Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2299
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: 40260
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.32
Found at i:160 original size:32 final size:28
Alignment explanation
Indices: 124--202 Score: 77
Period size: 32 Copynumber: 2.5 Consensus size: 28
114 GACATATGAA
124 AATATATTAAGATATTATTTAAATATAATCAT
1 AATATATTAA-ATATTATTT-AATATAA--AT
156 AATATATTAAATCAATATTATTTAATATAAAT
1 AATATATT--A--AATATTATTTAATATAAAT
188 AATCATATTAAATAT
1 AAT-ATATTAAATAT
203 CAAAATATTA
Statistics
Matches: 42, Mismatches: 0, Indels: 13
0.76 0.00 0.24
Matches are distributed among these distances:
29 5 0.12
31 1 0.02
32 13 0.31
33 5 0.12
34 8 0.19
35 9 0.21
36 1 0.02
ACGTcount: A:0.52, C:0.04, G:0.01, T:0.43
Consensus pattern (28 bp):
AATATATTAAATATTATTTAATATAAAT
Found at i:179 original size:35 final size:33
Alignment explanation
Indices: 135--200 Score: 98
Period size: 33 Copynumber: 1.9 Consensus size: 33
125 ATATATTAAG
135 ATATTATTTAAATATAATCATAAT-ATATTAAATCA
1 ATATTATTT-AATATAA--ATAATCATATTAAATCA
170 ATATTATTTAATATAAATAATCATATTAAAT
1 ATATTATTTAATATAAATAATCATATTAAAT
201 ATCAAAATAT
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
32 5 0.17
33 9 0.30
34 7 0.23
35 9 0.30
ACGTcount: A:0.52, C:0.05, G:0.00, T:0.44
Consensus pattern (33 bp):
ATATTATTTAATATAAATAATCATATTAAATCA
Found at i:201 original size:19 final size:19
Alignment explanation
Indices: 148--202 Score: 51
Period size: 19 Copynumber: 2.9 Consensus size: 19
138 TTATTTAAAT
* *
148 ATAATCATAATATAT-TAA
1 ATAATCATATTAAATATAA
*
166 ATCAAT-ATTATTTAATATAA
1 AT-AATCA-TATTAAATATAA
186 ATAATCATATTAAATAT
1 ATAATCATATTAAATAT
203 CAAAATATTA
Statistics
Matches: 29, Mismatches: 4, Indels: 7
0.73 0.10 0.17
Matches are distributed among these distances:
18 3 0.10
19 20 0.69
20 6 0.21
ACGTcount: A:0.53, C:0.05, G:0.00, T:0.42
Consensus pattern (19 bp):
ATAATCATATTAAATATAA
Found at i:205 original size:35 final size:35
Alignment explanation
Indices: 135--215 Score: 96
Period size: 35 Copynumber: 2.3 Consensus size: 35
125 ATATATTAAG
135 ATATTATTTAAATATAATCATAATATATTAAATC-A
1 ATATTATTTAAATATAA-CATAATATATTAAATCAA
170 ATATTATTT-AATATAA-ATAATCATATTAAATATCAAA
1 ATATTATTTAAATATAACATAAT-ATATT-AA-ATC-AA
207 ATATTATTT
1 ATATTATTT
216 TTTTTATGTA
Statistics
Matches: 41, Mismatches: 0, Indels: 8
0.84 0.00 0.16
Matches are distributed among these distances:
32 5 0.12
33 5 0.12
34 9 0.22
35 12 0.29
37 10 0.24
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.44
Consensus pattern (35 bp):
ATATTATTTAAATATAACATAATATATTAAATCAA
Found at i:17842 original size:51 final size:51
Alignment explanation
Indices: 17782--17914 Score: 212
