Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009247.1 Hibiscus syriacus cultivar Beakdansim tig00112888_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: 1479039
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 8
Found at i:422236 original size:37 final size:37
Alignment explanation
Indices: 422186--422259 Score: 139
Period size: 37 Copynumber: 2.0 Consensus size: 37
422176 CGGATGTAAC
*
422186 TGGATGGTTCGTGTATCGAAGAGGAAGAGGAAAAATA
1 TGGATGGTTCGTGTATCGAACAGGAAGAGGAAAAATA
422223 TGGATGGTTCGTGTATCGAACAGGAAGAGGAAAAATA
1 TGGATGGTTCGTGTATCGAACAGGAAGAGGAAAAATA
422260 ACATATGAGA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 36 1.00
ACGTcount: A:0.38, C:0.07, G:0.34, T:0.22
Consensus pattern (37 bp):
TGGATGGTTCGTGTATCGAACAGGAAGAGGAAAAATA
Found at i:426308 original size:198 final size:199
Alignment explanation
Indices: 425923--426321 Score: 597
Period size: 198 Copynumber: 2.0 Consensus size: 199
425913 TGATTTTCGG
* * *
425923 TTGGCTCATGCCTCTTAACTATATGGCTTCAATCTTCTAGTACTACTGAGACAGATTTCAACATC
1 TTGGCTCATGCCACTCAACTATATGGCTTCAATCTTCTACTACTACTGAGACAGATTTCAACATC
*
425988 TTTGTCATTCAATTTACAAAAATTTGAATCATAAAAGAAAGACATAGAAACGCCAAAATCTGTAG
66 TTTGTCATTCAATTTACAAAAA-TTGAATCATAAAAGAAAGACATAGAAACACCAAAATCTGTAG
**
426053 CAGAAATGTTGGGAAAGTTCTAAGGCAACAAAAGGAATAAAGGAAATTGAAAGACAAGGTGAATA
130 CAGAAATGTTGGGAAAGTTCTAAAACAACAAAAGGAATAAAGGAAATTGAAAGACAAGGTGAATA
426118 TTCTA
195 TTCTA
* * *
426123 TTGGCTCATGCCACTCAACTATATGGCTTCAATCTTCTTCTACTACTGAGACAGATTTTAGCATC
1 TTGGCTCATGCCACTCAACTATATGGCTTCAATCTTCTACTACTACTGAGACAGATTTCAACATC
* *
426188 TTTGTCATTCAATTTACAAACA-TGAATCATAAAAGAAAGGCATAGAAACACCAAAA-CTTGTAG
66 TTTGTCATTCAATTTACAAAAATTGAATCATAAAAGAAAGACATAGAAACACCAAAATC-TGTAG
* *** * *
426251 CAGAAATGTTGGG-AAGCTTTTAAAACAACAAAAGGAATAAAGGCGGTTGAAAGACAAGGTTAGT
130 CAGAAATGTTGGGAAAG-TTCTAAAACAACAAAAGGAATAAAGGAAATTGAAAGACAAGGTGAAT
426315 ATTCTA
194 ATTCTA
426321 T
1 T
426322 CTAAAAAACT
Statistics
Matches: 180, Mismatches: 17, Indels: 6
0.89 0.08 0.03
Matches are distributed among these distances:
197 4 0.02
198 96 0.53
200 80 0.44
ACGTcount: A:0.39, C:0.16, G:0.17, T:0.28
Consensus pattern (199 bp):
TTGGCTCATGCCACTCAACTATATGGCTTCAATCTTCTACTACTACTGAGACAGATTTCAACATC
TTTGTCATTCAATTTACAAAAATTGAATCATAAAAGAAAGACATAGAAACACCAAAATCTGTAGC
AGAAATGTTGGGAAAGTTCTAAAACAACAAAAGGAATAAAGGAAATTGAAAGACAAGGTGAATAT
TCTA
Found at i:430804 original size:256 final size:259
Alignment explanation
Indices: 430345--430863 Score: 810
Period size: 256 Copynumber: 2.0 Consensus size: 259
430335 GGAAGTGTCT
* *
430345 TAGCACTAATACTAAAATGTCTTAGCAGTGGTACAAAAAGTGCATTCGCACTGAATCAAAAGGGC
1 TAGCACTAATACTAAAATGCCTTAGCACTGGTACAAAAAGTG-ATTCGCACTGAATCAAAAGGGC
*** * *
430410 ATTTTCACTGATACAAAAGTGTCGTAGCAATGGGGAAGAGAAGCCAGACATCTATGCTCGCAGAA
65 ATCCGCACTAATACAAAAGTGACGTAGCAATGGGGAAGAGAAGCCAGACATCTATGCTCGCAGAA
* *
430475 TCGAATAATACATACGTACACTTAAGTAACCCGGGTGTCCTCGTTGTTTCCCGAGTGTCAACAAA
130 TCGAATAATACATACGTACACTCAAGTAACCCGGGTGTACTCGTTGTTTCCCGAGTGTCAACAAA
*
430540 TACTAG-TTTATGTCACATAATTTGATGTTGTTATTCATAAGGGTTCGAGTATTATTATCACTTG
195 GACTAGTTTTATGTCACATAATTTGATGTTGTTATTCATAAGGGTTCGAGTATTATTATCACTTG
* **
430604 TAGCACTAATACTAAAGTGCCTTAGCACTGGTAC-AAAAGTG-TTCGCACTGAATCAAAAGTTCA
1 TAGCACTAATACTAAAATGCCTTAGCACTGGTACAAAAAGTGATTCGCACTGAATCAAAAGGGCA
* * *
430667 TCCGCACTAATACAAAAGTGACGTAGCACTGGGGAAGAGAATCTAGACATCTATGCTCGCAGAAT
66 TCCGCACTAATACAAAAGTGACGTAGCAATGGGGAAGAGAAGCCAGACATCTATGCTCGCAGAAT
* * * * *
430732 CGAATAGTAGATATGTACGCTCAAGTAATCCGGGTGTACTCGTTGTTTCCCGAGTGTCAACAAAG
131 CGAATAATACATACGTACACTCAAGTAACCCGGGTGTACTCGTTGTTTCCCGAGTGTCAACAAAG
*
430797 GCTAGTTTTATGTCACATAATTTGATGTTGTTATTCATAAGGGTTCGAGTATTATTATCACTTG
196 ACTAGTTTTATGTCACATAATTTGATGTTGTTATTCATAAGGGTTCGAGTATTATTATCACTTG
430861 TAG
1 TAG
430864 TCTCATTTAA
Statistics
Matches: 237, Mismatches: 22, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
256 138 0.58
257 61 0.26
258 7 0.03
259 31 0.13
ACGTcount: A:0.32, C:0.18, G:0.21, T:0.29
Consensus pattern (259 bp):
TAGCACTAATACTAAAATGCCTTAGCACTGGTACAAAAAGTGATTCGCACTGAATCAAAAGGGCA
TCCGCACTAATACAAAAGTGACGTAGCAATGGGGAAGAGAAGCCAGACATCTATGCTCGCAGAAT
CGAATAATACATACGTACACTCAAGTAACCCGGGTGTACTCGTTGTTTCCCGAGTGTCAACAAAG
ACTAGTTTTATGTCACATAATTTGATGTTGTTATTCATAAGGGTTCGAGTATTATTATCACTTG
Found at i:431100 original size:18 final size:20
Alignment explanation
Indices: 431057--431104 Score: 66
Period size: 18 Copynumber: 2.5 Consensus size: 20
431047 CTGATATAGT
431057 GTATCGATACTACCTCAATG
1 GTATCGATACTACCTCAATG
431077 GTATCGATACT-CC-C-ATG
1 GTATCGATACTACCTCAATG
431094 AGTATCGATAC
1 -GTATCGATAC
431105 CAAAATGACA
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
17 3 0.11
18 11 0.41
19 2 0.07
20 11 0.41
ACGTcount: A:0.29, C:0.25, G:0.17, T:0.29
Consensus pattern (20 bp):
GTATCGATACTACCTCAATG
Found at i:432263 original size:15 final size:16
Alignment explanation
Indices: 432222--432268 Score: 51
Period size: 16 Copynumber: 2.9 Consensus size: 16
432212 CAATTAAACT
**
432222 ATTCGATATTAAAAAAA
1 ATTC-ATATTAAATTAA
*
432239 ATTCATATTAGATTAA
1 ATTCATATTAAATTAA
432255 ATT-ATATTAAATTA
1 ATTCATATTAAATTA
432269 TGGGTGAACT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
15 10 0.38
16 12 0.46
17 4 0.15
ACGTcount: A:0.51, C:0.04, G:0.04, T:0.40
Consensus pattern (16 bp):
ATTCATATTAAATTAA
Found at i:439358 original size:22 final size:22
Alignment explanation
Indices: 439324--439372 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 22
439314 TAGCACTGGT
* *
439324 AAGTGCATTCACACTGAAT-CAA
1 AAGTGAATCCACACT-AATACAA
439346 AAGTGAATCCACACTAATACAA
1 AAGTGAATCCACACTAATACAA
439368 AAGTG
1 AAGTG
439373 TCGTGGCACT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 3 0.12
22 21 0.88
ACGTcount: A:0.45, C:0.20, G:0.14, T:0.20
Consensus pattern (22 bp):
AAGTGAATCCACACTAATACAA
Found at i:440260 original size:64 final size:63
Alignment explanation
Indices: 440170--440324 Score: 195
Period size: 64 Copynumber: 2.4 Consensus size: 63
440160 TGCACCCATT
* * *
440170 TCGAATGCATTTTGTGTACCGATGCACAAGCTATGCATCGATGCACTCTTGAAAAT-TTTGAAAC
1 TCGAATGCATTTT-TGTACCGATGCACAAACCATGCATCGATGCACTCCTG--AATCTTTGAAAC
440234 A
63 A
* **
440235 TCGAATGCATTTTTGTACCGATGCACAAACCATGCATCGATTCACTCCTGGCTCTTTGAAACA
1 TCGAATGCATTTTTGTACCGATGCACAAACCATGCATCGATGCACTCCTGAATCTTTGAAACA
**
440298 TCGAATGCAATTAGTGTACCGATGCAC
1 TCGAATGC-ATTTTTGTACCGATGCAC
440325 CCCTAGTGTA
Statistics
Matches: 80, Mismatches: 8, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
62 1 0.01
63 17 0.21
64 49 0.61
65 13 0.16
ACGTcount: A:0.29, C:0.23, G:0.18, T:0.30
Consensus pattern (63 bp):
TCGAATGCATTTTTGTACCGATGCACAAACCATGCATCGATGCACTCCTGAATCTTTGAAACA
Found at i:448354 original size:12 final size:13
Alignment explanation
Indices: 448324--448349 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
448314 GAGTAATTTG
448324 TAATTTCAAAAAT
1 TAATTTCAAAAAT
448337 TAATTTCAAAAAT
1 TAATTTCAAAAAT
448350 GATTTTCCAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.54, C:0.08, G:0.00, T:0.38
Consensus pattern (13 bp):
TAATTTCAAAAAT
Found at i:454558 original size:23 final size:23
Alignment explanation
Indices: 454532--454581 Score: 73
Period size: 23 Copynumber: 2.2 Consensus size: 23
454522 GTAGTGGGAA
* *
454532 AAGGAGGTATGAGATGGCAAGAG
1 AAGGAGGTAAGAGATAGCAAGAG
*
454555 AAGGAGGTAAGAGATAGCTAGAG
1 AAGGAGGTAAGAGATAGCAAGAG
454578 AAGG
1 AAGG
454582 CACATGACTG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.42, C:0.04, G:0.42, T:0.12
Consensus pattern (23 bp):
AAGGAGGTAAGAGATAGCAAGAG
Found at i:456824 original size:31 final size:30
Alignment explanation
Indices: 456774--456859 Score: 79
Period size: 31 Copynumber: 2.9 Consensus size: 30
456764 GTTTTAATCC
* * *
456774 AAAAAAATATTCTAAATACTTAT-TTCGACT
1 AAAAATATATTTTAGATACTTATATT-GACT
* *
456804 -AAAATGATAATTTTAGATACTCATATTGATT
1 AAAAAT-AT-ATTTTAGATACTTATATTGACT
456835 AAAAATATATTTTAGATA-TTATATT
1 AAAAATATATTTTAGATACTTATATT
456860 CTTTTAAATA
Statistics
Matches: 46, Mismatches: 6, Indels: 9
0.75 0.10 0.15
Matches are distributed among these distances:
29 10 0.22
30 12 0.26
31 17 0.37
32 7 0.15
ACGTcount: A:0.45, C:0.07, G:0.06, T:0.42
Consensus pattern (30 bp):
AAAAATATATTTTAGATACTTATATTGACT
Found at i:462359 original size:103 final size:103
Alignment explanation
Indices: 462180--462383 Score: 266
Period size: 103 Copynumber: 2.0 Consensus size: 103
462170 AAAACATATT
* * * * * *
462180 AGCACACACAATGCTATCATATCATAATCATAATATGCAAACAAAGTGCAATCACATCAGAAATA
1 AGCACACACAATGCTATCACATCAGAATCATAACATGCAAACAAAGTGAAATCACATAAAAAATA
* * * *
462245 TACTAGTGTACCTACCGGTAACACTACTGTATATCATA
66 TACCAGTGTACCCACCGGTAACACCACAGTATATCATA
* * * *
462283 AGCACACA-AAGTGCTATCACATCGGATTCATAACATGCACACAAAGTGAAATCATATAAAAAAT
1 AGCACACACAA-TGCTATCACATCAGAATCATAACATGCAAACAAAGTGAAATCACATAAAAAAT
462347 ATACCAGTGTACCCACCGGTAACACCACAGTATATCA
65 ATACCAGTGTACCCACCGGTAACACCACAGTATATCA
462384 ATCACTCCAC
Statistics
Matches: 86, Mismatches: 14, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
102 2 0.02
103 84 0.98
ACGTcount: A:0.42, C:0.24, G:0.12, T:0.23
Consensus pattern (103 bp):
AGCACACACAATGCTATCACATCAGAATCATAACATGCAAACAAAGTGAAATCACATAAAAAATA
TACCAGTGTACCCACCGGTAACACCACAGTATATCATA
Found at i:467290 original size:22 final size:22
Alignment explanation
Indices: 467265--467315 Score: 84
Period size: 22 Copynumber: 2.3 Consensus size: 22
467255 TAATACGAAT
* *
467265 GCACTTTTGTATTAGTGCTAAG
1 GCACTTTAGTATTAGTGCCAAG
467287 GCACTTTAGTATTAGTGCCAAG
1 GCACTTTAGTATTAGTGCCAAG
467309 GCACTTT
1 GCACTTT
467316 CGTTATTAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.24, C:0.18, G:0.22, T:0.37
Consensus pattern (22 bp):
GCACTTTAGTATTAGTGCCAAG
Found at i:472388 original size:23 final size:22
Alignment explanation
Indices: 472359--472421 Score: 90
Period size: 23 Copynumber: 2.8 Consensus size: 22
472349 CTCCTACAGG
472359 GGGGAATCGGTTCCCCTTCAAAA
1 GGGGAATCGGTTCCCCTTC-AAA
*
472382 GGGGAATCGGTTCCCCTTCAAG
1 GGGGAATCGGTTCCCCTTCAAA
* *
472404 GGGGTATCGATTCCCCTT
1 GGGGAATCGGTTCCCCTT
472422 GCACCAAAAC
Statistics
Matches: 37, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
22 18 0.49
23 19 0.51
ACGTcount: A:0.19, C:0.27, G:0.29, T:0.25
Consensus pattern (22 bp):
GGGGAATCGGTTCCCCTTCAAA
Found at i:472412 original size:22 final size:22
Alignment explanation
Indices: 472335--472421 Score: 84
Period size: 22 Copynumber: 3.9 Consensus size: 22
472325 CAGAACCTCC
* * * *
472335 AGGGGGTATTGATTCTCCTACA
1 AGGGGGAATCGATTCCCCTTCA
* *
472357 GGGGGGAATCGGTTCCCCTTCAA
1 AGGGGGAATCGATTCCCCTTC-A
* *
472380 AAGGGGAATCGGTTCCCCTTCA
1 AGGGGGAATCGATTCCCCTTCA
*
472402 AGGGGGTATCGATTCCCCTT
1 AGGGGGAATCGATTCCCCTT
472422 GCACCAAAAC
Statistics
Matches: 53, Mismatches: 11, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
22 33 0.62
23 20 0.38
ACGTcount: A:0.20, C:0.24, G:0.30, T:0.26
Consensus pattern (22 bp):
AGGGGGAATCGATTCCCCTTCA
Found at i:476214 original size:33 final size:33
Alignment explanation
Indices: 476177--476246 Score: 131
Period size: 33 Copynumber: 2.1 Consensus size: 33
476167 CAATAAAAAG
*
476177 TTTGCTAAAAGTTAGAATAGTAAAATATATACA
1 TTTGCTAAAAGTTAGAATAGAAAAATATATACA
476210 TTTGCTAAAAGTTAGAATAGAAAAATATATACA
