Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013878.1 Kokia drynarioides strain JFW-HI SEQ_128906, 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: 323362
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 33 characters in sequence are not A, C, G, or T
File 1 of 2
Found at i:5704 original size:16 final size:16
Alignment explanation
Indices: 5660--5706 Score: 51
Period size: 16 Copynumber: 2.9 Consensus size: 16
5650 GGGGAATGTG
*
5660 TAAAAAAACAT-AAATA
1 TAAATAAACATGAAA-A
*
5676 TAAATAGACATGAAAA
1 TAAATAAACATGAAAA
*
5692 TAAATAAAGATGAAA
1 TAAATAAACATGAAA
5707 TAAGAATAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
16 23 0.88
17 3 0.12
ACGTcount: A:0.68, C:0.04, G:0.09, T:0.19
Consensus pattern (16 bp):
TAAATAAACATGAAAA
Found at i:6663 original size:155 final size:153
Alignment explanation
Indices: 6266--7025 Score: 760
Period size: 146 Copynumber: 5.0 Consensus size: 153
6256 GCAAAATTAA
** * *
6266 TTTTTTTTTTGT-AAGCAAAATCGTTACTTTTCTTAAAAATCAAAACTTTTATTTTGAAAT-GAT
1 TTTTTTTTTT-TAAAG-AAAATCACTATTTTTCTTAAAAATCAAAACTTTTATTTCGAAATAG-T
* * *
6329 TAAGAAAAATC-AAACTTTATTTAAAAATTTAAACTTTTTTCTTTAAAATGACTAAAAACATA--
63 TAAAAAAAATCAAAACTTTGTTTAAAAATTTAAAC-TTTTACTTTAAAATGACTAAAAA-ATAGT
* *
6391 TTTTTATTTTTAAAAACCTATA-TTTTC
126 TTTTTATTTTTAAAAATCTAAACTTTTC
* * * * * * * *
6418 TCTTTCTTTTAAAAAAAAATCACTATTTTTCTTAAAAATGAAAACTTTTATTTTGAAACACTTAA
1 TTTTTTTTTTTAAAGAAAATCACTATTTTTCTTAAAAATCAAAACTTTTATTTCGAAATAGTT--
* * **
6483 AAAAAAAATAAAAAACTTTGTTTAAAAATTTAAAATTTTAAATTAAAATGACTAAAAAATAGTTT
64 AAAAAAAAT-CAAAACTTTGTTTAAAAATTTAAACTTTTACTTTAAAATGACTAAAAAATAGTTT
* *
6548 TTTATTTTTTAAAATCTAAACTTTTT
128 TTTATTTTTAAAAATCTAAACTTTTC
* *
6574 TTTTTTTTTTTTAAGAAAATCACTATTTTTCTTAAAAAT-AAAATTTTTTATTTCGAAATAGTTA
1 TTTTTTTTTTTAAAGAAAATCACTATTTTTCTTAAAAATCAAAA-CTTTTATTTCGAAATAGTT-
** *
6638 AAAAAAAAATCAAAACTTTGTTTAAAAATTTAAACTTTTAAATTATAATGACT-AAAAATAGTTT
64 -AAAAAAAATCAAAACTTTGTTTAAAAATTTAAACTTTTACTTTAAAATGACTAAAAAATAGTTT
6702 TTTATTTTTAAAAATCTAAA-----C
128 TTTATTTTTAAAAATCTAAACTTTTC
* * * * * * *
6723 -TTTTATTTTTAAATAAAATCACTATTTTTATTAAAAATAAAAAATTTTTATTTCAAAATAATT-
1 TTTTTTTTTTTAAAGAAAATCACTATTTTTCTTAAAAAT-CAAAACTTTTATTTCGAAATAGTTA
* ** *
6786 AAAAAAGTCAAAACTTTGTTTAAAAATTTAAACTTTT-CTTTAAAATGTTTAAAAAA-ACATATT
65 AAAAAAATCAAAACTTTGTTTAAAAATTTAAACTTTTACTTTAAAATGACTAAAAAATA-GT-TT
**
6849 TTTATTTAAAAAAATCTAAAC-TTTC
128 TTTATTTTTAAAAATCTAAACTTTTC
* * * *
6874 ---TATTTTTTAAAGAAAGA-CATTATTTTTCTTAAAAATCGAAACTTTTATTTCTAAATAGTT-
1 TTTTTTTTTTTAAAGAAA-ATCACTATTTTTCTTAAAAATCAAAACTTTTATTTCGAAATAGTTA
* * * *
6934 --AAAAATCAAAATTTTATTTAAAAATTTAAATTTTTTCTTTAAAATGACTAAAAAATAGTTTTT
65 AAAAAAATCAAAACTTTGTTTAAAAATTTAAACTTTTACTTTAAAATGACTAAAAAATAGTTTTT
*
6997 TATTTTTAAAAATTTAAACTTTTC
130 TATTTTTAAAAATCTAAACTTTTC
7021 TTTTT
1 TTTTT
7026 AAAAAATTAA
Statistics
Matches: 511, Mismatches: 71, Indels: 54
0.80 0.11 0.08
Matches are distributed among these distances:
145 9 0.02
146 93 0.18
147 42 0.08
148 54 0.11
149 46 0.09
150 6 0.01
151 42 0.08
152 10 0.02
153 11 0.02
154 50 0.10
155 84 0.16
156 64 0.13
ACGTcount: A:0.44, C:0.08, G:0.04, T:0.45
Consensus pattern (153 bp):
TTTTTTTTTTTAAAGAAAATCACTATTTTTCTTAAAAATCAAAACTTTTATTTCGAAATAGTTAA
AAAAAATCAAAACTTTGTTTAAAAATTTAAACTTTTACTTTAAAATGACTAAAAAATAGTTTTTT
ATTTTTAAAAATCTAAACTTTTC
Found at i:6860 original size:49 final size:50
Alignment explanation
Indices: 6804--7023 Score: 133
Period size: 49 Copynumber: 4.5 Consensus size: 50
6794 CAAAACTTTG
6804 TTTAAAAATTTAAACTTTTCTTTAAAATGTTTAAAAAA-ACATATTTTTA
1 TTTAAAAATTTAAACTTTTCTTTAAAATGTTTAAAAAAGACATATTTTTA
*
6853 TTTAAAAAAATCTAAAC-TTTCTATT----T-TTTAAAGAAAGACATTATTTTT-
1 TTT--AAAAATTTAAACTTTTCT-TTAAAATGTTTAAA-AAAGACA-TATTTTTA
* ** * * * * *
6901 CTTAAAAATCGAAACTTTTATTTCTAAATAG-TT-AAAAA-TCAAAATTTTA
1 TTTAAAAATTTAAACTTTTCTTT-AAAAT-GTTTAAAAAAGACATATTTTTA
* ** * *
6950 TTTAAAAATTTAAATTTTTTCTTTAAAATGACTAAAAAATA-GT-TTTTTA
1 TTTAAAAATTTAAA-CTTTTCTTTAAAATGTTTAAAAAAGACATATTTTTA
6999 TTTTTAAAAATTTAAACTTTTCTTT
1 --TTTAAAAATTTAAACTTTTCTTT
7024 TTAAAAAATT
Statistics
Matches: 131, Mismatches: 19, Indels: 41
0.69 0.10 0.21
Matches are distributed among these distances:
46 19 0.15
47 8 0.06
48 11 0.08
49 33 0.25
50 28 0.21
51 30 0.23
52 2 0.02
ACGTcount: A:0.43, C:0.07, G:0.03, T:0.47
Consensus pattern (50 bp):
TTTAAAAATTTAAACTTTTCTTTAAAATGTTTAAAAAAGACATATTTTTA
Found at i:6958 original size:29 final size:30
Alignment explanation
Indices: 6902--6958 Score: 80
Period size: 29 Copynumber: 1.9 Consensus size: 30
6892 ATTATTTTTC
* **
6902 TTAAAAATCGAAACTTTTATTTCTAAATAG
1 TTAAAAATCGAAAATTTTATTTAAAAATAG
6932 TTAAAAATC-AAAATTTTATTTAAAAAT
1 TTAAAAATCGAAAATTTTATTTAAAAAT
6959 TTAAATTTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
29 15 0.62
30 9 0.38
ACGTcount: A:0.49, C:0.07, G:0.04, T:0.40
Consensus pattern (30 bp):
TTAAAAATCGAAAATTTTATTTAAAAATAG
Found at i:7019 original size:22 final size:22
Alignment explanation
Indices: 6994--7041 Score: 69
Period size: 22 Copynumber: 2.2 Consensus size: 22
6984 AAAAATAGTT
* *
6994 TTTTATTTTTAAAAATTTAAAC
1 TTTTATTTTTAAAAAATTAAAA
*
7016 TTTTCTTTTTAAAAAATTAAAA
1 TTTTATTTTTAAAAAATTAAAA
7038 TTTT
1 TTTT
7042 TCCCAAGATC
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.40, C:0.04, G:0.00, T:0.56
Consensus pattern (22 bp):
TTTTATTTTTAAAAAATTAAAA
Found at i:7025 original size:23 final size:23
Alignment explanation
Indices: 6994--7043 Score: 66
Period size: 23 Copynumber: 2.2 Consensus size: 23
6984 AAAAATAGTT
* *
6994 TTTTATTTTT-AAAAATTTAAAC
1 TTTTCTTTTTAAAAAATTAAAAC
*
7016 TTTTCTTTTTAAAAAATTAAAAT
1 TTTTCTTTTTAAAAAATTAAAAC
7039 TTTTC
1 TTTTC
7044 CCAAGATCAA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
22 9 0.38
23 15 0.62
ACGTcount: A:0.38, C:0.06, G:0.00, T:0.56
Consensus pattern (23 bp):
TTTTCTTTTTAAAAAATTAAAAC
Found at i:7874 original size:42 final size:42
Alignment explanation
Indices: 7801--8398 Score: 722
Period size: 42 Copynumber: 14.3 Consensus size: 42
7791 TTGAAATGAG
* * *
7801 AATGCTAAAGAAATGTAAAT-AGACCT-CACACCTGGGCCTTTA
1 AATGC-AATGAAAAGTAAATGA-ACCTCCACACCTGGGCCTCTA
*
7843 AATGCAACGAAAAGTAAATGAACCTCCACACCTGGGCCTCTA
1 AATGCAATGAAAAGTAAATGAACCTCCACACCTGGGCCTCTA
* *
7885 AATGCAATGAAAAGTAAATGGACCTCCACACCTGGGCATCTA
1 AATGCAATGAAAAGTAAATGAACCTCCACACCTGGGCCTCTA
* * * *
7927 AATACAATGAAAAGTAAATGGACCTCCACACATGGGCCTCCA
1 AATGCAATGAAAAGTAAATGAACCTCCACACCTGGGCCTCTA
* **
7969 AATGCAATGAAAAGTAAATGGACCTCCACACCTAAGCCTCTA
1 AATGCAATGAAAAGTAAATGAACCTCCACACCTGGGCCTCTA
* * * * *
8011 ATTGCCATGAAAAGTAAATGGACCTCCACACCTAGGCCTTTA
1 AATGCAATGAAAAGTAAATGAACCTCCACACCTGGGCCTCTA
* * *
8053 AATGCGATGAAAAGTAAATGAACCTCCACACTTAGGCCTCTA
1 AATGCAATGAAAAGTAAATGAACCTCCACACCTGGGCCTCTA
* * * *
8095 AATGCAATGAAAAATAAATGGACCTCTACACCTAGGCCTCTA
1 AATGCAATGAAAAGTAAATGAACCTCCACACCTGGGCCTCTA
* *
8137 AATGCGATGAAAAGTAAAT-AGACCTCCACACCTAGGCCTCTA
1 AATGCAATGAAAAGTAAATGA-ACCTCCACACCTGGGCCTCTA
* * *
8179 AATGCGATGAAAAGTAAATG-ACCACCACACCTCGGCCTCTA
1 AATGCAATGAAAAGTAAATGAACCTCCACACCTGGGCCTCTA
* * * * *
8220 AATACGATGAAAAGTAAATGGACTTCCACACTTGGGCCTCTA
1 AATGCAATGAAAAGTAAATGAACCTCCACACCTGGGCCTCTA
* * *
8262 AATGTAATGAAAAGTAAATGAACCTCCACACTTGGGCCTCTC
1 AATGCAATGAAAAGTAAATGAACCTCCACACCTGGGCCTCTA
* *
8304 AATGCAACGAAAAGTAAAT-AGACCTCCACACCTGGGCTTCTA
1 AATGCAATGAAAAGTAAATGA-ACCTCCACACCTGGGCCTCTA
* * *
8346 AATGCAATGAAAAGTAAATGAACCTCCAC-CCTTAGACCTATA
1 AATGCAATGAAAAGTAAATGAACCTCCACACC-TGGGCCTCTA
8388 AATGCAATGAA
1 AATGCAATGAA
8399 TGTTTTCCTT
Statistics
Matches: 492, Mismatches: 56, Indels: 16
0.87 0.10 0.03
Matches are distributed among these distances:
41 57 0.12
42 434 0.88
43 1 0.00
ACGTcount: A:0.38, C:0.25, G:0.16, T:0.20
Consensus pattern (42 bp):
AATGCAATGAAAAGTAAATGAACCTCCACACCTGGGCCTCTA
Found at i:8842 original size:20 final size:20
Alignment explanation
Indices: 8801--8842 Score: 50
Period size: 20 Copynumber: 2.1 Consensus size: 20
8791 GCTCTCTCTA
* *
8801 TTTTTTCTTCTTTTTTTTTG
1 TTTTTTCTTCTTTTCTTGTG
8821 TTTTTTCTATC-TTTCTTGTG
1 TTTTTTCT-TCTTTTCTTGTG
8841 TT
1 TT
8843 ACTTTTCTTG
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 17 0.89
21 2 0.11
ACGTcount: A:0.02, C:0.12, G:0.07, T:0.79
Consensus pattern (20 bp):
TTTTTTCTTCTTTTCTTGTG
Found at i:11432 original size:55 final size:56
Alignment explanation
Indices: 11372--11544 Score: 190
Period size: 55 Copynumber: 3.1 Consensus size: 56
11362 AACGCTCTTT
* *
11372 CCGAGCTGA-AATAGCTTTACGCTCTAACCAAGACGTAAGTAGTCTAAAGCTCTAC
1 CCGAGCTGATAATAGCATTACGCTCTAACCGAGACGTAAGTAGTCTAAAGCTCTAC
* * * * **
11427 CCGAGC-AATAACAGCATTGCGCTCTAACTGAGACGTAAGTAGTCTGTAGCTCTAC
1 CCGAGCTGATAATAGCATTACGCTCTAACCGAGACGTAAGTAGTCTAAAGCTCTAC
* * * * * * *
11482 TCGAGCT-ATAATAGCATTATGCTCTAATCGAGACATAAGCAGGCCAAAGCTCTAC
1 CCGAGCTGATAATAGCATTACGCTCTAACCGAGACGTAAGTAGTCTAAAGCTCTAC
11537 CCGAGCTG
1 CCGAGCTG
11545 TAAGTAAATC
Statistics
Matches: 94, Mismatches: 21, Indels: 5
0.78 0.17 0.04
Matches are distributed among these distances:
54 1 0.01
55 93 0.99
ACGTcount: A:0.31, C:0.25, G:0.20, T:0.23
Consensus pattern (56 bp):
CCGAGCTGATAATAGCATTACGCTCTAACCGAGACGTAAGTAGTCTAAAGCTCTAC
Found at i:11548 original size:28 final size:28
Alignment explanation
Indices: 11516--11576 Score: 77
Period size: 28 Copynumber: 2.2 Consensus size: 28
11506 TAATCGAGAC
**
11516 ATAAGCAGGCCAAAGCTCTACCCGAGCT
1 ATAAGCAAACCAAAGCTCTACCCGAGCT
* * *
11544 GTAAGTAAATCAAAGCTCTACCCGAGCT
1 ATAAGCAAACCAAAGCTCTACCCGAGCT
11572 ATAAG
1 ATAAG
11577 TAGAGTATTG
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.36, C:0.26, G:0.20, T:0.18
Consensus pattern (28 bp):
ATAAGCAAACCAAAGCTCTACCCGAGCT
Found at i:31144 original size:28 final size:30
Alignment explanation
Indices: 31112--31212 Score: 125
Period size: 30 Copynumber: 3.4 Consensus size: 30
31102 AAAGGGTCGA
* *
31112 AAAATGAAATTTCAGAGAA-TTT-AGGGTT
1 AAAATGTAATTTCAGAAAATTTTAAGGGTT
**
31140 AAAATGTAATTTTGGAAAATTTTAAGGGTT
1 AAAATGTAATTTCAGAAAATTTTAAGGGTT
**
31170 AAAATGTAATTTTGGAAAATTTTTAAGGGTT
1 AAAATGTAATTTCAGAAAA-TTTTAAGGGTT
31201 AAAATGTAATTT
