Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold533
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: 86003
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.31
Warning! 7068 characters in sequence are not A, C, G, or T
Found at i:60 original size:21 final size:21
Alignment explanation
Indices: 2--87 Score: 57
Period size: 21 Copynumber: 4.0 Consensus size: 21
1 G
* *
2 ACCCTTAAATCCTAAACCCTAA
1 ACCCCTAAATCCT-AACCCTTA
* * **
24 ATCCCTAACTATTAACCCTTA
1 ACCCCTAAATCCTAACCCTTA
*
45 ACCCCTAACTCCTAA-CCTCTA
1 ACCCCTAAATCCTAACCCT-TA
* * *
66 AACCTTAAATCCCAACCCTTA
1 ACCCCTAAATCCTAACCCTTA
87 A
1 A
88 ACCATGATCC
Statistics
Matches: 49, Mismatches: 13, Indels: 5
0.73 0.19 0.07
Matches are distributed among these distances:
20 3 0.06
21 35 0.71
22 11 0.22
ACGTcount: A:0.36, C:0.38, G:0.00, T:0.26
Consensus pattern (21 bp):
ACCCCTAAATCCTAACCCTTA
Found at i:321 original size:41 final size:42
Alignment explanation
Indices: 262--566 Score: 498
Period size: 41 Copynumber: 7.4 Consensus size: 42
252 AACCAAATCT
262 TCAAAAACGCCGCTAAAGGCCTGAGCATTAGCGGCGCTTCCA
1 TCAAAAACGCCGCTAAAGGCCTGAGCATTAGCGGCGCTTCCA
304 T-AAAAACGCCGCTAAAGGCCTGAGCATTAGCGGCGCTTCCA
1 TCAAAAACGCCGCTAAAGGCCTGAGCATTAGCGGCGCTTCCA
345 T-AAAAACGCCGCTAAAGGCCTGAGCATTAGCGGCGCTTCC-
1 TCAAAAACGCCGCTAAAGGCCTGAGCATTAGCGGCGCTTCCA
* * *
385 TCACAAACGCCGCTAAAGGCCTAAGCATTAGCGGCGCTT-TA
1 TCAAAAACGCCGCTAAAGGCCTGAGCATTAGCGGCGCTTCCA
*
426 TCAAAAACGCCGCTAAAGGCATGAGCATTAGCGGCGCTTCC-
1 TCAAAAACGCCGCTAAAGGCCTGAGCATTAGCGGCGCTTCCA
*
467 TCAAAAACGCCGCTAAAGGCCTGAGCATTAGCGGCGCTT-TA
1 TCAAAAACGCCGCTAAAGGCCTGAGCATTAGCGGCGCTTCCA
*
508 TCAAAAACGCCGCTAAAGGCCTAAGCATTAGCGGCGCTTCC-
1 TCAAAAACGCCGCTAAAGGCCTGAGCATTAGCGGCGCTTCCA
*
549 TCAAAAACGCCACTAAAG
1 TCAAAAACGCCGCTAAAG
567 CCCCGAAAAC
Statistics
Matches: 246, Mismatches: 12, Indels: 11
0.91 0.04 0.04
Matches are distributed among these distances:
40 1 0.00
41 244 0.99
42 1 0.00
ACGTcount: A:0.30, C:0.30, G:0.23, T:0.17
Consensus pattern (42 bp):
TCAAAAACGCCGCTAAAGGCCTGAGCATTAGCGGCGCTTCCA
Found at i:7105 original size:56 final size:55
Alignment explanation
Indices: 7032--7185 Score: 202
Period size: 56 Copynumber: 2.7 Consensus size: 55
7022 AGTAGTTACA
*
7032 TAGGAATCAAATTGCTAAAACATAATATCCCATAATAATATCCTATAACATCCTAT
1 TAGGAATCAAA-TGCTAAAACATAATATCCCATAATAATATCCTATAACATCCCAT
* * * *
7088 TAGGAATCAAACTGCTAAGATATAATATCTCATAATAATATCCTATAATATCCCAT
1 TAGGAATCAAA-TGCTAAAACATAATATCCCATAATAATATCCTATAACATCCCAT
*
7144 TAGGAATCAAATGGCTAAAAAGATAATA-CCTCATAATAATAT
1 TAGGAATCAAAT-GCT-AAAACATAATATCC-CATAATAATAT
7186 ATCAACAAAT
Statistics
Matches: 86, Mismatches: 9, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
55 1 0.01
56 65 0.76
57 20 0.23
ACGTcount: A:0.45, C:0.17, G:0.08, T:0.30
Consensus pattern (55 bp):
TAGGAATCAAATGCTAAAACATAATATCCCATAATAATATCCTATAACATCCCAT
Found at i:13162 original size:15 final size:15
Alignment explanation
Indices: 13142--13183 Score: 59
Period size: 15 Copynumber: 2.8 Consensus size: 15
13132 TAATTAATTA
13142 TTATTATTATTGTA-T
1 TTATTATTATT-TACT
*
13157 TTATTATTACTTACT
1 TTATTATTATTTACT
13172 TTATTATTATTT
1 TTATTATTATTT
