Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold3261.1
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: 147108
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.32
Warning! 84 characters in sequence are not A, C, G, or T
Found at i:2260 original size:65 final size:65
Alignment explanation
Indices: 2183--2311 Score: 192
Period size: 65 Copynumber: 2.0 Consensus size: 65
2173 ATGGGCTCAA
*
2183 ATTACCACAAGGCCCAATAACGAGGTCAAAGGCCA-AGCAAATGCG-T-ATGAAACTAAATGGAA
1 ATTACCACAAGGCCCAATAACGAGGTCAAAGGCCAGA-AAAATGCGCTCA--AAACTAAATGGAA
2245 CCG
63 CCG
*
2248 ATTACCATAAGGCCCAATAACGAGGTCAAAGGCCAGAAAAATGCGCTCAAAACTAAATGGAACC
1 ATTACCACAAGGCCCAATAACGAGGTCAAAGGCCAGAAAAATGCGCTCAAAACTAAATGGAACC
2312 ATTCAAGAAT
Statistics
Matches: 59, Mismatches: 2, Indels: 6
0.88 0.03 0.09
Matches are distributed among these distances:
65 56 0.95
66 2 0.03
67 1 0.02
ACGTcount: A:0.43, C:0.23, G:0.20, T:0.14
Consensus pattern (65 bp):
ATTACCACAAGGCCCAATAACGAGGTCAAAGGCCAGAAAAATGCGCTCAAAACTAAATGGAACCG
Found at i:16302 original size:20 final size:19
Alignment explanation
Indices: 16268--16315 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 19
16258 CAACTCAACT
16268 TTAGCTCAACGAGCTCATTC
1 TTAGCTCAACGAGCTCA-TC
** *
16288 TTAGCTCAATTAGCTTATC
1 TTAGCTCAACGAGCTCATC
16307 TTAAGCTCA
1 TT-AGCTCA
16316 TTTTAGTTCG
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
19 4 0.17
20 20 0.83
ACGTcount: A:0.27, C:0.25, G:0.12, T:0.35
Consensus pattern (19 bp):
TTAGCTCAACGAGCTCATC
Found at i:30615 original size:22 final size:22
Alignment explanation
Indices: 30587--30630 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
30577 TTTTGAACCA
30587 TTACCATTTCGTACCAAATCCC
1 TTACCATTTCGTACCAAATCCC
* *
30609 TTACCATTTTGTACCAATTCCC
1 TTACCATTTCGTACCAAATCCC
30631 AAATATAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.25, C:0.34, G:0.05, T:0.36
Consensus pattern (22 bp):
TTACCATTTCGTACCAAATCCC
Found at i:32296 original size:18 final size:18
Alignment explanation
Indices: 32275--32318 Score: 63
Period size: 18 Copynumber: 2.4 Consensus size: 18
32265 AAAGGAAGAC
32275 AGAAAAAGA-AATTGAAAA
1 AGAAAAAGACAA-TGAAAA
32293 AGAAAAAGACAATGAAAA
1 AGAAAAAGACAATGAAAA
32311 AGAGAAAA
1 AGA-AAAA
32319 AAAGAGATTG
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
18 18 0.75
19 6 0.25
ACGTcount: A:0.73, C:0.02, G:0.18, T:0.07
Consensus pattern (18 bp):
AGAAAAAGACAATGAAAA
Found at i:34104 original size:33 final size:34
Alignment explanation
Indices: 34067--34138 Score: 110
Period size: 33 Copynumber: 2.1 Consensus size: 34
34057 GAGTTAGTTT
*
34067 ATTAAATTTAGTTCAGCTCAAATAAGTGTTAG-A
1 ATTAAATTTAATTCAGCTCAAATAAGTGTTAGTA
* *
34100 ATTAATTTTAATTCAGCTTAAATAAGTGTTAGTA
1 ATTAAATTTAATTCAGCTCAAATAAGTGTTAGTA
34134 ATTAA
1 ATTAA
34139 TTTGTTTAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
33 29 0.83
34 6 0.17
ACGTcount: A:0.40, C:0.07, G:0.12, T:0.40
Consensus pattern (34 bp):
ATTAAATTTAATTCAGCTCAAATAAGTGTTAGTA
Found at i:41778 original size:82 final size:82
Alignment explanation
Indices: 41641--41803 Score: 299
Period size: 82 Copynumber: 2.0 Consensus size: 82
41631 TCCTGACGCT
* *
41641 TATTGTGAATGGGAATCTAAGATTGAACTTATGTTTCGGTATTATAAATGTCCGGATGATTAAAA
1 TATTGTGAATGGGAATCTAAGATTGAACTCATGTTTCGGTATTATAAATGTCCGGATGATGAAAA
*
41706 GGTAGCGTTAGCAACAC
66 GGTAGCATTAGCAACAC
41723 TATTGTGAATGGGAATCTAAGATTGAACTCATGTTTCGGTATTATAAATGTCCGGATGATGAAAA
1 TATTGTGAATGGGAATCTAAGATTGAACTCATGTTTCGGTATTATAAATGTCCGGATGATGAAAA
41788 GGTAGCATTAGCAACA
66 GGTAGCATTAGCAACA
41804 TTGGAATTTT
Statistics
Matches: 78, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
82 78 1.00
ACGTcount: A:0.34, C:0.11, G:0.23, T:0.32
Consensus pattern (82 bp):
TATTGTGAATGGGAATCTAAGATTGAACTCATGTTTCGGTATTATAAATGTCCGGATGATGAAAA
GGTAGCATTAGCAACAC
Found at i:48202 original size:28 final size:27
Alignment explanation
Indices: 48151--48223 Score: 76
Period size: 28 Copynumber: 2.7 Consensus size: 27
