Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008280.1 Hibiscus syriacus cultivar Beakdansim tig00110940_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: 3557051
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 12 of 17
Found at i:2510865 original size:22 final size:22
Alignment explanation
Indices: 2510839--2510883 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 22
2510829 ATCTAATAAT
*
2510839 ACTGTATATTAATTATATATTA
1 ACTGTATATTAACTATATATTA
2510861 ACTGTATATTAACTATATATTA
1 ACTGTATATTAACTATATATTA
2510883 A
1 A
2510884 TATGTCTTTC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.42, C:0.07, G:0.04, T:0.47
Consensus pattern (22 bp):
ACTGTATATTAACTATATATTA
Found at i:2514611 original size:13 final size:13
Alignment explanation
Indices: 2514593--2514617 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2514583 CCCTTCCCAA
2514593 GAAAAGGAAAAAG
1 GAAAAGGAAAAAG
2514606 GAAAAGGAAAAA
1 GAAAAGGAAAAA
2514618 CTACTTTCTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (13 bp):
GAAAAGGAAAAAG
Found at i:2524565 original size:26 final size:26
Alignment explanation
Indices: 2524527--2524577 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 26
2524517 TGATTTTATG
2524527 TTAAAAAATAAATT-TATAAATTTTAA
1 TTAAAAAATAAATTATA-AAATTTTAA
2524553 TTAATAAAA-AAATTATAAAATTTTA
1 TTAA-AAAATAAATTATAAAATTTTA
2524578 GAATGACAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
26 17 0.74
27 6 0.26
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (26 bp):
TTAAAAAATAAATTATAAAATTTTAA
Found at i:2526782 original size:21 final size:21
Alignment explanation
Indices: 2526758--2526811 Score: 99
Period size: 21 Copynumber: 2.5 Consensus size: 21
2526748 TTTAAGTCAG
2526758 AGTTTAAGGTTTAGGGTTTAT
1 AGTTTAAGGTTTAGGGTTTAT
2526779 AGTTTAAGGTTTAGGGTTTAT
1 AGTTTAAGGTTTAGGGTTTAT
2526800 AGTTTAAAGGTT
1 AGTTT-AAGGTT
2526812 ACGAGGTTAT
Statistics
Matches: 32, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
21 26 0.81
22 6 0.19
ACGTcount: A:0.26, C:0.00, G:0.28, T:0.46
Consensus pattern (21 bp):
AGTTTAAGGTTTAGGGTTTAT
Found at i:2526821 original size:22 final size:22
Alignment explanation
Indices: 2526758--2526835 Score: 94
Period size: 21 Copynumber: 3.7 Consensus size: 22
2526748 TTTAAGTCAG
2526758 AGTTT-AAGGTTTAGGGTTTAT
1 AGTTTAAAGGTTTAGGGTTTAT
2526779 AGTTT-AAGGTTTAGGGTTTAT
1 AGTTTAAAGGTTTAGGGTTTAT
2526800 AGTTTAAAGG-TTACGAGG-TTAT
1 AGTTTAAAGGTTTA-G-GGTTTAT
*
2526822 GGTTTAAA-GTTTAG
1 AGTTTAAAGGTTTAG
2526836 AGTTATCAAT
Statistics
Matches: 52, Mismatches: 1, Indels: 8
0.85 0.02 0.13
Matches are distributed among these distances:
21 31 0.60
22 19 0.37
23 2 0.04
ACGTcount: A:0.27, C:0.01, G:0.28, T:0.44
Consensus pattern (22 bp):
AGTTTAAAGGTTTAGGGTTTAT
Found at i:2537726 original size:8 final size:8
Alignment explanation
Indices: 2537714--2537773 Score: 111
Period size: 8 Copynumber: 7.5 Consensus size: 8
2537704 AATATCAATA
*
2537714 TACATACA
1 TACATACG
2537722 TACATACG
1 TACATACG
2537730 TACATACG
1 TACATACG
2537738 TACATACG
1 TACATACG
2537746 TACATACG
1 TACATACG
2537754 TACATACG
1 TACATACG
2537762 TACATACG
1 TACATACG
2537770 TACA
1 TACA
2537774 ACTTACGGAA
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
8 51 1.00
ACGTcount: A:0.40, C:0.25, G:0.10, T:0.25
Consensus pattern (8 bp):
TACATACG
Found at i:2552349 original size:21 final size:22
Alignment explanation
Indices: 2552307--2552351 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 22
2552297 CTTTGGCTCC
2552307 AAACAAAATCTGAATCTGGTTCG
1 AAACAAAATCTGAA-CTGGTTCG
*
2552330 AAACAAAATCTGGA-TGGTTCG
1 AAACAAAATCTGAACTGGTTCG
2552351 A
1 A
2552352 GTGTTTTGCA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 8 0.38
23 13 0.62
ACGTcount: A:0.40, C:0.16, G:0.20, T:0.24
Consensus pattern (22 bp):
AAACAAAATCTGAACTGGTTCG
Found at i:2553409 original size:8 final size:9
Alignment explanation
Indices: 2553391--2553421 Score: 53
Period size: 9 Copynumber: 3.3 Consensus size: 9
2553381 TTCTATAAGA
2553391 TTTTTATTT
1 TTTTTATTT
2553400 TTTTTATTTT
1 TTTTTA-TTT
2553410 TTTTTATTT
1 TTTTTATTT
2553419 TTT
1 TTT
2553422 GCAATTTTCA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
9 12 0.57
10 9 0.43
ACGTcount: A:0.10, C:0.00, G:0.00, T:0.90
Consensus pattern (9 bp):
TTTTTATTT
Found at i:2553410 original size:10 final size:10
Alignment explanation
Indices: 2553391--2553421 Score: 55
Period size: 10 Copynumber: 3.2 Consensus size: 10
2553381 TTCTATAAGA
2553391 TTTTTA-TTT
1 TTTTTATTTT
2553400 TTTTTATTTT
1 TTTTTATTTT
2553410 TTTTTATTTT
1 TTTTTATTTT
2553420 TT
1 TT
2553422 GCAATTTTCA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 6 0.29
10 15 0.71
ACGTcount: A:0.10, C:0.00, G:0.00, T:0.90
Consensus pattern (10 bp):
TTTTTATTTT
Found at i:2553429 original size:19 final size:19
Alignment explanation
Indices: 2553391--2553429 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
2553381 TTCTATAAGA
** *
2553391 TTTTTATTTTTTTTATTTT
1 TTTTTATTTTTTGCAATTT
2553410 TTTTTATTTTTTGCAATTT
1 TTTTTATTTTTTGCAATTT
2553429 T
1 T
2553430 CATAGGCAAT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.13, C:0.03, G:0.03, T:0.82
Consensus pattern (19 bp):
TTTTTATTTTTTGCAATTT
Found at i:2561607 original size:166 final size:164
Alignment explanation
Indices: 2561333--2561671 Score: 644
Period size: 166 Copynumber: 2.1 Consensus size: 164
2561323 AGGGCTGCCA
2561333 ATTGGGAAGCGGACAGTCTAGCTAAAGATGGAATTGGTTGATTAGCTGCCTTTGTATTTGAGGAG
1 ATTGGGAAGCGGACAGTCTAGCTAAAGATGGAATTGGTTGATTAGCTGCCTTTGTATTTGAGGAG
2561398 TTGGAGTGGATGTTTCATTTTGTTTCTGCAGGTTTTGTTCTCAGTATTATGTAATTTGTGTCTAC
66 TTGGAGTGGATGTTTCATTTTGTTTCTGCAGGTTTTGTTCTCAGTATTATGTAATTTGTGTCTAC
2561463 GCTTTCCACTGATAGTGGTTTTTAAGTCTTATGCTT
131 GCTTT-C-CTGATAGTGGTTTTTAAGTCTTATGCTT
2561499 ATTGGGAAGCGGACAGTCTAGCTAAAGATGGAATTGGTTGATTAGCTGCCTTTGTATTTGAGGAG
1 ATTGGGAAGCGGACAGTCTAGCTAAAGATGGAATTGGTTGATTAGCTGCCTTTGTATTTGAGGAG
2561564 TTGGAGTGGATGTTTCATTTTGTTTCTGCAGGTTTTGTTCTCAGTATTATGTAATTTGTGTCTAC
66 TTGGAGTGGATGTTTCATTTTGTTTCTGCAGGTTTTGTTCTCAGTATTATGTAATTTGTGTCTAC
2561629 GCTTTCCTGATAGTGGTTTTTAAGTCTTATGCTT
131 GCTTTCCTGATAGTGGTTTTTAAGTCTTATGCTT
2561663 -TCTGGGAAG
1 AT-TGGGAAG
2561672 GTTTATTTTG
Statistics
Matches: 172, Mismatches: 0, Indels: 4
0.98 0.00 0.02
Matches are distributed among these distances:
163 1 0.01
164 35 0.20
165 1 0.01
166 135 0.78
ACGTcount: A:0.20, C:0.12, G:0.27, T:0.42
Consensus pattern (164 bp):
ATTGGGAAGCGGACAGTCTAGCTAAAGATGGAATTGGTTGATTAGCTGCCTTTGTATTTGAGGAG
TTGGAGTGGATGTTTCATTTTGTTTCTGCAGGTTTTGTTCTCAGTATTATGTAATTTGTGTCTAC
GCTTTCCTGATAGTGGTTTTTAAGTCTTATGCTT
Found at i:2565731 original size:133 final size:133
Alignment explanation
Indices: 2565493--2565758 Score: 532
Period size: 133 Copynumber: 2.0 Consensus size: 133
2565483 TAGTAAAGTT
2565493 GTGGATTGAATCAAGTGGCCGAGTTCTTCACCTATGATTTTCAGCTCACTAGTCAAGGAAATTAG
1 GTGGATTGAATCAAGTGGCCGAGTTCTTCACCTATGATTTTCAGCTCACTAGTCAAGGAAATTAG
2565558 TGCACTGGTAGAAGATAGAAGTGTTGTTGTAAAACATGTTAGTAGAATTGTGAATTGTAAAGCCG
66 TGCACTGGTAGAAGATAGAAGTGTTGTTGTAAAACATGTTAGTAGAATTGTGAATTGTAAAGCCG
2565623 ATG
131 ATG
2565626 GTGGATTGAATCAAGTGGCCGAGTTCTTCACCTATGATTTTCAGCTCACTAGTCAAGGAAATTAG
1 GTGGATTGAATCAAGTGGCCGAGTTCTTCACCTATGATTTTCAGCTCACTAGTCAAGGAAATTAG
2565691 TGCACTGGTAGAAGATAGAAGTGTTGTTGTAAAACATGTTAGTAGAATTGTGAATTGTAAAGCCG
66 TGCACTGGTAGAAGATAGAAGTGTTGTTGTAAAACATGTTAGTAGAATTGTGAATTGTAAAGCCG
2565756 ATG
131 ATG
2565759 AATTAGCTAA
Statistics
Matches: 133, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
133 133 1.00
ACGTcount: A:0.31, C:0.13, G:0.26, T:0.31
Consensus pattern (133 bp):
GTGGATTGAATCAAGTGGCCGAGTTCTTCACCTATGATTTTCAGCTCACTAGTCAAGGAAATTAG
TGCACTGGTAGAAGATAGAAGTGTTGTTGTAAAACATGTTAGTAGAATTGTGAATTGTAAAGCCG
ATG
Found at i:2566696 original size:13 final size:13
Alignment explanation
Indices: 2566678--2566704 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
2566668 GAGCTGGTTT
2566678 TGTTTACCTCTTC
1 TGTTTACCTCTTC
2566691 TGTTTACCTCTTC
1 TGTTTACCTCTTC
2566704 T
1 T
2566705 TTTGAATCTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.07, C:0.30, G:0.07, T:0.56
Consensus pattern (13 bp):
TGTTTACCTCTTC
Found at i:2581911 original size:12 final size:12
Alignment explanation
Indices: 2581894--2581924 Score: 53
Period size: 12 Copynumber: 2.5 Consensus size: 12
2581884 GAGATTAAAC
2581894 ATTAAGCAAATT
1 ATTAAGCAAATT
2581906 ATTAAGCAAATT
1 ATTAAGCAAATT
2581918 ATGTAAG
1 AT-TAAG
2581925 ATGAAAGAAC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 14 0.78
13 4 0.22
ACGTcount: A:0.48, C:0.06, G:0.13, T:0.32
Consensus pattern (12 bp):
ATTAAGCAAATT
Found at i:2582206 original size:152 final size:151
Alignment explanation
Indices: 2581918--2582342 Score: 464
Period size: 152 Copynumber: 2.8 Consensus size: 151
2581908 TAAGCAAATT
* *
2581918 ATGTAAGATGAAAGAACTATACCTCCATGGAAATGGGTTCTTCAATGATCACTGCTTCAGTTGCC
1 ATGTAAGATGAAAGAACTATACCACCATGGAAATGGGTTCTTGAATGATCACTGCTTCAGTTGCC
* * *
2581983 ATTTTTCCCTGCAGAAGTTA-CGGAATTCGAGTTCG-GTAACACTAAAGAAAACTGCCCGTGAGT
66 ATTTTTTCCTGCAGAAGTAATC-GAATTCGAGTTCGAG-AACACTAAAG-AAACTGCACGTGAGT
** * * * *
2582046 ATGGACATTCTTAAACTGTTAATC
128 ATAAACATTCATAAACTATGAAGC
* * * *
2582070 ATGTAAGATGAAAGAACTTTACCACCATGGAAATGGATTCTTGAATGATCACTGCTTCGGTTGCA
1 ATGTAAGATGAAAGAACTATACCACCATGGAAATGGGTTCTTGAATGATCACTGCTTCAGTTGCC
**
2582135 ATTTTTTCCTGCAGAAGTAATCGAATTCGAGTT-GAAGAACACTAAAGAAACTGTCTACG-GTTT
66 ATTTTTTCCTGCAGAAGTAATCGAATTCGAGTTCG-AGAACACTAAAGAAACTG-C-ACGTGAGT
* * *
2582198 CTAAACATTCATAAATTATGGAGC
128 ATAAACATTCATAAACTATGAAGC
* * ** *
2582222 ATAG-AAGATAAAAAAAAACCCTACCACCATGGAAACGGGTTCTTGAATGATCACTGCTTCAGTT
1 AT-GTAAGAT--GAAAGAACTATACCACCATGGAAATGGGTTCTTGAATGATCACTGCTTCAGTT
*
2582286 GCCATTTATTTCCTGCAGAAGAATAATCGAATTTCGAGTTCGAGAATACTAAAGAAA
63 GCCATTT-TTTCCTGCAGAAG--TAATCGAA-TTCGAGTTCGAGAACACTAAAGAAA
2582343 ACTACCTATG
Statistics
Matches: 231, Mismatches: 29, Indels: 20
0.82 0.10 0.07
Matches are distributed among these distances:
151 7 0.03
152 123 0.53
153 5 0.02
154 52 0.23
155 13 0.06
157 8 0.03
158 22 0.10
159 1 0.00
ACGTcount: A:0.34, C:0.18, G:0.19, T:0.29
Consensus pattern (151 bp):
ATGTAAGATGAAAGAACTATACCACCATGGAAATGGGTTCTTGAATGATCACTGCTTCAGTTGCC
ATTTTTTCCTGCAGAAGTAATCGAATTCGAGTTCGAGAACACTAAAGAAACTGCACGTGAGTATA
AACATTCATAAACTATGAAGC
Found at i:2583259 original size:7 final size:7
Alignment explanation
Indices: 2583247--2583271 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
2583237 ATAACATTGA
2583247 AATTATT
1 AATTATT
2583254 AATTATT
1 AATTATT
2583261 AATTATT
1 AATTATT
2583268 AATT
1 AATT
2583272 GGAGTGATCA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (7 bp):
AATTATT
Found at i:2585455 original size:27 final size:28
Alignment explanation
Indices: 2585402--2585464 Score: 83
Period size: 27 Copynumber: 2.3 Consensus size: 28
2585392 CAGGGATTGG
* *
2585402 GGGTATTTTAGGTTATTTCACACTTCAA
1 GGGTATTTTAGGTCATTTCACAATTCAA
* *
2585430 GGGTATTTT-GGTCATTTTATAATTCAA
1 GGGTATTTTAGGTCATTTCACAATTCAA
2585457 GGGTATTT
1 GGGTATTT
2585465 ATTTCATTTC
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
27 22 0.71
28 9 0.29
ACGTcount: A:0.24, C:0.10, G:0.21, T:0.46
Consensus pattern (28 bp):
GGGTATTTTAGGTCATTTCACAATTCAA
Found at i:2591627 original size:23 final size:23
Alignment explanation
Indices: 2591578--2591627 Score: 64
Period size: 23 Copynumber: 2.2 Consensus size: 23
2591568 GGTTCAAGTA
*
2591578 CAAACTCGAATTTGAGCTTGAAC
1 CAAACTCGAATTTGAGCTTCAAC
* * *
2591601 CAAACTTGAATTTGAGTTTCAAT
1 CAAACTCGAATTTGAGCTTCAAC
2591624 CAAA
1 CAAA
2591628 TTAAGTCTAA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.38, C:0.18, G:0.14, T:0.30
Consensus pattern (23 bp):
CAAACTCGAATTTGAGCTTCAAC
Found at i:2591696 original size:26 final size:26
Alignment explanation
Indices: 2591667--2591716 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 26
2591657 TTTTTCAAGC
* *
2591667 TCGAGTCAAACTTCTAATTTTTAATT
1 TCGAGTAAAACTTCAAATTTTTAATT
*
2591693 TCGAGTAAAACTTGAAATTTTTAA
1 TCGAGTAAAACTTCAAATTTTTAA
2591717 GTTCACGAGC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.36, C:0.12, G:0.10, T:0.42
Consensus pattern (26 bp):
TCGAGTAAAACTTCAAATTTTTAATT
