Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2499
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: 35935
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Found at i:205 original size:78 final size:70
Alignment explanation
Indices: 17--283 Score: 286
Period size: 67 Copynumber: 3.8 Consensus size: 70
7 CAAAATTAAA
* *
17 AACCTC-GCGTGTCCTGAGGCTC-ACTCACCTCTCG-AATATGAGTTGATTTTGAAAACAGAAAT
1 AACCTCAGCGTGT-CTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTGAAAA-AAAAAA
*
79 TG-AAAT
64 AGAAAAT
*
85 -ACCTCAGC--GTCTGAGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTGAAACAAATTAAA
1 AACCTCAGCGTGTCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTGAAA-AAA--AAA
147 AAGAAAAT
63 AAGAAAAT
* *
155 AAAAACCTCAGCGTGTCCTGAGGCTCAACTCACACTCTCGCAATATGAGTTGATTTT-AAAACAG
1 ---AACCTCAGCGTGT-CTGAGGCTCAACTCAC-CTCTCGCAATATGAGTTGATTTTGAAAAAAA
**
219 AAAATTAAAT
61 AAAAGAAAAT
*
229 TACCTCAGCGTGTC-GAGGCTCAACTCACCTCT-GCAATATGAGTTGA-TTTGAAAAA
1 AACCTCAGCGTGTCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTGAAAAA
284 GTAGAAATTA
Statistics
Matches: 172, Mismatches: 11, Indels: 33
0.80 0.05 0.15
Matches are distributed among these distances:
65 9 0.05
66 16 0.09
67 44 0.26
68 7 0.04
69 18 0.10
70 5 0.03
71 12 0.07
74 16 0.09
76 4 0.02
77 19 0.11
78 22 0.13
ACGTcount: A:0.34, C:0.22, G:0.17, T:0.27
Consensus pattern (70 bp):
AACCTCAGCGTGTCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTGAAAAAAAAAAAG
AAAAT
Found at i:268 original size:145 final size:141
Alignment explanation
Indices: 8--281 Score: 430
Period size: 145 Copynumber: 1.9 Consensus size: 141
1 ATGAAAC
8 AAAATTAAAAACCTCGCGTGTCCTGAGGCTCACTCACCTCTCGAATATGAGTTGATTTTGAAAAC
1 AAAATTAAAAACCTCGCGTGTCCTGAGGCTCACTCACCTCTCGAATATGAGTTGATTTTGAAAAC
*
73 AGAAATTGAAATACCTCAGCGTCTGAGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTGAAA
66 AGAAATTGAAATACCTCAGCGTCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGA-TTTGAAA
138 CAAATTAAAAAG
130 CAAATTAAAAAG
150 AAAA-TAAAAACCTCAGCGTGTCCTGAGGCTCAACTCACACTCTCGCAATATGAGTTGATTTT-A
1 AAAATTAAAAACCTC-GCGTGTCCTGAGGCTC-ACTCAC-CTCTCG-AATATGAGTTGATTTTGA
*
213 AAACAGAAAATT-AAATTACCTCAGCGTGTCGAGGCTCAACTCACCTCT-GCAATATGAGTTGAT
62 AAACAG-AAATTGAAA-TACCTCAGCGTCT-GAGGCTCAACTCACCTCTCGCAATATGAGTTGAT
276 TTGAAA
124 TTGAAA
282 AAGTAGAAAT
Statistics
Matches: 123, Mismatches: 2, Indels: 12
0.90 0.01 0.09
Matches are distributed among these distances:
141 10 0.08
142 20 0.16
143 6 0.05
144 23 0.19
145 47 0.38
146 17 0.14
ACGTcount: A:0.35, C:0.21, G:0.17, T:0.27
Consensus pattern (141 bp):
AAAATTAAAAACCTCGCGTGTCCTGAGGCTCACTCACCTCTCGAATATGAGTTGATTTTGAAAAC
AGAAATTGAAATACCTCAGCGTCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTGAAAC
AAATTAAAAAG
Found at i:442 original size:51 final size:51
Alignment explanation
