Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011948.1 Corchorus capsularis cultivar CVL-1 contig11969, 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: 131968
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:2407 original size:33 final size:33
Alignment explanation
Indices: 2278--2417 Score: 158
Period size: 33 Copynumber: 4.2 Consensus size: 33
2268 AAGGATCATG
* ** * *
2278 TGGCCGGTTGTGGC-CGGGCATGGCCATGTCGCG
1 TGGCCGG-TGTTGCGCGGGCATCTCCAAGTCGCA
* *
2311 TGGCCGGTGATG-GCCGGGCATCTCCAAGTCACA
1 TGGCCGGTGTTGCG-CGGGCATCTCCAAGTCGCA
* *
2344 TGCCCGATGTTGCGCGGGCATCTCCAAGTCGCA
1 TGGCCGGTGTTGCGCGGGCATCTCCAAGTCGCA
*
2377 TGGCCGGTGTTGCGCGGGCATCTCCAAGTCGCG
1 TGGCCGGTGTTGCGCGGGCATCTCCAAGTCGCA
2410 TGGCCGGT
1 TGGCCGGT
2418 CACAAGTGCT
Statistics
Matches: 90, Mismatches: 14, Indels: 6
0.82 0.13 0.05
Matches are distributed among these distances:
32 3 0.03
33 86 0.96
34 1 0.01
ACGTcount: A:0.11, C:0.30, G:0.38, T:0.21
Consensus pattern (33 bp):
TGGCCGGTGTTGCGCGGGCATCTCCAAGTCGCA
Found at i:3736 original size:11 final size:11
Alignment explanation
Indices: 3722--3747 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
3712 AATACATTGA
3722 AAATATTTTTC
1 AAATATTTTTC
3733 AAATATTTTTC
1 AAATATTTTTC
3744 AAAT
1 AAAT
3748 TTATTAAATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.42, C:0.08, G:0.00, T:0.50
Consensus pattern (11 bp):
AAATATTTTTC
Found at i:3923 original size:13 final size:13
Alignment explanation
Indices: 3904--3938 Score: 63
Period size: 13 Copynumber: 2.8 Consensus size: 13
3894 ATTTCTTGCT
3904 TAAAAAAAAT-TA
1 TAAAAAAAATATA
3916 TAAAAAAAATATA
1 TAAAAAAAATATA
3929 TAAAAAAAAT
1 TAAAAAAAAT
3939 TCATTGTTGT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
12 10 0.45
13 12 0.55
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (13 bp):
TAAAAAAAATATA
Found at i:7576 original size:21 final size:21
Alignment explanation
Indices: 7550--7599 Score: 75
Period size: 21 Copynumber: 2.4 Consensus size: 21
7540 CAGCAGCTTC
*
7550 TTCTTCTTCCTCT-TTTTCACT
1 TTCTTCTTCCT-TGTTCTCACT
7571 TTCTTCTTCCTTGTTCTCACT
1 TTCTTCTTCCTTGTTCTCACT
7592 TTCTTCTT
1 TTCTTCTT
7600 TTTCTTCTTC
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
20 1 0.04
21 26 0.96
ACGTcount: A:0.04, C:0.32, G:0.02, T:0.62
Consensus pattern (21 bp):
TTCTTCTTCCTTGTTCTCACT
Found at i:14481 original size:26 final size:27
Alignment explanation
Indices: 14440--14490 Score: 86
Period size: 26 Copynumber: 1.9 Consensus size: 27
14430 CCAAGCCGTT
14440 ACAACAACCAAGCTTTCCCCAAGCTTG
1 ACAACAACCAAGCTTTCCCCAAGCTTG
*
14467 ACAAC-ACCGAGCTTTCCCCAAGCT
1 ACAACAACCAAGCTTTCCCCAAGCT
14491 CAAACAAGTG
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
26 18 0.78
27 5 0.22
ACGTcount: A:0.31, C:0.39, G:0.12, T:0.18
Consensus pattern (27 bp):
ACAACAACCAAGCTTTCCCCAAGCTTG
Found at i:14497 original size:27 final size:27
Alignment explanation
Indices: 14440--14497 Score: 73
Period size: 26 Copynumber: 2.1 Consensus size: 27
14430 CCAAGCCGTT
**
14440 ACAACAACCAAGCTTTCCCCAAGCTTG
1 ACAACAACCAAGCTTTCCCCAAGCTAA
*
14467 ACAAC-ACCGAGCTTTCCCCAAGCTCAA
1 ACAACAACCAAGCTTTCCCCAAGCT-AA
14494 ACAA
1 ACAA
14498 GTGCTCCCCA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
26 18 0.67
27 9 0.33
ACGTcount: A:0.36, C:0.38, G:0.10, T:0.16
Consensus pattern (27 bp):
ACAACAACCAAGCTTTCCCCAAGCTAA
Found at i:14901 original size:76 final size:76
Alignment explanation
Indices: 14802--14950 Score: 201
Period size: 76 Copynumber: 2.0 Consensus size: 76
14792 TTCTATTGGG
* * *
14802 TCCTTATATACTCAGATCTGCCTCCAACGATCAT-TCTCCACATTAAATGCAAATCTTTCAAATC
1 TCCTTAAATACTCAGATCTGCCTCCAACGATCATAT-TCCACATCAAATCCAAATCTTTCAAATC
14866 TGTCAATTTGTT
65 TGTCAATTTGTT
* * ** * *
14878 TCCTTAAATACTTAGATTTGCCTCCAACGATCATATTCTTCATCAATTCCACATCTTTCAAATCT
1 TCCTTAAATACTCAGATCTGCCTCCAACGATCATATTCCACATCAAATCCAAATCTTTCAAATCT
14943 GTCAATTT
66 GTCAATTT
14951 ATGGCGTTGA
Statistics
Matches: 63, Mismatches: 9, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
76 62 0.98
77 1 0.02
ACGTcount: A:0.29, C:0.26, G:0.07, T:0.38
Consensus pattern (76 bp):
TCCTTAAATACTCAGATCTGCCTCCAACGATCATATTCCACATCAAATCCAAATCTTTCAAATCT
GTCAATTTGTT
Found at i:18514 original size:19 final size:18
Alignment explanation
Indices: 18490--18525 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
18480 TGATGATTTA
18490 TTGAAGATAATTTGAAGAT
1 TTGAAGATAA-TTGAAGAT
*
18509 TTGAAGATTATTGAAGA
1 TTGAAGATAATTGAAGA
18526 ATTATTTCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.42, C:0.00, G:0.22, T:0.36
Consensus pattern (18 bp):
TTGAAGATAATTGAAGAT
Found at i:25521 original size:11 final size:10
Alignment explanation
Indices: 25505--25557 Score: 56
Period size: 11 Copynumber: 5.2 Consensus size: 10
25495 AAGTTCGTGT
25505 TTGAAGATTTA
1 TTGAAGA-TTA
*
25516 TTGAAGATAA
1 TTGAAGATTA
25526 TTTGAAGA-T-
1 -TTGAAGATTA
25535 TTGAAGATTA
1 TTGAAGATTA
25545 TTGAAGAATTA
1 TTGAAG-ATTA
25556 TT
1 TT
25558 TCAATAAGCA
Statistics
Matches: 36, Mismatches: 2, Indels: 8
0.78 0.04 0.17
Matches are distributed among these distances:
8 7 0.19
9 1 0.03
10 8 0.22
11 20 0.56
ACGTcount: A:0.40, C:0.00, G:0.19, T:0.42
Consensus pattern (10 bp):
TTGAAGATTA
Found at i:25540 original size:19 final size:18
Alignment explanation
Indices: 25516--25551 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
25506 TGAAGATTTA
25516 TTGAAGATAATTTGAAGAT
1 TTGAAGATAA-TTGAAGAT
*
25535 TTGAAGATTATTGAAGA
1 TTGAAGATAATTGAAGA
25552 ATTATTTCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.42, C:0.00, G:0.22, T:0.36
Consensus pattern (18 bp):
TTGAAGATAATTGAAGAT
Found at i:27948 original size:22 final size:22
Alignment explanation
Indices: 27912--27955 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
27902 AATTGCAGGA
*
27912 CAACTTCGGCCCAGAACTTATT
1 CAACTTCGGCACAGAACTTATT
* *
27934 CAACTTCGGGACAGAAGTTATT
