Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009189.1 Hibiscus syriacus cultivar Beakdansim tig00112762_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: 966119
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.33
File 4 of 4
Found at i:872851 original size:19 final size:19
Alignment explanation
Indices: 872829--872877 Score: 89
Period size: 19 Copynumber: 2.6 Consensus size: 19
872819 ATCGCAACGA
872829 GAAAATCGCAATACGAAAT
1 GAAAATCGCAATACGAAAT
*
872848 GAAAATCGCAATGCGAAAT
1 GAAAATCGCAATACGAAAT
872867 GAAAATCGCAA
1 GAAAATCGCAA
872878 CGAGAAAATC
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.51, C:0.16, G:0.18, T:0.14
Consensus pattern (19 bp):
GAAAATCGCAATACGAAAT
Found at i:872884 original size:19 final size:18
Alignment explanation
Indices: 872829--872884 Score: 67
Period size: 19 Copynumber: 2.9 Consensus size: 18
872819 ATCGCAACGA
*
872829 GAAAATCGCAATACGAAAT
1 GAAAATCGCAAGA-GAAAT
*
872848 GAAAATCGCAATGCGAAAT
1 GAAAATCGCAA-GAGAAAT
872867 GAAAATCGCAACGAGAAA
1 GAAAATCGCAA-GAGAAA
872885 ATCGCAATGC
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
19 32 1.00
ACGTcount: A:0.52, C:0.16, G:0.20, T:0.12
Consensus pattern (18 bp):
GAAAATCGCAAGAGAAAT
Found at i:872940 original size:20 final size:20
Alignment explanation
Indices: 872915--872952 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
872905 TCGCATTGCG
* *
872915 ATTTTCTCGTTGCGATAGCC
1 ATTTTCGCGTTACGATAGCC
872935 ATTTTCGCGTTACGATAG
1 ATTTTCGCGTTACGATAG
872953 TCAAATGAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.18, C:0.21, G:0.21, T:0.39
Consensus pattern (20 bp):
ATTTTCGCGTTACGATAGCC
Found at i:874033 original size:24 final size:23
Alignment explanation
Indices: 874005--874058 Score: 81
Period size: 24 Copynumber: 2.3 Consensus size: 23
873995 AGTATTCGAA
* *
874005 ATTTGATCTTGGTCAATACCCGG
1 ATTTGATATTGGTCAATACACGG
874028 ACTTTGATATTGGTCAATACACGG
1 A-TTTGATATTGGTCAATACACGG
874052 ATTTGAT
1 ATTTGAT
874059 GATGTTTCAG
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
23 7 0.25
24 21 0.75
ACGTcount: A:0.26, C:0.17, G:0.20, T:0.37
Consensus pattern (23 bp):
ATTTGATATTGGTCAATACACGG
Found at i:874249 original size:12 final size:12
Alignment explanation
Indices: 874232--874256 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
874222 ATATAATCCT
874232 GAAGAAGAAAAA
1 GAAGAAGAAAAA
874244 GAAGAAGAAAAA
1 GAAGAAGAAAAA
874256 G
1 G
874257 TCCCCGAGAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:876591 original size:33 final size:32
Alignment explanation
Indices: 876544--876670 Score: 166
Period size: 33 Copynumber: 3.9 Consensus size: 32
876534 GGAAATTACT
*
876544 ATCGCAATGCGAAATGAAAATCGCAATGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGA-AGA
* *
876577 ATCGCAATGTGAAATGAAAATCGCAACGCTAA-T
1 ATCGCAATGCGAAATGAAAATCGCAACG--AAGA
*
876610 TTCGCAATGCGAAATGAAAATCGCAACGAAGGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAA-GA
*
876643 ATCGCAATGCGAAATGAAAATCGTAACG
1 ATCGCAATGCGAAATGAAAATCGCAACG
876671 CGAATTTAAT
Statistics
Matches: 82, Mismatches: 8, Indels: 8
0.84 0.08 0.08
Matches are distributed among these distances:
31 2 0.02
33 78 0.95
34 1 0.01
35 1 0.01
ACGTcount: A:0.43, C:0.17, G:0.22, T:0.17
Consensus pattern (32 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAAGA
Found at i:876627 original size:66 final size:66
Alignment explanation
Indices: 876545--876677 Score: 214
Period size: 66 Copynumber: 2.0 Consensus size: 66
876535 GAAATTACTA
* * *
876545 TCGCAATGCGAAATGAAAATCGCAATG-AGAGAATCGCAATGTGAAATGAAAATCGCAACGCTAA
1 TCGCAATGCGAAATGAAAATCGCAACGAAG-GAATCGCAATGCGAAATGAAAATCGCAACGCGAA
876609 TT
65 TT
*
876611 TCGCAATGCGAAATGAAAATCGCAACGAAGGAATCGCAATGCGAAATGAAAATCGTAACGCGAAT
1 TCGCAATGCGAAATGAAAATCGCAACGAAGGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
876676 T
66 T
876677 T
1 T
876678 AATTTCACGT
Statistics
Matches: 62, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
66 60 0.97
67 2 0.03
ACGTcount: A:0.42, C:0.17, G:0.22, T:0.19
Consensus pattern (66 bp):
TCGCAATGCGAAATGAAAATCGCAACGAAGGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
T
Found at i:876851 original size:14 final size:14
Alignment explanation
Indices: 876832--876868 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
876822 CATCAATTAA
876832 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
876846 ACAAATCACCTTTT
1 ACAAATCAACTTTT
876860 ACAAATCAA
1 ACAAATCAA
876869 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.24, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:878279 original size:42 final size:41
Alignment explanation
Indices: 878220--878425 Score: 164
Period size: 42 Copynumber: 4.9 Consensus size: 41
878210 GTGAATCGGG
* *
878220 CTCTTGAATGGTGGGAGGGACCTCTTCAACGATGACAGTGGC
1 CTCTTGAACGGTGGGAGGGA-CTCTTCAAGGATGACAGTGGC
* * *
878262 CTCTTGAACGGTGGGAGGGGACTC-TCGAGGAATGATAGGGGC
1 CTCTTGAACGGTGGGA-GGGACTCTTCAAGG-ATGACAGTGGC
* * * * * *
878304 CTCTTCAATGATAGGAGTGGACTCTTGAGGGATGACAGTGGC
1 CTCTTGAACGGTGGGAG-GGACTCTTCAAGGATGACAGTGGC
* * *
878346 CTCTTGAACGGTGGGAGGGGACTC-TCGAGGAATGATAGGGGC
1 CTCTTGAACGGTGGGA-GGGACTCTTCAAGG-ATGACAGTGGC
* * * * *
878388 CTCTTCAACGATAGGAGTGGACTCTTGAGGGATGACAG
1 CTCTTGAACGGTGGGAG-GGACTCTTCAAGGATGACAG
878426 GCGAGTCGGG
Statistics
Matches: 126, Mismatches: 30, Indels: 16
0.73 0.17 0.09
Matches are distributed among these distances:
41 9 0.07
42 106 0.84
43 11 0.09
ACGTcount: A:0.23, C:0.18, G:0.37, T:0.22
Consensus pattern (41 bp):
CTCTTGAACGGTGGGAGGGACTCTTCAAGGATGACAGTGGC
Found at i:878286 original size:21 final size:21
Alignment explanation
Indices: 878220--878286 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
878210 GTGAATCGGG
*
878220 CTCTTGAATGGTGGGA-GGGA
1 CTCTTGAACGGTGGGAGGGGA
* * ** * *
878240 CCTCTTCAACGATGACAGTGGC
1 -CTCTTGAACGGTGGGAGGGGA
878262 CTCTTGAACGGTGGGAGGGGA
1 CTCTTGAACGGTGGGAGGGGA
878283 CTCT
1 CTCT
878287 CGAGGAATGA
Statistics
Matches: 32, Mismatches: 13, Indels: 2
0.68 0.28 0.04
Matches are distributed among these distances:
21 30 0.94
22 2 0.06
ACGTcount: A:0.19, C:0.21, G:0.36, T:0.24
Consensus pattern (21 bp):
CTCTTGAACGGTGGGAGGGGA
Found at i:878361 original size:84 final size:84
Alignment explanation
Indices: 878250--878425 Score: 343
Period size: 84 Copynumber: 2.1 Consensus size: 84
