Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009463.1 Hibiscus syriacus cultivar Beakdansim tig00113726_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: 3931635
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 12 of 20
Found at i:2293722 original size:21 final size:20
Alignment explanation
Indices: 2293644--2293715 Score: 83
Period size: 20 Copynumber: 3.5 Consensus size: 20
2293634 TTCTAAACTT
*
2293644 AAAATCGCAACATGAAAATG
1 AAAATCGCAACACGAAAATG
2293664 AAAATCGCAACACGAAAATG
1 AAAATCGCAACACGAAAATG
** *
2293684 ACTATCACAACGA-GAGAAATG
1 AAAATCGCAAC-ACGA-AAATG
2293705 AAAATCGCAAC
1 AAAATCGCAAC
2293716 TAGAGAATCG
Statistics
Matches: 43, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
20 29 0.67
21 14 0.33
ACGTcount: A:0.53, C:0.19, G:0.15, T:0.12
Consensus pattern (20 bp):
AAAATCGCAACACGAAAATG
Found at i:2293736 original size:33 final size:33
Alignment explanation
Indices: 2293699--2293779 Score: 119
Period size: 33 Copynumber: 2.5 Consensus size: 33
2293689 CACAACGAGA
2293699 GAAATGAAAATCGCAACT-AGAGAATCGCAACGC
1 GAAATGAAAATCGCAA-TGAGAGAATCGCAACGC
*
2293732 GAAATGAAAATCGCAATGAGATAATCGCAACGC
1 GAAATGAAAATCGCAATGAGAGAATCGCAACGC
**
2293765 GAAACCAAAATCGCA
1 GAAATGAAAATCGCA
2293780 TTGCGATTTT
Statistics
Matches: 44, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
32 1 0.02
33 43 0.98
ACGTcount: A:0.47, C:0.21, G:0.20, T:0.12
Consensus pattern (33 bp):
GAAATGAAAATCGCAATGAGAGAATCGCAACGC
Found at i:2293797 original size:19 final size:19
Alignment explanation
Indices: 2293775--2293906 Score: 139
Period size: 19 Copynumber: 7.1 Consensus size: 19
2293765 GAAACCAAAA
*
2293775 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
2293794 TCGCGTTGCGATTTTAATT
1 TCGCGTTGCGATTTTCATT
2293813 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
2293827 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
* **
2293846 TCGCGTTACGATAGTCATT
1 TCGCGTTGCGATTTTCATT
*
2293865 TCCACGTTGCGATTTTCATT
1 T-CGCGTTGCGATTTTCATT
*
2293885 CTCTCGTTGCGATTTTCATT
1 -TCGCGTTGCGATTTTCATT
2293905 TC
1 TC
2293907 AACCAAAAGA
Statistics
Matches: 93, Mismatches: 13, Indels: 14
0.77 0.11 0.12
Matches are distributed among these distances:
14 10 0.11
16 3 0.03
17 2 0.02
19 46 0.49
20 31 0.33
21 1 0.01
ACGTcount: A:0.14, C:0.23, G:0.18, T:0.45
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:2293877 original size:20 final size:19
Alignment explanation
Indices: 2293830--2293907 Score: 57
Period size: 20 Copynumber: 4.0 Consensus size: 19
2293820 GCGATTCTCT
** *
2293830 CGTTGCGATTTTCATTTCG
1 CGTTGCGATAGTCATTTCA
*
2293849 CGTTACGATAGTCATTTCCA
1 CGTTGCGATAGTCATTT-CA
** *
2293869 CGTTGCGATTTTCATTCTCT
1 CGTTGCGATAGTCATT-TCA
**
2293889 CGTTGCGATTTTCATTTCA
1 CGTTGCGATAGTCATTTCA
2293908 ACCAAAAGAC
Statistics
Matches: 48, Mismatches: 9, Indels: 4
0.79 0.15 0.07
Matches are distributed among these distances:
19 16 0.33
20 31 0.65
21 1 0.02
ACGTcount: A:0.15, C:0.23, G:0.17, T:0.45
Consensus pattern (19 bp):
CGTTGCGATAGTCATTTCA
Found at i:2295997 original size:94 final size:94
Alignment explanation
Indices: 2295595--2295974 Score: 638
Period size: 94 Copynumber: 4.1 Consensus size: 94
2295585 TAGATTGCTT
* *
2295595 AGTAAATTTATTCGGTTGCTGCCAATACTGCTAAACTGTTTATTCTTTAACACTGTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
2295660 ATTTGTCTTTTGTTTTGTCTTTTGGTTG-A
66 ATTTGTC-TTTGTTTTGTCTTTTGGTTGAA
*
2295689 AGTAAATTTATTTGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
2295754 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
*
2295783 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
* * *
2295848 ATTTTTTTTTGTTTTATCTTTTGGTTGAA
66 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
* * * *
2295877 AGTAAATTTGTTCGGTTGCTGACAATTCTGCTAAACTGTGTATTCTTTAATACTCTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
2295942 ATTTGTCTTTGTTTTGTCTTTTGGTTG-A
66 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
2295970 AGTAA
1 AGTAA
2295975 TGCAATCCAT
Statistics
Matches: 271, Mismatches: 14, Indels: 3
0.94 0.05 0.01
Matches are distributed among these distances:
93 26 0.10
94 245 0.90
ACGTcount: A:0.22, C:0.12, G:0.19, T:0.48
Consensus pattern (94 bp):
AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:2296170 original size:14 final size:14
Alignment explanation
Indices: 2296151--2296206 Score: 58
Period size: 14 Copynumber: 3.6 Consensus size: 14
2296141 TCATTTCGCA
2296151 TTGCGATTCTCTCG
1 TTGCGATTCTCTCG
*
2296165 TTGCGATTTTCATTTCG
1 TTGCGA--TTC-TCTCG
2296182 CATTGCGATTCTCTCG
1 --TTGCGATTCTCTCG
2296198 TTGCGATTC
1 TTGCGATTC
2296207 ATTTCGCGTT
Statistics
Matches: 35, Mismatches: 2, Indels: 10
0.74 0.04 0.21
Matches are distributed among these distances:
14 15 0.43
16 7 0.20
17 7 0.20
19 6 0.17
ACGTcount: A:0.11, C:0.25, G:0.20, T:0.45
Consensus pattern (14 bp):
TTGCGATTCTCTCG
Found at i:2296174 original size:33 final size:33
Alignment explanation
Indices: 2296137--2296221 Score: 147
Period size: 33 Copynumber: 2.6 Consensus size: 33
2296127 TCGCGTTGAT
2296137 ATTTTCATTTCGCATTGCGATTCTCTCGTTGCG
1 ATTTTCATTTCGCATTGCGATTCTCTCGTTGCG
2296170 ATTTTCATTTCGCATTGCGATTCTCTCGTTGCG
1 ATTTTCATTTCGCATTGCGATTCTCTCGTTGCG
*
2296203 A--TTCATTTCGCGTTGCGAT
1 ATTTTCATTTCGCATTGCGAT
2296222 AGTCATTTTT
Statistics
Matches: 51, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
31 17 0.33
33 34 0.67
ACGTcount: A:0.13, C:0.24, G:0.19, T:0.45
Consensus pattern (33 bp):
ATTTTCATTTCGCATTGCGATTCTCTCGTTGCG
Found at i:2296189 original size:19 final size:19
Alignment explanation
Indices: 2296137--2296191 Score: 66
Period size: 19 Copynumber: 3.2 Consensus size: 19
2296127 TCGCGTTGAT
2296137 ATTTTCATTTCGCATTGCG
1 ATTTTCATTTCGCATTGCG
*
2296156 A--TTC-TCTCG--TTGCG
1 ATTTTCATTTCGCATTGCG
2296170 ATTTTCATTTCGCATTGCG
1 ATTTTCATTTCGCATTGCG
2296189 ATT
1 ATT
2296192 CTCTCGTTGC
Statistics
Matches: 29, Mismatches: 2, Indels: 10
0.71 0.05 0.24
Matches are distributed among these distances:
14 6 0.21
16 7 0.24
17 7 0.24
19 9 0.31
ACGTcount: A:0.15, C:0.22, G:0.16, T:0.47
Consensus pattern (19 bp):
ATTTTCATTTCGCATTGCG
Found at i:2296722 original size:42 final size:42
Alignment explanation
Indices: 2296646--2296734 Score: 106
Period size: 42 Copynumber: 2.1 Consensus size: 42
2296636 GACTCGCCTG
* * *
2296646 TCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCCCCTA
1 TCATCCCTCAAGAGTCCACTCCCAGCGTTCAAGAGGCCCCTA
* * * * *
2296688 TCATTCCTCGAGAGTCCCCTCCCAGCGTTCAAGAGGCCACTG
1 TCATCCCTCAAGAGTCCACTCCCAGCGTTCAAGAGGCCCCTA
2296730 TCATC
1 TCATC
2296735 GTTGAAGAGG
Statistics
Matches: 38, Mismatches: 9, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
42 38 1.00
ACGTcount: A:0.21, C:0.37, G:0.18, T:0.24
Consensus pattern (42 bp):
TCATCCCTCAAGAGTCCACTCCCAGCGTTCAAGAGGCCCCTA
Found at i:2298134 original size:14 final size:14
Alignment explanation
Indices: 2298115--2298148 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
2298105 TGTTTAATTT
2298115 ATTTGTAAAAGATG
1 ATTTGTAAAAGATG
*
2298129 ATTTGTAAAAGTTG
1 ATTTGTAAAAGATG
2298143 ATTTGT
1 ATTTGT
2298149 TTAATTGATG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.35, C:0.00, G:0.21, T:0.44
Consensus pattern (14 bp):
ATTTGTAAAAGATG
Found at i:2298315 original size:33 final size:33
Alignment explanation
Indices: 2298271--2298346 Score: 125
Period size: 33 Copynumber: 2.3 Consensus size: 33
2298261 ATGCGAAATG
*
2298271 AAAATCACAACGCGAAATGAAAATCACAACGAC
1 AAAATCGCAACGCGAAATGAAAATCACAACGAC
**
2298304 AAAATCGCAACGCGAAATGAAAATTGCAACGAC
1 AAAATCGCAACGCGAAATGAAAATCACAACGAC
2298337 AAAATCGCAA
1 AAAATCGCAA
2298347 AGCAAAACTA
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 40 1.00
ACGTcount: A:0.53, C:0.22, G:0.14, T:0.11
Consensus pattern (33 bp):
AAAATCGCAACGCGAAATGAAAATCACAACGAC
Found at i:2298332 original size:19 final size:19
Alignment explanation
Indices: 2298255--2298334 Score: 80
Period size: 19 Copynumber: 4.5 Consensus size: 19
2298245 AAAAATGACT
*
2298255 ATCGCAATGCGAAATGAAA
1 ATCGCAACGCGAAATGAAA
*
2298274 ATCACAACGCGAAATGAAA
1 ATCGCAACGCGAAATGAAA
* *
2298293 ATCACAA--CG--A-CAAA
1 ATCGCAACGCGAAATGAAA
2298307 ATCGCAACGCGAAATGAAA
1 ATCGCAACGCGAAATGAAA
*
2298326 ATTGCAACG
1 ATCGCAACG
2298335 ACAAAATCGC
Statistics
Matches: 50, Mismatches: 6, Indels: 10
0.76 0.09 0.15
Matches are distributed among these distances:
14 9 0.18
15 1 0.02
16 2 0.04
17 2 0.04
18 1 0.02
19 35 0.70
ACGTcount: A:0.49, C:0.21, G:0.17, T:0.12
Consensus pattern (19 bp):
ATCGCAACGCGAAATGAAA
Found at i:2298359 original size:19 final size:20
Alignment explanation
Indices: 2298337--2298382 Score: 60
Period size: 19 Copynumber: 2.4 Consensus size: 20
2298327 TTGCAACGAC
2298337 AAAATCGCAAA-GCAAAACT
1 AAAATCGCAAACGCAAAACT
*
2298356 AAAATCG-AAACGCGAAACT
1 AAAATCGCAAACGCAAAACT
*
2298375 AAATTCGC
1 AAAATCGC
2298383 GTTGCGATTT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
18 3 0.13
19 20 0.87
ACGTcount: A:0.52, C:0.22, G:0.13, T:0.13
Consensus pattern (20 bp):
AAAATCGCAAACGCAAAACT
Found at i:2298451 original size:34 final size:33
Alignment explanation
Indices: 2298382--2298506 Score: 214
Period size: 33 Copynumber: 3.8 Consensus size: 33
2298372 ACTAAATTCG
* * *
2298382 CGTTGCGATTTTCATTTCGCTTTGCGATTCCCT
1 CGTTGCGATTTTCATTTCGCATTGCAATTCTCT
2298415 CGTTGCGATTTTCATTTTCGCATTGCAATTCTCT
1 CGTTGCGATTTTCA-TTTCGCATTGCAATTCTCT
2298449 CGTTGCGATTTTCATTTCGCATTGCAATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCAATTCTCT
2298482 CGTTGCGATTTTCATTTCGCATTGC
1 CGTTGCGATTTTCATTTCGCATTGC
2298507 GATAGTCATT
Statistics
Matches: 88, Mismatches: 3, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
33 58 0.66
34 30 0.34
ACGTcount: A:0.13, C:0.25, G:0.17, T:0.46
Consensus pattern (33 bp):
CGTTGCGATTTTCATTTCGCATTGCAATTCTCT
Found at i:2298490 original size:67 final size:66
Alignment explanation
Indices: 2298382--2298506 Score: 214
Period size: 67 Copynumber: 1.9 Consensus size: 66
2298372 ACTAAATTCG
* *
2298382 CGTTGCGATTTTCATTTCGCTTTGCGATTCCCTCGTTGCGATTTTCATTTTCGCATTGCAATTCT
1 CGTTGCGATTTTCATTTCGCATTGCAATTCCCTCGTTGCGATTTTCA-TTTCGCATTGCAATTCT
2298447 CT
65 CT
*
2298449 CGTTGCGATTTTCATTTCGCATTGCAATTCTCTCGTTGCGATTTTCATTTCGCATTGC
1 CGTTGCGATTTTCATTTCGCATTGCAATTCCCTCGTTGCGATTTTCATTTCGCATTGC
2298507 GATAGTCATT
Statistics
