Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1548
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: 66296
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Found at i:1439 original size:13 final size:13
Alignment explanation
Indices: 1421--1446 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1411 CAATTTTTTG
1421 TGTATCGATACAT
1 TGTATCGATACAT
1434 TGTATCGATACAT
1 TGTATCGATACAT
1447 ACTTGCTGTA
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:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1531 original size:20 final size:20
Alignment explanation
Indices: 1506--1578 Score: 101
Period size: 20 Copynumber: 3.6 Consensus size: 20
1496 CAACTTTTTT
1506 ATGTATCGATACATTGCAAC
1 ATGTATCGATACATTGCAAC
****
1526 ATGTATCGATACATCTTTTTC
1 ATGTATCGATACAT-TGCAAC
1547 ATGTATCGATACATTGCAAC
1 ATGTATCGATACATTGCAAC
1567 ATGTATCGATAC
1 ATGTATCGATAC
1579 TTTGAATTGT
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
20 28 0.64
21 16 0.36
ACGTcount: A:0.32, C:0.19, G:0.14, T:0.36
Consensus pattern (20 bp):
ATGTATCGATACATTGCAAC
Found at i:1544 original size:41 final size:41
Alignment explanation
Indices: 1485--1578 Score: 170
Period size: 41 Copynumber: 2.3 Consensus size: 41
1475 CTGCCAAGAA
*
1485 ATGTATCGATACAACTTTTTTATGTATCGATACATTGCAAC
1 ATGTATCGATACAACTTTTTCATGTATCGATACATTGCAAC
*
1526 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
1 ATGTATCGATACAACTTTTTCATGTATCGATACATTGCAAC
1567 ATGTATCGATAC
1 ATGTATCGATAC
1579 TTTGAATTGT
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 51 1.00
ACGTcount: A:0.31, C:0.18, G:0.13, T:0.38
Consensus pattern (41 bp):
ATGTATCGATACAACTTTTTCATGTATCGATACATTGCAAC
Found at i:1560 original size:21 final size:21
Alignment explanation
Indices: 1485--1560 Score: 91
Period size: 21 Copynumber: 3.7 Consensus size: 21
1475 CTGCCAAGAA
* *
1485 ATGTATCGATACAACTTTTTT
1 ATGTATCGATACATCTTTTTC
****
1506 ATGTATCGATACAT-TGCAAC
1 ATGTATCGATACATCTTTTTC
1526 ATGTATCGATACATCTTTTTC
1 ATGTATCGATACATCTTTTTC
1547 ATGTATCGATACAT
1 ATGTATCGATACAT
1561 TGCAACATGT
Statistics
Matches: 44, Mismatches: 10, Indels: 2
0.79 0.18 0.04
Matches are distributed among these distances:
20 15 0.34
21 29 0.66
ACGTcount: A:0.30, C:0.17, G:0.12, T:0.41
Consensus pattern (21 bp):
ATGTATCGATACATCTTTTTC
Found at i:4049 original size:13 final size:13
Alignment explanation
Indices: 4031--4068 Score: 67
Period size: 13 Copynumber: 2.9 Consensus size: 13
4021 ATAATCACCC
4031 TGTATCGATACAG
1 TGTATCGATACAG
*
4044 TGTATCGATACAT
1 TGTATCGATACAG
4057 TGTATCGATACA
1 TGTATCGATACA
4069 AAGAAAAATG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.34
Consensus pattern (13 bp):
TGTATCGATACAG
Found at i:4082 original size:20 final size:20
Alignment explanation
Indices: 4057--4133 Score: 73
Period size: 20 Copynumber: 3.6 Consensus size: 20
4047 ATCGATACAT
4057 TGTATCGATACAAAGAAAAA
1 TGTATCGATACAAAGAAAAA
* *
4077 TGTATCGATACATAGAATTTCCAGA
1 TGTATCGATACAAAGAA-----AAA
* *
4102 TGTATCGATACACAGAAACA
1 TGTATCGATACAAAGAAAAA
4122 TGTATCGATACA
1 TGTATCGATACA
4134 TTTTGGACAT
Statistics
Matches: 48, Mismatches: 4, Indels: 10
0.77 0.06 0.16
Matches are distributed among these distances:
20 30 0.62
25 18 0.38