13184 TTATTTACCC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
14 2 0.08
15 22 0.92
ACGTcount: A:0.26, C:0.05, G:0.02, T:0.67
Consensus pattern (15 bp):
TTATTATTATTTACT
Found at i:14548 original size:27 final size:27
Alignment explanation
Indices: 14495--14550 Score: 67
Period size: 27 Copynumber: 2.1 Consensus size: 27
14485 ATATATATTC
* *
14495 AATTATAAAAATGCAACACGCACTTTT
1 AATTATAAAAATACAACACACACTTTT
* * *
14522 AATTATAAAAATATAACACATATTTTT
1 AATTATAAAAATACAACACACACTTTT
14549 AA
1 AA
14551 GCACTAAATA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.50, C:0.12, G:0.04, T:0.34
Consensus pattern (27 bp):
AATTATAAAAATACAACACACACTTTT
Found at i:15082 original size:21 final size:18
Alignment explanation
Indices: 15026--15092 Score: 73
Period size: 18 Copynumber: 3.6 Consensus size: 18
15016 AAAAAATTAT
*
15026 TTTAAAAATATTTTAAAA
1 TTTAAAAAAATTTTAAAA
**
15044 TTTAAAAAAATTAAAAAA
1 TTTAAAAAAATTTTAAAA
15062 GTATGTAAAAAAATTTTAAAA
1 -T-T-TAAAAAAATTTTAAAA
15083 -TTAAAAAAAT
1 TTTAAAAAAAT
15093 AAATATACTT
Statistics
Matches: 41, Mismatches: 5, Indels: 7
0.77 0.09 0.13
Matches are distributed among these distances:
17 9 0.22
18 16 0.39
19 1 0.02
20 1 0.02
21 14 0.34
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.34
Consensus pattern (18 bp):
TTTAAAAAAATTTTAAAA
Found at i:17898 original size:27 final size:29
Alignment explanation
Indices: 17864--17935 Score: 103
Period size: 27 Copynumber: 2.5 Consensus size: 29
17854 AATACATATA
*
17864 TTTAATTATAAAAATGCAATAC-ACTTTT
1 TTTAATTATAAAAATGCAATACAAATTTT
*
17892 TTT-ATTATAAAAATGTAATACATAATTTT
1 TTTAATTATAAAAATGCAATACA-AATTTT
17921 TTTAATTATAAAAAT
1 TTTAATTATAAAAAT
17936 ATAACACATA
Statistics
Matches: 39, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
27 17 0.44
28 3 0.08
29 8 0.21
30 11 0.28
ACGTcount: A:0.46, C:0.06, G:0.03, T:0.46
Consensus pattern (29 bp):
TTTAATTATAAAAATGCAATACAAATTTT
Found at i:17929 original size:30 final size:30
Alignment explanation
Indices: 17864--17951 Score: 119
Period size: 30 Copynumber: 3.0 Consensus size: 30
17854 AATACATATA
*
17864 TTTAATTATAAAAATGCAATAC--ACTTTT
1 TTTAATTATAAAAATGTAATACATACTTTT
*
17892 TTT-ATTATAAAAATGTAATACATAATTTT
1 TTTAATTATAAAAATGTAATACATACTTTT
* *
17921 TTTAATTATAAAAATATAACACATACTTTT
1 TTTAATTATAAAAATGTAATACATACTTTT
17951 T
1 T
17952 AAGCACTAAA
Statistics
Matches: 52, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
27 17 0.33
28 3 0.06
29 8 0.15
30 24 0.46
ACGTcount: A:0.44, C:0.08, G:0.02, T:0.45
Consensus pattern (30 bp):
TTTAATTATAAAAATGTAATACATACTTTT
Found at i:18246 original size:13 final size:13
Alignment explanation
Indices: 18228--18255 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
18218 AGTAGATTCA
18228 TTTATAATTAATG
1 TTTATAATTAATG
18241 TTTATAATTAATG
1 TTTATAATTAATG
18254 TT
1 TT
18256 GAATTTTTAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.36, C:0.00, G:0.07, T:0.57
Consensus pattern (13 bp):
TTTATAATTAATG
Found at i:23288 original size:19 final size:20
Alignment explanation
Indices: 23252--23301 Score: 77
Period size: 19 Copynumber: 2.6 Consensus size: 20
23242 ATAACAAAAA
23252 CAAAATAATTTTCAAAAATT
1 CAAAATAATTTTCAAAAATT
