Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01023636.1 Corchorus olitorius cultivar O-4 contig23669, 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: 53529
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.31
Found at i:5895 original size:17 final size:15
Alignment explanation
Indices: 5877--5926 Score: 61
Period size: 15 Copynumber: 3.5 Consensus size: 15
5867 AAGACATGTT
5877 TTTTCAAGAAAATTG
1 TTTTCAAGAAAATTG
*
5892 TTTTCAAGAAAA-GG
1 TTTTCAAGAAAATTG
5906 TTTTC-A-AAAATATG
1 TTTTCAAGAAAAT-TG
5920 TTTTCAA
1 TTTTCAA
5927 AAAGGTTTTG
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
12 4 0.13
13 1 0.03
14 12 0.40
15 13 0.43
ACGTcount: A:0.40, C:0.08, G:0.12, T:0.40
Consensus pattern (15 bp):
TTTTCAAGAAAATTG
Found at i:5910 original size:14 final size:13
Alignment explanation
Indices: 5877--5935 Score: 57
Period size: 14 Copynumber: 4.3 Consensus size: 13
5867 AAGACATGTT
*
5877 TTTTCAAGAAAATTG
1 TTTTCAA-AAAA-GG
5892 TTTTCAAGAAAAGG
1 TTTTCAA-AAAAGG
*
5906 TTTTCAAAAATATG
1 TTTTCAAAAA-AGG
5920 TTTTC-AAAAAGG
1 TTTTCAAAAAAGG
5932 TTTT
1 TTTT
5936 GAGTCCTTTA
Statistics
Matches: 40, Mismatches: 3, Indels: 5
0.83 0.06 0.10
Matches are distributed among these distances:
12 6 0.15
13 7 0.17
14 15 0.38
15 12 0.30
ACGTcount: A:0.39, C:0.07, G:0.14, T:0.41
Consensus pattern (13 bp):
TTTTCAAAAAAGG
Found at i:5929 original size:26 final size:27
Alignment explanation
Indices: 5885--5935 Score: 79
Period size: 26 Copynumber: 1.9 Consensus size: 27
5875 TTTTTTCAAG
5885 AAAATTGTTTTCAAGAAAAGGTTTTCA
1 AAAATTGTTTTCAAGAAAAGGTTTTCA
5912 AAAATATGTTTTC-A-AAAAGGTTTT
1 AAAAT-TGTTTTCAAGAAAAGGTTTT
5936 GAGTCCTTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
26 10 0.43
27 6 0.26
28 7 0.30
ACGTcount: A:0.41, C:0.06, G:0.14, T:0.39
Consensus pattern (27 bp):
AAAATTGTTTTCAAGAAAAGGTTTTCA
Found at i:6594 original size:11 final size:10
Alignment explanation
Indices: 6573--6598 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
6563 CAACTCAAAG
6573 AAAAAAGAAA
1 AAAAAAGAAA
6583 AAAAAAGAAA
1 AAAAAAGAAA
6593 AAAAAA
1 AAAAAA
6599 CTCAGCCTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.92, C:0.00, G:0.08, T:0.00
Consensus pattern (10 bp):
AAAAAAGAAA
Found at i:6831 original size:100 final size:100
Alignment explanation
Indices: 6654--6833 Score: 247
Period size: 100 Copynumber: 1.8 Consensus size: 100
6644 GAGGGATCCA
* * *
6654 AGTTGAAAACCCGCGAAGGGCGGCTTGGGTCCATCGGAGGTCACTTGAGTTGAAAACCCGAAAAG
1 AGTTGAAAACCCGAGAAGGGCGGCTTGGGTCCATCGGAGGTCACTTAAGTTGAAAACCAGAAAAG
6719 GGCGACTCAAGTGAAGGATGAAAAGGAGGAACTTG
66 GGCGACTCAAGTGAAGGATGAAAAGGAGGAACTTG
* * * * * *
6754 AGTTGAAAACCTGAAGAA-GGCGGCTTGGGTCCATCGGGGGTTACTTAAGTTGAAGACCATAGAA
1 AGTTGAAAACCCG-AGAAGGGCGGCTTGGGTCCATCGGAGGTCACTTAAGTTGAAAACCAGAAAA
6818 -GGCGACTCAAAGTGAA
65 GGGCGACTC-AAGTGAA
6834 AAGAAGATGT
Statistics
Matches: 69, Mismatches: 9, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
99 8 0.12
100 58 0.84
101 3 0.04
ACGTcount: A:0.32, C:0.17, G:0.33, T:0.18
Consensus pattern (100 bp):
AGTTGAAAACCCGAGAAGGGCGGCTTGGGTCCATCGGAGGTCACTTAAGTTGAAAACCAGAAAAG
GGCGACTCAAGTGAAGGATGAAAAGGAGGAACTTG
Found at i:9017 original size:67 final size:67
Alignment explanation
Indices: 8908--9067 Score: 250
Period size: 67 Copynumber: 2.4 Consensus size: 67
8898 AGAAGAACAC
* * *
8908 CGGAAGACGGTTTGTTAGAAAGAATTTTCAAATGCTGATTGGAAGACAATCTCATTAAGGATTAC
1 CGGAAGACGGTTTGCTAGAAAGAATTTTCAAATGCTGATTGGAAGACAATCTCACTAAGGAATAC
*
8973 -C
66 AT
*
8974 CTGGAAGACGGTTTGCTAGAAAGAATTTTCAAATGTTGATTGGAAGACAATCTCACTAAGGAATA
1 C-GGAAGACGGTTTGCTAGAAAGAATTTTCAAATGCTGATTGGAAGACAATCTCACTAAGGAATA
9039 CAT
65 CAT
*
9042 CGGAATACGGTTTGCTAGAAAGAATT
1 CGGAAGACGGTTTGCTAGAAAGAATT
9068 CTCCAGAAGT
Statistics
Matches: 86, Mismatches: 6, Indels: 3
0.91 0.06 0.03
Matches are distributed among these distances:
66 1 0.01
67 84 0.98
68 1 0.01
ACGTcount: A:0.36, C:0.13, G:0.23, T:0.28
