Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1813
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: 63819
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.34
Found at i:2593 original size:21 final size:22
Alignment explanation
Indices: 2546--2586 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
2536 AAAATTATTT
*
2546 TATTTAAATTTTAATAAAAAAC
1 TATTTAAAATTTAATAAAAAAC
2568 T-TTTAAAATTTAATAAAAA
1 TATTTAAAATTTAATAAAAA
2587 GTATTTATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 17 0.94
22 1 0.06
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.41
Consensus pattern (22 bp):
TATTTAAAATTTAATAAAAAAC
Found at i:2724 original size:15 final size:15
Alignment explanation
Indices: 2688--2729 Score: 50
Period size: 15 Copynumber: 2.7 Consensus size: 15
2678 TATAGATTTT
2688 TATTATTTTAAATAA
1 TATTATTTTAAATAA
*
2703 TAATATTTTATAA-AA
1 TATTATTTTA-AATAA
2718 TATTATTATTAA
1 TATTATT-TTAA
2730 TAAGTTTTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
15 18 0.78
16 5 0.22
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
TATTATTTTAAATAA
Found at i:2834 original size:16 final size:16
Alignment explanation
Indices: 2789--2836 Score: 62
Period size: 15 Copynumber: 2.9 Consensus size: 16
2779 AGATTAGATC
2789 AAAAATTTAAAATATTAA
1 AAAAATTTAAAA-A-TAA
*
2807 AAAAATAT-AAAATAA
1 AAAAATTTAAAAATAA
2822 AAAAATTTAAAAATA
1 AAAAATTTAAAAATA
2837 TAGTGACTAA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
15 10 0.37
16 7 0.26
17 3 0.11
18 7 0.26
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (16 bp):
AAAAATTTAAAAATAA
Found at i:4041 original size:13 final size:13
Alignment explanation
Indices: 4023--4069 Score: 55
Period size: 13 Copynumber: 3.8 Consensus size: 13
4013 TGTAAAGATT
4023 TAAATATATTTAA
1 TAAATATATTTAA
4036 TAAATATATTT-A
1 TAAATATATTTAA
*
4048 -AAATACA-TTAA
1 TAAATATATTTAA
*
4059 TAAAAATATTT
1 TAAATATATTT
4070 TAAAATCAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
10 2 0.07
11 7 0.25
12 6 0.21
13 13 0.46
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (13 bp):
TAAATATATTTAA
Found at i:11559 original size:6 final size:6
Alignment explanation
Indices: 11548--11577 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
11538 AAATAAATTA
11548 TATATT TATATT TATATT TATATT TATATT
1 TATATT TATATT TATATT TATATT TATATT
11578 AATTATATTC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (6 bp):
TATATT
Found at i:12131 original size:20 final size:19
Alignment explanation
Indices: 12107--12155 Score: 71
Period size: 19 Copynumber: 2.5 Consensus size: 19
12097 CAGATTAATT
12107 ATATTTATTTAATATTAAAA
1 ATATTT-TTTAATATTAAAA
* *
12127 TTATTTTTAAATATTAAAA
1 ATATTTTTTAATATTAAAA
12146 ATATTTTTTA
1 ATATTTTTTA
12156 TTAATTTTAA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
19 20 0.80
20 5 0.20
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (19 bp):
ATATTTTTTAATATTAAAA
Found at i:12135 original size:22 final size:22
Alignment explanation
Indices: 12103--12166 Score: 64
Period size: 22 Copynumber: 3.0 Consensus size: 22
12093 ATTTCAGATT
*
12103 AATTATATTTATTTAATATTAA
1 AATTATTTTTATTTAATATTAA
12125 AATTATTTTTA---AATATTAA
1 AATTATTTTTATTTAATATTAA
* *
12144 AAATATTTTT-TATTAATTTTAA
1 AATTATTTTTAT-TTAATATTAA
12166 A
1 A
12167 TTAGATTTTT
Statistics
Matches: 35, Mismatches: 3, Indels: 8
0.76 0.07 0.17
Matches are distributed among these distances:
19 17 0.49
22 18 0.51
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (22 bp):
AATTATTTTTATTTAATATTAA
Found at i:12236 original size:14 final size:14
Alignment explanation
Indices: 12205--12234 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
12195 TTTCAAATCT
12205 AAATAAAAAGTAAA
1 AAATAAAAAGTAAA
12219 AAATAAAAA-TAAA
1 AAATAAAAAGTAAA
12232 AAA
1 AAA
12235 ATCTTGTTCC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 7 0.44
14 9 0.56
ACGTcount: A:0.83, C:0.00, G:0.03, T:0.13
Consensus pattern (14 bp):
AAATAAAAAGTAAA
Found at i:14835 original size:337 final size:337
Alignment explanation
Indices: 14220--14893 Score: 1339
Period size: 337 Copynumber: 2.0 Consensus size: 337
14210 CATTTATTAA
14220 ACGGCAGGAAAAAAGAAAAAACTAAGATTGGCTTCCAGTTCTAAGTTCAATGTTTGTTCAAAGTG
