Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01005719.1 Kokia drynarioides strain JFW-HI SEQ_119950, 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: 21799
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.34
Found at i:2574 original size:17 final size:17
Alignment explanation
Indices: 2552--2584 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
2542 ACACGACCTG
2552 TCACATGGCTGTGTGGC
1 TCACATGGCTGTGTGGC
*
2569 TCACATGGGTGTGTGG
1 TCACATGGCTGTGTGG
2585 AAGGGGTCAG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.12, C:0.18, G:0.39, T:0.30
Consensus pattern (17 bp):
TCACATGGCTGTGTGGC
Found at i:3557 original size:21 final size:21
Alignment explanation
Indices: 3501--3558 Score: 64
Period size: 21 Copynumber: 2.7 Consensus size: 21
3491 AAAACTTTAA
*
3501 AAATATTAACTCTATTAAACAGT
1 AAATATTAACT-T-TTAAACAAT
*
3524 AAATGA-TATCTTTTAAACAAT
1 AAAT-ATTAACTTTTAAACAAT
3545 AAATATTAACTTTT
1 AAATATTAACTTTT
3559 TTTTCAAATT
Statistics
Matches: 30, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
20 1 0.03
21 19 0.63
22 1 0.03
23 8 0.27
24 1 0.03
ACGTcount: A:0.47, C:0.10, G:0.03, T:0.40
Consensus pattern (21 bp):
AAATATTAACTTTTAAACAAT
Found at i:4670 original size:96 final size:97
Alignment explanation
Indices: 4496--4682 Score: 263
Period size: 96 Copynumber: 1.9 Consensus size: 97
4486 AACTTTGGAA
* *
4496 AAGGATATTCAATTATCTCGATTTGAAGAAAAGTCGCACCTAGTAAGTTAAGGCACAAATTTTCA
1 AAGGATATTCAATTATCTCGATTTGAAGAAAAATCGCACCAAGTAAGTTAAGGCACAAATTTTCA
* *
4561 GAATCAGAGAT-AAAGAACATTGCCTCGATCT
66 AAATCAGAAATAAAAGAACATTGCCTCGATCT
* * *
4592 AAGGGTATTCGATTAT-TCCGATTTGAAGAAAAATCGCGCCAAGTAAGTTAAGGCACAAATTTTC
1 AAGGATATTCAATTATCT-CGATTTGAAGAAAAATCGCACCAAGTAAGTTAAGGCACAAATTTTC
*
4656 AAAACTCA-AAATAAAAGAATATTGCCT
65 AAAA-TCAGAAATAAAAGAACATTGCCT
4683 TAATTTTAAA
Statistics
Matches: 80, Mismatches: 8, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
95 1 0.01
96 63 0.79
97 16 0.20
ACGTcount: A:0.40, C:0.16, G:0.17, T:0.27
Consensus pattern (97 bp):
AAGGATATTCAATTATCTCGATTTGAAGAAAAATCGCACCAAGTAAGTTAAGGCACAAATTTTCA
AAATCAGAAATAAAAGAACATTGCCTCGATCT
Found at i:4936 original size:28 final size:28
Alignment explanation
Indices: 4905--4966 Score: 72
Period size: 28 Copynumber: 2.2 Consensus size: 28
