Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold369
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: 402231
ACGTcount: A:0.32, C:0.16, G:0.15, T:0.32
Warning! 19069 characters in sequence are not A, C, G, or T
File 1 of 2
Found at i:1068 original size:9 final size:9
Alignment explanation
Indices: 1054--1086 Score: 52
Period size: 9 Copynumber: 3.9 Consensus size: 9
1044 TAAGTATAGT
1054 TAAGTTATG
1 TAAGTTATG
1063 TAAGTTATG
1 TAAGTTATG
1072 T-A-TTATG
1 TAAGTTATG
1079 TAAGTTAT
1 TAAGTTAT
1087 TCATTACCCA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
7 6 0.27
8 2 0.09
9 14 0.64
ACGTcount: A:0.33, C:0.00, G:0.18, T:0.48
Consensus pattern (9 bp):
TAAGTTATG
Found at i:1264 original size:34 final size:34
Alignment explanation
Indices: 1219--1388 Score: 123
Period size: 34 Copynumber: 4.7 Consensus size: 34
1209 TATAATATTA
*
1219 ATGTAAGTTATGTATAATATTAATTAATTAAGTT
1 ATGTAATTTATGTATAATATTAATTAATTAAGTT
*
1253 ATGTAATTTATGTATAATATTAATGTAAGTTATGTAT
1 ATGTAATTTATGTATAATATTAAT-TAA-TTAAGT-T
* * * * *
1290 AATATTAATTAAT-TA-AGTTATGTAATTTATGTATA-AT
1 -AT-GTAATTTATGTATA-ATAT-TAATTAAT-TA-AGTT
1327 AT-TAATGTAAGTTATGTATAATATTAATTAATTAAGTT
1 ATGTAA--T---TTATGTATAATATTAATTAATTAAGTT
1365 ATGTAATTTATGTATAATATTAAT
1 ATGTAATTTATGTATAATATTAAT
1389 GTAAGTTATG
Statistics
Matches: 106, Mismatches: 12, Indels: 36
0.69 0.08 0.23
Matches are distributed among these distances:
34 43 0.41
35 3 0.03
36 8 0.08
37 6 0.06
38 16 0.15
39 24 0.23
40 5 0.05
41 1 0.01
ACGTcount: A:0.41, C:0.00, G:0.11, T:0.48
Consensus pattern (34 bp):
ATGTAATTTATGTATAATATTAATTAATTAAGTT
Found at i:1285 original size:22 final size:22
Alignment explanation
Indices: 1253--1298 Score: 83
Period size: 22 Copynumber: 2.1 Consensus size: 22
1243 TAATTAAGTT
*
1253 ATGTAATTTATGTATAATATTA
1 ATGTAAGTTATGTATAATATTA
1275 ATGTAAGTTATGTATAATATTA
1 ATGTAAGTTATGTATAATATTA
1297 AT
1 AT
1299 TAATTAAGTT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.41, C:0.00, G:0.11, T:0.48
Consensus pattern (22 bp):
ATGTAAGTTATGTATAATATTA
Found at i:1341 original size:22 final size:22
Alignment explanation
Indices: 1309--1354 Score: 83
Period size: 22 Copynumber: 2.1 Consensus size: 22
1299 TAATTAAGTT
*
1309 ATGTAATTTATGTATAATATTA
1 ATGTAAGTTATGTATAATATTA
1331 ATGTAAGTTATGTATAATATTA
1 ATGTAAGTTATGTATAATATTA
1353 AT
1 AT
1355 TAATTAAGTT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.41, C:0.00, G:0.11, T:0.48
Consensus pattern (22 bp):
ATGTAAGTTATGTATAATATTA
Found at i:1344 original size:65 final size:56
Alignment explanation
Indices: 1204--1961 Score: 1001
Period size: 56 Copynumber: 13.1 Consensus size: 56
1194 TGAAAATTAA
1204 TTATGTATAATATTAATGTAAGTTATGTATAATATTAATTAATTAAGTTATGTAAT
1 TTATGTATAATATTAATGTAAGTTATGTATAATATTAATTAATTAAGTTATGTAAT
1260 TTATGTATAATATTAATGTAAGTTATGTATAATATTAATTAATTAAGTTATGTAAT
1 TTATGTATAATATTAATGTAAGTTATGTATAATATTAATTAATTAAGTTATGTAAT
1316 TTATGTATAATATTAATGTAAGTTATGTATAATATTAATTAATTAAGTTATGTAAT
1 TTATGTATAATATTAATGTAAGTTATGTATAATATTAATTAATTAAGTTATGTAAT
1372 TTATGTATAATATTAATGTAAGTTATGTATAATATTAATTAATTAAGTTATGTAAT
1 TTATGTATAATATTAATGTAAGTTATGTATAATATTAATTAATTAAGTTATGTAAT
* * * *** *
1428 TTATGTATAATATTAATGTAAGTTATGCA-ATTTATGAA-TAATTATAAAAATGTAAG
1 TTATGTATAATATTAATGTAAGTTATGTATA-ATATTAATTAATTA-AGTTATGTAAT
*
1484 TTATGTA-AGT-TGTAAGCTATGTAAGTTATGTATAATATTAATTAATTAAGTTATGTAAGT
1 TTATGTATAATAT-T-A---ATGTAAGTTATGTATAATATTAATTAATTAAGTTATGTAA-T
* * * *
1544 TGTAAGT-TATTACTGTAAGCAATGTAATTTATGTGT-A-A-TAATTAATTAAGTTATGTAAT