ACGTcount: A:0.43, C:0.16, G:0.16, T:0.26
Consensus pattern (20 bp):
TGTATCGATACAAAGAAAAA
Found at i:6163 original size:15 final size:15
Alignment explanation
Indices: 6143--6173 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
6133 ATTTCGTTTG
*
6143 GAGCTTCTTCATTTT
1 GAGCTTCCTCATTTT
6158 GAGCTTCCTCATTTT
1 GAGCTTCCTCATTTT
6173 G
1 G
6174 GACATTTTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.23, G:0.16, T:0.48
Consensus pattern (15 bp):
GAGCTTCCTCATTTT
Found at i:10253 original size:13 final size:13
Alignment explanation
Indices: 10235--10260 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
10225 CAATTTTTTG
10235 TGTATCGATACAT
1 TGTATCGATACAT
10248 TGTATCGATACAT
1 TGTATCGATACAT
10261 ACTTGCTGTA
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:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:10345 original size:20 final size:20
Alignment explanation
Indices: 10320--10392 Score: 101
Period size: 20 Copynumber: 3.6 Consensus size: 20
10310 CAACTTTTTT
10320 ATGTATCGATACATTGCAAC
1 ATGTATCGATACATTGCAAC
****
10340 ATGTATCGATACATCTTTTTC
1 ATGTATCGATACAT-TGCAAC
10361 ATGTATCGATACATTGCAAC
1 ATGTATCGATACATTGCAAC
10381 ATGTATCGATAC
1 ATGTATCGATAC
10393 TTTGAATTGT
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
20 28 0.64
21 16 0.36
ACGTcount: A:0.32, C:0.19, G:0.14, T:0.36
Consensus pattern (20 bp):
ATGTATCGATACATTGCAAC
Found at i:10358 original size:41 final size:41
Alignment explanation
Indices: 10299--10392 Score: 170
Period size: 41 Copynumber: 2.3 Consensus size: 41
10289 CTGCCAAGAA
*
10299 ATGTATCGATACAACTTTTTTATGTATCGATACATTGCAAC
1 ATGTATCGATACAACTTTTTCATGTATCGATACATTGCAAC
*
10340 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
1 ATGTATCGATACAACTTTTTCATGTATCGATACATTGCAAC
10381 ATGTATCGATAC
1 ATGTATCGATAC
10393 TTTGAATTGT
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 51 1.00
ACGTcount: A:0.31, C:0.18, G:0.13, T:0.38
Consensus pattern (41 bp):
ATGTATCGATACAACTTTTTCATGTATCGATACATTGCAAC
Found at i:10374 original size:21 final size:21
Alignment explanation
Indices: 10299--10374 Score: 91
Period size: 21 Copynumber: 3.7 Consensus size: 21
10289 CTGCCAAGAA
* *
10299 ATGTATCGATACAACTTTTTT
1 ATGTATCGATACATCTTTTTC
****
10320 ATGTATCGATACAT-TGCAAC
1 ATGTATCGATACATCTTTTTC
10340 ATGTATCGATACATCTTTTTC
1 ATGTATCGATACATCTTTTTC
10361 ATGTATCGATACAT
1 ATGTATCGATACAT
10375 TGCAACATGT
Statistics
Matches: 44, Mismatches: 10, Indels: 2
0.79 0.18 0.04
Matches are distributed among these distances:
20 15 0.34
21 29 0.66
ACGTcount: A:0.30, C:0.17, G:0.12, T:0.41
Consensus pattern (21 bp):
ATGTATCGATACATCTTTTTC
Found at i:11784 original size:20 final size:19
Alignment explanation
Indices: 11732--11785 Score: 56
Period size: 19 Copynumber: 2.8 Consensus size: 19
11722 AAAAAGACAG
* *
11732 AATGTATTGATACATTGAA
1 AATGTATCGATACATTCAA
11751 AATGTATC-ATTACATTCATA
1 AATGTATCGA-TACATTCA-A
*
11771 CATGTATCGATACAT
1 AATGTATCGATACAT
11786 CTGGGTAAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
18 1 0.03
19 14 0.48
20 13 0.45
21 1 0.03
ACGTcount: A:0.39, C:0.13, G:0.11, T:0.37
Consensus pattern (19 bp):
AATGTATCGATACATTCAA
Found at i:16738 original size:20 final size:21
Alignment explanation
