Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008497.1 Hibiscus syriacus cultivar Beakdansim tig00111342_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: 1504768
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32
File 2 of 6
Found at i:271255 original size:19 final size:19
Alignment explanation
Indices: 271233--271281 Score: 55
Period size: 19 Copynumber: 2.6 Consensus size: 19
271223 TCGGGTCGGG
*
271233 TCAGACCGGTCAAACTGGT
1 TCAGACCGGTCAAACCGGT
* *
271252 TCAGACCAGTCAGACCGGT
1 TCAGACCGGTCAAACCGGT
271271 TC-GAACCGGTC
1 TCAG-ACCGGTC
271282 GAAATCGATT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
18 1 0.04
19 24 0.96
ACGTcount: A:0.24, C:0.31, G:0.27, T:0.18
Consensus pattern (19 bp):
TCAGACCGGTCAAACCGGT
Found at i:273892 original size:237 final size:236
Alignment explanation
Indices: 273478--273953 Score: 817
Period size: 237 Copynumber: 2.0 Consensus size: 236
273468 GCGGGGTGAA
* **
273478 TGTTAAGAATAGAGTGATGCCAGTTGGAGAGATTGCCAGCTGGAGCTGTTAGTTACTAACCGTTT
1 TGTTAAGAATAGAGTGATGCCAGCTACAGAGATTGCCAGCTGGAGCTGTTAGTTACTAACCGTTT
*
273543 CTATTAAGGTTAGTTATTCAGTTAAGCCAGCTTTCTATTGGGTTGAACTTATAGTGTTAACCCGT
66 CTATTAAGGTTAGTTATTCAGTTAAGCCAACTTTCTATTGGGTTGAACTTATAGTGTTAACCCGT
*
273608 TAAGAAAAACATGTGGCTATATAAGAAGACCTTCTGGTCAAGGGCTAGATCAATCTAATAGCCTA
131 TAAGAAAAACATGTGGCTATATAAGAAGACCTTCTGGTCAAGGGCTAGATCAATCTAATAGCCAA
273673 CATTTTCTTTCATTTCACCTCTCTTTACTTCTGGTTTAAAC
196 CATTTTCTTTCATTTCACCTCTCTTTACTTCTGGTTTAAAC
* * * * * *
273714 TGTTAAGAATAGAGTGGTGTCAGCTACAGGGATTGTCAGTTGGAGTTGTTAGTTACTAACCGTTT
1 TGTTAAGAATAGAGTGATGCCAGCTACAGAGATTGCCAGCTGGAGCTGTTAGTTACTAACCGTTT
*
273779 CTGTTAAGGTTAGTTTATTCAGTTAAGCCAACTTTCTATTGGGTTGAACTTATAGTGTTAACCCG
66 CTATTAAGGTTAG-TTATTCAGTTAAGCCAACTTTCTATTGGGTTGAACTTATAGTGTTAACCCG
*
273844 TTAAGAAAAGCATGTGGCTATATAAGAAGACCTTCTGGTCAAGGGCTAGATCAATCTAATAGCCA
130 TTAAGAAAAACATGTGGCTATATAAGAAGACCTTCTGGTCAAGGGCTAGATCAATCTAATAGCCA
*
273909 ACATTTTCTTTCCTTTCACCTCTCTTTACTTCTGGTTTAAAC
195 ACATTTTCTTTCATTTCACCTCTCTTTACTTCTGGTTTAAAC
273951 TGT
1 TGT
273954 GTTGTTAGCA
Statistics
Matches: 225, Mismatches: 14, Indels: 1
0.94 0.06 0.00
Matches are distributed among these distances:
236 68 0.30
237 157 0.70
ACGTcount: A:0.27, C:0.17, G:0.20, T:0.36
Consensus pattern (236 bp):
TGTTAAGAATAGAGTGATGCCAGCTACAGAGATTGCCAGCTGGAGCTGTTAGTTACTAACCGTTT
CTATTAAGGTTAGTTATTCAGTTAAGCCAACTTTCTATTGGGTTGAACTTATAGTGTTAACCCGT
TAAGAAAAACATGTGGCTATATAAGAAGACCTTCTGGTCAAGGGCTAGATCAATCTAATAGCCAA
CATTTTCTTTCATTTCACCTCTCTTTACTTCTGGTTTAAAC
Found at i:295230 original size:19 final size:19
Alignment explanation
Indices: 295206--295247 Score: 75
Period size: 19 Copynumber: 2.2 Consensus size: 19
295196 ATAGTCTGAT
*
295206 GATTATTTTATGATTTGAA
1 GATTATTTTATGATTTAAA
295225 GATTATTTTATGATTTAAA
1 GATTATTTTATGATTTAAA
295244 GATT
1 GATT
295248 CAATAAAATA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.33, C:0.00, G:0.14, T:0.52
Consensus pattern (19 bp):
GATTATTTTATGATTTAAA
Found at i:308108 original size:16 final size:16
Alignment explanation
Indices: 308068--308110 Score: 51
Period size: 11 Copynumber: 3.0 Consensus size: 16
308058 CTCTCCCCTC
308068 AATCAATGTACCCTTG
1 AATCAATGTACCCTTG
308084 -A--AA--TACCCTTG
1 AATCAATGTACCCTTG
308095 AATCAATGTACCCTTG
1 AATCAATGTACCCTTG
308111 TAAACAGGAC
Statistics
Matches: 22, Mismatches: 0, Indels: 10
0.69 0.00 0.31
Matches are distributed among these distances:
11 8 0.36
12 1 0.05
13 2 0.09
14 2 0.09
15 1 0.05
16 8 0.36
ACGTcount: A:0.33, C:0.26, G:0.12, T:0.30
Consensus pattern (16 bp):
AATCAATGTACCCTTG
Found at i:312055 original size:135 final size:134
Alignment explanation
Indices: 311686--312074 Score: 441
Period size: 130 Copynumber: 2.9 Consensus size: 134
311676 GACGACACTG
* * * * *
311686 CTCATCCGCGATGAAGAGAATCTTGGCCATCTTTAGGAAAGATGATAACATGGTTCCATTCTGC-
1 CTCATACGTGATGAAGAG-TTCTTGGCCATCTTTAGG-AAGGTGATAACATGGTTCC-TAC-GCG
* * * * * *
311750 -TGGGGACGGCTGGTTATCTGAGGTTGACACGGCTCATACGTGATGAAGAGTTCTGGTCAGGGGA
62 ATGAGGACGGCTGGTTATCTAAGGTTGACACGGCTCCTACGTGATGAGGAGATCTGGTCAGAGGA
**
311814 TGACATTA
127 TGACACGA
* * *
311822 CTCATACATGATGAAGAGTTCTTGGCCATC--TA--AAGGTGATAACACGGTTCCTACGTGATGA
1 CTCATACGTGATGAAGAGTTCTTGGCCATCTTTAGGAAGGTGATAACATGGTTCCTACGCGATGA
* * *
311883 GGACGGCTGGTTATCTAAGGGTGACACGGTTCCTACGTGATGAGGAAATCTGGTC-GAAGGATGA
66 GGACGGCTGGTTATCTAAGGTTGACACGGCTCCTACGTGATGAGGAGATCTGGTCAG-AGGATGA
311947 CACGA
130 CACGA
* *
311952 CTCATGCGTGATGAAGAGTTCTTGGCCATCTTTAGGAAGGGTGATAACTTGGTTCCTACGCGATG
1 CTCATACGTGATGAAGAGTTCTTGGCCATCTTTAGGAA-GGTGATAACATGGTTCCTACGCGATG
* * ***
312017 AGGATGGCTGGTTATCTAATGTTGACGTTGCTCCTACGTGATGAGGAGATCTGGTCAG
65 AGGACGGCTGGTTATCTAAGGTTGACACGGCTCCTACGTGATGAGGAGATCTGGTCAG
312075 CTGATGTTGA
Statistics
Matches: 212, Mismatches: 32, Indels: 18
0.81 0.12 0.07
Matches are distributed among these distances:
128 1 0.00
129 3 0.01
130 104 0.49
132 2 0.01
133 2 0.01
134 2 0.01
135 82 0.39
136 16 0.08
ACGTcount: A:0.25, C:0.18, G:0.30, T:0.28
Consensus pattern (134 bp):
CTCATACGTGATGAAGAGTTCTTGGCCATCTTTAGGAAGGTGATAACATGGTTCCTACGCGATGA
GGACGGCTGGTTATCTAAGGTTGACACGGCTCCTACGTGATGAGGAGATCTGGTCAGAGGATGAC
ACGA
Found at i:313030 original size:23 final size:22
Alignment explanation
Indices: 312978--313035 Score: 55
Period size: 23 Copynumber: 2.6 Consensus size: 22
312968 CTTGAACCCT
* *
312978 CCTTTATTTATTTTTTTTCTTTTT
1 CCTTT-TTTATTTTTTTTC-ATTC
* *
313002 CATTTTTCATTTTTTTTCATTC
1 CCTTTTTTATTTTTTTTCATTC
313024 CCTTTTTT-TTTT
1 CCTTTTTTATTTT
313036 AAGTGTAATA
Statistics
Matches: 28, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
21 4 0.14
22 8 0.29
23 12 0.43
24 4 0.14
ACGTcount: A:0.09, C:0.16, G:0.00, T:0.76
Consensus pattern (22 bp):
CCTTTTTTATTTTTTTTCATTC
Found at i:332025 original size:18 final size:18
Alignment explanation
Indices: 331980--332026 Score: 55
Period size: 18 Copynumber: 2.8 Consensus size: 18
331970 CACATCAGCA
331980 ATTT-TTAA-AAA-AATT
1 ATTTATTAATAAATAATT
331995 ATTTATTAATAAATAATT
1 ATTTATTAATAAATAATT
* *
332013 ATTTTTTACTAAAT
1 ATTTATTAATAAAT
332027 TAAAAACAGA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
15 4 0.15
16 4 0.15
17 3 0.11
18 16 0.59
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (18 bp):
ATTTATTAATAAATAATT
Found at i:332812 original size:414 final size:415
Alignment explanation
Indices: 331699--333345 Score: 2471
Period size: 414 Copynumber: 4.0 Consensus size: 415
331689 AAGAGAGACA
* * * * * *
331699 TAATGCAAACAAATACCCCCAACATTTGATAATATATGCAATTTTGTCCCAATTATTTTTTTTTT
1 TAATGCAAACAAATACCCCTAACGTTTGACAATATATGCAATTTTGCCCCTATTATTTTTTTTTG
* * * *
331764 AAACATTTGACCCCCACGTTTCATTTTGGATCAAAAAGCACCCTCGTTAGATGAAAACTGTTAGT
66 GAACATTTGACCCCCACGTTTCATTTTGGGTCAAAAAACACCCTCGTTGGATGAAAACTGTTAGT
* * *
331829 CAACTGACGGTCAACGTCTGAAGTTGACTCAACAAGAACATGTGGAGGGAGATATTGACGTGACA
131 CAACTGACGGTCAACGTCTGAAGCTGACTCAACAAGAACATGTGGAGGGAGATACTGACGTGGCA
* * *
331894 TGTCCATATCATAGTAGATTATGACGTGACAGAT-CATGTAGACTAAATGCTGACATGGCATGTC
196 TGTCCACATCATAGTAGATGATGACGTGACAGATCCACGTAGACTAAATGCTGACATGGCATGTC
* * *
331958 CACATGTGATGGCACATCAGCAA--TTTTTAAAAAAATTATTTATTAATAAATAATTATTTTTTA
261 CACGTGTGATGCCACATCAGCAATTTTTTTAAAAAAATTATTTAATAATAAATAATTATTTTTTA
* * *
332021 CTAAATTAAAAACAGA-CAATCAGATGCTGTCACATGACATATAGATTTTTTATTAAATTGAGAT
326 CTAAATTAATAACA-ATCAATCAGATGTTGTCACATGACACATAGATTTTTTATTAAATTGAGAT
*
332085 AGGAGGGATTAAACATCCACAAATTT
390 AGGAGGGATTAAACCTCCACAAATTT
*
332111 TAATGCAAACAAATACCCCTAACGTTTGACAATATATGCAATTTTGCCCCTA-TAATTTTTTTTG
1 TAATGCAAACAAATACCCCTAACGTTTGACAATATATGCAATTTTGCCCCTATTATTTTTTTTTG
*
332175 GAACATTTGACCCCCATGTTTCATTTTGGGTCAAAAAAACACCCTCGTTGGATGAAAACTGTTAG
66 GAACATTTGACCCCCACGTTTCATTTTGGGTC-AAAAAACACCCTCGTTGGATGAAAACTGTTAG
332240 TCAACTGACGGTCAACGTCTGAAGCTGACTCAACAAGAACATGTGGAGGGAGATACTGACGTGGC
130 TCAACTGACGGTCAACGTCTGAAGCTGACTCAACAAGAACATGTGGAGGGAGATACTGACGTGGC
* * * * * *
332305 ATGTTCATATTACAGTAGATGATGACGTGACAGATCCACATAGACTAAATGTTGACATGGCATGT
195 ATGTCCACATCATAGTAGATGATGACGTGACAGATCCACGTAGACTAAATGCTGACATGGCATGT
* * *
332370 CCACGTGTGATGCCACGTCAGTAATTTTTTTAAAAAAAATTATTTAATAATAAATAATTACTTTT
260 CCACGTGTGATGCCACATCAGCAATTTTTTT-AAAAAAATTATTTAATAATAAATAATTATTTTT
*
332435 TACTAAATTAATAACAATCAATCAGATGTTGTCACATGACACATAAATTTTTTATTAAATTGAGA
324 TACTAAATTAATAACAATCAATCAGATGTTGTCACATGACACATAGATTTTTTATTAAATTGAGA
*
332500 TAGGAGGGATTAAACCTCCAAAAATTT
389 TAGGAGGGATTAAACCTCCACAAATTT
* * * * *
332527 TAATGCAAATAAATACTCCTAACGTTTGACAATATATACAATTTT-CCCCTATTGTTGTTTTTTG
1 TAATGCAAACAAATACCCCTAACGTTTGACAATATATGCAATTTTGCCCCTATTATTTTTTTTTG
*
332591 GAACATTTGA-CCCCACGTTTCATTTTGGGTCAAAAAACACCATCGTTGGATGAAAAAC-GTTAG
66 GAACATTTGACCCCCACGTTTCATTTTGGGTCAAAAAACACCCTCGTTGGATG-AAAACTGTTAG
* * * *
332654 TCAACTGACGGTCAACGTCTGAAGCTGACTCATCAAGAACATGTGGAGGGAGATGCTAATGTGGC
130 TCAACTGACGGTCAACGTCTGAAGCTGACTCAACAAGAACATGTGGAGGGAGATACTGACGTGGC
*
332719 ATGTCCACATCATAGTAGATGATGACGTGACAGATCCACGTAGACTAAATACTGACATGGCATGT
195 ATGTCCACATCATAGTAGATGATGACGTGACAGATCCACGTAGACTAAATGCTGACATGGCATGT
* * * *
332784 TCACGTGTGATGCCACGTC-GACAATTTTTTT-TAAAAATTAATTAATAATAAATAATTATTTTT
260 CCACGTGTGATGCCACATCAG-CAATTTTTTTAAAAAAATTATTTAATAATAAATAATTATTTTT
* * *
332847 TACTAAATTAATAACAGTCAATCAGATGTTGTCACATGGCACATGGATTTTTTATTAAATTGAGA
324 TACTAAATTAATAACAATCAATCAGATGTTGTCACATGACACATAGATTTTTTATTAAATTGAGA
332912 TAGGAGGGATTAAACCTCCACAAATTT
389 TAGGAGGGATTAAACCTCCACAAATTT
* * * *
332939 TAATGCAAATAAATACCCCTAACGTTTGACAATATATGCAATTTTGCCCTTATTGTTTTTTTTTT
1 TAATGCAAACAAATACCCCTAACGTTTGACAATATATGCAATTTTGCCCCTATTATTTTTTTTTG
* * *
333004 GAACATTTGACCCCCACGTTTCATTTTGGGTCAAAAAGCACTCTCGTTGGATGAAAATTGTTAGT
66 GAACATTTGACCCCCACGTTTCATTTTGGGTCAAAAAACACCCTCGTTGGATGAAAACTGTTAGT
* *
333069 CAACTGACGGTCAACGTCTGAAGCTGACTCAACAAGAACATGTGGAGGAAGATGCTGACGTGGCA
131 CAACTGACGGTCAACGTCTGAAGCTGACTCAACAAGAACATGTGGAGGGAGATACTGACGTGGCA
* *
333134 TGTCC-CTATTATAGTAGATGATGACGTGACAGATCCACGTAGACTAAATGCTGGCATGGCATGT
196 TGTCCAC-ATCATAGTAGATGATGACGTGACAGATCCACGTAGACTAAATGCTGACATGGCATGT
** **
333198 CCACGTGTGATGCCACATCAATAATTTTTTTTTAAAAA--A--TAATAATAAATAATTATTTTTT
260 CCACGTGTGATGCCACATCAGCAATTTTTTTAAAAAAATTATTTAATAATAAATAATTATTTTTT
* * *
333259 ACTAAATTAATAACAACCAATCAGATGTTGTCACACGACACAT-GTATTTTTTATTAAATTAAGA
325 ACTAAATTAATAACAATCAATCAGATGTTGTCACATGACACATAG-ATTTTTTATTAAATTGAGA
333323 TAGGAGGGATTAAACCTCCACAA
389 TAGGAGGGATTAAACCTCCACAA
333346 TTGAACCTCG
Statistics
Matches: 1131, Mismatches: 88, Indels: 33
0.90 0.07 0.03
Matches are distributed among these distances:
410 1 0.00
411 141 0.12
412 329 0.29
413 79 0.07
414 362 0.32
415 43 0.04
416 176 0.16
ACGTcount: A:0.35, C:0.17, G:0.17, T:0.32
Consensus pattern (415 bp):
TAATGCAAACAAATACCCCTAACGTTTGACAATATATGCAATTTTGCCCCTATTATTTTTTTTTG
GAACATTTGACCCCCACGTTTCATTTTGGGTCAAAAAACACCCTCGTTGGATGAAAACTGTTAGT
CAACTGACGGTCAACGTCTGAAGCTGACTCAACAAGAACATGTGGAGGGAGATACTGACGTGGCA
TGTCCACATCATAGTAGATGATGACGTGACAGATCCACGTAGACTAAATGCTGACATGGCATGTC
CACGTGTGATGCCACATCAGCAATTTTTTTAAAAAAATTATTTAATAATAAATAATTATTTTTTA
CTAAATTAATAACAATCAATCAGATGTTGTCACATGACACATAGATTTTTTATTAAATTGAGATA
GGAGGGATTAAACCTCCACAAATTT
Found at i:333265 original size:28 final size:29
Alignment explanation
Indices: 333217--333271 Score: 76
Period size: 28 Copynumber: 1.9 Consensus size: 29
333207 ATGCCACATC
*
333217 AATAATTTTTTTTTAAAAAA-TAATAATA
1 AATAATTATTTTTTAAAAAATTAATAATA
**
333245 AATAATTATTTTTTACTAAATTAATAA
1 AATAATTATTTTTTAAAAAATTAATAA
333272 CAACCAATCA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
28 17 0.74
29 6 0.26
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (29 bp):
AATAATTATTTTTTAAAAAATTAATAATA
Found at i:336135 original size:18 final size:18
Alignment explanation
Indices: 336109--336158 Score: 66
Period size: 18 Copynumber: 2.8 Consensus size: 18
336099 TTGAAATCTC
* *
336109 AACTTAAAGGAGATAAAT
1 AACTCAAAGAAGATAAAT
336127 AACTCAAAGTAA-ATAAAT
1 AACTCAAAG-AAGATAAAT
336145 AACTCAAAGAAGAT
1 AACTCAAAGAAGAT
336159 GAACTCTTCT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
17 2 0.07
