Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold278
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: 1156311
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 38162 characters in sequence are not A, C, G, or T
File 1 of 4
Found at i:11333 original size:11 final size:11
Alignment explanation
Indices: 11306--11337 Score: 50
Period size: 10 Copynumber: 3.1 Consensus size: 11
11296 CTTGTAGATT
11306 AAAGAA-GAAA
1 AAAGAATGAAA
11316 AAA-AATGAAA
1 AAAGAATGAAA
11326 AAAGAATGAAA
1 AAAGAATGAAA
11337 A
1 A
11338 GCAATAAGCA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
9 2 0.10
10 10 0.50
11 8 0.40
ACGTcount: A:0.78, C:0.00, G:0.16, T:0.06
Consensus pattern (11 bp):
AAAGAATGAAA
Found at i:32459 original size:17 final size:17
Alignment explanation
Indices: 32437--32472 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
32427 TGGGCTTTTG
32437 TGGTCTGGTATTAAGAT
1 TGGTCTGGTATTAAGAT
32454 TGGTCTGGTATTAAGAT
1 TGGTCTGGTATTAAGAT
32471 TG
1 TG
32473 TTTTTATCTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.22, C:0.06, G:0.31, T:0.42
Consensus pattern (17 bp):
TGGTCTGGTATTAAGAT
Found at i:34331 original size:29 final size:28
Alignment explanation
Indices: 34265--34322 Score: 91
Period size: 29 Copynumber: 2.1 Consensus size: 28
34255 TTCTTCTGTT
*
34265 AAATAAAAGTAGAGGGACTAAATTCCTGA
1 AAATAAAAGTAGAGGGACTAAATT-CTCA
34294 AAATAAAAGTAGAGGGACTAAATT-TCA
1 AAATAAAAGTAGAGGGACTAAATTCTCA
34321 AA
1 AA
34323 TGTACAAAGA
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
27 4 0.14
29 24 0.86
ACGTcount: A:0.52, C:0.09, G:0.19, T:0.21
Consensus pattern (28 bp):
AAATAAAAGTAGAGGGACTAAATTCTCA
Found at i:56875 original size:19 final size:18
Alignment explanation
Indices: 56851--56930 Score: 55
Period size: 16 Copynumber: 4.6 Consensus size: 18
56841 CATTTATTTG
56851 TTTATTTCATTCATAATTA
1 TTTATTT-ATTCATAATTA
56870 TTTATTT-TT-AT-ATT-
1 TTTATTTATTCATAATTA
*
56884 TTGATTTTATTCATAATTA
1 TTTA-TTTATTCATAATTA
* *
56903 TATCTTTTTATTC--AACTA
1 T-T-TATTTATTCATAATTA
56921 TTTATTTATT
1 TTTATTTATT
56931 TTTATTAAAG
Statistics
Matches: 49, Mismatches: 5, Indels: 17
0.69 0.07 0.24
Matches are distributed among these distances:
14 3 0.06
15 6 0.12
16 11 0.22
17 5 0.10
18 8 0.16
19 8 0.16
20 8 0.16
ACGTcount: A:0.28, C:0.07, G:0.01, T:0.64
Consensus pattern (18 bp):
TTTATTTATTCATAATTA
Found at i:56880 original size:33 final size:32
Alignment explanation
Indices: 56843--56914 Score: 90
Period size: 33 Copynumber: 2.2 Consensus size: 32
56833 CATTCATTCA
* *
56843 TTTATTTGTTTATTTCATTCATAATTATTTATT
1 TTTATTT-TTGATTTCATTCATAATTATATATT
* *
56876 TTTATATTTTGATTTTATTCATAATTATATCTT
1 TTTAT-TTTTGATTTCATTCATAATTATATATT
56909 TTTATT
1 TTTATT
56915 CAACTATTTA
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
32 1 0.03
33 31 0.91
34 2 0.06
ACGTcount: A:0.25, C:0.06, G:0.03, T:0.67
Consensus pattern (32 bp):
TTTATTTTTGATTTCATTCATAATTATATATT
Found at i:57995 original size:14 final size:15
Alignment explanation
Indices: 57978--58006 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
57968 TGTATTCTAA
57978 TATTT-ATATTTTTT
1 TATTTAATATTTTTT
57992 TATTTAATATTTTTT
1 TATTTAATATTTTTT
58007 ATTAAAATTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 5 0.36
15 9 0.64
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (15 bp):
TATTTAATATTTTTT
Found at i:63722 original size:50 final size:50
Alignment explanation
Indices: 63655--64059 Score: 431
Period size: 50 Copynumber: 8.1 Consensus size: 50
63645 TTTCTTGTAC
* * * * * * * *
63655 TGCCAAAGCCATATCCCAGATATGGTCTTACATGAGAGTTCTAATATAGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACTTCTCATCTCGG
* * **
63705 TGCCTATGCCATGTCCCAGACATGGTCTTACGGGGGACCTT-TCATCTCGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGA-CTTCTCATCTCGG
* *
63755 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTTATCTCGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACTTCTCATCTCGG
* * *
63805 TGCCAACGCCATGTCCCAGACATGGTCTTATATGAGACCTCTCATCTCGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACTTCTCATCTCGG
* * *
63855 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGATGTTTTC-TGTAC--
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGA-CTTCTCATCT-CGG
** * * * * * *
63904 TGCCAATTCCATATCCCAAATATAGTCTTACATGGGAGTTCTCATATCGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACTTCTCATCTCGG
* * * ** *
63954 TGCCCATGCCATGTCCCAAACATGGTCTTACGGGGGACCTCTCATCTCGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACTTCTCATCTCGG
* *
64004 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTTATCTCGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACTTCTCATCTCGG
64054 TGCCAA
1 TGCCAA
64060 NNNNNNNNNN
Statistics
Matches: 298, Mismatches: 50, Indels: 14
0.82 0.14 0.04
Matches are distributed among these distances:
48 6 0.02
49 35 0.12
50 251 0.84
51 6 0.02
ACGTcount: A:0.22, C:0.29, G:0.21, T:0.27
Consensus pattern (50 bp):
TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACTTCTCATCTCGG
Found at i:65390 original size:16 final size:17
Alignment explanation
Indices: 65364--65399 Score: 65
Period size: 16 Copynumber: 2.2 Consensus size: 17
65354 GTTTTTTATT
65364 TTTCGAATTTAGGGTTA
1 TTTCGAATTTAGGGTTA
65381 TTTC-AATTTAGGGTTA
1 TTTCGAATTTAGGGTTA
65397 TTT
1 TTT
65400 AGGGTTATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 15 0.79
17 4 0.21
ACGTcount: A:0.22, C:0.06, G:0.19, T:0.53
Consensus pattern (17 bp):
TTTCGAATTTAGGGTTA
Found at i:66373 original size:6 final size:6
Alignment explanation
Indices: 65406--66357 Score: 1635
Period size: 6 Copynumber: 158.7 Consensus size: 6
65396 ATTTAGGGTT
* * * *
65406 ATTTCG ATTTCG ATTTCA ATTTTG ATTTCG ATTAT-G A-TTCTA ATTTTG
1 ATTTCG ATTTCG ATTTCG ATTTCG ATTTCG ATT-TCG ATTTC-G ATTTCG
* * * * ** ** *
65454 ATTTCG ATTTTG ATTTTG ATTTCA ATTTTG A-AAC- ACTCACTG ATTTTG
1 ATTTCG ATTTCG ATTTCG ATTTCG ATTTCG ATTTCG A-TTTC-G ATTTCG
* * * * * * *
65502 ATTTTG ACTTT-G ATTTCA ATTTTG ATTTTG ATTTTG ATTTTG ATTTTG
1 ATTTCG A-TTTCG ATTTCG ATTTCG ATTTCG ATTTCG ATTTCG ATTTCG
*
65550 ATTTTG ATTTCG ATTTCG ATTTCG ATTTCG ATTTCG ATTTCG ATTTCG
1 ATTTCG ATTTCG ATTTCG ATTTCG ATTTCG ATTTCG ATTTCG ATTTCG
65598 ATTTCG ATTTCG ATTTCG ATTTCG ATTTCG ATTTCG ATTTCG ATTTCG
1 ATTTCG ATTTCG ATTTCG ATTTCG ATTTCG ATTTCG ATTTCG ATTTCG
65646 ATTTCG ATTTCG ATTTCG ATTTCG ATTTCG ATTTCG ATTTCG ATTTCG
1 ATTTCG ATTTCG ATTTCG ATTTCG ATTTCG ATTTCG ATTTCG ATTTCG
65694 ATTTCG ATTTCG ATTTCG ATTTCG ATTTCG ATTTCG ATTTCG ATTTCG
1 ATTTCG ATTTCG ATTTCG ATTTCG ATTTCG ATTTCG ATTTCG ATTTCG
65742 ATTTCG ATTTCG ATTTCG ATTTCG ATTTCG ATTTCG ATTTCG ATTTCG
1 ATTTCG ATTTCG ATTTCG ATTTCG ATTTCG ATTTCG ATTTCG ATTTCG
65790 ATTTCG ATTTCG ATTTCG ATTTCG ATTTCG ATTTCG ATTTCG ATTTCG
1 ATTTCG ATTTCG ATTTCG ATTTCG ATTTCG ATTTCG ATTTCG ATTTCG
65838 ATTTCG ATTTCG ATTTCG ATTTCG ATTTCG ATTTCG ATTTCG ATTTCG
1 ATTTCG ATTTCG ATTTCG ATTTCG ATTTCG ATTTCG ATTTCG ATTTCG
65886 ATTTCG ATTTCG ATTTCG ATTTCG ATTTCG ATTTCG ATTTCG ATTTCG
1 ATTTCG ATTTCG ATTTCG ATTTCG ATTTCG ATTTCG ATTTCG ATTTCG
65934 ATTTCG ATTTCG ATTTCG ATTTCG ATTTCG ATTTCG ATTTCG ATTTCG
1 ATTTCG ATTTCG ATTTCG ATTTCG ATTTCG ATTTCG ATTTCG ATTTCG
65982 ATTTCG ATTTCG ATTTCG ATTTCG ATTTCG ATTTCG ATTTCG ATTTCG
1 ATTTCG ATTTCG ATTTCG ATTTCG ATTTCG ATTTCG ATTTCG ATTTCG
66030 ATTTCG ATTTCG ATTTCG ATTTCG ATTTCG ATTTCG ATTTCG ATTTCG
1 ATTTCG ATTTCG ATTTCG ATTTCG ATTTCG ATTTCG ATTTCG ATTTCG
66078 ATTTCG ATTTCG ATTTCG ATTTCG ATTTCG ATTTCG ATTTCG ATTTCG
1 ATTTCG ATTTCG ATTTCG ATTTCG ATTTCG ATTTCG ATTTCG ATTTCG
66126 ATTTCG ATTTCG ATTTCG ATTTCG ATTTCG ATTTCG ATTTCG ATTTCG
1 ATTTCG ATTTCG ATTTCG ATTTCG ATTTCG ATTTCG ATTTCG ATTTCG
66174 ATTTCG ATTTCG ATTTCG ATTTCG ATTTCG ATTTCG ATTTCG ATTTCG
1 ATTTCG ATTTCG ATTTCG ATTTCG ATTTCG ATTTCG ATTTCG ATTTCG
66222 ATTTCG ATTTCG ATTTCG ATTTCG ATTTCG ATTTCG ATTTCG ATTTCG
1 ATTTCG ATTTCG ATTTCG ATTTCG ATTTCG ATTTCG ATTTCG ATTTCG
66270 ATTTCG ATTTCG ATTTCG ATTTCG ATTTCG ATTTCG ATTTCG ATTTCG
1 ATTTCG ATTTCG ATTTCG ATTTCG ATTTCG ATTTCG ATTTCG ATTTCG
66318 ATTTCG ATTTCG ATTTCG ATTTCG ATTTCG ATTTCG ATTT
1 ATTTCG ATTTCG ATTTCG ATTTCG ATTTCG ATTTCG ATTT
66358 AAGGTTATTT
Statistics
Matches: 912, Mismatches: 24, Indels: 20
0.95 0.03 0.02
Matches are distributed among these distances:
4 2 0.00
5 4 0.00
6 898 0.98
7 7 0.01
8 1 0.00
ACGTcount: A:0.18, C:0.15, G:0.16, T:0.51
Consensus pattern (6 bp):
ATTTCG
Found at i:66687 original size:62 final size:61
Alignment explanation
Indices: 66616--66736 Score: 215
Period size: 62 Copynumber: 2.0 Consensus size: 61
66606 TTGTATATTA
*
66616 TTGTCTGCCATGTGCATGACAAAAATGGTTGTGTTTGTATTAAATTATTTTTGTATTGGTTG
1 TTGTCTGCCATGTGCATGACAAAAATGGTTGAGTTTGTATTAAATTA-TTTTGTATTGGTTG
*
66678 TTGTCTGCCATGTGCATGACAGAAATGGTTGAGTTTGTATTAAATTATTTTGTATTGGT
1 TTGTCTGCCATGTGCATGACAAAAATGGTTGAGTTTGTATTAAATTATTTTGTATTGGT
66737 CATTTTCTGA
Statistics
Matches: 57, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
61 12 0.21
62 45 0.79
ACGTcount: A:0.23, C:0.08, G:0.23, T:0.45
Consensus pattern (61 bp):
TTGTCTGCCATGTGCATGACAAAAATGGTTGAGTTTGTATTAAATTATTTTGTATTGGTTG
Found at i:75126 original size:77 final size:78
Alignment explanation
Indices: 75044--75203 Score: 295
Period size: 77 Copynumber: 2.1 Consensus size: 78
75034 ATATATTTTA
*
75044 ATTAAGTATAATAATATTAATTTCATATTAATTACATGAAAAAAAAATTTTTTATTTGTTGAATA
1 ATTAAGTATAATAATATTAATTTCATATTAATTACATGAAAAAAAAATATTTTATTTGTTGAATA
75109 AAAAACA-TTAAC
66 AAAAACACTTAAC
*
75121 ATTAAGTATAATAATATTAATTTCATATTAATTACATGAAATAAAAATATTTTATTTGTTGAATA
1 ATTAAGTATAATAATATTAATTTCATATTAATTACATGAAAAAAAAATATTTTATTTGTTGAATA
75186 AAAAACACTTAAC
66 AAAAACACTTAAC
75199 ATTAA
1 ATTAA
75204 AATATATTAG
Statistics
Matches: 80, Mismatches: 2, Indels: 1
0.96 0.02 0.01
Matches are distributed among these distances:
77 70 0.88
78 10 0.12
ACGTcount: A:0.49, C:0.06, G:0.05, T:0.40
Consensus pattern (78 bp):
ATTAAGTATAATAATATTAATTTCATATTAATTACATGAAAAAAAAATATTTTATTTGTTGAATA
AAAAACACTTAAC
Found at i:89910 original size:6 final size:6
Alignment explanation
Indices: 89899--89943 Score: 54
Period size: 6 Copynumber: 7.5 Consensus size: 6
89889 AGTTTATTTG
* * * *
89899 TTTTAT TTTTAT TTTTAT TTTTCT TCTTAT GTTTAT TGTTAT TTT
1 TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTT
89944 CTTAGACTTA
Statistics
Matches: 31, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
6 31 1.00
ACGTcount: A:0.13, C:0.04, G:0.04, T:0.78
Consensus pattern (6 bp):
TTTTAT
Found at i:94222 original size:22 final size:21
Alignment explanation
Indices: 94182--94222 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
94172 TTAGGCTTGG
*
94182 TAGAGACTTTATTACACATGT
1 TAGAGACTTAATTACACATGT
*
94203 TAGAGACTGTAATTAGACAT
1 TAGAGACT-TAATTACACAT
94223 TGTGAAACTC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 8 0.47
22 9 0.53
ACGTcount: A:0.37, C:0.12, G:0.17, T:0.34
Consensus pattern (21 bp):
TAGAGACTTAATTACACATGT
Found at i:94708 original size:29 final size:29
Alignment explanation
