among these distances:
9 16 0.46
10 12 0.34
11 7 0.20
ACGTcount: A:0.17, C:0.25, G:0.25, T:0.33
Consensus pattern (9 bp):
AACCGGTTT
Found at i:67403 original size:20 final size:21
Alignment explanation
Indices: 67378--67416 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
67368 GGCTGCTGGA
67378 AACCGGTT-TAACCGGTTTTC
1 AACCGGTTCTAACCGGTTTTC
*
67398 AACCGGTTCTGACCGGTTT
1 AACCGGTTCTAACCGGTTT
67417 GACCGGTTTC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.18, C:0.26, G:0.23, T:0.33
Consensus pattern (21 bp):
AACCGGTTCTAACCGGTTTTC
Found at i:67414 original size:10 final size:9
Alignment explanation
Indices: 67379--67439 Score: 59
Period size: 10 Copynumber: 6.3 Consensus size: 9
67369 GCTGCTGGAA
*
67379 ACCGGTTTA
1 ACCGGTTTG
*
67388 ACCGGTTTTCA
1 ACCGG-TTT-G
67399 ACCGGTTCTG
1 ACCGGTT-TG
67409 ACCGGTTTG
1 ACCGGTTTG
67418 ACCGGTTTCG
1 ACCGGTTT-G
*
67428 ACCGGTCTG
1 ACCGGTTTG
67437 ACC
1 ACC
67440 CGACCGACCG
Statistics
Matches: 46, Mismatches: 2, Indels: 8
0.82 0.04 0.14
Matches are distributed among these distances:
9 19 0.41
10 20 0.43
11 7 0.15
ACGTcount: A:0.15, C:0.30, G:0.26, T:0.30
Consensus pattern (9 bp):
ACCGGTTTG
Found at i:67423 original size:19 final size:19
Alignment explanation
Indices: 67399--67439 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
67389 CCGGTTTTCA
*
67399 ACCGG-TTCTGACCGGTTTG
1 ACCGGTTTC-GACCGGTCTG
67418 ACCGGTTTCGACCGGTCTG
1 ACCGGTTTCGACCGGTCTG
67437 ACC
1 ACC
67440 CGACCGACCG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 17 0.85
20 3 0.15
ACGTcount: A:0.12, C:0.32, G:0.29, T:0.27
Consensus pattern (19 bp):
ACCGGTTTCGACCGGTCTG
Found at i:67449 original size:18 final size:18
Alignment explanation
Indices: 67436--67485 Score: 66
Period size: 18 Copynumber: 2.8 Consensus size: 18
67426 CGACCGGTCT
67436 GACCCGACCGACCGACCC
1 GACCCGACCGACCGACCC
**
67454 GACCCGACCG-TTGACCC
1 GACCCGACCGACCGACCC
67471 GACCCGACCCGACCG
1 GACCCGA-CCGACCG
67486 GACCGTTGAT
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
17 12 0.46
18 13 0.50
19 1 0.04
ACGTcount: A:0.20, C:0.52, G:0.24, T:0.04
Consensus pattern (18 bp):
GACCCGACCGACCGACCC
Found at i:67477 original size:27 final size:26
Alignment explanation
Indices: 67443--67494 Score: 86
Period size: 27 Copynumber: 2.0 Consensus size: 26
67433 TCTGACCCGA
67443 CCGACCGACCCGACCCGACCGTTGAC
1 CCGACCGACCCGACCCGACCGTTGAC
*
67469 CCGACCCGACCCGACCGGACCGTTGA
1 CCGA-CCGACCCGACCCGACCGTTGA
67495 TCGTTGACCG
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
26 4 0.17
27 20 0.83
ACGTcount: A:0.19, C:0.48, G:0.25, T:0.08
Consensus pattern (26 bp):
CCGACCGACCCGACCCGACCGTTGAC
Found at i:67490 original size:5 final size:5
Alignment explanation
Indices: 67436--67489 Score: 58
Period size: 5 Copynumber: 10.8 Consensus size: 5
67426 CGACCGGTCT
* *
67436 GACCC GA-CC GA-CC GACCC GACCC GACCGTT GACCC GACCC GACCC GACCG
1 GACCC GACCC GACCC GACCC GACCC GACC--C GACCC GACCC GACCC GACCC
67486 GACC
1 GACC
67490 GTTGATCGTT
Statistics
Matches: 43, Mismatches: 3, Indels: 6
0.83 0.06 0.12
Matches are distributed among these distances:
4 8 0.19
5 31 0.72
7 4 0.09
ACGTcount: A:0.20, C:0.52, G:0.24, T:0.04
Consensus pattern (5 bp):
GACCC
Found at i:73345 original size:20 final size:20
Alignment explanation
Indices: 73308--73366 Score: 75
Period size: 21 Copynumber: 2.9 Consensus size: 20
73298 CAGAACCCTA
*
73308 GGGGGTATCGATTCCC-CTAT
1 GGGGGGATCGATTCCCTC-AT
*
73328 GGGGGGAATCGGTTCCCTCAT