18 25 0.89
19 1 0.04
ACGTcount: A:0.58, C:0.10, G:0.12, T:0.20
Consensus pattern (18 bp):
AACTCAAAGAAGATAAAT
Found at i:338632 original size:2 final size:2
Alignment explanation
Indices: 338625--338651 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
338615 TTCACAATTT
338625 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
338652 CAACCATAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:345264 original size:26 final size:24
Alignment explanation
Indices: 345233--345293 Score: 70
Period size: 25 Copynumber: 2.4 Consensus size: 24
345223 AGAATAAGAG
345233 AAAATAAAAAAATATTAATA-AAATA
1 AAAATAAAAAAA-A-TAATATAAATA
*
345258 ATAAATAAATAAAAATAATATTAATA
1 A-AAATAAA-AAAAATAATATAAATA
345284 AAAATAAAAA
1 AAAATAAAAA
345294 TCATTTTTAA
Statistics
Matches: 32, Mismatches: 1, Indels: 7
0.80 0.03 0.17
Matches are distributed among these distances:
24 2 0.06
25 13 0.41
26 13 0.41
27 4 0.12
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (24 bp):
AAAATAAAAAAAATAATATAAATA
Found at i:345274 original size:22 final size:22
Alignment explanation
Indices: 345239--345294 Score: 62
Period size: 21 Copynumber: 2.6 Consensus size: 22
345229 AGAGAAAATA
**
345239 AAAAAATATTAATAA-AATAAT
1 AAAAAATAAAAATAATAATAAT
*
345260 AAATAAATAAAAATAATATTAAT
1 AAA-AAATAAAAATAATAATAAT
345283 -AAAAATAAAAAT
1 AAAAAATAAAAAT
345295 CATTTTTAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
21 13 0.43
22 12 0.40
23 5 0.17
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (22 bp):
AAAAAATAAAAATAATAATAAT
Found at i:345281 original size:31 final size:30
Alignment explanation
Indices: 345234--345294 Score: 97
Period size: 31 Copynumber: 2.0 Consensus size: 30
345224 GAATAAGAGA
345234 AAATAAAAAAATATTAAT-AAAATAATAAAT
1 AAATAAAAAAATATTAATAAAAATAA-AAAT
345264 AAATAAAAATAATATTAATAAAAATAAAAAT
1 AAATAAAAA-AATATTAATAAAAATAAAAAT
345295 CATTTTTAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
30 9 0.31
31 13 0.45
32 7 0.24
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (30 bp):
AAATAAAAAAATATTAATAAAAATAAAAAT
Found at i:345330 original size:38 final size:37
Alignment explanation
Indices: 345288--345404 Score: 137
Period size: 38 Copynumber: 3.1 Consensus size: 37
345278 TTAATAAAAA
** * *
345288 TAAAAATCATTTTTAAAACTATATATTATATATGCTTT
1 TAAAAATTGTTTTTAAAACTATATAATATATAT-ATTT
* *
345326 TAAAAATTGTTTTCAAAACCATATAATATATATATTT
1 TAAAAATTGTTTTTAAAACTATATAATATATATATTT
*
345363 TCAAAAATTGTCTTTAAAACTATATAATATATAT-TTT
1 T-AAAAATTGTTTTTAAAACTATATAATATATATATTT
*
345400 CAAAA
1 TAAAA
345405 TTATATATTA
Statistics
Matches: 68, Mismatches: 10, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
36 4 0.06
37 7 0.10
38 57 0.84
ACGTcount: A:0.45, C:0.09, G:0.03, T:0.44
Consensus pattern (37 bp):
TAAAAATTGTTTTTAAAACTATATAATATATATATTT
Found at i:345411 original size:99 final size:98
Alignment explanation
Indices: 345296--345495 Score: 244
Period size: 99 Copynumber: 2.0 Consensus size: 98
345286 AATAAAAATC
* * *
345296 ATTTTTAAAACTATATATTATATATGCTTTTAAAAAT-TGTTTTCAAAACCATATA-ATATATAT
1 ATTTTCAAAACTATATATTATATAT-ATTTTAAAAATAT-TTTTAAAAACCATATATATATATAT
**
345359 ATTTTCAAAA-ATTGTCTTTAAAACTATATAATATAT
64 ATTTTCAAAATATT-T-TCAAAAACTATATAATATAT
* * ** *
345395 ATTTTCAAAATTATATATTATATATATTTTTAAAATATTTTTAAAAATTATATATTATATATATT
1 ATTTTCAAAACTATATATTATATATATTTTAAAAATATTTTTAAAAACCATATA-TATATATATA
345460 TTTTCAAAATATTTTCAAAAACTATATAATATAT
65 TTTTCAAAATATTTTCAAAAACTATATAATATAT
345494 AT
1 AT
345496 ATATTTCAAA
Statistics
Matches: 87, Mismatches: 10, Indels: 8
0.83 0.10 0.08
Matches are distributed among these distances:
98 22 0.25
99 44 0.51
100 18 0.21
101 3 0.03
ACGTcount: A:0.45, C:0.06, G:0.01, T:0.48
Consensus pattern (98 bp):
ATTTTCAAAACTATATATTATATATATTTTAAAAATATTTTTAAAAACCATATATATATATATAT
TTTCAAAATATTTTCAAAAACTATATAATATAT
Found at i:345417 original size:25 final size:25
Alignment explanation
Indices: 345383--345430 Score: 78
Period size: 25 Copynumber: 1.9 Consensus size: 25
345373 TCTTTAAAAC
345383 TATATAATATATATTTTCAAAATTA
1 TATATAATATATATTTTCAAAATTA
* *
345408 TATATTATATATATTTTTAAAAT
1 TATATAATATATATTTTCAAAAT
345431 ATTTTTAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (25 bp):
TATATAATATATATTTTCAAAATTA
Found at i:345419 original size:61 final size:61
Alignment explanation
Indices: 345335--345461 Score: 159
Period size: 61 Copynumber: 2.1 Consensus size: 61
345325 TTAAAAATTG
*
345335 TTTTCAAAACCATATAATATATATATTTTCAAAA-ATTGTCTTTAAAACTATATA-ATATATA
1 TTTTCAAAACCATATAATATATATATTTTCAAAATATT-T-TTAAAAACTATATATATATATA
** * * *
345396 TTTTCAAAATTATATATTATATATATTTTTAAAATATTTTTAAAAATTATATATTATATATA
1 TTTTCAAAACCATATAATATATATATTTTCAAAATATTTTTAAAAACTATATA-TATATATA
345458 TTTT
1 TTTT
345462 TTCAAAATAT
Statistics
Matches: 57, Mismatches: 6, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
60 12 0.21
61 31 0.54
62 14 0.25
ACGTcount: A:0.44, C:0.06, G:0.01, T:0.50
Consensus pattern (61 bp):
TTTTCAAAACCATATAATATATATATTTTCAAAATATTTTTAAAAACTATATATATATATA
Found at i:345469 original size:39 final size:38
Alignment explanation
Indices: 345391--345519 Score: 170
Period size: 39 Copynumber: 3.3 Consensus size: 38
345381 ACTATATAAT
*
345391 ATATATTTTCAAAATTATATATTATATATATTTTT-AAA
1 ATAT-TTTTAAAAATTATATATTATATATATTTTTCAAA
345429 ATATTTTTAAAAATTATATATTATATATATTTTTTCAAA
1 ATATTTTTAAAAATTATATATTATATATA-TTTTTCAAA
* * * *
345468 ATATTTTCAAAAACTATATAATATATATATATTTCAAAA
1 ATATTTTTAAAAATTATATATTATATATATTTTTC-AAA
*
345507 ATATTTTAAAAAA
1 ATATTTTTAAAAA
345520 AAACTCCTAA
Statistics
Matches: 82, Mismatches: 6, Indels: 5
0.88 0.06 0.05
Matches are distributed among these distances:
37 24 0.29
38 14 0.17
39 44 0.54
ACGTcount: A:0.48, C:0.04, G:0.00, T:0.48
Consensus pattern (38 bp):
ATATTTTTAAAAATTATATATTATATATATTTTTCAAA
Found at i:349685 original size:12 final size:12
Alignment explanation
Indices: 349665--349702 Score: 53
Period size: 12 Copynumber: 3.3 Consensus size: 12
349655 TTTATAAATA
349665 CCTCGCATCTCT
1 CCTCGCATCTCT
*
349677 CCTCACA--TCT
1 CCTCGCATCTCT
349687 CCTCGCATCTCT
1 CCTCGCATCTCT
349699 CCTC
1 CCTC
349703 TCTTATAAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
10 9 0.41
12 13 0.59
ACGTcount: A:0.11, C:0.53, G:0.05, T:0.32
Consensus pattern (12 bp):
CCTCGCATCTCT
Found at i:353206 original size:35 final size:34
Alignment explanation
Indices: 353121--353207 Score: 97
Period size: 35 Copynumber: 2.5 Consensus size: 34
353111 ATTTGGTATT
*
353121 TAAATACAACAAACTTACAATAAGAATTAAATGG
1 TAAATACAACAAAATTACAATAAGAATTAAATGG
* *
353155 TAAATGATAACCAAATTACAATAACTGATATTAAATGG
1 TAAAT-ACAACAAAATTACAATAA--GA-ATTAAATGG
353193 T-AATA-AACAAAATTA
1 TAAATACAACAAAATTA
353208 ACTGAAATAT
Statistics
Matches: 45, Mismatches: 4, Indels: 7
0.80 0.07 0.12
Matches are distributed among these distances:
34 5 0.11
35 24 0.53
36 1 0.02
37 5 0.11
38 10 0.22
ACGTcount: A:0.55, C:0.10, G:0.08, T:0.26
Consensus pattern (34 bp):
TAAATACAACAAAATTACAATAAGAATTAAATGG
Found at i:353440 original size:9 final size:9
Alignment explanation
Indices: 353429--353481 Score: 54
Period size: 9 Copynumber: 5.9 Consensus size: 9
353419 GTCATCATCG
*
353429 TCGTCGTCG
1 TCGTCGTCA
353438 TCGTCGTCA
1 TCGTCGTCA
* *
353447 -CTATCATCA
1 TC-GTCGTCA
353456 TCGTCGTCA
1 TCGTCGTCA
*
353465 TCGTCGTCC
1 TCGTCGTCA
353474 TCGTCGTC
1 TCGTCGTC
353482 CTGAGCAGGT
Statistics
Matches: 36, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
8 1 0.03
9 34 0.94
10 1 0.03
ACGTcount: A:0.09, C:0.36, G:0.21, T:0.34
Consensus pattern (9 bp):
TCGTCGTCA
Found at i:355469 original size:111 final size:111
Alignment explanation
Indices: 355275--355607 Score: 594
Period size: 111 Copynumber: 3.0 Consensus size: 111
355265 ATTACAAAAA
* *
355275 TTAATTCTTACTCTAATAATCATGCATTGAATAAATCAACTAATTATTACTAATAATTTAAATTA
1 TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAATTATTACTAATAATTTAAATTA
355340 AATTAAAACGTTAAAATGTTACCGTATCAGCAAAGTGTCGAGATAT
66 AATTAAAACGTTAAAATGTTACCGTATCAGCAAAGTGTCGAGATAT
* * *
355386 TTAATTCTTAATCTAATAATCATGCATTAAATAACTCAACTAATTATTACTAGTAATTTAATTTA
1 TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAATTATTACTAATAATTTAAATTA
*
355451 AATTAAAACGTTAAAATGTTACCGTATCAGCAAAGTATCGAGATAT
66 AATTAAAACGTTAAAATGTTACCGTATCAGCAAAGTGTCGAGATAT
*
355497 TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAAATATTACTAATAATTTAAATTA
1 TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAATTATTACTAATAATTTAAATTA
*
355562 AATTAAAACGTTAAAATGTTACCGTATCAGCAAAGTGTAGAGATAT
66 AATTAAAACGTTAAAATGTTACCGTATCAGCAAAGTGTCGAGATAT
355608 ATGATTTTCA
Statistics
Matches: 210, Mismatches: 12, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
111 210 1.00
ACGTcount: A:0.44, C:0.12, G:0.08, T:0.36
Consensus pattern (111 bp):
TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAATTATTACTAATAATTTAAATTA
AATTAAAACGTTAAAATGTTACCGTATCAGCAAAGTGTCGAGATAT
Found at i:355929 original size:50 final size:49
Alignment explanation
Indices: 355875--355972 Score: 108
Period size: 50 Copynumber: 2.0 Consensus size: 49
355865 AGATACTCAG
* *
355875 GTATAGAGC-GGATCAGAGGGCGCGCTATACCTACGTGGCGCCAGATCACC
1 GTATAGAGCAGG--CAGAGGGCGCGCTATACCCACGTGGCGCCAAATCACC
** * *
355925 GTATATCGCAAGGCAGGGGGCGCTCTATACCCACGTGGCGCCAAATCA
1 GTATAGAGC-AGGCAGAGGGCGCGCTATACCCACGTGGCGCCAAATCA
355973 TCATATAGCG
Statistics
Matches: 40, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
50 38 0.95
52 2 0.05
ACGTcount: A:0.24, C:0.29, G:0.31, T:0.16
Consensus pattern (49 bp):
GTATAGAGCAGGCAGAGGGCGCGCTATACCCACGTGGCGCCAAATCACC
Found at i:357977 original size:41 final size:41
Alignment explanation
Indices: 357932--358013 Score: 128
Period size: 41 Copynumber: 2.0 Consensus size: 41
357922 AAATTGAAAA
* *
357932 TAAATTAATAATTTAAAGACCTAATCAAGAAAAATACAAAT
1 TAAATTAATAATCTAAAGACCAAATCAAGAAAAATACAAAT
* *
357973 TAAATTATTAATCTAAAGACCAAATCAAGAAAAGTACAAAT
1 TAAATTAATAATCTAAAGACCAAATCAAGAAAAATACAAAT
358014 ATTGCACATA
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
41 37 1.00
ACGTcount: A:0.57, C:0.11, G:0.06, T:0.26
Consensus pattern (41 bp):
TAAATTAATAATCTAAAGACCAAATCAAGAAAAATACAAAT
Found at i:362699 original size:20 final size:20
Alignment explanation
Indices: 362674--362716 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
362664 ACAGATATTT
* *
362674 TTTCTTTGTATGTCTACTTA
1 TTTCTTTGTATGTATACCTA
362694 TTTCTTTGTATGTATACCTA
1 TTTCTTTGTATGTATACCTA
362714 TTT
1 TTT
362717 GCTTATAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.16, C:0.14, G:0.09, T:0.60
Consensus pattern (20 bp):
TTTCTTTGTATGTATACCTA
Found at i:367704 original size:2 final size:2
Alignment explanation
Indices: 367697--367748 Score: 104
Period size: 2 Copynumber: 26.0 Consensus size: 2
367687 ATCATAACAC
367697 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
367739 TA TA TA TA TA
1 TA TA TA TA TA
367749 GAGGCAAAAT
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:367934 original size:14 final size:14
Alignment explanation
Indices: 367915--367947 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
367905 CGCTGGGCAT
367915 CCGAGGCCATCCGA
1 CCGAGGCCATCCGA
367929 CCGAGGCCATCCGA
1 CCGAGGCCATCCGA
*
367943 ACGAG
1 CCGAG
367948 CTATGCGAGG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.24, C:0.39, G:0.30, T:0.06
Consensus pattern (14 bp):
CCGAGGCCATCCGA
Found at i:367968 original size:10 final size:10
Alignment explanation
Indices: 367953--368009 Score: 51
Period size: 10 Copynumber: 5.4 Consensus size: 10
367943 ACGAGCTATG
367953 CGAGGGCATC
1 CGAGGGCATC
*
367963 CGAGGGCAAC
1 CGAGGGCATC
*
367973 CGAGCGAGCTATG
1 CGAG-G-GC-ATC
*
367986 CGAGGGAATC
1 CGAGGGCATC
*
367996 CGAGGGCAAC
1 CGAGGGCATC
368006 CGAG
1 CGAG
368010 CGAGGGTAGG
Statistics
Matches: 37, Mismatches: 7, Indels: 6
0.74 0.14 0.12
Matches are distributed among these distances:
10 27 0.73
11 2 0.05
12 3 0.08
13 5 0.14
ACGTcount: A:0.26, C:0.26, G:0.40, T:0.07
Consensus pattern (10 bp):
CGAGGGCATC
Found at i:367981 original size:33 final size:33
Alignment explanation
