Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold43
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: 2559314
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 13088 characters in sequence are not A, C, G, or T
File 4 of 19
Found at i:455238 original size:16 final size:17
Alignment explanation
Indices: 455213--455247 Score: 63
Period size: 16 Copynumber: 2.1 Consensus size: 17
455203 CCAAGCTCGC
455213 AAAATCTTAAACTTAAA
1 AAAATCTTAAACTTAAA
455230 AAAAT-TTAAACTTAAA
1 AAAATCTTAAACTTAAA
455246 AA
1 AA
455248 CCAAAGCCCA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 13 0.72
17 5 0.28
ACGTcount: A:0.63, C:0.09, G:0.00, T:0.29
Consensus pattern (17 bp):
AAAATCTTAAACTTAAA
Found at i:455861 original size:16 final size:17
Alignment explanation
Indices: 455827--455861 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 17
455817 TATGCATTAG
455827 TTTATATAGAAGTCCTTT
1 TTTATATAGAAGT-CTTT
455845 TTTATATAGAAGT-TTT
1 TTTATATAGAAGTCTTT
455861 T
1 T
455862 CTTCAATTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 4 0.24
18 13 0.76
ACGTcount: A:0.29, C:0.06, G:0.11, T:0.54
Consensus pattern (17 bp):
TTTATATAGAAGTCTTT
Found at i:456939 original size:16 final size:16
Alignment explanation
Indices: 456918--456981 Score: 60
Period size: 16 Copynumber: 4.1 Consensus size: 16
456908 TTCGAGCTCA
*
456918 GATCATTTTAGATTCG
1 GATCATTTCAGATTCG
*
456934 GATCATTTCGGATTCG
1 GATCATTTCAGATTCG
* * *
456950 GATCA-ATCGGGTTCG
1 GATCATTTCAGATTCG
456965 GATC-TTTCTAGATTCG
1 GATCATTTC-AGATTCG
456981 G
1 G
456982 GTCAATTGCG
Statistics
Matches: 39, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
15 14 0.36
16 25 0.64
ACGTcount: A:0.20, C:0.17, G:0.25, T:0.38
Consensus pattern (16 bp):
GATCATTTCAGATTCG
Found at i:456964 original size:15 final size:16
Alignment explanation
Indices: 456928--456968 Score: 57
Period size: 15 Copynumber: 2.6 Consensus size: 16
456918 GATCATTTTA
*
456928 GATTCGGATCATTTCG
1 GATTCGGATCATATCG
456944 GATTCGGATCA-ATCG
1 GATTCGGATCATATCG
*
456959 GGTTCGGATC
1 GATTCGGATC
456969 TTTCTAGATT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 12 0.52
16 11 0.48
ACGTcount: A:0.20, C:0.20, G:0.29, T:0.32
Consensus pattern (16 bp):
GATTCGGATCATATCG
Found at i:457412 original size:38 final size:36
Alignment explanation
Indices: 457334--457411 Score: 102
Period size: 38 Copynumber: 2.1 Consensus size: 36
457324 AATATTTAAT
* *
457334 AAATATATAATATATATTTTAGACTTTTATAAGATAA
1 AAATATATAATATATATGTAAGACTTTTATAAGA-AA
457371 AAATATATATATATATATGTAAGACTTTTTTATAAGAAA
1 AAATATATA-ATATATATGTAAGAC--TTTTATAAGAAA
457410 AA
1 AA
457412 TTGCAAACGA
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
37 9 0.25
38 13 0.36
39 4 0.11
40 10 0.28
ACGTcount: A:0.50, C:0.03, G:0.06, T:0.41
Consensus pattern (36 bp):
AAATATATAATATATATGTAAGACTTTTATAAGAAA
Found at i:458049 original size:2 final size:2
Alignment explanation
Indices: 458042--458070 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
458032 ATTTCCAAAC
458042 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
458071 AAATCAAAGT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:460725 original size:23 final size:23
Alignment explanation
Indices: 460680--460731 Score: 59
Period size: 23 Copynumber: 2.3 Consensus size: 23
460670 ATTACAAAAT
* *
460680 AATAAAAATTTAGTTAATCTTAA
1 AATAAAAATTTAATTAATATTAA
* *
460703 AATAATAATTTAATTACTATTAA
1 AATAAAAATTTAATTAATATTAA
*
460726 ATTAAA
1 AATAAA
460732 TTATTATTAA
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.54, C:0.04, G:0.02, T:0.40
Consensus pattern (23 bp):
AATAAAAATTTAATTAATATTAA
Found at i:461108 original size:23 final size:23
Alignment explanation
Indices: 461065--461108 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
461055 TTTATCTTTA
**
461065 AATTTTTTTAAATAATGATAATT
1 AATTTTTTTAAATAAAAATAATT
461088 AATTTTTTTAAATAAAAATAA
1 AATTTTTTTAAATAAAAATAA
461109 CATAATATAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (23 bp):
AATTTTTTTAAATAAAAATAATT
Found at i:461114 original size:24 final size:23
Alignment explanation
Indices: 461065--461114 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 23
461055 TTTATCTTTA
** *
461065 AATTTTTTTAAATAATGATAATT
1 AATTTTTTTAAATAAAAATAAAT
461088 AATTTTTTTAAATAAAAATAACAT
1 AATTTTTTTAAATAAAAATAA-AT
461112 AAT
1 AAT
461115 ATATTAATAT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
23 19 0.83
24 4 0.17
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.46
Consensus pattern (23 bp):
AATTTTTTTAAATAAAAATAAAT
Found at i:462641 original size:2 final size:2
Alignment explanation
Indices: 462634--462659 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
462624 ATTGAACGAG
462634 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
462660 TTTATATGTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:463321 original size:46 final size:46
Alignment explanation
Indices: 463269--463360 Score: 175
Period size: 46 Copynumber: 2.0 Consensus size: 46
463259 TTTAATTTTT
*
463269 AAATAAATTAAGTAAATTCAAATTTTAATATCAAATCTAAGGTTAA
1 AAATAAATTAAGTAAATTCAAATTTAAATATCAAATCTAAGGTTAA
463315 AAATAAATTAAGTAAATTCAAATTTAAATATCAAATCTAAGGTTAA
1 AAATAAATTAAGTAAATTCAAATTTAAATATCAAATCTAAGGTTAA
463361 TCTCGAATGA
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
46 45 1.00
ACGTcount: A:0.53, C:0.07, G:0.07, T:0.34
Consensus pattern (46 bp):
AAATAAATTAAGTAAATTCAAATTTAAATATCAAATCTAAGGTTAA
Found at i:464505 original size:30 final size:27
Alignment explanation
Indices: 464437--464516 Score: 79
Period size: 28 Copynumber: 2.7 Consensus size: 27
464427 GGCTTAACCT
*
464437 ATTTTTTTAATGAACTTAATATTTTTAAA
1 ATTTTTTTAA--AATTTAATATTTTTAAA
464466 ATTTATTTTAAAATTTAATATTTTTATTTAA
1 ATTT-TTTTAAAATTTAATATTTTTA---AA
*
464497 ATTTTTTTAAATATTAAATA
1 ATTTTTTTAAA-ATTTAATA
464517 AACTTTCAAA
Statistics
Matches: 44, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
28 14 0.32
29 4 0.09
30 13 0.30
31 13 0.30
ACGTcount: A:0.40, C:0.01, G:0.01, T:0.57
Consensus pattern (27 bp):
ATTTTTTTAAAATTTAATATTTTTAAA
Found at i:465031 original size:14 final size:15
Alignment explanation
Indices: 465007--465035 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
464997 CCCCTTGTCG
465007 CCCCCCTCCCCCCCA
1 CCCCCCTCCCCCCCA
465022 CCCCCC-CCCCCCCA
1 CCCCCCTCCCCCCCA
465036 ACTCCCCCAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 8 0.57
15 6 0.43
ACGTcount: A:0.07, C:0.90, G:0.00, T:0.03
Consensus pattern (15 bp):
CCCCCCTCCCCCCCA
Found at i:465503 original size:31 final size:28
Alignment explanation
Indices: 465468--465525 Score: 71
Period size: 30 Copynumber: 2.0 Consensus size: 28
465458 TTTATTATAT
*
465468 TTTTAAAATATTATTTTTATTTAAATAATTA
1 TTTT-AAATATTAATTTT-TTTAAA-AATTA
*
465499 TTTTATATATTAATTTTTTTAAAAATT
1 TTTTAAATATTAATTTTTTTAAAAATT
465526 TATAAGTGAG
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
28 4 0.16
29 6 0.24
30 11 0.44
31 4 0.16
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (28 bp):
TTTTAAATATTAATTTTTTTAAAAATTA
Found at i:465634 original size:16 final size:16
Alignment explanation
Indices: 465597--465644 Score: 60
Period size: 17 Copynumber: 2.9 Consensus size: 16
465587 TTAATGATAA
*
465597 TATAATTATTTTTATT
1 TATAATTAATTTTATT
*
465613 TTTATATTAATATTTATT
1 TATA-ATTAAT-TTTATT
465631 TATAATTAATTTTA
1 TATAATTAATTTTA
465645 AATAAATTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
16 7 0.26
17 11 0.41
18 9 0.33
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (16 bp):
TATAATTAATTTTATT
Found at i:469261 original size:20 final size:20
Alignment explanation
Indices: 469233--469277 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
469223 TTTATTTTTC
** *
469233 TTTTCAATTTGAAATATTAA
1 TTTTCAATTAAAAATAGTAA
*
469253 TTTTTAATTAAAAATAGTAA
1 TTTTCAATTAAAAATAGTAA
469273 TTTTC
1 TTTTC
469278 TCATATGTAA
Statistics
