Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01022859.1 Corchorus olitorius cultivar O-4 contig22892, 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: 26201
ACGTcount: A:0.32, C:0.17, G:0.21, T:0.29
Found at i:1857 original size:41 final size:40
Alignment explanation
Indices: 1799--2020 Score: 134
Period size: 40 Copynumber: 5.5 Consensus size: 40
1789 CCTTTCGACT
*
1799 GGGAAAGGCAAATTGGGAAATGTAAACAACACCTTCCGGTG
1 GGGAAAGGCAAACTGGG-AATGTAAACAACACCTTCCGGTG
* * *
1840 GGGAAAGGCAAACTGGGAATAGCAAACAACAGC-TCCGGGG
1 GGGAAAGGCAAACTGGGAAT-GTAAACAACACCTTCCGGTG
* * *
1880 GGGAAGGGCAAAC-AGGAAT-TAAAACAACACCTTCCGATG
1 GGGAAAGGCAAACTGGGAATGT-AAACAACACCTTCCGGTG
* * ** * * *
1919 AGGAAGGGCAAGAAAAGCAGG-CT-TAAACAACACTTTCCGATG
1 GGGAAAGGC-A-AACTG--GGAATGTAAACAACACCTTCCGGTG
* * *
1961 AGGAAGGGCAAAAC-GAGAAT-TAAAACAACACCTTCCGGTG
1 GGGAAAGGC-AAACTGGGAATGT-AAACAACACCTTCCGGTG
* *
2001 GGGAAGGGCAAGACAGGGAA
1 GGGAAAGGCAA-ACTGGGAA
2021 AAGTAGGTTT
Statistics
Matches: 147, Mismatches: 22, Indels: 24
0.76 0.11 0.12
Matches are distributed among these distances:
38 10 0.07
39 22 0.15
40 49 0.33
41 34 0.23
42 28 0.19
43 2 0.01
44 2 0.01
ACGTcount: A:0.40, C:0.18, G:0.30, T:0.12
Consensus pattern (40 bp):
GGGAAAGGCAAACTGGGAATGTAAACAACACCTTCCGGTG
Found at i:1890 original size:40 final size:41
Alignment explanation
Indices: 1799--1915 Score: 125
Period size: 41 Copynumber: 2.9 Consensus size: 41
1789 CCTTTCGACT
* * *
1799 GGGAAAGGCAAATTGGGAAATGTAAACAACACCTTCCGGTG
1 GGGAAAGGCAAACTGGGAAATGCAAACAACACCTTCCGGGG
*
1840 GGGAAAGGCAAACTGGG-AATAGCAAACAACAGC-TCCGGGG
1 GGGAAAGGCAAACTGGGAAAT-GCAAACAACACCTTCCGGGG
* * **
1880 GGGAAGGGCAAAC-AGG-AATTAAAACAACACCTTCCG
1 GGGAAAGGCAAACTGGGAAATGCAAACAACACCTTCCG
1916 ATGAGGAAGG
Statistics
Matches: 65, Mismatches: 9, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
38 9 0.14
39 9 0.14
40 21 0.32
41 26 0.40
ACGTcount: A:0.38, C:0.20, G:0.30, T:0.12
Consensus pattern (41 bp):
GGGAAAGGCAAACTGGGAAATGCAAACAACACCTTCCGGGG
Found at i:1957 original size:42 final size:42
Alignment explanation
Indices: 1895--2363 Score: 217
Period size: 40 Copynumber: 10.8 Consensus size: 42
1885 GGGCAAACAG
1895 GAATTAAAACAACACCTTCCGATGAGGAAGGGCAAGAAAAGCA
1 GAATTAAAACAACACCTTCCGATGAGGAAGGGCAAGAAAAG-A
** * *
1938 GGCTT-AAACAACACTTTCCGATGAGGAAGGGC-A-AAACGA
1 GAATTAAAACAACACCTTCCGATGAGGAAGGGCAAGAAAAGA
* * *
1977 GAATTAAAACAACACCTTCCGGTGGGGAAGGGCAAGACAGGGAAAA
1 GAATTAAAACAACACCTTCCGATGAGGAAGGGCAAGA-A---AAGA
* * * *** * *
2023 GTAGGTTTAAACGACACCTTTTAATGAGGAAGGGC-A-AAACGG