878240 CCTCTTCAAC
*
878250 GATGACAGTGGCCTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGGGGCCTCTTCAATGA
1 GATGACAGTGGCCTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGGGGCCTCTTCAACGA
878315 TAGGAGTGGACTCTTGAGG
66 TAGGAGTGGACTCTTGAGG
878334 GATGACAGTGGCCTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGGGGCCTCTTCAACGA
1 GATGACAGTGGCCTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGGGGCCTCTTCAACGA
878399 TAGGAGTGGACTCTTGAGG
66 TAGGAGTGGACTCTTGAGG
878418 GATGACAG
1 GATGACAG
878426 GCGAGTCGGG
Statistics
Matches: 91, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
84 91 1.00
ACGTcount: A:0.23, C:0.17, G:0.38, T:0.22
Consensus pattern (84 bp):
GATGACAGTGGCCTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGGGGCCTCTTCAACGA
TAGGAGTGGACTCTTGAGG
Found at i:878804 original size:88 final size:90
Alignment explanation
Indices: 878642--878825 Score: 264
Period size: 88 Copynumber: 2.0 Consensus size: 90
878632 ATATTTCAAA
* * * *
878642 ACTTCAACAAAAATACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGTTTA
1 ACTTCAACAAAAAGACAAAACAAAAACAAAAACTAACTTCACAGTGTT--A-AATAAACAGTTTA
878707 GCAGAATTGGCAGCAACCGAATAAATTT
63 GCAGAATTGGCAGCAACCGAATAAATTT
* *
878735 ACTTCAACCAAAAGACAAAACAAAAAGAAAAACT-ACTTCACAGTGTT-AATAAACAGTTTAGCA
1 ACTTCAACAAAAAGACAAAACAAAAACAAAAACTAACTTCACAGTGTTAAATAAACAGTTTAGCA
*
878798 GTATTGGCAGCAACCGAATAAATTT
66 GAATTGGCAGCAACCGAATAAATTT
878823 ACT
1 ACT
878826 AAGCAATCTA
Statistics
Matches: 84, Mismatches: 7, Indels: 5
0.88 0.07 0.05
Matches are distributed among these distances:
88 42 0.50
92 13 0.15
93 29 0.35
ACGTcount: A:0.48, C:0.18, G:0.12, T:0.22
Consensus pattern (90 bp):
ACTTCAACAAAAAGACAAAACAAAAACAAAAACTAACTTCACAGTGTTAAATAAACAGTTTAGCA
GAATTGGCAGCAACCGAATAAATTT
Found at i:879028 original size:63 final size:63
Alignment explanation
Indices: 878969--879110 Score: 151
Period size: 63 Copynumber: 2.3 Consensus size: 63
878959 CTTAGAGCGG
* * *
878969 CAACCTCAC-CACGTAAAGTAGACACCTCCACACGCCATGCACCATCGTTATCGCGTAGAGTAC
1 CAACCTC-CTCACGCAAAGCAGACACCTCCACACGCCATGCACCATCGTTATCGCGTAGAGCAC
* * * *** * *
879032 CGATCTCCTCACGCAAGGCATTGACCTCTACACGCCATGCACCATCGTTATCGCGTAGAGTAC
1 CAACCTCCTCACGCAAAGCAGACACCTCCACACGCCATGCACCATCGTTATCGCGTAGAGCAC
* *
879095 CGATCTCCTCACGCAA
1 CAACCTCCTCACGCAA
879111 GGCATTGACC
Statistics
Matches: 69, Mismatches: 9, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
62 1 0.01
63 68 0.99
ACGTcount: A:0.27, C:0.37, G:0.17, T:0.20
Consensus pattern (63 bp):
CAACCTCCTCACGCAAAGCAGACACCTCCACACGCCATGCACCATCGTTATCGCGTAGAGCAC
Found at i:879111 original size:63 final size:63
Alignment explanation
Indices: 878992--879122 Score: 253
Period size: 63 Copynumber: 2.1 Consensus size: 63
878982 TAAAGTAGAC
878992 ACCTCCACACGCCATGCACCATCGTTATCGCGTAGAGTACCGATCTCCTCACGCAAGGCATTG
1 ACCTCCACACGCCATGCACCATCGTTATCGCGTAGAGTACCGATCTCCTCACGCAAGGCATTG
*
879055 ACCTCTACACGCCATGCACCATCGTTATCGCGTAGAGTACCGATCTCCTCACGCAAGGCATTG
1 ACCTCCACACGCCATGCACCATCGTTATCGCGTAGAGTACCGATCTCCTCACGCAAGGCATTG
879118 ACCTC
1 ACCTC
879123 ATCACGTAAC
Statistics
Matches: 67, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
63 67 1.00
ACGTcount: A:0.24, C:0.37, G:0.18, T:0.21
Consensus pattern (63 bp):
ACCTCCACACGCCATGCACCATCGTTATCGCGTAGAGTACCGATCTCCTCACGCAAGGCATTG
Found at i:880642 original size:33 final size:33
Alignment explanation
Indices: 880600--880695 Score: 165
Period size: 33 Copynumber: 2.9 Consensus size: 33
880590 ATGAGATAAT
**
880600 GAGAATCGCAACGCGAAATGACTATCGCAACGA
1 GAGAATCGCAACGCGAAATGAAAATCGCAACGA
*
880633 GAGAATCGCAACGCGAAATGAAAATCGTAACGA
1 GAGAATCGCAACGCGAAATGAAAATCGCAACGA
880666 GAGAATCGCAACGCGAAATGAAAATCGCAA
1 GAGAATCGCAACGCGAAATGAAAATCGCAA
880696 TGCGATTTTG
Statistics
Matches: 59, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 59 1.00
ACGTcount: A:0.44, C:0.21, G:0.24, T:0.11
Consensus pattern (33 bp):
GAGAATCGCAACGCGAAATGAAAATCGCAACGA
Found at i:880664 original size:19 final size:19
Alignment explanation
Indices: 880575--880700 Score: 92
Period size: 19 Copynumber: 7.1 Consensus size: 19
880565 TCTTTTGGTT
* *
880575 GAAATGAAAATCGCAATGA
1 GAAATGAAAATCGCAACGC
*
880594 GATAATGAGAATCGCAACGC
1 GA-AATGAAAATCGCAACGC
**
880614 GAAATGACTATCGCAA--C
1 GAAATGAAAATCGCAACGC
*
880631 G--A-GAGAATCGCAACGC
1 GAAATGAAAATCGCAACGC
*
880647 GAAATGAAAATCGTAA--C
1 GAAATGAAAATCGCAACGC
*
880664 G--A-GAGAATCGCAACGC
1 GAAATGAAAATCGCAACGC
*
880680 GAAATGAAAATCGCAATGC
1 GAAATGAAAATCGCAACGC
880699 GA
1 GA
880701 TTTTGGTTTC
Statistics
Matches: 83, Mismatches: 13, Indels: 22
0.70 0.11 0.19
Matches are distributed among these distances:
14 18 0.22
15 2 0.02
16 4 0.05
17 4 0.05
18 2 0.02
19 37 0.45
20 16 0.19
ACGTcount: A:0.44, C:0.18, G:0.24, T:0.13
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGC
Found at i:880718 original size:19 final size:19
Alignment explanation
Indices: 880696--880762 Score: 62
Period size: 19 Copynumber: 3.5 Consensus size: 19
880686 AAAATCGCAA
*
880696 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGATTTCGCGT
* *
880715 TGCGTTTTTTATTTCGCGT
1 TGCGATTTTGATTTCGCGT
* * *
880734 TGCGATAGTTAATTCCGCGT
1 TGCGAT-TTTGATTTCGCGT
*
880754 TGTGATTTT
1 TGCGATTTT
880763 CATTCTCGAA
Statistics
Matches: 38, Mismatches: 9, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
19 23 0.61
20 15 0.39
ACGTcount: A:0.10, C:0.15, G:0.25, T:0.49
Consensus pattern (19 bp):
TGCGATTTTGATTTCGCGT
Found at i:881365 original size:20 final size:20
Alignment explanation
Indices: 881280--881373 Score: 91
Period size: 20 Copynumber: 4.7 Consensus size: 20
881270 CGCTATGTAA
* *
881280 ATCGCGTTGCGAAAGTCAGA
1 ATCGCGTTGCGATAGTCAGT
*
881300 ATCGCGTTGCGAAAGTCAGT
1 ATCGCGTTGCGATAGTCAGT
* * *
881320 ATCTCGTTGCGATTTTGT-ATT
1 ATCGCGTTGCGA--TAGTCAGT
*
881341 ATCGCATTGCGATAGTCAGT
1 ATCGCGTTGCGATAGTCAGT
*
881361 ATCGCATTGCGAT
1 ATCGCGTTGCGAT
881374 TTTCCCAATT
Statistics
Matches: 62, Mismatches: 9, Indels: 6
0.81 0.12 0.08
Matches are distributed among these distances:
19 3 0.05
20 45 0.73
21 12 0.19
22 2 0.03
ACGTcount: A:0.23, C:0.19, G:0.26, T:0.32
Consensus pattern (20 bp):
ATCGCGTTGCGATAGTCAGT
Found at i:881392 original size:41 final size:41
Alignment explanation
Indices: 881300--881394 Score: 111