Matches: 20, Mismatches: 5, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.40, C:0.04, G:0.04, T:0.51
Consensus pattern (20 bp):
TTTTCAATTAAAAATAGTAA
Found at i:469842 original size:2 final size:2
Alignment explanation
Indices: 469835--469864 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
469825 AATAAAACTC
469835 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
469865 GTTTGCTCTA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:470243 original size:96 final size:97
Alignment explanation
Indices: 470069--470264 Score: 288
Period size: 96 Copynumber: 2.0 Consensus size: 97
470059 CGTGGGGCCG
* * * *
470069 TCAGACATATTATGGTTCTCTTATCCCACAACCTCTCGAGGCCATTTGCTACATCCCTTTTGCTA
1 TCAGACATATTATGGTTCTCTTATCCCACAACCTCTCGAGCCCATTTGCTACATCCCTCTTCCCA
470134 GCCCATCAACCTTACAGGCCCCACTATTCACC
66 GCCCATCAACCTTACAGGCCCCACTATTCACC
* * *
470166 TCAGACATGTTATGG-T-TCTTATCCCACAACCTCTCTAGCCCATTTTGCTACATCTCTCTTCCC
1 TCAGACATATTATGGTTCTCTTATCCCACAACCTCTCGAGCCCA-TTTGCTACATCCCTCTTCCC
* *
470229 AGCCCATCCACCTTACAGGCCTCACTATTCACC
65 AGCCCATCAACCTTACAGGCCCCACTATTCACC
470262 TCA
1 TCA
470265 CCTACTACAA
Statistics
Matches: 89, Mismatches: 9, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
95 24 0.27
96 51 0.57
97 14 0.16
ACGTcount: A:0.22, C:0.37, G:0.10, T:0.31
Consensus pattern (97 bp):
TCAGACATATTATGGTTCTCTTATCCCACAACCTCTCGAGCCCATTTGCTACATCCCTCTTCCCA
GCCCATCAACCTTACAGGCCCCACTATTCACC
Found at i:475290 original size:20 final size:22
Alignment explanation
Indices: 475238--475290 Score: 67
Period size: 20 Copynumber: 2.5 Consensus size: 22
475228 AGTATTATGT
475238 TAATATATATATATATAATCCAA
1 TAATATATAT-TATATAATCCAA
*
475261 T-ATATATATTA-ATAAT-TAA
1 TAATATATATTATATAATCCAA
475280 TAATATATATT
1 TAATATATATT
475291 TGTTTTCTCT
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
19 3 0.11
20 14 0.50
21 2 0.07
22 8 0.29
23 1 0.04
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.45
Consensus pattern (22 bp):
TAATATATATTATATAATCCAA
Found at i:476349 original size:25 final size:24
Alignment explanation
Indices: 476302--476355 Score: 63
Period size: 25 Copynumber: 2.2 Consensus size: 24
476292 AAATAATATA
* * *
476302 TTTAATATATATTTTATTTTTATT
1 TTTAATATATATATTATATTTATG
*
476326 TTTAATAATTTATATTATATTTATG
1 TTTAAT-ATATATATTATATTTATG
476351 TTTAA
1 TTTAA
476356 ATTATAGAAC
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
24 6 0.24
25 19 0.76
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (24 bp):
TTTAATATATATATTATATTTATG
Found at i:476962 original size:15 final size:15
Alignment explanation
Indices: 476938--477014 Score: 57
Period size: 15 Copynumber: 5.0 Consensus size: 15
476928 TTTTTATTAT
476938 TATTAAATTTAAAAAA
1 TATT-AATTTAAAAAA
* * *
476954 TATTCATTT-AATAT
1 TATTAATTTAAAAAA
476968 TATTAAATTTAAAAAA
1 TATT-AATTTAAAAAA
* * * *
476984 TATTTATTTTAATAT
1 TATTAATTTAAAAAA
476999 TATTATATTTAAAAAA
1 TATTA-ATTTAAAAAA
477015 ATAAAAATTT
Statistics
Matches: 44, Mismatches: 14, Indels: 6
0.69 0.22 0.09
Matches are distributed among these distances:
14 7 0.16
15 19 0.43
16 18 0.41
ACGTcount: A:0.51, C:0.01, G:0.00, T:0.48
Consensus pattern (15 bp):
TATTAATTTAAAAAA
Found at i:476995 original size:31 final size:31
Alignment explanation
Indices: 476929--477014 Score: 138
Period size: 30 Copynumber: 2.8 Consensus size: 31
476919 TGTCATTAAT
*
476929 TTTTATTATTATTAAATTTAAAAAATATTCA
1 TTTTAATATTATTAAATTTAAAAAATATTCA
*
476960 -TTTAATATTATTAAATTTAAAAAATATTTA
1 TTTTAATATTATTAAATTTAAAAAATATTCA
*
476990 TTTTAATATTATTATATTTAAAAAA
1 TTTTAATATTATTAAATTTAAAAAA
477015 ATAAAAATTT
Statistics
Matches: 51, Mismatches: 3, Indels: 2
0.91 0.05 0.04
Matches are distributed among these distances:
30 28 0.55
31 23 0.45
ACGTcount: A:0.48, C:0.01, G:0.00, T:0.51
Consensus pattern (31 bp):
TTTTAATATTATTAAATTTAAAAAATATTCA
Found at i:477030 original size:30 final size:29
Alignment explanation
Indices: 476934--477032 Score: 108
Period size: 30 Copynumber: 3.3 Consensus size: 29
476924 TTAATTTTTA
*
476934 TTATTATTAAATTTAAAAAATATTCATTT
1 TTATTATTAAATTTAAAAAATATTAATTT
* *
476963 AATATTATTAAATTTAAAAAATATTTATTT
1 -TTATTATTAAATTTAAAAAATATTAATTT
* **
476993 TAATATTATTATATTTAAAAAAATAAAAATTT
1 T--TATTATTAAATTT-AAAAAATATTAATTT
477025 TTATTATT
1 TTATTATT
477033 TTCTTAATTT
Statistics
Matches: 59, Mismatches: 7, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
30 34 0.58
31 12 0.20
32 13 0.22
ACGTcount: A:0.48, C:0.01, G:0.00, T:0.51
Consensus pattern (29 bp):
TTATTATTAAATTTAAAAAATATTAATTT
Found at i:477328 original size:6 final size:6
Alignment explanation
Indices: 477309--477354 Score: 65
Period size: 6 Copynumber: 7.7 Consensus size: 6
477299 ACGTAATGAA
* * *
477309 AGAGAC AGAGAG AGAAAG AGAGAG AGAGAG AGAGAG AGAGAC AGAG
1 AGAGAG AGAGAG AGAGAG AGAGAG AGAGAG AGAGAG AGAGAG AGAG
477355 GGATTGTCAA
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
6 36 1.00
ACGTcount: A:0.52, C:0.04, G:0.43, T:0.00
Consensus pattern (6 bp):
AGAGAG
Found at i:477328 original size:10 final size:10
Alignment explanation
Indices: 477309--477354 Score: 65
Period size: 10 Copynumber: 4.6 Consensus size: 10
477299 ACGTAATGAA
*
477309 AGAGACAGAG
1 AGAGAGAGAG
*
477319 AGAGAAAGAG
1 AGAGAGAGAG
477329 AGAGAGAGAG
1 AGAGAGAGAG
477339 AGAGAGAGAG
1 AGAGAGAGAG
*
477349 ACAGAG
1 AGAGAG
477355 GGATTGTCAA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
10 33 1.00
ACGTcount: A:0.52, C:0.04, G:0.43, T:0.00
Consensus pattern (10 bp):
AGAGAGAGAG
Found at i:477348 original size:8 final size:8
Alignment explanation
Indices: 477309--477354 Score: 65
Period size: 8 Copynumber: 5.8 Consensus size: 8
477299 ACGTAATGAA
*
477309 AGAGACAG
1 AGAGAGAG
*
477317 AGAGAGAA
1 AGAGAGAG
477325 AGAGAGAG
1 AGAGAGAG
477333 AGAGAGAG
1 AGAGAGAG
477341 AGAGAGAG
1 AGAGAGAG
*
477349 ACAGAG
1 AGAGAG
477355 GGATTGTCAA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
8 34 1.00
ACGTcount: A:0.52, C:0.04, G:0.43, T:0.00
Consensus pattern (8 bp):
AGAGAGAG
Found at i:477462 original size:5 final size:5
Alignment explanation
Indices: 477438--477475 Score: 53
Period size: 5 Copynumber: 7.8 Consensus size: 5
477428 AAAATAAATG
477438 GAAAA -AAAA TGAAAA G-AAA GAAAA GAAAA GAAAA GAAA
1 GAAAA GAAAA -GAAAA GAAAA GAAAA GAAAA GAAAA GAAA
477476 GTAAGAGTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
4 8 0.27
5 18 0.60
6 4 0.13
ACGTcount: A:0.79, C:0.00, G:0.18, T:0.03
Consensus pattern (5 bp):
GAAAA
Found at i:477470 original size:19 final size:19
Alignment explanation
Indices: 477438--477476 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
477428 AAAATAAATG
477438 GAAAAAAAATGAAAAGAAA
1 GAAAAAAAATGAAAAGAAA
477457 GAAAAGAAAA-GAAAAGAAA
1 GAAAA-AAAATGAAAAGAAA
477476 G
1 G
477477 TAAGAGTTTG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 15 0.79
20 4 0.21
ACGTcount: A:0.77, C:0.00, G:0.21, T:0.03
Consensus pattern (19 bp):
GAAAAAAAATGAAAAGAAA
Found at i:478981 original size:3 final size:3
Alignment explanation
Indices: 478964--479006 Score: 59
Period size: 3 Copynumber: 14.3 Consensus size: 3
478954 AAGTTCCTGA
* * *
478964 TCT TCT TCG TAT TCT TCT TCT TCT TCT TCG TCT TCT TCT TCT T
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT T
479007 GTTTCCTGCA
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.02, C:0.30, G:0.05, T:0.63
Consensus pattern (3 bp):
TCT
Found at i:479812 original size:17 final size:19
Alignment explanation
Indices: 479766--479812 Score: 55
Period size: 18 Copynumber: 2.6 Consensus size: 19
479756 TAAGATATAG
479766 TAAATT-ATTATTTAAATA
1 TAAATTAATTATTTAAATA
*
479784 AAAATATAATTA-TTAAAT-
1 TAAAT-TAATTATTTAAATA
479802 TAAATTAATTA
1 TAAATTAATTA
479813 ATTATGTTTA
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
17 6 0.24
18 8 0.32
19 7 0.28
20 4 0.16
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (19 bp):
