Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D05
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: 64368997
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1610000 characters in sequence are not A, C, G, or T
File 127 of 208
Found at i:41777607 original size:46 final size:45
Alignment explanation
Indices: 41777556--41777653 Score: 160
Period size: 46 Copynumber: 2.2 Consensus size: 45
41777546 TTAAAAATTT
*
41777556 AAATTAAGTCAAGCATTTGTTATAGTTTAATAAATTAATACAAACA
1 AAATTAAGTCAAGCATTTGTTATAATTTAATAAATTAATACAAA-A
* *
41777602 AAATTAAGTCAAGCATTTTTTATAATTTAATAAATTAATTCAAAA
1 AAATTAAGTCAAGCATTTGTTATAATTTAATAAATTAATACAAAA
41777647 AAATTAA
1 AAATTAA
41777654 CACAATCTTG
Statistics
Matches: 49, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
45 8 0.16
46 41 0.84
ACGTcount: A:0.50, C:0.07, G:0.06, T:0.37
Consensus pattern (45 bp):
AAATTAAGTCAAGCATTTGTTATAATTTAATAAATTAATACAAAA
Found at i:41784820 original size:29 final size:29
Alignment explanation
Indices: 41784786--41784847 Score: 124
Period size: 29 Copynumber: 2.1 Consensus size: 29
41784776 TAGGTTTATG
41784786 CTTTTGAAGTTTATGTTTGGTTTGATGAA
1 CTTTTGAAGTTTATGTTTGGTTTGATGAA
41784815 CTTTTGAAGTTTATGTTTGGTTTGATGAA
1 CTTTTGAAGTTTATGTTTGGTTTGATGAA
41784844 CTTT
1 CTTT
41784848 GGAGCTTTGA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 33 1.00
ACGTcount: A:0.19, C:0.05, G:0.23, T:0.53
Consensus pattern (29 bp):
CTTTTGAAGTTTATGTTTGGTTTGATGAA
Found at i:41789526 original size:26 final size:26
Alignment explanation
Indices: 41789468--41789526 Score: 64
Period size: 26 Copynumber: 2.2 Consensus size: 26
41789458 CCACCATAAA
*
41789468 AATTTGAAGCAAATAACCCATTTCGAT
1 AATTT-AAGCAAACAACCCATTTCGAT
** * *
41789495 TTTTTAAGCAAACAATCCATTTCGGT
1 AATTTAAGCAAACAACCCATTTCGAT
41789521 AATTTA
1 AATTTA
41789527 TTTCTACCAA
Statistics
Matches: 25, Mismatches: 7, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
26 22 0.88
27 3 0.12
ACGTcount: A:0.37, C:0.17, G:0.10, T:0.36
Consensus pattern (26 bp):
AATTTAAGCAAACAACCCATTTCGAT
Found at i:41789730 original size:9 final size:10
Alignment explanation
Indices: 41789704--41789729 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
41789694 CTAGTTAATT
41789704 AAAAAAACAA
1 AAAAAAACAA
41789714 AAAAAAACAA
1 AAAAAAACAA
41789724 AAAAAA
1 AAAAAA
41789730 CTAATGTTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.92, C:0.08, G:0.00, T:0.00
Consensus pattern (10 bp):
AAAAAAACAA
Found at i:41791837 original size:28 final size:29
Alignment explanation
Indices: 41791797--41791856 Score: 79
Period size: 28 Copynumber: 2.1 Consensus size: 29
41791787 ATTTAATTTT
*
41791797 AATTTTAATTAAATAAATAA-AAATAATTA
1 AATTCTAATTAAA-AAATAACAAATAATTA
*
41791826 AATTCTAA-TAAAAAATAACATATAATTA
1 AATTCTAATTAAAAAATAACAAATAATTA
41791854 AAT
1 AAT
41791857 GAAGGTAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
27 6 0.21
28 15 0.54
29 7 0.25
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.35
Consensus pattern (29 bp):
AATTCTAATTAAAAAATAACAAATAATTA
Found at i:41792303 original size:84 final size:84
Alignment explanation
Indices: 41792144--41792302 Score: 221
Period size: 84 Copynumber: 1.9 Consensus size: 84
41792134 TAGGAGATCT
* * * *
41792144 AAAGTATAATTTTACTATATATTAATGAATAATTTCTTTATTTATAAGAGGATTAAATTGAAAAT
1 AAAGTATAATTTCACTACATATTAATGAATAATTTCTCTATTTATAAGAGGACTAAATTGAAAAT
* *
41792209 TTTTTATTTTTAAGGGGCC
66 GTTTCATTTTTAAGGGGCC
* ** *
41792228 AAAGTGTAATTTCACTACATATTAATTTATAGTTTCTCTATTTATAAGAGGACTAAATTG-AAAT
1 AAAGTATAATTTCACTACATATTAATGAATAATTTCTCTATTTATAAGAGGACTAAATTGAAAAT
41792292 GTTTCATTTTT
66 GTTTCATTTTT
41792303 TTTGGGGTAA
Statistics
Matches: 65, Mismatches: 10, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
83 13 0.20
84 52 0.80
ACGTcount: A:0.36, C:0.07, G:0.11, T:0.45
Consensus pattern (84 bp):
AAAGTATAATTTCACTACATATTAATGAATAATTTCTCTATTTATAAGAGGACTAAATTGAAAAT
GTTTCATTTTTAAGGGGCC
Found at i:41794130 original size:46 final size:46
Alignment explanation
Indices: 41794063--41794170 Score: 191
Period size: 46 Copynumber: 2.3 Consensus size: 46
41794053 CGCCGTTTTA
*
41794063 ACAAGATCTACTATCTACGATCTACT-CTGCTGCCAAATACAGGAAG
1 ACAAGATCTGCTATCTACGATCTACTCCT-CTGCCAAATACAGGAAG
41794109 ACAAGATCTGCTATCTACGATCTACTCCTCTGCCAAATACAGGAAG
1 ACAAGATCTGCTATCTACGATCTACTCCTCTGCCAAATACAGGAAG
41794155 ACAAGATCTGCTATCT
1 ACAAGATCTGCTATCT
41794171 TTAATTTGTT
Statistics
Matches: 60, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
46 58 0.97
47 2 0.03
ACGTcount: A:0.33, C:0.27, G:0.15, T:0.25
Consensus pattern (46 bp):
ACAAGATCTGCTATCTACGATCTACTCCTCTGCCAAATACAGGAAG
Found at i:41794680 original size:24 final size:24
Alignment explanation
Indices: 41794625--41794682 Score: 64
Period size: 24 Copynumber: 2.4 Consensus size: 24
41794615 CGGATTGCCC
41794625 CCACTGTAATCTTCAGAGTTCAAT
1 CCACTGTAATCTTCAGAGTTCAAT
*** *
41794649 CTGTTGTAATCTTCA-AGGTTCAGT
1 CCACTGTAATCTTCAGA-GTTCAAT
41794673 CCACTGTAAT
1 CCACTGTAAT
41794683 TTTGGGACAT
Statistics
Matches: 26, Mismatches: 7, Indels: 2
0.74 0.20 0.06
Matches are distributed among these distances:
23 1 0.04
24 25 0.96
ACGTcount: A:0.26, C:0.22, G:0.16, T:0.36
Consensus pattern (24 bp):
CCACTGTAATCTTCAGAGTTCAAT
Found at i:41795694 original size:20 final size:20
Alignment explanation
Indices: 41795669--41795728 Score: 79
Period size: 20 Copynumber: 3.0 Consensus size: 20
41795659 CCTAGGCTTC
41795669 TCATTTTTCTTTTTCTTCTTT
1 TCATTTTTCTTTTT-TTCTTT
*
41795690 T-A-TTTTCTTTTTTCCTTT
1 TCATTTTTCTTTTTTTCTTT
*
41795708 TCTTTTTTCTTTTTTTCTTT
1 TCATTTTTCTTTTTTTCTTT
41795728 T
1 T
41795729 TTTCTTTTTT
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
18 6 0.18
19 10 0.29
20 17 0.50
21 1 0.03
ACGTcount: A:0.03, C:0.17, G:0.00, T:0.80
Consensus pattern (20 bp):
TCATTTTTCTTTTTTTCTTT
Found at i:41795697 original size:13 final size:12
Alignment explanation
Indices: 41795672--41795742 Score: 76
Period size: 13 Copynumber: 5.8 Consensus size: 12
41795662 AGGCTTCTCA
41795672 TTTTTCTTTTTCT
1 TTTTTC-TTTTCT
*
41795685 TCTTTTATTTTCT
1 T-TTTTCTTTTCT
41795698 TTTTTCCTTTTCT
1 TTTTT-CTTTTCT
41795711 TTTTTCTTTT-T
1 TTTTTCTTTTCT
41795722 TTCTTT-TTTTCT
1 TT-TTTCTTTTCT
41795734 TTTTT-TTTT
1 TTTTTCTTTT
41795743 AACATTTTTT
Statistics
Matches: 52, Mismatches: 2, Indels: 10
0.81 0.03 0.16
Matches are distributed among these distances:
11 14 0.27
12 15 0.29
13 19 0.37
14 4 0.08
ACGTcount: A:0.01, C:0.14, G:0.00, T:0.85
Consensus pattern (12 bp):
TTTTTCTTTTCT
Found at i:41795708 original size:7 final size:7
Alignment explanation
Indices: 41795672--41795742 Score: 69
Period size: 7 Copynumber: 10.4 Consensus size: 7
41795662 AGGCTTCTCA
41795672 TTTTTC-
1 TTTTTCT
41795678 TTTTTCT
1 TTTTTCT
*
41795685 TCTTT-T
1 TTTTTCT
*
41795691 ATTTTCT
1 TTTTTCT
41795698 TTTTTC-
1 TTTTTCT
*
41795704 CTTTTCT
1 TTTTTCT
41795711 TTTTTCTT
1 TTTTTC-T
41795719 TTTTTCTT
1 TTTTTC-T
41795727 TTTTTCT
1 TTTTTCT
41795734 TTTTT-T
1 TTTTTCT
41795740 TTT
1 TTT
41795743 AACATTTTTT
Statistics
Matches: 55, Mismatches: 6, Indels: 8
0.80 0.09 0.12
Matches are distributed among these distances:
6 19 0.35
7 21 0.38
8 15 0.27
ACGTcount: A:0.01, C:0.14, G:0.00, T:0.85
Consensus pattern (7 bp):
TTTTTCT
Found at i:41795739 original size:8 final size:8
Alignment explanation
Indices: 41795672--41795739 Score: 72
Period size: 8 Copynumber: 8.6 Consensus size: 8
41795662 AGGCTTCTCA
41795672 TTTTTCTT
1 TTTTTCTT
41795680 TTTCTTCTT
1 TTT-TTCTT
41795689 TTATTT-TCT
1 TT-TTTCT-T
41795698 TTTTTC--
1 TTTTTCTT
*
41795704 CTTTTC-T
1 TTTTTCTT
41795711 TTTTTCTT
1 TTTTTCTT
41795719 TTTTTCTT
1 TTTTTCTT
41795727 TTTTTCTT
1 TTTTTCTT
41795735 TTTTT
1 TTTTT
41795740 TTTAACATTT
Statistics
Matches: 52, Mismatches: 2, Indels: 12
0.79 0.03 0.18
Matches are distributed among these distances:
6 5 0.10
7 5 0.10
8 29 0.56
9 12 0.23
10 1 0.02
ACGTcount: A:0.01, C:0.15, G:0.00, T:0.84
Consensus pattern (8 bp):
TTTTTCTT
Found at i:41795740 original size:20 final size:20
Alignment explanation
Indices: 41795678--41795742 Score: 78
Period size: 20 Copynumber: 3.2 Consensus size: 20
41795668 CTCATTTTTC
*
41795678 TTTTTCTTCTTTTATTTTCTT
1 TTTTTCTT-TTTTTTTTTCTT
* *
41795699 TTTTCCTTTTCTTTTTTCTT
1 TTTTTCTTTTTTTTTTTCTT
41795719 TTTTTCTTTTTTTCTTTT-TT
1 TTTTTCTTTTTTT-TTTTCTT
41795739 TTTT
1 TTTT
41795743 AACATTTTTT
Statistics
Matches: 38, Mismatches: 5, Indels: 3
0.83 0.11 0.07
Matches are distributed among these distances:
20 27 0.71
21 11 0.29
ACGTcount: A:0.02, C:0.14, G:0.00, T:0.85
Consensus pattern (20 bp):
TTTTTCTTTTTTTTTTTCTT
Found at i:41795751 original size:28 final size:28
Alignment explanation
Indices: 41795672--41795742 Score: 85
Period size: 26 Copynumber: 2.6 Consensus size: 28
41795662 AGGCTTCTCA
* *
41795672 TTTTTCTTTTTCTTCTTT-TA-TTTTCT
1 TTTTTCCTTTTCTTTTTTCTATTTTTCT
*
41795698 TTTTTCCTTTTCTTTTTTCTTTTTTTCT
1 TTTTTCCTTTTCTTTTTTCTATTTTTCT
*
41795726 TTTTTTCTTTT-TTTTTT
1 TTTTTCCTTTTCTTTTTT
41795743 AACATTTTTT
Statistics
Matches: 39, Mismatches: 4, Indels: 3
0.85 0.09 0.07
Matches are distributed among these distances:
26 16 0.41
27 7 0.18
28 16 0.41
ACGTcount: A:0.01, C:0.14, G:0.00, T:0.85
Consensus pattern (28 bp):
TTTTTCCTTTTCTTTTTTCTATTTTTCT
Found at i:41798068 original size:12 final size:12
Alignment explanation
Indices: 41798037--41798070 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
41798027 CTTTTCTAGT
41798037 TGTTCTTGCATC
1 TGTTCTTGCATC
**
41798049 TGGGCTTGCATC
1 TGTTCTTGCATC
41798061 TGTTCTTGCA
1 TGTTCTTGCA
41798071 ATTGCTCTAA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.09, C:0.24, G:0.24, T:0.44
Consensus pattern (12 bp):
TGTTCTTGCATC
Found at i:41798236 original size:19 final size:20
Alignment explanation
Indices: 41798212--41798258 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 20
41798202 TGTGAAAATC
*
41798212 TAATGCATATG-ATGCAATG
1 TAATGCAAATGCATGCAATG
*
41798231 TAATGCAAATGCATGGAATG
1 TAATGCAAATGCATGCAATG
41798251 -AATGCAAA
1 TAATGCAAA
41798259 AAGAAAGAGA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 18 0.72
20 7 0.28
ACGTcount: A:0.43, C:0.11, G:0.21, T:0.26
Consensus pattern (20 bp):
TAATGCAAATGCATGCAATG
Found at i:41804158 original size:18 final size:18
Alignment explanation
Indices: 41804137--41804172 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
41804127 TATTACAAGA
41804137 TTATGACACACTTATAAT
1 TTATGACACACTTATAAT
41804155 TTATGACACACTTATAAT
1 TTATGACACACTTATAAT
