Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000558.1 Hibiscus syriacus cultivar Beakdansim tig00001091_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: 180436
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 1 of 2
Found at i:2004 original size:21 final size:20
Alignment explanation
Indices: 1962--2001 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
1952 GAAAATATAC
1962 TATTTAAATTTAATTATAAA
1 TATTTAAATTTAATTATAAA
*
1982 TATTTATATTTTAA-TATAAA
1 TATTTA-AATTTAATTATAAA
2002 ATAAATTATT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 12 0.67
21 6 0.33
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (20 bp):
TATTTAAATTTAATTATAAA
Found at i:2184 original size:12 final size:12
Alignment explanation
Indices: 2167--2199 Score: 52
Period size: 11 Copynumber: 2.9 Consensus size: 12
2157 TCCACCTATG
2167 ATTATTTTTTTA
1 ATTATTTTTTTA
2179 ATTA-TTTTTTA
1 ATTATTTTTTTA
2190 ATT-TTTTTTT
1 ATTATTTTTTT
2200 GTTGCCCTCC
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
11 16 0.80
12 4 0.20
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (12 bp):
ATTATTTTTTTA
Found at i:14727 original size:62 final size:62
Alignment explanation
Indices: 14626--14743 Score: 164
Period size: 62 Copynumber: 1.9 Consensus size: 62
14616 TTTTTTTACA
* * *
14626 CATCAAAATATGAATTTCTAAAGCTCCATTTCACACTTGCTTTTATTCTTGTTTCTACCACG
1 CATCAAAATATGAACTTCTAAAGCTACATTTCACACTTGCTTTTATTCTAGTTTCTACCACG
* * ** *
14688 CATCAAAGTGTGAACTTCTAAAGCTACATTTGGCTCTTGCTTTTATTCTAGTTTCT
1 CATCAAAATATGAACTTCTAAAGCTACATTTCACACTTGCTTTTATTCTAGTTTCT
14744 GTCTCTTAAA
Statistics
Matches: 48, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
62 48 1.00
ACGTcount: A:0.25, C:0.22, G:0.11, T:0.42
Consensus pattern (62 bp):
CATCAAAATATGAACTTCTAAAGCTACATTTCACACTTGCTTTTATTCTAGTTTCTACCACG
Found at i:16593 original size:27 final size:27
Alignment explanation
Indices: 16553--16611 Score: 100
Period size: 27 Copynumber: 2.2 Consensus size: 27
16543 ATTATTTTCT
*
16553 TTATTATATAATGTAATTATTTAATTA
1 TTATTATATAATGTAATTATCTAATTA
*
16580 TTATTATATGATGTAATTATCTAATTA
1 TTATTATATAATGTAATTATCTAATTA
16607 TTATT
1 TTATT
16612 TTGGTTCTAT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.37, C:0.02, G:0.05, T:0.56
Consensus pattern (27 bp):
TTATTATATAATGTAATTATCTAATTA
Found at i:16853 original size:26 final size:27
Alignment explanation
Indices: 16793--16855 Score: 67
Period size: 26 Copynumber: 2.4 Consensus size: 27
16783 TTTAACGATG
*
16793 AAATAATATATTTTTAATAATATTTTAA
1 AAATAATA-ATGTTTAATAATATTTTAA
** *
16821 TTA-AATAATGTTTATTAAT-TTTTAA
1 AAATAATAATGTTTAATAATATTTTAA
16846 AAATAATAAT
1 AAATAATAAT
16856 AACTTAATTA
Statistics
Matches: 28, Mismatches: 6, Indels: 4
0.74 0.16 0.11
Matches are distributed among these distances:
25 7 0.25
26 16 0.57
27 4 0.14
28 1 0.04
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (27 bp):
AAATAATAATGTTTAATAATATTTTAA
Found at i:31535 original size:21 final size:22
Alignment explanation
Indices: 31511--31562 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 22
31501 TTTATTTTTT
*
31511 AAATTTAATTA-TTTAACTTTC
1 AAATTTAATTACTCTAACTTTC
* *
31532 AAA-TTACTCACTCTAACTTTC
1 AAATTTAATTACTCTAACTTTC
31553 AAATTTAATT
1 AAATTTAATT
31563 TCTTATTTTA
Statistics
Matches: 24, Mismatches: 5, Indels: 3
0.75 0.16 0.09
Matches are distributed among these distances:
20 5 0.21
21 15 0.62
22 4 0.17
ACGTcount: A:0.38, C:0.15, G:0.00, T:0.46
Consensus pattern (22 bp):
AAATTTAATTACTCTAACTTTC
Found at i:31853 original size:31 final size:31
Alignment explanation
Indices: 31818--31882 Score: 103
Period size: 31 Copynumber: 2.1 Consensus size: 31
31808 AACATTATAG
**
31818 TTTGGTGCTAACTTATGGTTTACCTTATATT
1 TTTGGTGCTAACTTAAAGTTTACCTTATATT
*
31849 TTTGGTGCTAACTTAAAGTTTACCTTATTTT
1 TTTGGTGCTAACTTAAAGTTTACCTTATATT
31880 TTT
1 TTT
31883 TTTCATTTAC
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.20, C:0.12, G:0.14, T:0.54
Consensus pattern (31 bp):
TTTGGTGCTAACTTAAAGTTTACCTTATATT
Found at i:35262 original size:135 final size:135
Alignment explanation
Indices: 35087--35347 Score: 389
Period size: 135 Copynumber: 1.9 Consensus size: 135
35077 GATCAACATG
* *
35087 TGTTTGATACAGAAGATGCTCAAGAAGGCAAGAGATGGTCCTCACAACCACAATCATCAGCTGCT
1 TGTTTGATACAGAAGATGCTCAAGAAGGCAAGAGATGGTCCTCACAACCACAACCATCACCTGCT
*
35152 CATTTTTCAGAATCAAAGCCTTTGTATAAAACTTCATCATATCCCCAGCAGCAACCAGAGCCTCT
66 CATTTTTCAGAATCAAAGCCTTTGTATAAAACTTCATCATATCCCAAGCAGCAACCAGAGCCTCT
35217 CTTCA
131 CTTCA
* * * *
35222 TGTTTGATACAGAAGACT-CTCAAGAAGGCAAGAGATGGTCCTCTCAGCCGCAACCATCTCCTGC
1 TGTTTGATACAGAAGA-TGCTCAAGAAGGCAAGAGATGGTCCTCACAACCACAACCATCACCTGC
* * * ** *
35286 TCGTTTTTCAGAATCAAAGCTTTTGTATAGAACTTTGTCATATCCCAATCAGCAACCAGAGC
65 TCATTTTTCAGAATCAAAGCCTTTGTATAAAACTTCATCATATCCCAAGCAGCAACCAGAGC
35348 TTCACTTCTC
Statistics
Matches: 112, Mismatches: 13, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
135 111 0.99
136 1 0.01
ACGTcount: A:0.31, C:0.26, G:0.17, T:0.26
Consensus pattern (135 bp):
TGTTTGATACAGAAGATGCTCAAGAAGGCAAGAGATGGTCCTCACAACCACAACCATCACCTGCT
CATTTTTCAGAATCAAAGCCTTTGTATAAAACTTCATCATATCCCAAGCAGCAACCAGAGCCTCT
CTTCA
Found at i:37269 original size:42 final size:42
Alignment explanation
Indices: 37210--37293 Score: 168
Period size: 42 Copynumber: 2.0 Consensus size: 42
37200 GGAATCGGTA
37210 AGGGGATAATAAAGAAAAAGGGAAGGGTCCTGTGTGAAGATC
1 AGGGGATAATAAAGAAAAAGGGAAGGGTCCTGTGTGAAGATC
37252 AGGGGATAATAAAGAAAAAGGGAAGGGTCCTGTGTGAAGATC
1 AGGGGATAATAAAGAAAAAGGGAAGGGTCCTGTGTGAAGATC
37294 GTGAACAACG
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 42 1.00
ACGTcount: A:0.40, C:0.07, G:0.36, T:0.17
Consensus pattern (42 bp):
AGGGGATAATAAAGAAAAAGGGAAGGGTCCTGTGTGAAGATC
Found at i:38326 original size:2 final size:2
Alignment explanation
Indices: 38313--38352 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
38303 ATCTGTAAAC
*
38313 AT AT AC AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
38353 GGACTTCATT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:43316 original size:29 final size:30
Alignment explanation
Indices: 43268--43341 Score: 82
Period size: 29 Copynumber: 2.5 Consensus size: 30
43258 TTATAACCAA
** *
43268 AATTATTTAATTATGAAATTTTAT-AAATTT
1 AATTA-TTAATTATTTAATTTAATAAAATTT
43298 AATTATTAATTATTTAATTTAATCAAAATTT
1 AATTATTAATTATTTAATTTAAT-AAAATTT
43329 AA-TATT-ATTATTT
1 AATTATTAATTATTT
43342 TTAATACAAA
Statistics
Matches: 39, Mismatches: 3, Indels: 5
0.83 0.06 0.11
Matches are distributed among these distances:
29 22 0.56
30 9 0.23
31 8 0.21
ACGTcount: A:0.43, C:0.01, G:0.01, T:0.54
Consensus pattern (30 bp):
AATTATTAATTATTTAATTTAATAAAATTT
Found at i:45497 original size:14 final size:16
Alignment explanation
Indices: 45480--45511 Score: 50
Period size: 14 Copynumber: 2.1 Consensus size: 16
45470 TTTTAAAATT
45480 TTTAAAT-TT-ACATC
1 TTTAAATCTTAACATC
45494 TTTAAATCTTAACATC
1 TTTAAATCTTAACATC
45510 TT
1 TT
45512 CACGTCTATA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 7 0.44
15 2 0.12
16 7 0.44
ACGTcount: A:0.34, C:0.16, G:0.00, T:0.50
Consensus pattern (16 bp):
TTTAAATCTTAACATC
Found at i:47649 original size:23 final size:23
Alignment explanation
Indices: 47618--47663 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
47608 TTGAATGAAG
*
47618 AAGATAAAATAAAAT-AAAAATGA
1 AAGACAAAA-AAAATGAAAAATGA
47641 AAGACAAAAAAAATGAAAAATGA
1 AAGACAAAAAAAATGAAAAATGA
47664 TGTGGATGAC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 5 0.24
23 16 0.76
ACGTcount: A:0.74, C:0.02, G:0.11, T:0.13
Consensus pattern (23 bp):
AAGACAAAAAAAATGAAAAATGA
Found at i:49014 original size:60 final size:60
Alignment explanation
Indices: 48945--49059 Score: 142
Period size: 60 Copynumber: 1.9 Consensus size: 60
48935 AAATAGTCAC
* * * *
48945 TCAACTATAGAGTGGTGTTTTATTGAGTC-CCTCGATTATTAACAGATACAAAATGATTCT
1 TCAACTATAGAGTCGTGTTTTATTGAGTCATCT-GACTATTAAAAGATACAAAATGATTCT
* * * *
49005 TCAACTATAGGGTCTTGTTTTGTTGAGTCATCTGACTATTAAAAGTTACAAAATG
1 TCAACTATAGAGTCGTGTTTTATTGAGTCATCTGACTATTAAAAGATACAAAATG
49060 GTCACCTGAC
Statistics
Matches: 46, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
60 44 0.96
61 2 0.04
ACGTcount: A:0.31, C:0.14, G:0.17, T:0.37
Consensus pattern (60 bp):
TCAACTATAGAGTCGTGTTTTATTGAGTCATCTGACTATTAAAAGATACAAAATGATTCT
Found at i:49191 original size:23 final size:21
Alignment explanation
Indices: 49149--49191 Score: 50
Period size: 23 Copynumber: 2.0 Consensus size: 21
49139 GTCGACTAAG
* *
49149 ATATGATAGTTTTTTGATATT
1 ATATGATAGTTTTATCATATT
49170 ATATGATCATGTTTTATCATAT
1 ATATGAT-A-GTTTTATCATAT
49192 CTCAATTATC
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 7 0.39
22 1 0.06
23 10 0.56
ACGTcount: A:0.30, C:0.05, G:0.12, T:0.53
Consensus pattern (21 bp):
ATATGATAGTTTTATCATATT
Found at i:57097 original size:14 final size:14
Alignment explanation
Indices: 57058--57101 Score: 61
Period size: 14 Copynumber: 3.1 Consensus size: 14
57048 CAATGAATCC
**
57058 TAAACCCTAAACCA
1 TAAACCCTAAATTA
*
57072 TAAATCCTAAATTA
1 TAAACCCTAAATTA
57086 TAAACCCTAAATTA
1 TAAACCCTAAATTA
57100 TA
1 TA
57102 CTTACCTCAT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 26 1.00
ACGTcount: A:0.50, C:0.23, G:0.00, T:0.27
Consensus pattern (14 bp):
TAAACCCTAAATTA
Found at i:59508 original size:20 final size:20
Alignment explanation
Indices: 59466--59548 Score: 87
Period size: 21 Copynumber: 4.0 Consensus size: 20