1 CAACTTCGGCACAGAACTTATT
27956 GTGCAGGACA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.30, C:0.25, G:0.18, T:0.27
Consensus pattern (22 bp):
CAACTTCGGCACAGAACTTATT
Found at i:27969 original size:52 final size:52
Alignment explanation
Indices: 27905--28004 Score: 182
Period size: 52 Copynumber: 1.9 Consensus size: 52
27895 GAAGAAGAAT
*
27905 TGCAGGACAACTTCGGCCCAGAACTTATTCAACTTCGGGACAGAAGTTATTG
1 TGCAGGACAACTTCGGCCCAGAACTTATACAACTTCGGGACAGAAGTTATTG
*
27957 TGCAGGACAACTTCGGCCCAGAACTTGTACAACTTCGGGACAGAAGTT
1 TGCAGGACAACTTCGGCCCAGAACTTATACAACTTCGGGACAGAAGTT
28005 GTTGCGGGAA
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 46 1.00
ACGTcount: A:0.29, C:0.24, G:0.24, T:0.23
Consensus pattern (52 bp):
TGCAGGACAACTTCGGCCCAGAACTTATACAACTTCGGGACAGAAGTTATTG
Found at i:28000 original size:22 final size:22
Alignment explanation
Indices: 27963--28006 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
27953 ATTGTGCAGG
*
27963 ACAACTTCGGCCCAGAACTTGT
1 ACAACTTCGGCACAGAACTTGT
* *
27985 ACAACTTCGGGACAGAAGTTGT
1 ACAACTTCGGCACAGAACTTGT
28007 TGCGGGAAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.30, C:0.25, G:0.23, T:0.23
Consensus pattern (22 bp):
ACAACTTCGGCACAGAACTTGT
Found at i:33076 original size:30 final size:28
Alignment explanation
Indices: 33042--33135 Score: 79
Period size: 30 Copynumber: 3.4 Consensus size: 28
33032 GGGTTGTGCT
33042 CGGTCATGTGCGATTGCTCCATGCCATGGC
1 CGGTCATGTGCG-TTGCTCCATG-CATGGC
* * *
33072 CGGTCATGTGC-TCGGT-CATG--TGTC
1 CGGTCATGTGCGTTGCTCCATGCATGGC
* *
33096 CGGTCTTGTGCGGTTGCCCCATGCAATGGC
1 CGGTCATGTGC-GTTGCTCCATGC-ATGGC
33126 CGGTCATGTG
1 CGGTCATGTG
33136 GGATCCCAGC
Statistics
Matches: 49, Mismatches: 9, Indels: 12
0.70 0.13 0.17
Matches are distributed among these distances:
24 13 0.27
26 2 0.04
27 8 0.16
28 3 0.06
30 23 0.47
ACGTcount: A:0.11, C:0.28, G:0.33, T:0.29
Consensus pattern (28 bp):
CGGTCATGTGCGTTGCTCCATGCATGGC
Found at i:37858 original size:11 final size:11
Alignment explanation
Indices: 37840--37871 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
37830 AATTGTCTTA
37840 AAATCTTCAAG
1 AAATCTTCAAG
*
37851 ATATCTTCAAG
1 AAATCTTCAAG
37862 AAATCTTCAA
1 AAATCTTCAA
37872 AACACGAACT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.44, C:0.19, G:0.06, T:0.31
Consensus pattern (11 bp):
AAATCTTCAAG
Found at i:43462 original size:21 final size:20
Alignment explanation
Indices: 43430--43468 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
43420 TAATCCACTA
*
43430 AAAACAATTAAACTAAATAT
1 AAAACAAGTAAACTAAATAT
*
43450 AAAACAAAGTAAATTAAAT
1 AAAAC-AAGTAAACTAAAT
43469 CTAGATCTAG
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 5 0.31
21 11 0.69
ACGTcount: A:0.67, C:0.08, G:0.03, T:0.23
Consensus pattern (20 bp):
AAAACAAGTAAACTAAATAT
Found at i:51417 original size:36 final size:36
Alignment explanation
Indices: 51381--51797 Score: 209
Period size: 37 Copynumber: 10.9 Consensus size: 36
51371 CATAGTACAT
* *
51381 AGTCAAAGTCTTAATTCAAGGAAATTAAGAAAACAT
1 AGTCAAAGTCTTAATTCAAGGTAATTAAGAAAACAC
*
51417 AGTCAAAGTCTTAATTCAAGGTAATTAAAAAAAGCAAACAC
1 AGTCAAAGTCTTAATTCAAGGTAATT-----AAGAAAACAC
*
51458 AGTCAAAGTCTTAATTCAGGGTAATTAAGAAAAGTAAACAC
1 AGTCAAAGTCTTAATTCAAGGTAATTAAG---A--AAACAC
*
51499 AGTCAAAGTCTTAATTCAGGGTAATTAAGAAAAGTAGGCAC
1 AGTCAAAGTCTTAATTCAAGGTAATTAAG-AAA--A--CAC
** *
51540 AGTCAAAGTCTTAATTCGGGGTAATTAAGTAAAA-GC
1 AGTCAAAGTCTTAATTCAAGGTAATTAAG-AAAACAC
* * * *
51576 AGTTAAAGAACTTAATTCAGGGTGATTAAGTAAAA-AC
1 AGTCAAAG-TCTTAATTCAAGGTAATTAAG-AAAACAC
* * * * *
51613 AGTTAAAGAACTTAATTCAGGGCAATTAAGTAAAA-GC
1 AGTCAAAG-TCTTAATTCAAGGTAATTAAG-AAAACAC
* * * *
51650 AGTTAAAAGAACTTAATTCAAGGCAATTAAGTAAAA-GC
1 AG-TCAAAG-TCTTAATTCAAGGTAATTAAG-AAAACAC
* * * * *
51688 AGTTAAAGAACTTAATTCAGGGTGATTAAGTAAAA-GC
1 AGTCAAAG-TCTTAATTCAAGGTAATTAAG-AAAACAC
* * * *
51725 AGTTAAAGAACTTAATT-AAGGGCAATTAAGTAAAA-GC
1 AGTCAAAG-TCTTAATTCAA-GGTAATTAAG-AAAACAC
* * *
51762 AGTTAAAAGAACTTAATTCAAGGCAATTAAGTAAAA
1 AG-TCAAAG-TCTTAATTCAAGGTAATTAAG-AAAA
51798 GCAATTAAAA
Statistics
Matches: 336, Mismatches: 26, Indels: 36
0.84 0.07 0.09
Matches are distributed among these distances:
36 37 0.11
37 127 0.38
38 64 0.19
39 6 0.02
41 102 0.30
ACGTcount: A:0.47, C:0.11, G:0.18, T:0.25
Consensus pattern (36 bp):
AGTCAAAGTCTTAATTCAAGGTAATTAAGAAAACAC
Found at i:51468 original size:41 final size:41
Alignment explanation
Indices: 51381--51576 Score: 258
Period size: 41 Copynumber: 4.9 Consensus size: 41
51371 CATAGTACAT
* * *
51381 AGTCAAAGTCTTAATTCAAGGAAATTAAG---A--AAACAT
1 AGTCAAAGTCTTAATTCAGGGTAATTAAGAAAAGCAAACAC
* *
51417 AGTCAAAGTCTTAATTCAAGGTAATTAAAAAAAGCAAACAC
1 AGTCAAAGTCTTAATTCAGGGTAATTAAGAAAAGCAAACAC
*
51458 AGTCAAAGTCTTAATTCAGGGTAATTAAGAAAAGTAAACAC
1 AGTCAAAGTCTTAATTCAGGGTAATTAAGAAAAGCAAACAC
* **
51499 AGTCAAAGTCTTAATTCAGGGTAATTAAGAAAAGTAGGCAC
1 AGTCAAAGTCTTAATTCAGGGTAATTAAGAAAAGCAAACAC
*
51540 AGTCAAAGTCTTAATTCGGGGTAATTAAGTAAAAGCA
1 AGTCAAAGTCTTAATTCAGGGTAATTAAG-AAAAGCA
51577 GTTAAAGAAC
Statistics
Matches: 144, Mismatches: 10, Indels: 6
0.90 0.06 0.04
Matches are distributed among these distances:
36 27 0.19
39 1 0.01
41 110 0.76
42 6 0.04
ACGTcount: A:0.46, C:0.12, G:0.17, T:0.24
Consensus pattern (41 bp):
AGTCAAAGTCTTAATTCAGGGTAATTAAGAAAAGCAAACAC
Found at i:51604 original size:37 final size:37
Alignment explanation
Indices: 51549--51977 Score: 624
Period size: 37 Copynumber: 11.5 Consensus size: 37
51539 CAGTCAAAGT
* *
51549 CTTAATTCGGGGTAATTAAGTAAAAGCAGTTAAAGAA
1 CTTAATTCAGGGCAATTAAGTAAAAGCAGTTAAAGAA
** *
51586 CTTAATTCAGGGTGATTAAGTAAAAACAGTTAAAGAA
1 CTTAATTCAGGGCAATTAAGTAAAAGCAGTTAAAGAA
51623 CTTAATTCAGGGCAATTAAGTAAAAGCAGTTAAAAGAA
1 CTTAATTCAGGGCAATTAAGTAAAAGCAGTT-AAAGAA
*
51661 CTTAATTCAAGGCAATTAAGTAAAAGCAGTTAAAGAA
1 CTTAATTCAGGGCAATTAAGTAAAAGCAGTTAAAGAA
**
51698 CTTAATTCAGGGTGATTAAGTAAAAGCAGTTAAAGAA