Consensus pattern (67 bp):
CGGAAGACGGTTTGCTAGAAAGAATTTTCAAATGCTGATTGGAAGACAATCTCACTAAGGAATAC
AT
Found at i:9146 original size:64 final size:64
Alignment explanation
Indices: 9071--9423 Score: 499
Period size: 64 Copynumber: 5.5 Consensus size: 64
9061 AAGAATTCTC
* *
9071 CAGAAGTGGATCGGAAGACGATCTTGTCAAGAATTACACCAGAAGATGGTTTCTCAAGAGTTTT
1 CAGAAGTTGATCGGAAGACGATCTTGTCAAGAAGTACACCAGAAGATGGTTTCTCAAGAGTTTT
* *
9135 CAGAAGTGGATCGGAAGACGATCTTGTCAAGAAGTACACCAGAAGACGGTTTCTCAAGAGTTTT
1 CAGAAGTTGATCGGAAGACGATCTTGTCAAGAAGTACACCAGAAGATGGTTTCTCAAGAGTTTT
* *
9199 CATAAGTTGATCGGAAGACGATCTTGTCAAGAAGTACACCAGAATATGGTTTCTCAAGAGTTTT
1 CAGAAGTTGATCGGAAGACGATCTTGTCAAGAAGTACACCAGAAGATGGTTTCTCAAGAGTTTT
* * * *
9263 CAAAAGTTGATCGGAAGACGATCTTGTCAAAAAGTACACCAGAAGATGGCTTCTCAACAGTTTT
1 CAGAAGTTGATCGGAAGACGATCTTGTCAAGAAGTACACCAGAAGATGGTTTCTCAAGAGTTTT
* * * * * * * * *
9327 CAGAAGTTGATCGGAAGACGATCTTGTTAAAAAGTATATCAGAGGATAGTGTCTCGAAAAGGTTT
1 CAGAAGTTGATCGGAAGACGATCTTGTCAAGAAGTACACCAGAAGATGGTTTCTC-AAGAGTTTT
* * *
9392 CAGAAGTCGATCGGAAGACGGTCTTGTTAAGA
1 CAGAAGTTGATCGGAAGACGATCTTGTCAAGA
9424 GATGCATCGA
Statistics
Matches: 264, Mismatches: 24, Indels: 1
0.91 0.08 0.00
Matches are distributed among these distances:
64 228 0.86
65 36 0.14
ACGTcount: A:0.34, C:0.16, G:0.25, T:0.26
Consensus pattern (64 bp):
CAGAAGTTGATCGGAAGACGATCTTGTCAAGAAGTACACCAGAAGATGGTTTCTCAAGAGTTTT
Found at i:9567 original size:50 final size:50
Alignment explanation
Indices: 9508--9677 Score: 250
Period size: 50 Copynumber: 3.4 Consensus size: 50
9498 TTCGGAAGCC
* * *
9508 AATTGGAAGATAGTTCAAAGGATAAGCAGAAGACGGTTCTTTTAAGATTG
1 AATTGGAAGACAGTTCAAAGGATAAGCGGAAGACGGTCCTTTTAAGATTG
* *
9558 AATTGGAAGACAGTTCAAAGGATAAGTGGAAGACGGTCCTTTTGAGATTG
1 AATTGGAAGACAGTTCAAAGGATAAGCGGAAGACGGTCCTTTTAAGATTG
* * *
9608 AATTGGAAGACAGTTCAAAGGATAAGCGGAAGACGATCCTTTAAATATTG
1 AATTGGAAGACAGTTCAAAGGATAAGCGGAAGACGGTCCTTTTAAGATTG
* *
9658 GATTGGAAGACAATTCAAAG
1 AATTGGAAGACAGTTCAAAG
9678 AAGTTGTTTC
Statistics
Matches: 108, Mismatches: 12, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
50 108 1.00
ACGTcount: A:0.38, C:0.10, G:0.26, T:0.25
Consensus pattern (50 bp):
AATTGGAAGACAGTTCAAAGGATAAGCGGAAGACGGTCCTTTTAAGATTG
Found at i:9591 original size:23 final size:23
Alignment explanation
Indices: 9561--9641 Score: 63
Period size: 23 Copynumber: 3.3 Consensus size: 23
9551 AAGATTGAAT
9561 TGGAAGACAGTTCAAAGGATAAG
1 TGGAAGACAGTTCAAAGGATAAG
* * *** *
9584 TGGAAGACGGTCCTTTTGAGATTGAAT
1 TGGAAGACAGTTC-AAAG-GA-T-AAG
9611 TGGAAGACAGTTCAAAGGATAAG
1 TGGAAGACAGTTCAAAGGATAAG
*
9634 CGGAAGAC
1 TGGAAGAC
9642 GATCCTTTAA
Statistics
Matches: 41, Mismatches: 13, Indels: 8
0.66 0.21 0.13
Matches are distributed among these distances:
23 20 0.49
24 2 0.05
25 4 0.10
26 2 0.05
27 13 0.32
ACGTcount: A:0.37, C:0.11, G:0.31, T:0.21
Consensus pattern (23 bp):
TGGAAGACAGTTCAAAGGATAAG
Found at i:9733 original size:27 final size:27
Alignment explanation
Indices: 9654--9738 Score: 84
Period size: 27 Copynumber: 3.2 Consensus size: 27
9644 TCCTTTAAAT
*
9654 ATTGGATTGGAAGACAATTCAAAGAAG
1 ATTGAATTGGAAGACAATTCAAAGAAG
* * ***
9681 -TTG-TTTCGGAAGACGATTCCCCGAAG
1 ATTGAATT-GGAAGACAATTCAAAGAAG
*
9707 ATTGAATTGGAAGAAAATTCAAAGAAG
1 ATTGAATTGGAAGACAATTCAAAGAAG
9734 ATTGA
1 ATTGA
9739 TCGGGAGACG
Statistics
Matches: 44, Mismatches: 11, Indels: 6
0.72 0.18 0.10
Matches are distributed among these distances:
25 2 0.05
26 18 0.41
27 22 0.50
28 2 0.05
ACGTcount: A:0.40, C:0.11, G:0.25, T:0.25
Consensus pattern (27 bp):
ATTGAATTGGAAGACAATTCAAAGAAG
Found at i:11311 original size:14 final size:14
Alignment explanation
Indices: 11292--11319 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
11282 AATAGATCAA
11292 GCATTGCACCAATC
1 GCATTGCACCAATC
11306 GCATTGCACCAATC
1 GCATTGCACCAATC
11320 ATGGCATTTC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.29, C:0.36, G:0.14, T:0.21
Consensus pattern (14 bp):
GCATTGCACCAATC
