Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2080
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: 44768
ACGTcount: A:0.32, C:0.17, G:0.20, T:0.31
Found at i:4850 original size:13 final size:15
Alignment explanation
Indices: 4820--4850 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
4810 TTCCAGATTT
4820 TCTTTTCTACCTCTC
1 TCTTTTCTACCTCTC
4835 TCTTTTCTACCTCTC
1 TCTTTTCTACCTCTC
4850 T
1 T
4851 GGAAAGTAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.06, C:0.39, G:0.00, T:0.55
Consensus pattern (15 bp):
TCTTTTCTACCTCTC
Found at i:4934 original size:15 final size:14
Alignment explanation
Indices: 4892--4941 Score: 50
Period size: 15 Copynumber: 3.5 Consensus size: 14
4882 TATAACTTGA
*
4892 ATGCAAATGATGTG
1 ATGCAAATGATGAG
4906 ATG-AAATGTTATGAG
1 ATGCAAATG--ATGAG
4921 ATGCAAATGCATGA-
1 ATGCAAATG-ATGAG
4935 ATGCAAA
1 ATGCAAA
4942 AAGAATATCG
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
13 5 0.16
14 10 0.32
15 11 0.35
16 5 0.16
ACGTcount: A:0.42, C:0.08, G:0.24, T:0.26
Consensus pattern (14 bp):
ATGCAAATGATGAG
Found at i:8809 original size:24 final size:24
Alignment explanation
Indices: 8764--8810 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
8754 ATATTAAAAG
*
8764 ATATATATATAAAATGTATACATA
1 ATATATATATAAAATATATACATA
*
8788 ATATA-ATATTAAAATATTTACAT
1 ATATATATA-TAAAATATATACAT
8811 GGTATATACA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 3 0.15
24 17 0.85
ACGTcount: A:0.53, C:0.04, G:0.02, T:0.40
Consensus pattern (24 bp):
ATATATATATAAAATATATACATA
Found at i:10300 original size:26 final size:25
Alignment explanation
Indices: 10243--10331 Score: 67
Period size: 26 Copynumber: 3.5 Consensus size: 25
10233 AGGAGGACAT
* *
10243 ATAAATAATAATATTAGA-ATAAAGTA
1 ATAAA-AATAATACTACATATAAA-TA
*
10269 ATTAAAAATAATACTATATATAAATA
1 A-TAAAAATAATACTACATATAAATA
*
10295 TATAAATATATATAC-ACATAT-AATA
1 -ATAAAAATA-ATACTACATATAAATA
*
10320 ATAATAATAATA
1 ATAAAAATAATA
10332 ATAATATGTA
Statistics
Matches: 53, Mismatches: 6, Indels: 11
0.76 0.09 0.16
Matches are distributed among these distances:
23 3 0.06
24 7 0.13
25 4 0.08
26 25 0.47
27 14 0.26
ACGTcount: A:0.61, C:0.03, G:0.02, T:0.34
Consensus pattern (25 bp):
ATAAAAATAATACTACATATAAATA
Found at i:10322 original size:20 final size:18
Alignment explanation
Indices: 10271--10338 Score: 54
Period size: 18 Copynumber: 3.8 Consensus size: 18
10261 ATAAAGTAAT
* *
10271 TAAAAATAATACTATATA
1 TAAATATAATAATATATA
10289 TAAATAT-ATAAATATATA
1 TAAATATAAT-AATATATA
10307 TACACATATAATAATA-ATA
1 TA-A-ATATAATAATATATA
*
10326 -ATA-ATAATAATAT
1 TAAATATAATAATAT
10339 GTATTAAATG
Statistics
Matches: 42, Mismatches: 3, Indels: 12
0.74 0.05 0.21
Matches are distributed among these distances:
15 9 0.21
16 1 0.02
17 2 0.05
18 16 0.38
19 4 0.10
20 8 0.19
21 2 0.05
ACGTcount: A:0.60, C:0.04, G:0.00, T:0.35
Consensus pattern (18 bp):
TAAATATAATAATATATA
Found at i:10662 original size:14 final size:15
Alignment explanation
Indices: 10645--10713 Score: 58
