Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002275.1 Hibiscus syriacus cultivar Beakdansim tig00004629_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: 179937
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:5282 original size:18 final size:18
Alignment explanation
Indices: 5259--5327 Score: 93
Period size: 18 Copynumber: 3.7 Consensus size: 18
5249 ACTGAATATT
5259 TGTCCCGAAGGACCACTA
1 TGTCCCGAAGGACCACTA
*
5277 TGTCCCAAAGGACCACTGA
1 TGTCCCGAAGGACCACT-A
* *
5296 TTGTTCCGAAGAACCACTA
1 -TGTCCCGAAGGACCACTA
5315 TGTCCCGAAGGAC
1 TGTCCCGAAGGAC
5328 AACTGATAAT
Statistics
Matches: 43, Mismatches: 6, Indels: 4
0.81 0.11 0.08
Matches are distributed among these distances:
18 27 0.63
19 2 0.05
20 14 0.33
ACGTcount: A:0.29, C:0.30, G:0.22, T:0.19
Consensus pattern (18 bp):
TGTCCCGAAGGACCACTA
Found at i:5306 original size:38 final size:38
Alignment explanation
Indices: 5258--5334 Score: 118
Period size: 38 Copynumber: 2.0 Consensus size: 38
5248 CACTGAATAT
* *
5258 TTGTCCCGAAGGACCACTATGTCCCAAAGGACCACTGA
1 TTGTCCCGAAGAACCACTATGTCCCAAAGGACAACTGA
* *
5296 TTGTTCCGAAGAACCACTATGTCCCGAAGGACAACTGA
1 TTGTCCCGAAGAACCACTATGTCCCAAAGGACAACTGA
5334 T
1 T
5335 AATCCCTCGA
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
38 35 1.00
ACGTcount: A:0.30, C:0.29, G:0.21, T:0.21
Consensus pattern (38 bp):
TTGTCCCGAAGAACCACTATGTCCCAAAGGACAACTGA
Found at i:12121 original size:18 final size:18
Alignment explanation
Indices: 12094--12166 Score: 83
Period size: 18 Copynumber: 3.9 Consensus size: 18
12084 ACTGAATATT
*
12094 TGTCCTGAAGGACCACTA
1 TGTCCCGAAGGACCACTA
12112 TGTCCCGAAGGACCACTGA
1 TGTCCCGAAGGACCACT-A
** *
12131 TTGTTACGAAGAACCACTA
1 -TGTCCCGAAGGACCACTA
*
12150 TATCCCGAAGGACCACT
1 TGTCCCGAAGGACCACT
12167 GATAATCCCT
Statistics
Matches: 45, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
18 29 0.64
19 2 0.04
20 14 0.31
ACGTcount: A:0.30, C:0.29, G:0.21, T:0.21
Consensus pattern (18 bp):
TGTCCCGAAGGACCACTA
Found at i:19681 original size:75 final size:75
Alignment explanation
Indices: 19576--19762 Score: 223
Period size: 75 Copynumber: 2.5 Consensus size: 75
19566 CATAAATAAA
* * * *
19576 GTCAAATATCAAGACTCAAACCACAATATTAAGTTTAGAATAATAAAATCCATAAACAAATCACA
1 GTCAAATCTTAAGACTCAAACCATAATATTAAGTCTAGAATAATAAAATCCATAAACAAATCACA
*
19641 ATATTAAAAT
66 ATAGTAAAAT
* * * * * * *
19651 GTTAAAT-TTCAATATTCAAACCATAATATTAACTCTAGAATAATAAAATTCATAATCAAATCAT
1 GTCAAATCTT-AAGACTCAAACCATAATATTAAGTCTAGAATAATAAAATCCATAAACAAATCAC
*
19715 AATAGTAAAGT
65 AATAGTAAAAT
* *
19726 GTCAAATCTTAAGACTCAAATCATATTATTAAGTCTA
1 GTCAAATCTTAAGACTCAAACCATAATATTAAGTCTA
19763 AAAAAATATT
Statistics
Matches: 92, Mismatches: 18, Indels: 4
0.81 0.16 0.04
Matches are distributed among these distances:
74 1 0.01
75 89 0.97
76 2 0.02
ACGTcount: A:0.49, C:0.14, G:0.06, T:0.30
Consensus pattern (75 bp):
GTCAAATCTTAAGACTCAAACCATAATATTAAGTCTAGAATAATAAAATCCATAAACAAATCACA
ATAGTAAAAT
Found at i:23967 original size:18 final size:18
Alignment explanation
Indices: 23944--23990 Score: 51
Period size: 18 Copynumber: 2.6 Consensus size: 18
23934 ATTATTCTAA
23944 TAATTATATTTTATTAAT
1 TAATTATATTTTATTAAT
**
23962 TAATTA-ATTATTATTTTT
1 TAATTATATT-TTATTAAT
*
23980 TATTTATATTT
1 TAATTATATTT
23991 AAAAAATTAG
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
17 3 0.12
18 18 0.75
19 3 0.12
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (18 bp):
TAATTATATTTTATTAAT
Found at i:26823 original size:18 final size:16
Alignment explanation
Indices: 26796--26829 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 16
26786 AGGAAGCCAT
26796 TTCGAAAAATGGAAAGA
1 TTCGAAAAAT-GAAAGA
26813 TTCGAAAAAATGAAAGA
1 TTCG-AAAAATGAAAGA
26830 AAAAAAACGA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 10 0.62
18 6 0.38
ACGTcount: A:0.56, C:0.06, G:0.21, T:0.18
Consensus pattern (16 bp):
TTCGAAAAATGAAAGA
Found at i:32270 original size:21 final size:20
Alignment explanation
Indices: 32184--32341 Score: 86
Period size: 21 Copynumber: 7.8 Consensus size: 20
32174 AAATGACCAA
**
32184 CAAAATCGCAACGCGA-AAT
1 CAAAATCGCAACGCGATTTT
* ***
32203 AAAAATCGCAACGCGATCCC
1 CAAAATCGCAACGCGATTTT
* ** *
32223 CAGAATCGCAAATC-AGTTTC
1 CAAAATCGCAACGCGA-TTTT
32243 CAAAATCGCAACGCGATTCTT
1 CAAAATCGCAACGCGATT-TT
* * * *
32264 GAAAATCGCAATGCGATAGTA
1 CAAAATCGCAACGCGAT-TTT
* **
32285 CAAATTCGCATTGCGATTTT
1 CAAAATCGCAACGCGATTTT
* *
32305 CCAAAATCGCAACGCGAATAT
1 -CAAAATCGCAACGCGATTTT
*
32326 GAAAATCGCAACGCGA
1 CAAAATCGCAACGCGA
32342 ACACATAAAT
Statistics
Matches: 104, Mismatches: 29, Indels: 11
0.72 0.20 0.08
Matches are distributed among these distances:
19 16 0.15
20 41 0.39
21 47 0.45
ACGTcount: A:0.39, C:0.25, G:0.17, T:0.19
Consensus pattern (20 bp):
CAAAATCGCAACGCGATTTT
Found at i:32370 original size:20 final size:20
Alignment explanation
Indices: 32308--32501 Score: 212
Period size: 20 Copynumber: 9.7 Consensus size: 20
32298 CGATTTTCCA
* ** *
32308 AAATCGCAACGCGAATATGA
1 AAATCGCAACGCGTATCCGT
* *
32328 AAATCGCAACGCG-AACACAT
1 AAATCGCAACGCGTATC-CGT
32348 AAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
32368 AAATCGCAACGTGTATCCGT
1 AAATCGCAACGCGTATCCGT
**
32388 AAATCGCAACGCGTATGGGT
1 AAATCGCAACGCGTATCCGT
* *
32408 AAATCGCAATGTGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
32428 ATATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
* * *
32448 AAATCGCAACG-ATAATACAT
1 AAATCGCAACGCGT-ATCCGT
32468 AAAATCGCAACGCGTATCCGT
1 -AAATCGCAACGCGTATCCGT
32489 AAATCGCAACGCG
1 AAATCGCAACGCG
32502 ATATTTAAAG
Statistics
Matches: 144, Mismatches: 25, Indels: 10
0.80 0.14 0.06
Matches are distributed among these distances:
19 2 0.01
20 124 0.86
21 17 0.12
22 1 0.01
ACGTcount: A:0.36, C:0.25, G:0.20, T:0.20
Consensus pattern (20 bp):
AAATCGCAACGCGTATCCGT
Found at i:32392 original size:60 final size:60
Alignment explanation
Indices: 32308--32501 Score: 244
Period size: 60 Copynumber: 3.2 Consensus size: 60
32298 CGATTTTCCA
* ** * *
32308 AAATCGCAACGCGAATATGAAAATCGCAACGCGAACACATAAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGT
* * *** * *
32368 AAATCGCAACGTGTATCCGTAAATCGCAACGCGTATGGGTAAATCGCAATGTGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGT
* **
32428 ATATCGCAACGCGTATCCGTAAATCGCAACGATAATACATAAAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACAT-AAATCGCAACGCGTATCCGT
32489 AAATCGCAACGCG
1 AAATCGCAACGCG
32502 ATATTTAAAG
Statistics
Matches: 110, Mismatches: 23, Indels: 1
0.82 0.17 0.01
Matches are distributed among these distances:
60 80 0.73
61 30 0.27
ACGTcount: A:0.36, C:0.25, G:0.20, T:0.20
Consensus pattern (60 bp):
AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGT
Found at i:32923 original size:33 final size:33
Alignment explanation
Indices: 32884--32954 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
32874 TTCACTTAGA
*
32884 TTTCATTTCGCGTTACGATTCTGTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
* *
32917 TTTCATTTCGCGTTGCTATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
32950 TTTCA
1 TTTCA
32955 AGTTAGTATT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.11, C:0.23, G:0.18, T:0.48
Consensus pattern (33 bp):
TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
Found at i:33078 original size:20 final size:20
Alignment explanation
Indices: 33034--33142 Score: 115
Period size: 20 Copynumber: 5.8 Consensus size: 20
33024 TGCAGAAGAG
*
33034 TCGCAACGAGATAAATGAAAA
1 TCGCAACGAGA-GAATGAAAA
***
33055 TCGCAACGAGAGAATGACTG
1 TCGCAACGAGAGAATGAAAA
33075 TCGCAACGAGAGAATGAAAA
1 TCGCAACGAGAGAATGAAAA
33095 TCGCAAC--GAG-A-G--AA
1 TCGCAACGAGAGAATGAAAA
*
33109 TCGCAACGCGA-AATGAAAA
1 TCGCAACGAGAGAATGAAAA
33128 TCGCAACGAGAGAAT
1 TCGCAACGAGAGAAT
33143 CGCAACGCGA
Statistics
Matches: 73, Mismatches: 8, Indels: 15
0.76 0.08 0.16
Matches are distributed among these distances:
14 9 0.12
16 4 0.05
17 2 0.03
18 3 0.04
19 12 0.16
20 32 0.44
21 11 0.15
ACGTcount: A:0.45, C:0.18, G:0.25, T:0.12
Consensus pattern (20 bp):
TCGCAACGAGAGAATGAAAA
Found at i:33098 original size:40 final size:36