Found at i:14508 original size:35 final size:34
Alignment explanation
Indices: 14461--14568 Score: 117
Period size: 35 Copynumber: 2.9 Consensus size: 34
14451 AGAACTTTGA
14461 AAAACTGAATGGGAACTTTCCCAATTTGAAAACTT
1 AAAACTG-ATGGGAACTTTCCCAATTTGAAAACTT
*
14496 AAAAGCTGATGGGAACTTTCCCAATTTTTTTAAAAAAAACTT
1 AAAA-CTGATGGGAACTTTCCCAA----TTT---GAAAACTT
*
14538 AAAACTGGTGGGAACTTTCCCAATTTGAAAA
1 AAAACTGATGGGAACTTTCCCAATTTGAAAA
14569 GAGCTAAATT
Statistics
Matches: 62, Mismatches: 3, Indels: 17
0.76 0.04 0.21
Matches are distributed among these distances:
34 4 0.06
35 20 0.32
36 3 0.05
37 3 0.05
39 3 0.05
41 18 0.29
42 11 0.18
ACGTcount: A:0.40, C:0.16, G:0.15, T:0.30
Consensus pattern (34 bp):
AAAACTGATGGGAACTTTCCCAATTTGAAAACTT
Found at i:15527 original size:39 final size:40
Alignment explanation
Indices: 15444--15529 Score: 97
Period size: 39 Copynumber: 2.2 Consensus size: 40
15434 TAAGACTCAA
* * **
15444 AAAGACCAAACCTATCTAAAGACCCAAACAAAAGAAAATT
1 AAAGCCCAAACCTATATAAAGACCCAAACAAAAGAAAAGC
15484 AAAGCCCAAACACTATATAAAG-CCC-AACAAAA-AATAAGC
1 AAAGCCCAAAC-CTATATAAAGACCCAAACAAAAGAA-AAGC
15523 AAAGCCC
1 AAAGCCC
15530 GAAGAGTTTT
Statistics
Matches: 40, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
38 2 0.05
39 16 0.40
40 13 0.32
41 9 0.22
ACGTcount: A:0.56, C:0.26, G:0.08, T:0.10
Consensus pattern (40 bp):
AAAGCCCAAACCTATATAAAGACCCAAACAAAAGAAAAGC
Found at i:17824 original size:43 final size:42
Alignment explanation
Indices: 17775--17875 Score: 130
Period size: 43 Copynumber: 2.4 Consensus size: 42
17765 GCTTGGTATG
*
17775 GAATTTGTAAGGGAAAGTATTTGGGCCCGAAAAGATTTGTAAA
1 GAATTTGTAAGGGAAAG-ATTTGGGCCCGAAAAGATTGGTAAA
* * * **
17818 GCATTTGTAAGGAAAAAGATTTGGGCCTGAAAAGATTGGTATG
1 GAATTTGTAAGG-GAAAGATTTGGGCCCGAAAAGATTGGTAAA
17861 GAATTTGTAAGGGAA
1 GAATTTGTAAGGGAA
17876 TAAATGGGCC
Statistics
Matches: 49, Mismatches: 8, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
42 2 0.04
43 43 0.88
44 4 0.08
ACGTcount: A:0.37, C:0.06, G:0.30, T:0.28
Consensus pattern (42 bp):
GAATTTGTAAGGGAAAGATTTGGGCCCGAAAAGATTGGTAAA
Found at i:18496 original size:65 final size:66
Alignment explanation
Indices: 18427--18564 Score: 163
Period size: 65 Copynumber: 2.1 Consensus size: 66
18417 TTTTAAAATA
* * *
18427 AGAAAGGCTTGTCTCAGGTCTAAAACTGAAAGA-AAACGTCCTGTCCGAGGTCGAAAATAAAAC-
1 AGAAAGACCTGTCTCAGGTCTAAAACTGAAAGATAAA-GACCTGTCCGAGGTCGAAAATAAAACT
18490 TG
65 TG
* ** ** * *
18492 AGAAAGACCTGTCTGAGGTCTGGAACTGAAAGATAAAGACCTGTTTGAGGTCGAAATTGAAACTT
1 AGAAAGACCTGTCTCAGGTCTAAAACTGAAAGATAAAGACCTGTCCGAGGTCGAAAATAAAACTT
18557 G
66 G
18558 AGAAAGA
1 AGAAAGA
18565 ACGACCAGTT
Statistics
Matches: 61, Mismatches: 10, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
65 49 0.80
66 12 0.20
ACGTcount: A:0.38, C:0.15, G:0.25, T:0.21
Consensus pattern (66 bp):
AGAAAGACCTGTCTCAGGTCTAAAACTGAAAGATAAAGACCTGTCCGAGGTCGAAAATAAAACTT
G
Found at i:18615 original size:39 final size:39
Alignment explanation
Indices: 18567--19363 Score: 1223
Period size: 39 Copynumber: 20.6 Consensus size: 39
18557 GAGAAAGAAC
* * *
18567 GACCAGTTTCTAGTCAACTTTGATAAATGCTAAAAAGAT
1 GACCTGTTTCCAGTCAACTTTGATAAATGCTGAAAAGAT
* *
18606 GACCTGTTTCCAATCAACTTTGATAAATGCTGAAAGGAT
1 GACCTGTTTCCAGTCAACTTTGATAAATGCTGAAAAGAT
18645 GACCTGTTTCCAGTCAACTTTG----A---T-AAAAGAT
1 GACCTGTTTCCAGTCAACTTTGATAAATGCTGAAAAGAT
*
18676 GACTTGTTTCCAGTCAACTTTGATAAATGCTGAAAAGAT
1 GACCTGTTTCCAGTCAACTTTGATAAATGCTGAAAAGAT
18715 GACCTGTTTCCAGTCAACTTTGATAAATGCTGAAAAGAT
1 GACCTGTTTCCAGTCAACTTTGATAAATGCTGAAAAGAT
*
18754 GACCTGTTTCCAGTCAACTTTGATAAATGCTGATAAGAT
1 GACCTGTTTCCAGTCAACTTTGATAAATGCTGAAAAGAT
*
18793 GACCTGTTTCCAGTCAACTTTGATGAATGCTGAAAAGAT
1 GACCTGTTTCCAGTCAACTTTGATAAATGCTGAAAAGAT
* **
18832 GACCTGTTTCCAGTCAACTTTGATGAATGCTGATGAGAT
1 GACCTGTTTCCAGTCAACTTTGATAAATGCTGAAAAGAT
* *
18871 GACCTGATTCCAGTCAACTTTGATAAATGCCGAAAAGAT
1 GACCTGTTTCCAGTCAACTTTGATAAATGCTGAAAAGAT
*
18910 GACCTGTTTCCAGTCAACTTTGATAAATGCTGATAAGAT
