Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000901.1 Hibiscus syriacus cultivar Beakdansim tig00001769_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: 118845
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:470 original size:11 final size:11
Alignment explanation
Indices: 454--491 Score: 60
Period size: 11 Copynumber: 3.5 Consensus size: 11
444 TTAATAATAA
454 AAAATAACAAT
1 AAAATAACAAT
465 AAAATAACAAT
1 AAAATAACAAT
*
476 -AAATAATAAT
1 AAAATAACAAT
486 AAAATA
1 AAAATA
492 TTATTATAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
10 9 0.36
11 16 0.64
ACGTcount: A:0.74, C:0.05, G:0.00, T:0.21
Consensus pattern (11 bp):
AAAATAACAAT
Found at i:479 original size:10 final size:10
Alignment explanation
Indices: 455--488 Score: 50
Period size: 10 Copynumber: 3.3 Consensus size: 10
445 TAATAATAAA
455 AAATAACAAT
1 AAATAACAAT
465 AAAATAACAAT
1 -AAATAACAAT
*
476 AAATAATAAT
1 AAATAACAAT
486 AAA
1 AAA
489 ATATTATTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
10 12 0.55
11 10 0.45
ACGTcount: A:0.74, C:0.06, G:0.00, T:0.21
Consensus pattern (10 bp):
AAATAACAAT
Found at i:479 original size:21 final size:21
Alignment explanation
Indices: 446--491 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
436 AATTAAAATT
*
446 AATAATAAAAAATAACAATAA
1 AATAACAAAAAATAACAATAA
* *
467 AATAACAATAAATAATAATAA
1 AATAACAAAAAATAACAATAA
488 AATA
1 AATA
492 TTATTATAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.74, C:0.04, G:0.00, T:0.22
Consensus pattern (21 bp):
AATAACAAAAAATAACAATAA
Found at i:566 original size:34 final size:34
Alignment explanation
Indices: 522--593 Score: 101
Period size: 34 Copynumber: 2.1 Consensus size: 34
512 TCCAAAAACC
522 TATATAATATATTTCAAAAAAATATTT-AAAATTA
1 TATATAATATATTT-AAAAAAATATTTCAAAATTA
* * *
556 TATATTATATATTTTAAAAAATATTTCTAAATTA
1 TATATAATATATTTAAAAAAATATTTCAAAATTA
590 TATA
1 TATA
594 GTTTTCGAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
33 11 0.32
34 23 0.68
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (34 bp):
TATATAATATATTTAAAAAAATATTTCAAAATTA
Found at i:621 original size:24 final size:24
Alignment explanation
Indices: 594--641 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 24
584 AAATTATATA
*
594 GTTTTCGAAATG-TTTTAAAACTAT
1 GTTTTC-AAATGATTTCAAAACTAT
618 GTTTTCAAATGATTTCAAAACTAT
1 GTTTTCAAATGATTTCAAAACTAT
642 ATATTATATG
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 5 0.23
24 17 0.77
ACGTcount: A:0.35, C:0.10, G:0.10, T:0.44
Consensus pattern (24 bp):
GTTTTCAAATGATTTCAAAACTAT
Found at i:694 original size:37 final size:36
Alignment explanation
Indices: 619--719 Score: 107
Period size: 37 Copynumber: 2.8 Consensus size: 36
609 TAAAACTATG
* * * **
619 TTTTC-AAATGATTTCAAAACTATATATTATATGTA
1 TTTTCAAAATGTTTTCAAAACCATATAATATATACA
654 TTTTCAAAATGTTTTCAAAATCCATATAATATATACA
1 TTTTCAAAATGTTTTCAAAA-CCATATAATATATACA
* *
691 TTTTTAAAATGTTTTTCAAAA-AATATAAT
1 TTTTCAAAATG-TTTTCAAAACCATATAAT
720 GTTTTCAAAC
Statistics
Matches: 56, Mismatches: 7, Indels: 5
0.82 0.10 0.07
Matches are distributed among these distances:
35 5 0.09
36 20 0.36
37 22 0.39
38 9 0.16
ACGTcount: A:0.43, C:0.09, G:0.04, T:0.45
Consensus pattern (36 bp):
TTTTCAAAATGTTTTCAAAACCATATAATATATACA
Found at i:724 original size:29 final size:29
Alignment explanation
Indices: 684--747 Score: 85
Period size: 29 Copynumber: 2.2 Consensus size: 29
674 TCCATATAAT
*
684 ATATACATTTTTAAAATGTTTTTCAAAAA
1 ATATACATTTTTAAAACGTTTTTCAAAAA
*
713 ATATA-ATGTTTTCAAACGTTTTTCAAAAA
1 ATATACAT-TTTTAAAACGTTTTTCAAAAA
742 ACTATA
1 A-TATA
748 TATTATATGC
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
28 2 0.06
29 25 0.81
30 4 0.13
ACGTcount: A:0.44, C:0.09, G:0.05, T:0.42
Consensus pattern (29 bp):
ATATACATTTTTAAAACGTTTTTCAAAAA
Found at i:785 original size:35 final size:34
Alignment explanation
Indices: 740--860 Score: 120
Period size: 35 Copynumber: 3.5 Consensus size: 34
730 GTTTTTCAAA
740 AAACTATATATTATATGCTTTTC-AAAATATTTTT
1 AAACTATATATTATATG-TTTTCAAAAATATTTTT
*
774 AAACCTATATA-TATAAGTTTTCTAAAAATATTTTT
1 AAA-CTATATATTATATGTTTTC-AAAAATATTTTT
* * * **
809 AAAGTCATATATTATATATTTCCAAAAATGATTTCA
1 AAACT-ATATATTATATGTTTTCAAAAAT-ATTTTT
*
845 AAACTATATATAATAT
1 AAACTATATATTATAT
861 ATACTAAAAA
Statistics
Matches: 72, Mismatches: 9, Indels: 11
0.78 0.10 0.12
Matches are distributed among these distances:
33 5 0.07
34 9 0.12
35 42 0.58
36 16 0.22
ACGTcount: A:0.44, C:0.09, G:0.03, T:0.44
Consensus pattern (34 bp):
AAACTATATATTATATGTTTTCAAAAATATTTTT
Found at i:1575 original size:84 final size:83
Alignment explanation
Indices: 1480--2617 Score: 1018
Period size: 83 Copynumber: 13.7 Consensus size: 83
1470 GAGCAGTGTA
* * * * *
1480 TCGAACTCGAAGGT-TTTCGGTGACAGATAACCCTTATCGAATTAAGTTATGCTGTAAATGATGT
1 TCGAACTCGAAGGTCTTT-GGTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATAT
* ** *
1544 GCCCTAGAAGCTGAATGTAA
65 G-CCTTGAAGCTGAGCGTAG
* *
1564 TCGAACTCGAAGGTATTTGTTGGCAGAT-ACCCTTCTCGACTTAAGTTATGCTGCAAATGATATG
1 TCGAACTCGAAGGTCTTTGGTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATATG
*
1628 CCTTGGAGCTGAGCGTAG
66 CCTTGAAGCTGAGCGTAG
* * * * * * *
1646 TCAAACTCGAA-GTCTTTTGGTGTCAGATAACCCTTCTAGCCTTGAGTTATGTTGTAAATGATAT
1 TCGAACTCGAAGGTC-TTTGGTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATAT
** *
1710 GCCTTGAAGCTGATTGTAA
65 GCCTTGAAGCTGAGCGTAG
* * * * * *
1729 TCGAGCTTGAGGGTC-TT--TGGCAGATATCCCTTCTCGACTTAAGTTA-GCTGTAAATGATGTG
1 TCGAACTCGAAGGTCTTTGGTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATATG
* * *
1790 CATTGGAG-TGAGAGTAG
66 CCTTGAAGCTGAGCGTAG
* *
1807 TCAAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATTCTGCAAATGATAT
1 TCGAACTCGAAGGTCTTTGG-TGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATAT
* *
1872 ACCTTGGAGCTGAGCGTAG