Indices: 341--440 Score: 141
Period size: 51 Copynumber: 1.9 Consensus size: 51
331 TGAAAACAGA
*
341 AATTG-AAATTACCTCACGTGTCTGAGGCTCAACTCATCTCGCAATATATG
1 AATTGAAAAATACCTCACGTGTCTGAGGCTCAACTCATCTCGCAATATATG
*
391 AATTGAAAAATACCTCA-GTGTGTTGAGGCTCAACTCACCTCTCGCAATAT
1 AATTGAAAAATACCTCACGTGT-CTGAGGCTCAACTCA--TCTCGCAATAT
441 GAGTTGATTT
Statistics
Matches: 44, Mismatches: 2, Indels: 5
0.86 0.04 0.10
Matches are distributed among these distances:
50 9 0.20
51 24 0.55
53 11 0.25
ACGTcount: A:0.31, C:0.24, G:0.16, T:0.29
Consensus pattern (51 bp):
AATTGAAAAATACCTCACGTGTCTGAGGCTCAACTCATCTCGCAATATATG
Found at i:498 original size:73 final size:72
Alignment explanation
Indices: 398--1018 Score: 870
Period size: 69 Copynumber: 8.8 Consensus size: 72
388 ATGAATTGAA
* *
398 AAATACCTCAGTGTGT--TGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTAAAAAAAC
1 AAATACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTT-TAAAAAC
461 AG-AATTG
65 AGAAATTG
*
468 AAATACCTCAGCATGTGACC-GAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTAAAAA
1 AAATACCTCAGC--GTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTAAAAA
532 CAGAAATTG
64 CAGAAATTG
* *
541 AAAATACCTCAGCGTGTCCTGAGGCTCAACTCA--TCTCGCAATATGAG-TGA-ATTTTGAAAA-
1 -AAATACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTAAAAAC
601 AGAAATTG
65 AGAAATTG
609 AAATACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAAA
1 AAATACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGA-TTTTTT-AAAAA
674 CAGAAATTG
64 CAGAAATTG
*
683 AAAATACCTCA-CGTGTCC-GAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTGAAAAC
1 -AAATACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTAAAAAC
746 AGAAATTG
65 AGAAATTG
* **
754 AAATACCTCAGCGTGTCC-GAGGCTCAACTCACCTCTCGCAATATAAGTTGATTTTTTTTGAAAC
1 AAATACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGA-TTTTTTAAAAAC
818 AGAAATTG
65 AGAAATTG
* * *
826 AAATACCTCAACGTGT-CTGAGGCTCAACTCA--TCTCGCAATATAAGTTGA--TTTTGAAAACA
1 AAATACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTAAAAACA
886 GAAATTG
66 GAAATTG
**
893 AAATTACCTCAGCGTGTCCTGAGGCTCAACTCATTTCTCGCAATATGAGTTGA---TTT-AAAAC
1 AAA-TACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTAAAAAC
954 AGAAATTG
65 AGAAATTG
*
962 AAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTAGCAATATGAGTTGATTTT
1 AAA-TACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTT
1019 GAAAACAAAA
Statistics
Matches: 506, Mismatches: 20, Indels: 48
0.88 0.03 0.08
Matches are distributed among these distances:
67 51 0.10
68 20 0.04
69 100 0.20
70 48 0.09
71 84 0.17
72 73 0.14
73 93 0.18
74 27 0.05
75 10 0.02
ACGTcount: A:0.33, C:0.21, G:0.17, T:0.29
Consensus pattern (72 bp):
AAATACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTAAAAACA
GAAATTG
Found at i:769 original size:71 final size:71