1 GACCTGTTTCCAGTCAACTTTGATAAATGCTGAAAAGAT
* * * * *
18949 GACCTATTTCCAATCAACTTTGATGAATGATGATAAGAT
1 GACCTGTTTCCAGTCAACTTTGATAAATGCTGAAAAGAT
* * *
18988 GACCTGTTTCCAATCAACTTTGATGAATGCTGATAAGAT
1 GACCTGTTTCCAGTCAACTTTGATAAATGCTGAAAAGAT
*
19027 GACCTGTTTCCGGTCAACTTTGATAAATGCTGAAAAGAT
1 GACCTGTTTCCAGTCAACTTTGATAAATGCTGAAAAGAT
*
19066 GACGTGTTTCCAGTCAACTTTGATAAATGCTGAAAAGAT
1 GACCTGTTTCCAGTCAACTTTGATAAATGCTGAAAAGAT
*
19105 GACTTGTTTCCAGTCAACTTTGATAAATGCTGAAAAGAT
1 GACCTGTTTCCAGTCAACTTTGATAAATGCTGAAAAGAT
* *
19144 GACCTGTTTCCAGTCAACTTCGATGAATGCTGAAAAGAT
1 GACCTGTTTCCAGTCAACTTTGATAAATGCTGAAAAGAT
* *
19183 GACCTGTTTCCAGTCAACTTTGATGAATGCTGATAAGAT
1 GACCTGTTTCCAGTCAACTTTGATAAATGCTGAAAAGAT
*
19222 GACCTGTTTCCAGTCAACTTTGATGAATGCTGAAAAGAT
1 GACCTGTTTCCAGTCAACTTTGATAAATGCTGAAAAGAT
*
19261 GACCTGTTTCCAGTCAACTTGGATAAATGCTGAAAAGAT
1 GACCTGTTTCCAGTCAACTTTGATAAATGCTGAAAAGAT
*
19300 GACTTGTTTCCAGTCAACTTTGATAAATGCTGAAAAGAT
1 GACCTGTTTCCAGTCAACTTTGATAAATGCTGAAAAGAT
* * *
19339 GACTTGTTTCCAGTTAACTTCGATA
1 GACCTGTTTCCAGTCAACTTTGATA
19364 CTTAACTGTT
Statistics
Matches: 703, Mismatches: 47, Indels: 16
0.92 0.06 0.02
Matches are distributed among these distances:
31 27 0.04
32 1 0.00
35 2 0.00
38 1 0.00
39 672 0.96
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.32
Consensus pattern (39 bp):
GACCTGTTTCCAGTCAACTTTGATAAATGCTGAAAAGAT
Found at i:27689 original size:11 final size:11
Alignment explanation
Indices: 27668--27707 Score: 64
Period size: 11 Copynumber: 3.7 Consensus size: 11
27658 GTATCCTAAG
27668 TTTTT-TTATT
1 TTTTTCTTATT
*
27678 TATTTCTTATT
1 TTTTTCTTATT
27689 TTTTTCTTATT
1 TTTTTCTTATT
27700 TTTTTCTT
1 TTTTTCTT
27708 TTTGATTATT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
10 4 0.15
11 23 0.85
ACGTcount: A:0.10, C:0.07, G:0.00, T:0.82
Consensus pattern (11 bp):
TTTTTCTTATT
Found at i:29546 original size:4 final size:4
Alignment explanation
Indices: 29537--29749 Score: 50
Period size: 4 Copynumber: 54.0 Consensus size: 4
29527 AGATTTTTTG
* * * *
29537 TTAT TTAT TTA- CTAT TTAT ATT-T TTAT TTAT TAAT TTAA CTA- TTAT
1 TTAT TTAT TTAT TTAT TTAT -TTAT TTAT TTAT TTAT TTAT TTAT TTAT
* ** * * * * *
29583 CTAT TTAT TTA- CAAT TTAT CTTTT TTAT TTAT TAAA TTAG CTA- TTAT
1 TTAT TTAT TTAT TTAT TTAT -TTAT TTAT TTAT TTAT TTAT TTAT TTAT
* * * * * * * *
29630 CTAT TTAT TTACT ATTAT CTAC TT-T TT-T TTAC TTAC CTAT TTAT CTAA
1 TTAT TTAT TTA-T -TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT
* * * * * * *
29678 TTA- TTAT CTAT ATAC CTAT TTAT CTT-T TTAT TTAT CTAT TATTT TTAC
1 TTAT TTAT TTAT TTAT TTAT TTAT -TTAT TTAT TTAT TTAT T-TAT TTAT
29726 TTAT TT-T TCTAT TTAT TTAT TTAT
1 TTAT TTAT T-TAT TTAT TTAT TTAT
29750 CAATTACTTT
Statistics
Matches: 147, Mismatches: 46, Indels: 32
0.65 0.20 0.14
Matches are distributed among these distances:
3 21 0.14
4 109 0.74
5 14 0.10
6 3 0.02
ACGTcount: A:0.27, C:0.10, G:0.00, T:0.63
Consensus pattern (4 bp):
TTAT
Found at i:29567 original size:27 final size:27
Alignment explanation
Indices: 29529--29593 Score: 71
Period size: 27 Copynumber: 2.4 Consensus size: 27
29519 ACCAAAAAAG
*
29529 ATTTTT-TGTTATTTATTT-ACTATTTAT
1 ATTTTTAT-TTATTAATTTAACTA-TTAT
29556 ATTTTTATTTATTAATTTAACTATTAT
1 ATTTTTATTTATTAATTTAACTATTAT
* *
29583 CTATTTATTTA
1 ATTTTTATTTA
29594 CAATTTATCT
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
27 28 0.85
28 5 0.15
ACGTcount: A:0.28, C:0.05, G:0.02, T:0.66
Consensus pattern (27 bp):
ATTTTTATTTATTAATTTAACTATTAT
Found at i:29627 original size:47 final size:47
Alignment explanation
Indices: 29538--29649 Score: 174
Period size: 47 Copynumber: 2.4 Consensus size: 47
29528 GATTTTTTGT
* *
29538 TATTTATTTACTATTTAT-ATTTTTATTTATTAATTTAACTATTATC
1 TATTTATTTACTATTTATCTTTTTTATTTATTAAATTAACTATTATC
* *
29584 TATTTATTTACAATTTATCTTTTTTATTTATTAAATTAGCTATTATC
1 TATTTATTTACTATTTATCTTTTTTATTTATTAAATTAACTATTATC
29631 TATTTATTTACTA-TTATCT
1 TATTTATTTACTATTTATCT