Indices: 367929--368013 Score: 134
Period size: 33 Copynumber: 2.6 Consensus size: 33
367919 GGCCATCCGA
* * * *
367929 CCGAGGCCATCCGAACGAGCTATGCGAGGGCAT
1 CCGAGGGCAACCGAGCGAGCTATGCGAGGGAAT
367962 CCGAGGGCAACCGAGCGAGCTATGCGAGGGAAT
1 CCGAGGGCAACCGAGCGAGCTATGCGAGGGAAT
367995 CCGAGGGCAACCGAGCGAG
1 CCGAGGGCAACCGAGCGAG
368014 GGTAGGTCAC
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 48 1.00
ACGTcount: A:0.26, C:0.28, G:0.38, T:0.08
Consensus pattern (33 bp):
CCGAGGGCAACCGAGCGAGCTATGCGAGGGAAT
Found at i:368061 original size:29 final size:29
Alignment explanation
Indices: 368015--368071 Score: 87
Period size: 29 Copynumber: 2.0 Consensus size: 29
368005 CCGAGCGAGG
368015 GTAGGTCACCATGCACTCCGGGCAACCTT
1 GTAGGTCACCATGCACTCCGGGCAACCTT
* * *
368044 GTAGGTCGCCATGTACTCCGGGCGACCT
1 GTAGGTCACCATGCACTCCGGGCAACCT
368072 ACCCTCGCTC
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.18, C:0.33, G:0.28, T:0.21
Consensus pattern (29 bp):
GTAGGTCACCATGCACTCCGGGCAACCTT
Found at i:368192 original size:20 final size:20
Alignment explanation
Indices: 368167--368220 Score: 90
Period size: 20 Copynumber: 2.7 Consensus size: 20
368157 CATAGCTCGT
368167 TCGGATGGCATCGGATGCTC
1 TCGGATGGCATCGGATGCTC
*
368187 TCGGATGGCATCGGATGCTT
1 TCGGATGGCATCGGATGCTC
*
368207 TCGGATGGCCTCGG
1 TCGGATGGCATCGG
368221 TCGGATGGCC
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.13, C:0.24, G:0.37, T:0.26
Consensus pattern (20 bp):
TCGGATGGCATCGGATGCTC
Found at i:368226 original size:14 final size:14
Alignment explanation
Indices: 368207--368248 Score: 75
Period size: 14 Copynumber: 3.0 Consensus size: 14
368197 TCGGATGCTT
368207 TCGGATGGCCTCGG
1 TCGGATGGCCTCGG
*
368221 TCGGATGGCCTCGA
1 TCGGATGGCCTCGG
368235 TCGGATGGCCTCGG
1 TCGGATGGCCTCGG
368249 ATGCCCATCA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
14 26 1.00
ACGTcount: A:0.10, C:0.29, G:0.40, T:0.21
Consensus pattern (14 bp):
TCGGATGGCCTCGG
Found at i:368589 original size:29 final size:29
Alignment explanation
Indices: 368546--368634 Score: 160
Period size: 29 Copynumber: 3.1 Consensus size: 29
368536 AACACCCCAC
368546 AGGTCGCTCGGATGCCATGGCGACCTCCA
1 AGGTCGCTCGGATGCCATGGCGACCTCCA
* *
368575 AGGTCGCCCGCATGCCATGGCGACCTCCA
1 AGGTCGCTCGGATGCCATGGCGACCTCCA
368604 AGGTCGCTCGGATGCCATGGCGACCTCCA
1 AGGTCGCTCGGATGCCATGGCGACCTCCA
368633 AG
1 AG
368635 CTCACTGTAG
Statistics
Matches: 56, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 56 1.00
ACGTcount: A:0.18, C:0.36, G:0.30, T:0.16
Consensus pattern (29 bp):
AGGTCGCTCGGATGCCATGGCGACCTCCA
Found at i:373850 original size:30 final size:30
Alignment explanation
Indices: 373807--373882 Score: 102
Period size: 30 Copynumber: 2.5 Consensus size: 30
373797 CACATTCATA
373807 TCACATGTT-CATATAAGC-TCCTAACTTCTT
1 TCACAT-TTACATATAAGCAT-CTAACTTCTT
* *
373837 TCACATTTACATATAATCATGTAACTTCTT
1 TCACATTTACATATAAGCATCTAACTTCTT
373867 TCACATTTACATATAA
1 TCACATTTACATATAA
373883 CATGGCTTAA
Statistics
Matches: 42, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
29 2 0.05
30 39 0.93
31 1 0.02
ACGTcount: A:0.33, C:0.22, G:0.04, T:0.41
Consensus pattern (30 bp):
TCACATTTACATATAAGCATCTAACTTCTT
Found at i:390689 original size:54 final size:49
Alignment explanation
Indices: 390605--390726 Score: 120
Period size: 54 Copynumber: 2.3 Consensus size: 49
390595 AAAAAATAAT
* *
390605 AATAAAAATGAGAAAAAGAAAAAGAAG-AAAAGAAGAAAAGAAAAGATGAGAAAA
1 AATAAAAATGA-AAAAA-AAAAAAAAGAAAAAAAAG-AAAGAAAA-AT--GAAAA
*
390659 AATAAAAATGAAAAAAAAATAAAAATGAAAAAAAAGAAAGAAAAATTAAAA
1 AATAAAAATGAAAAAAAAA-AAAAA-GAAAAAAAAGAAAGAAAAATGAAAA
* *
390710 GAGAAAAATGAAAAAAA
1 AATAAAAATGAAAAAAA
390727 GAGAAATAAA
Statistics
Matches: 60, Mismatches: 5, Indels: 9
0.81 0.07 0.12
Matches are distributed among these distances:
51 19 0.32
52 3 0.05
53 11 0.18
54 20 0.33
55 7 0.12
ACGTcount: A:0.77, C:0.00, G:0.15, T:0.08
Consensus pattern (49 bp):
AATAAAAATGAAAAAAAAAAAAAAGAAAAAAAAGAAAGAAAAATGAAAA
Found at i:390691 original size:26 final size:25
Alignment explanation
Indices: 390608--390726 Score: 91
Period size: 26 Copynumber: 4.6 Consensus size: 25
390598 AAATAATAAT
*
390608 AAAAATGAGAAAAAGAAA-AAGAAGAA
1 AAAAATGA-AAAAA-AAATAAAAAGAA
*
390634 AAGAA-GAAAAGAAAAGATGAGAAAA-AA
1 AAAAATGAAAA-AAAA-AT-A-AAAAGAA
390661 TAAAAATGAAAAAAAAATAAAAATGAA
1 -AAAAATGAAAAAAAAATAAAAA-GAA
* * * *
390688 AAAAAAGAAAGAAAAATTAAAAGAG
1 AAAAATGAAAAAAAAATAAAAAGAA
390713 AAAAATGAAAAAAA
1 AAAAATGAAAAAAA
390727 GAGAAATAAA
Statistics
Matches: 75, Mismatches: 9, Indels: 19
0.73 0.09 0.18
Matches are distributed among these distances:
24 5 0.07
25 23 0.31
26 24 0.32
27 7 0.09
28 11 0.15
29 5 0.07
ACGTcount: A:0.77, C:0.00, G:0.15, T:0.08
Consensus pattern (25 bp):
AAAAATGAAAAAAAAATAAAAAGAA
Found at i:390714 original size:14 final size:14
Alignment explanation
Indices: 390561--390723 Score: 55
Period size: 14 Copynumber: 11.9 Consensus size: 14
390551 TTTCGCTTGA
390561 AGAAGAAAT-AAAAG
1 AGAA-AAATGAAAAG
390575 AGAAAAA--AAAA-
1 AGAAAAATGAAAAG
* *
390586 CGAAAAATGAAAAA
1 AGAAAAATGAAAAG
* * *
390600 ATAATAATAAAAATG
1 AGAAAAATGAAAA-G
390615 AGAAAAA-GAAAAAG
1 AGAAAAATG-AAAAG
*
390629 AAGAAAAGAAGAAAAG
1 -AGAAAA-ATGAAAAG
* *
390645 A-AAAGATGAGAAAAA
1 AGAAAAAT--GAAAAG
*
390660 ATAAAAATG-AAA-
1 AGAAAAATGAAAAG
390672 A-AAAAAT-AAAA-
1 AGAAAAATGAAAAG
*
390683 ATGAAAAA--AAAGAA
1 A-GAAAAATGAAA-AG
*
390697 AGAAAAATTAAAAG
1 AGAAAAATGAAAAG
390711 AGAAAAATGAAAA
1 AGAAAAATGAAAA
390724 AAAGAGAAAT
Statistics
Matches: 116, Mismatches: 15, Indels: 36
0.69 0.09 0.22
Matches are distributed among these distances:
11 16 0.14
12 8 0.07
13 23 0.20
14 32 0.28
15 25 0.22
16 11 0.09
17 1 0.01
ACGTcount: A:0.76, C:0.01, G:0.15, T:0.09
Consensus pattern (14 bp):
AGAAAAATGAAAAG
Found at i:390727 original size:17 final size:17
Alignment explanation
Indices: 390608--390732 Score: 88
Period size: 17 Copynumber: 7.7 Consensus size: 17
390598 AAATAATAAT
*
390608 AAAAATGAGAAAAA-GA
1 AAAAAAGAGAAAAATGA
*
390624 AAAAGA-AG-AAAA-GA
1 AAAAAAGAGAAAAATGA
* *
390638 AGAAAAGA-AAAGATGA
1 AAAAAAGAGAAAAATGA
* *
390654 GAAAAA-ATAAAAATGA
1 AAAAAAGAGAAAAATGA
* *
390670 AAAAAAAATAAAAATGA
1 AAAAAAGAGAAAAATGA
390687 AAAAAA-AGAAAGAA--A
1 AAAAAAGAGAAA-AATGA
390702 AATTAAAAGAGAAAAATGA
1 AA--AAAAGAGAAAAATGA
390721 AAAAAAGAGAAA
1 AAAAAAGAGAAA
390733 TAAAAGGAGG
Statistics
Matches: 88, Mismatches: 10, Indels: 21
0.74 0.08 0.18
Matches are distributed among these distances:
14 10 0.11
15 10 0.11
16 26 0.30
17 34 0.39
18 5 0.06
19 3 0.03
ACGTcount: A:0.77, C:0.00, G:0.16, T:0.07
Consensus pattern (17 bp):
AAAAAAGAGAAAAATGA
Found at i:390727 original size:91 final size:91
Alignment explanation
Indices: 390561--390732 Score: 217
Period size: 91 Copynumber: 1.9 Consensus size: 91
390551 TTTCGCTTGA
* * *
390561 AGAAGAAATAAAAGAGAAAAAAAAACGAAAAATGAAAAAATAATAATAAAAATGAGAAAAAGAAA
1 AGAAAAAATAAAAGAGAAAAAAAAACGAAAAATGAAAAAATAAAAAGAAAAATGAGAAAAAGAAA
*
390626 AAGAAGAAAAGAAGAAAAGAAAAGATG
66 AAGAAAAAAAG-AGAAAAGAAAAGATG
* * *
390653 AGAAAAAATAAAA-ATGAAAAAAAAA-TAAAAATGAAAAAA-AAGAAAGAAAAATTA-AAAGAGA
1 AGAAAAAATAAAAGA-GAAAAAAAAACGAAAAATGAAAAAATAA-AAAGAAAAATGAGAAAAAGA
390714 AAAATGAAAAAAAGAGAAA
64 AAAA-GAAAAAAAGAGAAA
390733 TAAAAGGAGG
Statistics
Matches: 70, Mismatches: 7, Indels: 8
0.82 0.08 0.09
Matches are distributed among these distances:
90 17 0.24
91 31 0.44
92 22 0.31
ACGTcount: A:0.76, C:0.01, G:0.15, T:0.08
Consensus pattern (91 bp):
AGAAAAAATAAAAGAGAAAAAAAAACGAAAAATGAAAAAATAAAAAGAAAAATGAGAAAAAGAAA
AAGAAAAAAAGAGAAAAGAAAAGATG
Found at i:390738 original size:44 final size:43
Alignment explanation
Indices: 390560--390738 Score: 123
Period size: 45 Copynumber: 4.0 Consensus size: 43
390550 ATTTCGCTTG
* * *
390560 AAGAAGAAATAAAAGAGAAAAA-AAAACGAAAAATGAAAAAATA-AT
1 AAGAAAAAATAAAA-AGAAAAAGAAAA--AAAGA-GAAAAAAAAGAT
* * *
390605 AATAAAAATGAGAAAAAGAAAAAGAAGAAAAGAAGAAAAGAAAAGAT
1 AAGAAAAA--ATAAAAAGAAAAAGAAAAAAAG-AGAAAA-AAAAGAT
* *
390652 GAGAAAAAATAAAAATGAAAAA-AAAATAAAAATGAAAAAAAAGA-
1 AAGAAAAAATAAAAA-GAAAAAGAAAA-AAAGA-GAAAAAAAAGAT
* *
390696 AAGAAAAATTAAAAGAGAAAAATGAAAAAAAGAGAAATAAAAG
1 AAGAAAAAATAAAA-AGAAAAA-GAAAAAAAGAGAAAAAAAAG
390739 GAGGGTTCAA
Statistics
Matches: 107, Mismatches: 15, Indels: 25
0.73 0.10 0.17
Matches are distributed among these distances:
44 27 0.25
45 35 0.33
46 29 0.27
47 16 0.15
ACGTcount: A:0.76, C:0.01, G:0.15, T:0.08
Consensus pattern (43 bp):
AAGAAAAAATAAAAAGAAAAAGAAAAAAAGAGAAAAAAAAGAT
Found at i:392131 original size:51 final size:51
Alignment explanation
Indices: 392065--392414 Score: 425
Period size: 51 Copynumber: 6.7 Consensus size: 51
392055 AAATTCGTTG
*
392065 GTTGAAGATCGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAAGTTC
1 GTTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAAGTTC
*
392116 GTTGAAAATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAAGTTC
1 GTTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAAGTTC
*
392167 G-TGAAGATTGAGTCCTATACTCTCTGAATAGGAATA-GGAGCTGACAAGTTC
1 GTTGAAGATTGAGTCCTATACTCTCTG-A-AGGAATAGGGAGCGGACAAGTTC
* *
392218 GTTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACACGTTT
1 GTTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAAGTTC
* * * ** *
392269 ATTGAAGATCGAGTCTTATACTCTCTGAAGGAATAGGGAGCGGACCCGTTT
1 GTTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAAGTTC
* * * * * *
392320 GTTGAAGATTATTCGAGTCTTATACTCCCTGAACGAATAGGGAGCAGACACGTTT
1 GTTGAAG---ATT-GAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAAGTTC
* *
392375 GTTGAAGATTGTTCAAGTCTTATACTCTCTGAATGAATAG
1 GTTGAAGATTG----AGTCCTATACTCTCTGAAGGAATAG
392415 AGAACATACA
Statistics
Matches: 268, Mismatches: 19, Indels: 20
0.87 0.06 0.07
Matches are distributed among these distances:
50 31 0.12
51 133 0.50
52 35 0.13
54 2 0.01
55 67 0.25
ACGTcount: A:0.29, C:0.16, G:0.26, T:0.28
Consensus pattern (51 bp):
GTTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAAGTTC
Found at i:392361 original size:55 final size:53
Alignment explanation
Indices: 392060--392474 Score: 408
Period size: 51 Copynumber: 7.9 Consensus size: 53
392050 GAAGCAAATT
*
392060 CGTTGGTTGAAG-A-TCGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACA
1 CGTTTGTTGAAGAATTCGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACA
* *
392111 AGTTCGTTGAA-AATT-GAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACA
1 CGTTTGTTGAAGAATTCGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACA
* * *
392162 AGTTCG-TGAAG-ATT-GAGTCCTATACTCTCTGAATAGGAATA-GGAGCTGACA
1 CGTTTGTTGAAGAATTCGAGTCCTATACTCTCTG-A-AGGAATAGGGAGCGGACA
* *
392213 AGTTCGTTGAAG-ATT-GAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACA
1 CGTTTGTTGAAGAATTCGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACA
* * *
392264 CGTTTATTGAAG-A-TCGAGTCTTATACTCTCTGAAGGAATAGGGAGCGGACC
1 CGTTTGTTGAAGAATTCGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACA
* * * *
392315 CGTTTGTTGAAGATTATTCGAGTCTTATACTCCCTGAACGAATAGGGAGCAGACA
1 CGTTTGTTGAAGA--ATTCGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACA
* * * * * * **
392370 CGTTTGTTGAAGATTGTTCAAGTCTTATACTCTCTGAATGAATAGAGAACATACA
1 CGTTTGTTGAAGA--ATTCGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACA
* * *
392425 CATTT-TATGAAGATTGTCCGAGTCTTATACT-TCCTGAAGGAATAGGGAGC
1 CGTTTGT-TGAAGAAT-T-CGAGTCCTATACTCT-CTGAAGGAATAGGGAGC
392475 AGGCTCGTCA
Statistics
Matches: 321, Mismatches: 27, Indels: 28
0.85 0.07 0.07
Matches are distributed among these distances:
50 32 0.10
51 133 0.41
52 33 0.10
53 1 0.00
54 4 0.01
55 118 0.37
ACGTcount: A:0.30, C:0.16, G:0.26, T:0.28
Consensus pattern (53 bp):
CGTTTGTTGAAGAATTCGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACA
Found at i:392450 original size:110 final size:108
Alignment explanation
Indices: 392076--392502 Score: 323
Period size: 110 Copynumber: 4.0 Consensus size: 108
392066 TTGAAGATCG
* * * * * * *
392076 AGTCCTATACTCTCTGAAGGAATAGGGAGCGGACA-AGTTCGTTGAA-A--AT-TGAGTCCTATA
1 AGTCTTATACTCTCTGAAGGAATAGAGAACAGACACA-TTTGTTGAAGATTATCCGAGTCTTATA