Matches: 55, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
66 11 0.20
67 44 0.80
ACGTcount: A:0.13, C:0.25, G:0.17, T:0.46
Consensus pattern (66 bp):
CGTTGCGATTTTCATTTCGCATTGCAATTCCCTCGTTGCGATTTTCATTTCGCATTGCAATTCTC
T
Found at i:2298528 original size:20 final size:19
Alignment explanation
Indices: 2298482--2298536 Score: 65
Period size: 20 Copynumber: 2.8 Consensus size: 19
2298472 GCAATTCTCT
**
2298482 CGTTGCGATTTTCATTTCG
1 CGTTGCGATAGTCATTTCG
*
2298501 CATTGCGATAGTCATTTCCG
1 CGTTGCGATAGTCATTT-CG
*
2298521 CGTTGCGATAGACATT
1 CGTTGCGATAGTCATT
2298537 AAGATGATTG
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 14 0.47
20 16 0.53
ACGTcount: A:0.18, C:0.22, G:0.22, T:0.38
Consensus pattern (19 bp):
CGTTGCGATAGTCATTTCG
Found at i:2302010 original size:20 final size:20
Alignment explanation
Indices: 2301983--2302126 Score: 175
Period size: 20 Copynumber: 7.2 Consensus size: 20
2301973 AAATCGCAAA
*
2301983 GCGA-TTACGTATTCTCGTT
1 GCGATTTACGTATTCGCGTT
*
2302002 GCGATTTAC-TAAATCGCGTT
1 GCGATTTACGT-ATTCGCGTT
* *
2302022 GCAATTTACGTAATCGCGTT
1 GCGATTTACGTATTCGCGTT
*
2302042 GCGATTTACGTATTCACGTT
1 GCGATTTACGTATTCGCGTT
2302062 GCGATTTACGTATTCGCGTT
1 GCGATTTACGTATTCGCGTT
* **
2302082 GCGATTTTCCAAATTCGCGTT
1 GCGA-TTTACGTATTCGCGTT
*
2302103 GCGATTTACGTATTCGCATT
1 GCGATTTACGTATTCGCGTT
2302123 GCGA
1 GCGA
2302127 ATTAGGAAAA
Statistics
Matches: 107, Mismatches: 14, Indels: 7
0.84 0.11 0.05
Matches are distributed among these distances:
19 5 0.05
20 84 0.79
21 18 0.17
ACGTcount: A:0.20, C:0.21, G:0.22, T:0.38
Consensus pattern (20 bp):
GCGATTTACGTATTCGCGTT
Found at i:2302030 original size:60 final size:60
Alignment explanation
Indices: 2301965--2302088 Score: 162
Period size: 60 Copynumber: 2.1 Consensus size: 60
2301955 TCTCGTTACG
*
2301965 ATTTACGTAAATCGCAAAGCGA-TTACGTATTCTCGTTGCGATTTAC-TAAATCGCGTTGCA
1 ATTTACGT-AATCGCAAAGCGATTTACGTATTCACGTTGCGATTTACGT-AATCGCGTTGCA
*** * *
2302025 ATTTACGTAATCGCGTTGCGATTTACGTATTCACGTTGCGATTTACGTATTCGCGTTGCG
1 ATTTACGTAATCGCAAAGCGATTTACGTATTCACGTTGCGATTTACGTAATCGCGTTGCA
2302085 ATTT
1 ATTT
2302089 TCCAAATTCG
Statistics
Matches: 56, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
59 10 0.18
60 45 0.80
61 1 0.02
ACGTcount: A:0.23, C:0.19, G:0.20, T:0.37
Consensus pattern (60 bp):
ATTTACGTAATCGCAAAGCGATTTACGTATTCACGTTGCGATTTACGTAATCGCGTTGCA
Found at i:2302031 original size:40 final size:41
Alignment explanation
Indices: 2301958--2302140 Score: 194
Period size: 40 Copynumber: 4.5 Consensus size: 41
2301948 GTCAGAATCT
* *** *
2301958 CGTTACGATTTACGTAAATCGCAAAGCGA-TTACGTATTCT
1 CGTTGCGATTTACGTAAATCGCGTTGCGATTTACGTATTCG
* *
2301998 CGTTGCGATTTAC-TAAATCGCGTTGCAATTTACGTAATCG
1 CGTTGCGATTTACGTAAATCGCGTTGCGATTTACGTATTCG
* *
2302038 CGTTGCGATTTACGT-ATTCACGTTGCGATTTACGTATTCG
1 CGTTGCGATTTACGTAAATCGCGTTGCGATTTACGTATTCG
* *
2302078 CGTTGCGATTTTC-CAAATTCGCGTTGCGATTTACGTATTCG
1 CGTTGCGATTTACGTAAA-TCGCGTTGCGATTTACGTATTCG
* * * *
2302119 CATTGCGAATTAGGAAAATCGC
1 CGTTGCGATTTACGTAAATCGC
2302141 AAAGCGAATT
Statistics
Matches: 118, Mismatches: 20, Indels: 9
0.80 0.14 0.06
Matches are distributed among these distances:
39 11 0.09
40 68 0.58
41 36 0.31
42 3 0.03
ACGTcount: A:0.24, C:0.20, G:0.21, T:0.35
Consensus pattern (41 bp):
CGTTGCGATTTACGTAAATCGCGTTGCGATTTACGTATTCG
Found at i:2302147 original size:21 final size:21
Alignment explanation
Indices: 2302123--2302163 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
2302113 TATTCGCATT
2302123 GCGAATTAGGAAAATCGCAAA
1 GCGAATTAGGAAAATCGCAAA
* *
2302144 GCGAATTTGGGAAATCGCAA
1 GCGAATTAGGAAAATCGCAA
2302164 TGTGATAGTC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.41, C:0.15, G:0.27, T:0.17
Consensus pattern (21 bp):
GCGAATTAGGAAAATCGCAAA
Found at i:2306782 original size:25 final size:25
Alignment explanation
Indices: 2306741--2306790 Score: 68
Period size: 24 Copynumber: 2.0 Consensus size: 25
2306731 TTTTATGAAC
2306741 TAAAACATGAATAATATTAAAAATAT
1 TAAAACATGAATAATA-TAAAAATAT
2306767 TAAAA-ATGAA-ATATATAAAAATAT
1 TAAAACATGAATA-ATATAAAAATAT
2306791 ATTGGTTAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
24 10 0.43
25 8 0.35
26 5 0.22
ACGTcount: A:0.64, C:0.02, G:0.04, T:0.30
Consensus pattern (25 bp):
TAAAACATGAATAATATAAAAATAT
Found at i:2306792 original size:26 final size:26
Alignment explanation
Indices: 2306741--2306793 Score: 65
Period size: 25 Copynumber: 2.0 Consensus size: 26
2306731 TTTTATGAAC
*
2306741 TAAAACATGAATAATATTAAAAATAT
1 TAAAACATGAATAATATAAAAAATAT
2306767 TAAAA-ATGAA-ATATATAAAAATATAT
1 TAAAACATGAATA-ATATAAAAA-ATAT
2306793 T
1 T
2306794 GGTTAAATTA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
24 1 0.04
25 13 0.54
26 10 0.42
ACGTcount: A:0.62, C:0.02, G:0.04, T:0.32
Consensus pattern (26 bp):
TAAAACATGAATAATATAAAAAATAT
Found at i:2323917 original size:13 final size:12
Alignment explanation
Indices: 2323899--2323937 Score: 51
Period size: 13 Copynumber: 3.1 Consensus size: 12
2323889 GTATTATGAT
2323899 TTTTCAAACATTG
1 TTTTCAAA-ATTG
*
2323912 TTTTCAAAATAG
1 TTTTCAAAATTG
2323924 TTTTCAAAGATTG
1 TTTTCAAA-ATTG
2323937 T
1 T
2323938 CCATTAGAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
12 11 0.48
13 12 0.52
ACGTcount: A:0.33, C:0.10, G:0.10, T:0.46
Consensus pattern (12 bp):
TTTTCAAAATTG
Found at i:2323928 original size:12 final size:13
Alignment explanation
Indices: 2323899--2323931 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
2323889 GTATTATGAT
*
2323899 TTTTCAAACATTG
1 TTTTCAAACATAG
2323912 TTTTCAAA-ATAG
1 TTTTCAAACATAG
2323924 TTTTCAAA
1 TTTTCAAA
2323932 GATTGTCCAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 11 0.58
13 8 0.42
ACGTcount: A:0.36, C:0.12, G:0.06, T:0.45
Consensus pattern (13 bp):
TTTTCAAACATAG
Found at i:2337841 original size:18 final size:18
Alignment explanation
Indices: 2337810--2337844 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
2337800 GAAAAAATTT
*
2337810 TCGTGGCACATTTTTTTG
1 TCGTGCCACATTTTTTTG
*
2337828 TCGTGCCACCTTTTTTT
1 TCGTGCCACATTTTTTT
2337845 CTTTTCCTTG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.09, C:0.23, G:0.17, T:0.51
Consensus pattern (18 bp):
TCGTGCCACATTTTTTTG
Found at i:2340177 original size:7 final size:7
Alignment explanation
Indices: 2340167--2340223 Score: 51
Period size: 7 Copynumber: 7.9 Consensus size: 7
2340157 GGTTTTTCAT
2340167 TTTTTTC
1 TTTTTTC
*
2340174 TTTTTCC
1 TTTTTTC
*
2340181 TTTTCCTC
1 TTTT-TTC
2340189 TTTTTTC
1 TTTTTTC
*
2340196 CTTTTTC
1 TTTTTTC
*
2340203 CTTTTTC
1 TTTTTTC
*
2340210 TCTTTTC
1 TTTTTTC
2340217 TTATTTT
1 TT-TTTT
2340224 AATTTTTTGT
Statistics
Matches: 40, Mismatches: 8, Indels: 3
0.78 0.16 0.06
Matches are distributed among these distances:
7 31 0.77
8 9 0.22
ACGTcount: A:0.02, C:0.23, G:0.00, T:0.75
Consensus pattern (7 bp):
TTTTTTC
Found at i:2340190 original size:15 final size:15
Alignment explanation
Indices: 2340172--2340216 Score: 56
Period size: 16 Copynumber: 2.9 Consensus size: 15
2340162 TTCATTTTTT
2340172 TCTTTTTCCTTTTCC
1 TCTTTTTCCTTTTCC
*
2340187 TCTTTTTTCCTTTTTC
1 TC-TTTTTCCTTTTCC
2340203 -CTTTTTCTCTTTTC
1 TCTTTTTC-CTTTTC
2340217 TTATTTTAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
14 6 0.23
15 8 0.31
16 12 0.46
ACGTcount: A:0.00, C:0.29, G:0.00, T:0.71
Consensus pattern (15 bp):
TCTTTTTCCTTTTCC
Found at i:2340199 original size:23 final size:23
Alignment explanation
Indices: 2340166--2340215 Score: 82
Period size: 23 Copynumber: 2.2 Consensus size: 23
2340156 TGGTTTTTCA
*
2340166 TTTTTTTCTTTTTCCTTTTCCTC
1 TTTTTTCCTTTTTCCTTTTCCTC
*
2340189 TTTTTTCCTTTTTCCTTTTTCTC
1 TTTTTTCCTTTTTCCTTTTCCTC
2340212 TTTT
1 TTTT
2340216 CTTATTTTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (23 bp):
TTTTTTCCTTTTTCCTTTTCCTC
Found at i:2340223 original size:23 final size:23
Alignment explanation
Indices: 2340167--2340223 Score: 73
Period size: 23 Copynumber: 2.5 Consensus size: 23
2340157 GGTTTTTCAT
2340167 TTTTTTC-TTTTTCCTTTTCCTC
1 TTTTTTCATTTTTCCTTTTCCTC
* *
2340189 TTTTTTCCTTTTTCCTTTTTCTC
1 TTTTTTCATTTTTCCTTTTCCTC
2340212 TTTTCTT-ATTTT
1 TTTT-TTCATTTT
2340224 AATTTTTTGT
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
22 7 0.23
23 22 0.71
24 2 0.06
ACGTcount: A:0.02, C:0.23, G:0.00, T:0.75
Consensus pattern (23 bp):
TTTTTTCATTTTTCCTTTTCCTC
Found at i:2342584 original size:46 final size:46
Alignment explanation
Indices: 2342516--2342994 Score: 764
Period size: 46 Copynumber: 10.4 Consensus size: 46
2342506 CACCCATATG
* *
2342516 CATTTCATGGTATCCTTTCATGCCATTTTATACGCTATTATACATTT
1 CATTT-ATGGCATCCTTTCATGCCCTTTTATACGCTATTATACATTT
* * *
2342563 CATTTCTGGCATCATTTCATGCCCTTTTATACTCTATTATACATTT
1 CATTTATGGCATCCTTTCATGCCCTTTTATACGCTATTATACATTT
* *
2342609 CATTTATGGAATCCTTTCATGCCCTTTTATATGCTATTATACATTT
1 CATTTATGGCATCCTTTCATGCCCTTTTATACGCTATTATACATTT
* * *
2342655 CATTTATGGCAGCATTTCATGCCCTTTTATACTCTATTATACATTT
1 CATTTATGGCATCCTTTCATGCCCTTTTATACGCTATTATACATTT
*
2342701 CATTTATGGCATCCTTTCATGCCCTTTTATACGCTATTCTACATTT
1 CATTTATGGCATCCTTTCATGCCCTTTTATACGCTATTATACATTT
* **
2342747 CATTTATGGCATCATTTCATGCCCTTTTATACTTTATTATACATTT
1 CATTTATGGCATCCTTTCATGCCCTTTTATACGCTATTATACATTT
2342793 CATTTATGGCATCCTTTCATGCCCTTTTATACGCTATTATACATTT
1 CATTTATGGCATCCTTTCATGCCCTTTTATACGCTATTATACATTT
* *
2342839 CATTTATGGCATCCTTTCATACCCTTTTATATGCTATTATACATTT
1 CATTTATGGCATCCTTTCATGCCCTTTTATACGCTATTATACATTT
*
2342885 CATTTATGGCATCCTTTCATGCCCTTTTATACACTATTATACATTT
1 CATTTATGGCATCCTTTCATGCCCTTTTATACGCTATTATACATTT
* *
2342931 CATTTATGGTATCCTTTCATG-CC-TTTATACACTATTATACATTT
1 CATTTATGGCATCCTTTCATGCCCTTTTATACGCTATTATACATTT
2342975 CATTTATGGCATCCTTTCAT
1 CATTTATGGCATCCTTTCAT
2342995 TTCTTTTATA
Statistics
Matches: 399, Mismatches: 33, Indels: 3
0.92 0.08 0.01
Matches are distributed among these distances:
44 40 0.10
45 2 0.01
46 352 0.88
47 5 0.01
ACGTcount: A:0.23, C:0.22, G:0.08, T:0.47
Consensus pattern (46 bp):
CATTTATGGCATCCTTTCATGCCCTTTTATACGCTATTATACATTT
Found at i:2343147 original size:60 final size:61
Alignment explanation
Indices: 2343082--2343290 Score: 195
Period size: 68 Copynumber: 3.2 Consensus size: 61
2343072 AATTGATATA
*
2343082 TTTTTGTCAAATGCACAACTAGGCCTCAAAG-CCTTTCATCTAACTGGCATAACCGACACC
1 TTTTTGTCAAATGCACAATTAGGCCTCAAAGTCCTTTCATCTAACTGGCATAACCGACACC
* **
2343142 TTTTTGTCAAATGCACAATTAGGCCTTAAAGGCACTTATCCTTTCATCTAACTGGCATAATTGAC
