Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009460.1 Hibiscus syriacus cultivar Beakdansim tig00113722_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: 2853300
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
File 6 of 14
Found at i:1012198 original size:14 final size:14
Alignment explanation
Indices: 1012181--1012210 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
1012171 AAATGATATT
*
1012181 ATTAAAAACATTAA
1 ATTAAAAACACTAA
1012195 ATTAAAAACACTAA
1 ATTAAAAACACTAA
1012209 AT
1 AT
1012211 ATTTATATGA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.63, C:0.10, G:0.00, T:0.27
Consensus pattern (14 bp):
ATTAAAAACACTAA
Found at i:1014452 original size:40 final size:39
Alignment explanation
Indices: 1014364--1014452 Score: 92
Period size: 40 Copynumber: 2.2 Consensus size: 39
1014354 TTTATGAATT
*
1014364 TAATATTAATAAAATATTTTAATATCATTTTAATCAAAA
1 TAATATTATTAAAATATTTTAATATCATTTTAATCAAAA
* * *
1014403 TATTAATTATTAAAATATATTTATTAAT-ATTTCTAAT-AATA
1 TAAT-ATTATTAAAATAT-TTTAAT-ATCATTT-TAATCAAAA
1014444 TAATATTAT
1 TAATATTAT
1014453 ATTTTTAATA
Statistics
Matches: 41, Mismatches: 5, Indels: 7
0.77 0.09 0.13
Matches are distributed among these distances:
39 3 0.07
40 17 0.41
41 15 0.37
42 6 0.15
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (39 bp):
TAATATTATTAAAATATTTTAATATCATTTTAATCAAAA
Found at i:1014479 original size:28 final size:27
Alignment explanation
Indices: 1014436--1014532 Score: 76
Period size: 28 Copynumber: 3.6 Consensus size: 27
1014426 TTAATATTTC
1014436 TAATAATAT--AATATTATATTTTTAA
1 TAATAATATAAAATATTATATTTTTAA
* *
1014461 T-ATTATGATAAAATAATTA-ATTTTATTA
1 TAATAAT-ATAAAAT-ATTATATTTT-TAA
* *
1014489 TAATAATATAAGATATTATATTTTTATTT
1 TAATAATATAAAATATTATATTTTTA--A
*
1014518 TAATAATATATAATA
1 TAATAATATAAAATA
1014533 AATTATTAAT
Statistics
Matches: 55, Mismatches: 8, Indels: 14
0.71 0.10 0.18
Matches are distributed among these distances:
24 4 0.07
25 3 0.05
27 13 0.24
28 18 0.33
29 17 0.31
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (27 bp):
TAATAATATAAAATATTATATTTTTAA
Found at i:1014486 original size:20 final size:21
Alignment explanation
Indices: 1014457--1014496 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
1014447 TATTATATTT
1014457 TTAATATTATGATAA-AATAA
1 TTAATATTATGATAATAATAA
* *
1014477 TTAATTTTATTATAATAATA
1 TTAATATTATGATAATAATA
1014497 TAAGATATTA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (21 bp):
TTAATATTATGATAATAATAA
Found at i:1014539 original size:29 final size:29
Alignment explanation
Indices: 1014455--1014539 Score: 75
Period size: 29 Copynumber: 2.9 Consensus size: 29
1014445 AATATTATAT
* * *
1014455 TTTTAATATTATGATAAAATAATTAATTTTA
1 TTTTAATAATAT-ATAATA-AATTATTTTTA
* *
1014486 TTATAATAATATA-AGAT-ATTATATTTTTA
1 TTTTAATAATATATA-ATAAAT-TATTTTTA
1014515 TTTTAATAATATATAATAAATTATT
1 TTTTAATAATATATAATAAATTATT
1014540 AATAAAATTT
Statistics
Matches: 43, Mismatches: 7, Indels: 10
0.72 0.12 0.17
Matches are distributed among these distances:
28 2 0.05
29 26 0.60
30 5 0.12
31 10 0.23
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (29 bp):
TTTTAATAATATATAATAAATTATTTTTA
Found at i:1014580 original size:27 final size:26
Alignment explanation
Indices: 1014550--1014614 Score: 69
Period size: 27 Copynumber: 2.4 Consensus size: 26
1014540 AATAAAATTT
* *
1014550 ATATTATTTATTAAT-TTCATAGAAATA
1 ATATTATTTATTAATAATAAT-G-AATA
*
1014577 ATATTATTAAATTAATAATAATGAATA
1 ATATTATT-TATTAATAATAATGAATA
1014604 ATATTATTTAT
1 ATATTATTTAT
1014615 ATATTTAATA
Statistics
Matches: 32, Mismatches: 4, Indels: 5
0.78 0.10 0.12
Matches are distributed among these distances:
26 2 0.06
27 20 0.62
28 7 0.22
29 3 0.09
ACGTcount: A:0.48, C:0.02, G:0.03, T:0.48
Consensus pattern (26 bp):
ATATTATTTATTAATAATAATGAATA
Found at i:1014630 original size:27 final size:27
Alignment explanation
Indices: 1014550--1014635 Score: 63
Period size: 27 Copynumber: 3.1 Consensus size: 27
1014540 AATAAAATTT
* *
1014550 ATATTATTTAT-TAATTTCATAGAAATA
1 ATATTATTTATAT-ATTTAATATAAATA
*
1014577 ATATTA-TTA-A-ATTAATAATAATGAATA
1 ATATTATTTATATATT--TAAT-ATAAATA
1014604 ATATTATTTATATATTTAATATTAATATA
1 ATATTATTTATATATTTAATA-TAA-ATA
1014633 ATA
1 ATA
1014636 ATCTAATAAT
Statistics
Matches: 46, Mismatches: 4, Indels: 16
0.70 0.06 0.24
Matches are distributed among these distances:
24 3 0.07
26 6 0.13
27 18 0.39
28 9 0.20
29 7 0.15
30 3 0.07
ACGTcount: A:0.49, C:0.01, G:0.02, T:0.48
Consensus pattern (27 bp):
ATATTATTTATATATTTAATATAAATA
Found at i:1014676 original size:23 final size:23
Alignment explanation
Indices: 1014650--1014694 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
1014640 AATAATATTT
1014650 TAATAAAGATATTTAAAATATAC
1 TAATAAAGATATTTAAAATATAC
* * *
1014673 TAATTAATATTTTTAAAATATA
1 TAATAAAGATATTTAAAATATA
1014695 ATATAACACT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.42
Consensus pattern (23 bp):
TAATAAAGATATTTAAAATATAC
Found at i:1016248 original size:30 final size:30
Alignment explanation
Indices: 1016212--1016274 Score: 92
Period size: 30 Copynumber: 2.1 Consensus size: 30
1016202 AGCTCCATAA
1016212 GTCGTCAAGTG-TTCCTGGAGACCTATGGAG
1 GTCGTCAAGTGCTT-CTGGAGACCTATGGAG
* *
1016242 GTCGTCATGTGCTTCTGGAGACCTATGGTG
1 GTCGTCAAGTGCTTCTGGAGACCTATGGAG
1016272 GTC
1 GTC
1016275 ACTGTAACAA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
30 28 0.93
31 2 0.07
ACGTcount: A:0.16, C:0.21, G:0.33, T:0.30
Consensus pattern (30 bp):
GTCGTCAAGTGCTTCTGGAGACCTATGGAG
Found at i:1020051 original size:21 final size:21
Alignment explanation
Indices: 1020025--1020100 Score: 125
Period size: 21 Copynumber: 3.6 Consensus size: 21
1020015 ATTGAATTTA
*
1020025 TCCCGAATGACCACATATATG
1 TCCCGAAGGACCACATATATG
*
1020046 TCCCGAAGGACCACATAAATG
1 TCCCGAAGGACCACATATATG
*
1020067 TCCCGAAGGATCACATATATG
1 TCCCGAAGGACCACATATATG
1020088 TCCCGAAGGACCA
1 TCCCGAAGGACCA
1020101 TTCCTTAAGG
Statistics
Matches: 50, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 50 1.00
ACGTcount: A:0.34, C:0.29, G:0.18, T:0.18
Consensus pattern (21 bp):
TCCCGAAGGACCACATATATG
Found at i:1020569 original size:65 final size:65
Alignment explanation
Indices: 1020500--1020660 Score: 202
Period size: 65 Copynumber: 2.5 Consensus size: 65
1020490 GAATTAAATT
* *
1020500 GAACATCGAATGCATTTCATGCATCGATGCACACA-CCATGCACCGATGCACTGAGGAT-TTTAT
1 GAACATCGAATGCATTTGATGCATCGATGCAC-CAGCCATGCACCGATGCACTCAGGATATTT-T
1020563 GA
64 GA
* * * * *
1020565 GAACATCGAATGCATTTGATGTATTGATGCACCAGCCATGCATCGATGCACTCTGGCTATTTTGA
1 GAACATCGAATGCATTTGATGCATCGATGCACCAGCCATGCACCGATGCACTCAGGATATTTTGA
* *
1020630 -AACATCGAATGCACTTGATCCATCGATGCAC
1 GAACATCGAATGCATTTGATGCATCGATGCAC
1020661 TCTTAGTGCA
Statistics
Matches: 83, Mismatches: 11, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
64 29 0.35
65 51 0.61
66 3 0.04
ACGTcount: A:0.29, C:0.24, G:0.20, T:0.27
Consensus pattern (65 bp):
GAACATCGAATGCATTTGATGCATCGATGCACCAGCCATGCACCGATGCACTCAGGATATTTTGA
Found at i:1029648 original size:29 final size:29
Alignment explanation
Indices: 1029606--1029666 Score: 122
Period size: 29 Copynumber: 2.1 Consensus size: 29
1029596 AGATGATAAC
1029606 TAAGCTTAAGGAAAGCTTAAGTTGTCTTA
1 TAAGCTTAAGGAAAGCTTAAGTTGTCTTA
1029635 TAAGCTTAAGGAAAGCTTAAGTTGTCTTA
1 TAAGCTTAAGGAAAGCTTAAGTTGTCTTA
1029664 TAA
1 TAA
1029667 TCAAAAGATG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 32 1.00
ACGTcount: A:0.36, C:0.10, G:0.20, T:0.34
Consensus pattern (29 bp):
TAAGCTTAAGGAAAGCTTAAGTTGTCTTA
Found at i:1029755 original size:12 final size:12
Alignment explanation
Indices: 1029738--1029762 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1029728 AAGAGTTGAT
1029738 AAGTTAAATTTG
1 AAGTTAAATTTG
1029750 AAGTTAAATTTG
1 AAGTTAAATTTG
1029762 A
1 A
1029763 CTTGTAATCA
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:0.44, C:0.00, G:0.16, T:0.40
Consensus pattern (12 bp):
AAGTTAAATTTG
Found at i:1031709 original size:20 final size:20
Alignment explanation
Indices: 1031686--1031725 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
1031676 GAAGATTGAT
*
1031686 GATCTTAAAACTTCTTTTAA
1 GATCATAAAACTTCTTTTAA
* *
1031706 GATCATCAATCTTCTTTTAA
1 GATCATAAAACTTCTTTTAA
1031726 TAAGGTTGGA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.33, C:0.17, G:0.05, T:0.45
Consensus pattern (20 bp):
GATCATAAAACTTCTTTTAA
Found at i:1035928 original size:22 final size:21
Alignment explanation
Indices: 1035893--1035938 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 21
1035883 GAAAATCTGA
*
1035893 TTTTTTTTTAAATTTTGATGT
1 TTTTTTTTTAAATTATGATGT
* *
1035914 TTTTTTTATTTAATTATGTTGT
1 TTTTTTT-TTAAATTATGATGT
1035936 TTT
1 TTT
1035939 CATTAAAACT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 7 0.33
22 14 0.67
ACGTcount: A:0.17, C:0.00, G:0.09, T:0.74
Consensus pattern (21 bp):
TTTTTTTTTAAATTATGATGT
Found at i:1037863 original size:17 final size:19
Alignment explanation
Indices: 1037835--1037883 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
1037825 TTTATGAGAA
1037835 CATCGAATGCACT-TGA-TG
1 CATCG-ATGCACTCTGAGTG
*
1037853 CATCGATGCACTCTTAGTG
1 CATCGATGCACTCTGAGTG
*
1037872 CACCGATGCACT
1 CATCGATGCACT
1037884 AAGGGTCCAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 7 0.26
18 7 0.26
19 13 0.48
ACGTcount: A:0.24, C:0.29, G:0.20, T:0.27
Consensus pattern (19 bp):
CATCGATGCACTCTGAGTG
Found at i:1041419 original size:41 final size:42
Alignment explanation
Indices: 1041367--1041582 Score: 179
Period size: 41 Copynumber: 5.2 Consensus size: 42
1041357 GTACAAGTTA
* * *
1041367 TTAGCGGCGTTTGT-ATAAAAATGCCACTAAAGTACGAGTAT
1 TTAGCGACGTTTATGATAAAAACGCCACTAAAGTACGAGTAT
* * * * *
1041408 TTTGCAACGTTTGTGCTTAAAACGCCAACTAAAGTACGA-TAAT
1 TTAGCGACGTTTATGATAAAAACGCC-ACTAAAGTACGAGT-AT
** * *
1041451 TTAGCGTTGTTTAT-ATAAAAGCGCCACTAAACTACGAGTAT
1 TTAGCGACGTTTATGATAAAAACGCCACTAAAGTACGAGTAT
* * *
1041492 TTAGCGGCGTTTATGCT-TAAACGCCACTAAAGTACGAGTAT
1 TTAGCGACGTTTATGATAAAAACGCCACTAAAGTACGAGTAT
* * * * * * *
1041533 TTAGTGGCATTTGTGCTTAAAACGCCACTAAAGTATGAGTAT
1 TTAGCGACGTTTATGATAAAAACGCCACTAAAGTACGAGTAT
*
1041575 TTACCGAC
1 TTAGCGAC
1041583 TCTTGTTCAA
Statistics
Matches: 140, Mismatches: 29, Indels: 11
0.78 0.16 0.06
Matches are distributed among these distances:
41 71 0.51
42 46 0.33
43 23 0.16
