Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020202.1 Corchorus olitorius cultivar O-4 contig20235, 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: 78897
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Found at i:3044 original size:40 final size:40
Alignment explanation
Indices: 2989--3069 Score: 153
Period size: 40 Copynumber: 2.0 Consensus size: 40
2979 TAAGCGGGTG
*
2989 ATTTTTTTTAAAAAATGCAATTTATTCCAACTGGTTCTGT
1 ATTTTTTTAAAAAAATGCAATTTATTCCAACTGGTTCTGT
3029 ATTTTTTTAAAAAAATGCAATTTATTCCAACTGGTTCTGT
1 ATTTTTTTAAAAAAATGCAATTTATTCCAACTGGTTCTGT
3069 A
1 A
3070 ACCCACGTGG
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
40 40 1.00
ACGTcount: A:0.32, C:0.12, G:0.10, T:0.46
Consensus pattern (40 bp):
ATTTTTTTAAAAAAATGCAATTTATTCCAACTGGTTCTGT
Found at i:4419 original size:13 final size:13
Alignment explanation
Indices: 4401--4425 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
4391 GTTATCAAAT
4401 TTACAGTAATTAG
1 TTACAGTAATTAG
4414 TTACAGTAATTA
1 TTACAGTAATTA
4426 CTGAAAAATT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.08, G:0.12, T:0.40
Consensus pattern (13 bp):
TTACAGTAATTAG
Found at i:5541 original size:16 final size:15
Alignment explanation
Indices: 5503--5544 Score: 57
Period size: 15 Copynumber: 2.7 Consensus size: 15
5493 ACAGAGGTTG
* *
5503 ACAGAAAGCAATTAA
1 ACAGAAAACAATGAA
5518 ACAGAAAACAATGAA
1 ACAGAAAACAATGAA
5533 ACTAGAAAACAA
1 AC-AGAAAACAA
5545 AGCAAAGTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
15 15 0.62
16 9 0.38
ACGTcount: A:0.64, C:0.14, G:0.12, T:0.10
Consensus pattern (15 bp):
ACAGAAAACAATGAA
Found at i:6350 original size:20 final size:18
Alignment explanation
Indices: 6311--6346 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
6301 TAGCCCTAAA
*
6311 AACTAGAAGAAAAACTAG
1 AACTAGAAGAAAAAATAG
6329 AACTAGAAGAGAAAAATA
1 AACTAGAAGA-AAAAATA
6347 AGAAGAGAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 10 0.62
19 6 0.38
ACGTcount: A:0.64, C:0.08, G:0.17, T:0.11
Consensus pattern (18 bp):
AACTAGAAGAAAAAATAG
Found at i:10982 original size:21 final size:20
Alignment explanation
Indices: 10958--10998 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
10948 TTTTTTTTCA
10958 AAAAACGCAAGACTCAAAATT
1 AAAAACGCAA-ACTCAAAATT
* *
10979 AAAAACGGAAATTCAAAATT
1 AAAAACGCAAACTCAAAATT
10999 TTTTTTTTCA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 9 0.50
21 9 0.50
ACGTcount: A:0.59, C:0.15, G:0.10, T:0.17
Consensus pattern (20 bp):
AAAAACGCAAACTCAAAATT
Found at i:11038 original size:30 final size:29
Alignment explanation
Indices: 10979--11035 Score: 89
Period size: 29 Copynumber: 2.0 Consensus size: 29
10969 ACTCAAAATT
*
10979 AAAAACGGAAATTCAAAATTTTTTTTTTC
1 AAAAACGGAAATACAAAATTTTTTTTTTC
11008 AAAAACGGAAA-ACACAAATTTTTTTTTT
1 AAAAACGGAAATACA-AAATTTTTTTTTT
11036 TCAGAAAAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
28 2 0.08
29 24 0.92
ACGTcount: A:0.44, C:0.11, G:0.07, T:0.39
Consensus pattern (29 bp):
AAAAACGGAAATACAAAATTTTTTTTTTC
Found at i:11054 original size:35 final size:34
Alignment explanation
Indices: 10994--11086 Score: 90
Period size: 35 Copynumber: 2.8 Consensus size: 34
10984 CGGAAATTCA
10994 AAATTTTTTTTTTC---AAAAACG--GAAAACAC
1 AAATTTTTTTTTTCAGAAAAAACGCAGAAAACAC
**
11023 AAATTTTTTTTTTTCAGAAAAAACGCAGAAAACGG
1 AAA-TTTTTTTTTTCAGAAAAAACGCAGAAAACAC
*
11058 AAATATTTTTTTT-AGATTAAAAACGCAGA
1 AAATTTTTTTTTTCAGA--AAAAACGCAGA
11087 CACAAAGAGA
Statistics
Matches: 53, Mismatches: 3, Indels: 10
0.80 0.05 0.15
Matches are distributed among these distances:
29 3 0.06
30 11 0.21
33 10 0.19
34 9 0.17
35 20 0.38
ACGTcount: A:0.44, C:0.11, G:0.11, T:0.34
Consensus pattern (34 bp):
AAATTTTTTTTTTCAGAAAAAACGCAGAAAACAC
Found at i:11386 original size:16 final size:15
Alignment explanation
Indices: 11348--11389 Score: 57
Period size: 15 Copynumber: 2.7 Consensus size: 15
11338 ACAGAGGTTG
* *
11348 ACAGAAAGCAATTAA
1 ACAGAAAACAATGAA
11363 ACAGAAAACAATGAA
1 ACAGAAAACAATGAA
11378 ACTAGAAAACAA
1 AC-AGAAAACAA
11390 AGCAAAGTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
15 15 0.62
16 9 0.38
ACGTcount: A:0.64, C:0.14, G:0.12, T:0.10
Consensus pattern (15 bp):
ACAGAAAACAATGAA
Found at i:12195 original size:20 final size:18
Alignment explanation
Indices: 12156--12191 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
12146 TAGCCCTAAA
*
12156 AACTAGAAGAAAAACTAG
1 AACTAGAAGAAAAAATAG
12174 AACTAGAAGAGAAAAATA
1 AACTAGAAGA-AAAAATA
12192 AGAAGAGAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 10 0.62
19 6 0.38
ACGTcount: A:0.64, C:0.08, G:0.17, T:0.11
Consensus pattern (18 bp):
AACTAGAAGAAAAAATAG
Found at i:13397 original size:22 final size:22
Alignment explanation
Indices: 13361--13422 Score: 63
Period size: 22 Copynumber: 2.8 Consensus size: 22
13351 ATTTCGATAA