Alignment explanation
Indices: 398--1031 Score: 865
Period size: 73 Copynumber: 9.0 Consensus size: 71
388 ATGAATTGAA
* * **
398 AAATACCTCAGTGTGT-TGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTAAAAAAACA
1 AAATACCTCAGCGTGTCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTT-TGAAAACA
462 G-AATTG
65 GAAATTG
* *
468 AAATACCTCAGCATGTGACCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTAAAAAC
1 AAATACCTCAGC--GTGTCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTGAAAAC
533 AGAAATTG
64 AGAAATTG
*
541 AAAATACCTCAGCGTGTCCTGAGGCTCAACTCA--TCTCGCAATATGAG-TGA-ATTTTGAAAA-
1 -AAATACCTCAGCGTGTCC-GAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTGAAAAC
601 AGAAATTG
64 AGAAATTG
609 AAATACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAAA
1 AAATACCTCAGCGTGTCC-GAGGCTCAACTCACCTCTCGCAATATGAGTTGA-TTTTTTG-AAAA
674 CAGAAATTG
63 CAGAAATTG
683 AAAATACCTCA-CGTGTCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTGAAAACA
1 -AAATACCTCAGCGTGTCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTGAAAACA
747 GAAATTG
65 GAAATTG
*
754 AAATACCTCAGCGTGTCCGAGGCTCAACTCACCTCTCGCAATATAAGTTGATTTTTTTTG-AAAC
1 AAATACCTCAGCGTGTCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGA--TTTTTTGAAAAC
818 AGAAATTG
64 AGAAATTG
* * *
826 AAATACCTCAACGTGTCTGAGGCTCAACTCA--TCTCGCAATATAAGTTGA--TTTTGAAAACAG
1 AAATACCTCAGCGTGTCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTGAAAACAG
887 AAATTG
66 AAATTG
**
893 AAATTACCTCAGCGTGTCCTGAGGCTCAACTCATTTCTCGCAATATGAGTTGA---TTT-AAAAC
1 AAA-TACCTCAGCGTGTCC-GAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTGAAAAC
954 AGAAATTG
64 AGAAATTG
*
962 AAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTAGCAATATGAGTTGA--TTTTGAAAAC
1 AAA-TACCTCAGCGTGTCC-GAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTGAAAAC
*
1025 AAAAATT
64 AGAAATT
1032 AAAAGGCTTA
Statistics
Matches: 522, Mismatches: 18, Indels: 47
0.89 0.03 0.08
Matches are distributed among these distances:
66 5 0.01
67 47 0.09
68 21 0.04
69 98 0.19
70 51 0.10
71 94 0.18
72 69 0.13
73 100 0.19
74 27 0.05
75 10 0.02
ACGTcount: A:0.33, C:0.21, G:0.17, T:0.29
Consensus pattern (71 bp):
AAATACCTCAGCGTGTCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTGAAAACAG
AAATTG
Found at i:793 original size:213 final size:213
Alignment explanation
Indices: 398--1208 Score: 950
Period size: 190 Copynumber: 3.9 Consensus size: 213
388 ATGAATTGAA
* **
398 AAATACCTCAGTGTGT-TGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTAAAAAAACA
1 AAATACCTCAGCGTGTCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTGAAAAACA
*
462 G-AATTG-AAATACCTCAGCATGTGACCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTT
66 GAAATTGAAAATACCTCAGC--GTGTCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTT
525 TTAAAAACAGAAATTGAAAATACCTCAGCGTGTCCTGAGGCTCAACTCA--TCTCGCAATATGAG