1 G-A-ATTAAAACAACACCTTCCGATGAGGAAGGGCAAGAAAAGA
* * * **
2065 GAATTAAAACAACACCTTTCGGTG-GAGAAGTGCAAGACAGGGA
1 GAATTAAAACAACACCTTCCGATGAG-GAAGGGCAAGA-AAAGA
* * * *
2108 AAATCAGGCTTAAACAACACCTTCCGATAAGGAAGGGCAA-AACA-A
1 GAAT-----TAAAACAACACCTTCCGATGAGGAAGGGCAAGAAAAGA
* ** * *
2153 GAATTTAAACAACACCTTTTGGTGGGGAAGGGCAAGACAGGGAA-A
1 GAATTAAAACAACACCTTCCGATGAGGAAGGGCAAGA-A---AAGA
* * * *
2198 AACAGGTTTAAACAACACCTTCCGATGAGGAAGGGC-A-AAACGG
1 GA-A--TTAAAACAACACCTTCCGATGAGGAAGGGCAAGAAAAGA
* * * *
2241 GAATTAAAAGAACACCTTCCGGTGGGGAAGGGCAAGACAGGGAAAA
1 GAATTAAAACAACACCTTCCGATGAGGAAGGGCAAGA-A---AAGA
* * *
2287 GCAGGTTTAAACAACACCTTCCGATGAGGAAGGGC-A-AAACGA
1 G-A-ATTAAAACAACACCTTCCGATGAGGAAGGGCAAGAAAAGA
* * *
2329 GAATTAAAACAATACCTTCCGGTGGGGAAGGGCAA
1 GAATTAAAACAACACCTTCCGATGAGGAAGGGCAA
2364 ACTGGGAATA
Statistics
Matches: 315, Mismatches: 74, Indels: 76
0.68 0.16 0.16
Matches are distributed among these distances:
39 5 0.02
40 128 0.41
41 8 0.03
42 37 0.12
43 11 0.03
45 10 0.03
46 10 0.03
47 6 0.02
48 99 0.31
49 1 0.00
ACGTcount: A:0.40, C:0.18, G:0.27, T:0.15
Consensus pattern (42 bp):
GAATTAAAACAACACCTTCCGATGAGGAAGGGCAAGAAAAGA
Found at i:2069 original size:88 final size:88
Alignment explanation
Indices: 1881--2376 Score: 686
Period size: 88 Copynumber: 5.7 Consensus size: 88
1871 GCTCCGGGGG
* *
1881 GGAAGGGC-AAAC-AGGAATTAAAACAACACCTTCCGATGAGGAAGGGC---A-A--GAAAAGCA
1 GGAAGGGCAAAACGA-GAATTAAAACAACACCTTCCGGTGGGGAAGGGCAAGACAGGGAAAAGCA
* *
1938 GGCTTAAACAACACTTTCCGATGA
65 GGTTTAAACAACACCTTCCGATGA
*
1962 GGAAGGGCAAAACGAGAATTAAAACAACACCTTCCGGTGGGGAAGGGCAAGACAGGGAAAAGTAG
1 GGAAGGGCAAAACGAGAATTAAAACAACACCTTCCGGTGGGGAAGGGCAAGACAGGGAAAAGCAG
* ***
2027 GTTTAAACGACACCTTTTAATGA
66 GTTTAAACAACACCTTCCGATGA
* * * * *
2050 GGAAGGGCAAAACGGGAATTAAAACAACACCTTTCGGTGGAGAAGTGCAAGACAGGGAAAATCAG
1 GGAAGGGCAAAACGAGAATTAAAACAACACCTTCCGGTGGGGAAGGGCAAGACAGGGAAAAGCAG
* *
2115 GCTTAAACAACACCTTCCGATAA
66 GTTTAAACAACACCTTCCGATGA
* * ** *
2138 GGAAGGGCAAAACAAGAATTTAAACAACACCTTTTGGTGGGGAAGGGCAAGACAGGGAAAAACAG
1 GGAAGGGCAAAACGAGAATTAAAACAACACCTTCCGGTGGGGAAGGGCAAGACAGGGAAAAGCAG
2203 GTTTAAACAACACCTTCCGATGA
66 GTTTAAACAACACCTTCCGATGA
* *
2226 GGAAGGGCAAAACGGGAATTAAAAGAACACCTTCCGGTGGGGAAGGGCAAGACAGGGAAAAGCAG
1 GGAAGGGCAAAACGAGAATTAAAACAACACCTTCCGGTGGGGAAGGGCAAGACAGGGAAAAGCAG
2291 GTTTAAACAACACCTTCCGATGA
66 GTTTAAACAACACCTTCCGATGA
* * *
2314 GGAAGGGCAAAACGAGAATTAAAACAATACCTTCCGGTGGGGAAGGGCAA-ACTGGGAATAGCA
1 GGAAGGGCAAAACGAGAATTAAAACAACACCTTCCGGTGGGGAAGGGCAAGACAGGGAAAAGCA
2377 AACATTGGGA
Statistics