65 GCCTTGAAGCTGAGCGTAG
* * * * * * * *
1891 CCGAACTCGAAGGTCTTTGGTTGTAGATAGCCCTTCTCGACTTAAGCTATGCTACAAAGGATTTA
1 TCGAACTCGAAGGTCTTTGGTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATAT-
* *
1956 CCCTCGAAGCTGAGCGTAG
65 GCCTTGAAGCTGAGCGTAG
** ** * * ** * *
1975 TCGAACTCGAAGGTCTTTATTAACAGATAA-CCTTCTAGCCTTGGGTTATG-TGTAAATGATGTG
1 TCGAACTCGAAGGTCTTTGGTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATATG
* * *
2038 CCTTTGAAGCTAAGTGTAA
66 CC-TTGAAGCTGAGCGTAG
* * * * *
2057 TCAAACTC-AGGGGATCTTTGGTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGC-AATGC
1 TCGAACTCGA-AGG-TCTTTGG--TGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGA
* **
2120 TGTGTTGTTG-AGCTGAGCGTAG
62 TATG-CCTTGAAGCTGAGCGTAG
* * * * * *
2142 TCAAACTCAAAGGTCTTTTGTTGGTAGATAACCCTTCTAGACTTAAGTTATGTTGCAAATG-TAT
1 TCGAACTCGAAGGTC-TTTGGTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATAT
*
2206 GCCTTGGAGCTGAGCGTAG
65 GCCTTGAAGCTGAGCGTAG
* * ** * *
2225 TCAAACTTGGGGGTCTTTGGTTGGCAGATAGCCCTTCTCGACTTAAGTTATGCTGCAAATGATGT
1 TCGAACTCGAAGGTCTTTGG-TGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATAT
*
2290 GTCGTT-AAGCTGAGCGTAG
65 G-CCTTGAAGCTGAGCGTAG
* * * * * * * * *
2309 TCAAACTCAAAGGTCTTTTGTTGGCAGATAACCTTTCTAGCCTTGAGTTATGCTGTAAATGTTAT
1 TCGAACTCGAAGGTC-TTTGGTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATAT
* *
2374 ACCTTGGAGCTGAGCGTAG
65 GCCTTGAAGCTGAGCGTAG
* * *
2393 TCGAACTCGAAGGTC-TT--TGGCAGATAGCCCTTCTCAACTTAAGTTATGCTGCAAATGATGGT
1 TCGAACTCGAAGGTCTTTGGTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGAT-AT
*
2455 GCCTTGGAGCTGAGCGTAG
65 GCCTTGAAGCTGAGCGTAG
* * * *
2474 TCGAACTCGAAGGTCTTTTGATGGCAGATATCCATTCTCGACTTAAGCTATGCTGCAAATGATAT
1 TCGAACTCGAAGGTC-TTTGGTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATAT
*
2539 GCCCTCGAAGCTGAGCGTAG
65 G-CCTTGAAGCTGAGCGTAG
* * * * * *
2559 TCGAACTCGAAGGTCTTTGTTGACATATAACCCTTCTAGTCTTGAA-TTATGCTGAAAAT
1 TCGAACTCGAAGGTCTTTGGTGGCAGATAACCCTTCTCGACTT-AAGTTATGCTGCAAAT
2618 AGATTCTTTA
Statistics
Matches: 849, Mismatches: 170, Indels: 70
0.78 0.16 0.06
Matches are distributed among these distances:
78 17 0.02
79 21 0.02
80 58 0.07
81 39 0.05
82 102 0.12
83 255 0.30
84 217 0.26
85 111 0.13
86 27 0.03
87 2 0.00
ACGTcount: A:0.25, C:0.19, G:0.24, T:0.32
Consensus pattern (83 bp):
TCGAACTCGAAGGTCTTTGGTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATATG
CCTTGAAGCTGAGCGTAG
Found at i:1680 original size:166 final size:168
Alignment explanation
Indices: 1483--2617 Score: 1138
Period size: 166 Copynumber: 6.8 Consensus size: 168
1473 CAGTGTATCG
* * * * * *
1483 AACTCGAAGGT-TTTCGGTGACAGATAACCCTTATCGAATTAAGTTATGCTGTAAATGATGTGCC
1 AACTCGAAGGTCTTTTGGTGGCAGATAACCCTTCTAGACTTAAGTTATGCTGTAAATGATATGCC
* ** * *
1547 CTAGAAGCTGAATGTAATCGAACTCGAAGGTATTTGTTGGCAGATA-CCCTTCTCGACTTAAGTT
66 CTTGAAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGTTGGCAGATAGCCCTTCTCGACTTAAGTT
*
1611 ATGCTGCAAATGATATGCCTTGGAGCTGAGCGTAGTCA
131 ATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCA
* * * *
1649 AACTCGAA-GTCTTTTGGTGTCAGATAACCCTTCTAGCCTTGAGTTATGTTGTAAATGATATG-C
1 AACTCGAAGGTCTTTTGGTGGCAGATAACCCTTCTAGACTTAAGTTATGCTGTAAATGATATGCC
** * * * * *
1712 CTTGAAGCTGATTGTAATCGAGCTTGAGGGTC--T-TTGGCAGATATCCCTTCTCGACTTAAGTT
66 CTTGAAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGTTGGCAGATAGCCCTTCTCGACTTAAGTT
* * *
1774 A-GCTGTAAATGATGTGCATTGGAG-TGAGAGTAGTCA
131 ATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCA
* * * *
1810 AACTCGAAGGTC-TTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATTCTGCAAATGATAT-A
1 AACTCGAAGGTCTTTTGG-TGGCAGATAACCCTTCTAGACTTAAGTTATGCTGTAAATGATATGC
* * *
1873 CCTTGGAGCTGAGCGTAGCCGAACTCGAAGGTCTTTGGTT-GTAGATAGCCCTTCTCGACTTAAG
65 CCTTGAAGCTGAGCGTAGTCGAACTCGAAGGTCTTT-GTTGGCAGATAGCCCTTCTCGACTTAAG
* * * * * * * *
1937 CTATGCTACAAAGGATTTACCCTCGAAGCTGAGCGTAGTCG
129 TTATGCTGCAAATGATGT-GCCTTGGAGCTGAGCGTAGTCA
** * ** *
1978 AACTCGAAGGTCTTTAT--TAACAGATAA-CCTTCTAGCCTTGGGTTATG-TGTAAATGATGTGC
1 AACTCGAAGGTCTTT-TGGTGGCAGATAACCCTTCTAGACTTAAGTTATGCTGTAAATGATATGC
* * * * * *
2039 CTTTGAAGCTAAGTGTAATCAAACTC-AGGGGATCTTTGGTTTGGCAGATAGCCCTTCTCGACTT
65 CCTTGAAGCTGAGCGTAGTCGAACTCGA-AGG-TCTTT-G-TTGGCAGATAGCCCTTCTCGACTT
* *
2103 AAGCTATGCTGC-AATGCTGTG--TTGTTGAGCTGAGCGTAGTCA
126 AAGTTATGCTGCAAATGATGTGCCTTG--GAGCTGAGCGTAGTCA
* * * * *
2145 AACTCAAAGGTCTTTTGTTGGTAGATAACCCTTCTAGACTTAAGTTATGTTGCAAATG-TATG-C
1 AACTCGAAGGTCTTTTGGTGGCAGATAACCCTTCTAGACTTAAGTTATGCTGTAAATGATATGCC
* * * **
2208 CTTGGAGCTGAGCGTAGTCAAACTTGGGGGTCTTTGGTTGGCAGATAGCCCTTCTCGACTTAAGT
66 CTTGAAGCTGAGCGTAGTCGAACTCGAAGGTCTTT-GTTGGCAGATAGCCCTTCTCGACTTAAGT
* *
2273 TATGCTGCAAATGATGTGTCGTT-AAGCTGAGCGTAGTCA
130 TATGCTGCAAATGATGTG-CCTTGGAGCTGAGCGTAGTCA
* * * * * * *
2312 AACTCAAAGGTCTTTTGTTGGCAGATAACCTTTCTAGCCTTGAGTTATGCTGTAAATGTTAT-AC
1 AACTCGAAGGTCTTTTGGTGGCAGATAACCCTTCTAGACTTAAGTTATGCTGTAAATGATATGCC
* *
2376 CTTGGAGCTGAGCGTAGTCGAACTCGAAGGTC--T-TTGGCAGATAGCCCTTCTCAACTTAAGTT
66 CTTGAAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGTTGGCAGATAGCCCTTCTCGACTTAAGTT
*
2438 ATGCTGCAAATGATGGTGCCTTGGAGCTGAGCGTAGTCG
131 ATGCTGCAAATGAT-GTGCCTTGGAGCTGAGCGTAGTCA
* * * * * *
2477 AACTCGAAGGTCTTTTGATGGCAGATATCCATTCTCGACTTAAGCTATGCTGCAAATGATATGCC
1 AACTCGAAGGTCTTTTGGTGGCAGATAACCCTTCTAGACTTAAGTTATGCTGTAAATGATATGCC
* * * * * *
2542 CTCGAAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGTTGACATATAACCCTTCTAGTCTTGAA-T
66 CTTGAAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGTTGGCAGATAGCCCTTCTCGACTT-AAGT
*
2606 TATGCTGAAAAT
130 TATGCTGCAAAT
2618 AGATTCTTTA
Statistics
Matches: 803, Mismatches: 127, Indels: 75
0.80 0.13 0.07
Matches are distributed among these distances:
161 24 0.03
162 95 0.12
163 20 0.02
164 46 0.06
165 135 0.17
166 166 0.21
167 130 0.16
168 92 0.11
169 83 0.10