1 TTTGCTAAAAGTTAGAATAGAAAAATATATACA
476243 TTTG
1 TTTG
476247 AACACATAAG
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.47, C:0.06, G:0.13, T:0.34
Consensus pattern (33 bp):
TTTGCTAAAAGTTAGAATAGAAAAATATATACA
Found at i:479235 original size:91 final size:91
Alignment explanation
Indices: 479077--479242 Score: 233
Period size: 91 Copynumber: 1.8 Consensus size: 91
479067 GGAATGTCAA
* *** * *
479077 TTCTTCTCATTATGAACTCATTCTCCCTCGTTGGTTGAGTTCTTCTCATTATGAACTCTCAACTG
1 TTCTTCTCATTATGAACTCATTCTCCCTCATTGGACAAGTCCTTCTCATTATGAACCCTCAACTG
*
479142 AAAATCTTGAACTAAGGTTGAACAAG
66 AAAATATTGAACTAAGGTTGAACAAG
* * * *
479168 TTCTTCTTATTATGAACTTATTCTCCCTCATTGGACAAGTCCTTCTCATTATGAACCCTCTATTG
1 TTCTTCTCATTATGAACTCATTCTCCCTCATTGGACAAGTCCTTCTCATTATGAACCCTCAACTG
479233 AAAATATTGA
66 AAAATATTGA
479243 GTCACCTCAT
Statistics
Matches: 64, Mismatches: 11, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
91 64 1.00
ACGTcount: A:0.27, C:0.22, G:0.12, T:0.39
Consensus pattern (91 bp):
TTCTTCTCATTATGAACTCATTCTCCCTCATTGGACAAGTCCTTCTCATTATGAACCCTCAACTG
AAAATATTGAACTAAGGTTGAACAAG
Found at i:479391 original size:105 final size:105
Alignment explanation
Indices: 479161--479451 Score: 318
Period size: 105 Copynumber: 2.7 Consensus size: 105
479151 AACTAAGGTT
* * * *
479161 GAACAAGTTCTTCTTATTATGAACTTATTCTCCCTCATT-GGACAAGTCCTTCTCATTATGAACC
1 GAACAAGTTATTCTCATTATGAAC--ATTCT-CCT--TTAGGACGAGTTCTTCTCATTATGAA--
* * * *
479225 CTCTAT-TGAAAATATTGAGTCACCTCATTCTACGGTGGACTTGGAAG
59 CTCT-TCTGGAAATGTTGAGTCACCTCATTCTACGGTGAACTTGAAAG
* * * *
479272 GAACACGTTCTTCTCATTATGAACTTTCTCTTTTAGGACGAGTTCTTCTCATTATGAACTCTTCT
1 GAACAAGTTATTCTCATTATGAACATTCTCCTTTAGGACGAGTTCTTCTCATTATGAACTCTTCT
* * *
479337 GGAAATGTTG-GTTCACCTCCTTCTATGGTGAATTTGAAAG
66 GGAAATGTTGAG-TCACCTCATTCTACGGTGAACTTGAAAG
*
479377 GAACAAGTTATTCTCATTATGAACATTCTCCTTTAGGACGAGTTCTTCTCATTATGAACTTTTCA
1 GAACAAGTTATTCTCATTATGAACATTCTCCTTTAGGACGAGTTCTTCTCATTATGAACTCTTC-
479442 TTGGAAATGT
65 -TGGAAATGT
479452 CGATCCTCAA
Statistics
Matches: 157, Mismatches: 18, Indels: 14
0.83 0.10 0.07
Matches are distributed among these distances:
104 2 0.01
105 95 0.61
106 2 0.01
107 30 0.19
108 2 0.01
109 4 0.03
111 22 0.14
ACGTcount: A:0.26, C:0.20, G:0.16, T:0.38
Consensus pattern (105 bp):
GAACAAGTTATTCTCATTATGAACATTCTCCTTTAGGACGAGTTCTTCTCATTATGAACTCTTCT
GGAAATGTTGAGTCACCTCATTCTACGGTGAACTTGAAAG
Found at i:479697 original size:135 final size:136
Alignment explanation
Indices: 479416--479844 Score: 668
Period size: 135 Copynumber: 3.2 Consensus size: 136
479406 CCTTTAGGAC
* * * *
479416 GAGTTCTTCTCATTATGAACTTTTC-ATTGGAAATGTCGAT-CCTCAAGCGAGGCT-TCACTGGT
1 GAGTTCTTCTCATTATGAAC-TCTCAATTGGAAATGTCAATCCCTCAAGTGAGG-TGTCACTGAT
* *
479478 TCGAAATACCGTGAATCGAGTGATAGGTCAAACAAGCTCTTATCATTATGAACTTCTTCTCCCTC
64 TCGAAATACCGTGAATCGAGTGATAGGTCGAACAAGCTCTTCTCATTATGAACTTCTTCTCCCTC
*
479543 TGTCAGAT
129 TGTCGGAT
479551 GAGTTCTTCTCATTATGAACTCTCAATTGGAAATGTCAATCCCTCAAGTGAGGTGTCACTGATTC
1 GAGTTCTTCTCATTATGAACTCTCAATTGGAAATGTCAATCCCTCAAGTGAGGTGTCACTGATTC
*
479616 GAAATACCGTGAATCGAGTAATAGGTCGAACAAGCTCTTCTCATTATGAACTTCTTCT-CCTCTG
66 GAAATACCGTGAATCGAGTGATAGGTCGAACAAGCTCTTCTCATTATGAACTTCTTCTCCCTCTG
479680 TCGGAT
131 TCGGAT
* * *
479686 GAGTTCTTCTCATTCTGAACTCTCAATTGGAAATATCAATCCCTCAAGTGAGGTGTTACTGATTC
1 GAGTTCTTCTCATTATGAACTCTCAATTGGAAATGTCAATCCCTCAAGTGAGGTGTCACTGATTC
* * * * *
479751 AAAATGCCGTGAATCAAGTGATAGGTCGAACAAGCTCTTCTCATTATGAACTCCTTCTCCCTCTT
66 GAAATACCGTGAATCGAGTGATAGGTCGAACAAGCTCTTCTCATTATGAACTTCTTCTCCCTCTG
479816 TCGGAT
131 TCGGAT
479822 GAGTTCTTCTCATTATGAACTCT
1 GAGTTCTTCTCATTATGAACTCT
479845 GTACTGGAAA
Statistics
Matches: 272, Mismatches: 18, Indels: 7
0.92 0.06 0.02
Matches are distributed among these distances:
134 3 0.01
135 161 0.59
136 108 0.40
ACGTcount: A:0.26, C:0.23, G:0.18, T:0.34
Consensus pattern (136 bp):
GAGTTCTTCTCATTATGAACTCTCAATTGGAAATGTCAATCCCTCAAGTGAGGTGTCACTGATTC
GAAATACCGTGAATCGAGTGATAGGTCGAACAAGCTCTTCTCATTATGAACTTCTTCTCCCTCTG
TCGGAT
Found at i:480209 original size:36 final size:37
Alignment explanation
Indices: 480128--480578 Score: 214
Period size: 40 Copynumber: 11.6 Consensus size: 37
480118 TGTCTTAAGT
* * ** * *
480128 GAGA-AAAATTTGGTTTTAAGAAAAACCATCTCAAGG
1 GAGATAAAATTTTGTTTCAAGGGAAACTATCTCAAGC
* * *
480164 GAGACAAAA-TTTGTTTCAAGGGAAACTGTCTCAAGA
1 GAGATAAAATTTTGTTTCAAGGGAAACTATCTCAAGC
480200 GAGATAAAA-TTTGTTTCAAGGGAAACTATCTCAAGC
1 GAGATAAAATTTTGTTTCAAGGGAAACTATCTCAAGC
* *
480236 GAGATAAAATCTTTTGTTTCGAGGGAAACTATCTAAAGC
1 GAGATAAAA--TTTTGTTTCAAGGGAAACTATCTCAAGC
* * ** *
480275 GAGATAAAATCTTCTGTTTCAAGGAAAAACAATCTTGAGT
1 GAGATAAAAT-TT-TGTTTCAAGG-GAAACTATCTCAAGC
* * * *
480315 GAGATAAAATCTTTTGTTTCAAGGAAAAACAATCTTGAA-T
1 GAGATAAAA--TTTTGTTTCAAGG-GAAACTATC-TCAAGC
* * * *
480355 GAGATAAAATCTTCTGTTTCAAGGAAAAATAATCTTGAA-T
1 GAGATAAAAT-TT-TGTTTCAAGGGAAACT-ATC-TCAAGC
* * * *
480395 GAGATAAAATCTTCTGTTTCAAGGAAAAACAATCTTGAA-T
1 GAGATAAAAT-TT-TGTTTCAAGG-GAAACTATC-TCAAGC
* * ** *
480435 GAGATAAAATCTTCTGTTTCAAGGAAAAACAATCTTGAGT
1 GAGATAAAAT-TT-TGTTTCAAGG-GAAACTATCTCAAGC
* * **
480475 GAGATAAAATCTTATGTTTCAAGGAAAAACAATCTTGAGC
1 GAGATAAAAT-TT-TGTTTCAAGG-GAAACTATCTCAAGC
* * * *
480515 GAGATAAAATCTTCTATTTCAAGGAAAAACAATCTTGAA-C
1 GAGATAAAAT-TT-TGTTTCAAGG-GAAACTATC-TCAAGC
*
480555 GAGATAAAATCTTCTATTTCAAGG
1 GAGATAAAAT-TT-TGTTTCAAGG
480579 AAAAACAATC
Statistics
Matches: 367, Mismatches: 32, Indels: 28
0.86 0.07 0.07
Matches are distributed among these distances:
36 66 0.18
37 5 0.01
38 3 0.01
39 51 0.14
40 231 0.63
41 10 0.03
42 1 0.00
ACGTcount: A:0.41, C:0.12, G:0.17, T:0.29
Consensus pattern (37 bp):
GAGATAAAATTTTGTTTCAAGGGAAACTATCTCAAGC
Found at i:480245 original size:72 final size:73
Alignment explanation
Indices: 480118--480338 Score: 194
Period size: 72 Copynumber: 2.9 Consensus size: 73
480108 AAGAGAAGCT
* * * * *
480118 TGTCTTAAGTGAGA-AAAATTTGGTTTTAAGAAAAACCATCTCAAGGGAGACAAAA-TTTGTTTC
1 TGTCTAAAGAGAGATAAAATTT-GTTTCAAGGAAAACCATCTCAAGCGAGACAAAATTTTGTTTC
480181 AAGGGAAAC
65 AAGGGAAAC
* * * *
480190 TGTCTCAAGAGAGATAAAATTTGTTTCAAGGGAAACTATCTCAAGCGAGATAAAATCTTTTGTTT
1 TGTCTAAAGAGAGATAAAATTTGTTTCAAGGAAAACCATCTCAAGCGAGACAAAA--TTTTGTTT
*
480255 CGAGGGAAAC
64 CAAGGGAAAC
* * * ** * *
480265 TATCTAAAGCGAGATAAAATCTTCTGTTTCAAGGAAAAACAATCTTGAGTGAGATAAAATCTTTT
1 TGTCTAAAGAGAGATAAAA--TT-TGTTTCAAGG-AAAACCATCTCAAGCGAGACAAAA--TTTT
480330 GTTTCAAGG
60 GTTTCAAGG
480339 AAAAACAATC
Statistics
Matches: 123, Mismatches: 18, Indels: 9
0.82 0.12 0.06
Matches are distributed among these distances:
72 39 0.32
73 7 0.06
75 32 0.26
77 2 0.02
78 10 0.08
79 33 0.27
ACGTcount: A:0.38, C:0.12, G:0.20, T:0.30
Consensus pattern (73 bp):
TGTCTAAAGAGAGATAAAATTTGTTTCAAGGAAAACCATCTCAAGCGAGACAAAATTTTGTTTCA
AGGGAAAC
Found at i:480326 original size:40 final size:40
Alignment explanation
Indices: 480236--480599 Score: 559
Period size: 40 Copynumber: 9.1 Consensus size: 40
480226 TATCTCAAGC
* * * * ** *
480236 GAGATAAAATCTTTTGTTTCGAGG-GAAACTATCTAAAGC
1 GAGATAAAATCTTCTGTTTCAAGGAAAAACAATCTTGAGT
480275 GAGATAAAATCTTCTGTTTCAAGGAAAAACAATCTTGAGT
1 GAGATAAAATCTTCTGTTTCAAGGAAAAACAATCTTGAGT
* *
480315 GAGATAAAATCTTTTGTTTCAAGGAAAAACAATCTTGAAT
1 GAGATAAAATCTTCTGTTTCAAGGAAAAACAATCTTGAGT
* *
480355 GAGATAAAATCTTCTGTTTCAAGGAAAAATAATCTTGAAT
1 GAGATAAAATCTTCTGTTTCAAGGAAAAACAATCTTGAGT
*
480395 GAGATAAAATCTTCTGTTTCAAGGAAAAACAATCTTGAAT
1 GAGATAAAATCTTCTGTTTCAAGGAAAAACAATCTTGAGT
480435 GAGATAAAATCTTCTGTTTCAAGGAAAAACAATCTTGAGT
1 GAGATAAAATCTTCTGTTTCAAGGAAAAACAATCTTGAGT
* *
480475 GAGATAAAATCTTATGTTTCAAGGAAAAACAATCTTGAGC
1 GAGATAAAATCTTCTGTTTCAAGGAAAAACAATCTTGAGT
* **
480515 GAGATAAAATCTTCTATTTCAAGGAAAAACAATCTTGAAC
1 GAGATAAAATCTTCTGTTTCAAGGAAAAACAATCTTGAGT
*
480555 GAGATAAAATCTTCTATTTCAAGGAAAAACAATCTTGAGT
1 GAGATAAAATCTTCTGTTTCAAGGAAAAACAATCTTGAGT
480595 GAGAT
1 GAGAT
480600 GAATCCTCTG
Statistics
Matches: 304, Mismatches: 20, Indels: 1
0.94 0.06 0.00
Matches are distributed among these distances:
39 22 0.07
40 282 0.93
ACGTcount: A:0.41, C:0.12, G:0.16, T:0.30
Consensus pattern (40 bp):
GAGATAAAATCTTCTGTTTCAAGGAAAAACAATCTTGAGT
Found at i:480423 original size:20 final size:20
Alignment explanation
Indices: 480360--480423 Score: 53
Period size: 20 Copynumber: 3.2 Consensus size: 20
480350 TGAATGAGAT
480360 AAAATCTTCTGTTTCAAGGA
1 AAAATCTTCTGTTTCAAGGA
** *
480380 AAAATAATC---TTGAATGAGA
1 AAAATCTTCTGTTTCAA-G-GA
480399 TAAAATCTTCTGTTTCAAGGA
1 -AAAATCTTCTGTTTCAAGGA
480420 AAAA
1 AAAA
480424 CAATCTTGAA
Statistics
Matches: 32, Mismatches: 6, Indels: 12
0.64 0.12 0.24
Matches are distributed among these distances:
17 4 0.12
18 1 0.03
19 2 0.06
20 18 0.56
21 2 0.06
22 1 0.03
23 4 0.12
ACGTcount: A:0.44, C:0.11, G:0.14, T:0.31
Consensus pattern (20 bp):
AAAATCTTCTGTTTCAAGGA
Found at i:480428 original size:23 final size:23
Alignment explanation
Indices: 480402--480470 Score: 62
Period size: 23 Copynumber: 3.3 Consensus size: 23
480392 AATGAGATAA
480402 AATCTTCTGTTTCAAGGAAAAAC
1 AATCTTCTGTTTCAAGGAAAAAC
* *
480425 AATC-T-TG----AATGAGATAA-
1 AATCTTCTGTTTCAAGGA-AAAAC
480442 AATCTTCTGTTTCAAGGAAAAAC
1 AATCTTCTGTTTCAAGGAAAAAC
480465 AATCTT
1 AATCTT
480471 GAGTGAGATA
Statistics
Matches: 34, Mismatches: 4, Indels: 16
0.63 0.07 0.30
Matches are distributed among these distances:
17 8 0.24
18 4 0.12
19 2 0.06
21 2 0.06
22 4 0.12
23 14 0.41
ACGTcount: A:0.41, C:0.14, G:0.13, T:0.32
Consensus pattern (23 bp):
AATCTTCTGTTTCAAGGAAAAAC
Found at i:480548 original size:23 final size:23
Alignment explanation
Indices: 480522--480590 Score: 60
Period size: 23 Copynumber: 3.3 Consensus size: 23
480512 AGCGAGATAA
480522 AATCTTCTATTTCAAGGAAAAAC
1 AATCTTCTATTTCAAGGAAAAAC
* * * *
480545 AATCTT-GA--ACGA-G-ATAA-
1 AATCTTCTATTTCAAGGAAAAAC
480562 AATCTTCTATTTCAAGGAAAAAC
1 AATCTTCTATTTCAAGGAAAAAC
480585 AATCTT
1 AATCTT
480591 GAGTGAGATG
Statistics
Matches: 32, Mismatches: 8, Indels: 12
0.62 0.15 0.23
Matches are distributed among these distances:
17 6 0.19
18 4 0.12
19 1 0.03
20 4 0.12
21 1 0.03
22 4 0.12
23 12 0.38
ACGTcount: A:0.43, C:0.16, G:0.10, T:0.30
Consensus pattern (23 bp):
AATCTTCTATTTCAAGGAAAAAC
Found at i:483440 original size:9 final size:9
Alignment explanation
Indices: 483426--483512 Score: 90
Period size: 9 Copynumber: 9.6 Consensus size: 9
483416 TTTCATTTCA
483426 TTTCTTTAT
1 TTTCTTTAT
483435 TTTCTTTATT
1 TTTCTTTA-T
483445 TTCTCTTTAT
1 TT-TCTTTAT
483455 TTTCTTTAT
1 TTTCTTTAT
483464 TTTCTTT-T
1 TTTCTTTAT
*
483472 TTCCTTT-T
1 TTTCTTTAT
*
483480 TTTCTTTTTT
1 TTTC-TTTAT
*
483490 TTTCTTTTT
1 TTTCTTTAT
483499 TTTCCTTT-T
1 TTT-CTTTAT
483508 TTTCT
1 TTTCT
483513 CTGATGGATG
Statistics
Matches: 71, Mismatches: 2, Indels: 11
0.85 0.02 0.13
Matches are distributed among these distances:
8 13 0.18
9 37 0.52
10 15 0.21
11 6 0.08
ACGTcount: A:0.05, C:0.15, G:0.00, T:0.80
Consensus pattern (9 bp):
TTTCTTTAT
Found at i:483462 original size:29 final size:26
Alignment explanation
Indices: 483426--483512 Score: 113
Period size: 28 Copynumber: 3.2 Consensus size: 26
483416 TTTCATTTCA
483426 TTTCTTTATTTTCTTTATTTTCTCTTTAT
1 TTTCTTTATTTTCTTT-TTTTC-CTTT-T
483455 TTTCTTTATTTTC-TTTTTTCCTTTT
1 TTTCTTTATTTTCTTTTTTTCCTTTT
*
483480 TTTCTTTTTTTTTCTTTTTTTTCCTTTT
1 TTTC-TTTATTTTC-TTTTTTTCCTTTT
483508 TTTCT