1 T-TATGTATAATA-T-T----AATGTAAGTTATGTATAATATTAATTAATTAAGTTATGTAAT
*
1603 TTATGTATAATATTAATGCAAGTTATGTATAATATTAATTAATTAAGTTATGTAAT
1 TTATGTATAATATTAATGTAAGTTATGTATAATATTAATTAATTAAGTTATGTAAT
*
1659 TTATGTATAATATTAATGCAAGTTATGTATAATATTAATTAATTAAGTTATGTAAT
1 TTATGTATAATATTAATGTAAGTTATGTATAATATTAATTAATTAAGTTATGTAAT
*
1715 TTATGTATAATATTAATGCAAGTTATGTATAATATTAATTAATTAAGTTATGTAAT
1 TTATGTATAATATTAATGTAAGTTATGTATAATATTAATTAATTAAGTTATGTAAT
*
1771 TTATGTATAATATTAATGCAAGTTATGTATAATATTAATTAATTAAGTTATGTAAT
1 TTATGTATAATATTAATGTAAGTTATGTATAATATTAATTAATTAAGTTATGTAAT
*
1827 TTATGTATAATATTAATGCAAGTTATGTAATATATGTATAATATTAATTAATTAAGTTATGTAAT
1 TTATGTATAATATTAAT----G-TA---AGT-TATGTATAATATTAATTAATTAAGTTATGTAAT
*
1892 TTATGTATAATATTAATGCAAGTTATGTAATATATGTATAATATTAATTAATTAAGTTATGTAAT
1 TTATGTATAATATTAAT----G-TA---AGT-TATGTATAATATTAATTAATTAAGTTATGTAAT
1957 TTATG
1 TTATG
1962 CACTCTCAAT
Statistics
Matches: 645, Mismatches: 27, Indels: 51
0.89 0.04 0.07
Matches are distributed among these distances:
53 13 0.02
54 2 0.00
55 11 0.02
56 422 0.65
57 1 0.00
58 5 0.01
59 31 0.05
60 29 0.04
61 8 0.01
62 1 0.00
63 16 0.02
64 2 0.00
65 103 0.16
66 1 0.00
ACGTcount: A:0.41, C:0.01, G:0.12, T:0.46
Consensus pattern (56 bp):
TTATGTATAATATTAATGTAAGTTATGTATAATATTAATTAATTAAGTTATGTAAT
Found at i:1397 original size:22 final size:22
Alignment explanation
Indices: 1365--1410 Score: 83
Period size: 22 Copynumber: 2.1 Consensus size: 22
1355 TAATTAAGTT
*
1365 ATGTAATTTATGTATAATATTA
1 ATGTAAGTTATGTATAATATTA
1387 ATGTAAGTTATGTATAATATTA
1 ATGTAAGTTATGTATAATATTA
1409 AT
1 AT
1411 TAATTAAGTT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.41, C:0.00, G:0.11, T:0.48
Consensus pattern (22 bp):
ATGTAAGTTATGTATAATATTA
Found at i:1432 original size:34 final size:33
Alignment explanation
Indices: 1387--1961 Score: 272
Period size: 34 Copynumber: 18.4 Consensus size: 33
1377 TATAATATTA
*
1387 ATGTAAGTTATGTATAATATTAATTAATTAAGTT
1 ATGTAATTTATGTATAATATTAA-TAATTAAGTT
*
1421 ATGTAATTTATGTATAATATTAAT--GTAAGTT
1 ATGTAATTTATGTATAATATTAATAATTAAGTT
* * *
1452 ATGCAATTTATGAATAAT-TATAAAAATGTAAGTT
1 ATGTAATTTATGTATAATAT-TAATAAT-TAAGTT
*
1486 ATGTAAGTTGTAAGCTATGTAAGTTATGT-ATAATATTAA-TT
1 ATGTAA-TT-TATG-TA--TAA--TAT-TAAT-A-ATTAAGTT
* ** * * **
1527 AAT-TAAGTTATGTAAGTTGTAAGTTATTACTGTAAGCA
1 -ATGTAATTTATGT-A-TAAT-A-TTAATAAT-TAAGTT
* *
1565 ATGTAATTTATGTGTAATA--ATTAATTAAGTT
1 ATGTAATTTATGTATAATATTAATAATTAAGTT
1596 ATGTAATTTATG-----TA-TAAT-ATT-A---
1 ATGTAATTTATGTATAATATTAATAATTAAGTT
* *
1618 ATGCAAGTTATGTATAATATTAATTAATTAAGTT
1 ATGTAATTTATGTATAATATTAA-TAATTAAGTT
1652 ATGTAATTTATG-----TA-TAAT-ATT-A---
1 ATGTAATTTATGTATAATATTAATAATTAAGTT
* *
1674 ATGCAAGTTATGTATAATATTAATTAATTAAGTT
1 ATGTAATTTATGTATAATATTAA-TAATTAAGTT
1708 ATGTAATTTATG-----TA-TAAT-ATT-A---
1 ATGTAATTTATGTATAATATTAATAATTAAGTT
* *
1730 ATGCAAGTTATGTATAATATTAATTAATTAAGTT
1 ATGTAATTTATGTATAATATTAA-TAATTAAGTT
1764 ATGTAATTTATG-----TA-TAAT-ATT-A---
1 ATGTAATTTATGTATAATATTAATAATTAAGTT
* *
1786 ATGCAAGTTATGTATAATATTAATTAATTAAGTT
1 ATGTAATTTATGTATAATATTAA-TAATTAAGTT
**
1820 ATGTAATTTATGTATAATATTAAT--GCAAGTT
1 ATGTAATTTATGTATAATATTAATAATTAAGTT
*
1851 ATGTAATATATGTATAATATTAATTAATTAAGTT
1 ATGTAATTTATGTATAATATTAA-TAATTAAGTT
**
1885 ATGTAATTTATGTATAATATTAAT--GCAAGTT
1 ATGTAATTTATGTATAATATTAATAATTAAGTT
*
1916 ATGTAATATATGTATAATATTAATTAATTAAGTT
1 ATGTAATTTATGTATAATATTAA-TAATTAAGTT
1950 ATGTAATTTATG
1 ATGTAATTTATG
1962 CACTCTCAAT
Statistics
Matches: 409, Mismatches: 55, Indels: 154
0.66 0.09 0.25
Matches are distributed among these distances:
22 40 0.10