*
23272 CAAAATAATTTT-TAAAATT
1 CAAAATAATTTTCAAAAATT
23291 CAAAAT-ATTTT
1 CAAAATAATTTT
23302 GAGGATATAT
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
18 5 0.17
19 12 0.41
20 12 0.41
ACGTcount: A:0.52, C:0.08, G:0.00, T:0.40
Consensus pattern (20 bp):
CAAAATAATTTTCAAAAATT
Found at i:26312 original size:41 final size:41
Alignment explanation
Indices: 26255--26337 Score: 148
Period size: 41 Copynumber: 2.0 Consensus size: 41
26245 TTGGGCAACC
*
26255 ACTTTCCCTTCAACCAACACAACTAAAATAAAAGGATTTGA
1 ACTTTCCCTTCAACCAACACAACTAAAACAAAAGGATTTGA
*
26296 ACTTTCCCTTCAACCAACACAACTAAAACAAAGGGATTTGA
1 ACTTTCCCTTCAACCAACACAACTAAAACAAAAGGATTTGA
26337 A
1 A
26338 TTTTTTATTA
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 40 1.00
ACGTcount: A:0.43, C:0.25, G:0.08, T:0.23
Consensus pattern (41 bp):
ACTTTCCCTTCAACCAACACAACTAAAACAAAAGGATTTGA
Found at i:29174 original size:25 final size:25
Alignment explanation
Indices: 29109--29162 Score: 83
Period size: 25 Copynumber: 2.2 Consensus size: 25
29099 GTTATTAGGG
* *
29109 TTACCGATTC-CAGCTCTTATGAGC
1 TTACCGATACTCAGCTCGTATGAGC
29133 TTACCGATACTCAGCTCGTATGAGC
1 TTACCGATACTCAGCTCGTATGAGC
29158 TTACC
1 TTACC
29163 ATTATTTAGC
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
24 9 0.33
25 18 0.67
ACGTcount: A:0.22, C:0.30, G:0.17, T:0.31
Consensus pattern (25 bp):
TTACCGATACTCAGCTCGTATGAGC
Found at i:45999 original size:5 final size:5
Alignment explanation
Indices: 45989--46021 Score: 66
Period size: 5 Copynumber: 6.6 Consensus size: 5
45979 TGATAAGTGG
45989 ATTTT ATTTT ATTTT ATTTT ATTTT ATTTT ATT
1 ATTTT ATTTT ATTTT ATTTT ATTTT ATTTT ATT
46022 AATAAAAGCA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 28 1.00
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (5 bp):
ATTTT
Found at i:68270 original size:21 final size:20
Alignment explanation
Indices: 68246--68315 Score: 65
Period size: 21 Copynumber: 3.5 Consensus size: 20
68236 TTTATTTTTA
68246 CTTTTTTATTAACTTTTATCT
1 CTTTTTTATTAA-TTTTATCT
* *
68267 CTTTTTTTTTAATTTT-TTT
1 CTTTTTTATTAATTTTATCT
68286 C-TTTTT-TTAAGTTTTATCT
1 CTTTTTTATTAA-TTTTATCT
*
68305 TTTTTCTTATT
1 CTTTT-TTATT
68316 TTATTTTGTT
Statistics
Matches: 40, Mismatches: 4, Indels: 9
0.75 0.08 0.17
Matches are distributed among these distances:
17 4 0.10
18 9 0.22
19 5 0.12
20 7 0.17
21 13 0.32
22 2 0.05
ACGTcount: A:0.14, C:0.10, G:0.01, T:0.74
Consensus pattern (20 bp):
CTTTTTTATTAATTTTATCT
Found at i:68292 original size:17 final size:17
Alignment explanation
Indices: 68270--68309 Score: 62
Period size: 17 Copynumber: 2.4 Consensus size: 17
68260 TTTATCTCTT
* *
68270 TTTTTTTAATTTTTTTC
1 TTTTTTTAAGTTTTATC
68287 TTTTTTTAAGTTTTATC
1 TTTTTTTAAGTTTTATC
68304 TTTTTT
1 TTTTTT
68310 CTTATTTTAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.12, C:0.05, G:0.03, T:0.80
Consensus pattern (17 bp):
TTTTTTTAAGTTTTATC
Found at i:68301 original size:38 final size:36
Alignment explanation
Indices: 68232--68322 Score: 98
Period size: 38 Copynumber: 2.5 Consensus size: 36
68222 CCTTCTTTTA
68232 TTTTTTTATTTTTACTTTTTTATTAACTTTTATCTCTT
1 TTTTTTTATTTTTA-TTTTTTATTAACTTTTATCT-TT
* *
68270 TTTTTTTAATTTTT-TTCTTTTTTTAAGTTTTATC-TT
