Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D04
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: 52479919
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.33
Warning! 336953 characters in sequence are not A, C, G, or T
File 103 of 173
Found at i:31821269 original size:20 final size:20
Alignment explanation
Indices: 31821244--31821283 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
31821234 AATATTTTCC
*
31821244 AGTAAATCATTTTACAGAAA
1 AGTAAAACATTTTACAGAAA
*
31821264 AGTAAAACATTTTCCAGAAA
1 AGTAAAACATTTTACAGAAA
31821284 TCATTTTACG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.50, C:0.12, G:0.10, T:0.28
Consensus pattern (20 bp):
AGTAAAACATTTTACAGAAA
Found at i:31821289 original size:34 final size:35
Alignment explanation
Indices: 31821232--31821298 Score: 109
Period size: 34 Copynumber: 1.9 Consensus size: 35
31821222 CAAACACCAG
*
31821232 AAAATATTTTCCAGTAAATCATTTTACAGAAAAGT
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
*
31821267 AAAACATTTTCCAG-AAATCATTTTACGGAAAA
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAA
31821299 TATTTTACTG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 17 0.57
35 13 0.43
ACGTcount: A:0.46, C:0.13, G:0.09, T:0.31
Consensus pattern (35 bp):
AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
Found at i:31822771 original size:21 final size:21
Alignment explanation
Indices: 31822746--31822786 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
31822736 TTTTGCTTCA
*
31822746 TCATTCTTG-TCCTTGCTCAAG
1 TCATT-TTGTTCCTTCCTCAAG
31822767 TCATTTTGTTCCTTCCTCAA
1 TCATTTTGTTCCTTCCTCAA
31822787 CAGTGGAGTC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 3 0.17
21 15 0.83
ACGTcount: A:0.15, C:0.29, G:0.10, T:0.46
Consensus pattern (21 bp):
TCATTTTGTTCCTTCCTCAAG
Found at i:31827315 original size:5 final size:5
Alignment explanation
Indices: 31827297--31827351 Score: 51
Period size: 5 Copynumber: 11.4 Consensus size: 5
31827287 GAAAGAAGAA
* * * * *
31827297 GAAA- GAAAG AAAAG GAAAG GAGAG GAAAG AAAAA G-AAG AAAAG GAAAG
1 GAAAG GAAAG GAAAG GAAAG GAAAG GAAAG GAAAG GAAAG GAAAG GAAAG
31827345 GAAAG GA
1 GAAAG GA
31827352 GAAGAAGAAG
Statistics
Matches: 39, Mismatches: 10, Indels: 3
0.75 0.19 0.06
Matches are distributed among these distances:
4 6 0.15
5 33 0.85
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (5 bp):
GAAAG
Found at i:31827359 original size:3 final size:3
Alignment explanation
Indices: 31827351--31827453 Score: 65
Period size: 3 Copynumber: 35.3 Consensus size: 3
31827341 AAAGGAAAGG
* * *
31827351 AGA AGA AGA AGA AGA AGA AGA AAA ATGAA AGA AAA AGA AGG A-A AGA
1 AGA AGA AGA AGA AGA AGA AGA AGA A-G-A AGA AGA AGA AGA AGA AGA
* * *
31827397 A-A AGG A-A AGG AGA AGA AGA AGA AGA A-A A-A AGAA AGA AAA AGA
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AG-A AGA AGA AGA
* *
31827439 AGG A-A AGA AAA AGA A
1 AGA AGA AGA AGA AGA A
31827454 AGGAGAAGAG
Statistics
Matches: 76, Mismatches: 16, Indels: 16
0.70 0.15 0.15
Matches are distributed among these distances:
2 9 0.12
3 61 0.80
4 4 0.05
5 2 0.03
ACGTcount: A:0.71, C:0.00, G:0.28, T:0.01
Consensus pattern (3 bp):
AGA
Found at i:31827383 original size:50 final size:50
Alignment explanation
Indices: 31827328--31827487 Score: 211
Period size: 50 Copynumber: 3.3 Consensus size: 50
31827318 GAGGAAAGAA
* * * *
31827328 AAAGAAGAA-AAGGAAAGGAAAGGAGAAGAAGAAGAAGAAGAAGAAAAATG
1 AAAGAAAAAGAAGGAAAGAAAAGGA-AAGGAGAAGAAGAAGAAGAAAAAAG
31827378 AAAGAAAAAGAAGGAAAGAAAAGGAAAGGAGAAGAAGAAGAAGAAAAAAG
1 AAAGAAAAAGAAGGAAAGAAAAGGAAAGGAGAAGAAGAAGAAGAAAAAAG
* *
31827428 AAAGAAAAAGAAGGAAAGAAAAAGAAAGGAGAAG-AGAA-AA-AAAAAGG
1 AAAGAAAAAGAAGGAAAGAAAAGGAAAGGAGAAGAAGAAGAAGAAAAAAG
* *
31827475 AAAGGAGAAGAAG
1 AAAGAAAAAGAAG
31827488 AGGGAAGGAA
Statistics
Matches: 101, Mismatches: 8, Indels: 5
0.89 0.07 0.04
Matches are distributed among these distances:
47 17 0.17
48 2 0.02
49 4 0.04
50 64 0.63
51 14 0.14
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.01
Consensus pattern (50 bp):
AAAGAAAAAGAAGGAAAGAAAAGGAAAGGAGAAGAAGAAGAAGAAAAAAG
Found at i:31827454 original size:6 final size:6
Alignment explanation
Indices: 31827322--31827454 Score: 65
Period size: 6 Copynumber: 21.2 Consensus size: 6
31827312 AAAGGAGAGG
* * * * * *
31827322 AAAGAA AAAGAAGA AAAGGA AAGGAA AGGAGAA GAAGAA GAAGAA GAAGAA
1 AAAGAA AAAG-A-A AAAGAA AAAGAA A-AAGAA AAAGAA AAAGAA AAAGAA
* * * *
31827373 AAATG-- AAAGAA AAAGAA GGAAAGAA AAGGAA AGGAGAA GAAGAA GAAGAA
1 AAA-GAA AAAGAA AAAGAA --AAAGAA AAAGAA A-AAGAA AAAGAA AAAGAA
*
31827423 AAA-AG AAAGAA AAAGAA GGAAAGAA AAAGAA A
1 AAAGAA AAAGAA AAAGAA --AAAGAA AAAGAA A
31827455 GGAGAAGAGA
Statistics
Matches: 99, Mismatches: 16, Indels: 24
0.71 0.12 0.17
Matches are distributed among these distances:
4 1 0.01
5 7 0.07
6 66 0.67
7 8 0.08
8 17 0.17
ACGTcount: A:0.71, C:0.00, G:0.29, T:0.01
Consensus pattern (6 bp):
AAAGAA
Found at i:31827477 original size:23 final size:22
Alignment explanation
Indices: 31827359--31827485 Score: 91
Period size: 23 Copynumber: 5.5 Consensus size: 22
31827349 GGAGAAGAAG
*
31827359 AAGAAGAAGAAGAAAAATGAAAGA
1 AAGAAGAAG-AGAAAAA-AAAAGA
31827383 AA-AAGAAG-GAAAGAAAAGGAAAGGA
1 AAGAAGAAGAG-AA-AAAA--AAA-GA
31827408 GAAGAAGAAGAAGAAAAAAGAAAGA
1 -AAGAAGAAG-AGAAAAAA-AAAGA
*
31827433 AA-AAGAAG-GAAAGAAAAAGA
1 AAGAAGAAGAGAAAAAAAAAGA
*
31827453 AAGGAGAAGAGAAAAAAAAAGGA
1 AAGAAGAAGAGAAAAAAAAA-GA
*
31827476 AAGGAGAAGA
1 AAGAAGAAGA
31827486 AGAGGGAAGG
Statistics
Matches: 87, Mismatches: 4, Indels: 25
0.75 0.03 0.22
Matches are distributed among these distances:
20 7 0.08
21 12 0.14
22 11 0.13
23 27 0.31
24 7 0.08
25 4 0.05
26 6 0.07
27 10 0.11
28 2 0.02
29 1 0.01
ACGTcount: A:0.70, C:0.00, G:0.29, T:0.01
Consensus pattern (22 bp):
AAGAAGAAGAGAAAAAAAAAGA
Found at i:31827503 original size:36 final size:35
Alignment explanation
Indices: 31827385--31827507 Score: 101
Period size: 33 Copynumber: 3.4 Consensus size: 35
31827375 ATGAAAGAAA
* *
31827385 AAGAAGG-AAAGAAAAGGAAAGGAGAAGAAGAAGAAGA
1 AAGAAGGAAAAAAAAAGGAAAGGAGAAGAAG-AG--GG
* * * *
31827422 AAAAAGAAAGAAAAAGAAGGAAAGAAAAAGAA-A-GG
1 AAGAAGGAA-AAAAA-AAGGAAAGGAGAAGAAGAGGG
31827457 -AGAAGAGAAAAAAAAAGGAAAGGAGAAGAAGAGGG
1 AAGAAG-GAAAAAAAAAGGAAAGGAGAAGAAGAGGG
31827492 AAGGAAGGAAAAAAAA
1 AA-GAAGGAAAAAAAA
31827508 GAAAAAAAAT
Statistics
Matches: 68, Mismatches: 10, Indels: 17
0.72 0.11 0.18
Matches are distributed among these distances:
33 14 0.21
34 10 0.15
35 5 0.07
36 10 0.15
37 9 0.13
38 2 0.03
39 4 0.06
40 14 0.21
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (35 bp):
AAGAAGGAAAAAAAAAGGAAAGGAGAAGAAGAGGG
Found at i:31827504 original size:33 final size:33
Alignment explanation
Indices: 31827335--31827516 Score: 94
Period size: 33 Copynumber: 5.5 Consensus size: 33
31827325 GAAAAAGAAG
* * *
31827335 AAAAGGAAAGGAAAGGAGAAGAAGAAGAAGAAGAAGA
1 AAAAGGAAAGAAAAAGA-AAGGAGAAG-AGAA-AA-A
* *
31827372 AAAATGAAAGAAAAAG-AA-G-GAA-AGAAAAG
1 AAAAGGAAAGAAAAAGAAAGGAGAAGAGAAAAA
* **
31827401 GAAAGGAGAAGAAGAAGAAGAAAAAAGAA-AG-AAAA
1 AAAAGGA-AAG-A-AA-AAGAAAGGAGAAGAGAAAAA
*
31827436 AGAAGGAAAGAAAAAGAAAGGAGAAGAGAAAAA
1 AAAAGGAAAGAAAAAGAAAGGAGAAGAGAAAAA
* *
31827469 AAAAGGAAAGGAGAAGAAGAGG-GAAG-GAAGGAAA
1 AAAAGGAAAGAAAAAGAA-AGGAGAAGAGAA--AAA
*
31827503 AAAAAGAAA-AAAAA
1 AAAAGGAAAGAAAAA
31827517 TAATTTTAAT
Statistics
Matches: 114, Mismatches: 19, Indels: 28
0.71 0.12 0.17
Matches are distributed among these distances:
29 5 0.04
30 5 0.04
31 15 0.13
32 9 0.08
33 33 0.29
34 19 0.17
35 10 0.09
36 5 0.04
37 13 0.11
ACGTcount: A:0.69, C:0.00, G:0.30, T:0.01
Consensus pattern (33 bp):
AAAAGGAAAGAAAAAGAAAGGAGAAGAGAAAAA
Found at i:31828221 original size:7 final size:8
Alignment explanation
Indices: 31828200--31828246 Score: 51
Period size: 8 Copynumber: 5.8 Consensus size: 8
31828190 TGAAATAATG
31828200 TAAAATTA
1 TAAAATTA
31828208 TAAAATTA
1 TAAAATTA
31828216 -AAAATTA
1 TAAAATTA
*
31828223 TAATATTTTA
1 TAA-A-ATTA
*
31828233 TAAAATAA
1 TAAAATTA
31828241 TAAAAT
1 TAAAAT
31828247 GCGGAGAAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
7 7 0.21
8 18 0.55
9 2 0.06
10 6 0.18
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (8 bp):
TAAAATTA
Found at i:31828424 original size:318 final size:319
Alignment explanation
Indices: 31827846--31828621 Score: 1360
Period size: 319 Copynumber: 2.4 Consensus size: 319
31827836 AATTGTATAT
* * * **
31827846 TTAATAAATTTCAAACATAATGCACTGAAGTAATGTAAAATGATAAAATTAAAAATTACGATATT
1 TTAATAAATTTCAAACATTATGCACTGAAATAATGTAAAATTATAAAATTAAAAATTATAATATT
* * *
31827911 TTTTAAAATAATAAAATGCGGATAAAAAAATACGAACAAATGGCCGAAGTAAGAGTGTATTACTA
66 TTATAAAATAATAAAATGCGGA-GAAAAAATACGAACAAATGGCCGAAGTAAGAGTGTATTACAA
*
31827976 ACTTTTTTAAAAATTCAGAAATAATTAATACAAATATTTCAAACAAAATGCATTGAAATAATATA
130 ACTTTTTTAAAAATTCAGAAATAATTAATACAAATATTTCAAACAAAATGCACTGAAATAATATA
31828041 AAATAAGAAAATAAGAAAATAAAATATTTTTATTGAAAGAAATAAAAATCGGAAAAATAATACGA
195 AAATAAGAAAATAAGAAAATAAAATATTTTTATTGAAAGAAATAAAAATCGGAAAAATAATACGA
31828106 GCAAAGGGCAGGGATAAGGG-TTTTTTCTTACACCAAATTAATTTAAAAAACACACTAAA
260 GCAAAGGGCAGGGATAAGGGTTTTTTTCTTACACCAAATTAATTTAAAAAACACACTAAA
31828165 TTAATAAATTTCAAACATTATGCACTGAAATAATGTAAAATTATAAAATTAAAAATTATAATATT
1 TTAATAAATTTCAAACATTATGCACTGAAATAATGTAAAATTATAAAATTAAAAATTATAATATT
*
31828230 TTATAAAATAATAAAATGCGGAGAAAAAATACGAACAAATGGCTGAAGTAAGAGTGTATTACAAA
66 TTATAAAATAATAAAATGCGGAGAAAAAATACGAACAAATGGCCGAAGTAAGAGTGTATTACAAA
*
31828295 CTTTTTTAAAAATTCAGAAATAATTAATACAAATATTTCAAACAAAATGCACTGGAATAATATAA
131 CTTTTTTAAAAATTCAGAAATAATTAATACAAATATTTCAAACAAAATGCACTGAAATAATATAA
* *
31828360 AATAATAAAATACA-AAAATAAAATATTTTTATTGAAAGTAATAAAAATC-GAGAAAATAATACG
196 AATAAGAAAATA-AGAAAATAAAATATTTTTATTGAAAGAAATAAAAATCGGA-AAAATAATACG
31828423 AGCAAAGGGCAGGGATAAGGGTTTTTTTCTTACACCAAATTAATTTAAAAAACACACTAAA
259 AGCAAAGGGCAGGGATAAGGGTTTTTTTCTTACACCAAATTAATTTAAAAAACACACTAAA
*
31828484 TTAATAAATTTCAAACATTATGCACTAAAATAATGTAAAATTATAAAATTAAAAATTATAATATT
1 TTAATAAATTTCAAACATTATGCACTGAAATAATGTAAAATTATAAAATTAAAAATTATAATATT
*
31828549 TTCTAAAATAATAAAATGCGGAGAAAAAAATACGAACAAATGGCCGAAGTAAGAGTGTATTACAA
66 TTATAAAATAATAAAATGCGGAG-AAAAAATACGAACAAATGGCCGAAGTAAGAGTGTATTACAA
31828614 ACTTTTTT
130 ACTTTTTT
31828622 TCAACTTGCA
Statistics
Matches: 437, Mismatches: 16, Indels: 7
0.95 0.03 0.02
Matches are distributed among these distances:
317 2 0.00
318 180 0.41
319 207 0.47
320 48 0.11
ACGTcount: A:0.51, C:0.09, G:0.11, T:0.29
Consensus pattern (319 bp):
TTAATAAATTTCAAACATTATGCACTGAAATAATGTAAAATTATAAAATTAAAAATTATAATATT
TTATAAAATAATAAAATGCGGAGAAAAAATACGAACAAATGGCCGAAGTAAGAGTGTATTACAAA
CTTTTTTAAAAATTCAGAAATAATTAATACAAATATTTCAAACAAAATGCACTGAAATAATATAA
AATAAGAAAATAAGAAAATAAAATATTTTTATTGAAAGAAATAAAAATCGGAAAAATAATACGAG
CAAAGGGCAGGGATAAGGGTTTTTTTCTTACACCAAATTAATTTAAAAAACACACTAAA
Found at i:31833734 original size:3 final size:3
Alignment explanation
Indices: 31833726--31833766 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
31833716 TAATACTAAG
31833726 AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AA
1 AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AA
31833767 TAATAATAAT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.68, C:0.32, G:0.00, T:0.00
Consensus pattern (3 bp):
AAC
Found at i:31833771 original size:3 final size:3
Alignment explanation
Indices: 31833765--31833789 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
31833755 CAACAACAAC
31833765 AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT A
31833790 GCTAAAACTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:31834077 original size:27 final size:27
Alignment explanation
Indices: 31834032--31834121 Score: 112
Period size: 27 Copynumber: 3.3 Consensus size: 27
31834022 GAGTAGTCCT
* *
31834032 GCCAATCAGTATGGAACCATTGGTGCT
1 GCCAATCAGTATGGCACCATTGGTGCC
*
31834059 GCCAACCTCA-T-TGGCACCATCGGTGCC
1 GCCAA--TCAGTATGGCACCATTGGTGCC
*
31834086 GCCAATCAGTATGGCACCTTTGGTGCC
1 GCCAATCAGTATGGCACCATTGGTGCC
31834113 GCCAATCAG
1 GCCAATCAG
31834122 AAACCCTCCA
Statistics
Matches: 54, Mismatches: 5, Indels: 8
0.81 0.07 0.12
Matches are distributed among these distances:
25 3 0.06
26 1 0.02
27 46 0.85
28 1 0.02
29 3 0.06
ACGTcount: A:0.22, C:0.31, G:0.24, T:0.22
Consensus pattern (27 bp):
GCCAATCAGTATGGCACCATTGGTGCC
Found at i:31837203 original size:46 final size:45
Alignment explanation
Indices: 31837094--31837475 Score: 399
Period size: 46 Copynumber: 8.3 Consensus size: 45
31837084 CTTACATATG
* *
31837094 ATCACTTATCAC-TTGTC-CCTGATCAGATAAGTGTAGCTAGGCT
1 ATCACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAGCT
* *
31837137 ACCACTTATCACTTTCTCACTTGATCAGATAAGTGTAGCTAAGGCT
1 ATCACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAA-GCT
*
31837183 AACACTTATCACTTTGTCACTTGATCAGATAA--GTA--T-AG--
1 ATCACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAGCT
*
31837221 --CACTTATCACTTTTTCACTTGATCAGATAAGTGTAGCTAAAGCT
1 ATCACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCT-AAGCT
* * * *
31837265 ACCACTTATCACTTTGTCTCTTGATCAGATAAGTATAGCCGAAGCT
1 ATCACTTATCACTTTGTCACTTGATCAGATAAGTGTAG-CTAAGCT
*
31837311 ATCACTTATCACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCT
1 ATCACTTATCAC---T---TTGTCACTTGATCAGATAAGTGTAG-CTAAGCT
31837363 ATCACTTATCACTTTCCACTTGTCACTTGATCAGATAAGTGTAGCTGAAGCT
1 ATCACTTATCAC--T----TTGTCACTTGATCAGATAAGTGTAGCT-AAGCT
* *
31837415 ATCACTTATCACTTTGTCACTTGATCAGATAAGTATAGCCGAAGCT
1 ATCACTTATCACTTTGTCACTTGATCAGATAAGTGTAG-CTAAGCT
*
31837461 ATTACTTATCACTTT
1 ATCACTTATCACTTT
31837476 CCACTTGTCA
Statistics
Matches: 298, Mismatches: 18, Indels: 43
0.83 0.05 0.12
Matches are distributed among these distances:
36 29 0.10
38 3 0.01
40 2 0.01
41 1 0.00
42 3 0.01
43 11 0.04
44 7 0.02
45 21 0.07
46 125 0.42
47 2 0.01
49 1 0.00
50 1 0.00
51 4 0.01
52 88 0.30
ACGTcount: A:0.29, C:0.22, G:0.15, T:0.35
Consensus pattern (45 bp):
ATCACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAGCT
Found at i:31837226 original size:36 final size:36
Alignment explanation
Indices: 31837185--31837303 Score: 130
Period size: 36 Copynumber: 3.0 Consensus size: 36
31837175 CTAAGGCTAA
31837185 CACTTATCACTTTGTCACTTGATCAGATAAGTATAG
1 CACTTATCACTTTGTCACTTGATCAGATAAGTATAG
*
31837221 CACTTATCACTTTTTCACTTGATCAGATAAGTGTAGCTAAAG
1 CACTTATCACTTTGTCACTTGATCAGATAA--GTA--T--AG
*
31837263 CTACCACTTATCACTTTGTCTCTTGATCAGATAAGTATAG
1 ----CACTTATCACTTTGTCACTTGATCAGATAAGTATAG
31837303 C
1 C
31837304 CGAAGCTATC
Statistics
Matches: 70, Mismatches: 3, Indels: 20
0.75 0.03 0.22
Matches are distributed among these distances:
36 30 0.43
38 3 0.04
40 3 0.04
42 3 0.04
44 3 0.04
46 28 0.40
ACGTcount: A:0.29, C:0.21, G:0.13, T:0.36
Consensus pattern (36 bp):
CACTTATCACTTTGTCACTTGATCAGATAAGTATAG
Found at i:31837246 original size:82 final size:82
Alignment explanation
Indices: 31837139--31837303 Score: 294
Period size: 82 Copynumber: 2.0 Consensus size: 82
31837129 GCTAGGCTAC
*
31837139 CACTTATCACTTTCTCACTTGATCAGATAAGTGTAGCTAAGGCTAACACTTATCACTTTGTCACT
1 CACTTATCACTTTCTCACTTGATCAGATAAGTGTAGCTAAAGCTAACACTTATCACTTTGTCACT
31837204 TGATCAGATAAGTATAG
66 TGATCAGATAAGTATAG
* * *
31837221 CACTTATCACTTTTTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTGTCTCT
1 CACTTATCACTTTCTCACTTGATCAGATAAGTGTAGCTAAAGCTAACACTTATCACTTTGTCACT
31837286 TGATCAGATAAGTATAG
66 TGATCAGATAAGTATAG
31837303 C
1 C
31837304 CGAAGCTATC
Statistics
Matches: 79, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
82 79 1.00
ACGTcount: A:0.30, C:0.21, G:0.14, T:0.35
Consensus pattern (82 bp):
CACTTATCACTTTCTCACTTGATCAGATAAGTGTAGCTAAAGCTAACACTTATCACTTTGTCACT
TGATCAGATAAGTATAG
Found at i:31837340 original size:52 final size:52
Alignment explanation
Indices: 31837267--31837495 Score: 335
Period size: 52 Copynumber: 4.5 Consensus size: 52
31837257 CTAAAGCTAC
* *
31837267 CACTTATCACTTTGTCTCTTGATCAGATAAGTATAGCCGAAGCTATCACTTAT
1 CACTTTTCAC-TTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACTTAT
*
31837320 CACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACTTAT
1 CACTTTTCACTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACTTAT
* * *
31837372 CACTTTCCACTTGTCACTTGATCAGATAAGTGTAGCTGAAGCTATCACTTAT
1 CACTTTTCACTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACTTAT
*
31837424 CAC---T---TTGTCACTTGATCAGATAAGTATAGCCGAAGCTATTACTTAT
1 CACTTTTCACTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACTTAT
*
31837470 CACTTTCCACTTGTCACTTGATCAGA
1 CACTTTTCACTTGTCACTTGATCAGA
31837496 AGTACTCAAA
Statistics
Matches: 160, Mismatches: 10, Indels: 13
0.87 0.05 0.07
Matches are distributed among these distances:
46 42 0.26
52 109 0.68
53 9 0.06
ACGTcount: A:0.28, C:0.23, G:0.14, T:0.35
Consensus pattern (52 bp):
CACTTTTCACTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACTTAT
Found at i:31837432 original size:98 final size:98
Alignment explanation
Indices: 31837221--31837495 Score: 373
Period size: 98 Copynumber: 2.8 Consensus size: 98
31837211 ATAAGTATAG
* ** *
31837221 CACTTATCACTTTTTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCAC--T----TT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACTTATCACTTTCCACTT
*
31837280 GTCTCTTGATCAGATAAGTATAGCCGAAGCTAT
66 GTCACTTGATCAGATAAGTATAGCCGAAGCTAT
31837313 CACTTATCACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACTTATCACTTT
1 CACTTATCAC---T---TTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACTTATCACTTT
* *
31837378 CCACTTGTCACTTGATCAGATAAGTGTAGCTGAAGCTAT
60 CCACTTGTCACTTGATCAGATAAGTATAGCCGAAGCTAT
* *
31837417 CACTTATCACTTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATTACTTATCACTTTCCACTT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACTTATCACTTTCCACTT
31837482 GTCACTTGATCAGA
66 GTCACTTGATCAGA
31837496 AGTACTCAAA
Statistics
Matches: 162, Mismatches: 9, Indels: 18
0.86 0.05 0.10
Matches are distributed among these distances:
92 10 0.06
95 1 0.01
98 107 0.66
100 1 0.01
101 1 0.01
104 42 0.26
ACGTcount: A:0.28, C:0.23, G:0.14, T:0.35
Consensus pattern (98 bp):
CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACTTATCACTTTCCACTT
GTCACTTGATCAGATAAGTATAGCCGAAGCTAT
Found at i:31850596 original size:42 final size:42
Alignment explanation
Indices: 31850537--31850635 Score: 164
Period size: 42 Copynumber: 2.4 Consensus size: 42
31850527 CAGTAGCTTC
31850537 ACACGGCCTGGCACAT-GGTCATGTAAGGCCATTTCGAAGGGT
1 ACACGGCCTGGCACATGGGTC-TGTAAGGCCATTTCGAAGGGT
31850579 ACACGGCCTGGCACATGGGTCTGTAAGGCCATTTCGAAGGGT
1 ACACGGCCTGGCACATGGGTCTGTAAGGCCATTTCGAAGGGT
**
31850621 ACACATCCTGGCACA
1 ACACGGCCTGGCACA
31850636 CGAGCGTGTG
Statistics
Matches: 54, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
42 50 0.93
43 4 0.07
ACGTcount: A:0.24, C:0.26, G:0.29, T:0.20
Consensus pattern (42 bp):
ACACGGCCTGGCACATGGGTCTGTAAGGCCATTTCGAAGGGT
Found at i:31851491 original size:38 final size:39
Alignment explanation
Indices: 31851440--31851548 Score: 148
Period size: 38 Copynumber: 2.8 Consensus size: 39
31851430 GTTTGATTCC
*
31851440 TTAATTATGTCATAATTTGAACATCATTAATATGAGT-T
1 TTAATTATGTCATAATTTGAACATCATTAATAAGAGTAT
* * *
31851478 TTAATTATGTCATAATCTAAATATCATTAATAAGAGTAT
1 TTAATTATGTCATAATTTGAACATCATTAATAAGAGTAT
* * *
31851517 TTAATTATGTCATAGTTTGGACATCTTTAATA
1 TTAATTATGTCATAATTTGAACATCATTAATA
31851549 CATGTTTTTA
Statistics
Matches: 60, Mismatches: 10, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
38 33 0.55
39 27 0.45
ACGTcount: A:0.38, C:0.08, G:0.10, T:0.44
Consensus pattern (39 bp):
TTAATTATGTCATAATTTGAACATCATTAATAAGAGTAT
Found at i:31851559 original size:39 final size:38
Alignment explanation
Indices: 31851440--31851559 Score: 125
Period size: 39 Copynumber: 3.1 Consensus size: 38
31851430 GTTTGATTCC
*
31851440 TTAATTATGTCATAATTTGAACATCATTAAT-ATGAGTT
1 TTAATTATGTCATAATTTGAACATCATTAATAATG-TTT
* * * * *
31851478 TTAATTATGTCATAATCTAAATATCATTAATAAGAGTAT
1 TTAATTATGTCATAATTTGAACATCATTAATAA-TGTTT
* * *
31851517 TTAATTATGTCATAGTTTGGACATCTTTAATACATGTTT
1 TTAATTATGTCATAATTTGAACATCATTAATA-ATGTTT
31851556 TTAA
1 TTAA
31851560 GTGTGTTTAA
Statistics
Matches: 65, Mismatches: 14, Indels: 5
0.77 0.17 0.06
Matches are distributed among these distances:
38 28 0.43
39 35 0.54
40 2 0.03
ACGTcount: A:0.37, C:0.08, G:0.10, T:0.45
Consensus pattern (38 bp):
TTAATTATGTCATAATTTGAACATCATTAATAATGTTT
Found at i:31857571 original size:20 final size:18
Alignment explanation
Indices: 31857524--31857572 Score: 57
Period size: 20 Copynumber: 2.7 Consensus size: 18
31857514 CAAGATAAAC
31857524 ATTAAATTAA-ATTTAAT
1 ATTAAATTAATATTTAAT
31857541 ATTAAGA-TAATCACTTTAAT
1 ATTAA-ATTAAT-A-TTTAAT
31857561 ATTAAATTAATA
1 ATTAAATTAATA
31857573 AAATACTATT
Statistics
Matches: 27, Mismatches: 0, Indels: 8
0.77 0.00 0.23
Matches are distributed among these distances:
17 8 0.30
18 1 0.04
19 3 0.11
20 15 0.56
ACGTcount: A:0.51, C:0.04, G:0.02, T:0.43
Consensus pattern (18 bp):
ATTAAATTAATATTTAAT
Found at i:31859249 original size:15 final size:15
Alignment explanation
Indices: 31859225--31859256 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
31859215 TGTGCATGCA
*
31859225 AAATATAAAAGACAT
1 AAATACAAAAGACAT
31859240 AAATACAAAAGACAT
1 AAATACAAAAGACAT
31859255 AA
1 AA
31859257 TAGTGAAATG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.69, C:0.09, G:0.06, T:0.16
Consensus pattern (15 bp):
AAATACAAAAGACAT
Found at i:31860564 original size:206 final size:206
Alignment explanation
Indices: 31860203--31860607 Score: 648
Period size: 206 Copynumber: 2.0 Consensus size: 206
31860193 GATAGTTGGT
* *
31860203 ATGTAAGTGTATACAAAAACTGTAGTGGTATCCACCCGAGGTAGAAGAAAGTGGTCTAAAAAGGA
1 ATGTAACTGTATACAAAAACTGTAGTGGTATCCACCCGAGGTAGAAGAAAGTGGTCTAAAAAGAA
*
31860268 TAATTGGGGCACAGATGTTCATTAATCATAATCAATATTAGCCAAGGTATATTTTGGATTAAAAC
66 TAATTGGGGCACAGATGTTCATTAATCATAATCAATATCAGCCAAGGTATATTTTGGATTAAAAC
*
31860333 TCATTAAGTTCTCCTGAACTTACAAAAAAAATATATTTATGTTTCAAGTAAAGTGGGATGTATTG
131 TCATTAAGTTCTCCTGAACTTACAAAAAAAATATATTTATGTTTCAAGTAAAGTGAGATGTATTG
31860398 CGTCGGGTGGC
196 CGTCGGGTGGC
* ** *
31860409 ATGTAACTGTATACCAAAACTGTAGTGGTATCTGCCCGAGGTAGAAGAAAGTGGTCTAAAAATAA
1 ATGTAACTGTATACAAAAACTGTAGTGGTATCCACCCGAGGTAGAAGAAAGTGGTCTAAAAAGAA
* * * *
31860474 TAGTTGGTGCACAGATGTTCATTAATCATAATCAATATCCGCCAAGGTATATTTTGGATTAAAGC
66 TAATTGGGGCACAGATGTTCATTAATCATAATCAATATCAGCCAAGGTATATTTTGGATTAAAAC
* *** * *
31860539 TCATTAAGTTCTCTTGAACTTACAAAAATGTTATATTTATGTTTCAGGTAAGGTGAGATGTATTG
131 TCATTAAGTTCTCCTGAACTTACAAAAAAAATATATTTATGTTTCAAGTAAAGTGAGATGTATTG
31860604 CGTC
196 CGTC
31860608 AGGAGGGAGG
Statistics
Matches: 181, Mismatches: 18, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
206 181 1.00
ACGTcount: A:0.35, C:0.13, G:0.21, T:0.32
Consensus pattern (206 bp):
ATGTAACTGTATACAAAAACTGTAGTGGTATCCACCCGAGGTAGAAGAAAGTGGTCTAAAAAGAA
TAATTGGGGCACAGATGTTCATTAATCATAATCAATATCAGCCAAGGTATATTTTGGATTAAAAC
TCATTAAGTTCTCCTGAACTTACAAAAAAAATATATTTATGTTTCAAGTAAAGTGAGATGTATTG
CGTCGGGTGGC
Found at i:31877384 original size:30 final size:30
Alignment explanation
Indices: 31877343--31877455 Score: 142
Period size: 30 Copynumber: 3.8 Consensus size: 30
31877333 GTGCAACAGA
*
31877343 CAGA-TCAGTTACAGATGCAGATATAGGTT
1 CAGATTCAGTTACAGATGCAGATATAGATT
* *
31877372 CAGATTCGGTTACTGATGCAGATACTA-ATAT
1 CAGATTCAGTTACAGATGCAGATA-TAGAT-T
*
31877403 -AGATTCAGTTACAGATGCAGATATAGATA
1 CAGATTCAGTTACAGATGCAGATATAGATT
*
31877432 CAAATTCAGTTACAGATGCAGATA
1 CAGATTCAGTTACAGATGCAGATA
31877456 AATGTACAAA
Statistics
Matches: 72, Mismatches: 7, Indels: 9
0.82 0.08 0.10
Matches are distributed among these distances:
29 6 0.08
30 63 0.88
31 3 0.04
ACGTcount: A:0.37, C:0.14, G:0.20, T:0.28
Consensus pattern (30 bp):
CAGATTCAGTTACAGATGCAGATATAGATT
Found at i:31877464 original size:30 final size:29
Alignment explanation
Indices: 31877347--31877470 Score: 124
Period size: 30 Copynumber: 4.1 Consensus size: 29
31877337 AACAGACAGA
* * *
31877347 TCAGTTACAGATGCAGATATAGGTTCAGAT
1 TCAGTTACAGATGCAGATA-AAGTACAAAT
* * * *
31877377 TCGGTTACTGATGCAGATACTAA-TATAGAT
1 TCAGTTACAGATGCAGATA--AAGTACAAAT
*
31877407 TCAGTTACAGATGCAGATATAGATACAAAT
1 TCAGTTACAGATGCAGATAAAG-TACAAAT
31877437 TCAGTTACAGATGCAGATAAATGTACAAAT
1 TCAGTTACAGATGCAGATAAA-GTACAAAT
31877467 TCAG
1 TCAG
31877471 ATCTTACCCT
Statistics
Matches: 79, Mismatches: 11, Indels: 8
0.81 0.11 0.08
Matches are distributed among these distances:
28 1 0.01
30 75 0.95
31 3 0.04
ACGTcount: A:0.38, C:0.14, G:0.19, T:0.29
Consensus pattern (29 bp):
TCAGTTACAGATGCAGATAAAGTACAAAT
Found at i:31877469 original size:60 final size:59
Alignment explanation
Indices: 31877347--31877470 Score: 151
Period size: 60 Copynumber: 2.1 Consensus size: 59
31877337 AACAGACAGA
* * * * * * *
31877347 TCAGTTACAGATGCAGATATAGGTTCAGATTCGGTTACTGATGCAGATACTAATATAGAT
1 TCAGTTACAGATGCAGATATAGATACAAATTCAGTTACAGATGCAGATAC-AATACAAAT
31877407 TCAGTTACAGATGCAGATATAGATACAAATTCAGTTACAGATGCAGATA-AATGTACAAAT
1 TCAGTTACAGATGCAGATATAGATACAAATTCAGTTACAGATGCAGATACAA--TACAAAT
31877467 TCAG
1 TCAG
31877471 ATCTTACCCT
Statistics
Matches: 55, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
58 2 0.04
60 53 0.96
ACGTcount: A:0.38, C:0.14, G:0.19, T:0.29
Consensus pattern (59 bp):
TCAGTTACAGATGCAGATATAGATACAAATTCAGTTACAGATGCAGATACAATACAAAT
Found at i:31877615 original size:23 final size:22
Alignment explanation
Indices: 31877583--31877628 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 22
31877573 CACTTTTTAG
31877583 AATAGCGCAGTCAAGCTGCCAGA
1 AATAGCGCAGT-AAGCTGCCAGA
* *
31877606 AATAGTGCAGTAATCTGCCAGA
1 AATAGCGCAGTAAGCTGCCAGA
31877628 A
1 A
31877629 TAAGATAAGT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 11 0.52
23 10 0.48
ACGTcount: A:0.37, C:0.22, G:0.24, T:0.17
Consensus pattern (22 bp):
AATAGCGCAGTAAGCTGCCAGA
Found at i:31879612 original size:15 final size:15
Alignment explanation
Indices: 31879592--31879620 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
31879582 TAATAGGGAA
31879592 ATGAATGAGAGAATG
1 ATGAATGAGAGAATG
31879607 ATGAATGAGAGAAT
1 ATGAATGAGAGAAT
31879621 AAACAAGAGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.48, C:0.00, G:0.31, T:0.21
Consensus pattern (15 bp):
ATGAATGAGAGAATG
Found at i:31893908 original size:19 final size:19
Alignment explanation
Indices: 31893886--31893959 Score: 78
Period size: 19 Copynumber: 3.9 Consensus size: 19
31893876 GAACGCATAC
31893886 TGGCACAT-AAGGTGCATCT
1 TGGCACATGAA-GTGCATCT
*
31893905 TGGCTCATGAAGTGCATCT
1 TGGCACATGAAGTGCATCT
* * *
31893924 TGGCGCATGAAGAGCGTCT
1 TGGCACATGAAGTGCATCT
* *
31893943 TAGCACATAAAGTGCAT
1 TGGCACATGAAGTGCAT
31893960 AAAATCGTAC
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
19 43 0.96
20 2 0.04
ACGTcount: A:0.27, C:0.20, G:0.27, T:0.26
Consensus pattern (19 bp):
TGGCACATGAAGTGCATCT
Found at i:31895482 original size:9 final size:9
Alignment explanation
Indices: 31895468--31895534 Score: 59
Period size: 9 Copynumber: 7.6 Consensus size: 9
31895458 TAATTTTATT
31895468 TTATAAAAA
1 TTATAAAAA
*
31895477 TTATAATAA
1 TTATAAAAA
*
31895486 -TAT--TAA
1 TTATAAAAA
31895492 TTATAAAAA
1 TTATAAAAA
31895501 TTATAATAAA
1 TTATAA-AAA
* *
31895511 TGAAAAATAA
1 TTATAAA-AA
31895521 TTATAAAAA
1 TTATAAAAA
31895530 TTATA
1 TTATA
31895535 TAGAGAATTG
Statistics
Matches: 47, Mismatches: 6, Indels: 10
0.75 0.10 0.16
Matches are distributed among these distances:
6 3 0.06
7 3 0.06
8 3 0.06
9 24 0.51
10 14 0.30
ACGTcount: A:0.61, C:0.00, G:0.01, T:0.37
Consensus pattern (9 bp):
TTATAAAAA
Found at i:31895563 original size:10 final size:10
Alignment explanation
Indices: 31895550--31895602 Score: 54
Period size: 10 Copynumber: 5.4 Consensus size: 10
31895540 AATTGTAGAG
31895550 AAAATATTAA
1 AAAATATTAA
* *
31895560 AAAATGTT-G
1 AAAATATTAA
*
31895569 AAAATAGTAA
1 AAAATATTAA
**
31895579 AAAATAAGAA
1 AAAATATTAA
31895589 AAAATATTAA
1 AAAATATTAA
31895599 AAAA
1 AAAA
31895603 AACATATAAA
Statistics
Matches: 33, Mismatches: 9, Indels: 2
0.75 0.20 0.05
Matches are distributed among these distances:
9 6 0.18
10 27 0.82
ACGTcount: A:0.70, C:0.00, G:0.08, T:0.23
Consensus pattern (10 bp):
AAAATATTAA
Found at i:31895632 original size:19 final size:19
Alignment explanation
Indices: 31895610--31895646 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
31895600 AAAAACATAT
31895610 AAATTGCAAAAATTATAAC
1 AAATTGCAAAAATTATAAC
*
31895629 AAATTGTAAAAATTATAA
1 AAATTGCAAAAATTATAA
31895647 AGAGTTATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.59, C:0.05, G:0.05, T:0.30
Consensus pattern (19 bp):
AAATTGCAAAAATTATAAC
Found at i:31895675 original size:21 final size:21
Alignment explanation
Indices: 31895635--31895676 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
31895625 TAACAAATTG
* * *
31895635 TAAAAATTATAAAGAGTTATT
1 TAAAAACTATAAAAAATTATT
31895656 TAAAAACTATAAAAAATTATT
1 TAAAAACTATAAAAAATTATT
31895677 AAACATATTA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.57, C:0.02, G:0.05, T:0.36
Consensus pattern (21 bp):
TAAAAACTATAAAAAATTATT
Found at i:31896096 original size:19 final size:20
Alignment explanation
Indices: 31896069--31896106 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 20
31896059 TTTTTTAAAA
* *
31896069 ATAATTTTTGTAAT-TTTTT
1 ATAACTTTTATAATGTTTTT
31896088 ATAACTTTTATAATGTTTT
1 ATAACTTTTATAATGTTTT
31896107 GCACTTTTAC
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 12 0.75
20 4 0.25
ACGTcount: A:0.29, C:0.03, G:0.05, T:0.63
Consensus pattern (20 bp):
ATAACTTTTATAATGTTTTT
Found at i:31904666 original size:11 final size:11
Alignment explanation
Indices: 31904650--31904707 Score: 57
Period size: 11 Copynumber: 5.2 Consensus size: 11
31904640 AGGTAAATAT
31904650 TATTTTATTAA
1 TATTTTATTAA
*
31904661 TATTTTGATTTGA
1 TATTTT-A-TTAA
*
31904674 TA-TTTATTTA
1 TATTTTATTAA
31904684 TATTTTATTAA
1 TATTTTATTAA
31904695 T-TTTTACTTAA
1 TATTTTA-TTAA
31904706 TA
1 TA
31904708 CATAAGGAAG
Statistics
Matches: 39, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
10 10 0.26
11 20 0.51
12 4 0.10
13 5 0.13
ACGTcount: A:0.31, C:0.02, G:0.03, T:0.64
Consensus pattern (11 bp):
TATTTTATTAA
Found at i:31905442 original size:22 final size:22
Alignment explanation
Indices: 31905389--31905461 Score: 65
Period size: 22 Copynumber: 3.3 Consensus size: 22
31905379 ATTTTAGCGC
* * * *
31905389 GCTTACCGTCTTGCACTTTAGC
1 GCTTACTGTTTTGCACTTCAGT
*
31905411 GCTTATTGTTTTGCACTTCAGT
1 GCTTACTGTTTTGCACTTCAGT
* * *
31905433 GCTTACTGTTCTACACTTCGGT
1 GCTTACTGTTTTGCACTTCAGT
*
31905455 GCCTACT
1 GCTTACT
31905462 ATTCAGAACT
Statistics
Matches: 41, Mismatches: 10, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
22 41 1.00
ACGTcount: A:0.14, C:0.27, G:0.18, T:0.41
Consensus pattern (22 bp):
GCTTACTGTTTTGCACTTCAGT
Found at i:31908362 original size:25 final size:25
Alignment explanation
Indices: 31908273--31908367 Score: 79
Period size: 25 Copynumber: 3.8 Consensus size: 25
31908263 TGTTCCGACC
* *
31908273 CACAGCTCGTTTGAGCATACCGATT
1 CACAACTCGTATGAGCATACCGATT
* * *
31908298 TATAGCTCGTGA-GAGCATACCGA-T
1 CACAACTCGT-ATGAGCATACCGATT
* *
31908322 CTACAAGTC-AAGTGAGCATACCGATT
1 C-ACAACTCGTA-TGAGCATACCGATT
31908348 CACAACTCGTATGAGCATAC