4895 AAAATGTGAT
* *
4905 TTTTGGATACCC-AGGGGAAAAATGGTAA
1 TTTTGGACACCCGA-GGGAAAAATGGAAA
* *
4933 TTTTGGACACTCGAGGGTAAAATGGAAA
1 TTTTGGACACCCGAGGGAAAAATGGAAA
4961 TTTTGG
1 TTTTGG
4967 GAAAGTTCGG
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
28 28 0.97
29 1 0.03
ACGTcount: A:0.32, C:0.10, G:0.29, T:0.29
Consensus pattern (28 bp):
TTTTGGACACCCGAGGGAAAAATGGAAA
Found at i:4996 original size:59 final size:58
Alignment explanation
Indices: 4922--5381 Score: 502
Period size: 59 Copynumber: 7.8 Consensus size: 58
4912 TACCCAGGGG
* * * ** *
4922 AAAAATGGTAA-TTTTGGACA-CTCGAGGGTAAAATGGAAATTTTGGGAAAGTTCGGGGT
1 AAAAATGG-AATTTTTGGA-AGTTCGAGGGTAAAATGGTAATTTTTGGAAAAATCGAGGT
*
4980 CAAAAATGGAATTTTTGGAAGTTCAAGGGTAAAATGGTAATTTTTGGAAAAATCGAGGT
1 -AAAAATGGAATTTTTGGAAGTTCGAGGGTAAAATGGTAATTTTTGGAAAAATCGAGGT
* *
5039 CAAAAATGGAA-TTTTGAAAATTCGAGGGTAAAATGGTAATTTTTGG-AAAATCGAGGT
1 -AAAAATGGAATTTTTGGAAGTTCGAGGGTAAAATGGTAATTTTTGGAAAAATCGAGGT
* *
5096 AAAAAAATGGATTTTTTGGAAGTTCGAGGGTAAAATGGTAATTTTTGGAGAAATCGAGGAT
1 --AAAAATGGAATTTTTGGAAGTTCGAGGGTAAAATGGTAATTTTTGGAAAAATCGAGG-T
** *
5157 AAAAATGGAATTTTTGGAAGTTTAAGGGTAAAATTGTAATTTTTGGAAAAAATCGAGGTT
1 AAAAATGGAATTTTTGGAAGTTCGAGGGTAAAATGGTAATTTTTGG-AAAAATCGAGG-T
* * * * **
5217 AAGAATGAAATTTTTGGAAGTTCGGGGGTAAAATGGTAATTTTTGGAAAATTTAAGGTT
1 AAAAATGGAATTTTTGGAAGTTCGAGGGTAAAATGGTAATTTTTGGAAAAATCGAGG-T
* * **
5276 AAAAATGGAATTTTTGAAAGTTCGAGGGTAAAAAT-GTAATTTTTAGAAAGTTCGAGGAT
1 AAAAATGGAATTTTTGGAAGTTCGAGGGT-AAAATGGTAATTTTTGGAAAAATCGAGG-T
* * *
5335 AAAGATGGAA-TTTTGGAAAGTTTGTGGGCTAAAAT-GTAATTTTTGGA
1 AAAAATGGAATTTTTGG-AAGTTCGAGGG-TAAAATGGTAATTTTTGGA
5382 CAGTTTAGGG
Statistics
Matches: 347, Mismatches: 44, Indels: 20
0.84 0.11 0.05
Matches are distributed among these distances:
57 11 0.03
58 49 0.14
59 220 0.63
60 66 0.19
61 1 0.00
ACGTcount: A:0.38, C:0.04, G:0.26, T:0.32
Consensus pattern (58 bp):
AAAAATGGAATTTTTGGAAGTTCGAGGGTAAAATGGTAATTTTTGGAAAAATCGAGGT
Found at i:5112 original size:30 final size:29
Alignment explanation
Indices: 4922--5353 Score: 263
Period size: 29 Copynumber: 14.7 Consensus size: 29
4912 TACCCAGGGG
* *
4922 AAAAATGGTAA-TTTTGGACACTCGAGGGT
1 AAAAATGGTAATTTTTGGAAAATCGA-GGT
* * * *
4951 -AAAATGGAAATTTTGGGAAAGTTCGGGGT
1 AAAAATGGTAATTTTTGGAAA-ATCGAGGT
