Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold204
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: 427869
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.34
File 1 of 3
Found at i:1076 original size:13 final size:13
Alignment explanation
Indices: 1058--1083 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1048 TACAGCAAGT
1058 ATGTATCGATACA
1 ATGTATCGATACA
1071 ATGTATCGATACA
1 ATGTATCGATACA
1084 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:3285 original size:21 final size:20
Alignment explanation
Indices: 3253--3291 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
3243 ATGCGCTAAA
*
3253 AAAAGATATAAACGATTTAG
1 AAAAGAAATAAACGATTTAG
*
3273 AAAAGAAATTAAATGATTT
1 AAAAGAAA-TAAACGATTT
3292 GCAAGTTGAA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 7 0.44
21 9 0.56
ACGTcount: A:0.56, C:0.03, G:0.13, T:0.28
Consensus pattern (20 bp):
AAAAGAAATAAACGATTTAG
Found at i:3333 original size:21 final size:21
Alignment explanation
Indices: 3300--3344 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
3290 TTGCAAGTTG
*
3300 AAATAAAGAAGTTGGCTAATGA
1 AAATAAAGAAGTTAGCTAA-GA
*
3322 AAATAATG-AGTTAGCTAAGA
1 AAATAAAGAAGTTAGCTAAGA
3342 AAA
1 AAA
3345 ATGAAAACTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 9 0.43
22 7 0.33
ACGTcount: A:0.53, C:0.04, G:0.20, T:0.22
Consensus pattern (21 bp):
AAATAAAGAAGTTAGCTAAGA
Found at i:4862 original size:13 final size:13
Alignment explanation
Indices: 4844--4869 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
4834 CAATTTTTTG
4844 TGTATCGATACAT
1 TGTATCGATACAT
4857 TGTATCGATACAT
1 TGTATCGATACAT
4870 ACTTGCTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:5608 original size:21 final size:21
Alignment explanation
Indices: 5567--5610 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
5557 CTCTCCTTTA
* *
5567 TCTCCCCCATTTATTAATAAT
1 TCTCCCCCATTAATCAATAAT
5588 TCTCCCCC-TTAATCAAGTAAT
1 TCTCCCCCATTAATCAA-TAAT
5609 TC
1 TC
5611 ATATCAAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 6 0.30
21 14 0.70
ACGTcount: A:0.27, C:0.32, G:0.02, T:0.39
Consensus pattern (21 bp):
TCTCCCCCATTAATCAATAAT
Found at i:7433 original size:13 final size:13
Alignment explanation
Indices: 7415--7440 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
7405 ATAATCACCC
7415 TGTATCGATACAA
1 TGTATCGATACAA
7428 TGTATCGATACAA
1 TGTATCGATACAA
7441 AGAAAAATGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:9538 original size:15 final size:15
Alignment explanation
Indices: 9518--9548 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
9508 ATTTCGTTTG
*
9518 GAGCTTCTTCATTTT
1 GAGCTTCCTCATTTT
9533 GAGCTTCCTCATTTT
1 GAGCTTCCTCATTTT
9548 G
1 G
9549 GACATTTTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.23, G:0.16, T:0.48
Consensus pattern (15 bp):
GAGCTTCCTCATTTT
Found at i:11381 original size:21 final size:21
Alignment explanation
Indices: 11352--11396 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
11342 AAGTTTTCAT
*
11352 TTTTCTTAGCTAAC-TCATTA
1 TTTTCTTAGCCAACTTCATTA
*
11372 TTTTCATTAGCCAACTTCTTTA
1 TTTTC-TTAGCCAACTTCATTA
11394 TTT
1 TTT
11397 CAACTTGCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 8 0.38
22 8 0.38
ACGTcount: A:0.22, C:0.20, G:0.04, T:0.53
Consensus pattern (21 bp):
TTTTCTTAGCCAACTTCATTA
Found at i:11566 original size:15 final size:16
Alignment explanation
Indices: 11537--11567 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
11527 TTGTTCTAGA
11537 TTTTCAATTTCATTAT
1 TTTTCAATTTCATTAT
11553 TTTTCAATTT-ATTAT
1 TTTTCAATTTCATTAT
11568 CTTCTTTTAG
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:0.26, C:0.10, G:0.00, T:0.65
Consensus pattern (16 bp):
TTTTCAATTTCATTAT
Found at i:13641 original size:13 final size:13
Alignment explanation
Indices: 13623--13648 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
13613 CAATTTTTTG
13623 TGTATCGATACAT
1 TGTATCGATACAT
13636 TGTATCGATACAT
1 TGTATCGATACAT
13649 ACTTGCTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:17804 original size:13 final size:13
Alignment explanation
Indices: 17786--17815 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
17776 ACAATGTCCC
*
17786 ATGTATCGTTACA
1 ATGTATCGATACA
17799 ATGTATCGATACA
1 ATGTATCGATACA
17812 ATGT
1 ATGT
17816 CCCATGTATC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.33, C:0.13, G:0.17, T:0.37
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:17806 original size:33 final size:33
Alignment explanation
Indices: 17769--17831 Score: 108
Period size: 33 Copynumber: 1.9 Consensus size: 33
17759 TTTTACTATA
* *
17769 TATCGTTACAATGTCCCATGTATCGTTACAATG
1 TATCGATACAATGTCCCATGTATCGATACAATG
17802 TATCGATACAATGTCCCATGTATCGATACA
1 TATCGATACAATGTCCCATGTATCGATACA
17832 TTTCACTTAG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 28 1.00
ACGTcount: A:0.30, C:0.22, G:0.14, T:0.33
Consensus pattern (33 bp):
TATCGATACAATGTCCCATGTATCGATACAATG
Found at i:17903 original size:19 final size:19
Alignment explanation
Indices: 17860--17932 Score: 83
Period size: 20 Copynumber: 3.7 Consensus size: 19
17850 CTACCAGTTT
*
17860 CATGTATCGATTCAATTGAG
1 CATGTATCGATACAA-TGAG
*
17880 TATGTATCGATACAATGAG
1 CATGTATCGATACAATGAG
* *
17899 CATGTATCGATACAAAGCAT
1 CATGTATCGATACAATG-AG
*
17919 AATGTATCGATACA
1 CATGTATCGATACA
17933 TCTGGATGTG
Statistics
Matches: 46, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
19 19 0.41
20 27 0.59
ACGTcount: A:0.37, C:0.15, G:0.18, T:0.30
Consensus pattern (19 bp):
CATGTATCGATACAATGAG
Found at i:23003 original size:14 final size:15
Alignment explanation
Indices: 22984--23013 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
22974 ATATTATTAA
22984 AATTTA-ATAATTTT
1 AATTTATATAATTTT
22998 AATTTATATAATTTT
1 AATTTATATAATTTT
23013 A
1 A
23014 TACGAGTTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 6 0.40
15 9 0.60
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (15 bp):
AATTTATATAATTTT
Found at i:26182 original size:2 final size:2
Alignment explanation
Indices: 26175--26210 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
26165 ATATTTCACC
*
26175 AT AT AT AT AT AT AT AT AT GT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
26211 CAATTGATGA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:28682 original size:76 final size:75
Alignment explanation
Indices: 28563--28842 Score: 237
Period size: 76 Copynumber: 3.7 Consensus size: 75
28553 AATTTGAATG
* * * **
28563 ATCAGTTTGAACCTTTA--AAGAGGTAAACCCTTTGGGAAGGCATAGCAATATTCTCATGCCTGA
1 ATCAATTTGAACCTTTAGGAAG-GTTAAAGCCTTTAAGAAGGCATAGCAATATTCTCA-GCCTGA
*
28626 AAAATTAAGATA
64 AAAATCAAGATA
* * * * *
28638 ATTAATTTGAACTTTTAGGAAGGTTAAAGCCTTTAAGAAGGCATAGCAACAATCTTGAGCCTTTG
1 ATCAATTTGAACCTTTAGGAAGGTTAAAGCCTTTAAGAAGGCATAGCAATATTC-TCAGCC--T-
* *
28703 GAAAAGTGAA-ATA
62 GAAAAATCAAGATA
* * * *
28716 ATCAATTTAAACCTTTAGGAAGGTTAAAGCCTTTGTA-AAGGTATAGCAATATTCTCAAACCT-A
1 ATCAATTTGAACCTTTAGGAAGGTTAAAGCCTTT-AAGAAGGCATAGCAATATTCTC-AGCCTGA
* *
28779 AGAAAGCCAGATA
64 A-AAATCAAGATA
* * * *
28792 ATCAAGTTGAACCTTTGGGAAGGTTAAGGCTTTTAAGAAGGCATAGCAATA
1 ATCAATTTGAACCTTTAGGAAGGTTAAAGCCTTTAAGAAGGCATAGCAATA
28843 GTCTTGAGCC
Statistics
Matches: 162, Mismatches: 32, Indels: 21
0.75 0.15 0.10
Matches are distributed among these distances:
74 2 0.01
75 18 0.11
76 75 0.46
77 6 0.04
78 52 0.32
79 9 0.06
ACGTcount: A:0.38, C:0.14, G:0.20, T:0.28
Consensus pattern (75 bp):
ATCAATTTGAACCTTTAGGAAGGTTAAAGCCTTTAAGAAGGCATAGCAATATTCTCAGCCTGAAA
AATCAAGATA
Found at i:28895 original size:154 final size:153
Alignment explanation
Indices: 28569--28982 Score: 388
Period size: 154 Copynumber: 2.7 Consensus size: 153
28559 AATGATCAGT
* ** **
28569 TTGAACCTTTAAAGAGG-TAAACCCTTTGGGAAGGCATAGCAATATTCTCATGCCTGAAAAATTA
1 TTGAACCTTTAAA-AGGTTAAACCCTTTGGAAAGGCATAGCAATATTCTCAAACCTGAAAAAGCA
* * *
28633 AGATAATTAATTTGAACTTTTAGGAAGGTTAAAGCCTTTAAGAAGGCATAGCAACAATCTTGAGC
65 AGATAATCAAGTTGAACCTTTAGGAAGGTTAAAGCCTTTAAGAAGGCATAGCAACAATCTTGAGC
* *
28698 CTTTGGAAAAGTGAAATAATCAAT
130 CTTTGGAAAAGCGAAATAATCAAG
* * * * *
28722 TTAAACCTTTAGGAAGGTTAAAGCCTTTGTAAAGGTATAGCAATATTCTCAAACCT-AAGAAAGC
1 TTGAACCTTTA-AAAGGTTAAACCCTTTGGAAAGGCATAGCAATATTCTCAAACCTGAA-AAAGC
* * * * * *
28786 CAGATAATCAAGTTGAACCTTTGGGAAGGTTAAGGCTTTTAAGAAGGCATAGCAATAGTCTTGAG
64 AAGATAATCAAGTTGAACCTTTAGGAAGGTTAAAGCCTTTAAGAAGGCATAGCAACAATCTTGAG
* *
28851 CCTTTAGG-AAGGCGAGATAATCAAG
129 CCTTT-GGAAAAGCGAAATAATCAAG
* ** * * * * ***
28876 TTGAACCTTTAAAATGGTTAAGGCTTTTTGGGAAGGCATAACAAGAATT-TCAAGCCTTTGGGTA
1 TTGAACCTTTAAAA-GGTTAA-ACCCTTTGGAAAGGCATAGCAA-TATTCTCAAACC--TGAAAA
* * *
28940 AGCGA-ATAACCAAGTTGAACCTTTAGGAAGGTTAAGGCCTTTA
61 AGCAAGATAATCAAGTTGAACCTTTAGGAAGGTTAAAGCCTTTA
28983 GGAAAAAAAG
Statistics
Matches: 209, Mismatches: 42, Indels: 17
0.78 0.16 0.06
Matches are distributed among these distances:
153 17 0.08
154 126 0.60
155 22 0.11
156 38 0.18
157 6 0.03
ACGTcount: A:0.36, C:0.14, G:0.21, T:0.28
Consensus pattern (153 bp):
TTGAACCTTTAAAAGGTTAAACCCTTTGGAAAGGCATAGCAATATTCTCAAACCTGAAAAAGCAA
GATAATCAAGTTGAACCTTTAGGAAGGTTAAAGCCTTTAAGAAGGCATAGCAACAATCTTGAGCC
TTTGGAAAAGCGAAATAATCAAG
Found at i:29097 original size:78 final size:78
Alignment explanation
Indices: 28591--29097 Score: 360
Period size: 78 Copynumber: 6.6 Consensus size: 78
28581 AGAGGTAAAC
* * * * *** * * *
28591 CCTTTGGGAAGGCATAGCAATATTCTCATGCC-TGAA-AAATTAAGATAATTAATTTGAACTTTT
1 CCTTTGAGAAGGCATAGCAACATTCTCAAGCCTTTAAGAAGGCAAGATAATCAAGTTGAACCTTT
*
28654 AGGAAGGTTAAAG
66 AGGAAGGTTAAGG
* * ** * *
28667 CCTTTAAGAAGGCATAGCAACAATCTTGAGCCTTTGGAA-AAGTG-AA-ATAATCAATTTAAACC
1 CCTTTGAGAAGGCATAGCAACATTCTCAAGCCTTT--AAGAAG-GCAAGATAATCAAGTTGAACC
*
28729 TTTAGGAAGGTTAAAG
63 TTTAGGAAGGTTAAGG
* * * * *
28745 CCTTTGTA-AAGGTATAGCAATATTCTCAAACC--TAAGAAAGCCAGATAATCAAGTTGAACCTT
1 CCTTTG-AGAAGGCATAGCAACATTCTCAAGCCTTTAAGAAGGCAAGATAATCAAGTTGAACCTT
*
28807 TGGGAAGGTTAAGG
65 TAGGAAGGTTAAGG
* * * * ** * *
28821 CTTTTAAGAAGGCATAGCAATAGTCTTGAGCCTTTAGGAAGGCGAGATAATCAAGTTGAACCTTT
1 CCTTTGAGAAGGCATAGCAACATTCTCAAGCCTTTAAGAAGGCAAGATAATCAAGTTGAACCTTT
*
28886 A-AAATGGTTAAGG
66 AGGAA-GGTTAAGG
* * * * ** * *
28899 CTTTTTGGGAAGGCATAACAAGAATT-TCAAGCCTTTGGGTAA-GCGA-ATAACCAAGTTGAACC
1 C-CTTTGAGAAGGCATAGCAA-CATTCTCAAGCCTTTAAG-AAGGCAAGATAATCAAGTTGAACC
28961 TTTAGGAAGGTTAAGG
63 TTTAGGAAGGTTAAGG
** * * **
28977 CCTTT-AGGAA-AAAAAGCAACATTCTCAAGACTTTAAGAAGGCAAGATAATCAAGTT-AAATTT
1 CCTTTGA-GAAGGCATAGCAACATTCTCAAGCCTTTAAGAAGGCAAGATAATCAAGTTGAACCTT