129 TT-AAAACAGAAATTG-AAATACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAG
588 -TGAATTTTGAAAAAGAAATTG
192 TTGAATTTTGAAAAAGAAATTG
609 AAATACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAAA
1 AAATACCTCAGCGTGT-CTGAGGCTCAACTCACCTCTCGCAATATGAGTTGA-TTTTTTGAAAAA
674 CAGAAATTGAAAATACCTCA-CGTGTCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTT
64 CAGAAATTGAAAATACCTCAGCGTGTCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTT
*
738 TTGAAAACAGAAATTGAAATACCTCAGCGTGTCC-GAGGCTCAACTCACCTCTCGCAATATAAGT
129 TT-AAAACAGAAATTGAAATACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGT
* *
802 TGATTTTTTTTGAAACAGAAATTG
193 TGA---ATTTTGAAAAAGAAATTG
* *
826 AAATACCTCAACGTGTCTGAGGCTCAACTCA--TCTCGCAATATAAGTTGA--TTTTG-AAAACA
1 AAATACCTCAGCGTGTCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTGAAAAACA
* **
886 GAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCATTTCTCGCAATATGAGTTGA---TT
66 GAAATTGAAAATACCTCAGCGTGTCC-GAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTT
*
948 TAAAACAGAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTAGCAATATGAGTT
130 TAAAACAGAAATTGAAA-TACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTT
*
1013 G-ATTTTGAAAACAAAAATT-
194 GAATTTTGAAAA-AGAAATTG
* *
1032 -AA-A----A--G-G-CT-----T-AACTCACCTCTCGCAATATGAG-TCA--ATTT--AAAACA
1 AAATACCTCAGCGTGTCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTGAAAAACA
* * * * * *
1076 TAAACTAAAAATACCTCGGCGTGCCCCGAGGCTCAACTCACTTCTCGCAATATGAGTTGA-TTTT
66 GAAATTGAAAATACCTCAGCGTG-TCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTT
* * * * * *
1140 GAAAA-AAAAATTAAAATACCTCAACGTGTCTTGAGGCTCAACTCATCTCTCGCAATATGAGTTG
130 TAAAACAGAAATTGAAATACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTG
1204 -ATTTT
195 AATTTT
1209 CCTTGGAAAG
Statistics
Matches: 544, Mismatches: 35, Indels: 63
0.85 0.05 0.10
Matches are distributed among these distances:
190 111 0.20
191 17 0.03
192 19 0.03
196 2 0.00
197 1 0.00
198 1 0.00
200 1 0.00
204 1 0.00
205 2 0.00
206 8 0.01
207 6 0.01
208 16 0.03
209 18 0.03
210 53 0.10
211 40 0.07
212 49 0.09
213 104 0.19
214 33 0.06
215 6 0.01
216 25 0.05
217 31 0.06
ACGTcount: A:0.34, C:0.21, G:0.17, T:0.29
Consensus pattern (213 bp):
AAATACCTCAGCGTGTCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTGAAAAACA
GAAATTGAAAATACCTCAGCGTGTCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTT
AAAACAGAAATTGAAATACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGA
ATTTTGAAAAAGAAATTG
Found at i:1128 original size:121 final size:120
Alignment explanation
Indices: 914--1155 Score: 349
Period size: 121 Copynumber: 2.0 Consensus size: 120
904 GCGTGTCCTG
** ** * * * *
914 AGGCTCAACTCATTTCTCGCAATATGAGTTGATTTAAAACAGAAATTGAAATTACCTCAGCGTGT