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.31
Consensus pattern (42 bp):
TTAGCGACGTTTATGATAAAAACGCCACTAAAGTACGAGTAT
Found at i:1041470 original size:84 final size:82
Alignment explanation
Indices: 1041375--1041536 Score: 218
Period size: 84 Copynumber: 2.0 Consensus size: 82
1041365 TATTAGCGGC
* * * * *
1041375 GTTTGTATAAAAATGCCACTAAAGTACGAGTATTTTGCAACGTTTGTGCTTAAAACGCCAACTAA
1 GTTTATATAAAAACGCCACTAAACTACGAGTATTTAGCAACGTTTATGCTT-AAACGCC-ACTAA
1041440 AGTACGA-TAATTTAGCGTT
64 AGTACGAGT-ATTTAGCGTT
* **
1041459 GTTTATATAAAAGCGCCACTAAACTACGAGTATTTAGCGGCGTTTATGCTTAAACGCCACTAAAG
1 GTTTATATAAAAACGCCACTAAACTACGAGTATTTAGCAACGTTTATGCTTAAACGCCACTAAAG
1041524 TACGAGTATTTAG
66 TACGAGTATTTAG
1041537 TGGCATTTGT
Statistics
Matches: 69, Mismatches: 8, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
82 18 0.26
83 8 0.12
84 43 0.62
ACGTcount: A:0.34, C:0.17, G:0.19, T:0.31
Consensus pattern (82 bp):
GTTTATATAAAAACGCCACTAAACTACGAGTATTTAGCAACGTTTATGCTTAAACGCCACTAAAG
TACGAGTATTTAGCGTT
Found at i:1041573 original size:42 final size:42
Alignment explanation
Indices: 1041384--1041577 Score: 198
Period size: 41 Copynumber: 4.6 Consensus size: 42
1041374 CGTTTGTATA
* * ** * *
1041384 AAAATGCCACTAAAGTACGAGTATTTTGCAACGTTTGTGCTT
1 AAAACGCCACTAAAGTACGAGTATTTAGCGGCATTTATGCTT
*** *
1041426 AAAACGCCAACTAAAGTACGA-TAATTTAGCGTTGTTTAT--AT
1 AAAACGCC-ACTAAAGTACGAGT-ATTTAGCGGCATTTATGCTT
* *
1041467 AAAAGCGCCACTAAACTACGAGTATTTAGCGGCGTTTATGCTT
1 AAAA-CGCCACTAAAGTACGAGTATTTAGCGGCATTTATGCTT
* *
1041510 -AAACGCCACTAAAGTACGAGTATTTAGTGGCATTTGTGCTT
1 AAAACGCCACTAAAGTACGAGTATTTAGCGGCATTTATGCTT
*
1041551 AAAACGCCACTAAAGTATGAGTATTTA
1 AAAACGCCACTAAAGTACGAGTATTTA
1041578 CCGACTCTTG
Statistics
Matches: 129, Mismatches: 16, Indels: 14
0.81 0.10 0.09
Matches are distributed among these distances:
41 64 0.50
42 41 0.32
43 24 0.19
ACGTcount: A:0.34, C:0.17, G:0.19, T:0.30
Consensus pattern (42 bp):
AAAACGCCACTAAAGTACGAGTATTTAGCGGCATTTATGCTT
Found at i:1051553 original size:16 final size:16
Alignment explanation
Indices: 1051532--1051562 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1051522 TAATTAAGCT
*
1051532 CTGAATTATTCAAATG
1 CTGAATGATTCAAATG
1051548 CTGAATGATTCAAAT
1 CTGAATGATTCAAAT
1051563 ACTCTATATG
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:0.39, C:0.13, G:0.13, T:0.35
Consensus pattern (16 bp):
CTGAATGATTCAAATG
Found at i:1051670 original size:27 final size:27
Alignment explanation
Indices: 1051611--1051663 Score: 88
Period size: 27 Copynumber: 2.0 Consensus size: 27
1051601 AATAATGGCT
*
1051611 CTGAATCATTCAGAATGTACTTTTGTA
1 CTGAATCATTCAGAATGTACTTCTGTA
*
1051638 CTGAATCATTCAGAATTTACTTCTGT
1 CTGAATCATTCAGAATGTACTTCTGT
1051664 GTTGAATTAG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.28, C:0.17, G:0.13, T:0.42
Consensus pattern (27 bp):
CTGAATCATTCAGAATGTACTTCTGTA
Found at i:1056195 original size:38 final size:39
Alignment explanation
Indices: 1056145--1056235 Score: 116
Period size: 37 Copynumber: 2.4 Consensus size: 39
1056135 TTTGTATAAT
1056145 ATTACAAATTATAAAATATTTATAT-ATTTTCTTTAAAAA
1 ATTA-AAATTATAAAATATTTATATAATTTTCTTTAAAAA
* * *
1056184 ATT-AAATT-TATAATATTTATATAATTTTTTTTACAAA
1 ATTAAAATTATAAAATATTTATATAATTTTCTTTAAAAA
*
1056221 ATTAAAAATATAAAA
1 ATTAAAATTATAAAA
1056236 AATGTTTAAT
Statistics
Matches: 44, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
36 13 0.30
37 20 0.45
38 4 0.09
39 7 0.16
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (39 bp):
ATTAAAATTATAAAATATTTATATAATTTTCTTTAAAAA
Found at i:1056727 original size:19 final size:19
Alignment explanation
Indices: 1056690--1056728 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
1056680 TTGATTTATG
* **
1056690 TAAAAATAAATATTTAAAT
1 TAAAAAAAAATATAAAAAT
1056709 TAAAAAAAAATATAAAAAT
1 TAAAAAAAAATATAAAAAT
1056728 T
1 T
1056729 CTTAATTTAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (19 bp):
TAAAAAAAAATATAAAAAT
Found at i:1057522 original size:29 final size:27
Alignment explanation
Indices: 1057490--1057561 Score: 67
Period size: 30 Copynumber: 2.6 Consensus size: 27
1057480 CTCCGTTATT
1057490 ATTTATTTTATTAATTATGTATGTTTAAA
1 ATTTATTTTATTAATTAT-TAT-TTTAAA
1057519 ATTTTATTTGTATCT-A-TATTATTTTAAA
1 A-TTTATTT-TAT-TAATTATTATTTTAAA
* *
1057547 AATTATATTATTAAT
1 ATTTATTTTATTAAT
1057562 ATTTATATAT
Statistics
Matches: 36, Mismatches: 2, Indels: 12
0.72 0.04 0.24
Matches are distributed among these distances:
25 1 0.03
26 4 0.11
27 5 0.14
28 7 0.19
29 4 0.11
30 10 0.28
31 4 0.11
32 1 0.03
ACGTcount: A:0.36, C:0.01, G:0.04, T:0.58
Consensus pattern (27 bp):
ATTTATTTTATTAATTATTATTTTAAA
Found at i:1057674 original size:25 final size:22
Alignment explanation
Indices: 1057640--1057688 Score: 64
Period size: 23 Copynumber: 2.2 Consensus size: 22
1057630 TATTTACATA
*
1057640 AATTTA-AAATTTAAAACAATACT
1 AATTTATAAAATTAAAA-AATA-T
1057663 AATTTATAAAATTAAAAAATAT
1 AATTTATAAAATTAAAAAATAT
1057685 AATT
1 AATT
1057689 AAAACATCTA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
22 5 0.21
23 10 0.42
24 9 0.38
ACGTcount: A:0.59, C:0.04, G:0.00, T:0.37
Consensus pattern (22 bp):
AATTTATAAAATTAAAAAATAT
Found at i:1059985 original size:20 final size:19
Alignment explanation
Indices: 1059960--1060013 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 19
1059950 GCGAAATAAA
1059960 AATCGCAACGCGATCTCCAG
1 AATCGCAACGCGATC-CCAG
** *
1059980 AATCGCAAATCAGTTCCCAG
1 AATCGCAACGC-GATCCCAG
1060000 AATCGCAACGCGAT
1 AATCGCAACGCGAT
1060014 TATGAAGAAT
Statistics
Matches: 27, Mismatches: 6, Indels: 3
0.75 0.17 0.08
Matches are distributed among these distances:
19 2 0.07
20 22 0.81
21 3 0.11
ACGTcount: A:0.33, C:0.31, G:0.19, T:0.17
Consensus pattern (19 bp):
AATCGCAACGCGATCCCAG
Found at i:1060107 original size:20 final size:20
Alignment explanation
Indices: 1060063--1060276 Score: 198
Period size: 20 Copynumber: 10.6 Consensus size: 20
1060053 GATTCTGACT
*
1060063 ATCGCAACGAGTATCCGTAAA
1 ATCGCAACGCGTATCCGT-AA
1060084 ATCGCAACGCGTATCCGTAA
1 ATCGCAACGCGTATCCGTAA
* *
1060104 ATCGCAACGAC-AATACGTAAA
1 ATCGCAACG-CGTATCCGT-AA
1060125 ATCGCAACGCGTATCCGTAA
1 ATCGCAACGCGTATCCGTAA
* * *
1060145 ATCGCAACGAGAATACGTAA
1 ATCGCAACGCGTATCCGTAA
*
1060165 ATCGCAACGCGTATCTGTAA
1 ATCGCAACGCGTATCCGTAA
* ** * **
1060185 ATAGCAACAAGAATATGTAA
1 ATCGCAACGCGTATCCGTAA
*
1060205 ATCGCAATGCGTATCCGTAA
1 ATCGCAACGCGTATCCGTAA
* *
1060225 ATCGCAACGAC-AATACGTAAA
1 ATCGCAACG-CGTATCCGT-AA
* *
1060246 ATTGCAATGCGTATCCGTAA
1 ATCGCAACGCGTATCCGTAA
*
1060266 ATCGTAACGCG
1 ATCGCAACGCG
1060277 ATTTTTAAAG
Statistics
Matches: 153, Mismatches: 34, Indels: 13
0.76 0.17 0.06
Matches are distributed among these distances:
20 104 0.68
21 49 0.32
ACGTcount: A:0.38, C:0.23, G:0.19, T:0.20
Consensus pattern (20 bp):
ATCGCAACGCGTATCCGTAA
Found at i:1060108 original size:41 final size:41
Alignment explanation
Indices: 1060063--1060274 Score: 302
Period size: 41 Copynumber: 5.2 Consensus size: 41
1060053 GATTCTGACT
* *
1060063 ATCGCAACGAGTATCCGTAAAATCGCAACGCGTATCCGTAA
1 ATCGCAACGAGAATACGTAAAATCGCAACGCGTATCCGTAA
*
1060104 ATCGCAACGACAATACGTAAAATCGCAACGCGTATCCGTAA
1 ATCGCAACGAGAATACGTAAAATCGCAACGCGTATCCGTAA
*
1060145 ATCGCAACGAGAATACGT-AAATCGCAACGCGTATCTGTAA
1 ATCGCAACGAGAATACGTAAAATCGCAACGCGTATCCGTAA
* * * *
1060185 ATAGCAACAAGAATATGT-AAATCGCAATGCGTATCCGTAA
1 ATCGCAACGAGAATACGTAAAATCGCAACGCGTATCCGTAA
* * *
1060225 ATCGCAACGACAATACGTAAAATTGCAATGCGTATCCGTAA
1 ATCGCAACGAGAATACGTAAAATCGCAACGCGTATCCGTAA
*
1060266 ATCGTAACG
1 ATCGCAACG
1060275 CGATTTTTAA
Statistics
Matches: 154, Mismatches: 16, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
40 70 0.45
41 84 0.55
ACGTcount: A:0.38, C:0.23, G:0.18, T:0.20
Consensus pattern (41 bp):
ATCGCAACGAGAATACGTAAAATCGCAACGCGTATCCGTAA
Found at i:1060837 original size:20 final size:20
Alignment explanation
Indices: 1060812--1060898 Score: 86
Period size: 20 Copynumber: 4.3 Consensus size: 20
1060802 TTCTAAACTT
*
1060812 AAAATCGCAACATGAAAATG
1 AAAATCGCAACACGAAAATG
1060832 AAAATCGCAACACGAAAATG
1 AAAATCGCAACACGAAAATG
** *
1060852 ACTATCGCAACGA-GAGAATG
1 AAAATCGCAAC-ACGAAAATG
** * *
1060872 ACTATCGCAACGCGGAAATG
1 AAAATCGCAACACGAAAATG
1060892 AAAATCG
1 AAAATCG
1060899 AAACGAGATA
Statistics
Matches: 56, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
20 55 0.98
21 1 0.02
ACGTcount: A:0.47, C:0.20, G:0.20, T:0.14
Consensus pattern (20 bp):
AAAATCGCAACACGAAAATG
Found at i:1060872 original size:40 final size:40
Alignment explanation
Indices: 1060812--1060906 Score: 102
Period size: 40 Copynumber: 2.4 Consensus size: 40
1060802 TTCTAAACTT
1060812 AAAATCGCAAC-ATGAAAATGAAAATCGCAACACGAAAATG
1 AAAATCGCAACGA-GAAAATGAAAATCGCAACACGAAAATG
** * ** * *
1060852 ACTATCGCAACGAGAGAATGACTATCGCAACGCGGAAATG
1 AAAATCGCAACGAGAAAATGAAAATCGCAACACGAAAATG
*
1060892 AAAATCGAAACGAGA
1 AAAATCGCAACGAGA
1060907 TAATCGCAAC
Statistics
Matches: 44, Mismatches: 10, Indels: 2
0.79 0.18 0.04
Matches are distributed among these distances:
40 43 0.98
41 1 0.02
ACGTcount: A:0.48, C:0.19, G:0.20, T:0.13
Consensus pattern (40 bp):
AAAATCGCAACGAGAAAATGAAAATCGCAACACGAAAATG
Found at i:1060990 original size:20 final size:21
Alignment explanation
Indices: 1060959--1061022 Score: 78
Period size: 20 Copynumber: 3.1 Consensus size: 21
1060949 CGCATTGCGA
*
1060959 TTCTCTCGTTGCGATTTTCAT
1 TTCTCGCGTTGCGATTTTCAT
**
1060980 TTC-CGCGTTGCGATAGTCA-
1 TTCTCGCGTTGCGATTTTCAT
*
1060999 TTCTCTCGTTGCGATTTTCAT
1 TTCTCGCGTTGCGATTTTCAT
1061020 TTC
1 TTC
1061023 AACCAAAAGA
Statistics
Matches: 35, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
19 3 0.09
20 26 0.74
21 6 0.17
ACGTcount: A:0.11, C:0.25, G:0.17, T:0.47
Consensus pattern (21 bp):
TTCTCGCGTTGCGATTTTCAT
Found at i:1063114 original size:94 final size:94
Alignment explanation
Indices: 1062712--1063091 Score: 674
Period size: 94 Copynumber: 4.1 Consensus size: 94
1062702 TAGATTGCTT
* *
1062712 AGTAAATTTATTCGGTTGCTGCCAATACTGCTAAACTGTTTATTCTTTAACACTGTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
1062777 ATTTGTCTTTTGTTTTGTCTTTTGGTTG-A
66 ATTTGTC-TTTGTTTTGTCTTTTGGTTGAA
*
1062806 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAAT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
1062871 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