41804173 GTAGGTGAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.39, C:0.17, G:0.06, T:0.39
Consensus pattern (18 bp):
TTATGACACACTTATAAT
Found at i:41813076 original size:50 final size:49
Alignment explanation
Indices: 41813013--41813200 Score: 187
Period size: 50 Copynumber: 3.8 Consensus size: 49
41813003 AAAGTGATGG
* **
41813013 TCACGTGTGTAGTACTATGTGTAGGCTACTACGTGTACCGGAACGAAAGA
1 TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGAA-GTTAGA
* * * * * *
41813063 TCGCATGTGTAGTACTATGTGCAGGCTACTATGCGTATCGGATAGCTTCGA
1 TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGA-AG-TTAGA
* * * * *
41813114 TCATGTGTGTAGTACTATGTGCAGGCTACTACGTGAACTAGAAAGTTTGA
1 TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTAC-CGGAAGTTAGA
* * *
41813164 TCTCGTATGTAGTACTATGTGAAGGCTACTACGTGTA
1 TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTA
41813201 TCAAATAATA
Statistics
Matches: 111, Mismatches: 24, Indels: 6
0.79 0.17 0.04
Matches are distributed among these distances:
50 73 0.66
51 36 0.32
52 2 0.02
ACGTcount: A:0.26, C:0.17, G:0.27, T:0.31
Consensus pattern (49 bp):
TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGAAGTTAGA
Found at i:41813202 original size:101 final size:101
Alignment explanation
Indices: 41813017--41813202 Score: 246
Period size: 101 Copynumber: 1.8 Consensus size: 101
41813007 TGATGGTCAC
* * * * *
41813017 GTGTGTAGTACTATGTGTAGGCTACTACGTGTACCGGAACGAAAGATCGCATGTGTAGTACTATG
1 GTGTGTAGTACTATGTGCAGGCTACTACGTGAACCAGAAAGAAAGATCGCATATGTAGTACTATG
* *
41813082 TGCAGGCTACTATGCGTATCGGATAGCTTCGATCAT
66 TGAAGGCTACTACGCGTATCGGATAGCTTCGATCAT
* *** * *
41813118 GTGTGTAGTACTATGTGCAGGCTACTACGTGAACTAGAAAGTTTGATCTCGTATGTAGTACTATG
1 GTGTGTAGTACTATGTGCAGGCTACTACGTGAACCAGAAAGAAAGATCGCATATGTAGTACTATG
*
41813183 TGAAGGCTACTACGTGTATC
66 TGAAGGCTACTACGCGTATC
41813203 AAATAATAAT
Statistics
Matches: 71, Mismatches: 14, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
101 71 1.00
ACGTcount: A:0.25, C:0.17, G:0.27, T:0.31
Consensus pattern (101 bp):
GTGTGTAGTACTATGTGCAGGCTACTACGTGAACCAGAAAGAAAGATCGCATATGTAGTACTATG
TGAAGGCTACTACGCGTATCGGATAGCTTCGATCAT
Found at i:41816905 original size:15 final size:16
Alignment explanation
Indices: 41816882--41816914 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
41816872 GAATCGATTG
*
41816882 TTTATTTTGTTTGTGT
1 TTTATTTTGTTTATGT
41816898 TTTA-TTTGTTTATGT
1 TTTATTTTGTTTATGT
41816913 TT
1 TT
41816915 ACACAACATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 12 0.75
16 4 0.25
ACGTcount: A:0.09, C:0.00, G:0.15, T:0.76
Consensus pattern (16 bp):
TTTATTTTGTTTATGT
Found at i:41824381 original size:20 final size:20
Alignment explanation
Indices: 41824343--41824381 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
41824333 TTAACTTAGT
*
41824343 CCAGCTCACTCGAGCTCAAG
1 CCAGCTCACTCGAGATCAAG
* *
41824363 CCAGCTCATTTGAGATCAA
1 CCAGCTCACTCGAGATCAA
41824382 TTCAGCTCAA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.28, C:0.33, G:0.18, T:0.21
Consensus pattern (20 bp):
CCAGCTCACTCGAGATCAAG
Found at i:41828524 original size:20 final size:22
Alignment explanation
Indices: 41828499--41828551 Score: 65
Period size: 20 Copynumber: 2.5 Consensus size: 22
41828489 GAATCATGTA
41828499 GGTATCAATACTAAT-ACA-AT
1 GGTATCAATACTAATCACATAT
* * *
41828519 GGTATCAATATTTATCATATAT
1 GGTATCAATACTAATCACATAT
41828541 GGTATCAATAC
1 GGTATCAATAC
41828552 CGATAAAAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
20 13 0.48
21 2 0.07
22 12 0.44
ACGTcount: A:0.40, C:0.13, G:0.11, T:0.36
Consensus pattern (22 bp):
GGTATCAATACTAATCACATAT
Found at i:41831575 original size:20 final size:20
Alignment explanation
Indices: 41831550--41831591 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
41831540 AATATAATTG
*
41831550 TTATTTGCTTCT-ATAACATT
1 TTATTTACTTCTCA-AACATT
41831570 TTATTTACTTCTCAAACATT
1 TTATTTACTTCTCAAACATT
41831590 TT
1 TT
41831592 CATTCCCCTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 19 0.95
21 1 0.05
ACGTcount: A:0.26, C:0.17, G:0.02, T:0.55
Consensus pattern (20 bp):
TTATTTACTTCTCAAACATT
Found at i:41835980 original size:14 final size:16
Alignment explanation
Indices: 41835961--41835993 Score: 52
Period size: 14 Copynumber: 2.2 Consensus size: 16
41835951 GGCAACCCAT
41835961 ATTTATTT-ATTTT-A
1 ATTTATTTAATTTTGA
41835975 ATTTATTTAATTTTGA
1 ATTTATTTAATTTTGA
41835991 ATT
1 ATT
41835994 AAGTTTAGAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 8 0.47
15 5 0.29
16 4 0.24
ACGTcount: A:0.30, C:0.00, G:0.03, T:0.67
Consensus pattern (16 bp):
ATTTATTTAATTTTGA
Found at i:41839237 original size:18 final size:18
Alignment explanation
Indices: 41839193--41839237 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 18
41839183 AAATTGCTAC
41839193 TAGTT-AAATTAATTAAT
1 TAGTTAAAATTAATTAAT
*
41839210 TAGTTTAAATTAATTAATT
1 TAGTTAAAATTAATTAA-T
41839229 TA-TTAAAAT
1 TAGTTAAAAT
41839238 CTGGACATAT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
17 5 0.20
18 17 0.68
19 3 0.12
ACGTcount: A:0.47, C:0.00, G:0.04, T:0.49
Consensus pattern (18 bp):
TAGTTAAAATTAATTAAT
Found at i:41842303 original size:33 final size:33
Alignment explanation
Indices: 41842266--41842331 Score: 132
Period size: 33 Copynumber: 2.0 Consensus size: 33
41842256 GCTGGAATAG
41842266 TTAATGCATATGTTTAGTTTATTTACCTAAGTT
1 TTAATGCATATGTTTAGTTTATTTACCTAAGTT
41842299 TTAATGCATATGTTTAGTTTATTTACCTAAGTT
1 TTAATGCATATGTTTAGTTTATTTACCTAAGTT
41842332 AAGTATTTAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.27, C:0.09, G:0.12, T:0.52
Consensus pattern (33 bp):
TTAATGCATATGTTTAGTTTATTTACCTAAGTT
Found at i:41850792 original size:28 final size:28
Alignment explanation
Indices: 41850729--41850854 Score: 200
Period size: 28 Copynumber: 4.5 Consensus size: 28
41850719 ATATTAAGTC
* *
41850729 CGCACACTCAGTGCTATATAATC-AACT
1 CGCACACTTAGTGCTACATAATCAAACT
*
41850756 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTACATAATCAAACT
*
41850784 CGCACACTTAGTGCTACATAATCAAGCT
1 CGCACACTTAGTGCTACATAATCAAACT
*
41850812 CGCACACTTAGTGCTACATAATCAAGCT
1 CGCACACTTAGTGCTACATAATCAAACT
41850840 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
41850855 GTACAATTTA
Statistics
Matches: 95, Mismatches: 3, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
27 22 0.23
28 73 0.77
ACGTcount: A:0.32, C:0.29, G:0.13, T:0.26
Consensus pattern (28 bp):
CGCACACTTAGTGCTACATAATCAAACT
Found at i:41853670 original size:39 final size:39
Alignment explanation
Indices: 41853614--41853839 Score: 187
Period size: 39 Copynumber: 5.7 Consensus size: 39
41853604 TTGAATGATG
*
41853614 TCCGGGCTAAG-TCCCGAAGGC-TTGTGCTAAG-TGAC-AATA
1 TCCGGACTAAGAT-CCGAAGGCATTGTGC-AAGAT-ACTAA-A
*
41853653 TCCGGACTAAGATCCGAAGGCATTTGTGCGAGATACTAAA
1 TCCGGACTAAGATCCGAAGGCA-TTGTGCAAGATACTAAA
* *
41853693 TCCGGACTAAGATCCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGACTAAGATCCGAAGGCA-TTGTGCAAGATACTAAA
* * * *
41853733 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGACTAAGATCCGAAGGCA-TTGTGCAAGATACTAAA
* * * *
41853772 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGACTAAGATCCGAAGGCA-TTGTGCAAGATACTAAA
**
41853811 TCCGGGTTAAG-TCCCGAAGGCATTTGTGC
1 TCCGGACTAAGAT-CCGAAGGCA-TTGTGC
41853840 GAATTACTAT
Statistics
Matches: 172, Mismatches: 9, Indels: 11
0.90 0.05 0.06
Matches are distributed among these distances:
39 92 0.53
40 71 0.41
41 9 0.05
ACGTcount: A:0.27, C:0.22, G:0.27, T:0.24
Consensus pattern (39 bp):
TCCGGACTAAGATCCGAAGGCATTGTGCAAGATACTAAA
Found at i:41853702 original size:40 final size:39
Alignment explanation
Indices: 41853614--41853876 Score: 304
Period size: 40 Copynumber: 6.6 Consensus size: 39
41853604 TTGAATGATG
*
41853614 TCCGGGCTAAGTCCCGAAGGC--TTGTGCTA-AGTGAC-AATA
1 TCCGGGCTAAGT-CCGAAGGCATTTGTGCGAGA-T-ACTAA-A
*
41853653 TCCGGACTAAGATCCGAAGGCATTTGTGCGAGATACTAAA
1 TCCGGGCTAAG-TCCGAAGGCATTTGTGCGAGATACTAAA
* *
41853693 TCCGGACTAAGATCCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAG-TCCGAAGGCATTTGTGCGAGATACTAAA
* *
41853733 TCCGGGCTAAGCCCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAGTCCGAAGGCATTTGTGCGAGATACTAAA
* *
41853772 TCCGGGCTAAGCCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCGAAGGCATTTGTGCGAGATACTAAA
*
41853811 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGA-ATTACTATAA
1 TCCGGGCTAAGT-CCGAAGGCATTTGTGCGAGA-TACTA-AA
*
41853852 -CCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGT-CCGAAGGCATTTG
41853877 AACGAGGAGC
Statistics
Matches: 204, Mismatches: 12, Indels: 15
0.88 0.05 0.06
Matches are distributed among these distances:
39 92 0.45
40 99 0.49
41 12 0.06
42 1 0.00
ACGTcount: A:0.27, C:0.22, G:0.27, T:0.24
Consensus pattern (39 bp):
TCCGGGCTAAGTCCGAAGGCATTTGTGCGAGATACTAAA
Found at i:41853749 original size:79 final size:79
Alignment explanation
Indices: 41853614--41853876 Score: 308
Period size: 79 Copynumber: 3.3 Consensus size: 79
41853604 TTGAATGATG
* *
41853614 TCCGGGCTAAGTCCCGAAGGC--TTGTGCTA-AGTGAC-AATATCCGGACTAAGAT-CCGAAGGC
1 TCCGGGCTAAGT-CCGAAGGCATTTGTGCGAGA-T-ACTAA-ATCCGGGCTAAG-TCCCGAAGGC
41853674 ATTTGTGCGAGATACTAAA
61 ATTTGTGCGAGATACTAAA
* *
41853693 TCCGGACTAAGATCCGAAGGCATTTGTGCGAGATACTAATTCCGGGCTAAG-CCCGAAGGCATTT
1 TCCGGGCTAAG-TCCGAAGGCATTTGTGCGAGATACTAAATCCGGGCTAAGTCCCGAAGGCATTT
*
41853757 GTGCGAGATACTAAT
65 GTGCGAGATACTAAA
* * *
41853772 TCCGGGCTAAGCCCGAAGGCATTTGTGCGAGTTACTAAATCCGGGTTAAGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCGAAGGCATTTGTGCGAGATACTAAATCCGGGCTAAGTCCCGAAGGCATTTG
41853837 TGCGA-ATTACTATAA
66 TGCGAGA-TACTA-AA
*
41853852 -CCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGT-CCGAAGGCATTTG
41853877 AACGAGGAGC
Statistics
Matches: 161, Mismatches: 13, Indels: 19
0.83 0.07 0.10
Matches are distributed among these distances:
78 36 0.22
79 87 0.54
80 27 0.17
81 10 0.06
82 1 0.01
ACGTcount: A:0.27, C:0.22, G:0.27, T:0.24
Consensus pattern (79 bp):
TCCGGGCTAAGTCCGAAGGCATTTGTGCGAGATACTAAATCCGGGCTAAGTCCCGAAGGCATTTG
TGCGAGATACTAAA
Found at i:41853898 original size:79 final size:77
Alignment explanation
Indices: 41853615--41853909 Score: 273
Period size: 79 Copynumber: 3.7 Consensus size: 77
41853605 TGAATGATGT
* * **
41853615 CCGGGCTAAGTCCCGAAGGC--TTGTGCTAAGTGACAATATCCGGACTAAGAT-CCGAAGGCATT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGC-GAG-GACTA-ATCCGGGTTAAG-TCCCGAAGGCATT
41853677 TGTGCGAGATACTAAA
62 TGTGCGAGATACTAAA
* * *
41853693 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTAATTCCGGGCTAAG-CCCGAAGGCATT