Indices: 94651--94708 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 29
94641 ATTTTTTGAA
* * *
94651 AATATTTACAAAAAAGACATCTAATTTTT
1 AATATTTACAAAAAAGACAACCAAATTTT
94680 AATATTTAC-AAAAAGAGCAACCAAATTTT
1 AATATTTACAAAAAAGA-CAACCAAATTTT
94709 GAAAATAGTT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
28 7 0.28
29 18 0.72
ACGTcount: A:0.50, C:0.12, G:0.05, T:0.33
Consensus pattern (29 bp):
AATATTTACAAAAAAGACAACCAAATTTT
Found at i:104260 original size:70 final size:70
Alignment explanation
Indices: 104179--104313 Score: 270
Period size: 70 Copynumber: 1.9 Consensus size: 70
104169 CTAATATTTT
104179 TATTTAATTTTTTTACTAGTATTATGTTATGACAAAAAAATTATATAACAAATATATTATAAAAA
1 TATTTAATTTTTTTACTAGTATTATGTTATGACAAAAAAATTATATAACAAATATATTATAAAAA
104244 TTAAA
66 TTAAA
104249 TATTTAATTTTTTTACTAGTATTATGTTATGACAAAAAAATTATATAACAAATATATTATAAAAA
1 TATTTAATTTTTTTACTAGTATTATGTTATGACAAAAAAATTATATAACAAATATATTATAAAAA
104314 AATTAAAATA
Statistics
Matches: 65, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
70 65 1.00
ACGTcount: A:0.48, C:0.04, G:0.04, T:0.43
Consensus pattern (70 bp):
TATTTAATTTTTTTACTAGTATTATGTTATGACAAAAAAATTATATAACAAATATATTATAAAAA
TTAAA
Found at i:104753 original size:28 final size:28
Alignment explanation
Indices: 104717--104781 Score: 78
Period size: 28 Copynumber: 2.4 Consensus size: 28
104707 TTAAATAAAC
* * * *
104717 TCAAATACCAAATTGATTATTGAAATAT
1 TCAAGTACCAAATTAAATATTAAAATAT
104745 TCAAGTACCAAATTAAATATTAAAATAT
1 TCAAGTACCAAATTAAATATTAAAATAT
*
104773 T-AGGTACCA
1 TCAAGTACCA
104782 CATGGTATAT
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
27 7 0.22
28 25 0.78
ACGTcount: A:0.48, C:0.12, G:0.08, T:0.32
Consensus pattern (28 bp):
TCAAGTACCAAATTAAATATTAAAATAT
Found at i:120227 original size:27 final size:27
Alignment explanation
Indices: 120189--120290 Score: 100
Period size: 27 Copynumber: 3.8 Consensus size: 27
120179 CACGACAACT
* * *
120189 AAGAATAGCCTTTGTGGCAAACTCTAG
1 AAGAATAACCTTAGTGGCAAACTCTAA
* *
120216 AAGAATAACCTTAGTTG-AGAACCCTAA
1 AAGAATAACCTTAGTGGCA-AACTCTAA
*
120243 AAGAATAACATTAGTGGCAAACTCTAA
1 AAGAATAACCTTAGTGGCAAACTCTAA
* *
120270 AAGGAAT-GCCTTTGTGGCAAA
1 AA-GAATAACCTTAGTGGCAAA
120291 TTCTGAATAG
Statistics
Matches: 61, Mismatches: 11, Indels: 6
0.78 0.14 0.08
Matches are distributed among these distances:
26 1 0.02
27 55 0.90
28 5 0.08
ACGTcount: A:0.40, C:0.17, G:0.20, T:0.24
Consensus pattern (27 bp):
AAGAATAACCTTAGTGGCAAACTCTAA
Found at i:124626 original size:15 final size:15
Alignment explanation
Indices: 124606--124647 Score: 59
Period size: 14 Copynumber: 2.9 Consensus size: 15
124596 TTCTTTCACT
124606 AACCCTAAAACCCAA
1 AACCCTAAAACCCAA
**
124621 AACCCT-AAACCTTA
1 AACCCTAAAACCCAA
124635 AACCCTAAAACCC
1 AACCCTAAAACCC
124648 TAAGACCAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
14 12 0.52
15 11 0.48
ACGTcount: A:0.48, C:0.40, G:0.00, T:0.12
Consensus pattern (15 bp):
AACCCTAAAACCCAA
Found at i:124636 original size:22 final size:22
Alignment explanation
Indices: 124606--124650 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 22
124596 TTCTTTCACT
124606 AACCCTAAAACCC-AAAACCCTA
1 AACCCT-AAACCCTAAAACCCTA
*
124628 AACCTTAAACCCTAAAACCCTA
1 AACCCTAAACCCTAAAACCCTA
124650 A
1 A
124651 GACCAAAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 6 0.29
22 15 0.71
ACGTcount: A:0.49, C:0.38, G:0.00, T:0.13
Consensus pattern (22 bp):
AACCCTAAACCCTAAAACCCTA
Found at i:124647 original size:8 final size:8
Alignment explanation
Indices: 124606--124650 Score: 60
Period size: 8 Copynumber: 6.0 Consensus size: 8
124596 TTCTTTCACT
124606 AACCCTAA
1 AACCCTAA
124614 AACCC-AA
1 AACCCTAA
124621 AACCCT-A
1 AACCCTAA
*
124628 AA-CCTTA
1 AACCCTAA
124635 AACCCTAA
1 AACCCTAA
124643 AACCCTAA
1 AACCCTAA
124651 GACCAAAAAT
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
6 3 0.09
7 13 0.39
8 17 0.52
ACGTcount: A:0.49, C:0.38, G:0.00, T:0.13
Consensus pattern (8 bp):
AACCCTAA
Found at i:147825 original size:24 final size:24
Alignment explanation
Indices: 147781--147849 Score: 111
Period size: 24 Copynumber: 2.8 Consensus size: 24
147771 ACTCTTTCAT
*
147781 GAGCTTCCCAATTAATGGCTCTCTG
1 GAGCTTCCCGA-TAATGGCTCTCTG
147806 GAGCTTCCCGATAATGGCTCTCTG
1 GAGCTTCCCGATAATGGCTCTCTG
*
147830 CAGCTTCCCGATAATGGCTC
1 GAGCTTCCCGATAATGGCTC
147850 GCTTGAACTT
Statistics
Matches: 42, Mismatches: 2, Indels: 1
0.93 0.04 0.02
Matches are distributed among these distances:
24 32 0.76
25 10 0.24
ACGTcount: A:0.19, C:0.30, G:0.22, T:0.29
Consensus pattern (24 bp):
GAGCTTCCCGATAATGGCTCTCTG
Found at i:147903 original size:24 final size:24
Alignment explanation
Indices: 147777--147947 Score: 100
Period size: 24 Copynumber: 7.0 Consensus size: 24
147767 AAAGACTCTT
**
147777 TCATGAGCTTCCCAATTAATGGCTC
1 TCATGAGCTT-CCTGTTAATGGCTC
* *
147802 TC-TGGAGCTTCCCGATAATGGCTC
1 TCAT-GAGCTTCCTGTTAATGGCTC
* *
147826 TC-TGCAGCTTCCCGATAATGGCTC
1 TCATG-AGCTTCCTGTTAATGGCTC
* * * ** **
147850 GCTTGAACTTTTTGATT-ATACCTC
1 TCATGAGCTTCCTG-TTAATGGCTC
*
147874 TTATGAGCTTCCTGTTAATGGCTC
1 TCATGAGCTTCCTGTTAATGGCTC
147898 TCATGAGCTTTCC-GTTACATGGCTC
1 TCATGAGC-TTCCTGTTA-ATGGCTC
*
147923 ACATGAGCTT-CTCGTTATATGGCTC
1 TCATGAGCTTCCT-GTTA-ATGGCTC
147948 AAGAGAGAGA
Statistics
Matches: 115, Mismatches: 22, Indels: 18
0.74 0.14 0.12
Matches are distributed among these distances:
23 4 0.03
24 71 0.62
25 40 0.35
ACGTcount: A:0.19, C:0.26, G:0.19, T:0.36
Consensus pattern (24 bp):
TCATGAGCTTCCTGTTAATGGCTC
Found at i:147941 original size:72 final size:72
Alignment explanation
Indices: 147806--147941 Score: 159
Period size: 72 Copynumber: 1.9 Consensus size: 72
147796 TGGCTCTCTG
* * * *
147806 GAGCTTCCCGATAATGGCTCTCTGCAGCTTCCCGATAATGGCTCGCTTGAACTTTTTGATTATAC
1 GAGCTTCCCGATAATGGCTCTCTGCAGCTTCCCGATAATGGCTCACATGAACTTCTCGATTATAC
147871 CTCTTAT
66 CTCTTAT
* * * * *
147878 GAGCTTCCTGTTAATGGCTCTCATG-AGCTTTCCGTTACATGGCTCACATGAGCTTCTCG-TTAT
1 GAGCTTCCCGATAATGGCTCTC-TGCAGCTTCCCGATA-ATGGCTCACATGAACTTCTCGATTAT
147941 A
64 A
147942 TGGCTCAAGA
Statistics
Matches: 53, Mismatches: 9, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
72 35 0.66
73 18 0.34
ACGTcount: A:0.19, C:0.26, G:0.19, T:0.36
Consensus pattern (72 bp):
GAGCTTCCCGATAATGGCTCTCTGCAGCTTCCCGATAATGGCTCACATGAACTTCTCGATTATAC
CTCTTAT
Found at i:147948 original size:25 final size:24
Alignment explanation
Indices: 147876--147948 Score: 87
Period size: 25 Copynumber: 3.0 Consensus size: 24
147866 TATACCTCTT
*
147876 ATGAGCTTC-CTGTTAATGGCTCTC
1 ATGAGCTTCTC-GTTAATGGCTCAC
147900 ATGAGCTT-TCCGTTACATGGCTCAC
1 ATGAGCTTCT-CGTTA-ATGGCTCAC
147925 ATGAGCTTCTCGTTATATGGCTCA
1 ATGAGCTTCTCGTTA-ATGGCTCA
147949 AGAGAGAGAG
Statistics
Matches: 43, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
24 12 0.28
25 30 0.70
26 1 0.02
ACGTcount: A:0.19, C:0.25, G:0.21, T:0.36
Consensus pattern (24 bp):
ATGAGCTTCTCGTTAATGGCTCAC
Found at i:151440 original size:59 final size:57
Alignment explanation
Indices: 151368--151497 Score: 172
Period size: 59 Copynumber: 2.2 Consensus size: 57
151358 GATAAAATTG
* * * *
151368 AATAGTTGGGTGACAATTTTGTAAC-TTTCATAGTTGAGTGACCAAAAAATAAATTTACT
1 AATAGTTAGGTGACAATTTTGTAACTTTTCATAATTGAGTCA-CAAAAAA-AAA-ATACT
* *
151427 AATAGTTAAGTGACCATTTTGTAACTTTTCATAATTGAGTCACAAAAAAAAAATACT
1 AATAGTTAGGTGACAATTTTGTAACTTTTCATAATTGAGTCACAAAAAAAAAATACT
151484 AATAGTTAGGTGAC
1 AATAGTTAGGTGAC
151498 GATTAGTGTA
Statistics
Matches: 63, Mismatches: 7, Indels: 4
0.85 0.09 0.05
Matches are distributed among these distances:
57 17 0.27
58 3 0.05
59 29 0.46
60 14 0.22
ACGTcount: A:0.40, C:0.11, G:0.15, T:0.34
Consensus pattern (57 bp):
AATAGTTAGGTGACAATTTTGTAACTTTTCATAATTGAGTCACAAAAAAAAAATACT
Found at i:151925 original size:23 final size:23
Alignment explanation
Indices: 151895--151944 Score: 61
Period size: 23 Copynumber: 2.2 Consensus size: 23
151885 AGAAATATAT
151895 AAAT-TATA-AAACTTTAAAA-AA
1 AAATATATATAAA-TTTAAAATAA
151916 AGAATATATATAAATTTAAAATAA
1 A-AATATATATAAATTTAAAATAA
151940 AAATA
1 AAATA
151945 AAATGAATAT
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
21 1 0.04
22 3 0.12
23 15 0.60
24 6 0.24
ACGTcount: A:0.66, C:0.02, G:0.02, T:0.30
Consensus pattern (23 bp):
AAATATATATAAATTTAAAATAA
Found at i:151930 original size:32 final size:31
Alignment explanation
Indices: 151876--152007 Score: 112
Period size: 30 Copynumber: 4.3 Consensus size: 31
151866 AATTTTGTCA
*
151876 AAAAATATAAGAA-ATATATAAATTATAAAACT
1 AAAAATAAAAGAATATATATAAATT-TAAAA-T
**
151908 TTAAA-AAAAGAATATATATAAATTTAAAAT
1 AAAAATAAAAGAATATATATAAATTTAAAAT
*
151938 AAAAATAAAATGAATATATA-AAA-TGAAAAT
1 AAAAATAAAA-GAATATATATAAATTTAAAAT
* * * * * *
151968 AAAAAGAGAA-TATATATTTAAAATAAAAAT
1 AAAAATAAAAGAATATATATAAATTTAAAAT
151998 AAAAATAAAA
1 AAAAATAAAA
152008 AAATTANNNN
Statistics
Matches: 82, Mismatches: 13, Indels: 12
0.77 0.12 0.11
Matches are distributed among these distances:
28 6 0.07
29 3 0.04
30 32 0.39
31 18 0.22
32 23 0.28
ACGTcount: A:0.68, C:0.01, G:0.05, T:0.27
Consensus pattern (31 bp):
AAAAATAAAAGAATATATATAAATTTAAAAT
Found at i:151958 original size:13 final size:13
Alignment explanation
Indices: 151942--151983 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
151932 TAAAATAAAA
151942 ATAAAATGAATAT
1 ATAAAATGAATAT
*
151955 ATAAAATGAAAAT
1 ATAAAATGAATAT
*
151968 A-AAAAGAGAATAT
1 ATAAAA-TGAATAT
151981 ATA
1 ATA
151984 TTTAAAATAA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
12 4 0.17
13 19 0.79
14 1 0.04
ACGTcount: A:0.67, C:0.00, G:0.10, T:0.24
Consensus pattern (13 bp):
ATAAAATGAATAT
Found at i:151980 original size:24 final size:24
Alignment explanation
Indices: 151932--152002 Score: 70
Period size: 24 Copynumber: 2.7 Consensus size: 24
151922 TATATAAATT
*
151932 TAAAATAAAAATAAAATGAATATA
1 TAAAATAAAAATAAAAAGAATATA
*
151956 TAAAATGAAAATAAAAAGAGAATATATA
1 TAAAATAAAAAT-AAAA-AG-A-ATATA
151984 TTTAAAATAAAAATAAAAA
1 --TAAAATAAAAATAAAAA
152003 TAAAAAAATT
Statistics
Matches: 38, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
24 11 0.29
25 4 0.11
26 1 0.03
27 1 0.03
28 6 0.16
29 4 0.11
30 11 0.29
ACGTcount: A:0.70, C:0.00, G:0.06, T:0.24
Consensus pattern (24 bp):
TAAAATAAAAATAAAAAGAATATA
Found at i:152328 original size:23 final size:23
Alignment explanation
Indices: 152302--152347 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 23
152292 NNNNNCCTTT
*
152302 ATTT-TTTATTTTTTATAAATTTA
1 ATTTATTTAATTTTTAT-AATTTA
152325 ATTTATTTAATTTTTATAATTTA
1 ATTTATTTAATTTTTATAATTTA
152348 TAATATTCTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 10 0.48
24 11 0.52
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (23 bp):
ATTTATTTAATTTTTATAATTTA
Found at i:153082 original size:21 final size:21
Alignment explanation
Indices: 153058--153098 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
153048 TATTTAAATT
153058 TAATTAACAATCT-AGATTAAC
1 TAATTAACAAT-TAAGATTAAC
*
153079 TAATTAATAATTAAGATTAA
1 TAATTAACAATTAAGATTAA
153099 GTTAGAAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 17 0.94
