Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr3
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: 42799318
ACGTcount: A:0.32, C:0.17, G:0.16, T:0.32
Warning! 891409 characters in sequence are not A, C, G, or T
File 19 of 141
Found at i:5751946 original size:23 final size:23
Alignment explanation
Indices: 5751896--5751958 Score: 90
Period size: 23 Copynumber: 2.7 Consensus size: 23
5751886 AATTTGGTTT
**
5751896 ATTTCGTACCAAAAGTTCCATACA
1 ATTTCGTACCAAAA-CCCCATACA
*
5751920 ATTTCGTACCAAAACCCCATACC
1 ATTTCGTACCAAAACCCCATACA
5751943 ATTTCGTACCAAAACC
1 ATTTCGTACCAAAACC
5751959 AACTCCATCT
Statistics
Matches: 36, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
23 22 0.61
24 14 0.39
ACGTcount: A:0.37, C:0.32, G:0.06, T:0.25
Consensus pattern (23 bp):
ATTTCGTACCAAAACCCCATACA
Found at i:5753012 original size:12 final size:12
Alignment explanation
Indices: 5752995--5753019 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
5752985 AAAATCTGAT
5752995 TTCAATGTGTAA
1 TTCAATGTGTAA
5753007 TTCAATGTGTAA
1 TTCAATGTGTAA
5753019 T
1 T
5753020 GTATAAGGGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.32, C:0.08, G:0.16, T:0.44
Consensus pattern (12 bp):
TTCAATGTGTAA
Found at i:5753509 original size:44 final size:44
Alignment explanation
Indices: 5753461--5753601 Score: 122
Period size: 44 Copynumber: 3.2 Consensus size: 44
5753451 ATTTTCTTGA
5753461 TTCTTGAAATCGCTCAAAACAACAAAATTGGACCAAGATTCGGT
1 TTCTTGAAATCGCTCAAAACAACAAAATTGGACCAAGATTCGGT
** *** * * * * * ** * *
5753505 TTCTTGACTTTTTTGAAAACAA-GAAAGTGAATCTTGATTTTCTTGA
1 TTCTTGAAATCGCTCAAAACAACAAAATTGGACCAAGA--TTC-GGT
5753551 TTCTTGAAATCGCTCAAAACAACAAAATTGGACCAAGATTCGGT
1 TTCTTGAAATCGCTCAAAACAACAAAATTGGACCAAGATTCGGT
5753595 TTCTTGA
1 TTCTTGA
5753602 CTTTTTTGAA
Statistics
Matches: 65, Mismatches: 28, Indels: 8
0.64 0.28 0.08
Matches are distributed among these distances:
43 9 0.14
44 24 0.37
45 6 0.09
46 17 0.26
47 9 0.14
ACGTcount: A:0.35, C:0.17, G:0.16, T:0.33
Consensus pattern (44 bp):
TTCTTGAAATCGCTCAAAACAACAAAATTGGACCAAGATTCGGT
Found at i:5753557 original size:90 final size:90
Alignment explanation
Indices: 5753444--5753638 Score: 390
Period size: 90 Copynumber: 2.2 Consensus size: 90
5753434 CAAGATTTGA
5753444 AATCTTGATTTTCTTGATTCTTGAAATCGCTCAAAACAACAAAATTGGACCAAGATTCGGTTTCT
1 AATCTTGATTTTCTTGATTCTTGAAATCGCTCAAAACAACAAAATTGGACCAAGATTCGGTTTCT
5753509 TGACTTTTTTGAAAACAAGAAAGTG
66 TGACTTTTTTGAAAACAAGAAAGTG
5753534 AATCTTGATTTTCTTGATTCTTGAAATCGCTCAAAACAACAAAATTGGACCAAGATTCGGTTTCT
1 AATCTTGATTTTCTTGATTCTTGAAATCGCTCAAAACAACAAAATTGGACCAAGATTCGGTTTCT
5753599 TGACTTTTTTGAAAACAAGAAAGTG
66 TGACTTTTTTGAAAACAAGAAAGTG
5753624 AATCTTGATTTTCTT
1 AATCTTGATTTTCTT
5753639 TTTCCTTCGT
Statistics
Matches: 105, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
90 105 1.00
ACGTcount: A:0.33, C:0.15, G:0.15, T:0.36
Consensus pattern (90 bp):
AATCTTGATTTTCTTGATTCTTGAAATCGCTCAAAACAACAAAATTGGACCAAGATTCGGTTTCT
TGACTTTTTTGAAAACAAGAAAGTG
Found at i:5753614 original size:44 final size:44
Alignment explanation
Indices: 5753476--5753616 Score: 122
Period size: 44 Copynumber: 3.2 Consensus size: 44
5753466 GAAATCGCTC
5753476 AAAACAACAAAATTGGACCAAGATTCGGTTTCTTGACTTTTTTG
1 AAAACAACAAAATTGGACCAAGATTCGGTTTCTTGACTTTTTTG
* * * * ** * * ** *** *
5753520 AAAACAA-GAAAGTGAATCTTGATTTTCTTGATTCTTGAAATCGCTC
1 AAAACAACAAAATTGGACCAAGA--TTC-GGTTTCTTGACTTTTTTG
5753566 AAAACAACAAAATTGGACCAAGATTCGGTTTCTTGACTTTTTTG
1 AAAACAACAAAATTGGACCAAGATTCGGTTTCTTGACTTTTTTG
5753610 AAAACAA
1 AAAACAA
5753617 GAAAGTGAAT
Statistics
Matches: 65, Mismatches: 28, Indels: 8
0.64 0.28 0.08
Matches are distributed among these distances:
43 9 0.14
44 24 0.37
45 6 0.09
46 17 0.26
47 9 0.14
ACGTcount: A:0.37, C:0.16, G:0.15, T:0.33
Consensus pattern (44 bp):
AAAACAACAAAATTGGACCAAGATTCGGTTTCTTGACTTTTTTG
Found at i:5754635 original size:39 final size:39
Alignment explanation
Indices: 5754552--5754639 Score: 99
Period size: 39 Copynumber: 2.3 Consensus size: 39
5754542 TGAAAATCAA
* * *
5754552 AAAAAGAAAAGAAAATTGAGAGAAAAAGAGGGAAAATTG
1 AAAAAGAAAAGAAAATAGAGAGAAAAAGAGGAAAAACTG
* *
5754591 TAAAAGAAAATGAAAATAGAGTGAAAAA-A-GAAAACACTG
1 AAAAAGAAAA-GAAAATAGAGAGAAAAAGAGGAAAA-ACTG
5754630 AAAAAGAAAA
1 AAAAAGAAAA
5754640 AGAATGTGAA
Statistics
Matches: 41, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
38 4 0.10
39 22 0.54
40 15 0.37
ACGTcount: A:0.67, C:0.02, G:0.20, T:0.10
Consensus pattern (39 bp):
AAAAAGAAAAGAAAATAGAGAGAAAAAGAGGAAAAACTG
Found at i:5757047 original size:26 final size:26
Alignment explanation
Indices: 5757018--5757067 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 26
5757008 AATTCAGTCG
5757018 AAAAAGCCAAAAAAAATTGAAAAATA
1 AAAAAGCCAAAAAAAATTGAAAAATA
* * * *
5757044 AAAAATCCAATAAATATTTAAAAA
1 AAAAAGCCAAAAAAAATTGAAAAA
5757068 AAGATTTAGC
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
26 20 1.00
ACGTcount: A:0.70, C:0.08, G:0.04, T:0.18
Consensus pattern (26 bp):
AAAAAGCCAAAAAAAATTGAAAAATA
Found at i:5759556 original size:18 final size:20
Alignment explanation
Indices: 5759535--5759584 Score: 68
Period size: 18 Copynumber: 2.5 Consensus size: 20
5759525 AAAGAAAGAC
5759535 AGAAAAAGA-AATCAAAAA-
1 AGAAAAAGAGAATCAAAAAG
*
5759553 AGAAAAAGAGAATGAAAAAG
1 AGAAAAAGAGAATCAAAAAG
5759573 AGAAAAAAGAGA
1 AG-AAAAAGAGA
5759585 TTGAGAGTGG
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
18 9 0.32
19 8 0.29
20 2 0.07
21 9 0.32
ACGTcount: A:0.74, C:0.02, G:0.20, T:0.04
Consensus pattern (20 bp):
AGAAAAAGAGAATCAAAAAG
Found at i:5764297 original size:12 final size:12
Alignment explanation
Indices: 5764280--5764310 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
5764270 TCCCGAAATT
*
5764280 AAAAAAATTTTG
1 AAAAAAATTGTG
5764292 AAAAAAATTGTG
1 AAAAAAATTGTG
5764304 AAAAAAA
1 AAAAAAA
5764311 AAAAAAAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.68, C:0.00, G:0.10, T:0.23
Consensus pattern (12 bp):
AAAAAAATTGTG
Found at i:5765554 original size:16 final size:16
Alignment explanation
Indices: 5765533--5765571 Score: 69
Period size: 16 Copynumber: 2.4 Consensus size: 16
5765523 AGATTTTGCA
*
5765533 AAAGAAATGAGTGAAG
1 AAAGAAACGAGTGAAG
5765549 AAAGAAACGAGTGAAG
1 AAAGAAACGAGTGAAG
5765565 AAAGAAA
1 AAAGAAA
5765572 ACAAGAAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.62, C:0.03, G:0.28, T:0.08
Consensus pattern (16 bp):
AAAGAAACGAGTGAAG
Found at i:5767388 original size:64 final size:64
Alignment explanation
Indices: 5767310--5767478 Score: 338
Period size: 64 Copynumber: 2.6 Consensus size: 64
5767300 CCAGGTCAAA
5767310 AATTTCATTGAATGAATTTTCTTGCTCATCTGACCAATAAAGGTGCTTGAACAAGACTTTGTTT
1 AATTTCATTGAATGAATTTTCTTGCTCATCTGACCAATAAAGGTGCTTGAACAAGACTTTGTTT
5767374 AATTTCATTGAATGAATTTTCTTGCTCATCTGACCAATAAAGGTGCTTGAACAAGACTTTGTTT
1 AATTTCATTGAATGAATTTTCTTGCTCATCTGACCAATAAAGGTGCTTGAACAAGACTTTGTTT
5767438 AATTTCATTGAATGAATTTTCTTGCTCATCTGACCAATAAA
1 AATTTCATTGAATGAATTTTCTTGCTCATCTGACCAATAAA
5767479 ATGCTGAATT
Statistics
Matches: 105, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
64 105 1.00
ACGTcount: A:0.31, C:0.16, G:0.14, T:0.39
Consensus pattern (64 bp):
AATTTCATTGAATGAATTTTCTTGCTCATCTGACCAATAAAGGTGCTTGAACAAGACTTTGTTT
Found at i:5771961 original size:50 final size:50
Alignment explanation
Indices: 5771886--5771982 Score: 140
Period size: 50 Copynumber: 1.9 Consensus size: 50
5771876 TGCACCCAAG
* * * *
5771886 AAGATTAAAGATGAATCGGCAAGAACTCTAGAAATTGGGGATTTTGAACA
1 AAGATTAAACACGAATCGGCAAGAACCCTAGAAATTGGGGAGTTTGAACA
* *
5771936 AAGATTAAACACGAATTGGCAAGAACCCTGGAAATTGGGGAGTTTGA
1 AAGATTAAACACGAATCGGCAAGAACCCTAGAAATTGGGGAGTTTGA
5771983 CCGATTCTTT
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
50 41 1.00
ACGTcount: A:0.40, C:0.11, G:0.26, T:0.23
Consensus pattern (50 bp):
AAGATTAAACACGAATCGGCAAGAACCCTAGAAATTGGGGAGTTTGAACA
Found at i:5779169 original size:105 final size:105
Alignment explanation
Indices: 5779045--5779253 Score: 400
Period size: 105 Copynumber: 2.0 Consensus size: 105
5779035 ACTTTTAAAG
5779045 AAAACTCAAGAGAGAATTCTTGGAGAAAAACTCAAAGAGAATTCTGCACTTAAACAAATCTGAAA
1 AAAACTCAAGAGAGAATTCTTGGAGAAAAACTCAAAGAGAATTCTGCACTTAAACAAATCTGAAA
*
5779110 TTTTTTGATCTAATTGAGAAATGAATACAAGGGGTGGCCA
66 ATTTTTGATCTAATTGAGAAATGAATACAAGGGGTGGCCA
5779150 AAAACTCAAGAGAGAATTCTTGGAGAAAAACTCAAAGAGAATTCTGCACTTAAACAAATCTGAAA
1 AAAACTCAAGAGAGAATTCTTGGAGAAAAACTCAAAGAGAATTCTGCACTTAAACAAATCTGAAA
*
5779215 ATTTTTGATCTAATTGAGAAGTGAATACAAGGGGTGGCC
66 ATTTTTGATCTAATTGAGAAATGAATACAAGGGGTGGCC
5779254 GACCATCATT
Statistics
Matches: 102, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
105 102 1.00
ACGTcount: A:0.43, C:0.13, G:0.20, T:0.24
Consensus pattern (105 bp):
AAAACTCAAGAGAGAATTCTTGGAGAAAAACTCAAAGAGAATTCTGCACTTAAACAAATCTGAAA
ATTTTTGATCTAATTGAGAAATGAATACAAGGGGTGGCCA
Found at i:5784137 original size:19 final size:20
Alignment explanation
Indices: 5784113--5784150 Score: 69
Period size: 19 Copynumber: 1.9 Consensus size: 20
5784103 TGAGCTGGTT
5784113 GGAGCTGAAA-TGAGCTAAG
1 GGAGCTGAAATTGAGCTAAG
5784132 GGAGCTGAAATTGAGCTAA
1 GGAGCTGAAATTGAGCTAA
5784151 AATCAGCTTG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 10 0.56
20 8 0.44
ACGTcount: A:0.37, C:0.11, G:0.34, T:0.18
Consensus pattern (20 bp):
GGAGCTGAAATTGAGCTAAG
Found at i:5787860 original size:28 final size:27
Alignment explanation
Indices: 5787797--5787948 Score: 241
Period size: 27 Copynumber: 5.6 Consensus size: 27
5787787 ATATTAAGTC
* * *
5787797 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAACT
*
5787824 CGCACACTTAGTGCTACATAATCAAACT
1 CGCACACTTAGTGCTACATAGTC-AACT
5787852 CGCACACTTAGTGCTACATAGTCAACT
1 CGCACACTTAGTGCTACATAGTCAACT
5787879 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTC-AACT
*
5787907 CGCACACTTAGTGCTACATAGTCAATT
1 CGCACACTTAGTGCTACATAGTCAACT
5787934 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
5787949 GCACAATTTA
Statistics
Matches: 119, Mismatches: 4, Indels: 4
0.94 0.03 0.03
Matches are distributed among these distances:
27 66 0.55
28 53 0.45
ACGTcount: A:0.31, C:0.29, G:0.14, T:0.26
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAACT
Found at i:5787881 original size:55 final size:55
Alignment explanation
Indices: 5787797--5787948 Score: 259
Period size: 55 Copynumber: 2.8 Consensus size: 55
5787787 ATATTAAGTC
* * *
5787797 CGCACACTCAGTGCTATATAATCAACTCGCACACTTAGTGCTACATAATCAAACT
1 CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCTACATAATCAAACT
*
5787852 CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCTACATAATCAAACT
*
5787907 CGCACACTTAGTGCTACATAGTCAATTCGCACACTTAGTGCT
1 CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCT
5787949 GCACAATTTA
Statistics
Matches: 92, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
55 92 1.00