1 -CCGGGCTAAG-TCCCGAAGGCATTTGTGCGAG-GACTAA-TCCGGGTTAAGTCCCGAAGGCATT
*
41853756 TGTGCGAGATACTAATT
62 TGTGCGAGATACTAA-A
*
41853773 CCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTAAATCCGGGTTAAGTCCCGAAGGCATTTG
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAG-GACT-AATCCGGGTTAAGTCCCGAAGGCATTTG
41853837 TGCGA-ATTACTATAA
64 TGCGAGA-TACTA-AA
* ** * *
41853852 CCGGGCTATGTCCCGAAGGCATTTGAACGAGGAGCTATATCC-GGTTAAATTCCGAAGG
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGGA-CTA-ATCCGGGTTAAGTCCCGAAGG
41853910 TACGCGATTT
Statistics
Matches: 185, Mismatches: 17, Indels: 28
0.80 0.07 0.12
Matches are distributed among these distances:
78 34 0.18
79 104 0.56
80 41 0.22
81 6 0.03
ACGTcount: A:0.27, C:0.22, G:0.27, T:0.24
Consensus pattern (77 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGGACTAATCCGGGTTAAGTCCCGAAGGCATTTGTG
CGAGATACTAAA
Found at i:41867922 original size:20 final size:22
Alignment explanation
Indices: 41867897--41867942 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 22
41867887 GAACATGGAC
*
41867897 TAAACAGCAT-GT-AGACAAAT
1 TAAACAACATGGTAAGACAAAT
*
41867917 TAAACAATATGGTAAGACAAAT
1 TAAACAACATGGTAAGACAAAT
41867939 TAAA
1 TAAA
41867943 AACTCTTAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 8 0.36
21 2 0.09
22 12 0.55
ACGTcount: A:0.54, C:0.11, G:0.13, T:0.22
Consensus pattern (22 bp):
TAAACAACATGGTAAGACAAAT
Found at i:41868165 original size:30 final size:30
Alignment explanation
Indices: 41868122--41868189 Score: 86
Period size: 30 Copynumber: 2.3 Consensus size: 30
41868112 TAAACTAAAT
*
41868122 TGAGCTTAAACGAGCTTAA-ATGAGCTCAAG
1 TGAGCTGAAACGAGCTTAATA-GAGCTCAAG
* *
41868152 TGAGCTGATACGAGCTTAATAGAGCTGAAG
1 TGAGCTGAAACGAGCTTAATAGAGCTCAAG
41868182 -GAGCTGAA
1 TGAGCTGAA
41868190 GATGAGCTAG
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
29 7 0.21
30 25 0.76
31 1 0.03
ACGTcount: A:0.35, C:0.15, G:0.28, T:0.22
Consensus pattern (30 bp):
TGAGCTGAAACGAGCTTAATAGAGCTCAAG
Found at i:41868197 original size:30 final size:30
Alignment explanation
Indices: 41868122--41868197 Score: 75
Period size: 30 Copynumber: 2.5 Consensus size: 30
41868112 TAAACTAAAT
* *
41868122 TGAGCTTAAACGAGCTTAAATGAGCTCAAG
1 TGAGCTGAGACGAGCTTAAATGAGCTCAAG
* *
41868152 TGAGCTGATACGAGCTT-AATAGAGCTGAAG
1 TGAGCTGAGACGAGCTTAAAT-GAGCTCAAG
*
41868182 -GAGCTGAAGATGAGCT
1 TGAGCTG-AGACGAGCT
41868198 AGAATCAGCT
Statistics
Matches: 39, Mismatches: 5, Indels: 4
0.81 0.10 0.08
Matches are distributed among these distances:
29 9 0.23
30 30 0.77
ACGTcount: A:0.34, C:0.14, G:0.29, T:0.22
Consensus pattern (30 bp):
TGAGCTGAGACGAGCTTAAATGAGCTCAAG
Found at i:41873293 original size:27 final size:27
Alignment explanation
Indices: 41873205--41873355 Score: 232
Period size: 27 Copynumber: 5.6 Consensus size: 27
41873195 ATATTAAGTC
* * *
41873205 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAACT
*
41873232 -GCACACTTAGTGCTACATAATCAAACT
1 CGCACACTTAGTGCTACATAGTC-AACT
41873259 CGCACACTTAGTGCTACATAGTCAACT
1 CGCACACTTAGTGCTACATAGTCAACT
41873286 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTC-AACT
*
41873314 CGCACACTTAGTGCTACATAGTCAATT
1 CGCACACTTAGTGCTACATAGTCAACT
41873341 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
41873356 GCACAATTTA
Statistics
Matches: 117, Mismatches: 4, Indels: 6
0.92 0.03 0.05
Matches are distributed among these distances:
26 20 0.17
27 49 0.42
28 48 0.41
ACGTcount: A:0.31, C:0.28, G:0.14, T:0.26
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAACT
Found at i:41873311 original size:55 final size:55
Alignment explanation
Indices: 41873205--41873355 Score: 250
Period size: 55 Copynumber: 2.8 Consensus size: 55
41873195 ATATTAAGTC
* * *
41873205 CGCACACTCAGTGCTATATAATCAACT-GCACACTTAGTGCTACATAATCAAACT
1 CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCTACATAATCAAACT
*
41873259 CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCTACATAATCAAACT
*
41873314 CGCACACTTAGTGCTACATAGTCAATTCGCACACTTAGTGCT
1 CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCT
41873356 GCACAATTTA
Statistics
Matches: 91, Mismatches: 5, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
54 24 0.26
55 67 0.74
ACGTcount: A:0.31, C:0.28, G:0.14, T:0.26
Consensus pattern (55 bp):
CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCTACATAATCAAACT
Found at i:41880620 original size:28 final size:27
Alignment explanation
Indices: 41880557--41880736 Score: 288
Period size: 28 Copynumber: 6.6 Consensus size: 27
41880547 ATATTAAGTC
* * *
41880557 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAACT
*
41880584 CGCACACTTAGTGCTACATAATCAAACT
1 CGCACACTTAGTGCTACATAGTC-AACT
41880612 CGCACACTTAGTGCTACATAGTCAACT
1 CGCACACTTAGTGCTACATAGTCAACT
41880639 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTC-AACT
41880667 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTC-AACT
*
41880695 CGCACACTTAGTGCTACATAGTCAATT
1 CGCACACTTAGTGCTACATAGTCAACT
41880722 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
41880737 GCACAATTTA
Statistics
Matches: 147, Mismatches: 4, Indels: 4
0.95 0.03 0.03
Matches are distributed among these distances:
27 66 0.45
28 81 0.55
ACGTcount: A:0.31, C:0.29, G:0.14, T:0.26
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAACT
Found at i:41880641 original size:55 final size:55
Alignment explanation
Indices: 41880557--41880736 Score: 299
Period size: 55 Copynumber: 3.3 Consensus size: 55
41880547 ATATTAAGTC
* * * *
41880557 CGCACACTCAGTGCTATATAATCAACTCGCACACTTAGTGCTACATAATCAAACT
1 CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCTACATAGTCAAACT
41880612 CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCTACATAGTCAAACT
*
41880667 CGCACACTTAGTGCTACATAGTCAAACTCGCACACTTAGTGCTACATAGTC-AATT
1 CGCACACTTAGTGCTACATAGTC-AACTCGCACACTTAGTGCTACATAGTCAAACT
41880722 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
41880737 GCACAATTTA
Statistics
Matches: 119, Mismatches: 5, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
55 92 0.77
56 27 0.23
ACGTcount: A:0.31, C:0.29, G:0.14, T:0.26
Consensus pattern (55 bp):
CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCTACATAGTCAAACT
Found at i:41880695 original size:83 final size:82
Alignment explanation
Indices: 41880557--41880736 Score: 306
Period size: 83 Copynumber: 2.2 Consensus size: 82
41880547 ATATTAAGTC
* *
41880557 CGCACACTCAGTGCTATATAATCAACTCGCACACTTAGTGCTACATAATCAAACTCGCACACTTA
1 CGCACACTTAGTGCTACATAATCAACTCGCACACTTAGTGCTACATAATCAAACTCGCACACTTA
41880622 GTGCTACATAGTCAACT
66 GTGCTACATAGTCAACT
* *
41880639 CGCACACTTAGTGCTACATAGTCAAACTCGCACACTTAGTGCTACATAGTCAAACTCGCACACTT
1 CGCACACTTAGTGCTACATAATC-AACTCGCACACTTAGTGCTACATAATCAAACTCGCACACTT
*
41880704 AGTGCTACATAGTCAATT
65 AGTGCTACATAGTCAACT
41880722 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
41880737 GCACAATTTA
Statistics
Matches: 92, Mismatches: 5, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
82 20 0.22
83 72 0.78
ACGTcount: A:0.31, C:0.29, G:0.14, T:0.26
Consensus pattern (82 bp):
CGCACACTTAGTGCTACATAATCAACTCGCACACTTAGTGCTACATAATCAAACTCGCACACTTA
GTGCTACATAGTCAACT
Found at i:41888497 original size:13 final size:14
Alignment explanation
Indices: 41888479--41888507 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
41888469 ATTTGAACTG
41888479 AACTAACT-AAATT
1 AACTAACTAAAATT
41888492 AACTAACTAAAATT
1 AACTAACTAAAATT
41888506 AA
1 AA
41888508 ATAATTTATT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 8 0.53
14 7 0.47
ACGTcount: A:0.59, C:0.14, G:0.00, T:0.28
Consensus pattern (14 bp):
AACTAACTAAAATT
Found at i:41888581 original size:20 final size:21
Alignment explanation
Indices: 41888556--41888597 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
41888546 AATAGAAAGA
*
41888556 TGGAAACGAGGTC-ATTGAGC
1 TGGAAACGAGCTCAATTGAGC
*
41888576 TGGAAATGAGCTCAATTGAGC
1 TGGAAACGAGCTCAATTGAGC
41888597 T
1 T
41888598 CAACAAGCTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 11 0.58
21 8 0.42
ACGTcount: A:0.31, C:0.14, G:0.31, T:0.24
Consensus pattern (21 bp):
TGGAAACGAGCTCAATTGAGC
Found at i:41897525 original size:20 final size:20
Alignment explanation
Indices: 41897497--41897541 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
41897487 TAATATGTCT
*
41897497 TGTCCTAACCGAATTAATTG
1 TGTCTTAACCGAATTAATTG
**
41897517 TGTCTTAACTTAATTAATTG
1 TGTCTTAACCGAATTAATTG
41897537 TGTCT
1 TGTCT
41897542 AGTTTTAATT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.27, C:0.16, G:0.13, T:0.44
Consensus pattern (20 bp):
TGTCTTAACCGAATTAATTG
Found at i:41898327 original size:22 final size:22
Alignment explanation
Indices: 41898253--41898347 Score: 73
Period size: 22 Copynumber: 4.2 Consensus size: 22
41898243 ACCTTTTGAT
* *
41898253 CCATTTACGTACCAAAACCTATA
1 CCATTT-CGTAACAAAACCTAAA
* * * * *
41898276 CCATTTTGTACCTACACCAAAAA
1 CCATTTCGTAACAAAACC-TAAA
*
41898299 CCCATTTCGTAACAAAACCTATA
1 -CCATTTCGTAACAAAACCTAAA
* *
41898322 CCATTTCATAACTAAACCTAAA
1 CCATTTCGTAACAAAACCTAAA
41898344 CCAT
1 CCAT
41898348 AATCAACCAA
Statistics
Matches: 56, Mismatches: 14, Indels: 5
0.75 0.19 0.07
Matches are distributed among these distances:
22 32 0.57
23 10 0.18
24 14 0.25
ACGTcount: A:0.40, C:0.31, G:0.03, T:0.26
Consensus pattern (22 bp):
CCATTTCGTAACAAAACCTAAA
Found at i:41898771 original size:39 final size:39
Alignment explanation
Indices: 41898728--41898805 Score: 113
Period size: 39 Copynumber: 2.0 Consensus size: 39
41898718 GTAGGTTTGC
*
41898728 AAAGTGTTTT-GAGAATAAGATAGGTGATGGTTCGGCTAA
1 AAAGTGTTTTAG-GAATAAGATAGGTGATGGCTCGGCTAA
* *
41898767 AAAGTGTTTTAGGGATAGGATAGGTGATGGCTCGGCTAA
1 AAAGTGTTTTAGGAATAAGATAGGTGATGGCTCGGCTAA
41898806 GGATAAAAAC
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
39 34 0.97
40 1 0.03
ACGTcount: A:0.31, C:0.06, G:0.33, T:0.29
Consensus pattern (39 bp):
AAAGTGTTTTAGGAATAAGATAGGTGATGGCTCGGCTAA
Found at i:41910028 original size:28 final size:28
Alignment explanation
Indices: 41909965--41910115 Score: 205
Period size: 28 Copynumber: 5.4 Consensus size: 28
41909955 ATATTAAGTC
*
41909965 CGCACACTCAGTGCTATATAATC-AACT
1 CGCACACTTAGTGCTATATAATCAAACT
41909992 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
* *
41910020 CGCACACTTAGTGCTACATAATCAAGCT
1 CGCACACTTAGTGCTATATAATCAAACT
* *
41910048 CGCACACTTAGTGCTACATAATCAAGCT
1 CGCACACTTAGTGCTATATAATCAAACT
* * * *
41910076 CGCACACTTAGTGCTGTACAATTTAAACC
1 CGCACACTTAGTGCTATATAA-TCAAACT
41910105 CGCACACTTAG
1 CGCACACTTAG
41910116 CGCCAATCTC