25 4 0.01
26 14 0.03
27 13 0.03
28 21 0.05
29 10 0.02
30 13 0.03
31 99 0.24
32 7 0.02
33 3 0.01
34 127 0.31
35 3 0.01
36 7 0.02
37 9 0.02
38 14 0.03
39 7 0.02
40 1 0.00
41 7 0.02
42 8 0.02
43 2 0.00
ACGTcount: A:0.41, C:0.02, G:0.12, T:0.46
Consensus pattern (33 bp):
ATGTAATTTATGTATAATATTAATAATTAAGTT
Found at i:1491 original size:9 final size:9
Alignment explanation
Indices: 1477--1553 Score: 62
Period size: 9 Copynumber: 9.2 Consensus size: 9
1467 AATTATAAAA
1477 ATGTAAGTT
1 ATGTAAGTT
1486 ATGTAAG-T
1 ATGTAAGTT
*
1494 -TGTAAGCT
1 ATGTAAGTT
1502 ATGTAAGTT
1 ATGTAAGTT
*
1511 ATGTATA-AT
1 ATGTA-AGTT
1520 AT-TAA-TT
1 ATGTAAGTT
1527 AAT-TAAGTT
1 -ATGTAAGTT
1536 ATGTAAG-T
1 ATGTAAGTT
1544 -TGTAAGTT
1 ATGTAAGTT
1552 AT
1 AT
1554 TACTGTAAGC
Statistics
Matches: 57, Mismatches: 3, Indels: 16
0.75 0.04 0.21
Matches are distributed among these distances:
7 14 0.25
8 13 0.23
9 29 0.51
10 1 0.02
ACGTcount: A:0.36, C:0.01, G:0.18, T:0.44
Consensus pattern (9 bp):
ATGTAAGTT
Found at i:1499 original size:16 final size:16
Alignment explanation
Indices: 1478--1553 Score: 59
Period size: 16 Copynumber: 4.6 Consensus size: 16
1468 ATTATAAAAA
1478 TGTAAGTTATGTAAGT
1 TGTAAGTTATGTAAGT
*
1494 TGTAAGCTATGTAAGTT
1 TGTAAGTTATGTAAG-T
*
1511 ATGTATA-ATAT-TAA-T
1 -TGTA-AGTTATGTAAGT
*
1526 TAATTAAGTTATGTAAGT
1 T--GTAAGTTATGTAAGT
1544 TGTAAGTTAT
1 TGTAAGTTAT
1554 TACTGTAAGC
Statistics
Matches: 47, Mismatches: 5, Indels: 16
0.69 0.07 0.24
Matches are distributed among these distances:
14 1 0.02
15 2 0.04
16 27 0.57
17 7 0.15
18 9 0.19
19 1 0.02
ACGTcount: A:0.36, C:0.01, G:0.18, T:0.45
Consensus pattern (16 bp):
TGTAAGTTATGTAAGT
Found at i:1505 original size:25 final size:26
Alignment explanation
Indices: 1476--1549 Score: 84
Period size: 25 Copynumber: 2.9 Consensus size: 26
1466 TAATTATAAA
1476 AATGTAAGTTATGTAAGTTGTAAGCT
1 AATGTAAGTTATGTAAGTTGTAAGCT
* *
1502 -ATGTAAGTTATGTATAATAT-TAA-TT
1 AATGTAAGTTATGTA-AGT-TGTAAGCT
1527 AAT-TAAGTTATGTAAGTTGTAAG
1 AATGTAAGTTATGTAAGTTGTAAG
1550 TTATTACTGT
Statistics
Matches: 40, Mismatches: 3, Indels: 11
0.74 0.06 0.20
Matches are distributed among these distances:
23 1 0.03
24 5 0.12
25 26 0.65
26 7 0.17
27 1 0.03
ACGTcount: A:0.38, C:0.01, G:0.19, T:0.42
Consensus pattern (26 bp):
AATGTAAGTTATGTAAGTTGTAAGCT
Found at i:4808 original size:15 final size:17
Alignment explanation
Indices: 4769--4801 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
4759 CTAACCCGAC
4769 CCTCTTAAAACCCTAAA
1 CCTCTTAAAACCCTAAA
*
4786 CCTCTTAAATCCCTAA
1 CCTCTTAAAACCCTAA
4802 CTCTTAACCA
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:0.36, C:0.36, G:0.00, T:0.27
Consensus pattern (17 bp):
CCTCTTAAAACCCTAAA
Found at i:4890 original size:14 final size:15
Alignment explanation
Indices: 4871--4901 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
4861 GACCAACCCT
4871 TAATCCCT-AATCCA
1 TAATCCCTAAATCCA
4885 TAATCCCTAAATCCA
1 TAATCCCTAAATCCA
4900 TA
1 TA
4902 TATATATAGT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 8 0.50
15 8 0.50
ACGTcount: A:0.39, C:0.32, G:0.00, T:0.29
Consensus pattern (15 bp):
TAATCCCTAAATCCA
Found at i:5980 original size:114 final size:114
Alignment explanation
Indices: 5666--6024 Score: 521
Period size: 113 Copynumber: 3.2 Consensus size: 114
5656 CGCTTTAACA
* * * * * *
5666 AAAACGCCGCTAAAAC-CTATATTATTCGCGGCGCTAATCTAAAAGCGCCACTAAAGTCACCGAA
1 AAAACGCCGCTAATACTC-ATATTATTAGCGGCGCTATTCAAAAAACGCCACTAATGTCACCGAA
*
5730 GTGTCTCCAAACGACGTCGTCTGGGGTTTAGTTTTTGCGGCATTTTTATA-