* * * ** *
392136 CTCTCTGAAGGAATAGGGAGCGGACAAGTTCGTGAAGA--TT-G
65 CTCCCTGAAGGAATAGGGAGCAGACACGTTTTTGAAGATTTTCA
* * * * *
392177 AGTCCTATACTCTCTGAATAGGAATAG-GAGCTGACA-AGTTCGTTGAAGA-T-T--GAGTCCTA
1 AGTCTTATACTCTCTG-A-AGGAATAGAGAACAGACACA-TTTGTTGAAGATTATCCGAGTCTTA
* * *
392236 TACTCTCTGAAGGAATAGGGAGCGGACACGTTTATTGAAGA---TCG
63 TACTCCCTGAAGGAATAGGGAGCAGACACGTTT-TTGAAGATTTTCA
* * * * * *
392280 AGTCTTATACTCTCTGAAGGAATAGGGAGCGGACCCGTTTGTTGAAGATTATTCGAGTCTTATAC
1 AGTCTTATACTCTCTGAAGGAATAGAGAACAGACACATTTGTTGAAGATTATCCGAGTCTTATAC
*
392345 TCCCTGAACGAATAGGGAGCAGACACGTTTGTTGAAGATTGTTCA
66 TCCCTGAAGGAATAGGGAGCAGACACGTTT-TTGAAGATT-TTCA
* * *
392390 AGTCTTATACTCTCTGAATGAATAGAGAACATACACATTT-TATGAAGATTGTCCGAGTCTTATA
1 AGTCTTATACTCTCTGAAGGAATAGAGAACAGACACATTTGT-TGAAGATTATCCGAGTCTTATA
* * * *
392454 CTTCCTGAAGGAATAGGGAGCAGGCTCGTCATTTGAAGATTTTTCA
65 CTCCCTGAAGGAATAGGGAGCAGACACGT-TTTTGAAGA-TTTTCA
392500 AGT
1 AGT
392503 TTCATTTATC
Statistics
Matches: 278, Mismatches: 29, Indels: 29
0.83 0.09 0.09
Matches are distributed among these distances:
101 24 0.09
102 78 0.28
103 33 0.12
104 1 0.00
106 44 0.16
109 1 0.00
110 94 0.34
111 3 0.01
ACGTcount: A:0.30, C:0.16, G:0.25, T:0.29
Consensus pattern (108 bp):
AGTCTTATACTCTCTGAAGGAATAGAGAACAGACACATTTGTTGAAGATTATCCGAGTCTTATAC
TCCCTGAAGGAATAGGGAGCAGACACGTTTTTGAAGATTTTCA
Found at i:400886 original size:12 final size:12
Alignment explanation
Indices: 400854--400893 Score: 50
Period size: 12 Copynumber: 3.6 Consensus size: 12
400844 TGCGGGAAAA
400854 TTAAAATC-A-T
1 TTAAAATCTATT
400864 TT-AAATCTATT
1 TTAAAATCTATT
*
400875 TTAAAATTTATT
1 TTAAAATCTATT
400887 TTAAAAT
1 TTAAAAT
400894 ATAGATTGAT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
9 5 0.19
10 3 0.12
11 3 0.12
12 15 0.58
ACGTcount: A:0.45, C:0.05, G:0.00, T:0.50
Consensus pattern (12 bp):
TTAAAATCTATT
Found at i:401230 original size:22 final size:22
Alignment explanation
Indices: 400880--401221 Score: 515
Period size: 22 Copynumber: 15.6 Consensus size: 22
400870 CTATTTTAAA
*
400880 ATTTATTTTAAAATATAGATTG
1 ATTTATTTTAAAATATGGATTG
400902 ATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAAATATGGATTG
400924 ATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAAATATGGATTG
* ***
400946 ATTTATTTTAAAATAT-AAAAA
1 ATTTATTTTAAAATATGGATTG
* *
400967 AATTATTTTAAAATATGAATTG
1 ATTTATTTTAAAATATGGATTG
***
400989 ATTTATTTTAAAATATGGAAAA
1 ATTTATTTTAAAATATGGATTG
401011 ATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAAATATGGATTG
401033 ATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAAATATGGATTG
401055 ATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAAATATGGATTG
***
401077 ATTTATTTTAAAATATGGAAAA
1 ATTTATTTTAAAATATGGATTG
*
401099 AGTTATTTTAAAATATGGATTG
1 ATTTATTTTAAAATATGGATTG
401121 ATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAAATATGGATTG
*
401143 ATTTATTTTAAAATATCGATTG
1 ATTTATTTTAAAATATGGATTG
*
401165 ATTTATTTTAAAATATGGATTA
1 ATTTATTTTAAAATATGGATTG
* *
401187 ATTTATTTTAAAATATGAATTA
1 ATTTATTTTAAAATATGGATTG
401209 ATTTATTTTAAAA
1 ATTTATTTTAAAA
401222 AATTCATTAT
Statistics
Matches: 290, Mismatches: 29, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
21 16 0.06
22 274 0.94
ACGTcount: A:0.42, C:0.00, G:0.10, T:0.48
Consensus pattern (22 bp):
ATTTATTTTAAAATATGGATTG
Found at i:404483 original size:2 final size:2
Alignment explanation
Indices: 404478--404542 Score: 130
Period size: 2 Copynumber: 32.5 Consensus size: 2
404468 ATTTTTTTAC
404478 AT AT AT AT AT 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 AT AT AT AT AT
404520 AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT A
404543 GTTTGCAAAT
Statistics
Matches: 63, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 63 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:404573 original size:38 final size:35
Alignment explanation
Indices: 404526--404780 Score: 157
Period size: 38 Copynumber: 7.0 Consensus size: 35
404516 ATATATATAT
* *
404526 ATATATATATATATATAGTTTGCAAATGGTTTTTGAAA
1 ATATATATA-ATATATAGTTTGAAAAT--ATTTTGAAA
*
404564 ATACGTATATAATATATAGCTTTTAAAATATTTTGAAA
1 ATA--TATATAATATATAG-TTTGAAAATATTTTGAAA
* *
404602 ATATATATAATATATAGTTTTTAAAATTATTTTTTAAA
1 ATATATATAATATATAG-TTTGAAAA-TA-TTTTGAAA
** *
404640 ACT-TATATAATATATAGTTTTTAAA-A--TCGAAA
1 A-TATATATAATATATAGTTTGAAAATATTTTGAAA
*
404672 ACT-TATATAATATATAGTTTTTAAAAAATATTTTTAGAAA
1 A-TATATATAATATATAG--TTT-GAAAATA-TTTT-GAAA
** * *
404712 ATATATAT-ATA-ATTTTTTTGAAAACATTTT-TAA
1 ATATATATAATATA-TAGTTTGAAAATATTTTGAAA
* *
404745 ATATGTATAATATATAGTTTGAAAATGTTTTTGAAA
1 ATATATATAATATATAGTTTGAAAAT-ATTTTGAAA
404781 TTTTGGAAAC
Statistics
Matches: 175, Mismatches: 22, Indels: 42
0.73 0.09 0.18
Matches are distributed among these distances:
32 21 0.12
33 9 0.05
34 15 0.09
35 13 0.07
36 30 0.17
37 12 0.07
38 37 0.21
39 15 0.09
40 23 0.13
ACGTcount: A:0.44, C:0.03, G:0.07, T:0.46
Consensus pattern (35 bp):
ATATATATAATATATAGTTTGAAAATATTTTGAAA
Found at i:404609 original size:36 final size:36
Alignment explanation
Indices: 404556--404764 Score: 186
Period size: 38 Copynumber: 5.8 Consensus size: 36
404546 TGCAAATGGT
*
404556 TTTTGAAAATACGTATATAATATATAGCTTTTAAAATA
1 TTTTGAAAATA--TATATAATATATAGTTTTTAAAATA
404594 TTTTGAAAATATATATAATATATAGTTTTTAAAATTA
1 TTTTGAAAATATATATAATATATAGTTTTTAAAA-TA
*
404631 TTTTTTAAAACT-TATATAATATATAGTTTTT-AAA-A
1 -TTTTGAAAA-TATATATAATATATAGTTTTTAAAATA
*
404666 --TCGAAAACT-TATATAATATATAGTTTTTAAAAAATA
1 TTTTGAAAA-TATATATAATATATAGTTTTT--AAAATA
* *
404702 TTTTTAGAAAATATATAT-ATA-AT-TTTTTTGAAAACA
1 -TTTT-GAAAATATATATAATATATAGTTTTT-AAAATA
* *
404738 TTTT-TAAATATGTATAATATATAGTTT
1 TTTTGAAAATATATATAATATATAGTTT
404765 GAAAATGTTT
Statistics
Matches: 145, Mismatches: 11, Indels: 32
0.77 0.06 0.17
Matches are distributed among these distances:
32 26 0.18
33 9 0.06
34 3 0.02
35 10 0.07
36 31 0.21
37 10 0.07
38 40 0.28
39 6 0.04
40 10 0.07
ACGTcount: A:0.44, C:0.03, G:0.06, T:0.47
Consensus pattern (36 bp):
TTTTGAAAATATATATAATATATAGTTTTTAAAATA
Found at i:404674 original size:32 final size:32
Alignment explanation
Indices: 404637--404697 Score: 122
Period size: 32 Copynumber: 1.9 Consensus size: 32
404627 ATTATTTTTT
404637 AAAACTTATATAATATATAGTTTTTAAAATCG
1 AAAACTTATATAATATATAGTTTTTAAAATCG
404669 AAAACTTATATAATATATAGTTTTTAAAA
1 AAAACTTATATAATATATAGTTTTTAAAA
404698 AATATTTTTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.49, C:0.05, G:0.05, T:0.41
Consensus pattern (32 bp):
AAAACTTATATAATATATAGTTTTTAAAATCG
Found at i:404721 original size:74 final size:74
Alignment explanation
Indices: 404555--404724 Score: 197
Period size: 70 Copynumber: 2.3 Consensus size: 74
404545 TTGCAAATGG
* *
404555 TTTTTGAAAATACGTATATAATATATAGCTTTTAAAATATTTTGAAAATATATATAATATATAGT
1 TTTTTGAAAATA-TTATATAATATATAGCTTTTAAAATA-TTCGAAAATATATATAATATATAGT
*
404620 TTTTAAAATTA
64 TTTTAAAAATA
* * *
404631 TTTTTTAAAA-CTTATATAATATATAG-TTTTTAAA-A-TCGAAAACT-TATATAATATATAGTT
1 TTTTTGAAAATATTATATAATATATAGCTTTTAAAATATTCGAAAA-TATATATAATATATAGTT
404691 TTTAAAAAATA
65 TTT-AAAAATA
404702 TTTTTAGAAAATATATATATAAT
1 TTTTT-GAAAATAT-TATATAAT
404725 TTTTTTGAAA
Statistics
Matches: 81, Mismatches: 8, Indels: 12
0.80 0.08 0.12
Matches are distributed among these distances:
70 25 0.31
71 12 0.15
72 5 0.06
73 8 0.10
74 22 0.27
76 9 0.11
ACGTcount: A:0.46, C:0.03, G:0.05, T:0.46
Consensus pattern (74 bp):
TTTTTGAAAATATTATATAATATATAGCTTTTAAAATATTCGAAAATATATATAATATATAGTTT
TTAAAAATA
Found at i:404839 original size:22 final size:20
Alignment explanation
Indices: 404814--404895 Score: 64
Period size: 20 Copynumber: 4.0 Consensus size: 20
404804 ATATAATATA
404814 TATTTGTTTTTATTATTTGTTT
1 TATTT-TTTTTATTATTT-TTT
404836 TATTTTATTTTTATT-TTATTTT
1 TA-TTT-TTTTTATTATT-TTTT
*
404858 TATTTTATTT-TTATTTATTT
1 TATTTTTTTTATTATTT-TTT
*
404878 TA-TTCTTTTATT-TTTTTT
1 TATTTTTTTTATTATTTTTT
404896 CCAAGTCCAA
Statistics
Matches: 51, Mismatches: 4, Indels: 14
0.74 0.06 0.20
Matches are distributed among these distances:
18 3 0.06
19 11 0.22
20 13 0.25
21 3 0.06
22 9 0.18
23 12 0.24
ACGTcount: A:0.16, C:0.01, G:0.02, T:0.80
Consensus pattern (20 bp):
TATTTTTTTTATTATTTTTT
Found at i:404849 original size:11 final size:11
Alignment explanation
Indices: 404820--404892 Score: 87
Period size: 11 Copynumber: 6.5 Consensus size: 11
404810 TATATATTTG
404820 TTTTTATTATT-
1 TTTTTATT-TTA
404831 TGTTTTATTTTA
1 T-TTTTATTTTA
404843 TTTTTATTTTA
1 TTTTTATTTTA
404854 TTTTTATTTTA
1 TTTTTATTTTA
404865 TTTTTA-TTTA
1 TTTTTATTTTA
*
404875 TTTTATTCTTTTA
1 -TTT-TTATTTTA
404888 TTTTT
1 TTTTT
404893 TTTCCAAGTC
Statistics
Matches: 56, Mismatches: 1, Indels: 10
0.84 0.01 0.15
Matches are distributed among these distances:
10 4 0.07
11 35 0.62
12 13 0.23
13 4 0.07
ACGTcount: A:0.16, C:0.01, G:0.01, T:0.81
Consensus pattern (11 bp):
TTTTTATTTTA
Found at i:404891 original size:5 final size:5
Alignment explanation
Indices: 404833--404881 Score: 64
Period size: 5 Copynumber: 9.4 Consensus size: 5
404823 TTATTATTTG
404833 TTTTA TTTTA TTTTTA TTTTA TTTTTA TTTTA TTTT- TATTTA TTTTA
1 TTTTA TTTTA -TTTTA TTTTA -TTTTA TTTTA TTTTA T-TTTA TTTTA
404880 TT
1 TT
404882 CTTTTATTTT
Statistics
Matches: 40, Mismatches: 0, Indels: 8
0.83 0.00 0.17
Matches are distributed among these distances:
4 1 0.03
5 28 0.70
6 11 0.28
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (5 bp):
TTTTA
Found at i:406082 original size:28 final size:26
Alignment explanation
Indices: 406051--406102 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 26
406041 GTTTTTATTA
*
406051 TTATTATATTTTTTATTCTTCTTTTCAC
1 TTATTAT-TTTTTTATT-TTCATTTCAC
*
406079 TTATTCTTTTTTTATTTTCATTTC
1 TTATTATTTTTTTATTTTCATTTC
406103 CCTATTTTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
26 7 0.32
27 9 0.41
28 6 0.27
ACGTcount: A:0.15, C:0.13, G:0.00, T:0.71
Consensus pattern (26 bp):
TTATTATTTTTTTATTTTCATTTCAC
Found at i:406116 original size:26 final size:27
Alignment explanation
Indices: 406059--406117 Score: 68
Period size: 26 Copynumber: 2.2 Consensus size: 27
406049 TATTATTATA
* *
406059 TTTTTTATTCTTCTTTTCACTTATTCT
1 TTTTTTATTCTTCATTTCACCTATTCT
*
406086 TTTTTTATT-TTCATTTC-CCTATTTT
1 TTTTTTATTCTTCATTTCACCTATTCT
406111 TATTTTT
1 T-TTTTT
406118 TTTCCTCTCT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
25 7 0.25
26 12 0.43
27 9 0.32
ACGTcount: A:0.12, C:0.15, G:0.00, T:0.73
Consensus pattern (27 bp):
TTTTTTATTCTTCATTTCACCTATTCT
Found at i:406201 original size:31 final size:32
Alignment explanation
Indices: 406143--406202 Score: 79
Period size: 32 Copynumber: 1.9 Consensus size: 32
406133 TTTTATTCAA
* *
406143 TTCTTTTTTTCGTTTTGACTTTTTTATTTATT
1 TTCTTTTTTTCGCTTTGACTTTATTATTTATT
406175 TTCTTTTTGTTC-CTTTGA-TTTATTATTT
1 TTCTTTTT-TTCGCTTTGACTTTATTATTT
406203 TAGTATTATA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
31 9 0.36
32 13 0.52
33 3 0.12
ACGTcount: A:0.10, C:0.10, G:0.07, T:0.73
Consensus pattern (32 bp):
TTCTTTTTTTCGCTTTGACTTTATTATTTATT
Found at i:406217 original size:20 final size:21
Alignment explanation
Indices: 406192--406236 Score: 58
Period size: 20 Copynumber: 2.2 Consensus size: 21
406182 TGTTCCTTTG
406192 ATTTA-TTATTTTAGTATTA-T
1 ATTTATTTA-TTTAGTATTATT
*
406212 ATTTATTTATTTATTATTATT
1 ATTTATTTATTTAGTATTATT
406233 ATTT
1 ATTT
406237 TTTTTTGTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
20 14 0.64
21 8 0.36
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.69
Consensus pattern (21 bp):
ATTTATTTATTTAGTATTATT
Found at i:412919 original size:18 final size:19
Alignment explanation
Indices: 412888--412938 Score: 63
Period size: 20 Copynumber: 2.8 Consensus size: 19
412878 AACATTCCTA
412888 GTAATCTT--ATTCC-CTG
1 GTAATCTTACATTCCACTG
*
412904 GTGATCTTACATTCCCACTG
1 GTAATCTTACATT-CCACTG
412924 GTAATCTTACATTCC
1 GTAATCTTACATTCC
412939 GCGAACCAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
16 7 0.24
18 3 0.10
19 4 0.14
20 15 0.52
ACGTcount: A:0.22, C:0.27, G:0.12, T:0.39
Consensus pattern (19 bp):
