Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019288.1 Corchorus olitorius cultivar O-4 contig19321, 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: 35323
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.32
Found at i:2488 original size:14 final size:14
Alignment explanation
Indices: 2469--2505 Score: 74
Period size: 14 Copynumber: 2.6 Consensus size: 14
2459 CTAAGCCTAT
2469 AATGATGTATTTAA
1 AATGATGTATTTAA
2483 AATGATGTATTTAA
1 AATGATGTATTTAA
2497 AATGATGTA
1 AATGATGTA
2506 ATATGCATGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.43, C:0.00, G:0.16, T:0.41
Consensus pattern (14 bp):
AATGATGTATTTAA
Found at i:2755 original size:25 final size:25
Alignment explanation
Indices: 2725--2772 Score: 87
Period size: 25 Copynumber: 1.9 Consensus size: 25
2715 ATGCAATGTC
2725 AAATTAGATTTGAGCTACATGAATG
1 AAATTAGATTTGAGCTACATGAATG
*
2750 AAATTAGCTTTGAGCTACATGAA
1 AAATTAGATTTGAGCTACATGAA
2773 CGCAAAATAC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.40, C:0.10, G:0.19, T:0.31
Consensus pattern (25 bp):
AAATTAGATTTGAGCTACATGAATG
Found at i:2969 original size:26 final size:28
Alignment explanation
Indices: 2912--3009 Score: 103
Period size: 27 Copynumber: 3.6 Consensus size: 28
2902 AAGTGGACTC
* * *
2912 AAAATGACCAACATGCCCCTGAATATG-
1 AAAATGACCAAAATGCCACTGAATGTGA
* * * *
2939 CAAATGACCAAAATTCC-CTTAGTGT-A
1 AAAATGACCAAAATGCCACTGAATGTGA
*
2965 AAAATGACCATAATGCCACTGAATGTGA
1 AAAATGACCAAAATGCCACTGAATGTGA
2993 AAAATGACCAAAATGCC
1 AAAATGACCAAAATGCC
3010 CCTATATTTT
Statistics
Matches: 56, Mismatches: 12, Indels: 5
0.77 0.16 0.07
Matches are distributed among these distances:
26 19 0.34
27 20 0.36
28 17 0.30
ACGTcount: A:0.43, C:0.22, G:0.14, T:0.20
Consensus pattern (28 bp):
AAAATGACCAAAATGCCACTGAATGTGA
Found at i:3007 original size:28 final size:27
Alignment explanation
Indices: 2912--3010 Score: 103
Period size: 26 Copynumber: 3.7 Consensus size: 27
2902 AAGTGGACTC
* *
2912 AAAATGACCAACATGCCCCTGAATATG-
1 AAAATGACCAAAATG-CCCTGAATGTGA
* * * *
2939 CAAATGACCAAAATTCCCTTAGTGT-A
1 AAAATGACCAAAATGCCCTGAATGTGA
*
2965 AAAATGACCATAATGCCACTGAATGTGA
1 AAAATGACCAAAATGCC-CTGAATGTGA
2993 AAAATGACCAAAATGCCC
1 AAAATGACCAAAATGCCC
3011 CTATATTTTT
Statistics
Matches: 57, Mismatches: 12, Indels: 6
0.76 0.16 0.08
Matches are distributed among these distances:
26 21 0.37
27 19 0.33
28 17 0.30
ACGTcount: A:0.42, C:0.23, G:0.14, T:0.20
Consensus pattern (27 bp):
AAAATGACCAAAATGCCCTGAATGTGA
Found at i:3393 original size:50 final size:50
Alignment explanation
Indices: 3315--3737 Score: 720
Period size: 50 Copynumber: 8.5 Consensus size: 50
3305 GAGAGATCCT
*
3315 CGAGTTTGGCTTGTGGAAAAGCTTATGTTGATAATTGACTCGTATGGAAA
1 CGAGTTTGGCTTGTGGAAAAGCCTATGTTGATAATTGACTCGTATGGAAA
* *
3365 CGAGCTTGGCTTGTGGAAAAGCCCATGTTGATAATTGACTCGTATGGAAA
1 CGAGTTTGGCTTGTGGAAAAGCCTATGTTGATAATTGACTCGTATGGAAA
*
3415 CGAGTTTGGCTTGTGGAAAAGGCTATGTTGATAATTGACTCGTATGGAAA
1 CGAGTTTGGCTTGTGGAAAAGCCTATGTTGATAATTGACTCGTATGGAAA
* *
3465 CGAGTTTGGCTTGTGGAAAAGCCTATGTTGATGATTGACTCGTATGGAGA
1 CGAGTTTGGCTTGTGGAAAAGCCTATGTTGATAATTGACTCGTATGGAAA
*
3515 CGAGTTTGGCTTGTGGAAAAGTCTATGTTGATAATTGACTCGTATGGAAA
1 CGAGTTTGGCTTGTGGAAAAGCCTATGTTGATAATTGACTCGTATGGAAA
* *
3565 CGAGTTCGACTTGTGGAAAAGCCTATGTTGATAATTGACTCGTATGGAAA
1 CGAGTTTGGCTTGTGGAAAAGCCTATGTTGATAATTGACTCGTATGGAAA
*
3615 CGAGTTTGGCTTGTGGAAAAGCCTATGTTGATAATTGACTTGTATGGAAA
1 CGAGTTTGGCTTGTGGAAAAGCCTATGTTGATAATTGACTCGTATGGAAA
* *
3665 CGAGTTTGGCTTGTGGAAAAGTCTGTGTTGATAATTGACTCGTATGGAAA
1 CGAGTTTGGCTTGTGGAAAAGCCTATGTTGATAATTGACTCGTATGGAAA
* *
3715 CGAGTTTGACTTATGGAAAAGCC
1 CGAGTTTGGCTTGTGGAAAAGCC
3738 AAAGCATTCG
Statistics
Matches: 349, Mismatches: 24, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
50 349 1.00
ACGTcount: A:0.28, C:0.12, G:0.29, T:0.32
Consensus pattern (50 bp):
CGAGTTTGGCTTGTGGAAAAGCCTATGTTGATAATTGACTCGTATGGAAA
Found at i:4368 original size:50 final size:50
Alignment explanation
Indices: 4311--4512 Score: 278
Period size: 50 Copynumber: 4.0 Consensus size: 50
4301 CTAAAATGCC
* ** * * *
4311 TTTTGAAAATCGACCTTTGGTCTTGATCTCACAAATGGAGTGCAATCTTA