*
29039 TAGGGATGGTTAAGG
65 TA-GGAAGGTTAAGG
** *
29054 CCTTTGAGAAGGCATAGCAACATTCTTGAGCCTTTTAGAAGGCA
1 CCTTTGAGAAGGCATAGCAACATTCTCAAGCCTTTAAGAAGGCA
29098 TAGCAATTGC
Statistics
Matches: 338, Mismatches: 70, Indels: 44
0.75 0.15 0.10
Matches are distributed among these distances:
74 3 0.01
75 9 0.03
76 101 0.30
77 38 0.11
78 144 0.43
79 39 0.12
80 4 0.01
ACGTcount: A:0.36, C:0.14, G:0.22, T:0.28
Consensus pattern (78 bp):
CCTTTGAGAAGGCATAGCAACATTCTCAAGCCTTTAAGAAGGCAAGATAATCAAGTTGAACCTTT
AGGAAGGTTAAGG
Found at i:29193 original size:83 final size:82
Alignment explanation
Indices: 29091--29265 Score: 269
Period size: 83 Copynumber: 2.1 Consensus size: 82
29081 GAGCCTTTTA
* *
29091 GAAGGCATAGCAATTGCCTTTAGGAAGACATAGCAAAAATCTCAAGCCTTTAGAAAGGTAAGATA
1 GAAGGCATAGCAATAGCCTTTAGGAAGACATAGCAAAAATCTCAAGCCTTTAGAAAGGCAAGATA
29156 ATTAATTTAAACCTTTGG
66 ATTAATTTAAACCTTT-G
* * * * *
29174 GAAGGCATAGCAATAGCCTTTGGGAAGACATAGCAACAATCTCGAGCCTTTGGGAAGGCAAGATA
1 GAAGGCATAGCAATAGCCTTTAGGAAGACATAGCAAAAATCTCAAGCCTTTAGAAAGGCAAGATA
29239 ATTAATTTAAACCTTTG
66 ATTAATTTAAACCTTTG
*
29256 GAAAGCATAG
1 GAAGGCATAG
29266 TAGTCTTAAG
Statistics
Matches: 84, Mismatches: 8, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
82 10 0.12
83 74 0.88
ACGTcount: A:0.38, C:0.15, G:0.22, T:0.25
Consensus pattern (82 bp):
GAAGGCATAGCAATAGCCTTTAGGAAGACATAGCAAAAATCTCAAGCCTTTAGAAAGGCAAGATA
ATTAATTTAAACCTTTG
Found at i:29254 original size:30 final size:30
Alignment explanation
Indices: 29220--29317 Score: 80
Period size: 30 Copynumber: 3.4 Consensus size: 30
29210 CAATCTCGAG
29220 CCTTTGGGAAGGCAAGATAATTAATTTAAA
1 CCTTTGGGAAGGCAAGATAATTAATTTAAA
* * * *
29250 CCTTT-GGAAAGCATAG-T-AGT--CTTAAG
1 CCTTTGGGAAGGCA-AGATAATTAATTTAAA
* ** *
29276 CCTCTAAGAAGGCAAGATAATGAATTTAAA
1 CCTTTGGGAAGGCAAGATAATTAATTTAAA
29306 CCTTTGGGAAGG
1 CCTTTGGGAAGG
29318 TATAGCAACA
Statistics
Matches: 48, Mismatches: 14, Indels: 12
0.65 0.19 0.16
Matches are distributed among these distances:
26 10 0.21
27 7 0.15
28 3 0.06
29 8 0.17
30 20 0.42
ACGTcount: A:0.37, C:0.13, G:0.22, T:0.28
Consensus pattern (30 bp):
CCTTTGGGAAGGCAAGATAATTAATTTAAA
Found at i:29434 original size:78 final size:77
Alignment explanation
Indices: 29306--29480 Score: 233
Period size: 78 Copynumber: 2.3 Consensus size: 77
29296 TGAATTTAAA
* * * * * *
29306 CCTTTGGGAAGGTATAGCAACATCCCAAGCCTTTGGGAAGGCAAGATAATTAAGTTGAACTTTTG
1 CCTTTGGAAAGGCATAACAACATCCCAAACCTTTGGGAAGGCAAGATAATTAAGTTAAACCTTTG
29371 AGAAAGTTAAGG
66 AGAAAGTTAAGG
* * *
29383 CCTTTGGAAAGGCATAACAACAATCTCAAACCTTTGGGAAGGCGAGATAATTTAGTTAAACCTTT
1 CCTTTGGAAAGGCATAACAAC-ATCCCAAACCTTTGGGAAGGCAAGATAATTAAGTTAAACCTTT
*
29448 GGGAAAGTTAAGG
65 GAGAAAGTTAAGG
**
29461 CCTTTTAAAAGGCATAACAA
1 CCTTTGGAAAGGCATAACAA
29481 TAGTCTTAAG
Statistics
Matches: 85, Mismatches: 12, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
77 18 0.21
78 67 0.79
ACGTcount: A:0.36, C:0.15, G:0.23, T:0.26
Consensus pattern (77 bp):
CCTTTGGAAAGGCATAACAACATCCCAAACCTTTGGGAAGGCAAGATAATTAAGTTAAACCTTTG
AGAAAGTTAAGG
Found at i:29501 original size:78 final size:78
Alignment explanation
Indices: 29332--29589 Score: 261
Period size: 78 Copynumber: 3.3 Consensus size: 78
29322 GCAACATCCC
* * * * *
29332 AAGCCTTTGGGAAGGCAAGATAATTAAGTTGAACTTTTGAGAAAGTTAAGGCCTTTGGAAAGGCA
1 AAGCCTTTAGGAAGGCGAGATAATTTAGTTGAACCTTTGGGAAAGTTAAGGCCTTTGGAAAGGCA
* * *
29397 TAACAACAATCTC
66 TAACAATAGTCTT
* * * **
29410 AAACCTTTGGGAAGGCGAGATAATTTAGTTAAACCTTTGGGAAAGTTAAGGCCTTTTAAAAGGCA
1 AAGCCTTTAGGAAGGCGAGATAATTTAGTTGAACCTTTGGGAAAGTTAAGGCCTTTGGAAAGGCA
29475 TAACAATAGTCTT
66 TAACAATAGTCTT
* ** * ** *
29488 AAGCCATTAGGAA-GATAAATAA-TTAGGTTGAACCTTTGGGAATA-TTAAAACCTTTGGCAAGG
1 AAGCCTTTAGGAAGGCGAGATAATTTA-GTTGAACCTTTGGGAA-AGTTAAGGCCTTTGGAAAGG
**
29550 CATGGCAATAGTCTT
64 CATAACAATAGTCTT
* *
29565 AAGCCTTTAGGAGGGCGACATAATT
1 AAGCCTTTAGGAAGGCGAGATAATT
29590 AGGTTAGGAA
Statistics
Matches: 146, Mismatches: 30, Indels: 7
0.80 0.16 0.04
Matches are distributed among these distances:
76 3 0.02
77 58 0.40
78 84 0.58
79 1 0.01
ACGTcount: A:0.36, C:0.14, G:0.23, T:0.28
Consensus pattern (78 bp):
AAGCCTTTAGGAAGGCGAGATAATTTAGTTGAACCTTTGGGAAAGTTAAGGCCTTTGGAAAGGCA
TAACAATAGTCTT
Found at i:31140 original size:11 final size:11
Alignment explanation
Indices: 31110--31163 Score: 51
Period size: 11 Copynumber: 4.9 Consensus size: 11
31100 ATTTTTTTAG
31110 TTTTAAATATA
1 TTTTAAATATA
*
31121 TTTTATTAAATGTA
1 --TT-TTAAATATA
31135 TTTTAAATATA
1 TTTTAAATATA
31146 TTTT--A-ATA
1 TTTTAAATATA
31154 TTTTAAATAT
1 TTTTAAATAT
31164 TAATTTAGTT
Statistics
Matches: 35, Mismatches: 2, Indels: 10
0.74 0.04 0.21
Matches are distributed among these distances:
8 7 0.20
9 1 0.03
10 1 0.03
11 14 0.40
12 2 0.06
13 2 0.06
14 8 0.23
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (11 bp):
TTTTAAATATA
Found at i:31179 original size:21 final size:19
Alignment explanation
Indices: 31133--31170 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
31123 TTATTAAATG
*
31133 TATTTTAAATATATTTTAA
1 TATTTTAAATATAATTTAA
31152 TATTTTAAATATTAATTTA
1 TATTTTAAATA-TAATTTA
31171 GTTATTTTAG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 11 0.65
20 6 0.35
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (19 bp):
TATTTTAAATATAATTTAA
Found at i:42648 original size:56 final size:56
Alignment explanation
Indices: 42540--42645 Score: 178
Period size: 56 Copynumber: 1.9 Consensus size: 56
42530 AATTAACTAG
* *
42540 ATGTATTGATATATTGAAAAATGTATCAATACATCTGGGTAAAAAGACAAATGTAT
1 ATGTATCGATACATTGAAAAATGTATCAATACATCTGGGTAAAAAGACAAATGTAT
*
42596 ATGTATCGATACATTGAAAAATGTATCGATACATCTGGGTAAAAA-ACAAA
1 ATGTATCGATACATTGAAAAATGTATCAATACATCTGGGTAAAAAGACAAA
42646 ATGCATTGAT
Statistics
Matches: 47, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
55 5 0.11
56 42 0.89
ACGTcount: A:0.45, C:0.09, G:0.16, T:0.29
Consensus pattern (56 bp):
ATGTATCGATACATTGAAAAATGTATCAATACATCTGGGTAAAAAGACAAATGTAT
Found at i:47590 original size:20 final size:20
Alignment explanation
Indices: 47565--47603 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
47555 GATGACATTG
47565 GCATTTGCCTTGTTTTAGGC
1 GCATTTGCCTTGTTTTAGGC
47585 GCATTTGCCTTGTTTTAGG
1 GCATTTGCCTTGTTTTAGG
47604 TGCTATTCCA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.10, C:0.18, G:0.26, T:0.46
Consensus pattern (20 bp):
GCATTTGCCTTGTTTTAGGC
Found at i:47953 original size:41 final size:41
Alignment explanation
Indices: 47908--48037 Score: 127
Period size: 41 Copynumber: 3.2 Consensus size: 41
47898 GGTCAATTTT
47908 TCTAACTCGTTAACTCGTATAGTTTAATTC-CGCTCAACCCC
1 TCTAACTCGTTAACTCGTATAGTTTAA-TCGCGCTCAACCCC
* * * * * *
47949 TCTAACTCATTGACTCATATGGTTTCATCGCGGTCAACCCC
1 TCTAACTCGTTAACTCGTATAGTTTAATCGCGCTCAACCCC
* * * ** * *
47990 TCTAACTAGTTAACTTGTATAGTTTCATCTTGATCAACCCT
1 TCTAACTCGTTAACTCGTATAGTTTAATCGCGCTCAACCCC
48031 TCTAACT
1 TCTAACT
48038 TGTTGACTTA
Statistics
Matches: 72, Mismatches: 16, Indels: 2
0.80 0.18 0.02
Matches are distributed among these distances:
40 2 0.03
41 70 0.97
ACGTcount: A:0.25, C:0.28, G:0.11, T:0.36
Consensus pattern (41 bp):
TCTAACTCGTTAACTCGTATAGTTTAATCGCGCTCAACCCC
Found at i:48320 original size:41 final size:40
Alignment explanation
Indices: 48255--48508 Score: 298
Period size: 41 Copynumber: 6.2 Consensus size: 40
48245 CACCCAATGC
* *
48255 TGACTTGTATAGTTTCATCTTAGTCAACCCTTCTAACTTGT
1 TGACTTGTATGGTTTCATCCTAGTCAACCCTT-TAACTTGT
*
48296 T-ACCTTGTATAGTTTCATCCTAGTCAACCCCTTTAACTTGT
1 TGA-CTTGTATGGTTTCATCCTAGTCAA-CCCTTTAACTTGT
*
48337 TGACTTGTATGGTTTCATCCTAGTCAACCTCTTTAACTCGT
1 TGACTTGTATGGTTTCATCCTAGTCAACC-CTTTAACTTGT
* * *
48378 TTACTCGTATGGTTTCAT-CTCGGTCAACCCTTCTAACTTGT
1 TGACTTGTATGGTTTCATCCT-AGTCAACCCTT-TAACTTGT
*
48419 TGACTTGTATGGTTTCATCCTAGTCAACCCCTTTAACTTAT
1 TGACTTGTATGGTTTCATCCTAGTCAA-CCCTTTAACTTGT
* * * *
48460 TGACTCGTATGGTTTCACCCT-GATCAAGCCCTCTAACTCGT
1 TGACTTGTATGGTTTCATCCTAG-TCAA-CCCTTTAACTTGT
48501 TGACTTGT
1 TGACTTGT
48509 CAGTTTTGTC
Statistics
Matches: 186, Mismatches: 18, Indels: 18
0.84 0.08 0.08
Matches are distributed among these distances:
40 9 0.05
41 164 0.88
42 13 0.07
ACGTcount: A:0.20, C:0.26, G:0.14, T:0.41
Consensus pattern (40 bp):
TGACTTGTATGGTTTCATCCTAGTCAACCCTTTAACTTGT
Found at i:48427 original size:123 final size:123
Alignment explanation
Indices: 48261--48501 Score: 362
Period size: 123 Copynumber: 2.0 Consensus size: 123
48251 ATGCTGACTT
*
48261 GTATAGTTTCATCTTAGTCAACCCTTCTAACTTGTTACCTTGTATAGTTTCATCCTAGTCAACCC
1 GTATAGTTTCATCTCAGTCAACCCTTCTAACTTGTTACCTTGTATAGTTTCATCCTAGTCAACCC
* * * *
48326 CTTTAACTTGTTGACTTGTATGGTTTCATCCT-AGTCAA-CCTCTTTAACTCGTTTACTC
66 CTTTAACTTATTGACTCGTATGGTTTCACCCTGA-TCAAGCC-CTCTAACTCGTTTACTC
* * *
48384 GTATGGTTTCATCTCGGTCAACCCTTCTAACTTGTTGA-CTTGTATGGTTTCATCCTAGTCAACC
1 GTATAGTTTCATCTCAGTCAACCCTTCTAACTTGTT-ACCTTGTATAGTTTCATCCTAGTCAACC
48448 CCTTTAACTTATTGACTCGTATGGTTTCACCCTGATCAAGCCCTCTAACTCGTT
65 CCTTTAACTTATTGACTCGTATGGTTTCACCCTGATCAAGCCCTCTAACTCGTT
48502 GACTTGTCAG
Statistics
Matches: 107, Mismatches: 8, Indels: 6
0.88 0.07 0.05
Matches are distributed among these distances:
123 103 0.96
124 4 0.04
ACGTcount: A:0.20, C:0.26, G:0.13, T:0.40
Consensus pattern (123 bp):
GTATAGTTTCATCTCAGTCAACCCTTCTAACTTGTTACCTTGTATAGTTTCATCCTAGTCAACCC
CTTTAACTTATTGACTCGTATGGTTTCACCCTGATCAAGCCCTCTAACTCGTTTACTC
Found at i:52071 original size:155 final size:154
Alignment explanation
Indices: 51713--52303 Score: 438
Period size: 155 Copynumber: 3.8 Consensus size: 154
51703 CGAAGGTATA
* * * ***
51713 CCCTAAAGCCATTTTAGTAATTTTTTTTAGAACCAAGTCTGATGTAGTTACTGGGATGCTTTTAT
1 CCCTAAAGGCATTTTAGTAA-TTTTTTTAGAACCAAGTCTCATGTAGTCACCAAGATGCTTTTAT
* * * * * * *
51778 GCCAAAGGTATACATTTAAGATAGGTTCACCCTTTATGATCATTTTCGAGTCCTTTAGGGTCATC
65 GCCAAAGGTATGCATTTAGGATAGGTTTACCCTCTATGATCATTTTCGAGTCCTTAAGGATCATA
*
51843 GAGATGCTTTCAAAATAAAAGTAGT
130 GAGATGCTTTCAAAATAAAAGTACT
** * * * *
51868 CTTTAAGGGCATTTT-GATTATTTTTCTTAGAACCGAGTCTCATATAGTCACCAAGATGCTTTTA
1 CCCTAAAGGCATTTTAG-TAATTTTT-TTAGAACCAAGTCTCATGTAGTCACCAAGATGCTTTTA
* * * * *
51932 TGCCAAAGGTTTGCATTTGGGATAGGTTTACCCTACTATGATCATTTTTGTGTCCTTAAGGATTA
64 TGCCAAAGGTATGCATTTAGGATAGGTTTACCCT-CTATGATCATTTTCGAGTCCTTAAGGATCA
* **
51997 CTAG-GATGCTTTTAGGATGAAAAG-ACT
128 -TAGAGATGCTTTCAAAAT-AAAAGTACT
* * * * *
52024 CCCTAAAGGCATTTTAGTAATTTTTTTAAAATCAAGTCCCATGTAGTCA-CTAGAATGCTTTCAT
1 CCCTAAAGGCATTTTAGTAATTTTTTTAGAACCAAGTCTCATGTAGTCACCAAG-ATGCTTTTAT
* * * * * ** * * *