1 GGGGGG-ATCGATTCCCTCAT
73349 GGGGGGATCGATTCCCTC
1 GGGGGGATCGATTCCCTC
73367 TGCACAAAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
20 16 0.47
21 17 0.50
22 1 0.03
ACGTcount: A:0.14, C:0.25, G:0.36, T:0.25
Consensus pattern (20 bp):
GGGGGGATCGATTCCCTCAT
Found at i:83864 original size:9 final size:9
Alignment explanation
Indices: 83850--83910 Score: 59
Period size: 9 Copynumber: 6.4 Consensus size: 9
83840 GGCTGCTGGA
83850 AACCGGTTT
1 AACCGGTTT
83859 AACCGGTTTT
1 AACCGG-TTT
83869 CAACCGGTTCT
1 -AACCGGTT-T
*
83880 GACCGGTTT
1 AACCGGTTT
*
83889 GACCGGTTT
1 AACCGGTTT
* *
83898 GACCGGTAT
1 AACCGGTTT
83907 AACC
1 AACC
83911 CGACCGACCG
Statistics
Matches: 46, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
9 27 0.59
10 12 0.26
11 7 0.15
ACGTcount: A:0.20, C:0.26, G:0.25, T:0.30
Consensus pattern (9 bp):
AACCGGTTT
Found at i:83875 original size:20 final size:21
Alignment explanation
Indices: 83850--83888 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
83840 GGCTGCTGGA
83850 AACCGGTT-TAACCGGTTTTC
1 AACCGGTTCTAACCGGTTTTC
*
83870 AACCGGTTCTGACCGGTTT
1 AACCGGTTCTAACCGGTTT
83889 GACCGGTTTG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.18, C:0.26, G:0.23, T:0.33
Consensus pattern (21 bp):
AACCGGTTCTAACCGGTTTTC
Found at i:83886 original size:10 final size:9
Alignment explanation
Indices: 83851--83904 Score: 63
Period size: 9 Copynumber: 5.7 Consensus size: 9
83841 GCTGCTGGAA
*
83851 ACCGGTTTA
1 ACCGGTTTG
*
83860 ACCGGTTTTCA
1 ACCGG-TTT-G
83871 ACCGGTTCTG
1 ACCGGTT-TG
83881 ACCGGTTTG
1 ACCGGTTTG
83890 ACCGGTTTG
1 ACCGGTTTG
83899 ACCGGT
1 ACCGGT
83905 ATAACCCGAC
Statistics
Matches: 41, Mismatches: 1, Indels: 6
0.85 0.02 0.12
Matches are distributed among these distances:
9 22 0.54
10 12 0.29
11 7 0.17
ACGTcount: A:0.15, C:0.26, G:0.28, T:0.31
Consensus pattern (9 bp):
ACCGGTTTG
Found at i:83973 original size:22 final size:19
Alignment explanation
Indices: 83908--83967 Score: 76
Period size: 17 Copynumber: 3.4 Consensus size: 19
83898 GACCGGTATA
*
83908 ACCCGACCG-ACCGACCCG
1 ACCCGACCGTTCCGACCCG
83926 ACCCGACCGTT--GACCCG
1 ACCCGACCGTTCCGACCCG
83943 ACCCGACCGTT--GACCCG
1 ACCCGACCGTTCCGACCCG
83960 ACCCGACC
1 ACCCGACC
83968 CGACCGGACC
Statistics
Matches: 40, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
17 31 0.77
18 9 0.22
ACGTcount: A:0.20, C:0.52, G:0.22, T:0.07
Consensus pattern (19 bp):
ACCCGACCGTTCCGACCCG
Found at i:83978 original size:5 final size:5
Alignment explanation
Indices: 83908--83977 Score: 63
Period size: 5 Copynumber: 13.6 Consensus size: 5
83898 GACCGGTATA
* *
83908 ACCCG A-CCG A-CCG ACCCG ACCCG ACCGTTG ACCCG ACCCG ACCGTTG
1 ACCCG ACCCG ACCCG ACCCG ACCCG ACC--CG ACCCG ACCCG ACC--CG
*
83955 ACCCG ACCCG ACCCG ACCGG ACC
1 ACCCG ACCCG ACCCG ACCCG ACC
83978 GTTGACCGTT
Statistics
Matches: 55, Mismatches: 5, Indels: 10
0.79 0.07 0.14
Matches are distributed among these distances:
4 8 0.15
5 39 0.71
7 8 0.15
ACGTcount: A:0.20, C:0.51, G:0.23, T:0.06
Consensus pattern (5 bp):
ACCCG
Found at i:83984 original size:17 final size:17
Alignment explanation
Indices: 83920--83967 Score: 96
Period size: 17 Copynumber: 2.8 Consensus size: 17
83910 CCGACCGACC
83920 GACCCGACCCGACCGTT
1 GACCCGACCCGACCGTT
83937 GACCCGACCCGACCGTT
1 GACCCGACCCGACCGTT
83954 GACCCGACCCGACC
1 GACCCGACCCGACC
83968 CGACCGGACC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 31 1.00
ACGTcount: A:0.19, C:0.50, G:0.23, T:0.08