1 CTTAATTCAGGGCAATTAAGTAAAAGCAGTTAAAGAA
*
51735 CTTAATTAAGGGCAATTAAGTAAAAGCAGTTAAAAGAA
1 CTTAATTCAGGGCAATTAAGTAAAAGCAGTT-AAAGAA
* *
51773 CTTAATTCAAGGCAATTAAGTAAAAGCAATTAAAAGAA
1 CTTAATTCAGGGCAATTAAGTAAAAGCAGTT-AAAGAA
* *
51811 CTTAATTCAAGACAATTAAGTAAAAGCAGTTAAAGAA
1 CTTAATTCAGGGCAATTAAGTAAAAGCAGTTAAAGAA
* *
51848 CTTAATTTAGGGCAATTAAGTAAAAGCAATTAAAGAA
1 CTTAATTCAGGGCAATTAAGTAAAAGCAGTTAAAGAA
* * *
51885 CTTAATTCAAGGTAGTTAAGTAAAAGCAGTTAAAGAA
1 CTTAATTCAGGGCAATTAAGTAAAAGCAGTTAAAGAA
* * *
51922 CTTAATTCAGGACAATTAAGTAAAGGCAGTTAAAGGA
1 CTTAATTCAGGGCAATTAAGTAAAAGCAGTTAAAGAA
* *
51959 CTTAATTCAGAGTAATTAA
1 CTTAATTCAGGGCAATTAA
51978 ATAAGAAAAG
Statistics
Matches: 354, Mismatches: 36, Indels: 4
0.90 0.09 0.01
Matches are distributed among these distances:
37 248 0.70
38 106 0.30
ACGTcount: A:0.47, C:0.09, G:0.18, T:0.26
Consensus pattern (37 bp):
CTTAATTCAGGGCAATTAAGTAAAAGCAGTTAAAGAA
Found at i:51684 original size:112 final size:112
Alignment explanation
Indices: 51562--51977 Score: 654
Period size: 112 Copynumber: 3.7 Consensus size: 112
51552 AATTCGGGGT
*** *
51562 AATTAAGTAAAAGCAGTTAAAGAACTTAATTCAGGGTGATTAAGTAAAAACAGTTAAAGAACTTA
1 AATTAAGTAAAAGCAGTTAAAGAACTTAATTCAGGACAATTAAGTAAAAGCAGTTAAAGAACTTA
51627 ATTCAGGGCAATTAAGTAAAAGCAGTTAAAAGAACTTAATTCAAGGC
66 ATTCAGGGCAATTAAGTAAAAGCAGTTAAAAGAACTTAATTCAAGGC
***
51674 AATTAAGTAAAAGCAGTTAAAGAACTTAATTCAGGGTGATTAAGTAAAAGCAGTTAAAGAACTTA
1 AATTAAGTAAAAGCAGTTAAAGAACTTAATTCAGGACAATTAAGTAAAAGCAGTTAAAGAACTTA
*
51739 ATTAAGGGCAATTAAGTAAAAGCAGTTAAAAGAACTTAATTCAAGGC
66 ATTCAGGGCAATTAAGTAAAAGCAGTTAAAAGAACTTAATTCAAGGC
* *
51786 AATTAAGTAAAAGCAATTAAAAGAACTTAATTCAAGACAATTAAGTAAAAGCAGTTAAAGAACTT
1 AATTAAGTAAAAGCAGTT-AAAGAACTTAATTCAGGACAATTAAGTAAAAGCAGTTAAAGAACTT
* * *
51851 AATTTAGGGCAATTAAGTAAAAGCAATT-AAAGAACTTAATTCAAGGT
65 AATTCAGGGCAATTAAGTAAAAGCAGTTAAAAGAACTTAATTCAAGGC
* * *
51898 AGTTAAGTAAAAGCAGTTAAAGAACTTAATTCAGGACAATTAAGTAAAGGCAGTTAAAGGACTTA
1 AATTAAGTAAAAGCAGTTAAAGAACTTAATTCAGGACAATTAAGTAAAAGCAGTTAAAGAACTTA
* *
51963 ATTCAGAGTAATTAA
66 ATTCAGGGCAATTAA
51978 ATAAGAAAAG
Statistics
Matches: 285, Mismatches: 18, Indels: 3
0.93 0.06 0.01
Matches are distributed among these distances:
111 56 0.20
112 161 0.56
113 68 0.24
ACGTcount: A:0.48, C:0.09, G:0.17, T:0.25
Consensus pattern (112 bp):
AATTAAGTAAAAGCAGTTAAAGAACTTAATTCAGGACAATTAAGTAAAAGCAGTTAAAGAACTTA
ATTCAGGGCAATTAAGTAAAAGCAGTTAAAAGAACTTAATTCAAGGC
Found at i:52030 original size:41 final size:41
Alignment explanation
Indices: 51980--52246 Score: 444
Period size: 41 Copynumber: 6.5 Consensus size: 41
51970 GTAATTAAAT
* * * *
51980 AAGAAAAGCACAAACTTAATTTCAAGAAAAGAAATTAGGCA
1 AAGACAAGCACAGACTTAATTTCAAGAAAGGAAATTAGGTA
*
52021 AAGACAAGCATAGACTTAATTTCAAGAAAGGAAATTAGGTA
1 AAGACAAGCACAGACTTAATTTCAAGAAAGGAAATTAGGTA
* *
52062 AAGACAAGCACAGACTTAATTTCAAGGATGGAAATTAGGTA
1 AAGACAAGCACAGACTTAATTTCAAGAAAGGAAATTAGGTA
*
52103 AAGACAAGCACAGACTTAATTTCAAGGAAGGAAATTAGGTA
1 AAGACAAGCACAGACTTAATTTCAAGAAAGGAAATTAGGTA
52144 AAGACAAGCACAGACTTAATTTCAAGAAAGGAAATTAGGTA
1 AAGACAAGCACAGACTTAATTTCAAGAAAGGAAATTAGGTA
* *
52185 AAGACAAGCAAAGACTTAATTTCAAGAAAGGACATTAGGTA
1 AAGACAAGCACAGACTTAATTTCAAGAAAGGAAATTAGGTA
52226 AAGACAAGCACAGACTTAATT
1 AAGACAAGCACAGACTTAATT
52247 CAGGGTAATT
Statistics
Matches: 213, Mismatches: 13, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
41 213 1.00
ACGTcount: A:0.49, C:0.12, G:0.19, T:0.20
Consensus pattern (41 bp):
AAGACAAGCACAGACTTAATTTCAAGAAAGGAAATTAGGTA
Found at i:52042 original size:187 final size:186
Alignment explanation
Indices: 51562--52013 Score: 524
Period size: 187 Copynumber: 2.4 Consensus size: 186
51552 AATTCGGGGT
* ** * * *
51562 AATTAAGTAAAAGCAGTT-AAAGAACTTAATTCAGGGTGATTAAGTAAAAACAGT-TAAAGAACT
1 AATTAAGTAAAAGCAGTTAAAAGAACTTAATTCAAGGCAATTAAAT-AAAACAATGAAAAGAACT
* ** ** * * *
51625 TAATTCAGGGCAATTAAGTAAAAGCAGTTAAAAGAACTTAATTCAAGGCAATTAAGTAAAAGCAG
65 TAATTCAAGAAAAGAAAGTAAAAGCAG-TCAAAGAACTTAATTTAAGGCAATTAAGTAAAAGCAA
* *
51690 TTAAAGAACTTAATTCAGGGTGATTAAGTAAAAGCAGTTAAAGAACTTAATTAAGGGC
129 TTAAAGAACTTAATTCAAGGTGATTAAGTAAAAGCAGTTAAAGAACTTAATTAAGGAC
* *
51748 AATTAAGTAAAAGCAGTTAAAAGAACTTAATTCAAGGCAATTAAGTAAAAGCAATTAAAAGAACT
1 AATTAAGTAAAAGCAGTTAAAAGAACTTAATTCAAGGCAATTAAATAAAA-CAATGAAAAGAACT
* ** * *
51813 TAATTCAAGACAATTAAGTAAAAGCAGTTAAAGAACTTAATTTAGGGCAATTAAGTAAAAGCAAT
65 TAATTCAAGAAAAGAAAGTAAAAGCAGTCAAAGAACTTAATTTAAGGCAATTAAGTAAAAGCAAT
*
51878 TAAAGAACTTAATTCAAGGT-AGTTAAGTAAAAGCAGTTAAAGAACTTAATTCAGGAC
130 TAAAGAACTTAATTCAAGGTGA-TTAAGTAAAAGCAGTTAAAGAACTTAATTAAGGAC
* * * * *
51935 AATTAAGTAAAGGCAGTT-AAAGGACTTAATTC-AGAGTAATTAAATAAGAA-AA-GCACA-AAC
1 AATTAAGTAAAAGCAGTTAAAAGAACTTAATTCAAG-GCAATTAAATAA-AACAATGAAAAGAAC
51995 TTAATTTCAAGAAAAGAAA
64 TTAA-TTCAAGAAAAGAAA
52014 TTAGGCAAAG
Statistics
Matches: 235, Mismatches: 24, Indels: 16
0.85 0.09 0.06
Matches are distributed among these distances:
183 7 0.03
184 13 0.06
185 4 0.02
186 46 0.20
187 132 0.56
188 33 0.14
ACGTcount: A:0.49, C:0.09, G:0.17, T:0.25
Consensus pattern (186 bp):
AATTAAGTAAAAGCAGTTAAAAGAACTTAATTCAAGGCAATTAAATAAAACAATGAAAAGAACTT
AATTCAAGAAAAGAAAGTAAAAGCAGTCAAAGAACTTAATTTAAGGCAATTAAGTAAAAGCAATT
AAAGAACTTAATTCAAGGTGATTAAGTAAAAGCAGTTAAAGAACTTAATTAAGGAC
Found at i:52047 original size:23 final size:22
Alignment explanation
Indices: 52021--52087 Score: 52
Period size: 23 Copynumber: 3.1 Consensus size: 22
52011 AAATTAGGCA
52021 AAGACAAGCATAGACTTAATTTC
1 AAGACAAGCA-AGACTTAATTTC
* ** *
52044 AAGA-AAGGAA-A-TT-AGGTA
1 AAGACAAGCAAGACTTAATTTC
52062 AAGACAAGCACAGACTTAATTTC
1 AAGACAAGCA-AGACTTAATTTC
52085 AAG
1 AAG
52088 GATGGAAATT
Statistics
Matches: 31, Mismatches: 8, Indels: 10
0.63 0.16 0.20
Matches are distributed among these distances:
18 6 0.19
19 6 0.19
20 2 0.06
21 2 0.06
22 6 0.19
23 9 0.29
ACGTcount: A:0.48, C:0.13, G:0.18, T:0.21
Consensus pattern (22 bp):
