Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007428.1 Hibiscus syriacus cultivar Beakdansim tig00020138_pilon, whole genome shotgun sequence
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: 917797
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 5
Found at i:152373 original size:19 final size:19
Alignment explanation
Indices: 152297--152375 Score: 87
Period size: 19 Copynumber: 4.4 Consensus size: 19
152287 CTTAATGTCT
**
152297 ATCGCAATGCGGAAATGACT
1 ATCGCAATGC-GAAATGAAA
152317 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
152336 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
152350 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
152369 ATCGCAA
1 ATCGCAA
152376 CGAGGGAATC
Statistics
Matches: 50, Mismatches: 4, Indels: 11
0.77 0.06 0.17
Matches are distributed among these distances:
14 10 0.20
15 1 0.02
16 2 0.04
17 2 0.04
18 1 0.02
19 24 0.48
20 10 0.20
ACGTcount: A:0.43, C:0.19, G:0.23, T:0.15
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:152575 original size:14 final size:14
Alignment explanation
Indices: 152556--152590 Score: 61
Period size: 14 Copynumber: 2.5 Consensus size: 14
152546 TCAATTAAAG
152556 AAATCAACTTTTAC
1 AAATCAACTTTTAC
*
152570 AAATCATCTTTTAC
1 AAATCAACTTTTAC
152584 AAATCAA
1 AAATCAA
152591 TTAAACAATC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.46, C:0.20, G:0.00, T:0.34
Consensus pattern (14 bp):
AAATCAACTTTTAC
Found at i:154007 original size:21 final size:21
Alignment explanation
Indices: 153941--154007 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
153931 GTGAATCGGG
*
153941 CTCTTGAATGGTGGGA-GGGA
1 CTCTTGAACGGTGGGAGGGGA
* * ** * *
153961 CCTCTTCAACGATGACAGTGGC
1 -CTCTTGAACGGTGGGAGGGGA
153983 CTCTTGAACGGTGGGAGGGGA
1 CTCTTGAACGGTGGGAGGGGA
154004 CTCT
1 CTCT
154008 CGAGGAATGA
Statistics
Matches: 32, Mismatches: 13, Indels: 2
0.68 0.28 0.04
Matches are distributed among these distances:
21 30 0.94
22 2 0.06
ACGTcount: A:0.19, C:0.21, G:0.36, T:0.24
Consensus pattern (21 bp):
CTCTTGAACGGTGGGAGGGGA
Found at i:154489 original size:21 final size:21
Alignment explanation
Indices: 154460--154531 Score: 78
Period size: 20 Copynumber: 3.6 Consensus size: 21
154450 TCTGGAACTT
154460 AAAATCGCAACGTGAAAAATG
1 AAAATCGCAACGTGAAAAATG
** * *
154481 ACTATCGCAACGAG-AGAATG
1 AAAATCGCAACGTGAAAAATG
*
154501 AAAATCGCAACGTG--AAATA
1 AAAATCGCAACGTGAAAAATG
154520 AAAATCGCAACG
1 AAAATCGCAACG
154532 AGAGAATCGC
Statistics
Matches: 42, Mismatches: 9, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
19 15 0.36
20 16 0.38
21 11 0.26
ACGTcount: A:0.49, C:0.18, G:0.19, T:0.14
Consensus pattern (21 bp):
AAAATCGCAACGTGAAAAATG
Found at i:154538 original size:39 final size:40
Alignment explanation
Indices: 154460--154538 Score: 117
Period size: 41 Copynumber: 2.0 Consensus size: 40
154450 TCTGGAACTT
*
154460 AAAATCGCAACGTGAAAAATGACTATCGCAACGAGAGAATG
1 AAAATCGCAACGTGAAAAA-GACAATCGCAACGAGAGAATG
154501 AAAATCGCAACGTGAAATAA-A-AATCGCAACGAGAGAAT
1 AAAATCGCAACGTGAAA-AAGACAATCGCAACGAGAGAAT
154539 CGCAATGTGA
Statistics
Matches: 36, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
39 16 0.44
40 1 0.03
41 17 0.47
42 2 0.06
ACGTcount: A:0.49, C:0.16, G:0.20, T:0.14
Consensus pattern (40 bp):
AAAATCGCAACGTGAAAAAGACAATCGCAACGAGAGAATG
Found at i:154588 original size:19 final size:18
Alignment explanation
Indices: 154564--154623 Score: 56
Period size: 19 Copynumber: 3.4 Consensus size: 18
154554 AAATAGCAAC
154564 GCGATTATAGTTTCGCGTT
1 GCGATTATA-TTTCGCGTT
*
154583 GCGATT-T-TGT--CGTT
1 GCGATTATATTTCGCGTT
*
154597 GCGATTTTCATTTCGCGTT
1 GCGATTAT-ATTTCGCGTT
154616 GCGATTAT
1 GCGATTAT
154624 CTCGTTGCGA
Statistics
Matches: 33, Mismatches: 3, Indels: 10
0.72 0.07 0.22
Matches are distributed among these distances:
14 10 0.30
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 17 0.52
ACGTcount: A:0.13, C:0.17, G:0.25, T:0.45
Consensus pattern (18 bp):
GCGATTATATTTCGCGTT
Found at i:154611 original size:33 final size:33
Alignment explanation
Indices: 154574--154643 Score: 122
Period size: 33 Copynumber: 2.1 Consensus size: 33
154564 GCGATTATAG
* *
154574 TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
1 TTTCGCGTTGCGATTATCTCGTTGCGATTTTCA
154607 TTTCGCGTTGCGATTATCTCGTTGCGATTTTCA
1 TTTCGCGTTGCGATTATCTCGTTGCGATTTTCA
154640 TTTC
1 TTTC
154644 AACCAAAAGA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.10, C:0.20, G:0.21, T:0.49
Consensus pattern (33 bp):
TTTCGCGTTGCGATTATCTCGTTGCGATTTTCA
Found at i:154846 original size:94 final size:94
Alignment explanation
Indices: 154734--155109 Score: 611
Period size: 94 Copynumber: 4.1 Consensus size: 94
154724 ATGGATTGCA
* *
154734 TTAC-TTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCAGAGTATTAAAGAATACACAGT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
* *
154798 TTAGCAGAATTGGTAGCAAACGAACAAAT
66 TTAGCAGAATTGGCAGCAACCGAACAAAT
154827 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
154892 TTAGCAGAATTGGCAGCAACCGAACAAAT
66 TTAGCAGAATTGGCAGCAACCGAACAAAT
* *
154921 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAGGAATACACATT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
*
154986 TTAGCAGAATTGGCAGCAACCGAATAAAT
66 TTAGCAGAATTGGCAGCAACCGAACAAAT
*
155015 TTAC-TTCAACCAAAAGACAAAACAAAAGACAAATACTAACTTCACAGTGTT----AATAAACAG
1 TTACTTTCAACCAAAAGACAAAAC-AAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAG
* *
155075 TTTAGCAGTATTGGCAGCAACCGAATAAAT
65 TTTAGCAGAATTGGCAGCAACCGAACAAAT
155105 TTACT
1 TTACT
155110 AAGCAATCTA
Statistics
Matches: 270, Mismatches: 10, Indels: 8
0.94 0.03 0.03
Matches are distributed among these distances:
90 40 0.15
93 23 0.09
94 207 0.77
ACGTcount: A:0.47, C:0.19, G:0.12, T:0.22
Consensus pattern (94 bp):
TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
TTAGCAGAATTGGCAGCAACCGAACAAAT
Found at i:155497 original size:21 final size:21
Alignment explanation
Indices: 155473--155547 Score: 52
Period size: 21 Copynumber: 3.7 Consensus size: 21
155463 GTGACGGGAT
155473 AGGTGATGGCTCTCGTTGTAG
1 AGGTGATGGCTCTCGTTGTAG
* ** *
155494 AGGTGTATAG-TCGGGTTG-ATC
1 AGGTG-ATGGCTCTCGTTGTA-G
*
155515 AGGTGATGGCTCT-G-GGT-G
1 AGGTGATGGCTCTCGTTGTAG
155533 AGGTGATGGCTCTCG
1 AGGTGATGGCTCTCG
155548 AAGTGGAGGA
Statistics
Matches: 41, Mismatches: 8, Indels: 12
0.67 0.13 0.20
Matches are distributed among these distances:
18 13 0.32
19 2 0.05
20 5 0.12
21 18 0.44
22 3 0.07
ACGTcount: A:0.15, C:0.13, G:0.41, T:0.31
Consensus pattern (21 bp):
AGGTGATGGCTCTCGTTGTAG
Found at i:156829 original size:20 final size:20
Alignment explanation
Indices: 156804--156866 Score: 76
Period size: 20 Copynumber: 3.1 Consensus size: 20
156794 TTTTGGTTGA
156804 AATGAAAATCGCAACGAGAG
1 AATGAAAATCGCAACGAGAG
156824 AATGAAAATCGCAACTCG-GA-
1 AATGAAAATCGCAA--CGAGAG
**
156844 AATGACTATCGCAACGAGAG
1 AATGAAAATCGCAACGAGAG
156864 AAT
1 AAT
156867 CGCAACGCGA
Statistics
Matches: 37, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
18 2 0.05
19 2 0.05
20 29 0.78
21 2 0.05
22 2 0.05
ACGTcount: A:0.46, C:0.17, G:0.22, T:0.14
Consensus pattern (20 bp):
AATGAAAATCGCAACGAGAG
Found at i:156911 original size:19 final size:19
Alignment explanation
Indices: 156864--156947 Score: 72
Period size: 19 Copynumber: 4.7 Consensus size: 19
156854 GCAACGAGAG
*
156864 AATCGCAACGCGAAATGAA
1 AATCACAACGCGAAATGAA
*
156883 AACCGA-AACGCGAAATGAA
1 AATC-ACAACGCGAAATGAA
*
156902 AATCACAA--CG--A-GAT
1 AATCACAACGCGAAATGAA
*
156916 AATCGCAACGCGAAATGAA
1 AATCACAACGCGAAATGAA
*
156935 AATCACAATGCGA
1 AATCACAACGCGA
156948 TTTTGGTTTC
Statistics
Matches: 50, Mismatches: 8, Indels: 14
0.69 0.11 0.19
Matches are distributed among these distances:
14 9 0.18
15 1 0.02
16 2 0.04
17 2 0.04
18 2 0.04
19 34 0.68
ACGTcount: A:0.49, C:0.21, G:0.19, T:0.11
Consensus pattern (19 bp):
AATCACAACGCGAAATGAA
Found at i:156911 original size:52 final size:53
Alignment explanation
Indices: 156810--156936 Score: 166
Period size: 52 Copynumber: 2.4 Consensus size: 53
156800 TTGAAATGAA
* * * * ** *
156810 AATCGCAACGAGAGAATGAAAATCGCAACTCGGAAATGACTATCGCAACGAGAG
1 AATCGCAACGCGA-AATGAAAACCGAAACGCGGAAATGAAAATCACAACGAGAG
*
156864 AATCGCAACGCGAAATGAAAACCGAAACGC-GAAATGAAAATCACAACGAGAT
1 AATCGCAACGCGAAATGAAAACCGAAACGCGGAAATGAAAATCACAACGAGAG
156916 AATCGCAACGCGAAATGAAAA
1 AATCGCAACGCGAAATGAAAA
156937 TCACAATGCG
Statistics
Matches: 65, Mismatches: 8, Indels: 2
0.87 0.11 0.03
Matches are distributed among these distances:
52 39 0.60
53 14 0.22
54 12 0.18
ACGTcount: A:0.47, C:0.20, G:0.21, T:0.11
Consensus pattern (53 bp):
AATCGCAACGCGAAATGAAAACCGAAACGCGGAAATGAAAATCACAACGAGAG
Found at i:157049 original size:20 final size:20
Alignment explanation
Indices: 156974--157064 Score: 89
Period size: 20 Copynumber: 4.5 Consensus size: 20
156964 CGATTATCTC
* *
156974 GTTGCGATTTTTA-TTTCGC
1 GTTGCGATTTTCATTTTCGT
156993 GTTGCGATTTTCATTTCTC-T
1 GTTGCGATTTTCATTT-TCGT
**
157013 CGTT-CTGATAGTCATTTTCGT
1 -GTTGC-GATTTTCATTTTCGT
*
157034 GTTGCGATTTTCATTTTCAT
1 GTTGCGATTTTCATTTTCGT
157054 GTTGCGATTTT
1 GTTGCGATTTT
157065 AAGTTTAGAA
Statistics
Matches: 59, Mismatches: 7, Indels: 11
0.77 0.09 0.14
Matches are distributed among these distances:
19 12 0.20
20 31 0.53
21 16 0.27
ACGTcount: A:0.12, C:0.16, G:0.19, T:0.53
Consensus pattern (20 bp):
GTTGCGATTTTCATTTTCGT
Found at i:157395 original size:25 final size:26
Alignment explanation
Indices: 157337--157388 Score: 79
Period size: 27 Copynumber: 2.0 Consensus size: 26
157327 TTTCCATTTC
*
157337 TGAATGATTGTGAGGGATTTCTGACCG
1 TGAATGGTTGTGAGGGATTTC-GACCG
157364 TGAATGGTTGTGAGGGATTTC-ACCG
1 TGAATGGTTGTGAGGGATTTCGACCG
157389 GCGATGGGGA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
25 4 0.17
27 20 0.83
ACGTcount: A:0.21, C:0.12, G:0.35, T:0.33
Consensus pattern (26 bp):
TGAATGGTTGTGAGGGATTTCGACCG
Found at i:157639 original size:20 final size:20
Alignment explanation
Indices: 157616--157709 Score: 116
Period size: 20 Copynumber: 4.7 Consensus size: 20
157606 CGATAGTCAG
*
157616 ATTCGCGTTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
* *
157636 ATTCGCATTGCGATTTTCCT
1 ATTCGCATTGCGATTTACGT
*
157656 AATTCGCATTGTGATTTACGT
1 -ATTCGCATTGCGATTTACGT
* *
157677 AATCGCGTTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
*
157697 ATTTGCATTGCGA
1 ATTCGCATTGCGA
157710 ATTAGGAAAA
Statistics
Matches: 61, Mismatches: 12, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
20 44 0.72
21 17 0.28
ACGTcount: A:0.19, C:0.19, G:0.21, T:0.40
Consensus pattern (20 bp):
ATTCGCATTGCGATTTACGT
Found at i:157732 original size:21 final size:21
Alignment explanation
Indices: 157706--157792 Score: 95
Period size: 21 Copynumber: 4.2 Consensus size: 21
157696 TATTTGCATT
157706 GCGAATTAGGAAAATCGCAAC
1 GCGAATTAGGAAAATCGCAAC
* * *
157727 GCGAA-TACGTAAATCGCAAT
1 GCGAATTAGGAAAATCGCAAC
*
157747 GCGAATTAGTAAAATCGCAAC
1 GCGAATTAGGAAAATCGCAAC
* * * *
157768 GCGATTTTGGGAAATCGCAAT
1 GCGAATTAGGAAAATCGCAAC
157789 GCGA
1 GCGA
157793 TAGTCAGAAC