1 AGGCTCAACTCACCTCTCGCAATATGAGTCAATTTAAAACAGAAACTAAAAATACCTCAGCGTGC
*
979 CCTGAGGCTCAACTCACCTCTAGCAATATGAGTTGATTTTGAAAACAAAAATTAAA
66 CCCGAGGCTCAACTCACCTCTAGCAATATGAGTTGATTTTGAAAA-AAAAATTAAA
* * *
1035 AGGCTTAACTCACCTCTCGCAATATGAGTCAATTTAAAACATAAACTAAAAATACCTCGGCGTGC
1 AGGCTCAACTCACCTCTCGCAATATGAGTCAATTTAAAACAGAAACTAAAAATACCTCAGCGTGC
* *
1100 CCCGAGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTGAAAAAAAAATTAAA
66 CCCGAGGCTCAACTCACCTCTAGCAATATGAGTTGATTTTGAAAAAAAAATTAAA
1155 A
1 A
1156 TACCTCAACG
Statistics
Matches: 107, Mismatches: 14, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
120 11 0.10
121 96 0.90
ACGTcount: A:0.37, C:0.21, G:0.15, T:0.27
Consensus pattern (120 bp):
AGGCTCAACTCACCTCTCGCAATATGAGTCAATTTAAAACAGAAACTAAAAATACCTCAGCGTGC
CCCGAGGCTCAACTCACCTCTAGCAATATGAGTTGATTTTGAAAAAAAAATTAAA
Found at i:1156 original size:69 final size:70
Alignment explanation
Indices: 1035--1208 Score: 203
Period size: 69 Copynumber: 2.5 Consensus size: 70
1025 AAAAATTAAA
* * * * * **
1035 AGGCTTAACTCACCTCTCGCAATATGAG-TCAATTTAAAACATAAACTAAAAATACCTCGGCGTG
1 AGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTAAAACATAAAATAAAAATACCTCAACGTG
1099 CCCCG
66 CCCCG
*
1104 AGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTGAAAA-A-AAAATTAAAATACCTCAACGT
1 AGGCTCAACTCACTTCTCGCAATATGAGTTGATTTT-AAAACATAAAATAAAAATACCTCAACGT
* **
1167 GTCTTG
65 GCCCCG
1173 AGGCTCAACTCA-TCTCTCGCAATATGAGTTGATTTT
1 AGGCTCAACTCACT-TCTCGCAATATGAGTTGATTTT
1209 CCTTGGAAAG
Statistics
Matches: 91, Mismatches: 11, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
68 1 0.01
69 80 0.88
70 6 0.07
71 4 0.04
ACGTcount: A:0.33, C:0.23, G:0.15, T:0.29
Consensus pattern (70 bp):
AGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTAAAACATAAAATAAAAATACCTCAACGTG
CCCCG
Found at i:9656 original size:20 final size:21
Alignment explanation
Indices: 9605--9660 Score: 64
Period size: 20 Copynumber: 2.8 Consensus size: 21
9595 ATACTACATC
9605 AATATGTACAT-ATATAAAAA
1 AATATGTACATAATATAAAAA
* * *
9625 AATACGT-GATAATAT-TAAA
1 AATATGTACATAATATAAAAA
9644 AATATGTACATAATATA
1 AATATGTACATAATATA
9661 GTGTTAAAAA
Statistics
Matches: 28, Mismatches: 5, Indels: 5
0.74 0.13 0.13
Matches are distributed among these distances:
19 11 0.39
20 17 0.61
ACGTcount: A:0.55, C:0.05, G:0.07, T:0.32
Consensus pattern (21 bp):
AATATGTACATAATATAAAAA
Found at i:9702 original size:22 final size:24
Alignment explanation
Indices: 9639--9703 Score: 80
Period size: 25 Copynumber: 2.8 Consensus size: 24
9629 CGTGATAATA
*
9639 TTAAAAATATGTACATAATATAGTG
1 TTAAAAATATATACATAATATAG-G
*
9664 TTAAAAATACATACATAATATA-G
1 TTAAAAATATATACATAATATAGG
*
9687 TT-AAGATATATACATAA
1 TTAAAAATATATACATAA
9704 GATAACATGT
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
22 13 0.36
23 3 0.08
25 20 0.56
ACGTcount: A:0.52, C:0.06, G:0.08, T:0.34