AAGACAAGCAAGACTTAATTTC
Found at i:52170 original size:23 final size:22
Alignment explanation
Indices: 52103--52211 Score: 54
Period size: 23 Copynumber: 5.2 Consensus size: 22
52093 AAATTAGGTA
52103 AAGACAAGCACAGACTTAATTTC
1 AAGACAAGCA-AGACTTAATTTC
* * ** *
52126 AAG-GAAGGAA-A-TT-AGGTA
1 AAGACAAGCAAGACTTAATTTC
52144 AAGACAAGCACAGACTTAATTTC
1 AAGACAAGCA-AGACTTAATTTC
* ** *
52167 AAGA-AAGGAA-A-TT-AGGTA
1 AAGACAAGCAAGACTTAATTTC
52185 AAGACAAGCAAAGACTTAATTTC
1 AAGACAAGC-AAGACTTAATTTC
52208 AAGA
1 AAGA
52212 AAGGACATTA
Statistics
Matches: 58, Mismatches: 18, Indels: 20
0.60 0.19 0.21
Matches are distributed among these distances:
18 11 0.19
19 11 0.19
20 5 0.09
21 4 0.07
22 12 0.21
23 15 0.26
ACGTcount: A:0.49, C:0.13, G:0.19, T:0.19
Consensus pattern (22 bp):
AAGACAAGCAAGACTTAATTTC
Found at i:52309 original size:36 final size:36
Alignment explanation
Indices: 52253--52386 Score: 184
Period size: 36 Copynumber: 3.7 Consensus size: 36
52243 AATTCAGGGT
52253 AATTAAGT-AAATCAGCAAAGACTTAATTCCACAAG
1 AATTAAGTAAAATCAGCAAAGACTTAATTCCACAAG
* *
52288 AATTAAGTAAAATCAGTAAAGACTTAATTTCACAAG
1 AATTAAGTAAAATCAGCAAAGACTTAATTCCACAAG
*
52324 AATTAAGTAAAATCAACAAAGACTTAA-TCCA-AAG
1 AATTAAGTAAAATCAGCAAAGACTTAATTCCACAAG
*
52358 ATGATTAAGTAAGATCAGTCAAAGACTTA
1 A--ATTAAGTAAAATCAG-CAAAGACTTA
52387 TCCCAAGGGG
Statistics
Matches: 88, Mismatches: 7, Indels: 6
0.87 0.07 0.06
Matches are distributed among these distances:
34 4 0.05
35 11 0.12
36 63 0.72
37 10 0.11
ACGTcount: A:0.50, C:0.13, G:0.12, T:0.25
Consensus pattern (36 bp):
AATTAAGTAAAATCAGCAAAGACTTAATTCCACAAG
Found at i:52463 original size:70 final size:69
Alignment explanation
Indices: 52381--52513 Score: 212
Period size: 70 Copynumber: 1.9 Consensus size: 69
52371 ATCAGTCAAA
* * * *
52381 GACTTATCCCAAGGGGATTAAGTAGAGTTAAGGACTTGATTCCAAGGAAGGGAATTAAGTAGATT
1 GACTTATCCCAAGGGAATTAAGTAGAGTCAAGGACTTAATTCCAAGAAAGGGAATTAAGTAGATT
52446 AAAG
66 AAAG
*
52450 GACTTGATTCCAAGGGAATTAAGTAGAGTCAAGGACTTAATTCCAAGAAAGGGAATTAAGTAGA
1 GACTT-ATCCCAAGGGAATTAAGTAGAGTCAAGGACTTAATTCCAAGAAAGGGAATTAAGTAGA
52514 GTCAATGATT
Statistics
Matches: 58, Mismatches: 5, Indels: 1
0.91 0.08 0.02
Matches are distributed among these distances:
69 5 0.09
70 53 0.91
ACGTcount: A:0.39, C:0.11, G:0.26, T:0.24
Consensus pattern (69 bp):
GACTTATCCCAAGGGAATTAAGTAGAGTCAAGGACTTAATTCCAAGAAAGGGAATTAAGTAGATT
AAAG
Found at i:52470 original size:33 final size:32
Alignment explanation
Indices: 52381--52496 Score: 126
Period size: 33 Copynumber: 3.4 Consensus size: 32
52371 ATCAGTCAAA
* *
52381 GACTT-ATCCCAAGGGGATTAAGTAGAGTTAAG
1 GACTTGATTCCAAGGGAATTAAGTAGA-TTAAG
52413 GACTTGATTCCAAGGAAGGGAATTAAGTAGATTAAAG
1 GACTTGATTCC----AAGGGAATTAAGTAGATT-AAG
*
52450 GACTTGATTCCAAGGGAATTAAGTAGAGTCAAG
1 GACTTGATTCCAAGGGAATTAAGTAGA-TTAAG
*
52483 GACTTAATTCCAAG
1 GACTTGATTCCAAG
52497 AAAGGGAATT
Statistics
Matches: 73, Mismatches: 4, Indels: 13
0.81 0.04 0.14
Matches are distributed among these distances:
32 5 0.07
33 36 0.49
34 1 0.01
36 2 0.03
37 29 0.40
ACGTcount: A:0.37, C:0.12, G:0.26, T:0.25
Consensus pattern (32 bp):
GACTTGATTCCAAGGGAATTAAGTAGATTAAG
Found at i:52516 original size:37 final size:37
Alignment explanation
Indices: 52391--52566 Score: 180
Period size: 37 Copynumber: 4.9 Consensus size: 37
52381 GACTTATCCC
* * *
52391 AAGGGGATTAAGTAGAGTTAAGGACTTGATTCCAAGG
1 AAGGGAATTAAGTAGAGTCAAGGACTTAATTCCAAGG
* * *
52428 AAGGGAATTAAGTAGATTAAAGGACTTGATTCC----
1 AAGGGAATTAAGTAGAGTCAAGGACTTAATTCCAAGG
*
52461 AAGGGAATTAAGTAGAGTCAAGGACTTAATTCCAAGA
1 AAGGGAATTAAGTAGAGTCAAGGACTTAATTCCAAGG
* * *
52498 AAGGGAATTAAGTAGAGTCAATGATTTAATTTCAAGG
1 AAGGGAATTAAGTAGAGTCAAGGACTTAATTCCAAGG
* * * * * *
52535 AATGAAATCATGTAAAGTCAGGGACTTAATTC
1 AAGGGAATTAAGTAGAGTCAAGGACTTAATTC
52567 AGAGTAGTTA
Statistics
Matches: 116, Mismatches: 19, Indels: 8
0.81 0.13 0.06
Matches are distributed among these distances:
33 30 0.26
37 86 0.74
ACGTcount: A:0.40, C:0.09, G:0.25, T:0.26
Consensus pattern (37 bp):
AAGGGAATTAAGTAGAGTCAAGGACTTAATTCCAAGG
Found at i:52534 original size:70 final size:70
Alignment explanation
Indices: 52381--52534 Score: 202
Period size: 70 Copynumber: 2.2 Consensus size: 70
52371 ATCAGTCAAA
* * * * * *
52381 GACTT-ATCCCAAGGGGATTAAGTAGAGTTAAGGACTTGATTCCAAGGAAGGGAATTAAGTAGAT
1 GACTTAATTCCAAGGGAATTAAGTAGAGTCAAGGACTTAATTCCAAGAAAGGGAATTAAGTAGAG
52445 TAAAG
66 TAAAG
*
52450 GACTTGATTCCAAGGGAATTAAGTAGAGTCAAGGACTTAATTCCAAGAAAGGGAATTAAGTAGAG
1 GACTTAATTCCAAGGGAATTAAGTAGAGTCAAGGACTTAATTCCAAGAAAGGGAATTAAGTAGAG
* *
52515 TCAAT
66 TAAAG
* *
52520 GATTTAATTTCAAGG
1 GACTTAATTCCAAGG
52535 AATGAAATCA
Statistics
Matches: 73, Mismatches: 11, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
69 5 0.07
70 68 0.93
ACGTcount: A:0.38, C:0.10, G:0.25, T:0.26
Consensus pattern (70 bp):
GACTTAATTCCAAGGGAATTAAGTAGAGTCAAGGACTTAATTCCAAGAAAGGGAATTAAGTAGAG
TAAAG
Found at i:52610 original size:32 final size:32
Alignment explanation
Indices: 52550--52611 Score: 97
Period size: 32 Copynumber: 1.9 Consensus size: 32
52540 AATCATGTAA
*
52550 AGTCAGGGACTTAATTCAGAGTAGTTAAGTCG
1 AGTCAGGGACTTAATTCAGAGTAATTAAGTCG
* *
52582 AGTCAGGGACTTAATTCGGGGTAATTAAGT
1 AGTCAGGGACTTAATTCAGAGTAATTAAGT
52612 AGCATCAATA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 27 1.00
ACGTcount: A:0.31, C:0.11, G:0.29, T:0.29
Consensus pattern (32 bp):
AGTCAGGGACTTAATTCAGAGTAATTAAGTCG
Found at i:52630 original size:36 final size:36
Alignment explanation
Indices: 52590--52777 Score: 238
Period size: 36 Copynumber: 5.2 Consensus size: 36
52580 CGAGTCAGGG
*
52590 ACTTAATTCGGGGTAATTAAGTAGCATCAATAAA-A
1 ACTTAATTCAGGGTAATTAAGTAGCATCAATAAAGA
52625 GACTTAATTCAGGGTAATTAAGTAG-AGTCAATAAAGA
1 -ACTTAATTCAGGGTAATTAAGTAGCA-TCAATAAAGA
* * * *
52662 ACTTAATTCAAGGCAATTAAGTAGCGTCAATAAAAGG
1 ACTTAATTCAGGGTAATTAAGTAGCATCAAT-AAAGA
* *