Statistics
Matches: 53, Mismatches: 12, Indels: 2
0.79 0.18 0.03
Matches are distributed among these distances:
20 17 0.32
21 36 0.68
ACGTcount: A:0.38, C:0.18, G:0.24, T:0.20
Consensus pattern (21 bp):
GCGAATTAGGAAAATCGCAAC
Found at i:157742 original size:61 final size:61
Alignment explanation
Indices: 157618--157743 Score: 137
Period size: 61 Copynumber: 2.1 Consensus size: 61
157608 ATAGTCAGAT
* * * * ** * *
157618 TCGCGTTGCGATTTACGTATTCGCATTGCGATTTTCCTAATTCGCATTGTGATTTACGTAA
1 TCGCGTTGCGATTTACGTATTCGCATTGCGAATTACCAAAATCGCAACGCGATATACGTAA
* **
157679 TCGCGTTGCGATTTACGTATTTGCATTGCGAATTAGGAAAATCGCAACGCGA-ATACGTAAA
1 TCGCGTTGCGATTTACGTATTCGCATTGCGAATTACCAAAATCGCAACGCGATATACGT-AA
157740 TCGC
1 TCGC
157744 AATGCGAATT
Statistics
Matches: 53, Mismatches: 11, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
60 5 0.09
61 48 0.91
ACGTcount: A:0.25, C:0.20, G:0.21, T:0.34
Consensus pattern (61 bp):
TCGCGTTGCGATTTACGTATTCGCATTGCGAATTACCAAAATCGCAACGCGATATACGTAA
Found at i:161398 original size:21 final size:22
Alignment explanation
Indices: 161368--161410 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
161358 ACTAAAATAA
161368 AAATAT-AAAAAATGCGAAAACC
1 AAATATAAAAAAATGC-AAAACC
161390 AAAT-TAAAAAAATGCAAAACC
1 AAATATAAAAAAATGCAAAACC
161411 TGATTTCGGG
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
21 7 0.35
22 13 0.65
ACGTcount: A:0.65, C:0.14, G:0.07, T:0.14
Consensus pattern (22 bp):
AAATATAAAAAAATGCAAAACC
Found at i:162400 original size:15 final size:16
Alignment explanation
Indices: 162373--162412 Score: 57
Period size: 17 Copynumber: 2.6 Consensus size: 16
162363 GCCTTCGGGT
162373 TATATAA-ATAATAA-
1 TATATAATATAATAAC
162387 TATATAATATAATAAC
1 TATATAATATAATAAC
162403 GTATATAATA
1 -TATATAATA
162413 AACGTCACTT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 7 0.30
15 7 0.30
17 9 0.39
ACGTcount: A:0.57, C:0.03, G:0.03, T:0.38
Consensus pattern (16 bp):
TATATAATATAATAAC
Found at i:163033 original size:34 final size:35
Alignment explanation
Indices: 162995--163062 Score: 93
Period size: 35 Copynumber: 2.0 Consensus size: 35
162985 GTAAATAAAG
* *
162995 TAGAAC-AGAGGAAGCGTCACACTTTCAATTCAAT
1 TAGAACGAGAGGAAGCATCACACTTACAATTCAAT
* *
163029 TAGAACGGGAGGAAGCATCACACTTACGATTCAA
1 TAGAACGAGAGGAAGCATCACACTTACAATTCAA
163063 GTAAAATGAA
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
34 6 0.21
35 23 0.79
ACGTcount: A:0.38, C:0.21, G:0.21, T:0.21
Consensus pattern (35 bp):
TAGAACGAGAGGAAGCATCACACTTACAATTCAAT
Found at i:163165 original size:77 final size:77
Alignment explanation
Indices: 163029--163174 Score: 202
Period size: 77 Copynumber: 1.9 Consensus size: 77
163019 TCAATTCAAT
** * * *
163029 TAGAACGGGAGGAAGCATCACACTTACGATTCAAGTAAAATGAAAGGATGCATAACACTTTTGAT
1 TAGAACGAAAGGAAGCATCACACTTACGATTCAAGTAAAATGAAAAGAGGCATAACACTTTCGAT
163094 TCTCGTCAAAAG
66 TCTCGTCAAAAG
* * * **
163106 TAGAACGAAAGGAAGCATCACACTTTCGTTTCAAGTAGAATGAAAAGAGGCATGGCACTTTCGAT
1 TAGAACGAAAGGAAGCATCACACTTACGATTCAAGTAAAATGAAAAGAGGCATAACACTTTCGAT
163171 TCTC
66 TCTC
163175 AATGACAGAA
Statistics
Matches: 59, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
77 59 1.00
ACGTcount: A:0.37, C:0.18, G:0.21, T:0.24
Consensus pattern (77 bp):
TAGAACGAAAGGAAGCATCACACTTACGATTCAAGTAAAATGAAAAGAGGCATAACACTTTCGAT
TCTCGTCAAAAG
Found at i:164425 original size:39 final size:39
Alignment explanation
Indices: 164382--164462 Score: 135
Period size: 39 Copynumber: 2.1 Consensus size: 39
164372 CTCATGATTT
*
164382 TATTAAAACCATGATAAACAATATAATACATAATAGTCA
1 TATTAAAACCATGATAAACAATATAATAAATAATAGTCA
* *
164421 TATTAAAATCATGATAAACAATATCATAAATAATAGTCA
1 TATTAAAACCATGATAAACAATATAATAAATAATAGTCA
164460 TAT
1 TAT
164463 CATATTCTTT
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
39 39 1.00
ACGTcount: A:0.53, C:0.11, G:0.05, T:0.31
Consensus pattern (39 bp):
TATTAAAACCATGATAAACAATATAATAAATAATAGTCA
Found at i:164657 original size:20 final size:19
Alignment explanation
Indices: 164632--164676 Score: 54
Period size: 20 Copynumber: 2.3 Consensus size: 19
164622 TTATTTAAGA
164632 TTCATAACTTAATTTCATAT
1 TTCATAACTTAATTTCA-AT
** *
164652 TTCATAGTTTATTTTCAAT
1 TTCATAACTTAATTTCAAT
164671 TTCATA
1 TTCATA
164677 GCCAATGCAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
19 8 0.36
20 14 0.64
ACGTcount: A:0.31, C:0.13, G:0.02, T:0.53
Consensus pattern (19 bp):
TTCATAACTTAATTTCAAT
Found at i:171515 original size:30 final size:30
Alignment explanation
Indices: 171481--171537 Score: 114
Period size: 30 Copynumber: 1.9 Consensus size: 30
171471 CAAAATAAAG
171481 AAAGGTTGAAGCATAATAAGTTTAAAAAAT
1 AAAGGTTGAAGCATAATAAGTTTAAAAAAT
171511 AAAGGTTGAAGCATAATAAGTTTAAAA
1 AAAGGTTGAAGCATAATAAGTTTAAAA
171538 GTACTCACTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.53, C:0.04, G:0.18, T:0.26
Consensus pattern (30 bp):
AAAGGTTGAAGCATAATAAGTTTAAAAAAT
Found at i:176763 original size:3 final size:3
Alignment explanation
Indices: 176755--176856 Score: 204
Period size: 3 Copynumber: 34.0 Consensus size: 3
176745 GCTTGGCATG
176755 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
176803 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
176851 TAT TAT
1 TAT TAT
176857 ACAAACCAGT
Statistics
Matches: 99, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 99 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:189241 original size:106 final size:106
Alignment explanation
Indices: 189048--190025 Score: 1395
Period size: 106 Copynumber: 9.3 Consensus size: 106
189038 CCAACAAGAG
* *
189048 TTCAACTTCACAGCGTAGGATATTGGACTCAAGACAACGCAAGTTCAACTTCACGACGAAGGGAC
1 TTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGAC
* *
189113 CGCTGGTTGTCAA-TATATAACTTCCCAATTTCAGAGTCAAT
66 CGCTGGTTGTCAACTA-ACAACTTCCCAATTTCAGAGCCAAT
*
189154 TTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGAAGAAGGGAC
1 TTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGAC
*
189219 CGCTGGTTGTCAACTAACAACTTCTCAATTTCAGAGCCAAT
66 CGCTGGTTGTCAACTAACAACTTCCCAATTTCAGAGCCAAT
* *
189260 TTCAACTTCACAACGAAGGATATTGGACTCCAGACAACACAAGTTCAACTTCACGACGAAGGGAC
1 TTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGAC
* * *
189325 CGCTGGTTGTCAACAAACAATTTCCCAATTTTAGAGCCAAT
66 CGCTGGTTGTCAACTAACAACTTCCCAATTTCAGAGCCAAT
*
189366 TTCAACTTCACAGCGAAGGATATTGGACTCAAGACAACGCAAGTTCAACTTCACGACGAAGGGAC
1 TTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGAC
*
189431 CACTGGTTGTCAA-TAAACAACTTCCCAATTTCAGAGCCAAT
66 CGCTGGTTGTCAACT-AACAACTTCCCAATTTCAGAGCCAAT
* *
189472 TTCAACTTCACAGCGAAGGATATTTGACTCTAGACAACGCAAGTTCAACTTCACGACGAAGGGAC
1 TTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGAC
* * *
189537 CGCTGGTTGTCAACAAACAACTTCTCAATTTTAGAGCCAAT
66 CGCTGGTTGTCAACTAACAACTTCCCAATTTCAGAGCCAAT
* * *
189578 TTCAACTTCACAACGAAGGATATTGGACTCCACACAACACAAGTTCAACTTCACGACGAAGGGAC
1 TTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGAC
* *
189643 CACTGGTTGTCAA-TAAACAATTTCCCAATTTCAGAGCCAAT
66 CGCTGGTTGTCAACT-AACAACTTCCCAATTTCAGAGCCAAT
* *
189684 TTCAACTTCACAGCGTAGGATATTGGACTCAAGACAACGCAAGTTCAACTTCACGACGAAGGGAC
1 TTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGAC
189749 CGCTGGTTGTCAA-TAAACAACTTCCCAATTTCAGAGCCAAT
66 CGCTGGTTGTCAACT-AACAACTTCCCAATTTCAGAGCCAAT
* * * * * * *
189790 TTTAACTTCTCAGCGAAGGATCTTGGAC-CCAAGACAACACAAGCTCAACTTCACAACGAAGGGG
1 TTCAACTTCACAGCGAAGGATATTGGACTCC-AGACAACGCAAGTTCAACTTCACGACGAAGGGA
** * * *
189854 TGGCTGATTGTCAAC-AA-AA-TT-TC-A-TTCAGAGTCAAT
65 CCGCTGGTTGTCAACTAACAACTTCCCAATTTCAGAGCCAAT
* * *
189890 TTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGAC
1 TTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGAC
* * * * * *
189955 GGCTGGTTGTCAACAAATAATTTCCCGATTCCAGAGCCAAT
66 CGCTGGTTGTCAACTAACAACTTCCCAATTTCAGAGCCAAT
*
189996 TTCAACTTCAC-GACGGAGGATATTGGACTC
1 TTCAACTTCACAG-CGAAGGATATTGGACTC
190026 AGAACAATGC
Statistics
Matches: 789, Mismatches: 69, Indels: 28
0.89 0.08 0.03
Matches are distributed among these distances:
100 80 0.10
101 4 0.01
102 3 0.00
103 4 0.01
104 3 0.00
105 5 0.01
106 688 0.87
107 2 0.00
ACGTcount: A:0.34, C:0.25, G:0.18, T:0.23
Consensus pattern (106 bp):
TTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGAC
CGCTGGTTGTCAACTAACAACTTCCCAATTTCAGAGCCAAT
Found at i:189625 original size:318 final size:317
Alignment explanation
Indices: 189048--190026 Score: 1583
Period size: 318 Copynumber: 3.1 Consensus size: 317
189038 CCAACAAGAG
189048 TTCAACTTCACAGCGTAGGATATTGGACTCAAGACAACGCAAGTTCAACTTCACGACGAAGGGAC
1 TTCAACTTCACAGCGTAGGATATTGGACTCAAGACAACGCAAGTTCAACTTCACGACGAAGGGAC
* * *
189113 CGCTGGTTGTCAATATATAACTTCCCAATTTCAGAGTCAATTTCAACTTCACAGCGAAGGATATT
66 CGCTGGTTGTCAATAAACAACTTCCCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATT
* *
189178 GGACTCCAGACAACGCAAGTTCAACTTCACGAAGAAGGGACCGCTGGTTGTCAACTAACAACTTC
131 GGACTCAAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAAC-AACAACTTC
189243 TCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACACAAGTTCAA
195 TCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACACAAGTTCAA
*
189308 CTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCCAATTTTAGAGCCAAT
260 CTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCCAATTTCAGAGCCAAT
*
189366 TTCAACTTCACAGCGAAGGATATTGGACTCAAGACAACGCAAGTTCAACTTCACGACGAAGGGAC
1 TTCAACTTCACAGCGTAGGATATTGGACTCAAGACAACGCAAGTTCAACTTCACGACGAAGGGAC
*
189431 CACTGGTTGTCAATAAACAACTTCCCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATT
66 CGCTGGTTGTCAATAAACAACTTCCCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATT
* *
189496 TGACTCTAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTC
131 GGACTCAAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAAC-AACAACTTC
* *
189561 TCAATTTTAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCACACAACACAAGTTCAA
195 TCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACACAAGTTCAA
* *
189626 CTTCACGACGAAGGGACCACTGGTTGTCAATAAACAATTTCCCAATTTCAGAGCCAAT
260 CTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCCAATTTCAGAGCCAAT
189684 TTCAACTTCACAGCGTAGGATATTGGACTCAAGACAACGCAAGTTCAACTTCACGACGAAGGGAC
1 TTCAACTTCACAGCGTAGGATATTGGACTCAAGACAACGCAAGTTCAACTTCACGACGAAGGGAC
* * *
189749 CGCTGGTTGTCAATAAACAACTTCCCAATTTCAGAGCCAATTTTAACTTCTCAGCGAAGGATCTT
66 CGCTGGTTGTCAATAAACAACTTCCCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATT
* * * * *** *
189814 GGACCCAAGACAACACAAGCTCAACTTCACAACGAAGGGGTGGCTGATTGTCAACAA-AA-TT-T
131 GGACTCAAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAACAACTTCT
* * *
189876 C-A-TTCAGAGTCAATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAAGTTCAAC
196 CAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACACAAGTTCAAC
* * * * *
189939 TTCACAACGAAGGGACGGCTGGTTGTCAACAAATAATTTCCCGATTCCAGAGCCAAT
261 TTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCCAATTTCAGAGCCAAT
*
189996 TTCAACTTCAC-GACGGAGGATATTGGACTCA
1 TTCAACTTCACAG-CGTAGGATATTGGACTCA
190027 GAACAATGCT
Statistics
Matches: 618, Mismatches: 42, Indels: 8
0.93 0.06 0.01
Matches are distributed among these distances:
311 1 0.00
312 134 0.22
313 1 0.00
314 2 0.00
315 2 0.00
316 2 0.00
317 2 0.00
318 474 0.77
ACGTcount: A:0.34, C:0.25, G:0.18, T:0.23
Consensus pattern (317 bp):
TTCAACTTCACAGCGTAGGATATTGGACTCAAGACAACGCAAGTTCAACTTCACGACGAAGGGAC
CGCTGGTTGTCAATAAACAACTTCCCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATT
GGACTCAAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAACAACTTCT
CAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACACAAGTTCAAC
TTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCCAATTTCAGAGCCAAT
Found at i:190818 original size:37 final size:37
Alignment explanation
Indices: 190756--190852 Score: 140
Period size: 37 Copynumber: 2.6 Consensus size: 37
190746 CCTTTTCGTC
*
190756 CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
1 CTACTATGATTCAAACTCCTAAAAATAGGATAGAATT
* * * *
190793 TTGCTATGATTCAAACTCCTTAAAATAGGATAGAGTT
1 CTACTATGATTCAAACTCCTAAAAATAGGATAGAATT
*
190830 CTACTATGATTTAAACTCCTAAA
1 CTACTATGATTCAAACTCCTAAA
190853 GATATGATCC
Statistics
Matches: 51, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
37 51 1.00
ACGTcount: A:0.39, C:0.16, G:0.12, T:0.32
Consensus pattern (37 bp):
CTACTATGATTCAAACTCCTAAAAATAGGATAGAATT
Found at i:191407 original size:2 final size:2
Alignment explanation
Indices: 191389--191481 Score: 165
Period size: 2 Copynumber: 48.0 Consensus size: 2
191379 TTTTTAATAC
191389 TA TA T- TA T- TA T- TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
191428 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
191470 TA TA TA TA TA TA
1 TA TA TA TA TA TA
191482 AAATATTTTA
Statistics
Matches: 88, Mismatches: 0, Indels: 6
0.94 0.00 0.06
Matches are distributed among these distances:
1 3 0.03
2 85 0.97
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:191703 original size:19 final size:17
Alignment explanation
Indices: 191671--191732 Score: 56
Period size: 18 Copynumber: 3.5 Consensus size: 17
191661 TTTTGATTTT
191671 TTTTCTATTATATTATA
1 TTTTCTATTATATTATA
191688 TTTTCATATTACTATTATTA
1 TTTTC-TATTA-TATTA-TA
* *
191708 TTGT-TATGATTATTAT-
1 TTTTCTATTA-TATTATA
191724 TTTTCTATT
1 TTTTCTATT
191733 TTACTCATTT
Statistics
Matches: 36, Mismatches: 5, Indels: 8
0.73 0.10 0.16
Matches are distributed among these distances:
16 3 0.08
17 9 0.25
18 14 0.39
19 5 0.14
20 5 0.14
ACGTcount: A:0.26, C:0.06, G:0.03, T:0.65
Consensus pattern (17 bp):
TTTTCTATTATATTATA
Found at i:191793 original size:13 final size:12
Alignment explanation
Indices: 191777--191824 Score: 53
Period size: 13 Copynumber: 3.8 Consensus size: 12
191767 CATTTATTTA
191777 TTTATTTTTTTCC
1 TTTATTTTTTT-C
191790 TTTATTTTTTTAC
1 TTTATTTTTTT-C
191803 -TTATTTTTATTC
1 TTTATTTTT-TTC
*
191815 TTCATTTTTT
1 TTTATTTTTT
191825 CATTTATTCA
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
12 10 0.32
13 21 0.68
ACGTcount: A:0.12, C:0.10, G:0.00, T:0.77
Consensus pattern (12 bp):
TTTATTTTTTTC
Found at i:191796 original size:25 final size:25
Alignment explanation
Indices: 191768--191844 Score: 75
Period size: 25 Copynumber: 2.9 Consensus size: 25
191758 TTAATATTTC
191768 ATTTATTTATTTATTTTTTTCCTTT
1 ATTTATTTATTTATTTTTTTCCTTT
* *
191793 ATTTTTTTACTTATTTTTATTCTTCATTT
1 ATTTATTTATTTATTTTT-TTC--C-TTT
*
191822 -TTTCATTTATTCATTTTTTTCCT
1 ATTT-ATTTATTTATTTTTTTCCT
191845 CTGACATCTT
Statistics
Matches: 42, Mismatches: 5, Indels: 10
0.74 0.09 0.18
Matches are distributed among these distances:
25 17 0.40
26 4 0.10
28 7 0.17
29 14 0.33
ACGTcount: A:0.16, C:0.12, G:0.00, T:0.73
Consensus pattern (25 bp):
ATTTATTTATTTATTTTTTTCCTTT
Found at i:191809 original size:12 final size:12
Alignment explanation
Indices: 191768--191824 Score: 53
Period size: 12 Copynumber: 4.6 Consensus size: 12
191758 TTAATATTTC
* *
191768 ATTTATTTATTT
1 ATTTTTTTACTT
*
191780 ATTTTTTTCCTTT
1 ATTTTTTTAC-TT
191793 ATTTTTTTACTT
1 ATTTTTTTACTT
191805 ATTTTTATT-CTT
1 ATTTTT-TTACTT
191817 CATTTTTT
1 -ATTTTTT
191825 CATTTATTCA
Statistics
Matches: 38, Mismatches: 4, Indels: 6
0.79 0.08 0.12
Matches are distributed among these distances:
12 19 0.50
13 19 0.50
ACGTcount: A:0.16, C:0.09, G:0.00, T:0.75
Consensus pattern (12 bp):
ATTTTTTTACTT
Found at i:194165 original size:16 final size:16
Alignment explanation
Indices: 194144--194186 Score: 86
Period size: 16 Copynumber: 2.7 Consensus size: 16
194134 ACTATTCAAA
194144 TGAATAGTAAATTTTG
1 TGAATAGTAAATTTTG
194160 TGAATAGTAAATTTTG
1 TGAATAGTAAATTTTG
194176 TGAATAGTAAA
1 TGAATAGTAAA
194187 AATTTTATCG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 27 1.00
ACGTcount: A:0.42, C:0.00, G:0.19, T:0.40
Consensus pattern (16 bp):
TGAATAGTAAATTTTG
Found at i:203989 original size:28 final size:28
Alignment explanation
Indices: 203958--204036 Score: 133
Period size: 28 Copynumber: 2.8 Consensus size: 28
203948 TTTAGGTACC
203958 TATTTTGA-CATAAAATACTTTAGACACT
1 TATTTTGACCA-AAAATACTTTAGACACT
203986 TATTTTGACCAAAAATACTTTAGACACT
1 TATTTTGACCAAAAATACTTTAGACACT
204014 TATTTTGACCAAAAAATACTTTA
1 TATTTTGACC-AAAAATACTTTA
204037 AAAAATTAAA
Statistics
Matches: 49, Mismatches: 0, Indels: 3
0.94 0.00 0.06
Matches are distributed among these distances:
28 35 0.71
29 14 0.29
ACGTcount: A:0.41, C:0.15, G:0.06, T:0.38
Consensus pattern (28 bp):
TATTTTGACCAAAAATACTTTAGACACT
Found at i:209971 original size:41 final size:41
Alignment explanation
Indices: 209902--209979 Score: 102
Period size: 41 Copynumber: 1.9 Consensus size: 41
209892 TGAAAAATAG
*
209902 TTTTGTTTTGAGTAAGATCTACTAGATCTATATTTTTGTAC
1 TTTTCTTTTGAGTAAGATCTACTAGATCTATATTTTTGTAC
* * * * *
209943 TTTTCTTTTGAGTAGGATTTATTGGATCTGTATTTTT
1 TTTTCTTTTGAGTAAGATCTACTAGATCTATATTTTT
209980 TCATTGTCCT
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
41 31 1.00
ACGTcount: A:0.21, C:0.08, G:0.17, T:0.55
Consensus pattern (41 bp):
TTTTCTTTTGAGTAAGATCTACTAGATCTATATTTTTGTAC
Found at i:214294 original size:45 final size:44
Alignment explanation
Indices: 214139--214295 Score: 133
Period size: 45 Copynumber: 3.5 Consensus size: 44
214129 TTTTGGCTTG
*
214139 TCCATCACATAAGGAGTTGGATCATC-ATCGCCTTTTTT-TTACGAT
1 TCCATCACATAAGAAGTTGGATCATCTAT--CCTTTTTTGTT-CGAT
* * * * *
214184 TCTAACACATAATAAGTTGGATTATC-ATCATTGTTTTGTTCGAT
1 TCCATCACATAAGAAGTTGGATCATCTATCCTT-TTTTGTTCGAT
* * * *
214228 TCCATCACAAAAGAAAG-TGGATCAACGTTTCCTTTTTTGCTCGAT
1 TCCATCACATAAG-AAGTTGGATCATC-TATCCTTTTTTGTTCGAT
*
214273 TCCATCACATAAGGAGTTGGATC
1 TCCATCACATAAGAAGTTGGATC
214296 TGCATTGACA
Statistics
Matches: 89, Mismatches: 17, Indels: 12
0.75 0.14 0.10
Matches are distributed among these distances:
43 3 0.03
44 26 0.29
45 56 0.63
46 4 0.04
ACGTcount: A:0.28, C:0.20, G:0.16, T:0.36
Consensus pattern (44 bp):
TCCATCACATAAGAAGTTGGATCATCTATCCTTTTTTGTTCGAT
Found at i:216171 original size:44 final size:44
Alignment explanation
Indices: 216118--216229 Score: 118
Period size: 44 Copynumber: 2.5 Consensus size: 44
216108 TTTTGGCTCG
216118 TCCATCACATAAGGAGTTGGATCAGCATCACAT-TTTTCCACGAT
1 TCCATCACATAAGGAGTTGGATCAGCATCAC-TCTTTTCCACGAT
* ** * * ***
216162 TCTATCACATAATAAGTGGGATTAGCATCACTCTTTTGTTCGAT
1 TCCATCACATAAGGAGTTGGATCAGCATCACTCTTTTCCACGAT
* *
216206 TCCATCACAGAAGGAGGTGGATCA
1 TCCATCACATAAGGAGTTGGATCA
216230 ATGTTTCTAT
Statistics
Matches: 52, Mismatches: 15, Indels: 2
0.75 0.22 0.03
Matches are distributed among these distances:
43 1 0.02
44 51 0.98
ACGTcount: A:0.29, C:0.21, G:0.19, T:0.30
Consensus pattern (44 bp):
TCCATCACATAAGGAGTTGGATCAGCATCACTCTTTTCCACGAT
Found at i:216536 original size:17 final size:16
Alignment explanation
Indices: 216513--216562 Score: 57
Period size: 15 Copynumber: 3.1 Consensus size: 16
216503 GAAGAAAATT
216513 AAAGAAAGAAATGAAAA
1 AAAGAAA-AAATGAAAA
* *
216530 AAGGAAACAAT-AAAA
1 AAAGAAAAAATGAAAA
*
216545 AAAGAGAAAATGAAAA
1 AAAGAAAAAATGAAAA
216561 AA
1 AA
216563 TAAATATAAA
Statistics
Matches: 27, Mismatches: 5, Indels: 3
0.77 0.14 0.09
Matches are distributed among these distances:
15 12 0.44
16 9 0.33
17 6 0.22
ACGTcount: A:0.76, C:0.02, G:0.16, T:0.06
Consensus pattern (16 bp):
AAAGAAAAAATGAAAA
Found at i:218161 original size:43 final size:43
Alignment explanation
Indices: 218097--218204 Score: 121
Period size: 43 Copynumber: 2.5 Consensus size: 43
218087 AAGATTCGAT
* *
218097 TCCATCACCA-AAGGAGATGGATCAACATTC-CTTTTTTAGTTAG
1 TCCATCA-CATAAGGAGTTGGATCAACA-TCACTTTTTTAGCTAG
* *
218140 TCCATCACATAAGGAGTTGGATCAACATCACTTTTTTCGCTAT
1 TCCATCACATAAGGAGTTGGATCAACATCACTTTTTTAGCTAG
* * *
218183 TCTACCACATAAGAAGTTGGAT
1 TCCATCACATAAGGAGTTGGAT
218205 TATCATAATG
Statistics
Matches: 56, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
42 4 0.07
43 52 0.93
ACGTcount: A:0.31, C:0.21, G:0.16, T:0.32
Consensus pattern (43 bp):
TCCATCACATAAGGAGTTGGATCAACATCACTTTTTTAGCTAG
Found at i:218302 original size:21 final size:21
Alignment explanation
Indices: 218272--218315 Score: 79
Period size: 21 Copynumber: 2.1 Consensus size: 21
218262 TTTGCTCGAT
*
218272 TCCATCACATAAGGAGTTGGA
1 TCCATAACATAAGGAGTTGGA
218293 TCCATAACATAAGGAGTTGGA
1 TCCATAACATAAGGAGTTGGA
218314 TC
1 TC
218316 TACATCGACC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.34, C:0.18, G:0.23, T:0.25
Consensus pattern (21 bp):
TCCATAACATAAGGAGTTGGA
Found at i:220298 original size:21 final size:22
Alignment explanation
Indices: 220272--220313 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 22
220262 TTTGCTCGAT
*
220272 TCCATCATATAAGGAG-TTGAA
1 TCCATCACATAAGGAGCTTGAA
220293 TCCATCACATAAGGAGCTTGA
1 TCCATCACATAAGGAGCTTGA
220314 TCTGCACCGA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 15 0.79
22 4 0.21
ACGTcount: A:0.36, C:0.19, G:0.19, T:0.26
Consensus pattern (22 bp):
TCCATCACATAAGGAGCTTGAA
Found at i:226239 original size:22 final size:23
Alignment explanation
Indices: 226194--226239 Score: 67
Period size: 22 Copynumber: 2.0 Consensus size: 23
226184 ATTTATCAGA
*
226194 TTTTAGTTGTGGAGATTCATGAG
1 TTTTAGTTGTGGAGATTCAGGAG
*
226217 TTTTAGTT-TGGAGATTCCGGAG
1 TTTTAGTTGTGGAGATTCAGGAG
226239 T
1 T
226240 GACTTTTCAG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 13 0.62
23 8 0.38
ACGTcount: A:0.20, C:0.07, G:0.30, T:0.43
Consensus pattern (23 bp):
TTTTAGTTGTGGAGATTCAGGAG
Found at i:233583 original size:36 final size:35
Alignment explanation
Indices: 233504--233594 Score: 94
Period size: 35 Copynumber: 2.6 Consensus size: 35
233494 CAAAGTGTCG
* ***
233504 TCTCGCTAGAGACAATTTTCTTAAAAACAATTTTG
1 TCTCGCTTGAGACAATTTTCTTAAAAACAATTCCA
*
233539 TCTTGCTTGAGACAATTTCTCTT-AAAACAAATTCCA
1 TCTCGCTTGAGACAATTT-TCTTAAAAAC-AATTCCA
* *
233575 TCTCGCTTGAGCCAGTTTTC
1 TCTCGCTTGAGACAATTTTC
233595 CCTTGAGATG
Statistics
Matches: 46, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
35 23 0.50
36 23 0.50
ACGTcount: A:0.29, C:0.22, G:0.12, T:0.37
Consensus pattern (35 bp):
TCTCGCTTGAGACAATTTTCTTAAAAACAATTCCA
Found at i:233957 original size:29 final size:29
Alignment explanation
Indices: 233916--234161 Score: 94
Period size: 29 Copynumber: 7.8 Consensus size: 29
233906 TTTGTCTCTC
*
233916 TTGAGA-CAGTTTCTCTTGAAACATCATCT
