Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01015957.1 Corchorus capsularis cultivar CVL-1 contig15978, 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: 51161
ACGTcount: A:0.33, C:0.19, G:0.19, T:0.29
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:1769 original size:21 final size:21
Alignment explanation
Indices: 1743--1806 Score: 85
Period size: 21 Copynumber: 3.0 Consensus size: 21
1733 GAATATTCTC
1743 ATCTGTACAGTAACAAATTTT
1 ATCTGTACAGTAACAAATTTT
* *
1764 ATCTGTACAGTAACAAATCTA
1 ATCTGTACAGTAACAAATTTT
*
1785 ATAC-GTACAGTAACCAATTTT
1 AT-CTGTACAGTAACAAATTTT
1806 A
1 A
1807 CTCTCACCGA
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
21 36 0.97
22 1 0.03
ACGTcount: A:0.41, C:0.17, G:0.09, T:0.33
Consensus pattern (21 bp):
ATCTGTACAGTAACAAATTTT
Found at i:9934 original size:25 final size:24
Alignment explanation
Indices: 9900--9958 Score: 84
Period size: 25 Copynumber: 2.5 Consensus size: 24
9890 TTCAAACCCT
*
9900 AAACTTCATTTCTAACAACTTCTTC
1 AAACTTCATTTCTAACAA-ATCTTC
*
9925 AAACTTCATTTTTAACAAATCTTC
1 AAACTTCATTTCTAACAAATCTTC
9949 AAA-TTCATTT
1 AAACTTCATTT
9959 TCCTTCATTT
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
23 7 0.22
24 8 0.25
25 17 0.53
ACGTcount: A:0.36, C:0.22, G:0.00, T:0.42
Consensus pattern (24 bp):
AAACTTCATTTCTAACAAATCTTC
Found at i:9997 original size:26 final size:26
Alignment explanation
Indices: 9968--10035 Score: 109
Period size: 26 Copynumber: 2.6 Consensus size: 26
9958 TTCCTTCATT
9968 TTAATCATAAACTAATTAAATACTAA
1 TTAATCATAAACTAATTAAATACTAA
* *
9994 TTAATAATAAACTAATTAGATACTAA
1 TTAATCATAAACTAATTAAATACTAA
*
10020 TTAAACATAAACTAAT
1 TTAATCATAAACTAAT
10036 AAACTAAGTA
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
26 38 1.00
ACGTcount: A:0.54, C:0.10, G:0.01, T:0.34
Consensus pattern (26 bp):
TTAATCATAAACTAATTAAATACTAA
Found at i:10059 original size:52 final size:51
Alignment explanation
Indices: 9968--10085 Score: 122
Period size: 52 Copynumber: 2.4 Consensus size: 51
9958 TTCCTTCATT
* *
9968 TTAATCATAAACTAATTAAATACTAATTAATAATAAACTAATTAGATACTAA
1 TTAAACATAAACTAATTAAATACTAATTAATAATAAACTAATTA-AAACTAA
* * *
10020 TTAAACATAAACTAA-TAAACTAAGTAATT-TTAATTAACTAATTAAAACTAA
1 TTAAACATAAACTAATTAAA-T-ACTAATTAATAATAAACTAATTAAAACTAA
10071 -T---CATAAACTAATTAA
1 TTAAACATAAACTAATTAA
10086 TATTAAAAAA
Statistics
Matches: 58, Mismatches: 5, Indels: 10
0.79 0.07 0.14
Matches are distributed among these distances:
47 10 0.17
48 3 0.05
50 1 0.02
51 10 0.17
52 28 0.48
53 6 0.10
ACGTcount: A:0.54, C:0.10, G:0.02, T:0.34
Consensus pattern (51 bp):
TTAAACATAAACTAATTAAATACTAATTAATAATAAACTAATTAAAACTAA
Found at i:10480 original size:2 final size:2
Alignment explanation
Indices: 10469--10512 Score: 58
Period size: 2 Copynumber: 23.5 Consensus size: 2
10459 GTAAATGTAA
*
10469 AT AT AT -T AT AT AT AT AT AT AT -T AT AT A- AT AA 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
10508 AT AT A
1 AT AT A
10513 ATAATAGTAG
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
1 3 0.08
2 34 0.92
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:10495 original size:22 final size:22
Alignment explanation
Indices: 10469--10518 Score: 68
Period size: 22 Copynumber: 2.4 Consensus size: 22
10459 GTAAATGTAA
* *
10469 ATATATTATATATATATATATT
1 ATATAATAAATATATATATATT
10491 ATATAATAAATATATATATA-T
1 ATATAATAAATATATATATATT
10512 A-ATAATA
1 ATATAATA
10519 GTAGTAATAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
20 6 0.23
21 2 0.08
22 18 0.69
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (22 bp):
ATATAATAAATATATATATATT
Found at i:10503 original size:20 final size:19
Alignment explanation
Indices: 10469--10518 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 19
10459 GTAAATGTAA
* *
10469 ATATATTATATATATATAT
1 ATATATAATAAATATATAT
10488 ATTATATAATAAATATATAT
1 A-TATATAATAAATATATAT
10508 ATATAATAATA
1 ATAT-ATAATA
10519 GTAGTAATAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
19 4 0.15
20 23 0.85
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (19 bp):
ATATATAATAAATATATAT
Found at i:11710 original size:15 final size:15
Alignment explanation
Indices: 11686--11715 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
11676 AGGCCTTGTC
11686 GGTGAAATTGAAAAT
1 GGTGAAATTGAAAAT
*
11701 GGTGAGATTGAAAAT
1 GGTGAAATTGAAAAT
11716 AATGATGACG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.43, C:0.00, G:0.30, T:0.27
Consensus pattern (15 bp):
GGTGAAATTGAAAAT
Found at i:13657 original size:123 final size:123
Alignment explanation
Indices: 13432--13684 Score: 299
Period size: 123 Copynumber: 2.1 Consensus size: 123