Period size: 14 Copynumber: 4.8 Consensus size: 15
10635 ATGGTAAAAA
10645 TAATAATAAT-GTAT
1 TAATAATAATAGTAT
* *
10659 TAATAAGAAT-GATAG
1 TAATAATAATAG-TAT
10674 TAATAA-AATAAG-AT
1 TAATAATAAT-AGTAT
10688 T-ATAATAATAGTAT
1 TAATAATAATAGTAT
*
10702 TAATAAAAATAG
1 TAATAATAATAG
10714 ACATAAAAAG
Statistics
Matches: 45, Mismatches: 4, Indels: 11
0.75 0.07 0.18
Matches are distributed among these distances:
13 6 0.13
14 21 0.47
15 17 0.38
16 1 0.02
ACGTcount: A:0.57, C:0.00, G:0.10, T:0.33
Consensus pattern (15 bp):
TAATAATAATAGTAT
Found at i:10706 original size:71 final size:71
Alignment explanation
Indices: 10555--10691 Score: 167
Period size: 71 Copynumber: 2.0 Consensus size: 71
10545 TAGTATTAAC
* * * *
10555 AAAATAATAATA--ATAATAATAATAATAATACATTAATAATAATATATGTTAATAAAAATAATA
1 AAAATAATAATATGGTAAAAATAATAATAATACATTAATAAGAATATATGTTAATAAAAATAAGA
10618 ATATAT
66 ATATAT
**
10624 AAAATAATAATATGGTAAAAATAATAATAATGTATTAATAAGAATGATA-G-TAAT-AAAATAAG
1 AAAATAATAATATGGTAAAAATAATAATAATACATTAATAAGAAT-ATATGTTAATAAAAATAAG
*
10686 ATTATA
65 AATATA
10692 ATAATAGTAT
Statistics
Matches: 58, Mismatches: 7, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
69 24 0.41
70 4 0.07
71 27 0.47
72 3 0.05
ACGTcount: A:0.61, C:0.01, G:0.06, T:0.33
Consensus pattern (71 bp):
AAAATAATAATATGGTAAAAATAATAATAATACATTAATAAGAATATATGTTAATAAAAATAAGA
ATATAT
Found at i:10764 original size:3 final size:3
Alignment explanation
Indices: 10388--10712 Score: 141
Period size: 3 Copynumber: 108.0 Consensus size: 3
10378 TTTAAAAATG
* * * * * *
10388 ATA ATA GTA ATA AAA ATA AAA ATA CTA GTG ATA ATA ATA ATA ATA ATAA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT-A
* * * *
10437 ATA GTA ATA ATA ATA CATTA ATA ATA ATA AT- ATG TTA ATA ACA ATA
1 ATA ATA ATA ATA ATA -A-TA ATA ATA ATA ATA ATA ATA ATA ATA ATA
* * * * *
10483 A-A TTA ATGA ATTA ATA A-C ATA ACA GTA AGTAA ATA A-A CATA AAA
1 ATA ATA AT-A A-TA ATA ATA ATA ATA ATA A-T-A ATA ATA -ATA ATA
* * * * *
10527 ATA A-A ATA ATT ATA ATA GTA GTA TTA ACA A-A ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
* * *
10573 ATA ATA ATA ATA CATTA ATA ATA ATA TATG TTA ATA AAA ATA ATA ATA
1 ATA ATA ATA ATA -A-TA ATA ATA ATA -ATA ATA ATA ATA ATA ATA ATA
* * * * *
10621 TATA A-A ATA ATA AT- ATG GTA AAA ATA ATA ATA AT- GTA TTA ATA
1 -ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
* * * * * * * *
10664 AGA ATG ATA GTA ATA A-A ATA A-G ATT ATA ATA ATA GTA TTA ATA AAA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
10710 ATA
1 ATA
10713 GACATAAAAA
Statistics
Matches: 237, Mismatches: 62, Indels: 46
0.69 0.18 0.13
Matches are distributed among these distances:
2 17 0.07
3 194 0.82
4 19 0.08
5 7 0.03
ACGTcount: A:0.60, C:0.02, G:0.06, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:11528 original size:3 final size:3
Alignment explanation
Indices: 11514--11564 Score: 75
Period size: 3 Copynumber: 16.7 Consensus size: 3
11504 TGTATTTCAA
* *