170 12 0.01
ACGTcount: A:0.25, C:0.19, G:0.24, T:0.32
Consensus pattern (168 bp):
AACTCGAAGGTCTTTTGGTGGCAGATAACCCTTCTAGACTTAAGTTATGCTGTAAATGATATGCC
CTTGAAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGTTGGCAGATAGCCCTTCTCGACTTAAGTT
ATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCA
Found at i:3869 original size:82 final size:87
Alignment explanation
Indices: 3739--3964 Score: 239
Period size: 82 Copynumber: 2.6 Consensus size: 87
3729 GGCTAGCTGA
* * * *
3739 ATCCGTAAAGTCGAGGCGTTTAACCAATTGCTCTAGAGGGACAGCTCAA-TAT-GTA-AA-CACC
1 ATCCATAAAGACGGGGCGTTTAACCAATTGCTCTAGAGGGACAACTCAATTATAGTATAATCACC
* * *
3800 TTTATCATGTTAGCTGAATCTT
66 TTTATCAGGCTAGCTGAATATT
* *
3822 ATCCAT-AAGCCGGGGCGTTTAACCAATTGC-CTTAGAGGGACATCTCAAGCTTTATTGTATAGT
1 ATCCATAAAGACGGGGCGTTTAACCAATTGCTC-TAGAGGGACAACTC-A-----A-T-TATAGT
3885 ATAATCACCTTTATCAGGCTAGCTGAATATT
57 ATAATCACCTTTATCAGGCTAGCTGAATATT
*
3916 ATCCATAAAGACGGGGCGTTTAACCAATTTCTCTAGAGGGACAACTCAA
1 ATCCATAAAGACGGGGCGTTTAACCAATTGCTCTAGAGGGACAACTCAA
3965 GCTTATTGTA
Statistics
Matches: 118, Mismatches: 10, Indels: 24
0.78 0.07 0.16
Matches are distributed among these distances:
81 1 0.01
82 35 0.30
83 6 0.05
88 1 0.01
89 1 0.01
91 3 0.03
92 3 0.03
93 2 0.02
94 30 0.25
95 35 0.30
96 1 0.01
ACGTcount: A:0.31, C:0.21, G:0.19, T:0.29
Consensus pattern (87 bp):
ATCCATAAAGACGGGGCGTTTAACCAATTGCTCTAGAGGGACAACTCAATTATAGTATAATCACC
TTTATCAGGCTAGCTGAATATT
Found at i:3984 original size:95 final size:94
Alignment explanation
Indices: 3796--3976 Score: 276
Period size: 94 Copynumber: 1.9 Consensus size: 94
3786 AATATGTAAA
* * * *
3796 CACCTTTATCATGTTAGCTGAATCTTATCCATAAGCCGGGGCGTTTAACCAATTGCCTTAGAGGG
1 CACCTTTATCAGGCTAGCTGAATATTATCCATAAGACGGGGCGTTTAACCAATTGCCTTAGAGGG
*
3861 ACATCTCAAGCTTTATTGTATAGTATAAT
66 ACAACTCAAGCTTTATTGTATAGTATAAT
*
3890 CACCTTTATCAGGCTAGCTGAATATTATCCATAAAGACGGGGCGTTTAACCAATT-TCTCTAGAG
1 CACCTTTATCAGGCTAGCTGAATATTATCCAT-AAGACGGGGCGTTTAACCAATTGCCT-TAGAG
3954 GGACAACTCAAGC-TTATTGTATA
64 GGACAACTCAAGCTTTATTGTATA
3977 TTTATAATTA
Statistics
Matches: 79, Mismatches: 6, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
94 41 0.52
95 38 0.48
ACGTcount: A:0.29, C:0.20, G:0.18, T:0.32
Consensus pattern (94 bp):
CACCTTTATCAGGCTAGCTGAATATTATCCATAAGACGGGGCGTTTAACCAATTGCCTTAGAGGG
ACAACTCAAGCTTTATTGTATAGTATAAT
Found at i:5894 original size:14 final size:14
Alignment explanation
Indices: 5875--5905 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
5865 CCCATACGGA
5875 GAATAAATTCCCAC
1 GAATAAATTCCCAC
*
5889 GAATAAATTTCCAC
1 GAATAAATTCCCAC
5903 GAA
1 GAA
5906 GACGTCGTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.45, C:0.23, G:0.10, T:0.23
Consensus pattern (14 bp):
GAATAAATTCCCAC
Found at i:6517 original size:12 final size:12
Alignment explanation
Indices: 6496--6530 Score: 54
Period size: 12 Copynumber: 2.9 Consensus size: 12
6486 ATGTTAATAT
6496 GATAATAAAAAA
1 GATAATAAAAAA
6508 -ATAGATAAAAAA
1 GATA-ATAAAAAA
6520 GATAATAAAAA
1 GATAATAAAAA
6531 TGAAAAAAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
11 3 0.14
12 15 0.71
13 3 0.14
ACGTcount: A:0.74, C:0.00, G:0.09, T:0.17
Consensus pattern (12 bp):
GATAATAAAAAA
Found at i:6587 original size:39 final size:40
Alignment explanation
Indices: 6503--6587 Score: 93
Period size: 39 Copynumber: 2.1 Consensus size: 40
6493 TATGATAATA
** *
6503 AAAAAATAGATAAAAAAGATAATAAAAATGAAAAAAATTT
1 AAAAAATAGATAAAAAAGATAATAAAAAACAAAAAAATGT
* * *
6543 TAAAAATA-CTAAAAATA-ATAATAAAAAACAAAATAATGT
1 AAAAAATAGATAAAAA-AGATAATAAAAAACAAAAAAATGT
6582 AAAAAA
1 AAAAAA
6588 ATAATAGCAA
Statistics
Matches: 37, Mismatches: 7, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
39 29 0.78
40 8 0.22
ACGTcount: A:0.73, C:0.02, G:0.05, T:0.20
Consensus pattern (40 bp):
AAAAAATAGATAAAAAAGATAATAAAAAACAAAAAAATGT
Found at i:7922 original size:15 final size:17
Alignment explanation
Indices: 7902--7941 Score: 57
Period size: 17 Copynumber: 2.5 Consensus size: 17
7892 TTAGACCTGG
*
7902 ATAATAAAA-CAAA-AA
1 ATAATAAAATAAAATAA
7917 ATAATAAAATAAAATAA
1 ATAATAAAATAAAATAA
7934 ATAATAAA
1 ATAATAAA
7942 TAATAAATAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 9 0.41
16 3 0.14
17 10 0.45
ACGTcount: A:0.78, C:0.03, G:0.00, T:0.20
Consensus pattern (17 bp):
ATAATAAAATAAAATAA
Found at i:8036 original size:31 final size:29
Alignment explanation
Indices: 8000--8084 Score: 93
Period size: 29 Copynumber: 2.9 Consensus size: 29
7990 AAACTATATA
8000 ATATATA-TTTCAAAAATATTTTAAAATT
1 ATATATATTTTCAAAAATATTTTAAAATT
* *
8028 ATATTATATTTTTTAAAAATGTTTTCAAAATT
1 ATA-TATA-TTTTCAAAAATATTTT-AAAATT
* *
8060 ATATA-GTTTTCGAAAATATTTTAAA
1 ATATATATTTTCAAAAATATTTTAAA
8085 CTATGTTTTC
Statistics
Matches: 47, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
28 6 0.13
29 17 0.36
31 15 0.32
32 9 0.19
ACGTcount: A:0.45, C:0.04, G:0.04, T:0.48
Consensus pattern (29 bp):
ATATATATTTTCAAAAATATTTTAAAATT
Found at i:8104 original size:24 final size:25
Alignment explanation
Indices: 8065--8113 Score: 66
Period size: 24 Copynumber: 2.0 Consensus size: 25
8055 AAATTATATA
*
8065 GTTTTCGAAAATATTT-TAAACTAT
1 GTTTTCGAAAATATTTCAAAACTAT
8089 GTTTTC-AAAATGATTTCAAAACTAT
1 GTTTTCGAAAAT-ATTTCAAAACTAT
8114 ATATAAGTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
23 5 0.23
24 10 0.45
25 7 0.32
ACGTcount: A:0.39, C:0.10, G:0.08, T:0.43
Consensus pattern (25 bp):
GTTTTCGAAAATATTTCAAAACTAT
Found at i:8168 original size:35 final size:34
Alignment explanation
Indices: 8102--8298 Score: 126
Period size: 36 Copynumber: 5.7 Consensus size: 34
8092 TTCAAAATGA
8102 TTTCAAAA-C-TAT-ATATAAGTATTTTCAAAATGTT
1 TTTCAAAACCATATAATATAA-T-TTTT-AAAATGTT
8136 TTTCAAAACCATATAATATACATTTTTAAAATGTT
1 TTTCAAAACCATATAATATA-ATTTTTAAAATGTT
* *
8171 TTTC-AAA--A-AT-ATATAATATTTTCAAACGTT