1 TTTTTGTCAAATGCACAATTAGGCCTCAAA-G------TCCTTTCATCTAACTGGCATAACCGAC
2343207 ACC
59 ACC
* * * **
2343210 TTTCTGTCAAATGCACAGTTAGGCCTCAAAGGCACTTAACCTTTCATCTAACTAGCATAATTGAC
1 TTTTTGTCAAATGCACAATTAGGCCTCAAA-G----T--CCTTTCATCTAACTGGCATAACCGAC
2343275 ACC
59 ACC
*
2343278 TTTCTGTCAAATG
1 TTTTTGTCAAATG
2343291 TACAGTTATG
Statistics
Matches: 128, Mismatches: 11, Indels: 12
0.85 0.07 0.08
Matches are distributed among these distances:
60 28 0.22
61 1 0.01
66 2 0.02
68 97 0.76
ACGTcount: A:0.30, C:0.26, G:0.13, T:0.31
Consensus pattern (61 bp):
TTTTTGTCAAATGCACAATTAGGCCTCAAAGTCCTTTCATCTAACTGGCATAACCGACACC
Found at i:2343296 original size:68 final size:68
Alignment explanation
Indices: 2343113--2343298 Score: 300
Period size: 68 Copynumber: 2.7 Consensus size: 68
2343103 GGCCTCAAAG
** * * *
2343113 CCTTTCATCTAACTGGCATAACCGACACCTTTTTGTCAAATGCACAATTAGGCCTTAAAGGCACT
1 CCTTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCACAGTTAGGCCTCAAAGGCACT
*
2343178 TAT
66 TAA
2343181 CCTTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCACAGTTAGGCCTCAAAGGCACT
1 CCTTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCACAGTTAGGCCTCAAAGGCACT
2343246 TAA
66 TAA
* *
2343249 CCTTTCATCTAACTAGCATAATTGACACCTTTCTGTCAAATGTACAGTTA
1 CCTTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCACAGTTA
2343299 TGCCATTAAT
Statistics
Matches: 110, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
68 110 1.00
ACGTcount: A:0.30, C:0.26, G:0.13, T:0.32
Consensus pattern (68 bp):
CCTTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCACAGTTAGGCCTCAAAGGCACT
TAA
Found at i:2343685 original size:24 final size:24
Alignment explanation
Indices: 2343640--2343685 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
2343630 CACCATACAT
* *
2343640 ATATACATCCATGACTACTGTAAC
1 ATATACATACATGACTAATGTAAC
2343664 ATATACATACAT-ACTAAATGTA
1 ATATACATACATGACT-AATGTA
2343686 CTCACATGGA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 3 0.16
24 16 0.84
ACGTcount: A:0.43, C:0.20, G:0.07, T:0.30
Consensus pattern (24 bp):
ATATACATACATGACTAATGTAAC
Found at i:2350873 original size:34 final size:33
Alignment explanation
Indices: 2350835--2350898 Score: 83
Period size: 33 Copynumber: 1.9 Consensus size: 33
2350825 TTCATGTTCA
* *
2350835 AAATTTCAAAACACTTCAATTACATTCTAAACCC
1 AAATTCCAAAACACTT-AATTACATTATAAACCC
**
2350869 AAATTCCAAAATGCTTAATTACATTATAAA
1 AAATTCCAAAACACTTAATTACATTATAAA
2350899 AACTAAATTA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
33 13 0.50
34 13 0.50
ACGTcount: A:0.47, C:0.20, G:0.02, T:0.31
Consensus pattern (33 bp):
AAATTCCAAAACACTTAATTACATTATAAACCC
Found at i:2351513 original size:35 final size:34
Alignment explanation
Indices: 2351467--2351540 Score: 112
Period size: 35 Copynumber: 2.1 Consensus size: 34
2351457 AAAATACTTT
*
2351467 AATTTAAGGTTTAGAATATAATTGAAGTATTTTGG
1 AATTTAAGGTTTAGAATATAATTGAAGT-TTTTAG
* *
2351502 AATTTAGGGTTTAGAATGTAATTGAAGTTTTTAG
1 AATTTAAGGTTTAGAATATAATTGAAGTTTTTAG
2351536 AATTT
1 AATTT
2351541 TGAGCATGAA
Statistics
Matches: 36, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
34 10 0.28
35 26 0.72
ACGTcount: A:0.35, C:0.00, G:0.20, T:0.45
Consensus pattern (34 bp):
AATTTAAGGTTTAGAATATAATTGAAGTTTTTAG
Found at i:2352228 original size:15 final size:15
Alignment explanation
Indices: 2352208--2352272 Score: 55
Period size: 15 Copynumber: 4.3 Consensus size: 15
2352198 TTGTCCGTTT
*
2352208 TTATTATTAATT-GTA
1 TTATTATT-ATTACTA
2352223 TTATTATTATTACTA
1 TTATTATTATTACTA
2352238 TTATTATATATATA-TA
1 TTATTAT-TAT-TACTA
*
2352254 TATAATATTATTA-TA
1 T-TATTATTATTACTA
2352269 TTAT
1 TTAT
2352273 ATTTGCATTT
Statistics
Matches: 43, Mismatches: 3, Indels: 9
0.78 0.05 0.16
Matches are distributed among these distances:
14 5 0.12
15 22 0.51
16 9 0.21
17 7 0.16
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.58
Consensus pattern (15 bp):
TTATTATTATTACTA
Found at i:2357887 original size:15 final size:15
Alignment explanation
Indices: 2357867--2357906 Score: 71
Period size: 15 Copynumber: 2.7 Consensus size: 15
2357857 CTACATGGAG
2357867 CGATGAAGAAGGTTC
1 CGATGAAGAAGGTTC
2357882 CGATGAAGAAGGTTC
1 CGATGAAGAAGGTTC
*
2357897 TGATGAAGAA
1 CGATGAAGAA
2357907 TAACAAGAAG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.38, C:0.10, G:0.33, T:0.20
Consensus pattern (15 bp):
CGATGAAGAAGGTTC
Found at i:2358074 original size:21 final size:21
Alignment explanation
Indices: 2358049--2358090 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
2358039 AAGACTTTAT
2358049 TTTCAAAATACAAAAATGAAA
1 TTTCAAAATACAAAAATGAAA
**
2358070 TTTCAAAATTGAAAAATGAAA
1 TTTCAAAATACAAAAATGAAA
2358091 ATAGTCTTAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.60, C:0.07, G:0.07, T:0.26
Consensus pattern (21 bp):
TTTCAAAATACAAAAATGAAA
Found at i:2361960 original size:22 final size:22
Alignment explanation
Indices: 2361909--2361961 Score: 63
Period size: 23 Copynumber: 2.4 Consensus size: 22
2361899 GGAGGTATCA
2361909 ATACCCCCTTGAAGGGGTACCG
1 ATACCCCCTTGAAGGGGTACCG
* *
2361931 ATCCCCCCTTTG-AGTGGGTACTG
1 ATACCCCC-TTGAAG-GGGTACCG
2361954 ATACCCCC
1 ATACCCCC
2361962 AGGAGAGTAC
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
22 9 0.35
23 17 0.65
ACGTcount: A:0.19, C:0.36, G:0.23, T:0.23
Consensus pattern (22 bp):
ATACCCCCTTGAAGGGGTACCG
Found at i:2369884 original size:22 final size:22
Alignment explanation
Indices: 2369859--2369945 Score: 138
Period size: 22 Copynumber: 4.0 Consensus size: 22
2369849 ATATCTACAT
2369859 TTTTCAAAGATGATAGATAATC
1 TTTTCAAAGATGATAGATAATC
**
2369881 TTTTCAAAGATGATAGATTCTC
1 TTTTCAAAGATGATAGATAATC
**
2369903 TTTTCAAAGATGATAGATTCTC
1 TTTTCAAAGATGATAGATAATC
2369925 TTTTCAAAGATGATAGATAAT
1 TTTTCAAAGATGATAGATAAT
2369946 TTTGGAGTCA
Statistics
Matches: 61, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 61 1.00
ACGTcount: A:0.37, C:0.10, G:0.14, T:0.39
Consensus pattern (22 bp):
TTTTCAAAGATGATAGATAATC
Found at i:2370606 original size:20 final size:20
Alignment explanation
Indices: 2370577--2370661 Score: 91
Period size: 20 Copynumber: 4.2 Consensus size: 20
2370567 CTCACAAATT
2370577 TGTAAATCCTTCGGGTCATC
1 TGTAAATCCTTCGGGTCATC
*
2370597 TGTAAGTCCTTCGGGTCATC
1 TGTAAATCCTTCGGGTCATC
* * * *
2370617 TGTAAGTCTTTCGAG-CATGA
1 TGTAAATCCTTCGGGTCAT-C
2370637 TGTTTAAATCCTTCGGGTCATC
1 TG--TAAATCCTTCGGGTCATC
2370659 TGT
1 TGT
2370662 CAGTGTTTCG
Statistics
Matches: 53, Mismatches: 8, Indels: 8
0.77 0.12 0.12
Matches are distributed among these distances:
19 3 0.06
20 35 0.66
22 12 0.23
23 3 0.06
ACGTcount: A:0.19, C:0.21, G:0.22, T:0.38
Consensus pattern (20 bp):
TGTAAATCCTTCGGGTCATC
Found at i:2370906 original size:12 final size:13
Alignment explanation
Indices: 2370889--2370956 Score: 70
Period size: 14 Copynumber: 5.3 Consensus size: 13
2370879 TGTTCGTTTT
2370889 TATTATTA-ATTA
1 TATTATTATATTA
2370901 TATTATTATTATTA
1 TATTATTA-TATTA
*
2370915 TATTA-CATATT-
1 TATTATTATATTA
*
2370926 TATTATATATAATA
1 TATTAT-TATATTA
*
2370940 TATTATTATATAA
1 TATTATTATATTA
2370953 TATT
1 TATT
2370957 TGCATTTACA
Statistics
Matches: 46, Mismatches: 5, Indels: 9
0.77 0.08 0.15
Matches are distributed among these distances:
11 5 0.11
12 12 0.26
13 14 0.30
14 15 0.33
ACGTcount: A:0.41, C:0.01, G:0.00, T:0.57
Consensus pattern (13 bp):
TATTATTATATTA
Found at i:2370911 original size:18 final size:18
Alignment explanation
Indices: 2370888--2370948 Score: 63
Period size: 18 Copynumber: 3.2 Consensus size: 18
2370878 TTGTTCGTTT
2370888 TTATTATTAATTATATTA
1 TTATTATTAATTATATTA
2370906 TTATTATTATATTACATATTTA
1 TTATTATTA-ATT--ATA-TTA
2370928 TTA-TATATAA-TATATTA
1 TTATTAT-TAATTATATTA
2370945 TTAT
1 TTAT
2370949 ATAATATTTG
Statistics
Matches: 37, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
17 6 0.16
18 12 0.32
19 3 0.08
20 1 0.03
21 7 0.19
22 8 0.22
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (18 bp):
TTATTATTAATTATATTA
Found at i:2383407 original size:31 final size:30
Alignment explanation
Indices: 2383361--2383447 Score: 104
Period size: 31 Copynumber: 2.8 Consensus size: 30
2383351 TTTGATAATA
*
2383361 TAATAATTATTTTATAGTA-TTTAGATAAATT
1 TAATAA-TATTTTATAATATTTTA-ATAAATT
*
2383392 TATTAATAATTTTATAATATTTTAATAAATT
1 TAATAAT-ATTTTATAATATTTTAATAAATT
*
2383423 TAATAAGTATTTTATAATTTTTTAA
1 TAATAA-TATTTTATAATATTTTAA
2383448 ACTTTATTGA
Statistics
Matches: 49, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
30 1 0.02
31 43 0.88
32 5 0.10
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.54
Consensus pattern (30 bp):
TAATAATATTTTATAATATTTTAATAAATT
Found at i:2384202 original size:31 final size:29
Alignment explanation
Indices: 2384167--2384253 Score: 93
Period size: 31 Copynumber: 2.8 Consensus size: 29
2384157 TCAATAAAGT
2384167 TTAAAAAATTATAAAATACTTATTAAATTTA
1 TTAAAAAA-TATAAAATA-TTATTAAATTTA
*
2384198 TTAAAAGAATATAAAATTATTAATAAATTTA
1 TTAAAA-AATATAAAA-TATTATTAAATTTA
* *
2384229 TCTAAATACTATAAAATAATTATTA
1 T-TAAAAAATATAAAAT-ATTATTA
2384254 TATTATCGAA
Statistics
Matches: 48, Mismatches: 4, Indels: 8
0.80 0.07 0.13
Matches are distributed among these distances:
30 1 0.02
31 39 0.81
32 8 0.17
ACGTcount: A:0.55, C:0.03, G:0.01, T:0.40
Consensus pattern (29 bp):
TTAAAAAATATAAAATATTATTAAATTTA
Found at i:2385780 original size:3 final size:3
Alignment explanation
Indices: 2385766--2385876 Score: 154
Period size: 3 Copynumber: 37.7 Consensus size: 3
2385756 CATCATCATC
2385766 ATT ATT -TT -TT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
* * * * * *
2385812 ATT ATT ATT CTT ATT CTT ATT ATT ATT ATA ATT ATT ATT ATC ATC ATC
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
2385860 ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT AT
2385877 GTGTTTCATT
Statistics
Matches: 99, Mismatches: 8, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
2 4 0.04
3 95 0.96
ACGTcount: A:0.32, C:0.05, G:0.00, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:2389257 original size:23 final size:24
Alignment explanation
Indices: 2389219--2389270 Score: 79
Period size: 23 Copynumber: 2.2 Consensus size: 24
2389209 ACCGAAGTGT
2389219 CACATAGAATTTGTCCCGAAGGAC
1 CACATAGAATTTGTCCCGAAGGAC
* *
2389243 CACATAG-ATTTGTCCTGAATGAC
1 CACATAGAATTTGTCCCGAAGGAC
2389266 CACAT
1 CACAT
2389271 GGAACCCCCG
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