Consensus pattern (17 bp):
GACCCGACCCGACCGTT
Found at i:83984 original size:22 final size:22
Alignment explanation
Indices: 83918--83984 Score: 84
Period size: 22 Copynumber: 3.0 Consensus size: 22
83908 ACCCGACCGA
*
83918 CCGACCCGACCCGACCGTTGAC
1 CCGACCCGACCGGACCGTTGAC
*
83940 CCGACCCGACCGTTGACC--CGAC
1 CCGACCCGACCG--GACCGTTGAC
83962 CCGACCCGACCGGACCGTTGAC
1 CCGACCCGACCGGACCGTTGAC
83984 C
1 C
83985 GTTGACCGTT
Statistics
Matches: 38, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
20 4 0.11
22 30 0.79
24 4 0.11
ACGTcount: A:0.18, C:0.49, G:0.24, T:0.09
Consensus pattern (22 bp):
CCGACCCGACCGGACCGTTGAC
Found at i:88560 original size:36 final size:37
Alignment explanation
Indices: 88493--88563 Score: 101
Period size: 36 Copynumber: 1.9 Consensus size: 37
88483 TATCCAGTGC
88493 TTCTTGAGCTTTATCTTCAAATCAATATTTTCCATGT
1 TTCTTGAGCTTTATCTTCAAATCAATATTTTCCATGT
* *
88530 TTCTTGAGCTATTAT-TT-ATATCAATGTTTTCCAT
1 TTCTTGAGCT-TTATCTTCAAATCAATATTTTCCAT
88564 CTTTTTTTCT
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
36 15 0.48
37 12 0.39
38 4 0.13
ACGTcount: A:0.24, C:0.17, G:0.08, T:0.51
Consensus pattern (37 bp):
TTCTTGAGCTTTATCTTCAAATCAATATTTTCCATGT
Found at i:89924 original size:21 final size:21
Alignment explanation
Indices: 89898--89937 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
89888 GAGTGTGATG
89898 ATATTGATATGACAATTTATA
1 ATATTGATATGACAATTTATA
* *
89919 ATATTGATGTGATAATTTA
1 ATATTGATATGACAATTTA
89938 AGGTGGTTAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.40, C:0.03, G:0.12, T:0.45
Consensus pattern (21 bp):
ATATTGATATGACAATTTATA
Found at i:94889 original size:18 final size:17
Alignment explanation
Indices: 94867--94906 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
94857 ATCAAAAACT
94867 AAAAATAAATATAAAATA
1 AAAAATAAATA-AAAATA
* *
94885 AAAAATTATTAAAAATA
1 AAAAATAAATAAAAATA
94902 AAAAA
1 AAAAA
94907 ATATTTTAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 11 0.55
18 9 0.45
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.23
Consensus pattern (17 bp):
AAAAATAAATAAAAATA
Found at i:94899 original size:17 final size:17
Alignment explanation
Indices: 94879--94911 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
94869 AAATAAATAT
*
94879 AAAATAAAAAATTATTA
1 AAAATAAAAAAATATTA
94896 AAAATAAAAAAATATT
1 AAAATAAAAAAATATT
94912 TTAAAAAATA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (17 bp):
AAAATAAAAAAATATTA
Found at i:94921 original size:20 final size:18
Alignment explanation
Indices: 94879--94918 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 18
94869 AAATAAATAT
94879 AAAAT-AAAAAATTATTA
1 AAAATAAAAAAATTATTA
*
94896 AAAATAAAAAAATATTTTA
1 AAAATAAAAAAAT-TATTA
94915 AAAA
1 AAAA
94919 ATATATATAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 5 0.25
18 7 0.35
19 8 0.40
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (18 bp):
AAAATAAAAAAATTATTA
Found at i:95072 original size:2 final size:2
Alignment explanation
Indices: 95065--95104 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
95055 ACTTTTACAC
95065 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
95105 GAATGGCGTA
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:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:95745 original size:21 final size:21
Alignment explanation
Indices: 95721--95765 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
95711 TTAATAGTAA
*
95721 TTTTAGTAATTTAATTTTTAT