1 TTTCAAAACCATATAATATAAT-TTTTAAAATGTT
* * *
8201 TTTCAAAAACTATATATATATATACTTTTCAAAATATT
1 TTTC-AAAACCATATA-ATATA-A-TTTTTAAAATGTT
* * *
8239 TTT-AAAATCATATTATATAAGTTTTCTAAAAATATT
1 TTTCAAAACCATATAATATAA-TTTT-T-AAAATGTT
*
8275 TTT-AAAAGCCATATATTATAATTT
1 TTTCAAAA-CCATATAATATAATTT
8299 CCAAAAATGA
Statistics
Matches: 132, Mismatches: 14, Indels: 32
0.74 0.08 0.18
Matches are distributed among these distances:
29 2 0.02
30 19 0.14
31 2 0.02
32 4 0.03
34 17 0.13
35 20 0.15
36 33 0.25
37 21 0.16
38 13 0.10
39 1 0.01
ACGTcount: A:0.43, C:0.09, G:0.03, T:0.45
Consensus pattern (34 bp):
TTTCAAAACCATATAATATAATTTTTAAAATGTT
Found at i:8381 original size:2 final size:2
Alignment explanation
Indices: 8374--8429 Score: 105
Period size: 2 Copynumber: 28.5 Consensus size: 2
8364 AATGAGTGTC
8374 TA TA TA TA TA TA TA TA TA TA TA TA -A TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
8415 TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA T
8430 TAAATCAAAA
Statistics
Matches: 53, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 52 0.98
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:8616 original size:24 final size:24
Alignment explanation
Indices: 8589--8639 Score: 68
Period size: 24 Copynumber: 2.1 Consensus size: 24
8579 GATGATTCAT
* *
8589 ATTTTAAATCATTAAT-TTAATTTA
1 ATTTT-AATCATAAATCTGAATTTA
8613 ATTTTAATCATAAATCTGAATTTA
1 ATTTTAATCATAAATCTGAATTTA
8637 ATT
1 ATT
8640 AAATAACGTC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
23 9 0.38
24 15 0.62
ACGTcount: A:0.41, C:0.06, G:0.02, T:0.51
Consensus pattern (24 bp):
ATTTTAATCATAAATCTGAATTTA
Found at i:9120 original size:379 final size:378
Alignment explanation
Indices: 8422--9181 Score: 1275
Period size: 379 Copynumber: 2.0 Consensus size: 378
8412 ATATATATAT
8422 ATATATATTAAATCAAAAGAATTATTATGATTTAAGTTGATATATTTTAATTATCATTCTATTTA
1 ATATATATTAAATCAAAAGAATTATTATGATTTAAGTTGATATATTTTAATTATCATTCTATTTA
8487 ATTGAAAGATTCGTTAGATGTCAATGCCTAATGGCATGCCTTTTATCACTTTTTTTGGCAATTTA
66 ATTGAAAGATTCGTTAGATGTCAATGCCTAATGGCATGCCTTTTATCACTTTTTTTGGCAATTTA
8552 TACGTGGATCGCTTCCATAAAAGAATGGATGATTCATATTTTAAATCATTAATTTAATTTAATTT
131 TACGTGGATCGCTTCCATAAAAGAATGGATGATTCATATTTTAAATCATTAATTTAATTTAATTT
*
8617 TAATCATAAATCTGAATTTAATTAAATAACGTCATTTAATTTTATTATTGATAAACTAATCATTC
196 TAATCATAAATCTAAATTTAATTAAATAACGTCATTTAATTTTATTATTGATAAACTAATCATTC
*
8682 ATATTAATATAAGGGCAAATTATATTTAGTACCTAATCTATCAGTTTTGATCTGTTTTAGTACCT
261 ATATTAATATAAGGGCAAATTATATTTAGTACCTAAACTATCAGTTTTGATCTGTTTTAGTACCT
* *
8747 AAACTTTTAATTTTTTTAAAACCATATCTAAAGTTTA-CTTTTGTTTCATTTTA
326 AAACTTTTAA-TTTTTTAAAACCATACCTAAAGTTTATCTTTTATTTCATTTTA
*
8800 ATATATATTAAATC-AAAGAATTATTATGATTTAAGTTTTGATATA-TTTAATTATCATT-TTTT
1 ATATATATTAAATCAAAAGAATTATTATGATTTAAG--TTGATATATTTTAATTATCATTCTATT
*
8862 TAATTGAAAGATTTCGTTAGATGTCAATGCCTAATGGCATGCCTTTTGTCACTTTTTTTTGGCAA
64 TAATTGAAAGA-TTCGTTAGATGTCAATGCCTAATGGCATGCCTTTTATCAC-TTTTTTTGGCAA
**
8927 TTTATACGTGGATCGCTTCCATAAAAAGAATGGATGATTTGTATTTTAAATCATTAATTTAATTT
127 TTTATACGTGGATCGCTTCCAT-AAAAGAATGGATGATTCATATTTTAAATCATTAATTTAA-TT
* *
8992 TAATTTTAATCA-AAGTCTAAATTTAATTAAATAACTTCATTTAATTTTTATTA-T-ATAAACTA
190 TAATTTTAATCATAAATCTAAATTTAATTAAATAACGTCATTTAA-TTTTATTATTGATAAACT-
*
9054 AATCATTCATGTTAATA-AAGGGCAAATTATATTTAGTACCTAAACTATCAGTTTTGATCTGTTT
253 AATCATTCATATTAATATAAGGGCAAATTATATTTAGTACCTAAACTATCAGTTTTGATCTGTTT
*
9118 TAGTACCTAAACTTTTAATTTTTTAAAACCATACCTAAAGTTTATTTTTTATTTCATTTTA
318 TAGTACCTAAACTTTTAATTTTTTAAAACCATACCTAAAGTTTATCTTTTATTTCATTTTA
9179 ATA
1 ATA
9182 CACCGTCGTT
Statistics
Matches: 361, Mismatches: 12, Indels: 17
0.93 0.03 0.04
Matches are distributed among these distances:
377 35 0.10
378 91 0.25
379 130 0.36
380 83 0.23
381 22 0.06
ACGTcount: A:0.35, C:0.11, G:0.09, T:0.45
Consensus pattern (378 bp):
ATATATATTAAATCAAAAGAATTATTATGATTTAAGTTGATATATTTTAATTATCATTCTATTTA
ATTGAAAGATTCGTTAGATGTCAATGCCTAATGGCATGCCTTTTATCACTTTTTTTGGCAATTTA
TACGTGGATCGCTTCCATAAAAGAATGGATGATTCATATTTTAAATCATTAATTTAATTTAATTT
TAATCATAAATCTAAATTTAATTAAATAACGTCATTTAATTTTATTATTGATAAACTAATCATTC
ATATTAATATAAGGGCAAATTATATTTAGTACCTAAACTATCAGTTTTGATCTGTTTTAGTACCT
AAACTTTTAATTTTTTAAAACCATACCTAAAGTTTATCTTTTATTTCATTTTA
Found at i:18998 original size:56 final size:57
Alignment explanation
Indices: 18927--19045 Score: 215
Period size: 56 Copynumber: 2.1 Consensus size: 57
18917 ATAGGAGATG
*
18927 AAAT-TATAAAATTGTAGGGAACGAAAATGTATTATCAAACATAAAATGTT-AAAAA
1 AAATCTATAAAATTGTAGGGAACGAAAACGTATTATCAAACATAAAATGTTAAAAAA
18982 AAATCTATAAAATTGTAGGGAACGAAAACGTATTATCAAACATAAAATGTTAAAAAA
1 AAATCTATAAAATTGTAGGGAACGAAAACGTATTATCAAACATAAAATGTTAAAAAA
19039 AAATCTA
1 AAATCTA
19046 AACTGTACAA
Statistics
Matches: 61, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
55 4 0.07
56 45 0.74
57 12 0.20
ACGTcount: A:0.55, C:0.08, G:0.12, T:0.26
Consensus pattern (57 bp):
AAATCTATAAAATTGTAGGGAACGAAAACGTATTATCAAACATAAAATGTTAAAAAA
Found at i:37098 original size:22 final size:22
Alignment explanation
Indices: 37070--37115 Score: 92
Period size: 22 Copynumber: 2.1 Consensus size: 22
37060 CATTATGCCC
37070 ATAGTTAACACAACACAGAACA
1 ATAGTTAACACAACACAGAACA
37092 ATAGTTAACACAACACAGAACA
1 ATAGTTAACACAACACAGAACA
37114 AT
1 AT
37116 GCTTCTAGAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.54, C:0.22, G:0.09, T:0.15
Consensus pattern (22 bp):
ATAGTTAACACAACACAGAACA
Found at i:48318 original size:14 final size:14
Alignment explanation
Indices: 48295--48334 Score: 62
Period size: 14 Copynumber: 2.8 Consensus size: 14
48285 AAAAATATTT
*
48295 AAATTAAAATCTAAG
1 AAATT-AAATATAAG
48310 AAATTAAATATAAG
1 AAATTAAATATAAG
48324 AAATTAAATAT
1 AAATTAAATAT
48335 GCAGGGGATT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
14 19 0.79
15 5 0.21
ACGTcount: A:0.62, C:0.03, G:0.05, T:0.30