48141 AATTCGGCTG
*
48151 AACTAAGACACATTAAAATGATGTAAT
1 AACTAAGACAAATTAAAATGATGTAAT
* *
48178 AAACTAAGACAAATTAATTAT-ATGTACT
1 -AACTAAGACAAATTAA-AATGATGTAAT
* *
48206 AACTAAAACATATTAAAA
1 AACTAAGACAAATTAAAA
48224 ACATGCATTA
Statistics
Matches: 38, Mismatches: 6, Indels: 4
0.79 0.12 0.08
Matches are distributed among these distances:
26 1 0.03
27 14 0.37
28 21 0.55
29 2 0.05
ACGTcount: A:0.55, C:0.11, G:0.07, T:0.27
Consensus pattern (27 bp):
AACTAAGACAAATTAAAATGATGTAAT
Found at i:48255 original size:28 final size:27
Alignment explanation
Indices: 48209--48264 Score: 67
Period size: 28 Copynumber: 2.0 Consensus size: 27
48199 ATGTACTAAC
* *
48209 TAAAACATATTAAAAACATGCATTAAAA
1 TAAAACAAATTAAAAACAT-AATTAAAA
* *
48237 TAAAACAAATTTAACACATAATTAAAA
1 TAAAACAAATTAAAAACATAATTAAAA
48264 T
1 T
48265 GTCTAGATTT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
27 8 0.33
28 16 0.67
ACGTcount: A:0.61, C:0.11, G:0.02, T:0.27
Consensus pattern (27 bp):
TAAAACAAATTAAAAACATAATTAAAA
Found at i:51341 original size:15 final size:16
Alignment explanation
Indices: 51321--51362 Score: 59
Period size: 15 Copynumber: 2.6 Consensus size: 16
51311 TTTTCTCGCA
51321 ATCTTTTTCTTTT-TC
1 ATCTTTTTCTTTTCTC
51336 ATCTTTTTCTTTTCTC
1 ATCTTTTTCTTTTCTC
51352 ACTCTCTTTTC
1 A-TCT-TTTTC
51363 ACTCTCTTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
15 13 0.54
16 3 0.12
17 3 0.12
18 5 0.21
ACGTcount: A:0.07, C:0.26, G:0.00, T:0.67
Consensus pattern (16 bp):
ATCTTTTTCTTTTCTC
Found at i:59079 original size:36 final size:36
Alignment explanation
Indices: 59039--59110 Score: 126
Period size: 36 Copynumber: 2.0 Consensus size: 36
59029 TAGTGACACT
59039 TTGAATTTTGAACAGAAAATAACTTCTCGAAAACCC
1 TTGAATTTTGAACAGAAAATAACTTCTCGAAAACCC
* *
59075 TTGAATTTTGAACAGAAAATAACTTTTCGACAACCC
1 TTGAATTTTGAACAGAAAATAACTTCTCGAAAACCC
59111 ATTCAAACTT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 34 1.00
ACGTcount: A:0.40, C:0.19, G:0.11, T:0.29
Consensus pattern (36 bp):
TTGAATTTTGAACAGAAAATAACTTCTCGAAAACCC
Found at i:60595 original size:14 final size:13
Alignment explanation
Indices: 60555--60596 Score: 50
Period size: 15 Copynumber: 3.1 Consensus size: 13
60545 TTCACTTGCC
60555 TCTTTTTCTCTCATT
1 TCTTTTTCTCT--TT
60570 TCTTTTTC-CTTT
1 TCTTTTTCTCTTT
60582 TCTATTTTCTCTTT
1 TCT-TTTTCTCTTT
60596 T
1 T
60597 TCCTCACACT
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
12 5 0.20
13 5 0.20
14 7 0.28
15 8 0.32
ACGTcount: A:0.05, C:0.24, G:0.00, T:0.71
Consensus pattern (13 bp):
TCTTTTTCTCTTT
Found at i:64473 original size:16 final size:17
Alignment explanation
Indices: 64451--64499 Score: 66
Period size: 18 Copynumber: 2.9 Consensus size: 17
64441 CTCCCAACAT
64451 TCATGCATTTTCA-GG-
1 TCATGCATTTTCATGGA
64466 TACATGCATTTTCAATGGA
1 T-CATGCATTTTC-ATGGA
64485 TCATGCATTTTCATG
1 TCATGCATTTTCATG
64500 ATACTATCCG
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
15 1 0.03
16 11 0.37
17 4 0.13
18 13 0.43
19 1 0.03
ACGTcount: A:0.24, C:0.18, G:0.16, T:0.41
Consensus pattern (17 bp):
TCATGCATTTTCATGGA
Found at i:66038 original size:20 final size:21
Alignment explanation
Indices: 66003--66041 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
65993 CAGCTCGTTG
66003 AGCTCAATTCAGCTCATTTCC
1 AGCTCAATTCAGCTCATTTCC
*
66024 AGCTC-ATTGAGCTCATTT
1 AGCTCAATTCAGCTCATTT
66042 GCTTGTTTGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.23, C:0.28, G:0.13, T:0.36
Consensus pattern (21 bp):
AGCTCAATTCAGCTCATTTCC
Found at i:66449 original size:13 final size:13
Alignment explanation
Indices: 66431--66456 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
66421 TGTGTCCTAA
66431 TATGAATTAAATT
1 TATGAATTAAATT
66444 TATGAATTAAATT
1 TATGAATTAAATT
66457 ACTTTCAGGT
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:0.46, C:0.00, G:0.08, T:0.46
Consensus pattern (13 bp):
TATGAATTAAATT
Found at i:67649 original size:10 final size:10
Alignment explanation