Period size: 41 Copynumber: 2.3 Consensus size: 41
881290 GAAAGTCAGA
* * * ** *
881300 ATCGCGTTGCGAAAGTCAGTATCTCGTTGCGATTTTGTATT
1 ATCGCGTTGCGATAGTCAGTATCGCATTGCGATTTTCCAAT
*
881341 ATCGCATTGCGATAGTCAGTATCGCATTGCGATTTTCCCAAT
1 ATCGCGTTGCGATAGTCAGTATCGCATTGCGATTTT-CCAAT
881383 -TCGCGTTGCGAT
1 ATCGCGTTGCGAT
881395 TTACTTATTC
Statistics
Matches: 45, Mismatches: 8, Indels: 2
0.82 0.15 0.04
Matches are distributed among these distances:
41 43 0.96
42 2 0.04
ACGTcount: A:0.20, C:0.21, G:0.23, T:0.36
Consensus pattern (41 bp):
ATCGCGTTGCGATAGTCAGTATCGCATTGCGATTTTCCAAT
Found at i:881484 original size:21 final size:21
Alignment explanation
Indices: 881444--881484 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
881434 ACTGTAGACC
**
881444 ATCGCAACGCGATTTCCAACT
1 ATCGCAACGCGAAATCCAACT
*
881465 ATCGCAACGCGAAATGCAAC
1 ATCGCAACGCGAAATCCAAC
881485 GCGAATTTGC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.34, C:0.32, G:0.17, T:0.17
Consensus pattern (21 bp):
ATCGCAACGCGAAATCCAACT
Found at i:881955 original size:22 final size:20
Alignment explanation
Indices: 881928--881970 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 20
881918 TGTTTATGAC
*
881928 ACATTTTTCTATATTTTTTTAT
1 ACATTTTT-TA-ATCTTTTTAT
881950 ACATTTTTTAATCTTTTTAT
1 ACATTTTTTAATCTTTTTAT
881970 A
1 A
881971 GGCCATTTGA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 10 0.50
21 2 0.10
22 8 0.40
ACGTcount: A:0.26, C:0.09, G:0.00, T:0.65
Consensus pattern (20 bp):
ACATTTTTTAATCTTTTTAT
Found at i:882795 original size:29 final size:29
Alignment explanation
Indices: 882762--882823 Score: 97
Period size: 29 Copynumber: 2.1 Consensus size: 29
882752 TGGTATGAAT
*
882762 GTTGGCTGGATTAGTCTGATTGCTTATTG
1 GTTGGCTGGACTAGTCTGATTGCTTATTG
* *
882791 GTTGGCTGGACTGGTCTGATTGCTTGTTG
1 GTTGGCTGGACTAGTCTGATTGCTTATTG
882820 GTTG
1 GTTG
882824 TCTATACTCT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.10, C:0.11, G:0.35, T:0.44
Consensus pattern (29 bp):
GTTGGCTGGACTAGTCTGATTGCTTATTG
Found at i:883268 original size:16 final size:16
Alignment explanation
Indices: 883249--883279 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
883239 AATCATGAAT
883249 AATATATGTAAGTTAA
1 AATATATGTAAGTTAA
*
883265 AATATATTTAAGTTA
1 AATATATGTAAGTTA
883280 TTAATTAAAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.48, C:0.00, G:0.10, T:0.42
Consensus pattern (16 bp):
AATATATGTAAGTTAA
Found at i:883396 original size:21 final size:19
Alignment explanation
Indices: 883376--883412 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
883366 ATATATATAA
883376 AAACTAAATTTAGTAATAT
1 AAACTAAATTTAGTAATAT
*
883395 AAAGTAAATTTAGTAATA
1 AAACTAAATTTAGTAATA
883413 ATATTATCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.54, C:0.03, G:0.08, T:0.35
Consensus pattern (19 bp):
AAACTAAATTTAGTAATAT
Found at i:886068 original size:30 final size:30
Alignment explanation
Indices: 886033--886114 Score: 101
Period size: 30 Copynumber: 2.7 Consensus size: 30
886023 TCAAGTGACT
*
886033 ATTTTGTAATAAATGATAACGTTAGTAACC
1 ATTTTGTAACAAATGATAACGTTAGTAACC
* * ***
886063 ATTTTGTAACAAACGATAATGTTAGTGGTC
1 ATTTTGTAACAAATGATAACGTTAGTAACC
*
886093 ATTTTGTGACAAATGATAACGT
1 ATTTTGTAACAAATGATAACGT
886115 CAACATTCTG
Statistics
Matches: 43, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
30 43 1.00
ACGTcount: A:0.37, C:0.10, G:0.17, T:0.37
Consensus pattern (30 bp):
ATTTTGTAACAAATGATAACGTTAGTAACC
Found at i:893154 original size:3 final size:3
Alignment explanation
Indices: 893146--893266 Score: 242
Period size: 3 Copynumber: 40.3 Consensus size: 3
893136 GGCTTCATTG
893146 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
893194 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
893242 TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA T
893267 ATAGAATAAC
Statistics
Matches: 118, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 118 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:893573 original size:19 final size:20
Alignment explanation
Indices: 893551--893592 Score: 61
Period size: 19 Copynumber: 2.1 Consensus size: 20
893541 ATTTTAATAT
893551 AATAATTT-TATAACA-TTTA
1 AATAATTTCT-TAACATTTTA
893570 AATAATTTCTTAACATTTTA
1 AATAATTTCTTAACATTTTA
893590 AAT
1 AAT
893593 CAAGCGAGCA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 13 0.62
20 8 0.38
ACGTcount: A:0.45, C:0.07, G:0.00, T:0.48
Consensus pattern (20 bp):
AATAATTTCTTAACATTTTA
Found at i:895218 original size:28 final size:28
Alignment explanation
Indices: 895181--895242 Score: 115
Period size: 28 Copynumber: 2.2 Consensus size: 28
895171 AATGACGAGA
895181 AATAATAATCTTTTCCCCATTGAGATTG
1 AATAATAATCTTTTCCCCATTGAGATTG
895209 AATAATAATCTTTTCCCCATTGAGATTG
1 AATAATAATCTTTTCCCCATTGAGATTG
*
895237 AGTAAT
1 AATAAT
895243 TTTAGGAACC
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 33 1.00
ACGTcount: A:0.34, C:0.16, G:0.11, T:0.39
Consensus pattern (28 bp):
AATAATAATCTTTTCCCCATTGAGATTG
Found at i:902081 original size:23 final size:23
Alignment explanation
Indices: 902055--902102 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 23
902045 ATAAAGTACA
*
902055 ATAACATACTAGGTAGCGCTTAT
1 ATAACATAATAGGTAGCGCTTAT
**
902078 ATAATGTAATAGGTAGCGCTTAT
1 ATAACATAATAGGTAGCGCTTAT
902101 AT
1 AT
902103 TTACCTATTT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.35, C:0.12, G:0.19, T:0.33
Consensus pattern (23 bp):
ATAACATAATAGGTAGCGCTTAT
Found at i:902411 original size:23 final size:23
Alignment explanation
Indices: 902385--902457 Score: 94
Period size: 23 Copynumber: 3.2 Consensus size: 23
902375 TAATTACTAA
*
902385 ATATAACCACTACCTATTACATT
1 ATATAACGACTACCTATTACATT
902408 ATATAAACGA-TACCTATTACATT
1 ATAT-AACGACTACCTATTACATT
* * *
902431 ATATAAGGGCTACCTATTACATC
1 ATATAACGACTACCTATTACATT
902454 ATAT
1 ATAT
902458 GTTTACCTAT
Statistics
Matches: 44, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
22 3 0.07
23 37 0.84
24 4 0.09
ACGTcount: A:0.40, C:0.21, G:0.05, T:0.34
Consensus pattern (23 bp):
ATATAACGACTACCTATTACATT
Found at i:902927 original size:39 final size:39
Alignment explanation
Indices: 902860--902984 Score: 225
Period size: 39 Copynumber: 3.2 Consensus size: 39
902850 TCAAGTTGTA
902860 GATTTTGATTTCC-TTTGCTTGGCATCATATGAGATTTG
1 GATTTTGATTTCCTTTTGCTTGGCATCATATGAGATTTG