1 CACAACTCGTATGAGCATAC
31908368 ATGCACATGA
Statistics
Matches: 54, Mismatches: 10, Indels: 12
0.71 0.13 0.16
Matches are distributed among these distances:
23 1 0.02
24 1 0.02
25 49 0.91
26 3 0.06
ACGTcount: A:0.31, C:0.25, G:0.20, T:0.24
Consensus pattern (25 bp):
CACAACTCGTATGAGCATACCGATT
Found at i:31914766 original size:96 final size:96
Alignment explanation
Indices: 31914575--31914759 Score: 298
Period size: 96 Copynumber: 1.9 Consensus size: 96
31914565 CTTACTTTTT
*
31914575 TCTCTAGTTGGATATTTCATTGGAAATTGGAAACCATTATGATCTTTTGAACTACACCAATAACA
1 TCTCTAGTTGGATATTTAATTGGAAATTGGAAACCATTATGATCTTTTGAACTACACCAATAACA
* *
31914640 TTGCATAAAAGGTGATATCTCAATCATATTC
66 TTGCACAAAAGGTGATAGCTCAATCATATTC
* * * *
31914671 TCTCTATTTGGATATTTAATTGGACATTGGAAACCCTTATGATCTTTTGAACTAGACCAATAACA
1 TCTCTAGTTGGATATTTAATTGGAAATTGGAAACCATTATGATCTTTTGAACTACACCAATAACA
*
31914736 TTTCACAAAAGGTGATAGCTCAAT
66 TTGCACAAAAGGTGATAGCTCAAT
31914760 TGTATTCCTC
Statistics
Matches: 81, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
96 81 1.00
ACGTcount: A:0.34, C:0.17, G:0.14, T:0.35
Consensus pattern (96 bp):
TCTCTAGTTGGATATTTAATTGGAAATTGGAAACCATTATGATCTTTTGAACTACACCAATAACA
TTGCACAAAAGGTGATAGCTCAATCATATTC
Found at i:31928148 original size:42 final size:43
Alignment explanation
Indices: 31928060--31928207 Score: 138
Period size: 43 Copynumber: 3.4 Consensus size: 43
31928050 GCATACGTCA
* * * *
31928060 CAGACGAGGTCTTACATGTAATCCAATATCGATGCCACTGTCC
1 CAGACAAGGTCTTACACGAAATCCAATATCGATGCCAATGTCC
** *
31928103 CAGACAAGGTCTTACACGAAATCTTATA-CGATGTCAATGTCC
1 CAGACAAGGTCTTACACGAAATCCAATATCGATGCCAATGTCC
* * **
31928145 CAGACATGGTCTTACACATAAATCTCAA-ATCGATGCCAACATCC
1 CAGACAAGGTCTTACAC-GAAATC-CAATATCGATGCCAATGTCC
* **
31928189 TAGACGTGGTCTTACACGA
1 CAGACAAGGTCTTACACGA
31928208 TATCATATAT
Statistics
Matches: 85, Mismatches: 17, Indels: 6
0.79 0.16 0.06
Matches are distributed among these distances:
42 28 0.33
43 30 0.35
44 27 0.32
ACGTcount: A:0.32, C:0.26, G:0.17, T:0.25
Consensus pattern (43 bp):
CAGACAAGGTCTTACACGAAATCCAATATCGATGCCAATGTCC
Found at i:31929306 original size:13 final size:13
Alignment explanation
Indices: 31929288--31929314 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
31929278 CACAAACGAT
31929288 AAAATTTTCACAC
1 AAAATTTTCACAC
31929301 AAAATTTTCACAC
1 AAAATTTTCACAC
31929314 A
1 A
31929315 TATAAATTAA
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:0.48, C:0.22, G:0.00, T:0.30
Consensus pattern (13 bp):
AAAATTTTCACAC
Found at i:31930430 original size:21 final size:21
Alignment explanation
Indices: 31930402--31930444 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
31930392 TAATGATATA
*
31930402 TATAAATTATATATTT-TTAT
1 TATAAATTACATATTTATTAT
31930422 TATACAATTACATATTTATTAT
1 TATA-AATTACATATTTATTAT
31930444 T
1 T
31930445 TTATTTATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 4 0.20
21 11 0.55
22 5 0.25
ACGTcount: A:0.40, C:0.05, G:0.00, T:0.56
Consensus pattern (21 bp):
TATAAATTACATATTTATTAT
Found at i:31933905 original size:42 final size:41
Alignment explanation
Indices: 31933844--31933984 Score: 151
Period size: 41 Copynumber: 3.3 Consensus size: 41
31933834 AGATATGAAA
31933844 TAAAA-AAAAAGAAGTGAAATTAATAAGTTGTTATTTTAAATTT
1 TAAAAGAAAAA-AA-TGAAATTAATAAGTT-TTATTTTAAATTT
* * *
31933887 TATAAGAAACAAATGAAATTAATAAGTTTTTTATTTAAA-TT
1 TAAAAGAAAAAAATGAAATTAATAAGTTTTAT-TTTAAATTT
* * * *
31933928 TAGAAGAAAAAAAAGAAATTAATTAGTTTGTAATTTAAATTT
1 TAAAAGAAAAAAATGAAATTAATAAGTTT-TATTTTAAATTT
31933970 TGAAAAGAAAAAAAT
1 T-AAAAGAAAAAAAT
31933985 ATTTTTGGAC
Statistics
Matches: 82, Mismatches: 11, Indels: 10
0.80 0.11 0.10
Matches are distributed among these distances:
41 36 0.44
42 25 0.30
43 17 0.21
44 4 0.05
ACGTcount: A:0.53, C:0.01, G:0.11, T:0.35
Consensus pattern (41 bp):
TAAAAGAAAAAAATGAAATTAATAAGTTTTATTTTAAATTT
Found at i:31937630 original size:18 final size:19
Alignment explanation
Indices: 31937596--31937632 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
31937586 GTAAACTAAG
31937596 TTAAATAAAACTAACCAAA
1 TTAAATAAAACTAACCAAA
*
31937615 TTAAGTAAAA-TAACCAAA
1 TTAAATAAAACTAACCAAA
31937633 CCAAATTACA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 8 0.47
19 9 0.53
ACGTcount: A:0.62, C:0.14, G:0.03, T:0.22
Consensus pattern (19 bp):
TTAAATAAAACTAACCAAA
Found at i:31941867 original size:13 final size:13
Alignment explanation
Indices: 31941849--31941875 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
31941839 CACAAATGAT
31941849 AAAATTTTCACAC
1 AAAATTTTCACAC
31941862 AAAATTTTCACAC
1 AAAATTTTCACAC
31941875 A
1 A
31941876 TATAAATTAA
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:0.48, C:0.22, G:0.00, T:0.30
Consensus pattern (13 bp):
AAAATTTTCACAC
Found at i:31958552 original size:26 final size:25
Alignment explanation
Indices: 31958517--31958592 Score: 107
Period size: 26 Copynumber: 3.0 Consensus size: 25
31958507 AATTATCCCT
31958517 ATTTTACCCTAGTAAAACTTTGACG
1 ATTTTACCCTAGTAAAACTTTGACG
*
31958542 ATTTTACCCCTAGTAAAACTTTAACG
1 ATTTTA-CCCTAGTAAAACTTTGACG
* *
31958568 ATTTTAACCCTAGCAAAATTTTGAC
1 ATTTT-ACCCTAGTAAAACTTTGAC
31958593 AAGTTTGCCT
Statistics
Matches: 45, Mismatches: 4, Indels: 3
0.87 0.08 0.06
Matches are distributed among these distances:
25 6 0.13
26 38 0.84
27 1 0.02
ACGTcount: A:0.34, C:0.21, G:0.09, T:0.36
Consensus pattern (25 bp):
ATTTTACCCTAGTAAAACTTTGACG
Found at i:31963158 original size:29 final size:28
Alignment explanation
Indices: 31963108--31963181 Score: 71
Period size: 29 Copynumber: 2.6 Consensus size: 28
31963098 TAGAGATAGT
*
31963108 CACAAAGGC-TTCCATGTTTAGAGATTTGT-
1 CACAAAGGCATTCC-T-TCTAGAGATTT-TC
* *
31963137 CACAGAGGCATTTCCTTCTAGAGGTTTTC
1 CACAAAGGCA-TTCCTTCTAGAGATTTTC
31963166 CACAAAGGCATTCCTT
1 CACAAAGGCATTCCTT
31963182 AACATTCAAT
Statistics
Matches: 38, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
28 7 0.18
29 26 0.68
30 1 0.03
31 4 0.11
ACGTcount: A:0.26, C:0.23, G:0.19, T:0.32
Consensus pattern (28 bp):
CACAAAGGCATTCCTTCTAGAGATTTTC
Found at i:31963445 original size:53 final size:54
Alignment explanation
Indices: 31963354--31963463 Score: 143
Period size: 53 Copynumber: 2.1 Consensus size: 54
31963344 TTCCTTAAAT
* *
31963354 TTTCTCATATGATGTCATAACCCACCAATTACGATCTTACACAATATGGTATTC
1 TTTCTCATATGATGCCATAACCCACCAATTACGATCTTACACAATATAGTATTC
* * * *
31963408 TTTC-CATATGATGCCATAACCCA-CAAGTTATGGTCTTACACGATATAGTCTTC
1 TTTCTCATATGATGCCATAACCCACCAA-TTACGATCTTACACAATATAGTATTC
31963461 TTT
1 TTT
31963464 AGTGTCATGG
Statistics
Matches: 49, Mismatches: 6, Indels: 3
0.84 0.10 0.05
Matches are distributed among these distances:
52 3 0.06
53 42 0.86
54 4 0.08
ACGTcount: A:0.29, C:0.24, G:0.11, T:0.36
Consensus pattern (54 bp):
TTTCTCATATGATGCCATAACCCACCAATTACGATCTTACACAATATAGTATTC
Found at i:31968377 original size:15 final size:15
Alignment explanation
Indices: 31968357--31968407 Score: 52
Period size: 15 Copynumber: 3.5 Consensus size: 15
31968347 ACAACTCGTT
31968357 AATGTAAGTGACTAA
1 AATGTAAGTGACTAA
* *
31968372 AATGTAA-T-ATTTTA
1 AATGTAAGTGA-CTAA
*
31968386 AATATAAGTGACTAA
1 AATGTAAGTGACTAA
31968401 AATGTAA
1 AATGTAA
31968408 CCTTAAGTAA
Statistics
Matches: 27, Mismatches: 6, Indels: 6
0.69 0.15 0.15
Matches are distributed among these distances:
13 1 0.04
14 9 0.33
15 16 0.59
16 1 0.04
ACGTcount: A:0.49, C:0.04, G:0.14, T:0.33
Consensus pattern (15 bp):
AATGTAAGTGACTAA
Found at i:31971536 original size:47 final size:49
Alignment explanation
Indices: 31971459--31971554 Score: 128
Period size: 47 Copynumber: 2.0 Consensus size: 49
31971449 AACATGTGAA
*
31971459 AATGTGATTATGTGATTTTCGTGTAAGACCATA-TCTGAGA-TATGGCATC
1 AATGTGATTATGTGATTTACGTGTAAGACCATAGT-TG-GACTATGGCATC
*
31971508 AATGTGA-TATGTGA-TTACGTGTAGGACCATAGTTGGACTATGGCATC
1 AATGTGATTATGTGATTTACGTGTAAGACCATAGTTGGACTATGGCATC
31971555 GAGAAAAACG
Statistics
Matches: 43, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
46 2 0.05
47 26 0.60
48 8 0.19
49 7 0.16
ACGTcount: A:0.28, C:0.12, G:0.25, T:0.34
Consensus pattern (49 bp):
AATGTGATTATGTGATTTACGTGTAAGACCATAGTTGGACTATGGCATC
Found at i:31974836 original size:26 final size:26
Alignment explanation
Indices: 31974800--31974850 Score: 84
Period size: 26 Copynumber: 2.0 Consensus size: 26
31974790 TTGAATAAAA
31974800 AGGGGTCGCTAAGTGCAGATTCCCCG
1 AGGGGTCGCTAAGTGCAGATTCCCCG
* *
31974826 AGGGGTTGCTAAGTGCTGATTCCCC
1 AGGGGTCGCTAAGTGCAGATTCCCC
31974851 AAATTATTGA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.18, C:0.25, G:0.33, T:0.24
Consensus pattern (26 bp):
AGGGGTCGCTAAGTGCAGATTCCCCG
Found at i:31974930 original size:43 final size:44
Alignment explanation
Indices: 31974865--31975063 Score: 159
Period size: 43 Copynumber: 4.7 Consensus size: 44
31974855 TATTGACTCT
* *
31974865 AAAGGTGGTTGCTAAGTT-CTAATTCCACCATATCTTTGATTGTG
1 AAAGGTGGTTGCTAA-TTGCTAATTCCACCGTATCATTGATTGTG
* * * *
31974909 AAAGG-GGTTGCTACTTGCTAATTCC-CCGTATCACTGAATAT-
1 AAAGGTGGTTGCTAATTGCTAATTCCACCGTATCATTGATTGTG
* * * * *
31974950 ATAGGTGGTTGCTAAGTGTTGATTCCACCGTATCCTTGATTGTG
1 AAAGGTGGTTGCTAATTGCTAATTCCACCGTATCATTGATTGTG
* *
31974994 AAAGG-GGTTGCT-ATGTGCTGATTCC-CCGTATCACTGAATT-T-
1 AAAGGTGGTTGCTAAT-TGCTAATTCCACCGTATCATTG-ATTGTG
*
31975035 AAA-GTGGTTGCTAAGTGCTGAA-TCCACCG
1 AAAGGTGGTTGCTAATTGCT-AATTCCACCG
31975064 AGTAACAGAT
Statistics
Matches: 123, Mismatches: 22, Indels: 22
0.74 0.13 0.13
Matches are distributed among these distances:
40 1 0.01
41 21 0.17
42 45 0.37
43 47 0.38
44 9 0.07
ACGTcount: A:0.24, C:0.19, G:0.24, T:0.34
Consensus pattern (44 bp):
AAAGGTGGTTGCTAATTGCTAATTCCACCGTATCATTGATTGTG
Found at i:31974975 original size:85 final size:84
Alignment explanation
Indices: 31974866--31975062 Score: 281
Period size: 85 Copynumber: 2.3 Consensus size: 84
31974856 ATTGACTCTA
* *
31974866 AAGGTGGTTGCTAAGT-TCTAATTCCACCATATCTTTGATTGTGAAAGGGGTTGCTACT-TGCTA
1 AAGGTGGTTGCTAAGTGT-TGATTCCACCATATCCTTGATTGTGAAAGGGGTTGCTA-TGTGCTA
31974929 ATTCCCCGTATCACTGAATAT
64 ATTCCCCGTATCACTGAATAT
* *
31974950 ATAGGTGGTTGCTAAGTGTTGATTCCACCGTATCCTTGATTGTGAAAGGGGTTGCTATGTGCTGA
1 A-AGGTGGTTGCTAAGTGTTGATTCCACCATATCCTTGATTGTGAAAGGGGTTGCTATGTGCTAA
*
31975015 TTCCCCGTATCACTGAATTT
65 TTCCCCGTATCACTGAATAT
* * *
31975035 AAAGTGGTTGCTAAGTGCTGAATCCACC
1 AAGGTGGTTGCTAAGTGTTGATTCCACC
31975063 GAGTAACAGA
Statistics
Matches: 102, Mismatches: 8, Indels: 6