52699 ACTTAATTCAGGGTAATTAAGT-GGAGTTAATAAAGA
1 ACTTAATTCAGGGTAATTAAGTAGCA-TCAATAAAGA
* *
52735 ACTTAATTCAGGGTAATTAAGTGGAATCAATAAAGA
1 ACTTAATTCAGGGTAATTAAGTAGCATCAATAAAGA
52771 ACTTAAT
1 ACTTAAT
52778 CTAAAAAGAG
Statistics
Matches: 133, Mismatches: 13, Indels: 12
0.84 0.08 0.08
Matches are distributed among these distances:
35 1 0.01
36 101 0.76
37 31 0.23
ACGTcount: A:0.43, C:0.10, G:0.19, T:0.28
Consensus pattern (36 bp):
ACTTAATTCAGGGTAATTAAGTAGCATCAATAAAGA
Found at i:52733 original size:73 final size:72
Alignment explanation
Indices: 52590--52777 Score: 279
Period size: 73 Copynumber: 2.6 Consensus size: 72
52580 CGAGTCAGGG
*
52590 ACTTAATTCGGGGTAATTAAGTAGCATCAATAAAAGACTTAATTCAGGGTAATTAAGTAGAGTCA
1 ACTTAATTCAGGGTAATTAAGTAGCATCAATAAAAGACTTAATTCAGGGTAATTAAGTAGAGTCA
52655 ATAAAGA
66 ATAAAGA
* * * * *
52662 ACTTAATTCAAGGCAATTAAGTAGCGTCAATAAAAGGACTTAATTCAGGGTAATTAAGTGGAGTT
1 ACTTAATTCAGGGTAATTAAGTAGCATCAATAAAA-GACTTAATTCAGGGTAATTAAGTAGAGTC
52727 AATAAAGA
65 AATAAAGA
* *
52735 ACTTAATTCAGGGTAATTAAGTGGAATCAAT-AAAGAACTTAAT
1 ACTTAATTCAGGGTAATTAAGTAGCATCAATAAAAG-ACTTAAT
52778 CTAAAAAGAG
Statistics
Matches: 103, Mismatches: 11, Indels: 4
0.87 0.09 0.03
Matches are distributed among these distances:
71 1 0.01
72 41 0.40
73 61 0.59
ACGTcount: A:0.43, C:0.10, G:0.19, T:0.28
Consensus pattern (72 bp):
ACTTAATTCAGGGTAATTAAGTAGCATCAATAAAAGACTTAATTCAGGGTAATTAAGTAGAGTCA
ATAAAGA
Found at i:52807 original size:109 final size:110
Alignment explanation
Indices: 52586--52816 Score: 276
Period size: 109 Copynumber: 2.1 Consensus size: 110
52576 AAGTCGAGTC
*
52586 AGGGACTTAATTCGGGGTAATTAAGTAGCATCAATAAAAGACTTAATTCAGGGTAATTAAGTAGA
1 AGGGACTTAATTCAGGGTAATTAAGTAGCATCAATAAAAGACTTAATTCAGGGTAATTAAGTAGA
* * * * * *
52651 GTCAATAAAGAACTTAATTCAAGGCAATTAAGTAGCGTCAATAAA
66 ATCAATAAAGAACTTAATTAAAAGCAATTAAGCAGAGACAATAAA
* * *
52696 A-GGACTTAATTCAGGGTAATTAAGT-GGAGTTAAT-AAAGAACTTAATTCAGGGTAATTAAGTG
1 AGGGACTTAATTCAGGGTAATTAAGTAGCA-TCAATAAAAG-ACTTAATTCAGGGTAATTAAGTA
52758 GAATCAATAAAGAACTTAATCTAAAAAG-AGATTAAGCA-AGACAAT-AA
64 GAATCAATAAAGAACTTAAT-T-AAAAGCA-ATTAAGCAGAGACAATAAA
*
52805 AGGGGCTTAATT
1 AGGGACTTAATT
52817 TATAAAAATT
Statistics
Matches: 104, Mismatches: 11, Indels: 12
0.82 0.09 0.09
Matches are distributed among these distances:
108 6 0.06
109 71 0.68
110 17 0.16
111 10 0.10
ACGTcount: A:0.44, C:0.10, G:0.20, T:0.26
Consensus pattern (110 bp):
AGGGACTTAATTCAGGGTAATTAAGTAGCATCAATAAAAGACTTAATTCAGGGTAATTAAGTAGA
ATCAATAAAGAACTTAATTAAAAGCAATTAAGCAGAGACAATAAA
Found at i:56280 original size:17 final size:17
Alignment explanation
Indices: 56239--56280 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
56229 GATTAAATTG
*
56239 ATTTTTGCTTGCATGTT
1 ATTTTTGCTTGAATGTT
*
56256 ATTATTGCTTGAAT-TT
1 ATTTTTGCTTGAATGTT
56272 AGTTTTTGC
1 A-TTTTTGC
56281 ATTTAGTTTA
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
16 3 0.14
17 18 0.86
ACGTcount: A:0.17, C:0.10, G:0.17, T:0.57
Consensus pattern (17 bp):
ATTTTTGCTTGAATGTT
Found at i:59618 original size:31 final size:31
Alignment explanation
Indices: 59583--59642 Score: 111
Period size: 31 Copynumber: 1.9 Consensus size: 31
59573 AGGGACTAAC
*
59583 AAAAGTTGGAGTGTGGGGGAAATATGATACG
1 AAAAGTTGAAGTGTGGGGGAAATATGATACG
59614 AAAAGTTGAAGTGTGGGGGAAATATGATA
1 AAAAGTTGAAGTGTGGGGGAAATATGATA
59643 AGACCTAATT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.38, C:0.02, G:0.37, T:0.23
Consensus pattern (31 bp):
AAAAGTTGAAGTGTGGGGGAAATATGATACG
Found at i:63170 original size:25 final size:25
Alignment explanation
Indices: 63137--63190 Score: 81
Period size: 25 Copynumber: 2.2 Consensus size: 25
63127 GATTTATTAC
* *
63137 TAGGCTTGATTATAGGAGATCTGAT
1 TAGGCTTGACTATAAGAGATCTGAT
*
63162 TAGGCTTGACTATAAGAGATTTGAT
1 TAGGCTTGACTATAAGAGATCTGAT
63187 TAGG
1 TAGG
63191 AGACGTGATT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.30, C:0.07, G:0.28, T:0.35
Consensus pattern (25 bp):
TAGGCTTGACTATAAGAGATCTGAT
Found at i:64284 original size:15 final size:15
Alignment explanation
Indices: 64263--64348 Score: 60
Period size: 13 Copynumber: 6.0 Consensus size: 15
64253 TATTACTAGG
64263 CTTGATTATAGGAGA
1 CTTGATTATAGGAGA
*
64278 TTTGA-T-TA-G-G-
1 CTTGATTATAGGAGA
*
64288 CTTGACTATAGGAGA
1 CTTGATTATAGGAGA
*
64303 TTTGA-T-TAGGAGA
1 CTTGATTATAGGAGA
*
64316 CGTGATTATAGGGATTGA
1 CTTGATTATA-GGA--GA
64334 CTTGATTATAGGAGA
1 CTTGATTATAGGAGA
64349 TAATAGGAAG
Statistics
Matches: 55, Mismatches: 6, Indels: 20
0.68 0.07 0.25
Matches are distributed among these distances:
10 4 0.07
11 2 0.04
12 3 0.05
13 13 0.24
14 4 0.07
15 12 0.22
16 3 0.05
17 3 0.05
18 11 0.20
ACGTcount: A:0.30, C:0.06, G:0.29, T:0.35
Consensus pattern (15 bp):
CTTGATTATAGGAGA
Found at i:64289 original size:25 final size:25
Alignment explanation
Indices: 64259--64312 Score: 99
Period size: 25 Copynumber: 2.2 Consensus size: 25
64249 CATCTATTAC
*
64259 TAGGCTTGATTATAGGAGATTTGAT
1 TAGGCTTGACTATAGGAGATTTGAT
64284 TAGGCTTGACTATAGGAGATTTGAT
1 TAGGCTTGACTATAGGAGATTTGAT
64309 TAGG
1 TAGG
64313 AGACGTGATT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.28, C:0.06, G:0.30, T:0.37
Consensus pattern (25 bp):
TAGGCTTGACTATAGGAGATTTGAT
Found at i:69687 original size:66 final size:66
Alignment explanation
Indices: 69581--69707 Score: 211
Period size: 66 Copynumber: 1.9 Consensus size: 66
69571 TTTCCCCAGA
* *
69581 GGGACAACTATTGGAAATTTACTAAATTCACCAATTTCTCTTCTCCTCTTT-TATTTATTTTTCA
1 GGGACAACTATTGGAAATTTACTAAATTCACCAATGTCTCTTCTCCCCTTTATA-TTATTTTTCA
69645 GG
65 GG
*
69647 GGGACAACTATTGGTAATTTACTAAATTCACCAATGTCTCTTCTCCCCTTTATATTATTTT
1 GGGACAACTATTGGAAATTTACTAAATTCACCAATGTCTCTTCTCCCCTTTATATTATTTT
69708 AAGAACAATC
Statistics
Matches: 57, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
66 55 0.96
67 2 0.04
ACGTcount: A:0.26, C:0.20, G:0.10, T:0.43
Consensus pattern (66 bp):