11514 TAT TAC TAT TAT TAT TAT TAT TAT TAT TGT TAT TAT TAT TAT TAT ATAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT -TAT
11563 TA
1 TA
11565 GTGTATACTT
Statistics
Matches: 43, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
3 40 0.93
4 3 0.07
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:11599 original size:158 final size:157
Alignment explanation
Indices: 11389--11684 Score: 522
Period size: 157 Copynumber: 1.9 Consensus size: 157
11379 CTTTATTAAA
*
11389 TATTATTATTATATATTAGTGTATACTTTTTATTATATACGTATATGCATATATATTTTGTATAT
1 TATTATTATTATATATTAGTGTATACTTTTTATTATATACGTATATGCATATATA-TTTATATAT
* *
11454 AGTATTATTTTTTATTACTTTATTTTAATATTTTTATTATATTTGC-TTTTTGTATTTCAATATT
65 AGTATTATTTTTTATTACTTTATTTTAATA-TTTTATTATATTTACTTTTTTGTATCTCAATATT
11518 ACTATTATTATTATTATTATTATTGTTAT
129 ACTATTATTATTATTATTATTATTGTTAT
*
11547 TATTATTATTATATATTAGTGTATACTTTTTATTATATACGTATATGTATATATATTTATATATA
1 TATTATTATTATATATTAGTGTATACTTTTTATTATATACGTATATGCATATATATTTATATATA
*
11612 GTATTATTTTTTATTACTTTATTTTAATATTTTATTATATTTACTTTTTTGTATCTCAATATTAT
66 GTATTATTTTTTATTACTTTATTTTAATATTTTATTATATTTACTTTTTTGTATCTCAATATTAC
11677 TATTATTA
131 TATTATTA
11685 ACGCTCTTAT
Statistics
Matches: 132, Mismatches: 5, Indels: 3
0.94 0.04 0.02
Matches are distributed among these distances:
156 14 0.11
157 64 0.48
158 54 0.41
ACGTcount: A:0.30, C:0.04, G:0.05, T:0.60
Consensus pattern (157 bp):
TATTATTATTATATATTAGTGTATACTTTTTATTATATACGTATATGCATATATATTTATATATA
GTATTATTTTTTATTACTTTATTTTAATATTTTATTATATTTACTTTTTTGTATCTCAATATTAC
TATTATTATTATTATTATTATTGTTAT
Found at i:11747 original size:3 final size:3
Alignment explanation
Indices: 11724--12200 Score: 221
Period size: 3 Copynumber: 159.0 Consensus size: 3
11714 TTTTTATGTC
* * * * * *
11724 TAT TTT TAT TAA TAC TAT TAT TA- TAA TCT TAT T-T TAT TAT TAT CAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* * * * *
11770 TCT TAT TAA TA- CAT TAT TAT TAT T-T T-T TAC CA- TAT TAT TAT T-T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* * *
11813 TAT ATAT TAT TAT TGT TAT TAA CAT ATAT TAT TAT TAAT GTAT TAT TAT
1 TAT -TAT TAT TAT TAT TAT TAT TAT -TAT TAT TAT T-AT -TAT TAT TAT
* * * * *
11862 TTT CTAT TAT T-T TAT TAA TAT CAT TGT TAT CAT T-T TAT TAT TAT
1 TAT -TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* * * *
11906 TAT TAT TAT TAT TAT TAT TAT TAT T-T TGT TAA TAT TAC TAT TAT AAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* * * *
11953 TAT T-T TAT TTT TAT GT-T TATT TACT TAC TGT TA- TGT TAT TAAT TCAT
1 TAT TAT TAT TAT TAT -TAT TA-T TA-T TAT TAT TAT TAT TAT T-AT T-AT
* * * * * *
12000 TAA T-T TAT TGT TAT AAA CA- TAT TAT TAT TAAT GTAT TAT TAT TAC
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T-AT -TAT TAT TAT TAT
* * *
12045 TATT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT CAC TAC TAT TAT
1 TA-T TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* * * * * * * * * * *
12091 TTT TAT TTT TAT TAC TAT TAT CAT TTT TAAA AAA AAT TAT TGT TAC
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT T-AT TAT TAT TAT TAT TAT