65 GTGTCTCCAAACGACGTCGTCT-GGGTTTAGTTTTTGCAGCATTTTTATAG
5780 AAAACGCCGCTAATACTCATA-TATTAGCGGCGCTATTCAAAAAACGCCACTAATGTCACCGAAG
1 AAAACGCCGCTAATACTCATATTATTAGCGGCGCTATTCAAAAAACGCCACTAATGTCACCGAAG
* *
5844 TGTCTCCAAACGACGTCGTCTGGGTTTTAGTTTTTACAGCATTTTTACAG
66 TGTCTCCAAACGACGTCGTCTGGG-TTTAGTTTTTGCAGCATTTTTATAG
* *
5894 AAAA-GCCGCTAATACTCATATTATTAGCGGCGCTATTCGAAAAACGCCAGTAATGTCACCGAAG
1 AAAACGCCGCTAATACTCATATTATTAGCGGCGCTATTCAAAAAACGCCACTAATGTCACCGAAG
* * * *
5958 TTTCTCCAAACGTCGTCGTCTGGGTTTAGTTTTTGCTGCGTTTTTATAG
66 TGTCTCCAAACGACGTCGTCTGGGTTTAGTTTTTGCAGCATTTTTATAG
6007 -AAACGCCGCTAATACTCA
1 AAAACGCCGCTAATACTCA
6025 ATCGGTTGCG
Statistics
Matches: 223, Mismatches: 17, Indels: 11
0.89 0.07 0.04
Matches are distributed among these distances:
112 6 0.03
113 131 0.59
114 85 0.38
115 1 0.00
ACGTcount: A:0.28, C:0.23, G:0.19, T:0.29
Consensus pattern (114 bp):
AAAACGCCGCTAATACTCATATTATTAGCGGCGCTATTCAAAAAACGCCACTAATGTCACCGAAG
TGTCTCCAAACGACGTCGTCTGGGTTTAGTTTTTGCAGCATTTTTATAG
Found at i:22288 original size:18 final size:18
Alignment explanation
Indices: 22253--22311 Score: 57
Period size: 18 Copynumber: 3.1 Consensus size: 18
22243 GAACAATGCC
22253 AAAAGGAAAAAAGGAAGAAA-
1 AAAA-GAAAAAA--AAGAAAG
22273 AAAAGAAAAGAAAAGAAAG
1 AAAAGAAAA-AAAAGAAAG
* *
22292 AAAATAAAAAAAAGGAAG
1 AAAAGAAAAAAAAGAAAG
22310 AA
1 AA
22312 GGAAAGAATG
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
18 16 0.46
19 13 0.37
20 6 0.17
ACGTcount: A:0.78, C:0.00, G:0.20, T:0.02
Consensus pattern (18 bp):
AAAAGAAAAAAAAGAAAG
Found at i:22292 original size:22 final size:24
Alignment explanation
Indices: 22261--22319 Score: 68
Period size: 22 Copynumber: 2.5 Consensus size: 24
22251 CCAAAAGGAA
* *
22261 AAAAGGAAGAAAA-AAAGAAAA-G
1 AAAAGAAAGAAAATAAAAAAAAGG
22283 AAAAGAAAGAAAATAAAAAAAAGG
1 AAAAGAAAGAAAATAAAAAAAAGG
22307 AAGAAGGAAAGAA
1 AA-AA-GAAAGAA
22320 TGAGTCAACG
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
22 12 0.39
23 7 0.23
24 3 0.10
25 2 0.06
26 7 0.23
ACGTcount: A:0.76, C:0.00, G:0.22, T:0.02
Consensus pattern (24 bp):
AAAAGAAAGAAAATAAAAAAAAGG
Found at i:22423 original size:41 final size:41
Alignment explanation
Indices: 22376--22459 Score: 150
Period size: 41 Copynumber: 2.0 Consensus size: 41
22366 GGAGAAGTGA
22376 AAAAATAATATTCCTCAATGCACACGTAGAGATTCGAACAT
1 AAAAATAATATTCCTCAATGCACACGTAGAGATTCGAACAT
* *
22417 AAAAATAATATTCCTTAATGCACACGTAGAGATTTGAACAT
1 AAAAATAATATTCCTCAATGCACACGTAGAGATTCGAACAT
22458 AA
1 AA
22460 GACCACTGAC
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 41 1.00
ACGTcount: A:0.45, C:0.17, G:0.12, T:0.26
Consensus pattern (41 bp):
AAAAATAATATTCCTCAATGCACACGTAGAGATTCGAACAT
Found at i:23777 original size:3 final size:3
Alignment explanation
Indices: 23769--23809 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
23759 TTTGAAGAGA
23769 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
23810 CGTGGTTCAA
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:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:25959 original size:2 final size:2
Alignment explanation
Indices: 25952--25988 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
25942 ATCTGAAAAA
25952 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
25989 TTTTGTGGCC
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:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:28129 original size:30 final size:26
Alignment explanation
Indices: 28095--28153 Score: 82
Period size: 30 Copynumber: 2.1 Consensus size: 26
28085 TTTTATGTAT
28095 TTATATTTTATAATTTAATAAATAATAAAA
