Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold282
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: 59809
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:1275 original size:46 final size:45
Alignment explanation
Indices: 1225--1396 Score: 215
Period size: 46 Copynumber: 3.8 Consensus size: 45
1215 TGGTTGAGCA
1225 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-G
* * * *
1271 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGAATGTAACTAG-GCA-
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACT-TATG-GA-T-GCGAAG
1317 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-G
* *
1363 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTA
1397 GGGGCGGGTT
Statistics
Matches: 108, Mismatches: 10, Indels: 16
0.81 0.07 0.12
Matches are distributed among these distances:
43 1 0.01
44 3 0.03
45 2 0.02
46 96 0.89
47 2 0.02
48 3 0.03
49 1 0.01
ACGTcount: A:0.22, C:0.22, G:0.28, T:0.29
Consensus pattern (45 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAAG
Found at i:1379 original size:92 final size:92
Alignment explanation
Indices: 1222--1391 Score: 313
Period size: 92 Copynumber: 1.8 Consensus size: 92
1212 GGATGGTTGA
* *
1222 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
1287 TGAGTCCGAGTTCGTGAATGTAACTAG
66 TGAGTCCGAGTTCGTGAATGTAACTAG
*
1314 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
1379 TGAGTCCGAGTTC
66 TGAGTCCGAGTTC
1392 ACTTAGGGGC
Statistics
Matches: 75, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
92 75 1.00
ACGTcount: A:0.21, C:0.22, G:0.29, T:0.28
Consensus pattern (92 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAATGTAACTAG
Found at i:8795 original size:46 final size:45
Alignment explanation
Indices: 8742--8914 Score: 174
Period size: 46 Copynumber: 3.8 Consensus size: 45
8732 TATTTGGACA
8742 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-G
* * * * *
8788 TCCGAACTCGTTGAGTTGAGTCAGAGTTC-GTGCAATGTAACTAG-GCA-
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACT--TATG-GA-T-GCGAAG
*
8835 TCCGAACTCGTTGAGTTGAGTCCGAGTTCATTTATGGATGCGAACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-G
* *
8881 -CATGAGCTCGTTGAGTTGAGTCCGAGTTCACTTA
1 TC-CGAACTCGTTGAGTTGAGTCCGAGTTCACTTA
8915 GGGGCGGGTT
Statistics
Matches: 104, Mismatches: 13, Indels: 20
0.76 0.09 0.15
Matches are distributed among these distances:
43 1 0.01
44 3 0.03
45 3 0.03
46 60 0.58
47 31 0.30
48 2 0.02
49 3 0.03
50 1 0.01
ACGTcount: A:0.23, C:0.20, G:0.28, T:0.30
Consensus pattern (45 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAAG
Found at i:8899 original size:93 final size:93
Alignment explanation
Indices: 8740--8909 Score: 279
Period size: 93 Copynumber: 1.8 Consensus size: 93
8730 GATATTTGGA
*
8740 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGTT
1 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGTCCGAACTCGTTGAGTT
8805 GAGTCAGAGTTCGTGCAATGTAACTAGG
66 GAGTCAGAGTTCGTGCAATGTAACTAGG
* * *
8833 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCATTTATGGATGCGAACG-CATGAGCTCGTTGAGT
