Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008695.1 Hibiscus syriacus cultivar Beakdansim tig00111725_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: 140010
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.31
Found at i:2895 original size:33 final size:33
Alignment explanation
Indices: 2831--2931 Score: 82
Period size: 33 Copynumber: 3.0 Consensus size: 33
2821 CTTGTTGATG
* * *
2831 AATG-AAGGATGAT-TTAATGGTGATGAAATGGT
1 AATGAAAGGATGATGTTATTGGCG-TGATATGGT
2863 AATGAAAGGATGATGTTATTGGCGTGATATGGT
1 AATGAAAGGATGATGTTATTGGCGTGATATGGT
* * *
2896 GATGGAATATGG-TGATGATATAGGCGTGATAATGGT
1 AAT-GAA-A-GGATGATGTTATTGGCGTGAT-ATGGT
2932 GATGGACAGA
Statistics
Matches: 57, Mismatches: 6, Indels: 8
0.80 0.08 0.11
Matches are distributed among these distances:
32 4 0.07
33 19 0.33
34 10 0.18
35 17 0.30
36 7 0.12
ACGTcount: A:0.33, C:0.02, G:0.34, T:0.32
Consensus pattern (33 bp):
AATGAAAGGATGATGTTATTGGCGTGATATGGT
Found at i:11320 original size:36 final size:35
Alignment explanation
Indices: 11227--11337 Score: 143
Period size: 35 Copynumber: 3.2 Consensus size: 35
11217 TTGGTGGTTA
* * *
11227 TATAGGCGTGAAATGGTGATAGAAGATGGTAAGGA
1 TATAGGCGTGAAATGGTGATGGAAGATGGTAATGT
* * * *
11262 TATAGGCTTGCAATGGTAATGGAAGATGGTGATGT
1 TATAGGCGTGAAATGGTGATGGAAGATGGTAATGT
11297 TATAGGCGTGAAAATGGTGATGGAAGATGGTAATGT
1 TATAGGCGTG-AAATGGTGATGGAAGATGGTAATGT
11333 T-TAGG
1 TATAGG
11338 TAGTATCTTA
Statistics
Matches: 64, Mismatches: 11, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
35 41 0.64
36 23 0.36
ACGTcount: A:0.32, C:0.04, G:0.36, T:0.28
Consensus pattern (35 bp):
TATAGGCGTGAAATGGTGATGGAAGATGGTAATGT
Found at i:15418 original size:8 final size:8
Alignment explanation
Indices: 15407--15431 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
15397 GAGAAAAATC
15407 AGAAAAGA
1 AGAAAAGA
15415 AGAAAAGA
1 AGAAAAGA
15423 AGAAAAGA
1 AGAAAAGA
15431 A
1 A
15432 AAGAAAAAGA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (8 bp):
AGAAAAGA
Found at i:15441 original size:16 final size:16
Alignment explanation
Indices: 15390--15441 Score: 52
Period size: 16 Copynumber: 3.1 Consensus size: 16
15380 TTGGAGTGCA
15390 AAAAGAAGAGAAAAATCAG
1 AAAAGAAGA-AAAAA--AG
*
15409 AAAAGAAGAAAAGAAG
1 AAAAGAAGAAAAAAAG
15425 AAAAGAA-AAGAAAAAG
1 AAAAGAAGAA-AAAAAG
15441 A
1 A
15442 GAAGTTCAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
15 2 0.07
16 15 0.50
18 4 0.13
19 9 0.30
ACGTcount: A:0.75, C:0.02, G:0.21, T:0.02
Consensus pattern (16 bp):
AAAAGAAGAAAAAAAG
Found at i:23757 original size:19 final size:21
Alignment explanation
Indices: 23733--23784 Score: 72
Period size: 21 Copynumber: 2.6 Consensus size: 21
23723 CGGCCAAGAG
*
23733 CATGTATCTTCA-TT-AAAAT
1 CATGTATTTTCATTTAAAAAT
*
23752 CATGTATTTTAATTTAAAAAT
1 CATGTATTTTCATTTAAAAAT
23773 CATGTATTTTCA
1 CATGTATTTTCA
23785 AAGGGGTTTC
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
19 10 0.36
20 2 0.07
21 16 0.57
ACGTcount: A:0.37, C:0.12, G:0.06, T:0.46
Consensus pattern (21 bp):
CATGTATTTTCATTTAAAAAT
Found at i:31364 original size:33 final size:32
Alignment explanation
Indices: 31302--31365 Score: 78
Period size: 33 Copynumber: 2.0 Consensus size: 32
31292 GCAAAAATTA
*
31302 AAGAAAGAAATGATTAAAATAGAATATGAAAG
1 AAGAAAGAAATGATTAAAAAAGAATATGAAAG
31334 AAGAAAGGAAATGA-TAAGAAAAGGAA-ATGAAA
1 AAGAAA-GAAATGATTAA-AAAA-GAATATGAAA
31366 TGGATAGAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
32 9 0.32
33 16 0.57
34 3 0.11
ACGTcount: A:0.64, C:0.00, G:0.22, T:0.14
Consensus pattern (32 bp):
AAGAAAGAAATGATTAAAAAAGAATATGAAAG
Found at i:31365 original size:21 final size:21
Alignment explanation
Indices: 31336--31375 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
31326 TATGAAAGAA
31336 GAAAGGAAAT-GATAAGAAAAG
1 GAAAGGAAATGGAT-AGAAAAG
*
31357 GAAATGAAATGGATAGAAA
1 GAAAGGAAATGGATAGAAA
31376 TGTTATCAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 14 0.82
22 3 0.18
ACGTcount: A:0.60, C:0.00, G:0.28, T:0.12
Consensus pattern (21 bp):
GAAAGGAAATGGATAGAAAAG
