Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000911.1 Hibiscus syriacus cultivar Beakdansim tig00001810_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: 162015
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.33
Found at i:2411 original size:34 final size:33
Alignment explanation
Indices: 2344--2412 Score: 93
Period size: 33 Copynumber: 2.1 Consensus size: 33
2334 ACATTTGCAA
*
2344 TATGTTATACCCCAAATTCCAAATAATTCAATT
1 TATGTTATACCCCAAATTCAAAATAATTCAATT
* * *
2377 TATGTTATACCCTAAATTCTAAAATACTTTAATT
1 TATGTTATACCCCAAATTC-AAAATAATTCAATT
2411 TA
1 TA
2413 GGGTTTAGAA
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
33 18 0.58
34 13 0.42
ACGTcount: A:0.39, C:0.17, G:0.03, T:0.41
Consensus pattern (33 bp):
TATGTTATACCCCAAATTCAAAATAATTCAATT
Found at i:6784 original size:24 final size:25
Alignment explanation
Indices: 6744--6794 Score: 63
Period size: 26 Copynumber: 2.1 Consensus size: 25
6734 ATGATGATAA
6744 TAAATATTTTATAA-TTT-AAAAAT
1 TAAATATTTTATAATTTTGAAAAAT
6767 TAAA-ATTTTCATATATTTTGAAAAAT
1 TAAATATTTT-ATA-ATTTTGAAAAAT
6793 TA
1 TA
6795 TTGACTTTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
22 5 0.21
23 7 0.29
24 1 0.04
25 3 0.12
26 8 0.33
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (25 bp):
TAAATATTTTATAATTTTGAAAAAT
Found at i:7700 original size:16 final size:17
Alignment explanation
Indices: 7679--7710 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
7669 TCAAACTAGA
7679 TTGAGTTT-AATGGGAT
1 TTGAGTTTAAATGGGAT
7695 TTGAGTTTAAATGGGA
1 TTGAGTTTAAATGGGA
7711 CTTATCACCC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.28, C:0.00, G:0.31, T:0.41
Consensus pattern (17 bp):
TTGAGTTTAAATGGGAT
Found at i:10544 original size:2 final size:2
Alignment explanation
Indices: 10537--10568 Score: 55
Period size: 2 Copynumber: 15.5 Consensus size: 2
10527 AACATGGAGT
10537 TA TA TA TA TA TA TA TA TA TA TA TA TA CTA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA T
10569 GAAAATGTGT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 27 0.93
3 2 0.07
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:11376 original size:23 final size:23
Alignment explanation
Indices: 11346--11400 Score: 83
Period size: 23 Copynumber: 2.4 Consensus size: 23
11336 GACATTTATA
*
11346 TTCGGTGCAATTCTACGCGGCAC
1 TTCGGTGCAATTCTACGCGACAC
*
11369 TTCGGTGCAATTCTACGTGACAC
1 TTCGGTGCAATTCTACGCGACAC
*
11392 TTTGGTGCA
1 TTCGGTGCA
11401 TTTATACGAG
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.18, C:0.25, G:0.25, T:0.31
Consensus pattern (23 bp):
TTCGGTGCAATTCTACGCGACAC
Found at i:13142 original size:39 final size:39
Alignment explanation
Indices: 13099--13221 Score: 131
Period size: 39 Copynumber: 3.2 Consensus size: 39
13089 AAATAATCAC
* *
13099 CCTCACCTTAGGTGTTATCTCCTTTATTACATTCAACAT
1 CCTCACCTTAGGTATTATCTCCTTTATTACACTCAACAT
* * *
13138 CCTCACCTTAGGAATTAT-TACCTTTATTACGCTCACCAT
1 CCTCACCTTAGGTATTATCT-CCTTTATTACACTCAACAT
* * * * **
13177 CATTACCTTAGGTATTACCGCCTTTATTACACTCATTAT
1 CCTCACCTTAGGTATTATCTCCTTTATTACACTCAACAT
13216 CCTCAC
1 CCTCAC
13222 ATTAAGCATT
Statistics
Matches: 67, Mismatches: 15, Indels: 4
0.78 0.17 0.05
Matches are distributed among these distances:
38 1 0.01
39 66 0.99
ACGTcount: A:0.24, C:0.30, G:0.07, T:0.38
Consensus pattern (39 bp):
CCTCACCTTAGGTATTATCTCCTTTATTACACTCAACAT
Found at i:19468 original size:140 final size:140
Alignment explanation
Indices: 19319--19578 Score: 369
Period size: 140 Copynumber: 1.9 Consensus size: 140
19309 TAAAATATGT
* * * *
19319 AGGCTCTAATATTAA-CACTAATTTGTTTTAACCAATTATTGTGTCGAATAATCAAAATAGTCCC
1 AGGCTCTAATATTAATC-CTAATTTATTTTAACCAATTATCGAGTCGAATAATCAAAATAGTCCA
* * ** *
19383 TCGGGCATGTTAATGCGATAGCTTATTCAAATTACCCCTTAAATTAAAGGACTAAAATGATAATA
65 TCGAGCATGTTAATGCGAGAGCCAATTCAAATTACCCCTTAAATTAAAGAACTAAAATGATAATA
19448 AACCTAAAGTG
130 AACCTAAAGTG
* * * *
19459 AGGCTCTAATATTAATCCTAATTTATTTTAACCAATTATCGAGTTGAATAATCGAAATGGTCTAT
1 AGGCTCTAATATTAATCCTAATTTATTTTAACCAATTATCGAGTCGAATAATCAAAATAGTCCAT
* *
19524 CGAGCATGTTAATGTGAGAGCCAATTCAAATTACTCCTTAAATTAAAGAACTAAA
66 CGAGCATGTTAATGCGAGAGCCAATTCAAATTACCCCTTAAATTAAAGAACTAAA
19579 GTATGAGAAA
Statistics
Matches: 104, Mismatches: 15, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
140 103 0.99
141 1 0.01
ACGTcount: A:0.38, C:0.16, G:0.13, T:0.33
Consensus pattern (140 bp):
AGGCTCTAATATTAATCCTAATTTATTTTAACCAATTATCGAGTCGAATAATCAAAATAGTCCAT
CGAGCATGTTAATGCGAGAGCCAATTCAAATTACCCCTTAAATTAAAGAACTAAAATGATAATAA
ACCTAAAGTG
Found at i:22655 original size:24 final size:24
Alignment explanation
Indices: 22623--22680 Score: 107
Period size: 24 Copynumber: 2.4 Consensus size: 24
22613 CCGATTCATT
22623 GAAGTCACTTCTTGAAGAATGTGA
1 GAAGTCACTTCTTGAAGAATGTGA
22647 GAAGTCACTTCTTGAAGAATGTGA
1 GAAGTCACTTCTTGAAGAATGTGA
*
22671 GAAGCCACTT
1 GAAGTCACTT
22681 TACGTAGGGT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 33 1.00
ACGTcount: A:0.33, C:0.16, G:0.24, T:0.28
Consensus pattern (24 bp):
GAAGTCACTTCTTGAAGAATGTGA
Found at i:24463 original size:85 final size:85
Alignment explanation
Indices: 24348--24655 Score: 411
Period size: 85 Copynumber: 3.6 Consensus size: 85
24338 GTCTTTTTAA
* * *
24348 ATGACGTGTGCTTCAATGACACGCAATGTAAGTCATATACGCGTGTCATAAATTTATGACACACA
1 ATGACGGGGGCTTCAATGACACGCAATGTAAGTCATACACGCGTGTCATAAATTTATGACACACA
* *
24413 AATGTATGTCA-AATAGATTT
66 AATGTGTGTCATATTA-ATTT
* ** * *
24433 ATGACGGGGGCTTCAATGACGCGCAATGTAAGTCATACATACGTGTCATAAATTTATGACGCATA
1 ATGACGGGGGCTTCAATGACACGCAATGTAAGTCATACACGCGTGTCATAAATTTATGACACACA
*
24498 AATGTGTGTCATCTTAATTT
66 AATGTGTGTCATATTAATTT
* * * * *
24518 ATGACGGGGGCTTTAATGACGCGCAATGTAAGTCATACATGTGTGTCATAAATTTATGACAAACA
1 ATGACGGGGGCTTCAATGACACGCAATGTAAGTCATACACGCGTGTCATAAATTTATGACACACA
*
24583 AATATGTGTCATATTAATTT
66 AATGTGTGTCATATTAATTT
* ** *
24603 ATGACGGAGGCTTCAATGACACGCAATGTAAGTCATACATACGCGTCATAAAT
1 ATGACGGGGGCTTCAATGACACGCAATGTAAGTCATACACGCGTGTCATAAAT
24656 GTGCGTCATA
Statistics
Matches: 197, Mismatches: 25, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
85 195 0.99
86 2 0.01
ACGTcount: A:0.34, C:0.16, G:0.20, T:0.30
Consensus pattern (85 bp):
ATGACGGGGGCTTCAATGACACGCAATGTAAGTCATACACGCGTGTCATAAATTTATGACACACA
AATGTGTGTCATATTAATTT
Found at i:24653 original size:170 final size:170
Alignment explanation
Indices: 24348--24655 Score: 474
Period size: 170 Copynumber: 1.8 Consensus size: 170
24338 GTCTTTTTAA
* * * *
24348 ATGACGTGTGCTTCAATGACACGCAATGTAAGTCATATACGCGTGTCATAAATTTATGACACACA
1 ATGACGGGGGCTTCAATGACACGCAATGTAAGTCATACACGCGTGTCATAAATTTATGACAAACA
* * * *
24413 AATGTATGTCAAATAGATTTATGACGGGGGCTTCAATGACGCGCAATGTAAGTCATACATACGTG
66 AATATATGTCAAATAGATTTATGACGGAGGCTTCAATGACACGCAATGTAAGTCATACATACGCG
24478 TCATAAATTTATGACGCATAAATGTGTGTCATCTTAATTT
131 TCATAAATTTATGACGCATAAATGTGTGTCATCTTAATTT
* * * *
24518 ATGACGGGGGCTTTAATGACGCGCAATGTAAGTCATACATGTGTGTCATAAATTTATGACAAACA
1 ATGACGGGGGCTTCAATGACACGCAATGTAAGTCATACACGCGTGTCATAAATTTATGACAAACA
* *
24583 AATATGTGTCATATTA-ATTTATGACGGAGGCTTCAATGACACGCAATGTAAGTCATACATACGC
66 AATATATGTCA-AATAGATTTATGACGGAGGCTTCAATGACACGCAATGTAAGTCATACATACGC
24647 GTCATAAAT
130 GTCATAAAT
24656 GTGCGTCATA
Statistics
Matches: 123, Mismatches: 14, Indels: 2
0.88 0.10 0.01
Matches are distributed among these distances:
170 120 0.98
171 3 0.02
ACGTcount: A:0.34, C:0.16, G:0.20, T:0.30
Consensus pattern (170 bp):
ATGACGGGGGCTTCAATGACACGCAATGTAAGTCATACACGCGTGTCATAAATTTATGACAAACA
AATATATGTCAAATAGATTTATGACGGAGGCTTCAATGACACGCAATGTAAGTCATACATACGCG
TCATAAATTTATGACGCATAAATGTGTGTCATCTTAATTT
Found at i:25830 original size:37 final size:36
Alignment explanation
Indices: 25789--25867 Score: 88
Period size: 37 Copynumber: 2.2 Consensus size: 36
25779 ATGAAAACTA
* *
25789 ATTAAATAACATGAA-AAAAAAATAAACGATAAAAAAT
1 ATTAAATAACATAAAGAAAAAAAT-AACAAT-AAAAAT
** *
25826 ATTAAATTTCATAAAGAAAAAAATAACAATGAAAAT
1 ATTAAATAACATAAAGAAAAAAATAACAATAAAAAT
25862 ATTAAA
1 ATTAAA
25868 AGGAAAAAAA
Statistics
Matches: 36, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
36 11 0.31
37 17 0.47
38 8 0.22
ACGTcount: A:0.67, C:0.05, G:0.05, T:0.23
Consensus pattern (36 bp):
ATTAAATAACATAAAGAAAAAAATAACAATAAAAAT
Found at i:26960 original size:8 final size:8
Alignment explanation
Indices: 26947--26974 Score: 56
Period size: 8 Copynumber: 3.5 Consensus size: 8
26937 AATAAGTAAT
26947 AAAATAGA
1 AAAATAGA
26955 AAAATAGA
1 AAAATAGA
26963 AAAATAGA
1 AAAATAGA
26971 AAAA
1 AAAA
26975 GAAGGAAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.79, C:0.00, G:0.11, T:0.11
Consensus pattern (8 bp):
AAAATAGA
Found at i:26983 original size:17 final size:16
Alignment explanation
Indices: 26947--26985 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
26937 AATAAGTAAT
*
26947 AAAATAGAAAAATAGA
1 AAAATAGAAAAAAAGA
*
26963 AAAATAGAAAAAGAAGG
1 AAAATAGAAAAA-AAGA
26980 AAAATA
1 AAAATA
26986 ATAATTATAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
16 12 0.60
17 8 0.40
ACGTcount: A:0.74, C:0.00, G:0.15, T:0.10
Consensus pattern (16 bp):
AAAATAGAAAAAAAGA
Found at i:27081 original size:12 final size:12
Alignment explanation
Indices: 27058--27119 Score: 56
Period size: 12 Copynumber: 5.0 Consensus size: 12
27048 AACTATATAT
27058 AATATGTTTCAAA
1 AATAT-TTTCAAA
27071 AATATTTTCAAA
1 AATATTTTCAAA
* *
27083 ACTATATATT-ATAT
1 A--ATATTTTCA-AA
27097 AAT-TTTTCAAA
1 AATATTTTCAAA
27108 AATATTTTCAAA
1 AATATTTTCAAA
27120 CTACATGTTA
Statistics
Matches: 40, Mismatches: 4, Indels: 11
0.73 0.07 0.20
Matches are distributed among these distances:
11 7 0.17
12 19 0.47
13 6 0.15
14 8 0.20
ACGTcount: A:0.47, C:0.08, G:0.02, T:0.44
Consensus pattern (12 bp):
AATATTTTCAAA
Found at i:27121 original size:36 final size:36
Alignment explanation
Indices: 26994--27280 Score: 160
Period size: 36 Copynumber: 7.8 Consensus size: 36
26984 TAATAATTAT
*
26994 AAAAATATTTTCAAAACTATATAATACATATATTTGTT-
1 AAAAATATTTTCAAAACTATAT-AT-TATATATTT-TTC
* * *
27032 AAAAAAATTGTTTTAAAACTATATA-TA-ATATGTTTC
1 AAAAATA-T-TTTCAAAACTATATATTATATATTTTTC
27068 AAAAATATTTTCAAAACTATATATTATATAATTTTTC
1 AAAAATATTTTCAAAACTATATATTATAT-ATTTTTC
* * *
27105 AAAAATATTTTC-AAACTACATGTTATATAGTTTTC
1 AAAAATATTTTCAAAACTATATATTATATATTTTTC
** *****
27140 AAATTTAAAAAAAAAAC-ATATATTATATATATTTTC
1 AAAAATATTTTCAAAACTATATATTATATAT-TTTTC
* * *
27176 AAAATGTTTTTTTAAAAAAAAC-ATATATTATATATATTTTC
1 AAAA--ATATTTT---CAAAACTATATATTATATAT-TTTTC
* *
27217 -AAAATGA-CTTAAAAACTATATATTATATATAATTTTTC
1 AAAAAT-ATTTTCAAAACTATATA-T-TATAT-ATTTTTC
* **
27255 -AAAATGTTTTGGAAACTATATATTAT
1 AAAAATATTTTCAAAACTATATATTAT
27281 GTATAAATTT
Statistics
Matches: 197, Mismatches: 33, Indels: 40
0.73 0.12 0.15
Matches are distributed among these distances:
34 14 0.07
35 32 0.16
36 47 0.24
37 21 0.11
38 38 0.19
39 4 0.02
40 16 0.08
41 25 0.13
ACGTcount: A:0.47, C:0.07, G:0.03, T:0.43
Consensus pattern (36 bp):
AAAAATATTTTCAAAACTATATATTATATATTTTTC
Found at i:27229 original size:38 final size:39
Alignment explanation
Indices: 27148--27261 Score: 137
Period size: 41 Copynumber: 2.9 Consensus size: 39
27138 TCAAATTTAA
**
27148 AAAAAAAACATATATTATATATATTTTCAAAATGTTTTTTT
1 AAAAAAAACATATATTATATATATTTTCAAAATG--TACTT
27189 AAAAAAAACATATATTATATATATTTTCAAAATG-ACTT
1 AAAAAAAACATATATTATATATATTTTCAAAATGTACTT
27227 ---AAAAACTATATATTATATATAATTTTTCAAAATGT
1 AAAAAAAAC-ATATATTATATAT-A-TTTTCAAAATGT
27262 TTTGGAAACT
Statistics
Matches: 67, Mismatches: 2, Indels: 10
0.85 0.03 0.13
Matches are distributed among these distances:
35 6 0.09
36 13 0.19
37 1 0.01
38 13 0.19
41 34 0.51
ACGTcount: A:0.49, C:0.06, G:0.03, T:0.42
Consensus pattern (39 bp):
AAAAAAAACATATATTATATATATTTTCAAAATGTACTT
Found at i:27271 original size:38 final size:37
Alignment explanation
Indices: 27192--27298 Score: 137
Period size: 38 Copynumber: 2.9 Consensus size: 37
27182 TTTTTTTAAA
27192 AAAAAC-ATATATTATATAT-ATTTTCAAAATGACTT
1 AAAAACTATATATTATATATAATTTTCAAAATGACTT
**
27227 AAAAACTATATATTATATATAATTTTTCAAAATGTTTT
1 AAAAACTATATATTATATATAA-TTTTCAAAATGACTT
** *
27265 GGAAACTATATATTATGTATAAATTTTCAAAATG
1 AAAAACTATATATTATATAT-AATTTTCAAAATG
27299 CTTTATAGTT
Statistics
Matches: 63, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
35 6 0.10
36 13 0.21
37 1 0.02
38 41 0.65
39 2 0.03
ACGTcount: A:0.46, C:0.07, G:0.06, T:0.42
Consensus pattern (37 bp):
AAAAACTATATATTATATATAATTTTCAAAATGACTT
Found at i:28278 original size:165 final size:165
Alignment explanation
Indices: 27883--28582 Score: 822
Period size: 165 Copynumber: 4.3 Consensus size: 165
27873 AATTTATTGA
* * * * * * * * *
27883 CAGATAGCCCTTCTTGCCTTGAGCTATGCTGTAAATGATGTG-CCTTGGAGCTGAGCATAGTCGA
1 CAGATAACCCTTCTAGACTTGAGTTATACTGTAAATGATGTGCCCTCGAAGCTGAGTATAATCGA
* * * * * ** *
27947 ACTC-AAAGGTCTTTGGCAGATAGCCCTTCTAGCCTTGAGCTATACCCCAAATGATGTGTCATT-
66 ACTCGAGA-GTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATTCTGCAAATGATGTG-CCTTG
* * *
28010 GAGTTGAGCGTAATCAAACTCAAAGGTCTTT-GTTGG
129 GAGCTGAGCGTAGTCAAACTCAAAGGTCTTTGGTTAG
* ** *
28046 CAGATAACCCTTCTAG-CATTGAGTTATGCTACAAATGATGTGCCCTCGAAGCTGAGTGTAATCG
1 CAGATAACCCTTCTAGAC-TTGAGTTATACTGTAAATGATGTGCCCTCGAAGCTGAGTATAATCG
* *
28110 AACTCGAGAGTCTTTAGCAGATAGCCCTTCTCGACTTAAGTTATTCTGCAAATGATGTGCCTTGG
65 AACTCGAGAGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATTCTGCAAATGATGTGCCTTGG
* *
28175 AGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTAG
130 AGCTGAGCGTAGTCAAACTCAAAGGTCTTTGGTTAG
* *
28211 CAGATAACCCTTCTCGACTTAAGTTATACTGTAAATGATGTGCCCTCGAAGCTGAGTATAATCGA
1 CAGATAACCCTTCTAGACTTGAGTTATACTGTAAATGATGTGCCCTCGAAGCTGAGTATAATCGA
* * * * *
28276 ACTCGAGGGTTTTTGACAGATAACCCTTCTCGACTTAAGCTATTCTGCAAATAATGTGCCTTGGA
66 ACTCGAGAGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATTCTGCAAATGATGTGCCTTGGA
* *
28341 GCTGAGCGTAGTCAAACTCGAAGGTCTTTCGGTGA-