Matches: 365, Mismatches: 42, Indels: 10
0.88 0.10 0.02
Matches are distributed among these distances:
81 8 0.02
82 35 0.10
83 1 0.00
85 1 0.00
86 1 0.00
87 11 0.03
88 308 0.84
ACGTcount: A:0.40, C:0.18, G:0.28, T:0.14
Consensus pattern (88 bp):
GGAAGGGCAAAACGAGAATTAAAACAACACCTTCCGGTGGGGAAGGGCAAGACAGGGAAAAGCAG
GTTTAAACAACACCTTCCGATGA
Found at i:2230 original size:48 final size:48
Alignment explanation
Indices: 2156--2323 Score: 190
Period size: 48 Copynumber: 3.7 Consensus size: 48
2146 AAAACAAGAA
** * *
2156 TTTAAACAACACCTTTTGGTGGGGAAGGGCAAGACAGGGAAAAACAGG
1 TTTAAACAACACCTTCCGATGAGGAAGGGCAAGACAGGGAAAAACAGG
*
2204 TTTAAACAACACCTTCCGATGAGGAAGGGCAAAAC-GGG----A-A--
1 TTTAAACAACACCTTCCGATGAGGAAGGGCAAGACAGGGAAAAACAGG
* * * * *
2244 TTAAAAGAACACCTTCCGGTGGGGAAGGGCAAGACAGGGAAAAGCAGG
1 TTTAAACAACACCTTCCGATGAGGAAGGGCAAGACAGGGAAAAACAGG
2292 TTTAAACAACACCTTCCGATGAGGAAGGGCAA
1 TTTAAACAACACCTTCCGATGAGGAAGGGCAA
2324 AACGAGAATT
Statistics
Matches: 97, Mismatches: 15, Indels: 16
0.76 0.12 0.12
Matches are distributed among these distances:
40 30 0.31
41 3 0.03
42 1 0.01
43 1 0.01
46 1 0.01
47 3 0.03
48 58 0.60
ACGTcount: A:0.38, C:0.18, G:0.29, T:0.15
Consensus pattern (48 bp):
TTTAAACAACACCTTCCGATGAGGAAGGGCAAGACAGGGAAAAACAGG
Found at i:11265 original size:19 final size:19
Alignment explanation
Indices: 11243--11280 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
11233 GATTAAGCTG
11243 GCCCATTACACTCAAGCCC
1 GCCCATTACACTCAAGCCC
* *
11262 GCCCATTGCACTTAAGCCC
1 GCCCATTACACTCAAGCCC
11281 ACAAGGAGGT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.24, C:0.45, G:0.13, T:0.18
Consensus pattern (19 bp):
GCCCATTACACTCAAGCCC
Found at i:14284 original size:44 final size:44
Alignment explanation
Indices: 14181--14609 Score: 282
Period size: 52 Copynumber: 9.3 Consensus size: 44
14171 TGGTAATAGA
* * *
14181 AAATTGAGAAATTAAAAAGGAATTTTGTATTTATAGAGAGTAAAAGT
1 AAATTG-GTAATTAAAAAGGAATTTGGTAATTA-A-AGAGTAAAAGT
* * *
14228 AAACTGGCAATTAAAAAGGAATTTGGTACTTAAAGAGTAAAAGT
1 AAATTGGTAATTAAAAAGGAATTTGGTAATTAAAGAGTAAAAGT
*
14272 AAATTGGTAATTAAAAAGGAATTTGGTAATTAAAAAAAAGTAAAAGT
1 AAATTGGTAATTAAAAAGGAATTTGGTAATT---AAAGAGTAAAAGT
* *
14319 AAATTGGTAATTAAGAA-GAATTTGGTAATTAAAGAGTAAAAGG
1 AAATTGGTAATTAAAAAGGAATTTGGTAATTAAAGAGTAAAAGT
* * **
14362 AAATTGGTAATTAAAAA-GAATTTGGTAAGTAAAAAG-AATTTGGT
1 AAATTGGTAATTAAAAAGGAATTTGGTAATTAAAGAGTAA--AAGT
** * * **
14406 AAA-T-AAAGAGT-AAAAGGAAATTGGTTAATT-TGGTAAGTAAAAAG-
1 AAATTGGTA-ATTAAAAAGGAATTTGG-TAATTAAAG--AGT-AAAAGT
* * * * *
14450 AATTTGATAATTAAAAA-GAATTTGGTAAATAAAGAGTACAAGG