Found at i:38668 original size:18 final size:17
Alignment explanation
Indices: 38610--38668 Score: 91
Period size: 17 Copynumber: 3.4 Consensus size: 17
38600 AAATTTTGGC
*
38610 TTTTTTGGCTCTTTTTTT
1 TTTTTTGCCT-TTTTTTT
38628 TTTTTTGCCTTTTTTTT
1 TTTTTTGCCTTTTTTTT
38645 TTTTTTGCCTTTTTTGTT
1 TTTTTTGCCTTTTTT-TT
38663 TTTTTT
1 TTTTTT
38669 TTTGAAAAAA
Statistics
Matches: 39, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
17 22 0.56
18 17 0.44
ACGTcount: A:0.00, C:0.10, G:0.08, T:0.81
Consensus pattern (17 bp):
TTTTTTGCCTTTTTTTT
Found at i:40340 original size:19 final size:20
Alignment explanation
Indices: 40316--40366 Score: 68
Period size: 20 Copynumber: 2.6 Consensus size: 20
40306 CGGCCAAGAG
* *
40316 CATGTATCTTCAT-TAAAAT
1 CATGTATTTTCATCAAAAAT
40335 CATGTATTTTCATCAAAAAT
1 CATGTATTTTCATCAAAAAT
*
40355 CCTGTATTTTCA
1 CATGTATTTTCA
40367 AAGGGGTTTT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 12 0.43
20 16 0.57
ACGTcount: A:0.33, C:0.18, G:0.06, T:0.43
Consensus pattern (20 bp):
CATGTATTTTCATCAAAAAT
Found at i:40760 original size:22 final size:21
Alignment explanation
Indices: 40719--40762 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 21
40709 CACCATCTCC
*
40719 ACTTCATCATCAACATCATCA
1 ACTTCATCATCAACACCATCA
*
40740 ACTTCATCCATCAAGACCATCA
1 ACTTCAT-CATCAACACCATCA
40762 A
1 A
40763 TTCCGCATCT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 7 0.35
22 13 0.65
ACGTcount: A:0.39, C:0.34, G:0.02, T:0.25
Consensus pattern (21 bp):
ACTTCATCATCAACACCATCA
Found at i:41089 original size:17 final size:17
Alignment explanation
Indices: 41061--41110 Score: 66
Period size: 18 Copynumber: 2.8 Consensus size: 17
41051 AATTGGAGTG
41061 CAAAAAGAAAGAAAAAGA-
1 CAAAAAG-AAGAAAAA-AT
41079 CAAAAAGAAGAAAAAAT
1 CAAAAAGAAGAAAAAAT
41096 CAGAAAAGAAGAAAA
1 CA-AAAAGAAGAAAA
41111 GAAAAGAAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
16 1 0.03
17 10 0.33
18 19 0.63
ACGTcount: A:0.76, C:0.06, G:0.16, T:0.02
Consensus pattern (17 bp):
CAAAAAGAAGAAAAAAT
Found at i:41115 original size:21 final size:19
Alignment explanation
Indices: 41061--41115 Score: 53
Period size: 21 Copynumber: 2.8 Consensus size: 19
41051 AATTGGAGTG
41061 CAAAAAG-AAAGAAAAAGA
1 CAAAAAGAAAAGAAAAAGA
41079 CAAAAAGAAGAA-AAAATCAGA
1 CAAAAAGAA-AAGAAAA--AGA
41100 -AAAGAAGAAAAGAAAA
1 CAAA-AAGAAAAGAAAA
41116 GAAATTCAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 9
0.77 0.00 0.22
Matches are distributed among these distances:
18 7 0.23
19 5 0.16
20 7 0.23
21 12 0.39
ACGTcount: A:0.76, C:0.05, G:0.16, T:0.02
Consensus pattern (19 bp):
CAAAAAGAAAAGAAAAAGA
Found at i:41118 original size:18 final size:18
Alignment explanation
Indices: 41081--41119 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
41071 GAAAAAGACA
*
41081 AAAAGAAGAAAAAATCAG
1 AAAAGAAGAAAAAATAAG
41099 AAAAGAAGAAAAGAA-AAG
1 AAAAGAAGAAAA-AATAAG
41117 AAA
1 AAA
41120 TTCAAAAGAG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 17 0.89
19 2 0.11
ACGTcount: A:0.77, C:0.03, G:0.18, T:0.03
Consensus pattern (18 bp):
AAAAGAAGAAAAAATAAG
Found at i:44466 original size:19 final size:20
Alignment explanation
Indices: 44442--44492 Score: 68
Period size: 20 Copynumber: 2.6 Consensus size: 20
44432 CGGCCAAGAG
* *
44442 CATGTATCTTCAT-TAAAAT
1 CATGTATTTTCATCAAAAAT
44461 CATGTATTTTCATCAAAAAT
1 CATGTATTTTCATCAAAAAT
*
44481 CCTGTATTTTCA
1 CATGTATTTTCA
44493 AAGGGGTTTC
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 12 0.43
20 16 0.57
ACGTcount: A:0.33, C:0.18, G:0.06, T:0.43
Consensus pattern (20 bp):
CATGTATTTTCATCAAAAAT
Found at i:44886 original size:22 final size:21
Alignment explanation
Indices: 44845--44888 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 21
44835 CACCATCTCC
*
44845 ACTTCATCATCAACATCATCA
1 ACTTCATCATCAACACCATCA
*
44866 ACTTCATCCATCAAGACCATCA
1 ACTTCAT-CATCAACACCATCA
44888 A
1 A
44889 TTCCGCAACC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 7 0.35
22 13 0.65
ACGTcount: A:0.39, C:0.34, G:0.02, T:0.25
Consensus pattern (21 bp):
