Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1386
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: 85536
ACGTcount: A:0.36, C:0.15, G:0.16, T:0.33
Found at i:885 original size:18 final size:19
Alignment explanation
Indices: 849--887 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
839 GGGCCACTCT
*
849 TTTTTTTTATTGATGTTCA
1 TTTTTTTTATTGATATTCA
*
868 TTTTTTTT-TTGCTATTCA
1 TTTTTTTTATTGATATTCA
886 TT
1 TT
888 CCCATTATTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 10 0.56
19 8 0.44
ACGTcount: A:0.13, C:0.08, G:0.08, T:0.72
Consensus pattern (19 bp):
TTTTTTTTATTGATATTCA
Found at i:10620 original size:11 final size:11
Alignment explanation
Indices: 10604--10675 Score: 74
Period size: 11 Copynumber: 6.1 Consensus size: 11
10594 CTTTTACACC
10604 CAAAAAAAAAA
1 CAAAAAAAAAA
10615 CAAAAAACAAAA
1 CAAAAAA-AAAA
10627 -AAAAACAAAAA
1 CAAAAA-AAAAA
*
10638 CAAGAAAAAAA
1 CAAAAAAAAAA
10649 CAAGAAAAAAATA
1 CAA-AAAAAAA-A
10662 GCGAAAAAAAAAA
1 -C-AAAAAAAAAA
10675 C
1 C
10676 CAGAAAGGGG
Statistics
Matches: 52, Mismatches: 2, Indels: 13
0.78 0.03 0.19
Matches are distributed among these distances:
11 24 0.46
12 16 0.31
13 2 0.04
14 8 0.15
15 2 0.04
ACGTcount: A:0.82, C:0.11, G:0.06, T:0.01
Consensus pattern (11 bp):
CAAAAAAAAAA
Found at i:10628 original size:17 final size:17
Alignment explanation
Indices: 10606--10656 Score: 77
Period size: 17 Copynumber: 2.9 Consensus size: 17
10596 TTTACACCCA
10606 AAAAAAAAACAAAAAAC
1 AAAAAAAAACAAAAAAC
10623 AAAAAAAAAC-AAAAAC
1 AAAAAAAAACAAAAAAC
10639 AAGAAAAAAACAAGAAAA
1 AA-AAAAAAACAA-AAAA
10657 AAATAGCGAA
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
16 8 0.26
17 18 0.58
18 1 0.03
19 4 0.13
ACGTcount: A:0.86, C:0.10, G:0.04, T:0.00
Consensus pattern (17 bp):
AAAAAAAAACAAAAAAC
Found at i:11989 original size:57 final size:57
Alignment explanation
Indices: 11895--12784 Score: 1271
Period size: 57 Copynumber: 15.5 Consensus size: 57
11885 TGTTCATCCC
* *
11895 TTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCCCACAAGTCAGTGGTACCT
1 TTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCACCT
* *
11952 TTTCAAAGCCCACAAATCAGTGGCACTCTTTTTAAAGCCCACAAGTCAGTGGCACCT
1 TTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCACCT
*
12009 TTTCAAAGCCCACAAATCAGTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCACTCT
1 TTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCAC-CT
12067 TTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCA-CT
1 TTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCACCT
* *
12123 CTTTCAAAGCCCACAAGTCAGTGGCACCCTTTTCAAAGCCCACAAATCAGTGGCACTCT
1 -TTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCAC-CT
12182 TTTCAAAGCCCACAAGTCAGTGGCACTC-TTTCAAAGCCCACAAGTCAGTGGCACTCT
1 TTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCAC-CT
12239 TTTCAAAGCCCACAAGTCAGTGGCACTC-TTTCAAAGCCCACAAGTCAGTGGCACCCT
1 TTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCA-CCT
* *
12296 TTTCAAAGCCCACAAATCAGTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCACCC
1 TTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCACCT
*
12353 TTTCAAATCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCACTCT
1 TTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCAC-CT
* *
12411 TTT-AAAGCCCACAAGTCAGTGGCACCCTTTTCAAAGCCCACAAATCAGTGGCACTCT
1 TTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCAC-CT
* * *
12468 TTTCAAAGCCCACAAGTCAATGGCAC-CTTTTCAAAGTCCACGAGTCAGTGGCACCT
1 TTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCACCT
* *
12524 TTTCAAAGCCCACGAGTCAGTGGCACTC-TTTCAAAGCCCACAAGTCAGTGGCACCC
1 TTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCACCT
* * *
12580 TTTC-AAGCCCACGAGTCAGTGGTAC-CTTTTCAAAGCCCACGAGTCAGTGGCA-CT
1 TTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCACCT
*
12634 CTTTCAAAGCCCACAAGTCAGTGGCAC-CCTTTCAAAGCCCACACAAGTCAGTGGCACTCCT
1 -TTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAG-CC-CACAAGTCAGTGGCA--CCT
* ** * * *
12695 TTT-AAAGCCTACGCAAGTCAGTAACACTCTTTTCAAAGCCCACATGTGTTAGTGACAACTCT
1 TTTCAAAGCC--CACAAGTCAGTGGCACTCTTTTCAAAGCCCACA--AGTCAGTGGC-AC-CT
*
12757 TTTCAAAGCCCACACAAGTTAGTGGCAC
1 TTTCAAAG-CC-CACAAGTCAGTGGCAC
12785 CATTTTTTTT
Statistics
Matches: 762, Mismatches: 45, Indels: 46
0.89 0.05 0.05
Matches are distributed among these distances:
54 2 0.00
55 48 0.06
56 85 0.11
57 406 0.53
58 147 0.19
59 8 0.01
60 7 0.01
61 18 0.02
62 21 0.03
63 18 0.02
64 2 0.00
ACGTcount: A:0.29, C:0.31, G:0.17, T:0.23
Consensus pattern (57 bp):
TTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCACCT
Found at i:12044 original size:86 final size:86
Alignment explanation
Indices: 11895--12790 Score: 1303
Period size: 86 Copynumber: 10.4 Consensus size: 86
11885 TGTTCATCCC
* *
11895 TTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCCCACAAGTCAGTGGTAC-CTTTTCAAA
1 TTTCAAAGCCCACAAGTCAGTGGCAC-CTTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAA
*
11959 GCCCACAAATCAGTGGCACTCT
65 GCCCACAAGTCAGTGGCACTCT
* *
11981 TTTTAAAGCCCACAAGTCAGTGGCACCTTTTCAAAGCCCACAAATCAGTGGCACTCTTTTCAAAG
1 TTTCAAAGCCCACAAGTCAGTGGCACCTTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAG
12046 CCCACAAGTCAGTGGCACTCT
66 CCCACAAGTCAGTGGCACTCT
12067 TTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCACTC-TTTCAAA
1 TTTCAAAGCCCACAAGTCAGTGGCAC-CTTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAA
*
12131 GCCCACAAGTCAGTGGCACCCT
65 GCCCACAAGTCAGTGGCACTCT
*
12153 TTTCAAAGCCCACAAATCAGTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCACTC-TTTCAAA
1 TTTCAAAGCCCACAAGTCAGTGGCAC-CTTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAA
12217 GCCCACAAGTCAGTGGCACTCT
65 GCCCACAAGTCAGTGGCACTCT
*
12239 TTTCAAAGCCCACAAGTCAGTGGCA-CTCTTTCAAAGCCCACAAGTCAGTGGCACCCTTTTCAAA
1 TTTCAAAGCCCACAAGTCAGTGGCACCT-TTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAA
*
12303 GCCCACAAATCAGTGGCACTCT
65 GCCCACAAGTCAGTGGCACTCT
* *
12325 TTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAATCCCACAAGTCAGTGGCACTCTTTTCAAAG
1 TTTCAAAGCCCACAAGTCAGTGGCACCTTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAG
12390 CCCACAAGTCAGTGGCACTCT
66 CCCACAAGTCAGTGGCACTCT
*
12411 TTT-AAAGCCCACAAGTCAGTGGCACCCTTTTCAAAGCCCACAAATCAGTGGCACTCTTTTCAAA
1 TTTCAAAGCCCACAAGTCAGTGGCA-CCTTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAA
*
12475 GCCCACAAGTCAATGGCAC-CT
65 GCCCACAAGTCAGTGGCACTCT
* * *
12496 TTTCAAAGTCCACGAGTCAGTGGCACCTTTTCAAAGCCCACGAGTCAGTGGCACTC-TTTCAAAG
1 TTTCAAAGCCCACAAGTCAGTGGCACCTTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAG
*
12560 CCCACAAGTCAGTGGCAC-CC
66 CCCACAAGTCAGTGGCACTCT
* * *
12580 TTTC-AAGCCCACGAGTCAGTGGTACCTTTTCAAAGCCCACGAGTCAGTGGCACTC-TTTCAAAG
1 TTTCAAAGCCCACAAGTCAGTGGCACCTTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAG
*
12643 CCCACAAGTCAGTGGCAC-CC
66 CCCACAAGTCAGTGGCACTCT
* **
12663 TTTCAAAGCCCACACAAGTCAGTGGCACTCCTTTT-AAAGCCTACGCAAGTCAGTAACACTCTTT
1 TTTCAAAG-CC-CACAAGTCAGTGGCA--CCTTTTCAAAGCC--CACAAGTCAGTGGCACTCTTT
* * *
12727 TCAAAGCCCACATGTGTTAGTGACAACTCT
60 TCAAAGCCCACA--AGTCAGTGGC-ACTCT
*
12757 TTTCAAAGCCCACACAAGTTAGTGGCACCATTTT
1 TTTCAAAG-CC-CACAAGTCAGTGGCACC-TTTT
12791 TTTTAAAAAA
Statistics
Matches: 750, Mismatches: 40, Indels: 33
0.91 0.05 0.04
Matches are distributed among these distances:
83 81 0.11
84 35 0.05
85 109 0.15
86 413 0.55
87 36 0.05
88 6 0.01
89 14 0.02
90 14 0.02
92 9 0.01
93 6 0.01
94 27 0.04
ACGTcount: A:0.28, C:0.31, G:0.17, T:0.23
Consensus pattern (86 bp):
TTTCAAAGCCCACAAGTCAGTGGCACCTTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAG
CCCACAAGTCAGTGGCACTCT
Found at i:12223 original size:143 final size:142
Alignment explanation
Indices: 11895--12784 Score: 1367
Period size: 143 Copynumber: 6.2 Consensus size: 142
11885 TGTTCATCCC
*
11895 TTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCCCACAAGTCAGTGGTACCTTTTCAAAG
1 TTTCAAAGCCCACAAGTCAGTGGCACT-CTTTCAAAGCCCACAAGTCAGTGGCACCTTTTCAAAG
* *
11960 CCCACAAATCAGTGGCACTCTTTTTAAAGCCCACAAGTCAGTGGCA-CCTTTTCAAAGCCCACAA
65 CCCACAAGTCAGTGGCACTC-TTTCAAAGCCCACAAGTCAGTGGCACCCTTTTCAAAGCCCACAA
12024 ATCAGTGGCACTCT
129 ATCAGTGGCACTCT
12038 TTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAA
1 TTTCAAAGCCCACAAGTCAGTGGCACTC-TTTCAAAGCCCACAAGTCAGTGGCAC-CTTTTCAAA
12103 GCCCACAAGTCAGTGGCACTCTTTCAAAGCCCACAAGTCAGTGGCACCCTTTTCAAAGCCCACAA
64 GCCCACAAGTCAGTGGCACTCTTTCAAAGCCCACAAGTCAGTGGCACCCTTTTCAAAGCCCACAA
12168 ATCAGTGGCACTCT
129 ATCAGTGGCACTCT
12182 TTTCAAAGCCCACAAGTCAGTGGCACTCTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAG
1 TTTCAAAGCCCACAAGTCAGTGGCACTCTTTCAAAGCCCACAAGTCAGTGGCAC-CTTTTCAAAG
12247 CCCACAAGTCAGTGGCACTCTTTCAAAGCCCACAAGTCAGTGGCACCCTTTTCAAAGCCCACAAA
65 CCCACAAGTCAGTGGCACTCTTTCAAAGCCCACAAGTCAGTGGCACCCTTTTCAAAGCCCACAAA
12312 TCAGTGGCACTCT
130 TCAGTGGCACTCT
* *
12325 TTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAATCCCACAAGTCAGTGGCACTCTTTTCAAAG
1 TTTCAAAGCCCACAAGTCAGTGGCACTCTTTCAAAGCCCACAAGTCAGTGGCAC-CTTTTCAAAG
*
12390 CCCACAAGTCAGTGGCACTCTTTTAAAGCCCACAAGTCAGTGGCACCCTTTTCAAAGCCCACAAA
65 CCCACAAGTCAGTGGCACTCTTTCAAAGCCCACAAGTCAGTGGCACCCTTTTCAAAGCCCACAAA
12455 TCAGTGGCACTCT
130 TCAGTGGCACTCT
* * *
12468 TTTCAAAGCCCACAAGTCAATGGCAC-CTTTTCAAAGTCCACGAGTCAGTGGCACCTTTTCAAAG
1 TTTCAAAGCCCACAAGTCAGTGGCACTC-TTTCAAAGCCCACAAGTCAGTGGCACCTTTTCAAAG
* * *
12532 CCCACGAGTCAGTGGCACTCTTTCAAAGCCCACAAGTCAGTGGCACCC-TTTC-AAGCCCACGAG
65 CCCACAAGTCAGTGGCACTCTTTCAAAGCCCACAAGTCAGTGGCACCCTTTTCAAAGCCCACAAA
*
12595 TCAGTGGTAC-CT
130 TCAGTGGCACTCT
* *
12607 TTTCAAAGCCCACGAGTCAGTGGCACTCTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGC
1 TTTCAAAGCCCACAAGTCAGTGGCACTCTTTCAAAGCCCACAAGTCAGTGGCACCTTTTCAAAG-
* * ** *
12672 CCACACAAGTCAGTGGCACTCCTTTTAAAGCCTACGCAAGTCAGTAACACTCTTTTCAAAGCCCA
65 CC-CACAAGTCAGTGGCACT-CTTTCAAAGCC--CACAAGTCAGTGGCACCCTTTTCAAAGCCCA
** * *
12737 CATGTGTTAGTGACAACTCT
126 CA--AATCAGTGGC-ACTCT
*
12757 TTTCAAAGCCCACACAAGTTAGTGGCAC
1 TTTCAAAG-CC-CACAAGTCAGTGGCAC
12785 CATTTTTTTT
Statistics
Matches: 696, Mismatches: 33, Indels: 27
0.92 0.04 0.04
Matches are distributed among these distances:
139 59 0.08
140 21 0.03
141 20 0.03
142 68 0.10
143 379 0.54
144 103 0.15
145 4 0.01
146 8 0.01
148 6 0.01
149 2 0.00
150 10 0.01
151 2 0.00
152 14 0.02
ACGTcount: A:0.29, C:0.31, G:0.17, T:0.23
Consensus pattern (142 bp):
TTTCAAAGCCCACAAGTCAGTGGCACTCTTTCAAAGCCCACAAGTCAGTGGCACCTTTTCAAAGC
CCACAAGTCAGTGGCACTCTTTCAAAGCCCACAAGTCAGTGGCACCCTTTTCAAAGCCCACAAAT
CAGTGGCACTCT
Found at i:13375 original size:20 final size:20
Alignment explanation
Indices: 13347--13421 Score: 87
Period size: 20 Copynumber: 3.8 Consensus size: 20
13337 TTTTACCCTG
13347 ATGTATCGATACATTTTTCA
1 ATGTATCGATACATTTTTCA
* * * *
13367 ATATATCGATACATGTATGA
1 ATGTATCGATACATTTTTCA
* * *