59456 ATCAGATTGT
*
59466 CCAGGGGGTATAGATTCCTCC
1 CCAGGGGGTACAGATTCC-CC
*
59487 CCAGGGGGTACCGATTCCCC
1 CCAGGGGGTACAGATTCCCC
* * *
59507 CCAAGGGGAACAGATCCCCCC
1 CCAGGGGGTACAGAT-TCCCC
59528 CCAGGGGGTATC-GATTCCCC
1 CCAGGGGGTA-CAGATTCCCC
59548 C
1 C
59549 TGTCTAACGG
Statistics
Matches: 51, Mismatches: 9, Indels: 5
0.78 0.14 0.08
Matches are distributed among these distances:
20 19 0.37
21 31 0.61
22 1 0.02
ACGTcount: A:0.19, C:0.37, G:0.28, T:0.16
Consensus pattern (20 bp):
CCAGGGGGTACAGATTCCCC
Found at i:60850 original size:19 final size:20
Alignment explanation
Indices: 60826--60873 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 20
60816 AACGATTTTC
*
60826 TTTTGAAAACAAAAAT-AGA
1 TTTTGAAAACAAAAATGAAA
* *
60845 TTTTGAAAGCCAAAATGAAA
1 TTTTGAAAACAAAAATGAAA
60865 TTTTGAAAA
1 TTTTGAAAA
60874 AGGATTTAGA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 14 0.58
20 10 0.42
ACGTcount: A:0.52, C:0.06, G:0.12, T:0.29
Consensus pattern (20 bp):
TTTTGAAAACAAAAATGAAA
Found at i:62341 original size:19 final size:21
Alignment explanation
Indices: 62312--62352 Score: 59
Period size: 19 Copynumber: 2.0 Consensus size: 21
62302 ATCAGATTGT
62312 CCAGAGGGTACAGATTC-CCC
1 CCAGAGGGTACAGATTCTCCC
*
62332 CCAG-GGGTACCGATTCTCCC
1 CCAGAGGGTACAGATTCTCCC
62352 C
1 C
62353 TGTCTAATGA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 11 0.58
20 8 0.42
ACGTcount: A:0.20, C:0.39, G:0.24, T:0.17
Consensus pattern (21 bp):
CCAGAGGGTACAGATTCTCCC
Found at i:63516 original size:11 final size:11
Alignment explanation
Indices: 63491--63563 Score: 58
Period size: 11 Copynumber: 6.5 Consensus size: 11
63481 ACCCGTCTTT
63491 GAGCTTCAAAT-
1 GAGCTT-AAATC
*
63502 GAGCTTGAATC
1 GAGCTTAAATC
*
63513 GAGCTCAAAGTC
1 GAGCTTAAA-TC
*
63525 GAGCTTGAATC
1 GAGCTTAAATC
* *
63536 GAGCTCAAAATT
1 GAGCT-TAAATC
*
63548 GAGCTTTAATC
1 GAGCTTAAATC
63559 GAGCT
1 GAGCT
63564 CGAGTTTCGA
Statistics
Matches: 48, Mismatches: 11, Indels: 6
0.74 0.17 0.09
Matches are distributed among these distances:
10 3 0.06
11 28 0.58
12 17 0.35
ACGTcount: A:0.32, C:0.19, G:0.23, T:0.26
Consensus pattern (11 bp):
GAGCTTAAATC
Found at i:63529 original size:23 final size:23
Alignment explanation
Indices: 63498--63564 Score: 100
Period size: 23 Copynumber: 3.0 Consensus size: 23
63488 TTTGAGCTTC
63498 AAAT-GAGCTTGAATCGAGCTCA
1 AAATCGAGCTTGAATCGAGCTCA
*
63520 AAGTCGAGCTTGAATCGAGCTCA
1 AAATCGAGCTTGAATCGAGCTCA
* *
63543 AAATTGAGCTTTAATCGAGCTC
1 AAATCGAGCTTGAATCGAGCTC
63565 GAGTTTCGAG
Statistics
Matches: 40, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
22 3 0.08
23 37 0.93
ACGTcount: A:0.33, C:0.19, G:0.22, T:0.25
Consensus pattern (23 bp):
AAATCGAGCTTGAATCGAGCTCA
Found at i:63900 original size:29 final size:31
Alignment explanation
Indices: 63868--63932 Score: 80
Period size: 31 Copynumber: 2.2 Consensus size: 31
63858 TAAATAAAAG
63868 TTTAATAT-TTTAAAATTAC-TAAATAAGTA
1 TTTAATATGTTTAAAATTACTTAAATAAGTA
** * *
63897 TTTAATATGTTTCTATTTGCTTAAATAAGTA
1 TTTAATATGTTTAAAATTACTTAAATAAGTA
63928 TTTAA
1 TTTAA
63933 CCTCTCAAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
29 8 0.27
30 7 0.23
31 15 0.50
ACGTcount: A:0.40, C:0.05, G:0.06, T:0.49
Consensus pattern (31 bp):
TTTAATATGTTTAAAATTACTTAAATAAGTA
Found at i:65288 original size:15 final size:16
Alignment explanation
Indices: 65263--65293 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
65253 AGAGTTCAAG
65263 CTTCTAGATATGGTTT
1 CTTCTAGATATGGTTT
65279 CTTC-AGATATGGTTT
1 CTTCTAGATATGGTTT
65294 GCTCATATAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 11 0.73
16 4 0.27
ACGTcount: A:0.19, C:0.13, G:0.19, T:0.48
Consensus pattern (16 bp):
CTTCTAGATATGGTTT
Found at i:67651 original size:14 final size:14
Alignment explanation
Indices: 67632--67670 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
67622 TAATGGGGAG
67632 TAATCCCTGCAAAA
1 TAATCCCTGCAAAA
*
67646 TAATCCCTGCGAAA
1 TAATCCCTGCAAAA
* *
67660 GAATCTCTGCA
1 TAATCCCTGCA
67671 TATAGACAGA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.36, C:0.28, G:0.13, T:0.23
Consensus pattern (14 bp):
TAATCCCTGCAAAA
Found at i:68144 original size:24 final size:23
Alignment explanation
Indices: 68086--68144 Score: 55
Period size: 24 Copynumber: 2.5 Consensus size: 23
68076 TGAAGAATAT
*
68086 TATTATGATGATGACGAAAATGA
1 TATTATGATGATGACGAAAAGGA
* ** *
68109 TGAATACAATGATGACGTAAACGGA
1 T-ATTATGATGATGACG-AAAAGGA
68134 TATTATGATGA
1 TATTATGATGA
68145 GAAAGATGAG
Statistics
Matches: 26, Mismatches: 8, Indels: 3
0.70 0.22 0.08
Matches are distributed among these distances:
23 1 0.04
24 19 0.73
25 6 0.23
ACGTcount: A:0.42, C:0.07, G:0.22, T:0.29
Consensus pattern (23 bp):
TATTATGATGATGACGAAAAGGA
Found at i:70607 original size:37 final size:36
Alignment explanation
Indices: 70548--70667 Score: 181
Period size: 35 Copynumber: 3.3 Consensus size: 36
70538 ATCCCATTAT
* *
70548 CATTTTTC-AACAAACATCTACCAAACTTTGAAAAAC
1 CATTTTTCAAAGAAACATTTACCAAACTTTG-AAAAC
*
70584 TATTTTTCAAAGAAACATTTACCAAACTTTGAAAAC
1 CATTTTTCAAAGAAACATTTACCAAACTTTGAAAAC
70620 CA-TTTTCAAAGAAACATTTACCAAACTTTGAAAAC
1 CATTTTTCAAAGAAACATTTACCAAACTTTGAAAAC
70655 CATTTTTTCAAAG
1 CA-TTTTTCAAAG
70668 TTGGTTACCA
Statistics
Matches: 77, Mismatches: 4, Indels: 5
0.90 0.05 0.06
Matches are distributed among these distances:
35 35 0.45
36 13 0.17
37 29 0.38
ACGTcount: A:0.43, C:0.20, G:0.05, T:0.32
Consensus pattern (36 bp):
CATTTTTCAAAGAAACATTTACCAAACTTTGAAAAC
Found at i:70623 original size:21 final size:21
Alignment explanation
Indices: 70599--70659 Score: 64
Period size: 21 Copynumber: 3.2 Consensus size: 21
70589 TTCAAAGAAA
70599 CATTTACCAAACTTTGAAAAC
1 CATTTACCAAACTTTGAAAAC
*
70620 CATTT-TCAAA----G-AAA-
1 CATTTACCAAACTTTGAAAAC
70634 CATTTACCAAACTTTGAAAAC
1 CATTTACCAAACTTTGAAAAC
70655 CATTT
1 CATTT
70660 TTTCAAAGTT
Statistics
Matches: 31, Mismatches: 2, Indels: 14
0.66 0.04 0.30
Matches are distributed among these distances:
14 5 0.16
15 7 0.23
16 1 0.03
19 1 0.03
20 7 0.23
21 10 0.32
ACGTcount: A:0.43, C:0.21, G:0.05, T:0.31
Consensus pattern (21 bp):
CATTTACCAAACTTTGAAAAC
Found at i:70676 original size:35 final size:36
Alignment explanation
Indices: 70550--70694 Score: 142
Period size: 35 Copynumber: 4.1 Consensus size: 36
70540 CCCATTATCA
*
70550 TTTTTCAACA-AACA-TCTACCAAACTTTGAAAAAC-T
1 TTTTTCAA-AGAACAGT-TACCAAACTTTGAAAACCAT
*
70585 ATTTTTCAAAGAAACATTTACCAAACTTTGAAAACCA-
1 -TTTTTCAAAG-AACAGTTACCAAACTTTGAAAACCAT
*
70622 -TTTTCAAAGAAACATTTACCAAACTTTGAAAACCAT
1 TTTTTCAAAG-AACAGTTACCAAACTTTGAAAACCAT
***
70658 TTTTTCAAAG-TTGGTTACCAAAC-TTGAAAACCAT
1 TTTTTCAAAGAACAGTTACCAAACTTTGAAAACCAT
70692 TTT
1 TTT
70695 AATACTTTCA
Statistics
Matches: 98, Mismatches: 5, Indels: 14
0.84 0.04 0.12
Matches are distributed among these distances:
34 14 0.14
35 45 0.46
36 8 0.08
37 30 0.31
38 1 0.01
ACGTcount: A:0.41, C:0.19, G:0.06, T:0.33
Consensus pattern (36 bp):
TTTTTCAAAGAACAGTTACCAAACTTTGAAAACCAT
Found at i:74756 original size:16 final size:16
Alignment explanation
Indices: 74732--74770 Score: 60
Period size: 16 Copynumber: 2.4 Consensus size: 16
74722 TATCGCCGAC
*
74732 CGAATTTCACTATTCA
1 CGAAATTCACTATTCA
74748 CGAAATTCACTATTCA
1 CGAAATTCACTATTCA
74764 CGTAAAT
1 CG-AAAT
74771 AGTAATGAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
16 17 0.81
17 4 0.19
ACGTcount: A:0.36, C:0.23, G:0.08, T:0.33
Consensus pattern (16 bp):
CGAAATTCACTATTCA
Found at i:75229 original size:37 final size:36
Alignment explanation
Indices: 75170--75288 Score: 179
Period size: 35 Copynumber: 3.3 Consensus size: 36
75160 ATCCCATTAT
* *
75170 CATTTTTC-AACAAACATCTACCAAACTTTGAAAAAC
1 CATTTTTCAAAGAAACATTTACCAAACTTTG-AAAAC
*
75206 TATTTTTCAAAGAAACATTTACCAAACTTTGAAAAC
1 CATTTTTCAAAGAAACATTTACCAAACTTTGAAAAC
75242 CA-TTTTCAAAGAAACATTTACCAAACTTTGAAAAC
1 CATTTTTCAAAGAAACATTTACCAAACTTTGAAAAC
75277 CATTTTTTCAAA
1 CA-TTTTTCAAA
75289 ATTGGTTACC
Statistics
Matches: 76, Mismatches: 4, Indels: 5
0.89 0.05 0.06
Matches are distributed among these distances:
35 35 0.46
36 13 0.17
37 28 0.37
ACGTcount: A:0.44, C:0.20, G:0.04, T:0.32
Consensus pattern (36 bp):
CATTTTTCAAAGAAACATTTACCAAACTTTGAAAAC
Found at i:75245 original size:21 final size:21
Alignment explanation
Indices: 75221--75281 Score: 64
Period size: 21 Copynumber: 3.2 Consensus size: 21
75211 TTCAAAGAAA
75221 CATTTACCAAACTTTGAAAAC
1 CATTTACCAAACTTTGAAAAC
*
75242 CATTT-TCAAA----G-AAA-
1 CATTTACCAAACTTTGAAAAC
75256 CATTTACCAAACTTTGAAAAC
1 CATTTACCAAACTTTGAAAAC
75277 CATTT
1 CATTT
75282 TTTCAAAATT
Statistics
Matches: 31, Mismatches: 2, Indels: 14
0.66 0.04 0.30
Matches are distributed among these distances:
14 5 0.16
15 7 0.23
16 1 0.03
19 1 0.03
20 7 0.23
21 10 0.32
ACGTcount: A:0.43, C:0.21, G:0.05, T:0.31
Consensus pattern (21 bp):
CATTTACCAAACTTTGAAAAC
Found at i:75298 original size:35 final size:37
Alignment explanation
Indices: 75172--75316 Score: 153
Period size: 35 Copynumber: 4.1 Consensus size: 37
75162 CCCATTATCA
* *
75172 TTTTTC-AACAAACA-TCTACCAAACTTTGAAAAAC-T
1 TTTTTCAAAGAAACAGT-TACCAAACTTTGAAAACCAT
*
75207 ATTTTTCAAAGAAACATTTACCAAACTTTGAAAACCA-
1 -TTTTTCAAAGAAACAGTTACCAAACTTTGAAAACCAT
*
75244 -TTTTCAAAGAAACATTTACCAAACTTTGAAAACCAT
1 TTTTTCAAAGAAACAGTTACCAAACTTTGAAAACCAT
***
75280 TTTTTC-AA-AATTGGTTACCAAA-TTTGAAAACCAT
1 TTTTTCAAAGAAACAGTTACCAAACTTTGAAAACCAT
75314 TTT
1 TTT
75317 AATACTTTCA
Statistics
Matches: 98, Mismatches: 6, Indels: 12