Period size: 51 Copynumber: 2.6 Consensus size: 51
17772 ATTTGCCTAC
* * *
17782 ATGTATCGATATATTGAATAATGTATCGATACATCTGGGTAAAAATCTAGA
1 ATGTATCGATACAATGAATAATGTATCGATACATCTGGGTAAAAACCTAGA
* *
17833 ATGTATCGATACAATGAAAAATGTATCGATACATCTGGGTAAAAACCTAGT
1 ATGTATCGATACAATGAATAATGTATCGATACATCTGGGTAAAAACCTAGA
*
17884 ATGTATCGATACAATGAATATTGTATCGATA
1 ATGTATCGATACAATGAATAATGTATCGATA
17915 TAATCAATCA
Statistics
Matches: 75, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
51 75 1.00
ACGTcount: A:0.40, C:0.11, G:0.17, T:0.32
Consensus pattern (51 bp):
ATGTATCGATACAATGAATAATGTATCGATACATCTGGGTAAAAACCTAGA
Found at i:18901 original size:32 final size:31
Alignment explanation
Indices: 18863--19279 Score: 433
Period size: 32 Copynumber: 13.0 Consensus size: 31
18853 TAGAAAGAGA
18863 TGCCACCAACTTGTGTGGGCTTTTAAAAGGGT
1 TGCCACCAACTTGTGTGGGC-TTTAAAAGGGT
* * * **
18895 TGCCACCGACATGGGTAAGCTTTAAGAAGGGT
1 TGCCACCAACTTGTGTGGGCTTTAA-AAGGGT
* * *
18927 TGCCACCAACTTGTGTGAGTTTTGAAAAAGGT
1 TGCCACCAACTTGTGTGGGCTTT-AAAAGGGT
* * *
18959 TGCCATCGACTTGTGTGGGCCTTTAAAAAAGGT
1 TGCCACCAACTTGTGTGGG-CTTT-AAAAGGGT
** *
18992 CACCACCAACTTATGTGGGCTTTAGAAAGGGT
1 TGCCACCAACTTGTGTGGGCTTTA-AAAGGGT
*
19024 CGCCACCAACTTGTGTGGGCTTTAGAAAGGGT
1 TGCCACCAACTTGTGTGGGCTTTA-AAAGGGT
** *
19056 CACCACCAACTTGTGTGGGCTTTAGAAATGGT
1 TGCCACCAACTTGTGTGGGCTTTA-AAAGGGT
* * **
19088 TACCACCGACTTGTGTGGGCATTGGAAAGGGT
1 TGCCACCAACTTGTGTGGGC-TTTAAAAGGGT
* *
19120 CGCCACCAACTTATGTGGGCTTTGAAGAA-GGT
1 TGCCACCAACTTGTGTGGGCTTT-AA-AAGGGT
*
19152 TGCCACCGACTTGTGTGGGCTTTAGAAAGGGT
1 TGCCACCAACTTGTGTGGGCTTTA-AAAGGGT
19184 TGCCACCAACTTGTGTGGGCTTTGAAGAA-GGT
1 TGCCACCAACTTGTGTGGGCTTT-AA-AAGGGT
* *
19216 TGCCATCGACTTGTGTGGGCTTTAGAAAGGGT
1 TGCCACCAACTTGTGTGGGCTTTA-AAAGGGT
19248 TGCCACCAACTTGTGTGGGCTTTAAGAAGGGT
1 TGCCACCAACTTGTGTGGGCTTTAA-AAGGGT
19280 AAAGGTGCCA
Statistics
Matches: 326, Mismatches: 45, Indels: 28
0.82 0.11 0.07
Matches are distributed among these distances:
31 15 0.05
32 277 0.85
33 34 0.10
ACGTcount: A:0.24, C:0.19, G:0.30, T:0.28
Consensus pattern (31 bp):
TGCCACCAACTTGTGTGGGCTTTAAAAGGGT
Found at i:18942 original size:64 final size:64
Alignment explanation
Indices: 18847--19279 Score: 495
Period size: 64 Copynumber: 6.8 Consensus size: 64
18837 CCAATGACAT
* * * *
18847 TGGGC-TTAGAAAGAGATGCCACCAACTTGTGTGGGCTTTTAAAAGGGTTGCCACCGACATGGG
1 TGGGCTTTAGAAAGGGTTGCCACCAACTTGTGTGGGCTTTTAAAAGGGTTGCCACCGACTTGTG
** * * *
18910 TAAGCTTTA-AGAAGGGTTGCCACCAACTTGTGTGAG-TTTTGAAAAAGGTTGCCATCGACTTGT
1 TGGGCTTTAGA-AAGGGTTGCCACCAACTTGTGTGGGCTTTT-AAAAGGGTTGCCACCGACTTGT
18973 G
64 G
* * ** * * *
18974 TGGGCCTTTAAAAAAGGTCACCACCAACTTATGTGGGC-TTTAGAAAGGGTCGCCACCAACTTGT