1 ACGGCAGGAAAAAAGAAAAAACTAAGATTGGCTTCCAGTTCTAAGTTCAATGTTTGTTCAAAGTG
14285 TAATTAATAAATTGATTTGTTTAAATTCAGCAAAAATAGTAAAAAAGAAAATTATAAATTATTAA
66 TAATTAATAAATTGATTTGTTTAAATTCAGCAAAAATAGTAAAAAAGAAAATTATAAATTATTAA
14350 TTAAATAATTTTTAATTAATGATTTTATTTAACAATATTTATATGGTTAAGGATACAAAATATTT
131 TTAAATAATTTTTAATTAATGATTTTATTTAACAATATTTATATGGTTAAGGATACAAAATATTT
14415 TTTTAAAAAAATATTTTTTATATTTAATTAATTATTTTTATAAAATTTAAAAAATAATATAATAA
196 TTTTAAAAAAATATTTTTTATATTTAATTAATTATTTTTATAAAATTTAAAAAATAATATAATAA
14480 TTATATATATATATATATATTTAAACTTTAACATGTGCTTATCCATTAACTTTTCCCTTAATGAA
261 TTATATATATATATATATATTTAAACTTTAACATGTGCTTATCCATTAACTTTTCCCTTAATGAA
14545 TATGTGGAATGT
326 TATGTGGAATGT
14557 ACGGCAGGAAAAAAGAAAAAACTAAGATTGGCTTCCAGTTCTAAGTTCAATGTTTGTTCAAAGTG
1 ACGGCAGGAAAAAAGAAAAAACTAAGATTGGCTTCCAGTTCTAAGTTCAATGTTTGTTCAAAGTG
14622 TAATTAATAAATTGATTTGTTTAAATTCAGCAAAAATAGTAAAAAAGAAAATTATAAATTATTAA
66 TAATTAATAAATTGATTTGTTTAAATTCAGCAAAAATAGTAAAAAAGAAAATTATAAATTATTAA
14687 TTAAATAATTTTTAATTAATGATTTTATTTAACAATATTTATATGGTTAAGGATACAAAATATTT
131 TTAAATAATTTTTAATTAATGATTTTATTTAACAATATTTATATGGTTAAGGATACAAAATATTT
*
14752 TTTTTAAAAAATATTTTTTATATTTAATTAATTATTTTTATAAAATTTAAAAAATAATATAATAA
196 TTTTAAAAAAATATTTTTTATATTTAATTAATTATTTTTATAAAATTTAAAAAATAATATAATAA
14817 TTATATATATATATATATATTTAAACTTTAACATGTGCTTATCCATTAACTTTTCCCTTAATGAA
261 TTATATATATATATATATATTTAAACTTTAACATGTGCTTATCCATTAACTTTTCCCTTAATGAA
14882 TATGTGGAATGT
326 TATGTGGAATGT
14894 TCCAGTTGTT
Statistics
Matches: 336, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
337 336 1.00
ACGTcount: A:0.43, C:0.07, G:0.09, T:0.41
Consensus pattern (337 bp):
ACGGCAGGAAAAAAGAAAAAACTAAGATTGGCTTCCAGTTCTAAGTTCAATGTTTGTTCAAAGTG
TAATTAATAAATTGATTTGTTTAAATTCAGCAAAAATAGTAAAAAAGAAAATTATAAATTATTAA
TTAAATAATTTTTAATTAATGATTTTATTTAACAATATTTATATGGTTAAGGATACAAAATATTT
TTTTAAAAAAATATTTTTTATATTTAATTAATTATTTTTATAAAATTTAAAAAATAATATAATAA
TTATATATATATATATATATTTAAACTTTAACATGTGCTTATCCATTAACTTTTCCCTTAATGAA
TATGTGGAATGT
Found at i:17651 original size:5 final size:6
Alignment explanation
Indices: 17636--17661 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
17626 TCAACTAGAA
17636 AAAAAG AAAAAG AAAAAG AAAAAG AA
1 AAAAAG AAAAAG AAAAAG AAAAAG AA
17662 GAACCTCAAG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (6 bp):
AAAAAG
Found at i:21535 original size:105 final size:104
Alignment explanation
Indices: 21412--21793 Score: 414
Period size: 105 Copynumber: 3.6 Consensus size: 104
21402 GAAATAACGA
* * * * *
21412 GGTTGGAGTATCCTCGATTGTGAAAAATTGGTATTTTTGGAAATAAAATCGGAATTGGAGTATCC
1 GGTTGGAGTATCCCCGATTATGAAAAATCGATA-TTTTGAAAATAAAATCGGAATTGGAGTATCC
21477 CCGATTAAAGGAGAAATTGGTGTTGTGAAAATAAAACCGG
65 CCGATTAAAGGAGAAATTGGTGTTGTGAAAATAAAACCGG
* **
21517 GGTTGGAGTATCCCCGATTATGAAAAATCGATATTTTGAAAATAAAGTCGGGGTTGGAGTATCCC
1 GGTTGGAGTATCCCCGATTATGAAAAATCGATATTTTGAAAATAAAATCGGAATTGGAGTAT-CC
* * * * ** ** *
21582 CTCAGAAATAACGG-G--GTTGGAGTATCCCCGATGAT-TAA-CGG
65 C-C-G-ATTAAAGGAGAAATTGGTGT-T--GTGAAAATAAAACCGG
* * * * * *
21623 GGTTGGAGTGTCCCCGATTGTGAAGAATTGGTATTTTTGGAAATAAAATCGGAATTGGAGTATCC
1 GGTTGGAGTATCCCCGATTATGAAAAATCGATA-TTTTGAAAATAAAATCGGAATTGGAGTATCC
21688 CCGATTAAAGGAGAAATTGGTGTTGTGAAAATAAAACCGG
65 CCGATTAAAGGAGAAATTGGTGTTGTGAAAATAAAACCGG
* **
21728 GGTTGGAGTATCCCCGATTATGAAAAATCGATATTTTGAAAATAAAGTCGGGGTTGGAGTATCCC
1 GGTTGGAGTATCCCCGATTATGAAAAATCGATATTTTGAAAATAAAATCGGAATTGGAGTATCCC
21793 C
66 C
21794 TCAGAAATAA
Statistics
Matches: 220, Mismatches: 44, Indels: 27
0.76 0.15 0.09
Matches are distributed among these distances:
103 10 0.05
104 58 0.26
105 71 0.32
106 42 0.19
107 29 0.13
108 10 0.05
ACGTcount: A:0.32, C:0.13, G:0.27, T:0.28
Consensus pattern (104 bp):
GGTTGGAGTATCCCCGATTATGAAAAATCGATATTTTGAAAATAAAATCGGAATTGGAGTATCCC
CGATTAAAGGAGAAATTGGTGTTGTGAAAATAAAACCGG
Found at i:21572 original size:51 final size:51
Alignment explanation
Indices: 21412--21793 Score: 288
Period size: 51 Copynumber: 7.3 Consensus size: 51
21402 GAAATAACGA
* * *
21412 GGTTGGAGTATCCTCGATTGTGAAAAATTGGTATTTTTGGAAATAAAATCGG
1 GGTTGGAGTATCCCCGATTATGAAAAATTGGTA-TTTTGAAAATAAAATCGG
** * * * * *
21464 AATTGGAGTATCCCCGATTAAAGGAGAAATTGGTGTTGTGAAAATAAAACCGG
1 GGTTGGAGTATCCCCGATT--ATGAAAAATTGGTATTTTGAAAATAAAATCGG