Found at i:2591946 original size:10 final size:10
Alignment explanation
Indices: 2591931--2591961 Score: 62
Period size: 10 Copynumber: 3.1 Consensus size: 10
2591921 AAGGTTGACT
2591931 TGAGTAAAGA
1 TGAGTAAAGA
2591941 TGAGTAAAGA
1 TGAGTAAAGA
2591951 TGAGTAAAGA
1 TGAGTAAAGA
2591961 T
1 T
2591962 CATGCTGGAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.48, C:0.00, G:0.29, T:0.23
Consensus pattern (10 bp):
TGAGTAAAGA
Found at i:2595865 original size:6 final size:6
Alignment explanation
Indices: 2595854--2595899 Score: 56
Period size: 6 Copynumber: 7.5 Consensus size: 6
2595844 AAACATAAAT
* * *
2595854 AAATAA AAATAA AAAGAC AAATAA AAATAA AAAAATA AAATAA AAA
1 AAATAA AAATAA AAATAA AAATAA AAATAA AAATA-A AAATAA AAA
2595900 ATAATAGTAG
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
6 28 0.85
7 5 0.15
ACGTcount: A:0.83, C:0.02, G:0.02, T:0.13
Consensus pattern (6 bp):
AAATAA
Found at i:2595893 original size:13 final size:13
Alignment explanation
Indices: 2595858--2595900 Score: 52
Period size: 13 Copynumber: 3.3 Consensus size: 13
2595848 ATAAATAAAT
*
2595858 AAAAATAAAA-AG
1 AAAAATAAAATAA
*
2595870 ACAAATAAAAATAA
1 AAAAAT-AAAATAA
2595884 AAAAATAAAATAA
1 AAAAATAAAATAA
2595897 AAAA
1 AAAA
2595901 TAATAGTAGT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
12 5 0.19
13 15 0.58
14 6 0.23
ACGTcount: A:0.84, C:0.02, G:0.02, T:0.12
Consensus pattern (13 bp):
AAAAATAAAATAA
Found at i:2595898 original size:12 final size:12
Alignment explanation
Indices: 2595850--2595903 Score: 51
Period size: 12 Copynumber: 4.5 Consensus size: 12
2595840 ATAGAAACAT
2595850 AAAT-AAAT-AA
1 AAATAAAATAAA
*
2595860 AAATAAAA-AGAC
1 AAATAAAATA-AA
2595872 AAATAAAAATAAAA
1 AAAT-AAAAT-AAA
2595886 AAATAAAATAAA
1 AAATAAAATAAA
2595898 AAATAA
1 AAATAA
2595904 TAGTAGTGAT
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
10 4 0.11
11 3 0.08
12 14 0.39
13 9 0.25
14 5 0.14
15 1 0.03
ACGTcount: A:0.81, C:0.02, G:0.02, T:0.15
Consensus pattern (12 bp):
AAATAAAATAAA
Found at i:2595898 original size:18 final size:18
Alignment explanation
Indices: 2595850--2595899 Score: 73
Period size: 18 Copynumber: 2.7 Consensus size: 18
2595840 ATAGAAACAT
2595850 AAATAAATAAAAATAAAA
1 AAATAAATAAAAATAAAA
* *
2595868 AGACAAATAAAAATAAAA
1 AAATAAATAAAAATAAAA
2595886 AAATAAAATAAAAA
1 AAAT-AAATAAAAA
2595900 ATAATAGTAG
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
18 18 0.67
19 9 0.33
ACGTcount: A:0.82, C:0.02, G:0.02, T:0.14
Consensus pattern (18 bp):
AAATAAATAAAAATAAAA
Found at i:2597207 original size:13 final size:14
Alignment explanation
Indices: 2597191--2597220 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
2597181 TAAAAACATA
2597191 AAAAGAAAAT-AAT
1 AAAAGAAAATGAAT
2597204 AAAAGAAAATGAAT
1 AAAAGAAAATGAAT
2597218 AAA
1 AAA
2597221 TAATAATAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 10 0.62
14 6 0.38
ACGTcount: A:0.77, C:0.00, G:0.10, T:0.13
Consensus pattern (14 bp):
AAAAGAAAATGAAT
Found at i:2597253 original size:18 final size:18
Alignment explanation
Indices: 2597216--2597252 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
2597206 AAGAAAATGA
2597216 ATAAATAATAATAATAAT
1 ATAAATAATAATAATAAT
*
2597234 ATAAATTAT-ATAAT-AT
1 ATAAATAATAATAATAAT
2597250 ATA
1 ATA
2597253 TTTTCTTCAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
16 5 0.28
17 5 0.28
18 8 0.44
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (18 bp):
ATAAATAATAATAATAAT
Found at i:2597283 original size:32 final size:31
Alignment explanation
Indices: 2597247--2597389 Score: 92
Period size: 31 Copynumber: 4.4 Consensus size: 31
2597237 AATTATATAA
* * * **
2597247 TATATATTTTCTTCAAAAATATTTTTTTAAAC
1 TATATATTATATTCAAAAA-AGTTTTCAAAAC
*
2597279 TATATATTATATTTAAAAAAGTTTTCAAAAC
1 TATATATTATATTCAAAAAAGTTTTCAAAAC
* *
2597310 TATATATTATATAGTTTTCAAAATA-TTTT-AAAAA
1 TATATA-T-TATA---TTCAAAAAAGTTTTCAAAAC
* * *
2597344 TATTATATAAGTTTTCAAAAAATGTTTTTAAAAC
1 TA-TATATTA-TATTCAAAAAA-GTTTTCAAAAC
2597378 TATATATTATAT
1 TATATATTATAT
2597390 AATTTTTTTC
Statistics
Matches: 86, Mismatches: 15, Indels: 20
0.71 0.12 0.17
Matches are distributed among these distances:
31 23 0.27
32 19 0.22
33 15 0.17
34 14 0.16
35 8 0.09
36 7 0.08
ACGTcount: A:0.44, C:0.06, G:0.03, T:0.48
Consensus pattern (31 bp):
TATATATTATATTCAAAAAAGTTTTCAAAAC
Found at i:2597410 original size:39 final size:37
Alignment explanation
Indices: 2597240--2597593 Score: 281
Period size: 39 Copynumber: 9.6 Consensus size: 37
2597230 TAATATAAAT
* ** * *
2597240 TATATAATATATATTTTCTTCAAAAATATTTTTTTAAAC
1 TATATATTATATAAGTT-TTCAAAAAT-GTTTTTAAAAC
* *
2597279 TATATA-T-TAT-A--TTT-AAAAAAGTTTTCAAAAC
1 TATATATTATATAAGTTTTCAAAAATGTTTTTAAAAC
*
2597310 TATATATTATAT-AGTTTTC-AAAAT-ATTTT-AAA-
1 TATATATTATATAAGTTTTCAAAAATGTTTTTAAAAC
2597342 -A-ATATTATATAAGTTTTCAAAAAATGTTTTTAAAAC
1 TATATATTATATAAGTTTTC-AAAAATGTTTTTAAAAC
*
2597378 TATATATTATATAATTTTTTTCAAAAATGTTTTTAAAAC
1 TATATATTATATAA--GTTTTCAAAAATGTTTTTAAAAC
* * * ** *
2597417 TATATGTTATATAATTTTTTAAAAAAACATTTTTAAAAT
1 TATATATTATATAA-GTTTT-CAAAAATGTTTTTAAAAC
*** *
2597456 TATATATTATATAA-TTTTCCAATTTTTTTTTTAAAAAAAC
1 TATATATTATATAAGTTTT-CAAAAATGTTTTT---AAAAC
*
2597496 TATATATTATATAAGTTTTC-AAAATGTTTTAAAAAC
1 TATATATTATATAAGTTTTCAAAAATGTTTTTAAAAC
*
2597532 TATATATTATATAAGTTTTC-AAAATGTTTTGAAAAC
1 TATATATTATATAAGTTTTCAAAAATGTTTTTAAAAC
*
2597568 TATATAATATATAAATGTTTTCAAAA
1 TATATATTATAT-AA-GTTTTCAAAA
2597594 CTATATATTA
Statistics
Matches: 261, Mismatches: 31, Indels: 46
0.77 0.09 0.14
Matches are distributed among these distances:
30 9 0.03
31 22 0.08
32 6 0.02
33 14 0.05
34 8 0.03
35 10 0.04
36 51 0.20
37 17 0.07
38 24 0.09
39 72 0.28
40 24 0.09
41 4 0.02
ACGTcount: A:0.44, C:0.05, G:0.03, T:0.47
Consensus pattern (37 bp):
TATATATTATATAAGTTTTCAAAAATGTTTTTAAAAC
Found at i:2597537 original size:36 final size:36
Alignment explanation
Indices: 2597294--2597683 Score: 256
Period size: 36 Copynumber: 10.8 Consensus size: 36
2597284 ATTATATTTA
* *
2597294 AAAAAGTTTTCAAAACTATATATTATAT-AGTTTTC
1 AAAATGTTTTAAAAACTATATATTATATAAGTTTTC
*
2597329 AAAATATTTT--AAA--A-ATATTATATAAGTTTTC
1 AAAATGTTTTAAAAACTATATATTATATAAGTTTTC
* *
2597360 AAAAAATGTTTTTAAAACTATATATTATATAATTTTTTTC
1 --AAAATGTTTTAAAAACTATATATTATATAA--GTTTTC
* * * *
2597400 AAAAATGTTTTTAAAACTATATGTTATATAATTTTTTAAA
1 -AAAATGTTTTAAAAACTATATATTATATAA-GTTTT--C
** * *
2597440 AAAACATTTTTAAAATTATATATTATATAA-TTTTCC
1 AAAATGTTTTAAAAACTATATATTATATAAGTTTT-C
** *
2597476 AATTTTTTTTTTAAAAAAACTATATATTATATAAGTTTTC
1 AA--AATGTTTT--AAAAACTATATATTATATAAGTTTTC
2597516 AAAATGTTTTAAAAACTATATATTATATAAGTTTTC
1 AAAATGTTTTAAAAACTATATATTATATAAGTTTTC
*
2597552 AAAATGTTTTGAAAACTATATA--ATAT-A----T-
1 AAAATGTTTTAAAAACTATATATTATATAAGTTTTC
*
2597580 -AAATGTTTTCAAAACTATATATTATATATA-TTTTC
1 AAAATGTTTTAAAAACTATATATTATATA-AGTTTTC
* * * * **
2597615 AAAATATTTTCAAAAACCATATAATATACAAACTTTC
1 AAAATGTTTT-AAAAACTATATATTATATAAGTTTTC
* *
2597652 AAAAATCGTTTTCTGAAAATTATATATTATAT
1 -AAAAT-G-TTT-TAAAAACTATATATTATAT
2597684 TTTGTCAAAA
Statistics
Matches: 288, Mismatches: 35, Indels: 59
0.75 0.09 0.15
Matches are distributed among these distances:
27 20 0.07
29 5 0.02
30 9 0.03
31 9 0.03
33 13 0.05
34 5 0.02
35 11 0.04
36 58 0.20
37 24 0.08
38 31 0.11
39 56 0.19
40 42 0.15
41 5 0.02
ACGTcount: A:0.45, C:0.07, G:0.04, T:0.45
Consensus pattern (36 bp):
AAAATGTTTTAAAAACTATATATTATATAAGTTTTC
Found at i:2597604 original size:63 final size:64
Alignment explanation
Indices: 2597517--2597642 Score: 193
Period size: 63 Copynumber: 2.0 Consensus size: 64
2597507 TAAGTTTTCA
* * *
2597517 AAATGTTTTAAAAACTATATATTATATA-AGTTTTCAAAATGTTTT-GAAAACTATATAATATAT
1 AAATGTTTTAAAAACTATATATTATATATA-TTTTCAAAATATTTTCAAAAACCATATAATATAT
*
2597580 AAATGTTTTCAAAACTATATATTATATATATTTTCAAAATATTTTCAAAAACCATATAATATA
1 AAATGTTTTAAAAACTATATATTATATATATTTTCAAAATATTTTCAAAAACCATATAATATA
2597643 CAAACTTTCA
Statistics
Matches: 57, Mismatches: 4, Indels: 3
0.89 0.06 0.05
Matches are distributed among these distances:
63 41 0.72
64 16 0.28
ACGTcount: A:0.47, C:0.07, G:0.04, T:0.42
Consensus pattern (64 bp):
AAATGTTTTAAAAACTATATATTATATATATTTTCAAAATATTTTCAAAAACCATATAATATAT
Found at i:2597605 original size:25 final size:27
Alignment explanation
Indices: 2597553--2597607 Score: 92
Period size: 27 Copynumber: 2.0 Consensus size: 27
2597543 TAAGTTTTCA
*
2597553 AAATGTTTTGAAAACTATATAATATAT
1 AAATGTTTTCAAAACTATATAATATAT
*
2597580 AAATGTTTTCAAAACTATATATTATAT
1 AAATGTTTTCAAAACTATATAATATAT
2597607 A
1 A
2597608 TATTTTCAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.47, C:0.05, G:0.05, T:0.42
Consensus pattern (27 bp):
AAATGTTTTCAAAACTATATAATATAT
Found at i:2597613 original size:25 final size:27
Alignment explanation
Indices: 2597553--2597618 Score: 82
Period size: 27 Copynumber: 2.5 Consensus size: 27
2597543 TAAGTTTTCA
* *
2597553 AAATGTTTTGAAAACTATATAATATAT
1 AAATATTTTCAAAACTATATAATATAT
*
2597580 AAATGTTTTCAAAACTATAT-AT-TAT
1 AAATATTTTCAAAACTATATAATATAT
*
2597605 ATATATTTTCAAAA
1 AAATATTTTCAAAA
2597619 TATTTTCAAA
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
25 15 0.42
26 2 0.06
27 19 0.53
ACGTcount: A:0.47, C:0.06, G:0.05, T:0.42
Consensus pattern (27 bp):
AAATATTTTCAAAACTATATAATATAT
Found at i:2597652 original size:37 final size:36
Alignment explanation
Indices: 2597580--2597655 Score: 89
Period size: 37 Copynumber: 2.1 Consensus size: 36
2597570 TATAATATAT
* * * * * *
2597580 AAATGTTTTCAAAACTATATATTATATATATTTTCA
1 AAATATTTTCAAAACCATATAATATACAAACTTTCA
2597616 AAATATTTTCAAAAACCATATAATATACAAACTTTCA
1 AAATATTTTC-AAAACCATATAATATACAAACTTTCA
2597653 AAA
1 AAA
2597656 ATCGTTTTCT
Statistics
Matches: 33, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
36 9 0.27
37 24 0.73
ACGTcount: A:0.49, C:0.12, G:0.01, T:0.38
Consensus pattern (36 bp):
AAATATTTTCAAAACCATATAATATACAAACTTTCA
Found at i:2597751 original size:15 final size:14
Alignment explanation
Indices: 2597731--2597762 Score: 55
Period size: 14 Copynumber: 2.2 Consensus size: 14
2597721 ACACATATAT
2597731 ATATATATAATAAAA
1 ATATATAT-ATAAAA
2597746 ATATATATATAAAA
1 ATATATATATAAAA
2597760 ATA
1 ATA
2597763 ACAAAATAAC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 9 0.53
15 8 0.47
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (14 bp):
ATATATATATAAAA
Found at i:2597763 original size:23 final size:23
Alignment explanation
Indices: 2597725--2597768 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
2597715 CTATATACAC
* * *
2597725 ATATATATATATATAATAAAAAT
1 ATATATATAAAAATAACAAAAAT
2597748 ATATATATAAAAATAACAAAA
1 ATATATATAAAAATAACAAAA
2597769 TAACTTCGGC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (23 bp):
ATATATATAAAAATAACAAAAAT
Found at i:2599330 original size:35 final size:35
Alignment explanation
Indices: 2599291--2599379 Score: 94
Period size: 34 Copynumber: 2.6 Consensus size: 35
2599281 AATGGTAATA
* * *
2599291 AACAAAACTAACCAAAATACATTAACAAA-AAGTCC
1 AACAAAATTAACCAAAATAAATTAA-AAATAAATCC
*
2599326 AACAAATTTAA-CAAAATAAATTAAAAATAAATCC
1 AACAAAATTAACCAAAATAAATTAAAAATAAATCC
* *
2599360 AACCAAATTAA-CGAAATAAA
1 AACAAAATTAACCAAAATAAA
2599380 GTAAGTATTA
Statistics
Matches: 46, Mismatches: 7, Indels: 3
0.82 0.12 0.05
Matches are distributed among these distances:
33 3 0.07
34 34 0.74
35 9 0.20
ACGTcount: A:0.63, C:0.17, G:0.02, T:0.18
Consensus pattern (35 bp):
AACAAAATTAACCAAAATAAATTAAAAATAAATCC
Found at i:2599341 original size:34 final size:34
Alignment explanation
Indices: 2599303--2599379 Score: 95
Period size: 34 Copynumber: 2.3 Consensus size: 34
2599293 CAAAACTAAC
* *
2599303 CAAAATACATTAACAAA-AAGTCCAA-CAAATTTAA
1 CAAAATAAATTAA-AAATAAATCCAACCAAA-TTAA
2599337 CAAAATAAATTAAAAATAAATCCAACCAAATTAA
1 CAAAATAAATTAAAAATAAATCCAACCAAATTAA
*
2599371 CGAAATAAA
1 CAAAATAAA
2599380 GTAAGTATTA
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
33 3 0.08
34 31 0.82
35 4 0.11
ACGTcount: A:0.62, C:0.16, G:0.03, T:0.19
Consensus pattern (34 bp):
CAAAATAAATTAAAAATAAATCCAACCAAATTAA
Found at i:2601682 original size:17 final size:19
Alignment explanation
Indices: 2601662--2601703 Score: 54
Period size: 17 Copynumber: 2.4 Consensus size: 19