1 AAAATGTAATTT
31213 TTAGGAAGCT
Statistics
Matches: 66, Mismatches: 4, Indels: 3
0.90 0.05 0.04
Matches are distributed among these distances:
28 15 0.23
29 3 0.05
30 25 0.38
31 23 0.35
ACGTcount: A:0.42, C:0.01, G:0.19, T:0.39
Consensus pattern (30 bp):
AAAATGTAATTTCAGAAAATTTTAAGGGTT
Found at i:31270 original size:30 final size:29
Alignment explanation
Indices: 31222--31371 Score: 144
Period size: 29 Copynumber: 5.1 Consensus size: 29
31212 TTTAGGAAGC
31222 TTGGG-GTCAAAATGTGATTTTGGAAAGGT
1 TTGGGAGTCAAAATGTGATTTTGGAAA-GT
* * *
31251 TTGGTAGTAAAAATATGATTTTGGGAAAGT
1 TTGGGAGTCAAAATGTGATTTT-GGAAAGT
* * *
31281 TTGGGGGTCAAGATGTGATTTTGGGAAGT
1 TTGGGAGTCAAAATGTGATTTTGGAAAGT
31310 TTGAGGA-TCAAAATGTGATTTTGGAAAAG-
1 TTG-GGAGTCAAAATGTGATTTTGG-AAAGT
* * **
31339 TTAGGTGTCAAAATGCAATTTTGGAAAAGT
1 TTGGGAGTCAAAATGTGATTTTGG-AAAGT
31369 TTG
1 TTG
31372 AGGATTAAAA
Statistics
Matches: 98, Mismatches: 17, Indels: 11
0.78 0.13 0.09
Matches are distributed among these distances:
28 2 0.02
29 51 0.52
30 40 0.41
31 5 0.05
ACGTcount: A:0.31, C:0.03, G:0.31, T:0.35
Consensus pattern (29 bp):
TTGGGAGTCAAAATGTGATTTTGGAAAGT
Found at i:31384 original size:30 final size:30
Alignment explanation
Indices: 31134--31550 Score: 223
Period size: 30 Copynumber: 14.0 Consensus size: 30
31124 CAGAGAATTT
* *
31134 AGGGTTAAAATGTAATTTTGGAAAATTTTA
1 AGGGTTAAAATGTAATTTTGGAAAAGTTTG
* *
31164 AGGGTTAAAATGTAATTTTGGAAAATTTTTA
1 AGGGTTAAAATGTAATTTTGGAAAA-GTTTG
*
31195 AGGGTTAAAATGTAATTTTTAGG--AAGCTTG
1 AGGGTTAAAATGTAA-TTTT-GGAAAAGTTTG
* * *
31225 -GGGTCAAAATGTGATTTTGGAAAGGTTTG
1 AGGGTTAAAATGTAATTTTGGAAAAGTTTG
* * * * *
31254 -GTAGTAAAAATATGATTTTGGGAAAGTTTG
1 AG-GGTTAAAATGTAATTTTGGAAAAGTTTG
* * * * *
31284 GGGGTCAAGATGTGATTTTGG-GAAGTTTG
1 AGGGTTAAAATGTAATTTTGGAAAAGTTTG
* * *
31313 AGGATCAAAATGTGATTTTGGAAAAG-TT-
1 AGGGTTAAAATGTAATTTTGGAAAAGTTTG
* *
31341 AGGTGTCAAAATGCAATTTTGGAAAAGTTTG
1 AGG-GTTAAAATGTAATTTTGGAAAAGTTTG
* * ** ** *
31372 AGGATTAAAATGCAACATTATAAGAGTTT-
1 AGGGTTAAAATGTAATTTTGGAAAAGTTTG
* * ** *
31401 AGGGGCTAAAATTTAATTTTAAAAAAGTTTA
1 A-GGGTTAAAATGTAATTTTGGAAAAGTTTG
* *
31432 AGGGTTAAAAATGTAATTTTGGAGAAGTTCG
1 AGGGTT-AAAATGTAATTTTGGAAAAGTTTG
** * *
31463 -GGGTTAAAATACAATTTT-GAATGAGTTCG
1 AGGGTTAAAATGTAATTTTGGAA-AAGTTTG
* * *
31492 -GAGGCTAAAATGTAATTTTAGAGAAGTTT-
1 AG-GGTTAAAATGTAATTTTGGAAAAGTTTG
* *
31521 AGGAGTCAAAATGCT-A-TTTGGAAGAGTTTG
1 AGG-GTTAAAATG-TAATTTTGGAAAAGTTTG
31551 GGGGCTCTTT
Statistics
Matches: 305, Mismatches: 61, Indels: 42
0.75 0.15 0.10
Matches are distributed among these distances:
27 2 0.01
28 9 0.03
29 95 0.31
30 145 0.48
31 48 0.16
32 4 0.01
33 2 0.01
ACGTcount: A:0.36, C:0.04, G:0.26, T:0.35
Consensus pattern (30 bp):
AGGGTTAAAATGTAATTTTGGAAAAGTTTG
Found at i:39373 original size:49 final size:49
Alignment explanation
Indices: 39318--39432 Score: 149
Period size: 49 Copynumber: 2.3 Consensus size: 49
39308 ACATCAGTCC
* *
39318 CTCTTTGTCGCGACATGGTCTTCAATTCCAAATGGTCCTTCAATCTCTA
1 CTCTTTGTCGCGACATGGTCCTCAATTCCAAATGGTCCTCCAATCTCTA
* * ** *
39367 CTCTTTGTCGCGACAGGGTCCTCAGTTCTGAATGGTCCTCCAATCTGTA
1 CTCTTTGTCGCGACATGGTCCTCAATTCCAAATGGTCCTCCAATCTCTA
* *
39416 TTCTTTGTCGTGACATG
1 CTCTTTGTCGCGACATG
39433 AAGGTCTTTT
Statistics
Matches: 56, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
49 56 1.00
ACGTcount: A:0.17, C:0.27, G:0.19, T:0.37
Consensus pattern (49 bp):
CTCTTTGTCGCGACATGGTCCTCAATTCCAAATGGTCCTCCAATCTCTA
Found at i:46876 original size:62 final size:62
Alignment explanation
Indices: 46779--46904 Score: 252
Period size: 62 Copynumber: 2.0 Consensus size: 62
46769 CCTCTAAATT
46779 TTGGGCCTATTCATTACTCATTTAGCTATGTAGTTGAATCTTATAGGGATTGATCTTCAATC
1 TTGGGCCTATTCATTACTCATTTAGCTATGTAGTTGAATCTTATAGGGATTGATCTTCAATC
46841 TTGGGCCTATTCATTACTCATTTAGCTATGTAGTTGAATCTTATAGGGATTGATCTTCAATC
1 TTGGGCCTATTCATTACTCATTTAGCTATGTAGTTGAATCTTATAGGGATTGATCTTCAATC
46903 TT
1 TT
46905 TTAATTTTGC
Statistics
Matches: 64, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
62 64 1.00
ACGTcount: A:0.24, C:0.16, G:0.17, T:0.43
Consensus pattern (62 bp):
TTGGGCCTATTCATTACTCATTTAGCTATGTAGTTGAATCTTATAGGGATTGATCTTCAATC
Found at i:49670 original size:17 final size:17
Alignment explanation
Indices: 49630--49668 Score: 71
Period size: 16 Copynumber: 2.4 Consensus size: 17
49620 TGAATATATT
49630 TTTAAATTTACTTTAAA
1 TTTAAATTTACTTTAAA
49647 TTTAAATTTA-TTTAAA
1 TTTAAATTTACTTTAAA
49663 TTTAAA
1 TTTAAA
49669 ATAAATAATG
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
16 12 0.55
17 10 0.45
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.54
Consensus pattern (17 bp):
TTTAAATTTACTTTAAA
Found at i:50268 original size:15 final size:16
Alignment explanation
Indices: 50239--50286 Score: 55
Period size: 15 Copynumber: 3.1 Consensus size: 16
50229 TAATATATAC
* *
50239 ATATATTAATATATTT
1 ATATATTTATGTATTT
*
50255 A-ATATTTATTTA-TT
1 ATATATTTATGTATTT
50269 ATATATTTATGTATTT
1 ATATATTTATGTATTT
50285 AT
1 AT
50287 TACTGACTAT
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
14 3 0.11
15 19 0.70
16 5 0.19
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (16 bp):
ATATATTTATGTATTT
Found at i:50278 original size:8 final size:8
Alignment explanation
Indices: 50239--50286 Score: 55
Period size: 8 Copynumber: 6.2 Consensus size: 8
50229 TAATATATAC
*
50239 ATATATTA
1 ATATATTT
50247 ATATATTT
1 ATATATTT
50255 A-ATATTT
1 ATATATTT
*
50262 ATTTA-TT
1 ATATATTT
50269 ATATATTT
1 ATATATTT
*
50277 ATGTATTT
1 ATATATTT
50285 AT
1 AT
50287 TACTGACTAT
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
7 13 0.38
8 21 0.62
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (8 bp):
ATATATTT
Found at i:51322 original size:30 final size:30
Alignment explanation
Indices: 51237--51323 Score: 101
Period size: 30 Copynumber: 2.9 Consensus size: 30
51227 CCCAAAACGT
* *
51237 CCCC-AAATTTTTCCAAAATTACATTTTAA
1 CCCCTAAACTTTTCTAAAATTACATTTTAA
51266 CCCCTAAAC--TTCGTGAAAATTACATTTTAA
1 CCCCTAAACTTTTC-T-AAAATTACATTTTAA
51296 -CCCTAAACTTTTCTAAAATTACCATTTT
1 CCCCTAAACTTTTCTAAAATTA-CATTTT
51324 GCCCTCGAAC
Statistics
Matches: 50, Mismatches: 2, Indels: 11
0.79 0.03 0.17
Matches are distributed among these distances:
28 3 0.06
29 19 0.38
30 25 0.50
31 3 0.06
ACGTcount: A:0.36, C:0.24, G:0.02, T:0.38
Consensus pattern (30 bp):
CCCCTAAACTTTTCTAAAATTACATTTTAA
Found at i:51328 original size:29 final size:29
Alignment explanation
Indices: 51310--51391 Score: 92
Period size: 29 Copynumber: 2.8 Consensus size: 29
51300 AAACTTTTCT
*
51310 AAAATTACCATTTTGCCCTCGAACATCCA
1 AAAATTACCATTTTGCCCTCAAACATCCA
* **
51339 AAAATTACCATTTTGCCTTCAAATTTCCAA
1 AAAATTACCATTTTGCCCTCAAACATCC-A
* * *
51369 AAAATCACCTTTTTGACCTCAAA
1 AAAATTACCATTTTGCCCTCAAA
51392 TTTTCCAAAA
Statistics
Matches: 44, Mismatches: 8, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
29 24 0.55
30 20 0.45
ACGTcount: A:0.37, C:0.27, G:0.05, T:0.32
Consensus pattern (29 bp):
AAAATTACCATTTTGCCCTCAAACATCCA
Found at i:51383 original size:30 final size:31
Alignment explanation
Indices: 51338--51401 Score: 87
Period size: 30 Copynumber: 2.1 Consensus size: 31
51328 TCGAACATCC
*
51338 AAAAATTACCATTTTG-CCTTCAAA-TTTCCA
1 AAAAATCACCATTTTGACC-TCAAATTTTCCA
*
51368 AAAAATCACCTTTTTGACCTCAAATTTTCCA
1 AAAAATCACCATTTTGACCTCAAATTTTCCA
51399 AAA
1 AAA
51402 GTTCAATTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
30 19 0.63
31 11 0.37
ACGTcount: A:0.39, C:0.23, G:0.03, T:0.34
Consensus pattern (31 bp):
AAAAATCACCATTTTGACCTCAAATTTTCCA
Found at i:51400 original size:31 final size:30
Alignment explanation
Indices: 51310--51401 Score: 89
Period size: 29 Copynumber: 3.1 Consensus size: 30
51300 AAACTTTTCT
* * * **
51310 AAAATTACCATTTTGCCCTCGAACATCC-A
1 AAAATCACCATTTTGCCTTCAAATTTCCAA
*
51339 AAAATTACCATTTTGCCTTCAAATTTCCAA
1 AAAATCACCATTTTGCCTTCAAATTTCCAA
*
51369 AAAATCACCTTTTTGACC-TCAAATTTTCCAA
1 AAAATCACCATTTTG-CCTTCAAA-TTTCCAA
51400 AA
1 AA
51402 GTTCAATTTT
Statistics
Matches: 54, Mismatches: 6, Indels: 4
0.84 0.09 0.06
Matches are distributed among these distances:
29 24 0.44
30 19 0.35
31 11 0.20
ACGTcount: A:0.37, C:0.26, G:0.04, T:0.33
Consensus pattern (30 bp):
AAAATCACCATTTTGCCTTCAAATTTCCAA
Found at i:61903 original size:25 final size:23
Alignment explanation
Indices: 61875--61941 Score: 62
Period size: 24 Copynumber: 2.7 Consensus size: 23
61865 CTTCTAGATT
61875 TTAGCTCATACGAGCCCAGATAAAA
1 TTAGCTC-TACGAGCCCAGA-AAAA
* * **
61900 TTAGCTCTCACAAGTCCAGAAAGG
1 TTAGCTCT-ACGAGCCCAGAAAAA
61924 TTAGCTCTTACGAGCCCA
1 TTAGCTC-TACGAGCCCA
61942 AAATGGTTAA
Statistics
Matches: 34, Mismatches: 6, Indels: 5
0.76 0.13 0.11
Matches are distributed among these distances:
24 17 0.50
25 17 0.50
ACGTcount: A:0.33, C:0.27, G:0.18, T:0.22
Consensus pattern (23 bp):
TTAGCTCTACGAGCCCAGAAAAA
Found at i:61949 original size:24 final size:24
Alignment explanation
Indices: 61900--61950 Score: 59
Period size: 24 Copynumber: 2.1 Consensus size: 24
61890 CCAGATAAAA
*
61900 TTAGCTCTCACAAGTCCAGAAAGG
1 TTAGCTCTCACAAGCCCAGAAAGG
* *
61924 TTAGCTCTTACGAGCCCA-AAATGG
1 TTAGCTCTCACAAGCCCAGAAA-GG
61948 TTA
1 TTA
61951 ACCATTATAC
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
23 3 0.13
24 20 0.87
ACGTcount: A:0.31, C:0.24, G:0.20, T:0.25
Consensus pattern (24 bp):
TTAGCTCTCACAAGCCCAGAAAGG
Found at i:63612 original size:5 final size:5
Alignment explanation
Indices: 63602--63646 Score: 56
Period size: 5 Copynumber: 8.6 Consensus size: 5
63592 TATAGTAATA
63602 TTTCT TTTCT TTTCTT TTTCT CTTTC- TTTCTT TTTCT TTTCT TTT
1 TTTCT TTTCT TTTC-T TTTCT -TTTCT TTTC-T TTTCT TTTCT TTT
63647 TCTTATTCAA
Statistics
Matches: 36, Mismatches: 0, Indels: 8
0.82 0.00 0.18
Matches are distributed among these distances:
4 4 0.11
5 19 0.53
6 13 0.36
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (5 bp):
TTTCT
Found at i:63622 original size:6 final size:6
Alignment explanation
Indices: 63602--63650 Score: 54
Period size: 6 Copynumber: 9.0 Consensus size: 6
63592 TATAGTAATA
*
63602 TTTC-T TTTC-T TTTCTT TTTCTC TTTC-- TTTCTT TTTC-T TTTCTT
