Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008016.1 Hibiscus syriacus cultivar Beakdansim tig00110482_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: 5469637
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 5 of 25
Found at i:973039 original size:16 final size:16
Alignment explanation
Indices: 973020--973057 Score: 76
Period size: 16 Copynumber: 2.4 Consensus size: 16
973010 TAAGACACTT
973020 AAGATCGAGCTTTCTA
1 AAGATCGAGCTTTCTA
973036 AAGATCGAGCTTTCTA
1 AAGATCGAGCTTTCTA
973052 AAGATC
1 AAGATC
973058 CACTTGTTCT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.34, C:0.18, G:0.18, T:0.29
Consensus pattern (16 bp):
AAGATCGAGCTTTCTA
Found at i:977690 original size:26 final size:26
Alignment explanation
Indices: 977627--977683 Score: 71
Period size: 27 Copynumber: 2.1 Consensus size: 26
977617 AAATTTGTGT
*
977627 AAAATTATAAAAATTTTATTCTTCTTT
1 AAAATTAT-AAAATTTTATTCTTCTTC
977654 AAAATTATAAAATTTTAATT-TTCCTTC
1 AAAATTATAAAATTTT-ATTCTT-CTTC
977681 AAA
1 AAA
977684 GTTTAAATCT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
26 10 0.37
27 17 0.63
ACGTcount: A:0.44, C:0.09, G:0.00, T:0.47
Consensus pattern (26 bp):
AAAATTATAAAATTTTATTCTTCTTC
Found at i:978592 original size:23 final size:23
Alignment explanation
Indices: 978519--978605 Score: 68
Period size: 23 Copynumber: 3.6 Consensus size: 23
978509 TTGTAATAAA
*
978519 AATATTACATTTATAATAAAAAT
1 AATATTAAATTTATAATAAAAAT
* * *
978542 AATATAAAATTACTAAAACAAAGGAAAT
1 AATATTAAATT--TATAA-TAA--AAAT
*
978570 AATATTATATTTATAATAAAAAT
1 AATATTAAATTTATAATAAAAAT
978593 AATA-TAAAGTTTA
1 AATATTAAA-TTTA
978606 CTTATGTTAG
Statistics
Matches: 49, Mismatches: 9, Indels: 12
0.70 0.13 0.17
Matches are distributed among these distances:
22 3 0.06
23 21 0.43
25 6 0.12
26 6 0.12
28 13 0.27
ACGTcount: A:0.59, C:0.03, G:0.03, T:0.34
Consensus pattern (23 bp):
AATATTAAATTTATAATAAAAAT
Found at i:978599 original size:28 final size:28
Alignment explanation
Indices: 978519--978599 Score: 66
Period size: 28 Copynumber: 3.1 Consensus size: 28
978509 TTGTAATAAA
*
978519 AATATTACATTTATAATAAAAATAATAT
1 AATATTATATTTATAATAAAAATAATAT
* * **
978547 AAAATTACTA---A-AA-CAAAGGAA-AT
1 AATATTA-TATTTATAATAAAAATAATAT
978570 AATATTATATTTATAATAAAAATAATAT
1 AATATTATATTTATAATAAAAATAATAT
978598 AA
1 AA
978600 AGTTTACTTA
Statistics
Matches: 37, Mismatches: 9, Indels: 14
0.62 0.15 0.23
Matches are distributed among these distances:
22 2 0.05
23 8 0.22
24 5 0.14
25 3 0.08
26 3 0.08
27 5 0.14
28 10 0.27
29 1 0.03
ACGTcount: A:0.60, C:0.04, G:0.02, T:0.33
Consensus pattern (28 bp):
AATATTATATTTATAATAAAAATAATAT
Found at i:979072 original size:6 final size:6
Alignment explanation
Indices: 979061--979094 Score: 59
Period size: 6 Copynumber: 5.7 Consensus size: 6
979051 TTTGCCTTTT
*
979061 ATCCTC ATCCTC ATCCTC ATCCTC AACCTC ATCC
1 ATCCTC ATCCTC ATCCTC ATCCTC ATCCTC ATCC
979095 CATGCAAGAG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.21, C:0.50, G:0.00, T:0.29
Consensus pattern (6 bp):
ATCCTC
Found at i:981046 original size:2 final size:2
Alignment explanation
Indices: 981039--981068 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
981029 CAAATTTCTC
981039 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
981069 CACAGCAGTC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:983861 original size:14 final size:13
Alignment explanation
Indices: 983841--983866 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
983831 TTCTGGTAAT
983841 TTTAAAAATTTTA
1 TTTAAAAATTTTA
983854 TTTAAAAATTTTA
1 TTTAAAAATTTTA
983867 AAAATAAAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (13 bp):
TTTAAAAATTTTA
Found at i:985179 original size:3 final size:3
Alignment explanation
Indices: 985164--985207 Score: 79
Period size: 3 Copynumber: 14.7 Consensus size: 3
985154 CATCTTCATA
*
985164 TTC TTC CTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
985208 TTCCTGTTCC
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (3 bp):
TTC
Found at i:991724 original size:12 final size:12
Alignment explanation
Indices: 991709--991733 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
991699 TATTAAGTAA
991709 TTAATATTTAAT
1 TTAATATTTAAT
991721 TTAATATTTAAT
1 TTAATATTTAAT
991733 T
1 T
991734 ATTTTAAAAA
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:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (12 bp):
TTAATATTTAAT
Found at i:992153 original size:21 final size:21
Alignment explanation
Indices: 992129--992175 Score: 94
Period size: 21 Copynumber: 2.2 Consensus size: 21
992119 TATCGCAAAT
992129 TCGCGTTGCGATAGTTGAAAA
1 TCGCGTTGCGATAGTTGAAAA
992150 TCGCGTTGCGATAGTTGAAAA
1 TCGCGTTGCGATAGTTGAAAA
992171 TCGCG
1 TCGCG
992176 GTTCGCGTTG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.26, C:0.17, G:0.30, T:0.28
Consensus pattern (21 bp):
TCGCGTTGCGATAGTTGAAAA
Found at i:992343 original size:11 final size:11
Alignment explanation
Indices: 992327--992366 Score: 66
Period size: 11 Copynumber: 3.8 Consensus size: 11
992317 AGTATTACCA
992327 CGACCACGACC
1 CGACCACGACC
992338 CGACCACGACC
1 CGACCACGACC
992349 CGACC-CGACC
1 CGACCACGACC
992359 CGA-CACGA
1 CGACCACGA
992367 GACGGACGGC
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
9 1 0.04
10 11 0.39
11 16 0.57
ACGTcount: A:0.28, C:0.53, G:0.20, T:0.00
Consensus pattern (11 bp):
CGACCACGACC
Found at i:992352 original size:5 final size:5
Alignment explanation
Indices: 992327--992362 Score: 54
Period size: 5 Copynumber: 6.8 Consensus size: 5
992317 AGTATTACCA
992327 CGACC ACGACC CGACC ACGACC CGACC CGACC CGAC
1 CGACC -CGACC CGACC -CGACC CGACC CGACC CGAC
992363 ACGAGACGGA
Statistics
Matches: 29, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
5 19 0.66
6 10 0.34
ACGTcount: A:0.25, C:0.56, G:0.19, T:0.00
Consensus pattern (5 bp):
CGACC
Found at i:992876 original size:6 final size:6
Alignment explanation
Indices: 992867--992891 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
992857 GTCGTGGTCG
992867 TGGTAA TGGTAA TGGTAA TGGTAA T
1 TGGTAA TGGTAA TGGTAA TGGTAA T
992892 ACGTGTGTTC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.32, C:0.00, G:0.32, T:0.36
Consensus pattern (6 bp):
TGGTAA
Found at i:993018 original size:22 final size:22
Alignment explanation
Indices: 992989--993082 Score: 113
Period size: 22 Copynumber: 4.4 Consensus size: 22
992979 AATTTGGAAA
992989 ATCGCAACGACAACTGTAGACT
1 ATCGCAACGACAACTGTAGACT
*
993011 TTCGCAACGACAACTGTAGACT
1 ATCGCAACGACAACTGTAGACT
* * **
993033 ATCGCAACG--AA-TTTGGAAA
1 ATCGCAACGACAACTGTAGACT
*
993052 ATCGCAATGACAACTGTAGACT
1 ATCGCAACGACAACTGTAGACT
993074 ATCGCAACG
1 ATCGCAACG
993083 CGAATTTACG
Statistics
Matches: 57, Mismatches: 12, Indels: 6
0.76 0.16 0.08
Matches are distributed among these distances:
19 12 0.21
20 2 0.04
21 2 0.04
22 41 0.72
ACGTcount: A:0.36, C:0.24, G:0.19, T:0.20
Consensus pattern (22 bp):
ATCGCAACGACAACTGTAGACT
Found at i:996640 original size:21 final size:22
Alignment explanation
Indices: 996593--996640 Score: 64
Period size: 21 Copynumber: 2.3 Consensus size: 22
996583 CCATCTCCGT
*
996593 AGGGTTACATTCCTAGCCCGCC
1 AGGGTTACATGCCTAGCCCGCC
*
996615 A-GGTTACATGCCTAGGCCG-C
1 AGGGTTACATGCCTAGCCCGCC
996635 AGGGTT
1 AGGGTT
996641 TTATGACACC
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
20 2 0.09
21 20 0.87
22 1 0.04
ACGTcount: A:0.19, C:0.29, G:0.29, T:0.23
Consensus pattern (22 bp):
AGGGTTACATGCCTAGCCCGCC
Found at i:997290 original size:17 final size:19
Alignment explanation
Indices: 997253--997291 Score: 55
Period size: 20 Copynumber: 2.1 Consensus size: 19
997243 TGATCATAAC
997253 ATTTCAATATGCATGCATAT
1 ATTTCAATATGCA-GCATAT
997273 ATTTCAATATG-A-CATAT
1 ATTTCAATATGCAGCATAT
997290 AT
1 AT
997292 AAATCATGTC
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 7 0.37
19 1 0.05
20 11 0.58
ACGTcount: A:0.38, C:0.13, G:0.08, T:0.41
Consensus pattern (19 bp):
ATTTCAATATGCAGCATAT
Found at i:997533 original size:23 final size:22
Alignment explanation
Indices: 997484--997570 Score: 129
Period size: 22 Copynumber: 3.9 Consensus size: 22
997474 TATTGATATT
*
997484 TGTCCCGAAGGACCACATGATA
1 TGTCCCGAAGGACCACTTGATA
997506 TGTCCCGAAGGACCACTTGAATA
1 TGTCCCGAAGGACCACTTG-ATA
*
997529 TGTCCCGAAGGACCACGTGATA
1 TGTCCCGAAGGACCACTTGATA
* *
997551 TATCCCAAAGGACCACTTGA
1 TGTCCCGAAGGACCACTTGA
997571 ACCCTCGACT
Statistics
Matches: 59, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
22 38 0.64
23 21 0.36
ACGTcount: A:0.31, C:0.28, G:0.22, T:0.20
Consensus pattern (22 bp):
TGTCCCGAAGGACCACTTGATA
Found at i:997550 original size:45 final size:45
Alignment explanation
Indices: 997484--997571 Score: 149
Period size: 45 Copynumber: 2.0 Consensus size: 45
997474 TATTGATATT
* *
997484 TGTCCCGAAGGACCACATGATATGTCCCGAAGGACCACTTGAATA
1 TGTCCCGAAGGACCACATGATATATCCCAAAGGACCACTTGAATA
*
997529 TGTCCCGAAGGACCACGTGATATATCCCAAAGGACCACTTGAA
1 TGTCCCGAAGGACCACATGATATATCCCAAAGGACCACTTGAA
997572 CCCTCGACTC
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
45 40 1.00
ACGTcount: A:0.32, C:0.27, G:0.22, T:0.19
Consensus pattern (45 bp):
TGTCCCGAAGGACCACATGATATATCCCAAAGGACCACTTGAATA
Found at i:1000057 original size:22 final size:23
Alignment explanation
Indices: 1000029--1000076 Score: 71
Period size: 22 Copynumber: 2.1 Consensus size: 23