1 TTTCT
483513 CTGATGGATG
Statistics
Matches: 54, Mismatches: 1, Indels: 8
0.86 0.02 0.13
Matches are distributed among these distances:
25 5 0.09
26 12 0.22
27 6 0.11
28 18 0.33
29 13 0.24
ACGTcount: A:0.05, C:0.15, G:0.00, T:0.80
Consensus pattern (26 bp):
TTTCTTTATTTTCTTTTTTTCCTTTT
Found at i:483489 original size:10 final size:10
Alignment explanation
Indices: 483476--483510 Score: 61
Period size: 10 Copynumber: 3.5 Consensus size: 10
483466 TCTTTTTTCC
483476 TTTTTTTCTT
1 TTTTTTTCTT
483486 TTTTTTTCTT
1 TTTTTTTCTT
*
483496 TTTTTTCCTT
1 TTTTTTTCTT
483506 TTTTT
1 TTTTT
483511 CTCTGATGGA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
10 24 1.00
ACGTcount: A:0.00, C:0.11, G:0.00, T:0.89
Consensus pattern (10 bp):
TTTTTTTCTT
Found at i:483492 original size:19 final size:20
Alignment explanation
Indices: 483468--483510 Score: 70
Period size: 19 Copynumber: 2.2 Consensus size: 20
483458 CTTTATTTTC
483468 TTTTTTCCTTTTTTT-CTTT
1 TTTTTTCCTTTTTTTCCTTT
*
483487 TTTTTTCTTTTTTTTCCTTT
1 TTTTTTCCTTTTTTTCCTTT
483507 TTTT
1 TTTT
483511 CTCTGATGGA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
19 14 0.64
20 8 0.36
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (20 bp):
TTTTTTCCTTTTTTTCCTTT
Found at i:486419 original size:55 final size:53
Alignment explanation
Indices: 486332--486481 Score: 162
Period size: 55 Copynumber: 2.7 Consensus size: 53
486322 TTTAAAGGAA
486332 GTCTTCAATCAGCTTT-AGATTTCTTCATTCATCAGATATCTTTCTTCACAG-ATCT
1 GTCTTCAATCAG-TTTAAGATTTCTTCATTCATC-GATATCTTTCTTCA-AGAAT-T
* * * * *
486387 GTCTTCAATCTGTTTAAGATTTCTTCAATCATCGAATGTTTTTCTTCATGAATT
1 GTCTTCAATCAGTTTAAGATTTCTTCATTCATCG-ATATCTTTCTTCAAGAATT
486441 GTTCTTCAATCAGTTTCAA-ATTTCTTCATTCATCGGATATC
1 G-TCTTCAATCAGTTT-AAGATTTCTTCATTCATC-GATATC
486482 CAATTTCATG
Statistics
Matches: 80, Mismatches: 9, Indels: 12
0.79 0.09 0.12
Matches are distributed among these distances:
54 7 0.09
55 70 0.88
56 3 0.04
ACGTcount: A:0.24, C:0.21, G:0.10, T:0.45
Consensus pattern (53 bp):
GTCTTCAATCAGTTTAAGATTTCTTCATTCATCGATATCTTTCTTCAAGAATT
Found at i:488368 original size:35 final size:35
Alignment explanation
Indices: 488329--488402 Score: 139
Period size: 35 Copynumber: 2.1 Consensus size: 35
488319 CAATAAAAAG
*
488329 TTTGCTAAAAGTTAGAATAGTAAAATATATATACA
1 TTTGCTAAAAGTTAGAATAGAAAAATATATATACA
488364 TTTGCTAAAAGTTAGAATAGAAAAATATATATACA
1 TTTGCTAAAAGTTAGAATAGAAAAATATATATACA
488399 TTTG
1 TTTG
488403 AACACATAAG
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 38 1.00
ACGTcount: A:0.47, C:0.05, G:0.12, T:0.35
Consensus pattern (35 bp):
TTTGCTAAAAGTTAGAATAGAAAAATATATATACA
Found at i:496418 original size:19 final size:19
Alignment explanation
Indices: 496394--496430 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
496384 TGCATTGGGC
496394 TATGAACATGAAAATAAGA
1 TATGAACATGAAAATAAGA
* *
496413 TATGAATATGAAATTAAG
1 TATGAACATGAAAATAAG
496431 TTATCAATCT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.54, C:0.03, G:0.16, T:0.27
Consensus pattern (19 bp):
TATGAACATGAAAATAAGA
Found at i:496450 original size:18 final size:19
Alignment explanation
Indices: 496401--496452 Score: 61
Period size: 19 Copynumber: 2.8 Consensus size: 19
496391 GGCTATGAAC
* *
496401 ATGAAAATAAGATATGAAT
1 ATGAAAATAAGTTATCAAT
*
496420 ATGAAATTAAGTTATCAAT
1 ATGAAAATAAGTTATCAAT
*
496439 CT-AAAATAAGTTAT
1 ATGAAAATAAGTTAT
496453 GAGTCCGAAA
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
18 11 0.39
19 17 0.61
ACGTcount: A:0.52, C:0.04, G:0.12, T:0.33
Consensus pattern (19 bp):
ATGAAAATAAGTTATCAAT
Found at i:496524 original size:13 final size:13
Alignment explanation
Indices: 496499--496559 Score: 65
Period size: 13 Copynumber: 4.8 Consensus size: 13
496489 CTAAAATGGG
496499 ATATGAATA-TGAA
1 ATATGAA-AGTGAA
*
496512 ATGTGAAAGTG-A
1 ATATGAAAGTGAA
496524 ATATGAAAGTGAA
1 ATATGAAAGTGAA
*
496537 ATATGAAAAT-AA
1 ATATGAAAGTGAA
496549 GATATGAAAGT
1 -ATATGAAAGT
496560 TTTGTATTTT
Statistics
Matches: 41, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
12 14 0.34
13 27 0.66
ACGTcount: A:0.52, C:0.00, G:0.21, T:0.26
Consensus pattern (13 bp):
ATATGAAAGTGAA
Found at i:496526 original size:19 final size:18
Alignment explanation
Indices: 496502--496537 Score: 63
Period size: 19 Copynumber: 1.9 Consensus size: 18
496492 AAATGGGATA
496502 TGAATATGAAATGTGAAAG
1 TGAATATGAAA-GTGAAAG
496521 TGAATATGAAAGTGAAA
1 TGAATATGAAAGTGAAA
496538 TATGAAAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 6 0.35
19 11 0.65
ACGTcount: A:0.50, C:0.00, G:0.25, T:0.25
Consensus pattern (18 bp):
TGAATATGAAAGTGAAAG
Found at i:496637 original size:39 final size:39
Alignment explanation
Indices: 496591--496671 Score: 117
Period size: 39 Copynumber: 2.1 Consensus size: 39
496581 AAAGAATATA
* * *
496591 ATATGACTATTATGTATGATATTGTTTATCATGACTTTG
1 ATATGACTATTATGTATGACACTATTTATCATGACTTTG
* *
496630 ATATGACTATTATGTATGACGCTATTTATCATGAGTTTG
1 ATATGACTATTATGTATGACACTATTTATCATGACTTTG
496669 ATA
1 ATA
496672 AAATCATGAG
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
39 37 1.00
ACGTcount: A:0.30, C:0.09, G:0.16, T:0.46
Consensus pattern (39 bp):
ATATGACTATTATGTATGACACTATTTATCATGACTTTG
Found at i:497937 original size:20 final size:20
Alignment explanation
Indices: 497912--497949 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
497902 CATTCATGCA
*
497912 TCTAGTTCGTTGAATAAAAT
1 TCTAGTTCATTGAATAAAAT
497932 TCTAGTTCATTGAATAAA
1 TCTAGTTCATTGAATAAA
497950 GTTGGTTCAT
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:0.37, C:0.11, G:0.13, T:0.39
Consensus pattern (20 bp):
TCTAGTTCATTGAATAAAAT
Found at i:498001 original size:17 final size:17
Alignment explanation
Indices: 497933--498003 Score: 63
Period size: 17 Copynumber: 4.2 Consensus size: 17
497923 GAATAAAATT
*
497933 CTAGTTCATTGAATAAA
1 CTAGTTCATTTAATAAA
* * *
497950 GTTGGTTCA-TTAATAAT
1 -CTAGTTCATTTAATAAA
* *
497967 CTAGTTCATTCAACAAA
1 CTAGTTCATTTAATAAA
*
497984 CTAGTTCATTTATTAAA
1 CTAGTTCATTTAATAAA
498001 CTA
1 CTA
498004 ACTCTTAATT
Statistics
Matches: 40, Mismatches: 12, Indels: 3
0.73 0.22 0.05
Matches are distributed among these distances:
16 6 0.15
17 28 0.70
18 6 0.15
ACGTcount: A:0.37, C:0.14, G:0.10, T:0.39
Consensus pattern (17 bp):
CTAGTTCATTTAATAAA
Found at i:500497 original size:22 final size:19
Alignment explanation
Indices: 500467--500508 Score: 50
Period size: 21 Copynumber: 2.1 Consensus size: 19
500457 TAAAAGAAGC
500467 ATGAAAGTTAGAGAAAAGAAA
1 ATGAAAGTT-G-GAAAAGAAA
500488 ATGAAGAGTTGGAAAA-AAA
1 ATGAA-AGTTGGAAAAGAAA
500507 AT
1 AT
500509 TTCTACTAAC
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
19 5 0.25
20 5 0.25
21 6 0.30
22 4 0.20
ACGTcount: A:0.60, C:0.00, G:0.24, T:0.17
Consensus pattern (19 bp):
ATGAAAGTTGGAAAAGAAA
Found at i:502012 original size:20 final size:18
Alignment explanation
Indices: 501979--502061 Score: 84
Period size: 17 Copynumber: 4.7 Consensus size: 18
501969 TCATTCATGC
* *
501979 ATCTAATTCGTTGAATAAA
1 ATCTAGTTCATTGAAT-AA
501998 ATTCTAGTTCATTGAATAA
1 A-TCTAGTTCATTGAATAA
502017 AGT-TAGTTCATT-AATAA
1 A-TCTAGTTCATTGAATAA
*
502034 A-CTAGTTCATTCAATAA
1 ATCTAGTTCATTGAATAA
502051 A-CTAGTTCATT
1 ATCTAGTTCATT
502062 TATTAAACTA
Statistics
Matches: 58, Mismatches: 3, Indels: 8
0.84 0.04 0.12
Matches are distributed among these distances:
16 9 0.16
17 22 0.38
18 9 0.16
19 5 0.09
20 13 0.22
ACGTcount: A:0.39, C:0.12, G:0.10, T:0.40
Consensus pattern (18 bp):
ATCTAGTTCATTGAATAA
Found at i:502034 original size:17 final size:17
Alignment explanation
Indices: 502001--502071 Score: 90
Period size: 17 Copynumber: 4.2 Consensus size: 17
501991 GAATAAAATT
*
502001 CTAGTTCATTGAATAAA
1 CTAGTTCATTCAATAAA
*
502018 GTTAGTTCATT-AATAAA
1 -CTAGTTCATTCAATAAA
502035 CTAGTTCATTCAATAAA
1 CTAGTTCATTCAATAAA
* *
502052 CTAGTTCATTTATTAAA
1 CTAGTTCATTCAATAAA
502069 CTA
1 CTA
502072 ACTCTTAATT
Statistics
Matches: 48, Mismatches: 4, Indels: 3
0.87 0.07 0.05
Matches are distributed among these distances:
16 9 0.19
17 30 0.62
18 9 0.19
ACGTcount: A:0.39, C:0.13, G:0.08, T:0.39
Consensus pattern (17 bp):
CTAGTTCATTCAATAAA
Found at i:508894 original size:22 final size:21
Alignment explanation
Indices: 508846--508917 Score: 65
Period size: 22 Copynumber: 3.3 Consensus size: 21
508836 ATTCTCTTCC
*
508846 CAGTGTTATGACACTTTTGTA-
1 CAGTGTGA-GACACTTTTGTAT
*
508867 CTAGTGTGAATACACTTTTGTAT
1 C-AGTGTG-AGACACTTTTGTAT
*
508890 CAGTGTTGAGACACTTTAGTAT
1 CAGTG-TGAGACACTTTTGTAT
*
508912 TAGTGT
1 CAGTGT
508918 CAAGGCACTT
Statistics
Matches: 42, Mismatches: 5, Indels: 8
0.76 0.09 0.15
Matches are distributed among these distances:
21 2 0.05
22 36 0.86
23 4 0.10
ACGTcount: A:0.25, C:0.12, G:0.21, T:0.42
Consensus pattern (21 bp):
CAGTGTGAGACACTTTTGTAT
Found at i:508927 original size:44 final size:44
Alignment explanation
Indices: 508846--508929 Score: 107
Period size: 44 Copynumber: 1.9 Consensus size: 44
508836 ATTCTCTTCC
* * *
508846 CAGTGTTATGACACTTTTGTACTAGTGTGAATACACTTTTGTAT
1 CAGTGTTATGACACTTTAGTACTAGTGTCAAGACACTTTTGTAT
* *
508890 CAGTGTTGA-GACACTTTAGTATTAGTGTCAAGGCACTTTT
1 CAGTGTT-ATGACACTTTAGTACTAGTGTCAAGACACTTTT
508930 ATTATTAAAT
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
44 33 0.97
45 1 0.03
ACGTcount: A:0.25, C:0.14, G:0.20, T:0.40
Consensus pattern (44 bp):
CAGTGTTATGACACTTTAGTACTAGTGTCAAGACACTTTTGTAT
Found at i:513936 original size:11 final size:11
Alignment explanation
Indices: 513901--513942 Score: 50
Period size: 11 Copynumber: 3.9 Consensus size: 11
513891 ACCTCTCATT
*
513901 ATTTTTAATTC
1 ATTTATAATTC
*
513912 ATTTATATTTC
1 ATTTATAATTC
*
513923 ATTTATAATAC
1 ATTTATAATTC
513934 ATTT-TAATT
1 ATTTATAATT
513943 ATTAAATTAA
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
10 4 0.15
11 22 0.85
ACGTcount: A:0.33, C:0.07, G:0.00, T:0.60
Consensus pattern (11 bp):
ATTTATAATTC
Found at i:516564 original size:19 final size:20
Alignment explanation
Indices: 516532--516569 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 20
516522 TGTGTTTAAT
**
516532 TTTACTTTTTATG-CAAATA
1 TTTACTTTGAATGCCAAATA
516551 TTTACTTTGAATGCCAAAT
1 TTTACTTTGAATGCCAAAT
516570 GTTTGAACTA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 11 0.69
20 5 0.31
ACGTcount: A:0.32, C:0.13, G:0.08, T:0.47
Consensus pattern (20 bp):
TTTACTTTGAATGCCAAATA
Found at i:522291 original size:37 final size:37
Alignment explanation
Indices: 522214--522291 Score: 84
Period size: 37 Copynumber: 2.1 Consensus size: 37
522204 TCGAAGGGCT
* * * * *
522214 ATATCCCCATTTTGATTTTTGTTTATGATTGGGATCC
1 ATATCCCCATTTTGATTTCTATTTATAACTGAGATCC
* * *
522251 ATATCCCCATTTTGATTTCTATTTCTAACTGATATTC
1 ATATCCCCATTTTGATTTCTATTTATAACTGAGATCC
522288 ATAT
1 ATAT
522292 TATGATTTGG
Statistics
Matches: 33, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
37 33 1.00
ACGTcount: A:0.23, C:0.18, G:0.10, T:0.49
Consensus pattern (37 bp):
ATATCCCCATTTTGATTTCTATTTATAACTGAGATCC
Found at i:524806 original size:13 final size:13
Alignment explanation
Indices: 524788--524813 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
524778 AAGGAAAAAC
524788 AATATATATATAT
1 AATATATATATAT
524801 AATATATATATAT
1 AATATATATATAT
524814 TTCTTTGATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (13 bp):