ACTTCATCATCAACACCATCA
Found at i:50654 original size:22 final size:21
Alignment explanation
Indices: 50626--50671 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 21
50616 AAAATAAATT
*
50626 AAAACCTTATCAG-AACACTCAC
1 AAAACCTCA-CAGTAACACTC-C
50648 AAAACCTCACAGTAACACTCC
1 AAAACCTCACAGTAACACTCC
50669 AAA
1 AAA
50672 GAAATTAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
21 7 0.32
22 15 0.68
ACGTcount: A:0.48, C:0.33, G:0.04, T:0.15
Consensus pattern (21 bp):
AAAACCTCACAGTAACACTCC
Found at i:51424 original size:16 final size:15
Alignment explanation
Indices: 51405--51443 Score: 60
Period size: 15 Copynumber: 2.5 Consensus size: 15
51395 TTTGATAATT
51405 AAGAAATGAAAATGGA
1 AAGAAATG-AAATGGA
*
51421 AAGAATTGAAATGGA
1 AAGAAATGAAATGGA
51436 AAGAAATG
1 AAGAAATG
51444 TTATCAAAGA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 14 0.67
16 7 0.33
ACGTcount: A:0.59, C:0.00, G:0.26, T:0.15
Consensus pattern (15 bp):
AAGAAATGAAATGGA
Found at i:51680 original size:36 final size:35
Alignment explanation
Indices: 51587--51697 Score: 152
Period size: 35 Copynumber: 3.2 Consensus size: 35
51577 TTGTTGGTTA
* * * *
51587 TATAGGCGTGAAATGGTGATAGAAGATGGTAAGGA
1 TATAGGCGTGAAATGGTGATGGAAGATGGTGATGT
* *
51622 TATAGGCGTGCAATGGTAATGGAAGATGGTGATGT
1 TATAGGCGTGAAATGGTGATGGAAGATGGTGATGT
51657 TATAGGCGTGAAAATGGTGATGGAAGATGGTGATGT
1 TATAGGCGTG-AAATGGTGATGGAAGATGGTGATGT
51693 T-TAGG
1 TATAGG
51698 TAGTATCTTA
Statistics
Matches: 67, Mismatches: 8, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
35 43 0.64
36 24 0.36
ACGTcount: A:0.32, C:0.04, G:0.38, T:0.27
Consensus pattern (35 bp):
TATAGGCGTGAAATGGTGATGGAAGATGGTGATGT
Found at i:55217 original size:19 final size:20
Alignment explanation
Indices: 55170--55219 Score: 66
Period size: 19 Copynumber: 2.5 Consensus size: 20
55160 GAAACCCATT
**
55170 TGAAAATACATGATTTTTGA
1 TGAAAATACATGATTTTAAA
55190 TGAAAATACATGA-TTTAAA
1 TGAAAATACATGATTTTAAA
*
55209 TGAAGATACAT
1 TGAAAATACAT
55220 ACTGTTGGCC
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
19 14 0.52
20 13 0.48
ACGTcount: A:0.46, C:0.06, G:0.14, T:0.34
Consensus pattern (20 bp):
TGAAAATACATGATTTTAAA
Found at i:62709 original size:55 final size:57
Alignment explanation
Indices: 62634--62759 Score: 152
Period size: 55 Copynumber: 2.3 Consensus size: 57
62624 AGATTCCCTT
* *
62634 TCGGACTCTTGCAC-CAATGTCTTAGCAAGCCCGATACTCTATCTT-GA-CTCAT-TA
1 TCGGACACTTGCACTCAATGTCTTAGCAAGCCCGATACTCTATCTTAAACCTC-TCTA
* * * * *
62688 TCGGACACTTGCACTTAATGTCTTGGCAAGCCCGATCCTCTGTCTTAAACCTCTCTG
1 TCGGACACTTGCACTCAATGTCTTAGCAAGCCCGATACTCTATCTTAAACCTCTCTA
62745 TCGGACACTTGCACT
1 TCGGACACTTGCACT
62760 AGTGTCTCGA
Statistics
Matches: 61, Mismatches: 7, Indels: 5
0.84 0.10 0.07
Matches are distributed among these distances:
54 13 0.21
55 27 0.44
56 2 0.03
57 19 0.31
ACGTcount: A:0.21, C:0.31, G:0.17, T:0.31
Consensus pattern (57 bp):
TCGGACACTTGCACTCAATGTCTTAGCAAGCCCGATACTCTATCTTAAACCTCTCTA
Found at i:65426 original size:2 final size:2
Alignment explanation
Indices: 65312--65413 Score: 168
Period size: 2 Copynumber: 49.5 Consensus size: 2
65302 AGTTATTTTC
65312 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
65354 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT ACT AT AGT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT A-T AT
*
65398 AT AT TT AT CAT AT AT A
1 AT AT AT AT -AT AT AT A
65414 CACATCTTAT
Statistics
Matches: 95, Mismatches: 2, Indels: 6
0.92 0.02 0.06
Matches are distributed among these distances:
2 89 0.94
3 6 0.06
ACGTcount: A:0.48, C:0.02, G:0.01, T:0.49
Consensus pattern (2 bp):
AT
Found at i:66978 original size:16 final size:18
Alignment explanation
Indices: 66948--67007 Score: 61
Period size: 17 Copynumber: 3.3 Consensus size: 18
66938 TTGGAGTGCA
66948 AAAAGAAAGAAAAAAA-C
1 AAAAGAAAGAAAAAAATC
*
66965 AAAAG-AAGAGAAAAATC
1 AAAAGAAAGAAAAAAATC
* *
66982 AAAAAAAAAAAAAGAAATTC
1 AAAAGAAAGAAAA-AAA-TC
67002 AAAAGA
1 AAAAGA
67008 GAAAACAAGC
Statistics
Matches: 34, Mismatches: 5, Indels: 5