TAAATTAATTATTTAAATA
Found at i:480418 original size:20 final size:20
Alignment explanation
Indices: 480395--480452 Score: 59
Period size: 19 Copynumber: 3.0 Consensus size: 20
480385 TTATAAAATA
*
480395 TATTACTATTT-TATTTTAAT
1 TATT-CTATTTATATTATAAT
*
480415 TATTTTATTTATATTATAAT
1 TATTCTATTTATATTATAAT
*
480435 TA-TCTAATTATATT-TAAT
1 TATTCTATTTATATTATAAT
480453 ATTATCGATT
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
18 4 0.12
19 15 0.45
20 14 0.42
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.62
Consensus pattern (20 bp):
TATTCTATTTATATTATAAT
Found at i:481184 original size:15 final size:14
Alignment explanation
Indices: 481142--481184 Score: 52
Period size: 15 Copynumber: 3.0 Consensus size: 14
481132 CCATCTTAAA
481142 AATTTTAAAAGATAT
1 AATTTT-AAAGATAT
481157 AATTTTAAA-ATAT
1 AATTTTAAAGATAT
*
481170 GATTATTAAAGATAT
1 AATT-TTAAAGATAT
481185 TTTTAAGCTT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
13 7 0.28
14 8 0.32
15 10 0.40
ACGTcount: A:0.51, C:0.00, G:0.07, T:0.42
Consensus pattern (14 bp):
AATTTTAAAGATAT
Found at i:481693 original size:15 final size:15
Alignment explanation
Indices: 481673--481728 Score: 53
Period size: 15 Copynumber: 3.6 Consensus size: 15
481663 TAAATTTTTT
481673 TTATTTTTAAATTAA
1 TTATTTTTAAATTAA
*
481688 TTATTTTT-TATCTAAA
1 TTATTTTTAAAT-T-AA
481704 TTTATTTTTAAATTTAA
1 -TTATTTTTAAA-TTAA
481721 -TATTTTTA
1 TTATTTTTA
481729 TTAAAATCTT
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
14 2 0.06
15 17 0.50
16 2 0.06
17 10 0.29
18 2 0.06
19 1 0.03
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (15 bp):
TTATTTTTAAATTAA
Found at i:482208 original size:22 final size:21
Alignment explanation
Indices: 482144--482213 Score: 70
Period size: 21 Copynumber: 3.2 Consensus size: 21
482134 ATCAAGGATA
482144 AAATTTAAAATAATTTAAAATTT
1 AAATTTAAAAT-A-TTAAAATTT
* *
482167 TATTTTAAAAT-TTAATAATTT
1 AAATTTAAAATATTAA-AATTT
*
482188 AAATTTAAAATGATCAAAATTT
1 AAATTTAAAAT-ATTAAAATTT
482210 AAAT
1 AAAT
482214 AATTTAATTT
Statistics
Matches: 39, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
20 4 0.10
21 14 0.36
22 9 0.23
23 12 0.31
ACGTcount: A:0.53, C:0.01, G:0.01, T:0.44
Consensus pattern (21 bp):
AAATTTAAAATATTAAAATTT
Found at i:482546 original size:18 final size:21
Alignment explanation
Indices: 482502--482566 Score: 61
Period size: 21 Copynumber: 3.3 Consensus size: 21
482492 AATTTTTATT
482502 TAAAT-TTAATTATAAAATATA
1 TAAATATT-ATTATAAAATATA
482523 TAAATATTATTATAAAA-A-A
1 TAAATATTATTATAAAATATA
*
482542 T-AATATT-TTA-ATAATATAA
1 TAAATATTATTATAAAATAT-A
482561 TAAATA
1 TAAATA
482567 ATAAAATAAT
Statistics
Matches: 38, Mismatches: 1, Indels: 11
0.76 0.02 0.22
Matches are distributed among these distances:
16 3 0.08
17 4 0.11
18 6 0.16
19 4 0.11
20 5 0.13
21 14 0.37
22 2 0.05
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (21 bp):
TAAATATTATTATAAAATATA
Found at i:482548 original size:15 final size:16
Alignment explanation
Indices: 482524--482576 Score: 56
Period size: 15 Copynumber: 3.4 Consensus size: 16
482514 TAAAATATAT
*
482524 AAATATTATTATAA-A
1 AAATAATATTATAATA
*
482539 AAATAATATTTTAATA
1 AAATAATATTATAATA
* *
482555 ATATAATA-AATAATA
1 AAATAATATTATAATA
482570 AAATAAT
1 AAATAAT
482577 TTTTAAAATT
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
15 23 0.74
16 8 0.26
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (16 bp):
AAATAATATTATAATA
Found at i:489055 original size:17 final size:17
Alignment explanation
Indices: 489011--489099 Score: 65
Period size: 17 Copynumber: 4.9 Consensus size: 17
489001 TGTGAACATA
*
489011 TATTAAAAATTATATTATT
1 TATTAAATA-TATATT-TT
*
489030 TAGTCAAATATATATTTT
1 TA-TTAAATATATATTTT
*
489048 TATTAAATATTTATTATT
1 TATTAAATATATATT-TT
*
489066 T-TT-AATATTTATTTAT
1 TATTAAATATATATTT-T
489082 TATTAAAATTATATATTT
1 TATT-AAA-TATATATTT
489100 AATATTTAAA
Statistics
Matches: 58, Mismatches: 5, Indels: 13
0.76 0.07 0.17
Matches are distributed among these distances:
15 1 0.02
16 12 0.21
17 15 0.26
18 7 0.12
19 10 0.17
20 13 0.22
ACGTcount: A:0.40, C:0.01, G:0.01, T:0.57
Consensus pattern (17 bp):
TATTAAATATATATTTT
Found at i:489067 original size:20 final size:20
Alignment explanation
Indices: 489042--489085 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
489032 GTCAAATATA
*
489042 TATTTTTATTAAATATTTAT
1 TATTTTTAATAAATATTTAT
**
489062 TATTTTTAATATTTATTTAT
1 TATTTTTAATAAATATTTAT
489082 TATT
1 TATT
489086 AAAATTATAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (20 bp):
TATTTTTAATAAATATTTAT
Found at i:489074 original size:16 final size:16
Alignment explanation
Indices: 489053--489107 Score: 60
Period size: 16 Copynumber: 3.5 Consensus size: 16
489043 ATTTTTATTA
489053 AATATTTATTATTTTT
1 AATATTTATTATTTTT
*
489069 AATATTTATTTATTATT
1 AATATTTA-TTATTTTT
* *
489086 AA-AATTA-TATATTT
1 AATATTTATTATTTTT
489100 AATATTTA
1 AATATTTA
489108 AATTTTTTAT
Statistics
Matches: 32, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
14 7 0.22
15 4 0.12
16 12 0.38
17 9 0.28
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (16 bp):
AATATTTATTATTTTT
Found at i:489101 original size:31 final size:33
Alignment explanation
Indices: 489036--489107 Score: 96
Period size: 31 Copynumber: 2.2 Consensus size: 33
489026 TATTTAGTCA
* *
489036 AATATATATTTTTATTAAATATTTATTATTTTT
1 AATATTTATTTTTATTAAATATTTATTATATTT
489069 AATATTTATTTATTATTAAA-A-TTA-TATATTT
1 AATATTTATTT-TTATTAAATATTTATTATATTT
489100 AATATTTA
1 AATATTTA
489108 AATTTTTTAT
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
31 14 0.39
32 3 0.08
33 11 0.31
34 8 0.22
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (33 bp):
AATATTTATTTTTATTAAATATTTATTATATTT
Found at i:489118 original size:20 final size:20
Alignment explanation
Indices: 489071--489118 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
489061 TTATTTTTAA
*
489071 TATTTATTTATTATTAAAAT
1 TATTTATTTAATATTAAAAT
* *
489091 TATATATTTAATATTTAAAT
1 TATTTATTTAATATTAAAAT
*
489111 TTTTTATT
1 TATTTATT
489119 GATTTAATAA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (20 bp):
TATTTATTTAATATTAAAAT
Found at i:491284 original size:179 final size:180
Alignment explanation
Indices: 490976--491331 Score: 554
Period size: 179 Copynumber: 2.0 Consensus size: 180
490966 AAGCAATACT
*
490976 TTTTTTTTAGTAGTATTCCATTTGTCGGTTCGATTAATAATCAAATCGAAATTTTATTAATTGAA
1 TTTTTTTTAGTAGTATTCAATTTGTCGGTTCGATTAATAATCAAATCGAAATTTTATTAATTGAA
* * *
491041 TTAACTAATTTTTTTTGTTAACTGTTAACCAAATCGAATTAAAAGAGATTTAAATTATATAAATC
66 TTAACTAATTTTTTTTGTTAACTGTTAACCAAATCGAATTAAAAGAAACTTAAATTAAATAAATC
* * * * *
491106 GAAATTATTTTAATTAATTCAGTTGGTTAACTGAATTTACTGAATTTTAG
131 AAAATTATGTCAATTAATTCAGTTGATTAACTGAATTAACTGAATTTTAG
* ** *
491156 TTTTTTTTAGTAGTATTCAATTTTTTTGTTCGATTAATAATCAAATCGAGATTTTATTAATTGAA
1 TTTTTTTTAGTAGTATTCAATTTGTCGGTTCGATTAATAATCAAATCGAAATTTTATTAATTGAA
*
491221 TTAACTAA-TTTTTTTGTTAA-TCGTTAATCAAATCGAATTAAAAGAAACTTAAATTAAATAAAT
66 TTAACTAATTTTTTTTGTTAACT-GTTAACCAAATCGAATTAAAAGAAACTTAAATTAAATAAAT
*
491284 CAAAATTATGTCAATTAATTCAGTTGATTAATTGAATTAACTGAATTT
130 CAAAATTATGTCAATTAATTCAGTTGATTAACTGAATTAACTGAATTT
491332 CAATTGTTTT
Statistics
Matches: 160, Mismatches: 15, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
178 1 0.01
179 91 0.57
180 68 0.43
ACGTcount: A:0.37, C:0.08, G:0.10, T:0.45
Consensus pattern (180 bp):
TTTTTTTTAGTAGTATTCAATTTGTCGGTTCGATTAATAATCAAATCGAAATTTTATTAATTGAA
TTAACTAATTTTTTTTGTTAACTGTTAACCAAATCGAATTAAAAGAAACTTAAATTAAATAAATC
AAAATTATGTCAATTAATTCAGTTGATTAACTGAATTAACTGAATTTTAG
Found at i:491459 original size:20 final size:18
Alignment explanation
Indices: 491434--491472 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
491424 GATTATATTT
491434 ATAATAAGTTAAAAACTTAA
1 ATAATAAG-T-AAAACTTAA
*
491454 ATAATATGTAAAACTTAA
1 ATAATAAGTAAAACTTAA
491472 A
1 A