1 TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT
63645 TTTCTT
1 TTTCTT
63651 ATTCAACATT
Statistics
Matches: 39, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
4 4 0.10
5 14 0.36
6 21 0.54
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (6 bp):
TTTCTT
Found at i:63631 original size:16 final size:15
Alignment explanation
Indices: 63602--63645 Score: 70
Period size: 16 Copynumber: 2.8 Consensus size: 15
63592 TATAGTAATA
63602 TTTCTTTTCTTTTCTT
1 TTTCTTTTC-TTTCTT
63618 TTTCTCTTTCTTTCTT
1 TTTCT-TTTCTTTCTT
63634 TTTCTTTTCTTT
1 TTTCTTTTCTTT
63646 TTCTTATTCA
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
15 7 0.26
16 16 0.59
17 4 0.15
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (15 bp):
TTTCTTTTCTTTCTT
Found at i:70221 original size:15 final size:16
Alignment explanation
Indices: 70201--70231 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
70191 ATTATTATGG
70201 TAACTCCCTT-GTTTA
1 TAACTCCCTTGGTTTA
70216 TAACTCCCTTGGTTTA
1 TAACTCCCTTGGTTTA
70232 AGGAATTTTC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 10 0.67
16 5 0.33
ACGTcount: A:0.19, C:0.26, G:0.10, T:0.45
Consensus pattern (16 bp):
TAACTCCCTTGGTTTA
Found at i:75246 original size:24 final size:24
Alignment explanation
Indices: 75219--75274 Score: 94
Period size: 24 Copynumber: 2.3 Consensus size: 24
75209 ACGAGTCTAG
*
75219 AAAGGTTAGCTCTTACGAGGCCAA
1 AAAGGTTAGCTCTTACGAGCCCAA
*
75243 AAAGGTTAGCTCTTACGAGCCCAG
1 AAAGGTTAGCTCTTACGAGCCCAA
75267 AAAGGTTA
1 AAAGGTTA
75275 ACCATTATAC
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.34, C:0.20, G:0.25, T:0.21
Consensus pattern (24 bp):
AAAGGTTAGCTCTTACGAGCCCAA
Found at i:89424 original size:16 final size:15
Alignment explanation
Indices: 89403--89447 Score: 54
Period size: 16 Copynumber: 2.9 Consensus size: 15
89393 TACATTTATG
89403 TTTATTTCTTTTTTA
1 TTTATTTCTTTTTTA
89418 CTTTATTTCTTCTTTTA
1 -TTTATTTCTT-TTTTA
* *
89435 TCTGTTTCTTTTT
1 TTTATTTCTTTTT
89448 AGATTCTATG
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
15 3 0.12
16 18 0.69
17 5 0.19
ACGTcount: A:0.09, C:0.13, G:0.02, T:0.76
Consensus pattern (15 bp):
TTTATTTCTTTTTTA
Found at i:91734 original size:17 final size:18
Alignment explanation
Indices: 91695--91736 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
91685 ATGCATAGCA
* *
91695 TTTAGTTGTCATTGTATT
1 TTTATTTGTCACTGTATT
91713 TTTATTTGTCACTGTA-T
1 TTTATTTGTCACTGTATT
91730 TTTATTT
1 TTTATTT
91737 AGTGCATTTG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 8 0.36
18 14 0.64
ACGTcount: A:0.17, C:0.07, G:0.12, T:0.64
Consensus pattern (18 bp):
TTTATTTGTCACTGTATT
Found at i:95886 original size:24 final size:24
Alignment explanation
Indices: 95858--95932 Score: 71
Period size: 24 Copynumber: 3.1 Consensus size: 24
95848 GAACCCAAAA
*
95858 TTAGCTCTCATGAGTCC-AGAAAGG
1 TTAGCTCTCACGAG-CCTAGAAAGG
* *
95882 TTAGCTCTTACGTGCCTAGAAAGG
1 TTAGCTCTCACGAGCCTAGAAAGG
* * * *
95906 TTAGCTCTTACAAGCCCAAAAAGG
1 TTAGCTCTCACGAGCCTAGAAAGG
95930 TTA
1 TTA
95933 ACCAGTATAT
Statistics
Matches: 43, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
23 2 0.05
24 41 0.95
ACGTcount: A:0.31, C:0.21, G:0.21, T:0.27
Consensus pattern (24 bp):
TTAGCTCTCACGAGCCTAGAAAGG
Found at i:96094 original size:82 final size:82
Alignment explanation
Indices: 95943--96096 Score: 220
Period size: 82 Copynumber: 1.9 Consensus size: 82
95933 ACCAGTATAT
* ** * *
95943 GATGCTACTCATACAAGATGATGAGAATCTGCAACATACGCGGAGACTCAGCCATCGATATGATC
1 GATGCTACTCACACAAGATGATGAGAATCTGCAACATACGCAAAGACTCAGCCATCGAAAGGATC
96008 CACAATTTCCCACTCTC
66 CACAATTTCCCACTCTC
* *
96025 GATGCTACTCACACAAGCTGATGAGAAT-TCGCAACATACGCAAAGACTCAGCCATCGAAAGGGT
1 GATGCTACTCACACAAGATGATGAGAATCT-GCAACATACGCAAAGACTCAGCCATCGAAAGGAT
*
96089 TCACAATT
65 CCACAATT
96097 CAGTATTCAT
Statistics
Matches: 63, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
81 1 0.02
82 62 0.98
ACGTcount: A:0.34, C:0.27, G:0.18, T:0.21
Consensus pattern (82 bp):
GATGCTACTCACACAAGATGATGAGAATCTGCAACATACGCAAAGACTCAGCCATCGAAAGGATC
CACAATTTCCCACTCTC
Found at i:101942 original size:30 final size:30
Alignment explanation
Indices: 101906--101981 Score: 91
Period size: 31 Copynumber: 2.5 Consensus size: 30
101896 TGCATATATG
* *
101906 AACTTTAATTTGGTGT-AATTATACACGTGA
1 AACTTTAATTTGAT-TCAAATATACACGTGA
* *
101936 AACTTTAATTGTGATTCAAATGTACACTTGA
1 AACTTTAATT-TGATTCAAATATACACGTGA
101967 AACTTTAATTTGATT
1 AACTTTAATTTGATT
101982 TAATCATACA
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
30 16 0.40
31 24 0.60
ACGTcount: A:0.34, C:0.11, G:0.13, T:0.42
Consensus pattern (30 bp):
AACTTTAATTTGATTCAAATATACACGTGA
Found at i:102404 original size:25 final size:25
Alignment explanation
Indices: 102370--102423 Score: 108
Period size: 25 Copynumber: 2.2 Consensus size: 25
102360 TCTATTCCGT
102370 CATGCCCTTTGCCTTGCGCAACTGA
1 CATGCCCTTTGCCTTGCGCAACTGA
102395 CATGCCCTTTGCCTTGCGCAACTGA
1 CATGCCCTTTGCCTTGCGCAACTGA
102420 CATG
1 CATG
102424 TCCACTGGTG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 29 1.00
ACGTcount: A:0.17, C:0.35, G:0.20, T:0.28
Consensus pattern (25 bp):
CATGCCCTTTGCCTTGCGCAACTGA
Found at i:106518 original size:26 final size:24
Alignment explanation
Indices: 106471--106519 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
106461 ATTCCAAAAA
**
106471 ATAAAAAATATTAAGTATTTTAAC
1 ATAAAAAATATTAAAAATTTTAAC
106495 ATAAAAAATATATAAAAATATTTAA
1 ATAAAAAATAT-TAAAAAT-TTTAA
106520 AATATTTTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 11 0.52
25 5 0.24
26 5 0.24
ACGTcount: A:0.61, C:0.02, G:0.02, T:0.35
Consensus pattern (24 bp):
ATAAAAAATATTAAAAATTTTAAC
Found at i:107595 original size:40 final size:40
Alignment explanation
Indices: 107549--107628 Score: 124
Period size: 40 Copynumber: 2.0 Consensus size: 40
107539 TAGCTATTCC
* * *
107549 TGAAATGTTATTATTCTAAATAAAATATGTTCCGAACTTT
1 TGAAATGTCATTATTCTAAACAAAAGATGTTCCGAACTTT
*
107589 TGAAATGTCATTATTCTAAACAAAAGATGTTCTGAACTTT
1 TGAAATGTCATTATTCTAAACAAAAGATGTTCCGAACTTT
107629 AATTATTCTC
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
40 36 1.00
ACGTcount: A:0.38, C:0.11, G:0.11, T:0.40
Consensus pattern (40 bp):
TGAAATGTCATTATTCTAAACAAAAGATGTTCCGAACTTT
Found at i:119196 original size:3 final size:3
Alignment explanation
Indices: 119188--119214 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
119178 TTGATGTTGT
119188 CAA CAA CAA CAA CAA CAA CAA CAA CAA
1 CAA CAA CAA CAA CAA CAA CAA CAA CAA
119215 TAATAATAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.33, G:0.00, T:0.00
Consensus pattern (3 bp):
CAA
Found at i:120480 original size:33 final size:34
Alignment explanation
Indices: 120443--120515 Score: 96
Period size: 34 Copynumber: 2.2 Consensus size: 34
120433 ATCAAATTAC
*
120443 TTTTTTATCCTTC-TTTTTAACGTTTCTTCTTC-A
1 TTTTTTATCCTTCTTTTTTAACATTTCTTC-TCAA
* *
120476 TTTTTTATTCTTCTTTTTTCACATTTCTTCTCAA
1 TTTTTTATCCTTCTTTTTTAACATTTCTTCTCAA
120510 TTTTTT
1 TTTTTT
120516 CTTCCAAGAA
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
33 14 0.40
34 21 0.60
ACGTcount: A:0.12, C:0.19, G:0.01, T:0.67
Consensus pattern (34 bp):
TTTTTTATCCTTCTTTTTTAACATTTCTTCTCAA
Found at i:121681 original size:24 final size:24
Alignment explanation
Indices: 121645--121903 Score: 207
Period size: 24 Copynumber: 10.8 Consensus size: 24
121635 TAACTCATGT
**
121645 ACGTTTATATTCGTCAGCTTGCAC
1 ACGTTTATGCTCGTCAGCTTGCAC
* ** *
121669 ACGTTTATGTTCGTCAGCTTATAT
1 ACGTTTATGCTCGTCAGCTTGCAC
* *
121693 ATGTTTATGCTCTTCAGCTTGCAC
1 ACGTTTATGCTCGTCAGCTTGCAC
*
121717 ACGTTTATGCTCGTCAGCTAT--AT
1 ACGTTTATGCTCGTCAGCT-TGCAC
** **
121740 ACGTTTACACTTATCAGCTTGCAC
1 ACGTTTATGCTCGTCAGCTTGCAC
* * ** *
121764 ATGTTTATGCTCATCAGCTTATAT
1 ACGTTTATGCTCGTCAGCTTGCAC
* *
121788 ACCTTTACGCTCGTCAGCTTGCAC
1 ACGTTTATGCTCGTCAGCTTGCAC
*
121812 ACGTTTACGCTCGTCAGCTTGCAC
1 ACGTTTATGCTCGTCAGCTTGCAC
* * * ** *
121836 ACGTTTACGCTCATCAACTTATAT
1 ACGTTTATGCTCGTCAGCTTGCAC
* ** *
121860 AAGTTTACACTCGTCAGTTTGCAC
1 ACGTTTATGCTCGTCAGCTTGCAC
*
121884 ACATTTATGCTCGTCAGCTT
1 ACGTTTATGCTCGTCAGCTT
121904 ATACGTTTAC
Statistics
Matches: 181, Mismatches: 51, Indels: 6
0.76 0.21 0.03
Matches are distributed among these distances:
22 1 0.01
23 16 0.09
24 163 0.90
25 1 0.01
ACGTcount: A:0.22, C:0.25, G:0.15, T:0.37
Consensus pattern (24 bp):
ACGTTTATGCTCGTCAGCTTGCAC
Found at i:121710 original size:48 final size:48
Alignment explanation
Indices: 121658--121847 Score: 249
Period size: 48 Copynumber: 4.0 Consensus size: 48
121648 TTTATATTCG
* * *
121658 TCAGCTTGCACACGTTTATGTTCGTCAGCTTATATATGTTTATGCTCT
1 TCAGCTTGCACACGTTTATGCTCGTCAGCTTATATACGTTTACGCTCT
*
121706 TCAGCTTGCACACGTTTATGCTCGTCAGC-TATATACGTTTACACT-T
1 TCAGCTTGCACACGTTTATGCTCGTCAGCTTATATACGTTTACGCTCT
* * * *
121752 ATCAGCTTGCACATGTTTATGCTCATCAGCTTATATACCTTTACGCTCG
1 -TCAGCTTGCACACGTTTATGCTCGTCAGCTTATATACGTTTACGCTCT
* ** *
121801 TCAGCTTGCACACGTTTACGCTCGTCAGCTTGCACACGTTTACGCTC
1 TCAGCTTGCACACGTTTATGCTCGTCAGCTTATATACGTTTACGCTC
121848 ATCAACTTAT
Statistics
Matches: 123, Mismatches: 16, Indels: 6
0.85 0.11 0.04
Matches are distributed among these distances:
46 1 0.01
47 40 0.33
48 82 0.67
ACGTcount: A:0.20, C:0.27, G:0.16, T:0.37
Consensus pattern (48 bp):
TCAGCTTGCACACGTTTATGCTCGTCAGCTTATATACGTTTACGCTCT
Found at i:121807 original size:95 final size:95
Alignment explanation
Indices: 121658--121830 Score: 274
Period size: 95 Copynumber: 1.8 Consensus size: 95
121648 TTTATATTCG
* * ** * *
121658 TCAGCTTGCACACGTTTATGTTCGTCAGCTTATATATGTTTATGCTCTTCAGCTTGCACACGTTT
1 TCAGCTTGCACACGTTTATGCTCATCAGCTTATATACCTTTACGCTCGTCAGCTTGCACACGTTT
*
121723 ATGCTCGTCAGCTATATACGTTTACACTTA
66 ACGCTCGTCAGCTATATACGTTTACACTTA
*
121753 TCAGCTTGCACATGTTTATGCTCATCAGCTTATATACCTTTACGCTCGTCAGCTTGCACACGTTT
1 TCAGCTTGCACACGTTTATGCTCATCAGCTTATATACCTTTACGCTCGTCAGCTTGCACACGTTT
121818 ACGCTCGTCAGCT
66 ACGCTCGTCAGCT
121831 TGCACACGTT
Statistics
Matches: 70, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
95 70 1.00
ACGTcount: A:0.20, C:0.26, G:0.16, T:0.38
Consensus pattern (95 bp):