52088 GCCAAAGGTGTGTATTTAGGATAGGTTTACCTTTTATAATCATTTTCGAGTTTTTAAGGGTTACC
65 GCCAAAGGTATGCATTTAGGATAGGTTTACCCTCTATGATCATTTTCGAGTCCTTAAGGATCA-T
* * ***
52153 A-AAATACTTTCATTTTAAAAGTA-T
129 AGAGATGCTTTCAAAATAAAAGTACT
** * * ** * * * * * *
52177 ACCCTAAAGGTGTTTAAATAATTTTCCTAGAATCAGGGTTTGATATAGTCACTAAGATGCTTTTA
1 -CCCTAAAGGCATTTTAGTAATTTTTTTAGAACCA-AGTCTCATGTAGTCACCAAGATGCTTTTA
* * * * * *
52242 TGCCAAAAGTTTGCATTTAGGATCGATTTACCCTTTTATGATCATTTTCAAGTCCTTTAAGG
64 TGCCAAAGGTATGCATTTAGGATAGGTTTACCC-TCTATGATCATTTTCGAGTCC-TTAAGG
52304 TTACCAAAGT
Statistics
Matches: 340, Mismatches: 82, Indels: 26
0.76 0.18 0.06
Matches are distributed among these distances:
153 6 0.02
154 70 0.21
155 175 0.51
156 75 0.22
157 14 0.04
ACGTcount: A:0.29, C:0.15, G:0.17, T:0.38
Consensus pattern (154 bp):
CCCTAAAGGCATTTTAGTAATTTTTTTAGAACCAAGTCTCATGTAGTCACCAAGATGCTTTTATG
CCAAAGGTATGCATTTAGGATAGGTTTACCCTCTATGATCATTTTCGAGTCCTTAAGGATCATAG
AGATGCTTTCAAAATAAAAGTACT
Found at i:52174 original size:310 final size:311
Alignment explanation
Indices: 51713--52289 Score: 696
Period size: 310 Copynumber: 1.9 Consensus size: 311
51703 CGAAGGTATA
* ** * * * *
51713 CCCTAAAGCCATTTTAGTAATTTTTTTTAGAACCAAGTCTGATGTAGTTACTGGGATGCTTTTAT
1 CCCTAAAGCCATTTTAGTAATTTTTTTTAAAACCAAGTCCCATGTAGTCACTAGAATGCTTTCAT
* *
51778 GCCAAAGGTATACATTTAAGATAGGTTCACCCTTTATGATCATTTTCGAGTCCTTTAGGGTCATC
66 GCCAAAGGTATACATTTAAGATAGGTTCACCCTTTATAATCATTTTCGAGTCCTTTAGGGTCACC
* * * ** * * * * * *
51843 GAGATGCTTTCAAAATAAAAGTAGT-CTTTAAGGGCAT-TTTGATTATTTTTCTTAGAA-CCGAG
131 AAAATACTTTCAAAATAAAAGTA-TACCCTAAAGG--TGTTTAAATAATTTTCCTAGAATCAGAG
* * *
51905 TCTCATATAGTCACCAAGATGCTTTTATGCCAAAGGTTTGCATTTGGGATAGGTTTACCCTACTA
193 TCTCATATAGTCACCAAGATGCTTTTATGCCAAAAGTTTGCATTTAGGATAGATTTACCCTACTA
51970 TGATCATTTTTGTGTCCTTAAGGATTACTAGGATGCTTTTAGGATGAAAAGACT
258 TGATCATTTTTGTGTCCTTAAGGATTACTAGGATGCTTTTAGGATGAAAAGACT
* *
52024 CCCTAAAGGCATTTTAGTAA-TTTTTTTAAAATCAAGTCCCATGTAGTCACTAGAATGCTTTCAT
1 CCCTAAAGCCATTTTAGTAATTTTTTTTAAAACCAAGTCCCATGTAGTCACTAGAATGCTTTCAT
* ** * * * * *
52088 GCCAAAGGTGTGTATTTAGGATAGGTTTACCTTTTATAATCATTTTCGAGT-TTTTAAGGGTTAC
66 GCCAAAGGTATACATTTAAGATAGGTTCACCCTTTATAATCATTTTCGAGTCCTTT-AGGGTCAC
*** * *
52152 CAAAATACTTTCATTTTAAAAGTATACCCTAAAGGTGTTTAAATAATTTTCCTAGAATCAGGGTT
130 CAAAATACTTTCAAAATAAAAGTATACCCTAAAGGTGTTTAAATAATTTTCCTAGAATCAGAGTC
* * * **
52217 TGATATAGTCACTAAGATGCTTTTATGCCAAAAGTTTGCATTTAGGATCGATTTACCCTTTTATG
195 TCATATAGTCACCAAGATGCTTTTATGCCAAAAGTTTGCATTTAGGATAGATTTACCCTACTATG
52282 ATCATTTT
260 ATCATTTT
52290 CAAGTCCTTT
Statistics
Matches: 219, Mismatches: 43, Indels: 9
0.81 0.16 0.03
Matches are distributed among these distances:
308 1 0.00
309 20 0.09
310 179 0.82
311 19 0.09
ACGTcount: A:0.29, C:0.15, G:0.17, T:0.39
Consensus pattern (311 bp):
CCCTAAAGCCATTTTAGTAATTTTTTTTAAAACCAAGTCCCATGTAGTCACTAGAATGCTTTCAT
GCCAAAGGTATACATTTAAGATAGGTTCACCCTTTATAATCATTTTCGAGTCCTTTAGGGTCACC
AAAATACTTTCAAAATAAAAGTATACCCTAAAGGTGTTTAAATAATTTTCCTAGAATCAGAGTCT
CATATAGTCACCAAGATGCTTTTATGCCAAAAGTTTGCATTTAGGATAGATTTACCCTACTATGA
TCATTTTTGTGTCCTTAAGGATTACTAGGATGCTTTTAGGATGAAAAGACT
Found at i:53282 original size:3 final size:3
Alignment explanation
Indices: 53274--53322 Score: 98
Period size: 3 Copynumber: 16.3 Consensus size: 3
53264 AATCAATAGG
53274 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
53322 A
1 A
53323 ATTTTGAAAA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 46 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:57949 original size:28 final size:27
Alignment explanation
Indices: 57888--57951 Score: 67
Period size: 28 Copynumber: 2.3 Consensus size: 27
57878 TTTTATTAAT
*
57888 TTTATATAAGATTATAAAATATTATATA
1 TTTATATAAGATTATAAAACATTATA-A
* *
57916 TTTATATAA-ATTTTGAAACATTAATAA
1 TTTATATAAGATTATAAAACATT-ATAA
57943 TTATATATA
1 TT-TATATA
57952 TAAATTTTTA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
27 13 0.42
28 18 0.58
ACGTcount: A:0.48, C:0.02, G:0.03, T:0.47
Consensus pattern (27 bp):
TTTATATAAGATTATAAAACATTATAA
Found at i:58719 original size:50 final size:50
Alignment explanation
Indices: 58635--58746 Score: 143
Period size: 50 Copynumber: 2.2 Consensus size: 50
58625 TTTCACAATT
* * * *
58635 TGTATTGATACATCCTTCATTGTATCGATACATCCTAGGTTTTAACCAGA
1 TGTATCGATACATCCTTCATTATATCAATACATCCTAGGTTTTAACCAAA
* * * * *
58685 TGTATCTATACATTCTTCATTATATCAATGCATCCTGGGTTTTACCCAAA
1 TGTATCGATACATCCTTCATTATATCAATACATCCTAGGTTTTAACCAAA
58735 TGTATCGATACA
1 TGTATCGATACA
58747 GGCATTTTTT
Statistics
Matches: 52, Mismatches: 10, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
50 52 1.00
ACGTcount: A:0.29, C:0.21, G:0.12, T:0.38
Consensus pattern (50 bp):
TGTATCGATACATCCTTCATTATATCAATACATCCTAGGTTTTAACCAAA
Found at i:59562 original size:8 final size:8
Alignment explanation
Indices: 59549--59573 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
59539 TTAGGACTCC
59549 CATGCATT
1 CATGCATT
59557 CATGCATT
1 CATGCATT
59565 CATGCATT
1 CATGCATT
59573 C
1 C
59574 TTGTGGTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.24, C:0.28, G:0.12, T:0.36
Consensus pattern (8 bp):
CATGCATT
Found at i:61248 original size:79 final size:78
Alignment explanation
Indices: 61115--61516 Score: 394
Period size: 79 Copynumber: 5.1 Consensus size: 78
61105 TTTTATATGT
* * ** *
61115 TTTTATTTCTAAAAAACTGATTTTCCACTATCGAAGATACTCCAACCCCGTTATTTCCGAGGGGA
1 TTTTATTTCTAAAACACTGATTTTCCACAATCGGGGATACTCCAA-CCCATTATTTCCGAGGGGA
* *
61180 TACTCCAACCTCGG
65 TACTCCAACCCCGA
* * * * *
61194 TTTTATTTCTAGAATATTGATTTTCCACAATCGGGGATACTCCAACCTCATTATTTTCGAGAGGA
1 TTTTATTTCTAAAACACTGATTTTCCACAATCGGGGATACTCCAACC-CATTATTTCCGAGGGGA
61259 TACTCCAACCCCGA
65 TACTCCAACCCCGA
* * * * ***
61273 TTTTATTTCTAAAACACTAATTTTCCACCATCGGGGATACTTCAACCCGTTATTTCCGAAAAGAT
1 TTTTATTTCTAAAACACTGATTTTCCACAATCGGGGATACTCCAACCCATTATTTCCGAGGGGAT
*
61338 ACTCCAACCCCTA
66 ACTCCAACCCCGA
* * * * *
61351 TTTTATTTCCAAAAACACCGATTTTTTTCACAATCGGGAATACTCCAAACCCATTATTTCTGAGG
1 TTTTATTT-CTAAAACACTGA--TTTTCCACAATCGGGGATACTCC-AACCCATTATTTCCGAGG
61416 GGATACTCCAACCCCGA
62 GGATACTCCAACCCCGA
* ** * * ** *
61433 TTTTATTTCAAAAACA-TCGATTTGTTTTACAATCGGGGATACTCCGACCCCCTTATTTTTGAAG
1 TTTTATTTCTAAAACACT-GA-TT-TTCCACAATCGGGGATACTCC-AACCCATTATTTCCGAGG
*
61497 AGATACTCCAACCCC-A
62 GGATACTCCAACCCCGA
61513 TTTT
1 TTTT
61517 TATCTCCAAA
Statistics
Matches: 272, Mismatches: 44, Indels: 13
0.83 0.13 0.04
Matches are distributed among these distances:
78 36 0.13
79 115 0.42
80 8 0.03
81 76 0.28
82 37 0.14
ACGTcount: A:0.29, C:0.26, G:0.12, T:0.33
Consensus pattern (78 bp):
TTTTATTTCTAAAACACTGATTTTCCACAATCGGGGATACTCCAACCCATTATTTCCGAGGGGAT
ACTCCAACCCCGA
Found at i:63314 original size:20 final size:21
Alignment explanation
Indices: 63289--63337 Score: 84
Period size: 20 Copynumber: 2.4 Consensus size: 21
63279 ATAAACCAAA
63289 GTATCGATATATAGAT-TTTT
1 GTATCGATATATAGATATTTT
63309 GTATCGATATATAGATATTTT
1 GTATCGATATATAGATATTTT
63330 -TATCGATA
1 GTATCGATA
63338 CATTAAGGTT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
20 24 0.86
21 4 0.14
ACGTcount: A:0.33, C:0.06, G:0.14, T:0.47
Consensus pattern (21 bp):
GTATCGATATATAGATATTTT
Found at i:63422 original size:20 final size:20
Alignment explanation
Indices: 63399--63452 Score: 108
Period size: 20 Copynumber: 2.7 Consensus size: 20
63389 CACATCCAGA
63399 TGTATCGATACATTATGCAT
1 TGTATCGATACATTATGCAT
63419 TGTATCGATACATTATGCAT
1 TGTATCGATACATTATGCAT
63439 TGTATCGATACATT
1 TGTATCGATACATT
63453 GTATCAATAC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.41
Consensus pattern (20 bp):
TGTATCGATACATTATGCAT
Found at i:65295 original size:21 final size:21
Alignment explanation
Indices: 65269--65318 Score: 82
Period size: 21 Copynumber: 2.4 Consensus size: 21
65259 CGACATTGAA
65269 GAAGAAGAGTTTGAATAAGCC
1 GAAGAAGAGTTTGAATAAGCC
*
65290 GAAGAAGAGTTTGAATAAGCT
1 GAAGAAGAGTTTGAATAAGCC
*
65311 AAAGAAGA
1 GAAGAAGA
65319 AAGCAATAGT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.48, C:0.06, G:0.28, T:0.18
Consensus pattern (21 bp):
GAAGAAGAGTTTGAATAAGCC
Found at i:67300 original size:14 final size:15
Alignment explanation
Indices: 67272--67300 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
67262 ATTTTCATCC
67272 TTTTGTATGTAAATA
1 TTTTGTATGTAAATA
67287 TTTTGTAT-TAAATA
1 TTTTGTATGTAAATA
67301 ATGAAAAAGA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 6 0.43
15 8 0.57
ACGTcount: A:0.34, C:0.00, G:0.10, T:0.55
Consensus pattern (15 bp):
TTTTGTATGTAAATA
Found at i:68236 original size:16 final size:16
Alignment explanation
Indices: 68212--68242 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
68202 AAAGGCTTTC
*
68212 AAAATTTTTAATAGAA
1 AAAAGTTTTAATAGAA
68228 AAAAGTTTTAATAGA
1 AAAAGTTTTAATAGA
68243 GGAAATGTTG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.55, C:0.00, G:0.10, T:0.35
Consensus pattern (16 bp):
AAAAGTTTTAATAGAA
Found at i:69656 original size:13 final size:13
Alignment explanation
Indices: 69621--69656 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 13
69611 AAAAACCCAG
69621 ATGTATCGATACA
1 ATGTATCGATACA
69634 ATGT-TC--TACA
1 ATGTATCGATACA
69644 ATGTATCGATACA
1 ATGTATCGATACA
69657 GGGTTACTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 6
0.77 0.00 0.23
Matches are distributed among these distances:
10 8 0.40
11 2 0.10
12 2 0.10
13 8 0.40
ACGTcount: A:0.36, C:0.17, G:0.14, T:0.33
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:72250 original size:19 final size:20
Alignment explanation
Indices: 72207--72258 Score: 88
Period size: 20 Copynumber: 2.6 Consensus size: 20
72197 CGCATCCAGA
*
72207 TGTATCGATACATTATGCTT
1 TGTATCGATACATTATGCAT
72227 TGTATCGATACATTAT-CAT
1 TGTATCGATACATTATGCAT
72246 TGTATCGATACAT
1 TGTATCGATACAT
72259 GAAACTGGCA
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
19 15 0.48
20 16 0.52
ACGTcount: A:0.29, C:0.15, G:0.13, T:0.42
Consensus pattern (20 bp):
TGTATCGATACATTATGCAT
Found at i:74836 original size:3 final size:3
Alignment explanation
Indices: 74828--74853 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
74818 TCAACCCAAA
74828 TCT TCT TCT TCT TCT TCT TCT TCT TC
1 TCT TCT TCT TCT TCT TCT TCT TCT TC
74854 CCTTTTCTCC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.00, C:0.35, G:0.00, T:0.65
Consensus pattern (3 bp):
TCT
Found at i:99511 original size:2 final size:2
Alignment explanation
Indices: 99504--99528 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
99494 GCTTTCTCAC