AATATATATATAT
Found at i:535983 original size:18 final size:19
Alignment explanation
Indices: 535948--535984 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
535938 CACGGAATGT
535948 AAGATTACCAGTGGGAATAA
1 AAGATTACCAG-GGGAATAA
535968 AAGATTACCA-GGGAATA
1 AAGATTACCAGGGGAATA
535985 GGATTACTGG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 7 0.41
20 10 0.59
ACGTcount: A:0.46, C:0.11, G:0.24, T:0.19
Consensus pattern (19 bp):
AAGATTACCAGGGGAATAA
Found at i:538230 original size:28 final size:30
Alignment explanation
Indices: 538173--538249 Score: 79
Period size: 28 Copynumber: 2.6 Consensus size: 30
538163 AATTCTATTT
* *
538173 AATATATAATATATATATAATTTTTTAAAA
1 AATATATAATATATATATAATTTCTGAAAA
*
538203 AATATAT-ATA-ATATATAGTTTCTGAAAA
1 AATATATAATATATATATAATTTCTGAAAA
* *
538231 TAT-TTTGAATATATATATA
1 AATATAT-AATATATATATA
538250 TATAATATAG
Statistics
Matches: 39, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
27 2 0.05
28 17 0.44
29 6 0.15
30 14 0.36
ACGTcount: A:0.49, C:0.01, G:0.04, T:0.45
Consensus pattern (30 bp):
AATATATAATATATATATAATTTCTGAAAA
Found at i:538247 original size:39 final size:37
Alignment explanation
Indices: 538201--538350 Score: 201
Period size: 38 Copynumber: 4.0 Consensus size: 37
538191 AATTTTTTAA
*
538201 AAAATATATATAATATATAGTTTCTGAAAATATTTTG
1 AAAATATATATAATATATAGTTTTTGAAAATATTTTG
* * *
538238 AATATATATATATATAATATAGTTTTTGAAAACAATTTG
1 AAAATATATATA-AT-ATATAGTTTTTGAAAATATTTTG
* *
538277 AAAATTTATATAATATATAGTTTTTGAAAAATATTTTA
1 AAAATATATATAATATATAGTTTTTG-AAAATATTTTG
* *
538315 AAAATATATATAATATATAGTTTTTTAAAACATTTT
1 AAAATATATATAATATATAGTTTTTGAAAATATTTT
538351 ATATATAATT
Statistics
Matches: 98, Mismatches: 12, Indels: 6
0.84 0.10 0.05
Matches are distributed among these distances:
37 32 0.33
38 36 0.37
39 30 0.31
ACGTcount: A:0.47, C:0.02, G:0.06, T:0.45
Consensus pattern (37 bp):
AAAATATATATAATATATAGTTTTTGAAAATATTTTG
Found at i:538362 original size:24 final size:24
Alignment explanation
Indices: 538327--538374 Score: 78
Period size: 24 Copynumber: 2.0 Consensus size: 24
538317 AATATATATA
* *
538327 ATATATAGTTTTTTAAAACATTTT
1 ATATATAATTTTTGAAAACATTTT
538351 ATATATAATTTTTGAAAACATTTT
1 ATATATAATTTTTGAAAACATTTT
538375 GAAAATATAT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.40, C:0.04, G:0.04, T:0.52
Consensus pattern (24 bp):
ATATATAATTTTTGAAAACATTTT
Found at i:538411 original size:5 final size:5
Alignment explanation
Indices: 538403--538597 Score: 327
Period size: 5 Copynumber: 39.0 Consensus size: 5
538393 TAGTTTTTGA
538403 ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT
1 ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT
538453 ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT
1 ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT
* * *
538503 ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAC ATTAC ATTAC
1 ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT
* * * *
538553 ATTAC ATTAC ATTAC ATTAC ATTAT ATTAT ATTAT ATTAT ATTAT
1 ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT
538598 TTGTTATTTT
Statistics
Matches: 188, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
5 188 1.00
ACGTcount: A:0.40, C:0.04, G:0.00, T:0.56
Consensus pattern (5 bp):
ATTAT
Found at i:538642 original size:20 final size:18
Alignment explanation
Indices: 538599--538645 Score: 51
Period size: 17 Copynumber: 2.5 Consensus size: 18
538589 TTATATTATT
538599 TGTTATTTTTCTTTTTTTA
1 TGTTA-TTTTCTTTTTTTA
*
538618 T-TTATTTTCTTTCCTTTTG
1 TGTTATTTTCTTT--TTTTA
538637 TGTTATTTT
1 TGTTATTTT
538646 GTCCTTAAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
17 8 0.33
18 3 0.12
19 6 0.25
20 7 0.29
ACGTcount: A:0.09, C:0.09, G:0.06, T:0.77
Consensus pattern (18 bp):
TGTTATTTTCTTTTTTTA
Found at i:542084 original size:16 final size:16
Alignment explanation
Indices: 542063--542102 Score: 80
Period size: 16 Copynumber: 2.5 Consensus size: 16
542053 TTTAACCATT
542063 CATTTATATGCATTTA
1 CATTTATATGCATTTA
542079 CATTTATATGCATTTA
1 CATTTATATGCATTTA
542095 CATTTATA
1 CATTTATA
542103 CGTTTAAAAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.33, C:0.12, G:0.05, T:0.50
Consensus pattern (16 bp):
CATTTATATGCATTTA
Found at i:542714 original size:18 final size:19
Alignment explanation
Indices: 542691--542729 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
542681 CGCATAAAAA
* *
542691 ATGTCCCGAATGACCA-AT
1 ATGTCCCAAAGGACCACAT
542709 ATGTCCCAAAGGACCACAT
1 ATGTCCCAAAGGACCACAT
542728 AT
1 AT
542730 CACATATGTC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 14 0.78
19 4 0.22
ACGTcount: A:0.36, C:0.28, G:0.15, T:0.21
Consensus pattern (19 bp):
ATGTCCCAAAGGACCACAT
Found at i:545877 original size:16 final size:16
Alignment explanation
Indices: 545858--545896 Score: 51
Period size: 18 Copynumber: 2.3 Consensus size: 16
545848 CATAACTTAA
545858 CAATATCTTATAATTC
1 CAATATCTTATAATTC
*
545874 CAATACATTTTATAATTC
1 CAAT--ATCTTATAATTC
545892 CAATA
1 CAATA
545897 CATTTCTATC
Statistics
Matches: 20, Mismatches: 1, Indels: 4
0.80 0.04 0.16
Matches are distributed among these distances:
16 5 0.25
18 15 0.75
ACGTcount: A:0.41, C:0.18, G:0.00, T:0.41
Consensus pattern (16 bp):
CAATATCTTATAATTC
Found at i:545886 original size:18 final size:18
Alignment explanation
Indices: 545865--545901 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
545855 TAACAATATC
545865 TTATAATTCCAATACATT
1 TTATAATTCCAATACATT
545883 TTATAATTCCAATACATT
1 TTATAATTCCAATACATT
545901 T
1 T
545902 CTATCATATA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.38, C:0.16, G:0.00, T:0.46
Consensus pattern (18 bp):
TTATAATTCCAATACATT
Found at i:549411 original size:20 final size:20
Alignment explanation
Indices: 549386--549460 Score: 114
Period size: 20 Copynumber: 3.8 Consensus size: 20
549376 CGAAACTCCC
*
549386 ATGCATCAATGCACCCCTTA
1 ATGCATCGATGCACCCCTTA
549406 ATGCATCGATGCACCCCTTA
1 ATGCATCGATGCACCCCTTA
*
549426 TTGCATCGATGCACCCCTTA
1 ATGCATCGATGCACCCCTTA
* *
549446 TTGCATCGATACACC
1 ATGCATCGATGCACC
549461 TTCAAATTTT
Statistics
Matches: 52, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 52 1.00
ACGTcount: A:0.25, C:0.35, G:0.13, T:0.27
Consensus pattern (20 bp):
ATGCATCGATGCACCCCTTA
Found at i:552159 original size:23 final size:23
Alignment explanation
Indices: 552129--552200 Score: 65
Period size: 23 Copynumber: 3.1 Consensus size: 23
552119 GTTCTACGCA
552129 GTCCTTCAGGACAATTATATGTG
1 GTCCTTCAGGACAATTATATGTG
* * * *
552152 GTCCTTCAGAACATTTCTATGCG
1 GTCCTTCAGGACAATTATATGTG
* * *
552175 GTACTTCGGGATAA-TACTATGTG
1 GTCCTTCAGGACAATTA-TATGTG
552198 GTC
1 GTC
552201 ATTCGAGACA
Statistics
Matches: 36, Mismatches: 12, Indels: 2
0.72 0.24 0.04
Matches are distributed among these distances:
22 1 0.03
23 35 0.97
ACGTcount: A:0.24, C:0.19, G:0.22, T:0.35
Consensus pattern (23 bp):
GTCCTTCAGGACAATTATATGTG
Found at i:552228 original size:23 final size:24
Alignment explanation
Indices: 552146--552253 Score: 68
Period size: 23 Copynumber: 4.6 Consensus size: 24
552136 AGGACAATTA
552146 TATGTGGTC-CTTC-AGAACATTTC
1 TATGTGG-CACTTCGAGAACATTTC
* * * *
552169 TATGCGGTACTTCGGGATA-A-TAC
1 TATGTGGCACTTCGAGA-ACATTTC
552192 TATGTGGTCA-TTCGAG-ACATTTC
1 TATGTGG-CACTTCGAGAACATTTC
*
552215 TATGTGGCACTTCGGTGCAA-ATTTC
1 TATGTGGCACTTC-GAG-AACATTTC
*
552240 TACGTGGCACTTCG
1 TATGTGGCACTTCG
552254 GTGTAATTTA
Statistics
Matches: 65, Mismatches: 10, Indels: 19
0.69 0.11 0.20
Matches are distributed among these distances:
21 1 0.02
22 3 0.05
23 35 0.54
24 7 0.11
25 18 0.28
26 1 0.02
ACGTcount: A:0.21, C:0.20, G:0.23, T:0.35
Consensus pattern (24 bp):
TATGTGGCACTTCGAGAACATTTC
Found at i:552267 original size:24 final size:25
Alignment explanation
Indices: 552218--552267 Score: 75
Period size: 25 Copynumber: 2.0 Consensus size: 25
552208 ACATTTCTAT
*
552218 GTGGCACTTCGGTGCAAATTTCTAC
1 GTGGCACTTCGGTGCAAATTTATAC
*
552243 GTGGCACTTCGGTG-TAATTTATAC
1 GTGGCACTTCGGTGCAAATTTATAC
552267 G
1 G
552268 AGTTTTGGTG
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 9 0.39
25 14 0.61
ACGTcount: A:0.20, C:0.20, G:0.26, T:0.34
Consensus pattern (25 bp):
GTGGCACTTCGGTGCAAATTTATAC
Found at i:561504 original size:17 final size:16
Alignment explanation
Indices: 561482--561516 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 16
561472 AGCTCTTCTC
561482 TCTAATTCTCTCCATAG
1 TCTAATTCTCTCCA-AG
561499 TCTAATTCTCTCCAAG
1 TCTAATTCTCTCCAAG
561515 TC
1 TC
561517 CAAATCTCCT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 4 0.22
17 14 0.78
ACGTcount: A:0.23, C:0.31, G:0.06, T:0.40
Consensus pattern (16 bp):
TCTAATTCTCTCCAAG
Found at i:564340 original size:18 final size:18
Alignment explanation
Indices: 564313--564350 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
564303 ATTCAGAAGT
564313 TTCTTCCTTTTAGTTTTG
1 TTCTTCCTTTTAGTTTTG
*
564331 TTCTTGCTTTTAGTTTTG
1 TTCTTCCTTTTAGTTTTG
564349 TT
1 TT
564351 ATTTGTTGTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.05, C:0.13, G:0.13, T:0.68
Consensus pattern (18 bp):
TTCTTCCTTTTAGTTTTG
Found at i:564474 original size:13 final size:13
Alignment explanation
Indices: 564456--564480 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
564446 TGAGGATTCT
564456 TGAAGGTTCTTTA
1 TGAAGGTTCTTTA
564469 TGAAGGTTCTTT
1 TGAAGGTTCTTT
564481 GGAAAATGGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.20, C:0.08, G:0.24, T:0.48
Consensus pattern (13 bp):
TGAAGGTTCTTTA
Found at i:570024 original size:13 final size:13
Alignment explanation
Indices: 570006--570032 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
569996 ACACACACAC
570006 ATATATATATATA
1 ATATATATATATA
570019 ATATATATATATA
1 ATATATATATATA
570032 A
1 A
570033 CATCGGCTCG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (13 bp):
ATATATATATATA
Found at i:571064 original size:17 final size:17
Alignment explanation
Indices: 571025--571078 Score: 54
Period size: 17 Copynumber: 3.0 Consensus size: 17
571015 CTCTTATATT
*
571025 AATAAAAAATGATATTATAA
1 AATAAAATAT-ATATT-T-A
571045 AATAAAATATATATTTA
1 AATAAAATATATATTTA
* *
571062 AATAATATTTATATTTA
1 AATAAAATATATATTTA
571079 TTATTTTAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
17 16 0.52
18 1 0.03
19 5 0.16
20 9 0.29
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (17 bp):
AATAAAATATATATTTA
Found at i:571068 original size:20 final size:21
Alignment explanation
Indices: 571018--571068 Score: 54
Period size: 20 Copynumber: 2.5 Consensus size: 21
571008 ATAAGCACTC
*
571018 TTATATTAATAAAAAATGATA
1 TTATAATAATAAAAAATGATA
*
571039 TTATAA-AATAAAATAT-ATA
1 TTATAATAATAAAAAATGATA
571058 TT-TAAATAATA
1 TTAT-AATAATA
571069 TTTATATTTA
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
18 1 0.04
19 7 0.27
20 13 0.50
21 5 0.19
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (21 bp):
TTATAATAATAAAAAATGATA
Found at i:571851 original size:14 final size:15
Alignment explanation
Indices: 571739--571857 Score: 123
Period size: 15 Copynumber: 7.5 Consensus size: 15
571729 TAATAAGGTT
571739 ATTTATTTTAAAATA
1 ATTTATTTTAAAATA
571754 ATTTATTTTAAAATA
1 ATTTATTTTAAAATA
*
571769 ATTTATTATAAAATA
1 ATTTATTTTAAAATA
*
571784 ATCTATTTTAAAATA
1 ATTTATTTTAAAATA
* *
571799 AATTATTATAAAATATGGA