491473 ACATCAAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 10 0.56
19 1 0.06
20 7 0.39
ACGTcount: A:0.59, C:0.05, G:0.05, T:0.31
Consensus pattern (18 bp):
ATAATAAGTAAAACTTAA
Found at i:491948 original size:22 final size:22
Alignment explanation
Indices: 491906--491952 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 22
491896 TTTAATTTTA
*
491906 ATTTTTATTTTTGAATATAATT
1 ATTTATATTTTTGAATATAATT
*
491928 ATTTATATATTTTG-ATTTAATT
1 ATTTATAT-TTTTGAATATAATT
491950 ATT
1 ATT
491953 AATTTGTACA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
22 17 0.77
23 5 0.23
ACGTcount: A:0.32, C:0.00, G:0.04, T:0.64
Consensus pattern (22 bp):
ATTTATATTTTTGAATATAATT
Found at i:492264 original size:15 final size:15
Alignment explanation
Indices: 492207--492287 Score: 65
Period size: 15 Copynumber: 5.3 Consensus size: 15
492197 TAATTTTAGA
*
492207 TTAAACTCAAAAAAT
1 TTAAACTTAAAAAAT
*
492222 TTAAATTTAAAAAATT
1 TTAAACTTAAAAAA-T
* **
492238 TTGAACGGAAAAAAT
1 TTAAACTTAAAAAAT
492253 TTAAACTTAAAAAGAT
1 TTAAACTTAAAAA-AT
***
492269 TCGGAC-TAAAAAAT
1 TTAAACTTAAAAAAT
492283 TTAAA
1 TTAAA
492288 AAAAATCAAA
Statistics
Matches: 49, Mismatches: 15, Indels: 5
0.71 0.22 0.07
Matches are distributed among these distances:
14 4 0.08
15 29 0.59
16 16 0.33
ACGTcount: A:0.56, C:0.07, G:0.07, T:0.30
Consensus pattern (15 bp):
TTAAACTTAAAAAAT
Found at i:492281 original size:31 final size:30
Alignment explanation
Indices: 492215--492287 Score: 85
Period size: 31 Copynumber: 2.4 Consensus size: 30
492205 GATTAAACTC
* *
492215 AAAAAATTTAAATTTAAAAAATTTTGAACGG
1 AAAAAATTTAAACTTAAAAAATTTCGAAC-G
* *
492246 AAAAAATTTAAACTTAAAAAGA-TTCGGACT
1 AAAAAATTTAAACTTAAAAA-ATTTCGAACG
492276 AAAAAATTTAAA
1 AAAAAATTTAAA
492288 AAAAATCAAA
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
30 12 0.32
31 24 0.65
32 1 0.03
ACGTcount: A:0.58, C:0.05, G:0.08, T:0.29
Consensus pattern (30 bp):
AAAAAATTTAAACTTAAAAAATTTCGAACG
Found at i:492580 original size:32 final size:34
Alignment explanation
Indices: 492544--492615 Score: 96
Period size: 34 Copynumber: 2.2 Consensus size: 34
492534 TAAAATATTT
*
492544 TTATATAAATTTTTATAA-A-TTA-ATAGTTTATA
1 TTATATAAA-TTTTAAAATATTTATATAGTTTATA
*
492576 TTATATAAATTTTAAAATATTTATATATTTTATA
1 TTATATAAATTTTAAAATATTTATATAGTTTATA
492610 TTATAT
1 TTATAT
492616 TTATATTTTA
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
31 7 0.20
32 10 0.29
33 3 0.09
34 15 0.43
ACGTcount: A:0.43, C:0.00, G:0.01, T:0.56
Consensus pattern (34 bp):
TTATATAAATTTTAAAATATTTATATAGTTTATA
Found at i:492615 original size:20 final size:19
Alignment explanation
Indices: 492571--492621 Score: 59
Period size: 18 Copynumber: 2.6 Consensus size: 19
492561 AATTAATAGT
*
492571 TTATATTATATAAATTTTAA
1 TTATATT-TATATATTTTAA
*
492591 -AATATTTATATATTTTATA
1 TTATATTTATATATTTTA-A
492610 TTATATTTATAT
1 TTATATTTATAT
492622 TTTAATTTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
18 10 0.38
19 6 0.23
20 10 0.38
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (19 bp):
TTATATTTATATATTTTAA
Found at i:493429 original size:21 final size:22
Alignment explanation
Indices: 493375--493423 Score: 73
Period size: 22 Copynumber: 2.2 Consensus size: 22
493365 ATTAAAATAA
493375 TAAAAAATTTATTTTATTAAAT
1 TAAAAAATTTATTTTATTAAAT
*
493397 TAAAAAATTTATGTTT-TTCAAT
1 TAAAAAATTTAT-TTTATTAAAT
493419 TAAAA
1 TAAAA
493424 TTTTATTAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
22 22 0.88
23 3 0.12
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (22 bp):
TAAAAAATTTATTTTATTAAAT
Found at i:493653 original size:15 final size:14
Alignment explanation
Indices: 493628--493661 Score: 50
Period size: 15 Copynumber: 2.4 Consensus size: 14
493618 TTAAAAATAT
493628 TTTTATATTTATAA
1 TTTTATATTTATAA
493642 TTTTATATTTTATAA
1 TTTTATA-TTTATAA
*
493657 ATTTA
1 TTTTA
493662 AATAAAATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 7 0.39
15 11 0.61
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (14 bp):
TTTTATATTTATAA
Found at i:493703 original size:20 final size:20
Alignment explanation
Indices: 493664--493700 Score: 67
Period size: 19 Copynumber: 1.9 Consensus size: 20
493654 TAAATTTAAA
493664 TAAAATATATTATTTTAATT
1 TAAAATATATTATTTTAATT
493684 TAAAA-ATATTATTTTAA
1 TAAAATATATTATTTTAA
493701 ATTGAATTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
19 12 0.71
20 5 0.29
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (20 bp):
TAAAATATATTATTTTAATT
Found at i:493880 original size:5 final size:5
Alignment explanation
Indices: 493870--493914 Score: 81
Period size: 5 Copynumber: 8.8 Consensus size: 5
493860 TATTTCATCA
493870 TATAT TATAT TATAT TATAT TATAAT TATAT TATAT TATAT TATA
1 TATAT TATAT TATAT TATAT TAT-AT TATAT TATAT TATAT TATA
493915 ACATAATGAA
Statistics
Matches: 39, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
5 34 0.87
6 5 0.13
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (5 bp):
TATAT
Found at i:493899 original size:21 final size:21
Alignment explanation
Indices: 493873--493915 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
493863 TTCATCATAT
493873 ATTATATTATATTATATTATA
1 ATTATATTATATTATATTATA
493894 ATTATATTATATTATATTATA
1 ATTATATTATATTATATTATA
493915 A
1 A
493916 CATAATGAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (21 bp):
ATTATATTATATTATATTATA
Found at i:493920 original size:26 final size:26
Alignment explanation
Indices: 493870--493921 Score: 86
Period size: 26 Copynumber: 2.0 Consensus size: 26
493860 TATTTCATCA
**
493870 TATATTATATTATATTATATTATAAT
1 TATATTATATTATATTATAACATAAT
493896 TATATTATATTATATTATAACATAAT
1 TATATTATATTATATTATAACATAAT
493922 GAAATGATAT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (26 bp):
TATATTATATTATATTATAACATAAT
Found at i:493931 original size:26 final size:26
Alignment explanation
Indices: 493876--493931 Score: 67
Period size: 26 Copynumber: 2.2 Consensus size: 26
493866 ATCATATATT
** * * *
493876 ATATTATATTATATTATAATTATATT
1 ATATTATATTATAACATAATGAAATG
493902 ATATTATATTATAACATAATGAAATG
1 ATATTATATTATAACATAATGAAATG
493928 ATAT
1 ATAT
493932 AATACAGAGA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.46, C:0.02, G:0.04, T:0.48
Consensus pattern (26 bp):
ATATTATATTATAACATAATGAAATG
Found at i:494338 original size:2 final size:2
Alignment explanation
Indices: 494331--494355 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
494321 GGTTTTAATT
494331 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 T
494356 GTTGGCTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:494501 original size:3 final size:3
Alignment explanation
Indices: 494493--494540 Score: 96
Period size: 3 Copynumber: 16.0 Consensus size: 3
494483 CTTTTATCAG
494493 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
494541 TTCAATTCAA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 45 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:497878 original size:16 final size:18
Alignment explanation
Indices: 497857--497902 Score: 53
Period size: 16 Copynumber: 2.7 Consensus size: 18
497847 AATCCACAAT
497857 AAACATTAAAAATC-AC-
1 AAACATTAAAAATCAACA
497873 AAACA-TAAATAATCAACA
1 AAACATTAAA-AATCAACA
*
497891 AAAGATTAAAAA
1 AAACATTAAAAA
497903 AAATACACAT
Statistics
Matches: 25, Mismatches: 1, Indels: 6
0.78 0.03 0.19
Matches are distributed among these distances:
15 4 0.16
16 9 0.36
17 2 0.08
18 6 0.24
19 4 0.16
ACGTcount: A:0.67, C:0.13, G:0.02, T:0.17
Consensus pattern (18 bp):
AAACATTAAAAATCAACA
Found at i:499145 original size:2 final size:2
Alignment explanation
Indices: 499138--499164 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
499128 AATTTTAGCT
499138 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
499165 TTGAGTAGAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:502674 original size:25 final size:25
Alignment explanation
Indices: 502614--502695 Score: 73