Indices: 67613--67663 Score: 57
Period size: 10 Copynumber: 5.1 Consensus size: 10
67603 AGTAAGTGAT
**
67613 TAAAAAAATT
1 TAAAAAAAAA
67623 TAAAAAAAAA
1 TAAAAAAAAA
**
67633 TCGAAAAAAA
1 TAAAAAAAAA
*
67643 TAAAAAAAAG
1 TAAAAAAAAA
67653 TAAAAAAAAA
1 TAAAAAAAAA
67663 T
1 T
67664 TCGTGGATTG
Statistics
Matches: 33, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
10 33 1.00
ACGTcount: A:0.78, C:0.02, G:0.04, T:0.16
Consensus pattern (10 bp):
TAAAAAAAAA
Found at i:68639 original size:6 final size:6
Alignment explanation
Indices: 68614--68712 Score: 74
Period size: 6 Copynumber: 16.0 Consensus size: 6
68604 TAATGAATTC
** * *
68614 GAAAAA GAAAGT GAAGAA GAAAAA GAAAACA -AAAAA GAAAAA GAAAAC
1 GAAAAA GAAAAA GAAAAA GAAAAA GAAAA-A GAAAAA GAAAAA GAAAAA
** * * *
68662 GAAAAA GTGAGA GAAAAA GAAAAT GAAGAAAA GAAAATT GAAAAA GAAAAA
1 GAAAAA GAAAAA GAAAAA GAAAAA G-A-AAAA GAAAA-A GAAAAA GAAAAA
68713 TATGAAAATG
Statistics
Matches: 70, Mismatches: 18, Indels: 10
0.71 0.18 0.10
Matches are distributed among these distances:
5 1 0.01
6 57 0.81
7 8 0.11
8 4 0.06
ACGTcount: A:0.73, C:0.02, G:0.20, T:0.05
Consensus pattern (6 bp):
GAAAAA
Found at i:68695 original size:14 final size:13
Alignment explanation
Indices: 68674--68711 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 13
68664 AAAAGTGAGA
68674 GAAAAAGAAAA-T
1 GAAAAAGAAAATT
68686 GAAGAAAAGAAAATT
1 G-A-AAAAGAAAATT
68701 GAAAAAGAAAA
1 GAAAAAGAAAA
68712 ATATGAAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
12 1 0.04
13 10 0.43
14 10 0.43
15 2 0.09
ACGTcount: A:0.74, C:0.00, G:0.18, T:0.08
Consensus pattern (13 bp):
GAAAAAGAAAATT
Found at i:68755 original size:17 final size:18
Alignment explanation
Indices: 68730--68769 Score: 55
Period size: 17 Copynumber: 2.3 Consensus size: 18
68720 ATGAGATTTC
68730 AAAAACAAAAT-AGAGTG
1 AAAAACAAAATGAGAGTG
* *
68747 AAAAGCAAAATGAGATTG
1 AAAAACAAAATGAGAGTG
68765 AAAAA
1 AAAAA
68770 GAAAGAGAGT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
17 10 0.53
18 9 0.47
ACGTcount: A:0.65, C:0.05, G:0.17, T:0.12
Consensus pattern (18 bp):
AAAAACAAAATGAGAGTG
Found at i:68768 original size:18 final size:18
Alignment explanation
Indices: 68717--68769 Score: 63
Period size: 18 Copynumber: 2.9 Consensus size: 18
68707 GAAAAATATG
*
68717 AAAATGAGATTTCAAAAAC
1 AAAATGAGA-TTGAAAAAC
* *
68736 AAAAT-AGAGTGAAAAGC
1 AAAATGAGATTGAAAAAC
68753 AAAATGAGATTGAAAAA
1 AAAATGAGATTGAAAAA
68770 GAAAGAGAGT
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
17 11 0.39
18 12 0.43
19 5 0.18
ACGTcount: A:0.60, C:0.06, G:0.17, T:0.17
Consensus pattern (18 bp):
AAAATGAGATTGAAAAAC
Found at i:68785 original size:36 final size:32
Alignment explanation
Indices: 68745--68811 Score: 80
Period size: 32 Copynumber: 2.0 Consensus size: 32
68735 CAAAATAGAG
*
68745 TGAAAAGCAAAATGAGATTGAAAAAGAAAGAGAGTT
1 TGAAAAG-AAAACGAG--TGAAAAAG-AAGAGAGTT
*
68781 TGAAAAGAAAACGAGTGAAGAAGAAGAGAGT
1 TGAAAAGAAAACGAGTGAAAAAGAAGAGAGT
68812 GCTCAAACAC
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
32 8 0.28
33 7 0.24
35 7 0.24
36 7 0.24
ACGTcount: A:0.55, C:0.03, G:0.28, T:0.13
Consensus pattern (32 bp):
TGAAAAGAAAACGAGTGAAAAAGAAGAGAGTT
Found at i:68796 original size:17 final size:16
Alignment explanation
Indices: 68745--68796 Score: 50
Period size: 17 Copynumber: 2.9 Consensus size: 16
68735 CAAAATAGAG
*
68745 TGAAAAGCAAAATGAGAT
1 TGAAAAG-AAAA-GAGTT
68763 TGAAAAAGAAAGAGAGTT
1 TG-AAAAGAAA-AGAGTT
68781 TGAAAAGAAAACGAGT
1 TGAAAAGAAAA-GAGT
68797 GAAGAAGAAG
Statistics
Matches: 30, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
16 1 0.03
17 12 0.40
18 11 0.37
19 6 0.20
ACGTcount: A:0.56, C:0.04, G:0.25, T:0.15
Consensus pattern (16 bp):
TGAAAAGAAAAGAGTT
Found at i:70079 original size:20 final size:21
Alignment explanation
Indices: 70044--70082 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
70034 CAGCTCGTTG
70044 AGCTCAATTCAGCTCATTTCC
1 AGCTCAATTCAGCTCATTTCC
*
70065 AGCTC-ATTGAGCTCATTT