ACGTcount: A:0.31, C:0.29, G:0.14, T:0.26
Consensus pattern (55 bp):
CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCTACATAATCAAACT
Found at i:5790627 original size:52 final size:52
Alignment explanation
Indices: 5790525--5790624 Score: 166
Period size: 51 Copynumber: 1.9 Consensus size: 52
5790515 TAAATAAAAT
*
5790525 CGACACAAGCAGAATTTAAAAGAAAAAAAATTGACAGTAAGAAATTAAAGAA
1 CGACACAAGCAGAATTTAAAAGAAAAAAAATTGACAGCAAGAAATTAAAGAA
* *
5790577 CGACACAAGTAGAATTTAAAAG-AAAAAAATTGAGAGCAAGAAATTAAA
1 CGACACAAGCAGAATTTAAAAGAAAAAAAATTGACAGCAAGAAATTAAA
5790625 AGATAAGTCC
Statistics
Matches: 45, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
51 24 0.53
52 21 0.47
ACGTcount: A:0.59, C:0.09, G:0.16, T:0.16
Consensus pattern (52 bp):
CGACACAAGCAGAATTTAAAAGAAAAAAAATTGACAGCAAGAAATTAAAGAA
Found at i:5791742 original size:9 final size:9
Alignment explanation
Indices: 5791728--5791753 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
5791718 TATTTGAAAA
5791728 GGTTCACAC
1 GGTTCACAC
5791737 GGTTCACAC
1 GGTTCACAC
5791746 GGTTCACA
1 GGTTCACA
5791754 AAGTTGCACA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.23, C:0.31, G:0.23, T:0.23
Consensus pattern (9 bp):
GGTTCACAC
Found at i:5792340 original size:145 final size:145
Alignment explanation
Indices: 5792077--5792367 Score: 519
Period size: 145 Copynumber: 2.0 Consensus size: 145
5792067 CGAAGCTCTG
*
5792077 TTGTTGAGTTAACCTTTGTCAAATGGAACTCAAACTTCATGTACAACCACAGAAACTGTTTAAGG
1 TTGTTGAGTTAACCTTTGTCAAATGGAACTCAAACTTCATGTACAACCACAGAAACCGTTTAAGG
*
5792142 CACGAATATAATTTGAAAAAAAATTTGGCAAATTTCGTTACCTTATTCAAAAACCAAGTATCAAA
66 CACGAATATAAATTGAAAAAAAATTTGGCAAATTTCGTTACCTTATTCAAAAACCAAGTATCAAA
5792207 ACAATAAAAAGTATT
131 ACAATAAAAAGTATT
5792222 TTGTTGAGTTAACCTTTGTCAAATGGAACTCAAACTTCATGTACAACCACAGAAACCGTTTAAGG
1 TTGTTGAGTTAACCTTTGTCAAATGGAACTCAAACTTCATGTACAACCACAGAAACCGTTTAAGG
****
5792287 CACGAATATAAATTGAAAATTTTTTTGGCAAATTTCGTTACCTTATTCAAAAACCAAGTATCAAA
66 CACGAATATAAATTGAAAAAAAATTTGGCAAATTTCGTTACCTTATTCAAAAACCAAGTATCAAA
*
5792352 ACAATAGAAAGTATT
131 ACAATAAAAAGTATT
5792367 T
1 T
5792368 GGACACAATA
Statistics
Matches: 139, Mismatches: 7, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
145 139 1.00
ACGTcount: A:0.41, C:0.16, G:0.13, T:0.31
Consensus pattern (145 bp):
TTGTTGAGTTAACCTTTGTCAAATGGAACTCAAACTTCATGTACAACCACAGAAACCGTTTAAGG
CACGAATATAAATTGAAAAAAAATTTGGCAAATTTCGTTACCTTATTCAAAAACCAAGTATCAAA
ACAATAAAAAGTATT
Found at i:5800458 original size:65 final size:65
Alignment explanation
Indices: 5800354--5800484 Score: 226
Period size: 65 Copynumber: 2.0 Consensus size: 65
5800344 AAATTAAACG
* * *
5800354 ATCAGCTTTTCATAGAATTTTAAGAGCTGTTACGATAAGAAGAAAAGAGAGAACTTGATGGAATA
1 ATCAGATTTTAATAGAATTCTAAGAGCTGTTACGATAAGAAGAAAAGAGAGAACTTGATGGAATA
*
5800419 ATCAGATTTTAATAGAATTCTAAGGGCTGTTACGATAAGAAGAAAAGAGAGAACTTGATGGAATA
1 ATCAGATTTTAATAGAATTCTAAGAGCTGTTACGATAAGAAGAAAAGAGAGAACTTGATGGAATA
5800484 A
1 A
5800485 GACGGCTCTT
Statistics
Matches: 62, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
65 62 1.00
ACGTcount: A:0.43, C:0.08, G:0.22, T:0.27
Consensus pattern (65 bp):
ATCAGATTTTAATAGAATTCTAAGAGCTGTTACGATAAGAAGAAAAGAGAGAACTTGATGGAATA
Found at i:5818583 original size:29 final size:29
Alignment explanation
Indices: 5818520--5818587 Score: 77
Period size: 29 Copynumber: 2.3 Consensus size: 29
5818510 TAATCAACCG
5818520 CGCACACTTAGTGCCATGTACTTTAAACT
1 CGCACACTTAGTGCCATGTACTTTAAACT
* **
5818549 CACACACTTAGTG-C-TGTACATTTCAAGTT
1 CGCACACTTAGTGCCATGTAC-TTT-AAACT
5818578 CGCACACTTA
1 CGCACACTTA
5818588 CCTTTTCCGC
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
27 5 0.15
28 4 0.12
29 24 0.73
ACGTcount: A:0.28, C:0.28, G:0.13, T:0.31
Consensus pattern (29 bp):
CGCACACTTAGTGCCATGTACTTTAAACT
Found at i:5818699 original size:174 final size:174
Alignment explanation
Indices: 5818409--5818832 Score: 803
Period size: 174 Copynumber: 2.4 Consensus size: 174
5818399 AACTCAAGGT
* *
5818409 ACTTACCTTTTCCGCTGTCCAAAATTGACTCGGTAAAGTCGCACCCTTCATGTAAATAATTTATA
1 ACTTACCTTTTCCGCTGTCCAAAATCGACTCGGTAAAGTCGCACCCTTAATGTAAATAATTTATA
5818474 GAAAATATATATTGGGTTCGCACACATAGTGCTTAATAATCAACCGCGCACACTTAGTGCCATGT
66 GAAAATATATATTGGGTTCGCACACATAGTGCTTAATAATCAACCGCGCACACTTAGTGCCATGT
**
5818539 ACTTTAAACTCACACACTTAGTGCTGTACATTTCAAGTTCGCAC
131 ACTTTAAACTCACACACTTAGTGCCATACATTTCAAGTTCGCAC
5818583 ACTTACCTTTTCCGCTGTCCAAAATCGACTCGGTAAAGTCGCACCCTTAATGTAAATAATTTATA
1 ACTTACCTTTTCCGCTGTCCAAAATCGACTCGGTAAAGTCGCACCCTTAATGTAAATAATTTATA
5818648 GAAAATATATATTGGGTTCGCACACATAGTGCTTAATAATCAACCGCGCACACTTAGTGCCATGT
66 GAAAATATATATTGGGTTCGCACACATAGTGCTTAATAATCAACCGCGCACACTTAGTGCCATGT
*
5818713 ACTTTAAACTCACACACTTAGTGCCATGCATTTCAAGTTCGCAC
131 ACTTTAAACTCACACACTTAGTGCCATACATTTCAAGTTCGCAC
5818757 ACTTACCTTTTCCGCTGTCCAAAATCGACTCGGTAAAGTCGCACCCTTAATGTAAATAATTTATA
1 ACTTACCTTTTCCGCTGTCCAAAATCGACTCGGTAAAGTCGCACCCTTAATGTAAATAATTTATA
5818822 GAAAATATATA
66 GAAAATATATA
5818833 GAACACTTAT
Statistics
Matches: 245, Mismatches: 5, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
174 245 1.00
ACGTcount: A:0.32, C:0.24, G:0.14, T:0.31
Consensus pattern (174 bp):
ACTTACCTTTTCCGCTGTCCAAAATCGACTCGGTAAAGTCGCACCCTTAATGTAAATAATTTATA
GAAAATATATATTGGGTTCGCACACATAGTGCTTAATAATCAACCGCGCACACTTAGTGCCATGT
ACTTTAAACTCACACACTTAGTGCCATACATTTCAAGTTCGCAC
Found at i:5818757 original size:29 final size:29
Alignment explanation
Indices: 5818694--5818761 Score: 84
Period size: 29 Copynumber: 2.3 Consensus size: 29
5818684 TAATCAACCG
*
5818694 CGCACACTTAGTGCCATGTACTTTAAACT
1 CGCACACTTAGTGCCATGCACTTTAAACT
* **
5818723 CACACACTTAGTGCCATGCA-TTTCAAGTT
1 CGCACACTTAGTGCCATGCACTTT-AAACT
5818752 CGCACACTTA
1 CGCACACTTA
5818762 CCTTTTCCGC
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
28 3 0.09
29 30 0.91
ACGTcount: A:0.28, C:0.29, G:0.13, T:0.29
Consensus pattern (29 bp):
CGCACACTTAGTGCCATGCACTTTAAACT
Found at i:5822837 original size:43 final size:43
Alignment explanation
Indices: 5822790--5822873 Score: 118
Period size: 43 Copynumber: 2.0 Consensus size: 43
5822780 ATGTTGTCAT
* *
5822790 TGTATTGA-GATTTCGTGTAAGA-CCATGTCTGGGACATTGGCAC
1 TGTATT-ATGATTTCATGTAAGAGCC-TGTCTGGGACAGTGGCAC
5822833 TGTATTATGATTTCATGTAAGAGCCTGTCTGGGACAGTGGC
1 TGTATTATGATTTCATGTAAGAGCCTGTCTGGGACAGTGGC
5822874 TTTGATACTT
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
42 1 0.03
43 34 0.92
44 2 0.05
ACGTcount: A:0.23, C:0.15, G:0.29, T:0.33
Consensus pattern (43 bp):
TGTATTATGATTTCATGTAAGAGCCTGTCTGGGACAGTGGCAC
Found at i:5822887 original size:43 final size:43
Alignment explanation
Indices: 5822798--5822923 Score: 114
Period size: 43 Copynumber: 2.9 Consensus size: 43
5822788 ATTGTATTGA
* * *
5822798 GATTTCGTGTAAGACCATGTCTGGGACATTGGCACTGTATTAT
1 GATTTCATGTAAGACCATGTCTGGGACAGTGGCACTGTACTAT
**
5822841 GATTTCATGTAAGAGCC-TGTCTGGGACAGTGGCTTTGATACT-T
1 GATTTCATGTAAGA-CCATGTCTGGGACAGTGGCACTG-TACTAT
* * * * *
5822884 GATTACATGTAAGGCCACGTCTAGGAC-GTTGGCATTGTAC
1 GATTTCATGTAAGACCATGTCTGGGACAG-TGGCACTGTAC
5822924 GAGCTTCTGA
Statistics
Matches: 69, Mismatches: 10, Indels: 9
0.78 0.11 0.10
Matches are distributed among these distances:
42 6 0.09
43 58 0.84
44 5 0.07
ACGTcount: A:0.23, C:0.17, G:0.27, T:0.33
Consensus pattern (43 bp):
GATTTCATGTAAGACCATGTCTGGGACAGTGGCACTGTACTAT
Found at i:5826171 original size:29 final size:29
Alignment explanation
Indices: 5826110--5826178 Score: 95
Period size: 29 Copynumber: 2.4 Consensus size: 29
5826100 GCTTGGAATT
* * *
5826110 GATTCGGGCCAAATGGGCCATATGAATCT
1 GATTTGGGCCTAATGGGCCATATGAATCA
*
5826139 GATTTGGGCCTAATGGGCCATATGAATGA
1 GATTTGGGCCTAATGGGCCATATGAATCA
5826168 GA-TTGGGCCTA
1 GATTTGGGCCTA
5826179 GTGAACCATA
Statistics
Matches: 36, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
28 9 0.25
29 27 0.75
ACGTcount: A:0.26, C:0.17, G:0.30, T:0.26
Consensus pattern (29 bp):
GATTTGGGCCTAATGGGCCATATGAATCA
Found at i:5826187 original size:28 final size:29
Alignment explanation
Indices: 5826127--5826190 Score: 76
Period size: 28 Copynumber: 2.2 Consensus size: 29
5826117 GCCAAATGGG
* **
5826127 CCATATGAATCTGATTTGGGCCTAATGGG
1 CCATATGAATCAGATTTGGGCCTAATGAA
* *
5826156 CCATATGAATGAGA-TTGGGCCTAGTGAA
1 CCATATGAATCAGATTTGGGCCTAATGAA
5826184 CCATATG
1 CCATATG
5826191 CATGTATGTA
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
28 18 0.60
29 12 0.40
ACGTcount: A:0.28, C:0.17, G:0.27, T:0.28
Consensus pattern (29 bp):
CCATATGAATCAGATTTGGGCCTAATGAA
Found at i:5827856 original size:95 final size:95
Alignment explanation
Indices: 5827693--5827881 Score: 369
Period size: 95 Copynumber: 2.0 Consensus size: 95
5827683 ATTCCAGCAT
*
5827693 GCACAAAGAATAGCACACATTTAGCTAAACGGAATATTTCGTAATACGCAATTTACCGATATCAA
1 GCACAAAGAATAGCACACATTTAGCTAAACGGAATATTTCATAATACGCAATTTACCGATATCAA
5827758 ACTTGCTTCACAACATTAACAACCCTTATG
66 ACTTGCTTCACAACATTAACAACCCTTATG
5827788 GCACAAAGAATAGCACACATTTAGCTAAACGGAATATTTCATAATACGCAATTTACCGATATCAA
1 GCACAAAGAATAGCACACATTTAGCTAAACGGAATATTTCATAATACGCAATTTACCGATATCAA
5827853 ACTTGCTTCACAACATTAACAACCCTTAT
66 ACTTGCTTCACAACATTAACAACCCTTAT
5827882 ATACATACAC
Statistics
Matches: 93, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
95 93 1.00
ACGTcount: A:0.40, C:0.23, G:0.11, T:0.26
Consensus pattern (95 bp):
GCACAAAGAATAGCACACATTTAGCTAAACGGAATATTTCATAATACGCAATTTACCGATATCAA
ACTTGCTTCACAACATTAACAACCCTTATG
Found at i:5828186 original size:40 final size:40
Alignment explanation
Indices: 5828095--5828437 Score: 494
Period size: 40 Copynumber: 8.6 Consensus size: 40
5828085 TCCTCGTTCA
* * * * *
5828095 AATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACAC-
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
5828134 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
5828174 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
5828214 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
5828254 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
5828294 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* * *
5828334 AATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCACA
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* * * * * * *
5828374 AAGGCCTTC-GGATCTTGATCCGGATATATTCACTTAGCAC-
1 AATGCCTTCGGGA-CTTAACCCGGATTTAATAAC-TCGCACG
* *
5828414 AAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAACCCGGA
5828438 CAGCATTCAA
Statistics
Matches: 280, Mismatches: 20, Indels: 7
0.91 0.07 0.02
Matches are distributed among these distances:
39 37 0.13
40 235 0.84
41 8 0.03
ACGTcount: A:0.27, C:0.27, G:0.21, T:0.25
Consensus pattern (40 bp):
AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
Found at i:5831618 original size:29 final size:29
Alignment explanation
Indices: 5831586--5831643 Score: 107
Period size: 29 Copynumber: 2.0 Consensus size: 29
5831576 AAATACTTTA
5831586 CATATTTTAACTCAATAACATCCATCATT
