Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01011394.1 Corchorus olitorius cultivar O-4 contig11427, 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: 39700
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.31
Found at i:4530 original size:29 final size:29
Alignment explanation
Indices: 4497--4555 Score: 109
Period size: 29 Copynumber: 2.0 Consensus size: 29
4487 ATGCAAACTC
*
4497 TATTCATGCTATTTGAAGAGATGACCTAA
1 TATTCATGCTATGTGAAGAGATGACCTAA
4526 TATTCATGCTATGTGAAGAGATGACCTAA
1 TATTCATGCTATGTGAAGAGATGACCTAA
4555 T
1 T
4556 GAAGCAAATC
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.34, C:0.14, G:0.19, T:0.34
Consensus pattern (29 bp):
TATTCATGCTATGTGAAGAGATGACCTAA
Found at i:5137 original size:22 final size:22
Alignment explanation
Indices: 5111--5152 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
5101 GTCATTTTCT
* *
5111 AATTCACTCTTGGCATTTAGTA
1 AATTCAATCTTCGCATTTAGTA
*
5133 AATTCAATGTTCGCATTTAG
1 AATTCAATCTTCGCATTTAG
5153 CATAGCTTAT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.29, C:0.17, G:0.14, T:0.40
Consensus pattern (22 bp):
AATTCAATCTTCGCATTTAGTA
Found at i:8154 original size:17 final size:17
Alignment explanation
Indices: 8127--8160 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
8117 CAATTTGTTT
8127 GCTTTTCTCTA-TGGCC
1 GCTTTTCTCTATTGGCC
8143 GCTTTATCTCTATTGGCC
1 GCTTT-TCTCTATTGGCC
8161 TTCAAGGCAG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 5 0.31
17 6 0.38
18 5 0.31
ACGTcount: A:0.09, C:0.29, G:0.18, T:0.44
Consensus pattern (17 bp):
GCTTTTCTCTATTGGCC
Found at i:11048 original size:13 final size:13
Alignment explanation
Indices: 11030--11054 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
11020 ATAGGCCTAA
11030 TAAGAGTAACTTG
1 TAAGAGTAACTTG
11043 TAAGAGTAACTT
1 TAAGAGTAACTT
11055 ATTTCTTCTC
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:0.20, T:0.32
Consensus pattern (13 bp):
TAAGAGTAACTTG
Found at i:14721 original size:22 final size:22
Alignment explanation
Indices: 14694--14743 Score: 82
Period size: 22 Copynumber: 2.3 Consensus size: 22
14684 AGTTTAATAG
14694 TTGCATTTTTGCATGGCACCTT
1 TTGCATTTTTGCATGGCACCTT
* *
14716 TTGCATTTTTGCATGGTATCTT
1 TTGCATTTTTGCATGGCACCTT
14738 TTGCAT
1 TTGCAT
14744 CCATCCTTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.14, C:0.18, G:0.18, T:0.50
Consensus pattern (22 bp):
TTGCATTTTTGCATGGCACCTT