1 AGCTCAATTCAGCTCATTT
70083 GCTTGTTTGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.23, C:0.28, G:0.13, T:0.36
Consensus pattern (21 bp):
AGCTCAATTCAGCTCATTTCC
Found at i:70490 original size:13 final size:13
Alignment explanation
Indices: 70472--70497 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
70462 TGTGTCCTAA
70472 TATGAATTAAATT
1 TATGAATTAAATT
70485 TATGAATTAAATT
1 TATGAATTAAATT
70498 GCTTTCAGGT
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:0.46, C:0.00, G:0.08, T:0.46
Consensus pattern (13 bp):
TATGAATTAAATT
Found at i:72304 original size:20 final size:20
Alignment explanation
Indices: 72247--72296 Score: 73
Period size: 20 Copynumber: 2.5 Consensus size: 20
72237 ATTTACCTCG
*
72247 ATTCAGCTCACATGAGTTTA
1 ATTCAGCTCACATGAGCTTA
* *
72267 ATTCAACTCACATAAGCTTA
1 ATTCAGCTCACATGAGCTTA
72287 ATTCAGCTCA
1 ATTCAGCTCA
72297 TTTGAGCTCA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.34, C:0.24, G:0.10, T:0.32
Consensus pattern (20 bp):
ATTCAGCTCACATGAGCTTA
Found at i:74707 original size:72 final size:72
Alignment explanation
Indices: 74621--74760 Score: 262
Period size: 72 Copynumber: 1.9 Consensus size: 72
74611 AAGCAAACTT
*
74621 CGAGTCAATAATCTTTCGAGATGATGAACAAAAAAGGACAAGTTATTCTTCGTATGCCTGAAAGA
1 CGAGTCAATAATCTTTCGAGATGATGAACAAAAAAGGACAAGTTATTCTTCGTATGCCTCAAAGA
74686 AGTACGA
66 AGTACGA
*
74693 CGAGTCAATAATCTTTCGAGATGATGAACAAAAAAGTACAAGTTATTCTTCGTATGCCTCAAAGA
1 CGAGTCAATAATCTTTCGAGATGATGAACAAAAAAGGACAAGTTATTCTTCGTATGCCTCAAAGA
74758 AGT
66 AGT
74761 CCCTTCCGGA
Statistics
Matches: 66, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
72 66 1.00
ACGTcount: A:0.39, C:0.16, G:0.19, T:0.26
Consensus pattern (72 bp):
CGAGTCAATAATCTTTCGAGATGATGAACAAAAAAGGACAAGTTATTCTTCGTATGCCTCAAAGA
AGTACGA
Found at i:74930 original size:18 final size:17
Alignment explanation
Indices: 74883--74977 Score: 59
Period size: 18 Copynumber: 5.4 Consensus size: 17
74873 TAATAAAATC
74883 AAAAA-AGAAGAAAAAG
1 AAAAAGAGAAGAAAAAG
* **
74899 AAAAGGTAGGTGAAAAAG
1 AAAAAG-AGAAGAAAAAG
* *
74917 AAAAAGAGAATGAATATG
1 AAAAAGAGAA-GAAAAAG
*
74935 AAAATGAGAAAAGAAAAAG
1 AAAA--AGAGAAGAAAAAG
* *
74954 -AGAAGTGAGAGAAAAAG
1 AAAAAGAGA-AGAAAAAG
74971 AAAAAGA
1 AAAAAGA
74978 AAAAGAGAAA
Statistics
Matches: 56, Mismatches: 16, Indels: 12
0.67 0.19 0.14
Matches are distributed among these distances:
16 7 0.12
17 10 0.18
18 29 0.52
19 5 0.09
20 5 0.09
ACGTcount: A:0.67, C:0.00, G:0.25, T:0.07
Consensus pattern (17 bp):
AAAAAGAGAAGAAAAAG
Found at i:74949 original size:31 final size:29
Alignment explanation
Indices: 74910--74986 Score: 102
Period size: 31 Copynumber: 2.6 Consensus size: 29
74900 AAAGGTAGGT
* *
74910 GAAAAAGAAAAAGAGAA-TGAATATGAAAAT
1 GAAAAAGAAAAAGAGAAGTG-AGA-GAAAAA
74940 GAGAAAAGAAAAAGAGAAGTGAGAGAAAAA
1 GA-AAAAGAAAAAGAGAAGTGAGAGAAAAA
74970 GAAAAAGAAAAAGAGAA
1 GAAAAAGAAAAAGAGAA
74987 AATTGAAAAA
Statistics
Matches: 43, Mismatches: 2, Indels: 5
0.86 0.04 0.10
Matches are distributed among these distances:
29 15 0.35
30 9 0.21
31 17 0.40
32 2 0.05
ACGTcount: A:0.69, C:0.00, G:0.25, T:0.06
Consensus pattern (29 bp):
GAAAAAGAAAAAGAGAAGTGAGAGAAAAA
Found at i:74980 original size:5 final size:6
Alignment explanation
Indices: 74910--75000 Score: 58
Period size: 6 Copynumber: 14.7 Consensus size: 6
74900 AAAGGTAGGT
* * * * * *
74910 GAAAAA GAAAAA GAGAAT GAATAT GAAAAT GAGAAAA GAAAAA G-AGAA
1 GAAAAA GAAAAA GAAAAA GAAAAA GAAAAA GA-AAAA GAAAAA GAAAAA
** *
74958 GTGAGA GAAAAA GAAAAA GAAAAA GAGAAAA TTGAAAAA GAAA
1 GAAAAA GAAAAA GAAAAA GAAAAA GA-AAAA --GAAAAA GAAA
75001 TTGAGATTGA
Statistics
Matches: 67, Mismatches: 13, Indels: 10
0.74 0.14 0.11
Matches are distributed among these distances:
5 4 0.06
6 48 0.72
7 9 0.13
8 4 0.06
9 2 0.03
ACGTcount: A:0.69, C:0.00, G:0.23, T:0.08
Consensus pattern (6 bp):
GAAAAA
Found at i:75025 original size:45 final size:42
Alignment explanation
Indices: 74932--75059 Score: 143