*
1062900 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
1062965 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
* * *
1062994 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAATACTCTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
1063059 ATTTGTCTTTGTTTTGTCTTTTGGTTG-A
66 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
1063087 AGTAA
1 AGTAA
1063092 TGTAATCCAT
Statistics
Matches: 278, Mismatches: 7, Indels: 3
0.97 0.02 0.01
Matches are distributed among these distances:
93 26 0.09
94 252 0.91
ACGTcount: A:0.21, C:0.13, G:0.19, T:0.47
Consensus pattern (94 bp):
AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:1063213 original size:14 final size:14
Alignment explanation
Indices: 1063194--1063221 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
1063184 AACGCGAAAT
1063194 GAATCGCAACGAGA
1 GAATCGCAACGAGA
1063208 GAATCGCAACGAGA
1 GAATCGCAACGAGA
1063222 AATGAAAATC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.43, C:0.21, G:0.29, T:0.07
Consensus pattern (14 bp):
GAATCGCAACGAGA
Found at i:1063272 original size:19 final size:19
Alignment explanation
Indices: 1063179--1063261 Score: 90
Period size: 19 Copynumber: 4.7 Consensus size: 19
1063169 AAAAATGACT
1063179 ATCGCAACGCGAAATG--A
1 ATCGCAACGCGAAATGAAA
*
1063196 ATCGCAA--CG--A-GAGA
1 ATCGCAACGCGAAATGAAA
*
1063210 ATCGCAACGAGAAATGAAA
1 ATCGCAACGCGAAATGAAA
*
1063229 ATCGCAATGCGAAATGAAA
1 ATCGCAACGCGAAATGAAA
1063248 ATCGCAACGCGAAA
1 ATCGCAACGCGAAA
1063262 CTATAATCGC
Statistics
Matches: 54, Mismatches: 5, Indels: 12
0.76 0.07 0.17
Matches are distributed among these distances:
12 1 0.02
13 1 0.02
14 8 0.15
15 2 0.04
16 1 0.02
17 7 0.13
18 1 0.02
19 33 0.61
ACGTcount: A:0.46, C:0.20, G:0.23, T:0.11
Consensus pattern (19 bp):
ATCGCAACGCGAAATGAAA
Found at i:1063357 original size:20 final size:20
Alignment explanation
Indices: 1063306--1063372 Score: 89
Period size: 20 Copynumber: 3.4 Consensus size: 20
1063296 GATTCTCTCG
* **
1063306 TTGCGATAGTAAAATTCGCA
1 TTGCGATAGTCATTTTCGCA
*
1063326 TTGCGATTGTCATTTTCGCA
1 TTGCGATAGTCATTTTCGCA
*
1063346 TTGCGATAGTCATTTTCGCG
1 TTGCGATAGTCATTTTCGCA
1063366 TTGCGAT
1 TTGCGAT
1063373 TTTAAGTTTC
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 41 1.00
ACGTcount: A:0.21, C:0.18, G:0.22, T:0.39
Consensus pattern (20 bp):
TTGCGATAGTCATTTTCGCA
Found at i:1063947 original size:21 final size:21
Alignment explanation
Indices: 1063856--1063959 Score: 93
Period size: 21 Copynumber: 5.0 Consensus size: 21
1063846 GACTCACCTG
*
1063856 TCATCGTTCAAGAGGCCTCCCA
1 TCATCGTTCAAGAGGCC-CCTA
1063878 T-ATCGTTCAAGAGGCCCCTA
1 TCATCGTTCAAGAGGCCCCTA
** * *
1063898 TCATCCCTCAAGAGTCCCCTC
1 TCATCGTTCAAGAGGCCCCTA
* * * *
1063919 CCACCGTTCAAGAGGCCACTG
1 TCATCGTTCAAGAGGCCCCTA
* *
1063940 TCATCGTTGAAGAGGTCCCT
1 TCATCGTTCAAGAGGCCCCT
1063960 CCCAACATTT
Statistics
Matches: 64, Mismatches: 17, Indels: 3
0.76 0.20 0.04
Matches are distributed among these distances:
20 4 0.06
21 59 0.92
22 1 0.02
ACGTcount: A:0.22, C:0.36, G:0.19, T:0.23
Consensus pattern (21 bp):
TCATCGTTCAAGAGGCCCCTA
Found at i:1063953 original size:42 final size:42
Alignment explanation
Indices: 1063881--1063963 Score: 105
Period size: 42 Copynumber: 2.0 Consensus size: 42
1063871 CCTCCCATAT
*
1063881 CGTTCAAGAGGCCCCTATCATCCCTCAAGA-GTCCCCTCCCAC
1 CGTTCAAGAGGCCACTATCATCCCTCAAGAGGT-CCCTCCCAC
* ** *
1063923 CGTTCAAGAGGCCACTGTCATCGTTGAAGAGGTCCCTCCCA
1 CGTTCAAGAGGCCACTATCATCCCTCAAGAGGTCCCTCCCA
1063964 ACATTTTAGA
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
42 33 0.94
43 2 0.06
ACGTcount: A:0.22, C:0.39, G:0.19, T:0.20
Consensus pattern (42 bp):
CGTTCAAGAGGCCACTATCATCCCTCAAGAGGTCCCTCCCAC
Found at i:1065336 original size:14 final size:14
Alignment explanation
Indices: 1065317--1065352 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
1065307 AATGTTTAAT
1065317 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
* *
1065331 TGATTTGTAAATGT
1 TGATTTGTAAAAGA
1065345 TGATTTGT
1 TGATTTGT
1065353 TTAATTGATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.22, T:0.47
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:1065503 original size:33 final size:34
Alignment explanation
Indices: 1065454--1065528 Score: 125
Period size: 33 Copynumber: 2.2 Consensus size: 34
1065444 AAAACAGACT
*
1065454 ATCGCAACGAGAGAATCGCAATGC-AAAATGAAA
1 ATCGCAACAAGAGAATCGCAATGCGAAAATGAAA
*
1065487 ATCGCAACAAGTGAATCGCAATGCGAAAATGAAA
1 ATCGCAACAAGAGAATCGCAATGCGAAAATGAAA
1065521 ATCGCAAC
1 ATCGCAAC
1065529 GCGAAACTAA
Statistics
Matches: 39, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
33 22 0.56
34 17 0.44
ACGTcount: A:0.47, C:0.20, G:0.20, T:0.13
Consensus pattern (34 bp):
ATCGCAACAAGAGAATCGCAATGCGAAAATGAAA
Found at i:1065525 original size:20 final size:19
Alignment explanation
Indices: 1065467--1065527 Score: 69
Period size: 14 Copynumber: 3.4 Consensus size: 19
1065457 GCAACGAGAG
1065467 AATCGCAATGCAAAATGAA
1 AATCGCAATGCAAAATGAA
*
1065486 AATCGCAA--C-AAGTG--
1 AATCGCAATGCAAAATGAA
1065500 AATCGCAATGCGAAAATGAA
1 AATCGCAATGC-AAAATGAA
1065520 AATCGCAA
1 AATCGCAA
1065528 CGCGAAACTA
Statistics
Matches: 34, Mismatches: 2, Indels: 11
0.72 0.04 0.23
Matches are distributed among these distances:
14 8 0.24
16 5 0.15
17 1 0.03
18 4 0.12
19 8 0.24
20 8 0.24
ACGTcount: A:0.49, C:0.18, G:0.18, T:0.15
Consensus pattern (19 bp):
AATCGCAATGCAAAATGAA
Found at i:1065601 original size:33 final size:33
Alignment explanation
Indices: 1065545--1065639 Score: 127
Period size: 33 Copynumber: 2.8 Consensus size: 33
1065535 CTAATTTCGT
*
1065545 GTTGCGATTTTCATTTTCGCATTGCGATTCACTC
1 GTTGTGATTTTCA-TTTCGCATTGCGATTCACTC
*
1065579 GTTGTGATTTTCATTTCGCATTGCGATTCTCTC
1 GTTGTGATTTTCATTTCGCATTGCGATTCACTC
** *
1065612 GTTGTGATAGTCATTTCTGCTTTGCGAT
1 GTTGTGATTTTCATTTC-GCATTGCGAT
1065640 AGTCAATTCC
Statistics
Matches: 55, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
33 34 0.62
34 21 0.38
ACGTcount: A:0.14, C:0.20, G:0.20, T:0.46
Consensus pattern (33 bp):
GTTGTGATTTTCATTTCGCATTGCGATTCACTC
Found at i:1065642 original size:20 final size:19
Alignment explanation
Indices: 1065617--1065699 Score: 87
Period size: 20 Copynumber: 4.2 Consensus size: 19
1065607 CTCTCGTTGT
1065617 GATAGTCATTTCTGCTTTGC
1 GATAGTCATTTC-GCTTTGC
* *
1065637 GATAGTCAATTCCGCATTGC
1 GATAGTC-ATTTCGCTTTGC
1065657 GATAGTCATTTC-CATGTTGC
1 GATAGTCATTTCGC-T-TTGC
*
1065677 GATAGTCATATTCGCGTTGC
1 GATAGTCAT-TTCGCTTTGC
1065697 GAT
1 GAT
1065700 TTCCGCGTTG
Statistics
Matches: 53, Mismatches: 5, Indels: 10
0.78 0.07 0.15
Matches are distributed among these distances:
18 1 0.02
19 4 0.08
20 40 0.75
21 7 0.13
22 1 0.02
ACGTcount: A:0.20, C:0.20, G:0.22, T:0.37
Consensus pattern (19 bp):
GATAGTCATTTCGCTTTGC
Found at i:1065677 original size:40 final size:39
Alignment explanation
Indices: 1065617--1065699 Score: 107
Period size: 40 Copynumber: 2.1 Consensus size: 39
1065607 CTCTCGTTGT
1065617 GATAGTCATTTCTGCTTTGCGATAGTCA-ATTCCGCATTGC
1 GATAGTCATTTCTGC-TTGCGATAGTCATATT-CGCATTGC
*
1065657 GATAGTCATTTCCATG-TTGCGATAGTCATATTCGCGTTGC
1 GATAGTCATTT-C-TGCTTGCGATAGTCATATTCGCATTGC
1065697 GAT
1 GAT
1065700 TTCCGCGTTG
Statistics
Matches: 39, Mismatches: 1, Indels: 6
0.85 0.02 0.13
Matches are distributed among these distances:
40 33 0.85
41 4 0.10
42 2 0.05
ACGTcount: A:0.20, C:0.20, G:0.22, T:0.37
Consensus pattern (39 bp):
GATAGTCATTTCTGCTTGCGATAGTCATATTCGCATTGC
Found at i:1068154 original size:24 final size:24
Alignment explanation
Indices: 1068120--1068173 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
1068110 CTGAAAAATC
1068120 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
* *
1068144 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
1068168 ATCAAA
1 ATCAAA
1068174 TTTCGAATAC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.41, C:0.20, G:0.19, T:0.20
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:1068187 original size:24 final size:24
Alignment explanation
Indices: 1068120--1068187 Score: 64
Period size: 24 Copynumber: 2.8 Consensus size: 24
1068110 CTGAAAAATC
* * *
1068120 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAGTCCGAATACTGACCAAG
** *
1068144 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAGTCCGAATACTGACCAAG
* *
1068168 ATCAAATTTCGAATACTGAC
1 ATCAAAGTCCGAATACTGAC
1068188 TAGTACTCAC
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 37 1.00
ACGTcount: A:0.38, C:0.21, G:0.18, T:0.24
Consensus pattern (24 bp):
ATCAAAGTCCGAATACTGACCAAG
Found at i:1069058 original size:20 final size:20
Alignment explanation
Indices: 1069033--1069100 Score: 118
Period size: 20 Copynumber: 3.4 Consensus size: 20
1069023 GTCAGAATCT
*
1069033 CGTTGCGATTTACATATTCG
1 CGTTGCGATTTACGTATTCG
*
1069053 CATTGCGATTTACGTATTCG
1 CGTTGCGATTTACGTATTCG
1069073 CGTTGCGATTTACGTATTCG
1 CGTTGCGATTTACGTATTCG
1069093 CGTTGCGA
1 CGTTGCGA
1069101 ATTAGGAAAA
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 45 1.00
ACGTcount: A:0.18, C:0.21, G:0.24, T:0.38
Consensus pattern (20 bp):
CGTTGCGATTTACGTATTCG
Found at i:1069121 original size:21 final size:21
Alignment explanation
Indices: 1069097--1069142 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
1069087 TATTCGCGTT
1069097 GCGAATTAGGAAAATCGCAAC
1 GCGAATTAGGAAAATCGCAAC
* * *
1069118 GCGAATTTGGGAAATCGCAAT
1 GCGAATTAGGAAAATCGCAAC
1069139 GCGA
1 GCGA
1069143 TAGTCAGAAT
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:0.37, C:0.17, G:0.28, T:0.17
Consensus pattern (21 bp):
GCGAATTAGGAAAATCGCAAC
Found at i:1069237 original size:20 final size:20
Alignment explanation
Indices: 1069193--1069445 Score: 262
Period size: 20 Copynumber: 12.6 Consensus size: 20
1069183 TATCAGAGAT
*
1069193 CGCGTTGCGAATTATC-GAT-
1 CGCGTTGCGATTTA-CGGATA
1069212 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
1069232 CGCGTTGCGATTTTACGTAT-
1 CGCGTTGCGA-TTTACGGATA
*
1069252 TGTCGTTGCGATTTACGGATA
1 CG-CGTTGCGATTTACGGATA
* * *
1069273 CGCATTGCGATTTACGTATT
1 CGCGTTGCGATTTACGGATA
* *
1069293 CTCGTTGCGATTTACAGATA
1 CGCGTTGCGATTTACGGATA
*
1069313 CGCGTTGCGATTTACAGATA
1 CGCGTTGCGATTTACGGATA
* *
1069333 CGCGTTGCGATTTACGTATT
1 CGCGTTGCGATTTACGGATA
*
1069353 CTCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
1069373 CGCGTTGCGATTTTATGTAT-