* * *
21517 GGTTGGAGTATCCCCGATTATGAAAAATCGATATTTTGAAAATAAAGTCGG
1 GGTTGGAGTATCCCCGATTATGAAAAATTGGTATTTTGAAAATAAAATCGG
* *** ** *
21568 GGTTGGAGTATCCCC--TCA-GAAATAACGGGGTTGGAGTATCCCCGATGAT-TAA-CGG
1 GGTTGGAGTATCCCCGATTATGAAA-AA-----TT-G-GTAT-TTTGAAAATAAAATCGG
* * * *
21623 GGTTGGAGTGTCCCCGATTGTGAAGAATTGGTATTTTTGGAAATAAAATCGG
1 GGTTGGAGTATCCCCGATTATGAAAAATTGGTA-TTTTGAAAATAAAATCGG
** * * * * *
21675 AATTGGAGTATCCCCGATTAAAGGAGAAATTGGTGTTGTGAAAATAAAACCGG
1 GGTTGGAGTATCCCCGATT--ATGAAAAATTGGTATTTTGAAAATAAAATCGG
* * *
21728 GGTTGGAGTATCCCCGATTATGAAAAATCGATATTTTGAAAATAAAGTCGG
1 GGTTGGAGTATCCCCGATTATGAAAAATTGGTATTTTGAAAATAAAATCGG
21779 GGTTGGAGTATCCCC
1 GGTTGGAGTATCCCC
21794 TCAGAAATAA
Statistics
Matches: 249, Mismatches: 62, Indels: 39
0.71 0.18 0.11
Matches are distributed among these distances:
48 4 0.02
49 4 0.02
50 6 0.02
51 82 0.33
52 37 0.15
53 64 0.26
54 20 0.08
55 18 0.07
56 4 0.02
57 7 0.03
58 3 0.01
ACGTcount: A:0.32, C:0.13, G:0.27, T:0.28
Consensus pattern (51 bp):
GGTTGGAGTATCCCCGATTATGAAAAATTGGTATTTTGAAAATAAAATCGG
Found at i:21628 original size:27 final size:28
Alignment explanation
Indices: 21565--21640 Score: 102
Period size: 27 Copynumber: 2.8 Consensus size: 28
21555 AAAATAAAGT
*
21565 CGGGGTTGGAGTATCCCCTCA-GAAATAA
1 CGGGGTTGGAGTATCCCC-GATGAAATAA
*
21593 CGGGGTTGGAGTATCCCCGATG-ATTAA
1 CGGGGTTGGAGTATCCCCGATGAAATAA
*
21620 CGGGGTTGGAGTGTCCCCGAT
1 CGGGGTTGGAGTATCCCCGAT
21641 TGTGAAGAAT
Statistics
Matches: 44, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
27 25 0.57
28 19 0.43
ACGTcount: A:0.21, C:0.21, G:0.34, T:0.24
Consensus pattern (28 bp):
CGGGGTTGGAGTATCCCCGATGAAATAA
Found at i:21658 original size:106 final size:106
Alignment explanation
Indices: 21369--21901 Score: 410
Period size: 105 Copynumber: 5.0 Consensus size: 106
21359 TGGAGTGTTT
* * * * * *
21369 CCTCGGAAGTAACGGGGTTGGAGTATCCCCGATGAAATAACGAGGTTGGAGTATCCTCGATTGTG
1 CCTCAGAAATAACGGGGTTGGAGTATCCCCGATG-ATTAACGGGGTTGGAGTATCCCCGATTATG
* * * *
21434 AAAAATTGGTATTTTTGGAAATAAAATCGGAATTGGAGTAT-C
65 AAAAATCGATA-TTTTGAAAATAAAATCGGAGTTGGAGTATCC
* * * * ** ** *
21476 CC-C-G-ATTAAAGGAGAAATTGGTGT-T--GTGAAAATAAAACCGGGGTTGGAGTATCCCCGAT
1 CCTCAGAAATAACGG-G--GTTGGAGTATCCCCGATGAT-TAA-CGGGGTTGGAGTATCCCCGAT
* *
21535 TATGAAAAATCGATATTTTGAAAATAAAGTCGGGGTTGGAGTATCC
61 TATGAAAAATCGATATTTTGAAAATAAAATCGGAGTTGGAGTATCC
* *
21581 CCTCAGAAATAACGGGGTTGGAGTATCCCCGATGATTAACGGGGTTGGAGTGTCCCCGATTGTGA
1 CCTCAGAAATAACGGGGTTGGAGTATCCCCGATGATTAACGGGGTTGGAGTATCCCCGATTATGA
* * * * *
21646 AGAATTGGTATTTTTGGAAATAAAATCGGAATTGGAGTAT-C
66 AAAATCGATA-TTTTGAAAATAAAATCGGAGTTGGAGTATCC
* * * * ** ** *
21687 CC-C-G-ATTAAAGGAGAAATTGGTGT-T--GTGAAAATAAAACCGGGGTTGGAGTATCCCCGAT
1 CCTCAGAAATAACGG-G--GTTGGAGTATCCCCGATGAT-TAA-CGGGGTTGGAGTATCCCCGAT
* *
21746 TATGAAAAATCGATATTTTGAAAATAAAGTCGGGGTTGGAGTATCC
61 TATGAAAAATCGATATTTTGAAAATAAAATCGGAGTTGGAGTATCC
* *
21792 CCTCAGAAATAACGGGGTTGGAGTATCCCCGATGATTAACGGGGTTGGAGTGTCCCCGATTGTGA
1 CCTCAGAAATAACGGGGTTGGAGTATCCCCGATGATTAACGGGGTTGGAGTATCCCCGATTATGA
* * * *
21857 AGAAATTGGTGTTTTTTTGGAAATAAAATCGGAGTTGGAGTATCC
66 A-AAA-T--CGATATTTTGAAAATAAAATCGGAGTTGGAGTATCC
21902 TCGATTATAG
Statistics
Matches: 325, Mismatches: 72, Indels: 55
0.72 0.16 0.12
Matches are distributed among these distances:
103 11 0.03
104 64 0.20
105 84 0.26
106 71 0.22
107 44 0.14
108 21 0.06
110 30 0.09
ACGTcount: A:0.31, C:0.13, G:0.28, T:0.28
Consensus pattern (106 bp):
CCTCAGAAATAACGGGGTTGGAGTATCCCCGATGATTAACGGGGTTGGAGTATCCCCGATTATGA
AAAATCGATATTTTGAAAATAAAATCGGAGTTGGAGTATCC
Found at i:21721 original size:211 final size:211
Alignment explanation
Indices: 21369--21958 Score: 959
Period size: 211 Copynumber: 2.8 Consensus size: 211
21359 TGGAGTGTTT
* * * * * *
21369 CCTCGGAAGTAACGGGGTTGGAGTATCCCCGATGAAATAACGAGGTTGGAGTATCCTCGATTGTG
1 CCTCAGAAATAACGGGGTTGGAGTATCCCCGATG-ATTAACGGGGTTGGAGTGTCCCCGATTGTG
*
21434 AAAAATTGGTATTTTTGGAAATAAAATCGGAATTGGAGTATCCCCGATTAAAGGAGAAATTGGTG
65 AAGAATTGGTATTTTTGGAAATAAAATCGGAATTGGAGTATCCCCGATTAAAGGAGAAATTGGTG
21499 TTGTGAAAATAAAACCGGGGTTGGAGTATCCCCGATTATGAAAAATCGATATTTTGAAAATAAAG
130 TTGTGAAAATAAAACCGGGGTTGGAGTATCCCCGATTATGAAAAATCGATATTTTGAAAATAAAG
21564 TCGGGGTTGGAGTATCC