13422 TATTAACCAA
* * *
13432 ATGAACCGAAAACTATTTTTTGTAAAACGTTAACCGAACCGAAGTATCCTATCCCGAACATCAAC
1 ATGAACCGAAAACTATTTTTTGTAAAACATTAACCGAACCAAAGAATCCTATCCCGAACATCAAC
* * * * *
13497 CGAACTGAAATATTTCGATTAACCAACCGGATGATATTTTAACATAAATTTTAAATTT
66 CGAACCGAAATATATCGATCAACCAACCGAATGATATTTTAACATAAATTTAAAATTT
* * * * * *
13555 ATGAACCGAACACTATTTTTTGTAAATCATTAACCGATCCAAAGAATCTTATTCCGAACATTAAC
1 ATGAACCGAAAACTATTTTTTGTAAAACATTAACCGAACCAAAGAATCCTATCCCGAACATCAAC
* ***** * *
13620 CGAACCGAAATATATCGGTCAATTGGTCGAATTATATTTTAACTTAAATTTAAAATTT
66 CGAACCGAAATATATCGATCAACCAACCGAATGATATTTTAACATAAATTTAAAATTT
*
13678 ATTAACC
1 ATGAACC
13685 AAATTAGTAT
Statistics
Matches: 107, Mismatches: 23, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
123 107 1.00
ACGTcount: A:0.39, C:0.19, G:0.11, T:0.32
Consensus pattern (123 bp):
ATGAACCGAAAACTATTTTTTGTAAAACATTAACCGAACCAAAGAATCCTATCCCGAACATCAAC
CGAACCGAAATATATCGATCAACCAACCGAATGATATTTTAACATAAATTTAAAATTT
Found at i:13761 original size:146 final size:147
Alignment explanation
Indices: 13555--13826 Score: 393
Period size: 146 Copynumber: 1.9 Consensus size: 147
13545 TTTTAAATTT
* * * *
13555 ATGAACCGAACACTATTTTTTGTAAATCATTAACCGATCCAAAGAATCTTATTCCGAACATTAAC
1 ATGAACCGAACACTATTGTTTGTAAAACATTAACCGAACCAAAGAATCCTATTCCGAACATTAAC
* * **
13620 CGAACCGAAATATATCGGTCAATTGGTCGAATTATATTTTAACTTAAATTTAAAATTTATTAACC
66 CGAACCAAAATATATCGGTCAATCGACCGAATTATATTTTAACTTAAATTTAAAATTTATTAACC
13685 AAATTAGTATTAACCGA
131 AAATTAGTATTAACCGA
* * * ** *
13702 ATGAACCGAATACTA-TGTTTGTAAAACATTAATCGAACCGAAGTTTCCTATTCCTAACATTAAC
1 ATGAACCGAACACTATTGTTTGTAAAACATTAACCGAACCAAAGAATCCTATTCCGAACATTAAC
* *
13766 CGAACCAAAATATTTCGGTTAATCGACCGAATTATATTTTAACTTAAATTTAAAATTTATT
66 CGAACCAAAATATATCGGTCAATCGACCGAATTATATTTTAACTTAAATTTAAAATTTATT
13827 TTACTATAAT
Statistics
Matches: 109, Mismatches: 16, Indels: 1
0.87 0.13 0.01
Matches are distributed among these distances:
146 95 0.87
147 14 0.13
ACGTcount: A:0.39, C:0.17, G:0.10, T:0.34
Consensus pattern (147 bp):
ATGAACCGAACACTATTGTTTGTAAAACATTAACCGAACCAAAGAATCCTATTCCGAACATTAAC
CGAACCAAAATATATCGGTCAATCGACCGAATTATATTTTAACTTAAATTTAAAATTTATTAACC
AAATTAGTATTAACCGA
Found at i:16631 original size:23 final size:22
Alignment explanation
Indices: 16595--16659 Score: 67
Period size: 23 Copynumber: 2.9 Consensus size: 22
16585 GAAGACCTCA
*
16595 ATATGAAATTTTGATAACCAAC
1 ATATGAAATATTGATAACCAAC
* * **
16617 ACTATGAGATGTTGATAACCTCC
1 A-TATGAAATATTGATAACCAAC
*
16640 ATATGATATATTGATAACCA
1 ATATGAAATATTGATAACCA
16660 CGTTATGAAA
Statistics
Matches: 35, Mismatches: 7, Indels: 2
0.80 0.16 0.05
Matches are distributed among these distances:
22 17 0.49
23 18 0.51
ACGTcount: A:0.40, C:0.15, G:0.12, T:0.32
Consensus pattern (22 bp):
ATATGAAATATTGATAACCAAC
Found at i:16723 original size:22 final size:22
Alignment explanation
Indices: 16596--16965 Score: 111
Period size: 22 Copynumber: 16.7 Consensus size: 22
16586 AAGACCTCAA
*
16596 TATGAAATTTTGATAACCAACAC
1 TATGAAATTTTGATAATC-ACAC
* *
16619 TATGAGATGTTGATAACCTC-CA-
1 TATGAAATTTTGATAA--TCACAC
* * * **
16641 TATGATATATTGATAACCACGT
1 TATGAAATTTTGATAATCACAC
* * *
16663 TATGAAAATTTAAAAACCTC-CA-
1 TATGAAATTTTGATAA--TCACAC
16685 TATG-AATTGTT-AGTAATCACAC
1 TATGAAATT-TTGA-TAATCACAC
*
16707 TCTGAAATTTTGATAATCACAC
1 TATGAAATTTTGATAATCACAC
* * *
16729 TATGAAATTGTGATAACCTCAC
1 TATGAAATTTTGATAATCACAC
* *
16751 TATGAAATTTTAATAAATCTTC-C
1 TATGAAATTTTGAT-AATC-ACAC
* **
16774 TATAAAATTTTGATAAACTTTC-C
1 TATGAAATTTTGAT-AA-TCACAC
* * *
16797 TATAAAATTTTGATAACCTC-C
1 TATGAAATTTTGATAATCACAC
** * *
16818 TTATGATTTTTTGAT-ATCCTCAT
1 -TATGAAATTTTGATAAT-CACAC
* * * *
16841 TATGAAACTTTGTTAATCTCCC
1 TATGAAATTTTGATAATCACAC
* *
16863 TATGAAATTTTGAT-TTACATAC
1 TATGAAATTTTGATAAT-CACAC
* * *
16885 TGTGAAATTTTGATAA-CCCTC
1 TATGAAATTTTGATAATCACAC
* * *
16906 TTGTGAAATTTTGA-AAACTAAAC
1 -TATGAAATTTTGATAATC-ACAC
* * *
16929 TATGAAATTTTCATAACCTTCA-
1 TATGAAATTTTGATAATC-ACAC
16951 TATGAAATTTTGATA
1 TATGAAATTTTGATA
16966 TCCTCCCTGA
Statistics
Matches: 262, Mismatches: 60, Indels: 51
0.70 0.16 0.14
Matches are distributed among these distances:
20 3 0.01
21 16 0.06
22 172 0.66
23 66 0.25
24 4 0.02
25 1 0.00
ACGTcount: A:0.36, C:0.15, G:0.10, T:0.39
Consensus pattern (22 bp):
TATGAAATTTTGATAATCACAC
Found at i:16781 original size:23 final size:23
Alignment explanation
Indices: 16750--16812 Score: 92
Period size: 23 Copynumber: 2.7 Consensus size: 23
16740 GATAACCTCA
* *
16750 CTATGAAATTTTAATAAA-TCTTC
1 CTATAAAATTTTGATAAACT-TTC
16773 CTATAAAATTTTGATAAACTTTC
1 CTATAAAATTTTGATAAACTTTC
16796 CTATAAAATTTTGATAA
1 CTATAAAATTTTGATAA
16813 CCTCCTTATG