1000019 TTTATGATAT
*
1000029 TTATTTAATATAATAATTAA-TA
1 TTATTTAATATAAAAATTAATTA
*
1000051 TTATTTATTATAAAAATTAATTA
1 TTATTTAATATAAAAATTAATTA
1000074 TTA
1 TTA
1000077 ATTTTAAAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 18 0.78
23 5 0.22
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (23 bp):
TTATTTAATATAAAAATTAATTA
Found at i:1000071 original size:26 final size:25
Alignment explanation
Indices: 1000003--1000073 Score: 74
Period size: 26 Copynumber: 2.8 Consensus size: 25
999993 TTTTTTAATT
* *
1000003 TTTATTTAAAAATTATTTTATGATA
1 TTTATTTAAAAATTAATTAATGATA
1000028 TTTATTTAATATAA-TAATTAAT-ATTA
1 TTTATTTAA-A-AATTAATTAATGA-TA
1000054 TTTATTATAAAAATTAATTA
1 TTTATT-TAAAAATTAATTA
1000074 TTAATTTTAA
Statistics
Matches: 39, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
25 12 0.31
26 22 0.56
27 5 0.13
ACGTcount: A:0.45, C:0.00, G:0.01, T:0.54
Consensus pattern (25 bp):
TTTATTTAAAAATTAATTAATGATA
Found at i:1004957 original size:21 final size:21
Alignment explanation
Indices: 1004928--1004974 Score: 69
Period size: 21 Copynumber: 2.2 Consensus size: 21
1004918 TTGAAAGGAA
*
1004928 CGATTCCTTGAGAA-AAATGAT
1 CGATCCCTTGA-AAGAAATGAT
1004949 CGATCCCTTGAAAGAAATGAT
1 CGATCCCTTGAAAGAAATGAT
1004970 CGATC
1 CGATC
1004975 ATTCTCTGTT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
20 2 0.08
21 22 0.92
ACGTcount: A:0.36, C:0.19, G:0.19, T:0.26
Consensus pattern (21 bp):
CGATCCCTTGAAAGAAATGAT
Found at i:1012671 original size:14 final size:14
Alignment explanation
Indices: 1012652--1012683 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
1012642 AGTTAAAAAT
1012652 TATTTTTAAATTAA
1 TATTTTTAAATTAA
*
1012666 TATTTTTATATTAA
1 TATTTTTAAATTAA
1012680 TATT
1 TATT
1012684 AGATTAATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (14 bp):
TATTTTTAAATTAA
Found at i:1019893 original size:20 final size:20
Alignment explanation
Indices: 1019846--1019895 Score: 73
Period size: 20 Copynumber: 2.5 Consensus size: 20
1019836 TATAGCTAAT
1019846 AGTTCTAGAACACAATGGAA
1 AGTTCTAGAACACAATGGAA
** *
1019866 AGAGCTAGAACACAATGGAG
1 AGTTCTAGAACACAATGGAA
1019886 AGTTCTAGAA
1 AGTTCTAGAA
1019896 TACTTTGGAA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.44, C:0.14, G:0.24, T:0.18
Consensus pattern (20 bp):
AGTTCTAGAACACAATGGAA
Found at i:1020520 original size:15 final size:15
Alignment explanation
Indices: 1020500--1020538 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
1020490 CCAAATCAAG
1020500 AATAAAGATTAAAAC
1 AATAAAGATTAAAAC
* * *
1020515 AATAAAGACTAAGAT
1 AATAAAGATTAAAAC
1020530 AATAAAGAT
1 AATAAAGAT
1020539 AAATAAAGAC
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.64, C:0.05, G:0.10, T:0.21
Consensus pattern (15 bp):
AATAAAGATTAAAAC
Found at i:1022399 original size:12 final size:13
Alignment explanation
Indices: 1022377--1022405 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
1022367 GTTAAGTTCT
1022377 TGAGAGAAGATAA
1 TGAGAGAAGATAA
1022390 TGAG-GAAGATAA
1 TGAGAGAAGATAA
1022402 TGAG
1 TGAG
1022406 TGTGACGGTG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 12 0.75
13 4 0.25
ACGTcount: A:0.48, C:0.00, G:0.34, T:0.17
Consensus pattern (13 bp):
TGAGAGAAGATAA
Found at i:1031884 original size:21 final size:21
Alignment explanation
Indices: 1031858--1031903 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
1031848 GAGTTCTGGG
* *
1031858 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
1031879 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
1031900 CAAG
1 CAAG
1031904 CGACAGAATT
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:0.30, C:0.28, G:0.26, T:0.15
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:1032669 original size:31 final size:31
Alignment explanation
Indices: 1032631--1032816 Score: 304
Period size: 31 Copynumber: 6.0 Consensus size: 31
1032621 AGGGTCGAGG
1032631 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
1032662 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
1032693 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
*
1032724 G-TTACCTATGTTCTTCGGAACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
*
1032754 GTTTACCTATGTCCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
* * *
1032785 GATTACCTAGGTTCTTCGGAATC-TATGGACT
1 GTTTACCTATGTTCTTCGGGA-CATATGGACT
1032816 G
1 G
1032817 GTCCTTCGGG
Statistics
Matches: 146, Mismatches: 7, Indels: 4
0.93 0.04 0.03
Matches are distributed among these distances:
30 29 0.20
31 116 0.79
32 1 0.01
ACGTcount: A:0.20, C:0.20, G:0.23, T:0.37
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGGGACATATGGACT
Found at i:1032702 original size:62 final size:61
Alignment explanation
Indices: 1032631--1032816 Score: 311
Period size: 61 Copynumber: 3.0 Consensus size: 61
1032621 AGGGTCGAGG
*
1032631 GTTTACCTATGTTCTTCGGGACATATGGACTGTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACTG-TTACCTATGTTCTTCGGAACATATGGACT
1032693 GTTTACCTATGTTCTTCGGGACATATGGACTGTTACCTATGTTCTTCGGAACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACTGTTACCTATGTTCTTCGGAACATATGGACT
* *
1032754 GTTTACCTATGTCCTTCGGGACATATGGACTGATTACCTAGGTTCTTCGGAATC-TATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACTG-TTACCTATGTTCTTCGGAA-CATATGGACT
1032816 G
1 G
1032817 GTCCTTCGGG
Statistics
Matches: 119, Mismatches: 3, Indels: 4
0.94 0.02 0.03
Matches are distributed among these distances:
61 59 0.50
62 59 0.50
63 1 0.01
ACGTcount: A:0.20, C:0.20, G:0.23, T:0.37
Consensus pattern (61 bp):
GTTTACCTATGTTCTTCGGGACATATGGACTGTTACCTATGTTCTTCGGAACATATGGACT
Found at i:1032791 original size:92 final size:92
Alignment explanation
Indices: 1032633--1032816 Score: 307
Period size: 92 Copynumber: 2.0 Consensus size: 92
1032623 GGTCGAGGGT
* * *
1032633 TTACCTATGTTCTTCGGGACATATGGACTGTTTACCTATGTTCTTCGGGACATATGGACTGTTTA
1 TTACCTATGTTCTTCGGAACATATGGACTGTTTACCTATGTCCTTCGGGACATATGGACTGATTA
* *
1032698 CCTATGTTCTTCGGGA-CATATGGACTG
66 CCTAGGTTCTTCGGAATC-TATGGACTG
1032725 TTACCTATGTTCTTCGGAACATATGGACTGTTTACCTATGTCCTTCGGGACATATGGACTGATTA
1 TTACCTATGTTCTTCGGAACATATGGACTGTTTACCTATGTCCTTCGGGACATATGGACTGATTA
1032790 CCTAGGTTCTTCGGAATCTATGGACTG
66 CCTAGGTTCTTCGGAATCTATGGACTG
1032817 GTCCTTCGGG
Statistics
Matches: 86, Mismatches: 5, Indels: 2
0.92 0.05 0.02
Matches are distributed among these distances:
92 85 0.99
93 1 0.01
ACGTcount: A:0.21, C:0.20, G:0.22, T:0.37
Consensus pattern (92 bp):
TTACCTATGTTCTTCGGAACATATGGACTGTTTACCTATGTCCTTCGGGACATATGGACTGATTA
CCTAGGTTCTTCGGAATCTATGGACTG
Found at i:1033640 original size:14 final size:14
Alignment explanation
Indices: 1033621--1033651 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
1033611 TATTTATACG
1033621 AAAAAAGAAAAAAA
1 AAAAAAGAAAAAAA
1033635 AAAAAAGAAAAAAA
1 AAAAAAGAAAAAAA
1033649 AAA
1 AAA
1033652 TTGTTGAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.94, C:0.00, G:0.06, T:0.00
Consensus pattern (14 bp):
AAAAAAGAAAAAAA
Found at i:1035839 original size:19 final size:20
Alignment explanation
Indices: 1035815--1035854 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
1035805 GTTCTGGGCA
* *
1035815 AGGGGAATCGGTA-CCCTTC
1 AGGGGAACCGATACCCCTTC
1035834 AGGGGAACCGATACCCCTTC
1 AGGGGAACCGATACCCCTTC
1035854 A
1 A
1035855 AGCGACAGAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 11 0.61
20 7 0.39
ACGTcount: A:0.25, C:0.30, G:0.28, T:0.17
Consensus pattern (20 bp):
AGGGGAACCGATACCCCTTC
Found at i:1036633 original size:31 final size:31
Alignment explanation
Indices: 1036575--1036759 Score: 295
Period size: 31 Copynumber: 6.0 Consensus size: 31
1036565 AGGGTCGAGG
1036575 GTTTACCTATGTTCTTCGGG--ATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
1036604 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
1036635 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
*
1036666 GTTTACCTATGTTCTTCGGAACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
*
1036697 GTTTACCTATGTCCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
* * *
1036728 GATTACCTAGGTTCTTCGGAATC-TATGGACT
1 GTTTACCTATGTTCTTCGGGA-CATATGGACT
1036759 G
1 G
1036760 GTCCTTCGGG
Statistics
Matches: 146, Mismatches: 7, Indels: 4
0.93 0.04 0.03
Matches are distributed among these distances:
29 20 0.14
31 125 0.86
32 1 0.01
ACGTcount: A:0.20, C:0.19, G:0.23, T:0.38
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGGGACATATGGACT
Found at i:1037968 original size:21 final size:21
Alignment explanation
Indices: 1037942--1037986 Score: 90
Period size: 21 Copynumber: 2.1 Consensus size: 21
1037932 TTAGACTGCA
1037942 AGCCTCAGCATCTATTCTGAT
1 AGCCTCAGCATCTATTCTGAT
1037963 AGCCTCAGCATCTATTCTGAT
1 AGCCTCAGCATCTATTCTGAT
1037984 AGC
1 AGC
1037987 AGACACAGAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.24, C:0.29, G:0.16, T:0.31
Consensus pattern (21 bp):
AGCCTCAGCATCTATTCTGAT
Found at i:1047439 original size:3 final size:3
Alignment explanation
Indices: 1047431--1047455 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
1047421 GAATTGGGTT
1047431 TTG TTG TTG TTG TTG TTG TTG TTG T
1 TTG TTG TTG TTG TTG TTG TTG TTG T
1047456 AATACTATTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.00, C:0.00, G:0.32, T:0.68
Consensus pattern (3 bp):
TTG
Found at i:1065877 original size:30 final size:30
Alignment explanation
Indices: 1065843--1065913 Score: 124