1 TTTTGAAAAGCGAATTTTGATCTTGAGCTCACAAATGGAATGCAATCTTA
* **
4361 TTTTGAAAAGCGAATTTTGATCTTGGGCTCACAAATGGAATGCAATCTCG
1 TTTTGAAAAGCGAATTTTGATCTTGAGCTCACAAATGGAATGCAATCTTA
* * *
4411 TTTTGAAAAGCGAATTTTGATCTTGAACTCACAAATGGAAAGCAATTTTA
1 TTTTGAAAAGCGAATTTTGATCTTGAGCTCACAAATGGAATGCAATCTTA
* *
4461 CTTTGAAAAGCGAATTTTGATCTTGGGCTCACAAATGGAATGCAATCTTA
1 TTTTGAAAAGCGAATTTTGATCTTGAGCTCACAAATGGAATGCAATCTTA
4511 TT
1 TT
4513 GTAAATATTC
Statistics
Matches: 131, Mismatches: 21, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
50 131 1.00
ACGTcount: A:0.32, C:0.15, G:0.19, T:0.34
Consensus pattern (50 bp):
TTTTGAAAAGCGAATTTTGATCTTGAGCTCACAAATGGAATGCAATCTTA
Found at i:4446 original size:100 final size:100
Alignment explanation
Indices: 4311--4508 Score: 315
Period size: 100 Copynumber: 2.0 Consensus size: 100
4301 CTAAAATGCC
* * * * ** *
4311 TTTTGAAAATCGACCTTTGGTCTTGATCTCACAAATGGAGTGCAATCTTATTTTGAAAAGCGAAT
1 TTTTGAAAAGCGAACTTTGATCTTGAACTCACAAATGGAAAGCAATCTTACTTTGAAAAGCGAAT
4376 TTTGATCTTGGGCTCACAAATGGAATGCAATCTCG
66 TTTGATCTTGGGCTCACAAATGGAATGCAATCTCG
* *
4411 TTTTGAAAAGCGAATTTTGATCTTGAACTCACAAATGGAAAGCAATTTTACTTTGAAAAGCGAAT
1 TTTTGAAAAGCGAACTTTGATCTTGAACTCACAAATGGAAAGCAATCTTACTTTGAAAAGCGAAT
4476 TTTGATCTTGGGCTCACAAATGGAATGCAATCT
66 TTTGATCTTGGGCTCACAAATGGAATGCAATCT
4509 TATTGTAAAT
Statistics
Matches: 89, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
100 89 1.00
ACGTcount: A:0.32, C:0.16, G:0.19, T:0.33
Consensus pattern (100 bp):
TTTTGAAAAGCGAACTTTGATCTTGAACTCACAAATGGAAAGCAATCTTACTTTGAAAAGCGAAT
TTTGATCTTGGGCTCACAAATGGAATGCAATCTCG
Found at i:5108 original size:14 final size:14
Alignment explanation
Indices: 5089--5131 Score: 61
Period size: 14 Copynumber: 3.0 Consensus size: 14
5079 CAATTCTCTT
5089 TTGATTTTTTTTGA
1 TTGATTTTTTTTGA
5103 TTGATTTTTTTT-A
1 TTGATTTTTTTTGA
5116 TTGATTGATTTTTTGA
1 TTGATT--TTTTTTGA
5132 ATTTCTTAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
13 7 0.27
14 12 0.46
15 6 0.23
16 1 0.04
ACGTcount: A:0.16, C:0.00, G:0.14, T:0.70
Consensus pattern (14 bp):
TTGATTTTTTTTGA
Found at i:5119 original size:17 final size:16
Alignment explanation
Indices: 5093--5129 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 16
5083 TCTCTTTTGA
5093 TTTTTTTTGATTGATT
1 TTTTTTTTGATTGATT
5109 TTTTTTATTGATTGATT
1 TTTTTT-TTGATTGATT
5126 TTTT
1 TTTT
5130 GAATTTCTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 6 0.30
17 14 0.70
ACGTcount: A:0.14, C:0.00, G:0.11, T:0.76
Consensus pattern (16 bp):
TTTTTTTTGATTGATT
Found at i:5533 original size:14 final size:16
Alignment explanation
Indices: 5511--5547 Score: 51
Period size: 14 Copynumber: 2.4 Consensus size: 16
5501 GTGCCTTTAA
*
5511 TTTCCTTTTTTC-A-T
1 TTTCATTTTTTCAATT
5525 TTTCATTTTTTCAATT
1 TTTCATTTTTTCAATT
5541 TTTCATT
1 TTTCATT
5548 CATTTTGATT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
14 11 0.55
15 1 0.05
16 8 0.40
ACGTcount: A:0.14, C:0.16, G:0.00, T:0.70
Consensus pattern (16 bp):
TTTCATTTTTTCAATT
Found at i:14115 original size:16 final size:16
Alignment explanation
Indices: 14094--14127 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
14084 TCTACAATGT
14094 AATCCCATTTACAAAA
1 AATCCCATTTACAAAA
14110 AATCCCATTTACAAAA
1 AATCCCATTTACAAAA
14126 AA
1 AA
14128 GAACCGAGGC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.53, C:0.24, G:0.00, T:0.24
Consensus pattern (16 bp):
AATCCCATTTACAAAA
Found at i:14841 original size:14 final size:14
Alignment explanation
Indices: 14822--14859 Score: 51
Period size: 14 Copynumber: 2.7 Consensus size: 14
14812 TTTATTATTA
14822 ATAATATATACAAT
1 ATAATATATACAAT
*
14836 ATAATATAT-TAAT
1 ATAATATATACAAT
14849 ATATATATATA
1 ATA-ATATATA
14860 TATATATTCG
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
13 6 0.29
14 15 0.71
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (14 bp):
ATAATATATACAAT
Found at i:14851 original size:22 final size:22
Alignment explanation
Indices: 14823--14867 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 22
14813 TTATTATTAA
14823 TAATATATACAATATA-ATATAT
1 TAATATATA-AATATATATATAT
*
14845 TAATATATATATATATATATAT
1 TAATATATAAATATATATATAT