1 TTGAGATCA-TTTCCCTTGAAACATCATCT
233945 TTGAGATCATTTCCCTTGAATTGA-ATTTTGTC-TCT
1 TTGAGATCATTTCCCTTGAA---ACA-----TCATCT
* *
233980 CTTGAGAT-AGATTCTCTTGAAACATCATCT
1 -TTGAGATCA-TTTCCCTTGAAACATCATCT
*
234010 TTGAGATCGTTTCCCTTGAAACGAATTTTGTC-TCT
1 TTGAGATCATTTCCCTTGAAAC--A-----TCATCT
*
234045 CTTGAGA-CAATTTCTCTTGAAACATCATCT
1 -TTGAGATC-ATTTCCCTTGAAACATCATCT
* *
234075 TTGAGATCGTTTCCCTTGAAAAGTATTTTGTC-TCT
1 TTGAGATCATTTCCCTTG-AAA-CA-----TCATCT
*
234110 CTTGAGA-CAATTTCTCTTGAAACATCATCT
1 -TTGAGATC-ATTTCCCTTGAAACATCATCT
*
234140 TTGAGATCGTTTCCCTTGAAAC
1 TTGAGATCATTTCCCTTGAAAC
234162 GATTTGTCTC
Statistics
Matches: 165, Mismatches: 16, Indels: 72
0.65 0.06 0.28
Matches are distributed among these distances:
29 72 0.44
30 16 0.10
31 3 0.02
32 1 0.01
33 1 0.01
34 3 0.02
35 15 0.09
36 54 0.33
ACGTcount: A:0.25, C:0.20, G:0.14, T:0.41
Consensus pattern (29 bp):
TTGAGATCATTTCCCTTGAAACATCATCT
Found at i:233977 original size:65 final size:65
Alignment explanation
Indices: 233839--234179 Score: 553
Period size: 65 Copynumber: 5.3 Consensus size: 65
233829 TTCAAACAAG
** *
233839 TTTTGTCTCTCTTGAGACAATTTCTCTTGAAACAAAGATCTTTGAGATTGTTTCCCTTGAAACGA
1 TTTTGTCTCTCTTGAGACAATTTCTCTTGAAAC-ATCATCTTTGAGATCGTTTCCCTTGAAACGA
233904 A
65 A
* * **
233905 TTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACATCATCTTTGAGATCATTTCCCTTGAATTGAA
1 TTTTGTCTCTCTTGAGACAATTTCTCTTGAAACATCATCTTTGAGATCGTTTCCCTTGAAACGAA
*
233970 TTTTGTCTCTCTTGAGATAGA-TTCTCTTGAAACATCATCTTTGAGATCGTTTCCCTTGAAACGA
1 TTTTGTCTCTCTTGAGACA-ATTTCTCTTGAAACATCATCTTTGAGATCGTTTCCCTTGAAACGA
234034 A
65 A
* *
234035 TTTTGTCTCTCTTGAGACAATTTCTCTTGAAACATCATCTTTGAGATCGTTTCCCTTGAAAAGTA
1 TTTTGTCTCTCTTGAGACAATTTCTCTTGAAACATCATCTTTGAGATCGTTTCCCTTGAAACGAA
234100 TTTTGTCTCTCTTGAGACAATTTCTCTTGAAACATCATCTTTGAGATCGTTTCCCTTGAAACG-A
1 TTTTGTCTCTCTTGAGACAATTTCTCTTGAAACATCATCTTTGAGATCGTTTCCCTTGAAACGAA
234164 -TTTGTCTCTCTTGAGA
1 TTTTGTCTCTCTTGAGA
234180 TGGTTTCTCT
Statistics
Matches: 257, Mismatches: 16, Indels: 7
0.92 0.06 0.03
Matches are distributed among these distances:
63 16 0.06
64 2 0.01
65 207 0.81
66 32 0.12
ACGTcount: A:0.24, C:0.20, G:0.15, T:0.41
Consensus pattern (65 bp):
TTTTGTCTCTCTTGAGACAATTTCTCTTGAAACATCATCTTTGAGATCGTTTCCCTTGAAACGAA
Found at i:234498 original size:83 final size:83
Alignment explanation
Indices: 234345--234538 Score: 253
Period size: 83 Copynumber: 2.3 Consensus size: 83
234335 AAAGATGGCA
* * * * *
234345 AGCCGTCCTCTTCACGTAGGAACTATGTTATCCACTAACCAAATCTCCTCATCACGTATGAGTCG
1 AGCCGTCCTCATCACGTAGGAACTATGTCATCCACCAACCAAATCTCCTCATCACGTAGGAGCCG
*
234410 TGTCAAACTTAAATAACC
66 CGTCAAACTTAAATAACC
** * * *
234428 AGTTGTCCTCATCACGTCGGAACTGTGTCATCCACCAACCAGATCTCCTCATCACGTAGGAGCCG
1 AGCCGTCCTCATCACGTAGGAACTATGTCATCCACCAACCAAATCTCCTCATCACGTAGGAGCCG
* *
234493 CGTCAACCTTAGATAACC
66 CGTCAAACTTAAATAACC
* *
234511 AGCCGTCCTCATCGCGTAGGAACCATGT
1 AGCCGTCCTCATCACGTAGGAACTATGT
234539 TATCATCATC
Statistics
Matches: 92, Mismatches: 19, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
83 92 1.00
ACGTcount: A:0.27, C:0.31, G:0.17, T:0.25
Consensus pattern (83 bp):
AGCCGTCCTCATCACGTAGGAACTATGTCATCCACCAACCAAATCTCCTCATCACGTAGGAGCCG
CGTCAAACTTAAATAACC
Found at i:234610 original size:217 final size:217
Alignment explanation
Indices: 234235--234657 Score: 546
Period size: 217 Copynumber: 1.9 Consensus size: 217
234225 CTTGTAGACC
* * *
234235 GTGTCATCCCCTAACCAAATCTCATCATCACGTAGGAGCCGCGTGACCCGTAGATAACCATCCAT
1 GTGTCATCCCCTAACCAAATCTCATCATCACGTAGGAGCCGCGTCAACCGTAGATAACCAGCCAT
* * * *
234300 CCTCATCACGTAGGAATCGTGTTATCATCATCACTAAAGATGGCAAGCCGTCCTCTTCACGTAGG
66 CCTCATCACGTAGGAACCATGTTATCATCATCACTAAAGATGGCAAGCCATCCTCATCACGTAGG
* * * * **
234365 AACTATGTTATCCACTAACCAAATCTCCTCATCACGTATGAGTCGTGTCAAACTTAAATAACCAG
131 AACTATGTCATCAACTAACCAAATCTCCTCATCACGTAGGAGCCGCATCAAACTTAAATAACCAG
**
234430 TTGTCCTCATCACGTCGGAACT
196 TCATCCTCATCACGTCGGAACT
* * * *
234452 GTGTCATCCACC-AACCAGATCTCCTCATCACGTAGGAGCCGCGTCAACCTTAGATAACCAGCCG
1 GTGTCATCC-CCTAACCAAATCTCATCATCACGTAGGAGCCGCGTCAACCGTAGATAACCAGCCA
* ** * *
234516 TCCTCATCGCGTAGGAACCATGTTATCATCATCGTTAAAGATGGTC-AGCTATCCTCATCGCGTA
65 TCCTCATCACGTAGGAACCATGTTATCATCATCACTAAAGATGG-CAAGCCATCCTCATCACGTA
* * * *
234580 GGAACTATGTCATCAA-TCGACCAGATCTCCTCATCACGTAGGAGCCGCATCAACCTTAGATAAC
129 GGAACTATGTCATCAACT-AACCAAATCTCCTCATCACGTAGGAGCCGCATCAAACTTAAATAAC
234644 CAGTCATCCTCATC
193 CAGTCATCCTCATC
234658 GCATAGGAAC
Statistics
Matches: 175, Mismatches: 28, Indels: 6
0.84 0.13 0.03
Matches are distributed among these distances:
216 1 0.01
217 171 0.98
218 3 0.02
ACGTcount: A:0.28, C:0.30, G:0.17, T:0.25
Consensus pattern (217 bp):
GTGTCATCCCCTAACCAAATCTCATCATCACGTAGGAGCCGCGTCAACCGTAGATAACCAGCCAT
CCTCATCACGTAGGAACCATGTTATCATCATCACTAAAGATGGCAAGCCATCCTCATCACGTAGG
AACTATGTCATCAACTAACCAAATCTCCTCATCACGTAGGAGCCGCATCAAACTTAAATAACCAG
TCATCCTCATCACGTCGGAACT
Found at i:234614 original size:134 final size:137
Alignment explanation
Indices: 234433--234807 Score: 445
Period size: 134 Copynumber: 2.7 Consensus size: 137
234423 TAACCAGTTG
* * * *
234433 TCCTCATCACGTCGGAACTGTGTCATCCACCAACCAGATCTCCTCATCACGTAGGAGCCGCGTCA
1 TCCTCATCACGTAGGAACTATGTCATCCATCGACCAGATCTCCTCATCACGTAGGAGCCGCGTCA
* * * *
234498 ACCTTAGATAACCAGCCGTCCTCATCGCGTAGGAACCATGTTAT-C-ATCATCGTTAAAGATGGT
66 ACCTTAGATAACCAGACATCCTCATCGCGTAGGAACCATGTTATCCAATCATCCTTAAAGATGGC
234561 C-AG-CTA
131 CAAGAC-A
* * *
234567 TCCTCATCGCGTAGGAACTATGTCATCAATCGACCAGATCTCCTCATCACGTAGGAGCCGCATCA
1 TCCTCATCACGTAGGAACTATGTCATCCATCGACCAGATCTCCTCATCACGTAGGAGCCGCGTCA
* * *
234632 ACCTTAGATAACCAGTCATCCTCATCGCATAGGAACCATGTTATCACCAATTATCCTTAAAGATG
66 ACCTTAGATAACCAGACATCCTCATCGCGTAGGAACCATGTTAT--CCAATCATCCTTAAAGATG
*
234697 GCCAAGACG
129 GCCAAGACA
* * * **
234706 TCCTCACCACGTAGGAA-AAGTGTCATCCATCGACCATATCTCCTCATCACGTAGGAGCCATGTC
1 TCCTCATCACGTAGGAACTA-TGTCATCCATCGACCAGATCTCCTCATCACGTAGGAGCCGCGTC
* * ** * *
234770 ACCCATAGATAGTCAGACTTCCTCATCACGTAGGAACC
65 AACCTTAGATAACCAGACATCCTCATCGCGTAGGAACC
234808 GTGCTACCTC
Statistics
Matches: 204, Mismatches: 30, Indels: 9
0.84 0.12 0.04
Matches are distributed among these distances:
134 99 0.49
137 1 0.00
138 17 0.08
139 86 0.42
140 1 0.00
ACGTcount: A:0.28, C:0.31, G:0.17, T:0.23
Consensus pattern (137 bp):
TCCTCATCACGTAGGAACTATGTCATCCATCGACCAGATCTCCTCATCACGTAGGAGCCGCGTCA
ACCTTAGATAACCAGACATCCTCATCGCGTAGGAACCATGTTATCCAATCATCCTTAAAGATGGC
CAAGACA
Found at i:235024 original size:3 final size:3
Alignment explanation
Indices: 235016--235079 Score: 128
Period size: 3 Copynumber: 21.3 Consensus size: 3
235006 ATTTTGTTAA
235016 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
235064 ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT A
235080 GAGGCCAAAT
Statistics
Matches: 61, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 61 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:239184 original size:23 final size:23
Alignment explanation
Indices: 239149--239248 Score: 67
Period size: 23 Copynumber: 4.6 Consensus size: 23
239139 AAATTTTAAA
239149 TTATT-ATATATTTTAGATATTTT
1 TTATTAATA-ATTTTAGATATTTT
239172 TTATTAATAA-TTT-G-TATTTAT
1 TTATTAATAATTTTAGATATTT-T
* *
239193 TTAGATTTAAAAATTTTA-A-A-TTA
1 TT--A-TTAATAATTTTAGATATTTT
239216 TTA-T-AT-ATTTTAGATATTTT
1 TTATTAATAATTTTAGATATTTT
239236 TTATTAATAATTT
1 TTATTAATAATTT
239249 GTATTTATTT
Statistics
Matches: 59, Mismatches: 4, Indels: 28
0.65 0.04 0.31
Matches are distributed among these distances:
17 6 0.10
18 2 0.03
19 2 0.03
20 10 0.17
21 6 0.10
22 5 0.08
23 13 0.22
24 11 0.19
25 4 0.07
ACGTcount: A:0.36, C:0.00, G:0.04, T:0.60
Consensus pattern (23 bp):
TTATTAATAATTTTAGATATTTT
Found at i:239234 original size:64 final size:64
Alignment explanation
Indices: 239133--239262 Score: 260
Period size: 64 Copynumber: 2.0 Consensus size: 64
239123 ACCATCGTAC
239133 ATTTAAAAATTTTAAATTATTATATATTTTAGATATTTTTTATTAATAATTTGTATTTATTTAG
1 ATTTAAAAATTTTAAATTATTATATATTTTAGATATTTTTTATTAATAATTTGTATTTATTTAG
239197 ATTTAAAAATTTTAAATTATTATATATTTTAGATATTTTTTATTAATAATTTGTATTTATTTAG
1 ATTTAAAAATTTTAAATTATTATATATTTTAGATATTTTTTATTAATAATTTGTATTTATTTAG
239261 AT
1 AT
239263 GCTTATATTC
Statistics
Matches: 66, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
64 66 1.00
ACGTcount: A:0.38, C:0.00, G:0.05, T:0.58
Consensus pattern (64 bp):
ATTTAAAAATTTTAAATTATTATATATTTTAGATATTTTTTATTAATAATTTGTATTTATTTAG
Found at i:239948 original size:23 final size:23
Alignment explanation
Indices: 239896--239955 Score: 66
Period size: 24 Copynumber: 2.6 Consensus size: 23
239886 AACCATAAGG
* * * *
239896 AACGTACCACAAGAGCTGATAAA
1 AACGTGCCACAAGAACAGAGAAA
239919 AAGCGTGCCACAAGAACAGAGAAA
1 AA-CGTGCCACAAGAACAGAGAAA
*
239943 AACGTGTCACAAG
1 AACGTGCCACAAG
239956 GATATATATT
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
23 12 0.39
24 19 0.61
ACGTcount: A:0.47, C:0.22, G:0.22, T:0.10
Consensus pattern (23 bp):
AACGTGCCACAAGAACAGAGAAA
Found at i:239998 original size:13 final size:13
Alignment explanation
Indices: 239980--240013 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
239970 TTTAAAAGTG
*
239980 AAAAAAGTCAAAC
1 AAAAAAATCAAAC
239993 AAAAAAATCAAAC
1 AAAAAAATCAAAC
*
240006 AAACAAAT
1 AAAAAAAT
240014 AATACTATGA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.74, C:0.15, G:0.03, T:0.09
Consensus pattern (13 bp):
AAAAAAATCAAAC
Found at i:240971 original size:20 final size:20
Alignment explanation
Indices: 240919--240971 Score: 54
Period size: 21 Copynumber: 2.6 Consensus size: 20
240909 TGATGTTGTT
*
240919 TTATTTTAATTTAGTCACTG
1 TTATTTTAATTTAGTCACTA
* *
240939 TAATTTTTGATTTAGAT-ACTA
1 TTA-TTTTAATTTAG-TCACTA
240960 TTATTTTAATTT
1 TTATTTTAATTT
240972 TTTGCATTTT
Statistics
Matches: 26, Mismatches: 5, Indels: 4
0.74 0.14 0.11
Matches are distributed among these distances:
20 10 0.38
21 15 0.58
22 1 0.04
ACGTcount: A:0.28, C:0.06, G:0.08, T:0.58
Consensus pattern (20 bp):
TTATTTTAATTTAGTCACTA
Found at i:241077 original size:5 final size:5
Alignment explanation
Indices: 241067--241091 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
241057 CAATTACGTC
241067 TTTAT TTTAT TTTAT TTTAT TTTAT
1 TTTAT TTTAT TTTAT TTTAT TTTAT
241092 ATTTTAATGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (5 bp):
TTTAT
Found at i:247148 original size:77 final size:76
Alignment explanation
Indices: 246931--247148 Score: 230
Period size: 77 Copynumber: 2.9 Consensus size: 76
246921 CTTGAGATTG
* * * *
246931 TTTTTCTT-AAAC-AGATTTTGTCTCACTTGAGAC-AGTTTTGCTCGAAAGAAGACATTTCATTT
1 TTTTTCTTAAAACAAGA-TTTGTCTCGCTTGAGACAATTTTTACTCGAAAGAAAACATTTCATTT
* * * * *
246993 GACTCGAGATTG
65 CACACAAGACTA
* * * *
247005 TTTTTCTTAAAACAAGATTTGTC-CTGCTTTAGATAATTTTTACTCGAAACAAGAAGATTT-ATT
1 TTTTTCTTAAAACAAGATTTGTCTC-GCTTGAGACAATTTTTACTCGAAAGAA-AACATTTCATT
247068 TCACACAAAGACTA
64 TCACAC-AAGACTA
* *
247082 TTTTTCTTAAAACAAGATTTGTCTCGCTTGAGACAATTTTTACTCGAAAGAAAATATTTCACTTC
1 TTTTTCTTAAAACAAGATTTGTCTCGCTTGAGACAATTTTTACTCGAAAGAAAACATTTCATTTC
247147 AC
66 AC
247149 TTAAGATTGT