Period size: 25 Copynumber: 3.3 Consensus size: 25
502604 TTTTTAAAAA
* *
502614 TTTAT-ATTTTAA-ATTAATTTAAT
1 TTTATAATATTAATATTAATATAAT
*
502637 TTTATTATAATT-ATATTAAATATATAT
1 TTTATAAT-ATTAATATT-AATATA-AT
*
502664 TTT-TAATATTAATATTTATATAAT
1 TTTATAATATTAATATTAATATAAT
502688 TTTATAAT
1 TTTATAAT
502696 TAAATTTAAA
Statistics
Matches: 48, Mismatches: 4, Indels: 12
0.75 0.06 0.19
Matches are distributed among these distances:
23 5 0.10
24 8 0.17
25 17 0.35
26 13 0.27
27 5 0.10
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (25 bp):
TTTATAATATTAATATTAATATAAT
Found at i:502683 original size:23 final size:22
Alignment explanation
Indices: 502657--502708 Score: 61
Period size: 23 Copynumber: 2.3 Consensus size: 22
502647 TTATATTAAA
*
502657 TATATATTTTTA-ATATTAATATT
1 TATATAATTTTATA-ATTAA-ATT
502680 TATATAATTTTATAATTAAATT
1 TATATAATTTTATAATTAAATT
*
502702 TAAATAA
1 TATATAA
502709 AATATTTTAT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
22 9 0.35
23 16 0.62
24 1 0.04
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (22 bp):
TATATAATTTTATAATTAAATT
Found at i:503416 original size:22 final size:21
Alignment explanation
Indices: 503380--503420 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
503370 AATAATGAGA
*
503380 TTTAATTAATCTTAATATTATC
1 TTTAATTAATATTAA-ATTATC
*
503402 TTTAATTATTATTAAATTA
1 TTTAATTAATATTAAATTA
503421 AATTATATCT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 4 0.24
22 13 0.76
ACGTcount: A:0.39, C:0.05, G:0.00, T:0.56
Consensus pattern (21 bp):
TTTAATTAATATTAAATTATC
Found at i:503771 original size:11 final size:11
Alignment explanation
Indices: 503748--503788 Score: 57
Period size: 11 Copynumber: 3.7 Consensus size: 11
503738 TGATTTATTT
503748 TTAA-ATAAAA
1 TTAATATAAAA
*
503758 TTAATATAATA
1 TTAATATAAAA
503769 TTAATATTAAAA
1 TTAATA-TAAAA
503781 TTAATATA
1 TTAATATA
503789 TATAATTGAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
10 4 0.15
11 13 0.48
12 10 0.37
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (11 bp):
TTAATATAAAA
Found at i:504031 original size:18 final size:18
Alignment explanation
Indices: 503998--504032 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
503988 AATTTCATAG
*
503998 TAATTAAAGATAATTTTA
1 TAATTAAAAATAATTTTA
*
504016 TAATTAAAAATTATTTT
1 TAATTAAAAATAATTTT
504033 GAGTAAAAAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (18 bp):
TAATTAAAAATAATTTTA
Found at i:504334 original size:5 final size:5
Alignment explanation
Indices: 504292--504345 Score: 51
Period size: 5 Copynumber: 10.6 Consensus size: 5
504282 AATTTAGGTG
504292 TAATAT TAATAT TATATT T-ATT T-ATT T-ATT TAAATT TAATT TAATT
1 TAAT-T TAAT-T TA-ATT TAATT TAATT TAATT T-AATT TAATT TAATT
504338 TAATT TAA
1 TAATT TAA
504346 GAATTCGGAT
Statistics
Matches: 45, Mismatches: 0, Indels: 7
0.87 0.00 0.13
Matches are distributed among these distances:
4 12 0.27
5 17 0.38
6 14 0.31
7 2 0.04
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (5 bp):
TAATT
Found at i:504702 original size:19 final size:18
Alignment explanation
Indices: 504680--504729 Score: 55
Period size: 18 Copynumber: 2.7 Consensus size: 18
504670 TAATTTTATT
*
504680 TAAATCTTTAAATATCAAA
1 TAAATATTTAAAT-TCAAA
* *
504699 TAAAAATTTAAATTTAAA
1 TAAATATTTAAATTCAAA
*
504717 TAAATAATTAAAT
1 TAAATATTTAAAT
504730 AAATATATTA
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
18 15 0.58
19 11 0.42
ACGTcount: A:0.58, C:0.04, G:0.00, T:0.38
Consensus pattern (18 bp):
TAAATATTTAAATTCAAA
Found at i:504719 original size:18 final size:20
Alignment explanation
Indices: 504686--504730 Score: 60
Period size: 18 Copynumber: 2.4 Consensus size: 20
504676 TATTTAAATC
504686 TTTAAATATCAAATAAA-AA
1 TTTAAATATCAAATAAATAA
*
504705 TTTAAAT-TTAAATAAATAA
1 TTTAAATATCAAATAAATAA
504724 -TTAAATA
1 TTTAAATA
504731 AATATATTAC
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
18 14 0.61
19 9 0.39
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (20 bp):
TTTAAATATCAAATAAATAA
Found at i:504982 original size:18 final size:17
Alignment explanation
Indices: 504959--504997 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 17
504949 TAATTTAGGG
504959 TTATTTATTTAATTTAAA
1 TTATTTATTTAATTT-AA
*
504977 TTATTTTTTTAATTTAA
1 TTATTTATTTAATTTAA
504994 TTAT
1 TTAT
504998 AAAAATATTA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
17 6 0.30
18 14 0.70
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (17 bp):
TTATTTATTTAATTTAA
Found at i:505030 original size:44 final size:43
Alignment explanation
Indices: 504982--505064 Score: 107
Period size: 44 Copynumber: 1.9 Consensus size: 43
504972 TTAAATTATT
**
504982 TTTTTAAT-TTAATTATAAA-AATATTATATATTATATAAATAAAA
1 TTTTTAATATT-ATT-TAAATAATAAAATATATTAT-TAAATAAAA
505026 TTTTTAATATTATTTAAATAATAAAATATATTATTAAAT
1 TTTTTAATATTATTTAAATAATAAAATATATTATTAAAT
505065 CAATTTAAAT
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
43 9 0.26
44 24 0.69
45 2 0.06
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (43 bp):
TTTTTAATATTATTTAAATAATAAAATATATTATTAAATAAAA
Found at i:508934 original size:15 final size:15
Alignment explanation
Indices: 508914--508950 Score: 65
Period size: 15 Copynumber: 2.5 Consensus size: 15
508904 TTCCCATTAC
*
508914 TATTATTATTGTTAT
1 TATTATTATTGTCAT
508929 TATTATTATTGTCAT
1 TATTATTATTGTCAT
508944 TATTATT
1 TATTATT
508951 TGTGATGACA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.27, C:0.03, G:0.05, T:0.65
Consensus pattern (15 bp):
TATTATTATTGTCAT
Found at i:511080 original size:22 final size:21
Alignment explanation
Indices: 511065--511107 Score: 72
Period size: 20 Copynumber: 2.1 Consensus size: 21
511055 AAAGACATAT
511065 ATAAT-ATTTTAAAAAGTAAA
1 ATAATAATTTTAAAAAGTAAA
511085 ATAATAATTTTAAAAA-TAAA
1 ATAATAATTTTAAAAAGTAAA
511105 ATA
1 ATA
511108 GAGTAAAGCG
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
20 12 0.55
21 10 0.45
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (21 bp):
ATAATAATTTTAAAAAGTAAA
Found at i:513653 original size:21 final size:20
Alignment explanation
Indices: 513628--513669 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
513618 TATATTATAT
*
513628 TTTTTAATTTAATTTTCAAAA
1 TTTTTAATTAAATTTT-AAAA
*
513649 TTTTTTATTAAATTTTAAAA
1 TTTTTAATTAAATTTTAAAA
513669 T
1 T
513670 ATAAAAAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 5 0.26
21 14 0.74
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (20 bp):
TTTTTAATTAAATTTTAAAA
Found at i:513659 original size:20 final size:22
Alignment explanation
Indices: 513626--513669 Score: 58
Period size: 20 Copynumber: 2.1 Consensus size: 22
513616 TCTATATTAT
513626 ATTTTTTAATTT-AATTTTCAAA
1 ATTTTTTAATTTAAATTTT-AAA
513648 ATTTTTT-A-TTAAATTTTAAA
1 ATTTTTTAATTTAAATTTTAAA
513668 AT
1 AT
513670 ATAAAAAAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
20 7 0.33
21 7 0.33
22 7 0.33
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (22 bp):
ATTTTTTAATTTAAATTTTAAA
Found at i:513911 original size:26 final size:27
Alignment explanation
Indices: 513875--513926 Score: 72
Period size: 26 Copynumber: 2.0 Consensus size: 27
513865 TTATTTGATA
513875 TAAATATTTTTAATA-TATTTAAATTTG
1 TAAATATTTTTAA-ACTATTTAAATTTG
*
513902 TAAATA-TTTTAAACTATTTATATTT
1 TAAATATTTTTAAACTATTTAAATTT
513927 ATATTTATAT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
25 1 0.04
26 16 0.70
27 6 0.26
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.56
Consensus pattern (27 bp):
TAAATATTTTTAAACTATTTAAATTTG
Found at i:513979 original size:24 final size:25
Alignment explanation
Indices: 513921--513979 Score: 59
Period size: 23 Copynumber: 2.4 Consensus size: 25
513911 TAAACTATTT
*
513921 ATATTTATATTTATATTTAAATATAA
1 ATATTT-TATATATATTTAAATATAA
* **
513947 CTA-AATATATATA-TTAAATATAA
1 ATATTTTATATATATTTAAATATAA
513970 ATATTTTATA
1 ATATTTTATA
513980 AAAATAAAAA