** *
4980 CAAAAATGG-AATTTTTGGAAGTTCAAGGGT
1 -AAAAATGGTAATTTTTGGAAAATCGA-GGT
5010 -AAAATGGTAATTTTTGGAAAAATCGAGGT
1 AAAAATGGTAATTTTTGG-AAAATCGAGGT
5039 CAAAAATGG-AA-TTTT-GAAAATTCGAGGGT
1 -AAAAATGGTAATTTTTGGAAAA-TCGA-GGT
5068 -AAAATGGTAATTTTTGGAAAATCGAGGT
1 AAAAATGGTAATTTTTGGAAAATCGAGGT
* **
5096 AAAAAAATGG-ATTTTTTGGAAGTTCGAGGGT
1 --AAAAATGGTAATTTTTGGAAAATCGA-GGT
5127 -AAAATGGTAATTTTTGGAGAAATCGAGGAT
1 AAAAATGGTAATTTTTGGA-AAATCGAGG-T
** **
5157 AAAAATGG-AATTTTTGGAAGTTTAAGGGT
1 AAAAATGGTAATTTTTGGAAAATCGA-GGT
*
5186 -AAAATTGTAATTTTTGGAAAAAATCGAGGTT
1 AAAAATGGTAATTTTTGG--AAAATCGAGG-T
* * ** *
5217 AAGAAT-GAAATTTTTGGAAGTTCGGGGGT
1 AAAAATGGTAATTTTTGGAAAATC-GAGGT
**
5246 -AAAATGGTAATTTTTGGAAAATTTAAGGTT
1 AAAAATGGTAATTTTTGGAAAA-TCGAGG-T
*
5276 AAAAATGG-AATTTTT-GAAAGTTCGAGGGT
1 AAAAATGGTAATTTTTGGAAA-ATCGA-GGT
* *
5305 AAAAAT-GTAATTTTTAGAAAGTTCGAGGAT
1 AAAAATGGTAATTTTTGGAAA-ATCGAGG-T
*
5335 AAAGATGG-AA-TTTTGGAAA
1 AAAAATGGTAATTTTTGGAAA
5354 GTTTGTGGGC
Statistics
Matches: 320, Mismatches: 44, Indels: 78
0.72 0.10 0.18
Matches are distributed among these distances:
27 11 0.03
28 44 0.14
29 113 0.35
30 94 0.29
31 54 0.17
32 4 0.01
ACGTcount: A:0.39, C:0.04, G:0.26, T:0.31
Consensus pattern (29 bp):
AAAAATGGTAATTTTTGGAAAATCGAGGT
Found at i:8062 original size:99 final size:97
Alignment explanation
Indices: 7750--8157 Score: 500
Period size: 99 Copynumber: 4.2 Consensus size: 97
7740 ATCCGCCATT
* *
7750 GCTTAAA--TTTCCTTTCATG-CTTCTGAGGTA-TAGGGTTCGCCATTGTGACTTAAACCTTTCC
1 GCTTAAATCTTTCCCTTCATGTC-TCTGAGGTACTA-GGTTCGCCATTGCGACTTAAACCTTT-C
* * * *
7811 CCTCTTGTCTTCGTGGTACTGGATTTGCCATTGTG
63 CCTTTTGTCTTCGTGGTACTGGATTCGCCGTTGCG
* * *
7846 GCTTAAATCTTTCCCTTTCATGCCTCTGAGGTACTAGATTCGCCATTGCGACTTAAACCTTTTCC
1 GCTTAAATCTTTCCC-TTCATGTCTCTGAGGTACTAGGTTCGCCATTGCGACTTAAACCTTTCCC
* * *
7911 TTGTGTCTTTGTGGTACTGGATTCGCCGTTACG
65 TTTTGTCTTCGTGGTACTGGATTCGCCGTTGCG
* * * *
7944 GCTTAAATCTTTCTCTTCATGTCTCTGAGGTACTAGGTTTGTCGTTGCGACTTAAACCTTTCCCT
1 GCTTAAATCTTTCCCTTCATGTCTCTGAGGTACTAGGTTCGCCATTGCGACTTAAACCTTTCCCT
* * * *
8009 TTTGTATCTTTGCGGTACTGGATTCACTGTTGCG
66 TTTG--TCTTCGTGGTACTGGATTCGCCGTTGCG
* * * *
8043 GCTTAGATTTTTCCCTTCATGTCTCTGAGGTACTAGGTTCGCCATTGAGACTTAAACCCTTCCCT
1 GCTTAAATCTTTCCCTTCATGTCTCTGAGGTACTAGGTTCGCCATTGCGACTTAAACCTTTCCCT