ACGTcount: A:0.51, C:0.07, G:0.05, T:0.37
Consensus pattern (21 bp):
TAATTAACAATTAAGATTAAC
Found at i:168370 original size:56 final size:56
Alignment explanation
Indices: 168281--168386 Score: 140
Period size: 56 Copynumber: 1.9 Consensus size: 56
168271 GAAATTATTG
* * * *
168281 AGCTTTGTGCCTAGCAGGCTTCGTGCCAATGAATTTATCAACCTTAGTGCTTAGCA
1 AGCTTTATGCCTAGCAGGCTCCATGCCAATGAATTTATAAACCTTAGTGCTTAGCA
*** *
168337 AGCTTTATGCCTAGCAGGCTCCATGCTGGTGAATTTATAAAGCTTAGTGC
1 AGCTTTATGCCTAGCAGGCTCCATGCCAATGAATTTATAAACCTTAGTGC
168387 CTAGTAGGTT
Statistics
Matches: 42, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
56 42 1.00
ACGTcount: A:0.24, C:0.22, G:0.23, T:0.32
Consensus pattern (56 bp):
AGCTTTATGCCTAGCAGGCTCCATGCCAATGAATTTATAAACCTTAGTGCTTAGCA
Found at i:168460 original size:80 final size:80
Alignment explanation
Indices: 168360--168602 Score: 256
Period size: 80 Copynumber: 3.0 Consensus size: 80
168350 GCAGGCTCCA
* * * * *
168360 TGCTGGTGAATTTATAAAGCTTAGTGCCTAGTAGGTTTTGTGTCGGTGTAGTTATCGGGCTTTGT
1 TGCTAGTGAATTTATCAAGCTTAGTGCTTAGTAGGCTTTGTATCGGTGTAGTTATCGGGCTTTGT
168425 GCCTATCAGACTTTG
66 GCCTATCAGACTTTG
* * ** * * * * *
168440 TGCTAGTGAATTTATCAAGCTTAATGATTAACAGGCTTTGTACCGGTGAACTTATTGGGCTTTAT
1 TGCTAGTGAATTTATCAAGCTTAGTGCTTAGTAGGCTTTGTATCGGTGTAGTTATCGGGCTTTGT
*
168505 GCCTAGT-AGGCTTTG
66 GCCTA-TCAGACTTTG
* * *** *
168520 TGCCAGTGAATCTATCAAGCTTAGTGCTTAGTAGGCTAAATATCGATGT-GATTATCGGGCTTTG
1 TGCTAGTGAATTTATCAAGCTTAGTGCTTAGTAGGCTTTGTATCGGTGTAG-TTATCGGGCTTTG
*
168584 TGCCTAGCAGACTTTG
65 TGCCTATCAGACTTTG
168600 TGC
1 TGC
168603 CGATGAATCA
Statistics
Matches: 128, Mismatches: 32, Indels: 6
0.77 0.19 0.04
Matches are distributed among these distances:
80 127 0.99
81 1 0.01
ACGTcount: A:0.21, C:0.16, G:0.26, T:0.37
Consensus pattern (80 bp):
TGCTAGTGAATTTATCAAGCTTAGTGCTTAGTAGGCTTTGTATCGGTGTAGTTATCGGGCTTTGT
GCCTATCAGACTTTG
Found at i:168552 original size:40 final size:40
Alignment explanation
Indices: 168365--168556 Score: 113
Period size: 40 Copynumber: 4.8 Consensus size: 40
168355 CTCCATGCTG
* * * * *
168365 GTGAATTTATAAAGCTTAGTGCCTAGTAGGTTTTGTGTCG
1 GTGAATCTATCAAGCTTAGTGCCTAGTAGGCTTTGTGCCA
* ** * * *
168405 GTGTAGT-TATCGGGCTTTGTGCCTA-TCAGACTTTGTGCTA
1 GTG-AATCTATCAAGCTTAGTGCCTAGT-AGGCTTTGTGCCA
* * ** ** * *
168445 GTGAATTTATCAAGCTTAATGATTAACAGGCTTTGTACCG
1 GTGAATCTATCAAGCTTAGTGCCTAGTAGGCTTTGTGCCA
***
168485 GTGAA-CTTATTGGGCTTTA-TGCCTAGTAGGCTTTGTGCCA
1 GTGAATC-TATCAAGC-TTAGTGCCTAGTAGGCTTTGTGCCA
*
168525 GTGAATCTATCAAGCTTAGTGCTTAGTAGGCT
1 GTGAATCTATCAAGCTTAGTGCCTAGTAGGCT
168557 AAATATCGAT
Statistics
Matches: 108, Mismatches: 36, Indels: 16
0.68 0.22 0.10
Matches are distributed among these distances:
39 6 0.06
40 96 0.89
41 6 0.06
ACGTcount: A:0.22, C:0.15, G:0.26, T:0.38
Consensus pattern (40 bp):
GTGAATCTATCAAGCTTAGTGCCTAGTAGGCTTTGTGCCA
Found at i:171672 original size:3 final size:3
Alignment explanation
Indices: 171664--171751 Score: 149
Period size: 3 Copynumber: 29.3 Consensus size: 3
171654 GAAAAACAAG
171664 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
* * *
171712 TCT TCT TAT TCT TAT TCT TAT TCT TCT TCT TCT TCT TCT T
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT T
171752 ATTATTATTC
Statistics
Matches: 79, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 79 1.00
ACGTcount: A:0.03, C:0.30, G:0.00, T:0.67
Consensus pattern (3 bp):
TCT
Found at i:171762 original size:12 final size:12
Alignment explanation
Indices: 171664--171763 Score: 128
Period size: 12 Copynumber: 8.3 Consensus size: 12
171654 GAAAAACAAG
*
171664 TCTTCTTCTTCT
1 TCTTCTTATTCT
*
171676 TCTTCTTCTTCT
1 TCTTCTTATTCT
*
171688 TCTTCTTCTTCT
1 TCTTCTTATTCT
*
171700 TCTTCTTCTTCT
1 TCTTCTTATTCT
171712 TCTTCTTATTCT
1 TCTTCTTATTCT
*
171724 TATTCTTATTCT
1 TCTTCTTATTCT
*
171736 TCTTCTTCTTCT
1 TCTTCTTATTCT
* *
171748 TCTTATTATTAT
1 TCTTCTTATTCT
171760 TCTT
1 TCTT
171764 TGTTTGCTAT
Statistics
Matches: 81, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 81 1.00
ACGTcount: A:0.06, C:0.27, G:0.00, T:0.67
Consensus pattern (12 bp):
TCTTCTTATTCT
Found at i:175625 original size:29 final size:30
Alignment explanation
Indices: 175556--175627 Score: 92
Period size: 31 Copynumber: 2.4 Consensus size: 30
175546 AAATTTCAAA
* *
175556 TTTATACATGAACATTAGTTTAATGTATAAT
1 TTTATACATGAACATTAATTT-ATGTACAAT
* *
175587 TTTATACATGAACTTTAATTT-TGTGCAAT
1 TTTATACATGAACATTAATTTATGTACAAT
175616 TTTATACATGAA
1 TTTATACATGAA
175628 ATTTTGATTT
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
29 18 0.49
31 19 0.51
ACGTcount: A:0.36, C:0.08, G:0.10, T:0.46
Consensus pattern (30 bp):
TTTATACATGAACATTAATTTATGTACAAT
Found at i:175856 original size:29 final size:31
Alignment explanation
Indices: 175788--175857 Score: 81
Period size: 31 Copynumber: 2.3 Consensus size: 31
175778 GAAATTAAAG
* * *
175788 TTTCATGTATATATTTGAACCAGTATCAAAT
1 TTTCATGTATATAATTGAACCAGAATCAAAA
* *
175819 TTTCGTGTATATAATTGTACCA-AATCAAAA
1 TTTCATGTATATAATTGAACCAGAATCAAAA
175849 TTT-ATGTAT
1 TTTCATGTAT
175858 CAAATTACAC
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
29 5 0.15
30 9 0.27
31 19 0.58
ACGTcount: A:0.36, C:0.11, G:0.10, T:0.43
Consensus pattern (31 bp):
TTTCATGTATATAATTGAACCAGAATCAAAA
Found at i:178579 original size:15 final size:15
Alignment explanation
Indices: 178559--178593 Score: 70
Period size: 15 Copynumber: 2.3 Consensus size: 15
178549 CCCTTTAACA
178559 AGACAAGAACTAAAG
1 AGACAAGAACTAAAG
178574 AGACAAGAACTAAAG
1 AGACAAGAACTAAAG
178589 AGACA
1 AGACA
178594 CTCAGATTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.60, C:0.14, G:0.20, T:0.06
Consensus pattern (15 bp):
AGACAAGAACTAAAG
Found at i:182016 original size:25 final size:25
Alignment explanation
Indices: 181987--182034 Score: 96
Period size: 25 Copynumber: 1.9 Consensus size: 25
181977 TTAAGGTAAA
181987 CTTGCAAAAGCTAGGTACTATATAG
1 CTTGCAAAAGCTAGGTACTATATAG
182012 CTTGCAAAAGCTAGGTACTATAT
1 CTTGCAAAAGCTAGGTACTATAT
182035 GAGATACACG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.35, C:0.17, G:0.19, T:0.29
Consensus pattern (25 bp):
CTTGCAAAAGCTAGGTACTATATAG
Found at i:182659 original size:21 final size:20
Alignment explanation
Indices: 182633--182675 Score: 68
Period size: 21 Copynumber: 2.1 Consensus size: 20
182623 TTGAACCCTG
*
182633 AACCTCAAACCCTAAATCCCA
1 AACCTCAAACCATAAA-CCCA
182654 AACCTCAAACCATAAACCCA
1 AACCTCAAACCATAAACCCA
182674 AA
1 AA
182676 TCTCGAATCT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
20 6 0.29
21 15 0.71
ACGTcount: A:0.49, C:0.40, G:0.00, T:0.12
Consensus pattern (20 bp):
AACCTCAAACCATAAACCCA
Found at i:191996 original size:18 final size:17
Alignment explanation
Indices: 191971--192006 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 17
191961 TTTAAAATAT
191971 AAACATCATTCATATCA
1 AAACATCATTCATATCA
*
191988 AAACAATCATTCATTTCA
1 AAAC-ATCATTCATATCA
192006 A
1 A
192007 TCACAATCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 4 0.24
18 13 0.76
ACGTcount: A:0.47, C:0.22, G:0.00, T:0.31
Consensus pattern (17 bp):
AAACATCATTCATATCA
Found at i:196724 original size:45 final size:45
Alignment explanation
Indices: 196660--196820 Score: 259
Period size: 45 Copynumber: 3.6 Consensus size: 45
196650 CAAAAATGAT
* *
196660 TAAGACCATAGTTGAAAGACATTATGGCACTATACCGGAAATAAA
1 TAAGACCATAGTTGAAAGACACTATGGCACTATACCGAAAATAAA
* *
196705 TAAGACCATATTTGAAAGACACTATGGCACTATACCAAAAATAAA
1 TAAGACCATAGTTGAAAGACACTATGGCACTATACCGAAAATAAA
*
196750 TAAGACCATAGTTGAAAGACACTATGGCACTATACCGAAAATGAA
1 TAAGACCATAGTTGAAAGACACTATGGCACTATACCGAAAATAAA
* *
196795 TAAGACCATAGTTAAAAGATACTATG
1 TAAGACCATAGTTGAAAGACACTATG
196821 ACATCTTGTT
Statistics
Matches: 107, Mismatches: 9, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
45 107 1.00
ACGTcount: A:0.46, C:0.16, G:0.16, T:0.22
Consensus pattern (45 bp):
TAAGACCATAGTTGAAAGACACTATGGCACTATACCGAAAATAAA
Found at i:196843 original size:45 final size:45
Alignment explanation
Indices: 196650--196845 Score: 191
Period size: 45 Copynumber: 4.4 Consensus size: 45
196640 TAATTGGCTT
* * *
196650 CAAAAAT-GATTAAGACCATAGTTGAAAGACATTATGGCACTATAC
1 CAAAAATAGA-TAAGACCATAGTTAAAAGACACTATGACACTATAC
** * * * *
196695 CGGAAATAAATAAGACCATATTTGAAAGACACTATGGCACTATAC
1 CAAAAATAGATAAGACCATAGTTAAAAGACACTATGACACTATAC
* * *
196740 CAAAAATAAATAAGACCATAGTTGAAAGACACTATGGCACTATAC
1 CAAAAATAGATAAGACCATAGTTAAAAGACACTATGACACTATAC
* * **
196785 CGAAAAT-GAATAAGACCATAGTTAAAAGATACTATGACATCT-TGT
1 CAAAAATAG-ATAAGACCATAGTTAAAAGACACTATGACA-CTATAC
*
196830 TAAAAATAGATAAGAC
1 CAAAAATAGATAAGAC
196846 TATGGCTGAA
Statistics
Matches: 130, Mismatches: 17, Indels: 8
0.84 0.11 0.05
Matches are distributed among these distances:
45 126 0.97
46 4 0.03
ACGTcount: A:0.47, C:0.15, G:0.15, T:0.23
Consensus pattern (45 bp):
CAAAAATAGATAAGACCATAGTTAAAAGACACTATGACACTATAC
Found at i:196843 original size:90 final size:90
Alignment explanation
Indices: 196650--196868 Score: 264
Period size: 90 Copynumber: 2.4 Consensus size: 90
196640 TAATTGGCTT
* *
196650 CAAAAAT-GATTAAGACCATAGTTGAAAGACATTATGGCACTATACCGGAAATAAATAAGACCAT
1 CAAAAATAGA-TAAGACCATAGTTGAAAGACACTATGGCACTATACCGAAAATAAATAAGACCAT
* * *
196714 ATTTGAAAGACACTATGGCACTATAC
65 AGTTAAAAGACACTATGACACTATAC
* *
196740 CAAAAATAAATAAGACCATAGTTGAAAGACACTATGGCACTATACCGAAAATGAATAAGACCATA
1 CAAAAATAGATAAGACCATAGTTGAAAGACACTATGGCACTATACCGAAAATAAATAAGACCATA
* **
196805 GTTAAAAGATACTATGACATCT-TGT
66 GTTAAAAGACACTATGACA-CTATAC
* * * *
196830 TAAAAATAGATAAGACTATGGCTGAAAGA-ACCTATGGCA
1 CAAAAATAGATAAGACCATAGTTGAAAGACA-CTATGGCA
196869 TCATGAACAA
Statistics
Matches: 111, Mismatches: 15, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
89 1 0.01
90 107 0.96
91 3 0.03
ACGTcount: A:0.46, C:0.16, G:0.16, T:0.23
Consensus pattern (90 bp):
CAAAAATAGATAAGACCATAGTTGAAAGACACTATGGCACTATACCGAAAATAAATAAGACCATA
GTTAAAAGACACTATGACACTATAC
Found at i:206559 original size:27 final size:27
Alignment explanation
Indices: 206500--206558 Score: 86
Period size: 27 Copynumber: 2.2 Consensus size: 27
206490 TCAATACGCC
206500 AGAAAATGAAA-CCTTTATGACAATCT
1 AGAAAATGAAAGCCTTTATGACAATCT
206526 AGAAAATGAAAGCCTTTATAGA-AATCT
1 AGAAAATGAAAGCCTTTAT-GACAATCT
206553 ATGAAA
1 A-GAAA
206559 TAGAAGCCTT
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
26 11 0.37
27 13 0.43
28 6 0.20
ACGTcount: A:0.49, C:0.12, G:0.14, T:0.25
Consensus pattern (27 bp):
AGAAAATGAAAGCCTTTATGACAATCT
Found at i:206565 original size:27 final size:26
Alignment explanation
Indices: 206503--206569 Score: 68
Period size: 27 Copynumber: 2.5 Consensus size: 26
206493 ATACGCCAGA
*
206503 AAAT-GAAACCTTTATGACAATCTAG
1 AAATAGAAGCCTTTATGACAATCTAG
206528 AAA-ATGAAAGCCTTTATAGA-AATCTATG
1 AAATA-G-AAGCCTTTAT-GACAATCTA-G
206556 AAATAGAAGCCTTT
1 AAATAGAAGCCTTT
206570 GTGGTGATCT
Statistics
Matches: 35, Mismatches: 1, Indels: 10
0.76 0.02 0.22
Matches are distributed among these distances:
25 3 0.09
26 1 0.03
27 23 0.66
28 7 0.20