GGGACAACTATTGGAAATTTACTAAATTCACCAATGTCTCTTCTCCCCTTTATATTATTTTTCAG
G
Found at i:75799 original size:17 final size:18
Alignment explanation
Indices: 75777--75810 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
75767 GTATCCGACC
75777 AGAAAAAGGA-AAAAAAA
1 AGAAAAAGGAGAAAAAAA
*
75794 AGAAAACGGAGAAAAAA
1 AGAAAAAGGAGAAAAAA
75811 GCAGTGGGTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.76, C:0.03, G:0.21, T:0.00
Consensus pattern (18 bp):
AGAAAAAGGAGAAAAAAA
Found at i:84820 original size:30 final size:30
Alignment explanation
Indices: 84786--84843 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
84776 CTGCAGAGAG
*
84786 TTTGAAAGAAAGCACAGAGTTTTGAGATAA
1 TTTGAAAGAAAGCACAGAGCTTTGAGATAA
* *
84816 TTTGAGAGAAAGCACGGAGCTTTGAGAT
1 TTTGAAAGAAAGCACAGAGCTTTGAGAT
84844 TTTGCGCAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.38, C:0.09, G:0.28, T:0.26
Consensus pattern (30 bp):
TTTGAAAGAAAGCACAGAGCTTTGAGATAA
Found at i:87175 original size:28 final size:29
Alignment explanation
Indices: 87117--87195 Score: 88
Period size: 28 Copynumber: 2.7 Consensus size: 29
87107 TAAATACCAA
* **
87117 AAAAAAATCCCTTATGTTTTGCTTTTGGGAC
1 AAAATAATCCCTTATG-TTT-CTTTCAGGAC
87148 AAAATAATCCCTTATGTTT-TTTCAGGAC
1 AAAATAATCCCTTATGTTTCTTTCAGGAC
* *
87176 AAATTAATCCCTTACGTTTC
1 AAAATAATCCCTTATGTTTC
87196 AAAAATGAGC
Statistics
Matches: 42, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
28 24 0.57
30 3 0.07
31 15 0.36
ACGTcount: A:0.30, C:0.19, G:0.11, T:0.39
Consensus pattern (29 bp):
AAAATAATCCCTTATGTTTCTTTCAGGAC
Found at i:87378 original size:29 final size:29
Alignment explanation
Indices: 87327--87414 Score: 162
Period size: 29 Copynumber: 3.1 Consensus size: 29
87317 AAGGGACTAA
87327 TTTGTCCC-AAA-AAAACATAAGGGATTT
1 TTTGTCCCAAAAGAAAACATAAGGGATTT
87354 TTTGTCCCAAAAGAAAACATAAGGGATTT
1 TTTGTCCCAAAAGAAAACATAAGGGATTT
87383 TTTGTCCCAAAAGAAAACATAAGGGATTT
1 TTTGTCCCAAAAGAAAACATAAGGGATTT
87412 TTT
1 TTT
87415 AGTATTTAGT
Statistics
Matches: 59, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
27 8 0.14
28 3 0.05
29 48 0.81
ACGTcount: A:0.40, C:0.14, G:0.16, T:0.31
Consensus pattern (29 bp):
TTTGTCCCAAAAGAAAACATAAGGGATTT
Found at i:88398 original size:31 final size:31
Alignment explanation
Indices: 88363--88429 Score: 116
Period size: 31 Copynumber: 2.2 Consensus size: 31
88353 TAAATTATAA
* *
88363 TTTTTCTTTTGGGACAAAATAATCCTTTATG
1 TTTTTCTTTTGGGACAAAAAAATCCCTTATG
88394 TTTTTCTTTTGGGACAAAAAAATCCCTTATG
1 TTTTTCTTTTGGGACAAAAAAATCCCTTATG
88425 TTTTT
1 TTTTT
88430 TTTCGGAACA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 34 1.00
ACGTcount: A:0.25, C:0.13, G:0.12, T:0.49
Consensus pattern (31 bp):
TTTTTCTTTTGGGACAAAAAAATCCCTTATG
Found at i:88634 original size:30 final size:31
Alignment explanation
Indices: 88598--88664 Score: 109
Period size: 30 Copynumber: 2.2 Consensus size: 31
88588 TTTTGAAATG
88598 TAAGGGATTAATTTGTCCCAAAA-AAAAACA
1 TAAGGGATTAATTTGTCCCAAAAGAAAAACA
* *
88628 TAAGGGATTATTTTGTCCCAAAAGCAAAACA
1 TAAGGGATTAATTTGTCCCAAAAGAAAAACA
88659 TAAGGG
1 TAAGGG
88665 TTTTTTTTTG
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
30 22 0.65
31 12 0.35
ACGTcount: A:0.45, C:0.13, G:0.18, T:0.24
Consensus pattern (31 bp):
TAAGGGATTAATTTGTCCCAAAAGAAAAACA
Found at i:90601 original size:15 final size:15
Alignment explanation
Indices: 90554--90602 Score: 53
Period size: 16 Copynumber: 3.1 Consensus size: 15
90544 CCTGAATCCA
90554 AAAAGACTCGAACCCG
1 AAAA-ACTCGAACCCG
* *
90570 AAAAAGTTCAAACCCG
1 AAAAA-CTCGAACCCG
*
90586 AAAAACTCGAATCCG
1 AAAAACTCGAACCCG
90601 AA
1 AA
90603 CCCGAACATG
Statistics
Matches: 27, Mismatches: 5, Indels: 3
0.77 0.14 0.09
Matches are distributed among these distances:
15 10 0.37
16 17 0.63
ACGTcount: A:0.49, C:0.27, G:0.14, T:0.10
Consensus pattern (15 bp):
AAAAACTCGAACCCG
Found at i:90929 original size:30 final size:30
Alignment explanation
Indices: 90842--90929 Score: 79
Period size: 30 Copynumber: 2.8 Consensus size: 30
90832 TTTAATTAGC
* *
90842 AAAAAATATTTATATACATTTATTATTTGAAAT
1 AAAATATAATTATATACA--TA-TATTTGAAAT
* * * *
90875 AAAATATATATTTTTTATAT-TATTTGGAAT
1 AAAATATA-ATTATATACATATATTTGAAAT
90905 AAAATATAATTATATACATATATTT
1 AAAATATAATTATATACATATATTT
90930 TAATATTTAT
Statistics
Matches: 44, Mismatches: 9, Indels: 7
0.73 0.15 0.12
Matches are distributed among these distances:
29 8 0.18
30 22 0.50
32 1 0.02
33 7 0.16
34 6 0.14
ACGTcount: A:0.47, C:0.02, G:0.03, T:0.48
Consensus pattern (30 bp):
AAAATATAATTATATACATATATTTGAAAT
Found at i:90941 original size:22 final size:22
Alignment explanation
Indices: 90930--90978 Score: 73
Period size: 21 Copynumber: 2.3 Consensus size: 22
90920 ACATATATTT
90930 TAATATTTATATAAATAAAATA
1 TAATATTTATATAAATAAAATA
* *
90952 TAATA-TTATATATATAATATA
1 TAATATTTATATAAATAAAATA
90973 TAATAT
1 TAATAT
90979 AAACGAACAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 19 0.79
22 5 0.21
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (22 bp):
TAATATTTATATAAATAAAATA
Found at i:91023 original size:22 final size:22
Alignment explanation
Indices: 90978--91024 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 22
90968 ATATATAATA
*
90978 TAAACGAACATAAACGATCTAT
1 TAAACGAACATAAACGAACTAT
*
91000 TAAATGAACAATAAACGAAC-AT
1 TAAACGAAC-ATAAACGAACTAT
91022 TAA
1 TAA
91025 TCGAGCTTGT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
22 13 0.59
23 9 0.41
ACGTcount: A:0.55, C:0.15, G:0.09, T:0.21
Consensus pattern (22 bp):
TAAACGAACATAAACGAACTAT
Found at i:91493 original size:17 final size:16
Alignment explanation
Indices: 91438--91493 Score: 51
Period size: 16 Copynumber: 3.4 Consensus size: 16
91428 GAATCAACAT
*
91438 GACCCAAATTTAATCT
1 GACCCAAATTTAATCC
* * *
91454 GTATCCAAA-TCAACCC
1 G-ACCCAAATTTAATCC
91470 GACCCAAATTTAATCC
1 GACCCAAATTTAATCC
91486 GAACCCAA
1 G-ACCCAA
91494 CATGACCCGC
Statistics