Period size: 45 Copynumber: 3.0 Consensus size: 42
74922 GAGAATGAAT
* *
74932 ATGAAAATGAGAAAA-GAAAAAGAGAAGTGAGAGAAAAAGAAA
1 ATGAAAAAGAGAAAATGAAAAAGA-AATTGAGAGAAAAAGAAA
* *
74974 AAGAAAAAGAGAAAATTGAAAAAGAAATTGAGATTGAAAAAGGAA
1 ATGAAAAAGAGAAAA-TGAAAAAGAAATTGAGA--GAAAAAGAAA
*
75019 GTGAAAAAGAGAAAATCGAAAAAGAAATTGA-AGAAATAAGA
1 ATGAAAAAGAGAAAAT-GAAAAAGAAATTGAGAGAAA-AAGA
75060 GAAAACGAGT
Statistics
Matches: 73, Mismatches: 7, Indels: 11
0.80 0.08 0.12
Matches are distributed among these distances:
42 17 0.23
43 10 0.14
44 10 0.14
45 36 0.49
ACGTcount: A:0.65, C:0.01, G:0.23, T:0.11
Consensus pattern (42 bp):
ATGAAAAAGAGAAAATGAAAAAGAAATTGAGAGAAAAAGAAA
Found at i:78440 original size:20 final size:20
Alignment explanation
Indices: 78384--78431 Score: 87
Period size: 20 Copynumber: 2.4 Consensus size: 20
78374 TTTACCTCGG
*
78384 TTCAGCTCACATGAGTTTAA
1 TTCAGCTCACATGAGCTTAA
78404 TTCAGCTCACATGAGCTTAA
1 TTCAGCTCACATGAGCTTAA
78424 TTCAGCTC
1 TTCAGCTC
78432 GTTTGAGCTC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.27, C:0.25, G:0.15, T:0.33
Consensus pattern (20 bp):
TTCAGCTCACATGAGCTTAA
Found at i:80524 original size:21 final size:24
Alignment explanation
Indices: 80498--80547 Score: 70
Period size: 21 Copynumber: 2.2 Consensus size: 24
80488 CTACTAATGT
80498 GTTCACAC-AAAA-ATTAAA-AGG
1 GTTCACACTAAAACATTAAAGAGG
*
80519 GTTCACACTAAAACATTAAAGATG
1 GTTCACACTAAAACATTAAAGAGG
80543 GTTCA
1 GTTCA
80548 TGAATTCAGC
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
21 8 0.32
22 4 0.16
23 6 0.24
24 7 0.28
ACGTcount: A:0.46, C:0.16, G:0.14, T:0.24
Consensus pattern (24 bp):
GTTCACACTAAAACATTAAAGAGG
Found at i:81243 original size:27 final size:27
Alignment explanation
Indices: 81205--81256 Score: 95
Period size: 27 Copynumber: 1.9 Consensus size: 27
81195 TCATTGAAGC
*
81205 ATCTTCATTGCTGTCCATGCATGTATT
1 ATCTTCAATGCTGTCCATGCATGTATT
81232 ATCTTCAATGCTGTCCATGCATGTA
1 ATCTTCAATGCTGTCCATGCATGTA
81257 CCTACAAACT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.21, C:0.23, G:0.15, T:0.40
Consensus pattern (27 bp):
ATCTTCAATGCTGTCCATGCATGTATT
Found at i:81913 original size:50 final size:52
Alignment explanation
Indices: 81763--81923 Score: 192
Period size: 50 Copynumber: 3.2 Consensus size: 52
81753 ATGATGCTTA
** * *
81763 AATGCATGATTTAA-TTAA-GATGCAAAC-TAAA-TGAACA-AATGAGTTACTT
1 AATGCATGACATAATTTAATGATGCAAACTTAAACT-AACATGA-GAGTTACAT
* *
81812 AATGCATGACATAATTTAATGATGCAGACTTAAACTAACATGGGAGTTACAT
1 AATGCATGACATAATTTAATGATGCAAACTTAAACTAACATGAGAGTTACAT
*
81864 AATGCATGTCATAATTT-ATGATGCAAACTT-AACTAACATGAGAGTTACAT
1 AATGCATGACATAATTTAATGATGCAAACTTAAACTAACATGAGAGTTACAT
81914 AATGCATGAC
1 AATGCATGAC
81924 TTTATTAAAT
Statistics
Matches: 97, Mismatches: 10, Indels: 9
0.84 0.09 0.08
Matches are distributed among these distances:
49 12 0.12
50 32 0.33
51 20 0.21
52 32 0.33
53 1 0.01
ACGTcount: A:0.42, C:0.13, G:0.16, T:0.30
Consensus pattern (52 bp):
AATGCATGACATAATTTAATGATGCAAACTTAAACTAACATGAGAGTTACAT
Found at i:83059 original size:17 final size:17
Alignment explanation
Indices: 83030--83083 Score: 72
Period size: 19 Copynumber: 3.0 Consensus size: 17
83020 GCAACTCATG
83030 TATTAATCTAAGATGAGT
1 TATTAA-CTAAGATGAGT
*
83048 TATTAACTAAGATGAAT
1 TATTAACTAAGATGAGT
83065 TCAATTAACTAAGATGAGT
1 T--ATTAACTAAGATGAGT
83084 AATTTATTCA
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
17 11 0.34
18 6 0.19
19 15 0.47
ACGTcount: A:0.43, C:0.07, G:0.15, T:0.35
Consensus pattern (17 bp):
TATTAACTAAGATGAGT
Found at i:85214 original size:86 final size:85
Alignment explanation
Indices: 85011--85230 Score: 271
Period size: 86 Copynumber: 2.5 Consensus size: 85
85001 CTTAAACTTT
* * *
85011 TTTTTTAAAAAAGCAATTAAACCCCTACTTTTTTTGCACTCAATTAGATACTTGAACTGGCAAAA
1 TTTTTCAAAAAAGCAATT-AACCCCT-CTTTTTTTGCACTCAATTGGATACTTGAACTGACAAAA
**
85076 TGCATCAAAAAGGCCTCAATTT
64 TGCATCAAAAAGGCCTCAATAC
* * *
85098 TTTTTCAAAAAATGTAATTAAGCTCTCTTTTTTTGCACTCAATTGGATACTTGAACTGACAAAAT