99504 AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG A
99529 TGCTTTAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:102500 original size:11 final size:11
Alignment explanation
Indices: 102472--102511 Score: 55
Period size: 11 Copynumber: 3.7 Consensus size: 11
102462 TTTTTAATTA
102472 TAAATTATC-T
1 TAAATTATCAT
*
102482 TTAATTATCAT
1 TAAATTATCAT
*
102493 TAAATTATAAT
1 TAAATTATCAT
102504 TAAATTAT
1 TAAATTAT
102512 TCTAATTATA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
10 8 0.31
11 18 0.69
ACGTcount: A:0.45, C:0.05, G:0.00, T:0.50
Consensus pattern (11 bp):
TAAATTATCAT
Found at i:102704 original size:16 final size:15
Alignment explanation
Indices: 102672--102705 Score: 50
Period size: 16 Copynumber: 2.2 Consensus size: 15
102662 AAAAAATATT
*
102672 TTTAATTTATTTTAA
1 TTTAATTTATATTAA
102687 TTTAATTATATATTAA
1 TTTAATT-TATATTAA
102703 TTT
1 TTT
102706 TGATATTAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 7 0.41
16 10 0.59
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (15 bp):
TTTAATTTATATTAA
Found at i:102734 original size:22 final size:20
Alignment explanation
Indices: 102678--102734 Score: 51
Period size: 22 Copynumber: 2.5 Consensus size: 20
102668 TATTTTTAAT
*
102678 TTATTTTAATTTAATTATATA
1 TTATTTTTA-TTAATTATATA
102699 TTAATTTTGATATTAATATATTATA
1 TT-ATTTT--TATTAAT-TA-TATA
102724 TTATTTTTATT
1 TTATTTTTATT
102735 TAAAAATAAG
Statistics
Matches: 30, Mismatches: 1, Indels: 9
0.75 0.03 0.22
Matches are distributed among these distances:
21 2 0.07
22 9 0.30
23 5 0.17
24 8 0.27
25 6 0.20
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (20 bp):
TTATTTTTATTAATTATATA
Found at i:104070 original size:21 final size:21
Alignment explanation
Indices: 103975--104063 Score: 133
Period size: 21 Copynumber: 4.2 Consensus size: 21
103965 TGTAGCCAAG
* *
103975 TGTATCAATAGATGTCAAGAT
1 TGTATCGATACATGTCAAGAT
*
103996 TGTATCGATACATGTCAAAAT
1 TGTATCGATACATGTCAAGAT
*
104017 AGTATCGATACATGTCAAGAT
1 TGTATCGATACATGTCAAGAT
*
104038 GGTATCGATACATGTCAAGAT
1 TGTATCGATACATGTCAAGAT
104059 TGTAT
1 TGTAT
104064 AAATACAATT
Statistics
Matches: 61, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 61 1.00
ACGTcount: A:0.36, C:0.12, G:0.19, T:0.33
Consensus pattern (21 bp):
TGTATCGATACATGTCAAGAT
Found at i:105639 original size:2 final size:2
Alignment explanation
Indices: 105632--105662 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
105622 ATCAAAGGTA
105632 AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
105663 TTGAAAAGAA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:106820 original size:33 final size:33
Alignment explanation
Indices: 106783--106849 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
106773 TTCAATGATT
106783 TGTATCGATACATAAAATGTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
*** *
106816 TGTATCGATACATATTTTTTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
106849 T
1 T
106850 TTAAGCTACT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.34, C:0.12, G:0.13, T:0.40
Consensus pattern (33 bp):
TGTATCGATACATAAAATGTTGTATCGATACAA
Found at i:106821 original size:13 final size:13
Alignment explanation
Indices: 106803--106827 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
106793 CATAAAATGT
106803 TGTATCGATACAA
1 TGTATCGATACAA
106816 TGTATCGATACA
1 TGTATCGATACA
106828 TATTTTTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:106908 original size:13 final size:13
Alignment explanation
Indices: 106890--106914 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
106880 ATTACTCAAA
106890 TGTATCGATACAT
1 TGTATCGATACAT
106903 TGTATCGATACA
1 TGTATCGATACA
106915 CTGATCTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:107016 original size:52 final size:52
Alignment explanation
Indices: 106923--107041 Score: 213
Period size: 52 Copynumber: 2.3 Consensus size: 52
106913 CACTGATCTT
*
106923 TGTATCGATACATGC-GGCAAATTTGCCCAGATGTATCGATACATTATAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
*
106974 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATTAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
107026 TGTATCGATACATGCA
1 TGTATCGATACATGCA
107042 AAGAACTTTT
Statistics
Matches: 65, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
51 15 0.23
52 50 0.77
ACGTcount: A:0.34, C:0.18, G:0.18, T:0.29
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
Found at i:111031 original size:25 final size:25
Alignment explanation
Indices: 111001--111085 Score: 161
Period size: 25 Copynumber: 3.4 Consensus size: 25
110991 TTTCAATAAT
111001 AAATCATTTTTAGCTTTTAATTTTG
1 AAATCATTTTTAGCTTTTAATTTTG
111026 AAATCATTTTTAGCTTTTAATTTTG
1 AAATCATTTTTAGCTTTTAATTTTG
111051 AAATCATTTTTAGCTTTTAATTTTG
1 AAATCATTTTTAGCTTTTAATTTTG
*
111076 AAATTATTTT
1 AAATCATTTT
111086 CTTAAATTTT
Statistics
Matches: 59, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
25 59 1.00
ACGTcount: A:0.29, C:0.07, G:0.07, T:0.56
Consensus pattern (25 bp):
AAATCATTTTTAGCTTTTAATTTTG
Found at i:111093 original size:21 final size:21
Alignment explanation
Indices: 111069--111117 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
111059 TTTAGCTTTT
111069 AATTTTGAAATT-ATTTTCTTA
1 AATTTT-AAATTCATTTTCTTA
* *
111090 AATTTTAAGTTCATTTTCTCA
1 AATTTTAAATTCATTTTCTTA
*
111111 AACTTTA
1 AATTTTA
111118 CTAAATGATC
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
20 4 0.17
21 20 0.83
ACGTcount: A:0.33, C:0.10, G:0.04, T:0.53
Consensus pattern (21 bp):
AATTTTAAATTCATTTTCTTA
Found at i:113097 original size:21 final size:21
Alignment explanation
Indices: 113073--113113 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
113063 TCGACGCATG
*
113073 TTAGGAGTGTAATGATACATA
1 TTAGGAGTATAATGATACATA
* *
113094 TTAGGATTATATTGATACAT
1 TTAGGAGTATAATGATACAT
113114 GATAGAATTG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.37, C:0.05, G:0.20, T:0.39
Consensus pattern (21 bp):
TTAGGAGTATAATGATACATA
Found at i:115195 original size:24 final size:24
Alignment explanation
Indices: 115175--115230 Score: 62
Period size: 24 Copynumber: 2.4 Consensus size: 24
115165 TTAATATATT
*
115175 TTTATAT-GATATAAATTATATAA
1 TTTATATAAATATAAATTATATAA
**
115198 TTTATATAAATATAAAAAATAT-A
1 TTTATATAAATATAAATTATATAA
115221 TATTATATAA
1 T-TTATATAA
115231 TTTGAAAATA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
23 9 0.32
24 19 0.68
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.45
Consensus pattern (24 bp):
TTTATATAAATATAAATTATATAA
Found at i:116713 original size:17 final size:16
Alignment explanation
Indices: 116693--116760 Score: 50
Period size: 17 Copynumber: 4.2 Consensus size: 16
116683 TAAGTCGATT
116693 TAAATTATAATTAAATA
1 TAAA-TATAATTAAATA
*
116710 TAAA-A-AATAAAATA
1 TAAATATAATTAAATA
* * *
116724 GAAATGTAATTAAATT
1 TAAATATAATTAAATA
* *
116740 TAAGTTATTATTAAATA
1 TAA-ATATAATTAAATA
116757 TAAA
1 TAAA
116761 CAATAAAACA
Statistics
Matches: 37, Mismatches: 11, Indels: 7
0.67 0.20 0.13
Matches are distributed among these distances:
14 11 0.30
15 1 0.03
16 9 0.24
17 16 0.43
ACGTcount: A:0.59, C:0.00, G:0.04, T:0.37
Consensus pattern (16 bp):
TAAATATAATTAAATA
Found at i:116755 original size:47 final size:47
Alignment explanation
Indices: 116690--116786 Score: 131
Period size: 47 Copynumber: 2.1 Consensus size: 47
116680 AAATAAGTCG
* * *
116690 ATTTAAATTATAATTAAATATAAAAAATAAAATAGAAATGTAATTAA
1 ATTTAAATTATAATTAAATATAAAAAATAAAACAAAAATATAATTAA
* * * *
116737 ATTTAAGTTATTATTAAATATAAACAATAAAACAAAAATATTATTAA
1 ATTTAAATTATAATTAAATATAAAAAATAAAACAAAAATATAATTAA
116784 ATT
1 ATT
116787 ATTAAATTTA
Statistics
Matches: 43, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
47 43 1.00
ACGTcount: A:0.59, C:0.02, G:0.03, T:0.36
Consensus pattern (47 bp):
ATTTAAATTATAATTAAATATAAAAAATAAAACAAAAATATAATTAA
Found at i:121770 original size:33 final size:33
Alignment explanation
Indices: 121728--121799 Score: 117
Period size: 33 Copynumber: 2.2 Consensus size: 33
121718 TTTAAGTAAG
*
121728 AAATCGAAATTGTTACAGATTACAAAATATAAT
1 AAATCGAAATTGTTACAAATTACAAAATATAAT
*
121761 AAATCGAAATTGTTACAAATTATAAAATATAAT
1 AAATCGAAATTGTTACAAATTACAAAATATAAT
*
121794 AGATCG
1 AAATCG
121800 CATAGTTATG
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.51, C:0.08, G:0.10, T:0.31
Consensus pattern (33 bp):
AAATCGAAATTGTTACAAATTACAAAATATAAT
Found at i:126639 original size:16 final size:16
Alignment explanation
Indices: 126620--126686 Score: 57
Period size: 16 Copynumber: 4.2 Consensus size: 16
126610 TAAGTTAATT
126620 ATTCGAGTCATTTTAA
1 ATTCGAGTCATTTTAA
* *
126636 ATTCGAATAATTTTAA
1 ATTCGAGTCATTTTAA
**
126652 ATTTC-AGTCATTTCGA
1 A-TTCGAGTCATTTTAA
*
126668 ATTCTGA-TCATTCTAA
1 ATTC-GAGTCATTTTAA
126684 ATT
1 ATT
126687 TAAGTTATTT
Statistics
Matches: 39, Mismatches: 9, Indels: 6
0.72 0.17 0.11
Matches are distributed among these distances:
15 3 0.08
16 32 0.82
17 4 0.10
ACGTcount: A:0.33, C:0.13, G:0.09, T:0.45
Consensus pattern (16 bp):
ATTCGAGTCATTTTAA
Found at i:127006 original size:19 final size:20
Alignment explanation
Indices: 126957--127009 Score: 56
Period size: 19 Copynumber: 2.8 Consensus size: 20
126947 TTACACGTTA
*
126957 ATAAT-TATTTATATAATTT
1 ATAATATATTCATATAATTT
* * *
126976 TTAACATGTTCATAT-ATTT
1 ATAATATATTCATATAATTT
126995 ATAATATATTCATAT
1 ATAATATATTCATAT
127010 TTTTGTGCTC
Statistics
Matches: 26, Mismatches: 7, Indels: 2
0.74 0.20 0.06
Matches are distributed among these distances:
19 19 0.73
20 7 0.27
ACGTcount: A:0.40, C:0.06, G:0.02, T:0.53
Consensus pattern (20 bp):
ATAATATATTCATATAATTT
Found at i:132167 original size:14 final size:14
Alignment explanation
Indices: 132150--132179 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
132140 TTATTTTATC
132150 ATAATAAAAAAATT
1 ATAATAAAAAAATT
*
132164 ATAATAAAATAATT
1 ATAATAAAAAAATT
132178 AT
1 AT
132180 TTTATGAGAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (14 bp):
ATAATAAAAAAATT
Found at i:132453 original size:25 final size:25
Alignment explanation
Indices: 132381--132454 Score: 64
Period size: 25 Copynumber: 2.9 Consensus size: 25
132371 AATAAAATAA
*
132381 AAATTAA-CTATTTTATAAGATAAATT
1 AAATTAATCTATATTA-AA-ATAAATT
*
132407 AAA-TAAT-TATTTTATTATAATAAATT
1 AAATTAATCTA---TATTAAAATAAATT
132433 AAATTAATCTATATTAAAATAA
1 AAATTAATCTATATTAAAATAA
132455 TTATTACAAT
Statistics
Matches: 39, Mismatches: 3, Indels: 13
0.71 0.05 0.24
Matches are distributed among these distances:
25 15 0.38
26 13 0.33
27 5 0.13
28 6 0.15