1 TTTTTTT-ATTTTTATT-TTTTATTAACTTTTATCTTT
*
68306 TTTTCTTA-TTTTATTTT
1 TTTTTTTATTTTTATTTT
68323 GTTTATTTAT
Statistics
Matches: 47, Mismatches: 3, Indels: 10
0.78 0.05 0.17
Matches are distributed among these distances:
34 6 0.13
35 3 0.06
36 8 0.17
37 2 0.04
38 22 0.47
39 6 0.13
ACGTcount: A:0.14, C:0.08, G:0.01, T:0.77
Consensus pattern (36 bp):
TTTTTTTATTTTTATTTTTTATTAACTTTTATCTTT
Found at i:68309 original size:9 final size:8
Alignment explanation
Indices: 68227--68346 Score: 68
Period size: 8 Copynumber: 14.9 Consensus size: 8
68217 GACACCCTTC
68227 TTTTATTT
1 TTTTATTT
68235 TTTTA--T
1 TTTTATTT
*
68241 TTTTACTT
1 TTTTATTT
*
68249 TTTTATTAAC
1 TTTTATT--T
*
68259 TTTTATCT
1 TTTTATTT
*
68267 CTTT-TTT
1 TTTTATTT
*
68274 TTTAATTT
1 TTTTATTT
*
68282 TTTTCTTT
1 TTTTATTT
**
68290 TTTTA-AG
1 TTTTATTT
68297 TTTTATCTT
1 TTTTAT-TT
* *
68306 TTTTCTTA
1 TTTTATTT
68314 TTTTATTT
1 TTTTATTT
68322 TGTTTATTT
1 T-TTTATTT
*
68331 ATTTATTT
1 TTTTATTT
68339 TATTTATT
1 T-TTTATT
68347 GTTATTAATT
Statistics
Matches: 82, Mismatches: 21, Indels: 17
0.68 0.17 0.14
Matches are distributed among these distances:
6 6 0.07
7 9 0.11
8 43 0.52
9 18 0.22
10 6 0.07
ACGTcount: A:0.16, C:0.06, G:0.02, T:0.77
Consensus pattern (8 bp):
TTTTATTT
Found at i:68317 original size:17 final size:17
Alignment explanation
Indices: 68232--68319 Score: 54
Period size: 17 Copynumber: 4.9 Consensus size: 17
68222 CCTTCTTTTA
*
68232 TTTTTTTATTTTTA-CT
1 TTTTTTTAGTTTTATCT
*
68248 TTTTTATTAACTTTTATCTCTT
1 TTTTT-TT-AGTTTTA--TC-T
* *
68270 TTTTTTTAATTTTTTTCT
1 TTTTTTT-AGTTTTATCT
*
68288 TTTTTTAAGTTTTATCT
1 TTTTTTTAGTTTTATCT
68305 TTTTTCTTA-TTTTAT
1 TTTTT-TTAGTTTTAT
68320 TTTGTTTATT
Statistics
Matches: 58, Mismatches: 7, Indels: 13
0.74 0.09 0.17
Matches are distributed among these distances:
16 5 0.09
17 21 0.36
18 15 0.26
19 2 0.03
21 9 0.16
22 6 0.10
ACGTcount: A:0.15, C:0.08, G:0.01, T:0.76
Consensus pattern (17 bp):
TTTTTTTAGTTTTATCT
Found at i:71463 original size:30 final size:30
Alignment explanation
Indices: 71427--71559 Score: 176
Period size: 30 Copynumber: 4.4 Consensus size: 30
71417 GTCGCAGAGC
* * * *
71427 AGTTCATATCACTCGGACATTGCCGGTTCA
1 AGTTCATATCACCCAGACATAGGCGGTTCA
71457 AGTTCATATCACCCAGACATAGGCGGTTCA
1 AGTTCATATCACCCAGACATAGGCGGTTCA
**
71487 AGTTCATATCACCCAGACATAGGCAATTCA
1 AGTTCATATCACCCAGACATAGGCGGTTCA
* *
71517 AGTTCATATCACCTAGACATAGGCGGTTCG
1 AGTTCATATCACCCAGACATAGGCGGTTCA
* *
71547 AGTTTATTTCACC
1 AGTTCATATCACC
71560 AAGAGCAACC
Statistics
Matches: 91, Mismatches: 12, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
30 91 1.00
ACGTcount: A:0.29, C:0.26, G:0.18, T:0.28
Consensus pattern (30 bp):
AGTTCATATCACCCAGACATAGGCGGTTCA
Found at i:74951 original size:22 final size:22
Alignment explanation
Indices: 74921--74982 Score: 81
Period size: 21 Copynumber: 2.8 Consensus size: 22
74911 AATTTTAAAA
* *
74921 TTAATAATTTATGAAAATTATAT
1 TTAA-AATTTATAAAAAATATAT
74944 TTAAAATTT-TAAAAAATATAT
1 TTAAAATTTATAAAAAATATAT
74965 TTAAAATATTATAAAAAA
1 TTAAAAT-TTATAAAAAA
74983 AACAATAAAT
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
21 17 0.49
22 7 0.20
23 11 0.31