1 TTTTTCAAAAAA-GCAATTAACCCCTCTTTTTTTGCACTCAATTGGATACTTGAACTGACAAAAT
*
85163 GCATCAAAAGGGCCCTCAA-AC
65 GCATCAAAAAGG-CCTCAATAC
* *
85184 TTTTTCAAAAAAACAATTAATCCCTGCTTTTTTTTTGCACTCAATTG
1 TTTTTCAAAAAAGCAATTAA-CCC--CTCTTTTTTTGCACTCAATTG
85231 CCAAAATGCA
Statistics
Matches: 114, Mismatches: 14, Indels: 9
0.83 0.10 0.07
Matches are distributed among these distances:
85 6 0.05
86 61 0.54
87 22 0.19
88 25 0.22
ACGTcount: A:0.35, C:0.20, G:0.10, T:0.35
Consensus pattern (85 bp):
TTTTTCAAAAAAGCAATTAACCCCTCTTTTTTTGCACTCAATTGGATACTTGAACTGACAAAATG
CATCAAAAAGGCCTCAATAC
Found at i:85467 original size:9 final size:9
Alignment explanation
Indices: 85454--85497 Score: 54
Period size: 9 Copynumber: 4.8 Consensus size: 9
85444 AGAAAAAGAT
85454 TATAAAA-A
1 TATAAAATA
85462 TCATAAAATA
1 T-ATAAAATA
85472 TATAAAATA
1 TATAAAATA
85481 TATAGAAATA
1 TATA-AAATA
*
85491 TAGAAAA
1 TATAAAA
85498 AGAAATATAA
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
8 1 0.03
9 21 0.66
10 10 0.31
ACGTcount: A:0.66, C:0.02, G:0.05, T:0.27
Consensus pattern (9 bp):
TATAAAATA
Found at i:85491 original size:19 final size:18
Alignment explanation
Indices: 85454--85498 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 18
85444 AGAAAAAGAT
85454 TATAAAAATCATAAAATA
1 TATAAAAATCATAAAATA
85472 TATAAAATAT-ATAGAAATA
1 TATAAAA-ATCATA-AAATA
*
85491 TAGAAAAA
1 TATAAAAA
85499 GAAATATAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
18 11 0.46
19 13 0.54
ACGTcount: A:0.67, C:0.02, G:0.04, T:0.27
Consensus pattern (18 bp):
TATAAAAATCATAAAATA
Found at i:88106 original size:17 final size:18
Alignment explanation
Indices: 88074--88107 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
88064 CATATAAGAA
88074 ACATAATTATAATGCAAG
1 ACATAATTATAATGCAAG
88092 ACATAATTA-AATGCAA
1 ACATAATTATAATGCAA
88108 ATTGAAGTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 7 0.44
18 9 0.56
ACGTcount: A:0.53, C:0.12, G:0.09, T:0.26
Consensus pattern (18 bp):
ACATAATTATAATGCAAG
Found at i:88213 original size:16 final size:16
Alignment explanation
Indices: 88177--88219 Score: 54
Period size: 15 Copynumber: 2.7 Consensus size: 16
88167 ATAATGCATG
88177 ACTTAATTAAATGCAA
1 ACTTAATTAAATGCAA
88193 ACTT-ATTAAATTG-AA
1 ACTTAATTAAA-TGCAA
88208 ATCTTAATTAAA
1 A-CTTAATTAAA
88220 AGTCTTTTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
15 9 0.38
16 9 0.38
17 6 0.25
ACGTcount: A:0.49, C:0.09, G:0.05, T:0.37
Consensus pattern (16 bp):
ACTTAATTAAATGCAA
Found at i:101444 original size:27 final size:29
Alignment explanation
Indices: 101414--101477 Score: 82
Period size: 27 Copynumber: 2.3 Consensus size: 29
101404 CAACACTTCA
*
101414 CTTTTTTTTATAA-CTTCAT-ATTTTTTT
1 CTTTTTTTTATAATCTTCATAATTCTTTT
*
101441 CTTTTTTTT-TAATTTTCATAATTCTTTT
1 CTTTTTTTTATAATCTTCATAATTCTTTT
101469 -TTTTTTTTA
1 CTTTTTTTTA
101478 CTTTTCCAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
26 3 0.09
27 22 0.69
28 7 0.22
ACGTcount: A:0.17, C:0.09, G:0.00, T:0.73
Consensus pattern (29 bp):
CTTTTTTTTATAATCTTCATAATTCTTTT
Found at i:101445 original size:26 final size:28
Alignment explanation
Indices: 101415--101477 Score: 78
Period size: 26 Copynumber: 2.3 Consensus size: 28
101405 AACACTTCAC
101415 TTTTTTTTATAA-CTTCAT-ATT-TTTT
1 TTTTTTTTATAATCTTCATAATTCTTTT
* *
101440 TCTTTTTTTTTAATTTTCATAATTCTTTT
1 T-TTTTTTTATAATCTTCATAATTCTTTT
101469 TTTTTTTTA
1 TTTTTTTTA
101478 CTTTTCCAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
25 1 0.03
26 10 0.32
27 5 0.16
28 10 0.32
29 5 0.16
ACGTcount: A:0.17, C:0.08, G:0.00, T:0.75
Consensus pattern (28 bp):
TTTTTTTTATAATCTTCATAATTCTTTT
Found at i:102770 original size:20 final size:20
Alignment explanation
Indices: 102745--102789 Score: 58
Period size: 20 Copynumber: 2.2 Consensus size: 20
102735 TAAATTCACA
102745 TAATTAAAAC-AAGACAC-AAT
1 TAATT-AAACTAAGAC-CTAAT
102765 TAATTAAACTAAGACCTAAT
1 TAATTAAACTAAGACCTAAT
102785 TAATT
1 TAATT
102790 CGGTTAGTAC