1 CATATTTTAACTCAATAACATCCATCATT
*
5831615 CATATTTTAACTTAATAACATCCATCATT
1 CATATTTTAACTCAATAACATCCATCATT
5831644 TACTCCATTA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.38, C:0.22, G:0.00, T:0.40
Consensus pattern (29 bp):
CATATTTTAACTCAATAACATCCATCATT
Found at i:5832872 original size:43 final size:42
Alignment explanation
Indices: 5832731--5832879 Score: 116
Period size: 43 Copynumber: 3.5 Consensus size: 42
5832721 CAATGCCAAT
5832731 GTCCTAGACGTGGTCTTACATGCT-ATC-TCAGATCGATGCCA-C
1 GTCC-AGACGTGGTCTTACATG-TAATCAT-AGATCGATGCCAGC
* * *
5832773 TGTCCTAGACAG-GGTCTTACACG-AATCA-A-ATACGATACC-GAT
1 -GTCC-AGAC-GTGGTCTTACATGTAATCATAGAT-CGATGCCAG-C
*
5832815 GTCCCAGACATGGTCTTACATGTAATCATAGATCGATGCCAGC
1 GT-CCAGACGTGGTCTTACATGTAATCATAGATCGATGCCAGC
5832858 GTCTCAGACGTGGTCTTACATG
1 GTC-CAGACGTGGTCTTACATG
5832880 AGAACGCATA
Statistics
Matches: 85, Mismatches: 8, Indels: 26
0.71 0.07 0.22
Matches are distributed among these distances:
40 2 0.02
41 23 0.27
42 11 0.13
43 45 0.53
44 4 0.05
ACGTcount: A:0.26, C:0.26, G:0.21, T:0.27
Consensus pattern (42 bp):
GTCCAGACGTGGTCTTACATGTAATCATAGATCGATGCCAGC
Found at i:5833956 original size:19 final size:18
Alignment explanation
Indices: 5833934--5833999 Score: 52
Period size: 19 Copynumber: 3.7 Consensus size: 18
5833924 GACTTATAAA
5833934 ACATTTAAACATTCAATTC
1 ACATTTAAACATTCAA-TC
5833953 ACA--TAAA-ATT-AATC
1 ACATTTAAACATTCAATC
5833967 A-ATTAATAAACAATTCAATC
1 ACATT--TAAAC-ATTCAATC
*
5833987 ACAATTAAACATT
1 ACATTTAAACATT
5834000 TTGTCCATAA
Statistics
Matches: 38, Mismatches: 1, Indels: 17
0.68 0.02 0.30
Matches are distributed among these distances:
13 1 0.03
14 3 0.08
15 2 0.05
16 3 0.08
17 8 0.21
18 3 0.08
19 11 0.29
20 5 0.13
21 2 0.05
ACGTcount: A:0.52, C:0.17, G:0.00, T:0.32
Consensus pattern (18 bp):
ACATTTAAACATTCAATC
Found at i:5836132 original size:20 final size:21
Alignment explanation
Indices: 5836095--5836135 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
5836085 CTTGTATAAC
5836095 TATCACCAAACATTCAAAATA
1 TATCACCAAACATTCAAAATA
*
5836116 TATCATCAAAC-TTCAAAATA
1 TATCACCAAACATTCAAAATA
5836136 CTCATGTATT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 9 0.47
21 10 0.53
ACGTcount: A:0.51, C:0.22, G:0.00, T:0.27
Consensus pattern (21 bp):
TATCACCAAACATTCAAAATA
Found at i:5842466 original size:18 final size:18
Alignment explanation
Indices: 5842417--5842468 Score: 77
Period size: 18 Copynumber: 2.9 Consensus size: 18
5842407 TGGCCAAATT
*
5842417 CAGTAACAGTAAAAAGTG
1 CAGTAACAGTAAACAGTG
*
5842435 TAGTAACAGTAAACAGTG
1 CAGTAACAGTAAACAGTG
*
5842453 CAGTATCAGTAAACAG
1 CAGTAACAGTAAACAG
5842469 AATACAAGTC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 30 1.00
ACGTcount: A:0.46, C:0.13, G:0.21, T:0.19
Consensus pattern (18 bp):
CAGTAACAGTAAACAGTG
Found at i:5846023 original size:38 final size:38
Alignment explanation
Indices: 5845961--5846302 Score: 173
Period size: 38 Copynumber: 8.0 Consensus size: 38
5845951 GGAATGAAAA
* ** * *
5845961 AACGTTGTGCTAAGCAGATGTACCAAGGTTATACATGT
1 AACGTGGTGCTAAGTGGATATACCACGGTTATACATGT
*
5845999 AACGTGGTGCTAAGTGGATATACCACGATTACACATATTGATACATGT
1 AACGTGGTGCTAAGTGGATATACCACG---------GTT-ATACATGT
* *
5846047 AACGTGGTGCTAAGTGGATATGCCACGGTTACATATATTGATTCATT
1 AACGTGGTGCTAAGTGGATATACCACGGTT--ATACA-TG------T
5846094 AACGTGGTGCTAAGTGGATATACCACGGTTATACATGT
1 AACGTGGTGCTAAGTGGATATACCACGGTTATACATGT
* **
5846132 AACGGGGTGCTAAGTGGATATACCATGATTACACATATTGATACATGT
1 AACGTGGTGCTAAGTGGATATA-C-------CAC-GGTT-ATACATGT
* ** *
5846180 AATGTGGTGCTAAGTGGATATGTCAGGGTTACATATATTTATTCAT-T
1 AACGTGGTGCTAAGTGGATATACCACGG-----T-TA--TA--CATGT
*
5846227 AACGTGGTGCTAAGTGGATATACCACGGTTAAACATGT
1 AACGTGGTGCTAAGTGGATATACCACGGTTATACATGT
*
5846265 AACGTGGTGCTAAGTGGATATGCCACGGTTATACATGT
1 AACGTGGTGCTAAGTGGATATACCACGGTTATACATGT
5846303 TAATTTGAAA
Statistics
Matches: 236, Mismatches: 29, Indels: 78
0.69 0.08 0.23
Matches are distributed among these distances:
37 3 0.01
38 81 0.34
39 4 0.02
40 6 0.03
41 4 0.02
42 1 0.00
44 4 0.02
45 5 0.02
46 5 0.02
47 59 0.25
48 64 0.27
ACGTcount: A:0.30, C:0.15, G:0.24, T:0.31
Consensus pattern (38 bp):
AACGTGGTGCTAAGTGGATATACCACGGTTATACATGT
Found at i:5846062 original size:48 final size:48
Alignment explanation
Indices: 5845991--5846262 Score: 325
Period size: 48 Copynumber: 5.9 Consensus size: 48
5845981 TACCAAGGTT
*
5845991 ATACATGTAACGTGGTGCTAAGTGGATATACCACGATTACACATATTG
1 ATACATGTAACGTGGTGCTAAGTGGATATACCACGGTTACACATATTG
* *
5846039 ATACATGTAACGTGGTGCTAAGTGGATATGCCACGGTTACATATATTG
1 ATACATGTAACGTGGTGCTAAGTGGATATACCACGGTTACACATATTG
*
5846087 ATTCAT-TAACGTGGTGCTAAGTGGATATACCACGG---------TT-
1 ATACATGTAACGTGGTGCTAAGTGGATATACCACGGTTACACATATTG
* * *
5846124 ATACATGTAACGGGGTGCTAAGTGGATATACCATGATTACACATATTG
1 ATACATGTAACGTGGTGCTAAGTGGATATACCACGGTTACACATATTG
* ** * * *
5846172 ATACATGTAATGTGGTGCTAAGTGGATATGTCAGGGTTACATATATTT
1 ATACATGTAACGTGGTGCTAAGTGGATATACCACGGTTACACATATTG
* *
5846220 ATTCAT-TAACGTGGTGCTAAGTGGATATACCACGGTTAAACAT
1 ATACATGTAACGTGGTGCTAAGTGGATATACCACGGTTACACAT
5846263 GTAACGTGGT
Statistics
Matches: 189, Mismatches: 24, Indels: 23
0.80 0.10 0.10
Matches are distributed among these distances:
37 5 0.03
38 28 0.15
47 61 0.32
48 95 0.50
ACGTcount: A:0.31, C:0.14, G:0.23, T:0.32
Consensus pattern (48 bp):
ATACATGTAACGTGGTGCTAAGTGGATATACCACGGTTACACATATTG
Found at i:5846141 original size:85 final size:86
Alignment explanation
Indices: 5846039--5846200 Score: 254
Period size: 85 Copynumber: 1.9 Consensus size: 86
5846029 ACACATATTG
* * * * *
5846039 ATACATGTAACGTGGTGCTAAGTGGATATGCCACGGTTACATATATTGATTCAT-TAACGTGGTG
1 ATACATGTAACGGGGTGCTAAGTGGATATACCACGATTACACATATTGATACATGTAACGTGGTG
5846103 CTAAGTGGATATACCACGGTT
66 CTAAGTGGATATACCACGGTT
* *
5846124 ATACATGTAACGGGGTGCTAAGTGGATATACCATGATTACACATATTGATACATGTAATGTGGTG
1 ATACATGTAACGGGGTGCTAAGTGGATATACCACGATTACACATATTGATACATGTAACGTGGTG
5846189 CTAAGTGGATAT
66 CTAAGTGGATAT
5846201 GTCAGGGTTA
Statistics
Matches: 69, Mismatches: 7, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
85 48 0.70
86 21 0.30
ACGTcount: A:0.30, C:0.14, G:0.25, T:0.31
Consensus pattern (86 bp):
ATACATGTAACGGGGTGCTAAGTGGATATACCACGATTACACATATTGATACATGTAACGTGGTG
CTAAGTGGATATACCACGGTT
Found at i:5846199 original size:133 final size:133
Alignment explanation
Indices: 5845961--5846300 Score: 545
Period size: 133 Copynumber: 2.6 Consensus size: 133
5845951 GGAATGAAAA
* ** * *
5845961 AACGTTGTGCTAAGCAGATGTACCAAGGTTATACATGTAACGTGGTGCTAAGTGGATATACCACG
1 AACGTGGTGCTAAGTGGATATACCACGGTTATACATGTAACGTGGTGCTAAGTGGATATACCACG
5846026 ATTACACATATTGATACATGTAACGTGGTGCTAAGTGGATATGCCACGGTTACATATATTGATTC
66 ATTACACATATTGATACATGTAACGTGGTGCTAAGTGGATATGCCACGGTTACATATATTGATTC
5846091 ATT
131 ATT
* *
5846094 AACGTGGTGCTAAGTGGATATACCACGGTTATACATGTAACGGGGTGCTAAGTGGATATACCATG
1 AACGTGGTGCTAAGTGGATATACCACGGTTATACATGTAACGTGGTGCTAAGTGGATATACCACG
* * * *
5846159 ATTACACATATTGATACATGTAATGTGGTGCTAAGTGGATATGTCAGGGTTACATATATTTATTC
66 ATTACACATATTGATACATGTAACGTGGTGCTAAGTGGATATGCCACGGTTACATATATTGATTC
5846224 ATT
131 ATT
* *
5846227 AACGTGGTGCTAAGTGGATATACCACGGTTAAACATGTAACGTGGTGCTAAGTGGATATGCCACG
1 AACGTGGTGCTAAGTGGATATACCACGGTTATACATGTAACGTGGTGCTAAGTGGATATACCACG
* *
5846292 GTTATACAT
66 ATTACACAT
5846301 GTTAATTTGA
Statistics
Matches: 190, Mismatches: 17, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
133 190 1.00
ACGTcount: A:0.30, C:0.15, G:0.24, T:0.31
Consensus pattern (133 bp):
AACGTGGTGCTAAGTGGATATACCACGGTTATACATGTAACGTGGTGCTAAGTGGATATACCACG
ATTACACATATTGATACATGTAACGTGGTGCTAAGTGGATATGCCACGGTTACATATATTGATTC
ATT
Found at i:5848419 original size:22 final size:22
Alignment explanation
Indices: 5848394--5848437 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
5848384 AATTATTAAC
*
5848394 ATAATGAATTTTAATTAATTTT
1 ATAATAAATTTTAATTAATTTT
* *
5848416 ATAATAAATTTTGATTATTTTT
1 ATAATAAATTTTAATTAATTTT
5848438 TATTGTTTTC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.39, C:0.00, G:0.05, T:0.57
Consensus pattern (22 bp):
ATAATAAATTTTAATTAATTTT
Found at i:5856695 original size:23 final size:23
Alignment explanation
Indices: 5856638--5856695 Score: 55
Period size: 23 Copynumber: 2.5 Consensus size: 23
5856628 ATTATTTTAT
*
5856638 GAAAAAGAAAGGAAATAATAAAA
1 GAAAAAAAAAGGAAATAATAAAA
* ** *
5856661 GAAATACTAAGGATAATAA-AAGA
1 GAAAAAAAAAGGA-AATAATAAAA
5856684 GAAAAAAAAAGG
1 GAAAAAAAAAGG
5856696 GGTTATTACC
Statistics
Matches: 27, Mismatches: 7, Indels: 2
0.75 0.19 0.06
Matches are distributed among these distances:
23 22 0.81
24 5 0.19
ACGTcount: A:0.69, C:0.02, G:0.19, T:0.10
Consensus pattern (23 bp):
GAAAAAAAAAGGAAATAATAAAA
Found at i:5858230 original size:56 final size:56
Alignment explanation
Indices: 5858139--5858261 Score: 176
Period size: 55 Copynumber: 2.2 Consensus size: 56
5858129 GAGATTGGCG
* * *
5858139 CTAAGTGTGCGGGTTTAAATTGTACAGCACTAAGTGTGCGAGTTTGATTATGTAGCA
1 CTAAGTGTGCGAGTTTAAATTATACAGCACTAAGTGTGCGAG-TTGATTATATAGCA
* *
5858196 CTAAGTGTGCGAGTTT-GATTATATAGCACTAAGTGTGCGAGTTGATTATATAGCA
1 CTAAGTGTGCGAGTTTAAATTATACAGCACTAAGTGTGCGAGTTGATTATATAGCA
*
5858251 CTGAGTGTGCG
1 CTAAGTGTGCG
5858262 GACTTAATAT
Statistics
Matches: 60, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
55 23 0.38
56 22 0.37
57 15 0.25
ACGTcount: A:0.26, C:0.12, G:0.28, T:0.33
Consensus pattern (56 bp):
CTAAGTGTGCGAGTTTAAATTATACAGCACTAAGTGTGCGAGTTGATTATATAGCA
Found at i:5858248 original size:27 final size:28
Alignment explanation
Indices: 5858139--5858261 Score: 176
Period size: 28 Copynumber: 4.4 Consensus size: 28
5858129 GAGATTGGCG
* * * *
5858139 CTAAGTGTGCGGGTTTAAATTGTACAGCA
1 CTAAGTGTGCGAGTTT-GATTATATAGCA
*
5858168 CTAAGTGTGCGAGTTTGATTATGTAGCA
1 CTAAGTGTGCGAGTTTGATTATATAGCA
5858196 CTAAGTGTGCGAGTTTGATTATATAGCA
1 CTAAGTGTGCGAGTTTGATTATATAGCA
5858224 CTAAGTGTGCGAG-TTGATTATATAGCA
1 CTAAGTGTGCGAGTTTGATTATATAGCA
*
5858251 CTGAGTGTGCG
1 CTAAGTGTGCG
5858262 GACTTAATAT
Statistics
Matches: 87, Mismatches: 7, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
27 24 0.28
28 48 0.55
29 15 0.17
ACGTcount: A:0.26, C:0.12, G:0.28, T:0.33
Consensus pattern (28 bp):
CTAAGTGTGCGAGTTTGATTATATAGCA
Found at i:5858272 original size:27 final size:27
Alignment explanation
Indices: 5858164--5858274 Score: 116
Period size: 28 Copynumber: 4.0 Consensus size: 27
5858154 TAAATTGTAC
* * *
5858164 AGCACTAAGTGTGCGAGTTTGATTATGT
1 AGCACTAAGTGTGCGA-CTTGAATATAT
* *
5858192 AGCACTAAGTGTGCGAGTTTGATTATAT
1 AGCACTAAGTGTGCGA-CTTGAATATAT
* *
5858220 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGACTTGAATATAT
*
5858247 AGCACTGAGTGTGCGGACTT-AATATAT
1 AGCACTAAGTGTGC-GACTTGAATATAT
5858274 A
1 A
5858275 CTTTTGAATC
Statistics
Matches: 77, Mismatches: 5, Indels: 3
0.91 0.06 0.04
Matches are distributed among these distances:
27 30 0.39
28 47 0.61
ACGTcount: A:0.29, C:0.12, G:0.26, T:0.33
Consensus pattern (27 bp):
AGCACTAAGTGTGCGACTTGAATATAT
Found at i:5861128 original size:15 final size:15
Alignment explanation
Indices: 5861108--5861137 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
5861098 TTTGTGTGCT
5861108 TAATTTGCAAAAAGG
1 TAATTTGCAAAAAGG
5861123 TAATTTGCAAAAAGG
1 TAATTTGCAAAAAGG
5861138 GCCTAATCTC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.47, C:0.07, G:0.20, T:0.27
Consensus pattern (15 bp):
TAATTTGCAAAAAGG
Found at i:5861376 original size:16 final size:17
Alignment explanation
Indices: 5861331--5861376 Score: 51
Period size: 16 Copynumber: 2.8 Consensus size: 17
5861321 AAAGTCATAT
5861331 TAATAAAATAAAAAGGA
1 TAATAAAATAAAAAGGA
* *
5861348 -AGA-AAATTCAAAAGGA
1 TA-ATAAAATAAAAAGGA
5861364 TAATAAAATAAAA
1 TAATAAAATAAAA
5861377 TTCAAACTAG
Statistics
Matches: 22, Mismatches: 4, Indels: 6
0.69 0.12 0.19
Matches are distributed among these distances:
16 13 0.59
17 9 0.41
ACGTcount: A:0.70, C:0.02, G:0.11, T:0.17
Consensus pattern (17 bp):
TAATAAAATAAAAAGGA
Found at i:5863346 original size:25 final size:25
Alignment explanation
Indices: 5863312--5863361 Score: 91
Period size: 25 Copynumber: 2.0 Consensus size: 25
5863302 TGTGTCTAAG
*
5863312 GCCGTGTGACCATTTAAAAGTTGAA
1 GCCGCGTGACCATTTAAAAGTTGAA
5863337 GCCGCGTGACCATTTAAAAGTTGAA
1 GCCGCGTGACCATTTAAAAGTTGAA
5863362 TTTTTTTTAA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.32, C:0.18, G:0.24, T:0.26
Consensus pattern (25 bp):
GCCGCGTGACCATTTAAAAGTTGAA
Found at i:5868226 original size:16 final size:16
Alignment explanation
Indices: 5868205--5868236 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
5868195 TATTAGCTAG
*
5868205 CCCATGCCCTAATTTT
1 CCCATGCCATAATTTT
5868221 CCCATGCCATAATTTT
1 CCCATGCCATAATTTT
5868237 TAAGTTTGTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.22, C:0.34, G:0.06, T:0.38
Consensus pattern (16 bp):
CCCATGCCATAATTTT
Found at i:5868946 original size:43 final size:43
Alignment explanation
Indices: 5868899--5869002 Score: 154
Period size: 43 Copynumber: 2.4 Consensus size: 43
5868889 AACGAGATGT
5868899 GATTATGTGTAAGACCATGTCTAGAACATTGGCATCATTATGA
1 GATTATGTGTAAGACCATGTCTAGAACATTGGCATCATTATGA
* * * **
5868942 GATTACGTGTAAGACCATGTCTGGGACATTGGCATCATTATTT
1 GATTATGTGTAAGACCATGTCTAGAACATTGGCATCATTATGA
*
5868985 GATTTTGTGTAAGACCAT
1 GATTATGTGTAAGACCAT
5869003 AGATGGGCTA
Statistics
Matches: 54, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
43 54 1.00
ACGTcount: A:0.29, C:0.14, G:0.22, T:0.35
Consensus pattern (43 bp):
GATTATGTGTAAGACCATGTCTAGAACATTGGCATCATTATGA
Found at i:5869019 original size:43 final size:43
Alignment explanation
Indices: 5868899--5869045 Score: 120
Period size: 43 Copynumber: 3.4 Consensus size: 43
5868889 AACGAGATGT
* * * * *
5868899 GATTATGTGTAAGACCATGTCTAGAACATTGGCATCATTATGA
1 GATTACGTGTAAGACCATGTATGGGACATCGGCATCATTATGA
* * **
5868942 GATTACGTGTAAGACCATGTCTGGGACATTGGCATCATTATTT
1 GATTACGTGTAAGACCATGTATGGGACATCGGCATCATTATGA
** *
5868985 GATTTTGTGTAAGACCATAG-ATGGG-CTATCGGCATCGA-TATGT
1 GATTACGTGTAAGACCAT-GTATGGGAC-ATCGGCATC-ATTATGA
* *
5869028 GATAACATGTAAGACCAT
1 GATTACGTGTAAGACCAT
5869046 ATCTAGGATA
Statistics
Matches: 87, Mismatches: 14, Indels: 6
0.81 0.13 0.06
Matches are distributed among these distances:
42 1 0.01
43 84 0.97
44 2 0.02
ACGTcount: A:0.30, C:0.15, G:0.23, T:0.32
Consensus pattern (43 bp):
GATTACGTGTAAGACCATGTATGGGACATCGGCATCATTATGA
Found at i:5869384 original size:26 final size:25
Alignment explanation
Indices: 5869353--5869406 Score: 90
Period size: 26 Copynumber: 2.1 Consensus size: 25
5869343 CTTTTAAAGC
5869353 TTACTTTGTGTGTTCTTTCCCCATT
1 TTACTTTGTGTGTTCTTTCCCCATT
*
5869378 TTNACTTTGTGTGTTCTTTCCCTATT
1 TT-ACTTTGTGTGTTCTTTCCCCATT
5869404 TTA
1 TTA
5869407 TAGATAATCA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
25 3 0.11
26 24 0.89
ACGTcount: A:0.09, C:0.20, G:0.11, T:0.57
Consensus pattern (25 bp):
TTACTTTGTGTGTTCTTTCCCCATT
Found at i:5871467 original size:37 final size:37
Alignment explanation
Indices: 5871417--5871490 Score: 121
Period size: 37 Copynumber: 2.0 Consensus size: 37
5871407 CTTGCTTCTT
* * *
5871417 TCCCTTCTGCTAGCTGCTATATATCAAAGTGAATAAA
1 TCCCTACTGCTAGCAGCTATAAATCAAAGTGAATAAA
5871454 TCCCTACTGCTAGCAGCTATAAATCAAAGTGAATAAA
1 TCCCTACTGCTAGCAGCTATAAATCAAAGTGAATAAA
5871491 AAATCCCAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
37 34 1.00
ACGTcount: A:0.36, C:0.22, G:0.14, T:0.28
Consensus pattern (37 bp):
TCCCTACTGCTAGCAGCTATAAATCAAAGTGAATAAA
Found at i:5872428 original size:27 final size:27
Alignment explanation
Indices: 5872397--5872602 Score: 132
Period size: 27 Copynumber: 7.6 Consensus size: 27
5872387 TTAGTTTACC
*
5872397 AAATTACCGAAATACCCTCGATTTGTA
1 AAATTACCGAAATACCCTCGATTTGCA
* * *
5872424 AAATTACCAAAATACCC-CTAATTTGGA
1 AAATTACCGAAATACCCTC-GATTTGCA
*
5872451 AAATTACCGAAATACCCTTGATTTAG-A
1 AAATTACCGAAATACCCTCGATTT-GCA
** * * *
5872478 AAATTACAAAAAT-CCCCCTAATTTACA
1 AAATTACCGAAATACCCTC-GATTTGCA
* * * **
5872505 AAATTACTGAAATACCCTTGACTTGTT
1 AAATTACCGAAATACCCTCGATTTGCA
* *
5872532 AAATTACC-AAAGTACCCCCGATTTACA
1 AAATTACCGAAA-TACCCTCGATTTGCA
* *** *
5872559 GAATTACCGTTTTACCTTCGATTTGCA
1 AAATTACCGAAATACCCTCGATTTGCA
**
5872586 AAATTATTGAAATACCC
1 AAATTACCGAAATACCC
5872603 CTGTAGGGTA
Statistics
Matches: 129, Mismatches: 42, Indels: 16
0.69 0.22 0.09
Matches are distributed among these distances:
26 7 0.05
27 118 0.91
28 4 0.03
ACGTcount: A:0.39, C:0.22, G:0.09, T:0.30
Consensus pattern (27 bp):
AAATTACCGAAATACCCTCGATTTGCA
Found at i:5872462 original size:54 final size:54
Alignment explanation
Indices: 5872391--5872567 Score: 221
Period size: 54 Copynumber: 3.3 Consensus size: 54
5872381 AATACTTTAG
* *
5872391 TTTACCAAATTACCGAAATACCCTCGATTTGTAAAATTACCAAAATACCCCTAA
1 TTTACAAAATTACCGAAATACCCTTGATTTGTAAAATTACCAAAATACCCCTAA
** * *
5872445 TTTGGAAAATTACCGAAATACCCTTGATTTAG-AAAATTACAAAAATCCCCCTAA
1 TTTACAAAATTACCGAAATACCCTTGATTT-GTAAAATTACCAAAATACCCCTAA
* * * * **
5872499 TTTACAAAATTACTGAAATACCCTTGACTTGTTAAATTACCAAAGTACCCCCGA
1 TTTACAAAATTACCGAAATACCCTTGATTTGTAAAATTACCAAAATACCCCTAA
*
5872553 TTTACAGAATTACCG
1 TTTACAAAATTACCG
5872568 TTTTACCTTC
Statistics
Matches: 103, Mismatches: 18, Indels: 4
0.82 0.14 0.03
Matches are distributed among these distances:
53 1 0.01
54 101 0.98
55 1 0.01
ACGTcount: A:0.40, C:0.23, G:0.08, T:0.29
Consensus pattern (54 bp):
TTTACAAAATTACCGAAATACCCTTGATTTGTAAAATTACCAAAATACCCCTAA
Found at i:5872617 original size:27 final size:27
Alignment explanation
Indices: 5872594--5872701 Score: 144
Period size: 27 Copynumber: 4.0 Consensus size: 27
5872584 CAAAATTATT
**
5872594 GAAATACCCCTGTAGGGTAGAATTATT
1 GAAATACCCCTGTAGGGTAGAATTACC
*
5872621 GAAATACCCTTGTAGGGTAGAATTACC
1 GAAATACCCCTGTAGGGTAGAATTACC
*
5872648 GAAATACCCCTATAGGGTAGAATTACC
1 GAAATACCCCTGTAGGGTAGAATTACC
* * * *
5872675 GAGATACCCTTGTGGGGTAAAATTACC
1 GAAATACCCCTGTAGGGTAGAATTACC
5872702 ATTTTGCCCT
Statistics
Matches: 71, Mismatches: 10, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 71 1.00
ACGTcount: A:0.33, C:0.19, G:0.22, T:0.26
Consensus pattern (27 bp):
GAAATACCCCTGTAGGGTAGAATTACC
Found at i:5872645 original size:54 final size:54
Alignment explanation
Indices: 5872585--5872701 Score: 162
Period size: 54 Copynumber: 2.2 Consensus size: 54
5872575 TTCGATTTGC
** * **
5872585 AAAATTATTGAAATACCCCTGTAGGGTAGAATTATTGAAATACCCTTGTAGGGT
1 AAAATTACCGAAATACCCCTATAGGGTAGAATTACCGAAATACCCTTGTAGGGT
* * *
5872639 AGAATTACCGAAATACCCCTATAGGGTAGAATTACCGAGATACCCTTGTGGGGT
1 AAAATTACCGAAATACCCCTATAGGGTAGAATTACCGAAATACCCTTGTAGGGT
5872693 AAAATTACC
1 AAAATTACC
5872702 ATTTTGCCCT
Statistics
Matches: 54, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
54 54 1.00
ACGTcount: A:0.35, C:0.17, G:0.21, T:0.27
Consensus pattern (54 bp):
AAAATTACCGAAATACCCCTATAGGGTAGAATTACCGAAATACCCTTGTAGGGT
Found at i:5872711 original size:27 final size:27
Alignment explanation
Indices: 5872681--5872744 Score: 67
Period size: 27 Copynumber: 2.4 Consensus size: 27
5872671 TACCGAGATA
*
5872681 CCCTTGTGGGGTAAAATTACCATTTTG
1 CCCTTGTGGGGTAAAATGACCATTTTG
* * **
5872708 CCCTTAG-GGTGTTAAATGACTGTTTTG
1 CCCTT-GTGGGGTAAAATGACCATTTTG
5872735 CCCTTGTGGG
1 CCCTTGTGGG
5872745 CAAGTGATTG
Statistics
Matches: 29, Mismatches: 6, Indels: 4
0.74 0.15 0.10
Matches are distributed among these distances:
26 1 0.03
27 27 0.93
28 1 0.03
ACGTcount: A:0.17, C:0.19, G:0.27, T:0.38
Consensus pattern (27 bp):
CCCTTGTGGGGTAAAATGACCATTTTG
Found at i:5873267 original size:22 final size:22
Alignment explanation
Indices: 5873216--5873277 Score: 72
Period size: 22 Copynumber: 2.8 Consensus size: 22
5873206 CCAATTATTT
*
5873216 TGATTATGGCTTTGCGCCAACA
1 TGATTATGGCTTTGTGCCAACA
* *
5873238 T-ACGTATGGCTTTGTGCCAACC
1 TGA-TTATGGCTTTGTGCCAACA
*
5873260 TGATTATGGCTGTGTGCC
1 TGATTATGGCTTTGTGCC
5873278 GTTATTATGG
Statistics
Matches: 33, Mismatches: 5, Indels: 4
0.79 0.12 0.10
Matches are distributed among these distances:
21 1 0.03
22 31 0.94
23 1 0.03
ACGTcount: A:0.18, C:0.23, G:0.26, T:0.34
Consensus pattern (22 bp):
TGATTATGGCTTTGTGCCAACA
Found at i:5873543 original size:25 final size:25
Alignment explanation
Indices: 5873512--5873599 Score: 133
Period size: 25 Copynumber: 3.6 Consensus size: 25
5873502 TTGCATTCAC
* *
5873512 ATTCTGATTCAGATTCTGTTACCTG
1 ATTCTGATTCTGATTCTGTCACCTG
* *
5873537 ATACTGA-TCTGATTCTGTCACCTA
1 ATTCTGATTCTGATTCTGTCACCTG
5873561 ATTCTGATTCTGATTCTGTCACCTG
1 ATTCTGATTCTGATTCTGTCACCTG
5873586 ATTCTGATTCTGAT
1 ATTCTGATTCTGAT
5873600 AATGTTTCTT
Statistics
Matches: 56, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
24 20 0.36
25 36 0.64
ACGTcount: A:0.20, C:0.22, G:0.15, T:0.43
Consensus pattern (25 bp):
ATTCTGATTCTGATTCTGTCACCTG
Found at i:5873620 original size:17 final size:18
Alignment explanation
Indices: 5873587--5873620 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
5873577 TGTCACCTGA
5873587 TTCTGATTCTGATAATGT
1 TTCTGATTCTGATAATGT
*
5873605 TTCTTATTCT-ATAATG
1 TTCTGATTCTGATAATG
5873621 GGTTAACGCC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.24, C:0.12, G:0.12, T:0.53
Consensus pattern (18 bp):
TTCTGATTCTGATAATGT
Found at i:5873971 original size:35 final size:35
Alignment explanation
Indices: 5873919--5873990 Score: 117
Period size: 35 Copynumber: 2.1 Consensus size: 35
5873909 AGTAAAGCCG
* *
5873919 TTGTAATTTTCTAGATTTTAAATTTGGAATTTTAT
1 TTGTAATTTTCGAGATTTCAAATTTGGAATTTTAT
*
5873954 TTGTAATTTTCGGGATTTCAAATTTGGAATTTTAT
1 TTGTAATTTTCGAGATTTCAAATTTGGAATTTTAT
5873989 TT
1 TT
5873991 ATTGTTCTTA
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
35 34 1.00
ACGTcount: A:0.26, C:0.04, G:0.14, T:0.56
Consensus pattern (35 bp):
TTGTAATTTTCGAGATTTCAAATTTGGAATTTTAT