13387 ATGTATCGATATATTCTGCA
1 ATGTATCGATACATTTTTCA
13407 ATGTATCGATACATT
1 ATGTATCGATACATT
13422 ATGTCTTTTT
Statistics
Matches: 43, Mismatches: 12, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
20 43 1.00
ACGTcount: A:0.33, C:0.13, G:0.13, T:0.40
Consensus pattern (20 bp):
ATGTATCGATACATTTTTCA
Found at i:13414 original size:40 final size:39
Alignment explanation
Indices: 13347--13424 Score: 111
Period size: 40 Copynumber: 2.0 Consensus size: 39
13337 TTTTACCCTG
* *
13347 ATGTATCGATACATTTTTCAATATATCGATACATGTATGA
1 ATGTATCGATACATTCTGCAATATATCGATACAT-TATGA
* *
13387 ATGTATCGATATATTCTGCAATGTATCGATACATTATG
1 ATGTATCGATACATTCTGCAATATATCGATACATTATG
13425 TCTTTTTACC
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
39 4 0.12
40 30 0.88
ACGTcount: A:0.33, C:0.13, G:0.14, T:0.40
Consensus pattern (39 bp):
ATGTATCGATACATTCTGCAATATATCGATACATTATGA
Found at i:17687 original size:26 final size:26
Alignment explanation
Indices: 17636--17687 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
17626 ATTTATTTTG
* *
17636 AATTTTTTTAATTAAGTTATTCTTTA
1 AATTTTATTAATTAAGTTATTATTTA
* *
17662 AATTTTATTAATTAATTTGTTATTTA
1 AATTTTATTAATTAAGTTATTATTTA
17688 CATAAAAAAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.33, C:0.02, G:0.04, T:0.62
Consensus pattern (26 bp):
AATTTTATTAATTAAGTTATTATTTA
Found at i:18648 original size:17 final size:17
Alignment explanation
Indices: 18626--18662 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
18616 TTGATAAATT
18626 TTTTATATAATTTTATA
1 TTTTATATAATTTTATA
**
18643 TTTTATATTTTTTTATA
1 TTTTATATAATTTTATA
18660 TTT
1 TTT
18663 ATTTTGATCT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (17 bp):
TTTTATATAATTTTATA
Found at i:19152 original size:17 final size:17
Alignment explanation
Indices: 19130--19166 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
19120 TGATTAAATT
19130 TTTTATATAATTTTATA
1 TTTTATATAATTTTATA
**
19147 TTTTATATTTTTTTATA
1 TTTTATATAATTTTATA
19164 TTT
1 TTT
19167 ATTTTGATCT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (17 bp):
TTTTATATAATTTTATA
Found at i:19270 original size:26 final size:25
Alignment explanation
Indices: 19225--19276 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 25
19215 CTCATCATGA
* *
19225 AAATTTTTTAATTAAGTTATTTTTT
1 AAATTTTTCAATTAAGTTATTATTT
*
19250 AAATTTTATCAATTAATTTATTATTT
1 AAATTTT-TCAATTAAGTTATTATTT
19276 A
1 A
19277 CATAAAAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
25 7 0.30
26 16 0.70
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.60
Consensus pattern (25 bp):
AAATTTTTCAATTAAGTTATTATTT
Found at i:20397 original size:16 final size:15
Alignment explanation
Indices: 20378--20453 Score: 57
Period size: 15 Copynumber: 4.9 Consensus size: 15
20368 ATACTTTGAT
20378 TTTAAGTTATTTTAAA
1 TTTAA-TTATTTTAAA
20394 TTTAAATTA-TTTAAA
1 TTT-AATTATTTTAAA
* * * *
20409 GTCTAAATCAATTAAAA
1 -T-TTAATTATTTTAAA
*
20426 TTTAATTTTTTTAAA
1 TTTAATTATTTTAAA
20441 TTTAATT-TTTTAA
1 TTTAATTATTTTAA
20454 TTTTTTTAAT
Statistics
Matches: 48, Mismatches: 8, Indels: 10
0.73 0.12 0.15
Matches are distributed among these distances:
14 6 0.12
15 22 0.46
16 12 0.25
17 8 0.17
ACGTcount: A:0.41, C:0.03, G:0.03, T:0.54
Consensus pattern (15 bp):
TTTAATTATTTTAAA
Found at i:20453 original size:14 final size:15
Alignment explanation
Indices: 20423--20451 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
20413 AAATCAATTA
20423 AAATTTAATTTTTTT
1 AAATTTAATTTTTTT
20438 AAATTTAATTTTTT
1 AAATTTAATTTTTT
20452 AATTTTTTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (15 bp):
AAATTTAATTTTTTT
Found at i:20457 original size:22 final size:23
Alignment explanation
Indices: 20426--20469 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
20416 TCAATTAAAA
*
20426 TTTAATTTTTTTAAATTTAATTT
1 TTTAATTTTTTTAAATTAAATTT
20449 TTTAATTTTTTT-AATTAAATT
1 TTTAATTTTTTTAAATTAAATT
20470 AAAATTTGAC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
22 8 0.40
23 12 0.60
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (23 bp):
TTTAATTTTTTTAAATTAAATTT
Found at i:21634 original size:2 final size:2
Alignment explanation
Indices: 21623--21660 Score: 62
Period size: 2 Copynumber: 20.0 Consensus size: 2
21613 ATTATAGGTC
21623 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
21661 ACTCGCGGTC
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
1 2 0.06
2 32 0.94
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:21785 original size:13 final size:13
Alignment explanation
Indices: 21756--21794 Score: 60
Period size: 13 Copynumber: 2.8 Consensus size: 13
21746 TGTATAAACT
21756 TGATAATATTATATA
1 TGAT-ATATT-TATA
21771 TGATATATTTATA
1 TGATATATTTATA
21784 TGATATATTTA
1 TGATATATTTA
21795 ATTTAAAATG
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
13 15 0.62
14 5 0.21
15 4 0.17
ACGTcount: A:0.41, C:0.00, G:0.08, T:0.51
Consensus pattern (13 bp):
TGATATATTTATA
Found at i:22864 original size:15 final size:15
Alignment explanation
Indices: 22844--22968 Score: 52
Period size: 15 Copynumber: 8.5 Consensus size: 15
22834 ATTTCATATT
*
22844 ATTTATTTTTATTAA
1 ATTTATTTTAATTAA
22859 ATTTATTTTAATTTAA
1 ATTTATTTTAA-TTAA
* *
22875 TTTGTTAATTTTATATTCA
1 -AT-TT-ATTTTA-ATTAA
** *
22894 ATAAATTTAAAATTAA
1 ATTTATTT-TAATTAA
*
22910 ATTTATTATAA--AA
1 ATTTATTTTAATTAA
22923 A-TT-TTTTAATTAA
1 ATTTATTTTAATTAA
22936 A-TTATTTT--TTAA