TCAGCTTGCACACGTTTATGCTCATCAGCTTATATACCTTTACGCTCGTCAGCTTGCACACGTTT
ACGCTCGTCAGCTATATACGTTTACACTTA
Found at i:121848 original size:72 final size:72
Alignment explanation
Indices: 121655--121903 Score: 268
Period size: 72 Copynumber: 3.5 Consensus size: 72
121645 ACGTTTATAT
* * ** * * ** *
121655 TCGTCAGCTTGCACACGTTTATGTTCGTCAGCTTATATATGTTTATGCTCTTCAGCTTGCACACG
1 TCGTCAGCTTGCACACGTTTACGCTCGTCAGCTTGCACATGTTTATGCTCATCAGCTTATATACG
*
121720 TTTATGC
66 TTTACGC
* * **
121727 TCGTCAGCTAT--ATACGTTTACACTTATCAGCTTGCACATGTTTATGCTCATCAGCTTATATAC
1 TCGTCAGCT-TGCACACGTTTACGCTCGTCAGCTTGCACATGTTTATGCTCATCAGCTTATATAC
*
121790 CTTTACGC
65 GTTTACGC
* * * *
121798 TCGTCAGCTTGCACACGTTTACGCTCGTCAGCTTGCACACGTTTACGCTCATCAACTTATATAAG
1 TCGTCAGCTTGCACACGTTTACGCTCGTCAGCTTGCACATGTTTATGCTCATCAGCTTATATACG
*
121863 TTTACAC
66 TTTACGC
* * *
121870 TCGTCAGTTTGCACACATTTATGCTCGTCAGCTT
1 TCGTCAGCTTGCACACGTTTACGCTCGTCAGCTT
121904 ATACGTTTAC
Statistics
Matches: 146, Mismatches: 28, Indels: 6
0.81 0.16 0.03
Matches are distributed among these distances:
70 1 0.01
71 54 0.37
72 90 0.62
73 1 0.01
ACGTcount: A:0.21, C:0.26, G:0.16, T:0.37
Consensus pattern (72 bp):
TCGTCAGCTTGCACACGTTTACGCTCGTCAGCTTGCACATGTTTATGCTCATCAGCTTATATACG
TTTACGC
Found at i:124262 original size:18 final size:18
Alignment explanation
Indices: 124239--124290 Score: 77
Period size: 18 Copynumber: 2.9 Consensus size: 18
124229 AAAATGAGGG
*
124239 AAATGATGTTCACATTTT
1 AAATGATGTTCACATTTC
*
124257 AAATGATGTTCACACTTC
1 AAATGATGTTCACATTTC
*
124275 AAATGATGTTAACATT
1 AAATGATGTTCACATT
124291 GATGGAAACG
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 30 1.00
ACGTcount: A:0.37, C:0.13, G:0.12, T:0.38
Consensus pattern (18 bp):
AAATGATGTTCACATTTC
Found at i:124719 original size:72 final size:71
Alignment explanation
Indices: 124627--124810 Score: 323
Period size: 72 Copynumber: 2.6 Consensus size: 71
124617 CAATGCTAAA
*
124627 CTAGTTTTATCAATAGTTGTTTATGTTTAGATTTTGGATATTGAATTTATGTTCTACTTATTTAT
1 CTAGTTTTATCAATAGTTGTTTATGTTT-GATTTTGGATATTGAATTCATGTTCTACTTATTTAT
124692 GTGTAAT
65 GTGTAAT
*
124699 CTAGTTTTATCAATAGTTGTTTATGTTTGGTTTTTGGATATTGAATTCATGTTCTACTTATTTAT
1 CTAGTTTTATCAATAGTTGTTTATGTTT-GATTTTGGATATTGAATTCATGTTCTACTTATTTAT
124764 GTGTAAT
65 GTGTAAT
*
124771 CTAGTTTTATCAATAGTTGTTTATATTTGATTTTGGATAT
1 CTAGTTTTATCAATAGTTGTTTATGTTTGATTTTGGATAT
124811 AAAATTTGTT
Statistics
Matches: 107, Mismatches: 5, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
71 11 0.10
72 96 0.90
ACGTcount: A:0.24, C:0.06, G:0.16, T:0.54
Consensus pattern (71 bp):
CTAGTTTTATCAATAGTTGTTTATGTTTGATTTTGGATATTGAATTCATGTTCTACTTATTTATG
TGTAAT
Found at i:126523 original size:21 final size:21
Alignment explanation
Indices: 126499--126544 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
126489 TACAATTTTG
126499 TTAAT-ATCTAAATATAAATAT
1 TTAATGAT-TAAATATAAATAT
* *
126520 TTAATGATTATATTTAAATAT
1 TTAATGATTAAATATAAATAT
126541 TTAA
1 TTAA
126545 AATATAGTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 20 0.91
22 2 0.09
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (21 bp):
TTAATGATTAAATATAAATAT
Found at i:126560 original size:20 final size:20
Alignment explanation
Indices: 126513--126569 Score: 62
Period size: 21 Copynumber: 2.8 Consensus size: 20
126503 TATCTAAATA
* *
126513 TAAATATTTAATGATTATATT
1 TAAATATTT-ATAAATATATT
126534 TAAATATTTA-AAATATAGTT
1 TAAATATTTATAAATATA-TT
*
126554 TATATATTTATAAATA
1 TAAATATTTATAAATA
126570 ATTCATATTA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
19 5 0.16
20 12 0.39
21 14 0.45
ACGTcount: A:0.47, C:0.00, G:0.04, T:0.49
Consensus pattern (20 bp):
TAAATATTTATAAATATATT
Found at i:137201 original size:23 final size:23
Alignment explanation
Indices: 137174--137222 Score: 98
Period size: 23 Copynumber: 2.1 Consensus size: 23
137164 AAAATGAAAC
137174 ATATTGTCATTATTGACAAATAG
1 ATATTGTCATTATTGACAAATAG
137197 ATATTGTCATTATTGACAAATAG
1 ATATTGTCATTATTGACAAATAG
137220 ATA
1 ATA
137223 AAAAGAATAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.41, C:0.08, G:0.12, T:0.39
Consensus pattern (23 bp):
ATATTGTCATTATTGACAAATAG
Found at i:142519 original size:41 final size:40
Alignment explanation
Indices: 142474--142552 Score: 104
Period size: 40 Copynumber: 1.9 Consensus size: 40
142464 TGGCGATTAG
* * *
142474 ACATAAAATGCCACAAAAAGTAAATCAATAGTGGCGTTTTT
1 ACAT-AAACGCCACAAAAAGTAAAACAATAATGGCGTTTTT
* *
142515 ACATAAACGCCGCAAAAGGTAAAACAATAATGGCGTTT
1 ACATAAACGCCACAAAAAGTAAAACAATAATGGCGTTT
142553 GTAGGAAAAA
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
40 29 0.88
41 4 0.12
ACGTcount: A:0.44, C:0.16, G:0.16, T:0.23
Consensus pattern (40 bp):
ACATAAACGCCACAAAAAGTAAAACAATAATGGCGTTTTT
Found at i:142686 original size:41 final size:41
Alignment explanation
Indices: 142559--142688 Score: 170
Period size: 41 Copynumber: 3.2 Consensus size: 41
142549 GTTTGTAGGA
* ** *
142559 AAAATGCCGCTAAATGTCAAAGCATTAGTTGCGCTTATGGG
1 AAAATGCCGCTAAAGGTCAAAGCATTAGCGGCGTTTATGGG
* * *
142600 AAAACGTCGCTAAAGGTCAAAGCATTAGCGGCTTTTATGGG
1 AAAATGCCGCTAAAGGTCAAAGCATTAGCGGCGTTTATGGG
* * *
142641 AAAATACCGCTAAAGGTTAGAGCATTAGCGGCGTTTATGGG
1 AAAATGCCGCTAAAGGTCAAAGCATTAGCGGCGTTTATGGG
142682 AAAATGC
1 AAAATGC
142689 TGCTGGAAAA
Statistics
Matches: 75, Mismatches: 14, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
41 75 1.00
ACGTcount: A:0.33, C:0.16, G:0.26, T:0.25
Consensus pattern (41 bp):
AAAATGCCGCTAAAGGTCAAAGCATTAGCGGCGTTTATGGG
Found at i:142698 original size:13 final size:13
Alignment explanation
Indices: 142680--142731 Score: 104
Period size: 13 Copynumber: 4.0 Consensus size: 13
142670 GGCGTTTATG
142680 GGAAAATGCTGCT
1 GGAAAATGCTGCT
142693 GGAAAATGCTGCT
1 GGAAAATGCTGCT
142706 GGAAAATGCTGCT
1 GGAAAATGCTGCT
142719 GGAAAATGCTGCT
1 GGAAAATGCTGCT
142732 AAAAGTCAGA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 39 1.00
ACGTcount: A:0.31, C:0.15, G:0.31, T:0.23
Consensus pattern (13 bp):
GGAAAATGCTGCT
Found at i:142784 original size:41 final size:40
Alignment explanation
Indices: 142722--142805 Score: 114
Period size: 41 Copynumber: 2.1 Consensus size: 40
142712 TGCTGCTGGA
* *
142722 AAATGCTGCTAAAAGTCAGAGCACTAGCGGCGTTTATGAGG
1 AAATGCTGCGAAAAGTAAGAGCACTAGCGGCGTTTAT-AGG
* * *
142763 AAATGCTGCGAAAGGTAAGAGCATTAGCGGTGTTTATAGG
1 AAATGCTGCGAAAAGTAAGAGCACTAGCGGCGTTTATAGG
142803 AAA
1 AAA
142806 AACGCCGCTA
Statistics
Matches: 38, Mismatches: 5, Indels: 1
0.86 0.11 0.02
Matches are distributed among these distances:
40 6 0.16
41 32 0.84
ACGTcount: A:0.35, C:0.13, G:0.30, T:0.23
Consensus pattern (40 bp):
AAATGCTGCGAAAAGTAAGAGCACTAGCGGCGTTTATAGG
Found at i:143123 original size:31 final size:27
Alignment explanation
Indices: 143087--143165 Score: 70
Period size: 31 Copynumber: 2.7 Consensus size: 27
143077 GATTACATCA
143087 AAATTAAAGTTTCATGTATACATATGAACC
1 AAATTAAAG-TTCATGTATA-AT-TGAACC
* *
143117 ACAATTAAAAATTCACGTGTATAATTGCACC
1 A-AATT-AAAGTTCA--TGTATAATTGAACC
143148 AAATTAAAGTT-ATGTATA
1 AAATTAAAGTTCATGTATA
143166 TAATTGCACA
Statistics
Matches: 42, Mismatches: 3, Indels: 12
0.74 0.05 0.21
Matches are distributed among these distances:
26 6 0.14
28 1 0.02
29 5 0.12
30 5 0.12
31 14 0.33
32 5 0.12
33 6 0.14
ACGTcount: A:0.44, C:0.13, G:0.10, T:0.33
Consensus pattern (27 bp):
AAATTAAAGTTCATGTATAATTGAACC
Found at i:143530 original size:30 final size:31
Alignment explanation
Indices: 143467--143540 Score: 98
Period size: 30 Copynumber: 2.4 Consensus size: 31
143457 TCGCAAATTA
* *
143467 ATACTTAAATTATGTCATTTTTTTCACGTTG
1 ATACTTAAATTATCTCATTTTTTTAACGTTG
*
143498 ATACTTAAATT-TCT-ATTTTTGTTAATGTTG
1 ATACTTAAATTATCTCATTTTT-TTAACGTTG
143528 ATACTTAAATTAT
1 ATACTTAAATTAT
143541 ACTCCGTTAT
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
29 6 0.16
30 20 0.53
31 12 0.32
ACGTcount: A:0.30, C:0.09, G:0.08, T:0.53
Consensus pattern (31 bp):
ATACTTAAATTATCTCATTTTTTTAACGTTG
Found at i:144582 original size:19 final size:19
Alignment explanation
Indices: 144543--144582 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
144533 ACATTACAAG
* *
144543 TTAAAATATATTTCAATTT
1 TTAAAATATATTTAAAATT
*
144562 TTAAAATTTATTTAAAATT
1 TTAAAATATATTTAAAATT
144581 TT
1 TT
144583 GATATAAAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (19 bp):
TTAAAATATATTTAAAATT
Found at i:144672 original size:41 final size:41
Alignment explanation
Indices: 144594--144673 Score: 106
Period size: 41 Copynumber: 2.0 Consensus size: 41
144584 ATATAAAAAT
* * ***
144594 AACATTAACGACGTTTATGAAAAAAATACTGTTAAAAATTA
1 AACAATAACAACGTTTATGAAAAAAATACTAAAAAAAATTA
*
144635 AACAATAACAACGTTTATGAAAAAAATTCTAAAAAAAAT
1 AACAATAACAACGTTTATGAAAAAAATACTAAAAAAAAT
144674 AATGTAATAA
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
41 33 1.00
ACGTcount: A:0.56, C:0.10, G:0.07, T:0.26
Consensus pattern (41 bp):
AACAATAACAACGTTTATGAAAAAAATACTAAAAAAAATTA
Found at i:144947 original size:45 final size:46
Alignment explanation
Indices: 144860--144947 Score: 115
Period size: 47 Copynumber: 1.9 Consensus size: 46
144850 TAAATCATAG
** *
144860 TTTCTCCTCTCTCAAAACTTCAAATTTCTCTAATCCCTAATCCTTAA
1 TTTCTCCTCTCTCAAAACCCCAAA-TTCTCAAATCCCTAATCCTTAA
**
144907 TTTCTCCTCTCTCAAAACCCCAAA-TCTCAAATTTCTAATCC
1 TTTCTCCTCTCTCAAAACCCCAAATTCTCAAATCCCTAATCC
144948 CTAAATATTT
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
45 14 0.39
47 22 0.61
ACGTcount: A:0.28, C:0.34, G:0.00, T:0.38
Consensus pattern (46 bp):
TTTCTCCTCTCTCAAAACCCCAAATTCTCAAATCCCTAATCCTTAA
Found at i:147943 original size:25 final size:25
Alignment explanation
Indices: 147906--147953 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
147896 ATTTAATTTA
* *
147906 AAAATAACTCAAAAATTTAATTACT
1 AAAACAACCCAAAAATTTAATTACT
*
147931 AAAACAACCCAAATATTTAATTA
1 AAAACAACCCAAAAATTTAATTA
147954 TTTAATTAGT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.56, C:0.15, G:0.00, T:0.29
Consensus pattern (25 bp):
AAAACAACCCAAAAATTTAATTACT
Found at i:148085 original size:42 final size:42
Alignment explanation
Indices: 148033--148246 Score: 241