1 TTATATTTTAT-A-TT-ATAAAT-ATAAAA
28125 TTATATTTTATATTATAAATATAAAA
1 TTATATTTTATATTATAAATATAAAA
28151 TTA
1 TTA
28154 ATATCATTTA
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
26 9 0.31
27 6 0.21
28 2 0.07
29 1 0.03
30 11 0.38
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (26 bp):
TTATATTTTATATTATAAATATAAAA
Found at i:28209 original size:23 final size:25
Alignment explanation
Indices: 28161--28209 Score: 68
Period size: 23 Copynumber: 2.0 Consensus size: 25
28151 TTAATATCAT
28161 TTAAAATAATAATTATAAAGTGTAA
1 TTAAAATAATAATTATAAAGTGTAA
28186 TTAAAAT-AT-ATTATAATAGT-TAA
1 TTAAAATAATAATTATAA-AGTGTAA
28209 T
1 T
28210 ACATAACATA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
23 11 0.48
24 5 0.22
25 7 0.30
ACGTcount: A:0.53, C:0.00, G:0.06, T:0.41
Consensus pattern (25 bp):
TTAAAATAATAATTATAAAGTGTAA
Found at i:28224 original size:18 final size:17
Alignment explanation
Indices: 28201--28237 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 17
28191 ATATATTATA
28201 ATAGTTAATACATAACAT
1 ATAGTTAATACA-AACAT
*
28219 ATAGTTAATATAAACAT
1 ATAGTTAATACAAACAT
28236 AT
1 AT
28238 TATATTATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 7 0.39
18 11 0.61
ACGTcount: A:0.51, C:0.08, G:0.05, T:0.35
Consensus pattern (17 bp):
ATAGTTAATACAAACAT
Found at i:31199 original size:146 final size:147
Alignment explanation
Indices: 31019--31311 Score: 579
Period size: 146 Copynumber: 2.0 Consensus size: 147
31009 CTTTTATTTT
31019 TATTTGAATATAAAAATCATGTATTAAAAAAAAAGAATGCAGTATAAGACTGGATTACTGTTGAA
1 TATTTGAATATAAAAATCATGTATTAAAAAAAAAGAATGCAGTATAAGACTGGATTACTGTTGAA
31084 GTAGCAAAAGTGAGTCTAATTATAAAATGACATAATGGTGCTTTCTATTACGTTTTCAAATGTAA
66 GTAGCAAAAGTGAGTCTAATTATAAAATGACATAATGGTGCTTTCTATTACGTTTTCAAATGTAA
31149 TAAATTTGTACTTTAAA
131 TAAATTTGTACTTTAAA
31166 TATTTGAATA-AAAAATCATGTATTAAAAAAAAAGAATGCAGTATAAGACTGGATTACTGTTGAA
1 TATTTGAATATAAAAATCATGTATTAAAAAAAAAGAATGCAGTATAAGACTGGATTACTGTTGAA
31230 GTAGCAAAAGTGAGTCTAATTATAAAATGACATAATGGTGCTTTCTATTACGTTTTCAAATGTAA
66 GTAGCAAAAGTGAGTCTAATTATAAAATGACATAATGGTGCTTTCTATTACGTTTTCAAATGTAA
31295 TAAATTTGTACTTTAAA
131 TAAATTTGTACTTTAAA
31312 AGTTACAATT
Statistics
Matches: 146, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
146 136 0.93
147 10 0.07
ACGTcount: A:0.42, C:0.08, G:0.15, T:0.34
Consensus pattern (147 bp):
TATTTGAATATAAAAATCATGTATTAAAAAAAAAGAATGCAGTATAAGACTGGATTACTGTTGAA
GTAGCAAAAGTGAGTCTAATTATAAAATGACATAATGGTGCTTTCTATTACGTTTTCAAATGTAA
TAAATTTGTACTTTAAA
Found at i:46567 original size:114 final size:115
Alignment explanation
Indices: 46357--46586 Score: 444
Period size: 114 Copynumber: 2.0 Consensus size: 115
46347 CCCGGGCAAA
*
46357 ATTGGCTATCTTAAAGTCTTTGCCCTGTTCTCGTTACACGACAACGAGCAAAGAGGGGCAGCTAT
1 ATTGCCTATCTTAAAGTCTTTGCCCTGTTCTCGTTACACGACAACGAGCAAAGAGGGGCAGCTAT
46422 AATACCCAATTTAGCCCGGGCTTAAATAAACAAAGGTCCCCAGTCCATTT
66 AATACCCAATTTAGCCCGGGCTTAAATAAACAAAGGTCCCCAGTCCATTT
46472 ATTGCCTAT-TTAAAGTCTTTGCCCTGTTCTCGTTACACGACAACGAGCAAAGAGGGGCAGCTAT
1 ATTGCCTATCTTAAAGTCTTTGCCCTGTTCTCGTTACACGACAACGAGCAAAGAGGGGCAGCTAT
46536 AATACCCAATTTAGCCCGGGCTTAAATAAACAAAGGTCCCCAGTCCATTT
66 AATACCCAATTTAGCCCGGGCTTAAATAAACAAAGGTCCCCAGTCCATTT
46586 A
1 A
46587 AAATCTTAAT
Statistics
Matches: 114, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
114 106 0.93
115 8 0.07
ACGTcount: A:0.30, C:0.25, G:0.19, T:0.26
Consensus pattern (115 bp):
ATTGCCTATCTTAAAGTCTTTGCCCTGTTCTCGTTACACGACAACGAGCAAAGAGGGGCAGCTAT
AATACCCAATTTAGCCCGGGCTTAAATAAACAAAGGTCCCCAGTCCATTT
Found at i:52324 original size:1 final size:1