GTAATCTTACATTCCACTG
Found at i:412930 original size:20 final size:20
Alignment explanation
Indices: 412901--412938 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
412891 ATCTTATTCC
*
412901 CTGGTGATCTTACATTCCCA
1 CTGGTAATCTTACATTCCCA
412921 CTGGTAATCTTACATTCC
1 CTGGTAATCTTACATTCC
412939 GCGAACCAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.21, C:0.29, G:0.13, T:0.37
Consensus pattern (20 bp):
CTGGTAATCTTACATTCCCA
Found at i:415631 original size:36 final size:36
Alignment explanation
Indices: 415567--415759 Score: 237
Period size: 36 Copynumber: 5.4 Consensus size: 36
415557 AAACATCGGA
*
415567 ACTTTCGATTCAAGT-GAACGGAAGGAAGCATCGAC
1 ACTTTCGATTCAAGTCGAACGGAATGAAGCATCGAC
* * *
415602 ACTTTTGATTCAAGTCGAACGGAATGAAGCATTGGC
1 ACTTTCGATTCAAGTCGAACGGAATGAAGCATCGAC
* * * *
415638 ACTTTCGATTCCAGACGAACGGAAAGAAGCATCGGC
1 ACTTTCGATTCAAGTCGAACGGAATGAAGCATCGAC
415674 ACTTTCGATTCAAGTCGAACGGAATGAAGCATCGAC
1 ACTTTCGATTCAAGTCGAACGGAATGAAGCATCGAC
* * * * * *
415710 CCTTTCGATTCAAGTTGAACAGAAGGAGGCGTC-AC
1 ACTTTCGATTCAAGTCGAACGGAATGAAGCATCGAC
*
415745 ACTTTCGATTAAAGT
1 ACTTTCGATTCAAGT
415760 GTTCATCTTT
Statistics
Matches: 136, Mismatches: 21, Indels: 2
0.86 0.13 0.01
Matches are distributed among these distances:
35 29 0.21
36 107 0.79
ACGTcount: A:0.32, C:0.21, G:0.24, T:0.23
Consensus pattern (36 bp):
ACTTTCGATTCAAGTCGAACGGAATGAAGCATCGAC
Found at i:417280 original size:35 final size:35
Alignment explanation
Indices: 417241--417376 Score: 170
Period size: 35 Copynumber: 3.9 Consensus size: 35
417231 TGAATAAGAA
417241 GAACGAAAGAAAGCATCGACACTTTCGATTCAAGT
1 GAACGAAAGAAAGCATCGACACTTTCGATTCAAGT
* * * *
417276 GAACGGAAGGAAGCATCAACACTTTCGATTGAA--
1 GAACGAAAGAAAGCATCGACACTTTCGATTCAAGT
* * *
417309 GAACGAAAGGAAGTATCGGCACTTTCGATTCAAGT
1 GAACGAAAGAAAGCATCGACACTTTCGATTCAAGT
*
417344 GAACGGAAGAAAGCATCCG-CACTTTCGATTCAA
1 GAACGAAAGAAAGCAT-CGACACTTTCGATTCAA
417377 ATGTTCATCT
Statistics
Matches: 86, Mismatches: 12, Indels: 6
0.83 0.12 0.06
Matches are distributed among these distances:
33 28 0.33
35 56 0.65
36 2 0.02
ACGTcount: A:0.38, C:0.20, G:0.23, T:0.20
Consensus pattern (35 bp):
GAACGAAAGAAAGCATCGACACTTTCGATTCAAGT
Found at i:417347 original size:68 final size:68
Alignment explanation
Indices: 417238--417373 Score: 218
Period size: 68 Copynumber: 2.0 Consensus size: 68
417228 AGATGAATAA
*
417238 GAAGAACGAAAGAAAGCATCGACACTTTCGATTCAAGTGAACGGAAGGAAGCATCAACACTTTCG
1 GAAGAACGAAAGAAAGCATCGACACTTTCGATTCAAGTGAACGGAAGAAAGCATCAACACTTTCG
417303 ATT
66 ATT
* * * **
417306 GAAGAACGAAAGGAAGTATCGGCACTTTCGATTCAAGTGAACGGAAGAAAGCATCCGCACTTTCG
1 GAAGAACGAAAGAAAGCATCGACACTTTCGATTCAAGTGAACGGAAGAAAGCATCAACACTTTCG
417371 ATT
66 ATT
417374 CAAATGTTCA
Statistics
Matches: 62, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
68 62 1.00
ACGTcount: A:0.38, C:0.19, G:0.24, T:0.20
Consensus pattern (68 bp):
GAAGAACGAAAGAAAGCATCGACACTTTCGATTCAAGTGAACGGAAGAAAGCATCAACACTTTCG
ATT
Found at i:418742 original size:43 final size:43
Alignment explanation
Indices: 418531--418774 Score: 319
Period size: 43 Copynumber: 5.7 Consensus size: 43
418521 TAACGATATA
* ** *
418531 TAGCGGCGTTTGTTGGACAAACGCCGCAATAGGTGTTGATATT
1 TAGCGGCGTTTTTTCCACAAACGCCGCAATAGGTGTTGAGATT
*
418574 TACCGGCG-TTTTTCCAACAAACGCCGCAATAGGTGTTGAGATT
1 TAGCGGCGTTTTTTCC-ACAAACGCCGCAATAGGTGTTGAGATT
* *
418617 TAGCGGCGTTTTTCCCACAAATGCCGCAATAGGTGTTGAGATT
1 TAGCGGCGTTTTTTCCACAAACGCCGCAATAGGTGTTGAGATT
* * ** *
418660 TAGCAGCATTTTCCCCACAAACGTCGCAATAGGTGTTGAGATT
1 TAGCGGCGTTTTTTCCACAAACGCCGCAATAGGTGTTGAGATT
*
418703 TAGCGGCGTTTTTTCCACAAACGCCGCAATAGGTCTTGAGATT
1 TAGCGGCGTTTTTTCCACAAACGCCGCAATAGGTGTTGAGATT
** * *
418746 TAGCGATGTTTTTCCCACAAACACCGCAA
1 TAGCGGCGTTTTTTCCACAAACGCCGCAA
418775 AAGATCTGGT
Statistics
Matches: 176, Mismatches: 23, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
42 4 0.02
43 166 0.94
44 6 0.03
ACGTcount: A:0.25, C:0.23, G:0.23, T:0.29
Consensus pattern (43 bp):
TAGCGGCGTTTTTTCCACAAACGCCGCAATAGGTGTTGAGATT
Found at i:418801 original size:43 final size:43
Alignment explanation
Indices: 418528--418820 Score: 173
Period size: 43 Copynumber: 6.8 Consensus size: 43
418518 AGGTAACGAT
* * ** * * * *
418528 ATATAGCGGCGTTTGTTGGACAAACGCCGCAATAGGTGTTGAT
1 ATATAGCGGCATTTTTTCCACAAACGCCGCAAAAGATCTTGAG
* * * * * *
418571 ATTTACCGGC-GTTTTTCCAACAAACGCCGCAATAGGTGTTGAG
1 ATATAGCGGCATTTTTTCC-ACAAACGCCGCAAAAGATCTTGAG
* * * * * * *
418614 ATTTAGCGGCGTTTTTCCCACAAATGCCGCAATAGGTGTTGAG
1 ATATAGCGGCATTTTTTCCACAAACGCCGCAAAAGATCTTGAG
* * ** * * * *
418657 ATTTAGCAGCATTTTCCCCACAAACGTCGCAATAGGTGTTGAG
1 ATATAGCGGCATTTTTTCCACAAACGCCGCAAAAGATCTTGAG
* * * *
418700 ATTTAGCGGCGTTTTTTCCACAAACGCCGCAATAGGTCTTGAG
1 ATATAGCGGCATTTTTTCCACAAACGCCGCAAAAGATCTTGAG
* *
418743 ATTTAGC-G-ATGTTTTTCCCACAAACACCGCAAAAGATC-TG-G
1 ATATAGCGGCAT-TTTTT-CCACAAACGCCGCAAAAGATCTTGAG
**
418784 TATATAGCGGCATTTTTTAGAACAAACGCCGCAAAAG
1 -ATATAGCGGCATTTTTT-CCACAAACGCCGCAAAAG
418821 GTCATATCTA
Statistics
Matches: 212, Mismatches: 31, Indels: 14
0.82 0.12 0.05
Matches are distributed among these distances:
41 2 0.01
42 18 0.08
43 184 0.87
44 8 0.04
ACGTcount: A:0.28, C:0.22, G:0.23, T:0.28
Consensus pattern (43 bp):
ATATAGCGGCATTTTTTCCACAAACGCCGCAAAAGATCTTGAG
Found at i:418809 original size:86 final size:85
Alignment explanation
Indices: 418510--418823 Score: 310
Period size: 86 Copynumber: 3.7 Consensus size: 85
418500 AAAAAAAAAT
*** * * ** * *
418510 GCCGCAATAGGTAACGATATATAGCGGCGTTTGTTGGACAAACGCCGCAATAGGTGTTGATATTT
1 GCCGCAATAGGTGTTGAGATATAGCGGCGTTTTTTCCACAAACGCCGCAATAGGTCTTGAGATTT
* * *
418575 ACCGGCGTTTTTCCAACAAAC
66 AGC-GAGTTTTTCCCACAAAC
* * * *
418596 GCCGCAATAGGTGTTGAGATTTAGCGGCGTTTTTCCCACAAATGCCGCAATAGGTGTTGAGATTT
1 GCCGCAATAGGTGTTGAGATATAGCGGCGTTTTTTCCACAAACGCCGCAATAGGTCTTGAGATTT
*
418661 AGC-AGCATTTTCCCCACAAAC
66 AGCGAG--TTTTTCCCACAAAC
* *
418682 GTCGCAATAGGTGTTGAGATTTAGCGGCGTTTTTTCCACAAACGCCGCAATAGGTCTTGAGATTT
1 GCCGCAATAGGTGTTGAGATATAGCGGCGTTTTTTCCACAAACGCCGCAATAGGTCTTGAGATTT
418747 AGCGATGTTTTTCCCACAAAC
66 AGCGA-GTTTTTCCCACAAAC
* * * * * ** *
418768 ACCGCAAAAGAT-CTG-GTATATAGCGGCATTTTTTAGAACAAACGCCGCAAAAGGTC
1 GCCGCAATAGGTGTTGAG-ATATAGCGGCGTTTTTT-CCACAAACGCCGCAATAGGTC
418824 ATATCTATAG
Statistics
Matches: 192, Mismatches: 30, Indels: 12
0.82 0.13 0.05
Matches are distributed among these distances:
84 2 0.01
85 17 0.09
86 171 0.89
87 1 0.01
88 1 0.01
ACGTcount: A:0.28, C:0.22, G:0.23, T:0.27
Consensus pattern (85 bp):
GCCGCAATAGGTGTTGAGATATAGCGGCGTTTTTTCCACAAACGCCGCAATAGGTCTTGAGATTT
AGCGAGTTTTTCCCACAAAC
Found at i:418809 original size:129 final size:130
Alignment explanation
Indices: 418527--418822 Score: 357
Period size: 129 Copynumber: 2.3 Consensus size: 130
418517 TAGGTAACGA
* * * *
418527 TATATAGCGGCGTTTGTTGGACAAACGCCGCAATAGGTGTTGATATTTACCGGCGTTTTTCCAAC
1 TATATAGCGGCATTTTTTGAACAAACGCCGCAATAGGTGTTGAGATTTACCGGCGTTTTTCCAAC
* * ** * * *
418592 AAACGCCGCAATAGGTGTTGAGATTTAGCGGCGTTTTTCCCACAAATGCCGCAATAGGTGTTGAG
66 AAACGCCGCAATAGGTCTTGAGATTTAGCGACGTTTTTCCCACAAACACCGCAAAAGATGCTGAG
* * **** * *
418657 -ATTTAGCAGCATTTTCCCCACAAACGTCGCAATAGGTGTTGAGATTTAGCGGCGTTTTTTCC-A
1 TATATAGCGGCATTTTTTGAACAAACGCCGCAATAGGTGTTGAGATTTACCGGCG-TTTTTCCAA
*
418720 CAAACGCCGCAATAGGTCTTGAGATTTAGCGATGTTTTTCCCACAAACACCGCAAAAGAT-CTG-
65 CAAACGCCGCAATAGGTCTTGAGATTTAGCGACGTTTTTCCCACAAACACCGCAAAAGATGCTGA
418783 G
130 G
*
418784 TATATAGCGGCATTTTTTAGAACAAACGCCGCAAAAGGT
1 TATATAGCGGCATTTTTT-GAACAAACGCCGCAATAGGT
418823 CATATCTATA
Statistics
Matches: 136, Mismatches: 27, Indels: 7
0.80 0.16 0.04
Matches are distributed among these distances:
127 1 0.01
128 15 0.11
129 113 0.83
130 7 0.05
ACGTcount: A:0.27, C:0.21, G:0.23, T:0.28
Consensus pattern (130 bp):
TATATAGCGGCATTTTTTGAACAAACGCCGCAATAGGTGTTGAGATTTACCGGCGTTTTTCCAAC
AAACGCCGCAATAGGTCTTGAGATTTAGCGACGTTTTTCCCACAAACACCGCAAAAGATGCTGAG
Found at i:418996 original size:21 final size:21
Alignment explanation
Indices: 418970--419028 Score: 73
Period size: 21 Copynumber: 2.8 Consensus size: 21
418960 ATTTTCCAAT
*
418970 AAACTTGACATCCATAACAAC
1 AAACTTGAAATCCATAACAAC
* *
418991 AAACTTAAAATCCATAACAAG
1 AAACTTGAAATCCATAACAAC
**
419012 AAAAATGAAATCCATAA
1 AAACTTGAAATCCATAA
419029 TAATAAATCA
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.56, C:0.20, G:0.05, T:0.19
Consensus pattern (21 bp):
AAACTTGAAATCCATAACAAC
Found at i:421997 original size:42 final size:41
Alignment explanation
Indices: 421951--422029 Score: 97
Period size: 41 Copynumber: 1.9 Consensus size: 41
421941 ACCTTTTATC
* *
421951 ATTTTATAGCGGCGTTT-TCTAAAAAACGCTGCTAAAGTACAT
1 ATTTT-TAGCGACGTTTGTCT-AAAAACGCCGCTAAAGTACAT
* *
421993 ATTTTTTGCGACGTTTGTGTAAAAACGCCGCTAAAGT
1 ATTTTTAGCGACGTTTGTCTAAAAACGCCGCTAAAGT
422030 TCTAATTTGT
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
41 25 0.78
42 7 0.22
ACGTcount: A:0.30, C:0.16, G:0.19, T:0.34
Consensus pattern (41 bp):
ATTTTTAGCGACGTTTGTCTAAAAACGCCGCTAAAGTACAT
Found at i:422190 original size:85 final size:86
Alignment explanation
Indices: 422005--422199 Score: 222
Period size: 85 Copynumber: 2.3 Consensus size: 86
421995 TTTTTGCGAC
* * *
422005 GTTTGTGTAAAAACGCCGCTAAAGT-TCTAATTTGTTGCAGCGTTTATTAGAAAAAAAGCCACTA
1 GTTTGTATAAAAACGCCGCTAAAGTATCAAATTTGTTGCAGCATTTATTAGAAAAAAAGCCACTA
**
422069 TAGAAGAACTCTATTGTGGCA
66 TAGAAGAACTCTATTGCAGCA
* * * *
422090 -TTTTTATAAAAACGCCGTTAAAGTAT-AAATCTT-TTGCGGCATTTGTTAGAAAAAAAACGCCA
1 GTTTGTATAAAAACGCCGCTAAAGTATCAAAT-TTGTTGCAGCATTTATTAG-AAAAAAA-GCCA
* *
422152 CTATAGATGGAC-CTATTGCAG-A
63 CTATAGAAGAACTCTATTGCAGCA
422174 GTTTGTATAAAAACGCCGCTAAAGTA
1 GTTTGTATAAAAACGCCGCTAAAGTA
422200 CTACTCTGTT
Statistics
Matches: 92, Mismatches: 13, Indels: 10
0.80 0.11 0.09
Matches are distributed among these distances:
84 38 0.41
85 40 0.43
86 14 0.15
ACGTcount: A:0.36, C:0.15, G:0.18, T:0.30
Consensus pattern (86 bp):
GTTTGTATAAAAACGCCGCTAAAGTATCAAATTTGTTGCAGCATTTATTAGAAAAAAAGCCACTA
TAGAAGAACTCTATTGCAGCA
Found at i:422219 original size:41 final size:41
Alignment explanation
Indices: 421959--422322 Score: 152
Period size: 41 Copynumber: 8.8 Consensus size: 41
421949 TCATTTTATA
* * * *
421959 GCGGCGTTT-TCTAAAAAACGCTGCTAAAGTACATA-TTTTTT
1 GCGGCGTTTGTAT-AAAAACGCCGCTAAAGTAC-TACTCTATT
* * * * * *
422000 GCGACGTTTGTGTAAAAACGCCGCTAAAGTTCTAATTTGTT
1 GCGGCGTTTGTATAAAAACGCCGCTAAAGTACTACTCTATT
* * * * * * * **
422041 GCAGCGTTTATTAGAAAAAAAGCCACTATAGAAGAACTCTATT
1 GCGGCGTTT-GTA-TAAAAACGCCGCTAAAGTACTACTCTATT
* * * * * *
422084 GTGGCATTTTTATAAAAACGCCGTTAAAGTA-TAAATCTTTT
1 GCGGCGTTTGTATAAAAACGCCGCTAAAGTACT-ACTCTATT
* * * *
422125 GCGGCATTTGTTAGAAAAAAAACGCCACTATAG-A-TGGAC-CTATT
1 GCGGCGTTTG-T---ATAAAAACGCCGCTAAAGTACT--ACTCTATT
* * *
422169 GCAGAGTTTGTATAAAAACGCCGCTAAAGTACTACTCTGTT
1 GCGGCGTTTGTATAAAAACGCCGCTAAAGTACTACTCTATT
* * ** * *
422210 GTGGCGTTTGT-TGAAAAACGTCATTACA-TATGTAC-CTATT
1 GCGGCGTTTGTAT-AAAAACGCCGCTAAAGTA-CTACTCTATT
* * * *
422250 GCGGCGTTTATATAAAAATGCCGCTATAGTACTACTCTATA
1 GCGGCGTTTGTATAAAAACGCCGCTAAAGTACTACTCTATT
*
422291 GCGGCGTTTGTTTAAGAAACGCCGCTAAAGTA
1 GCGGCGTTTGTATAA-AAACGCCGCTAAAGTA
422323 TCATTTTGTG
Statistics
Matches: 234, Mismatches: 70, Indels: 37
0.69 0.21 0.11
Matches are distributed among these distances:
40 48 0.21
41 111 0.47
42 22 0.09
43 25 0.11
44 13 0.06
45 15 0.06
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.32
Consensus pattern (41 bp):
GCGGCGTTTGTATAAAAACGCCGCTAAAGTACTACTCTATT
Found at i:422220 original size:85 final size:84
Alignment explanation
Indices: 422005--422302 Score: 275
Period size: 81 Copynumber: 3.6 Consensus size: 84
421995 TTTTTGCGAC
* * * * *
422005 GTTTGTGTAAAAACGCCGCTAAAGTTCTAATTTGTTGCAGCGTTTATTAGAAAAAAA-GCCACTA
1 GTTTGTATAAAAACGCCGCTAAAGTACTAATCTGTTGCGGCGTTTGTTAGAAAAAAACGCCACTA
* *
422069 TAGAAGAACTCTATTGTGGCA
66 TAGATGAAC-CTATTGCGG-A
* * * *
422090 -TTTTTATAAAAACGCCGTTAAAGTA-TAAATCTTTTGCGGCATTTGTTAGAAAAAAAACGCCAC
1 GTTTGTATAAAAACGCCGCTAAAGTACT-AATCTGTTGCGGCGTTTGTTAG-AAAAAAACGCCAC
* *
422153 TATAGATGGACCTATTGCAGA
64 TATAGATGAACCTATTGCGGA