Statistics
Matches: 113, Mismatches: 9, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
27 22 0.19
28 76 0.67
29 15 0.13
ACGTcount: A:0.32, C:0.28, G:0.13, T:0.26
Consensus pattern (28 bp):
CGCACACTTAGTGCTATATAATCAAACT
Found at i:41928634 original size:47 final size:47
Alignment explanation
Indices: 41928489--41928914 Score: 683
Period size: 47 Copynumber: 9.1 Consensus size: 47
41928479 CCCTTCGGGA
* * * * * * *
41928489 CTTATCACATTTATGCACTTTCACATCCATCACGTTGGCCACTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
41928536 CCTGTCACATATATACACTTTCACATTCA-CACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
41928582 CTTATCACATATATACACTTTCACATTCATCACATCGTCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
41928629 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
41928676 CTTATCACCTATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
41928723 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTTGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
41928770 CTTATCACACATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* * *
41928817 CTTATCACACATATACACTTTCACATTCATCACGTCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
41928864 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
41928911 CTTA
1 CTTA
41928915 CTATCATTTC
Statistics
Matches: 353, Mismatches: 25, Indels: 2
0.93 0.07 0.01
Matches are distributed among these distances:
46 40 0.11
47 313 0.89
ACGTcount: A:0.28, C:0.31, G:0.09, T:0.32
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:41932301 original size:70 final size:70
Alignment explanation
Indices: 41932183--41932315 Score: 248
Period size: 70 Copynumber: 1.9 Consensus size: 70
41932173 TTGCATGCCC
41932183 AACAGCACCTTAAATACATGTCTATGCTTTACATTAAATTCGGCCAACACCTCCTTTATTGCTGC
1 AACAGCACCTTAAATACATGTCTATGCTTTACATTAAATTCGGCCAACACCTCCTTTATTGCTGC
41932248 TGTTG
66 TGTTG
* *
41932253 AACATCACCTTAAATGCATGTCTATGCTTTACATTAAATTCGGCCAACACCTCCTTTATTGCT
1 AACAGCACCTTAAATACATGTCTATGCTTTACATTAAATTCGGCCAACACCTCCTTTATTGCT
41932316 ACTGATTTAA
Statistics
Matches: 61, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
70 61 1.00
ACGTcount: A:0.28, C:0.26, G:0.11, T:0.35
Consensus pattern (70 bp):
AACAGCACCTTAAATACATGTCTATGCTTTACATTAAATTCGGCCAACACCTCCTTTATTGCTGC
TGTTG
Found at i:41934250 original size:21 final size:18
Alignment explanation
Indices: 41934208--41934252 Score: 54
Period size: 21 Copynumber: 2.3 Consensus size: 18
41934198 TTTTTCAAAC
41934208 TCTTTTTCAAATCCTCTT
1 TCTTTTTCAAATCCTCTT
*
41934226 TCTTTTATCACATCACTCATT
1 TCTTTT-TCAAATC-CTC-TT
41934247 TCTTTT
1 TCTTTT
41934253 GTACTCTCAT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
18 6 0.26
19 6 0.26
20 3 0.13
21 8 0.35
ACGTcount: A:0.18, C:0.27, G:0.00, T:0.56
Consensus pattern (18 bp):
TCTTTTTCAAATCCTCTT
Found at i:41934386 original size:15 final size:16
Alignment explanation
Indices: 41934361--41934392 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
41934351 TATCTCACAC
41934361 TCATCTTCTTTTTCTT
1 TCATCTTCTTTTTCTT
41934377 TCAT-TTCTTTTTCTT
1 TCATCTTCTTTTTCTT
41934392 T
1 T
41934393 TTCATTTTCT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 12 0.75
16 4 0.25
ACGTcount: A:0.06, C:0.22, G:0.00, T:0.72
Consensus pattern (16 bp):
TCATCTTCTTTTTCTT
Found at i:41935278 original size:25 final size:27
Alignment explanation
Indices: 41935241--41935301 Score: 83
Period size: 26 Copynumber: 2.3 Consensus size: 27
41935231 TCAATCACTT
41935241 TTTTTTTTCAATT-TCG-ATTTTTTTTC
1 TTTTTTTTCAATTCT-GAATTTTTTTTC
41935267 TTTTTTTT-AATTCTGAATTTTTTTTC
1 TTTTTTTTCAATTCTGAATTTTTTTTC
41935293 TTCTTTTTT
1 TT-TTTTTT
41935302 TCTTCAATAC
Statistics
Matches: 32, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
25 5 0.16
26 21 0.66
27 6 0.19
ACGTcount: A:0.11, C:0.10, G:0.03, T:0.75
Consensus pattern (27 bp):
TTTTTTTTCAATTCTGAATTTTTTTTC
Found at i:41935377 original size:12 final size:12
Alignment explanation
Indices: 41935347--41935388 Score: 59
Period size: 11 Copynumber: 3.5 Consensus size: 12
41935337 GAATACAAAC
41935347 TTTTTTTTGAA-
1 TTTTTTTTGAAT
41935358 TTTTTTTTGAAT
1 TTTTTTTTGAAT
*
41935370 TTTTTTTTCAAGT
1 TTTTTTTTGAA-T
41935383 TTTTTT
1 TTTTTT
41935389 AACAATACCG
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
11 11 0.39
12 10 0.36
13 7 0.25
ACGTcount: A:0.14, C:0.02, G:0.07, T:0.76
Consensus pattern (12 bp):
TTTTTTTTGAAT
Found at i:41935388 original size:11 final size:11
Alignment explanation
Indices: 41935347--41935376 Score: 60
Period size: 11 Copynumber: 2.7 Consensus size: 11
41935337 GAATACAAAC
41935347 TTTTTTTTGAA
1 TTTTTTTTGAA
41935358 TTTTTTTTGAA
1 TTTTTTTTGAA
41935369 TTTTTTTT
1 TTTTTTTT
41935377 TCAAGTTTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.13, C:0.00, G:0.07, T:0.80
Consensus pattern (11 bp):
TTTTTTTTGAA
Found at i:41936650 original size:70 final size:70
Alignment explanation
Indices: 41936532--41936668 Score: 247
Period size: 70 Copynumber: 2.0 Consensus size: 70
41936522 TTGCATGCCC
41936532 AACAGCACCTTAAATACATGTCTATGCTTTACATTAAATTCGGCCAACACCTCCTTTATTGCTGC
1 AACAGCACCTTAAATACATGTCTATGCTTTACATTAAATTCGGCCAACACCTCCTTTATTGCTGC
41936597 TGTTG
66 TGTTG
* * *
41936602 AACATCACCTTAAATGCATGTCTATGCTTTACATTAAATTCGGCCAACACCTCCTTTGTTGCTGC
1 AACAGCACCTTAAATACATGTCTATGCTTTACATTAAATTCGGCCAACACCTCCTTTATTGCTGC
41936667 TG
66 TG
41936669 ATTTAATTCA
Statistics
Matches: 64, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
70 64 1.00
ACGTcount: A:0.26, C:0.26, G:0.13, T:0.34
Consensus pattern (70 bp):
AACAGCACCTTAAATACATGTCTATGCTTTACATTAAATTCGGCCAACACCTCCTTTATTGCTGC
TGTTG
Found at i:41938285 original size:26 final size:26
Alignment explanation
Indices: 41938253--41938359 Score: 117
Period size: 26 Copynumber: 4.1 Consensus size: 26
41938243 AACACACCAA
*
41938253 TATCGCAGCAAAGTTGCCAGTATCAG
1 TATCGCAGCAAAGCTGCCAGTATCAG
*
41938279 TAACGCAGCAAAGCTGCCAGTAAT-AG
1 TATCGCAGCAAAGCTGCCAGT-ATCAG
* * * *
41938305 TATCACAGTAGAGCTGCCAATATCAG
1 TATCGCAGCAAAGCTGCCAGTATCAG
* * *
41938331 TATTGCAGCAAAGCTACCAGTAACAG
1 TATCGCAGCAAAGCTGCCAGTATCAG
41938357 TAT
1 TAT
41938360 TTGTGGCAAA
Statistics
Matches: 65, Mismatches: 14, Indels: 4
0.78 0.17 0.05
Matches are distributed among these distances:
25 2 0.03
26 61 0.94
27 2 0.03
ACGTcount: A:0.36, C:0.22, G:0.21, T:0.21
Consensus pattern (26 bp):
TATCGCAGCAAAGCTGCCAGTATCAG
Found at i:41938619 original size:27 final size:27
Alignment explanation
Indices: 41938549--41938907 Score: 384
Period size: 27 Copynumber: 13.3 Consensus size: 27
41938539 AGGGGTATAA
* *
41938549 CGGTTATTTTACCCCTCG-GGAGTATTT
1 CGGTAATTTTACCCTTCGAGG-GTATTT
* *
41938576 CGGTAATTTTACCCTTCGGGGGCATTT
1 CGGTAATTTTACCCTTCGAGGGTATTT
* *
41938603 CGGTAATTTTACTCTTCGAGGGCATTT
1 CGGTAATTTTACCCTTCGAGGGTATTT
** * *
41938630 CAATAATTTTACCCATCAAGGGTATTT
1 CGGTAATTTTACCCTTCGAGGGTATTT
* **
41938657 TGGTAATTTTACCCTTTAAGGGTATTT
1 CGGTAATTTTACCCTTCGAGGGTATTT
* *
41938684 CGATAATTTTACCTTTCGAGGGTATTT
1 CGGTAATTTTACCCTTCGAGGGTATTT
* * *
41938711 CGATAATTTTACCCTTTGAGGGAATTT
1 CGGTAATTTTACCCTTCGAGGGTATTT
** *
41938738 TTGTAATTTTACCCTTTGAGGGTATTT
1 CGGTAATTTTACCCTTCGAGGGTATTT
41938765 CGGTAATTTTACCCTTCGA-GGTATTT
1 CGGTAATTTTACCCTTCGAGGGTATTT
* * *
41938791 TGATAATTTTACCCTTCGGGGGTATTT
1 CGGTAATTTTACCCTTCGAGGGTATTT
*
41938818 CGGTAATTTTACCCTTCGTGGGTATTT
1 CGGTAATTTTACCCTTCGAGGGTATTT
* * *
41938845 AGATAATTTCACCCTTCGAGGGTA-TT
1 CGGTAATTTTACCCTTCGAGGGTATTT
* *
41938871 CTAGTAATTTTACCCATT-AAGGGTATTT
1 C-GGTAATTTTACCC-TTCGAGGGTATTT
*
41938899 CAGTAATTT
1 CGGTAATTT
41938908 GCCCACGAAT
Statistics
Matches: 281, Mismatches: 46, Indels: 10
0.83 0.14 0.03
Matches are distributed among these distances:
26 25 0.09
27 249 0.89
28 7 0.02
ACGTcount: A:0.22, C:0.17, G:0.19, T:0.42
Consensus pattern (27 bp):
CGGTAATTTTACCCTTCGAGGGTATTT
Found at i:41945432 original size:18 final size:19
Alignment explanation
Indices: 41945404--41945450 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 19
41945394 TAGCAGTATA
41945404 AAATATAAAAA-TAAAAACC
1 AAAT-TAAAAACTAAAAACC
* *
41945423 CAATTAAAAACTTAAAACC
1 AAATTAAAAACTAAAAACC
41945442 AAATTAAAA
1 AAATTAAAA
41945451 TGCTTTATTA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
18 6 0.25
19 18 0.75
ACGTcount: A:0.68, C:0.13, G:0.00, T:0.19
Consensus pattern (19 bp):
AAATTAAAAACTAAAAACC
Found at i:41945931 original size:26 final size:26
Alignment explanation
Indices: 41945859--41945964 Score: 117
Period size: 26 Copynumber: 4.1 Consensus size: 26
41945849 AACACACCAA
41945859 TATCGCAGCAAAGCTACCAGTATAC--
1 TATCGCAGCAAAGCTACCAGTA-ACAG
* * *
41945884 TAACACAGCAAAGCTACTAGTAACAG
1 TATCGCAGCAAAGCTACCAGTAACAG
* * *
41945910 TATCGCAGCAGAGCTGCCAGTATCAG
1 TATCGCAGCAAAGCTACCAGTAACAG
* *
41945936 TATCGCAACAAAGCTGCCAGTAACAG
1 TATCGCAGCAAAGCTACCAGTAACAG
41945962 TAT
1 TAT
41945965 TTGTGGCAAA
Statistics
Matches: 67, Mismatches: 12, Indels: 3
0.82 0.15 0.04
Matches are distributed among these distances:
24 2 0.03
25 19 0.28
26 46 0.69
ACGTcount: A:0.37, C:0.25, G:0.19, T:0.19
Consensus pattern (26 bp):
TATCGCAGCAAAGCTACCAGTAACAG
Found at i:41946240 original size:27 final size:27
Alignment explanation
Indices: 41946174--41946394 Score: 157
Period size: 27 Copynumber: 8.2 Consensus size: 27
41946164 AACCCTCAGA
* *
41946174 GGTATTTCT-ATAATTTTACCCTTCAAG
1 GGTATTT-TGATAATTTTACCTTTCGAG
** ** *
41946201 GGCGTTTCAATAATTTTACCTTTCAAG
1 GGTATTTTGATAATTTTACCTTTCGAG
* **
41946228 GGCATTTTGATAACATTACCCTTT-GA-
1 GGTATTTTGATAATTTTA-CCTTTCGAG
* * * *
41946254 GATATTTCGGTAATTTTACCTATCGAG
1 GGTATTTTGATAATTTTACCTTTCGAG
* *
41946281 GGTAATTT-AGTAATTTTATGCTTT-GAG
1 GGTATTTTGA-TAATTTTA-CCTTTCGAG
* **
41946308 GGTATTTTGCTAATTTTACCCATCGAG
1 GGTATTTTGATAATTTTACCTTTCGAG
*
41946335 GGTATTTTGATAATTTTACCCTTCGAG
1 GGTATTTTGATAATTTTACCTTTCGAG
* *
41946362 GGTATTCTGGTAATTTTACTCTTT-GAG
1 GGTATTTTGATAATTTTAC-CTTTCGAG
41946389 GGTATT
1 GGTATT
41946395 CGAAGGTATT
Statistics
Matches: 152, Mismatches: 33, Indels: 18
0.75 0.16 0.09
Matches are distributed among these distances:
25 4 0.03
26 16 0.11
27 121 0.80
28 11 0.07
ACGTcount: A:0.24, C:0.14, G:0.18, T:0.43
Consensus pattern (27 bp):
GGTATTTTGATAATTTTACCTTTCGAG
Found at i:41946397 original size:37 final size:37
Alignment explanation
Indices: 41946356--41946431 Score: 107
Period size: 37 Copynumber: 2.1 Consensus size: 37
41946346 AATTTTACCC
* * * *
41946356 TTCGAGGGTATTCTGGTAATTTTACTCTTTGAGGGTA
1 TTCGAAGGTATTCTGGTAATGTTACCCTTAGAGGGTA