1 AAATTGGTAATTAAAAAGGAATTTGGTAATTAAAGAGTAAAAGT
*
14493 AAATTGGTTAATTTGGTAAGTAAAAAGAATTTGGTAATTAAAGAGTAAAAGT
1 AAATTGG-TAA--T--T-A--AAAAGGAATTTGGTAATTAAAGAGTAAAAGT
* *
14545 AAATTGGTTAATTTTGTAATTAAAAAGAATTTGGTAATTAAAGAGTAAAAGC
1 AAATTGG-TAA---T-T-A--AAAAGGAATTTGGTAATTAAAGAGTAAAAGT
14597 AAATTGGTTAATT
1 AAATTGG-TAATT
14610 TGGTAATTAA
Statistics
Matches: 313, Mismatches: 42, Indels: 53
0.77 0.10 0.13
Matches are distributed among these distances:
42 11 0.04
43 62 0.20
44 56 0.18
45 15 0.05
46 43 0.14
47 35 0.11
48 2 0.01
49 2 0.01
51 4 0.01
52 80 0.26
53 3 0.01
ACGTcount: A:0.49, C:0.01, G:0.20, T:0.30
Consensus pattern (44 bp):
AAATTGGTAATTAAAAAGGAATTTGGTAATTAAAGAGTAAAAGT
Found at i:14343 original size:90 final size:91
Alignment explanation
Indices: 14181--14396 Score: 294
Period size: 90 Copynumber: 2.4 Consensus size: 91
14171 TGGTAATAGA
* * * * * *
14181 AAATTGAGAAATTAAAAAGGAATTTTGT-ATTTATAGAGAGTAAAAGTAAACTGGCAATTAAAAA
1 AAATTG-GTAATTAAAAAGGAATTTGGTAATTAAAAAAAAGTAAAAGTAAACTGGCAATTAAAAA
* *
14245 GGAATTTGGTACTTAAAGAGTAAAAGT
65 GGAATTTGGTAATTAAAGAGTAAAAGG
* * *
14272 AAATTGGTAATTAAAAAGGAATTTGGTAATTAAAAAAAAGTAAAAGTAAATTGGTAATTAAGAA-
1 AAATTGGTAATTAAAAAGGAATTTGGTAATTAAAAAAAAGTAAAAGTAAACTGGCAATTAAAAAG
14336 GAATTTGGTAATTAAAGAGTAAAAGG
66 GAATTTGGTAATTAAAGAGTAAAAGG
*
14362 AAATTGGTAATTAAAAA-GAATTTGGTAAGTAAAAA
1 AAATTGGTAATTAAAAAGGAATTTGGTAATTAAAAA
14397 GAATTTGGTA
Statistics
Matches: 112, Mismatches: 12, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
89 17 0.15
90 60 0.54
91 35 0.31
ACGTcount: A:0.51, C:0.01, G:0.19, T:0.28
Consensus pattern (91 bp):
AAATTGGTAATTAAAAAGGAATTTGGTAATTAAAAAAAAGTAAAAGTAAACTGGCAATTAAAAAG
GAATTTGGTAATTAAAGAGTAAAAGG
Found at i:14345 original size:18 final size:18
Alignment explanation
Indices: 14322--14482 Score: 94
Period size: 18 Copynumber: 8.7 Consensus size: 18
14312 TAAAAGTAAA
*
14322 TTGGTAATTAAGAAGAAT
1 TTGGTAATTAAAAAGAAT
*
14340 TTGGTAATTAAAGAGTAAAAGGAAA
1 TTGGTAATT----A--AAAA-GAAT
14365 TTGGTAATTAAAAAGAAT
1 TTGGTAATTAAAAAGAAT
*
14383 TTGGTAAGTAAAAAGAAT
1 TTGGTAATTAAAAAGAAT
* *
14401 TTGGTAAATAAAGAGTAA-
1 TTGGTAATTAAAAAG-AAT
** * ****
14419 AAGGAAATT--GGTTAAT
1 TTGGTAATTAAAAAGAAT
*
14435 TTGGTAAGTAAAAAGAAT
1 TTGGTAATTAAAAAGAAT
*
14453 TTGATAATTAAAAAGAAT
1 TTGGTAATTAAAAAGAAT
*
14471 TTGGTAAATAAA
1 TTGGTAATTAAA
14483 GAGTACAAGG
Statistics
Matches: 107, Mismatches: 25, Indels: 22
0.69 0.16 0.14
Matches are distributed among these distances:
15 2 0.02
16 6 0.06
18 76 0.71
19 6 0.06
21 1 0.01
22 1 0.01