14867 T
1 T
14868 CGGTCGGGTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 5 0.24
22 16 0.76
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (22 bp):
TAATATATAAATATATATATAT
Found at i:15409 original size:25 final size:25
Alignment explanation
Indices: 15381--15430 Score: 82
Period size: 25 Copynumber: 2.0 Consensus size: 25
15371 TTATGCAATG
*
15381 TGAAATTAGATTTGAGCTGCATGAA
1 TGAAATTAGATTTGAGCTACATGAA
*
15406 TGAAATTAGCTTTGAGCTACATGAA
1 TGAAATTAGATTTGAGCTACATGAA
15431 CGCAAAATAC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.36, C:0.10, G:0.22, T:0.32
Consensus pattern (25 bp):
TGAAATTAGATTTGAGCTACATGAA
Found at i:15627 original size:26 final size:27
Alignment explanation
Indices: 15570--15668 Score: 103
Period size: 26 Copynumber: 3.7 Consensus size: 27
15560 AAGTGGACTC
* * *
15570 AAAATGACCAACATGCCCCTGAATATG-
1 AAAATGACCAAAATG-CCCTAAATGTGA
* * *
15597 CAAATGACCAAAATGCCCTTAGTGT-A
1 AAAATGACCAAAATGCCCTAAATGTGA
*
15623 AAAATGACCATAATGCCACTAAATGTGA
1 AAAATGACCAAAATGCC-CTAAATGTGA
15651 AAAATGACCAAAATGCCC
1 AAAATGACCAAAATGCCC
15669 CTGGATTTTT
Statistics
Matches: 59, Mismatches: 10, Indels: 6
0.79 0.13 0.08
Matches are distributed among these distances:
26 22 0.37
27 20 0.34
28 17 0.29
ACGTcount: A:0.43, C:0.23, G:0.14, T:0.19
Consensus pattern (27 bp):
AAAATGACCAAAATGCCCTAAATGTGA
Found at i:18867 original size:38 final size:39
Alignment explanation
Indices: 18771--18880 Score: 161
Period size: 39 Copynumber: 2.9 Consensus size: 39
18761 GGTTGTGCAT
*
18771 AGTGGACCCGTACCTCAGGGGGTTAAACTGATGGTAAAG
1 AGTGGACCCGTACCTCAGGGGGTTAAACTGTTGGTAAAG
* * *
18810 AGTGGACTCATACCACAGGGGGTTAAACTGTTGGT-AAG
1 AGTGGACCCGTACCTCAGGGGGTTAAACTGTTGGTAAAG
*
18848 AGTGGACCCGTGCCTCAGGGGGTT-AACTGTTGG
1 AGTGGACCCGTACCTCAGGGGGTTAAACTGTTGG
18881 CTAGACTCGA
Statistics
Matches: 63, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
37 9 0.14
38 23 0.37
39 31 0.49
ACGTcount: A:0.25, C:0.18, G:0.35, T:0.23
Consensus pattern (39 bp):
AGTGGACCCGTACCTCAGGGGGTTAAACTGTTGGTAAAG
Found at i:18921 original size:6 final size:6
Alignment explanation
Indices: 18910--18959 Score: 84
Period size: 6 Copynumber: 8.3 Consensus size: 6
18900 CGTTAATGGA
18910 TGATTG TGATTG TGATTG TGATTG TGATTG TGATT- TCGATTG TGATTG
1 TGATTG TGATTG TGATTG TGATTG TGATTG TGATTG T-GATTG TGATTG
18958 TG
1 TG
18960 GTGCAGCCTG
Statistics
Matches: 42, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
5 1 0.02
6 40 0.95
7 1 0.02
ACGTcount: A:0.16, C:0.02, G:0.32, T:0.50
Consensus pattern (6 bp):
TGATTG
Found at i:21297 original size:65 final size:64
Alignment explanation
Indices: 21214--21506 Score: 226
Period size: 65 Copynumber: 4.5 Consensus size: 64
21204 TTCGCCCTTT
* * *
21214 GACCGAAAGGGCATTTTTGGAAA-GTAGAATA-A-ACTGAAATGCAAAAATGATGAAACTGACCA
1 GACCGAAAGGGTATTTTTGGAAATG-AAAATACACACTGAAATG-AAAAA-GACGAAA-TGA-CA
21276 TTTC
61 TTTC
* *
21280 -ACCGAAAGGGTATTTTTGGAAATGAAAATACTACACTTAAATGTAAAAGACGAAATGACATTTC
1 GACCGAAAGGGTATTTTTGGAAATGAAAATAC-ACACTGAAATGAAAAAGACGAAATGACATTTC
* * **
21344 GACCGAAAGGGTA-TTTTGGAAATTTGAAAATTA-A-ACTTAAATGCAAAAGACGGAAATGACCC
1 GACCGAAAGGGTATTTTTGGAAA--TGAAAA-TACACACTGAAATGAAAAAGAC-GAAATGACAT
21406 TTC
62 TTC
* * * * * **
21409 GACCGAAAGGGTGTTTTGGGAATTTGAAAATTA-A-ACTTAAATGCAAAAGACGGAAATGACCCT
1 GACCGAAAGGGTATTTTTGGAA-ATGAAAA-TACACACTGAAATGAAAAAGAC-GAAATGACATT
21472 TC
63 TC
* * *
21474 GACCGAAAGGGTGTTTTCGGAATTTGAAAATAC
1 GACCGAAAGGGTATTTTTGGAA-ATGAAAATAC
21507 TAACAACCTT
Statistics
Matches: 203, Mismatches: 12, Indels: 25
0.85 0.05 0.10
Matches are distributed among these distances:
64 33 0.16
65 135 0.67
66 20 0.10
67 7 0.03
68 8 0.04
ACGTcount: A:0.41, C:0.13, G:0.21, T:0.25
Consensus pattern (64 bp):
GACCGAAAGGGTATTTTTGGAAATGAAAATACACACTGAAATGAAAAAGACGAAATGACATTTC
Found at i:21366 original size:64 final size:65
Alignment explanation
Indices: 21280--21504 Score: 294
Period size: 65 Copynumber: 3.5 Consensus size: 65
21270 TGACCATTTC
* * * *
21280 ACCGAAAGGGTATTTTTGGAA-ATGAAAATACTACACTTAAATGTAAAAGAC-GAAATGACATTT
1 ACCGAAAGGGTATTTTCGGAATATGAAAAT--TAAACTTAAATGCAAAAGACGGAAATGACACTT
21343 CG
64 CG
* *