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (22 bp):
TTAAAATTTATAAAAAATATAT
Found at i:75041 original size:25 final size:24
Alignment explanation
Indices: 75012--75081 Score: 63
Period size: 24 Copynumber: 2.9 Consensus size: 24
75002 CATATCTTTA
*
75012 AAAATAATATATTTTAAATAATTTG
1 AAAATAATA-ATTTAAAATAATTTG
* *
75037 AAAATCATAGTTTAAAATAATTT-
1 AAAATAATAATTTAAAATAATTTG
* *
75060 ACAAATCATAA-TTAAAAAAATT
1 A-AAATAATAATTTAAAATAATT
75082 ATAAAACAAA
Statistics
Matches: 39, Mismatches: 5, Indels: 4
0.81 0.10 0.08
Matches are distributed among these distances:
23 11 0.28
24 20 0.51
25 8 0.21
ACGTcount: A:0.56, C:0.04, G:0.03, T:0.37
Consensus pattern (24 bp):
AAAATAATAATTTAAAATAATTTG
Found at i:75077 original size:24 final size:23
Alignment explanation
Indices: 75027--75107 Score: 78
Period size: 24 Copynumber: 3.4 Consensus size: 23
75017 AATATATTTT
* *
75027 AAATAATTTGAAAATCATAGTTTA
1 AAATAATTT-AAAATCATAATTAA
75051 AAATAATTTACAAATCATAATTAA
1 AAATAATTTA-AAATCATAATTAA
75075 AAA-AATTATAAAA-CA-AATTAA
1 AAATAATT-TAAAATCATAATTAA
75096 AATATACATTTA
1 AA-ATA-ATTTA
75108 TAATATTATA
Statistics
Matches: 50, Mismatches: 2, Indels: 11
0.79 0.03 0.17
Matches are distributed among these distances:
21 8 0.16
22 3 0.06
23 11 0.22
24 28 0.56
ACGTcount: A:0.58, C:0.06, G:0.02, T:0.33
Consensus pattern (23 bp):
AAATAATTTAAAATCATAATTAA
Found at i:75113 original size:140 final size:140
Alignment explanation
Indices: 74952--75683 Score: 1419
Period size: 140 Copynumber: 5.2 Consensus size: 140
74942 ATTTAAAATT
* * * * *
74952 TTAAAAAATATATTTAAAATATTATAAAAAAAACAATAAATTTGAAAGGTCATATCTTTAAAAAT
1 TTAAAATATACATTTATAATATTATAAAACAAATAATAAATTTGAAAGGTCATATCTTTAAAAAT
75017 AATATATTTTAAATAATTTGAAAATCATAGTTTAAAATAATTTACAAATCATAATTAAAAAAATT
66 AATATATTTTAAATAATTTGAAAATCATAGTTTAAAATAATTTACAAATCATAATTAAAAAAATT
75082 ATAAAACAAA
131 ATAAAACAAA
75092 TTAAAATATACATTTATAATATTATAAAACAAATAATAAATTTGAAAGGTCATATCTTTAAAAAT
1 TTAAAATATACATTTATAATATTATAAAACAAATAATAAATTTGAAAGGTCATATCTTTAAAAAT
75157 AATATATTTTAAATAATTTGAAAATCATAGTTTAAAATAATTTACAAATCATAATTAAAAAAATT
66 AATATATTTTAAATAATTTGAAAATCATAGTTTAAAATAATTTACAAATCATAATTAAAAAAATT
75222 ATAAAACAAA
131 ATAAAACAAA
75232 TTAAAATATACATTTATAATATTATAAAACAAATAATAAATTTGAAAGGTCATATCTTTAAAAAT
1 TTAAAATATACATTTATAATATTATAAAACAAATAATAAATTTGAAAGGTCATATCTTTAAAAAT
75297 AATATATTTTAAATAATTTGAAAATCATAGTTTAAAATAATTTACAAATCATAATTAAAAAAATT
66 AATATATTTTAAATAATTTGAAAATCATAGTTTAAAATAATTTACAAATCATAATTAAAAAAATT
75362 ATAAAACAAA
131 ATAAAACAAA
75372 TTAAAATATACATTTATAATATTATAAAACAAATAATAAATTTGAAAGGTCATATCTTTAAAAAT
1 TTAAAATATACATTTATAATATTATAAAACAAATAATAAATTTGAAAGGTCATATCTTTAAAAAT
75437 AATATATTTTAAATAATTTGAAAATCATAGTTTAAAATAATTTACAAATCATAATTAAAAAAATT
66 AATATATTTTAAATAATTTGAAAATCATAGTTTAAAATAATTTACAAATCATAATTAAAAAAATT
75502 ATAAAACAAA
131 ATAAAACAAA
75512 TTAAAATATACATTTATAATATTATAAAACAAATAATAAATTTGAAAGGTCATATCTTTAAAAAT
1 TTAAAATATACATTTATAATATTATAAAACAAATAATAAATTTGAAAGGTCATATCTTTAAAAAT
75577 AATATATTTTAAATAATTTGAAAATCATAGTTTAAAATAATTTACAAATCATAATTAAAAAAATT
66 AATATATTTTAAATAATTTGAAAATCATAGTTTAAAATAATTTACAAATCATAATTAAAAAAATT
75642 ATAAAACAAA
131 ATAAAACAAA