Found at i:5883318 original size:27 final size:27
Alignment explanation
Indices: 5883257--5883308 Score: 77
Period size: 27 Copynumber: 1.9 Consensus size: 27
5883247 TCATACATCT
5883257 CTTAGGGGCATAACAGTTATTTTATCA
1 CTTAGGGGCATAACAGTTATTTTATCA
** *
5883284 CACAGGGGCATAATAGTTATTTTAT
1 CTTAGGGGCATAACAGTTATTTTAT
5883309 TGATTAGGGG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.31, C:0.13, G:0.19, T:0.37
Consensus pattern (27 bp):
CTTAGGGGCATAACAGTTATTTTATCA
Found at i:5887836 original size:47 final size:47
Alignment explanation
Indices: 5887779--5888028 Score: 330
Period size: 47 Copynumber: 5.4 Consensus size: 47
5887769 ATTGATGTAC
* * *
5887779 AAGTATATATATGTGATAGGGCCGAGTGGCCAATGTGATGAATGTGA
1 AAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGA
** ** * * *
5887826 AAGTGTATATATGTGATGGGGTTGAGTGACCAACGTGATGAATGTGA
1 AAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGA
5887873 AAGTG-----ATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGA
1 AAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGA
* * *
5887915 AAGTGTATATATGAGATAAGACCTAATGGCCAATGTGATGAATGTGA
1 AAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGA
*
5887962 AAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATGGATGTGA
1 AAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGA
*
5888009 AAGTGTATAAATGTGATAAG
1 AAGTGTATATATGTGATAAG
5888029 TCCCGAAGGG
Statistics
Matches: 177, Mismatches: 21, Indels: 10
0.85 0.10 0.05
Matches are distributed among these distances:
42 35 0.20
47 142 0.80
ACGTcount: A:0.34, C:0.08, G:0.31, T:0.28
Consensus pattern (47 bp):
AAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGA
Found at i:5887898 original size:89 final size:90
Alignment explanation
Indices: 5887788--5888028 Score: 315
Period size: 89 Copynumber: 2.6 Consensus size: 90
5887778 CAAGTATATA
* * * *** *
5887788 TATGTGATAGGGCCGAGTGGCCAATGTGATGAATGTGAAAGTGTATATATGTGAT-GGGGTTGAG
1 TATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTATATATGTGATAAGACCT-AA
5887852 TGACCAACGTGATGAATGTGAAAGTG
65 TGACCAACGTGATGAATGTGAAAGTG
*
5887878 -ATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTATATATGAGATAAGACCTAAT
1 TATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTATATATGTGATAAGACCTAAT
* *
5887942 GGCCAATGTGATGAATGTGAAAGTG
66 GACCAACGTGATGAATGTGAAAGTG
* *
5887967 TATATATGTGATAAGGCCGAATGGCCAATGTGATGGATGTGAAAGTGTATAAATGTGATAAG
1 ----TATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTATATATGTGATAAG
5888029 TCCCGAAGGG
Statistics
Matches: 132, Mismatches: 13, Indels: 8
0.86 0.08 0.05
Matches are distributed among these distances:
89 76 0.58
90 2 0.02
94 54 0.41
ACGTcount: A:0.33, C:0.08, G:0.32, T:0.27
Consensus pattern (90 bp):
TATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTATATATGTGATAAGACCTAAT
GACCAACGTGATGAATGTGAAAGTG
Found at i:5901015 original size:40 final size:40
Alignment explanation
Indices: 5900947--5901094 Score: 244
Period size: 40 Copynumber: 3.7 Consensus size: 40
5900937 NNNNNNNNCT
*
5900947 CAAATGCCTTCGGGACTTAGCCCAGTTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
* *
5900987 CAATTGCCTTCGGGACTTGGCCCGGTTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
*
5901027 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
*
5901067 CAAATGCCTTCAGG-CTTAGCCCGGTTAT
1 CAAATGCCTTCGGGACTTAGCCCGGTTAT
5901095 CAATCCAAAT
Statistics
Matches: 100, Mismatches: 8, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
39 13 0.13
40 87 0.87
ACGTcount: A:0.24, C:0.28, G:0.22, T:0.26
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
Found at i:5901784 original size:51 final size:51
Alignment explanation
Indices: 5901708--5901809 Score: 186
Period size: 51 Copynumber: 2.0 Consensus size: 51
5901698 ATTCATAAGT
5901708 GCATAGATACTATGTTACAAACAATTATTTCCTTGCTTAGCAGCCGAACCA
1 GCATAGATACTATGTTACAAACAATTATTTCCTTGCTTAGCAGCCGAACCA
* *
5901759 GCATAGATACTATGTTACCAACAATTATTTCCTTGCTTAGTAGCCGAACCA
1 GCATAGATACTATGTTACAAACAATTATTTCCTTGCTTAGCAGCCGAACCA
5901810 ATATACACAT
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
51 49 1.00
ACGTcount: A:0.32, C:0.24, G:0.14, T:0.30
Consensus pattern (51 bp):
GCATAGATACTATGTTACAAACAATTATTTCCTTGCTTAGCAGCCGAACCA
Found at i:5908765 original size:40 final size:40
Alignment explanation
Indices: 5908695--5909631 Score: 1691
Period size: 40 Copynumber: 23.5 Consensus size: 40
5908685 AAACCAAGTA
** ** *
5908695 CCTTCGGGGTTTAG-CCGGATATAGCT-ACTCGCTGAAAGG
1 CCTTCGGGACTTAGCCCGGATATAG-TAACTCGCACAAATG
* * * *
5908734 CCTTTGGGACTTAGCCTGGTTATAGTAACTCGCACAATTG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
* * * * *
5908774 CCTTTGGCACTTAGTCCGGTTATAGTAACTCGCACAATTG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
* *
5908814 CCTTCGGGACTTGGCCCGGTTATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
5908854 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
5908894 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
5908934 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
5908974 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
5909014 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
5909054 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
5909094 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
5909134 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
5909174 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
5909214 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
5909254 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
5909294 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
5909334 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
5909374 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
5909414 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
5909454 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
5909494 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
5909534 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
5909574 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
*
5909614 CCTTCAGG-CTTAGCCCGG
1 CCTTCGGGACTTAGCCCGG
5909632 TTATCAATCC
Statistics
Matches: 876, Mismatches: 20, Indels: 4
0.97 0.02 0.00
Matches are distributed among these distances:
39 22 0.03
40 854 0.97
ACGTcount: A:0.26, C:0.27, G:0.23, T:0.24
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
Found at i:5915399 original size:22 final size:23
Alignment explanation
Indices: 5915377--5915428 Score: 65
Period size: 23 Copynumber: 2.3 Consensus size: 23
5915367 ATGTTTTTAC
5915377 TTTTATTTTAT-TTTAAGACTACT
1 TTTTATTTT-TCTTTAAGACTACT
5915400 TTTTATTTTTCTTTAAG-CTTA-T
1 TTTTATTTTTCTTTAAGAC-TACT
5915422 TTTTATT
1 TTTTATT
5915429 AGGATTTATA
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
22 10 0.37
23 17 0.63
ACGTcount: A:0.21, C:0.08, G:0.04, T:0.67
Consensus pattern (23 bp):
TTTTATTTTTCTTTAAGACTACT
Found at i:5916373 original size:13 final size:13
Alignment explanation
Indices: 5916355--5916381 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
5916345 TACCTCCACG
5916355 ATTAACCCTTAGT
1 ATTAACCCTTAGT
5916368 ATTAACCCTTAGT
1 ATTAACCCTTAGT
5916381 A
1 A
5916382 AACCCCGTTG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.33, C:0.22, G:0.07, T:0.37
Consensus pattern (13 bp):
ATTAACCCTTAGT
Found at i:5925562 original size:28 final size:27
Alignment explanation
Indices: 5925495--5925596 Score: 123
Period size: 27 Copynumber: 3.7 Consensus size: 27
5925485 TTAGTTTACC
* * *
5925495 AAATTACCAAAATACCCTTGATTAGCA
1 AAATTACCAAAATACCCCTGATTTGTA
*
5925522 AAATTACCAAAATACCCCTGGTTTGTA
1 AAATTACCAAAATACCCCTGATTTGTA
* *
5925549 AAATTACCAAAAATATCCCTAATTTGTA
1 AAATTACC-AAAATACCCCTGATTTGTA
**
5925577 AAATTACTGAAATACCCCTG
1 AAATTACCAAAATACCCCTG
5925597 TAGGGTAGAA
Statistics
Matches: 63, Mismatches: 11, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
27 40 0.63
28 23 0.37
ACGTcount: A:0.42, C:0.22, G:0.08, T:0.28
Consensus pattern (27 bp):
AAATTACCAAAATACCCCTGATTTGTA
Found at i:5925608 original size:27 final size:27
Alignment explanation
Indices: 5925578--5925799 Score: 293
Period size: 27 Copynumber: 8.2 Consensus size: 27
5925568 TAATTTGTAA
5925578 AATTACTGAAATACCCCTGTAGGGTAG
1 AATTACTGAAATACCCCTGTAGGGTAG
* * * *
5925605 AATTATTGAAATACCTCTGCAAGGTAG
1 AATTACTGAAATACCCCTGTAGGGTAG
*
5925632 AATTA-TCGAAATACCCTTGTAGGGTAG
1 AATTACT-GAAATACCCCTGTAGGGTAG
*
5925659 AATTACCGAAATACCCCTGTAGGGTAG
1 AATTACTGAAATACCCCTGTAGGGTAG
* * *
5925686 AATTATTGAAATACCCCTATAAGGTAG
1 AATTACTGAAATACCCCTGTAGGGTAG
** *
5925713 AATTACCAAAATAACCCTGTAGGGTAG
1 AATTACTGAAATACCCCTGTAGGGTAG
*
5925740 AATTACTGAAATACCCTTGTAGGGTAG
1 AATTACTGAAATACCCCTGTAGGGTAG
* *
5925767 AAATACTAAAATACCCCTGTAGGGTAG
1 AATTACTGAAATACCCCTGTAGGGTAG
5925794 AATTAC
1 AATTAC
5925800 CGAGGTACCC
Statistics
Matches: 165, Mismatches: 28, Indels: 4
0.84 0.14 0.02
Matches are distributed among these distances:
26 1 0.01
27 164 0.99
ACGTcount: A:0.37, C:0.17, G:0.19, T:0.27
Consensus pattern (27 bp):
AATTACTGAAATACCCCTGTAGGGTAG
Found at i:5925809 original size:54 final size:54
Alignment explanation
Indices: 5925578--5925828 Score: 279
Period size: 54 Copynumber: 4.6 Consensus size: 54
5925568 TAATTTGTAA
* * *** * * *
5925578 AATTACTGAAATACCCCTGTAGGGTAGAATTATTGAAATACCTCTGCAAGGTAG
1 AATTACCGAAATACCCTTGTAGGGTAGAATTACCAAAATACCCCTGTAGGGTAG
* *
5925632 AATTATCGAAATACCCTTGTAGGGTAGAATTACCGAAATACCCCTGTAGGGTAG
1 AATTACCGAAATACCCTTGTAGGGTAGAATTACCAAAATACCCCTGTAGGGTAG
** * * * *
5925686 AATTATTGAAATACCCCTATAAGGTAGAATTACCAAAATAACCCTGTAGGGTAG
1 AATTACCGAAATACCCTTGTAGGGTAGAATTACCAAAATACCCCTGTAGGGTAG
* * *
5925740 AATTACTGAAATACCCTTGTAGGGTAGAAATACTAAAATACCCCTGTAGGGTAG
1 AATTACCGAAATACCCTTGTAGGGTAGAATTACCAAAATACCCCTGTAGGGTAG
** * *
5925794 AATTACCGAGGTACCCTCGTGGGGT-GAAATTACCA
1 AATTACCGAAATACCCTTGTAGGGTAG-AATTACCA
5925829 TTTTGCCCCT
Statistics
Matches: 168, Mismatches: 28, Indels: 2
0.85 0.14 0.01
Matches are distributed among these distances:
53 1 0.01
54 167 0.99
ACGTcount: A:0.35, C:0.18, G:0.21, T:0.26
Consensus pattern (54 bp):
AATTACCGAAATACCCTTGTAGGGTAGAATTACCAAAATACCCCTGTAGGGTAG
Found at i:5925826 original size:81 final size:80
Alignment explanation
Indices: 5925578--5925802 Score: 333
Period size: 81 Copynumber: 2.8 Consensus size: 80
5925568 TAATTTGTAA
* * *
5925578 AATTACTGAAATACCCCTGTAGGGTAGAATTATTGAAATACCTCTGCAAGGTAGAATTATCGAAA
1 AATTACTGAAATACCCCTGTAGGGTAGAATTATTGAAATACCCCTGTAAGGTAGAATTACCGAAA
5925643 TACCCTTGTAGGGTAG
66 TACCC-TGTAGGGTAG
* * *
5925659 AATTACCGAAATACCCCTGTAGGGTAGAATTATTGAAATACCCCTATAAGGTAGAATTACCAAAA
1 AATTACTGAAATACCCCTGTAGGGTAGAATTATTGAAATACCCCTGTAAGGTAGAATTACCGAAA
5925724 TAACCCTGTAGGGTAG
66 T-ACCCTGTAGGGTAG
* * * * *
5925740 AATTACTGAAATACCCTTGTAGGGTAGAAATACTAAAATACCCCTGTAGGGTAGAATTACCGA