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
23 36 0.97
24 1 0.03
ACGTcount: A:0.41, C:0.11, G:0.05, T:0.43
Consensus pattern (23 bp):
CTATAAAATTTTGATAAACTTTC
Found at i:17000 original size:20 final size:20
Alignment explanation
Indices: 16931--17003 Score: 85
Period size: 19 Copynumber: 3.6 Consensus size: 20
16921 AACTAAACTA
* *
16931 TGAAATTTTCATAACCTTCAT
1 TGAAATTTTGATATCCTTC-T
* *
16952 ATGAAATTTTGATATCCTCCC
1 -TGAAATTTTGATATCCTTCT
16973 TG-AATTTTGATATCCTTCT
1 TGAAATTTTGATATCCTTCT
16992 TGAAATTTTGAT
1 TGAAATTTTGAT
17004 TACTCCATAA
Statistics
Matches: 44, Mismatches: 6, Indels: 4
0.81 0.11 0.07
Matches are distributed among these distances:
19 17 0.39
20 11 0.25
22 16 0.36
ACGTcount: A:0.29, C:0.16, G:0.10, T:0.45
Consensus pattern (20 bp):
TGAAATTTTGATATCCTTCT
Found at i:17176 original size:22 final size:21
Alignment explanation
Indices: 17085--17312 Score: 110
Period size: 22 Copynumber: 10.5 Consensus size: 21
17075 GAAATACCAC
17085 TATGAAATTTTTG-TAATCACAT
1 TATGAAA-TTTTGATAATCAC-T
* * * *
17107 TCTGAAAATTTGATAACCTCTT
1 TATGAAATTTTGATAATCAC-T
* * * * *
17129 TATAAAATTTTGTTGACCCCT
1 TATGAAATTTTGATAATCACT
*
17150 CTATGAAATTCTGATAATCACAT
1 -TATGAAATTTTGATAATCAC-T
*
17173 TATGTAATTTTGATAACCTCACT
1 TATGAAATTTTGATAA--TCACT
**
17196 T-TGAAATTTTGATAATCTTT
1 TATGAAATTTTGATAATCACT
17216 CTAT-AAATTTTGATAATCCGATCT
1 -TATGAAATTTTGATAAT-C-A-CT
*
17240 CTATGAAATTTCGATAATCACTT
1 -TATGAAATTTTGATAATCAC-T
*
17263 TATGAGA-TTTGATAA-C-CTT
1 TATGAAATTTTGATAATCAC-T
* * *
17282 CTATAAAATTTTGGTACTC-CT
1 -TATGAAATTTTGATAATCACT
17303 TATGAAATTT
1 TATGAAATTT
17313 AGACTTTTAT
Statistics
Matches: 159, Mismatches: 32, Indels: 32
0.71 0.14 0.14
Matches are distributed among these distances:
19 3 0.02
20 18 0.11
21 33 0.21
22 78 0.49
23 5 0.03
24 10 0.06
25 12 0.08
ACGTcount: A:0.33, C:0.14, G:0.10, T:0.43
Consensus pattern (21 bp):
TATGAAATTTTGATAATCACT
Found at i:17274 original size:46 final size:43
Alignment explanation
Indices: 17112--17292 Score: 138
Period size: 44 Copynumber: 4.1 Consensus size: 43
17102 CACATTCTGA
* * * * * *
17112 AAATTT-GATAACCTCTTTATAAAATTTTGTTGACCCCTCTATG
1 AAATTTCGATAATCACTTTAT-GAATTTTGATAACCTCTCTATG
* * *
17155 AAA-TTCTGATAATCACATTATGTAATTTTGATAACCTCACTTTG
1 AAATTTC-GATAATCACTTTATG-AATTTTGATAACCTCTCTATG
* * *
17199 AAATTTTGATAATC-TTTCTATAAATTTTGATAATCCGATCTCTATG
1 AAATTTCGATAATCACTT-TATGAATTTTGATAA-CC--TCTCTATG
*
17245 AAATTTCGATAATCACTTTATGAGA-TTTGATAACCT-TCTATA
1 AAATTTCGATAATCACTTTATGA-ATTTTGATAACCTCTCTATG
17287 AAATTT
1 AAATTT
17293 TGGTACTCCT
Statistics
Matches: 109, Mismatches: 19, Indels: 21
0.73 0.13 0.14
Matches are distributed among these distances:
42 13 0.12
43 16 0.15
44 42 0.39
45 4 0.04
46 31 0.28
47 3 0.03
ACGTcount: A:0.34, C:0.15, G:0.09, T:0.43
Consensus pattern (43 bp):
AAATTTCGATAATCACTTTATGAATTTTGATAACCTCTCTATG
Found at i:17346 original size:22 final size:22
Alignment explanation
Indices: 17317--17385 Score: 70
Period size: 22 Copynumber: 3.2 Consensus size: 22
17307 AAATTTAGAC
* *
17317 TTTT-ATAACCTTCATATGAAA
1 TTTTGATAACCTACCTATGAAA
*
17338 TTTTGATAACC-ACGCTATAAAA
1 TTTTGATAACCTAC-CTATGAAA
* *
17360 TTTTGATAACCTCCCCATGAAA
1 TTTTGATAACCTACCTATGAAA
17382 TTTT
1 TTTT
17386 TAATGAAATT
Statistics
Matches: 39, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
21 5 0.13
22 33 0.85
23 1 0.03
ACGTcount: A:0.35, C:0.19, G:0.07, T:0.39
Consensus pattern (22 bp):
TTTTGATAACCTACCTATGAAA
Found at i:17568 original size:68 final size:66
Alignment explanation
Indices: 17490--17619 Score: 154
Period size: 68 Copynumber: 1.9 Consensus size: 66
17480 ATTAACCACC
* * *
17490 CTATGAAATTTCAATAACCAACC-CAAGAGATTTTAATAACCTGATCCTATGAAATTTTGGTAAC
1 CTATGAAATTTCAATAACC-ACCTCAAGAAATTATAATAACC--ATCCTATGAAATTTTGATAAC
17554 TACA
63 TACA
** * * *
17558 CTATGAAATTTTGATAACCTCCTCATGAAATTATAATAACCATCTTATGAAATTTTGATAAC
1 CTATGAAATTTCAATAACCACCTCAAGAAATTATAATAACCATCCTATGAAATTTTGATAAC
17620 CACATAGAGA
Statistics
Matches: 53, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
66 19 0.36
67 2 0.04
68 32 0.60
ACGTcount: A:0.39, C:0.18, G:0.09, T:0.34
Consensus pattern (66 bp):
CTATGAAATTTCAATAACCACCTCAAGAAATTATAATAACCATCCTATGAAATTTTGATAACTAC
A
Found at i:17585 original size:22 final size:21
Alignment explanation
Indices: 17534--17620 Score: 95
Period size: 22 Copynumber: 4.0 Consensus size: 21
17524 AATAACCTGA
*
17534 TCCTATGAAATTTTGGTAA-C
1 TCCTATGAAATTTTGATAACC
17554 TACACTATGAAATTTTGATAACC
1 T-C-CTATGAAATTTTGATAACC
* *
17577 TCCTCATGAAATTATAATAACC
1 TCCT-ATGAAATTTTGATAACC
*
17599 ATCTTATGAAATTTTGATAACC
1 -TCCTATGAAATTTTGATAACC