29 1 0.03
ACGTcount: A:0.45, C:0.13, G:0.13, T:0.28
Consensus pattern (26 bp):
AAATAGAAGCCTTTATGACAATCTAG
Found at i:213463 original size:6 final size:6
Alignment explanation
Indices: 213452--213482 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
213442 ATAAGTATAT
*
213452 TAATTA TGATTA TAATTA TAATTA TAATTA T
1 TAATTA TAATTA TAATTA TAATTA TAATTA T
213483 TGTTGGTAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (6 bp):
TAATTA
Found at i:214808 original size:12 final size:12
Alignment explanation
Indices: 214791--214816 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
214781 GTTTCATGTT
214791 TTTCAACAATTA
1 TTTCAACAATTA
214803 TTTCAACAATTA
1 TTTCAACAATTA
214815 TT
1 TT
214817 ATAAGTGGTG
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:0.38, C:0.15, G:0.00, T:0.46
Consensus pattern (12 bp):
TTTCAACAATTA
Found at i:221191 original size:48 final size:48
Alignment explanation
Indices: 221124--221221 Score: 169
Period size: 48 Copynumber: 2.0 Consensus size: 48
221114 GTCATGCATA
* * *
221124 CATAGCCTGTCATCTACTTAGGATTAAGGTATACCATAATTTGAACGT
1 CATAGCCTGCCATCCACTTAGGATTAAGGAATACCATAATTTGAACGT
221172 CATAGCCTGCCATCCACTTAGGATTAAGGAATACCATAATTTGAACGT
1 CATAGCCTGCCATCCACTTAGGATTAAGGAATACCATAATTTGAACGT
221220 CA
1 CA
221222 CAAGTGAATA
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
48 47 1.00
ACGTcount: A:0.33, C:0.21, G:0.16, T:0.30
Consensus pattern (48 bp):
CATAGCCTGCCATCCACTTAGGATTAAGGAATACCATAATTTGAACGT
Found at i:222114 original size:8 final size:8
Alignment explanation
Indices: 222097--222159 Score: 74
Period size: 8 Copynumber: 7.8 Consensus size: 8
222087 TTTTTTGAAG
222097 TATATTAT
1 TATATTAT
*
222105 TATTTTAT
1 TATATTAT
*
222113 TATATT-G
1 TATATTAT
*
222120 TAAATTATAT
1 TATA-T-TAT
222130 TATATTAT
1 TATATTAT
222138 TATATTAT
1 TATATTAT
222146 TATATTAT
1 TATATTAT
222154 TATATT
1 TATATT
222160 TTAAATAAAC
Statistics
Matches: 46, Mismatches: 6, Indels: 6
0.79 0.10 0.10
Matches are distributed among these distances:
7 3 0.07
8 38 0.83
9 2 0.04
10 3 0.07
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.62
Consensus pattern (8 bp):
TATATTAT
Found at i:224944 original size:119 final size:120
Alignment explanation
Indices: 224733--224971 Score: 462
Period size: 119 Copynumber: 2.0 Consensus size: 120
224723 GTGAATGATA
*
224733 TATGGAATTAAAGCTTGTTGAGTCTTTTTTCATGAAAAAATATCGGTTTAACAAAAAGAGTTTTA
1 TATGGAATTAAAGCTTGTTGAGTCTATTTTCATGAAAAAATATCGGTTTAACAAAAAGAGTTTTA
224798 TATTTTAAGATATTTGAATTTTCGTGACACAGGGTCAGAACAG-TTTTGGTGTCC
66 TATTTTAAGATATTTGAATTTTCGTGACACAGGGTCAGAACAGTTTTTGGTGTCC
224852 TATGGAATTAAAGCTTGTTGAGTCTATTTTCATGAAAAAATATCGGTTTAACAAAAAGAGTTTTA
1 TATGGAATTAAAGCTTGTTGAGTCTATTTTCATGAAAAAATATCGGTTTAACAAAAAGAGTTTTA
224917 TATTTTAAGATATTTGAATTTTCGTGACACAGGGTCAGAACAGTTTTTGGTGTCC
66 TATTTTAAGATATTTGAATTTTCGTGACACAGGGTCAGAACAGTTTTTGGTGTCC
224972 CCTGTTTTGA
Statistics
Matches: 118, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
119 107 0.91
120 11 0.09
ACGTcount: A:0.32, C:0.10, G:0.19, T:0.38
Consensus pattern (120 bp):
TATGGAATTAAAGCTTGTTGAGTCTATTTTCATGAAAAAATATCGGTTTAACAAAAAGAGTTTTA
TATTTTAAGATATTTGAATTTTCGTGACACAGGGTCAGAACAGTTTTTGGTGTCC
Found at i:228544 original size:39 final size:39
Alignment explanation
Indices: 228490--228627 Score: 213
Period size: 39 Copynumber: 3.5 Consensus size: 39
228480 AACATGTTTT
*
228490 TGAGTATTGTGATATATGCTTGAATGTTATGTGATTAGA
1 TGAGTATTGTGATATATGCTTGAATGTTATGTGATTATA
* *
228529 TGAGTGTTGTGATATATGCTTGAATGTTATGTGGTTATA
1 TGAGTATTGTGATATATGCTTGAATGTTATGTGATTATA
* *
228568 TGTGTATTGTGATATATGCTTGAATGTTATGCGATTATA
1 TGAGTATTGTGATATATGCTTGAATGTTATGTGATTATA
* *
228607 TGTGTAATGTGATATATGCTT
1 TGAGTATTGTGATATATGCTT
228628 AAAAGAGAAT
Statistics
Matches: 91, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
39 91 1.00
ACGTcount: A:0.25, C:0.04, G:0.25, T:0.46
Consensus pattern (39 bp):
TGAGTATTGTGATATATGCTTGAATGTTATGTGATTATA
Found at i:233521 original size:51 final size:51
Alignment explanation
Indices: 233441--233729 Score: 300
Period size: 51 Copynumber: 5.7 Consensus size: 51
233431 NNNNNNGGTA
* *
233441 CACATAGTAGCCTTCACTTAGTACTACACATGTGACCATCATTTATCGATT
1 CACATAGTAGCCTTCACCTAGTACTACACATGTGACCATAATTTATCGATT
* * * * * *
233492 CACGTAGTAGCCTTCACACT-GTACTACACACGTGACCA-AAGCTTCTCGGTA
1 CACATAGTAGCCTTCAC-CTAGTACTACACATGTGACCATAA-TTTATCGATT
* * *
233543 CACATTGTAGCCTTCACTTAGTACTACACATGTGACCATCATTTATCGATT
1 CACATAGTAGCCTTCACCTAGTACTACACATGTGACCATAATTTATCGATT
* * * * * *
233594 CACTTAGTAGCCTTCACGC-AGTACTACACACGTGACCA-AAGCTTCTCGGTA
1 CACATAGTAGCCTTCAC-CTAGTACTACACATGTGACCATAA-TTTATCGATT
* * * *
233645 CACATTGTAGCCTTTACTTAGTACTACACATGTGACCATAATATATCGATT
1 CACATAGTAGCCTTCACCTAGTACTACACATGTGACCATAATTTATCGATT
*
233696 CACGTAGTAGCCTTCACGC-AGTACTACACATGTG
1 CACATAGTAGCCTTCAC-CTAGTACTACACATGTG
233730 TTCTTCGATA
Statistics
Matches: 189, Mismatches: 40, Indels: 18
0.77 0.16 0.07
Matches are distributed among these distances:
50 3 0.02
51 182 0.96
52 4 0.02
ACGTcount: A:0.28, C:0.27, G:0.15, T:0.29
Consensus pattern (51 bp):
CACATAGTAGCCTTCACCTAGTACTACACATGTGACCATAATTTATCGATT
Found at i:233618 original size:102 final size:102
Alignment explanation
Indices: 233437--233725 Score: 515
Period size: 102 Copynumber: 2.8 Consensus size: 102
233427 NNNNNNNNNN
*
233437 GGTACACATAGTAGCCTTCACTTAGTACTACACATGTGACCATCATTTATCGATTCACGTAGTAG
1 GGTACACATTGTAGCCTTCACTTAGTACTACACATGTGACCATCATTTATCGATTCACGTAGTAG
* *
233502 CCTTCACACTGTACTACACACGTGACCAAAGCTTCTC
66 CCTTCACGCAGTACTACACACGTGACCAAAGCTTCTC
*
233539 GGTACACATTGTAGCCTTCACTTAGTACTACACATGTGACCATCATTTATCGATTCACTTAGTAG
1 GGTACACATTGTAGCCTTCACTTAGTACTACACATGTGACCATCATTTATCGATTCACGTAGTAG
233604 CCTTCACGCAGTACTACACACGTGACCAAAGCTTCTC
66 CCTTCACGCAGTACTACACACGTGACCAAAGCTTCTC
* * *
233641 GGTACACATTGTAGCCTTTACTTAGTACTACACATGTGACCATAATATATCGATTCACGTAGTAG
1 GGTACACATTGTAGCCTTCACTTAGTACTACACATGTGACCATCATTTATCGATTCACGTAGTAG
233706 CCTTCACGCAGTACTACACA
66 CCTTCACGCAGTACTACACA
233726 TGTGTTCTTC
Statistics
Matches: 179, Mismatches: 8, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
102 179 1.00
ACGTcount: A:0.29, C:0.27, G:0.15, T:0.29
Consensus pattern (102 bp):
GGTACACATTGTAGCCTTCACTTAGTACTACACATGTGACCATCATTTATCGATTCACGTAGTAG
CCTTCACGCAGTACTACACACGTGACCAAAGCTTCTC
Found at i:241629 original size:19 final size:20
Alignment explanation
Indices: 241587--241639 Score: 90
Period size: 20 Copynumber: 2.7 Consensus size: 20
241577 AATTATAAAA
241587 AAAAATTCAAAATAATTTTC
1 AAAAATTCAAAATAATTTTC
241607 AAAAATTCAAAATAATTTT-
1 AAAAATTCAAAATAATTTTC
*
241626 AAAAATTTAAAATA
1 AAAAATTCAAAATA
241640 TTTATAACAA
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
19 13 0.41
20 19 0.59
ACGTcount: A:0.60, C:0.06, G:0.00, T:0.34
Consensus pattern (20 bp):
AAAAATTCAAAATAATTTTC
Found at i:241642 original size:9 final size:8
Alignment explanation
Indices: 241623--241715 Score: 51
Period size: 8 Copynumber: 10.4 Consensus size: 8
241613 TCAAAATAAT
241623 TTTAAAAA
1 TTTAAAAA
241631 TTTAAAATA
1 TTTAAAA-A
241640 TTTATAACAA
1 TTTA-AA-AA
*
241650 TTTTAAAA
1 TTTAAAAA
***
241658 TTTATATTT
1 TTTA-AAAA
241667 TTTAAAAA
1 TTTAAAAA
241675 TTCTAAAAAA
1 TT-T-AAAAA
241685 TATATAAAGAAA
1 T-T-T-AA-AAA
*
241697 TTTAAAAT
1 TTTAAAAA
241705 TTTAAAAA
1 TTTAAAAA
241713 TTT
1 TTT
241716 TCTAAAACAA
Statistics
Matches: 66, Mismatches: 11, Indels: 16
0.71 0.12 0.17
Matches are distributed among these distances:
8 27 0.41
9 15 0.23
10 13 0.20
11 7 0.11
12 4 0.06
ACGTcount: A:0.53, C:0.02, G:0.01, T:0.44
Consensus pattern (8 bp):
TTTAAAAA
Found at i:241651 original size:19 final size:19
Alignment explanation
Indices: 241587--241663 Score: 70
Period size: 19 Copynumber: 4.1 Consensus size: 19
241577 AATTATAAAA
*
241587 AAAAATTCAAAATAATTT-T
1 AAAAATTTAAAAT-ATTTAT
*
241606 CAAAAATTCAAAATAATTT-T
1 -AAAAATTTAAAAT-ATTTAT
241626 AAAAATTTAAAATATTTAT
1 AAAAATTTAAAATATTTAT
* *
241645 AACAATTTTAAA-ATTTAT
1 AAAAATTTAAAATATTTAT
241663 A
1 A
241664 TTTTTTAAAA
Statistics
Matches: 53, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
18 11 0.21
19 23 0.43
20 19 0.36
ACGTcount: A:0.56, C:0.05, G:0.00, T:0.39
Consensus pattern (19 bp):
AAAAATTTAAAATATTTAT
Found at i:241660 original size:18 final size:18
Alignment explanation
Indices: 241620--241715 Score: 56
Period size: 18 Copynumber: 5.3 Consensus size: 18
241610 AATTCAAAAT
241620 AATTT-TAAAAATTTAAA
1 AATTTATAAAAATTTAAA
* *
241637 ATATTTATAACAATTTTAA
1 A-ATTTATAAAAATTTAAA
***
241656 AATTTAT-ATTTTTTAAA
1 AATTTATAAAAATTTAAA
241673 AATTCTA-AAAAATATATAAA
1 AATT-TATAAAAAT-T-TAAA
* *
241693 GAAATT-TAAAATTTTAAA
1 -AATTTATAAAAATTTAAA
241711 AATTT
1 AATTT
241716 TCTAAAACAA
Statistics
Matches: 59, Mismatches: 12, Indels: 16
0.68 0.14 0.18
Matches are distributed among these distances:
17 15 0.25
18 18 0.31
19 13 0.22
20 10 0.17
21 3 0.05
ACGTcount: A:0.53, C:0.02, G:0.01, T:0.44
Consensus pattern (18 bp):
AATTTATAAAAATTTAAA
Found at i:241716 original size:9 final size:9
Alignment explanation
Indices: 241600--241716 Score: 62
Period size: 10 Copynumber: 12.7 Consensus size: 9
241590 AATTCAAAAT
241600 AATTTTCAAA
1 AATTTT-AAA
**
241610 AATTCAAAA
1 AATTTTAAA
241619 TAATTTTAAA
1 -AATTTTAAA
241629 AA-TTTAAA
1 AATTTTAAA
*
241637 ATATTTATAAC
1 A-ATTT-TAAA
241648 AATTTT-AA
1 AATTTTAAA
*
241656 AA-TTTATA
1 AATTTTAAA
**
241664 TTTTTTAAA
1 AATTTTAAA
*
241673 AATTCTAAAA
1 AATT-TTAAA
*
241683 AATATATAAA
1 AAT-TTTAAA
*
241693 GAAATTT-AA
1 -AATTTTAAA
241702 AATTTTAAA
1 AATTTTAAA
241711 AATTTT
1 AATTTT
241717 CTAAAACAAT
Statistics
Matches: 79, Mismatches: 18, Indels: 21
0.67 0.15 0.18
Matches are distributed among these distances:
7 3 0.04
8 16 0.20
9 24 0.30
10 29 0.37
11 7 0.09
ACGTcount: A:0.53, C:0.03, G:0.01, T:0.43
Consensus pattern (9 bp):
AATTTTAAA
Found at i:248063 original size:52 final size:52
Alignment explanation
Indices: 247979--248147 Score: 160
Period size: 52 Copynumber: 3.2 Consensus size: 52
247969 GTACATAGTA
** ** *
247979 CCTGCTAAATAATTACTGGCTCAAAGCTTGCTAAATAATCATCGACTCAAAG
1 CCTGCTAAATAAACACCAGCTCAAAGCCTGCTAAATAATCATCGACTCAAAG
* * * * *
248031 CCTGCTAGATAAGCGCCAGCTCAAGGCCTGCTAAATAATCACTTG-CTCAAAG
1 CCTGCTAAATAAACACCAGCTCAAAGCCTGCTAAATAATCA-TCGACTCAAAG
* * * * * * * *
248083 GCTGTTAAATAAACATCGGCTCAAAGCCTGCTAAACAAACATCGACTTAAGG
1 CCTGCTAAATAAACACCAGCTCAAAGCCTGCTAAATAATCATCGACTCAAAG
248135 CCTGCTAAATAAA
1 CCTGCTAAATAAA
248148 GTACATCCCG
Statistics
Matches: 91, Mismatches: 24, Indels: 4
0.76 0.20 0.03
Matches are distributed among these distances:
51 2 0.02
52 87 0.96
53 2 0.02
ACGTcount: A:0.36, C:0.25, G:0.16, T:0.23
Consensus pattern (52 bp):
CCTGCTAAATAAACACCAGCTCAAAGCCTGCTAAATAATCATCGACTCAAAG
Found at i:248122 original size:26 final size:26
Alignment explanation
Indices: 247979--248147 Score: 137
Period size: 26 Copynumber: 6.5 Consensus size: 26
247969 GTACATAGTA
247979 CCTGCTAAATAATTAC-T-GGCTCAAAG
1 CCTGCTAAATAA--ACATCGGCTCAAAG
* * *
248005 CTTGCTAAATAATCATCGACTCAAAG