0.77 0.11 0.11
Matches are distributed among these distances:
16 9 0.26
17 10 0.29
18 5 0.15
19 3 0.09
20 7 0.21
ACGTcount: A:0.78, C:0.05, G:0.12, T:0.05
Consensus pattern (18 bp):
AAAAGAAAGAAAAAAATC
Found at i:71553 original size:17 final size:16
Alignment explanation
Indices: 71515--71553 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 16
71505 ATTGGAGTGC
71515 AAAAAGAAAGAAAAAG
1 AAAAAGAAAGAAAAAG
*
71531 ATAAAAGAAGAGAAAAAT
1 A-AAAAGAA-AGAAAAAG
71549 AAAAA
1 AAAAA
71554 AAAATCAATA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
16 1 0.05
17 11 0.55
18 8 0.40
ACGTcount: A:0.79, C:0.00, G:0.15, T:0.05
Consensus pattern (16 bp):
AAAAAGAAAGAAAAAG
Found at i:71554 original size:18 final size:17
Alignment explanation
Indices: 71515--71554 Score: 53
Period size: 18 Copynumber: 2.3 Consensus size: 17
71505 ATTGGAGTGC
71515 AAAAAGAAAGAAAAAGA
1 AAAAAGAAAGAAAAAGA
* *
71532 TAAAAGAAGAGAAAAATA
1 AAAAAGAA-AGAAAAAGA
71550 AAAAA
1 AAAAA
71555 AAATCAATAG
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
17 7 0.37
18 12 0.63
ACGTcount: A:0.80, C:0.00, G:0.15, T:0.05
Consensus pattern (17 bp):
AAAAAGAAAGAAAAAGA
Found at i:76099 original size:18 final size:17
Alignment explanation
Indices: 76076--76125 Score: 59
Period size: 18 Copynumber: 2.9 Consensus size: 17
76066 AAATTGGAGT
76076 ACAAAAAGAAAGAAAAA
1 ACAAAAAGAAAGAAAAA
76093 GAC-AAAAGAATAGAAAAA
1 -ACAAAAAGAA-AGAAAAA
*
76111 TCAAAAA-AAAGAAAA
1 ACAAAAAGAAAGAAAA
76126 GAAAAGAAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
16 6 0.21
17 10 0.34
18 13 0.45
ACGTcount: A:0.78, C:0.06, G:0.12, T:0.04
Consensus pattern (17 bp):
ACAAAAAGAAAGAAAAA
Found at i:76101 original size:17 final size:16
Alignment explanation
Indices: 76079--76125 Score: 58
Period size: 17 Copynumber: 2.8 Consensus size: 16
76069 TTGGAGTACA
76079 AAAAGAAAGAAAAAGAC
1 AAAAGAAAGAAAAA-AC
*
76096 AAAAGAATAGAAAAATC
1 AAAAGAA-AGAAAAAAC
*
76113 AAAAAAAAGAAAA
1 AAAAGAAAGAAAA
76126 GAAAAGAAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
16 6 0.22
17 14 0.52
18 7 0.26
ACGTcount: A:0.79, C:0.04, G:0.13, T:0.04
Consensus pattern (16 bp):
AAAAGAAAGAAAAAAC
Found at i:82304 original size:19 final size:20
Alignment explanation
Indices: 82263--82313 Score: 77
Period size: 19 Copynumber: 2.6 Consensus size: 20
82253 GAAACCCCTT
*
82263 TGAAAATACATGATTTTTGA
1 TGAAAATACATGATTTTTAA
82283 TGAAAATACATGA-TTTTAA
1 TGAAAATACATGATTTTTAA
*
82302 TGAAGATACATG
1 TGAAAATACATG
82314 CTCTTGGCCG
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 16 0.55
20 13 0.45
ACGTcount: A:0.43, C:0.06, G:0.16, T:0.35
Consensus pattern (20 bp):
TGAAAATACATGATTTTTAA
Found at i:85743 original size:33 final size:33
Alignment explanation
Indices: 85682--85779 Score: 81
Period size: 33 Copynumber: 2.9 Consensus size: 33
85672 GTTGATGAAT
* * *
85682 GAAGGATGAT-TTAATGGTGATGAAATGGTAAGG
1 GAAGGATGATGTTATTGGCG-TGATATGGTAAGG
* *
85715 GAAGGATGATGTTATTGGCGTGATATGGTGATG
1 GAAGGATGATGTTATTGGCGTGATATGGTAAGG
* * *
85748 GAAGATGGTGATGATATAGGCGTGATAATGGT
1 GAAG--GATGATGTTATTGGCGTGAT-ATGGT
85780 GATGGACTAT
Statistics
Matches: 53, Mismatches: 8, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
33 24 0.45
34 7 0.13
35 17 0.32
36 5 0.09
ACGTcount: A:0.31, C:0.02, G:0.38, T:0.30
Consensus pattern (33 bp):
GAAGGATGATGTTATTGGCGTGATATGGTAAGG
Found at i:85792 original size:36 final size:36
Alignment explanation
Indices: 85721--85833 Score: 165
Period size: 36 Copynumber: 3.2 Consensus size: 36
85711 AAGGGAAGGA
* * *
85721 TGATGTTATTGGCGTGAT-ATGGTGATGGAAGATGG
1 TGATGATATAGGCGTGATAATGGTGATGGAATATGG
*
85756 TGATGATATAGGCGTGATAATGGTGATGGACTATGG
1 TGATGATATAGGCGTGATAATGGTGATGGAATATGG
* *
85792 TGATGATATAGGCGTGATAATGGAGATGGATTATGG
1 TGATGATATAGGCGTGATAATGGTGATGGAATATGG
85828 TGATGA
1 TGATGA
85834 AAATAGTATC
Statistics
Matches: 71, Mismatches: 6, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
35 16 0.23
36 55 0.77
ACGTcount: A:0.27, C:0.04, G:0.37, T:0.32
Consensus pattern (36 bp):
TGATGATATAGGCGTGATAATGGTGATGGAATATGG