902898 GATTTTGATTTCCTTTTGCTTGGCATCATATGAGATTTG
1 GATTTTGATTTCCTTTTGCTTGGCATCATATGAGATTTG
* *
902937 GATTTTGATTTCCTTTTGCTTGGCACCATATGAGCTTTG
1 GATTTTGATTTCCTTTTGCTTGGCATCATATGAGATTTG
902976 GATTTTGAT
1 GATTTTGAT
902985 GAGCATCGGA
Statistics
Matches: 84, Mismatches: 2, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
38 13 0.15
39 71 0.85
ACGTcount: A:0.18, C:0.14, G:0.21, T:0.48
Consensus pattern (39 bp):
GATTTTGATTTCCTTTTGCTTGGCATCATATGAGATTTG
Found at i:903266 original size:18 final size:18
Alignment explanation
Indices: 903243--903279 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
903233 CGAAATATAT
903243 ATTGAAATTCAAACTCAA
1 ATTGAAATTCAAACTCAA
* *
903261 ATTGAAATTTAAATTCAA
1 ATTGAAATTCAAACTCAA
903279 A
1 A
903280 CTCCAATTAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.51, C:0.11, G:0.05, T:0.32
Consensus pattern (18 bp):
ATTGAAATTCAAACTCAA
Found at i:903555 original size:25 final size:25
Alignment explanation
Indices: 903527--903577 Score: 84
Period size: 25 Copynumber: 2.0 Consensus size: 25
903517 TTAATCCAAA
*
903527 TAATGTACCCATAACAATGTTCAAT
1 TAATGTACCCACAACAATGTTCAAT
*
903552 TAATGTACCCACAACAATGTTTAAT
1 TAATGTACCCACAACAATGTTCAAT
903577 T
1 T
903578 GATTTGTTGT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.39, C:0.20, G:0.08, T:0.33
Consensus pattern (25 bp):
TAATGTACCCACAACAATGTTCAAT
Found at i:903870 original size:21 final size:22
Alignment explanation
Indices: 903845--903896 Score: 77
Period size: 23 Copynumber: 2.3 Consensus size: 22
903835 ACACTTTACA
*
903845 ATATAACCACTACCTATTACATT
1 ATATAAACA-TACCTATTACATT
903868 ATATAAACGATACCTATTACATT
1 ATATAAAC-ATACCTATTACATT
903891 ATATAA
1 ATATAA
903897 GGGCTACCTA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
23 26 0.96
24 1 0.04
ACGTcount: A:0.44, C:0.19, G:0.02, T:0.35
Consensus pattern (22 bp):
ATATAAACATACCTATTACATT
Found at i:903881 original size:23 final size:23
Alignment explanation
Indices: 903855--903917 Score: 90
Period size: 23 Copynumber: 2.7 Consensus size: 23
903845 ATATAACCAC
903855 TACCTATTACATTATATAAACGA
1 TACCTATTACATTATATAAACGA
** *
903878 TACCTATTACATTATATAAGGGC
1 TACCTATTACATTATATAAACGA
*
903901 TACCTATTACATCATAT
1 TACCTATTACATTATAT
903918 GTTTACCTAT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.38, C:0.19, G:0.06, T:0.37
Consensus pattern (23 bp):
TACCTATTACATTATATAAACGA
Found at i:904300 original size:21 final size:22
Alignment explanation
Indices: 904275--904326 Score: 77
Period size: 23 Copynumber: 2.3 Consensus size: 22
904265 ACACTTTACA
*
904275 ATATAACCACTACCTATTACATT
1 ATATAAACA-TACCTATTACATT
904298 ATATAAACGATACCTATTACATT
1 ATATAAAC-ATACCTATTACATT
904321 ATATAA
1 ATATAA
904327 GGGCTACCTA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
23 26 0.96
24 1 0.04
ACGTcount: A:0.44, C:0.19, G:0.02, T:0.35
Consensus pattern (22 bp):
ATATAAACATACCTATTACATT
Found at i:904311 original size:23 final size:23
Alignment explanation
Indices: 904285--904347 Score: 90
Period size: 23 Copynumber: 2.7 Consensus size: 23
904275 ATATAACCAC
904285 TACCTATTACATTATATAAACGA
1 TACCTATTACATTATATAAACGA
** *
904308 TACCTATTACATTATATAAGGGC
1 TACCTATTACATTATATAAACGA
*
904331 TACCTATTACATCATAT
1 TACCTATTACATTATAT
904348 GTTTACCTAT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.38, C:0.19, G:0.06, T:0.37
Consensus pattern (23 bp):
TACCTATTACATTATATAAACGA
Found at i:907503 original size:22 final size:23
Alignment explanation
Indices: 907472--907514 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
907462 TTCCACAGTG
907472 AAAAAAGTATAGACAC-TTTTAT
1 AAAAAAGTATAGACACATTTTAT
* *
907494 AAAAAGGTATCGACACATTTT
1 AAAAAAGTATAGACACATTTT
907515 TATACCGGTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 14 0.78
23 4 0.22
ACGTcount: A:0.47, C:0.12, G:0.12, T:0.30
Consensus pattern (23 bp):
AAAAAAGTATAGACACATTTTAT
Found at i:908026 original size:183 final size:183
Alignment explanation
Indices: 907510--908202 Score: 1223
Period size: 183 Copynumber: 3.8 Consensus size: 183
907500 GTATCGACAC
*
907510 ATTTTTATACCGGTTATATTACAAAATTATCTATTACATTATAAATCTGGGTTCCGATGTGTAAA
1 ATTTTTATACCGGTTATATTACAAAATTATCTATTACATTATAAATATGGGTTCCGATGTGTAAA
*
907575 TGTCGACACTTTTTTAAATGGTATCGACACATTTTTCTTCCAATCTGAACATAAAGTACCGACAC
66 TGTCGACACTTTTTTAAATGGTATCGACACATTTTTCTTCCAATCTGGACATAAAGTACCGACAC
*
907640 AATATTAGAAAGTGTCGATAAAGGTTGTAGACCTATTCGCTCATAAAACCGGT
131 AATATTAGAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGGT
907693 A-TTTTATACCGGTTATATTACAAAATTATCTATTACATTATAAATATGGGTTCCGATGTGTAAA
1 ATTTTTATACCGGTTATATTACAAAATTATCTATTACATTATAAATATGGGTTCCGATGTGTAAA
907757 TGTCGACAC-TTTTTAAATGGTATCGACACATTTTTCTTCCAATCTGGACATAAAGTACCGACAC
66 TGTCGACACTTTTTTAAATGGTATCGACACATTTTTCTTCCAATCTGGACATAAAGTACCGACAC
907821 AATATTAGAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGGT
131 AATATTAGAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGGT
907874 ATTTTTATACCGGTTATATTACAAAATTATCTATTACATTATAAATATGGGTTCCGATGTGTAAA
1 ATTTTTATACCGGTTATATTACAAAATTATCTATTACATTATAAATATGGGTTCCGATGTGTAAA
*
907939 TGTCGACACTTTTTTAAATGGTATCGACACTTTTTTCTTCCAATCTGGACATAAAGTACCGACAC
66 TGTCGACACTTTTTTAAATGGTATCGACACATTTTTCTTCCAATCTGGACATAAAGTACCGACAC
908004 AATATTAGAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGGT
131 AATATTAGAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGGT
* * *
908057 ATATTTATACCGGTTATATTACAAAATTATCTATTACATTATAAATCTGGGTTCCGATGTTTTTT
1 ATTTTTATACCGGTTATATTACAAAATTATCTATTACATTATAAATATGGGTTCCGATG---TGT
* * * *
908122 CAA--TCGACACTTTTTTAAATGGTATCGACACATTTTTCTTTCATTCTGGACATAAAGTACAGA
63 AAATGTCGACACTTTTTTAAATGGTATCGACACATTTTTCTTCCAATCTGGACATAAAGTACCGA
*
908185 CACAATATTAAAAAGTGT
128 CACAATATTAGAAAGTGT
908203 GAAAACTTTG
Statistics
Matches: 492, Mismatches: 13, Indels: 9
0.96 0.03 0.02
Matches are distributed among these distances:
181 107 0.22
182 143 0.29
183 165 0.34
184 73 0.15
186 4 0.01
ACGTcount: A:0.33, C:0.16, G:0.14, T:0.36
Consensus pattern (183 bp):
ATTTTTATACCGGTTATATTACAAAATTATCTATTACATTATAAATATGGGTTCCGATGTGTAAA
TGTCGACACTTTTTTAAATGGTATCGACACATTTTTCTTCCAATCTGGACATAAAGTACCGACAC
AATATTAGAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGGT
Found at i:909402 original size:3 final size:3
Alignment explanation
Indices: 909394--909468 Score: 78