1 CCTGCTAAATAAACATCGGCTCAAAG
* * ** * *
248031 CCTGCTAGATAAGCGCCAGCTCAAGG
1 CCTGCTAAATAAACATCGGCTCAAAG
* *
248057 CCTGCTAAATAATCA-CTTGCTCAAAG
1 CCTGCTAAATAAACATC-GGCTCAAAG
* *
248083 GCTGTTAAATAAACATCGGCTCAAAG
1 CCTGCTAAATAAACATCGGCTCAAAG
* * * *
248109 CCTGCTAAACAAACATCGACTTAAGG
1 CCTGCTAAATAAACATCGGCTCAAAG
248135 CCTGCTAAATAAA
1 CCTGCTAAATAAA
248148 GTACATCCCG
Statistics
Matches: 112, Mismatches: 27, Indels: 8
0.76 0.18 0.05
Matches are distributed among these distances:
24 1 0.01
25 2 0.02
26 108 0.96
27 1 0.01
ACGTcount: A:0.36, C:0.25, G:0.16, T:0.23
Consensus pattern (26 bp):
CCTGCTAAATAAACATCGGCTCAAAG
Found at i:248135 original size:78 final size:78
Alignment explanation
Indices: 247979--248146 Score: 205
Period size: 78 Copynumber: 2.2 Consensus size: 78
247969 GTACATAGTA
* * * * *
247979 CCTGCTAAATAATTACTGGCTCAAAGCTTGCTAAATAATCATCGACTCAAAGCCTGCTAGATAAG
1 CCTGCTAAATAATCACTGGCTCAAAGCTTGCTAAATAAACATCGACTCAAAGCCTGCTAAACAAA
248044 CGCCAGCTCAAGG
66 CGCCAGCTCAAGG
* * *
248057 CCTGCTAAATAATCACTTGCTCAAAGGC-TGTTAAATAAACATCGGCTCAAAGCCTGCTAAACAA
1 CCTGCTAAATAATCACTGGCTCAAA-GCTTGCTAAATAAACATCGACTCAAAGCCTGCTAAACAA
** *
248121 ACATC-GACTTAAGG
65 ACGCCAG-CTCAAGG
248135 CCTGCTAAATAA
1 CCTGCTAAATAA
248147 AGTACATCCC
Statistics
Matches: 77, Mismatches: 11, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
77 1 0.01
78 74 0.96
79 2 0.03
ACGTcount: A:0.36, C:0.25, G:0.16, T:0.23
Consensus pattern (78 bp):
CCTGCTAAATAATCACTGGCTCAAAGCTTGCTAAATAAACATCGACTCAAAGCCTGCTAAACAAA
CGCCAGCTCAAGG
Found at i:252595 original size:68 final size:68
Alignment explanation
Indices: 252515--252810 Score: 313
Period size: 68 Copynumber: 4.5 Consensus size: 68
252505 TGCTATGATA
* * * *
252515 TTACACAATATGATCCCATATTTAATGTCCTGGCAGACTCTATATGTTGCCATAGCTGAGCTACA
1 TTACACATTATGAACCCATGTTTAATGTCCTGGCAGACTCCATATGTTGCCATAGCTGAGCTACA
252580 GTC
66 GTC
* * ** * * *
252583 TTACACATTATGAACTCATGCTTAATAACTTGGCAGATTCCATATGTTGCCATAGCTAAGCTAC-
1 TTACACATTATGAACCCATGTTTAATGTCCTGGCAGACTCCATATGTTGCCATAGCTGAGCTACA
*
252647 GACC
66 G-TC
* * * *
252651 TTACACATTATGAAGCCATGTTTAA--T-C--G--GATTCCATATGTTGTCATCGCTGAGCTACA
1 TTACACATTATGAACCCATGTTTAATGTCCTGGCAGACTCCATATGTTGCCATAGCTGAGCTACA
*
252709 ATC
66 GTC
* * * *
252712 TTACATATTATGAACCTATGTTTAATGTCCTAGTAGACTCCATATGTTGCCATAG-TCGAGCTAC
1 TTACACATTATGAACCCATGTTTAATGTCCTGGCAGACTCCATATGTTGCCATAGCT-GAGCTAC
*
252776 GGTC
65 AGTC
252780 TTACACATTATGAACCCATGTTTAATGTCCT
1 TTACACATTATGAACCCATGTTTAATGTCCT
252811 AACAAACTCC
Statistics
Matches: 186, Mismatches: 32, Indels: 20
0.78 0.13 0.08
Matches are distributed among these distances:
61 49 0.26
63 2 0.01
64 1 0.01
66 1 0.01
67 2 0.01
68 131 0.70
ACGTcount: A:0.28, C:0.22, G:0.16, T:0.34
Consensus pattern (68 bp):
TTACACATTATGAACCCATGTTTAATGTCCTGGCAGACTCCATATGTTGCCATAGCTGAGCTACA
GTC
Found at i:252737 original size:129 final size:129
Alignment explanation
Indices: 252556--252805 Score: 333
Period size: 129 Copynumber: 1.9 Consensus size: 129
252546 GGCAGACTCT
* * * *
252556 ATATGTTGCCATAGCTGAGCTACAGTCTTACACATTATGAACTCATGCTTAATAACTTGGCAGAT
1 ATATGTTGCCATAGCTGAGCTACAATCTTACACATTATGAACTCATGCTTAATAACCTAGCAGAC
*
252621 TCCATATGTTGCCATAG-CTAAGCTACGACCTTACACATTATGAAGCCATGTTTAATCGGATTCC
66 TCCATATGTTGCCATAGTC-AAGCTACGACCTTACACATTATGAACCCATGTTTAATCGGATTCC
* * * * ** *
252685 ATATGTTGTCATCGCTGAGCTACAATCTTACATATTATGAAC-CTATGTTTAATGTCCTAGTAGA
1 ATATGTTGCCATAGCTGAGCTACAATCTTACACATTATGAACTC-ATGCTTAATAACCTAGCAGA
* **
252749 CTCCATATGTTGCCATAGTCGAGCTACGGTCTTACACATTATGAACCCATGTTTAAT
65 CTCCATATGTTGCCATAGTCAAGCTACGACCTTACACATTATGAACCCATGTTTAAT
252806 GTCCTAACAA
Statistics
Matches: 104, Mismatches: 15, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
128 1 0.01
129 102 0.98
130 1 0.01
ACGTcount: A:0.29, C:0.22, G:0.16, T:0.34
Consensus pattern (129 bp):
ATATGTTGCCATAGCTGAGCTACAATCTTACACATTATGAACTCATGCTTAATAACCTAGCAGAC
TCCATATGTTGCCATAGTCAAGCTACGACCTTACACATTATGAACCCATGTTTAATCGGATTCC
Found at i:256006 original size:3 final size:3
Alignment explanation
Indices: 255986--256037 Score: 52
Period size: 3 Copynumber: 17.3 Consensus size: 3
255976 TAATAGCAAC
* * *
255986 AAT AGT AAT AAT ATT AAT AAT AAT AA- AAGT AGT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA-T AAT AAT AAT AAT AAT
*
256031 GAT AAT A
1 AAT AAT A
256038 CCAACACAAT
Statistics
Matches: 39, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
2 2 0.05
3 36 0.92
4 1 0.03
ACGTcount: A:0.60, C:0.00, G:0.08, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:257845 original size:50 final size:49
Alignment explanation
Indices: 257791--257933 Score: 153
Period size: 50 Copynumber: 2.9 Consensus size: 49
257781 TCTACTCCGT
* *
257791 TGCAATGCCAGGGAAACAAGATTCACCTTTGTAGCTTAAAT-TTATTTAAC
1 TGCAATGTCGGGGAAACAAGATTCA-CTTTGTAGCTTAAATCTTA-TTAAC
* * * * *
257841 TGCAATGTTGGGGAAACAAGATTCGTCGTTGTAGCTTCAATCTTATTAAT
1 TGCAATGTCGGGGAAACAAGATTC-ACTTTGTAGCTTAAATCTTATTAAC
* * *
257891 TGCAATGTCGGGGAAGCAAAATTCACTGTTGTAGCTTCAATCT
1 TGCAATGTCGGGGAAACAAGATTCACT-TTGTAGCTTAAATCT
257934 GTTCCTCTAC
Statistics
Matches: 78, Mismatches: 12, Indels: 6
0.81 0.12 0.06
Matches are distributed among these distances:
49 1 0.01
50 74 0.95
51 3 0.04
ACGTcount: A:0.30, C:0.17, G:0.20, T:0.33
Consensus pattern (49 bp):
TGCAATGTCGGGGAAACAAGATTCACTTTGTAGCTTAAATCTTATTAAC
Found at i:258177 original size:43 final size:43
Alignment explanation
Indices: 258130--258351 Score: 160
Period size: 43 Copynumber: 5.1 Consensus size: 43
258120 TGCTACTCAT
258130 GGAGACAAGGCTGTGGTCTTCGATCTACTCCACTACTGCTTAG
1 GGAGACAAGGCTGTGGTCTTCGATCTACTCCACTACTGCTTAG
* ** * * * * *
258173 GGAGATC-AGATCTGTAATTTTCAACCTACTCCACTGCTGCTCAG
1 GGAGA-CAAG-GCTGTGGTCTTCGATCTACTCCACTACTGCTTAG
* **
258217 GGAGACAAGGCTG-GAGACTTCGATCTGGTCCACTACTGCTTAG
1 GGAGACAAGGCTGTG-GTCTTCGATCTACTCCACTACTGCTTAG
* ** ** * * * * *
258260 GGAGATAAAATCTGTAATTTTCAACCTACTCCACTGCTGCTCAG
1 GGAGA-CAAGGCTGTGGTCTTCGATCTACTCCACTACTGCTTAG
* * * * *
258304 GGAGACAAGGCTGGGGACTTCGATCTGCTTCACTACTACTTAG
1 GGAGACAAGGCTGTGGTCTTCGATCTACTCCACTACTGCTTAG
258347 GGAGA
1 GGAGA
258352 TAAGATCTGT
Statistics
Matches: 126, Mismatches: 47, Indels: 12
0.68 0.25 0.06
Matches are distributed among these distances:
43 63 0.50
44 63 0.50
ACGTcount: A:0.25, C:0.24, G:0.24, T:0.27
Consensus pattern (43 bp):
GGAGACAAGGCTGTGGTCTTCGATCTACTCCACTACTGCTTAG
Found at i:258205 original size:44 final size:44
Alignment explanation
Indices: 258090--258545 Score: 289
Period size: 44 Copynumber: 10.4 Consensus size: 44
258080 ATACAGGAAT
* * * * * * *
258090 ATAAGATTTGTTATTTTCAACCTACTCTACTGCTACTCATGGAG
1 ATAAGATCTGTAATCTTCAACCTACTCCACTACTGCTCAGGGAG
* * ** * * *
258134 ACAAG-GCTGTGGTCTTCGATCTACTCCACTACTGCTTAGGGAG
1 ATAAGATCTGTAATCTTCAACCTACTCCACTACTGCTCAGGGAG
* * *
258177 ATCAGATCTGTAATTTTCAACCTACTCCACTGCTGCTCAGGGAG
1 ATAAGATCTGTAATCTTCAACCTACTCCACTACTGCTCAGGGAG
* * * * * ** *
258221 ACAAG-GCTGGAGA-CTTCGATCTGGTCCACTACTGCTTAGGGAG
1 ATAAGATCTGTA-ATCTTCAACCTACTCCACTACTGCTCAGGGAG
* * *
258264 ATAAAATCTGTAATTTTCAACCTACTCCACTGCTGCTCAGGGAG
1 ATAAGATCTGTAATCTTCAACCTACTCCACTACTGCTCAGGGAG
* * ** * * * * * *
258308 ACAAG-GCTGGGGA-CTTCGATCTGCTTCACTACTACTTAGGGAG
1 ATAAGATCT-GTAATCTTCAACCTACTCCACTACTGCTCAGGGAG
* * *
258351 ATAAGATCTGTAATTTTCAACCTACTCCAC-AGCTACTAAGGGAG
1 ATAAGATCTGTAATCTTCAACCTACTCCACTA-CTGCTCAGGGAG
* ** * * *
258395 ATAAGGTCTACAATCTCCAACCTACTCCACTGCTGCTCAAGGAG
1 ATAAGATCTGTAATCTTCAACCTACTCCACTACTGCTCAGGGAG
* ** *
258439 ATAAGGTCTACAATCTTCAACCTACTCCACTGCTGCTCAGGGAG
1 ATAAGATCTGTAATCTTCAACCTACTCCACTACTGCTCAGGGAG
* * * * *
258483 ATAAG-GCTTGTCATCTTCGATC-AGCTCCACTACTGCTTAGGGAG
1 ATAAGATC-TGTAATCTTCAACCTA-CTCCACTACTGCTCAGGGAG
*
258527 ATAATATCTGTAATTCTTC
1 ATAAGATCTGTAA-TCTTC
258546 GGTCTGCTCC
Statistics
Matches: 309, Mismatches: 90, Indels: 25
0.73 0.21 0.06
Matches are distributed among these distances:
43 93 0.30
44 210 0.68
45 6 0.02
ACGTcount: A:0.27, C:0.25, G:0.20, T:0.29
Consensus pattern (44 bp):
ATAAGATCTGTAATCTTCAACCTACTCCACTACTGCTCAGGGAG
Found at i:258209 original size:87 final size:87
Alignment explanation
Indices: 258090--258541 Score: 521
Period size: 87 Copynumber: 5.2 Consensus size: 87
258080 ATACAGGAAT
* * * * *
258090 ATAAGATTTGTTATTTTCAACCTACTCTACTGCTACTCATGGAGACAAGGCTGTGGTCTTCGATC
1 ATAAGATCTGTAATTTTCAACCTACTCCACTGCTGCTCAGGGAGACAAGGCTGTGGTCTTCGATC
258155 TACTCCACTACTGCTTAGGGAG
66 TACTCCACTACTGCTTAGGGAG
* *
258177 ATCAGATCTGTAATTTTCAACCTACTCCACTGCTGCTCAGGGAGACAAGGCTG-GAGACTTCGAT
1 ATAAGATCTGTAATTTTCAACCTACTCCACTGCTGCTCAGGGAGACAAGGCTGTG-GTCTTCGAT
**
258241 CTGGTCCACTACTGCTTAGGGAG
65 CTACTCCACTACTGCTTAGGGAG
* * *
258264 ATAAAATCTGTAATTTTCAACCTACTCCACTGCTGCTCAGGGAGACAAGGCTGGGGACTTCGATC
1 ATAAGATCTGTAATTTTCAACCTACTCCACTGCTGCTCAGGGAGACAAGGCTGTGGTCTTCGATC
* * *
258329 TGCTTCACTACTACTTAGGGAG
66 TACTCCACTACTGCTTAGGGAG
* * * * **** * * *
258351 ATAAGATCTGTAATTTTCAACCTACTCCACAGCTACTAAGGGAGATAAGGTCTACAATCTCCAAC
1 ATAAGATCTGTAATTTTCAACCTACTCCACTGCTGCTCAGGGAGACAAGG-CTGTGGTCTTCGAT
* * *
258416 CTACTCCACTGCTGCTCAAGGAG
65 CTACTCCACTACTGCTTAGGGAG
* ** * * **
258439 ATAAGGTCTACAATCTTCAACCTACTCCACTGCTGCTCAGGGAGATAAGGCTTGTCATCTTCGAT
1 ATAAGATCTGTAATTTTCAACCTACTCCACTGCTGCTCAGGGAGACAAGGC-TGTGGTCTTCGAT
258504 C-AGCTCCACTACTGCTTAGGGAG
65 CTA-CTCCACTACTGCTTAGGGAG
*
258527 ATAATATCTGTAATT
1 ATAAGATCTGTAATT
258542 CTTCGGTCTG
Statistics
Matches: 306, Mismatches: 54, Indels: 9
0.83 0.15 0.02
Matches are distributed among these distances:
86 1 0.00
87 203 0.66
88 102 0.33
ACGTcount: A:0.27, C:0.25, G:0.20, T:0.29
Consensus pattern (87 bp):
ATAAGATCTGTAATTTTCAACCTACTCCACTGCTGCTCAGGGAGACAAGGCTGTGGTCTTCGATC
TACTCCACTACTGCTTAGGGAG
Found at i:258805 original size:216 final size:217
Alignment explanation
Indices: 258463--258967 Score: 764
Period size: 216 Copynumber: 2.3 Consensus size: 217
258453 CTTCAACCTA
* * ** *
258463 CTCCACTGCTGCTCAGGGAGATAAGGCTTGTCATCTTCGATCAGCTCCACTACTGCTTAGGGAGA
1 CTCCACTACTGCTTAGGGAGATAAGATTTGTCATCTTCGATCTGCTCCACTACTGCTTAGGGAGA
* * *
258528 TAATATCTGTAATTCTTCGGTCTGCTCCGCTACAACCTCAGAGTGATAAGACCTTATGCGATCTA
66 TAAGATCTG-AATTCTTCGGTCTGCTCCGCTACAACCTCAGAGAGATAAGACCTGATGCGATCTA
*
258593 CTCTACTACAACTTCAGAGAGATAAGATCTTTTATTTTAATCCACTCCACTACAACTTCAGGGAG
130 CTCTACTACAACTTCAGAGAGATAAGATCTTTTATTTTAATCCACTCCACTACAACTTCAGAGAG
258658 ATAGGATTACTGG-TTTCAATCTG
195 ATAGGATTACTGGCTTT-AATCTG
* * *
258681 TTCCACTACTGCTTAGGGAGATAAGATTTGTGATCTTTGATCTGCTCCACTACTGCTTAGGGAGA
1 CTCCACTACTGCTTAGGGAGATAAGATTTGTCATCTTCGATCTGCTCCACTACTGCTTAGGGAGA
* ** *
258746 TAAGATCTG-CTTCTTCGGTCTGCTCCGCTGTAACCTCAGGGAGATAAGACCTGATGCGATCTAC
66 TAAGATCTGAATTCTTCGGTCTGCTCCGCTACAACCTCAGAGAGATAAGACCTGATGCGATCTAC
** *
258810 TCTACTGTAACTTCAGAGAGATAAGATCTTTTATTTTAATCCACTCCACTGCAACTTCAGAGAGA
131 TCTACTACAACTTCAGAGAGATAAGATCTTTTATTTTAATCCACTCCACTACAACTTCAGAGAGA
*
258875 TATGATTACTGGCTTTAATCTG
196 TAGGATTACTGGCTTTAATCTG
* *
258897 CTCCACTACTGCTTAGGGAGATAAGATCTGCCATCTTCGATCTGCTCCACTAC-GACTTAGGGAG