Found at i:89247 original size:15 final size:15
Alignment explanation
Indices: 89216--89262 Score: 55
Period size: 14 Copynumber: 3.3 Consensus size: 15
89206 TTTTGCTTCA
*
89216 CTTTTTCTTTGCTTT
1 CTTTTTCTTTTCTTT
*
89231 -TTTTT-TATTC-TT
1 CTTTTTCTTTTCTTT
89243 CTTTTTCTTTTCTTT
1 CTTTTTCTTTTCTTT
89258 CTTTT
1 CTTTT
89263 GCACTCCAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 6
0.74 0.09 0.17
Matches are distributed among these distances:
12 2 0.08
13 8 0.31
14 9 0.35
15 7 0.27
ACGTcount: A:0.02, C:0.17, G:0.02, T:0.79
Consensus pattern (15 bp):
CTTTTTCTTTTCTTT
Found at i:89712 original size:33 final size:33
Alignment explanation
Indices: 89670--89739 Score: 88
Period size: 33 Copynumber: 2.1 Consensus size: 33
89660 GTTGATGAAT
*
89670 GAAGGATGAT-TTAATGGTGATGAAATGGTAATG
1 GAAGGATGATGTTAATGGCG-TGAAATGGTAATG
* * *
89703 GAAGGATGATGTTATTGGCGTGATATGGTGATG
1 GAAGGATGATGTTAATGGCGTGAAATGGTAATG
89736 GAAG
1 GAAG
89740 ATGGTGATGA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
33 25 0.78
34 7 0.22
ACGTcount: A:0.31, C:0.01, G:0.37, T:0.30
Consensus pattern (33 bp):
GAAGGATGATGTTAATGGCGTGAAATGGTAATG
Found at i:89780 original size:36 final size:36
Alignment explanation
Indices: 89709--89821 Score: 165
Period size: 36 Copynumber: 3.2 Consensus size: 36
89699 AATGGAAGGA
* * *
89709 TGATGTTATTGGCGTGAT-ATGGTGATGGAAGATGG
1 TGATGATATAGGCGTGATAATGGTGATGGAATATGG
*
89744 TGATGATATAGGCGTGATAATGGTGATGGACTATGG
1 TGATGATATAGGCGTGATAATGGTGATGGAATATGG
* *
89780 TGATGATATAGGCGTGATAATGGAGATGGATTATGG
1 TGATGATATAGGCGTGATAATGGTGATGGAATATGG
89816 TGATGA
1 TGATGA
89822 AAATAGTATT
Statistics
Matches: 71, Mismatches: 6, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
35 16 0.23
36 55 0.77
ACGTcount: A:0.27, C:0.04, G:0.37, T:0.32
Consensus pattern (36 bp):
TGATGATATAGGCGTGATAATGGTGATGGAATATGG
Found at i:91785 original size:24 final size:25
Alignment explanation
Indices: 91739--91793 Score: 60
Period size: 24 Copynumber: 2.3 Consensus size: 25
91729 ACAGTTATGC
*
91739 CACTTGAAGTTCAAAAAGATGTG-T
1 CACTTGAAGTGCAAAAAGATGTGAT
* * *
91763 CACTTGAAGTGCCACAAGTTGTGAT
1 CACTTGAAGTGCAAAAAGATGTGAT
91788 CA-TTGA
1 CACTTGA
91794 GGCTCCAAGT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
24 23 0.88
25 3 0.12
ACGTcount: A:0.33, C:0.16, G:0.22, T:0.29
Consensus pattern (25 bp):
CACTTGAAGTGCAAAAAGATGTGAT
Found at i:94239 original size:24 final size:24
Alignment explanation
Indices: 94212--94262 Score: 59
Period size: 24 Copynumber: 2.1 Consensus size: 24
94202 CTCAGAAAAC
* *
94212 AAAATGAAGCACTC-AAAAGAAAGA
1 AAAATCAAGAACTCAAAAAG-AAGA
*
94236 AAAATCCAGAACTCAAAAAGAAGA
1 AAAATCAAGAACTCAAAAAGAAGA
94260 AAA
1 AAA
94263 GCAAAGAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
24 18 0.78
25 5 0.22
ACGTcount: A:0.65, C:0.14, G:0.14, T:0.08
Consensus pattern (24 bp):
AAAATCAAGAACTCAAAAAGAAGA
Found at i:94267 original size:15 final size:15
Alignment explanation
Indices: 94256--94284 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
94246 ACTCAAAAAG
94256 AAGAAAAGCAAAGAA
1 AAGAAAAGCAAAGAA
94271 AAGAAAAG-AAAGAA
1 AAGAAAAGCAAAGAA
94285 GTTGAAGCAC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 6 0.43
15 8 0.57
ACGTcount: A:0.76, C:0.03, G:0.21, T:0.00
Consensus pattern (15 bp):
AAGAAAAGCAAAGAA
Found at i:95610 original size:24 final size:25
Alignment explanation
Indices: 95564--95618 Score: 60
Period size: 24 Copynumber: 2.3 Consensus size: 25
95554 ACAGTTATGC
*
95564 CACTTGAAGTTCAAAAAGATGTG-T
1 CACTTGAAGTGCAAAAAGATGTGAT
* * *
95588 CACTTGAAGTGCCACAAGTTGTGAT
1 CACTTGAAGTGCAAAAAGATGTGAT
95613 CA-TTGA
1 CACTTGA
95619 GGCTCCAAGT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
24 23 0.88
25 3 0.12
ACGTcount: A:0.33, C:0.16, G:0.22, T:0.29
Consensus pattern (25 bp):
CACTTGAAGTGCAAAAAGATGTGAT
Found at i:98048 original size:24 final size:24
Alignment explanation
Indices: 98027--98077 Score: 68
Period size: 24 Copynumber: 2.1 Consensus size: 24
98017 CTCGGAAAAC
*
98027 AAAATGAAGCACTCAAAAGAAAGA