Alignment explanation
Indices: 33027--33142 Score: 139
Period size: 33 Copynumber: 3.1 Consensus size: 36
33017 TTCAATTTGC
*
33027 AGAAGAGTCGCAACGAGATAAATGAAAATCGCAACGAG
1 AGAATAGTCGCAACGAG--AAATGAAAATCGCAACGAG
33065 AGAATGACTGTCGCAACGAGAGAATGAAAATCGCAACGAG
1 AGAAT-A--GTCGCAACGAGA-AATGAAAATCGCAACGAG
*
33105 AG-A-A-TCGCAACGCGAAATGAAAATCGCAACGAG
1 AGAATAGTCGCAACGAGAAATGAAAATCGCAACGAG
33138 AGAAT
1 AGAAT
33143 CGCAACGCGA
Statistics
Matches: 70, Mismatches: 2, Indels: 15
0.80 0.02 0.17
Matches are distributed among these distances:
33 20 0.29
34 11 0.16
37 1 0.01
38 4 0.06
39 3 0.04
40 20 0.29
41 11 0.16
ACGTcount: A:0.46, C:0.17, G:0.26, T:0.11
Consensus pattern (36 bp):
AGAATAGTCGCAACGAGAAATGAAAATCGCAACGAG
Found at i:33112 original size:14 final size:14
Alignment explanation
Indices: 33093--33149 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
33083 AGAGAATGAA
33093 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
33107 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
33126 AATCGCAACGAGAG
1 AATCGCAACGAGAG
33140 AATCGCAACG
1 AATCGCAACG
33150 CGAAACCAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.28
ACGTcount: A:0.44, C:0.23, G:0.25, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:33127 original size:33 final size:33
Alignment explanation
Indices: 33046--33165 Score: 150
Period size: 33 Copynumber: 3.4 Consensus size: 33
33036 GCAACGAGAT
*
33046 AAATGAAAATCGCAACGAGAGAATGACTGTCGCAACGAG
1 AAATGAAAATCGCAACGAGAG-A--A---TCGCAACGCG
33085 AGAATGAAAATCGCAACGAGAGAATCGCAACGCG
1 A-AATGAAAATCGCAACGAGAGAATCGCAACGCG
33119 AAATGAAAATCGCAACGAGAGAATCGCAACGCG
1 AAATGAAAATCGCAACGAGAGAATCGCAACGCG
**
33152 AAACCAAAATCGCA
1 AAATGAAAATCGCA
33166 TTGCGATTTT
Statistics
Matches: 77, Mismatches: 3, Indels: 8
0.88 0.03 0.09
Matches are distributed among these distances:
33 44 0.57
34 10 0.13
37 1 0.01
39 2 0.03
40 20 0.26
ACGTcount: A:0.46, C:0.21, G:0.23, T:0.10
Consensus pattern (33 bp):
AAATGAAAATCGCAACGAGAGAATCGCAACGCG
Found at i:33183 original size:19 final size:19
Alignment explanation
Indices: 33161--33288 Score: 87
Period size: 19 Copynumber: 7.1 Consensus size: 19
33151 GAAACCAAAA
*
33161 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
33180 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
33194 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
33213 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
33227 TCTCGTTGCGATTTTCATTT
1 TCGCGTTGCGATTTTCA-TT
* ***
33247 CTCTCGTTGCGACAGTCATT
1 -TCGCGTTGCGATTTTCATT
*
33267 CTCTCGTTGCGATTTTCATT
1 -TCGCGTTGCGATTTTCATT
33287 TC
1 TC
33289 AACCAAAAGA
Statistics
Matches: 87, Mismatches: 10, Indels: 24
0.72 0.08 0.20
Matches are distributed among these distances:
14 20 0.23
16 6 0.07
17 6 0.07
19 22 0.25
20 19 0.22
21 14 0.16
ACGTcount: A:0.11, C:0.25, G:0.19, T:0.45
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:33202 original size:14 final size:14
Alignment explanation
Indices: 33183--33239 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
33173 TTTCATTTCG
33183 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
33197 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
33216 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
33230 CGTTGCGATT
1 CGTTGCGATT
33240 TTCATTTCTC
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
16 3 0.08
17 3 0.08
19 10 0.28
ACGTcount: A:0.09, C:0.25, G:0.23, T:0.44
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:33208 original size:33 final size:33
Alignment explanation
Indices: 33166--33288 Score: 165
Period size: 33 Copynumber: 3.5 Consensus size: 33
33156 CAAAATCGCA
33166 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
33199 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
*
33232 TTGCGATTTTCATTTCTCTCGTTGCGACAGTCATTCTCTCG
1 TTGCGATTTTCA-TT-TCGCGTT--G-C-G--ATTCTCTCG
33273 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
33289 AACCAAAAGA
Statistics
Matches: 81, Mismatches: 1, Indels: 10
0.88 0.01 0.11
Matches are distributed among these distances:
33 45 0.56
34 2 0.02
35 6 0.07
37 1 0.01
38 1 0.01
39 3 0.04
40 2 0.02
41 21 0.26
ACGTcount: A:0.11, C:0.24, G:0.19, T:0.46
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
Found at i:33250 original size:21 final size:21
Alignment explanation
Indices: 33224--33288 Score: 96
Period size: 21 Copynumber: 3.1 Consensus size: 21
33214 CGCGTTGCGA
33224 TTCTCTCGTTGCGATTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
***
33245 TTCTCTCGTTGCGACAGTCA-
1 TTCTCTCGTTGCGATTTTCAT
33265 TTCTCTCGTTGCGATTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
33286 TTC
1 TTC
33289 AACCAAAAGA
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
20 17 0.46
21 20 0.54
ACGTcount: A:0.11, C:0.26, G:0.15, T:0.48
Consensus pattern (21 bp):
TTCTCTCGTTGCGATTTTCAT
Found at i:35140 original size:93 final size:93
Alignment explanation
Indices: 34981--35449 Score: 904
Period size: 93 Copynumber: 5.1 Consensus size: 93
34971 TAGATTGCTT
*
34981 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
35046 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
35074 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
*
35139 TTTGTCTTTGTTTTGTCTTTTGGTTTAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
35167 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
35232 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
*
35260 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAATTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
35325 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
35353 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
35418 TTTGTCTTTGTTTTGTCTTTTGGTTG-A
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
35445 AGTAA
1 AGTAA
35450 TGCAATCCAT
Statistics
Matches: 371, Mismatches: 5, Indels: 1
0.98 0.01 0.00
Matches are distributed among these distances:
92 6 0.02
93 365 0.98
ACGTcount: A:0.22, C:0.13, G:0.19, T:0.46
Consensus pattern (93 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:35537 original size:19 final size:19
Alignment explanation
Indices: 35497--35625 Score: 125
Period size: 19 Copynumber: 7.3 Consensus size: 19
35487 TAGTTTACTT
* *
35497 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAAC-CAAAA
35517 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
**
35536 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAACCAAAA
*
35555 TCGCAA--CG--A-CAGAA
1 TCGCAACGCGAAACCAAAA
35569 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
*
35588 TCGCAA--CG--A-CAAGA
1 TCGCAACGCGAAACCAAAA
35602 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
35621 TCGCA
1 TCGCA
35626 TTGCGATTTT
Statistics
Matches: 90, Mismatches: 9, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 19 0.21
15 2 0.02
16 4 0.04
17 4 0.04
18 2 0.02
19 46 0.51
20 13 0.14
ACGTcount: A:0.46, C:0.29, G:0.17, T:0.09
Consensus pattern (19 bp):
TCGCAACGCGAAACCAAAA
Found at i:35576 original size:33 final size:32
Alignment explanation
Indices: 35533--35625 Score: 150
Period size: 33 Copynumber: 2.8 Consensus size: 32
35523 CGCGAAACCA
**
35533 AAATCGCAACGCGAAATGAAAATCGCAACGAC
1 AAATCGCAACGCGAAACCAAAATCGCAACGAC
35565 AGAATCGCAACGCGAAACCAAAATCGCAACGAC
1 A-AATCGCAACGCGAAACCAAAATCGCAACGAC
35598 AAGATCGCAACGCGAAACCAAAATCGCA
1 AA-ATCGCAACGCGAAACCAAAATCGCA
35626 TTGCGATTTT
Statistics
Matches: 57, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
32 2 0.04
33 55 0.96
ACGTcount: A:0.46, C:0.28, G:0.18, T:0.08
Consensus pattern (32 bp):
AAATCGCAACGCGAAACCAAAATCGCAACGAC
Found at i:35623 original size:52 final size:52
Alignment explanation
Indices: 35497--35625 Score: 140
Period size: 52 Copynumber: 2.5 Consensus size: 52
35487 TAGTTTACTT
**
35497 TCGCAACACGAAACTTAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
1 TCGCAACACGAAACACAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
* * *
35549 T-G-AAAATCGCAACGACAGAATCGCAACGCGAAACCAAAATCGCAACGAC-AAGA
1 TCGCAACA-CGAAAC-ACAAAATCGCAACGCGAAACCAAAATCGCAACG-CGAA-A
*
35602 TCGCAACGCGAAAC-CAAAATCGCA