1 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGTC-CGAACTCGTTGAGT
*
8897 TGAGTCCGAGTTC
65 TGAGTCAGAGTTC
8910 ACTTAGGGGC
Statistics
Matches: 71, Mismatches: 5, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
92 1 0.01
93 70 0.99
ACGTcount: A:0.22, C:0.20, G:0.28, T:0.29
Consensus pattern (93 bp):
CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGTCCGAACTCGTTGAGTT
GAGTCAGAGTTCGTGCAATGTAACTAGG
Found at i:11607 original size:39 final size:40
Alignment explanation
Indices: 11563--11728 Score: 232
Period size: 40 Copynumber: 4.2 Consensus size: 40
11553 CCTTCAGAAT
* *
11563 TTAG-CCGGATATAGCT-ACTTGCTCAAATGCCTTCGGGAC
1 TTAGCCCGGATATAG-TAACTCGCACAAATGCCTTCGGGAC
*
11602 TTAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGGAC
1 TTAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGAC
*
11642 TTAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGG-C
1 TTAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGAC
* *
11681 TTAGCCCGGA-ATTAGTCACTAGCACAAATGCCTTCGGGAC
1 TTAGCCCGGATA-TAGTAACTCGCACAAATGCCTTCGGGAC
11721 TTAGCCCG
1 TTAGCCCG
11729 ATTATCATCC
Statistics
Matches: 117, Mismatches: 6, Indels: 7
0.90 0.05 0.05
Matches are distributed among these distances:
38 1 0.01
39 39 0.33
40 77 0.66
ACGTcount: A:0.24, C:0.28, G:0.23, T:0.25
Consensus pattern (40 bp):
TTAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGAC
Found at i:11630 original size:40 final size:40
Alignment explanation
Indices: 11586--11733 Score: 237
Period size: 40 Copynumber: 3.7 Consensus size: 40
11576 GCTACTTGCT
11586 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
11626 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
* * *
11666 CAAATGCCTTCGGG-CTTAGCCCGG-AATTAGTCACTAGCA
1 CAAATGCCTTCGGGACTTAGCCCGGTTA-TAGTAACTCGCA
*
11705 CAAATGCCTTCGGGACTTAGCCCGATTAT
1 CAAATGCCTTCGGGACTTAGCCCGGTTAT
11734 CATCCGAATA
Statistics
Matches: 100, Mismatches: 5, Indels: 6
0.90 0.05 0.05
Matches are distributed among these distances:
38 1 0.01
39 34 0.34
40 64 0.64
41 1 0.01
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
Found at i:11687 original size:79 final size:80
Alignment explanation
Indices: 11586--11733 Score: 237
Period size: 79 Copynumber: 1.9 Consensus size: 80
11576 GCTACTTGCT
* *
11586 CAAATGCCTTCGGGACTTAGCCCGG-TTATAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCG
1 CAAATGCCTTCGGGACTTAGCCCGGAAT-TAGTAACTAGCACAAATGCCTTCGGGACTTAGCCCG
*
11650 GTTATAGTAACTCGCA
65 ATTATAGTAACTCGCA
*
11666 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTCACTAGCACAAATGCCTTCGGGACTTAGCCCGA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTAACTAGCACAAATGCCTTCGGGACTTAGCCCGA
11730 TTAT
66 TTAT
11734 CATCCGAATA
Statistics
Matches: 63, Mismatches: 4, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
79 48 0.76
80 15 0.24
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.25
Consensus pattern (80 bp):
CAAATGCCTTCGGGACTTAGCCCGGAATTAGTAACTAGCACAAATGCCTTCGGGACTTAGCCCGA
TTATAGTAACTCGCA
Found at i:12335 original size:24 final size:24
Alignment explanation
Indices: 12308--12356 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