Consensus pattern (24 bp):
TTAAAAATATATACATAATATAGG
Found at i:9792 original size:52 final size:47
Alignment explanation
Indices: 9724--9856 Score: 141
Period size: 44 Copynumber: 2.8 Consensus size: 47
9714 AAAAAAATAT
*
9724 ATATATATAAATAATATAATATTAAAGATATATACATAAAATAGTATAAA
1 ATATATATATATAATATAATATT-AAGATATATACATAAAATA-T-TAAA
* *
9774 ATATATATATACGTAATATAA-ATTTAA-A-ATATACCTAATATATTAAA
1 ATATATATATA--TAATATAATA-TTAAGATATATACATAAAATATTAAA
*
9821 AGA-ATATATATAATATAATATTAAGATATATA-ATAA
1 ATATATATATATAATATAATATTAAGATATATACATAA
9857 TAACAAAAAA
Statistics
Matches: 72, Mismatches: 5, Indels: 17
0.77 0.05 0.18
Matches are distributed among these distances:
44 12 0.17
45 5 0.07
46 12 0.17
47 6 0.08
48 1 0.01
49 12 0.17
50 11 0.15
51 3 0.04
52 10 0.14
ACGTcount: A:0.57, C:0.03, G:0.04, T:0.36
Consensus pattern (47 bp):
ATATATATATATAATATAATATTAAGATATATACATAAAATATTAAA
Found at i:10376 original size:30 final size:30
Alignment explanation
Indices: 10340--10454 Score: 194
Period size: 30 Copynumber: 3.8 Consensus size: 30
10330 TAGGTACAAG
* *
10340 TGGTGGTGGAGAAGGTGTGGCTAGTGGAGT
1 TGGTGGTGGAAAAGGAGTGGCTAGTGGAGT
*
10370 TGGTGGTGGAAAAAGAGTGGCTAGTGGAGT
1 TGGTGGTGGAAAAGGAGTGGCTAGTGGAGT
*
10400 TGGTGGTGGAAAAGGTGTGGCTAGTGGAGT
1 TGGTGGTGGAAAAGGAGTGGCTAGTGGAGT
10430 TGGTGGTGGAAAAGGAGTGGCTAGT
1 TGGTGGTGGAAAAGGAGTGGCTAGT
10455 TGAGAAAAGT
Statistics
Matches: 79, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 79 1.00
ACGTcount: A:0.22, C:0.03, G:0.50, T:0.25
Consensus pattern (30 bp):
TGGTGGTGGAAAAGGAGTGGCTAGTGGAGT
Found at i:16927 original size:12 final size:12
Alignment explanation
Indices: 16893--16927 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
16883 TAAAAAAAAC
16893 TATTTTATTTAA
1 TATTTTATTTAA
* *
16905 TATTCTGTTTAA
1 TATTTTATTTAA
16917 TATTTTATTTA
1 TATTTTATTTA
16928 TTTAATTTCT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.29, C:0.03, G:0.03, T:0.66
Consensus pattern (12 bp):
TATTTTATTTAA
Found at i:21495 original size:15 final size:16
Alignment explanation
Indices: 21477--21514 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
21467 ATTTATGTAA
*
21477 TTTTATATATA-AAAT
1 TTTTATATAAACAAAT
*
21492 TTTTATTTAAACAAAT
1 TTTTATATAAACAAAT
21508 TTTTATA
1 TTTTATA
21515 AATTATTATC
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
15 9 0.47
16 10 0.53
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (16 bp):
TTTTATATAAACAAAT
Found at i:23413 original size:17 final size:18
Alignment explanation
Indices: 23377--23419 Score: 52
Period size: 17 Copynumber: 2.4 Consensus size: 18
23367 GCCCACAAAT
*
23377 TTCCTTTTTTGTCATTCC
1 TTCCTTTCTTGTCATTCC
*
23395 TTCCTTTCTT-TCTTTCC
1 TTCCTTTCTTGTCATTCC
*
23412 TTCTTTTC
1 TTCCTTTC
23420 CACGTTCTCC
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