Period size: 3 Copynumber: 25.0 Consensus size: 3
909384 ACTTGTTTGG
* * * **
909394 ATC ATC ATC TTC ATC ATC ATC ATC ATC ATC GTC ATC ATC TTC ATC GCC
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC
* * *
909442 AGC TTC ATC GTC ATC ATC ATC ATC ATC
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC
909469 GTCAGCTTCA
Statistics
Matches: 57, Mismatches: 15, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
3 57 1.00
ACGTcount: A:0.25, C:0.35, G:0.05, T:0.35
Consensus pattern (3 bp):
ATC
Found at i:910488 original size:198 final size:199
Alignment explanation
Indices: 910131--910648 Score: 984
Period size: 198 Copynumber: 2.6 Consensus size: 199
910121 CCCCACTAGG
910131 CCGGATATAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGA
1 CCGG-TATAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGA
910196 TTTTGGGATCGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTCCATTCAT
65 TTTTGGGATCGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTCCATTCAT
910261 TCTGGGAAAAAAGTATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCA
130 TCTGGGAAAAAAGTATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCA
910326 TAAAA
195 TAAAA
910331 CCGGTATAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGAT
1 CCGGTATAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGAT
910396 TTTGGGATCGACAC-TTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTCCATTCATT
66 TTTGGGATCGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTCCATTCATT
910460 CTGGGAAAAAAGTATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCAT
131 CTGGGAAAAAAGTATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCAT
910525 AAAA
196 AAAA
*
910529 CTGGTATAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGAT
1 CCGGTATAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGAT
* *
910594 TTTGGGATTGACACTTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTT
66 TTTGGGATCGACAC-TTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTT
910649 GGCCATATTG
Statistics
Matches: 313, Mismatches: 3, Indels: 4
0.98 0.01 0.01
Matches are distributed among these distances:
198 196 0.63
199 75 0.24
200 42 0.13
ACGTcount: A:0.30, C:0.15, G:0.17, T:0.37
Consensus pattern (199 bp):
CCGGTATAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGAT
TTTGGGATCGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTCCATTCATT
CTGGGAAAAAAGTATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCAT
AAAA
Found at i:910799 original size:19 final size:19
Alignment explanation
Indices: 910767--910814 Score: 80
Period size: 19 Copynumber: 2.6 Consensus size: 19
910757 TTATATTCAC
910767 ATACAAAA-TATAAATCGT
1 ATACAAAATTATAAATCGT
*
910785 ATACAAAATTATAAATCTT
1 ATACAAAATTATAAATCGT
910804 ATACAAAATTA
1 ATACAAAATTA
910815 ACTCGACATT
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
18 8 0.29
19 20 0.71
ACGTcount: A:0.56, C:0.10, G:0.02, T:0.31
Consensus pattern (19 bp):
ATACAAAATTATAAATCGT
Found at i:912714 original size:21 final size:21
Alignment explanation
Indices: 912674--912738 Score: 69
Period size: 21 Copynumber: 3.1 Consensus size: 21
912664 CCCCTTATTC
* *
912674 CTCTCGAGTGTATCTTCGACT
1 CTCTCGAGTTTCTCTTCGACT
*
912695 CTCTCGAGTTTCTCTACGACT
1 CTCTCGAGTTTCTCTTCGACT
* *
912716 -TGATCAAGTTTCTCTTCGACT
1 CT-CTCGAGTTTCTCTTCGACT
912737 CT
1 CT
912739 TGATTGTCTT
Statistics
Matches: 36, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
20 1 0.03
21 34 0.94
22 1 0.03
ACGTcount: A:0.15, C:0.29, G:0.15, T:0.40
Consensus pattern (21 bp):
CTCTCGAGTTTCTCTTCGACT
Found at i:915013 original size:19 final size:19
Alignment explanation
Indices: 914958--915004 Score: 76
Period size: 20 Copynumber: 2.4 Consensus size: 19
914948 ATCCGGTATC
914958 ATTTTACCGGTTTTATCAT
1 ATTTTACCGGTTTTATCAT
*
914977 TTTGTTACCGGTTTTATCAT
1 ATT-TTACCGGTTTTATCAT
914997 ATTTTACC
1 ATTTTACC
915005 TGTTATATCG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 7 0.28
20 18 0.72
ACGTcount: A:0.19, C:0.17, G:0.11, T:0.53
Consensus pattern (19 bp):
ATTTTACCGGTTTTATCAT
Found at i:915149 original size:20 final size:20
Alignment explanation
Indices: 915124--915182 Score: 77
Period size: 20 Copynumber: 3.0 Consensus size: 20
915114 ACTTTTAAAT
915124 TTACCGGTTTTATCATTTTG
1 TTACCGGTTTTATCATTTTG
*
915144 TTACCGGTTTTATCATATT-
1 TTACCGGTTTTATCATTTTG
*
915163 TTACCTGG-TATATCATTTTG
1 TTACC-GGTTTTATCATTTTG
915183 GATCGATATA
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
19 14 0.41
20 20 0.59
ACGTcount: A:0.19, C:0.15, G:0.14, T:0.53
Consensus pattern (20 bp):
TTACCGGTTTTATCATTTTG
Found at i:915645 original size:224 final size:224
Alignment explanation
Indices: 915233--915670 Score: 765
Period size: 224 Copynumber: 2.0 Consensus size: 224
915223 TTAAAACTGC
*
915233 TTTTAAAGTTATGTAATTTATGTTTCAATTTATTTAATAGTGTTTCATGTTTTTCACCTACAATA
1 TTTTAAAGTTATGTAATTTATGTTTCAATTTATTTAATAGTGTTTCATGTTTTCCACCTACAATA
*
915298 TTAATTTAATAATTTAATTTACACAAAATTATATTTGATGTTTTGATATTTTATAAAATATTATT
66 TTAATTTAATAATTTAATTTACACAAAAATATATTTGATGTTTTGATATTTTATAAAATATTATT
* *
915363 TAGAATTTAAATTTAACAATATTAACCAAATATAATAATAAATATGTTTTCAACAGTGAAATAAG
131 TAGAATTTAAATTTAACAATATTAACCAAAGATAATAATAAATATATTTTCAACAGTGAAATAAG
915428 TATGGACACTTTTATAAAATGATATACTT
196 TATGGACACTTTTATAAAATGATATACTT
915457 TTTTGAAAGTTATGTAATTTATGTTTCAATTT-TTTAATAGTGTTTCATGTTTTCCACCTACAAT
1 TTTT-AAAGTTATGTAATTTATGTTTCAATTTATTTAATAGTGTTTCATGTTTTCCACCTACAAT
*
915521 ATTAATTTAATAATTTCATTTACACAAAAA-ATTATTTGATTGTTTTGATATTTTATAAAATATT
65 ATTAATTTAATAATTTAATTTACACAAAAATA-TATTTGA-TGTTTTGATATTTTATAAAATATT
* *
915585 ATTTAGATTTTAAATTTAACAATATTAACTAAAGATAATAATAAATATATTTTC-ACAGTGAAAT
128 ATTTAGAATTTAAATTTAACAATATTAACCAAAGATAATAATAAATATATTTTCAACAGTGAAAT
915649 AAGTATGGACACTTTTATAAAA
193 AAGTATGGACACTTTTATAAAA
915671 AGGATAGATA
Statistics
Matches: 204, Mismatches: 7, Indels: 6
0.94 0.03 0.03
Matches are distributed among these distances:
223 1 0.00
224 102 0.50
225 101 0.50
ACGTcount: A:0.39, C:0.07, G:0.08, T:0.45
Consensus pattern (224 bp):
TTTTAAAGTTATGTAATTTATGTTTCAATTTATTTAATAGTGTTTCATGTTTTCCACCTACAATA
TTAATTTAATAATTTAATTTACACAAAAATATATTTGATGTTTTGATATTTTATAAAATATTATT
TAGAATTTAAATTTAACAATATTAACCAAAGATAATAATAAATATATTTTCAACAGTGAAATAAG
TATGGACACTTTTATAAAATGATATACTT
Found at i:918070 original size:2 final size:2