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
19 5 0.22
20 18 0.78
ACGTcount: A:0.53, C:0.13, G:0.04, T:0.29
Consensus pattern (20 bp):
TAATTAAACTAAGACCTAAT
Found at i:105022 original size:30 final size:32
Alignment explanation
Indices: 104987--105073 Score: 97
Period size: 33 Copynumber: 2.7 Consensus size: 32
104977 ATAATATGAG
* *
104987 TCTTTAATTATGTCTTG-TTTATTAA-ATGCA
1 TCTTTAATTATGTCTTGCATTATTAATATACA
*
105017 TCTTTAATTAATGTCTTGCATTATTAATCTACA
1 TCTTTAATT-ATGTCTTGCATTATTAATATACA
* *
105050 TCTTTTAATTATGACATGCATTAT
1 TC-TTTAATTATGTCTTGCATTAT
105074 GTGTTCTGCA
Statistics
Matches: 48, Mismatches: 5, Indels: 5
0.83 0.09 0.09
Matches are distributed among these distances:
30 9 0.19
31 8 0.17
32 7 0.15
33 17 0.35
34 7 0.15
ACGTcount: A:0.29, C:0.13, G:0.08, T:0.51
Consensus pattern (32 bp):
TCTTTAATTATGTCTTGCATTATTAATATACA
Found at i:110664 original size:109 final size:109
Alignment explanation
Indices: 110470--110798 Score: 554
Period size: 109 Copynumber: 3.0 Consensus size: 109
110460 TGGATTAAGA
* * *
110470 TTTAAGAGGATATTTGGCTATTTGGTCCAATGAG--AAATCGAAACCCAGCACATTAGGGCACAT
1 TTTAAAAGGATATTTGGCTATTTGGTCGAATGAGAAAAATCGAAACCCAGCACATTAGGGCACGT
*
110533 TTTCTCGAATTTCCAAACGCAAAACATTGCCTTATTTTGAAATT
66 TTTCTCGAATTTCCAAATGCAAAACATTGCCTTATTTTGAAATT
*
110577 TTTAAAAGGATATTTGGCTATTTGGTCGAATGAGAAAAATCGAAACCCAGCACATTAGGGCATGT
1 TTTAAAAGGATATTTGGCTATTTGGTCGAATGAGAAAAATCGAAACCCAGCACATTAGGGCACGT
*
110642 TTTCTCGAATTTCCAAATGCAAAACATTGCCTTATTTTAAAATT
66 TTTCTCGAATTTCCAAATGCAAAACATTGCCTTATTTTGAAATT
*
110686 TTTAAAAGGATATTTGGCTATTTGGTCGAACGAGAAAAATCGAAACCCAGCACATTAGGGCACGT
1 TTTAAAAGGATATTTGGCTATTTGGTCGAATGAGAAAAATCGAAACCCAGCACATTAGGGCACGT
* *
110751 TTTCTAGAATTTCCAAATGCAAAACATTACCTTATTTTGAAATCT
66 TTTCTCGAATTTCCAAATGCAAAACATTGCCTTATTTTGAAAT-T
110796 TTT
1 TTT
110799 TAAACAGATA
Statistics
Matches: 208, Mismatches: 11, Indels: 3
0.94 0.05 0.01
Matches are distributed among these distances:
107 32 0.15
109 172 0.83
110 4 0.02
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Consensus pattern (109 bp):
TTTAAAAGGATATTTGGCTATTTGGTCGAATGAGAAAAATCGAAACCCAGCACATTAGGGCACGT
TTTCTCGAATTTCCAAATGCAAAACATTGCCTTATTTTGAAATT
Found at i:111530 original size:321 final size:321
Alignment explanation
Indices: 110948--111589 Score: 1248
Period size: 321 Copynumber: 2.0 Consensus size: 321
110938 AAATCAAAAC
110948 ATTTTTTCGAAATAATAATGAAAATGTAAATAAAGAAATAAACAAAGAAAATGACCATAAAAATA
1 ATTTTTTCGAAATAATAATGAAAATGTAAATAAAGAAATAAACAAAGAAAATGACCATAAAAATA
111013 TAAAAGATATATATGCGTATATACATAAAATTATGGAAATATGAAAAAATATATGTATGTATATA
66 TAAAAGATATATATGCGTATATACATAAAATTATGGAAATATGAAAAAATATATGTATGTATATA
*
111078 TTTCAAAATTATTGTATAAAATATACATACATATATAAATAAAAGTAGGCATATACATACATATA
131 TTTCAAAATTATTGTATAAAATATACATACATATATAAATAAAAGTAAGCATATACATACATATA
111143 CGTATATATATTAAAATATGTATATGTACATGCATGTATATAAAAATTATAGAAGGTATATAAAA
196 CGTATATATATTAAAATATGTATATGTACATGCATGTATATAAAAATTATAGAAGGTATATAAAA
111208 GTATGTATATATATATGAAAATAGAATACGTACATAGATATATAGATATGCATATAAGTTA
261 GTATGTATATATATATGAAAATAGAATACGTACATAGATATATAGATATGCATATAAGTTA
111269 ATTTTTTCGAAATAATAATGAAAATGTAAATAAAGAAATAAACAAAGAAAATGACCATAAAAATA
1 ATTTTTTCGAAATAATAATGAAAATGTAAATAAAGAAATAAACAAAGAAAATGACCATAAAAATA
111334 TAAAAGATATATATGCGTATATACATAAAATTATGGAAATATGAAAAAATATATGTATGTATATA
66 TAAAAGATATATATGCGTATATACATAAAATTATGGAAATATGAAAAAATATATGTATGTATATA
*
111399 TTTCAAAATTATTGTATAAAATATACATACATATATAAATATAAGTAAGCATATACATACATATA
131 TTTCAAAATTATTGTATAAAATATACATACATATATAAATAAAAGTAAGCATATACATACATATA
111464 CGTATATATATTAAAATATGTATATGTACATGCATGTATATAAAAATTATAGAAGGTATATAAAA
196 CGTATATATATTAAAATATGTATATGTACATGCATGTATATAAAAATTATAGAAGGTATATAAAA
* *
111529 GTGTGTATATATATATGAAAATAGAATATGTACATAGATATATAGATATGCATATAAGTTA
261 GTATGTATATATATATGAAAATAGAATACGTACATAGATATATAGATATGCATATAAGTTA
111590 TAAAATATGA
Statistics
Matches: 317, Mismatches: 4, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
321 317 1.00