1 TGGG-CTTTAGAAAGGGTTGCCACCAACTTGTGTGGGCTTTTA-AAAGGGTTGCCACCGACTTGT
19038 G
64 G
** * *
19039 TGGGCTTTAGAAAGGGTCACCACCAACTTGTGTGGGC-TTTAGAAATGGTTACCACCGACTTGTG
1 TGGGCTTTAGAAAGGGTTGCCACCAACTTGTGTGGGCTTTTA-AAAGGGTTGCCACCGACTTGTG
* * * * *
19103 TGGGCATTGGAAAGGGTCGCCACCAACTTATGTGGGCTTTGAAGAA-GGTTGCCACCGACTTGTG
1 TGGGCTTTAGAAAGGGTTGCCACCAACTTGTGTGGGCTTTTAA-AAGGGTTGCCACCGACTTGTG
* *
19167 TGGGCTTTAGAAAGGGTTGCCACCAACTTGTGTGGGCTTTGAAGAA-GGTTGCCATCGACTTGTG
1 TGGGCTTTAGAAAGGGTTGCCACCAACTTGTGTGGGCTTTTAA-AAGGGTTGCCACCGACTTGTG
19231 TGGGCTTTAGAAAGGGTTGCCACCAACTTGTGTGGGC-TTTAAGAAGGGT
1 TGGGCTTTAGAAAGGGTTGCCACCAACTTGTGTGGGCTTTTAA-AAGGGT
19280 AAAGGTGCCA
Statistics
Matches: 321, Mismatches: 39, Indels: 19
0.85 0.10 0.05
Matches are distributed among these distances:
63 15 0.05
64 250 0.78
65 55 0.17
66 1 0.00
ACGTcount: A:0.24, C:0.19, G:0.30, T:0.27
Consensus pattern (64 bp):
TGGGCTTTAGAAAGGGTTGCCACCAACTTGTGTGGGCTTTTAAAAGGGTTGCCACCGACTTGTG
Found at i:19346 original size:32 final size:32
Alignment explanation
Indices: 19305--19749 Score: 259
Period size: 27 Copynumber: 14.8 Consensus size: 32
19295 TTGTGGACTT
*
19305 AAAATGGTGCCATGGAGTTATGGACTTGAAAAG
1 AAAA-GGTGCCATGGAGTTGTGGACTTGAAAAG
19338 AAAAGGTGCCATGGAGTTGTGGACTT----A-
1 AAAAGGTGCCATGGAGTTGTGGACTTGAAAAG
* *
19365 AAATGGTGCCATGGAGTTATGGACTTGAAAAG
1 AAAAGGTGCCATGGAGTTGTGGACTTGAAAAG
*
19397 AAAAGGTGCTATGGAGTTGTGGACTT----A-
1 AAAAGGTGCCATGGAGTTGTGGACTTGAAAAG
* *
19424 AAAAGGTGCCATGGAGTTGGGGACTTGAAAGG
1 AAAAGGTGCCATGGAGTTGTGGACTTGAAAAG
**
19456 AAAAGGTGCCACAGAGTTGTGGACTT-AAAAG
1 AAAAGGTGCCATGGAGTTGTGGACTTGAAAAG
* * * * *
19487 ----GGTGCCACGAAGTTATGGATTTGAAAAC
1 AAAAGGTGCCATGGAGTTGTGGACTTGAAAAG
* *
19515 AAAATGGTGCCATGGATTTGTGGGCTT-AAAAG
1 AAAA-GGTGCCATGGAGTTGTGGACTTGAAAAG
*** * *
19547 ----GGTGCCACAAAGTTGCGAACTT-AAAAG
1 AAAAGGTGCCATGGAGTTGTGGACTTGAAAAG
* * *
19574 ----GGTGCCACGGAGTTATGGACTTGAAAGG
1 AAAAGGTGCCATGGAGTTGTGGACTTGAAAAG
** *
19602 AAAAAGGTGCCACAGAGTTGTGGACAT-AAAAG
1 -AAAAGGTGCCATGGAGTTGTGGACTTGAAAAG
*** *
19634 ----GGTGCCACAAAGTTGTGGACTTGAAAGG
1 AAAAGGTGCCATGGAGTTGTGGACTTGAAAAG
*** * * *
19662 AAAAGGTGCCACAAAGCTGTGAACTTAAAAAGG
1 AAAAGGTGCCATGGAGTTGTGGACTTGAAAA-G
* ** *
19695 AAGAGGTGCCACAGAGCTGTGGACTT-AAAAG
1 AAAAGGTGCCATGGAGTTGTGGACTTGAAAAG
* *
19726 GAAAGGTGCCACGGAGTTGTGGAC
1 AAAAGGTGCCATGGAGTTGTGGAC
19750 CCGAAGAAGA
Statistics
Matches: 328, Mismatches: 56, Indels: 58
0.74 0.13 0.13
Matches are distributed among these distances:
27 123 0.38
28 14 0.04
31 26 0.08
32 102 0.31
33 63 0.19
ACGTcount: A:0.34, C:0.13, G:0.32, T:0.21
Consensus pattern (32 bp):
AAAAGGTGCCATGGAGTTGTGGACTTGAAAAG
Found at i:19348 original size:59 final size:59