1 ATTTATT-TTAAA-AT--A
571818 TTGATTTATTTTTAAAATA
1 ---ATTTA-TTTTAAAATA
571837 ATTTATTTT-AAATA
1 ATTTATTTTAAAATA
571851 ATTTATT
1 ATTTATT
571858 AGTATGGATT
Statistics
Matches: 88, Mismatches: 8, Indels: 17
0.78 0.07 0.15
Matches are distributed among these distances:
14 12 0.14
15 51 0.58
16 9 0.10
17 2 0.02
19 2 0.02
21 2 0.02
22 8 0.09
23 2 0.02
ACGTcount: A:0.45, C:0.01, G:0.03, T:0.51
Consensus pattern (15 bp):
ATTTATTTTAAAATA
Found at i:571874 original size:18 final size:18
Alignment explanation
Indices: 571851--571907 Score: 59
Period size: 18 Copynumber: 3.4 Consensus size: 18
571841 ATTTTAAATA
571851 ATTTATTAGTATGGATTG
1 ATTTATTAGTATGGATTG
* * *
571869 ATTTATT--T-T-AAATA
1 ATTTATTAGTATGGATTG
571883 ATTTATTAGTATGGATTG
1 ATTTATTAGTATGGATTG
571901 ATTTATT
1 ATTTATT
571908 TTAAAATATG
Statistics
Matches: 29, Mismatches: 6, Indels: 8
0.67 0.14 0.19
Matches are distributed among these distances:
14 9 0.31
15 1 0.03
16 2 0.07
17 1 0.03
18 16 0.55
ACGTcount: A:0.32, C:0.00, G:0.14, T:0.54
Consensus pattern (18 bp):
ATTTATTAGTATGGATTG
Found at i:571875 original size:32 final size:32
Alignment explanation
Indices: 571837--572324 Score: 341
Period size: 32 Copynumber: 16.4 Consensus size: 32
571827 TTTTAAAATA
571837 ATTTATTTTAAATAATTTATTAGTATGGATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTG
571869 ATTTATTTTAAATAATTTATTAGTATGGATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTG
571901 ATTTA-TTT---TAA---A--A-TATGGATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTG
*
571923 ATTTATTTTAAATAATTTATTAGTATGAATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTG
** **
571955 ATTTATTTTAAA-ATATGGATT-G-ATTTATT-
1 ATTTATTTTAAATA-ATTTATTAGTATGGATTG
* * * * * *
571984 ATTGTAGTTGTATGGATTGATTTATT--T-T-AAATA
1 ATT-TA-TT-T-T-AAATAATTTATTAGTATGGATTG
* * * ** * *
572017 ATTTATTAGTATGGATTGATTTATT--T-TAAAATA
1 ATTTATT--T-T-AAATAATTTATTAGTATGGATTG
572050 ATTTATTTTAAATAATTTATTAGTATGGATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTG
* *
572082 ATTTA--TT--GT-A---GTT-GTATGGATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTG
572105 ATTTATTTTAAATAATTTATTAGTATGGATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTG
572137 ATTTATTTT--A-AA---A-TA-T-T-GATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTG
572159 ATTTATTTTAAATAATTTATTAGTATGGATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTG
* *
572191 ATTTA--TT--AT--TGTAGTT-GTATGAATTG
1 ATTTATTTTAAATAATTTA-TTAGTATGGATTG
572217 ATTTATTTTAAATAATTTATTAGTATGGATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTG
572249 ATTTATTTTAAATAATTTATTAGTATGGATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTG
*
572281 ATTTATTTTAAATAATTTATTAATATGGATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTG
572313 ATTTATTTTAAA
1 ATTTATTTTAAA
572325 ATATGGATTG
Statistics
Matches: 377, Mismatches: 28, Indels: 102
0.74 0.06 0.20
Matches are distributed among these distances:
22 28 0.07
23 20 0.05
24 4 0.01
25 7 0.02
26 21 0.06
27 4 0.01
28 10 0.03
29 17 0.05
30 16 0.04
31 17 0.05
32 210 0.56
33 17 0.05
34 6 0.02
ACGTcount: A:0.34, C:0.00, G:0.13, T:0.53
Consensus pattern (32 bp):
ATTTATTTTAAATAATTTATTAGTATGGATTG
Found at i:571908 original size:80 final size:79
Alignment explanation
Indices: 571716--572197 Score: 290
Period size: 80 Copynumber: 6.0 Consensus size: 79
571706 TATTAAAATA
*
571716 ATTTTAAATAATTTA--A-TAAGG-TTATTTA-TTTTAAAATAATTTATTTTAAAATAATTTATT
1 ATTTTAAATAATTTATTAGTATGGATTATTTATTTTTAAAATAATTTATTTT-AAATAATTTATT
* * *
571776 A-TA--AAATAATCT
65 AGTATGAATTGATTT
* *
571788 ATTTTAAAATAAATTATTATAAAATATGGATTGATTTATTTTTAAAATAATTTATTTTAAATAAT
1 ATTTT-AAAT-AA-T-TTAT-TAGTATGGATT-ATTTATTTTTAAAATAATTTATTTTAAATAAT
*
571853 TTATTAGTATGGATTGATTT
60 TTATTAGTATGAATTGATTT
*
571873 ATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGATTTATTTTAAATAA
1 ATTTTAAATAATTTATTAGTATGGATT-ATTTATTTTTAAA-AT--A---ATTTATTTTAAATAA
571938 TTTATTAGTATGAATTGATTT
59 TTTATTAGTATGAATTGATTT
** ** * ** * *
571959 ATTTTAAA-ATATGGATT-G-ATTTATTATTGTAGTTGTATGGATTGATTTATTTTAAATAATTT
1 ATTTTAAATA-ATTTATTAGTATGGATTATT-TA-TT-TTTAAAATAATTTATTTTAAATAATTT
*
572021 ATTAGTATGGATTGATTT
62 ATTAGTATGAATTGATTT
** * ** * * *
572039 ATTTTAAAATAATTTATT--T-TAAATAATTTA---TTAGTATGGATTGA-TTT--AT--TGTAG
1 ATTTT-AAATAATTTATTAGTATGGATTATTTATTTTTAAAAT-AATTTATTTTAAATAATTTA-
*
572093 TT-GTATGGATTGATTT
63 TTAGTATGAATTGATTT
*
572109 ATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATTGATTGATTTATTTTAAATAA
1 ATTTTAAATAATTTATTAGTATGGATT-ATTTATTTTTAAA-A-T-A---ATTTATTTTAAATAA
*
572174 TTTATTAGTATGGATTGATTT
59 TTTATTAGTATGAATTGATTT
572195 ATT
1 ATT
572198 ATTGTAGTTG
Statistics
Matches: 323, Mismatches: 40, Indels: 80
0.73 0.09 0.18
Matches are distributed among these distances:
69 12 0.04
70 22 0.07
71 3 0.01
72 10 0.03
73 9 0.03
74 8 0.02
75 6 0.02
76 5 0.02
77 1 0.00
78 2 0.01
79 3 0.01
80 72 0.22
81 20 0.06
82 23 0.07
83 27 0.08
84 13 0.04
85 17 0.05
86 70 0.22
ACGTcount: A:0.37, C:0.00, G:0.11, T:0.52
Consensus pattern (79 bp):
ATTTTAAATAATTTATTAGTATGGATTATTTATTTTTAAAATAATTTATTTTAAATAATTTATTA
GTATGAATTGATTT
Found at i:571917 original size:22 final size:22
Alignment explanation
Indices: 571892--571934 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
571882 AATTTATTAG
571892 TATGGATTGATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAAA
571914 TATGGATTGATTTATTTTAAA
1 TATGGATTGATTTATTTTAAA
571935 TAATTTATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.35, C:0.00, G:0.14, T:0.51
Consensus pattern (22 bp):
TATGGATTGATTTATTTTAAAA
Found at i:571929 original size:54 final size:54
Alignment explanation
Indices: 571860--571983 Score: 239
Period size: 54 Copynumber: 2.3 Consensus size: 54
571850 AATTTATTAG
*
571860 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATGAATTGATTTATTTTAAAA
571914 TATGGATTGATTTATTTTAAATAATTTATTAGTATGAATTGATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATGAATTGATTTATTTTAAAA
571968 TATGGATTGATTTATT
1 TATGGATTGATTTATT
571984 ATTGTAGTTG
Statistics
Matches: 69, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
54 69 1.00
ACGTcount: A:0.35, C:0.00, G:0.13, T:0.52
Consensus pattern (54 bp):
TATGGATTGATTTATTTTAAATAATTTATTAGTATGAATTGATTTATTTTAAAA
Found at i:571955 original size:134 final size:127
Alignment explanation
Indices: 571769--572301 Score: 484
Period size: 134 Copynumber: 4.2 Consensus size: 127
571759 TTTTAAAATA
* * * *
571769 ATTTATTATAAAATAATCTATTTTAAAATAAATTATTATAAAATATGGATTGATTTATTTTTAAA
1 ATTTATTTTAAAATAATTTATTTT-AAAT-AA-T-TTAT-TAGTATGGATTGATTTATTTTTAAA
571834 ATAATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAATAATTTATTAGTATGGAT
61 ATAATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAATAATTTATTAGTATGGAT
571899 TG
126 TG
*
571901 ATTTATTTTAAAATATGGATTGATTTATTTTAAATAATTTATTAGTATGAATTGATTTA-TTTTA
1 ATTTATTTT-AAA-AT--A---ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTTA
* *
571965 AAATATGGATTGA-TTT--ATTATTGTAGTT-GTATGGATTGATTTATTTTAAATAATTTATTAG
59 AAATA---ATTTATTTTAAATAATT-TA-TTAGTATGGATTGATTTATTTTAAATAATTTATTAG
572026 TATGGATTG
119 TATGGATTG
572035 ATTTATTTTAAAATAATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTGTAGTTGTATG
1 ATTTATTTTAAAATAATTTATTTTAAATAATTTATTAGTATGGATTGATTTA-T-T--TT-TA--
* * *
572100 GATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTT--A-AA---A-TA-T-T-G
59 AAATAATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAATAATTTATTAGTATGG
572155 ATTG
124 ATTG
* ** ** * * *
572159 ATTTATTTT-AAATAATTTA--TT-AGT-ATGGATT-G-ATTTATT-ATTGTAGTTGTATGAATT
1 ATTTATTTTAAAATAATTTATTTTAAATAATTTATTAGTATGGATTGATT-TA-TT-TTTAAAAT
*
572216 GATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTG
63 AATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTG
572281 ATTTATTTT-AAATAATTTATT
1 ATTTATTTTAAAATAATTTATT
572302 AATATGGATT
Statistics
Matches: 342, Mismatches: 22, Indels: 82
0.77 0.05 0.18
Matches are distributed among these distances:
112 45 0.13
114 2 0.01
115 4 0.01
116 4 0.01
117 8 0.02
118 2 0.01
119 7 0.02
120 3 0.01
121 3 0.01
122 24 0.07
123 10 0.03
124 14 0.04
125 1 0.00
126 1 0.00
127 38 0.11
128 1 0.00
130 2 0.01
131 2 0.01
132 17 0.05
133 28 0.08
134 90 0.26
135 16 0.05
136 6 0.02
137 2 0.01
138 4 0.01
139 8 0.02
ACGTcount: A:0.35, C:0.00, G:0.12, T:0.53
Consensus pattern (127 bp):
ATTTATTTTAAAATAATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTTAAAATAAT
TTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTG
Found at i:572041 original size:112 final size:112
Alignment explanation
Indices: 571914--572476 Score: 612
Period size: 112 Copynumber: 5.1 Consensus size: 112
571904 TATTTTAAAA
571914 TATGGATTGATTTATTTTAAATAATTTATTAGTATGAATTGATTTATTTTAAAATATGGATTGAT
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATGAATTGATTTATTTTAAAATATGGATTGAT
571979 TTATTATTGTAGTTGTATGGATTGATTTATTTTAAATAATTTATTAG
66 TTATTATTGTAGTTGTATGGATTGATTTATTTTAAATAATTTATTAG
* * *
572026 TATGGATTGATTTATTTTAAAATAATTTATT--T-T-AAATAATTTA--TT--AGTATGGATTGA
1 TATGGATTGATTTATTTT-AAATAATTTATTAGTATGAATTGATTTATTTTAAAATATGGATTGA
572083 --T-TTATTGTAGTTGTATGGATTGATTTATTTTAAATAATTTATTAG
65 TTTATTATTGTAGTTGTATGGATTGATTTATTTTAAATAATTTATTAG
* * * * ** * * *
572128 TATGGATTGATTTATTTTAAA-ATATTGATT-G-ATTTATTTTAAATAATTTATTAGTATGGATT
1 TATGGATTGATTTATTTTAAATA-ATTTATTAGTA-TGAATTGATTTATTTTA-AAATATGGATT
*
572190 GATTTATTATTGTAGTTGTATGAATTGATTTATTTTAAATAATTTATTAG
63 GATTTATTATTGTAGTTGTATGGATTGATTTATTTTAAATAATTTATTAG
* **
572240 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAATAATTTATTAAT
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATGAATTGATTTATTTT-AA-AA--TATGGAT
* * *** * *
572305 ATGGATTGATTTATTTTA-AAATATGGATTGATTTA---T---TACTGTAGTT-G
62 -T-GATTTA-TTATTGTAGTTGTATGGATTGATTTATTTTAAATAATTTA-TTAG
* * *
572352 TATAGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTGAAATATGGATTGAT
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATGAATTGATTTATTTTAAAATATGGATTGAT
*
572417 TTATTATTGTAGTTGTATGAATTGATTTATTTTAAATAATTTATTAG
66 TTATTATTGTAGTTGTATGGATTGATTTATTTTAAATAATTTATTAG
*
572464 TATGGATTTATTT
1 TATGGATTGATTT
572477 TAAAAATATG
Statistics
Matches: 374, Mismatches: 44, Indels: 66
0.77 0.09 0.14
Matches are distributed among these distances:
100 1 0.00
101 9 0.02
102 62 0.17
103 2 0.01
104 5 0.01
105 18 0.05
106 20 0.05
107 3 0.01
108 5 0.01
109 21 0.06
110 3 0.01
111 5 0.01
112 160 0.43
113 25 0.07
114 3 0.01
115 1 0.00
116 5 0.01
117 1 0.00
118 18 0.05
119 7 0.02
ACGTcount: A:0.33, C:0.00, G:0.14, T:0.53
Consensus pattern (112 bp):
TATGGATTGATTTATTTTAAATAATTTATTAGTATGAATTGATTTATTTTAAAATATGGATTGAT
TTATTATTGTAGTTGTATGGATTGATTTATTTTAAATAATTTATTAG
Found at i:572064 original size:14 final size:15
Alignment explanation
Indices: 572035--572070 Score: 65
Period size: 14 Copynumber: 2.5 Consensus size: 15
572025 GTATGGATTG
572035 ATTTATTTTAAAATA
1 ATTTATTTTAAAATA
572050 ATTTATTTT-AAATA
1 ATTTATTTTAAAATA
572064 ATTTATT
1 ATTTATT
572071 AGTATGGATT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 12 0.57
15 9 0.43
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (15 bp):
ATTTATTTTAAAATA
Found at i:572191 original size:214 final size:212
Alignment explanation
Indices: 571812--572341 Score: 600