131 GCTGAGCGTAGTCAAACTCAAAGGTCTTT-GGTTAG
* *
28376 CAGATAACCCTTCTAGCCTTGAGTTATGA-TGTAAATGATGTGCCCTCGAAGCTGAGTGTAATCG
1 CAGATAACCCTTCTAGACTTGAGTTAT-ACTGTAAATGATGTGCCCTCGAAGCTGAGTATAATCG
* * * * *
28440 AACTCGAGGGTCTTTGGCAGATAGCCCTTCTCAACTTACGCTATGT-TGTAAATGATGTGTCTTG
65 AACTCGAGAGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTAT-TCTGCAAATGATGTGCCTTG
* * * *
28504 GAGATGAGCATAGTCGAACTCAAAGGTCTTTGGTTGG
129 GAGCTGAGCGTAGTCAAACTCAAAGGTCTTTGGTTAG
* * * *
28541 CAGATAACCCTTCTTGACTTAAGTTATATTGTGAATGATGTG
1 CAGATAACCCTTCTAGACTTGAGTTATACTGTAAATGATGTG
28583 GCTTGGAGTT
Statistics
Matches: 464, Mismatches: 62, Indels: 20
0.85 0.11 0.04
Matches are distributed among these distances:
162 1 0.00
163 38 0.08
164 94 0.20
165 324 0.70
166 7 0.02
ACGTcount: A:0.26, C:0.20, G:0.24, T:0.31
Consensus pattern (165 bp):
CAGATAACCCTTCTAGACTTGAGTTATACTGTAAATGATGTGCCCTCGAAGCTGAGTATAATCGA
ACTCGAGAGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATTCTGCAAATGATGTGCCTTGGA
GCTGAGCGTAGTCAAACTCAAAGGTCTTTGGTTAG
Found at i:28532 original size:330 final size:328
Alignment explanation
Indices: 27883--28640 Score: 953
Period size: 330 Copynumber: 2.3 Consensus size: 328
27873 AATTTATTGA
* * * * * * * *
27883 CAGATAGCCCTTCTTGCCTTGAGCTATGCTGTAAATGATGTGCCTTGGAGCTGAGCATAGTCGAA
1 CAGATAACCCTTCTTGACTTAAGTTATACTGTAAATGATGTGCCTCGAAGCTGAGCATAATCGAA
* * * * *
27948 CTCAAAGGTCTTTGGCAGATAGCCCTTCTAGCCTTGAGCTATACCCCAAATGATGTGTCATTGAG
66 CTCAAAGGTCTTTGACAGATAACCCTTCTAGACTTAAGCTATACCCCAAATAATGTGTCATTGAG
* * * *
28013 TTGAGCGTAATCAAACTCAAAGGTCTTTGTTGGCAGATAACCCTTCTAGCATTGAGTTATGCTAC
131 CTGAGCGTAATCAAACTCAAAGGTCTTTGGTGACAGATAACCCTTCTAGCATTGAGTTATGATAC
*
28078 AAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGAGAGTCTTTAGCAGATAGCCCTTCTCG
196 AAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGAGAGTCTTTAGCAGATAGCCCTTCTCA
* * * *
28143 ACTTAAGTTATTCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGT
261 ACTTAAGCTATTCTGCAAATGATGTGCCTTGGAGATGAGCATAGTCGAACTCAAAGGTCTTTGGT
28208 TAG
326 TAG
* *
28211 CAGATAACCCTTCTCGACTTAAGTTATACTGTAAATGATGTGCCCTCGAAGCTGAGTATAATCGA
1 CAGATAACCCTTCTTGACTTAAGTTATACTGTAAATGATGTG-CCTCGAAGCTGAGCATAATCGA
* * * * * ** *
28276 ACTCGAGGGTTTTTGACAGATAACCCTTCTCGACTTAAGCTATTCTGCAAATAATGTG-CCTTGG
65 ACTCAAAGGTCTTTGACAGATAACCCTTCTAGACTTAAGCTATACCCCAAATAATGTGTCATT-G
* * *
28340 AGCTGAGCGTAGTCAAACTCGAAGGTCTTTCGGTGACAGATAACCCTTCTAGCCTTGAGTTATGA
129 AGCTGAGCGTAATCAAACTCAAAGGTCTTT-GGTGACAGATAACCCTTCTAGCATTGAGTTATGA
** * *
28405 TGTAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGAGGGTCTTTGGCAGATAGCCCTTC
193 TACAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGAGAGTCTTTAGCAGATAGCCCTTC
* * *
28470 TCAACTTACGCTATGT-TGTAAATGATGTGTCTTGGAGATGAGCATAGTCGAACTCAAAGGTCTT
258 TCAACTTAAGCTAT-TCTGCAAATGATGTGCCTTGGAGATGAGCATAGTCGAACTCAAAGGTCTT
*
28534 TGGTTGG
322 TGGTTAG
* * * * * * * *
28541 CAGATAACCCTTCTTGACTTAAGTTATATTGTGAATGATGTGGCTTGGAGTTGAGCGTAGTCGAA
1 CAGATAACCCTTCTTGACTTAAGTTATACTGTAAATGATGTGCCTCGAAGCTGAGCATAATCGAA
**
28606 CTTGAAGGTCTTTTGGTGACAGATAACCCTTCTAG
66 CTCAAAGGTC--TT--TGACAGATAACCCTTCTAG
28641 CCTTGAGTTA
Statistics
Matches: 365, Mismatches: 57, Indels: 11
0.84 0.13 0.03
Matches are distributed among these distances:
328 39 0.11
329 115 0.32
330 190 0.52
331 3 0.01
333 18 0.05
ACGTcount: A:0.25, C:0.20, G:0.24, T:0.31
Consensus pattern (328 bp):
CAGATAACCCTTCTTGACTTAAGTTATACTGTAAATGATGTGCCTCGAAGCTGAGCATAATCGAA
CTCAAAGGTCTTTGACAGATAACCCTTCTAGACTTAAGCTATACCCCAAATAATGTGTCATTGAG
CTGAGCGTAATCAAACTCAAAGGTCTTTGGTGACAGATAACCCTTCTAGCATTGAGTTATGATAC
AAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGAGAGTCTTTAGCAGATAGCCCTTCTCA
ACTTAAGCTATTCTGCAAATGATGTGCCTTGGAGATGAGCATAGTCGAACTCAAAGGTCTTTGGT
TAG
Found at i:28562 original size:249 final size:246
Alignment explanation
Indices: 27880--28976 Score: 1009
Period size: 249 Copynumber: 4.4 Consensus size: 246
27870 ACCAATTTAT
* * * * * * *
27880 TGACAGATAGCCCTTCTTGCCTTGAGCTATGCTGTAAATGATGTGCCTTGGAGCTGAGCATAGTC
1 TGACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCTCGAAGCTGAGCGTAATC
* * * ** *
27945 GAACTCAAAGGTCTTTGGCAGATAGCCCTTCT-AGCCTTGAGCTATACCCCAAATGATGTGTCAT
66 GAACTCGAAGGTCTTTGGCAGATAGCCCTTCTCA-ACTTAAGCTATACTGCAAATGATGTG-CCT
* * *
28009 T-GAGTTGAGCGTAATCAAACTCAAAGGTCTTTGTTGGCAGATAACCCTTCTAG-CATTGAGTTA
129 TGGAGTTGAGCATAATCGAACTCAAAGGTCTTTGTTGGCAGATAACCCTTCTAGAC-TTAAGTTA
* * * * * *
28072 TGCTACAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCG-AGAGTCTTT--
193 TTCTGCAAATGATGTG-CCTTGGAGCTGAGCGTAGTCGAACTCGAAG-GTCTTTGG
* * * * * * * * * *
28125 AG-CAGATAGCCCTTCTCGACTTAAGTTATTCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTC
1 TGACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCTCGAAGCTGAGCGTAATC
* * * *
28189 GAACTCGAAGGTCTTTGGTTAGCAGATAACCCTTCTCGACTTAAGTTATACTGTAAATGATGTGC
66 GAACTCGAAGGTCTTT-G---GCAGATAGCCCTTCTCAACTTAAGCTATACTGCAAATGATGTG-
* * * * * * * * *
28254 CCTCGAAGCTGAGTATAATCGAACTC-GAGG-GTTT-TTGACAGATAACCCTTCTCGACTTAAGC
126 CCTTGGAGTTGAGCATAATCGAACTCAAAGGTCTTTGTTGGCAGATAACCCTTCTAGACTTAAGT
* *
28316 TATTCTGCAAATAATGTGCCTTGGAGCTGAGCGTAGTCAAACTCGAAGGTCTTTCGG
191 TATTCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTT-GG
* *
28373 TGACAGATAACCCTTCTAGCCTTGAGTTATGATGTAAATGATGTGCCCTCGAAGCTGAGTGTAAT
1 TGACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTG-CCTCGAAGCTGAGCGTAAT
* * ** * *
28438 CGAACTCGAGGGTCTTTGGCAGATAGCCCTTCTCAACTTACGCTATGTTGTAAATGATGTGTCTT
65 CGAACTCGAAGGTCTTTGGCAGATAGCCCTTCTCAACTTAAGCTATACTGCAAATGATGTGCCTT
* * *
28503 GGAGATGAGCATAGTCGAACTCAAAGGTCTTTGGTTGGCAGATAACCCTTCTTGACTTAAGTTAT
130 GGAGTTGAGCATAATCGAACTCAAAGGTCTTT-GTTGGCAGATAACCCTTCTAGACTTAAGTTAT
** * * *
28568 AT-TGTGAATGATGTGGCTTGGAGTTGAGCGTAGTCGAACTTGAAGGTCTTTTGG
194 -TCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTC-TTTGG
* *
28622 TGACAGATAACCCTTCTAGCCTTGAGTTATGCTATAAATGATGTGCCCTCGAAGCTGAGTGTAAT
1 TGACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTG-CCTCGAAGCTGAGCGTAAT
* * * * * * **
28687 AGAACTCGAACGTCTTTGGTAGATAGCCCTTCTCGACTTAAGATATGCTGCAAATGACATGCCTT
65 CGAACTCGAAGGTCTTTGGCAGATAGCCCTTCTCAACTTAAGCTATACTGCAAATGATGTGCCTT
* * * *
28752 GGAGTTGAGCGTAGTCGAACTCAAAGGTCTTTGGTTGGCAGATAACCCTTCTAGCCTTGAGTTAT
130 GGAGTTGAGCATAATCGAACTCAAAGGTCTTT-GTTGGCAGATAACCCTTCTAGACTTAAGTTAT
* * ** * * * * *
28817 GT-TGTAAATGATGTGCCCTCAATACTGAGTGTAATCGAACTAGAGGGTCTTT-G
194 -TCTGCAAATGATGTGCCTTGGA-GCTGAGCGTAGTCGAACTCGAAGGTCTTTGG
* * * * * ** * * *
28870 -G-CAGATAGCCCTTCTCGACTTAAGCTATGCTACAAATGATGTGCCTTGGAGCTGAGCGTAGTC
1 TGACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCTCGAAGCTGAGCGTAATC
* *
28933 GAACTCGAAGGTCTTTGTTGGCAGATAACCCTTCTCGACTTAAG
66 GAACTCGAAGGTC--T-TTGGCAGATAGCCCTTCTCAACTTAAG
28977 TTATGCAGCA
Statistics
Matches: 708, Mismatches: 121, Indels: 43
0.81 0.14 0.05
Matches are distributed among these distances:
244 70 0.10
245 77 0.11
246 115 0.16
247 9 0.01
248 66 0.09
249 316 0.45
250 55 0.08
ACGTcount: A:0.25, C:0.20, G:0.24, T:0.30
Consensus pattern (246 bp):
TGACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCTCGAAGCTGAGCGTAATC
GAACTCGAAGGTCTTTGGCAGATAGCCCTTCTCAACTTAAGCTATACTGCAAATGATGTGCCTTG
GAGTTGAGCATAATCGAACTCAAAGGTCTTTGTTGGCAGATAACCCTTCTAGACTTAAGTTATTC
TGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGG
Found at i:28590 original size:414 final size:413
Alignment explanation
Indices: 27879--28989 Score: 1268
Period size: 414 Copynumber: 2.7 Consensus size: 413
27869 GACCAATTTA
* * * * * * * ** *
27879 TTGACAGATAGCCCTTCTTGCCTTGAGCTATGCTGTAAATGATGTGCCTTGGAGCTGAGCATAGT
1 TTGACAGATAACCCTTCTCGACTTAAGATATGCTGCAAATAACATGCCTTGGAGCTGAGCGTAGT
* * * ***
27944 CGAACTCAAAGGTCTTT-G--G-CAGATAGCCCTTCTAGCCTTGAGCTAT-ACCCCAAATGATGT
66 CAAACTCAAAGGTCTTTGGTTGACAGATAACCCTTCTAGCCTTGAGTTATGA-TGTAAATGATGT
* * * * * * *
28004 G---TCATTGAGTTGAGCGTAATCAAACTCA-AAGGTCTTTGTTGGCAGATAACCCTTCT-AGCA
130 GCCCTCAAT-A-CTGAGTGTAATCGAACT-AGAGGGTC--T-TTGGCAGATAGCCCTTCTCAAC-
* * * * * ** * *
28064 TTGAGTTATGCTACAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTC-GAGAGTC--T-TT
188 TTAAGCTATGCTACAAATGATGTG-CCTTGGAGATGAGCATAGTCGAACTCAAAG-GTCTTTGTT
* *
28125 AGCAGATAGCCCTTCTCGACTTAAGTTATTCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCG
251 GGCAGATAACCCTTCTCGACTTAAGTTATTCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCG
* * *
28190 AACTCGAAGGTC-TTTGGTTAGCAGATAACCCTTCTCGACTTAAGTTATACTGTAAATGATGTGC
316 AACTCGAAGGTCTTTTGGTGA-CAGATAACCCTTCTAGACTTAAGTTATACTATAAATGATGTGC
* ** *
28254 CCTCGAAGCTGAGTATAATCGAACTCGAGGGTTT
380 CCTCGAAGCTGAGTATAATAGAACTCGAACGTCT
* * **
28288 TTGACAGATAACCCTTCTCGACTTAAGCTATTCTGCAAATAATGTGCCTTGGAGCTGAGCGTAGT
1 TTGACAGATAACCCTTCTCGACTTAAGATATGCTGCAAATAACATGCCTTGGAGCTGAGCGTAGT
*
28353 CAAACTCGAAGGTCTTTCGG-TGACAGATAACCCTTCTAGCCTTGAGTTATGATGTAAATGATGT
66 CAAACTCAAAGGTCTTT-GGTTGACAGATAACCCTTCTAGCCTTGAGTTATGATGTAAATGATGT
* * *
28417 GCCCTCGAA-GCTGAGTGTAATCGAACTCGAGGGTCTTTGGCAGATAGCCCTTCTCAACTTACGC
130 GCCCTC-AATACTGAGTGTAATCGAACTAGAGGGTCTTTGGCAGATAGCCCTTCTCAACTTAAGC
* ** *
28481 TATGTTGTAAATGATGTGTCTTGGAGATGAGCATAGTCGAACTCAAAGGTCTTTGGTTGGCAGAT
194 TATGCTACAAATGATGTGCCTTGGAGATGAGCATAGTCGAACTCAAAGGTCTTT-GTTGGCAGAT
* ** * * *
28546 AACCCTTCTTGACTTAAGTTATAT-TGTGAATGATGTGGCTTGGAGTTGAGCGTAGTCGAACTTG
258 AACCCTTCTCGACTTAAGTTAT-TCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCG
* * *
28610 AAGGTCTTTTGGTGACAGATAACCCTTCTAGCCTTGAGTTATGCTATAAATGATGTGCCCTCGAA
322 AAGGTCTTTTGGTGACAGATAACCCTTCTAGACTTAAGTTATACTATAAATGATGTGCCCTCGAA
*
28675 GCTGAGTGTAATAGAACTCGAACGTCT
387 GCTGAGTATAATAGAACTCGAACGTCT
** * * *
28702 TTGGTAGATAGCCCTTCTCGACTTAAGATATGCTGCAAATGACATGCCTTGGAGTTGAGCGTAGT
1 TTGACAGATAACCCTTCTCGACTTAAGATATGCTGCAAATAACATGCCTTGGAGCTGAGCGTAGT
* * *
28767 CGAACTCAAAGGTCTTTGGTTGGCAGATAACCCTTCTAGCCTTGAGTTATGTTGTAAATGATGTG
66 CAAACTCAAAGGTCTTTGGTTGACAGATAACCCTTCTAGCCTTGAGTTATGATGTAAATGATGTG
*
28832 CCCTCAATACTGAGTGTAATCGAACTAGAGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTA
131 CCCTCAATACTGAGTGTAATCGAACTAGAGGGTCTTTGGCAGATAGCCCTTCTCAACTTAAGCTA
* * *
28897 TGCTACAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGTTGGCAGATAAC
196 TGCTACAAATGATGTGCCTTGGAGATGAGCATAGTCGAACTCAAAGGTCTTTGTTGGCAGATAAC
* *
28962 CCTTCTCGACTTAAGTTATGCAGCAAAT
261 CCTTCTCGACTTAAGTTATTCTGCAAAT
28990 AGTTTCTTCA
Statistics
Matches: 595, Mismatches: 86, Indels: 38
0.83 0.12 0.05
Matches are distributed among these distances:
409 72 0.12
410 22 0.04
411 38 0.06
412 5 0.01
413 74 0.12
414 373 0.63
415 8 0.01
416 2 0.00
417 1 0.00
ACGTcount: A:0.26, C:0.20, G:0.24, T:0.31
Consensus pattern (413 bp):
TTGACAGATAACCCTTCTCGACTTAAGATATGCTGCAAATAACATGCCTTGGAGCTGAGCGTAGT
CAAACTCAAAGGTCTTTGGTTGACAGATAACCCTTCTAGCCTTGAGTTATGATGTAAATGATGTG
CCCTCAATACTGAGTGTAATCGAACTAGAGGGTCTTTGGCAGATAGCCCTTCTCAACTTAAGCTA
TGCTACAAATGATGTGCCTTGGAGATGAGCATAGTCGAACTCAAAGGTCTTTGTTGGCAGATAAC
CCTTCTCGACTTAAGTTATTCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGG
TCTTTTGGTGACAGATAACCCTTCTAGACTTAAGTTATACTATAAATGATGTGCCCTCGAAGCTG
AGTATAATAGAACTCGAACGTCT
Found at i:28727 original size:165 final size:164
Alignment explanation
Indices: 28537--28982 Score: 606
Period size: 165 Copynumber: 2.7 Consensus size: 164
28527 AGGTCTTTGG
* * * ** ** *
28537 TTGGCAGATAACCCTTCTTGACTTAAGTTATATTGTGAATGATGTGGCTTGGAGTTGAGCGTAGT
1 TTGGCAGATAGCCCTTCTCGACTTAAGATATGCTGCAAATGATGTGCCTTGGAGTTGAGCGTAGT
* *
28602 CGAACTTGAAGGTCTTTTGGTGACAGATAACCCTTCTAGCCTTGAGTTATGCTATAAATGATGTG
66 CGAACTCGAAGGTC-TTTGGTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTATAAATGATGTG
* *
28667 CCCTCGAA-GCTGAGTGTAATAGAACTCGAACGTCT
130 CCCTC-AATACTGAGTGTAATAGAACTAGAACGTCT
* **
28702 TTGGTAGATAGCCCTTCTCGACTTAAGATATGCTGCAAATGACATGCCTTGGAGTTGAGCGTAGT
1 TTGGCAGATAGCCCTTCTCGACTTAAGATATGCTGCAAATGATGTGCCTTGGAGTTGAGCGTAGT
* * *
28767 CGAACTCAAAGGTCTTTGGTTGGCAGATAACCCTTCTAGCCTTGAGTTATGTTGTAAATGATGTG
66 CGAACTCGAAGGTCTTTGG-TGGCAGATAACCCTTCTAGCCTTGAGTTATGCTATAAATGATGTG
* **
28832 CCCTCAATACTGAGTGTAATCGAACTAGAGGGTCT
130 CCCTCAATACTGAGTGTAATAGAACTAGAACGTCT
* * *
28867 TTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTACAAATGATGTGCCTTGGAGCTGAGCGTAGT
1 TTGGCAGATAGCCCTTCTCGACTTAAGATATGCTGCAAATGATGTGCCTTGGAGTTGAGCGTAGT
* * * *
28932 CGAACTCGAAGGTCTTTGTTGGCAGATAACCCTTCTCGACTTAAGTTATGC
66 CGAACTCGAAGGTCTTTGGTGGCAGATAACCCTTCTAGCCTTGAGTTATGC
28983 AGCAAATAGT
Statistics
Matches: 246, Mismatches: 33, Indels: 5
0.87 0.12 0.02
Matches are distributed among these distances:
164 35 0.14
165 211 0.86
ACGTcount: A:0.25, C:0.19, G:0.25, T:0.31
Consensus pattern (164 bp):
TTGGCAGATAGCCCTTCTCGACTTAAGATATGCTGCAAATGATGTGCCTTGGAGTTGAGCGTAGT
CGAACTCGAAGGTCTTTGGTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTATAAATGATGTGC
CCTCAATACTGAGTGTAATAGAACTAGAACGTCT
Found at i:30215 original size:83 final size:84
Alignment explanation
Indices: 30111--30331 Score: 214
Period size: 95 Copynumber: 2.5 Consensus size: 84
30101 AGCTAGCTGG
*
30111 ATCCATAAAGCCGAGGCGTTTAACCAATTGCTCTAGAGGGACAGC-TTA-ATA-TATAAACACCT
1 ATCCATAAAGCAG-GGCGTTTAACCAATT-CTCTAGAGGGACAGCTTTATATAGTATAAACACCT
* *
30173 TTATCAGGTTAGCTGAATTTT
64 TTATCAGGCTAGCTGAATATT
* *
30194 ATCCATAAAGTCAGGGTGTTTAACCAATTCCCTTAGAGGGACAGCTCAAGCTTTATTGTATAGTA
1 ATCCATAAAG-CAGGGCGTTTAACCAATTCTC-TAGAGGG--A---C-AGCTTTA---TATAGTA
**
30259 TAATTACCTTTATCAGGCTAGCTGAATATT
55 TAAACACCTTTATCAGGCTAGCTGAATATT
*
30289 ATCCATAAAGCCAGGGCGTTTAACCAATTTCTCTATAGGGACA
1 ATCCATAAAG-CAGGGCGTTTAACCAA-TTCTCTAGAGGGACA
30332 ACTCAAGCTT
Statistics
Matches: 112, Mismatches: 11, Indels: 24
0.76 0.07 0.16
Matches are distributed among these distances:
82 2 0.02
83 31 0.28
84 2 0.02
85 1 0.01
88 1 0.01
89 4 0.04
90 4 0.04
93 1 0.01
94 3 0.03
95 59 0.53
96 4 0.04
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.31
Consensus pattern (84 bp):