17621 ACATAGAGAC
Statistics
Matches: 56, Mismatches: 6, Indels: 8
0.80 0.09 0.11
Matches are distributed among these distances:
20 1 0.02
21 3 0.05
22 47 0.84
23 5 0.09
ACGTcount: A:0.37, C:0.17, G:0.09, T:0.37
Consensus pattern (21 bp):
TCCTATGAAATTTTGATAACC
Found at i:17621 original size:22 final size:22
Alignment explanation
Indices: 17519--17621 Score: 86
Period size: 22 Copynumber: 4.6 Consensus size: 22
17509 AACCCAAGAG
* *
17519 ATTTTAATAACCTGATCCTATGAA
1 ATTTTGATAACC--ATCTTATGAA
*
17543 ATTTTGGTAACTACA-C-TATGAA
1 ATTTTGATAAC--CATCTTATGAA
*
17565 ATTTTGATAACC-TCCTCATGAA
1 ATTTTGATAACCAT-CTTATGAA
* *
17587 ATTATAATAACCATCTTATGAA
1 ATTTTGATAACCATCTTATGAA
17609 ATTTTGATAACCA
1 ATTTTGATAACCA
17622 CATAGAGACA
Statistics
Matches: 64, Mismatches: 9, Indels: 14
0.74 0.10 0.16
Matches are distributed among these distances:
20 1 0.02
21 1 0.02
22 49 0.77
23 2 0.03
24 10 0.16
26 1 0.02
ACGTcount: A:0.38, C:0.17, G:0.09, T:0.37
Consensus pattern (22 bp):
ATTTTGATAACCATCTTATGAA
Found at i:17821 original size:19 final size:20
Alignment explanation
Indices: 17790--17827 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
17780 TATTGACATT
17790 TAAAAATTGAAATT-AAAAG
1 TAAAAATTGAAATTCAAAAG
17809 TAAAATATT-AAATTCAAAA
1 TAAAA-ATTGAAATTCAAAA
17828 AATAATAGTA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.63, C:0.03, G:0.05, T:0.29
Consensus pattern (20 bp):
TAAAAATTGAAATTCAAAAG
Found at i:18174 original size:31 final size:31
Alignment explanation
Indices: 18139--18198 Score: 104
Period size: 31 Copynumber: 1.9 Consensus size: 31
18129 TGGCAATTTA
18139 GAAATATGTTTTAAAGAA-AAGGGTACAATTG
1 GAAATATGTTTTAAA-AATAAGGGTACAATTG
18170 GAAATATGTTTTAAAAATAAGGGTACAAT
1 GAAATATGTTTTAAAAATAAGGGTACAAT
18199 CGAAAAACAT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
30 2 0.07
31 26 0.93
ACGTcount: A:0.47, C:0.03, G:0.20, T:0.30
Consensus pattern (31 bp):
GAAATATGTTTTAAAAATAAGGGTACAATTG
Found at i:18322 original size:22 final size:22
Alignment explanation
Indices: 18297--18339 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
18287 TAAATGAAAT
18297 ATTTATACGAAATTATGATAAC
1 ATTTATACGAAATTATGATAAC
* **
18319 ATTTTTATTAAATTATGATAA
1 ATTTATACGAAATTATGATAA
18340 TTACACTATT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.44, C:0.05, G:0.07, T:0.44
Consensus pattern (22 bp):
ATTTATACGAAATTATGATAAC
Found at i:18373 original size:41 final size:41
Alignment explanation
Indices: 18312--18420 Score: 150
Period size: 41 Copynumber: 2.7 Consensus size: 41
18302 TACGAAATTA
* *
18312 TGATAACATT-TTTATTAAATTATGATAATTACACTATTTT
1 TGATAACCTTCTTTATGAAATTATGATAATTACACTATTTT
18352 TGATAACCTTCTTTATGAAATTATGATAATTACACTATTTT
1 TGATAACCTTCTTTATGAAATTATGATAATTACACTATTTT
* * * *
18393 TTATGA-CGTCTTTATGAAATTTTGATAA
1 TGATAACCTTCTTTATGAAATTATGATAA
18421 CCTTCCTATG
Statistics
Matches: 62, Mismatches: 6, Indels: 2
0.89 0.09 0.03
Matches are distributed among these distances:
40 29 0.47
41 33 0.53
ACGTcount: A:0.35, C:0.09, G:0.08, T:0.48
Consensus pattern (41 bp):
TGATAACCTTCTTTATGAAATTATGATAATTACACTATTTT
Found at i:18745 original size:23 final size:23
Alignment explanation
Indices: 18719--18776 Score: 80
Period size: 23 Copynumber: 2.5 Consensus size: 23
18709 CCTCGCTATG
* *
18719 AAATTTTGATAAACCTTCCAATA
1 AAATTTTGATAAAACTCCCAATA
**
18742 AAATTTTGATAAAACTCCCTGTA
1 AAATTTTGATAAAACTCCCAATA
18765 AAATTTTGATAA
1 AAATTTTGATAA
18777 CCTCATGAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.43, C:0.14, G:0.07, T:0.36
Consensus pattern (23 bp):
AAATTTTGATAAAACTCCCAATA
Found at i:18808 original size:16 final size:18
Alignment explanation
Indices: 18765--18812 Score: 55
Period size: 16 Copynumber: 2.7 Consensus size: 18
18755 ACTCCCTGTA
*
18765 AAATTTTGATAACCTCATG
1 AAATTTTGATAA-CTCATC
*
18784 AAATCTTGATAACT-A-C
1 AAATTTTGATAACTCATC
18800 AAATTTTGATAAC
1 AAATTTTGATAAC
18813 CTCCCTATGA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
16 12 0.46
17 1 0.04
18 2 0.08
19 11 0.42
ACGTcount: A:0.42, C:0.15, G:0.08, T:0.35
Consensus pattern (18 bp):
AAATTTTGATAACTCATC
Found at i:18829 original size:22 final size:22
Alignment explanation
Indices: 18405--18961 Score: 220
Period size: 22 Copynumber: 25.6 Consensus size: 22
18395 ATGACGTCTT
*
18405 TATGAAATTTTGATAACCTTCC
1 TATGAAATTTTGATAACCTCCC
** * *
18427 TATGAAATTTCAATAACGAT-AC
1 TATGAAATTTTGATAAC-CTCCC
* * ***
18449 TATGAAATTTCGAGAACCTTTT
1 TATGAAATTTTGATAACCTCCC
* ** *
18471 TAT-AATTTTTTTTAACCAT-CT
1 TATGAAATTTTGATAACC-TCCC
18492 TATGAAATTTT-ATTAACCTCCC
1 TATGAAATTTTGA-TAACCTCCC
* * *
18514 TAAGGAATTTTTTGA-AGACCTCAC
1 T-ATGAA-ATTTTGATA-ACCTCCC