**
13361 CCTATGAAAACTTGATAACCACT
1 CCTATGAAATTTTGATAACC-CT
* * *
13384 -CTGTGAAATTTTGATAATCTT
1 CCTATGAAATTTTGATAACCCT
13405 CCTATGAAATTTTGATAA
1 CCTATGAAATTTTGATAA
13423 TCACACTATA
Statistics
Matches: 32, Mismatches: 6, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
21 1 0.03
22 31 0.97
ACGTcount: A:0.35, C:0.16, G:0.11, T:0.37
Consensus pattern (22 bp):
CCTATGAAATTTTGATAACCCT
Found at i:13431 original size:22 final size:20
Alignment explanation
Indices: 13331--13422 Score: 62
Period size: 22 Copynumber: 4.4 Consensus size: 20
13321 GTGAAAATTA
*
13331 TTTGATAACATCATTATGAAAT
1 TTTGATAACA-C-CTATGAAAT
* *
13353 TTCGAT-A-ACCTATGAAAA
1 TTTGATAACACCTATGAAAT
* *
13371 CTTGATAACCACTCTGTGAAAT
1 TTTGATAA-CAC-CTATGAAAT
*
13393 TTTGATAATCTTCCTATGAAAT
1 TTTGATAA-C-ACCTATGAAAT
13415 TTTGATAA
1 TTTGATAA
13423 TCACACTATA
Statistics
Matches: 54, Mismatches: 11, Indels: 10
0.72 0.15 0.13
Matches are distributed among these distances:
18 11 0.20
19 2 0.04
20 1 0.02
21 3 0.06
22 36 0.67
23 1 0.02
ACGTcount: A:0.37, C:0.14, G:0.11, T:0.38
Consensus pattern (20 bp):
TTTGATAACACCTATGAAAT
Found at i:13576 original size:21 final size:23
Alignment explanation
Indices: 13527--13606 Score: 62
Period size: 22 Copynumber: 3.6 Consensus size: 23
13517 CTCTTTATTT
* *
13527 AATTTTGATAA-CATCTCC-ATAA
1 AATTTTGATAACCTTC-CCAATGA
13549 AATTTTTG-TAACCTT-CCAATGA
1 AA-TTTTGATAACCTTCCCAATGA
* *
13571 AATTTTGTTAA-CTTCCCTATGA
1 AATTTTGATAACCTTCCCAATGA
*
13593 AACTTTGATAACCT
1 AATTTTGATAACCT
13607 CCCCCCCCCC
Statistics
Matches: 47, Mismatches: 5, Indels: 11
0.75 0.08 0.17
Matches are distributed among these distances:
21 10 0.21
22 28 0.60
23 9 0.19
ACGTcount: A:0.34, C:0.19, G:0.07, T:0.40
Consensus pattern (23 bp):
AATTTTGATAACCTTCCCAATGA
Found at i:13719 original size:22 final size:22
Alignment explanation
Indices: 13620--13812 Score: 99
Period size: 22 Copynumber: 8.7 Consensus size: 22
13610 CCCCCCCCCA
*
13620 ATGAAATTTTGATAACCACACT
1 ATGAAATTTTGATAACCACTCT
*
13642 AT-AAATTTTGATAACC-TTCGT
1 ATGAAATTTTGATAACCACTC-T
* *
13663 ATAAAATTTTGGTAACGACACTCT
1 ATGAAATTTTGATAAC--CACTCT
* * ** *
13687 AAGAAAATTTGATAACCTTTTT
1 ATGAAATTTTGATAACCACTCT
* *
13709 ATGAAATTTTGGTAACGC-CTGT
1 ATGAAATTTTGATAAC-CACTCT
* * * *
13731 ATAAAATGTTGATAACTACACT
1 ATGAAATTTTGATAACCACTCT
** * *
13753 ATGACGTTTTGATAACCTC-CAA
1 ATGAAATTTTGATAACCACTC-T
*
13775 ATGAAATTTT-AGTAACCACACT
1 ATGAAATTTTGA-TAACCACTCT
* *
13797 AAGAAAATTTGATAAC
1 ATGAAATTTTGATAAC
13813 TTTCCTATGT
Statistics
Matches: 125, Mismatches: 35, Indels: 22
0.69 0.19 0.12
Matches are distributed among these distances:
20 1 0.01
21 19 0.15
22 86 0.69
23 3 0.02
24 14 0.11
25 2 0.02
ACGTcount: A:0.39, C:0.15, G:0.12, T:0.34
Consensus pattern (22 bp):
ATGAAATTTTGATAACCACTCT
Found at i:15306 original size:119 final size:118
Alignment explanation
Indices: 15058--15408 Score: 598
Period size: 119 Copynumber: 3.0 Consensus size: 118
15048 TGTTAACACG
* *
15058 TTTGGAATCTAAGAATTAAGGAGTAATTTATACCATTTTTATTGGAAGAGTTGGTTTGAAGTGG-
1 TTTGGGATCTAAGAATTAAGGAGTAATTTATACTATTTTTATTGGAAGAGTTGGTTTGAAGTGGA
* *
15122 AAATTTAAGGACTTGAAATTCCTCAAAACAATATTCATAGTTGTGGTGGAGCG
66 AAATTTAAGGACTTGAAATTCCTCAAAACAATATTCATGGTTGTGGTGGAGCC
*
15175 TTTGGGACCTAAGAATTAAGGAGTAATTTATACTATTTTTA-TGGAAGAGTTGGTTTGAAGTGGA
1 TTTGGGATCTAAGAATTAAGGAGTAATTTATACTATTTTTATTGGAAGAGTTGGTTTGAAGTGGA
15239 AAATTTAAGGACTTGAGAAATTCCTCAAAACAATATTCATGGTTGTGGTGGAGCC
66 AAATTTAAGGACTT--GAAATTCCTCAAAACAATATTCATGGTTGTGGTGGAGCC
*
15294 TTTGGGATCTAAGAATTAAGGAGTAATTTATACTATTTTTATTGGAAGAGTTGGTTTGAAATGGA
1 TTTGGGATCTAAGAATTAAGGAGTAATTTATACTATTTTTATTGGAAGAGTTGGTTTGAAGTGGA
* *
15359 AAAATGAAGGACTTGAAATTCCTCAAAACAATATTCATGGTTGTGGTGGA
66 AAATTTAAGGACTTGAAATTCCTCAAAACAATATTCATGGTTGTGGTGGA
15409 TGTTCTTCCA
Statistics
Matches: 221, Mismatches: 9, Indels: 7
0.93 0.04 0.03
Matches are distributed among these distances:
116 22 0.10
117 52 0.24
118 36 0.16
119 77 0.35
120 34 0.15
ACGTcount: A:0.34, C:0.08, G:0.24, T:0.34
Consensus pattern (118 bp):
TTTGGGATCTAAGAATTAAGGAGTAATTTATACTATTTTTATTGGAAGAGTTGGTTTGAAGTGGA
AAATTTAAGGACTTGAAATTCCTCAAAACAATATTCATGGTTGTGGTGGAGCC
Found at i:15614 original size:16 final size:16
Alignment explanation
Indices: 15578--15627 Score: 66
Period size: 16 Copynumber: 3.1 Consensus size: 16
15568 TATAATACTA
*
15578 ATATTCTTATTAGTCATT
1 ATATTATTATTA-T-ATT
15596 ATATTATTATTATATT
1 ATATTATTATTATATT
15612 ATATTATTATT-TATT
1 ATATTATTATTATATT
15627 A
1 A
15628 CTTTCCAATT
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
15 5 0.16
16 14 0.45
17 1 0.03
18 11 0.35
ACGTcount: A:0.34, C:0.04, G:0.02, T:0.60
Consensus pattern (16 bp):
ATATTATTATTATATT
Found at i:15727 original size:8 final size:8
Alignment explanation
Indices: 15704--15744 Score: 55
Period size: 8 Copynumber: 4.9 Consensus size: 8