23 19 0.73
24 7 0.27
ACGTcount: A:0.33, C:0.25, G:0.17, T:0.25
Consensus pattern (24 bp):
CACATAGAATTTGTCCCGAAGGAC
Found at i:2391136 original size:24 final size:27
Alignment explanation
Indices: 2391091--2391142 Score: 65
Period size: 24 Copynumber: 2.0 Consensus size: 27
2391081 TAAATTTTAT
* *
2391091 TATTCAGTTTTGTTTTATTTTAGTCAC
1 TATTCAGTTTTGTTTGATTTTAGCCAC
2391118 TATT-AGTTTT-TTTGA-TTTAGCCAC
1 TATTCAGTTTTGTTTGATTTTAGCCAC
2391142 T
1 T
2391143 GTTTTTTTCT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
24 9 0.39
25 4 0.17
26 6 0.26
27 4 0.17
ACGTcount: A:0.19, C:0.12, G:0.12, T:0.58
Consensus pattern (27 bp):
TATTCAGTTTTGTTTGATTTTAGCCAC
Found at i:2391962 original size:22 final size:23
Alignment explanation
Indices: 2391934--2391989 Score: 89
Period size: 22 Copynumber: 2.5 Consensus size: 23
2391924 TATACCCATA
2391934 GTACCGATACT-TCTCTTCTAAG
1 GTACCGATACTCTCTCTTCTAAG
2391956 GTACCGATA-TCTCTCTTCTAAG
1 GTACCGATACTCTCTCTTCTAAG
*
2391978 GTACTGATACTC
1 GTACCGATACTC
2391990 ACTTCAATAT
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
21 1 0.03
22 28 0.90
23 2 0.06
ACGTcount: A:0.23, C:0.27, G:0.14, T:0.36
Consensus pattern (23 bp):
GTACCGATACTCTCTCTTCTAAG
Found at i:2396316 original size:39 final size:38
Alignment explanation
Indices: 2396272--2396354 Score: 96
Period size: 40 Copynumber: 2.1 Consensus size: 38
2396262 TTTTGGAAGT
*
2396272 AGAAAAAT-GTTCTATTTCGTGGGTATAACGAATTTGAAA
1 AGAAAAATAGTT-T-TTTCGTGGGTATAACAAATTTGAAA
* *
2396311 AGAAAAATAAAGTTTTTTTGTGGGTATAACAAATTTGAGA
1 AGAAAAAT--AGTTTTTTCGTGGGTATAACAAATTTGAAA
2396351 AGAA
1 AGAA
2396355 GAAAATTTAG
Statistics
Matches: 38, Mismatches: 3, Indels: 5
0.83 0.07 0.11
Matches are distributed among these distances:
39 8 0.21
40 26 0.68
41 1 0.03
42 3 0.08
ACGTcount: A:0.42, C:0.05, G:0.20, T:0.33
Consensus pattern (38 bp):
AGAAAAATAGTTTTTTCGTGGGTATAACAAATTTGAAA
Found at i:2397193 original size:6 final size:6
Alignment explanation
Indices: 2397182--2397227 Score: 83
Period size: 6 Copynumber: 7.7 Consensus size: 6
2397172 CTTAAAAAGA
*
2397182 AGAAGG AGAAGG AGAAGG AGAAGG AGAAGG AGAAGG AGAAGA AGAA
1 AGAAGG AGAAGG AGAAGG AGAAGG AGAAGG AGAAGG AGAAGG AGAA
2397228 TTGGGGAGGA
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
6 39 1.00
ACGTcount: A:0.54, C:0.00, G:0.46, T:0.00
Consensus pattern (6 bp):
AGAAGG
Found at i:2399065 original size:19 final size:18
Alignment explanation
Indices: 2399029--2399070 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 18
2399019 AATATATAAC
*
2399029 TTATCTTTAATTTCAATA
1 TTATTTTTAATTTCAATA
2399047 TATATTTTTATATTT-AATA
1 T-TATTTTTA-ATTTCAATA
2399066 TTATT
1 TTATT
2399071 AATAAATATC
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
18 5 0.24
19 12 0.57
20 4 0.19
ACGTcount: A:0.33, C:0.05, G:0.00, T:0.62
Consensus pattern (18 bp):
TTATTTTTAATTTCAATA
Found at i:2400912 original size:14 final size:15
Alignment explanation
Indices: 2400886--2400927 Score: 56
Period size: 14 Copynumber: 3.1 Consensus size: 15
2400876 TATATGTAAT
2400886 ACATAGTTTTTGAAA
1 ACATAGTTTTTGAAA
2400901 ACATAG-TTTTGAAA
1 ACATAGTTTTTGAAA
2400915 AC---GTTTTTGAAA
1 ACATAGTTTTTGAAA
2400927 A
1 A
2400928 TATGTATAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
11 1 0.04
12 9 0.35
14 10 0.38
15 6 0.23
ACGTcount: A:0.40, C:0.07, G:0.14, T:0.38
Consensus pattern (15 bp):
ACATAGTTTTTGAAA
Found at i:2400974 original size:38 final size:37
Alignment explanation
Indices: 2400903--2401003 Score: 157
Period size: 38 Copynumber: 2.7 Consensus size: 37
2400893 TTTTGAAAAC
*
2400903 ATAGTTTTGAAAACGTTTTTGAAAATATGTATAATAT
1 ATAGTTTTGAAAACATTTTTGAAAATATGTATAATAT
2400940 ATAGTTTTGAAAACATTTTTCGAAAATATGTATAATAT
1 ATAGTTTTGAAAACATTTTT-GAAAATATGTATAATAT
**
2400978 ATAGTTTTTGAAAACCCTTTTGAAAA
1 ATAG-TTTTGAAAACATTTTTGAAAA
2401004 CACACACACA
Statistics
Matches: 59, Mismatches: 3, Indels: 3
0.91 0.05 0.05
Matches are distributed among these distances:
37 19 0.32
38 26 0.44
39 14 0.24
ACGTcount: A:0.41, C:0.06, G:0.12, T:0.42
Consensus pattern (37 bp):
ATAGTTTTGAAAACATTTTTGAAAATATGTATAATAT
Found at i:2401010 original size:2 final size:2
Alignment explanation
Indices: 2401003--2401041 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
2400993 CCTTTTGAAA
2401003 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
2401042 TATATATATA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.49, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:2401046 original size:2 final size:2
Alignment explanation
Indices: 2401041--2401075 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
2401031 ACACACACAC
2401041 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2401076 GTTTTTGAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2413615 original size:44 final size:44
Alignment explanation
Indices: 2413559--2413647 Score: 142
Period size: 44 Copynumber: 2.0 Consensus size: 44
2413549 CATTTCTTCT
* *
2413559 TACTTCATTTCATTTCCTTGTGAATTTAATTTTCTTTCATTTTG
1 TACTTCATTTCATCTCCTTGTGAATTTAATTTTCTTTAATTTTG
* *
2413603 TACTTCGTTTCATCTCCTTTTGAATTTAATTTTCTTTAATTTTG
1 TACTTCATTTCATCTCCTTGTGAATTTAATTTTCTTTAATTTTG
2413647 T
1 T
2413648 GTGGGATGTT
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
44 41 1.00
ACGTcount: A:0.18, C:0.16, G:0.07, T:0.60
Consensus pattern (44 bp):
TACTTCATTTCATCTCCTTGTGAATTTAATTTTCTTTAATTTTG
Found at i:2418555 original size:14 final size:15
Alignment explanation
Indices: 2418529--2418596 Score: 80
Period size: 12 Copynumber: 5.1 Consensus size: 15
2418519 TATATATAAT
2418529 ACATAGTTTTTGAAA
1 ACATAGTTTTTGAAA
2418544 ACATAG-TTTTG-AA
1 ACATAGTTTTTGAAA
2418557 A-AT-GTTTTTGAAA
1 ACATAGTTTTTGAAA
2418570 ACATAG-TTTTG-AA
1 ACATAGTTTTTGAAA
2418583 A-AT-GTTTTTGAAA
1 ACATAGTTTTTGAAA
2418596 A
1 A
2418597 TATGTATAAT
Statistics
Matches: 47, Mismatches: 0, Indels: 14
0.77 0.00 0.23
Matches are distributed among these distances:
11 2 0.04
12 14 0.30
13 12 0.26
14 12 0.26
15 7 0.15
ACGTcount: A:0.40, C:0.04, G:0.15, T:0.41
Consensus pattern (15 bp):
ACATAGTTTTTGAAA
Found at i:2418563 original size:26 final size:26
Alignment explanation
Indices: 2418534--2418596 Score: 126
Period size: 26 Copynumber: 2.4 Consensus size: 26
2418524 ATAATACATA
2418534 GTTTTTGAAAACATAGTTTTGAAAAT
1 GTTTTTGAAAACATAGTTTTGAAAAT
2418560 GTTTTTGAAAACATAGTTTTGAAAAT
1 GTTTTTGAAAACATAGTTTTGAAAAT
2418586 GTTTTTGAAAA
1 GTTTTTGAAAA
2418597 TATGTATAAT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 37 1.00
ACGTcount: A:0.38, C:0.03, G:0.16, T:0.43
Consensus pattern (26 bp):
GTTTTTGAAAACATAGTTTTGAAAAT
Found at i:2418629 original size:38 final size:39
Alignment explanation
Indices: 2418517--2418663 Score: 149
Period size: 38 Copynumber: 3.8 Consensus size: 39
2418507 TTATACATAT
*
2418517 AATATATATAATACATAGTTTTTGAAAACATAGTTTTGAA
1 AATATATATAATACATAG-TTTTGAAAACATATTTTTGAA
* * * * *
2418557 AATGTTTTTGAAAACATAGTTTTG-AAA-ATGTTTTTGAA
1 AATATATAT-AATACATAGTTTTGAAAACATATTTTTGAA
* *
2418595 AATATGTATAATATATAGTTTTGAAAACAT-TTTTTGAA
1 AATATATATAATACATAGTTTTGAAAACATATTTTTGAA
** *
2418633 AATATATATAATTTATAGTTTT-TAAACATAT
1 AATATATATAATACATAGTTTTGAAAACATAT
2418664 ATATATATAT
Statistics
Matches: 89, Mismatches: 14, Indels: 10
0.79 0.12 0.09
Matches are distributed among these distances:
37 18 0.20
38 47 0.53
39 5 0.06
40 11 0.12
41 8 0.09
ACGTcount: A:0.42, C:0.03, G:0.10, T:0.44
Consensus pattern (39 bp):
AATATATATAATACATAGTTTTGAAAACATATTTTTGAA
Found at i:2418663 original size:26 final size:26
Alignment explanation
Indices: 2418625--2418715 Score: 116
Period size: 25 Copynumber: 3.5 Consensus size: 26
2418615 TTGAAAACAT
2418625 TTTTTGAAAATATATATAATTTATAG
1 TTTTTGAAAATATATATAATTTATAG
*
2418651 TTTTT-AAACATATATAT-ATATATAG
1 TTTTTGAAA-ATATATATAATTTATAG
*
2418676 TTTTTGAAAAAATATATAATATATATAG
1 TTTTTGAAAATATATATAAT-T-TATAG
2418704 -TTTTGAAAATAT
1 TTTTTGAAAATAT
2418716 TTTTCGAAAA
Statistics
Matches: 56, Mismatches: 4, Indels: 9
0.81 0.06 0.13
Matches are distributed among these distances:
25 22 0.39
26 18 0.32
27 11 0.20
28 5 0.09
ACGTcount: A:0.45, C:0.01, G:0.07, T:0.47
Consensus pattern (26 bp):
TTTTTGAAAATATATATAATTTATAG
Found at i:2418666 original size:28 final size:27
Alignment explanation
Indices: 2418625--2418715 Score: 86
Period size: 28 Copynumber: 3.4 Consensus size: 27
2418615 TTGAAAACAT
*
2418625 TTTTTGAAA-ATATATATAATTTATAG
1 TTTTTAAAATATATATATAATTTATAG
2418651 TTTTTAAACATATATATAT-A--TATAG
1 TTTTTAAA-ATATATATATAATTTATAG
2418676 TTTTTGAAAA-A-ATATATAATATATATAG
1 TTTTT-AAAATATATATATAAT-T-TATAG
*
2418704 TTTTGAAAATAT
1 TTTTTAAAATAT
2418716 TTTTCGAAAA
Statistics
Matches: 53, Mismatches: 2, Indels: 17
0.74 0.03 0.24
Matches are distributed among these distances:
23 6 0.11
24 2 0.04
25 11 0.21
26 10 0.19
27 6 0.11
28 18 0.34
ACGTcount: A:0.45, C:0.01, G:0.07, T:0.47
Consensus pattern (27 bp):
TTTTTAAAATATATATATAATTTATAG
Found at i:2418745 original size:36 final size:36
Alignment explanation
Indices: 2418684--2418843 Score: 166
Period size: 36 Copynumber: 4.5 Consensus size: 36
2418674 AGTTTTTGAA
*
2418684 AAAATATATAATATATATAGTTTTGAAAATATTTTTCG
1 AAAACATAT-ATA-ATATAGTTTTGAAAATATTTTTCG
* *
2418722 AAAACATTTATAATATAATTTTGAAAATATTTTTCG
1 AAAACATATATAATATAGTTTTGAAAATATTTTTCG
**
2418758 AAAACATATATAATATAGTTTTGAAAACCTTTTT-G
1 AAAACATATATAATATAGTTTTGAAAATATTTTTCG
* * ** *
2418793 -AAATATATAT-ATATAGTTTTTAAAA-CGTTTTCTA
1 AAAACATATATAATATAGTTTTGAAAATATTTTTC-G
*
2418827 AAAACACATATAATATA
1 AAAACATATATAATATA
2418844 TATTTTTTGA
Statistics
Matches: 105, Mismatches: 13, Indels: 10
0.82 0.10 0.08
Matches are distributed among these distances:
32 5 0.05
33 14 0.13
34 9 0.09
35 9 0.09
36 58 0.55
37 3 0.03
38 7 0.07
ACGTcount: A:0.46, C:0.06, G:0.06, T:0.42
Consensus pattern (36 bp):
AAAACATATATAATATAGTTTTGAAAATATTTTTCG
Found at i:2418755 original size:12 final size:12
Alignment explanation
Indices: 2418704--2418761 Score: 55
Period size: 13 Copynumber: 4.8 Consensus size: 12
2418694 ATATATATAG
2418704 TTTTGAAAATAT
1 TTTTGAAAATAT
*
2418716 TTTTCGAAAACAT
1 TTTT-GAAAATAT
* * *
2418729 TTAT-AATATAA
1 TTTTGAAAATAT
2418740 TTTTGAAAATAT
1 TTTTGAAAATAT
2418752 TTTTCGAAAA
1 TTTT-GAAAA
2418762 CATATATAAT
Statistics
Matches: 35, Mismatches: 8, Indels: 5
0.73 0.17 0.10
Matches are distributed among these distances:
11 7 0.20
12 13 0.37
13 15 0.43
ACGTcount: A:0.43, C:0.05, G:0.07, T:0.45
Consensus pattern (12 bp):
TTTTGAAAATAT
Found at i:2418922 original size:18 final size:17
Alignment explanation
Indices: 2418895--2419003 Score: 123
Period size: 18 Copynumber: 6.2 Consensus size: 17
2418885 CATATACATA
* *
2418895 TATATGTTATATGTGTAT
1 TATATATTATAT-TATAT
2418913 TATATATTATATTATA-
1 TATATATTATATTATAT
*
2418929 TATATATTATATTATAA
1 TATATATTATATTATAT
2418946 TATAGTATTATATTATAT
1 TATA-TATTATATTATAT
2418964 TATA-ATATAGTATTATAT
1 TATATAT-TA-TATTATAT
2418982 TATATATTATTTATTATAT
1 TATATATTA--TATTATAT
2419001 TAT
1 TAT
2419004 GGTTTATTAT
Statistics
Matches: 81, Mismatches: 4, Indels: 11
0.84 0.04 0.11
Matches are distributed among these distances:
16 18 0.22
17 9 0.11
18 41 0.51
19 13 0.16
ACGTcount: A:0.39, C:0.00, G:0.05, T:0.56
Consensus pattern (17 bp):
TATATATTATATTATAT
Found at i:2418925 original size:5 final size:5
Alignment explanation
Indices: 2418915--2419003 Score: 92
Period size: 5 Copynumber: 16.6 Consensus size: 5
2418905 ATGTGTATTA
2418915 TATAT TATAT TATAT ATATAT TATAT TATAAT ATAGTAT TATAT TATAT
1 TATAT TATAT TATAT -TATAT TATAT TAT-AT -TA-TAT TATAT TATAT
2418964 TATAAT ATAGTAT TATAT TATA- TATTAT T-TAT TATAT TAT
1 TAT-AT -TA-TAT TATAT TATAT TA-TAT TATAT TATAT TAT
2419004 GGTTTATTAT
Statistics
Matches: 74, Mismatches: 0, Indels: 20
0.79 0.00 0.21
Matches are distributed among these distances:
4 6 0.08
5 44 0.59
6 14 0.19
7 8 0.11
8 2 0.03
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (5 bp):
TATAT
Found at i:2418936 original size:23 final size:22
Alignment explanation
Indices: 2418877--2419000 Score: 87
Period size: 23 Copynumber: 5.6 Consensus size: 22
2418867 GTTTTTGAAA
* * *
2418877 ATATAATACATATACATATA-T
1 ATATTATATATATATATATATT
* * *
2418898 ATGTTATATGTGTATTATATATT
1 ATATTATATATATA-TATATATT
2418921 ATATTATATATATAT-TATATT
1 ATATTATATATATATATATATT
*
2418942 ATAATATAGTAT-TATATTATATT
1 ATATTATA-TATATATA-TATATT
*
2418965 ATAATATAGTATTATATTATATATT
1 ATATTATA-TA-TATA-TATATATT
2418990 AT-TTAT-TATAT
1 ATATTATATATAT
2419001 TATGGTTTAT
Statistics
Matches: 84, Mismatches: 11, Indels: 16
0.76 0.10 0.14
Matches are distributed among these distances:
21 28 0.33
22 11 0.13
23 29 0.35
24 4 0.05
25 10 0.12
26 2 0.02
ACGTcount: A:0.42, C:0.02, G:0.04, T:0.52
Consensus pattern (22 bp):
ATATTATATATATATATATATT
Found at i:2420321 original size:18 final size:18
Alignment explanation
Indices: 2420298--2420347 Score: 55
Period size: 18 Copynumber: 2.8 Consensus size: 18
2420288 TGACATGTTA
2420298 TTTATTTTATTTTATATT
1 TTTATTTTATTTTATATT
* * *
2420316 TTTATTTTCTTTTTTCTT
1 TTTATTTTATTTTATATT
* *
2420334 TTTCTTTTAATTTA
1 TTTATTTTATTTTA
2420348 ATCAATTTTC
Statistics
Matches: 25, Mismatches: 7, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.16, C:0.06, G:0.00, T:0.78
Consensus pattern (18 bp):
TTTATTTTATTTTATATT
Found at i:2428080 original size:21 final size:21
Alignment explanation
Indices: 2428040--2428131 Score: 94
Period size: 21 Copynumber: 4.4 Consensus size: 21
2428030 GCGTTCTATT
* * *
2428040 TGGTCCTTCGGGACACATATG
1 TGGTCCTTTGGAACATATATG
* * *
2428061 TGATCCTTTAGAATATATATG
1 TGGTCCTTTGGAACATATATG
* * * *
2428082 CGGTCCTTCGGGACATATATT
1 TGGTCCTTTGGAACATATATG
2428103 TGGTCCTTTGGAACATATATG
1 TGGTCCTTTGGAACATATATG
2428124 TGGTCCTT
1 TGGTCCTT
2428132 AGGGACAATT
Statistics
Matches: 54, Mismatches: 17, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
21 54 1.00
ACGTcount: A:0.22, C:0.18, G:0.23, T:0.37
Consensus pattern (21 bp):
TGGTCCTTTGGAACATATATG
Found at i:2428110 original size:42 final size:42
Alignment explanation
Indices: 2428041--2428138 Score: 133
Period size: 42 Copynumber: 2.3 Consensus size: 42
2428031 CGTTCTATTT
*
2428041 GGTCCTTCGGGACACATATGTGATCCTTTAGAATATATATGC
1 GGTCCTTCGGGACACATATGTGATCCTTTAGAACATATATGC
* * * * *
2428083 GGTCCTTCGGGACATATATTTGGTCCTTTGGAACATATATGT
1 GGTCCTTCGGGACACATATGTGATCCTTTAGAACATATATGC
*
2428125 GGTCCTTAGGGACA
1 GGTCCTTCGGGACA
2428139 ATTCTATGTG
Statistics
Matches: 49, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
42 49 1.00
ACGTcount: A:0.23, C:0.18, G:0.24, T:0.34
Consensus pattern (42 bp):
GGTCCTTCGGGACACATATGTGATCCTTTAGAACATATATGC
Found at i:2428150 original size:23 final size:23
Alignment explanation
Indices: 2428078--2428208 Score: 96
Period size: 21 Copynumber: 6.0 Consensus size: 23
2428068 TTAGAATATA
* *
2428078 TATGCGGTCCTTCGGGAC-A-TA
1 TATGTGGTCCTTCGGGACAATTC
* * * *
2428099 TATTTGGTCCTTTGGAAC-A-TA
1 TATGTGGTCCTTCGGGACAATTC
*
2428120 TATGTGGTCCTTAGGGACAATTC
1 TATGTGGTCCTTCGGGACAATTC
*
2428143 TATGTGGTCATTCGGGACAA-T-
1 TATGTGGTCCTTCGGGACAATTC
*
2428164 TATGTAGGT-TTTCGGGACAATTC
1 TATGT-GGTCCTTCGGGACAATTC
* * *
2428187 TACGAGGTCCTTCGGAACAATT
1 TATGTGGTCCTTCGGGACAATT
2428209 TTATATGGCA
Statistics
Matches: 89, Mismatches: 15, Indels: 10
0.78 0.13 0.09
Matches are distributed among these distances:
21 47 0.53
22 9 0.10
23 33 0.37
ACGTcount: A:0.23, C:0.18, G:0.25, T:0.34
Consensus pattern (23 bp):
TATGTGGTCCTTCGGGACAATTC
Found at i:2428490 original size:23 final size:23
Alignment explanation
Indices: 2428425--2428490 Score: 69
Period size: 23 Copynumber: 2.9 Consensus size: 23
2428415 GTAATAGATG
* * *
2428425 AAAGTATGTGACTATATGATATG
1 AAAGTATGTAACTATATGTTATA
* * *
2428448 AAAGTATGTAAATGTGTGTTATA
1 AAAGTATGTAACTATATGTTATA
*
2428471 AAAGTATGTAACTACATGTT
1 AAAGTATGTAACTATATGTT
2428491 TCATTAGTTC
Statistics
Matches: 33, Mismatches: 10, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.39, C:0.05, G:0.20, T:0.36
Consensus pattern (23 bp):
AAAGTATGTAACTATATGTTATA
Found at i:2430467 original size:43 final size:43
Alignment explanation
Indices: 2430397--2430525 Score: 152
Period size: 43 Copynumber: 3.0 Consensus size: 43
2430387 AGTCTAAATT
* * *
2430397 CCAAACTATCAATCCACATATACACCAAACTAAT-ATATTAAAA
1 CCAAAGTAACAATCCACAAATACACCAAACT-ATCATATTAAAA
* * * *
2430440 CCAAAGTAACAATTCACAAATTCACCAAAGTATCATATTACAA
1 CCAAAGTAACAATCCACAAATACACCAAACTATCATATTAAAA
* * *
2430483 CCAATGTAACAATCCATAAATACACTAAACTATCATATTAAAA
1 CCAAAGTAACAATCCACAAATACACCAAACTATCATATTAAAA
2430526 GCATCCTTGA
Statistics
Matches: 71, Mismatches: 14, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
42 2 0.03
43 69 0.97
ACGTcount: A:0.50, C:0.23, G:0.02, T:0.24
Consensus pattern (43 bp):
CCAAAGTAACAATCCACAAATACACCAAACTATCATATTAAAA
Found at i:2434056 original size:23 final size:23
Alignment explanation
Indices: 2434022--2434078 Score: 98
Period size: 23 Copynumber: 2.5 Consensus size: 23
2434012 CTTTGCTTCT
2434022 GATTTA-GTATGCATGTTTATAA
1 GATTTATGTATGCATGTTTATAA
*
2434044 GATTTATGTATGCATGTTTATGA
1 GATTTATGTATGCATGTTTATAA
2434067 GATTTATGTATG
1 GATTTATGTATG
2434079 TCCGACAAGA
Statistics
Matches: 33, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
22 6 0.18
23 27 0.82
ACGTcount: A:0.28, C:0.04, G:0.21, T:0.47
Consensus pattern (23 bp):
GATTTATGTATGCATGTTTATAA
Found at i:2436526 original size:13 final size:13
Alignment explanation
Indices: 2436493--2436529 Score: 65
Period size: 13 Copynumber: 2.8 Consensus size: 13
2436483 CAGATCCATG
*
2436493 AAACTTTATCCCC
1 AAACTTTTTCCCC
2436506 AAACTTTTTCCCC
1 AAACTTTTTCCCC
2436519 AAACTTTTTCC
1 AAACTTTTTCC
2436530 TAGCTCGTCT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.27, C:0.35, G:0.00, T:0.38
Consensus pattern (13 bp):
AAACTTTTTCCCC
Found at i:2437155 original size:24 final size:24
Alignment explanation
Indices: 2437118--2437172 Score: 92
Period size: 24 Copynumber: 2.2 Consensus size: 24
2437108 GGCATAAATG
*
2437118 TTCTTCTATAATCGCATCATTTTGA
1 TTCTT-TATAATCGAATCATTTTGA
2437143 TTCTTTATAATCGAATCATTTTGA
1 TTCTTTATAATCGAATCATTTTGA
2437167 TTCTTT
1 TTCTTT
2437173 GACAAATCCT
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
24 24 0.83
25 5 0.17
ACGTcount: A:0.24, C:0.16, G:0.07, T:0.53
Consensus pattern (24 bp):
TTCTTTATAATCGAATCATTTTGA
Found at i:2439870 original size:12 final size:12
Alignment explanation
Indices: 2439853--2439893 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 12
2439843 TATTTTTATA
2439853 GAAAATAAAAAT
1 GAAAATAAAAAT
2439865 GAAAAT--AAAT
1 GAAAATAAAAAT
2439875 GAAAATGAAAATAT
1 GAAAAT-AAAA-AT
2439889 GAAAA
1 GAAAA
2439894 CATAAAAACG
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
10 10 0.40
12 6 0.24
13 2 0.08
14 7 0.28
ACGTcount: A:0.71, C:0.00, G:0.12, T:0.17
Consensus pattern (12 bp):
GAAAATAAAAAT
Found at i:2439879 original size:16 final size:16
Alignment explanation
Indices: 2439855--2439887 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
2439845 TTTTTATAGA
2439855 AAATAAAAATGAAAAT
1 AAATAAAAATGAAAAT
*
2439871 AAATGAAAATGAAAAT
1 AAATAAAAATGAAAAT
2439887 A
1 A
2439888 TGAAAACATA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.73, C:0.00, G:0.09, T:0.18
Consensus pattern (16 bp):
AAATAAAAATGAAAAT
Found at i:2440472 original size:15 final size:15
Alignment explanation
Indices: 2440452--2440480 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
2440442 AATACCTTTT
2440452 AAAAATAATTTTAAG
1 AAAAATAATTTTAAG
2440467 AAAAATAATTTTAA
1 AAAAATAATTTTAA
2440481 AAGATAAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.34
Consensus pattern (15 bp):
AAAAATAATTTTAAG
Found at i:2442200 original size:24 final size:25
Alignment explanation
Indices: 2442159--2442209 Score: 86
Period size: 24 Copynumber: 2.1 Consensus size: 25
2442149 TTGGGTTTGC
2442159 TTGTAAATGGGGCCTCCAGCCTACT
1 TTGTAAATGGGGCCTCCAGCCTACT
*
2442184 TTGT-AATTGGGCCTCCAGCCTACT
1 TTGTAAATGGGGCCTCCAGCCTACT
2442208 TT
1 TT
2442210 ATAGTTTGGC
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
24 21 0.84
25 4 0.16
ACGTcount: A:0.18, C:0.27, G:0.22, T:0.33
Consensus pattern (25 bp):
TTGTAAATGGGGCCTCCAGCCTACT
Found at i:2442254 original size:2 final size:2
Alignment explanation
Indices: 2442247--2442272 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2442237 AATAATAATA
2442247 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
2442273 GTGGGACAAA
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:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2442568 original size:81 final size:82
Alignment explanation
Indices: 2442394--2442596 Score: 275
Period size: 81 Copynumber: 2.5 Consensus size: 82
2442384 TAATGAGAAA
* * * * * *