Alignment explanation
Indices: 19280--19553 Score: 377
Period size: 59 Copynumber: 4.6 Consensus size: 59
19270 TAAGAAGGGT
** * *
19280 AAAGGTGCCACAGATTTGTGGACTTAAAATGGTGCCATGGAGTTATGGACTTGAAAAGA
1 AAAGGTGCCATGGAGTTGTGGACTTAAAAGGGTGCCATGGAGTTATGGACTTGAAAAGA
*
19339 AAAGGTGCCATGGAGTTGTGGACTTAAAATGGTGCCATGGAGTTATGGACTTGAAAAGA
1 AAAGGTGCCATGGAGTTGTGGACTTAAAAGGGTGCCATGGAGTTATGGACTTGAAAAGA
* * ** *
19398 AAAGGTGCTATGGAGTTGTGGACTTAAAAAGGTGCCATGGAGTTGGGGACTTGAAAGGA
1 AAAGGTGCCATGGAGTTGTGGACTTAAAAGGGTGCCATGGAGTTATGGACTTGAAAAGA
** * * * *
19457 AAAGGTGCCACAGAGTTGTGGACTTAAAAGGGTGCCACGAAGTTATGGATTTGAAAACA
1 AAAGGTGCCATGGAGTTGTGGACTTAAAAGGGTGCCATGGAGTTATGGACTTGAAAAGA
* *
19516 AAATGGTGCCATGGATTTGTGGGCTTAAAAGGGTGCCA
1 AAA-GGTGCCATGGAGTTGTGGACTTAAAAGGGTGCCA
19554 CAAAGTTGCG
Statistics
Matches: 191, Mismatches: 23, Indels: 1
0.89 0.11 0.00
Matches are distributed among these distances:
59 161 0.84
60 30 0.16
ACGTcount: A:0.32, C:0.11, G:0.32, T:0.24
Consensus pattern (59 bp):
AAAGGTGCCATGGAGTTGTGGACTTAAAAGGGTGCCATGGAGTTATGGACTTGAAAAGA
Found at i:19569 original size:87 final size:87
Alignment explanation
Indices: 19456--19648 Score: 262
Period size: 87 Copynumber: 2.2 Consensus size: 87
19446 ACTTGAAAGG
* * * * *
19456 AAAA-GGTGCCACAGAGTTGTGGACTTAAAAGGGTGCCACGAAGTTATGGATTTGAAAACAAAAT
1 AAAAGGGTGCCACAAAGTTGCGAACTTAAAAGGGTGCCACGAAGTTATGGACTTGAAAACAAAAA
** * * *
19520 GGTGCCATGGATTTGTGGGCTT
66 GGTGCCACAGAGTTGTGGACAT
* **
19542 AAAAGGGTGCCACAAAGTTGCGAACTTAAAAGGGTGCCACGGAGTTATGGACTTGAAAGGAAAAA
1 AAAAGGGTGCCACAAAGTTGCGAACTTAAAAGGGTGCCACGAAGTTATGGACTTGAAAACAAAAA
19607 GGTGCCACAGAGTTGTGGACAT
66 GGTGCCACAGAGTTGTGGACAT
19629 AAAAGGGTGCCACAAAGTTG
1 AAAAGGGTGCCACAAAGTTG
19649 TGGACTTGAA
Statistics
Matches: 93, Mismatches: 13, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
86 4 0.04
87 89 0.96
ACGTcount: A:0.34, C:0.14, G:0.31, T:0.21
Consensus pattern (87 bp):
AAAAGGGTGCCACAAAGTTGCGAACTTAAAAGGGTGCCACGAAGTTATGGACTTGAAAACAAAAA
GGTGCCACAGAGTTGTGGACAT
Found at i:19612 original size:33 final size:32
Alignment explanation
Indices: 19569--19749 Score: 185
Period size: 33 Copynumber: 5.8 Consensus size: 32
19559 TTGCGAACTT
* * *
19569 AAAAGGGTGCCACGGAGTTATGGACTTGAAAGG
1 AAAA-GGTGCCACAGAGTTGTGGACTTAAAAGG
*
19602 AAAAAGGTGCCACAGAGTTGTGGACATAAAA-G
1 -AAAAGGTGCCACAGAGTTGTGGACTTAAAAGG
* *
19634 ----GGTGCCACAAAGTTGTGGACTTGAAAGG
1 AAAAGGTGCCACAGAGTTGTGGACTTAAAAGG
* * *
19662 AAAAGGTGCCACAAAGCTGTGAACTTAAAAAGG
1 AAAAGGTGCCACAGAGTTGTGGACTT-AAAAGG
* *
19695 AAGAGGTGCCACAGAGCTGTGGACTTAAAAGG
1 AAAAGGTGCCACAGAGTTGTGGACTTAAAAGG
*
19727 -AAAGGTGCCACGGAGTTGTGGAC
1 AAAAGGTGCCACAGAGTTGTGGAC
19750 CCGAAGAAGA
Statistics
Matches: 125, Mismatches: 16, Indels: 15