24 3 0.03
25 12 0.11
ACGTcount: A:0.50, C:0.00, G:0.20, T:0.30
Consensus pattern (18 bp):
TTGGTAATTAAAAAGAAT
Found at i:14389 original size:61 final size:62
Alignment explanation
Indices: 14313--14505 Score: 244
Period size: 70 Copynumber: 3.0 Consensus size: 62
14303 AAAAAAAAGT
* * *
14313 AAAAGTAAATTGGTAATTAAGAAGAATTTGGTAATTAAAGAGTAAAAGGAAATTGG-TAATTA
1 AAAAG-AATTTGGTAATTAAAAAGAATTTGGTAAATAAAGAGTAAAAGGAAATTGGTTAATTA
*
14375 AAAAGAATTTGGTAAGTAAAAAGAATTTGGTAAATAAAGAGTAAAAGGAAATTGGTTAATTTGGT
1 AAAAGAATTTGGTAATTAAAAAGAATTTGGTAAATAAAGAGTAAAAGGAAATTGGTTAA-----T
14440 AAGTA
61 ---TA
* *
14445 AAAAGAATTTGATAATTAAAAAGAATTTGGTAAATAAAGAGTACAAGGAAATTGGTTAATT
1 AAAAGAATTTGGTAATTAAAAAGAATTTGGTAAATAAAGAGTAAAAGGAAATTGGTTAATT
14506 TGGTAAGTAA
Statistics
Matches: 115, Mismatches: 7, Indels: 18
0.82 0.05 0.13
Matches are distributed among these distances:
61 46 0.40
62 9 0.08
65 1 0.01
67 1 0.01
70 58 0.50
ACGTcount: A:0.50, C:0.01, G:0.21, T:0.29
Consensus pattern (62 bp):
AAAAGAATTTGGTAATTAAAAAGAATTTGGTAAATAAAGAGTAAAAGGAAATTGGTTAATTA
Found at i:14436 original size:34 final size:34
Alignment explanation
Indices: 14398--14516 Score: 105
Period size: 34 Copynumber: 3.4 Consensus size: 34
14388 AAGTAAAAAG
14398 AATTTGGTAAATAAAGAGTAAAAGGAAATTGGTT
1 AATTTGGTAAATAAAGAGTAAAAGGAAATTGGTT
* * *** ****
14432 AATTTGGTAAGTAAAAAG-AATTTGATAATTAAAAAG
1 AATTTGGTAAATAAAGAGTAAAAGGA-AATT--GGTT
*
14468 AATTTGGTAAATAAAGAGTACAAGGAAATTGGTT
1 AATTTGGTAAATAAAGAGTAAAAGGAAATTGGTT
*
14502 AATTTGGTAAGTAAA
1 AATTTGGTAAATAAA
14517 AAGAATTTGG
Statistics
Matches: 61, Mismatches: 20, Indels: 8
0.69 0.22 0.09
Matches are distributed among these distances:
33 4 0.07
34 34 0.56
36 20 0.33
37 3 0.05
ACGTcount: A:0.48, C:0.01, G:0.21, T:0.30
Consensus pattern (34 bp):
AATTTGGTAAATAAAGAGTAAAAGGAAATTGGTT
Found at i:14447 original size:70 final size:70
Alignment explanation
Indices: 14365--14534 Score: 304
Period size: 70 Copynumber: 2.4 Consensus size: 70
14355 TAAAAGGAAA
* *
14365 TTGGTAATTAAAAAGAATTTGGTAAGTAAAAAGAATTTGGTAAATAAAGAGTAAAAGGAAATTGG
1 TTGGTAAGTAAAAAGAATTTGGTAATTAAAAAGAATTTGGTAAATAAAGAGTAAAAGGAAATTGG
14430 TTAAT
66 TTAAT
* *
14435 TTGGTAAGTAAAAAGAATTTGATAATTAAAAAGAATTTGGTAAATAAAGAGTACAAGGAAATTGG
1 TTGGTAAGTAAAAAGAATTTGGTAATTAAAAAGAATTTGGTAAATAAAGAGTAAAAGGAAATTGG
14500 TTAAT
66 TTAAT
14505 TTGGTAAGTAAAAAGAATTTGGTAATTAAA
1 TTGGTAAGTAAAAAGAATTTGGTAATTAAA
14535 GAGTAAAAGT
Statistics
Matches: 95, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
70 95 1.00
ACGTcount: A:0.48, C:0.01, G:0.21, T:0.31