2601652 ATTAATTAAA
2601662 TAAAATA-TTAAA-AAATT
1 TAAAATACTTAAATAAATT
2601679 T-AAATACTTAAATAAATT
1 TAAAATACTTAAATAAATT
*
2601697 AAAAATA
1 TAAAATA
2601704 AAATATTAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
16 5 0.24
17 6 0.29
18 5 0.24
19 5 0.24
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.33
Consensus pattern (19 bp):
TAAAATACTTAAATAAATT
Found at i:2601691 original size:24 final size:23
Alignment explanation
Indices: 2601647--2601724 Score: 56
Period size: 24 Copynumber: 3.3 Consensus size: 23
2601637 TATATCTGCA
*
2601647 AAAAAATTAATTAA-ATAAAATATT
1 AAAAAATTAA--AATATTAAATATT
*
2601671 AAAAAATTTAAATACTTAAATAAATT
1 AAAAAATTAAAATA-TTAAAT--ATT
2601697 -AAAAA-TAAAATATTAAATA-T
1 AAAAAATTAAAATATTAAATATT
2601717 AATAAAAT
1 AA-AAAAT
2601725 ATACCTTAAA
Statistics
Matches: 44, Mismatches: 3, Indels: 15
0.71 0.05 0.24
Matches are distributed among these distances:
20 1 0.02
21 2 0.05
22 6 0.14
23 7 0.16
24 20 0.45
25 5 0.11
26 3 0.07
ACGTcount: A:0.67, C:0.01, G:0.00, T:0.32
Consensus pattern (23 bp):
AAAAAATTAAAATATTAAATATT
Found at i:2604397 original size:35 final size:35
Alignment explanation
Indices: 2604347--2604485 Score: 179
Period size: 35 Copynumber: 3.9 Consensus size: 35
2604337 TGAATAAGAA
* **
2604347 GAACGGAAAGAAGCATTGGCACTTTCGATTCAAGT
1 GAACGGAAGGAAGCATCAGCACTTTCGATTCAAGT
* *
2604382 GAACAGAAGGAAGCATCAGCACTTTCGATTCAAGAA
1 GAACGGAAGGAAGCATCAGCACTTTCGATTCAAG-T
* * *
2604418 GAACGAAAGGAAGCATCGGCATTTTCGATTCAAGT
1 GAACGGAAGGAAGCATCAGCACTTTCGATTCAAGT
* *
2604453 GAACGGGAGGAAGCATAAGCACTTTCGATTCAA
1 GAACGGAAGGAAGCATCAGCACTTTCGATTCAA
2604486 TTGTTCATAT
Statistics
Matches: 88, Mismatches: 15, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
35 58 0.66
36 30 0.34
ACGTcount: A:0.37, C:0.18, G:0.25, T:0.20
Consensus pattern (35 bp):
GAACGGAAGGAAGCATCAGCACTTTCGATTCAAGT
Found at i:2604421 original size:71 final size:71
Alignment explanation
Indices: 2604342--2604485 Score: 227
Period size: 71 Copynumber: 2.0 Consensus size: 71
2604332 GAAGGTGAAT
* *
2604342 AAGAAGAACGGAAA-GAAGCATTGGCACTTTCGATTCAAGTGAACAGAAGGAAGCATCAGCACTT
1 AAGAAGAAC-GAAAGGAAGCATCGGCACTTTCGATTCAAGTGAACAGAAGGAAGCATAAGCACTT
2604406 TCGATTC
65 TCGATTC
* * *
2604413 AAGAAGAACGAAAGGAAGCATCGGCATTTTCGATTCAAGTGAACGGGAGGAAGCATAAGCACTTT
1 AAGAAGAACGAAAGGAAGCATCGGCACTTTCGATTCAAGTGAACAGAAGGAAGCATAAGCACTTT
2604478 CGATTC
66 CGATTC
2604484 AA
1 AA
2604486 TTGTTCATAT
Statistics
Matches: 67, Mismatches: 5, Indels: 2
0.91 0.07 0.03
Matches are distributed among these distances:
70 4 0.06
71 63 0.94
ACGTcount: A:0.38, C:0.17, G:0.25, T:0.19
Consensus pattern (71 bp):
AAGAAGAACGAAAGGAAGCATCGGCACTTTCGATTCAAGTGAACAGAAGGAAGCATAAGCACTTT
CGATTC
Found at i:2606190 original size:17 final size:18
Alignment explanation
Indices: 2606157--2606190 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
2606147 TTTACTGTCA
2606157 TTTTGTTGTCTTAATTTC
1 TTTTGTTGTCTTAATTTC
*
2606175 TTTTGTT-TCTTTATTT
1 TTTTGTTGTCTTAATTT
2606191 ATTGATTTGG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.09, C:0.09, G:0.09, T:0.74
Consensus pattern (18 bp):
TTTTGTTGTCTTAATTTC
Found at i:2607061 original size:22 final size:22
Alignment explanation
Indices: 2606999--2607057 Score: 59
Period size: 22 Copynumber: 2.7 Consensus size: 22
2606989 TTTACATTCT
2606999 TTTTTATTGAATTTTATT-CAC
1 TTTTTATTGAATTTTATTACAC
* ***
2607020 TTTTAATTCTTTTTTTATTACA-
1 TTTTTATT-GAATTTTATTACAC
2607042 TTTTTATTGAATTTTA
1 TTTTTATTGAATTTTA
2607058 ATTATATGAA
Statistics
Matches: 28, Mismatches: 8, Indels: 4
0.70 0.20 0.10
Matches are distributed among these distances:
21 12 0.43
22 14 0.50
23 2 0.07
ACGTcount: A:0.24, C:0.07, G:0.03, T:0.66
Consensus pattern (22 bp):
TTTTTATTGAATTTTATTACAC
Found at i:2608521 original size:4 final size:4
Alignment explanation
Indices: 2608512--2608750 Score: 451
Period size: 4 Copynumber: 59.8 Consensus size: 4
2608502 TGATCTTAGA
2608512 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
2608560 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
2608608 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
2608656 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
* * *
2608704 GTAT GTAT GTAT GTAT GTAT GTAC GTAC GTAC GTAT GTAT GTAT GTA
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTA
2608751 CGTACGTACG
Statistics
Matches: 233, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
4 233 1.00
ACGTcount: A:0.25, C:0.01, G:0.25, T:0.49
Consensus pattern (4 bp):
GTAT
Found at i:2608755 original size:4 final size:4
Alignment explanation
Indices: 2608724--2608770 Score: 67
Period size: 4 Copynumber: 11.8 Consensus size: 4
2608714 ATGTATGTAT
* * *
2608724 GTAC GTAC GTAC GTAT GTAT GTAT GTAC GTAC GTAC GTAC GTAC GTA
1 GTAC GTAC GTAC GTAC GTAC GTAC GTAC GTAC GTAC GTAC GTAC GTA
2608771 ATATGATGAC
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
4 41 1.00
ACGTcount: A:0.26, C:0.17, G:0.26, T:0.32
Consensus pattern (4 bp):
GTAC
Found at i:2609988 original size:20 final size:20
Alignment explanation
Indices: 2609963--2610003 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
2609953 TAGGGAGAGG
2609963 ATTGAAAGGTTAAGACCTTT
1 ATTGAAAGGTTAAGACCTTT
2609983 ATTGAAAGGTTAAGACCTTT
1 ATTGAAAGGTTAAGACCTTT
2610003 A
1 A
2610004 AATGAAATGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.37, C:0.10, G:0.20, T:0.34
Consensus pattern (20 bp):
ATTGAAAGGTTAAGACCTTT
Found at i:2615251 original size:20 final size:20
Alignment explanation
Indices: 2615226--2615266 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
2615216 CAGGGAGATG
2615226 ATTGAAAGGTTAAGACCTTT
1 ATTGAAAGGTTAAGACCTTT
2615246 ATTGAAAGGTTAAGACCTTT
1 ATTGAAAGGTTAAGACCTTT
2615266 A
1 A
2615267 AATGAAATGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.37, C:0.10, G:0.20, T:0.34
Consensus pattern (20 bp):
ATTGAAAGGTTAAGACCTTT
Found at i:2615385 original size:22 final size:23
Alignment explanation
Indices: 2615354--2615399 Score: 67
Period size: 22 Copynumber: 2.0 Consensus size: 23
2615344 GAGTGAAATG
2615354 AAATAATTAAGTA-TTTTCATGA
1 AAATAATTAAGTATTTTTCATGA
* *
2615376 AAATACTTAATTATTTTTCATGA
1 AAATAATTAAGTATTTTTCATGA
2615399 A
1 A
2615400 TAGTCATGAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 11 0.52
23 10 0.48
ACGTcount: A:0.43, C:0.07, G:0.07, T:0.43
Consensus pattern (23 bp):
AAATAATTAAGTATTTTTCATGA
Found at i:2618840 original size:6 final size:6
Alignment explanation
Indices: 2618829--2618867 Score: 53
Period size: 6 Copynumber: 6.7 Consensus size: 6
2618819 TTTAACATAG
* *
2618829 TATTAA TATTAA TATTAA TATTAA T-TTTA TTTTAA TATT
1 TATTAA TATTAA TATTAA TATTAA TATTAA TATTAA TATT
2618868 TTGATATAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
5 4 0.14
6 25 0.86
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (6 bp):
TATTAA
Found at i:2620099 original size:2 final size:2
Alignment explanation
Indices: 2620094--2620130 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
2620084 ATCTTAATTA
2620094 AT 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 AT A
2620131 AAGACATTTA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2624230 original size:111 final size:111
Alignment explanation
Indices: 2623896--2624318 Score: 645
Period size: 111 Copynumber: 3.8 Consensus size: 111
2623886 GGGAAGATTA
* *
2623896 AATCAGGGTAGACTTGTTCCGCTGTCACTCGGGGAATATCAAATCTT-AAAAGAGATGGATCTGT
1 AATCAGGGTAGACTTGTTCCGCTGTCACTCAGGGAATATCAAATCTTGAAAA-AGAGGGATCTGT
2623960 TCCGCTTCCTCTGAGGGAATATCAGATCTGGGAAAGTTGATTCATTG
65 TCCGCTTCCTCTGAGGGAATATCAGATCTGGGAAAGTTGATTCATTG
* * *
2624007 AATCAGGGTAGACTTGTTCTGCTGTCACTCAGGGAATATCAAATCTTG--AAAGAGAGATCTATT
1 AATCAGGGTAGACTTGTTCCGCTGTCACTCAGGGAATATCAAATCTTGAAAAAGAGGGATCTGTT
** * * *
2624070 CCGCTTTTTCTGAGGGAATATCATATATGGGAAAGTTGATTTATTG
66 CCGCTTCCTCTGAGGGAATATCAGATCTGGGAAAGTTGATTCATTG
*
2624116 AATCAGGGTAGACTTGTTCCGCTGTCACTCAGGAAATATCAAATCTTGAAAAAGAGGGATCTGTT
1 AATCAGGGTAGACTTGTTCCGCTGTCACTCAGGGAATATCAAATCTTGAAAAAGAGGGATCTGTT
*
2624181 TCGCTTCCTCTGAGGGAATATCAGATCTGGGAAAGTTGATTCATTG
66 CCGCTTCCTCTGAGGGAATATCAGATCTGGGAAAGTTGATTCATTG
* * *
2624227 AATCAGGGTAGACTTGTTCCGCTGTCACTCAGGGAATATCAAATCTTTAAAAAGAGTGATATGTT
1 AATCAGGGTAGACTTGTTCCGCTGTCACTCAGGGAATATCAAATCTTGAAAAAGAGGGATCTGTT
* * *
2624292 CCACTTCTTCTGAAGGGAATATTAGAT
66 CCGCTTCCTCTG-AGGGAATATCAGAT
2624319 AGATGGATTT
Statistics
Matches: 280, Mismatches: 28, Indels: 7
0.89 0.09 0.02
Matches are distributed among these distances:
109 97 0.35
110 2 0.01
111 168 0.60
112 13 0.05
ACGTcount: A:0.29, C:0.16, G:0.23, T:0.31
Consensus pattern (111 bp):
AATCAGGGTAGACTTGTTCCGCTGTCACTCAGGGAATATCAAATCTTGAAAAAGAGGGATCTGTT
CCGCTTCCTCTGAGGGAATATCAGATCTGGGAAAGTTGATTCATTG
Found at i:2624740 original size:17 final size:17
Alignment explanation
Indices: 2624718--2624756 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 17
2624708 TTGGACCCAC
2624718 CCTCTTCTTCAGGTTCA
1 CCTCTTCTTCAGGTTCA
* *
2624735 CCTCTTCTTTAGGTTTA
1 CCTCTTCTTCAGGTTCA
2624752 CCTCT
1 CCTCT
2624757 CTAAATACGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.10, C:0.33, G:0.10, T:0.46
Consensus pattern (17 bp):
CCTCTTCTTCAGGTTCA
Found at i:2634450 original size:4 final size:4
Alignment explanation
Indices: 2634441--2634465 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
2634431 TTTGCTTCGA
2634441 AAAT AAAT AAAT AAAT AAAT AAAT A
1 AAAT AAAT AAAT AAAT AAAT AAAT A
2634466 CATGCACAAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (4 bp):
AAAT
Found at i:2635039 original size:3 final size:3
Alignment explanation
Indices: 2635031--2635076 Score: 85
Period size: 3 Copynumber: 15.7 Consensus size: 3
2635021 AATAATTATT
2635031 TAA TAA TAA TAA TAA TAA TAA T-A TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
2635077 TTCAGGACGA
Statistics
Matches: 42, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 2 0.05
3 40 0.95
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:2635073 original size:23 final size:23
Alignment explanation
Indices: 2635021--2635077 Score: 96
Period size: 23 Copynumber: 2.5 Consensus size: 23
2635011 ACCTGTAAAA
* *
2635021 AATAATTATTTAATAATAATAAT
1 AATAATAATATAATAATAATAAT
2635044 AATAATAATATAATAATAATAAT
1 AATAATAATATAATAATAATAAT
2635067 AATAATAATAT
1 AATAATAATAT
2635078 TCAGGACGAA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (23 bp):
AATAATAATATAATAATAATAAT
Found at i:2637421 original size:38 final size:38
Alignment explanation
Indices: 2637378--2637455 Score: 156
Period size: 38 Copynumber: 2.1 Consensus size: 38
2637368 GTACAAAAAT
2637378 CAAGTCAAGCTCAACATGCTTGAACTTAGAATGCTGAA
1 CAAGTCAAGCTCAACATGCTTGAACTTAGAATGCTGAA
2637416 CAAGTCAAGCTCAACATGCTTGAACTTAGAATGCTGAA
1 CAAGTCAAGCTCAACATGCTTGAACTTAGAATGCTGAA
2637454 CA
1 CA
2637456 GGATTGGCAC
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 40 1.00
ACGTcount: A:0.37, C:0.22, G:0.18, T:0.23
Consensus pattern (38 bp):
CAAGTCAAGCTCAACATGCTTGAACTTAGAATGCTGAA
Found at i:2639603 original size:45 final size:45
Alignment explanation
Indices: 2639548--2639639 Score: 139
Period size: 45 Copynumber: 2.0 Consensus size: 45
2639538 GTTGAAGGAG
*
2639548 CATGCATGGGACCAAGGGCATTATCAACACGCATTGAAGAAGCAT
1 CATGCATGGGACCAAGAGCATTATCAACACGCATTGAAGAAGCAT
* * * *
2639593 CATGTATGGGACCATGAGCATTATCAACAGGCATTGAAGGAGCAT
1 CATGCATGGGACCAAGAGCATTATCAACACGCATTGAAGAAGCAT
2639638 CA
1 CA
2639640 CATGGGTTGT
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
45 42 1.00
ACGTcount: A:0.35, C:0.21, G:0.25, T:0.20
Consensus pattern (45 bp):
CATGCATGGGACCAAGAGCATTATCAACACGCATTGAAGAAGCAT
Found at i:2639693 original size:15 final size:15
Alignment explanation
Indices: 2639675--2639711 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
2639665 CATCGGTTGA
2639675 TGGAGCAGGTG-ATGG
1 TGGAGCAGGTGCA-GG
2639690 TGGAGCAGGTGCAGG
1 TGGAGCAGGTGCAGG
2639705 TGGAGCA
1 TGGAGCA
2639712 TGCTCTGGTG
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
15 20 0.95
16 1 0.05
ACGTcount: A:0.22, C:0.11, G:0.51, T:0.16
Consensus pattern (15 bp):
TGGAGCAGGTGCAGG
Found at i:2643677 original size:2 final size:2
Alignment explanation
Indices: 2643670--2643700 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