Period size: 30 Copynumber: 2.4 Consensus size: 30
1065833 ATATGTAACT
1065843 TTTATTTATTTATTTATTTTGAATAATTTA
1 TTTATTTATTTATTTATTTTGAATAATTTA
* *
1065873 TTTATTTATTCATTTATTTTGAATGATTTA
1 TTTATTTATTTATTTATTTTGAATAATTTA
1065903 TTTATTTATTT
1 TTTATTTATTT
1065914 TGAATAATTT
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 38 1.00
ACGTcount: A:0.27, C:0.01, G:0.04, T:0.68
Consensus pattern (30 bp):
TTTATTTATTTATTTATTTTGAATAATTTA
Found at i:1065901 original size:22 final size:22
Alignment explanation
Indices: 1065876--1065931 Score: 94
Period size: 22 Copynumber: 2.5 Consensus size: 22
1065866 TAATTTATTT
* *
1065876 ATTTATTCATTTATTTTGAATG
1 ATTTATTTATTTATTTTGAATA
1065898 ATTTATTTATTTATTTTGAATA
1 ATTTATTTATTTATTTTGAATA
1065920 ATTTATTTATTT
1 ATTTATTTATTT
1065932 GTTTGAAGGG
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.29, C:0.02, G:0.05, T:0.64
Consensus pattern (22 bp):
ATTTATTTATTTATTTTGAATA
Found at i:1065931 original size:4 final size:4
Alignment explanation
Indices: 1065843--1065913 Score: 61
Period size: 4 Copynumber: 16.8 Consensus size: 4
1065833 ATATGTAACT
* * *
1065843 TTTA TTTA TTTA TTTA TTTTGA ATAA TTTA TTTA TTTA TTCA TTTA TTTTGA
1 TTTA TTTA TTTA TTTA -TTT-A TTTA TTTA TTTA TTTA TTTA TTTA -TTT-A
* *
1065895 ATGA TTTA TTTA TTTA TTT
1 TTTA TTTA TTTA TTTA TTT
1065914 TGAATAATTT
Statistics
Matches: 53, Mismatches: 10, Indels: 8
0.75 0.14 0.11
Matches are distributed among these distances:
4 43 0.81
5 8 0.15
6 2 0.04
ACGTcount: A:0.27, C:0.01, G:0.04, T:0.68
Consensus pattern (4 bp):
TTTA
Found at i:1073582 original size:20 final size:21
Alignment explanation
Indices: 1073538--1073577 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
1073528 CCCTCTTTGA
*
1073538 AGGGGAACCGATTCCCCCCAC
1 AGGGGAACCGATACCCCCCAC
*
1073559 AGGGGAATCGATACCCCCC
1 AGGGGAACCGATACCCCCC
1073578 TAGGGTTCTG
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:0.40, G:0.25, T:0.10
Consensus pattern (21 bp):
AGGGGAACCGATACCCCCCAC
Found at i:1083363 original size:20 final size:21
Alignment explanation
Indices: 1083319--1083374 Score: 78
Period size: 20 Copynumber: 2.7 Consensus size: 21
1083309 CAGTTTCCAA
* *
1083319 ATTCGCAACGCGAATATCCAG
1 ATTCGCAACGCGATTATCAAG
*
1083340 ATTCGCAACGCGATTGT-AAG
1 ATTCGCAACGCGATTATCAAG
1083360 ATTCGCAACGCGATT
1 ATTCGCAACGCGATT
1083375 TTGAAAAATA
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
20 17 0.53
21 15 0.47
ACGTcount: A:0.30, C:0.25, G:0.21, T:0.23
Consensus pattern (21 bp):
ATTCGCAACGCGATTATCAAG
Found at i:1083445 original size:22 final size:20
Alignment explanation
Indices: 1083385--1083464 Score: 74
Period size: 19 Copynumber: 3.9 Consensus size: 20
1083375 TTGAAAAATA
*
1083385 TGTTGCGATAGTTAAAA-TG
1 TGTTGCGATAGTGAAAAGTG
*
1083404 TGTTGCGAGAGTTTGAAAAACGTG
1 TGTTGCGATAG--TG-AAAA-GTG
1083428 TTGTTGCGATAGTGAAAAG-G
1 -TGTTGCGATAGTGAAAAGTG
*
1083448 TGTTGCAATAGTGAAAA
1 TGTTGCGATAGTGAAAA
1083465 ATCCAAAATA
Statistics
Matches: 51, Mismatches: 4, Indels: 12
0.76 0.06 0.18
Matches are distributed among these distances:
19 26 0.51
20 1 0.02
21 2 0.04
22 8 0.16
23 2 0.04
24 2 0.04
25 10 0.20
ACGTcount: A:0.33, C:0.06, G:0.30, T:0.31
Consensus pattern (20 bp):
TGTTGCGATAGTGAAAAGTG
Found at i:1083852 original size:21 final size:21
Alignment explanation
Indices: 1083828--1083909 Score: 110
Period size: 21 Copynumber: 3.9 Consensus size: 21
1083818 TCGTAATGCA
*
1083828 AACTTTGACTATCGCAACGTG
1 AACTTAGACTATCGCAACGTG
**
1083849 AACTTAGACTATCGCAACGCA
1 AACTTAGACTATCGCAACGTG
* *
1083870 AACTTCGACTATCGTAACGTG
1 AACTTAGACTATCGCAACGTG
*
1083891 AACTTGGACTATCGCAACG
1 AACTTAGACTATCGCAACG
1083910 AATTTGGACT
Statistics
Matches: 52, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 52 1.00
ACGTcount: A:0.32, C:0.26, G:0.18, T:0.24
Consensus pattern (21 bp):
AACTTAGACTATCGCAACGTG
Found at i:1083873 original size:42 final size:42
Alignment explanation
Indices: 1083825--1083909 Score: 143
Period size: 42 Copynumber: 2.0 Consensus size: 42
1083815 AAATCGTAAT
*
1083825 GCAAACTTTGACTATCGCAACGTGAACTTAGACTATCGCAAC
1 GCAAACTTCGACTATCGCAACGTGAACTTAGACTATCGCAAC
* *
1083867 GCAAACTTCGACTATCGTAACGTGAACTTGGACTATCGCAAC
1 GCAAACTTCGACTATCGCAACGTGAACTTAGACTATCGCAAC
1083909 G
1 G
1083910 AATTTGGACT
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
42 40 1.00
ACGTcount: A:0.32, C:0.26, G:0.19, T:0.24
Consensus pattern (42 bp):
GCAAACTTCGACTATCGCAACGTGAACTTAGACTATCGCAAC
Found at i:1083954 original size:19 final size:19
Alignment explanation
Indices: 1083926--1083963 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
1083916 GACTAACATA
*
1083926 AATTTGAAAAATCGCAACG
1 AATTTAAAAAATCGCAACG
1083945 AATTTAAAAAATCGCAACG
1 AATTTAAAAAATCGCAACG
1083964 CGAACTTGGA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.50, C:0.16, G:0.13, T:0.21
Consensus pattern (19 bp):
AATTTAAAAAATCGCAACG
Found at i:1084970 original size:17 final size:17
Alignment explanation
Indices: 1084922--1084971 Score: 50
Period size: 17 Copynumber: 3.0 Consensus size: 17
1084912 AATCAACCCG
*
1084922 AACCCAAAAATGA-CTCG
1 AACCCAAAAATGATC-CA
* *
1084939 AA-CCAGAATTGATCCA
1 AACCCAAAAATGATCCA
1084955 AACCCAAAAATGATCCA
1 AACCCAAAAATGATCCA
1084972 GACTTGAACC
Statistics
Matches: 26, Mismatches: 5, Indels: 4
0.74 0.14 0.11
Matches are distributed among these distances:
16 11 0.42
17 15 0.58
ACGTcount: A:0.48, C:0.28, G:0.10, T:0.14
Consensus pattern (17 bp):
AACCCAAAAATGATCCA
Found at i:1091049 original size:21 final size:22
Alignment explanation
Indices: 1091020--1091069 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 22
1091010 ATTCCTATTC
* *
1091020 AAAATTAAAAAGACTTAAGA-A
1 AAAAATAAAAAGACATAAGATA
*
1091041 AAAAAT-AAAAGACATAATATA
1 AAAAATAAAAAGACATAAGATA
1091062 AAAAATAA
1 AAAAATAA
1091070 GAGAACTAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
20 11 0.46
21 12 0.50
22 1 0.04
ACGTcount: A:0.72, C:0.04, G:0.06, T:0.18
Consensus pattern (22 bp):
AAAAATAAAAAGACATAAGATA
Found at i:1091080 original size:21 final size:21
Alignment explanation
Indices: 1091027--1091069 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 21
1091017 TTCAAAATTA
* *
1091027 AAAAGACTTAAGA-AAAAAAT
1 AAAAGACATAATATAAAAAAT
1091047 AAAAGACATAATATAAAAAAT
1 AAAAGACATAATATAAAAAAT
1091068 AA
1 AA
1091070 GAGAACTAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 11 0.55
21 9 0.45
ACGTcount: A:0.72, C:0.05, G:0.07, T:0.16
Consensus pattern (21 bp):
AAAAGACATAATATAAAAAAT
Found at i:1098656 original size:21 final size:21
Alignment explanation
Indices: 1098630--1098669 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
1098620 CCCCCTTTGA
*
1098630 AGGGGAACCGATTCCCCCCAC
1 AGGGGAACCGATACCCCCCAC
*
1098651 AGGGGAATCGATACCCCCC
1 AGGGGAACCGATACCCCCC
1098670 TGGGGTTCTG
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:0.40, G:0.25, T:0.10
Consensus pattern (21 bp):
AGGGGAACCGATACCCCCCAC
Found at i:1102482 original size:25 final size:24
Alignment explanation
Indices: 1102443--1102491 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 24
1102433 AGGTATCCCT
* *
1102443 AAAAAATAAAAAAATGTTAGATAA
1 AAAAAATAAAAAAATATTAAATAA
*
1102467 AAAATAATAAATAAATATTAAATAA
1 AAAA-AATAAAAAAATATTAAATAA
1102492 TCAAAGGGAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
24 4 0.19
25 17 0.81
ACGTcount: A:0.71, C:0.00, G:0.04, T:0.24
Consensus pattern (24 bp):
AAAAAATAAAAAAATATTAAATAA
Found at i:1103621 original size:35 final size:35
Alignment explanation
Indices: 1103548--1103622 Score: 114
Period size: 35 Copynumber: 2.1 Consensus size: 35
1103538 CGTCACGTCC
* **
1103548 AGTAAGGCCCTGAGCACACAGCCGATGAACCGGTA
1 AGTAAGGCCCTGAGCACACAGCCGAGGAACCGCCA
*
1103583 AGTAAGGCCCTGAGCACACAGCCGAGGAACCTCCA
1 AGTAAGGCCCTGAGCACACAGCCGAGGAACCGCCA
1103618 AGTAA
1 AGTAA
1103623 TCTTCCTCCA
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.33, C:0.29, G:0.27, T:0.11
Consensus pattern (35 bp):
AGTAAGGCCCTGAGCACACAGCCGAGGAACCGCCA
Found at i:1103726 original size:24 final size:24
Alignment explanation
Indices: 1103699--1103789 Score: 112
Period size: 24 Copynumber: 3.8 Consensus size: 24
1103689 CATAATTCAA
1103699 GTCAAGTATCATATCAGAATCCAG
1 GTCAAGTATCATATCAGAATCCAG
* *
1103723 GTCATGTATCATATCAGAATCCAT
1 GTCAAGTATCATATCAGAATCCAG
*
1103747 GTCAA-TATCAGATCAGAATCCAG
1 GTCAAGTATCATATCAGAATCCAG
* * * *
1103770 ATTAGGTATCATAACAGAAT
1 GTCAAGTATCATATCAGAAT
1103790 TCAAATTTGA
Statistics
Matches: 56, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
23 18 0.32
24 38 0.68
ACGTcount: A:0.38, C:0.19, G:0.15, T:0.27
Consensus pattern (24 bp):
GTCAAGTATCATATCAGAATCCAG
Found at i:1103769 original size:47 final size:48
Alignment explanation
Indices: 1103699--1103789 Score: 130
Period size: 47 Copynumber: 1.9 Consensus size: 48
1103689 CATAATTCAA
* * * *
1103699 GTCAAGTATCATATCAGAATCCAGGTCATGTATCATATCAGAATCCAT
1 GTCAAGTATCAGATCAGAATCCAGATCAGGTATCATAACAGAATCCAT
*
1103747 GTCAA-TATCAGATCAGAATCCAGATTAGGTATCATAACAGAAT
1 GTCAAGTATCAGATCAGAATCCAGATCAGGTATCATAACAGAAT
1103790 TCAAATTTGA
Statistics
Matches: 38, Mismatches: 5, Indels: 1
0.86 0.11 0.02
Matches are distributed among these distances:
47 33 0.87
48 5 0.13
ACGTcount: A:0.38, C:0.19, G:0.15, T:0.27
Consensus pattern (48 bp):
GTCAAGTATCAGATCAGAATCCAGATCAGGTATCATAACAGAATCCAT