1 CGCGTTGCGA-TTTACGGATA
* **
1069393 TGTCGTTGTAATTTACGGATA
1 CG-CGTTGCGATTTACGGATA
1069414 CGCGTTGCGATTTTACGGATA
1 CGCGTTGCGA-TTTACGGATA
*
1069435 CTCGTTGCGAT
1 CGCGTTGCGAT
1069446 AGCCAGAATC
Statistics
Matches: 193, Mismatches: 32, Indels: 17
0.80 0.13 0.07
Matches are distributed among these distances:
18 1 0.01
19 16 0.08
20 126 0.65
21 50 0.26
ACGTcount: A:0.19, C:0.19, G:0.25, T:0.37
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:1073116 original size:25 final size:25
Alignment explanation
Indices: 1073065--1073116 Score: 61
Period size: 26 Copynumber: 2.1 Consensus size: 25
1073055 TAAGATTTCA
* **
1073065 AATACAATATTTATTTAAATGTGAT
1 AATACAATATTGATTTAAATGAAAT
1073090 AATACAAGTATTGATTTAAAT-AAAT
1 AATACAA-TATTGATTTAAATGAAAT
1073115 AA
1 AA
1073117 AAAAAATGAC
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
25 11 0.48
26 12 0.52
ACGTcount: A:0.50, C:0.04, G:0.08, T:0.38
Consensus pattern (25 bp):
AATACAATATTGATTTAAATGAAAT
Found at i:1075897 original size:27 final size:27
Alignment explanation
Indices: 1075858--1075912 Score: 94
Period size: 27 Copynumber: 2.0 Consensus size: 27
1075848 ATTGTTGGGA
1075858 CTTAACATATGAATTTAGTGGTTTTAT
1 CTTAACATATGAATTTAGTGGTTTTAT
1075885 CTTAACA-AGTGAATTTAGTGGTTTTAT
1 CTTAACATA-TGAATTTAGTGGTTTTAT
1075912 C
1 C
1075913 AGGTAAGTAT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
26 1 0.04
27 26 0.96
ACGTcount: A:0.29, C:0.09, G:0.16, T:0.45
Consensus pattern (27 bp):
CTTAACATATGAATTTAGTGGTTTTAT
Found at i:1077965 original size:3 final size:3
Alignment explanation
Indices: 1077957--1078011 Score: 58
Period size: 3 Copynumber: 18.0 Consensus size: 3
1077947 CATTTAAATT
* * *
1077957 TTA TTA TTA TTA TTA -AA TTTA TTA TTA CTAA ATA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA -TTA TTA TTA -TTA TTA TTA TTA TTA TTA
1078003 TTA TTA TTA
1 TTA TTA TTA
1078012 ATATATATAT
Statistics
Matches: 43, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
2 1 0.02
3 39 0.91
4 3 0.07
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (3 bp):
TTA
Found at i:1078019 original size:28 final size:29
Alignment explanation
Indices: 1077958--1078033 Score: 82
Period size: 31 Copynumber: 2.5 Consensus size: 29
1077948 ATTTAAATTT
*
1077958 TATTATTATTATTAAATTTATTATTACTAAA
1 TATTATTATTATT--ATTTATTATTAATAAA
*
1077989 TATTATTATTATTA-TTATTATTAATATA
1 TATTATTATTATTATTTATTATTAATAAA
1078017 TATATATATATATATTA
1 TAT-TAT-TAT-TATTA
1078034 CAAGCCCAAA
Statistics
Matches: 40, Mismatches: 2, Indels: 6
0.83 0.04 0.12
Matches are distributed among these distances:
28 15 0.38
29 4 0.10
30 3 0.08
31 18 0.45
ACGTcount: A:0.42, C:0.01, G:0.00, T:0.57
Consensus pattern (29 bp):
TATTATTATTATTATTTATTATTAATAAA
Found at i:1078074 original size:21 final size:21
Alignment explanation
Indices: 1078050--1078090 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
1078040 CAAAGGACCC
1078050 GGAGGCCCGTTT-TACAAATCT
1 GGAGGCCCGTTTAT-CAAATCT
1078071 GGAGGCCCGTTTATCAAATC
1 GGAGGCCCGTTTATCAAATC
1078091 CCAAACCCAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 18 0.95
22 1 0.05
ACGTcount: A:0.24, C:0.24, G:0.24, T:0.27
Consensus pattern (21 bp):
GGAGGCCCGTTTATCAAATCT
Found at i:1079405 original size:11 final size:11
Alignment explanation
Indices: 1079389--1079458 Score: 54
Period size: 11 Copynumber: 6.0 Consensus size: 11
1079379 TTCATTTTAA
1079389 TTATTATTATT
1 TTATTATTATT
1079400 TTATTATTACTT
1 TTATTATTA-TT
1079412 TTGA-TA-TATGT
1 TT-ATTATTAT-T
1079423 TTAAATTATTATCT
1 TT--ATTATTAT-T
* *
1079437 TCATGATTATT
1 TTATTATTATT
1079448 TTATTATTATT
1 TTATTATTATT
1079459 ATTAAGTTAT
Statistics
Matches: 47, Mismatches: 6, Indels: 12
0.72 0.09 0.18
Matches are distributed among these distances:
10 1 0.02
11 24 0.51
12 14 0.30
13 3 0.06
14 5 0.11
ACGTcount: A:0.29, C:0.04, G:0.04, T:0.63
Consensus pattern (11 bp):
TTATTATTATT
Found at i:1079869 original size:141 final size:140
Alignment explanation
Indices: 1079573--1079852 Score: 327
Period size: 141 Copynumber: 2.0 Consensus size: 140
1079563 ATAAAACATA
* * * *
1079573 TTTTGATATATATTTATTTTTTAATATCTAAGAAAAGAGCTGTCTTAAAATACCTAGAAGTCCTT
1 TTTTAATATATATTTATTTTTTAATATCAAAGAAAAGAACTGTCTTAAAACACCTAGAAGTCCTT
* * * * * *
1079638 TTCTGATATTCTTAAATAAATAAATGTCCTACTTTTATAAATTGTATATATATTAATCTATTTTT
66 TTCTGATATTCTTAAATAAATAAATATCCTACTTTTATAAATTATAAATATATTAA-CAATTATA
*
1079703 TTAGATAAATG
130 GTAGATAAATG
* * *
1079714 TTTTAATATTTATTTATTTTTTAATATCAAAGGAAGGAACTGTCTTAAAACACCTAGAAG-CTCT
1 TTTTAATATATATTTATTTTTTAATATCAAAGAAAAGAACTGTCTTAAAACACCTAGAAGTC-CT
* *
1079778 TTTCTGATATT-TCTAAATAAATAAATATCTTA-TTTATATAAATTAATAAATTTACTTAA-AAT
65 TTTCTGATATTCT-TAAATAAATAAATATCCTACTTT-TATAAATT-ATAAATATA-TTAACAAT
1079840 TATAGTA-ATAAAT
126 TATAGTAGATAAAT
1079853 TTAAATTAAA
Statistics
Matches: 118, Mismatches: 16, Indels: 11
0.81 0.11 0.08
Matches are distributed among these distances:
140 11 0.09
141 97 0.82
142 6 0.05
143 4 0.03
ACGTcount: A:0.39, C:0.09, G:0.07, T:0.45
Consensus pattern (140 bp):
TTTTAATATATATTTATTTTTTAATATCAAAGAAAAGAACTGTCTTAAAACACCTAGAAGTCCTT
TTCTGATATTCTTAAATAAATAAATATCCTACTTTTATAAATTATAAATATATTAACAATTATAG
TAGATAAATG
Found at i:1084671 original size:2 final size:2
Alignment explanation
Indices: 1084664--1084701 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
1084654 TTATCCTTTA
1084664 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1084702 CCTTGGTTGT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1084912 original size:16 final size:15
Alignment explanation
Indices: 1084886--1084917 Score: 55
Period size: 16 Copynumber: 2.1 Consensus size: 15
1084876 CTTGTCCAAC
1084886 AAAGAAAGAAGAAAA
1 AAAGAAAGAAGAAAA
1084901 AAAGAGAAGAAGAAAA
1 AAAGA-AAGAAGAAAA
1084917 A
1 A
1084918 GGAAAATTGA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 5 0.31
16 11 0.69
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (15 bp):
AAAGAAAGAAGAAAA
Found at i:1087500 original size:114 final size:115
Alignment explanation
Indices: 1087300--1087613 Score: 504
Period size: 115 Copynumber: 2.7 Consensus size: 115
1087290 GAATGTGCTC
*
1087300 ATAGCATCTTCTGGAAGTGTTCTTTGAATTATCTGATCTGATTTGGTATGAACTCCAAAATCAAT
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTTGGTATGAACTCCAAAATCAAT
* * *
1087365 CATTAGATTTGAAAGATGAA-TTTGCTCATGGTAGAAATAAGGAGACTCA
66 CATTGGATTTGAAAGATGAATTTTGCTCATAGTAGAAATAAGGAGACCCA
*
1087414 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTTGGTATGAATTCCAAAATCAAT
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTTGGTATGAACTCCAAAATCAAT
1087479 CATTGGATTTGAAAGATGAATTTTGCTCATAGTAGAAATAAGGAGACCCA
66 CATTGGATTTGAAAGATGAATTTTGCTCATAGTAGAAATAAGGAGACCCA
* * * * * * *
1087529 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATATGATCTGATTCGGTAGGAACCCCAGAACCGAT
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTTGGTATGAACTCCAAAATCAAT
*
1087594 CATTGGAATTGAAAGATGAA
66 CATTGGATTTGAAAGATGAA
1087614 CTGCATGATC
Statistics
Matches: 185, Mismatches: 14, Indels: 1
0.93 0.07 0.00
Matches are distributed among these distances:
114 82 0.44
115 103 0.56
ACGTcount: A:0.32, C:0.14, G:0.21, T:0.33
Consensus pattern (115 bp):
ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTTGGTATGAACTCCAAAATCAAT
CATTGGATTTGAAAGATGAATTTTGCTCATAGTAGAAATAAGGAGACCCA
Found at i:1089829 original size:54 final size:53
Alignment explanation
Indices: 1089758--1089912 Score: 238
Period size: 54 Copynumber: 2.9 Consensus size: 53
1089748 GAAATCTTGG
1089758 CAGAAGCCACAGTAAAGGATGAATGTGTTGTCAAATGTTTTACGAACATCTGAA
1 CAGAAGCCACAG-AAAGGATGAATGTGTTGTCAAATGTTTTACGAACATCTGAA
* *
1089812 CAGAAACCACATGAAAGGATGAATGTGTTGTCAAATGTTTTACGAACATCTGAG
1 CAGAAGCCACA-GAAAGGATGAATGTGTTGTCAAATGTTTTACGAACATCTGAA
***
1089866 CAGAAGCCACAGGAAAGGATGAATGCACTGTCAAATGTTTTACGAAC
1 CAGAAGCCACA-GAAAGGATGAATGTGTTGTCAAATGTTTTACGAAC
1089913 CTGCTATTCT
Statistics
Matches: 93, Mismatches: 7, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
54 92 0.99
55 1 0.01
ACGTcount: A:0.37, C:0.16, G:0.23, T:0.24
Consensus pattern (53 bp):
CAGAAGCCACAGAAAGGATGAATGTGTTGTCAAATGTTTTACGAACATCTGAA
Found at i:1091059 original size:76 final size:76
Alignment explanation
Indices: 1090979--1091696 Score: 1348
Period size: 76 Copynumber: 9.5 Consensus size: 76
1090969 CTATTTCCCA
*
1090979 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAACCTTCGGGATCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGATCTTTTTGATGTTTTCAA
1091044 AGCCTTAGGGT
66 AGCCTTAGGGT
*
1091055 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGATCTTTTTGATGTTTTCAA
1091120 AGCCTTAGGGT
66 AGCCTTAGGGT
*
1091131 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGATCTTTTTGATGTTTTCAA
*
1091196 AGCCTTCGGGT
66 AGCCTTAGGGT
1091207 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGATCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGATCTTTTTGATGTTTTCAA
1091272 AGCCTTAGGGT
66 AGCCTTAGGGT
1091283 CATCTGTAAGTCCTTCAGTGCATGATGTTTCC-AAAAGCCTTCGGGATCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGATCTTTTTGATGTTTTCAA
1091347 AGCCTTAGGGT
66 AGCCTTAGGGT
1091358 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGATCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGATCTTTTTGATGTTTTCAA
1091423 AGCCTTAGGGT
66 AGCCTTAGGGT
1091434 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGATCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGATCTTTTTGATGTTTTCAA
1091499 AGCCTTAGGGT
66 AGCCTTAGGGT
*
1091510 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGATCTTTTTGATGTTTTCAA
1091575 AGCCTTAGGGT
66 AGCCTTAGGGT
*
1091586 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGATCTTTTTGATGTTTTCAA
*
1091651 AGCCTTCGGGT
66 AGCCTTAGGGT
* *
1091662 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAA
1091697 CATTTCAATC
Statistics
Matches: 632, Mismatches: 9, Indels: 2
0.98 0.01 0.00
Matches are distributed among these distances:
75 75 0.12
76 557 0.88
ACGTcount: A:0.22, C:0.20, G:0.21, T:0.36
Consensus pattern (76 bp):
CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGATCTTTTTGATGTTTTCAA
AGCCTTAGGGT
Found at i:1091679 original size:379 final size:379
Alignment explanation
Indices: 1090979--1091696 Score: 1373
Period size: 379 Copynumber: 1.9 Consensus size: 379
1090969 CTATTTCCCA