Statistics
Matches: 118, Mismatches: 18, Indels: 13
0.79 0.12 0.09
Matches are distributed among these distances:
74 9 0.08
75 16 0.14
76 30 0.25
77 62 0.53
78 1 0.01
ACGTcount: A:0.32, C:0.17, G:0.13, T:0.39
Consensus pattern (76 bp):
TTTTTCTTAAAACAAGATTTGTCTCGCTTGAGACAATTTTTACTCGAAAGAAAACATTTCATTTC
ACACAAGACTA
Found at i:247224 original size:39 final size:39
Alignment explanation
Indices: 247165--248005 Score: 1265
Period size: 39 Copynumber: 21.6 Consensus size: 39
247155 TTGTTTTTAA
* *
247165 AGAAGATTGTATCTCGCTTGAGATAGTTTCCCTCGAAAC
1 AGAAGATTTTGTCTCGCTTGAGATAGTTTCCCTCGAAAC
* *
247204 ACAAGATTTTGTCTCACTTGAGATAGTTTCCCTCGAAAC
1 AGAAGATTTTGTCTCGCTTGAGATAGTTTCCCTCGAAAC
* *
247243 AGAAGATTTTATCTTGCTTGAGATAGTTTCCCTCGAAAC
1 AGAAGATTTTGTCTCGCTTGAGATAGTTTCCCTCGAAAC
* *
247282 AGAAGATTGTATCTCGCTTGAGATAGTTTCCCTCGAAAC
1 AGAAGATTTTGTCTCGCTTGAGATAGTTTCCCTCGAAAC
* *
247321 AAAAGATTTTGTCTCACTTGAGATAGTTTCCCTCGAAAC
1 AGAAGATTTTGTCTCGCTTGAGATAGTTTCCCTCGAAAC
*
247360 AGAAGATTTTATCTCGCTTGAGATAGTTTCCCTCGAAAC
1 AGAAGATTTTGTCTCGCTTGAGATAGTTTCCCTCGAAAC
* *
247399 AGAAGATTGTATCTCGCTTGAGATAGTTTCCCTCGAAAC
1 AGAAGATTTTGTCTCGCTTGAGATAGTTTCCCTCGAAAC
* *
247438 ACAAGATTTTGTCTCACTTGAGATAGTTTCCCTCGAAAC
1 AGAAGATTTTGTCTCGCTTGAGATAGTTTCCCTCGAAAC
* *
247477 AGAAGATTTTATCTCGCTTGAGATAGTTTCCCTCAAAAC
1 AGAAGATTTTGTCTCGCTTGAGATAGTTTCCCTCGAAAC
* *
247516 AGAA-ATTTTTTTCTCACTTGAGATAGTTTCCCTCGAAAC
1 AGAAGA-TTTTGTCTCGCTTGAGATAGTTTCCCTCGAAAC
* * *
247555 AGAAGATTTTATCTCACTTGAGATAGTTTCCCTCGAAAT
1 AGAAGATTTTGTCTCGCTTGAGATAGTTTCCCTCGAAAC
* *
247594 AGAAGATTTTTTCTCGCTTGAGATAGTTTCCCTAGAAAC
1 AGAAGATTTTGTCTCGCTTGAGATAGTTTCCCTCGAAAC
*
247633 AGAAGATTTTGTCTCGCTTGAGATAGTTTCCCTAGAAAC
1 AGAAGATTTTGTCTCGCTTGAGATAGTTTCCCTCGAAAC
*
247672 AGAAGATTTTGTCTCGCTTGAGATAGTTTCCCTCAAAAC
1 AGAAGATTTTGTCTCGCTTGAGATAGTTTCCCTCGAAAC
*
247711 AGAAGATTTTGTCTCACTTGAGATAGTTTCCCTCGAAAC
1 AGAAGATTTTGTCTCGCTTGAGATAGTTTCCCTCGAAAC
* *
247750 AGAAGATTTTATCTCACTTGAGATAGTTTCCCTCGAAAC
1 AGAAGATTTTGTCTCGCTTGAGATAGTTTCCCTCGAAAC
* * *
247789 AGAAGATTTTATCTCGCTTGAGATAGTTTTCCTAGAAAC
1 AGAAGATTTTGTCTCGCTTGAGATAGTTTCCCTCGAAAC
*
247828 AGAAGATTTTGTCTCGCTTGAGATAGTTTCCCTCAAAAC
1 AGAAGATTTTGTCTCGCTTGAGATAGTTTCCCTCGAAAC
* * * * *
247867 ATAATATTTTGTCTCGCTTGATATAGTTTCCCT-AAAAT
1 AGAAGATTTTGTCTCGCTTGAGATAGTTTCCCTCGAAAC
* *
247905 AGAAGATTTTGTCTCGCTTGAGATAGTTTCCCTCAAAAT
1 AGAAGATTTTGTCTCGCTTGAGATAGTTTCCCTCGAAAC
*
247944 AGAAGATTTTGTCTCACTTGAGATAGTTTCCCTCGAAAC
1 AGAAGATTTTGTCTCGCTTGAGATAGTTTCCCTCGAAAC
*
247983 AGAAAATTTTGTCTTC-CTTGAGA
1 AGAAGATTTTGTC-TCGCTTGAGA
248006 CATTTTTCTT
Statistics
Matches: 739, Mismatches: 59, Indels: 8
0.92 0.07 0.01
Matches are distributed among these distances:
38 35 0.05
39 701 0.95
40 3 0.00
ACGTcount: A:0.29, C:0.20, G:0.17, T:0.34
Consensus pattern (39 bp):
AGAAGATTTTGTCTCGCTTGAGATAGTTTCCCTCGAAAC
Found at i:248436 original size:44 final size:44
Alignment explanation
Indices: 248364--248575 Score: 172
Period size: 44 Copynumber: 4.8 Consensus size: 44
248354 TTGTTCAACT
* * * * *
248364 TTTTGCTCGATTCTATCACAGAATGAGGTAGATCAGCACCGACA
1 TTTTGTTCGATTCCATCACAGAAGGAGGTGGATCAGCATCGACA
* * * ***
248408 TCTTGTTCGATTCCATCACAGAAGGAGGTGGATCAACATTTGTTT
1 TTTTGTTCGATTCCATCACAGAAGGAGGTGGATCAGCA-TCGACA
* * * * * * * *
248453 TTTCTGCTCAAATCCATCGCAGAAGGAGTTGGATCAGCGTCAACT
1 TTT-TGTTCGATTCCATCACAGAAGGAGGTGGATCAGCATCGACA
* * * *
248498 TTTTGTTCGATTCTATCACAAAAGGAAGTAGATCAGCATCGACA
1 TTTTGTTCGATTCCATCACAGAAGGAGGTGGATCAGCATCGACA
* * *
248542 TATCGTTCGATTCCATCATAGAAGGAGGTGGATC
1 TTTTGTTCGATTCCATCACAGAAGGAGGTGGATC
248576 GACATTTTTA
Statistics
Matches: 124, Mismatches: 42, Indels: 4
0.73 0.25 0.02
Matches are distributed among these distances:
44 88 0.71
45 8 0.06
46 28 0.23
ACGTcount: A:0.28, C:0.20, G:0.22, T:0.30
Consensus pattern (44 bp):
TTTTGTTCGATTCCATCACAGAAGGAGGTGGATCAGCATCGACA
Found at i:248658 original size:50 final size:49
Alignment explanation
Indices: 248604--248699 Score: 140
Period size: 50 Copynumber: 1.9 Consensus size: 49
248594 CAAATCCATC
*
248604 GTAGAAGGATTTGGATCAGCGTCAAATT-TTAGCTCGATTCTATCACAGAA
1 GTAGAAGGAGTTGGATCAGCGTCAAATTCTT-GCTCGATTC-ATCACAGAA
* *
248654 GTAGAAGGAGTTGGATCAGCTTCAACTTCTTGCTCGATTCATCACA
1 GTAGAAGGAGTTGGATCAGCGTCAAATTCTTGCTCGATTCATCACA
248700 ATGGAGTTGA
Statistics
Matches: 42, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
49 6 0.14
50 34 0.81
51 2 0.05
ACGTcount: A:0.29, C:0.19, G:0.22, T:0.30
Consensus pattern (49 bp):
GTAGAAGGAGTTGGATCAGCGTCAAATTCTTGCTCGATTCATCACAGAA
Found at i:256644 original size:15 final size:16
Alignment explanation
Indices: 256616--256656 Score: 59
Period size: 17 Copynumber: 2.6 Consensus size: 16
256606 GGGCCTCGAG
256616 CTATATAA-ATAATAA
1 CTATATAATATAATAA
256631 -TATATAATATAATAA
1 CTATATAATATAATAA
256646 CGTATATAATA
1 C-TATATAATA
256657 AACGTCACTC
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
14 7 0.30
15 7 0.30
17 9 0.39
ACGTcount: A:0.56, C:0.05, G:0.02, T:0.37
Consensus pattern (16 bp):
CTATATAATATAATAA
Found at i:257079 original size:46 final size:46
Alignment explanation
Indices: 257027--257178 Score: 152
Period size: 46 Copynumber: 3.4 Consensus size: 46
257017 TAGATTACTT
* *
257027 CACTACTCTTCGGTGAAGATTTCATACTTTGCTGAAAAATCTGTTC
1 CACTACTCTTCCGTGAAGATTTCATACTTTGCTGAAAAATTTGTTC
** * * **
257073 CACTACTCTTTTGTG--GAGTTCAGA-TTTG-TGATTGAATTTGCTTC
1 CACTACTCTTCCGTGAAGATTTCATACTTTGCTGA-AAAATTTG-TTC
* * *
257117 CACTACTCTTCCATGGAG-TTTGATACTTTGCTGAAAAATTTGTTC
1 CACTACTCTTCCGTGAAGATTTCATACTTTGCTGAAAAATTTGTTC
257162 CACTACTCTTCCGTGAA
1 CACTACTCTTCCGTGAA
257179 AATGAATTGA
Statistics
Matches: 83, Mismatches: 17, Indels: 13
0.73 0.15 0.12
Matches are distributed among these distances:
42 3 0.04
43 9 0.11
44 22 0.27
45 22 0.27
46 24 0.29
47 3 0.04
ACGTcount: A:0.23, C:0.21, G:0.16, T:0.39
Consensus pattern (46 bp):
CACTACTCTTCCGTGAAGATTTCATACTTTGCTGAAAAATTTGTTC
Found at i:258179 original size:22 final size:22
Alignment explanation
Indices: 258154--258202 Score: 98
Period size: 22 Copynumber: 2.2 Consensus size: 22
258144 AAAGCTTTGG
258154 TCTTTGAAAAGAGAATCTATCA
1 TCTTTGAAAAGAGAATCTATCA
258176 TCTTTGAAAAGAGAATCTATCA
1 TCTTTGAAAAGAGAATCTATCA
258198 TCTTT
1 TCTTT
258203 ACAAAATGTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.37, C:0.14, G:0.12, T:0.37
Consensus pattern (22 bp):
TCTTTGAAAAGAGAATCTATCA
Found at i:259032 original size:40 final size:40
Alignment explanation
Indices: 258988--259084 Score: 149
Period size: 40 Copynumber: 2.4 Consensus size: 40
258978 TCTGAAATGA
*
258988 GCCTTCAATATGCCCCATATTTTATTTCTGACTAAAAAAG
1 GCCTTCAATATGCCCCACATTTTATTTCTGACTAAAAAAG
** * *
259028 GCCTTCAGCATGCCCCACATTTTATTTCTGACTGAAATAG
1 GCCTTCAATATGCCCCACATTTTATTTCTGACTAAAAAAG
259068 GCCTTCAATATGCCCCA
1 GCCTTCAATATGCCCCA
259085 ACCTTGGCTA
Statistics
Matches: 50, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
40 50 1.00
ACGTcount: A:0.28, C:0.28, G:0.12, T:0.32
Consensus pattern (40 bp):
GCCTTCAATATGCCCCACATTTTATTTCTGACTAAAAAAG
Found at i:270950 original size:28 final size:28
Alignment explanation
Indices: 270919--270997 Score: 133
Period size: 28 Copynumber: 2.8 Consensus size: 28
270909 TTTAGGTACC
270919 TATTTTGA-CATAAAATACTTTAGACACT
1 TATTTTGACCA-AAAATACTTTAGACACT
270947 TATTTTGACCAAAAATACTTTAGACACT
1 TATTTTGACCAAAAATACTTTAGACACT
270975 TATTTTGACCAAAAAATACTTTA
1 TATTTTGACC-AAAAATACTTTA
270998 AATAATTAAA
Statistics
Matches: 49, Mismatches: 0, Indels: 3
0.94 0.00 0.06
Matches are distributed among these distances:
28 35 0.71
29 14 0.29
ACGTcount: A:0.41, C:0.15, G:0.06, T:0.38
Consensus pattern (28 bp):
TATTTTGACCAAAAATACTTTAGACACT
Found at i:279320 original size:17 final size:16
Alignment explanation
Indices: 279297--279346 Score: 57
Period size: 15 Copynumber: 3.1 Consensus size: 16
279287 GAAGAAAATT
279297 AAAGAAAGAAATGAAAA
1 AAAGAAA-AAATGAAAA
* *
279314 AAGGAAACAAT-AAAA
1 AAAGAAAAAATGAAAA
*
279329 AAAGAGAAAATGAAAA
1 AAAGAAAAAATGAAAA
279345 AA
1 AA
279347 TAAATATAAA
Statistics
Matches: 27, Mismatches: 5, Indels: 3
0.77 0.14 0.09
Matches are distributed among these distances:
15 12 0.44
16 9 0.33
17 6 0.22
ACGTcount: A:0.76, C:0.02, G:0.16, T:0.06
Consensus pattern (16 bp):
AAAGAAAAAATGAAAA
Found at i:281087 original size:21 final size:21
Alignment explanation
Indices: 281057--281100 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
281047 TTTGCTCGAT
* *
281057 TCCATCACATAATGAGTTGGA
1 TCCATAACATAAGGAGTTGGA
281078 TCCATAACATAAGGAGTTGGA
1 TCCATAACATAAGGAGTTGGA
281099 TC
1 TC
281101 TGCATCGACC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.34, C:0.18, G:0.20, T:0.27
Consensus pattern (21 bp):
TCCATAACATAAGGAGTTGGA
Found at i:289049 original size:22 final size:21
Alignment explanation
Indices: 289000--289049 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 21
288990 TTTTTATTTA
289000 TCAGA-TTTTAGTTTGGAGAT
1 TCAGAGTTTTAGTTTGGAGAT
*
289020 TCATGAGTTTTTGTTTGGAGATT
1 TCA-GAGTTTTAGTTTGGAGA-T
289043 TCAGAGT
1 TCAGAGT
289050 GACTTTTCAG
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
20 3 0.12
21 2 0.08
22 17 0.65
23 4 0.15
ACGTcount: A:0.22, C:0.06, G:0.26, T:0.46
Consensus pattern (21 bp):
TCAGAGTTTTAGTTTGGAGAT
Found at i:296398 original size:37 final size:36
Alignment explanation
Indices: 296347--296436 Score: 92
Period size: 36 Copynumber: 2.5 Consensus size: 36
296337 TTTGAGATTT
**
296347 TTTCTCTCGAAACAAAGTGTCGTCTCGCTAGAGACAA
1 TTTCTCTTAAAACAAA-TGTCGTCTCGCTAGAGACAA
* * * * *
296384 TTT-TCTTAAAAACAAATTTTGTCTTGCTTGTGACAA
1 TTTCTCTT-AAAACAAATGTCGTCTCGCTAGAGACAA
296420 TTTCTCTTAAAACAAAT
1 TTTCTCTTAAAACAAAT
296437 TCCATCTCGC
Statistics
Matches: 44, Mismatches: 7, Indels: 5
0.79 0.12 0.09
Matches are distributed among these distances:
36 30 0.68
37 14 0.32
ACGTcount: A:0.32, C:0.19, G:0.12, T:0.37
Consensus pattern (36 bp):
TTTCTCTTAAAACAAATGTCGTCTCGCTAGAGACAA
Found at i:296449 original size:36 final size:36
Alignment explanation
Indices: 296369--296460 Score: 96
Period size: 36 Copynumber: 2.6 Consensus size: 36
296359 CAAAGTGTCG
* ***
296369 TCTCGCTAGAGACAATTTTCTTAAAAACAAATTTTG
1 TCTCGCTTGAGACAATTTTCTTAAAAACAAATTCCA
* *
296405 TCTTGCTTGTGACAATTTCTCTT-AAAACAAATTCCA
1 TCTCGCTTGAGACAATTT-TCTTAAAAACAAATTCCA
* *
296441 TCTCGCTTGAGCCAGTTTTC
1 TCTCGCTTGAGACAATTTTC
296461 CCTTGAGATG
Statistics
Matches: 45, Mismatches: 10, Indels: 3
0.78 0.17 0.05
Matches are distributed among these distances:
35 2 0.04
36 39 0.87
37 4 0.09
ACGTcount: A:0.28, C:0.22, G:0.12, T:0.38
Consensus pattern (36 bp):
TCTCGCTTGAGACAATTTTCTTAAAAACAAATTCCA
Found at i:296820 original size:29 final size:29
Alignment explanation
Indices: 296780--296895 Score: 85
Period size: 29 Copynumber: 3.8 Consensus size: 29
296770 TTTTTCTCTC
*
296780 TTGAGACAGTTTCTCTTGAAACATCATCT
1 TTGAGACAGTTTCCCTTGAAACATCATCT
*
296809 TTGAGATC-GTTTCCCTTGAAATGAATTTTGTC-TCT
1 TTGAGA-CAGTTTCCCTTGAAA--CA-----TCATCT
* *
296844 CTTGAGACAATTTCTCTTGAAACATCATCT
1 -TTGAGACAGTTTCCCTTGAAACATCATCT