1 ATTTATTTTAATTAA
*
22948 A-TTATTATCAATT-A
1 ATTTATT-TTAATTAA
22962 ATTTATT
1 ATTTATT
22969 ATTTACATGA
Statistics
Matches: 83, Mismatches: 14, Indels: 26
0.67 0.11 0.21
Matches are distributed among these distances:
11 5 0.06
12 12 0.14
13 9 0.11
14 6 0.07
15 19 0.23
16 17 0.20
17 2 0.02
18 3 0.04
19 9 0.11
20 1 0.01
ACGTcount: A:0.40, C:0.02, G:0.01, T:0.58
Consensus pattern (15 bp):
ATTTATTTTAATTAA
Found at i:23185 original size:65 final size:65
Alignment explanation
Indices: 23114--23265 Score: 295
Period size: 65 Copynumber: 2.3 Consensus size: 65
23104 CAAGAGAAAC
*
23114 AAATAAACGTTTAAATTTGGTTATTGAAATCTTAAGTTAATAACAGTAAGTTTGATAATTTTTTA
1 AAATAAACGTTTAAATTTGGTTATTGAAATCTTAAGTTAATAACAATAAGTTTGATAATTTTTTA
23179 AAATAAACGTTTAAATTTGGTTATTGAAATCTTAAGTTAATAACAATAAGTTTGATAATTTTTTA
1 AAATAAACGTTTAAATTTGGTTATTGAAATCTTAAGTTAATAACAATAAGTTTGATAATTTTTTA
23244 AAATAAACGTTTAAATTTGGTT
1 AAATAAACGTTTAAATTTGGTT
23266 TTATTTGTAA
Statistics
Matches: 86, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
65 86 1.00
ACGTcount: A:0.41, C:0.05, G:0.12, T:0.43
Consensus pattern (65 bp):
AAATAAACGTTTAAATTTGGTTATTGAAATCTTAAGTTAATAACAATAAGTTTGATAATTTTTTA
Found at i:24672 original size:12 final size:12
Alignment explanation
Indices: 24603--24699 Score: 55
Period size: 12 Copynumber: 8.5 Consensus size: 12
24593 ATATTTAGTT
24603 TATATTTTAAAAA
1 TATA-TTTAAAAA
* **
24616 TTTTATTTAAATT
1 -TATATTTAAAAA
*
24629 TTTATTT-AAAA
1 TATATTTAAAAA
*
24640 T-TATTAAAAAA
1 TATATTTAAAAA
*
24651 TATAATT--AAA
1 TATATTTAAAAA
*
24661 TATATTTATAAA
1 TATATTTAAAAA
24673 TA-A-TTAAAAA
1 TATATTTAAAAA
*
24683 TTTATTTAAAAA
1 TATATTTAAAAA
24695 T-TATT
1 TATATT
24700 ATTATATTAA
Statistics
Matches: 66, Mismatches: 11, Indels: 15
0.72 0.12 0.16
Matches are distributed among these distances:
10 20 0.30
11 14 0.21
12 23 0.35
13 6 0.09
14 3 0.05
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (12 bp):
TATATTTAAAAA
Found at i:24683 original size:22 final size:22
Alignment explanation
Indices: 24658--24700 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
24648 AAATATAATT
*
24658 AAATATATTTATAAATAATTAA
1 AAATATATTTAAAAATAATTAA
* *
24680 AAATTTATTTAAAAATTATTA
1 AAATATATTTAAAAATAATTA
24701 TTATATTAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (22 bp):
AAATATATTTAAAAATAATTAA
Found at i:26555 original size:22 final size:22
Alignment explanation
Indices: 26512--26560 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 22
26502 CTCCATAAGG
*
26512 AAAAGTTGAAGAATTTTGAGAA
1 AAAAGTTGAAGAATTTGGAGAA
*
26534 GAAAGTTGAA-AATTTGGCAGAA
1 AAAAGTTGAAGAATTTGG-AGAA
26556 AAAAG
1 AAAAG
26561 AGACAGAGTG
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
21 6 0.26
22 17 0.74
ACGTcount: A:0.51, C:0.02, G:0.24, T:0.22
Consensus pattern (22 bp):
AAAAGTTGAAGAATTTGGAGAA
Found at i:29619 original size:3 final size:3
Alignment explanation
Indices: 29599--29636 Score: 51
Period size: 3 Copynumber: 13.0 Consensus size: 3
29589 TTTCTATTTG
* *
29599 AAT ATT AAT AAT TA- AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
29637 CAATGAAAGT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
2 1 0.03
3 29 0.97
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (3 bp):
AAT
Found at i:29854 original size:16 final size:17
Alignment explanation
Indices: 29835--29871 Score: 60
Period size: 16 Copynumber: 2.3 Consensus size: 17
29825 TTTAAGATAC
29835 TTTAAT-TTTAAATTAT
1 TTTAATATTTAAATTAT
29851 TTT-ATATTTAAATTAT
1 TTTAATATTTAAATTAT
29867 TTTAA
1 TTTAA
29872 ATTCAAGTCA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
15 2 0.11
16 16 0.84
17 1 0.05
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (17 bp):
TTTAATATTTAAATTAT
Found at i:30566 original size:20 final size:20
Alignment explanation
Indices: 30541--30586 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
30531 AAGAATTGAA
*
30541 GAGGGATACAAGAGAGGGAT
1 GAGGGATACAAGAGAGGGAG
**
30561 GAGGGATACTTGAGAGGGAG
1 GAGGGATACAAGAGAGGGAG
30581 GAGGGA
1 GAGGGA
30587 GCCTCTATTT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.35, C:0.04, G:0.50, T:0.11
Consensus pattern (20 bp):
GAGGGATACAAGAGAGGGAG
Found at i:30661 original size:25 final size:25
Alignment explanation
Indices: 30623--30707 Score: 73
Period size: 27 Copynumber: 3.2 Consensus size: 25
30613 CCCATTTTGT
30623 AATAAAAATTAGCCACAAATTTTGACA
1 AATAAAAA-TAGCCAC-AATTTTGACA
* * *
30650 AATAAACA-AGCCTCCATATTTGACA
1 AATAAAAATAGCCACAAT-TTTGACA
* *
30675 AATACAAAATAACCACCATTTTTGACA
1 AATA-AAAATAGCCA-CAATTTTGACA
30702 AATAAA
1 AATAAA
30708 TGGGTGGCTT
Statistics
Matches: 46, Mismatches: 8, Indels: 9
0.73 0.13 0.14
Matches are distributed among these distances:
24 2 0.04
25 16 0.35
26 5 0.11
27 21 0.46
28 2 0.04
ACGTcount: A:0.51, C:0.19, G:0.06, T:0.25
Consensus pattern (25 bp):
AATAAAAATAGCCACAATTTTGACA
Found at i:32625 original size:21 final size:22
Alignment explanation
Indices: 32587--32632 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 22
32577 ATCTGTTGAA
* **
32587 ACTCCACCTGTTTTGGAGTA-T
1 ACTCCACCTGCTGCGGAGTACT
32608 ACTCCACCTGCTGCGGAGTACT
1 ACTCCACCTGCTGCGGAGTACT
32630 ACT
1 ACT
32633 TGTCTGAACA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 17 0.81
22 4 0.19
ACGTcount: A:0.20, C:0.30, G:0.20, T:0.30
Consensus pattern (22 bp):
ACTCCACCTGCTGCGGAGTACT
Found at i:37433 original size:11 final size:11