0.84 0.05 0.10
Matches are distributed among these distances:
34 15 0.15
35 45 0.46
36 8 0.08
37 29 0.30
38 1 0.01
ACGTcount: A:0.42, C:0.19, G:0.06, T:0.34
Consensus pattern (37 bp):
TTTTTCAAAGAAACAGTTACCAAACTTTGAAAACCAT
Found at i:80728 original size:2 final size:2
Alignment explanation
Indices: 80721--80746 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
80711 CCATTTAAAT
80721 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
80747 ATTTATATTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:80781 original size:19 final size:21
Alignment explanation
Indices: 80716--80782 Score: 59
Period size: 21 Copynumber: 3.3 Consensus size: 21
80706 TATGACCATT
* *
80716 TAAAT-TATATATATATATATA
1 TAAATATATA-ATTTATATTTA
* *
80737 TATATATATAATTTATATTTC
1 TAAATATATAATTTATATTTA
*
80758 GAAATAT-TAATTTA-ATTTA
1 TAAATATATAATTTATATTTA
80777 TAAATA
1 TAAATA
80783 CATATAAATA
Statistics
Matches: 37, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
19 9 0.24
20 7 0.19
21 17 0.46
22 4 0.11
ACGTcount: A:0.48, C:0.01, G:0.01, T:0.49
Consensus pattern (21 bp):
TAAATATATAATTTATATTTA
Found at i:85617 original size:2 final size:2
Alignment explanation
Indices: 85610--85635 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
85600 GATGTTACAA
85610 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
85636 GTATGTTTCA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:92842 original size:21 final size:21
Alignment explanation
Indices: 92791--92843 Score: 72
Period size: 21 Copynumber: 2.5 Consensus size: 21
92781 ATTATGACTA
92791 TCGCAATGCGATTTTCCAATT
1 TCGCAATGCGATTTTCCAATT
**
92812 TCGCGTTGCGATTTTCCCAA-T
1 TCGCAATGCGATTTT-CCAATT
92833 TCGCAATGCGA
1 TCGCAATGCGA
92844 ATAAGTAAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
21 23 0.85
22 4 0.15
ACGTcount: A:0.21, C:0.26, G:0.19, T:0.34
Consensus pattern (21 bp):
TCGCAATGCGATTTTCCAATT
Found at i:92876 original size:21 final size:20
Alignment explanation
Indices: 92833--92879 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 20
92823 TTTTCCCAAT
*
92833 TCGCAATGCGAATAAGTAAA
1 TCGCAATGCGAATAAGAAAA
**
92853 TCGCAATGCGAATTTGGAAAA
1 TCGCAATGCGAA-TAAGAAAA
92874 TCGCAA
1 TCGCAA
92880 CGCGGTACTG
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
20 12 0.52
21 11 0.48
ACGTcount: A:0.40, C:0.17, G:0.21, T:0.21
Consensus pattern (20 bp):
TCGCAATGCGAATAAGAAAA
Found at i:92897 original size:41 final size:41
Alignment explanation
Indices: 92870--93006 Score: 143
Period size: 41 Copynumber: 3.4 Consensus size: 41
92860 GCGAATTTGG
*
92870 AAAATCGCAACGCGGTACTGACTATCGCAACGCGATAATAC
1 AAAATCGCAACGCGATACTGACTATCGCAACGCGATAATAC
* * * *
92911 AAAATCGCAACGCGATACTGACTTTCGCAAC-TGATACT-T
1 AAAATCGCAACGCGATACTGACTATCGCAACGCGATAATAC
** * * * *
92950 AATTTCGCAACTCAATACTGACTTTCGCAACGAGATAATAC
1 AAAATCGCAACGCGATACTGACTATCGCAACGCGATAATAC
* *
92991 ATAATCGCAATGCGAT
1 AAAATCGCAACGCGAT
93007 TTTCAAAGAG
Statistics
Matches: 76, Mismatches: 18, Indels: 4
0.78 0.18 0.04
Matches are distributed among these distances:
39 27 0.36
40 10 0.13
41 39 0.51
ACGTcount: A:0.36, C:0.25, G:0.16, T:0.23
Consensus pattern (41 bp):
AAAATCGCAACGCGATACTGACTATCGCAACGCGATAATAC
Found at i:92898 original size:20 final size:20
Alignment explanation
Indices: 92873--92986 Score: 88
Period size: 20 Copynumber: 5.7 Consensus size: 20
92863 AATTTGGAAA
*
92873 ATCGCAACGCGGTACTGACT
1 ATCGCAACGCGATACTGACT
* *
92893 ATCGCAACGCGATAAT-ACAAA
1 ATCGCAACGCGATACTGAC--T
92914 ATCGCAACGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* * * *
92934 TTCGCAAC-TGATACTTAAT
1 ATCGCAACGCGATACTGACT
* * *
92953 TTCGCAACTCAATACTGACT
1 ATCGCAACGCGATACTGACT
* *
92973 TTCGCAACGAGATA
1 ATCGCAACGCGATA
92987 ATACATAATC
Statistics
Matches: 74, Mismatches: 16, Indels: 8
0.76 0.16 0.08
Matches are distributed among these distances:
19 18 0.24
20 39 0.53
21 15 0.20
22 2 0.03
ACGTcount: A:0.33, C:0.26, G:0.17, T:0.24
Consensus pattern (20 bp):
ATCGCAACGCGATACTGACT
Found at i:92948 original size:19 final size:20
Alignment explanation
Indices: 92915--92980 Score: 89
Period size: 20 Copynumber: 3.4 Consensus size: 20
92905 TAATACAAAA
*
92915 TCGCAACGCGATACTGACTT
1 TCGCAACTCGATACTGACTT
* *
92935 TCGCAACT-GATACTTAATT
1 TCGCAACTCGATACTGACTT
*
92954 TCGCAACTCAATACTGACTT
1 TCGCAACTCGATACTGACTT
92974 TCGCAAC
1 TCGCAAC
92981 GAGATAATAC
Statistics
Matches: 39, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
19 17 0.44
20 22 0.56
ACGTcount: A:0.29, C:0.29, G:0.14, T:0.29
Consensus pattern (20 bp):
TCGCAACTCGATACTGACTT
Found at i:93201 original size:22 final size:22
Alignment explanation
Indices: 93173--93216 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
93163 CACTCTCTCA
93173 CCCATCTCCGACGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
*
93195 CCCATCTCCGGCGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
93217 TATCTCCATC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.20, C:0.45, G:0.16, T:0.18
Consensus pattern (22 bp):
CCCATCTCCGACGAAATCCGTC
Found at i:93518 original size:20 final size:20
Alignment explanation
Indices: 93464--93537 Score: 78
Period size: 20 Copynumber: 3.8 Consensus size: 20
93454 AAATCGCAAC
* *
93464 GCGATTTT-ATTCTCTCGTT
1 GCGATTTTCATTTTCGCGTT
** **
93483 GCGATAGTCAAATTCGCGTT
1 GCGATTTTCATTTTCGCGTT
*
93503 GCGATTTTCATTTTCGTGTT
1 GCGATTTTCATTTTCGCGTT
93523 GCGATTTTCATTTTC
1 GCGATTTTCATTTTC
93538 AGAAACTATT
Statistics
Matches: 43, Mismatches: 11, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
19 6 0.14
20 37 0.86
ACGTcount: A:0.15, C:0.19, G:0.19, T:0.47
Consensus pattern (20 bp):
GCGATTTTCATTTTCGCGTT
Found at i:93728 original size:25 final size:24
Alignment explanation
Indices: 93674--93728 Score: 58
Period size: 25 Copynumber: 2.2 Consensus size: 24
93664 TGTTTATTAT
* *
93674 TGTTTTTGGTATATCTTCACAGTG
1 TGTTTTTGGTATATCTTAACAGTA
93698 TAGTTTTTGGTATATC-TAACTTAGTA
1 T-GTTTTTGGTATATCTTAAC--AGTA
93724 TGTTT
1 TGTTT
93729 ATTGTTTTTG
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
24 4 0.15
25 18 0.69
26 4 0.15
ACGTcount: A:0.20, C:0.09, G:0.18, T:0.53
Consensus pattern (24 bp):
TGTTTTTGGTATATCTTAACAGTA
Found at i:94878 original size:18 final size:18
Alignment explanation
Indices: 94857--94904 Score: 87
Period size: 18 Copynumber: 2.7 Consensus size: 18
94847 TCCACTTCGG
94857 GAGCCATCACCTCACCCA
1 GAGCCATCACCTCACCCA
*
94875 GAGCTATCACCTCACCCA
1 GAGCCATCACCTCACCCA
94893 GAGCCATCACCT
1 GAGCCATCACCT
94905 GATCGACCCG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.27, C:0.46, G:0.12, T:0.15
Consensus pattern (18 bp):
GAGCCATCACCTCACCCA
Found at i:95499 original size:19 final size:20
Alignment explanation
Indices: 95445--95511 Score: 73
Period size: 20 Copynumber: 3.4 Consensus size: 20
95435 TAGTTTACTT
* *
95445 TCGCAACACGAAAATGACTA
1 TCGCAACGCGGAAATGACTA
*
95465 TCGCAACGCGGAAATGGCTA
1 TCGCAACGCGGAAATGACTA
* **
95485 TCGCAATGC-GAAATGAAAA
1 TCGCAACGCGGAAATGACTA
95504 TCGCAACG
1 TCGCAACG
95512 ACAAAATCGC
Statistics
Matches: 39, Mismatches: 8, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
19 14 0.36
20 25 0.64
ACGTcount: A:0.39, C:0.24, G:0.22, T:0.15
Consensus pattern (20 bp):
TCGCAACGCGGAAATGACTA
Found at i:95531 original size:33 final size:33
Alignment explanation
Indices: 95484--95575 Score: 157
Period size: 33 Copynumber: 2.8 Consensus size: 33
95474 GGAAATGGCT
*
95484 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAATGTGAAATGAAAATCGCAACGACAAA
*
95517 ATCGCAATATGAAATGAAAATCGCAACGACAAA
1 ATCGCAATGTGAAATGAAAATCGCAACGACAAA
*
95550 ATCGCAACGTGAAATGAAAATCGCAA
1 ATCGCAATGTGAAATGAAAATCGCAA
95576 TGCGATTTGT
Statistics
Matches: 55, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 55 1.00
ACGTcount: A:0.49, C:0.20, G:0.17, T:0.14
Consensus pattern (33 bp):
ATCGCAATGTGAAATGAAAATCGCAACGACAAA
Found at i:95571 original size:19 final size:18
Alignment explanation
Indices: 95494--95575 Score: 63
Period size: 14 Copynumber: 4.9 Consensus size: 18
95484 ATCGCAATGC
95494 GAAATGAAAATCGCAAC-
1 GAAATGAAAATCGCAACT
* *
95511 G--A-CAAAATCGCAATAT
1 GAAATGAAAATCGCAA-CT
95527 GAAATGAAAATCGCAAC-
1 GAAATGAAAATCGCAACT
*
95544 G--A-CAAAATCGCAACGT
1 GAAATGAAAATCGCAAC-T
95560 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
95576 TGCGATTTGT
Statistics
Matches: 49, Mismatches: 6, Indels: 18
0.67 0.08 0.25
Matches are distributed among these distances:
14 21 0.43
15 2 0.04
16 2 0.04
17 2 0.04
18 2 0.04
19 20 0.41
ACGTcount: A:0.51, C:0.18, G:0.17, T:0.13
Consensus pattern (18 bp):
GAAATGAAAATCGCAACT
Found at i:95611 original size:14 final size:14
Alignment explanation
Indices: 95592--95650 Score: 64
Period size: 14 Copynumber: 3.9 Consensus size: 14
95582 TTGTGTTTCG
95592 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
95606 CGTTGCGATTTTCATTT
1 CGTTGCGA-TTT--TGT
95623 CGCATTGCGATTTTGT
1 CG--TTGCGATTTTGT
95639 CGTTGCGATTTT
1 CGTTGCGATTTT
95651 CATTTCGCAT
Statistics
Matches: 38, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
14 18 0.47
15 3 0.08
16 4 0.11
17 4 0.11
18 3 0.08
19 6 0.16
ACGTcount: A:0.10, C:0.17, G:0.24, T:0.49
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:95624 original size:33 final size:33
Alignment explanation
Indices: 95587--95669 Score: 157
Period size: 33 Copynumber: 2.5 Consensus size: 33
95577 GCGATTTGTG
*
95587 TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