195 TCGGGGTTGGAGTATCC
21581 CCTCAGAAATAACGGGGTTGGAGTATCCCCGATGATTAACGGGGTTGGAGTGTCCCCGATTGTGA
1 CCTCAGAAATAACGGGGTTGGAGTATCCCCGATGATTAACGGGGTTGGAGTGTCCCCGATTGTGA
21646 AGAATTGGTATTTTTGGAAATAAAATCGGAATTGGAGTATCCCCGATTAAAGGAGAAATTGGTGT
66 AGAATTGGTATTTTTGGAAATAAAATCGGAATTGGAGTATCCCCGATTAAAGGAGAAATTGGTGT
21711 TGTGAAAATAAAACCGGGGTTGGAGTATCCCCGATTATGAAAAATCGATATTTTGAAAATAAAGT
131 TGTGAAAATAAAACCGGGGTTGGAGTATCCCCGATTATGAAAAATCGATATTTTGAAAATAAAGT
21776 CGGGGTTGGAGTATCC
196 CGGGGTTGGAGTATCC
21792 CCTCAGAAATAACGGGGTTGGAGTATCCCCGATGATTAACGGGGTTGGAGTGTCCCCGATTGTGA
1 CCTCAGAAATAACGGGGTTGGAGTATCCCCGATGATTAACGGGGTTGGAGTGTCCCCGATTGTGA
* * * * **
21857 AGAAATTGGTGTTTTTTTGGAAATAAAATCGGAGTTGGAGTATCCTCGATTATA-GA-AAATTAA
66 AG-AATT-G-GTATTTTTGGAAATAAAATCGGAATTGGAGTATCCCCGATTAAAGGAGAAATTGG
* * * * * *
21920 TGTTTTGAAAGTAAAATCGGAGTTGGAATATCCTCGATT
128 TGTTGTGAAAATAAAACCGGGGTTGGAGTATCCCCGATT
21959 GTGGAGAATT
Statistics
Matches: 356, Mismatches: 19, Indels: 6
0.93 0.05 0.02
Matches are distributed among these distances:
211 239 0.67
212 74 0.21
213 3 0.01
214 40 0.11
ACGTcount: A:0.31, C:0.13, G:0.27, T:0.28
Consensus pattern (211 bp):
CCTCAGAAATAACGGGGTTGGAGTATCCCCGATGATTAACGGGGTTGGAGTGTCCCCGATTGTGA
AGAATTGGTATTTTTGGAAATAAAATCGGAATTGGAGTATCCCCGATTAAAGGAGAAATTGGTGT
TGTGAAAATAAAACCGGGGTTGGAGTATCCCCGATTATGAAAAATCGATATTTTGAAAATAAAGT
CGGGGTTGGAGTATCC
Found at i:21839 original size:27 final size:28
Alignment explanation
Indices: 21776--21851 Score: 102
Period size: 27 Copynumber: 2.8 Consensus size: 28
21766 AAAATAAAGT
*
21776 CGGGGTTGGAGTATCCCCTCA-GAAATAA
1 CGGGGTTGGAGTATCCCC-GATGAAATAA
*
21804 CGGGGTTGGAGTATCCCCGATG-ATTAA
1 CGGGGTTGGAGTATCCCCGATGAAATAA
*
21831 CGGGGTTGGAGTGTCCCCGAT
1 CGGGGTTGGAGTATCCCCGAT
21852 TGTGAAGAAA
Statistics
Matches: 44, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
27 25 0.57
28 19 0.43
ACGTcount: A:0.21, C:0.21, G:0.34, T:0.24
Consensus pattern (28 bp):
CGGGGTTGGAGTATCCCCGATGAAATAA
Found at i:24334 original size:13 final size:13
Alignment explanation
Indices: 24316--24341 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
24306 ACAAAGATCC
24316 ATGTATCGATACA
1 ATGTATCGATACA
24329 ATGTATCGATACA
1 ATGTATCGATACA
24342 CAGAAAAATG
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:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:24337 original size:33 final size:33
Alignment explanation
Indices: 24295--24361 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
24285 AAAATTTCCA
***
24295 AATGTATCGATACAAAGATCCATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
*
24328 AATGTATCGATACACAGAAAAATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
24361 A
1 A
24362 TTTCCTTGGC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.43, C:0.16, G:0.15, T:0.25
Consensus pattern (33 bp):
AATGTATCGATACAAAGAAAAATGTATCGATAC
Found at i:24405 original size:19 final size:18
Alignment explanation
Indices: 24381--24448 Score: 83
Period size: 19 Copynumber: 3.9 Consensus size: 18
24371 CAGTAGCTAA
24381 TTATGTATCGATACAATAC
1 TTATGTATCGATACAA-AC
24400 TTATGTATCGATAC--A-
1 TTATGTATCGATACAAAC
24415 -T-TGTATCGATACAAAAC
1 TTATGTATCGATAC-AAAC
24432 TTATGTATCGATACAAA
1 TTATGTATCGATACAAA
24449 TTGTTGAATT
Statistics
Matches: 43, Mismatches: 0, Indels: 13
0.77 0.00 0.23
Matches are distributed among these distances:
13 11 0.26
14 1 0.02
16 2 0.05
18 4 0.09
19 25 0.58
ACGTcount: A:0.38, C:0.15, G:0.12, T:0.35
Consensus pattern (18 bp):
TTATGTATCGATACAAAC
Found at i:24421 original size:13 final size:13
Alignment explanation
Indices: 24403--24427 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
24393 ACAATACTTA
24403 TGTATCGATACAT
1 TGTATCGATACAT
24416 TGTATCGATACA
1 TGTATCGATACA
24428 AAACTTATGT
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:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:24425 original size:32 final size:32
Alignment explanation
Indices: 24384--24446 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
24374 TAGCTAATTA
*
24384 TGTATCGATACAATACTTATGTATCGATACAT
1 TGTATCGATACAAAACTTATGTATCGATACAT
24416 TGTATCGATACAAAACTTATGTATCGATACA
1 TGTATCGATACAAAACTTATGTATCGATACA