Alignment explanation
Indices: 918063--918091 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
918053 TTTTCTTAGT
918063 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
918092 TTGAAGAATC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:921319 original size:23 final size:27
Alignment explanation
Indices: 921293--921346 Score: 71
Period size: 26 Copynumber: 2.1 Consensus size: 27
921283 ACAGAAGATT
*
921293 ATATTAT-C-AACG-AAGAATACAT-A
1 ATATTATGCAAACGTAAGAAAACATCA
921316 ATATTATGCAAACGTAAGAAAACATCA
1 ATATTATGCAAACGTAAGAAAACATCA
921343 ATAT
1 ATAT
921347 ATTGCATGTA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
23 7 0.27
24 1 0.04
25 4 0.15
26 9 0.35
27 5 0.19
ACGTcount: A:0.52, C:0.13, G:0.09, T:0.26
Consensus pattern (27 bp):
ATATTATGCAAACGTAAGAAAACATCA
Found at i:924629 original size:14 final size:14
Alignment explanation
Indices: 924608--924644 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
924598 TAATACCCTA
924608 AATAAATTTATTAT
1 AATAAATTTATTAT
*
924622 ATTAAATTTATTAT
1 AATAAATTTATTAT
924636 AATAAATTT
1 AATAAATTT
924645 GATTTTTTAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (14 bp):
AATAAATTTATTAT
Found at i:926879 original size:28 final size:29
Alignment explanation
Indices: 926813--926881 Score: 86
Period size: 29 Copynumber: 2.4 Consensus size: 29
926803 TAAATGGACT
* * *
926813 TAATTGATTTTTTATTAAGTTTGATGGCA
1 TAATTGATTTTTTAGTAAGTTTGAAGACA
*
926842 TCATTGATTTTTTAGTAAGTTTGAAGAC-
1 TAATTGATTTTTTAGTAAGTTTGAAGACA
*
926870 TAATTTATTTTT
1 TAATTGATTTTT
926882 AAAGAAATAA
Statistics
Matches: 34, Mismatches: 6, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
28 10 0.29
29 24 0.71
ACGTcount: A:0.28, C:0.04, G:0.14, T:0.54
Consensus pattern (29 bp):
TAATTGATTTTTTAGTAAGTTTGAAGACA
Found at i:929169 original size:2 final size:2
Alignment explanation
Indices: 929157--929221 Score: 112
Period size: 2 Copynumber: 32.5 Consensus size: 2
929147 AATATGAGAT
*
929157 TA TA TA GA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
929199 TA TA TA TA TA TA TA TA TA GA TA T
1 TA TA TA TA TA TA TA TA TA TA TA T
929222 TGATAGAACT
Statistics
Matches: 59, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 59 1.00
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.48
Consensus pattern (2 bp):
TA
Found at i:930191 original size:23 final size:23
Alignment explanation
Indices: 930154--930244 Score: 128
Period size: 23 Copynumber: 4.0 Consensus size: 23
930144 ATTATTATAT
*
930154 GGCACTACGGTGCAATTCTACGC
1 GGCACTCCGGTGCAATTCTACGC
*
930177 GGTACTCCGGTGCAATTCTACGC
1 GGCACTCCGGTGCAATTCTACGC
* *
930200 GGCACTCTGGTGCAATTCTACGT
1 GGCACTCCGGTGCAATTCTACGC
* *
930223 GGCACTTCGGTGCAATTATACG
1 GGCACTCCGGTGCAATTCTACG
930245 AGCTGTGGTG
Statistics
Matches: 60, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 60 1.00
ACGTcount: A:0.20, C:0.27, G:0.26, T:0.26
Consensus pattern (23 bp):
GGCACTCCGGTGCAATTCTACGC
Found at i:931243 original size:20 final size:19
Alignment explanation
Indices: 931208--931261 Score: 72
Period size: 20 Copynumber: 2.7 Consensus size: 19
931198 AAATCGCAAC
931208 GCGATTTTAGTTTCGCGTT
1 GCGATTTTAGTTTCGCGTT
*
931227 GCGATTTTCATTTTCGCGTT
1 GCGATTTT-AGTTTCGCGTT
*
931247 GCGAATTTAAGTTTC
1 GCG-ATTTTAGTTTC
931262 AGAAACTACT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
19 8 0.27
20 18 0.60
21 4 0.13
ACGTcount: A:0.15, C:0.17, G:0.22, T:0.46
Consensus pattern (19 bp):
GCGATTTTAGTTTCGCGTT
Found at i:932668 original size:42 final size:41
Alignment explanation
Indices: 932573--932671 Score: 126
Period size: 42 Copynumber: 2.4 Consensus size: 41
932563 CCCCCCACTT
* * * *
932573 CGAGAGCCATCACCTGATCGAGCTGATTCTACATCTCGACA
1 CGAGAGCCATCACCTGATCGAGCCGATTATACACCTCCACA
*
932614 CTCAGAGCCATCACCTGATCGAGCCGATTATACACCTCCACAA
1 C-GAGAGCCATCACCTGATCGAGCCGATTATACACCTCCAC-A
*
932657 CGAGAGTCATCACCT
1 CGAGAGCCATCACCT
932672 ATTCCATCAC
Statistics
Matches: 49, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
41 1 0.02
42 46 0.94
43 2 0.04
ACGTcount: A:0.28, C:0.34, G:0.17, T:0.20
Consensus pattern (41 bp):
CGAGAGCCATCACCTGATCGAGCCGATTATACACCTCCACA
Found at i:932833 original size:21 final size:21
Alignment explanation
Indices: 932780--932835 Score: 76
Period size: 21 Copynumber: 2.7 Consensus size: 21
932770 GTTAGGGGAG
* *
932780 TTACGTGATGAAGTCAGTGCT
1 TTACGTGATGAGGTCAGTACT
*
932801 TTACGTGATGAGGTCGGTACT
1 TTACGTGATGAGGTCAGTACT
*
932822 TTACGTGGTGAGGT
1 TTACGTGATGAGGT
932836 ATATGTTTTA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.20, C:0.12, G:0.34, T:0.34
Consensus pattern (21 bp):
TTACGTGATGAGGTCAGTACT
Found at i:932846 original size:42 final size:41
Alignment explanation
Indices: 932799--932898 Score: 119
Period size: 42 Copynumber: 2.4 Consensus size: 41
932789 GAAGTCAGTG
*
932799 CTTTACGTGATGAGGTCGGTACTTTACGTGGTGAGGTATATG
1 CTTTACGTGATGAGGT-GGTACTTTACGTGGTGAGGTATATA
* * ** *
932841 TTTTACGCGATGACAATGGTACTTTACGTGGTGAGGTATCTA
1 CTTTACGTGATGA-GGTGGTACTTTACGTGGTGAGGTATATA
*
932883 CTTTACGTGATAAGGT
1 CTTTACGTGATGAGGT
932899 AGTCGCTCTA
Statistics
Matches: 46, Mismatches: 11, Indels: 3
0.77 0.18 0.05
Matches are distributed among these distances:
41 1 0.02
42 44 0.96
43 1 0.02
ACGTcount: A:0.22, C:0.13, G:0.29, T:0.36
Consensus pattern (41 bp):
CTTTACGTGATGAGGTGGTACTTTACGTGGTGAGGTATATA
Found at i:932898 original size:21 final size:21
Alignment explanation
Indices: 932860--932899 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
932850 ATGACAATGG
* *
932860 TACTTTACGTGGTGAGGTATC
1 TACTTTACGTGATAAGGTATC
932881 TACTTTACGTGATAAGGTA
1 TACTTTACGTGATAAGGTA
932900 GTCGCTCTAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.25, C:0.12, G:0.25, T:0.38
Consensus pattern (21 bp):
TACTTTACGTGATAAGGTATC
Found at i:933013 original size:4 final size:4
Alignment explanation
Indices: 933004--933045 Score: 66
Period size: 4 Copynumber: 10.5 Consensus size: 4
932994 TTTTTAAGTA
* *
933004 TTAT TTAT TTAT TTAT TTAT TTAT TTAT GTAT TAAT TTAT TT
1 TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TT
933046 TTAGCGGCCC
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
4 34 1.00
ACGTcount: A:0.26, C:0.00, G:0.02, T:0.71
Consensus pattern (4 bp):
TTAT
Found at i:933238 original size:42 final size:42