ACGTcount: A:0.53, C:0.03, G:0.01, T:0.43
Consensus pattern (25 bp):
AAATTAATCTATATTAAAATAAATT
Found at i:133771 original size:14 final size:14
Alignment explanation
Indices: 133754--133781 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
133744 ATTTTATGTT
133754 TTAAATTATTTTAA
1 TTAAATTATTTTAA
133768 TTAAATTATTTTAA
1 TTAAATTATTTTAA
133782 AAAACCTATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (14 bp):
TTAAATTATTTTAA
Found at i:138578 original size:2 final size:2
Alignment explanation
Indices: 138571--138609 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
138561 TTGAACAATA
138571 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
138610 AGTTCAAGAG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:139311 original size:2 final size:2
Alignment explanation
Indices: 139304--139340 Score: 56
Period size: 2 Copynumber: 18.5 Consensus size: 2
139294 TTGTTTCATT
* *
139304 TA TA TA TA TG TA TA TA TA TA TA TA TA TA TT TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
139341 TTGTATCATA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.54
Consensus pattern (2 bp):
TA
Found at i:139319 original size:10 final size:10
Alignment explanation
Indices: 139304--139351 Score: 60
Period size: 10 Copynumber: 4.7 Consensus size: 10
139294 TTGTTTCATT
139304 TATATATATG
1 TATATATATG
*
139314 TATATATATA
1 TATATATATG
*
139324 TATATATATT
1 TATATATATG
*
139334 TATATATTTG
1 TATATATATG
139344 TATCATAT
1 TAT-ATAT
139352 TAATGTTTAG
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
10 29 0.88
11 4 0.12
ACGTcount: A:0.40, C:0.02, G:0.04, T:0.54
Consensus pattern (10 bp):
TATATATATG
Found at i:140090 original size:14 final size:14
Alignment explanation
Indices: 140071--140099 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
140061 TTTGAAGTAT
140071 CTATGTTTGATATA
1 CTATGTTTGATATA
140085 CTATGTTTGATATA
1 CTATGTTTGATATA
140099 C
1 C
140100 GTGTATGACA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.28, C:0.10, G:0.14, T:0.48
Consensus pattern (14 bp):
CTATGTTTGATATA
Found at i:143061 original size:13 final size:12
Alignment explanation
Indices: 143041--143078 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
143031 ATTTGACATA
*
143041 TAAATTTTCAAT
1 TAAATTTTTAAT
143053 TAAATTTTT-AT
1 TAAATTTTTAAT
143064 TAATATTTTTAAT
1 TAA-ATTTTTAAT
143077 TA
1 TA
143079 TTTTTGATTA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
11 5 0.22
12 14 0.61
13 4 0.17
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.58
Consensus pattern (12 bp):
TAAATTTTTAAT
Found at i:144513 original size:62 final size:62
Alignment explanation
Indices: 144437--144561 Score: 250
Period size: 62 Copynumber: 2.0 Consensus size: 62
144427 AAGGATCATT
144437 GAGAAAACCTAGCATTTTTGGTTAAAATGGTCATTTCTAACATTAAATTTCCCCTATATAGG
1 GAGAAAACCTAGCATTTTTGGTTAAAATGGTCATTTCTAACATTAAATTTCCCCTATATAGG
144499 GAGAAAACCTAGCATTTTTGGTTAAAATGGTCATTTCTAACATTAAATTTCCCCTATATAGG
1 GAGAAAACCTAGCATTTTTGGTTAAAATGGTCATTTCTAACATTAAATTTCCCCTATATAGG
144561 G
1 G
144562 CATTATGAGT
Statistics
Matches: 63, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
62 63 1.00
ACGTcount: A:0.34, C:0.16, G:0.15, T:0.35
Consensus pattern (62 bp):
GAGAAAACCTAGCATTTTTGGTTAAAATGGTCATTTCTAACATTAAATTTCCCCTATATAGG
Found at i:148392 original size:19 final size:19
Alignment explanation
Indices: 148368--148430 Score: 75
Period size: 19 Copynumber: 3.6 Consensus size: 19
148358 AAACAGTAAC
148368 TGTATCGATACATAAGTGT
1 TGTATCGATACATAAGTGT
148387 TGTATCGATAC--AA----
1 TGTATCGATACATAAGTGT
*
148400 TGCATCGATACATAAGTGT
1 TGTATCGATACATAAGTGT
148419 TGTATCGATACA
1 TGTATCGATACA
148431 ATGTATCACT
Statistics
Matches: 36, Mismatches: 2, Indels: 12
0.72 0.04 0.24
Matches are distributed among these distances:
13 10 0.28
15 2 0.06
17 2 0.06
19 22 0.61
ACGTcount: A:0.33, C:0.14, G:0.19, T:0.33
Consensus pattern (19 bp):
TGTATCGATACATAAGTGT
Found at i:148412 original size:32 final size:32
Alignment explanation
Indices: 148371--148433 Score: 126
Period size: 32 Copynumber: 2.0 Consensus size: 32
148361 CAGTAACTGT
148371 ATCGATACATAAGTGTTGTATCGATACAATGC
1 ATCGATACATAAGTGTTGTATCGATACAATGC
148403 ATCGATACATAAGTGTTGTATCGATACAATG
1 ATCGATACATAAGTGTTGTATCGATACAATG
148434 TATCACTACA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.35, C:0.14, G:0.19, T:0.32
Consensus pattern (32 bp):
ATCGATACATAAGTGTTGTATCGATACAATGC
Found at i:162365 original size:19 final size:18
Alignment explanation
Indices: 162336--162390 Score: 65
Period size: 18 Copynumber: 3.0 Consensus size: 18
162326 GCGTCCTCCG
**
162336 CAAAAAAAAAAAATGAAA
1 CAAAAAAAAAAAAACAAA
162354 CAAAACAAAAAAAAACAAA
1 CAAAA-AAAAAAAAACAAA
* *
162373 CAAAAAAACAACAACAAA
1 CAAAAAAAAAAAAACAAA
162391 AAGGGTCCGA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
18 16 0.50
19 16 0.50
ACGTcount: A:0.82, C:0.15, G:0.02, T:0.02
Consensus pattern (18 bp):
CAAAAAAAAAAAAACAAA
Found at i:162373 original size:14 final size:14
Alignment explanation
Indices: 162351--162392 Score: 59
Period size: 14 Copynumber: 2.9 Consensus size: 14
162341 AAAAAAAATG
162351 AAACAAAACAAAAAA
1 AAAC-AAACAAAAAA
162366 AAACAAACAAAAAA
1 AAACAAACAAAAAA
162380 ACAAC-AACAAAAA
1 A-AACAAACAAAAA
162393 GGGTCCGAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
14 19 0.73
15 7 0.27
ACGTcount: A:0.83, C:0.17, G:0.00, T:0.00
Consensus pattern (14 bp):
AAACAAACAAAAAA
Found at i:162377 original size:12 final size:11
Alignment explanation
Indices: 162355--162392 Score: 51
Period size: 12 Copynumber: 3.4 Consensus size: 11
162345 AAAATGAAAC
162355 AAAACAA-AAA
1 AAAACAACAAA
162365 AAAACAAACAAA
1 AAAAC-AACAAA
162377 AAAACAACAACA
1 AAAACAACAA-A
162389 AAAA
1 AAAA
162393 GGGTCCGAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
10 5 0.20
11 7 0.28
12 13 0.52
ACGTcount: A:0.84, C:0.16, G:0.00, T:0.00
Consensus pattern (11 bp):
AAAACAACAAA
Found at i:163864 original size:28 final size:28
Alignment explanation
Indices: 163824--163906 Score: 148
Period size: 28 Copynumber: 3.0 Consensus size: 28
163814 CATTCCTCAC
163824 CCTTCAAAAGCCCACAAGTCAGTGGCAA
1 CCTTCAAAAGCCCACAAGTCAGTGGCAA
*
163852 CCTTCAAAAGCCCACAAGTTAGTGGCAA
1 CCTTCAAAAGCCCACAAGTCAGTGGCAA
*
163880 CCTTCAAAAGCCCACAAGTCCGTGGCA
1 CCTTCAAAAGCCCACAAGTCAGTGGCA
163907 TTTTTTTCCT
Statistics
Matches: 52, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
28 52 1.00
ACGTcount: A:0.34, C:0.33, G:0.18, T:0.16
Consensus pattern (28 bp):
CCTTCAAAAGCCCACAAGTCAGTGGCAA
Found at i:163952 original size:32 final size:32
Alignment explanation
Indices: 163887--163976 Score: 108
Period size: 32 Copynumber: 2.8 Consensus size: 32
163877 CAACCTTCAA
* **
163887 AAGCCCACAAGTCCGTGGCATTTTTTTCCTTTT
1 AAGCCCACAACTCCGTGGCA-CCTTTTCCTTTT
*
163920 AAGCCCACAACTCCGTGGCACCTTTTCTTTTT
1 AAGCCCACAACTCCGTGGCACCTTTTCCTTTT
* * *
163952 AAGTCCATAACTCTGTGGCACCTTT
1 AAGCCCACAACTCCGTGGCACCTTT
163977 AAACCCAACA
Statistics
Matches: 50, Mismatches: 7, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
32 31 0.62
33 19 0.38
ACGTcount: A:0.20, C:0.30, G:0.14, T:0.36
Consensus pattern (32 bp):
AAGCCCACAACTCCGTGGCACCTTTTCCTTTT
Found at i:164058 original size:75 final size:75
Alignment explanation
Indices: 163935--164174 Score: 399
Period size: 75 Copynumber: 3.2 Consensus size: 75
163925 CACAACTCCG
*
163935 TGGCACCTTTTCTTTTTAAGTCCATAACTCTGTGGCACCTTTAAACCCAACATCGCTGGCCTTGA
1 TGGCACCTTTTCTTTTTAAGTCCATAACTCCGTGGCACCTTTAAACCCAACATCGCTGGCCTTGA
164000 ATCAGCATAT
66 ATCAGCATAT
*
164010 TGGCACCTTTTCTTTTTAAGTCCATAACTCCGTGGCACCTTTAAACCCAACATCGCTGGCCTTAA
1 TGGCACCTTTTCTTTTTAAGTCCATAACTCCGTGGCACCTTTAAACCCAACATCGCTGGCCTTGA
164075 ATCAGCATAT
66 ATCAGCATAT
* * * * * *
164085 TGGCACATTTTCTTTTTAAGTCCACAACTTCTTGGCACCTTTAAGCCCAATATCGCTGGCCTTGA
1 TGGCACCTTTTCTTTTTAAGTCCATAACTCCGTGGCACCTTTAAACCCAACATCGCTGGCCTTGA
164150 ATCAGCATAT
66 ATCAGCATAT
*
164160 TGGCACCTTGTCTTT
1 TGGCACCTTTTCTTT
164175 AAGACCAATG
Statistics
Matches: 154, Mismatches: 11, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
75 154 1.00
ACGTcount: A:0.23, C:0.28, G:0.15, T:0.34
Consensus pattern (75 bp):
TGGCACCTTTTCTTTTTAAGTCCATAACTCCGTGGCACCTTTAAACCCAACATCGCTGGCCTTGA
ATCAGCATAT
Found at i:164183 original size:48 final size:48
Alignment explanation
Indices: 164123--164353 Score: 264
Period size: 48 Copynumber: 5.0 Consensus size: 48
164113 TTCTTGGCAC
*
164123 CTTTAAGCCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTGT
1 CTTTAAGACCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTGT
* * *
164171 CTTTAAGACCAATGTCGCTGCCCTTGAATCAGCACATTGGCA------
1 CTTTAAGACCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTGT
* *
164213 ---TAAGCCCAATATCACTGGCCTTGAATCAGCATATTGGCACCTTGT
1 CTTTAAGACCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTGT
* * * *
164258 TTTTAAGACCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTCAT
1 CTTTAAGACCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTT-GT
* * *
164307 CTTTAAGACCGATATCGTTGGCCTTGAATCAACATATTGGCATCCTT
1 CTTTAAGACCAATATCGCTGGCCTTGAATCAGCATATTGGCA-CCTT
164354 AACATTCCTA
Statistics
Matches: 152, Mismatches: 20, Indels: 20
0.79 0.10 0.10
Matches are distributed among these distances:
39 34 0.22
48 77 0.51
49 37 0.24
50 4 0.03
ACGTcount: A:0.25, C:0.26, G:0.18, T:0.30
Consensus pattern (48 bp):
CTTTAAGACCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTGT
Found at i:164235 original size:39 final size:39
Alignment explanation
Indices: 164174--164251 Score: 111
Period size: 39 Copynumber: 2.0 Consensus size: 39
164164 ACCTTGTCTT
* *
164174 TAAGACCAATGTCGCTGCCCTTGAATCAGCACATTGGCA
1 TAAGACCAATATCACTGCCCTTGAATCAGCACATTGGCA
* * *
164213 TAAGCCCAATATCACTGGCCTTGAATCAGCATATTGGCA
1 TAAGACCAATATCACTGCCCTTGAATCAGCACATTGGCA
164252 CCTTGTTTTT
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
39 34 1.00
ACGTcount: A:0.29, C:0.27, G:0.19, T:0.24
Consensus pattern (39 bp):
TAAGACCAATATCACTGCCCTTGAATCAGCACATTGGCA
Found at i:164272 original size:87 final size:87
Alignment explanation
Indices: 164126--164299 Score: 321
Period size: 87 Copynumber: 2.0 Consensus size: 87
164116 TTGGCACCTT
*
164126 TAAGCCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTGTCTTTAAGACCAATGTCGCTG
1 TAAGCCCAATATCACTGGCCTTGAATCAGCATATTGGCACCTTGTCTTTAAGACCAATGTCGCTG
164191 CCCTTGAATCAGCACATTGGCA
66 CCCTTGAATCAGCACATTGGCA
*
164213 TAAGCCCAATATCACTGGCCTTGAATCAGCATATTGGCACCTTGTTTTTAAGACCAATGTCGCTG
1 TAAGCCCAATATCACTGGCCTTGAATCAGCATATTGGCACCTTGTCTTTAAGACCAATGTCGCTG