Alignment explanation
Indices: 37417--37441 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
37407 ATTCCCAAAC
37417 TTTTTTTCTTT
1 TTTTTTTCTTT
37428 TTTTTTTCTTT
1 TTTTTTTCTTT
37439 TTT
1 TTT
37442 GGTAAATGGC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.00, C:0.08, G:0.00, T:0.92
Consensus pattern (11 bp):
TTTTTTTCTTT
Found at i:38909 original size:40 final size:41
Alignment explanation
Indices: 38816--38919 Score: 124
Period size: 40 Copynumber: 2.6 Consensus size: 41
38806 TATTAAATAT
38816 ATTTATTTAAATTTAATT-TGATTTAAAATATAAATATTAAA
1 ATTTATTTAAATTTAATTAT-ATTTAAAATATAAATATTAAA
* * *
38857 TTTTATTTAAATTTAGTTATATTTATAA-AT-AATAATTAAA
1 ATTTATTTAAATTTAATTATATTTAAAATATAAAT-ATTAAA
* *
38897 ATTTATTAAAATTTATTTATATT
1 ATTTATTTAAATTTAATTATATT
38920 ATATTTTTTA
Statistics
Matches: 55, Mismatches: 6, Indels: 5
0.83 0.09 0.08
Matches are distributed among these distances:
39 3 0.05
40 28 0.51
41 23 0.42
42 1 0.02
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (41 bp):
ATTTATTTAAATTTAATTATATTTAAAATATAAATATTAAA
Found at i:38929 original size:14 final size:14
Alignment explanation
Indices: 38907--38958 Score: 52
Period size: 14 Copynumber: 3.6 Consensus size: 14
38897 ATTTATTAAA
38907 ATTTATTTATATTAT
1 ATTT-TTTATATTAT
38922 ATTTTTTATAATT-T
1 ATTTTTTAT-ATTAT
* *
38936 ATTTTTTAAAATAT
1 ATTTTTTATATTAT
*
38950 AATTTTTAT
1 ATTTTTTAT
38959 TAATTTAATA
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
13 2 0.06
14 22 0.71
15 7 0.23
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (14 bp):
ATTTTTTATATTAT
Found at i:40166 original size:18 final size:19
Alignment explanation
Indices: 40131--40172 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 19
40121 GCAAAAATTG
*
40131 TATAAAATTAGTTTTGTTA
1 TATAAAATTAGATTTGTTA
40150 TATAAAATTA-ATTTGTTA
1 TATAAAATTAGATTTGTTA
*
40168 AATAA
1 TATAA
40173 TTGAATATTG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 11 0.52
19 10 0.48
ACGTcount: A:0.45, C:0.00, G:0.07, T:0.48
Consensus pattern (19 bp):
TATAAAATTAGATTTGTTA
Found at i:40462 original size:3 final size:3
Alignment explanation
Indices: 40456--40485 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
40446 TTAATTATTA
40456 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
40486 CAATGGAAGT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:40718 original size:16 final size:16
Alignment explanation
Indices: 40699--40742 Score: 52
Period size: 16 Copynumber: 2.8 Consensus size: 16
40689 ATCTTGAATC
* *
40699 ATTTTAATTTTAAATT
1 ATTTTAAATTAAAATT
40715 ATTTTAAATTAAAATT
1 ATTTTAAATTAAAATT
* *
40731 AATTAAAATTAA
1 ATTTTAAATTAA
40743 TTTTTTAATT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (16 bp):
ATTTTAAATTAAAATT
Found at i:43352 original size:7 final size:7
Alignment explanation
Indices: 43328--43373 Score: 56
Period size: 7 Copynumber: 6.3 Consensus size: 7
43318 TTCAAATCAA
*
43328 TTAAAAT
1 TTAAATT
43335 TTAAATTTT
1 TTAAA--TT
*
43344 TTTAATT
1 TTAAATT
43351 TTAAATT
1 TTAAATT
43358 TTAAATT
1 TTAAATT
43365 TTAAATT
1 TTAAATT
43372 TT
1 TT
43374 TTTAATTAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
7 29 0.85
9 5 0.15
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (7 bp):
TTAAATT
Found at i:43382 original size:14 final size:15
Alignment explanation
Indices: 43332--43384 Score: 58
Period size: 14 Copynumber: 3.6 Consensus size: 15
43322 AATCAATTAA
43332 AATTTAAATTTTTTT
1 AATTTAAATTTTTTT
*
43347 AATTTTAAA--TTTTA
1 AA-TTTAAATTTTTTT
43361 AATTTTAAATTTTTTT
1 AA-TTTAAATTTTTTT
43377 AA-TTAAAT
1 AATTTAAAT
43385 CAAAATCTAG
Statistics
Matches: 33, Mismatches: 2, Indels: 7
0.79 0.05 0.17
Matches are distributed among these distances:
14 19 0.58
15 2 0.06
16 12 0.36
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (15 bp):
AATTTAAATTTTTTT
Found at i:45075 original size:16 final size:16
Alignment explanation
Indices: 45053--45106 Score: 74
Period size: 16 Copynumber: 3.4 Consensus size: 16
45043 TATAATCAAG
45053 TTATTTTGTATTTAAA
1 TTATTTTGTATTTAAA
*
45069 ATATTTT-TATTTTAAA
1 TTATTTTGTA-TTTAAA
*
45085 TTATTTTGAATTTAAA
1 TTATTTTGTATTTAAA
45101 TTATTT
1 TTATTT
45107 CGAGCTCAAG
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
15 2 0.06
16 30 0.91
17 1 0.03
ACGTcount: A:0.33, C:0.00, G:0.04, T:0.63
Consensus pattern (16 bp):
TTATTTTGTATTTAAA
Found at i:46681 original size:18 final size:18
Alignment explanation
Indices: 46658--46694 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
46648 AAGATAATAA
46658 TATTAATCTTTTATTTAT
1 TATTAATCTTTTATTTAT
46676 TATTAATCTTTTATTTAT
1 TATTAATCTTTTATTTAT
46694 T
1 T
46695 TATCTGTCGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.27, C:0.05, G:0.00, T:0.68
Consensus pattern (18 bp):
TATTAATCTTTTATTTAT
Found at i:49686 original size:36 final size:35
Alignment explanation
Indices: 49640--49750 Score: 143
Period size: 36 Copynumber: 3.1 Consensus size: 35
49630 TTAAAAAGAT
*
49640 AAAAAA-CTTAAAGTGCTTTAAATACATTATTTTAA
1 AAAAAATCTTAAAGTACTTTAAATACATTA-TTTAA
* *
49675 AAAAAATCTTAAAGCACTTTAAATATATTATTTAA
1 AAAAAATCTTAAAGTACTTTAAATACATTATTTAA
* *
49710 AGAAAAGATCCTAAAGTACTTTAAGTACATTATTTAA
1 A-AAAA-ATCTTAAAGTACTTTAAATACATTATTTAA
49747 AAAA
1 AAAA
49751 TAAAAGAAAT
Statistics
Matches: 66, Mismatches: 7, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
35 12 0.18
36 27 0.41
37 27 0.41