1090979 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAACCTTCGGGATCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAACCTTCGGGATCTTTTTGATGTTTTCAA
1091044 AGCCTTAGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTT
66 AGCCTTAGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTT
1091109 GATGTTTTCAAAGCCTTAGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTC
131 GATGTTTTCAAAGCCTTAGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTC
*
1091174 GGGAGCTTTTTGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCC
196 GGGAGCTTTTTGATGTTTTCAAAGCCTTAGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCC
* *
1091239 AAAAAGCCTTCGGGATCTTTTTGATGTTTTCAAAGCCTTAGGGTCATCTGTAAGTCCTTCAGTGC
261 AAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAGCCTTAGGGTCATCTGTAAGCCCTTCAGTGC
1091304 ATGATGTTTCCAAAAGCCTTCGGGATCTTTTTGATGTTTTCAAAGCCTTAGGGT
326 ATGATGTTTCCAAAAGCCTTCGGGATCTTTTTGATGTTTTCAAAGCCTTAGGGT
*
1091358 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGATCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAACCTTCGGGATCTTTTTGATGTTTTCAA
*
1091423 AGCCTTAGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGATCTTTTT
66 AGCCTTAGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTT
1091488 GATGTTTTCAAAGCCTTAGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTC
131 GATGTTTTCAAAGCCTTAGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTC
1091553 GGGAGCTTTTTGATGTTTTCAAAGCCTTAGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCC
196 GGGAGCTTTTTGATGTTTTCAAAGCCTTAGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCC
*
1091618 AAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGCCCTTCAGTGC
261 AAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAGCCTTAGGGTCATCTGTAAGCCCTTCAGTGC
*
1091683 ATGATGTTTTCAAA
326 ATGATGTTTCCAAA
1091697 CATTTCAATC
Statistics
Matches: 332, Mismatches: 7, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
379 332 1.00
ACGTcount: A:0.22, C:0.20, G:0.21, T:0.36
Consensus pattern (379 bp):
CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAACCTTCGGGATCTTTTTGATGTTTTCAA
AGCCTTAGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTT
GATGTTTTCAAAGCCTTAGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTC
GGGAGCTTTTTGATGTTTTCAAAGCCTTAGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCC
AAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAGCCTTAGGGTCATCTGTAAGCCCTTCAGTGC
ATGATGTTTCCAAAAGCCTTCGGGATCTTTTTGATGTTTTCAAAGCCTTAGGGT
Found at i:1091830 original size:3 final size:3
Alignment explanation
Indices: 1091824--1091884 Score: 70
Period size: 3 Copynumber: 20.0 Consensus size: 3
1091814 CATTTAAATT
* * *
1091824 TTA TTA TTA TTA TTA -AA TTTA TTA TTA CTAA ATA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA -TTA TTA TTA -TTA TTA TTA TTA TTA TTA
1091870 TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA
1091885 ATATATATAT
Statistics
Matches: 49, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
2 1 0.02
3 45 0.92
4 3 0.06
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.61
Consensus pattern (3 bp):
TTA
Found at i:1091862 original size:34 final size:31
Alignment explanation
Indices: 1091818--1091896 Score: 95
Period size: 34 Copynumber: 2.4 Consensus size: 31
1091808 TTTTTTCATT
*
1091818 TAAATTTTATTATTATTATTAAATTTATTATTAC
1 TAAATATTATTATTATTATT--A-TTATTATTAC
*
1091852 TAAATATTATTATTATTATTATTATTATTAT
1 TAAATATTATTATTATTATTATTATTATTAC
1091883 TAATATATATATTA
1 TAA-ATAT-TATTA
1091897 CAAGCCCAAA
Statistics
Matches: 41, Mismatches: 2, Indels: 5
0.85 0.04 0.10
Matches are distributed among these distances:
31 12 0.29
32 5 0.12
33 5 0.12
34 19 0.46
ACGTcount: A:0.41, C:0.01, G:0.00, T:0.58
Consensus pattern (31 bp):
TAAATATTATTATTATTATTATTATTATTAC
Found at i:1091895 original size:15 final size:16
Alignment explanation
Indices: 1091825--1091896 Score: 94
Period size: 15 Copynumber: 4.5 Consensus size: 16
1091815 ATTTAAATTT
1091825 TATTATTATTATTAAA
1 TATTATTATTATTAAA
*
1091841 T-TTATTATTACTAAA
1 TATTATTATTATTAAA
*
1091856 TATTATTATTATT-AT
1 TATTATTATTATTAAA
1091871 TATTATTATTATTAATA
1 TATTATTATTATTAA-A
1091888 TATATATTA
1 TAT-TATTA
1091897 CAAGCCCAAA
Statistics
Matches: 48, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
15 28 0.58
16 12 0.25
17 3 0.06
18 5 0.10
ACGTcount: A:0.40, C:0.01, G:0.00, T:0.58
Consensus pattern (16 bp):
TATTATTATTATTAAA
Found at i:1091951 original size:21 final size:21
Alignment explanation
Indices: 1091913--1091953 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
1091903 CAAAGGACCC
*
1091913 GGAGGCCCGTTTTACAAATCT
1 GGAGGCCCGTTATACAAATCT
1091934 GGAGGCCCGGTTAT-CAAATC
1 GGAGGCCC-GTTATACAAATC
1091954 CCAAACCTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.24, C:0.24, G:0.27, T:0.24
Consensus pattern (21 bp):
GGAGGCCCGTTATACAAATCT
Found at i:1093724 original size:141 final size:139
Alignment explanation
Indices: 1093434--1093707 Score: 303
Period size: 141 Copynumber: 2.0 Consensus size: 139
1093424 AACATATTTG
* *
1093434 ATATATATTTATTTTTAATATCTAAGAAAAGAGCTGTCTTAAAATACCTAGAAGTCCTTTTCTGA
1 ATATATATTTATTTTTAATATCAAAGAAAAGAGCTGTCTTAAAACACCTAGAAGTCCTTTTCTGA
* * * * * **
1093499 TATTCTTAAATAAATAAATGTTATACTTTTATAAATTGTATATATATTAATCTATTTTTTTAGAT
66 TATTCTTAAATAAATAAATATTATACTTTTATAAATTATAAATATATTAA-CAATTATAGTAGAT
1093564 AAATGTTTTA
130 AAATGTTTTA
*
1093574 ATATTTATTTATTTTTTAATATCAAAGGAAGAA-A-CTGTCTTAAAACACCTAGAAG-CTCTTTT
1 ATATATATTTA-TTTTTAATATCAAA-GAA-AAGAGCTGTCTTAAAACACCTAGAAGTC-CTTTT
*
1093636 CTGATATT-TCTAAATAAATAAATATCT-TA-TTTATATAAATTAATAAATTTACTTAA-AATTA
62 CTGATATTCT-TAAATAAATAAATAT-TATACTTT-TATAAATT-ATAAATATA-TTAACAATTA
1093697 TAGTA-ATAAAT
122 TAGTAGATAAAT
1093708 TTAAATTAAA
Statistics
Matches: 114, Mismatches: 11, Indels: 18
0.80 0.08 0.13
Matches are distributed among these distances:
140 21 0.18
141 76 0.67
142 11 0.10
143 6 0.05
ACGTcount: A:0.41, C:0.08, G:0.07, T:0.44
Consensus pattern (139 bp):
ATATATATTTATTTTTAATATCAAAGAAAAGAGCTGTCTTAAAACACCTAGAAGTCCTTTTCTGA
TATTCTTAAATAAATAAATATTATACTTTTATAAATTATAAATATATTAACAATTATAGTAGATA
AATGTTTTA
Found at i:1101797 original size:82 final size:82
Alignment explanation
Indices: 1101657--1101819 Score: 290
Period size: 82 Copynumber: 2.0 Consensus size: 82
1101647 CTTAATACGC
* *
1101657 TAAATATGAACTTATCAAGTAATTCAATGGTGAAAAAGAATATTGTTCTCTTTAAAAGATTCATG
1 TAAATATGAACTTAACAAGTAATTCAATGGTGAAAAAGAATATTGTTCTCTTTAAAAGATTCAAG
*
1101722 TTCGAGCAATTATGTTG
66 TTCGAGAAATTATGTTG
*
1101739 TAAATATGAACTTAACAAGTAATTCAATGGTGAAAAAGAATATTGTTCTCTTTTAAAGATTCAAG
1 TAAATATGAACTTAACAAGTAATTCAATGGTGAAAAAGAATATTGTTCTCTTTAAAAGATTCAAG
1101804 TTCGAGAAATTATGTT
66 TTCGAGAAATTATGTT
1101820 TACAAGATTT
Statistics
Matches: 77, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
82 77 1.00
ACGTcount: A:0.39, C:0.09, G:0.15, T:0.36
Consensus pattern (82 bp):
TAAATATGAACTTAACAAGTAATTCAATGGTGAAAAAGAATATTGTTCTCTTTAAAAGATTCAAG
TTCGAGAAATTATGTTG
Found at i:1102153 original size:34 final size:34
Alignment explanation
Indices: 1102105--1102170 Score: 105
Period size: 34 Copynumber: 1.9 Consensus size: 34
1102095 TAAATGGTGT
* *
1102105 CATTGCCAGGATTCATTAAGAGCAGTGAGGCTGC
1 CATTGCCAGGATTCATGAAGACCAGTGAGGCTGC
*
1102139 CATTGCCAGTATTCATGAAGACCAGTGAGGCT
1 CATTGCCAGGATTCATGAAGACCAGTGAGGCT
1102171 TTAACATATT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
34 29 1.00
ACGTcount: A:0.27, C:0.21, G:0.27, T:0.24
Consensus pattern (34 bp):
CATTGCCAGGATTCATGAAGACCAGTGAGGCTGC
Found at i:1118022 original size:14 final size:14
Alignment explanation
Indices: 1117999--1118032 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
1117989 ATAATAATAA
*
1117999 TAAT-AAATATTTT
1 TAATAAAATATATT
1118012 TAATAAAATATATT
1 TAATAAAATATATT
1118026 TAATAAA
1 TAATAAA
1118033 TTAAAATTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 4 0.21
14 15 0.79
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (14 bp):
TAATAAAATATATT
Found at i:1119087 original size:13 final size:13
Alignment explanation
Indices: 1119069--1119094 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1119059 TCATACACAA
1119069 GAGAAAAAAATTT
1 GAGAAAAAAATTT
1119082 GAGAAAAAAATTT
1 GAGAAAAAAATTT
1119095 CAATCCTTAT
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:0.62, C:0.00, G:0.15, T:0.23
Consensus pattern (13 bp):
GAGAAAAAAATTT
Found at i:1121361 original size:24 final size:22
Alignment explanation
Indices: 1121301--1121373 Score: 57
Period size: 20 Copynumber: 3.4 Consensus size: 22
1121291 TATATATCTA
1121301 CAATTAATTAAATATATGTTTT
1 CAATTAATTAAATATATGTTTT
* *
1121323 -AA-TAATCCAAA-ATATTTAATTT
1 CAATTAAT-TAAATATATGT--TTT
*
1121345 CAATTAATTAAATATAT-ATTT
1 CAATTAATTAAATATATGTTTT
1121366 -AATTAATT
1 CAATTAATT
1121374 TGAAATAATA
Statistics
Matches: 41, Mismatches: 4, Indels: 14
0.69 0.07 0.24
Matches are distributed among these distances:
20 17 0.41
21 8 0.20
22 3 0.07
23 5 0.12
24 8 0.20
ACGTcount: A:0.47, C:0.05, G:0.01, T:0.47
Consensus pattern (22 bp):
CAATTAATTAAATATATGTTTT
Found at i:1121371 original size:20 final size:21
Alignment explanation
Indices: 1121302--1121373 Score: 67
Period size: 22 Copynumber: 3.4 Consensus size: 21
1121292 ATATATCTAC
**
1121302 AATTAATTAAATATATGTTTT
1 AATTAATTAAATATATAATTT
* *
1121323 AA-TAATCCAAAATATTTAATTT
1 AATTAAT--TAAATATATAATTT
1121345 CAATTAATTAAATATAT-ATTT
1 -AATTAATTAAATATATAATTT
1121366 AATTAATT
1 AATTAATT
1121374 TGAAATAATA
Statistics
Matches: 41, Mismatches: 6, Indels: 9
0.73 0.11 0.16
Matches are distributed among these distances:
20 12 0.29
21 6 0.15
22 17 0.41
23 2 0.05
24 4 0.10
ACGTcount: A:0.47, C:0.04, G:0.01, T:0.47
Consensus pattern (21 bp):
AATTAATTAAATATATAATTT
Found at i:1121450 original size:90 final size:89
Alignment explanation
Indices: 1121335--1121509 Score: 305
Period size: 90 Copynumber: 2.0 Consensus size: 89
1121325 TAATCCAAAA
* * *
1121335 TATTTAATTTCAATTAATTAAATATATATTTAATTAATTTGAAATAATAAAATCCCTAATATGAT
1 TATTAAATTCCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAA-CCCTAATATGAT
1121400 TAGGGTAACTTGGATATAAAATGAT
65 TAGGGTAACTTGGATATAAAATGAT
1121425 TATTAAATTCCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAACCCTAATATGATT
1 TATTAAATTCCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAACCCTAATATGATT
*
1121490 AGGGTAACTTGGCTATAAAA