Found at i:1106107 original size:13 final size:13
Alignment explanation
Indices: 1106089--1106146 Score: 89
Period size: 13 Copynumber: 4.5 Consensus size: 13
1106079 CAGTGGTCAA
*
1106089 CGGGTCAACAGGT
1 CGGGTCAACGGGT
1106102 CGGGTCAACGGGT
1 CGGGTCAACGGGT
*
1106115 CGGGTAAACGGGT
1 CGGGTCAACGGGT
*
1106128 CGGGTAAACGGGT
1 CGGGTCAACGGGT
1106141 CGGGTC
1 CGGGTC
1106147 GGGTTATGAC
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
13 42 1.00
ACGTcount: A:0.19, C:0.21, G:0.45, T:0.16
Consensus pattern (13 bp):
CGGGTCAACGGGT
Found at i:1109516 original size:3 final size:3
Alignment explanation
Indices: 1109510--1109552 Score: 59
Period size: 3 Copynumber: 14.0 Consensus size: 3
1109500 TATATACATG
* *
1109510 TTA TTA TAA ATA TTA TTTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA TTA
1109553 ATTCTATTAA
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
3 32 0.91
4 3 0.09
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (3 bp):
TTA
Found at i:1112152 original size:26 final size:27
Alignment explanation
Indices: 1112122--1112174 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
1112112 GACATATTGT
*
1112122 GCATT-TTGTTATTTTTTTTTACATTC
1 GCATTATTGTTACTTTTTTTTACATTC
* *
1112148 GCATTATTTTTCCTTTTTTTTACATTC
1 GCATTATTGTTACTTTTTTTTACATTC
1112175 ACATGTCTCA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
26 5 0.22
27 18 0.78
ACGTcount: A:0.15, C:0.15, G:0.06, T:0.64
Consensus pattern (27 bp):
GCATTATTGTTACTTTTTTTTACATTC
Found at i:1112549 original size:168 final size:168
Alignment explanation
Indices: 1112265--1112607 Score: 650
Period size: 168 Copynumber: 2.0 Consensus size: 168
1112255 GTGTCACCAT
*
1112265 ATCCAGGGAAATCTATGAAGCCCCGTACCCCAGGTAGTATGATGAGAACGCTCGTTGCGAAAATC
1 ATCCAAGGAAATCTATGAAGCCCCGTACCCCAGGTAGTATGATGAGAACGCTCGTTGCGAAAATC
*
1112330 ATAGCGGAGTCCCAGGGCGCACTATCAAGAATTACTCCACAATCAAGAGAATCATACAGAAAATA
66 ATAGAGGAGTCCCAGGGCGCACTATCAAGAATTACTCCACAATCAAGAGAATCATACAGAAAATA
*
1112395 CGTAACAAGAATCGGATCAACTTCAACAACTTGGGGGC
131 CGTAACAAGAATCGGATCAACTTCAACAACTTGGGGCC
1112433 ATCCAAGGAAATCTATGAAGCCCCGTACCCCAGGTAGTATGATGAGAACGCTCGTTGCGAAAATC
1 ATCCAAGGAAATCTATGAAGCCCCGTACCCCAGGTAGTATGATGAGAACGCTCGTTGCGAAAATC
1112498 ATAGAGGAGTCCCAGGGCGCACTATCAAGAATTACTCCACAATCAAGAGAATCATACAGAAAATA
66 ATAGAGGAGTCCCAGGGCGCACTATCAAGAATTACTCCACAATCAAGAGAATCATACAGAAAATA
*
1112563 CGTAACAAGAATCGGATCAACTTTAACAACTTGGGGCC
131 CGTAACAAGAATCGGATCAACTTCAACAACTTGGGGCC
1112601 ATCCAAG
1 ATCCAAG
1112608 TGAGGAAGAT
Statistics
Matches: 171, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
168 171 1.00
ACGTcount: A:0.36, C:0.24, G:0.21, T:0.19
Consensus pattern (168 bp):
ATCCAAGGAAATCTATGAAGCCCCGTACCCCAGGTAGTATGATGAGAACGCTCGTTGCGAAAATC
ATAGAGGAGTCCCAGGGCGCACTATCAAGAATTACTCCACAATCAAGAGAATCATACAGAAAATA
CGTAACAAGAATCGGATCAACTTCAACAACTTGGGGCC
Found at i:1114422 original size:105 final size:105
Alignment explanation
Indices: 1114240--1115980 Score: 2394
Period size: 105 Copynumber: 16.9 Consensus size: 105
1114230 GAGAGCGGAT
1114240 TTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTTCAGAGCCAATTTC
1 TTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTTCAGAGCCAATTTC
*
1114305 AACTTCACAACGAAGGATATTGGACTCCACACAACGCAAG
66 AACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAG
* * *
1114345 TTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACATTTCCCAATTTCAGAGCCAATTTT
1 TTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTTCAGAGCCAATTTC
* *
1114410 AACTTCACAACGAAGGGTATTGGATTCCAGACAACGCAAG
66 AACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAG
*
1114450 TTCAACTTCACGATGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTTCAGAGCCAATTTC
1 TTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTTCAGAGCCAATTTC
*
1114515 AACTTCACAACGAAGGATATTGGACTCCACACAACGCAAG
66 AACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAG
* *
1114555 TTCAACTTCACGACGAAGGGACCGCTGGTTGTCAA-TAA-A-----CAATTTC----CCAATTTT
1 TTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTTCAGAGCCAATTTC
* ***
1114609 AACTTCACAACGAAGGATATTGGACTCAAGACAGTACAAG
66 AACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAG
* ** * *
1114649 TTCAACTTCACGACGAAGGGACCACTGACTGTCAAACAAACAACTTCTCAATCTCAGAGCCAATT
1 TTCAACTTCACGACGAAGGGACCGCTGGTTGTC-AACAAAC-ATTTCTCAATTTCAGAGCCAATT
1114714 TCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAG
64 TCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAG
* * *
1114756 TTCAACTTCACGACAAAGGGACTGCTGGTTGTCAA-TAA-A-----CAATTTC----CCAATTTC
1 TTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTTCAGAGCCAATTTC
* ***
1114810 AACTTCACAACGAAGGATATTGGACTCAAGACAGTACAAG
66 AACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAG
** * *
1114850 TTCAACTTCACGACGAAGGGACCGCTGACTGTCAAACAAACAACTTCTCAATTTCAGGGCCAATT
1 TTCAACTTCACGACGAAGGGACCGCTGGTTGTC-AACAAAC-ATTTCTCAATTTCAGAGCCAATT
1114915 TCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAG
64 TCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAG
* *
1114957 TTCAACTTCACAACGAAGGGACCGCTGGTTGTCAA-TAA-A-----CAATTTC----CCAATTTC
1 TTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTTCAGAGCCAATTTC
* ***
1115011 AACTTCACAACGAAGGATATTGGACTCAAGACAGTACAAG
66 AACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAG
**
1115051 TTCAACTTCACGACGAAGGGACCGCTGACTGT---C-AAC--TTCTCAATTTCAGAGCCAATTTC
1 TTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTTCAGAGCCAATTTC
* * *
1115110 AACTTCACAACAAAGGGTATTGGATTCCAGACAACGCAAG
66 AACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAG
1115150 TTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTTCAGAGCCAATTTC
1 TTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTTCAGAGCCAATTTC
*
1115215 AACTTCACAACGAAGGATATTGGACTCCACACAACGCAAG
66 AACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAG
* *
1115255 TTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACATTTCCCAATTTCAGAGCCAATTTC
1 TTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTTCAGAGCCAATTTC
*
1115320 AACTTCACAACGAAGGGTATTGGACTCCAGACAACGCAAG
66 AACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAG
1115360 TTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTTCAGAGCCAATTTC
1 TTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTTCAGAGCCAATTTC
1115425 AACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAG
66 AACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAG
* * * *
1115465 TTCAACTTCACGACGAAGGGACCACTGGTTTTCAATAAATATTTCTCAATTTCAGAGCCAATTTC
1 TTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTTCAGAGCCAATTTC
* *
1115530 AACTTCACAGCGAAGGATATTGGACTCCAGATAACGCAAG
66 AACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAG
* *
1115570 TTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTTTAGAGCCAATTT
1 TTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAAC-ATTTCTCAATTTCAGAGCCAATTT
* *
1115635 CAACTTCACAATGAAGGATATTGGACTCCAGACAACGTAAG
65 CAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAG
* * *
1115676 TTCAACTTCACGATGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTTTAGAGCCAATTT
1 TTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAAC-ATTTCTCAATTTCAGAGCCAATTT
1115741 CAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAG
65 CAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAG
* * * ** *
1115782 TTCAACTTCACGACGAAGGGATCGCTGGTTGTCAATAAACAATTTCCCAGGTTCAGAGTCAATTT
1 TTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAAC-ATTTCTCAATTTCAGAGCCAATTT
* * * *
1115847 CAACTTCACAACGAAGGATATTAGACTCGAGACAGCACAAG
65 CAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAG
* * * ** * * * *
1115888 CTCAACTTCAC-AGCGAAGGGGCGGCTGACTGTCAACAAACAACTTC-CTAGTTCCAGGGCCAAT
1 TTCAACTTCACGA-CGAAGGGACCGCTGGTTGTCAACAAAC-ATTTCTC-AATTTCAGAGCCAAT
* *
1115951 TTCAACTTCACGACGGAGGATATTGGACTC
63 TTCAACTTCACAACGAAGGATATTGGACTC
1115981 GGAGCAACTT
Statistics
Matches: 1462, Mismatches: 129, Indels: 89
0.87 0.08 0.05
Matches are distributed among these distances:
91 2 0.00
94 218 0.15
95 11 0.01
96 4 0.00
98 22 0.02
99 71 0.05
102 1 0.00
103 19 0.01
104 2 0.00
105 634 0.43
106 333 0.23
107 145 0.10
ACGTcount: A:0.34, C:0.25, G:0.18, T:0.23
Consensus pattern (105 bp):
TTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTTCAGAGCCAATTTC
AACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAG
Found at i:1116222 original size:36 final size:37
Alignment explanation
Indices: 1116176--1116259 Score: 118
Period size: 37 Copynumber: 2.3 Consensus size: 37
1116166 TTGAATATAT
*
1116176 TTTC-CTTGAAACAAA-TTTCGTCTCCCTTGAGACAT
1 TTTCTCTTGAAACAAAGTTTCGTCTCCCTTGAGACAG
* * *
1116211 TTTCTTTTGAAACAAAGTTTTGTCTCTCTTGAGACAG
1 TTTCTCTTGAAACAAAGTTTCGTCTCCCTTGAGACAG
1116248 TTTCTCTTGAAA
1 TTTCTCTTGAAA
1116260 GAAAAAAACC
Statistics
Matches: 42, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
35 4 0.10
36 10 0.24
37 28 0.67
ACGTcount: A:0.25, C:0.20, G:0.13, T:0.42
Consensus pattern (37 bp):
TTTCTCTTGAAACAAAGTTTCGTCTCCCTTGAGACAG
Found at i:1116446 original size:84 final size:84
Alignment explanation
Indices: 1116298--1116480 Score: 213
Period size: 84 Copynumber: 2.2 Consensus size: 84
1116288 GAAACACCAA
* *
1116298 ACCTTCGAGCTCGATTACACTCAACTCCAAGACACATCATTTGCAACACAGCTCAAGGCAAGAAG
1 ACCTTCGAGTTCGACTACACTCAACTCCAAGACACATCATTTGCAACACAGCTCAAGGCAAGAAG
*