Alignment explanation
Indices: 933178--933275 Score: 133
Period size: 42 Copynumber: 2.3 Consensus size: 42
933168 GATTCACCTG
* * * *
933178 TCATCGTTCAAGATGCCCCTCCTATCATTCAAGAGGCCCCTC
1 TCATCGTTCAAGAGGCCCCTCCCACCATTCAAGAGGCCCCTA
* *
933220 TCATCGTTCAAGAGGCCCCTCCCACCGTTCAAGAGGCCTCTA
1 TCATCGTTCAAGAGGCCCCTCCCACCATTCAAGAGGCCCCTA
*
933262 TCATTGTTCAAGAG
1 TCATCGTTCAAGAG
933276 CCCGATTCAC
Statistics
Matches: 49, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
42 49 1.00
ACGTcount: A:0.22, C:0.35, G:0.17, T:0.26
Consensus pattern (42 bp):
TCATCGTTCAAGAGGCCCCTCCCACCATTCAAGAGGCCCCTA
Found at i:933270 original size:21 final size:21
Alignment explanation
Indices: 933178--933275 Score: 117
Period size: 21 Copynumber: 4.7 Consensus size: 21
933168 GATTCACCTG
*
933178 TCATCGTTCAAGATGCCCCTC
1 TCATCGTTCAAGAGGCCCCTC
*
933199 -CTATCATTCAAGAGGCCCCTC
1 TC-ATCGTTCAAGAGGCCCCTC
933220 TCATCGTTCAAGAGGCCCCTC
1 TCATCGTTCAAGAGGCCCCTC
* * * *
933241 CCACCGTTCAAGAGGCCTCTA
1 TCATCGTTCAAGAGGCCCCTC
*
933262 TCATTGTTCAAGAG
1 TCATCGTTCAAGAG
933276 CCCGATTCAC
Statistics
Matches: 65, Mismatches: 10, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
20 1 0.02
21 63 0.97
22 1 0.02
ACGTcount: A:0.22, C:0.35, G:0.17, T:0.26
Consensus pattern (21 bp):
TCATCGTTCAAGAGGCCCCTC
Found at i:935975 original size:149 final size:149
Alignment explanation
Indices: 935702--936005 Score: 599
Period size: 149 Copynumber: 2.0 Consensus size: 149
935692 CGAAGTGCCC
935702 CGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAATTCCTTAAGAAT
1 CGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAATTCCTTAAGAAT
935767 CATATACATATACTATGGATCAAGTATGTGTCTTTCAAGACTTCACACAGGTTCCAAAGGATATA
66 CATATACATATACTATGGATCAAGTATGTGTCTTTCAAGACTTCACACAGGTTCCAAAGGATATA
935832 CATATGTCCTAAAGAACCG
131 CATATGTCCTAAAGAACCG
935851 CGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAATTCCTTAAGAAT
1 CGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAATTCCTTAAGAAT
*
935916 CATATACATATACTATGGATCAAGTATGTGTCTTTCAAGACTTCACACAGGTTCTAAAGGATATA
66 CATATACATATACTATGGATCAAGTATGTGTCTTTCAAGACTTCACACAGGTTCCAAAGGATATA
935981 CATATGTCCTAAAGAACCG
131 CATATGTCCTAAAGAACCG
936000 CGTAGA
1 CGTAGA
936006 CCCTCTACCC
Statistics
Matches: 154, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
149 154 1.00
ACGTcount: A:0.36, C:0.20, G:0.16, T:0.28
Consensus pattern (149 bp):
CGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAATTCCTTAAGAAT
CATATACATATACTATGGATCAAGTATGTGTCTTTCAAGACTTCACACAGGTTCCAAAGGATATA
CATATGTCCTAAAGAACCG
Found at i:936120 original size:24 final size:26
Alignment explanation
Indices: 936093--936153 Score: 72
Period size: 30 Copynumber: 2.3 Consensus size: 26
936083 TATCGCGTAG
936093 ACATAGTAT-TTT-CATACCTTTATC
1 ACATAGTATATTTACATACCTTTATC
936117 ACATAGGCATATCATTTACATACCTTTATC
1 ACATA-G--TAT-ATTTACATACCTTTATC
936147 ACATAGT
1 ACATAGT
936154 TCATATAACT
Statistics
Matches: 31, Mismatches: 0, Indels: 9
0.77 0.00 0.22
Matches are distributed among these distances:
24 5 0.16
25 1 0.03
27 4 0.13
29 4 0.13
30 17 0.55
ACGTcount: A:0.33, C:0.21, G:0.07, T:0.39
Consensus pattern (26 bp):
ACATAGTATATTTACATACCTTTATC
Found at i:942287 original size:149 final size:146
Alignment explanation
Indices: 942020--942320 Score: 575
Period size: 149 Copynumber: 2.0 Consensus size: 146
942010 CGAAGTGCCC
942020 CGTAGAATTGCACCGTAGTGCCATATAATGTCCATAAGGACCACATAGAATTCCTTAAGAATCAT
1 CGTAGAATTGCACCGTAGTGCCATATAATGTCCATAAGGACCACATAGAATTCCTTAAGAATCAT
942085 ATACATATACTATGGATCAAGTATGTGTCTTTCAAGACTTCACACAGGTTCCAAAGGATATACAT
66 ATACATATACTATGGATCAAGTATGTGTCTTTCAAGACTTCACACAGGTTCCAAAGGATATACAT
942150 ATGTCCTAAAGAACCG
131 ATGTCCTAAAGAACCG
942166 CGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAATTCCTTAAGAAT
1 CGTAGAATTGCACCGTAGTGCC--AT-ATAATGTCCATAAGGACCACATAGAATTCCTTAAGAAT
942231 CATATACATATACTATGGATCAAGTATGTGTCTTTCAAGACTTCACACAGGTTCCAAAGGATATA
63 CATATACATATACTATGGATCAAGTATGTGTCTTTCAAGACTTCACACAGGTTCCAAAGGATATA
942296 CATATGTCCTAAAGAACCG
128 CATATGTCCTAAAGAACCG
942315 CGTAGA
1 CGTAGA
942321 CCCTCTACCC
Statistics
Matches: 152, Mismatches: 0, Indels: 3
0.98 0.00 0.02
Matches are distributed among these distances:
146 22 0.14
148 2 0.01
149 128 0.84
ACGTcount: A:0.36, C:0.20, G:0.17, T:0.27
Consensus pattern (146 bp):
CGTAGAATTGCACCGTAGTGCCATATAATGTCCATAAGGACCACATAGAATTCCTTAAGAATCAT
ATACATATACTATGGATCAAGTATGTGTCTTTCAAGACTTCACACAGGTTCCAAAGGATATACAT
ATGTCCTAAAGAACCG
Found at i:942435 original size:24 final size:26
Alignment explanation
Indices: 942408--942468 Score: 72
Period size: 30 Copynumber: 2.3 Consensus size: 26
942398 TATCGCGTAG
942408 ACATAGTAT-TTT-CATACCTTTATC
1 ACATAGTATATTTACATACCTTTATC
942432 ACATAGGCATATCATTTACATACCTTTATC
1 ACATA-G--TAT-ATTTACATACCTTTATC
942462 ACATAGT
1 ACATAGT
942469 TCATATAACT
Statistics
Matches: 31, Mismatches: 0, Indels: 9
0.77 0.00 0.22
Matches are distributed among these distances:
24 5 0.16
25 1 0.03
27 4 0.13
29 4 0.13
30 17 0.55
ACGTcount: A:0.33, C:0.21, G:0.07, T:0.39
Consensus pattern (26 bp):
ACATAGTATATTTACATACCTTTATC
Found at i:945998 original size:16 final size:15
Alignment explanation
Indices: 945976--946014 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
945966 GAAATTATTG
945976 AAAAATTATATAGAAA
1 AAAAATTATATA-AAA
* *
945992 TAAAATTATGTAAAA
1 AAAAATTATATAAAA
946007 AAAAATTA
1 AAAAATTA
946015 GAGATGAGGA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
15 10 0.50
16 10 0.50
ACGTcount: A:0.67, C:0.00, G:0.05, T:0.28
Consensus pattern (15 bp):
AAAAATTATATAAAA
Found at i:946198 original size:20 final size:20
Alignment explanation
Indices: 946151--946343 Score: 96
Period size: 20 Copynumber: 9.7 Consensus size: 20
946141 CAAAACATTT
*
946151 GTGTTGCGAAAATAAAA--C
1 GTGTTGCGAAATTAAAATTC
* *
946169 CTGGTGCGAAATTAAAATTC
1 GTGTTGCGAAATTAAAATTC
946189 GTGTTGCG-AATTCGAAAA-TC
1 GTGTTGCGAAATT--AAAATTC
* **
946209 GAGTTGCGAAAACAAAATTC
1 GTGTTGCGAAATTAAAATTC
* *
946229 GCGTTG-GGAATTCAGAAA-TC
1 GTGTTGCGAAATT-A-AAATTC
* * *
946249 GAGTTGCGAATTTGAAATTC
1 GTGTTGCGAAATTAAAATTC
* *
946269 AGTGTTGCGAATTTGAAATTC
1 -GTGTTGCGAAATTAAAATTC
* *
946290 AGTGTTGCGAATTTTGAAA-TC
1 -GTGTTGCGAA-ATTAAAATTC
* * *
946311 GCGTTGCGAATTTGGAAATT-
1 GTGTTGCGAAATT-AAAATTC
946331 GTGTTGCGAAATT
1 GTGTTGCGAAATT