Found at i:16906 original size:9 final size:9
Alignment explanation
Indices: 16896--16932 Score: 51
Period size: 8 Copynumber: 4.3 Consensus size: 9
16886 AGAAATGAAG
*
16896 AAGAAGAAG
1 AAGAAGAAA
16905 AA-AAGAAA
1 AAGAAGAAA
16913 AAGAAGAAA
1 AAGAAGAAA
16922 AAGAA-AAA
1 AAGAAGAAA
16930 AAG
1 AAG
16933 GGGGAATCTA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
8 13 0.50
9 13 0.50
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (9 bp):
AAGAAGAAA
Found at i:16907 original size:17 final size:17
Alignment explanation
Indices: 16885--16929 Score: 58
Period size: 17 Copynumber: 2.8 Consensus size: 17
16875 TTAGGGTTAA
* *
16885 AAGAAATGAAGAAGAAG
1 AAGAAAAGAAAAAGAAG
16902 AAGAAAAGAAAAAGAAG
1 AAGAAAAGAAAAAGAAG
16919 -A-AAAAGAAAAA
1 AAGAAAAGAAAAA
16930 AAGGGGGAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
15 10 0.38
16 1 0.04
17 15 0.58
ACGTcount: A:0.76, C:0.00, G:0.22, T:0.02
Consensus pattern (17 bp):
AAGAAAAGAAAAAGAAG
Found at i:16910 original size:14 final size:14
Alignment explanation
Indices: 16893--16929 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
16883 AAAAGAAATG
*
16893 AAGAAGAAGAAGAA
1 AAGAAAAAGAAGAA
16907 AAGAAAAAGAAGAAA
1 AAGAAAAAGAAG-AA
16922 AAGAAAAA
1 AAGAAAAA
16930 AAGGGGGAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
14 11 0.52
15 10 0.48
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (14 bp):
AAGAAAAAGAAGAA
Found at i:17962 original size:30 final size:30
Alignment explanation
Indices: 17927--18011 Score: 116
Period size: 31 Copynumber: 2.8 Consensus size: 30
17917 TTTCTTAAGC
*
17927 AAATTCAAAAGAAGATTTTGGAAAATAAGG
1 AAATTCAAAAGAAGATTTTGGAAAATAAAG
* *
17957 TAATTCCAAAAGGAGATTTTGGAAAATAAAG
1 AAATT-CAAAAGAAGATTTTGGAAAATAAAG
**
17988 AAACCCAAAAGAAGATTTTGGAAA
1 AAATTCAAAAGAAGATTTTGGAAA
18012 TTAATAAAAT
Statistics
Matches: 47, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
30 22 0.47
31 25 0.53
ACGTcount: A:0.52, C:0.07, G:0.19, T:0.22
Consensus pattern (30 bp):
AAATTCAAAAGAAGATTTTGGAAAATAAAG
Found at i:17967 original size:31 final size:30
Alignment explanation
Indices: 17928--18011 Score: 116
Period size: 30 Copynumber: 2.8 Consensus size: 30
17918 TTCTTAAGCA
*
17928 AATT-CAAAAGAAGATTTTGGAAAATAAGG
1 AATTCCAAAAGAAGATTTTGGAAAATAAAG
*
17957 TAATTCCAAAAGGAGATTTTGGAAAATAAAG
1 -AATTCCAAAAGAAGATTTTGGAAAATAAAG
**
17988 AAACCCAAAAGAAGATTTTGGAAA
1 AATTCCAAAAGAAGATTTTGGAAA