75652 TTAAAATATACATTTATAATATTATAAAACAA
1 TTAAAATATACATTTATAATATTATAAAACAA
75684 TTTAAAGAAA
Statistics
Matches: 587, Mismatches: 5, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
140 587 1.00
ACGTcount: A:0.55, C:0.06, G:0.03, T:0.36
Consensus pattern (140 bp):
TTAAAATATACATTTATAATATTATAAAACAAATAATAAATTTGAAAGGTCATATCTTTAAAAAT
AATATATTTTAAATAATTTGAAAATCATAGTTTAAAATAATTTACAAATCATAATTAAAAAAATT
ATAAAACAAA
Found at i:75181 original size:25 final size:24
Alignment explanation
Indices: 75152--75221 Score: 63
Period size: 24 Copynumber: 2.9 Consensus size: 24
75142 CATATCTTTA
*
75152 AAAATAATATATTTTAAATAATTTG
1 AAAATAATA-ATTTAAAATAATTTG
* *
75177 AAAATCATAGTTTAAAATAATTT-
1 AAAATAATAATTTAAAATAATTTG
* *
75200 ACAAATCATAA-TTAAAAAAATT
1 A-AAATAATAATTTAAAATAATT
75222 ATAAAACAAA
Statistics
Matches: 39, Mismatches: 5, Indels: 4
0.81 0.10 0.08
Matches are distributed among these distances:
23 11 0.28
24 20 0.51
25 8 0.21
ACGTcount: A:0.56, C:0.04, G:0.03, T:0.37
Consensus pattern (24 bp):
AAAATAATAATTTAAAATAATTTG
Found at i:75217 original size:24 final size:23
Alignment explanation
Indices: 75167--75247 Score: 78
Period size: 24 Copynumber: 3.4 Consensus size: 23
75157 AATATATTTT
* *
75167 AAATAATTTGAAAATCATAGTTTA
1 AAATAATTT-AAAATCATAATTAA
75191 AAATAATTTACAAATCATAATTAA
1 AAATAATTTA-AAATCATAATTAA
75215 AAA-AATTATAAAA-CA-AATTAA
1 AAATAATT-TAAAATCATAATTAA
75236 AATATACATTTA
1 AA-ATA-ATTTA
75248 TAATATTATA
Statistics
Matches: 50, Mismatches: 2, Indels: 11
0.79 0.03 0.17
Matches are distributed among these distances:
21 8 0.16
22 3 0.06
23 11 0.22
24 28 0.56
ACGTcount: A:0.58, C:0.06, G:0.02, T:0.33
Consensus pattern (23 bp):
AAATAATTTAAAATCATAATTAA
Found at i:75321 original size:25 final size:24
Alignment explanation
Indices: 75292--75361 Score: 63
Period size: 24 Copynumber: 2.9 Consensus size: 24
75282 CATATCTTTA
*
75292 AAAATAATATATTTTAAATAATTTG
1 AAAATAATA-ATTTAAAATAATTTG
* *
75317 AAAATCATAGTTTAAAATAATTT-
1 AAAATAATAATTTAAAATAATTTG
* *
75340 ACAAATCATAA-TTAAAAAAATT
1 A-AAATAATAATTTAAAATAATT
75362 ATAAAACAAA
Statistics
Matches: 39, Mismatches: 5, Indels: 4
0.81 0.10 0.08
Matches are distributed among these distances:
23 11 0.28
24 20 0.51
25 8 0.21
ACGTcount: A:0.56, C:0.04, G:0.03, T:0.37
Consensus pattern (24 bp):
AAAATAATAATTTAAAATAATTTG
Found at i:75357 original size:24 final size:23
Alignment explanation
Indices: 75307--75387 Score: 78
Period size: 24 Copynumber: 3.4 Consensus size: 23
75297 AATATATTTT
* *
75307 AAATAATTTGAAAATCATAGTTTA
1 AAATAATTT-AAAATCATAATTAA
75331 AAATAATTTACAAATCATAATTAA
1 AAATAATTTA-AAATCATAATTAA
75355 AAA-AATTATAAAA-CA-AATTAA
1 AAATAATT-TAAAATCATAATTAA
75376 AATATACATTTA
1 AA-ATA-ATTTA
75388 TAATATTATA
Statistics
Matches: 50, Mismatches: 2, Indels: 11
0.79 0.03 0.17
Matches are distributed among these distances:
21 8 0.16
22 3 0.06
23 11 0.22
24 28 0.56
ACGTcount: A:0.58, C:0.06, G:0.02, T:0.33
Consensus pattern (23 bp):
AAATAATTTAAAATCATAATTAA
Found at i:75461 original size:25 final size:24
Alignment explanation
Indices: 75432--75501 Score: 63
Period size: 24 Copynumber: 2.9 Consensus size: 24
75422 CATATCTTTA