Consensus pattern (14 bp):
AAATTAAATATAAG
Found at i:51947 original size:16 final size:16
Alignment explanation
Indices: 51922--51954 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
51912 CGTTGATGTA
*
51922 TACATGAATAAACTCT
1 TACATCAATAAACTCT
51938 TACATCAATAAACTCT
1 TACATCAATAAACTCT
51954 T
1 T
51955 GGCATTAATT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.42, C:0.21, G:0.03, T:0.33
Consensus pattern (16 bp):
TACATCAATAAACTCT
Found at i:53075 original size:17 final size:17
Alignment explanation
Indices: 53052--53101 Score: 59
Period size: 17 Copynumber: 2.9 Consensus size: 17
53042 TCTAAACTGA
53052 AAATAAATATTCTTTTTG
1 AAATAAATATT-TTTTTG
*
53070 -AATAAAT-TTATTTTG
1 AAATAAATATTTTTTTG
53085 AATATAAATATTTTTTT
1 AA-ATAAATATTTTTTT
53102 TTATTTAAGA
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
15 5 0.19
16 3 0.11
17 13 0.48
18 6 0.22
ACGTcount: A:0.40, C:0.02, G:0.04, T:0.54
Consensus pattern (17 bp):
AAATAAATATTTTTTTG
Found at i:54507 original size:21 final size:22
Alignment explanation
Indices: 54483--54523 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
54473 TTAGGAATGT
* *
54483 TGGAGCAAAGTAG-GGAAAATA
1 TGGAGAAAAATAGAGGAAAATA
54504 TGGAGAAAAATAGAGGAAAA
1 TGGAGAAAAATAGAGGAAAA
54524 GTAGAAGTAG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 11 0.65
22 6 0.35
ACGTcount: A:0.54, C:0.02, G:0.32, T:0.12
Consensus pattern (22 bp):
TGGAGAAAAATAGAGGAAAATA
Found at i:56754 original size:29 final size:27
Alignment explanation
Indices: 56712--56767 Score: 94
Period size: 29 Copynumber: 2.0 Consensus size: 27
56702 CTTCCTTGAA
56712 CGAGAGGATCATTTTTGAATTGTTTTATG
1 CGAGAGGATCA-TTTTGAATT-TTTTATG
56741 CGAGAGGATCATTTTGAATTTTTTATG
1 CGAGAGGATCATTTTGAATTTTTTATG
56768 TGACAACAGA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
27 7 0.26
28 9 0.33
29 11 0.41
ACGTcount: A:0.25, C:0.07, G:0.23, T:0.45
Consensus pattern (27 bp):
CGAGAGGATCATTTTGAATTTTTTATG
Found at i:69067 original size:15 final size:15
Alignment explanation
Indices: 69047--69143 Score: 151
Period size: 15 Copynumber: 6.5 Consensus size: 15
69037 TTCCAGAAAA
69047 TGAATTACTGGAATT
1 TGAATTACTGGAATT
69062 TGAATTACTGGAATT
1 TGAATTACTGGAATT
69077 TGAATTACTGGAATT
1 TGAATTACTGGAATT
**
69092 TGAATTACTGGAAAA
1 TGAATTACTGGAATT
69107 TGAATTACTGGAATT
1 TGAATTACTGGAATT
**
69122 TGAATT-CTGGAAAA
1 TGAATTACTGGAATT
69136 TGAATTAC
1 TGAATTAC
69144 ATTTCTGTAA
Statistics
Matches: 75, Mismatches: 6, Indels: 2
0.90 0.07 0.02
Matches are distributed among these distances:
14 12 0.16
15 63 0.84
ACGTcount: A:0.37, C:0.07, G:0.20, T:0.36
Consensus pattern (15 bp):
TGAATTACTGGAATT
Found at i:69081 original size:30 final size:30
Alignment explanation
Indices: 69042--69143 Score: 179
Period size: 30 Copynumber: 3.4 Consensus size: 30
69032 TGGTTTTCCA
69042 GAAAATGAATTACTGGAATTTGAATTACTG
1 GAAAATGAATTACTGGAATTTGAATTACTG
**
69072 GAATTTGAATTACTGGAATTTGAATTACTG
1 GAAAATGAATTACTGGAATTTGAATTACTG
69102 GAAAATGAATTACTGGAATTTGAATT-CTG
1 GAAAATGAATTACTGGAATTTGAATTACTG
69131 GAAAATGAATTAC
1 GAAAATGAATTAC
69144 ATTTCTGTAA
Statistics
Matches: 68, Mismatches: 4, Indels: 1
0.93 0.05 0.01
Matches are distributed among these distances:
29 16 0.24
30 52 0.76
ACGTcount: A:0.39, C:0.07, G:0.20, T:0.34
Consensus pattern (30 bp):
GAAAATGAATTACTGGAATTTGAATTACTG
Found at i:69149 original size:20 final size:20
Alignment explanation
Indices: 69126--69195 Score: 131
Period size: 20 Copynumber: 3.5 Consensus size: 20
69116 GGAATTTGAA
69126 TTCTGGAAAATGAATTACAT
1 TTCTGGAAAATGAATTACAT
*
69146 TTCTGTAAAATGAATTACAT
1 TTCTGGAAAATGAATTACAT
69166 TTCTGGAAAATGAATTACAT
1 TTCTGGAAAATGAATTACAT
69186 TTCTGGAAAA
1 TTCTGGAAAA
69196 CATCTGGAAA
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 48 1.00
ACGTcount: A:0.40, C:0.10, G:0.14, T:0.36
Consensus pattern (20 bp):
TTCTGGAAAATGAATTACAT
Found at i:69418 original size:29 final size:27
Alignment explanation
Indices: 69362--69427 Score: 78
Period size: 28 Copynumber: 2.3 Consensus size: 27
69352 TTTACTAAAA
* *
69362 TATTATTGAAATATATAAATAATATTAT
1 TATTATT-AAATATATAAAAAAAATTAT
69390 TCATTATTAAATATATAAAAAAAATTTAT
1 T-ATTATTAAATATATAAAAAAAA-TTAT
69419 TATATATTA
1 TAT-TATTA
69428 TTAATAAATA
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
28 17 0.52
29 16 0.48
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.45
Consensus pattern (27 bp):
TATTATTAAATATATAAAAAAAATTAT
Found at i:69469 original size:23 final size:23
Alignment explanation
Indices: 69421--69481 Score: 65
Period size: 23 Copynumber: 2.7 Consensus size: 23
69411 AAATTTATTA
*
69421 TATATTATTAATAA-ATAATATCT
1 TATATTATT-ATAATATAATATAT
69444 TATATTATTATAATATAAT-TGAT
1 TATATTATTATAATATAATAT-AT
*
69467 TATTTTA-TATAATAT
1 TATATTATTATAATAT
69482 TAAAAATATA
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
22 13 0.38
23 21 0.62
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.52
Consensus pattern (23 bp):
TATATTATTATAATATAATATAT
Found at i:69499 original size:22 final size:23
Alignment explanation
Indices: 69474--69517 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
69464 GATTATTTTA
69474 TATAATATTAAAAATA-TAATAT
1 TATAATATTAAAAATATTAATAT
* *
69496 TATATTATTATAAATATTAATA
1 TATAATATTAAAAATATTAATA
69518 AATATATTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 14 0.74
23 5 0.26
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (23 bp):
TATAATATTAAAAATATTAATAT
Found at i:69522 original size:22 final size:22
Alignment explanation
Indices: 69478--69534 Score: 64
Period size: 21 Copynumber: 2.6 Consensus size: 22
69468 ATTTTATATA
* *
69478 ATATTAAAAATA-TAATATTAT
1 ATATTATAAATATTAATATAAT
69499 ATTATTATAAATATTAATA-AAT
1 A-TATTATAAATATTAATATAAT
*
69521 ATATTTTAAATATT
1 ATATTATAAATATT