0.88 0.07 0.05
Matches are distributed among these distances:
84 26 0.25
85 75 0.74
86 1 0.01
ACGTcount: A:0.23, C:0.19, G:0.23, T:0.35
Consensus pattern (84 bp):
AAGGTGGTTGCTAAGTGTTGATTCCACCATATCCTTGATTGTGAAAGGGGTTGCTATGTGCTAAT
TCCCCGTATCACTGAATAT
Found at i:31977361 original size:153 final size:153
Alignment explanation
Indices: 31976932--31977754 Score: 1133
Period size: 153 Copynumber: 5.4 Consensus size: 153
31976922 TTAGTGTGTT
* *
31976932 TTTTTATTGAAAGTAATAAAATCCGGTAAAAAAAATACGAACAACAAAGGGCTGAAATAAGGGTT
1 TTTTTATTAAAAGTAATAAAATCC-G-AAAAAAAATACG---AACAAAGGGCCGAAATAAGGG-T
*
31976997 TTTTTTAAATTTAAATAAAAAAACACACTAAATGAATACATTTCAAACATAATGTACTAAAATAA
60 TTTTTTAAATTT-AATTAAAAAACACACTAAATGAATACATTTCAAACATAATGTACTAAAATAA
31977062 TGTAAAATAATAAAATACGAAAATAATATA
124 TGTAAAATAATAAAATACGAAAATAATATA
* * **
31977092 TTTTTATTAAAAGTAATAAAATCC--AAAAAAATACGAATAAATGGTTGAAATAA-GGTTTTTTT
1 TTTTTATTAAAAGTAATAAAATCCGAAAAAAAATACGAACAAAGGGCCGAAATAAGGGTTTTTTT
*
31977154 AAATTTAAATAAAAAACACACTAAATGAATACATTTCAAACATAATGTACTAAAATAATGTAAAA
66 AAATTTAATTAAAAAACACACTAAATGAATACATTTCAAACATAATGTACTAAAATAATGTAAAA
31977219 TAATAAAATTA-GAAAATAATATA
131 TAATAAAA-TACGAAAATAATATA
*
31977242 -TTTT-TTAAAAGTAATAAAATCCAGAAAAAAAATACGAACAAAGGGCCGAAATAATGGTTTTTT
1 TTTTTATTAAAAGTAATAAAATCC-GAAAAAAAATACGAACAAAGGGCCGAAATAAGGGTTTTTT
* * * *
31977305 TAAAATTTATTTAAAAAACACAATAAATTAATACATTTCAAATATAATGTACTAAAATAATGTAA
65 T-AAATTTAATTAAAAAACACACTAAATGAATACATTTCAAACATAATGTACTAAAATAATGTAA
*
31977370 ACTAATAAAATACGAAAATAATATA
129 AATAATAAAATACGAAAATAATATA
** * * * *
31977395 TTTTTATTGGAAGTAATAAAATCCGAAAAAAAATACTAACAAATGGTCGAAATAAAGGTTTTTTT
1 TTTTTATTAAAAGTAATAAAATCCGAAAAAAAATACGAACAAAGGGCCGAAATAAGGGTTTTTTT
* * * * *
31977460 TAATTTATTTAAAAAACACAGTAAATTAATATATTTCAAACATAATGTACTAAAATAATGTAAAA
66 AAATTTAATTAAAAAACACACTAAATGAATACATTTCAAACATAATGTACTAAAATAATGTAAAA
31977525 TAATAAAATACGAAAATAATATA
131 TAATAAAATACGAAAATAATATA
* * *
31977548 TTTTTATTGAAAGTAATAAAATCTGAAAAAAAAATACGAATAAAGGGCCGAAATAAGGGTTTTTT
1 TTTTTATTAAAAGTAATAAAATCCG-AAAAAAAATACGAACAAAGGGCCGAAATAAGGGTTTTTT
* * *
31977613 TAAATTTAAATAAAAAACACACTAAATGAATATATTTCAAACATAATGTACTAAAATAATTTAAA
65 TAAATTTAATTAAAAAACACACTAAATGAATACATTTCAAACATAATGTACTAAAATAATGTAAA
*
31977678 ATAATAAAATTA-GAAAATAGTATA
130 ATAATAAAA-TACGAAAATAATATA
** * * *
31977702 -TTTT-TTAAAAGTAATAAAATTCAAAAAAAAAATACGAATAAAGAGCCAAAATA
1 TTTTTATTAAAAGTAATAAAA-TCCGAAAAAAAATACGAACAAAGGGCCGAAATA
31977755 CAAACAATTG
Statistics
Matches: 605, Mismatches: 46, Indels: 32
0.89 0.07 0.05
Matches are distributed among these distances:
148 18 0.03
149 4 0.01
150 77 0.13
151 40 0.07
152 54 0.09
153 206 0.34
154 154 0.25
155 18 0.03
156 11 0.02
160 23 0.04
ACGTcount: A:0.54, C:0.08, G:0.09, T:0.30
Consensus pattern (153 bp):
TTTTTATTAAAAGTAATAAAATCCGAAAAAAAATACGAACAAAGGGCCGAAATAAGGGTTTTTTT
AAATTTAATTAAAAAACACACTAAATGAATACATTTCAAACATAATGTACTAAAATAATGTAAAA
TAATAAAATACGAAAATAATATA
Found at i:31982768 original size:24 final size:23
Alignment explanation
Indices: 31982741--31982785 Score: 54
Period size: 24 Copynumber: 1.9 Consensus size: 23
31982731 ATTTTAGTTT
31982741 TTTTGAAAAAAAACAATAAAATTA
1 TTTTGAAAAAAAA-AATAAAATTA
** *
31982765 TTTTTTAAAAAAAGATAAAAT
1 TTTTGAAAAAAAAAATAAAAT
31982786 GAGTGGTCAA
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
23 7 0.39
24 11 0.61
ACGTcount: A:0.60, C:0.02, G:0.04, T:0.33
Consensus pattern (23 bp):
TTTTGAAAAAAAAAATAAAATTA
Found at i:31982990 original size:18 final size:18
Alignment explanation
Indices: 31982940--31982982 Score: 86
Period size: 18 Copynumber: 2.4 Consensus size: 18
31982930 TCTTAAAAAC
31982940 ACTTTTGGGCCAAAAAGT
1 ACTTTTGGGCCAAAAAGT
31982958 ACTTTTGGGCCAAAAAGT
1 ACTTTTGGGCCAAAAAGT
31982976 ACTTTTG
1 ACTTTTG
31982983 AGCAAAAACT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.30, C:0.16, G:0.21, T:0.33
Consensus pattern (18 bp):
ACTTTTGGGCCAAAAAGT
Found at i:31986787 original size:11 final size:11
Alignment explanation
Indices: 31986771--31986812 Score: 57
Period size: 11 Copynumber: 3.6 Consensus size: 11
31986761 TAGCTATTTA
31986771 TAATAAAATAT
1 TAATAAAATAT
31986782 TAATAAAATAT
1 TAATAAAATAT
*
31986793 CTCATTAAAATAT
1 -T-AATAAAATAT
31986806 TAATAAA
1 TAATAAA
31986813 GTAATATTTA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
11 16 0.59
12 2 0.07
13 9 0.33
ACGTcount: A:0.60, C:0.05, G:0.00, T:0.36
Consensus pattern (11 bp):
TAATAAAATAT
Found at i:31990367 original size:17 final size:17
Alignment explanation
Indices: 31990345--31990378 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
31990335 ATGATGGAGG
31990345 TTTAGACTT-GGAAGAAA
1 TTTAGA-TTAGGAAGAAA
31990362 TTTAGATTAGGAAGAAA
1 TTTAGATTAGGAAGAAA
31990379 ATCCAGGAAC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 2 0.12
17 14 0.88
ACGTcount: A:0.44, C:0.03, G:0.24, T:0.29
Consensus pattern (17 bp):
TTTAGATTAGGAAGAAA
Found at i:31995304 original size:61 final size:61
Alignment explanation
Indices: 31995238--31995424 Score: 186
Period size: 61 Copynumber: 3.1 Consensus size: 61
31995228 TATAGTATCG
31995238 TATATTATGATTTTAGTAAATTCATATAAAAATATTTATTATTAAGAATTTTATTAAATTA
1 TATATTATGATTTTAGTAAATTCATATAAAAATATTTATTATTAAGAATTTTATTAAATTA
* * ** * * * * * * * *
31995299 TATATTTTAATTAAAATATATTTA-ATAATAATTATTTCA-AATT-A-TATTTTA-TAGTATCA
1 TATATTATGATTTTAGTAAATTCATATAA-AAATATTT-ATTATTAAGAATTTTATTA-AATTA
* *
31995358 TATATTATGATTTTAGTAAATTCATATAAGAATATTGATTATTAAGAATTTTATTAAATTA
1 TATATTATGATTTTAGTAAATTCATATAAAAATATTTATTATTAAGAATTTTATTAAATTA
31995419 TATATT
1 TATATT
31995425 TTAATTAAAA
Statistics
Matches: 92, Mismatches: 26, Indels: 16
0.69 0.19 0.12
Matches are distributed among these distances:
58 3 0.03
59 34 0.37
60 10 0.11
61 42 0.46
62 3 0.03
ACGTcount: A:0.43, C:0.02, G:0.05, T:0.50
Consensus pattern (61 bp):
TATATTATGATTTTAGTAAATTCATATAAAAATATTTATTATTAAGAATTTTATTAAATTA
Found at i:31995313 original size:18 final size:17
Alignment explanation
Indices: 31995285--31995319 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
31995275 ATTATTAAGA
*
31995285 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
31995302 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
31995320 TTAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:31995329 original size:120 final size:120
Alignment explanation
Indices: 31995190--31995505 Score: 569
Period size: 120 Copynumber: 2.6 Consensus size: 120
31995180 AAGTAGATTA
* * *
31995190 TAAAAAATATTTAATAATAATTATTTTAAATTATATTTTATAGTATCGTATATTATGATTTTAGT
1 TAAAATATATTTAATAATAATTATTTCAAATTATATTTTATAGTATCATATATTATGATTTTAGT
*
31995255 AAATTCATATAAAAATATTTATTATTAAGAATTTTATTAAATTATATATTTTAAT
66 AAATTCATATAAAAATATTGATTATTAAGAATTTTATTAAATTATATATTTTAAT
31995310 TAAAATATATTTAATAATAATTATTTCAAATTATATTTTATAGTATCATATATTATGATTTTAGT
1 TAAAATATATTTAATAATAATTATTTCAAATTATATTTTATAGTATCATATATTATGATTTTAGT
*
31995375 AAATTCATATAAGAATATTGATTATTAAGAATTTTATTAAATTATATATTTTAAT
66 AAATTCATATAAAAATATTGATTATTAAGAATTTTATTAAATTATATATTTTAAT
*
31995430 TAAAATATATTTAATAATAATTATTTCAAATTATATTATATAGTATCATATATTATGATTTTAGT
1 TAAAATATATTTAATAATAATTATTTCAAATTATATTTTATAGTATCATATATTATGATTTTAGT
*
31995495 AAATTTATATA
66 AAATTCATATA
31995506 TTTTATTAAA
Statistics
Matches: 189, Mismatches: 7, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
120 189 1.00
ACGTcount: A:0.44, C:0.02, G:0.04, T:0.49
Consensus pattern (120 bp):
TAAAATATATTTAATAATAATTATTTCAAATTATATTTTATAGTATCATATATTATGATTTTAGT
AAATTCATATAAAAATATTGATTATTAAGAATTTTATTAAATTATATATTTTAAT
Found at i:31995453 original size:54 final size:54
Alignment explanation
Indices: 31995275--31995454 Score: 164
Period size: 54 Copynumber: 3.1 Consensus size: 54
31995265 AAAAATATTT
31995275 ATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATA
1 ATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATA
* * * * ** *
31995329 ATTATTTCAAATTATATTTTATAGTATCATATATTATGATTTT-AGTAAATTCATATAAGAATAT
1 ATTA-TT--AA-GA-ATTTTAT--TA-AAT-TA-TAT-ATTTTAATTAAAAT-ATAT-TTAATAA
*
31995393 TG
53 TA
31995395 ATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATA
1 ATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATA
31995449 ATTATT
1 ATTATT
31995455 TCAAATTATA
Statistics
Matches: 96, Mismatches: 16, Indels: 28
0.69 0.11 0.20
Matches are distributed among these distances:
54 15 0.16
55 11 0.11
56 9 0.09
57 4 0.04
58 3 0.03
59 9 0.09
61 9 0.09
62 3 0.03
63 4 0.04
64 9 0.09
65 11 0.11
66 9 0.09
ACGTcount: A:0.44, C:0.02, G:0.04, T:0.50
Consensus pattern (54 bp):
ATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATA
Found at i:31995482 original size:61 final size:61
Alignment explanation
Indices: 31995297--31995482 Score: 174
Period size: 57 Copynumber: 3.1 Consensus size: 61
31995287 TTTATTAAAT
*
31995297 TATATATTTTAATTAAAATATATTTAATAATAATTATTTCAAATTATATTTTATAGTATCA
1 TATATATTTTAATTAAAATATATTTAATAATAATTATTTCAAATTATATTATATAGTATCA
* * * * * * *
31995358 TATATTATGATTTTAGT-AAAT-TCATATAAGAAT-ATTGATTATTAAGA--ATTTTAT-TA-AA
1 TATA-TAT--TTTAATTAAAATAT-ATTTAATAATAATT-ATT-TCAA-ATTATATTATATAGTA
31995416 T--
59 TCA
31995417 TATATATTTTAATTAAAATATATTTAATAATAATTATTTCAAATTATATTATATAGTATCA
1 TATATATTTTAATTAAAATATATTTAATAATAATTATTTCAAATTATATTATATAGTATCA
31995478 TATAT
1 TATAT
31995483 TATGATTTTA
Statistics
Matches: 94, Mismatches: 15, Indels: 32
0.67 0.11 0.23
Matches are distributed among these distances:
55 1 0.01
56 8 0.09
57 21 0.22
58 9 0.10
59 6 0.06
61 11 0.12
62 9 0.10
63 20 0.21
64 8 0.09
65 1 0.01
ACGTcount: A:0.44, C:0.03, G:0.04, T:0.49
Consensus pattern (61 bp):
TATATATTTTAATTAAAATATATTTAATAATAATTATTTCAAATTATATTATATAGTATCA
Found at i:31995541 original size:26 final size:26
Alignment explanation
Indices: 31995429--31995541 Score: 63
Period size: 26 Copynumber: 4.2 Consensus size: 26
31995419 TATATTTTAA
*
31995429 TTAAAATATATTTAATAATAATTAT-
1 TTAAATTATATTTAATAATAATTATG
31995454 TTCAAATTATATTATATAGTATCATATATTATG
1 TT-AAATTATATT-TA-A-TA--ATA-ATTATG
** * * * *
31995487 ATTTTAGTAAATTT-AT-AT-ATTTTA
1 -TTAAATTATATTTAATAATAATTATG
31995511 TTAAATTATATTTAATAATAATTATG
1 TTAAATTATATTTAATAATAATTATG
31995537 TTAAA
1 TTAAA
31995542 ATATGATTAA
Statistics
Matches: 63, Mismatches: 13, Indels: 23
0.64 0.13 0.23
Matches are distributed among these distances:
23 9 0.14
24 6 0.10
25 4 0.06
26 20 0.32
27 2 0.03
28 1 0.02
29 3 0.05
30 1 0.02