*
164278 GCCTTGAATCAGCACATTGGCA
66 CCCTTGAATCAGCACATTGGCA
164300 CCTTCATCTT
Statistics
Matches: 84, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
87 84 1.00
ACGTcount: A:0.26, C:0.26, G:0.20, T:0.28
Consensus pattern (87 bp):
TAAGCCCAATATCACTGGCCTTGAATCAGCATATTGGCACCTTGTCTTTAAGACCAATGTCGCTG
CCCTTGAATCAGCACATTGGCA
Found at i:165217 original size:19 final size:19
Alignment explanation
Indices: 165193--165255 Score: 75
Period size: 19 Copynumber: 3.6 Consensus size: 19
165183 AAACAGTAAC
165193 TGTATCGATACATAAGTGT
1 TGTATCGATACATAAGTGT
165212 TGTATCGATAC--AA----
1 TGTATCGATACATAAGTGT
165225 TGTATCGATACATAAGTGT
1 TGTATCGATACATAAGTGT
*
165244 TGTATCCATACA
1 TGTATCGATACA
165256 ATGTATCACT
Statistics
Matches: 37, Mismatches: 1, Indels: 12
0.74 0.02 0.24
Matches are distributed among these distances:
13 11 0.30
15 2 0.05
17 2 0.05
19 22 0.59
ACGTcount: A:0.33, C:0.14, G:0.17, T:0.35
Consensus pattern (19 bp):
TGTATCGATACATAAGTGT
Found at i:165230 original size:13 final size:13
Alignment explanation
Indices: 165212--165236 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
165202 ACATAAGTGT
165212 TGTATCGATACAA
1 TGTATCGATACAA
165225 TGTATCGATACA
1 TGTATCGATACA
165237 TAAGTGTTGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:165234 original size:32 final size:32
Alignment explanation
Indices: 165193--165262 Score: 131
Period size: 32 Copynumber: 2.2 Consensus size: 32
165183 AAACAGTAAC
*
165193 TGTATCGATACATAAGTGTTGTATCGATACAA
1 TGTATCGATACATAAGTGTTGTATCCATACAA
165225 TGTATCGATACATAAGTGTTGTATCCATACAA
1 TGTATCGATACATAAGTGTTGTATCCATACAA
165257 TGTATC
1 TGTATC
165263 ACTACAAAGC
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 37 1.00
ACGTcount: A:0.33, C:0.14, G:0.17, T:0.36
Consensus pattern (32 bp):
TGTATCGATACATAAGTGTTGTATCCATACAA
Found at i:169532 original size:20 final size:19
Alignment explanation
Indices: 169507--169622 Score: 55
Period size: 20 Copynumber: 6.1 Consensus size: 19
169497 CATTTTATAC
*
169507 TTGCATCCACGTTACATGCT
1 TTGCATCCACATT-CATGCT
169527 TTGCAT-CATCATTTCATGCT
1 TTGCATCCA-CA-TTCATGCT
* *
169547 TT-CA-CAACCTTCATGCT
1 TTGCATCCACATTCATGCT
169564 TTGCAT-CATCATTTCATG-T
1 TTGCATCCA-CA-TTCATGCT
* * * *
169583 TTTCA-CAACTTTCATACT
1 TTGCATCCACATTCATGCT
**
169601 TTGCATCTTCATTTCATGCT
1 TTGCATCCACA-TTCATGCT
169621 TT
1 TT
169623 CACAACTTTC
Statistics
Matches: 71, Mismatches: 14, Indels: 22
0.66 0.13 0.21
Matches are distributed among these distances:
17 15 0.21
18 10 0.14
19 14 0.20
20 30 0.42
21 2 0.03
ACGTcount: A:0.21, C:0.27, G:0.09, T:0.44
Consensus pattern (19 bp):
TTGCATCCACATTCATGCT
Found at i:169537 original size:39 final size:37
Alignment explanation
Indices: 169494--169634 Score: 138
Period size: 37 Copynumber: 3.8 Consensus size: 37
169484 TTGTTTGCTG
* * *
169494 CATCATTTTATACTTGCATCCACGTTACATGCTTTGCAT
1 CATCATTTCATACTTGCA-CAACCTT-CATGCTTTGCAT
* *
169533 CATCATTTCATGCTTTCACAACCTTCATGCTTTGCAT
1 CATCATTTCATACTTGCACAACCTTCATGCTTTGCAT
** * * *
169570 CATCATTTCATGTTTTCACAACTTTCATACTTTGCAT
1 CATCATTTCATACTTGCACAACCTTCATGCTTTGCAT
* * * *
169607 CTTCATTTCATGCTTTCACAACTTTCAT
1 CATCATTTCATACTTGCACAACCTTCAT
169635 TCATTCATCA
Statistics
Matches: 92, Mismatches: 10, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
37 72 0.78
38 5 0.05
39 15 0.16
ACGTcount: A:0.23, C:0.27, G:0.07, T:0.43
Consensus pattern (37 bp):
CATCATTTCATACTTGCACAACCTTCATGCTTTGCAT
Found at i:169569 original size:37 final size:37
Alignment explanation
Indices: 169521--169634 Score: 192
Period size: 37 Copynumber: 3.1 Consensus size: 37
169511 ATCCACGTTA
*
169521 CATGCTTTGCATCATCATTTCATGCTTTCACAACCTT
1 CATGCTTTGCATCATCATTTCATGCTTTCACAACTTT
*
169558 CATGCTTTGCATCATCATTTCATGTTTTCACAACTTT
1 CATGCTTTGCATCATCATTTCATGCTTTCACAACTTT
* *
169595 CATACTTTGCATCTTCATTTCATGCTTTCACAACTTT
1 CATGCTTTGCATCATCATTTCATGCTTTCACAACTTT
169632 CAT
1 CAT
169635 TCATTCATCA
Statistics
Matches: 72, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
37 72 1.00
ACGTcount: A:0.22, C:0.27, G:0.07, T:0.44
Consensus pattern (37 bp):
CATGCTTTGCATCATCATTTCATGCTTTCACAACTTT
Found at i:169680 original size:24 final size:26
Alignment explanation
Indices: 169646--169700 Score: 69
Period size: 24 Copynumber: 2.2 Consensus size: 26
169636 CATTCATCAT
*
169646 TTTTTTTATTTTTGATAA-TT-TTGA
1 TTTTTTGATTTTTGATAATTTCTTGA
**
169670 TTTTTTGATTTTTTTTAATTTCTTGA
1 TTTTTTGATTTTTGATAATTTCTTGA
169696 TTTTT
1 TTTTT
169701 AATTTTTTTA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
24 15 0.58
25 2 0.08
26 9 0.35
ACGTcount: A:0.16, C:0.02, G:0.07, T:0.75
Consensus pattern (26 bp):
TTTTTTGATTTTTGATAATTTCTTGA
Found at i:169683 original size:26 final size:25
Alignment explanation
Indices: 169666--169714 Score: 73
Period size: 24 Copynumber: 2.0 Consensus size: 25
169656 TTTGATAATT
*
169666 TTGATTTTTTGATTTTTTTTAATTTC
1 TTGA-TTTTTAATTTTTTTTAATTTC
169692 TTGATTTTTAA-TTTTTTTAATTT
1 TTGATTTTTAATTTTTTTTAATTT
169715 TTATCATTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 12 0.55
25 6 0.27
26 4 0.18
ACGTcount: A:0.18, C:0.02, G:0.06, T:0.73
Consensus pattern (25 bp):
TTGATTTTTAATTTTTTTTAATTTC
Found at i:169685 original size:18 final size:17
Alignment explanation
Indices: 169644--169751 Score: 69
Period size: 18 Copynumber: 6.4 Consensus size: 17
169634 TTCATTCATC
169644 ATTTTTTTTA-TTTTTG
1 ATTTTTTTTATTTTTTG
** *
169660 ATAATTTTGATTTTTTG
1 ATTTTTTTTATTTTTTG
*
169677 ATTTTTTTTAATTTCTTG
1 ATTTTTTTT-ATTTTTTG
** *
169695 ATTTTTAAT-TTTTTTA
1 ATTTTTTTTATTTTTTG
* * *
169711 ATTTTTATCATTATGTT-
1 ATTTTTTTTATT-TTTTG
*
169728 ATTATTTTTTATTTTATG
1 ATT-TTTTTTATTTTTTG
169746 ATTTTT
1 ATTTTT
169752 CCAAACAAAT
Statistics
Matches: 68, Mismatches: 18, Indels: 11
0.70 0.19 0.11
Matches are distributed among these distances:
16 19 0.28
17 22 0.32
18 27 0.40
ACGTcount: A:0.20, C:0.02, G:0.06, T:0.72
Consensus pattern (17 bp):
ATTTTTTTTATTTTTTG
Found at i:169686 original size:33 final size:33
Alignment explanation
Indices: 169644--169708 Score: 89
Period size: 33 Copynumber: 2.0 Consensus size: 33
169634 TTCATTCATC
*
169644 ATTTTTTTT-ATTT-TTGATAATTTTGATTTTTTG
1 ATTTTTTTTAATTTCTTGAT--TTTTAATTTTTTG
169677 ATTTTTTTTAATTTCTTGATTTTTAATTTTTT
1 ATTTTTTTTAATTTCTTGATTTTTAATTTTTT
169709 TAATTTTTAT
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
33 20 0.69
34 4 0.14
35 5 0.17
ACGTcount: A:0.18, C:0.02, G:0.06, T:0.74
Consensus pattern (33 bp):
ATTTTTTTTAATTTCTTGATTTTTAATTTTTTG
Found at i:170730 original size:42 final size:41
Alignment explanation
Indices: 170681--171589 Score: 524
Period size: 42 Copynumber: 21.5 Consensus size: 41
170671 AAGGTCCTTG
* *
170681 GGTCAAAGCCGACAAGCAAACTTTAGATGAGGCAGTCTCCA
1 GGTCAAAGCCGACAGGCAGACTTTAGATGAGGCAGTCTCCA
* * * **
170722 GGTTCAAAGCCAACAGGCAGAC-TGAG-GGTAGAAAAGTCTCCAA
1 GG-TCAAAGCCGACAGGCAGACTTTAGATG-AG-GCAGTCTCC-A
* * * * *
170765 GGTCAAAGCCGATAGGCAGACCTTAGATAAGGTATTCTCCA
1 GGTCAAAGCCGACAGGCAGACTTTAGATGAGGCAGTCTCCA
* * * *
170806 GGGTCAAAGCCAACAGACAGACTTTAGATGAAGCAGTCTTCAA
1 -GGTCAAAGCCGACAGGCAGACTTTAGATGAGGCAGTC-TCCA
** *
170849 GGTCAAAGCCGACAGGCAGACTGAAGAAT-AGGAATGTCTCCA
1 GGTCAAAGCCGACAGGCAGACTTTAG-ATGAGGCA-GTCTCCA
* * * *
170891 GGGTTAAAGCTGACAGGCAGAATTTAGATGAGGCAGTCTTCA
1 -GGTCAAAGCCGACAGGCAGACTTTAGATGAGGCAGTCTCCA
* * * ** *
170933 GGGTCAAAGTCGATAGGCAAACTGAAAGAT-AGGAAAGTCTCCA
1 -GGTCAAAGCCGACAGGCAGACT-TTAGATGAGG-CAGTCTCCA
* *
170976 GGGTCAAAGTCGACAGGCAGACTTTAGATGAGGCAATCTCCA
1 -GGTCAAAGCCGACAGGCAGACTTTAGATGAGGCAGTCTCCA
* ** * * *
171018 GGGTCAAAACCGACAGGCAGACTGAAG-GGTAGGAAAGTCTTCA
1 -GGTCAAAGCCGACAGGCAGACTTTAGATG-AGG-CAGTCTCCA
* ** * *
171061 GGGTTAAATTCGACAAGCAGACTTTAGATGAGGCAGTCTTCA
1 -GGTCAAAGCCGACAGGCAGACTTTAGATGAGGCAGTCTCCA
* * **
171103 GAGTCAAAGCCGACAGGCAGAC-TGAG-GGTAGAAAAGTCTCCAA
1 G-GTCAAAGCCGACAGGCAGACTTTAGATG-AG-GCAGTCTCC-A
* * * * * * * *
171146 GGTCAAAGCCAATAGGTAGACCTTAAATAAGGCAGCCTCTA
1 GGTCAAAGCCGACAGGCAGACTTTAGATGAGGCAGTCTCCA
* * * * *
171187 GGGTCAAAGCCGACAGGAAGACCTTAGATAAAGCAGTCTCTAA
1 -GGTCAAAGCCGACAGGCAGACTTTAGATGAGGCAGTCTC-CA
* * ** **
171230 GGTCAAAGCTGATAGATAGACTTTAGATGAGGCAGTCTTTA
1 GGTCAAAGCCGACAGGCAGACTTTAGATGAGGCAGTCTCCA
** * **
171271 GGGTCAAAGCCGACAGGCAGACTGAAGGAT-AGGTAAGTCTTTA
1 -GGTCAAAGCCGACAGGCAGACTTTA-GATGAGG-CAGTCTCCA
* * * *
171314 GCGTCAAAGTCGACAAGCAGACTTTAGATGAGGTAGTCTCTA
1 G-GTCAAAGCCGACAGGCAGACTTTAGATGAGGCAGTCTCCA
* * * * * * *
171356 GAGTCAAAGTCGACAAGTAGACTGATGGAT-AGGAAAGTCTCTA
1 G-GTCAAAGCCGACAGGCAGACT-TTAGATGAGG-CAGTCTCCA
* * *
171399 GGATCAAAGCTGACAGGTAGACTTTAGATGAGGCAGTCTTCA
1 GG-TCAAAGCCGACAGGCAGACTTTAGATGAGGCAGTCTCCA
** * * ** *
171441 GGGTCAAAGCCGACAGGCAGACTGAAGGGTAAGAAAGTCTCTAA
1 -GGTCAAAGCCGACAGGCAGACTTTA-GATGAGGCAGTCTC-CA
* *
171485 GGTCAAAGCTGACAGGCAGACTTTAGATAAGGCAGTCTCCAA
1 GGTCAAAGCCGACAGGCAGACTTTAGATGAGGCAGTCTCC-A
** * *
171527 GGTCAAAGCCGACAGGCAGACTAAAAGAT-AGGAAAGTCTCTA
1 GGTCAAAGCCGACAGGCAGACT-TTAGATGAGG-CAGTCTCCA
*
171569 GAATCAAAGCCGACAGGCAGA
1 G-GTCAAAGCCGACAGGCAGA
171590 TTGAAGGGTA
Statistics
Matches: 671, Mismatches: 155, Indels: 82
0.74 0.17 0.09
Matches are distributed among these distances:
40 2 0.00
41 17 0.03
42 409 0.61
43 241 0.36
44 2 0.00
ACGTcount: A:0.35, C:0.19, G:0.28, T:0.18
Consensus pattern (41 bp):
GGTCAAAGCCGACAGGCAGACTTTAGATGAGGCAGTCTCCA
Found at i:170776 original size:84 final size:84
Alignment explanation
Indices: 170681--171032 Score: 223
Period size: 85 Copynumber: 4.2 Consensus size: 84
170671 AAGGTCCTTG
* * * *
170681 GGTCAAAGCCGACAAGCAAACTTTAGATGAGGCAGTCTCCAGGTTCAAAGCCAACAGGCAGAC-T
1 GGTCAAAGCCGACAAGCAAACCTTAGATAAGGCAGTCTCCAGGGTCAAAGCCAACAGACAGACTT
*
170745 GAGGGTAGAA-AAGTCTCCAA
66 GA-GAT-GAAGAAGTCTCCAA
* * * * *
170765 GGTCAAAGCCGATAGGCAGACCTTAGATAAGGTATTCTCCAGGGTCAAAGCCAACAGACAGACTT
1 GGTCAAAGCCGACAAGCAAACCTTAGATAAGGCAGTCTCCAGGGTCAAAGCCAACAGACAGACTT
* * *
170830 TAGATGAAGCAGTCTTCAA
66 GAGATGAAGAAGTCTCCAA
* * * * * ** *
170849 GGTCAAAGCCGACAGGCAGA-CTGAAGA-ATAGGAATGTCTCCAGGGTTAAAGCTGACAGGCAGA
1 GGTCAAAGCCGACAAGCAAACCT-TAGATA-AGGCA-GTCTCCAGGGTCAAAGCCAACAGACAGA
* * * * * *
170912 ATTTAGATGAGGCAGTCTTCAG
63 CTTGAGATGAAGAAGTCTCCAA
* * * * * * * *
170934 GGTCAAAGTCGATAGGCAAA-CTGAAAGAT-AGGAAAGTCTCCAGGGTCAAAGTCGACAGGCAGA
1 GGTCAAAGCCGACAAGCAAACCT--TAGATAAGG-CAGTCTCCAGGGTCAAAGCCAACAGACAGA
* * *
170997 CTTTAGATGAGGCAA-TCTCCAG
63 CTTGAGATGAAG-AAGTCTCCAA
*
171019 GGTCAAAACCGACA
1 GGTCAAAGCCGACA
171033 GGCAGACTGA
Statistics
Matches: 222, Mismatches: 37, Indels: 17