18012 TTAATAAAAT
Statistics
Matches: 48, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
30 25 0.52
31 23 0.48
ACGTcount: A:0.51, C:0.07, G:0.19, T:0.23
Consensus pattern (30 bp):
AATTCCAAAAGAAGATTTTGGAAAATAAAG
Found at i:22682 original size:14 final size:15
Alignment explanation
Indices: 22657--22695 Score: 53
Period size: 15 Copynumber: 2.6 Consensus size: 15
22647 CAAGAAACGT
22657 TTTTCAAGAAAA-AAG
1 TTTTCAA-AAAATAAG
*
22672 TTTTCAAAAAATGAG
1 TTTTCAAAAAATAAG
22687 TTTTCAAAA
1 TTTTCAAAA
22696 GGTTTTGGGT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 4 0.18
15 18 0.82
ACGTcount: A:0.49, C:0.08, G:0.10, T:0.33
Consensus pattern (15 bp):
TTTTCAAAAAATAAG
Found at i:25067 original size:14 final size:14
Alignment explanation
Indices: 25030--25079 Score: 52
Period size: 14 Copynumber: 3.6 Consensus size: 14
25020 AAAAGACACA
25030 AAAGA-GAGTTCAAG
1 AAAGAGGAG-TCAAG
25044 AAATGAGGAGGT-AAG
1 AAA-GAGGA-GTCAAG
25059 AAAGAGGAGTCAAG
1 AAAGAGGAGTCAAG
25073 -AAGAGGA
1 AAAGAGGA
25080 AAGGGACAGA
Statistics
Matches: 32, Mismatches: 0, Indels: 9
0.78 0.00 0.22
Matches are distributed among these distances:
13 9 0.28
14 11 0.34
15 8 0.25
16 3 0.09
17 1 0.03
ACGTcount: A:0.50, C:0.04, G:0.36, T:0.10
Consensus pattern (14 bp):
AAAGAGGAGTCAAG
Found at i:25792 original size:67 final size:64
Alignment explanation
Indices: 25644--25965 Score: 337
Period size: 64 Copynumber: 4.9 Consensus size: 64
25634 AGAGCATTTT
* * * * *
25644 AGAAGTACACC-GAAAGACGGTTTGCTAGAAAGAATTTTCA-AATGTTGATTGGAAGACAATCTC
1 AGAAGTACACCAG-AAGATGGTTT-CT--AAAGAGTTTTCAGAA-GTTGATCGGAAGACGATCTT
*
25707 ATTGA
61 A-TCA
* * * * * *
25712 GGAA-TACATCAGAAGACGGTTTACTAGAAACAATTTTCAGAAGATGATCGGAAGACGATCTTAT
1 AGAAGTACACCAGAAGATGGTTT-CT--AAAGAGTTTTCAGAAGTTGATCGGAAGACGATCTTAT
25776 CA
63 CA
* * * * *
25778 AGAAGTACACCAGAAGATGGTTTCTCAAGAGTTTTCAGATGTTGATCGAAAGATGATCTTGTCA
1 AGAAGTACACCAGAAGATGGTTTCTAAAGAGTTTTCAGAAGTTGATCGGAAGACGATCTTATCA
* * *
25842 AGAAGTACACCAGAAGATGGTTTCTCAAA-AGTTTTCAGAAGTTGATCGGAAGATGATTTTGTCA
1 AGAAGTACACCAGAAGATGGTTTCT-AAAGAGTTTTCAGAAGTTGATCGGAAGACGATCTTATCA
*
25906 AGAAGTACACCAGAAGATGGTTTCTCAAGAGTTTTCAGAAGTTGATCGGAAGACGATCTT
1 AGAAGTACACCAGAAGATGGTTTCTAAAGAGTTTTCAGAAGTTGATCGGAAGACGATCTT
25966 GTTAAGAGAT
Statistics
Matches: 222, Mismatches: 27, Indels: 14
0.84 0.10 0.05
Matches are distributed among these distances:
63 2 0.01