* * * * * *
12137 TAT TAT TCT T-T TAC CATT TAA TACA TAT TAT TAC TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TA-T TAT TA-T TAT TAT TAT TAT TAT TAT TAT
12183 TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT
12201 CTTTGTGGGT
Statistics
Matches: 353, Mismatches: 92, Indels: 58
0.70 0.18 0.12
Matches are distributed among these distances:
2 26 0.07
3 291 0.82
4 34 0.10
5 2 0.01
ACGTcount: A:0.32, C:0.06, G:0.02, T:0.60
Consensus pattern (3 bp):
TAT
Found at i:11763 original size:19 final size:20
Alignment explanation
Indices: 11739--11776 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
11729 TTATTAATAC
11739 TATTATTAT-AATCTTATTT
1 TATTATTATCAATCTTATTT
*
11758 TATTATTATCATTCTTATT
1 TATTATTATCAATCTTATT
11777 AATACATTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.29, C:0.08, G:0.00, T:0.63
Consensus pattern (20 bp):
TATTATTATCAATCTTATTT
Found at i:11789 original size:14 final size:14
Alignment explanation
Indices: 11729--11791 Score: 51
Period size: 14 Copynumber: 4.4 Consensus size: 14
11719 ATGTCTATTT
11729 TTATTAATACTATTA
1 TTATTAATAC-ATTA
11744 TTA-TAAT-C-TTA
1 TTATTAATACATTA
* *
11755 TTTTATTATTATCATTC
1 --TTATTAATA-CATTA
11772 TTATTAATACATTA
1 TTATTAATACATTA
11786 TTATTA
1 TTATTA
11792 TTTTTTACCA
Statistics
Matches: 38, Mismatches: 4, Indels: 13
0.69 0.07 0.24
Matches are distributed among these distances:
11 3 0.08
13 4 0.11
14 17 0.45
15 11 0.29
16 1 0.03
17 2 0.05
ACGTcount: A:0.35, C:0.08, G:0.00, T:0.57
Consensus pattern (14 bp):
TTATTAATACATTA
Found at i:11808 original size:32 final size:32
Alignment explanation
Indices: 11772--11963 Score: 113
Period size: 35 Copynumber: 5.7 Consensus size: 32
11762 ATTATCATTC
*
11772 TTATTAATACATTATTATTATTTT-TTACCATA
1 TTATTAATA-ATTATTATTATTTTATTACTATA
* *
11804 TTATTATTTTATATATTATTATTGTTATTAACATATA
1 TTATTA-ATAAT-TATTATTATT-TTATT-AC-TATA
* * * *
11841 TTATTATTAATGTATTATTATTTT-CTATTATT
1 TTATTAATAAT-TATTATTATTTTATTACTATA
* * *
11873 TTATTAATATCATTGTTATCATTTTATTATTATTA
1 TTATTAATA--ATTATTATTATTTTATTACTA-TA
* * *
11908 TTATTATTATTATTATTATTATTTTGTTAATATTA
1 TTATTA--ATAATTATTATTATTTTATTACTA-TA
*
11943 CTATT-ATAATTATT-TTATTTT
1 TTATTAATAATTATTATTATTTT
11964 TATGTTTATT
Statistics
Matches: 128, Mismatches: 20, Indels: 25
0.74 0.12 0.14
Matches are distributed among these distances:
31 7 0.05
32 27 0.21
33 22 0.17
34 10 0.08
35 35 0.27
36 16 0.12
37 11 0.09
ACGTcount: A:0.32, C:0.04, G:0.02, T:0.62
Consensus pattern (32 bp):
TTATTAATAATTATTATTATTTTATTACTATA
Found at i:11961 original size:58 final size:61
Alignment explanation
Indices: 11839--12059 Score: 162
Period size: 58 Copynumber: 3.7 Consensus size: 61
11829 TATTAACATA
* * * *
11839 TATTATTATTAATGTATTATTATTTTCTATTATTTTATTAATATCATTGTTATCATTTTAT
1 TATTATTATTAATGTATTATTATTATCTATTATTTTATTAATATCACTATTATAATTTTAT
* *
11900 TATTATTATT-AT-TATTATTATTAT-TATTATTTTGTTAATATTACTATTATAA--TTAT
1 TATTATTATTAATGTATTATTATTATCTATTATTTTATTAATATCACTATTATAATTTTAT