1 TCGCAACACGAAACACAAAATCGCA
35626 TTGCGATTTT
Statistics
Matches: 62, Mismatches: 9, Indels: 12
0.75 0.11 0.14
Matches are distributed among these distances:
50 3 0.05
51 6 0.10
52 42 0.68
53 3 0.05
54 6 0.10
55 2 0.03
ACGTcount: A:0.46, C:0.29, G:0.17, T:0.09
Consensus pattern (52 bp):
TCGCAACACGAAACACAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
Found at i:35643 original size:19 final size:19
Alignment explanation
Indices: 35621--35793 Score: 168
Period size: 19 Copynumber: 9.6 Consensus size: 19
35611 GAAACCAAAA
*
35621 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
35640 TCGCGTTGCGA--TTC-TT
1 TCGCGTTGCGATTTTCATT
35656 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
* *
35673 TCGCATTGCGA--TTC-TG
1 TCGCGTTGCGATTTTCATT
35689 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
**
35706 TCGCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTCATT
**
35725 TCGCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTCATT
* *
35744 TCTCGTTGCGATTATCATT
1 TCGCGTTGCGATTTTCATT
*
35763 TCGCGTTGCGATTTTAAGTT
1 TCGCGTTGCGATTTTCA-TT
*
35783 TCGTGTTGCGA
1 TCGCGTTGCGA
35794 AAGTAAACTA
Statistics
Matches: 128, Mismatches: 15, Indels: 21
0.78 0.09 0.13
Matches are distributed among these distances:
14 15 0.12
16 11 0.09
17 11 0.09
19 79 0.62
20 12 0.09
ACGTcount: A:0.11, C:0.19, G:0.24, T:0.46
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:35662 original size:14 final size:14
Alignment explanation
Indices: 35643--35699 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
35633 TTTCATTTCG
35643 CGTTGCGATTCTTT
1 CGTTGCGATTCTTT
35657 CGTTGCGATTTTCATTT
1 CGTTGCGA--TTC-TTT
*
35674 CGCATTGCGATTCTGT
1 CG--TTGCGATTCTTT
35690 CGTTGCGATT
1 CGTTGCGATT
35700 TTCATTTCGC
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 16 0.43
16 7 0.19
17 8 0.22
19 6 0.16
ACGTcount: A:0.11, C:0.21, G:0.23, T:0.46
Consensus pattern (14 bp):
CGTTGCGATTCTTT
Found at i:35751 original size:38 final size:38
Alignment explanation
Indices: 35621--35793 Score: 168
Period size: 33 Copynumber: 4.8 Consensus size: 38
35611 GAAACCAAAA
*
35621 TCGCATTGCGATTTTCATTTCGCGTTGCGA-T-TC-TT
1 TCGCGTTGCGATTTTCATTTCGCGTTGCGATTATCATT
* *
35656 T--CGTTGCGATTTTCATTTCGCATTGCGA-T-TC-TG
1 TCGCGTTGCGATTTTCATTTCGCGTTGCGATTATCATT
* **
35689 T--CGTTGCGATTTTCATTTCGCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTCATTTCGCGTTGCGATTATCATT
** *
35725 TCGCGTTGCGATTTTGGTTTCTCGTTGCGATTATCATT
1 TCGCGTTGCGATTTTCATTTCGCGTTGCGATTATCATT
* *
35763 TCGCGTTGCGATTTTAAGTTTCGTGTTGCGA
1 TCGCGTTGCGATTTTCA-TTTCGCGTTGCGA
35794 AAGTAAACTA
Statistics
Matches: 116, Mismatches: 16, Indels: 8
0.83 0.11 0.06
Matches are distributed among these distances:
33 56 0.48
34 1 0.01
35 2 0.02
36 2 0.02
38 44 0.38
39 11 0.09
ACGTcount: A:0.11, C:0.19, G:0.24, T:0.46
Consensus pattern (38 bp):
TCGCGTTGCGATTTTCATTTCGCGTTGCGATTATCATT
Found at i:37736 original size:14 final size:14
Alignment explanation
Indices: 37717--37752 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
37707 ATTGTTTAAT
37717 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
37731 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
37745 TGATTTGT
1 TGATTTGT
37753 GTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.22, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:37875 original size:19 final size:19
Alignment explanation
Indices: 37859--37936 Score: 112
Period size: 19 Copynumber: 4.4 Consensus size: 19
37849 AAAAATGACT
37859 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
37878 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
37897 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
37911 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
37930 ATCGCAA
1 ATCGCAA
37937 CGAGAGAATC
Statistics
Matches: 52, Mismatches: 2, Indels: 10
0.81 0.03 0.16
Matches are distributed among these distances:
14 10 0.19
15 1 0.02
16 2 0.04
17 2 0.04
18 1 0.02
19 36 0.69
ACGTcount: A:0.46, C:0.18, G:0.22, T:0.14
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:37915 original size:14 final size:14
Alignment explanation
Indices: 37896--37950 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
37886 GCGAAATGAA
37896 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
37910 AATCGCAATGCGAAATGAA
1 AATCGCAA--CG--A-GAG
37929 AATCGCAACGAGAG
1 AATCGCAACGAGAG
37943 AATCGCAA
1 AATCGCAA
37951 TGCGATTTTA
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
14 18 0.53
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.29
ACGTcount: A:0.45, C:0.20, G:0.24, T:0.11
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:37968 original size:33 final size:33
Alignment explanation
Indices: 37877--37955 Score: 158
Period size: 33 Copynumber: 2.4 Consensus size: 33
37867 GCGAAATGAA
37877 AATCGCAATGCGAAATGAAAATCGCAACGAGAG
1 AATCGCAATGCGAAATGAAAATCGCAACGAGAG
37910 AATCGCAATGCGAAATGAAAATCGCAACGAGAG
1 AATCGCAATGCGAAATGAAAATCGCAACGAGAG
37943 AATCGCAATGCGA
1 AATCGCAATGCGA
37956 TTTTAATTTC
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 46 1.00
ACGTcount: A:0.44, C:0.19, G:0.24, T:0.13
Consensus pattern (33 bp):
AATCGCAATGCGAAATGAAAATCGCAACGAGAG
Found at i:37973 original size:19 final size:19
Alignment explanation
Indices: 37945--38147 Score: 203
Period size: 19 Copynumber: 11.7 Consensus size: 19
37935 AACGAGAGAA
* *
37945 TCGCAATGCGATTTTAATT
1 TCGCATTGCGATTTTCATT
*
37964 TCGCATTGCGA--TTC-TC
1 TCGCATTGCGATTTTCATT
37980 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
37997 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
38016 TCGCATTGCGA--TTC-TC
1 TCGCATTGCGATTTTCATT
38032 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
38049 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
38068 TCGCATTGCGA--TTC-TC
1 TCGCATTGCGATTTTCATT
38084 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
38101 TCCGCATTGCGATTTTCA--
1 T-CGCATTGCGATTTTCATT
*
38119 T-G--TTGGGATTTTCATT
1 TCGCATTGCGATTTTCATT
38135 TCGCATTGCGATT
1 TCGCATTGCGATT
38148 CTCTCGTTGC
Statistics
Matches: 153, Mismatches: 10, Indels: 42
0.75 0.05 0.20
Matches are distributed among these distances:
14 29 0.19
16 23 0.15
17 19 0.12
18 3 0.02
19 67 0.44
20 12 0.08
ACGTcount: A:0.15, C:0.22, G:0.18, T:0.45
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:38007 original size:52 final size:52
Alignment explanation
Indices: 37945--38119 Score: 323
Period size: 52 Copynumber: 3.3 Consensus size: 52
37935 AACGAGAGAA
* *
37945 TCGCAATGCGATTTTAATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATT
1 TCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATT
37997 TCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATT
1 TCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATT
38049 TCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATT
1 TCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATT
38101 TCCGCATTGCGATTTTCAT
1 T-CGCATTGCGATTTTCAT
38120 GTTGGGATTT
Statistics
Matches: 120, Mismatches: 2, Indels: 1
0.98 0.02 0.01
Matches are distributed among these distances:
52 103 0.86
53 17 0.14
ACGTcount: A:0.15, C:0.23, G:0.17, T:0.45
Consensus pattern (52 bp):
TCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATT
Found at i:38169 original size:33 final size:33
Alignment explanation
Indices: 37951--38161 Score: 223
Period size: 33 Copynumber: 6.2 Consensus size: 33
37941 AGAATCGCAA
*
37951 TGCGATTTTAATTTCGCATTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCATTGCGATTCTCTCGT
*
37984 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCAT
1 TGCGATTTTCATTTCGCATTGCGA--TTC-TCTCG--T
* * * * *
38022 TGCGATTCTCTCGTTGCG-ATTTTC-ATT-TCGCAT
1 TGCGATT-T-TCATTTCGCA-TTGCGATTCTCTCGT
38055 TGCGATTTTCATTTCGCATTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCATTGCGATTCTCTCGT
*
38088 TGCGATTTTCATTTCCGCATTGCGATTTTCAT-GT
1 TGCGATTTTCATTT-CGCATTGCGATTCTC-TCGT
*
38122 TGGGATTTTCATTTCGCATTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCATTGCGATTCTCTCGT
38155 TGCGATT
1 TGCGATT
38162 GTAATTTCCG
Statistics
Matches: 147, Mismatches: 17, Indels: 28