1 AAAATCAAGCACTCAAAAGAAAGA
*
98051 AAAATCCAGCACTCAAAA-AGAAGA
1 AAAATCAAGCACTCAAAAGA-AAGA
98075 AAA
1 AAA
98078 GCAAAGAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
23 1 0.04
24 23 0.96
ACGTcount: A:0.63, C:0.16, G:0.14, T:0.08
Consensus pattern (24 bp):
AAAATCAAGCACTCAAAAGAAAGA
Found at i:98082 original size:15 final size:15
Alignment explanation
Indices: 98071--98099 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
98061 ACTCAAAAAG
98071 AAGAAAAGCAAAGAA
1 AAGAAAAGCAAAGAA
98086 AAGAAAAG-AAAGAA
1 AAGAAAAGCAAAGAA
98100 GTTGAAGCAC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 6 0.43
15 8 0.57
ACGTcount: A:0.76, C:0.03, G:0.21, T:0.00
Consensus pattern (15 bp):
AAGAAAAGCAAAGAA
Found at i:99423 original size:24 final size:25
Alignment explanation
Indices: 99377--99431 Score: 60
Period size: 24 Copynumber: 2.3 Consensus size: 25
99367 ACAGTTATGC
*
99377 CACTTGAAGTTCAAAAAGATGTG-T
1 CACTTGAAGTGCAAAAAGATGTGAT
* * *
99401 CACTTGAAGTGCCACAAGTTGTGAT
1 CACTTGAAGTGCAAAAAGATGTGAT
99426 CA-TTGA
1 CACTTGA
99432 GGCTCCAAGT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
24 23 0.88
25 3 0.12
ACGTcount: A:0.33, C:0.16, G:0.22, T:0.29
Consensus pattern (25 bp):
CACTTGAAGTGCAAAAAGATGTGAT
Found at i:102083 original size:30 final size:31
Alignment explanation
Indices: 102047--102106 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 31
102037 CTTAGCTTTA
**
102047 TATTATGTTTACATATGTTTTAGAT-TCATT
1 TATTATGTTTACATATCATTTAGATATCATT
*
102077 TATTATGTTTGCATATCATTTAGATATCAT
1 TATTATGTTTACATATCATTTAGATATCAT
102107 GGCAGCATGT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 22 0.85
31 4 0.15
ACGTcount: A:0.28, C:0.08, G:0.10, T:0.53
Consensus pattern (31 bp):
TATTATGTTTACATATCATTTAGATATCATT
Found at i:103050 original size:20 final size:19
Alignment explanation
Indices: 103003--103053 Score: 57
Period size: 20 Copynumber: 2.6 Consensus size: 19
102993 CGGCCAAGAG
* *
103003 CATGTATCTTCATTAAAAT
1 CATGTATTTTCATAAAAAT
**
103022 CATACATTTTCATCAAAAAT
1 CATGTATTTTCAT-AAAAAT
103042 CATGTATTTTCA
1 CATGTATTTTCA
103054 AAGGGGTTTT
Statistics
Matches: 25, Mismatches: 6, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
19 10 0.40
20 15 0.60
ACGTcount: A:0.37, C:0.18, G:0.04, T:0.41
Consensus pattern (19 bp):
CATGTATTTTCATAAAAAT
Found at i:109241 original size:22 final size:21
Alignment explanation
Indices: 109200--109243 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 21
109190 CACCATCTCC
*
109200 ACTTCATCATCAACATCATCA
1 ACTTCATCATCAACACCATCA
*
109221 ACTTCATCCATCAAGACCATCA
1 ACTTCAT-CATCAACACCATCA
109243 A
1 A
109244 TTCCGCAACC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 7 0.35
22 13 0.65
ACGTcount: A:0.39, C:0.34, G:0.02, T:0.25
Consensus pattern (21 bp):
ACTTCATCATCAACACCATCA
Found at i:117086 original size:13 final size:11
Alignment explanation
Indices: 117045--117129 Score: 66
Period size: 11 Copynumber: 7.2 Consensus size: 11
117035 ACAATCTATC
117045 CATCACCATTAT
1 CATCACCA-TAT
*
117057 CA-CGCCTATAT
1 CATCACC-ATAT
117068 CATCACCATAGT
1 CATCACCATA-T
117080 CCATCACCATTAT
1 -CATCACCA-TAT
*
117093 CA-CGCCTATAT
1 CATCACC-ATAT
117104 CATCACCATATT
1 CATCACCATA-T
117116 CCATCACCATAT
1 -CATCACCATAT
117128 CA
1 CA
117130 CGCCTATATT
Statistics
Matches: 60, Mismatches: 4, Indels: 19
0.72 0.05 0.23
Matches are distributed among these distances:
11 24 0.40
12 15 0.25
13 19 0.32
14 2 0.03
ACGTcount: A:0.32, C:0.36, G:0.04, T:0.28
Consensus pattern (11 bp):
CATCACCATAT
Found at i:117090 original size:36 final size:36
Alignment explanation
Indices: 117043--117146 Score: 183
Period size: 36 Copynumber: 2.9 Consensus size: 36
117033 ATACAATCTA
117043 TCCATCACCATTATCACGCCTATATCATCACCATAG
1 TCCATCACCATTATCACGCCTATATCATCACCATAG
*
117079 TCCATCACCATTATCACGCCTATATCATCACCATAT
1 TCCATCACCATTATCACGCCTATATCATCACCATAG
*
117115 TCCATCACCA-TATCACGCCTATATTATCACCA
1 TCCATCACCATTATCACGCCTATATCATCACCA
117147 ACTTATAAAT
Statistics
Matches: 66, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