29650 ACTTTTTTTT
Statistics
Matches: 60, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
46 23 0.38
47 37 0.62
ACGTcount: A:0.29, C:0.08, G:0.01, T:0.62
Consensus pattern (47 bp):
TATTTATTTACTATTTATCTTTTTTATTTATTAAATTAACTATTATC
Found at i:29671 original size:59 final size:63
Alignment explanation
Indices: 29608--29728 Score: 144
Period size: 64 Copynumber: 2.0 Consensus size: 63
29598 TTATCTTTTT
* *
29608 TATTTAT-TAA-ATTAGCTAT-TATCTATTTAT-TTACTA-TTATCTACTTTTTTTTACTTACC
1 TATTTATCTAATATTAGCTATATACCTATTTATCTTACTATTTATCTA-TTATTTTTACTTACC
* **
29667 TATTTATCTAATTATTATCTATATACCTATTTATCTTTTTATTTATCTATTATTTTTACTTA
1 TATTTATCTAA-TATTAGCTATATACCTATTTATCTTACTATTTATCTATTATTTTTACTTA
29729 TTTTTCTATT
Statistics
Matches: 51, Mismatches: 5, Indels: 7
0.81 0.08 0.11
Matches are distributed among these distances:
59 7 0.14
60 3 0.06
62 8 0.16
63 10 0.20
64 16 0.31
65 7 0.14
ACGTcount: A:0.27, C:0.12, G:0.01, T:0.60
Consensus pattern (63 bp):
TATTTATCTAATATTAGCTATATACCTATTTATCTTACTATTTATCTATTATTTTTACTTACC
Found at i:29696 original size:27 final size:28
Alignment explanation
Indices: 29663--29716 Score: 83
Period size: 27 Copynumber: 2.0 Consensus size: 28
29653 TTTTTTTACT
29663 TACCTATTTATCTAATTA-TTATCTATA
1 TACCTATTTATCTAATTATTTATCTATA
**
29690 TACCTATTTATCTTTTTATTTATCTAT
1 TACCTATTTATCTAATTATTTATCTAT
29717 TATTTTTACT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
27 16 0.67
28 8 0.33
ACGTcount: A:0.28, C:0.15, G:0.00, T:0.57
Consensus pattern (28 bp):
TACCTATTTATCTAATTATTTATCTATA
Found at i:31314 original size:43 final size:42
Alignment explanation
Indices: 31264--31364 Score: 130
Period size: 43 Copynumber: 2.4 Consensus size: 42
31254 GCTTGGTATG
*
31264 GAATTTGTAAGGGAAAGTATTTGGGCCCGAAAAGATTTGTAAA
1 GAATTTGTAAGGGAAAG-ATTTGGGCCCGAAAAGATTGGTAAA
* * * **
31307 GCATTTGTAAGGAAAAAGATTTGGGCCTGAAAAGATTGGTATG
1 GAATTTGTAAGG-GAAAGATTTGGGCCCGAAAAGATTGGTAAA
31350 GAATTTGTAAGGGAA
1 GAATTTGTAAGGGAA
31365 TAAATGGGCC
Statistics
Matches: 49, Mismatches: 8, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
42 2 0.04
43 43 0.88
44 4 0.08
ACGTcount: A:0.37, C:0.06, G:0.30, T:0.28
Consensus pattern (42 bp):
GAATTTGTAAGGGAAAGATTTGGGCCCGAAAAGATTGGTAAA
Found at i:33415 original size:30 final size:30
Alignment explanation
Indices: 33339--33436 Score: 126
Period size: 31 Copynumber: 3.3 Consensus size: 30
33329 AACCTTTTCT
*
33339 TAAACAAATCCAAAAGAAGATTTTGGAAAA
1 TAAATAAATCCAAAAGAAGATTTTGGAAAA
* *
33369 TAAGTTAATTCCAAAAGAAGATTTTGGAAAA
1 TAA-ATAAATCCAAAAGAAGATTTTGGAAAA
* *
33400 TAAATAAACCCAAAAGAGGATTTTGG-AAA
1 TAAATAAATCCAAAAGAAGATTTTGGAAAA
*
33429 TCAATAAA
1 TAAATAAA
33437 ATTGATCAAG
Statistics
Matches: 59, Mismatches: 8, Indels: 3
0.84 0.11 0.04
Matches are distributed among these distances:
29 10 0.17
30 22 0.37
31 27 0.46
ACGTcount: A:0.53, C:0.09, G:0.14, T:0.23
Consensus pattern (30 bp):
TAAATAAATCCAAAAGAAGATTTTGGAAAA
Found at i:34410 original size:27 final size:27
Alignment explanation
Indices: 34365--34443 Score: 140
Period size: 27 Copynumber: 2.9 Consensus size: 27
34355 GAACCTACCC
*
34365 GGGTCGAAGTGGGAAGATCCACTGCTG
1 GGGTCGAAGTGGGAGGATCCACTGCTG
*
34392 GGGTCGAAGTGTGAGGATCCACTGCTG
1 GGGTCGAAGTGGGAGGATCCACTGCTG
34419 GGGTCGAAGTGGGAGGATCCACTGC
1 GGGTCGAAGTGGGAGGATCCACTGC
34444 GGCAACAGTC
Statistics
Matches: 49, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 49 1.00
ACGTcount: A:0.20, C:0.19, G:0.42, T:0.19
Consensus pattern (27 bp):
GGGTCGAAGTGGGAGGATCCACTGCTG
Found at i:36262 original size:2 final size:2
Alignment explanation
Indices: 36257--36299 Score: 77
Period size: 2 Copynumber: 21.5 Consensus size: 2
36247 GATGTGTGTG
*
36257 TA TA TA TA TA TA TA TA TA TA TA TA TA GA 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
36299 T
1 T
36300 TTCTAAAATG
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (2 bp):
TA
Found at i:36838 original size:69 final size:68
Alignment explanation