Indices: 16705--16761 Score: 55
Period size: 20 Copynumber: 2.7 Consensus size: 21
16695 TTTATTAGCA
16705 ATGTAT-TTTAATATAATAATT
1 ATGTATATTT-ATATAATAATT
* *
16726 -TGTATATTTATATCATATTT
1 ATGTATATTTATATAATAATT
*
16746 ATATCATATTTATATA
1 ATGT-ATATTTATATA
16762 TTTTTATGTG
Statistics
Matches: 29, Mismatches: 4, Indels: 5
0.76 0.11 0.13
Matches are distributed among these distances:
20 14 0.48
21 5 0.17
22 10 0.34
ACGTcount: A:0.39, C:0.04, G:0.04, T:0.54
Consensus pattern (21 bp):
ATGTATATTTATATAATAATT
Found at i:16745 original size:11 final size:11
Alignment explanation
Indices: 16729--16760 Score: 64
Period size: 11 Copynumber: 2.9 Consensus size: 11
16719 AATAATTTGT
16729 ATATTTATATC
1 ATATTTATATC
16740 ATATTTATATC
1 ATATTTATATC
16751 ATATTTATAT
1 ATATTTATAT
16761 ATTTTTATGT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.38, C:0.06, G:0.00, T:0.56
Consensus pattern (11 bp):
ATATTTATATC
Found at i:16815 original size:30 final size:32
Alignment explanation
Indices: 16779--16838 Score: 88
Period size: 32 Copynumber: 1.9 Consensus size: 32
16769 GTGTCATAAT
16779 TATATTTA-AA-AAATATTATATAAATTTTGA
1 TATATTTATAATAAATATTATATAAATTTTGA
**
16809 TATATTTATAATTTATATTATATAAATTTT
1 TATATTTATAATAAATATTATATAAATTTT
16839 AATACGTTCG
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
30 8 0.31
31 2 0.08
32 16 0.62
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (32 bp):
TATATTTATAATAAATATTATATAAATTTTGA
Found at i:16818 original size:18 final size:17
Alignment explanation
Indices: 16791--16839 Score: 50
Period size: 16 Copynumber: 2.9 Consensus size: 17
16781 TATTTAAAAA
16791 ATATTATATAAATTTTGAT
1 ATATT-TATAAATTTT-AT
16810 ATATTTAT-AA-TTTAT
1 ATATTTATAAATTTTAT
*
16825 AT-TATATAAATTTTA
1 ATATTTATAAATTTTA
16840 ATACGTTCGT
Statistics
Matches: 27, Mismatches: 1, Indels: 7
0.77 0.03 0.20
Matches are distributed among these distances:
14 4 0.15
15 6 0.22
16 7 0.26
17 2 0.07
18 3 0.11
19 5 0.19
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (17 bp):
ATATTTATAAATTTTAT
Found at i:16882 original size:23 final size:22
Alignment explanation
Indices: 16855--16928 Score: 84
Period size: 23 Copynumber: 3.5 Consensus size: 22
16845 TTCGTATATT
16855 TATATCATATTCATATTATTTTG
1 TATATCATATT-ATATTATTTTG
*
16878 TATATCATATTATATT-TTATG
1 TATATCATATTATATTATTTTG
*
16899 T-TAT-ATATTA-ATTATTTTT
1 TATATCATATTATATTATTTTG
*
16918 TATATTATATT
1 TATATCATATT
16929 TTTATCATAT
Statistics
Matches: 45, Mismatches: 3, Indels: 8
0.80 0.05 0.14
Matches are distributed among these distances:
18 3 0.07
19 10 0.22
20 6 0.13
21 10 0.22
22 5 0.11
23 11 0.24
ACGTcount: A:0.32, C:0.04, G:0.03, T:0.61
Consensus pattern (22 bp):
TATATCATATTATATTATTTTG
Found at i:16897 original size:40 final size:39
Alignment explanation
Indices: 16849--16928 Score: 90
Period size: 40 Copynumber: 2.0 Consensus size: 39
16839 AATACGTTCG
16849 TATATTTATATCATAT-TCATATTATTTTGTATATCATAT
1 TATATTTATATCATATATCA-ATTATTTTGTATATCATAT
* * * * *
16888 TATATTTTATGTTATATATTAATTATTTTTTATATTATAT
1 TATA-TTTATATCATATATCAATTATTTTGTATATCATAT
16928 T
1 T
16929 TTTATCATAT
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
39 4 0.12
40 28 0.82
41 2 0.06