2643660 TTCAAAACTT
2643670 TA TA TA 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 TA TA TA T
2643701 TTCATATTGC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2644887 original size:41 final size:41
Alignment explanation
Indices: 2644830--2644908 Score: 140
Period size: 41 Copynumber: 1.9 Consensus size: 41
2644820 GTTTTTCGGC
2644830 CTTACTGCAATGAATCCATCTGTGAAAACCAAGATTTTGGG
1 CTTACTGCAATGAATCCATCTGTGAAAACCAAGATTTTGGG
* *
2644871 CTTACTGCAATGAATCCATCTGTGAGAATCAAGATTTT
1 CTTACTGCAATGAATCCATCTGTGAAAACCAAGATTTT
2644909 AGAGCAGATC
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 36 1.00
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.32
Consensus pattern (41 bp):
CTTACTGCAATGAATCCATCTGTGAAAACCAAGATTTTGGG
Found at i:2649562 original size:20 final size:20
Alignment explanation
Indices: 2649527--2649578 Score: 61
Period size: 20 Copynumber: 2.6 Consensus size: 20
2649517 GATTCAATCA
* *
2649527 GTATCGATATCAAAGGG-GG
1 GTATCGATACCAAAGGGAAG
*
2649546 TGTATCGATACCGAAGGGAAG
1 -GTATCGATACCAAAGGGAAG
2649567 GTATCGATACCA
1 GTATCGATACCA
2649579 TTTCAAAACA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
20 26 0.96
21 1 0.04
ACGTcount: A:0.33, C:0.15, G:0.31, T:0.21
Consensus pattern (20 bp):
GTATCGATACCAAAGGGAAG
Found at i:2650188 original size:47 final size:47
Alignment explanation
Indices: 2650063--2650301 Score: 356
Period size: 47 Copynumber: 5.1 Consensus size: 47
2650053 TAAATCGAAT
*
2650063 CCATAAACTAAAATGCATGAAATGATGCATTAAGGCATGAAAGGATG
1 CCATAAACTAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATG
* ** * * *
2650110 CCAT-AATTAAAATGCATGAAAATATGGATTAAGGTATAAAAGGATG
1 CCATAAACTAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATG
* *
2650156 TCATAAACTAAAATGCACGAAAGGATGCATTAAGGCATGAAAGGATG
1 CCATAAACTAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATG
* * *
2650203 TCAT-AATTAAAATGCATGAAATGATGCATTAAGGCATGAAAGGATG
1 CCATAAACTAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATG
2650249 CCATAAACTAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATG
1 CCATAAACTAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATG
2650296 CCATAA
1 CCATAA
2650302 TTTAAATATA
Statistics
Matches: 170, Mismatches: 20, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
46 81 0.48
47 89 0.52
ACGTcount: A:0.45, C:0.11, G:0.21, T:0.22
Consensus pattern (47 bp):
CCATAAACTAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATG
Found at i:2650199 original size:20 final size:20
Alignment explanation
Indices: 2650174--2650296 Score: 102
Period size: 20 Copynumber: 5.5 Consensus size: 20
2650164 TAAAATGCAC
2650174 GAAAGGATGCATTAAGGCAT
1 GAAAGGATGCATTAAGGCAT
*
2650194 GAAAGGATGTCATAATTAAAATGCAT
1 GAAAGGATG-C---ATT--AAGGCAT
*
2650220 GAAATGATGCATTAAGGCAT
1 GAAAGGATGCATTAAGGCAT
*
2650240 GAAAGGATGCCATAAACTAAAATGCAT
1 GAAAGGATG-CAT----T--AAGGCAT
2650267 GAAAGGATGCATTAAGGCAT
1 GAAAGGATGCATTAAGGCAT
2650287 GAAAGGATGC
1 GAAAGGATGC
2650297 CATAATTTAA
Statistics
Matches: 84, Mismatches: 6, Indels: 26
0.72 0.05 0.22
Matches are distributed among these distances:
20 39 0.46
21 4 0.05
22 4 0.05
24 3 0.04
25 2 0.02
26 17 0.20
27 15 0.18
ACGTcount: A:0.43, C:0.11, G:0.25, T:0.21
Consensus pattern (20 bp):
GAAAGGATGCATTAAGGCAT
Found at i:2650223 original size:93 final size:93
Alignment explanation
Indices: 2650063--2650308 Score: 404
Period size: 93 Copynumber: 2.6 Consensus size: 93
2650053 TAAATCGAAT
*
2650063 CCATAAACTAAAATGCATGAAATGATGCATTAAGGCATGAAAGGATGCCATAATTAAAATGCATG
1 CCATAAACTAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGCCATAATTAAAATGCATG
* *
2650128 AAAAT-ATGGATTAAGGTATAAAAGGATG
66 -AAATGATGCATTAAGGCATAAAAGGATG
* * *
2650156 TCATAAACTAAAATGCACGAAAGGATGCATTAAGGCATGAAAGGATGTCATAATTAAAATGCATG
1 CCATAAACTAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGCCATAATTAAAATGCATG
*
2650221 AAATGATGCATTAAGGCATGAAAGGATG
66 AAATGATGCATTAAGGCATAAAAGGATG
*
2650249 CCATAAACTAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGCCATAATTTAAAT
1 CCATAAACTAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGCCATAATTAAAAT
2650309 ATATATAAAT
Statistics
Matches: 141, Mismatches: 11, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
92 4 0.03
93 137 0.97
ACGTcount: A:0.45, C:0.11, G:0.21, T:0.23
Consensus pattern (93 bp):
CCATAAACTAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGCCATAATTAAAATGCATG
AAATGATGCATTAAGGCATAAAAGGATG
Found at i:2656496 original size:20 final size:20
Alignment explanation
Indices: 2656468--2656519 Score: 59
Period size: 20 Copynumber: 2.6 Consensus size: 20
2656458 GATTCAATCA
* * * *
2656468 GTATCGATACCAAAGGGGAT
1 GTATTGATACCAAAGAGAAG
*
2656488 GTATTGATACCGAAGAGAAG
1 GTATTGATACCAAAGAGAAG
2656508 GTATTGATACCA
1 GTATTGATACCA
2656520 TTTCAAAACA
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.37, C:0.13, G:0.27, T:0.23
Consensus pattern (20 bp):
GTATTGATACCAAAGAGAAG
Found at i:2656567 original size:19 final size:21
Alignment explanation
Indices: 2656543--2656596 Score: 67
Period size: 19 Copynumber: 2.6 Consensus size: 21
2656533 TGTAAAAATT
2656543 GTATCGATACCATAATA-GG-
1 GTATCGATACCATAATATGGA
* *
2656562 GTATCGGTACCATAGTATGGTA
1 GTATCGATACCATAATATGG-A
2656584 GTATCGATACCAT
1 GTATCGATACCAT
2656597 GGTAGGGGTA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
19 15 0.52
20 2 0.07
22 12 0.41
ACGTcount: A:0.31, C:0.17, G:0.22, T:0.30
Consensus pattern (21 bp):
GTATCGATACCATAATATGGA
Found at i:2656718 original size:22 final size:22
Alignment explanation
Indices: 2656693--2656738 Score: 92
Period size: 22 Copynumber: 2.1 Consensus size: 22
2656683 AAGTAATGTT
2656693 TAAGTGTAATTGTTAGGAGATA
1 TAAGTGTAATTGTTAGGAGATA
2656715 TAAGTGTAATTGTTAGGAGATA
1 TAAGTGTAATTGTTAGGAGATA
2656737 TA
1 TA
2656739 CTAACAATTG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.37, C:0.00, G:0.26, T:0.37
Consensus pattern (22 bp):
TAAGTGTAATTGTTAGGAGATA
Found at i:2656747 original size:22 final size:22
Alignment explanation
Indices: 2656700--2656748 Score: 55
Period size: 22 Copynumber: 2.2 Consensus size: 22
2656690 GTTTAAGTGT
* **
2656700 AATTGTTAGGAGATATAAGTGT
1 AATTGTTAGGAGATATAACTAC
2656722 AATTGTTAGGAGATAT-ACTAAC
1 AATTGTTAGGAGATATAACT-AC
2656744 AATTG
1 AATTG
2656749 ACATTAAACA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
21 2 0.09
22 21 0.91
ACGTcount: A:0.39, C:0.04, G:0.22, T:0.35
Consensus pattern (22 bp):
AATTGTTAGGAGATATAACTAC
Found at i:2657157 original size:47 final size:47
Alignment explanation
Indices: 2657029--2657318 Score: 433
Period size: 47 Copynumber: 6.2 Consensus size: 47
2657019 GCTCTAAATC
* *
2657029 GGAT-CCATAAACTAAAATGCATGAAATGATGCATCAAGGCATGAAA
1 GGATGCCATAAACTAAAATGCATGAAAGGATGCATTAAGGCATGAAA
* * *
2657075 GGATGCCAT-AATTAAAATGCATGAAAGGATACATTAAGGCATAAAA
1 GGATGCCATAAACTAAAATGCATGAAAGGATGCATTAAGGCATGAAA
* *
2657121 GGATGTCATAAACTAAAATGCATGAAAGGATGCATTAATGCATGAAA
1 GGATGCCATAAACTAAAATGCATGAAAGGATGCATTAAGGCATGAAA
* * * * *
2657168 GGATGTCAT-AATTAAAATGCAAGAAATGATGCATTAATGCATGAAA
1 GGATGCCATAAACTAAAATGCATGAAAGGATGCATTAAGGCATGAAA
*
2657214 GGATGCCATAAACTAAAATGCATGAAATGATGCATTAAGGCATGAAA
1 GGATGCCATAAACTAAAATGCATGAAAGGATGCATTAAGGCATGAAA
2657261 GGATGCCATAAACTAAAATGCATGAAAGGATGCATTAAGGCATGAAA
1 GGATGCCATAAACTAAAATGCATGAAAGGATGCATTAAGGCATGAAA
*
2657308 GGATGTCATAA
1 GGATGCCATAA
2657319 TTTAAATATA
Statistics
Matches: 222, Mismatches: 19, Indels: 5
0.90 0.08 0.02
Matches are distributed among these distances:
46 86 0.39
47 136 0.61
ACGTcount: A:0.45, C:0.12, G:0.21, T:0.22
Consensus pattern (47 bp):
GGATGCCATAAACTAAAATGCATGAAAGGATGCATTAAGGCATGAAA
Found at i:2657203 original size:93 final size:93
Alignment explanation
Indices: 2657034--2657318 Score: 462
Period size: 93 Copynumber: 3.1 Consensus size: 93
2657024 AAATCGGATC
*
2657034 CATAAACTAAAATGCATGAAATGATGCATCAAGGCATGAAAGGATGCCATAATTAAAATGCATGA
1 CATAAACTAAAATGCATGAAATGATGCATTAAGGCATGAAAGGATGCCATAATTAAAATGCATGA
* *
2657099 AAGGATACATTAAGGCATAAAAGGATGT
66 AAGGATGCATTAAGGCATGAAAGGATGT
* * * *
2657127 CATAAACTAAAATGCATGAAAGGATGCATTAATGCATGAAAGGATGTCATAATTAAAATGCAAGA
1 CATAAACTAAAATGCATGAAATGATGCATTAAGGCATGAAAGGATGCCATAATTAAAATGCATGA
* * *
2657192 AATGATGCATTAATGCATGAAAGGATGC
66 AAGGATGCATTAAGGCATGAAAGGATGT
*
2657220 CATAAACTAAAATGCATGAAATGATGCATTAAGGCATGAAAGGATGCCATAAACTAAAATGCATG
1 CATAAACTAAAATGCATGAAATGATGCATTAAGGCATGAAAGGATGCCAT-AATTAAAATGCATG
2657285 AAAGGATGCATTAAGGCATGAAAGGATGT
65 AAAGGATGCATTAAGGCATGAAAGGATGT
2657314 CATAA
1 CATAA
2657319 TTTAAATATA
Statistics
Matches: 173, Mismatches: 18, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
93 130 0.75
94 43 0.25
ACGTcount: A:0.46, C:0.12, G:0.21, T:0.22
Consensus pattern (93 bp):
CATAAACTAAAATGCATGAAATGATGCATTAAGGCATGAAAGGATGCCATAATTAAAATGCATGA
AAGGATGCATTAAGGCATGAAAGGATGT
Found at i:2657286 original size:140 final size:139
Alignment explanation
Indices: 2657041--2657325 Score: 471
Period size: 140 Copynumber: 2.0 Consensus size: 139
2657031 ATCCATAAAC
* *
2657041 TAAAATGCATGAAATGATGCATCAAGGCATGAAAGGATGCCATAATTAAAATGCATGAAAGGATA
1 TAAAATGCAAGAAATGATGCATCAAGGCATGAAAGGATGCCATAACTAAAATGCATGAAAGGATA
* *
2657106 CATTAAGGCATAAAAGGATGTCATAAACTAAAATGCATGAAAGGATGCATTAATGCATGAAAGGA
66 CATTAAGGCATAAAAGGATGCCATAAACTAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGA
2657171 TGTCATAAT
131 TGTCATAAT
* * *
2657180 TAAAATGCAAGAAATGATGCATTAATGCATGAAAGGATGCCATAAACTAAAATGCATGAAATGAT
1 TAAAATGCAAGAAATGATGCATCAAGGCATGAAAGGATGCCAT-AACTAAAATGCATGAAAGGAT
* *
2657245 GCATTAAGGCATGAAAGGATGCCATAAACTAAAATGCATGAAAGGATGCATTAAGGCATGAAAGG
65 ACATTAAGGCATAAAAGGATGCCATAAACTAAAATGCATGAAAGGATGCATTAAGGCATGAAAGG
2657310 ATGTCATAAT
130 ATGTCATAAT
*
2657320 TTAAAT
1 TAAAAT
2657326 ATATATAAAC
Statistics
Matches: 135, Mismatches: 10, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
139 40 0.30
140 95 0.70
ACGTcount: A:0.45, C:0.11, G:0.21, T:0.23
Consensus pattern (139 bp):
TAAAATGCAAGAAATGATGCATCAAGGCATGAAAGGATGCCATAACTAAAATGCATGAAAGGATA
CATTAAGGCATAAAAGGATGCCATAAACTAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGA
TGTCATAAT
Found at i:2657620 original size:21 final size:21
Alignment explanation
Indices: 2657594--2657641 Score: 87
Period size: 21 Copynumber: 2.3 Consensus size: 21
2657584 TCACGCGTAG
2657594 GTAAAAGCAAAGATTAACTAA
1 GTAAAAGCAAAGATTAACTAA
*
2657615 GTAAAAGCAAAGATTAACTGA
1 GTAAAAGCAAAGATTAACTAA
2657636 GTAAAA
1 GTAAAA
2657642 AGTGTTTTTG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.56, C:0.08, G:0.17, T:0.19
Consensus pattern (21 bp):
GTAAAAGCAAAGATTAACTAA
Found at i:2670703 original size:80 final size:81
Alignment explanation
Indices: 2670601--2670762 Score: 317
Period size: 80 Copynumber: 2.0 Consensus size: 81
2670591 ATGCAAATCA
2670601 CGAGATCTACAGTTTGTAAATTCATAAAAAAGGAGATAATTTGTCGGTATGGATTGCCAGAAAGA
1 CGAGATCTACAGTTTGTAAATTCATAAAAAAGGAGATAATTTGTCGGTATGGATTGCCAGAAAGA
2670666 A-TGTCACAGATAATG
66 ATTGTCACAGATAATG
2670681 CGAGATCTACAGTTTGTAAATTCATAAAAAAGGAGATAATTTGTCGGTATGGATTGCCAGAAAGA
1 CGAGATCTACAGTTTGTAAATTCATAAAAAAGGAGATAATTTGTCGGTATGGATTGCCAGAAAGA
2670746 ATTGTCACAGATAATG
66 ATTGTCACAGATAATG
2670762 C
1 C
2670763 CACTAATTTG
Statistics
Matches: 81, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
80 66 0.81
81 15 0.19
ACGTcount: A:0.38, C:0.12, G:0.22, T:0.28
Consensus pattern (81 bp):
CGAGATCTACAGTTTGTAAATTCATAAAAAAGGAGATAATTTGTCGGTATGGATTGCCAGAAAGA
ATTGTCACAGATAATG
Found at i:2671150 original size:8 final size:8
Alignment explanation
Indices: 2671130--2671197 Score: 50
Period size: 8 Copynumber: 8.0 Consensus size: 8
2671120 AAAAGAGAAC
2671130 AAAT-AAA
1 AAATGAAA
*
2671137 AGATGAAA
1 AAATGAAA
2671145 AAATGAAAAA
1 AAATG--AAA
*
2671155 AAAAGAAAA
1 AAATG-AAA
2671164 AAATG-AA
1 AAATGAAA
2671171 AAATGAAAAA
1 AAATG--AAA
2671181 GAAATGAAA
1 -AAATGAAA
2671190 AAATGAAA
1 AAATGAAA
2671198 GAGAAAAAGG
Statistics
Matches: 50, Mismatches: 4, Indels: 13
0.75 0.06 0.19
Matches are distributed among these distances:
7 10 0.20
8 15 0.30
9 11 0.22
10 9 0.18
11 5 0.10
ACGTcount: A:0.76, C:0.00, G:0.13, T:0.10
Consensus pattern (8 bp):
AAATGAAA
Found at i:2671162 original size:18 final size:18