Consensus pattern (70 bp):
TTGGTAAGTAAAAAGAATTTGGTAATTAAAAAGAATTTGGTAAATAAAGAGTAAAAGGAAATTGG
TTAAT
Found at i:14506 original size:104 final size:106
Alignment explanation
Indices: 14398--14655 Score: 241
Period size: 104 Copynumber: 2.4 Consensus size: 106
14388 AAGTAAAAAG
* *
14398 AATTTGGTAAATAAAGAGTAAAAGGAAATTGGTTAATT-TG-GT-AAGTAAA-AAG-AA-TTTGA
1 AATTTGGT-AATAAA-AGTAAAAAGAAATTGG-TAATTAAGAGTAAAGTAAATAAGTAATTTTG-
* *
14457 TAATTAAAAAGAATTTGGTAAATAAAGAGTACAAGGAAATTGGTT
62 TAATTAAAAAGAATTTGGTAAATAAAGAGTAAAAGCAAATTGGTT
* **
14502 AATTTGG---T--AAGTAAAAAGAATTTGGTAATTAAAGAGTAAAAGTAAATTGGTTAATTTTGT
1 AATTTGGTAATAAAAGTAAAAAGAAATTGGTAATT-AAGAGT-AAAGTAAATAAG-TAATTTTGT
*
14562 AATTAAAAAGAATTTGGTAATTAAAGAGTAAAAGCAAATTGGTT
63 AATTAAAAAGAATTTGGTAAATAAAGAGTAAAAGCAAATTGGTT
*
14606 AATTTGGTAATTAAGAAAGTAAAATGAAATTGGGATAATTAAAGAGTAAA
1 AATTTGGTAA-T-A-AAAGTAAAAAGAAATT-GG-TAATT-AAGAGTAAA
14656 ATGAATTGGA
Statistics
Matches: 125, Mismatches: 10, Indels: 29
0.76 0.06 0.18
Matches are distributed among these distances:
96 5 0.04
97 14 0.11
98 2 0.02
99 2 0.02
100 1 0.01
101 7 0.06
102 1 0.01
104 58 0.46
105 4 0.03
108 1 0.01
112 13 0.10
113 5 0.04
114 12 0.10
ACGTcount: A:0.48, C:0.01, G:0.20, T:0.31
Consensus pattern (106 bp):
AATTTGGTAATAAAAGTAAAAAGAAATTGGTAATTAAGAGTAAAGTAAATAAGTAATTTTGTAAT
TAAAAAGAATTTGGTAAATAAAGAGTAAAAGCAAATTGGTT
Found at i:14601 original size:26 final size:25
Alignment explanation
Indices: 14463--14609 Score: 88
Period size: 25 Copynumber: 5.7 Consensus size: 25
14453 TTGATAATTA
* *
14463 AAAAGAATTTGG-TAAATAAAGAGT
1 AAAAGAAATTGGTTAATTAAAGAGT
* **
14487 ACAAGGAAATTGGTTAATT-TGGTAAGT
1 A-AAAGAAATTGGTTAATTAAAG--AGT
*
14514 AAAAAGAATTTGG-TAATTAAAGAGT
1 -AAAAGAAATTGGTTAATTAAAGAGT
** *
14539 AAAAGTAAATTGGTTAATT-TTGTAATT
1 AAAAG-AAATTGGTTAATTAAAG--AGT
*
14566 AAAAAGAATTTGG-TAATTAAAGAGT
1 -AAAAGAAATTGGTTAATTAAAGAGT
14591 AAAAGCAAATTGGTTAATT
1 AAAAG-AAATTGGTTAATT
14610 TGGTAATTAA
Statistics
Matches: 91, Mismatches: 18, Indels: 26
0.67 0.13 0.19
Matches are distributed among these distances:
24 11 0.12
25 28 0.31
26 24 0.26
27 22 0.24
28 6 0.07
ACGTcount: A:0.47, C:0.01, G:0.20, T:0.32
Consensus pattern (25 bp):
AAAAGAAATTGGTTAATTAAAGAGT
Found at i:14615 original size:34 final size:35
Alignment explanation
Indices: 14572--14638 Score: 102
Period size: 35 Copynumber: 1.9 Consensus size: 35
14562 AATTAAAAAG
*
14572 AATTTGGTAATTAA-AGAGTAAAA-GCAAATTGGTT
1 AATTTGGTAATTAAGAAAGTAAAATG-AAATTGGTT
14606 AATTTGGTAATTAAGAAAGTAAAATGAAATTGG
1 AATTTGGTAATTAAGAAAGTAAAATGAAATTGG