ACGTcount: A:0.51, C:0.05, G:0.11, T:0.33
Consensus pattern (321 bp):
ATTTTTTCGAAATAATAATGAAAATGTAAATAAAGAAATAAACAAAGAAAATGACCATAAAAATA
TAAAAGATATATATGCGTATATACATAAAATTATGGAAATATGAAAAAATATATGTATGTATATA
TTTCAAAATTATTGTATAAAATATACATACATATATAAATAAAAGTAAGCATATACATACATATA
CGTATATATATTAAAATATGTATATGTACATGCATGTATATAAAAATTATAGAAGGTATATAAAA
GTATGTATATATATATGAAAATAGAATACGTACATAGATATATAGATATGCATATAAGTTA
Found at i:112961 original size:20 final size:20
Alignment explanation
Indices: 112925--112962 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
112915 TTGAGCTAAA
*
112925 ATTGAGCTGAATTGAGCTCG
1 ATTGAGCTGAATCGAGCTCG
*
112945 ATTGAGCTGGATCGAGCT
1 ATTGAGCTGAATCGAGCT
112963 TCATTTTGCA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.24, C:0.16, G:0.32, T:0.29
Consensus pattern (20 bp):
ATTGAGCTGAATCGAGCTCG
Found at i:117375 original size:11 final size:11
Alignment explanation
Indices: 117359--117397 Score: 60
Period size: 11 Copynumber: 3.5 Consensus size: 11
117349 TGTACAAATT
117359 TTTTTTTCAAA
1 TTTTTTTCAAA
*
117370 TTTTTTTAAAA
1 TTTTTTTCAAA
117381 TTTTTTTCAAAA
1 TTTTTTTC-AAA
117393 TTTTT
1 TTTTT
117398 CACAATCACT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
11 17 0.68
12 8 0.32
ACGTcount: A:0.28, C:0.05, G:0.00, T:0.67
Consensus pattern (11 bp):
TTTTTTTCAAA
Found at i:127316 original size:50 final size:50
Alignment explanation
Indices: 127238--127336 Score: 189
Period size: 50 Copynumber: 2.0 Consensus size: 50
127228 ATTCATTTGT
127238 GAGTTTATTCAACTCTCTAAATTCGTTTAAGACTCAAGCTCACTTATCTG
1 GAGTTTATTCAACTCTCTAAATTCGTTTAAGACTCAAGCTCACTTATCTG
*
127288 GAGTTTATTCAACTCTCTAAATTTGTTTAAGACTCAAGCTCACTTATCT
1 GAGTTTATTCAACTCTCTAAATTCGTTTAAGACTCAAGCTCACTTATCT
127337 AGCATAGCTA
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
50 48 1.00
ACGTcount: A:0.28, C:0.21, G:0.11, T:0.39
Consensus pattern (50 bp):
GAGTTTATTCAACTCTCTAAATTCGTTTAAGACTCAAGCTCACTTATCTG
Found at i:129417 original size:40 final size:39
Alignment explanation
Indices: 129341--129417 Score: 93
Period size: 40 Copynumber: 1.9 Consensus size: 39
129331 GAATTAGTTT
* **
129341 GGGCCTTAGCCCGTTCAGATACAGTCTCAGAAATACATTA
1 GGGCCTTAGCCCATTCAGATACAGAATCAG-AATACATTA
129381 GGGCCTTAGCCCATATCAGATACAGAATGCAG-ATACA
1 GGGCCTTAGCCCAT-TCAGATACAGAAT-CAGAATACA
129418 GTAAATCAGA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
40 18 0.56
41 11 0.34
42 3 0.09
ACGTcount: A:0.32, C:0.25, G:0.21, T:0.22
Consensus pattern (39 bp):
GGGCCTTAGCCCATTCAGATACAGAATCAGAATACATTA
Found at i:134794 original size:11 final size:11
Alignment explanation
Indices: 134770--134802 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
134760 CAGCTCCATG
134770 AGCTCAAA-TC
1 AGCTCAAATTC
134780 AGCTCAAATTC
1 AGCTCAAATTC
*
134791 AGCTCAATTTC
1 AGCTCAAATTC
134802 A
1 A
134803 TTTAGACATT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
10 8 0.38
11 13 0.62
ACGTcount: A:0.36, C:0.27, G:0.09, T:0.27
Consensus pattern (11 bp):
AGCTCAAATTC
Found at i:140459 original size:27 final size:27
Alignment explanation
Indices: 140429--140606 Score: 180
Period size: 27 Copynumber: 6.6 Consensus size: 27
140419 ATATTGAGCC
* *
140429 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAATCAACT
* * *
140456 CGCACACTTAATGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAATCAACT
*
140483 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAATC-AACT
** * *
140511 CGCACACTTAGTGCCGCATGATCAATT
1 CGCACACTTAGTGCTACATAATCAACT
* **
140538 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAATCAACT
* *
140565 CGCACACTTAGTGCAACATAGTCAAAC-
1 CGCACACTTAGTGCTACATAATC-AACT
140592 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
140607 GTACAATTTA
Statistics
Matches: 125, Mismatches: 22, Indels: 8
0.81 0.14 0.05
Matches are distributed among these distances:
27 101 0.81
28 24 0.19
ACGTcount: A:0.31, C:0.29, G:0.14, T:0.26
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAATCAACT
Done.