69535 TTAATAATTA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
21 13 0.42
22 13 0.42
23 5 0.16
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (22 bp):
ATATTATAAATATTAATATAAT
Found at i:69533 original size:52 final size:53
Alignment explanation
Indices: 69418--69548 Score: 142
Period size: 52 Copynumber: 2.5 Consensus size: 53
69408 AAAAAATTTA
* * **
69418 TTATATATTATTAATAAATAATATCTTATATTATTATAATATAATTGATTATT
1 TTATATAATATTAATAAATAATATATTATATTATTATAATATAATAAATTATT
69471 TTATATAATATTAA-AAAT-ATAATATTATATTATTATAAATATTAATAAATATATT
1 TTATATAATATTAATAAATAAT-ATATTATATTATTAT-AATA-TAATAAAT-TATT
* * *
69526 TTAAAT-ATTTTAATAATTAATAT
1 TTATATAATATTAATAAATAATAT
69549 TTTGATGAAA
Statistics
Matches: 65, Mismatches: 7, Indels: 10
0.79 0.09 0.12
Matches are distributed among these distances:
51 2 0.03
52 18 0.28
53 17 0.26
54 12 0.18
55 14 0.22
56 2 0.03
ACGTcount: A:0.48, C:0.01, G:0.01, T:0.50
Consensus pattern (53 bp):
TTATATAATATTAATAAATAATATATTATATTATTATAATATAATAAATTATT
Found at i:69760 original size:42 final size:43
Alignment explanation
Indices: 69696--69816 Score: 190
Period size: 42 Copynumber: 2.8 Consensus size: 43
69686 ATGAATTACA
* *
69696 TTCCAGAAAACGAATTACGTGAAACAAACACGGGAAAAC-GTT
1 TTCCGGAAAACGAATTACGTGAAACAAACACGGAAAAACAGTT
*
69738 TTCCGGAAAACGAATTACGTGAAACAAACACGGAAAAACATTT
1 TTCCGGAAAACGAATTACGTGAAACAAACACGGAAAAACAGTT
* *
69781 TTCCGTAAAACGAATTACGTGAAACAAACACTGAAA
1 TTCCGGAAAACGAATTACGTGAAACAAACACGGAAA
69817 TTCGGGGAAA
Statistics
Matches: 73, Mismatches: 5, Indels: 1
0.92 0.06 0.01
Matches are distributed among these distances:
42 37 0.51
43 36 0.49
ACGTcount: A:0.46, C:0.19, G:0.17, T:0.18
Consensus pattern (43 bp):
TTCCGGAAAACGAATTACGTGAAACAAACACGGAAAAACAGTT
Found at i:69934 original size:28 final size:29
Alignment explanation
Indices: 69900--69985 Score: 86
Period size: 31 Copynumber: 2.9 Consensus size: 29
69890 AATTGGTCCC
69900 TAAAATTTTAAATATTTTAATTTCATCCT
1 TAAAATTTTAAATATTTTAATTTCATCCT
* *
69929 T-AAATTATAATTATTATTTTAAATT-AGTCCT
1 TAAAATTTTAA--A-TATTTTAATTTCA-TCCT
* *
69960 TAAAATTTTGAACATTTTAATTTCAT
1 TAAAATTTTAAATATTTTAATTTCAT
69986 TCTCAAACTA
Statistics
Matches: 45, Mismatches: 6, Indels: 12
0.71 0.10 0.19
Matches are distributed among these distances:
28 8 0.18
29 11 0.24
30 4 0.09
31 15 0.33
32 7 0.16
ACGTcount: A:0.38, C:0.08, G:0.02, T:0.51
Consensus pattern (29 bp):
TAAAATTTTAAATATTTTAATTTCATCCT
Found at i:70012 original size:60 final size:60
Alignment explanation
Indices: 69888--70057 Score: 173
Period size: 60 Copynumber: 2.8 Consensus size: 60
69878 TACCTCGTTT
* * * * * * *
69888 TAAATTGGTCCCTAAAATTTTAAATATTTTAATTTCATCCTTAAATTATAATTATTATTT
1 TAAATTGGTCCCTAAAATTTTGAACATTTTAATTTCATCCTCAAACTATAACTATCATTC
* * *
69948 TAAATTAGTCCTTAAAATTTTGAACATTTTAATTTCATTCTCAAACTATAACCT-TCATTC
1 TAAATTGGTCCCTAAAATTTTGAACATTTTAATTTCATCCTCAAACTATAA-CTATCATTC
* * * * *
70008 TAAATTGGTCCCCAAACTTCTTGAACATTCTGATTTCATCC-CAAATTATA
1 TAAATTGGTCCCTAAAATT-TTGAACATTTTAATTTCATCCTCAAACTATA
70058 CATATATATC
Statistics
Matches: 90, Mismatches: 18, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
60 71 0.79
61 19 0.21
ACGTcount: A:0.35, C:0.17, G:0.05, T:0.44
Consensus pattern (60 bp):
TAAATTGGTCCCTAAAATTTTGAACATTTTAATTTCATCCTCAAACTATAACTATCATTC
Found at i:70078 original size:29 final size:29
Alignment explanation
Indices: 70046--70129 Score: 150
Period size: 29 Copynumber: 2.9 Consensus size: 29
70036 TCTGATTTCA
*
70046 TCCCAAATTATACATATATATCAGTCCCT
1 TCCCAAATTATACGTATATATCAGTCCCT
70075 TCCCAAATTATACGTATATATCAGTCCCT
1 TCCCAAATTATACGTATATATCAGTCCCT
*
70104 TCCCAAATTATACGTATATATTAGTC
1 TCCCAAATTATACGTATATATCAGTC
70130 ACATCTCTTG
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 53 1.00
ACGTcount: A:0.33, C:0.25, G:0.06, T:0.36
Consensus pattern (29 bp):
TCCCAAATTATACGTATATATCAGTCCCT
Found at i:73110 original size:19 final size:19
Alignment explanation
Indices: 73049--73110 Score: 54
Period size: 19 Copynumber: 3.2 Consensus size: 19
73039 TTAATATTAT
* *
73049 AATTTTATTATAATATTTA
1 AATTTAATTATAATTTTTA
* * *
73068 AA-TTAGTTTTAATTTTTTTC
1 AATTTAATTATAA--TTTTTA
73088 AATTTAATTATAATTTTTA
1 AATTTAATTATAATTTTTA
73107 AATT
1 AATT
73111 AGTTTACGAT
Statistics
Matches: 32, Mismatches: 8, Indels: 6
0.70 0.17 0.13
Matches are distributed among these distances:
18 7 0.22
19 11 0.34
20 6 0.19
21 8 0.25
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.60
Consensus pattern (19 bp):
AATTTAATTATAATTTTTA
Found at i:73322 original size:16 final size:16
Alignment explanation
Indices: 73301--73343 Score: 77
Period size: 16 Copynumber: 2.7 Consensus size: 16
73291 GATTAAACAT
73301 TGAATGATTCAAATGA
1 TGAATGATTCAAATGA
*
73317 TGAATGATTTAAATGA
1 TGAATGATTCAAATGA
73333 TGAATGATTCA
1 TGAATGATTCA
73344 GAGGCTCTTA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 25 1.00
ACGTcount: A:0.42, C:0.05, G:0.19, T:0.35
Consensus pattern (16 bp):
TGAATGATTCAAATGA
Found at i:74534 original size:8 final size:8
Alignment explanation
Indices: 74511--74544 Score: 50
Period size: 8 Copynumber: 4.2 Consensus size: 8
74501 ATTCGATTAA
*
74511 TATGTACA
1 TATGTACG
74519 TATGTACG
1 TATGTACG
74527 TATGTACG
1 TATGTACG
*
74535 TAGGTACG
1 TATGTACG
74543 TA
1 TA
74545 CATACGTACA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
8 24 1.00
ACGTcount: A:0.29, C:0.12, G:0.24, T:0.35
Consensus pattern (8 bp):
TATGTACG
Found at i:74550 original size:8 final size:8
Alignment explanation
Indices: 74539--74563 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
74529 TGTACGTAGG
74539 TACGTACA
1 TACGTACA
74547 TACGTACA
1 TACGTACA
74555 TACGTACA
1 TACGTACA
74563 T
1 T
74564 GATATAAGTC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.36, C:0.24, G:0.12, T:0.28
Consensus pattern (8 bp):
TACGTACA