1 AATTACTGAAATACCCCTGTAGGGTAGAATTATTGAAATACCCCTGTAAGGTAGAATTACCGA
5925803 GGTACCCTCG
Statistics
Matches: 129, Mismatches: 14, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
81 125 0.97
82 4 0.03
ACGTcount: A:0.37, C:0.17, G:0.20, T:0.26
Consensus pattern (80 bp):
AATTACTGAAATACCCCTGTAGGGTAGAATTATTGAAATACCCCTGTAAGGTAGAATTACCGAAA
TACCCTGTAGGGTAG
Found at i:5931345 original size:29 final size:29
Alignment explanation
Indices: 5931310--5931378 Score: 95
Period size: 29 Copynumber: 2.4 Consensus size: 29
5931300 TGAGATTGGT
* *
5931310 ACTAAGTGTGCGGGCTTGAAA-TGCATGGC
1 ACTAAGTGTGCGAG-TTGAAAGTACATGGC
*
5931339 ACTAAGTGTGCGAGTTTAAAGTACATGGC
1 ACTAAGTGTGCGAGTTGAAAGTACATGGC
5931368 ACTAAGTGTGC
1 ACTAAGTGTGC
5931379 TTGGTTGATT
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
28 5 0.14
29 31 0.86
ACGTcount: A:0.28, C:0.16, G:0.30, T:0.26
Consensus pattern (29 bp):
ACTAAGTGTGCGAGTTGAAAGTACATGGC
Found at i:5939503 original size:29 final size:29
Alignment explanation
Indices: 5939468--5939540 Score: 103
Period size: 29 Copynumber: 2.5 Consensus size: 29
5939458 GTTGTGAGAT
* *
5939468 TGGCACTAAGTGTGCGGGCTTGAAA-TGCA
1 TGGCACTAAGTGTGCGAG-TTGAAAGTACA
*
5939497 TGGCACTAAGTGTGCGAGTTTAAAGTACA
1 TGGCACTAAGTGTGCGAGTTGAAAGTACA
5939526 TGGCACTAAGTGTGC
1 TGGCACTAAGTGTGC
5939541 ATGGTTGATT
Statistics
Matches: 40, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
28 5 0.12
29 35 0.88
ACGTcount: A:0.26, C:0.16, G:0.32, T:0.26
Consensus pattern (29 bp):
TGGCACTAAGTGTGCGAGTTGAAAGTACA
Found at i:5941772 original size:20 final size:19
Alignment explanation
Indices: 5941736--5941786 Score: 54
Period size: 20 Copynumber: 2.7 Consensus size: 19
5941726 AATGGTTATT
*
5941736 TTGTAAA-GTTGTAAAATAA
1 TTGTAAATG-TGTGAAATAA
5941755 GTTGTAAATGTGTGAAATAA
1 -TTGTAAATGTGTGAAATAA
5941775 TTG-AAAT-TGTGA
1 TTGTAAATGTGTGA
5941787 GTTGCTATAG
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
17 5 0.17
18 4 0.14
19 3 0.10
20 16 0.55
21 1 0.03
ACGTcount: A:0.41, C:0.00, G:0.22, T:0.37
Consensus pattern (19 bp):
TTGTAAATGTGTGAAATAA
Found at i:5948427 original size:16 final size:15
Alignment explanation
Indices: 5948396--5948438 Score: 52
Period size: 16 Copynumber: 2.7 Consensus size: 15
5948386 TTTGATGAAT
5948396 TGAA-TTACTTAACTA
1 TGAACTTAC-TAACTA
5948411 TGAACTTACTAAGCTA
1 TGAACTTACTAA-CTA
5948427 TGAAGCTTACTA
1 TGAA-CTTACTA
5948439 TGTGTTATTT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
15 7 0.28
16 11 0.44
17 7 0.28
ACGTcount: A:0.37, C:0.16, G:0.12, T:0.35
Consensus pattern (15 bp):
TGAACTTACTAACTA
Found at i:5951915 original size:27 final size:27
Alignment explanation
Indices: 5951856--5952034 Score: 268
Period size: 27 Copynumber: 6.6 Consensus size: 27
5951846 TAAATTGTAC
*
5951856 AGCACTAAGTGTGCGAGTTGGACTATGT
1 AGCACTAAGTGTGCGAATT-GACTATGT
5951884 AGCACTAAGTGTGCGAATTGACTATGT
1 AGCACTAAGTGTGCGAATTGACTATGT
*
5951911 TGCACTAAGTGTGCGAATTGACTATGT
1 AGCACTAAGTGTGCGAATTGACTATGT
*
5951938 TGCACTAAGTGTGCGAATTGACTATGT
1 AGCACTAAGTGTGCGAATTGACTATGT
* *
5951965 AGCACTAAGTGTGCGAGTTTGATTATGT
1 AGCACTAAGTGTGCGA-ATTGACTATGT
* *
5951993 AGCACTAAGTGTGCGAGTTGACTATAT
1 AGCACTAAGTGTGCGAATTGACTATGT
*
5952020 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
5952035 GACTTAATAT
Statistics
Matches: 141, Mismatches: 9, Indels: 3
0.92 0.06 0.02
Matches are distributed among these distances:
27 98 0.70
28 43 0.30
ACGTcount: A:0.26, C:0.15, G:0.28, T:0.31
Consensus pattern (27 bp):
AGCACTAAGTGTGCGAATTGACTATGT
Found at i:5951998 original size:82 final size:82
Alignment explanation
Indices: 5951856--5952034 Score: 270
Period size: 82 Copynumber: 2.2 Consensus size: 82
5951846 TAAATTGTAC
* *
5951856 AGCACTAAGTGTGCGAGTTGGACTATGTAGCACTAAGTGTGCGAATTGACTATGTTGCACTAAGT
1 AGCACTAAGTGTGCGAATTGGACTATGTAGCACTAAGTGTGCGAATTGACTATGTAGCACTAAGT
*
5951921 GTGCGAATTGACTATGT
66 GTGCGAATTGACTATAT
* * *
5951938 TGCACTAAGTGTGCGAATT-GACTATGTAGCACTAAGTGTGCGAGTTTGATTATGTAGCACTAAG
1 AGCACTAAGTGTGCGAATTGGACTATGTAGCACTAAGTGTGCGA-ATTGACTATGTAGCACTAAG
*
5952002 TGTGCGAGTTGACTATAT
65 TGTGCGAATTGACTATAT
*
5952020 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
5952035 GACTTAATAT
Statistics
Matches: 87, Mismatches: 9, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
81 24 0.28
82 63 0.72
ACGTcount: A:0.26, C:0.15, G:0.28, T:0.31
Consensus pattern (82 bp):
AGCACTAAGTGTGCGAATTGGACTATGTAGCACTAAGTGTGCGAATTGACTATGTAGCACTAAGT
GTGCGAATTGACTATAT
Found at i:5960111 original size:27 final size:27
Alignment explanation
Indices: 5960081--5960257 Score: 167
Period size: 27 Copynumber: 6.5 Consensus size: 27
5960071 AAATTGTACA
* * *
5960081 GCACTAAGGGTGCGATTTGACTATGTT
1 GCACTAAGTGTGCGAATTGACTATGTG
* * *
5960108 GCACTCAGTGTGCGAAATGAATATGAT-
1 GCACTAAGTGTGCGAATTGACTATG-TG
* *
5960135 GCACTAAGTGTGCGAATTGACCATGCG
1 GCACTAAGTGTGCGAATTGACTATGTG
*
5960162 GCACTAAGTGTGCGAGATGGACTATGTG
1 GCACTAAGTGTGCGA-ATTGACTATGTG
* * * *
5960190 GCACTAAGTGTGCGATTTGATTACGTA
1 GCACTAAGTGTGCGAATTGACTATGTG
* * * *
5960217 GCACTAAGTGTGCGAGTTGATTATATA
1 GCACTAAGTGTGCGAATTGACTATGTG
*
5960244 GCACTGAGTGTGCG
1 GCACTAAGTGTGCG
5960258 GGCTCAATAA
Statistics
Matches: 125, Mismatches: 22, Indels: 6
0.82 0.14 0.04
Matches are distributed among these distances:
27 100 0.80
28 25 0.20
ACGTcount: A:0.26, C:0.16, G:0.30, T:0.28
Consensus pattern (27 bp):
GCACTAAGTGTGCGAATTGACTATGTG
Found at i:5960200 original size:82 final size:81
Alignment explanation
Indices: 5960081--5960236 Score: 197
Period size: 82 Copynumber: 1.9 Consensus size: 81
5960071 AAATTGTACA
* * * * *
5960081 GCACTAAGGGTGCGATTTGACTATGTTGCACTCAGTGTGCGAAATGAATATG-ATGCACTAAGTG
1 GCACTAAGGGTGCGAATGGACTATGTGGCACTAAGTGTGCGAAATGAATACGTA-GCACTAAGTG
5960145 TGCGAATTGACCATGCG
65 TGCGAATTGACCATGCG
* ** *
5960162 GCACTAAGTGTGCGAGATGGACTATGTGGCACTAAGTGTGCGATTTGATTACGTAGCACTAAGTG
1 GCACTAAGGGTGCGA-ATGGACTATGTGGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTG
*
5960227 TGCGAGTTGA
65 TGCGAATTGA
5960237 TTATATAGCA
Statistics
Matches: 63, Mismatches: 10, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
81 14 0.22
82 48 0.76
83 1 0.02
ACGTcount: A:0.26, C:0.16, G:0.30, T:0.28
Consensus pattern (81 bp):
GCACTAAGGGTGCGAATGGACTATGTGGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTGT
GCGAATTGACCATGCG
Found at i:5960221 original size:55 final size:54
Alignment explanation
Indices: 5960081--5960257 Score: 187
Period size: 54 Copynumber: 3.3 Consensus size: 54
5960071 AAATTGTACA
* * * *
5960081 GCACTAAGGGTGCGATTTGACTATGTTGCACTCAGTGTGCGAAATGAATATGAT
1 GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAGATGAATATGAT
* * ** *
5960135 GCACTAAGTGTGCGAATTGACCATGCGGCACTAAGTGTGCGAGATGGACTATG-T
1 GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAGAT-GAATATGAT
* * * *
5960189 GGCACTAAGTGTGCGATTTGATTACGTAGCACTAAGTGTGCGAGTTGATTAT-AT
1 -GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAGATGAATATGAT
*
5960243 AGCACTGAGTGTGCG
1 -GCACTAAGTGTGCG
5960258 GGCTCAATAA
Statistics
Matches: 102, Mismatches: 18, Indels: 6
0.81 0.14 0.05
Matches are distributed among these distances:
54 58 0.57
55 44 0.43
ACGTcount: A:0.26, C:0.16, G:0.30, T:0.28
Consensus pattern (54 bp):
GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAGATGAATATGAT
Found at i:5960248 original size:82 final size:81
Alignment explanation
Indices: 5960077--5960257 Score: 193
Period size: 82 Copynumber: 2.2 Consensus size: 81
5960067 GATTAAATTG
* * * * * *
5960077 TACAGCACTAAGGGTGCGATTTGACTATGTTGCACTCAGTGTGCGAAATGAATATGATGCACTAA
1 TACAGCACTAAGTGTGCGAATGGACTATGTGGCACTAAGTGTGCGAAATGAATACGATGCACTAA
5960142 GTGTGCGAATTGACCA
66 GTGTGCGAATTGACCA
* * ** *
5960158 TGCGGCACTAAGTGTGCGAGATGGACTATGTGGCACTAAGTGTGCGATTTGATTACG-TAGCACT
1 TACAGCACTAAGTGTGCGA-ATGGACTATGTGGCACTAAGTGTGCGAAATGAATACGAT-GCACT
* **
5960222 AAGTGTGCGAGTTGATTA
64 AAGTGTGCGAATTGACCA
* *
5960240 TATAGCACTGAGTGTGCG
1 TACAGCACTAAGTGTGCG
5960258 GGCTCAATAA
Statistics
Matches: 80, Mismatches: 18, Indels: 3
0.79 0.18 0.03
Matches are distributed among these distances:
81 17 0.21
82 63 0.79
ACGTcount: A:0.27, C:0.16, G:0.29, T:0.28
Consensus pattern (81 bp):
TACAGCACTAAGTGTGCGAATGGACTATGTGGCACTAAGTGTGCGAAATGAATACGATGCACTAA
GTGTGCGAATTGACCA
Found at i:5967338 original size:44 final size:45
Alignment explanation
Indices: 5967240--5967338 Score: 137
Period size: 44 Copynumber: 2.2 Consensus size: 45
5967230 TACTATGTGA
* *
5967240 ACCGGGTACCATTGACTATAAAAGTGGTTGCTATGTGCTGATTCC
1 ACCGAGTATCATTGACTATAAAAGTGGTTGCTATGTGCTGATTCC
* * *
5967285 ACTGAGTATCATTGATTAT-AAGGTGGTTGCTATGTGCTGATTCC
1 ACCGAGTATCATTGACTATAAAAGTGGTTGCTATGTGCTGATTCC
*
5967329 ACCGTGTATC
1 ACCGAGTATC
5967339 TGTTATTATT
Statistics
Matches: 47, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
44 32 0.68
45 15 0.32
ACGTcount: A:0.23, C:0.18, G:0.24, T:0.34
Consensus pattern (45 bp):
ACCGAGTATCATTGACTATAAAAGTGGTTGCTATGTGCTGATTCC
Found at i:5967593 original size:13 final size:13
Alignment explanation
Indices: 5967575--5967600 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
5967565 AATACTCAGT
5967575 TTGGATTGAACGC
1 TTGGATTGAACGC
5967588 TTGGATTGAACGC
1 TTGGATTGAACGC
5967601 GGGATTGAGT
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:0.23, C:0.15, G:0.31, T:0.31
Consensus pattern (13 bp):
TTGGATTGAACGC
Found at i:5996622 original size:50 final size:50
Alignment explanation
Indices: 5996556--5996741 Score: 164
Period size: 50 Copynumber: 3.7 Consensus size: 50
5996546 GAGGATGAGA
* * **
5996556 TCCCAAGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAGG
1 TCCCACGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGACAAC
* * * * *
5996606 TCCCCCGTAAGACCATGTCTGTGACATGGTATAT-GCACTGATATGACAAC
1 TCCCACGTAAGACCATGTCTGGGACATGGCAT-TGGCACCGAGATGACAAC
* * * * *
5996656 TCCCATGTAAGACCATATCTGGGATATGGCATTGGCA--GTACAGGA-AAC
1 TCCCACGTAAGACCATGTCTGGGACATGGCATTGGCACCG-AGATGACAAC
* * *
5996704 ATCCCATGTAAGACCATGTCTGGGACATAGCTTTGGCA
1 -TCCCACGTAAGACCATGTCTGGGACATGGCATTGGCA
5996742 TTTTATTATC
Statistics
Matches: 111, Mismatches: 21, Indels: 9
0.79 0.15 0.06
Matches are distributed among these distances:
48 4 0.04
49 38 0.34
50 68 0.61
51 1 0.01
ACGTcount: A:0.28, C:0.23, G:0.25, T:0.23
Consensus pattern (50 bp):
TCCCACGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGACAAC
Found at i:5996960 original size:12 final size:12
Alignment explanation
Indices: 5996943--5996981 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
5996933 ATGAGTTATT
5996943 TAAGTAAGCAAG
1 TAAGTAAGCAAG
*
5996955 TAAGTAAACAAG
1 TAAGTAAGCAAG
* *
5996967 TAAGAAAGTAAG
1 TAAGTAAGCAAG
5996979 TAA
1 TAA
5996982 AGAAGAAACG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.56, C:0.05, G:0.21, T:0.18
Consensus pattern (12 bp):
TAAGTAAGCAAG
Found at i:6004725 original size:13 final size:13