64 142 0.64
65 2 0.01
66 7 0.03
67 63 0.28
68 6 0.03
ACGTcount: A:0.36, C:0.14, G:0.23, T:0.27
Consensus pattern (64 bp):
AGAAGTACACCAGAAGATGGTTTCTAAAGAGTTTTCAGAAGTTGATCGGAAGACGATCTTATCA
Found at i:25836 original size:64 final size:64
Alignment explanation
Indices: 25745--25972 Score: 375
Period size: 64 Copynumber: 3.6 Consensus size: 64
25735 CTAGAAACAA
* *
25745 TTTTCAGAAGATGATCGGAAGACGATCTTATCAAGAAGTACACCAGAAGATGGTTTCTCAAGAG
1 TTTTCAGAAGTTGATCGGAAGACGATCTTGTCAAGAAGTACACCAGAAGATGGTTTCTCAAGAG
* * * *
25809 TTTTCAGATGTTGATCGAAAGATGATCTTGTCAAGAAGTACACCAGAAGATGGTTTCTCAAAAG
1 TTTTCAGAAGTTGATCGGAAGACGATCTTGTCAAGAAGTACACCAGAAGATGGTTTCTCAAGAG
* *
25873 TTTTCAGAAGTTGATCGGAAGATGATTTTGTCAAGAAGTACACCAGAAGATGGTTTCTCAAGAG
1 TTTTCAGAAGTTGATCGGAAGACGATCTTGTCAAGAAGTACACCAGAAGATGGTTTCTCAAGAG
*
25937 TTTTCAGAAGTTGATCGGAAGACGATCTTGTTAAGA
1 TTTTCAGAAGTTGATCGGAAGACGATCTTGTCAAGA
25973 GATGCACCGA
Statistics
Matches: 151, Mismatches: 13, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
64 151 1.00
ACGTcount: A:0.34, C:0.14, G:0.24, T:0.29
Consensus pattern (64 bp):
TTTTCAGAAGTTGATCGGAAGACGATCTTGTCAAGAAGTACACCAGAAGATGGTTTCTCAAGAG
Found at i:26276 original size:101 final size:98
Alignment explanation
Indices: 26199--26478 Score: 371
Period size: 101 Copynumber: 2.8 Consensus size: 98
26189 TGATTTTCTC
* * *
26199 AAGATTGAATTGGAAGACAGTTCAAAGGATAAGCGAAAGACGGCCCCTTTTTAAGATTCAATTGG
1 AAGATTGAATTGGAAGACAGTTCAAAGGATAAGCGGAAGACGG-TCC-TTTTAAGATTGAATTGG
*
26264 AAGACAGTTCAAAGGATAAGCAGAAGACAGTCCTTTT
64 AAGACAGTTCAAAGGATAAGCAGAAGAGA-T-CTTTT
* * *
26301 AAAATTGAATTGGAAGATAGTTCAAAGGATAAGCGGAAGACGGTCCTTTTAAGATTGAATTGGAT
1 AAGATTGAATTGGAAGACAGTTCAAAGGATAAGCGGAAGACGGTCCTTTTAAGATTGAATTGGAA
* * *
26366 GACAGTTTAAAGGATAAGCAGAAGGCGGTCCTTTTT
66 GACAGTTCAAAGGATAAGCAGAA-GAGAT-C-TTTT
* * *
26402 AAGATTGAATTGGAAGACAGTTCAAAGAATAAGCGGAAGACGGTCCTTTTAATATTGGATTGGAA
1 AAGATTGAATTGGAAGACAGTTCAAAGGATAAGCGGAAGACGGTCCTTTTAAGATTGAATTGGAA
*
26467 GACAATTCAAAG
66 GACAGTTCAAAG
26479 AAATTCATTC
Statistics
Matches: 158, Mismatches: 18, Indels: 5
0.87 0.10 0.03
Matches are distributed among these distances:
100 42 0.27
101 76 0.48
102 40 0.25
ACGTcount: A:0.38, C:0.12, G:0.25, T:0.25
Consensus pattern (98 bp):
AAGATTGAATTGGAAGACAGTTCAAAGGATAAGCGGAAGACGGTCCTTTTAAGATTGAATTGGAA
GACAGTTCAAAGGATAAGCAGAAGAGATCTTTT
Found at i:26425 original size:151 final size:152