1 TTTTAGTAATTTAATATTTAT
* *
95742 TTTTAGTATTTTTATATTTAT
1 TTTTAGTAATTTAATATTTAT
95763 TTT
1 TTT
95766 AAAATATTTA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.24, C:0.00, G:0.04, T:0.71
Consensus pattern (21 bp):
TTTTAGTAATTTAATATTTAT
Found at i:95780 original size:22 final size:22
Alignment explanation
Indices: 95755--95810 Score: 60
Period size: 23 Copynumber: 2.5 Consensus size: 22
95745 TAGTATTTTT
*
95755 ATATTTAT-TTTAAAATATTTAA
1 ATATTTATATTTAAAAT-TTAAA
*
95777 ATATTTTATATTTTAAATTTAAA
1 ATA-TTTATATTTAAAATTTAAA
95800 ATATTATATAT
1 ATATT-TATAT
95811 ATATTTTTAA
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
22 5 0.17
23 17 0.59
24 7 0.24
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (22 bp):
ATATTTATATTTAAAATTTAAA
Found at i:97598 original size:13 final size:13
Alignment explanation
Indices: 97580--97627 Score: 69
Period size: 13 Copynumber: 3.7 Consensus size: 13
97570 TTTATGAATA
97580 GTGAACAATACCC
1 GTGAACAATACCC
* * *
97593 GTGAACAGTAACA
1 GTGAACAATACCC
97606 GTGAACAATACCC
1 GTGAACAATACCC
97619 GTGAACAAT
1 GTGAACAAT
97628 GGAAGAATCA
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
13 29 1.00
ACGTcount: A:0.42, C:0.23, G:0.19, T:0.17
Consensus pattern (13 bp):
GTGAACAATACCC
Found at i:98197 original size:48 final size:45
Alignment explanation
Indices: 98118--98244 Score: 166
Period size: 48 Copynumber: 2.8 Consensus size: 45
98108 TATAAAATTT
* *
98118 CTTACCATTTATCCCATAAGCTCATATGCTTATTTTTACCAAAATA
1 CTTACCATTTATTCCATAAGCTCATAAGCTTATTTTT-CCAAAATA
* *
98164 CTTACCATTTAAATTCCATAAGCTCGTAAGCTTATTTTTCCAATATA
1 CTTACCATTT--ATTCCATAAGCTCATAAGCTTATTTTTCCAAAATA
* *
98211 CTTGCCA-TTATTCCGTAAGCTCATAAGCTTATTT
1 CTTACCATTTATTCCATAAGCTCATAAGCTTATTT
98245 GCATGGTTAC
Statistics
Matches: 72, Mismatches: 7, Indels: 6
0.85 0.08 0.07
Matches are distributed among these distances:
44 23 0.32
46 12 0.17
47 13 0.18
48 24 0.33
ACGTcount: A:0.30, C:0.23, G:0.07, T:0.40
Consensus pattern (45 bp):
CTTACCATTTATTCCATAAGCTCATAAGCTTATTTTTCCAAAATA
Found at i:98397 original size:40 final size:40
Alignment explanation
Indices: 98348--98430 Score: 166
Period size: 40 Copynumber: 2.1 Consensus size: 40
98338 CACCGTAGTG
98348 TTACACATAAGGTCGTGCCCACCATATACACCGAAGTGTA
1 TTACACATAAGGTCGTGCCCACCATATACACCGAAGTGTA
98388 TTACACATAAGGTCGTGCCCACCATATACACCGAAGTGTA
1 TTACACATAAGGTCGTGCCCACCATATACACCGAAGTGTA
98428 TTA
1 TTA
98431 TAAACCTGCA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 43 1.00
ACGTcount: A:0.33, C:0.27, G:0.17, T:0.24
Consensus pattern (40 bp):
TTACACATAAGGTCGTGCCCACCATATACACCGAAGTGTA
Found at i:103002 original size:8 final size:8
Alignment explanation
Indices: 102991--103045 Score: 69
Period size: 8 Copynumber: 6.8 Consensus size: 8
102981 AAGAAAAGAG
102991 AAAAAT-A
1 AAAAATAA
102998 AAAAAT-A
1 AAAAATAA
103005 AAAAATAA
1 AAAAATAA
103013 AAAAATAA
1 AAAAATAA
103021 AGAAAATAGA
1 A-AAAATA-A
103031 CAAAAATAA
1 -AAAAATAA
103040 AAAAAT
1 AAAAAT
103046 GGGTTGTCTT
Statistics
Matches: 44, Mismatches: 0, Indels: 7
0.86 0.00 0.14
Matches are distributed among these distances:
7 13 0.30
8 16 0.36
9 7 0.16
10 7 0.16
11 1 0.02
ACGTcount: A:0.82, C:0.02, G:0.04, T:0.13
Consensus pattern (8 bp):
AAAAATAA
Found at i:103007 original size:6 final size:7
Alignment explanation
Indices: 102991--103021 Score: 53
Period size: 7 Copynumber: 4.3 Consensus size: 7
102981 AAGAAAAGAG
102991 AAAAATA
1 AAAAATA
102998 AAAAATA