946344 GGAGTTCGCG
Statistics
Matches: 141, Mismatches: 20, Indels: 26
0.75 0.11 0.14
Matches are distributed among these distances:
18 14 0.10
19 17 0.12
20 57 0.40
21 46 0.33
22 7 0.05
ACGTcount: A:0.32, C:0.12, G:0.25, T:0.31
Consensus pattern (20 bp):
GTGTTGCGAAATTAAAATTC
Found at i:946226 original size:40 final size:40
Alignment explanation
Indices: 946173--946362 Score: 150
Period size: 40 Copynumber: 4.7 Consensus size: 40
946163 TAAAACCTGG
946173 TGCGAAATTAAAATTCGTGTTGCGAATTCGAAAATCGAGT
1 TGCGAAATTAAAATTCGTGTTGCGAATTCGAAAATCGAGT
** * *
946213 TGCGAAAACAAAATTCGCGTTGGGAATTC-AGAAATCGAGT
1 TGCGAAATTAAAATTCGTGTTGCGAATTCGA-AAATCGAGT
* * * * *
946253 TGCGAATTTGAAATTCAGTGTTGCGAATTTGAAATTCAGTGT
1 TGCGAAATTAAAATTC-GTGTTGCGAATTCGAAAATC-GAGT
* * * * * * *
946295 TGCGAATTTTGAAA-TCGCGTTGCGAATTTGGAAATTGTGT
1 TGCGAA-ATTAAAATTCGTGTTGCGAATTCGAAAATCGAGT
** * *
946335 TGCGAAATTGGAGTTCGCGTTGCGAATT
1 TGCGAAATTAAAATTCGTGTTGCGAATT
946363 TGTTGTTCAT
Statistics
Matches: 124, Mismatches: 20, Indels: 12
0.79 0.13 0.08
Matches are distributed among these distances:
39 5 0.04
40 70 0.56
41 30 0.24
42 12 0.10
43 7 0.06
ACGTcount: A:0.30, C:0.12, G:0.26, T:0.32
Consensus pattern (40 bp):
TGCGAAATTAAAATTCGTGTTGCGAATTCGAAAATCGAGT
Found at i:946247 original size:21 final size:21
Alignment explanation
Indices: 946223--946362 Score: 114
Period size: 20 Copynumber: 6.9 Consensus size: 21
946213 TGCGAAAACA
* * *
946223 AAATTCGCGTTGGGAATTCAG
1 AAATTCGTGTTGCGAATTCTG
*
946244 AAA-TCGAGTTGCGAATT-TG
1 AAATTCGTGTTGCGAATTCTG
946263 AAATTCAGTGTTGCGAATT-TG
1 AAATTC-GTGTTGCGAATTCTG
*
946284 AAATTCAGTGTTGCGAATTTTG
1 AAATTC-GTGTTGCGAATTCTG
*
946306 AAA-TCGCGTTGCGAATT-TGG
1 AAATTCGTGTTGCGAATTCT-G
*
946326 AAATT-GTGTTGCGAAAT-TG
1 AAATTCGTGTTGCGAATTCTG
* * *
946345 GAGTTCGCGTTGCGAATT
1 AAATTCGTGTTGCGAATT
946363 TGTTGTTCAT
Statistics
Matches: 102, Mismatches: 11, Indels: 13
0.81 0.09 0.10
Matches are distributed among these distances:
19 9 0.09
20 50 0.49
21 38 0.37
22 5 0.05
ACGTcount: A:0.27, C:0.11, G:0.27, T:0.34
Consensus pattern (21 bp):
AAATTCGTGTTGCGAATTCTG
Found at i:946267 original size:27 final size:21
Alignment explanation
Indices: 946251--946364 Score: 130
Period size: 20 Copynumber: 5.6 Consensus size: 21
946241 CAGAAATCGA
946251 GTTGCGAATTTGAAATTCAGT
1 GTTGCGAATTTGAAATTCAGT
946272 GTTGCGAATTTGAAATTCAGT
1 GTTGCGAATTTGAAATTCAGT
*
946293 GTTGCGAATTTTGAAA-TC-GC
1 GTTGCGAA-TTTGAAATTCAGT
946313 GTTGCGAATTTGGAAATT--GT
1 GTTGCGAATTT-GAAATTCAGT
* * * *
946333 GTTGCGAAATTGGAGTTC-GC
1 GTTGCGAATTTGAAATTCAGT
946353 GTTGCGAATTTG
1 GTTGCGAATTTG
946365 TTGTTCATTT
Statistics
Matches: 82, Mismatches: 7, Indels: 9
0.84 0.07 0.09
Matches are distributed among these distances:
19 7 0.09
20 36 0.44
21 32 0.39
22 7 0.09
ACGTcount: A:0.25, C:0.11, G:0.28, T:0.37
Consensus pattern (21 bp):
GTTGCGAATTTGAAATTCAGT
Found at i:946346 original size:20 final size:21
Alignment explanation
Indices: 946251--946343 Score: 97
Period size: 21 Copynumber: 4.5 Consensus size: 21
946241 CAGAAATCGA
946251 GTTGCG-AATTTGAAATTCAGT
1 GTTGCGAAATTTGAAATT-AGT
946272 GTTGCG-AATTTGAAATTCAGT
1 GTTGCGAAATTTGAAATT-AGT
* * *
946293 GTTGCGAATTTTGAAA-TCGC
1 GTTGCGAAATTTGAAATTAGT
946313 GTTGCG-AATTTGGAAATT-GT
1 GTTGCGAAATTT-GAAATTAGT
946333 GTTGCGAAATT
1 GTTGCGAAATT
946344 GGAGTTCGCG
Statistics
Matches: 63, Mismatches: 5, Indels: 8
0.83 0.07 0.11
Matches are distributed among these distances:
19 4 0.06
20 18 0.29
21 33 0.52
22 8 0.13
ACGTcount: A:0.27, C:0.10, G:0.26, T:0.38
Consensus pattern (21 bp):
GTTGCGAAATTTGAAATTAGT
Found at i:946356 original size:20 final size:21
Alignment explanation
Indices: 946173--946360 Score: 99
Period size: 20 Copynumber: 9.3 Consensus size: 21
946163 TAAAACCTGG
* *
946173 TGCGAAATT-AAAATTCGTGT
1 TGCGAAATTGGAAATTCGCGT
* * *
946193 TGCG-AATTCGAAAATCGAGT
1 TGCGAAATTGGAAATTCGCGT
***
946213 TGCGAAA-ACAAAATTCGCGT
1 TGCGAAATTGGAAATTCGCGT
* * *
946233 TG-GGAATTCAGAAA-TCGAGT
1 TGCGAAATT-GGAAATTCGCGT
* *
946253 TGCG-AATTTGAAATTCAGTGT
1 TGCGAAATTGGAAATTC-GCGT
* *
946274 TGCG-AATTTGAAATTCAGTGT
1 TGCGAAATTGGAAATTC-GCGT
* *
946295 TGCGAATTTTGAAA-TCGCGT
1 TGCGAAATTGGAAATTCGCGT
* *
946315 TGCGAATTTGGAAATT-GTGT
1 TGCGAAATTGGAAATTCGCGT
*
946335 TGCGAAATTGG-AGTTCGCGT
1 TGCGAAATTGGAAATTCGCGT
946355 TGCGAA
1 TGCGAA
946361 TTTGTTGTTC
Statistics
Matches: 137, Mismatches: 21, Indels: 20
0.77 0.12 0.11
Matches are distributed among these distances:
19 14 0.10
20 78 0.57
21 37 0.27
22 8 0.06
ACGTcount: A:0.30, C:0.12, G:0.26, T:0.31
Consensus pattern (21 bp):
TGCGAAATTGGAAATTCGCGT
Found at i:954716 original size:54 final size:54
Alignment explanation
Indices: 954658--954785 Score: 202
Period size: 54 Copynumber: 2.4 Consensus size: 54
954648 GTTGATTTTG
* * *
954658 TTCTAGAAATTTGGTTTCCAGTAATGGTGCCACTAGATGCCGAGTTTGAATCCC
1 TTCTAGAAATTTGGTTTCCAGAAATGATGACACTAGATGCCGAGTTTGAATCCC
* * *
954712 TTCTAGAAATTTGATTTCCAGAAATGATGACACTAGTTGCCGAGTTTGATTCCC
1 TTCTAGAAATTTGGTTTCCAGAAATGATGACACTAGATGCCGAGTTTGAATCCC
954766 TTCTAGAAATTTGGTTTCCA
1 TTCTAGAAATTTGGTTTCCA
954786 ATTATGATCC
Statistics
Matches: 67, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
54 67 1.00
ACGTcount: A:0.26, C:0.19, G:0.20, T:0.36
Consensus pattern (54 bp):
TTCTAGAAATTTGGTTTCCAGAAATGATGACACTAGATGCCGAGTTTGAATCCC
Found at i:955453 original size:14 final size:14
Alignment explanation
Indices: 955434--955462 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
955424 TCATCACCTG
955434 ACAATGTAAGAAGA
1 ACAATGTAAGAAGA
955448 ACAATGTAAGAAGA
1 ACAATGTAAGAAGA
955462 A
1 A
955463 ACTAATCACT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.59, C:0.07, G:0.21, T:0.14
Consensus pattern (14 bp):
ACAATGTAAGAAGA
Found at i:965771 original size:2 final size:2
Alignment explanation
Indices: 965764--965831 Score: 102
Period size: 2 Copynumber: 34.5 Consensus size: 2
965754 ATAAAGGAAA
**
965764 AT AT AT AT GC AT AT AT AT -T AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
965805 AT AT AT AT AT AT AT AT TT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
965832 AAACTTTGGG
Statistics
Matches: 59, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
1 1 0.02
2 58 0.98
ACGTcount: A:0.47, C:0.01, G:0.01, T:0.50
Consensus pattern (2 bp):
AT
Done.