Statistics
Matches: 25, Mismatches: 7, Indels: 4
0.69 0.19 0.11
Matches are distributed among these distances:
23 12 0.48
24 11 0.44
26 2 0.08
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (25 bp):
ATATTTTATATATATTTAAATATAA
Found at i:514307 original size:22 final size:21
Alignment explanation
Indices: 514285--514354 Score: 63
Period size: 22 Copynumber: 3.3 Consensus size: 21
514275 GCTTATCTAT
514285 TATTTAAAAAATATTAT-A-A
1 TATTTAAAAAATATTATAATA
* *
514304 TATTTAAAAAAAATTATATTAA
1 TATTTAAAAAATATTATAAT-A
* *
514326 TATTTATAAAATTTTATAATTA
1 TATTTAAAAAATATTATAA-TA
*
514348 AATTTAA
1 TATTTAA
514355 TAATTTTTTT
Statistics
Matches: 39, Mismatches: 8, Indels: 5
0.75 0.15 0.10
Matches are distributed among these distances:
19 16 0.41
22 22 0.56
23 1 0.03
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (21 bp):
TATTTAAAAAATATTATAATA
Found at i:514309 original size:19 final size:19
Alignment explanation
Indices: 514285--514345 Score: 68
Period size: 19 Copynumber: 3.1 Consensus size: 19
514275 GCTTATCTAT
514285 TATTTAAAAAATATTATAA
1 TATTTAAAAAATATTATAA
*
514304 TATTTAAAAAAAATTATATTAA
1 TATTTAAAAAATA-T-TA-TAA
* *
514326 TATTTATAAAATTTTATAA
1 TATTTAAAAAATATTATAA
514345 T
1 T
514346 TAAATTTAAT
Statistics
Matches: 35, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
19 16 0.46
20 3 0.09
21 3 0.09
22 13 0.37
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (19 bp):
TATTTAAAAAATATTATAA
Found at i:514793 original size:22 final size:21
Alignment explanation
Indices: 514768--514822 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 21
514758 TAGCTGTTTA
* *
514768 AATATTAAAATATTTTTATATT
1 AATATTTAAATA-TTTTATAAT
*
514790 AATATTTATATATTTTATAAT
1 AATATTTAAATATTTTATAAT
*
514811 AAAATTTAAATA
1 AATATTTAAATA
514823 AAAATATTTT
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
21 18 0.64
22 10 0.36
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (21 bp):
AATATTTAAATATTTTATAAT
Found at i:515697 original size:20 final size:20
Alignment explanation
Indices: 515664--515727 Score: 53
Period size: 20 Copynumber: 3.1 Consensus size: 20
515654 GATATAAAAA
**
515664 TATAATATTTTAAATATAAT
1 TATAATATAATAAATATAAT
515684 TATAATATAATAAA-AT-A-
1 TATAATATAATAAATATAAT
515701 TATAAATATATATCAAATATAAAT
1 TAT-AATATA-AT-AAATAT-AAT
515725 TAT
1 TAT
515728 TAAGAATCGG
Statistics
Matches: 35, Mismatches: 2, Indels: 10
0.74 0.04 0.21
Matches are distributed among these distances:
17 3 0.09
18 7 0.20
19 4 0.11
20 15 0.43
21 2 0.06
23 1 0.03
24 3 0.09
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (20 bp):
TATAATATAATAAATATAAT
Found at i:516065 original size:2 final size:2
Alignment explanation
Indices: 516058--516089 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
516048 CACATGCTAC
516058 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
516090 TAAAATCGAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:516185 original size:17 final size:17
Alignment explanation
Indices: 516163--516195 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
516153 TAGTTCGATA
*
516163 TATTAAGTTAAATAATT
1 TATTAACTTAAATAATT
516180 TATTAACTTAAATAAT
1 TATTAACTTAAATAAT
516196 ATTAAATTGA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.48, C:0.03, G:0.03, T:0.45
Consensus pattern (17 bp):
TATTAACTTAAATAATT
Found at i:517894 original size:15 final size:15
Alignment explanation
Indices: 517875--517951 Score: 63
Period size: 15 Copynumber: 5.3 Consensus size: 15
517865 TATTATTAAT
*
517875 ATATTTAAATATATT
1 ATATTTAAATATATA
517890 ATATTT-AATA-ATA
1 ATATTTAAATATATA
* *
517903 AAATTTAAA-ATAAAA
1 ATATTTAAATAT-ATA
*
517918 ATATTTAAAAATA-A
1 ATATTTAAATATATA
* *
517932 ATATTTTAATATATT
1 ATATTTAAATATATA
517947 ATATT
1 ATATT
517952 AATATTTGCA
Statistics
Matches: 50, Mismatches: 7, Indels: 10
0.75 0.10 0.15
Matches are distributed among these distances:
13 8 0.16
14 18 0.36
15 22 0.44
16 2 0.04
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (15 bp):
ATATTTAAATATATA
Found at i:517909 original size:28 final size:29
Alignment explanation
Indices: 517875--517955 Score: 96
Period size: 28 Copynumber: 2.9 Consensus size: 29
517865 TATTATTAAT
517875 ATATTTAAATATATTATATTTAATAATAA
1 ATATTTAAATATATTATATTTAATAATAA
** *
517904 A-ATTTAAA-ATAAAAATATTTAAAAATAA
1 ATATTTAAATAT-ATTATATTTAATAATAA
*
517932 ATATTTTAATATATTATA-TTAATA
1 ATATTTAAATATATTATATTTAATA
517956 TTTGCATTTA
Statistics
Matches: 42, Mismatches: 7, Indels: 7
0.75 0.12 0.12
Matches are distributed among these distances:
27 2 0.05
28 27 0.64
29 11 0.26
30 2 0.05
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (29 bp):
ATATTTAAATATATTATATTTAATAATAA
Found at i:518398 original size:22 final size:22
Alignment explanation
Indices: 518373--518425 Score: 54
Period size: 22 Copynumber: 2.4 Consensus size: 22
518363 TTAAGTTATT
518373 TAAATTTTTAAATTTAAT-AAAA
1 TAAATTTTTAAA-TTAATAAAAA
* * *
518395 TAAAATATTAAATTACTAAAAA
1 TAAATTTTTAAATTAATAAAAA
*
518417 TTAATTTTT
1 TAAATTTTT
518426 TTAAAAAAAT
Statistics
Matches: 24, Mismatches: 6, Indels: 2
0.75 0.19 0.06
Matches are distributed among these distances:
21 4 0.17
22 20 0.83
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (22 bp):
TAAATTTTTAAATTAATAAAAA
Found at i:518700 original size:38 final size:39
Alignment explanation
Indices: 518658--518734 Score: 97
Period size: 39 Copynumber: 2.0 Consensus size: 39
518648 TGACTTAATT
*
518658 TAAATTATT-ATTTAATAA-ATAAAA-ATATTTTTATTTAA
1 TAAA-TATTAATTAAATAATATAAAATA-ATTTTTATTTAA
*
518696 TAAATATTAATTAAATAATATTAAATAATTTTTATTTAA
1 TAAATATTAATTAAATAATATAAAATAATTTTTATTTAA
518735 ATACTTTTTA
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
37 4 0.12
38 12 0.35
39 17 0.50
40 1 0.03
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (39 bp):
TAAATATTAATTAAATAATATAAAATAATTTTTATTTAA
Found at i:518723 original size:25 final size:25
Alignment explanation
Indices: 518689--518737 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 25
518679 AAAATATTTT
*
518689 TATTTAATAAATATTAATTAAATAA
1 TATTAAATAAATATTAATTAAATAA
* * *
518714 TATTAAATAATTTTTATTTAAATA
1 TATTAAATAAATATTAATTAAATA
518738 CTTTTTACGA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (25 bp):
TATTAAATAAATATTAATTAAATAA
Found at i:521467 original size:2 final size:2
Alignment explanation
Indices: 521462--521497 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
521452 TATGTATGTA
521462 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
521498 AACAAAAGAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:524066 original size:17 final size:17
Alignment explanation
Indices: 524044--524078 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
524034 TCTCTGTACA
524044 CATGTCCGAATACGCAT
1 CATGTCCGAATACGCAT
524061 CATGTCCGAATACGCAT
1 CATGTCCGAATACGCAT
524078 C
1 C
524079 GAATAAGGGT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.29, C:0.31, G:0.17, T:0.23
Consensus pattern (17 bp):
CATGTCCGAATACGCAT
Found at i:525267 original size:2 final size:2
Alignment explanation
Indices: 525260--525296 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
525250 GATATAAGTT
525260 TA TA 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 TA TA T
525297 GATCTATGTC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:526202 original size:205 final size:205
Alignment explanation
Indices: 525850--526261 Score: 824
Period size: 205 Copynumber: 2.0 Consensus size: 205
525840 TTTATTTATC
525850 ACAATGTCAATAAATCAAATAATGTTACTTAAAATTTTTAAAGGTAATACAAATAAATTTATTTT
1 ACAATGTCAATAAATCAAATAATGTTACTTAAAATTTTTAAAGGTAATACAAATAAATTTATTTT
525915 TAATGGAACGACATCTTTTAGCTTATTAATAGTGTATACGCATCAAAAATAAATTCTTGTAAATT
66 TAATGGAACGACATCTTTTAGCTTATTAATAGTGTATACGCATCAAAAATAAATTCTTGTAAATT
525980 TGGACATGAATTGAACTTCAAAAATTAAATCCTTTTACTTCATAGATCTCTTTTGAAAACAAAGG
131 TGGACATGAATTGAACTTCAAAAATTAAATCCTTTTACTTCATAGATCTCTTTTGAAAACAAAGG