1 CTCCACTACTGCTTAGGGAGATAAGATTTGTCATCTTCGATCTGCTCCACTACTG-CTTAGGGAG
258961 ATAAGAT
65 ATAAGAT
258968 TTGTAATTTC
Statistics
Matches: 260, Mismatches: 25, Indels: 6
0.89 0.09 0.02
Matches are distributed among these distances:
215 1 0.00
216 191 0.73
217 3 0.01
218 65 0.25
ACGTcount: A:0.26, C:0.23, G:0.19, T:0.31
Consensus pattern (217 bp):
CTCCACTACTGCTTAGGGAGATAAGATTTGTCATCTTCGATCTGCTCCACTACTGCTTAGGGAGA
TAAGATCTGAATTCTTCGGTCTGCTCCGCTACAACCTCAGAGAGATAAGACCTGATGCGATCTAC
TCTACTACAACTTCAGAGAGATAAGATCTTTTATTTTAATCCACTCCACTACAACTTCAGAGAGA
TAGGATTACTGGCTTTAATCTG
Found at i:261216 original size:12 final size:11
Alignment explanation
Indices: 261175--261274 Score: 58
Period size: 12 Copynumber: 8.4 Consensus size: 11
261165 TGATTTTGAC
*
261175 TTTTTCTTCTT
1 TTTTTTTTCTT
261186 CTTTTTCTTTCTT
1 -TTTTT-TTTCTT
261199 TTTTTTGTTCTT
1 TTTTTT-TTCTT
261211 TTTTTTATT-TT
1 TTTTTT-TTCTT
** *
261222 TTGATTTTATT
1 TTTTTTTTCTT
*
261233 TTTTTATTACTT
1 TTTTT-TTTCTT
261245 TTTTTAATTTCAATT
1 TTTTT--TTTC--TT
*
261260 TTTCTTTTCTT
1 TTTTTTTTCTT
261271 TTTT
1 TTTT
261275 GATTTTGATT
Statistics
Matches: 70, Mismatches: 11, Indels: 15
0.73 0.11 0.16
Matches are distributed among these distances:
10 2 0.03
11 17 0.24
12 32 0.46
13 13 0.19
15 6 0.09
ACGTcount: A:0.09, C:0.10, G:0.02, T:0.79
Consensus pattern (11 bp):
TTTTTTTTCTT
Found at i:261223 original size:22 final size:22
Alignment explanation
Indices: 261174--261222 Score: 64
Period size: 22 Copynumber: 2.3 Consensus size: 22
261164 TTGATTTTGA
261174 CTTTTTCTTCTTCTTTTTCTTT
1 CTTTTTCTTCTTCTTTTTCTTT
* *
261196 CTTTTTTTTGTTCTTTTT-TTT
1 CTTTTTCTTCTTCTTTTTCTTT
*
261217 ATTTTT
1 CTTTTT
261223 TGATTTTATT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
21 8 0.33
22 16 0.67
ACGTcount: A:0.02, C:0.14, G:0.02, T:0.82
Consensus pattern (22 bp):
CTTTTTCTTCTTCTTTTTCTTT
Found at i:261229 original size:13 final size:13
Alignment explanation
Indices: 261213--261280 Score: 50
Period size: 13 Copynumber: 5.3 Consensus size: 13
261203 TTGTTCTTTT
261213 TTTTATTTTTTGA
1 TTTTATTTTTTGA
*
261226 TTTTATTTTTTTA
1 TTTTATTTTTTGA
* *
261239 TTACT-TTTTTTAA
1 TT-TTATTTTTTGA
* * *
261252 TTTCAATTTTT-C
1 TTTTATTTTTTGA
*
261264 TTTTCTTTTTTGA
1 TTTTATTTTTTGA
261277 TTTT
1 TTTT
261281 GATTGTGATT
Statistics
Matches: 41, Mismatches: 11, Indels: 6
0.71 0.19 0.10
Matches are distributed among these distances:
12 8 0.20
13 32 0.78
14 1 0.02
ACGTcount: A:0.15, C:0.06, G:0.03, T:0.76
Consensus pattern (13 bp):
TTTTATTTTTTGA
Found at i:261229 original size:25 final size:25
Alignment explanation
Indices: 261209--261280 Score: 71
Period size: 26 Copynumber: 2.9 Consensus size: 25
261199 TTTTTTGTTC
261209 TTTTTT-TTA-TTTTTTGATTTTAT
1 TTTTTTATTACTTTTTTGATTTTAT
* *
261232 TTTTTTATTACTTTTTTTAATTTCAAT
1 TTTTTTATTAC-TTTTTTGATTT-TAT
261259 TTTTCTT-TT-CTTTTTTGATTTT
1 TTTT-TTATTACTTTTTTGATTTT
261281 GATTGTGATT
Statistics
Matches: 40, Mismatches: 4, Indels: 9
0.75 0.08 0.17
Matches are distributed among these distances:
23 6 0.15
24 3 0.08
25 10 0.25
26 11 0.28
27 8 0.20
28 2 0.05
ACGTcount: A:0.14, C:0.06, G:0.03, T:0.78
Consensus pattern (25 bp):
TTTTTTATTACTTTTTTGATTTTAT
Found at i:268678 original size:71 final size:71
Alignment explanation
Indices: 268588--268730 Score: 166
Period size: 71 Copynumber: 2.0 Consensus size: 71
268578 AATCTACCAT
* **
268588 ATTTGGACAGCTTTTATACATAAATTTGAACAGCATTTATATACCAA-A-TTAGA-CAACATTTT
1 ATTTGGACAGCATAAATACATAAATTTGAACAGCA--TATATA-CAACAGTTAGAGCAACATTTT
268650 CACACCAAA
63 CACACCAAA
* ** * *
268659 ATTTGGACAGCATAAATACATCAATTTGGGCAGCATATATACAACAGTTTGAGCAACATTTTTAC
1 ATTTGGACAGCATAAATACATAAATTTGAACAGCATATATACAACAGTTAGAGCAACATTTTCAC
268724 ACCAAA
66 ACCAAA
268730 A
1 A
268731 CTGGATAGCA
Statistics
Matches: 61, Mismatches: 8, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
68 3 0.05
69 7 0.11
70 4 0.07
71 47 0.77
ACGTcount: A:0.41, C:0.18, G:0.11, T:0.30
Consensus pattern (71 bp):
ATTTGGACAGCATAAATACATAAATTTGAACAGCATATATACAACAGTTAGAGCAACATTTTCAC
ACCAAA
Found at i:268685 original size:23 final size:23
Alignment explanation
Indices: 268658--268701 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
268648 TTCACACCAA
268658 AATTTGGACAGCATAAATACATC
1 AATTTGGACAGCATAAATACATC
* *
268681 AATTTGGGCAGCATATATACA
1 AATTTGGACAGCATAAATACA
268702 ACAGTTTGAG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.41, C:0.16, G:0.16, T:0.27
Consensus pattern (23 bp):
AATTTGGACAGCATAAATACATC
Found at i:268709 original size:23 final size:23
Alignment explanation
Indices: 268658--268709 Score: 68
Period size: 23 Copynumber: 2.3 Consensus size: 23
268648 TTCACACCAA
*
268658 AATTTGGACAGCATAAATACATC
1 AATTTGGACAGCATAAATACAAC
* *
268681 AATTTGGGCAGCATATATACAAC
1 AATTTGGACAGCATAAATACAAC
*
268704 AGTTTG
1 AATTTG
268710 AGCAACATTT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.38, C:0.15, G:0.17, T:0.29
Consensus pattern (23 bp):
AATTTGGACAGCATAAATACAAC
Found at i:268766 original size:47 final size:47
Alignment explanation
Indices: 268726--268992 Score: 453
Period size: 47 Copynumber: 5.7 Consensus size: 47
268716 ATTTTTACAC
* * *
268726 CAAAACTGGATAGCATATATGCAACAAATTGGGCAGCATTTAAGCAT
1 CAAAATTGGACAGCATATATGTAACAAATTGGGCAGCATTTAAGCAT
* * *
268773 CAAAATTAGACATCATATATGTAACAAATTGGGCAGCATTTAATCAT
1 CAAAATTGGACAGCATATATGTAACAAATTGGGCAGCATTTAAGCAT
268820 CAAAATTGGACAGCATATATGTAACAAATTGGGCAGCATTTAAGCAT
1 CAAAATTGGACAGCATATATGTAACAAATTGGGCAGCATTTAAGCAT
268867 CAAAATTGGACAGCATATATGTAACAAATTGGGCAGCATTTAAGCAT
1 CAAAATTGGACAGCATATATGTAACAAATTGGGCAGCATTTAAGCAT
*
268914 CAAAATTGGACAGCATATATGTAACAAATTGGGTAGCATTTAAGCAT
1 CAAAATTGGACAGCATATATGTAACAAATTGGGCAGCATTTAAGCAT
* *
268961 CAAAATTGGACAACATATTTGTAACAAATTGG
1 CAAAATTGGACAGCATATATGTAACAAATTGG
268993 TTCAACTCAT
Statistics
Matches: 208, Mismatches: 12, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
47 208 1.00
ACGTcount: A:0.41, C:0.15, G:0.18, T:0.27
Consensus pattern (47 bp):
CAAAATTGGACAGCATATATGTAACAAATTGGGCAGCATTTAAGCAT
Found at i:268800 original size:24 final size:24
Alignment explanation
Indices: 268726--268992 Score: 188
Period size: 23 Copynumber: 11.4 Consensus size: 24
268716 ATTTTTACAC
* * *
268726 CAAAACTGGATAGCATATATGCAA
1 CAAAATTGGACAGCATATATGTAA
* * * * *
268750 C-AAATTGGGCAGCATTTAAGCAT
1 CAAAATTGGACAGCATATATGTAA
* *
268773 CAAAATTAGACATCATATATGTAA
1 CAAAATTGGACAGCATATATGTAA
* * * *
268797 C-AAATTGGGCAGCATTTAAT-CAT
1 CAAAATTGGACAGCATAT-ATGTAA
268820 CAAAATTGGACAGCATATATGTAA
1 CAAAATTGGACAGCATATATGTAA
* * * * *
268844 C-AAATTGGGCAGCATTTAAGCAT
1 CAAAATTGGACAGCATATATGTAA
268867 CAAAATTGGACAGCATATATGTAA
1 CAAAATTGGACAGCATATATGTAA
* * * * *
268891 C-AAATTGGGCAGCATTTAAGCAT
1 CAAAATTGGACAGCATATATGTAA
268914 CAAAATTGGACAGCATATATGTAA
1 CAAAATTGGACAGCATATATGTAA
** * * * *
268938 C-AAATTGGGTAGCATTTAAGCAT
1 CAAAATTGGACAGCATATATGTAA
* *
268961 CAAAATTGGACAACATATTTGTAA
1 CAAAATTGGACAGCATATATGTAA
268985 C-AAATTGG
1 CAAAATTGG
268993 TTCAACTCAT
Statistics
Matches: 179, Mismatches: 57, Indels: 15
0.71 0.23 0.06
Matches are distributed among these distances:
23 93 0.52
24 86 0.48
ACGTcount: A:0.41, C:0.15, G:0.18, T:0.27
Consensus pattern (24 bp):
CAAAATTGGACAGCATATATGTAA
Found at i:268836 original size:141 final size:141
Alignment explanation
Indices: 268684--268978 Score: 421
Period size: 141 Copynumber: 2.1 Consensus size: 141
268674 ATACATCAAT
* ** * *
268684 TTGGGCAGCATATATACAACAGTTTGAGCAACATTTTTA-CACCAAAACTGGATAGCATATATGC
1 TTGGACAGCATATATACAACAAATTGAGCAACA-TTTAAGCACCAAAACTGGACAGCATATATGC
*
268748 AACAAATTGGGCAGCATTTAAGCATCAAAATTAGACATCATATATGTAACAAATTGGGCAGCATT
65 AACAAATTGGGCAGCATTTAAGCATCAAAATTAGACAGCATATATGTAACAAATTGGGCAGCATT
*
268813 TAATCATCAAAA
130 TAAGCATCAAAA
** * * * * *
268825 TTGGACAGCATATATGTAACAAATTGGGCAGCATTTAAGCATCAAAATTGGACAGCATATATGTA
1 TTGGACAGCATATATACAACAAATTGAGCAACATTTAAGCACCAAAACTGGACAGCATATATGCA
* *
268890 ACAAATTGGGCAGCATTTAAGCATCAAAATTGGACAGCATATATGTAACAAATTGGGTAGCATTT
66 ACAAATTGGGCAGCATTTAAGCATCAAAATTAGACAGCATATATGTAACAAATTGGGCAGCATTT
268955 AAGCATCAAAA
131 AAGCATCAAAA
*
268966 TTGGACAACATAT
1 TTGGACAGCATAT
268979 TTGTAACAAA
Statistics
Matches: 136, Mismatches: 17, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
140 4 0.03
141 132 0.97
ACGTcount: A:0.40, C:0.16, G:0.17, T:0.27
Consensus pattern (141 bp):
TTGGACAGCATATATACAACAAATTGAGCAACATTTAAGCACCAAAACTGGACAGCATATATGCA
ACAAATTGGGCAGCATTTAAGCATCAAAATTAGACAGCATATATGTAACAAATTGGGCAGCATTT
AAGCATCAAAA
Found at i:269922 original size:43 final size:45
Alignment explanation
Indices: 269875--269959 Score: 115
Period size: 43 Copynumber: 1.9 Consensus size: 45
269865 TAATCACGTA
269875 TCGATGCC-ACTGTCCCAGACAG-GGTCTCACACG-TAA-ACACAAG
1 TCGATGCCAAC-GTCCCAGAC-GTGGTCTCACACGATAACACACAAG
*
269918 TCGATGCCAACGTCCCAGACGTGGTCTTACACGATAACACAC
1 TCGATGCCAACGTCCCAGACGTGGTCTCACACGATAACACAC
269960 CTCGAAAATC
Statistics
Matches: 37, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
42 1 0.03
43 27 0.73
44 5 0.14
45 4 0.11
ACGTcount: A:0.29, C:0.33, G:0.20, T:0.18
Consensus pattern (45 bp):
TCGATGCCAACGTCCCAGACGTGGTCTCACACGATAACACACAAG
Found at i:271127 original size:14 final size:15
Alignment explanation
Indices: 271108--271136 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
271098 TCACGAAACT
271108 TTCACACAT-ATAAA
1 TTCACACATAATAAA
271122 TTCACACATAATAAA
1 TTCACACATAATAAA
271137 AATAGAAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.52, C:0.21, G:0.00, T:0.28
Consensus pattern (15 bp):
TTCACACATAATAAA
Found at i:285426 original size:19 final size:20
Alignment explanation
Indices: 285394--285431 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
285384 GGATCATTTT
285394 GAAAAAACACAAAAAAATTG
1 GAAAAAACACAAAAAAATTG
*
285414 GAAAAAATA-AAAAAAATT
1 GAAAAAACACAAAAAAATT
285432 AAAAATAGGG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.74, C:0.05, G:0.08, T:0.13
Consensus pattern (20 bp):
GAAAAAACACAAAAAAATTG
Found at i:299453 original size:31 final size:31
Alignment explanation
Indices: 299418--299477 Score: 120
Period size: 31 Copynumber: 1.9 Consensus size: 31
299408 TAAAAATATA
299418 TTCAAAATTTTCATATATTTGAAAAGCCAAT
1 TTCAAAATTTTCATATATTTGAAAAGCCAAT
299449 TTCAAAATTTTCATATATTTGAAAAGCCA
1 TTCAAAATTTTCATATATTTGAAAAGCCA
299478 TTAAATGAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.42, C:0.13, G:0.07, T:0.38
Consensus pattern (31 bp):
TTCAAAATTTTCATATATTTGAAAAGCCAAT
Found at i:300102 original size:24 final size:24
Alignment explanation
Indices: 300086--300137 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
300076 AATCAAAGTC
300086 AAATATATTATGTTAATAAATACT
1 AAATATATTATGTTAATAAATACT
** *
300110 AAATATATTATACTCATAAATACT
1 AAATATATTATGTTAATAAATACT
300134 AAAT
1 AAAT
300138 CTTCTAGAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.52, C:0.08, G:0.02, T:0.38
Consensus pattern (24 bp):
AAATATATTATGTTAATAAATACT
Found at i:304518 original size:24 final size:24
Alignment explanation