0.80 0.13 0.06
Matches are distributed among these distances:
83 6 0.03
84 90 0.41
85 119 0.54
86 7 0.03
ACGTcount: A:0.35, C:0.20, G:0.27, T:0.18
Consensus pattern (84 bp):
GGTCAAAGCCGACAAGCAAACCTTAGATAAGGCAGTCTCCAGGGTCAAAGCCAACAGACAGACTT
GAGATGAAGAAGTCTCCAA
Found at i:170927 original size:85 final size:85
Alignment explanation
Indices: 170756--171589 Score: 796
Period size: 85 Copynumber: 9.8 Consensus size: 85
170746 AGGGTAGAAA
* * * * * **
170756 AGTCTCCAAGGTCAAAGCCGATAGGCAGACCT-TA-GATAAGG-TATTCTCCAGGGTCAAAGCCA
1 AGTCTTCAAGGTCAAAGCCGACAGGCAGA-CTGAAGGAT-AGGAAAGTCTCCAGGGTCAAAGCTG
* *
170818 ACAGACAGACTTTAGATGAAGC
64 ACAGGCAGACTTTAGATGAGGC
* * *
170840 AGTCTTCAAGGTCAAAGCCGACAGGCAGACTGAAGAATAGGAATGTCTCCAGGGTTAAAGCTGAC
1 AGTCTTCAAGGTCAAAGCCGACAGGCAGACTGAAGGATAGGAAAGTCTCCAGGGTCAAAGCTGAC
*
170905 AGGCAGAATTTAGATGAGGC
66 AGGCAGACTTTAGATGAGGC
* * * * *
170925 AGTCTTCAGGGTCAAAGTCGATAGGCAAACTGAAAGATAGGAAAGTCTCCAGGGTCAAAG-TCGA
1 AGTCTTCAAGGTCAAAGCCGACAGGCAGACTGAAGGATAGGAAAGTCTCCAGGGTCAAAGCT-GA
170989 CAGGCAGACTTTAGATGAGGC
65 CAGGCAGACTTTAGATGAGGC
* * * * * * * *
171010 AATCTCCAGGGTCAAAACCGACAGGCAGACTGAAGGGTAGGAAAGTCTTCAGGGTTAAA-TTCGA
1 AGTCTTCAAGGTCAAAGCCGACAGGCAGACTGAAGGATAGGAAAGTCTCCAGGGTCAAAGCT-GA
*
171074 CAAGCAGACTTTAGATGAGGC
65 CAGGCAGACTTTAGATGAGGC
* * * **
171095 AGTCTTC-AGAGTCAAAGCCGACAGGCAGACTG-AGGGTAGAAAAGTCTCCAAGGTCAAAGCCAA
1 AGTCTTCAAG-GTCAAAGCCGACAGGCAGACTGAAGGATAGGAAAGTCTCCAGGGTCAAAGCTGA
* * * * *
171158 TAGGTAGACCTTAAATAAGGC
65 CAGGCAGACTTTAGATGAGGC
* * * * * *
171179 AG-CCTCTAGGGTCAAAGCCGACAGGAAGACCT-TA-GATA--AAGCAGTCTCTAAGGTCAAAGC
1 AGTCTTC-AAGGTCAAAGCCGACAGGCAGA-CTGAAGGATAGGAA--AGTCTCCAGGGTCAAAGC
* **
171239 TGATAGATAGACTTTAGATGAGGC
62 TGACAGGCAGACTTTAGATGAGGC
* * * ** *
171263 AGTCTTTAGGGTCAAAGCCGACAGGCAGACTGAAGGATAGGTAAGTCTTTAGCGTCAAAG-TCGA
1 AGTCTTCAAGGTCAAAGCCGACAGGCAGACTGAAGGATAGGAAAGTCTCCAGGGTCAAAGCT-GA
* *
171327 CAAGCAGACTTTAGATGAGGT
65 CAGGCAGACTTTAGATGAGGC
* * * * * * *
171348 AGTC-TCTAGAGTCAAAGTCGACAAGTAGACTGATGGATAGGAAAGTCTCTAGGATCAAAGCTGA
1 AGTCTTCAAG-GTCAAAGCCGACAGGCAGACTGAAGGATAGGAAAGTCTCCAGGGTCAAAGCTGA
*
171412 CAGGTAGACTTTAGATGAGGC
65 CAGGCAGACTTTAGATGAGGC
* * * * *
171433 AGTCTTCAGGGTCAAAGCCGACAGGCAGACTGAAGGGTAAGAAAGTCTCTAAGGTCAAAGCTGAC
1 AGTCTTCAAGGTCAAAGCCGACAGGCAGACTGAAGGATAGGAAAGTCTCCAGGGTCAAAGCTGAC
*
171498 AGGCAGACTTTAGATAAGGC
66 AGGCAGACTTTAGATGAGGC
* * * * ** *
171518 AGTCTCCAAGGTCAAAGCCGACAGGCAGACTAAAAGATAGGAAAGTCTCTAGAATCAAAGCCGAC
1 AGTCTTCAAGGTCAAAGCCGACAGGCAGACTGAAGGATAGGAAAGTCTCCAGGGTCAAAGCTGAC
171583 AGGCAGA
66 AGGCAGA
171590 TTGAAGGGTA
Statistics
Matches: 618, Mismatches: 110, Indels: 43
0.80 0.14 0.06
Matches are distributed among these distances:
82 2 0.00
83 7 0.01
84 156 0.25
85 448 0.72
86 4 0.01
87 1 0.00
ACGTcount: A:0.35, C:0.19, G:0.28, T:0.19
Consensus pattern (85 bp):
AGTCTTCAAGGTCAAAGCCGACAGGCAGACTGAAGGATAGGAAAGTCTCCAGGGTCAAAGCTGAC
AGGCAGACTTTAGATGAGGC
Found at i:171449 original size:338 final size:339
Alignment explanation
Indices: 170800--171547 Score: 898
Period size: 338 Copynumber: 2.2 Consensus size: 339
170790 GATAAGGTAT
* * * * * *
170800 TCTCCAGGGTCAAAGCCAACAGACAGACTTTAGATGAA-GCAGTCTTCAAGGTCAAAGCCGACAG
1 TCTCCAAGGTCAAAGCCAACAGGCAGACCTTAAAT-AAGGCAGCCTCCAAGGTCAAAGCCGACAG
* * * * * * * * ** *
170864 GCAGA-CTGAAGA-ATAGGAATGTCTCCAGGGTTAAAGCTGACAGGCAGAATTTAGATGAGGCAG
65 GAAGACCT-TAGATA-AAGCA-GTCTCTAAGGTCAAAGCTGATAGATAGACTTTAGATGAGGCAG
* * * *
170927 TCTTCAGGGTCAAAGTCGATAGGCAAACTGAAAGATAGGAAAGTCTCCAGGGTCAAAGTCGACAG
127 TCTTCAGGGTCAAAGCCGACAGGCAAACTGAAAGATAGGAAAGTCTCCAGCGTCAAAGTCGACAA
* * *
170992 GCAGACTTTAGATGAGGCAATCTCCAGGGTCAAAACCGACAGGCAGACTGAAGGGTAGGAAAGTC
192 GCAGACTTTAGATGAGGCAATCTCCAGAGTCAAAACCGACAAGCAGACTGAAGGATAGGAAAGTC
* * *
171057 TTCAGGGTTAAATTCGACAAGCAGACTTTAGATGAGGCAGTCTTCAGAGTCAAAGCCGACAGGCA
257 TTCAGGATCAAACTCGACAAGCAGACTTTAGATGAGGCAGTCTTCAGAGTCAAAGCCGACAGGCA
171122 GACTG-AGGGT-AGAAAAG
322 GACTGAAGGGTAAG-AAAG
* * * *
171139 TCTCCAAGGTCAAAGCCAATAGGTAGACCTTAAATAAGGCAGCCTCTAGGGTCAAAGCCGACAGG
1 TCTCCAAGGTCAAAGCCAACAGGCAGACCTTAAATAAGGCAGCCTCCAAGGTCAAAGCCGACAGG
171204 AAGACCTTAGATAAAGCAGTCTCTAAGGTCAAAGCTGATAGATAGACTTTAGATGAGGCAGTCTT
66 AAGACCTTAGATAAAGCAGTCTCTAAGGTCAAAGCTGATAGATAGACTTTAGATGAGGCAGTCTT
* * * * **
171269 TAGGGTCAAAGCCGACAGGCAGACTGAAGGATAGGTAAGTCTTTAGCGTCAAAGTCGACAAGCAG
131 CAGGGTCAAAGCCGACAGGCAAACTGAAAGATAGGAAAGTCTCCAGCGTCAAAGTCGACAAGCAG
* * * ** * *
171334 ACTTTAGATGAGGTAGTCTCTAGAGTCAAAGTCGACAAGTAGACTGATGGATAGGAAAGTC-TCT
196 ACTTTAGATGAGGCAATCTCCAGAGTCAAAACCGACAAGCAGACTGAAGGATAGGAAAGTCTTC-
* * *
171398 AGGATCAAAGCT-GACAGGTAGACTTTAGATGAGGCAGTCTTCAGGGTCAAAGCCGACAGGCAGA
260 AGGATCAAA-CTCGACAAGCAGACTTTAGATGAGGCAGTCTTCAGAGTCAAAGCCGACAGGCAGA
171462 CTGAAGGGTAAGAAAG
324 CTGAAGGGTAAGAAAG
* ** * * *
171478 TCTCTAAGGTCAAAGCTGACAGGCAGACTTTAGATAAGGCAGTCTCCAAGGTCAAAGCCGACAGG
1 TCTCCAAGGTCAAAGCCAACAGGCAGACCTTAAATAAGGCAGCCTCCAAGGTCAAAGCCGACAGG
*
171543 CAGAC
66 AAGAC
171548 TAAAAGATAG
Statistics
Matches: 344, Mismatches: 58, Indels: 14
0.83 0.14 0.03
Matches are distributed among these distances:
337 2 0.01
338 207 0.60
339 130 0.38
340 5 0.01
ACGTcount: A:0.34, C:0.19, G:0.28, T:0.19
Consensus pattern (339 bp):
TCTCCAAGGTCAAAGCCAACAGGCAGACCTTAAATAAGGCAGCCTCCAAGGTCAAAGCCGACAGG
AAGACCTTAGATAAAGCAGTCTCTAAGGTCAAAGCTGATAGATAGACTTTAGATGAGGCAGTCTT
CAGGGTCAAAGCCGACAGGCAAACTGAAAGATAGGAAAGTCTCCAGCGTCAAAGTCGACAAGCAG
ACTTTAGATGAGGCAATCTCCAGAGTCAAAACCGACAAGCAGACTGAAGGATAGGAAAGTCTTCA
GGATCAAACTCGACAAGCAGACTTTAGATGAGGCAGTCTTCAGAGTCAAAGCCGACAGGCAGACT
GAAGGGTAAGAAAG
Found at i:171468 original size:423 final size:423
Alignment explanation
Indices: 170765--171548 Score: 1078
Period size: 423 Copynumber: 1.9 Consensus size: 423
170755 AAGTCTCCAA
* * * * * *
170765 GGTCAAAGCCGATAGGCAGACCTTAGATAAGGTATTCTCCAGGGTCAAAGCCAACAGACAGACTT
1 GGTCAAAGCCGACAGGAAGACCTTAGATAAAGCAGTCTCCAAGGTCAAAGCCAACAGACAGACTT
*
170830 TAGATGAAGCAGTCTTCAAGGTCAAAGCCGACAGGCAGACTGAAGAATAGGAATGTCTCCAGGGT
66 TAGATGAAGCAGTCTTCAAGGTCAAAGCCGACAGGCAGACTGAAGAATAGGAATGTCTCCAGCGT
* * * * *
170895 TAAAGCTGACAGGCAGAATTTAGATGAGGCAGTCTTCAGGGTCAAAGTCGATAGGCAAACTGAAA
131 CAAAGCTGACAAGCAGAATTTAGATGAGGCAGTCTTCAGAGTCAAAGTCGACAAGCAAACTGAAA
*
170960 GATAGGAAAGTCTCCAGGGTCAAAGTCGACAGGCAGACTTTAGATGAGGCAATCTCCAGGGTCAA
196 GATAGGAAAGTCTCCAGGATCAAAGTCGACAGGCAGACTTTAGATGAGGCAATCTCCAGGGTCAA
* * * *
171025 AACCGACAGGCAGACTGAAGGGTAGGAAAGTCT-TCAGGGTTAAA-TTCGACAAGCAGACTTTAG
261 AACCGACAGGCAGACTGAAGGGTAAGAAAGTCTCT-AAGGTCAAAGCT-GACAAGCAGACTTTAG
* *
171088 ATGAGGCAGTCTTC-AGAGTCAAAGCCGACAGGCAGACTGAGGGTAGAAAAGTCTCCAAGGTCAA
324 ATAAGGCAGTCTCCAAG-GTCAAAGCCGACAGGCAGACTGAGGGTAGAAAAGTCTCCAAGGTCAA
171152 AGCCAATAGGTAGACCTTAAATAAGGCAGCCTCTAG
388 AGCCAATAGGTAGACCTTAAATAAGGCAGCCTCTAG
* ** * *
171188 GGTCAAAGCCGACAGGAAGACCTTAGATAAAGCAGTCTCTAAGGTCAAAGCTGATAGATAGACTT
1 GGTCAAAGCCGACAGGAAGACCTTAGATAAAGCAGTCTCCAAGGTCAAAGCCAACAGACAGACTT
* * * * **
171253 TAGATGAGGCAGTCTTTAGGGTCAAAGCCGACAGGCAGACTGAAGGATAGGTAA-GTCTTTAGCG
66 TAGATGAAGCAGTCTTCAAGGTCAAAGCCGACAGGCAGACTGAAGAATAGG-AATGTCTCCAGCG
* * * *
171317 TCAAAG-TCGACAAGCAGACTTTAGATGAGGTAGTC-TCTAGAGTCAAAGTCGACAAGTAGACTG
130 TCAAAGCT-GACAAGCAGAATTTAGATGAGGCAGTCTTC-AGAGTCAAAGTCGACAAGCAAACTG
** * * * *
171380 ATGGATAGGAAAGTCTCTAGGATCAAAG-CTGACAGGTAGACTTTAGATGAGGCAGTCTTCAGGG
193 AAAGATAGGAAAGTCTCCAGGATCAAAGTC-GACAGGCAGACTTTAGATGAGGCAATCTCCAGGG
* *
171444 TCAAAGCCGACAGGCAGACTGAAGGGTAAGAAAGTCTCTAAGGTCAAAGCTGACAGGCAGACTTT
257 TCAAAACCGACAGGCAGACTGAAGGGTAAGAAAGTCTCTAAGGTCAAAGCTGACAAGCAGACTTT
171509 AGATAAGGCAGTCTCCAAGGTCAAAGCCGACAGGCAGACT
322 AGATAAGGCAGTCTCCAAGGTCAAAGCCGACAGGCAGACT
171549 AAAAGATAGG
Statistics
Matches: 312, Mismatches: 42, Indels: 14
0.85 0.11 0.04
Matches are distributed among these distances:
422 4 0.01
423 302 0.97
424 6 0.02
ACGTcount: A:0.34, C:0.19, G:0.28, T:0.19
Consensus pattern (423 bp):
GGTCAAAGCCGACAGGAAGACCTTAGATAAAGCAGTCTCCAAGGTCAAAGCCAACAGACAGACTT
TAGATGAAGCAGTCTTCAAGGTCAAAGCCGACAGGCAGACTGAAGAATAGGAATGTCTCCAGCGT
CAAAGCTGACAAGCAGAATTTAGATGAGGCAGTCTTCAGAGTCAAAGTCGACAAGCAAACTGAAA
GATAGGAAAGTCTCCAGGATCAAAGTCGACAGGCAGACTTTAGATGAGGCAATCTCCAGGGTCAA
AACCGACAGGCAGACTGAAGGGTAAGAAAGTCTCTAAGGTCAAAGCTGACAAGCAGACTTTAGAT
AAGGCAGTCTCCAAGGTCAAAGCCGACAGGCAGACTGAGGGTAGAAAAGTCTCCAAGGTCAAAGC
CAATAGGTAGACCTTAAATAAGGCAGCCTCTAG
Found at i:179913 original size:22 final size:23
Alignment explanation
Indices: 179888--179932 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 23
179878 ATTCTTATTA
*
179888 ATTAAGCAAATAATG-ATGAATG
1 ATTAAGAAAATAATGTATGAATG
* *
179910 ATTATGAAAATTATGTATGAATG
1 ATTAAGAAAATAATGTATGAATG
179933 CCACGACTAT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
22 12 0.63
23 7 0.37
ACGTcount: A:0.47, C:0.02, G:0.18, T:0.33
Consensus pattern (23 bp):
ATTAAGAAAATAATGTATGAATG
Found at i:184895 original size:20 final size:19
Alignment explanation
Indices: 184870--184948 Score: 58
Period size: 20 Copynumber: 4.1 Consensus size: 19
184860 CATTTCATAC
*
184870 TTGCATCCACGTTACATGCT
1 TTGCATCCACATT-CATGCT
184890 TTGCAT-CATCATTTCATGCT
1 TTGCATCCA-CA-TTCATGCT
* *
184910 TT-CA-CAACCTTCATGCT
1 TTGCATCCACATTCATGCT
184927 TTGCAT-CATCATTTCATGCT
1 TTGCATCCA-CA-TTCATGCT
184947 TT
1 TT
184949 CAAAACTTTC
Statistics
Matches: 47, Mismatches: 5, Indels: 14
0.71 0.08 0.21
Matches are distributed among these distances:
17 10 0.21
18 4 0.09
19 6 0.13
20 25 0.53
21 2 0.04
ACGTcount: A:0.20, C:0.28, G:0.10, T:0.42
Consensus pattern (19 bp):
TTGCATCCACATTCATGCT
Found at i:184924 original size:17 final size:17
Alignment explanation
Indices: 184901--184997 Score: 95
Period size: 17 Copynumber: 5.4 Consensus size: 17
184891 TGCATCATCA
184901 TTTCATGCTTTCACAAC
1 TTTCATGCTTTCACAAC
* *
184918 CTTCATGCTTTGCATCATC
1 TTTCATGCTTT-CA-CAAC
*
184937 ATTTCATGCTTTCAAAAC
1 -TTTCATGCTTTCACAAC
**
184955 TTTCATGCTTTACATCTTC
1 TTTCATGCTTT-CA-CAAC
184974 ATTTCATGCTTTCACAAC
1 -TTTCATGCTTTCACAAC
184992 TTTCAT
1 TTTCAT
184998 TCATTCATCA
Statistics
Matches: 64, Mismatches: 10, Indels: 12
0.74 0.12 0.14
Matches are distributed among these distances:
17 27 0.42
18 8 0.12
19 8 0.12
20 21 0.33
ACGTcount: A:0.23, C:0.27, G:0.06, T:0.44
Consensus pattern (17 bp):
TTTCATGCTTTCACAAC
Found at i:184931 original size:37 final size:37
Alignment explanation
Indices: 184857--184997 Score: 192
Period size: 37 Copynumber: 3.8 Consensus size: 37
184847 TTGTTTACCG
* * * *
184857 CATCATTTCATACTTGCATCCACGTTACATGCTTTGCAT