* * * *
422174 GTTTGTATAAAAACGCCGCTAAAGTACTACTCTGTTGTGGCGTTTGTT-G--AAAAACGTCATTA
1 GTTTGTATAAAAACGCCGCTAAAGTACTAATCTGTTGCGGCGTTTGTTAGAAAAAAACGCCACTA
* * * *
422236 CATATGTACCTATTGCGGC
66 TAGATGAACCTATTGCGGA
* * * * * *
422255 GTTTATATAAAAATGCCGCTATAGTACTACTCTATAGCGGCGTTTGTT
1 GTTTGTATAAAAACGCCGCTAAAGTACTAATCTGTTGCGGCGTTTGTT
422303 TAAGAAACGC
Statistics
Matches: 176, Mismatches: 32, Indels: 14
0.79 0.14 0.06
Matches are distributed among these distances:
81 67 0.38
83 1 0.01
84 40 0.23
85 53 0.30
86 15 0.09
ACGTcount: A:0.32, C:0.16, G:0.19, T:0.33
Consensus pattern (84 bp):
GTTTGTATAAAAACGCCGCTAAAGTACTAATCTGTTGCGGCGTTTGTTAGAAAAAAACGCCACTA
TAGATGAACCTATTGCGGA
Found at i:426301 original size:3 final size:3
Alignment explanation
Indices: 426293--426328 Score: 56
Period size: 3 Copynumber: 12.0 Consensus size: 3
426283 CAATCTCAGA
426293 TCT TCT TCTT TCT TC- TCT TCT TCT TCT TCT TCT TCT
1 TCT TCT TC-T TCT TCT TCT TCT TCT TCT TCT TCT TCT
426329 ACGGCTGTTG
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
2 2 0.06
3 26 0.84
4 3 0.10
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
TCT
Found at i:427546 original size:19 final size:19
Alignment explanation
Indices: 427524--427593 Score: 70
Period size: 19 Copynumber: 3.6 Consensus size: 19
427514 TTATTTTATT
*
427524 TTATTATTTATTTTTTTAA
1 TTATTATTTATTTATTTAA
427543 TTATTATTTGA-TTATTTAA
1 TTATTATTT-ATTTATTTAA
* * *
427562 TTGTAAATTTATTTAATTAA
1 TTAT-TATTTATTTATTTAA
*
427582 TTAATATTTATT
1 TTATTATTTATT
427594 AATTGTAGTT
Statistics
Matches: 41, Mismatches: 7, Indels: 6
0.76 0.13 0.11
Matches are distributed among these distances:
19 27 0.66
20 14 0.34
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.64
Consensus pattern (19 bp):
TTATTATTTATTTATTTAA
Found at i:427547 original size:16 final size:16
Alignment explanation
Indices: 427513--427580 Score: 57
Period size: 16 Copynumber: 4.1 Consensus size: 16
427503 TAAGTACTCA
*
427513 ATTATTTTATTTTATT
1 ATTATTTTATTTAATT
427529 ATTTATTTT-TTTAATT
1 A-TTATTTTATTTAATT
427545 ATTATTTGATTATTTAATT
1 ATTA-TT--TTATTTAATT
* * *
427564 GTAAATTTATTTAATT
1 ATTATTTTATTTAATT
427580 A
1 A
427581 ATTAATATTT
Statistics
Matches: 42, Mismatches: 5, Indels: 10
0.74 0.09 0.18
Matches are distributed among these distances:
15 3 0.07
16 20 0.48
17 7 0.17
18 3 0.07
19 9 0.21
ACGTcount: A:0.31, C:0.00, G:0.03, T:0.66
Consensus pattern (16 bp):
ATTATTTTATTTAATT
Found at i:428572 original size:2 final size:2
Alignment explanation
Indices: 428565--428596 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
428555 TTATAGAATG
428565 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
428597 TAAATAGGTG
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:433482 original size:15 final size:15
Alignment explanation
Indices: 433464--433494 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
433454 CAGGGTATCC
433464 ATGTAGATAAAGAGA
1 ATGTAGATAAAGAGA
433479 ATGTAGATAAAGAGA
1 ATGTAGATAAAGAGA
433494 A
1 A
433495 GGTCAAGGCA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.55, C:0.00, G:0.26, T:0.19
Consensus pattern (15 bp):
ATGTAGATAAAGAGA
Found at i:436287 original size:30 final size:30
Alignment explanation
Indices: 436251--436334 Score: 89
Period size: 30 Copynumber: 2.8 Consensus size: 30
436241 TGTAGAGAGT
* *
436251 GATGATGAGAAGGATGAGGAGGATGAGGAC
1 GATGATGAGAAGGACGAGGAGGAGGAGGAC
* * * * *
436281 GATGATGACAACGAGGAGGAAGAGGTGGAC
1 GATGATGAGAAGGACGAGGAGGAGGAGGAC
436311 GATGATGATG-AGGACGAGGAGGAG
1 GATGATGA-GAAGGACGAGGAGGAG
436335 CAACATATAA
Statistics
Matches: 43, Mismatches: 10, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
30 43 1.00
ACGTcount: A:0.36, C:0.06, G:0.46, T:0.12
Consensus pattern (30 bp):
GATGATGAGAAGGACGAGGAGGAGGAGGAC
Found at i:436935 original size:54 final size:54
Alignment explanation
Indices: 436853--436957 Score: 165
Period size: 54 Copynumber: 1.9 Consensus size: 54
436843 TGTCTCCTCG
* * *
436853 TGGAAAAGACATAATTATTGGAACAACATATACACATGAATATTCTCATACTCA
1 TGGAAAAGACATAACTATTGCAACAACATATACACATGAATATTCCCATACTCA
* *
436907 TGGAAAAGGCATAACTATTGCAACAACATATGCACATGAATATTCCCATAC
1 TGGAAAAGACATAACTATTGCAACAACATATACACATGAATATTCCCATAC
436958 ATACATATAT
Statistics
Matches: 46, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
54 46 1.00
ACGTcount: A:0.43, C:0.19, G:0.12, T:0.26
Consensus pattern (54 bp):
TGGAAAAGACATAACTATTGCAACAACATATACACATGAATATTCCCATACTCA
Found at i:436962 original size:4 final size:4
Alignment explanation
Indices: 436953--436994 Score: 75
Period size: 4 Copynumber: 10.5 Consensus size: 4
436943 TGAATATTCC
*
436953 CATA CATA CATA TATA CATA CATA CATA CATA CATA CATA CA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CA
436995 CTGGGGGAAT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
4 36 1.00
ACGTcount: A:0.50, C:0.24, G:0.00, T:0.26
Consensus pattern (4 bp):
CATA
Found at i:459478 original size:35 final size:36
Alignment explanation
Indices: 459439--459533 Score: 102
Period size: 35 Copynumber: 2.6 Consensus size: 36
459429 TTTGAAAATG
* *
459439 TATATAATATATAGTTTTAAAACCGTTTCTGAAAATA
1 TATATAATATATAGTTTTAAAA-CGTTTCTAAAAACA
* * * *
459476 TATATTATA-AAATTTTTAAAACGTTTTTAAAAACA
1 TATATAATATATAGTTTTAAAACGTTTCTAAAAACA
*
459511 TGTATAATATATAGTTTTTAAAA
1 TATATAATATATAG-TTTTAAAA
459534 GCATTTTGGA
Statistics
Matches: 46, Mismatches: 10, Indels: 4
0.77 0.17 0.07
Matches are distributed among these distances:
35 18 0.39
36 12 0.26
37 16 0.35
ACGTcount: A:0.45, C:0.05, G:0.06, T:0.43
Consensus pattern (36 bp):
TATATAATATATAGTTTTAAAACGTTTCTAAAAACA
Found at i:459480 original size:37 final size:36
Alignment explanation
Indices: 459417--459533 Score: 112
Period size: 37 Copynumber: 3.2 Consensus size: 36
459407 TATACATAAT
* *
459417 TTTTGAAAACATTT-TGAAAATGTATATAATATATAG
1 TTTT-AAAACGTTTCTGAAAATATATATAATATATAG
* * *
459453 TTTTAAAACCGTTTCTGAAAATATATATTATA-AAAT
1 TTTTAAAA-CGTTTCTGAAAATATATATAATATATAG
* * * *
459489 TTTTAAAACGTTTTTAAAAACATGTATAATATATAG
1 TTTTAAAACGTTTCTGAAAATATATATAATATATAG
459525 TTTTTAAAA
1 -TTTTAAAA
459534 GCATTTTGGA
Statistics
Matches: 65, Mismatches: 12, Indels: 7
0.77 0.14 0.08
Matches are distributed among these distances:
35 22 0.34
36 20 0.31
37 23 0.35
ACGTcount: A:0.44, C:0.05, G:0.08, T:0.43
Consensus pattern (36 bp):
TTTTAAAACGTTTCTGAAAATATATATAATATATAG
Found at i:462079 original size:17 final size:18
Alignment explanation
Indices: 462047--462080 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
462037 CTCACTAACC
*
462047 CTTTTATTTTTTTGTTCT
1 CTTTTATTTTTGTGTTCT
462065 CTTTTA-TTTTGTGTTC
1 CTTTTATTTTTGTGTTC
462081 ATCGTTTGCA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.06, C:0.12, G:0.09, T:0.74
Consensus pattern (18 bp):
CTTTTATTTTTGTGTTCT
Found at i:462716 original size:19 final size:19
Alignment explanation
Indices: 462692--462737 Score: 83
Period size: 19 Copynumber: 2.4 Consensus size: 19
462682 ATTTAGACAT
462692 TTTGCATTTCGTTATTTTC
1 TTTGCATTTCGTTATTTTC
*
462711 TTTGCATTTTGTTATTTTC
1 TTTGCATTTCGTTATTTTC
462730 TTTGCATT
1 TTTGCATT
462738 CACATTAACT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.11, C:0.13, G:0.11, T:0.65
Consensus pattern (19 bp):
TTTGCATTTCGTTATTTTC
Found at i:466509 original size:84 final size:83
Alignment explanation
Indices: 466105--466865 Score: 840
Period size: 84 Copynumber: 9.2 Consensus size: 83
466095 GCTCAAGGCC
* * *
466105 AGAAGGGCTACCTGCCACC-AAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTT
1 AGAAGGGTTATCTGCCACCAAAGACCTTTGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTT
* *
466169 GCAGAATAGCTTAAGTCG
66 GCAGCATAACTTAAGTCG
* * * * * * * * *
466187 AGAAGGGCTATCTG---CCAAAGACCCTTAAGTTCGATTACACTCAACTTCAAGGGCATAACATT
1 AGAAGGGTTATCTGCCACCAAAGACCTTTGAGTTCGACTACGCTCAGCTCCAA-GGCACATCATT
* * * * *
466249 TACAACATAACTCAAGGCT
65 TGCAGCATAACTTAAGTCG
** * * *
466268 AGAAGGGTTATCTGTTAGCAAAGACCTTTGAGTTTGACTACGCTCAGCTCCTAGGCACATCATTT
1 AGAAGGGTTATCTGCCACCAAAGACCTTTGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTT
* *
466333 GCAGAATAGCTTAAGTCG
66 GCAGCATAACTTAAGTCG
* *** * * * *
466351 AGAAGGGCTATCTG---CCAAAGACCCCCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATT
1 AGAAGGGTTATCTGCCACCAAAGACCTTTGAGTTCGACTACGCTCAGC-TCCAAGGCACATCATT
466413 TGCAGCATAACTTAAGTCG
65 TGCAGCATAACTTAAGTCG
* **
466432 AGAAGGGTTATCTGCCAACCAAAGACCTTTGAGTTCGACTACGCTCGGCTCCAAGGCATGTCATT
1 AGAAGGGTTATCTGCC-ACCAAAGACCTTTGAGTTCGACTACGCTCAGCTCCAAGGCACATCATT
* *
466497 TGCAGCACAACTTAAGTCT
65 TGCAGCATAACTTAAGTCG
* *
466516 AGAAGGGTTGTCTACCACCAAAAGACCTTTGAGTTCGACTACGCTCAGCTCCAAGGCACATCATT
1 AGAAGGGTTATCTGCCACC-AAAGACCTTTGAGTTCGACTACGCTCAGCTCCAAGGCACATCATT
* * *
466581 TGCAGAATAGCTTAAGTCA
65 TGCAGCATAACTTAAGTCG
*** * * * *
466600 AGAAGGGTTATCTG---CCAAAGACCCCCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATT
1 AGAAGGGTTATCTGCCACCAAAGACCTTTGAGTTCGACTACGCTCAGC-TCCAAGGCACATCATT
466662 TGCAGCATAACTTAAGTCG
65 TGCAGCATAACTTAAGTCG
* **
466681 AGAAGGGTTATCTGCCAACCAAAGACCTTTGAGTTCGACTACGCTCAGCTCCAAGGTATGTCATT
1 AGAAGGGTTATCTGCC-ACCAAAGACCTTTGAGTTCGACTACGCTCAGCTCCAAGGCACATCATT
* *
466746 TGCAGCACAACTTAAGTCT
65 TGCAGCATAACTTAAGTCG
*
466765 AGAAGGGTTGTCTGCCACCAAAAGACCTTTGAGTTCGACTACGCTCAGCTCCAAGGCACATCATT
1 AGAAGGGTTATCTGCCACC-AAAGACCTTTGAGTTCGACTACGCTCAGCTCCAAGGCACATCATT
* *
466830 TGCAGAATAGCTTAAGTCG
65 TGCAGCATAACTTAAGTCG
* *
466849 AGAAGAGCTATCTGCCA
1 AGAAGGGTTATCTGCCA
466866 AAGACCTCCG
Statistics
Matches: 556, Mismatches: 106, Indels: 32
0.80 0.15 0.05
Matches are distributed among these distances:
79 2 0.00
80 74 0.13
81 123 0.22
82 13 0.02
83 40 0.07
84 253 0.46
85 51 0.09
ACGTcount: A:0.29, C:0.25, G:0.21, T:0.24
Consensus pattern (83 bp):
AGAAGGGTTATCTGCCACCAAAGACCTTTGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTT
GCAGCATAACTTAAGTCG
Found at i:466562 original size:249 final size:249
Alignment explanation
Indices: 466105--466911 Score: 1187
Period size: 249 Copynumber: 3.3 Consensus size: 249
466095 GCTCAAGGCC
* ** * * * *
466105 AGAAGGGCTACCTGCCACCAAGACCTTCGAGTTCGACTACGCTCAGC-TCCAAGGCACATCATTT
1 AGAAGGGCTATCTGCCA--AAGACCCCCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATTT
* * * * * * *
466169 GCAGAATAGCTTAAGTCGAGAAGGGCTATCTG----CCAAAGACCCTTAAGTTCGATTACACTCA
64 GCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTTGAGTTCGACTACGCTCA
* * ** * * * * * * ** *
466230 ACTTCAAGGGCATAACATTTACAACATAACTCAAGGCTAGAAGGGTTATCTGTTAGC-AAAGACC
129 GCTCCAA-GGCATGTCATTTGCAGCACAACTTAAGTCTAGAAGGGTTGTCTGCCACCAAAAGACC
* *
466294 TTTGAGTTTGACTACGCTCAGCTCCTAGGCACATCATTTGCAGAATAGCTTAAGTCG
193 TTTGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGAATAGCTTAAGTCG
466351 AGAAGGGCTATCTGCCAAAGACCCCCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTGC
1 AGAAGGGCTATCTGCCAAAGACCCCCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTGC
*
466416 AGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTTGAGTTCGACTACGCTCGGC
66 AGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTTGAGTTCGACTACGCTCAGC
*
466481 TCCAAGGCATGTCATTTGCAGCACAACTTAAGTCTAGAAGGGTTGTCTACCACCAAAAGACCTTT
131 TCCAAGGCATGTCATTTGCAGCACAACTTAAGTCTAGAAGGGTTGTCTGCCACCAAAAGACCTTT
*
466546 GAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGAATAGCTTAAGTCA
196 GAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGAATAGCTTAAGTCG
*
466600 AGAAGGGTTATCTGCCAAAGACCCCCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTGC
1 AGAAGGGCTATCTGCCAAAGACCCCCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTGC
466665 AGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTTGAGTTCGACTACGCTCAGC
66 AGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTTGAGTTCGACTACGCTCAGC
*
466730 TCCAAGGTATGTCATTTGCAGCACAACTTAAGTCTAGAAGGGTTGTCTGCCACCAAAAGACCTTT
131 TCCAAGGCATGTCATTTGCAGCACAACTTAAGTCTAGAAGGGTTGTCTGCCACCAAAAGACCTTT
466795 GAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGAATAGCTTAAGTCG
196 GAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGAATAGCTTAAGTCG
* * * *