ACGTcount: A:0.50, C:0.09, G:0.06, T:0.34
Consensus pattern (35 bp):
AAAAAATCTTAAAGTACTTTAAATACATTATTTAA
Found at i:51891 original size:32 final size:31
Alignment explanation
Indices: 51817--51901 Score: 91
Period size: 31 Copynumber: 2.7 Consensus size: 31
51807 GTATGAATTA
* * *
51817 TTTTGAATTTAAATTATTTT-CGATTTAAATC
1 TTTTAAATTTAAATCATTTTAAG-TTTAAATC
* *
51848 TTTTAAGTTTAAGTCATTTTAAGTTTAAAGTC
1 TTTTAAATTTAAATCATTTTAAGTTTAAA-TC
*
51880 TTTTAAATTTAAATTATTTTAA
1 TTTTAAATTTAAATCATTTTAA
51902 ATTCGGGCTT
Statistics
Matches: 44, Mismatches: 8, Indels: 3
0.80 0.15 0.05
Matches are distributed among these distances:
31 22 0.50
32 22 0.50
ACGTcount: A:0.34, C:0.05, G:0.07, T:0.54
Consensus pattern (31 bp):
TTTTAAATTTAAATCATTTTAAGTTTAAATC
Found at i:51902 original size:16 final size:16
Alignment explanation
Indices: 51812--51904 Score: 89
Period size: 16 Copynumber: 5.9 Consensus size: 16
51802 ATTAAGTATG
*
51812 AATTATTTTGAATTTA
1 AATTATTTTAAATTTA
**
51828 AATTATTTTCGATTTA
1 AATTATTTTAAATTTA
* *
51844 AA-TCTTTTAAGTTTA
1 AATTATTTTAAATTTA
* * *
51859 AGTCATTTTAAGTTTA
1 AATTATTTTAAATTTA
* *
51875 AAGTCTTTTAAATTTA
1 AATTATTTTAAATTTA
51891 AATTATTTTAAATT
1 AATTATTTTAAATT
51905 CGGGCTTGTG
Statistics
Matches: 60, Mismatches: 16, Indels: 2
0.77 0.21 0.03
Matches are distributed among these distances:
15 10 0.17
16 50 0.83
ACGTcount: A:0.35, C:0.04, G:0.06, T:0.54
Consensus pattern (16 bp):
AATTATTTTAAATTTA
Found at i:52353 original size:7 final size:7
Alignment explanation
Indices: 52341--52390 Score: 55
Period size: 7 Copynumber: 6.9 Consensus size: 7
52331 GTAAAATTAT
52341 TATTTTA
1 TATTTTA
52348 TATTTTA
1 TATTTTA
**
52355 TAAAATTA
1 T-ATTTTA
52363 TTATTTTA
1 -TATTTTA
52371 TATTTTA
1 TATTTTA
*
52378 TATGTTA
1 TATTTTA
52385 TATTTT
1 TATTTT
52391 TAGTTAAAAA
Statistics
Matches: 35, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
7 26 0.74
8 8 0.23
9 1 0.03
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (7 bp):
TATTTTA
Found at i:52358 original size:23 final size:23
Alignment explanation
Indices: 52332--52379 Score: 96
Period size: 23 Copynumber: 2.1 Consensus size: 23
52322 TTACCGAAGG
52332 TAAAATTATTATTTTATATTTTA
1 TAAAATTATTATTTTATATTTTA
52355 TAAAATTATTATTTTATATTTTA
1 TAAAATTATTATTTTATATTTTA
52378 TA
1 TA
52380 TGTTATATTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (23 bp):
TAAAATTATTATTTTATATTTTA
Found at i:52947 original size:56 final size:56
Alignment explanation
Indices: 52885--52991 Score: 196
Period size: 56 Copynumber: 1.9 Consensus size: 56
52875 CTTTATTTCC
52885 AAATTTTATTTTTATTACAAAATGAGAATTTTAATCGAAAGAAAAAGTTATGAAAT
1 AAATTTTATTTTTATTACAAAATGAGAATTTTAATCGAAAGAAAAAGTTATGAAAT
* *
52941 AAATTTTATTTTTATTACAAAATGAGAATTTTAGTCGAAAGGAAAAGTTAT
1 AAATTTTATTTTTATTACAAAATGAGAATTTTAATCGAAAGAAAAAGTTAT
52992 TATTTTTATA
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
56 49 1.00
ACGTcount: A:0.46, C:0.04, G:0.12, T:0.38
Consensus pattern (56 bp):
AAATTTTATTTTTATTACAAAATGAGAATTTTAATCGAAAGAAAAAGTTATGAAAT
Found at i:56140 original size:16 final size:15
Alignment explanation
Indices: 56114--56144 Score: 53
Period size: 16 Copynumber: 2.0 Consensus size: 15
56104 ATAAAAAAGA
56114 ATTTTTTATTATTTT
1 ATTTTTTATTATTTT
56129 ATTTTGTTATTATTTT
1 ATTTT-TTATTATTTT
56145 TTATTTTTCA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 5 0.33
16 10 0.67
ACGTcount: A:0.19, C:0.00, G:0.03, T:0.77
Consensus pattern (15 bp):
ATTTTTTATTATTTT
Found at i:57513 original size:5 final size:5
Alignment explanation
Indices: 57505--57558 Score: 72
Period size: 5 Copynumber: 10.8 Consensus size: 5
57495 GCATGAAAGC
* * * *
57505 AATGC AATGA AATGC AATGA AATGA AATGA AATGA AATGC AATGC AATGA
1 AATGA AATGA AATGA AATGA AATGA AATGA AATGA AATGA AATGA AATGA
57555 AATG
1 AATG
57559 TTTTTGAAAT
Statistics
Matches: 44, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
5 44 1.00
ACGTcount: A:0.52, C:0.07, G:0.20, T:0.20
Consensus pattern (5 bp):
AATGA
Found at i:57520 original size:10 final size:10
Alignment explanation
Indices: 57505--57558 Score: 81
Period size: 10 Copynumber: 5.4 Consensus size: 10
57495 GCATGAAAGC
57505 AATGCAATGA
1 AATGCAATGA
57515 AATGCAATGA
1 AATGCAATGA
*
57525 AATGAAATGA
1 AATGCAATGA
* *
57535 AATGAAATGC
1 AATGCAATGA
57545 AATGCAATGA
1 AATGCAATGA
57555 AATG
1 AATG
57559 TTTTTGAAAT
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
10 40 1.00
ACGTcount: A:0.52, C:0.07, G:0.20, T:0.20
Consensus pattern (10 bp):
AATGCAATGA
Found at i:57523 original size:15 final size:15
Alignment explanation
Indices: 57497--57558 Score: 90
Period size: 15 Copynumber: 4.2 Consensus size: 15
57487 CATTTCATGC
*
57497 ATGAAA-GCAATGCA
1 ATGAAATGCAATGAA
57511 ATGAAATGCAATGAA
1 ATGAAATGCAATGAA
*
57526 ATGAAATGAAATGAA
1 ATGAAATGCAATGAA
*
57541 ATGCAATGCAATGAA
1 ATGAAATGCAATGAA
57556 ATG
1 ATG
57559 TTTTTGAAAT
Statistics
Matches: 43, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
14 6 0.14
15 37 0.86
ACGTcount: A:0.52, C:0.08, G:0.21, T:0.19
Consensus pattern (15 bp):
ATGAAATGCAATGAA
Found at i:57585 original size:14 final size:14
Alignment explanation
Indices: 57566--57592 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
57556 ATGTTTTTGA
57566 AATGCATGAAATGG
1 AATGCATGAAATGG
57580 AATGCATGAAATG
1 AATGCATGAAATG
57593 AAAATTATGC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.44, C:0.07, G:0.26, T:0.22