1116363 GGCTATTTACCAACCAAAG
66 GGCTATCTACCAACCAAAG
* * ** * * * * * *
1116382 ACCTTCGAGTTCGACTACGCTCAGCTCTGAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAG
1 ACCTTCGAGTTCGACTACACTCAACTCCAAGACACATCATTTGCAACACAGCTCAAGGCAAGAAG
* *
1116447 GGTTATCTGCCAACCAAAG
66 GGCTATCTACCAACCAAAG
*
1116466 ACCTGACGAGTTCGA
1 ACCT-TCGAGTTCGA
1116481 TTTCATTCAG
Statistics
Matches: 82, Mismatches: 16, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
84 73 0.89
85 9 0.11
ACGTcount: A:0.31, C:0.28, G:0.20, T:0.21
Consensus pattern (84 bp):
ACCTTCGAGTTCGACTACACTCAACTCCAAGACACATCATTTGCAACACAGCTCAAGGCAAGAAG
GGCTATCTACCAACCAAAG
Found at i:1117715 original size:4 final size:4
Alignment explanation
Indices: 1117706--1117782 Score: 54
Period size: 4 Copynumber: 18.8 Consensus size: 4
1117696 TGGGTTTATT
*
1117706 TTTA TTTA TTTA TTTC TATT- TTTA -TT- TTTA TTTTA TTTTA TTTA TTTA
1 TTTA TTTA TTTA TTTA T-TTA TTTA TTTA TTTA -TTTA -TTTA TTTA TTTA
*
1117754 TTTTC TTTGA TTTA TTT- TTTA TTTTA TTT
1 -TTTA TTT-A TTTA TTTA TTTA -TTTA TTT
1117783 TTATTTTTAC
Statistics
Matches: 61, Mismatches: 3, Indels: 18
0.74 0.04 0.22
Matches are distributed among these distances:
3 9 0.15
4 31 0.51
5 21 0.34
ACGTcount: A:0.18, C:0.03, G:0.01, T:0.78
Consensus pattern (4 bp):
TTTA
Found at i:1117737 original size:18 final size:18
Alignment explanation
Indices: 1117700--1117790 Score: 105
Period size: 18 Copynumber: 4.8 Consensus size: 18
1117690 TTATTTTGGG
1117700 TTTATTTTTATTTATTTAT
1 TTTATTTTTATTT-TTTAT
1117719 TTCTATTTTTA-TTTTTAT
1 TT-TATTTTTATTTTTTAT
1117737 TTTA-TTTTATTTATTTAT
1 TTTATTTTTATTT-TTTAT
*
1117755 TTTCTTTGATTTATTTTTTAT
1 TTT-ATT--TTTATTTTTTAT
1117776 TTTATTTTTATTTTT
1 TTTATTTTTATTTTT
1117791 ACGATTTATT
Statistics
Matches: 63, Mismatches: 2, Indels: 15
0.79 0.03 0.19
Matches are distributed among these distances:
16 5 0.08
17 4 0.06
18 24 0.38
19 4 0.06
20 11 0.17
21 8 0.13
22 7 0.11
ACGTcount: A:0.18, C:0.02, G:0.01, T:0.79
Consensus pattern (18 bp):
TTTATTTTTATTTTTTAT
Found at i:1117739 original size:5 final size:5
Alignment explanation
Indices: 1117700--1117789 Score: 71
Period size: 5 Copynumber: 17.6 Consensus size: 5
1117690 TTATTTTGGG
1117700 TTTAT TTT-T ATTTA- TTTAT TTCTATT TTTATT TTTAT TTTAT TTTA-
1 TTTAT TTTAT -TTTAT TTTAT TT-TA-T TTTA-T TTTAT TTTAT TTTAT
* * *
1117746 TTTA- TTTAT TTTCT TTGAT TTATTT TTTAT TTTATT TTTAT TTT
1 TTTAT TTTAT TTTAT TTTAT TT-TAT TTTAT TTTA-T TTTAT TTT
1117790 TACGATTTAT
Statistics
Matches: 71, Mismatches: 6, Indels: 16
0.76 0.06 0.17
Matches are distributed among these distances:
4 13 0.18
5 37 0.52
6 18 0.25
7 3 0.04
ACGTcount: A:0.18, C:0.02, G:0.01, T:0.79
Consensus pattern (5 bp):
TTTAT
Found at i:1117750 original size:40 final size:40
Alignment explanation
Indices: 1117700--1117788 Score: 134
Period size: 36 Copynumber: 2.3 Consensus size: 40
1117690 TTATTTTGGG
1117700 TTTATTTTTATTTATTTA-TTTCTATT--TTTA-TTTTTAT
1 TTTATTTTTATTTATTTATTTTCT-TTGATTTATTTTTTAT
1117737 TTTA-TTTTATTTATTTATTTTCTTTGATTTATTTTTTAT
1 TTTATTTTTATTTATTTATTTTCTTTGATTTATTTTTTAT
1117776 TTTATTTTTATTT
1 TTTATTTTTATTT
1117789 TTACGATTTA
Statistics
Matches: 47, Mismatches: 0, Indels: 7
0.87 0.00 0.13
Matches are distributed among these distances:
36 15 0.32
37 9 0.19
38 4 0.09
39 11 0.23
40 8 0.17
ACGTcount: A:0.18, C:0.02, G:0.01, T:0.79
Consensus pattern (40 bp):
TTTATTTTTATTTATTTATTTTCTTTGATTTATTTTTTAT
Found at i:1121790 original size:14 final size:15
Alignment explanation
Indices: 1121767--1121799 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
1121757 GAGTTTTATG
*
1121767 AAAATTATAAT-TTA
1 AAAATGATAATATTA
1121781 AAAATGATAATATTA
1 AAAATGATAATATTA
1121796 AAAA
1 AAAA
1121800 ATATTTTTAG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 10 0.59
15 7 0.41
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (15 bp):
AAAATGATAATATTA
Found at i:1123116 original size:30 final size:29
Alignment explanation
Indices: 1123080--1123172 Score: 96
Period size: 32 Copynumber: 3.0 Consensus size: 29
1123070 ATAACCACTA
* *
1123080 TCCATATGTTCTGAAGAACATAGGTAACTG
1 TCCATATGTCCCGAAG-ACATAGGTAACTG
* *
1123110 TCCATATGTCCCAAAGGACATAGGTAATCCTA
1 TCCATATGTCCCGAA-GACATAGGTAA--CTG
*
1123142 TCCATATGTCCCGAATGACATAGATAACTG
1 TCCATATGTCCCGAA-GACATAGGTAACTG
1123172 T
1 T
1123173 TGAAAACATT
Statistics
Matches: 52, Mismatches: 8, Indels: 6
0.79 0.12 0.09
Matches are distributed among these distances:
30 25 0.48
31 1 0.02
32 26 0.50
ACGTcount: A:0.33, C:0.22, G:0.17, T:0.28
Consensus pattern (29 bp):
TCCATATGTCCCGAAGACATAGGTAACTG
Found at i:1123151 original size:32 final size:30
Alignment explanation
Indices: 1123076--1123170 Score: 109
Period size: 30 Copynumber: 3.1 Consensus size: 30
1123066 CCGAATAACC
* * *
1123076 ACTATCCATATGTTCTGAAGAACATAGGTA
1 ACTATCCATATGTCCCGAAGGACATAGGTA
* *
1123106 ACTGTCCATATGTCCCAAAGGACATAGGTA
1 ACTATCCATATGTCCCGAAGGACATAGGTA
* *
1123136 ATCCTATCCATATGTCCCGAATGACATAGATA
1 A--CTATCCATATGTCCCGAAGGACATAGGTA
1123168 ACT
1 ACT
1123171 GTTGAAAACA
Statistics
Matches: 54, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
30 28 0.52
32 26 0.48
ACGTcount: A:0.35, C:0.22, G:0.16, T:0.27
Consensus pattern (30 bp):
ACTATCCATATGTCCCGAAGGACATAGGTA
Found at i:1133514 original size:104 final size:104
Alignment explanation
Indices: 1133298--1133507 Score: 375
Period size: 104 Copynumber: 2.0 Consensus size: 104
1133288 ACACTTTTAG
* * *
1133298 GACATTCTCGGTTGTTTGACCAATCTTTTTATTGATATACTTTTTAGGGTTGAATTTGACGTTCG
1 GACATTCTCGGTCGTTTGACCAATCTTTTTATTGATATACTTTTTAGGGTTGAATTTGACATTCA
*
1133363 TCTAAATAGATGTAGATGACACTTATATGTATTATTGTT
66 TCTAAATAGATGTAAATGACACTTATATGTATTATTGTT
1133402 GACATTCTCGGTCGTTTGACCAATCTTTTTATTGATATACTTTTTAGGGTTGAATTTGACATTCA
1 GACATTCTCGGTCGTTTGACCAATCTTTTTATTGATATACTTTTTAGGGTTGAATTTGACATTCA
*
1133467 TCTAAATAGATGTAAATGATACTTATATGTATTATTGTT
66 TCTAAATAGATGTAAATGACACTTATATGTATTATTGTT
1133506 GA
1 GA
1133508 TCTTCTCTGC
Statistics
Matches: 101, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
104 101 1.00
ACGTcount: A:0.27, C:0.11, G:0.17, T:0.45
Consensus pattern (104 bp):
GACATTCTCGGTCGTTTGACCAATCTTTTTATTGATATACTTTTTAGGGTTGAATTTGACATTCA
TCTAAATAGATGTAAATGACACTTATATGTATTATTGTT
Found at i:1135075 original size:23 final size:23
Alignment explanation
Indices: 1135031--1135076 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
1135021 AAATGTTTTT
*
1135031 ATTTTAACTAATTTAACTTTAAA
1 ATTTTAACTAATTTAACATTAAA
1135054 ATTTTAACTAATTTTAA-ATTAAA
1 ATTTTAACTAA-TTTAACATTAAA
1135077 TTAATAGTGC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 16 0.76
24 5 0.24
ACGTcount: A:0.46, C:0.07, G:0.00, T:0.48
Consensus pattern (23 bp):
ATTTTAACTAATTTAACATTAAA
Found at i:1135095 original size:38 final size:38
Alignment explanation
Indices: 1135053--1135128 Score: 109
Period size: 38 Copynumber: 2.0 Consensus size: 38
1135043 TTAACTTTAA
* *
1135053 AATTTTAACTAATTT-TAAATTAAATTAATAGTGCTTAT
1 AATTTTAAAT-ATTTATAAATTAAATTAATAATGCTTAT
*
1135091 AATTTTAAATTTTTATAAATTAAATTAATAATGCTTAT
1 AATTTTAAATATTTATAAATTAAATTAATAATGCTTAT
1135129 CGTTAATTAA
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
37 3 0.09
38 31 0.91
ACGTcount: A:0.43, C:0.04, G:0.04, T:0.49
Consensus pattern (38 bp):
AATTTTAAATATTTATAAATTAAATTAATAATGCTTAT
Found at i:1146836 original size:4 final size:4
Alignment explanation
Indices: 1146820--1146859 Score: 53
Period size: 4 Copynumber: 10.0 Consensus size: 4
1146810 TGAAATGAAC
* * *
1146820 ATAT ATTT ATAT ATAT ATAT ATAT ATAT ATGT ATAA ATAT
1 ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT
1146860 TATTATAAAC
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
4 30 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (4 bp):
ATAT
Found at i:1146836 original size:6 final size:6
Alignment explanation
Indices: 1146820--1146859 Score: 53
Period size: 6 Copynumber: 6.7 Consensus size: 6
1146810 TGAAATGAAC
* * *
1146820 ATATAT TTATAT ATATAT ATATAT ATATAT GTATAA ATAT
1 ATATAT ATATAT ATATAT ATATAT ATATAT ATATAT ATAT
1146860 TATTATAAAC
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (6 bp):
ATATAT
Found at i:1146846 original size:10 final size:10
Alignment explanation
Indices: 1146820--1146859 Score: 53
Period size: 10 Copynumber: 4.0 Consensus size: 10
1146810 TGAAATGAAC
*
1146820 ATATATTTAT
1 ATATATATAT
1146830 ATATATATAT
1 ATATATATAT
1146840 ATATATATAT
1 ATATATATAT
* *
1146850 GTATAAATAT
1 ATATATATAT
1146860 TATTATAAAC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 27 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (10 bp):
ATATATATAT
Found at i:1146866 original size:12 final size:14
Alignment explanation
Indices: 1146828--1146868 Score: 50
Period size: 14 Copynumber: 3.1 Consensus size: 14
1146818 ACATATATTT
* *
1146828 ATATATATATATAT
1 ATATATATGTATAA
1146842 ATATATATGTATAA
1 ATATATATGTATAA
1146856 ATAT-TAT-TATAA
1 ATATATATGTATAA
1146868 A
1 A
1146869 CATGTTTTAC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
12 6 0.24
13 3 0.12
14 16 0.64
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.46
Consensus pattern (14 bp):
ATATATATGTATAA
Found at i:1149470 original size:31 final size:31
Alignment explanation
Indices: 1149432--1149587 Score: 251
Period size: 31 Copynumber: 5.0 Consensus size: 31
1149422 CCCGAATGAC