ATCCATAAAGCAGGGCGTTTAACCAATTCTCTAGAGGGACAGCTTTATATAGTATAAACACCTTT
ATCAGGCTAGCTGAATATT
Found at i:30329 original size:95 final size:94
Alignment explanation
Indices: 30159--30354 Score: 268
Period size: 95 Copynumber: 2.1 Consensus size: 94
30149 GGACAGCTTA
** * * * *
30159 ATATATAAACACCTTTATCAGGTTAGCTGAATTTTATCCATAAAGTCAGGGTGTTTAACCAATTC
1 ATATATAATTACCTTTATCAGGCTAGCTGAATATTATCCATAAAGCCAGGGCGTTTAACCAATTC
* * *
30224 CCTTAGAGGGACAGCTCAAGCTTTATTGT
66 CCTTAGAGGGACAACTCAAGCTTCATTAT
30253 ATAGTATAATTACCTTTATCAGGCTAGCTGAATATTATCCATAAAGCCAGGGCGTTTAACCAATT
1 ATA-TATAATTACCTTTATCAGGCTAGCTGAATATTATCCATAAAGCCAGGGCGTTTAACCAATT
* *
30318 -TCTCTATAGGGACAACTCAAGCTTCATTAT
65 CCCT-TAGAGGGACAACTCAAGCTTCATTAT
30348 ATATATA
1 ATATATA
30355 TAATATTATA
Statistics
Matches: 89, Mismatches: 11, Indels: 4
0.86 0.11 0.04
Matches are distributed among these distances:
94 9 0.10
95 80 0.90
ACGTcount: A:0.33, C:0.18, G:0.15, T:0.34
Consensus pattern (94 bp):
ATATATAATTACCTTTATCAGGCTAGCTGAATATTATCCATAAAGCCAGGGCGTTTAACCAATTC
CCTTAGAGGGACAACTCAAGCTTCATTAT
Found at i:32429 original size:11 final size:11
Alignment explanation
Indices: 32388--32430 Score: 50
Period size: 11 Copynumber: 3.9 Consensus size: 11
32378 GTGTAGTTGC
* *
32388 TTTGTTTGTGT
1 TTTGGTTGTTT
* *
32399 TTTGGTTGGTG
1 TTTGGTTGTTT
32410 TTTGGTTGTTT
1 TTTGGTTGTTT
32421 TTTGGTTGTT
1 TTTGGTTGTT
32431 GGTTTTTTCG
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
11 26 1.00
ACGTcount: A:0.00, C:0.00, G:0.33, T:0.67
Consensus pattern (11 bp):
TTTGGTTGTTT
Found at i:32940 original size:25 final size:28
Alignment explanation
Indices: 32908--32970 Score: 78
Period size: 28 Copynumber: 2.3 Consensus size: 28
32898 TGGACCTTAA
* *
32908 AATAAAATAA-AAA-AAGAA-AAATATT
1 AATAAAATAATAAATAAAAACAAATAAT
32933 AATAAAATAATAAATAAAAACAAATAAT
1 AATAAAATAATAAATAAAAACAAATAAT
32961 AATAATAATA
1 AATAA-AATA
32971 TATTATAATA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
25 10 0.31
26 3 0.09
27 4 0.12
28 11 0.34
29 4 0.12
ACGTcount: A:0.75, C:0.02, G:0.02, T:0.22
Consensus pattern (28 bp):
AATAAAATAATAAATAAAAACAAATAAT
Found at i:32967 original size:31 final size:32
Alignment explanation
Indices: 32905--32982 Score: 81
Period size: 31 Copynumber: 2.5 Consensus size: 32
32895 TGTTGGACCT
*
32905 TAAAAT-A-AAATAAAAAAAGAAAAATATTAA
1 TAAAATAATAAATAAAAAAAGAAAAATAATAA
* *
32935 TAAAATAATAAATAAAAACA-AATAATAATAA
1 TAAAATAATAAATAAAAAAAGAAAAATAATAA
* *
32966 TAATATATTATAATAAA
1 TAAAATAATA-AATAAA
32983 TTTTTTCAAA
Statistics
Matches: 40, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
30 6 0.15
31 18 0.45
32 16 0.40
ACGTcount: A:0.72, C:0.01, G:0.01, T:0.26
Consensus pattern (32 bp):
TAAAATAATAAATAAAAAAAGAAAAATAATAA
Found at i:32996 original size:29 final size:29
Alignment explanation
Indices: 32964--33037 Score: 71
Period size: 32 Copynumber: 2.5 Consensus size: 29
32954 AAATAATAAT
32964 AATAATATATTATAATAAATT-TTTTCAAA
1 AATAATATATTATAA-AAATTGTTTTCAAA
* *
32993 AATATTATATATTTTTAAAAGTTGTTTTCAAA
1 AATA--ATATA-TTATAAAAATTGTTTTCAAA
*
33025 ACT-ATATATTATA
1 AATAATATATTATA
33038 TATGTCTTCA
Statistics
Matches: 37, Mismatches: 4, Indels: 9
0.74 0.08 0.18
Matches are distributed among these distances:
28 4 0.11
29 9 0.24
31 9 0.24
32 15 0.41
ACGTcount: A:0.46, C:0.04, G:0.03, T:0.47
Consensus pattern (29 bp):
AATAATATATTATAAAAATTGTTTTCAAA
Found at i:33106 original size:39 final size:39
Alignment explanation
Indices: 32994--33289 Score: 290
Period size: 39 Copynumber: 7.5 Consensus size: 39
32984 TTTTTCAAAA
* **
32994 ATATTATAT-A-TTTTTAAAAGTTGTTTTC-AAAACTAT
1 ATATTATATAAGTTTTCAAAAAATGTTTTCAAAAACTAT
* * *
33030 ATATTATATATGTCTTCAAAATATGTTTTC-AAAACTAT
1 ATATTATATAAGTTTTCAAAAAATGTTTTCAAAAACTAT
33068 ATATTATATAAGTTTTCAAAAAAATGTTTTC-AAAACTAT
1 ATATTATATAAGTTTTC-AAAAAATGTTTTCAAAAACTAT
*
33107 ATATTATATAAGTTTTCAAAAAAAATGTTTTCAAAAATTAT
1 ATATTATATAAGTTTTC--AAAAAATGTTTTCAAAAACTAT
* ***
33148 ATATTATATATTATATATATTTTCAAAATGTTTTCAAAAACTAT
1 ATATTATATA--A-GT-T-TTCAAAAAATGTTTTCAAAAACTAT
*
33192 ATATTATATATATATTTTC--AAAATGTTTTCAAAAAACTAT
1 ATATTATATA-A-GTTTTCAAAAAATGTTTTC-AAAAACTAT
33232 ATATTATAT-A-TATTTC--AAAATGTTTTCAAAAAACTAT
1 ATATTATATAAGT-TTTCAAAAAATGTTTTC-AAAAACTAT
33269 ATATTATATAAGTTTTCAAAA
1 ATATTATATAAGTTTTCAAAA
33290 CTATATATTA
Statistics
Matches: 229, Mismatches: 15, Indels: 28
0.84 0.06 0.10
Matches are distributed among these distances:
36 10 0.04
37 34 0.15
38 43 0.19
39 49 0.21
40 34 0.15
41 19 0.08
42 1 0.00
43 6 0.03
44 30 0.13
45 1 0.00
46 2 0.01
ACGTcount: A:0.44, C:0.07, G:0.04, T:0.45
Consensus pattern (39 bp):
ATATTATATAAGTTTTCAAAAAATGTTTTCAAAAACTAT
Found at i:33162 original size:48 final size:44
Alignment explanation
Indices: 33128--33482 Score: 266
Period size: 39 Copynumber: 8.4 Consensus size: 44
33118 GTTTTCAAAA
*
33128 AAAATGTTTTCAAAAATTATATATTATATATTATATATATTTTC
1 AAAATGTTTTCAAAAACTATATATTATATATTATATATATTTTC
33172 AAAATGTTTTCAAAAAC--TATA-TAT-TA-TATATATATTTTC
1 AAAATGTTTTCAAAAACTATATATTATATATTATATATATTTTC
*
33211 AAAATGTTTTC--AAA--A-A-ACTATATATTATATATA-TTTC
1 AAAATGTTTTCAAAAACTATATATTATATATTATATATATTTTC
*
33248 AAAATGTTTTCAAAAAACTATATATTATATAAGTTTTCAAAACTATATATTAT-
1 AAAATGTTTTC-AAAAACTATATATTATAT-A---TT----A-TATATATTTTC
* * * * *
33301 ATAA-GTTTTCAAAAAATGTTTTCAAAACTATATATTATATA-AGTTTTC
1 AAAATGTTTTC-AAAAA--CTAT--ATATTATATATTATATATA-TTTTC
*
33349 AAAATGTTTTCAAAAAC--TATA-TAT-TA-TACATATATTTTC
1 AAAATGTTTTCAAAAACTATATATTATATATTATATATATTTTC
*
33388 AAAATGTTTTC--AAA--A-A-ACTATATATTATATATATTTTC
1 AAAATGTTTTCAAAAACTATATATTATATATTATATATATTTTC
33426 AAAATGTTTTCAAAAACTATATA-T-TATA-TATATATATTTT-
1 AAAATGTTTTCAAAAACTATATATTATATATTATATATATTTTC
33466 AAAATGTTTTCAAAAAC
1 AAAATGTTTTCAAAAAC
33483 AATTTTCTAA
Statistics
Matches: 258, Mismatches: 14, Indels: 82
0.73 0.04 0.23
Matches are distributed among these distances:
35 2 0.01
36 8 0.03
37 25 0.10
38 31 0.12
39 45 0.17
40 28 0.11
41 18 0.07
42 12 0.05
43 3 0.01
44 24 0.09
45 1 0.00
46 1 0.00
47 7 0.03
48 11 0.04
49 6 0.02
52 15 0.06
53 9 0.03
54 4 0.02
55 1 0.00
56 7 0.03
ACGTcount: A:0.45, C:0.08, G:0.03, T:0.44
Consensus pattern (44 bp):
AAAATGTTTTCAAAAACTATATATTATATATTATATATATTTTC
Found at i:33287 original size:27 final size:27
Alignment explanation
Indices: 33253--33316 Score: 114
Period size: 25 Copynumber: 2.4 Consensus size: 27
33243 ATTTCAAAAT
33253 GTTTTCAAAAAACTATATATTATATAA
1 GTTTTCAAAAAACTATATATTATATAA
33280 GTTTTC--AAAACTATATATTATATAA
1 GTTTTCAAAAAACTATATATTATATAA
33305 GTTTTCAAAAAA
1 GTTTTCAAAAAA
33317 TGTTTTCAAA
Statistics
Matches: 35, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
25 25 0.71
27 10 0.29
ACGTcount: A:0.47, C:0.08, G:0.05, T:0.41
Consensus pattern (27 bp):
GTTTTCAAAAAACTATATATTATATAA
Found at i:33322 original size:38 final size:37
Alignment explanation
Indices: 33280--33482 Score: 279
Period size: 38 Copynumber: 5.3 Consensus size: 37
33270 TATTATATAA
33280 GTTTTC-AAAACTATATATTATATA-AGTTTTCAAAAAAT
1 GTTTTCAAAAACTATATATTATATATA-TTTTC--AAAAT
33318 GTTTTC-AAAACTATATATTATATA-AGTTTTCAAAAT
1 GTTTTCAAAAACTATATATTATATATA-TTTTCAAAAT
33354 GTTTTCAAAAACTATATATTATACATATATTTTCAAAAT
1 GTTTTCAAAAACTATATATTAT--ATATATTTTCAAAAT
33393 GTTTTCAAAAAACTATATATTATATATATTTTCAAAAT
1 GTTTTC-AAAAACTATATATTATATATATTTTCAAAAT
*
33431 GTTTTCAAAAACTATATATTATATATATATATTTTAAAAT
1 GTTTTCAAAAACTATATA-T-TATATATAT-TTTCAAAAT
33471 GTTTTCAAAAAC
1 GTTTTCAAAAAC
33483 AATTTTCTAA
Statistics
Matches: 156, Mismatches: 1, Indels: 14
0.91 0.01 0.08
Matches are distributed among these distances:
36 11 0.07
37 27 0.17
38 53 0.34
39 28 0.18
40 37 0.24
ACGTcount: A:0.44, C:0.08, G:0.04, T:0.44
Consensus pattern (37 bp):
GTTTTCAAAAACTATATATTATATATATTTTCAAAAT
Found at i:33334 original size:63 final size:61
Alignment explanation
Indices: 33224--33352 Score: 199
Period size: 63 Copynumber: 2.1 Consensus size: 61
33214 ATGTTTTCAA
33224 AAAACTATATATTATATATATTTCAAAATGTTTTCAAAAAACTATATATTATATAAGTTTTC
1 AAAACTATATATTATATATATTTCAAAATGTTTTC-AAAAACTATATATTATATAAGTTTTC
33286 AAAACTATATATTATATA-AGTTTTCAAAAAATGTTTTC-AAAACTATATATTATATAAGTTTTC
1 AAAACTATATATTATATATA--TTTC--AAAATGTTTTCAAAAACTATATATTATATAAGTTTTC
33349 AAAA
1 AAAA
33353 TGTTTTCAAA
Statistics
Matches: 63, Mismatches: 0, Indels: 7
0.90 0.00 0.10
Matches are distributed among these distances:
61 1 0.02
62 18 0.29
63 33 0.52
65 11 0.17
ACGTcount: A:0.47, C:0.08, G:0.04, T:0.42
Consensus pattern (61 bp):
AAAACTATATATTATATATATTTCAAAATGTTTTCAAAAACTATATATTATATAAGTTTTC
Found at i:33387 original size:102 final size:101
Alignment explanation
Indices: 33177--33481 Score: 318
Period size: 102 Copynumber: 2.8 Consensus size: 101
33167 TTTTCAAAAT
33177 GTTTTCAAAAACTATATATTATATATATATTTTCAAAATGTTTTCAAAAAACTATATATTATATA
1 GTTTTC-AAAACTATATATTATATATATATTTTCAAAATGTTTTC-AAAAACTATATATTATATA
33242 TATTTCAAAATGTTTTCAAAAAACTATATATTATATAA
64 TATTTCAAAATGTTTTCAAAAAACTATATATTATATAA
*
33280 GTTTTCAAAACTATATATTATATA-A-GTTTTCAAAAAATGTTTTC-AAAACTATATATTATATA
1 GTTTTCAAAACTATATATTATATATATATTTTC--AAAATGTTTTCAAAAACTATATATTATATA
33342 -AGTTTTCAAAATGTTTTC-AAAAACTATATATTATACATATATTTTCAAAA
64 TA--TTTCAAAATGTTTTCAAAAAAC--TATA-TAT---TATA---T---AA
33392 TGTTTTCAAAAAACTATATA-T-TATATATATTTTCAAAATGTTTTCAAAAACTATATATTATAT
1 -GTTTTC--AAAACTATATATTATATATATATTTTCAAAATGTTTTCAAAAAC--TATA-TAT-T
*
33455 ATATATATTTTAAAATGTTTTCAAAAA
59 ATATATATTTCAAAATGTTTTCAAAAA
33482 CAATTTTCTA
Statistics
Matches: 171, Mismatches: 3, Indels: 41
0.80 0.01 0.19
Matches are distributed among these distances:
99 1 0.01
100 29 0.17
101 16 0.09
102 33 0.19
103 9 0.05
106 4 0.02
109 1 0.01
112 2 0.01
113 21 0.12
114 7 0.04
115 16 0.09
116 4 0.02
117 17 0.10
118 10 0.06
119 1 0.01
ACGTcount: A:0.45, C:0.08, G:0.04, T:0.44
Consensus pattern (101 bp):
GTTTTCAAAACTATATATTATATATATATTTTCAAAATGTTTTCAAAAACTATATATTATATATA
TTTCAAAATGTTTTCAAAAAACTATATATTATATAA
Found at i:33482 original size:77 final size:76
Alignment explanation
Indices: 32998--33482 Score: 467
Period size: 77 Copynumber: 6.4 Consensus size: 76
32988 TCAAAAATAT
* * *
32998 TATATAT-TTTTAAAAGTTGTTTTC-AAAACTATATATTATATATGTCTTCAAAATATGTTTTC-
1 TATATATATTTTAAAA-ATGTTTTCAAAAACTATATATTATATAAGTTTTC-AAA-ATGTTTTCA
33060 AAAACTATATATTA
63 AAAACTATATATTA
*
33074 TATA-AGT-TTTCAAAAAAATGTTTTC-AAAACTATATATTATATAAGTTTTCAAAAAAAATGTT
1 TATATA-TATTT--TAAAAATGTTTTCAAAAACTATATATTATATAAGTTTTC----AAAATGTT
*
33136 TTCAAAAATTATATATTATATA
59 TTCAAAAA--CTATA-TAT-TA
* *
33158 TTATATATATTTTCAAAATGTTTTCAAAAACTATATATTATATATATATTTTCAAAATGTTTTCA
1 -TATATATATTTTAAAAATGTTTTCAAAAACTATATATTATATA-A-GTTTTCAAAATGTTTTC-
33223 AAAAACTATATA-T-
62 AAAAACTATATATTA
*
33236 TATATATA-TTTCAAAATGTTTTCAAAAAACTATATA-T-TAT-A----T---AA-GTTTTC-AA
1 TATATATATTTTAAAAATGTTTTC-AAAAACTATATATTATATAAGTTTTCAAAATGTTTTCAAA
33288 AACTATATATTA
65 AACTATATATTA
** * **
33300 TATAAGTTTTCAAAAAATGTTTTC-AAAACTATATATTATATAAGTTTTCAAAATGTTTTCAAAA
1 TATATATATTTTAAAAATGTTTTCAAAAACTATATATTATATAAGTTTTCAAAATGTTTTCAAAA
33364 ACTATATATTA
66 ACTATATATTA
* *
33375 TACATATATTTTCAAAATGTTTTCAAAAAACTATATATTATATATA-TTTTCAAAATGTTTTCAA
1 TATATATATTTTAAAAATGTTTTC-AAAAACTATATATTATATA-AGTTTTCAAAATGTTTTCAA
33439 AAACTATATATTA
64 AAACTATATATTA
*
33452 TATATATATATTTTAAAATGTTTTCAAAAAC
1 TATATATAT-TTTAAAAATGTTTTCAAAAAC
33483 AATTTTCTAA
Statistics
Matches: 347, Mismatches: 24, Indels: 75
0.78 0.05 0.17
Matches are distributed among these distances:
62 11 0.03
63 12 0.03
64 12 0.03
65 17 0.05
66 1 0.00
68 1 0.00
70 1 0.00
73 3 0.01
74 6 0.02
75 35 0.10
76 24 0.07
77 113 0.33
78 19 0.05
79 9 0.03
80 8 0.02
81 2 0.01
82 8 0.02
83 14 0.04
84 18 0.05
85 23 0.07
86 5 0.01
87 5 0.01
ACGTcount: A:0.44, C:0.08, G:0.04, T:0.44
Consensus pattern (76 bp):
TATATATATTTTAAAAATGTTTTCAAAAACTATATATTATATAAGTTTTCAAAATGTTTTCAAAA
ACTATATATTA
Found at i:34573 original size:16 final size:16
Alignment explanation
Indices: 34552--34584 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
34542 CGATTGATTT
*
34552 TTGGGTTGGGTCAATA
1 TTGGGTTAGGTCAATA
34568 TTGGGTTAGGTCAATA
1 TTGGGTTAGGTCAATA
34584 T
1 T
34585 CGCATCGGTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.21, C:0.06, G:0.33, T:0.39
Consensus pattern (16 bp):
TTGGGTTAGGTCAATA
Found at i:35046 original size:117 final size:120
Alignment explanation
Indices: 34925--35166 Score: 275
Period size: 117 Copynumber: 2.0 Consensus size: 120
34915 TGAAACTACG
* * *
34925 TATATAATATATAGTTTTT-AATA-GTTTTT-AAAAC-TATATAATATATAGTTTTAAAAAAGAC
1 TATATAATATATAGTTTTTGAAAACATTTTTGAAAACATATAT-AT-TATAGTTTT-AAAAACAC
* *
34986 ATTTTAGAAAATATATATAATATATAATTTTT-AAAATCATTTTGAAAA-CTTATATA-
63 ATTTTAGAAAACATATATAATATATAATTTTTGAAAAT-ATTTTGAAAACCATATATAT
* **
35042 TATAT-ATATATAGTTTTTGAAAACATTTTTGAAAACATATATATTATAGTTTTGAAAACATTTT
1 TATATAATATATAGTTTTTGAAAACATTTTTGAAAACATATATATTATAGTTTTAAAAACACATT
* * * * *
35106 TTTGAAAACATATATATTATATAGTTTTTGAAGATATTTTTAAAACCATATATAT
66 TTAGAAAACATATATAATATATAATTTTTGAAAATATTTTGAAAACCATATATAT
35161 TATATA
1 TATATA
35167 GTTTTGAAAA
Statistics
Matches: 104, Mismatches: 13, Indels: 13
0.80 0.10 0.10
Matches are distributed among these distances:
116 13 0.12
117 49 0.47
118 25 0.24
119 12 0.12
120 5 0.05
ACGTcount: A:0.44, C:0.04, G:0.06, T:0.45
Consensus pattern (120 bp):
TATATAATATATAGTTTTTGAAAACATTTTTGAAAACATATATATTATAGTTTTAAAAACACATT
TTAGAAAACATATATAATATATAATTTTTGAAAATATTTTGAAAACCATATATAT
Found at i:35052 original size:42 final size:43
Alignment explanation
Indices: 34996--35089 Score: 133
Period size: 43 Copynumber: 2.3 Consensus size: 43
34986 ATTTTAGAAA
*
34996 ATATATATA-ATATATAATTTTT-AAAATCA-TTTTGAAAACTT
1 ATATATATATATATATAATTTTTGAAAA-CATTTTTGAAAACAT
*
35037 ATATATATATATATATAGTTTTTGAAAACATTTTTGAAAACAT
1 ATATATATATATATATAATTTTTGAAAACATTTTTGAAAACAT