1 CATCATTTCATGCTTTCA-CAAC-TTTCATGCTTTGCAT
*
184896 CATCATTTCATGCTTTCACAACCTTCATGCTTTGCAT
1 CATCATTTCATGCTTTCACAACTTTCATGCTTTGCAT
* *
184933 CATCATTTCATGCTTTCAAAACTTTCATGCTTTACAT
1 CATCATTTCATGCTTTCACAACTTTCATGCTTTGCAT
*
184970 CTTCATTTCATGCTTTCACAACTTTCAT
1 CATCATTTCATGCTTTCACAACTTTCAT
184998 TCATTCATCA
Statistics
Matches: 92, Mismatches: 10, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
37 73 0.79
38 3 0.03
39 16 0.17
ACGTcount: A:0.23, C:0.28, G:0.07, T:0.42
Consensus pattern (37 bp):
CATCATTTCATGCTTTCACAACTTTCATGCTTTGCAT
Found at i:184980 original size:20 final size:20
Alignment explanation
Indices: 184884--184985 Score: 99
Period size: 20 Copynumber: 5.4 Consensus size: 20
184874 ATCCACGTTA
*
184884 CATGCTTTGCATCATCATTT
1 CATGCTTTACATCATCATTT
* *
184904 CATGCTTT-CA-CAAC-CTT
1 CATGCTTTACATCATCATTT
*
184921 CATGCTTTGCATCATCATTT
1 CATGCTTTACATCATCATTT
* *
184941 CATGCTTT-CA-AAAC-TTT
1 CATGCTTTACATCATCATTT
*
184958 CATGCTTTACATCTTCATTT
1 CATGCTTTACATCATCATTT
184978 CATGCTTT
1 CATGCTTT
184986 CACAACTTTC
Statistics
Matches: 67, Mismatches: 9, Indels: 12
0.76 0.10 0.14
Matches are distributed among these distances:
17 21 0.31
18 9 0.13
19 8 0.12
20 29 0.43
ACGTcount: A:0.22, C:0.26, G:0.08, T:0.44
Consensus pattern (20 bp):
CATGCTTTACATCATCATTT
Found at i:185020 original size:8 final size:8
Alignment explanation
Indices: 185009--185075 Score: 64
Period size: 8 Copynumber: 7.6 Consensus size: 8
184999 CATTCATCAT
185009 TTTTTTTA
1 TTTTTTTA
185017 TTTTTTATAA
1 TTTTTT-T-A
185027 TTTTTATT-
1 TTTTT-TTA
185035 TTTTTGATTGA
1 TTTTT--TT-A
185046 TTTTTTTA
1 TTTTTTTA
185054 TTTTTTTAA
1 TTTTTTT-A
185063 TTTTTTTA
1 TTTTTTTA
185071 TTTTT
1 TTTTT
185076 ATCATTATGT
Statistics
Matches: 52, Mismatches: 0, Indels: 14
0.79 0.00 0.21
Matches are distributed among these distances:
8 25 0.48
9 14 0.27
10 7 0.13
11 6 0.12
ACGTcount: A:0.16, C:0.00, G:0.03, T:0.81
Consensus pattern (8 bp):
TTTTTTTA
Found at i:185021 original size:9 final size:9
Alignment explanation
Indices: 185007--185075 Score: 54
Period size: 9 Copynumber: 7.7 Consensus size: 9
184997 TTCATTCATC
185007 ATTTTTTTT
1 ATTTTTTTT
185016 A--TTTTTT
1 ATTTTTTTT
**
185023 ATAATTTTT
1 ATTTTTTTT
*
185032 ATTTTTTTG
1 ATTTTTTTT
185041 ATTGATTTTTT
1 ATT--TTTTTT
185052 -TATTTTTTT
1 AT-TTTTTTT
*
185061 AATTTTTTT
1 ATTTTTTTT
185070 ATTTTT
1 ATTTTT
185076 ATCATTATGT
Statistics
Matches: 47, Mismatches: 7, Indels: 12
0.71 0.11 0.18
Matches are distributed among these distances:
7 7 0.15
9 33 0.70
10 1 0.02
11 6 0.13
ACGTcount: A:0.17, C:0.00, G:0.03, T:0.80
Consensus pattern (9 bp):
ATTTTTTTT
Found at i:185037 original size:17 final size:17
Alignment explanation
Indices: 185009--185077 Score: 77
Period size: 17 Copynumber: 3.9 Consensus size: 17
184999 CATTCATCAT
185009 TTTTTTTATTTTTTATAA
1 TTTTTTTA-TTTTTATAA
*
185027 TTTTTATT-TTTTTGATTGA
1 TTTTT-TTATTTTT-A-TAA
*
185046 TTTTTTTATTTTTTTAA
1 TTTTTTTATTTTTATAA
185063 TTTTTTTATTTTTAT
1 TTTTTTTATTTTTAT
185078 CATTATGTTA
Statistics
Matches: 43, Mismatches: 4, Indels: 9
0.77 0.07 0.16
Matches are distributed among these distances:
17 21 0.49
18 8 0.19
19 14 0.33
ACGTcount: A:0.17, C:0.00, G:0.03, T:0.80
Consensus pattern (17 bp):
TTTTTTTATTTTTATAA
Found at i:185058 original size:37 final size:37
Alignment explanation
Indices: 185009--185098 Score: 112
Period size: 37 Copynumber: 2.4 Consensus size: 37
184999 CATTCATCAT
* *
185009 TTTTTTTATTTTTTATAA-TTTTTATTTTTTTGATTGA
1 TTTTTTTATTTTTTATAATTTTTTATTTTTATCATT-A
185046 TTTTTTTATTTTTT-TAATTTTTTTATTTTTATCATTA
1 TTTTTTTATTTTTTATAA-TTTTTTATTTTTATCATTA
* *
185083 TGTTATTATTTTTTAT
1 TTTTTTTATTTTTTAT
185099 TTTATGATTT
Statistics
Matches: 46, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
36 3 0.07
37 27 0.59
38 16 0.35
ACGTcount: A:0.19, C:0.01, G:0.03, T:0.77
Consensus pattern (37 bp):
TTTTTTTATTTTTTATAATTTTTTATTTTTATCATTA
Found at i:207025 original size:16 final size:16
Alignment explanation
Indices: 207004--207034 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
206994 AATCTTTCTT
207004 AAGAAAAAAAAAAGAA
1 AAGAAAAAAAAAAGAA
*
207020 AAGAAAAGAAAAAGA
1 AAGAAAAAAAAAAGA
207035 GGTTAAGGAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (16 bp):
AAGAAAAAAAAAAGAA
Found at i:208092 original size:17 final size:19
Alignment explanation
Indices: 208057--208102 Score: 53
Period size: 17 Copynumber: 2.5 Consensus size: 19
208047 AAATTATTTT
208057 TTAATTTTTTTAATTTT-AA
1 TTAA-TTTTTTAATTTTAAA
208076 -TAATTTTTT-ATTATTAAA
1 TTAATTTTTTAATT-TTAAA
208094 TTAATTTTT
1 TTAATTTTT
208103 ATGAATTCAC
Statistics
Matches: 24, Mismatches: 0, Indels: 6
0.80 0.00 0.20
Matches are distributed among these distances:
16 3 0.12
17 8 0.33
18 5 0.21
19 8 0.33
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (19 bp):
TTAATTTTTTAATTTTAAA
Found at i:208640 original size:18 final size:18
Alignment explanation
Indices: 208614--208648 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
208604 TAATTATAAT
208614 TTTTATTAACATGTAAAG
1 TTTTATTAACATGTAAAG
* *
208632 TTTTGTTAACTTGTAAA
1 TTTTATTAACATGTAAA
208649 TTATATCATA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.34, C:0.06, G:0.11, T:0.49
Consensus pattern (18 bp):
TTTTATTAACATGTAAAG
Found at i:210190 original size:3 final size:3
Alignment explanation
Indices: 210182--210208 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
210172 AGTGAAAAAC
210182 AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT
210209 TCTAGGGACT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:211208 original size:19 final size:19
Alignment explanation
Indices: 211184--211222 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
211174 TTTGGATTTA
211184 TTATAATATATTA-TAATAT
1 TTATAA-ATATTATTAATAT
*
211203 TTATAAATGTTATTAATAT
1 TTATAAATATTATTAATAT
211222 T
1 T
211223 CTAGATAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 5 0.28
19 13 0.72
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.54
Consensus pattern (19 bp):
TTATAAATATTATTAATAT
Found at i:213965 original size:13 final size:13
Alignment explanation
Indices: 213947--213971 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
213937 TTTGAATTTA
213947 AATTAATTTAAAT
1 AATTAATTTAAAT
213960 AATTAATTTAAA
1 AATTAATTTAAA
213972 GTAAAAGAGG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (13 bp):
AATTAATTTAAAT
Found at i:215579 original size:19 final size:19
Alignment explanation
Indices: 215555--215592 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
215545 CAAAGATTAA
*
215555 AATAATCTTTTAAATAAAT
1 AATAATCTCTTAAATAAAT
215574 AATAATCTCTTAAATAAAT
1 AATAATCTCTTAAATAAAT
215593 TTATAAAATG
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:0.53, C:0.08, G:0.00, T:0.39
Consensus pattern (19 bp):
AATAATCTCTTAAATAAAT
Found at i:215821 original size:22 final size:23
Alignment explanation
Indices: 215796--215838 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
215786 ATAATGTAAC
215796 ATACAAATCATCA-TAATAAAAT
1 ATACAAATCATCATTAATAAAAT
* *
215818 ATACATATTATCATTAATAAA
1 ATACAAATCATCATTAATAAA
215839 TTATTTACAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 11 0.61
23 7 0.39
ACGTcount: A:0.56, C:0.12, G:0.00, T:0.33
Consensus pattern (23 bp):
ATACAAATCATCATTAATAAAAT
Found at i:216394 original size:16 final size:16
Alignment explanation
Indices: 216350--216430 Score: 51
Period size: 15 Copynumber: 5.1 Consensus size: 16
216340 CTAAGTGTTT
* *
216350 AACTCAAAATAACCTA
1 AACTTAAAATAATCTA
*
216366 AA-TAAAAATTAATCTA
1 AACTTAAAA-TAATCTA
*
216382 AACTTAAAATAAT-TT
1 AACTTAAAATAATCTA
* *
216397 AATTTAAAATAA-CTT
1 AACTTAAAATAATCTA
* *
216412 AATTTAAAAATAATTTA
1 AACTT-AAAATAATCTA
216429 AA
1 AA
216431 ACTTTTAAAA
Statistics
Matches: 53, Mismatches: 7, Indels: 9
0.77 0.10 0.13
Matches are distributed among these distances:
15 24 0.45
16 21 0.40
17 8 0.15
ACGTcount: A:0.58, C:0.09, G:0.00, T:0.33
Consensus pattern (16 bp):
AACTTAAAATAATCTA
Found at i:216405 original size:15 final size:15
Alignment explanation
Indices: 216385--216429 Score: 72
Period size: 15 Copynumber: 2.9 Consensus size: 15
216375 TAATCTAAAC
216385 TTAAAATAATTTAAT
1 TTAAAATAATTTAAT
*
216400 TTAAAATAACTTAAT
1 TTAAAATAATTTAAT
216415 TTAAAAATAATTTAA
1 TT-AAAATAATTTAA
216430 AACTTTTAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
15 16 0.59
16 11 0.41
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (15 bp):
TTAAAATAATTTAAT
Found at i:216793 original size:18 final size:18
Alignment explanation
Indices: 216756--216835 Score: 60
Period size: 18 Copynumber: 4.4 Consensus size: 18
216746 TGTATATATT
*
216756 ATATTATAATTATTTTTAAA
1 ATATTATAA--ATTTATAAA
216776 ATATTATAAATTTATAAA
1 ATATTATAAATTTATAAA
* **
216794 ATTTTA-ATAATTTATATT
1 ATATTATA-AATTTATAAA
216812 ATA-TA-AAATTT-TAAA
1 ATATTATAAATTTATAAA
216827 ATAATTATA
1 AT-ATTATA
216836 TTTTATATAT
Statistics
Matches: 49, Mismatches: 7, Indels: 10
0.74 0.11 0.15
Matches are distributed among these distances:
15 4 0.08
16 6 0.12
17 6 0.12
18 24 0.49
20 9 0.18
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (18 bp):
ATATTATAAATTTATAAA
Found at i:216808 original size:26 final size:25
Alignment explanation
Indices: 216769--216850 Score: 89
Period size: 25 Copynumber: 3.2 Consensus size: 25
216759 TTATAATTAT
216769 TTTTAAAATATTATAAATTTATAAAA
1 TTTTAAAATATTAT-AATTTATAAAA
216795 TTTTAATAAT-TTAT-ATTATATAAAA
1 TTTTAA-AATATTATAATT-TATAAAA
* *
216820 TTTTAAAATAATTATATTTTAT-ATA
1 TTTTAAAAT-ATTATAATTTATAAAA
216845 TTTTAA
1 TTTTAA
216851 TTATTTATAT
Statistics
Matches: 49, Mismatches: 2, Indels: 11
0.79 0.03 0.18
Matches are distributed among these distances:
24 6 0.12
25 21 0.43
26 17 0.35
27 5 0.10
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (25 bp):
TTTTAAAATATTATAATTTATAAAA
Found at i:216841 original size:33 final size:34
Alignment explanation
Indices: 216761--216843 Score: 84
Period size: 33 Copynumber: 2.5 Consensus size: 34
216751 ATATTATATT
* *
216761 ATAATTAT-TTTTAAAATATTATAAATTTATAAA
1 ATAATTATATTTTATATTATTATAAATTTATAAA
* *
216794 AT-TTTAATAATTTATATTA-TATAAAATTT-TAAA
1 ATAATT-ATATTTTATATTATTAT-AAATTTATAAA
216827 ATAATTATATTTTATAT
1 ATAATTATATTTTATAT
216844 ATTTTAATTA
Statistics
Matches: 40, Mismatches: 6, Indels: 8
0.74 0.11 0.15
Matches are distributed among these distances:
32 2 0.05
33 23 0.57
34 15 0.38
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (34 bp):
ATAATTATATTTTATATTATTATAAATTTATAAA
Done.