2442394 TATGCTCCAATTTTCTTTCGGGGGATATCAGACTTGATATGTTCCTCTTTTTCAGGTAGTCAGAT
1 TATGCTCCACTCTTCTTTCAGGGGAGATCAGACTTGATTTGTTCCTCTTTTTCAGGTAATCAGAT
*
2442459 CAACTTTGGAAGACGGT
66 CAACTTTGGAAGACGGG
* * * *
2442476 TCTGCTCCACTCTTCTTTTAGGGTAGATCAGACTTGATTTGTTCCTCTTTTT-GGGTAATCAGAT
1 TATGCTCCACTCTTCTTTCAGGGGAGATCAGACTTGATTTGTTCCTCTTTTTCAGGTAATCAGAT
*
2442540 CAATTTTGGAAGACGGG
66 CAACTTTGGAAGACGGG
2442557 TATGCTCCACTCTTCTTTCAGGGGAGATC-GAACTTGATTT
1 TATGCTCCACTCTTCTTTCAGGGGAGATCAG-ACTTGATTT
2442597 TTCTTTGGAA
Statistics
Matches: 105, Mismatches: 15, Indels: 3
0.85 0.12 0.02
Matches are distributed among these distances:
80 1 0.01
81 60 0.57
82 44 0.42
ACGTcount: A:0.21, C:0.19, G:0.22, T:0.38
Consensus pattern (82 bp):
TATGCTCCACTCTTCTTTCAGGGGAGATCAGACTTGATTTGTTCCTCTTTTTCAGGTAATCAGAT
CAACTTTGGAAGACGGG
Found at i:2442623 original size:56 final size:56
Alignment explanation
Indices: 2442544--2442751 Score: 215
Period size: 56 Copynumber: 3.7 Consensus size: 56
2442534 TCAGATCAAT
* * * *
2442544 TTTGGAAGACGGGTATGCTCCACTCTTCTTTCAGGGGAGATC-GAACTTGATTTTTC
1 TTTGGAAAATGGGTCTGCTCCACTCTTCTTTCAGGGGAGATCAG-ACTTGATATTTC
* *
2442600 TTTGGAAAATGGGTCTGCTCCACTCTTCTTTCAGGGGAGATCATAATTGATATTTC
1 TTTGGAAAATGGGTCTGCTCCACTCTTCTTTCAGGGGAGATCAGACTTGATATTTC
* ** * * ** **
2442656 TTTGGAAAATTGGT-TGACTATACTCTTCTTTCA-GGGAGATAAGACTCGGGAAATC
1 TTTGGAAAATGGGTCTG-CTCCACTCTTCTTTCAGGGGAGATCAGACTTGATATTTC
* * *
2442711 TTTGGAAAATGAGTCTGCTCCACTATTCTTTCAGTGGAGAT
1 TTTGGAAAATGGGTCTGCTCCACTCTTCTTTCAGGGGAGAT
2442752 AAAACTATAT
Statistics
Matches: 125, Mismatches: 23, Indels: 8
0.80 0.15 0.05
Matches are distributed among these distances:
55 41 0.33
56 84 0.67
ACGTcount: A:0.24, C:0.17, G:0.23, T:0.36
Consensus pattern (56 bp):
TTTGGAAAATGGGTCTGCTCCACTCTTCTTTCAGGGGAGATCAGACTTGATATTTC
Found at i:2442740 original size:55 final size:54
Alignment explanation
Indices: 2442598--2442753 Score: 152
Period size: 55 Copynumber: 2.8 Consensus size: 54
2442588 ACTTGATTTT
* * * * **
2442598 TCTTTGGAAAATGGGTCTGCTCCACTCTTCTTTCAGGGGAGATCATAATTGATATT
1 TCTTTGGAAAAT-GGTCTGCTCCACTCTTCTTTCA-GGGAGATAAGAATCGAGAAA
** * *
2442654 TCTTTGGAAAATTGGT-TGACTATACTCTTCTTTCAGGGAGATAAGACTCGGGAAA
1 TCTTTGGAAAA-TGGTCTG-CTCCACTCTTCTTTCAGGGAGATAAGAATCGAGAAA
*
2442709 TCTTTGGAAAATGAGTCTGCTCCACTATTCTTTCAGTGGAGATAA
1 TCTTTGGAAAATG-GTCTGCTCCACTCTTCTTTCAG-GGAGATAA
2442754 AACTATATAT
Statistics
Matches: 82, Mismatches: 13, Indels: 10
0.78 0.12 0.10
Matches are distributed among these distances:
54 2 0.02
55 41 0.50
56 38 0.46
57 1 0.01
ACGTcount: A:0.26, C:0.17, G:0.22, T:0.35
Consensus pattern (54 bp):
TCTTTGGAAAATGGTCTGCTCCACTCTTCTTTCAGGGAGATAAGAATCGAGAAA
Found at i:2442979 original size:62 final size:62
Alignment explanation
Indices: 2442888--2443035 Score: 208
Period size: 62 Copynumber: 2.4 Consensus size: 62
2442878 ATCAAATTAG
* * * * *
2442888 AAAGAATTAACTTCTCTTTACGAGGAAGTCAAGGATTGACTCTGCTGGGGAGTCAATG-ATAAC
1 AAAG-ATTGACTTCTTTTTACGAGAAAGTCAAGGATTGACTCTGATGGGGAGTC-AGGAATAAC
* *
2442951 AACGATTGACTTCTTTTTATGAGAAAGTCAAGGATTGACTCTGATGGGGAGTCAGGAATAAC
1 AAAGATTGACTTCTTTTTACGAGAAAGTCAAGGATTGACTCTGATGGGGAGTCAGGAATAAC
2443013 AAAGATTGACTTCTTTTTACGAG
1 AAAGATTGACTTCTTTTTACGAG
2443036 GCTCCTCTGG
Statistics
Matches: 75, Mismatches: 9, Indels: 3
0.86 0.10 0.03
Matches are distributed among these distances:
61 2 0.03
62 70 0.93
63 3 0.04
ACGTcount: A:0.32, C:0.14, G:0.24, T:0.30
Consensus pattern (62 bp):
AAAGATTGACTTCTTTTTACGAGAAAGTCAAGGATTGACTCTGATGGGGAGTCAGGAATAAC
Found at i:2443478 original size:42 final size:41
Alignment explanation
Indices: 2443401--2443494 Score: 100
Period size: 42 Copynumber: 2.3 Consensus size: 41
2443391 AGGTTTTATG
* *
2443401 GATGGCCCGAAGGACTTATCATCTTGCTCAGAAGACTGACA
1 GATGACCCGAAGGACTTATCATCATGCTCAGAAGACTGACA
* * * **
2443442 GATGACCCGAAGGATTTAATCATCATGTTC-GAAAGACTTATT
1 GATGACCCGAAGGACTT-ATCATCATGCTCAG-AAGACTGACA
2443484 GATGACCCGAA
1 GATGACCCGAA
2443495 TGCCATACAA
Statistics
Matches: 44, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
41 16 0.36
42 28 0.64
ACGTcount: A:0.32, C:0.21, G:0.22, T:0.24
Consensus pattern (41 bp):
GATGACCCGAAGGACTTATCATCATGCTCAGAAGACTGACA
Found at i:2443967 original size:240 final size:239
Alignment explanation
Indices: 2443526--2444430 Score: 1196
Period size: 239 Copynumber: 3.8 Consensus size: 239
2443516 AGTTTAATAG
* * *
2443526 GTAAGAAACTTTGGTA-AT-TTCTTTCTTACTTTTAAAAAATTTCATTTT-C-TAAAATATTAAA
1 GTAAGAAACTTTGG-AGATCTT-TTTCTTACTTTTCAAAAATTTCATTTTACAAAAAAGATTAAA
* * ** * * ** ** **
2443587 TAAAAAACTTTAAAAATTGTTTTCTCATTTTTTGAAAATCACGCGAAAACATCTTGGTCGAAGGT
64 TGAGAAACTTTGGAAATCGCTTTCTCATTTTTCAAAAATCACTTGAAAACATCTTGCCCGAAGGT
* *
2443652 CTTATAGATGGCCCAAAGGACTTATCATCTTGCTCGAAAGACTGACAGATGACCAGAAGGATTTA
129 CTTATAGATGGCCCGAAGGACTTATCATCTTGCTCGAAAGACTGACAGATGACCTGAAGGATTTA
*
2443717 ATCATCATGCTCGAAAGACTTACTGATGGCCCGAAAGACTTACTAA
194 ATCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTACTAA
* *
2443763 GTGAGAAA-TGTTGGAGATCTTTTTCTTACTTTTTAAAAATTTCATTTTACAAAAAAAGATTAAA
1 GTAAGAAACT-TTGGAGATCTTTTTCTTACTTTTCAAAAATTTCATTTTAC-AAAAAAGATTAAA
*
2443827 TGAGAAACTTTGGAAATCACTTTCTCATTTTTCAAAAATCACTTGAAAACATCTTGCCCGAAGGT
64 TGAGAAACTTTGGAAATCGCTTTCTCATTTTTCAAAAATCACTTGAAAACATCTTGCCCGAAGGT
* * *
2443892 CTTATAGATGGCCTGAAGGACTTATCATTTTGCTCGAAAGACTGACAGATGACCTTAAGGATTTA
129 CTTATAGATGGCCCGAAGGACTTATCATCTTGCTCGAAAGACTGACAGATGACCTGAAGGATTTA
** *
2443957 ATCATCATGCTCGAAAGACTTACTGATATCCCGAAGGACATACTAA
194 ATCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTACTAA
* * *
2444003 GTTAGAAACTTTGGAGATCGTTTTCTTACTTTTCAAAAATTTCATTTTACAAAAAATATTAAATG
1 GTAAGAAACTTTGGAGATCTTTTTCTTACTTTTCAAAAATTTCATTTTACAAAAAAGATTAAATG
* ** * * *
2444068 AGAAACTTTGGAAATTGCTTTCTCATTTTTTGAAAACCACTTGAAAACATCTTGTCCGAACGTCT
66 AGAAACTTTGGAAATCGCTTTCTCATTTTTCAAAAATCACTTGAAAACATCTTGCCCGAAGGTCT
* * * * * * *
2444133 TATAGTTGGCCCGAAGGAGTTATCATCTTGCTTGAAAGACTCAAAAATGA-CTCGAATGATTTAA
131 TATAGATGGCCCGAAGGACTTATCATCTTGCTCGAAAGACTGACAGATGACCT-GAAGGATTTAA
* *
2444197 TCATCATGCACGAAAGACTTACTGATGGCTCGAAGGACTTACTAA
195 TCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTACTAA
2444242 GTAAGAAACTTTGGAGAT-TATTTTCTTACTTTTCAAAAATTTCATTTTACAAAAAAGATTAAAT
1 GTAAGAAACTTTGGAGATCT-TTTTCTTACTTTTCAAAAATTTCATTTTACAAAAAAGATTAAAT
*
2444306 GAGAAAC-TTGGAAATCGCTTTCTCATTTTTCAAAAAGCACTTGAAAACATCTTGCCCGAAGGTC
65 GAGAAACTTTGGAAATCGCTTTCTCATTTTTCAAAAATCACTTGAAAACATCTTGCCCGAAGGTC
** * * * * * **
2444370 TTATAGATGATCCGAAGTATTTAATCATCATGCTCGAAAGACTCACTGATGGTCTGAAGGA
130 TTATAGATGGCCCGAAGGACTT-ATCATCTTGCTCGAAAGACTGACAGATGACCTGAAGGA
2444431 CTTACTAAGT
Statistics
Matches: 584, Mismatches: 73, Indels: 20
0.86 0.11 0.03
Matches are distributed among these distances:
236 2 0.00
237 39 0.07
238 73 0.12
239 258 0.44
240 211 0.36
241 1 0.00
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.33
Consensus pattern (239 bp):
GTAAGAAACTTTGGAGATCTTTTTCTTACTTTTCAAAAATTTCATTTTACAAAAAAGATTAAATG
AGAAACTTTGGAAATCGCTTTCTCATTTTTCAAAAATCACTTGAAAACATCTTGCCCGAAGGTCT
TATAGATGGCCCGAAGGACTTATCATCTTGCTCGAAAGACTGACAGATGACCTGAAGGATTTAAT
CATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTACTAA
Found at i:2444516 original size:197 final size:197
Alignment explanation
Indices: 2444191--2444608 Score: 653
Period size: 197 Copynumber: 2.1 Consensus size: 197
2444181 GACTCGAATG
* *
2444191 ATTTAATCATCATGCACGAAAGACTTACTGATGGCTCGAAGGACTTACTAAGTAAGAAACTTTGG
1 ATTTAATCATCATGCTCGAAAGACTCACTGATGGCTCGAAGGACTTACTAAGTAAGAAACTTTGG
*
2444256 AGATTATTTTCTTACTTTTCAAAAATTTCATTTTACAAAAAAGATTAAATGAGAAACTTGGAAAT
66 AGATCATTTTCTTACTTTTCAAAAATTTCATTTTACAAAAAAGATTAAATGAGAAACTTGGAAAT
* * *
2444321 CGCTTTCTCATTTTTCAAAAAGCACTTGAAAACATCTTGCCCGAAGGTCTTATAGATGATCCGAA
131 CGCTTTCCCATTTTTCAAAAAGCACTTGAAAACATCTTGCCCGAAAGTCTTATAGATGACCCGAA
*
2444386 GT
196 GA
2444388 ATTTAATCATCATGCTCGAAAGACTCACTGATGG-TCTGAAGGACTTACTAAGTAAGAAACTTTG
1 ATTTAATCATCATGCTCGAAAGACTCACTGATGGCTC-GAAGGACTTACTAAGTAAGAAACTTTG
* *
2444452 GAGATCGTTTTCTTACTTTTCAAAAATTTCA-TTTACAAAAAGGATTAAATGAGAAACTTTGGAA
65 GAGATCATTTTCTTACTTTTCAAAAATTTCATTTTACAAAAAAGATTAAATGAGAAAC-TTGGAA
* * * * *
2444516 ATCGCTTTCCCATTTTTCGAAAATCACTTGAAAACATCTTTCCTGAAAGTCTTATAGATGGCCCG
129 ATCGCTTTCCCATTTTTCAAAAAGCACTTGAAAACATCTTGCCCGAAAGTCTTATAGATGACCCG
2444581 AAGA
194 AAGA
* *
2444585 ACTT-ATCATCTTGCTCGAAAGACT
1 ATTTAATCATCATGCTCGAAAGACT
2444609 GACAGATAAT
Statistics
Matches: 203, Mismatches: 16, Indels: 5
0.91 0.07 0.02
Matches are distributed among these distances:
196 46 0.23
197 157 0.77
ACGTcount: A:0.35, C:0.17, G:0.15, T:0.33
Consensus pattern (197 bp):
ATTTAATCATCATGCTCGAAAGACTCACTGATGGCTCGAAGGACTTACTAAGTAAGAAACTTTGG
AGATCATTTTCTTACTTTTCAAAAATTTCATTTTACAAAAAAGATTAAATGAGAAACTTGGAAAT
CGCTTTCCCATTTTTCAAAAAGCACTTGAAAACATCTTGCCCGAAAGTCTTATAGATGACCCGAA
GA
Found at i:2453502 original size:2 final size:2
Alignment explanation
Indices: 2453490--2453518 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
2453480 ATAATATTAA
2453490 AT AT A- 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
2453519 GTGGGACGAA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2457446 original size:2 final size:2
Alignment explanation
Indices: 2457439--2457467 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
2457429 CTTCAGAAAC
2457439 AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
2457468 AAACTCTCTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:2458883 original size:131 final size:131
Alignment explanation
Indices: 2458748--2459009 Score: 366
Period size: 131 Copynumber: 2.0 Consensus size: 131
2458738 ATAAGAATGG
* * * * *
2458748 TGATAACACGGTTCCTACGTGATGAGGA-TGACTGGTTATCT-TGGGGTGACATGGCTCCTACAT
1 TGATAAAACGATTCCTACGTGATCAGGACAG-CTGGTTATCTAT-GGGTAACATGGCTCCTACAT
* *
2458811 GATGAGGAGGTTTGGTCGGGGGATGACACAGTTCCTACGTGATGAGGATGACATGCCATCTTTAG
64 GATGAGGAGGTATGGTCGGGGGATGACACAGTTCCTACGTGATGAGGATGACATGCCATCCTTAG
2458876 GGA
129 GGA
* * * *
2458879 TGATAAAATGATTCCTACGTGATCAGGACAGTTGGTTGTCTATGGGTAACATGGCTCCTACGTGA
1 TGATAAAACGATTCCTACGTGATCAGGACAGCTGGTTATCTATGGGTAACATGGCTCCTACATGA
* * *
2458944 TGAGGAGGTATGGTCGGTGGATGACACAGTTCCTATGTGATGAGGATGTCATGCCATCCTTAGGG
66 TGAGGAGGTATGGTCGGGGGATGACACAGTTCCTACGTGATGAGGATGACATGCCATCCTTAGGG
2459009 A
131 A
2459010 ATTGTTTCAA
Statistics