466849 AGAAGAGCTATCTGCCAAAGACCTCCGAGTTCGATTACACTCAACTTCG-GGGTCATATCATTT
1 AGAAGGGCTATCTGCCAAAGACCCCCGAGTTCGATTACACTCAGCTTCGAGGG-CACATCATTT
466912 ACAACATAGC
Statistics
Matches: 512, Mismatches: 42, Indels: 11
0.91 0.07 0.02
Matches are distributed among these distances:
244 24 0.05
245 44 0.09
246 16 0.03
248 40 0.08
249 388 0.76
ACGTcount: A:0.29, C:0.25, G:0.21, T:0.24
Consensus pattern (249 bp):
AGAAGGGCTATCTGCCAAAGACCCCCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTGC
AGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTTGAGTTCGACTACGCTCAGC
TCCAAGGCATGTCATTTGCAGCACAACTTAAGTCTAGAAGGGTTGTCTGCCACCAAAAGACCTTT
GAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGAATAGCTTAAGTCG
Found at i:466711 original size:165 final size:164
Alignment explanation
Indices: 466124--466865 Score: 825
Period size: 165 Copynumber: 4.5 Consensus size: 164
466114 ACCTGCCACC
*
466124 AAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGAATAGCTTAAGTCGAG
1 AAGACCTTTGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGAATAGCTTAAGTCGAG
* * * * * * *
466189 AAGGGCTATCTG---CCAAAGACCCTTAAGTTCGATTACACTCAACTTCAAGGGCATAACATTTA
66 AAGGGCTATCTGCCACCAAAGACCCTTGAGTTCGACTACACTCAGCTCCAA-GGCACATCATTTG
* * *
466251 CA-ACATAACTCAAGGCTAGAAGGGTTATCTGTTAGCA
130 CAGA-ATAACTTAAGTCTAGAAGGGTTATCTG--ACCA
* *
466288 AAGACCTTTGAGTTTGACTACGCTCAGCTCCTAGGCACATCATTTGCAGAATAGCTTAAGTCGAG
1 AAGACCTTTGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGAATAGCTTAAGTCGAG
** * * *
466353 AAGGGCTATCTG---CCAAAGACCCCCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTG
66 AAGGGCTATCTGCCACCAAAGACCCTTGAGTTCGACTACACTCAGC-TCCAAGGCACATCATTTG
* *
466415 CAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCA
130 CAGAATAACTTAAGTCTAGAAGGGTTATCTG---ACCA
* ** * * * *
466453 AAGACCTTTGAGTTCGACTACGCTCGGCTCCAAGGCATGTCATTTGCAGCACAACTTAAGTCTAG
1 AAGACCTTTGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGAATAGCTTAAGTCGAG
* * * * *
466518 AAGGGTTGTCTACCACCAAAAGACCTTTGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTG
66 AAGGGCTATCTGCCACC-AAAGACCCTTGAGTTCGACTACACTCAGCTCCAAGGCACATCATTTG
* *
466583 CAGAATAGCTTAAGTCAAGAAGGGTTATCTG-CCA
130 CAGAATAACTTAAGTCTAGAAGGGTTATCTGACCA
*** * * * * * *
466617 AAGACCCCCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTGCAGCATAACTTAAGTCGA
1 AAGACCTTTGAGTTCGACTACGCTCAGC-TCCAAGGCACATCATTTGCAGAATAGCTTAAGTCGA
* * * * **
466682 GAAGGGTTATCTGCCAACCAAAGACCTTTGAGTTCGACTACGCTCAGCTCCAAGGTATGTCATTT
65 GAAGGGCTATCTGCC-ACCAAAGACCCTTGAGTTCGACTACACTCAGCTCCAAGGCACATCATTT
* * *
466747 GCAGCACAACTTAAGTCTAGAAGGGTTGTCTGCCACCAA
129 GCAGAATAACTTAAGTCTAGAAGGGTTATCTG--ACC-A
466786 AAGACCTTTGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGAATAGCTTAAGTCGAG
1 AAGACCTTTGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGAATAGCTTAAGTCGAG
*
466851 AAGAGCTATCTGCCA
66 AAGGGCTATCTGCCA
466866 AAGACCTCCG
Statistics
Matches: 490, Mismatches: 75, Indels: 23
0.83 0.13 0.04
Matches are distributed among these distances:
164 162 0.33
165 183 0.37
166 3 0.01
167 1 0.00
168 93 0.19
169 48 0.10
ACGTcount: A:0.30, C:0.25, G:0.21, T:0.24
Consensus pattern (164 bp):
AAGACCTTTGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGAATAGCTTAAGTCGAG
AAGGGCTATCTGCCACCAAAGACCCTTGAGTTCGACTACACTCAGCTCCAAGGCACATCATTTGC
AGAATAACTTAAGTCTAGAAGGGTTATCTGACCA
Found at i:467642 original size:35 final size:35
Alignment explanation
Indices: 467531--467694 Score: 107
Period size: 37 Copynumber: 4.4 Consensus size: 35
467521 GCAAACGGTC
*
467531 TTTGAAAATACT-TATAATATACATAATTTTTGAAAACAT
1 TTTGAAAATA-TATATAATAT--A-AATTTTT-AAAACGT
* * **
467570 TTTGAAAATGTATATAATATATAGGTTTAAAACCGT
1 TTTGAAAATATATATAATATAAATTTTTAAAA-CGT
*
467606 TTCTGAAAATATATATTATA-AAATTTTTAAAACGTT
1 TT-TGAAAATATATATAATATAAATTTTTAAAACG-T
* * * * *
467642 TTTAAAAACATGTATAATATATAGTTTTTAAAAGCAT
1 TTTGAAAATATATATAATATA-AATTTTTAAAA-CGT
*
467679 TTTGGAAATTATATAT
1 TTT-GAAAATATATAT
467695 TACATATTTT
Statistics
Matches: 97, Mismatches: 20, Indels: 17
0.72 0.15 0.13
Matches are distributed among these distances:
35 19 0.20
36 21 0.22
37 30 0.31
38 10 0.10
39 17 0.18
ACGTcount: A:0.44, C:0.05, G:0.09, T:0.42
Consensus pattern (35 bp):
TTTGAAAATATATATAATATAAATTTTTAAAACGT
Found at i:469032 original size:10 final size:9
Alignment explanation
Indices: 469017--469069 Score: 52
Period size: 9 Copynumber: 5.4 Consensus size: 9
469007 TTTATTTATC
469017 ATTTTTTTCT
1 ATTTTTTT-T
469027 ATTTTTTTT
1 ATTTTTTTT
469036 ATTTATTTTT
1 ATTT-TTTTT
* *
469046 AAGCTTATTTT
1 -A-TTTTTTTT
469057 ATTTTTTTT
1 ATTTTTTTT
469066 ATTT
1 ATTT
469070 ATTCTTTTCC
Statistics
Matches: 36, Mismatches: 4, Indels: 7
0.77 0.09 0.15
Matches are distributed among these distances:
9 15 0.42
10 14 0.39
11 5 0.14
12 2 0.06
ACGTcount: A:0.17, C:0.04, G:0.02, T:0.77
Consensus pattern (9 bp):
ATTTTTTTT
Found at i:471292 original size:19 final size:20
Alignment explanation
Indices: 471268--471306 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 20
471258 ATAAAAATTT
*
471268 AAAATTATCATATA-TTTTA
1 AAAATTATAATATACTTTTA
*
471287 AAAATTTTAATATACTTTTA
1 AAAATTATAATATACTTTTA
471307 TTACTCTTGA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 12 0.71
20 5 0.29
ACGTcount: A:0.46, C:0.05, G:0.00, T:0.49
Consensus pattern (20 bp):
AAAATTATAATATACTTTTA
Found at i:473082 original size:41 final size:42
Alignment explanation
Indices: 472987--473161 Score: 318
Period size: 41 Copynumber: 4.2 Consensus size: 42
472977 GATTCGCAAC
472987 GCGATAGTCGAAGTTCGCGTTGCGATTCATTCCAAATTCGTT
1 GCGATAGTCGAAGTTCGCGTTGCGATTCATTCCAAATTCGTT
473029 GCGATAGTCGAAGTTCGCGTTGCGATTCATTCCAAA-TCGTT
1 GCGATAGTCGAAGTTCGCGTTGCGATTCATTCCAAATTCGTT
*
473070 GCGATAGGCGAAGTTCGCGTTGCGATTCATTCC-AATTCGTT
1 GCGATAGTCGAAGTTCGCGTTGCGATTCATTCCAAATTCGTT
*
473111 GCGACAGTCGAAGTTCGCGTTGCGATTCATTCCAAATTCGTT
1 GCGATAGTCGAAGTTCGCGTTGCGATTCATTCCAAATTCGTT
473153 GCGATAGTC
1 GCGATAGTC
473162 CAAATATTGC
Statistics
Matches: 127, Mismatches: 4, Indels: 4
0.94 0.03 0.03
Matches are distributed among these distances:
40 2 0.02
41 73 0.57
42 52 0.41
ACGTcount: A:0.21, C:0.22, G:0.25, T:0.31
Consensus pattern (42 bp):
GCGATAGTCGAAGTTCGCGTTGCGATTCATTCCAAATTCGTT
Found at i:473152 original size:21 final size:21
Alignment explanation
Indices: 473004--473157 Score: 108
Period size: 21 Copynumber: 7.4 Consensus size: 21
472994 TCGAAGTTCG
473004 CGTTGCGATTCATTCCAAATT
1 CGTTGCGATTCATTCCAAATT
* * *
473025 CGTTGCGA-T-AGTCGAAGTT
1 CGTTGCGATTCATTCCAAATT
473044 CGCGTTGCGATTCATTCCAAA-T
1 --CGTTGCGATTCATTCCAAATT
** * *
473066 CGTTGCGA-T-AGGCGAAGTT
1 CGTTGCGATTCATTCCAAATT
473085 CGCGTTGCGATTCATTCC-AATT
1 --CGTTGCGATTCATTCCAAATT
* * *
473107 CGTTGCGA--CAGTCGAAGTT
1 CGTTGCGATTCATTCCAAATT
473126 CGCGTTGCGATTCATTCCAAATT
1 --CGTTGCGATTCATTCCAAATT
473149 CGTTGCGAT
1 CGTTGCGAT
473158 AGTCCAAATA
Statistics
Matches: 99, Mismatches: 20, Indels: 28
0.67 0.14 0.19
Matches are distributed among these distances:
18 8 0.08
19 12 0.12
20 17 0.17
21 41 0.41
22 6 0.06
23 15 0.15
ACGTcount: A:0.21, C:0.23, G:0.24, T:0.32
Consensus pattern (21 bp):
CGTTGCGATTCATTCCAAATT
Found at i:473263 original size:19 final size:21
Alignment explanation
Indices: 473239--473296 Score: 75
Period size: 24 Copynumber: 2.7 Consensus size: 21
473229 CACGTATTAC
473239 CACGACCACGACCC-A-GGAT
1 CACGACCACGACCCGAGGGAT
473258 CACGACCACGACCCGGGATGGGAT
1 CACGACCACGACCC--GA-GGGAT
473282 CACGACCACGACCCG
1 CACGACCACGACCCG
473297 GGACAGGACG
Statistics
Matches: 34, Mismatches: 0, Indels: 7
0.83 0.00 0.17
Matches are distributed among these distances:
19 14 0.41
22 2 0.06
24 18 0.53
ACGTcount: A:0.28, C:0.41, G:0.26, T:0.05
Consensus pattern (21 bp):
CACGACCACGACCCGAGGGAT
Found at i:473286 original size:24 final size:24
Alignment explanation
Indices: 473254--473299 Score: 92
Period size: 24 Copynumber: 1.9 Consensus size: 24
473244 CCACGACCCA
473254 GGATCACGACCACGACCCGGGATG
1 GGATCACGACCACGACCCGGGATG
473278 GGATCACGACCACGACCCGGGA
1 GGATCACGACCACGACCCGGGA
473300 CAGGACGGCG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.26, C:0.35, G:0.33, T:0.07
Consensus pattern (24 bp):
GGATCACGACCACGACCCGGGATG
Found at i:475480 original size:75 final size:75
Alignment explanation
Indices: 475357--475507 Score: 266
Period size: 75 Copynumber: 2.0 Consensus size: 75
475347 TTGATTTTTC
* *
475357 AGTGTAAATTATGGTTTATTTGCAGCGATGGACATTTCAGAGACTGGAGTTCAAAAGCCTGGTTC
1 AGTGTAAATTATGGTTTATTTGCAGCGATGGACACTTAAGAGACTGGAGTTCAAAAGCCTGGTTC
*
475422 TGCTACTCCA
66 TGCTACACCA
*
475432 AGTGTAAATTATGGTTTATTTGCAGCGATGTACACTTAAGAGACTGGAGTTCAAAAGCCTGGTTC
1 AGTGTAAATTATGGTTTATTTGCAGCGATGGACACTTAAGAGACTGGAGTTCAAAAGCCTGGTTC
475497 TGCTACACCA
66 TGCTACACCA
475507 A
1 A
475508 AACTGTAGGT
Statistics
Matches: 72, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
75 72 1.00
ACGTcount: A:0.28, C:0.17, G:0.23, T:0.31
Consensus pattern (75 bp):
AGTGTAAATTATGGTTTATTTGCAGCGATGGACACTTAAGAGACTGGAGTTCAAAAGCCTGGTTC
TGCTACACCA
Found at i:477879 original size:83 final size:84
Alignment explanation
Indices: 477782--477940 Score: 232
Period size: 84 Copynumber: 1.9 Consensus size: 84
477772 AAAAAATCTC
* * * *
477782 TTAATTTTTATGCTAATTATAGATAACATATTTT-ATAAAAATAATTTACAAACCAAATTAGCAC
1 TTAATTTATATGCTAATTAAAAATAACATATTTTAAAAAAAATAATTTACAAACCAAATTAGCAC
477846 ATT-TTTTTAATGATTATAT
66 -TTATTTTTAATGATTATAT
* * *
477865 TTAATTTATATGCTAATTAAAAATGATATATTTTAAAAAAAATAATTTACATACCAAATTAGCAC
1 TTAATTTATATGCTAATTAAAAATAACATATTTTAAAAAAAATAATTTACAAACCAAATTAGCAC
477930 TTATTTTTAAT
66 TTATTTTTAAT
477941 TTCCTCCATA
Statistics
Matches: 67, Mismatches: 7, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
83 31 0.46
84 36 0.54
ACGTcount: A:0.44, C:0.08, G:0.04, T:0.43
Consensus pattern (84 bp):
TTAATTTATATGCTAATTAAAAATAACATATTTTAAAAAAAATAATTTACAAACCAAATTAGCAC
TTATTTTTAATGATTATAT
Found at i:489039 original size:78 final size:77
Alignment explanation
Indices: 488888--489045 Score: 239
Period size: 77 Copynumber: 2.0 Consensus size: 77
488878 ATACTAAACC
* * *
488888 ACAATAGAAATAAGCGAATCTCCATTTTTGTAAAAAAATATTAAATTAATTATTGGGTAAAGAAA
1 ACAATAGAAATAAGAGAATCTCCA-TTTTGTAAAAAAATATTAAATTAATTATCGGGCAAAGAAA
488953 AATGAAAAAAAAA
65 AATGAAAAAAAAA
*
488966 ACAATAGAAATAAGAGCATCTCCA-TTT-TAAAAAAATATTAAATTTAATTTATCGGGCAAAGAA
1 ACAATAGAAATAAGAGAATCTCCATTTTGTAAAAAAATATTAAA-TTAA-TTATCGGGCAAAGAA
489029 AAATGAAAAAAAAA
64 AAATGAAAAAAAAA
489043 ACA
1 ACA
489046 CTACGTACCC
Statistics
Matches: 74, Mismatches: 4, Indels: 5
0.89 0.05 0.06
Matches are distributed among these distances:
75 15 0.20
76 7 0.09
77 30 0.41
78 22 0.30
ACGTcount: A:0.56, C:0.08, G:0.11, T:0.25
Consensus pattern (77 bp):
ACAATAGAAATAAGAGAATCTCCATTTTGTAAAAAAATATTAAATTAATTATCGGGCAAAGAAAA
ATGAAAAAAAAA
Found at i:492236 original size:26 final size:26
Alignment explanation
Indices: 492185--492236 Score: 61
Period size: 26 Copynumber: 2.0 Consensus size: 26
492175 GATAGACATC
* **
492185 ATTTGAGTTTTCTTTTTTTATTTAAT
1 ATTTGAGTTTTCTTTTTTAACATAAT
492211 ATTTGAGTTTT-TTTTATTAACATAAT
1 ATTTGAGTTTTCTTTT-TTAACATAAT
492237 CTCTAAAATT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
25 4 0.18
26 18 0.82
ACGTcount: A:0.25, C:0.04, G:0.08, T:0.63
Consensus pattern (26 bp):
ATTTGAGTTTTCTTTTTTAACATAAT
Found at i:493915 original size:26 final size:26
Alignment explanation
Indices: 493886--493941 Score: 85
Period size: 26 Copynumber: 2.2 Consensus size: 26
493876 TACTTCATGC
493886 TTATAATTATTGGTGTTAATTAAATG
1 TTATAATTATTGGTGTTAATTAAATG
** *
493912 TTATTGTTTTTGGTGTTAATTAAATG
1 TTATAATTATTGGTGTTAATTAAATG
493938 TTAT
1 TTAT
493942 TGTTTTTGTC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.29, C:0.00, G:0.16, T:0.55
Consensus pattern (26 bp):
TTATAATTATTGGTGTTAATTAAATG
Found at i:493942 original size:26 final size:26
Alignment explanation
Indices: 493895--493949 Score: 110
Period size: 26 Copynumber: 2.1 Consensus size: 26
493885 CTTATAATTA
493895 TTGGTGTTAATTAAATGTTATTGTTT
1 TTGGTGTTAATTAAATGTTATTGTTT
493921 TTGGTGTTAATTAAATGTTATTGTTT