* * * *
11956 T-TTATT-TTTATGT-TTATTTACTTA-CTGTTATGTTATTAAT-TCATTAATT-T-ATTGTTAT
1 TATTATTATTAATGTATTA-TTA-TTATCTATTATTTTATTAATATCACT-ATTATAATT-TTAT
12014 AAACATATTATTATTAATGTATTATTATTA-CTATTTATTATTATTA
1 -----TATTATTATTAATGTATTATTATTATCTA-TTATT-TTATTA
12060 TTATTATTAT
Statistics
Matches: 127, Mismatches: 14, Indels: 33
0.73 0.08 0.19
Matches are distributed among these distances:
54 2 0.02
55 11 0.09
56 13 0.10
57 18 0.14
58 27 0.21
59 11 0.09
60 2 0.02
61 10 0.08
63 1 0.01
64 10 0.08
65 13 0.10
66 9 0.07
ACGTcount: A:0.31, C:0.04, G:0.04, T:0.61
Consensus pattern (61 bp):
TATTATTATTAATGTATTATTATTATCTATTATTTTATTAATATCACTATTATAATTTTAT
Found at i:26049 original size:90 final size:88
Alignment explanation
Indices: 25925--26331 Score: 374
Period size: 88 Copynumber: 4.6 Consensus size: 88
25915 GAGTGGATCA
*
25925 AAAATTACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGACGATGAGCCTTAACCCC
1 AAAATTACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGATGATGAGCCTTAACCCC
*
25990 CTAAGCAGTAGGGTAATAGGCGAG
66 CTAAGCAGTAGGGTAATAGGC-TG
* * * * *
26014 AAAATGACAGATCTTTATCTCCCTAAGCAATAGTGGAGTAGATCAAAGATGGTGAGTCTTAA-CC
1 AAAATTACAGATC-TTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGATGATGAGCCTTAACCC
* *
26078 CCTAAGCAATAGGGTAACT-GACTG
65 CCTAAGCAGTAGGGTAA-TAGGCTG
* * * * *** * * *
26102 AAAA-TACAGATCCTATTTCCCTAAGCAATAGTGGAGCGGATCGAAA-ATGGCAAGCTTTATCTC
1 AAAATTACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATC-AAAGATGATGAGCCTTAACCC
* * * ** *
26165 TCTGAGCAGCAGTGG-AGCAAGCTG
65 CCTAAGCAGTAG-GGTAATAGGCTG
* * *
26189 AAGATTACAGATCTTATCTCCCTAAGCAGCAGTGGAGCAGATCGAAGATGATGAGCAGGCTTTAA
1 AAAATTACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGATGATGAGC---C-TTAA
* * *
26254 CTCCCTAAACAGTAGGGTAAAAGGCTGG
62 CCCCCTAAGCAGTAGGGTAATAGGCT-G
** *
26282 AGGATTACAAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATTAAAGAT
1 AAAATTAC-AGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGAT
26332 AGCAAACCTT
Statistics
Matches: 252, Mismatches: 51, Indels: 25
0.77 0.16 0.08
Matches are distributed among these distances:
86 35 0.14
87 28 0.11
88 46 0.18
89 32 0.13
90 44 0.17
91 2 0.01
92 19 0.08
93 8 0.03
94 38 0.15
ACGTcount: A:0.34, C:0.19, G:0.24, T:0.23
Consensus pattern (88 bp):
AAAATTACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGATGATGAGCCTTAACCCC
CTAAGCAGTAGGGTAATAGGCTG
Found at i:26236 original size:44 final size:44
Alignment explanation
Indices: 25888--26463 Score: 227
Period size: 44 Copynumber: 13.0 Consensus size: 44
25878 TAAATTTCGG
* * * ** * *
25888 CAGATCCTATCTCCTTAAGCAATAGTGGAGTGGATCAAAAATTA
1 CAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATTA
* **
25932 CAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGACGA
1 CAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATTA
* * * * ** * * *
25976 -TGAGCCTTAACCCCCTAAGCAGTAG-GGTAATAG-GCGAGAAAATGA
1 CAGA-TCTTATCTCCCTAAGCAGTAGTGG-AGCAGATC--GAAGATTA
* * *
26021 CAGATCTTTATCTCCCTAAGCAATAGTGGAGTAGATCAAAGATGGT-