66 AGGGTAACTTGGATATAAAA
1121510 GGGTGTGTTA
Statistics
Matches: 81, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
89 32 0.40
90 49 0.60
ACGTcount: A:0.45, C:0.07, G:0.09, T:0.39
Consensus pattern (89 bp):
TATTAAATTCCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAACCCTAATATGATT
AGGGTAACTTGGATATAAAATGAT
Found at i:1121712 original size:14 final size:14
Alignment explanation
Indices: 1121693--1121720 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
1121683 TTCATTGTTG
1121693 TCCTTGTTGTTTTT
1 TCCTTGTTGTTTTT
1121707 TCCTTGTTGTTTTT
1 TCCTTGTTGTTTTT
1121721 CAAGGAACCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.00, C:0.14, G:0.14, T:0.71
Consensus pattern (14 bp):
TCCTTGTTGTTTTT
Found at i:1131088 original size:20 final size:21
Alignment explanation
Indices: 1131063--1131171 Score: 107
Period size: 21 Copynumber: 5.3 Consensus size: 21
1131053 TTTTCCCAAT
*
1131063 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
1131083 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
*
1131104 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
1131124 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
*
1131145 TCGCAATGCGATAATAA-AAAA
1 TCGCAATGCGA-ATTAAGAAAA
1131166 TCGCAA
1 TCGCAA
1131172 CGAGATACTT
Statistics
Matches: 70, Mismatches: 16, Indels: 5
0.77 0.18 0.05
Matches are distributed among these distances:
20 27 0.39
21 41 0.59
22 2 0.03
ACGTcount: A:0.43, C:0.17, G:0.22, T:0.17
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:1131108 original size:41 final size:41
Alignment explanation
Indices: 1131063--1131173 Score: 188
Period size: 41 Copynumber: 2.7 Consensus size: 41
1131053 TTTTCCCAAT
1131063 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
1131104 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
*
1131145 TCGCAATGCGATAATAA-AAAATCGCAACG
1 TCGCAATGCG--AATAAGTAAATCGCAACG
1131174 AGATACTTAC
Statistics
Matches: 67, Mismatches: 1, Indels: 3
0.94 0.01 0.04
Matches are distributed among these distances:
41 51 0.76
42 11 0.16
43 5 0.07
ACGTcount: A:0.42, C:0.18, G:0.23, T:0.17
Consensus pattern (41 bp):
TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
Found at i:1131191 original size:20 final size:20
Alignment explanation
Indices: 1131166--1131238 Score: 119
Period size: 20 Copynumber: 3.6 Consensus size: 20
1131156 TAATAAAAAA
* *
1131166 TCGCAACGAGATACTTACTT
1 TCGCAACGCGATACTGACTT
1131186 TCGCAACGCGATACTGACTT
1 TCGCAACGCGATACTGACTT
*
1131206 TCGCAACGCGATTCTGACTT
1 TCGCAACGCGATACTGACTT
1131226 TCGCAACGCGATA
1 TCGCAACGCGATA
1131239 ATACATAATC
Statistics
Matches: 49, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 49 1.00
ACGTcount: A:0.26, C:0.29, G:0.19, T:0.26
Consensus pattern (20 bp):
TCGCAACGCGATACTGACTT
Found at i:1133122 original size:18 final size:18
Alignment explanation
Indices: 1133096--1133140 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
1133086 TCCACTTCGG
*
1133096 GAGCCATCACCTCGCCCA
1 GAGCCATCACCTCACCCA
*
1133114 GAGCTATCACCTCACCCA
1 GAGCCATCACCTCACCCA
1133132 GAGCCATCA
1 GAGCCATCA
1133141 TCTGATCGAC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.27, C:0.44, G:0.16, T:0.13
Consensus pattern (18 bp):
GAGCCATCACCTCACCCA
Found at i:1133676 original size:19 final size:20
Alignment explanation
Indices: 1133622--1133687 Score: 71
Period size: 20 Copynumber: 3.4 Consensus size: 20
1133612 TAGTTTACTT
* *
1133622 TCGCAACACGAAAATGACTA
1 TCGCAACGCGGAAATGACTA
*
1133642 TCGCAACGCGGAAATGGCTA
1 TCGCAACGCGGAAATGACTA
* **
1133662 TCGCAATGC-GAAATGAAAA
1 TCGCAACGCGGAAATGACTA
1133681 TCGCAAC
1 TCGCAAC
1133688 AACAAAATCG
Statistics
Matches: 38, Mismatches: 8, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
19 13 0.34
20 25 0.66
ACGTcount: A:0.39, C:0.24, G:0.21, T:0.15
Consensus pattern (20 bp):
TCGCAACGCGGAAATGACTA
Found at i:1133719 original size:32 final size:33
Alignment explanation
Indices: 1133661--1133751 Score: 157
Period size: 32 Copynumber: 2.8 Consensus size: 33
1133651 GGAAATGGCT
1133661 ATCGCAATGCGAAATGAAAATCGCAACAACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACAACAAA
*
1133694 ATCGCAATGCGAAATG-AAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACAACAAA
*
1133726 ATCGCAACGCGAAATGAAAATCGCAA
1 ATCGCAATGCGAAATGAAAATCGCAA
1133752 TGCGATTTGT
Statistics
Matches: 55, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
32 30 0.55
33 25 0.45
ACGTcount: A:0.48, C:0.22, G:0.18, T:0.12
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACAACAAA
Found at i:1133734 original size:14 final size:14
Alignment explanation
Indices: 1133677--1133734 Score: 62
Period size: 14 Copynumber: 3.9 Consensus size: 14
1133667 ATGCGAAATG
*
1133677 AAAATCGCAACAAC
1 AAAATCGCAACGAC
*
1133691 AAAATCGCAATGCGAA
1 AAAATCGCAA--CGAC
1133707 ATGAAATCGCAACGAC
1 A--AAATCGCAACGAC
1133723 AAAATCGCAACG
1 AAAATCGCAACG
1133735 CGAAATGAAA
Statistics
Matches: 37, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
14 21 0.57
16 7 0.19
18 9 0.24
ACGTcount: A:0.50, C:0.24, G:0.16, T:0.10
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:1133826 original size:19 final size:19
Alignment explanation
Indices: 1133763--1133885 Score: 96
Period size: 20 Copynumber: 6.7 Consensus size: 19
1133753 GCGATTTGTG
1133763 TTTCGCGTTGCGA-TTTCA
1 TTTCGCGTTGCGATTTTCA
1133781 TTTCGCGTTGCGA-TTT--
1 TTTCGCGTTGCGATTTTCA
*
1133797 TGT--CGTTGCGATTTTCA
1 TTTCGCGTTGCGATTTTCA
* ***
1133814 TTTCGCATTGCGATAGCCA
1 TTTCGCGTTGCGATTTTCA
* **
1133833 TTTCCGCGTTGTGATAGTCA
1 TTT-CGCGTTGCGATTTTCA
*
1133853 TTTCGCGTTGCGATTTTAA
1 TTTCGCGTTGCGATTTTCA
*
1133872 GTTTCGTGTTGCGA
1 -TTTCGCGTTGCGA
1133886 AAGTAAACTA
Statistics
Matches: 84, Mismatches: 14, Indels: 12
0.76 0.13 0.11
Matches are distributed among these distances:
14 8 0.10
15 3 0.04
16 2 0.02
17 2 0.02
18 16 0.19
19 25 0.30
20 28 0.33
ACGTcount: A:0.13, C:0.20, G:0.24, T:0.43
Consensus pattern (19 bp):
TTTCGCGTTGCGATTTTCA
Found at i:1133854 original size:20 final size:19
Alignment explanation
Indices: 1133763--1133866 Score: 87
Period size: 19 Copynumber: 5.7 Consensus size: 19
1133753 GCGATTTGTG
*
1133763 TTTCGCGTTGCGAT-TTCA
1 TTTCGCGTTGCGATAGTCA
1133781 TTTCGCGTTGCG--A-T--
1 TTTCGCGTTGCGATAGTCA
**
1133795 TTT-GTCGTTGCGATTTTCA
1 TTTCG-CGTTGCGATAGTCA
* *
1133814 TTTCGCATTGCGATAGCCA
1 TTTCGCGTTGCGATAGTCA
*
1133833 TTTCCGCGTTGTGATAGTCA
1 TTT-CGCGTTGCGATAGTCA
1133853 TTTCGCGTTGCGAT
1 TTTCGCGTTGCGAT
1133867 TTTAAGTTTC
Statistics
Matches: 68, Mismatches: 9, Indels: 17
0.72 0.10 0.18
Matches are distributed among these distances:
13 1 0.01
14 10 0.15
16 1 0.01
17 1 0.01
18 12 0.18
19 26 0.38
20 17 0.25
ACGTcount: A:0.12, C:0.21, G:0.24, T:0.42
Consensus pattern (19 bp):
TTTCGCGTTGCGATAGTCA
Found at i:1135753 original size:14 final size:14
Alignment explanation
Indices: 1135734--1135769 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
1135724 ATTGTTTAAT
1135734 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
* *
1135748 TGATTTGTAAATGT
1 TGATTTGTAAAAGA
1135762 TGATTTGT
1 TGATTTGT
1135770 TTAATTGATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.22, T:0.47
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:1135895 original size:14 final size:14
Alignment explanation
Indices: 1135876--1135929 Score: 63
Period size: 14 Copynumber: 3.5 Consensus size: 14
1135866 CGAAATGGCT
1135876 ATCGCAACGAGAAA
1 ATCGCAACGAGAAA
1135890 ATCGCAATGCGAAATGAAA
1 ATCGCAA--CG--A-GAAA
1135909 ATCGCAACGAGAAA
1 ATCGCAACGAGAAA
1135923 ATCGCAA
1 ATCGCAA
1135930 TGCGATTTTC
Statistics
Matches: 35, Mismatches: 0, Indels: 10
0.78 0.00 0.22
Matches are distributed among these distances:
14 18 0.51
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 11 0.31
ACGTcount: A:0.48, C:0.20, G:0.20, T:0.11
Consensus pattern (14 bp):
ATCGCAACGAGAAA
Found at i:1135947 original size:33 final size:33
Alignment explanation
Indices: 1135857--1135934 Score: 120
Period size: 33 Copynumber: 2.4 Consensus size: 33
1135847 AAAACAAACT
* ***
1135857 ATCGCAACGCGAAATGGCTATCGCAACGAGAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAAA
1135890 ATCGCAATGCGAAATGAAAATCGCAACGAGAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAAA
1135923 ATCGCAATGCGA
1 ATCGCAATGCGA
1135935 TTTTCATTTC
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 41 1.00
ACGTcount: A:0.42, C:0.22, G:0.23, T:0.13
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAAA
Found at i:1135978 original size:20 final size:20
Alignment explanation
Indices: 1135953--1136010 Score: 89
Period size: 20 Copynumber: 2.9 Consensus size: 20
1135943 TCGCATTGCG
*
1135953 ATTTTCTCGTTGCGATAGCC
1 ATTTTCACGTTGCGATAGCC
*
1135973 ATTTTCACATTGCGATAGCC
1 ATTTTCACGTTGCGATAGCC
*
1135993 ATTTTCGCGTTGCGATAG
1 ATTTTCACGTTGCGATAG
1136011 TCAAATGAAT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.19, C:0.22, G:0.21, T:0.38
Consensus pattern (20 bp):
ATTTTCACGTTGCGATAGCC
Found at i:1137094 original size:24 final size:24
Alignment explanation
Indices: 1137067--1137120 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
1137057 GTATTCGAAA
* *
1137067 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATATTGGTCAATACACGGAC
*
1137091 TTTGATATTGGTCAATACACGGAT
1 TTTGATATTGGTCAATACACGGAC
1137115 TTTGAT
1 TTTGAT
1137121 GATGTTTCAG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.24, C:0.17, G:0.20, T:0.39
Consensus pattern (24 bp):
TTTGATATTGGTCAATACACGGAC
Found at i:1137306 original size:12 final size:12
Alignment explanation
Indices: 1137289--1137313 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1137279 ATATAATCCT
1137289 GAAGAAGAAAAA
1 GAAGAAGAAAAA
1137301 GAAGAAGAAAAA
1 GAAGAAGAAAAA
1137313 G
1 G
1137314 TCCCCGAAGA
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:1139009 original size:42 final size:42
Alignment explanation
Indices: 1138920--1139012 Score: 114
Period size: 42 Copynumber: 2.2 Consensus size: 42
1138910 CCTCTTCAAC
* * * * *
1138920 AATGACAGTGGCCTCTTGAACGGTGGGAGGGGACTCTCGAGG
1 AATGATAGGGGCCTCTTCAACGATAGGAGGGGACTCTCGAGG
* *
1138962 AATGATAGGGGCCTCTTCAACGATAGGAGTGGACTCTTGAGG
1 AATGATAGGGGCCTCTTCAACGATAGGAGGGGACTCTCGAGG
*
1139004 GATGATAGG
1 AATGATAGG
1139013 CGAGTCGGGC
Statistics
Matches: 43, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
42 43 1.00