31 3 0.05
32 6 0.10
33 6 0.10
34 2 0.03
ACGTcount: A:0.44, C:0.02, G:0.04, T:0.50
Consensus pattern (26 bp):
TTAAATTATATTTAATAATAATTATG
Found at i:31995728 original size:39 final size:41
Alignment explanation
Indices: 31995668--31995773 Score: 126
Period size: 44 Copynumber: 2.5 Consensus size: 41
31995658 TTTCCTTATG
* *
31995668 CTATTACACCTCTATTACATTCAACCAAACACAAGAA-TAC
1 CTATTACGCCTCTATTACATTCAACCAAACAAAAGAATTAC
31995708 C-ATTACGCCTCTATTTCATTCCATTCAACCAAACAAAAGAATTAC
1 CTATTACGCCTCTA-TT-A---CATTCAACCAAACAAAAGAATTAC
*
31995753 CTATTACGCCTCTATTCCATT
1 CTATTACGCCTCTATTACATT
31995774 ACACATCTAT
Statistics
Matches: 56, Mismatches: 3, Indels: 13
0.78 0.04 0.18
Matches are distributed among these distances:
39 11 0.20
40 3 0.05
41 5 0.09
44 19 0.34
45 6 0.11
46 12 0.21
ACGTcount: A:0.36, C:0.30, G:0.04, T:0.30
Consensus pattern (41 bp):
CTATTACGCCTCTATTACATTCAACCAAACAAAAGAATTAC
Found at i:31995748 original size:44 final size:46
Alignment explanation
Indices: 31995685--31995773 Score: 146
Period size: 44 Copynumber: 2.0 Consensus size: 46
31995675 ACCTCTATTA
* *
31995685 CATTCAACCAAACACAAGAA-TACC-ATTACGCCTCTATTTCATTC
1 CATTCAACCAAACAAAAGAATTACCTATTACGCCTCTATTCCATTC
31995729 CATTCAACCAAACAAAAGAATTACCTATTACGCCTCTATTCCATT
1 CATTCAACCAAACAAAAGAATTACCTATTACGCCTCTATTCCATT
31995774 ACACATCTAT
Statistics
Matches: 41, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
44 19 0.46
45 4 0.10
46 18 0.44
ACGTcount: A:0.37, C:0.30, G:0.04, T:0.28
Consensus pattern (46 bp):
CATTCAACCAAACAAAAGAATTACCTATTACGCCTCTATTCCATTC
Found at i:31996719 original size:3 final size:3
Alignment explanation
Indices: 31996711--31996762 Score: 104
Period size: 3 Copynumber: 17.3 Consensus size: 3
31996701 CTACTTCTTA
31996711 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
31996759 ATT A
1 ATT A
31996763 CTCCTCAATA
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 49 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:31998338 original size:14 final size:14
Alignment explanation
Indices: 31998297--31998339 Score: 50
Period size: 14 Copynumber: 3.0 Consensus size: 14
31998287 AACATAAGTG
*
31998297 ATTAAAATATAATA
1 ATTAAAATAAAATA
* *
31998311 TTTTAAATATAAATA
1 ATTAAAATA-AAATA
31998326 ATTAAAATAAAATA
1 ATTAAAATAAAATA
31998340 TGAAATAAAT
Statistics
Matches: 23, Mismatches: 5, Indels: 2
0.77 0.17 0.07
Matches are distributed among these distances:
14 12 0.52
15 11 0.48
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (14 bp):
ATTAAAATAAAATA
Found at i:31998347 original size:21 final size:20
Alignment explanation
Indices: 31998315--31998353 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
31998305 ATAATATTTT
*
31998315 AAATATAAATAATTAAAATA
1 AAATATAAATAAATAAAATA
31998335 AAATATGAAATAAATAAAA
1 AAATAT-AAATAAATAAAA
31998354 GTGACTATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.72, C:0.00, G:0.03, T:0.26
Consensus pattern (20 bp):
AAATATAAATAAATAAAATA
Found at i:32007327 original size:6 final size:6
Alignment explanation
Indices: 32007316--32007350 Score: 70
Period size: 6 Copynumber: 5.8 Consensus size: 6
32007306 GATTCGATTT
32007316 TATTAC TATTAC TATTAC TATTAC TATTAC TATTA
1 TATTAC TATTAC TATTAC TATTAC TATTAC TATTA
32007351 TTCTTCTTTG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.34, C:0.14, G:0.00, T:0.51
Consensus pattern (6 bp):
TATTAC
Found at i:32007684 original size:21 final size:21
Alignment explanation
Indices: 32007655--32007707 Score: 79
Period size: 21 Copynumber: 2.5 Consensus size: 21
32007645 AGCGGTGGTG
* *
32007655 GTGAAATTAGATACTATGGCA
1 GTGAGATTAGATACTATAGCA
*
32007676 GTGAGATTAGATACTGTAGCA
1 GTGAGATTAGATACTATAGCA
32007697 GTGAGATTAGA
1 GTGAGATTAGA
32007708 AATAATGGTG
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.36, C:0.08, G:0.28, T:0.28
Consensus pattern (21 bp):
GTGAGATTAGATACTATAGCA
Found at i:32008306 original size:11 final size:10
Alignment explanation
Indices: 32008246--32008304 Score: 73
Period size: 11 Copynumber: 5.5 Consensus size: 10
32008236 CAACTAAATC
32008246 ATTTCTCTCA
1 ATTTCTCTCA
32008256 ATTTCTCTCTA
1 ATTTCTCTC-A
*
32008267 ATATTCTCTAA
1 AT-TTCTCTCA
32008278 ATTTCCTCTCA
1 ATTT-CTCTCA
32008289 ATTTCCTCTCA
1 ATTT-CTCTCA
32008300 ATTTC
1 ATTTC
32008305 CTATTTAAAA
Statistics
Matches: 44, Mismatches: 2, Indels: 6
0.85 0.04 0.12
Matches are distributed among these distances:
10 12 0.27
11 26 0.59
12 6 0.14
ACGTcount: A:0.22, C:0.29, G:0.00, T:0.49
Consensus pattern (10 bp):
ATTTCTCTCA
Found at i:32009493 original size:7 final size:7
Alignment explanation
Indices: 32009483--32009507 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
32009473 TTAGTATTTA
32009483 GTATTAT
1 GTATTAT
32009490 GTATTAT
1 GTATTAT
32009497 GTATTAT
1 GTATTAT
32009504 GTAT
1 GTAT
32009508 ATAACTAATA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.28, C:0.00, G:0.16, T:0.56
Consensus pattern (7 bp):
GTATTAT
Found at i:32009493 original size:14 final size:15
Alignment explanation
Indices: 32009476--32009507 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
32009466 TTGGTATTTA
32009476 GTATTTA-GTATTAT
1 GTATTTATGTATTAT
32009490 GTA-TTATGTATTAT
1 GTATTTATGTATTAT
32009504 GTAT
1 GTAT
32009508 ATAACTAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 3
0.84 0.00 0.16
Matches are distributed among these distances:
13 3 0.19
14 13 0.81
ACGTcount: A:0.28, C:0.00, G:0.16, T:0.56
Consensus pattern (15 bp):
GTATTTATGTATTAT
Found at i:32010054 original size:30 final size:29
Alignment explanation
Indices: 32010016--32010099 Score: 89
Period size: 30 Copynumber: 2.8 Consensus size: 29
32010006 TCAACGAGGC
* *
32010016 CCAAACAATCACCCAACCCATCATCAGCA
1 CCAAACAATCACCCAACCCAGCAACAGCA
*
32010045 CCAATACAATCA-TCAGACCCAGCAACAGCA
1 CCAA-ACAATCACCCA-ACCCAGCAACAGCA
* *
32010075 CCGACACAGTCACCCAACCCAGCAA
1 CC-AAACAATCACCCAACCCAGCAA
32010100 TTCAACCGAC
Statistics
Matches: 45, Mismatches: 6, Indels: 7
0.78 0.10 0.12
Matches are distributed among these distances:
29 6 0.13
30 36 0.80
31 3 0.07
ACGTcount: A:0.40, C:0.43, G:0.08, T:0.08
Consensus pattern (29 bp):
CCAAACAATCACCCAACCCAGCAACAGCA
Found at i:32010172 original size:18 final size:18
Alignment explanation
Indices: 32010149--32010191 Score: 68
Period size: 18 Copynumber: 2.4 Consensus size: 18
32010139 TGCCAGGTGC
*
32010149 GTATCCTAGCCCTTTTAT
1 GTATCCTAACCCTTTTAT
32010167 GTATCCTAACCCTTTTAT
1 GTATCCTAACCCTTTTAT
*
32010185 GTTTCCT
1 GTATCCT
32010192 TTTTCTAGTC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.16, C:0.28, G:0.09, T:0.47
Consensus pattern (18 bp):
GTATCCTAACCCTTTTAT
Found at i:32010471 original size:21 final size:21
Alignment explanation
Indices: 32010447--32010490 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
32010437 AGATCCCCTA
* *
32010447 CCGGAGGAACCAGAATCCTCG
1 CCGGAGCAACCAGAACCCTCG
*
32010468 CCGGAGCAACCATAACCCTCG
1 CCGGAGCAACCAGAACCCTCG
32010489 CC
1 CC
32010491 AGAAGCTGGA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.27, C:0.41, G:0.23, T:0.09
Consensus pattern (21 bp):
CCGGAGCAACCAGAACCCTCG
Found at i:32014235 original size:19 final size:19
Alignment explanation
Indices: 32014211--32014248 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
32014201 TTGATACAAC
32014211 AAATTAATTATCAATACCA
1 AAATTAATTATCAATACCA
*
32014230 AAATTAATTATCGATACCA
1 AAATTAATTATCAATACCA
32014249 CTATTTTTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.50, C:0.16, G:0.03, T:0.32
Consensus pattern (19 bp):
AAATTAATTATCAATACCA
Found at i:32015505 original size:18 final size:19
Alignment explanation
Indices: 32015482--32015529 Score: 62
Period size: 19 Copynumber: 2.6 Consensus size: 19
32015472 ATATGAGTTT
* *
32015482 ATGCACTT-ATGTGCTAGG
1 ATGCACTTCATGTGCCAAG
*
32015500 ATGCACTTCGTGTGCCAAG
1 ATGCACTTCATGTGCCAAG
32015519 ATGCACTTCAT
1 ATGCACTTCAT
32015530 TCGCTAATAT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
18 8 0.32
19 17 0.68
ACGTcount: A:0.23, C:0.23, G:0.23, T:0.31
Consensus pattern (19 bp):
ATGCACTTCATGTGCCAAG
Found at i:32017213 original size:13 final size:13
Alignment explanation
Indices: 32017177--32017213 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
32017167 AAACCTAAGA
32017177 AAAGAGAAAATCT
1 AAAGAGAAAATCT
**
32017190 AAAGACTAAATCT
1 AAAGAGAAAATCT
32017203 AAAGAGAAAAT
1 AAAGAGAAAAT
32017214 TATACAAAGT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.62, C:0.08, G:0.14, T:0.16
Consensus pattern (13 bp):
AAAGAGAAAATCT
Found at i:32025247 original size:21 final size:20
Alignment explanation
Indices: 32025215--32025257 Score: 59
Period size: 21 Copynumber: 2.1 Consensus size: 20
32025205 TCAAGGTGTC
*
32025215 TTCTAGGGTATGTCACGACA
1 TTCTAGGCTATGTCACGACA
*
32025235 TTCTCAGGCTATGTCGCGACA
1 TTCT-AGGCTATGTCACGACA
32025256 TT
1 TT
32025258 AAAGGCAGCC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 4 0.20
21 16 0.80
ACGTcount: A:0.21, C:0.23, G:0.23, T:0.33
Consensus pattern (20 bp):
TTCTAGGCTATGTCACGACA
Found at i:32036349 original size:46 final size:46
Alignment explanation
Indices: 32036258--32036350 Score: 123
Period size: 46 Copynumber: 2.0 Consensus size: 46
32036248 TCGCATTAAG
* * *
32036258 TGGTTATAAATCTCTAAGACATTGATTCTGACGGACATTTGCAAAC
1 TGGTAATAAATCTCTAAGACATTGATTCTGACGGAAATTTACAAAC
* * * *
32036304 TGGTAATAAATCTTTAAGACATTTATTTTGATGGAAATTTACAAAC
1 TGGTAATAAATCTCTAAGACATTGATTCTGACGGAAATTTACAAAC
32036350 T
1 T
32036351 TTAGATAGAG
Statistics
Matches: 40, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
46 40 1.00
ACGTcount: A:0.35, C:0.13, G:0.15, T:0.37
Consensus pattern (46 bp):
TGGTAATAAATCTCTAAGACATTGATTCTGACGGAAATTTACAAAC
Found at i:32037521 original size:45 final size:45
Alignment explanation
Indices: 32037472--32037648 Score: 160
Period size: 45 Copynumber: 3.9 Consensus size: 45
32037462 CGTGTTTTCA
* * *
32037472 CATGATGCCATAGTGTCTTTTGGCTATGGTCTTACTTATTTCTAC
1 CATGATGCCATAGCGTCTGTTGGCTATGGTCTTACTCATTTCTAC
* **
32037517 CATGATGCCATAGCGTCTGTTGGCTATGGTCTTACTCATTTTTTT
1 CATGATGCCATAGCGTCTGTTGGCTATGGTCTTACTCATTTCTAC
* * ** * **
32037562 CATGATGCCATAACATCT-TTCAACTATGGTTCTTACTCATTTTTTT
1 CATGATGCCATAGCGTCTGTT-GGCTATGG-TCTTACTCATTTCTAC
* * **
32037608 CATGATGCCATAACATCT-TTCAACTATGGTCTTACTCATTT
1 CATGATGCCATAGCGTCTGTT-GGCTATGGTCTTACTCATTT
32037649 TTGCAGTGAC
Statistics
Matches: 120, Mismatches: 10, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