Period size: 214 Copynumber: 2.5 Consensus size: 212
571802 TATTATAAAA
*
571812 TATGGATTGATTTATTTTTAAAATAATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTT
1 TATGGATTGATTTA-TTTTAAAATAATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTG
* * *
571877 TAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGATTTATTTTAAATAATTTA
65 TAAAT-ATGTATTAGGATGGATTGATTTATTTTAAAATATGGATTGATTTATTTTAAATAATTGA
** * *
571942 TTAGTATGAATTGATTTATTTTAAAATATGGATTGATTTATTATTGTAGTTGTATGGATTGATTT
129 TTAGTATGAATTGAAATAATTTAAAATATGGATTGATTTATTATTGTAGTTGTATGAATTGATTT
572007 ATTTTAAATAATTTATTAG
194 ATTTTAAATAATTTATTAG
572026 TATGGATTGATTTATTTTAAAATAATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTGT
1 TATGGATTGATTTATTTTAAAATAATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTGT
* * * * *
572091 -AGT-TGTA-T-GGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAA-AT
66 AAATATGTATTAGGATGGATTGA-TTT--AT--TTTA-AAATATGGATTGATTTATTTTAAATA-
* * * * *
572151 ATTGATT-G-ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTATTGTAGTTGTATGAA
124 ATTGATTAGTA-TGAATTGAAATAATTTA-AAATATGGATTGATTTATTATTGTAGTTGTATGAA
572214 TTGATTTATTTTAAATAATTTATTAG
187 TTGATTTATTTTAAATAATTTATTAG
*
572240 TATGGATTG---------------ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTT
1 TATGGATTGATTTATTTTAAAATAATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTGT
* **
572290 AAATAATTTATTAATATGGATTGATTTATTTTAAAATATGGATTGATTTATT
66 AAAT-ATGTATTAGGATGGATTGATTTATTTTAAAATATGGATTGATTTATT
572342 ACTGTAGTTG
Statistics
Matches: 275, Mismatches: 27, Indels: 44
0.79 0.08 0.13
Matches are distributed among these distances:
198 17 0.06
199 44 0.16
200 2 0.01
201 2 0.01
202 3 0.01
203 4 0.01
204 7 0.03
208 8 0.03
209 4 0.01
210 3 0.01
211 2 0.01
212 3 0.01
213 67 0.24
214 109 0.40
ACGTcount: A:0.34, C:0.00, G:0.13, T:0.53
Consensus pattern (212 bp):
TATGGATTGATTTATTTTAAAATAATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTGT
AAATATGTATTAGGATGGATTGATTTATTTTAAAATATGGATTGATTTATTTTAAATAATTGATT
AGTATGAATTGAAATAATTTAAAATATGGATTGATTTATTATTGTAGTTGTATGAATTGATTTAT
TTTAAATAATTTATTAG
Found at i:572219 original size:80 final size:79
Alignment explanation
Indices: 572119--572527 Score: 304
Period size: 80 Copynumber: 5.0 Consensus size: 79
572109 ATTTTAAATA
*
572119 ATTTATTAGTATGGATTGATTTATTTTAAAATATTGATTGATTTATTTTAAATAATTTATTAGTA
1 ATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGATTTATTTTAAATAATTTATTAGTA
572184 TGGATTGATTTATT
66 TGGATTGATTTATT
*
572198 ATTGTAGTT-GTATGAATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAT
1 ATT-TA-TTAGTATGGATTGATTTA-TTT---TAA---A--A-TATGGATTGATTTATTTTAAAT
572262 AATTTATTAGTATGGATTGATTTATTTTAAAT
54 AATTTATTAGTATGGATTGATTTA---T---T
* ** *
572294 AATTTATTAATATGGATTGATTTATTTTAAAATATGGATTGATTTA--TTACTGTAGTTGTA-TA
1 -ATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGATTTATTTTA-AATAATT-TATTA
* * *
572356 G-ATTGATTTATTTTAAATA
63 GTATGGATTGA-TTT--ATT
* * *
572375 ATTTATTAGTATGGATTGATTTATTTTGAAATATGGATTGATTTATTATT--GTAGTTGTA-T-G
1 ATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGATTTATT-TTAAATAATT-TATTAG
* * * *
572436 AATTGATTTATTTTAAATA
64 TATGGATTGA-TTT--ATT
572455 ATTTATTAGTAT-G---GATTTATTTTAAAAATATGGATTGATTTATTTTAAATAATTTATTAGT
1 ATTTATTAGTATGGATTGATTTATTTT-AAAATATGGATTGATTTATTTTAAATAATTTATTAGT
*
572516 ATGGATTCATTT
65 ATGGATTGATTT
572528 TAAAAATATG
Statistics
Matches: 278, Mismatches: 18, Indels: 69
0.76 0.05 0.19
Matches are distributed among these distances:
76 12 0.04
77 21 0.08
78 8 0.03
79 13 0.05
80 99 0.36
81 5 0.02
83 2 0.01
84 14 0.05
85 10 0.04
86 16 0.06
87 3 0.01
89 2 0.01
90 45 0.16
92 3 0.01
93 1 0.00
95 5 0.02
96 16 0.06
97 3 0.01
ACGTcount: A:0.33, C:0.00, G:0.14, T:0.53
Consensus pattern (79 bp):
ATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGATTTATTTTAAATAATTTATTAGTA
TGGATTGATTTATT
Found at i:572251 original size:144 final size:143
Alignment explanation
Indices: 572095--572527 Score: 470
Period size: 144 Copynumber: 3.1 Consensus size: 143
572085 TATTGTAGTT
572095 GTATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATTGATTGA
1 GTATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTT-AAATATTGATTGA
572160 TTTATTTTAAATAATTTATTAGTATGGATTGATTTATTATTGTAGTTGTATGAATTGATTTATTT
65 TTTATTTTAAATAATTTATTAGTATGGATTGATTTATTATTGTAGTTGTATGAATTGATTTATTT
572225 TAAATAATTTATTA
130 TAAATAATTTATTA
* *
572239 GTATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAATAATTTATTAA
1 GTATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAT-ATTGATTGA
* * ** * * * *
572304 TATGGA-TTGATTTATTTTA-AAATATGGATTGATTTATTACTGTAGTTGTAT-AGATTGATTTA
65 T-T-TATTTTAAATAATTTATTAGTATGGATTGATTTATTATTGTAGTTGTATGA-ATTGATTTA
572366 TTTTAAATAATTTATTA
127 TTTTAAATAATTTATTA
** * ** *
572383 GTATGGATTGATTTATTTTGAAAT-ATGGATT-G-AT---TT-A-TTATTGTAGTTGTATGAATT
1 GTATGGATTGATTTATTTT-AAATAATTTATTAGTATGGATTGATTTATTTTAAATAT-TG-ATT
**** *
572440 GATTTATTTTAAATAATTTATTAGTAT-G---GATTTA-T-TT-TAAAAATATGGATTGATTTAT
63 GATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTATTGTAGTTGTATGAATTGATTTAT
572498 TTTAAATAATTTATTA
128 TTTAAATAATTTATTA
*
572514 GTATGGATTCATTT
1 GTATGGATTGATTT
572528 TAAAAATATG
Statistics
Matches: 247, Mismatches: 32, Indels: 33
0.79 0.10 0.11
Matches are distributed among these distances:
131 44 0.18
132 1 0.00
133 1 0.00
134 6 0.02
136 2 0.01
137 20 0.08
138 10 0.04
139 2 0.01
142 2 0.01
143 6 0.02
144 138 0.56
145 14 0.06
146 1 0.00
ACGTcount: A:0.33, C:0.00, G:0.14, T:0.52
Consensus pattern (143 bp):
GTATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAATATTGATTGAT
TTATTTTAAATAATTTATTAGTATGGATTGATTTATTATTGTAGTTGTATGAATTGATTTATTTT
AAATAATTTATTA
Found at i:572398 original size:18 final size:18
Alignment explanation
Indices: 572375--572422 Score: 51
Period size: 22 Copynumber: 2.4 Consensus size: 18
572365 ATTTTAAATA
*
572375 ATTTATTAGTATGGATTG
1 ATTTATTAATATGGATTG
572393 ATTTATTTTGAAATATGGATTG
1 ATTTA--TT--AATATGGATTG
572415 ATTTATTA
1 ATTTATTA
572423 TTGTAGTTGT
Statistics
Matches: 25, Mismatches: 1, Indels: 8
0.74 0.03 0.24
Matches are distributed among these distances:
18 6 0.24
20 4 0.16
22 15 0.60
ACGTcount: A:0.31, C:0.00, G:0.17, T:0.52
Consensus pattern (18 bp):
ATTTATTAATATGGATTG
Found at i:572495 original size:51 final size:51
Alignment explanation
Indices: 572432--572564 Score: 248
Period size: 51 Copynumber: 2.6 Consensus size: 51
572422 ATTGTAGTTG
* *
572432 TATGAATTGATTTATTTTAAATAATTTATTAGTATGGATTTATTTTAAAAA
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTCATTTTAAAAA
572483 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTCATTTTAAAAA
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTCATTTTAAAAA
572534 TATGGATTGATTTATTTTAAATAATTTATTA
1 TATGGATTGATTTATTTTAAATAATTTATTA
572565 TTGTAGTTGT
Statistics
Matches: 80, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
51 80 1.00
ACGTcount: A:0.38, C:0.01, G:0.11, T:0.51
Consensus pattern (51 bp):
TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTCATTTTAAAAA
Found at i:572614 original size:31 final size:31
Alignment explanation
Indices: 572579--572637 Score: 100
Period size: 31 Copynumber: 1.9 Consensus size: 31
572569 AGTTGTATGG
* *
572579 ATTATTTAAATTTCAGTATTGTAAAACTAAA
1 ATTATTTAAATCTCAGTATTGCAAAACTAAA
572610 ATTATTTAAATCTCAGTATTGCAAAACT
1 ATTATTTAAATCTCAGTATTGCAAAACT
572638 CTTTTAAGTT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.42, C:0.10, G:0.07, T:0.41
Consensus pattern (31 bp):
ATTATTTAAATCTCAGTATTGCAAAACTAAA
Found at i:575642 original size:2 final size:2
Alignment explanation
Indices: 575635--575709 Score: 150
Period size: 2 Copynumber: 37.5 Consensus size: 2
575625 GGGTGATTTT
575635 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
575677 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
575710 TTTAAGAAAT
Statistics
Matches: 73, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 73 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:576399 original size:37 final size:37
Alignment explanation
Indices: 576358--576434 Score: 136
Period size: 37 Copynumber: 2.1 Consensus size: 37
576348 CTGAGTTGGA
*
576358 CCTGAAAATTATGGATCTAAATCCGACCTGAGAACGG
1 CCTGAAAATTATGGATCTAAACCCGACCTGAGAACGG
*
576395 CCTGAAAATTATGGATCTAAACCCGACCTGAGAATGG
1 CCTGAAAATTATGGATCTAAACCCGACCTGAGAACGG
576432 CCT
1 CCT
576435 AGACCCGAAT
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.34, C:0.23, G:0.21, T:0.22
Consensus pattern (37 bp):
CCTGAAAATTATGGATCTAAACCCGACCTGAGAACGG
Found at i:578455 original size:18 final size:17
Alignment explanation
Indices: 578427--578484 Score: 73
Period size: 18 Copynumber: 3.3 Consensus size: 17
578417 TAATATAAAA
578427 TTATATATAAACTATAT
1 TTATATATAAACTATAT
578444 TTATACTATAAACTATAT
1 TTATA-TATAAACTATAT
578462 AATTAT-TATAAACTATAT
1 --TTATATATAAACTATAT
*
578480 GTATA
1 TTATA
578485 AATTATATTT
Statistics
Matches: 36, Mismatches: 1, Indels: 8
0.80 0.02 0.18
Matches are distributed among these distances:
16 3 0.08
17 5 0.14
18 24 0.67
20 4 0.11
ACGTcount: A:0.47, C:0.07, G:0.02, T:0.45
Consensus pattern (17 bp):
TTATATATAAACTATAT
Found at i:578535 original size:98 final size:98
Alignment explanation
Indices: 578432--578621 Score: 308
Period size: 98 Copynumber: 1.9 Consensus size: 98
578422 TAAAATTATA
*
578432 TATAAACTATATTTATACTATAAACTATATAATTATTATAAACTATATGTATAAATTATATTTAT
1 TATAAACTATATTTATACTATAAACTATATAATTATTATAAACTATATATATAAATTATATTTAT
578497 GTGAACTATATATATAAACTATGTATACAAAAT
66 GTGAACTATATATATAAACTATGTATACAAAAT
* * * *
578530 TATAAACTATATTTATATTATAAGCTATATAATTATTATAAGCTATATATATAAATTATGTTTAT
1 TATAAACTATATTTATACTATAAACTATATAATTATTATAAACTATATATATAAATTATATTTAT
* * *
578595 TTGAATTATATATATAAACTATTTATA
66 GTGAACTATATATATAAACTATGTATA
578622 TAAACTATAT
Statistics
Matches: 84, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
98 84 1.00
ACGTcount: A:0.45, C:0.06, G:0.04, T:0.45
Consensus pattern (98 bp):
TATAAACTATATTTATACTATAAACTATATAATTATTATAAACTATATATATAAATTATATTTAT
GTGAACTATATATATAAACTATGTATACAAAAT
Found at i:578551 original size:18 final size:18
Alignment explanation
Indices: 578528--578582 Score: 67
Period size: 18 Copynumber: 3.1 Consensus size: 18
578518 TGTATACAAA
*
578528 ATTATAAACTATATTTAT
1 ATTATAAGCTATATTTAT
*
578546 ATTATAAGCTATA-TAATT
1 ATTATAAGCTATATTTA-T
*
578564 ATTATAAGCTATATATAT
1 ATTATAAGCTATATTTAT
578582 A
1 A
578583 AATTATGTTT
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
17 2 0.06
18 28 0.90
19 1 0.03
ACGTcount: A:0.45, C:0.05, G:0.04, T:0.45
Consensus pattern (18 bp):
ATTATAAGCTATATTTAT
Found at i:578623 original size:13 final size:15
Alignment explanation
Indices: 578601--578734 Score: 72
Period size: 15 Copynumber: 9.3 Consensus size: 15
578591 TTATTTGAAT
578601 TATATATATAAACTA
1 TATATATATAAACTA
578616 T-T-TATATAAACTA
1 TATATATATAAACTA
*
578629 TATATGTATAAAC--
1 TATATATATAAACTA
*
578642 --TATA-A-AAAGTA
1 TATATATATAAACTA
* *
578653 TATAGTTTATAAAATA
1 TATA-TATATAAACTA
*
578669 TTATTTATATTAATA-TA
1 -TATATATA-TAA-ACTA
* *
578686 GTGTATATATATA-TA
1 -TATATATATAAACTA
*
578701 TATATATAAAAACTA
1 TATATATATAAACTA
*
578716 TATATGTATAAACTA
1 TATATATATAAACTA
578731 TATA
1 TATA
578735 AAATATATAG
Statistics
Matches: 90, Mismatches: 16, Indels: 26