*
8108 TTATGTCTTCGTGGTACTGGATTCGCTGTTGCG
66 TT-TGTCTTCGTGGTACTGGATTCGCCGTTGCG
8141 GCTTAAATCTTTCCCTT
1 GCTTAAATCTTTCCCTT
8158 TCAATTCATG
Statistics
Matches: 268, Mismatches: 36, Indels: 14
0.84 0.11 0.04
Matches are distributed among these distances:
96 7 0.03
97 47 0.18
98 87 0.32
99 122 0.46
100 5 0.02
ACGTcount: A:0.16, C:0.24, G:0.20, T:0.40
Consensus pattern (97 bp):
GCTTAAATCTTTCCCTTCATGTCTCTGAGGTACTAGGTTCGCCATTGCGACTTAAACCTTTCCCT
TTTGTCTTCGTGGTACTGGATTCGCCGTTGCG
Found at i:8156 original size:49 final size:49
Alignment explanation
Indices: 7798--8158 Score: 261
Period size: 49 Copynumber: 7.3 Consensus size: 49
7788 GCCATTGTGA
* * * * *
7798 CTTAAACCTTTCCCCTCT-TGTCTTCGTGGTACTGGATTTGCCATTGTGG
1 CTTAAACCTTT-CCCTTTATGTCTTCGAGGTACTGGATTCGCCGTTGCGG
* * * * *
7847 CTTAAATCTTTCCCTTTCATG-CCTCTGAGGTACTAGATTCGCCATTGCGA
1 CTTAAACCTTTCCCTTT-ATGTCTTC-GAGGTACTGGATTCGCCGTTGCGG
* * * * *
7897 CTTAAACCTTTTCC-TTGTGTCTTTGTGGTACTGGATTCGCCGTTACGG
1 CTTAAACCTTTCCCTTTATGTCTTCGAGGTACTGGATTCGCCGTTGCGG
* * * * * *
7945 CTTAAATCTTTCTCTTCATGTC-TCTGAGGTACTAGG-TTTGTCGTTGCGA
1 CTTAAACCTTTCCCTTTATGTCTTC-GAGGTACT-GGATTCGCCGTTGCGG
* * * *
7994 CTTAAACCTTTCCCTTT-TGTATCTTTGCGGTACTGGATTCACTGTTGCGG
1 CTTAAACCTTTCCCTTTATG--TCTTCGAGGTACTGGATTCGCCGTTGCGG
* ** * * * *
8044 CTTAGATTTTTCCCTTCATGTC-TCTGAGGTACTAGG-TTCGCCATTGAGA
1 CTTAAACCTTTCCCTTTATGTCTTC-GAGGTACT-GGATTCGCCGTTGCGG
* * *
8093 CTTAAACCCTTCCCTTTATGTCTTCGTGGTACTGGATTCGCTGTTGCGG
1 CTTAAACCTTTCCCTTTATGTCTTCGAGGTACTGGATTCGCCGTTGCGG
*
8142 CTTAAATCTTTCCCTTT
1 CTTAAACCTTTCCCTTT
8159 CAATTCATGG
Statistics
Matches: 234, Mismatches: 62, Indels: 32
0.71 0.19 0.10
Matches are distributed among these distances:
48 43 0.18
49 119 0.51
50 69 0.29
51 3 0.01
ACGTcount: A:0.15, C:0.25, G:0.19, T:0.41
Consensus pattern (49 bp):
CTTAAACCTTTCCCTTTATGTCTTCGAGGTACTGGATTCGCCGTTGCGG
Found at i:18328 original size:59 final size:59
Alignment explanation
Indices: 18233--18626 Score: 325
Period size: 59 Copynumber: 6.7 Consensus size: 59
18223 ACTTGGGCGG
* * * * * ** **
18233 AAATGGTAA-TTTTAGACACTCGGGGGCAAAACGGTAATTTTGGGAAAGTTTGGGGTCAA
1 AAATGG-AATTTTTAGAAATTCGAGGGTAAAATGGTAATTTTGGGAAAAATCAGGGTCAA
* * * * * *
18292 AAATAGAATTTTTAGATATCCGAAGGTAAAATGGTAATTTTTGGAACAATCAGGGTC-A