12298 CGCCTATAAC
12308 CGAATACATGCAACACCAATCTAT
1 CGAATACATGCAACACCAATCTAT
12332 CGAATACATGCAACACCAATCTAT
1 CGAATACATGCAACACCAATCTAT
12356 C
1 C
12357 TCATGTGGCC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.41, C:0.31, G:0.08, T:0.20
Consensus pattern (24 bp):
CGAATACATGCAACACCAATCTAT
Found at i:16673 original size:20 final size:20
Alignment explanation
Indices: 16631--16678 Score: 53
Period size: 20 Copynumber: 2.5 Consensus size: 20
16621 TAAATTCTAA
** *
16631 AAAGATAAATACATTTAATT
1 AAAGATAAATACAGATAACT
*
16651 AAAGATAAATAGAGATAACT
1 AAAGATAAATACAGATAACT
16671 AAA-ATAAA
1 AAAGATAAA
16679 ATCCTAAAAT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 5 0.21
20 19 0.79
ACGTcount: A:0.62, C:0.04, G:0.08, T:0.25
Consensus pattern (20 bp):
AAAGATAAATACAGATAACT
Found at i:16724 original size:15 final size:15
Alignment explanation
Indices: 16704--16736 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
16694 TAATCCTAAT
16704 AATTATCCTAATATA
1 AATTATCCTAATATA
16719 AATTATCCTAATATA
1 AATTATCCTAATATA
16734 AAT
1 AAT
16737 AAAATGGAGT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.48, C:0.12, G:0.00, T:0.39
Consensus pattern (15 bp):
AATTATCCTAATATA
Found at i:26927 original size:78 final size:78
Alignment explanation
Indices: 26773--26971 Score: 233
Period size: 77 Copynumber: 2.6 Consensus size: 78
26763 GATTGTATTA
* * * * *
26773 TGTTTCAAACA-AAAATTCAATTGAACAATCTTGTTTCAAGATTTATTCCTACTGTTTGATAGGA
1 TGTTTCAAACAGAAAA-TCAATTGAAAAATTTTGTTTCAGGATTTATTCCTACTGTTTAAAAGGA
***
26837 TTTGTTTGA-TTTT
65 TTTGTGCAATTTTT
* **
26850 TGTTTCAAACAGAAAATCAATTGAAAAATTTTGTTTCAGGATGTTATTCTTGTTGTTTAAAAGGA
1 TGTTTCAAACAGAAAATCAATTGAAAAATTTTGTTTCAGGAT-TTATTCCTACTGTTTAAAAGGA
26915 TTTGTGCAATTTTTT
65 TTTGTGCAA-TTTTT
* *
26930 TGTTTCAAACAG-AAATCAATTGAATAATTATGTTTCAGGATT
1 TGTTTCAAACAGAAAATCAATTGAAAAATTTTGTTTCAGGATT
26972 CTTTTCCTGC
Statistics
Matches: 105, Mismatches: 13, Indels: 7
0.84 0.10 0.06
Matches are distributed among these distances:
77 34 0.32
78 28 0.27
79 27 0.26
80 16 0.15
ACGTcount: A:0.32, C:0.10, G:0.15, T:0.44
Consensus pattern (78 bp):
TGTTTCAAACAGAAAATCAATTGAAAAATTTTGTTTCAGGATTTATTCCTACTGTTTAAAAGGAT
TTGTGCAATTTTT
Found at i:27006 original size:79 final size:77
Alignment explanation
Indices: 26773--27006 Score: 238
Period size: 79 Copynumber: 3.0 Consensus size: 77
26763 GATTGTATTA
* * * * *
26773 TGTTTCAAACAAAAATTCAATTGAACAATCTTGTTTCAAGATTTATTCCTACTGTTTGATAGGAT
1 TGTTTCAAACAGAAA-TCAATTGAAAAAT-TTGTTTCAGGATTTATTCCTGCTGTTTAATAGGAT
*
26838 TTGTTTGA--TTTT
64 TTGTTCGATTTTTT
* * *
26850 TGTTTCAAACAGAAAATCAATTGAAAAATTTTGTTTCAGGATGTTATTCTTGTTGTTTAAAAGGA
1 TGTTTCAAACAG-AAATCAATTGAAAAA-TTTGTTTCAGGAT-TTATTCCTGCTGTTTAATAGGA
* *
26915 TTTGTGCAATTTTTT
63 TTTGTTCGATTTTTT
* * * * *
26930 TGTTTCAAACAGAAATCAATTGAATAATTATGTTTCAGGATTCTTTTCCTGCTGCTCAATAGAAT
1 TGTTTCAAACAGAAATCAATTGAAAAATT-TGTTTCAGGATT-TATTCCTGCTGTTTAATAGGAT
*
26995 TTATTCGATTTT
64 TTGTTCGATTTT
27007 GTTAACAAAA
Statistics
Matches: 128, Mismatches: 22, Indels: 12
0.79 0.14 0.07
Matches are distributed among these distances:
77 33 0.26
78 30 0.23
79 49 0.38
80 16 0.12
ACGTcount: A:0.30, C:0.11, G:0.14, T:0.44
Consensus pattern (77 bp):
TGTTTCAAACAGAAATCAATTGAAAAATTTGTTTCAGGATTTATTCCTGCTGTTTAATAGGATTT
GTTCGATTTTTT
Found at i:29124 original size:40 final size:40
Alignment explanation
Indices: 29069--29149 Score: 153
Period size: 40 Copynumber: 2.0 Consensus size: 40
29059 ACCTACCATT
*
29069 CCTTTGAACATCAACATGTACACATGAAACCAACTGTATG
1 CCTTTGAACATCAACATATACACATGAAACCAACTGTATG
29109 CCTTTGAACATCAACATATACACATGAAACCAACTGTATG
1 CCTTTGAACATCAACATATACACATGAAACCAACTGTATG
29149 C
1 C
29150 ATTTCCTTTT
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
40 40 1.00
ACGTcount: A:0.38, C:0.26, G:0.11, T:0.25
Consensus pattern (40 bp):
CCTTTGAACATCAACATATACACATGAAACCAACTGTATG
Found at i:35964 original size:26 final size:26
Alignment explanation
Indices: 35935--35990 Score: 60
Period size: 26 Copynumber: 2.2 Consensus size: 26
35925 GTAAAAGGAA
*
35935 AAAAAAATTGGGGGTTTGACGG-AAGT
1 AAAAAAATTGAGGGTTTGA-GGAAAGT
***
35961 AAAAGTTTTGAGGGTTTGAGGAAAGT
1 AAAAAAATTGAGGGTTTGAGGAAAGT
35987 AAAA
1 AAAA
35991 GTTTTAGGGG
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
25 2 0.08
26 23 0.92
ACGTcount: A:0.41, C:0.02, G:0.32, T:0.25
Consensus pattern (26 bp):
AAAAAAATTGAGGGTTTGAGGAAAGT
Found at i:35983 original size:25 final size:26
Alignment explanation
Indices: 35946--35999 Score: 85
Period size: 26 Copynumber: 2.1 Consensus size: 26
35936 AAAAAATTGG
35946 GGGTTTGACGG-AAGTAAAAGTTTTGA
1 GGGTTTGACGGAAAGTAAAAGTTTT-A
35972 GGGTTTGA-GGAAAGTAAAAGTTTTA
1 GGGTTTGACGGAAAGTAAAAGTTTTA
35997 GGG
1 GGG
36000 GAAGTAAAAG
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
25 6 0.22
26 21 0.78
ACGTcount: A:0.31, C:0.02, G:0.37, T:0.30
Consensus pattern (26 bp):
GGGTTTGACGGAAAGTAAAAGTTTTA
Found at i:36006 original size:18 final size:18
Alignment explanation
Indices: 35983--36020 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
35973 GGTTTGAGGA
35983 AAGTAAAAGTTTTAGGGG
1 AAGTAAAAGTTTTAGGGG
36001 AAGTAAAAGTTTTAGGGG
1 AAGTAAAAGTTTTAGGGG
36019 AA
1 AA
36021 AATAAGGAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.42, C:0.00, G:0.32, T:0.26
Consensus pattern (18 bp):
AAGTAAAAGTTTTAGGGG
Found at i:41400 original size:114 final size:113
Alignment explanation
Indices: 41200--41605 Score: 442
Period size: 115 Copynumber: 3.5 Consensus size: 113
41190 TAATTTTTCC
* ** * * *
41200 TCATTTTTTGAAAACATAAAAGCCTAAATTGGTATCGATACCAACTATGGGTATCAATAGTTATG
1 TCATTTTTTCAAAACATCGAAGCCGAAATTGGTATCGATACCAGCTATGGGTATCAATACTTATG
* *
41265 G-CTTGATATTGATACATTGGTGATGGTATCGATACTTAGGATTTATTTT
66 GTC-TGGTATCGATACATTGGTGAT-GTATCGATACTTAGGATTTATTTT
* * * **
41314 TCATTTTTTGAAAACATCGAAGTCGAAATTGGTATTGATACCAGCTATGGGTATTGATACTTATG
1 TCATTTTTTCAAAACATCGAAGCCGAAATTGGTATCGATACCAGCTATGGGTATCAATACTTATG
* *
41379 GTCTGGTATCAATACTTTGGTGATTGTATCGATACTTAGGATTTATTTT
66 GTCTGGTATCGATACATTGGTGA-TGTATCGATACTTAGGATTTATTTT
** * * * ** *
41428 TCATTTTCCCTAAACATCGAAAGACAAAATTGGTATCGATAATAGCTATGGGTATCAATTCTTA-
1 TCATTTTTTCAAAACATCG-AAGCCGAAATTGGTATCGATACCAGCTATGGGTATCAATACTTAT