14639 GATAATTAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
34 14 0.47
35 15 0.50
36 1 0.03
ACGTcount: A:0.46, C:0.01, G:0.21, T:0.31
Consensus pattern (35 bp):
AATTTGGTAATTAAGAAAGTAAAATGAAATTGGTT
Found at i:14656 original size:87 final size:85
Alignment explanation
Indices: 14565--14819 Score: 289
Period size: 87 Copynumber: 3.0 Consensus size: 85
14555 ATTTTGTAAT
*
14565 TAAAAAGAATTTGGTAATTAAAGAGTAAAAGCAAATTGGTTAATTTGGTAATTAAGAAAGTAAAA
1 TAAAAAGAATTTGGTAATTAAAGAGTAAAAG-AAATTGGTAAATTTGGTAATTAAGAAAGTAAAA
14630 TGAAATTGGGATAATTAAAGAG
65 TGAAATTGGG-TAATTAAAGAG
*
14652 TAAAATGAA-TTGGATAATTAAAGAGT------AATTGGTAAAATTTGGTAATTAAGAAA-TAAA
1 TAAAAAGAATTTGG-TAATTAAAGAGTAAAAGAAATTGGT-AAATTTGGTAATTAAGAAAGTAAA
*
14709 ATGAACTT-GGTAATTAAAGAG
64 ATGAAATTGGGTAATTAAAGAG
* * * * *
14730 TAAAGTAA-AATTTGGCAATCAAAAAGTAAAAAGGAAATTGGTCAACTTGGTAATTAA-AAAGTA
1 TAAA--AAGAATTTGGTAATTAAAGAGT-AAAA-GAAATTGGTAAATTTGGTAATTAAGAAAGTA
14793 AAATGAAATTGGGTAATTAAAGAG
62 AAATGAAATTGGGTAATTAAAGAG
14817 TAA
1 TAA
14820 TTGGTAAAAT
Statistics
Matches: 143, Mismatches: 10, Indels: 30
0.78 0.05 0.16
Matches are distributed among these distances:
78 15 0.10
79 13 0.09
80 23 0.16
81 18 0.13
85 3 0.02
86 28 0.20
87 43 0.30
ACGTcount: A:0.50, C:0.02, G:0.20, T:0.28
Consensus pattern (85 bp):
TAAAAAGAATTTGGTAATTAAAGAGTAAAAGAAATTGGTAAATTTGGTAATTAAGAAAGTAAAAT
GAAATTGGGTAATTAAAGAG
Found at i:14666 original size:25 final size:26
Alignment explanation
Indices: 14609--14876 Score: 117
Period size: 26 Copynumber: 9.8 Consensus size: 26
14599 ATTGGTTAAT
*
14609 TTGG-TAATTAAGAAAGTAAAATGAAA
1 TTGGATAATTAA-AGAGTAAAATGAAA
14635 TTGGGATAATTAAAGAGTAAAATG-AA
1 TT-GGATAATTAAAGAGTAAAATGAAA
*
14661 TTGGATAATTAAAGAGT-AATTGGTAAAA
1 TTGGATAATTAAAGAGTAAAAT-G--AAA
* *
14689 TTTGG-TAATT-AAGAAATAAAATGAAC
1 -TTGGATAATTAAAG-AGTAAAATGAAA
* *
14715 TTGG-TAATTAAAGAGTAAAGTAAAA
1 TTGGATAATTAAAGAGTAAAATGAAA
* * * *
14740 TTTGG-CAATCAAAAAGTAAAAAGGAAA
1 -TTGGATAATTAAAGAGT-AAAATGAAA
*
14767 TTGGTCAACTTGGTAATTAAAAAGTAAAATGAAA
1 TTGG---A-----TAATTAAAGAGTAAAATGAAA
* *
14801 TTGGGTAATTAAAGAGT-AATTGGTAAAA
1 TTGGATAATTAAAGAGTAAAAT-G--AAA
*
14829 TTGGATAATT-AAGAAGTAAGA-GAAAA
1 TTGGATAATTAAAG-AGTAAAATG-AAA
*
14855 TTTGG-TAATTAAAGGGTAAAAT
1 -TTGGATAATTAAAGAGTAAAAT
14877 CTGGTAATGA
Statistics
Matches: 187, Mismatches: 26, Indels: 57
0.69 0.10 0.21
Matches are distributed among these distances:
24 3 0.02
25 36 0.19
26 54 0.29
27 32 0.17
28 32 0.17
29 8 0.04
34 12 0.06
35 10 0.05
ACGTcount: A:0.49, C:0.02, G:0.21, T:0.28
Consensus pattern (26 bp):