0.80 0.10 0.10
Matches are distributed among these distances:
27 23 0.18
28 1 0.01
31 20 0.16
32 27 0.22
33 50 0.40
34 4 0.03
ACGTcount: A:0.36, C:0.14, G:0.33, T:0.17
Consensus pattern (32 bp):
AAAAGGTGCCACAGAGTTGTGGACTTAAAAGG
Found at i:19693 original size:60 final size:59
Alignment explanation
Indices: 19542--19746 Score: 223
Period size: 60 Copynumber: 3.4 Consensus size: 59
19532 TTGTGGGCTT
* * *
19542 AAAAGGGTGCCACAAAGTTGCGAACTTAAAAGGGTGCCACGGAGTTATGGACTTGAAAGG
1 AAAA-GGTGCCACAAAGTTGTGAACTTAAAAGGGTGCCACAGAGTTGTGGACTTGAAAGG
* * * *
19602 AAAAAGGTGCCACAGAGTTGTGGACATAAAAGGGTGCCACAAAGTTGTGGACTTGAAAGG
1 -AAAAGGTGCCACAAAGTTGTGAACTTAAAAGGGTGCCACAGAGTTGTGGACTTGAAAGG
* * *
19662 AAAAGGTGCCACAAAGCTGTGAACTTAAAAAGGAAGAGGTGCCACAGAGCTGTGGACTTAAAAGG
1 AAAAGGTGCCACAAAGTTGTGAACTT---AA--AAG-GGTGCCACAGAGTTGTGGACTTGAAAGG
**
19727 -AAAGGTGCCACGGAGTTGTG
1 AAAAGGTGCCACAAAGTTGTG
19747 GACCCGAAGA
Statistics
Matches: 121, Mismatches: 17, Indels: 9
0.82 0.12 0.06
Matches are distributed among these distances:
59 22 0.18
60 48 0.40
61 4 0.03
62 2 0.02
64 20 0.17
65 25 0.21
ACGTcount: A:0.36, C:0.15, G:0.32, T:0.18
Consensus pattern (59 bp):
AAAAGGTGCCACAAAGTTGTGAACTTAAAAGGGTGCCACAGAGTTGTGGACTTGAAAGG
Found at i:20695 original size:13 final size:13
Alignment explanation
Indices: 20677--20702 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
20667 TACAATGTTC
20677 ATGTATCGATACT
1 ATGTATCGATACT
20690 ATGTATCGATACT
1 ATGTATCGATACT
20703 GTGCATTATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
ATGTATCGATACT
Found at i:21291 original size:22 final size:23
Alignment explanation
Indices: 21252--21299 Score: 80
Period size: 23 Copynumber: 2.1 Consensus size: 23
21242 TTTCCTTTTC
21252 TCTCCCCCTTAATAAAAAAAATT
1 TCTCCCCCTTAATAAAAAAAATT
*
21275 TCTCCCCCTTAAT-AAAACAATT
1 TCTCCCCCTTAATAAAAAAAATT
21297 TCT
1 TCT
21300 TTTAATCACA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
22 11 0.46
23 13 0.54
ACGTcount: A:0.38, C:0.29, G:0.00, T:0.33
Consensus pattern (23 bp):
TCTCCCCCTTAATAAAAAAAATT
Found at i:22534 original size:23 final size:25
Alignment explanation
Indices: 22489--22534 Score: 60
Period size: 24 Copynumber: 1.9 Consensus size: 25
22479 CCGGGAAAAG
* *
22489 GTGGTGGGTTGCCCGGTCTGTGAGT
1 GTGGTGGGCTGCCCAGTCTGTGAGT
22514 GTGG-GGGCTGCCCAGT-TGTGA
1 GTGGTGGGCTGCCCAGTCTGTGA
22535 CCTGGAGTGC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 5 0.26
24 10 0.53
25 4 0.21
ACGTcount: A:0.07, C:0.17, G:0.48, T:0.28
Consensus pattern (25 bp):
GTGGTGGGCTGCCCAGTCTGTGAGT
Found at i:23006 original size:13 final size:13
Alignment explanation
Indices: 22988--23012 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