Found at i:77158 original size:2 final size:2
Alignment explanation
Indices: 77151--77175 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
77141 ATTTCAAAGA
77151 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
77176 GAGAGAGAGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:80939 original size:13 final size:15
Alignment explanation
Indices: 80919--80960 Score: 56
Period size: 14 Copynumber: 3.1 Consensus size: 15
80909 TATAATCGGT
80919 TATA-ATAATA-ATA
1 TATATATAATATATA
80932 -ATATATAATATATA
1 TATATATAATATATA
80946 TATATAT-ATATATA
1 TATATATAATATATA
80960 T
1 T
80961 GAACATAACA
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
12 3 0.12
13 6 0.23
14 11 0.42
15 6 0.23
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (15 bp):
TATATATAATATATA
Found at i:80944 original size:2 final size:2
Alignment explanation
Indices: 80932--80960 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
80922 AATAATAATA
80932 AT AT AT A- 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
80961 GAACATAACA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:88421 original size:2 final size:2
Alignment explanation
Indices: 88416--88443 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
88406 ACACACACAC
88416 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
88444 TAATAATATG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:89768 original size:12 final size:12
Alignment explanation
Indices: 89751--89777 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
89741 AAACCTACTC
89751 CAATACTAAAAA
1 CAATACTAAAAA
89763 CAATACTAAAAA
1 CAATACTAAAAA
89775 CAA
1 CAA
89778 ATCCCACAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.67, C:0.19, G:0.00, T:0.15
Consensus pattern (12 bp):
CAATACTAAAAA
Found at i:96344 original size:39 final size:39
Alignment explanation
Indices: 96285--96735 Score: 513
Period size: 39 Copynumber: 11.7 Consensus size: 39
96275 TTGTTTTTAA
* * * * *
96285 AGAATATTTTATCTCACTTGAGATGGTTTCTCTCGAAAT
1 AGAAGATTTTATCTCGCTTGAGATAGTTTCCCTCGAAAC
* * *
96324 AGAATATTTTATCTTGCTTGAGATAGTTTCCCTCGAAAT
1 AGAAGATTTTATCTCGCTTGAGATAGTTTCCCTCGAAAC
* *
96363 AAAAGATTTTATCTCCCTTGAGATAGTTTCCCTCGAAAC
1 AGAAGATTTTATCTCGCTTGAGATAGTTTCCCTCGAAAC
* * *
96402 AAAAGATTTTATCTCGCTTGAGATAGTTTCCCTCAAAAT
1 AGAAGATTTTATCTCGCTTGAGATAGTTTCCCTCGAAAC
*
96441 AGAAGATTTTATCTCGCTTGAGATAGTTTCCCTTGAAAC
1 AGAAGATTTTATCTCGCTTGAGATAGTTTCCCTCGAAAC
* *
96480 ACAACATTTTATCTCGCTTGAGATAGTTTCCCTCGAAAC
1 AGAAGATTTTATCTCGCTTGAGATAGTTTCCCTCGAAAC
*
96519 AAAAGATTTTATCTCGCTTGAGATAGTTTCCCTCGAAAC
1 AGAAGATTTTATCTCGCTTGAGATAGTTTCCCTCGAAAC
* *
96558 ATAAGATTTTATCTCGCTTGAGATAGTTTCCCTCGAAAT
1 AGAAGATTTTATCTCGCTTGAGATAGTTTCCCTCGAAAC
* * *
96597 AGAAGATTTTATCTTGCTTGAGATAGTTTCCATTGAAAC
1 AGAAGATTTTATCTCGCTTGAGATAGTTTCCCTCGAAAC
* ** * * * *
96636 --AAG-TTTTGTCTTTCTTGTGACAGTTTCTCTTGAAAC
1 AGAAGATTTTATCTCGCTTGAGATAGTTTCCCTCGAAAC
* * * *
96672 --AA-ATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAAC
1 AGAAGATTTTATCTCGCTTGAGATAGTTTCCCTCGAAAC
* * *
96708 AAGAA-A-TGTATCTCACTTGAGATGGTTT
1 -AGAAGATTTTATCTCGCTTGAGATAGTTT
96736 TTCTTAAAAC
Statistics
Matches: 366, Mismatches: 42, Indels: 9
0.88 0.10 0.02
Matches are distributed among these distances:
36 59 0.16
37 3 0.01
38 17 0.05
39 287 0.78
ACGTcount: A:0.29, C:0.18, G:0.16, T:0.38
Consensus pattern (39 bp):
AGAAGATTTTATCTCGCTTGAGATAGTTTCCCTCGAAAC
Found at i:96669 original size:36 final size:35
Alignment explanation
Indices: 96603--96710 Score: 135
Period size: 36 Copynumber: 3.0 Consensus size: 35
96593 AAATAGAAGA
* * *
96603 TTTTATCTTGCTTGAGATAGTTTCCATTGAAACAAG
1 TTTTGTCTTTCTTGAGACAGTTTCC-TTGAAACAAG
* *
96639 TTTTGTCTTTCTTGTGACAGTTTCTCTTGAAACAAA
1 TTTTGTCTTTCTTGAGACAGTTTC-CTTGAAACAAG
*
96675 TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAG
1 TTTTGTCTTTCTTGAGACAGTTT-CCTTGAAACAAG
96711 AAATGTATCT
Statistics
Matches: 62, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
36 60 0.97
37 2 0.03
ACGTcount: A:0.24, C:0.18, G:0.16, T:0.43
Consensus pattern (35 bp):
TTTTGTCTTTCTTGAGACAGTTTCCTTGAAACAAG
Found at i:96819 original size:76 final size:74
Alignment explanation
Indices: 96660--96827 Score: 178
Period size: 75 Copynumber: 2.3 Consensus size: 74
96650 TTGTGACAGT
* * ** *
96660 TTCTCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAGAAATGTATCTCACT
1 TTCTCTTAAAACAAATTTCGTCTCGATCGAGACAGTTTCCCTTGAAACAAGAAATGTATCTCACT
* *
96725 TGAGATGGT
66 CGAGATGGA
* * * * *
96734 TTTTCTTAAAACCAATTTCGTCTCGATCGAGACAATTTTCTCTTGAAACAAGAAATTTTATCTCA
1 TTCTCTTAAAACAAATTTCGTCTCGATCGAGAC-AGTTTCCCTTGAAACAAGAAA-TGTATCTCA
96799 CTCGAGA-GAGA
64 CTCGAGATG-GA
*
96810 TTCTCTT-AAACATATTTC
1 TTCTCTTAAAACAAATTTC
96828 TTATTAATTT
Statistics
Matches: 76, Mismatches: 15, Indels: 5
0.79 0.16 0.05
Matches are distributed among these distances:
74 26 0.34
75 29 0.38
76 21 0.28
ACGTcount: A:0.30, C:0.20, G:0.13, T:0.37
Consensus pattern (74 bp):
TTCTCTTAAAACAAATTTCGTCTCGATCGAGACAGTTTCCCTTGAAACAAGAAATGTATCTCACT
CGAGATGGA
Found at i:100302 original size:25 final size:25
Alignment explanation
Indices: 100274--100323 Score: 82
Period size: 25 Copynumber: 2.0 Consensus size: 25
100264 CATTATTTTC
*
100274 CAAAAAATGTACCCATAACAATGTT
1 CAAAAAATGTACCCACAACAATGTT
*
100299 CAAATAATGTACCCACAACAATGTT
1 CAAAAAATGTACCCACAACAATGTT
100324 TAATTGATTT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.46, C:0.22, G:0.08, T:0.24
Consensus pattern (25 bp):
CAAAAAATGTACCCACAACAATGTT
Found at i:103030 original size:24 final size:24
Alignment explanation
Indices: 103003--103049 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
102993 CAAAATCCGA
103003 GTATTAACCAAGATCAAAGTTCGG
1 GTATTAACCAAGATCAAAGTTCGG
* *
103027 GTATTGACCAAGATCAAATTTCG
1 GTATTAACCAAGATCAAAGTTCG