24447 AATTGTTGAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.37, C:0.16, G:0.13, T:0.35
Consensus pattern (32 bp):
TGTATCGATACAAAACTTATGTATCGATACAT
Found at i:24528 original size:21 final size:21
Alignment explanation
Indices: 24504--24560 Score: 105
Period size: 21 Copynumber: 2.7 Consensus size: 21
24494 CATTTGTAGG
24504 ATGTATCGATACATTCCACAA
1 ATGTATCGATACATTCCACAA
*
24525 ATGTATCGATACATTCTACAA
1 ATGTATCGATACATTCCACAA
24546 ATGTATCGATACATT
1 ATGTATCGATACATT
24561 TAAATTTTTT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.37, C:0.19, G:0.11, T:0.33
Consensus pattern (21 bp):
ATGTATCGATACATTCCACAA
Found at i:25685 original size:22 final size:21
Alignment explanation
Indices: 25668--25725 Score: 64
Period size: 21 Copynumber: 2.8 Consensus size: 21
25658 TTAAAAGTTG
25668 CATTCTTTTATCCAAAAAATA
1 CATTCTTTTATCCAAAAAATA
* ** *
25689 CATTCTTTTGTCCAACCATTA
1 CATTCTTTTATCCAAAAAATA
25710 CA-TCATTTTATCCAAA
1 CATTC-TTTTATCCAAA
25726 TATACCTTTT
Statistics
Matches: 30, Mismatches: 6, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
20 2 0.07
21 28 0.93
ACGTcount: A:0.34, C:0.24, G:0.02, T:0.40
Consensus pattern (21 bp):
CATTCTTTTATCCAAAAAATA
Found at i:32854 original size:22 final size:23
Alignment explanation
Indices: 32820--32864 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 23
32810 TCGAAAAAAA
32820 AAAAAAAAAAAAG-GGGCTTTCC
1 AAAAAAAAAAAAGTGGGCTTTCC
** *
32842 AAAAAAACCAAAGTGGGTTTTCC
1 AAAAAAAAAAAAGTGGGCTTTCC
32865 GATTGAGTGG
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
22 11 0.58
23 8 0.42
ACGTcount: A:0.49, C:0.16, G:0.18, T:0.18
Consensus pattern (23 bp):
AAAAAAAAAAAAGTGGGCTTTCC
Found at i:33258 original size:11 final size:11
Alignment explanation
Indices: 33220--33260 Score: 55
Period size: 11 Copynumber: 3.5 Consensus size: 11
33210 AAATTTAGGT
33220 AAAAAAGAAAG
1 AAAAAAGAAAG
*
33231 AAAGAAGATGAAG
1 AAAAAAGA--AAG
33244 AAAAAAGAAAG
1 AAAAAAGAAAG
33255 AAAAAA
1 AAAAAA
33261 ATATGAAATG
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
11 16 0.62
13 10 0.38
ACGTcount: A:0.78, C:0.00, G:0.20, T:0.02
Consensus pattern (11 bp):
AAAAAAGAAAG
Found at i:40040 original size:17 final size:17
Alignment explanation
Indices: 40020--40053 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
40010 ACCTAATCCT
40020 AAAAAAAAAAAAAAACC
1 AAAAAAAAAAAAAAACC
40037 AAAAAAAAAAAAAAACC
1 AAAAAAAAAAAAAAACC
40054 TTTTCACCCT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.88, C:0.12, G:0.00, T:0.00
Consensus pattern (17 bp):
AAAAAAAAAAAAAAACC
Found at i:41131 original size:30 final size:31
Alignment explanation
Indices: 41074--41131 Score: 82
Period size: 30 Copynumber: 1.9 Consensus size: 31
41064 TACTGTGAAC
* *
41074 CTTTTCAAAGTCCACGACTCAGTGGCATTTT
1 CTTTTCAAAGTCCACAACTCAGGGGCATTTT
*
41105 CTTTT-AAAGTCCACAACTCTGGGGCAT
1 CTTTTCAAAGTCCACAACTCAGGGGCAT
41132 CCTTTAAGTC
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
30 19 0.79
31 5 0.21
ACGTcount: A:0.24, C:0.26, G:0.17, T:0.33
Consensus pattern (31 bp):
CTTTTCAAAGTCCACAACTCAGGGGCATTTT
Found at i:41191 original size:27 final size:27
Alignment explanation
Indices: 41150--42248 Score: 1890
Period size: 27 Copynumber: 41.1 Consensus size: 27
41140 TCACACTTTG
41150 CCTTTTAAAGTCCACAACTCCGTGGCAC
1 CCTTTT-AAGTCCACAACTCCGTGGCAC
*
41178 CCTTTTAAGTCCACAACT-CTTGGCAC
1 CCTTTTAAGTCCACAACTCCGTGGCAC
*
41204 CCTTTTAAAGTCCACAACTCCGTGGTAC
1 CCTTTT-AAGTCCACAACTCCGTGGCAC
*
41232 CTCTTTTAAGTCCACAACTCTGTGGCAC
1 C-CTTTTAAGTCCACAACTCCGTGGCAC
*
41260 CCTTTTAAGTCCACAACTCCGTGGCAT
1 CCTTTTAAGTCCACAACTCCGTGGCAC
* *
41287 TCTTTTAAGTCCACAACTCTGTGGCAC
1 CCTTTTAAGTCCACAACTCCGTGGCAC
41314 CCTTTTAAGTCCACAACTCCGTGGCA-
1 CCTTTTAAGTCCACAACTCCGTGGCAC
41340 CCTTTTAAGTCCACAACTCCGTGGC-C
1 CCTTTTAAGTCCACAACTCCGTGGCAC
41366 CCTTTTAAGTCCACAACTCCGTGGCAC
1 CCTTTTAAGTCCACAACTCCGTGGCAC
41393 CCTTTTAAGTCCACAACTCCGTGGCAC
1 CCTTTTAAGTCCACAACTCCGTGGCAC
41420 CCTTTTAAGTCCACAACTCCGTGGCAC
1 CCTTTTAAGTCCACAACTCCGTGGCAC
41447 CCTTTTAAGTCCACAACTCCGTGGCATC
1 CCTTTTAAGTCCACAACTCCGTGGCA-C
41475 CCTTTTAAGTCCACAACTCCGTGGC-C
1 CCTTTTAAGTCCACAACTCCGTGGCAC
41501 CCTTTTAAGTCCACAACTCCGTGGCAC
1 CCTTTTAAGTCCACAACTCCGTGGCAC
41528 CCTTTTAAGTCCACAACTCCGTGGCA-
1 CCTTTTAAGTCCACAACTCCGTGGCAC