Matches: 30, Mismatches: 7, Indels: 5
0.71 0.17 0.12
Matches are distributed among these distances:
15 6 0.20
16 12 0.40
17 12 0.40
ACGTcount: A:0.39, C:0.32, G:0.07, T:0.21
Consensus pattern (16 bp):
GACCCAAATTTAATCC
Found at i:91502 original size:32 final size:32
Alignment explanation
Indices: 91386--91493 Score: 94
Period size: 32 Copynumber: 3.4 Consensus size: 32
91376 ACCAAATCCG
* * * * *
91386 AATCCGAACCTAAATTAAGCTGACACAAA-TT
1 AATCCGAACCCAAATCAACCCGACCCAAATTT
* **
91417 AA-CCTGAACCCGAATCAACATGACCCAAATTT
1 AATCC-GAACCCAAATCAACCCGACCCAAATTT
* * *
91449 AATCTGTATCCAAATCAACCCGACCCAAATTT
1 AATCCGAACCCAAATCAACCCGACCCAAATTT
91481 AATCCGAACCCAA
1 AATCCGAACCCAA
91494 CATGACCCGC
Statistics
Matches: 59, Mismatches: 15, Indels: 5
0.75 0.19 0.06
Matches are distributed among these distances:
30 2 0.03
31 20 0.34
32 36 0.61
33 1 0.02
ACGTcount: A:0.42, C:0.30, G:0.08, T:0.20
Consensus pattern (32 bp):
AATCCGAACCCAAATCAACCCGACCCAAATTT
Found at i:94752 original size:32 final size:32
Alignment explanation
Indices: 94716--94820 Score: 131
Period size: 32 Copynumber: 3.3 Consensus size: 32
94706 TTTAAGTCGA
*
94716 GTTCGGGTCAAATTTGGGTCGGGTTGATTCGG
1 GTTCGGGTCAAATTTGGGTCAGGTTGATTCGG
* *
94748 GTTCGGGTTAAATTTGGGAT-AGGTTGATTCAG
1 GTTCGGGTCAAATTTGGG-TCAGGTTGATTCGG
* * *
94780 GTTCGGGTCAATTTTGGATCAGGTTAATTCGG
1 GTTCGGGTCAAATTTGGGTCAGGTTGATTCGG
*
94812 GTTGGGGTC
1 GTTCGGGTC
94821 CGGATTGGGT
Statistics
Matches: 62, Mismatches: 9, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
31 1 0.02
32 60 0.97
33 1 0.02
ACGTcount: A:0.16, C:0.10, G:0.37, T:0.36
Consensus pattern (32 bp):
GTTCGGGTCAAATTTGGGTCAGGTTGATTCGG
Found at i:95049 original size:16 final size:16
Alignment explanation
Indices: 95030--95103 Score: 55
Period size: 15 Copynumber: 4.7 Consensus size: 16
95020 GGGTTCAGGT
95030 TTTTTTGGGTTTGAGA
1 TTTTTTGGGTTTGAGA
* *
95046 TTTTTCGGATTCT--GA
1 TTTTTTGGGTT-TGAGA
*
95061 TTTTTTCGGGTTTGAGC
1 TTTTTT-GGGTTTGAGA
* * *
95078 TTTTTCGGG-TTCAGG
1 TTTTTTGGGTTTGAGA
95093 TTTTTTGGGTT
1 TTTTTTGGGTT
95104 CGGATTCAGA
Statistics
Matches: 44, Mismatches: 9, Indels: 10
0.70 0.14 0.16
Matches are distributed among these distances:
15 20 0.45
16 17 0.39
17 7 0.16
ACGTcount: A:0.08, C:0.08, G:0.28, T:0.55
Consensus pattern (16 bp):
TTTTTTGGGTTTGAGA
Found at i:95053 original size:32 final size:32
Alignment explanation
Indices: 95017--95103 Score: 122
Period size: 32 Copynumber: 2.8 Consensus size: 32
95007 TTTTTTCAAG
95017 TTCGGGTTCAGGTTTTTTTGGGTTTGAGATTT
1 TTCGGGTTCAGGTTTTTTTGGGTTTGAGATTT
* * * * *
95049 TTCGGATTCTGATTTTTTCGGGTTTGAGCTTT
1 TTCGGGTTCAGGTTTTTTTGGGTTTGAGATTT
95081 TTCGGGTTCAGG-TTTTTTGGGTT
1 TTCGGGTTCAGGTTTTTTTGGGTT
95104 CGGATTCAGA
Statistics
Matches: 46, Mismatches: 9, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
31 10 0.22
32 36 0.78
ACGTcount: A:0.08, C:0.09, G:0.30, T:0.53
Consensus pattern (32 bp):
TTCGGGTTCAGGTTTTTTTGGGTTTGAGATTT
Found at i:95081 original size:15 final size:15
Alignment explanation
Indices: 95030--95088 Score: 64
Period size: 16 Copynumber: 3.7 Consensus size: 15
95020 GGGTTCAGGT
*
95030 TTTTTTGGGTTTGAG
1 TTTTTCGGGTTTGAG
* *
95045 ATTTTTCGGATTCTGAT
1 -TTTTTCGGGTT-TGAG
95062 TTTTTCGGGTTTGAG
1 TTTTTCGGGTTTGAG
95077 CTTTTTCGGGTT
1 -TTTTTCGGGTT
95089 CAGGTTTTTT
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
15 3 0.08
16 30 0.83
17 3 0.08
ACGTcount: A:0.08, C:0.08, G:0.27, T:0.56
Consensus pattern (15 bp):
TTTTTCGGGTTTGAG
Found at i:95096 original size:15 final size:15
Alignment explanation
Indices: 95017--95104 Score: 59
Period size: 16 Copynumber: 5.6 Consensus size: 15
95007 TTTTTTCAAG
95017 TTCGGGTTCAGGTTTT
1 TTCGGGTTCAGG-TTT
* * *
95033 TTTGGGTTTGAGATTT
1 TTCGGG-TTCAGGTTT
* * *
95049 TTCGGATTCTGATTTT
1 TTCGGGTTCAG-GTTT
* *
95065 TTCGGGTTTGAGCTTT
1 TTCGGG-TTCAGGTTT
95081 TTCGGGTTCAGGTTT
1 TTCGGGTTCAGGTTT
*
95096 TTTGGGTTC
1 TTCGGGTTC
95105 GGATTCAGAC
Statistics
Matches: 54, Mismatches: 15, Indels: 7
0.71 0.20 0.09
Matches are distributed among these distances:
15 18 0.33
16 29 0.54
17 7 0.13
ACGTcount: A:0.08, C:0.10, G:0.30, T:0.52
Consensus pattern (15 bp):
TTCGGGTTCAGGTTT
Found at i:95252 original size:10 final size:10
Alignment explanation
Indices: 95237--95268 Score: 55
Period size: 10 Copynumber: 3.2 Consensus size: 10
95227 ATCTAGAACT
95237 TAGCTTTGAC
1 TAGCTTTGAC
*
95247 TAGCTTCGAC
1 TAGCTTTGAC
95257 TAGCTTTGAC
1 TAGCTTTGAC
95267 TA
1 TA
95269 ATATGGATAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.22, C:0.22, G:0.19, T:0.38
Consensus pattern (10 bp):
TAGCTTTGAC
Found at i:95657 original size:21 final size:18
Alignment explanation
Indices: 95626--95683 Score: 55
Period size: 18 Copynumber: 3.1 Consensus size: 18
95616 ATGTATTTGG
*
95626 TTTGTGGGTAGGTATAGT
1 TTTGTAGGTAGGTATAGT
* *
95644 TTTCGGTAATGTAGCTAT-GT
1 TTT--GT-AGGTAGGTATAGT
95664 TTTGTAGGTAGGTATAGT
1 TTTGTAGGTAGGTATAGT
95682 TT
1 TT
95684 CCAATTTTCA
Statistics
Matches: 31, Mismatches: 5, Indels: 8
0.70 0.11 0.18
Matches are distributed among these distances:
17 8 0.26
18 9 0.29
20 7 0.23
21 7 0.23
ACGTcount: A:0.19, C:0.03, G:0.31, T:0.47
Consensus pattern (18 bp):
TTTGTAGGTAGGTATAGT
Found at i:96756 original size:20 final size:21
Alignment explanation
Indices: 96718--96758 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
96708 AGGTCTACTT
96718 GTTATCATCTCCAAAAGAACA
1 GTTATCATCTCCAAAAGAACA
96739 GTTATCATCTCC-AAAGAACA
1 GTTATCATCTCCAAAAGAACA
96759 ACTCCGAAGC
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 8 0.40
21 12 0.60
ACGTcount: A:0.41, C:0.24, G:0.10, T:0.24
Consensus pattern (21 bp):
GTTATCATCTCCAAAAGAACA
Found at i:117532 original size:33 final size:33
Alignment explanation
Indices: 117429--117533 Score: 104
Period size: 33 Copynumber: 3.2 Consensus size: 33
117419 TTGCAAAGAG
* * * *