Period size: 42 Copynumber: 4.8 Consensus size: 42
148023 AATTAAATAT
*
148033 TTAATTATTAA-AGACAATCCAAATATTTAATTATTTAATTAG
1 TTAATTATTAACA-ACAACCCAAATATTTAATTATTTAATTAG
148075 TTAATTATTAACAACAACCCAAATATTTAATTATTTAATTAG
1 TTAATTATTAACAACAACCCAAATATTTAATTATTTAATTAG
*
148117 TTAATTATTAACAACAACCCAAATATTTAATTATTTAATTTTAT
1 TTAATTATTAACAACAACCCAAATATTTAATTATTTAA--TTAG
* *
148161 TTAATTAAAATTTTAATTACTAAAAACAATCTAAATATTTAATTATTTAATTAG
1 TTAATT---A--TT-A--AC----AACAACCCAAATATTTAATTATTTAATTAG
*
148215 TTAATTATTAATAACAACCCAAATATTTAATT
1 TTAATTATTAACAACAACCCAAATATTTAATT
148247 CAAAATATTT
Statistics
Matches: 149, Mismatches: 8, Indels: 30
0.80 0.04 0.16
Matches are distributed among these distances:
42 95 0.64
43 1 0.01
44 9 0.06
46 1 0.01
47 1 0.01
48 1 0.01
49 4 0.03
50 1 0.01
51 1 0.01
52 2 0.01
54 9 0.06
56 24 0.16
ACGTcount: A:0.46, C:0.09, G:0.02, T:0.43
Consensus pattern (42 bp):
TTAATTATTAACAACAACCCAAATATTTAATTATTTAATTAG
Found at i:148177 original size:98 final size:100
Alignment explanation
Indices: 148053--148323 Score: 374
Period size: 98 Copynumber: 2.8 Consensus size: 100
148043 AAGACAATCC
* * * *
148053 AAATATTTAATTATTTAAT--TAGTTAATTATTAACAACAACCCAAATATTTAATTATTTAATTA
1 AAATATTTAATTAATTAATAATATTTAATTATTAAAAACAATCCAAATATTTAATTATTTAATTA
148116 GTTAATTATTAACAACAACCCAAATATTTAATT-A
66 GTTAATTATTAACAACAACCCAAATATTTAATTCA
* * * *
148150 TTTAAT-TTTATTTAATTAA-AAT-TTTAATTACTAAAAACAATCTAAATATTTAATTATTTAAT
1 --AAATATTTAATTAATTAATAATATTTAATTATTAAAAACAATCCAAATATTTAATTATTTAAT
*
148212 TAGTTAATTATTAATAACAACCCAAATATTTAATTCA
64 TAGTTAATTATTAACAACAACCCAAATATTTAATTCA
* *
148249 AAATATTTAATTATTTAATTATATTTAATTATTAAAAACAATCCAAATATTTAATTATTTAATTA
1 AAATATTTAATTAATTAATAATATTTAATTATTAAAAACAATCCAAATATTTAATTATTTAATTA
*
148314 GTTATTTATT
66 GTTAATTATT
148324 TGCAACTATG
Statistics
Matches: 150, Mismatches: 16, Indels: 11
0.85 0.09 0.06
Matches are distributed among these distances:
97 3 0.02
98 91 0.61
99 7 0.05
100 49 0.33
ACGTcount: A:0.45, C:0.08, G:0.01, T:0.45
Consensus pattern (100 bp):
AAATATTTAATTAATTAATAATATTTAATTATTAAAAACAATCCAAATATTTAATTATTTAATTA
GTTAATTATTAACAACAACCCAAATATTTAATTCA
Found at i:148295 original size:58 final size:56
Alignment explanation
Indices: 148193--148304 Score: 179
Period size: 58 Copynumber: 2.0 Consensus size: 56
148183 AAAACAATCT
*
148193 AAATATTTAATTATTTAATTAGTTAATTATTAATAACAACCCAAATATTTAATTCA
1 AAATATTTAATTATTTAATTAGTTAATTATTAAAAACAACCCAAATATTTAATTCA
* *
148249 AAATATTTAATTATTTAATTATATTTAATTATTAAAAACAATCCAAATATTTAATT
1 AAATATTTAATTATTTAA-T-TAGTTAATTATTAAAAACAACCCAAATATTTAATT
148305 ATTTAATTAG
Statistics
Matches: 51, Mismatches: 3, Indels: 2
0.91 0.05 0.04
Matches are distributed among these distances:
56 18 0.35
57 1 0.02
58 32 0.63
ACGTcount: A:0.47, C:0.07, G:0.01, T:0.45
Consensus pattern (56 bp):
AAATATTTAATTATTTAATTAGTTAATTATTAAAAACAACCCAAATATTTAATTCA
Found at i:149531 original size:23 final size:23
Alignment explanation
Indices: 149502--149545 Score: 88
Period size: 23 Copynumber: 1.9 Consensus size: 23
149492 GCAATCTTCT
149502 TTTATCTTATCTATGATCATCCC
1 TTTATCTTATCTATGATCATCCC
149525 TTTATCTTATCTATGATCATC
1 TTTATCTTATCTATGATCATC
149546 TCTAGAGTGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.23, C:0.23, G:0.05, T:0.50
Consensus pattern (23 bp):
TTTATCTTATCTATGATCATCCC
Found at i:154095 original size:43 final size:41
Alignment explanation
Indices: 153993--154104 Score: 100
Period size: 43 Copynumber: 2.6 Consensus size: 41
153983 AAATTTGTTA
* *
153993 ATTTTAGCGGTGTTTGTGGGAAAAACGCAGCTAAAGAACATT
1 ATTTTAGTGGTGTTTGTGGG-AAAGCGCAGCTAAAGAACATT
** ** *
154035 ATTTATAGTGGCATTTGTGGGAGAAGCGCATTTAAAGACCATGT
1 ATTT-TAGTGGTGTTTGTGGGA-AAGCGCAGCTAAAGAACAT-T
154079 -TCTTTAGTGGTGTTTGTGAGGAAAGC
1 AT-TTTAGTGGTGTTTGTG-GGAAAGC
154105 ATCGCTAAAG
Statistics
Matches: 56, Mismatches: 9, Indels: 9
0.76 0.12 0.12
Matches are distributed among these distances:
42 5 0.09
43 45 0.80
44 6 0.11
ACGTcount: A:0.29, C:0.11, G:0.29, T:0.32
Consensus pattern (41 bp):
ATTTTAGTGGTGTTTGTGGGAAAGCGCAGCTAAAGAACATT
Found at i:154238 original size:43 final size:43
Alignment explanation
Indices: 154191--154323 Score: 149
Period size: 43 Copynumber: 3.1 Consensus size: 43
154181 ATTTAGCCAC
* * * *
154191 GTTTGTGAGACAAGCGTCGTTAAAGACCATATTTTTTAACGGG
1 GTTTGTGAGAAAAGCGTCGCTAAAGATCATGTTTTTTAACGGG
* * * * *
154234 GTTTGTGAAAAAAGTGTTGCTAAAGATCATGTTTTTTAACAGC
1 GTTTGTGAGAAAAGCGTCGCTAAAGATCATGTTTTTTAACGGG
* * * *
154277 GTTTGTGGGAAAAACGTCGCTAAAGATCATGTTCTTTAGCGGG
1 GTTTGTGAGAAAAGCGTCGCTAAAGATCATGTTTTTTAACGGG
154320 GTTT
1 GTTT
154324 ATGGGAAGGC
Statistics
Matches: 72, Mismatches: 18, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
43 72 1.00
ACGTcount: A:0.28, C:0.12, G:0.26, T:0.35
Consensus pattern (43 bp):
GTTTGTGAGAAAAGCGTCGCTAAAGATCATGTTTTTTAACGGG
Found at i:156086 original size:16 final size:15
Alignment explanation
Indices: 156053--156092 Score: 55
Period size: 16 Copynumber: 2.6 Consensus size: 15
156043 TGTTAAAATC
156053 TTTAAAAATTATATT
1 TTTAAAAATTATATT
156068 TTTAAATAATTA-ATAT
1 TTTAAA-AATTATAT-T
156084 TTTAAAAAT
1 TTTAAAAAT
156093 AAAATAAAAG
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
15 11 0.48
16 12 0.52
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (15 bp):
TTTAAAAATTATATT
Found at i:157787 original size:76 final size:76
Alignment explanation
Indices: 157661--157809 Score: 280
Period size: 76 Copynumber: 2.0 Consensus size: 76
157651 GGTTTTAATG
157661 TTGGTTTTAATTGAATCTTTTGCACGGCCAGGACAAGATTTAAAGGTAATTGGTGCTCTTACAGC
1 TTGGTTTTAATTGAATCTTTTGCACGGCCAGGACAAGATTTAAAGGTAATTGGTGCTCTTACAGC
157726 CACTTAGACGC
66 CACTTAGACGC
* *
157737 TTGGTTTTAATTGAATCTTTTGCATGGCCAGGACAAGATTTAAAGGTAATTGGTGCTCTTACATC
1 TTGGTTTTAATTGAATCTTTTGCACGGCCAGGACAAGATTTAAAGGTAATTGGTGCTCTTACAGC
157802 CACTTAGA
66 CACTTAGA
157810 GGCTGGGTAG
Statistics
Matches: 71, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
76 71 1.00
ACGTcount: A:0.27, C:0.17, G:0.21, T:0.35
Consensus pattern (76 bp):
TTGGTTTTAATTGAATCTTTTGCACGGCCAGGACAAGATTTAAAGGTAATTGGTGCTCTTACAGC
CACTTAGACGC
Found at i:161953 original size:17 final size:17
Alignment explanation
Indices: 161931--161965 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
161921 TAACTTCCCA
161931 GCACCACACGACCGTGT
1 GCACCACACGACCGTGT
161948 GCACCACACGACCGTGT
1 GCACCACACGACCGTGT
161965 G
1 G
161966 GTCGATTTTC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.23, C:0.40, G:0.26, T:0.11
Consensus pattern (17 bp):
GCACCACACGACCGTGT
Found at i:163638 original size:6 final size:7
Alignment explanation
Indices: 163624--163658 Score: 54
Period size: 7 Copynumber: 5.1 Consensus size: 7
163614 AAAATATAAA
163624 TTCATTT
1 TTCATTT
163631 TTCATTT
1 TTCATTT
*
163638 TTCAGTT
1 TTCATTT
163645 TTCA-TT
1 TTCATTT
163651 TTCATTT
1 TTCATTT
163658 T
1 T
163659 GGAGAAAACC
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
6 6 0.23
7 20 0.77
ACGTcount: A:0.14, C:0.14, G:0.03, T:0.69
Consensus pattern (7 bp):
TTCATTT
Found at i:168698 original size:47 final size:47
Alignment explanation
Indices: 168629--168739 Score: 168
Period size: 47 Copynumber: 2.4 Consensus size: 47
168619 AAGGTGGATG
* *
168629 AAGTGATAGTTTATCTACAAAAGTGATGGCTTGTCCACAATATCATA
1 AAGTGACAGTTTATCTACAAAAGTGATGGCTAGTCCACAATATCATA
* * * *
168676 AAGTGGCAGTTTATCTACAAAAGTGGTGGCTAGTCCACAATATTATT
1 AAGTGACAGTTTATCTACAAAAGTGATGGCTAGTCCACAATATCATA
168723 AAGTGACAGTTTATCTA
1 AAGTGACAGTTTATCTA
168740 AATTACTATG
Statistics
Matches: 57, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
47 57 1.00
ACGTcount: A:0.34, C:0.14, G:0.19, T:0.32
Consensus pattern (47 bp):
AAGTGACAGTTTATCTACAAAAGTGATGGCTAGTCCACAATATCATA
Found at i:170627 original size:25 final size:26
Alignment explanation
Indices: 170590--170660 Score: 83
Period size: 25 Copynumber: 2.8 Consensus size: 26
170580 CATCCATTTT
*
170590 TTATCCCAG-TAAAATTTTGACGATA
1 TTATCCCTGATAAAATTTTGACGATA
* * *
170615 TTATCTC-GATAAAATTTTGATGATT
1 TTATCCCTGATAAAATTTTGACGATA
*
170640 TTATCCCTGGTAAAATTTTGA
1 TTATCCCTGATAAAATTTTGA
170661 AAAAAATGTA
Statistics
Matches: 39, Mismatches: 5, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
24 1 0.03
25 26 0.67
26 12 0.31
ACGTcount: A:0.32, C:0.13, G:0.13, T:0.42
Consensus pattern (26 bp):
TTATCCCTGATAAAATTTTGACGATA
Found at i:173996 original size:21 final size:21
Alignment explanation
Indices: 173972--174022 Score: 84
Period size: 21 Copynumber: 2.4 Consensus size: 21
173962 CTAGTGATGT
* *
173972 TTCTACTGTAACAAGTCATGC
1 TTCTACCGAAACAAGTCATGC
173993 TTCTACCGAAACAAGTCATGC
1 TTCTACCGAAACAAGTCATGC
174014 TTCTACCGA
1 TTCTACCGA
174023 TACTAAAAAC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.29, C:0.27, G:0.14, T:0.29
Consensus pattern (21 bp):
TTCTACCGAAACAAGTCATGC
Found at i:179093 original size:41 final size:41
Alignment explanation
Indices: 179030--179249 Score: 257
Period size: 41 Copynumber: 5.4 Consensus size: 41
179020 TGTATAAATT
* ** *
179030 GAAGACTCATGTCTTGAGATGAGCATGAAATTATATTAAAG
1 GAAGACTCATGACTCAAGATGAGCATGAGATTATATTAAAG
**
179071 GAAGACTCGCGACTCGAA-ATGAGCATGAGATTATATTAAAG
1 GAAGACTCATGACTC-AAGATGAGCATGAGATTATATTAAAG
* * * *
179112 GAAGACTCATGTCTCAGGGTGAGCATGAGTTTATATTAAAG
1 GAAGACTCATGACTCAAGATGAGCATGAGATTATATTAAAG
* *
179153 GAAGACTCATGTCTCAAGGTGAGCATGAGATTATATTAAAG
1 GAAGACTCATGACTCAAGATGAGCATGAGATTATATTAAAG
* *
179194 GAAGACT-GT-ATCTCAAGATGAGAATGAGATTATATTTAAAG
1 GAAGACTCATGA-CTCAAGATGAGCATGAGATTATA-TTAAAG
*
179235 GAAGACTTATGACTC
1 GAAGACTCATGACTC
179250 GGTAGATCGT
Statistics
Matches: 154, Mismatches: 19, Indels: 11
0.84 0.10 0.06
Matches are distributed among these distances:
40 23 0.15
41 125 0.81
42 5 0.03
43 1 0.01
ACGTcount: A:0.37, C:0.12, G:0.24, T:0.27
Consensus pattern (41 bp):
GAAGACTCATGACTCAAGATGAGCATGAGATTATATTAAAG
Found at i:179275 original size:81 final size:81
Alignment explanation
Indices: 179030--179279 Score: 245
Period size: 82 Copynumber: 3.1 Consensus size: 81
179020 TGTATAAATT
* ** * * ** **
179030 GAAGACTCATGTCTTGAGATGAGCATGAAATTATATTAAAGGAAGACTCGCGACTCGAAATGAGC