0.77 0.09 0.15
Matches are distributed among these distances:
31 9 0.06
32 6 0.04
33 71 0.48
34 29 0.20
35 6 0.04
36 4 0.03
37 2 0.01
38 8 0.05
39 3 0.02
40 9 0.06
ACGTcount: A:0.14, C:0.22, G:0.18, T:0.46
Consensus pattern (33 bp):
TGCGATTTTCATTTCGCATTGCGATTCTCTCGT
Found at i:40452 original size:12 final size:12
Alignment explanation
Indices: 40435--40459 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
40425 TCTTCGGGGA
40435 CTTTTTCTTCTT
1 CTTTTTCTTCTT
40447 CTTTTTCTTCTT
1 CTTTTTCTTCTT
40459 C
1 C
40460 AGGATTATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:40668 original size:24 final size:24
Alignment explanation
Indices: 40634--40680 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
40624 CTGAAACATC
40634 ATCAAAATCCGTG-TATTGACCAAT
1 ATCAAAATCCG-GATATTGACCAAT
*
40658 ATCAAAGTCCGGATATTGACCAA
1 ATCAAAATCCGGATATTGACCAA
40681 GACCAAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.38, C:0.21, G:0.15, T:0.26
Consensus pattern (24 bp):
ATCAAAATCCGGATATTGACCAAT
Found at i:41390 original size:20 final size:20
Alignment explanation
Indices: 41362--41551 Score: 204
Period size: 20 Copynumber: 9.5 Consensus size: 20
41352 AAATTTCAGT
* * * *
41362 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATACGC
*
41382 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
41402 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
41422 GTTGCGATATACGGATACGC
1 GTTGCGATTTACGGATACGC
* **
41442 ATTGCGATTTACCCATACGC
1 GTTGCGATTTACGGATACGC
*
41462 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATACGC
41482 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
* *
41502 GTTGCGATTTATGTG-TTCGC
1 GTTGCGATTTACG-GATACGC
* ** *
41522 GTTGCGATTTTCATATTCGC
1 GTTGCGATTTACGGATACGC
41542 GTTGCGATTT
1 GTTGCGATTT
41552 TGGAAAATCG
Statistics
Matches: 146, Mismatches: 20, Indels: 8
0.84 0.11 0.05
Matches are distributed among these distances:
19 2 0.01
20 142 0.97
21 2 0.01
ACGTcount: A:0.19, C:0.19, G:0.25, T:0.36
Consensus pattern (20 bp):
GTTGCGATTTACGGATACGC
Found at i:41568 original size:21 final size:21
Alignment explanation
Indices: 41538--41620 Score: 78
Period size: 21 Copynumber: 4.0 Consensus size: 21
41528 ATTTTCATAT
*
41538 TCGCGTTGCGATTTTGGAAAA
1 TCGCATTGCGATTTTGGAAAA
* * * **
41559 TCGCAATGCGAATTTGTACTA
1 TCGCATTGCGATTTTGGAAAA
*
41580 TCGCATTGCGATTTT-TAAGAA
1 TCGCATTGCGATTTTGGAA-AA
*
41601 TCGCGTTGCGATTTTGGAAA
1 TCGCATTGCGATTTTGGAAA
41621 CTGATTTGCG
Statistics
Matches: 48, Mismatches: 12, Indels: 4
0.75 0.19 0.06
Matches are distributed among these distances:
20 2 0.04
21 44 0.92
22 2 0.04
ACGTcount: A:0.25, C:0.16, G:0.24, T:0.35
Consensus pattern (21 bp):
TCGCATTGCGATTTTGGAAAA
Found at i:41611 original size:42 final size:43
Alignment explanation
Indices: 41518--41616 Score: 100
Period size: 42 Copynumber: 2.4 Consensus size: 43
41508 ATTTATGTGT
*
41518 TCGCGTTGCG-ATTT-TCATATTCGCGTTGCGATTTTGGAAAA
1 TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTTTGGAAAA
** *
41559 TCGCAATGCGAATTTGT-ACTA-TCGCATTGCGATTTT-TAAGAA
1 TCGCGTTGCGAATTTGTCA-TATTCGCATTGCGATTTTGGAA-AA
*
41601 TCGCGTTGCGATTTTG
1 TCGCGTTGCGAATTTG
41617 GAAACTGATT
Statistics
Matches: 47, Mismatches: 7, Indels: 7
0.77 0.11 0.11
Matches are distributed among these distances:
41 10 0.21
42 34 0.72
43 3 0.06
ACGTcount: A:0.21, C:0.17, G:0.23, T:0.38
Consensus pattern (43 bp):
TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTTTGGAAAA
Found at i:41887 original size:28 final size:28
Alignment explanation
Indices: 41855--41945 Score: 123
Period size: 28 Copynumber: 3.2 Consensus size: 28
41845 GACTGACCGG
*
41855 TTCAATCGAGAACCGTTGTTTAGTCCGA
1 TTCAATCGAGAACCGTTGTCTAGTCCGA
41883 TTCAATC-AGGAACCGTTGTCTAGTCCGA
1 TTCAATCGA-GAACCGTTGTCTAGTCCGA
* *
41911 TTCAATCG-GAAATCGTTGTCTAGTCCGG
1 TTCAATCGAG-AACCGTTGTCTAGTCCGA
41939 TTCAATC
1 TTCAATC
41946 TAGACCGATT
Statistics
Matches: 57, Mismatches: 3, Indels: 6
0.86 0.05 0.09
Matches are distributed among these distances:
27 2 0.04
28 55 0.96
ACGTcount: A:0.24, C:0.23, G:0.21, T:0.32
Consensus pattern (28 bp):
TTCAATCGAGAACCGTTGTCTAGTCCGA
Found at i:42761 original size:18 final size:18
Alignment explanation
Indices: 42729--42763 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
42719 CCGGTTCTTC
*
42729 CGACCGGTCGGACCAGTT
1 CGACCGGTCGAACCAGTT
*
42747 CGACCGGTTGAACCAGT
1 CGACCGGTCGAACCAGT
42764 GAACAGGTAG
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:0.20, C:0.31, G:0.31, T:0.17
Consensus pattern (18 bp):
CGACCGGTCGAACCAGTT
Found at i:43177 original size:12 final size:12
Alignment explanation
Indices: 43162--43186 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
43152 AATGAAAGTT
43162 TAAATATTAAAA
1 TAAATATTAAAA
43174 TAAATATTAAAA
1 TAAATATTAAAA
43186 T
1 T
43187 GGACCAAACT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (12 bp):
TAAATATTAAAA
Found at i:48693 original size:16 final size:17
Alignment explanation
Indices: 48662--48695 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
48652 TGTATCGCCG
*
48662 ACAAAATTTTACTATTC
1 ACAAAATTTCACTATTC
48679 ACAAAA-TTCACTATTC
1 ACAAAATTTCACTATTC
48695 A
1 A
48696 TGCAAATAGT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 10 0.62
17 6 0.38
ACGTcount: A:0.44, C:0.21, G:0.00, T:0.35
Consensus pattern (17 bp):
ACAAAATTTCACTATTC
Found at i:58074 original size:2 final size:2
Alignment explanation
Indices: 58069--58121 Score: 106
Period size: 2 Copynumber: 26.5 Consensus size: 2
58059 TATATCTTGT
58069 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
58111 TA TA TA TA TA T
1 TA TA TA TA TA T
58122 TGCTCGGACA
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 51 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:66094 original size:2 final size:2
Alignment explanation
Indices: 66087--66111 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
66077 ATCTTTGTGC
66087 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
66112 TTTGGTAGCC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:68065 original size:21 final size:20
Alignment explanation
Indices: 68036--68077 Score: 50
Period size: 20 Copynumber: 2.0 Consensus size: 20
68026 TGTCGGTACG
68036 TATCAATACTATTAA-AATATA
1 TATCAATAC-A-TAACAATATA
*
68057 TATCGATACATAACAATATA
1 TATCAATACATAACAATATA
68077 T
1 T
68078 CAGATAAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
19 3 0.16
20 8 0.42
21 8 0.42
ACGTcount: A:0.50, C:0.12, G:0.02, T:0.36
Consensus pattern (20 bp):
TATCAATACATAACAATATA
Found at i:68515 original size:183 final size:181
Alignment explanation
Indices: 68035--68515 Score: 614
Period size: 183 Copynumber: 2.6 Consensus size: 181
68025 TTGTCGGTAC
* * * * *
68035 GTATCAATACTATTA-AAATATATATCGATACATAACAATATATCAGATAAAAATATGAGAAAAC
1 GTATC-ATACT-TTATAAACATGTATCGATACATAACAATATAACAGGTAAAAATATGACAAAAC
* * *
68099 -ATGTTCA-ATATTATAAAACCGGTAAAGCGCTACAGGATATGTTGAAA-GTATCGATTTCATTC
64 GGT-TTCATA-ATGATAAAACCGGTAAAGCGCTACAGGATATGTT-AAAGGTATCAATTTCATTC
* *
68161 AAATAAGTATCGACATTTTTGAAATTTAAAATAAAAGCAATAATAAAGCCTATAAA
126 AAATAAGTATCGACACTTTTGAAATTTAAAAGAAAAGCAATAATAAAGCCTATAAA
* *
68217 GTATCAGTACTTTATAAACATGTATCGATACACAACAATATAACAGGAAAAAATATGACAAAACC
1 GTATCA-TACTTTATAAACATGTATCGATACATAACAATATAACAGGTAAAAATATGACAAAA-C
* * * *
68282 GGTTTCATAATGATAAAACCGGTAAAGCGATATTA-GATATGTTGAAGGTATCAATTTCATTTAA
64 GGTTTCATAATGATAAAACCGGTAAAGCGCTA-CAGGATATGTTAAAGGTATCAATTTCATTCAA
* * **
68346 ATAAGTATCGATACTTTTGGAATTTAAAAG-AAAGACAATAATAGCGCCTATAAA
128 ATAAGTATCGACACTTTTGAAATTTAAAAGAAAAG-CAATAATAAAGCCTATAAA
68400 GTATCGATACTTTATAAACATGTATCGATACATAACAATATAACAGGTAAAAATATGACAAAATC
1 GTATC-ATACTTTATAAACATGTATCGATACATAACAATATAACAGGTAAAAATATGACAAAA-C
* * *
68465 GGTTTCATAATGACAAAACCAGTAAAGCGCTACCGGATATGTTAAAGGTAT
64 GGTTTCATAATGATAAAACCGGTAAAGCGCTACAGGATATGTTAAAGGTAT
68516 AGATACTTTA
Statistics
Matches: 260, Mismatches: 29, Indels: 19
0.84 0.09 0.06
Matches are distributed among these distances:
181 4 0.02
182 56 0.22
183 196 0.75
184 4 0.02
ACGTcount: A:0.45, C:0.13, G:0.14, T:0.28