1 TTTCGCATTGCGATTTTGTCGTTGCGATTTTCA
95620 TTTCGCATTGCGATTTTGTCGTTGCGATTTTCA
1 TTTCGCATTGCGATTTTGTCGTTGCGATTTTCA
95653 TTTCGCATTGCGATTTT
1 TTTCGCATTGCGATTTT
95670 CATTTCGCAT
Statistics
Matches: 49, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 49 1.00
ACGTcount: A:0.11, C:0.18, G:0.22, T:0.49
Consensus pattern (33 bp):
TTTCGCATTGCGATTTTGTCGTTGCGATTTTCA
Found at i:95626 original size:52 final size:51
Alignment explanation
Indices: 95570--95685 Score: 135
Period size: 52 Copynumber: 2.2 Consensus size: 51
95560 GAAATGAAAA
* * * * *
95570 TCGCAATGCGATTTGT-GTTTCGCGTTGCGATTTTGTCGTTGCGATTTTCATT
1 TCGCATTGCGATTTGTCGTTGCGAGTTGC-ATTTCG-CATTGCGATTTTCATT
* *
95622 TCGCATTGCGATTTTGTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATT
1 TCGCATTGCGA-TTTGTCGTTGCGAGTTGCATTTCGCATTGCGATTTTCATT
95674 TCGCATTGCGAT
1 TCGCATTGCGAT
95686 AGCCATTTCC
Statistics
Matches: 55, Mismatches: 7, Indels: 5
0.82 0.10 0.07
Matches are distributed among these distances:
51 1 0.02
52 36 0.65
53 10 0.18
54 8 0.15
ACGTcount: A:0.13, C:0.19, G:0.22, T:0.46
Consensus pattern (51 bp):
TCGCATTGCGATTTGTCGTTGCGAGTTGCATTTCGCATTGCGATTTTCATT
Found at i:95632 original size:19 final size:19
Alignment explanation
Indices: 95608--95685 Score: 112
Period size: 19 Copynumber: 4.4 Consensus size: 19
95598 GATTTTGTCG
95608 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
95627 TTGCGA-TTT--TGTCG--
1 TTGCGATTTTCATTTCGCA
95641 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
95660 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
95679 TTGCGAT
1 TTGCGAT
95686 AGCCATTTCC
Statistics
Matches: 52, Mismatches: 2, Indels: 10
0.81 0.03 0.16
Matches are distributed among these distances:
14 6 0.12
15 3 0.06
16 4 0.08
17 4 0.08
18 3 0.06
19 32 0.62
ACGTcount: A:0.14, C:0.19, G:0.19, T:0.47
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:95692 original size:19 final size:19
Alignment explanation
Indices: 95650--95713 Score: 83
Period size: 19 Copynumber: 3.3 Consensus size: 19
95640 GTTGCGATTT
**
95650 TCATTTCGCATTGCGATTT
1 TCATTTCGCATTGCGATAG
95669 TCATTTCGCATTGCGATAG
1 TCATTTCGCATTGCGATAG
* *
95688 CCATTTCCGCGTTGCGATAG
1 TCATTT-CGCATTGCGATAG
95708 TCATTT
1 TCATTT
95714 TCGTACGAAA
Statistics
Matches: 39, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
19 22 0.56
20 17 0.44
ACGTcount: A:0.17, C:0.23, G:0.19, T:0.41
Consensus pattern (19 bp):
TCATTTCGCATTGCGATAG
Found at i:95799 original size:27 final size:28
Alignment explanation
Indices: 95733--95801 Score: 76
Period size: 25 Copynumber: 2.6 Consensus size: 28
95723 AGTAAACTAT
* *
95733 TCTTCTTCTTGAATGTTTATATATGTTG
1 TCTTCTTCTAGAATGTTTATATAAGTTG
95761 TCTT-TT-TA-AATGTTTATATAAG-TG
1 TCTTCTTCTAGAATGTTTATATAAGTTG
95785 -CTTACTTCTAGAATGTT
1 TCTT-CTTCTAGAATGTT
95802 ATCTGATGCA
Statistics
Matches: 35, Mismatches: 2, Indels: 9
0.76 0.04 0.20
Matches are distributed among these distances:
23 3 0.09
24 2 0.06
25 15 0.43
26 3 0.09
27 8 0.23
28 4 0.11
ACGTcount: A:0.23, C:0.10, G:0.13, T:0.54
Consensus pattern (28 bp):
TCTTCTTCTAGAATGTTTATATAAGTTG
Found at i:96102 original size:21 final size:20
Alignment explanation
Indices: 96076--96144 Score: 66
Period size: 21 Copynumber: 3.4 Consensus size: 20
96066 CTGTCATTCC
96076 TCAAGAGTCCCCTCCAATCGT
1 TCAAGAGTCCCCTCC-ATCGT
* * **
96097 TCAAGAGGCCCCTATCATCCC
1 TCAAGAGTCCCCT-CCATCGT
* *
96118 TCAAGAGTCCCCCCCACCGT
1 TCAAGAGTCCCCTCCATCGT
96138 TCAAGAG
1 TCAAGAG
96145 GCCACTGTCA
Statistics
Matches: 37, Mismatches: 10, Indels: 3
0.74 0.20 0.06
Matches are distributed among these distances:
20 10 0.27
21 26 0.70
22 1 0.03
ACGTcount: A:0.25, C:0.41, G:0.16, T:0.19
Consensus pattern (20 bp):
TCAAGAGTCCCCTCCATCGT
Found at i:96156 original size:41 final size:42
Alignment explanation
Indices: 96066--96156 Score: 130
Period size: 41 Copynumber: 2.2 Consensus size: 42
96056 CCCGACTCAC
* * *
96066 CTGTCATTCCTCAAGAGTCCCCTCCAATCGTTCAAGAGGCCC
1 CTGTCATCCCTCAAGAGTCCCCTCCAACCGTTCAAGAGGCCA
* *
96108 CTATCATCCCTCAAGAGTCCCC-CCCACCGTTCAAGAGGCCA
1 CTGTCATCCCTCAAGAGTCCCCTCCAACCGTTCAAGAGGCCA
96149 CTGTCATC
1 CTGTCATC
96157 GTTGAAGAGG
Statistics
Matches: 43, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
41 23 0.53
42 20 0.47
ACGTcount: A:0.22, C:0.41, G:0.15, T:0.22
Consensus pattern (42 bp):
CTGTCATCCCTCAAGAGTCCCCTCCAACCGTTCAAGAGGCCA
Found at i:98020 original size:32 final size:32
Alignment explanation
Indices: 97979--98108 Score: 172
Period size: 32 Copynumber: 3.9 Consensus size: 32
97969 GAAAATTACT
97979 ATCGCAATGCGAAATG-AAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGA-A
*
98011 ATCGCAATGCGAAATGAAAATCGCAACGAGAT
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAA
*
98043 TTCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAAATCGCAA--CG--A-G-AA
98081 ATCGCAATGCGAAATGAAAATCGCAACG
1 ATCGCAATGCGAAATGAAAATCGCAACG
98109 CGAATTTAGT
Statistics
Matches: 87, Mismatches: 4, Indels: 10
0.86 0.04 0.10
Matches are distributed among these distances:
32 41 0.47
33 14 0.16
34 2 0.02
36 3 0.03
37 1 0.01
38 26 0.30
ACGTcount: A:0.44, C:0.18, G:0.22, T:0.15
Consensus pattern (32 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAA
Found at i:98034 original size:19 final size:19
Alignment explanation
Indices: 97979--98112 Score: 148
Period size: 19 Copynumber: 7.7 Consensus size: 19
97969 GAAAATTACT
97979 ATCGCAATGCGAAATG-AA
1 ATCGCAATGCGAAATGAAA
*
97997 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
98011 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
98030 ATCGCAA--CG--A-G-AT
1 ATCGCAATGCGAAATGAAA
*
98043 TTCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
98062 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
98081 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
98100 ATCGCAACGCGAA
1 ATCGCAATGCGAA
98113 TTTAGTTTCG
Statistics
Matches: 97, Mismatches: 7, Indels: 23
0.76 0.06 0.18
Matches are distributed among these distances:
13 8 0.08
14 10 0.10
15 3 0.03
16 4 0.04
17 3 0.03
18 9 0.09
19 60 0.62
ACGTcount: A:0.44, C:0.19, G:0.22, T:0.15
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:98174 original size:14 final size:14
Alignment explanation
Indices: 98123--98211 Score: 52
Period size: 14 Copynumber: 5.7 Consensus size: 14
98113 TTTAGTTTCG
* *
98123 CGTTGCGATTTTGT
1 CGTTGCGATTCTCT
*
98137 CGTTGCGATTTCATTTCG
1 CGTTGCGA-TTC---TCT
98155 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
* *
98169 CGTTGCAATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
98188 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
98202 CGTTGCGATT
1 CGTTGCGATT
98212 TCTTTTCGCA
Statistics
Matches: 58, Mismatches: 8, Indels: 18
0.69 0.10 0.21
Matches are distributed among these distances:
14 29 0.50
15 2 0.03
16 3 0.05
17 6 0.10
18 9 0.16
19 9 0.16
ACGTcount: A:0.10, C:0.22, G:0.22, T:0.45
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:98187 original size:33 final size:32
Alignment explanation
Indices: 98118--98228 Score: 168
Period size: 32 Copynumber: 3.4 Consensus size: 32
98108 GCGAATTTAG
* *
98118 TTTCGCGTTGCGATTTTGTCGTTGCGATTTCA
1 TTTCGCGTTGCGATTCTCTCGTTGCGATTTCA
*
98150 TTTCGCGTTGCGATTCTCTCGTTGCAATTTTCA
1 TTTCGCGTTGCGATTCTCTCGTTGCGA-TTTCA
*
98183 TTTCGCGTTGCGATTCTCTCGTTGCGATTTCT
1 TTTCGCGTTGCGATTCTCTCGTTGCGATTTCA
*
98215 TTTCGCATTGCGAT
1 TTTCGCGTTGCGAT
98229 AGTACTTTTA
Statistics
Matches: 72, Mismatches: 6, Indels: 2
0.90 0.08 0.03
Matches are distributed among these distances:
32 41 0.57
33 31 0.43
ACGTcount: A:0.10, C:0.23, G:0.22, T:0.46
Consensus pattern (32 bp):
TTTCGCGTTGCGATTCTCTCGTTGCGATTTCA
Found at i:98353 original size:14 final size:14
Alignment explanation
Indices: 98334--98369 Score: 56
Period size: 13 Copynumber: 2.6 Consensus size: 14
98324 CATCAATTAA
*
98334 ACAAATCAACTTTT
1 ACAAATCAACCTTT
98348 ACAAATC-ACCTTT
1 ACAAATCAACCTTT
98361 ACAAATCAA
1 ACAAATCAA
98370 TTAAACAATC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
13 12 0.60
14 8 0.40
ACGTcount: A:0.47, C:0.25, G:0.00, T:0.28
Consensus pattern (14 bp):
ACAAATCAACCTTT
Found at i:99479 original size:21 final size:21
Alignment explanation
Indices: 99434--99524 Score: 58
Period size: 21 Copynumber: 4.3 Consensus size: 21
99424 GTGGGAGGAC
* * * *
99434 CTCTTCAACGATGGCAGTGGC
1 CTCTTGAACGATGGGAGGGGA
99455 CTCTTGAACGATGGGAGGGGA
1 CTCTTGAACGATGGGAGGGGA
* * ** *
99476 CTCTCG-AGGAATGATAGGGGC
1 CTCTTGAACG-ATGGGAGGGGA
* * *
99497 CTCTTCAACGATAGGAGTGGA
1 CTCTTGAACGATGGGAGGGGA
99518 CTCTTGA
1 CTCTTGA
99525 GGGATGACAG
Statistics
Matches: 50, Mismatches: 18, Indels: 4
0.69 0.25 0.06
Matches are distributed among these distances:
20 2 0.04
21 46 0.92
22 2 0.04
ACGTcount: A:0.23, C:0.21, G:0.33, T:0.23
Consensus pattern (21 bp):
CTCTTGAACGATGGGAGGGGA
Found at i:99507 original size:42 final size:42
Alignment explanation
Indices: 99452--99531 Score: 115
Period size: 42 Copynumber: 1.9 Consensus size: 42
99442 CGATGGCAGT
* *
99452 GGCCTCTTGAACGATGGGAGGGGACTCTCGAGGAATGATAGG
1 GGCCTCTTCAACGATAGGAGGGGACTCTCGAGGAATGATAGG
* * *
99494 GGCCTCTTCAACGATAGGAGTGGACTCTTGAGGGATGA
1 GGCCTCTTCAACGATAGGAGGGGACTCTCGAGGAATGA
99532 CAGGTGAGTC
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
42 33 1.00
ACGTcount: A:0.24, C:0.17, G:0.38, T:0.21
Consensus pattern (42 bp):
GGCCTCTTCAACGATAGGAGGGGACTCTCGAGGAATGATAGG
Found at i:101633 original size:19 final size:19
Alignment explanation