* * * *
1149432 CAGTCCATA-GATTCCGAAAAACCTAGGTAAT
1 CAGTCCATATG-TCCCGAAGAACATAGGTAAA
1149463 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1149494 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
*
1149525 CAGTCCATATGTTCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1149556 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1149587 C
1 C
1149588 CCTCGACCCT
Statistics
Matches: 118, Mismatches: 6, Indels: 2
0.94 0.05 0.02
Matches are distributed among these distances:
31 117 0.99
32 1 0.01
ACGTcount: A:0.38, C:0.22, G:0.19, T:0.21
Consensus pattern (31 bp):
CAGTCCATATGTCCCGAAGAACATAGGTAAA
Found at i:1149807 original size:59 final size:58
Alignment explanation
Indices: 1149706--1149820 Score: 133
Period size: 59 Copynumber: 2.0 Consensus size: 58
1149696 CACATATCTT
* * * * *
1149706 TTCTTTTCAGTCACGTATCACATGTACGTGTAATCATTTATCTCATAATCACATGTTCC
1 TTCTCTTCAGTCACATACCACATGTACGTGTAATCATATATCTAAT-ATCACATGTTCC
* * *
1149765 TTCTCTTCTGTCACATACCACATGTATGTGTAAAT-ATATATCTAATATCATATGTT
1 TTCTCTTCAGTCACATACCACATGTACGTGT-AATCATATATCTAATATCACATGTT
1149821 ACATTTTCAT
Statistics
Matches: 47, Mismatches: 8, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
58 9 0.19
59 35 0.74
60 3 0.06
ACGTcount: A:0.28, C:0.21, G:0.10, T:0.42
Consensus pattern (58 bp):
TTCTCTTCAGTCACATACCACATGTACGTGTAATCATATATCTAATATCACATGTTCC
Found at i:1152807 original size:95 final size:94
Alignment explanation
Indices: 1152639--1152823 Score: 246
Period size: 95 Copynumber: 2.0 Consensus size: 94
1152629 TATAATATTA
** *
1152639 TATATATACAATAAAGCTTGAGTTGTCCCTCTAGAGAAATTGGTTAAAAGCCCCGGCTTTATAGA
1 TATATATACAATAAAGCTTGAGCAGTCCCTCTAGAGAAATTGGTTAAAAGCCCCGACTTTATAGA
* *
1152704 TAATATTCAGCTAGCCTGATAAAGGCGAT
66 TAAGATTCAGCTAACCTGATAAAGGCGAT
* * ** *
1152733 TATACTATACAATAAAGTTTGAGCAGTCCCTCTA-AGGCAATTGGTTAAACTCCCCGACTTTATG
1 TATA-TATACAATAAAGCTTGAGCAGTCCCTCTAGA-GAAATTGGTTAAAAGCCCCGACTTTATA
*
1152797 GATAAGATTCAGCTAACCTGATGAAGG
64 GATAAGATTCAGCTAACCTGATAAAGG
1152824 TATTTACATA
Statistics
Matches: 78, Mismatches: 11, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
94 5 0.06
95 73 0.94
ACGTcount: A:0.34, C:0.18, G:0.19, T:0.29
Consensus pattern (94 bp):
TATATATACAATAAAGCTTGAGCAGTCCCTCTAGAGAAATTGGTTAAAAGCCCCGACTTTATAGA
TAAGATTCAGCTAACCTGATAAAGGCGAT
Found at i:1154393 original size:99 final size:99
Alignment explanation
Indices: 1154229--1154421 Score: 298
Period size: 99 Copynumber: 1.9 Consensus size: 99
1154219 ATTTCATAAC
* *
1154229 CAATTTCAACTTCACAGCGAAGGATATTGGACCCAAGACAACACAAGCTCAACTTCACGACGAAG
1 CAATTTCAACTTCACAACGAAGGATATTGGACCCAAGACAACACAAGCTCAACTTCAAGACGAAG
*
1154294 GGGCGTCTG-CTTGTCAACAAACAACTTTCAGAGT
66 GGGCGGCTGAC-TGTCAACAAACAACTTTCAGAGT
* * **
1154328 CAATTTCAACTTCACAACGAAGGATATTGGACTCAAGACAGCACAAGCTCAACTTCAAGGTGAAG
1 CAATTTCAACTTCACAACGAAGGATATTGGACCCAAGACAACACAAGCTCAACTTCAAGACGAAG
*
1154393 GGGCGGCTGACTGTCAACAAACAATTTTC
66 GGGCGGCTGACTGTCAACAAACAACTTTC
1154422 CAGTTCCAAA
Statistics
Matches: 85, Mismatches: 8, Indels: 2
0.89 0.08 0.02
Matches are distributed among these distances:
99 84 0.99
100 1 0.01
ACGTcount: A:0.35, C:0.25, G:0.20, T:0.21
Consensus pattern (99 bp):
CAATTTCAACTTCACAACGAAGGATATTGGACCCAAGACAACACAAGCTCAACTTCAAGACGAAG
GGGCGGCTGACTGTCAACAAACAACTTTCAGAGT
Found at i:1154999 original size:11 final size:11
Alignment explanation
Indices: 1154976--1155020 Score: 58
Period size: 11 Copynumber: 4.3 Consensus size: 11
1154966 TGGAATGAAC
1154976 ATATATT-TAT
1 ATATATTATAT
1154986 ATATATTATAT
1 ATATATTATAT
*
1154997 ATATATTGTAT
1 ATATATTATAT
*
1155008 AAATATTAT-T
1 ATATATTATAT
1155018 ATA
1 ATA
1155021 AACATGTTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
10 10 0.33
11 20 0.67
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.53
Consensus pattern (11 bp):
ATATATTATAT
Found at i:1156236 original size:22 final size:22
Alignment explanation
Indices: 1156169--1156236 Score: 52
Period size: 22 Copynumber: 3.1 Consensus size: 22
1156159 TACTTAATTA
1156169 TATTT-TTCTATTTAT-TTACTA-
1 TATTTATT-TATTTATGTTA-TAT
* * * * *
1156190 TATTTATCTATTTTTGGTGTTT
1 TATTTATTTATTTATGTTATAT
1156212 TATTTATTTATTTATGTTATAT
1 TATTTATTTATTTATGTTATAT
1156234 TAT
1 TAT
1156237 ACCATTTTTT
Statistics
Matches: 34, Mismatches: 10, Indels: 5
0.69 0.20 0.10
Matches are distributed among these distances:
21 12 0.35
22 22 0.65
ACGTcount: A:0.22, C:0.04, G:0.06, T:0.68
Consensus pattern (22 bp):
TATTTATTTATTTATGTTATAT
Found at i:1156709 original size:4 final size:4
Alignment explanation
Indices: 1156696--1156869 Score: 59
Period size: 4 Copynumber: 40.5 Consensus size: 4
1156686 TACTTACTTC
*
1156696 TTAT TATAT TTATT TTATT TTATT TTATT TTAT CTTAT TT-T TTAT TCAGT
1 TTAT T-TAT TTA-T TTA-T TTA-T TTA-T TTAT -TTAT TTAT TTAT TTA-T
* * * * *
1156746 TTAT TTAAT ATT-T TTAT CATCAT TTTT TTA- TTAT ATGT TTCT TTATT
1 TTAT TT-AT -TTAT TTAT --TTAT TTAT TTAT TTAT TTAT TTAT TTA-T
* * ** *
1156793 TTATT TTTT TTCT TTGAT TTAT TTAT TTAT TTAT TCCT TTCAT TTGAC
1 TTA-T TTAT TTAT TT-AT TTAT TTAT TTAT TTAT TTAT TT-AT TT-AT
* *
1156841 TTAT TTA- ATAT TTTT TTAT TTAT TTAT TT
1 TTAT TTAT TTAT TTAT TTAT TTAT TTAT TT
1156870 CATCTAACAT
Statistics
Matches: 130, Mismatches: 25, Indels: 30
0.70 0.14 0.16
Matches are distributed among these distances:
3 10 0.08
4 66 0.51
5 49 0.38
6 5 0.04
ACGTcount: A:0.21, C:0.06, G:0.02, T:0.71
Consensus pattern (4 bp):
TTAT
Found at i:1156712 original size:5 final size:5
Alignment explanation
Indices: 1156699--1156736 Score: 58
Period size: 5 Copynumber: 7.4 Consensus size: 5
1156689 TTACTTCTTA
*
1156699 TTATAT TTATT TTATT TTATT TTATT TTATC TTATT TT
1 TTAT-T TTATT TTATT TTATT TTATT TTATT TTATT TT
1156737 TTATTCAGTT
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
5 26 0.87
6 4 0.13
ACGTcount: A:0.21, C:0.03, G:0.00, T:0.76
Consensus pattern (5 bp):
TTATT
Found at i:1163365 original size:16 final size:17
Alignment explanation
Indices: 1163333--1163365 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
1163323 AAATTAGGGG
*
1163333 TTTGGGGTTTGAGAAAT
1 TTTGGGCTTTGAGAAAT
1163350 TTTGGGCTTT-AGAAAT
1 TTTGGGCTTTGAGAAAT
1163366 AACGATAATA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.24, C:0.03, G:0.30, T:0.42
Consensus pattern (17 bp):
TTTGGGCTTTGAGAAAT
Found at i:1165330 original size:19 final size:19
Alignment explanation
Indices: 1165302--1165353 Score: 77
Period size: 19 Copynumber: 2.7 Consensus size: 19
1165292 CTAGGCTCGA
*
1165302 ATCGACTCAATTCGATTTG
1 ATCGATTCAATTCGATTTG
*
1165321 ATCGATTCAATTCAATTTG
1 ATCGATTCAATTCGATTTG
*
1165340 ATCGTTTCAATTCG
1 ATCGATTCAATTCG
1165354 GTTCGCTTAG
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.27, C:0.19, G:0.13, T:0.40
Consensus pattern (19 bp):
ATCGATTCAATTCGATTTG
Found at i:1170948 original size:33 final size:33
Alignment explanation
Indices: 1170918--1170984 Score: 86
Period size: 34 Copynumber: 2.1 Consensus size: 33
1170908 CAGAAAACTG
1170918 AAAAT-GAAAAT-TATTTTCTGAAAACAAAAACAA
1 AAAATAGAAAATAT-TTTTCT-AAAACAAAAACAA
*
1170951 AAAATAGAAAATATTTTTCTAAAAC-CAAACAA
1 AAAATAGAAAATATTTTTCTAAAACAAAAACAA
1170983 AA
1 AA
1170985 TTCCCATATA
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
32 8 0.26
33 10 0.32
34 12 0.39
35 1 0.03
ACGTcount: A:0.61, C:0.10, G:0.04, T:0.24
Consensus pattern (33 bp):
AAAATAGAAAATATTTTTCTAAAACAAAAACAA
Found at i:1171104 original size:27 final size:27
Alignment explanation
Indices: 1171072--1171127 Score: 94
Period size: 27 Copynumber: 2.1 Consensus size: 27
1171062 ACTCCTAAAA
* *
1171072 TTTTATAATTTCACCTTGCTTAAAATC
1 TTTTATAATTTCACCTGGCATAAAATC
1171099 TTTTATAATTTCACCTGGCATAAAATC
1 TTTTATAATTTCACCTGGCATAAAATC
1171126 TT
1 TT
1171128 AAGTTCCTGT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.30, C:0.18, G:0.05, T:0.46
Consensus pattern (27 bp):
TTTTATAATTTCACCTGGCATAAAATC
Found at i:1174859 original size:17 final size:14
Alignment explanation
Indices: 1174835--1174886 Score: 63
Period size: 13 Copynumber: 3.6 Consensus size: 14
1174825 TGAAGTTCTA
1174835 ATTTTCTTTCATCTT
1 ATTTTCTTTCAT-TT
1174850 CATCTTTCTTTC-TTT
1 -AT-TTTCTTTCATTT
1174865 ATTTTCTTTCA-TT
1 ATTTTCTTTCATTT
1174878 ATTTTCTTT
1 ATTTTCTTT
1174887 TCACAGTGCT
Statistics
Matches: 34, Mismatches: 0, Indels: 7
0.83 0.00 0.17
Matches are distributed among these distances:
13 19 0.56
14 2 0.06
15 2 0.06
16 3 0.09
17 8 0.24
ACGTcount: A:0.12, C:0.19, G:0.00, T:0.69
Consensus pattern (14 bp):
ATTTTCTTTCATTT
Found at i:1175531 original size:13 final size:13
Alignment explanation
Indices: 1175493--1175544 Score: 54
Period size: 13 Copynumber: 4.2 Consensus size: 13
1175483 TATTTTCTCA
1175493 TTATTTTTTTA-T
1 TTATTTTTTTATT
* * *
1175505 TCAATATTTT-TT
1 TTATTTTTTTATT
1175517 TTATTTTTTTATT
1 TTATTTTTTTATT
*
1175530 TTATTTATTTATT
1 TTATTTTTTTATT
1175543 TT
1 TT
1175545 CATTAATTTT
Statistics
Matches: 31, Mismatches: 7, Indels: 3
0.76 0.17 0.07
Matches are distributed among these distances:
12 15 0.48
13 16 0.52
ACGTcount: A:0.19, C:0.02, G:0.00, T:0.79
Consensus pattern (13 bp):
TTATTTTTTTATT
Found at i:1177568 original size:18 final size:20
Alignment explanation
Indices: 1177540--1177576 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
1177530 TCGAAACAAA
1177540 AAAAAACTAATT-AGTATTT
1 AAAAAACTAATTGAGTATTT