103050 AATACTGACT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.36, C:0.17, G:0.19, T:0.28
Consensus pattern (24 bp):
GTATTAACCAAGATCAAAGTTCGG
Found at i:103058 original size:24 final size:24
Alignment explanation
Indices: 103009--103058 Score: 64
Period size: 24 Copynumber: 2.1 Consensus size: 24
102999 CCGAGTATTA
** *
103009 ACCAAGATCAAAGTTCGGGTATTG
1 ACCAAGATCAAAGTTCGAATACTG
*
103033 ACCAAGATCAAATTTCGAATACTG
1 ACCAAGATCAAAGTTCGAATACTG
103057 AC
1 AC
103059 TAGTACTCAC
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.38, C:0.20, G:0.18, T:0.24
Consensus pattern (24 bp):
ACCAAGATCAAAGTTCGAATACTG
Found at i:103820 original size:14 final size:15
Alignment explanation
Indices: 103786--103823 Score: 60
Period size: 16 Copynumber: 2.5 Consensus size: 15
103776 GAAATCATTG
103786 AAAAATTATATAGAA
1 AAAAATTATATAGAA
103801 ATAAAATTATATA-AA
1 A-AAAATTATATAGAA
103816 AAAAATTA
1 AAAAATTA
103824 GAGATGGAGA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 7 0.32
15 4 0.18
16 11 0.50
ACGTcount: A:0.68, C:0.00, G:0.03, T:0.29
Consensus pattern (15 bp):
AAAAATTATATAGAA
Found at i:104003 original size:19 final size:18
Alignment explanation
Indices: 103960--104006 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 18
103950 CAAAACATTT
103960 GTGTTGCGAAACTAAAAC
1 GTGTTGCGAAACTAAAAC
* * *
103978 CTGTTGCGAAATTAAATTC
1 GTGTTGCGAAACTAAA-AC
103997 GTGTTGCGAA
1 GTGTTGCGAA
104007 TTTGAAAATC
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
18 14 0.58
19 10 0.42
ACGTcount: A:0.32, C:0.15, G:0.23, T:0.30
Consensus pattern (18 bp):
GTGTTGCGAAACTAAAAC
Found at i:104024 original size:21 final size:21
Alignment explanation
Indices: 104000--104058 Score: 73
Period size: 21 Copynumber: 2.8 Consensus size: 21
103990 TAAATTCGTG
104000 TTGCGAATTTGAAAATCAAAA
1 TTGCGAATTTGAAAATCAAAA
* ***
104021 TTGCGAATTTGAAATTCAGTG
1 TTGCGAATTTGAAAATCAAAA
*
104042 TTGCGAATTTGGAAATC
1 TTGCGAATTTGAAAATC
104059 GCGTTACGAA
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.36, C:0.10, G:0.20, T:0.34
Consensus pattern (21 bp):
TTGCGAATTTGAAAATCAAAA
Found at i:104045 original size:42 final size:40
Alignment explanation
Indices: 103981--104058 Score: 120
Period size: 42 Copynumber: 1.9 Consensus size: 40
103971 CTAAAACCTG
103981 TTGCGAAATTAAATTCGTGTTGCGAATTTGAAAATCAAAA
1 TTGCGAAATTAAATTCGTGTTGCGAATTTGAAAATCAAAA
* *
104021 TTGCGAATTTGAAATTCAGTGTTGCGAATTTGGAAATC
1 TTGCGAAATT-AAATTC-GTGTTGCGAATTTGAAAATC
104059 GCGTTACGAA
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
40 9 0.26
41 6 0.18
42 19 0.56
ACGTcount: A:0.35, C:0.10, G:0.21, T:0.35
Consensus pattern (40 bp):
TTGCGAAATTAAATTCGTGTTGCGAATTTGAAAATCAAAA
Found at i:105947 original size:5 final size:5
Alignment explanation
Indices: 105937--105973 Score: 74
Period size: 5 Copynumber: 7.4 Consensus size: 5
105927 GAGAGGAAGA
105937 GATAG GATAG GATAG GATAG GATAG GATAG GATAG GA
1 GATAG GATAG GATAG GATAG GATAG GATAG GATAG GA
105974 ACTGTTGAGA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 32 1.00
ACGTcount: A:0.41, C:0.00, G:0.41, T:0.19
Consensus pattern (5 bp):
GATAG
Found at i:114920 original size:35 final size:36
Alignment explanation
Indices: 114853--114923 Score: 117
Period size: 36 Copynumber: 2.0 Consensus size: 36
114843 TGATTTTAAG
114853 TCGAATTTATGTTTTATACTAATAATTATTAAATCT
1 TCGAATTTATGTTTTATACTAATAATTATTAAATCT
* *
114889 TCGAATTTATGTTTTTTA-TTATAATTATTAAATCT
1 TCGAATTTATGTTTTATACTAATAATTATTAAATCT
114924 ATTTAATAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
35 16 0.48
36 17 0.52
ACGTcount: A:0.34, C:0.07, G:0.06, T:0.54
Consensus pattern (36 bp):
TCGAATTTATGTTTTATACTAATAATTATTAAATCT
Found at i:115161 original size:141 final size:139
Alignment explanation
Indices: 114972--115242 Score: 395
Period size: 141 Copynumber: 1.9 Consensus size: 139
114962 ATGAGGATTT
* * * *
114972 TATTGTTATTGTTATTATAAGTCTTCGAATTTAATCAATTTGTTAAGGTAAACAAA-CTATAAC-
1 TATTGTTATTGTTATTATAAATATTCAAATTTAATCAATTTGGTAAGGTAAA-AAATCTATAACA
*
115035 TAATTATTAAATATTCGAATTTAAGTTAAGGTAAAAATTTCAAAAAACAATATTTTACTCATGTT
65 TAATTATTAAATATTCGAATTTAAGTTAAGGTAAAAAATTCAAAAAA-AATA--TTACTCATGTT
115100 TATGATGTTATTA
127 TATGATGTTATTA
*
115113 TATT-TTATTGTTATTTATAAATATTCAAATTTAATCAATTTGGTAAGGTAAAAAATTTATAACT
1 TATTGTTATTGTTA-TTATAAATATTCAAATTTAATCAATTTGGTAAGGTAAAAAATCTATAAC-
*
115177 GATAATTATTAAATCTTCGAATTTAAGTTAAGGTAAAAAATTCAAAAAAAATATTACTCATGTTT
64 -ATAATTATTAAATATTCGAATTTAAGTTAAGGTAAAAAATTCAAAAAAAATATTACTCATGTTT
115242 A
128 A
115243 CAAAATAAAT
Statistics
Matches: 118, Mismatches: 7, Indels: 10
0.87 0.05 0.07
Matches are distributed among these distances:
140 12 0.10
141 57 0.48
143 4 0.03
144 45 0.38
ACGTcount: A:0.42, C:0.07, G:0.09, T:0.42
Consensus pattern (139 bp):
TATTGTTATTGTTATTATAAATATTCAAATTTAATCAATTTGGTAAGGTAAAAAATCTATAACAT
AATTATTAAATATTCGAATTTAAGTTAAGGTAAAAAATTCAAAAAAAATATTACTCATGTTTATG
ATGTTATTA
Found at i:116247 original size:17 final size:18
Alignment explanation
Indices: 116225--116266 Score: 50
Period size: 17 Copynumber: 2.4 Consensus size: 18
116215 GTAAAATTAT
116225 AAATAAAGAAATAAA-TA
1 AAATAAAGAAATAAAGTA
** *
116242 AAATAACTAAATAAAGTT
1 AAATAAAGAAATAAAGTA
116260 AAATAAA
1 AAATAAA
116267 TTAATTTAAA
Statistics
Matches: 20, Mismatches: 4, Indels: 1
0.80 0.16 0.04
Matches are distributed among these distances:
17 13 0.65
18 7 0.35
ACGTcount: A:0.71, C:0.02, G:0.05, T:0.21
Consensus pattern (18 bp):
AAATAAAGAAATAAAGTA
Found at i:116281 original size:10 final size:10
Alignment explanation
Indices: 116263--116287 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
116253 TAAAGTTAAA
116263 TAAATTAATT
1 TAAATTAATT
116273 TAAATTAATT
1 TAAATTAATT
116283 TAAAT
1 TAAAT
116288 AGTATAATTA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (10 bp):
TAAATTAATT
Done.