44 2 0.02
45 73 0.61
46 45 0.38
ACGTcount: A:0.21, C:0.21, G:0.14, T:0.44
Consensus pattern (45 bp):
CATGATGCCATAGCGTCTGTTGGCTATGGTCTTACTCATTTCTAC
Found at i:32037649 original size:45 final size:45
Alignment explanation
Indices: 32037495--32037682 Score: 218
Period size: 45 Copynumber: 4.2 Consensus size: 45
32037485 TGTCTTTTGG
* * ** * * **
32037495 CTATGGTCTTACTTATTTCTACCATGATGCCATAGCGTCTGTT-GG
1 CTATGGTCTTACTCATTTTTTTCATGATGCCATAACATCT-TTCAA
32037540 CTATGGTCTTACTCATTTTTTTCATGATGCCATAACATCTTTCAA
1 CTATGGTCTTACTCATTTTTTTCATGATGCCATAACATCTTTCAA
32037585 CTATGGTTCTTACTCATTTTTTTCATGATGCCATAACATCTTTCAA
1 CTATGG-TCTTACTCATTTTTTTCATGATGCCATAACATCTTTCAA
* ** * *
32037631 CTATGGTCTTACTCA-TTTTTGCAGTGACACTATAACATCTTTCAG
1 CTATGGTCTTACTCATTTTTTTCA-TGATGCCATAACATCTTTCAA
32037676 CTATGGT
1 CTATGGT
32037683 ATTTGTAAGA
Statistics
Matches: 127, Mismatches: 13, Indels: 6
0.87 0.09 0.04
Matches are distributed among these distances:
44 9 0.07
45 73 0.57
46 45 0.35
ACGTcount: A:0.22, C:0.22, G:0.13, T:0.43
Consensus pattern (45 bp):
CTATGGTCTTACTCATTTTTTTCATGATGCCATAACATCTTTCAA
Found at i:32038200 original size:22 final size:22
Alignment explanation
Indices: 32038160--32038201 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
32038150 TGTTATTTTT
*
32038160 TATTAAAATGTTAAAATAATAA
1 TATTAAAATGTAAAAATAATAA
32038182 TATTAAAA-GTAAAACATAAT
1 TATTAAAATGTAAAA-ATAAT
32038202 TTAAGGTTGT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.60, C:0.02, G:0.05, T:0.33
Consensus pattern (22 bp):
TATTAAAATGTAAAAATAATAA
Found at i:32039021 original size:13 final size:13
Alignment explanation
Indices: 32039003--32039123 Score: 91
Period size: 13 Copynumber: 9.3 Consensus size: 13
32038993 TAAATGTGTA
32039003 ATATGAAATGGTT
1 ATATGAAATGGTT
*
32039016 ATATGAGATGGTT
1 ATATGAAATGGTT
*
32039029 ATTTGAAATGGTT
1 ATATGAAATGGTT
**
32039042 ATAT-AAATGAAT
1 ATATGAAATGGTT
* * *
32039054 AAATAAAATGATT
1 ATATGAAATGGTT
*
32039067 ATATGAATTGGTT
1 ATATGAAATGGTT
**
32039080 ATATAGAAATAATT
1 ATAT-GAAATGGTT
* * *
32039094 ATATTAAGTGTTT
1 ATATGAAATGGTT
* *
32039107 ATACGAAATGTTT
1 ATATGAAATGGTT
32039120 ATAT
1 ATAT
32039124 AGATAAATAT
Statistics
Matches: 83, Mismatches: 23, Indels: 4
0.75 0.21 0.04
Matches are distributed among these distances:
12 9 0.11
13 64 0.77
14 10 0.12
ACGTcount: A:0.42, C:0.01, G:0.17, T:0.40
Consensus pattern (13 bp):
ATATGAAATGGTT
Found at i:32052041 original size:15 final size:15
Alignment explanation
Indices: 32052018--32052047 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
32052008 GCATAACTGT
*
32052018 TCCTGAGGTAAAGAA
1 TCCTCAGGTAAAGAA
32052033 TCCTCAGGTAAAGAA
1 TCCTCAGGTAAAGAA
32052048 CATTTACAAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.40, C:0.17, G:0.23, T:0.20
Consensus pattern (15 bp):
TCCTCAGGTAAAGAA
Found at i:32058797 original size:38 final size:38
Alignment explanation
Indices: 32058746--32058821 Score: 152
Period size: 38 Copynumber: 2.0 Consensus size: 38
32058736 ATGAAGCAAC
32058746 ATTTCTCTATGTTTGTTAACTAAATCTTGCTTTTCCTT
1 ATTTCTCTATGTTTGTTAACTAAATCTTGCTTTTCCTT
32058784 ATTTCTCTATGTTTGTTAACTAAATCTTGCTTTTCCTT
1 ATTTCTCTATGTTTGTTAACTAAATCTTGCTTTTCCTT
32058822 TTCTCACATG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 38 1.00
ACGTcount: A:0.18, C:0.18, G:0.08, T:0.55
Consensus pattern (38 bp):
ATTTCTCTATGTTTGTTAACTAAATCTTGCTTTTCCTT
Found at i:32069735 original size:27 final size:27
Alignment explanation
Indices: 32069705--32069757 Score: 70
Period size: 27 Copynumber: 2.0 Consensus size: 27
32069695 AATGAGTGTA
*
32069705 ATTAATCAAAAGATAAATCTTTTGATC
1 ATTAATCAAAAGATAAATCATTTGATC
* * *
32069732 ATTAGTCAAAAGTTATATCATTTGAT
1 ATTAATCAAAAGATAAATCATTTGAT
32069758 TTTTGAAAAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.42, C:0.09, G:0.09, T:0.40
Consensus pattern (27 bp):
ATTAATCAAAAGATAAATCATTTGATC
Found at i:32077549 original size:45 final size:45
Alignment explanation
Indices: 32077485--32077572 Score: 167
Period size: 45 Copynumber: 2.0 Consensus size: 45
32077475 TTAGAGACAA
32077485 GAGTAGAAACTTTGAAAGAGAAAGGATAAAAAGAAGAATGTCTTG
1 GAGTAGAAACTTTGAAAGAGAAAGGATAAAAAGAAGAATGTCTTG
*
32077530 GAGTAGAAACTTTGAAAGAGAAAGGATAAAAAGAATAATGTCT
1 GAGTAGAAACTTTGAAAGAGAAAGGATAAAAAGAAGAATGTCT
32077573 AGCCCTCCAC
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
45 42 1.00
ACGTcount: A:0.50, C:0.05, G:0.25, T:0.20
Consensus pattern (45 bp):
GAGTAGAAACTTTGAAAGAGAAAGGATAAAAAGAAGAATGTCTTG
Found at i:32089630 original size:42 final size:42
Alignment explanation
Indices: 32089569--32089650 Score: 121
Period size: 42 Copynumber: 2.0 Consensus size: 42
32089559 CCTAGAAAAA
* *
32089569 AATTTAAAAAAGGAGAAGATAATCTTGCGTTGTT-GAAAATG
1 AATTTAAAAAAGGAGAAGATAAACATGCGTTGTTGGAAAATG
*
32089610 AATTTAAAAATAGGAGAAGATAAACATGGGTTGTTGGAAAA
1 AATTTAAAAA-AGGAGAAGATAAACATGCGTTGTTGGAAAA
32089651 AAGCTATAAA
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
41 10 0.28
42 21 0.58
43 5 0.14
ACGTcount: A:0.46, C:0.04, G:0.23, T:0.27
Consensus pattern (42 bp):
AATTTAAAAAAGGAGAAGATAAACATGCGTTGTTGGAAAATG
Found at i:32091560 original size:17 final size:19
Alignment explanation
Indices: 32091533--32091567 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
32091523 ACATAGTCGG
32091533 TTTCATATTT-CCCTTAGC
1 TTTCATATTTCCCCTTAGC
32091551 TTTC-TATTTCCCCTTAG
1 TTTCATATTTCCCCTTAG
32091568 AGGATGAGGG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.14, C:0.29, G:0.06, T:0.51
Consensus pattern (19 bp):
TTTCATATTTCCCCTTAGC
Found at i:32094308 original size:16 final size:16
Alignment explanation
Indices: 32094287--32094326 Score: 62
Period size: 16 Copynumber: 2.5 Consensus size: 16
32094277 CGTTTGGTTC
*
32094287 GCTGTAATTGAATAGA
1 GCTGTAATGGAATAGA
32094303 GCTGTAATGGAATAGA
1 GCTGTAATGGAATAGA
*
32094319 ACTGTAAT
1 GCTGTAAT
32094327 AGTAATTCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.38, C:0.07, G:0.25, T:0.30
Consensus pattern (16 bp):
GCTGTAATGGAATAGA
Found at i:32094359 original size:45 final size:44
Alignment explanation
Indices: 32094308--32094400 Score: 143
Period size: 44 Copynumber: 2.1 Consensus size: 44
32094298 ATAGAGCTGT
*
32094308 AATGGAATAGAACTGTAATAGTAATTCAAT-TGTTTGGTTGAATGG
1 AATGGAATAGAACTGGAATAGT-ATTC-ATGTGTTTGGTTGAATGG
*
32094353 AATGGAATAGAACTGGAATAGTATTCTTGTGTTTGGTTGAATGG
1 AATGGAATAGAACTGGAATAGTATTCATGTGTTTGGTTGAATGG
32094397 AATG
1 AATG
32094401 ATGTTGTAAT
Statistics
Matches: 45, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
43 1 0.02
44 23 0.51
45 21 0.47
ACGTcount: A:0.33, C:0.04, G:0.27, T:0.35
Consensus pattern (44 bp):
AATGGAATAGAACTGGAATAGTATTCATGTGTTTGGTTGAATGG
Found at i:32094529 original size:34 final size:32
Alignment explanation
Indices: 32094494--32094568 Score: 87
Period size: 33 Copynumber: 2.2 Consensus size: 32
32094484 GTTATTAAAT
*
32094494 TTTAATAATATTATTAATATAAATAATAAATAA
1 TTTAATAATATT-TTAACATAAATAATAAATAA
* * *
32094527 TTTAATCATATTTTAACATAATTATTAAATATAA
1 TTTAATAATATTTTAACATAAATAAT-AA-ATAA
32094561 TTTAATAA
1 TTTAATAA
32094569 AAAATATATA
Statistics
Matches: 35, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
32 11 0.31
33 13 0.37
34 11 0.31
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (32 bp):
TTTAATAATATTTTAACATAAATAATAAATAA
Found at i:32094876 original size:23 final size:21
Alignment explanation
Indices: 32094850--32094908 Score: 73
Period size: 23 Copynumber: 2.6 Consensus size: 21
32094840 TCATTAGTTT
32094850 ATATGTCATAATATCCAAACATA
1 ATAT-TCAT-ATATCCAAACATA
*
32094873 ATATTCATATATTAACAAACATA
1 ATATTCATATA-T-CCAAACATA
32094896 ATATTCATATATC
1 ATATTCATATATC
32094909 AATAAAAAGA
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
21 3 0.09
22 6 0.19
23 23 0.72
ACGTcount: A:0.47, C:0.15, G:0.02, T:0.36
Consensus pattern (21 bp):
ATATTCATATATCCAAACATA
Found at i:32100614 original size:23 final size:23
Alignment explanation
Indices: 32100587--32100705 Score: 148
Period size: 23 Copynumber: 5.2 Consensus size: 23
32100577 AGTGTTATTG
* *
32100587 ATCAGTGGTAACTTCGGGTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
* *
32100610 TTCAGTGGTAGCTACGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
*
32100633 ATCAGTGGTAGCTTTGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
* * * *
32100656 TTCAGTGCTAGCTACGGCTACGT
1 ATCAGTGGTAGCTTCGGCTACAT
*
32100679 ATCAGTGGTAGCTTCGGTTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
32100702 ATCA
1 ATCA
32100706 ATGTGGCACT
Statistics
Matches: 79, Mismatches: 17, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 79 1.00
ACGTcount: A:0.23, C:0.20, G:0.25, T:0.32
Consensus pattern (23 bp):
ATCAGTGGTAGCTTCGGCTACAT
Found at i:32100655 original size:46 final size:46
Alignment explanation
Indices: 32100587--32100701 Score: 176
Period size: 46 Copynumber: 2.5 Consensus size: 46
32100577 AGTGTTATTG
* * *
32100587 ATCAGTGGTAACTTCGGGTACATTTCAGTGGTAGCTACGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACATTTCAGTGCTAGCTACGGCTACAT
* *
32100633 ATCAGTGGTAGCTTTGGCTACATTTCAGTGCTAGCTACGGCTACGT
1 ATCAGTGGTAGCTTCGGCTACATTTCAGTGCTAGCTACGGCTACAT
*
32100679 ATCAGTGGTAGCTTCGGTTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
32100702 ATCAATGTGG
Statistics
Matches: 62, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
46 62 1.00
ACGTcount: A:0.22, C:0.20, G:0.26, T:0.32
Consensus pattern (46 bp):
ATCAGTGGTAGCTTCGGCTACATTTCAGTGCTAGCTACGGCTACAT
Found at i:32101090 original size:24 final size:24
Alignment explanation
Indices: 32101056--32101101 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
32101046 TATATGAAAT
* *
32101056 ATAAATTTTAAATATTTTTAAACA
1 ATAAATATTAAATATTTATAAACA
*
32101080 ATAAATATTAATTATTTATAAA
1 ATAAATATTAAATATTTATAAA
32101102 ATTTAATTAG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (24 bp):
ATAAATATTAAATATTTATAAACA
Found at i:32103195 original size:16 final size:16
Alignment explanation
Indices: 32103174--32103204 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
32103164 CTATGCATGC
*
32103174 AAAATATAAAAGACAA
1 AAAATACAAAAGACAA
32103190 AAAATACAAAAGACA
1 AAAATACAAAAGACA
32103205 TATTAGTGAA
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:0.74, C:0.10, G:0.06, T:0.10
Consensus pattern (16 bp):
AAAATACAAAAGACAA
Found at i:32104826 original size:28 final size:28