1177559 AAAAAA-TAATTGAGTATT
1 AAAAAACTAATTGAGTATT
1177577 ATAATTTAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 5 0.29
19 12 0.71
ACGTcount: A:0.54, C:0.03, G:0.08, T:0.35
Consensus pattern (20 bp):
AAAAAACTAATTGAGTATTT
Found at i:1182515 original size:22 final size:24
Alignment explanation
Indices: 1182472--1182536 Score: 62
Period size: 26 Copynumber: 2.7 Consensus size: 24
1182462 AAAATAAATA
* * *
1182472 AATAATTAATTAATTAA-ATTTT-
1 AATAAATAAATAAATAATATTTTG
*
1182494 AATAAATAAATAAATAATTTTTTTG
1 AATAAATAAATAAATAA-TATTTTG
1182519 AAGTAAATAAATAAATAA
1 AA-TAAATAAATAAATAA
1182537 AAATTACCTC
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
22 14 0.40
24 4 0.11
25 2 0.06
26 15 0.43
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.40
Consensus pattern (24 bp):
AATAAATAAATAAATAATATTTTG
Found at i:1182914 original size:4 final size:4
Alignment explanation
Indices: 1182905--1182946 Score: 57
Period size: 4 Copynumber: 10.0 Consensus size: 4
1182895 ATATCCCTTC
*
1182905 AAAT AAAT AAAT AAAT AAAT AATT CAAAAT AAAT AAAT AAAT
1 AAAT AAAT AAAT AAAT AAAT AAAT --AAAT AAAT AAAT AAAT
1182947 CATTAATTTA
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
4 31 0.91
6 3 0.09
ACGTcount: A:0.71, C:0.02, G:0.00, T:0.26
Consensus pattern (4 bp):
AAAT
Found at i:1182939 original size:30 final size:30
Alignment explanation
Indices: 1182905--1182983 Score: 104
Period size: 30 Copynumber: 2.6 Consensus size: 30
1182895 ATATCCCTTC
1182905 AAATAAATAAATAAATAAATAATTCAAAAT
1 AAATAAATAAATAAATAAATAATTCAAAAT
* * * *
1182935 AAATAAATAAATCATTAATTTATTCAAAAT
1 AAATAAATAAATAAATAAATAATTCAAAAT
* *
1182965 AAATGAATAAAGAAATAAA
1 AAATAAATAAATAAATAAA
1182984 AAAAATGATT
Statistics
Matches: 40, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
30 40 1.00
ACGTcount: A:0.66, C:0.04, G:0.03, T:0.28
Consensus pattern (30 bp):
AAATAAATAAATAAATAAATAATTCAAAAT
Found at i:1183001 original size:19 final size:18
Alignment explanation
Indices: 1182977--1183024 Score: 69
Period size: 19 Copynumber: 2.6 Consensus size: 18
1182967 ATGAATAAAG
1182977 AAATAAAAAAAATGATTCA
1 AAATAAAAAAAA-GATTCA
*
1182996 AAATAAACAAAAAGGTTCA
1 AAATAAA-AAAAAGATTCA
1183015 AAATAAAAAA
1 AAATAAAAAA
1183025 TAAATAAAAG
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
18 3 0.11
19 19 0.70
20 5 0.19
ACGTcount: A:0.71, C:0.06, G:0.06, T:0.17
Consensus pattern (18 bp):
AAATAAAAAAAAGATTCA
Found at i:1184155 original size:3 final size:3
Alignment explanation
Indices: 1184149--1184213 Score: 130
Period size: 3 Copynumber: 21.7 Consensus size: 3
1184139 GTAAAAAAAT
1184149 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1184197 ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA AT
1184214 GGCGCTCTTG
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 62 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:1186723 original size:39 final size:38
Alignment explanation
Indices: 1186658--1186738 Score: 128
Period size: 39 Copynumber: 2.1 Consensus size: 38
1186648 TCATTAGTGC
*
1186658 TTATGAGTTTATTACTATTAGAATTAATTATTAGTATT
1 TTATGAGTTTATTACGATTAGAATTAATTATTAGTATT
1186696 TTATGAGTTGTATTACGATTACG-ATTAATTATTAGTATT
1 TTATGAGTT-TATTACGATTA-GAATTAATTATTAGTATT
1186735 TTAT
1 TTAT
1186739 TAGTAACTCT
Statistics
Matches: 40, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
38 9 0.22
39 30 0.75
40 1 0.03
ACGTcount: A:0.32, C:0.04, G:0.12, T:0.52
Consensus pattern (38 bp):
TTATGAGTTTATTACGATTAGAATTAATTATTAGTATT
Found at i:1195298 original size:39 final size:39
Alignment explanation
Indices: 1195240--1195314 Score: 132
Period size: 39 Copynumber: 1.9 Consensus size: 39
1195230 GGAGTGTGAA
*
1195240 TTATATTACGATTAGGATTAATTATTAATATTTTATGAG
1 TTATATTACGATTAAGATTAATTATTAATATTTTATGAG
*
1195279 TTATATTACGATTAAGATTAGTTATTAATATTTTAT
1 TTATATTACGATTAAGATTAATTATTAATATTTTAT
1195315 TTTACTACTA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
39 34 1.00
ACGTcount: A:0.36, C:0.03, G:0.11, T:0.51
Consensus pattern (39 bp):
TTATATTACGATTAAGATTAATTATTAATATTTTATGAG
Found at i:1198440 original size:29 final size:29
Alignment explanation
Indices: 1198398--1198473 Score: 116
Period size: 29 Copynumber: 2.6 Consensus size: 29
1198388 GGAGCATGAG
*
1198398 GGAGTGCATGGCGACCTACAAAGTCTCCC
1 GGAGTGCATGGCGACCTACAAAGTCGCCC
*
1198427 GGAGTGCATGGCGACCTACAAGGTCGCCC
1 GGAGTGCATGGCGACCTACAAAGTCGCCC
* *
1198456 GGAGGGCATGTCGACCTA
1 GGAGTGCATGGCGACCTA
1198474 TGCTTGGGGA
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
29 43 1.00
ACGTcount: A:0.22, C:0.29, G:0.33, T:0.16
Consensus pattern (29 bp):
GGAGTGCATGGCGACCTACAAAGTCGCCC
Found at i:1198538 original size:19 final size:19
Alignment explanation
Indices: 1198514--1198552 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
1198504 GTAGGTTGCC
1198514 CGGAAGGCATGGCGACCTA
1 CGGAAGGCATGGCGACCTA
1198533 CGGAAGGCATGGCGACCTA
1 CGGAAGGCATGGCGACCTA
1198552 C
1 C
1198553 AGCCAACAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.26, C:0.28, G:0.36, T:0.10
Consensus pattern (19 bp):
CGGAAGGCATGGCGACCTA
Found at i:1214641 original size:55 final size:55
Alignment explanation
Indices: 1214559--1214672 Score: 212
Period size: 55 Copynumber: 2.1 Consensus size: 55
1214549 TAGTTCATAT
1214559 AAAAGTGATTGCCTATTATATTTAAAATTGCCTTTTGTTTT-AAAAAATATTATTA
1 AAAAGTGATTGCCTATTATATTTAAAATTGCCTTTTGTTTTAAAAAAATA-TATTA
1214614 AAAAGTGATTGCCTATTATATTTAAAATTGCCTTTTGTTTTAAAAAAATATATTA
1 AAAAGTGATTGCCTATTATATTTAAAATTGCCTTTTGTTTTAAAAAAATATATTA
1214669 AAAA
1 AAAA
1214673 TAAGTATCTA
Statistics
Matches: 58, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
55 50 0.86
56 8 0.14
ACGTcount: A:0.41, C:0.07, G:0.09, T:0.43
Consensus pattern (55 bp):
AAAAGTGATTGCCTATTATATTTAAAATTGCCTTTTGTTTTAAAAAAATATATTA
Found at i:1214690 original size:55 final size:55
Alignment explanation
Indices: 1214570--1214690 Score: 156
Period size: 55 Copynumber: 2.2 Consensus size: 55
1214560 AAAGTGATTG
* * * *
1214570 CCTATTATATTTAAAATTGCCTTTTGTTTTAAAAAATATTATTAAAAAGTGATTG
1 CCTATAATATTTAAAATTGCCTTTTGTTTTAAAAAATATTATTAAAAAGTAAGTA
*
1214625 CCTATTATATTTAAAATTGCCTTTTGTTTTAAAAAA-ATATATTAAAAA-TAAGTA
1 CCTATAATATTTAAAATTGCCTTTTGTTTTAAAAAATAT-TATTAAAAAGTAAGTA
*
1214679 TCTAATAATATT
1 CCT-ATAATATT
1214691 ATTTTTATTC
Statistics
Matches: 59, Mismatches: 5, Indels: 4
0.87 0.07 0.06
Matches are distributed among these distances:
54 7 0.12
55 52 0.88
ACGTcount: A:0.41, C:0.07, G:0.07, T:0.45
Consensus pattern (55 bp):
CCTATAATATTTAAAATTGCCTTTTGTTTTAAAAAATATTATTAAAAAGTAAGTA
Found at i:1217090 original size:4 final size:4
Alignment explanation
Indices: 1217081--1217125 Score: 54
Period size: 4 Copynumber: 10.8 Consensus size: 4
1217071 CAAATTATCA
* *
1217081 GAGG GAGG GAGG GAGAA GAGG GAGG GAGAA GAGG GAGG GAGG GAG
1 GAGG GAGG GAGG GAG-G GAGG GAGG GAG-G GAGG GAGG GAGG GAG
1217126 AGAGAAAGAG
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
4 29 0.83
5 6 0.17
ACGTcount: A:0.33, C:0.00, G:0.67, T:0.00
Consensus pattern (4 bp):
GAGG
Found at i:1217102 original size:17 final size:17
Alignment explanation
Indices: 1217080--1217126 Score: 66
Period size: 17 Copynumber: 3.0 Consensus size: 17
1217070 ACAAATTATC
1217080 AGAGGGAGGGAGGGAG-
1 AGAGGGAGGGAGGGAGA
1217096 A-A--GAGGGAGGGAGA
1 AGAGGGAGGGAGGGAGA
1217110 AGAGGGAGGGAGGGAGA
1 AGAGGGAGGGAGGGAGA
1217127 GAGAAAGAGA
Statistics
Matches: 27, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
13 11 0.41
14 1 0.04
15 2 0.07
16 1 0.04
17 12 0.44
ACGTcount: A:0.36, C:0.00, G:0.64, T:0.00
Consensus pattern (17 bp):
AGAGGGAGGGAGGGAGA
Found at i:1217103 original size:13 final size:13
Alignment explanation
Indices: 1217085--1217121 Score: 74
Period size: 13 Copynumber: 2.8 Consensus size: 13
1217075 TTATCAGAGG
1217085 GAGGGAGGGAGAA
1 GAGGGAGGGAGAA
1217098 GAGGGAGGGAGAA
1 GAGGGAGGGAGAA
1217111 GAGGGAGGGAG
1 GAGGGAGGGAG
1217122 GGAGAGAGAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.35, C:0.00, G:0.65, T:0.00
Consensus pattern (13 bp):
GAGGGAGGGAGAA
Found at i:1221370 original size:25 final size:25
Alignment explanation
Indices: 1221308--1221373 Score: 91
Period size: 24 Copynumber: 2.7 Consensus size: 25
1221298 TTTATTTTTA
*
1221308 AACT-AAACCATAAATCATTTAAAC
1 AACTAAAACCATAAACCATTTAAAC
*
1221332 AA-TAAAACCCTAAACCATTTAAAC
1 AACTAAAACCATAAACCATTTAAAC
*
1221356 AACTAAAACCTTAAACCA
1 AACTAAAACCATAAACCA
1221374 CTATCTAAAA
Statistics
Matches: 37, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
23 1 0.03
24 22 0.59
25 14 0.38
ACGTcount: A:0.55, C:0.24, G:0.00, T:0.21
Consensus pattern (25 bp):
AACTAAAACCATAAACCATTTAAAC
Found at i:1221386 original size:21 final size:19
Alignment explanation
Indices: 1221360--1221400 Score: 64
Period size: 21 Copynumber: 2.1 Consensus size: 19
1221350 TTAAACAACT
1221360 AAAACCTTAAACCACTATCTA
1 AAAACCTTAAACC-CT-TCTA
1221381 AAAACCTTAAACCCTTCTA
1 AAAACCTTAAACCCTTCTA
1221400 A
1 A
1221401 CATAAACAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
19 5 0.25
20 2 0.10
21 13 0.65
ACGTcount: A:0.46, C:0.29, G:0.00, T:0.24
Consensus pattern (19 bp):
AAAACCTTAAACCCTTCTA
Found at i:1222803 original size:4 final size:4
Alignment explanation
Indices: 1222794--1222838 Score: 54
Period size: 4 Copynumber: 10.8 Consensus size: 4
1222784 TTGATTATCA
* *