21345 ACCGAAAGGGTATTTT-GGAAATTTGAAAATTAAACTTAAATGCAAAAGACGGAAATGACCCTTC
1 ACCGAAAGGGTATTTTCGG-AATATGAAAATTAAACTTAAATGCAAAAGACGGAAATGACACTTC
21409 G
65 G
* * * *
21410 ACCGAAAGGGTGTTTTGGGAATTTGAAAATTAAACTTAAATGCAAAAGACGGAAATGACCCTTCG
1 ACCGAAAGGGTATTTTCGGAATATGAAAATTAAACTTAAATGCAAAAGACGGAAATGACACTTCG
* *
21475 ACCGAAAGGGTGTTTTCGGAATTTGAAAAT
1 ACCGAAAGGGTATTTTCGGAATATGAAAAT
21505 ACTAACAACC
Statistics
Matches: 149, Mismatches: 7, Indels: 8
0.91 0.04 0.05
Matches are distributed among these distances:
64 20 0.13
65 120 0.81
66 9 0.06
ACGTcount: A:0.40, C:0.13, G:0.21, T:0.26
Consensus pattern (65 bp):
ACCGAAAGGGTATTTTCGGAATATGAAAATTAAACTTAAATGCAAAAGACGGAAATGACACTTCG
Found at i:25920 original size:43 final size:45
Alignment explanation
Indices: 25856--25949 Score: 120
Period size: 43 Copynumber: 2.1 Consensus size: 45
25846 ATAAACTGAA
*
25856 GAATTGAGGAAAGACCACCCTGAATCA-A-GTAAATTGATGCATT
1 GAATTGAAGAAAGACCACCCTGAATCATAGGTAAATTGATGCATT
* * *
25899 GAATTGAAGAAAGGCCGCCCTGGATCATTGAGGTAAATTGATGCATT
1 GAATTGAAGAAAGACCACCCTGAATCA-T-AGGTAAATTGATGCATT
25946 GAAT
1 GAAT
25950 AATTGAAATT
Statistics
Matches: 43, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
43 23 0.53
46 1 0.02
47 19 0.44
ACGTcount: A:0.36, C:0.15, G:0.24, T:0.24
Consensus pattern (45 bp):
GAATTGAAGAAAGACCACCCTGAATCATAGGTAAATTGATGCATT
Found at i:25961 original size:22 final size:22
Alignment explanation
Indices: 25933--26443 Score: 242
Period size: 22 Copynumber: 23.0 Consensus size: 22
25923 TCATTGAGGT
* *
25933 AAATTGATGCATTGAATAATTG
1 AAATTGAAGCATTGAAGAATTG
*
25955 AAATTGAATCATTGAAGAATTG
1 AAATTGAAGCATTGAAGAATTG
* *
25977 AAAGTGAAGTATTGAAGAATTG
1 AAATTGAAGCATTGAAGAATTG
* * *
25999 AAAGTGAATCATTGAAGGATTG
1 AAATTGAAGCATTGAAGAATTG
* *
26021 AAAATGAAGCATTGAAGTATT-
1 AAATTGAAGCATTGAAGAATTG
*
26042 AAACTTGAAGCATTGAAAAATTTG
1 AAA-TTGAAGCATTGAAGAA-TTG
*
26066 AAATTGAAACATTGAAGAATTG
1 AAATTGAAGCATTGAAGAATTG
** * *
26088 AAATTGAAATATTGAATAATTA
1 AAATTGAAGCATTGAAGAATTG
* * *
26110 AAATTGAAACATTGAAGGACTG
1 AAATTGAAGCATTGAAGAATTG
* *
26132 AGATTGAAGAATTG-A-AATTG
1 AAATTGAAGCATTGAAGAATTG
**
26152 AAGCATTGAAATATTG-A-AATTG
1 AA--ATTGAAGCATTGAAGAATTG
*
26174 AAACATTGAAGAATTGAATTTGAGGAATTG
1 -AA-ATTGAAGCATTG-A----A-GAATTG
* * *
26204 AAATTGAAACATTGAAGGATCG
1 AAATTGAAGCATTGAAGAATTG
* *
26226 AAATCGGAGCATTGAAGAATTG
1 AAATTGAAGCATTGAAGAATTG
* * *
26248 AATTTGAA--ATTGAGGCATTGG
1 AAATTGAAGCATTGAAGAATT-G
26269 AGAATTGAA--ATTGAA-ACATTG
1 A-AATTGAAGCATTGAAGA-ATTG
26290 AATGATTGAA--ATTGAA-ACATTG
1 AA--ATTGAAGCATTGAAGA-ATTG
26312 AAATACTGAA--ATTGAA-ACATTG
1 AAAT--TGAAGCATTGAAGA-ATTG
*
26334 AGGAATTGAA--TTTG-A-AATTG
1 A--AATTGAAGCATTGAAGAATTG
* *
26354 AAGCATTGAAGGATTG-A-ATTTG
1 AA--ATTGAAGCATTGAAGAATTG
*
26376 AAATTGAAGCATTGGAGAATTGG
1 AAATTGAAGCATTGAAGAATT-G
* **
26399 AGAATTGAAGTATTGACA-TTTTG
1 A-AATTGAAGCATTGA-AGAATTG
26422 AAATTGGAA-CATTGAAGAATTG
1 AAATT-GAAGCATTGAAGAATTG
26444 CATCTCAAGA
Statistics
Matches: 391, Mismatches: 64, Indels: 68
0.75 0.12 0.13
Matches are distributed among these distances:
18 1 0.00
20 38 0.10
21 12 0.03
22 274 0.70
23 26 0.07
24 20 0.05
25 1 0.00
27 1 0.00
28 11 0.03
29 2 0.01
30 5 0.01
ACGTcount: A:0.44, C:0.05, G:0.22, T:0.30
Consensus pattern (22 bp):
AAATTGAAGCATTGAAGAATTG
Found at i:25962 original size:14 final size:14
Alignment explanation
Indices: 25943--26666 Score: 148
Period size: 14 Copynumber: 49.9 Consensus size: 14
25933 AAATTGATGC
*
25943 ATTGAATAATTGAA
1 ATTGAAGAATTGAA
**
25957 ATTGAATCATTGAAGA
1 ATTGAAGAATTG-A-A
*
25973 ATTG-A-AAGTGAA
1 ATTGAAGAATTGAA
25985 GTATTGAAGAATTGAA
1 --ATTGAAGAATTGAA
* **
26001 AGTGAATCATTGAA
1 ATTGAAGAATTGAA
26015 GGATTGAA-AA-TGAA
1 --ATTGAAGAATTGAA
*
26029 GCATTGAAGTATT-AA
1 --ATTGAAGAATTGAA
*
26044 ACTTGAAGCATTGAAAA
1 A-TTGAAGAATTG--AA
26061 ATTTG-A-AATTGAAA
1 A-TTGAAGAATTG-AA
26075 CATTGAAGAATTGAA
1 -ATTGAAGAATTGAA
26090 ATTGAA-ATATTGAATA
1 ATTGAAGA-ATTG-A-A
26106 ATT-AA-AATTGAAA
1 ATTGAAGAATTG-AA
* * *
26119 CATTGAAGGACTGAG
1 -ATTGAAGAATTGAA
26134 ATTGAAGAATTGAA
1 ATTGAAGAATTGAA
*
26148 ATTGAAGCATTGAAA
1 ATTGAAGAATTG-AA
26163 TATTG-A-AATTGAAA