Consensus pattern (181 bp):
GTATCATACTTTATAAACATGTATCGATACATAACAATATAACAGGTAAAAATATGACAAAACGG
TTTCATAATGATAAAACCGGTAAAGCGCTACAGGATATGTTAAAGGTATCAATTTCATTCAAATA
AGTATCGACACTTTTGAAATTTAAAAGAAAAGCAATAATAAAGCCTATAAA
Found at i:71095 original size:66 final size:66
Alignment explanation
Indices: 70965--71095 Score: 172
Period size: 66 Copynumber: 2.0 Consensus size: 66
70955 AGGGGGAAGT
* * *
70965 GGGTGGAAAAATAGATGGAGTGGTGAAAGAAGTTAAAGATTTGAGGGGTGAACTTAAGATGGTGA
1 GGGTGGAAAAATAGATGGAGTGGTGAAAGAAGTTAAAGAATTGAGGGGTGAACTGAAGAGGGTGA
71030 C
66 C
* * *** * *
71031 GGGTGGAAAAATTGATGGAGTGGTGAAGGAAGTTGTGGAATTGAGGGGTGAACTGACGGGGGTGA
1 GGGTGGAAAAATAGATGGAGTGGTGAAAGAAGTTAAAGAATTGAGGGGTGAACTGAAGAGGGTGA
71096 AAGGGGTGGT
Statistics
Matches: 55, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
66 55 1.00
ACGTcount: A:0.32, C:0.03, G:0.43, T:0.22
Consensus pattern (66 bp):
GGGTGGAAAAATAGATGGAGTGGTGAAAGAAGTTAAAGAATTGAGGGGTGAACTGAAGAGGGTGA
C
Found at i:71985 original size:20 final size:20
Alignment explanation
Indices: 71940--71985 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 20
71930 GTTTATATAA
*
71940 AGTATCGTTACTTTTTGTAC
1 AGTATCGATACTTTTTGTAC
*
71960 ATGTATCGATACTTTTTGTCC
1 A-GTATCGATACTTTTTGTAC
71981 AGTAT
1 AGTAT
71986 GCTTCCCAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
20 5 0.22
21 18 0.78
ACGTcount: A:0.22, C:0.15, G:0.15, T:0.48
Consensus pattern (20 bp):
AGTATCGATACTTTTTGTAC
Found at i:74515 original size:14 final size:14
Alignment explanation
Indices: 74498--74525 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
74488 TTTAAATGTT
74498 TGAGAACAAATGGA
1 TGAGAACAAATGGA
74512 TGAGAACAAATGGA
1 TGAGAACAAATGGA
74526 CCGCCTTTGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.50, C:0.07, G:0.29, T:0.14
Consensus pattern (14 bp):
TGAGAACAAATGGA
Found at i:75849 original size:15 final size:15
Alignment explanation
Indices: 75828--75876 Score: 53
Period size: 15 Copynumber: 3.1 Consensus size: 15
75818 TTGACCCGAC
75828 CCGTTGACCCGTTGA
1 CCGTTGACCCGTTGA
* * *
75843 TCGTTGATCTGTTGA
1 CCGTTGACCCGTTGA
75858 CCGTTGACCGGCGTTGA
1 CCGTTGACC--CGTTGA
75875 CC
1 CC
75877 ACTGTTGACC
Statistics
Matches: 26, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
15 19 0.73
17 7 0.27
ACGTcount: A:0.12, C:0.29, G:0.29, T:0.31
Consensus pattern (15 bp):
CCGTTGACCCGTTGA
Found at i:78610 original size:43 final size:42
Alignment explanation
Indices: 78535--78628 Score: 170
Period size: 43 Copynumber: 2.2 Consensus size: 42
78525 GGGCCTTACT
78535 TGGTGTGTTGGTGGGTTATGGTTCTAGGGAACCTACACATTA
1 TGGTGTGTTGGTGGGTTATGGTTCTAGGGAACCTACACATTA
*
78577 TGGTGTGTTGGTGGGTGTATGGTTCTGGGGAACCTACACATTA
1 TGGTGTGTTGGTGGGT-TATGGTTCTAGGGAACCTACACATTA
78620 TGGTGTGTT
1 TGGTGTGTT
78629 TGGTTGGAGG
Statistics
Matches: 50, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
42 16 0.32
43 34 0.68
ACGTcount: A:0.16, C:0.11, G:0.36, T:0.37
Consensus pattern (42 bp):
TGGTGTGTTGGTGGGTTATGGTTCTAGGGAACCTACACATTA
Found at i:81400 original size:3 final size:3
Alignment explanation
Indices: 81382--81449 Score: 97
Period size: 3 Copynumber: 23.3 Consensus size: 3
81372 TTTCATTAAA
*
81382 ATT ATT CTT AATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A-T ATT
1 ATT ATT ATT -ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
81427 A-T ATT ATT ATT ATT ATT A-T ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT A
81450 CAAATAAATA
Statistics
Matches: 59, Mismatches: 2, Indels: 8
0.86 0.03 0.12
Matches are distributed among these distances:
2 6 0.10
3 51 0.86
4 2 0.03
ACGTcount: A:0.35, C:0.01, G:0.00, T:0.63
Consensus pattern (3 bp):
ATT
Found at i:81446 original size:22 final size:23
Alignment explanation
Indices: 81382--81449 Score: 102
Period size: 22 Copynumber: 2.9 Consensus size: 23
81372 TTTCATTAAA
*
81382 ATTATTCTTAATTATTATTATTATT
1 ATTATTATT-ATTATTA-TATTATT
81407 ATTATTATTATTATTATATTA-T
1 ATTATTATTATTATTATATTATT
81429 ATTATTATTATTATTATATTA
1 ATTATTATTATTATTATATTA
81450 CAAATAAATA
Statistics
Matches: 42, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
22 22 0.52
23 5 0.12
24 7 0.17
25 8 0.19
ACGTcount: A:0.35, C:0.01, G:0.00, T:0.63
Consensus pattern (23 bp):
ATTATTATTATTATTATATTATT
Found at i:85359 original size:12 final size:13
Alignment explanation
Indices: 85342--85370 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
85332 ACATTCACAT
85342 ATTTACA-TTTGC
1 ATTTACATTTTGC
85354 ATTTACATTTTGC
1 ATTTACATTTTGC
85367 ATTT
1 ATTT
85371 TTTTCATTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 7 0.44
13 9 0.56
ACGTcount: A:0.24, C:0.14, G:0.07, T:0.55
Consensus pattern (13 bp):
ATTTACATTTTGC
Found at i:88093 original size:7 final size:8
Alignment explanation
Indices: 88065--88093 Score: 51
Period size: 8 Copynumber: 3.8 Consensus size: 8
88055 TTATACTTGA
88065 AAAAAAGG
1 AAAAAAGG
88073 AAAAAAGG
1 AAAAAAGG
88081 AAAAAA-G
1 AAAAAAGG
88088 AAAAAA
1 AAAAAA
88094 ATTAAACCAA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
7 7 0.33
8 14 0.67
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (8 bp):
AAAAAAGG
Found at i:93623 original size:46 final size:46
Alignment explanation
Indices: 93519--94233 Score: 1098
Period size: 46 Copynumber: 15.6 Consensus size: 46
93509 TATTTCCAAT
93519 ATCTGTAAGTCCTTCAGTGCATGATGTTATCAAAAACCCTTCGGGTC
1 ATCTGTAAGTCCTTCAGTGCATGATGTTATCAAAAA-CCTTCGGGTC
*
93566 ATCTGTAAGTCCTTCAGTGCATGATGTTATCAAAAACCTTCGTGTC
1 ATCTGTAAGTCCTTCAGTGCATGATGTTATCAAAAACCTTCGGGTC
** * * * * *
93612 ATCACTAAGTCCTTCAGTGTATGATGTTTTC-AAAACCTCCAGGAC
1 ATCTGTAAGTCCTTCAGTGCATGATGTTATCAAAAACCTTCGGGTC
*
93657 ATCTGTAAGTCTTTCAGTGCATGATGTTATCAAAAACCTTCGGGTC
1 ATCTGTAAGTCCTTCAGTGCATGATGTTATCAAAAACCTTCGGGTC
*
93703 ATCTGTAAGTCCTTTAGTGCATGATGTTATCAAAAACCTTCGGGTC
1 ATCTGTAAGTCCTTCAGTGCATGATGTTATCAAAAACCTTCGGGTC
**
93749 ATCTGTAAGTCCTTCAGTGCATGATGTTATCAAAAACCTTTAGGTC
1 ATCTGTAAGTCCTTCAGTGCATGATGTTATCAAAAACCTTCGGGTC
93795 ATCTGTAAGTCCTTCAGTGCATGATGTTATCAAAAACCTTCGGGTC
1 ATCTGTAAGTCCTTCAGTGCATGATGTTATCAAAAACCTTCGGGTC
* * * *
93841 ATCTGTAAGCCCTTCAGTGCATGTTGTTTTC-AAAACCTCCGGGTC
1 ATCTGTAAGTCCTTCAGTGCATGATGTTATCAAAAACCTTCGGGTC
*
93886 ATCTGTAAGCCCTTCAGTGCATGATGTTATCAAAAACCTTCGGGTC
1 ATCTGTAAGTCCTTCAGTGCATGATGTTATCAAAAACCTTCGGGTC
93932 ATCTGTAAGTCCTTCAGTGCATGATGTTATCAAAAACCTTCGGGTC
1 ATCTGTAAGTCCTTCAGTGCATGATGTTATCAAAAACCTTCGGGTC
* * *
93978 ATCTGTAAGCCCTTCAGTGCATGATGTTTTTC-AAAACCTTCGAGTC
1 ATCTGTAAGTCCTTCAGTGCATGATG-TTATCAAAAACCTTCGGGTC
*
94024 ATCTGTAAGTCCTTCAGTGCATGATGTTATCAAAAACCTTCAGGTC
1 ATCTGTAAGTCCTTCAGTGCATGATGTTATCAAAAACCTTCGGGTC
*
94070 ATCTATAAGTCCTTCAGTGCATGATGTTATCAAAAACCTTCGGGTC
1 ATCTGTAAGTCCTTCAGTGCATGATGTTATCAAAAACCTTCGGGTC
* *
94116 ATCTGTAAGTCCTTCAATGCATGATGTTTTC-AAAACCTTCGGGTC
1 ATCTGTAAGTCCTTCAGTGCATGATGTTATCAAAAACCTTCGGGTC
* * * *
94161 ATTTTTAAGCCCTTCAGTGCATGATGTTTTC-AAAACCTTCGGGTC
1 ATCTGTAAGTCCTTCAGTGCATGATGTTATCAAAAACCTTCGGGTC
* * *
94206 ATCTGCAAGCCCTTCAGTGCACGATGTT
1 ATCTGTAAGTCCTTCAGTGCATGATGTT
94234 TTTAAAACCT
Statistics
Matches: 612, Mismatches: 52, Indels: 10
0.91 0.08 0.01
Matches are distributed among these distances:
45 161 0.26
46 411 0.67
47 40 0.07
ACGTcount: A:0.26, C:0.23, G:0.18, T:0.33
Consensus pattern (46 bp):
ATCTGTAAGTCCTTCAGTGCATGATGTTATCAAAAACCTTCGGGTC
Found at i:93921 original size:229 final size:229
Alignment explanation
Indices: 93519--94233 Score: 1107
Period size: 229 Copynumber: 3.1 Consensus size: 229
93509 TATTTCCAAT
* **
93519 ATCTGTAAGTCCTTCAGTGCATGATGTTATCAAAAACCCTTCGGGTCATCTGTAAGTCCTTCAGT
1 ATCTGTAAGCCCTTCAGTGCATGATGTTATCAAAAA-CCTTTAGGTCATCTGTAAGTCCTTCAGT
* *
93584 GCATGATGTTATCAAAAACCTTCGTGTCATC-ACTAAGTCCTTCAGTGTATGATGTTTTCAAAAC
65 GCATGATGTTATCAAAAACCTTCGGGTCATCTA-TAAGTCCTTCAGTGCATGATGTTTTCAAAAC
* * *
93648 CTCCAGGACATCTGTAAGTCTTTCAGTGCATGATGTTATCAAAAACCTTCGGGTCATCTGTAAGT
129 CTCCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTATCAAAAACCTTCGGGTCATCTGTAAGT
*
93713 CCTTTAGTGCATGATGTTATCAAAAACCTTCGGGTC
194 CCTTCAGTGCATGATGTTATCAAAAACCTTCGGGTC
*