41554 CCTTTTAAGTCCAC-ACTCCGTGGCAC
1 CCTTTTAAGTCCACAACTCCGTGGCAC
41580 CCTTTTAAGTCCACAACTCCGTGGCAC
1 CCTTTTAAGTCCACAACTCCGTGGCAC
41607 CCTTTTAAGTCCACAACTCCGTGGCAC
1 CCTTTTAAGTCCACAACTCCGTGGCAC
41634 CCTTTTAAGTCCACAACTCCGTGGCAC
1 CCTTTTAAGTCCACAACTCCGTGGCAC
41661 CCTTTTAAGTCCACAACTCCGTGGCAC
1 CCTTTTAAGTCCACAACTCCGTGGCAC
41688 CCTTTTAAGT-CACAACTCCGTGGCAAC
1 CCTTTTAAGTCCACAACTCCGTGGC-AC
41715 CCTTTTAAGTCCACAACTCCGTGGCAC
1 CCTTTTAAGTCCACAACTCCGTGGCAC
41742 CCTTTTAAGTCCACAACTCCGTGGCAC
1 CCTTTTAAGTCCACAACTCCGTGGCAC
41769 CCTTTTAAGTCCACAACT-CGTGGCAC
1 CCTTTTAAGTCCACAACTCCGTGGCAC
41795 CCTTTTAAGT-CACAACTCCGTGGCAC
1 CCTTTTAAGTCCACAACTCCGTGGCAC
41821 CCTTTTAAGTCCACAA--CCGTGGCAC
1 CCTTTTAAGTCCACAACTCCGTGGCAC
41846 CCTTTTAAGTCCACAA--CCGTGGCAC
1 CCTTTTAAGTCCACAACTCCGTGGCAC
*
41871 TCTTTTAAGTCCACAACT--GTGGCAC
1 CCTTTTAAGTCCACAACTCCGTGGCAC
41896 CCTTTTAAGTCCACAACTCCGTGGCA-
1 CCTTTTAAGTCCACAACTCCGTGGCAC
41922 CCTTTTAAGTCCACAACT-CGTGGCAC
1 CCTTTTAAGTCCACAACTCCGTGGCAC
41948 CCTTTTAAGTCCACAACTCCGTGGCAC
1 CCTTTTAAGTCCACAACTCCGTGGCAC
41975 CCTTTTAAGTCCACAACTCCGTGGCATC
1 CCTTTTAAGTCCACAACTCCGTGGCA-C
*
42003 CCTTTTAAGTTCACAACTCCGTGGCAC
1 CCTTTTAAGTCCACAACTCCGTGGCAC
*
42030 CCTTTTAGGTCCACAACTCCGTGGCAC
1 CCTTTTAAGTCCACAACTCCGTGGCAC
42057 CCTTTTAAGTCCACAACTCCGTGGCAC
1 CCTTTTAAGTCCACAACTCCGTGGCAC
* *
42084 TCTTTTAAGTCCACAACTCTGTGGCAC
1 CCTTTTAAGTCCACAACTCCGTGGCAC
42111 CCTTTTAAAGTCCACAACTCCGTGGCAC
1 CCTTTT-AAGTCCACAACTCCGTGGCAC
42139 CCTTTTAAGTCCACAACTCCGTGGCAC
1 CCTTTTAAGTCCACAACTCCGTGGCAC
42166 CCTTTTAAGTCCACAACTCCGTGGCAC
1 CCTTTTAAGTCCACAACTCCGTGGCAC
*
42193 CCTTTTAAGTCCACAACTCCGTGGCAT
1 CCTTTTAAGTCCACAACTCCGTGGCAC
* *
42220 CCTTTTAAATCCACAACTCTGTGGCAC
1 CCTTTTAAGTCCACAACTCCGTGGCAC
42247 CC
1 CC
42249 ATTCCAAAGC
Statistics
Matches: 1024, Mismatches: 26, Indels: 43
0.94 0.02 0.04
Matches are distributed among these distances:
25 98 0.10
26 203 0.20
27 593 0.58
28 125 0.12
29 5 0.00
ACGTcount: A:0.22, C:0.35, G:0.15, T:0.27
Consensus pattern (27 bp):
CCTTTTAAGTCCACAACTCCGTGGCAC
Found at i:42289 original size:32 final size:32
Alignment explanation
Indices: 42231--43337 Score: 1358
Period size: 32 Copynumber: 35.8 Consensus size: 32
42221 CTTTTAAATC
* * *
42231 CACAACTCTGTGGC-ACCCATTCCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
42262 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
42294 CACAAGTCGGTGGCAACCCATTTCAAAG-CC-
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
* * * *
42324 CACAAGTCAGTGGC-A-TCTTTTCAAAGTCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
* * *
42354 CACAAGTTGGTGGC-ATCC-TTTCAAAGTCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
* *
42384 CACAAGTTGGTGGC-ATCC-TTTCAAAG-CC-
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
* *
42412 CACAAGTCAGTGGC-ATCC-TTTCAAAG-CC-
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
*
42440 CACAAGTCGGTGGCAATCCATTTCAAAG-CC-
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
*
42470 CACAAGT--GTGGC-A-TCA-TTCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
*
42497 CACAAGTCGGTGGCAACCCATTCCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
*
42529 CACAAGTCGGTGGACAAACCCATTCCAAAAGGCCCA
1 CACAAGTCGGTGG-C-AACCCATTTC-AAA-GCCCA
42565 CACAAGTC-GTGGCAACCCA-TTCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
* *
42595 CACAACGTCCGGT-GCAACCCA-TCCAAAGGCCA
1 CACAA-GT-CGGTGGCAACCCATTTCAAAGCCCA
*
42627 CAAAAGTCGGTGGCAA-CCA-TTCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
*
42657 CACAAGTCGGTGGCAACCCATTTCAAGGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
42689 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
*
42721 CACAAGTCGGTGGCAACCCATTCCAAAG-CCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
42752 CACAAGTCGGTGGCAACCCA-TTCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
42783 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
* *
42815 CATAAGTCGGTGGCAACCCATTCCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
42847 CACAAGTCTGGTGGCAA-CCATTTCAAAGCCCA
1 CACAAGTC-GGTGGCAACCCATTTCAAAGCCCA
* * *
42879 CACAAGTC-GTGGC-A-TCTTTTCAAAGTCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
* *
42908 CACAAGTTGGTGGC-ATCC-TTTCAAAG-CC-