22978 ATAAACCCTT
22988 TGTATCGATACAC
1 TGTATCGATACAC
23001 TGTATCGATACA
1 TGTATCGATACA
23013 TCTGAGTTTT
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:0.32, C:0.20, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAC
Found at i:29180 original size:19 final size:20
Alignment explanation
Indices: 29136--29187 Score: 72
Period size: 20 Copynumber: 2.6 Consensus size: 20
29126 TTACAAGCCA
29136 ATGTATCGATACATTTGGTC
1 ATGTATCGATACATTTGGTC
*
29156 ATGTATCGATACGTCTT-GT-
1 ATGTATCGATACAT-TTGGTC
29175 ATGTATCGATACA
1 ATGTATCGATACA
29188 AACAGTTAAG
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
19 12 0.41
20 15 0.52
21 2 0.07
ACGTcount: A:0.27, C:0.15, G:0.19, T:0.38
Consensus pattern (20 bp):
ATGTATCGATACATTTGGTC
Found at i:29275 original size:13 final size:13
Alignment explanation
Indices: 29257--29281 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
29247 TACAGTGGTC
29257 ATGTATCGATACA
1 ATGTATCGATACA
29270 ATGTATCGATAC
1 ATGTATCGATAC
29282 TGTGCATTAT
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:29299 original size:33 final size:32
Alignment explanation
Indices: 29240--29302 Score: 90
Period size: 33 Copynumber: 1.9 Consensus size: 32
29230 ATCTTTGCAA
*
29240 GTATCGATACAGTGGTCATGTATCGATACAAT
1 GTATCGATACAGTGATCATGTATCGATACAAT
* *
29272 GTATCGATACTGTGCATTATGTATCGATACA
1 GTATCGATACAGTG-ATCATGTATCGATACA
29303 TCTGAAGGTG
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
32 13 0.48
33 14 0.52
ACGTcount: A:0.30, C:0.16, G:0.21, T:0.33
Consensus pattern (32 bp):
GTATCGATACAGTGATCATGTATCGATACAAT
Found at i:29941 original size:13 final size:13
Alignment explanation
Indices: 29923--29950 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
29913 ATATGATGCC
29923 ATATCCGACTTGT
1 ATATCCGACTTGT
29936 ATATCCGACTTGT
1 ATATCCGACTTGT
29949 AT
1 AT
29951 CTCAGGCATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.25, C:0.21, G:0.14, T:0.39
Consensus pattern (13 bp):
ATATCCGACTTGT
Found at i:30643 original size:13 final size:13
Alignment explanation
Indices: 30625--30651 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
30615 ACATTATGCT
30625 TTGTATCGATACA
1 TTGTATCGATACA
30638 TTGTATCGATACA
1 TTGTATCGATACA
30651 T
1 T
30652 GATCATTGTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.41
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:30648 original size:33 final size:32
Alignment explanation
Indices: 30606--30670 Score: 103
Period size: 32 Copynumber: 2.0 Consensus size: 32
30596 CATACCCAGA
* *
30606 TGTATCGATACATTATGCTTTGTATCGATACAT
1 TGTATCGATACATGAT-CATTGTATCGATACAT
30639 TGTATCGATACATGATCATTGTATCGATACAT
1 TGTATCGATACATGATCATTGTATCGATACAT
30671 GGACAATTGT