Consensus pattern (14 bp):
AATGCATGAAATGG
Found at i:57646 original size:15 final size:16
Alignment explanation
Indices: 57622--57656 Score: 56
Period size: 15 Copynumber: 2.3 Consensus size: 16
57612 ATGTTACGTG
57622 AAAA-GCATGAAAT-A
1 AAAATGCATGAAATGA
57636 AAAATGCATGAAATGA
1 AAAATGCATGAAATGA
57652 AAAAT
1 AAAAT
57657 ATGTGAAATG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 4 0.21
15 9 0.47
16 6 0.32
ACGTcount: A:0.63, C:0.06, G:0.14, T:0.17
Consensus pattern (16 bp):
AAAATGCATGAAATGA
Found at i:60404 original size:21 final size:21
Alignment explanation
Indices: 60380--60443 Score: 51
Period size: 21 Copynumber: 3.1 Consensus size: 21
60370 TATTTACATT
60380 TTGTTTTCTAAATAATGTACA
1 TTGTTTTCTAAATAATGTACA
* * * * **
60401 TTG-TATAT-ATTAATATATT
1 TTGTTTTCTAAATAATGTACA
*
60420 TTGTTTGCTAAATAATGTACA
1 TTGTTTTCTAAATAATGTACA
60441 TTG
1 TTG
60444 CATAGACTAT
Statistics
Matches: 28, Mismatches: 13, Indels: 4
0.62 0.29 0.09
Matches are distributed among these distances:
19 10 0.36
20 5 0.18
21 13 0.46
ACGTcount: A:0.33, C:0.06, G:0.11, T:0.50
Consensus pattern (21 bp):
TTGTTTTCTAAATAATGTACA
Found at i:65804 original size:16 final size:17
Alignment explanation
Indices: 65785--65816 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
65775 TTTCGAGTTT
65785 AAATTAT-TTTGATTCG
1 AAATTATGTTTGATTCG
65801 AAATTATGTTTGATTC
1 AAATTATGTTTGATTC
65817 AAGTTTAGTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.31, C:0.06, G:0.12, T:0.50
Consensus pattern (17 bp):
AAATTATGTTTGATTCG
Found at i:66008 original size:18 final size:18
Alignment explanation
Indices: 65985--66029 Score: 81
Period size: 18 Copynumber: 2.5 Consensus size: 18
65975 TAACACAATA
65985 ATTATATAAAATTAATTT
1 ATTATATAAAATTAATTT
66003 ATTATATAAAATTAATTT
1 ATTATATAAAATTAATTT
*
66021 ATTAAATAA
1 ATTATATAA
66030 TTAAATATTA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (18 bp):
ATTATATAAAATTAATTT
Found at i:66630 original size:20 final size:20
Alignment explanation
Indices: 66593--66629 Score: 67
Period size: 19 Copynumber: 1.9 Consensus size: 20
66583 ATTTAAAAAT
66593 TTTTAAATCACATTTTTTAC
1 TTTTAAATCACATTTTTTAC
66613 TTTTAAA-CACATTTTTT
1 TTTTAAATCACATTTTTT
66630 TCAATTCAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.30, C:0.14, G:0.00, T:0.57
Consensus pattern (20 bp):
TTTTAAATCACATTTTTTAC
Found at i:67519 original size:68 final size:68
Alignment explanation
Indices: 67410--67547 Score: 240
Period size: 68 Copynumber: 2.0 Consensus size: 68
67400 GGTAATCAGT
67410 GGCAGAACCGAAAAGGCACCAAATAATGAAATTGCTAAGGTCATTTTATGAAGCGCTAAAAAATC
1 GGCAGAACCGAAAAGGCACCAAATAATGAAATTGCTAAGGTCATTTTATGAAGCGCTAAAAAATC
67475 GGA
66 GGA
* * * *
67478 GGCAGAATCGGAAAGGCACCAAATGATGAAATTGCTAAGGTCATTTTATGAAGCGCTACAAAATC
1 GGCAGAACCGAAAAGGCACCAAATAATGAAATTGCTAAGGTCATTTTATGAAGCGCTAAAAAATC
67543 GGA
66 GGA
67546 GG
1 GG
67548 AATTGGCATT
Statistics
Matches: 66, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
68 66 1.00
ACGTcount: A:0.40, C:0.16, G:0.25, T:0.20
Consensus pattern (68 bp):
GGCAGAACCGAAAAGGCACCAAATAATGAAATTGCTAAGGTCATTTTATGAAGCGCTAAAAAATC
GGA
Found at i:67630 original size:18 final size:18
Alignment explanation
Indices: 67607--67642 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
67597 ATAGTCTTTG
67607 TTATTTT-ATTTCTCCATT
1 TTATTTTAATTT-TCCATT
67625 TTATTTTAATTTTCCATT
1 TTATTTTAATTTTCCATT
67643 AATTATTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 13 0.76
19 4 0.24
ACGTcount: A:0.19, C:0.14, G:0.00, T:0.67
Consensus pattern (18 bp):
TTATTTTAATTTTCCATT
Found at i:67929 original size:17 final size:18
Alignment explanation
Indices: 67896--67938 Score: 70
Period size: 17 Copynumber: 2.4 Consensus size: 18
67886 AACACAAACA
67896 TTATATAAAATTAATTTG
1 TTATATAAAATTAATTTG
67914 TTATATAAAA-TAATTTG
1 TTATATAAAATTAATTTG
*
67931 TTAAATAA
1 TTATATAA
67939 TTAAATATTT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 14 0.58
18 10 0.42
ACGTcount: A:0.49, C:0.00, G:0.05, T:0.47
Consensus pattern (18 bp):
TTATATAAAATTAATTTG
Found at i:68451 original size:16 final size:16
Alignment explanation
Indices: 68421--68465 Score: 56
Period size: 16 Copynumber: 2.8 Consensus size: 16
68411 ATTCTTTTGC
* *
68421 ATTTAAAATACTTTA-
1 ATTTAAATTATTTTAG
68436 ATCTTAAATTATTTTAG
1 AT-TTAAATTATTTTAG
68453 ATTTAAATTATTT
1 ATTTAAATTATTT
68466 CAAATTCAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
15 2 0.08
16 22 0.85
17 2 0.08
ACGTcount: A:0.40, C:0.04, G:0.02, T:0.53
Consensus pattern (16 bp):
ATTTAAATTATTTTAG
Found at i:72390 original size:28 final size:29
Alignment explanation
Indices: 72331--72390 Score: 72
Period size: 29 Copynumber: 2.1 Consensus size: 29
72321 TAACCAAAAA
*
72331 AAAAATTATTATTTTTATAATAAATTTTT
1 AAAAATTATTATTTTTATAATAAATTTAT
72360 AAAAATT-TTAATTTTTCA-AATAAA-TTAT
1 AAAAATTATT-ATTTTT-ATAATAAATTTAT
72388 AAA
1 AAA
72391 GTGACCCATT
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
28 8 0.29
29 19 0.68
30 1 0.04
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (29 bp):
AAAAATTATTATTTTTATAATAAATTTAT
Found at i:73094 original size:15 final size:15
Alignment explanation
Indices: 73063--73105 Score: 52
Period size: 15 Copynumber: 2.8 Consensus size: 15
73053 TTATGGGTCA
*
73063 ATAATATATAAATTTG
1 ATAATAT-TATATTTG
73079 ATAATATTATATTTG
1 ATAATATTATATTTG