Alignment explanation
Indices: 32104772--32104824 Score: 72
Period size: 27 Copynumber: 1.9 Consensus size: 28
32104762 CACTTATAAT
** *
32104772 ATTTTTTATTTTTTTTATTTTTTAAATG
1 ATTTTTTATTTTTAATATTTTTAAAATG
32104800 ATTTTTTA-TTTTAATATTTTTAAAA
1 ATTTTTTATTTTTAATATTTTTAAAA
32104825 ATTTCAAAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
27 14 0.64
28 8 0.36
ACGTcount: A:0.28, C:0.00, G:0.02, T:0.70
Consensus pattern (28 bp):
ATTTTTTATTTTTAATATTTTTAAAATG
Found at i:32110785 original size:16 final size:18
Alignment explanation
Indices: 32110764--32110797 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
32110754 AATTCGTGTA
32110764 GGGCCCA-G-GACCCATT
1 GGGCCCACGCGACCCATT
32110780 GGGCCCACGCGACCCATT
1 GGGCCCACGCGACCCATT
32110798 TTAGTCAAAC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.44
17 1 0.06
18 8 0.50
ACGTcount: A:0.18, C:0.41, G:0.29, T:0.12
Consensus pattern (18 bp):
GGGCCCACGCGACCCATT
Found at i:32113111 original size:49 final size:50
Alignment explanation
Indices: 32113028--32113209 Score: 213
Period size: 50 Copynumber: 3.7 Consensus size: 50
32113018 TTATTGAGAC
* **
32113028 TATGAGAGGTCCCATGTAAAACCATGCCTGGGACATGGCGTTGGCACCGA
1 TATGAGAGGTCCCATGTAAGACCATATCTGGGACATGGCGTTGGCACCGA
* *
32113078 GATGAGAGGTCCCAT-TAAGACCATGTCTGGGACATGGCGTTGGCACCGA
1 TATGAGAGGTCCCATGTAAGACCATATCTGGGACATGGCGTTGGCACCGA
* * ** * * * *
32113127 TATGTGAGGCCCCCCGTAAGACCATATCTGGGACATCGCATGGGCACCTA
1 TATGAGAGGTCCCATGTAAGACCATATCTGGGACATGGCGTTGGCACCGA
** *
32113177 TATGAGAACTCCCATGTAAGATCATATCTGGGA
1 TATGAGAGGTCCCATGTAAGACCATATCTGGGA
32113210 TGTGTCATTG
Statistics
Matches: 111, Mismatches: 20, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
49 42 0.38
50 69 0.62
ACGTcount: A:0.26, C:0.24, G:0.28, T:0.21
Consensus pattern (50 bp):
TATGAGAGGTCCCATGTAAGACCATATCTGGGACATGGCGTTGGCACCGA
Found at i:32119604 original size:30 final size:30
Alignment explanation
Indices: 32119568--32119625 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
32119558 TCCGAGCTTT
*
32119568 GGGGCAAAAGTGTAATTATGTAAAAGTTTA
1 GGGGCAAAAGTATAATTATGTAAAAGTTTA
* * *
32119598 GGGGCAAAATTATAATTTTGTCAAAGTT
1 GGGGCAAAAGTATAATTATGTAAAAGTT
32119626 AGAGTCGAGG
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.38, C:0.05, G:0.24, T:0.33
Consensus pattern (30 bp):
GGGGCAAAAGTATAATTATGTAAAAGTTTA
Found at i:32120072 original size:50 final size:50
Alignment explanation
Indices: 32119976--32120198 Score: 223
Period size: 50 Copynumber: 4.3 Consensus size: 50
32119966 AGATCTCATA
* *
32119976 TAAGACCATGTCTGGGACATGGCATTGCCATCATTGAGATAATGAGAGGTCCCATG
1 TAAGACCATGTCTGGGACATGGCGTTGGCA-C--T--GAT-ATGAGAGGTCCCATG
*** *
32120032 TAAGACCATGTCTCAAACATGGCGTTGGCACTGAGATGAGAGGTCCCATG
1 TAAGACCATGTCTGGGACATGGCGTTGGCACTGATATGAGAGGTCCCATG
* * * **
32120082 TAAGACCATGTTTGGGACATGGCGTTGGCACCGATATGTGAGGTCCCCCG
1 TAAGACCATGTCTGGGACATGGCGTTGGCACTGATATGAGAGGTCCCATG
* * * **
32120132 TAAGACCATATCTGGGACATCGCATTGGCACCT-ATATGAGAACTCCCATG
1 TAAGACCATGTCTGGGACATGGCGTTGGCA-CTGATATGAGAGGTCCCATG
*
32120182 TAAGACCATATCTGGGA
1 TAAGACCATGTCTGGGA
32120199 TGTGGCATTG
Statistics
Matches: 141, Mismatches: 25, Indels: 8
0.81 0.14 0.05
Matches are distributed among these distances:
50 111 0.79
51 3 0.02
53 1 0.01
55 1 0.01
56 25 0.18
ACGTcount: A:0.27, C:0.22, G:0.26, T:0.24
Consensus pattern (50 bp):
TAAGACCATGTCTGGGACATGGCGTTGGCACTGATATGAGAGGTCCCATG
Found at i:32130852 original size:16 final size:16
Alignment explanation
Indices: 32130821--32130850 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
32130811 CACGTACCTC
32130821 TTTTTTAAAATATTTA
1 TTTTTTAAAATATTTA
32130837 TTTTTT-AAATATTT
1 TTTTTTAAAATATTT
32130851 TACTTTGCCT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (16 bp):
TTTTTTAAAATATTTA
Found at i:32131126 original size:3 final size:3
Alignment explanation
Indices: 32131118--32131155 Score: 58
Period size: 3 Copynumber: 12.7 Consensus size: 3
32131108 ATTCAAAAAA
* *
32131118 CAT CAT CAT TAT CAT CAT CAT CAT CAT TAT CAT CAT CA
1 CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CA
32131156 CTATAGTTAC
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.34, C:0.29, G:0.00, T:0.37
Consensus pattern (3 bp):
CAT
Found at i:32143504 original size:12 final size:12
Alignment explanation
Indices: 32143487--32143511 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
32143477 TAACAAATAA
32143487 CATAGAAGCACC
1 CATAGAAGCACC
32143499 CATAGAAGCACC
1 CATAGAAGCACC
32143511 C
1 C
32143512 CAAGGAGAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.40, C:0.36, G:0.16, T:0.08
Consensus pattern (12 bp):
CATAGAAGCACC
Found at i:32147311 original size:50 final size:50
Alignment explanation
Indices: 32147256--32147449 Score: 194
Period size: 50 Copynumber: 3.9 Consensus size: 50
32147246 CATTGAGATT
* *
32147256 ATGAGAGGTCCCATGTAAGACCATGTCTAGGACATGGCGTTGGCACCGAG
1 ATGAGAGGTCCCATGTAAGACCATGTCTAGGACATGGCATTGGCACCGAC
** * *
32147306 ATGAGAGGTCCCCCGTAAGACCATGTCTAGGACATGGCATGGGCACCGAT
1 ATGAGAGGTCCCATGTAAGACCATGTCTAGGACATGGCATTGGCACCGAC
** * * * *
32147356 ATGAGAACTCCAATGTAAGACTATATCTAGGATATGGCATTGGCA--GTAC
1 ATGAGAGGTCCCATGTAAGACCATGTCTAGGACATGGCATTGGCACCG-AC
** * ** * *
32147405 AAAAAACATCCCATGTAAGACCATGTCTGGGACATGGCTTTGGCA
1 ATGAGAGGTCCCATGTAAGACCATGTCTAGGACATGGCATTGGCA
32147450 TGTTATTATC
Statistics
Matches: 117, Mismatches: 26, Indels: 3
0.80 0.18 0.02
Matches are distributed among these distances:
48 1 0.01
49 35 0.30
50 81 0.69
ACGTcount: A:0.30, C:0.22, G:0.27, T:0.22
Consensus pattern (50 bp):
ATGAGAGGTCCCATGTAAGACCATGTCTAGGACATGGCATTGGCACCGAC
Found at i:32155195 original size:8 final size:8
Alignment explanation
Indices: 32155182--32155223 Score: 57
Period size: 8 Copynumber: 5.1 Consensus size: 8
32155172 TTTAAATGAT
32155182 TCCATTTC
1 TCCATTTC
32155190 TCCATTTC
1 TCCATTTC
*
32155198 TCCATGTTT
1 TCCAT-TTC
32155207 TCCATTTC
1 TCCATTTC
*
32155215 TCAATTTC
1 TCCATTTC
32155223 T
1 T
32155224 ATTCATTTTG
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
8 23 0.77
9 7 0.23
ACGTcount: A:0.14, C:0.31, G:0.02, T:0.52
Consensus pattern (8 bp):
TCCATTTC
Found at i:32165242 original size:15 final size:15
Alignment explanation
Indices: 32165222--32165250 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
32165212 GTATTGTTGC
32165222 TTGATAACACGGTGA
1 TTGATAACACGGTGA
32165237 TTGATAACACGGTG
1 TTGATAACACGGTG
32165251 TGTCAAGCAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.31, C:0.14, G:0.28, T:0.28
Consensus pattern (15 bp):
TTGATAACACGGTGA
Found at i:32168159 original size:49 final size:49
Alignment explanation
Indices: 32168068--32168164 Score: 149
Period size: 49 Copynumber: 2.0 Consensus size: 49
32168058 ATCTATTTAT
** * * *
32168068 AGGTTGAAAAACCTTATTCTAATCAATGTCGAATAGATGAAGTGTAGTA
1 AGGTTGAAAAACCTTATTCTAATCAATGTAAAATAAAAGAAGTATAGTA
32168117 AGGTTGAAAAACCTTATTCTAATCAATGTAAAATAAAAGAAGTATAGT
1 AGGTTGAAAAACCTTATTCTAATCAATGTAAAATAAAAGAAGTATAGT
32168165 TCTATATAAA
Statistics
Matches: 43, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
49 43 1.00
ACGTcount: A:0.43, C:0.09, G:0.18, T:0.30
Consensus pattern (49 bp):
AGGTTGAAAAACCTTATTCTAATCAATGTAAAATAAAAGAAGTATAGTA
Found at i:32174650 original size:10 final size:11
Alignment explanation
Indices: 32174604--32174652 Score: 50
Period size: 10 Copynumber: 4.5 Consensus size: 11
32174594 ACTTGTTAGT
32174604 AAAATATTATA
1 AAAATATTATA
32174615 AAAA-AGTTATGA
1 AAAATA-TTAT-A
*
32174627 AAATTATT-TA
1 AAAATATTATA
32174637 AAAATATTA-A
1 AAAATATTATA
32174647 AAAATA
1 AAAATA
32174653 GGTTTAAACA
Statistics
Matches: 32, Mismatches: 2, Indels: 9
0.74 0.05 0.21
Matches are distributed among these distances:
10 16 0.50
11 9 0.28
12 6 0.19
13 1 0.03
ACGTcount: A:0.63, C:0.00, G:0.04, T:0.33
Consensus pattern (11 bp):
AAAATATTATA
Found at i:32174896 original size:13 final size:13
Alignment explanation
Indices: 32174870--32174902 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
32174860 AAAAGTACAT
32174870 AAATAATTTTAAA
1 AAATAATTTTAAA
32174883 AAAT-ATTTTAAA
1 AAATAATTTTAAA
*
32174895 AATTAATT
1 AAATAATT
32174903 ATTTTTGTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
12 11 0.61
13 7 0.39
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (13 bp):
AAATAATTTTAAA
Found at i:32177251 original size:15 final size:14
Alignment explanation
Indices: 32177193--32177244 Score: 65
Period size: 14 Copynumber: 3.9 Consensus size: 14
32177183 ATTTGATTTA
32177193 ATATAAATTTTTTT
1 ATATAAATTTTTTT
* *
32177207 -TA-AAA-ATTGTT
1 ATATAAATTTTTTT
32177218 ATATAAATTTTTTT
1 ATATAAATTTTTTT
32177232 ATATAAATTTTTT
1 ATATAAATTTTTT
32177245 ACCTATATTC
Statistics
Matches: 31, Mismatches: 4, Indels: 6
0.76 0.10 0.15
Matches are distributed among these distances:
11 4 0.13
12 5 0.16
13 5 0.16
14 17 0.55
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (14 bp):
ATATAAATTTTTTT
Found at i:32178163 original size:30 final size:30
Alignment explanation
Indices: 32178129--32178185 Score: 87
Period size: 30 Copynumber: 1.9 Consensus size: 30
32178119 GCATAGAAAT
* **
32178129 TAGTACATTAAGTATGTGTAAATTTTTATA
1 TAGTACATTAAATATGTACAAATTTTTATA
32178159 TAGTACATTAAATATGTACAAATTTTT
1 TAGTACATTAAATATGTACAAATTTTT
32178186 CCTCATACTA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.39, C:0.05, G:0.11, T:0.46
Consensus pattern (30 bp):
TAGTACATTAAATATGTACAAATTTTTATA
Found at i:32178956 original size:22 final size:22
Alignment explanation
Indices: 32178917--32178958 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
32178907 TTAAAATCAA
*
32178917 AACAAAAACAAAGAAAGAAAGT
1 AACAAAAAAAAAGAAAGAAAGT
32178939 AACAAAAAAAGAAG-AAGAAA
1 AACAAAAAAA-AAGAAAGAAA
32178959 AAAGACAGTG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 15 0.83
23 3 0.17
ACGTcount: A:0.76, C:0.07, G:0.14, T:0.02
Consensus pattern (22 bp):
AACAAAAAAAAAGAAAGAAAGT
Found at i:32192780 original size:22 final size:22
Alignment explanation
Indices: 32192755--32192802 Score: 69
Period size: 22 Copynumber: 2.2 Consensus size: 22
32192745 ACTAAGAGCC
* *
32192755 ATAAACAGGATAGCTATAAGCT
1 ATAAACAGAATAGCTACAAGCT
*
32192777 ATAAACAGAATGGCTACAAGCT
1 ATAAACAGAATAGCTACAAGCT
32192799 ATAA
1 ATAA
32192803 GTACAGTACT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.48, C:0.15, G:0.17, T:0.21
Consensus pattern (22 bp):
ATAAACAGAATAGCTACAAGCT
Done.