1 AAATGGAATTTTTAGAAATTCGAGGGTAAAATGGTAATTTTGGGAAAAATCAGGGTCAA
* * * * *
18350 AAATGAAATTTTTAGAAGTTCGAGGGTAAAATGGTAATTTTTGGAAAAAATTAGGGTTAA
1 AAATGGAATTTTTAGAAATTCGAGGGTAAAATGGTAA-TTTTGGGAAAAATCAGGGTCAA
* *
18410 AAATGGAATTTTTGGAAATTCGAGGGTAAAATGGTAATTTTTGGAAAAATC-GAGGTCAA
1 AAATGGAATTTTTAGAAATTCGAGGGTAAAATGGTAATTTTGGGAAAAATCAG-GGTCAA
* ** ** * * *
18469 AAATGGAATTTTTGGAAATTCGAGGGTAAAATGGTTTTTTTTTGAGAAAT-TGAGGTTAA
1 AAATGGAATTTTTAGAAATTCGAGGGTAAAATGGTAATTTTGGGAAAAATCAG-GGTCAA
* * * * ** *
18528 AAATGGAATTTTTGGAAGTTTGGGGGTAAAATGACAATTTTTGGAAAAATC-GAGGTCAA
1 AAATGGAATTTTTAGAAATTCGAGGGTAAAATGGTAATTTTGGGAAAAATCAG-GGTCAA
* * *
18587 AAATGGAATTTTTGGAAGTT-TAGGGGT-AAATGGTAATTTT
1 AAATGGAATTTTTAGAAATTCGA-GGGTAAAATGGTAATTTT
18627 AAAAAAAAAA
Statistics
Matches: 277, Mismatches: 51, Indels: 15
0.81 0.15 0.04
Matches are distributed among these distances:
58 46 0.17
59 196 0.71
60 35 0.13
ACGTcount: A:0.37, C:0.05, G:0.26, T:0.33
Consensus pattern (59 bp):
AAATGGAATTTTTAGAAATTCGAGGGTAAAATGGTAATTTTGGGAAAAATCAGGGTCAA
Found at i:18359 original size:29 final size:28
Alignment explanation
Indices: 18316--18603 Score: 224
Period size: 29 Copynumber: 9.8 Consensus size: 28
18306 GATATCCGAA
18316 GGTAAAATGGTAATTTTTGGAACAATC-AG
1 GGTAAAATGG-AATTTTTGGAA-AATCGAG
* * **
18345 GGTCAAAATGAAATTTTTAGAAGTTCGAG
1 GGT-AAAATGGAATTTTTGGAAAATCGAG
*
18374 GGTAAAATGGTAATTTTTGGAAAAAAT-TAG
1 GGTAAAATGG-AATTTTTGG--AAAATCGAG
*
18404 GGTTAAAAATGGAATTTTTGGAAATTCGAG
1 GG-T-AAAATGGAATTTTTGGAAAATCGAG
18434 GGTAAAATGGTAATTTTTGGAAAAATCGA-
1 GGTAAAATGG-AATTTTTGG-AAAATCGAG
*
18463 GGTCAAAAATGGAATTTTTGGAAATTCGAG
1 GGT--AAAATGGAATTTTTGGAAAATCGAG
** * *
18493 GGTAAAATGGTTTTTTTTTGAGAAATTGAG
1 GGTAAAATGG-AATTTTTGGA-AAATCGAG
* ** * *
18523 GTTAAAAATGGAATTTTTGGAAGTTTGGG
1 GGT-AAAATGGAATTTTTGGAAAATCGAG
*
18552 GGTAAAATGACAATTTTTGGAAAAATCGA-
1 GGTAAAATG-GAATTTTTGG-AAAATCGAG
18581 GGTCAAAAATGGAATTTTTGGAA
1 GGT--AAAATGGAATTTTTGGAA
18604 GTTTAGGGGT
Statistics
Matches: 207, Mismatches: 32, Indels: 40
0.74 0.11 0.14
Matches are distributed among these distances:
28 28 0.14
29 78 0.38
30 61 0.29
31 33 0.16
32 7 0.03
ACGTcount: A:0.38, C:0.04, G:0.25, T:0.33
Consensus pattern (28 bp):
GGTAAAATGGAATTTTTGGAAAATCGAG
Found at i:18439 original size:118 final size:119