ACGTcount: A:0.25, C:0.16, G:0.38, T:0.22
Consensus pattern (42 bp):
AATGATAGGGGCCTCTTCAACGATAGGAGGGGACTCTCGAGG
Found at i:1141094 original size:33 final size:33
Alignment explanation
Indices: 1141037--1141135 Score: 144
Period size: 33 Copynumber: 3.0 Consensus size: 33
1141027 ATGAGATAAT
*
1141037 GAGAATCGCAACGCGGAAATGACTATCGCAACGA
1 GAGAATCGCAACGC-GAAATGACTATCGCAACCA
*
1141071 GAGAATCGCAACGCGAAATGACTATCGCGACCA
1 GAGAATCGCAACGCGAAATGACTATCGCAACCA
* **
1141104 GACAATCGCAACGCGAAATGAAAATCGCAACC
1 GAGAATCGCAACGCGAAATGACTATCGCAACC
1141136 GCGAAATAAA
Statistics
Matches: 59, Mismatches: 6, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
33 45 0.76
34 14 0.24
ACGTcount: A:0.39, C:0.26, G:0.23, T:0.11
Consensus pattern (33 bp):
GAGAATCGCAACGCGAAATGACTATCGCAACCA
Found at i:1141129 original size:19 final size:19
Alignment explanation
Indices: 1141012--1141177 Score: 109
Period size: 20 Copynumber: 9.1 Consensus size: 19
1141002 TCTTTTGGTT
* *
1141012 GAAATGAAAATCGCAATGA
1 GAAATGAAAATCGCAACGC
*
1141031 GATAATGAGAATCGCAACGC
1 GA-AATGAAAATCGCAACGC
**
1141051 GGAAATGACTATCGCAA--C
1 -GAAATGAAAATCGCAACGC
*
1141069 G--A-GAGAATCGCAACGC
1 GAAATGAAAATCGCAACGC
** *
1141085 GAAATGACTATCGCGAC-C
1 GAAATGAAAATCGCAACGC
*
1141103 ---A-GACAATCGCAACGC
1 GAAATGAAAATCGCAACGC
1141118 GAAATGAAAATCGCAACCGC
1 GAAATGAAAATCGCAA-CGC
*
1141138 GAAATAAAAATCGCAACGC
1 GAAATGAAAATCGCAACGC
** *
1141157 GAAACAAAAATCGCAATGC
1 GAAATGAAAATCGCAACGC
1141176 GA
1 GA
1141178 TTTTTATTTC
Statistics
Matches: 118, Mismatches: 16, Indels: 26
0.74 0.10 0.16
Matches are distributed among these distances:
14 19 0.16
15 3 0.03
16 2 0.02
17 1 0.01
18 4 0.03
19 43 0.36
20 44 0.37
21 2 0.02
ACGTcount: A:0.44, C:0.22, G:0.22, T:0.12
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGC
Found at i:1141189 original size:19 final size:19
Alignment explanation
Indices: 1141167--1141208 Score: 66
Period size: 19 Copynumber: 2.2 Consensus size: 19
1141157 GAAACAAAAA
1141167 TCGCAATGCGATTTTTATT
1 TCGCAATGCGATTTTTATT
* *
1141186 TCGCATTGCGTTTTTTATT
1 TCGCAATGCGATTTTTATT
1141205 TCGC
1 TCGC
1141209 GTTGCGATAG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.14, C:0.19, G:0.17, T:0.50
Consensus pattern (19 bp):
TCGCAATGCGATTTTTATT
Found at i:1141213 original size:19 final size:19
Alignment explanation
Indices: 1141173--1141239 Score: 89
Period size: 19 Copynumber: 3.5 Consensus size: 19
1141163 AAAATCGCAA
*
1141173 TGCGATTTTTATTTCGCAT
1 TGCGATTTTTATTTCGCGT
*
1141192 TGCGTTTTTTATTTCGCGT
1 TGCGATTTTTATTTCGCGT
**
1141211 TGCGATAGTTATTTCTGCGT
1 TGCGATTTTTATTTC-GCGT
1141231 TGCGATTTT
1 TGCGATTTT
1141240 CATTCTCGAA
Statistics
Matches: 40, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
19 29 0.73
20 11 0.28
ACGTcount: A:0.12, C:0.15, G:0.21, T:0.52
Consensus pattern (19 bp):
TGCGATTTTTATTTCGCGT
Found at i:1141781 original size:20 final size:20
Alignment explanation
Indices: 1141756--1141808 Score: 88
Period size: 20 Copynumber: 2.6 Consensus size: 20
1141746 GCGCTATGTA
1141756 AATCGCGTTGCGAAAGTCAG
1 AATCGCGTTGCGAAAGTCAG
1141776 AATCGCGTTGCGAAAGTCAG
1 AATCGCGTTGCGAAAGTCAG
* *
1141796 TATCTCGTTGCGA
1 AATCGCGTTGCGA
1141809 TTTTGTATTA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.26, C:0.21, G:0.28, T:0.25
Consensus pattern (20 bp):
AATCGCGTTGCGAAAGTCAG
Found at i:1141842 original size:20 final size:20
Alignment explanation
Indices: 1141817--1141870 Score: 99
Period size: 20 Copynumber: 2.7 Consensus size: 20
1141807 GATTTTGTAT
1141817 TATCGCATTGCGATAGTAAG
1 TATCGCATTGCGATAGTAAG
*
1141837 TATCGCATTGCGATAGTCAG
1 TATCGCATTGCGATAGTAAG
1141857 TATCGCATTGCGAT
1 TATCGCATTGCGAT
1141871 TTTCCCAATT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.26, C:0.19, G:0.24, T:0.31
Consensus pattern (20 bp):
TATCGCATTGCGATAGTAAG
Found at i:1141855 original size:61 final size:61
Alignment explanation
Indices: 1141757--1141873 Score: 162
Period size: 61 Copynumber: 1.9 Consensus size: 61
1141747 CGCTATGTAA
* * * * *
1141757 ATCGCGTTGCGAAAGTCAGAATCGCGTTGCGAAAGTCAGTATCTCGTTGCGATTTTGTATT
1 ATCGCATTGCGAAAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTTGTATT
* * *
1141818 ATCGCATTGCGATAGTAAGTATCGCATTGCGATAGTCAGTATCGCATTGCGATTTT
1 ATCGCATTGCGAAAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTT
1141874 CCCAATTCGC
Statistics
Matches: 48, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
61 48 1.00
ACGTcount: A:0.24, C:0.18, G:0.25, T:0.33
Consensus pattern (61 bp):
ATCGCATTGCGAAAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTTGTATT
Found at i:1141889 original size:61 final size:61
Alignment explanation
Indices: 1141757--1141891 Score: 155
Period size: 61 Copynumber: 2.2 Consensus size: 61
1141747 CGCTATGTAA
* * * * * ** *
1141757 ATCGCGTTGCGAAAGTCAGAATCGCGTTGCGAAAGTCAGTATCTCGTTGCGATTTTGTATT
1 ATCGCGTTGCGATAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTTCCAAT
* * *
1141818 ATCGCATTGCGATAGTAAGTATCGCATTGCGATAGTCAGTATCGCATTGCGATTTTCCCAAT
1 ATCGCGTTGCGATAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTT-CCAAT
1141880 -TCGCGTTGCGAT
1 ATCGCGTTGCGAT
1141892 TTACTTATTC
Statistics
Matches: 61, Mismatches: 12, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
61 59 0.97
62 2 0.03
ACGTcount: A:0.23, C:0.20, G:0.24, T:0.33
Consensus pattern (61 bp):
ATCGCGTTGCGATAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTTCCAAT
Found at i:1145104 original size:58 final size:59
Alignment explanation
Indices: 1145032--1145142 Score: 154
Period size: 59 Copynumber: 1.9 Consensus size: 59
1145022 ATGATACATC
* *
1145032 GACTATAGAGTATTACTTTGTTAAGT-CACCGACTATCAAAAGTTATAAAATGAACCCT
1 GACTATAGAGTATTACTTTATTAAGTCCACCGACTATCAAAAATTATAAAATGAACCCT
* * *
1145090 GACTATAG-GATATTACTTTATTGAGTCCATCGACTATTAAAAATTATAAAATG
1 GACTATAGAG-TATTACTTTATTAAGTCCACCGACTATCAAAAATTATAAAATG
1145143 GTCACCTAAC
Statistics
Matches: 46, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
57 1 0.02
58 22 0.48
59 23 0.50
ACGTcount: A:0.39, C:0.14, G:0.14, T:0.33
Consensus pattern (59 bp):
GACTATAGAGTATTACTTTATTAAGTCCACCGACTATCAAAAATTATAAAATGAACCCT
Found at i:1145781 original size:35 final size:35
Alignment explanation
Indices: 1145732--1145834 Score: 109
Period size: 35 Copynumber: 2.9 Consensus size: 35
1145722 AAAACAGTCC
* *
1145732 TCAATTTCATTCTAAA-CCTCAAATTCCAAAGTAAG
1 TCAATTTCACTCTAAACCCT-AAATTCCAAAATAAG
*
1145767 TCAATTTCACTCTAAACCCTAAATTCCAAAATAAT
1 TCAATTTCACTCTAAACCCTAAATTCCAAAATAAG
** * * * *
1145802 TCAATTAAATTTTAAACCCCAAATTCTAAAATA
1 TCAATTTCACTCTAAACCCTAAATTCCAAAATA
1145835 CTTCAAATAC
Statistics
Matches: 58, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
35 55 0.95
36 3 0.05
ACGTcount: A:0.44, C:0.22, G:0.02, T:0.32
Consensus pattern (35 bp):
TCAATTTCACTCTAAACCCTAAATTCCAAAATAAG
Found at i:1147501 original size:35 final size:35
Alignment explanation
Indices: 1147453--1147564 Score: 143
Period size: 35 Copynumber: 3.2 Consensus size: 35
1147443 TCTAAACCTT
* * *
1147453 AAATTGAAGTATTTTAGAATTTGGGGTTTAGAATT
1 AAATTGAATTATTTTGGAATTTGGGGTTTAGAATG
* * *
1147488 TAATTGAATTATTTTGGAATTTAGGGTTTAGAGTG
1 AAATTGAATTATTTTGGAATTTGGGGTTTAGAATG
* * *
1147523 AAATTGAATTACTTTGGAATTTGAGGTTTATAATG
1 AAATTGAATTATTTTGGAATTTGGGGTTTAGAATG
1147558 AAATTGA
1 AAATTGA
1147565 GGACTGTTTT
Statistics
Matches: 65, Mismatches: 12, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
35 65 1.00
ACGTcount: A:0.34, C:0.01, G:0.22, T:0.43
Consensus pattern (35 bp):
AAATTGAATTATTTTGGAATTTGGGGTTTAGAATG
Found at i:1148049 original size:19 final size:20
Alignment explanation
Indices: 1148007--1148055 Score: 64
Period size: 19 Copynumber: 2.5 Consensus size: 20
1147997 ATTTGTTTAG
* *
1148007 GTTAATTGAATTTAAGTTGG
1 GTTAATTGAAATTAAGTTGA
*
1148027 GTTAATTTAAATT-AGTTGA
1 GTTAATTGAAATTAAGTTGA
1148046 GTTAATTGAA
1 GTTAATTGAA
1148056 TGTCATACAT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
19 14 0.56
20 11 0.44
ACGTcount: A:0.35, C:0.00, G:0.20, T:0.45
Consensus pattern (20 bp):
GTTAATTGAAATTAAGTTGA
Found at i:1148640 original size:2 final size:2
Alignment explanation
Indices: 1148633--1148658 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1148623 ATTTATCTTT
1148633 TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC
1148659 CACTTATTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:1155340 original size:20 final size:19
Alignment explanation
Indices: 1155219--1155552 Score: 151
Period size: 20 Copynumber: 16.6 Consensus size: 19
1155209 AAATGACCAA
* **
1155219 CAAATTCGCAACGTGATCT
1 CAAATTCGCAACGCGAAGT
* *
1155238 CAAATTCGTAACGCGAACT
1 CAAATTCGCAACGCGAAGT
* * *
1155257 CTAATTTCGCAACTC-AATTT
1 C-AAATTCGCAACGCGAA-GT
1155277 CCAAATTCGCAACGCGAATATGT
1 -CAAATTCGCAACGCG-A-A-GT
* *
1155300 -AAA-TCGTAACACAGAAGT
1 CAAATTCGCAACGC-GAAGT
1155318 CAAATTCGCAACGCGATAGT
1 CAAATTCGCAACGCGA-AGT
**
1155338 CAAATTCGCAATACTGAAGT
1 CAAATTCGCAACGC-GAAGT
*
1155358 CAAATTCGTAACGCGAA-T
1 CAAATTCGCAACGCGAAGT
1155376 CTGTAAA-TCGCAACGCGAATTTGT
1 C---AAATTCGCAACGCGAA---GT
* *
1155400 -AAA-TCGCAACACATAAGT
1 CAAATTCGCAACGC-GAAGT
* *
1155418 CAAATTCGCAATAGAGAAGT
1 CAAATTCGCAA-CGCGAAGT
* * *
1155438 CAAATTCGAAACACTGAATTT
1 CAAATTCGCAACGC-GAA-GT
* *
1155459 CAAATTCGCAACACTGAATTT
1 CAAATTCGCAACGC-GAA-GT
* *
1155480 CAAATTCGCAACACTGAATTT
1 CAAATTCGCAACGC-GAA-GT
* *
1155501 CAAATTCGCAACACTGAATTT
1 CAAATTCGCAACGC-GAA-GT
1155522 CAAATTCGCAACGCGAAAGT
1 CAAATTCGCAACGCG-AAGT
1155542 CAAATTCGCAA
1 CAAATTCGCAA
1155553 AGCGCGTTTA
Statistics
Matches: 256, Mismatches: 34, Indels: 49
0.76 0.10 0.14
Matches are distributed among these distances:
18 6 0.02
19 31 0.12
20 124 0.48
21 90 0.35
22 1 0.00
23 3 0.01
24 1 0.00
ACGTcount: A:0.39, C:0.23, G:0.14, T:0.24
Consensus pattern (19 bp):
CAAATTCGCAACGCGAAGT
Found at i:1155346 original size:80 final size:80
Alignment explanation
Indices: 1155237--1155385 Score: 187
Period size: 80 Copynumber: 1.9 Consensus size: 80
1155227 CAACGTGATC
* * *
1155237 TCAAATTCGTAACGCGAACTCTAATTTCGC-A-ACTCAATTTCCAAATTCGCAACGCGAATATGT
1 TCAAATTCGCAACGCGAACTCTAAATTCGCAATACTCAA-GT-CAAATTCGCAACGCGAATATGT
1155300 AAATCGTAACACAGAAG
64 AAATCGTAACACAGAAG
* * * *
1155317 TCAAATTCGCAACGCGATAGTC-AAATTCGCAATACTGAAGTCAAATTCGTAACGCGAATCTGTA
1 TCAAATTCGCAACGCGA-ACTCTAAATTCGCAATACTCAAGTCAAATTCGCAACGCGAATATGTA