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
* *
42936 CACAAGTCAGTGGC-ATCC-TTTCAAAG-CC-
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
*
42964 CACAAGTCGGTGGCAATCCATTTCAAAG--C-
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
** * *
42993 CACAAGTTAGTGGC-A-TC-TTCCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
43022 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
*
43054 CACAAGTCGGTGGCAACCCATTCCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
43086 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
43118 CACAAGTCGGTGGC-ACCCATTTTCAAAGCCCA
1 CACAAGTCGGTGGCAACCCA-TTTCAAAGCCCA
*
43150 CATAAGTCGGTGGCAAACCCATTTCAAAGCCCA
1 CACAAGTCGGTGGC-AACCCATTTCAAAGCCCA
43183 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
43215 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
* *
43247 CACAAGTCGGTGGCGACCCTTTTCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
* *
43279 CACAAGTCGGGGGCAACCCATTTAAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
** ** *
43311 TGCAAGTTAGTGGCAACCCTTTTCAAA
1 CACAAGTCGGTGGCAACCCATTTCAAA
43338 TCACCATTTT
Statistics
Matches: 974, Mismatches: 63, Indels: 77
0.87 0.06 0.07
Matches are distributed among these distances:
25 7 0.01
26 11 0.01
27 9 0.01
28 94 0.10
29 65 0.07
30 157 0.16
31 84 0.09
32 469 0.48
33 42 0.04
34 16 0.02
35 7 0.01
36 13 0.01
ACGTcount: A:0.31, C:0.33, G:0.19, T:0.18
Consensus pattern (32 bp):
CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
Found at i:43421 original size:45 final size:47
Alignment explanation
Indices: 43370--43488 Score: 127
Period size: 49 Copynumber: 2.5 Consensus size: 47
43360 GTCCGATATT
*
43370 GCTGGCCTTGAATCAGCATATTGG-CACCTTT-CTAAGCCCAATGTC
1 GCTGGCCTTGAATCAGCACATTGGCCACCTTTCCTAAGCCCAATGTC
* * * *
43415 GCTGGCCTTGAGTCAGCACATTGGTCCACTTTTCCCTTAGCCCGATGTC
1 GCTGGCCTTGAATCAGCACATTGG-CCACCTTT-CCTAAGCCCAATGTC
* *
43464 GCTGACCTTGAAAT-GGCACATTGGC
1 GCTGGCCTTG-AATCAGCACATTGGC
43489 ATTCCTCTCA
Statistics
Matches: 61, Mismatches: 8, Indels: 7
0.80 0.11 0.09
Matches are distributed among these distances:
45 22 0.36
47 6 0.10
48 1 0.02
49 30 0.49
50 2 0.03
ACGTcount: A:0.19, C:0.29, G:0.23, T:0.29
Consensus pattern (47 bp):
GCTGGCCTTGAATCAGCACATTGGCCACCTTTCCTAAGCCCAATGTC
Found at i:44214 original size:1 final size:1
Alignment explanation
Indices: 44170--44197 Score: 56
Period size: 1 Copynumber: 28.0 Consensus size: 1
44160 GGGAGGGATC
44170 AAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAA
44198 GGGGCTTTCC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 27 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:44220 original size:22 final size:23
Alignment explanation
Indices: 44186--44230 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 23
44176 AAAAAAAAAA
44186 AAAAAAAAAAAAG-GGGCTTTCC
1 AAAAAAAAAAAAGTGGGCTTTCC
** *
44208 AAAAAAACCAAAGTGGGTTTTCC
1 AAAAAAAAAAAAGTGGGCTTTCC
44231 GATTGAGTGG
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
22 11 0.58
23 8 0.42
ACGTcount: A:0.49, C:0.16, G:0.18, T:0.18
Consensus pattern (23 bp):
AAAAAAAAAAAAGTGGGCTTTCC
Found at i:44623 original size:11 final size:11
Alignment explanation
Indices: 44585--44625 Score: 55
Period size: 11 Copynumber: 3.5 Consensus size: 11
44575 AAATTTAGGT
44585 AAAAAAGAAAG
1 AAAAAAGAAAG
*
44596 AAAGAAGATGAAG
1 AAAAAAGA--AAG
44609 AAAAAAGAAAG
1 AAAAAAGAAAG
44620 AAAAAA
1 AAAAAA
44626 AATATGAAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
11 16 0.62
13 10 0.38
ACGTcount: A:0.78, C:0.00, G:0.20, T:0.02
Consensus pattern (11 bp):
AAAAAAGAAAG
Found at i:45019 original size:2 final size:2
Alignment explanation
Indices: 45006--45050 Score: 81
Period size: 2 Copynumber: 22.5 Consensus size: 2
44996 TTATTTTATT
*
45006 TA TA TG TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
45048 TA T
1 TA T
45051 TTTGAAAATC
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (2 bp):
TA
Found at i:49382 original size:21 final size:22
Alignment explanation
Indices: 49357--49397 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
49347 AACATGCTGT
49357 AAATGCATGAAACAT-AGCTCA
1 AAATGCATGAAACATGAGCTCA
*
49378 AAATGCATGAATCATGAGCT
1 AAATGCATGAAACATGAGCT