15694 AATGAGGATA
15704 TATCTTATC
1 TATCTTA-C
15713 TTATCTTAC
1 -TATCTTAC
*
15722 TATCTTAG
1 TATCTTAC
15730 TATCTTAC
1 TATCTTAC
15738 TATCTTA
1 TATCTTA
15745 TCTTACTATT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
8 21 0.72
9 1 0.03
10 7 0.24
ACGTcount: A:0.24, C:0.20, G:0.02, T:0.54
Consensus pattern (8 bp):
TATCTTAC
Found at i:15727 original size:13 final size:13
Alignment explanation
Indices: 15709--15753 Score: 63
Period size: 13 Copynumber: 3.2 Consensus size: 13
15699 GGATATATCT
15709 TATCTTATCTTAC
1 TATCTTATCTTAC
15722 TATCTTAGTATCTTAC
1 TATC-T--TATCTTAC
15738 TATCTTATCTTAC
1 TATCTTATCTTAC
15751 TAT
1 TAT
15754 TATATAAAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
13 15 0.52
14 1 0.03
15 1 0.03
16 12 0.41
ACGTcount: A:0.24, C:0.20, G:0.02, T:0.53
Consensus pattern (13 bp):
TATCTTATCTTAC
Found at i:15735 original size:16 final size:16
Alignment explanation
Indices: 15714--15744 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
15704 TATCTTATCT
15714 TATCTTACTATCTTAG
1 TATCTTACTATCTTAG
15730 TATCTTACTATCTTA
1 TATCTTACTATCTTA
15745 TCTTACTATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.26, C:0.19, G:0.03, T:0.52
Consensus pattern (16 bp):
TATCTTACTATCTTAG
Found at i:16521 original size:23 final size:22
Alignment explanation
Indices: 16480--16566 Score: 66
Period size: 26 Copynumber: 3.5 Consensus size: 22
16470 GACTGTAGAT
* *
16480 TGGTGGAAAATTTGATGAAGAAC
1 TGGT-GAAAACTTGTTGAAGAAC
16503 TGAGTGAAAACTTGTTGAAGAACAAC
1 TG-GTGAAAACTTGTTGAAG---AAC
*
16529 TTGGTGAAGACTTGTTGAAGAAC
1 -TGGTGAAAACTTGTTGAAGAAC
16552 TTTGGTGAATAACTT
1 --TGGTGAA-AACTT
16567 TGGTAGAGAC
Statistics
Matches: 53, Mismatches: 4, Indels: 12
0.77 0.06 0.17
Matches are distributed among these distances:
23 18 0.34
24 10 0.19
25 4 0.08
26 19 0.36
27 2 0.04
ACGTcount: A:0.36, C:0.08, G:0.26, T:0.30
Consensus pattern (22 bp):
TGGTGAAAACTTGTTGAAGAAC
Found at i:16565 original size:13 final size:13
Alignment explanation
Indices: 16529--16612 Score: 79
Period size: 13 Copynumber: 6.8 Consensus size: 13
16519 GAAGAACAAC
16529 TTGGTGAAG-AC-
1 TTGGTGAAGAACT
*
16540 TTGTTGAAGAACT
1 TTGGTGAAGAACT
*
16553 TTGGTGAATAACT
1 TTGGTGAAGAACT
16566 TTGGT--AGAGAC-
1 TTGGTGAAGA-ACT
*
16577 TTGCTGAAGAACT
1 TTGGTGAAGAACT
* *
16590 TTGATGAATAACT
1 TTGGTGAAGAACT
16603 TTGGTGAAGA
1 TTGGTGAAGA
16613 CTTGTTTCAC
Statistics
Matches: 58, Mismatches: 9, Indels: 10
0.75 0.12 0.13
Matches are distributed among these distances:
11 14 0.24
12 6 0.10
13 38 0.66
ACGTcount: A:0.31, C:0.08, G:0.27, T:0.33
Consensus pattern (13 bp):
TTGGTGAAGAACT
Found at i:16577 original size:37 final size:37
Alignment explanation
Indices: 16529--16618 Score: 146
Period size: 37 Copynumber: 2.4 Consensus size: 37
16519 GAAGAACAAC
*
16529 TTGGTGAAGACTTGTTGAAGAACTTTGGTGAATAACT
1 TTGGTGAAGACTTGTTGAAGAACTTTGATGAATAACT
*
16566 TTGGT-AGAGACTTGCTGAAGAACTTTGATGAATAACT
1 TTGGTGA-AGACTTGTTGAAGAACTTTGATGAATAACT
16603 TTGGTGAAGACTTGTT
1 TTGGTGAAGACTTGTT
16619 TCACTCTTGG
Statistics
Matches: 48, Mismatches: 3, Indels: 4
0.87 0.05 0.07
Matches are distributed among these distances:
36 1 0.02
37 46 0.96
38 1 0.02
ACGTcount: A:0.29, C:0.09, G:0.27, T:0.36
Consensus pattern (37 bp):
TTGGTGAAGACTTGTTGAAGAACTTTGATGAATAACT
Found at i:18325 original size:29 final size:29
Alignment explanation
Indices: 18270--18326 Score: 71
Period size: 29 Copynumber: 2.0 Consensus size: 29
18260 CCCATTTTCT
* *
18270 TTGAATTTTGTTCTTAAAAGCTGCTGTTA
1 TTGAATTTTGTTCATAAAAGCTACTGTTA
*
18299 TTGAATTTAT-TTCATAAAAGTTACTGTT
1 TTGAATTT-TGTTCATAAAAGCTACTGTT
18327 GTTTTCAAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 23 0.96
30 1 0.04
ACGTcount: A:0.28, C:0.09, G:0.14, T:0.49
Consensus pattern (29 bp):
TTGAATTTTGTTCATAAAAGCTACTGTTA
Found at i:31446 original size:132 final size:132
Alignment explanation
Indices: 31209--31459 Score: 403
Period size: 132 Copynumber: 1.9 Consensus size: 132
31199 TATTGAGTTT
* * *
31209 CAGGTTGCGAAATTGAACTTCTTGTGACATCTTGGTTAAGGAGATTCGAGTCCAACACATTATTG
1 CAGGTTGCCAAATTGAACTTCTTGCGACATCTTGGTTAAGGAGATTCGAGTACAACACATTATTG
* **
31274 TTCCAAAAGTTTTGTGACTGGTTCCATGCCAACCGCAATGAATTATCATCCCCAACTGGAAAATT
66 TTCCAAAAGTTTTGTGACTGGTACCATGCCAACAACAATGAATTATCATCCCCAACTGGAAAATT
31339 AC
131 AC
*
31341 CAGGTTGCCAAATTGAACTTGTTGCGACATCTTGGTTAAGGAGATTCGAGTACAACACATTATTG
1 CAGGTTGCCAAATTGAACTTCTTGCGACATCTTGGTTAAGGAGATTCGAGTACAACACATTATTG
* ** *
31406 TTCCAAAAGTTTTGTGATTGGTAGGATGGCAACAACAATGAATTATCATCCCCA
66 TTCCAAAAGTTTTGTGACTGGTACCATGCCAACAACAATGAATTATCATCCCCA
31460 TGATAAACTG
Statistics
Matches: 108, Mismatches: 11, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
132 108 1.00
ACGTcount: A:0.30, C:0.20, G:0.20, T:0.30
Consensus pattern (132 bp):
CAGGTTGCCAAATTGAACTTCTTGCGACATCTTGGTTAAGGAGATTCGAGTACAACACATTATTG