Indices: 101583--101675 Score: 106
Period size: 19 Copynumber: 5.1 Consensus size: 19
101573 TCTTTTGGTT
*
101583 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGC
*
101602 GATAATGAGAATCGCAACGC
1 GA-AATGAAAATCGCAACGC
101622 GAAATGAAAATCGCAA--C
1 GAAATGAAAATCGCAACGC
*
101639 G--A-GAGAATCGCAACGC
1 GAAATGAAAATCGCAACGC
*
101655 GAAATGAAAATCGCAATGC
1 GAAATGAAAATCGCAACGC
101674 GA
1 GA
101676 TTTGGTTTCG
Statistics
Matches: 62, Mismatches: 6, Indels: 12
0.77 0.08 0.15
Matches are distributed among these distances:
14 10 0.16
15 1 0.02
16 2 0.03
17 2 0.03
18 1 0.02
19 29 0.47
20 17 0.27
ACGTcount: A:0.46, C:0.18, G:0.24, T:0.12
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGC
Found at i:101650 original size:33 final size:33
Alignment explanation
Indices: 101608--101670 Score: 126
Period size: 33 Copynumber: 1.9 Consensus size: 33
101598 ACGAGATAAT
101608 GAGAATCGCAACGCGAAATGAAAATCGCAACGA
1 GAGAATCGCAACGCGAAATGAAAATCGCAACGA
101641 GAGAATCGCAACGCGAAATGAAAATCGCAA
1 GAGAATCGCAACGCGAAATGAAAATCGCAA
101671 TGCGATTTGG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.46, C:0.21, G:0.24, T:0.10
Consensus pattern (33 bp):
GAGAATCGCAACGCGAAATGAAAATCGCAACGA
Found at i:101692 original size:18 final size:17
Alignment explanation
Indices: 101671--101734 Score: 65
Period size: 18 Copynumber: 3.5 Consensus size: 17
101661 AAAATCGCAA
*
101671 TGCGATTTGGTTTCGCGT
1 TGCGATTT-ATTTCGCGT
*
101689 TGCGATTTTTATTCGCGT
1 TGCGATTTAT-TTCGCGT
101707 TGCGATAGTTATTTCCGCGT
1 TGCGAT--TTATTT-CGCGT
101727 TGCGATTT
1 TGCGATTT
101735 TCATTCTCGA
Statistics
Matches: 40, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
17 1 0.03
18 23 0.57
19 2 0.05
20 14 0.35
ACGTcount: A:0.11, C:0.17, G:0.27, T:0.45
Consensus pattern (17 bp):
TGCGATTTATTTCGCGT
Found at i:101727 original size:20 final size:18
Alignment explanation
Indices: 101682--101732 Score: 66
Period size: 18 Copynumber: 2.7 Consensus size: 18
101672 GCGATTTGGT
**
101682 TTCGCGTTGCGATTTTTA
1 TTCGCGTTGCGATAGTTA
101700 TTCGCGTTGCGATAGTTA
1 TTCGCGTTGCGATAGTTA
101718 TTTCCGCGTTGCGAT
1 -TT-CGCGTTGCGAT
101733 TTTCATTCTC
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
18 16 0.55
19 2 0.07
20 11 0.38
ACGTcount: A:0.12, C:0.20, G:0.25, T:0.43
Consensus pattern (18 bp):
TTCGCGTTGCGATAGTTA
Found at i:102311 original size:41 final size:40
Alignment explanation
Indices: 102255--102365 Score: 132
Period size: 41 Copynumber: 2.7 Consensus size: 40
102245 CGATAGTAAG
* *
102255 ATTCGCATTGCGATTTACGTATTCGCATTGCGATTTTCCT
1 ATTCGCATTGCGATTTACCTATTCGCATTGCGATTTACCT
* * * * *
102295 AATTCGCATTGTGATTTACTTAATCGCGTTGCGATTTACGT
1 -ATTCGCATTGCGATTTACCTATTCGCATTGCGATTTACCT
*
102336 ATTCGCATTGCGATTTTCCTAATTCGCATT
1 ATTCGCATTGCGATTTACCT-ATTCGCATT
102366 ACCAGAGTCT
Statistics
Matches: 58, Mismatches: 11, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
40 17 0.29
41 41 0.71
ACGTcount: A:0.20, C:0.21, G:0.17, T:0.42
Consensus pattern (40 bp):
ATTCGCATTGCGATTTACCTATTCGCATTGCGATTTACCT
Found at i:102350 original size:20 final size:20
Alignment explanation
Indices: 102237--102365 Score: 134
Period size: 20 Copynumber: 6.3 Consensus size: 20
102227 GCTATGTAAA
* *
102237 TCGCATTGCGATAGTAAG-AT
1 TCGCATTGCGAT-TTACGTAT
102257 TCGCATTGCGATTTACGTAT
1 TCGCATTGCGATTTACGTAT
* *
102277 TCGCATTGCGATTTTCCTAAT
1 TCGCATTGCGATTTACGT-AT
* * *
102298 TCGCATTGTGATTTACTTAA
1 TCGCATTGCGATTTACGTAT
*
102318 TCGCGTTGCGATTTACGTAT
1 TCGCATTGCGATTTACGTAT
* *
102338 TCGCATTGCGATTTTCCTAAT
1 TCGCATTGCGATTTACGT-AT
102359 TCGCATT
1 TCGCATT
102366 ACCAGAGTCT
Statistics
Matches: 91, Mismatches: 15, Indels: 5
0.82 0.14 0.05
Matches are distributed among these distances:
19 3 0.03
20 62 0.68
21 26 0.29
ACGTcount: A:0.21, C:0.20, G:0.19, T:0.40
Consensus pattern (20 bp):
TCGCATTGCGATTTACGTAT
Found at i:105160 original size:24 final size:23
Alignment explanation
Indices: 105101--105160 Score: 57
Period size: 24 Copynumber: 2.5 Consensus size: 23
105091 ATTATGAAGA
*
105101 ATATTATGATGATGACGAAAATG
1 ATATTATGATGATGACGAAAAGG
* ** *
105124 ATGAATACAATGATGACGTAAACGG
1 AT-ATTATGATGATGACG-AAAAGG
105149 ATATTATGATGA
1 ATATTATGATGA
105161 GAAAGATGAG
Statistics
Matches: 27, Mismatches: 8, Indels: 3
0.71 0.21 0.08
Matches are distributed among these distances:
23 2 0.07
24 19 0.70
25 6 0.22
ACGTcount: A:0.43, C:0.07, G:0.22, T:0.28
Consensus pattern (23 bp):
ATATTATGATGATGACGAAAAGG
Found at i:112621 original size:19 final size:20
Alignment explanation
Indices: 112565--112622 Score: 55
Period size: 19 Copynumber: 2.8 Consensus size: 20
112555 TTTTATGACC
*
112565 ATTTAAGTTATATATATATATA
1 ATTTAA-TT-TATAAATATATA
**
112587 ATTTATATTTCGAAATAT-TA
1 ATTTA-ATTTATAAATATATA
112607 ATTTAATTTATAAATA
1 ATTTAATTTATAAATA
112623 CATATAAATA
Statistics
Matches: 30, Mismatches: 5, Indels: 5
0.75 0.12 0.12
Matches are distributed among these distances:
19 9 0.30
20 7 0.23
21 6 0.20
22 7 0.23
23 1 0.03
ACGTcount: A:0.45, C:0.02, G:0.03, T:0.50
Consensus pattern (20 bp):
ATTTAATTTATAAATATATA
Found at i:117458 original size:2 final size:2
Alignment explanation
Indices: 117451--117500 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
117441 GATGTTACAA
117451 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
117493 AT AT AT AT
1 AT AT AT AT
117501 CAGTTTAAAA
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:124686 original size:21 final size:21
Alignment explanation
Indices: 124635--124687 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 21
124625 ATTATGACTA
*
124635 TCGCAATGCAATTTTCCAATT
1 TCGCAATGCGATTTTCCAATT
**
124656 TCGCGTTGCGATTTTCCCAA-T
1 TCGCAATGCGATTTT-CCAATT
124677 TCGCAATGCGA
1 TCGCAATGCGA
124688 ATAAGTAAAT
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
21 22 0.85
22 4 0.15
ACGTcount: A:0.23, C:0.26, G:0.17, T:0.34
Consensus pattern (21 bp):
TCGCAATGCGATTTTCCAATT
Found at i:124707 original size:41 final size:42
Alignment explanation
Indices: 124662--124765 Score: 111
Period size: 42 Copynumber: 2.5 Consensus size: 42
124652 AATTTCGCGT
* * * *
124662 TGCGATTTTCCCAATTCGCAATGCGAA-TAAGTAAATCGCAA
1 TGCGAATTTCCAAAATCGCAATGCGAATTAAGAAAATCGCAA
** **
124703 TGCGAATTTGGAAAATCGCAATGCGAATTTGGAAAATCGCAA
1 TGCGAATTTCCAAAATCGCAATGCGAATTAAGAAAATCGCAA
**
124745 TGCGAATTTGGAAAATCGCAA
1 TGCGAATTTCCAAAATCGCAA
124766 CGCGGTACTG
Statistics
Matches: 54, Mismatches: 8, Indels: 1
0.86 0.13 0.02
Matches are distributed among these distances:
41 22 0.41
42 32 0.59
ACGTcount: A:0.37, C:0.17, G:0.21, T:0.25
Consensus pattern (42 bp):
TGCGAATTTCCAAAATCGCAATGCGAATTAAGAAAATCGCAA
Found at i:124720 original size:21 final size:21
Alignment explanation
Indices: 124677--124765 Score: 144
Period size: 21 Copynumber: 4.3 Consensus size: 21
124667 TTTTCCCAAT
** *
124677 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTTGGAAAA
124697 TCGCAATGCGAATTTGGAAAA
1 TCGCAATGCGAATTTGGAAAA
124718 TCGCAATGCGAATTTGGAAAA
1 TCGCAATGCGAATTTGGAAAA
124739 TCGCAATGCGAATTTGGAAAA
1 TCGCAATGCGAATTTGGAAAA
124760 TCGCAA
1 TCGCAA
124766 CGCGGTACTG
Statistics
Matches: 65, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
20 12 0.18
21 53 0.82
ACGTcount: A:0.39, C:0.16, G:0.22, T:0.22
Consensus pattern (21 bp):
TCGCAATGCGAATTTGGAAAA
Found at i:124784 original size:20 final size:20
Alignment explanation
Indices: 124759--124873 Score: 97
Period size: 20 Copynumber: 5.7 Consensus size: 20
124749 AATTTGGAAA
*
124759 ATCGCAACGCGGTACTGACT
1 ATCGCAACGCGATACTGACT
* *
124779 ATCGCAACGCGATAAT-ACAAA
1 ATCGCAACGCGATACTGAC--T
124800 ATCGCAACGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* * * *
124820 TTCGCAACTCGATACTTAAT
1 ATCGCAACGCGATACTGACT
* * *
124840 TTCGCAACTCAATACTGACT
1 ATCGCAACGCGATACTGACT
* *
124860 TTCGCAACGAGATA
1 ATCGCAACGCGATA
124874 ATACATAATC
Statistics
Matches: 77, Mismatches: 15, Indels: 6
0.79 0.15 0.06
Matches are distributed among these distances:
19 2 0.03
20 58 0.75
21 15 0.19
22 2 0.03
ACGTcount: A:0.33, C:0.27, G:0.17, T:0.23
Consensus pattern (20 bp):
ATCGCAACGCGATACTGACT
Found at i:124801 original size:41 final size:41
Alignment explanation
Indices: 124756--124887 Score: 158
Period size: 41 Copynumber: 3.2 Consensus size: 41
124746 GCGAATTTGG
* *
124756 AAAATCGCAACGCGGTACTGACTATCGCAACGCGATAATAC
1 AAAATCGCAACGCGATACTGACTTTCGCAACGCGATAATAC
* * *
124797 AAAATCGCAACGCGATACTGACTTTCGCAACTCGATACT-T
1 AAAATCGCAACGCGATACTGACTTTCGCAACGCGATAATAC
** * * *
124837 AATTTCGCAACTCAATACTGACTTTCGCAACGAGATAATAC
1 AAAATCGCAACGCGATACTGACTTTCGCAACGCGATAATAC
*
124878 ATAATCGCAA
1 AAAATCGCAA
124888 TACGATTTTC
Statistics
Matches: 74, Mismatches: 16, Indels: 2
0.80 0.17 0.02
Matches are distributed among these distances:
40 32 0.43
41 42 0.57
ACGTcount: A:0.36, C:0.26, G:0.15, T:0.23
Consensus pattern (41 bp):
AAAATCGCAACGCGATACTGACTTTCGCAACGCGATAATAC
Found at i:125088 original size:22 final size:22
Alignment explanation
Indices: 125060--125103 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
125050 CACTCTCTCA
125060 CCCATCTCCGACGAAATTCGTC
1 CCCATCTCCGACGAAATTCGTC
* *
125082 CCCATCTCTGGCGAAATTCGTC
1 CCCATCTCCGACGAAATTCGTC
125104 TATCTCCATC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.20, C:0.39, G:0.16, T:0.25
Consensus pattern (22 bp):
CCCATCTCCGACGAAATTCGTC
Found at i:125405 original size:20 final size:20
Alignment explanation
Indices: 125382--125424 Score: 77
Period size: 20 Copynumber: 2.1 Consensus size: 20