Alignment explanation
Indices: 2671141--2671192 Score: 61
Period size: 18 Copynumber: 2.8 Consensus size: 18
2671131 AATAAAAGAT
2671141 GAAAAAATGAAAAAAAAA
1 GAAAAAATGAAAAAAAAA
*
2671159 GAAAAAAATGAAAAATGAAA
1 G-AAAAAATGAAAAA-AAAA
*
2671179 -AAGAAATGAAAAAA
1 GAAAAAATGAAAAAA
2671193 TGAAAGAGAA
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
18 13 0.45
19 13 0.45
20 3 0.10
ACGTcount: A:0.79, C:0.00, G:0.13, T:0.08
Consensus pattern (18 bp):
GAAAAAATGAAAAAAAAA
Found at i:2671163 original size:26 final size:28
Alignment explanation
Indices: 2671134--2671197 Score: 89
Period size: 26 Copynumber: 2.4 Consensus size: 28
2671124 GAGAACAAAT
*
2671134 AAAAGATGAAAAAATGAAAAA-AAAAGA
1 AAAAAATGAAAAAATGAAAAAGAAAAGA
*
2671161 AAAAAATG-AAAAATGAAAAAGAAATG-
1 AAAAAATGAAAAAATGAAAAAGAAAAGA
2671187 AAAAAATGAAA
1 AAAAAATGAAA
2671198 GAGAAAAAGG
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
26 20 0.61
27 13 0.39
ACGTcount: A:0.77, C:0.00, G:0.14, T:0.09
Consensus pattern (28 bp):
AAAAAATGAAAAAATGAAAAAGAAAAGA
Found at i:2671193 original size:19 final size:19
Alignment explanation
Indices: 2671145--2671203 Score: 68
Period size: 19 Copynumber: 3.2 Consensus size: 19
2671135 AAAGATGAAA
* *
2671145 AAATGAAAAAA-AAAGAAAA
1 AAATGAAAAAATGAA-AAAG
2671164 AAATG-AAAAATGAAAAAG
1 AAATGAAAAAATGAAAAAG
*
2671182 AAATGAAAAAATGAAAGAG
1 AAATGAAAAAATGAAAAAG
2671201 AAA
1 AAA
2671204 AAGGAGGGTT
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
18 13 0.37
19 22 0.63
ACGTcount: A:0.76, C:0.00, G:0.15, T:0.08
Consensus pattern (19 bp):
AAATGAAAAAATGAAAAAG
Found at i:2671205 original size:26 final size:26
Alignment explanation
Indices: 2671134--2671205 Score: 85
Period size: 26 Copynumber: 2.8 Consensus size: 26
2671124 GAGAACAAAT
*
2671134 AAAAGATGAAAAAATGAAAAAAAAAGA
1 AAAAAATGA-AAAATGAAAAAAAAAGA
*
2671161 AAAAAATGAAAAATGAAAAAGAAATG-
1 AAAAAATGAAAAATGAAAAA-AAAAGA
*
2671187 AAAAAATGAAAGA-GAAAAA
1 AAAAAATGAAAAATGAAAAA
2671206 GGAGGGTTTG
Statistics
Matches: 41, Mismatches: 3, Indels: 4
0.85 0.06 0.08
Matches are distributed among these distances:
25 6 0.15
26 23 0.56
27 12 0.29
ACGTcount: A:0.76, C:0.00, G:0.15, T:0.08
Consensus pattern (26 bp):
AAAAAATGAAAAATGAAAAAAAAAGA
Found at i:2672748 original size:115 final size:110
Alignment explanation
Indices: 2672517--2672802 Score: 381
Period size: 115 Copynumber: 2.6 Consensus size: 110
2672507 CATTTCTATT
*
2672517 AAGAGTTCATAATGAGAAGAACTCGTCCTAAAGG-G-A-AAGTTCATAATGAGAAGAACTTGTT-
1 AAGAGTTCATAATGAGAAGAACTCATCC-AAAGGAGAAGAAGTTCATAATGAGAAGAACTTGTTC
2672578 --CCTTTCAAGTCCCATCACAGAAAGATGGATCAACATTTTCAGTG
65 AACCTTTCAAGTCCCATCACAGAAAGATGGATCAACATTTTCAGTG
2672622 AAGAGTTCATAATGAGAAGAACTCATCCAAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTC
1 AAGAGTTCATAATGAGAAGAACTCATCCAAAGG-AGAAGAAGTTCATAATGAGAAGAACTTGTTC
** ** *
2672687 AACCTTGGT-TTGATTTCATCACAGAAGGAGGTGGATCAACATTTTCAGTG
65 AACCTT--TCAAG-TCCCATCACAGAA--AGATGGATCAACATTTTCAGTG
*
2672737 AAGAGTTCATAATGAGAAGAACTCATCCAACAAGAGAAGAAGTTCATAATGAGAA-AACTTGTTC
1 AAGAGTTCATAATGAGAAGAACTCATCCAA-AGGAGAAGAAGTTCATAATGAGAAGAACTTGTTC
2672801 AA
65 AA
2672803 TCCAACGCTT
Statistics
Matches: 161, Mismatches: 7, Indels: 17
0.87 0.04 0.09
Matches are distributed among these distances:
104 5 0.03
105 27 0.17
106 1 0.01
107 1 0.01
108 25 0.16
111 4 0.02
112 1 0.01
113 12 0.07
114 11 0.07
115 72 0.45
116 2 0.01
ACGTcount: A:0.40, C:0.15, G:0.21, T:0.25
Consensus pattern (110 bp):
AAGAGTTCATAATGAGAAGAACTCATCCAAAGGAGAAGAAGTTCATAATGAGAAGAACTTGTTCA
ACCTTTCAAGTCCCATCACAGAAAGATGGATCAACATTTTCAGTG
Found at i:2673533 original size:221 final size:219
Alignment explanation
Indices: 2673150--2673570 Score: 792
Period size: 221 Copynumber: 1.9 Consensus size: 219
2673140 ATGGAAGGCT
2673150 AAAAAAAATTGTTAGTGGAAGTTATAGACCCACGCAACTACATTCTACCTAAACCATCACCAAAG
1 AAAAAAAATTGTTAGTGGAAGTTATAGACCCACGCAACTACATTCTACCTAAACCATCACCAAAG
2673215 TCAGCAAATCCAACAAATCTCACCTAACCCATCAACATCTTACCAAAACGTAAGAAAAAAGGAAA
66 TCAGCAAATCCAACAAATCTCACCTAACCCATCAACATCTTACCAAAACGTAAGAAAAAAGGAAA
2673280 GGAAACAAGGGGATTCGGTGAGGATGGAAACCAT-AAAGGAGGAGAGAAAAAGAGAGGGAGGGAA
131 GGAAACAAGGGGATTCGGTGAGGATGGAAACCATAAAAGGA-G-GAGAAAAA-AGAGGGAGGGAA
2673344 GAAAAACACATTGAAAAAAGATCGGAG
193 GAAAAACACATTGAAAAAAGATCGGAG
2673371 AAAAAAAATTGTTAGTGGAAGTTATAGACCCACGCAACTACATTCTACCTAAACCATCACCAAAG
1 AAAAAAAATTGTTAGTGGAAGTTATAGACCCACGCAACTACATTCTACCTAAACCATCACCAAAG
2673436 TCAGCAAATCCAACAAATCTCACCTAACCCATCAACATCTTACCAAAACGTAAGAAAAAAAGGAA
66 TCAGCAAATCCAACAAATCTCACCTAACCCATCAACATCTTACCAAAACGTAAG-AAAAAAGGAA
2673501 AGG-AACAAGGGGATTCGGTGAGGATGGAAACCATAAAAGGAGGAGAAAAAAGAGGGAGGGAAGA
130 AGGAAACAAGGGGATTCGGTGAGGATGGAAACCATAAAAGGAGGAGAAAAAAGAGGGAGGGAAGA
2673565 AAAACA
195 AAAACA
2673571 GGGGAATTGA
Statistics
Matches: 198, Mismatches: 0, Indels: 6
0.97 0.00 0.03
Matches are distributed among these distances:
219 20 0.10
220 8 0.04
221 151 0.76
222 19 0.10
ACGTcount: A:0.47, C:0.19, G:0.20, T:0.14
Consensus pattern (219 bp):
AAAAAAAATTGTTAGTGGAAGTTATAGACCCACGCAACTACATTCTACCTAAACCATCACCAAAG
TCAGCAAATCCAACAAATCTCACCTAACCCATCAACATCTTACCAAAACGTAAGAAAAAAGGAAA
GGAAACAAGGGGATTCGGTGAGGATGGAAACCATAAAAGGAGGAGAAAAAAGAGGGAGGGAAGAA
AAACACATTGAAAAAAGATCGGAG
Found at i:2677573 original size:149 final size:143
Alignment explanation
Indices: 2677384--2677778 Score: 422
Period size: 149 Copynumber: 2.6 Consensus size: 143
2677374 ACACAAAAAT
* * *
2677384 CTTGTCAAGGTTTGTTGATTCATTATATATGCCATTGATTCTTGTTGCTGAATATTATGTTGTTT
1 CTTGTGAAGGTTTGTTGAATCA-TATATATGCCATTGATTCTTGTTGCTGAATATTATGTTCTTT
*
2677449 CGGGTTTTAGTCAATATTCGATGAATCCGCAAAG-TTTTAGGCTAACATAAGCGCACATAGACCC
65 CGGGTTTTAGTCAATATTCGATGAATCCGCAAAGTTTTTAGGCTAACATAAGCACACATAG-CCC
2677513 ACGTCAATAGTCATAGCAGAG
129 -CG-C----GTCATAGCAGAG
2677534 CTTGTGAAGGTTTGTTGAATCATATATATGCCATTGATTCTTGTTGCTGAATATTATGTTCTTTC
1 CTTGTGAAGGTTTGTTGAATCATATATATGCCATTGATTCTTGTTGCTGAATATTATGTTCTTTC
*
2677599 GGGTCATAGTAGATATTGTTGGTGAATA-TCTG-TGAATCCGCAAAGTTTTTAGGCTAACATAAG
66 GGGT--T--T---TA------GTCAATATTC-GATGAATCCGCAAAGTTTTTAGGCTAACATAAG
*
2677662 CACACATAGGCCCGCGTCATAGCAGAG
117 CACACATAGCCCCGCGTCATAGCAGAG
* * *
2677689 CTTCTGAAGG-TTGTTGAATCATATGTATTCCATTGATTCTTGTTGCTG-ATATTATGTTCTTTC
1 CTTGTGAAGGTTTGTTGAATCATATATATGCCATTGATTCTTGTTGCTGAATATTATGTTCTTTC
* ** *
2677752 CGGTCATAGTCGATATTGTCGATGAAT
66 GGGTTTTAGTCAATA-T-TCGATGAAT
2677779 ATCTGTGAAT
Statistics
Matches: 212, Mismatches: 14, Indels: 45
0.78 0.05 0.17
Matches are distributed among these distances:
140 5 0.02
142 1 0.00
143 7 0.03
146 2 0.01
149 46 0.22
150 20 0.09
151 1 0.00
153 19 0.09
154 36 0.17
155 21 0.10
156 2 0.01
159 1 0.00
160 2 0.01
161 17 0.08
162 32 0.15
ACGTcount: A:0.26, C:0.16, G:0.21, T:0.38
Consensus pattern (143 bp):
CTTGTGAAGGTTTGTTGAATCATATATATGCCATTGATTCTTGTTGCTGAATATTATGTTCTTTC
GGGTTTTAGTCAATATTCGATGAATCCGCAAAGTTTTTAGGCTAACATAAGCACACATAGCCCCG
CGTCATAGCAGAG
Found at i:2677778 original size:153 final size:155
Alignment explanation
Indices: 2677470--2677935 Score: 534
Period size: 153 Copynumber: 3.0 Consensus size: 155
2677460 CAATATTCGA
*
2677470 TGAATCCGCAAAG-TTTTAGGCTAACATAAGCGCACATAGACCCACGTCAATAGTCATAGCAGAG
1 TGAATCCGCAAAGTTTTTAGGCTAACATAAGCGCACATAG-GCC-CG-C----GTCATAGCAGAG
2677534 CTTGTGAAGGTTTGTTGAATCATATATATGCCATTGATTCTTGTTGCTGAATATTATGTTCTTTC
59 CTTGTGAAGGTTTGTTGAATCATATATATGCCATTGATTCTTGTTGCTGAATATTATGTTCTTTC
* * * *
2677599 GGGTCATAGTAGATATTGTTGGTGAATATCTG
124 CGGTCATAGTCGATATTGTCGATGAATATCTG
* *
2677631 TGAATCCGCAAAGTTTTTAGGCTAACATAAGCACACATAGGCCCGCGTCATAGCAGAGCTTCTGA
1 TGAATCCGCAAAGTTTTTAGGCTAACATAAGCGCACATAGGCCCGCGTCATAGCAGAGCTTGTGA
* *
2677696 AGG-TTGTTGAATCATATGTATTCCATTGATTCTTGTTGCTG-ATATTATGTTCTTTCCGGTCAT
66 AGGTTTGTTGAATCATATATATGCCATTGATTCTTGTTGCTGAATATTATGTTCTTTCCGGTCAT
2677759 AGTCGATATTGTCGATGAATATCTG
131 AGTCGATATTGTCGATGAATATCTG
* * * * * * * * ** * * *
2677784 TGAATCTGCAGAGTTTCT-GGAT-A-TTAAGTGGAAATAGGCTTGTGT-TTGGCAGAGCTTGTGA
1 TGAATCCGCAAAGTTTTTAGGCTAACATAAGCGCACATAGGCCCGCGTCATAGCAGAGCTTGTGA
* * * *
2677845 AGGTTTGTTGAATCATTACATATGCCATTGATTCTTGTGGCTGAATTTTATGTTC-TTCCGGGCT
66 AGGTTTGTTGAATCA-TATATATGCCATTGATTCTTGTTGCTGAATATTATGTTCTTTCCGGTC-
*
2677909 ATAGTCAATGTATTGTCGATGAATATC
129 ATAGTCGA--TATTGTCGATGAATATC
2677936 CTAGAATCTG
Statistics
Matches: 267, Mismatches: 31, Indels: 21
0.84 0.10 0.07
Matches are distributed among these distances:
149 16 0.06
150 25 0.09
151 31 0.12
152 20 0.07
153 58 0.22
154 53 0.20
155 21 0.08
159 1 0.00
160 2 0.01
161 15 0.06
162 25 0.09
ACGTcount: A:0.26, C:0.15, G:0.23, T:0.36
Consensus pattern (155 bp):
TGAATCCGCAAAGTTTTTAGGCTAACATAAGCGCACATAGGCCCGCGTCATAGCAGAGCTTGTGA
AGGTTTGTTGAATCATATATATGCCATTGATTCTTGTTGCTGAATATTATGTTCTTTCCGGTCAT
AGTCGATATTGTCGATGAATATCTG
Found at i:2678001 original size:151 final size:154
Alignment explanation
Indices: 2677526--2678086 Score: 436
Period size: 154 Copynumber: 3.7 Consensus size: 154
2677516 TCAATAGTCA
* *
2677526 TAGCAGAGCTTGTGAAGG-TTTGTTGAATCA-TATATATGCCATTGATTCTTGTTGCTGAATATT
1 TAGCAGAACTTGTGAAGGTTTTGTTGAATCATTATATATGCCATTGATTCTTGTTGCTGAATTTT
* * * * * * * *
2677589 ATGTTCTTTCGGG-TCATAGTAGA-TATTGTTGGTGAATAT-CTGTGAATCCGCAAAGTTTTTAG
66 ATGTTCTTCCGGGCT-ATAGTCGATTATTGTCGATGAATATCCTGAGAATCTGCAGAG-TTTCAG
* * ** * *
2677651 GCTA-ACATAAGCA-CACATAGGCCCGCGTCA
129 G--AGA-TTAAG-AGGA-ATAGGCTTGTGT-T
* * * * *
2677681 TAGCAGAGCTTCTGAAGG--TTGTTGAATCA-TATGTATTCCATTGATTCTTGTTGCTG-ATATT
1 TAGCAGAACTTGTGAAGGTTTTGTTGAATCATTATATATGCCATTGATTCTTGTTGCTGAATTTT
* * *
2677742 ATGTTCTTTCCGGTC-ATAGTCGA-TATTGTCGATGAATAT-CTGTGAATCTGCAGAGTTTCTGG
66 ATGTTC-TTCCGGGCTATAGTCGATTATTGTCGATGAATATCCTGAGAATCTGCAGAGTTTCAGG
* *
2677804 ATATTAAGTGGAAATAGGCTTGTGTT
130 AGATTAAGAGG-AATAGGCTTGTGTT
* * * *
2677830 TGGCAGAGCTTGTGAAGG-TTTGTTGAATCATTACATATGCCATTGATTCTTGTGGCTGAATTTT
1 TAGCAGAACTTGTGAAGGTTTTGTTGAATCATTATATATGCCATTGATTCTTGTTGCTGAATTTT
* *
2677894 ATGTTCTTCCGGGCTATAGTCAATGTATTGTCGATGAATATCCT-AGAATCTGGA-AGTTT-AGG
66 ATGTTCTTCCGGGCTATAGTCGAT-TATTGTCGATGAATATCCTGAGAATCTGCAGAGTTTCAGG
2677956 TAGATTAAGAGG-A-A-G-TTGTGTCT
130 -AGATTAAGAGGAATAGGCTTGTGT-T
*
2677979 TAGCAGAACTTGTGAAGGGGTTTTTTTTGGAATCATTATATATGCCATTGA---TTGTTGCTGAA
1 TAGCAGAACTTGTGAA--GG-TTTTGTT-GAATCATTATATATGCCATTGATTCTTGTTGCTGAA
* ** * *
2678041 TTTTATGTTATTTTGGG-TTTAGTGGATATATTGTCGATGAATATCC
62 TTTTATGTTCTTCCGGGCTATAGTCGAT-TATTGTCGATGAATATCC
2678087 GCAAATCCAG
Statistics
Matches: 342, Mismatches: 45, Indels: 43
0.80 0.10 0.10
Matches are distributed among these distances:
148 6 0.02
149 32 0.09
150 51 0.15
151 59 0.17
152 24 0.07
153 65 0.19
154 86 0.25
155 19 0.06
ACGTcount: A:0.25, C:0.12, G:0.24, T:0.39
Consensus pattern (154 bp):
TAGCAGAACTTGTGAAGGTTTTGTTGAATCATTATATATGCCATTGATTCTTGTTGCTGAATTTT
ATGTTCTTCCGGGCTATAGTCGATTATTGTCGATGAATATCCTGAGAATCTGCAGAGTTTCAGGA
GATTAAGAGGAATAGGCTTGTGTT
Found at i:2696173 original size:15 final size:15
Alignment explanation
Indices: 2696153--2696183 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
2696143 CAGACTAAAT
2696153 TACATCAATCCAAAC
1 TACATCAATCCAAAC
2696168 TACATCAATCCAAAC
1 TACATCAATCCAAAC
2696183 T
1 T
2696184 CTTAGACCAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.45, C:0.32, G:0.00, T:0.23
Consensus pattern (15 bp):
TACATCAATCCAAAC
Found at i:2704500 original size:20 final size:20
Alignment explanation
Indices: 2704475--2704514 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
2704465 TTTGAGAATA
2704475 TGCAAATAGTGAATAGGCTT
1 TGCAAATAGTGAATAGGCTT
2704495 TGCAAATAGTGAATAGGCTT
1 TGCAAATAGTGAATAGGCTT
2704515 GACGAAGTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.35, C:0.10, G:0.25, T:0.30
Consensus pattern (20 bp):
TGCAAATAGTGAATAGGCTT
Found at i:2704883 original size:20 final size:20
Alignment explanation
Indices: 2704834--2704881 Score: 89
Period size: 20 Copynumber: 2.5 Consensus size: 20
2704824 AAATTCAACA
2704834 TGAGGATTTCTATTCACTCC
1 TGAGGATTTCTATTCACTCC
2704854 TGAGGATTTCTATTCACTCC
1 TGAGGATTTCTATTCACTCC
2704874 TGA-GATTT
1 TGAGGATTT
2704882 TCAGTTGTCT
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
19 5 0.18
20 23 0.82
ACGTcount: A:0.21, C:0.21, G:0.17, T:0.42
Consensus pattern (20 bp):