Indices: 36744--36885 Score: 205
Period size: 74 Copynumber: 2.0 Consensus size: 68
36734 CAAGGTTTTT
*
36744 ACAAAAACACAATTTTATGTCACTTCCTAAATGAAT-AACCACCTAGCAGATAGTTATTCATGTT
1 ACAAAAACACAATTTTATGTCACTTCCTAAATGAATCAACCACCTAGCAGATAGTTACTCATGTT
36808 ATA
66 ATA
*
36811 ACAAAAACACAAGTTATTATGTCACTTCCTAAATGAATCACCAAATCACCTAGCAGATAGTTACT
1 ACAAAAACACAA-TT-TTATGTCACTTCCTAAATGAAT---C-AACCACCTAGCAGATAGTTACT
36876 CATGTTATA
60 CATGTTATA
36885 A
1 A
36886 TTGAAACAAG
Statistics
Matches: 66, Mismatches: 2, Indels: 7
0.88 0.03 0.09
Matches are distributed among these distances:
67 12 0.18
68 2 0.03
69 22 0.33
74 30 0.45
ACGTcount: A:0.41, C:0.20, G:0.09, T:0.30
Consensus pattern (68 bp):
ACAAAAACACAATTTTATGTCACTTCCTAAATGAATCAACCACCTAGCAGATAGTTACTCATGTT
ATA
Found at i:38279 original size:157 final size:157
Alignment explanation
Indices: 38035--38357 Score: 520
Period size: 157 Copynumber: 2.1 Consensus size: 157
38025 ATGACAAAAT
* * *
38035 TTCCTGGGGTTACCCGGGCGCGGGGTGGGGTTGCCCGGGCAACCCCATGAAGTTTCCTCAATTTC
1 TTCCTGGGGTTACCCAGGCGCGCGGTGGGGTTGCCCGGGCAACCCCAGGAAGTTTCCTCAATTTC
* * * *
38100 ATTATATATGGCGGCATTTGAGGCCTTAAACGCCACTAAAATAGCGGCGTTTTATAAACAAAACG
66 ATTATATATGACGGCATCTGAGGCCTGAAACGCCACTAAAATAGCAGCGTTTTATAAACAAAACG
38165 CCGCCATATATAATAAAATTGATAAAC
131 CCGCCATATATAATAAAATTGATAAAC
* * *
38192 TTCCTGGGGTTGCCCAGGCGCGCGGTGGGGTTGCCCGGGCAAGCCCAGGAAGTTTCCTCCATTTC
1 TTCCTGGGGTTACCCAGGCGCGCGGTGGGGTTGCCCGGGCAACCCCAGGAAGTTTCCTCAATTTC
* *
38257 ATTATATATGACGGCGTCTGAGGCCTGAAACGCCACTAAAATAGCAGCGTTTTATAACCAAAACG
66 ATTATATATGACGGCATCTGAGGCCTGAAACGCCACTAAAATAGCAGCGTTTTATAAACAAAACG
* *
38322 CCGCCATATATAATGAAATTGATTAAC
131 CCGCCATATATAATAAAATTGATAAAC
38349 TTCCTGGGG
1 TTCCTGGGG
38358 AGGAAGTTTC
Statistics
Matches: 152, Mismatches: 14, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
157 152 1.00
ACGTcount: A:0.26, C:0.24, G:0.25, T:0.25
Consensus pattern (157 bp):
TTCCTGGGGTTACCCAGGCGCGCGGTGGGGTTGCCCGGGCAACCCCAGGAAGTTTCCTCAATTTC
ATTATATATGACGGCATCTGAGGCCTGAAACGCCACTAAAATAGCAGCGTTTTATAAACAAAACG
CCGCCATATATAATAAAATTGATAAAC
Found at i:47487 original size:2 final size:2
Alignment explanation
Indices: 47480--47515 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
47470 AAAGTGGTAA
*
47480 AC AC AC AC AC AC AC AC AC AA AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
47516 TATTTGTGAG
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.53, C:0.47, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:51981 original size:51 final size:51
Alignment explanation
Indices: 51853--52051 Score: 319
Period size: 51 Copynumber: 3.9 Consensus size: 51
51843 ATTGAAGAGT
* *
51853 CGTCTTCCGCTTATCCTTTGAACTGTCTTACAATTCAATCTT-AAAAGGAC
1 CGTCTTCCGCTTATTCTTTGAACTGTCTTCCAATTCAATCTTAAAAAGGAC
* * *
51903 CGTCTTCCGCTTATCCTTTAAACTGTCTTCCAATTTAATCTTAAAAAGGAC
1 CGTCTTCCGCTTATTCTTTGAACTGTCTTCCAATTCAATCTTAAAAAGGAC
* *
51954 CGTCTTCCGCTTATTCTTTGAATTGTCTTCCAATTCAAACTTAAAAAGGAC
1 CGTCTTCCGCTTATTCTTTGAACTGTCTTCCAATTCAATCTTAAAAAGGAC
*
52005 CGTCTTCCGCTTATTCTTTGAACTGTCTTCCAATTCAATCCTAAAAA
1 CGTCTTCCGCTTATTCTTTGAACTGTCTTCCAATTCAATCTTAAAAA
52052 TCATCTTTCG
Statistics
Matches: 137, Mismatches: 11, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
50 39 0.28
51 98 0.72
ACGTcount: A:0.27, C:0.26, G:0.11, T:0.37
Consensus pattern (51 bp):
CGTCTTCCGCTTATTCTTTGAACTGTCTTCCAATTCAATCTTAAAAAGGAC
Found at i:52394 original size:64 final size:64
Alignment explanation
Indices: 52272--52889 Score: 695
Period size: 64 Copynumber: 9.6 Consensus size: 64
52262 CCGGTGCATC
* ** * * * *
52272 TCTTAACAAGATCGTCTTTCCGATCAACTTCTGAACCTT-TCGAAAAAACTATCCTCTGGTGTAC
1 TCTTGACAAGATCGTC-TTCCGATCAACTTCTGAAAATTGTTG-AGAAACCATCTTCTGGTGTAC
52336 T
64 T
* * * * * *
52337 TCTTGACGAGATCGTCCTCCAATCATCTTCTGAAAATTGCTGAGAAACCATCTTCTGGCGTACT
1 TCTTGACAAGATCGTCTTCCGATCAACTTCTGAAAATTGTTGAGAAACCATCTTCTGGTGTACT
* *
52401 TCTTTGACAAGATCGTCTTCCGATCAACTTCTGAAAACTGTCGAGAAACCATCTTCTGGTGTACT