125372 GATAGTCAAA
125382 TTCGCGTTGCGATTTTCATT
1 TTCGCGTTGCGATTTTCATT
*
125402 TTCGTGTTGCGATTTTCATT
1 TTCGCGTTGCGATTTTCATT
125422 TTC
1 TTC
125425 AGAAACTATT
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:0.09, C:0.19, G:0.19, T:0.53
Consensus pattern (20 bp):
TTCGCGTTGCGATTTTCATT
Found at i:125615 original size:25 final size:24
Alignment explanation
Indices: 125561--125615 Score: 58
Period size: 25 Copynumber: 2.2 Consensus size: 24
125551 TGTTTATTAT
* *
125561 TGTTTTTGGTATATCTTCACAGTG
1 TGTTTTTGGTATATCTTAACAGTA
125585 TAGTTTTTGGTATATC-TAACTTAGTA
1 T-GTTTTTGGTATATCTTAAC--AGTA
125611 TGTTT
1 TGTTT
125616 ATTGTTTTTG
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
24 4 0.15
25 18 0.69
26 4 0.15
ACGTcount: A:0.20, C:0.09, G:0.18, T:0.53
Consensus pattern (24 bp):
TGTTTTTGGTATATCTTAACAGTA
Found at i:126374 original size:2 final size:2
Alignment explanation
Indices: 126367--126450 Score: 159
Period size: 2 Copynumber: 42.0 Consensus size: 2
126357 TGCACCTTTC
126367 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
126409 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AC AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
126451 CCACGCATAC
Statistics
Matches: 80, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
2 80 1.00
ACGTcount: A:0.50, C:0.01, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:126868 original size:30 final size:30
Alignment explanation
Indices: 126723--126851 Score: 206
Period size: 30 Copynumber: 4.3 Consensus size: 30
126713 GAAGGACCTA
* *
126723 TCCAGAGGTCACAAAGA-CCCCGGTAACTG
1 TCCAGAGGTCATAAAGATCCTCGGTAACTG
*
126752 TCCAGAGGTCATAAAGATCCTCGGTAACTA
1 TCCAGAGGTCATAAAGATCCTCGGTAACTG
*
126782 TCCAGAGGTCATAAAGATCCTCGGTAATTG
1 TCCAGAGGTCATAAAGATCCTCGGTAACTG
126812 TCCAGAGGTCATAAAGATCCTCGGTAACTG
1 TCCAGAGGTCATAAAGATCCTCGGTAACTG
*
126842 TCCATAGGTC
1 TCCAGAGGTC
126852 CCGAAGAACC
Statistics
Matches: 92, Mismatches: 7, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
29 16 0.17
30 76 0.83
ACGTcount: A:0.30, C:0.25, G:0.22, T:0.22
Consensus pattern (30 bp):
TCCAGAGGTCATAAAGATCCTCGGTAACTG
Found at i:126868 original size:60 final size:60
Alignment explanation
Indices: 126720--126868 Score: 201
Period size: 60 Copynumber: 2.5 Consensus size: 60
126710 CCCGAAGGAC
**
126720 CTATCCAGAGGTCACAAAG-ACCCCGGTAACTGTCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCACAAAGAACCTAGGTAACTGTCCAGAGGTCATAAAGATCCTCGGTAA
* * * *
126779 CTATCCAGAGGTCATAAAGATCCTCGGTAATTGTCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCACAAAGAACCTAGGTAACTGTCCAGAGGTCATAAAGATCCTCGGTAA
* * * *
126839 CTGTCCATAGGTCCCGAAGAACCTAGGTAA
1 CTATCCAGAGGTCACAAAGAACCTAGGTAA
126869 ACTTTCCATA
Statistics
Matches: 78, Mismatches: 11, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
59 18 0.23
60 60 0.77
ACGTcount: A:0.32, C:0.25, G:0.22, T:0.21
Consensus pattern (60 bp):
CTATCCAGAGGTCACAAAGAACCTAGGTAACTGTCCAGAGGTCATAAAGATCCTCGGTAA
Found at i:128080 original size:21 final size:21
Alignment explanation
Indices: 128050--128094 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
128040 ATTCTGTCGT
* *
128050 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
128071 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
128092 TTG
1 TTG
128095 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:128519 original size:178 final size:178
Alignment explanation
Indices: 128220--128576 Score: 714
Period size: 178 Copynumber: 2.0 Consensus size: 178
128210 TTATTTCATC
128220 TTAAACCTCAAAATCCTATCTTCCATATGAGATTCAAAAATCATACCAAATTTTCTATATGTTCT
1 TTAAACCTCAAAATCCTATCTTCCATATGAGATTCAAAAATCATACCAAATTTTCTATATGTTCT
128285 AAATCCAATTATATCACTCCAAATCTCTTAATTTAACTATTGACAAGTCAAATTTAACTTCAAAT
66 AAATCCAATTATATCACTCCAAATCTCTTAATTTAACTATTGACAAGTCAAATTTAACTTCAAAT
128350 TCTACTTATCAATTCCTTTCCAAAATTTCATATAAAAACTCCAAATCT
131 TCTACTTATCAATTCCTTTCCAAAATTTCATATAAAAACTCCAAATCT
128398 TTAAACCTCAAAATCCTATCTTCCATATGAGATTCAAAAATCATACCAAATTTTCTATATGTTCT
1 TTAAACCTCAAAATCCTATCTTCCATATGAGATTCAAAAATCATACCAAATTTTCTATATGTTCT
128463 AAATCCAATTATATCACTCCAAATCTCTTAATTTAACTATTGACAAGTCAAATTTAACTTCAAAT
66 AAATCCAATTATATCACTCCAAATCTCTTAATTTAACTATTGACAAGTCAAATTTAACTTCAAAT
128528 TCTACTTATCAATTCCTTTCCAAAATTTCATATAAAAACTCCAAATCT
131 TCTACTTATCAATTCCTTTCCAAAATTTCATATAAAAACTCCAAATCT
128576 T
1 T
128577 AATCTCTCTA
Statistics
Matches: 179, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
178 179 1.00
ACGTcount: A:0.39, C:0.22, G:0.03, T:0.37
Consensus pattern (178 bp):
TTAAACCTCAAAATCCTATCTTCCATATGAGATTCAAAAATCATACCAAATTTTCTATATGTTCT
AAATCCAATTATATCACTCCAAATCTCTTAATTTAACTATTGACAAGTCAAATTTAACTTCAAAT
TCTACTTATCAATTCCTTTCCAAAATTTCATATAAAAACTCCAAATCT
Found at i:131060 original size:2 final size:2
Alignment explanation
Indices: 131053--131086 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
131043 TGCACCTTTC
*
131053 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AC AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
131087 CCACGCATAC
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:131412 original size:30 final size:30
Alignment explanation
Indices: 131356--131475 Score: 208
Period size: 30 Copynumber: 4.1 Consensus size: 30
131346 GAAGGACCTA
* *
131356 TCCAGAGGTCACAAAGA-CCCCGGTAACTG
1 TCCAGAGGTCATAAAGATCCTCGGTAACTG
131385 TCCAGAGGTCATAAAGATCCTCGGTAACTG
1 TCCAGAGGTCATAAAGATCCTCGGTAACTG
131415 TCCAGAGGTCATAAAGATCCTCGGTAACTG
1 TCCAGAGGTCATAAAGATCCTCGGTAACTG
131445 TCCAGAGGTCATAAAGATCCTCGGTAA-TG
1 TCCAGAGGTCATAAAGATCCTCGGTAACTG
131474 TC
1 TC
131476 ATAGTCCCGA
Statistics
Matches: 88, Mismatches: 2, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
29 20 0.23
30 68 0.77
ACGTcount: A:0.30, C:0.25, G:0.23, T:0.22
Consensus pattern (30 bp):
TCCAGAGGTCATAAAGATCCTCGGTAACTG
Found at i:131819 original size:27 final size:29
Alignment explanation
Indices: 131773--131828 Score: 71
Period size: 27 Copynumber: 2.0 Consensus size: 29
131763 TTCTCACCCA
**
131773 ATCACATTTATTCAGGT-AAA-CATACTT
1 ATCACATTTATTCACCTAAAATCATACTT
*
131800 ATCATATTTATTCACCTAAAATCATACTT
1 ATCACATTTATTCACCTAAAATCATACTT
131829 CATATAACAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
27 14 0.58
28 3 0.12
29 7 0.29
ACGTcount: A:0.38, C:0.20, G:0.04, T:0.39
Consensus pattern (29 bp):
ATCACATTTATTCACCTAAAATCATACTT
Found at i:132118 original size:19 final size:19
Alignment explanation
Indices: 132081--132119 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
132071 CACTTATACA
132081 CTTTTATATCACATAAACT
1 CTTTTATATCACATAAACT
132100 CTTTTATATCACATAAACT
1 CTTTTATATCACATAAACT
132119 C
1 C
132120 ATATATATAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.36, C:0.23, G:0.00, T:0.41
Consensus pattern (19 bp):
CTTTTATATCACATAAACT
Found at i:132126 original size:19 final size:19
Alignment explanation
Indices: 132085--132127 Score: 68
Period size: 19 Copynumber: 2.3 Consensus size: 19
132075 TATACACTTT
* *
132085 TATATCACATAAACTCTTT
1 TATATCACATAAACTCATA
132104 TATATCACATAAACTCATA
1 TATATCACATAAACTCATA
132123 TATAT
1 TATAT
132128 ATAGATCATG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.42, C:0.19, G:0.00, T:0.40
Consensus pattern (19 bp):
TATATCACATAAACTCATA
Found at i:134267 original size:18 final size:18
Alignment explanation
Indices: 134239--134286 Score: 78
Period size: 18 Copynumber: 2.7 Consensus size: 18
134229 TCCACTTCGG
134239 GAGCCATCACCTCACCCA
1 GAGCCATCACCTCACCCA
* *
134257 TAGCTATCACCTCACCCA
1 GAGCCATCACCTCACCCA
134275 GAGCCATCACCT
1 GAGCCATCACCT
134287 GATCGACCCG
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.27, C:0.46, G:0.10, T:0.17
Consensus pattern (18 bp):
GAGCCATCACCTCACCCA
Found at i:134852 original size:20 final size:20
Alignment explanation
Indices: 134827--134872 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
134817 TAGTTTACTT
134827 TCGCAACACGAAAATGACTA
1 TCGCAACACGAAAATGACTA
* * *
134847 TCGCAACGCGGAAATGGCTA
1 TCGCAACACGAAAATGACTA
134867 TCGCAA
1 TCGCAA
134873 TGCGAATTGA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.37, C:0.26, G:0.22, T:0.15
Consensus pattern (20 bp):
TCGCAACACGAAAATGACTA
Found at i:134930 original size:33 final size:33
Alignment explanation
Indices: 134884--134957 Score: 112
Period size: 33 Copynumber: 2.2 Consensus size: 33
134874 GCGAATTGAG
* *
134884 AATCGCAATGACAAAATCGCAATATGAAATGAA
1 AATCGCAACGACAAAATCGCAACATGAAATGAA
* *
134917 AATTGCAACGACAAAATCGCAACGTGAAATGAA
1 AATCGCAACGACAAAATCGCAACATGAAATGAA
134950 AATCGCAA
1 AATCGCAA
134958 TGCGATTTGT
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.50, C:0.18, G:0.16, T:0.16
Consensus pattern (33 bp):
AATCGCAACGACAAAATCGCAACATGAAATGAA
Found at i:134993 original size:14 final size:14
Alignment explanation
Indices: 134974--135032 Score: 55
Period size: 14 Copynumber: 3.9 Consensus size: 14
134964 TTGTGTTTCG
134974 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
134988 CGTTGCGATTTTCATTTT
1 CGTTGCGA--TT--TTGT
*
135006 GCATTGCGATTTTGT
1 -CGTTGCGATTTTGT
135021 CGTTGCGATTTT
1 CGTTGCGATTTT
135033 CATTTCGCAT
Statistics
Matches: 36, Mismatches: 4, Indels: 10
0.72 0.08 0.20
Matches are distributed among these distances:
14 19 0.53
15 3 0.08
16 2 0.06
17 2 0.06
18 3 0.08
19 7 0.19
ACGTcount: A:0.10, C:0.15, G:0.24, T:0.51
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:135013 original size:33 final size:33
Alignment explanation