35 21 0.32
36 45 0.68
ACGTcount: A:0.31, C:0.37, G:0.04, T:0.29
Consensus pattern (36 bp):
TCCATCACCATTATCACGCCTATATCATCACCATAG
Found at i:117630 original size:14 final size:15
Alignment explanation
Indices: 117596--117642 Score: 51
Period size: 14 Copynumber: 3.1 Consensus size: 15
117586 AATTTGGAGT
117596 GCAAAAGAAAGAAAA
1 GCAAAAGAAAGAAAA
*
117611 GAAAAAG-AAGAAAA
1 GCAAAAGAAAGAAAA
*
117625 TCAAAAGCAAAAGAAAA
1 GCAAAAG--AAAGAAAA
117642 G
1 G
117643 TGAAGCAAGT
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
14 12 0.48
15 6 0.24
17 7 0.28
ACGTcount: A:0.72, C:0.06, G:0.19, T:0.02
Consensus pattern (15 bp):
GCAAAAGAAAGAAAA
Found at i:121602 original size:13 final size:11
Alignment explanation
Indices: 121561--121645 Score: 66
Period size: 11 Copynumber: 7.2 Consensus size: 11
121551 ACAATCTATC
121561 CATCACCATTAT
1 CATCACCA-TAT
*
121573 CA-CGCCTATAT
1 CATCACC-ATAT
121584 CATCACCATAGT
1 CATCACCATA-T
121596 CCATCACCATTAT
1 -CATCACCA-TAT
*
121609 CA-CGCCTATAT
1 CATCACC-ATAT
121620 CATCACCATATT
1 CATCACCATA-T
121632 CCATCACCATAT
1 -CATCACCATAT
121644 CA
1 CA
121646 CGCCTATATT
Statistics
Matches: 60, Mismatches: 4, Indels: 19
0.72 0.05 0.23
Matches are distributed among these distances:
11 24 0.40
12 15 0.25
13 19 0.32
14 2 0.03
ACGTcount: A:0.32, C:0.36, G:0.04, T:0.28
Consensus pattern (11 bp):
CATCACCATAT
Found at i:121606 original size:36 final size:36
Alignment explanation
Indices: 121559--121662 Score: 183
Period size: 36 Copynumber: 2.9 Consensus size: 36
121549 ATACAATCTA
121559 TCCATCACCATTATCACGCCTATATCATCACCATAG
1 TCCATCACCATTATCACGCCTATATCATCACCATAG
*
121595 TCCATCACCATTATCACGCCTATATCATCACCATAT
1 TCCATCACCATTATCACGCCTATATCATCACCATAG
*
121631 TCCATCACCA-TATCACGCCTATATTATCACCA
1 TCCATCACCATTATCACGCCTATATCATCACCA
121663 ACTTATAAAT
Statistics
Matches: 66, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
35 21 0.32
36 45 0.68
ACGTcount: A:0.31, C:0.37, G:0.04, T:0.29
Consensus pattern (36 bp):
TCCATCACCATTATCACGCCTATATCATCACCATAG
Found at i:127408 original size:27 final size:28
Alignment explanation
Indices: 127378--127439 Score: 74
Period size: 27 Copynumber: 2.2 Consensus size: 28
127368 CTTTTCTTTG
* **
127378 CTTTTCTTCTTTTTGAGTGC-TGGATTT
1 CTTTTCTTCTTTTGGAGTGCTTCAATTT
127405 C-TTTCTTTCTTTTGGAGTGCTTCAATTT
1 CTTTTC-TTCTTTTGGAGTGCTTCAATTT
127433 CTTTTCT
1 CTTTTCT
127440 GATTTTTTTT
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
26 4 0.14
27 14 0.48
28 7 0.24
29 4 0.14
ACGTcount: A:0.08, C:0.18, G:0.15, T:0.60
Consensus pattern (28 bp):
CTTTTCTTCTTTTGGAGTGCTTCAATTT
Found at i:133164 original size:17 final size:17
Alignment explanation
Indices: 133072--133193 Score: 77
Period size: 17 Copynumber: 7.1 Consensus size: 17
133062 TTTAAACATG
* *
133072 TAGTTCATTGATTAAAT
1 TAGTTCATTAATTAAAC
* * *
133089 TATTTCATTCATTGAAC
1 TAGTTCATTAATTAAAC
* ** *
133106 TATTTCATTAAAGATTAC
1 TAGTTCATTAATTA-AAC
* *
133124 AAGTTCATTGAA-TAAAGT
1 TAGTTCATT-AATTAAA-C
133142 TAGTTCATTAATTAAAC
1 TAGTTCATTAATTAAAC
*
133159 TAGTTCATT-ATCAAAC
1 TAGTTCATTAATTAAAC
* *
133175 TAGATCATTTATTAAAC
1 TAGTTCATTAATTAAAC
133192 TA
1 TA
133194 ACTCTTAATT
Statistics
Matches: 81, Mismatches: 19, Indels: 10
0.74 0.17 0.09
Matches are distributed among these distances:
16 14 0.17
17 43 0.53
18 22 0.27
19 2 0.02
ACGTcount: A:0.39, C:0.11, G:0.08, T:0.42
Consensus pattern (17 bp):
TAGTTCATTAATTAAAC
Found at i:134934 original size:36 final size:36
Alignment explanation
Indices: 134882--134994 Score: 174
Period size: 36 Copynumber: 3.2 Consensus size: 36
134872 GATACTATTT
*
134882 TCATCACCATAATCCATCTCCATTATCACGCCTATA
1 TCATCACCATAATCCATCACCATTATCACGCCTATA
*
134918 TCATCACCATAGTCCATCACCATTATCACGCCTATA
1 TCATCACCATAATCCATCACCATTATCACGCCTATA
* *
134954 TCATCACCATATTCCATCACCA-TATCACGCCAATA
1 TCATCACCATAATCCATCACCATTATCACGCCTATA
*
134989 ACATCA
1 TCATCA
134995 TCCTTCCATT
Statistics
Matches: 72, Mismatches: 5, Indels: 1
0.92 0.06 0.01
Matches are distributed among these distances:
35 17 0.24