0.68 0.12 0.20
Matches are distributed among these distances:
9 3 0.03
10 1 0.01
11 3 0.03
13 14 0.16
14 12 0.13
15 32 0.36
16 10 0.11
17 14 0.16
18 1 0.01
ACGTcount: A:0.49, C:0.04, G:0.04, T:0.43
Consensus pattern (15 bp):
TATATATATAAACTA
Found at i:578721 original size:87 final size:88
Alignment explanation
Indices: 578601--578782 Score: 269
Period size: 87 Copynumber: 2.1 Consensus size: 88
578591 TTATTTGAAT
* *
578601 TATATATATAAACTATTTATATAAACTATATATGTATAAACTATA-AAAAGTATATAGTTTATAA
1 TATATATATAAACTATATATAAAAACTATATATGTATAAACTATATAAAA-TATATAGTTTATAA
* *
578665 AATATTATTTATATTAATATAGTG
65 AATATAATTTATATTAATATAGTA
* **
578689 TATATATATATA-TATATATAAAAACTATATATGTATAAACTATATAAAATATATAGTTTATATG
1 TATATATATAAACTATATATAAAAACTATATATGTATAAACTATATAAAATATATAGTTTATAAA
*
578753 TTATAATTTATATTAATATAGTA
66 ATATAATTTATATTAATATAGTA
578776 TATATAT
1 TATATAT
578783 GTATGCATTA
Statistics
Matches: 85, Mismatches: 8, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
87 70 0.82
88 15 0.18
ACGTcount: A:0.48, C:0.03, G:0.05, T:0.45
Consensus pattern (88 bp):
TATATATATAAACTATATATAAAAACTATATATGTATAAACTATATAAAATATATAGTTTATAAA
ATATAATTTATATTAATATAGTA
Found at i:578734 original size:17 final size:16
Alignment explanation
Indices: 578681--578734 Score: 54
Period size: 17 Copynumber: 3.2 Consensus size: 16
578671 ATTTATATTA
*
578681 ATATAGTGTATATATAT
1 ATATA-TGTATAAATAT
* *
578698 ATATATATATAAAAACT
1 ATATATGTATAAATA-T
578715 ATATATGTATAAACTAT
1 ATATATGTATAAA-TAT
578732 ATA
1 ATA
578735 AAATATATAG
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
16 7 0.23
17 22 0.73
18 1 0.03
ACGTcount: A:0.50, C:0.04, G:0.06, T:0.41
Consensus pattern (16 bp):
ATATATGTATAAATAT
Found at i:578905 original size:2 final size:2
Alignment explanation
Indices: 578898--578949 Score: 59
Period size: 2 Copynumber: 25.0 Consensus size: 2
578888 TCATATAGTT
** *
578898 TA TA TA TA TA GG TA TA TA TA TA TA TA TA TA TA TA TA GTT TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA
578941 TA TA CTA TA
1 TA TA -TA TA
578950 CATGGTTTAT
Statistics
Matches: 42, Mismatches: 6, Indels: 4
0.81 0.12 0.08
Matches are distributed among these distances:
2 39 0.93
3 3 0.07
ACGTcount: A:0.44, C:0.02, G:0.06, T:0.48
Consensus pattern (2 bp):
TA
Found at i:578983 original size:7 final size:7
Alignment explanation
Indices: 578971--579075 Score: 90
Period size: 7 Copynumber: 15.0 Consensus size: 7
578961 CATATATTAG
578971 GGTTTAT
1 GGTTTAT
*
578978 GGTTTAG
1 GGTTTAT
578985 GGTTTAT
1 GGTTTAT
*
578992 GATTTAT
1 GGTTTAT
578999 GGTTTAT
1 GGTTTAT
579006 GGTTTA-
1 GGTTTAT
579012 GGATTTAT
1 GG-TTTAT
*
579020 TGTTTAT
1 GGTTTAT
*
579027 GGTTTAA
1 GGTTTAT
*
579034 AGTTTA-
1 GGTTTAT
579040 GAGTTTA-
1 G-GTTTAT
579047 GAGTTTAT
1 G-GTTTAT
* *
579055 GATTTAG
1 GGTTTAT
*
579062 GGTTTAA
1 GGTTTAT
579069 GGTTTAT
1 GGTTTAT
579076 ATAAACTATA
Statistics
Matches: 80, Mismatches: 14, Indels: 8
0.78 0.14 0.08
Matches are distributed among these distances:
6 2 0.03
7 76 0.95
8 2 0.03
ACGTcount: A:0.22, C:0.00, G:0.27, T:0.51
Consensus pattern (7 bp):
GGTTTAT
Found at i:578999 original size:21 final size:21
Alignment explanation
Indices: 578973--579075 Score: 102
Period size: 21 Copynumber: 4.9 Consensus size: 21
578963 TATATTAGGG
578973 TTTATGGTTTAGGGTTTATGA
1 TTTATGGTTTAGGGTTTATGA
* *
578994 TTTATGGTTTATGGTTTAGGA
1 TTTATGGTTTAGGGTTTATGA
* * *
579015 TTTATTGTTTATGGTTTA-AA
1 TTTATGGTTTAGGGTTTATGA
*
579035 GTTTA-GAGTTTAGAGTTTATGA
1 -TTTATG-GTTTAGGGTTTATGA
* *
579057 TTTAGGGTTTAAGGTTTAT
1 TTTATGGTTTAGGGTTTAT
579076 ATAAACTATA
Statistics
Matches: 68, Mismatches: 10, Indels: 8
0.79 0.12 0.09
Matches are distributed among these distances:
20 1 0.01
21 65 0.96
22 2 0.03
ACGTcount: A:0.22, C:0.00, G:0.25, T:0.52
Consensus pattern (21 bp):
TTTATGGTTTAGGGTTTATGA
Found at i:579006 original size:28 final size:28
Alignment explanation
Indices: 578971--579075 Score: 115
Period size: 28 Copynumber: 3.8 Consensus size: 28
578961 CATATATTAG
578971 GGTTTATGGTTTAGGGTTTATGATTTAT
1 GGTTTATGGTTTAGGGTTTATGATTTAT
*
578999 GGTTTATGGTTTAGGATTTATTG-TTTAT
1 GGTTTATGGTTTAGGGTTTA-TGATTTAT
** *
579027 GGTTTAAAGTTTAGAGTTTA-GAGTTTAT
1 GGTTTATGGTTTAGGGTTTATGA-TTTAT
* * *
579055 GATTTAGGGTTTAAGGTTTAT
1 GGTTTATGGTTTAGGGTTTAT
579076 ATAAACTATA
Statistics
Matches: 63, Mismatches: 10, Indels: 7
0.79 0.12 0.09
Matches are distributed among these distances:
26 1 0.02
28 60 0.95
29 2 0.03
ACGTcount: A:0.22, C:0.00, G:0.27, T:0.51
Consensus pattern (28 bp):
GGTTTATGGTTTAGGGTTTATGATTTAT
Found at i:579310 original size:19 final size:20
Alignment explanation
Indices: 579297--579341 Score: 83
Period size: 19 Copynumber: 2.3 Consensus size: 20
579287 AATTTTTCTA
579297 TTCCCTCTAAATTTCTCAAT
1 TTCCCTCTAAATTTCTCAAT
579317 TTCCCTCTAAA-TTCTCAAT
1 TTCCCTCTAAATTTCTCAAT
579336 TTCCCT
1 TTCCCT
579342 TATATTTTCA
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
19 14 0.56
20 11 0.44
ACGTcount: A:0.22, C:0.33, G:0.00, T:0.44
Consensus pattern (20 bp):
TTCCCTCTAAATTTCTCAAT
Found at i:579458 original size:2 final size:2
Alignment explanation
Indices: 579451--579543 Score: 134
Period size: 2 Copynumber: 46.5 Consensus size: 2
579441 ACTTTGAATA
579451 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
* * * *
579493 AT AT AT AT A- AGT AT AG AC AT AA AT AA AT AT AT AT AT AT AT AT
1 AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
579535 AT AT AT AT A
1 AT AT AT AT A
579544 ATTAAACTTA
Statistics
Matches: 82, Mismatches: 7, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
1 1 0.01
2 80 0.98
3 1 0.01
ACGTcount: A:0.53, C:0.01, G:0.02, T:0.44
Consensus pattern (2 bp):
AT
Found at i:580155 original size:19 final size:20
Alignment explanation
Indices: 580115--580158 Score: 72
Period size: 19 Copynumber: 2.2 Consensus size: 20
580105 GGGAATTGGG
*
580115 AATTTAGAGGGAAATTGAAA
1 AATTTAGAGGGAAATAGAAA
580135 AATTTAGAGGG-AATAGAAA
1 AATTTAGAGGGAAATAGAAA
580154 AATTT
1 AATTT
580159 GGGAAGTTGA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
19 12 0.52
20 11 0.48
ACGTcount: A:0.50, C:0.00, G:0.23, T:0.27
Consensus pattern (20 bp):
AATTTAGAGGGAAATAGAAA
Found at i:580646 original size:23 final size:23
Alignment explanation
Indices: 580620--580663 Score: 88
Period size: 23 Copynumber: 1.9 Consensus size: 23
580610 TTATTTTTTC
580620 TTTATATAAATTAAACTATATCA
1 TTTATATAAATTAAACTATATCA
580643 TTTATATAAATTAAACTATAT
1 TTTATATAAATTAAACTATAT
580664 TTATTTTCCT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.48, C:0.07, G:0.00, T:0.45
Consensus pattern (23 bp):
TTTATATAAATTAAACTATATCA
Found at i:585294 original size:21 final size:21
Alignment explanation
Indices: 585268--585307 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
585258 CAGAACCCCA
*
585268 GGGGGGTATCGATTCCCCTGT
1 GGGGGGAATCGATTCCCCTGT
*
585289 GGGGGGAATCGGTTCCCCT
1 GGGGGGAATCGATTCCCCT
585308 TCAAAGGGGG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.10, C:0.25, G:0.40, T:0.25
Consensus pattern (21 bp):
GGGGGGAATCGATTCCCCTGT
Found at i:585339 original size:21 final size:23
Alignment explanation
Indices: 585288--585339 Score: 72
Period size: 23 Copynumber: 2.3 Consensus size: 23
585278 GATTCCCCTG
585288 TGGGGGGAATCGGTTCCCCTTCA
1 TGGGGGGAATCGGTTCCCCTTCA
**
585311 AAGGGGGAATCGGTT-CCC-TCA
1 TGGGGGGAATCGGTTCCCCTTCA
585332 TGGGGGGA
1 TGGGGGGA
585340 TCAATTCCCT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
21 9 0.36
22 3 0.12
23 13 0.52
ACGTcount: A:0.17, C:0.21, G:0.40, T:0.21
Consensus pattern (23 bp):
TGGGGGGAATCGGTTCCCCTTCA
Found at i:595762 original size:16 final size:16
Alignment explanation
Indices: 595741--595771 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
595731 GAGATCATGT
595741 TGCTGTTTGGAGCTAC
1 TGCTGTTTGGAGCTAC
595757 TGCTGTTTGGAGCTA
1 TGCTGTTTGGAGCTA
595772 TTGTTATGCT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.13, C:0.16, G:0.32, T:0.39
Consensus pattern (16 bp):
TGCTGTTTGGAGCTAC
Found at i:596151 original size:15 final size:15
Alignment explanation
Indices: 596131--596162 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
596121 GTGATTTCTC
596131 TGTCTTTTGTGTATT
1 TGTCTTTTGTGTATT
596146 TGTCTTTTGTGTATT
1 TGTCTTTTGTGTATT
596161 TG
1 TG
596163 GTTGACAAAG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.06, C:0.06, G:0.22, T:0.66
Consensus pattern (15 bp):
TGTCTTTTGTGTATT
Found at i:596459 original size:44 final size:44
Alignment explanation
Indices: 596396--596479 Score: 141
Period size: 44 Copynumber: 1.9 Consensus size: 44
596386 TGTGAGCAAA
*
596396 CTTCACAAGTTTGCATTTGTTAAAATATATATTCTCTTTGTAAG
1 CTTCACAAGCTTGCATTTGTTAAAATATATATTCTCTTTGTAAG
* *
596440 CTTCACAAGCTTGTATTTGTTAAAATATATATTTTCTTTG
1 CTTCACAAGCTTGCATTTGTTAAAATATATATTCTCTTTG
596480 CTTTTTGTTA
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
44 37 1.00
ACGTcount: A:0.29, C:0.13, G:0.11, T:0.48
Consensus pattern (44 bp):
CTTCACAAGCTTGCATTTGTTAAAATATATATTCTCTTTGTAAG
Found at i:596930 original size:16 final size:16
Alignment explanation
Indices: 596909--596939 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
596899 GTATTTAACT
*
596909 GATTCATACCTGAACC
1 GATTCAGACCTGAACC
596925 GATTCAGACCTGAAC
1 GATTCAGACCTGAAC
596940 TGAAATTTTG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.32, C:0.29, G:0.16, T:0.23
Consensus pattern (16 bp):
GATTCAGACCTGAACC
Found at i:598129 original size:15 final size:15
Alignment explanation
Indices: 598109--598140 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
598099 GTGATTTCTC
598109 TGTCTTTTGTGTATT
1 TGTCTTTTGTGTATT
598124 TGTCTTTTGTGTATT
1 TGTCTTTTGTGTATT
598139 TG
1 TG
598141 GTTGACAAAG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.06, C:0.06, G:0.22, T:0.66
Consensus pattern (15 bp):
TGTCTTTTGTGTATT
Found at i:598437 original size:44 final size:44
Alignment explanation
Indices: 598374--598457 Score: 141
Period size: 44 Copynumber: 1.9 Consensus size: 44
598364 TGTGAGCAAA
* *
598374 CTTCACAAGTTTGCATTTGTTAAAATATATATTCTCTTTGTAAG
1 CTTCACAAGCTTACATTTGTTAAAATATATATTCTCTTTGTAAG
*
598418 CTTCACAAGCTTACATTTGTTAAAATATATATTTTCTTTG
1 CTTCACAAGCTTACATTTGTTAAAATATATATTCTCTTTG
598458 CTTTTTGTTA
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
44 37 1.00
ACGTcount: A:0.30, C:0.14, G:0.10, T:0.46
Consensus pattern (44 bp):
CTTCACAAGCTTACATTTGTTAAAATATATATTCTCTTTGTAAG
Found at i:598907 original size:16 final size:16
Alignment explanation
Indices: 598886--598916 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
598876 GTATTTAACT
*
598886 GATTCATACCTGAACC
1 GATTCAGACCTGAACC
598902 GATTCAGACCTGAAC
1 GATTCAGACCTGAAC
598917 TGACAGCGAC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.32, C:0.29, G:0.16, T:0.23
Consensus pattern (16 bp):
GATTCAGACCTGAACC
Found at i:599752 original size:13 final size:13
Alignment explanation
Indices: 599736--599773 Score: 58
Period size: 13 Copynumber: 2.9 Consensus size: 13
599726 GCTACTGTTA
599736 TGTTGTTTGGAGT
1 TGTTGTTTGGAGT
*
599749 TGTTGTTTGGATT
1 TGTTGTTTGGAGT
*
599762 TATTGTTTGGAG
1 TGTTGTTTGGAG
599774 CTATTTTTAG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.11, C:0.00, G:0.34, T:0.55
Consensus pattern (13 bp):
TGTTGTTTGGAGT