Alignment explanation
Indices: 52313--52437 Score: 79
Period size: 1 Copynumber: 125.0 Consensus size: 1
52303 GATTCAGTTC
* * * * * * * *
52313 AAAACAAAAAAAAACAAAAACAAAAACAAAAAAACAAAAAAACAAAAAAAAAACAAAAAAACAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
* * * * * * * * * * *
52378 AAAATAGAAAAAAGAAAAAAGAGAACAAAAAAGAATAAAAAACAAAAAGAAACAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
52438 CCTCTACCGA
Statistics
Matches: 86, Mismatches: 38, Indels: 0
0.69 0.31 0.00
Matches are distributed among these distances:
1 86 1.00
ACGTcount: A:0.85, C:0.09, G:0.05, T:0.02
Consensus pattern (1 bp):
A
Found at i:52334 original size:16 final size:16
Alignment explanation
Indices: 52313--52435 Score: 96
Period size: 16 Copynumber: 7.6 Consensus size: 16
52303 GATTCAGTTC
52313 AAAACAAAAA-AAAACA
1 AAAACAAAAACAAAA-A
52329 AAAACAAAAACAAAAA
1 AAAACAAAAACAAAAA
52345 AACAA-AAAAACAAAAAA
1 AA-AACAAAAAC-AAAAA
52362 AAAACAAAAA-AACAAA
1 AAAACAAAAACAA-AAA
* *
52378 AAAATAGAAAA-AAGAA
1 AAAACA-AAAACAAAAA
* *
52394 AAAA-GAGAACAAAAA
1 AAAACAAAAACAAAAA
52409 AGAATA-AAAAACAAAAA
1 A-AA-ACAAAAACAAAAA
*
52426 GAAACAAAAA
1 AAAACAAAAA
52436 AACCTCTACC
Statistics
Matches: 89, Mismatches: 8, Indels: 20
0.76 0.07 0.17
Matches are distributed among these distances:
14 3 0.03
15 8 0.09
16 44 0.49
17 34 0.38
ACGTcount: A:0.85, C:0.09, G:0.05, T:0.02
Consensus pattern (16 bp):
AAAACAAAAACAAAAA
Found at i:52351 original size:27 final size:26
Alignment explanation
Indices: 52312--52436 Score: 114
Period size: 27 Copynumber: 4.6 Consensus size: 26
52302 AGATTCAGTT
52312 CAAAACAAA-AAAAAACAAAAACAAAAA
1 CAAAA-AAACAAAAAACAAAAA-AAAAA
52339 CAAAAAAACAAAAAAACAAAAAAAAAA
1 CAAAAAAAC-AAAAAACAAAAAAAAAA
52366 CAAAAAAACAAAAAA-ATAGAAAAAAGAA
1 CAAAAAAACAAAAAACA-A-AAAAAA-AA
*
52394 -AAAAGAGAACAAAAAAGAATAAAAAACAA
1 CAAAA-A-AACAAAAAACAA-AAAAAA-AA
*
52423 -AAAGAAACAAAAAA
1 CAAAAAAACAAAAAA
52437 ACCTCTACCG
Statistics
Matches: 87, Mismatches: 3, Indels: 16
0.82 0.03 0.15
Matches are distributed among these distances:
25 1 0.01
26 10 0.11
27 38 0.44
28 16 0.18
29 21 0.24
30 1 0.01
ACGTcount: A:0.84, C:0.10, G:0.05, T:0.02
Consensus pattern (26 bp):
CAAAAAAACAAAAAACAAAAAAAAAA
Found at i:52946 original size:13 final size:14
Alignment explanation
Indices: 52928--52958 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
52918 AAAATGACGA
52928 AAAAATG-AAAAGT
1 AAAAATGAAAAAGT
52941 AAAAATGAAAAAGT
1 AAAAATGAAAAAGT
52955 AAAA
1 AAAA
52959 GTGGAGAGGC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 7 0.41
14 10 0.59
ACGTcount: A:0.74, C:0.00, G:0.13, T:0.13
Consensus pattern (14 bp):
AAAAATGAAAAAGT
Found at i:54288 original size:89 final size:89
Alignment explanation
Indices: 54137--54954 Score: 1115
Period size: 89 Copynumber: 9.2 Consensus size: 89
54127 CGGTGAAACA
* *
54137 ACCAGCCTTGCCTCCCTGGGTTTGCAGCGGAGTAGACTAAATATAGCAGATCTTGCCTTCCTGTA
1 ACCAGCCTTGCCTCCCTGGGTTTGCAGCGGAGCAGACTGAATATAGCAGATCTTGCCTTCCTGTA
*
54202 CTGACAGCGAAGCAGATCAAAGTC
66 CTGACAGCGAAGCAGATCAAAGAC
54226 ACCAGCCTTGCCTCCCTGGGTTTGCAGCGGAGCAGACTGAATATAGCAGATCTTGCCTTCCTGTA
1 ACCAGCCTTGCCTCCCTGGGTTTGCAGCGGAGCAGACTGAATATAGCAGATCTTGCCTTCCTGTA
*
54291 CTGACAGCGAAGTAGATCAAAGAC
66 CTGACAGCGAAGCAGATCAAAGAC
* * *
54315 ACCAACCTTGCCTCCCTGGATTTGCAGCGGAGCAAACTGAATATAGCAGATCTTGCCTTCCTGTA
1 ACCAGCCTTGCCTCCCTGGGTTTGCAGCGGAGCAGACTGAATATAGCAGATCTTGCCTTCCTGTA
54380 CTGACAGCGAAGCAGATCAAAGAC
66 CTGACAGCGAAGCAGATCAAAGAC
54404 ACCAGCCTTGCCTCCCTGGGTTTGCAGCGGAGCAGACTGAATATAGCAGATCTTGCCTTCCTGTA