TTCCAAAAGTTTTGTGACTGGTACCATGCCAACAACAATGAATTATCATCCCCAACTGGAAAATT
AC
Found at i:40722 original size:45 final size:45
Alignment explanation
Indices: 40672--40798 Score: 218
Period size: 45 Copynumber: 2.8 Consensus size: 45
40662 AATTCTACTT
*
40672 CATCTCTAGGTAATTCATCAAAACAAACCTAATATTATACTCCTC
1 CATCTCTAGGTAATTCATCAAAATAAACCTAATATTATACTCCTC
* *
40717 CATCTCTAGGTAATTCATCAAAATAAAGCTAATATTCTACTCCTC
1 CATCTCTAGGTAATTCATCAAAATAAACCTAATATTATACTCCTC
*
40762 CATCTCTAGGCAATTCATCAAAATAAACCTAATATTA
1 CATCTCTAGGTAATTCATCAAAATAAACCTAATATTA
40799 ATTGTTGCTT
Statistics
Matches: 76, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
45 76 1.00
ACGTcount: A:0.39, C:0.24, G:0.06, T:0.31
Consensus pattern (45 bp):
CATCTCTAGGTAATTCATCAAAATAAACCTAATATTATACTCCTC
Found at i:41622 original size:300 final size:301
Alignment explanation
Indices: 41071--41677 Score: 1146
Period size: 300 Copynumber: 2.0 Consensus size: 301
41061 TGGAAAGGTG
41071 GAAATATACCAAACATAAGCAACTAATAGAAACCTTAATAAGAAGGAAATTGAATATTAAATAAA
1 GAAATATACCAAACATAAGCAACTAATAGAAACCTTAATAAGAAGGAAATTGAATATTAAAT-AA
41136 TAAAAAACAATTTTTTGTAAAATAAAATAGGAATAAGGAAATGTTAAATTTAAGTATCAAATAAT
65 TAAAAAACAATTTTTTGTAAAATAAAATAGGAATAAGGAAATGTTAAATTTAAGTATCAAATAAT
41201 ATAATCAACAAATTAATCCAGATTTACCTCAAAATGTTGCGGTGAGAAGTGAAATCTCACCACTT
130 ATAATCAACAAATTAATCCAGATTTACCTCAAAATGTTGCGGTGAGAAGTGAAATCTCACCACTT
41266 CAGGCTATGTCATCCTAAGGCGCTGCTAAATTAAATGGAAGGATCTTATCAACGTCCACCTGGAA
195 CAGGCTATGTCATCCTAAGGCGCTGCTAAATTAAATGGAAGGATCTTATCAACGTCCACCTGGAA
*
41331 ATTTTAGGAAACAGAACGGAGTCTAGGTGAAACCAATTCAGA
260 ATTTTAGGAAACAGAACGGAGTCCAGGTGAAACCAATTCAGA
41373 GAAATATACCAAACATAAGCAACTAATAGAAACCTTAATAAGAAGGAAATTGAATATTAAAT-A-
1 GAAATATACCAAACATAAGCAACTAATAGAAACCTTAATAAGAAGGAAATTGAATATTAAATAAT
41436 AAAAAACAATTTTTTTGTAAAATAAAATAGGAATAAGGAAATGTTAAATTTAAGTATCAAATAAT
66 AAAAAACAA-TTTTTTGTAAAATAAAATAGGAATAAGGAAATGTTAAATTTAAGTATCAAATAAT
41501 ATAATCAACAAATTAATCCAGATTTACCTCAAAATGTTGCGGTGAGAAGTGAAATCTCACCACTT
130 ATAATCAACAAATTAATCCAGATTTACCTCAAAATGTTGCGGTGAGAAGTGAAATCTCACCACTT
* *
41566 CAGGCTATGTCATCCTAAGGCGTTGCTAAATTAAATGGAAGGATCTTATTAACGTCCACCTGGAA
195 CAGGCTATGTCATCCTAAGGCGCTGCTAAATTAAATGGAAGGATCTTATCAACGTCCACCTGGAA
*
41631 ATTTTAGGAAACAGAACGGAGTCCATGTGAAACCAATTCAGA
260 ATTTTAGGAAACAGAACGGAGTCCAGGTGAAACCAATTCAGA
41673 GAAAT
1 GAAAT
41678 GTTAGGGAAG
Statistics
Matches: 300, Mismatches: 4, Indels: 4
0.97 0.01 0.01
Matches are distributed among these distances:
299 9 0.03
300 229 0.76
302 62 0.21
ACGTcount: A:0.44, C:0.14, G:0.15, T:0.26
Consensus pattern (301 bp):
GAAATATACCAAACATAAGCAACTAATAGAAACCTTAATAAGAAGGAAATTGAATATTAAATAAT
AAAAAACAATTTTTTGTAAAATAAAATAGGAATAAGGAAATGTTAAATTTAAGTATCAAATAATA
TAATCAACAAATTAATCCAGATTTACCTCAAAATGTTGCGGTGAGAAGTGAAATCTCACCACTTC
AGGCTATGTCATCCTAAGGCGCTGCTAAATTAAATGGAAGGATCTTATCAACGTCCACCTGGAAA
TTTTAGGAAACAGAACGGAGTCCAGGTGAAACCAATTCAGA
Found at i:44125 original size:51 final size:51
Alignment explanation
Indices: 44028--44125 Score: 119
Period size: 51 Copynumber: 1.9 Consensus size: 51
44018 TTCATATTTA
* **
44028 TCTTGTTTAGATCTTGTCTCCGGACAAACAAACACTCTTTTAGTGTTTTTC
1 TCTTGTTTAGATCTTGTCTCCGGACAAACAAACACTCGTACAGTGTTTTTC
* *
44079 TCTTGTTTCA-ATCTTGTCTCTGGACATACAAACACT-GTACACGTGTT
1 TCTTGTTT-AGATCTTGTCTCCGGACAAACAAACACTCGTACA-GTGTT
44126 CTTCATTCAG
Statistics
Matches: 40, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
50 2 0.05
51 37 0.93
52 1 0.03
ACGTcount: A:0.22, C:0.22, G:0.14, T:0.41
Consensus pattern (51 bp):
TCTTGTTTAGATCTTGTCTCCGGACAAACAAACACTCGTACAGTGTTTTTC
Found at i:46120 original size:82 final size:82
Alignment explanation
Indices: 45971--46134 Score: 211
Period size: 82 Copynumber: 2.0 Consensus size: 82
45961 ACTTAATTAA
* * * * * * *
45971 TTCAAAAAATGAACATGTGTCAACTCCATAACCCACTTGTGGAGTCCAAAATTTGCATCGCCTGT
1 TTCAAAAAATGAACATATGTCAACTCCACAACCCACTTGTAGAGTCCAAAATTTACACCACCGGT
*
46036 GTATCAAATAATTACCC
66 GTATCAAATAATCACCC
* * ** *
46053 TTCAAAAAATGGACATATGTTAACTCCACAACCCGTTTGTAGAGTCCAAAATTTATACCACCGGT
1 TTCAAAAAATGAACATATGTCAACTCCACAACCCACTTGTAGAGTCCAAAATTTACACCACCGGT
46118 GTATCAAATAATCACCC
66 GTATCAAATAATCACCC
46135 AACAATTAAT
Statistics
Matches: 69, Mismatches: 13, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
82 69 1.00
ACGTcount: A:0.35, C:0.24, G:0.13, T:0.27
Consensus pattern (82 bp):
TTCAAAAAATGAACATATGTCAACTCCACAACCCACTTGTAGAGTCCAAAATTTACACCACCGGT
GTATCAAATAATCACCC
Found at i:51483 original size:93 final size:94
Alignment explanation
Indices: 51308--51496 Score: 317
Period size: 93 Copynumber: 2.0 Consensus size: 94
51298 AATTTAAACA
* *
51308 ATGTCATTTAAAAAAATATATTTTAAAAAATCTAATATATTTAAGCTTTTTAATGAAATTAGTAA
1 ATGTCATTTAAAAAAATATATTTTAAAAAATCTAATATATCTAAACTTTTTAATGAAATTAGTAA
*
51373 TATGGTAAAAATAAAATAGGTATAAGGAT