* * *
18538 TAT-AAAGTTTTAATAACTTCCA
1 TATGAAA-TTTTGATAACCTCCC
* * * *
18560 AATGAAATTTTGACAACCAACAC
1 TATGAAATTTTGATAACC-TCCC
* *
18583 TAT-AAGATGTTGATAACCTCCA
1 TATGAA-ATTTTGATAACCTCCC
* * * **
18605 TATGATATATTGATAACCACGT
1 TATGAAATTTTGATAACCTCCC
** * * *
18627 TATGAAAAGTTAAAAACCTCCA
1 TATGAAATTTTGATAACCTCCC
* * * ***
18649 TATG-AATTGTCAGTAATCAGAC
1 TATGAAATTTTGA-TAACCTCCC
* * *
18671 TCTGAAATTTTGATAATCAT-AC
1 TATGAAATTTTGATAA-CCTCCC
* *
18693 TATGAAATTGTGATAACCTCGC
1 TATGAAATTTTGATAACCTCCC
*
18715 TATGAAATTTTGATAAACCTTCC
1 TATGAAATTTTGAT-AACCTCCC
* * *
18738 AATAAAATTTTGATAAAACTCCC
1 TATGAAATTTTGAT-AACCTCCC
* *
18761 TGTAAAATTTTGATAACCT--C
1 TATGAAATTTTGATAACCTCCC
*
18781 -ATGAAATCTTGATAA-----C
1 TATGAAATTTTGATAACCTCCC
*
18797 TA-CAAATTTTGATAACCTCCC
1 TATGAAATTTTGATAACCTCCC
** **
18818 TATGATTTTTTGATAACCTCAT
1 TATGAAATTTTGATAACCTCCC
* *
18840 TATGAAATTTTGTTAATCTCCC
1 TATGAAATTTTGATAACCTCCC
* * *
18862 TATGAAATTTTGATCTACAT-AC
1 TATGAAATTTTGAT-AACCTCCC
* *
18884 TATGAAATTTTGATAACCTTCT
1 TATGAAATTTTGATAACCTCCC
* *
18906 TATGAAATTTTGATAACCTTCA
1 TATGAAATTTTGATAACCTCCC
*
18928 TATGAAATTTTGATATCCTCCC
1 TATGAAATTTTGATAACCTCCC
18950 --TGAAATTTTGAT
1 TATGAAATTTTGAT
18962 TACTCCATAA
Statistics
Matches: 393, Mismatches: 112, Indels: 62
0.69 0.20 0.11
Matches are distributed among these distances:
16 12 0.03
17 1 0.00
19 12 0.03
20 13 0.03
21 27 0.07
22 246 0.63
23 70 0.18
24 11 0.03
25 1 0.00
ACGTcount: A:0.36, C:0.16, G:0.10, T:0.38
Consensus pattern (22 bp):
TATGAAATTTTGATAACCTCCC
Found at i:18863 original size:44 final size:43
Alignment explanation
Indices: 18405--19146 Score: 235
Period size: 44 Copynumber: 17.4 Consensus size: 43
18395 ATGACGTCTT
* ** *
18405 TATGAAATTTTGATAACCTTCCTATGAAATTTCAATAACGAT-A
1 TATGAAATTTTGATAACCTCCCTATGAAATTTTGATAAC-CTCA
* * *** * ** *
18448 CTATGAAATTTCGAGAACCTTTTTAT-AATTTTTTTTAACCATCT
1 -TATGAAATTTTGATAACCTCCCTATGAAATTTTGATAACC-TCA
* *
18492 TATGAAATTTT-ATTAACCTCCCTAAGGAATTTTTTGA-AGACCTCA
1 TATGAAATTTTGA-TAACCTCCCT-ATGAA-ATTTTGATA-ACCTCA
* * ** * *
18537 CTAT-AAAGTTTTAATAACTTCCAAATGAAATTTTGACAACCAACA
1 -TATGAAA-TTTTGATAACCTCCCTATGAAATTTTGATAACC-TCA
* * * * * *
18582 CTAT-AAGATGTTGATAACCTCCATATGATATATTGATAACCACGT
1 -TATGAA-ATTTTGATAACCTCCCTATGAAATTTTGATAACCTC-A
** * * * * * * **
18627 TATGAAAAGTTAAAAACCTCCATATG-AATTGTCAGTAATCAGA
1 TATGAAATTTTGATAACCTCCCTATGAAATTTTGA-TAACCTCA
* * * * *
18670 CTCTGAAATTTTGATAATCAT-ACTATGAAATTGTGATAACCTCGC
1 -TATGAAATTTTGATAA-CCTCCCTATGAAATTTTGATAACCTC-A
* * * * *
18715 TATGAAATTTTGATAAACCTTCCAATAAAATTTTGATAAAACTCCC
1 TATGAAATTTTGAT-AACCTCCCTATGAAATTTTGAT-AACCT-CA
* * *
18761 TGTAAAATTTTGATAACCT--C-ATGAAATCTTGATAA---C-
1 TATGAAATTTTGATAACCTCCCTATGAAATTTTGATAACCTCA
* **
18797 TA-CAAATTTTGATAACCTCCCTATGATTTTTTGATAACCTCA
1 TATGAAATTTTGATAACCTCCCTATGAAATTTTGATAACCTCA
* * * *
18839 TTATGAAATTTTGTTAATCTCCCTATGAAATTTTGATCTACAT-A
1 -TATGAAATTTTGATAACCTCCCTATGAAATTTTGAT-AACCTCA
* *
18883 CTATGAAATTTTGATAACCTTCTTATGAAATTTTGATAACCTTCA
1 -TATGAAATTTTGATAACCTCCCTATGAAATTTTGATAACC-TCA
* *
18928 TATGAAATTTTGATATCCTCCC--TGAAATTTTGATTA-CTCCA
1 TATGAAATTTTGATAACCTCCCTATGAAATTTTGATAACCT-CA
* * * * *
18969 TAATAAAAGTTTAATAACCTTCC--T--AA-TTTGGTAACCAT-A
1 T-ATGAAATTTTGATAACCTCCCTATGAAATTTTGATAACC-TCA
* *
19008 CTATGAAATTTTGATAACCTCCCCA-G-AA-----AT-ACCAC-
1 -TATGAAATTTTGATAACCTCCCTATGAAATTTTGATAACCTCA
* * ** * * *
19043 TATGAAATTTTGGTAATCAT-ATTTTGAAAATTTGATAACCTCTT
1 TATGAAATTTTGATAA-CCTCCCTATGAAATTTTGATAACCTC-A
* * *
19087 TATGAAATTTTGATAACCTCTCTATAAAATTTTGTTAACCCCTC-
1 TATGAAATTTTGATAACCTCCCTATGAAATTTTGATAA--CCTCA
19131 TATGAAATTTTGATAA
1 TATGAAATTTTGATAA
19147 TCATATTATG
Statistics
Matches: 521, Mismatches: 118, Indels: 118
0.69 0.16 0.16
Matches are distributed among these distances:
34 15 0.03
35 18 0.03
36 6 0.01
37 3 0.01
38 12 0.02
39 24 0.05
40 5 0.01
41 12 0.02
42 46 0.09
43 37 0.07
44 216 0.41
45 81 0.16
46 44 0.08
47 2 0.00
ACGTcount: A:0.36, C:0.17, G:0.10, T:0.38
Consensus pattern (43 bp):
TATGAAATTTTGATAACCTCCCTATGAAATTTTGATAACCTCA
Found at i:19022 original size:191 final size:190
Alignment explanation
Indices: 18673--19028 Score: 406
Period size: 191 Copynumber: 1.9 Consensus size: 190
18663 AATCAGACTC
18673 TGAAATTTTGATAATCATACTATGAAATTGTGATAACCTCGCTATGAAATTTTGATAAACCTTCC
1 TGAAATTTTGATAATCATACTATGAAATTGTGATAACCTCGCTATGAAATTTTGATAAACCTTCC
* * *
18738 AATAAAATTTTGATAAAACTCCCTGTAAAATTTTGATAACCTCATGAAATCTTGATAACTACAAA
66 AATAAAATTTTGATAAAACTCCCTG-AAAATTTTGATAACCTAATAAAATCTTAATAACTACAAA
* **
18803 TTTTGATAACCTCCCTATGATTTTTTGATAACCTCATTATGAAATTTTGTTAATCTCCCTA