TGAGGATTTCTATTCACTCC
Found at i:2707559 original size:28 final size:28
Alignment explanation
Indices: 2707490--2707578 Score: 115
Period size: 28 Copynumber: 3.1 Consensus size: 28
2707480 GCCAAGACCA
* *
2707490 TCTAGGGATTTATGTAAATGAAAATGCT
1 TCTACGGATTAATGTAAATGAAAATGCT
2707518 TCTTCGACGGATTAATGTAAATGAAAATGCT
1 TC-T--ACGGATTAATGTAAATGAAAATGCT
* *
2707549 TCTACGGATTAATGTAAGTGGAAATGCT
1 TCTACGGATTAATGTAAATGAAAATGCT
2707577 TC
1 TC
2707579 ACACATTTGG
Statistics
Matches: 54, Mismatches: 4, Indels: 6
0.84 0.06 0.09
Matches are distributed among these distances:
28 27 0.50
29 1 0.02
30 1 0.02
31 25 0.46
ACGTcount: A:0.34, C:0.11, G:0.21, T:0.34
Consensus pattern (28 bp):
TCTACGGATTAATGTAAATGAAAATGCT
Found at i:2710170 original size:59 final size:60
Alignment explanation
Indices: 2710060--2710192 Score: 173
Period size: 59 Copynumber: 2.2 Consensus size: 60
2710050 AGTCGATAAC
*
2710060 CATTTTGTAACTTTTAATAGTTGAAGAACCCAACAAAACAACATCACATAGTCAAAGGAT
1 CATTTTGTAACTTTTAATAATTGAAGAACCCAACAAAACAACATCACATAGTCAAAGGAT
* * * * *
2710120 TATTTTGTAATTTTTAATAATTGAAG-ACTCAACAAAACAATA-CACTATAGTCAAATGAT
1 CATTTTGTAACTTTTAATAATTGAAGAACCCAACAAAACAACATCAC-ATAGTCAAAGGAT
2710179 CATTTGTGT-ACTTT
1 CATTT-TGTAACTTT
2710193 ACCCTATTTA
Statistics
Matches: 63, Mismatches: 8, Indels: 5
0.83 0.11 0.07
Matches are distributed among these distances:
58 3 0.05
59 34 0.54
60 26 0.41
ACGTcount: A:0.41, C:0.15, G:0.11, T:0.34
Consensus pattern (60 bp):
CATTTTGTAACTTTTAATAATTGAAGAACCCAACAAAACAACATCACATAGTCAAAGGAT
Found at i:2712683 original size:21 final size:21
Alignment explanation
Indices: 2712653--2712695 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
2712643 ACAAGTTTAA
*
2712653 AAATAGGGAAAAGAAGATGGC
1 AAATAAGGAAAAGAAGATGGC
2712674 AAATAAGGAAAAGAAGATGGC
1 AAATAAGGAAAAGAAGATGGC
2712695 A
1 A
2712696 TTGGGCAATT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.56, C:0.05, G:0.30, T:0.09
Consensus pattern (21 bp):
AAATAAGGAAAAGAAGATGGC
Found at i:2714933 original size:30 final size:30
Alignment explanation
Indices: 2714897--2714970 Score: 139
Period size: 30 Copynumber: 2.5 Consensus size: 30
2714887 CTCGAGGCTG
2714897 CGAGGAAGAATACTGATTGAAGAGAGAAAC
1 CGAGGAAGAATACTGATTGAAGAGAGAAAC
2714927 CGAGGAAGAATACTGATTGAAGAGAGAAAC
1 CGAGGAAGAATACTGATTGAAGAGAGAAAC
*
2714957 CGAGGAAGAGTACT
1 CGAGGAAGAATACT
2714971 AACAGGCCTC
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
30 43 1.00
ACGTcount: A:0.45, C:0.11, G:0.31, T:0.14
Consensus pattern (30 bp):
CGAGGAAGAATACTGATTGAAGAGAGAAAC
Found at i:2716677 original size:3 final size:3
Alignment explanation
Indices: 2716669--2716766 Score: 160
Period size: 3 Copynumber: 32.7 Consensus size: 3
2716659 TTTTTATCCA
* *
2716669 TAT TAT TAT TAT TAG TAT TTT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* *
2716717 TAC TAT TAT TAT TAT TAT TAT TAT TAT TAT CAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
2716765 TA
1 TA
2716767 AATATATATT
Statistics
Matches: 87, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
3 87 1.00
ACGTcount: A:0.33, C:0.02, G:0.01, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:2718964 original size:18 final size:17
Alignment explanation
Indices: 2718941--2718991 Score: 50
Period size: 18 Copynumber: 2.9 Consensus size: 17
2718931 TTCTTTTCAA
2718941 ATTTTTTATTTATTTAT
1 ATTTTTTATTTATTTAT
*
2718958 -TATTTTTATAATATTTAT
1 AT-TTTTTAT-TTATTTAT
*
2718976 ATGTTTTATTTTATTT
1 ATTTTTTA-TTTATTT
2718992 GCAAGTATTT
Statistics
Matches: 27, Mismatches: 3, Indels: 7
0.73 0.08 0.19
Matches are distributed among these distances:
16 1 0.04
17 7 0.26
18 17 0.63
19 2 0.07
ACGTcount: A:0.25, C:0.00, G:0.02, T:0.73
Consensus pattern (17 bp):
ATTTTTTATTTATTTAT
Found at i:2719013 original size:13 final size:15
Alignment explanation
Indices: 2718982--2719018 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 15
2718972 TTATATGTTT
2718982 TATTTTATTTGCAAG
1 TATTTTATTTGCAAG
2718997 TATTTTATTT-C-AG
1 TATTTTATTTGCAAG
2719010 TA-TTTATTT
1 TATTTTATTT
2719019 TTCTGTCAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 7 0.32
13 4 0.18
14 1 0.05
15 10 0.45
ACGTcount: A:0.24, C:0.05, G:0.08, T:0.62
Consensus pattern (15 bp):
TATTTTATTTGCAAG
Found at i:2722360 original size:14 final size:15
Alignment explanation
Indices: 2722331--2722363 Score: 59
Period size: 14 Copynumber: 2.3 Consensus size: 15
2722321 TTATTATTTT
2722331 ATTTATTAAGTTAAA
1 ATTTATTAAGTTAAA
2722346 ATTTATTAA-TTAAA
1 ATTTATTAAGTTAAA
2722360 ATTT
1 ATTT
2722364 GAAAAAATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 9 0.50
15 9 0.50
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (15 bp):
ATTTATTAAGTTAAA
Found at i:2729638 original size:16 final size:16
Alignment explanation
Indices: 2729617--2729675 Score: 66
Period size: 16 Copynumber: 3.5 Consensus size: 16
2729607 GCTTGAAGAA
2729617 AAAAGAAAAAAGAAAG
1 AAAAGAAAAAAGAAAG
*
2729633 AAAAGAAAAAA-ATAG
1 AAAAGAAAAAAGAAAG
2729648 AAAATGAAAAAAAGAGAAG
1 AAAA-G-AAAAAAGA-AAG
2729667 AAAAAGAAA
1 -AAAAGAAA
2729676 GGGGGTCAAG
Statistics
Matches: 36, Mismatches: 2, Indels: 8
0.78 0.04 0.17
Matches are distributed among these distances:
15 7 0.19
16 12 0.33
17 6 0.17
18 4 0.11
19 3 0.08
20 4 0.11
ACGTcount: A:0.80, C:0.00, G:0.17, T:0.03
Consensus pattern (16 bp):
AAAAGAAAAAAGAAAG
Found at i:2729676 original size:15 final size:14
Alignment explanation
Indices: 2729617--2729676 Score: 59
Period size: 15 Copynumber: 4.0 Consensus size: 14
2729607 GCTTGAAGAA
2729617 AAAAGAAAAAAGAAAG
1 AAAAG-AAAAA-AAAG
2729633 AAAAGAAAAAAATAG
1 AAAAGAAAAAAA-AG
2729648 AAAATG-AAAAAAAG
1 AAAA-GAAAAAAAAG
*
2729662 AGAAGAAAAAGAAAG
1 AAAAGAAAAA-AAAG
2729677 GGGGTCAAGG
Statistics
Matches: 39, Mismatches: 1, Indels: 9
0.80 0.02 0.18
Matches are distributed among these distances:
13 1 0.03
14 11 0.28
15 21 0.54
16 6 0.15
ACGTcount: A:0.78, C:0.00, G:0.18, T:0.03
Consensus pattern (14 bp):
AAAAGAAAAAAAAG
Found at i:2731099 original size:83 final size:84
Alignment explanation
Indices: 2730709--2731101 Score: 686
Period size: 83 Copynumber: 4.7 Consensus size: 84
2730699 CATTAAATGA
* *
2730709 AAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATTTGATCTGG-TTGGACAG
1 AAGATGAATTTGCTAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGACAG
2730773 AACCAATCATTGAATTTGG
66 AACCAATCATTGAATTTGG
* *
2730792 AAGATGAATATGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGG-CAG
1 AAGATGAATTTGCTAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGACAG
*
2730856 AACCAATCATTAAATTTGG
66 AACCAATCATTGAATTTGG
*
2730875 AAGATGAATTTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGG-TTGGACAG
1 AAGATGAATTTGCTAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGACAG
*
2730939 AACCAATCATTGAATTTAG
66 AACCAATCATTGAATTTGG
*
2730958 AAGATGAATTTGTTAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGG-CAG
1 AAGATGAATTTGCTAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGACAG
2731022 AACCAATCATTGAATTTGG
66 AACCAATCATTGAATTTGG
2731041 AAGATGAATTTGCTAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGG
1 AAGATGAATTTGCTAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGG
2731102 TAAGAACTAC
Statistics
Matches: 295, Mismatches: 12, Indels: 6
0.94 0.04 0.02
Matches are distributed among these distances:
82 4 0.01
83 283 0.96
84 8 0.03
ACGTcount: A:0.27, C:0.13, G:0.23, T:0.37
Consensus pattern (84 bp):
AAGATGAATTTGCTAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGACAG
AACCAATCATTGAATTTGG
Found at i:2732037 original size:113 final size:112
Alignment explanation
Indices: 2731834--2732504 Score: 916
Period size: 113 Copynumber: 5.9 Consensus size: 112
2731824 ATTCAAATCT
*
2731834 ATCATTTGATGGATTATCATTGCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAA
1 ATCATTTGATGGATTAACATTGCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAA
* *
2731899 GAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGTTTGAATTC
66 GAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTG-CTGAATTC
* * *
2731947 ATCACTTGATGGATTATCATTGCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGAAA
1 ATCATTTGATGGATTAACATTGCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAA
* * * *
2732012 AAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTCAAATC
66 GAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTGAATTC
* *
2732059 TATCATTTGATGGATTAACATTCCCAGAGAA-GTTCATAATGAGAAGAATTCATCTGAAGAAGGA
1 -ATCATTTGATGGATTAACATTGCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
* * *
2732123 AGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTCAAATC
65 AGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTGAATTC
* *** * *
2732171 TATCACTTGATGGATTATTTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
1 -ATCATTTGATGGATTAACATTGCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
* * *
2732236 ATAATAAGTTCATAATGAGAAGAACTTGTTCAATCTTTTGCTTGAATTC
65 AGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGC-TGAATTC
* *
2732285 ATCATTTGATGGATCAACATTGCCAG-GTAGAGTTCATAATGAGAAGAACTCGTCATCTGAAGAA
1 ATCATTTGATGGATTAACATTGCCAGAGAAG-GTTCATAATGAGAAGAA--C-TCATCTGAAGAA
*
2732349 GGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAATCTTTTGCATGAATTC
62 GGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGC-TGAATTC
* * * ** *
2732401 ATCAATTGATGGATCAACATTTCTGGAGAA-GTTCATAATGAGAAGAACTCATCTGAAGAAGAAA
1 ATCATTTGATGGATTAACATTGCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAA
* * *
2732465 GAAGAGGTTCATAATAAGAAGAACTTGTTCAACTTTTTGC
66 GAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGC
2732505 ATAATTCTAT
Statistics
Matches: 505, Mismatches: 45, Indels: 17
0.89 0.08 0.03
Matches are distributed among these distances:
112 162 0.32
113 235 0.47
114 5 0.01
115 18 0.04
116 83 0.16
117 2 0.00
ACGTcount: A:0.38, C:0.13, G:0.20, T:0.30
Consensus pattern (112 bp):
ATCATTTGATGGATTAACATTGCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAA
GAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTGAATTC
Found at i:2732143 original size:24 final size:23
Alignment explanation
Indices: 2732100--2732144 Score: 56
Period size: 24 Copynumber: 1.9 Consensus size: 23
2732090 GTTCATAATG
*
2732100 AGAAGAATTCATCTGAAGAAGGA
1 AGAAGAATTCATATGAAGAAGGA
2732123 AGAAGAAGTTCATAATG-AGAAG
1 AGAAGAA-TTCAT-ATGAAGAAG
2732145 AATTTGTTCA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
23 7 0.37
24 10 0.53
25 2 0.11
ACGTcount: A:0.49, C:0.07, G:0.27, T:0.18
Consensus pattern (23 bp):
AGAAGAATTCATATGAAGAAGGA
Found at i:2732218 original size:225 final size:225
Alignment explanation
Indices: 2731826--2732504 Score: 963
Period size: 225 Copynumber: 3.0 Consensus size: 225
2731816 TAGCAAAGAT
* *
2731826 TCAAATCTATCATTTGATGGATTATCATTGCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGA
1 TCAAATCTATCATTTGATGGATTAACATTGCCAGAGAA-GTTCATAATGAGAAGAATTCATCTGA
* **
2731891 AGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGTTTGAAT-TCATCACTTG
65 AGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTCAAATCT-ATCACTTG
* *
2731955 ATGGATTATCATTGCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGAAAAAAGAAGT
129 ATGGATTATCATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGAAAAAAGAAGT
*
2732020 TCATAATGAGAAGAATTTGTTCAACCTTTTGC
194 TCATAATGAGAAGAACTTGTTCAACCTTTTGC
*
2732052 TCAAATCTATCATTTGATGGATTAACATTCCCAGAGAAGTTCATAATGAGAAGAATTCATCTGAA
1 TCAAATCTATCATTTGATGGATTAACATTGCCAGAGAAGTTCATAATGAGAAGAATTCATCTGAA
2732117 GAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTCAAATCTATCACTTGAT
66 GAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTCAAATCTATCACTTGAT
** * * *
2732182 GGATTATTTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAATAATAAGTTC
131 GGATTATCATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGAAAAAAGAAGTTC
*
2732247 ATAATGAGAAGAACTTGTTCAATCTTTTGC
196 ATAATGAGAAGAACTTGTTCAACCTTTTGC
** *
2732277 TTGAAT-TCATCATTTGATGGATCAACATTGCCAG-GTAGAGTTCATAATGAGAAGAACTCGTCA
1 TCAAATCT-ATCATTTGATGGATTAACATTGCCAGAG-A-AGTTCATAATGAGAAGAA-T--TCA
* * * *
2732340 TCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAATCTTTTGCATGAATTC-ATC
60 TCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGC-TCAAATCTATC