Found at i:599778 original size:13 final size:13
Alignment explanation
Indices: 599738--599778 Score: 55
Period size: 13 Copynumber: 3.2 Consensus size: 13
599728 TACTGTTATG
*
599738 TTGTTTGGAGTTG
1 TTGTTTGGAGTTA
*
599751 TTGTTTGGATTTA
1 TTGTTTGGAGTTA
*
599764 TTGTTTGGAGCTA
1 TTGTTTGGAGTTA
599777 TT
1 TT
599779 TTTAGATCAT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.12, C:0.02, G:0.29, T:0.56
Consensus pattern (13 bp):
TTGTTTGGAGTTA
Found at i:600122 original size:15 final size:15
Alignment explanation
Indices: 600102--600133 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
600092 GTGATTTCTC
600102 TGTCTTTTGTGTATT
1 TGTCTTTTGTGTATT
600117 TGTCTTTTGTGTATT
1 TGTCTTTTGTGTATT
600132 TG
1 TG
600134 GTTGACAAAG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.06, C:0.06, G:0.22, T:0.66
Consensus pattern (15 bp):
TGTCTTTTGTGTATT
Found at i:600430 original size:44 final size:44
Alignment explanation
Indices: 600367--600450 Score: 150
Period size: 44 Copynumber: 1.9 Consensus size: 44
600357 TGTGAGCAAA
*
600367 CTTCACAAGTTTGCATTTGTTAAAATATATATTCTCTTTGTAAG
1 CTTCACAAGCTTGCATTTGTTAAAATATATATTCTCTTTGTAAG
*
600411 CTTCACAAGCTTGCATTTGTTAAAATATATATTTTCTTTG
1 CTTCACAAGCTTGCATTTGTTAAAATATATATTCTCTTTG
600451 CTTTTTGTTA
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
44 38 1.00
ACGTcount: A:0.29, C:0.14, G:0.11, T:0.46
Consensus pattern (44 bp):
CTTCACAAGCTTGCATTTGTTAAAATATATATTCTCTTTGTAAG
Found at i:600900 original size:16 final size:16
Alignment explanation
Indices: 600879--600909 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
600869 GTATTTAATT
*
600879 GATTCATACCTGAACC
1 GATTCAGACCTGAACC
600895 GATTCAGACCTGAAC
1 GATTCAGACCTGAAC
600910 TGACAGCGAC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.32, C:0.29, G:0.16, T:0.23
Consensus pattern (16 bp):
GATTCAGACCTGAACC
Found at i:611604 original size:20 final size:20
Alignment explanation
Indices: 611557--612012 Score: 434
Period size: 20 Copynumber: 22.2 Consensus size: 20
611547 AATGACCAAC
**
611557 AAAATCGCAACGCGA-TATC
1 AAAATCGCAACGCGATTAAG
* *
611576 AAAACCGCAACGCGATTTAG
1 AAAATCGCAACGCGATTAAG
* * *
611596 AAAAGCGCAACGTTGA-AAAG
1 AAAATCGCAACG-CGATTAAG
* * ***
611616 AAGATCGCAACACGATCTTCC
1 AAAATCGCAACGCGAT-TAAG
* * *
611637 AAGAATCGCAATGCGATTCAT
1 AA-AATCGCAACGCGATTAAG
***
611658 AAAATCGCAACGCGATCTTCC
1 AAAATCGCAACGCGAT-TAAG
*
611679 AAGAATCGCAACGCGATTCAG
1 AA-AATCGCAACGCGATTAAG
*
611700 AAAATCGCAACGCGATTCAG
1 AAAATCGCAACGCGATTAAG
*
611720 AAAATCGCAACGCGATTCAG
1 AAAATCGCAACGCGATTAAG
***
611740 AAAATCGCAACGCGATCTTCC
1 AAAATCGCAACGCGAT-TAAG
611761 AAGAATCGCAACGCGATTAAG
1 AA-AATCGCAACGCGATTAAG
611782 AAAATCGCAACGCGATTAAG
1 AAAATCGCAACGCGATTAAG
***
611802 AAAATCGCAACGCGATCTTCC
1 AAAATCGCAACGCGAT-TAAG
*
611823 AAGAATCGCAACGCGATTCAG
1 AA-AATCGCAACGCGATTAAG
611844 AAAATCGCAACGCGATTCCAAG
1 AAAATCGCAACGCGATT--AAG
611866 --AATCGCAACGCGATTAAG
1 AAAATCGCAACGCGATTAAG
611884 AAAATCGCAACGCGATTAAG
1 AAAATCGCAACGCGATTAAG
* ***
611904 AGAATCGCAACGCGATCTTCC
1 AAAATCGCAACGCGAT-TAAG
611925 AAGAATCGCAACGCGATTAAG
1 AA-AATCGCAACGCGATTAAG
611946 AAAATCGCAACGCGATTAAG
1 AAAATCGCAACGCGATTAAG
***
611966 AAAATCGCAACGCGATCTTCC
1 AAAATCGCAACGCGAT-TAAG
611987 AAGAATCGCAACGCGATTAAG
1 AA-AATCGCAACGCGATTAAG
612008 AAAAT
1 AAAAT
612013 GAGTAAATTC
Statistics
Matches: 362, Mismatches: 56, Indels: 37
0.80 0.12 0.08
Matches are distributed among these distances:
18 3 0.01
19 16 0.04
20 224 0.62
21 36 0.10
22 83 0.23
ACGTcount: A:0.40, C:0.25, G:0.19, T:0.16
Consensus pattern (20 bp):
AAAATCGCAACGCGATTAAG
Found at i:611667 original size:62 final size:62
Alignment explanation
Indices: 611557--611981 Score: 435
Period size: 62 Copynumber: 6.9 Consensus size: 62
611547 AATGACCAAC
* * * * * *
611557 AAAATCGCAACGCGAT-AT-CAA-AACCGCAACGCGATTTAGAAAAGCGCAACGTTGA-AAAG
1 AAAATCGCAACGCGATCTTCCAAGAATCGCAACGCGATTCAGAAAATCGCAACG-CGATTAAG
* * * * ***
611616 AAGATCGCAACACGATCTTCCAAGAATCGCAATGCGATTCATAAAATCGCAACGCGATCTTCC
1 AAAATCGCAACGCGATCTTCCAAGAATCGCAACGCGATTCAGAAAATCGCAACGCGAT-TAAG
* *
611679 AAGAATCGCAACGCGA--TT-CAGAAAATCGCAACGCGATTCAGAAAATCGCAACGCGATTCAG
1 AA-AATCGCAACGCGATCTTCCA-AGAATCGCAACGCGATTCAGAAAATCGCAACGCGATTAAG
*
611740 AAAATCGCAACGCGATCTTCCAAGAATCGCAACGCGATTAAGAAAATCGCAACGCGATTAAG
1 AAAATCGCAACGCGATCTTCCAAGAATCGCAACGCGATTCAGAAAATCGCAACGCGATTAAG
611802 AAAATCGCAACGCGATCTTCCAAGAATCGCAACGCGATTCAGAAAATCGCAACGCGATTCCAAG
1 AAAATCGCAACGCGATCTTCCAAGAATCGCAACGCGATTCAGAAAATCGCAACGCGATT--AAG
*** * * ***
611866 --AATCGCAACGCGAT-TAAGAA-AATCGCAACGCGATTAAGAGAATCGCAACGCGATCTTCC
1 AAAATCGCAACGCGATCTTCCAAGAATCGCAACGCGATTCAGAAAATCGCAACGCGAT-TAAG
*** *
611925 AAGAATCGCAACGCGAT-TAAGAA-AATCGCAACGCGATTAAGAAAATCGCAACGCGAT
1 AA-AATCGCAACGCGATCTTCCAAGAATCGCAACGCGATTCAGAAAATCGCAACGCGAT
611982 CTTCCAAGAA
Statistics
Matches: 316, Mismatches: 34, Indels: 29
0.83 0.09 0.08
Matches are distributed among these distances:
59 14 0.04
60 46 0.15
61 14 0.04
62 224 0.71
63 4 0.01
64 14 0.04
ACGTcount: A:0.40, C:0.25, G:0.20, T:0.16
Consensus pattern (62 bp):
AAAATCGCAACGCGATCTTCCAAGAATCGCAACGCGATTCAGAAAATCGCAACGCGATTAAG
Found at i:611726 original size:82 final size:81
Alignment explanation
Indices: 611557--612003 Score: 525
Period size: 82 Copynumber: 5.4 Consensus size: 81
611547 AATGACCAAC
* ** * * *
611557 AAAATCGCAACGCGATATCAA-AACCGCAACGCGAT-TTAGAA-AAGCGCAACGTTGA-AAAGAA
1 AAAATCGCAACGCGAT-TCAAGAATCGCAACGCGATCTTCCAAGAATCGCAACG-CGATTAAGAA
* * ***
611618 GATCGCAACACGATCTTCC
64 AATCGCAACGCGAT-TAAG
* * *
611637 AAGAATCGCAATGCGATTCATAAAATCGCAACGCGATCTTCCAAGAATCGCAACGCGATTCAGAA
1 AA-AATCGCAACGCGATTCA-AGAATCGCAACGCGATCTTCCAAGAATCGCAACGCGATTAAGAA
*
611702 AATCGCAACGCGATTCAG
64 AATCGCAACGCGATTAAG
*
611720 AAAATCGCAACGCGATTCAGAAAATCGCAACGCGATCTTCCAAGAATCGCAACGCGATTAAGAAA
1 AAAATCGCAACGCGATTCA-AGAATCGCAACGCGATCTTCCAAGAATCGCAACGCGATTAAGAAA
611785 ATCGCAACGCGATTAAG
65 ATCGCAACGCGATTAAG
*
611802 AAAATCGCAACGCGATCTTCCAAGAATCGCAACGCGA--TT-CAGAAAATCGCAACGCGATTCCA
1 AAAATCGCAACGCGA--TT-CAAGAATCGCAACGCGATCTTCCA-AGAATCGCAACGCGATT--A
611864 AG--AATCGCAACGCGATTAAG
60 AGAAAATCGCAACGCGATTAAG
*
611884 AAAATCGCAACGCGATTAAGAGAATCGCAACGCGATCTTCCAAGAATCGCAACGCGATTAAGAAA
1 AAAATCGCAACGCGATTCA-AGAATCGCAACGCGATCTTCCAAGAATCGCAACGCGATTAAGAAA
611949 ATCGCAACGCGATTAAG
65 ATCGCAACGCGATTAAG
611966 AAAATCGCAACGCGATCTTCCAAGAATCGCAACGCGAT
1 AAAATCGCAACGCGA--TT-CAAGAATCGCAACGCGAT
612004 TAAGAAAATG
Statistics
Matches: 324, Mismatches: 22, Indels: 38
0.84 0.06 0.10
Matches are distributed among these distances:
79 1 0.00
80 25 0.08
81 16 0.05
82 206 0.64
83 11 0.03
84 62 0.19
85 3 0.01
ACGTcount: A:0.39, C:0.25, G:0.19, T:0.16
Consensus pattern (81 bp):
AAAATCGCAACGCGATTCAAGAATCGCAACGCGATCTTCCAAGAATCGCAACGCGATTAAGAAAA
TCGCAACGCGATTAAG
Found at i:611982 original size:62 final size:61
Alignment explanation
Indices: 611640--612012 Score: 493
Period size: 62 Copynumber: 6.0 Consensus size: 61
611630 ATCTTCCAAG
* * * *
611640 AATCGCAATGCGATTCATAAAATCGCAACGCGATCTTCCAAGAATCGCAACGCGATTCAGAA
1 AATCGCAACGCGATTAAGAAAATCGCAACGCGAT-TTCCAAGAATCGCAACGCGATTAAGAA
* * ***
611702 AATCGCAACGCGATTCAGAAAATCGCAACGCGA-TT-CAGAAAATCGCAACGCGATCTTCCAA
1 AATCGCAACGCGATTAAGAAAATCGCAACGCGATTTCCA-AGAATCGCAACGCGAT-TAAGAA
*** ***
611763 GAATCGCAACGCGATTAAGAAAATCGCAACGCGATTAAGAA-AATCGCAACGCGATCTTCCAA
1 -AATCGCAACGCGATTAAGAAAATCGCAACGCGATTTCCAAGAATCGCAACGCGAT-TAAGAA
*
611825 GAATCGCAACGCGATTCAGAAAATCGCAACGCGA-TTCCAAGAATCGCAACGCGATTAAGAA
1 -AATCGCAACGCGATTAAGAAAATCGCAACGCGATTTCCAAGAATCGCAACGCGATTAAGAA
*
611886 AATCGCAACGCGATTAAGAGAATCGCAACGCGATCTTCCAAGAATCGCAACGCGATTAAGAA
1 AATCGCAACGCGATTAAGAAAATCGCAACGCGAT-TTCCAAGAATCGCAACGCGATTAAGAA
611948 AATCGCAACGCGATTAAGAAAATCGCAACGCGATCTTCCAAGAATCGCAACGCGATTAAGAA
1 AATCGCAACGCGATTAAGAAAATCGCAACGCGAT-TTCCAAGAATCGCAACGCGATTAAGAA
612010 AAT
1 AAT
612013 GAGTAAATTC
Statistics
Matches: 284, Mismatches: 19, Indels: 16
0.89 0.06 0.05
Matches are distributed among these distances:
59 2 0.01
60 48 0.17
61 9 0.03
62 222 0.78
63 2 0.01
64 1 0.00
ACGTcount: A:0.39, C:0.25, G:0.19, T:0.17
Consensus pattern (61 bp):
AATCGCAACGCGATTAAGAAAATCGCAACGCGATTTCCAAGAATCGCAACGCGATTAAGAA
Found at i:612119 original size:6 final size:6
Alignment explanation
Indices: 612108--612177 Score: 105
Period size: 6 Copynumber: 12.5 Consensus size: 6
612098 GACACGTATT
612108 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACC-CG
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
612155 ACC-CG ACC-CG ACC-CG ACC-CG ACC
1 ACCACG ACCACG ACCACG ACCACG ACC
612178 CGAGACGAGA
Statistics
Matches: 64, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
5 25 0.39
6 39 0.61
ACGTcount: A:0.29, C:0.54, G:0.17, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:612808 original size:6 final size:5
Alignment explanation
Indices: 612754--612804 Score: 75
Period size: 5 Copynumber: 9.6 Consensus size: 5
612744 CCGTCTCGTC
612754 TCGGG TCGGG TCGGG TCGGG TCGGG TCGGG TCGTGG TCGTGG TCGTGG
1 TCGGG TCGGG TCGGG TCGGG TCGGG TCGGG TCG-GG TCG-GG TCG-GG
612802 TCG
1 TCG
612805 TGGTAATACG
Statistics
Matches: 45, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
5 28 0.62
6 17 0.38
ACGTcount: A:0.00, C:0.20, G:0.55, T:0.25
Consensus pattern (5 bp):
TCGGG
Found at i:614803 original size:12 final size:12
Alignment explanation
Indices: 614786--614810 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
614776 TCTTCGGGGA
614786 CTTTTTCTTCTT
1 CTTTTTCTTCTT
614798 CTTTTTCTTCTT
1 CTTTTTCTTCTT
614810 C
1 C
614811 AGGATTATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:615019 original size:24 final size:24
Alignment explanation
Indices: 614985--615031 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
614975 CTGAAACATC
614985 ATCAAAATCCGTG-TATTGACCAAT
1 ATCAAAATCCG-GATATTGACCAAT
*
615009 ATCAAAGTCCGGATATTGACCAA
1 ATCAAAATCCGGATATTGACCAA
615032 GACCAAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.38, C:0.21, G:0.15, T:0.26
Consensus pattern (24 bp):
ATCAAAATCCGGATATTGACCAAT
Found at i:615742 original size:20 final size:20
Alignment explanation
Indices: 615714--615963 Score: 234
Period size: 20 Copynumber: 12.5 Consensus size: 20
615704 AAATTTCAGT
* * *
615714 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGC
**
615734 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCGC
* * *
615754 ATTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGC
* **
615774 GTTGTGATTTACGGATTATC
1 GTTGCGATTTACGGATTCGC
* *
615794 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGC
* *
615814 ATTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
* *
615834 GTTGCGATATACGGATACGC
1 GTTGCGATTTACGGATTCGC
* **
615854 ATTGCGATTTACCCATAT-GC
1 GTTGCGATTTACGGAT-TCGC
*
615874 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
*
615894 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
*
615914 GTTGCGATTTATGTG-TTCGC
1 GTTGCGATTTACG-GATTCGC
* **
615934 GTTGCGATTTTCATATTCGC
1 GTTGCGATTTACGGATTCGC
615954 GTTGCGATTT
1 GTTGCGATTT
615964 TGGAAAATCG
Statistics
Matches: 192, Mismatches: 34, Indels: 8
0.82 0.15 0.03
Matches are distributed among these distances:
20 191 0.99
21 1 0.01
ACGTcount: A:0.20, C:0.18, G:0.24, T:0.38
Consensus pattern (20 bp):
GTTGCGATTTACGGATTCGC
Done.