*
75432 AAAATAATATATTTTAAATAATTTG
1 AAAATAATA-ATTTAAAATAATTTG
* *
75457 AAAATCATAGTTTAAAATAATTT-
1 AAAATAATAATTTAAAATAATTTG
* *
75480 ACAAATCATAA-TTAAAAAAATT
1 A-AAATAATAATTTAAAATAATT
75502 ATAAAACAAA
Statistics
Matches: 39, Mismatches: 5, Indels: 4
0.81 0.10 0.08
Matches are distributed among these distances:
23 11 0.28
24 20 0.51
25 8 0.21
ACGTcount: A:0.56, C:0.04, G:0.03, T:0.37
Consensus pattern (24 bp):
AAAATAATAATTTAAAATAATTTG
Found at i:75497 original size:24 final size:23
Alignment explanation
Indices: 75447--75527 Score: 78
Period size: 24 Copynumber: 3.4 Consensus size: 23
75437 AATATATTTT
* *
75447 AAATAATTTGAAAATCATAGTTTA
1 AAATAATTT-AAAATCATAATTAA
75471 AAATAATTTACAAATCATAATTAA
1 AAATAATTTA-AAATCATAATTAA
75495 AAA-AATTATAAAA-CA-AATTAA
1 AAATAATT-TAAAATCATAATTAA
75516 AATATACATTTA
1 AA-ATA-ATTTA
75528 TAATATTATA
Statistics
Matches: 50, Mismatches: 2, Indels: 11
0.79 0.03 0.17
Matches are distributed among these distances:
21 8 0.16
22 3 0.06
23 11 0.22
24 28 0.56
ACGTcount: A:0.58, C:0.06, G:0.02, T:0.33
Consensus pattern (23 bp):
AAATAATTTAAAATCATAATTAA
Found at i:75601 original size:25 final size:24
Alignment explanation
Indices: 75572--75641 Score: 63
Period size: 24 Copynumber: 2.9 Consensus size: 24
75562 CATATCTTTA
*
75572 AAAATAATATATTTTAAATAATTTG
1 AAAATAATA-ATTTAAAATAATTTG
* *
75597 AAAATCATAGTTTAAAATAATTT-
1 AAAATAATAATTTAAAATAATTTG
* *
75620 ACAAATCATAA-TTAAAAAAATT
1 A-AAATAATAATTTAAAATAATT
75642 ATAAAACAAA
Statistics
Matches: 39, Mismatches: 5, Indels: 4
0.81 0.10 0.08
Matches are distributed among these distances:
23 11 0.28
24 20 0.51
25 8 0.21
ACGTcount: A:0.56, C:0.04, G:0.03, T:0.37
Consensus pattern (24 bp):
AAAATAATAATTTAAAATAATTTG
Found at i:75637 original size:24 final size:23
Alignment explanation
Indices: 75587--75667 Score: 78
Period size: 24 Copynumber: 3.4 Consensus size: 23
75577 AATATATTTT
* *
75587 AAATAATTTGAAAATCATAGTTTA
1 AAATAATTT-AAAATCATAATTAA
75611 AAATAATTTACAAATCATAATTAA
1 AAATAATTTA-AAATCATAATTAA
75635 AAA-AATTATAAAA-CA-AATTAA
1 AAATAATT-TAAAATCATAATTAA
75656 AATATACATTTA
1 AA-ATA-ATTTA
75668 TAATATTATA
Statistics
Matches: 50, Mismatches: 2, Indels: 11
0.79 0.03 0.17
Matches are distributed among these distances:
21 8 0.16
22 3 0.06
23 11 0.22
24 28 0.56
ACGTcount: A:0.58, C:0.06, G:0.02, T:0.33
Consensus pattern (23 bp):
AAATAATTTAAAATCATAATTAA
Found at i:76092 original size:34 final size:36
Alignment explanation
Indices: 76054--76126 Score: 96
Period size: 36 Copynumber: 2.1 Consensus size: 36
76044 ACAGCCCCTC
* *
76054 ATTATTATTGTTT-TAA-GTTTTGTACCTAAATTCA
1 ATTATTATTCTTTCCAAGGTTTTGTACCTAAATTCA
* *
76088 ATTATTATTCTTTCCAAGGTTTTTTAGCTAAATTCA
1 ATTATTATTCTTTCCAAGGTTTTGTACCTAAATTCA
76124 ATT
1 ATT
76127 CTAGCAACAA
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
34 12 0.36
35 2 0.06
36 19 0.58
ACGTcount: A:0.29, C:0.11, G:0.08, T:0.52
Consensus pattern (36 bp):
ATTATTATTCTTTCCAAGGTTTTGTACCTAAATTCA
Found at i:78815 original size:17 final size:17
Alignment explanation
Indices: 78786--78818 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
78776 TGAATAAAAA
78786 AATAATAATTTTTTTTG