Alignment explanation
Indices: 18290--18686 Score: 459
Period size: 118 Copynumber: 3.4 Consensus size: 119
18280 GTTTGGGGTC
* * * * * *
18290 AAAAATAGAATTTTTAGATATCCGAAGGTAAAATGGTAATTTTTGGAACAATC-AGGGTC-AAAA
1 AAAAATGGAATTTTTGGAAATTCGAGGGTAAAATGGTAATTTTTGGAAAAATCGA-GGTCAAAAA
* * *
18353 TGAAATTTTTAGAAGTTCGAGGGTAAAATGGTAATTTTTGGAAAAAATT-AGGGTT
65 TGGAATTTTTGGAAGTTCGAGGGTAAAATGGTAATTTTTAGAAAAAATTGA-GGTT
18408 AAAAATGGAATTTTTGGAAATTCGAGGGTAAAATGGTAATTTTTGGAAAAATCGAGGTCAAAAAT
1 AAAAATGGAATTTTTGGAAATTCGAGGGTAAAATGGTAATTTTTGGAAAAATCGAGGTCAAAAAT
* ** * *
18473 GGAATTTTTGGAAATTCGAGGGTAAAATGGTTTTTTTTTG-AGAAATTGAGGTT
66 GGAATTTTTGGAAGTTCGAGGGTAAAATGGTAATTTTTAGAAAAAATTGAGGTT
* * * **
18526 AAAAATGGAATTTTTGGAAGTTTGGGGGTAAAATGACAATTTTTGGAAAAATCGAGGTCAAAAAT
1 AAAAATGGAATTTTTGGAAATTCGAGGGTAAAATGGTAATTTTTGGAAAAATCGAGGTCAAAAAT
* * * *
18591 GGAATTTTTGGAAGTT-TAGGGGT-AAATGGTAATTTTAAAAAAAAAATCGAGGTT
66 GGAATTTTTGGAAGTTCGA-GGGTAAAATGGTAATTTT-TAGAAAAAATTGAGGTT
** *
18645 -AAAATGGAA-TTTTGGAAAGTTTAAGGGTAAAATTGTAATTTT
1 AAAAATGGAATTTTTGGAAA-TTCGAGGGTAAAATGGTAATTTT
18687 GAAAAGCTTA
Statistics
Matches: 239, Mismatches: 33, Indels: 14
0.84 0.12 0.05
Matches are distributed among these distances:
117 20 0.08
118 167 0.70
119 52 0.22
ACGTcount: A:0.39, C:0.04, G:0.24, T:0.33
Consensus pattern (119 bp):
AAAAATGGAATTTTTGGAAATTCGAGGGTAAAATGGTAATTTTTGGAAAAATCGAGGTCAAAAAT
GGAATTTTTGGAAGTTCGAGGGTAAAATGGTAATTTTTAGAAAAAATTGAGGTT
Found at i:18591 original size:177 final size:177
Alignment explanation
Indices: 18286--18686 Score: 438
Period size: 177 Copynumber: 2.3 Consensus size: 177
18276 GAAAGTTTGG
* * * * * *
18286 GGTCAAAAATAGAATTTTTAGATATCCGAAGGTAAAATGGTAATTTTTGGAACAATCAGGGTCAA
1 GGTCAAAAATGGAATTTTTGGAAATTCGAGGGTAAAATGGTAATTTTTGGAACAATCAGGGTAAA
** * *
18351 AATGAAATTTTTAGAAGTTCGAGGGTAAAATGGTAATTTTTGGAAAAAATTAGGGTTAAAAATGG
66 AATGAAATTTTTAGAAGTTCGAGGGTAAAATGACAATTTTTGGAAAAAATGAGGGTCAAAAATGG
***
18416 AATTTTTGGAAATTCGA-GGGTAAAATGGTAATTTT-TGGAAAAATCGA
131 AATTTTTGGAAATT-GAGGGGT-AAATGGTAATTTTAAAAAAAAATCGA
** * * *
18463 GGTCAAAAATGGAATTTTTGGAAATTCGAGGGTAAAATGGTTTTTTTTTGAGAA-ATTGAGGTTA
1 GGTCAAAAATGGAATTTTTGGAAATTCGAGGGTAAAATGG-TAATTTTTG-GAACAATCAGGGTA
* * * *
18527 AAAATGGAATTTTTGGAAGTTTGGGGGTAAAATGACAATTTTTGG-AAAAATCGA-GGTCAAAAA