1 GAAGACTCATATCTCAAGATGAGAATGAGATTATATTAAAGGAAGACTCATGACTC-AGGTGAGC
*
179095 ATGAGATTATATTAAAG
65 ATAAGATTATATTAAAG
* * * * * *
179112 GAAGACTCATGTCTCAGGGTGAGCATGAGTTTATATTAAAGGAAGACTCATGTCTCAAGGTGAGC
1 GAAGACTCATATCTCAAGATGAGAATGAGATTATATTAAAGGAAGACTCATGACTC-AGGTGAGC
*
179177 ATGAGATTATATTAAAG
65 ATAAGATTATATTAAAG
* * *
179194 GAAGACT-GTATCTCAAGATGAGAATGAGATTATATTTAAAGGAAGACTTATGACTC-GGTAGAT
1 GAAGACTCATATCTCAAGATGAGAATGAGATTATA-TTAAAGGAAGACTCATGACTCAGGT-GAG
*
179257 CGTAAGATTAT-TTAAAAG
64 CATAAGATTATATT-AAAG
179275 GAAGA
1 GAAGA
179280 TTTATGACTC
Statistics
Matches: 142, Mismatches: 23, Indels: 7
0.83 0.13 0.04
Matches are distributed among these distances:
80 5 0.04
81 41 0.29
82 96 0.68
ACGTcount: A:0.38, C:0.11, G:0.24, T:0.27
Consensus pattern (81 bp):
GAAGACTCATATCTCAAGATGAGAATGAGATTATATTAAAGGAAGACTCATGACTCAGGTGAGCA
TAAGATTATATTAAAG
Found at i:183159 original size:11 final size:11
Alignment explanation
Indices: 183139--183217 Score: 72
Period size: 11 Copynumber: 6.9 Consensus size: 11
183129 TATATTTTAA
183139 AAAATAATTTT
1 AAAATAATTTT
*
183150 AAATTAATTTT
1 AAAATAATTTT
**
183161 AAAATAATTAAA
1 AAAATAATT-TT
183173 AAAAGTATATTTT
1 AAAA-TA-ATTTT
183186 AAAAAATAATTTT
1 --AAAATAATTTT
183199 --AATAATTTT
1 AAAATAATTTT
183208 AAAATAATTT
1 AAAATAATTT
183218 CCTGACGTGG
Statistics
Matches: 55, Mismatches: 6, Indels: 14
0.73 0.08 0.19
Matches are distributed among these distances:
9 9 0.16
11 26 0.47
12 4 0.07
13 7 0.13
14 5 0.09
15 4 0.07
ACGTcount: A:0.56, C:0.00, G:0.01, T:0.43
Consensus pattern (11 bp):
AAAATAATTTT
Found at i:183213 original size:20 final size:22
Alignment explanation
Indices: 183121--183217 Score: 62
Period size: 20 Copynumber: 4.4 Consensus size: 22
183111 TGATGATTTT
183121 AATAATTTT-A-T-ATTTTAAAA
1 AATAATTTTAAGTAATTTT-AAA
*
183141 AATAATTTTAAATTAATTTT-AA
1 AATAATTTT-AAGTAATTTTAAA
**
183163 AATAATTAAAAAAAGTATATTTTAAAA
1 AATAATT---TTAAGTA-ATTTT-AAA
183190 AATAATTTTAA-TAATTTT-AA
1 AATAATTTTAAGTAATTTTAAA
183210 AATAATTT
1 AATAATTT
183218 CCTGACGTGG
Statistics
Matches: 62, Mismatches: 5, Indels: 20
0.71 0.06 0.23
Matches are distributed among these distances:
20 19 0.31
22 15 0.24
23 3 0.05
24 11 0.18
25 5 0.08
27 9 0.15
ACGTcount: A:0.54, C:0.00, G:0.01, T:0.45
Consensus pattern (22 bp):
AATAATTTTAAGTAATTTTAAA
Found at i:185634 original size:41 final size:41
Alignment explanation
Indices: 185571--185798 Score: 305
Period size: 41 Copynumber: 5.5 Consensus size: 41
185561 ACTTGATGTA
* *
185571 TAAATGGAAGGCTCATGTCTCGAGATAAGCATGAGATTATAT
1 TAAA-GGAAGACTCATGTCTCGAGATGAGCATGAGATTATAT
* * *
185613 TAAAGGAAGACTCGTGACTCGAAATGAGCATGAGATTATAT
1 TAAAGGAAGACTCATGTCTCGAGATGAGCATGAGATTATAT
*
185654 TAAAGGAAGACTCATGTCTC-AGGGTGAGCATGAGATTATAT
1 TAAAGGAAGACTCATGTCTCGA-GATGAGCATGAGATTATAT
* * *
185695 TAAAGGAAGACTCATGTCGCAAGGTGAGCATGAGATTATAT
1 TAAAGGAAGACTCATGTCTCGAGATGAGCATGAGATTATAT
* *
185736 TAAAGGAAGACTCGTGTCTCGGGATGAGCATGAGATTATATT
1 TAAAGGAAGACTCATGTCTCGAGATGAGCATGAGATTATA-T
* *
185778 TAAAGGAAGACTTATGACTCG
1 TAAAGGAAGACTCATGTCTCG
185799 GTAGATTGTA
Statistics
Matches: 165, Mismatches: 18, Indels: 6
0.87 0.10 0.03
Matches are distributed among these distances:
40 1 0.01
41 140 0.85
42 24 0.15
ACGTcount: A:0.36, C:0.12, G:0.26, T:0.26
Consensus pattern (41 bp):
TAAAGGAAGACTCATGTCTCGAGATGAGCATGAGATTATAT
Found at i:185813 original size:82 final size:79
Alignment explanation
Indices: 185571--185827 Score: 270
Period size: 82 Copynumber: 3.1 Consensus size: 79
185561 ACTTGATGTA
* * * *
185571 TAAATGGAAGGCTCATGTCTCGAGATAAGCATGAGATTATATTAAAGGAAGACTCGTGACTCGAA
1 TAAA-GGAAGACTCATGTCTCGGGATGAGCATGAGATTATATTAAAGGAAGACTCATGACTCG--
*
185636 ATGAGCATG-AGATTATAT
63 GT-AG-ATGTAGATTATAT
* *
185654 TAAAGGAAGACTCATGTCTCAGGG-TGAGCATGAGATTATATTAAAGGAAGACTCATGTCGCAAG
1 TAAAGGAAGACTCATGTCTC-GGGATGAGCATGAGATTATATTAAAGGAAGACTCATGACTC--G
185718 GTGAGCATG-AGATTATAT
63 GT-AG-ATGTAGATTATAT
* *
185736 TAAAGGAAGACTCGTGTCTCGGGATGAGCATGAGATTATATTTAAAGGAAGACTTATGACTCGGT
1 TAAAGGAAGACTCATGTCTCGGGATGAGCATGAGATTATA-TTAAAGGAAGACTCATGACTCGGT
*
185801 AGATTGTAAGATTGT-T
65 AGA-TGT-AGATTATAT
185817 TAAAAGGAAGA
1 T-AAAGGAAGA
185828 TCTGCGACTC
Statistics
Matches: 153, Mismatches: 12, Indels: 19
0.83 0.07 0.10
Matches are distributed among these distances:
79 1 0.01
80 4 0.03
81 8 0.05
82 115 0.75
83 24 0.16
84 1 0.01
ACGTcount: A:0.36, C:0.11, G:0.26, T:0.27
Consensus pattern (79 bp):
TAAAGGAAGACTCATGTCTCGGGATGAGCATGAGATTATATTAAAGGAAGACTCATGACTCGGTA
GATGTAGATTATAT
Found at i:188634 original size:19 final size:20
Alignment explanation
Indices: 188603--188655 Score: 72
Period size: 19 Copynumber: 2.7 Consensus size: 20
188593 TGAAGAATCT
*
188603 AATTTTATTTATTTTAATTA
1 AATTTTATTTATTTTAATAA
*
188623 AATTTT-TTTATTTTTATAA
1 AATTTTATTTATTTTAATAA
*
188642 AATTTTAGTTATTT
1 AATTTTATTTATTT
188656 ATATGTTTTA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
19 17 0.59
20 12 0.41
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (20 bp):
AATTTTATTTATTTTAATAA
Found at i:191323 original size:57 final size:57
Alignment explanation
Indices: 191262--191521 Score: 448
Period size: 57 Copynumber: 4.6 Consensus size: 57
191252 ACAACGACGG
* * * *
191262 CAATGAGAATGCAAGACAGAATGAGAACAATGATCTTGTTCAGATCAACACCAACAA
1 CAATGAGAATGCAGGCCAAAATGAGAACAATGATCCTGTTCAGATCAACACCAACAA
*
191319 CAATGAGAATGCAGGCCAAAATGAGAACAACGATCCTGTTCAGATCAACACCAACAA
1 CAATGAGAATGCAGGCCAAAATGAGAACAATGATCCTGTTCAGATCAACACCAACAA
191376 CAATGAGAATGCAGGCCAAAATGAGAACAATGATCCTGTTCAGATCAACACCAACAA
1 CAATGAGAATGCAGGCCAAAATGAGAACAATGATCCTGTTCAGATCAACACCAACAA
* *
191433 CAATGAGAATGCAGGCCAAAATGAGGACAATGATCCTGTTCAGATCAACACCAGCAA
1 CAATGAGAATGCAGGCCAAAATGAGAACAATGATCCTGTTCAGATCAACACCAACAA
*
191490 CAATGAGAATGCAGGCCAAAATGAGAATAATG
1 CAATGAGAATGCAGGCCAAAATGAGAACAATG
191522 CTGCTGAGGG
Statistics
Matches: 193, Mismatches: 10, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
57 193 1.00
ACGTcount: A:0.44, C:0.21, G:0.19, T:0.16
Consensus pattern (57 bp):
CAATGAGAATGCAGGCCAAAATGAGAACAATGATCCTGTTCAGATCAACACCAACAA
Found at i:191495 original size:30 final size:30
Alignment explanation
Indices: 191287--191495 Score: 85
Period size: 30 Copynumber: 7.3 Consensus size: 30
191277 ACAGAATGAG
* *
191287 AACAATGATCTTGTTCAGATCAACACCAAC
1 AACAATGATCATGTTCAGATCAACACCAGC
** ** * **
191317 AACAATGAGAATG--CAGGCCAAAATGAG-
1 AACAATGATCATGTTCAGATCAACACCAGC
* * *
191344 AACAACGATCCTGTTCAGATCAACACCAAC
1 AACAATGATCATGTTCAGATCAACACCAGC
** ** * **
191374 AACAATGAGAATG--CAGGCCAAAATGAG-
1 AACAATGATCATGTTCAGATCAACACCAGC
* *
191401 AACAATGATCCTGTTCAGATCAACACCAAC
1 AACAATGATCATGTTCAGATCAACACCAGC
** ** * **
191431 AACAATGAGAATG--CAGGCCAAAATGAG-
1 AACAATGATCATGTTCAGATCAACACCAGC
* *
191458 GACAATGATCCTGTTCAGATCAACACCAGC
1 AACAATGATCATGTTCAGATCAACACCAGC
191488 AACAATGA
1 AACAATGA
191496 GAATGCAGGC
Statistics
Matches: 113, Mismatches: 57, Indels: 18
0.60 0.30 0.10
Matches are distributed among these distances:
27 28 0.25
28 24 0.21
29 25 0.22
30 36 0.32
ACGTcount: A:0.43, C:0.23, G:0.17, T:0.16
Consensus pattern (30 bp):
AACAATGATCATGTTCAGATCAACACCAGC
Found at i:194760 original size:10 final size:10
Alignment explanation
Indices: 194745--194769 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
194735 TGGAAAGAAG
194745 GAAAATTTGA
1 GAAAATTTGA
194755 GAAAATTTGA
1 GAAAATTTGA
194765 GAAAA
1 GAAAA
194770 CAATTAGAAG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.56, C:0.00, G:0.20, T:0.24
Consensus pattern (10 bp):
GAAAATTTGA
Found at i:197997 original size:35 final size:35
Alignment explanation
Indices: 197958--198027 Score: 140
Period size: 35 Copynumber: 2.0 Consensus size: 35
197948 AGCGGTTGAA
197958 ACAAGGATCAGTTGGAGCATGAATGATTTTCTTGG
1 ACAAGGATCAGTTGGAGCATGAATGATTTTCTTGG
197993 ACAAGGATCAGTTGGAGCATGAATGATTTTCTTGG
1 ACAAGGATCAGTTGGAGCATGAATGATTTTCTTGG
198028 GAGGGATTTT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.29, C:0.11, G:0.29, T:0.31
Consensus pattern (35 bp):
ACAAGGATCAGTTGGAGCATGAATGATTTTCTTGG
Found at i:198847 original size:38 final size:37
Alignment explanation
Indices: 198804--198886 Score: 89
Period size: 37 Copynumber: 2.2 Consensus size: 37
198794 ACAATTTTAA
* *
198804 TCTAGAATTACG-CCAAAACATGTCG-CTGCATGAGCACT
1 TCTAG-ATTACGAACAAAAC-TGTCGTC-GCATGAACACT
*
198842 TCTAGATTGCGAACAAAACTGTCGTCGCATGAACACT
1 TCTAGATTACGAACAAAACTGTCGTCGCATGAACACT
*
198879 TCCAGATT
1 TCTAGATT
198887 GCACCCAAAA
Statistics
Matches: 39, Mismatches: 4, Indels: 5
0.81 0.08 0.10
Matches are distributed among these distances:
37 27 0.69
38 12 0.31
ACGTcount: A:0.31, C:0.25, G:0.18, T:0.25
Consensus pattern (37 bp):
TCTAGATTACGAACAAAACTGTCGTCGCATGAACACT
Found at i:198865 original size:37 final size:38
Alignment explanation
Indices: 198817--198888 Score: 103
Period size: 37 Copynumber: 1.9 Consensus size: 38
198807 AGAATTACGC
* *
198817 CAAAACATGTCG-CTGCATGAGCACTTCTAGATTGCGAA
1 CAAAACATGTCGTC-GCATGAACACTTCCAGATTGCGAA
198855 CAAAAC-TGTCGTCGCATGAACACTTCCAGATTGC
1 CAAAACATGTCGTCGCATGAACACTTCCAGATTGC
198889 ACCCAAAACT
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
37 24 0.77
38 7 0.23
ACGTcount: A:0.31, C:0.26, G:0.19, T:0.24
Consensus pattern (38 bp):
CAAAACATGTCGTCGCATGAACACTTCCAGATTGCGAA
Found at i:198896 original size:37 final size:37
Alignment explanation
Indices: 198816--198898 Score: 98
Period size: 37 Copynumber: 2.2 Consensus size: 37
198806 TAGAATTACG
* *
198816 CCAAAACATGTCGCTGCATGAGCACTTCTAGATTGCGA
1 CCAAAAC-TGTCGCTGCATGAACACTTCCAGATTGCGA
*
198854 ACAAAACTGTCG-TCGCATGAACACTTCCAGATTGC-A
1 CCAAAACTGTCGCT-GCATGAACACTTCCAGATTGCGA
198890 CCCAAAACT
1 -CCAAAACT
198899 ATCATCGTAG
Statistics
Matches: 39, Mismatches: 4, Indels: 5
0.81 0.08 0.10
Matches are distributed among these distances:
36 2 0.05
37 31 0.79
38 6 0.15
ACGTcount: A:0.33, C:0.29, G:0.17, T:0.22
Consensus pattern (37 bp):
CCAAAACTGTCGCTGCATGAACACTTCCAGATTGCGA
Found at i:199063 original size:27 final size:26
Alignment explanation