*
41946393 TTCGAAGGTATTCTGGTAATGTTACCCTTAGAGTGTA
1 TTCGAAGGTATTCTGGTAATGTTACCCTTAGAGGGTA
41946430 TT
1 TT
41946432 TCGATAATTT
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
37 34 1.00
ACGTcount: A:0.21, C:0.12, G:0.25, T:0.42
Consensus pattern (37 bp):
TTCGAAGGTATTCTGGTAATGTTACCCTTAGAGGGTA
Found at i:41946430 original size:27 final size:27
Alignment explanation
Indices: 41946409--41946527 Score: 118
Period size: 27 Copynumber: 4.4 Consensus size: 27
41946399 GGTATTCTGG
* *
41946409 TAATGTTACCCTTAGAGTGTATTTCGA
1 TAATTTTACCCTTAGAGGGTATTTCGA
* *
41946436 TAATTTTACCCTTCGTGGGTA-TTCTGA
1 TAATTTTACCCTTAGAGGGTATTTC-GA
* *
41946463 TAATTTTACCCTTTGAGGGTATTTCGG
1 TAATTTTACCCTTAGAGGGTATTTCGA
* *
41946490 TAATTTTTCCCAATT-GAGGGTATTTCAA
1 TAATTTTACCC--TTAGAGGGTATTTCGA
41946518 TAA-TTTACCC
1 TAATTTTACCC
41946528 ATGAATCTAA
Statistics
Matches: 77, Mismatches: 11, Indels: 8
0.80 0.11 0.08
Matches are distributed among these distances:
26 3 0.04
27 55 0.71
28 17 0.22
29 2 0.03
ACGTcount: A:0.24, C:0.17, G:0.17, T:0.43
Consensus pattern (27 bp):
TAATTTTACCCTTAGAGGGTATTTCGA
Found at i:41946440 original size:64 final size:64
Alignment explanation
Indices: 41946330--41946459 Score: 154
Period size: 64 Copynumber: 2.0 Consensus size: 64
41946320 ATTTTACCCA
* * * * * * *
41946330 TCGAGGGTATTTTGATAATTTTACCCTTCGAGGGTATTCTGGTAATTTTACTCTTTGAGGGTAT
1 TCGAAGGTATTCTGATAATGTTACCCTTAGAGGGTATTCTGATAATTTTACCCTTCGAGGGTAT
* * *
41946394 TCGAAGGTATTCTGGTAATGTTACCCTTAGAGTGTATT-TCGATAATTTTACCCTTCGTGGGTAT
1 TCGAAGGTATTCTGATAATGTTACCCTTAGAGGGTATTCT-GATAATTTTACCCTTCGAGGGTAT
41946458 TC
1 TC
41946460 TGATAATTTT
Statistics
Matches: 55, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
63 1 0.02
64 54 0.98
ACGTcount: A:0.21, C:0.15, G:0.22, T:0.42
Consensus pattern (64 bp):
TCGAAGGTATTCTGATAATGTTACCCTTAGAGGGTATTCTGATAATTTTACCCTTCGAGGGTAT
Found at i:41946467 original size:91 final size:91
Alignment explanation
Indices: 41946308--41946485 Score: 266
Period size: 91 Copynumber: 2.0 Consensus size: 91
41946298 ATGCTTTGAG
* * * * *
41946308 GGTATTTTGCTAATTTTACCCATCGAGGGTATTTTGATAATTTTACCCTTCGAGGGTATTCTGGT
1 GGTATTCTGCTAATGTTACCCATAGAGGGTATTTCGATAATTTTACCCTTCGAGGGTATTCTGAT
*
41946373 AATTTTACTCTTTGAGGGTATTCGAA
66 AATTTTACCCTTTGAGGGTATTCGAA
* * * *
41946399 GGTATTCTGGTAATGTTACCCTTAGAGTGTATTTCGATAATTTTACCCTTCGTGGGTATTCTGAT
1 GGTATTCTGCTAATGTTACCCATAGAGGGTATTTCGATAATTTTACCCTTCGAGGGTATTCTGAT
41946464 AATTTTACCCTTTGAGGGTATT
66 AATTTTACCCTTTGAGGGTATT
41946486 TCGGTAATTT
Statistics
Matches: 77, Mismatches: 10, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
91 77 1.00
ACGTcount: A:0.21, C:0.15, G:0.21, T:0.43
Consensus pattern (91 bp):
GGTATTCTGCTAATGTTACCCATAGAGGGTATTTCGATAATTTTACCCTTCGAGGGTATTCTGAT
AATTTTACCCTTTGAGGGTATTCGAA
Found at i:41946525 original size:54 final size:53
Alignment explanation
Indices: 41946393--41946527 Score: 130
Period size: 54 Copynumber: 2.5 Consensus size: 53
41946383 TTTGAGGGTA
* ** *
41946393 TTCGAAGGTATTCTGGTAATGTTACCCTTAGAGTGTATTTCGATAATTTTACCC
1 TTCGAGGGTATTCTAATAAT-TTACCCTTAGAGGGTATTTCGATAATTTTACCC
* * * * *
41946447 TTCGTGGGTATTCTGATAATTTTACCCTTTGAGGGTATTTCGGTAATTTTTCCC
1 TTCGAGGGTATTCTAATAA-TTTACCCTTAGAGGGTATTTCGATAATTTTACCC
41946501 AATT-GAGGGTATT-TCAATAATTTACCC
1 --TTCGAGGGTATTCT-AATAATTTACCC
41946528 ATGAATCTAA
Statistics
Matches: 68, Mismatches: 9, Indels: 8
0.80 0.11 0.09
Matches are distributed among these distances:
54 53 0.78
55 13 0.19
56 2 0.03
ACGTcount: A:0.23, C:0.16, G:0.19, T:0.42
Consensus pattern (53 bp):
TTCGAGGGTATTCTAATAATTTACCCTTAGAGGGTATTTCGATAATTTTACCC
Found at i:41950688 original size:14 final size:14
Alignment explanation
Indices: 41950669--41950695 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
41950659 ACATGCATAA
41950669 AATGACCAAATTCT
1 AATGACCAAATTCT
41950683 AATGACCAAATTC
1 AATGACCAAATTC
41950696 CATTCAACAC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.44, C:0.22, G:0.07, T:0.26
Consensus pattern (14 bp):
AATGACCAAATTCT
Found at i:41951191 original size:9 final size:9
Alignment explanation
Indices: 41951172--41951208 Score: 58
Period size: 9 Copynumber: 4.1 Consensus size: 9
41951162 TGAGTTTTCG
41951172 AATTCGAAT
1 AATTCGAAT
41951181 AACTT-GAAT
1 AA-TTCGAAT
41951190 AATTCGAAT
1 AATTCGAAT
41951199 AATTCGAAT
1 AATTCGAAT
41951208 A
1 A
41951209 TCAAACTATA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
8 2 0.08
9 22 0.85
10 2 0.08
ACGTcount: A:0.46, C:0.11, G:0.11, T:0.32
Consensus pattern (9 bp):
AATTCGAAT
Found at i:41953786 original size:29 final size:29
Alignment explanation
Indices: 41953751--41953912 Score: 182
Period size: 29 Copynumber: 5.6 Consensus size: 29
41953741 GATTGTCAAA
*
41953751 ACCATCCCTTTTCAT-TTTCGATGGTCGTC
1 ACCATCCCTTTTCATAGTT-GATGGTCGTC
41953780 ACCATCCCTTTTCATAGTTGATGGTCGTC
1 ACCATCCCTTTTCATAGTTGATGGTCGTC
* * **
41953809 ACCATGCCTTTTCATAGTTGATAGTCGAA
1 ACCATCCCTTTTCATAGTTGATGGTCGTC
* * *
41953838 ACTATCCCTTTTCATTAATCGATGGTCGTC
1 ACCATCCCTTTTCA-TAGTTGATGGTCGTC
* * **
41953868 ACCATCCCTTTTCATAGTTGATAGTTGAA
1 ACCATCCCTTTTCATAGTTGATGGTCGTC
*
41953897 ACTATCCCTTTTCATA
1 ACCATCCCTTTTCATA
41953913 TTCGATGCTT
Statistics
Matches: 111, Mismatches: 20, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
29 86 0.77
30 25 0.23
ACGTcount: A:0.22, C:0.26, G:0.14, T:0.39
Consensus pattern (29 bp):
ACCATCCCTTTTCATAGTTGATGGTCGTC
Found at i:41953879 original size:59 final size:58
Alignment explanation
Indices: 41953751--41953919 Score: 223
Period size: 59 Copynumber: 2.9 Consensus size: 58
41953741 GATTGTCAAA
* * ** * * *
41953751 ACCATCCCTTTTCAT-TTTCGATGGTCGTCACCATCCCTTTTCATAGTTGATGGTCGTC
1 ACCATCCCTTTTCATAGTT-GATAGTCGAAACTATCCCTTTTCATAATCGATGGTCGTC
*
41953809 ACCATGCCTTTTCATAGTTGATAGTCGAAACTATCCCTTTTCATTAATCGATGGTCGTC
1 ACCATCCCTTTTCATAGTTGATAGTCGAAACTATCCCTTTTCA-TAATCGATGGTCGTC
* *
41953868 ACCATCCCTTTTCATAGTTGATAGTTGAAACTATCCCTTTTCATATTCGATG
1 ACCATCCCTTTTCATAGTTGATAGTCGAAACTATCCCTTTTCATAATCGATG
41953920 CTTGTCGATA
Statistics
Matches: 98, Mismatches: 11, Indels: 4
0.87 0.10 0.04
Matches are distributed among these distances:
58 42 0.43
59 56 0.57
ACGTcount: A:0.21, C:0.25, G:0.14, T:0.39
Consensus pattern (58 bp):
ACCATCCCTTTTCATAGTTGATAGTCGAAACTATCCCTTTTCATAATCGATGGTCGTC
Found at i:41953907 original size:88 final size:87
Alignment explanation
Indices: 41953739--41953912 Score: 249
Period size: 88 Copynumber: 2.0 Consensus size: 87
41953729 TTTCTTTTAA
* * *
41953739 TTGATTGTCAAAACCATCCCTTTTCATTTTCGATGGTCGTCACCATCCCTTTTCATAGTTGATGG
1 TTGATAGTCAAAACCATCCCTTTTCATTATCGATGGTCGTCACCATCCCTTTTCATAGTTGATAG
** *
41953804 TCGTCACCATGCCTTTTCATAG
66 TCGAAACCATCCCTTTTCATAG
* *
41953826 TTGATAGTCGAAACTATCCCTTTTCATTAATCGATGGTCGTCACCATCCCTTTTCATAGTTGATA
1 TTGATAGTCAAAACCATCCCTTTTCATT-ATCGATGGTCGTCACCATCCCTTTTCATAGTTGATA
* *
41953891 GTTGAAACTATCCCTTTTCATA
65 GTCGAAACCATCCCTTTTCATA
41953913 TTCGATGCTT
Statistics
Matches: 76, Mismatches: 10, Indels: 1
0.87 0.11 0.01
Matches are distributed among these distances:
87 25 0.33
88 51 0.67
ACGTcount: A:0.22, C:0.25, G:0.14, T:0.39
Consensus pattern (87 bp):
TTGATAGTCAAAACCATCCCTTTTCATTATCGATGGTCGTCACCATCCCTTTTCATAGTTGATAG
TCGAAACCATCCCTTTTCATAG
Found at i:41962201 original size:20 final size:20
Alignment explanation
Indices: 41962148--41962204 Score: 55
Period size: 20 Copynumber: 2.9 Consensus size: 20
41962138 AGGCATACCA
41962148 AAGTACAAACAGGGGCACGC
1 AAGTACAAACAGGGGCACGC
***
41962168 ATA-TACATTTAGGGGCAC-C
1 A-AGTACAAACAGGGGCACGC
41962187 GAAGTACAAACAGGGGCA
1 -AAGTACAAACAGGGGCA
41962205 TGTATGTGCA
Statistics
Matches: 28, Mismatches: 6, Indels: 6
0.70 0.15 0.15
Matches are distributed among these distances:
19 2 0.07
20 25 0.89
21 1 0.04
ACGTcount: A:0.39, C:0.21, G:0.28, T:0.12
Consensus pattern (20 bp):
AAGTACAAACAGGGGCACGC
Found at i:41967232 original size:46 final size:46
Alignment explanation
Indices: 41967180--41967273 Score: 154
Period size: 46 Copynumber: 2.0 Consensus size: 46
41967170 ATAGTGTGGC
* *
41967180 GTTCATCATATACCAAGGTTCTTATCA-TCATTTATAGTGGGTCGAG
1 GTTCATCATATACCAAGGTTCCTATCATTC-TTGATAGTGGGTCGAG
41967226 GTTCATCATATACCAAGGTTCCTATCATTCTTGATAGTGGGTCGAG
1 GTTCATCATATACCAAGGTTCCTATCATTCTTGATAGTGGGTCGAG
41967272 GT
1 GT
41967274 CTTTTCTTTG
Statistics
Matches: 45, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
46 43 0.96
47 2 0.04
ACGTcount: A:0.24, C:0.18, G:0.21, T:0.36
Consensus pattern (46 bp):
GTTCATCATATACCAAGGTTCCTATCATTCTTGATAGTGGGTCGAG
Found at i:41968467 original size:19 final size:18
Alignment explanation
Indices: 41968416--41968459 Score: 51
Period size: 18 Copynumber: 2.7 Consensus size: 18
41968406 TCATCATCTC
41968416 CTTTTT-TCTC-T-TTTT
1 CTTTTTGTCTCATATTTT
*
41968431 CTTTTTGTTTCATATTTT
1 CTTTTTGTCTCATATTTT
41968449 CTTTTT-TCTCA
1 CTTTTTGTCTCA
41968460 ATCATTTTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
15 6 0.25
16 3 0.12
17 5 0.21
18 10 0.42
ACGTcount: A:0.07, C:0.18, G:0.02, T:0.73
Consensus pattern (18 bp):
CTTTTTGTCTCATATTTT
Found at i:41970186 original size:20 final size:21
Alignment explanation
Indices: 41970142--41970186 Score: 58
Period size: 20 Copynumber: 2.2 Consensus size: 21
41970132 AAGCTAGGTT
41970142 GAGCTCAAATGAGCTTAAATA
1 GAGCTCAAATGAGCTTAAATA
* *
41970163 -AGCTCAAGTGAGCTT-ATTA
1 GAGCTCAAATGAGCTTAAATA
41970182 GAGCT
1 GAGCT
41970187 GAATGGAGCT
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
19 3 0.14
20 18 0.86
ACGTcount: A:0.36, C:0.16, G:0.22, T:0.27
Consensus pattern (21 bp):
GAGCTCAAATGAGCTTAAATA
Found at i:41977839 original size:10 final size:11
Alignment explanation
Indices: 41977815--41977848 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
41977805 AGGCATAAAG
*
41977815 ATGTTCACACC
1 ATGTTCAGACC
41977826 ATGTTCAG-CC
1 ATGTTCAGACC
41977836 ATGTTCAGACC
1 ATGTTCAGACC
41977847 AT
1 AT
41977849 ATGTGATGCG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
10 10 0.48
11 11 0.52
ACGTcount: A:0.26, C:0.29, G:0.15, T:0.29
Consensus pattern (11 bp):
ATGTTCAGACC
Found at i:41980219 original size:12 final size:13
Alignment explanation
Indices: 41980189--41980222 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
41980179 TACAGTTTCA
*
41980189 AAAAAAACAATTTG
1 AAAAAAA-AATTCG
41980203 AAAAAAAAATTCG
1 AAAAAAAAATTCG
41980216 AAAAAAA
1 AAAAAAA
41980223 GGAAGAGAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 12 0.63
14 7 0.37
ACGTcount: A:0.74, C:0.06, G:0.06, T:0.15