1 CAGATC-TTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGAT--TA
* * * * * *
26067 GAG-TCTTAAC-CCCTAAGCAATAG-GGTAACTGA-CTGAA-AATA
1 CAGATCTTATCTCCCTAAGCAGTAGTGG-AGCAGATC-GAAGATTA
* * * * * **
26108 CAGATCCTATTTCCCTAAGCAATAGTGGAGCGGATCGAAAATGG
1 CAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATTA
* * * * *
26152 CA-AGCTTTATCTCTCTGAGCAGCAGTGGAGCA-AGCTGAAGATTA
1 CAGATC-TTATCTCCCTAAGCAGTAGTGGAGCAGATC-GAAGATTA
*
26196 CAGATCTTATCTCCCTAAGCAGCAGTGGAGCAGATCGAAGATGATGA
1 CAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGAT--T-A
* * * ** * * *
26243 GCAG-GCTTTAACTCCCTAAACAGTAG-GGTAAAAGGCTGGAGGATTA
1 -CAGATC-TTATCTCCCTAAGCAGTAGTGG-AGCA-GATCGAAGATTA
**
26289 CAAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATTAAAGA-TA
1 C-AGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATTA
* * * * * *
26333 GCAAACCTTATCTCTCTAA--AGTTGCAGAGAGCATG-TTGAAG-TTA
1 -CAGATCTTATCTCCCTAAGCAGTAG-TG-GAGCA-GATCGAAGATTA
* * * * * *
26377 CA-AGTCTTATCTCTCTGAAGCTGTAGCGGAGCATATTGAAGATAA
1 CAGA-TCTTATCTCCCT-AAGCAGTAGTGGAGCAGATCGAAGATTA
26422 CAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGAT
1 CAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGAT
26464 ACCAAACCTT
Statistics
Matches: 393, Mismatches: 95, Indels: 88
0.68 0.16 0.15
Matches are distributed among these distances:
40 1 0.00
41 2 0.01
42 13 0.03
43 61 0.16
44 186 0.47
45 40 0.10
46 51 0.13
47 11 0.03
48 21 0.05
49 7 0.02
ACGTcount: A:0.33, C:0.19, G:0.23, T:0.24
Consensus pattern (44 bp):
CAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATTA
Found at i:30378 original size:16 final size:15
Alignment explanation
Indices: 30353--30387 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
30343 TAGATCTAAG
30353 TTTTTATAGTTTTAGT
1 TTTTTATAG-TTTAGT
*
30369 TTTTTTTAGTTTAGT
1 TTTTTATAGTTTAGT
30384 TTTT
1 TTTT
30388 AAATAAAACG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 10 0.56
16 8 0.44
ACGTcount: A:0.14, C:0.00, G:0.11, T:0.74
Consensus pattern (15 bp):
TTTTTATAGTTTAGT
Found at i:35109 original size:104 final size:103
Alignment explanation
Indices: 34929--35151 Score: 367
Period size: 104 Copynumber: 2.2 Consensus size: 103
34919 TGTATATAAA
** * *
34929 AGGGGTTGCTGTGTGCTGATTCCCCGATTTATGGGTGGTGCTATGTGCGTGATCCACCATATCTT
1 AGGGGTTGCTAAGTGCTGATTCCCCGATTCATGGGTGGTGCTAAGTGCGTGATCCACCATATCTT
34994 TGAAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCCCG
66 TGAAATGTGAAAGGGGGTTGCTATGTGCTGATT-CCCCG
* *
35033 AGGGGTTGCTAAGTGCTGATTCCCCGGTTCATTGGTGGTGCTAAGTGCGAT-ATCCACCATATCT
1 AGGGGTTGCTAAGTGCTGATTCCCCGATTCATGGGTGGTGCTAAGTGCG-TGATCCACCATATCT
35097 TTGAAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCCG
65 TTGAAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCCG
35136 AGGGGTTGCTAAGTGC
1 AGGGGTTGCTAAGTGC
35152 GATATCCATT
Statistics
Matches: 112, Mismatches: 6, Indels: 3
0.93 0.05 0.02
Matches are distributed among these distances:
103 21 0.19
104 90 0.80
105 1 0.01
ACGTcount: A:0.18, C:0.19, G:0.32, T:0.31