Indices: 304476--304527 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
304466 AATCAAAGTC
** *
304476 AAATATATTATGTTAATAAATGCT
1 AAATATATTATACTAATAAATACT
*
304500 AAATATATTATACTCATAAATACT
1 AAATATATTATACTAATAAATACT
304524 AAAT
1 AAAT
304528 CTCCTAGAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.50, C:0.08, G:0.04, T:0.38
Consensus pattern (24 bp):
AAATATATTATACTAATAAATACT
Found at i:306970 original size:54 final size:55
Alignment explanation
Indices: 306888--306996 Score: 202
Period size: 54 Copynumber: 2.0 Consensus size: 55
306878 TGGCAAAAAG
306888 ATTTGGAATTGTGTTCATTATAACCATAATTTTATTTACTAA-TTGTAAATTAAT
1 ATTTGGAATTGTGTTCATTATAACCATAATTTTATTTACTAATTTGTAAATTAAT
*
306942 ATTTGGAATTGTGTTCATTATAACCATAATTTTATTTATTAATTTGTAAATTAAT
1 ATTTGGAATTGTGTTCATTATAACCATAATTTTATTTACTAATTTGTAAATTAAT
306997 TTATATGTAT
Statistics
Matches: 53, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
54 41 0.77
55 12 0.23
ACGTcount: A:0.35, C:0.06, G:0.09, T:0.50
Consensus pattern (55 bp):
ATTTGGAATTGTGTTCATTATAACCATAATTTTATTTACTAATTTGTAAATTAAT
Found at i:307011 original size:2 final size:2
Alignment explanation
Indices: 306998--307027 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
306988 TAAATTAATT
*
306998 TA TA TG TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
307028 GTTCAAAGAC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
TA
Found at i:308574 original size:17 final size:15
Alignment explanation
Indices: 308546--308579 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 15
308536 ACATGAAAAG
308546 AGAAAAAAAAAAGAA
1 AGAAAAAAAAAAGAA
308561 AGAAAGAAAGAAAAGAA
1 AGAAA-AAA-AAAAGAA
308578 AG
1 AG
308580 GGAAATTATG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 5 0.29
16 3 0.18
17 9 0.53
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (15 bp):
AGAAAAAAAAAAGAA
Found at i:311883 original size:29 final size:29
Alignment explanation
Indices: 311846--311901 Score: 85
Period size: 29 Copynumber: 1.9 Consensus size: 29
311836 TAATGAGTAA
311846 AATGACACATTTAAAAAAAATCTAAAAAT
1 AATGACACATTTAAAAAAAATCTAAAAAT
* * *
311875 AATGACACATTTGAAAATATTCTAAAA
1 AATGACACATTTAAAAAAAATCTAAAA
311902 TTCCTTTGAG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 24 1.00
ACGTcount: A:0.57, C:0.11, G:0.05, T:0.27
Consensus pattern (29 bp):
AATGACACATTTAAAAAAAATCTAAAAAT
Found at i:312629 original size:29 final size:27
Alignment explanation
Indices: 312564--312632 Score: 77
Period size: 29 Copynumber: 2.4 Consensus size: 27
312554 TCTTAGTAAA
312564 TTTAAAATTTAATATATATTTTTTTAT
1 TTTAAAATTTAATATATATTTTTTTAT
*
312591 TTATAGAAATTTAAT-TACTCTATTTTTTAT
1 TT-TA-AAATTTAATATA-TAT-TTTTTTAT
312621 TCTTAAAATTTA
1 T-TTAAAATTTA
312633 TGTTCAACTG
Statistics
Matches: 36, Mismatches: 1, Indels: 8
0.80 0.02 0.18
Matches are distributed among these distances:
27 2 0.06
28 4 0.11
29 18 0.50
30 11 0.31
31 1 0.03
ACGTcount: A:0.36, C:0.04, G:0.01, T:0.58
Consensus pattern (27 bp):
TTTAAAATTTAATATATATTTTTTTAT
Found at i:318205 original size:19 final size:19
Alignment explanation
Indices: 318181--318218 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
318171 ACTATTTAGA
*
318181 AAAAAAATACATTAATCAT
1 AAAAAAATACATCAATCAT
318200 AAAAAAATACATCAATCAT
1 AAAAAAATACATCAATCAT
318219 CTCGTTAGGT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.63, C:0.13, G:0.00, T:0.24
Consensus pattern (19 bp):
AAAAAAATACATCAATCAT
Found at i:320817 original size:24 final size:23
Alignment explanation
Indices: 320780--320825 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 23
320770 AATACACTTT
*
320780 GATTTGATTATTAACCAAAATTGA
1 GATTTGATTATTAA-AAAAATTGA
320804 GATTTGAGTT-TTAAAAAAATTG
1 GATTTGA-TTATTAAAAAAATTG
320826 CAAATATTCA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
23 7 0.35
24 11 0.55
25 2 0.10
ACGTcount: A:0.41, C:0.04, G:0.15, T:0.39
Consensus pattern (23 bp):
GATTTGATTATTAAAAAAATTGA
Found at i:326522 original size:26 final size:26
Alignment explanation
Indices: 326447--326523 Score: 86
Period size: 26 Copynumber: 3.0 Consensus size: 26
326437 CACCAATATT
* *
326447 GCAGCAAAGCTGCAAGTAATAGCAAC
1 GCAGCAAAGCTGCAAGTAATAGTATC
*
326473 GCAGCAGAGCTGCCAA-T-ATCAGTATC
1 GCAGCAAAGCTG-CAAGTAAT-AGTATC
*
326499 GCAGCAAAGCTGCTAGTAATAGTAT
1 GCAGCAAAGCTGCAAGTAATAGTAT
326524 ATGTGGCACA
Statistics
Matches: 42, Mismatches: 5, Indels: 8
0.76 0.09 0.15
Matches are distributed among these distances:
25 4 0.10
26 33 0.79
27 5 0.12
ACGTcount: A:0.36, C:0.22, G:0.23, T:0.18
Consensus pattern (26 bp):
GCAGCAAAGCTGCAAGTAATAGTATC
Found at i:326777 original size:27 final size:27
Alignment explanation
Indices: 326758--326933 Score: 255
Period size: 27 Copynumber: 6.5 Consensus size: 27
326748 GGTATAACAA
326758 TCATTTTACCCTATGGGGGTATTTCAG
1 TCATTTTACCCTATGGGGGTATTTCAG
*
326785 TCATTTTACCCTATAGGGGTATTTCAG
1 TCATTTTACCCTATGGGGGTATTTCAG
*
326812 TCATTTTACCCTATGGGGGTATTTCAA
1 TCATTTTACCCTATGGGGGTATTTCAG
*
326839 TCATTTTACCCTATGAGGGTATTTC-G
1 TCATTTTACCCTATGGGGGTATTTCAG
** ** *
326865 ATCCCTTTAATCTATGGGGGTATTTTAG
1 -TCATTTTACCCTATGGGGGTATTTCAG
*
326893 TCATTTTACCCTATGGGGGTATTTCCG
1 TCATTTTACCCTATGGGGGTATTTCAG
326920 TCATTTTACCCTAT
1 TCATTTTACCCTAT
326934 AAGTATCTAT
Statistics
Matches: 130, Mismatches: 17, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
27 129 0.99
28 1 0.01
ACGTcount: A:0.20, C:0.19, G:0.19, T:0.42
Consensus pattern (27 bp):
TCATTTTACCCTATGGGGGTATTTCAG
Found at i:331108 original size:20 final size:20
Alignment explanation
Indices: 331069--331108 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
331059 TATTTTTGAA
*
331069 ATGTTATGTTTTAGTCACAT
1 ATGTTATGTTTTAGTAACAT
331089 ATGTTATTGTTTT-GTAACAT
1 ATGTTA-TGTTTTAGTAACAT
331109 TTTAGTCTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 12 0.67
21 6 0.33
ACGTcount: A:0.25, C:0.07, G:0.15, T:0.53
Consensus pattern (20 bp):
ATGTTATGTTTTAGTAACAT
Found at i:331266 original size:22 final size:22
Alignment explanation
Indices: 331241--331286 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 22
331231 TTTTGAGTAA
*
331241 TTTAAATTTTCTTTTATGTTCT
1 TTTAAATTTCCTTTTATGTTCT
* * *
331263 TTTAACTTTCCTTTTTTTTTCT
1 TTTAAATTTCCTTTTATGTTCT
331285 TT
1 TT
331287 ATTTTCCATT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.13, C:0.13, G:0.02, T:0.72
Consensus pattern (22 bp):
TTTAAATTTCCTTTTATGTTCT
Found at i:331827 original size:22 final size:22
Alignment explanation
Indices: 331802--331855 Score: 54
Period size: 22 Copynumber: 2.5 Consensus size: 22
331792 AAAAGAGAAT
331802 GGAAAAAAAAAAGAAAAAAAAA
1 GGAAAAAAAAAAGAAAAAAAAA
**** * *
331824 GGAAAGTCTAAAGAACATAAAA
1 GGAAAAAAAAAAGAAAAAAAAA
331846 GGAAAAAAAA
1 GGAAAAAAAA
331856 TTAAATTGCT
Statistics
Matches: 22, Mismatches: 10, Indels: 0
0.69 0.31 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.74, C:0.04, G:0.17, T:0.06
Consensus pattern (22 bp):
GGAAAAAAAAAAGAAAAAAAAA
Found at i:332890 original size:3 final size:3
Alignment explanation
Indices: 332882--332911 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
332872 ATTAACATAA
332882 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
332912 CAATATAAAA
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:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:336500 original size:36 final size:36
Alignment explanation
Indices: 336460--336533 Score: 148
Period size: 36 Copynumber: 2.1 Consensus size: 36
336450 ATTTGTTGTG
336460 TAGTAGAGTTGGGTAGGAAGTTTTCTGAAATAATTA
1 TAGTAGAGTTGGGTAGGAAGTTTTCTGAAATAATTA
336496 TAGTAGAGTTGGGTAGGAAGTTTTCTGAAATAATTA
1 TAGTAGAGTTGGGTAGGAAGTTTTCTGAAATAATTA
336532 TA
1 TA
336534 CATTTCGTTT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 38 1.00
ACGTcount: A:0.34, C:0.03, G:0.27, T:0.36
Consensus pattern (36 bp):
TAGTAGAGTTGGGTAGGAAGTTTTCTGAAATAATTA
Found at i:340006 original size:45 final size:45
Alignment explanation
Indices: 339911--340007 Score: 115
Period size: 45 Copynumber: 2.2 Consensus size: 45
339901 ACTGGAGTAG
* * *
339911 AAACTGCTATTGTAGGTGAACTCAGCTAACAGCAAAAACTCTTAG
1 AAACTACTATTGTAGGTGAACTCAGCTAACAGCAAAAACTCCTAC
* * *
339956 AAACTACTATTGTAGGTGAACTCGGCTAAC-GACAGAAACTCCTCC
1 AAACTACTATTGTAGGTGAACTCAGCTAACAG-CAAAAACTCCTAC
*
340001 CAACTAC
1 AAACTAC
340008 CTCAAAAATC
Statistics
Matches: 44, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
44 1 0.02
45 43 0.98
ACGTcount: A:0.36, C:0.25, G:0.16, T:0.23
Consensus pattern (45 bp):
AAACTACTATTGTAGGTGAACTCAGCTAACAGCAAAAACTCCTAC
Found at i:345591 original size:22 final size:22
Alignment explanation
Indices: 345566--345607 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
345556 ACTTTAACCC
345566 CAAAATTAGAA-AAAAATAATAG
1 CAAAATT-GAATAAAAATAATAG
345588 CAAAATTGAATAAAAATAAT
1 CAAAATTGAATAAAAATAAT
345608 GGCAGCAACC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 3 0.16
22 16 0.84
ACGTcount: A:0.67, C:0.05, G:0.07, T:0.21
Consensus pattern (22 bp):
CAAAATTGAATAAAAATAATAG
Found at i:348052 original size:15 final size:17
Alignment explanation
Indices: 348032--348063 Score: 50
Period size: 15 Copynumber: 2.0 Consensus size: 17
348022 ATTCAATGTA
348032 AATAAT-ATTTA-AAAT
1 AATAATCATTTATAAAT
348047 AATAATCATTTATAAAT
1 AATAATCATTTATAAAT
348064 TAAAAAATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 6 0.40
16 5 0.33
17 4 0.27
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.41
Consensus pattern (17 bp):
AATAATCATTTATAAAT
Found at i:349076 original size:22 final size:22
Alignment explanation
Indices: 349028--349069 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
349018 TAGGGGCTAC
* *
349028 TGTCTTTAGACAAAAGCTTGCA
1 TGTCTTGAGACAAAAGCTTACA
349050 TGTCTTGAGACAAAAGCTTA
1 TGTCTTGAGACAAAAGCTTA
349070 TTTGTCTCGA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.33, C:0.17, G:0.19, T:0.31
Consensus pattern (22 bp):
TGTCTTGAGACAAAAGCTTACA
Found at i:355137 original size:43 final size:43
Alignment explanation
Indices: 355018--355129 Score: 147
Period size: 43 Copynumber: 2.6 Consensus size: 43
355008 CTCGTACAAC
* *
355018 GCCAACGTCCCAAACATGGTCTTACATGTAAACACAGATCGAT
1 GCCAACGTCCCAGACATGGTCTTACATGAAAACACAGATCGAT
**
355061 GCC-ACTGTCCCAGATGTGGTCTTACATGAAAACACA-AGTCGAT
1 GCCAAC-GTCCCAGACATGGTCTTACATGAAAACACAGA-TCGAT
*
355104 GCCAACGTCCCAGACATGGTCCTACA
1 GCCAACGTCCCAGACATGGTCTTACA
355130 CAAAAACATT
Statistics
Matches: 59, Mismatches: 7, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
42 3 0.05
43 54 0.92
44 2 0.03
ACGTcount: A:0.31, C:0.29, G:0.19, T:0.21
Consensus pattern (43 bp):
GCCAACGTCCCAGACATGGTCTTACATGAAAACACAGATCGAT
Found at i:381713 original size:11 final size:11
Alignment explanation
Indices: 381697--381721 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
381687 TCATCTATTC
381697 TAAATATTGTT
1 TAAATATTGTT
381708 TAAATATTGTT
1 TAAATATTGTT
381719 TAA
1 TAA
381722 CAATATATTA
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:0.40, C:0.00, G:0.08, T:0.52
Consensus pattern (11 bp):
TAAATATTGTT