Consensus pattern (13 bp):
AAAAAAAAATTCG
Found at i:41988406 original size:47 final size:47
Alignment explanation
Indices: 41988299--41988835 Score: 804
Period size: 47 Copynumber: 11.1 Consensus size: 47
41988289 GAAATGATAG
41988299 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG--TATATATGTGA
*
41988348 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGAGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
41988395 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATAGATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG--TATAT--ATGTGA
*
41988446 TAAGGCCTAATGGCCGATGTGATTAATGTGAAAGTGTATATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG--TATATATGTGA
41988495 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG----TATATATGTGA
*
41988546 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATACGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
* *
41988593 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGCGTATATATGAGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
41988640 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG----TATATATGTGA
*
41988691 TAGGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
41988738 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
* * * * * * * *
41988785 CAGGGCCGAGTGGCCAACGTGATGGATGTGAAAGTGTATAAATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
41988832 TAAG
1 TAAG
41988836 TCCCAAAGGG
Statistics
Matches: 456, Mismatches: 22, Indels: 22
0.91 0.04 0.04
Matches are distributed among these distances:
47 233 0.51
49 82 0.18
51 141 0.31
ACGTcount: A:0.33, C:0.09, G:0.30, T:0.29
Consensus pattern (47 bp):
TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
Found at i:41988478 original size:98 final size:96
Alignment explanation
Indices: 41988299--41988835 Score: 825
Period size: 98 Copynumber: 5.6 Consensus size: 96
41988289 GAAATGATAG
41988299 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCG
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCG
*
41988364 ATGTGATGAATGTGAAAGTGTATATATGAGA
66 ATGTGATGAATGTGAAAGTGTATATATGTGA
41988395 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATAGATGTGATAAGGCCTAATGGC
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATAT--ATGTGATAAGGCCTAATGGC
*
41988460 CGATGTGATTAATGTGAAAGTGTATATATATGTGA
64 CGATGTGATGAATGTGAAAGTG--TATATATGTGA
41988495 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATATGTGATAAGGCCTAATGGC
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG--TATATATATGTGATAAGGCCTAATGGC
*
41988560 CGATGTGATGAATGTGAAAGTGTATATACGTGA
64 CGATGTGATGAATGTGAAAGTGTATATATGTGA
* *
41988593 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGCG--TATATATGAGATAAGGCCTAATGGCCG
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCG
41988656 ATGTGATGAATGTGAAAGTGTATATATATATGTGA
66 ATGTGATGAATGTGAAAGTG----TATATATGTGA
*
41988691 TAGGGCCTAATGGCCGATGTGATGAATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCG
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCG
41988754 ATGTGATGAATGTGAAAGTGTATATATGTGA
66 ATGTGATGAATGTGAAAGTGTATATATGTGA
* * * * * * *
41988785 CAGGGCCGAGTGGCCAACGTGATGGATGTGAAAGTGTATA-A-ATGTGATAAG
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAG
41988836 TCCCAAAGGG
Statistics
Matches: 413, Mismatches: 16, Indels: 26
0.91 0.04 0.06
Matches are distributed among these distances:
94 97 0.23
95 1 0.00
96 45 0.11
98 176 0.43
100 87 0.21
102 7 0.02
ACGTcount: A:0.33, C:0.09, G:0.30, T:0.29
Consensus pattern (96 bp):
TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCG
ATGTGATGAATGTGAAAGTGTATATATGTGA
Found at i:41988684 original size:145 final size:146
Alignment explanation
Indices: 41988299--41988824 Score: 839
Period size: 145 Copynumber: 3.6 Consensus size: 146
41988289 GAAATGATAG
41988299 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCG
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG-ATATATATGTGATAAGGCCTAATGGCCG
*
41988364 ATGTGATGAATGTGAAAGTG----TATATATGAGATAAGGCCTAATGGCCGATGTGATGAATGTG
65 ATGTGATGAATGTGAAAGTGTATATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTG
41988425 AAAGTGTATATATAGATGTGA
130 AAAGTG--TATAT--ATGTGA
*
41988446 TAAGGCCTAATGGCCGATGTGATTAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCG
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG-ATATATATGTGATAAGGCCTAATGGCCG
41988511 ATGTGATGAATGTGAAAGTGTATATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTG
65 ATGTGATGAATGTGAAAGTGTATATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTG
*
41988576 AAAGTGTATATACGTGA
130 AAAGTGTATATATGTGA
* *
41988593 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGCG-TATATATGAGATAAGGCCTAATGGCCGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGATATATATGTGATAAGGCCTAATGGCCGA
*
41988657 TGTGATGAATGTGAAAGTGTATATATATATGTGATAGGGCCTAATGGCCGATGTGATGAATGTGA
66 TGTGATGAATGTGAAAGTGTATATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGA
41988722 AAGTGTATATATGTGA
131 AAGTGTATATATGTGA
* * * * *
41988738 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG-TATATATGTGACAGGGCCGAGTGGCCAA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGATATATATGTGATAAGGCCTAATGGCCGA
* *
41988802 CGTGATGGATGTGAAAGTGTATA
66 TGTGATGAATGTGAAAGTGTATA
41988825 AATGTGATAA
Statistics
Matches: 358, Mismatches: 17, Indels: 10
0.93 0.04 0.03
Matches are distributed among these distances:
145 184 0.51
147 123 0.34
149 5 0.01
151 46 0.13
ACGTcount: A:0.32, C:0.09, G:0.30, T:0.29
Consensus pattern (146 bp):
TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGATATATATGTGATAAGGCCTAATGGCCGA
TGTGATGAATGTGAAAGTGTATATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGA
AAGTGTATATATGTGA
Found at i:41989010 original size:37 final size:37
Alignment explanation
Indices: 41988954--41989032 Score: 122
Period size: 37 Copynumber: 2.1 Consensus size: 37
41988944 CCGAGCTCTA
* * *
41988954 AAGACCCGATGACTACGTGTGGGGATTTTGTCCGGGT
1 AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
*
41988991 AAGACCCGATAACTTCGTGTGGAGATTATGTCCGGGT
1 AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
41989028 AAGAC
1 AAGAC
41989033 TTCGTAATAA
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.24, C:0.19, G:0.32, T:0.25
Consensus pattern (37 bp):
AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
Found at i:41992188 original size:12 final size:12
Alignment explanation
Indices: 41992173--41992203 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
41992163 TCTTTTGTTT
*
41992173 TTTTTCTAACTC
1 TTTTTCAAACTC
41992185 TTTTTCAAACTC
1 TTTTTCAAACTC
41992197 TTTTTCA
1 TTTTTCA
41992204 TTTTCTTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.19, C:0.23, G:0.00, T:0.58
Consensus pattern (12 bp):
TTTTTCAAACTC
Found at i:41992213 original size:13 final size:12
Alignment explanation
Indices: 41992183--41992225 Score: 59
Period size: 12 Copynumber: 3.6 Consensus size: 12
41992173 TTTTTCTAAC
**
41992183 TCTTTTTCAAAC
1 TCTTTTTCAATT
*
41992195 TCTTTTTCATTT
1 TCTTTTTCAATT
41992207 TCTTTTTCAATT
1 TCTTTTTCAATT
41992219 TCTTTTT
1 TCTTTTT
41992226 GTTTCATCTA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
12 27 1.00
ACGTcount: A:0.14, C:0.19, G:0.00, T:0.67
Consensus pattern (12 bp):
TCTTTTTCAATT
Found at i:41994687 original size:10 final size:10
Alignment explanation
Indices: 41994673--41994708 Score: 54
Period size: 10 Copynumber: 3.6 Consensus size: 10
41994663 TAAGCTAGGT
41994673 TGAGCTCAAA
1 TGAGCTCAAA
* *
41994683 CGAGCTTAAA
1 TGAGCTCAAA
41994693 TGAGCTCAAA
1 TGAGCTCAAA
41994703 TGAGCT
1 TGAGCT
41994709 GATTCGAGCT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
10 22 1.00
ACGTcount: A:0.36, C:0.19, G:0.22, T:0.22
Consensus pattern (10 bp):
TGAGCTCAAA
Found at i:41996900 original size:17 final size:16
Alignment explanation
Indices: 41996880--41996924 Score: 72
Period size: 16 Copynumber: 2.8 Consensus size: 16
41996870 TTGTACAATT
41996880 TTTTTTTAATTTCAAAA
1 TTTTTTTAATTTC-AAA
41996897 TTTTTTTAATTTCAAA
1 TTTTTTTAATTTCAAA
*
41996913 TTTTTTAAATTT
1 TTTTTTTAATTT
41996925 TTAGGAGTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
16 14 0.52
17 13 0.48
ACGTcount: A:0.31, C:0.04, G:0.00, T:0.64
Consensus pattern (16 bp):
TTTTTTTAATTTCAAA
Found at i:41998745 original size:4 final size:4
Alignment explanation
Indices: 41998724--41998759 Score: 56
Period size: 4 Copynumber: 9.0 Consensus size: 4
41998714 GTTGTAAAGT
41998724 TTTA TTT- TTTA TTTTA TTTA TTTA TTTA TTTA TTTA
1 TTTA TTTA TTTA -TTTA TTTA TTTA TTTA TTTA TTTA
41998760 CTTAGTTTAA
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
3 3 0.10
4 23 0.77
5 4 0.13
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (4 bp):
TTTA
Found at i:42001286 original size:29 final size:29
Alignment explanation
Indices: 42001247--42001306 Score: 102
Period size: 29 Copynumber: 2.1 Consensus size: 29
42001237 TTGTTGACAC
*
42001247 CACACGGGTGTGTGGCTAGCCGTGTGTGA
1 CACACGGGTGTGTGGCCAGCCGTGTGTGA
*
42001276 CACATGGGTGTGTGGCCAGCCGTGTGTGA
1 CACACGGGTGTGTGGCCAGCCGTGTGTGA
42001305 CA
1 CA
42001307 TATGACCATG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.15, C:0.22, G:0.40, T:0.23
Consensus pattern (29 bp):
CACACGGGTGTGTGGCCAGCCGTGTGTGA
Found at i:42001318 original size:29 final size:29
Alignment explanation
Indices: 42001257--42001318 Score: 70
Period size: 29 Copynumber: 2.1 Consensus size: 29
42001247 CACACGGGTG
* ****
42001257 TGTGGCTAGCCGTGTGTGACACATGGGTG
1 TGTGGCCAGCCGTGTGTGACACATGACCA
*
42001286 TGTGGCCAGCCGTGTGTGACATATGACCA
1 TGTGGCCAGCCGTGTGTGACACATGACCA
42001315 TGTG
1 TGTG
42001319 ATGGGTGAGT
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.16, C:0.19, G:0.37, T:0.27
Consensus pattern (29 bp):
TGTGGCCAGCCGTGTGTGACACATGACCA
Found at i:42004303 original size:25 final size:25
Alignment explanation
Indices: 42004267--42004332 Score: 62
Period size: 26 Copynumber: 2.6 Consensus size: 25
42004257 AATATATGTT
**
42004267 TTAATT-TGGTCTTAGTTCATACATC
1 TTAATTGT-GTCTTAGTTCATACAAA
* *
42004292 TTAATTGTGTCTAAAGTTGATACAAA
1 TTAATTGTGTCT-TAGTTCATACAAA
42004318 TTAAATTGTGTCTTA
1 TT-AATTGTGTCTTA
42004333 TTAGTGAATT
Statistics
Matches: 33, Mismatches: 5, Indels: 5
0.77 0.12 0.12
Matches are distributed among these distances:
25 10 0.30
26 13 0.39
27 10 0.30
ACGTcount: A:0.30, C:0.11, G:0.14, T:0.45
Consensus pattern (25 bp):
TTAATTGTGTCTTAGTTCATACAAA
Found at i:42006463 original size:21 final size:21
Alignment explanation
Indices: 42006408--42006463 Score: 60