17 13 0.59
18 9 0.41
ACGTcount: A:0.02, C:0.30, G:0.02, T:0.65
Consensus pattern (18 bp):
TTCCTTTCTTGTCATTCC
Found at i:23452 original size:17 final size:17
Alignment explanation
Indices: 23430--23501 Score: 60
Period size: 17 Copynumber: 4.2 Consensus size: 17
23420 CACGTTCTCC
23430 TTTTGTTATTTCTTTCT
1 TTTTGTTATTTCTTTCT
*
23447 TTTTGTTATTATTTTTCCT
1 TTTTGTTATT-TCTTT-CT
* *
23466 TTTTATT-TTTATTT-T
1 TTTTGTTATTTCTTTCT
*
23481 TATT-TTATTTCTTTTCT
1 TTTTGTTATTTC-TTTCT
23498 TTTT
1 TTTT
23502 TATTCTCAAC
Statistics
Matches: 44, Mismatches: 6, Indels: 10
0.73 0.10 0.17
Matches are distributed among these distances:
14 2 0.05
15 7 0.16
16 3 0.07
17 18 0.41
18 6 0.14
19 8 0.18
ACGTcount: A:0.10, C:0.08, G:0.03, T:0.79
Consensus pattern (17 bp):
TTTTGTTATTTCTTTCT
Found at i:23469 original size:19 final size:18
Alignment explanation
Indices: 23430--23486 Score: 62
Period size: 19 Copynumber: 3.2 Consensus size: 18
23420 CACGTTCTCC
*
23430 TTTTGTTATT-TCTTTCT
1 TTTTGTTATTATTTTTCT
23447 TTTTGTTATTATTTTTCCT
1 TTTTGTTATTATTTTT-CT
* * *
23466 TTTTATTTTTATTTTTAT
1 TTTTGTTATTATTTTTCT
23484 TTT
1 TTT
23487 ATTTCTTTTC
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
17 10 0.29
18 8 0.24
19 16 0.47
ACGTcount: A:0.11, C:0.07, G:0.04, T:0.79
Consensus pattern (18 bp):
TTTTGTTATTATTTTTCT
Found at i:23633 original size:19 final size:19
Alignment explanation
Indices: 23609--23649 Score: 82
Period size: 19 Copynumber: 2.2 Consensus size: 19
23599 TTCCTTCTCC
23609 TCTACTTCTACGATTCAAA
1 TCTACTTCTACGATTCAAA
23628 TCTACTTCTACGATTCAAA
1 TCTACTTCTACGATTCAAA
23647 TCT
1 TCT
23650 CTTATAAGTC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.29, C:0.27, G:0.05, T:0.39
Consensus pattern (19 bp):
TCTACTTCTACGATTCAAA
Found at i:29876 original size:15 final size:15
Alignment explanation
Indices: 29856--29907 Score: 50
Period size: 15 Copynumber: 3.2 Consensus size: 15
29846 ACTACAAAAC
29856 ATTTATTATTAATAT
1 ATTTATTATTAATAT
*
29871 ATTTATAATTGTAATAAAT
1 ATTTATTA-T-TAAT--AT
*
29890 ATTTATTATTAAAAT
1 ATTTATTATTAATAT
29905 ATT
1 ATT
29908 AACATTGAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 8
0.73 0.07 0.20
Matches are distributed among these distances:
15 12 0.40
16 1 0.03
17 7 0.23
18 1 0.03
19 9 0.30
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (15 bp):
ATTTATTATTAATAT
Found at i:29971 original size:16 final size:16
Alignment explanation
Indices: 29940--29976 Score: 58
Period size: 16 Copynumber: 2.3 Consensus size: 16
29930 ATGCTAATAA
29940 TATTATTTAAAATTAT
1 TATTATTTAAAATTAT
29956 TATT-TTTAAAATTTAT
1 TATTATTTAAAA-TTAT
29972 TATTA
1 TATTA
29977 AAATAAAATC
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
15 7 0.37
16 12 0.63
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (16 bp):
TATTATTTAAAATTAT
Done.