TTGGATAATTAAAGAGTAAAATGAAA
Found at i:14698 original size:53 final size:51
Alignment explanation
Indices: 14609--14876 Score: 159
Period size: 53 Copynumber: 4.9 Consensus size: 51
14599 ATTGGTTAAT
* * * *
14609 TTGGTAATTAAGAAAGTAAAATGAAATTGGGATAATTAAAGAGTAAAATGAA-
1 TTGGTAATTAA-AGAGTAAAGTAAAATTTGG-TAATTAAAGAGTAAAATGAAC
* *
14661 TTGGATAATTAAAGAGTAATTGGTAAAATTTGGTAATT-AAGAAATAAAATGAAC
1 TTGG-TAATTAAAGAGTAA--AGTAAAATTTGGTAATTAAAG-AGTAAAATGAAC
* * *
14715 TTGGTAATTAAAGAGTAAAGTAAAATTTGGCAATCAAAAAGTAAAAAGGAAATTGGTCAAC
1 TTGGTAATTAAAGAGTAAAGTAAAATTTGGTAATTAAAGAGT----A--AAA-T-G--AAC
* * * * * *
14776 TTGGTAATTAAAAAGTAAAATGAAATTGGGTAATTAAAGAGT-AATTGGTAAAA
1 TTGGTAATTAAAGAGTAAAGTAAAATTTGGTAATTAAAGAGTAAAAT-G--AAC
*
14829 TTGGATAATT-AAGAAGTAAGAG-AAAATTTGGTAATTAAAGGGTAAAAT
1 TTGG-TAATTAAAG-AGTAA-AGTAAAATTTGGTAATTAAAGAGTAAAAT
14877 CTGGTAATGA
Statistics
Matches: 169, Mismatches: 27, Indels: 37
0.73 0.12 0.16
Matches are distributed among these distances:
51 16 0.09
52 15 0.09
53 48 0.28
54 42 0.25
55 5 0.03
57 3 0.02
58 1 0.01
59 1 0.01
61 38 0.22
ACGTcount: A:0.49, C:0.02, G:0.21, T:0.28
Consensus pattern (51 bp):
TTGGTAATTAAAGAGTAAAGTAAAATTTGGTAATTAAAGAGTAAAATGAAC
Found at i:14846 original size:54 final size:53
Alignment explanation
Indices: 14765--14873 Score: 139
Period size: 54 Copynumber: 2.0 Consensus size: 53
14755 GTAAAAAGGA
* *
14765 AATTGGTCAACTTGGTAATTAAAAAGTAAAATG-AAATTGGGTAATTAAAGAGT
1 AATTGGTAAAATTGGTAATTAAAAAGTAAAA-GAAAATTGGGTAATTAAAGAGT
* * * *
14818 AATTGGTAAAATTGGATAATTAAGAAGTAAGAGAAAATTTGGTAATTAAAGGGT
1 AATTGGTAAAATTGG-TAATTAAAAAGTAAAAGAAAATTGGGTAATTAAAGAGT
14872 AA
1 AA
14874 AATCTGGTAA
Statistics
Matches: 48, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
53 14 0.29
54 34 0.71
ACGTcount: A:0.47, C:0.02, G:0.22, T:0.29
Consensus pattern (53 bp):
AATTGGTAAAATTGGTAATTAAAAAGTAAAAGAAAATTGGGTAATTAAAGAGT
Found at i:26031 original size:27 final size:27
Alignment explanation
Indices: 25918--26025 Score: 198
Period size: 27 Copynumber: 4.0 Consensus size: 27
25908 GCACTTAGGT
*
25918 CATTTAGGGGCATTTTGGTCATTTTTA
1 CATTCAGGGGCATTTTGGTCATTTTTA
*
25945 CATTCAGGGGCATTTTGGTCATTTTAA
1 CATTCAGGGGCATTTTGGTCATTTTTA
25972 CATTCAGGGGCATTTTGGTCATTTTTA
1 CATTCAGGGGCATTTTGGTCATTTTTA
25999 CATTCAGGGGCATTTTGGTCATTTTTA
1 CATTCAGGGGCATTTTGGTCATTTTTA
26026 AGTTCACATT
Statistics
Matches: 78, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 78 1.00
ACGTcount: A:0.19, C:0.14, G:0.22, T:0.44
Consensus pattern (27 bp):
CATTCAGGGGCATTTTGGTCATTTTTA
Done.