Matches: 115, Mismatches: 14, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
131 113 0.98
132 2 0.02
ACGTcount: A:0.24, C:0.16, G:0.32, T:0.28
Consensus pattern (131 bp):
TGATAAAACGATTCCTACGTGATCAGGACAGCTGGTTATCTATGGGTAACATGGCTCCTACATGA
TGAGGAGGTATGGTCGGGGGATGACACAGTTCCTACGTGATGAGGATGACATGCCATCCTTAGGG
A
Found at i:2459222 original size:67 final size:67
Alignment explanation
Indices: 2459009--2459371 Score: 350
Period size: 67 Copynumber: 5.4 Consensus size: 67
2458999 ATCCTTAGGG
* * * *
2459009 AATT-GTTTCAAGGGAAACAGACTCAATGATGA--TTGTTTCAATAGAAACTGTCTCAAGATAGA
1 AATTCGTTTCAAGGGAAAC-GACTCAAAGATGATTTTGTTTTAAGAGAAACTGTCTCAAGAGAGA
2459071 CAA
65 CAA
*
2459074 AACTT-GTTTCAAGGGAAATGACTCAAAGATGATTTT-TTTTAAGAGAAACTGTCTC-A-AGAGA
1 AA-TTCGTTTCAAGGGAAACGACTCAAAGATGATTTTGTTTTAAGAGAAACTGTCTCAAGAGAGA
2459135 CAA
65 CAA
** *
2459138 AATTCGTTTCAAGGGAAACGACAAAAAGATGATTTTGTTTTAAGAGAAATTGTCTCAAGAGAGAC
1 AATTCGTTTCAAGGGAAACGACTCAAAGATGATTTTGTTTTAAGAGAAACTGTCTCAAGAGAGAC
2459203 AA
66 AA
* * * * *
2459205 AATTCGTTTCAATGGAAACAACTCAATGATGATTTTGTTTTAAGAGAAACTGTCTTAAAAGAGAC
1 AATTCGTTTCAAGGGAAACGACTCAAAGATGATTTTGTTTTAAGAGAAACTGTCTCAAGAGAGAC
2459270 -A
66 AA
* * * * * * * * *
2459271 ATTTTGTTTGAAGGGAAATGATATCAAAGATTGTTTTTTGTTTCATGAGAAACAGTCTCAAG-GA
1 AATTCGTTTCAAGGGAAACGA-CTCAAAGA-TG-ATTTTGTTTTAAGAGAAACTGTCTCAAGAGA
*
2459335 -AAATA
63 GACA-A
* * *
2459340 AGATTTGTTTCAAGAGAAATAGACTCAAAGAT
1 A-ATTCGTTTCAAGGGAAA-CGACTCAAAGAT
2459372 TATAAATCTT
Statistics
Matches: 247, Mismatches: 37, Indels: 24
0.80 0.12 0.08
Matches are distributed among these distances:
63 2 0.01
64 37 0.15
65 33 0.13
66 49 0.20
67 74 0.30
68 4 0.02
69 25 0.10
70 21 0.09
71 2 0.01
ACGTcount: A:0.40, C:0.11, G:0.19, T:0.30
Consensus pattern (67 bp):
AATTCGTTTCAAGGGAAACGACTCAAAGATGATTTTGTTTTAAGAGAAACTGTCTCAAGAGAGAC
AA
Found at i:2459384 original size:36 final size:36
Alignment explanation
Indices: 2459307--2459396 Score: 92
Period size: 36 Copynumber: 2.5 Consensus size: 36
2459297 AAGATTGTTT
* * * *
2459307 TTTGTTTCATGAGAAACAGTCTCAAGGAAAATAAGA
1 TTTGTTTCAAGAGAAATAGACTCAAAGAAAATAAGA
**
2459343 TTTGTTTCAAGAGAAATAGACTCAAAGATTATAA-A
1 TTTGTTTCAAGAGAAATAGACTCAAAGAAAATAAGA
* *
2459378 TCTTGTTTCCAGTGAAATA
1 T-TTGTTTCAAGAGAAATA
2459397 ATTTCAGAAT
Statistics
Matches: 45, Mismatches: 8, Indels: 2
0.82 0.15 0.04
Matches are distributed among these distances:
35 2 0.04
36 43 0.96
ACGTcount: A:0.40, C:0.11, G:0.17, T:0.32
Consensus pattern (36 bp):
TTTGTTTCAAGAGAAATAGACTCAAAGAAAATAAGA
Found at i:2459680 original size:22 final size:22
Alignment explanation
Indices: 2459648--2459699 Score: 86
Period size: 22 Copynumber: 2.4 Consensus size: 22
2459638 GAGGAAACAT
*
2459648 CTTTAGAAGATCTGATTATTGA
1 CTTTAGGAGATCTGATTATTGA
*
2459670 CTTTAGGAGATCTGATTGTTGA
1 CTTTAGGAGATCTGATTATTGA
2459692 CTTTAGGA
1 CTTTAGGA
2459700 AGTCAAATCT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.27, C:0.10, G:0.23, T:0.40
Consensus pattern (22 bp):
CTTTAGGAGATCTGATTATTGA
Found at i:2465636 original size:2 final size:2
Alignment explanation
Indices: 2465629--2465654 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2465619 TTTAGAAACC
2465629 GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA
2465655 AAACTCTCTC
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:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:2468399 original size:21 final size:20
Alignment explanation
Indices: 2468353--2468399 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 20
2468343 TTATAGGAGG
* * *
2468353 GTATCGATACTGAAGAATCG
1 GTATCGATACTAAAAAATCA
2468373 GTATCGATACTAAAAATATCA
1 GTATCGATACTAAAAA-ATCA
2468394 GTATCG
1 GTATCG
2468400 GTACAATCCT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
20 14 0.61
21 9 0.39
ACGTcount: A:0.38, C:0.15, G:0.19, T:0.28
Consensus pattern (20 bp):
GTATCGATACTAAAAAATCA
Found at i:2474738 original size:22 final size:22
Alignment explanation
Indices: 2474713--2474762 Score: 73
Period size: 22 Copynumber: 2.3 Consensus size: 22
2474703 ATTTGTTAAG
* *
2474713 GCACTTTATTATCAATGCTAAT
1 GCACTTTAGTATCAATGCTAAC
*
2474735 GCACTTTAGTATCAGTGCTAAC
1 GCACTTTAGTATCAATGCTAAC
2474757 GCACTT
1 GCACTT
2474763 CCTTACCAGT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.28, C:0.22, G:0.14, T:0.36
Consensus pattern (22 bp):
GCACTTTAGTATCAATGCTAAC
Found at i:2478549 original size:19 final size:19
Alignment explanation
Indices: 2478527--2478563 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
2478517 AGAAGCTGAT
2478527 TTTTTTTAATAAAA-AAAAC
1 TTTTTTTAA-AAAATAAAAC
2478546 TTTTTTTAAAAAATAAAA
1 TTTTTTTAAAAAATAAAA
2478564 TAATGAAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 4 0.24
19 13 0.76
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.43
Consensus pattern (19 bp):
TTTTTTTAAAAAATAAAAC
Found at i:2479363 original size:6 final size:6
Alignment explanation
Indices: 2479352--2479387 Score: 72
Period size: 6 Copynumber: 6.0 Consensus size: 6
2479342 CCATCTTAGT
2479352 TTTTTG TTTTTG TTTTTG TTTTTG TTTTTG TTTTTG
1 TTTTTG TTTTTG TTTTTG TTTTTG TTTTTG TTTTTG
2479388 GATAATTTTG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 30 1.00
ACGTcount: A:0.00, C:0.00, G:0.17, T:0.83
Consensus pattern (6 bp):
TTTTTG
Found at i:2480770 original size:14 final size:14
Alignment explanation
Indices: 2480741--2480774 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
2480731 TTATATGTAT
2480741 ATTTTAATTATATA
1 ATTTTAATTATATA
* *
2480755 ATTTTAATTTTTTA
1 ATTTTAATTATATA
2480769 ATTTTA
1 ATTTTA
2480775 TAAGATCTTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (14 bp):
ATTTTAATTATATA
Found at i:2499759 original size:116 final size:117
Alignment explanation
Indices: 2499541--2499760 Score: 293
Period size: 116 Copynumber: 1.9 Consensus size: 117
2499531 TTTCAAATCA
* *
2499541 AAATTTTCTTTTTCAATACTTTCAAATTTCATTTTTGAGAGCTCTAAATCCTTCTTCAATATTTC
1 AAATTTTCTTTTTCAATACTTTCAAATTTCATTTTTGAAAGCTCTAAATCCTTCTTCAACATTTC
* *
2499606 ATTTTGATTTTCAAAATCCATTTTAGTTTCTAGAAGAAGTTTGTTTAATTTG
66 ATTTTGATTTTCAAAATCCATTTTACTTTCTAAAAGAAGTTTGTTTAATTTG
* * * * *
2499658 AAATTTTCTTTTTCAA-AGTTTTCAGATTTCA-TTTTGAAAGCTCTGACTCCTTTTTCAACATTT
1 AAATTTTCTTTTTCAATA-CTTTCAAATTTCATTTTTGAAAGCTCTAAATCCTTCTTCAACATTT
* * *
2499721 CATTTTGATTTTCCAAGTCTATTTTAACTTTC-AAAAGAAG
65 CATTTTGATTTTCAAAATCCATTTT-ACTTTCTAAAAGAAG
2499761 ATCATTTTTA
Statistics
Matches: 89, Mismatches: 12, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
116 57 0.64
117 32 0.36
ACGTcount: A:0.28, C:0.15, G:0.09, T:0.48
Consensus pattern (117 bp):
AAATTTTCTTTTTCAATACTTTCAAATTTCATTTTTGAAAGCTCTAAATCCTTCTTCAACATTTC
ATTTTGATTTTCAAAATCCATTTTACTTTCTAAAAGAAGTTTGTTTAATTTG
Found at i:2502910 original size:19 final size:20
Alignment explanation
Indices: 2502885--2502930 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 20
2502875 GACCAACAAA
* * *
2502885 ATCGCAATGCGATTTCTAAT
1 ATCGCAACGCGATCTCCAAT
2502905 -TCGCAACGCGATCTCCAAT
1 ATCGCAACGCGATCTCCAAT
2502924 ATCGCAA
1 ATCGCAA
2502931 ATTCGCGCTA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
19 16 0.73
20 6 0.27
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.26
Consensus pattern (20 bp):
ATCGCAACGCGATCTCCAAT
Found at i:2502976 original size:21 final size:21
Alignment explanation
Indices: 2502945--2503057 Score: 86
Period size: 21 Copynumber: 5.5 Consensus size: 21
2502935 GCGCTACATT
*
2502945 TCGCATTGCGATAGTTGAAAA
1 TCGCGTTGCGATAGTTGAAAA
* * ** **
2502966 TCGTGTTGCGAT-TTTCCATT
1 TCGCGTTGCGATAGTTGAAAA
2502986 TCGCGTTGCGATAGTTGAAAA
1 TCGCGTTGCGATAGTTGAAAA
* * ** **
2503007 TCGCGTTGCGGT-TTTCCATT
1 TCGCGTTGCGATAGTTGAAAA
*
2503027 TCGCGTTGTGATAGTTGAAAA
1 TCGCGTTGCGATAGTTGAAAA
2503048 TCGCGTTGCG
1 TCGCGTTGCG
2503058 GTTTTCCATT
Statistics
Matches: 63, Mismatches: 27, Indels: 4
0.67 0.29 0.04
Matches are distributed among these distances:
20 27 0.43
21 36 0.57
ACGTcount: A:0.19, C:0.18, G:0.27, T:0.36
Consensus pattern (21 bp):
TCGCGTTGCGATAGTTGAAAA
Found at i:2502989 original size:41 final size:41
Alignment explanation
Indices: 2502941--2503079 Score: 242
Period size: 41 Copynumber: 3.4 Consensus size: 41
2502931 ATTCGCGCTA
* * *
2502941 CATTTCGCATTGCGATAGTTGAAAATCGTGTTGCGATTTTC
1 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGGTTTTC
2502982 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGGTTTTC
1 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGGTTTTC
*
2503023 CATTTCGCGTTGTGATAGTTGAAAATCGCGTTGCGGTTTTC
1 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGGTTTTC
2503064 CATTTCGCGTTGCGAT
1 CATTTCGCGTTGCGAT
2503080 TTTCCATTTC
Statistics
Matches: 93, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 93 1.00
ACGTcount: A:0.18, C:0.19, G:0.25, T:0.38
Consensus pattern (41 bp):
CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGGTTTTC
Found at i:2502995 original size:20 final size:20
Alignment explanation
Indices: 2502970--2503139 Score: 137
Period size: 20 Copynumber: 8.4 Consensus size: 20
2502960 TGAAAATCGT
2502970 GTTGCGATTTTCCATTTCGC
1 GTTGCGATTTTCCATTTCGC
* ** **
2502990 GTTGCGATAGTTGAAAATCGC
1 GTTGCGAT-TTTCCATTTCGC
*
2503011 GTTGCGGTTTTCCATTTCGC
1 GTTGCGATTTTCCATTTCGC
* * ** **
2503031 GTTGTGATAGTTGAAAATCGC
1 GTTGCGAT-TTTCCATTTCGC
*
2503052 GTTGCGGTTTTCCATTTCGC
1 GTTGCGATTTTCCATTTCGC
2503072 GTTGCGATTTTCCATTTCGC
1 GTTGCGATTTTCCATTTCGC
* * * *
2503092 GTTGCAATAGTTACA-GT-GTC
1 GTTGCGAT-TTTCCATTTCG-C
2503112 GTTGCGATTTTCCATTTCGC
1 GTTGCGATTTTCCATTTCGC
2503132 GTTGCGAT
1 GTTGCGAT
2503140 AGTCTACAGT
Statistics
Matches: 110, Mismatches: 34, Indels: 12
0.71 0.22 0.08
Matches are distributed among these distances:
19 5 0.05
20 73 0.66
21 32 0.29
ACGTcount: A:0.15, C:0.20, G:0.25, T:0.40
Consensus pattern (20 bp):
GTTGCGATTTTCCATTTCGC
Found at i:2503083 original size:61 final size:60
Alignment explanation
Indices: 2503007--2503139 Score: 187
Period size: 61 Copynumber: 2.2 Consensus size: 60
2502997 TAGTTGAAAA
* ** *
2503007 TCGCGTTGCGGTTTTCCATTTCGCGTTGTGATAGTTGAAAATCG-CGTTGCGGTTTTCCATT
1 TCGCGTTGCGATTTTCCATTTCGCGTTGCAATAGTT-AAAAT-GTCGTTGCGATTTTCCATT
* *
2503068 TCGCGTTGCGATTTTCCATTTCGCGTTGCAATAGTTACAGTGTCGTTGCGATTTTCCATT
1 TCGCGTTGCGATTTTCCATTTCGCGTTGCAATAGTTAAAATGTCGTTGCGATTTTCCATT
2503128 TCGCGTTGCGAT
1 TCGCGTTGCGAT
2503140 AGTCTACAGT
Statistics
Matches: 65, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