35080 ATATAT-TATA
1 ATATATATATA
35090 GTTTTGAAAA
Statistics
Matches: 48, Mismatches: 2, Indels: 5
0.87 0.04 0.09
Matches are distributed among these distances:
41 9 0.19
42 18 0.38
43 21 0.44
ACGTcount: A:0.46, C:0.04, G:0.04, T:0.46
Consensus pattern (43 bp):
ATATATATATATATATAATTTTTGAAAACATTTTTGAAAACAT
Found at i:35070 original size:12 final size:12
Alignment explanation
Indices: 35055--35079 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
35045 ATATATATAG
35055 TTTTTGAAAACA
1 TTTTTGAAAACA
35067 TTTTTGAAAACA
1 TTTTTGAAAACA
35079 T
1 T
35080 ATATATTATA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.40, C:0.08, G:0.08, T:0.44
Consensus pattern (12 bp):
TTTTTGAAAACA
Found at i:35108 original size:37 final size:39
Alignment explanation
Indices: 35039--35177 Score: 184
Period size: 37 Copynumber: 3.7 Consensus size: 39
35029 GAAAACTTAT
35039 ATATATATATATATAGTTTTTGAAAACA-TTTTTGAAAAC
1 ATATATAT-TATATAGTTTTTGAAAACATTTTTTGAAAAC
35078 ATATATA-T-TATAG-TTTTGAAAACATTTTTTTGAAAAC
1 ATATATATTATATAGTTTTTGAAAACA-TTTTTTGAAAAC
* *
35115 ATATATATTATATAGTTTTTGAAGATA-TTTTT-AAAACC
1 ATATATATTATATAGTTTTTGAAAACATTTTTTGAAAA-C
35153 ATATATATTATATAG-TTTTGAAAAC
1 ATATATATTATATAGTTTTTGAAAAC
35178 TTATATAATA
Statistics
Matches: 90, Mismatches: 4, Indels: 14
0.83 0.04 0.13
Matches are distributed among these distances:
35 11 0.12
36 5 0.06
37 31 0.34
38 22 0.24
39 12 0.13
40 9 0.10
ACGTcount: A:0.42, C:0.05, G:0.08, T:0.45
Consensus pattern (39 bp):
ATATATATTATATAGTTTTTGAAAACATTTTTTGAAAAC
Found at i:35171 original size:25 final size:24
Alignment explanation
Indices: 35143--35200 Score: 71
Period size: 25 Copynumber: 2.3 Consensus size: 24
35133 TTGAAGATAT
* *
35143 TTTTAAAACCATATATATTATATAG
1 TTTTAAAA-CATATATAATAAATAG
*
35168 TTTTGAAAACTTATATAATAAATAG
1 TTTT-AAAACATATATAATAAATAG
35193 TTTTAAAA
1 TTTTAAAA
35201 TCATTTTGAA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
24 4 0.14
25 21 0.72
26 4 0.14
ACGTcount: A:0.47, C:0.05, G:0.05, T:0.43
Consensus pattern (24 bp):
TTTTAAAACATATATAATAAATAG
Found at i:35289 original size:33 final size:32
Alignment explanation
Indices: 35168--35386 Score: 141
Period size: 34 Copynumber: 6.7 Consensus size: 32
35158 TATTATATAG
35168 TTTTGAAAACTTATATAATAAATAGTTTTAAAATCA-
1 TTTTGAAAA-TTATA-AAT--ATAGTTTTAAAA-CAT
* * ***
35204 TTTTGAAATTTATATAATATA-TAGTTGAAATTTT
1 TTTTGAAAATTATA-AATATAGT--TTTAAAACAT
*
35238 TTTTGAAACA-TAT-AATATAGTTTTAAAACGT
1 TTTTGAAA-ATTATAAATATAGTTTTAAAACAT
35269 TTTTGAAAATTATAACATATAGTTTTAAAACAT
1 TTTTGAAAATTATAA-ATATAGTTTTAAAACAT
* * *
35302 TTTTG-AAATTATATAGTATATGGTTTGAAAATAT
1 TTTTGAAAATTATA-A--ATATAGTTTTAAAACAT
35336 TTTTG-AAA-TAT--ATATAGTTTTAAAACAT
1 TTTTGAAAATTATAAATATAGTTTTAAAACAT
** *
35364 TTTTTTAAATATATATATATAGT
1 TTTTGAAAAT-TATAAATATAGT
35387 ATTTTATTTT
Statistics
Matches: 149, Mismatches: 19, Indels: 33
0.74 0.09 0.16
Matches are distributed among these distances:
28 18 0.12
29 3 0.02
30 1 0.01
31 20 0.13
32 16 0.11
33 36 0.24
34 38 0.26
35 9 0.06
36 8 0.05
ACGTcount: A:0.42, C:0.03, G:0.08, T:0.47
Consensus pattern (32 bp):
TTTTGAAAATTATAAATATAGTTTTAAAACAT
Found at i:35342 original size:34 final size:33
Alignment explanation
Indices: 35042--35386 Score: 170
Period size: 33 Copynumber: 10.4 Consensus size: 33
35032 AACTTATATA
* *
35042 TATATATATATAGTTTTTGAAAACATTTTTGAAAA
1 TATATATATATAG-TTTT-AAAATATTTTTGAAAT
* * *
35077 CATATATATTATAGTTTTGAAAACATTTTTTTGAAAACA
1 TATATATA-TATAGTTTT--AAA-ATATTTTTG-AAA-T
*
35116 TATATATTATATAGTTTTTGAAGATATTTTT-AAA-
1 TATATA-TATATAG-TTTT-AAAATATTTTTGAAAT
** * *
35150 -A-CCATATATA---TT-ATATAGTTTTGAAAACT
1 TATATATATATAGTTTTAAAATATTTTTG-AAA-T
*
35179 TATATAATAAATAGTTTTAAAATCA-TTTTGAAATT
1 TATAT-ATATATAGTTTTAAAAT-ATTTTTGAAA-T
* * *
35214 TATATAATATATAG-TTGAAATTTTTTTTGAAA-
1 TATAT-ATATATAGTTTTAAAATATTTTTGAAAT
* **
35246 CATATA-ATATAGTTTTAAAACGTTTTTGAAAAT
1 TATATATATATAGTTTTAAAATATTTTTG-AAAT
* *
35279 TATA-ACATATAGTTTTAAAACATTTTTGAAAT
1 TATATATATATAGTTTTAAAATATTTTTGAAAT
* *
35311 TATATAGTATATGGTTTGAAAATATTTTTG--A-
1 TATATA-TATATAGTTTTAAAATATTTTTGAAAT
* *
35342 -A-ATATATATAGTTTTAAAACATTTTTTTAAA-
1 TATATATATATAGTTTTAAAATA-TTTTTGAAAT
35373 TATATATATATAGT
1 TATATATATATAGT
35387 ATTTTATTTT
Statistics
Matches: 243, Mismatches: 36, Indels: 64
0.71 0.10 0.19
Matches are distributed among these distances:
25 8 0.03
27 5 0.02
28 14 0.06
29 8 0.03
30 8 0.03
31 19 0.08
32 25 0.10
33 37 0.15
34 33 0.14
35 30 0.12
36 19 0.08
37 8 0.03
38 10 0.04
39 13 0.05
40 6 0.02
ACGTcount: A:0.42, C:0.04, G:0.08, T:0.46
Consensus pattern (33 bp):
TATATATATATAGTTTTAAAATATTTTTGAAAT
Found at i:35431 original size:18 final size:19
Alignment explanation
Indices: 35397--35443 Score: 71
Period size: 18 Copynumber: 2.6 Consensus size: 19
35387 ATTTTATTTT
*
35397 TTATTTATTT-CTTGTTTA
1 TTATTTATTTACTCGTTTA
35415 TTA-TTATTTACTCGTTTA
1 TTATTTATTTACTCGTTTA
35433 TTATTTATTTA
1 TTATTTATTTA
35444 TTTATTTTTA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
17 6 0.23
18 13 0.50
19 7 0.27
ACGTcount: A:0.21, C:0.06, G:0.04, T:0.68
Consensus pattern (19 bp):
TTATTTATTTACTCGTTTA
Found at i:35447 original size:15 final size:15
Alignment explanation
Indices: 35390--35453 Score: 55
Period size: 15 Copynumber: 4.5 Consensus size: 15
35380 ATATAGTATT
35390 TTATTT-TTTATTTA
1 TTATTTATTTATTTA
*
35404 TT-TCTTGTTTA-TTA
1 TTAT-TTATTTATTTA
* **
35418 TTATTTACTCGTTTA
1 TTATTTATTTATTTA
35433 TTATTTATTTATTTA
1 TTATTTATTTATTTA
35448 TT-TTTA
1 TTATTTA
35454 GGTCTATCAT
Statistics
Matches: 39, Mismatches: 7, Indels: 8
0.72 0.13 0.15
Matches are distributed among these distances:
13 1 0.03
14 16 0.41
15 22 0.56
ACGTcount: A:0.20, C:0.05, G:0.03, T:0.72
Consensus pattern (15 bp):
TTATTTATTTATTTA
Found at i:36977 original size:26 final size:26
Alignment explanation
Indices: 36948--37003 Score: 67
Period size: 26 Copynumber: 2.2 Consensus size: 26
36938 AAAGTTAACA
36948 TTTTTAATATTCGTTCTAATTATTAT
1 TTTTTAATATTCGTTCTAATTATTAT
* * * * *
36974 TTTTTAGTATTCTTTTTTATTTTTAT
1 TTTTTAATATTCGTTCTAATTATTAT
37000 TTTT
1 TTTT
37004 CCCTATCTCG
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.20, C:0.05, G:0.04, T:0.71
Consensus pattern (26 bp):
TTTTTAATATTCGTTCTAATTATTAT
Found at i:38224 original size:17 final size:17
Alignment explanation
Indices: 38204--38236 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
38194 CTCACTAACC
38204 CTTTTATTTTATGTTCT
1 CTTTTATTTTATGTTCT
*
38221 CTTTTATTTTGTGTTC
1 CTTTTATTTTATGTTC
38237 ATCGTTTGCA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.09, C:0.12, G:0.09, T:0.70
Consensus pattern (17 bp):
CTTTTATTTTATGTTCT
Found at i:38894 original size:19 final size:19
Alignment explanation
Indices: 38859--38904 Score: 67
Period size: 19 Copynumber: 2.5 Consensus size: 19
38849 TATTTAGACA
38859 TTTTGCA-TTTCTTATTTT
1 TTTTGCATTTTCTTATTTT
*
38877 TTTTGCATTTTGTTATTTT
1 TTTTGCATTTTCTTATTTT
*
38896 CTTTGCATT
1 TTTTGCATT
38905 CACATTAACT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
18 7 0.28
19 18 0.72
ACGTcount: A:0.11, C:0.11, G:0.09, T:0.70
Consensus pattern (19 bp):
TTTTGCATTTTCTTATTTT
Found at i:42209 original size:164 final size:164
Alignment explanation
Indices: 41939--43434 Score: 1949
Period size: 164 Copynumber: 9.0 Consensus size: 164
41929 TGCAGCTTAG
* * ** **
41939 CTCAAGGCTAGAAGGGCTACCTGCCACC-AAGACCTTCAAGTTCGACTACGCTCAGCTCCAAGGC
1 CTCAAGGCTAGAAGGGTTATCTGTTACCAAAGACCTTTGAGTTCGACTACGCTCAGCTCCAAGGC
* * *
42003 ACATCATTTGCAGAATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGATCCTCAAGTTCGATTAC
66 ACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCTCGAGTTCGATTAC
* *
42068 ACTCAGCTTCAAGGGCATAACATTTACAGCATAA
131 ACTCAGCTTCGAGGGCATATCATTTACAGCATAA
* *
42102 CTCAAGGCTAGAAGGGTTATCTGTTAGCAAAGACCTTTGAGTTCGACTACGCTCAGCTCCTAGGC
1 CTCAAGGCTAGAAGGGTTATCTGTTACCAAAGACCTTTGAGTTCGACTACGCTCAGCTCCAAGGC
* **
42167 ACATCATTTGCAGAATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCTTAAGTTCGATTAC
66 ACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCTCGAGTTCGATTAC
* *
42232 ACTCAGCTTCAAGGGCATAACATTTACAGCATAA
131 ACTCAGCTTCGAGGGCATATCATTTACAGCATAA
** *
42266 CTCAAGGCTAGAAGGGTTATCTGTTAGAAAAGACCTTTGAGTTCGACTACGCTCAGCTCCTAGGC
1 CTCAAGGCTAGAAGGGTTATCTGTTACCAAAGACCTTTGAGTTCGACTACGCTCAGCTCCAAGGC
* ** *
42331 ACATCATTTGCAGAATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCTTAAGTTCGGTTAC
66 ACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCTCGAGTTCGATTAC
* *
42396 ACTCAGCTTCAAGGGCATAACATTTACAGCATAA
131 ACTCAGCTTCGAGGGCATATCATTTACAGCATAA
* *
42430 CTCAAGGCTAGAAGGGTTCTCTGTTAGCAAAGACCTTTGAGTTCGACTACGCTCAGCTCCAAGGC
1 CTCAAGGCTAGAAGGGTTATCTGTTACCAAAGACCTTTGAGTTCGACTACGCTCAGCTCCAAGGC
* * *
42495 ACATCATTTGCAGAATAGCTTAAGTCAAGAAGGGCTATCTGCCAAAGACCCCCGAGTTCGATTAC
66 ACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCTCGAGTTCGATTAC
*
42560 ACTCAGCTTCGAGGGCACATCATTTACAGCATAA
131 ACTCAGCTTCGAGGGCATATCATTTACAGCATAA
* **** * * * *
42594 CTCAAGGCTAGAAGGGTTATCTGTGACCAAAAGACCCCCAAGTTCGATTACACTCAGCTTCGAGG
1 CTCAAGGCTAGAAGGGTTATCTGTTACC-AAAGACCTTTGAGTTCGACTACGCTCAGC-TCCAAG
* * *
42659 GCACATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTC
64 GCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTG----CCAAAGACCCTCGAGTTC
* *
42724 GATTACACTCAGC-TCTGAGGGCATATCATTTGCAGCACAA
125 GATTACACTCAGCTTC-GAGGGCATATCATTTACAGCATAA
* * * ** * *
42764 CTTAAGTCTAGAAGGGTTGTCTGCCAACAAAAGACCTTTGAGTTTGACTACGCTCAGCTCCAAGG
1 CTCAAGGCTAGAAGGGTTATCTG-TTACCAAAGACCTTTGAGTTCGACTACGCTCAGCTCCAAGG
* * *
42829 CACCTCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATTTGCCAAAGACCCCCGAGTTCGATTA
65 CACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCTCGAGTTCGATTA
*
42894 CACTCAGCTTCGAGGGCACATCATTTACAGCATAA
130 CACTCAGCTTCGAGGGCATATCATTTACAGCATAA
*
42929 CTCAAGGCTAGAAGGGTTATCTGTGACCAAAAGACCTTTGAGTTCGACTACGCTCAGCTCCAAGG
1 CTCAAGGCTAGAAGGGTTATCTGTTACC-AAAGACCTTTGAGTTCGACTACGCTCAGCTCCAAGG
* *
42994 CACATCATTTGCAGCATAGCTTAAGTCGAGGAGGGCTATCTGCCAAAGACCTTCGAGTTCGATTA
65 CACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCTCGAGTTCGATTA
* *
43059 CACTCAGC-TCTGAGGGCACATCATTTGCAGCATAA
130 CACTCAGCTTC-GAGGGCATATCATTTACAGCATAA
* * * * **
43094 CTTAAGTCAAGAAGGGGTATCTGCCAACCAAAGACCTTTGAGTTCGACTACGCTCAGCTCCAAGG
1 CTCAAGGCTAGAAGGGTTATCTG-TTACCAAAGACCTTTGAGTTCGACTACGCTCAGCTCCAAGG
* * *
43159 CATATCATTTGCAGCATAACTTAAGTCGATAAGGGCTATCTGCCAAAGACCCTCGAGTTCGATTA
65 CACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCTCGAGTTCGATTA
* * *
43224 CACTCAGCTTCGAGGACATATCATTTGCAGCACAA
130 CACTCAGCTTCGAGGGCATATCATTTACAGCATAA
* * * ** * * *
43259 CTTAAGTCTAGAAGGGTTGTCTGCCAACCAAAGACCTTTGAGTTCGATTACGCTCAGCTTCGAGG
1 CTCAAGGCTAGAAGGGTTATCTG-TTACCAAAGACCTTTGAGTTCGACTACGCTCAGC-TCCAAG
* * * * * *
43324 GCACATCATTTGCAGCATAACTCAAGGCTAGAAGGGTTATCTGTCACCAAAAGACCTTCGAGTTC
64 GCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTG---CC-AAAGACCCTCGAGTTC
* * *
43389 GATTACACTCAG-TTC-AGAGGCAAACCAGATTTACAGCATAG
125 GATTACACTCAGCTTCGAG-GGCATATC--ATTTACAGCATAA
43430 CTCAA
1 CTCAA
43435 TGCAAAAAGG
Statistics
Matches: 1197, Mismatches: 114, Indels: 36
0.89 0.08 0.03
Matches are distributed among these distances:
163 23 0.02
164 474 0.40
165 417 0.35
166 91 0.08
168 2 0.00
169 55 0.05
170 119 0.10
171 16 0.01
ACGTcount: A:0.30, C:0.25, G:0.21, T:0.24
Consensus pattern (164 bp):
CTCAAGGCTAGAAGGGTTATCTGTTACCAAAGACCTTTGAGTTCGACTACGCTCAGCTCCAAGGC
ACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCTCGAGTTCGATTAC
ACTCAGCTTCGAGGGCATATCATTTACAGCATAA
Found at i:42648 original size:85 final size:84
Alignment explanation
Indices: 41926--43408 Score: 1344
Period size: 85 Copynumber: 17.9 Consensus size: 84
41916 TAAACAAACT
* * * * * * ** * * *
41926 ATTTGCAGCTTAGCTCAAGGCTAGAAGGGCTACCTGCCACC-AAGACCTTCAAGTTCGACTACGC
1 ATTTGCAGCATAACTTAAGTCTAGAAGGGTTATCTGTGACCAAAGACCTTCGAGTTCGATTACAC
* *
41990 TCAGC-TCCAAGGCACATC
66 TCAGCTTCGAGGGCACATC
* * * * *
42008 ATTTGCAGAATAGCTTAAGTCGAGAAGGGCTATC--TG-CCAAAGATCC-TCAAGTTCGATTACA
1 ATTTGCAGCATAACTTAAGTCTAGAAGGGTTATCTGTGACCAAAGA-CCTTCGAGTTCGATTACA
* * *
42069 CTCAGCTTCAAGGGCATAAC
65 CTCAGCTTCGAGGGCACATC
* * * * * * * *
42089 ATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTTAGCAAAGACCTTTGAGTTCGACTACGC
1 ATTTGCAGCATAACTTAAGTCTAGAAGGGTTATCTGTGACCAAAGACCTTCGAGTTCGATTACAC
* *
42154 TCAGCTCCTA-GGCACATC
66 TCAGCTTCGAGGGCACATC
* * * * *
42172 ATTTGCAGAATAGCTTAAGTCGAGAAGGGCTATC--TG-CCAAAGACCCTT-AAGTTCGATTACA
1 ATTTGCAGCATAACTTAAGTCTAGAAGGGTTATCTGTGACCAAAGA-CCTTCGAGTTCGATTACA
* * *
42233 CTCAGCTTCAAGGGCATAAC
65 CTCAGCTTCGAGGGCACATC
* * * * ** * * *
42253 ATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTTAGAAAAGACCTTTGAGTTCGACTACGC
1 ATTTGCAGCATAACTTAAGTCTAGAAGGGTTATCTGTGACCAAAGACCTTCGAGTTCGATTACAC
* *
42318 TCAGCTCCTA-GGCACATC
66 TCAGCTTCGAGGGCACATC
* * * * * *
42336 ATTTGCAGAATAGCTTAAGTCGAGAAGGGCTATC--TG-CCAAAGACCCTT-AAGTTCGGTTACA
1 ATTTGCAGCATAACTTAAGTCTAGAAGGGTTATCTGTGACCAAAGA-CCTTCGAGTTCGATTACA
* * *
42397 CTCAGCTTCAAGGGCATAAC
65 CTCAGCTTCGAGGGCACATC
* * * * * * * * *
42417 ATTTACAGCATAACTCAAGGCTAGAAGGGTTCTCTGTTAGCAAAGACCTTTGAGTTCGACTACGC
1 ATTTGCAGCATAACTTAAGTCTAGAAGGGTTATCTGTGACCAAAGACCTTCGAGTTCGATTACAC
* *
42482 TCAGC-TCCAAGGCACATC
66 TCAGCTTCGAGGGCACATC
* * * * **
42500 ATTTGCAGAATAGCTTAAGTCAAGAAGGGCTATC--TG-CCAAAGACCCCCGAGTTCGATTACAC
1 ATTTGCAGCATAACTTAAGTCTAGAAGGGTTATCTGTGACCAAAGACCTTCGAGTTCGATTACAC
42562 TCAGCTTCGAGGGCACATC
66 TCAGCTTCGAGGGCACATC
* * * ** *
42581 ATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTGACCAAAAGACCCCCAAGTTCGATTACA
1 ATTTGCAGCATAACTTAAGTCTAGAAGGGTTATCTGTGACC-AAAGACCTTCGAGTTCGATTACA
42646 CTCAGCTTCGAGGGCACATC
65 CTCAGCTTCGAGGGCACATC
* **
42666 ATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGATTACA
1 ATTTGCAGCATAACTTAAGTCTAGAAGGGTTATCTG-TGACCAAAGACCTTCGAGTTCGATTACA
*
42731 CTCAGC-TCTGAGGGCATATC
65 CTCAGCTTC-GAGGGCACATC
* * ** * * * * *
42751 ATTTGCAGCACAACTTAAGTCTAGAAGGGTTGTCTGCCAACAAAAGACCTTTGAGTTTGACTACG
1 ATTTGCAGCATAACTTAAGTCTAGAAGGGTTATCTG-TGACCAAAGACCTTCGAGTTCGATTACA
* * *
42816 CTCAGC-TCCAAGGCACCTC
65 CTCAGCTTCGAGGGCACATC
* * * **
42835 ATTTGCAGCATAGCTTAAGTCGAGAAGGGCTAT-T-TG-CCAAAGACCCCCGAGTTCGATTACAC
1 ATTTGCAGCATAACTTAAGTCTAGAAGGGTTATCTGTGACCAAAGACCTTCGAGTTCGATTACAC
42897 TCAGCTTCGAGGGCACATC
66 TCAGCTTCGAGGGCACATC
* * * * * *
42916 ATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTGACCAAAAGACCTTTGAGTTCGACTACG
1 ATTTGCAGCATAACTTAAGTCTAGAAGGGTTATCTGTGACC-AAAGACCTTCGAGTTCGATTACA
* *
42981 CTCAGC-TCCAAGGCACATC
65 CTCAGCTTCGAGGGCACATC
* * * *
43000 ATTTGCAGCATAGCTTAAGTCGAGGAGGGCTATC--TG-CCAAAGACCTTCGAGTTCGATTACAC
1 ATTTGCAGCATAACTTAAGTCTAGAAGGGTTATCTGTGACCAAAGACCTTCGAGTTCGATTACAC
43062 TCAGC-TCTGAGGGCACATC
66 TCAGCTTC-GAGGGCACATC
* * ** * * *
43081 ATTTGCAGCATAACTTAAGTCAAGAAGGGGTATCTGCCAACCAAAGACCTTTGAGTTCGACTACG
1 ATTTGCAGCATAACTTAAGTCTAGAAGGGTTATCTG-TGACCAAAGACCTTCGAGTTCGATTACA
* * *
43146 CTCAGC-TCCAAGGCATATC
65 CTCAGCTTCGAGGGCACATC
* * * *
43165 ATTTGCAGCATAACTTAAGTCGATAAGGGCTATC--TG-CCAAAGACCCTCGAGTTCGATTACAC
1 ATTTGCAGCATAACTTAAGTCTAGAAGGGTTATCTGTGACCAAAGACCTTCGAGTTCGATTACAC
* *
43227 TCAGCTTCGAGGACATATC
66 TCAGCTTCGAGGGCACATC
* * ** * *
43246 ATTTGCAGCACAACTTAAGTCTAGAAGGGTTGTCTGCCAACCAAAGACCTTTGAGTTCGATTACG
1 ATTTGCAGCATAACTTAAGTCTAGAAGGGTTATCTG-TGACCAAAGACCTTCGAGTTCGATTACA
43311 CTCAGCTTCGAGGGCACATC
65 CTCAGCTTCGAGGGCACATC
* * *
43331 ATTTGCAGCATAACTCAAGGCTAGAAGGGTTATCTGTCACCAAAAGACCTTCGAGTTCGATTACA
1 ATTTGCAGCATAACTTAAGTCTAGAAGGGTTATCTGTGACC-AAAGACCTTCGAGTTCGATTACA
43396 CTCAG-TTCAGAGG
65 CTCAGCTTC-GAGG
43409 CAAACCAGAT
Statistics
Matches: 1125, Mismatches: 233, Indels: 83
0.78 0.16 0.06
Matches are distributed among these distances:
79 2 0.00
80 175 0.16
81 269 0.24
82 31 0.03
83 119 0.11
84 195 0.17
85 331 0.29
86 3 0.00
ACGTcount: A:0.30, C:0.25, G:0.21, T:0.25
Consensus pattern (84 bp):
ATTTGCAGCATAACTTAAGTCTAGAAGGGTTATCTGTGACCAAAGACCTTCGAGTTCGATTACAC
TCAGCTTCGAGGGCACATC
Found at i:44148 original size:38 final size:37
Alignment explanation
Indices: 44032--44349 Score: 261
Period size: 38 Copynumber: 8.6 Consensus size: 37
44022 ATATATACAT
*
44032 ATTTTGAAACTACGTATATAATATATAGTTTTT--AAT-
1 ATTTTGAAA--ACATATATAATATATAGTTTTTAAAATC
* * *
44068 AGTTTTTAAAAC-TATATAATATATAGTTTTAAAAAAGAC
1 A-TTTTGAAAACATATATAATATATAGTTTT-TAAAA-TC
* *
44107 ATTTTAGAAAATATATATAATATATAATTTTTAAAATC
1 ATTTT-GAAAACATATATAATATATAGTTTTTAAAATC
*
44145 ATTTTGAAAACTTATATATATATATAGTTTTTGAAAA-C
1 ATTTTGAAAACATATATA-ATATATAGTTTTT-AAAATC
*
44183 ATTTTTGAAAACATATAT-AT-TATAGTTTTGAAAA-C
1 A-TTTTGAAAACATATATAATATATAGTTTTTAAAATC
* *
44218 ATTTTTTTGAAAACATATATATTATATAGTTTTTGAAGAT-
1 A---TTTTGAAAACATATATAATATATAGTTTTT-AAAATC
* * *
44258 ATTTTTAAAACCATATATATTATATAGTTTTTAAAACC
1 ATTTTGAAAA-CATATATAATATATAGTTTTTAAAATC
*
44296 ATTTTGAAAAC-T-TATAATAAATAG--TTT-AAATC
1 ATTTTGAAAACATATATAATATATAGTTTTTAAAATC
**
44328 ATTTTG-AAATTTATATAATATA
1 ATTTTGAAAACATATATAATATA
44350 GTTGAAATTT
Statistics
Matches: 236, Mismatches: 25, Indels: 45
0.77 0.08 0.15
Matches are distributed among these distances:
31 3 0.01
32 11 0.05
33 11 0.05
34 18 0.08
35 18 0.08
36 11 0.05
37 51 0.22
38 55 0.23
39 37 0.16
40 21 0.09
ACGTcount: A:0.44, C:0.05, G:0.07, T:0.45
Consensus pattern (37 bp):
ATTTTGAAAACATATATAATATATAGTTTTTAAAATC
Found at i:44189 original size:12 final size:12
Alignment explanation
Indices: 44172--44196 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
44162 ATATATATAG
44172 TTTTTGAAAACA
1 TTTTTGAAAACA
44184 TTTTTGAAAACA
1 TTTTTGAAAACA
44196 T
1 T
44197 ATATATTATA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.40, C:0.08, G:0.08, T:0.44
Consensus pattern (12 bp):
TTTTTGAAAACA
Found at i:44472 original size:34 final size:31
Alignment explanation
Indices: 44158--44491 Score: 164
Period size: 33 Copynumber: 9.9 Consensus size: 31
44148 TTGAAAACTT
44158 ATATATATATATAGTTTTTGAAAACATTTTTGAAAA
1 ATATATA-ATATAG-TTTT-AAAACATTTTTG--AA
*
44194 CATATATATTATAGTTTTGAAAACATTTTTTTGAAAA
1 -ATATATAATATAGTTTT-AAAACA--TTTTTG--AA
* * *
44231 CATATATATTATATAGTTTTTGAAGATATTTTTAAAA
1 -ATATATA--ATATAG-TTTT-AAAACATTTTT-GAA
44268 CCATATATATTATATAGTTTTTAAAACCA-TTTTGAA
1 --ATATATA--ATATAG-TTTTAAAA-CATTTTTGAA
*
44304 A-ACTTATAATAAATAG-TTTAAATCA-TTTTGAA
1 ATA--TATAAT--ATAGTTTTAAAACATTTTTGAA
* ***
44336 ATTTATATAATATAG-TTGAAATTTTTTTTGAA
1 A--TATATAATATAGTTTTAAAACATTTTTGAA
* *
44368 ACATATAATATAGTTTTAAAACGTTTTTGAA
1 ATATATAATATAGTTTTAAAACATTTTTGAA
44399 A-ATTATAACATATAGTTTTAAAACATTTTTGAA
1 ATA-TAT-A-ATATAGTTTTAAAACATTTTTGAA
* *
44432 ATTATATAGTATATGGTTTTGAAAATATTTTTG-A
1 A-TATATA--ATATAGTTTT-AAAACATTTTTGAA
44466 A-ATAT-ATATAGTTTTAAAACATTTTT
1 ATATATAATATAGTTTTAAAACATTTTT
44492 TTTAAATATA
Statistics
Matches: 250, Mismatches: 23, Indels: 57
0.76 0.07 0.17
Matches are distributed among these distances:
28 10 0.04
29 9 0.04
30 12 0.05
31 27 0.11
32 23 0.09
33 40 0.16
34 15 0.06
35 32 0.13
36 7 0.03
37 34 0.14
38 27 0.11
39 5 0.02
40 9 0.04
ACGTcount: A:0.41, C:0.04, G:0.08, T:0.46
Consensus pattern (31 bp):
ATATATAATATAGTTTTAAAACATTTTTGAA
Found at i:44491 original size:96 final size:94
Alignment explanation
Indices: 44278--44491 Score: 249
Period size: 96 Copynumber: 2.2 Consensus size: 94
44268 CCATATATAT
* *
44278 TATATAGTTTTTAAAACCA-TTTTGAAAACTTATAATAAATAGTTTAAATCATTTTGAAATTTAT
1 TATATAG-TTTTAAAA-CATTTTTGAAAACTTATAACAAATAGTTTAAAACATTTTGAAATTTAT
* *
44342 ATAATATAGTTGAAATTTTTTTTGAAACATA
64 ATAATATAGTTGAAAATATTTTTGAAACATA
* *
44373 TAATATAGTTTTAAAACGTTTTTGAAAA-TTATAACATATAGTTTTAAAACATTTTTGAAA-TTA
1 T-ATATAGTTTTAAAACATTTTTGAAAACTTATAACAAATAG-TTTAAAACA-TTTTGAAATTTA
*
44436 TATAGTATATGGTTTTGAAAATATTTTTG-AA-ATA
63 TATA--ATATAG--TTGAAAATATTTTTGAAACATA
44470 TATATAGTTTTAAAACATTTTT
1 TATATAGTTTTAAAACATTTTT
44492 TTTAAATATA
Statistics
Matches: 103, Mismatches: 8, Indels: 15
0.82 0.06 0.12
Matches are distributed among these distances:
94 12 0.12
95 33 0.32
96 34 0.33
97 9 0.09
98 2 0.02
99 13 0.13
ACGTcount: A:0.41, C:0.04, G:0.08, T:0.46
Consensus pattern (94 bp):
TATATAGTTTTAAAACATTTTTGAAAACTTATAACAAATAGTTTAAAACATTTTGAAATTTATAT
AATATAGTTGAAAATATTTTTGAAACATA
Found at i:44510 original size:35 final size:34
Alignment explanation
Indices: 44046--44512 Score: 207
Period size: 38 Copynumber: 13.4 Consensus size: 34
44036 TGAAACTACG
* * * *
44046 TATATAATATATAGTTTT-TAATAGTTTTTAAAA
1 TATATATTATATAGTTTTAAAACATTTTTTAAAA
* **
44079 CTATATAATATATAGTTTTAAAAAAGACATTTTAGAAAA
1 -TATATATTATATAGTTTT---AAA-ACATTTTTTAAAA
* *
44118 TATATATAATATATAATTTTTAAAATCA-TTTTGAAAA
1 TATATAT--TATAT-AGTTTTAAAA-CATTTTTTAAAA
*
44155 CTTATATATATATATAGTTTTTGAAAACATTTTTGAAAA
1 --TATATAT-TATATAG-TTTT-AAAACATTTTTTAAAA
*
44194 CATATA-TATTATAGTTTTGAAAACATTTTTTTGAAAACA
1 TATATATTA-TATAGTTTT-AAAACA-TTTTTT--AAA-A
* * *
44233 TATATATTATATAGTTTTTGAAGATATTTTTAAAACCA
1 TATATATTATATAG-TTTT-AAAACATTTTTTAAA--A
*
44271 TATATATTATATAGTTTTTAAAACCA-TTTTGAAAA
1 TATATATTATATAG-TTTTAAAA-CATTTTTTAAAA
* * * *
44306 CT-TATAATAAATAG-TTTAAATCA--TTTTGAAA
1 -TATATATTATATAGTTTTAAAACATTTTTTAAAA
* * * ** *
44337 TTTATATAATATAG--TTGAAATTTTTTTTGAAA
1 TATATATTATATAGTTTTAAAACATTTTTTAAAA
* * *
44369 CATATA--ATATAGTTTTAAAACGTTTTTGAAAA
1 TATATATTATATAGTTTTAAAACATTTTTTAAAA
** * *
44401 T-TATAACATATAGTTTTAAAACATTTTTGAAAT
1 TATATATTATATAGTTTTAAAACATTTTTTAAAA
* * * *
44434 TATATAGTATATGGTTTTGAAA-ATATTTTT--GA
1 TATATATTATATAGTTTTAAAACAT-TTTTTAAAA
*
44466 -A-ATA-TATATAGTTTTAAAACATTTTTTTTAAA
1 TATATATTATATAGTTTTAAAACA-TTTTTTAAAA
44498 TATATATTATATAGT
1 TATATATTATATAGT
44513 ATTTTATTTT
Statistics
Matches: 343, Mismatches: 50, Indels: 79
0.73 0.11 0.17
Matches are distributed among these distances:
29 13 0.04
30 20 0.06
31 21 0.06
32 28 0.08
33 34 0.10
34 41 0.12
35 32 0.09
36 11 0.03
37 28 0.08
38 49 0.14
39 45 0.13
40 16 0.05
41 5 0.01
ACGTcount: A:0.43, C:0.04, G:0.07, T:0.46
Consensus pattern (34 bp):
TATATATTATATAGTTTTAAAACATTTTTTAAAA
Found at i:44531 original size:4 final size:4
Alignment explanation
Indices: 44515--44577 Score: 53
Period size: 4 Copynumber: 16.8 Consensus size: 4
44505 TATATAGTAT
* * * **
44515 TTTA TTT- TTTA TTTA TTT- CTTG TTTA -TTA -TTA TTTA CTCG TTTA
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA
44559 TTTA TTTA TTTA TTTA TTT
1 TTTA TTTA TTTA TTTA TTT
44578 TTAGGTCTAT
Statistics
Matches: 47, Mismatches: 9, Indels: 6
0.76 0.15 0.10
Matches are distributed among these distances:
3 11 0.23
4 36 0.77
ACGTcount: A:0.19, C:0.05, G:0.03, T:0.73
Consensus pattern (4 bp):
TTTA
Found at i:44570 original size:12 final size:11
Alignment explanation
Indices: 44515--44579 Score: 60
Period size: 12 Copynumber: 5.8 Consensus size: 11
44505 TATATAGTAT
44515 TTTATTTTTTA
1 TTTATTTTTTA
* *
44526 TTTATTTCTTG
1 TTTATTTTTTA
*
44537 TTTA-TTATTA
1 TTTATTTTTTA
**
44547 TTTACTCGTTTA
1 TTTA-TTTTTTA
44559 TTTATTTATTTA
1 TTTATTT-TTTA
44571 TTTATTTTT
1 TTTATTTTT
44580 AGGTCTATCA
Statistics
Matches: 42, Mismatches: 9, Indels: 6
0.74 0.16 0.11
Matches are distributed among these distances:
10 8 0.19
11 16 0.38
12 18 0.43
ACGTcount: A:0.18, C:0.05, G:0.03, T:0.74
Consensus pattern (11 bp):
TTTATTTTTTA
Found at i:45236 original size:25 final size:28
Alignment explanation
Indices: 45208--45258 Score: 72
Period size: 25 Copynumber: 1.9 Consensus size: 28
45198 GAAAACCCAT
*
45208 ATCATCA-AACC-CACAC-AAAAACAGA
1 ATCATCATAACCAAACACGAAAAACAGA
45233 ATCATCATAACCAAACACGAAAAACA
1 ATCATCATAACCAAACACGAAAAACA
45259 CAAGCCAACA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
25 7 0.32
26 4 0.18
27 4 0.18
28 7 0.32
ACGTcount: A:0.57, C:0.29, G:0.04, T:0.10
Consensus pattern (28 bp):
ATCATCATAACCAAACACGAAAAACAGA
Found at i:45250 original size:27 final size:27
Alignment explanation
Indices: 45189--45260 Score: 76
Period size: 26 Copynumber: 2.6 Consensus size: 27
45179 CCACAGTAAG
*
45189 CCAAACACAGAAAACCCATATCATCAAA
1 CCAAACACA-AAAACACATATCATCAAA
* *
45217 CC-CACACAAAAACAGA-ATCATCATAA
1 CCAAACACAAAAACACATATCATCA-AA
45243 CCAAACACGAAAAACACA
1 CCAAACAC-AAAAACACA
45261 AGCCAACAGC
Statistics
Matches: 36, Mismatches: 5, Indels: 6
0.77 0.11 0.13
Matches are distributed among these distances:
25 7 0.19
26 10 0.28
27 9 0.25
28 10 0.28
ACGTcount: A:0.56, C:0.32, G:0.04, T:0.08
Consensus pattern (27 bp):
CCAAACACAAAAACACATATCATCAAA
Found at i:47663 original size:20 final size:18
Alignment explanation
Indices: 47635--47679 Score: 54
Period size: 20 Copynumber: 2.4 Consensus size: 18
47625 AATGTTAAAT
*
47635 AATAGAATAGAATAAAATAA
1 AATAAAATAGAA-AAAA-AA
*
47655 AATAAAATAGAAAATAAA
1 AATAAAATAGAAAAAAAA
47673 AATAAAA
1 AATAAAA
47680 ATATCAAATA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
18 9 0.39
19 3 0.13
20 11 0.48
ACGTcount: A:0.76, C:0.00, G:0.07, T:0.18
Consensus pattern (18 bp):
AATAAAATAGAAAAAAAA
Found at i:47670 original size:12 final size:11
Alignment explanation
Indices: 47645--47692 Score: 53
Period size: 13 Copynumber: 4.1 Consensus size: 11
47635 AATAGAATAG
47645 AATAAAAT-AA
1 AATAAAATAAA
47655 AATAAAATAGAA
1 AATAAAATA-AA
47667 AATAAAAATAAA
1 AAT-AAAATAAA
47679 AATATCAAATAAA
1 AATA--AAATAAA
47692 A
1 A
47693 TATTAAAGAG
Statistics
Matches: 33, Mismatches: 0, Indels: 7
0.82 0.00 0.17
Matches are distributed among these distances:
10 8 0.24
11 1 0.03
12 10 0.30
13 14 0.42
ACGTcount: A:0.77, C:0.02, G:0.02, T:0.19
Consensus pattern (11 bp):
AATAAAATAAA
Found at i:47692 original size:18 final size:18
Alignment explanation
Indices: 47648--47694 Score: 60
Period size: 18 Copynumber: 2.6 Consensus size: 18
47638 AGAATAGAAT
47648 AAAATAAAAT-AAAATAG
1 AAAATAAAATAAAAATAG
*
47665 AAAATAAAAATAAAAATAT
1 AAAAT-AAAATAAAAATAG
*
47684 CAAATAAAATA
1 AAAATAAAATA
47695 TTAAAGAGAT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
17 5 0.19
18 11 0.42
19 10 0.38
ACGTcount: A:0.77, C:0.02, G:0.02, T:0.19
Consensus pattern (18 bp):
AAAATAAAATAAAAATAG
Found at i:47926 original size:2 final size:2
Alignment explanation
Indices: 47919--47950 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
47909 ATGACCCTCG
47919 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
47951 GTGTGTGTGT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:47955 original size:2 final size:2
Alignment explanation
Indices: 47950--47991 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
47940 TATATATATA
47950 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
47992 CGCGCGCGCG
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:49039 original size:19 final size:20
Alignment explanation
Indices: 48982--49047 Score: 57
Period size: 19 Copynumber: 3.4 Consensus size: 20
48972 ATAAATAAAC
* *
48982 ATAATAATATA-ATATATATA
1 ATAA-AATATATACATATACA
* *
49002 ATATAATA-ATACATGTACA
1 ATAAAATATATACATATACA
49021 ATAAAATATATA-ATATACA
1 ATAAAATATATACATATACA
49040 TATAAAAT
1 -ATAAAAT
49048 GTTTTCAAAA
Statistics
Matches: 37, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
18 1 0.03
19 23 0.62
20 13 0.35
ACGTcount: A:0.59, C:0.05, G:0.02, T:0.35
Consensus pattern (20 bp):
ATAAAATATATACATATACA
Found at i:49093 original size:39 final size:39
Alignment explanation
Indices: 49043--49320 Score: 427
Period size: 39 Copynumber: 7.1 Consensus size: 39
49033 ATATACATAT
*
49043 AAAATGTTTTCAAAAACTATATATTATATATATGTTTTC
1 AAAATGTTTTCAAAAACTATATATTATATATATATTTTC
*
49082 AAAATATTTTCAAAAACTATTATATATATATATATATATATTC
1 AAAATGTTTTCAAAAACTA-TATAT-TATATATATAT-T-TTC
49125 AAAATGTTTT-AAAAACTATATATTATATATATATTTTC
1 AAAATGTTTTCAAAAACTATATATTATATATATATTTTC
* *
49163 AAAATGTTTTCAAAAACTATATATTATATATATGTTTTT