296874 TTGAGATC-GTTTCCCTTGAAAC
1 TTGAGA-CAGTTTCCCTTGAAAC
296896 GAATTTTGTC
Statistics
Matches: 68, Mismatches: 7, Indels: 24
0.69 0.07 0.24
Matches are distributed among these distances:
29 38 0.56
30 5 0.07
31 1 0.01
34 1 0.01
35 4 0.06
36 19 0.28
ACGTcount: A:0.25, C:0.21, G:0.15, T:0.40
Consensus pattern (29 bp):
TTGAGACAGTTTCCCTTGAAACATCATCT
Found at i:296926 original size:65 final size:65
Alignment explanation
Indices: 296705--296915 Score: 345
Period size: 65 Copynumber: 3.3 Consensus size: 65
296695 TTCAAAAAAG
* ** *
296705 TTTTGTCTCTCTCGAGACAATTTCTCTTGAAACAAAGATCTTTGAGATTGTTTCCCTTGAAATG-
1 TTTTGTCTCTCTTGAGACAATTTCTCTTGAAAC-ATCATCTTTGAGATCGTTTCCCTTGAAATGA
296769 A
65 A
*
296770 TTTT-TCTCTCTTGAGACAGTTTCTCTTGAAACATCATCTTTGAGATCGTTTCCCTTGAAATGAA
1 TTTTGTCTCTCTTGAGACAATTTCTCTTGAAACATCATCTTTGAGATCGTTTCCCTTGAAATGAA
*
296834 TTTTGTCTCTCTTGAGACAATTTCTCTTGAAACATCATCTTTGAGATCGTTTCCCTTGAAACGAA
1 TTTTGTCTCTCTTGAGACAATTTCTCTTGAAACATCATCTTTGAGATCGTTTCCCTTGAAATGAA
296899 TTTTGTCTCTCTTGAGA
1 TTTTGTCTCTCTTGAGA
296916 TGGTTTCTCT
Statistics
Matches: 137, Mismatches: 7, Indels: 4
0.93 0.05 0.03
Matches are distributed among these distances:
63 27 0.20
64 31 0.23
65 79 0.58
ACGTcount: A:0.24, C:0.20, G:0.15, T:0.42
Consensus pattern (65 bp):
TTTTGTCTCTCTTGAGACAATTTCTCTTGAAACATCATCTTTGAGATCGTTTCCCTTGAAATGAA
Found at i:297260 original size:83 final size:83
Alignment explanation
Indices: 297085--297278 Score: 235
Period size: 83 Copynumber: 2.3 Consensus size: 83
297075 AAAGATGGCA
* * * * * * * *
297085 AGCCGTCCTCTTCACGTAGGAACTGTGTTATCCACTAACCAGATCTCCTTATCACGTATGAGTCG
1 AGCCGTCCTCATCACATAGGAACTGTGTCATCCACCAACCAAATCTCCTCATCACGTAGGAGCCG
*
297150 TGTCAACCTTAAATAACC
66 CGTCAACCTTAAATAACC
** *
297168 AGTTGTCCTCATCACATCGGAACTGTGTCATCCACCAACCAAATCTCCTCATCACGTAGGAGCCG
1 AGCCGTCCTCATCACATAGGAACTGTGTCATCCACCAACCAAATCTCCTCATCACGTAGGAGCCG
*
297233 CGTCAACCTTAGATAACC
66 CGTCAACCTTAAATAACC
* * * *
297251 AGCCATCCTCATCGCGTAGGAACCGTGT
1 AGCCGTCCTCATCACATAGGAACTGTGT
297279 TATCATCATC
Statistics
Matches: 91, Mismatches: 20, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
83 91 1.00
ACGTcount: A:0.26, C:0.31, G:0.17, T:0.25
Consensus pattern (83 bp):
AGCCGTCCTCATCACATAGGAACTGTGTCATCCACCAACCAAATCTCCTCATCACGTAGGAGCCG
CGTCAACCTTAAATAACC
Found at i:297350 original size:217 final size:217
Alignment explanation
Indices: 296975--297385 Score: 535
Period size: 217 Copynumber: 1.9 Consensus size: 217
296965 TTGTAGGACC
* * *
296975 GTGTCATCCCCTAACCAAATCTCATCATCACGTAGGAGCCGCGTGACCCGTAGATAACCATCCAT
1 GTGTCATCCCCTAACCAAATCTCATCATCACGTAGGAGCCGCGTCAACCGTAGATAACCAGCCAT
* * *
297040 CCTCATCACGTAGGAATCGTGTTATCATCATCACTAAAGATGGCAAGCCGTCCTCTTCACGTAGG
66 CCTCATCACGTAGGAACCGTGTTATCATCATCACTAAAGATGGCAAGCCATCCTCATCACGTAGG
* * * * * * **
297105 AACTGTGTTATCCACTAACCAGATCTCCTTATCACGTATG-AGTCGTGTCAACCTTAAATAACCA
131 AACTATGTCATCAACTAACCAAATCTCCTCATCACGTA-GAAGCCGCATCAACCTTAAATAACCA
297169 GTTGTCCTCATCACATCGGAACT
195 GTTGTCCTCATCACATCGGAACT
* *
297192 GTGTCATCCACC-AACCAAATCTCCTCATCACGTAGGAGCCGCGTCAACCTTAGATAACCAGCCA
1 GTGTCATCC-CCTAACCAAATCTCATCATCACGTAGGAGCCGCGTCAACCGTAGATAACCAGCCA
* * * *
297256 TCCTCATCGCGTAGGAACCGTGTTATCATCATC-CGTAAATATGGTC-AGCTATCCTCATCGCGT
65 TCCTCATCACGTAGGAACCGTGTTATCATCATCAC-TAAAGATGG-CAAGCCATCCTCATCACGT
* * *
297319 ATGAACTATGTCATCAA-TCGACCAAATCTCCTCATCACGTAGAAGCCGCATCAACCTTAGATAA
128 AGGAACTATGTCATCAACT-AACCAAATCTCCTCATCACGTAGAAGCCGCATCAACCTTAAATAA
297383 CCA
192 CCA
297386 ATCATCCTCA
Statistics
Matches: 166, Mismatches: 23, Indels: 10
0.83 0.12 0.05
Matches are distributed among these distances:
216 3 0.02
217 160 0.96
218 3 0.02
ACGTcount: A:0.28, C:0.30, G:0.16, T:0.25
Consensus pattern (217 bp):
GTGTCATCCCCTAACCAAATCTCATCATCACGTAGGAGCCGCGTCAACCGTAGATAACCAGCCAT
CCTCATCACGTAGGAACCGTGTTATCATCATCACTAAAGATGGCAAGCCATCCTCATCACGTAGG
AACTATGTCATCAACTAACCAAATCTCCTCATCACGTAGAAGCCGCATCAACCTTAAATAACCAG
TTGTCCTCATCACATCGGAACT
Found at i:297519 original size:139 final size:134
Alignment explanation
Indices: 297173--297547 Score: 368
Period size: 134 Copynumber: 2.8 Consensus size: 134
297163 TAACCAGTTG
* * *
297173 TCCTCATCACATCGGAACT-GTGTCATCCACCAACCAAATCTCCTCATCACGTAGGAGCCGCGTC
1 TCCTCATCACGTAGGAACTAGTGTCATCCACCGACCAAATCTCCTCATCACGTA-GAGCCGCGTC
* * * * *
297237 AACCTTAGATAACCAGCCATCCTCATCGCGTAGGAACCGTGTTATCATCATCCGTAAATATGGTC
65 AACCTTAGATAACCAACCATCCTCATCGCGTAGGAACCATGTTATCATCATCCCTAAAGATGGCC
297302 AGCTA
130 AGCTA
* * * * *
297307 TCCTCATCGCGTATGAACTA-TGTCATCAATCGACCAAATCTCCTCATCACGTAGAAGCCGCATC
1 TCCTCATCACGTAGGAACTAGTGTCATCCACCGACCAAATCTCCTCATCACGTAG-AGCCGCGTC
* *
297371 AACCTTAGATAACCAATCATCCTCAAT-GCGTAGGAACCATGTTATCACCAATTATCCCTAAAGA
65 AACCTTAGATAACCAACCATCCTC-ATCGCGTAGGAACCATGTTAT---C-ATCATCCCTAAAGA
297435 TGGCCAAGAC-A
125 TGGCC-AG-CTA
* * * **
297446 TCCTCA-CTATGTAGGAA-TAGTGTAATCCACCGACCATATCTCCTCATCACGTATGAGCCATGT
1 TCCTCATC-ACGTAGGAACTAGTGTCATCCACCGACCAAATCTCCTCATCACGTA-GAGCCGCGT
* * * * *
297509 CACCCATAGATAATCAGA-CTTCCTCATCACGTAGGAACC
64 CAACCTTAGATAACCA-ACCATCCTCATCGCGTAGGAACC
297548 GTGCTACCTC
Statistics
Matches: 197, Mismatches: 30, Indels: 23
0.79 0.12 0.09
Matches are distributed among these distances:
133 1 0.01
134 92 0.47
135 2 0.01
137 1 0.01
138 20 0.10
139 78 0.40
140 3 0.02
ACGTcount: A:0.30, C:0.31, G:0.15, T:0.24
Consensus pattern (134 bp):
TCCTCATCACGTAGGAACTAGTGTCATCCACCGACCAAATCTCCTCATCACGTAGAGCCGCGTCA
ACCTTAGATAACCAACCATCCTCATCGCGTAGGAACCATGTTATCATCATCCCTAAAGATGGCCA
GCTA
Found at i:297761 original size:3 final size:3
Alignment explanation
Indices: 297753--297810 Score: 116
Period size: 3 Copynumber: 19.3 Consensus size: 3
297743 ATTTTGTTAA
297753 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
297801 ATT ATT ATT A
1 ATT ATT ATT A
297811 GAGGCCAAAT
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 55 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:301569 original size:8 final size:8
Alignment explanation
Indices: 301558--301606 Score: 53
Period size: 8 Copynumber: 6.0 Consensus size: 8
301548 ATTTAGATAT
301558 TTTTTATA
1 TTTTTATA
301566 TTTTTATTA
1 TTTTTA-TA
* *
301575 ATTATATA
1 TTTTTATA
*
301583 ATTTTATA
1 TTTTTATA
*
301591 TTTTTAAA
1 TTTTTATA
301599 TTTTTATA
1 TTTTTATA
301607 GTTTCACATC
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
8 28 0.82
9 6 0.18
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (8 bp):
TTTTTATA
Found at i:302737 original size:13 final size:13
Alignment explanation
Indices: 302719--302752 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
302709 TTTAAAAGTG
*
302719 AAAAAAGTCAAAC
1 AAAAAAATCAAAC
302732 AAAAAAATCAAAC
1 AAAAAAATCAAAC
*
302745 AAACAAAT
1 AAAAAAAT
302753 AATACTATGA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.74, C:0.15, G:0.03, T:0.09
Consensus pattern (13 bp):
AAAAAAATCAAAC
Found at i:307247 original size:20 final size:22
Alignment explanation
Indices: 307208--307248 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 22
307198 ACTAAAATAA
307208 AAATATAAAAAATGCGAAAACC
1 AAATATAAAAAATGCGAAAACC
307230 AAAT-TAAAAAATGC-AAAAC
1 AAATATAAAAAATGCGAAAAC
307249 ATGATTTTGG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 5 0.26
21 10 0.53
22 4 0.21
ACGTcount: A:0.66, C:0.12, G:0.07, T:0.15
Consensus pattern (22 bp):
AAATATAAAAAATGCGAAAACC
Found at i:308319 original size:12 final size:14
Alignment explanation
Indices: 308294--308334 Score: 55
Period size: 15 Copynumber: 2.8 Consensus size: 14
308284 GCCTTTGGGC
308294 TATATAAATAATAA
1 TATATAAATAATAA
308308 TATATAATATAATAA
1 TATATAA-ATAATAA
*
308323 TGTATATAATAA
1 TATATA-AATAA
308335 ACGTCACTCG
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
14 7 0.29
15 16 0.67
16 1 0.04
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (14 bp):
TATATAAATAATAA
Found at i:308321 original size:15 final size:16
Alignment explanation
Indices: 308294--308333 Score: 57
Period size: 17 Copynumber: 2.6 Consensus size: 16
308284 GCCTTTGGGC
308294 TATATAA-ATAATAA-
1 TATATAATATAATAAG
308308 TATATAATATAATAATG
1 TATATAATATAATAA-G
308325 TATATAATA
1 TATATAATA
308334 AACGTCACTC
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 7 0.30
15 7 0.30
17 9 0.39
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.40
Consensus pattern (16 bp):
TATATAATATAATAAG
Found at i:308843 original size:44 final size:44
Alignment explanation
Indices: 308704--308852 Score: 158
Period size: 44 Copynumber: 3.3 Consensus size: 44
308694 TATATTACTT
* *
308704 CACTACTCTTTCGTGAAGATTTCATACTTTGCTGAAAAATTTGTTC
1 CACTACTCTTCCGTGGAG-TTTCATACTTT-CTGAAAAATTTGTTC
** * * **
308750 CACTACTCTTTTGTGGAG-TTCAGA-TTTGTGATTGAATTTGCTTC
1 CACTACTCTTCCGTGGAGTTTCATACTTTCTGA-AAAATTTG-TTC
*
308794 CACTACTCTTCCGTGGAGTTTGATACTTTCTGAAAAATTTGTTC
1 CACTACTCTTCCGTGGAGTTTCATACTTTCTGAAAAATTTGTTC
*
308838 TACTACTCTTCCGTG
1 CACTACTCTTCCGTG
308853 AAAATGAATT
Statistics
Matches: 85, Mismatches: 14, Indels: 10
0.78 0.13 0.09
Matches are distributed among these distances:
42 3 0.04
43 9 0.11
44 41 0.48
45 10 0.12
46 22 0.26
ACGTcount: A:0.21, C:0.20, G:0.16, T:0.42
Consensus pattern (44 bp):
CACTACTCTTCCGTGGAGTTTCATACTTTCTGAAAAATTTGTTC
Found at i:309855 original size:22 final size:22
Alignment explanation
Indices: 309830--309898 Score: 120
Period size: 22 Copynumber: 3.1 Consensus size: 22
309820 AGCTTTGGTA
309830 TTTGAAAAGAGAGTCTATCATC
1 TTTGAAAAGAGAGTCTATCATC
309852 TTTGAAAAGAGAGTCTATCATC
1 TTTGAAAAGAGAGTCTATCATC
* *
309874 TTTGAAAAGAGAATCTATTATC
1 TTTGAAAAGAGAGTCTATCATC
309896 TTT
1 TTT
309899 ACAAAATGTA
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 45 1.00
ACGTcount: A:0.36, C:0.12, G:0.16, T:0.36
Consensus pattern (22 bp):
TTTGAAAAGAGAGTCTATCATC
Found at i:310614 original size:40 final size:40
Alignment explanation
Indices: 310555--310657 Score: 143
Period size: 40 Copynumber: 2.6 Consensus size: 40
310545 TTTTTGTCTT
* *
310555 AAATGGGCCTTCAGTATGCCCCATATTTTATTTCTGACTA
1 AAATGGGCCTTCAGCATGCCCCACATTTTATTTCTGACTA
* *
310595 AAATGGGCCTTTAGCATGCCCCACATTTTATTTCTGACTG
1 AAATGGGCCTTCAGCATGCCCCACATTTTATTTCTGACTA
* **
310635 AAATAGGCCTTCAATATGCCCCA
1 AAATGGGCCTTCAGCATGCCCCA
310658 ACCTTTGCTA
Statistics
Matches: 55, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
40 55 1.00
ACGTcount: A:0.26, C:0.25, G:0.16, T:0.33
Consensus pattern (40 bp):
AAATGGGCCTTCAGCATGCCCCACATTTTATTTCTGACTA
Found at i:317381 original size:15 final size:16
Alignment explanation
Indices: 317354--317393 Score: 57
Period size: 17 Copynumber: 2.6 Consensus size: 16
317344 GCCTTCGGGT
317354 TATATAA-ATAATAA-
1 TATATAATATAATAAC
317368 TATATAATATAATAAC
1 TATATAATATAATAAC
317384 GTATATAATA
1 -TATATAATA
317394 AACGTCACTT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 7 0.30
15 7 0.30
17 9 0.39
ACGTcount: A:0.57, C:0.03, G:0.03, T:0.38
Consensus pattern (16 bp):
TATATAATATAATAAC
Found at i:319327 original size:39 final size:39
Alignment explanation
Indices: 319284--319364 Score: 126
Period size: 39 Copynumber: 2.1 Consensus size: 39