Period size: 21 Copynumber: 2.7 Consensus size: 21
42006398 AAAGAAAAGA
*
42006408 GAAAGAAAAGAAAACGGGATT
1 GAAAGAAAAGAAAACGGGAGT
** *
42006429 GAAA-AATGGAAAAAGGAGAGT
1 GAAAGAAAAGAAAACGG-GAGT
42006450 GAAAGAAAAGAAAA
1 GAAAGAAAAGAAAA
42006464 TGTTAAAGAT
Statistics
Matches: 27, Mismatches: 6, Indels: 3
0.75 0.17 0.08
Matches are distributed among these distances:
20 9 0.33
21 11 0.41
22 7 0.26
ACGTcount: A:0.62, C:0.02, G:0.29, T:0.07
Consensus pattern (21 bp):
GAAAGAAAAGAAAACGGGAGT
Found at i:42012600 original size:20 final size:20
Alignment explanation
Indices: 42012554--42012600 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
42012544 AGCTCGTTTC
*
42012554 CAGCTCACTCGAGCTCAAGT
1 CAGCTCACTCAAGCTCAAGT
* * *
42012574 CAACTCATTCAAGCTCAATT
1 CAGCTCACTCAAGCTCAAGT
42012594 CAGCTCA
1 CAGCTCA
42012601 ATCTTAACCC
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.30, C:0.34, G:0.13, T:0.23
Consensus pattern (20 bp):
CAGCTCACTCAAGCTCAAGT
Found at i:42017215 original size:21 final size:21
Alignment explanation
Indices: 42017189--42017245 Score: 71
Period size: 21 Copynumber: 2.7 Consensus size: 21
42017179 TTGGTATTTG
42017189 GGAATTGGTACGAAATGATAT
1 GGAATTGGTACGAAATGATAT
*
42017210 GGAATTGGT-CTGAAATGGTAT
1 GGAATTGGTAC-GAAATGATAT
*
42017231 GGTATTTGGTACGAA
1 GG-AATTGGTACGAA
42017246 TTGGTAATGG
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
20 1 0.03
21 20 0.65
22 9 0.29
23 1 0.03
ACGTcount: A:0.32, C:0.05, G:0.32, T:0.32
Consensus pattern (21 bp):
GGAATTGGTACGAAATGATAT
Found at i:42018824 original size:12 final size:11
Alignment explanation
Indices: 42018791--42018821 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
42018781 GAAATTCGAA
*
42018791 GAAAAAAAATC
1 GAAAAAAAATT
42018802 GAAAAAAAATT
1 GAAAAAAAATT
42018813 GAAAAAAAA
1 GAAAAAAAA
42018822 ATTTCGAAGT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.77, C:0.03, G:0.10, T:0.10
Consensus pattern (11 bp):
GAAAAAAAATT
Found at i:42019936 original size:21 final size:20
Alignment explanation
Indices: 42019891--42019938 Score: 53
Period size: 21 Copynumber: 2.4 Consensus size: 20
42019881 TGCAAGCGAG
*
42019891 AAAGAGAAATTGAAAGAAAA
1 AAAGAAAAATTGAAAGAAAA
*
42019911 GAAGAAAAGATTGAAA-AAGAA
1 AAAGAAAA-ATTGAAAGAA-AA
42019932 AAAGAAA
1 AAAGAAA
42019939 TCCAAAAAGA
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
20 8 0.35
21 15 0.65
ACGTcount: A:0.71, C:0.00, G:0.21, T:0.08
Consensus pattern (20 bp):
AAAGAAAAATTGAAAGAAAA
Found at i:42025299 original size:10 final size:9
Alignment explanation
Indices: 42025276--42025352 Score: 91
Period size: 10 Copynumber: 7.9 Consensus size: 9
42025266 TGCGAATAAC
*
42025276 GAGCTAAAT
1 GAGCTGAAT
42025285 GAGCTGAATT
1 GAGCTGAA-T
42025295 GAGCTCGAAT
1 GAGCT-GAAT
42025305 GAGCTCGAAT
1 GAGCT-GAAT
42025315 GAGCATGAAT
1 GAGC-TGAAT
42025325 GAGCTGAATT
1 GAGCTGAA-T
42025335 GAGCTCGAAT
1 GAGCT-GAAT
42025345 GAGCTGAA
1 GAGCTGAA
42025353 CCGCATGAAA
Statistics
Matches: 62, Mismatches: 1, Indels: 10
0.85 0.01 0.14
Matches are distributed among these distances:
9 14 0.23
10 41 0.66
11 7 0.11
ACGTcount: A:0.34, C:0.14, G:0.30, T:0.22
Consensus pattern (9 bp):
GAGCTGAAT
Found at i:42025307 original size:20 final size:20
Alignment explanation
Indices: 42025282--42025352 Score: 110
Period size: 20 Copynumber: 3.5 Consensus size: 20
42025272 TAACGAGCTA
42025282 AATGAGCTGAATTGAGCTCG
1 AATGAGCTGAATTGAGCTCG
42025302 AATGAGCTCGAA-TGAGCAT-G
1 AATGAGCT-GAATTGAGC-TCG
42025322 AATGAGCTGAATTGAGCTCG
1 AATGAGCTGAATTGAGCTCG
42025342 AATGAGCTGAA
1 AATGAGCTGAA
42025353 CCGCATGAAA
Statistics
Matches: 47, Mismatches: 0, Indels: 8
0.85 0.00 0.15
Matches are distributed among these distances:
19 4 0.09
20 39 0.83
21 4 0.09
ACGTcount: A:0.34, C:0.14, G:0.30, T:0.23
Consensus pattern (20 bp):
AATGAGCTGAATTGAGCTCG
Found at i:42027314 original size:20 final size:20
Alignment explanation
Indices: 42027289--42027339 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
42027279 TTGTACGGGA
* *
42027289 TTTGCACTTTGGTGCCTCTG
1 TTTGCACTTCGATGCCTCTG
42027309 TTTGCACTTCGATGCCTCTG
1 TTTGCACTTCGATGCCTCTG
* *
42027329 TATACACTTCG
1 TTTGCACTTCG
42027340 GTGTCCCTAT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.12, C:0.27, G:0.20, T:0.41
Consensus pattern (20 bp):
TTTGCACTTCGATGCCTCTG
Found at i:42027559 original size:7 final size:7
Alignment explanation
Indices: 42027547--42027571 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
42027537 GATATTAATA
42027547 AATGTTC
1 AATGTTC
42027554 AATGTTC
1 AATGTTC
42027561 AATGTTC
1 AATGTTC
42027568 AATG
1 AATG
42027572 AATTACTTGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.32, C:0.12, G:0.16, T:0.40
Consensus pattern (7 bp):
AATGTTC
Found at i:42033881 original size:8 final size:8
Alignment explanation
Indices: 42033850--42033881 Score: 55
Period size: 8 Copynumber: 4.0 Consensus size: 8
42033840 AGTAATAGAA
*
42033850 ATGCAACA
1 ATGCAACC
42033858 ATGCAACC
1 ATGCAACC
42033866 ATGCAACC
1 ATGCAACC
42033874 ATGCAACC
1 ATGCAACC
42033882 CATCCCAATC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
8 23 1.00
ACGTcount: A:0.41, C:0.34, G:0.12, T:0.12
Consensus pattern (8 bp):
ATGCAACC
Found at i:42034170 original size:23 final size:23
Alignment explanation
Indices: 42034143--42034197 Score: 56
Period size: 26 Copynumber: 2.3 Consensus size: 23
42034133 ATGATCAGCA
* *
42034143 CAAAGCCACCAGTAGCATCGCAG
1 CAAAGCCAACAGCAGCATCGCAG
*
42034166 CAAAGTTGCCAACAGCAGTATCGCAG
1 CAAA---GCCAACAGCAGCATCGCAG
42034192 CAAAGC
1 CAAAGC
42034198 TGCCAATAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 6
0.74 0.09 0.17
Matches are distributed among these distances:
23 6 0.23
26 20 0.77
ACGTcount: A:0.36, C:0.31, G:0.22, T:0.11
Consensus pattern (23 bp):
CAAAGCCAACAGCAGCATCGCAG
Found at i:42034211 original size:26 final size:26
Alignment explanation
Indices: 42034159--42034212 Score: 72
Period size: 26 Copynumber: 2.1 Consensus size: 26
42034149 CACCAGTAGC
* *
42034159 ATCGCAGCAAAGTTGCCAACAGCAGT
1 ATCGCAGCAAAGCTGCCAACAACAGT
* *
42034185 ATCGCAGCAAAGCTGCCAATAATAGT
1 ATCGCAGCAAAGCTGCCAACAACAGT
42034211 AT
1 AT
42034213 ATATGGCCAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.37, C:0.24, G:0.20, T:0.19
Consensus pattern (26 bp):
ATCGCAGCAAAGCTGCCAACAACAGT
Found at i:42034332 original size:24 final size:24
Alignment explanation
Indices: 42034301--42034402 Score: 105
Period size: 24 Copynumber: 4.2 Consensus size: 24
42034291 GCCATGCTCA
42034301 AAATCAGTCATACAAATCACAGAC
1 AAATCAGTCATACAAATCACAGAC
* * *
42034325 AAATCAGTCATACCAATCATATAC
1 AAATCAGTCATACAAATCACAGAC
* ** * *
42034349 AAATCACTCATTTAAATCACTGAA
1 AAATCAGTCATACAAATCACAGAC
** *
42034373 AAATCAGTCATTTACATCACAGAC
1 AAATCAGTCATACAAATCACAGAC
42034397 AAATCA
1 AAATCA
42034403 ACCATTTACA
Statistics
Matches: 63, Mismatches: 15, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
24 63 1.00
ACGTcount: A:0.47, C:0.24, G:0.06, T:0.24
Consensus pattern (24 bp):
AAATCAGTCATACAAATCACAGAC
Found at i:42034408 original size:24 final size:24
Alignment explanation
Indices: 42034347--42034412 Score: 71
Period size: 24 Copynumber: 2.8 Consensus size: 24
42034337 CCAATCATAT
* *
42034347 ACAAATC-ACTCATTTAAATCACTG
1 ACAAATCAAC-CATTTACATCACAG
* **
42034371 AAAAATCAGTCATTTACATCACAG
1 ACAAATCAACCATTTACATCACAG
42034395 ACAAATCAACCATTTACA
1 ACAAATCAACCATTTACA
42034413 CTCGAAAGGC
Statistics
Matches: 33, Mismatches: 8, Indels: 2
0.77 0.19 0.05
Matches are distributed among these distances:
24 33 1.00
ACGTcount: A:0.45, C:0.24, G:0.05, T:0.26
Consensus pattern (24 bp):
ACAAATCAACCATTTACATCACAG
Found at i:42034533 original size:27 final size:27
Alignment explanation
Indices: 42034429--42034681 Score: 154
Period size: 27 Copynumber: 9.4 Consensus size: 27
42034419 AGGCAAAATA
*
42034429 GTCA-TTTACCCT-CTAGGGGCATTACA
1 GTCATTTTACCCTAC-AGGGGCATTACG
* * ** * **
42034455 GTCATTTTACCTTATATTGGTATTTTG
1 GTCATTTTACCCTACAGGGGCATTACG
* * *
42034482 GTCATTTAACCCTAC-GGGGATATTATG
1 GTCATTTTACCCTACAGGGG-CATTACG
*
42034509 ATCATTTTACCCTACAGGGGCATTACG
1 GTCATTTTACCCTACAGGGGCATTACG
** ** *
42034536 GTCATTTTACCCT-GTGGGGGTTTTCG
1 GTCATTTTACCCTACAGGGGCATTACG
* *
42034562 GTCATTTTACCTTATAGGGGCATTACG
1 GTCATTTTACCCTACAGGGGCATTACG
* * *
42034589 GTCATTTTACCCTATAGTGGCATTACA
1 GTCATTTTACCCTACAGGGGCATTACG
* ** ** * *
42034616 GTCATTTTACCTTATGGGGGTTTTTCA
1 GTCATTTTACCCTACAGGGGCATTACG
* * * *
42034643 GTCATTTTACCTTACAAGGGTATTTCG
1 GTCATTTTACCCTACAGGGGCATTACG
*
42034670 GTAATTTTACCC
1 GTCATTTTACCC
42034682 ATCGAGGGTA
Statistics
Matches: 176, Mismatches: 46, Indels: 9
0.76 0.20 0.04
Matches are distributed among these distances:
26 26 0.15
27 146 0.83
28 4 0.02
ACGTcount: A:0.21, C:0.20, G:0.20, T:0.40
Consensus pattern (27 bp):
GTCATTTTACCCTACAGGGGCATTACG
Found at i:42034648 original size:134 final size:133
Alignment explanation
Indices: 42034429--42034681 Score: 301
Period size: 134 Copynumber: 1.9 Consensus size: 133
42034419 AGGCAAAATA
* * * * ***
42034429 GTCATTTACCCTCTAGGGGCATTACAGTCATTTTACCTTATATTGGTATTTTGGTCATTTAACCC
1 GTCATTTACCCTATAGGGGCATTACAGTCATTTTACCCTATAGTGGCATTACAGTCATTTAACCC
* * *
42034494 TACGGGGATATTATGATCATTTTACCCTACAGGGGCATTACGGTCATTTTACCCTGTGGGGGTTT
66 TACGGGGATATTATCATCATTTTACCCTACAAGGGCATTACGGTAATTTTACCCTGTGGGGGTTT
42034559 TCG
131 TCG
* * *
42034562 GTCATTTTACCTTATAGGGGCATTACGGTCATTTTACCCTATAGTGGCATTACAGTCATTTTACC
1 GTCA-TTTACCCTATAGGGGCATTACAGTCATTTTACCCTATAGTGGCATTACAGTCATTTAACC
* * * * * * *
42034627 TTATGGGGGT-TTTTCAGTCATTTTACCTTACAAGGGTATTTCGGTAATTTTACCC
65 CTACGGGGATATTATCA-TCATTTTACCCTACAAGGGCATTACGGTAATTTTACCC
42034682 ATCGAGGGTA
Statistics
Matches: 98, Mismatches: 20, Indels: 3
0.81 0.17 0.02
Matches are distributed among these distances:
133 8 0.08
134 90 0.92
ACGTcount: A:0.21, C:0.20, G:0.20, T:0.40
Consensus pattern (133 bp):
GTCATTTACCCTATAGGGGCATTACAGTCATTTTACCCTATAGTGGCATTACAGTCATTTAACCC
TACGGGGATATTATCATCATTTTACCCTACAAGGGCATTACGGTAATTTTACCCTGTGGGGGTTT
TCG
Found at i:42034841 original size:27 final size:27
Alignment explanation
Indices: 42034659--42034829 Score: 254
Period size: 27 Copynumber: 6.3 Consensus size: 27
42034649 TTACCTTACA
*
42034659 AGGGTATTTCGGTAATTTTACCCATCG
1 AGGGTATTTCGATAATTTTACCCATCG
*
42034686 AGGGTATTTCGATAGTTTTACCCATCG
1 AGGGTATTTCGATAATTTTACCCATCG
* * *
42034713 GGGGTATTTCGATAATCTTACCCATCA
1 AGGGTATTTCGATAATTTTACCCATCG
* *
42034740 AGGGTATTT-TAGTAATTTTACCCGTCG
1 AGGGTATTTCGA-TAATTTTACCCATCG