Alignment explanation
Indices: 6004702--6004737 Score: 54
Period size: 13 Copynumber: 2.8 Consensus size: 13
6004692 CCGTGTGAGT
*
6004702 CACACGACCTAGC
1 CACACGGCCTAGC
*
6004715 CACATGGCCTAGC
1 CACACGGCCTAGC
6004728 CACACGGCCT
1 CACACGGCCT
6004738 TGTGACCCCT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.25, C:0.44, G:0.19, T:0.11
Consensus pattern (13 bp):
CACACGGCCTAGC
Found at i:6016506 original size:13 final size:13
Alignment explanation
Indices: 6016488--6016517 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
6016478 AGCCCAAACT
6016488 CAATTACCCAACC
1 CAATTACCCAACC
6016501 CAATTACCCAACC
1 CAATTACCCAACC
6016514 CAAT
1 CAAT
6016518 AAAACTAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.40, C:0.43, G:0.00, T:0.17
Consensus pattern (13 bp):
CAATTACCCAACC
Found at i:6016669 original size:9 final size:9
Alignment explanation
Indices: 6016657--6016742 Score: 93
Period size: 9 Copynumber: 9.4 Consensus size: 9
6016647 AAAATAAAAA
6016657 AATTCGGGT
1 AATTCGGGT
*
6016666 AATTCAGGT
1 AATTCGGGT
*
6016675 ATTTTTC-GGT
1 A--ATTCGGGT
*
6016685 AATTCGGTT
1 AATTCGGGT
*
6016694 AATTCGGTT
1 AATTCGGGT
*
6016703 AATTCGGTT
1 AATTCGGGT
6016712 AATTCGGGT
1 AATTCGGGT
6016721 AATTCGGGT
1 AATTCGGGT
*
6016730 AATTCGGCT
1 AATTCGGGT
6016739 AATT
1 AATT
6016743 TTTAACCAAA
Statistics
Matches: 68, Mismatches: 6, Indels: 6
0.85 0.08 0.08
Matches are distributed among these distances:
8 3 0.04
9 58 0.85
10 4 0.06
11 3 0.04
ACGTcount: A:0.23, C:0.12, G:0.24, T:0.41
Consensus pattern (9 bp):
AATTCGGGT
Found at i:6019911 original size:28 final size:27
Alignment explanation
Indices: 6019880--6019945 Score: 69
Period size: 30 Copynumber: 2.3 Consensus size: 27
6019870 ATAAAAAAAG
**
6019880 AATAATTAAAATTATAAAATTTATTAGA
1 AATAATTAAAACCATAAAATTTATTA-A
*
6019908 AATAAATTAAAAACCATATAATTTATTAA
1 AAT-AATT-AAAACCATAAAATTTATTAA
*
6019937 AAAAATTAA
1 AATAATTAA
6019946 TTTATTAAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 5
0.78 0.10 0.12
Matches are distributed among these distances:
27 2 0.06
28 7 0.22
29 7 0.22
30 16 0.50
ACGTcount: A:0.61, C:0.03, G:0.02, T:0.35
Consensus pattern (27 bp):
AATAATTAAAACCATAAAATTTATTAA
Found at i:6019937 original size:19 final size:19
Alignment explanation
Indices: 6019913--6019961 Score: 75
Period size: 17 Copynumber: 2.7 Consensus size: 19
6019903 TTAGAAATAA
6019913 ATTAAAAACCATATAATTT
1 ATTAAAAACCATATAATTT
*
6019932 ATTAAAAA-AAT-TAATTT
1 ATTAAAAACCATATAATTT
6019949 ATTAAAAACCATA
1 ATTAAAAACCATA
6019962 AAAATAGAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
17 14 0.54
18 4 0.15
19 8 0.31
ACGTcount: A:0.57, C:0.08, G:0.00, T:0.35
Consensus pattern (19 bp):
ATTAAAAACCATATAATTT
Found at i:6020024 original size:10 final size:10
Alignment explanation
Indices: 6020009--6020068 Score: 77
Period size: 10 Copynumber: 5.9 Consensus size: 10
6019999 AATTAAAACC
6020009 ATAAAATTTT
1 ATAAAATTTT
*
6020019 ATAAAAATAATT
1 AT-AAAAT-TTT
*
6020031 A-AATATTTT
1 ATAAAATTTT
6020040 ATAAAATTTT
1 ATAAAATTTT
6020050 ATAAAATTTT
1 ATAAAATTTT
6020060 ATAAAATTT
1 ATAAAATTT
6020069 ATTTTTCTCA
Statistics
Matches: 43, Mismatches: 4, Indels: 6
0.81 0.08 0.11
Matches are distributed among these distances:
9 3 0.07
10 32 0.74
11 5 0.12
12 3 0.07
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (10 bp):
ATAAAATTTT
Found at i:6020315 original size:20 final size:20
Alignment explanation
Indices: 6020292--6020410 Score: 78
Period size: 20 Copynumber: 5.8 Consensus size: 20
6020282 TTATTTTTTC
*
6020292 TAAATTTTTATGGTTTTTAA
1 TAAATTTTTATAGTTTTTAA
**
6020312 TAAATTATTTTATAAATTTT-A
1 TAAA-T-TTTTATAGTTTTTAA
* *
6020333 TAAAATTTTATTGTTTTTAA
1 TAAATTTTTATAGTTTTTAA
** * * * *
6020353 TTTATTTCTAAAATTTTTTA
1 TAAATTTTTATAGTTTTTAA
* *
6020373 TAAATTTTAATGATTTTTTAA
1 TAAATTTTTAT-AGTTTTTAA
*
6020394 TAATTTTTTATAGTTTT
1 TAAATTTTTATAGTTTT
6020411 AATTCTAAAA
Statistics
Matches: 70, Mismatches: 25, Indels: 8
0.68 0.24 0.08
Matches are distributed among these distances:
19 10 0.14
20 28 0.40
21 22 0.31
22 10 0.14
ACGTcount: A:0.34, C:0.01, G:0.04, T:0.61
Consensus pattern (20 bp):
TAAATTTTTATAGTTTTTAA
Found at i:6020349 original size:41 final size:40
Alignment explanation
Indices: 6020287--6020405 Score: 120
Period size: 41 Copynumber: 3.0 Consensus size: 40
6020277 ATAAATTATT
* * *
6020287 TTTTCTAAATTTTTATGGTTTTTAATAAATTATTTTATAAA
1 TTTTATAAAATTTTATTGTTTTTAAT-AATTATTTTATAAA
6020328 TTTTATAAAATTTTATTGTTTTTAAT--TTATTTCTA-AAA
1 TTTTATAAAATTTTATTGTTTTTAATAATTATTT-TATAAA
* *
6020366 TTTTTTATAAATTTTAATGATTTTTTAATAATT-TTTTATA
1 TTTTATA-AAATTTTATTG--TTTTTAATAATTATTTTATA
6020406 GTTTTAATTC
Statistics
Matches: 66, Mismatches: 5, Indels: 13
0.79 0.06 0.15
Matches are distributed among these distances:
38 15 0.23
39 12 0.18
41 33 0.50
42 4 0.06
43 2 0.03
ACGTcount: A:0.34, C:0.02, G:0.03, T:0.61
Consensus pattern (40 bp):
TTTTATAAAATTTTATTGTTTTTAATAATTATTTTATAAA
Found at i:6020381 original size:30 final size:28
Alignment explanation
Indices: 6020347--6020414 Score: 75
Period size: 30 Copynumber: 2.3 Consensus size: 28
6020337 ATTTTATTGT
6020347 TTTTAATTTATTTCTAA-AATTTTTTATAAA
1 TTTTAATTT-TTT-TAATAATTTTTTAT-AA
*
6020377 TTTTAATGATTTTTTAATAATTTTTTATAG
1 TTTTAAT--TTTTTTAATAATTTTTTATAA
6020407 TTTTAATT
1 TTTTAATT
6020415 CTAAAATGAA
Statistics
Matches: 34, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
28 1 0.03
30 18 0.53
31 13 0.38
32 2 0.06
ACGTcount: A:0.32, C:0.01, G:0.03, T:0.63
Consensus pattern (28 bp):
TTTTAATTTTTTTAATAATTTTTTATAA
Found at i:6022201 original size:15 final size:15
Alignment explanation
Indices: 6022181--6022210 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
6022171 CTTTTTGACA
6022181 AAATTGCAATATGTT
1 AAATTGCAATATGTT
6022196 AAATTGCAATATGTT
1 AAATTGCAATATGTT
6022211 TTGCAAATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.40, C:0.07, G:0.13, T:0.40
Consensus pattern (15 bp):
AAATTGCAATATGTT
Found at i:6035510 original size:45 final size:46
Alignment explanation
Indices: 6035418--6035512 Score: 174
Period size: 47 Copynumber: 2.1 Consensus size: 46
6035408 GTATAAAGGT
6035418 ACTTTTATCAGTTATGATACATACACAAAAAAAAATATTCATAATAA
1 ACTTTTATCAGTTATGATACATACAC-AAAAAAAATATTCATAATAA
6035465 ACTTTTATCAGTTATGATACATACAC-AAAAAAATATTCATAATAA
1 ACTTTTATCAGTTATGATACATACACAAAAAAAATATTCATAATAA
6035510 ACT
1 ACT
6035513 CAAATTATAT
Statistics
Matches: 48, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
45 22 0.46
47 26 0.54
ACGTcount: A:0.49, C:0.14, G:0.04, T:0.33
Consensus pattern (46 bp):
ACTTTTATCAGTTATGATACATACACAAAAAAAATATTCATAATAA
Found at i:6036618 original size:37 final size:37
Alignment explanation
Indices: 6036567--6036717 Score: 162
Period size: 37 Copynumber: 4.0 Consensus size: 37
6036557 TGTACAGGTA
*
6036567 TATGCACTTTGTGTGCCAATATGCACTTATGTGCTAG
1 TATGCACTTCGTGTGCCAATATGCACTTATGTGCTAG
* *
6036604 TATGCACTTCGTGTGCCAGGA-ATGCGCTTATGCGCTAG
1 TATGCACTTCGTGTGCCA--ATATGCACTTATGTGCTAG
* * * * * *
6036642 TATGCACTTCGTGTGCTAGTATGCGCTTGTGGGCCAAG
1 TATGCACTTCGTGTGCCAATATGCACTTATGTG-CTAG
*
6036680 -ATGCACTTTGTGTGCCAATATGCACTATATGTGCTAG
1 TATGCACTTCGTGTGCCAATATGCACT-TATGTGCTAG
6036717 T
1 T
6036718 TTCTATTACT
Statistics
Matches: 93, Mismatches: 15, Indels: 11
0.78 0.13 0.09
Matches are distributed among these distances:
37 53 0.57
38 39 0.42
39 1 0.01
ACGTcount: A:0.20, C:0.21, G:0.26, T:0.34
Consensus pattern (37 bp):
TATGCACTTCGTGTGCCAATATGCACTTATGTGCTAG
Found at i:6036713 original size:19 final size:18
Alignment explanation
Indices: 6036566--6036705 Score: 102
Period size: 19 Copynumber: 7.5 Consensus size: 18
6036556 CTGTACAGGT
6036566 ATATGCACTTTGTGTGCCA
1 ATATGCAC-TTGTGTGCCA
* *
6036585 ATATGCACTTATGTGCTA
1 ATATGCACTTGTGTGCCA
*
6036603 GTATGCACTTCGTGTGCCA
1 ATATGCACTT-GTGTGCCA
* * * *
6036622 GGA-ATGCGCTTATGCGCTA
1 --ATATGCACTTGTGTGCCA
* *
6036641 GTATGCACTTCGTGTGCTA
1 ATATGCACTT-GTGTGCCA
* * *
6036660 GTATGCGCTTGTGGGCCA
1 ATATGCACTTGTGTGCCA
*
6036678 AGATGCACTTTGTGTGCCA
1 ATATGCAC-TTGTGTGCCA
6036697 ATATGCACT
1 ATATGCACT
6036706 ATATGTGCTA
Statistics
Matches: 93, Mismatches: 22, Indels: 13
0.73 0.17 0.10
Matches are distributed among these distances:
18 36 0.39
19 50 0.54
20 7 0.08
ACGTcount: A:0.20, C:0.21, G:0.26, T:0.33
Consensus pattern (18 bp):
ATATGCACTTGTGTGCCA
Found at i:6039925 original size:4 final size:4
Alignment explanation
Indices: 6039912--6040062 Score: 284
Period size: 4 Copynumber: 37.8 Consensus size: 4
6039902 ACACACACAC
*
6039912 ACAT ATAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
*
6039960 ACAT ACAT ACAT ACAT ACAT ATAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
6040008 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
6040056 ACAT ACA
1 ACAT ACA
6040063 ACAACTTCTC
Statistics
Matches: 143, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
4 143 1.00
ACGTcount: A:0.50, C:0.24, G:0.00, T:0.26
Consensus pattern (4 bp):
ACAT
Found at i:6044354 original size:14 final size:15
Alignment explanation
Indices: 6044335--6044363 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
6044325 ACTAAAAATG
6044335 CTATGGCAAA-GATA
1 CTATGGCAAATGATA
6044349 CTATGGCAAATGATA
1 CTATGGCAAATGATA
6044364 GAAGGTTTAC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.71
15 4 0.29
ACGTcount: A:0.41, C:0.14, G:0.21, T:0.24
Consensus pattern (15 bp):
CTATGGCAAATGATA
Found at i:6045747 original size:13 final size:13
Alignment explanation
Indices: 6045731--6045763 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
6045721 GATTAGAAAT
*
6045731 TAAATAACTAATA
1 TAAATAAATAATA
6045744 TAAATAAATAATA
1 TAAATAAATAATA
6045757 -AAATAAA
1 TAAATAAA
6045764 CAAATGGTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 7 0.37
13 12 0.63
ACGTcount: A:0.70, C:0.03, G:0.00, T:0.27
Consensus pattern (13 bp):
TAAATAAATAATA
Found at i:6056079 original size:6 final size:6
Alignment explanation
Indices: 6056068--6056093 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
6056058 GAGCTACAGT
6056068 AAAAGC AAAAGC AAAAGC AAAAGC AA
1 AAAAGC AAAAGC AAAAGC AAAAGC AA
6056094 GCACAAAATG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.69, C:0.15, G:0.15, T:0.00
Consensus pattern (6 bp):
AAAAGC
Found at i:6060122 original size:22 final size:22
Alignment explanation
Indices: 6060089--6060133 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 22
6060079 TAGTTTTAGG
*
6060089 TTTAGTTTTCTCTA-AGTTTTC
1 TTTAGTTTTCTCTACACTTTTC
6060110 TTTAGTTTTTCTCTACACTTTTC
1 TTTAG-TTTTCTCTACACTTTTC
6060133 T
1 T
6060134 AGGGTTTTCT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 5 0.24
22 9 0.43
23 7 0.33
ACGTcount: A:0.13, C:0.18, G:0.07, T:0.62
Consensus pattern (22 bp):
TTTAGTTTTCTCTACACTTTTC
Found at i:6063395 original size:17 final size:19
Alignment explanation