* * * ** *
2732404 AATTGATGGATCAACATTTCTGGAG-AAGTTCATAATGAGAAGAACTCATCTGAAGAAGAAAGAA
124 ACTTGATGGATTATCATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGAAAAAA
* * *
2732468 GAGGTTCATAATAAGAAGAACTTGTTCAACTTTTTGC
189 GAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGC
2732505 ATAATTCTAT
Statistics
Matches: 408, Mismatches: 37, Indels: 14
0.89 0.08 0.03
Matches are distributed among these distances:
224 2 0.00
225 201 0.49
226 55 0.13
227 1 0.00
228 69 0.17
229 75 0.18
230 5 0.01
ACGTcount: A:0.38, C:0.13, G:0.19, T:0.30
Consensus pattern (225 bp):
TCAAATCTATCATTTGATGGATTAACATTGCCAGAGAAGTTCATAATGAGAAGAATTCATCTGAA
GAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTCAAATCTATCACTTGAT
GGATTATCATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGAAAAAAGAAGTTC
ATAATGAGAAGAACTTGTTCAACCTTTTGC
Found at i:2732267 original size:338 final size:340
Alignment explanation
Indices: 2731826--2732504 Score: 1024
Period size: 338 Copynumber: 2.0 Consensus size: 340
2731816 TAGCAAAGAT
* *
2731826 TCAAATCTATCATTTGATGGATTATCATTGCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGA
1 TCAAATCTATCACTTGATGGATTATCATTGCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGA
* *
2731891 AGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGTTTGAATTCATCACTTGA
66 AGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTGAATTCATCACTTGA
* *
2731956 TGGATTATCATTGCCAGAGAAG-GTTCATAATGAGAAGAA-C-TCATCTGAAGAAGAAAAAAGAA
131 TGGATCAACATTGCCAG-GAAGAGTTCATAATGAGAAGAACCGTCATCTGAAGAAGAAAAAAGAA
* * *
2732018 GTTCATAATGAGAAGAATTTGTTCAACCTTTTGC-TCAAATCTATCATTTGATGGATTAACATTC
195 GTTCATAATGAGAAGAACTTGTTCAACCTTTTGCATCAAATC-ATCAATTGATGGATCAACATTC
* * *
2732082 CCAGAGAAGTTCATAATGAGAAGAATTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAA
259 CCAGAGAAGTTCATAATGAGAAGAACTCATCTGAAGAAGAAAGAAGAAGTTCATAATAAGAAGAA
*
2732147 TTTGTTCAACCTTTTGC
324 CTTGTTCAACCTTTTGC
** *
2732164 TCAAATCTATCACTTGATGGATTATTTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGA
1 TCAAATCTATCACTTGATGGATTATCATTGCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGA
* * * *
2732229 AGAAGGAATAATAAGTTCATAATGAGAAGAACTTGTTCAATCTTTTGCTTGAATTCATCATTTGA
66 AGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTGAATTCATCACTTGA
* * *
2732294 TGGATCAACATTGCCAGGTAGAGTTCATAATGAGAAGAACTCGTCATCTGAAGAAGGAAGAAGAA
131 TGGATCAACATTGCCAGGAAGAGTTCATAATGAGAAGAAC-CGTCATCTGAAGAAGAAAAAAGAA
* * * *
2732359 GTTCATAATGAGAAGAACTTGTTCAATCTTTTGCATGAATTCATCAATTGATGGATCAACATTTC
195 GTTCATAATGAGAAGAACTTGTTCAACCTTTTGCATCAAATCATCAATTGATGGATCAACATTCC
** *
2732424 TGGAGAAGTTCATAATGAGAAGAACTCATCTGAAGAAGAAAGAAGAGGTTCATAATAAGAAGAAC
260 CAGAGAAGTTCATAATGAGAAGAACTCATCTGAAGAAGAAAGAAGAAGTTCATAATAAGAAGAAC
*
2732489 TTGTTCAACTTTTTGC
325 TTGTTCAACCTTTTGC
2732505 ATAATTCTAT
Statistics
Matches: 305, Mismatches: 31, Indels: 7
0.89 0.09 0.02
Matches are distributed among these distances:
337 3 0.01
338 151 0.50
340 1 0.00
341 145 0.48
342 5 0.02
ACGTcount: A:0.38, C:0.13, G:0.19, T:0.30
Consensus pattern (340 bp):
TCAAATCTATCACTTGATGGATTATCATTGCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGA
AGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTGAATTCATCACTTGA
TGGATCAACATTGCCAGGAAGAGTTCATAATGAGAAGAACCGTCATCTGAAGAAGAAAAAAGAAG
TTCATAATGAGAAGAACTTGTTCAACCTTTTGCATCAAATCATCAATTGATGGATCAACATTCCC
AGAGAAGTTCATAATGAGAAGAACTCATCTGAAGAAGAAAGAAGAAGTTCATAATAAGAAGAACT
TGTTCAACCTTTTGC
Found at i:2732830 original size:3 final size:3
Alignment explanation
Indices: 2732822--2732934 Score: 199
Period size: 3 Copynumber: 37.7 Consensus size: 3
2732812 TTTTTATCCA
*
2732822 TAT TAT TAT TAT TAG TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
*
2732870 TAT TAT TAT TAC TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
*
2732918 CAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TA
2732935 AATATATATT
Statistics
Matches: 104, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 104 1.00
ACGTcount: A:0.34, C:0.02, G:0.01, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:2739581 original size:87 final size:87
Alignment explanation
Indices: 2739435--2739609 Score: 334
Period size: 87 Copynumber: 2.0 Consensus size: 87
2739425 CACAATGACA
2739435 AGGATTAAATCTCAACGAAAACCCATGTCCTAATGCATGTAGGACATTTTTAAGGACTCTTAAAC
1 AGGATTAAATCTCAACGAAAACCCATGTCCTAATGCATGTAGGACATTTTTAAGGACTCTTAAAC
2739500 ACTAAACAGATTGAAATCCAAT
66 ACTAAACAGATTGAAATCCAAT
2739522 AGGATTAAAT-TCAACGAAAACCCCATGTCCTAATGCATGTAGGACATTTTTAAGGACTCTTAAA
1 AGGATTAAATCTCAACGAAAA-CCCATGTCCTAATGCATGTAGGACATTTTTAAGGACTCTTAAA
2739586 CACTAAACAGATTGAAATCCAAT
65 CACTAAACAGATTGAAATCCAAT
2739609 A
1 A
2739610 AAATCATAAA
Statistics
Matches: 87, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
86 10 0.11
87 77 0.89
ACGTcount: A:0.41, C:0.19, G:0.14, T:0.26
Consensus pattern (87 bp):
AGGATTAAATCTCAACGAAAACCCATGTCCTAATGCATGTAGGACATTTTTAAGGACTCTTAAAC
ACTAAACAGATTGAAATCCAAT
Found at i:2741197 original size:9 final size:9
Alignment explanation
Indices: 2741183--2741216 Score: 52
Period size: 9 Copynumber: 3.8 Consensus size: 9
2741173 GAAAAGGGAA
2741183 AAATAAAAT
1 AAATAAAAT
2741192 AAATAAAAT
1 AAATAAAAT
2741201 AAAT-AAAT
1 AAATAAAAT
2741209 AAGATAAA
1 AA-ATAAA
2741217 GGAAAAAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
8 6 0.26
9 15 0.65
10 2 0.09
ACGTcount: A:0.76, C:0.00, G:0.03, T:0.21
Consensus pattern (9 bp):
AAATAAAAT
Found at i:2741204 original size:13 final size:13
Alignment explanation
Indices: 2741182--2741216 Score: 52
Period size: 13 Copynumber: 2.6 Consensus size: 13
2741172 GGAAAAGGGA
2741182 AAAATAAAATAAAT
1 AAAAT-AAATAAAT
2741196 AAAATAAATAAAT
1 AAAATAAATAAAT
*
2741209 AAGATAAA
1 AAAATAAA
2741217 GGAAAAAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
13 15 0.75
14 5 0.25
ACGTcount: A:0.77, C:0.00, G:0.03, T:0.20
Consensus pattern (13 bp):
AAAATAAATAAAT
Found at i:2741738 original size:18 final size:17
Alignment explanation
Indices: 2741715--2741757 Score: 52
Period size: 18 Copynumber: 2.5 Consensus size: 17
2741705 ATATATACAT
2741715 ATAATAATAATAACATAA
1 ATAATAATAATAA-ATAA
* *
2741733 ATAATAAAAATAAATGA
1 ATAATAATAATAAATAA
2741750 ATAA-AATA
1 ATAATAATA
2741758 TCCATATAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
16 3 0.14
17 7 0.32
18 12 0.55
ACGTcount: A:0.70, C:0.02, G:0.02, T:0.26
Consensus pattern (17 bp):
ATAATAATAATAAATAA
Found at i:2741754 original size:14 final size:13
Alignment explanation
Indices: 2741717--2741755 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 13
2741707 ATATACATAT
2741717 AATAATAATAACATA
1 AATAATAA-AA-ATA
2741732 AATAATAAAAATA
1 AATAATAAAAATA
2741745 AATGAATAAAA
1 AAT-AATAAAA
2741756 TATCCATATA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 6 0.26
14 9 0.39
15 8 0.35
ACGTcount: A:0.72, C:0.03, G:0.03, T:0.23
Consensus pattern (13 bp):
AATAATAAAAATA
Found at i:2743086 original size:105 final size:105
Alignment explanation
Indices: 2742754--2743794 Score: 1567
Period size: 105 Copynumber: 10.0 Consensus size: 105
2742744 CATTGTTCCA
* * ** *
2742754 AGTCCAATATCCTCCGTCGTGAAGTTGAAATTGGCTCTG-GAACCGGGAAATTGTTTGTTGACAA
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAG-ATTGGGAAGTTG-TTGTTGACAA
* * * *
2742818 CCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCG
64 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
** * *
2742860 AGTCCAATATCCTTCG-TGTGAAGTTGAAATTGAATCTGA-A-T--GAAATT-TTGTTGACAAGC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAACC
2742919 AGCGGTCCC-T--TCGTGAAGTTGAACTTGCGTTGTCTGG
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* * *
2742956 AGTCCAATATCTTTCGTTGTGAAGTTGAAATTGGCTCTGGGATTGGGAAGTTGTTGTTGACAAAC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAACC
*
2743021 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGG
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* * *
2743061 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGA-A-T--GAAATT-TTGTTGACAAGC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAACC
2743121 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* *
2743161 AGTCCAATATCCTTCGTTGTGAAG-TGAAATTGGCTCTGAGATTGGAAAGTTGTTGTTGACAAGC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAACC
*
2743225 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGG
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
2743265 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAACC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAACC
2743330 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* * **
2743370 AGTCCAATATCCTCCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGAAAGTTGTTGTTGACAAGA
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAACC
*
2743435 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGG
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
2743475 AGTCCAATATCCTTCGTTGTGAAGTTGAAA-TGGCTCTGAGATTGGGAAGTTGTTGTTGACAACC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAACC
2743539 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* * * *
2743579 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAAATTGTTTATTGACAA
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGG-AAGTTG-TTGTTGACAA
*
2743644 CCAGCGGTCCCTTTGTCGTGAAGTTGAACTTGCGTTGTCTGG
64 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* *
2743686 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAAC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTG-TTGTTGACAAC
* * * *
2743751 CAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCG
65 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
2743792 AGT
1 AGT
2743795 GCCACGATAT
Statistics
Matches: 862, Mismatches: 54, Indels: 38
0.90 0.06 0.04
Matches are distributed among these distances:
96 39 0.05
97 20 0.02
98 2 0.00
99 35 0.04
100 74 0.09
101 17 0.02
102 20 0.02
103 6 0.01
104 176 0.20
105 303 0.35
106 75 0.09
107 95 0.11
ACGTcount: A:0.22, C:0.18, G:0.27, T:0.33
Consensus pattern (105 bp):
AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAACC
AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
Found at i:2743511 original size:209 final size:208
Alignment explanation
Indices: 2742754--2743825 Score: 1569
Period size: 209 Copynumber: 5.1 Consensus size: 208
2742744 CATTGTTCCA
* **
2742754 AGTCCAATATCCTCCGTCGTGAAGTTGAAATTGGCTCTG-GAACCGGGAAA-TTGTTTGTTGACA
1 AGTCCAATATCCTCCGTTGTGAAGTTGAAATTGGCTCTGAG-A-TTGGAAAGTTG-TTGTTGACA
* * ** *
2742817 ACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGAGTCCAATATCCTTCG-TGTGA
63 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGGAGTCCAATATCCTTCGTTGTGA
** * *
2742881 AGTTGAAATTGAATCTGAA-T-GAAATT-TTGTTGACAAGCAGCGGTCCC-T--TCGTGAAGTTG
128 AGTTGAAATTGGCTCTGAATTGGAAGTTGTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTG
2742940 AACTTGCGTTGTCTGG
193 AACTTGCGTTGTCTGG
* * * * *
2742956 AGTCCAATATCTTTCGTTGTGAAGTTGAAATTGGCTCTGGGATTGGGAAGTTGTTGTTGACAAAC
1 AGTCCAATATCCTCCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGAAAGTTGTTGTTGACAACC
*
2743021 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGGAGTCCAATATCCTTCGCTGTGAAGT
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGGAGTCCAATATCCTTCGTTGTGAAGT
* *
2743086 TGAAATTGGCTCTGAA-T-GAAATT-TTGTTGACAAGCAGCGGTCCCTTCGTCGTGAAGTTGAAC
131 TGAAATTGGCTCTGAATTGGAAGTTGTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAAC
2743148 TTGCGTTGTCTGG
196 TTGCGTTGTCTGG
* *
2743161 AGTCCAATATCCTTCGTTGTGAAG-TGAAATTGGCTCTGAGATTGGAAAGTTGTTGTTGACAAGC
1 AGTCCAATATCCTCCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGAAAGTTGTTGTTGACAACC
2743225 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGGAGTCCAATATCCTTCGTTGTGAAGT
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGGAGTCCAATATCCTTCGTTGTGAAGT
2743290 TGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGA
131 TGAAATTGGCTCTGA-ATT-GGAAGTTGTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGA
2743355 ACTTGCGTTGTCTGG
194 ACTTGCGTTGTCTGG
**
2743370 AGTCCAATATCCTCCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGAAAGTTGTTGTTGACAAGA
1 AGTCCAATATCCTCCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGAAAGTTGTTGTTGACAACC
2743435 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGGAGTCCAATATCCTTCGTTGTGAAGT
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGGAGTCCAATATCCTTCGTTGTGAAGT
2743500 TGAAA-TGGCTCTGAGATTGGGAAGTTGTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGA
131 TGAAATTGGCTCTGA-ATT-GGAAGTTGTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGA
2743564 ACTTGCGTTGTCTGG
194 ACTTGCGTTGTCTGG
* * * * *
2743579 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAAATTGTTTATTGACAA
1 AGTCCAATATCCTCCGTTGTGAAGTTGAAATTGGCTCTGAGATT-GGAAAGTTG-TTGTTGACAA
* *
2743644 CCAGCGGTCCCTTTGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAA
64 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGGAGTCCAATATCCTTCGTTGTGAA
* *
2743709 GTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAACCAGCCGTCCCTTCGTTGTGAAGT
129 GTTGAAATTGGCTCTG-AATTG-GAAGTTG-TTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGT
* *
2743774 TGAACTTGTGTTGTCTCG
191 TGAACTTGCGTTGTCTGG
* * *
2743792 AGTGCCACGATATTCTCCGTCGTGGAGTTGAAAT
1 AGT-CCA--ATATCCTCCGTTGTGAAGTTGAAAT
2743826 CGCGGATGGC
Statistics
Matches: 808, Mismatches: 41, Indels: 28
0.92 0.05 0.03
Matches are distributed among these distances:
201 66 0.08
202 90 0.11
203 2 0.00
204 116 0.14
205 51 0.06
206 1 0.00
208 5 0.01
209 189 0.23
210 117 0.14
211 78 0.10
212 18 0.02
213 52 0.06
214 3 0.00
216 20 0.02
ACGTcount: A:0.22, C:0.18, G:0.27, T:0.33
Consensus pattern (208 bp):
AGTCCAATATCCTCCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGAAAGTTGTTGTTGACAACC
AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGGAGTCCAATATCCTTCGTTGTGAAGT
TGAAATTGGCTCTGAATTGGAAGTTGTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAAC
TTGCGTTGTCTGG
Found at i:2743577 original size:314 final size:314
Alignment explanation
Indices: 2742754--2743794 Score: 1576
Period size: 314 Copynumber: 3.3 Consensus size: 314
2742744 CATTGTTCCA
* **
2742754 AGTCCAATATCCTCCGTCGTGAAGTTGAAATTGGCTCTG-GAACCGGGAAATTGTTTGTTGACAA
1 AGTCCAATATCCTCCGTTGTGAAGTTGAAATTGGCTCTGAG-A--TTGAAATTGTTTGTTGACAA
* * *
2742818 CCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGAGTCCAATATCCTTCG-TGTGAA
63 CCAGCCGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAA
** *
2742882 GTTGAAATTGAATCTGA-A-T--GAAATT-TTGTTGACAAGCAGCGGTCCC-T--TCGTGAAGTT
128 GTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAGCAGCGGTCCCTTCGTCGTGAAGTT
* *
2742939 GAACTTGCGTTGTCTGGAGTCCAATATCTTTCGTTGTGAAGTTGAAATTGGCTCTGGGATTGGGA
193 GAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGA
* *
2743004 AGTTGTTGTTGACAAACAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGG
258 AGTTGTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* * *
2743061 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGA-A-TGAAA-T-TTTGTTGACAAGCA
1 AGTCCAATATCCTCCGTTGTGAAGTTGAAATTGGCTCTGAGATTGAAATTGTTTGTTGACAACCA
*
2743122 GCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAG-T
66 GCCGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTT
*
2743186 GAAATTGGCTCTGAGATTGGAAAGTTGTTGTTGACAAGCAGCGGTCCCTTCGTCGTGAAGTTGAA
131 GAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAGCAGCGGTCCCTTCGTCGTGAAGTTGAA
*
2743251 CTTGCATTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGT
196 CTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGT
2743316 TGTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
261 TGTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
*
2743370 AGTCCAATATCCTCCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGAAAGTTG-TTGTTGACAAG
1 AGTCCAATATCCTCCGTTGTGAAGTTGAAATTGGCTCTGAGATT-GAAA-TTGTTTGTTGACAAC
* * *
2743434 AAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGGAGTCCAATATCCTTCGTTGTGAAG
64 CAGCCGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAG
*
2743499 TTGAAA-TGGCTCTGAGATTGGGAAGTTGTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTG
129 TTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAGCAGCGGTCCCTTCGTCGTGAAGTTG
* *
2743563 AACTTGCGTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAA
194 AACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGG-A
* * *
2743628 AATTGTTTATTGACAACCAGCGGTCCCTTTGTCGTGAAGTTGAACTTGCGTTGTCTGG
258 AGTTG-TTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* *
2743686 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAAC
1 AGTCCAATATCCTCCGTTGTGAAGTTGAAATTGGCTCTGAGATTGA-AA-TTGTTTGTTGACAAC
* * *
2743751 CAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGAGT
64 CAGCCGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGT
2743795 GCCACGATAT
Statistics
Matches: 674, Mismatches: 39, Indels: 32
0.90 0.05 0.04
Matches are distributed among these distances:
301 77 0.11
302 9 0.01
303 5 0.01
305 4 0.01
306 22 0.03
307 37 0.05
309 165 0.24
310 1 0.00
311 1 0.00
312 4 0.01
314 191 0.28
315 12 0.02
316 98 0.15
317 48 0.07
ACGTcount: A:0.22, C:0.18, G:0.27, T:0.33
Consensus pattern (314 bp):
AGTCCAATATCCTCCGTTGTGAAGTTGAAATTGGCTCTGAGATTGAAATTGTTTGTTGACAACCA
GCCGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTT
GAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAGCAGCGGTCCCTTCGTCGTGAAGTTGAA
CTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGT
TGTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
Found at i:2744159 original size:29 final size:27
Alignment explanation
Indices: 2744093--2744149 Score: 69
Period size: 29 Copynumber: 2.0 Consensus size: 27
2744083 GCCTGTCTGG
*
2744093 AATCTTGATTCTTGAATCTTCAAATTTT
1 AATCATGA-TCTTGAATCTTCAAATTTT
*
2744121 GATCCATGATCTTGAATTCTTCAAATTTT
1 AAT-CATGATCTTGAA-TCTTCAAATTTT
2744150 CAAATCTGAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
28 9 0.36
29 16 0.64
ACGTcount: A:0.28, C:0.16, G:0.09, T:0.47
Consensus pattern (27 bp):
AATCATGATCTTGAATCTTCAAATTTT
Found at i:2744622 original size:36 final size:35
Alignment explanation
Indices: 2744572--2744843 Score: 187
Period size: 36 Copynumber: 7.9 Consensus size: 35
2744562 CAAGATTTTG
*
2744572 TGTTTCAAGAGAAACTGTCTCATAGGAGACAAAATT
1 TGTTTCAAGGGAAACTGTCTCA-AGGAGACAAAATT
* ** **
2744608 TGTTTCGAGGGAAACAATCTCAA--AG---ATTTT
1 TGTTTCAAGGGAAACTGTCTCAAGGAGACAAAATT
*
2744638 GTGTTTCAAGAGAAACTGTCTCAAAGGAGACAAAATT
1 -TGTTTCAAGGGAAACTGTCTC-AAGGAGACAAAATT
* * *
2744675 TGTTTCAAGGGAAATTATCTCAAGAGAGACGAAATT
1 TGTTTCAAGGGAAACTGTCTCAAG-GAGACAAAATT
** * * *
2744711 CATTTCAAGGGAAA-TGTTTTCAA--TG-----TTT
1 TGTTTCAAGGGAAACTG-TCTCAAGGAGACAAAATT
2744739 ATGTTTC-AGGAGAAACTGTCTCAAGGGAGACAAAATT
1 -TGTTTCAAGG-GAAACTGTCTCAA-GGAGACAAAATT
* *
2744776 T-TGTTCAAAGGAAACTGTCTCAAGAGAGACAAAGTT
1 TGT-TTCAAGGGAAACTGTCTCAAG-GAGACAAAATT
2744812 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAA
1 TGTTTCAAGGGAAACTGTCTCAAG-GAGACAA
2744844 TGGTGAGCAC
Statistics
Matches: 182, Mismatches: 30, Indels: 48
0.70 0.12 0.18
Matches are distributed among these distances:
28 5 0.03
29 13 0.07
30 5 0.03
31 17 0.09
32 3 0.02
33 3 0.02
34 2 0.01
35 7 0.04
36 119 0.65
37 8 0.04
ACGTcount: A:0.37, C:0.13, G:0.22, T:0.28
Consensus pattern (35 bp):
TGTTTCAAGGGAAACTGTCTCAAGGAGACAAAATT
Found at i:2744635 original size:67 final size:67
Alignment explanation
Indices: 2744563--2744697 Score: 234
Period size: 67 Copynumber: 2.0 Consensus size: 67
2744553 AGATAAATTC
* *
2744563 AAGATTTTGTGTTTCAAGAGAAACTGTCTCATAGGAGACAAAATTTGTTTCGAGGGAAACAATCT
1 AAGATTTTGTGTTTCAAGAGAAACTGTCTCAAAGGAGACAAAATTTGTTTCAAGGGAAACAATCT
2744628 CA
66 CA
**
2744630 AAGATTTTGTGTTTCAAGAGAAACTGTCTCAAAGGAGACAAAATTTGTTTCAAGGGAAATTATCT
1 AAGATTTTGTGTTTCAAGAGAAACTGTCTCAAAGGAGACAAAATTTGTTTCAAGGGAAACAATCT
2744695 CA
66 CA
2744697 A
1 A
2744698 GAGAGACGAA
Statistics
Matches: 64, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
67 64 1.00
ACGTcount: A:0.37, C:0.13, G:0.20, T:0.30
Consensus pattern (67 bp):
AAGATTTTGTGTTTCAAGAGAAACTGTCTCAAAGGAGACAAAATTTGTTTCAAGGGAAACAATCT
CA
Found at i:2744772 original size:101 final size:101
Alignment explanation
Indices: 2744639--2744825 Score: 279
Period size: 101 Copynumber: 1.9 Consensus size: 101
2744629 AAAGATTTTG
* *
2744639 TGTTTCAAGAGAAACTGTCTCAAAGGAGACAAAA-TTTGTTTCAAGGGAAATTATCTCAAGAGAG
1 TGTTTCAAGAGAAACTGTCTCAAAGGAGACAAAATTTTG-TTCAAAGGAAACTATCTCAAGAGAG
2744703 ACGAAA-TTCATTTCAAGGGAAATGTTTTCAATGTTTA
65 AC-AAAGTTCATTTCAAGGGAAATGTTTTCAATGTTTA
* * *
2744740 TGTTTCAGGAGAAACTGTCTCAAGGGAGACAAAATTTTGTTCAAAGGAAACTGTCTCAAGAGAGA
1 TGTTTCAAGAGAAACTGTCTCAAAGGAGACAAAATTTTGTTCAAAGGAAACTATCTCAAGAGAGA
**
2744805 CAAAGTTTGTTTCAAGGGAAA
66 CAAAGTTCATTTCAAGGGAAA
2744826 CTGTCTCAAG
Statistics
Matches: 77, Mismatches: 7, Indels: 4
0.88 0.08 0.05
Matches are distributed among these distances:
100 3 0.04
101 70 0.91
102 4 0.05
ACGTcount: A:0.37, C:0.12, G:0.22, T:0.28
Consensus pattern (101 bp):
TGTTTCAAGAGAAACTGTCTCAAAGGAGACAAAATTTTGTTCAAAGGAAACTATCTCAAGAGAGA
CAAAGTTCATTTCAAGGGAAATGTTTTCAATGTTTA
Found at i:2745313 original size:18 final size:18
Alignment explanation
Indices: 2745286--2745321 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
2745276 TGATGAATCC
* *
2745286 CCAAAGATGCCTCAATAT
1 CCAAAAATGCCCCAATAT
2745304 CCAAAAATGCCCCAATAT
1 CCAAAAATGCCCCAATAT
2745322 TTGATGTTGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.42, C:0.31, G:0.08, T:0.19
Consensus pattern (18 bp):
CCAAAAATGCCCCAATAT
Found at i:2745810 original size:22 final size:22
Alignment explanation
Indices: 2745733--2745803 Score: 106
Period size: 22 Copynumber: 3.2 Consensus size: 22
2745723 TTGTGTTTGG
*
2745733 TCAAAGGTTTGGCATTTGATGC
1 TCAAAGGTTTGACATTTGATGC
*
2745755 TCAAAGGTTTAACATTTGATGC
1 TCAAAGGTTTGACATTTGATGC
* *
2745777 TTAAAGGTTTGACATTGGATGC
1 TCAAAGGTTTGACATTTGATGC
2745799 TCAAA
1 TCAAA
2745804 AGATTGATGG
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 43 1.00
ACGTcount: A:0.30, C:0.13, G:0.23, T:0.35
Consensus pattern (22 bp):
TCAAAGGTTTGACATTTGATGC
Found at i:2746497 original size:16 final size:17
Alignment explanation
Indices: 2746450--2746498 Score: 50
Period size: 17 Copynumber: 2.9 Consensus size: 17
2746440 TTCTTTTTGA
2746450 TTTTTGCTCTTTTT-TCC
1 TTTTT-CTCTTTTTCTCC
2746467 TTTTGT-TCTTGTTTCT-C
1 TTTT-TCTCTT-TTTCTCC
2746484 TTTTTCTCTTTTTCT
1 TTTTTCTCTTTTTCT
2746499 TTGTTTTTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 9
0.76 0.00 0.24
Matches are distributed among these distances:
16 10 0.36
17 16 0.57
18 2 0.07
ACGTcount: A:0.00, C:0.20, G:0.06, T:0.73
Consensus pattern (17 bp):
TTTTTCTCTTTTTCTCC
Found at i:2746498 original size:23 final size:22
Alignment explanation
Indices: 2746460--2746533 Score: 71
Period size: 22 Copynumber: 3.2 Consensus size: 22
2746450 TTTTTGCTCT
*
2746460 TTTTTCCTTTTGTTCTTGTTTCTC
1 TTTTTGCTTTT-TTCTTGTTT-TC
2746484 TTTTT-CTCTTTTTCTTTGTTTT-
1 TTTTTGCT-TTTTTC-TTGTTTTC
*
2746506 TTTTTGCTTTTTTGCTTCTTTTC
1 TTTTTGCTTTTTT-CTTGTTTTC
2746529 TTTTT
1 TTTTT
2746534 TGTTCTTGAT
Statistics
Matches: 44, Mismatches: 1, Indels: 11
0.79 0.02 0.20
Matches are distributed among these distances:
22 16 0.36
23 14 0.32
24 14 0.32
ACGTcount: A:0.00, C:0.16, G:0.07, T:0.77
Consensus pattern (22 bp):
TTTTTGCTTTTTTCTTGTTTTC
Found at i:2746533 original size:16 final size:16
Alignment explanation
Indices: 2746467--2746540 Score: 57
Period size: 16 Copynumber: 4.6 Consensus size: 16
2746457 TCTTTTTTCC
*
2746467 TTTTGTTCTTGTTTCTCT
1 TTTTGTTCTT-TTGCT-T
* *
2746485 TTTT-CTCTTTTTCTT
1 TTTTGTTCTTTTGCTT
2746500 TGTTT-TT-TTTTGCTT
1 T-TTTGTTCTTTTGCTT
2746515 TTTTGCTTCTTTT-CTT
1 TTTTG-TTCTTTTGCTT
2746531 TTTTGTTCTT
1 TTTTGTTCTT
2746541 GATTAGATCT
Statistics
Matches: 49, Mismatches: 3, Indels: 11
0.78 0.05 0.17
Matches are distributed among these distances:
14 3 0.06
15 15 0.31
16 19 0.39
17 8 0.16
18 4 0.08
ACGTcount: A:0.00, C:0.15, G:0.08, T:0.77
Consensus pattern (16 bp):
TTTTGTTCTTTTGCTT
Found at i:2749596 original size:9 final size:9
Alignment explanation
Indices: 2749582--2749615 Score: 52
Period size: 9 Copynumber: 3.8 Consensus size: 9
2749572 GAAAAGGGAA
2749582 AAATAAAAT
1 AAATAAAAT
2749591 AAATAAAAT
1 AAATAAAAT
2749600 AAAT-AAAT
1 AAATAAAAT
2749608 AAGATAAA
1 AA-ATAAA
2749616 GGAAAAAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
8 6 0.26
9 15 0.65
10 2 0.09
ACGTcount: A:0.76, C:0.00, G:0.03, T:0.21
Consensus pattern (9 bp):
AAATAAAAT
Done.