1 TC-TTGACAAGATCGTCTTCCGATCAACTTCTGAAAATTGTTGAGAAACCATCTTCTGGTGTACT
** * *
52466 TCTTGACAAGATCGTCTTCCGATCATGTTCTGAAATTTTATTGAGAAACCATCTTCTGGTGTACT
1 TCTTGACAAGATCGTCTTCCGATCAACTTCTGAAA-ATTGTTGAGAAACCATCTTCTGGTGTACT
* * * *
52531 TCTTGATAAGATCGTCTTCCGCTCAACTTTTGAAAATTGGTT-AGAAACCATCTTCTAGTGTACT
1 TCTTGACAAGATCGTCTTCCGATCAACTTCTGAAAATT-GTTGAGAAACCATCTTCTGGTGTACT
* * * * * *
52595 GCTTGACAAGATCGCCTTCCGGTCGACTTCTAAAAATTCTTGAGAAACCATCTTCTGGTGTACT
1 TCTTGACAAGATCGTCTTCCGATCAACTTCTGAAAATTGTTGAGAAACCATCTTCTGGTGTACT
* * * * * * *
52659 TTTTAACGAGGTCGGCTTCCGA-CTAACTTTTGAAAATT-TTCGGGAAACCATCTTCTGGTGTAC
1 TCTTGACAAGATCGTCTTCCGATC-AACTTCTGAAAATTGTT-GAGAAACCATCTTCTGGTGTAC
52722 T
64 T
* * * * * * *
52723 TCTTGACAAGATTGTCTTCCGATCAATTTTTGAAATTTTTTTGAGACACCATCTTCTGGCGTACT
1 TCTTGACAAGATCGTCTTCCGATCAACTTCTGAAA-ATTGTTGAGAAACCATCTTCTGGTGTACT
** *
52788 TCTTGACAAGATCGTCTTCCGATCAACTTAGGAAAATTTTTGAGAAACCATCTTCTGGTGTACT
1 TCTTGACAAGATCGTCTTCCGATCAACTTCTGAAAATTGTTGAGAAACCATCTTCTGGTGTACT
* * *
52852 TTTTGACGAGATCGTCTTCCGATCAACTCCTGAAAATT
1 TCTTGACAAGATCGTCTTCCGATCAACTTCTGAAAATT
52890 CTTTCTAGCA
Statistics
Matches: 465, Mismatches: 78, Indels: 21
0.82 0.14 0.04
Matches are distributed among these distances:
63 5 0.01
64 276 0.59
65 182 0.39
66 2 0.00
ACGTcount: A:0.26, C:0.23, G:0.17, T:0.35
Consensus pattern (64 bp):
TCTTGACAAGATCGTCTTCCGATCAACTTCTGAAAATTGTTGAGAAACCATCTTCTGGTGTACT
Found at i:52464 original size:129 final size:127
Alignment explanation
Indices: 52272--52891 Score: 685
Period size: 129 Copynumber: 4.8 Consensus size: 127
52262 CCGGTGCATC
* ** * * *
52272 TCTTAACAAGATCGTCTTTCCGATCAACTTCTG-AACCTTTCGAAAAAACTATCCTCTGGTGTAC
1 TCTTGACAAGATCGTC-TTCCGATCAACTTCTGAAAATTTTCG-AGAAACCATCTTCTGGTGTAC
* * *
52336 TTCTTGACGAGATCGTCCTCCAATCATCTTCTGAAAATTGCTGAGAAACCATCTTCTGGCGTACT
64 TTCTTGACAAGATCGTCTTCCGATCATCTTCTGAAAATT-CTGAGAAACCATCTTCTGGCGTACT
* *
52401 TCTTTGACAAGATCGTCTTCCGATCAACTTCTGAAAACTGTCGAGAAACCATCTTCTGGTGTACT
1 TC-TTGACAAGATCGTCTTCCGATCAACTTCTGAAAATTTTCGAGAAACCATCTTCTGGTGTACT
* * * *
52466 TCTTGACAAGATCGTCTTCCGATCATGTTCTGAAATTTTATTGAGAAACCATCTTCTGGTGTACT
65 TCTTGACAAGATCGTCTTCCGATCATCTTCTGAAA-ATT-CTGAGAAACCATCTTCTGGCGTACT
* * * *
52531 TCTTGATAAGATCGTCTTCCGCTCAACTTTTGAAAATTGGTT--AGAAACCATCTTCTAGTGTAC
1 TCTTGACAAGATCGTCTTCCGATCAACTTCTGAAAATT--TTCGAGAAACCATCTTCTGGTGTAC
* * * * *
52594 TGCTTGACAAGATCGCCTTCCGGTCGA-CTTCTAAAAATTCTTGAGAAACCATCTTCTGGTGTAC
64 TTCTTGACAAGATCGTCTTCCGATC-ATCTTCTGAAAATTC-TGAGAAACCATCTTCTGGCGTAC
52658 T
127 T
* * * * * * *
52659 TTTTAACGAGGTCGGCTTCCGA-CTAACTTTTGAAAATTTTCGGGAAACCATCTTCTGGTGTACT
1 TCTTGACAAGATCGTCTTCCGATC-AACTTCTGAAAATTTTCGAGAAACCATCTTCTGGTGTACT
* * * * *
52723 TCTTGACAAGATTGTCTTCCGATCAAT-TTTTGAAATTTTTTTGAGACACCATCTTCTGGCGTAC
65 TCTTGACAAGATCGTCTTCCGATC-ATCTTCTGAAA--ATTCTGAGAAACCATCTTCTGGCGTAC
52787 T
127 T
** *
52788 TCTTGACAAGATCGTCTTCCGATCAACTTAGGAAAATTTTTGAGAAACCATCTTCTGGTGTACTT
1 TCTTGACAAGATCGTCTTCCGATCAACTTCTGAAAATTTTCGAGAAACCATCTTCTGGTGTACTT
* * * *
52853 TTTGACGAGATCGTCTTCCGATCAACTCCTGAAAATTCT
66 CTTGACAAGATCGTCTTCCGATCATCTTCTGAAAATTCT
52892 TTCTAGCAAA
Statistics
Matches: 412, Mismatches: 64, Indels: 32
0.81 0.13 0.06
Matches are distributed among these distances:
126 2 0.00
127 4 0.01
128 103 0.25
129 251 0.61
130 51 0.12
131 1 0.00
ACGTcount: A:0.25, C:0.23, G:0.17, T:0.35
Consensus pattern (127 bp):
TCTTGACAAGATCGTCTTCCGATCAACTTCTGAAAATTTTCGAGAAACCATCTTCTGGTGTACTT
CTTGACAAGATCGTCTTCCGATCATCTTCTGAAAATTCTGAGAAACCATCTTCTGGCGTACT
Found at i:52759 original size:257 final size:258
Alignment explanation
Indices: 52272--52892 Score: 752
Period size: 257 Copynumber: 2.4 Consensus size: 258
52262 CCGGTGCATC
* ** ** * * * * *
52272 TCTTAACAAGATCGTCTTTCCGATCAACTTCTGAACCTT-TCGAAAAAACTATCCTCTGGTGTAC
1 TCTTGACAAGATCGTC-TTCCGATCAACTTAGGAAAATTGTTG-AGAAACCATCTTCTAGTGTAC
* * * *
52336 TTCTTGACGAGATCGTCC-TCCAATCATCTTCTGAAAATTGC-TGAGAAACCATCTTCTGGCGTA