1222794 GAGG GAGG GAGG GAGAA GAGG GAGG GAGAA GAGG GAGG GAGG GAG
1 GAGG GAGG GAGG GAG-G GAGG GAGG GAG-G GAGG GAGG GAGG GAG
1222839 AGAGAAAGAG
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
4 29 0.83
5 6 0.17
ACGTcount: A:0.33, C:0.00, G:0.67, T:0.00
Consensus pattern (4 bp):
GAGG
Found at i:1222815 original size:17 final size:17
Alignment explanation
Indices: 1222793--1222839 Score: 66
Period size: 17 Copynumber: 3.0 Consensus size: 17
1222783 ATTGATTATC
1222793 AGAGGGAGGGAGGGAG-
1 AGAGGGAGGGAGGGAGA
1222809 A-A--GAGGGAGGGAGA
1 AGAGGGAGGGAGGGAGA
1222823 AGAGGGAGGGAGGGAGA
1 AGAGGGAGGGAGGGAGA
1222840 GAGAAAGAGA
Statistics
Matches: 27, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
13 11 0.41
14 1 0.04
15 2 0.07
16 1 0.04
17 12 0.44
ACGTcount: A:0.36, C:0.00, G:0.64, T:0.00
Consensus pattern (17 bp):
AGAGGGAGGGAGGGAGA
Found at i:1222816 original size:13 final size:13
Alignment explanation
Indices: 1222798--1222834 Score: 74
Period size: 13 Copynumber: 2.8 Consensus size: 13
1222788 TTATCAGAGG
1222798 GAGGGAGGGAGAA
1 GAGGGAGGGAGAA
1222811 GAGGGAGGGAGAA
1 GAGGGAGGGAGAA
1222824 GAGGGAGGGAG
1 GAGGGAGGGAG
1222835 GGAGAGAGAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.35, C:0.00, G:0.65, T:0.00
Consensus pattern (13 bp):
GAGGGAGGGAGAA
Found at i:1227079 original size:25 final size:25
Alignment explanation
Indices: 1227017--1227082 Score: 91
Period size: 24 Copynumber: 2.7 Consensus size: 25
1227007 TTTATTTTTA
*
1227017 AACT-AAACCATAAATCATTTAAAC
1 AACTAAAACCATAAACCATTTAAAC
*
1227041 AA-TAAAACCCTAAACCATTTAAAC
1 AACTAAAACCATAAACCATTTAAAC
*
1227065 AACTAAAACCTTAAACCA
1 AACTAAAACCATAAACCA
1227083 CTATCTAAAA
Statistics
Matches: 37, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
23 1 0.03
24 22 0.59
25 14 0.38
ACGTcount: A:0.55, C:0.24, G:0.00, T:0.21
Consensus pattern (25 bp):
AACTAAAACCATAAACCATTTAAAC
Found at i:1227095 original size:21 final size:19
Alignment explanation
Indices: 1227069--1227109 Score: 64
Period size: 21 Copynumber: 2.1 Consensus size: 19
1227059 TTAAACAACT
1227069 AAAACCTTAAACCACTATCTA
1 AAAACCTTAAACC-CT-TCTA
1227090 AAAACCTTAAACCCTTCTA
1 AAAACCTTAAACCCTTCTA
1227109 A
1 A
1227110 CATAAACAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
19 5 0.25
20 2 0.10
21 13 0.65
ACGTcount: A:0.46, C:0.29, G:0.00, T:0.24
Consensus pattern (19 bp):
AAAACCTTAAACCCTTCTA
Found at i:1241105 original size:19 final size:18
Alignment explanation
Indices: 1241083--1241142 Score: 57
Period size: 19 Copynumber: 3.2 Consensus size: 18
1241073 ACCGGTCTAA
1241083 ACCGGTCTGAATCGGCTTG
1 ACCGGTCTGAATCGG-TTG
* *
1241102 ACCGATCTAAATCGGTCTG
1 ACCGGTCTGAATCGGT-TG
* *
1241121 ACCAGTCTGAACCGGGTTG
1 ACCGGTCTGAATC-GGTTG
1241140 ACC
1 ACC
1241143 CGACCCAGTG
Statistics
Matches: 33, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
18 1 0.03
19 29 0.88
20 3 0.09
ACGTcount: A:0.22, C:0.28, G:0.27, T:0.23
Consensus pattern (18 bp):
ACCGGTCTGAATCGGTTG
Found at i:1241110 original size:29 final size:29
Alignment explanation
Indices: 1241066--1241121 Score: 94
Period size: 29 Copynumber: 1.9 Consensus size: 29
1241056 AATGTTTGAC
*
1241066 CGGCTTGACCGGTCTAAACCGGTCTGAAT
1 CGGCTTGACCGATCTAAACCGGTCTGAAT
*
1241095 CGGCTTGACCGATCTAAATCGGTCTGA
1 CGGCTTGACCGATCTAAACCGGTCTGA
1241122 CCAGTCTGAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.21, C:0.27, G:0.27, T:0.25
Consensus pattern (29 bp):
CGGCTTGACCGATCTAAACCGGTCTGAAT
Found at i:1241194 original size:29 final size:29
Alignment explanation
Indices: 1241151--1241236 Score: 129
Period size: 29 Copynumber: 3.0 Consensus size: 29
1241141 CCCGACCCAG
*
1241151 TGATATTTTGATAATTATTTTGAAAAAAA
1 TGATATTTTGGTAATTATTTTGAAAAAAA
**
1241180 TGATATTTTGGTAATTATTTTGAAAAAGG
1 TGATATTTTGGTAATTATTTTGAAAAAAA
*
1241209 TGATATTTTGGTAATTA-TTTAAAAAAAA
1 TGATATTTTGGTAATTATTTTGAAAAAAA
1241237 GTGCCATTTT
Statistics
Matches: 51, Mismatches: 6, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
28 8 0.16
29 43 0.84
ACGTcount: A:0.42, C:0.00, G:0.14, T:0.44
Consensus pattern (29 bp):
TGATATTTTGGTAATTATTTTGAAAAAAA
Found at i:1244964 original size:23 final size:23
Alignment explanation
Indices: 1244938--1244998 Score: 95
Period size: 23 Copynumber: 2.7 Consensus size: 23
1244928 CTCATATAAA
*
1244938 TGCACCGAAGTGCCACATAGAAT
1 TGCACCGTAGTGCCACATAGAAT
* *
1244961 TGCACCGTAGTGCCGCGTAGAAT
1 TGCACCGTAGTGCCACATAGAAT
1244984 TGCACCGTAGTGCCA
1 TGCACCGTAGTGCCA
1244999 TGTAATAATG
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.26, C:0.28, G:0.26, T:0.20
Consensus pattern (23 bp):
TGCACCGTAGTGCCACATAGAAT
Found at i:1245185 original size:103 final size:103
Alignment explanation
Indices: 1245006--1245334 Score: 640
Period size: 103 Copynumber: 3.2 Consensus size: 103
1244996 CCATGTAATA
*
1245006 ATGTCCCGAAGGACCACATATCATTCCTTAAGAATCATATACATATACTGGGGATCAAGTATGTG
1 ATGTCCCGAAGGACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTG
1245071 TCTCACCAGACTTCACACATGTTCCAAAGAATACATAT
66 TCTCACCAGACTTCACACATGTTCCAAAGAATACATAT
1245109 ATGTCCCGAAGGACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTG
1 ATGTCCCGAAGGACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTG
1245174 TCTCACCAGACTTCACACATGTTCCAAAGAATACATAT
66 TCTCACCAGACTTCACACATGTTCCAAAGAATACATAT
1245212 ATGTCCCGAAGGACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTG
1 ATGTCCCGAAGGACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTG
1245277 TCTCACCAGACTTCACACATGTTCCAAAGAATACATAT
66 TCTCACCAGACTTCACACATGTTCCAAAGAATACATAT
*
1245315 ATGTCCTGAAGGACCACATA
1 ATGTCCCGAAGGACCACATA
1245335 GACCCTCGAC
Statistics
Matches: 224, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
103 224 1.00
ACGTcount: A:0.36, C:0.23, G:0.14, T:0.27
Consensus pattern (103 bp):
ATGTCCCGAAGGACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTG
TCTCACCAGACTTCACACATGTTCCAAAGAATACATAT
Found at i:1246444 original size:16 final size:16
Alignment explanation
Indices: 1246423--1246453 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1246413 TGTAATACAG
*
1246423 ATAACCACATATAATT
1 ATAACCACACATAATT
1246439 ATAACCACACATAAT
1 ATAACCACACATAAT
1246454 CATGTCCATG
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:0.52, C:0.23, G:0.00, T:0.26
Consensus pattern (16 bp):
ATAACCACACATAATT
Found at i:1251807 original size:15 final size:15
Alignment explanation
Indices: 1251789--1251818 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
1251779 TGCACGTGCC
1251789 TCCCCCGCGCGTGGA
1 TCCCCCGCGCGTGGA
1251804 TCCCCCGCGCGTGGA
1 TCCCCCGCGCGTGGA
1251819 GAAGATTCGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.07, C:0.47, G:0.33, T:0.13
Consensus pattern (15 bp):
TCCCCCGCGCGTGGA
Found at i:1251917 original size:18 final size:18
Alignment explanation
Indices: 1251894--1251941 Score: 96
Period size: 18 Copynumber: 2.7 Consensus size: 18
1251884 CGAACCGGGT
1251894 TGACCCGACCCGTTGACC
1 TGACCCGACCCGTTGACC
1251912 TGACCCGACCCGTTGACC
1 TGACCCGACCCGTTGACC
1251930 TGACCCGACCCG
1 TGACCCGACCCG
1251942 GTGATATTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 30 1.00
ACGTcount: A:0.17, C:0.46, G:0.23, T:0.15
Consensus pattern (18 bp):
TGACCCGACCCGTTGACC
Found at i:1252010 original size:28 final size:29
Alignment explanation
Indices: 1251942--1252019 Score: 106
Period size: 28 Copynumber: 2.7 Consensus size: 29
1251932 ACCCGACCCG
** *
1251942 GTGATATTTTAGG-AATTATTTTTAAAATG
1 GTGATATTTT-GGTAATTATTTCGAAAATA
1251971 GTGATATTTTGGTAATTATTTCGAAAA-A
1 GTGATATTTTGGTAATTATTTCGAAAATA
1251999 GTGATATTTTGGTAATTATTT
1 GTGATATTTTGGTAATTATTT
1252020 AAAAAAAATA
Statistics
Matches: 45, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
28 23 0.51
29 22 0.49
ACGTcount: A:0.32, C:0.01, G:0.18, T:0.49
Consensus pattern (29 bp):
GTGATATTTTGGTAATTATTTCGAAAATA
Found at i:1252034 original size:28 final size:28
Alignment explanation
Indices: 1251972--1252042 Score: 90
Period size: 28 Copynumber: 2.5 Consensus size: 28
1251962 TTTAAAATGG
** *
1251972 TGATATTTTGGTAATTATTTCGAAAAAG
1 TGATATTTTGGTAATTATTTAAAAAAAA
1252000 TGATATTTTGGTAATTATTTAAAAAAAA
1 TGATATTTTGGTAATTATTTAAAAAAAA
*
1252028 T-ATTATTTTCGTAAT
1 TGA-TATTTTGGTAAT
1252043 AGTTGACTGT
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
27 1 0.03
28 37 0.97
ACGTcount: A:0.38, C:0.03, G:0.13, T:0.46
Consensus pattern (28 bp):
TGATATTTTGGTAATTATTTAAAAAAAA
Found at i:1259599 original size:16 final size:16
Alignment explanation
Indices: 1259575--1259608 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
1259565 TATCGCCGAC
*
1259575 CGAATTTCACTATTCA
1 CGAAATTCACTATTCA
1259591 CGAAATTCACTATTCA
1 CGAAATTCACTATTCA
1259607 CG
1 CG
1259609 TGAATAGTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.32, C:0.26, G:0.09, T:0.32
Consensus pattern (16 bp):
CGAAATTCACTATTCA
Found at i:1260111 original size:21 final size:22
Alignment explanation
Indices: 1260068--1260111 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
1260058 ATATTTTTCA
*
1260068 AAAAAACATTTACCAAACTTTG
1 AAAAAACATTTACCAAACGTTG
*
1260090 AAAAAACATTTTCCAAA-GTTG
1 AAAAAACATTTACCAAACGTTG
1260111 A
1 A
1260112 TTGCCAAACT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 4 0.20
22 16 0.80
ACGTcount: A:0.50, C:0.16, G:0.07, T:0.27
Consensus pattern (22 bp):
AAAAAACATTTACCAAACGTTG
Done.