64 AAAATGAAATTTTTAGAAGTTCGAGGGTAAAATGACAATTTTTGGAAAAAAT-GAGGGTCAAAAA
* *
18590 TGGAATTTTTGGAAGTTTAGGGGTAAATGGTAATTTTAAAAAAAAAATCGA
128 TGGAATTTTTGGAAATTGAGGGGTAAATGGTAATTTT-AAAAAAAAATCGA
* ** *
18641 GGT-TAAAATGGAA-TTTTGGAAAGTTTAAGGGTAAAATTGTAATTTT
1 GGTCAAAAATGGAATTTTTGGAAA-TTCGAGGGTAAAATGGTAATTTT
18687 GAAAAGCTTA
Statistics
Matches: 187, Mismatches: 30, Indels: 15
0.81 0.13 0.06
Matches are distributed among these distances:
176 28 0.15
177 91 0.49
178 65 0.35
179 3 0.02
ACGTcount: A:0.39, C:0.04, G:0.24, T:0.33
Consensus pattern (177 bp):
GGTCAAAAATGGAATTTTTGGAAATTCGAGGGTAAAATGGTAATTTTTGGAACAATCAGGGTAAA
AATGAAATTTTTAGAAGTTCGAGGGTAAAATGACAATTTTTGGAAAAAATGAGGGTCAAAAATGG
AATTTTTGGAAATTGAGGGGTAAATGGTAATTTTAAAAAAAAATCGA
Found at i:18635 original size:59 final size:60
Alignment explanation
Indices: 18286--18691 Score: 376
Period size: 59 Copynumber: 6.9 Consensus size: 60
18276 GAAAGTTTGG
* * * * * *
18286 GGTCAAAAATAGAATTTTTAG-A-TATCCGAAGGTAAAATGGTAATTTTTGGAACAATC-A
1 GGTCAAAAATGGAATTTTTGGAAGT-TTCGAGGGTAAAATGGTAATTTTTGAAAAAATCGA
* * *
18344 GGGTC-AAAATGAAATTTTTAGAAG-TTCGAGGGTAAAATGGTAATTTTTGGAAAAAAT-TA
1 -GGTCAAAAATGGAATTTTTGGAAGTTTCGAGGGTAAAATGGTAATTTTT-GAAAAAATCGA
* * *
18403 GGGTTAAAAATGGAATTTTTGGAA-ATTCGAGGGTAAAATGGTAATTTTTGGAAAAATCGA
1 -GGTCAAAAATGGAATTTTTGGAAGTTTCGAGGGTAAAATGGTAATTTTTGAAAAAATCGA
* ** * *
18463 GGTCAAAAATGGAATTTTTGGAA-ATTCGAGGGTAAAATGGTTTTTTTTTG-AGAAATTGA
1 GGTCAAAAATGGAATTTTTGGAAGTTTCGAGGGTAAAATGG-TAATTTTTGAAAAAATCGA
* * ** *
18522 GGTTAAAAATGGAATTTTTGGAAGTTT-GGGGGTAAAATGACAATTTTTGGAAAAATCGA
1 GGTCAAAAATGGAATTTTTGGAAGTTTCGAGGGTAAAATGGTAATTTTTGAAAAAATCGA
* **
18581 GGTCAAAAATGGAATTTTTGGAAGTTTAG-GGGT-AAATGGTAATTTTAAAAAAAAAATCGA
1 GGTCAAAAATGGAATTTTTGGAAGTTTCGAGGGTAAAATGGTAATTTT--TGAAAAAATCGA
* * *
18641 GGT-TAAAATGGAA-TTTTGGAAAGTTT-AAGGGTAAAATTGTAA-TTTTGAAAA
1 GGTCAAAAATGGAATTTTTGG-AAGTTTCGAGGGTAAAATGGTAATTTTTGAAAA
18692 GCTTAGGGTC
Statistics
Matches: 295, Mismatches: 36, Indels: 34
0.81 0.10 0.09
Matches are distributed among these distances:
57 4 0.01
58 59 0.20
59 161 0.55
60 71 0.24
ACGTcount: A:0.39, C:0.04, G:0.24, T:0.33
Consensus pattern (60 bp):
GGTCAAAAATGGAATTTTTGGAAGTTTCGAGGGTAAAATGGTAATTTTTGAAAAAATCGA
Found at i:18686 original size:29 final size:27