130 TTTTGATAACCTCACTATGAAATTTTGATAACCTCATTATGAAATTTTGTTAATCTCCCTA
* * *
18864 TGAAATTTTGAT-CTACATACTATGAAATTTTGATAACCTTC-TTATGAAATTTTGAT-AACCTT
1 TGAAATTTTGATAAT-CATACTATGAAATTGTGATAACC-TCGCTATGAAATTTTGATAAACCTT
* ** *
18926 -CATATGAAATTTTGAT-ATCCTCCCTG-AAATTTTGATTACTCCATAATAAAAGT-TTAATAAC
64 CCA-ATAAAATTTTGATAAAACTCCCTGAAAATTTTGA-TA-ACC-TAATAAAA-TCTTAATAA-
* * *
18987 CTTCCTAA-TTTGGTAACCAT-ACTATGAAATTTTGATAACCTC
123 C-TACAAATTTTGATAACC-TCACTATGAAATTTTGATAACCTC
19029 CCCAGAAATA
Statistics
Matches: 139, Mismatches: 16, Indels: 20
0.79 0.09 0.11
Matches are distributed among these distances:
187 9 0.06
188 2 0.01
189 12 0.09
190 31 0.22
191 78 0.56
192 7 0.05
ACGTcount: A:0.35, C:0.17, G:0.09, T:0.39
Consensus pattern (190 bp):
TGAAATTTTGATAATCATACTATGAAATTGTGATAACCTCGCTATGAAATTTTGATAAACCTTCC
AATAAAATTTTGATAAAACTCCCTGAAAATTTTGATAACCTAATAAAATCTTAATAACTACAAAT
TTTGATAACCTCACTATGAAATTTTGATAACCTCATTATGAAATTTTGTTAATCTCCCTA
Found at i:19130 original size:24 final size:22
Alignment explanation
Indices: 19069--19146 Score: 104
Period size: 22 Copynumber: 3.6 Consensus size: 22
19059 TCATATTTTG
*
19069 AAAA-TTTGATAACCTCTTTAT
1 AAAATTTTGATAACCTCTCTAT
*
19090 GAAATTTTGATAACCTCTCTAT
1 AAAATTTTGATAACCTCTCTAT
* *
19112 AAAATTTTGTTAACCCCTCTAT
1 AAAATTTTGATAACCTCTCTAT
*
19134 GAAATTTTGATAA
1 AAAATTTTGATAA
19147 TCATATTATG
Statistics
Matches: 49, Mismatches: 7, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
21 3 0.06
22 46 0.94
ACGTcount: A:0.36, C:0.15, G:0.08, T:0.41
Consensus pattern (22 bp):
AAAATTTTGATAACCTCTCTAT
Found at i:19156 original size:22 final size:21
Alignment explanation
Indices: 19043--19168 Score: 85
Period size: 22 Copynumber: 5.8 Consensus size: 21
19033 GAAATACCAC
*
19043 TATGAAATTTTGGTAATCATAT
1 TATGAAATTTTGATAATCAT-T
* *
19065 TTTGAAAATTTGATAACCTC-TT
1 TATGAAATTTTGATAA--TCATT
*
19087 TATGAAATTTTGATAACCTC-TC
1 TATGAAATTTTGATAA--TCATT
* * * * *
19109 TATAAAATTTTGTTAACCCCTC
1 TATGAAATTTTGATAA-TCATT
19131 TATGAAATTTTGATAATCATAT
1 TATGAAATTTTGATAATCAT-T
*
19153 TATGTAATTTTGATAA
1 TATGAAATTTTGATAA
19169 CCGCGTTTTG
Statistics
Matches: 85, Mismatches: 15, Indels: 8
0.79 0.14 0.07
Matches are distributed among these distances:
21 4 0.05
22 78 0.92
23 1 0.01
24 2 0.02
ACGTcount: A:0.35, C:0.11, G:0.10, T:0.44
Consensus pattern (21 bp):
TATGAAATTTTGATAATCATT
Found at i:19162 original size:44 final size:44
Alignment explanation
Indices: 19042--19187 Score: 152
Period size: 44 Copynumber: 3.3 Consensus size: 44
19032 AGAAATACCA
* * * *
19042 CTATGAAATTTTGGTAATCATATTTTGAAAATTTGATAACCTCT
1 CTATGAAATTTTGATAATCATATTATGAAATTTTGATAACCCCT
* * * * *
19086 TTATGAAATTTTGATAA-CCTCTCTATAAAATTTTGTTAACCCCT
1 CTATGAAATTTTGATAATCATAT-TATGAAATTTTGATAACCCCT
* *
19130 CTATGAAATTTTGATAATCATATTATGTAATTTTGATAACCGCGT
1 CTATGAAATTTTGATAATCATATTATGAAATTTTGATAACC-CCT
*
19175 -TTTGAAATTTTGA
1 CTATGAAATTTTGA
19188 AATTGGATCA
Statistics
Matches: 82, Mismatches: 17, Indels: 6
0.78 0.16 0.06
Matches are distributed among these distances:
43 3 0.04
44 74 0.90
45 5 0.06
ACGTcount: A:0.33, C:0.12, G:0.11, T:0.44
Consensus pattern (44 bp):
CTATGAAATTTTGATAATCATATTATGAAATTTTGATAACCCCT
Found at i:19303 original size:38 final size:37
Alignment explanation
Indices: 19245--19340 Score: 126
Period size: 38 Copynumber: 2.6 Consensus size: 37
19235 ATCTAAGCCC
*
19245 AAATAGGACGTT-GAAGACAAAGACAAAA-AGCAAAATT
1 AAATAAGACGTTGGAA-ACAAAGACAAAAGA-CAAAATT
19282 AAATACA-ACGATTGGAAACAAAGACAAAAGACAAAATT
1 AAATA-AGACG-TTGGAAACAAAGACAAAAGACAAAATT
19320 AAATAAGACGTTGGAAACAAA
1 AAATAAGACGTTGGAAACAAA
19341 AAGTCAAATT
Statistics
Matches: 53, Mismatches: 1, Indels: 10
0.83 0.02 0.16
Matches are distributed among these distances:
37 20 0.38
38 29 0.55
39 4 0.08
ACGTcount: A:0.58, C:0.11, G:0.17, T:0.14
Consensus pattern (37 bp):
AAATAAGACGTTGGAAACAAAGACAAAAGACAAAATT
Found at i:19311 original size:37 final size:38
Alignment explanation
Indices: 19245--19340 Score: 128
Period size: 37 Copynumber: 2.6 Consensus size: 38
19235 ATCTAAGCCC
*
19245 AAATAGGACGTT-GAAGACAAAGACAAAAAG-CAAAATT
1 AAATAAGACGTTGGAA-ACAAAGACAAAAAGACAAAATT
19282 AAATACA-ACGATTGGAAACAAAGAC-AAAAGACAAAATT
1 AAATA-AGACG-TTGGAAACAAAGACAAAAAGACAAAATT
19320 AAATAAGACGTTGGAAACAAA
1 AAATAAGACGTTGGAAACAAA
19341 AAGTCAAATT
Statistics
Matches: 53, Mismatches: 1, Indels: 10
0.83 0.02 0.16
Matches are distributed among these distances:
37 25 0.47
38 25 0.47
39 3 0.06
ACGTcount: A:0.58, C:0.11, G:0.17, T:0.14
Consensus pattern (38 bp):
AAATAAGACGTTGGAAACAAAGACAAAAAGACAAAATT
Found at i:19526 original size:32 final size:31
Alignment explanation
Indices: 19490--19557 Score: 93