1 -ATTGAAGAATTG-AA
26177 CATTGAAGAATTGAA
1 -ATTGAAGAATTGAA
* *
26192 TTTGAGGAATTGAA
1 ATTGAAGAATTGAA
26206 ATTGAA-ACATTGAA
1 ATTGAAGA-ATTGAA
* * *
26220 GGATCG-A-AATCGGAGC
1 --ATTGAAGAAT-TGA-A
26236 ATTGAAGAATTGAA
1 ATTGAAGAATTGAA
* *
26250 TTTG-A-AATTGAGGC
1 ATTGAAGAATTGA--A
*
26264 ATTGGAGAATTGAA
1 ATTGAAGAATTGAA
26278 ATTGAA-ACATTG-A
1 ATTGAAGA-ATTGAA
26291 A-T---G-ATTGAA
1 ATTGAAGAATTGAA
26300 ATTGAA-ACATTGAA
1 ATTGAAGA-ATTGAA
26314 ATACTG-A-AATTGAAA
1 AT--TGAAGAATTG-AA
*
26329 CATTGAGGAATTGAA
1 -ATTGAAGAATTGAA
*
26344 TTTG-A-AATTGAA
1 ATTGAAGAATTGAA
*
26356 GCATTGAAGGATTGAA
1 --ATTGAAGAATTGAA
*
26372 TTTG-A-AATTGAA
1 ATTGAAGAATTGAA
*
26384 GCATTGGAGAATTGGAGA
1 --ATTGAAGAATT-GA-A
*
26402 ATTGAAGTATTGACA
1 ATTGAAGAATTGA-A
*
26417 TTTTG-A-AATTGGAA
1 -ATTGAAGAATT-GAA
*
26431 CATTGAAGAATTG-C
1 -ATTGAAGAATTGAA
*
26445 ATCTCAAGAATTGAA
1 AT-TGAAGAATTGAA
*
26460 ATTGAAGCATTGAAA
1 ATTGAAGAATTG-AA
26475 TATTG-A-AATTGAA
1 -ATTGAAGAATTGAA
26488 GCATTGAAGAATTGAA
1 --ATTGAAGAATTGAA
* *
26504 TTTGAA-ACATTAAAAA
1 ATTGAAGA-ATT--GAA
26520 ATTGAA-ATATTGAAGA
1 ATTGAAGA-ATTG-A-A
*
26536 ATTG-A-ATTTGAA
1 ATTGAAGAATTGAA
* *
26548 GGATTGAAGGATTAAA
1 --ATTGAAGAATTGAA
**
26564 ATTGAACCATTGAAA
1 ATTGAAGAATTG-AA
26579 TATTG-A-AATTGAAA
1 -ATTGAAGAATTG-AA
*
26593 CATTGAAGATTTGAA
1 -ATTGAAGAATTGAA
*
26608 TTTGAAGAATTGAAA
1 ATTGAAGAATTG-AA
*
26623 TATTGAA-CATTGAAAA
1 -ATTGAAGAATTG--AA
*
26639 AGTGAAGAATTGGATA
1 ATTGAAGAATT-GA-A
26655 ATTGAAGAATTG
1 ATTGAAGAATTG
26667 GAGCATTGGA
Statistics
Matches: 535, Mismatches: 82, Indels: 185
0.67 0.10 0.23
Matches are distributed among these distances:
8 4 0.01
9 2 0.00
10 1 0.00
12 22 0.04
13 16 0.03
14 252 0.47
15 81 0.15
16 147 0.27
17 9 0.02
18 1 0.00
ACGTcount: A:0.45, C:0.05, G:0.21, T:0.30
Consensus pattern (14 bp):
ATTGAAGAATTGAA
Found at i:25998 original size:44 final size:44
Alignment explanation
Indices: 25933--26699 Score: 417
Period size: 44 Copynumber: 17.5 Consensus size: 44
25923 TCATTGAGGT
* * *
25933 AAATTGATGCATTGAATAATTGAAATTGAATCATTGAAGAATTG
1 AAATTGAAGCATTGAAGAATTGAAATTGAAACATTGAAGAATTG
* * * * *
25977 AAAGTGAAGTATTGAAGAATTGAAAGTGAATCATTGAAGGATTG
1 AAATTGAAGCATTGAAGAATTGAAATTGAAACATTGAAGAATTG
* * * *
26021 AAAATGAAGCATTGAAGTATT-AAACTTGAAGCATTGAAAAATTTG
1 AAATTGAAGCATTGAAGAATTGAAA-TTGAAACATTGAAGAA-TTG
* * * *
26066 AAATTGAAACATTGAAGAATTGAAATTGAAATATTGAATAATTA
1 AAATTGAAGCATTGAAGAATTGAAATTGAAACATTGAAGAATTG
* * *
26110 AAATTGAAACATTGAAG----G--ACTG--AGATTGAAGAATTG
1 AAATTGAAGCATTGAAGAATTGAAATTGAAACATTGAAGAATTG
26146 AAATTGAAGCATTGAA-ATATTGAAATTGAAACATTGAAGAATTG
1 AAATTGAAGCATTGAAGA-ATTGAAATTGAAACATTGAAGAATTG
* * *
26190 -AA-T------TTGAGGAATTGAAATTGAAACATTGAAGGATCG
1 AAATTGAAGCATTGAAGAATTGAAATTGAAACATTGAAGAATTG
* * * *
26226 AAATCGGAGCATTGAAGAATTGAATTTGAAATTGAGGCATTGGAGAATTG
1 AAATTGAAGCATTGAAGAATTGAAATTG-AA---A--CATTGAAGAATTG
* *
26276 AAATTGAAACATTGAATG-ATTGAAATTGAAACATTGAA-ATACTG
1 AAATTGAAGCATTGAA-GAATTGAAATTGAAACATTGAAGA-ATTG
* * *
26320 AAATTGAAACATTGAGGAATTGAATTTGAAATTGAAGCATTGAAGGATTG
1 AAATTGAAGCATT---GAA--GAA-TTGAAATTGAAACATTGAAGAATTG
* * * *
26370 AATTTGAA--ATTGAAGCATTGGAGAATTGGAGA-ATTGAAGTATTG
1 AAATTGAAGCATTGAAGAATT-GA-AATT-GAAACATTGAAGAATTG
* * *
26414 ACATTTTGAA--ATTGGAA-CATTGAAGAATTG---CATCTCAAGAATTG
1 A-A-ATTGAAGCATT-GAAGAATTG-A-AATTGAAACAT-TGAAGAATTG
*
26458 AAATTGAAGCATTGAA-ATATTGAAATTGAAGCATTGAAGAATTG
1 AAATTGAAGCATTGAAGA-ATTGAAATTGAAACATTGAAGAATTG
* * *
26502 AATTTGAAACATT--A-AA---AAATTGAAATATTGAAGAATTG
1 AAATTGAAGCATTGAAGAATTGAAATTGAAACATTGAAGAATTG
* * * * *
26540 AATTTGAAGGATTGAAGGATTAAAATTGAACCATTGAA-ATATTG
1 AAATTGAAGCATTGAAGAATTGAAATTGAAACATTGAAGA-ATTG
* * *
26584 AAATTGAAACATTGAAGATTTGAATTTGAAGA-ATTGAA-ATATTG
1 AAATTGAAGCATTGAAGAATTGAAATTGAA-ACATTGAAGA-ATTG
** * * *
26628 AACATTGAAAAAGTGAAGAATTGGATAATTGAAGA-ATTGGAGCATTGG
1 AA-ATTGAAGCATTGAAGAATT-GA-AATTGAA-ACATTGAAGAATT-G
* *
26676 ATAATTGAAGAATTGAAAAATTGA
1 A-AATTGAAGCATTGAAGAATTGA
26700 GGCTAATTGA
Statistics
Matches: 577, Mismatches: 81, Indels: 127
0.74 0.10 0.16
Matches are distributed among these distances:
36 54 0.09
37 3 0.01
38 34 0.06
40 3 0.01