93749 ATCTGTAAGTCCTTCAGTGCATGATGTTATCAAAAACCTTTAGGTCATCTGTAAGTCCTTCAGTG
1 ATCTGTAAGCCCTTCAGTGCATGATGTTATCAAAAACCTTTAGGTCATCTGTAAGTCCTTCAGTG
* * *
93814 CATGATGTTATCAAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGTTGTTTTCAAAACCT
66 CATGATGTTATCAAAAACCTTCGGGTCATCTATAAGTCCTTCAGTGCATGATGTTTTCAAAACCT
*
93879 CCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTATCAAAAACCTTCGGGTCATCTGTAAGTCC
131 CCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTATCAAAAACCTTCGGGTCATCTGTAAGTCC
93944 TTCAGTGCATGATGTTATCAAAAACCTTCGGGTC
196 TTCAGTGCATGATGTTATCAAAAACCTTCGGGTC
* *
93978 ATCTGTAAGCCCTTCAGTGCATGATGTTTTTC-AAAACC-TTCGAGTCATCTGTAAGTCCTTCAG
1 ATCTGTAAGCCCTTCAGTGCATGATG-TTATCAAAAACCTTTAG-GTCATCTGTAAGTCCTTCAG
* *
94041 TGCATGATGTTATCAAAAACCTTCAGGTCATCTATAAGTCCTTCAGTGCATGATGTTATCAAAAA
64 TGCATGATGTTATCAAAAACCTTCGGGTCATCTATAAGTCCTTCAGTGCATGATGTTTTC-AAAA
* * * * *
94106 CCTTCGGGTCATCTGTAAGTCCTTCAATGCATGATGTTTTC-AAAACCTTCGGGTCATTTTTAAG
128 CCTCCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTATCAAAAACCTTCGGGTCATCTGTAAG
* *
94170 CCCTTCAGTGCATGATGTTTTC-AAAACCTTCGGGTC
193 TCCTTCAGTGCATGATGTTATCAAAAACCTTCGGGTC
* *
94206 ATCTGCAAGCCCTTCAGTGCACGATGTT
1 ATCTGTAAGCCCTTCAGTGCATGATGTT
94234 TTTAAAACCT
Statistics
Matches: 451, Mismatches: 30, Indels: 11
0.92 0.06 0.02
Matches are distributed among these distances:
227 2 0.00
228 41 0.09
229 327 0.73
230 81 0.18
ACGTcount: A:0.26, C:0.23, G:0.18, T:0.33
Consensus pattern (229 bp):
ATCTGTAAGCCCTTCAGTGCATGATGTTATCAAAAACCTTTAGGTCATCTGTAAGTCCTTCAGTG
CATGATGTTATCAAAAACCTTCGGGTCATCTATAAGTCCTTCAGTGCATGATGTTTTCAAAACCT
CCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTATCAAAAACCTTCGGGTCATCTGTAAGTCC
TTCAGTGCATGATGTTATCAAAAACCTTCGGGTC
Found at i:94063 original size:26 final size:26
Alignment explanation
Indices: 94034--94110 Score: 76
Period size: 26 Copynumber: 3.2 Consensus size: 26
94024 ATCTGTAAGT
94034 CCTTCAGTGCATGATGTTATCAAAAA
1 CCTTCAGTGCATGATGTTATCAAAAA
* * **
94060 CCTTCAG-G--TCAT-CTAT--AAGT
1 CCTTCAGTGCATGATGTTATCAAAAA
94080 CCTTCAGTGCATGATGTTATCAAAAA
1 CCTTCAGTGCATGATGTTATCAAAAA
94106 CCTTC
1 CCTTC
94111 GGGTCATCTG
Statistics
Matches: 37, Mismatches: 8, Indels: 12
0.65 0.14 0.21
Matches are distributed among these distances:
20 9 0.24
21 1 0.03
22 3 0.08
23 6 0.16
24 3 0.08
25 1 0.03
26 14 0.38
ACGTcount: A:0.30, C:0.23, G:0.14, T:0.32
Consensus pattern (26 bp):
CCTTCAGTGCATGATGTTATCAAAAA
Found at i:94199 original size:25 final size:25
Alignment explanation
Indices: 94126--94200 Score: 70
Period size: 25 Copynumber: 3.2 Consensus size: 25
94116 ATCTGTAAGT
*
94126 CCTTCAATGCATGATGTTTTCAAAA
1 CCTTCAGTGCATGATGTTTTCAAAA
* * **
94151 CCTTC-G-G-GTCAT-TTTT-AAGC
1 CCTTCAGTGCATGATGTTTTCAAAA
94171 CCTTCAGTGCATGATGTTTTCAAAA
1 CCTTCAGTGCATGATGTTTTCAAAA
94196 CCTTC
1 CCTTC
94201 GGGTCATCTG
Statistics
Matches: 36, Mismatches: 9, Indels: 10
0.65 0.16 0.18
Matches are distributed among these distances:
20 7 0.19
21 5 0.14
22 4 0.11
23 4 0.11
24 4 0.11
25 12 0.33
ACGTcount: A:0.24, C:0.24, G:0.15, T:0.37
Consensus pattern (25 bp):
CCTTCAGTGCATGATGTTTTCAAAA
Found at i:98986 original size:23 final size:23
Alignment explanation
Indices: 98960--99029 Score: 131
Period size: 23 Copynumber: 3.0 Consensus size: 23
98950 AATGAGTATG
98960 TTTATCGTTATTCTATAACGGTA
1 TTTATCGTTATTCTATAACGGTA
98983 TTTATCGTTATTCTATAACGGTA
1 TTTATCGTTATTCTATAACGGTA
*
99006 TTTATCGTTATTCTATAACAGTA
1 TTTATCGTTATTCTATAACGGTA
99029 T
1 T
99030 ATATTATCAC
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
23 46 1.00
ACGTcount: A:0.27, C:0.13, G:0.11, T:0.49
Consensus pattern (23 bp):
TTTATCGTTATTCTATAACGGTA
Found at i:104345 original size:2 final size:2
Alignment explanation
Indices: 104338--104379 Score: 75
Period size: 2 Copynumber: 21.0 Consensus size: 2
104328 AGTCTAAATT
*
104338 TA TA TA TA TA TA TA TC TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
104380 AATAAATTTT
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:107011 original size:23 final size:22
Alignment explanation
Indices: 106985--107027 Score: 68
Period size: 23 Copynumber: 1.9 Consensus size: 22
106975 TATAAAAAAT
106985 TATTTTTTATTAAATATTTTTGA
1 TATTTTTTATTAAAT-TTTTTGA
*
107008 TATTTTTTATTTAATTTTTT
1 TATTTTTTATTAAATTTTTT
107028 AAATAATTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 5 0.26
23 14 0.74
ACGTcount: A:0.26, C:0.00, G:0.02, T:0.72
Consensus pattern (22 bp):
TATTTTTTATTAAATTTTTTGA
Found at i:109448 original size:17 final size:17
Alignment explanation
Indices: 109422--109454 Score: 50
Period size: 16 Copynumber: 1.9 Consensus size: 17
109412 TTTTATTTTT
109422 AATTTATTTAAGTATTTA
1 AATTTATTTAA-TATTTA
109440 AATTT-TTTAATATTT
1 AATTTATTTAATATTT
109455 TATTTAATTA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 5 0.33
17 5 0.33
18 5 0.33
ACGTcount: A:0.36, C:0.00, G:0.03, T:0.61
Consensus pattern (17 bp):
AATTTATTTAATATTTA
Found at i:109456 original size:17 final size:19
Alignment explanation
Indices: 109415--109456 Score: 54
Period size: 17 Copynumber: 2.4 Consensus size: 19
109405 TTTAATATTT
*
109415 TATTTTTAATTTATTTAAG
1 TATTTTAAATTTATTTAAG
109434 TA-TTTAAATTT-TTTAA-
1 TATTTTAAATTTATTTAAG
109450 TATTTTA
1 TATTTTA
109457 TTTAATTAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
16 2 0.10
17 9 0.43
18 8 0.38
19 2 0.10
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.64
Consensus pattern (19 bp):
TATTTTAAATTTATTTAAG
Found at i:114418 original size:19 final size:17
Alignment explanation
Indices: 114378--114412 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
114368 GTATAACTAA
114378 TATACAGTTTTTTCTAT
1 TATACAGTTTTTTCTAT
114395 TATACAGTTTTTTCTAT
1 TATACAGTTTTTTCTAT
114412 T
1 T
114413 GTATACTAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.23, C:0.11, G:0.06, T:0.60
Consensus pattern (17 bp):
TATACAGTTTTTTCTAT
Found at i:121001 original size:21 final size:21
Alignment explanation
Indices: 120955--121002 Score: 53
Period size: 21 Copynumber: 2.3 Consensus size: 21
120945 TCATCCCAAC
* *
120955 ATTATTAATATTGTTATTTGT
1 ATTAATAATATTATTATTTGT
*
120976 TTTAATAATATTATTATTAT-T
1 ATTAATAATATTATTATT-TGT
120997 ATTAAT
1 ATTAAT
121003 TTTTTTTTTA
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
21 21 0.95
22 1 0.05
ACGTcount: A:0.35, C:0.00, G:0.04, T:0.60
Consensus pattern (21 bp):
ATTAATAATATTATTATTTGT
Found at i:123334 original size:130 final size:131
Alignment explanation
Indices: 123149--123459 Score: 439
Period size: 131 Copynumber: 2.4 Consensus size: 131
123139 GCTTTAATTC
* * * *
123149 ATGAGAGGTCATTTATTCTCGATTGGAAATAATCAGATATTA-CAGCTTTATCTCGAGTCAATAT
1 ATGAGAGGTCATTTATTCTCGATTGGAAATAATTAGATATTATC-GTTTTAGCTCGAATCAATAT
*
123213 TG-ATTTTAAGACGGAATAGTGATATCTCTTCATTTCAATTG-GAGTAATAAATGACTACTTTAA
65 TGAATTTTAAGACGAAATAGTGATATCTCTTCATTTCAATTGAG-GTAATAAATGACTACTTTAA
123276 GGA
129 GGA
* * * *
123279 ATGAGAGGTTATTTATTCTCAATTGGAAATCATTAGATATTATCGTTTTCGCTCGAATCAATATT
1 ATGAGAGGTCATTTATTCTCGATTGGAAATAATTAGATATTATCGTTTTAGCTCGAATCAATATT
**
123344 GAATTTTAAGACGAAATAGTGATATCTCTTCATTTCAATTGAGGTAATAAATGACTGTTTTAAGG
66 GAATTTTAAGACGAAATAGTGATATCTCTTCATTTCAATTGAGGTAATAAATGACTACTTTAAGG
*
123409 C
131 A
* * * *
123410 ATGAAATGTCATTTATTCTCGATTGAAAATAATTAGATATTATCATTTTA
1 ATGAGAGGTCATTTATTCTCGATTGGAAATAATTAGATATTATCGTTTTA
123460 TCTCTTAAAA
Statistics
Matches: 158, Mismatches: 20, Indels: 5
0.86 0.11 0.03
Matches are distributed among these distances:
130 56 0.35
131 101 0.64
132 1 0.01
ACGTcount: A:0.34, C:0.11, G:0.16, T:0.39
Consensus pattern (131 bp):
ATGAGAGGTCATTTATTCTCGATTGGAAATAATTAGATATTATCGTTTTAGCTCGAATCAATATT
GAATTTTAAGACGAAATAGTGATATCTCTTCATTTCAATTGAGGTAATAAATGACTACTTTAAGG
A
Found at i:124326 original size:30 final size:30
Alignment explanation
Indices: 124292--124349 Score: 82
Period size: 30 Copynumber: 1.9 Consensus size: 30
124282 TAATTTTTTT
124292 AAAAAATATAAATTAAACCT-TCAAATTTAA
1 AAAAAAT-TAAATTAAACCTCTCAAATTTAA
* *
124322 AAAAAATTAATTTAAACCTCTGAAATTT
1 AAAAAATTAAATTAAACCTCTCAAATTT
124350 TTAAAATTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 11 0.44