66 TATGGTAAAAATAAAATAGATATAAGGAT
* * *
51402 ATGTCATTT-AAGAAATATATTTTAAAAATTCTAATATATCTAAACTTTTTAATTAAATTAGTAA
1 ATGTCATTTAAAAAAATATATTTTAAAAAATCTAATATATCTAAACTTTTTAATGAAATTAGTAA
51466 TATGGTAAAAATAAAATAGATATAAGGAT
66 TATGGTAAAAATAAAATAGATATAAGGAT
51495 AT
1 AT
51497 TAAATTTAAG
Statistics
Matches: 89, Mismatches: 6, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
93 80 0.90
94 9 0.10
ACGTcount: A:0.49, C:0.04, G:0.10, T:0.38
Consensus pattern (94 bp):
ATGTCATTTAAAAAAATATATTTTAAAAAATCTAATATATCTAAACTTTTTAATGAAATTAGTAA
TATGGTAAAAATAAAATAGATATAAGGAT
Found at i:51540 original size:93 final size:92
Alignment explanation
Indices: 51353--51630 Score: 244
Period size: 93 Copynumber: 3.0 Consensus size: 92
51343 TATATTTAAG
* * *
51353 CTTTTTAATGAAATTAGTAATATGGTAAAAATAAAATAGGTATAAGGATATGT-CATTTAAG-AA
1 CTTTTTAATTAAATTAGTAATATGGTAAAAATAAAATAGATATAAGGATAT-TAAATTTAAGTAA
*** * ** * * *
51416 ATATATTTTAAAAATTCTAATAT-ATCTAAA
65 ATA-AAAATAGAGTTTTTAGT-TGAT-AAAA
51446 CTTTTTAATTAAATTAGTAATATGGTAAAAATAAAATAGATATAAGGATATTAAATTTAAGTAAA
1 CTTTTTAATTAAATTAGTAATATGGTAAAAATAAAATAGATATAAGGATATTAAATTTAAGTAAA
*
51511 TAAAGATAGAGTTTTTAGTTGAGTAAAA
66 TAAAAATAGAGTTTTTAGTTGA-TAAAA
* ** * * * * * * * *
51539 CTATAAAAGTAAA--A-TAAAATGGTAAAAATGAAATAGTTATAATGATATTAGATTTAATTGAA
1 CTTTTTAATTAAATTAGTAATATGGTAAAAATAAAATAGATATAAGGATATTAAATTTAAGTAAA
51601 TAAAAATAGAGTTTTTAGTTGACTAAAA
66 TAAAAATAGAGTTTTTAGTTGA-TAAAA
51629 CT
1 CT
51631 ATAAAAGTTT
Statistics
Matches: 156, Mismatches: 25, Indels: 11
0.81 0.13 0.06
Matches are distributed among these distances:
90 69 0.44
91 1 0.01
92 2 0.01
93 78 0.50
94 6 0.04
ACGTcount: A:0.49, C:0.03, G:0.13, T:0.36
Consensus pattern (92 bp):
CTTTTTAATTAAATTAGTAATATGGTAAAAATAAAATAGATATAAGGATATTAAATTTAAGTAAA
TAAAAATAGAGTTTTTAGTTGATAAAA
Found at i:51586 original size:90 final size:90
Alignment explanation
Indices: 51467--51638 Score: 272
Period size: 90 Copynumber: 1.9 Consensus size: 90
51457 AATTAGTAAT
*
51467 ATGGTAAAAATAAAATAGATATAAGGATATTAAATTTAAGTAAATAAAGATAGAGTTTTTAGTTG
1 ATGGTAAAAATAAAATAGATATAAGGATATTAAATTTAAGTAAATAAAAATAGAGTTTTTAGTTG
*
51532 AGTAAAACTATAAAAGTAAAATAAA
66 ACTAAAACTATAAAAGTAAAATAAA
* * * * * *
51557 ATGGTAAAAATGAAATAGTTATAATGATATTAGATTTAATTGAATAAAAATAGAGTTTTTAGTTG
1 ATGGTAAAAATAAAATAGATATAAGGATATTAAATTTAAGTAAATAAAAATAGAGTTTTTAGTTG
51622 ACTAAAACTATAAAAGT
66 ACTAAAACTATAAAAGT
51639 TTAAACAATG
Statistics
Matches: 74, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
90 74 1.00
ACGTcount: A:0.51, C:0.02, G:0.15, T:0.33
Consensus pattern (90 bp):
ATGGTAAAAATAAAATAGATATAAGGATATTAAATTTAAGTAAATAAAAATAGAGTTTTTAGTTG
ACTAAAACTATAAAAGTAAAATAAA
Found at i:51812 original size:15 final size:17
Alignment explanation
Indices: 51787--51818 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
51777 GAAAAGATAA
51787 AAATATACAAA-TAAAC
1 AAATATACAAACTAAAC
51803 AAAT-TACAAACTAAAC
1 AAATATACAAACTAAAC
51819 TCACATCCCC
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 6 0.40
16 9 0.60
ACGTcount: A:0.66, C:0.16, G:0.00, T:0.19
Consensus pattern (17 bp):
AAATATACAAACTAAAC
Found at i:52127 original size:26 final size:26
Alignment explanation
Indices: 52096--52150 Score: 74
Period size: 26 Copynumber: 2.1 Consensus size: 26
52086 CAATCCAAAG
* *
52096 AAAATAATAAGTTCCGTCTAATCAGA
1 AAAATAACAAGTTCCGTCTAACCAGA
* *
52122 AAAATAACAAGTTCGGTCTAGCCAGA
1 AAAATAACAAGTTCCGTCTAACCAGA
52148 AAA
1 AAA
52151 CACTTAACCC
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.47, C:0.16, G:0.15, T:0.22
Consensus pattern (26 bp):
AAAATAACAAGTTCCGTCTAACCAGA
Found at i:52746 original size:214 final size:214
Alignment explanation
Indices: 52377--52806 Score: 824
Period size: 214 Copynumber: 2.0 Consensus size: 214
52367 TATTTGATTA
52377 TATATACTATATATTATTTTTAGTGACTATGGAAATTACTTAAAGGCCAAATTGAGGATTAATGT
1 TATATACTATATATTATTTTTAGTGACTATGGAAATTACTTAAAGGCCAAATTGAGGATTAATGT
52442 GGTGCCTCCTTTTGCCTTTTTTTGGTCTTTTCTCACTTTTCGAAAGACTAAAAAGGCCCTCGATG
66 GGTGCCTCCTTTTGCCTTTTTTTGGTCTTTTCTCACTTTTCGAAAGACTAAAAAGGCCCTCGATG
52507 AATTTCCTTAATTATTTTTCATGCTGCCCTTTTTTGTAATTTACTGCTTTTATATTTATGATTAA
131 AATTTCCTTAATTATTTTTCATGCTGCCCTTTTTTGTAATTTACTGCTTTTATATTTATGATTAA
52572 GTGTGTTTTAATTACATAT
196 GTGTGTTTTAATTACATAT
*
52591 TATATACTATATATTATTTTTAGTGACTATGGAAATTACTTAAAGGCCAAATTGAGTATTAATGT
1 TATATACTATATATTATTTTTAGTGACTATGGAAATTACTTAAAGGCCAAATTGAGGATTAATGT
* *
52656 GGTGCCTCCTTTTGGCTTTTTTTGGTCTTTTCTCACTTTTCGGAAGACTAAAAAGGCCCTCGATG
66 GGTGCCTCCTTTTGCCTTTTTTTGGTCTTTTCTCACTTTTCGAAAGACTAAAAAGGCCCTCGATG
*
52721 AATTTCCTTAATTATTTTTCATGCTGCCCTTTTTTGTAATTTACTGTTTTTATATTTATGATTAA
131 AATTTCCTTAATTATTTTTCATGCTGCCCTTTTTTGTAATTTACTGCTTTTATATTTATGATTAA
52786 GTGTGTTTTAATTACATAT
196 GTGTGTTTTAATTACATAT
52805 TA
1 TA
52807 ATTGTGTGTA
Statistics
Matches: 212, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