526045 TACAAAATTG
196 TACAAAATTG
526055 ACAATGTCAATAAATCAAATAATGTTACTTAAAATTTTTAAAGGTAATACAAATAAATTTATTTT
1 ACAATGTCAATAAATCAAATAATGTTACTTAAAATTTTTAAAGGTAATACAAATAAATTTATTTT
526120 TAATGGAACGACATCTTTTAGCTTATTAATAGTGTATACGCATCAAAAATAAATTCTTGTAAATT
66 TAATGGAACGACATCTTTTAGCTTATTAATAGTGTATACGCATCAAAAATAAATTCTTGTAAATT
526185 TGGACATGAATTGAACTTCAAAAATTAAATCCTTTTACTTCATAGATCTCTTTTGAAAACAAAGG
131 TGGACATGAATTGAACTTCAAAAATTAAATCCTTTTACTTCATAGATCTCTTTTGAAAACAAAGG
526250 TACAAAATTG
196 TACAAAATTG
526260 AC
1 AC
526262 CTCCGTGCAT
Statistics
Matches: 207, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
205 207 1.00
ACGTcount: A:0.42, C:0.12, G:0.10, T:0.36
Consensus pattern (205 bp):
ACAATGTCAATAAATCAAATAATGTTACTTAAAATTTTTAAAGGTAATACAAATAAATTTATTTT
TAATGGAACGACATCTTTTAGCTTATTAATAGTGTATACGCATCAAAAATAAATTCTTGTAAATT
TGGACATGAATTGAACTTCAAAAATTAAATCCTTTTACTTCATAGATCTCTTTTGAAAACAAAGG
TACAAAATTG
Found at i:527137 original size:4 final size:4
Alignment explanation
Indices: 527128--527170 Score: 86
Period size: 4 Copynumber: 10.8 Consensus size: 4
527118 ATAACAAAAG
527128 AATA AATA AATA AATA AATA AATA AATA AATA AATA AATA AAT
1 AATA AATA AATA AATA AATA AATA AATA AATA AATA AATA AAT
527171 TACATGTTTG
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 39 1.00
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (4 bp):
AATA
Found at i:528333 original size:16 final size:17
Alignment explanation
Indices: 528312--528358 Score: 55
Period size: 16 Copynumber: 2.8 Consensus size: 17
528302 AAATTATTTT
528312 AATTACTATTAAATT-A
1 AATTACTATTAAATTCA
528328 AATTAC-ATTATAATTCA
1 AATTACTATTA-AATTCA
528345 AA-TACATATTAAAT
1 AATTAC-TATTAAAT
528359 ATTTAAAATT
Statistics
Matches: 27, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
15 4 0.15
16 13 0.48
17 6 0.22
18 4 0.15
ACGTcount: A:0.51, C:0.09, G:0.00, T:0.40
Consensus pattern (17 bp):
AATTACTATTAAATTCA
Found at i:529980 original size:20 final size:21
Alignment explanation
Indices: 529955--529998 Score: 65
Period size: 20 Copynumber: 2.2 Consensus size: 21
529945 TTTGAATATA
*
529955 ATAAAAAATA-TATTATAAAT
1 ATAAAAAATATTATAATAAAT
529975 AT-AAAAATATTATAATAAAT
1 ATAAAAAATATTATAATAAAT
529995 ATAA
1 ATAA
529999 TATTATATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
19 7 0.33
20 13 0.62
21 1 0.05
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (21 bp):
ATAAAAAATATTATAATAAAT
Found at i:529984 original size:17 final size:18
Alignment explanation
Indices: 529954--529993 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
529944 TTTTGAATAT
529954 AATAAAAAATATATTATA
1 AATAAAAAATATATTATA
*
529972 AATATAAAA-ATATTAT-
1 AATAAAAAATATATTATA
529988 AATAAA
1 AATAAA
529994 TATAATATTA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
16 5 0.25
17 7 0.35
18 8 0.40
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.33
Consensus pattern (18 bp):
AATAAAAAATATATTATA
Found at i:530000 original size:17 final size:17
Alignment explanation
Indices: 529951--530005 Score: 53
Period size: 20 Copynumber: 3.2 Consensus size: 17
529941 TAATTTTGAA
529951 TATAATAAA-A-AATA-
1 TATAATAAATATAATAT
*
529965 TATTATAAATATAAAAATAT
1 TATAATAAATAT---AATAT
529985 TATAATAAATATAATAT
1 TATAATAAATATAATAT
530002 TATA
1 TATA
530006 TTTTTAAATA
Statistics
Matches: 33, Mismatches: 2, Indels: 9
0.75 0.05 0.20
Matches are distributed among these distances:
14 8 0.24
15 1 0.03
17 9 0.27
19 4 0.12
20 11 0.33
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (17 bp):
TATAATAAATATAATAT
Found at i:533850 original size:2 final size:2
Alignment explanation
Indices: 533843--533871 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
533833 AAGCAATGTG
533843 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 T
533872 TTTTTTTTGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:534685 original size:15 final size:15
Alignment explanation
Indices: 534665--534708 Score: 56
Period size: 15 Copynumber: 3.0 Consensus size: 15
534655 GCATTATATT
534665 TTTAGTATTATTAAA
1 TTTAGTATTATTAAA
*
534680 TTTAGTATT-TTAACT
1 TTTAGTATTATTAA-A
534695 TTTA-TATTATTAAA
1 TTTAGTATTATTAAA
534709 ATTATAACAA
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
14 8 0.32
15 17 0.68
ACGTcount: A:0.36, C:0.02, G:0.05, T:0.57
Consensus pattern (15 bp):
TTTAGTATTATTAAA
Found at i:535304 original size:2 final size:2
Alignment explanation
Indices: 535246--535289 Score: 81
Period size: 2 Copynumber: 22.5 Consensus size: 2
535236 GTGGTGTTTA
535246 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
535287 AT A
1 AT A
535290 CACACTTAAT
Statistics
Matches: 41, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.02
2 40 0.98
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:535873 original size:22 final size:22
Alignment explanation
Indices: 535824--535873 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 22
535814 ATTAAAAATT
* *
535824 TAAATTTTAAAATTATTAAATA
1 TAAATTTTAAAATAATTAAACA
*
535846 TTAATTTTAAAA-AATTAATACA
1 TAAATTTTAAAATAATTAA-ACA
535868 TAAATT
1 TAAATT
535874 AATTAAATTA
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
21 5 0.22
22 18 0.78
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (22 bp):
TAAATTTTAAAATAATTAAACA
Found at i:537267 original size:2 final size:2
Alignment explanation
Indices: 537262--537289 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
537252 TAATAAATTA
537262 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
537290 GTGTGTGTGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:537294 original size:2 final size:2
Alignment explanation
Indices: 537289--537313 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
537279 TATATATATA
537289 TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG T
537314 AACTGTTAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:540422 original size:19 final size:18
Alignment explanation
Indices: 540398--540441 Score: 56
Period size: 16 Copynumber: 2.5 Consensus size: 18
540388 AAAATATAAA
540398 AATATTAATATAATTTTTT
1 AATATTAAT-TAATTTTTT
540417 AATATT--TTAATTTTTT
1 AATATTAATTAATTTTTT
*
540433 AATAGTAAT
1 AATATTAAT
540442 GAGCTTAGTA
Statistics
Matches: 22, Mismatches: 1, Indels: 5
0.79 0.04 0.18
Matches are distributed among these distances:
16 14 0.64
17 1 0.05
18 1 0.05
19 6 0.27
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (18 bp):
AATATTAATTAATTTTTT
Found at i:541184 original size:17 final size:17
Alignment explanation
Indices: 541154--541186 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
541144 AATTTACATG
541154 TAAAAAAATAAATTATT
1 TAAAAAAATAAATTATT
541171 TAAATAAAAT-AATTAT
1 TAAA-AAAATAAATTAT
541187 CTATTTTACA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (17 bp):
TAAAAAAATAAATTATT
Found at i:544793 original size:14 final size:14
Alignment explanation
Indices: 544774--544802 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
544764 TGTATCCCTT
544774 TGAATAAGATGTCA
1 TGAATAAGATGTCA
544788 TGAATAAGATGTCA
1 TGAATAAGATGTCA
544802 T
1 T
544803 AAGATATGGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.41, C:0.07, G:0.21, T:0.31
Consensus pattern (14 bp):
TGAATAAGATGTCA
Found at i:545414 original size:43 final size:39
Alignment explanation
Indices: 545306--545421 Score: 214
Period size: 39 Copynumber: 3.0 Consensus size: 39
545296 TTGAGTGTGT
* *
545306 CATGAACAATTGAATTAAATTTTAAATAAATAATATATA
1 CATGAATAATTAAATTAAATTTTAAATAAATAATATATA
545345 CATGAATAATTAAATTAAATTTTAAATAAATAATATATA
1 CATGAATAATTAAATTAAATTTTAAATAAATAATATATA
545384 CATGAATAATTAAATTAAATTTTAAATAAATAATATAT
1 CATGAATAATTAAATTAAATTTTAAATAAATAATATAT
545422 TTTTTCATTC
Statistics
Matches: 75, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
39 75 1.00
ACGTcount: A:0.55, C:0.03, G:0.03, T:0.38
Consensus pattern (39 bp):
CATGAATAATTAAATTAAATTTTAAATAAATAATATATA