36 55 0.76
ACGTcount: A:0.33, C:0.36, G:0.04, T:0.27
Consensus pattern (36 bp):
TCATCACCATAATCCATCACCATTATCACGCCTATA
Found at i:134937 original size:13 final size:11
Alignment explanation
Indices: 134882--134980 Score: 67
Period size: 13 Copynumber: 8.3 Consensus size: 11
134872 GATACTATTT
134882 TCATCACCATAA
1 TCATCACCAT-A
*
134894 TCCATCTCCATTA
1 T-CATCACCA-TA
*
134907 TCA-CGCCTATA
1 TCATCACC-ATA
134918 TCATCACCATA
1 TCATCACCATA
134929 GTCCATCACCATTA
1 -T-CATCACCA-TA
*
134943 TCA-CGCCTATA
1 TCATCACC-ATA
134954 TCATCACCATA
1 TCATCACCATA
134965 TTCCATCACCATA
1 -T-CATCACCATA
134978 TCA
1 TCA
134981 CGCCAATAAC
Statistics
Matches: 71, Mismatches: 5, Indels: 23
0.72 0.05 0.23
Matches are distributed among these distances:
11 24 0.34
12 16 0.23
13 28 0.39
14 3 0.04
ACGTcount: A:0.31, C:0.36, G:0.03, T:0.29
Consensus pattern (11 bp):
TCATCACCATA
Found at i:135009 original size:33 final size:33
Alignment explanation
Indices: 134894--135033 Score: 97
Period size: 36 Copynumber: 4.1 Consensus size: 33
134884 ATCACCATAA
* * *
134894 TCCATCTCCATTATCACGCCTATATCATCA-CCAT
1 TCCATCACCA-TATCACGCCAATAACATCATCC-T
* *
134928 AGTCCATCACCATTATCACGCCTATATCATCA-CCATAT
1 --TCCATCACCA-TATCACGCCAATAACATCATCC---T
134966 TCCATCACCATATCACGCCAATAACATCATCCT
1 TCCATCACCATATCACGCCAATAACATCATCCT
* * * *
134999 TCCATTACCATTTCATCACCATTAA-ATCATCCT
1 TCCATCACCATATCA-CGCCAATAACATCATCCT
135032 TC
1 TC
135034 ATTCATCAAC
Statistics
Matches: 93, Mismatches: 7, Indels: 11
0.84 0.06 0.10
Matches are distributed among these distances:
33 24 0.26
34 7 0.08
35 17 0.18
36 43 0.46
38 2 0.02
ACGTcount: A:0.30, C:0.36, G:0.03, T:0.31
Consensus pattern (33 bp):
TCCATCACCATATCACGCCAATAACATCATCCT
Found at i:139428 original size:36 final size:36
Alignment explanation
Indices: 139371--139488 Score: 175
Period size: 36 Copynumber: 3.3 Consensus size: 36
139361 TTATAAGATA
* *
139371 CTATTTCATCACCATAATCCATCTCCATTATCACGC
1 CTATATCATCACCATAATCCATCACCATTATCACGC
*
139407 CTATATCATCACCATAGTCCATCACCATTATCACGC
1 CTATATCATCACCATAATCCATCACCATTATCACGC
*
139443 CTATATCATCACCATATTCCATCACCA-TATCACGC
1 CTATATCATCACCATAATCCATCACCATTATCACGC
* *
139478 CAATAACATCA
1 CTATATCATCA
139489 TCCTTCCATT
Statistics
Matches: 76, Mismatches: 6, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
35 17 0.22
36 59 0.78
ACGTcount: A:0.32, C:0.36, G:0.03, T:0.29
Consensus pattern (36 bp):
CTATATCATCACCATAATCCATCACCATTATCACGC
Found at i:139431 original size:13 final size:11
Alignment explanation
Indices: 139376--139474 Score: 67
Period size: 13 Copynumber: 8.3 Consensus size: 11
139366 AGATACTATT
139376 TCATCACCATAA
1 TCATCACCAT-A
*
139388 TCCATCTCCATTA
1 T-CATCACCA-TA
*
139401 TCA-CGCCTATA
1 TCATCACC-ATA
139412 TCATCACCATA
1 TCATCACCATA
139423 GTCCATCACCATTA
1 -T-CATCACCA-TA
*
139437 TCA-CGCCTATA
1 TCATCACC-ATA
139448 TCATCACCATA
1 TCATCACCATA
139459 TTCCATCACCATA
1 -T-CATCACCATA
139472 TCA
1 TCA
139475 CGCCAATAAC
Statistics
Matches: 71, Mismatches: 5, Indels: 23
0.72 0.05 0.23
Matches are distributed among these distances:
11 24 0.34
12 16 0.23
13 28 0.39
14 3 0.04
ACGTcount: A:0.31, C:0.36, G:0.03, T:0.29
Consensus pattern (11 bp):
TCATCACCATA
Found at i:139503 original size:33 final size:33
Alignment explanation
Indices: 139388--139527 Score: 97
Period size: 36 Copynumber: 4.1 Consensus size: 33
139378 ATCACCATAA
* * *
139388 TCCATCTCCATTATCACGCCTATATCATCA-CCAT
1 TCCATCACCA-TATCACGCCAATAACATCATCC-T
* *
139422 AGTCCATCACCATTATCACGCCTATATCATCA-CCATAT
1 --TCCATCACCA-TATCACGCCAATAACATCATCC---T
139460 TCCATCACCATATCACGCCAATAACATCATCCT
1 TCCATCACCATATCACGCCAATAACATCATCCT
* * * *
139493 TCCATTACCATTTCATCACCATTAA-ATCATCCT
1 TCCATCACCATATCA-CGCCAATAACATCATCCT
139526 TC
1 TC
139528 ATTCATCAAC
Statistics
Matches: 93, Mismatches: 7, Indels: 11
0.84 0.06 0.10
Matches are distributed among these distances:
33 24 0.26
34 7 0.08
35 17 0.18
36 43 0.46
38 2 0.02
ACGTcount: A:0.30, C:0.36, G:0.03, T:0.31
Consensus pattern (33 bp):
TCCATCACCATATCACGCCAATAACATCATCCT
Done.