Indices: 199006--199064 Score: 75
Period size: 27 Copynumber: 2.3 Consensus size: 26
198996 ATTGCACCCA
199006 AGAA-TGTCGTTGCATGAACATGTAC
1 AGAATTGTCGTTGCATGAACATGTAC
* * *
199031 AAAATTGTCGCTTGCATGAACGTGTCC
1 AGAATTGTCG-TTGCATGAACATGTAC
199058 AGAATTG
1 AGAATTG
199065 CGCCCAGAAT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
25 3 0.11
26 5 0.18
27 20 0.71
ACGTcount: A:0.31, C:0.17, G:0.24, T:0.29
Consensus pattern (26 bp):
AGAATTGTCGTTGCATGAACATGTAC
Found at i:209941 original size:15 final size:15
Alignment explanation
Indices: 209917--209948 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
209907 CCCATAAAGC
209917 GGTGGAAATTGAGGT
1 GGTGGAAATTGAGGT
*
209932 GGTGGGAATTGAGGT
1 GGTGGAAATTGAGGT
209947 GG
1 GG
209949 CAATTGGTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.22, C:0.00, G:0.53, T:0.25
Consensus pattern (15 bp):
GGTGGAAATTGAGGT
Found at i:210150 original size:18 final size:18
Alignment explanation
Indices: 210127--210162 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
210117 ACTAGAAAAT
210127 GAAAACATATAAGGGTTA
1 GAAAACATATAAGGGTTA
210145 GAAAACATATAAGGGTTA
1 GAAAACATATAAGGGTTA
210163 TGATACAAAC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.50, C:0.06, G:0.22, T:0.22
Consensus pattern (18 bp):
GAAAACATATAAGGGTTA
Found at i:211760 original size:21 final size:21
Alignment explanation
Indices: 211732--211820 Score: 74
Period size: 21 Copynumber: 4.2 Consensus size: 21
211722 AATTAAGTTA
211732 TAAA-ATTAATATAAAATAAT
1 TAAATATTAATATAAAATAAT
* *
211752 TAAATATTACTAAAAAATAAT
1 TAAATATTAATATAAAATAAT
* * * *
211773 TAAATTATAAAAACAAAATAAGA
1 TAAA-TATTAATATAAAATAA-T
*
211796 TAAATAAATAATATAAAA-AAT
1 TAAAT-ATTAATATAAAATAAT
211817 TAAA
1 TAAA
211821 ATGAACTCTT
Statistics
Matches: 53, Mismatches: 12, Indels: 7
0.74 0.17 0.10
Matches are distributed among these distances:
20 4 0.08
21 22 0.42
22 15 0.28
23 12 0.23
ACGTcount: A:0.67, C:0.02, G:0.01, T:0.29
Consensus pattern (21 bp):
TAAATATTAATATAAAATAAT
Found at i:211781 original size:48 final size:47
Alignment explanation
Indices: 211701--211816 Score: 137
Period size: 48 Copynumber: 2.5 Consensus size: 47
211691 AGCTATTCAC
* ** *
211701 ATAAA-AAATATT-TAAAAAATTAATTAAGTTATAAAATTAATATAAA
1 ATAAATAAATATTATAAAAAA-TAATTAAATTATAAAAACAAAATAAA
* *
211747 ATAATTAAATATTACTAAAAAATAATTAAATTATAAAAACAAAATAAG
1 ATAAATAAATATTA-TAAAAAATAATTAAATTATAAAAACAAAATAAA
*
211795 ATAAATAAATAATATAAAAAAT
1 ATAAATAAATATTATAAAAAAT
211817 TAAAATGAAC
Statistics
Matches: 59, Mismatches: 8, Indels: 5
0.82 0.11 0.07
Matches are distributed among these distances:
46 4 0.07
47 15 0.25
48 33 0.56
49 7 0.12
ACGTcount: A:0.66, C:0.02, G:0.02, T:0.31
Consensus pattern (47 bp):
ATAAATAAATATTATAAAAAATAATTAAATTATAAAAACAAAATAAA
Found at i:211946 original size:19 final size:19
Alignment explanation
Indices: 211922--211960 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
211912 GAAATTTGTG
*
211922 TAAAAAATTTAGCGAATTT
1 TAAAAAATTTAGAGAATTT
* *
211941 TAAAAACTTTTGAGAATTT
1 TAAAAAATTTAGAGAATTT
211960 T
1 T
211961 GAGAGCTTTA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.44, C:0.05, G:0.10, T:0.41
Consensus pattern (19 bp):
TAAAAAATTTAGAGAATTT
Found at i:212411 original size:30 final size:30
Alignment explanation
Indices: 212343--212411 Score: 93
Period size: 30 Copynumber: 2.3 Consensus size: 30
212333 TAAACCCAAA
** * * *
212343 TAAAAATGCTTAATACACGAAATATTATAT
1 TAAAAATATTTAATACACAAAACACTATAT
212373 TAAAAATATTTAATACACAAAACACTATAT
1 TAAAAATATTTAATACACAAAACACTATAT
212403 TAAAAATAT
1 TAAAAATAT
212412 CCAATTTCTT
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
30 34 1.00
ACGTcount: A:0.55, C:0.10, G:0.03, T:0.32
Consensus pattern (30 bp):
TAAAAATATTTAATACACAAAACACTATAT
Found at i:216599 original size:22 final size:22
Alignment explanation
Indices: 216575--216645 Score: 126
Period size: 22 Copynumber: 3.3 Consensus size: 22
216565 ATAAAATCTT
216575 TTTTTTTTG-TCAAATTGATCA
1 TTTTTTTTGATCAAATTGATCA
*
216596 TTTTTTTGGATCAAATTGATCA
1 TTTTTTTTGATCAAATTGATCA
216618 TTTTTTTTGATCAAATTGATCA
1 TTTTTTTTGATCAAATTGATCA
216640 TTTTTT
1 TTTTTT
216646 AACGGTCTTG
Statistics
Matches: 47, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
21 8 0.17
22 39 0.83
ACGTcount: A:0.24, C:0.08, G:0.10, T:0.58
Consensus pattern (22 bp):
TTTTTTTTGATCAAATTGATCA
Found at i:216814 original size:9 final size:9
Alignment explanation
Indices: 216792--216838 Score: 53
Period size: 9 Copynumber: 5.2 Consensus size: 9
216782 AAATTATTTT
216792 TTAAAA-TA
1 TTAAAATTA
216800 -TAAAATTA
1 TTAAAATTA
216808 TTAAAATTAA
1 TTAAAATT-A
*
216818 TTTAAAAATA
1 -TTAAAATTA
216828 TTAAAATTA
1 TTAAAATTA
216837 TT
1 TT
216839 TTTTTGAAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 7
0.79 0.05 0.17
Matches are distributed among these distances:
7 5 0.15
8 2 0.06
9 17 0.52
10 2 0.06
11 7 0.21
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (9 bp):
TTAAAATTA
Found at i:216832 original size:29 final size:29
Alignment explanation
Indices: 216779--216838 Score: 86
Period size: 29 Copynumber: 2.1 Consensus size: 29
216769 GTAAATGATT
* *
216779 TTAAAATTATTTTTTAAAATATAAAATTA
1 TTAAAATTATATTTAAAAATATAAAATTA
216808 TTAAAATTA-ATTTAAAAATATTAAAATTA
1 TTAAAATTATATTTAAAAATA-TAAAATTA
216837 TT
1 TT
216839 TTTTTGAAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
28 9 0.32
29 19 0.68
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (29 bp):
TTAAAATTATATTTAAAAATATAAAATTA
Found at i:218572 original size:24 final size:26
Alignment explanation
Indices: 218536--218584 Score: 66
Period size: 24 Copynumber: 2.0 Consensus size: 26
218526 AAACACATTT
*
218536 ACCCACTTAGCAATCCTTTGGGTTCG
1 ACCCACTTAGCAATACTTTGGGTTCG
*
218562 ACCC-CTT-GCAATACTTTGTGTTC
1 ACCCACTTAGCAATACTTTGGGTTC
218585 CATCGGAATT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 14 0.67
25 3 0.14
26 4 0.19
ACGTcount: A:0.18, C:0.31, G:0.16, T:0.35
Consensus pattern (26 bp):
ACCCACTTAGCAATACTTTGGGTTCG
Found at i:220418 original size:36 final size:36
Alignment explanation
Indices: 220349--220455 Score: 110
Period size: 36 Copynumber: 3.0 Consensus size: 36
220339 TCATATGATA
* * * *
220349 TCTTCAAGTTTCCTAGT-AATTAAACTCATACGAGC
1 TCTTCAAGTTACCCAGTAAATTCAACTCTTACGAGC
* * * *
220384 TTTTCACA-TTTCTCATTAAATTCAACTCTTACGAGC
1 TCTTCA-AGTTACCCAGTAAATTCAACTCTTACGAGC
*
220420 TCTTCAAGTTACCCAGTAAATTCAGCTCTTACGAGC
1 TCTTCAAGTTACCCAGTAAATTCAACTCTTACGAGC
220456 CAGTATAGTA
Statistics
Matches: 58, Mismatches: 11, Indels: 5
0.78 0.15 0.07
Matches are distributed among these distances:
35 12 0.21
36 46 0.79
ACGTcount: A:0.29, C:0.25, G:0.10, T:0.36
Consensus pattern (36 bp):
TCTTCAAGTTACCCAGTAAATTCAACTCTTACGAGC
Found at i:220479 original size:19 final size:19
Alignment explanation
Indices: 220455--220492 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
220445 CTCTTACGAG
* *
220455 CCAGTATAGTATATTGCTC
1 CCAGTATAATATATGGCTC
220474 CCAGTATAATATATGGCTC
1 CCAGTATAATATATGGCTC
220493 TTTTGAATCT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.29, C:0.21, G:0.16, T:0.34
Consensus pattern (19 bp):
CCAGTATAATATATGGCTC
Found at i:223371 original size:16 final size:16
Alignment explanation
Indices: 223352--223383 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
223342 CTATCCTCTA
223352 TTTCAACTGAAGAAAG
1 TTTCAACTGAAGAAAG
223368 TTTCAACTGAAGAAAG
1 TTTCAACTGAAGAAAG
223384 GGATCGAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.44, C:0.12, G:0.19, T:0.25
Consensus pattern (16 bp):
TTTCAACTGAAGAAAG
Found at i:224652 original size:18 final size:18
Alignment explanation
Indices: 224629--224668 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
224619 ATTCCGATAA
*
224629 AATCGAAAAAACTTGGTT
1 AATCGAAAAAACTCGGTT
**
224647 AATCGATCAAACTCGGTT
1 AATCGAAAAAACTCGGTT
224665 AATC
1 AATC
224669 TATCGGGGTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.40, C:0.17, G:0.15, T:0.28
Consensus pattern (18 bp):
AATCGAAAAAACTCGGTT
Found at i:226674 original size:24 final size:24
Alignment explanation
Indices: 226618--226727 Score: 132
Period size: 24 Copynumber: 4.6 Consensus size: 24
226608 ATTAGTTGGT
* *
226618 GAGCGTAAACGCAAAGTGGCT-AGC
1 GAGCATAAACGTAAAGTGGCTGA-C
*
226642 GAGCGTAAACGTAAAGTGGCTGAC
1 GAGCATAAACGTAAAGTGGCTGAC
* * **
226666 AAGCATAAACGTGAAGTGTTTGAC
1 GAGCATAAACGTAAAGTGGCTGAC
*
226690 GAGCATAAACATAAAGTGGCTGAC
1 GAGCATAAACGTAAAGTGGCTGAC
226714 GAGCATAAACGTAA
1 GAGCATAAACGTAA
226728 TTGAAACTTG
Statistics
Matches: 73, Mismatches: 12, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
24 72 0.99
25 1 0.01
ACGTcount: A:0.38, C:0.16, G:0.28, T:0.17
Consensus pattern (24 bp):
GAGCATAAACGTAAAGTGGCTGAC
Found at i:228067 original size:19 final size:20
Alignment explanation
Indices: 228022--228068 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 20
228012 GCCCCTATTC
**
228022 CTCAAATTTTTCAACTTTTT
1 CTCAAATTTTTCAACTTTGA
* *
228042 CTTAAATTTTTGAA-TTTGA
1 CTCAAATTTTTCAACTTTGA
228061 CTCAAATT
1 CTCAAATT
228069 AGTCCTGAAT
Statistics
Matches: 22, Mismatches: 5, Indels: 1
0.79 0.18 0.04
Matches are distributed among these distances:
19 10 0.45
20 12 0.55
ACGTcount: A:0.30, C:0.15, G:0.04, T:0.51
Consensus pattern (20 bp):
CTCAAATTTTTCAACTTTGA
Found at i:237624 original size:21 final size:21
Alignment explanation
Indices: 237585--237625 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
237575 AAAGTTAACA
*
237585 ATCAACGGTCAAAGGTCAACT
1 ATCAACGGTCAAAGATCAACT
*
237606 ATCAACGGTCAACGATCAAC
1 ATCAACGGTCAAAGATCAAC
237626 CAACGGTCAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.39, C:0.27, G:0.17, T:0.17
Consensus pattern (21 bp):
ATCAACGGTCAAAGATCAACT
Found at i:237625 original size:14 final size:14
Alignment explanation
Indices: 237586--237625 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
237576 AAGTTAACAA
* *
237586 TCAACGGTCAAAGG
1 TCAACGATCAACGG
*
237600 TCAACTATCAACGG
1 TCAACGATCAACGG
237614 TCAACGATCAAC
1 TCAACGATCAAC
237626 CAACGGTCAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.38, C:0.28, G:0.17, T:0.17