41 2 0.00
42 18 0.03
43 18 0.03
44 244 0.42
45 63 0.11
46 25 0.04
47 24 0.04
48 24 0.04
49 4 0.01
50 60 0.10
51 1 0.00
ACGTcount: A:0.45, C:0.05, G:0.21, T:0.30
Consensus pattern (44 bp):
AAATTGAAGCATTGAAGAATTGAAATTGAAACATTGAAGAATTG
Found at i:26081 original size:8 final size:7
Alignment explanation
Indices: 25943--26699 Score: 131
Period size: 8 Copynumber: 102.7 Consensus size: 7
25933 AAATTGATGC
25943 ATTGAATA
1 ATTGAA-A
25951 ATTG-AA
1 ATTGAAA
*
25957 ATTGAATC
1 ATTGAA-A
25965 ATTGAAGA
1 ATTGAA-A
25973 ATTG-AA
1 ATTGAAA
* *
25979 AGTGAAGT
1 ATTGAA-A
25987 ATTGAAGA
1 ATTGAA-A
25995 ATTG-AA
1 ATTGAAA
* *
26001 AGTGAATC
1 ATTGAA-A
*
26009 ATTGAAGG
1 ATTGAA-A
26017 ATTGAAA
1 ATTGAAA
*
26024 A-TGAAGC
1 ATTGAA-A
*
26031 ATTGAAGT
1 ATTGAA-A
26039 ATT-AAA
1 ATTGAAA
* *
26045 CTTGAAGC
1 ATTGAA-A
26053 ATTGAAAA
1 ATTG-AAA
26061 ATTTG-AA
1 A-TTGAAA
26068 ATTGAAA
1 ATTGAAA
26075 CATTGAAGA
1 -ATTGAA-A
26084 ATTG-AA
1 ATTGAAA
26090 ATTGAAA
1 ATTGAAA
26097 TATTGAATA
1 -ATTGAA-A
26106 ATT-AAA
1 ATTGAAA
26112 ATTGAAA
1 ATTGAAA
*
26119 CATTGAAGG
1 -ATTGAA-A
* *
26128 ACTG-AG
1 ATTGAAA
26134 ATTGAAGA
1 ATTGAA-A
26142 ATTG-AA
1 ATTGAAA
*
26148 ATTGAAGC
1 ATTGAA-A
26156 ATTGAAA
1 ATTGAAA
26163 TATTG-AA
1 -ATTGAAA
26170 ATTGAAA
1 ATTGAAA
26177 CATTGAAGA
1 -ATTGAA-A
26186 ATTG-AA
1 ATTGAAA
* *
26192 TTTGAGGA
1 ATTGA-AA
26200 ATTG-AA
1 ATTGAAA
26206 ATTGAAA
1 ATTGAAA
*
26213 CATTGAAGG
1 -ATTGAA-A
*
26222 ATCG-AA
1 ATTGAAA
* **
26228 ATCGGAGC
1 AT-TGAAA
26236 ATTGAAGA
1 ATTGAA-A
26244 ATTG-AA
1 ATTGAAA
*
26250 TTTG-AA
1 ATTGAAA
**
26256 ATTGAGGC
1 ATTGA-AA
*
26264 ATTGGAGA
1 ATT-GAAA
26272 ATTG-AA
1 ATTGAAA
26278 ATTGAAA
1 ATTGAAA
*
26285 CATTGAATG
1 -ATTGAA-A
26294 ATTG-AA
1 ATTGAAA
26300 ATTGAAA
1 ATTGAAA
26307 CATTGAAA
1 -ATTGAAA
*
26315 TACTG-AA
1 -ATTGAAA
26322 ATTGAAA
1 ATTGAAA
*
26329 CATTGAGGA
1 -ATTGA-AA
26338 ATTG-AA
1 ATTGAAA
*
26344 TTTG-AA
1 ATTGAAA
*
26350 ATTGAAGC
1 ATTGAA-A
*
26358 ATTGAAGG
1 ATTGAA-A
26366 ATTG-AA
1 ATTGAAA
*
26372 TTTG-AA
1 ATTGAAA
*
26378 ATTGAAGC
1 ATTGAA-A
*
26386 ATTGGAGA
1 ATT-GAAA
*
26394 ATTGGAGA
1 ATT-GAAA
*
26402 ATTGAAGT
1 ATTGAA-A
*
26410 ATTGACAT
1 ATTGA-AA
*
26418 TTTG-AA
1 ATTGAAA
*
26424 ATTGGAAC
1 ATT-GAAA
26432 ATTGAAGA
1 ATTGAA-A
*
26440 ATTG--C
1 ATTGAAA
*
26445 ATCTCAAGA
1 AT-TGAA-A
26454 ATTG-AA
1 ATTGAAA
*
26460 ATTGAAGC
1 ATTGAA-A
26468 ATTGAAA
1 ATTGAAA
26475 TATTG-AA
1 -ATTGAAA
*
26482 ATTGAAGC
1 ATTGAA-A
26490 ATTGAAGA
1 ATTGAA-A
26498 ATTG-AA
1 ATTGAAA
*
26504 TTTGAAA
1 ATTGAAA
*
26511 CATTAAAAA
1 -ATT-GAAA
26520 ATTGAAA
1 ATTGAAA
26527 TATTGAAGA
1 -ATTGAA-A
26536 ATTG-AA
1 ATTGAAA
* *
26542 TTTGAAGG
1 ATTGAA-A
*
26550 ATTGAAGG
1 ATTGAA-A
26558 ATT-AAA
1 ATTGAAA
*
26564 ATTGAACC
1 ATTGAA-A
26572 ATTGAAA
1 ATTGAAA
26579 TATTG-AA
1 -ATTGAAA
26586 ATTGAAA
1 ATTGAAA
26593 CATTGAAGA
1 -ATTGAA-A
*
26602 TTTG-AA
1 ATTGAAA
*
26608 TTTGAAGA
1 ATTGAA-A
26616 ATTGAAA
1 ATTGAAA
*
26623 TATTGAAC
1 -ATTGAAA
26631 ATTGAAAA
1 ATTG-AAA
*
26639 AGTGAAGA
1 ATTGAA-A
*
26647 ATTGGATA
1 ATT-GAAA
26655 ATTGAAGA
1 ATTGAA-A
**
26663 ATTGGAGC
1 ATT-GAAA
*
26671 ATTGGATA
1 ATT-GAAA
26679 ATTGAAGA
1 ATTGAA-A
26687 ATTGAAAA
1 ATTG-AAA
26695 ATTGA
1 ATTGA
26700 GGCTAATTGA
Statistics
Matches: 559, Mismatches: 100, Indels: 181
0.67 0.12 0.22
Matches are distributed among these distances:
5 2 0.00
6 126 0.23
7 95 0.17
8 309 0.55
9 27 0.05
ACGTcount: A:0.45, C:0.04, G:0.21, T:0.30
Consensus pattern (7 bp):
ATTGAAA
Found at i:26229 original size:58 final size:58
Alignment explanation
Indices: 26077--26666 Score: 255
Period size: 58 Copynumber: 9.9 Consensus size: 58
26067 AATTGAAACA
* * * * *
26077 TTGAAGAATTGAAATTGAAATATTGAATAATTAAAATTGAAACATTGAAGGACTGAGA-
1 TTGAAGAATTGAAATTGAAACATTGAAAAATTGAAATTGAAACATTGAAGAATTGA-AT
* *
26135 TTGAAGAATTGAAATTGAAGCATTGAAATATTGAAATTGAAACATTGAAGAATTGAAT
1 TTGAAGAATTGAAATTGAAACATTGAAAAATTGAAATTGAAACATTGAAGAATTGAAT
* ** * * * *
26193 TTGAGGAATTGAAATTGAAACATTGAAGGATCGAAATCGGAGCATTGAAGAATTGAAT
1 TTGAAGAATTGAAATTGAAACATTGAAAAATTGAAATTGAAACATTGAAGAATTGAAT
* * * *
26251 TTG-A-AATTG--A--G--GCATTGGAGAATTGAAATTGAAACATTGAATG-ATTGAAA