1 AAAATGTTTTCAAAAACTATATATTATATATATATTTTC
*
49202 AAATTGTTTTCAAAAACTATATA-T-TATATATATTTTC
1 AAAATGTTTTCAAAAACTATATATTATATATATATTTTC
*
49239 AAAATGTTTTCAAAAACTATATATTATATATATTTTTTC
1 AAAATGTTTTCAAAAACTATATATTATATATATATTTTC
* *
49278 AAAATGTTTTCAAAAACTATATATTATATACATATTTTA
1 AAAATGTTTTCAAAAACTATATATTATATATATATTTTC
49317 AAAA
1 AAAA
49321 AAATTATATT
Statistics
Matches: 219, Mismatches: 13, Indels: 14
0.89 0.05 0.06
Matches are distributed among these distances:
37 33 0.15
38 15 0.07
39 119 0.54
40 16 0.07
41 15 0.07
42 9 0.04
43 12 0.05
ACGTcount: A:0.44, C:0.07, G:0.03, T:0.46
Consensus pattern (39 bp):
AAAATGTTTTCAAAAACTATATATTATATATATATTTTC
Found at i:49240 original size:76 final size:75
Alignment explanation
Indices: 49042--49307 Score: 399
Period size: 76 Copynumber: 3.4 Consensus size: 75
49032 AATATACATA
*
49042 TAAAATGTTTTCAAAAACTATATATTATATATATGTTTTCAAAATATTTTCAAAAACTATTATAT
1 TAAAATGTTTTCAAAAACTATATATTATATATA--TTTTCAAAATGTTTTCAAAAACTA-TATAT
49107 ATATATATATATATATT
63 -TATATATAT-T-T-TT
*
49124 CAAAATGTTTT-AAAAACTATATATTATATATATATTTTCAAAATGTTTTCAAAAACTATATATT
1 TAAAATGTTTTCAAAAACTATATA-T-TATATATATTTTCAAAATGTTTTCAAAAACTATATATT
49188 ATATATATGTTTT
64 ATATATAT-TTTT
*
49201 TAAATTGTTTTCAAAAACTATATATTATATATATTTTCAAAATGTTTTCAAAAACTATATATTAT
1 TAAAATGTTTTCAAAAACTATATATTATATATATTTTCAAAATGTTTTCAAAAACTATATATTAT
49266 ATATATTTTT
66 ATATATTTTT
49276 TCAAAATGTTTTCAAAAACTATATATTATATA
1 T-AAAATGTTTTCAAAAACTATATATTATATA
49308 CATATTTTAA
Statistics
Matches: 174, Mismatches: 6, Indels: 14
0.90 0.03 0.07
Matches are distributed among these distances:
75 5 0.03
76 75 0.43
77 12 0.07
78 13 0.07
79 10 0.06
80 5 0.03
81 35 0.20
82 11 0.06
83 8 0.05
ACGTcount: A:0.44, C:0.07, G:0.03, T:0.47
Consensus pattern (75 bp):
TAAAATGTTTTCAAAAACTATATATTATATATATTTTCAAAATGTTTTCAAAAACTATATATTAT
ATATATTTTT
Found at i:52736 original size:13 final size:11
Alignment explanation
Indices: 52685--52744 Score: 57
Period size: 11 Copynumber: 5.1 Consensus size: 11
52675 TTTGGCCTGC
*
52685 AATAATAATAAT
1 AATAA-AATAAA
*
52697 AATAAAATAAC
1 AATAAAATAAA
*
52708 ATTAAAATAAA
1 AATAAAATAAA
52719 AATAAAATAGATA
1 AATAAAATA-A-A
52732 AATAAAAATAAA
1 AAT-AAAATAAA
52744 A
1 A
52745 GAACCGGGCG
Statistics
Matches: 41, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
11 22 0.54
12 8 0.20
13 5 0.12
14 6 0.15
ACGTcount: A:0.73, C:0.02, G:0.02, T:0.23
Consensus pattern (11 bp):
AATAAAATAAA
Found at i:52820 original size:26 final size:26
Alignment explanation
Indices: 52782--52834 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 26
52772 CGGGTATGGG
** *
52782 TCGGGTATCGGATTGAATTTGATTAT
1 TCGGGTATCGGATCAAATTTGAATAT
*
52808 TCGGGTATTGGATCAAATTTGAATAT
1 TCGGGTATCGGATCAAATTTGAATAT
52834 T
1 T
52835 TTATTCGAGT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.26, C:0.08, G:0.25, T:0.42
Consensus pattern (26 bp):
TCGGGTATCGGATCAAATTTGAATAT
Found at i:53358 original size:108 final size:108
Alignment explanation
Indices: 53169--53384 Score: 432
Period size: 108 Copynumber: 2.0 Consensus size: 108
53159 GGGAAGTCGT
53169 TTGTTGGAAATTTTAAAATTACTTTATATTTTAATTTTTTTATATAGTTTTTTATTAAAAATATA
1 TTGTTGGAAATTTTAAAATTACTTTATATTTTAATTTTTTTATATAGTTTTTTATTAAAAATATA
53234 TTTTTGTCATCTAAAATTCAAGTTTTCTTTTAAGAATTTTAAA
66 TTTTTGTCATCTAAAATTCAAGTTTTCTTTTAAGAATTTTAAA
53277 TTGTTGGAAATTTTAAAATTACTTTATATTTTAATTTTTTTATATAGTTTTTTATTAAAAATATA
1 TTGTTGGAAATTTTAAAATTACTTTATATTTTAATTTTTTTATATAGTTTTTTATTAAAAATATA
53342 TTTTTGTCATCTAAAATTCAAGTTTTCTTTTAAGAATTTTAAA
66 TTTTTGTCATCTAAAATTCAAGTTTTCTTTTAAGAATTTTAAA
53385 AGTTTAAATT
Statistics
Matches: 108, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
108 108 1.00
ACGTcount: A:0.34, C:0.05, G:0.06, T:0.55
Consensus pattern (108 bp):
TTGTTGGAAATTTTAAAATTACTTTATATTTTAATTTTTTTATATAGTTTTTTATTAAAAATATA
TTTTTGTCATCTAAAATTCAAGTTTTCTTTTAAGAATTTTAAA
Found at i:54215 original size:26 final size:25
Alignment explanation
Indices: 54186--54251 Score: 89
Period size: 26 Copynumber: 2.5 Consensus size: 25
54176 TTCAGAGTTA
54186 TCGAGTC-AAGTCGAGCTCAACAATAC
1 TCGAGTCGAA-TCG-GCTCAACAATAC
54212 TCGAGCTCGAATCGGCTCAACAATAC
1 TCGAG-TCGAATCGGCTCAACAATAC
54238 TCGAGTTCGAATCG
1 TCGAG-TCGAATCG
54252 ACTCGATTAC
Statistics
Matches: 37, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
26 30 0.81
27 5 0.14
28 2 0.05
ACGTcount: A:0.30, C:0.27, G:0.21, T:0.21
Consensus pattern (25 bp):
TCGAGTCGAATCGGCTCAACAATAC
Found at i:54584 original size:44 final size:42
Alignment explanation
Indices: 54467--54636 Score: 137
Period size: 43 Copynumber: 3.9 Consensus size: 42
54457 TAAAACTTTT
* *
54467 TACCTTTATAATTTAGG-TCTATGTTTTTTTTCAATCTTAATTTC
1 TACCTTTATAATTGAGGCTCTA--TTTTTTTTCAATC-TCATTTC
** * * ** * *
54511 TATATTTATAATTGAGACCCCTAAGTTTTTTCAATCTCAGTTA
1 TACCTTTATAATTGAG-GCTCTATTTTTTTTCAATCTCATTTC
*
54554 TACCTTTATAATTGAGGCCTCTATTTTTTTT-AATGTCGATTTC
1 TACCTTTATAATTGAGG-CTCTATTTTTTTTCAATCTC-ATTTC
* * *
54597 TACCTTTATAATTAAGGTTACTATTTTTTTTCAATTTCAT
1 TACCTTTATAATTGAGGCT-CTATTTTTTTTCAATCTCAT
54637 AAAATTTTTA
Statistics
Matches: 98, Mismatches: 22, Indels: 13
0.74 0.17 0.10
Matches are distributed among these distances:
42 6 0.06
43 60 0.61
44 29 0.30
46 3 0.03
ACGTcount: A:0.25, C:0.15, G:0.08, T:0.52
Consensus pattern (42 bp):
TACCTTTATAATTGAGGCTCTATTTTTTTTCAATCTCATTTC
Found at i:59152 original size:440 final size:440
Alignment explanation
Indices: 58331--59213 Score: 1631
Period size: 440 Copynumber: 2.0 Consensus size: 440
58321 ATGTGCTTCG
* * *
58331 TCCTGGAATGAAAAGACGGATTCTGTTTTCGAACCTCTTGATGTAGCAACAATGATCTGCTTGAC
1 TCCTGGAATGAAAAGACGGATTCTGTTGTCAAACATCTTGATGTAGCAACAATGATCTGCTTGAC
*
58396 ATATGGTAAAACCACTACTACTCATGAAACTATCAAACTTCTTGTACCATTGTCTAGGAGTTTGT
66 ATATGGTAAAACCACTACTACTCATGAAACTATCAAACTTCTTGTACAATTGTCTAGGAGTTTGT
* * *
58461 TTTAAACCATACAAGCTCTTCTTCAAACTGCATATCAGGTTTTTTTTGCCTGCCTCTATGAAGCC
131 TTTAAACCATACAAACTCTTCTTCAAACTGCATACCAGGTTTTTCTTGCCTGCCTCTATGAAGCC
58526 TTCTGGCTGCCTCATATATATTTATTCCTCCAAATCACCATGAAGGAAAGCTGTCTTTACATCTA
196 TTCTGGCTGCCTCATATATATTTATTCCTCCAAATCACCATGAAGGAAAGCTGTCTTTACATCTA
* *
58591 ACTGCTCAAGATGTAGATTTTCTGCAGCTACAATTTTCAACACCAGTCTGATTGTAGACAGTTTC
261 ACTGCTCAAGATGTAGATTTTCTACAACTACAATTTTCAACACCAGTCTGATTGTAGACAGTTTC
58656 ATGACTGGAGAGAAAATTTCATTGTAGTCAATACCTTCTTTTTGCTGAAAACCTTTGACAACCAA
326 ATGACTGGAGAGAAAATTTCATTGTAGTCAATACCTTCTTTTTGCTGAAAACCTTTGACAACCAA
58721 TCTGGCTTTGTAGCGTTTGCTCCCATCGTGCTCTTCATTGATCCTATAAA
391 TCTGGCTTTGTAGCGTTTGCTCCCATCGTGCTCTTCATTGATCCTATAAA
58771 TCCTGGAATGAAAAGACGGATTCTGTTGTCAAACATCTTGATGTAGCAACAATGATCTGCTTGAC
1 TCCTGGAATGAAAAGACGGATTCTGTTGTCAAACATCTTGATGTAGCAACAATGATCTGCTTGAC
* *
58836 ATCTGGTAAAACCACTGCTACTCATGAAACTATCAAACTTCTTGTACAATTGTCTAGGAGTTTGT
66 ATATGGTAAAACCACTACTACTCATGAAACTATCAAACTTCTTGTACAATTGTCTAGGAGTTTGT
58901 TTTAAACCATACAAACTCTTCTTCAAACTGCATACCAGGTTTTTCTTGCCTGCCTCTATGAAGCC
131 TTTAAACCATACAAACTCTTCTTCAAACTGCATACCAGGTTTTTCTTGCCTGCCTCTATGAAGCC
*
58966 TTCTGGCTGCCTCATATATATTTCTTCCTCCAAATCACCATGAAGGAAAGCTGTCTTTACATCTA
196 TTCTGGCTGCCTCATATATATTTATTCCTCCAAATCACCATGAAGGAAAGCTGTCTTTACATCTA
59031 ACTGCTCAAGATGTAGATTTTCTACAACTACAATTTTCAACACCAGTCTGATTGTAGACAGTTTC
261 ACTGCTCAAGATGTAGATTTTCTACAACTACAATTTTCAACACCAGTCTGATTGTAGACAGTTTC
*
59096 ATGACTGGAGAGAAAATTTCATTGTAGTCAATACTTTCTTTTTGCTGAAAACCTTTGACAACCAA
326 ATGACTGGAGAGAAAATTTCATTGTAGTCAATACCTTCTTTTTGCTGAAAACCTTTGACAACCAA
* *
59161 TCTGGCTTTGTAGCGTTTGCTCCCATCGTGCTCTTCCTTGATCCTGTAAA
391 TCTGGCTTTGTAGCGTTTGCTCCCATCGTGCTCTTCATTGATCCTATAAA
59211 TCC
1 TCC
59214 ACTTGTTATG
Statistics
Matches: 428, Mismatches: 15, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
440 428 1.00
ACGTcount: A:0.28, C:0.23, G:0.16, T:0.34
Consensus pattern (440 bp):
TCCTGGAATGAAAAGACGGATTCTGTTGTCAAACATCTTGATGTAGCAACAATGATCTGCTTGAC
ATATGGTAAAACCACTACTACTCATGAAACTATCAAACTTCTTGTACAATTGTCTAGGAGTTTGT
TTTAAACCATACAAACTCTTCTTCAAACTGCATACCAGGTTTTTCTTGCCTGCCTCTATGAAGCC
TTCTGGCTGCCTCATATATATTTATTCCTCCAAATCACCATGAAGGAAAGCTGTCTTTACATCTA
ACTGCTCAAGATGTAGATTTTCTACAACTACAATTTTCAACACCAGTCTGATTGTAGACAGTTTC
ATGACTGGAGAGAAAATTTCATTGTAGTCAATACCTTCTTTTTGCTGAAAACCTTTGACAACCAA
TCTGGCTTTGTAGCGTTTGCTCCCATCGTGCTCTTCATTGATCCTATAAA
Found at i:62120 original size:28 final size:28
Alignment explanation
Indices: 62080--62141 Score: 115
Period size: 28 Copynumber: 2.2 Consensus size: 28
62070 TGGGAGAAAG
62080 AAATGATTTTTGGGATAGTTTTGAAGCT
1 AAATGATTTTTGGGATAGTTTTGAAGCT
*
62108 AAATGATTTTTGGGATGGTTTTGAAGCT
1 AAATGATTTTTGGGATAGTTTTGAAGCT
62136 AAATGA
1 AAATGA
62142 GCTAGGGTAT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 33 1.00
ACGTcount: A:0.31, C:0.03, G:0.26, T:0.40
Consensus pattern (28 bp):
AAATGATTTTTGGGATAGTTTTGAAGCT
Found at i:64874 original size:79 final size:79
Alignment explanation
Indices: 64726--65062 Score: 568
Period size: 79 Copynumber: 4.3 Consensus size: 79
64716 TATGCTCTTT
*
64726 ATGCA-CCATATGCATTATTCTTTTATGCTGACAATGTACCCATATACATTTCAGCTATGATATC
1 ATGCACCCATATGCATTATTCTTTTATGCTGACAATGTACCCATATACATTTCAGCTATGACATC
*
64790 TTTTCATGCCAATA
66 CTTTCATGCCAATA
* * * * * *
64804 ATACACCTATATGCATTATTCTTTTATGTTGATAATGTACCCATATTCATTTCAGCTATGGCATC
1 ATGCACCCATATGCATTATTCTTTTATGCTGACAATGTACCCATATACATTTCAGCTATGACATC
64869 CTTTCATGCCAATA
66 CTTTCATGCCAATA
64883 ATGCACCCATATGCATTATTCTTTTATGCTGACAATGTACCCATATACATTTCAGCTATGACATC
1 ATGCACCCATATGCATTATTCTTTTATGCTGACAATGTACCCATATACATTTCAGCTATGACATC
*
64948 CTCTCATGCCAATA
66 CTTTCATGCCAATA
* *
64962 ATGCACCCATATGCATTATTCTTTTATACTGACAATGTACCCATATACATTTCAGCTATGGCATC
1 ATGCACCCATATGCATTATTCTTTTATGCTGACAATGTACCCATATACATTTCAGCTATGACATC
65027 CTTTCATGCCAATA
66 CTTTCATGCCAATA
65041 ATGCACCCATATGCATTATTCT
1 ATGCACCCATATGCATTATTCT
65063 CTTACTCAAT
Statistics
Matches: 240, Mismatches: 18, Indels: 1
0.93 0.07 0.00
Matches are distributed among these distances:
78 4 0.02
79 236 0.98
ACGTcount: A:0.29, C:0.24, G:0.10, T:0.37
Consensus pattern (79 bp):
ATGCACCCATATGCATTATTCTTTTATGCTGACAATGTACCCATATACATTTCAGCTATGACATC
CTTTCATGCCAATA
Found at i:65176 original size:68 final size:68
Alignment explanation
Indices: 65086--65408 Score: 502
Period size: 68 Copynumber: 4.8 Consensus size: 68
65076 ACTTAACCGC
* *
65086 TCATCTAACTGGCATAATTGACACCTTTTTGTCAAATACACAGTTAGGCCTCAAAGGCACTTAGC
1 TCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCACAGTTAGGCCTCAAAGGCACTTAGC
65151 CTT
66 CTT
*
65154 TCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCACAGTTAGGCTTCAAAGGCACTTAGC
1 TCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCACAGTTAGGCCTCAAAGGCACTTAGC
65219 CTT
66 CTT
*
65222 TCATCTAACTGGCATAATTGGCACCTTTCTGTCAAATGCACAGTTAGGCCTCAAAGGCACTTAGC
1 TCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCACAGTTAGGCCTCAAAGGCACTTAGC
65287 CTT
66 CTT
** * * * * *
65290 TCATCTAACTGATATAGTTAACACCTTTCTGTCAAATGTACAGTTAGTCCTCAAAGGTACTTAGC
1 TCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCACAGTTAGGCCTCAAAGGCACTTAGC
65355 CTT
66 CTT
* ** * *
65358 TCATCTAGCTAACATAATTGACACCTTTATGTCAAATGCACAGCTAGGCCT
1 TCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCACAGTTAGGCCT
65409 TTAATCTTTT
Statistics
Matches: 233, Mismatches: 22, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
68 233 1.00
ACGTcount: A:0.29, C:0.25, G:0.15, T:0.31
Consensus pattern (68 bp):
TCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCACAGTTAGGCCTCAAAGGCACTTAGC
CTT
Found at i:65824 original size:59 final size:59
Alignment explanation
Indices: 65760--66025 Score: 426
Period size: 59 Copynumber: 4.5 Consensus size: 59
65750 TTTCCCATAC
* * * * * * *
65760 GGAAATTCATACACTTAGGATGAATTTCTTATTATTTTAGCACAC-AAGGTGCCCCATCT
1 GGAAATTCATACACTTAGTATGAATTCCTTCTCATGTTAGCACACGAA-GTGCCCTATAT
* *
65819 AGAAATTCATACACTTAGTATGAATTCCTTCCCATGTTAGCACACGAAGTGCCCTATAT
1 GGAAATTCATACACTTAGTATGAATTCCTTCTCATGTTAGCACACGAAGTGCCCTATAT
*
65878 GGAAATTCATACAGTTAGTATGAATTCCTTCTCATGTTAGCACACGAAGTGCCCTATAT
1 GGAAATTCATACACTTAGTATGAATTCCTTCTCATGTTAGCACACGAAGTGCCCTATAT
65937 GGAAATTCATACACTTAGTATGAATTCCTTCTCATGTTAGCACACGAAGTGCCCTATAT
1 GGAAATTCATACACTTAGTATGAATTCCTTCTCATGTTAGCACACGAAGTGCCCTATAT
65996 GGAAATTCATACACTTAGTATGAATTCCTT
1 GGAAATTCATACACTTAGTATGAATTCCTT
66026 AACATTTTGC
Statistics
Matches: 193, Mismatches: 13, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
59 191 0.99
60 2 0.01
ACGTcount: A:0.31, C:0.21, G:0.15, T:0.33
Consensus pattern (59 bp):
GGAAATTCATACACTTAGTATGAATTCCTTCTCATGTTAGCACACGAAGTGCCCTATAT
Found at i:66529 original size:94 final size:96
Alignment explanation
Indices: 66406--66592 Score: 306
Period size: 94 Copynumber: 2.0 Consensus size: 96
66396 TACTTCTATG
*** * *
66406 CTATGGTACCGATACCCCCTTTTGGTATCGATACCAA-TTTTAGGTTCGATGTTTCCTAGTATCG
1 CTATGGTACCGATACCCCCTTCCAGTATCGATACCAATTTTTAGATTCGATGATTCCTAGTATCG
66470 ATA-CCTTACCATGGTATCGATACTACCATC
66 ATACCCTTACCATGGTATCGATACTACCATC
*
66500 CTATGGTACCGATACCCCCTTCCAGTATCGATACCAATTTTTAGATTCGATGATTCCTGGTATCG
1 CTATGGTACCGATACCCCCTTCCAGTATCGATACCAATTTTTAGATTCGATGATTCCTAGTATCG
66565 ATACCCTTACCATGGTATCGATACTACC
66 ATACCCTTACCATGGTATCGATACTACC
66593 TCTTCGGTAT
Statistics
Matches: 85, Mismatches: 6, Indels: 2
0.91 0.06 0.02
Matches are distributed among these distances:
94 34 0.40
95 27 0.32
96 24 0.28
ACGTcount: A:0.24, C:0.27, G:0.16, T:0.34
Consensus pattern (96 bp):
CTATGGTACCGATACCCCCTTCCAGTATCGATACCAATTTTTAGATTCGATGATTCCTAGTATCG
ATACCCTTACCATGGTATCGATACTACCATC
Found at i:67188 original size:43 final size:43
Alignment explanation
Indices: 67127--67212 Score: 163
Period size: 43 Copynumber: 2.0 Consensus size: 43
67117 AAAAATTTAC
67127 CTTTGGAACTATGGAGGAGAGCAACCCACGGGAGAGAAGAATA
1 CTTTGGAACTATGGAGGAGAGCAACCCACGGGAGAGAAGAATA
*
67170 CTTTGGAACTATGGAGGAGTGCAACCCACGGGAGAGAAGAATA
1 CTTTGGAACTATGGAGGAGAGCAACCCACGGGAGAGAAGAATA
67213 AGAGGAAGAG