214 212 1.00
ACGTcount: A:0.26, C:0.14, G:0.14, T:0.46
Consensus pattern (214 bp):
TATATACTATATATTATTTTTAGTGACTATGGAAATTACTTAAAGGCCAAATTGAGGATTAATGT
GGTGCCTCCTTTTGCCTTTTTTTGGTCTTTTCTCACTTTTCGAAAGACTAAAAAGGCCCTCGATG
AATTTCCTTAATTATTTTTCATGCTGCCCTTTTTTGTAATTTACTGCTTTTATATTTATGATTAA
GTGTGTTTTAATTACATAT
Found at i:53812 original size:42 final size:42
Alignment explanation
Indices: 53753--53833 Score: 144
Period size: 42 Copynumber: 1.9 Consensus size: 42
53743 GCTAAGTCTT
53753 GAAAATTCTCTGTAAATTAAGAAATACTCAACTCAAATCATA
1 GAAAATTCTCTGTAAATTAAGAAATACTCAACTCAAATCATA
* *
53795 GAAAATTCTTTGTAAATTAAGAAATATTCAACTCAAATC
1 GAAAATTCTCTGTAAATTAAGAAATACTCAACTCAAATC
53834 CTGATCCTTA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 37 1.00
ACGTcount: A:0.47, C:0.15, G:0.07, T:0.31
Consensus pattern (42 bp):
GAAAATTCTCTGTAAATTAAGAAATACTCAACTCAAATCATA
Found at i:53832 original size:21 final size:21
Alignment explanation
Indices: 53766--53832 Score: 57
Period size: 21 Copynumber: 3.2 Consensus size: 21
53756 AATTCTCTGT
*
53766 AAATTAAGAAATACTCAACTC
1 AAATTAAGAAATATTCAACTC
* ** *
53787 AAATCATAGAAA-ATTC-TTTGT
1 AAATTA-AGAAATATTCAACT-C
53808 AAATTAAGAAATATTCAACTC
1 AAATTAAGAAATATTCAACTC
53829 AAAT
1 AAAT
53833 CCTGATCCTT
Statistics
Matches: 33, Mismatches: 9, Indels: 8
0.66 0.18 0.16
Matches are distributed among these distances:
20 6 0.18
21 21 0.64
22 6 0.18
ACGTcount: A:0.51, C:0.13, G:0.06, T:0.30
Consensus pattern (21 bp):
AAATTAAGAAATATTCAACTC
Found at i:53969 original size:55 final size:55
Alignment explanation
Indices: 53899--54010 Score: 156
Period size: 55 Copynumber: 2.0 Consensus size: 55
53889 TTTATTTTGT
* *
53899 AGAATAATTAAGTAGAGATAGGGAGAATAGGATTTA-T-TAACATTTATTGTGTGAA
1 AGAATAATTAAGTAGAGATA-AGAG-ATAGAATTTATTATAACATTTATTGTGTGAA
* *
53954 AGAATAATTAAGTAGAGATAAGAGGTAGAATTTATTATAATATTTATTGTGTGAA
1 AGAATAATTAAGTAGAGATAAGAGATAGAATTTATTATAACATTTATTGTGTGAA
54009 AG
1 AG
54011 GAAACGGATA
Statistics
Matches: 51, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
53 8 0.16
54 4 0.08
55 39 0.76
ACGTcount: A:0.43, C:0.01, G:0.22, T:0.34
Consensus pattern (55 bp):
AGAATAATTAAGTAGAGATAAGAGATAGAATTTATTATAACATTTATTGTGTGAA
Found at i:58402 original size:178 final size:178
Alignment explanation
Indices: 58097--58426 Score: 479
Period size: 178 Copynumber: 1.9 Consensus size: 178
58087 TAAGCTCAAA
* * **
58097 TTATGTAATATTAAGTAGACCGTCTATTTCCGTTAACCGAAACAATTAATTCTTTGGAAGCAATT
1 TTATATAATATTAAGTAGACCGTCTATTCCCGTTAACCGAAACAACAAATTCTTTGGAAGCAATT
* *
58162 TTTATACCTTGAATATTAAATTTAGTTTTCGAGTCCTTCATAAAAGTTGTAGATCTTGGAACAAC
66 TTTATACCTTGAACATTAAATTTAGTTTTCGAGTCCTTCATAAAAGTTGTAGATCATGGAACAAC
*
58227 CTTTCAAGAGACACTTGAATCATCTCAATCAGACATCTGTAGCAAAAG
131 CTTTCAAGAGACACTTAAATCATCTCAATCAGACATCTGTAGCAAAAG
*
58275 TTATATAATATTAAGT-GAACCGTCTATTCCCGTTAACCGAAACAACAAATT-TTTCGGAAG-TA
1 TTATATAATATTAAGTAG-ACCGTCTATTCCCGTTAACCGAAACAACAAATTCTTT-GGAAGCAA
* *
58337 TTTTTGATA-CTTGAAACATTAAATTTAGTTTTCGAGTCCTTCTTGAAAGTTGTAGATCATGGAA
64 TTTTT-ATACCTTG-AACATTAAATTTAGTTTTCGAGTCCTTCATAAAAGTTGTAGATCATGGAA
* * *
58401 CAATCTTTTAATAGACACTTAAATCA
127 CAACCTTTCAAGAGACACTTAAATCA
58427 CCTTAATTGG
Statistics
Matches: 135, Mismatches: 13, Indels: 8
0.87 0.08 0.05
Matches are distributed among these distances:
177 14 0.10
178 121 0.90
ACGTcount: A:0.35, C:0.16, G:0.14, T:0.36
Consensus pattern (178 bp):
TTATATAATATTAAGTAGACCGTCTATTCCCGTTAACCGAAACAACAAATTCTTTGGAAGCAATT
TTTATACCTTGAACATTAAATTTAGTTTTCGAGTCCTTCATAAAAGTTGTAGATCATGGAACAAC
CTTTCAAGAGACACTTAAATCATCTCAATCAGACATCTGTAGCAAAAG
Found at i:58459 original size:178 final size:178
Alignment explanation
Indices: 58094--58471 Score: 469
Period size: 178 Copynumber: 2.1 Consensus size: 178
58084 TCATAAGCTC
* * **
58094 AAATTATGTAATATTAAGTAGACCGTCTATTTCCGTTAACCGAAACAATTAATTCTTTGGAAGCA
1 AAATTATATAATATTAAGTAGACCGTCTATTCCCGTTAACCGAAACAACAAATTCTTTGGAAGCA
* *
58159 ATTTTTATACCTTGAATATTAAATTTAGTTTTCGAGTCCTTCATAAAAGTTGTAGATCTTGGAAC
66 ATTTTTATACCTTGAACATTAAATTTAGTTTTCGAGTCCTTCATAAAAGTTGTAGATCATGGAAC
* * * * *
58224 AACCTTTCAAGAGACACTTGAATCATCTCAATCAGACATCTGTAGCAA
131 AACCTTTCAAGAGACACTTAAATCACCTCAATCAGACAACCGAAGCAA
*
58272 AAGTTATATAATATTAAGT-GAACCGTCTATTCCCGTTAACCGAAACAACAAATT-TTTCGGAAG
1 AAATTATATAATATTAAGTAG-ACCGTCTATTCCCGTTAACCGAAACAACAAATTCTTT-GGAAG
* * *
58335 -TATTTTTGATA-CTTGAAACATTAAATTTAGTTTTCGAGTCCTTCTTGAAAGTTGTAGATCATG
64 CAATTTTT-ATACCTTG-AACATTAAATTTAGTTTTCGAGTCCTTCATAAAAGTTGTAGATCATG
* * * * ** *
58398 GAACAATCTTTTAATAGACACTTAAATCACCTTAATTGGATAACCGAAG-AGA
127 GAACAACCTTTCAAGAGACACTTAAATCACCTCAATCAGACAACCGAAGCA-A
*
58450 AAATTATATAATATTAAATAGA
1 AAATTATATAATATTAAGTAGA
58472 TCGTTTAGCC
Statistics
Matches: 170, Mismatches: 24, Indels: 12
0.83 0.12 0.06
Matches are distributed among these distances:
177 15 0.09
178 154 0.91
179 1 0.01
ACGTcount: A:0.37, C:0.15, G:0.13, T:0.35
Consensus pattern (178 bp):
AAATTATATAATATTAAGTAGACCGTCTATTCCCGTTAACCGAAACAACAAATTCTTTGGAAGCA
ATTTTTATACCTTGAACATTAAATTTAGTTTTCGAGTCCTTCATAAAAGTTGTAGATCATGGAAC
AACCTTTCAAGAGACACTTAAATCACCTCAATCAGACAACCGAAGCAA
Found at i:59804 original size:77 final size:79
Alignment explanation
Indices: 59642--59806 Score: 262
Period size: 77 Copynumber: 2.1 Consensus size: 79
59632 ATATATATTA
* * *
59642 AATTGATTGATTGATTTGAATATATTTGCTCCAATTAGAATCAATTAGTACTAAAATGATATTAA
1 AATTGATTGATTGATTTGAATATACTTGATCCAATTAGAATCAATTAATACT-AAATGATATTAA
59707 ATTGATTGATTCATT
65 ATTGATTGATTCATT
59722 AATTGATTGATTGATTTGAATAT-CTTGATCCAATTAGAATCAATTAATACT-AATGATATTAAA
1 AATTGATTGATTGATTTGAATATACTTGATCCAATTAGAATCAATTAATACTAAATGATATTAAA
*
59785 TTGATTGATTGATT
66 TTGATTGATTCATT
*
59799 GATTGATT
1 AATTGATT
59807 TGAATATTGA
Statistics
Matches: 80, Mismatches: 5, Indels: 3
0.91 0.06 0.03
Matches are distributed among these distances:
77 32 0.40
79 25 0.31
80 23 0.29
ACGTcount: A:0.37, C:0.07, G:0.13, T:0.43
Consensus pattern (79 bp):
AATTGATTGATTGATTTGAATATACTTGATCCAATTAGAATCAATTAATACTAAATGATATTAAA
TTGATTGATTCATT
Found at i:59836 original size:67 final size:68
Alignment explanation
Indices: 59723--59853 Score: 201
Period size: 67 Copynumber: 1.9 Consensus size: 68
59713 TGATTCATTA
* *
59723 ATTGATTGATTGATTTGAATATCTTGATCCAATTAGAATCAATTAATACTAATGATATTAAATTG
1 ATTGATTGATTGATTTGAATA-CTTGATCAAATTAAAATCAATTAATACTAATGATATTAAATTG
59788 ATTG
65 ATTG
* * *
59792 ATTGATTGATTGATTTGAATA-TTGATCAAATTAAAATCAATTAATATTAATGTTATTTAATT
1 ATTGATTGATTGATTTGAATACTTGATCAAATTAAAATCAATTAATACTAATGATATTAAATT
59854 TTGAATTTTA
Statistics
Matches: 57, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
67 36 0.63
69 21 0.37
ACGTcount: A:0.39, C:0.05, G:0.11, T:0.44
Consensus pattern (68 bp):
ATTGATTGATTGATTTGAATACTTGATCAAATTAAAATCAATTAATACTAATGATATTAAATTGA
TTG
Found at i:62327 original size:19 final size:20
Alignment explanation
Indices: 62303--62340 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
62293 CAATAATGTT
62303 TTTTG-TTTTTTGTTTTTTG
1 TTTTGTTTTTTTGTTTTTTG
62322 TTTTGTTTTTTTGTTTTTT
1 TTTTGTTTTTTTGTTTTTT
62341 TTGCATAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 5 0.28
20 13 0.72
ACGTcount: A:0.00, C:0.00, G:0.13, T:0.87
Consensus pattern (20 bp):
TTTTGTTTTTTTGTTTTTTG
Found at i:62341 original size:8 final size:7
Alignment explanation
Indices: 62299--62340 Score: 68
Period size: 7 Copynumber: 6.1 Consensus size: 7
62289 TTCTCAATAA
62299 TGTTTTT
1 TGTTTTT
62306 TGTTTTT
1 TGTTTTT
62313 TGTTTTT
1 TGTTTTT
*
62320 TGTTTTG
1 TGTTTTT
62327 T-TTTTT
1 TGTTTTT
62333 TGTTTTT
1 TGTTTTT
62340 T
1 T
62341 TTGCATAAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
6 5 0.16
7 27 0.84
ACGTcount: A:0.00, C:0.00, G:0.14, T:0.86
Consensus pattern (7 bp):
TGTTTTT
Found at i:66025 original size:13 final size:13
Alignment explanation
Indices: 66007--66039 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
65997 TGCTCTTGCT
66007 CTGTTTTTTTACC
1 CTGTTTTTTTACC
*
66020 CTG-TTTTTTCCC
1 CTGTTTTTTTACC
66032 CTGTTTTT
1 CTGTTTTT
66040 GCCAACTGTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
12 11 0.61
13 7 0.39
ACGTcount: A:0.03, C:0.24, G:0.09, T:0.64
Consensus pattern (13 bp):
CTGTTTTTTTACC
Found at i:67488 original size:6 final size:6
Alignment explanation
Indices: 67477--67510 Score: 68
Period size: 6 Copynumber: 5.7 Consensus size: 6
67467 CGTCATGAAT
67477 TTTTAA TTTTAA TTTTAA TTTTAA TTTTAA TTTT
1 TTTTAA TTTTAA TTTTAA TTTTAA TTTTAA TTTT
67511 TTGATTCCAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (6 bp):
TTTTAA
Found at i:73082 original size:128 final size:119
Alignment explanation
Indices: 72811--73126 Score: 352
Period size: 128 Copynumber: 2.6 Consensus size: 119
72801 ATGTAGCTAG
* *
72811 TGCCTCGTTAAAAACCTTAAG-CTGGAAAACCCAATGGGACAAAACC-AGTCATAAGGAAAAAAG
1 TGCCTCATTAAAAACCTTAAGTC-GGAAAACCCAATGGGACAAAACCGA-TCATAAGGGAAAAAG
** * * *
72874 AGTGCAGCATATCAAGTCCATTTGTCTTCTGGACAAATATTACATGTGCTCTTTAT
64 AGTGCAGCATATCAAGTCCATTTGTCTTCAAGACAAACATTAAATGTGCTCATTAT
** * *
72930 TGCCTCATTAAAAACCTTGTGTCGGAAAACCCAATGGGACAAAACCGAACAGAAGGGAAAAAGAG
1 TGCCTCATTAAAAACCTTAAGTCGGAAAACCCAATGGGACAAAACCGATCATAAGGGAAAAAGAG
* *
72995 TGCTAGAGCA-ATTTAAGTCCATGTAAATGTCTTCAAGACAATTACATCTAAATGTGCT-ATTGT
66 TGC---AGCATA-TCAAGTCCAT-T---TGTCTTCAAGACAA--ACAT-TAAATGTGCTCATTAT
**
73058 TGCCTCATTAAAAACCTTAAGTCGGAAAACCCTGTGGGACAAAACCGATCATAAGGGAAAAAGAG
1 TGCCTCATTAAAAACCTTAAGTCGGAAAACCCAATGGGACAAAACCGATCATAAGGGAAAAAGAG
73123 TGCA
66 TGCA
73127 ACGCACTTTA
Statistics
Matches: 165, Mismatches: 19, Indels: 20
0.81 0.09 0.10
Matches are distributed among these distances:
119 58 0.35
120 2 0.01
121 1 0.01
122 13 0.08
123 1 0.01
125 1 0.01