ACGTcount: A:0.33, C:0.04, G:0.03, T:0.61
Consensus pattern (39 bp):
TATATTTATATCATATATCAATTATTTTGTATATCATAT
Found at i:16904 original size:12 final size:12
Alignment explanation
Indices: 16884--16930 Score: 60
Period size: 12 Copynumber: 4.0 Consensus size: 12
16874 TTTGTATATC
16884 ATATTATATTTT
1 ATATTATATTTT
* *
16896 ATGTTATATATT
1 ATATTATATTTT
*
16908 A-ATTATTTTTT
1 ATATTATATTTT
16919 ATATTATATTTT
1 ATATTATATTTT
16931 TATCATATAA
Statistics
Matches: 28, Mismatches: 6, Indels: 2
0.78 0.17 0.06
Matches are distributed among these distances:
11 8 0.29
12 20 0.71
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (12 bp):
ATATTATATTTT
Found at i:17240 original size:4 final size:4
Alignment explanation
Indices: 17231--17255 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
17221 AAAGGGGTTC
17231 TTAT TTAT TTAT TTAT TTAT TTAT T
1 TTAT TTAT TTAT TTAT TTAT TTAT T
17256 ATATACTTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
TTAT
Found at i:18486 original size:17 final size:17
Alignment explanation
Indices: 18464--18496 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
18454 ATTAGATAAT
18464 TTTTTTCTTTTTCTTTG
1 TTTTTTCTTTTTCTTTG
*
18481 TTTTTTTTTTTTCTTT
1 TTTTTTCTTTTTCTTT
18497 TTTGGATTTG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.00, C:0.09, G:0.03, T:0.88
Consensus pattern (17 bp):
TTTTTTCTTTTTCTTTG
Found at i:26573 original size:40 final size:40
Alignment explanation
Indices: 26518--26597 Score: 151
Period size: 40 Copynumber: 2.0 Consensus size: 40
26508 TCAATCATGG
*
26518 GTAATGGAAAAAAGAGTCAATAGTTACCAAAGTAGTGGAT
1 GTAATGGAAAAAAGAGTCAATAGCTACCAAAGTAGTGGAT
26558 GTAATGGAAAAAAGAGTCAATAGCTACCAAAGTAGTGGAT
1 GTAATGGAAAAAAGAGTCAATAGCTACCAAAGTAGTGGAT
26598 TGGAGTAAAG
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
40 39 1.00
ACGTcount: A:0.45, C:0.09, G:0.25, T:0.21
Consensus pattern (40 bp):
GTAATGGAAAAAAGAGTCAATAGCTACCAAAGTAGTGGAT
Found at i:28801 original size:13 final size:13
Alignment explanation
Indices: 28783--28807 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
28773 ACCCTAAATA
28783 AAAATAAAATAAT
1 AAAATAAAATAAT
28796 AAAATAAAATAA
1 AAAATAAAATAA
28808 GAACGTAATA
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:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (13 bp):
AAAATAAAATAAT
Found at i:31972 original size:13 final size:13
Alignment explanation
Indices: 31954--31980 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
31944 AAAGTTACTC
31954 AAACTTAGATGTG
1 AAACTTAGATGTG
31967 AAACTTAGATGTG
1 AAACTTAGATGTG
31980 A
1 A
31981 GTATTGGACA
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:0.07, G:0.22, T:0.30
Consensus pattern (13 bp):
AAACTTAGATGTG
Found at i:35414 original size:18 final size:17
Alignment explanation
Indices: 35387--35425 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 17
35377 AAAAATTTTT
35387 AATTAAAATATAATATA
1 AATTAAAATATAATATA
*
35404 AATTAAAA-ATATTATA
1 AATTAAAATATAATATA
*
35420 TATTAA
1 AATTAA
35426 TTATATTTAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
16 12 0.60
17 8 0.40
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (17 bp):
AATTAAAATATAATATA
Found at i:35457 original size:40 final size:39
Alignment explanation