Consensus pattern (103 bp):
AGGGGTTGCTAAGTGCTGATTCCCCGATTCATGGGTGGTGCTAAGTGCGTGATCCACCATATCTT
TGAAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCCG
Found at i:35203 original size:70 final size:72
Alignment explanation
Indices: 35071--35221 Score: 243
Period size: 71 Copynumber: 2.1 Consensus size: 72
35061 TCATTGGTGG
* *
35071 TGCTAAGTGCGATATCCACCATATCTTTGAAATGTGAAAGGGGGTTGCTATGTGCTGATT-CCCC
1 TGCTAAGTGCGATATCCACCATATATTTGAAATGTAAAAGGGGGTTGCTATGTGCTGATTCCCCC
35135 GAGGGGT
66 GAGGGGT
***
35142 TGCTAAGTGCGATATCCATTGTATATTTGAAATG-AAAAGGGGGTTGCTATGTGCTGATTCCCCC
1 TGCTAAGTGCGATATCCACCATATATTTGAAATGTAAAAGGGGGTTGCTATGTGCTGATTCCCCC
35206 GAGGGGT
66 GAGGGGT
35213 TGCTAAGTG
1 TGCTAAGTG
35222 ATGATTCCCC
Statistics
Matches: 74, Mismatches: 5, Indels: 2
0.91 0.06 0.02
Matches are distributed among these distances:
70 24 0.32
71 50 0.68
ACGTcount: A:0.23, C:0.17, G:0.30, T:0.30
Consensus pattern (72 bp):
TGCTAAGTGCGATATCCACCATATATTTGAAATGTAAAAGGGGGTTGCTATGTGCTGATTCCCCC
GAGGGGT
Found at i:42660 original size:104 final size:104
Alignment explanation
Indices: 42480--42703 Score: 378
Period size: 104 Copynumber: 2.2 Consensus size: 104
42470 TGTATATAAA
** * *
42480 AGGGGTTGCTGTGTGCTGATTCCCCGATTTATGGGTGGTGCTATGTGCGTGATCCACCATATCTT
1 AGGGGTTGCTAAGTGCTGATTCCCCGATTCATGGGTGGTGCTAAGTGCGTGATCCACCATATCTT
42545 TGAAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCCCG
66 TGAAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCCCG
* *
42584 AGGGGTTGCTAAGTGCTGATTCCCCGGTTCATTGGTGGTGCTAAGTGCGAT-ATCCACCATATCT
1 AGGGGTTGCTAAGTGCTGATTCCCCGATTCATGGGTGGTGCTAAGTGCG-TGATCCACCATATCT
42648 TTGAAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCCCG
65 TTGAAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCCCG
42688 AGGGGTTGCTAAGTGC
1 AGGGGTTGCTAAGTGC
42704 GATATCCATT
Statistics
Matches: 113, Mismatches: 6, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
104 112 0.99
105 1 0.01
ACGTcount: A:0.18, C:0.19, G:0.32, T:0.31
Consensus pattern (104 bp):
AGGGGTTGCTAAGTGCTGATTCCCCGATTCATGGGTGGTGCTAAGTGCGTGATCCACCATATCTT
TGAAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCCCG
Found at i:42755 original size:71 final size:72
Alignment explanation
Indices: 42622--42773 Score: 252
Period size: 71 Copynumber: 2.1 Consensus size: 72
42612 TCATTGGTGG
* *
42622 TGCTAAGTGCGATATCCACCATATCTTTGAAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCCC
1 TGCTAAGTGCGATATCCACCATATATTTGAAATGTAAAAGGGGGTTGCTATGTGCTGATTCCCCC
42687 GAGGGGT
66 GAGGGGT
***
42694 TGCTAAGTGCGATATCCATTGTATATTTGAAATG-AAAAGGGGGTTGCTATGTGCTGATTCCCCC
1 TGCTAAGTGCGATATCCACCATATATTTGAAATGTAAAAGGGGGTTGCTATGTGCTGATTCCCCC
42758 GAGGGGT
66 GAGGGGT
42765 TGCTAAGTG
1 TGCTAAGTG
42774 ATGATTCCCC
Statistics
Matches: 75, Mismatches: 5, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
71 45 0.60
72 30 0.40
ACGTcount: A:0.23, C:0.17, G:0.30, T:0.30
Consensus pattern (72 bp):
TGCTAAGTGCGATATCCACCATATATTTGAAATGTAAAAGGGGGTTGCTATGTGCTGATTCCCCC
GAGGGGT
Done.