1 TTGAAGAATTGAAATTGAAACATTGAAAAATTGAAATTGAAACATTGAA-GAATTGAAT
* * *
26301 TTGAA-ACATTGAAATACTG-AA-ATTGAAACATTGAGGAATTG-AA-TTTG-A-AATTGAAGCA
1 TTGAAGA-ATTGAAAT--TGAAACATTGAAAAATTGA--AATTGAAACATTGAAGAATTGAA--T
* * ** * *
26359 TTGAAGGATTGAATTTG-AA-ATTGAAGCATTGGAGAATTGGAGA-ATTGAAGTATTGACATT
1 TTGAAGAATTGAAATTGAAACATTGAAAAATT-GA-AATT-GAAACATTGAAGAATTGA-A-T
*
26419 TTG-A-AATTGGAACATTGAAGA-ATTGCATCTCAAGAATTGAAATTGAAGCATTGAAATATTGA
1 TTGAAGAATT-GAA-ATTGAA-ACATTG-A----AA-AATTGAAATTGAAACATTG--A-A--G-
*
26481 AATTGAAGCA
51 AATTGAA--T
* * * *
26491 TTGAAGAATTGAATTTGAAACATTAAAAAATTGAAATATTGAAGA-ATTG-A-ATTTGAAGGA
1 TTGAAGAATTGAAATTGAAACATTGAAAAATTG-AA-ATTGAA-ACATTGAAGAATTGAA--T
* * * * *
26551 TTGAAGGATTAAAATTGAACCATTGAAATATTGAAATTGAAACATTGAAGATTTGAAT
1 TTGAAGAATTGAAATTGAAACATTGAAAAATTGAAATTGAAACATTGAAGAATTGAAT
* *
26609 TTGAAGAATTGAAATATTG-AACATTGAAAAAGTGAAGAATTGGATA-ATTGAAGAATTG
1 TTGAAGAATTG-AA-ATTGAAACATTGAAAAATTG-A-AATT-GAAACATTGAAGAATTG
26667 GAGCATTGGA
Statistics
Matches: 412, Mismatches: 65, Indels: 107
0.71 0.11 0.18
Matches are distributed among these distances:
50 32 0.08
51 3 0.01
52 5 0.01
54 2 0.00
56 30 0.07
57 6 0.01
58 155 0.38
59 24 0.06
60 63 0.15
61 17 0.04
62 8 0.02
63 1 0.00
64 1 0.00
65 2 0.00
66 13 0.03
67 7 0.02
68 14 0.03
69 1 0.00
71 4 0.01
72 16 0.04
73 4 0.01
74 4 0.01
ACGTcount: A:0.44, C:0.05, G:0.21, T:0.30
Consensus pattern (58 bp):
TTGAAGAATTGAAATTGAAACATTGAAAAATTGAAATTGAAACATTGAAGAATTGAAT
Found at i:26255 original size:50 final size:49
Alignment explanation
Indices: 26201--26378 Score: 172
Period size: 50 Copynumber: 3.7 Consensus size: 49
26191 ATTTGAGGAA
* * *
26201 TTGAAATTGAAACATTGAAGGATCGAAATCGGAGCATTGAAGAATTGAAT
1 TTGAAATTGAAACATTGAAGGATCGAAATTGAAACATTG-AGAATTGAAT
** * * *
26251 TTGAAATTGAGGCATTGGAGAATTGAAATTGAAACATT--GAA-TG-A-
1 TTGAAATTGAAACATTGAAGGATCGAAATTGAAACATTGAGAATTGAAT
26295 TTGAAATTGAAACATTGAA--ATACTGAAATTGAAACATTGAGGAATTGAAT
1 TTGAAATTGAAACATTGAAGGAT-C-GAAATTGAAACATTGA-GAATTGAAT
* * *
26345 TTGAAATTGAAGCATTGAAGGATTGAATTTGAAA
1 TTGAAATTGAAACATTGAAGGATCGAAATTGAAA
26379 TTGAAGCATT
Statistics
Matches: 103, Mismatches: 15, Indels: 20
0.75 0.11 0.14
Matches are distributed among these distances:
42 2 0.02
44 30 0.29
45 1 0.01
46 2 0.02
47 6 0.06
48 2 0.02
49 1 0.01
50 57 0.55
52 2 0.02
ACGTcount: A:0.43, C:0.06, G:0.22, T:0.29
Consensus pattern (49 bp):
TTGAAATTGAAACATTGAAGGATCGAAATTGAAACATTGAGAATTGAAT
Found at i:26378 original size:72 final size:72
Alignment explanation
Indices: 26189--26378 Score: 215
Period size: 72 Copynumber: 2.6 Consensus size: 72
26179 TTGAAGAATT
* * * * * * *
26189 GAATTTGAGGAATTGAAATTGAAACATTGAAGGATCGAAATCGGAGCATTGAAGAATTGAATTTG
1 GAATTGGA-GAATTGAAATTGAAACATTGAAGGATTGAAATTGAAACATTGAAGAACTGAAATTG
26254 AAATTGAG
65 AAATTGAG
* *
26262 GCATTGGAGAATTGAAATTGAAACATTGAATGATTGAAATTGAAACATTGAA-ATACTGAAATTG
1 GAATTGGAGAATTGAAATTGAAACATTGAAGGATTGAAATTGAAACATTGAAGA-ACTGAAATTG
26326 AAACATTGAG
65 -AA-ATTGAG
* * *
26336 GAATT-GA-ATTTGAAATTGAAGCATTGAAGGATTGAATTTGAAA
1 GAATTGGAGAATTGAAATTGAAACATTGAAGGATTGAAATTGAAA
26379 TTGAAGCATT
Statistics
Matches: 100, Mismatches: 14, Indels: 7
0.83 0.12 0.06
Matches are distributed among these distances:
71 1 0.01
72 79 0.79
73 10 0.10
74 10 0.10
ACGTcount: A:0.43, C:0.05, G:0.23, T:0.29
Consensus pattern (72 bp):
GAATTGGAGAATTGAAATTGAAACATTGAAGGATTGAAATTGAAACATTGAAGAACTGAAATTGA
AATTGAG
Found at i:26405 original size:24 final size:23
Alignment explanation
Indices: 26369--26443 Score: 64
Period size: 23 Copynumber: 3.3 Consensus size: 23
26359 TTGAAGGATT
*
26369 GAATTTGAAATTGAAGCATTGGA
1 GAATTGGAAATTGAAGCATTGGA
*
26392 GAATTGGAGAATTGAAGTATT-GA
1 GAATTGGA-AATTGAAGCATTGGA
* * * *
26415 CATTTTGAAATTGGAA-CATTGAA
1 GAATTGGAAATT-GAAGCATTGGA
26438 GAATTG
1 GAATTG
26444 CATCTCAAGA
Statistics
Matches: 39, Mismatches: 10, Indels: 6
0.71 0.18 0.11
Matches are distributed among these distances:
22 7 0.18
23 21 0.54
24 11 0.28
ACGTcount: A:0.39, C:0.04, G:0.25, T:0.32
Consensus pattern (23 bp):
GAATTGGAAATTGAAGCATTGGA
Found at i:26479 original size:22 final size:23
Alignment explanation