Found at i:545859 original size:27 final size:28
Alignment explanation
Indices: 545818--545871 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 28
545808 TAATCATAAA
* * *
545818 AAAATATTTTTATTTAA-ATTTAATTAT
1 AAAATATATTAATTTAATATATAATTAT
545845 AAAATATATTAATTTAATATATAATTA
1 AAAATATATTAATTTAATATATAATTA
545872 GTATTTTAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
27 15 0.65
28 8 0.35
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (28 bp):
AAAATATATTAATTTAATATATAATTAT
Found at i:548598 original size:19 final size:19
Alignment explanation
Indices: 548576--548619 Score: 63
Period size: 19 Copynumber: 2.3 Consensus size: 19
548566 TAAATTTTAT
548576 TAATAATA-AAAAATTATAA
1 TAATAATATAAAAA-TATAA
548595 TAATAATATAAAAATATAA
1 TAATAATATAAAAATATAA
548614 TGAATA
1 T-AATA
548620 CCTATAACTA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 14 0.61
20 9 0.39
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.32
Consensus pattern (19 bp):
TAATAATATAAAAATATAA
Found at i:550404 original size:22 final size:22
Alignment explanation
Indices: 550376--550417 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
550366 ATTAAAAAAT
550376 TATTTTTAT-ATTAATATTTATA
1 TATTTTTATAATTAA-ATTTATA
550398 TATTTTTATAATTAAATTTA
1 TATTTTTATAATTAAATTTA
550418 AATAAAAATA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
22 14 0.74
23 5 0.26
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (22 bp):
TATTTTTATAATTAAATTTATA
Found at i:550539 original size:20 final size:20
Alignment explanation
Indices: 550500--550545 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 20
550490 TTTTTTAAAA
*
550500 AATTTTAATTATATTTTAAT
1 AATTTTAATTATATTATAAT
*
550520 -ATTTTAATATTTATTATAAT
1 AATTTTAAT-TATATTATAAT
550540 AATTTT
1 AATTTT
550546 TTAAAATTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
19 8 0.36
20 9 0.41
21 5 0.23
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (20 bp):
AATTTTAATTATATTATAAT
Found at i:550603 original size:24 final size:24
Alignment explanation
Indices: 550561--550617 Score: 71
Period size: 24 Copynumber: 2.4 Consensus size: 24
550551 ATTTAAATTG
*
550561 ATTTTATTAAAATTATTATTTAATA
1 ATTTAATTAAAATTATTATTTAA-A
* *
550586 A-TTAATTAATATTTTTATTTAAA
1 ATTTAATTAAAATTATTATTTAAA
550609 ATTTAATTA
1 ATTTAATTA
550618 TAAAAAATAT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
23 2 0.07
24 25 0.89
25 1 0.04
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (24 bp):
ATTTAATTAAAATTATTATTTAAA
Found at i:550640 original size:19 final size:19
Alignment explanation
Indices: 550611--550655 Score: 56
Period size: 19 Copynumber: 2.3 Consensus size: 19
550601 TATTTAAAAT
550611 TTAATTATAAAAA-ATATATA
1 TTAA-TATAAAAATA-ATATA
*
550631 TTAATATAAAAATAATATT
1 TTAATATAAAAATAATATA
550650 TTAATA
1 TTAATA
550656 ATATAATGAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
19 18 0.78
20 5 0.22
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (19 bp):
TTAATATAAAAATAATATA
Found at i:550941 original size:15 final size:15
Alignment explanation
Indices: 550916--550980 Score: 94
Period size: 15 Copynumber: 4.3 Consensus size: 15
550906 TATTCGGAGT
550916 TTTTAAATTTAATTA
1 TTTTAAATTTAATTA
* *
550931 TTTTGAGTTTAATTA
1 TTTTAAATTTAATTA
550946 TTTTAAATTTAATTA
1 TTTTAAATTTAATTA
*
550961 TTATTAATTTTAATTA
1 TT-TTAAATTTAATTA
550977 TTTT
1 TTTT
550981 TTTATTATAT
Statistics
Matches: 44, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
15 30 0.68
16 14 0.32
ACGTcount: A:0.34, C:0.00, G:0.03, T:0.63
Consensus pattern (15 bp):
TTTTAAATTTAATTA
Found at i:550952 original size:30 final size:31
Alignment explanation
Indices: 550916--550980 Score: 105
Period size: 30 Copynumber: 2.1 Consensus size: 31
550906 TATTCGGAGT
*
550916 TTTTAAATTTAATTATT-TTGAGTTTAATTA
1 TTTTAAATTTAATTATTATTAAGTTTAATTA
*
550946 TTTTAAATTTAATTATTATTAATTTTAATTA
1 TTTTAAATTTAATTATTATTAAGTTTAATTA
550977 TTTT
1 TTTT
550981 TTTATTATAT
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
30 17 0.53
31 15 0.47
ACGTcount: A:0.34, C:0.00, G:0.03, T:0.63
Consensus pattern (31 bp):
TTTTAAATTTAATTATTATTAAGTTTAATTA
Found at i:551024 original size:28 final size:27
Alignment explanation
Indices: 550979--551038 Score: 68
Period size: 28 Copynumber: 2.2 Consensus size: 27
550969 TTTAATTATT
* *
550979 TTTTTATTATATTATTTTA-AGTTTAAA
1 TTTTTATTAAATTATTTTATAATTT-AA
*
551006 TTTTTATTAAAATTTTTTTATAATTTAA
1 TTTTTATT-AAATTATTTTATAATTTAA
551034 TTTTT
1 TTTTT
551039 GAATATTAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
27 8 0.29
28 16 0.57
29 4 0.14
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.67
Consensus pattern (27 bp):
TTTTTATTAAATTATTTTATAATTTAA
Found at i:552400 original size:22 final size:22
Alignment explanation
Indices: 552356--552399 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
552346 AAATTTTTTT
*
552356 ATTTTATATATCATTAAATAAA
1 ATTTTAAATATCATTAAATAAA
*
552378 ATTTTAAATTTCA-TAAATAAA
1 ATTTTAAATATCATTAAATAAA
552399 A
1 A
552400 AAAATTATTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 9 0.45
22 11 0.55
ACGTcount: A:0.52, C:0.05, G:0.00, T:0.43
Consensus pattern (22 bp):
ATTTTAAATATCATTAAATAAA
Found at i:552606 original size:23 final size:24
Alignment explanation
Indices: 552546--552607 Score: 74
Period size: 26 Copynumber: 2.5 Consensus size: 24
552536 ATTTAAATAA
552546 TATTAAAT-ATAAAATATTTTTAT
1 TATTAAATAATAAAATATTTTTAT
*
552569 AATTAAATTTAAATAAAA-ATTTTTAT
1 TATTAAA--T-AATAAAATATTTTTAT
552595 TATTAAATAATAA
1 TATTAAATAATAA
552608 TTAAAATCAA
Statistics
Matches: 33, Mismatches: 2, Indels: 8
0.77 0.05 0.19
Matches are distributed among these distances:
23 11 0.33
24 1 0.03
25 1 0.03
26 14 0.42
27 6 0.18
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (24 bp):
TATTAAATAATAAAATATTTTTAT
Found at i:552612 original size:27 final size:27
Alignment explanation
Indices: 552554--552614 Score: 79
Period size: 26 Copynumber: 2.3 Consensus size: 27
552544 AATATTAAAT
*
552554 ATAAAATATTTTTATAATTAAATTTAA
1 ATAAAATATTTTTATAATTAAATATAA
*
552581 ATAAAA-ATTTTTATTATTAAATAATAA
1 ATAAAATATTTTTATAATTAAAT-ATAA
*
552608 TTAAAAT
1 ATAAAAT
552615 CAAATTAATA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
26 15 0.52
27 14 0.48
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (27 bp):
ATAAAATATTTTTATAATTAAATATAA
Found at i:552613 original size:26 final size:24
Alignment explanation
Indices: 552546--552614 Score: 68
Period size: 26 Copynumber: 2.8 Consensus size: 24
552536 ATTTAAATAA
*
552546 TATTAAATATAA-AATATTTTTAT
1 TATTAAATATAATAAAATTTTTAT
* *
552569 AATTAAATTTAAATAAAAATTTTTAT
1 TATTAAATAT-AAT-AAAATTTTTAT
552595 TATTAAATAATAATTAAAAT
1 TATTAAAT-ATAA-TAAAAT
552615 CAAATTAATA
Statistics
Matches: 36, Mismatches: 5, Indels: 7
0.75 0.10 0.15
Matches are distributed among these distances:
23 8 0.22
24 2 0.06
26 24 0.67
27 2 0.06
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (24 bp):
TATTAAATATAATAAAATTTTTAT
Found at i:552802 original size:6 final size:6
Alignment explanation
Indices: 552784--552828 Score: 72
Period size: 6 Copynumber: 7.5 Consensus size: 6
552774 GCCCCCCCTA
* *
552784 GTCCAT GTGCAT GTCCAT GTCCAT GTGCAT GTCCAT GTCCAT GTC
1 GTCCAT GTCCAT GTCCAT GTCCAT GTCCAT GTCCAT GTCCAT GTC
552829 TAAACAAGGA
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
6 35 1.00
ACGTcount: A:0.16, C:0.29, G:0.22, T:0.33
Consensus pattern (6 bp):
GTCCAT
Found at i:552807 original size:18 final size:18
Alignment explanation
Indices: 552784--552827 Score: 88
Period size: 18 Copynumber: 2.4 Consensus size: 18
552774 GCCCCCCCTA
552784 GTCCATGTGCATGTCCAT
1 GTCCATGTGCATGTCCAT
552802 GTCCATGTGCATGTCCAT
1 GTCCATGTGCATGTCCAT
552820 GTCCATGT
1 GTCCATGT
552828 CTAAACAAGG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.16, C:0.27, G:0.23, T:0.34
Consensus pattern (18 bp):
GTCCATGTGCATGTCCAT
Done.