Indices: 35396--35501 Score: 105
Period size: 40 Copynumber: 2.7 Consensus size: 39
35386 TAATTAAAAT
**
35396 ATAATATAA-ATTAAAAATATTATATATTAATTATATTTAA
1 ATAA-ATAATATTAAATTTATTATATATTAATTATATTT-A
*
35436 ATAAATAATATTAAATTTATTATAT-TATATTTATATTTA
1 ATAAATAATATTAAATTTATTATATAT-TAATTATATTTA
35475 ATAAAT-ATA-TAATATTTA-TATTATATT
1 ATAAATAATATTAA-ATTTATTA-TATATT
35502 TTTATATAAT
Statistics
Matches: 58, Mismatches: 3, Indels: 12
0.79 0.04 0.16
Matches are distributed among these distances:
37 5 0.09
38 12 0.21
39 13 0.22
40 28 0.48
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (39 bp):
ATAAATAATATTAAATTTATTATATATTAATTATATTTA
Found at i:35495 original size:13 final size:13
Alignment explanation
Indices: 35450--35520 Score: 62
Period size: 11 Copynumber: 5.8 Consensus size: 13
35440 ATAATATTAA
*
35450 ATTTATTATATTAT
1 ATTTA-TATATAAT
*
35464 ATTTATATTTAAT
1 ATTTATATATAAT
*
35477 A--AATATATAAT
1 ATTTATATATAAT
35488 ATTTATAT-T-AT
1 ATTTATATATAAT
*
35499 ATTTTTATATAAT
1 ATTTATATATAAT
35512 ATTTA-ATAT
1 ATTTATATAT
35521 TATTGAATAA
Statistics
Matches: 46, Mismatches: 7, Indels: 10
0.73 0.11 0.16
Matches are distributed among these distances:
11 18 0.39
12 6 0.13
13 17 0.37
14 5 0.11
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (13 bp):
ATTTATATATAAT
Found at i:35507 original size:24 final size:24
Alignment explanation
Indices: 35443--35523 Score: 83
Period size: 24 Copynumber: 3.3 Consensus size: 24
35433 TAAATAAATA
* *
35443 ATATTAAATTTATTATATTATATTT
1 ATATTATATTT-TTATATAATATTT
***
35468 ATATT-TAATAAATATATAATATTT
1 ATATTAT-ATTTTTATATAATATTT
35492 ATATTATATTTTTATATAATATTT
1 ATATTATATTTTTATATAATATTT
35516 AATATTAT
1 -ATATTAT
35524 TGAATAAAAT
Statistics
Matches: 45, Mismatches: 8, Indels: 6
0.76 0.14 0.10
Matches are distributed among these distances:
24 30 0.67
25 15 0.33
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (24 bp):
ATATTATATTTTTATATAATATTT
Found at i:43303 original size:2 final size:2
Alignment explanation
Indices: 43296--43332 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
43286 ATCATCTTCT
43296 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
43333 TGTAAAAAAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:44067 original size:23 final size:23
Alignment explanation
Indices: 44029--44117 Score: 66
Period size: 22 Copynumber: 4.1 Consensus size: 23
44019 AAGATCATTT
44029 TATTATTTTTA-A--AATAAAAA
1 TATTATTTTTATATTAATAAAAA
***
44049 TATTATTTTTATATTAATATTTA
1 TATTATTTTTATATTAATAAAAA
44072 TA-TATTTTTATAATT-ATAAAAA
1 TATTATTTTTAT-ATTAATAAAAA
* *
44094 -ATTATATTTAT-TAAATAAATAA
1 TATTATTTTTATATTAATAAA-AA
44116 TA
1 TA
44118 AATCAGATCG
Statistics
Matches: 53, Mismatches: 8, Indels: 13
0.72 0.11 0.18
Matches are distributed among these distances:
20 12 0.23
21 7 0.13
22 23 0.43
23 11 0.21
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (23 bp):
TATTATTTTTATATTAATAAAAA
Found at i:44106 original size:42 final size:41
Alignment explanation
Indices: 44027--44107 Score: 96
Period size: 42 Copynumber: 2.0 Consensus size: 41
44017 ATAAGATCAT
*
44027 TTTATTATTTTTAAAATAAAAATATTATTTTTATATTAATA
1 TTTATTATTTTTAAAATAAAAATATTATTATTATATTAATA