319274 CTCATGATTT
*
319284 TATTAAAACCATGATAAAAAATATAATACATAATAGTCA
1 TATTAAAACCATGATAAAAAATATAATAAATAATAGTCA
* * *
319323 TATTAAAATCATGATAAACAATATCATAAATAATAGTCA
1 TATTAAAACCATGATAAAAAATATAATAAATAATAGTCA
319362 TAT
1 TAT
319365 CATATTCTTT
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
39 38 1.00
ACGTcount: A:0.54, C:0.10, G:0.05, T:0.31
Consensus pattern (39 bp):
TATTAAAACCATGATAAAAAATATAATAAATAATAGTCA
Found at i:332694 original size:3 final size:3
Alignment explanation
Indices: 332686--332741 Score: 105
Period size: 3 Copynumber: 19.0 Consensus size: 3
332676 ACTTGGCATG
332686 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T-T TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
332733 TAT TAT TAT
1 TAT TAT TAT
332742 ACAAACCAGT
Statistics
Matches: 52, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 2 0.04
3 50 0.96
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:340447 original size:12 final size:12
Alignment explanation
Indices: 340430--340461 Score: 64
Period size: 12 Copynumber: 2.7 Consensus size: 12
340420 TTCCTCGACC
340430 GACCAAGAGGAA
1 GACCAAGAGGAA
340442 GACCAAGAGGAA
1 GACCAAGAGGAA
340454 GACCAAGA
1 GACCAAGA
340462 TAAGTGGTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.50, C:0.19, G:0.31, T:0.00
Consensus pattern (12 bp):
GACCAAGAGGAA
Found at i:341752 original size:12 final size:12
Alignment explanation
Indices: 341735--341759 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
341725 TCAATATCTT
341735 TTATTTATTTAA
1 TTATTTATTTAA
341747 TTATTTATTTAA
1 TTATTTATTTAA
341759 T
1 T
341760 CTTTATCTTT
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:0.00, G:0.00, T:0.68
Consensus pattern (12 bp):
TTATTTATTTAA
Found at i:342201 original size:11 final size:11
Alignment explanation
Indices: 342185--342219 Score: 61
Period size: 11 Copynumber: 3.2 Consensus size: 11
342175 CGCTTCGAGA
*
342185 AAAAAAAGAAG
1 AAAAAAACAAG
342196 AAAAAAACAAG
1 AAAAAAACAAG
342207 AAAAAAACAAG
1 AAAAAAACAAG
342218 AA
1 AA
342220 GAACAAGAGA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
11 23 1.00
ACGTcount: A:0.83, C:0.06, G:0.11, T:0.00
Consensus pattern (11 bp):
AAAAAAACAAG
Found at i:360477 original size:51 final size:51
Alignment explanation
Indices: 360369--360478 Score: 134
Period size: 51 Copynumber: 2.1 Consensus size: 51
360359 ATTAAATGAA
*** *
360369 ATTTTTTGAGGGGTCAAATAAGATATTTCCTATCAATTTAGCTTGACAGTT
1 ATTTTTTGAGGGGTCAAATAAGATATTTCCTATCAATTTAAAATGACACTT
*
360420 ATTTTTTGAGGGTTCAAATAAGATATTTCCTAAT-AATTTAAAAAATG-CACTT
1 ATTTTTTGAGGGGTCAAATAAGATATTTCCT-ATCAATTT--AAAATGACACTT
360472 ATTTTTT
1 ATTTTTT
360479 ATTTTAGAGA
Statistics
Matches: 51, Mismatches: 5, Indels: 5
0.84 0.08 0.08
Matches are distributed among these distances:
51 35 0.69
52 13 0.25
53 3 0.06
ACGTcount: A:0.33, C:0.10, G:0.14, T:0.44
Consensus pattern (51 bp):
ATTTTTTGAGGGGTCAAATAAGATATTTCCTATCAATTTAAAATGACACTT
Found at i:361215 original size:40 final size:38
Alignment explanation
Indices: 361131--361216 Score: 118
Period size: 38 Copynumber: 2.2 Consensus size: 38
361121 TTGAAGCATG
* *
361131 TATAACATATAGTTTTTAGAAAACGGTTATTGAAAACA
1 TATAATATATAGTTTTTAAAAAACGGTTATTGAAAACA
* *
361169 TATAATATATAGTTTTTAAAAAATCGGTTTTTTGAAAATA
1 TATAATATATAGTTTTTAAAAAA-CGG-TTATTGAAAACA
361209 TATAATAT
1 TATAATAT
361217 GATTTTGAAA
Statistics
Matches: 42, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
38 21 0.50
39 3 0.07
40 18 0.43
ACGTcount: A:0.44, C:0.05, G:0.10, T:0.41
Consensus pattern (38 bp):
TATAATATATAGTTTTTAAAAAACGGTTATTGAAAACA
Found at i:361328 original size:37 final size:38
Alignment explanation
Indices: 361280--361367 Score: 124
Period size: 39 Copynumber: 2.3 Consensus size: 38
361270 TGAATATATG
* *
361280 TAATATATAGTTCT-GAAAAATATTTTGAAATTATAAA
1 TAATATATAGTTCTAAAAAAATATTTTGAAAATATAAA
* *
361317 TAATATATAGTTTTTAAAAAAATATTTTGAAAATATATA
1 TAATATATAG-TTCTAAAAAAATATTTTGAAAATATAAA
361356 TAATATATAGTT
1 TAATATATAGTT
361368 TTCGAAAACA
Statistics
Matches: 45, Mismatches: 4, Indels: 3
0.87 0.08 0.06
Matches are distributed among these distances:
37 10 0.22
38 5 0.11
39 30 0.67
ACGTcount: A:0.49, C:0.01, G:0.07, T:0.43
Consensus pattern (38 bp):
TAATATATAGTTCTAAAAAAATATTTTGAAAATATAAA
Found at i:361338 original size:39 final size:39
Alignment explanation
Indices: 361295--361369 Score: 132
Period size: 39 Copynumber: 1.9 Consensus size: 39
361285 TATAGTTCTG
*
361295 AAAAATATTTTGAAATTATAAATAATATATAGTTTTTAA
1 AAAAATATTTTGAAAATATAAATAATATATAGTTTTTAA
*
361334 AAAAATATTTTGAAAATATATATAATATATAGTTTT
1 AAAAATATTTTGAAAATATAAATAATATATAGTTTT
361370 CGAAAACATA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
39 34 1.00
ACGTcount: A:0.51, C:0.00, G:0.05, T:0.44
Consensus pattern (39 bp):
AAAAATATTTTGAAAATATAAATAATATATAGTTTTTAA
Found at i:361375 original size:26 final size:25
Alignment explanation
Indices: 361341--361403 Score: 99
Period size: 26 Copynumber: 2.5 Consensus size: 25
361331 TAAAAAAATA
* *
361341 TTTTGAAAATATATATAATATATAG
1 TTTTGAAAACATATATAATAGATAG
361366 TTTTCGAAAACATATATAATAGATAG
1 TTTT-GAAAACATATATAATAGATAG
361392 TTTTGAAAACAT
1 TTTTGAAAACAT
361404 TTTTTAAAAT
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
25 12 0.34
26 23 0.66
ACGTcount: A:0.46, C:0.05, G:0.10, T:0.40
Consensus pattern (25 bp):
TTTTGAAAACATATATAATAGATAG
Found at i:361429 original size:37 final size:36
Alignment explanation
Indices: 361372--361468 Score: 140
Period size: 37 Copynumber: 2.6 Consensus size: 36
361362 ATAGTTTTCG
*
361372 AAAACATATATAATAGATAGTTTTGAAAACATTTTTT
1 AAAA-ATATATAATACATAGTTTTGAAAACATTTTTT
*
361409 AAAATATATATAATATATAGTTTTGAAAACATTTTTT
1 AAAA-ATATATAATACATAGTTTTGAAAACATTTTTT
* *
361446 GAAAACATATAATACATAGTTTT
1 AAAAATATATAATACATAGTTTT
361469 TTTTTAAAAA
Statistics
Matches: 55, Mismatches: 5, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
36 17 0.31
37 38 0.69
ACGTcount: A:0.46, C:0.05, G:0.07, T:0.41
Consensus pattern (36 bp):
AAAAATATATAATACATAGTTTTGAAAACATTTTTT
Found at i:361447 original size:13 final size:13
Alignment explanation
Indices: 361429--361453 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
361419 TAATATATAG
361429 TTTTGAAAACATT
1 TTTTGAAAACATT
361442 TTTTGAAAACAT
1 TTTTGAAAACAT
361454 ATAATACATA
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:0.40, C:0.08, G:0.08, T:0.44
Consensus pattern (13 bp):
TTTTGAAAACATT
Found at i:361613 original size:5 final size:5
Alignment explanation
Indices: 361603--361672 Score: 54
Period size: 5 Copynumber: 13.6 Consensus size: 5
361593 TATATACATA
* ** *
361603 TTATT TTATT TTATT TTATT TTCTAT TTACC TT-TT TTATT TTATT TACTTTT
1 TTATT TTATT TTATT TTATT TTAT-T TTATT TTATT TTATT TTATT T--TATT
361655 TTATT TT-TT CTTATT TTA
1 TTATT TTATT -TTATT TTA
361673 GTTCCGAGTC
Statistics
Matches: 51, Mismatches: 8, Indels: 12
0.72 0.11 0.17
Matches are distributed among these distances:
4 4 0.08
5 38 0.75
6 5 0.10
7 4 0.08
ACGTcount: A:0.17, C:0.07, G:0.00, T:0.76
Consensus pattern (5 bp):
TTATT
Found at i:361662 original size:18 final size:19
Alignment explanation
Indices: 361616--361662 Score: 71
Period size: 18 Copynumber: 2.5 Consensus size: 19
361606 TTTTATTTTA
361616 TTTTATTTTCTATTTACCTT
1 TTTTATTTT-TATTTACCTT
361636 TTTTA-TTTTATTTA-CTT
1 TTTTATTTTTATTTACCTT
361653 TTTTATTTTT
1 TTTTATTTTT
361663 TCTTATTTTA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
17 8 0.31
18 10 0.38
19 3 0.12
20 5 0.19
ACGTcount: A:0.15, C:0.09, G:0.00, T:0.77
Consensus pattern (19 bp):
TTTTATTTTTATTTACCTT
Found at i:361671 original size:17 final size:17
Alignment explanation
Indices: 361603--361661 Score: 68
Period size: 17 Copynumber: 3.4 Consensus size: 17
361593 TATATACATA
361603 TTATTTTATTTTA-TTTT
1 TTATTTTA-TTTACTTTT
*
361620 ATT-TTCTATTTACCTTTT
1 -TTATTTTATTTA-CTTTT
361638 TTATTTTATTTACTTTT
1 TTATTTTATTTACTTTT
361655 TTATTTT
1 TTATTTT
361662 TTCTTATTTT
Statistics
Matches: 36, Mismatches: 2, Indels: 7
0.80 0.04 0.16
Matches are distributed among these distances:
16 4 0.11
17 18 0.50
18 14 0.39
ACGTcount: A:0.17, C:0.07, G:0.00, T:0.76
Consensus pattern (17 bp):
TTATTTTATTTACTTTT
Found at i:370568 original size:3 final size:3
Alignment explanation
Indices: 370560--370631 Score: 101
Period size: 3 Copynumber: 23.7 Consensus size: 3
370550 GTTTTATTTA
* *
370560 TAT TAT TAT TAT TA- TAT TAT TATT TAT TAT ATAT TTT TAT TAT TAA
1 TAT TAT TAT TAT TAT TAT TAT TA-T TAT TAT -TAT TAT TAT TAT TAT
370606 TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TA
370632 CAAACAGGCC
Statistics
Matches: 62, Mismatches: 4, Indels: 6
0.86 0.06 0.08
Matches are distributed among these distances:
2 2 0.03
3 54 0.87
4 6 0.10
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:372026 original size:28 final size:28
Alignment explanation
Indices: 371972--372026 Score: 67
Period size: 28 Copynumber: 2.0 Consensus size: 28
371962 TTATTAGTTT
** *
371972 TTATTATTTTTACTTTCATTTATTATAG
1 TTATTATTTAAACTTTCATATATTATAG
372000 TTATTATTTAAACTTT-ATATATATATA
1 TTATTATTTAAACTTTCATATAT-TATA
372027 TTTAAAATAT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
27 5 0.22
28 18 0.78
ACGTcount: A:0.33, C:0.05, G:0.02, T:0.60
Consensus pattern (28 bp):
TTATTATTTAAACTTTCATATATTATAG
Found at i:372039 original size:22 final size:22
Alignment explanation
Indices: 371992--372046 Score: 57
Period size: 21 Copynumber: 2.7 Consensus size: 22
371982 TACTTTCATT
*
371992 TATTATAGT-TAT-TATTTAAAC
1 TATTATA-TATATATATTTAAAA
372013 T-TTATATATATATATTTAAAA
1 TATTATATATATATATTTAAAA
372034 TATTAT-TAT-TATA
1 TATTATATATATATA
372047 AATATATATA
Statistics
Matches: 30, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
19 1 0.03
20 12 0.40
21 13 0.43
22 4 0.13
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.55
Consensus pattern (22 bp):
TATTATATATATATATTTAAAA
Found at i:372071 original size:28 final size:28
Alignment explanation
Indices: 372014--372067 Score: 74
Period size: 28 Copynumber: 2.0 Consensus size: 28
372004 TATTTAAACT
* * *
372014 TTATATATATATATTTAAAATATTATTA
1 TTATAAATATATATATAAAATAATATTA
372042 TTATAAATATATATAT-AAATAATATT
1 TTATAAATATATATATAAAATAATATT
372068 TATTTATTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
27 9 0.39
28 14 0.61
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (28 bp):
TTATAAATATATATATAAAATAATATTA
Found at i:372084 original size:43 final size:45
Alignment explanation
Indices: 372034--372123 Score: 114
Period size: 45 Copynumber: 2.0 Consensus size: 45
372024 ATATTTAAAA
372034 TATTATTA-TTATAAAT-ATATATATAAATAATATTTATT-TATTT
1 TATTATTATTTATAAATCATATATATAAATAAT-TTTATTCTATTT
* * * *
372077 TATTATTATTTTTAAATCTTTTATATAAATTATTTTATTCTATTT
1 TATTATTATTTATAAATCATATATATAAATAATTTTATTCTATTT
372122 TA
1 TA
372124 ATTAAAGAAA
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
43 8 0.20
44 13 0.32
45 19 0.47
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (45 bp):
TATTATTATTTATAAATCATATATATAAATAATTTTATTCTATTT