1 ACCAGCCTTGCCTCCCTGGGTTTGCAGCGGAGCAGACTGAATATAGCAGATCTTGCCTTCCTGTA
54469 CTGACAGCGAAGCAGATCAAAGAC
66 CTGACAGCGAAGCAGATCAAAGAC
* ** *
54493 ACCAGCCTTGCATCATTGGG-TTACAGCGGAGCAGACTGAATATAGCAGATCTTGCCTTCCTGTA
1 ACCAGCCTTGCCTCCCTGGGTTTGCAGCGGAGCAGACTGAATATAGCAGATCTTGCCTTCCTGTA
*
54557 CTAACAGCGAAGCAGATCAAAGAC
66 CTGACAGCGAAGCAGATCAAAGAC
*
54581 ACCAGCCTTGCCTCCCTGGG-TTGCAGCGGAGCAGACTGAATATAGCAGATCTTGCCTTCTTGTA
1 ACCAGCCTTGCCTCCCTGGGTTTGCAGCGGAGCAGACTGAATATAGCAGATCTTGCCTTCCTGTA
* *
54645 CTGACAACGAAGCAGATCGAAGAC
66 CTGACAGCGAAGCAGATCAAAGAC
* *
54669 ACCAGCCTTGCCTCCCTGGGTTTGCAGCAGAGCAGACTGAATATGGCAGATCTTGCCTTCCTGTA
1 ACCAGCCTTGCCTCCCTGGGTTTGCAGCGGAGCAGACTGAATATAGCAGATCTTGCCTTCCTGTA
* *
54734 CTGACAGAGAAGCAGATCGAAA-AG
66 CTGACAGCGAAGCAGATC-AAAGAC
* ** * * * ** * * * *
54758 ACCAGCCTTGTCTCCCTGGG-CAGTAGTGGAGTAGGTTAAAAAATGGCAGATCTTACCTTCCTGT
1 ACCAGCCTTGCCTCCCTGGGTTTGCAGCGGAGCAGACT-GAATATAGCAGATCTTGCCTTCCTGT
* * *
54822 ACTGACAGAGAAGCAGATCGAAGAT
65 ACTGACAGCGAAGCAGATCAAAGAC
* * * * * ** * * * * *
54847 ACCAGCCTTGTCTCCCTGGG-TAGTAGTGGAGTAGGTTAAAAATAACAGATCCTGCCTTCTTGTA
1 ACCAGCCTTGCCTCCCTGGGTTTGCAGCGGAGCAGACTGAATATAGCAGATCTTGCCTTCCTGTA
* * * *
54911 CTAACAGAGAAGCAGATCGAAGAG
66 CTGACAGCGAAGCAGATCAAAGAC
* *
54935 ACCAGCCTTGTCTCCTTGGG
1 ACCAGCCTTGCCTCCCTGGG
54955 CAGTTGAGTA
Statistics
Matches: 671, Mismatches: 54, Indels: 9
0.91 0.07 0.01
Matches are distributed among these distances:
88 240 0.36
89 429 0.64
90 2 0.00
ACGTcount: A:0.27, C:0.26, G:0.24, T:0.22
Consensus pattern (89 bp):
ACCAGCCTTGCCTCCCTGGGTTTGCAGCGGAGCAGACTGAATATAGCAGATCTTGCCTTCCTGTA
CTGACAGCGAAGCAGATCAAAGAC
Found at i:54441 original size:178 final size:176
Alignment explanation
Indices: 54137--54954 Score: 1089
Period size: 177 Copynumber: 4.6 Consensus size: 176
54127 CGGTGAAACA
* *
54137 ACCAGCCTTGCCTCCCTGGGTTTGCAGCGGAGTAGACTAAATATAGCAGATCTTGCCTTCCTGTA
1 ACCAGCCTTGCCTCCCT-GGTTTGCAGCGGAGCAGACTGAATATAGCAGATCTTGCCTTCCTGTA
*
54202 CTGACAGCGAAGCAGATCAAAGTCACCAGCCTTGCCTCCCTGGGTTTGCAGCGGAGCAGACTGAA
65 CTGACAGCGAAGCAGATCAAAGACACCAGCCTTGCCTCCCTGGG-TTGCAGCGGAGCAGACTGAA
*
54267 TATAGCAGATCTTGCCTTCCTGTACTGACAGCGAAGTAGATCAAAGAC
129 TATAGCAGATCTTGCCTTCCTGTACTGACAGCGAAGCAGATCAAAGAC
* *
54315 ACCAACCTTGCCTCCCTGGATTTGCAGCGGAGCAAACTGAATATAGCAGATCTTGCCTTCCTGTA
1 ACCAGCCTTGCCTCCCTGG-TTTGCAGCGGAGCAGACTGAATATAGCAGATCTTGCCTTCCTGTA
54380 CTGACAGCGAAGCAGATCAAAGACACCAGCCTTGCCTCCCTGGGTTTGCAGCGGAGCAGACTGAA
65 CTGACAGCGAAGCAGATCAAAGACACCAGCCTTGCCTCCCTGGG-TTGCAGCGGAGCAGACTGAA
54445 TATAGCAGATCTTGCCTTCCTGTACTGACAGCGAAGCAGATCAAAGAC
129 TATAGCAGATCTTGCCTTCCTGTACTGACAGCGAAGCAGATCAAAGAC
* ** * *
54493 ACCAGCCTTGCATCATTGGGTTACAGCGGAGCAGACTGAATATAGCAGATCTTGCCTTCCTGTAC
1 ACCAGCCTTGCCTCCCTGGTTTGCAGCGGAGCAGACTGAATATAGCAGATCTTGCCTTCCTGTAC
*
54558 TAACAGCGAAGCAGATCAAAGACACCAGCCTTGCCTCCCTGGGTTGCAGCGGAGCAGACTGAATA
66 TGACAGCGAAGCAGATCAAAGACACCAGCCTTGCCTCCCTGGGTTGCAGCGGAGCAGACTGAATA
* * *
54623 TAGCAGATCTTGCCTTCTTGTACTGACAACGAAGCAGATCGAAGAC
131 TAGCAGATCTTGCCTTCCTGTACTGACAGCGAAGCAGATCAAAGAC
* *
54669 ACCAGCCTTGCCTCCCTGGGTTTGCAGCAGAGCAGACTGAATATGGCAGATCTTGCCTTCCTGTA
1 ACCAGCCTTGCCTCCCT-GGTTTGCAGCGGAGCAGACTGAATATAGCAGATCTTGCCTTCCTGTA
* * * ** * * * ** *
54734 CTGACAGAGAAGCAGATCGAAA-AGACCAGCCTTGTCTCCCTGGGCAGTAGTGGAGTAGGTTAAA
65 CTGACAGCGAAGCAGATC-AAAGACACCAGCCTTGCCTCCCTGGGTTGCAGCGGAGCAGACT-GA
* * * * * *
54798 AAATGGCAGATCTTACCTTCCTGTACTGACAGAGAAGCAGATCGAAGAT
128 ATATAGCAGATCTTGCCTTCCTGTACTGACAGCGAAGCAGATCAAAGAC
* * * * * * ** * * * * *
54847 ACCAGCCTTGTCTCCCTGGGTAGTAGTGGAGTAGGTTAAAAATAACAGATCCTGCCTTCTTGTAC