* * *
41492 -GTCCCTGGTATCGATACCTTGGTGAATGTATCAATACTTAGTATTTATTTT
65 GGT--CTGGTATCGATACATTGGTG-ATGTATCGATACTTAGGATTTATTTT
* * *
41543 TCATTTTTTTCAAAACATCGAAGCCGAATTTAGTATCGATACAAGC-ATTGGGTATCAATACTT
1 TCA-TTTTTTCAAAACATCGAAGCCGAAATTGGTATCGATACCAGCTA-TGGGTATCAATACTT
41606 TTGGCACTGG
Statistics
Matches: 245, Mismatches: 39, Indels: 15
0.82 0.13 0.05
Matches are distributed among these distances:
113 2 0.01
114 113 0.46
115 116 0.47
116 14 0.06
ACGTcount: A:0.30, C:0.14, G:0.17, T:0.38
Consensus pattern (113 bp):
TCATTTTTTCAAAACATCGAAGCCGAAATTGGTATCGATACCAGCTATGGGTATCAATACTTATG
GTCTGGTATCGATACATTGGTGATGTATCGATACTTAGGATTTATTTT
Found at i:44740 original size:29 final size:29
Alignment explanation
Indices: 44708--44814 Score: 117
Period size: 29 Copynumber: 3.7 Consensus size: 29
44698 GCTATCTTTG
* * *
44708 TTATAAGAAAGTCTTTGTAGCTATCTCAA
1 TTATAAGAAAGCCTTTGTGGCAATCTCAA
* * * *
44737 TTATAAGGAAGTCTTTTTGGCGATCTCAA
1 TTATAAGAAAGCCTTTGTGGCAATCTCAA
* *
44766 TTATAATG-AAGCCTTTTTGGCAATCTCTA
1 TTATAA-GAAAGCCTTTGTGGCAATCTCAA
44795 TTATAAGAAAGCCTTTGTGG
1 TTATAAGAAAGCCTTTGTGG
44815 TGACCTTTGT
Statistics
Matches: 68, Mismatches: 8, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
28 1 0.01
29 66 0.97
30 1 0.01
ACGTcount: A:0.30, C:0.14, G:0.18, T:0.38
Consensus pattern (29 bp):
TTATAAGAAAGCCTTTGTGGCAATCTCAA
Found at i:49561 original size:31 final size:31
Alignment explanation
Indices: 49526--49595 Score: 122
Period size: 31 Copynumber: 2.3 Consensus size: 31
49516 ATACAATTTG
49526 TTTTCTCTTCTATTTAACACAAATCTTTTCT
1 TTTTCTCTTCTATTTAACACAAATCTTTTCT
*
49557 TTTTCTCTTCTATTTAATACAAATCTTTTCT
1 TTTTCTCTTCTATTTAACACAAATCTTTTCT
*
49588 TTCTCTCT
1 TTTTCTCT
49596 CTCTCTCTCT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
31 37 1.00
ACGTcount: A:0.20, C:0.23, G:0.00, T:0.57
Consensus pattern (31 bp):
TTTTCTCTTCTATTTAACACAAATCTTTTCT
Found at i:56838 original size:33 final size:33
Alignment explanation
Indices: 56766--56838 Score: 76
Period size: 33 Copynumber: 2.2 Consensus size: 33
56756 GTTCCTCTGA
** * * *
56766 CTTTCAGTGAAGAAACTCCTGCCATTCTTCCAT
1 CTTTCAGCAAAGAAACTCCTACAATTCCTCCAT
*
56799 CATTCAGCAAAGAAACTCCTACAATTCCT-CAT
1 CTTTCAGCAAAGAAACTCCTACAATTCCTCCAT
56831 CCTTTCAG
1 -CTTTCAG
56839 TGAGGGAACT
Statistics
Matches: 32, Mismatches: 7, Indels: 2
0.78 0.17 0.05
Matches are distributed among these distances:
32 3 0.09
33 29 0.91
ACGTcount: A:0.29, C:0.32, G:0.10, T:0.30
Consensus pattern (33 bp):
CTTTCAGCAAAGAAACTCCTACAATTCCTCCAT
Found at i:56920 original size:31 final size:33
Alignment explanation
Indices: 56875--56944 Score: 83
Period size: 31 Copynumber: 2.2 Consensus size: 33
56865 CATCGGGTCC
*
56875 GGAAACTCAGACCATTTCTAC-AACAT-GGTGA
1 GGAAACTCAGACCATTCCTACAAACATGGGTGA
* *
56906 GGAAACTACA-ACCATTCCTGCAAACTTGGGTGA
1 GGAAACT-CAGACCATTCCTACAAACATGGGTGA
56939 GGAAAC
1 GGAAAC
56945 AACTGCTACT
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
31 16 0.48
32 6 0.18
33 11 0.33
ACGTcount: A:0.36, C:0.23, G:0.21, T:0.20
Consensus pattern (33 bp):
GGAAACTCAGACCATTCCTACAAACATGGGTGA
Done.