44068 TTTATATATTTTTATAATTATAAAAA-ATTA-TATT-TATTAA
1 TTTAT-TATTTTTA-AA--ATAAAAATATTATTATTATATTAA
44108 ATAAATAATA
Statistics
Matches: 35, Mismatches: 1, Indels: 7
0.81 0.02 0.16
Matches are distributed among these distances:
41 5 0.14
42 14 0.40
43 5 0.14
44 4 0.11
45 7 0.20
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (41 bp):
TTTATTATTTTTAAAATAAAAATATTATTATTATATTAATA
Found at i:44147 original size:13 final size:14
Alignment explanation
Indices: 44116--44148 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
44106 AAATAAATAA
*
44116 TAAATCAGATCGAT
1 TAAATCAAATCGAT
44130 TAAATCAAATCG-T
1 TAAATCAAATCGAT
44143 TAAATC
1 TAAATC
44149 TTATGTTTAG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 7 0.39
14 11 0.61
ACGTcount: A:0.45, C:0.15, G:0.09, T:0.30
Consensus pattern (14 bp):
TAAATCAAATCGAT
Found at i:47484 original size:6 final size:6
Alignment explanation
Indices: 47473--47497 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
47463 AATTAAGATG
47473 TGATTA TGATTA TGATTA TGATTA T
1 TGATTA TGATTA TGATTA TGATTA T
47498 AATTTCTAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.32, C:0.00, G:0.16, T:0.52
Consensus pattern (6 bp):
TGATTA
Found at i:47893 original size:16 final size:16
Alignment explanation
Indices: 47872--47932 Score: 65
Period size: 16 Copynumber: 3.9 Consensus size: 16
47862 ATTAATTTTT
47872 ATATTTTAAATATAAA
1 ATATTTTAAATATAAA
47888 ATATTTTAAATAT--A
1 ATATTTTAAATATAAA
* *
47902 AT-TATAAAATATAAA
1 ATATTTTAAATATAAA
*
47917 ATATATTCAAATATAA
1 ATAT-TTTAAATATAA
47933 TATAATATGA
Statistics
Matches: 37, Mismatches: 4, Indels: 7
0.77 0.08 0.15
Matches are distributed among these distances:
13 8 0.22
14 3 0.08
15 3 0.08
16 14 0.38
17 9 0.24
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (16 bp):
ATATTTTAAATATAAA
Found at i:47913 original size:29 final size:29
Alignment explanation
Indices: 47879--47937 Score: 93
Period size: 29 Copynumber: 2.0 Consensus size: 29
47869 TTTATATTTT
*
47879 AAATATAAAATAT-TTTAAATATAATTATA
1 AAATATAAAATATATTCAAATATAA-TATA
47908 AAATATAAAATATATTCAAATATAATATA
1 AAATATAAAATATATTCAAATATAATATA
47937 A
1 A
47938 TATGACTAGA
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
29 18 0.64
30 10 0.36
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (29 bp):
AAATATAAAATATATTCAAATATAATATA
Found at i:48369 original size:27 final size:27
Alignment explanation
Indices: 48330--48407 Score: 70
Period size: 32 Copynumber: 2.7 Consensus size: 27
48320 AATAATTAAA
*
48330 ATATAATAT--ATATTTTTTAAAATTT
1 ATATAATATAAATATTTTTTAAAAATT
48355 ATATAATATAAATATTTAATGTGTTAAAAATT
1 ATATAATATAAATA-TT--T-T-TTAAAAATT
48387 ATATAAATATAAAATATTTTT
1 ATAT-AATAT-AAATATTTTT
48408 AAACACAATT
Statistics
Matches: 43, Mismatches: 1, Indels: 14
0.74 0.02 0.24
Matches are distributed among these distances:
25 9 0.21
27 3 0.07
28 2 0.05
29 1 0.02
30 2 0.05
31 2 0.05
32 12 0.28
33 7 0.16
34 5 0.12
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (27 bp):
ATATAATATAAATATTTTTTAAAAATT
Found at i:52178 original size:2 final size:2
Alignment explanation
Indices: 52171--52201 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
52161 TGTAGACAAC
52171 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