1 AATAATAATTTTTTTTG
78803 AATAA-AATATTTTTTT
1 AATAATAAT-TTTTTTT
78819 ATATTTTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 3 0.20
17 12 0.80
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (17 bp):
AATAATAATTTTTTTTG
Found at i:78824 original size:10 final size:11
Alignment explanation
Indices: 78808--78840 Score: 50
Period size: 10 Copynumber: 3.0 Consensus size: 11
78798 TTTTGAATAA
78808 AATATTTTTTT
1 AATATTTTTTT
78819 -ATATTTTTTT
1 AATATTTTTTT
78829 AATAATTTTTTT
1 AAT-ATTTTTTT
78841 TAAAAAAATA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
10 10 0.50
11 2 0.10
12 8 0.40
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (11 bp):
AATATTTTTTT
Found at i:79318 original size:22 final size:22
Alignment explanation
Indices: 79293--79379 Score: 129
Period size: 22 Copynumber: 3.7 Consensus size: 22
79283 TCTATATTTA
79293 GTATGAATATTGTAATTTTTTT
1 GTATGAATATTGTAATTTTTTT
79315 GTATGAATATTGTAATTTTTTT
1 GTATGAATATTGTAATTTTTTT
79337 GTATGAATATTGTAATATTATAATTTT
1 GTATGAATATTGT-A-ATT-T--TTTT
79364 GTATGAATATTGTAAT
1 GTATGAATATTGTAAT
79380 GTCGGTATAT
Statistics
Matches: 60, Mismatches: 0, Indels: 7
0.90 0.00 0.10
Matches are distributed among these distances:
22 35 0.58
23 1 0.02
24 3 0.05
25 3 0.05
26 1 0.02
27 17 0.28
ACGTcount: A:0.32, C:0.00, G:0.14, T:0.54
Consensus pattern (22 bp):
GTATGAATATTGTAATTTTTTT
Found at i:79426 original size:47 final size:48
Alignment explanation
Indices: 79298--79426 Score: 165
Period size: 47 Copynumber: 2.7 Consensus size: 48
79288 ATTTAGTATG
* **
79298 AATATTGTAATTTTTTTGTATGAATATTGTAATTTTTTTGTATGAATATTGT
1 AATATTGTAA-TTTTTTGTATGAATATTGTAA--TGTCGGTAT-AATATTGT
*
79350 AATATTATAA--TTTTGTATGAATATTGTAATGTCGGTAT-ATATTGT
1 AATATTGTAATTTTTTGTATGAATATTGTAATGTCGGTATAATATTGT
79395 AATATTGTAATTTTTTGTATGAATATTGTAAT
1 AATATTGTAATTTTTTGTATGAATATTGTAAT
79427 TATTTTATAA
Statistics
Matches: 70, Mismatches: 5, Indels: 9
0.83 0.06 0.11
Matches are distributed among these distances:
45 16 0.23
47 26 0.37
49 19 0.27
52 9 0.13
ACGTcount: A:0.32, C:0.01, G:0.14, T:0.53
Consensus pattern (48 bp):
AATATTGTAATTTTTTGTATGAATATTGTAATGTCGGTATAATATTGT
Found at i:79497 original size:19 final size:19
Alignment explanation
Indices: 79475--79512 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
79465 TATAAATTTA
*
79475 TTAGTAACTTATTAGTAAT
1 TTAGTAACTTATTACTAAT
*
79494 TTAGTAATTTATTACTAAT
1 TTAGTAACTTATTACTAAT
79513 AAATTAAATT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.37, C:0.05, G:0.08, T:0.50
Consensus pattern (19 bp):
TTAGTAACTTATTACTAAT
Found at i:79770 original size:27 final size:28
Alignment explanation
Indices: 79732--79808 Score: 115
Period size: 27 Copynumber: 2.9 Consensus size: 28
79722 CCAGCCCGGC
*
79732 CCATTGGCGCCTCTCAGAAT-GGCACCA
1 CCATTGGCGCCTCCCAGAATAGGCACCA
*
79759 CCATTGGCGCCTCCCAG-GTAGGCACCA
1 CCATTGGCGCCTCCCAGAATAGGCACCA
79786 CCATTGGCGCCTCCCAG-ATAGGC
1 CCATTGGCGCCTCCCAGAATAGGC
79809 GCCAATACTA
Statistics
Matches: 46, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
26 1 0.02
27 45 0.98
ACGTcount: A:0.19, C:0.39, G:0.25, T:0.17
Consensus pattern (28 bp):
CCATTGGCGCCTCCCAGAATAGGCACCA
Done.