Alignment explanation
Indices: 26199--26478 Score: 429
Period size: 151 Copynumber: 1.8 Consensus size: 152
26189 TGATTTTCTC
26199 AAGATTGAATTGGAAGACAGTTCAAAGGATAAGCGAAAGACGGCCCCTTTTTAAGATTCAATTGG
1 AAGATTGAATTGGAAGACAGTTCAAAGGATAAGCGAAAGACGGCCCCTTTTTAAGATTCAATTGG
* * *
26264 AAGACAGTTCAAAGGATAAGCAGAAGACAGTCCTTTTAAAATTGAATTGGAAGATAGTTCAAAGG
66 AAGACAGTTCAAAGAATAAGCAGAAGACAGTCCTTTTAAAATTGAATTGGAAGACAATTCAAAGG
26329 ATAAGCGGAAGACGGTCCTTTT
131 ATAAGCGGAAGACGGTCCTTTT
* * * * *
26351 AAGATTGAATTGGATGACAGTTTAAAGGATAAGC-AGAAGGCGG-TCCTTTTTAAGATTGAATTG
1 AAGATTGAATTGGAAGACAGTTCAAAGGATAAGCGA-AAGACGGCCCCTTTTTAAGATTCAATTG
* * * *
26414 GAAGACAGTTCAAAGAATAAGCGGAAGACGGTCCTTTTAATATTGGATTGGAAGACAATTCAAAG
65 GAAGACAGTTCAAAGAATAAGCAGAAGACAGTCCTTTTAAAATTGAATTGGAAGACAATTCAAAG
26479 AAATTCATTC
Statistics
Matches: 115, Mismatches: 12, Indels: 3
0.88 0.09 0.02
Matches are distributed among these distances:
151 77 0.67
152 38 0.33
ACGTcount: A:0.38, C:0.12, G:0.25, T:0.25
Consensus pattern (152 bp):
AAGATTGAATTGGAAGACAGTTCAAAGGATAAGCGAAAGACGGCCCCTTTTTAAGATTCAATTGG
AAGACAGTTCAAAGAATAAGCAGAAGACAGTCCTTTTAAAATTGAATTGGAAGACAATTCAAAGG
ATAAGCGGAAGACGGTCCTTTT
Found at i:26480 original size:50 final size:50
Alignment explanation
Indices: 26199--26478 Score: 398
Period size: 50 Copynumber: 5.5 Consensus size: 50
26189 TGATTTTCTC
* *
26199 AAGATTGAATTGGAAGACAGTTCAAAGGATAAGCGAAAGACGGCCCCTTTTT
1 AAGATTGAATTGGAAGACAGTTCAAAGGATAAGCGGAAGACGG-TCC-TTTT
* * *
26251 AAGATTCAATTGGAAGACAGTTCAAAGGATAAGCAGAAGACAGTCCTTTT
1 AAGATTGAATTGGAAGACAGTTCAAAGGATAAGCGGAAGACGGTCCTTTT
* *
26301 AAAATTGAATTGGAAGATAGTTCAAAGGATAAGCGGAAGACGGTCCTTTT
1 AAGATTGAATTGGAAGACAGTTCAAAGGATAAGCGGAAGACGGTCCTTTT
* * * *
26351 AAGATTGAATTGGATGACAGTTTAAAGGATAAGCAGAAGGCGGTCCTTTTT
1 AAGATTGAATTGGAAGACAGTTCAAAGGATAAGCGGAAGACGGTCC-TTTT
*
26402 AAGATTGAATTGGAAGACAGTTCAAAGAATAAGCGGAAGACGGTCCTTTT
1 AAGATTGAATTGGAAGACAGTTCAAAGGATAAGCGGAAGACGGTCCTTTT
* * *
26452 AATATTGGATTGGAAGACAATTCAAAG
1 AAGATTGAATTGGAAGACAGTTCAAAG
26479 AAATTCATTC
Statistics
Matches: 203, Mismatches: 24, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
50 117 0.58
51 47 0.23
52 39 0.19
ACGTcount: A:0.38, C:0.12, G:0.25, T:0.25
Consensus pattern (50 bp):
AAGATTGAATTGGAAGACAGTTCAAAGGATAAGCGGAAGACGGTCCTTTT
Found at i:31770 original size:40 final size:39
Alignment explanation
Indices: 31671--32249 Score: 616