52202 CACCATTACA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:53853 original size:34 final size:34
Alignment explanation
Indices: 53810--53912 Score: 127
Period size: 34 Copynumber: 3.0 Consensus size: 34
53800 AAGATAAGTT
* * *
53810 CACCTAACACACCTAATATGTTTACCTAATACAC
1 CACCTAACACACTTAATATATTTACCTAACACAC
*
53844 CACCTAACACACTTAATATATTACTCACCTAACATAC
1 CACCTAACACACTTAATATATT--T-ACCTAACACAC
*
53881 CACC-AATACACTTAATATATTTACCTAACACA
1 CACCTAACACACTTAATATATTTACCTAACACA
53913 TTTAATAAAA
Statistics
Matches: 60, Mismatches: 6, Indels: 7
0.82 0.08 0.10
Matches are distributed among these distances:
33 9 0.15
34 21 0.35
36 17 0.28
37 13 0.22
ACGTcount: A:0.41, C:0.31, G:0.01, T:0.27
Consensus pattern (34 bp):
CACCTAACACACTTAATATATTTACCTAACACAC
Found at i:53931 original size:12 final size:12
Alignment explanation
Indices: 53914--53939 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
53904 CCTAACACAT
53914 TTAATAAAAATA
1 TTAATAAAAATA
53926 TTAATAAAAATA
1 TTAATAAAAATA
53938 TT
1 TT
53940 CTAATACTCC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (12 bp):
TTAATAAAAATA
Found at i:62091 original size:17 final size:19
Alignment explanation
Indices: 62055--62096 Score: 61
Period size: 17 Copynumber: 2.3 Consensus size: 19
62045 TTTAAATTTT
*
62055 TTTAAAAAAATTTAATATA
1 TTTATAAAAATTTAATATA
62074 TTTATAAAAA-TT-ATATA
1 TTTATAAAAATTTAATATA
62091 TTTATA
1 TTTATA
62097 TTTATATTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 11 0.50
18 2 0.09
19 9 0.41
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (19 bp):
TTTATAAAAATTTAATATA
Found at i:62107 original size:17 final size:17
Alignment explanation
Indices: 62087--62121 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
62077 ATAAAAATTA
* *
62087 TATATTTATATTTATAT
1 TATATATATATATATAT
62104 TATATATATATATATAT
1 TATATATATATATATAT
62121 T
1 T
62122 TGACATCAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (17 bp):
TATATATATATATATAT
Found at i:63186 original size:29 final size:26
Alignment explanation
Indices: 63114--63195 Score: 51
Period size: 29 Copynumber: 3.0 Consensus size: 26
63104 TTTGAATTAC
* *
63114 TTTATT-TTTTAAGTAAT-TTTATATT
1 TTTATTATATTAAGTAAATTTTAT-TT
* *
63139 TTTATTATATCAAAATAAATTTTTATTT
1 TTTATTATAT-TAAGTAAA-TTTTATTT
*
63167 TTTATGTATACTTAAGTAAACTCTTATTT
1 TTTAT-TATA-TTAAGTAAA-TTTTATTT
63196 CAAATAATAT
Statistics
Matches: 43, Mismatches: 8, Indels: 8
0.73 0.14 0.14
Matches are distributed among these distances:
25 6 0.14
26 2 0.05
27 5 0.12
28 7 0.16
29 22 0.51
30 1 0.02
ACGTcount: A:0.33, C:0.05, G:0.04, T:0.59
Consensus pattern (26 bp):
TTTATTATATTAAGTAAATTTTATTT
Found at i:63260 original size:30 final size:30
Alignment explanation
Indices: 63220--63309 Score: 110
Period size: 30 Copynumber: 3.0 Consensus size: 30
63210 AATTTATGTC
*
63220 AAAAACTTATTTAAGTATAAATTAAAAATT
1 AAAAATTTATTTAAGTATAAATTAAAAATT
* * *
63250 AAGAATTTATTT-TGATATAAATTAAAGATT
1 AAAAATTTATTTAAG-TATAAATTAAAAATT
* *
63280 AAAAATTTATTTAAATGTAAATTAAAAATT
1 AAAAATTTATTTAAGTATAAATTAAAAATT
63310 TATTTGAATG
Statistics
Matches: 49, Mismatches: 9, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
29 1 0.02
30 48 0.98
ACGTcount: A:0.53, C:0.01, G:0.06, T:0.40