Alignment explanation
Indices: 18644--18724 Score: 90
Period size: 29 Copynumber: 2.9 Consensus size: 27
18634 AAATCGAGGT
*
18644 TAAAATGGAATTTTGGAAAGTTTAAGGG
1 TAAAATTGAATTTTGGAAAGTTT-AGGG
* *
18672 TAAAATTGTAATTTTGAAAAGCTTAGGG
1 TAAAATTG-AATTTTGGAAAGTTTAGGG
*
18700 TCAAAGATAGAATTTTGGAAAGTTT
1 T-AAA-ATTGAATTTTGGAAAGTTT
18725 GGGGGCTACA
Statistics
Matches: 44, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
28 12 0.27
29 29 0.66
30 3 0.07
ACGTcount: A:0.40, C:0.02, G:0.23, T:0.35
Consensus pattern (27 bp):
TAAAATTGAATTTTGGAAAGTTTAGGG
Found at i:20479 original size:17 final size:18
Alignment explanation
Indices: 20452--20533 Score: 96
Period size: 17 Copynumber: 4.6 Consensus size: 18
20442 CAAATTTAAT
*
20452 TAAATTCAAATTT-AAAA
1 TAAATTTAAATTTAAAAA
*
20469 CAAATTTAAATTTTAAAAAA
1 TAAATTTAAA-TTT-AAAAA
* *
20489 TAAAGTTAAATTT-AAGA
1 TAAATTTAAATTTAAAAA
20506 TAAATTTAAATTTAAAAA
1 TAAATTTAAATTTAAAAA
20524 TAAATTTAAA
1 TAAATTTAAA
20534 ACCATTTTAA
Statistics
Matches: 54, Mismatches: 7, Indels: 7
0.79 0.10 0.10
Matches are distributed among these distances:
17 23 0.43
18 16 0.30
19 3 0.06
20 12 0.22
ACGTcount: A:0.59, C:0.02, G:0.02, T:0.37
Consensus pattern (18 bp):
TAAATTTAAATTTAAAAA
Found at i:20501 original size:37 final size:35
Alignment explanation
Indices: 20459--20533 Score: 105
Period size: 37 Copynumber: 2.1 Consensus size: 35
20449 AATTAAATTC
20459 AAATTTAAAACAAATTTAAATTTTAAAAAATAAAGTT
1 AAATTTAAAACAAATTTAAA-TTT-AAAAATAAAGTT
* * *
20496 AAATTTAAGATAAATTTAAATTTAAAAATAAATTT
1 AAATTTAAAACAAATTTAAATTTAAAAATAAAGTT
20531 AAA
1 AAA
20534 ACCATTTTAA
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
35 14 0.40
36 3 0.09
37 18 0.51
ACGTcount: A:0.60, C:0.01, G:0.03, T:0.36
Consensus pattern (35 bp):
AAATTTAAAACAAATTTAAATTTAAAAATAAAGTT
Found at i:20841 original size:17 final size:18
Alignment explanation
Indices: 20804--20841 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
20794 TATTTGTGAA
*
20804 AATTTTAAAAATTATTAT
1 AATTTTAAAAATAATTAT
*
20822 AATTTT-AAAATAATTTT
1 AATTTTAAAAATAATTAT
20839 AAT
1 AAT
20842 ATATTTTACA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 12 0.67
18 6 0.33
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (18 bp):
AATTTTAAAAATAATTAT
Done.