1155381 AATCG
65 AATCG
1155386 CAACGCGAAT
Statistics
Matches: 59, Mismatches: 7, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
80 49 0.83
81 5 0.08
82 5 0.08
ACGTcount: A:0.37, C:0.23, G:0.15, T:0.25
Consensus pattern (80 bp):
TCAAATTCGCAACGCGAACTCTAAATTCGCAATACTCAAGTCAAATTCGCAACGCGAATATGTAA
ATCGTAACACAGAAG
Found at i:1155407 original size:80 final size:81
Alignment explanation
Indices: 1155278--1155538 Score: 252
Period size: 80 Copynumber: 3.2 Consensus size: 81
1155268 ACTCAATTTC
* *
1155278 CAAATTCGCAACGCGAATATGTAAATCGTAACACAGAA---GTCAAATTCGCAACGCGATAGTCA
1 CAAATTCGCAACGCGAAT-TGTAAATCGCAACACAGAATTTGT-AAATTCGCAACACGATAGTCA
1155340 AATTCGCAATACTGAAGT
64 AATTCGCAATACTGAAGT
* *
1155358 CAAATTCGTAACGCGAATCTGTAAATCGCAACGC-GAATTTGTAAA-TCGCAACAC-ATAAGTCA
1 CAAATTCGCAACGCGAAT-TGTAAATCGCAACACAGAATTTGTAAATTCGCAACACGAT-AGTCA
**
1155420 AATTCGCAATAGAGAAGT
64 AATTCGCAATACTGAAGT
* * * * *
1155438 CAAATTCGAAACACTGAATT-TCAAATTCGCAACACTGAATTT-CAAATTCGCAACACTGA-ATT
1 CAAATTCGCAACGC-GAATTGT-AAA-TCGCAACACAGAATTTGTAAATTCGCAACAC-GATA-G
* *
1155500 TCAAATTCGCAACACTGAATTT
61 TCAAATTCGCAATACTGAA-GT
1155522 CAAATTCGCAACGCGAA
1 CAAATTCGCAACGCGAA
1155539 AGTCAAATTC
Statistics
Matches: 150, Mismatches: 18, Indels: 23
0.79 0.09 0.12
Matches are distributed among these distances:
79 6 0.04
80 75 0.50
81 18 0.12
82 18 0.12
83 19 0.13
84 14 0.09
ACGTcount: A:0.40, C:0.22, G:0.15, T:0.23
Consensus pattern (81 bp):
CAAATTCGCAACGCGAATTGTAAATCGCAACACAGAATTTGTAAATTCGCAACACGATAGTCAAA
TTCGCAATACTGAAGT
Found at i:1155463 original size:21 final size:21
Alignment explanation
Indices: 1155337--1155552 Score: 191
Period size: 21 Copynumber: 10.6 Consensus size: 21
1155327 AACGCGATAG
* *
1155337 TCAAATTCGCAATACTGAA-G
1 TCAAATTCGCAACACTGAATT
* *
1155357 TCAAATTCGTAACGC-GAATCT
1 TCAAATTCGCAACACTGAAT-T
*
1155378 GT-AAA-TCGCAACGC-GAATT
1 -TCAAATTCGCAACACTGAATT
* *
1155397 TGTAAA-TCGCAACACAT-AA-G
1 T-CAAATTCGCAACAC-TGAATT
* ** *
1155417 TCAAATTCGCAATAGAGAA-G
1 TCAAATTCGCAACACTGAATT
*
1155437 TCAAATTCGAAACACTGAATT
1 TCAAATTCGCAACACTGAATT
1155458 TCAAATTCGCAACACTGAATT
1 TCAAATTCGCAACACTGAATT
1155479 TCAAATTCGCAACACTGAATT
1 TCAAATTCGCAACACTGAATT
1155500 TCAAATTCGCAACACTGAATT
1 TCAAATTCGCAACACTGAATT
* **
1155521 TCAAATTCGCAACGC-GAAAG
1 TCAAATTCGCAACACTGAATT
1155541 TCAAATTCGCAA
1 TCAAATTCGCAA
1155553 AGCGCGTTTA
Statistics
Matches: 166, Mismatches: 20, Indels: 20
0.81 0.10 0.10
Matches are distributed among these distances:
18 1 0.01
19 7 0.04
20 76 0.46
21 81 0.49
22 1 0.01
ACGTcount: A:0.40, C:0.22, G:0.14, T:0.25
Consensus pattern (21 bp):
TCAAATTCGCAACACTGAATT
Found at i:1155737 original size:22 final size:22
Alignment explanation
Indices: 1155712--1155769 Score: 77
Period size: 22 Copynumber: 2.7 Consensus size: 22
1155702 CTACGGCGAC
1155712 ATCCGTCCCTATCTCCGACGAA
1 ATCCGTCCCTATCTCCGACGAA
*
1155734 ATCCGTTCCC-ATCTCCGGCGAA
1 ATCCG-TCCCTATCTCCGACGAA
1155756 ATCCGT--CTATCTCC
1 ATCCGTCCCTATCTCC
1155770 ATCTCTCAGA
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
19 1 0.03
20 6 0.18
21 1 0.03
22 21 0.64
23 4 0.12
ACGTcount: A:0.19, C:0.41, G:0.14, T:0.26
Consensus pattern (22 bp):
ATCCGTCCCTATCTCCGACGAA
Found at i:1156199 original size:20 final size:20
Alignment explanation
Indices: 1156148--1156199 Score: 59
Period size: 20 Copynumber: 2.6 Consensus size: 20
1156138 ATTGCAATGC
*
1156148 AATTTTAGTTTCGCGTTGCG
1 AATTTAAGTTTCGCGTTGCG
* * * *
1156168 ATTTTCATTTTCGCGTTGTG
1 AATTTAAGTTTCGCGTTGCG
1156188 AATTTAAGTTTC
1 AATTTAAGTTTC
1156200 AAAAACTACT
Statistics
Matches: 25, Mismatches: 7, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.17, C:0.13, G:0.19, T:0.50
Consensus pattern (20 bp):
AATTTAAGTTTCGCGTTGCG
Found at i:1158328 original size:64 final size:64
Alignment explanation
Indices: 1158202--1158337 Score: 157
Period size: 64 Copynumber: 2.1 Consensus size: 64
1158192 CAAGGTGTAC
* * * ** *
1158202 CGATGCACATGAAGTGCATCGATGCACTCTTTTAAAATACAAACATCGAATTCCATCAATGCAT
1 CGATGCATAAGAAGTGCATCGATGCACCCCCTTAAAATACAAACATCGAATACCATCAATGCAT
* ** **
1158266 CGATGCATAAGAAGTGCATCGATGCACCCCCCTT-AAATATAAACATCGAATAGGATTTATGCAT
1 CGATGCATAAGAAGTGCATCGATGCA-CCCCCTTAAAATACAAACATCGAATACCATCAATGCAT
1158330 CGATGCAT
1 CGATGCAT
1158338 GGTGTGGTGC
Statistics
Matches: 60, Mismatches: 11, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
64 56 0.93
65 4 0.07
ACGTcount: A:0.35, C:0.23, G:0.16, T:0.26
Consensus pattern (64 bp):
CGATGCATAAGAAGTGCATCGATGCACCCCCTTAAAATACAAACATCGAATACCATCAATGCAT
Found at i:1158651 original size:25 final size:25
Alignment explanation
Indices: 1158596--1158657 Score: 72
Period size: 25 Copynumber: 2.4 Consensus size: 25
1158586 ATAAGTCTAG
*
1158596 ATTCAATATTTTGATACATGATCACA
1 ATTC-ATATTATGATACATGATCACA
* *
1158622 TTTCATATTATGATACATGA-CATGA
1 ATTCATATTATGATACATGATCA-CA
1158647 ATTCATATTAT
1 ATTCATATTAT
1158658 ATGCATTAAG
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
24 2 0.06
25 26 0.84
26 3 0.10
ACGTcount: A:0.37, C:0.13, G:0.08, T:0.42
Consensus pattern (25 bp):
ATTCATATTATGATACATGATCACA
Found at i:1159008 original size:21 final size:21
Alignment explanation
Indices: 1158982--1159024 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
1158972 GCACTACGGT
1158982 GCAATTCTACGCGGCACTTCG
1 GCAATTCTACGCGGCACTTCG
*
1159003 GCAATTCTACGTGGCACTTCG
1 GCAATTCTACGCGGCACTTCG
1159024 G
1 G
1159025 TGCATTTATA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.19, C:0.30, G:0.26, T:0.26
Consensus pattern (21 bp):
GCAATTCTACGCGGCACTTCG
Found at i:1165109 original size:19 final size:19
Alignment explanation
Indices: 1165085--1165130 Score: 74
Period size: 19 Copynumber: 2.4 Consensus size: 19
1165075 CAAGGTGTAC
1165085 CGATGCACATGAAGTGCAT
1 CGATGCACATGAAGTGCAT
*
1165104 CGATGCATATGAAGTGCAT
1 CGATGCACATGAAGTGCAT
*
1165123 CAATGCAC
1 CGATGCAC
1165131 TCTTTTAAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.33, C:0.22, G:0.24, T:0.22
Consensus pattern (19 bp):
CGATGCACATGAAGTGCAT
Found at i:1165933 original size:23 final size:23
Alignment explanation
Indices: 1165882--1165943 Score: 79
Period size: 23 Copynumber: 2.7 Consensus size: 23
1165872 ACAATCTTAT
*
1165882 ATGGCACTACGGTGCAATTCTAC
1 ATGGCACTTCGGTGCAATTCTAC
* *
1165905 ACGGCACTTCGGTGCAATTCTAT
1 ATGGCACTTCGGTGCAATTCTAC
* *
1165928 TTGGCATTTCGGTGCA
1 ATGGCACTTCGGTGCA
1165944 TTTATACGAG
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.21, C:0.24, G:0.24, T:0.31
Consensus pattern (23 bp):
ATGGCACTTCGGTGCAATTCTAC
Found at i:1167116 original size:63 final size:63
Alignment explanation
Indices: 1167049--1167168 Score: 154
Period size: 63 Copynumber: 1.9 Consensus size: 63
1167039 AGGTCGATAC
* * * *
1167049 TTTACGTGAAGACAATGGTGC-ATGGCGTGATGAGGTATGGT-CTTTACGTGGTGAGGTGGATGT
1 TTTACGCGAAGACAATGGTGCGAT-ACGTGATGAGGTAT-CTACTTTACGTGATGAGGTGGATGT
* *
1167112 TTTACGCGATGACAATGGTGCGCTACGTGATGAGGTATCTACTTTACGTGATGAGGT
1 TTTACGCGAAGACAATGGTGCGATACGTGATGAGGTATCTACTTTACGTGATGAGGT
1167169 AGCCGCTCTA
Statistics
Matches: 49, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
62 1 0.02
63 47 0.96
64 1 0.02
ACGTcount: A:0.22, C:0.12, G:0.34, T:0.32
Consensus pattern (63 bp):
TTTACGCGAAGACAATGGTGCGATACGTGATGAGGTATCTACTTTACGTGATGAGGTGGATGT
Found at i:1167180 original size:21 final size:21
Alignment explanation
Indices: 1167134--1167183 Score: 64
Period size: 21 Copynumber: 2.4 Consensus size: 21
1167124 CAATGGTGCG
* *
1167134 CTACGTGATGAGGTATCTACT
1 CTACGTGATGAGGTAGCCACT
* *
1167155 TTACGTGATGAGGTAGCCGCT
1 CTACGTGATGAGGTAGCCACT
1167176 CTACGTGA
1 CTACGTGA
1167184 GATTGTTTCA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.22, C:0.20, G:0.28, T:0.30
Consensus pattern (21 bp):
CTACGTGATGAGGTAGCCACT
Found at i:1167513 original size:42 final size:42
Alignment explanation
Indices: 1167466--1167584 Score: 138
Period size: 42 Copynumber: 2.8 Consensus size: 42
1167456 GATTCACCTG
* *
1167466 TCATCGTTCAAGAGGCGCCTCCTATCA-TTCAAGAGG-CTCATC
1 TCATCGTTCAAGAGGCCCCTCCCA-CAGTTCAAGAGGCCTC-TC
*
1167508 TCATCGTTCAAGAGGCCCCTCCCACAGTTCAAGAGGCCTCTG
1 TCATCGTTCAAGAGGCCCCTCCCACAGTTCAAGAGGCCTCTC
*
1167550 TCATCGTTCAATG-GGTCCCTCCCATC-GTTCAAGAG
1 TCATCGTTCAA-GAGGCCCCTCCCA-CAGTTCAAGAG
1167585 CCCGATTCAC
Statistics
Matches: 69, Mismatches: 4, Indels: 8
0.85 0.05 0.10
Matches are distributed among these distances:
41 2 0.03
42 62 0.90
43 5 0.07
ACGTcount: A:0.22, C:0.33, G:0.20, T:0.25
Consensus pattern (42 bp):
TCATCGTTCAAGAGGCCCCTCCCACAGTTCAAGAGGCCTCTC
Found at i:1167558 original size:21 final size:21
Alignment explanation
Indices: 1167466--1167584 Score: 97
Period size: 21 Copynumber: 5.7 Consensus size: 21
1167456 GATTCACCTG
1167466 TCATCGTTCAAGAGGCGC-CTC
1 TCATCGTTCAAGAGGC-CTCTC
*
1167487 -CTATCATTCAAGAGG-CTCATC
1 TC-ATCGTTCAAGAGGCCTC-TC
*
1167508 TCATCGTTCAAGAGGCCCCTC
1 TCATCGTTCAAGAGGCCTCTC
* *
1167529 CCA-CAGTTCAAGAGGCCTCTG
1 TCATC-GTTCAAGAGGCCTCTC
1167550 TCATCGTTCAATG-GGTCC-CTC
1 TCATCGTTCAA-GAGG-CCTCTC
*
1167571 CCATCGTTCAAGAG
1 TCATCGTTCAAGAG
1167585 CCCGATTCAC
Statistics
Matches: 79, Mismatches: 9, Indels: 20
0.73 0.08 0.19
Matches are distributed among these distances:
19 1 0.01
20 4 0.05
21 67 0.85
22 7 0.09
ACGTcount: A:0.22, C:0.33, G:0.20, T:0.25
Consensus pattern (21 bp):
TCATCGTTCAAGAGGCCTCTC
Found at i:1169530 original size:24 final size:24
Alignment explanation
Indices: 1169481--1169530 Score: 57
Period size: 24 Copynumber: 2.1 Consensus size: 24
1169471 CCGAGTATTA
* *
1169481 ACCAAGATCAAAGTTCAGGTATTG
1 ACCAAGATCAAAGTTCAGATACTG
*
1169505 ACCAAGATCAAATTTC-GAATACTG
1 ACCAAGATCAAAGTTCAG-ATACTG
1169529 AC
1 AC
1169531 TAGTACTCAC
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
23 1 0.05
24 21 0.95
ACGTcount: A:0.40, C:0.20, G:0.16, T:0.24
Consensus pattern (24 bp):
ACCAAGATCAAAGTTCAGATACTG
Found at i:1170281 original size:16 final size:16
Alignment explanation
Indices: 1170259--1170298 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
1170249 GAAATCATTG
*
1170259 AAAAATTATATAGAAA
1 AAAAATTATATAAAAA
* *
1170275 TAAAATTATGTAAAAA
1 AAAAATTATATAAAAA
1170291 AAAAATTA
1 AAAAATTA
1170299 GAGATGAGGA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.68, C:0.00, G:0.05, T:0.28
Consensus pattern (16 bp):
AAAAATTATATAAAAA
Done.