Period size: 31 Copynumber: 2.2 Consensus size: 31
19480 TTTAGTAATG
*
19490 ACAATTCAGAAATATGTTTTTAAAAA-AAGGGT
1 ACAATT-AGAAATAT-ATTTTAAAAATAAGGGT
*
19522 ACAATTGGAAATATATTTTAAAAATAAGGGT
1 ACAATTAGAAATATATTTTAAAAATAAGGGT
19553 ACAAT
1 ACAAT
19558 CGGAAAACAT
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
30 9 0.27
31 18 0.55
32 6 0.18
ACGTcount: A:0.49, C:0.06, G:0.15, T:0.31
Consensus pattern (31 bp):
ACAATTAGAAATATATTTTAAAAATAAGGGT
Found at i:19543 original size:30 final size:32
Alignment explanation
Indices: 19498--19563 Score: 100
Period size: 31 Copynumber: 2.1 Consensus size: 32
19488 TGACAATTCA
* *
19498 GAAATATGTTTTTAAAAA-AAGGGTACAATTG
1 GAAATATGATTTTAAAAATAAGGGTACAATCG
19529 GAAATAT-ATTTTAAAAATAAGGGTACAATCG
1 GAAATATGATTTTAAAAATAAGGGTACAATCG
19560 GAAA
1 GAAA
19564 ACATAAAGTT
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
30 9 0.28
31 23 0.72
ACGTcount: A:0.48, C:0.05, G:0.18, T:0.29
Consensus pattern (32 bp):
GAAATATGATTTTAAAAATAAGGGTACAATCG
Found at i:19599 original size:2 final size:2
Alignment explanation
Indices: 19592--19638 Score: 69
Period size: 2 Copynumber: 23.5 Consensus size: 2
19582 TTCGTACTTT
*
19592 TA TA TA TA GTA TA GA TA -A 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
19634 TA TA T
1 TA TA T
19639 TTGGAGAGGT
Statistics
Matches: 41, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
1 1 0.02
2 38 0.93
3 2 0.05
ACGTcount: A:0.49, C:0.00, G:0.04, T:0.47
Consensus pattern (2 bp):
TA
Found at i:21259 original size:6 final size:6
Alignment explanation
Indices: 21249--21291 Score: 77
Period size: 6 Copynumber: 7.2 Consensus size: 6
21239 CTGCCATACA
*
21249 AAAAAA AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG A
1 AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG A
21292 GAGAGCAAGG
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 36 1.00
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (6 bp):
AAAAAG
Found at i:22736 original size:80 final size:78
Alignment explanation
Indices: 22642--22789 Score: 233
Period size: 80 Copynumber: 1.9 Consensus size: 78
22632 TTGATTGACC
* *
22642 TCAAATTTAGGGTTTACAATCTTTAAATAGTCTCAGGAAATAACGAAAATTAAATAAAAATAAAG
1 TCAAATTTAGGGTTTACAACCTTTAAATAGTCTCAGAAAATAACGAAAATTAAA-AAAAATAAA-
22707 AAAGCAAAAAAACAG
64 AAAGCAAAAAAACAG
* * *
22722 TCAAATTTATGGTTTACAACCTTTAAATGGTGTCAGAAAATAACGAAAATTAAAAAAAATAAAAA
1 TCAAATTTAGGGTTTACAACCTTTAAATAGTCTCAGAAAATAACGAAAATTAAAAAAAATAAAAA
22787 AGC
66 AGC
22790 CCCAAAACAG
Statistics
Matches: 63, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
78 5 0.08
79 9 0.14
80 49 0.78
ACGTcount: A:0.53, C:0.10, G:0.12, T:0.25
Consensus pattern (78 bp):
TCAAATTTAGGGTTTACAACCTTTAAATAGTCTCAGAAAATAACGAAAATTAAAAAAAATAAAAA
AGCAAAAAAACAG
Found at i:30441 original size:74 final size:75
Alignment explanation
Indices: 30264--30672 Score: 610
Period size: 75 Copynumber: 5.5 Consensus size: 75
30254 TCACGAAAAA
* * * *
30264 TCTAATCGAGGTCGAACGTCCAAGCAGATGTAACCCGTAGACGGCTGAGCGCCTAGACTGGCGCC
1 TCTAAGCGAGGTCGAACGTCCAAGCAGACGTCACCCGCAGACGGCTGAGCGCCTAGACTGGCGCC
*
30329 CCCGTATATC
66 CCCGTATAGC
* * * *
30339 TCTAAGCAAGGTCGAACGTCCAAGCAGACGTCACCCGCAGATGGTTAAGCGCCTAGACTGGCGCC
1 TCTAAGCGAGGTCGAACGTCCAAGCAGACGTCACCCGCAGACGGCTGAGCGCCTAGACTGGCGCC
30404 CCGCGTA-A-C
66 CC-CGTATAGC
30413 TCTAAGCGAGGTCGAACGTCCAAGCAGACGTCACCCGCAGACGGCTGAGCGCCTAGACTGGCGCC
1 TCTAAGCGAGGTCGAACGTCCAAGCAGACGTCACCCGCAGACGGCTGAGCGCCTAGACTGGCGCC
30478 CCCGTATAGC
66 CCCGTATAGC
* * * *
30488 TCTAAGCGAGGTTGAACGTCTAAGCGGACGTCACCCGCAGACGGTTGAGCGCCTAGACTGGCGCC
1 TCTAAGCGAGGTCGAACGTCCAAGCAGACGTCACCCGCAGACGGCTGAGCGCCTAGACTGGCGCC
30553 CCGCGTA-A-C
66 CC-CGTATAGC
*
30562 TCTAAGCGAGGTCGAACGTCCAAGGAGACGTCACCCGCAGACGGCTGAGCGCCTAGACTGGCGCC
1 TCTAAGCGAGGTCGAACGTCCAAGCAGACGTCACCCGCAGACGGCTGAGCGCCTAGACTGGCGCC
*
30627 CTCGTATAGC
66 CCCGTATAGC
* * *
30637 TCCAAGCGGGGTCGAACGTCCAAACAGACGTCACCC
1 TCTAAGCGAGGTCGAACGTCCAAGCAGACGTCACCC
30673 ACAAGAGTCC
Statistics
Matches: 302, Mismatches: 26, Indels: 12
0.89 0.08 0.04
Matches are distributed among these distances:
73 8 0.03
74 128 0.42
75 158 0.52
76 8 0.03
ACGTcount: A:0.24, C:0.33, G:0.29, T:0.15
Consensus pattern (75 bp):
TCTAAGCGAGGTCGAACGTCCAAGCAGACGTCACCCGCAGACGGCTGAGCGCCTAGACTGGCGCC
CCCGTATAGC
Found at i:30539 original size:149 final size:149
Alignment explanation
Indices: 30264--30672 Score: 674
Period size: 149 Copynumber: 2.7 Consensus size: 149
30254 TCACGAAAAA
* * * *
30264 TCTAATCGAGGTCGAACGTCCAAGCAGATGTAACCCGTAGACGGCTGAGCGCCTAGACTGGCGCC
1 TCTAAGCGAGGTCGAACGTCCAAGCAGACGTCACCCGCAGACGGCTGAGCGCCTAGACTGGCGCC
* * *