Consensus pattern (30 bp):
AAAAATTTATTTAAGTATAAATTAAAAATT
Found at i:63294 original size:24 final size:23
Alignment explanation
Indices: 63277--63329 Score: 83
Period size: 23 Copynumber: 2.4 Consensus size: 23
63267 TAAATTAAAG
63277 ATTAAAAATTTATTTAAATGTAA
1 ATTAAAAATTTATTTAAATGTAA
*
63300 ATTAAAAATTTATTTGAATGT-A
1 ATTAAAAATTTATTTAAATGTAA
63322 A-TAAAAAT
1 ATTAAAAAT
63330 ATAAAGTTTA
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
21 7 0.24
22 2 0.07
23 20 0.69
ACGTcount: A:0.53, C:0.00, G:0.06, T:0.42
Consensus pattern (23 bp):
ATTAAAAATTTATTTAAATGTAA
Found at i:65356 original size:23 final size:24
Alignment explanation
Indices: 65312--65356 Score: 65
Period size: 23 Copynumber: 1.9 Consensus size: 24
65302 TTAATAATTA
* *
65312 TTTATTTATATCATATTTATATAT
1 TTTATTTATATCATAATCATATAT
65336 TTTA-TTATATCATAATCATAT
1 TTTATTTATATCATAATCATAT
65357 TTAAAGTATT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 15 0.79
24 4 0.21
ACGTcount: A:0.36, C:0.07, G:0.00, T:0.58
Consensus pattern (24 bp):
TTTATTTATATCATAATCATATAT
Found at i:65424 original size:17 final size:17
Alignment explanation
Indices: 65364--65426 Score: 53
Period size: 17 Copynumber: 3.8 Consensus size: 17
65354 TATTTAAAGT
* *
65364 ATTTTAAAATTAAATAA
1 ATTTTAATATTATATAA
65381 ATTTTAACATATTA-AT-A
1 ATTTT-A-ATATTATATAA
*
65398 A--TTCATATTATATAA
1 ATTTTAATATTATATAA
65413 ATTTTAATATTATA
1 ATTTTAATATTATA
65427 ATTTATTATT
Statistics
Matches: 37, Mismatches: 3, Indels: 12
0.71 0.06 0.23
Matches are distributed among these distances:
13 6 0.16
14 2 0.05
15 4 0.11
17 17 0.46
18 3 0.08
19 5 0.14
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.48
Consensus pattern (17 bp):
ATTTTAATATTATATAA
Found at i:65459 original size:32 final size:35
Alignment explanation
Indices: 65403--65475 Score: 91
Period size: 32 Copynumber: 2.2 Consensus size: 35
65393 TAATAATTCA
*
65403 TATTATATAAATTTTAATATTATAATT-TA-TTAT
1 TATTATATAAATTGTAATATTATAATTATATTTAT
*
65436 T-TTATATAAATTGTATTCA-TATAATTATATTTAT
1 TATTATATAAATTGTAAT-ATTATAATTATATTTAT
65470 TATTAT
1 TATTAT
65476 CACATTCACT
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
32 21 0.62
33 4 0.12
34 5 0.15
35 4 0.12
ACGTcount: A:0.40, C:0.01, G:0.01, T:0.58
Consensus pattern (35 bp):
TATTATATAAATTGTAATATTATAATTATATTTAT
Found at i:65697 original size:30 final size:31
Alignment explanation
Indices: 65663--65723 Score: 81
Period size: 30 Copynumber: 2.0 Consensus size: 31
65653 TACATTTGAT
* *
65663 TTATTGAATAAAATTAAA-AAAGTAA-AATAA
1 TTATTCAATAAAATGAAATAAA-TAAGAATAA
65693 TTATTCAATAAAATGAAATAAATAAGAATAA
1 TTATTCAATAAAATGAAATAAATAAGAATAA
65724 GTATGATTGA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
30 19 0.70
31 8 0.30
ACGTcount: A:0.62, C:0.02, G:0.07, T:0.30
Consensus pattern (31 bp):
TTATTCAATAAAATGAAATAAATAAGAATAA
Found at i:65974 original size:6 final size:6
Alignment explanation
Indices: 65963--65988 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
65953 ATAACATAAA
65963 ATATTT ATATTT ATATTT ATATTT AT
1 ATATTT ATATTT ATATTT ATATTT AT
65989 CTTTTAATAA
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:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (6 bp):
ATATTT
Done.