Indices: 134969--135048 Score: 142
Period size: 33 Copynumber: 2.4 Consensus size: 33
134959 GCGATTTGTG
*
134969 TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
1 TTTCGCATTGCGATTTTGTCGTTGCGATTTTCA
*
135002 TTTTGCATTGCGATTTTGTCGTTGCGATTTTCA
1 TTTCGCATTGCGATTTTGTCGTTGCGATTTTCA
135035 TTTCGCATTGCGAT
1 TTTCGCATTGCGAT
135049 AGCCATTTCC
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 44 1.00
ACGTcount: A:0.11, C:0.17, G:0.23, T:0.49
Consensus pattern (33 bp):
TTTCGCATTGCGATTTTGTCGTTGCGATTTTCA
Found at i:135045 original size:19 final size:19
Alignment explanation
Indices: 134990--135048 Score: 65
Period size: 19 Copynumber: 3.4 Consensus size: 19
134980 GATTTTGTCG
*
134990 TTGCGATTTTCATTTTGCA
1 TTGCGATTTTCATTTCGCA
*
135009 TTGCGA-TTT--TGTCG--
1 TTGCGATTTTCATTTCGCA
135023 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
135042 TTGCGAT
1 TTGCGAT
135049 AGCCATTTCC
Statistics
Matches: 32, Mismatches: 3, Indels: 10
0.71 0.07 0.22
Matches are distributed among these distances:
14 6 0.19
15 3 0.09
16 3 0.09
17 4 0.12
18 3 0.09
19 13 0.41
ACGTcount: A:0.14, C:0.17, G:0.20, T:0.49
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:135067 original size:20 final size:19
Alignment explanation
Indices: 135033--135087 Score: 65
Period size: 20 Copynumber: 2.8 Consensus size: 19
135023 TTGCGATTTT
*
135033 CATTTCGCATTGCGATAGC
1 CATTTCGCGTTGCGATAGC
*
135052 CATTTCCGCGTTGCGATAGT
1 CATTT-CGCGTTGCGATAGC
*
135072 CATTTTCGTGTTGCGA
1 CA-TTTCGCGTTGCGA
135088 AAGTAAACTA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
19 5 0.16
20 23 0.74
21 3 0.10
ACGTcount: A:0.16, C:0.24, G:0.24, T:0.36
Consensus pattern (19 bp):
CATTTCGCGTTGCGATAGC
Found at i:135468 original size:21 final size:20
Alignment explanation
Indices: 135442--135510 Score: 66
Period size: 21 Copynumber: 3.4 Consensus size: 20
135432 CTGTCATTCC
135442 TCAAGAGTCCCCTCCAATCGT
1 TCAAGAGTCCCCTCC-ATCGT
* * **
135463 TCAAGAGGCCCCTATCATCCC
1 TCAAGAGTCCCCT-CCATCGT
* *
135484 TCAAGAGTCCCCCCCACCGT
1 TCAAGAGTCCCCTCCATCGT
135504 TCAAGAG
1 TCAAGAG
135511 GCCACTGTCA
Statistics
Matches: 37, Mismatches: 10, Indels: 3
0.74 0.20 0.06
Matches are distributed among these distances:
20 10 0.27
21 26 0.70
22 1 0.03
ACGTcount: A:0.25, C:0.41, G:0.16, T:0.19
Consensus pattern (20 bp):
TCAAGAGTCCCCTCCATCGT
Found at i:135522 original size:41 final size:42
Alignment explanation
Indices: 135432--135522 Score: 130
Period size: 41 Copynumber: 2.2 Consensus size: 42
135422 CCCGACTCAC
* * *
135432 CTGTCATTCCTCAAGAGTCCCCTCCAATCGTTCAAGAGGCCC
1 CTGTCATCCCTCAAGAGTCCCCTCCAACCGTTCAAGAGGCCA
* *
135474 CTATCATCCCTCAAGAGTCCCC-CCCACCGTTCAAGAGGCCA
1 CTGTCATCCCTCAAGAGTCCCCTCCAACCGTTCAAGAGGCCA
135515 CTGTCATC
1 CTGTCATC
135523 GTTGAAGAGG
Statistics
Matches: 43, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
41 23 0.53
42 20 0.47
ACGTcount: A:0.22, C:0.41, G:0.15, T:0.22
Consensus pattern (42 bp):
CTGTCATCCCTCAAGAGTCCCCTCCAACCGTTCAAGAGGCCA
Found at i:137407 original size:19 final size:19
Alignment explanation
Indices: 137385--137482 Score: 90
Period size: 19 Copynumber: 5.7 Consensus size: 19
137375 GGAAATTACT
137385 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
137404 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
137418 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
**
137437 ATCGCAA--CG--A-GGGA
1 ATCGCAATGCGAAATGAAA
137451 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
137470 ATCGCAACGCGAA
1 ATCGCAATGCGAA
137483 TTTAGTTTCG
Statistics
Matches: 62, Mismatches: 7, Indels: 20
0.70 0.08 0.22
Matches are distributed among these distances:
14 19 0.31
15 2 0.03
16 4 0.06
17 4 0.06
18 2 0.03
19 31 0.50
ACGTcount: A:0.44, C:0.19, G:0.24, T:0.12
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:137427 original size:33 final size:33
Alignment explanation
Indices: 137385--137478 Score: 179
Period size: 33 Copynumber: 2.8 Consensus size: 33
137375 GGAAATTACT
137385 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
*
137418 ATCGCAATGCGAAATGAAAATCGCAACGAGGGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
137451 ATCGCAATGCGAAATGAAAATCGCAACG
1 ATCGCAATGCGAAATGAAAATCGCAACG
137479 CGAATTTAGT
Statistics
Matches: 60, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 60 1.00
ACGTcount: A:0.44, C:0.19, G:0.24, T:0.13
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:137513 original size:19 final size:18
Alignment explanation
Indices: 137478--137605 Score: 92
Period size: 19 Copynumber: 7.3 Consensus size: 18
137468 AAATCGCAAC
*
137478 GCGAATTTAGTTTCGCGTT
1 GCGATTTTA-TTTCGCGTT
137497 GCGATTTTAGTTTCGCGTT
1 GCGATTTTA-TTTCGCGTT
*
137516 GCGA-TTT-TGT--CGTT
1 GCGATTTTATTTCGCGTT
*
137530 GCGATTTTCATTTCGCATT
1 GCGATTTT-ATTTCGCGTT
* * *
137549 ACGA---T-TCTCTCGTT
1 GCGATTTTATTTCGCGTT
137563 GCGATTTTCATTTCGCGTT
1 GCGATTTT-ATTTCGCGTT
*
137582 GCGATTTTCATTTCGCATT
1 GCGATTTT-ATTTCGCGTT
137601 GCGAT
1 GCGAT
137606 AGTACTTTTT
Statistics
Matches: 87, Mismatches: 12, Indels: 20
0.73 0.10 0.17
Matches are distributed among these distances:
14 17 0.20
15 3 0.03
16 3 0.03
17 3 0.03
18 3 0.03
19 58 0.67
ACGTcount: A:0.13, C:0.20, G:0.22, T:0.45
Consensus pattern (18 bp):
GCGATTTTATTTCGCGTT
Found at i:137535 original size:33 final size:33
Alignment explanation
Indices: 137488--137590 Score: 145
Period size: 33 Copynumber: 3.1 Consensus size: 33
137478 GCGAATTTAG
*
137488 TTTCGCGTTGCGATTTT-AGTTTCGCGTTGCGAT
1 TTTCTCGTTGCGATTTTCA-TTTCGCGTTGCGAT
* * *
137521 TTTGTCGTTGCGATTTTCATTTCGCATTACGAT
1 TTTCTCGTTGCGATTTTCATTTCGCGTTGCGAT
*
137554 TCTCTCGTTGCGATTTTCATTTCGCGTTGCGAT
1 TTTCTCGTTGCGATTTTCATTTCGCGTTGCGAT
137587 TTTC
1 TTTC
137591 ATTTCGCATT
Statistics
Matches: 60, Mismatches: 9, Indels: 2
0.85 0.13 0.03
Matches are distributed among these distances:
33 59 0.98
34 1 0.02
ACGTcount: A:0.11, C:0.20, G:0.21, T:0.48
Consensus pattern (33 bp):
TTTCTCGTTGCGATTTTCATTTCGCGTTGCGAT
Found at i:137731 original size:14 final size:14
Alignment explanation
Indices: 137712--137747 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
137702 CATCAATTAA
137712 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
137726 ACAAATCACCTTTT
1 ACAAATCAACTTTT
137740 ACAAATCA
1 ACAAATCA
137748 TTAAACAATC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.44, C:0.25, G:0.00, T:0.31
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:139162 original size:21 final size:21
Alignment explanation
Indices: 139096--139162 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
139086 GTGAATCGGG
*
139096 CTCTTGAATGGTGGGA-GGGA
1 CTCTTGAACGGTGGGAGGGGA
* * ** * *
139116 CCTCTTCAACGATGACAGTGGC
1 -CTCTTGAACGGTGGGAGGGGA
139138 CTCTTGAACGGTGGGAGGGGA
1 CTCTTGAACGGTGGGAGGGGA
139159 CTCT
1 CTCT
139163 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:139553 original size:13 final size:13
Alignment explanation
Indices: 139535--139559 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
139525 TTACTTCAAC
139535 CAAAAAGACAAAA
1 CAAAAAGACAAAA
139548 CAAAAAGACAAA
1 CAAAAAGACAAA
139560 TACTAACTTC
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:0.76, C:0.16, G:0.08, T:0.00
Consensus pattern (13 bp):
CAAAAAGACAAAA
Found at i:139619 original size:92 final size:90
Alignment explanation
Indices: 139436--139621 Score: 268
Period size: 92 Copynumber: 2.0 Consensus size: 90
139426 ATTTCAAACT
139436 TTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGTTTAGC
1 TTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAAT--A-AGTTTAGC
* *
139501 AGAATTGGCAGCAATCGAATAAATTTAC
63 AGAATTAGCAGCAACCGAATAAATTTAC
139529 TTCAACCAAAAAGACAAAACAAAAAGACAAATACTAACTTCACAGTGTTAATA-AAT-AGTTTAG
1 TTCAACC-AAAAGACAAAAC--AAAGACAAATACTAACTTCACAGTGTTAA-AGAATAAGTTTAG
*
139592 CAGTATTAGCAGCAACCGAATAAATTTAC
62 CAGAATTAGCAGCAACCGAATAAATTTAC
139621 T
1 T
139622 AAGCAATCTA
Statistics
Matches: 86, Mismatches: 3, Indels: 9
0.88 0.03 0.09
Matches are distributed among these distances:
92 34 0.40
93 7 0.08
94 12 0.14
96 32 0.37
97 1 0.01
ACGTcount: A:0.48, C:0.18, G:0.12, T:0.23
Consensus pattern (90 bp):
TTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATAAGTTTAGCAGA
ATTAGCAGCAACCGAATAAATTTAC
Found at i:141047 original size:19 final size:19
Alignment explanation
Indices: 140963--141093 Score: 146
Period size: 19 Copynumber: 7.1 Consensus size: 19
140953 TCTTTTGGTT
*
140963 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGC
**
140982 GATAATGACTATCGCAACGC
1 GA-AATGAAAATCGCAACGC
**
141002 GAAATGACTATCGCAACGC
1 GAAATGAAAATCGCAACGC
141021 GAAATGAAAATCGCAACGC
1 GAAATGAAAATCGCAACGC
*
141040 GAAATGAAAAACGCAA--C
1 GAAATGAAAATCGCAACGC
*
141057 G--A-GAGAATCGCAACGC
1 GAAATGAAAATCGCAACGC
*
141073 GAAATGAAAATCGCAATGC
1 GAAATGAAAATCGCAACGC
141092 GA
1 GA
141094 TTTTGGTTTC
Statistics
Matches: 96, Mismatches: 10, Indels: 12
0.81 0.08 0.10
Matches are distributed among these distances:
14 9 0.09
15 1 0.01
16 2 0.02
17 2 0.02
18 1 0.01
19 65 0.68
20 16 0.17
ACGTcount: A:0.45, C:0.21, G:0.22, T:0.12
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGC
Found at i:141122 original size:19 final size:19
Alignment explanation
Indices: 141089--141133 Score: 72
Period size: 19 Copynumber: 2.4 Consensus size: 19
141079 AAAATCGCAA
*
141089 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGATTTCGCGT
*
141108 TGCGATTTTTATTTCGCGT
1 TGCGATTTTGATTTCGCGT
141127 TGCGATT
1 TGCGATT