126 12 0.07
128 68 0.41
129 9 0.05
ACGTcount: A:0.38, C:0.19, G:0.19, T:0.23
Consensus pattern (119 bp):
TGCCTCATTAAAAACCTTAAGTCGGAAAACCCAATGGGACAAAACCGATCATAAGGGAAAAAGAG
TGCAGCATATCAAGTCCATTTGTCTTCAAGACAAACATTAAATGTGCTCATTAT
Found at i:76977 original size:65 final size:62
Alignment explanation
Indices: 76898--77285 Score: 272
Period size: 60 Copynumber: 6.4 Consensus size: 62
76888 GAAAGGTAAA
* * *
76898 ATCATGACAACTTCTGGTGTCAATTGAATAAAATTATGACATCTTCAAATGTCTATTGGAAATTT
1 ATCATGACAACTTCTGGTGTCAATTGAATAAAATTATGACATCTTCAAATATCAATT-GAAA--G
* *
76963 ATCATGACAACTTCTGGTGTCAATTGAATAAAATTATGACATCTTCAAGTATCAATTGCAAG
1 ATCATGACAACTTCTGGTGTCAATTGAATAAAATTATGACATCTTCAAATATCAATTGAAAG
* * * * *** * * *
77025 ATCATGACAACTTCTGGTGTCAATTG--CAAGATCATGACAACTTCTGGTGTCAATTGCAAC
1 ATCATGACAACTTCTGGTGTCAATTGAATAAAATTATGACATCTTCAAATATCAATTGAAAG
* * * * *** * *
77085 ATCATGACAACTTCTGGTGTCAATTG--CAAGATCATGACAACTTCTGGTGTCAATTGCAAG
1 ATCATGACAACTTCTGGTGTCAATTGAATAAAATTATGACATCTTCAAATATCAATTGAAAG
* * ** * *** * *
77145 AT-ATGACAACTTCTGGTGTCAATTG--CAAGAGCATGACAACTTCTGGTGTCAATTGCAAG
1 ATCATGACAACTTCTGGTGTCAATTGAATAAAATTATGACATCTTCAAATATCAATTGAAAG
* * * ** * *** * *
77204 ATTATGACAACTTCTGGTGTCATTTG--TAAGACCATGACAACTTCTGGTGTCAATTGTAAG
1 ATCATGACAACTTCTGGTGTCAATTGAATAAAATTATGACATCTTCAAATATCAATTGAAAG
*
77264 ACCATGACAACTTCTGGTGTCA
1 ATCATGACAACTTCTGGTGTCA
77286 TTTGTAAGTA
Statistics
Matches: 301, Mismatches: 21, Indels: 7
0.91 0.06 0.02
Matches are distributed among these distances:
59 58 0.19
60 160 0.53
62 26 0.09
64 3 0.01
65 54 0.18
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Consensus pattern (62 bp):
ATCATGACAACTTCTGGTGTCAATTGAATAAAATTATGACATCTTCAAATATCAATTGAAAG
Found at i:77182 original size:149 final size:151
Alignment explanation
Indices: 76963--77285 Score: 497
Period size: 149 Copynumber: 2.1 Consensus size: 151
76953 TTGGAAATTT
* * *
76963 ATCATGACAACTTCTGGTGTCAATTGAATAAAATTATGACATCTTCAAGTATCAATTGCAAGATC
1 ATCATGACAACTTCTGGTGTCAATTG-ACAAAATTATGACAACTTCAAGTATCAATTGCAAGAGC
*
77028 ATGACAACTTCTGGTGTCAATTGCAAGATCATGACAACTTCTGGTGTCAATTGCAACATCATGAC
65 ATGACAACTTCTGGTGTCAATTGCAAGATCATGACAACTTCTGGTGTCAATTGCAACACCATGAC
77093 AACTTCTGGTGTCAATTGCAAG
130 AACTTCTGGTGTCAATTGCAAG
* ** *
77115 ATCATGACAACTTCTGGTGTCAATTG-CAAGA-TATGACAACTTCTGGTGTCAATTGCAAGAGCA
1 ATCATGACAACTTCTGGTGTCAATTGACAAAATTATGACAACTTCAAGTATCAATTGCAAGAGCA
* * * *
77178 TGACAACTTCTGGTGTCAATTGCAAGATTATGACAACTTCTGGTGTCATTTGTAAGACCATGACA
66 TGACAACTTCTGGTGTCAATTGCAAGATCATGACAACTTCTGGTGTCAATTGCAACACCATGACA
*
77243 ACTTCTGGTGTCAATTGTAAG
131 ACTTCTGGTGTCAATTGCAAG
*
77264 ACCATGACAACTTCTGGTGTCA
1 ATCATGACAACTTCTGGTGTCA
77286 TTTGTAAGTA
Statistics
Matches: 157, Mismatches: 14, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
149 128 0.82
150 3 0.02
152 26 0.17
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.31
Consensus pattern (151 bp):
ATCATGACAACTTCTGGTGTCAATTGACAAAATTATGACAACTTCAAGTATCAATTGCAAGAGCA
TGACAACTTCTGGTGTCAATTGCAAGATCATGACAACTTCTGGTGTCAATTGCAACACCATGACA
ACTTCTGGTGTCAATTGCAAG
Found at i:77293 original size:30 final size:30
Alignment explanation
Indices: 76963--77285 Score: 486
Period size: 30 Copynumber: 10.7 Consensus size: 30
76953 TTGGAAATTT
* *
76963 ATCATGACAACTTCTGGTGTCAATTGAATAAA
1 ATCATGACAACTTCTGGTGTCAATTG--CAAG
* * ** *
76995 ATTATGACATCTTCAAGTATCAATTGCAAG
1 ATCATGACAACTTCTGGTGTCAATTGCAAG
77025 ATCATGACAACTTCTGGTGTCAATTGCAAG
1 ATCATGACAACTTCTGGTGTCAATTGCAAG
*
77055 ATCATGACAACTTCTGGTGTCAATTGCAAC
1 ATCATGACAACTTCTGGTGTCAATTGCAAG
77085 ATCATGACAACTTCTGGTGTCAATTGCAAG
1 ATCATGACAACTTCTGGTGTCAATTGCAAG
77115 ATCATGACAACTTCTGGTGTCAATTGCAAG
1 ATCATGACAACTTCTGGTGTCAATTGCAAG
77145 AT-ATGACAACTTCTGGTGTCAATTGCAAG
1 ATCATGACAACTTCTGGTGTCAATTGCAAG
*
77174 AGCATGACAACTTCTGGTGTCAATTGCAAG
1 ATCATGACAACTTCTGGTGTCAATTGCAAG
* * *
77204 ATTATGACAACTTCTGGTGTCATTTGTAAG
1 ATCATGACAACTTCTGGTGTCAATTGCAAG
* *
77234 ACCATGACAACTTCTGGTGTCAATTGTAAG
1 ATCATGACAACTTCTGGTGTCAATTGCAAG
*
77264 ACCATGACAACTTCTGGTGTCA
1 ATCATGACAACTTCTGGTGTCA
77286 TTTGTAAGTA
Statistics
Matches: 268, Mismatches: 22, Indels: 4
0.91 0.07 0.01
Matches are distributed among these distances:
29 28 0.10
30 219 0.82
32 21 0.08
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.31
Consensus pattern (30 bp):
ATCATGACAACTTCTGGTGTCAATTGCAAG
Found at i:78658 original size:31 final size:31
Alignment explanation
Indices: 78623--78684 Score: 106
Period size: 31 Copynumber: 2.0 Consensus size: 31
78613 AAAGTTATTA
* *
78623 ATGAATATTGTGATTATTCATGAATCAAGAG
1 ATGAATATTGTAAATATTCATGAATCAAGAG
78654 ATGAATATTGTAAATATTCATGAATCAAGAG
1 ATGAATATTGTAAATATTCATGAATCAAGAG
78685 TTCTCTTGTG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.42, C:0.06, G:0.18, T:0.34
Consensus pattern (31 bp):
ATGAATATTGTAAATATTCATGAATCAAGAG
Done.