1 AAAAATA
103005 AAAAATAA
1 AAAAAT-A
103013 AAAAATA
1 AAAAATA
103020 AA
1 AA
103022 GAAAATAGAC
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
7 16 0.70
8 7 0.30
ACGTcount: A:0.87, C:0.00, G:0.00, T:0.13
Consensus pattern (7 bp):
AAAAATA
Found at i:103008 original size:14 final size:15
Alignment explanation
Indices: 102991--103043 Score: 63
Period size: 17 Copynumber: 3.3 Consensus size: 15
102981 AAGAAAAGAG
102991 AAAAAT-AAAAAATA
1 AAAAATAAAAAAATA
103005 AAAAATAAAAAAATAA
1 AAAAATAAAAAAAT-A
103021 AGAAAATAGACAAAAATA
1 A-AAAATA-A-AAAAATA
103039 AAAAA
1 AAAAA
103044 ATGGGTTGTC
Statistics
Matches: 34, Mismatches: 0, Indels: 7
0.83 0.00 0.17
Matches are distributed among these distances:
14 6 0.18
15 7 0.21
16 2 0.06
17 10 0.29
18 3 0.09
19 6 0.18
ACGTcount: A:0.83, C:0.02, G:0.04, T:0.11
Consensus pattern (15 bp):
AAAAATAAAAAAATA
Found at i:105616 original size:20 final size:20
Alignment explanation
Indices: 105588--105757 Score: 164
Period size: 20 Copynumber: 8.6 Consensus size: 20
105578 CTCTAAGGAG
* *
105588 AAGTATCGATACTCTTGCTA
1 AAGTATCGAAACTCTTGCCA
*
105608 AAGTTTCGAAACTCTTGCCA
1 AAGTATCGAAACTCTTGCCA
* *
105628 AAGTAT-GAAAATTCTTACCA
1 AAGTATCG-AAACTCTTGCCA
* * * *
105648 AAGTATTGATACTCTTACGA
1 AAGTATCGAAACTCTTGCCA
* *
105668 AAGTATGGAAACTCTTACCA
1 AAGTATCGAAACTCTTGCCA
*
105688 AAGTATGGAAACTCTTGCCA
1 AAGTATCGAAACTCTTGCCA
* *
105708 AAGTATGGAAACTCTTGCTA
1 AAGTATCGAAACTCTTGCCA
* **
105728 AAGTATGGAAACTCTTAACA
1 AAGTATCGAAACTCTTGCCA
105748 AAGTAT-GAAA
1 AAGTATCGAAA
105758 ACTTTTACCA
Statistics
Matches: 131, Mismatches: 17, Indels: 5
0.86 0.11 0.03
Matches are distributed among these distances:
19 5 0.04
20 125 0.95
21 1 0.01
ACGTcount: A:0.38, C:0.17, G:0.16, T:0.29
Consensus pattern (20 bp):
AAGTATCGAAACTCTTGCCA
Found at i:105633 original size:40 final size:40
Alignment explanation
Indices: 105588--105776 Score: 207
Period size: 40 Copynumber: 4.7 Consensus size: 40
105578 CTCTAAGGAG
* * * * * * *
105588 AAGTATCGATACTCTTGCTAAAGTTTCGAAACTCTTGCCA
1 AAGTATGGAAACTCTTACCAAAGTATGGAAACTCTTACCA
* * * * *
105628 AAGTATGAAAATTCTTACCAAAGTATTGATACTCTTACGA
1 AAGTATGGAAACTCTTACCAAAGTATGGAAACTCTTACCA
*
105668 AAGTATGGAAACTCTTACCAAAGTATGGAAACTCTTGCCA
1 AAGTATGGAAACTCTTACCAAAGTATGGAAACTCTTACCA
* * *
105708 AAGTATGGAAACTCTTGCTAAAGTATGGAAACTCTTAACA
1 AAGTATGGAAACTCTTACCAAAGTATGGAAACTCTTACCA
* * *
105748 AAGTATGAAAACTTTTACCAAAGCATGGA
1 AAGTATGGAAACTCTTACCAAAGTATGGA
105777 TACTATTTCC
Statistics
Matches: 123, Mismatches: 26, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
40 123 1.00
ACGTcount: A:0.38, C:0.17, G:0.16, T:0.29
Consensus pattern (40 bp):
AAGTATGGAAACTCTTACCAAAGTATGGAAACTCTTACCA
Found at i:105662 original size:60 final size:60
Alignment explanation
Indices: 105588--105780 Score: 253
Period size: 60 Copynumber: 3.2 Consensus size: 60
105578 CTCTAAGGAG
* * * *
105588 AAGTATCGATACTCTTGCTAAAGTTTCGAAACTCTTGCCAAAGTATGAAAATTCTTACCA
1 AAGTATGGATACTCTTGCTAAAGTATGGAAACTCTTACCAAAGTATGAAAATTCTTACCA
* * * * * *
105648 AAGTATTGATACTCTTACGAAAGTATGGAAACTCTTACCAAAGTATGGAAACTCTTGCCA
1 AAGTATGGATACTCTTGCTAAAGTATGGAAACTCTTACCAAAGTATGAAAATTCTTACCA
* *
105708 AAGTATGGAAACTCTTGCTAAAGTATGGAAACTCTTAACAAAGTATGAAAACTT-TTACCA
1 AAGTATGGATACTCTTGCTAAAGTATGGAAACTCTTACCAAAGTATGAAAA-TTCTTACCA
*
105768 AAGCATGGATACT
1 AAGTATGGATACT
105781 ATTTCCCTAA
Statistics
Matches: 113, Mismatches: 19, Indels: 2
0.84 0.14 0.01
Matches are distributed among these distances:
60 112 0.99
61 1 0.01
ACGTcount: A:0.38, C:0.18, G:0.16, T:0.29
Consensus pattern (60 bp):
AAGTATGGATACTCTTGCTAAAGTATGGAAACTCTTACCAAAGTATGAAAATTCTTACCA
Found at i:105759 original size:20 final size:20
Alignment explanation
Indices: 105615--105776 Score: 207
Period size: 20 Copynumber: 8.1 Consensus size: 20
105605 CTAAAGTTTC
*
105615 GAAACTCTTGCCAAAGTATG
1 GAAACTCTTACCAAAGTATG
* * *
105635 AAAATTCTTACCAAAGTATT
1 GAAACTCTTACCAAAGTATG
* *
105655 GATACTCTTACGAAAGTATG
1 GAAACTCTTACCAAAGTATG
105675 GAAACTCTTACCAAAGTATG
1 GAAACTCTTACCAAAGTATG
*
105695 GAAACTCTTGCCAAAGTATG
1 GAAACTCTTACCAAAGTATG
* *
105715 GAAACTCTTGCTAAAGTATG
1 GAAACTCTTACCAAAGTATG
*
105735 GAAACTCTTAACAAAGTATG
1 GAAACTCTTACCAAAGTATG
* * *
105755 AAAACTTTTACCAAAGCATG
1 GAAACTCTTACCAAAGTATG
105775 GA
1 GA
105777 TACTATTTCC
Statistics
Matches: 121, Mismatches: 21, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 121 1.00
ACGTcount: A:0.40, C:0.17, G:0.16, T:0.27
Consensus pattern (20 bp):
GAAACTCTTACCAAAGTATG
Found at i:111560 original size:20 final size:20
Alignment explanation
Indices: 111537--111668 Score: 158
Period size: 20 Copynumber: 6.6 Consensus size: 20
111527 GATACTCTTT
111537 CCAAAGTATGGAAACTTTTA
1 CCAAAGTATGGAAACTTTTA
* *
111557 CCAAAATATGTAAA-TTATTA
1 CCAAAGTATGGAAACTT-TTA
* *
111577 CCAGAGTATGAAAACTTTTA
1 CCAAAGTATGGAAACTTTTA
* *
111597 CCAAAATATGGAAACTCTTA
1 CCAAAGTATGGAAACTTTTA
** *
111617 AAAAAGTATGGGAACTTTTA
1 CCAAAGTATGGAAACTTTTA
111637 CCAAAGTATGGAAACTTTTA
1 CCAAAGTATGGAAACTTTTA
*
111657 CCAAAATATGGA
1 CCAAAGTATGGA
111669 TACTCTTGCC
Statistics
Matches: 92, Mismatches: 18, Indels: 4
0.81 0.16 0.04
Matches are distributed among these distances:
19 2 0.02
20 88 0.96
21 2 0.02
ACGTcount: A:0.44, C:0.14, G:0.14, T:0.29
Consensus pattern (20 bp):
CCAAAGTATGGAAACTTTTA
Found at i:111607 original size:60 final size:60
Alignment explanation
Indices: 111537--111675 Score: 174
Period size: 60 Copynumber: 2.3 Consensus size: 60
111527 GATACTCTTT
* * * * *
111537 CCAAAGTATGGAAACTTTTACCAAAA-TAT-GTAAATTATTACCAGAGTATGAAAACTTTTA
1 CCAAAATATGGAAACTCTTA-AAAAAGTATGGGAAATT-TTACCAAAGTATGAAAACTTTTA
* *
111597 CCAAAATATGGAAACTCTTAAAAAAGTATGGGAACTTTTACCAAAGTATGGAAACTTTTA
1 CCAAAATATGGAAACTCTTAAAAAAGTATGGGAAATTTTACCAAAGTATGAAAACTTTTA
*
111657 CCAAAATATGGATACTCTT
1 CCAAAATATGGAAACTCTT
111676 GCCCTCGTAT
Statistics
Matches: 69, Mismatches: 8, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
59 4 0.06
60 60 0.87
61 5 0.07
ACGTcount: A:0.42, C:0.14, G:0.13, T:0.30
Consensus pattern (60 bp):
CCAAAATATGGAAACTCTTAAAAAAGTATGGGAAATTTTACCAAAGTATGAAAACTTTTA
Found at i:115351 original size:29 final size:28
Alignment explanation
Indices: 115319--115425 Score: 81
Period size: 29 Copynumber: 3.7 Consensus size: 28
115309 TATTTTACAC
115319 AAATAGCACATTTTTTAAAATAATTACCA
1 AAATAGCACATTTTTTAAAATAATT-CCA
** ** *
115348 AAATAGCACCCTTTTCGAATTAATTCTCA
1 AAATAGCACATTTTTTAAAATAATTC-CA
* * *
115377 AAATAGCAACA-ATTTTGAATTAATTCCCA
1 AAATAGC-ACATTTTTTAAAATAATT-CCA
* *
115406 AAATATCACTTTTTTTAAAA
1 AAATAGCACATTTTTTAAAA
115426 AAAAAAAATT
Statistics
Matches: 61, Mismatches: 13, Indels: 8
0.74 0.16 0.10
Matches are distributed among these distances:
28 3 0.05
29 55 0.90
30 3 0.05
ACGTcount: A:0.43, C:0.17, G:0.05, T:0.36
Consensus pattern (28 bp):
AAATAGCACATTTTTTAAAATAATTCCA
Found at i:115446 original size:92 final size:92
Alignment explanation
Indices: 115335--115502 Score: 255