Indices: 6063369--6063413 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 19
6063359 CAAGATAAAC
6063369 ATTAAAATAA-AT-TTAAT
1 ATTAAAATAACATCTTAAT
*
6063386 ATTAAGATAATCATCTTAAT
1 ATTAAAATAA-CATCTTAAT
6063406 ATTAAAAT
1 ATTAAAAT
6063414 TAATAATATA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
17 9 0.39
19 2 0.09
20 12 0.52
ACGTcount: A:0.53, C:0.04, G:0.02, T:0.40
Consensus pattern (19 bp):
ATTAAAATAACATCTTAAT
Found at i:6070411 original size:25 final size:27
Alignment explanation
Indices: 6070382--6070439 Score: 66
Period size: 26 Copynumber: 2.2 Consensus size: 27
6070372 TCTATAACAT
*
6070382 AAATATTAAATTAA-ATTAAA-TATTA
1 AAATATTAAATTAATATTAAATTAATA
**
6070407 AAATAATTACTTTAATATTAAATTAATA
1 AAAT-ATTAAATTAATATTAAATTAATA
6070435 AAATA
1 AAATA
6070440 CTATTAAGAT
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
25 4 0.15
26 8 0.30
27 7 0.26
28 8 0.30
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.40
Consensus pattern (27 bp):
AAATATTAAATTAATATTAAATTAATA
Found at i:6070480 original size:37 final size:35
Alignment explanation
Indices: 6070423--6070492 Score: 88
Period size: 37 Copynumber: 1.9 Consensus size: 35
6070413 TTACTTTAAT
*
6070423 ATTAAATTAATAAAATACTATTAAGATAAGTATTGA
1 ATTAAATTAATAAAATACTATTAAAATAA-TATTGA
*
6070459 ATTAAATTTAATATTAA-ACTATTAAAATAATATT
1 ATTAAA-TTAATA-AAATACTATTAAAATAATATT
6070493 ATTTTTGGAA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
36 10 0.33
37 18 0.60
38 2 0.07
ACGTcount: A:0.53, C:0.03, G:0.04, T:0.40
Consensus pattern (35 bp):
ATTAAATTAATAAAATACTATTAAAATAATATTGA
Found at i:6071512 original size:26 final size:26
Alignment explanation
Indices: 6071476--6071526 Score: 93
Period size: 26 Copynumber: 2.0 Consensus size: 26
6071466 CACCAATTTT
6071476 GCAGCAAAGCTACCAGAAATAGTATC
1 GCAGCAAAGCTACCAGAAATAGTATC
*
6071502 GCAGCAAAGCTACCAGTAATAGTAT
1 GCAGCAAAGCTACCAGAAATAGTAT
6071527 ATGTGGCAGA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.41, C:0.22, G:0.20, T:0.18
Consensus pattern (26 bp):
GCAGCAAAGCTACCAGAAATAGTATC
Found at i:6071754 original size:27 final size:27
Alignment explanation
Indices: 6071700--6071841 Score: 164
Period size: 27 Copynumber: 5.4 Consensus size: 27
6071690 GGGTATAACA
*
6071700 GTCATTTTA-CC-ATGTGGGTATTTCG
1 GTCATTTTATCCTATGGGGGTATTTCG
*
6071725 GTCATTTTATCCTATGGGGGTATTTTG
1 GTCATTTTATCCTATGGGGGTATTTCG
* * *
6071752 GTCATTTTACCCTACGAGGGTATTTCG
1 GTCATTTTATCCTATGGGGGTATTTCG
* * *
6071779 GTCATTTTACCCTAT-GGGGTCTTCCG
1 GTCATTTTATCCTATGGGGGTATTTCG
* * *
6071805 GTCATTTTATCCTACGGAGGTATTTCA
1 GTCATTTTATCCTATGGGGGTATTTCG
6071832 GTCATTTTAT
1 GTCATTTTAT
6071842 TGACCTCACG
Statistics
Matches: 98, Mismatches: 16, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
25 9 0.09
26 23 0.23
27 66 0.67
ACGTcount: A:0.17, C:0.18, G:0.22, T:0.43
Consensus pattern (27 bp):
GTCATTTTATCCTATGGGGGTATTTCG
Found at i:6071827 original size:53 final size:54
Alignment explanation
Indices: 6071715--6071840 Score: 175
Period size: 53 Copynumber: 2.4 Consensus size: 54
6071705 TTTACCATGT
* **
6071715 GGGTATTTCGGTCATTTTATCCTATGGGGGTATTTTGGTCATTTTACCCTACGA
1 GGGTATTTCGGTCATTTTACCCTATGGGGGTATTCCGGTCATTTTACCCTACGA
* *
6071769 GGGTATTTCGGTCATTTTACCCTAT-GGGGTCTTCCGGTCATTTTATCCTACG-
1 GGGTATTTCGGTCATTTTACCCTATGGGGGTATTCCGGTCATTTTACCCTACGA
*
6071821 GAGGTATTTCAGTCATTTTA
1 G-GGTATTTCGGTCATTTTA
6071841 TTGACCTCAC
Statistics
Matches: 65, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
52 1 0.02
53 40 0.62
54 24 0.37
ACGTcount: A:0.17, C:0.18, G:0.23, T:0.42
Consensus pattern (54 bp):
GGGTATTTCGGTCATTTTACCCTATGGGGGTATTCCGGTCATTTTACCCTACGA
Found at i:6079280 original size:27 final size:26
Alignment explanation
Indices: 6079250--6079419 Score: 187
Period size: 27 Copynumber: 6.3 Consensus size: 26
6079240 GGGTATAATA
*
6079250 GTCATTTTAACCTATGTGGGTATTTTG
1 GTCATTTTACCCTATG-GGGTATTTTG
* *
6079277 GTCATTTTACCCGATGGCGGTGTTTTG
1 GTCATTTTACCCTATGG-GGTATTTTG
* * *
6079304 GTTATTTTACCCTACAGGGGTATTTCG
1 GTCATTTTACCCTA-TGGGGTATTTTG
*
6079331 GTCATTTTCCCCTATAGGGGTATTTTG
1 GTCATTTTACCCTAT-GGGGTATTTTG
* *
6079358 GTTATTTTACCCTATGAGGGTATTTCG
1 GTCATTTTACCCTATG-GGGTATTTTG
* *
6079385 GTTATTTTACCCTACGGGGTATTTTG
1 GTCATTTTACCCTATGGGGTATTTTG
*
6079411 ATCATTTTA
1 GTCATTTTA
6079420 TTGACCTCAC
Statistics
Matches: 120, Mismatches: 19, Indels: 9
0.81 0.13 0.06
Matches are distributed among these distances:
26 18 0.15
27 100 0.83
28 2 0.02
ACGTcount: A:0.17, C:0.16, G:0.22, T:0.45
Consensus pattern (26 bp):
GTCATTTTACCCTATGGGGTATTTTG
Found at i:6079388 original size:81 final size:80
Alignment explanation
Indices: 6079250--6079419 Score: 227
Period size: 81 Copynumber: 2.1 Consensus size: 80
6079240 GGGTATAATA
* *
6079250 GTCATTTTAACCTATGTGGGTATTTTGGTCATTTTACCCGATGGCGGTGTTTTGGTTATTTTACC
1 GTCATTTTAACCTATGTGGGTATTTTGGTCATTTTACCCGATGGCGGTATTTCGGTTATTTTACC
6079315 CTACAGGGGTATTTCG
66 CTAC-GGGGTATTTCG
** * *
6079331 GTCATTTTCCCCTATAG-GGGTATTTTGGTTATTTTACCCTATGAG-GGTATTTCGGTTATTTTA
1 GTCATTTTAACCTAT-GTGGGTATTTTGGTCATTTTACCCGATG-GCGGTATTTCGGTTATTTTA
*
6079394 CCCTACGGGGTATTTTG
64 CCCTACGGGGTATTTCG
*
6079411 ATCATTTTA
1 GTCATTTTA
6079420 TTGACCTCAC
Statistics
Matches: 78, Mismatches: 9, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
80 17 0.22
81 59 0.76
82 2 0.03
ACGTcount: A:0.17, C:0.16, G:0.22, T:0.45
Consensus pattern (80 bp):
GTCATTTTAACCTATGTGGGTATTTTGGTCATTTTACCCGATGGCGGTATTTCGGTTATTTTACC
CTACGGGGTATTTCG
Found at i:6081217 original size:24 final size:25
Alignment explanation
Indices: 6081185--6081235 Score: 68
Period size: 24 Copynumber: 2.1 Consensus size: 25
6081175 AAATATCATA
*
6081185 TTAATTTTAATTAATTTAAA-TAAT
1 TTAATTTTAATTAATTAAAATTAAT
* *
6081209 TTAATTTTATTTGATTAAAATTAAT
1 TTAATTTTAATTAATTAAAATTAAT
6081234 TT
1 TT
6081236 CCCGAAAAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
24 17 0.74
25 6 0.26
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (25 bp):
TTAATTTTAATTAATTAAAATTAAT
Found at i:6083997 original size:63 final size:63
Alignment explanation
Indices: 6083896--6084023 Score: 220
Period size: 63 Copynumber: 2.0 Consensus size: 63
6083886 AGCCACGAAC
6083896 ATTGAGGGTTAGATAGAAATAATTTGGAGGTTTAAAAAATGAAATTGAATGAATAGTGAATAG
1 ATTGAGGGTTAGATAGAAATAATTTGGAGGTTTAAAAAATGAAATTGAATGAATAGTGAATAG
* * * *
6083959 ATTGAGGGTTAGGTAGAAATAATTTGGAGGTTTTAAAAATGAAATTGAGTGAGTAGTGAATAG
1 ATTGAGGGTTAGATAGAAATAATTTGGAGGTTTAAAAAATGAAATTGAATGAATAGTGAATAG
6084022 AT
1 AT
6084024 GGTCCGATAT
Statistics
Matches: 61, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
63 61 1.00
ACGTcount: A:0.41, C:0.00, G:0.27, T:0.31
Consensus pattern (63 bp):
ATTGAGGGTTAGATAGAAATAATTTGGAGGTTTAAAAAATGAAATTGAATGAATAGTGAATAG
Found at i:6089766 original size:27 final size:26
Alignment explanation
Indices: 6089703--6089759 Score: 78
Period size: 26 Copynumber: 2.2 Consensus size: 26
6089693 TAAAACTCTT
*
6089703 TTAAAAGAAAACTCAAGAGAAATTAT
1 TTAAAAGAAAACTCAAGAGAAATTAG
* *
6089729 TTAAAAGAAAACTCACAGAGAATTTCG
1 TTAAAAGAAAACTCA-AGAGAAATTAG
6089756 TTAA
1 TTAA
6089760 TTGAAAAACA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
26 15 0.56
27 12 0.44
ACGTcount: A:0.53, C:0.11, G:0.12, T:0.25
Consensus pattern (26 bp):
TTAAAAGAAAACTCAAGAGAAATTAG
Found at i:6101684 original size:27 final size:26
Alignment explanation
Indices: 6101624--6101684 Score: 70
Period size: 27 Copynumber: 2.3 Consensus size: 26
6101614 TTGTTAAAAC
*
6101624 TTATCTAAAAGAAAACTCAAGAGAATT
1 TTAT-TAAAAGAAAAATCAAGAGAATT
*
6101651 TCT-TTAAAATAAAAATCAAAGAGAATT
1 T-TATTAAAAGAAAAATC-AAGAGAATT
6101678 TTATTAA
1 TTATTAA
6101685 CCCAAAAGCA
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
26 12 0.41
27 16 0.55
28 1 0.03
ACGTcount: A:0.52, C:0.08, G:0.08, T:0.31
Consensus pattern (26 bp):
TTATTAAAAGAAAAATCAAGAGAATT
Found at i:6105137 original size:22 final size:23
Alignment explanation
Indices: 6105112--6105155 Score: 63
Period size: 22 Copynumber: 1.9 Consensus size: 23
6105102 GATTTTCCCG
6105112 ACTTCATTTCCCC-AATTTCCTA
1 ACTTCATTTCCCCAAATTTCCTA
*
6105134 ACTTCGTTTCCCCTAAATTTCC
1 ACTTCATTTCCCC-AAATTTCC
6105156 CTAAGTTATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 12 0.63
24 7 0.37
ACGTcount: A:0.20, C:0.36, G:0.02, T:0.41
Consensus pattern (23 bp):
ACTTCATTTCCCCAAATTTCCTA
Found at i:6106363 original size:3 final size:3
Alignment explanation
Indices: 6106355--6106384 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
6106345 GGTGATTCAT
6106355 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
6106385 ATGATTTTCT
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):
TTA
Found at i:6108886 original size:43 final size:43
Alignment explanation
Indices: 6108815--6109060 Score: 348
Period size: 43 Copynumber: 5.7 Consensus size: 43
6108805 ACAGTATTTT
* * * *
6108815 TAGCGGCTTTTGTGGAAAAAGCGTCGCTAAAGGTCTTGAGCTG
1 TAGCGGCGTTTGTGGAAAAAGCGCCGCTAAAGGTCTTGATCTA
* *
6108858 TAGCAGCGTTTGTGGAAAAAGCACCGCTAAAGGTCTTGATCTA
1 TAGCGGCGTTTGTGGAAAAAGCGCCGCTAAAGGTCTTGATCTA
* *
6108901 TAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCTTGAGCTA
1 TAGCGGCGTTTGTGGAAAAAGCGCCGCTAAAGGTCTTGATCTA
* * * *
6108944 TTGCGGCATTTGTGGAAAAAACGCCGCTAAAGGTCCTGATCTA
1 TAGCGGCGTTTGTGGAAAAAGCGCCGCTAAAGGTCTTGATCTA
*
6108987 TAGCGGCGTTTGTGGAAAAAGCGCCGCTAAAGGTCCTGATCTA
1 TAGCGGCGTTTGTGGAAAAAGCGCCGCTAAAGGTCTTGATCTA
* * *
6109030 TAGCAGCATTTGTGGGAAAAGCGCCGCTAAA
1 TAGCGGCGTTTGTGGAAAAAGCGCCGCTAAA
6109061 AACCTATTTT
Statistics
Matches: 181, Mismatches: 22, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
43 181 1.00
ACGTcount: A:0.27, C:0.19, G:0.30, T:0.24
Consensus pattern (43 bp):
TAGCGGCGTTTGTGGAAAAAGCGCCGCTAAAGGTCTTGATCTA
Found at i:6109047 original size:129 final size:129
Alignment explanation
Indices: 6108817--6109060 Score: 389
Period size: 129 Copynumber: 1.9 Consensus size: 129
6108807 AGTATTTTTA
* * * * *
6108817 GCGGCTTTTGTGGAAAAAGCGTCGCTAAAGGTCTTGAGCTGTAGCAGCGTTTGTGGAAAAAGCAC
1 GCGGCATTTGTGGAAAAAACGCCGCTAAAGGTCCTGAGCTATAGCAGCGTTTGTGGAAAAAGCAC
* * *
6108882 CGCTAAAGGTCTTGATCTATAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCTTGAGCTATT
66 CGCTAAAGGTCCTGATCTATAGCAGCATTTGTGGGAAAAGCGCCGCTAAAGGTCTTGAGCTATT
* * *
6108946 GCGGCATTTGTGGAAAAAACGCCGCTAAAGGTCCTGATCTATAGCGGCGTTTGTGGAAAAAGCGC
1 GCGGCATTTGTGGAAAAAACGCCGCTAAAGGTCCTGAGCTATAGCAGCGTTTGTGGAAAAAGCAC
6109011 CGCTAAAGGTCCTGATCTATAGCAGCATTTGTGGGAAAAGCGCCGCTAAA
66 CGCTAAAGGTCCTGATCTATAGCAGCATTTGTGGGAAAAGCGCCGCTAAA
6109061 AACCTATTTT
Statistics
Matches: 104, Mismatches: 11, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
129 104 1.00
ACGTcount: A:0.27, C:0.19, G:0.30, T:0.24
Consensus pattern (129 bp):
GCGGCATTTGTGGAAAAAACGCCGCTAAAGGTCCTGAGCTATAGCAGCGTTTGTGGAAAAAGCAC
CGCTAAAGGTCCTGATCTATAGCAGCATTTGTGGGAAAAGCGCCGCTAAAGGTCTTGAGCTATT
Done.