141134 CTCTCGTTGC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.09, C:0.16, G:0.27, T:0.49
Consensus pattern (19 bp):
TGCGATTTTGATTTCGCGT
Found at i:141740 original size:20 final size:20
Alignment explanation
Indices: 141688--141922 Score: 120
Period size: 20 Copynumber: 11.6 Consensus size: 20
141678 GCTATGTAAA
* *
141688 TCGCATTGCGATAGTAAG-AT
1 TCGCATTGCGAT-TTACGTAT
141708 TCGCATTGCGATTTACGTAT
1 TCGCATTGCGATTTACGTAT
* *
141728 TCGCATTGCGATTTTCCTAAT
1 TCGCATTGCGATTTACGT-AT
* * *
141749 TCGCATTGTGATTTACTTAA
1 TCGCATTGCGATTTACGTAT
*
141769 TCGCGTTGCGATTTACGTAT
1 TCGCATTGCGATTTACGTAT
* * * * *
141789 TCGCATTACGAATTATGAAAA
1 TCGCATTGCGATTTACG-TAT
** * *
141810 TCGCAACGCGA-ATACGTAAA
1 TCGCATTGCGATTTACGT-AT
* * * *
141830 TCGCAATGCGAATTAGGAAAAT
1 TCGCATTGCGATTTACG--TAT
*
141852 T-GCATTGCGATAGT-CAGTA-
1 TCGCATTGCGAT-TTAC-GTAT
* **
141871 TCGCATTGCGATTTTTCAAAT
1 TCGCATTGCGA-TTTACGTAT
*
141892 TCGCATTGCGATTTACTTAT
1 TCGCATTGCGATTTACGTAT
141912 TCGCATTGCGA
1 TCGCATTGCGA
141923 ATTGGGAAAA
Statistics
Matches: 162, Mismatches: 40, Indels: 26
0.71 0.18 0.11
Matches are distributed among these distances:
19 4 0.02
20 104 0.64
21 50 0.31
22 4 0.02
ACGTcount: A:0.27, C:0.19, G:0.20, T:0.34
Consensus pattern (20 bp):
TCGCATTGCGATTTACGTAT
Found at i:141812 original size:41 final size:41
Alignment explanation
Indices: 141685--141937 Score: 149
Period size: 41 Copynumber: 6.2 Consensus size: 41
141675 GGCGCTATGT
* * * *
141685 AAATCGCATTGCGATAGTAAG-ATTCGCATTGCGATTTACG-
1 AAATCGCATTGCGAT-TTACGTATTCGCATTGCGAATTAGGA
* * * * * * **
141725 TATTCGCATTGCGATTTTCCTAATTCGCATTGTGATTTA-CT
1 AAATCGCATTGCGATTTACGT-ATTCGCATTGCGAATTAGGA
* * * *
141766 TAATCGCGTTGCGATTTACGTATTCGCATTACGAATTATGA
1 AAATCGCATTGCGATTTACGTATTCGCATTGCGAATTAGGA
** * * *
141807 AAATCGCAACGCGA-ATACGTAAATCGCAATGCGAATTAGGA
1 AAATCGCATTGCGATTTACGT-ATTCGCATTGCGAATTAGGA
* * * ***
141848 AAATTGCATTGCGATAGT-CAGTA-TCGCATTGCGATTTTTCA
1 AAATCGCATTGCGAT-TTAC-GTATTCGCATTGCGAATTAGGA
* * *
141889 AATTCGCATTGCGATTTACTTATTCGCATTGCGAATTGGGA
1 AAATCGCATTGCGATTTACGTATTCGCATTGCGAATTAGGA
141930 AAATCGCA
1 AAATCGCA
141938 ACGCGAAATT
Statistics
Matches: 159, Mismatches: 44, Indels: 19
0.72 0.20 0.09
Matches are distributed among these distances:
39 1 0.01
40 35 0.22
41 118 0.74
42 2 0.01
43 3 0.02
ACGTcount: A:0.29, C:0.18, G:0.20, T:0.33
Consensus pattern (41 bp):
AAATCGCATTGCGATTTACGTATTCGCATTGCGAATTAGGA
Found at i:141860 original size:21 final size:21
Alignment explanation
Indices: 141797--141861 Score: 69
Period size: 21 Copynumber: 3.1 Consensus size: 21
141787 ATTCGCATTA
* *
141797 CGAATTATGAAAATCGCAACG
1 CGAATTACGAAAATCGCAATG
*
141818 CGAA-TACGTAAATCGCAATG
1 CGAATTACGAAAATCGCAATG
* * *
141838 CGAATTAGGAAAATTGCATTG
1 CGAATTACGAAAATCGCAATG
141859 CGA
1 CGA
141862 TAGTCAGTAT
Statistics
Matches: 36, Mismatches: 7, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 17 0.47
21 19 0.53
ACGTcount: A:0.40, C:0.17, G:0.22, T:0.22
Consensus pattern (21 bp):
CGAATTACGAAAATCGCAATG
Found at i:141964 original size:21 final size:22
Alignment explanation
Indices: 141912--141964 Score: 74
Period size: 21 Copynumber: 2.5 Consensus size: 22
141902 ATTTACTTAT
141912 TCGCATTGCG-AATTGGGAAAA
1 TCGCATTGCGAAATTGGGAAAA
**
141933 TCGCAACGCGAAATT-GGAAAA
1 TCGCATTGCGAAATTGGGAAAA
141954 TCGCATTGCGA
1 TCGCATTGCGA
141965 TAGTCATAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
21 23 0.85
22 4 0.15
ACGTcount: A:0.34, C:0.19, G:0.26, T:0.21
Consensus pattern (22 bp):
TCGCATTGCGAAATTGGGAAAA
Found at i:148667 original size:16 final size:17
Alignment explanation
Indices: 148631--148675 Score: 56
Period size: 16 Copynumber: 2.7 Consensus size: 17
148621 TTAAAAAAAT
**
148631 ATAATAAAATAAATTAA
1 ATAATAAAATAAAGAAA
148648 ATAATAAAA-AAAGAAA
1 ATAATAAAATAAAGAAA
*
148664 ATAATATAATAA
1 ATAATAAAATAA
148676 TGAATATTAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
16 13 0.54
17 11 0.46
ACGTcount: A:0.73, C:0.00, G:0.02, T:0.24
Consensus pattern (17 bp):
ATAATAAAATAAAGAAA
Found at i:149486 original size:57 final size:56
Alignment explanation
Indices: 149368--149487 Score: 127
Period size: 57 Copynumber: 2.1 Consensus size: 56
149358 TTAAAAGACT
* * **
149368 TAAAACTATTTAAACTAAAATACCTAAAAAATAATATAATATTCTAAATCCTATAC
1 TAAAACTATTTAAACTAAAATACCTAAAAAATAAGATAATATTATAAATAATATAC
* * * *
149424 AAAAACATATTTAAGCTAAAATACCTAAAACA-AAGATAA-ATTATAAAAATAATATTC
1 TAAAAC-TATTTAAACTAAAATACCTAAAAAATAAGATAATATTAT--AAATAATATAC
149481 TAAAACT
1 TAAAACT
149488 TAATTAAAAT
Statistics
Matches: 52, Mismatches: 9, Indels: 6
0.78 0.13 0.09
Matches are distributed among these distances:
55 4 0.08
56 12 0.23
57 36 0.69
ACGTcount: A:0.57, C:0.12, G:0.02, T:0.29
Consensus pattern (56 bp):
TAAAACTATTTAAACTAAAATACCTAAAAAATAAGATAATATTATAAATAATATAC
Found at i:149623 original size:76 final size:76
Alignment explanation
Indices: 149420--149599 Score: 324
Period size: 76 Copynumber: 2.4 Consensus size: 76
149410 TCTAAATCCT
* * *
149420 ATACAAAAACATATTTAAGCTAAAATACCTAAAACAAAGATAAATTATAAAAATAATATTCTAAA
1 ATACTAAAACCTATTTAAACTAAAATACCTAAAACAAAGATAAATTATAAAAATAATATTCTAAA
149485 ACTTAATTAAA
66 ACTTAATTAAA
149496 ATACTAAAACCTATTTAAACTAAAATACCTAAAACAAAGATAAATTATAAAAATAATATTCTAAA
1 ATACTAAAACCTATTTAAACTAAAATACCTAAAACAAAGATAAATTATAAAAATAATATTCTAAA
149561 ACTTAATTAAA
66 ACTTAATTAAA
*
149572 ATATTAAAACCTATTTAAACTAAAATAC
1 ATACTAAAACCTATTTAAACTAAAATAC
149600 AAAGATAAAA
Statistics
Matches: 100, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
76 100 1.00
ACGTcount: A:0.58, C:0.12, G:0.02, T:0.29
Consensus pattern (76 bp):
ATACTAAAACCTATTTAAACTAAAATACCTAAAACAAAGATAAATTATAAAAATAATATTCTAAA
ACTTAATTAAA
Found at i:149931 original size:245 final size:247
Alignment explanation
Indices: 149500--149991 Score: 862
Period size: 245 Copynumber: 2.0 Consensus size: 247
149490 ATTAAAATAC
149500 TAAAACCTATTTAAACTAAAATACCTAAAACAAAGATAAATTATAAAAATAATATTCTAAAACTT
1 TAAAACCTATTTAAACTAAAATACCTAAAACAAAGATAAATTATAAAAATAATATTCTAAAACTT
149565 AATTAAAATATTAAAACCTATTTAAACTAAAATACAAAGATAAAATATAATGTTTAAAATATTAT
66 AATTAAAATATTAAAACCTATTTAAACTAAAATACAAAGATAAAATATAATGTTTAAAATATTAT
* * ** *
149630 CCTAAACTTGAGTTTAATCCAAATCCGAATTCTAACCAGTTTTGATTCTGAAAAT-AAAGAATCT
131 CCTAAACTTGAGTTTAATCCAAATCCGAATTCCAACCAGCTTTGATTCCAAAAATAAAAAAATCT
* * **
149694 ACAGAATTGTGTTTTTT-TATGCAATTTCTATAATCTTATGTCCTGTACAGA
196 ACAGAATTGTATTTTTTGTATGCAATTTCCATAATCTTACATCCTGTACAGA
*
149745 TAAAACCTATTTAAACTAAAATACCTAAAACAAAGATAAATTATGAAAATAATATTCTAAAACTT
1 TAAAACCTATTTAAACTAAAATACCTAAAACAAAGATAAATTATAAAAATAATATTCTAAAACTT
*
149810 AATTAAAATATTAAAACCTATTTAAACTAAAATACAAAGATAAAATATAATGTTTAAAATGTTAT
66 AATTAAAATATTAAAACCTATTTAAACTAAAATACAAAGATAAAATATAATGTTTAAAATATTAT
149875 CCTAAACTTGAGTTTAATCCAAATCCGAATTCCAACCAGCTTTGATTCCAAAAATAAAAAAATCT
131 CCTAAACTTGAGTTTAATCCAAATCCGAATTCCAACCAGCTTTGATTCCAAAAATAAAAAAATCT
*
149940 ACAGAATTGTATTTTTTGTGTGCAATTTCCATAATCTTACATCCTGTACAGA
196 ACAGAATTGTATTTTTTGTATGCAATTTCCATAATCTTACATCCTGTACAGA
149992 AAATGAATTA
Statistics
Matches: 233, Mismatches: 12, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
245 179 0.77
246 24 0.10
247 30 0.13
ACGTcount: A:0.46, C:0.14, G:0.07, T:0.34
Consensus pattern (247 bp):
TAAAACCTATTTAAACTAAAATACCTAAAACAAAGATAAATTATAAAAATAATATTCTAAAACTT
AATTAAAATATTAAAACCTATTTAAACTAAAATACAAAGATAAAATATAATGTTTAAAATATTAT
CCTAAACTTGAGTTTAATCCAAATCCGAATTCCAACCAGCTTTGATTCCAAAAATAAAAAAATCT
ACAGAATTGTATTTTTTGTATGCAATTTCCATAATCTTACATCCTGTACAGA
Found at i:150273 original size:2 final size:2
Alignment explanation
Indices: 150266--150313 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
150256 GATGTTACAA
150266 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
150308 AT AT AT
1 AT AT AT
150314 TAAGTTTAAA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:155677 original size:23 final size:23
Alignment explanation
Indices: 155611--155696 Score: 88
Period size: 23 Copynumber: 3.7 Consensus size: 23
155601 TCATATAAAT
155611 TTGCACCGAAGTGCCACGTAGAA
1 TTGCACCGAAGTGCCACGTAGAA
* *
155634 TTTGTC-CCGAAAG-ACCGCGTAGAGA
1 -TTG-CACCG-AAGTGCCACGTAGA-A
155659 -TGCACCGAAGTGCCACGTAGAA
1 TTGCACCGAAGTGCCACGTAGAA
*
155681 TTGCACCGTAGTGCCA
1 TTGCACCGAAGTGCCA
155697 TATAATATGT
Statistics
Matches: 51, Mismatches: 5, Indels: 13
0.74 0.07 0.19
Matches are distributed among these distances:
22 5 0.10
23 27 0.53
24 14 0.27
25 5 0.10
ACGTcount: A:0.28, C:0.27, G:0.27, T:0.19
Consensus pattern (23 bp):
TTGCACCGAAGTGCCACGTAGAA
Found at i:159483 original size:2 final size:2
Alignment explanation
Indices: 159476--159509 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
159466 GATAGAAGTG
159476 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
159510 TACATAAGCT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:159948 original size:22 final size:22
Alignment explanation
Indices: 159920--160009 Score: 144
Period size: 22 Copynumber: 4.1 Consensus size: 22
159910 AGTCGAGGGT
159920 TATACAGTGGTCCTTCGGGACA
1 TATACAGTGGTCCTTCGGGACA
*
159942 TATACAGTGGTCTTTCGGGACA
1 TATACAGTGGTCCTTCGGGACA
159964 TATACAGTGGTCCTTCGGGACA
1 TATACAGTGGTCCTTCGGGACA
* **
159986 TATACAATGGTTTTTCGGGACA
1 TATACAGTGGTCCTTCGGGACA
160008 TA
1 TA
160010 ATGGTCCTTC
Statistics
Matches: 63, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 63 1.00
ACGTcount: A:0.24, C:0.19, G:0.26, T:0.31
Consensus pattern (22 bp):
TATACAGTGGTCCTTCGGGACA
Done.