1 TTGGTGTTAATTAAATGTTATTGTTT
493947 TTG
1 TTG
493950 TCTGATAAGG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.22, C:0.00, G:0.20, T:0.58
Consensus pattern (26 bp):
TTGGTGTTAATTAAATGTTATTGTTT
Found at i:510389 original size:40 final size:41
Alignment explanation
Indices: 510309--510415 Score: 117
Period size: 42 Copynumber: 2.6 Consensus size: 41
510299 ACTGTTTGAA
* * * * *
510309 CAGTGCAAAAAATACTGTGTTGATTCAAACAGTGCTGAAAAAT
1 CAGTGAAAAAAAT-CAGT-TTGGTTCAAACAATGCAGAAAAAT
510352 CAGTG-AAAAAATCAGTTTGGTTCAAACAATGCAGAAAAAT
1 CAGTGAAAAAAATCAGTTTGGTTCAAACAATGCAGAAAAAT
* *
510392 AATTGGAAAAAAATCAGTTTGGTT
1 CAGT-GAAAAAAATCAGTTTGGTT
510416 TGAACTGTGC
Statistics
Matches: 56, Mismatches: 6, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
40 23 0.41
41 4 0.07
42 24 0.43
43 5 0.09
ACGTcount: A:0.44, C:0.11, G:0.19, T:0.26
Consensus pattern (41 bp):
CAGTGAAAAAAATCAGTTTGGTTCAAACAATGCAGAAAAAT
Found at i:510403 original size:42 final size:40
Alignment explanation
Indices: 510332--510415 Score: 114
Period size: 40 Copynumber: 2.0 Consensus size: 40
510322 ACTGTGTTGA
* * *
510332 TTCAAACAGTGCTGAAAAATCAGTGAAAAAATCAGTTTGG
1 TTCAAACAATGCAGAAAAATAAGTGAAAAAATCAGTTTGG
*
510372 TTCAAACAATGCAGAAAAATAATTGGAAAAAAATCAGTTTGG
1 TTCAAACAATGCAGAAAAATAAGT-G-AAAAAATCAGTTTGG
510414 TT
1 TT
510416 TGAACTGTGC
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
40 20 0.53
41 1 0.03
42 17 0.45
ACGTcount: A:0.45, C:0.11, G:0.18, T:0.26
Consensus pattern (40 bp):
TTCAAACAATGCAGAAAAATAAGTGAAAAAATCAGTTTGG
Found at i:512348 original size:18 final size:18
Alignment explanation
Indices: 512325--512360 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
512315 TTAATTTCCT
512325 TTATTTATTTATTTGAGA
1 TTATTTATTTATTTGAGA
512343 TTATTTATTTATTTGAGA
1 TTATTTATTTATTTGAGA
512361 AGAAATGAAT
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:0.28, C:0.00, G:0.11, T:0.61
Consensus pattern (18 bp):
TTATTTATTTATTTGAGA
Found at i:513028 original size:24 final size:25
Alignment explanation
Indices: 513001--513056 Score: 71
Period size: 26 Copynumber: 2.2 Consensus size: 25
512991 TGTCTAATAG
*
513001 ATAAAAATTGTA-GTTA-GATGAATT
1 ATAAAAATTCTAGGTTATG-TGAATT
513025 ATAAAAATTCTAGTGTTATGTGAATT
1 ATAAAAATTCTAG-GTTATGTGAATT
513051 ATAAAA
1 ATAAAA
513057 GATACATTAA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
24 11 0.39
26 16 0.57
27 1 0.04
ACGTcount: A:0.46, C:0.02, G:0.14, T:0.38
Consensus pattern (25 bp):
ATAAAAATTCTAGGTTATGTGAATT
Found at i:519642 original size:21 final size:21
Alignment explanation
Indices: 519588--519649 Score: 97
Period size: 21 Copynumber: 3.0 Consensus size: 21
519578 CCAGCTATTC
* * *
519588 CAACAATCCGTACGGGTATTA
1 CAACAACCCGTATGGGAATTA
519609 CAACAACCCGTATGGGAATTA
1 CAACAACCCGTATGGGAATTA
519630 CAACAACCCGTATGGGAATT
1 CAACAACCCGTATGGGAATT
519650 CTTTGCCCTT
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 38 1.00
ACGTcount: A:0.35, C:0.24, G:0.19, T:0.21
Consensus pattern (21 bp):
CAACAACCCGTATGGGAATTA
Found at i:526640 original size:27 final size:27
Alignment explanation
Indices: 526609--526679 Score: 74
Period size: 27 Copynumber: 2.6 Consensus size: 27
526599 GATCATAAGG
*
526609 GTATTTAGGTCATTTTAGTA-CTCGAGT
1 GTATTTAGGTCATTTTAG-AGCTCGAGA
* *
526636 TTATTTTA-GTCATTTTAGAGCTCTAGA
1 GTA-TTTAGGTCATTTTAGAGCTCGAGA
*
526663 GTATTTTGGTCATTTTA
1 GTATTTAGGTCATTTTA
526680 ATCAATTCAG
Statistics
Matches: 36, Mismatches: 5, Indels: 6
0.77 0.11 0.13
Matches are distributed among these distances:
26 4 0.11
27 28 0.78
28 4 0.11
ACGTcount: A:0.23, C:0.10, G:0.18, T:0.49
Consensus pattern (27 bp):
GTATTTAGGTCATTTTAGAGCTCGAGA
Found at i:527702 original size:24 final size:24
Alignment explanation
Indices: 527661--527707 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 24
527651 TTAGCTTGAC
* *
527661 TAAACTGGATCGGATCGGATCGGT
1 TAAACTAGACCGGATCGGATCGGT
* *
527685 TAAACTAGACCGGTTCGGCTCGG
1 TAAACTAGACCGGATCGGATCGG
527708 CTACAGAGAA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.23, C:0.21, G:0.32, T:0.23
Consensus pattern (24 bp):
TAAACTAGACCGGATCGGATCGGT
Found at i:529869 original size:51 final size:51
Alignment explanation
Indices: 529807--530009 Score: 282
Period size: 51 Copynumber: 4.0 Consensus size: 51
529797 ACATTTACAC
*
529807 TTATATATGAATCATATCAATTTAAACTATAATAAATTCAAAAAAATATTA
1 TTATATTTGAATCATATCAATTTAAACTATAATAAATTCAAAAAAATATTA
** *
529858 TTATATTTGAATCATATCAATTTAAACTATAATAAATTCAAAAAGTTATCA
1 TTATATTTGAATCATATCAATTTAAACTATAATAAATTCAAAAAAATATTA
* * * **
529909 TTATATTTGAGTTATATCAATTTGAACTATAATAAATTTTAAAAAATATTA
1 TTATATTTGAATCATATCAATTTAAACTATAATAAATTCAAAAAAATATTA
* *
529960 TTATATTTTAATTATATCAATTTAAACTATAATAAAATT-ATAAAAAATAT
1 TTATATTTGAATCATATCAATTTAAACTATAAT-AAATTCA-AAAAAATAT
530010 AAATAAAAAT
Statistics
Matches: 134, Mismatches: 16, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
51 120 0.90
52 14 0.10
ACGTcount: A:0.49, C:0.06, G:0.03, T:0.41
Consensus pattern (51 bp):
TTATATTTGAATCATATCAATTTAAACTATAATAAATTCAAAAAAATATTA
Found at i:530035 original size:18 final size:18
Alignment explanation
Indices: 530011--530050 Score: 64
Period size: 17 Copynumber: 2.3 Consensus size: 18
530001 AAAAAATATA
530011 AATAAAAATATA-ATTAT
1 AATAAAAATATATATTAT
*
530028 AATAAAAATATATTTTAT
1 AATAAAAATATATATTAT
530046 AATAA
1 AATAA
530051 CTCACTATTA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
17 12 0.57
18 9 0.43
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (18 bp):
AATAAAAATATATATTAT
Found at i:530582 original size:27 final size:27
Alignment explanation
Indices: 530544--530600 Score: 114
Period size: 27 Copynumber: 2.1 Consensus size: 27
530534 AACCAACAGC
530544 ATTGCCAATAGACAACATTAAAATATG
1 ATTGCCAATAGACAACATTAAAATATG
530571 ATTGCCAATAGACAACATTAAAATATG
1 ATTGCCAATAGACAACATTAAAATATG
530598 ATT
1 ATT
530601 TTATGACATC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.47, C:0.14, G:0.11, T:0.28
Consensus pattern (27 bp):
ATTGCCAATAGACAACATTAAAATATG
Found at i:531088 original size:20 final size:21
Alignment explanation
Indices: 531063--531102 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
531053 TGTTTGGTTC
531063 TGAATG-GAACCATTCAGCGT
1 TGAATGTGAACCATTCAGCGT
531083 TGAATGTTGAACCATTCAGC
1 TGAATG-TGAACCATTCAGC
531103 ATTTAGCGTG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 6 0.33
22 12 0.67
ACGTcount: A:0.30, C:0.20, G:0.23, T:0.28
Consensus pattern (21 bp):
TGAATGTGAACCATTCAGCGT
Found at i:537796 original size:23 final size:23
Alignment explanation
Indices: 537768--537812 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
537758 TACTTTATTT
537768 ATTTTTCATTATTTT-TTATTCAG
1 ATTTTT-ATTATTTTATTATTCAG
*
537791 ATTTTTATTTTTTTATTATTCA
1 ATTTTTATTATTTTATTATTCA
537813 TTTTTAGTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 7 0.35
23 13 0.65
ACGTcount: A:0.22, C:0.07, G:0.02, T:0.69
Consensus pattern (23 bp):
ATTTTTATTATTTTATTATTCAG
Found at i:548899 original size:60 final size:60
Alignment explanation
Indices: 548755--548901 Score: 136
Period size: 60 Copynumber: 2.5 Consensus size: 60
548745 AATTTAGGGT
* ** * * *
548755 AAAG-TACACAAATGGTC-CCCGACTATAGGGTATTATTTTATTAAGTCCCTCTATTATTA
1 AAAGTTACA-AAATGATCACCCGACTATAGAATATTATATTATTAAGTCCCTCGACTATTA
* * * * * * *
548814 CATGTTATAAAATGATCATCTGACTATAGAATGTTATATTATTAAGTCTCTCGACTATTA
1 AAAGTTACAAAATGATCACCCGACTATAGAATATTATATTATTAAGTCCCTCGACTATTA
* *
548874 AAAGTTACGAAATGATTACCCGACTATA
1 AAAGTTACAAAATGATCACCCGACTATA
548902 ATTTATCATT
Statistics
Matches: 66, Mismatches: 20, Indels: 3
0.74 0.22 0.03
Matches are distributed among these distances:
59 9 0.14
60 57 0.86
ACGTcount: A:0.35, C:0.16, G:0.13, T:0.35
Consensus pattern (60 bp):
AAAGTTACAAAATGATCACCCGACTATAGAATATTATATTATTAAGTCCCTCGACTATTA
Found at i:548950 original size:39 final size:37
Alignment explanation
Indices: 548891--548965 Score: 105
Period size: 39 Copynumber: 2.0 Consensus size: 37
548881 CGAAATGATT
* *
548891 ACCCGACTATAATTTATCATTTTTTGTTTAAAAATTAAC
1 ACCCGACTATAACTCATCA-TTTTTG-TTAAAAATTAAC
*
548930 ACCCGACTATAACTCGTCATTTTTGTTAAAAATTAA
1 ACCCGACTATAACTCATCATTTTTGTTAAAAATTAA
548966 TGGTTGTCTA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
37 11 0.33
38 6 0.18
39 16 0.48
ACGTcount: A:0.36, C:0.17, G:0.07, T:0.40
Consensus pattern (37 bp):
ACCCGACTATAACTCATCATTTTTGTTAAAAATTAAC
Found at i:550279 original size:14 final size:14
Alignment explanation
Indices: 550225--550282 Score: 70
Period size: 14 Copynumber: 4.4 Consensus size: 14
550215 AGAAATGGAT
550225 TGTTCGTTCATTTA
1 TGTTCGTTCATTTA
*
550239 TGTTTGTTCATTTA
1 TGTTCGTTCATTTA
*
550253 TG-T--TT-ACTTA
1 TGTTCGTTCATTTA
550263 TGTTCGTTCATTTA
1 TGTTCGTTCATTTA
550277 TGTTCG
1 TGTTCG
550283 AACAGAGGGT
Statistics
Matches: 37, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
10 6 0.16
11 3 0.08
13 3 0.08
14 25 0.68
ACGTcount: A:0.14, C:0.12, G:0.16, T:0.59
Consensus pattern (14 bp):
TGTTCGTTCATTTA
Found at i:550587 original size:10 final size:10
Alignment explanation
Indices: 550588--550617 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
550578 GTTTATGTTC
*
550588 GTTCGTTTAC
1 GTTCGTTTAT
550598 GTTCGTTTAT
1 GTTCGTTTAT
550608 GTTCGTTTAT
1 GTTCGTTTAT
550618 CATTTAAATG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.10, C:0.13, G:0.20, T:0.57
Consensus pattern (10 bp):
GTTCGTTTAT
Found at i:550588 original size:14 final size:14
Alignment explanation
Indices: 550569--550614 Score: 64
Period size: 14 Copynumber: 3.6 Consensus size: 14
550559 TGTTTGCTTG
550569 TGTTCGTTCGTTTA
1 TGTTCGTTCGTTTA
550583 TGTTCGTTCGTTTA
1 TGTTCGTTCGTTTA
550597 ----CGTTCGTTTA
1 TGTTCGTTCGTTTA
550607 TGTTCGTT
1 TGTTCGTT
550615 TATCATTTAA
Statistics
Matches: 28, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
10 10 0.36
14 18 0.64
ACGTcount: A:0.07, C:0.15, G:0.22, T:0.57
Consensus pattern (14 bp):
TGTTCGTTCGTTTA
Found at i:552116 original size:15 final size:15
Alignment explanation
Indices: 552096--552211 Score: 60
Period size: 15 Copynumber: 7.6 Consensus size: 15
552086 TCGGGTCGGG
552096 TATATATATTTAAAT
1 TATATATATTTAAAT
*
552111 TATATATATATAAA-
1 TATATATATTTAAAT
* *
552125 TAT-TATATATATAT
1 TATATATATTTAAAT
* *
552139 TTTAATTTAATTTAAAT
1 TAT-ATAT-ATTTAAAT
* *
552156 TAAAT-TAATTAATAT
1 TATATATATTTAA-AT
* *
552171 TATATAT-TATATAT
1 TATATATATTTAAAT
*
552185 ATATATATATTATATAT
1 -TATATATATT-TAAAT
552202 ATATATATAT
1 -TATATATAT
552212 ATAATTATTT
Statistics
Matches: 78, Mismatches: 14, Indels: 16
0.72 0.13 0.15
Matches are distributed among these distances:
13 9 0.12
14 12 0.15
15 29 0.37
16 6 0.08
17 22 0.28
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (15 bp):
TATATATATTTAAAT
Found at i:552183 original size:2 final size:2
Alignment explanation
Indices: 552167--552214 Score: 75
Period size: 2 Copynumber: 25.5 Consensus size: 2
552157 AAATTAATTA
552167 AT AT -T AT AT AT -T AT AT AT AT AT AT AT AT -T AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
552206 AT AT AT AT A
1 AT AT AT AT A
552215 ATTATTTTTA
Statistics
Matches: 43, Mismatches: 0, Indels: 6
0.88 0.00 0.12
Matches are distributed among these distances:
1 3 0.07
2 40 0.93
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:552206 original size:17 final size:17
Alignment explanation
Indices: 552096--552211 Score: 98
Period size: 17 Copynumber: 6.9 Consensus size: 17
552086 TCGGGTCGGG
* *
552096 TATATATATTTAAATTA
1 TATATATATATATATTA
*
552113 TATATATATAAATATTA
1 TATATATATATATATTA
*
552130 TATATATAT-TTTAATT-
1 TATATATATATAT-ATTA
* * *
552146 TA-ATTTAAATTAAATTA
1 TATATATATA-TATATTA
552163 -AT-TAATATTATATATTA
1 TATAT-ATA-TATATATTA
552180 TATATATATATATATTA
1 TATATATATATATATTA
552197 TATATATATATATAT
1 TATATATATATATAT
552212 ATAATTATTT
Statistics
Matches: 78, Mismatches: 12, Indels: 18
0.72 0.11 0.17
Matches are distributed among these distances:
15 4 0.05
16 8 0.10
17 59 0.76
18 6 0.08
19 1 0.01
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (17 bp):
TATATATATATATATTA
Done.