Period size: 92 Copynumber: 1.8 Consensus size: 92
115325 CACATTTTTT
* * * ***
115335 AAAATAATTACCAAAATAGCACCCTTTTCGAATTAATTCTCAAAATAGCAACAATTTTGAATTAA
1 AAAAAAATTACCAAAATAGCACCCATTTCGAATTAATTCCCAAAATAGCAACAAAACTGAATTAA
115400 TTCCCAAAATATCACTTTTTTTAAAAA
66 TTCCCAAAATATCACTTTTTTTAAAAA
* *
115427 AAAAAAATTACCAAAATAGCACCCATTTCGAATTAATTCCCAGAATAGCACCAAAACTGAATTAA
1 AAAAAAATTACCAAAATAGCACCCATTTCGAATTAATTCCCAAAATAGCAACAAAACTGAATTAA
*
115492 TTCTCAAAATA
66 TTCCCAAAATA
115503 GCACCGGTCA
Statistics
Matches: 67, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
92 67 1.00
ACGTcount: A:0.46, C:0.19, G:0.05, T:0.29
Consensus pattern (92 bp):
AAAAAAATTACCAAAATAGCACCCATTTCGAATTAATTCCCAAAATAGCAACAAAACTGAATTAA
TTCCCAAAATATCACTTTTTTTAAAAA
Found at i:122719 original size:29 final size:29
Alignment explanation
Indices: 122667--122820 Score: 98
Period size: 29 Copynumber: 5.3 Consensus size: 29
122657 CATTTTACAC
* ** *
122667 AAATAGCACACTTTTTAAAATAATTACCA
1 AAATAGCACCCTTTTCGAATTAATTACCA
* *
122696 AAATATCACCCTTTTCGAATTAATT-CTAA
1 AAATAGCACCCTTTTCGAATTAATTAC-CA
* * *
122725 AAATAGCACCAATTTT-GAATTAATTCCCT
1 AAATAGCACC-CTTTTCGAATTAATTACCA
* * * ** * * *
122754 GAGTATCACTTTTTTTGAA-AAATTATCA
1 AAATAGCACCCTTTTCGAATTAATTACCA
* *
122782 AAATAGCACCCATTTCGAATTAATTCCCA
1 AAATAGCACCCTTTTCGAATTAATTACCA
122811 AAATAGCACC
1 AAATAGCACC
122821 AAAACTGAAT
Statistics
Matches: 91, Mismatches: 29, Indels: 10
0.70 0.22 0.08
Matches are distributed among these distances:
28 22 0.24
29 64 0.70
30 5 0.05
ACGTcount: A:0.40, C:0.20, G:0.06, T:0.33
Consensus pattern (29 bp):
AAATAGCACCCTTTTCGAATTAATTACCA
Found at i:122830 original size:86 final size:87
Alignment explanation
Indices: 122678--122836 Score: 230
Period size: 86 Copynumber: 1.8 Consensus size: 87
122668 AATAGCACAC
* * * ***
122678 TTTTTAAAATAATTACCAAAATATCACCCTTTTCGAATTAATTCTAAAAATAGCACCAATTTTGA
1 TTTTTAAAATAATTACCAAAATAGCACCCATTTCGAATTAATTCCAAAAATAGCACCAAAACTGA
122743 ATTAATTCCCTGAGTATCACTT
66 ATTAATTCCCTGAGTATCACTT
* * *
122765 TTTTTGAAA-AATTATCAAAATAGCACCCATTTCGAATTAATTCCCAAAATAGCACCAAAACTGA
1 TTTTTAAAATAATTACCAAAATAGCACCCATTTCGAATTAATTCCAAAAATAGCACCAAAACTGA
122829 ATTAATTC
66 ATTAATTC
122837 TCAGAATAGC
Statistics
Matches: 63, Mismatches: 9, Indels: 1
0.86 0.12 0.01
Matches are distributed among these distances:
86 55 0.87
87 8 0.13
ACGTcount: A:0.40, C:0.19, G:0.06, T:0.35
Consensus pattern (87 bp):
TTTTTAAAATAATTACCAAAATAGCACCCATTTCGAATTAATTCCAAAAATAGCACCAAAACTGA
ATTAATTCCCTGAGTATCACTT
Found at i:122889 original size:18 final size:18
Alignment explanation
Indices: 122857--122918 Score: 81
Period size: 18 Copynumber: 3.5 Consensus size: 18
122847 ACCGTTCAAA
*
122857 GATCAAC-GATCGGGTCG
1 GATCAACGGGTCGGGTCG
*
122874 GATTAACGGGTCGGGTCG
1 GATCAACGGGTCGGGTCG
*
122892 GGTCAACGGGTCGGGTCG
1 GATCAACGGGTCGGGTCG
*
122910 GGTCAACGG
1 GATCAACGG
122919 TCATGACCGG
Statistics
Matches: 40, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
17 6 0.15
18 34 0.85
ACGTcount: A:0.18, C:0.21, G:0.44, T:0.18
Consensus pattern (18 bp):
GATCAACGGGTCGGGTCG
Found at i:124277 original size:25 final size:25
Alignment explanation
Indices: 124233--124305 Score: 80
Period size: 26 Copynumber: 2.9 Consensus size: 25
124223 GATTTCATTA
*
124233 TTCTTCTTTTTTCTAGTTTTACAAAG
1 TTCTTCTTTTTTTTA-TTTTACAAAG
124259 TTCTTCTTTTTTTTATTTT-C-AAG
1 TTCTTCTTTTTTTTATTTTACAAAG
124282 TT-TTCATTTTCATTTTATTTTACA
1 TTCTTC-TTTT--TTTTATTTTACA