Indices: 26454--26600 Score: 89
Period size: 22 Copynumber: 6.6 Consensus size: 23
26444 CATCTCAAGA
26454 ATTGAA-ATTGAAGCATTGAAAT
1 ATTGAACATTGAAGCATTGAAAT
26476 ATTGAA-ATTGAAGCATTGAAGA-
1 ATTGAACATTGAAGCATTGAA-AT
* * * *
26498 ATTGAA-TTTGAAACATTAAAAA
1 ATTGAACATTGAAGCATTGAAAT
* *
26520 ATTGAAATATTGAAGAATTG-AAT
1 ATTG-AACATTGAAGCATTGAAAT
* *
26543 -TTGAAGGATTGAAGGATT-AAA-
1 ATTGAA-CATTGAAGCATTGAAAT
**
26564 ATTGAACCATTGAAATATTG-AA-
1 ATTGAA-CATTGAAGCATTGAAAT
26586 ATTGAAACATTGAAG
1 ATTG-AACATTGAAG
26601 ATTTGAATTT
Statistics
Matches: 101, Mismatches: 15, Indels: 18
0.75 0.11 0.13
Matches are distributed among these distances:
21 3 0.03
22 83 0.82
23 7 0.07
24 8 0.08
ACGTcount: A:0.47, C:0.04, G:0.18, T:0.31
Consensus pattern (23 bp):
ATTGAACATTGAAGCATTGAAAT
Found at i:26606 original size:22 final size:22
Alignment explanation
Indices: 26518--26699 Score: 116
Period size: 22 Copynumber: 8.0 Consensus size: 22
26508 AAACATTAAA
**
26518 AAATTGAAATATTGAAGAATTG
1 AAATTGAAGCATTGAAGAATTG
* * * *
26540 AATTTGAAGGATTGAAGGATTA
1 AAATTGAAGCATTGAAGAATTG
*
26562 AAATTGAACCATTGAA-ATATTG
1 AAATTGAAGCATTGAAGA-ATTG
* *
26584 AAATTGAAACATTGAAGATTTG
1 AAATTGAAGCATTGAAGAATTG
* *
26606 AATTTGAAGAATTGAA-ATATTG
1 AAATTGAAGCATTGAAGA-ATTG
** *
26628 AACATTGAAAAAGTGAAGAATTGG
1 AA-ATTGAAGCATTGAAGAATT-G
* * *
26652 ATAATTGAAGAATTGGAGCATTGG
1 A-AATTGAAGCATTGAAGAATT-G
* *
26676 ATAATTGAAGAATTGAAAAATTG
1 A-AATTGAAGCATTGAAGAATTG
26699 A
1 A
26700 GGCTAATTGA
Statistics
Matches: 127, Mismatches: 26, Indels: 13
0.77 0.16 0.08
Matches are distributed among these distances:
21 1 0.01
22 69 0.54
23 17 0.13
24 39 0.31
25 1 0.01
ACGTcount: A:0.46, C:0.03, G:0.21, T:0.30
Consensus pattern (22 bp):
AAATTGAAGCATTGAAGAATTG
Found at i:27889 original size:4 final size:4
Alignment explanation
Indices: 27880--27920 Score: 50
Period size: 4 Copynumber: 10.8 Consensus size: 4
27870 ACTTTTAATT
* *
27880 TTTC TTTC TTTT TTTC TTTC TTTT TTTC TTT- TTT- TTTC TTT
1 TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTT
27921 TTTACATCTT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
3 6 0.19
4 26 0.81
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (4 bp):
TTTC
Found at i:27923 original size:12 final size:12
Alignment explanation
Indices: 27878--27920 Score: 72
Period size: 12 Copynumber: 3.8 Consensus size: 12
27868 TCACTTTTAA
27878 TTTTTCTTTCTT
1 TTTTTCTTTCTT
27890 TTTTTCTTTCTT
1 TTTTTCTTTCTT
27902 TTTTTC-TT-TT
1 TTTTTCTTTCTT
27912 TTTTTCTTT
1 TTTTTCTTT
27921 TTTACATCTT
Statistics
Matches: 30, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
10 8 0.27
11 4 0.13
12 18 0.60
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (12 bp):
TTTTTCTTTCTT
Found at i:31836 original size:29 final size:28
Alignment explanation
Indices: 31794--31976 Score: 180
Period size: 29 Copynumber: 6.5 Consensus size: 28
31784 ATTTACTTTT
31794 ATTTTGGTCATTTTGGTACATCCAAGGGC
1 ATTTTGGTCATTTT-GTACATCCAAGGGC
*
31823 ATTTTGATCATTTTG--CATGACCAAGGGC
1 ATTTTGGTCATTTTGTACAT--CCAAGGGC
31851 ATTTTGGTCATTTTTGTACATCCAAGGGC
1 ATTTTGGTCA-TTTTGTACATCCAAGGGC
* *
31880 ATTTTGGTCATTTTTTCACATTC-AGTGGC
1 ATTTTGGTCATTTTGT-ACATCCAAG-GGC
* *
31909 ATTATGGTCATTTT-TACA-CTAAGGGC
1 ATTTTGGTCATTTTGTACATCCAAGGGC
* * * *
31935 ATTTTGGTCA-TTTGCATATTCAGGGGC
1 ATTTTGGTCATTTTGTACATCCAAGGGC
*
31962 ATGTTGGTCATTTTG
1 ATTTTGGTCATTTTG
31977 AGTCCACTTT
Statistics
Matches: 129, Mismatches: 14, Indels: 23
0.78 0.08 0.14
Matches are distributed among these distances:
25 3 0.02
26 17 0.13
27 19 0.15
28 30 0.23
29 57 0.44
31 3 0.02
ACGTcount: A:0.21, C:0.16, G:0.22, T:0.42
Consensus pattern (28 bp):
ATTTTGGTCATTTTGTACATCCAAGGGC
Found at i:32143 original size:25 final size:25
Alignment explanation
Indices: 32115--32162 Score: 87
Period size: 25 Copynumber: 1.9 Consensus size: 25
32105 GTATTTTGCG
32115 TTCATGTAGCTCAAAGCTAATTTCA
1 TTCATGTAGCTCAAAGCTAATTTCA
*
32140 TTCATGTAGCTCAAATCTAATTT
1 TTCATGTAGCTCAAAGCTAATTT
32163 GACATTGCAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.31, C:0.19, G:0.10, T:0.40
Consensus pattern (25 bp):
TTCATGTAGCTCAAAGCTAATTTCA
Done.