Period size: 40 Copynumber: 14.6 Consensus size: 39
31661 TTGGCTAATA
* *
31671 AAAAAATGATCCTGAGCAGGATTCTGAAA-TGA-TTGAT
1 AAAAAATGATCCTGAGCAGGATTTTGAAATTAATTTGAT
** * *
31708 AAAACAATGATCCTGAATAGGATTCTGAAATTAATTTGGT
1 AAAA-AATGATCCTGAGCAGGATTTTGAAATTAATTTGAT
* * * * ** *
31748 AAAACAAGGATCTTGAGCAGGATTGTG--ATTGA-CAGGT
1 AAAA-AATGATCCTGAGCAGGATTTTGAAATTAATTTGAT
** * *
31785 AAAGAAATGATCCTGAATAGGATTCTGAAATTAATATGAT
1 AAA-AAATGATCCTGAGCAGGATTTTGAAATTAATTTGAT
** *** *
31825 AAAGCGATGATCCTGAATGGGATTCTGAAATTAATTTGAT
1 AAA-AAATGATCCTGAGCAGGATTTTGAAATTAATTTGAT
* * *
31865 AAACCAATGATTCTGAGCAGAATTTTGAAATTAATTTGAT
1 AAA-AAATGATCCTGAGCAGGATTTTGAAATTAATTTGAT
* * *
31905 AAAAGATGATCCTGAGCAGGATTCTGAAA-TGA-TTGAT
1 AAAAAATGATCCTGAGCAGGATTTTGAAATTAATTTGAT
* *
31942 AAAACAATGATCATGAGCAGGGTTTTGAAATTAATTTGAT
1 AAAA-AATGATCCTGAGCAGGATTTTGAAATTAATTTGAT
* *
31982 AAAAAGATGATCCTTAGCAGGATTTTGAGATTAATTTGAT
1 AAAAA-ATGATCCTGAGCAGGATTTTGAAATTAATTTGAT
*
32022 AAAAAAAGGATCCTGAGCAGGATTTTGAAATTAATTTGAT
1 -AAAAAATGATCCTGAGCAGGATTTTGAAATTAATTTGAT
32062 AAAAAAGATGATCCTGAGCAGGATTTTGAAATTAATTTGAT
1 -AAAAA-ATGATCCTGAGCAGGATTTTGAAATTAATTTGAT
*
32103 AAAGAAA-GAATCCTGAGCAGGATTCTGAAATTAATTTGAT
1 AAA-AAATG-ATCCTGAGCAGGATTTTGAAATTAATTTGAT
32143 AAAAAGATGATCCTGAGCAGGATTTTGAAATTAATTTGAT
1 AAAAA-ATGATCCTGAGCAGGATTTTGAAATTAATTTGAT
32183 AAAAAGATGATCCTGAGCAGGATTTTGAAATTAATTTGAT
1 AAAAA-ATGATCCTGAGCAGGATTTTGAAATTAATTTGAT
*
32223 AAAGTAAGGATGATCCTGACCAGGATT
1 AAA--AA--ATGATCCTGAGCAGGATT
32250 AAAACACATA
Statistics
Matches: 467, Mismatches: 55, Indels: 34
0.84 0.10 0.06
Matches are distributed among these distances:
37 36 0.08
38 51 0.11
39 33 0.07
40 286 0.61
41 41 0.09
42 2 0.00
43 18 0.04
ACGTcount: A:0.40, C:0.09, G:0.21, T:0.30
Consensus pattern (39 bp):
AAAAAATGATCCTGAGCAGGATTTTGAAATTAATTTGAT
Found at i:31908 original size:157 final size:157
Alignment explanation
Indices: 31668--32225 Score: 676
Period size: 157 Copynumber: 3.5 Consensus size: 157
31658 GAATTGGCTA
* * * **
31668 ATAAAAAAATGATCCTGAGCAGGATTCTGAAA-TGA-TTGATAAAACAATGATCCTGAATAGGAT
1 ATAAAAAGATGATCCTGAGCAGGATTCTGAAATTAATTTGATAAAAAAATGATCCTGAGCAGGAT
* * * * ** *
31731 TCTGAAATTAATTTGGTAAAACAAGGATCTTGAGCAGGATTGTG-ATTGACAGGTAAAGAAATGA
66 TTTGAAATTAATTTGATAAAA-AAGGATCCTGAGCAGGATTCTGAATTGATTGATAAAGAAATGA
** *
31795 TCCTGAATAGGATTCTGAAATTAATATG
130 TCCTGAGCAGGATTCTGAAATTAATTTG