59 1 0.02
60 31 0.48
61 33 0.51
ACGTcount: A:0.14, C:0.21, G:0.25, T:0.41
Consensus pattern (60 bp):
TCGCGTTGCGATTTTCCATTTCGCGTTGCAATAGTTAAAATGTCGTTGCGATTTTCCATT
Found at i:2503162 original size:41 final size:40
Alignment explanation
Indices: 2503071--2503184 Score: 192
Period size: 41 Copynumber: 2.8 Consensus size: 40
2503061 TTCCATTTCG
2503071 CGTTGCGATTTTCCATTTCGCGTTGCAATAGTTACAGTGT
1 CGTTGCGATTTTCCATTTCGCGTTGCAATAGTTACAGTGT
*
2503111 CGTTGCGATTTTCCATTTCGCGTTGCGATAGTCTACAGTGT
1 CGTTGCGATTTTCCATTTCGCGTTGCAATAGT-TACAGTGT
* *
2503152 CGTTGTGATTTTCCATTTCGCGTTGCTATAGTT
1 CGTTGCGATTTTCCATTTCGCGTTGCAATAGTT
2503185 TTAAAAATGG
Statistics
Matches: 70, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
40 32 0.46
41 38 0.54
ACGTcount: A:0.15, C:0.20, G:0.23, T:0.42
Consensus pattern (40 bp):
CGTTGCGATTTTCCATTTCGCGTTGCAATAGTTACAGTGT
Found at i:2507679 original size:22 final size:22
Alignment explanation
Indices: 2507654--2507697 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
2507644 AGGACCATTG
2507654 GATATATCCCGAAAGACCACTA
1 GATATATCCCGAAAGACCACTA
* * *
2507676 GATATGTCCTGAATGACCACTA
1 GATATATCCCGAAAGACCACTA
2507698 TAACCCTCGA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.36, C:0.25, G:0.16, T:0.23
Consensus pattern (22 bp):
GATATATCCCGAAAGACCACTA
Found at i:2508378 original size:64 final size:64
Alignment explanation
Indices: 2508285--2508404 Score: 177
Period size: 64 Copynumber: 1.9 Consensus size: 64
2508275 ACAAATCACC
* * * *
2508285 TTCGATGTTTTAATCTTAAGGGGGTGCATCGATGCACTACTTGTGCATCGATACACTTATGGCA
1 TTCGATGTTTTAATCTTAAAGGAGTGCATCGATACACTACATGTGCATCGATACACTTATGGCA
* * *
2508349 TTCGATGTTTTTATTTTAAAGGAGTGCATCGATACACTTCATGTGCATCGATACAC
1 TTCGATGTTTTAATCTTAAAGGAGTGCATCGATACACTACATGTGCATCGATACAC
2508405 CTTGAACAAT
Statistics
Matches: 49, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
64 49 1.00
ACGTcount: A:0.25, C:0.18, G:0.21, T:0.36
Consensus pattern (64 bp):
TTCGATGTTTTAATCTTAAAGGAGTGCATCGATACACTACATGTGCATCGATACACTTATGGCA
Found at i:2513700 original size:64 final size:64
Alignment explanation
Indices: 2513587--2513747 Score: 153
Period size: 64 Copynumber: 2.5 Consensus size: 64
2513577 TCCATAACGT
* * * * *
2513587 GTGCATCGATGCACTACCTATGCATCGGTACACAAATCACCTTCGATGTTTTAATCTTAAGGGG
1 GTGCATCGATGCACTACCTATGCATCGATACACAAATCACATTCAATGTTTTAATCTTAAAGGA
* ** ** * *
2513651 GTGCATCGATGTACTACCCT-TGCATCGATACACTTATGGCATTCAATGTTTTTATTTTAAAGGA
1 GTGCATCGATGCACTA-CCTATGCATCGATACACAAATCACATTCAATGTTTTAATCTTAAAGGA
* * * * *
2513715 GTGCATCAATACACTTCATGTGCATCGATACAC
1 GTGCATCGATGCACTACCTATGCATCGATACAC
2513748 CTTGAACAAT
Statistics
Matches: 78, Mismatches: 17, Indels: 4
0.79 0.17 0.04
Matches are distributed among these distances:
63 2 0.03
64 73 0.94
65 3 0.04
ACGTcount: A:0.27, C:0.22, G:0.18, T:0.32
Consensus pattern (64 bp):
GTGCATCGATGCACTACCTATGCATCGATACACAAATCACATTCAATGTTTTAATCTTAAAGGA
Found at i:2515113 original size:130 final size:131
Alignment explanation
Indices: 2514812--2515181 Score: 472
Period size: 130 Copynumber: 2.8 Consensus size: 131
2514802 TAATTCTAAG
* * *
2514812 AGAGAAAACGATAATATCTAATTATTTACAATCGAAAATAAATAACCTCTCATGCCTTAAAGCAA
1 AGAGAAAACAATAATATCTAATTATTTCCAATCGAAAATAAATAACCTCTCATGCCTTAAAGCAG
* * * *
2514877 TCATTTATTACTCCAACCGGAATGAAGAGATATCACTATTTCGTCTTAAAATTCAATAGTGGTTC
66 TCATTTATTACTCCAACCGAAATGAAGAGATATCACTATTTCATCTTAAAAATCAATAGTGATTC
*
2514942 G
131 A
* * * *
2514943 AGAGAGAACTATAATATCTAATTATTTCCAATCGAGAATAAATGACCTCTCATGCCTTAAAGCAG
1 AGAGAAAACAATAATATCTAATTATTTCCAATCGAAAATAAATAACCTCTCATGCCTTAAAGCAG
* * ** *
2515008 TCATTTATTACTTCAATCGAAATGAA-ATTTATCACTATTTCATCTTAAAAATCAATATTGATTC
66 TCATTTATTACTCCAACCGAAATGAAGAGATATCACTATTTCATCTTAAAAATCAATAGTGATTC
2515072 A
131 A
* * * * *
2515073 AGAGAAAACAATAATATCTAATTATTCCCAATAGATAATAAATAACCTCTCACGCCTTAAAACAG
1 AGAGAAAACAATAATATCTAATTATTTCCAATCGAAAATAAATAACCTCTCATGCCTTAAAGCAG
* ** * * *
2515138 TTATTTATTACTCTGACCGAAGTGAAAAGATATTACTACTTTCA
66 TCATTTATTACTCCAACCGAAATGAAGAGATATCACTA-TTTCA
2515182 ATGTTAATTC
Statistics
Matches: 204, Mismatches: 33, Indels: 3
0.85 0.14 0.01
Matches are distributed among these distances:
130 109 0.53
131 90 0.44
132 5 0.02
ACGTcount: A:0.40, C:0.18, G:0.10, T:0.32
Consensus pattern (131 bp):
AGAGAAAACAATAATATCTAATTATTTCCAATCGAAAATAAATAACCTCTCATGCCTTAAAGCAG
TCATTTATTACTCCAACCGAAATGAAGAGATATCACTATTTCATCTTAAAAATCAATAGTGATTC
A
Found at i:2517309 original size:3 final size:3
Alignment explanation
Indices: 2517301--2517329 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
2517291 AAACAAAACA
2517301 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
2517330 CCCAAACAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:2518954 original size:20 final size:21
Alignment explanation
Indices: 2518929--2518980 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
2518919 TTTTCCCAAT
*
2518929 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
2518949 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
2518970 TCGCAATGCGA
1 TCGCAATGCGA
2518981 TACTGACTAT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
20 11 0.42
21 15 0.58
ACGTcount: A:0.38, C:0.19, G:0.25, T:0.17
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:2519071 original size:20 final size:20
Alignment explanation
Indices: 2519023--2519075 Score: 88
Period size: 20 Copynumber: 2.6 Consensus size: 20
2519013 TAATACAAAA
* *
2519023 TCGCAACGAGATACTGACTT
1 TCGCAACGCGATTCTGACTT
2519043 TCGCAACGCGATTCTGACTT
1 TCGCAACGCGATTCTGACTT
2519063 TCGCAACGCGATT
1 TCGCAACGCGATT
2519076 TACATAGCGC
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:0.25, C:0.28, G:0.21, T:0.26
Consensus pattern (20 bp):
TCGCAACGCGATTCTGACTT
Found at i:2519638 original size:19 final size:19
Alignment explanation
Indices: 2519593--2519640 Score: 53
Period size: 19 Copynumber: 2.5 Consensus size: 19
2519583 TTCGAGAATG
*
2519593 AAAATCGCAACGCGGAAAT
1 AAAATCGCAACGCGGAAAC
*
2519612 AACTATCGCAACGC-GAAACC
1 AA-AATCGCAACGCGGAAA-C
2519632 AAAATCGCA
1 AAAATCGCA
2519641 TTGCGATTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
19 12 0.50
20 12 0.50
ACGTcount: A:0.46, C:0.27, G:0.17, T:0.10
Consensus pattern (19 bp):
AAAATCGCAACGCGGAAAC
Found at i:2519658 original size:19 final size:19
Alignment explanation
Indices: 2519636--2519814 Score: 145
Period size: 19 Copynumber: 10.1 Consensus size: 19
2519626 GAAACCAAAA
*
2519636 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
2519655 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
2519669 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
2519688 TCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
2519707 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* **
2519721 TCTCGTTGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
2519740 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* **
2519754 TCTCGTTGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
*
2519773 TCCGCGTTGCGATTCTCATT
1 T-CGCGTTGCGATTTTCATT
*
2519793 ATCTCGTTGCGATTTTCATT
1 -TCGCGTTGCGATTTTCATT
2519813 TC
1 TC
2519815 AACCAAAAGA
Statistics
Matches: 129, Mismatches: 14, Indels: 34
0.73 0.08 0.19
Matches are distributed among these distances:
14 30 0.23
16 7 0.05
17 8 0.06
19 52 0.40
20 31 0.24
21 1 0.01
ACGTcount: A:0.12, C:0.24, G:0.21, T:0.44
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:2519719 original size:52 final size:52
Alignment explanation
Indices: 2519636--2519752 Score: 207
Period size: 52 Copynumber: 2.2 Consensus size: 52
2519626 GAAACCAAAA
* **
2519636 TCGCATTGCGATTTTCATTTCGCGTTGCGATTCTCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATTTCGCGTTGCGATTCTCTCGTTGCGATAGTCATT
2519688 TCGCGTTGCGATTTTCATTTCGCGTTGCGATTCTCTCGTTGCGATAGTCATT
1 TCGCGTTGCGATTTTCATTTCGCGTTGCGATTCTCTCGTTGCGATAGTCATT
2519740 TCGCGTTGCGATT
1 TCGCGTTGCGATT
2519753 CTCTCGTTGC
Statistics
Matches: 62, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
52 62 1.00
ACGTcount: A:0.11, C:0.23, G:0.22, T:0.44
Consensus pattern (52 bp):
TCGCGTTGCGATTTTCATTTCGCGTTGCGATTCTCTCGTTGCGATAGTCATT
Found at i:2519728 original size:33 final size:33
Alignment explanation
Indices: 2519691--2519789 Score: 171
Period size: 33 Copynumber: 3.0 Consensus size: 33
2519681 TTTCATTTCG
**
2519691 CGTTGCGATTTTCATTTCGCGTTGCGATTCTCT
1 CGTTGCGATAGTCATTTCGCGTTGCGATTCTCT
2519724 CGTTGCGATAGTCATTTCGCGTTGCGATTCTCT
1 CGTTGCGATAGTCATTTCGCGTTGCGATTCTCT
2519757 CGTTGCGATAGTCATTTCCGCGTTGCGATTCTC
1 CGTTGCGATAGTCATTT-CGCGTTGCGATTCTC
2519790 ATTATCTCGT
Statistics
Matches: 63, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
33 48 0.76
34 15 0.24
ACGTcount: A:0.11, C:0.25, G:0.23, T:0.40
Consensus pattern (33 bp):
CGTTGCGATAGTCATTTCGCGTTGCGATTCTCT
Found at i:2519729 original size:14 final size:14
Alignment explanation
Indices: 2519710--2519765 Score: 58
Period size: 14 Copynumber: 3.6 Consensus size: 14
2519700 TTTCATTTCG
2519710 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
2519724 CGTTGCGATAGTCATTTCG
1 CGTTGCGAT--TC---TCT
2519743 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
2519757 CGTTGCGAT
1 CGTTGCGAT
2519766 AGTCATTTCC
Statistics
Matches: 35, Mismatches: 2, Indels: 10
0.74 0.04 0.21
Matches are distributed among these distances:
14 20 0.57
16 2 0.06
17 2 0.06
19 11 0.31
ACGTcount: A:0.11, C:0.25, G:0.25, T:0.39
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:2521980 original size:42 final size:42
Alignment explanation
Indices: 2521934--2522106 Score: 188
Period size: 42 Copynumber: 4.1 Consensus size: 42
2521924 CCTATCGTTG
*
2521934 AAGAGGCCCCTATCATTCCTCGAGAGTCCCCTCCCACCATTC
1 AAGAGGCCACTATCATTCCTCGAGAGTCCCCTCCCACCATTC
* * * * * * *
2521976 AAGAGGCCACTGTCATCCCTCAAGAGTCCACTCCTATCATTG
1 AAGAGGCCACTATCATTCCTCGAGAGTCCCCTCCCACCATTC
* * *
2522018 AAGAGGCCCCTATCATTCCTCGAGAGTCCCCTCCCACCGTTT
1 AAGAGGCCACTATCATTCCTCGAGAGTCCCCTCCCACCATTC
* * *
2522060 AAGAGGCCACTGTCA-TCGTTGAAGAGGT-CCCTCCCACCATTC
1 AAGAGGCCACTATCATTCCTCG-AGA-GTCCCCTCCCACCATTC
2522102 AAGAG
1 AAGAG
2522107 CCCGATTCAC
Statistics
Matches: 106, Mismatches: 23, Indels: 4
0.80 0.17 0.03
Matches are distributed among these distances:
41 4 0.04
42 100 0.94
43 2 0.02
ACGTcount: A:0.24, C:0.36, G:0.18, T:0.22
Consensus pattern (42 bp):
AAGAGGCCACTATCATTCCTCGAGAGTCCCCTCCCACCATTC
Done.