124306 TTTTATTTTT
Statistics
Matches: 41, Mismatches: 1, Indels: 9
0.80 0.02 0.18
Matches are distributed among these distances:
22 3 0.07
23 9 0.22
24 1 0.02
25 13 0.32
26 15 0.37
ACGTcount: A:0.18, C:0.14, G:0.04, T:0.64
Consensus pattern (25 bp):
TTCTTCTTTTTTTTATTTTACAAAG
Found at i:124307 original size:12 final size:11
Alignment explanation
Indices: 124269--124314 Score: 56
Period size: 12 Copynumber: 3.8 Consensus size: 11
124259 TTCTTCTTTT
124269 TTTTATTTTCAA
1 TTTTATTTTC-A
124281 GTTTTCATTTTCA
1 -TTTT-ATTTTCA
124294 TTTTATTTTACA
1 TTTTATTTT-CA
124306 TTTTATTTT
1 TTTTATTTT
124315 TAAATATGCT
Statistics
Matches: 31, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
11 5 0.16
12 15 0.48
13 5 0.16
14 6 0.19
ACGTcount: A:0.20, C:0.09, G:0.02, T:0.70
Consensus pattern (11 bp):
TTTTATTTTCA
Found at i:124316 original size:18 final size:17
Alignment explanation
Indices: 124282--124314 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
124272 TATTTTCAAG
124282 TTTTCATTTTCATTTTA
1 TTTTCATTTTCATTTTA
124299 TTTTACATTTT-ATTTT
1 TTTT-CATTTTCATTTT
124315 TAAATATGCT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.18, C:0.09, G:0.00, T:0.73
Consensus pattern (17 bp):
TTTTCATTTTCATTTTA
Found at i:133266 original size:7 final size:7
Alignment explanation
Indices: 133254--133328 Score: 50
Period size: 7 Copynumber: 10.7 Consensus size: 7
133244 ATCATGTGCA
133254 AAAAAAG
1 AAAAAAG
133261 AAAAAAG
1 AAAAAAG
133268 AAAAAA-
1 AAAAAAG
*
133274 AAGAAAG
1 AAAAAAG
**
133281 -AAACTG
1 AAAAAAG
*
133287 TTCAAAAAG
1 --AAAAAAG
133296 AAAAAAAGG
1 -AAAAAA-G
133305 AAAAAAG
1 AAAAAAG
133312 --AAAAG
1 AAAAAAG
133317 AAAAAAG
1 AAAAAAG
133324 AAAAA
1 AAAAA
133329 TTGGAAAAAC
Statistics
Matches: 53, Mismatches: 8, Indels: 14
0.71 0.11 0.19
Matches are distributed among these distances:
5 5 0.09
6 8 0.15
7 24 0.45
8 11 0.21
9 5 0.09
ACGTcount: A:0.79, C:0.03, G:0.15, T:0.04
Consensus pattern (7 bp):
AAAAAAG
Found at i:133321 original size:12 final size:13
Alignment explanation
Indices: 133299--133327 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
133289 CAAAAAGAAA
133299 AAAAGGAAAAAAG
1 AAAAGGAAAAAAG
133312 AAAA-GAAAAAAG
1 AAAAGGAAAAAAG
133324 AAAA
1 AAAA
133328 ATTGGAAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 12 0.75
13 4 0.25
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (13 bp):
AAAAGGAAAAAAG
Found at i:133337 original size:43 final size:43
Alignment explanation
Indices: 133252--133342 Score: 105
Period size: 43 Copynumber: 2.1 Consensus size: 43
133242 AAATCATGTG
* *
133252 CAAAAAAAGAAAAAAGAAAAAAAAGAAAGAAACTGTTCAAAAA
1 CAAAAAAAGAAAAAAGAAAAAAAAGAAAGAAAATGTGCAAAAA
* * *
133295 GAAAAAAAGGAAAAAAGAAAAGAAA-AAAGAAAAAT-TGGAAAAA
1 CAAAAAAA-GAAAAAAGAAAAAAAAGAAAG-AAAATGTGCAAAAA
133338 CAAAA
1 CAAAA
133343 CAACAACAAA
Statistics
Matches: 40, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
43 21 0.52
44 19 0.47
ACGTcount: A:0.76, C:0.04, G:0.14, T:0.05
Consensus pattern (43 bp):
CAAAAAAAGAAAAAAGAAAAAAAAGAAAGAAAATGTGCAAAAA
Found at i:144379 original size:12 final size:12
Alignment explanation
Indices: 144364--144388 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
144354 TAATCTTTCT
144364 ATCAATCCTTTA
1 ATCAATCCTTTA
144376 ATCAATCCTTTA
1 ATCAATCCTTTA
144388 A
1 A
144389 AATCCCTAAT
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:0.36, C:0.24, G:0.00, T:0.40
Consensus pattern (12 bp):
ATCAATCCTTTA
Done.