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 15 0.50
33 15 0.50
ACGTcount: A:0.29, C:0.15, G:0.15, T:0.40
Consensus pattern (32 bp):
TGTATCGATACATGATCATTGTATCGATACAT
Found at i:30660 original size:19 final size:18
Alignment explanation
Indices: 30635--30692 Score: 89
Period size: 19 Copynumber: 3.1 Consensus size: 18
30625 TTGTATCGAT
30635 ACATTGTATCGATACATG
1 ACATTGTATCGATACATG
30653 ATCATTGTATCGATACATGG
1 A-CATTGTATCGATACAT-G
30673 ACAATTGTATCGATACATG
1 AC-ATTGTATCGATACATG
30692 A
1 A
30693 AACTAGTAGT
Statistics
Matches: 37, Mismatches: 0, Indels: 5
0.88 0.00 0.12
Matches are distributed among these distances:
18 1 0.03
19 19 0.51
20 17 0.46
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Consensus pattern (18 bp):
ACATTGTATCGATACATG
Found at i:30681 original size:20 final size:20
Alignment explanation
Indices: 30636--30691 Score: 89
Period size: 20 Copynumber: 2.9 Consensus size: 20
30626 TGTATCGATA
30636 CATTGTATCGATACAT-GAT
1 CATTGTATCGATACATGGAT
30655 CATTGTATCGATACATGGA-
1 CATTGTATCGATACATGGAT
30674 CAATTGTATCGATACATG
1 C-ATTGTATCGATACATG
30692 AAACTAGTAG
Statistics
Matches: 35, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
19 17 0.49
20 18 0.51
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.34
Consensus pattern (20 bp):
CATTGTATCGATACATGGAT
Found at i:30745 original size:20 final size:20
Alignment explanation
Indices: 30720--30773 Score: 74
Period size: 20 Copynumber: 2.7 Consensus size: 20
30710 CTACCACTGT
*
30720 TTGTATCGATACATGGT-ACA
1 TTGTATCGATACATGATGA-A
30740 TTGTATCGATACATGATGAA
1 TTGTATCGATACATGATGAA
*
30760 TTGTGTCGATACAT
1 TTGTATCGATACAT
30774 TGCTTGTAAC
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
20 30 0.97
21 1 0.03
ACGTcount: A:0.30, C:0.13, G:0.20, T:0.37
Consensus pattern (20 bp):
TTGTATCGATACATGATGAA
Found at i:33254 original size:15 final size:15
Alignment explanation
Indices: 33234--33272 Score: 60
Period size: 15 Copynumber: 2.6 Consensus size: 15
33224 TCATGATAGG
*
33234 GCTTGGGTAAGGTGC
1 GCTTGGGTAAAGTGC
33249 GCTTGGGTAAAGTGC
1 GCTTGGGTAAAGTGC
*
33264 ACTTGGGTA
1 GCTTGGGTA
33273 GTAAGGATCG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.18, C:0.13, G:0.41, T:0.28
Consensus pattern (15 bp):
GCTTGGGTAAAGTGC
Found at i:37212 original size:13 final size:13
Alignment explanation
Indices: 37190--37228 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
37180 CATTATTCAA
37190 TGTATCGATACAT
1 TGTATCGATACAT
*
37203 TGTATTGATACAT
1 TGTATCGATACAT
37216 TGTATCGATACAT
1 TGTATCGATACAT
37229 CTGGGAATTT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.31, C:0.13, G:0.15, T:0.41
Consensus pattern (13 bp):
TGTATCGATACAT
Done.