Found at i:381641 original size:22 final size:22
Alignment explanation
Indices: 381616--381692 Score: 88
Period size: 22 Copynumber: 3.5 Consensus size: 22
381606 ATCTACACTT
381616 TTCAAAGATGATAGATTCTTTC
1 TTCAAAGATGATAGATTCTTTC
381638 TTCAAAGATGATAGCATATC--TC
1 TTCAAAGATGATAG-AT-TCTTTC
* *
381660 TTTAAAGATGATAGTTTCTCTT-
1 TTCAAAGATGATAGATTCT-TTC
381682 TTCAAAGATGA
1 TTCAAAGATGA
381693 AAGCTTTATT
Statistics
Matches: 47, Mismatches: 3, Indels: 10
0.78 0.05 0.17
Matches are distributed among these distances:
20 2 0.04
21 1 0.02
22 39 0.83
23 3 0.06
24 2 0.04
ACGTcount: A:0.34, C:0.13, G:0.14, T:0.39
Consensus pattern (22 bp):
TTCAAAGATGATAGATTCTTTC
Found at i:382247 original size:124 final size:124
Alignment explanation
Indices: 382067--382726 Score: 920
Period size: 124 Copynumber: 5.4 Consensus size: 124
382057 CATTTGATGG
382067 ATCAACTTTTCCAGAGAAAGTTCATAATAAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCAT
1 ATCAACTTTTCCAGAGAAAGTTCATAATAAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCAT
*
382132 AATGAGAAGAACTTGTTCAACCTTTTGCATGACTCTATCACAGAAAGAGATAGATCATC
66 AATGAGAAGAACTTGTTCAACCTTTTGCATGACTCTATCACAGAAAGAGATAGATCAAC
*
382191 ATCAACTTTTCTAGAGAAAGTTCATAATAAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCAT
1 ATCAACTTTTCCAGAGAAAGTTCATAATAAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCAT
*
382256 AATGAGAAGAACTTGTTCAACCTTTTGCATGACTCTATCACAGAAGGAGATAGATCAAC
66 AATGAGAAGAACTTGTTCAACCTTTTGCATGACTCTATCACAGAAAGAGATAGATCAAC
*
382315 ATCAACTTTTCCAGAGAAAGTTCATAATAATAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCAT
1 ATCAACTTTTCCAGAGAAAGTTCATAATAAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCAT
*
382380 AATGAGAAGAACTTGTTCAACCTTTTGCATGACTCTATCACAGAAGGAGATAGATCAAC
66 AATGAGAAGAACTTGTTCAACCTTTTGCATGACTCTATCACAGAAAGAGATAGATCAAC
* * *
382439 ATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAGGGAAGAATAAGTTCAT
1 ATCAACTTTTCCAGAGAAAGTTCATAATAAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCAT
* * * * ** *
382504 AATGAGAAGAGCTTGTTCAACCTTTTGCTTCAAT-TCATCAC-----TCGATGGATC-A-
66 AATGAGAAGAACTTGTTCAACCTTTTGCATGACTCT-ATCACAGAAAGAGATAGATCAAC
* *
382556 A-C-A--TTGCCAG-GTAGAAGTTCATAATGAGAAGAACTCATCTGAAG-AGGAAGAAGAAGTTC
1 ATCAACTTTTCCAGAG-A-AAGTTCATAATAAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTC
* * * * * *
382615 ATAATGAGAACAATTTGTTCAGCCTTTTGCATGACTCTATCAC-GGAAGAAGATAAATCAGC
64 ATAATGAGAAGAACTTGTTCAACCTTTTGCATGACTCTATCACAGAAAG-AGATAGATCAAC
* ** * *
382676 ATCAACATTTCCAGA-AGTGTTCATAATGAGAATAACTCATCTGAAGAAGGA
1 ATCAACTTTTCCAGAGAAAGTTCATAATAAGAAGAACTCATCTGAAGAAGGA
382727 GAATAATTTA
Statistics
Matches: 484, Mismatches: 35, Indels: 35
0.87 0.06 0.06
Matches are distributed among these distances:
112 1 0.00
113 54 0.11
114 31 0.06
115 1 0.00
116 1 0.00
117 1 0.00
118 7 0.01
119 7 0.01
120 1 0.00
121 1 0.00
122 28 0.06
123 6 0.01
124 345 0.71
ACGTcount: A:0.40, C:0.16, G:0.19, T:0.25
Consensus pattern (124 bp):
ATCAACTTTTCCAGAGAAAGTTCATAATAAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCAT
AATGAGAAGAACTTGTTCAACCTTTTGCATGACTCTATCACAGAAAGAGATAGATCAAC
Found at i:382982 original size:3 final size:3
Alignment explanation
Indices: 382974--383045 Score: 92
Period size: 3 Copynumber: 23.7 Consensus size: 3
382964 GTTTTATTTA
* *
382974 TAT TAT TAT TA- TAT TAT TAT TATT TAT TAT ATAT TTT TAT TAT TAA
1 TAT TAT TAT TAT TAT TAT TAT TA-T TAT TAT -TAT TAT TAT TAT TAT
*
383020 TAT TAT TAT TAA TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TA
383046 CAAACAGGCC
Statistics
Matches: 60, Mismatches: 6, Indels: 6
0.83 0.08 0.08
Matches are distributed among these distances:
2 2 0.03
3 52 0.87
4 6 0.10
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:384443 original size:28 final size:28
Alignment explanation
Indices: 384389--384443 Score: 67
Period size: 28 Copynumber: 2.0 Consensus size: 28
384379 TTATTAGTTT
** *
384389 TTATTATTTTTACTTTCATTTATTATAG
1 TTATTATTTAAACTTTCATATATTATAG
384417 TTATTATTTAAACTTT-ATATATATATA
1 TTATTATTTAAACTTTCATATAT-TATA
384444 TTTAAAATAT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
27 5 0.22
28 18 0.78
ACGTcount: A:0.33, C:0.05, G:0.02, T:0.60
Consensus pattern (28 bp):
TTATTATTTAAACTTTCATATATTATAG
Found at i:384456 original size:22 final size:22
Alignment explanation
Indices: 384409--384463 Score: 57
Period size: 21 Copynumber: 2.7 Consensus size: 22
384399 TACTTTCATT
*
384409 TATTATAGT-TAT-TATTTAAAC
1 TATTATA-TATATATATTTAAAA
384430 T-TTATATATATATATTTAAAA
1 TATTATATATATATATTTAAAA
384451 TATTAT-TAT-TATA
1 TATTATATATATATA
384464 AATATATATA
Statistics
Matches: 30, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
19 1 0.03
20 12 0.40
21 13 0.43
22 4 0.13
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.55
Consensus pattern (22 bp):
TATTATATATATATATTTAAAA
Found at i:384488 original size:28 final size:28
Alignment explanation
Indices: 384431--384484 Score: 74
Period size: 28 Copynumber: 2.0 Consensus size: 28
384421 TATTTAAACT
* * *
384431 TTATATATATATATTTAAAATATTATTA
1 TTATAAATATATATATAAAATAATATTA
384459 TTATAAATATATATAT-AAATAATATT
1 TTATAAATATATATATAAAATAATATT
384485 TATTTATTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
27 9 0.39
28 14 0.61
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (28 bp):
TTATAAATATATATATAAAATAATATTA
Found at i:384501 original size:43 final size:45
Alignment explanation
Indices: 384451--384540 Score: 114
Period size: 45 Copynumber: 2.0 Consensus size: 45
384441 ATATTTAAAA
384451 TATTATTA-TTATAAAT-ATATATATAAATAATATTTATT-TATTT
1 TATTATTATTTATAAATCATATATATAAATAAT-TTTATTCTATTT
* * * *
384494 TATTATTATTTTTAAATCTTTTATATAAATTATTTTATTCTATTT
1 TATTATTATTTATAAATCATATATATAAATAATTTTATTCTATTT
384539 TA
1 TA
384541 ATTAAAGGAA
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
43 8 0.20
44 13 0.32
45 19 0.47
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (45 bp):
TATTATTATTTATAAATCATATATATAAATAATTTTATTCTATTT
Found at i:395637 original size:51 final size:51
Alignment explanation
Indices: 395529--395638 Score: 134
Period size: 51 Copynumber: 2.1 Consensus size: 51
395519 ATTAAATGAA
*** *
395529 ATTTTTTGAGGGGTCAAATAAGATATTTCCTATCAATTTAGCTTGACAGTT
1 ATTTTTTGAGGGGTCAAATAAGATATTTCCTATCAATTTAAAATGACACTT
*
395580 ATTTTTTGAGGGTTCAAATAAGATATTTCCTAAT-AATTTAAAAAATG-CACTT
1 ATTTTTTGAGGGGTCAAATAAGATATTTCCT-ATCAATTT--AAAATGACACTT
395632 ATTTTTT
1 ATTTTTT
395639 ATTTTAGAGA
Statistics
Matches: 51, Mismatches: 5, Indels: 5
0.84 0.08 0.08
Matches are distributed among these distances:
51 35 0.69
52 13 0.25
53 3 0.06
ACGTcount: A:0.33, C:0.10, G:0.14, T:0.44
Consensus pattern (51 bp):
ATTTTTTGAGGGGTCAAATAAGATATTTCCTATCAATTTAAAATGACACTT
Found at i:406136 original size:30 final size:30
Alignment explanation
Indices: 406100--406179 Score: 99
Period size: 31 Copynumber: 2.6 Consensus size: 30
406090 CCTTTTCATT
406100 TAAGTACCTAAAGTATTTTTTTAG-TCAAAA
1 TAAGTACCTAAAGTATTTTTTT-GTTCAAAA
* * *
406130 TAAGTACATAAAGTTATATTTTTGTTTAAAA
1 TAAGTACCTAAAG-TATTTTTTTGTTCAAAA
*
406161 TAGGTACCTAAAGTATTTT
1 TAAGTACCTAAAGTATTTT
406180 GTCAAAATAT
Statistics
Matches: 42, Mismatches: 6, Indels: 4
0.81 0.12 0.08
Matches are distributed among these distances:
30 18 0.43
31 24 0.57
ACGTcount: A:0.39, C:0.07, G:0.11, T:0.42
Consensus pattern (30 bp):
TAAGTACCTAAAGTATTTTTTTGTTCAAAA
Found at i:406161 original size:31 final size:31
Alignment explanation
Indices: 406100--406209 Score: 92
Period size: 31 Copynumber: 3.7 Consensus size: 31
406090 CCTTTTCATT
*
406100 TAAGTACCTAAAG-TATTTTTTTAGTCAAAA
1 TAAGTACCTAAAGTTATATTTTTAGTCAAAA
* *
406130 TAAGTACATAAAGTTATATTTTT-GTTTAAAA
1 TAAGTACCTAAAGTTATATTTTTAG-TCAAAA
*
406161 TAGGTACCTAAAG---TA-TTTT-GTCAAAA
1 TAAGTACCTAAAGTTATATTTTTAGTCAAAA
* *
406187 TATGTACC-AAAGTAATCATTTTT
1 TAAGTACCTAAAGTTAT-ATTTTT
406210 TATCGAAGTA
Statistics
Matches: 66, Mismatches: 7, Indels: 14
0.76 0.08 0.16
Matches are distributed among these distances:
25 4 0.06
26 12 0.18
27 5 0.08
28 3 0.05
29 1 0.02
30 17 0.26
31 24 0.36
ACGTcount: A:0.39, C:0.09, G:0.11, T:0.41
Consensus pattern (31 bp):
TAAGTACCTAAAGTTATATTTTTAGTCAAAA
Found at i:406383 original size:29 final size:29
Alignment explanation
Indices: 406297--406375 Score: 135
Period size: 28 Copynumber: 2.8 Consensus size: 29
406287 TTTAGGTACC
*
406297 TATTTTGA-CATAAAATACTTTAGACACT
1 TATTTTGACCAAAAAATACTTTAGACACT
406325 TATTTTGACC-AAAAATACTTTAGACACT
1 TATTTTGACCAAAAAATACTTTAGACACT
406353 TATTTTGACCAAAAAATACTTTA
1 TATTTTGACCAAAAAATACTTTA
406376 AATACTTAAA
Statistics
Matches: 48, Mismatches: 1, Indels: 3
0.92 0.02 0.06
Matches are distributed among these distances:
28 35 0.73
29 13 0.27
ACGTcount: A:0.41, C:0.15, G:0.06, T:0.38
Consensus pattern (29 bp):
TATTTTGACCAAAAAATACTTTAGACACT
Found at i:411104 original size:44 final size:44
Alignment explanation
Indices: 411002--411162 Score: 148
Period size: 44 Copynumber: 3.6 Consensus size: 44
410992 TTTTGGCTTG
* * *
411002 TCCATCATATAAGGAGTTGGATCATCATCACCTTTTTT-TACGAT
1 TCCATCACATAAGAAGTTGGATCATCATCA-CTTTTTTGTTCGAT
* * * *
411046 TCTACCACATAAGAAGTTGGATTATCATCACTTTTTTGTTTGAT
1 TCCATCACATAAGAAGTTGGATCATCATCACTTTTTTGTTCGAT
* * * *
411090 TCCATCACAAAAGAAAG-TGGATCAACGTTTC-CTTTTTTGCTCGAT
1 TCCATCACATAAG-AAGTTGGATCATC--ATCACTTTTTTGTTCGAT
*
411135 TCCATCACATAAGGAGTTGGATCCATCA
1 TCCATCACATAAGAAGTTGGAT-CATCA
411163 CATAAGGAGT
Statistics
Matches: 92, Mismatches: 19, Indels: 12
0.75 0.15 0.10
Matches are distributed among these distances:
43 7 0.08
44 48 0.52
45 32 0.35
46 5 0.05
ACGTcount: A:0.29, C:0.20, G:0.15, T:0.36
Consensus pattern (44 bp):
TCCATCACATAAGAAGTTGGATCATCATCACTTTTTTGTTCGAT
Found at i:411161 original size:21 final size:21
Alignment explanation
Indices: 411135--411178 Score: 79
Period size: 21 Copynumber: 2.1 Consensus size: 21
411125 TTTGCTCGAT
*
411135 TCCATCACATAAGGAGTTGGA
1 TCCATCACATAAGGAGTCGGA
411156 TCCATCACATAAGGAGTCGGA
1 TCCATCACATAAGGAGTCGGA
411177 TC
1 TC
411179 TGCATCAACC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.32, C:0.23, G:0.23, T:0.23
Consensus pattern (21 bp):
TCCATCACATAAGGAGTCGGA
Found at i:413405 original size:20 final size:20
Alignment explanation
Indices: 413380--413422 Score: 77
Period size: 20 Copynumber: 2.1 Consensus size: 20
413370 TATGGGATTG
413380 AGGGTAATTGTGACTTTTGT
1 AGGGTAATTGTGACTTTTGT
*
413400 AGGGTAATTGTGTCTTTTGT
1 AGGGTAATTGTGACTTTTGT
413420 AGG
1 AGG
413423 TTCGTCATCT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.19, C:0.05, G:0.33, T:0.44
Consensus pattern (20 bp):
AGGGTAATTGTGACTTTTGT
Found at i:415093 original size:21 final size:21
Alignment explanation
Indices: 415063--415106 Score: 79
Period size: 21 Copynumber: 2.1 Consensus size: 21
415053 TTTGCTCGAT
*
415063 TCCATCACATAAGGAGTTGGA
1 TCCATAACATAAGGAGTTGGA
415084 TCCATAACATAAGGAGTTGGA
1 TCCATAACATAAGGAGTTGGA
415105 TC
1 TC
415107 AACATCACTT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.34, C:0.18, G:0.23, T:0.25
Consensus pattern (21 bp):
TCCATAACATAAGGAGTTGGA
Done.