30329 CCCGTATATCTCTAAGCAAGGTCGAACGTCCAAGCAGACGTCACCCGCAGATGGTTAAGCGCCTA
66 CCCGTATAGCTCTAAGCGAGGTCGAACGTCCAAGCAGACGTCACCCGCAGACGGTTAAGCGCCTA
30394 GACTGGCGCCCCGCGTAAC
131 GACTGGCGCCCCGCGTAAC
30413 TCTAAGCGAGGTCGAACGTCCAAGCAGACGTCACCCGCAGACGGCTGAGCGCCTAGACTGGCGCC
1 TCTAAGCGAGGTCGAACGTCCAAGCAGACGTCACCCGCAGACGGCTGAGCGCCTAGACTGGCGCC
* * * *
30478 CCCGTATAGCTCTAAGCGAGGTTGAACGTCTAAGCGGACGTCACCCGCAGACGGTTGAGCGCCTA
66 CCCGTATAGCTCTAAGCGAGGTCGAACGTCCAAGCAGACGTCACCCGCAGACGGTTAAGCGCCTA
30543 GACTGGCGCCCCGCGTAAC
131 GACTGGCGCCCCGCGTAAC
*
30562 TCTAAGCGAGGTCGAACGTCCAAGGAGACGTCACCCGCAGACGGCTGAGCGCCTAGACTGGCGCC
1 TCTAAGCGAGGTCGAACGTCCAAGCAGACGTCACCCGCAGACGGCTGAGCGCCTAGACTGGCGCC
* * * *
30627 CTCGTATAGCTCCAAGCGGGGTCGAACGTCCAAACAGACGTCACCC
66 CCCGTATAGCTCTAAGCGAGGTCGAACGTCCAAGCAGACGTCACCC
30673 ACAAGAGTCC
Statistics
Matches: 241, Mismatches: 19, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
149 241 1.00
ACGTcount: A:0.24, C:0.33, G:0.29, T:0.15
Consensus pattern (149 bp):
TCTAAGCGAGGTCGAACGTCCAAGCAGACGTCACCCGCAGACGGCTGAGCGCCTAGACTGGCGCC
CCCGTATAGCTCTAAGCGAGGTCGAACGTCCAAGCAGACGTCACCCGCAGACGGTTAAGCGCCTA
GACTGGCGCCCCGCGTAAC
Found at i:34355 original size:21 final size:21
Alignment explanation
Indices: 34329--34375 Score: 76
Period size: 21 Copynumber: 2.2 Consensus size: 21
34319 GTCAACCCGC
*
34329 CAAAATTCGAAATTTGAATTT
1 CAAAATTCGAAATTCGAATTT
*
34350 CAAAATTTGAAATTCGAATTT
1 CAAAATTCGAAATTCGAATTT
34371 CAAAA
1 CAAAA
34376 AAAACATACG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.47, C:0.11, G:0.09, T:0.34
Consensus pattern (21 bp):
CAAAATTCGAAATTCGAATTT
Found at i:36004 original size:6 final size:6
Alignment explanation
Indices: 35993--36021 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
35983 GATGCTTATC
35993 TATTTA TATTTA TATTTA TATTTA TATTT
1 TATTTA TATTTA TATTTA TATTTA TATTT
36022 TCATTTACAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (6 bp):
TATTTA
Found at i:37204 original size:50 final size:50
Alignment explanation
Indices: 37149--37255 Score: 205
Period size: 50 Copynumber: 2.1 Consensus size: 50
37139 AAAGAAAACA
*
37149 AAATATAGTAATTATATAAATAAATGAGAAAATAAGAGGTGGAACTTTAG
1 AAATATAGTAATTATATAAATAAATGAGAAAATAAGAGGGGGAACTTTAG
37199 AAATATAGTAATTATATAAATAAATGAGAAAATAAGAGGGGGAACTTTAG
1 AAATATAGTAATTATATAAATAAATGAGAAAATAAGAGGGGGAACTTTAG
37249 AAATATA
1 AAATATA
37256 TATATGGATA
Statistics
Matches: 56, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
50 56 1.00
ACGTcount: A:0.53, C:0.02, G:0.18, T:0.27
Consensus pattern (50 bp):
AAATATAGTAATTATATAAATAAATGAGAAAATAAGAGGGGGAACTTTAG
Found at i:42927 original size:22 final size:22
Alignment explanation
Indices: 42902--42947 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
42892 GAACATAACT
42902 ATTAAAATG-GTTGACCATGTTG
1 ATTAAAA-GAGTTGACCATGTTG
*
42924 ATTAAAAGAGTTGGCCATGTTG
1 ATTAAAAGAGTTGACCATGTTG
42946 AT
1 AT
42948 GCATTAAACA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 1 0.05
22 21 0.95
ACGTcount: A:0.33, C:0.09, G:0.24, T:0.35
Consensus pattern (22 bp):
ATTAAAAGAGTTGACCATGTTG
Found at i:45361 original size:2 final size:2
Alignment explanation
Indices: 45354--45403 Score: 63
Period size: 2 Copynumber: 27.0 Consensus size: 2
45344 ACAAAATTGT
45354 GA GA GA GA GA GA GA GA G- GA G- GA GA GA GA GA G- GA G- GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
*
45392 GA GC GA GA GA GA
1 GA GA GA GA GA GA
45404 TTACCTTCAA
Statistics
Matches: 42, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
1 4 0.10
2 38 0.90
ACGTcount: A:0.44, C:0.02, G:0.54, T:0.00
Consensus pattern (2 bp):
GA
Found at i:45379 original size:14 final size:14
Alignment explanation
Indices: 45360--45394 Score: 70
Period size: 14 Copynumber: 2.5 Consensus size: 14
45350 TTGTGAGAGA
45360 GAGAGAGAGAGGAG
1 GAGAGAGAGAGGAG
45374 GAGAGAGAGAGGAG
1 GAGAGAGAGAGGAG
45388 GAGAGAG
1 GAGAGAG
45395 CGAGAGAGAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.43, C:0.00, G:0.57, T:0.00
Consensus pattern (14 bp):
GAGAGAGAGAGGAG
Found at i:48112 original size:18 final size:18
Alignment explanation
Indices: 48089--48177 Score: 106
Period size: 18 Copynumber: 4.9 Consensus size: 18
48079 CAAAGGTTCT
*
48089 TGCGGCAGCGGAACATCC
1 TGCGGCAGTGGAACATCC
* *
48107 TGCGGCAATGGAACATTC
1 TGCGGCAGTGGAACATCC
*
48125 TGCAGCAGTGGAACATCC
1 TGCGGCAGTGGAACATCC
* *
48143 TGCGGCATTAGAACATCC
1 TGCGGCAGTGGAACATCC
* *
48161 TGCGGCAATGGAGCATC
1 TGCGGCAGTGGAACATC
48178 TGCCTGTACA
Statistics
Matches: 59, Mismatches: 12, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
18 59 1.00
ACGTcount: A:0.26, C:0.27, G:0.29, T:0.18
Consensus pattern (18 bp):
TGCGGCAGTGGAACATCC
Done.