30 14 0.56
ACGTcount: A:0.55, C:0.10, G:0.02, T:0.33
Consensus pattern (30 bp):
AAAAAATTAAATTAAACCTCTCAAATTTAA
Found at i:124355 original size:29 final size:29
Alignment explanation
Indices: 124287--124355 Score: 68
Period size: 29 Copynumber: 2.3 Consensus size: 29
124277 GACTCTAATT
124287 TTTTTAAAAAATATAAATTAAACCTTCAAA
1 TTTTT-AAAAATATAAATTAAACCTTCAAA
* * * *
124317 -TTTAAAAAAAATTAATTTAAACCTCTGAAA
1 TTTTTAAAAATA-TAAATTAAACCT-TCAAA
124347 TTTTTAAAA
1 TTTTTAAAA
124356 TTTTAAGTTG
Statistics
Matches: 31, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
28 6 0.19
29 14 0.45
30 4 0.13
31 7 0.23
ACGTcount: A:0.52, C:0.09, G:0.01, T:0.38
Consensus pattern (29 bp):
TTTTTAAAAATATAAATTAAACCTTCAAA
Found at i:125271 original size:28 final size:30
Alignment explanation
Indices: 125215--125271 Score: 73
Period size: 31 Copynumber: 1.9 Consensus size: 30
125205 AATTTGAATT
* *
125215 TTAACTATAATATAATATAAATTTTTTATCA
1 TTAACTATAATATAATAT-AATATGTTATCA
125246 TTAACTATAATAT-ATAT-ATATGTTAT
1 TTAACTATAATATAATATAATATGTTAT
125272 AATTTGAATA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
28 7 0.29
30 4 0.17
31 13 0.54
ACGTcount: A:0.44, C:0.05, G:0.02, T:0.49
Consensus pattern (30 bp):
TTAACTATAATATAATATAATATGTTATCA
Found at i:125343 original size:2 final size:2
Alignment explanation
Indices: 125304--125328 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
125294 TATTAATTTC
125304 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 A
125329 ATTAAAAATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:127781 original size:5 final size:5
Alignment explanation
Indices: 127773--127914 Score: 284
Period size: 5 Copynumber: 28.4 Consensus size: 5
127763 GATCCGGTTT
127773 ATATC ATATC ATATC ATATC ATATC ATATC ATATC ATATC ATATC ATATC
1 ATATC ATATC ATATC ATATC ATATC ATATC ATATC ATATC ATATC ATATC
127823 ATATC ATATC ATATC ATATC ATATC ATATC ATATC ATATC ATATC ATATC
1 ATATC ATATC ATATC ATATC ATATC ATATC ATATC ATATC ATATC ATATC
127873 ATATC ATATC ATATC ATATC ATATC ATATC ATATC ATATC AT
1 ATATC ATATC ATATC ATATC ATATC ATATC ATATC ATATC AT
127915 GTTCATGTGC
Statistics
Matches: 137, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 137 1.00
ACGTcount: A:0.40, C:0.20, G:0.00, T:0.40
Consensus pattern (5 bp):
ATATC
Found at i:130506 original size:15 final size:15
Alignment explanation
Indices: 130426--130499 Score: 55
Period size: 15 Copynumber: 4.9 Consensus size: 15
130416 TTAATTTACA
* *
130426 TTTTAATTTAATTGT
1 TTTTTATTTTATTGT
130441 TTTTT-TTGTT-TT-T
1 TTTTTATT-TTATTGT
* *
130454 TTCTTCTTTTAATTGT
1 TTTTTATTTT-ATTGT
130470 TTTTTAAGTTTTATTGT
1 TTTTT-A-TTTTATTGT
130487 TTTTTATTTTATT
1 TTTTTATTTTATT
130500 TCTTTTTCTG
Statistics
Matches: 47, Mismatches: 5, Indels: 14
0.71 0.08 0.21
Matches are distributed among these distances:
13 7 0.15
14 6 0.13
15 14 0.30
16 6 0.13
17 10 0.21
18 4 0.09
ACGTcount: A:0.15, C:0.03, G:0.07, T:0.76
Consensus pattern (15 bp):
TTTTTATTTTATTGT
Found at i:130580 original size:44 final size:43
Alignment explanation
Indices: 130426--130615 Score: 142
Period size: 44 Copynumber: 4.2 Consensus size: 43
130416 TTAATTTACA
*
130426 TTTTAATTTAATTGTTTTTT-TTGTTTTTTTCTTCTTTT-AATTGTT
1 TTTTAATTT-ATT-TTTTTTATT-TCTTTTTCTTCTTTTAAATTG-T
* *
130471 TTTTAAGTTTTATTGTTTTTTATTTTATTTCTTTTTCTGCTTTT-AATT-A
1 TTTTAA--TTTA-----TTTT-TTTTATTTCTTTTTCTTCTTTTAAATTGT
***
130520 TTTT-ATTT-TAAATTTTATTTCTTTTTCTTC-TTTAAATTGT
1 TTTTAATTTATTTTTTTTATTTCTTTTTCTTCTTTTAAATTGT
130560 TCTTTAAATTTATTTTTTTTATTTCTTTTTCTTCTTTTTAAATTGT
1 T-TTT-AATTTATTTTTTTTATTTCTTTTTCTTC-TTTTAAATTGT
130606 TTTTAATTTA
1 TTTTAATTTA
130616 ATTTAATTTT
Statistics
Matches: 117, Mismatches: 11, Indels: 35
0.72 0.07 0.21
Matches are distributed among these distances:
38 3 0.03
39 21 0.18
40 2 0.02
41 3 0.03
43 4 0.03
44 25 0.21
45 9 0.08
46 15 0.13
47 3 0.03
48 1 0.01
49 4 0.03
50 2 0.02
51 23 0.20
52 2 0.02
ACGTcount: A:0.17, C:0.06, G:0.04, T:0.72
Consensus pattern (43 bp):
TTTTAATTTATTTTTTTTATTTCTTTTTCTTCTTTTAAATTGT
Found at i:130624 original size:90 final size:89
Alignment explanation
Indices: 130426--130625 Score: 194
Period size: 90 Copynumber: 2.2 Consensus size: 89
130416 TTAATTTACA
* * * * *
130426 TTTTAATTTAATTGT--TTTTTTTGTTTTTTTCTTCTTTTAATTGTTTTTTAAGTTTTATTGTTT
1 TTTTAATTTAATT-TAATTTTATTGTCTTTTTCTTCTTTAAATTGTTCTTTAAGATTTATTGTTT
**
130489 TTTATTTTATTTCTTTTTCTGCTTT
65 TTTATTTTATTTCTTTTTCTAATTT
* * *
130514 TAATTATTTTATTTTAAATTTTATT-TCTTTTTCTTCTTTAAATTGTTCTTTAA-ATTTATT-TT
1 T-TTTAATTTAATTT-AATTTTATTGTCTTTTTCTTCTTTAAATTGTTCTTTAAGATTTATTGTT
* *
130576 TTTTATTTCTTTTTCTTCTTTTTAAATTGT
64 TTTTATTT-TATTTCTT-TTTCT-AATT-T
130606 TTTTAATTTAATTTAATTTT
1 TTTTAATTTAATTTAATTTT
130626 TTATTTTCCC
Statistics
Matches: 89, Mismatches: 15, Indels: 14
0.75 0.13 0.12
Matches are distributed among these distances:
88 12 0.13
89 22 0.25
90 35 0.39
91 18 0.20
92 2 0.02
ACGTcount: A:0.18, C:0.06, G:0.04, T:0.72
Consensus pattern (89 bp):
TTTTAATTTAATTTAATTTTATTGTCTTTTTCTTCTTTAAATTGTTCTTTAAGATTTATTGTTTT
TTATTTTATTTCTTTTTCTAATTT
Found at i:132378 original size:28 final size:28
Alignment explanation
Indices: 132320--132379 Score: 66
Period size: 28 Copynumber: 2.1 Consensus size: 28
132310 TTTCGTAAAC
* * *
132320 TTTAGGTTTTGGGTTGAGTTTCGCGAGT
1 TTTAGGTTTTGGGTTGAGTTCCACGAAT
* * *
132348 TTTATGTTTTTGGTTGAGTTCCATGAAT
1 TTTAGGTTTTGGGTTGAGTTCCACGAAT
132376 TTTA
1 TTTA
132380 AAGTGATCTT
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.15, C:0.07, G:0.27, T:0.52
Consensus pattern (28 bp):
TTTAGGTTTTGGGTTGAGTTCCACGAAT
Found at i:149013 original size:18 final size:19
Alignment explanation
Indices: 148992--149027 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
148982 TTTTTTGAAA
148992 TTTTAG-CTTTTTTTTTGT
1 TTTTAGCCTTTTTTTTTGT
*
149010 TTTTTGCCTTTTTTTTTG
1 TTTTAGCCTTTTTTTTTG
149028 CCTTTTTTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.03, C:0.08, G:0.11, T:0.78
Consensus pattern (19 bp):
TTTTAGCCTTTTTTTTTGT
Found at i:149034 original size:13 final size:13
Alignment explanation
Indices: 149004--149037 Score: 52
Period size: 13 Copynumber: 2.6 Consensus size: 13
148994 TTAGCTTTTT
149004 TTTTGTTTTTTGCC
1 TTTT-TTTTTTGCC
149018 -TTTTTTTTTGCC
1 TTTTTTTTTTGCC
149030 TTTTTTTT
1 TTTTTTTT
149038 GTTTTTTTGA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
12 9 0.47
13 10 0.53
ACGTcount: A:0.00, C:0.12, G:0.09, T:0.79
Consensus pattern (13 bp):
TTTTTTTTTTGCC
Found at i:151306 original size:24 final size:23
Alignment explanation
Indices: 151264--151319 Score: 58
Period size: 24 Copynumber: 2.3 Consensus size: 23
151254 TATTGTTATG
*
151264 TTTAAAATAAAAATAATTATTTAA
1 TTTAAAATAAAAATAATTA-ATAA
* * *
151288 TTTAAAATAGATATCATTAATAA
1 TTTAAAATAAAAATAATTAATAA
151311 TGTTAAAAT
1 T-TTAAAAT
151320 TTACATTTTC
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
23 4 0.15
24 23 0.85
ACGTcount: A:0.54, C:0.02, G:0.04, T:0.41
Consensus pattern (23 bp):
TTTAAAATAAAAATAATTAATAA
Found at i:157540 original size:84 final size:84
Alignment explanation
Indices: 157391--158384 Score: 1107
Period size: 84 Copynumber: 11.9 Consensus size: 84
157381 GACAGTATAG
* * * * * * *
157391 CTCAAGGCAAGAAGTGCTATTTGCCAACAAAAGACCTTCGAGTTCGACTATGTTTAGCTCAAAGG
1 CTCAAGGCTAGAAGGGCTATCTGCCAACAAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGG
** *
157456 CACATCATTTGCAATATAG
66 CACATCATTTGCAGCATAA
* * * *
157475 CTCAAGGCAAGAAGGGCTATCTACCACCAAAAGACCTTCGAGTTCGACTACGCTCAGCTTCAAGG
1 CTCAAGGCTAGAAGGGCTATCTGCCAACAAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGG
*
157540 CACATCATTTGTAGCATAA
66 CACATCATTTGCAGCATAA
* * *
157559 -TGCAAGGCTAGAAGGGTTATCTGCCAACAAAAGACCTTCAAGTTCGACTACGCTTAGCTCCAAG
1 CT-CAAGGCTAGAAGGGCTATCTGCCAACAAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAG
* *
157623 GCACATAATTTGCAGCATAG
65 GCACATCATTTGCAGCATAA
* * * * * * * *
157643 CTTAAGTCGAGAAGGGCTATCTGTCACCAAAAGACCTTCGAGTTCGACTACACTTAGCTCTAAGG
1 CTCAAGGCTAGAAGGGCTATCTGCCAACAAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGG
* * *
157708 TACATTATTTGCAACATAA
66 CACATCATTTGCAGCATAA
* * * *
157727 CTTAAGGCTAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCAACTACGCTCAGCTCTAAGG
1 CTCAAGGCTAGAAGGGCTATCTGCCAACAAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGG
*
157792 CACATCATTTGCAGCATAG
66 CACATCATTTGCAGCATAA
* * * * * * *
157811 CTTAAGTCGAGAAGGGCTATCTGTCAACCAAAGACCTTCGAGTTCTACTACGCTCATCTCCAAGG
1 CTCAAGGCTAGAAGGGCTATCTGCCAACAAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGG
*
157876 CACATCATTTGTAGCATAA
66 CACATCATTTGCAGCATAA
* * * * * *
157895 CTCAAGGCTAGAAGGGTTATATTCCAACAAAAGACCTTCGAGTTCTACTACGTTCAACTCCAAGG
1 CTCAAGGCTAGAAGGGCTATCTGCCAACAAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGG
*
157960 CATATCATTTGCAGCATAA
66 CACATCATTTGCAGCATAA
* * * * ** *
157979 CTCAAGGCTAAAAGGGTTATCTTCCAACCAAAA-ACCTTTGAGTTTTACTACGCTCAACTCCAAG
1 CTCAAGGCTAGAAGGGCTATCTGCCAA-CAAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAG
*
158043 GCACATTATTTGCAGCATAA
65 GCACATCATTTGCAGCATAA
* * * * * *
158063 CTTAA-GTTGAGAAGGGCTATCTACCAACCAAAGACCTTCGAGTTCGACTATGCTTAGCTCCAAG
1 CTCAAGGCT-AGAAGGGCTATCTGCCAACAAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAG
*
158127 GCACATCATTTGTAGCATAA
65 GCACATCATTTGCAGCATAA
* *
158147 CTCAAGGCTAGAAGGGTTATCTGGCAACAAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGG
1 CTCAAGGCTAGAAGGGCTATCTGCCAACAAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGG
* **
158212 CACATCATTTACAATATAA
66 CACATCATTTGCAGCATAA
* * * * * *
158231 CTCAAGGCTAGAAGGGTTATCTGTCAAC-AAAGACCTTCAAGTTCGATTACACTCAGCTCAAAGG
1 CTCAAGGCTAGAAGGGCTATCTGCCAACAAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGG
* *
158295 CACATCATTTGTAGCATAG
66 CACATCATTTGCAGCATAA
* * * * * * * * * * *
158314 CTTAAGTCGAGAAGGGCTATCTGTCATC-AAAGATCTTAGAGTTCGATTACACTAAGCTCAAAGG
1 CTCAAGGCTAGAAGGGCTATCTGCCAACAAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGG
*
158378 CAAATCA
66 CACATCA
158385 AATTCCCAGC
Statistics
Matches: 781, Mismatches: 123, Indels: 13
0.85 0.13 0.01
Matches are distributed among these distances:
83 114 0.15
84 659 0.84
85 8 0.01
ACGTcount: A:0.32, C:0.24, G:0.19, T:0.25
Consensus pattern (84 bp):
CTCAAGGCTAGAAGGGCTATCTGCCAACAAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGG
CACATCATTTGCAGCATAA
Found at i:160739 original size:26 final size:24
Alignment explanation
Indices: 160703--160765 Score: 65
Period size: 26 Copynumber: 2.5 Consensus size: 24
160693 ATTAAATATT
160703 ATTTTGTATTTATGAGTTT-GGGTTGA
1 ATTTTGTATTT-T--GTTTAGGGTTGA
*
160729 ATTTTTTATTTTGTTTAGGGTTGA
1 ATTTTGTATTTTGTTTAGGGTTGA
160753 ATATCTTGTATTT
1 AT-T-TTGTATTT
160766 CGGGTTTGAT
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
23 4 0.12
24 9 0.28
25 2 0.06
26 17 0.53
ACGTcount: A:0.19, C:0.02, G:0.21, T:0.59
Consensus pattern (24 bp):
ATTTTGTATTTTGTTTAGGGTTGA
Found at i:162387 original size:31 final size:30
Alignment explanation
Indices: 162314--162388 Score: 107
Period size: 30 Copynumber: 2.5 Consensus size: 30
162304 TAAATTGAAC
*
162314 ACTTTAGATACATATTTTGACAACAAAAAA
1 ACTTTAGATACTTATTTTGACAACAAAAAA
*
162344 ACTTTA-AGTACTTATTTTGACAACAAAGATA
1 ACTTTAGA-TACTTATTTTGACAACAAA-AAA
162375 ACTTTAGATACTTA
1 ACTTTAGATACTTA
162389 AATAGAAAGA
Statistics
Matches: 40, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
29 1 0.03
30 24 0.60
31 14 0.35
32 1 0.03
ACGTcount: A:0.44, C:0.13, G:0.08, T:0.35
Consensus pattern (30 bp):
ACTTTAGATACTTATTTTGACAACAAAAAA
Found at i:164594 original size:2 final size:2
Alignment explanation
Indices: 164587--164612 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
164577 TTTGATAACA
164587 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
164613 CACACATATT
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:164679 original size:2 final size:2
Alignment explanation
Indices: 164672--164703 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
164662 AAAGATTAAC
164672 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
164704 TAATACTAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:168842 original size:42 final size:41
Alignment explanation
Indices: 168796--168921 Score: 114
Period size: 44 Copynumber: 3.0 Consensus size: 41
168786 TATAGCGGCC
168796 TTTTTATATTAAAACGCCGCTATTGACAATTATATAGTGGAG
1 TTTTTATA-TAAAACGCCGCTATTGACAATTATATAGTGGAG
* * * *
168838 TTTTTAGTCAT-AAACGCCGCAAATT-ATCTAA-CACTTTAGTGGCG
1 TTTTTA-T-ATAAAACGCCGC-TATTGA-C-AATTA-TATAGTGGAG
*
168882 TTTTTATAATAAAACGCCGCTATTGACAATTTTATAGTGG
1 TTTTTAT-ATAAAACGCCGCTATTGACAATTATATAGTGG
168922 CATTTTTTTG
Statistics
Matches: 66, Mismatches: 9, Indels: 18
0.71 0.10 0.19
Matches are distributed among these distances:
42 25 0.38
43 14 0.21
44 27 0.41
ACGTcount: A:0.32, C:0.15, G:0.16, T:0.37
Consensus pattern (41 bp):
TTTTTATATAAAACGCCGCTATTGACAATTATATAGTGGAG
Found at i:168895 original size:86 final size:85
Alignment explanation
Indices: 168795--168991 Score: 256
Period size: 86 Copynumber: 2.3 Consensus size: 85
168785 ATATAGCGGC
* *
168795 CTTTTTATATTAAAACGCCGCTATTGACAATTATATAGTGG-AGTTTTTAGTCATAAAC-GCCGC
1 CTTTTTATAATAAAACGCCGCTATTGACAATTATATAGTGGCAGTTTTTAGT-ATAAACAG-CAC
* *
168858 AAATTATCTAACACTTTAGTGG
64 AAATAATCTAAAACTTTAGTGG
* * *
168880 CGTTTTTATAATAAAACGCCGCTATTGACAATTTTATAGTGGCATTTTTTTGTATAAACAGCACA
1 C-TTTTTATAATAAAACGCCGCTATTGACAATTATATAGTGGCAGTTTTTAGTATAAACAGCACA
168945 AATAATCTAAAACTTTAGTGG
65 AATAATCTAAAACTTTAGTGG
** *
168966 CTTTTT-TTGTAAAACGCCGGTATTGA
1 CTTTTTATAATAAAACGCCGCTATTGA
168992 TTATGTATTT
Statistics
Matches: 99, Mismatches: 10, Indels: 7
0.85 0.09 0.06
Matches are distributed among these distances:
84 17 0.17
85 6 0.06
86 67 0.68
87 9 0.09
ACGTcount: A:0.32, C:0.15, G:0.15, T:0.38
Consensus pattern (85 bp):
CTTTTTATAATAAAACGCCGCTATTGACAATTATATAGTGGCAGTTTTTAGTATAAACAGCACAA
ATAATCTAAAACTTTAGTGG
Found at i:168930 original size:44 final size:43
Alignment explanation
Indices: 168796--168929 Score: 125
Period size: 42 Copynumber: 3.1 Consensus size: 43
168786 TATAGCGGCC
* *
168796 TTTTTATATTAAAACGCCGCTATTGACAATTATATAGTGG-AG
1 TTTTTATAATAAAACGCCGCTATTGACAATTTTATAGTGGCAG
* * **
168838 TTTTTAGTCAT-AAACGCCGCAAATT-ATCTAACACTT-TAGTGGC-G
1 TTTTTA-TAATAAAACGCCGC-TATTGA-C-AA-TTTTATAGTGGCAG
*
168882 TTTTTATAATAAAACGCCGCTATTGACAATTTTATAGTGGCAT
1 TTTTTATAATAAAACGCCGCTATTGACAATTTTATAGTGGCAG
168925 TTTTT
1 TTTTT
168930 TGTATAAACA
Statistics
Matches: 71, Mismatches: 11, Indels: 19
0.70 0.11 0.19
Matches are distributed among these distances:
41 2 0.03
42 25 0.35
43 18 0.25
44 25 0.35
45 1 0.01
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.40
Consensus pattern (43 bp):
TTTTTATAATAAAACGCCGCTATTGACAATTTTATAGTGGCAG
Found at i:169147 original size:21 final size:21
Alignment explanation
Indices: 169123--169166 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
169113 CATGACATAT
* *
169123 ATAACAACAAACTTTAATTCC
1 ATAACAACAAACTTAAAATCC
169144 ATAACAACAAACTTAAAATCC
1 ATAACAACAAACTTAAAATCC
169165 AT
1 AT
169167 TATAGTAAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.52, C:0.23, G:0.00, T:0.25
Consensus pattern (21 bp):
ATAACAACAAACTTAAAATCC
Found at i:173887 original size:24 final size:24
Alignment explanation
Indices: 173855--173910 Score: 103
Period size: 24 Copynumber: 2.3 Consensus size: 24
173845 GGGACCTGGT
*
173855 AAGCCATTAATGGTGTAGGCATCA
1 AAGCCATTAATGGTATAGGCATCA
173879 AAGCCATTAATGGTATAGGCATCA
1 AAGCCATTAATGGTATAGGCATCA
173903 AAGCCATT
1 AAGCCATT
173911 TGGTGCAGTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.36, C:0.18, G:0.21, T:0.25
Consensus pattern (24 bp):
AAGCCATTAATGGTATAGGCATCA
Found at i:176604 original size:20 final size:20
Alignment explanation
Indices: 176579--176620 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
176569 AATGATTATG
*
176579 AACCGATTT-TCATGTCTTCC
1 AACCGATTTAT-AGGTCTTCC
176599 AACCGATTTATAGGTCTTCC
1 AACCGATTTATAGGTCTTCC
176619 AA
1 AA
176621 TCAAGTCAGG
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:0.26, G:0.12, T:0.36
Consensus pattern (20 bp):
AACCGATTTATAGGTCTTCC
Done.