73094 AT-ATAATTATAT
1 ATAAT-ATTATAT
73106 GATATATTTA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
14 2 0.08
15 16 0.64
16 7 0.28
ACGTcount: A:0.47, C:0.00, G:0.05, T:0.49
Consensus pattern (15 bp):
ATAATATTATATTTG
Found at i:73131 original size:21 final size:21
Alignment explanation
Indices: 73102--73150 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
73092 TGATATAATT
* * *
73102 ATATGATATATTTAATTAAAA
1 ATATAATATAATTAAATAAAA
*
73123 ATATAATATAATTAAATATAA
1 ATATAATATAATTAAATAAAA
73144 ATATAAT
1 ATATAAT
73151 TATGGTAATG
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (21 bp):
ATATAATATAATTAAATAAAA
Found at i:73343 original size:30 final size:31
Alignment explanation
Indices: 73308--73389 Score: 98
Period size: 31 Copynumber: 2.7 Consensus size: 31
73298 ATAAATAGAT
* *
73308 TTTTATTTATGTTTA-TTTATGTATTTT-AAA
1 TTTTATTTATATTTAGTTTATAT-TTTTAAAA
73338 TTTTATTTATATTTAGTTTATATTTTTAAAA
1 TTTTATTTATATTTAGTTTATATTTTTAAAA
*
73369 TTTTAATTTA-ATTTAATTTAT
1 TTTT-ATTTATATTTAGTTTAT
73390 TTAAAATTAA
Statistics
Matches: 46, Mismatches: 3, Indels: 5
0.85 0.06 0.09
Matches are distributed among these distances:
30 18 0.39
31 23 0.50
32 5 0.11
ACGTcount: A:0.30, C:0.00, G:0.04, T:0.66
Consensus pattern (31 bp):
TTTTATTTATATTTAGTTTATATTTTTAAAA
Found at i:73371 original size:26 final size:27
Alignment explanation
Indices: 73362--73424 Score: 83
Period size: 30 Copynumber: 2.2 Consensus size: 27
73352 AGTTTATATT
73362 TTTAAAATTTTAATTTAATTTAATTTA
1 TTTAAAATTTTAATTTAATTTAATTTA
73389 TTTAAAATTAATTATATTTACATTT-ATTTA
1 TTTAAAATT--TTA-ATTTA-ATTTAATTTA
73419 TTTAAA
1 TTTAAA
73425 TTAAGTAAAT
Statistics
Matches: 32, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
27 9 0.28
29 3 0.09
30 16 0.50
31 4 0.12
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (27 bp):
TTTAAAATTTTAATTTAATTTAATTTA
Found at i:73397 original size:16 final size:16
Alignment explanation
Indices: 73378--73424 Score: 55
Period size: 15 Copynumber: 3.1 Consensus size: 16
73368 ATTTTAATTT
73378 AATTTAATTTATTTAA
1 AATTTAATTTATTTAA
73394 AA-TTAATTATATTT-A
1 AATTTAATT-TATTTAA
*
73409 CATTT-ATTTATTTAA
1 AATTTAATTTATTTAA
73424 A
1 A
73425 TTAAGTAAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 7
0.74 0.06 0.20
Matches are distributed among these distances:
14 5 0.19
15 12 0.46
16 9 0.35
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (16 bp):
AATTTAATTTATTTAA
Found at i:73472 original size:32 final size:31
Alignment explanation
Indices: 73422--73489 Score: 91
Period size: 32 Copynumber: 2.2 Consensus size: 31
73412 TTATTTATTT
* *
73422 AAATTAAGTAAATTTATTTAAAAATATTAAA
1 AAATTAAGTAAATATATTTAAAAATAATAAA
* *
73453 AAATATAATTAAATATATTTATAAATAATAAA
1 AAAT-TAAGTAAATATATTTAAAAATAATAAA
73485 AAATT
1 AAATT
73490 TATTTATAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
31 5 0.16
32 27 0.84
ACGTcount: A:0.60, C:0.00, G:0.01, T:0.38
Consensus pattern (31 bp):
AAATTAAGTAAATATATTTAAAAATAATAAA
Found at i:73478 original size:22 final size:22
Alignment explanation
Indices: 73430--73536 Score: 65
Period size: 22 Copynumber: 4.8 Consensus size: 22
73420 TTAAATTAAG
* * * *
73430 TAAATTTATTTAAAAATATTAA
1 TAAATATAATTAAATATATTTA
*
73452 AAAATATAATTAAATATATTTA
1 TAAATATAATTAAATATATTTA
* *
73474 TAAATAATAA-AAAATTTATTTA
1 TAAAT-ATAATTAAATATATTTA
* * *
73496 TAAATTATTATTATATTAAATTTA
1 TAAA-TATAATTA-AATATATTTA
* *
73520 -AATTATTATTAAATATA
1 TAAATATAATTAAATATA
73537 AAATCATAAA
Statistics
Matches: 65, Mismatches: 16, Indels: 9
0.72 0.18 0.10
Matches are distributed among these distances:
21 4 0.06
22 46 0.71
23 8 0.12
24 7 0.11
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (22 bp):
TAAATATAATTAAATATATTTA
Found at i:73531 original size:17 final size:16
Alignment explanation
Indices: 73505--73538 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
73495 ATAAATTATT
*
73505 ATTATATTAAATTTAA
1 ATTATATTAAATATAA
73521 ATTATTATTAAATATAA
1 ATTA-TATTAAATATAA
73538 A
1 A
73539 ATCATAAAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 4 0.25
17 12 0.75
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (16 bp):
ATTATATTAAATATAA
Found at i:74383 original size:26 final size:25
Alignment explanation
Indices: 74294--74384 Score: 67
Period size: 26 Copynumber: 3.4 Consensus size: 25
74284 ATATTTGTAG
* *
74294 ATATAAAATATTTAATTTTTATTACT
1 ATATAAAATATTTAATATTT-TTATT
* * *
74320 ATATAAAACATGAATTTGATATCTTAATT
1 ATAT-AAA-AT--ATTTAATATTTTTATT
*
74349 ATAT-TAATATTTAATATATTTTATT
1 ATATAAAATATTTAATAT-TTTTATT
74374 ATATAAAATAT
1 ATATAAAATAT
74385 AAATTGAACA
Statistics
Matches: 49, Mismatches: 10, Indels: 12
0.69 0.14 0.17
Matches are distributed among these distances:
24 8 0.16
25 9 0.18
26 11 0.22
27 4 0.08
28 2 0.04
29 7 0.14
30 8 0.16
ACGTcount: A:0.45, C:0.03, G:0.02, T:0.49
Consensus pattern (25 bp):
ATATAAAATATTTAATATTTTTATT
Found at i:75376 original size:22 final size:22
Alignment explanation
Indices: 75333--75381 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 22
75323 CTCCATAAGG
*
75333 AAAAGTTGAAGAATTTTGAGAA
1 AAAAGTTGAAGAATTTGGAGAA
*
75355 GAAAGTTGAA-AATTTGGCAGAA
1 AAAAGTTGAAGAATTTGG-AGAA
75377 AAAAG
1 AAAAG
75382 AGACAGAGTG
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
21 6 0.26
22 17 0.74
ACGTcount: A:0.51, C:0.02, G:0.24, T:0.22
Consensus pattern (22 bp):
AAAAGTTGAAGAATTTGGAGAA
Done.