** *** ** * *
31823 ATAAAGCGATGATCCTGAATGGGATTCTGAAATTAATTTGATAAACCAATGATTCTGAGCAGAAT
1 ATAAAAAGATGATCCTGAGCAGGATTCTGAAATTAATTTGATAAAAAAATGATCCTGAGCAGGAT
* * *
31888 TTTGAAATTAATTTGATAAAAGATGATCCTGAGCAGGATTCTGAAATGATTGATAAA-ACAATGA
66 TTTGAAATTAATTTGATAAAAAAGGATCCTGAGCAGGATTCTGAATTGATTGATAAAGA-AATGA
* * *
31952 TCATGAGCAGGGTTTTGAAATTAATTTG
130 TCCTGAGCAGGATTCTGAAATTAATTTG
* * * *
31980 ATAAAAAGATGATCCTTAGCAGGATTTTGAGATTAATTTGATAAAAAAAGGATCCTGAGCAGGAT
1 ATAAAAAGATGATCCTGAGCAGGATTCTGAAATTAATTTGATAAAAAAATGATCCTGAGCAGGAT
* *
32045 TTTGAAATTAATTTGATAAAAAAGATGATCCTGAGCAGGATTTTGAAATTAATTTGATAAAGAAA
66 TTTGAAATTAATTTGATAAAAAAG--GATCCTGAGCAGGATTCTG-AATTGA-TTGATAAAGAAA
32110 -GAATCCTGAGCAGGATTCTGAAATTAATTTG
127 TG-ATCCTGAGCAGGATTCTGAAATTAATTTG
* *
32141 ATAAAAAGATGATCCTGAGCAGGATTTTGAAATTAATTTGATAAAAAGATGATCCTGAGCAGGAT
1 ATAAAAAGATGATCCTGAGCAGGATTCTGAAATTAATTTGATAAAAAAATGATCCTGAGCAGGAT
32206 TTTGAAATTAATTTGATAAA
66 TTTGAAATTAATTTGATAAA
32226 GTAAGGATGA
Statistics
Matches: 340, Mismatches: 53, Indels: 14
0.84 0.13 0.03
Matches are distributed among these distances:
155 26 0.08
156 21 0.06
157 152 0.45
159 18 0.05
160 5 0.01
161 117 0.34
162 1 0.00
ACGTcount: A:0.40, C:0.09, G:0.20, T:0.31
Consensus pattern (157 bp):
ATAAAAAGATGATCCTGAGCAGGATTCTGAAATTAATTTGATAAAAAAATGATCCTGAGCAGGAT
TTTGAAATTAATTTGATAAAAAAGGATCCTGAGCAGGATTCTGAATTGATTGATAAAGAAATGAT
CCTGAGCAGGATTCTGAAATTAATTTG
Found at i:32343 original size:23 final size:22
Alignment explanation
Indices: 32317--32377 Score: 68
Period size: 22 Copynumber: 2.7 Consensus size: 22
32307 GACTTGTCAG
*
32317 AATTAATACCCTGAGGTTTCTGA
1 AATT-ATACCCGGAGGTTTCTGA
* *
32340 AATTGTGCCCGGAGGTTTCTGA
1 AATTATACCCGGAGGTTTCTGA
* *
32362 AATTGTGCCCGGAGGT
1 AATTATACCCGGAGGT
32378 CTTACAAATG
Statistics
Matches: 35, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
22 31 0.89
23 4 0.11
ACGTcount: A:0.23, C:0.18, G:0.28, T:0.31
Consensus pattern (22 bp):
AATTATACCCGGAGGTTTCTGA
Found at i:32354 original size:22 final size:22
Alignment explanation
Indices: 32329--32377 Score: 98
Period size: 22 Copynumber: 2.2 Consensus size: 22
32319 TTAATACCCT
32329 GAGGTTTCTGAAATTGTGCCCG
1 GAGGTTTCTGAAATTGTGCCCG
32351 GAGGTTTCTGAAATTGTGCCCG
1 GAGGTTTCTGAAATTGTGCCCG
32373 GAGGT
1 GAGGT
32378 CTTACAAATG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.18, C:0.16, G:0.35, T:0.31
Consensus pattern (22 bp):
GAGGTTTCTGAAATTGTGCCCG
Done.