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 42 1.00
ACGTcount: A:0.36, C:0.16, G:0.33, T:0.15
Consensus pattern (43 bp):
CTTTGGAACTATGGAGGAGAGCAACCCACGGGAGAGAAGAATA
Found at i:69273 original size:26 final size:28
Alignment explanation
Indices: 69235--69291 Score: 66
Period size: 29 Copynumber: 2.1 Consensus size: 28
69225 TATCATTTAA
69235 AAATAATTATAAA-ATA-ATTAATTTTT
1 AAATAATTATAAACATATATTAATTTTT
*
69261 AAATAAATT-TAAACTATATATTATTTTTT
1 AAAT-AATTATAAAC-ATATATTAATTTTT
69290 AA
1 AA
69292 CAATGATAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
26 8 0.31
27 4 0.15
28 3 0.12
29 11 0.42
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (28 bp):
AAATAATTATAAACATATATTAATTTTT
Found at i:71669 original size:11 final size:11
Alignment explanation
Indices: 71655--71717 Score: 51
Period size: 11 Copynumber: 5.9 Consensus size: 11
71645 ATAATTAAAT
*
71655 TTATCAAGTTA
1 TTATCAAATTA
* *
71666 TTATAAAATAA
1 TTATCAAATTA
*
71677 TTATTAAATT-
1 TTATCAAATTA
71687 TTATCAAATTA
1 TTATCAAATTA
71698 TTA--AAATTCA
1 TTATCAAATT-A
*
71708 TTATTAAATT
1 TTATCAAATT
71718 TATCAATCTT
Statistics
Matches: 42, Mismatches: 6, Indels: 7
0.76 0.11 0.13
Matches are distributed among these distances:
9 5 0.12
10 13 0.31
11 19 0.45
12 5 0.12
ACGTcount: A:0.46, C:0.05, G:0.02, T:0.48
Consensus pattern (11 bp):
TTATCAAATTA
Found at i:71699 original size:32 final size:31
Alignment explanation
Indices: 71633--71723 Score: 130
Period size: 31 Copynumber: 2.9 Consensus size: 31
71623 ACCATTGTGA
* *
71633 TATTATAAAATAATAATTAAATTTATCAAGT
1 TATTATAAAATAATTATTAAATTTATCAAAT
71664 TATTATAAAATAATTATTAAATTTTATCAAAT
1 TATTATAAAATAATTATTAAA-TTTATCAAAT
* *
71696 TATTA-AAATTCATTATTAAATTTATCAA
1 TATTATAAAATAATTATTAAATTTATCAA
71724 TCTTCACTTT
Statistics
Matches: 55, Mismatches: 4, Indels: 3
0.89 0.06 0.05
Matches are distributed among these distances:
30 8 0.15
31 33 0.60
32 14 0.25
ACGTcount: A:0.49, C:0.04, G:0.01, T:0.45
Consensus pattern (31 bp):
TATTATAAAATAATTATTAAATTTATCAAAT
Found at i:72312 original size:37 final size:36
Alignment explanation
Indices: 72205--72322 Score: 150
Period size: 35 Copynumber: 3.3 Consensus size: 36
72195 TGGCAACCAA
*
72205 CTTTGAAAAAATGGTTTTCAAAGTTTGGTAAATGCTT
1 CTTTGAAAAAA-GGTTTTCAAAGTTTGGTAAATGTTT
*
72242 CTTTG-AAAACGGTTTTCAAAGTTTGGTAAATGTTT
1 CTTTGAAAAAAGGTTTTCAAAGTTTGGTAAATGTTT
* * *
72277 CTTTGAAAAATAGTTTTTCAAAGTTTGATAGATGTTT
1 CTTTGAAAAA-AGGTTTTCAAAGTTTGGTAAATGTTT
*
72314 -GTTGAAAAA
1 CTTTGAAAAA
72323 TCATAATGAG
Statistics
Matches: 72, Mismatches: 7, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
35 29 0.40
36 16 0.22
37 27 0.38
ACGTcount: A:0.33, C:0.07, G:0.19, T:0.42
Consensus pattern (36 bp):
CTTTGAAAAAAGGTTTTCAAAGTTTGGTAAATGTTT
Found at i:73538 original size:15 final size:15
Alignment explanation
Indices: 73514--73545 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
73504 AGGCAGATCG
*
73514 AAATCCAGAACGGGA
1 AAATCAAGAACGGGA
73529 AAATCAAGAACGGGA
1 AAATCAAGAACGGGA
73544 AA
1 AA
73546 TAAATATTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.53, C:0.16, G:0.25, T:0.06
Consensus pattern (15 bp):
AAATCAAGAACGGGA
Found at i:76863 original size:21 final size:21
Alignment explanation
Indices: 76839--76934 Score: 76
Period size: 21 Copynumber: 5.2 Consensus size: 21
76829 AACTTTGAAA
76839 AAATGGTTTTCAAAGTTTGGT
1 AAATGGTTTTCAAAGTTTGGT
*
76860 AAAT-G-TTTC----TTT-GA
1 AAATGGTTTTCAAAGTTTGGT
76874 AAATGGTTTTCAAAGTTTGGT
1 AAATGGTTTTCAAAGTTTGGT
*
76895 AAAT-G-TTTC----TTT-GA
1 AAATGGTTTTCAAAGTTTGGT
76909 AAATGGTTTTCAAAGTTTGGT
1 AAATGGTTTTCAAAGTTTGGT
76930 AAATG
1 AAATG
76935 TTTCTTTGAA
Statistics
Matches: 57, Mismatches: 4, Indels: 28
0.64 0.04 0.31
Matches are distributed among these distances:
14 10 0.18
15 8 0.14
16 8 0.14
19 8 0.14
20 8 0.14
21 15 0.26
ACGTcount: A:0.30, C:0.05, G:0.21, T:0.44
Consensus pattern (21 bp):
AAATGGTTTTCAAAGTTTGGT
Found at i:76980 original size:36 final size:36
Alignment explanation
Indices: 76831--76984 Score: 242
Period size: 35 Copynumber: 4.3 Consensus size: 36
76821 TGGCAACCAA
76831 CTTTGAAAAAATGGTTTTCAAAGTTTGGTAAATGTTT
1 CTTTG-AAAAATGGTTTTCAAAGTTTGGTAAATGTTT
76868 CTTTG-AAAATGGTTTTCAAAGTTTGGTAAATGTTT
1 CTTTGAAAAATGGTTTTCAAAGTTTGGTAAATGTTT
76903 CTTTG-AAAATGGTTTTCAAAGTTTGGTAAATGTTT
1 CTTTGAAAAATGGTTTTCAAAGTTTGGTAAATGTTT
* *
76938 CTTTGAAAAATAGTTTTTCAAAGTTTGGTAGATGTTT
1 CTTTGAAAAAT-GGTTTTCAAAGTTTGGTAAATGTTT
*
76975 -GTTGAAAAAT
1 CTTTGAAAAAT
76985 CATAATGGGA
Statistics
Matches: 112, Mismatches: 3, Indels: 5
0.93 0.03 0.04
Matches are distributed among these distances:
35 70 0.62
36 14 0.12
37 28 0.25
ACGTcount: A:0.31, C:0.05, G:0.19, T:0.44
Consensus pattern (36 bp):
CTTTGAAAAATGGTTTTCAAAGTTTGGTAAATGTTT
Found at i:81359 original size:15 final size:15
Alignment explanation
Indices: 81339--81378 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
81329 TAATTGGGTT
81339 TTATTATTATTATTG-
1 TTATTATTATT-TTGA
*
81354 TTATTATAATTTTGA
1 TTATTATTATTTTGA
81369 TTATTATTAT
1 TTATTATTAT
81379 AAGTTTGGTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
14 3 0.14
15 19 0.86
ACGTcount: A:0.30, C:0.00, G:0.05, T:0.65
Consensus pattern (15 bp):
TTATTATTATTTTGA
Found at i:83139 original size:26 final size:26
Alignment explanation
Indices: 83110--83168 Score: 118
Period size: 26 Copynumber: 2.3 Consensus size: 26
83100 AACACCATTT
83110 TGCATAATATGTATGATATCCTCATG
1 TGCATAATATGTATGATATCCTCATG
83136 TGCATAATATGTATGATATCCTCATG
1 TGCATAATATGTATGATATCCTCATG
83162 TGCATAA
1 TGCATAA
83169 CTCGACATAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 33 1.00
ACGTcount: A:0.32, C:0.15, G:0.15, T:0.37
Consensus pattern (26 bp):
TGCATAATATGTATGATATCCTCATG
Found at i:96172 original size:56 final size:55
Alignment explanation
Indices: 95530--96507 Score: 1003
Period size: 54 Copynumber: 17.9 Consensus size: 55
95520 GAAGCAAATT
* ** * *
95530 AAGATTGTTTGAGTTCTAT--TCCCTGAAGCAAGAGGGAGTAAACCTGTAGACAG
1 AAGATTGTTCGAGTTCTATACTCCCTGAAGCAAGAGGGAGCGAACCCGTAGGCAG
* *
95583 AAGATTGTTCGAGTTC-CTACTCCCTGAAGCAAGAGGGAGCGAACCCATAGGCAG
1 AAGATTGTTCGAGTTCTATACTCCCTGAAGCAAGAGGGAGCGAACCCGTAGGCAG
* * * * *
95637 AAGATTGTTTGTGATC-CTACTCCCTGAAGCAAGAGGGAGCGAACCCGTAGACAG
1 AAGATTGTTCGAGTTCTATACTCCCTGAAGCAAGAGGGAGCGAACCCGTAGGCAG
*
95691 AAGATTGTTCGAGTTC--TACTCCCTGAAGCAAGAGGGAGCGAACCCGTAGGTAG
1 AAGATTGTTCGAGTTCTATACTCCCTGAAGCAAGAGGGAGCGAACCCGTAGGCAG
* * * * * *
95744 AAGATTGTTTGTGTTCCTA-A-TCCCTGAGGCAAGAGAGAGTGAACCCATAGGCAG
1 AAGATTGTTCGAGTT-CTATACTCCCTGAAGCAAGAGGGAGCGAACCCGTAGGCAG
* * *
95798 AAGATTGTTCGAGTTC-CTACTTCCTGAAGCAAGAGGGAGCGAACCCATAGGCAG
1 AAGATTGTTCGAGTTCTATACTCCCTGAAGCAAGAGGGAGCGAACCCGTAGGCAG
* * * * * *
95852 AAGATTGTTTGAGTTC-CTAGTCCCTGAAGCAAGAGGGAGCGAACCTGTATGCAA
1 AAGATTGTTCGAGTTCTATACTCCCTGAAGCAAGAGGGAGCGAACCCGTAGGCAG
* * * * * * * *
95906 AAGATTGTTCGAGTTCCTAT--TCCATCAACCTAGAGAGAGAGAACCCATAGGTAG
1 AAGATTGTTCGAGTT-CTATACTCCCTGAAGCAAGAGGGAGCGAACCCGTAGGCAG
* * * * * ** *
95960 ATGATTATTCGAGTTCTATACTCCCTGAAAGAAAGAGGGAGCAAACCCATTTGTAG
1 AAGATTGTTCGAGTTCTATACTCCCTG-AAGCAAGAGGGAGCGAACCCGTAGGCAG
*
96016 AAGATTGTTCGAGTTC-CTACTCCCTGAAGCAAGAGGGAGCGAACCCGTAGGCAG
1 AAGATTGTTCGAGTTCTATACTCCCTGAAGCAAGAGGGAGCGAACCCGTAGGCAG
* *
96070 AAGATTGTTCGAGTTC-CTACTCCCTGAAGCAAGAGGGAGAGAACCCGTAGGCAG
1 AAGATTGTTCGAGTTCTATACTCCCTGAAGCAAGAGGGAGCGAACCCGTAGGCAG
* * * **
96124 ATGATTTTTCGAGTTCTATACTCCCTGAAGGAAAGAGGGAGCGAACCCGTTTGCAG
1 AAGATTGTTCGAGTTCTATACTCCCTGAA-GCAAGAGGGAGCGAACCCGTAGGCAG
* * * * * * *
96180 AAGATTATTTGAGATCTATACTCCCTGAAAGAAAGAGGGAGCAAACTCGTTGGCAG
1 AAGATTGTTCGAGTTCTATACTCCCTG-AAGCAAGAGGGAGCGAACCCGTAGGCAG
* * ****
96236 AAGATTGTTCGAGTTCTATACTCCCTGAAAGAAAGAGGGAGCAAACCCGTTTTTAG
1 AAGATTGTTCGAGTTCTATACTCCCTG-AAGCAAGAGGGAGCGAACCCGTAGGCAG
* * * * * *
96292 AAGATTATTCGAGTTCTATACTCCCTGAAAGAAAGAGGGAACGAACCCTTTGGTAG
1 AAGATTGTTCGAGTTCTATACTCCCTG-AAGCAAGAGGGAGCGAACCCGTAGGCAG
* * * *
96348 AAGAATGTTCGAGTTCTATACTCCCTAAAAGAAAGAGGGAGCGAACCCGTTGGCAG
1 AAGATTGTTCGAGTTCTATACTCCCT-GAAGCAAGAGGGAGCGAACCCGTAGGCAG
* * * * *
96404 AAGATTATTCGATTTCTATACTCCCTGAAGCAAAAGGGAGTGAACCCGTTGGCAG
1 AAGATTGTTCGAGTTCTATACTCCCTGAAGCAAGAGGGAGCGAACCCGTAGGCAG
* * * ** * *
96459 AAGAATGTTCGCGTTCTATACTACCTGAAGTGATAGGGAGCAAACCCGT
1 AAGATTGTTCGAGTTCTATACTCCCTGAAGCAAGAGGGAGCGAACCCGT
96508 TTTACAAAGA
Statistics
Matches: 786, Mismatches: 123, Indels: 30
0.84 0.13 0.03
Matches are distributed among these distances:
52 1 0.00
53 69 0.09
54 350 0.45
55 90 0.11
56 274 0.35
57 2 0.00
ACGTcount: A:0.31, C:0.20, G:0.26, T:0.23
Consensus pattern (55 bp):
AAGATTGTTCGAGTTCTATACTCCCTGAAGCAAGAGGGAGCGAACCCGTAGGCAG
Found at i:96720 original size:15 final size:15
Alignment explanation
Indices: 96700--96739 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
96690 TAATTGGGTT
96700 TTATTATTATTATT-G
1 TTATTATTATT-TTGG
*
96715 TTATTATAATTTTGG
1 TTATTATTATTTTGG
96730 TTATTATTAT
1 TTATTATTAT
96740 AAGTTTGGTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
14 2 0.09
15 20 0.91
ACGTcount: A:0.28, C:0.00, G:0.07, T:0.65
Consensus pattern (15 bp):
TTATTATTATTTTGG
Found at i:96736 original size:18 final size:17
Alignment explanation
Indices: 96715--96753 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 17
96705 ATTATTATTG
*
96715 TTATTATAATTTTGGTTA
1 TTATTATAAGTTTGG-TA
96733 TTATTATAAGTTTGGTA
1 TTATTATAAGTTTGGTA
96750 TTAT
1 TTAT
96754 ATAGTTTTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
17 6 0.30
18 14 0.70
ACGTcount: A:0.28, C:0.00, G:0.13, T:0.59
Consensus pattern (17 bp):
TTATTATAAGTTTGGTA
Found at i:96769 original size:2 final size:2
Alignment explanation
Indices: 96764--96791 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
96754 ATAGTTTTTA
96764 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
96792 GCAAATAATT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:112831 original size:12 final size:12
Alignment explanation
Indices: 112814--112839 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
112804 TAACTCCAAT
112814 GAATTAGTATTG
1 GAATTAGTATTG
112826 GAATTAGTATTG
1 GAATTAGTATTG
112838 GA
1 GA
112840 GGAAGAAGCT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.35, C:0.00, G:0.27, T:0.38
Consensus pattern (12 bp):
GAATTAGTATTG
Found at i:121406 original size:18 final size:18
Alignment explanation
Indices: 121385--121419 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
121375 ATTTTCACTA
*
121385 TTGATGATGGTTTTTTTG
1 TTGATGATGATTTTTTTG
*
121403 TTGATTATGATTTTTTT
1 TTGATGATGATTTTTTT
121420 ATTATTTTAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.14, C:0.00, G:0.20, T:0.66
Consensus pattern (18 bp):
TTGATGATGATTTTTTTG
Found at i:121767 original size:3 final size:3
Alignment explanation
Indices: 121759--121822 Score: 119
Period size: 3 Copynumber: 21.3 Consensus size: 3
121749 AAAATCAAAT
*
121759 ATA ATA ATA ATA ATA ATA ATA ACA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
121807 ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA A
121823 CGGTCTCTGG
Statistics
Matches: 59, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
3 59 1.00
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (3 bp):
ATA
Found at i:122200 original size:130 final size:130
Alignment explanation
Indices: 122004--122489 Score: 551
Period size: 130 Copynumber: 3.7 Consensus size: 130
121994 GAGATTTTTA
* * * * * * *
122004 AAGATGAAATCTG-AAAAGGTATCTGCTCCACTGTTCTTCAGGGTAGATCAGATTTAGAAATGTT
1 AAGATCAAATCTGAAAAAGGGATATGCTCCACTGCTCTTCAGGGTAGATCAGATCTAAAAACGTT
*
122068 GATTCATTCCACTACTCTTCAGGGAAGATTGAATCGAGGTAGATTTGTTCAACTGCTCCTCATAG
66 GATTCATTCCACTACTCTTCAGGGAAGATTGAATCGAGGTAGATTTGTTCCACTGCTCCTCATAG
* * * *
122133 AAGATCAAATCTGAAAAAGGGATCTGCTCCGCTGCTCTTTAGGGTAGATCAGATCTAAAAACATT
1 AAGATCAAATCTGAAAAAGGGATATGCTCCACTGCTCTTCAGGGTAGATCAGATCTAAAAACGTT
** * * * * * * *
122198 GATTCATTTTATTGCACTTCAGGGAAGATTGAATCGAGTTAAATTTGTCCCACTGCTCCTCATGG
66 GATTCATTCCACTACTCTTCAGGGAAGATTGAATCGAGGTAGATTTGTTCCACTGCTCCTCATAG
* ** * **
122263 AAGATCAAATCTAAGAAAAGGGATATGCTCTGCTGCTCTTCAGGGTAGATCATATCTTAAAAATT
1 AAGATCAAATCTGA-AAAAGGGATATGCTCCACTGCTCTTCAGGGTAGATCAGATC-TAAAAACG
* * * * * * *
122328 TTGATTCATTCCATTGCTTTTCAGGGAAGATTGAATCGAGGTAGACTTGATCCACTACTCCTCAG
64 TTGATTCATTCCACTACTCTTCAGGGAAGATTGAATCGAGGTAGATTTGTTCCACTGCTCCTCAT
122393 AG
129 AG
* * * * **
122395 AAGATCAAATCTGGAAAAGGGGATATGTTCCACTGCTCTTCAAGGTAGATCAAATCTGGAAACGT
1 AAGATCAAATCT-GAAAAAGGGATATGCTCCACTGCTCTTCAGGGTAGATCAGATCTAAAAACGT
* * *
122460 TGATTCATTCCACTATTCTTAAGGAAAGAT
65 TGATTCATTCCACTACTCTTCAGGGAAGAT
122490 CAAATCGAAT
Statistics
Matches: 298, Mismatches: 55, Indels: 6
0.83 0.15 0.02
Matches are distributed among these distances:
129 12 0.04
130 111 0.37
131 66 0.22
132 108 0.36
133 1 0.00
ACGTcount: A:0.31, C:0.18, G:0.20, T:0.31
Consensus pattern (130 bp):
AAGATCAAATCTGAAAAAGGGATATGCTCCACTGCTCTTCAGGGTAGATCAGATCTAAAAACGTT
GATTCATTCCACTACTCTTCAGGGAAGATTGAATCGAGGTAGATTTGTTCCACTGCTCCTCATAG
Found at i:122471 original size:45 final size:45
Alignment explanation
Indices: 122378--122495 Score: 107
Period size: 45 Copynumber: 2.6 Consensus size: 45
122368 GTAGACTTGA
* * *
122378 TCCACTACTCCTCA-GAGAAGATCAAATCTGGAAAAGGGGATATGT
1 TCCACTACTCTTAAGGA-AAGATCAAATCTGGAAAAGGGGATATAT
* * * **
122423 TCCACTGCTCTTCAAGG-TAGATCAAATCTGGAAACGTTGAT-TCAT
1 TCCACTACTCTT-AAGGAAAGATCAAATCTGGAAAAGGGGATAT-AT
*
122468 TCCACTATTCTTAAGGAAAGATCAAATC
1 TCCACTACTCTTAAGGAAAGATCAAATC
122496 GAATTCGATT
Statistics
Matches: 58, Mismatches: 11, Indels: 8
0.75 0.14 0.10
Matches are distributed among these distances:
44 5 0.09
45 51 0.88
46 1 0.02
47 1 0.02
ACGTcount: A:0.34, C:0.21, G:0.18, T:0.27
Consensus pattern (45 bp):
TCCACTACTCTTAAGGAAAGATCAAATCTGGAAAAGGGGATATAT
Found at i:123810 original size:15 final size:15