64 TGCTTGACAAGATCG-CCTTCCGATCAACTTCTGAAAATT-CTTGAGAAACCATCTTCTGGCGTA
* *
52399 CTTCTTTGACAAGATCGTCTTCCGATCAACTTCTGAAAACTGTCGAGAAACCATCTTCTGGTGTA
127 CTTCTTTAACAAGATCGGCTTCCGATCAACTTCTGAAAACTGTCGAGAAACCATCTTCTGGTGTA
*
52464 CTTCTTGACAAGATCGTCTTCCGATCATGTTCTGAAATTTTATTGAGAAACCATCTTCTGGTGTA
192 CTTCTTGACAAGATCGTCTTCCGATCATGTTCTGAAATTTTATTGAGAAACCATCTTCTGGCGTA
52529 CT
257 CT
* * **
52531 TCTTGATAAGATCGTCTTCCGCTCAACTTTTGAAAATTGGTT-AGAAACCATCTTCTAGTGTACT
1 TCTTGACAAGATCGTCTTCCGATCAACTTAGGAAAATT-GTTGAGAAACCATCTTCTAGTGTACT
* * * *
52595 GCTTGACAAGATCGCCTTCCGGTCGACTTCTAAAAATTCTTGAGAAACCATCTTCTGGTGTACTT
65 GCTTGACAAGATCGCCTTCCGATCAACTTCTGAAAATTCTTGAGAAACCATCTTCTGGCGTACTT
* * * * * *
52660 -TTTAACGAGGTCGGCTTCCGA-CTAACTTTTGAAAATTTTCGGGAAACCATCTTCTGGTGTACT
130 CTTTAACAAGATCGGCTTCCGATC-AACTTCTGAAAACTGTCGAGAAACCATCTTCTGGTGTACT
* * * *
52723 TCTTGACAAGATTGTCTTCCGATCAAT-TTTTGAAATTTTTTTGAGACACCATCTTCTGGCGTAC
194 TCTTGACAAGATCGTCTTCCGATC-ATGTTCTGAAATTTTATTGAGAAACCATCTTCTGGCGTAC
52787 T
258 T
* * *
52788 TCTTGACAAGATCGTCTTCCGATCAACTTAGGAAAATTTTTGAGAAACCATCTTCTGGTGTACTT
1 TCTTGACAAGATCGTCTTCCGATCAACTTAGGAAAATTGTTGAGAAACCATCTTCTAGTGTACTG
* * * *
52853 TTTGACGAGATCGTCTTCCGATCAACTCCTGAAAATTCTT
66 CTTGACAAGATCGCCTTCCGATCAACTTCTGAAAATTCTT
52893 TCTAGCAAAC
Statistics
Matches: 309, Mismatches: 46, Indels: 16
0.83 0.12 0.04
Matches are distributed among these distances:
256 3 0.01
257 201 0.65
258 90 0.29
259 14 0.05
260 1 0.00
ACGTcount: A:0.25, C:0.23, G:0.17, T:0.35
Consensus pattern (258 bp):
TCTTGACAAGATCGTCTTCCGATCAACTTAGGAAAATTGTTGAGAAACCATCTTCTAGTGTACTG
CTTGACAAGATCGCCTTCCGATCAACTTCTGAAAATTCTTGAGAAACCATCTTCTGGCGTACTTC
TTTAACAAGATCGGCTTCCGATCAACTTCTGAAAACTGTCGAGAAACCATCTTCTGGTGTACTTC
TTGACAAGATCGTCTTCCGATCATGTTCTGAAATTTTATTGAGAAACCATCTTCTGGCGTACT
Found at i:52888 original size:193 final size:192
Alignment explanation
Indices: 52280--52889 Score: 733
Period size: 193 Copynumber: 3.2 Consensus size: 192
52270 TCTCTTAACA
** * * *
52280 AGATCGTCTTTCCGATCAACTTCTG-AACCTTTCGAAAAAACTATCCTCTGGTGTACTTCTTGAC
1 AGATCGTC-TTCCGATCAACTTCTGAAAATTTTCG-AGAAACCATCTTCTGGTGTACTTCTTGAC
* * * * * *
52344 GAGATCGTCCTCCAATC-ATCTTCTGAAAATTGCTGAGAAACCATCTTCTGGCGTACTTCTTTGA
64 AAGATCGTCTTCCGATCAAT-TTTTGAAATTTGTTGAGAAACCATCTTCTGGCGTACTTC-TTGA
* * * *
52408 CAAGATCGTCTTCCGATCAACTTCTGAAAACTGTCGAGAAACCATCTTCTGGTGTACTTCTTGAC
127 CAAGATCGTCTTCCGATCAACTTCTGAAAATTCTTGAGAAACCATCTTCTGGTGTACTTTTTGAC
*
52473 A
192 G
** * * *
52474 AGATCGTCTTCCGATCATGTTCTGAAATTTTATTGAGAAACCATCTTCTGGTGTACTTCTTGATA
1 AGATCGTCTTCCGATCAACTTCTGAAAATTT-TCGAGAAACCATCTTCTGGTGTACTTCTTGACA
* * * * * *
52539 AGATCGTCTTCCGCTCAACTTTTGAAAATTGGTT-AGAAACCATCTTCTAGTGTACTGCTTGACA
65 AGATCGTCTTCCGATCAATTTTTG-AAATTTGTTGAGAAACCATCTTCTGGCGTACTTCTTGACA
* * * * *
52603 AGATCGCCTTCCGGTCGACTTCTAAAAATTCTTGAGAAACCATCTTCTGGTGTACTTTTTAACG
129 AGATCGTCTTCCGATCAACTTCTGAAAATTCTTGAGAAACCATCTTCTGGTGTACTTTTTGACG
* * * *
52667 AGGTCGGCTTCCGA-CTAACTTTTGAAAATTTTCGGGAAACCATCTTCTGGTGTACTTCTTGACA
1 AGATCGTCTTCCGATC-AACTTCTGAAAATTTTCGAGAAACCATCTTCTGGTGTACTTCTTGACA
* * *
52731 AGATTGTCTTCCGATCAATTTTTGAAATTTTTTTGAGACACCATCTTCTGGCGTACTTCTTGACA
65 AGATCGTCTTCCGATCAATTTTTGAAA-TTTGTTGAGAAACCATCTTCTGGCGTACTTCTTGACA
** *
52796 AGATCGTCTTCCGATCAACTTAGGAAAATTTTTGAGAAACCATCTTCTGGTGTACTTTTTGACG
129 AGATCGTCTTCCGATCAACTTCTGAAAATTCTTGAGAAACCATCTTCTGGTGTACTTTTTGACG
*
52860 AGATCGTCTTCCGATCAACTCCTGAAAATT
1 AGATCGTCTTCCGATCAACTTCTGAAAATT
52890 CTTTCTAGCA
Statistics
Matches: 347, Mismatches: 61, Indels: 17
0.82 0.14 0.04
Matches are distributed among these distances:
191 3 0.01
192 56 0.16
193 203 0.59
194 76 0.22
195 9 0.03
ACGTcount: A:0.25, C:0.23, G:0.17, T:0.35
Consensus pattern (192 bp):
AGATCGTCTTCCGATCAACTTCTGAAAATTTTCGAGAAACCATCTTCTGGTGTACTTCTTGACAA
GATCGTCTTCCGATCAATTTTTGAAATTTGTTGAGAAACCATCTTCTGGCGTACTTCTTGACAAG
ATCGTCTTCCGATCAACTTCTGAAAATTCTTGAGAAACCATCTTCTGGTGTACTTTTTGACG
Done.