Found at i:383180 original size:8 final size:8
Alignment explanation
Indices: 383163--383192 Score: 51
Period size: 8 Copynumber: 3.8 Consensus size: 8
383153 CTAATTTATT
383163 TCTTCTTC
1 TCTTCTTC
*
383171 TCTTCCTC
1 TCTTCTTC
383179 TCTTCTTC
1 TCTTCTTC
383187 TCTTCT
1 TCTTCT
383193 CCCCAAGTCA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.00, C:0.40, G:0.00, T:0.60
Consensus pattern (8 bp):
TCTTCTTC
Found at i:384756 original size:24 final size:23
Alignment explanation
Indices: 384704--384750 Score: 80
Period size: 21 Copynumber: 2.1 Consensus size: 23
384694 TTATCTAATT
384704 TAAAATAAATAAATTATTAAAAA
1 TAAAATAAATAAATTATTAAAAA
384727 TAAAATAAA-AAA-TATTAAAAA
1 TAAAATAAATAAATTATTAAAAA
384748 TAA
1 TAA
384751 TAAAATTCAG
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
21 12 0.50
22 3 0.12
23 9 0.38
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (23 bp):
TAAAATAAATAAATTATTAAAAA
Found at i:384829 original size:11 final size:11
Alignment explanation
Indices: 384801--384844 Score: 54
Period size: 11 Copynumber: 3.9 Consensus size: 11
384791 TATTTTCAAG
384801 TTAATTAATTT
1 TTAATTAATTT
*
384812 TTTATT-ATTAT
1 TTAATTAATT-T
384823 TTAATTAATTT
1 TTAATTAATTT
384834 TTAATTCAATT
1 TTAATT-AATT
384845 CTATTAAGAT
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
10 3 0.11
11 18 0.64
12 7 0.25
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (11 bp):
TTAATTAATTT
Found at i:390727 original size:14 final size:15
Alignment explanation
Indices: 390708--390736 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
390698 ATTACTGGAC
390708 TAAAAAT-TTTAAGT
1 TAAAAATATTTAAGT
390722 TAAAAATATTTAAGT
1 TAAAAATATTTAAGT
390737 ATAATGACTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 7 0.50
15 7 0.50
ACGTcount: A:0.52, C:0.00, G:0.07, T:0.41
Consensus pattern (15 bp):
TAAAAATATTTAAGT
Found at i:392851 original size:105 final size:102
Alignment explanation
Indices: 392670--392895 Score: 330
Period size: 105 Copynumber: 2.2 Consensus size: 102
392660 TATTGAATAT
* * *
392670 AAAGGGGGTTGCTAAGTGCTGATTCCCCCAAGGGGTTGCTAAGTGTTGATTCCCCGAATCACTGG
1 AAAGGGGGTTGCTAAGTGCTAAATCCCCCAAGGGGTTGCTAAGTGCTGATTCCCCGAATCACTGG
392735 TGGTTGCTAAGTGCTGACTCCACCGTATCTTTAAATGTA
66 TGGTTGCTAAGTGCTGACTCCACCGTATC--TAAATGTA
* *
392774 AAAGGGGGTTGCTAAGTGCTAAATCCCCCTAAGGGGTTGCTACGTGCTGATTCCCC-AGATCATT
1 AAAGGGGGTTGCTAAGTGCTAAATCCCCC-AAGGGGTTGCTAAGTGCTGATTCCCCGA-ATCACT
* * *
392838 GGTGGTTGCTAAGTGCTGATTCCACCGTATCTAAGTGTG
64 GGTGGTTGCTAAGTGCTGACTCCACCGTATCTAAATGTA
392877 AAA-GGGGTTGCTAAGTGCT
1 AAAGGGGGTTGCTAAGTGCT
392896 GATTCCCCGA
Statistics
Matches: 112, Mismatches: 8, Indels: 6
0.89 0.06 0.05
Matches are distributed among these distances:
102 16 0.14
103 9 0.08
104 28 0.25
105 59 0.53
ACGTcount: A:0.22, C:0.20, G:0.28, T:0.29
Consensus pattern (102 bp):
AAAGGGGGTTGCTAAGTGCTAAATCCCCCAAGGGGTTGCTAAGTGCTGATTCCCCGAATCACTGG
TGGTTGCTAAGTGCTGACTCCACCGTATCTAAATGTA
Found at i:392854 original size:33 final size:33
Alignment explanation
Indices: 392808--393014 Score: 137
Period size: 33 Copynumber: 5.7 Consensus size: 33
392798 CCCCCTAAGG
*
392808 GGTTGCTACGTGCTGATTCCCC-AGATCATTGGT
1 GGTTGCTAAGTGCTGATTCCCCGA-ATCATTGGT
* *
392841 GGTTGCTAAGTGCTGATTCCACCGTATCTAAGTGTGAAAGG
1 GGTTGCTAAGTGCTGATTCC-CCGAATC--A-T-TG---GT
392882 GGTTGCTAAGTGCTGATTCCCCGAATCATTGGT
1 GGTTGCTAAGTGCTGATTCCCCGAATCATTGGT
* * * *
392915 GGTTGCTAAGCGCTGATCCCACCGTATCTTAAATGTGAAAGG
1 GGTTGCTAAGTGCTGATTCC-CCGAATC----AT-TG---GT
* * *
392957 GGTTGCTAAGTGTTGATTCCCCGACTCATGGGT
1 GGTTGCTAAGTGCTGATTCCCCGAATCATTGGT
*
392990 GGTTGCTAAGTGCTGAATCCACCGA
1 GGTTGCTAAGTGCTGATTCC-CCGA
393015 TAACGGATAA
Statistics
Matches: 137, Mismatches: 18, Indels: 37
0.71 0.09 0.19
Matches are distributed among these distances:
33 57 0.42
34 15 0.11
36 4 0.03
37 4 0.03
38 5 0.04
39 2 0.01
40 6 0.04
41 26 0.19
42 18 0.13
ACGTcount: A:0.21, C:0.21, G:0.28, T:0.30
Consensus pattern (33 bp):
GGTTGCTAAGTGCTGATTCCCCGAATCATTGGT
Found at i:392886 original size:41 final size:40
Alignment explanation
Indices: 392841--392976 Score: 151
Period size: 41 Copynumber: 3.5 Consensus size: 40
392831 GATCATTGGT
392841 GGTTGCTAAGTGCTGATTCCACCGTATCTAAGTGTGAAAGG
1 GGTTGCTAAGTGCTGATTCCACCGTATCTAA-TGTGAAAGG
* *
392882 GGTTGCTAAGTGCTGATTCC-CCGAATC--AT-TG---GT
1 GGTTGCTAAGTGCTGATTCCACCGTATCTAATGTGAAAGG
* *
392915 GGTTGCTAAGCGCTGATCCCACCGTATCTTAAATGTGAAAGG
1 GGTTGCTAAGTGCTGATTCCACCGTATC-T-AATGTGAAAGG
*
392957 GGTTGCTAAGTGTTGATTCC
1 GGTTGCTAAGTGCTGATTCC
392977 CCGACTCATG
Statistics
Matches: 77, Mismatches: 9, Indels: 17
0.75 0.09 0.17
Matches are distributed among these distances:
33 19 0.25
34 6 0.08
36 2 0.03
37 1 0.01
38 3 0.04
39 2 0.03
40 6 0.08
41 20 0.26
42 18 0.23
ACGTcount: A:0.22, C:0.19, G:0.28, T:0.31
Consensus pattern (40 bp):
GGTTGCTAAGTGCTGATTCCACCGTATCTAATGTGAAAGG
Found at i:392930 original size:74 final size:75
Alignment explanation
Indices: 392804--393013 Score: 325
Period size: 75 Copynumber: 2.8 Consensus size: 75
392794 AAATCCCCCT
*
392804 AAGGGGTTGCTACGTGCTGATTCCCC-AGATCATTGGTGGTTGCTAAGTGCTGATTCCACCGTAT
1 AAGGGGTTGCTAAGTGCTGATTCCCCGA-ATCATTGGTGGTTGCTAAGTGCTGATTCCACCGTAT
*
392868 C-TAAGTGTGA
65 CTTAAATGTGA
* *
392878 AAGGGGTTGCTAAGTGCTGATTCCCCGAATCATTGGTGGTTGCTAAGCGCTGATCCCACCGTATC
1 AAGGGGTTGCTAAGTGCTGATTCCCCGAATCATTGGTGGTTGCTAAGTGCTGATTCCACCGTATC
392943 TTAAATGTGA
66 TTAAATGTGA
* * * *
392953 AAGGGGTTGCTAAGTGTTGATTCCCCGACTCATGGGTGGTTGCTAAGTGCTGAATCCACCG
1 AAGGGGTTGCTAAGTGCTGATTCCCCGAATCATTGGTGGTTGCTAAGTGCTGATTCCACCG
393014 ATAACGGATA
Statistics
Matches: 124, Mismatches: 10, Indels: 3
0.91 0.07 0.02
Matches are distributed among these distances:
74 60 0.48
75 64 0.52
ACGTcount: A:0.21, C:0.21, G:0.29, T:0.30
Consensus pattern (75 bp):
AAGGGGTTGCTAAGTGCTGATTCCCCGAATCATTGGTGGTTGCTAAGTGCTGATTCCACCGTATC
TTAAATGTGA
Found at i:399924 original size:104 final size:102
Alignment explanation
Indices: 399782--400014 Score: 369
Period size: 104 Copynumber: 2.3 Consensus size: 102
399772 TATTGAATAT
*
399782 AAAGGGGGTTGCTAAGTGCTGATTCCCTCAAGGGGTTGCTAAGTGCTGATTCCCCGAATCACTGG
1 AAAGGGGGTTGCTAAGTGCTGATTCCCCCAAGGGGTTGCTAAGTGCTGATTCCCCGAATCACTGG
399847 TGGTTGCTAAGTGCTGACTCCACCGTATCTTTAAAAGTA
66 TGGTTGCTAAGTGCTGACTCCACCGTATC--TAAAAGTA
*
399886 AAAGGGGGTTGCTAAGTGCTGATTCCCCCAAGGGGTTGCTAAGTGCTGATTCCCCGAATCATTGG
1 AAAGGGGGTTGCTAAGTGCTGATTCCCCCAAGGGGTTGCTAAGTGCTGATTCCCCGAATCACTGG
** * ** *
399951 TGGTTGCTAAGTGCTGGTTCCACCGTATCTGAGTGTG
66 TGGTTGCTAAGTGCTGACTCCACCGTATCTAAAAGTA
399988 AAA-GGGGTTGCTAAGTGCTGATTCCCC
1 AAAGGGGGTTGCTAAGTGCTGATTCCCC
400015 GAATCATTGG
Statistics
Matches: 121, Mismatches: 8, Indels: 3
0.92 0.06 0.02
Matches are distributed among these distances:
101 24 0.20
102 7 0.06
104 90 0.74
ACGTcount: A:0.21, C:0.21, G:0.29, T:0.29
Consensus pattern (102 bp):
AAAGGGGGTTGCTAAGTGCTGATTCCCCCAAGGGGTTGCTAAGTGCTGATTCCCCGAATCACTGG
TGGTTGCTAAGTGCTGACTCCACCGTATCTAAAAGTA
Found at i:400004 original size:74 final size:75
Alignment explanation
Indices: 399915--400124 Score: 332
Period size: 75 Copynumber: 2.8 Consensus size: 75
399905 TGATTCCCCC
*
399915 AAGGGGTTGCTAAGTGCTGATTCCCCGAATCATTGGTGGTTGCTAAGTGCTGGTTCCACCGTATC
1 AAGGGGTTGCTAAGTGCTGATTCCCCGAATCATTGGTGGTTGCTAAGTGCTGATTCCACCGTATC
* *
399980 -TGAGTGTGA
66 TTAAATGTGA
* * *
399989 AAGGGGTTGCTAAGTGCTGATTCCCCGAATCATTGGTGGTTCCTAAGTGCTGATCCCACCGTTTC
1 AAGGGGTTGCTAAGTGCTGATTCCCCGAATCATTGGTGGTTGCTAAGTGCTGATTCCACCGTATC
400054 TTAAATGTGA
66 TTAAATGTGA
* * *
400064 AAGGGGTTACTAAGTGCTGATTCCCCGACTCATTGGTGGTTGCTAAGTGCTGAATCCACCG
1 AAGGGGTTGCTAAGTGCTGATTCCCCGAATCATTGGTGGTTGCTAAGTGCTGATTCCACCG
400125 ATAACGGATA
Statistics
Matches: 124, Mismatches: 11, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
74 61 0.49
75 63 0.51
ACGTcount: A:0.20, C:0.21, G:0.28, T:0.30
Consensus pattern (75 bp):
AAGGGGTTGCTAAGTGCTGATTCCCCGAATCATTGGTGGTTGCTAAGTGCTGATTCCACCGTATC
TTAAATGTGA
Found at i:401289 original size:326 final size:326
Alignment explanation
Indices: 400696--401349 Score: 1308
Period size: 326 Copynumber: 2.0 Consensus size: 326
400686 AATAAACTGT
400696 ACTAATTGGCGAACCAAAAATTCTGAAAAGTTTATGGTGGAAAGATATATGAGTCTAGTTTTGGC
1 ACTAATTGGCGAACCAAAAATTCTGAAAAGTTTATGGTGGAAAGATATATGAGTCTAGTTTTGGC
400761 AAAAATTTACAGAATCCAATTTTGATCCCTGTAGCTCCAGATAAAAATAAATTAGGGACCGTGAC
66 AAAAATTTACAGAATCCAATTTTGATCCCTGTAGCTCCAGATAAAAATAAATTAGGGACCGTGAC
400826 TCAGAAAACAGCTTGCTAGAAATTGAACAATTAATGAAATTTAAGTGTGATTAAAATCATGTTAC
131 TCAGAAAACAGCTTGCTAGAAATTGAACAATTAATGAAATTTAAGTGTGATTAAAATCATGTTAC
400891 TATGTAATCATGTGAGGAATTTATTTATTTGTCATATGTTTACTTACTAAGCTATATGCTTACTC
196 TATGTAATCATGTGAGGAATTTATTTATTTGTCATATGTTTACTTACTAAGCTATATGCTTACTC
400956 GTTTTTATTTTTCCTTGATTATAGTGACATCAACTTTTTGGGTATTTTGCAACTAATACTTTGGA
261 GTTTTTATTTTTCCTTGATTATAGTGACATCAACTTTTTGGGTATTTTGCAACTAATACTTTGGA
401021 A
326 A
401022 ACTAATTGGCGAACCAAAAATTCTGAAAAGTTTATGGTGGAAAGATATATGAGTCTAGTTTTGGC
1 ACTAATTGGCGAACCAAAAATTCTGAAAAGTTTATGGTGGAAAGATATATGAGTCTAGTTTTGGC
401087 AAAAATTTACAGAATCCAATTTTGATCCCTGTAGCTCCAGATAAAAATAAATTAGGGACCGTGAC
66 AAAAATTTACAGAATCCAATTTTGATCCCTGTAGCTCCAGATAAAAATAAATTAGGGACCGTGAC
401152 TCAGAAAACAGCTTGCTAGAAATTGAACAATTAATGAAATTTAAGTGTGATTAAAATCATGTTAC
131 TCAGAAAACAGCTTGCTAGAAATTGAACAATTAATGAAATTTAAGTGTGATTAAAATCATGTTAC
401217 TATGTAATCATGTGAGGAATTTATTTATTTGTCATATGTTTACTTACTAAGCTATATGCTTACTC
196 TATGTAATCATGTGAGGAATTTATTTATTTGTCATATGTTTACTTACTAAGCTATATGCTTACTC
401282 GTTTTTATTTTTCCTTGATTATAGTGACATCAACTTTTTGGGTATTTTGCAACTAATACTTTGGA
261 GTTTTTATTTTTCCTTGATTATAGTGACATCAACTTTTTGGGTATTTTGCAACTAATACTTTGGA
401347 A
326 A
401348 AC
1 AC
401350 ATGGCATGTA
Statistics
Matches: 328, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
326 328 1.00
ACGTcount: A:0.34, C:0.13, G:0.17, T:0.36
Consensus pattern (326 bp):
ACTAATTGGCGAACCAAAAATTCTGAAAAGTTTATGGTGGAAAGATATATGAGTCTAGTTTTGGC
AAAAATTTACAGAATCCAATTTTGATCCCTGTAGCTCCAGATAAAAATAAATTAGGGACCGTGAC
TCAGAAAACAGCTTGCTAGAAATTGAACAATTAATGAAATTTAAGTGTGATTAAAATCATGTTAC
TATGTAATCATGTGAGGAATTTATTTATTTGTCATATGTTTACTTACTAAGCTATATGCTTACTC
GTTTTTATTTTTCCTTGATTATAGTGACATCAACTTTTTGGGTATTTTGCAACTAATACTTTGGA
A
Found at i:403356 original size:16 final size:16
Alignment explanation
Indices: 403335--403366 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
403325 TCGTCAATAC
403335 ATACTTCCAAAACTCT
1 ATACTTCCAAAACTCT
403351 ATACTTCCAAAACTCT
1 ATACTTCCAAAACTCT
403367 TTTAAACCTG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.38, C:0.31, G:0.00, T:0.31
Consensus pattern (16 bp):
ATACTTCCAAAACTCT
Found at i:406122 original size:20 final size:20
Alignment explanation
Indices: 406099--406142 Score: 79
Period size: 20 Copynumber: 2.2 Consensus size: 20
406089 AGTTTTGGGA
*
406099 TTTTAATTTGAGTTTAAATC
1 TTTTAATTCGAGTTTAAATC
406119 TTTTAATTCGAGTTTAAATC
1 TTTTAATTCGAGTTTAAATC
406139 TTTT
1 TTTT
406143 GGGTTCAGGT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.27, C:0.07, G:0.09, T:0.57
Consensus pattern (20 bp):
TTTTAATTCGAGTTTAAATC
Done.