Consensus pattern (14 bp):
TCAACGATCAACGG
Found at i:237724 original size:20 final size:21
Alignment explanation
Indices: 237699--237745 Score: 69
Period size: 20 Copynumber: 2.3 Consensus size: 21
237689 GGTTTACTTA
*
237699 GTTTGGGTCAAAA-GGTTTGG
1 GTTTGGGTCAAAAGGGTCTGG
*
237719 GTTTGGTTCAAAAGGGTCTGG
1 GTTTGGGTCAAAAGGGTCTGG
237740 GTTTGG
1 GTTTGG
237746 TGATATTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
20 12 0.50
21 12 0.50
ACGTcount: A:0.17, C:0.06, G:0.40, T:0.36
Consensus pattern (21 bp):
GTTTGGGTCAAAAGGGTCTGG
Found at i:237742 original size:21 final size:20
Alignment explanation
Indices: 237699--237746 Score: 69
Period size: 21 Copynumber: 2.4 Consensus size: 20
237689 GGTTTACTTA
* *
237699 GTTTGGGTCAAAAGGTTTGG
1 GTTTGGTTCAAAAGGTCTGG
237719 GTTTGGTTCAAAAGGGTCTGG
1 GTTTGGTTCAAAA-GGTCTGG
237740 GTTTGGT
1 GTTTGGT
237747 GATATTAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
20 12 0.48
21 13 0.52
ACGTcount: A:0.17, C:0.06, G:0.40, T:0.38
Consensus pattern (20 bp):
GTTTGGTTCAAAAGGTCTGG
Found at i:244435 original size:20 final size:21
Alignment explanation
Indices: 244410--244459 Score: 57
Period size: 20 Copynumber: 2.4 Consensus size: 21
244400 TGGTTCACTT
*
244410 GGTTTGGATCAAAA-GGCTTG
1 GGTTTGGATCAAAAGGGCTTA
* * *
244430 GGTTTGGTTTAAAAGGGTTTA
1 GGTTTGGATCAAAAGGGCTTA
244451 GGTTTGGAT
1 GGTTTGGAT
244460 TTGGCTGGAG
Statistics
Matches: 24, Mismatches: 5, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
20 12 0.50
21 12 0.50
ACGTcount: A:0.22, C:0.04, G:0.36, T:0.38
Consensus pattern (21 bp):
GGTTTGGATCAAAAGGGCTTA
Found at i:247205 original size:21 final size:20
Alignment explanation
Indices: 247156--247207 Score: 52
Period size: 21 Copynumber: 2.5 Consensus size: 20
247146 TGTGCTAGTT
*
247156 CTACCGATACAAGTATGATTT
1 CTACCGATACAAGTATGA-TA
*
247177 CTATCGATACAAGTCATGCA-A
1 CTACCGATACAAGT-ATG-ATA
247198 CTACCGATAC
1 CTACCGATAC
247208 CAAAAACTCC
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
21 22 0.85
22 3 0.12
23 1 0.04
ACGTcount: A:0.35, C:0.25, G:0.13, T:0.27
Consensus pattern (20 bp):
CTACCGATACAAGTATGATA
Found at i:259808 original size:18 final size:17
Alignment explanation
Indices: 259785--259818 Score: 59
Period size: 18 Copynumber: 1.9 Consensus size: 17
259775 TCAGCAATTT
259785 TTTCTTCTTTTTCTTTTC
1 TTTCTTCTTTTT-TTTTC
259803 TTTCTTCTTTTTTTTT
1 TTTCTTCTTTTTTTTT
259819 AAATGACTGA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 4 0.25
18 12 0.75
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (17 bp):
TTTCTTCTTTTTTTTTC
Found at i:266885 original size:115 final size:115
Alignment explanation
Indices: 266678--266910 Score: 457
Period size: 115 Copynumber: 2.0 Consensus size: 115
266668 ATAATCAATG
266678 TCAATGCAATTAGAGTTAAACTTCAGAGTTAAAATAATTTTAGAGAACATGGTTGCACCCTTTAA
1 TCAATGCAATTAGAGTTAAACTTCAGAGTTAAAATAATTTTAGAGAACATGGTTGCACCCTTTAA
266743 TTGGTCAAATAACTCATCGATCCGAGGCAATGGATACTTATTCTTGATTA
66 TTGGTCAAATAACTCATCGATCCGAGGCAATGGATACTTATTCTTGATTA
266793 TCAATGCAATTAGAGTTAAACTTCAGAGTTAAAATAATTTTAGAGAACATGGTTGCACCCTTTAA
1 TCAATGCAATTAGAGTTAAACTTCAGAGTTAAAATAATTTTAGAGAACATGGTTGCACCCTTTAA
*
266858 TTGGTCAAATAACTCATCGATCGGAGGCAATGGATACTTATTCTTGATTA
66 TTGGTCAAATAACTCATCGATCCGAGGCAATGGATACTTATTCTTGATTA
266908 TCA
1 TCA
266911 CCTTATTTAG
Statistics
Matches: 117, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
115 117 1.00
ACGTcount: A:0.35, C:0.15, G:0.17, T:0.33
Consensus pattern (115 bp):
TCAATGCAATTAGAGTTAAACTTCAGAGTTAAAATAATTTTAGAGAACATGGTTGCACCCTTTAA
TTGGTCAAATAACTCATCGATCCGAGGCAATGGATACTTATTCTTGATTA
Found at i:269426 original size:21 final size:21
Alignment explanation
Indices: 269402--269449 Score: 78
Period size: 21 Copynumber: 2.3 Consensus size: 21
269392 CTGTGTAGAC
269402 TTCTATCGATACTTGTGCTAG
1 TTCTATCGATACTTGTGCTAG
*
269423 TTCTACCGATACTTGTGCTAG
1 TTCTATCGATACTTGTGCTAG
*
269444 TACTAT
1 TTCTAT
269450 AAACTACCGA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.21, C:0.21, G:0.17, T:0.42
Consensus pattern (21 bp):
TTCTATCGATACTTGTGCTAG
Found at i:274614 original size:3 final size:3
Alignment explanation
Indices: 274608--274659 Score: 54
Period size: 3 Copynumber: 17.3 Consensus size: 3
274598 AGAAGTGAAG
* *
274608 GAA GAA GAA GAA GAA GAA GGAA -AA GAA GAA GAA AAA GAG GAA GGAA
1 GAA GAA GAA GAA GAA GAA -GAA GAA GAA GAA GAA GAA GAA GAA -GAA
274654 -AA GAA G
1 GAA GAA G
274660 TCAAGGCAAA
Statistics
Matches: 41, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
2 4 0.10
3 31 0.76
4 6 0.15
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:274623 original size:12 final size:12
Alignment explanation
Indices: 274608--274659 Score: 70
Period size: 12 Copynumber: 4.3 Consensus size: 12
274598 AGAAGTGAAG
274608 GAAGAA-GAAGAA
1 GAAGAAGGAA-AA
274620 GAAGAAGGAAAA
1 GAAGAAGGAAAA
*
274632 GAAGAAGAAAAA
1 GAAGAAGGAAAA
*
274644 GAGGAAGGAAAA
1 GAAGAAGGAAAA
274656 GAAG
1 GAAG
274660 TCAAGGCAAA
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
12 32 0.91
13 3 0.09
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (12 bp):
GAAGAAGGAAAA
Found at i:274623 original size:24 final size:23
Alignment explanation
Indices: 274596--274659 Score: 82
Period size: 21 Copynumber: 2.9 Consensus size: 23
274586 AAAACAAGTG
274596 GAAGAAGTGAAGGAAGAAGAAGAA
1 GAAGAAG-GAAGGAAGAAGAAGAA
274620 GAAGAAGGAA--AAGAAGAAGAA
1 GAAGAAGGAAGGAAGAAGAAGAA
*
274641 AAAG-AGGAAGGAA-AAGAAG
1 GAAGAAGGAAGGAAGAAGAAG
274660 TCAAGGCAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 7
0.82 0.02 0.16
Matches are distributed among these distances:
20 5 0.14
21 20 0.54
22 2 0.05
23 3 0.08
24 7 0.19
ACGTcount: A:0.62, C:0.00, G:0.36, T:0.02
Consensus pattern (23 bp):
GAAGAAGGAAGGAAGAAGAAGAA
Found at i:290311 original size:19 final size:19
Alignment explanation
Indices: 290287--290330 Score: 63
Period size: 19 Copynumber: 2.3 Consensus size: 19
290277 TAAAAAAATT
*
290287 AAAATTCA-AAAAACTATAA
1 AAAATTCATAAAAA-TACAA
290306 AAAATTCATAAAAATACAA
1 AAAATTCATAAAAATACAA
290325 AAAATT
1 AAAATT
290331 AGCATGGAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 18 0.78
20 5 0.22
ACGTcount: A:0.68, C:0.09, G:0.00, T:0.23
Consensus pattern (19 bp):
AAAATTCATAAAAATACAA
Found at i:290935 original size:31 final size:31
Alignment explanation
Indices: 290893--291010 Score: 88
Period size: 31 Copynumber: 3.9 Consensus size: 31
290883 TTAATATAAT
*
290893 ATTTGGTACCTAAACTTGACACTTTTT-TTAA
1 ATTTGGAACCTAAACTTGACACTTTTTGTT-A
*
290924 ATTTGGAACCTAAACTTG----TTTTTGGTCCA
1 ATTTGGAACCTAAACTTGACACTTTTT-GT-TA
* **
290953 ATTT-GATA-GTCAAACTTGACACTTTTTCCTA
1 ATTTGGA-ACCT-AAACTTGACACTTTTTGTTA
*
290984 ATTTGGTACCTAAACTTGACACTTTTT
1 ATTTGGAACCTAAACTTGACACTTTTT
291011 TTTTAAGTTG
Statistics
Matches: 68, Mismatches: 8, Indels: 22
0.69 0.08 0.22
Matches are distributed among these distances:
27 5 0.07
28 3 0.04
29 14 0.21
31 39 0.57
32 2 0.03
33 5 0.07
ACGTcount: A:0.27, C:0.18, G:0.12, T:0.43
Consensus pattern (31 bp):
ATTTGGAACCTAAACTTGACACTTTTTGTTA
Found at i:291028 original size:31 final size:31
Alignment explanation
Indices: 290964--291031 Score: 93
Period size: 31 Copynumber: 2.2 Consensus size: 31
290954 TTTGATAGTC
*
290964 AAACTTGACACTTTTTCCTAATTTGGTACCT
1 AAACTTGACACTTTTTCCTAAGTTGGTACCT
**
290995 AAACTTGACACTTTTTTTTTAAGTTGGTA-CT
1 AAACTTGACAC-TTTTTCCTAAGTTGGTACCT
291026 AAACTT
1 AAACTT
291032 TTTGGGATCC
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
31 19 0.58
32 14 0.42
ACGTcount: A:0.28, C:0.18, G:0.10, T:0.44
Consensus pattern (31 bp):
AAACTTGACACTTTTTCCTAAGTTGGTACCT
Found at i:291077 original size:90 final size:91
Alignment explanation
Indices: 290893--291086 Score: 243
Period size: 90 Copynumber: 2.1 Consensus size: 91
290883 TTAATATAAT
* *
290893 ATTTGGTACCTAAACTTGACACTTTTTTTAAATTTGGAACCTAAACTTGTTTTTGGTCCAATTTG
1 ATTTGGTACCTAAACTTGACACTTTTTTTAAAGTTGGAACCTAAACTTGTTTTGGGTCCAATTTG
*
290958 ATAGTCAAACTTGACACTTTTTCCTA
66 ATACTCAAACTTGACACTTTTTCCTA
* *
290984 ATTTGGTACCTAAACTTGACACTTTTTTTTTAAGTTGGTA-CTAAAC-T-TTTTGGGATCCAATT
1 ATTTGGTACCTAAACTTGACAC-TTTTTTTAAAGTTGGAACCTAAACTTGTTTTGGG-TCCAATT
* ** *
291046 TGGTACTTGAACTT-ACCTCTTTTTCCTA
64 TGATACTCAAACTTGA-CACTTTTTCCTA
*
291074 ATTTAGTACCTAA
1 ATTTGGTACCTAA
291087 TATTAAGCCT
Statistics
Matches: 90, Mismatches: 10, Indels: 7
0.84 0.09 0.07
Matches are distributed among these distances:
89 7 0.08
90 41 0.46
91 28 0.31
92 14 0.16
ACGTcount: A:0.26, C:0.18, G:0.12, T:0.44
Consensus pattern (91 bp):
ATTTGGTACCTAAACTTGACACTTTTTTTAAAGTTGGAACCTAAACTTGTTTTGGGTCCAATTTG
ATACTCAAACTTGACACTTTTTCCTA
Found at i:294295 original size:17 final size:17
Alignment explanation
Indices: 294244--294296 Score: 54
Period size: 17 Copynumber: 3.1 Consensus size: 17
294234 TTTTTGAAAT
*
294244 TTTTAATAATGTCAATAA
1 TTTTAATAATTTC-ATAA
* **
294262 ATTT-ATAATTTTTTAA
1 TTTTAATAATTTCATAA
294278 TTTTAATAATTTCATAA
1 TTTTAATAATTTCATAA
294295 TT
1 TT
294297 GGGTAAATTG
Statistics
Matches: 27, Mismatches: 7, Indels: 3
0.73 0.19 0.08
Matches are distributed among these distances:
16 6 0.22
17 18 0.67
18 3 0.11
ACGTcount: A:0.40, C:0.04, G:0.02, T:0.55
Consensus pattern (17 bp):
TTTTAATAATTTCATAA
Found at i:305258 original size:23 final size:23
Alignment explanation
Indices: 305228--305394 Score: 271
Period size: 23 Copynumber: 7.3 Consensus size: 23
305218 TCATAGGTCC
305228 ATTTAAGCATAAATCACATTAAT
1 ATTTAAGCATAAATCACATTAAT
* *
305251 ATTTAAGCATAAATCATATTAAC
1 ATTTAAGCATAAATCACATTAAT
*
305274 ATTTAAGCATAAATCACATTGAT
1 ATTTAAGCATAAATCACATTAAT
* * *
305297 ATTTAAGCATAAATTATATTAAC
1 ATTTAAGCATAAATCACATTAAT
305320 ATTTAAGCATAAATCACATTAAT
1 ATTTAAGCATAAATCACATTAAT
305343 ATTTAAGCATAAATCACATTAAT
1 ATTTAAGCATAAATCACATTAAT
*
305366 ATTTAAGCATAAATTACATTAAT
1 ATTTAAGCATAAATCACATTAAT
305389 ATTTAA
1 ATTTAA
305395 CACATTTAAT
Statistics
Matches: 131, Mismatches: 13, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 131 1.00
ACGTcount: A:0.47, C:0.11, G:0.05, T:0.37
Consensus pattern (23 bp):
ATTTAAGCATAAATCACATTAAT
Done.