Alignment explanation
Indices: 123778--123825 Score: 59
Period size: 15 Copynumber: 3.4 Consensus size: 15
123768 TTTCAATTAT
123778 TTTC-TTTTTC-TT-
1 TTTCTTTTTTCTTTC
123790 TTTCTTTTTTCTTTC
1 TTTCTTTTTTCTTTC
123805 TTTCTTTTATT-TTTC
1 TTTCTTTT-TTCTTTC
123820 TTTCTT
1 TTTCTT
123826 CAGACAAAGT
Statistics
Matches: 32, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
12 4 0.12
13 6 0.19
14 2 0.06
15 18 0.56
16 2 0.06
ACGTcount: A:0.02, C:0.17, G:0.00, T:0.81
Consensus pattern (15 bp):
TTTCTTTTTTCTTTC
Found at i:123817 original size:19 final size:18
Alignment explanation
Indices: 123774--123825 Score: 61
Period size: 19 Copynumber: 2.8 Consensus size: 18
123764 TTTTTTTCAA
*
123774 TTATTTTCTTTTTCTTTTT
1 TTATTTT-TCTTTCTTTTT
*
123793 CT-TTTTTCTTTCTTTCTT
1 TTATTTTTCTTTCTTT-TT
123811 TTATTTTTCTTTCTT
1 TTATTTTTCTTTCTT
123826 CAGACAAAGT
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
17 8 0.29
18 7 0.25
19 13 0.46
ACGTcount: A:0.04, C:0.15, G:0.00, T:0.81
Consensus pattern (18 bp):
TTATTTTTCTTTCTTTTT
Found at i:126037 original size:18 final size:18
Alignment explanation
Indices: 126014--126049 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
126004 TCTCATTTTT
126014 GTTCACTATAAACCCCAA
1 GTTCACTATAAACCCCAA
126032 GTTCACTATAAACCCCAA
1 GTTCACTATAAACCCCAA
126050 AAGCTTCCCA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.39, C:0.33, G:0.06, T:0.22
Consensus pattern (18 bp):
GTTCACTATAAACCCCAA
Found at i:135124 original size:11 final size:12
Alignment explanation
Indices: 135100--135149 Score: 50
Period size: 11 Copynumber: 4.2 Consensus size: 12
135090 AGATCTCATG
*
135100 AAAAATACATAC
1 AAAAATACAAAC
135112 AAAAATA-AAAC
1 AAAAATACAAAC
135123 AAAAATTACAAAC
1 AAAAA-TACAAAC
* *
135136 ATATAT-CAAAC
1 AAAAATACAAAC
135147 AAA
1 AAA
135150 TAAGATTAAT
Statistics
Matches: 32, Mismatches: 4, Indels: 5
0.78 0.10 0.12
Matches are distributed among these distances:
11 15 0.47
12 10 0.31
13 7 0.22
ACGTcount: A:0.70, C:0.14, G:0.00, T:0.16
Consensus pattern (12 bp):
AAAAATACAAAC
Found at i:137176 original size:25 final size:24
Alignment explanation
Indices: 137124--137178 Score: 65
Period size: 25 Copynumber: 2.2 Consensus size: 24
137114 GGGTTGTTTG
* *
137124 GTTTGGGTCGGACCAGTCGGGTCG
1 GTTTGGGTCGGACCAGTCGGGCCA
* *
137148 GTTTGGGCTTGGACCAGTTGGGCCA
1 GTTTGGG-TCGGACCAGTCGGGCCA
137173 GTTTGG
1 GTTTGG
137179 CTCTTTGTAA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
24 7 0.27
25 19 0.73
ACGTcount: A:0.09, C:0.18, G:0.44, T:0.29
Consensus pattern (24 bp):
GTTTGGGTCGGACCAGTCGGGCCA
Found at i:146076 original size:44 final size:42
Alignment explanation
Indices: 145973--146195 Score: 338
Period size: 44 Copynumber: 5.2 Consensus size: 42
145963 AGCATGGGAA
* *
145973 AACTGTAAGGCTTACCCTTGCACACAGCAAAGGAACCTGGGA
1 AACTGTAAGGCTTACCCTTGCACACAGCAAAGGGACCTGGGG
*
146015 AACTGTAAGGCTTACCCTTGTACACAGCAAAGGGACCTAGTGGG
1 AACTGTAAGGCTTACCCTTGCACACAGCAAAGGGACCT-G-GGG
* *
146059 AACTGTAAGGCTTACCCTTGCACACAGCAAAGAGACATGGGGG
1 AACTGTAAGGCTTACCCTTGCACACAGCAAAGGGACCT-GGGG
146102 AACTGTAAGGCTTACCCTTGCACACAGCAAAGGGACCTGGGGG
1 AACTGTAAGGCTTACCCTTGCACACAGCAAAGGGACCT-GGGG
* *
146145 AAACTGTAAGGCTTATCCTTGCACACAACAAAGGGACCTGGGG
1 -AACTGTAAGGCTTACCCTTGCACACAGCAAAGGGACCTGGGG
146188 AACTGTAA
1 AACTGTAA
146196 CGATAATTAA
Statistics
Matches: 167, Mismatches: 11, Indels: 6
0.91 0.06 0.03
Matches are distributed among these distances:
42 44 0.26
43 49 0.29
44 74 0.44
ACGTcount: A:0.32, C:0.24, G:0.26, T:0.18
Consensus pattern (42 bp):
AACTGTAAGGCTTACCCTTGCACACAGCAAAGGGACCTGGGG
Found at i:146134 original size:87 final size:85
Alignment explanation
Indices: 145972--146195 Score: 342
Period size: 87 Copynumber: 2.6 Consensus size: 85
145962 GAGCATGGGA
* *
145972 AAACTGTAAGGCTTACCCTTGCACACAGCAAAGGAACCTGGGAAACTGTAAGGCTTACCCTTGTA
1 AAACTGTAAGGCTTACCCTTGCACACAGCAAAGG-ACCTGGGGAACTGTAAGGCTTACCCTTGCA
*
146037 CACAGCAAAGGGACCTAGTGGG
65 CACAGCAAAGGGACCT-GGGGG
*
146059 -AACTGTAAGGCTTACCCTTGCACACAGCAAAGAGACATGGGGGAACTGTAAGGCTTACCCTTGC
1 AAACTGTAAGGCTTACCCTTGCACACAGCAAAG-GACCT-GGGGAACTGTAAGGCTTACCCTTGC
146123 ACACAGCAAAGGGACCTGGGGG
64 ACACAGCAAAGGGACCTGGGGG
* *
146145 AAACTGTAAGGCTTATCCTTGCACACAACAAAGGGACCTGGGGAACTGTAA
1 AAACTGTAAGGCTTACCCTTGCACACAGCAAA-GGACCTGGGGAACTGTAA
146196 CGATAATTAA
Statistics
Matches: 126, Mismatches: 7, Indels: 9
0.89 0.05 0.06
Matches are distributed among these distances:
86 51 0.40
87 74 0.59
88 1 0.01
ACGTcount: A:0.32, C:0.24, G:0.26, T:0.18
Consensus pattern (85 bp):
AAACTGTAAGGCTTACCCTTGCACACAGCAAAGGACCTGGGGAACTGTAAGGCTTACCCTTGCAC
ACAGCAAAGGGACCTGGGGG
Found at i:146721 original size:27 final size:27
Alignment explanation
Indices: 146664--146725 Score: 72
Period size: 27 Copynumber: 2.3 Consensus size: 27
146654 TTTATATTAT
* *
146664 TATTATTATTATAATAATTATTATTAT
1 TATTATTATTATAATAATTATTATAAA
* *
146691 TATTATTATTAT-TTTATTATTAATAAA
1 TATTATTATTATAATAATTATT-ATAAA
146718 TATTATTA
1 TATTATTA
146726 CAGGCCCAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
26 7 0.23
27 23 0.77
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (27 bp):
TATTATTATTATAATAATTATTATAAA
Found at i:146725 original size:3 final size:3
Alignment explanation
Indices: 146649--146712 Score: 87
Period size: 3 Copynumber: 21.7 Consensus size: 3
146639 TTCATTTAAA
* *
146649 TAT TAT T-T ATAT TAT TAT TAT TAT TAT AAT AAT TAT TAT TAT TAT
1 TAT TAT TAT -TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
146694 TAT TAT TAT T-T TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TA
146713 ATAAATATTA
Statistics
Matches: 56, Mismatches: 2, Indels: 6
0.88 0.03 0.09
Matches are distributed among these distances:
2 3 0.05
3 52 0.93
4 1 0.02
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:148310 original size:20 final size:20
Alignment explanation
Indices: 148285--148327 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
148275 ATATTTTATA
148285 AATTATATATTAATTGTTTT
1 AATTATATATTAATTGTTTT
* * *
148305 AATTATTTATTTATTTTTTT
1 AATTATATATTAATTGTTTT
148325 AAT
1 AAT
148328 ATCGAGGAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (20 bp):
AATTATATATTAATTGTTTT
Found at i:159630 original size:15 final size:15
Alignment explanation
Indices: 159601--159688 Score: 80
Period size: 15 Copynumber: 6.1 Consensus size: 15
159591 TACTATGCTT
*
159601 GAAGAAAAAATAAAAA
1 GAAGAAAAGA-AAAAA
159617 GAAGAAAAGAAAAAA
1 GAAGAAAAGAAAAAA
*
159632 AAAGAAAAAGAAAAAA
1 GAAG-AAAAGAAAAAA
159648 -AAG--AAGAAAAAA
1 GAAGAAAAGAAAAAA
159660 G-AGAAGAAGAAAAAA
1 GAAGAA-AAGAAAAAA
*
159675 -AA-AAGAGAAAAAA
1 GAAGAAAAGAAAAAA
159688 G
1 G
159689 GGGGTCAAGA
Statistics
Matches: 62, Mismatches: 3, Indels: 16
0.77 0.04 0.20
Matches are distributed among these distances:
12 11 0.18
13 8 0.13
14 2 0.03
15 21 0.34
16 20 0.32
ACGTcount: A:0.81, C:0.00, G:0.18, T:0.01
Consensus pattern (15 bp):
GAAGAAAAGAAAAAA
Found at i:159649 original size:33 final size:32
Alignment explanation
Indices: 159605--159678 Score: 96
Period size: 33 Copynumber: 2.3 Consensus size: 32
159595 ATGCTTGAAG
*
159605 AAAAAATAAAAAGAAGAAAAGAA-AAAAAAAGA
1 AAAAAAAAAAAAGAAGAAAA-AAGAAAAAAAGA
* *
159637 AAAAGAAAAAAAAGAAGAAAAAAGAGAAGAAGA
1 AAAA-AAAAAAAAGAAGAAAAAAGAAAAAAAGA
159670 AAAAAAAAA
1 AAAAAAAAA
159679 GAGAAAAAAG
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
32 11 0.30
33 26 0.70
ACGTcount: A:0.84, C:0.00, G:0.15, T:0.01
Consensus pattern (32 bp):
AAAAAAAAAAAAGAAGAAAAAAGAAAAAAAGA
Found at i:159667 original size:40 final size:39
Alignment explanation
Indices: 159605--159687 Score: 105
Period size: 40 Copynumber: 2.1 Consensus size: 39
159595 ATGCTTGAAG
* *
159605 AAAAAATAAAAAGAAGAAAAGAA-AAAAAAAGAAAAAGAA
1 AAAAAAGAAAAAAAAGAAAAGAAGAAAAAAA-AAAAAGAA
* *
159644 AAAAAAGAAGAAAAAAGAGAAGAAGAAAAAAAAAAGAGAA
1 AAAAAAGAA-AAAAAAGAAAAGAAGAAAAAAAAAAAAGAA
159684 AAAA
1 AAAA
159688 GGGGGTCAAG
Statistics
Matches: 38, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
39 8 0.21
40 23 0.61
41 7 0.18
ACGTcount: A:0.83, C:0.00, G:0.16, T:0.01
Consensus pattern (39 bp):
AAAAAAGAAAAAAAAGAAAAGAAGAAAAAAAAAAAAGAA
Found at i:159673 original size:28 final size:27
Alignment explanation
Indices: 159612--159688 Score: 97
Period size: 27 Copynumber: 2.9 Consensus size: 27
159602 AAGAAAAAAT
*
159612 AAAAAG-AAGAAAAGAA-AAAAAA-AG
1 AAAAAGAAAAAAAAGAAGAAAAAAGAG
159636 AAAAAGAAAAAAAAGAAGAAAAAAGAG
1 AAAAAGAAAAAAAAGAAGAAAAAAGAG
* *
159663 AAGAAGAAAAAAAAAAGAGAAAAAAG
1 AAAAAGAAAAAAAAGA-AGAAAAAAG
159689 GGGGTCAAGA
Statistics
Matches: 46, Mismatches: 3, Indels: 4
0.87 0.06 0.08
Matches are distributed among these distances:
24 6 0.13
25 9 0.20
26 6 0.13
27 16 0.35
28 9 0.20
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (27 bp):
AAAAAGAAAAAAAAGAAGAAAAAAGAG
Found at i:160516 original size:113 final size:109
Alignment explanation
Indices: 160375--160580 Score: 295
Period size: 113 Copynumber: 1.9 Consensus size: 109
160365 TGGTAGAAAT
* * *
160375 AAGGAGGCCCAATAGCATCTTCTAGAAGTATTCTTTGAGTTATCTGATCTGGTTTTGGTATAAAC
1 AAGGAGACCCAATAGCATCTTCTAGAAGTATTC-TTGAGTTATCTGATCTGG-TTCGGTAGAAAC
*
160440 CCCAAAACCAATCATTAGATTTGAAAGATGAATTTGCTCATAGTAGAA
64 CCC-AAACCAATCATTAGAATT-AAAGATGAATTTGCTCATAGTAGAA
* * *
160488 AAGGAGACCCAATAGCATCTTCTGGAAGTGTTCTTGAGTTATCTGATCTGGTTCGGTAGGAACCC
1 AAGGAGACCCAATAGCATCTTCTAGAAGTATTCTTGAGTTATCTGATCTGGTTCGGTAGAAACCC
* *
160553 CAGACCAATTATTAGAATTAAAGATGAA
66 CAAACCAATCATTAGAATTAAAGATGAA
160581 CTGCATGATC
Statistics
Matches: 84, Mismatches: 9, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
109 9 0.11
110 15 0.18
111 12 0.14
112 18 0.21
113 30 0.36
ACGTcount: A:0.33, C:0.17, G:0.20, T:0.30
Consensus pattern (109 bp):
AAGGAGACCCAATAGCATCTTCTAGAAGTATTCTTGAGTTATCTGATCTGGTTCGGTAGAAACCC
CAAACCAATCATTAGAATTAAAGATGAATTTGCTCATAGTAGAA
Found at i:161509 original size:112 final size:112
Alignment explanation
Indices: 161293--162013 Score: 606
Period size: 109 Copynumber: 6.5 Consensus size: 112
161283 GATTTAAATC
* * ** * * *
161293 CATCATTTAATGGATCAACATTTTCAGTTAGAGTTCATAATAAGAAGAACAACTTATCTGAAGAG
1 CATCATTCAATGGATCAACATTTCCAGAGAAAGTTCATAAT--G-AGAAGAACTTATCTGAAGAA
* *
161358 GAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTCGAATT
63 GAAGAAGAAGTTCATAATGAGAAGAGCTTGTTCAACCTTTTGCTTGAATT
* *
161408 CATCATTCAATGGATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTTATCTGAAAAAAGA
1 CATCATTCAATGGATCAACATTTCCAGAGAAAGTTCATAATGAGAAGAACTTATCTG-AAGAAGA
*
161473 AGAAGAAGTTCA-AATGAGAAGAGCTTGTTCAACCTTTTGCTCGAATT
65 AGAAGAAGTTCATAATGAGAAGAGCTTGTTCAACCTTTTGCTTGAATT
* * * * * ** *
161520 CATCATTCGATGGATCATCGTTGCC--AGAAGGTTCATAATGAGAAGAACTTATCAT-CTGAGGA
1 CATCATTCAATGGATCAACATTTCCAGAGAAAGTTCATAATGAGAAGAACTTATC-TGAAGAAGA
161582 AGAAGAAGTTCA-AATGAGAAGAGCTTGTTCAACCTTTTTGCTTG--TT
65 AGAAGAAGTTCATAATGAGAAGAGCTTGTTCAACC-TTTTGCTTGAATT
*** * * *
161628 CTATCACAGAAAAAGATAGATCAGCATTAACATTTCCAGTCG--AGTTCATAATGAGAAGAACTC
1 C-AT--C--ATTCA-AT-G----G-ATCAACATTTCCAG-AGAAAGTTCATAATGAGAAGAACTT
* *
161691 ATCTGAAGAAGGAAG-AGAAGTTCATAATGAGAAGA-ATTGTTCAACTTTTTG-TTGAATT
53 ATCTGAAGAA-GAAGAAGAAGTTCATAATGAGAAGAGCTTGTTCAACCTTTTGCTTGAATT
* * *
161749 CATCATTCGATGGATCATCATTTCAAGAGAAAGTTCATAATGAGAAGAACTTAT-TGAAGAAG--
1 CATCATTCAATGGATCAACATTTCCAGAGAAAGTTCATAATGAGAAGAACTTATCTGAAGAAGAA
* *
161811 GAAGAAGTTCATAAT-AGAAGAGCTTGTTCAACCTTTTGTTTAAATT
66 GAAGAAGTTCATAATGAGAAGAGCTTGTTCAACCTTTTGCTTGAATT
* * *
161857 CATC-GT---TGGATAAACATTGCC--AG--AGTTCATAATGAGAA-AACTCGTCATCTGAAGAA
1 CATCATTCAATGGATCAACATTTCCAGAGAAAGTTCATAATGAGAAGAACT--T-ATCTGAAGAA
* * *
161913 GAAG-A-AA-TTCAT-ATGAG-AGAAGAATTGTTCAA-CTTTTGTTTAAATT
63 GAAGAAGAAGTTCATAATGAGAAG-AG-CTTGTTCAACCTTTTGCTTGAATT
* * * *
161959 CATCACTCGATGGATCAACTTTTCCAGAG-AAGTTCATAATGAGAAGAATTTATCT
1 CATCATTCAATGGATCAACATTTCCAGAGAAAGTTCATAATGAGAAGAACTTATCT
162014 AA
Statistics
Matches: 502, Mismatches: 59, Indels: 98
0.76 0.09 0.15
Matches are distributed among these distances:
99 4 0.01
100 15 0.03
101 5 0.01
102 31 0.06
103 19 0.04
104 12 0.02
105 1 0.00
106 19 0.04
107 32 0.06
108 18 0.04
109 72 0.14
110 61 0.12
111 2 0.00
112 69 0.14
113 19 0.04
114 3 0.01
115 38 0.08
116 1 0.00
118 1 0.00
119 4 0.01
120 16 0.03
121 45 0.09
122 14 0.03
123 1 0.00
ACGTcount: A:0.37, C:0.14, G:0.19, T:0.30
Consensus pattern (112 bp):
CATCATTCAATGGATCAACATTTCCAGAGAAAGTTCATAATGAGAAGAACTTATCTGAAGAAGAA
GAAGAAGTTCATAATGAGAAGAGCTTGTTCAACCTTTTGCTTGAATT
Found at i:161949 original size:102 final size:102
Alignment explanation
Indices: 161669--161962 Score: 307
Period size: 102 Copynumber: 2.8 Consensus size: 102
161659 ATTTCCAGTC
161669 GAGTTCATAATGAGAAGAA--CTCATCTGAAGAAGGAAGAGAAGTTCATAATGAGAAGAATTGTT
1 GAGTTCATAATGAGAAGAACTCTCATCTGAAGAAGGAAGA-AA-TTCATAA-GAGAAGAATTGTT
* * * * * *
161732 CAACTTTTTGTTGAATTCATCATTCGATGGATCATCATTTCAAGA
63 CAAC-TTTTGTTTAAAT--TCA-TCGATGGATAAACATTGC-ACA
* * *
161777 GAAAGTTCATAATGAGAAGAACT-T-AT-TGAAGAAGGAAGAAGTTCATAATAGAAGAGCTTGTT
1 G--AGTTCATAATGAGAAGAACTCTCATCTGAAGAAGGAAGAAATTCATAAGAGAAGA-ATTGTT
*
161839 CAACCTTTTGTTTAAATTCATCGTTGGATAAACATTGC-CA
63 CAA-CTTTTGTTTAAATTCATCGATGGATAAACATTGCACA
161879 GAGTTCATAATGAGAA-AACTCGTCATCTGAAGAA-GAAGAAATTCATATGAGAGAAGAATTGTT
1 GAGTTCATAATGAGAAGAACTC-TCATCTGAAGAAGGAAGAAATTCATA--AGAGAAGAATTGTT
161942 CAACTTTTGTTTAAATTCATC
63 CAACTTTTGTTTAAATTCATC
161963 ACTCGATGGA
Statistics
Matches: 161, Mismatches: 13, Indels: 30
0.79 0.06 0.15
Matches are distributed among these distances:
99 4 0.02
100 15 0.09
101 1 0.01
102 34 0.21
103 15 0.09
104 21 0.13
105 3 0.02
106 6 0.04
107 25 0.16
108 3 0.02
109 13 0.08
110 20 0.12
111 1 0.01
ACGTcount: A:0.38, C:0.12, G:0.19, T:0.31
Consensus pattern (102 bp):
GAGTTCATAATGAGAAGAACTCTCATCTGAAGAAGGAAGAAATTCATAAGAGAAGAATTGTTCAA
CTTTTGTTTAAATTCATCGATGGATAAACATTGCACA
Done.