49398 GTTAACATGA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.44, C:0.17, G:0.17, T:0.22
Consensus pattern (22 bp):
AAATGCATGAAACATGAGCTCA
Found at i:50320 original size:51 final size:52
Alignment explanation
Indices: 50236--50363 Score: 179
Period size: 51 Copynumber: 2.5 Consensus size: 52
50226 CGAAATATAA
50236 AAATTTGCCTGCATGTATTGATACATTTCATAGTGTAAT-GATACATCTGGGC
1 AAATTTGCCTGCATGTATTGATACATTTCATAGTGT-ATCGATACATCTGGGC
** *
50288 AAATTTGCCTTTATGTA-TGATACATTTCATAGTGTATCGATACATTTGGGC
1 AAATTTGCCTGCATGTATTGATACATTTCATAGTGTATCGATACATCTGGGC
* * *
50339 AAATTTACTTGCATGTATGGATACA
1 AAATTTGCCTGCATGTATTGATACA
50364 AAGATCAGTG
Statistics
Matches: 66, Mismatches: 8, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
50 2 0.03
51 43 0.65
52 21 0.32
ACGTcount: A:0.30, C:0.14, G:0.18, T:0.38
Consensus pattern (52 bp):
AAATTTGCCTGCATGTATTGATACATTTCATAGTGTATCGATACATCTGGGC
Found at i:50390 original size:13 final size:13
Alignment explanation
Indices: 50372--50396 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
50362 CAAAGATCAG
50372 TGTATCGATACAA
1 TGTATCGATACAA
50385 TGTATCGATACA
1 TGTATCGATACA
50397 TTTGAGTAAT
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):
TGTATCGATACAA
Found at i:50503 original size:19 final size:18
Alignment explanation
Indices: 50479--50542 Score: 75
Period size: 19 Copynumber: 3.7 Consensus size: 18
50469 GTAGATACAT
50479 TGTATCGATACAACAGTTA
1 TGTATCGATACAACA-TTA
50498 TGTATCGAT---ACA--A
1 TGTATCGATACAACATTA
50511 TGTATCGATACAACACTTA
1 TGTATCGATACAACA-TTA
50530 TGTATCGATACAA
1 TGTATCGATACAA
50543 ATCGTTGAAT
Statistics
Matches: 39, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
13 10 0.26
16 6 0.15
19 23 0.59
ACGTcount: A:0.38, C:0.17, G:0.14, T:0.31
Consensus pattern (18 bp):
TGTATCGATACAACATTA
Found at i:50515 original size:13 final size:13
Alignment explanation
Indices: 50497--50523 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
50487 TACAACAGTT
50497 ATGTATCGATACA
1 ATGTATCGATACA
50510 ATGTATCGATACA
1 ATGTATCGATACA
50523 A
1 A
50524 CACTTATGTA
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:0.41, C:0.15, G:0.15, T:0.30
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:50515 original size:32 final size:32
Alignment explanation
Indices: 50441--50542 Score: 154
Period size: 32 Copynumber: 3.2 Consensus size: 32
50431 AGCTTCATAG
* *
50441 CGATACATTGTATCGATACAAAACTTATGTA-
1 CGATACAATGTATCGATACAACACTTATGTAT
* *
50472 -GATACATTGTATCGATACAACAGTTATGTAT
1 CGATACAATGTATCGATACAACACTTATGTAT
50503 CGATACAATGTATCGATACAACACTTATGTAT
1 CGATACAATGTATCGATACAACACTTATGTAT
50535 CGATACAA
1 CGATACAA
50543 ATCGTTGAAT
Statistics
Matches: 65, Mismatches: 4, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
30 28 0.43
32 37 0.57
ACGTcount: A:0.38, C:0.17, G:0.14, T:0.31
Consensus pattern (32 bp):
CGATACAATGTATCGATACAACACTTATGTAT
Found at i:59700 original size:175 final size:175
Alignment explanation
Indices: 59409--59759 Score: 675
Period size: 175 Copynumber: 2.0 Consensus size: 175
59399 GGATTCATGA
59409 GTTCCCCTAAGCGGAAGCTCTTGTGCAAGGGTGGGAACAACATAGGTTCTGATTCCTAATTCTAT
1 GTTCCCCTAAGCGGAAGCTCTTGTGCAAGGGTGGGAACAACATAGGTTCTGATTCCTAATTCTAT
59474 CCCATTAACCTAGCCATTCTCTTTTCATGAGCTTTTTGAGCTTGCCTTCTTTACTGATGAGTGTT
66 CCCATTAACCTAGCCATTCTCTTTTCATGAGCTTTTTGAGCTTGCCTTCTTTACTGATGAGTGTT
*
59539 TGATTTAAACCCTAACCCTCATTTGTCGACCTTGTTGCTGACTTG
131 TGATTTAAACCCTAACCCTCATTTGTCGACCTTGTTGCTAACTTG
*
59584 GTTCCCCTAAGCGGAAGCTCTTGTGCAAGGGTGGGAACACCATAGGTTCTGATTCCTAATTCTAT
1 GTTCCCCTAAGCGGAAGCTCTTGTGCAAGGGTGGGAACAACATAGGTTCTGATTCCTAATTCTAT
*
59649 CCTATTAACCTAGCCATTCTCTTTTCATGAGCTTTTTGAGCTTGCCTTCTTTACTGATGAGTGTT
66 CCCATTAACCTAGCCATTCTCTTTTCATGAGCTTTTTGAGCTTGCCTTCTTTACTGATGAGTGTT
59714 TGATTTAAACCCTAACCCTCATTTGTCGACCTTGTTGCTAACTTG
131 TGATTTAAACCCTAACCCTCATTTGTCGACCTTGTTGCTAACTTG
59759 G
1 G
59760 AGTGCTCGAT
Statistics
Matches: 173, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
175 173 1.00
ACGTcount: A:0.21, C:0.24, G:0.19, T:0.37
Consensus pattern (175 bp):
GTTCCCCTAAGCGGAAGCTCTTGTGCAAGGGTGGGAACAACATAGGTTCTGATTCCTAATTCTAT
CCCATTAACCTAGCCATTCTCTTTTCATGAGCTTTTTGAGCTTGCCTTCTTTACTGATGAGTGTT
TGATTTAAACCCTAACCCTCATTTGTCGACCTTGTTGCTAACTTG
Done.