42034767 AGGGTATTTCGATAATTTTACCCATCG
1 AGGGTATTTCGATAATTTTACCCATCG
*
42034794 AGGGCATTTCGATAATTTTACCCATCG
1 AGGGTATTTCGATAATTTTACCCATCG
42034821 AGGGTATTT
1 AGGGTATTT
42034830 GGTAATTATT
Statistics
Matches: 127, Mismatches: 15, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
26 1 0.01
27 125 0.98
28 1 0.01
ACGTcount: A:0.24, C:0.18, G:0.21, T:0.37
Consensus pattern (27 bp):
AGGGTATTTCGATAATTTTACCCATCG
Found at i:42037025 original size:20 final size:20
Alignment explanation
Indices: 42037002--42037039 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
42036992 CCTCTATTTG
* *
42037002 CACTTCGGTGTCCCTGTTCA
1 CACTACGGTGCCCCTGTTCA
42037022 CACTACGGTGCCCCTGTT
1 CACTACGGTGCCCCTGTT
42037040 TGCACATTTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.11, C:0.37, G:0.21, T:0.32
Consensus pattern (20 bp):
CACTACGGTGCCCCTGTTCA
Found at i:42037579 original size:13 final size:13
Alignment explanation
Indices: 42037563--42037588 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
42037553 AATGTTCAAG
42037563 TGAAATGGTTATA
1 TGAAATGGTTATA
42037576 TGAAATGGTTATA
1 TGAAATGGTTATA
42037589 AGGAAAAATA
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:0.38, C:0.00, G:0.23, T:0.38
Consensus pattern (13 bp):
TGAAATGGTTATA
Found at i:42051532 original size:12 final size:12
Alignment explanation
Indices: 42051515--42051543 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
42051505 ATGTCGAAGG
42051515 AAAAAAATTCAA
1 AAAAAAATTCAA
42051527 AAAAAAATTCAA
1 AAAAAAATTCAA
42051539 AAAAA
1 AAAAA
42051544 TGCAAGTTGT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.79, C:0.07, G:0.00, T:0.14
Consensus pattern (12 bp):
AAAAAAATTCAA
Found at i:42052497 original size:24 final size:24
Alignment explanation
Indices: 42052470--42052524 Score: 65
Period size: 24 Copynumber: 2.3 Consensus size: 24
42052460 ATAAAATAGC
*
42052470 AAAAGATAAAGAAAAAGAAATTGA
1 AAAAGAGAAAGAAAAAGAAATTGA
* * * *
42052494 AAAAGAGAAAGAGAGAGGATTTGA
1 AAAAGAGAAAGAAAAAGAAATTGA
42052518 AAAAGAG
1 AAAAGAG
42052525 TGTGAGCCAG
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.64, C:0.00, G:0.25, T:0.11
Consensus pattern (24 bp):
AAAAGAGAAAGAAAAAGAAATTGA
Found at i:42052606 original size:18 final size:19
Alignment explanation
Indices: 42052572--42052612 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
42052562 ATGAAAAAAG
*
42052572 AAAAAAAGAAATTGAGACA
1 AAAAAAAGAAATCGAGACA
*
42052591 AAAAAAAGAAA-CGAGAGA
1 AAAAAAAGAAATCGAGACA
42052609 AAAA
1 AAAA
42052613 GAGACAAGCG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 9 0.45
19 11 0.55
ACGTcount: A:0.73, C:0.05, G:0.17, T:0.05
Consensus pattern (19 bp):
AAAAAAAGAAATCGAGACA
Found at i:42052609 original size:28 final size:27
Alignment explanation
Indices: 42052565--42052619 Score: 65
Period size: 28 Copynumber: 2.0 Consensus size: 27
42052555 AGAGAAAATG
**
42052565 AAAAAAGAAAAAAAGAAATTGAGACAA
1 AAAAAAGAAAAAAAGAAAAAGAGACAA
* *
42052592 AAAAAAGAAACGAGAGAAAAAGAGACAA
1 AAAAAAGAAA-AAAAGAAAAAGAGACAA
42052620 GCGAACCAGA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
27 10 0.43
28 13 0.57
ACGTcount: A:0.73, C:0.05, G:0.18, T:0.04
Consensus pattern (27 bp):
AAAAAAGAAAAAAAGAAAAAGAGACAA
Found at i:42056996 original size:48 final size:48
Alignment explanation
Indices: 42056944--42057049 Score: 137
Period size: 48 Copynumber: 2.2 Consensus size: 48
42056934 ATTGTCTTTC
*
42056944 TTTCTTTTTCAATTT-TCTCT-TTTTCCTCACA-CTTTTGTTCAATCTCAA
1 TTTCTTTTTCAATTTCTCTCTCTTTT--TCACATCCTTT-TTCAATCTCAA
* *
42056992 TTTCTTTTTCGATTTCTTTCTCTTTTTCACATCCTTTTTCAATCTCAA
1 TTTCTTTTTCAATTTCTCTCTCTTTTTCACATCCTTTTTCAATCTCAA
42057040 TTTCTTTTTC
1 TTTCTTTTTC
42057050 CATGACACTC
Statistics
Matches: 52, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
48 40 0.77
49 8 0.15
50 4 0.08
ACGTcount: A:0.14, C:0.25, G:0.02, T:0.59
Consensus pattern (48 bp):
TTTCTTTTTCAATTTCTCTCTCTTTTTCACATCCTTTTTCAATCTCAA
Found at i:42058093 original size:12 final size:13
Alignment explanation
Indices: 42058074--42058108 Score: 70
Period size: 13 Copynumber: 2.7 Consensus size: 13
42058064 ATATACTTCG
42058074 ATTTTTTTTTTGA
1 ATTTTTTTTTTGA
42058087 ATTTTTTTTTTGA
1 ATTTTTTTTTTGA
42058100 ATTTTTTTT
1 ATTTTTTTT
42058109 CAAATTTCCT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.14, C:0.00, G:0.06, T:0.80
Consensus pattern (13 bp):
ATTTTTTTTTTGA
Found at i:42061909 original size:10 final size:10
Alignment explanation
Indices: 42061894--42061927 Score: 59
Period size: 10 Copynumber: 3.3 Consensus size: 10
42061884 GTTTCGAAGG
42061894 AAAAAAATTC
1 AAAAAAATTC
42061904 AAAAAAAATTC
1 -AAAAAAATTC
42061915 AAAAAAATTC
1 AAAAAAATTC
42061925 AAA
1 AAA
42061928 TTGTAATTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
10 13 0.57
11 10 0.43
ACGTcount: A:0.74, C:0.09, G:0.00, T:0.18
Consensus pattern (10 bp):
AAAAAAATTC
Found at i:42061910 original size:11 final size:11
Alignment explanation
Indices: 42061894--42061927 Score: 61
Period size: 11 Copynumber: 3.2 Consensus size: 11
42061884 GTTTCGAAGG
42061894 AAAAAAATTCA
1 AAAAAAATTCA
42061905 AAAAAAATTC-
1 AAAAAAATTCA
42061915 AAAAAAATTCA
1 AAAAAAATTCA
42061926 AA
1 AA
42061928 TTGTAATTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
10 10 0.45
11 12 0.55
ACGTcount: A:0.74, C:0.09, G:0.00, T:0.18
Consensus pattern (11 bp):
AAAAAAATTCA
Found at i:42084390 original size:27 final size:27
Alignment explanation
Indices: 42084359--42084535 Score: 185
Period size: 27 Copynumber: 6.5 Consensus size: 27
42084349 ATATTGAGCC
* ** * *
42084359 CGCACACTTAGTGCTATGTAATCAACT
1 CGCACACTTAGTGCCACATAGTCAATT
* * *
42084386 CGCACACTTAGTGCCACGTAATCAAAT
1 CGCACACTTAGTGCCACATAGTCAATT
* *
42084413 CGGACACTTAGTGCCACATAGTCCATTT
1 CGCACACTTAGTGCCACATAGT-CAATT
* *
42084441 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCCACATAGTCAATT
* *
42084468 CGCACACTTAGTG-CATCATATTCATTT
1 CGCACACTTAGTGCCA-CATAGTCAATT
* *
42084495 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCCACATAGTCAATT
42084522 CGCACACTTAGTGC
1 CGCACACTTAGTGC
42084536 TGTACAATTT
Statistics
Matches: 127, Mismatches: 20, Indels: 6
0.83 0.13 0.04
Matches are distributed among these distances:
26 1 0.01
27 103 0.81
28 23 0.18
ACGTcount: A:0.28, C:0.28, G:0.16, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCCACATAGTCAATT
Found at i:42084426 original size:54 final size:54
Alignment explanation
Indices: 42084359--42084536 Score: 205
Period size: 54 Copynumber: 3.3 Consensus size: 54
42084349 ATATTGAGCC
* ** * *
42084359 CGCACACTTAGTGCTATGTAATCAACTCGCACACTTAGTGCCACGTAATCAAAT
1 CGCACACTTAGTGCTATATAATCATTTCGCACACTTAGTGCCACATAGTCAAAT
* * * * * * *
42084413 CGGACACTTAGTGCCACATAGTCCATTTCGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTATATAAT-CATTTCGCACACTTAGTGCCACATAGTCAAAT
* *
42084468 CGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTAT-ATAATCATTTCGCACACTTAGTGCCACATAGTCAAAT
42084522 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
42084537 GTACAATTTA
Statistics
Matches: 102, Mismatches: 19, Indels: 5
0.81 0.15 0.04
Matches are distributed among these distances:
54 60 0.59
55 42 0.41
ACGTcount: A:0.28, C:0.28, G:0.16, T:0.28
Consensus pattern (54 bp):
CGCACACTTAGTGCTATATAATCATTTCGCACACTTAGTGCCACATAGTCAAAT
Found at i:42084502 original size:82 final size:81
Alignment explanation
Indices: 42084380--42084535 Score: 206
Period size: 82 Copynumber: 1.9 Consensus size: 81
42084370 TGCTATGTAA
* * * **
42084380 TCAACTCGCACACTTAGTGCCACGTAATCAAATCGGACACTTAGTGCCACATAGTCCATTTCGCA
1 TCAACTCGCACACTTAGTGCCACATAATCAAATCGCACACTTAGTGCAACATAGT-CAAATCGCA
42084445 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * **
42084462 TCAATTCGCACACTTAGTG-CATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAATCGCA
1 TCAACTCGCACACTTAGTGCCA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCA
42084526 CACTTAGTGC
65 CACTTAGTGC
42084536 TGTACAATTT
Statistics
Matches: 64, Mismatches: 9, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
81 19 0.30
82 45 0.70
ACGTcount: A:0.28, C:0.29, G:0.16, T:0.27
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCCACATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCAC
ACTTAGTGCCGCATGG
Found at i:42101185 original size:27 final size:26
Alignment explanation
Indices: 42101155--42101232 Score: 111
Period size: 27 Copynumber: 2.9 Consensus size: 26
42101145 GGCATAACGG
*
42101155 TCATTTTACCCCATGGGGGTATTTCGA
1 TCATTTT-CCCCTTGGGGGTATTTCGA
*
42101182 TCATTTTCCCCTTCGGGGGTATTTCGG
1 TCATTTTCCCCTT-GGGGGTATTTCGA
42101209 TCATTTTCCCCTTTGGGGGTATTT
1 TCATTTTCCCC-TTGGGGGTATTT
42101233 TAGTAATTTT
Statistics
Matches: 47, Mismatches: 2, Indels: 4
0.89 0.04 0.08
Matches are distributed among these distances:
26 5 0.11
27 40 0.85
28 2 0.04
ACGTcount: A:0.12, C:0.23, G:0.23, T:0.42
Consensus pattern (26 bp):
TCATTTTCCCCTTGGGGGTATTTCGA
Found at i:42101241 original size:27 final size:27
Alignment explanation
Indices: 42101169--42101249 Score: 92
Period size: 27 Copynumber: 3.0 Consensus size: 27
42101159 TTTACCCCAT
*
42101169 GGGGGTATTTC-GATCATTTTCCCCTTC
1 GGGGGTATTTCAG-TAATTTTCCCCTTC
* * *
42101196 GGGGGTATTTCGGTCATTTTCCCCTTT
1 GGGGGTATTTCAGTAATTTTCCCCTTC
* *
42101223 GGGGGTATTTTAGTAATTTTACCCTTC
1 GGGGGTATTTCAGTAATTTTCCCCTTC
42101250 AAAGATATTT
Statistics
Matches: 47, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
27 46 0.98
28 1 0.02
ACGTcount: A:0.12, C:0.21, G:0.23, T:0.43
Consensus pattern (27 bp):
GGGGGTATTTCAGTAATTTTCCCCTTC
Found at i:42104481 original size:22 final size:22
Alignment explanation
Indices: 42104456--42104497 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
42104446 TACAAAGTTG
42104456 ATAAT-AAT-TAA-TATATATT
1 ATAATAAATATAATTATATATT
42104475 ATAATAAATATAATTATATATT
1 ATAATAAATATAATTATATATT
42104497 A
1 A
42104498 GTTATTATCA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
19 5 0.25
20 3 0.15
21 3 0.15
22 9 0.45
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (22 bp):
ATAATAAATATAATTATATATT
Found at i:42104484 original size:16 final size:15
Alignment explanation
Indices: 42104459--42104492 Score: 50
Period size: 16 Copynumber: 2.2 Consensus size: 15
42104449 AAAGTTGATA
*
42104459 ATAATTAATATATATT
1 ATAATAAATATA-ATT
42104475 ATAATAAATATAATT
1 ATAATAAATATAATT
42104490 ATA
1 ATA
42104493 TATTAGTTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 6 0.35
16 11 0.65
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (15 bp):
ATAATAAATATAATT
Done.