117429 TGTTTTAGATGTTGTTTGCGATGATACTAAACC
1 TGTTTTAGGTGTTGTTTGCGATGAAACAAAATC
** * *
117462 TAATTT-GAGTGTTGTTTGCGATGACACTAAATC
1 TGTTTTAG-GTGTTGTTTGCGATGAAACAAAATC
* *
117495 TGTTTTAGGTGTTGTTTGTGATGAAACAAAATT
1 TGTTTTAGGTGTTGTTTGCGATGAAACAAAATC
117528 TGTTTT
1 TGTTTT
117534 GGATGCTAAT
Statistics
Matches: 59, Mismatches: 11, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
32 1 0.02
33 57 0.97
34 1 0.02
ACGTcount: A:0.25, C:0.09, G:0.22, T:0.45
Consensus pattern (33 bp):
TGTTTTAGGTGTTGTTTGCGATGAAACAAAATC
Found at i:120236 original size:21 final size:21
Alignment explanation
Indices: 120212--120252 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
120202 TTTTCAAGGA
* *
120212 TAGATTTGAATCTAACACAAC
1 TAGATTCGAATCAAACACAAC
*
120233 TAGATTCGTATCAAACACAA
1 TAGATTCGAATCAAACACAA
120253 TGAGGTGAGC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.44, C:0.20, G:0.10, T:0.27
Consensus pattern (21 bp):
TAGATTCGAATCAAACACAAC
Found at i:127015 original size:435 final size:437
Alignment explanation
Indices: 126277--127340 Score: 1160
Period size: 437 Copynumber: 2.4 Consensus size: 437
126267 TGTGTATTTT
* * * *
126277 TTTG-TCTATTTATCCGATTAAGCTGTTTCAAGTGTCTATTAAAAGGTTAA-ATCATGATCTACA
1 TTTGTTCTATTTGTCCGATTAAGCTGATTCAAGTGTCTATTAAAA-GATAATTTCATGATCTACA
* * * * * * *
126340 ATTTTCATTAAGAACTCAAAAGTCAATTTTAATATCTT-GATTCTAAAAAATACTTCCGAAATTT
65 ACTTTCATGAAGGACTCAAAAGTAAATTTTTATAT-TTCAATTCTAAAAAATGCTTCCGAAATTT
* * * * * * ** * *
126404 TGTGGTTTTGATTGCCGGTTTATTTAATATCGTATAATTTTTTTTCCACATGTCCGATTTAAGTT
129 TGTCGTTTCGATTGACGGTCTATTTAATAACATATAATTTTTGATCCACATGTCCAATTAAAGTT
* * * * * * * * * *
126469 ATTGAAGTGTTGGTTAAAAAGTTATTGCATGATTTACGACTTTCATGAAGGATCCGAAAGCTAAA
194 ATTCAAGTGTAGATTAAAAAGTTACTGCATAATCTACGACATTCATAAAGAACCCGAAAGCTAAA
* * * *
126534 TTTGATTTACGAGTTTCGTGAAGGGTTCAAAAGGGAATTTTTATGTTTTAAGATCTCCATTAACA
259 TTTGATCTACGAGTTTCATGAAGAGTTCAAAAGGGAATTTTTATGTTTCAAGATCTCCATTAACA
* ** *
126599 AACATATTCTTATTTGGATTATTTATCAAATTACCCTCATACTTTTCTACTTTATACTACTTAGT
324 AACATATTCTTATTTGAATTAGATATCAAATCACCCTCATACTTTTCTACTTTATACTACTTAGT
* *
126664 CCTTAACAAAT-CTATCTTAATCTAATGTTTA-AGTT-TTAGTTTTTTA-TTC
389 CCTTAACAAATCCTATCTTAATC-AAT-TTAACACTTATT--TTTTTTAGTTC
** * *
126713 TTTGTTCTATTTGTCCGATTAAATTGATTCATGTGTCTATTAAAAGATAATTTCATTATCTACAA
1 TTTGTTCTATTTGTCCGATTAAGCTGATTCAAGTGTCTATTAAAAGATAATTTCATGATCTACAA
* * * *
126778 CTTTCATGAAGGATTCAAAAGAAAATTTTTATATTTCAATT-AAAAAAATGCTTCCTAAA-TTTG
66 CTTTCATGAAGGACTCAAAAGTAAATTTTTATATTTCAATTCTAAAAAATGCTTCCGAAATTTTG
* * *
126841 TTCGTTTCGATTTATGGTCTATTTAATAACATATAATTTTTGATCCACATGTCCAATTAAATTTA
131 -TCGTTTCGATTGACGGTCTATTTAATAACATATAATTTTTGATCCACATGTCCAATTAAAGTTA
* * *
126906 TTCAAGTGTAGATTAAAAGGTTACTGTATAATCTACGACATTCATAAAGAACCCGAAAG-TTAAT
195 TTCAAGTGTAGATTAAAAAGTTACTGCATAATCTACGACATTCATAAAGAACCCGAAAGCTAAAT
* *
126970 TTGATCTATGAGTTTCATGAAGAGTTCAAAAGGGAATTTTTATGTTTCAAGATCTTCATTAACAA
260 TTGATCTACGAGTTTCATGAAGAGTTCAAAAGGGAATTTTTATGTTTCAAGATCTCCATTAACAA
* * * * * *
127035 ATATTTTCTTATTTGAATTAGATATCAAATCATCCTCATACTTTTCTATTTTATGCTATTTAGTC
325 ACATATTCTTATTTGAATTAGATATCAAATCACCCTCATACTTTTCTACTTTATACTACTTAGTC
** * * *
127100 CTTGCCAAATCCTATCTTATTCGATTTAACACTTCATTTTTTTTAGTTTT
390 CTTAACAAATCCTATCTTAATCAATTTAACACTT-ATTTTTTTTAG-TTC
* * * * * * *
127150 TTTGTTCTATTTGTCCAATTAAGGTAATTCAGGTGTTTATTAAAAGGTAATTTTATGATCTACAA
1 TTTGTTCTATTTGTCCGATTAAGCTGATTCAAGTGTCTATTAAAAGATAATTTCATGATCTACAA
* * * * **
127215 CTCTCATGAAAGACTCAAATGTTAATTTTTATATTTCAATTCTAAAAAATGCTTTTGAAATTTTG
66 CTTTCATGAAGGACTCAAAAGTAAATTTTTATATTTCAATTCTAAAAAATGCTTCCGAAATTTTG
* ** * * *
127280 T-GATTTCGGTTGACAATCTATTTAATATATCATATTATTTTTGATCCAGATGTCCGATTAA
131 TCG-TTTCGATTGACGGTCTATTTAATA-A-CATATAATTTTTGATCCACATGTCCAATTAA
127341 TAAATTCACA
Statistics
Matches: 518, Mismatches: 95, Indels: 26
0.81 0.15 0.04
Matches are distributed among these distances:
434 3 0.01
435 142 0.27
436 133 0.26
437 173 0.33
438 34 0.07
439 5 0.01
440 28 0.05
ACGTcount: A:0.32, C:0.13, G:0.12, T:0.43
Consensus pattern (437 bp):
TTTGTTCTATTTGTCCGATTAAGCTGATTCAAGTGTCTATTAAAAGATAATTTCATGATCTACAA
CTTTCATGAAGGACTCAAAAGTAAATTTTTATATTTCAATTCTAAAAAATGCTTCCGAAATTTTG
TCGTTTCGATTGACGGTCTATTTAATAACATATAATTTTTGATCCACATGTCCAATTAAAGTTAT
TCAAGTGTAGATTAAAAAGTTACTGCATAATCTACGACATTCATAAAGAACCCGAAAGCTAAATT
TGATCTACGAGTTTCATGAAGAGTTCAAAAGGGAATTTTTATGTTTCAAGATCTCCATTAACAAA
CATATTCTTATTTGAATTAGATATCAAATCACCCTCATACTTTTCTACTTTATACTACTTAGTCC
TTAACAAATCCTATCTTAATCAATTTAACACTTATTTTTTTTAGTTC
Found at i:130918 original size:32 final size:32
Alignment explanation
Indices: 130877--130941 Score: 130
Period size: 32 Copynumber: 2.0 Consensus size: 32
130867 GCGCGCGGGC
130877 AAAATCTAGTATATATATAAAGGAATTGGGTT
1 AAAATCTAGTATATATATAAAGGAATTGGGTT
130909 AAAATCTAGTATATATATAAAGGAATTGGGTT
1 AAAATCTAGTATATATATAAAGGAATTGGGTT
130941 A
1 A
130942 CTCGTTCAAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.45, C:0.03, G:0.18, T:0.34
Consensus pattern (32 bp):
AAAATCTAGTATATATATAAAGGAATTGGGTT
Found at i:131510 original size:13 final size:12
Alignment explanation
Indices: 131492--131521 Score: 51
Period size: 13 Copynumber: 2.4 Consensus size: 12
131482 ATTAGTATAA
131492 ATTATCATTAATC
1 ATTATCATT-ATC
131505 ATTATCATTATC
1 ATTATCATTATC
131517 ATTAT
1 ATTAT
131522 ATATACAAGA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 8 0.47
13 9 0.53
ACGTcount: A:0.37, C:0.13, G:0.00, T:0.50
Consensus pattern (12 bp):
ATTATCATTATC
Found at i:131511 original size:6 final size:6
Alignment explanation
Indices: 131492--131521 Score: 51
Period size: 6 Copynumber: 4.8 Consensus size: 6
131482 ATTAGTATAA
131492 ATTATC ATTAATC ATTATC ATTATC ATTAT
1 ATTATC ATT-ATC ATTATC ATTATC ATTAT
131522 ATATACAAGA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
6 17 0.74
7 6 0.26
ACGTcount: A:0.37, C:0.13, G:0.00, T:0.50
Consensus pattern (6 bp):
ATTATC
Done.