1 ACCAGCCTTGCCTCCCTGGTTTGCAGCGGAGCAGACTGAATATAGCAGATCTTGCCTTCCTGTAC
* * * * * *
54912 TAACAGAGAAGCAGATCGAAGAGACCAGCCTTGTCTCCTTGGG
66 TGACAGCGAAGCAGATCAAAGACACCAGCCTTGCCTCCCTGGG
54955 CAGTTGAGTA
Statistics
Matches: 574, Mismatches: 61, Indels: 11
0.89 0.09 0.02
Matches are distributed among these distances:
176 81 0.14
177 247 0.43
178 246 0.43
ACGTcount: A:0.27, C:0.26, G:0.24, T:0.22
Consensus pattern (176 bp):
ACCAGCCTTGCCTCCCTGGTTTGCAGCGGAGCAGACTGAATATAGCAGATCTTGCCTTCCTGTAC
TGACAGCGAAGCAGATCAAAGACACCAGCCTTGCCTCCCTGGGTTGCAGCGGAGCAGACTGAATA
TAGCAGATCTTGCCTTCCTGTACTGACAGCGAAGCAGATCAAAGAC
Found at i:55709 original size:132 final size:133
Alignment explanation
Indices: 55460--55774 Score: 384
Period size: 132 Copynumber: 2.4 Consensus size: 133
55450 NNNNNNNNNT
* * ** * * *
55460 ACAGAGCTGATCTCCCTAAGCAGTAGTGGAGCAGATCAAAAATGGCAGATTTTACCTCCCTGTGG
1 ACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATTGAAGATGGCGGATTTTACCTCCCTGGGG
* *
55525 TTACAGTGGAGTGCATTGAAGCCAATAATTCTACTTCCCTGGGTAGCAGTGGAATAGATTAAAG-
66 TTACAGTGGAGTACATTGAAGCCAATAATTCTACTTCCCTGGGTAGCAGTGGAATAGATCAAAGA
*
55589 ATT
131 ATA
* * * * *
55592 TCGGATCTTATTTCCCTAAGCGGTAGTAGAGCAGATTGAAGATGGCGGATTTTACCTCCCTGGGG
1 ACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATTGAAGATGGCGGATTTTACCTCCCTGGGG
* * * *
55657 TTACAGTGGAGTACATTGAAGCCAGTAATTCTATCTT-CCT-GGTCGACAGTGGAATCGATCGAA
66 TTACAGTGGAGTACATTGAAGCCAATAATTCTA-CTTCCCTGGGTAG-CAGTGGAATAGATCAAA
55720 GAATA
129 GAATA
* * * *
55725 ACAGATCTTATCTCCCTAAGCAGTAGTGGAGTAGACTGATGACGGCGGAT
1 ACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATTGAAGATGGCGGAT
55775 CTTGTTTCCT
Statistics
Matches: 152, Mismatches: 28, Indels: 5
0.82 0.15 0.03
Matches are distributed among these distances:
131 4 0.03
132 102 0.67
133 46 0.30
ACGTcount: A:0.28, C:0.19, G:0.26, T:0.27
Consensus pattern (133 bp):
ACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATTGAAGATGGCGGATTTTACCTCCCTGGGG
TTACAGTGGAGTACATTGAAGCCAATAATTCTACTTCCCTGGGTAGCAGTGGAATAGATCAAAGA
ATA
Found at i:61715 original size:24 final size:24
Alignment explanation
Indices: 61652--61703 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
61642 TTTCTAGAAG
* * *
61652 ATTTAGTATTTATAAGTATAATAT
1 ATTTAGCATTTATTAGCATAATAT
61676 ATTTAGCATTTATTAGCATAATAT
1 ATTTAGCATTTATTAGCATAATAT
61700 ATTT
1 ATTT
61704 GACTTTGATT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.38, C:0.04, G:0.08, T:0.50
Consensus pattern (24 bp):
ATTTAGCATTTATTAGCATAATAT
Found at i:63586 original size:31 final size:31
Alignment explanation
Indices: 63548--63628 Score: 110
Period size: 31 Copynumber: 2.6 Consensus size: 31
63538 GATTTTTTTG
*
63548 AAAGTTTTCATTTAAGTCATT-ACATTATTCA
1 AAAGTTTTCATTTAAGTCATTGA-ACTATTCA
* *
63579 AAAGTTTTCATTTGAGTCATTGAACTATTCG
1 AAAGTTTTCATTTAAGTCATTGAACTATTCA
*
63610 AAAGTTTTTATTTAAGTCA
1 AAAGTTTTCATTTAAGTCA
63629 CTCGATTGTT
Statistics
Matches: 44, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
31 43 0.98
32 1 0.02
ACGTcount: A:0.33, C:0.11, G:0.11, T:0.44
Consensus pattern (31 bp):
AAAGTTTTCATTTAAGTCATTGAACTATTCA
Found at i:65061 original size:2 final size:2
Alignment explanation
Indices: 65056--65095 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
65046 TGAGCTTTGC
*
65056 AT AT AT AT AT AT AT AT AT AT AC AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
65096 TTCCAATATC
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:67066 original size:28 final size:28
Alignment explanation
Indices: 67032--67103 Score: 110
Period size: 28 Copynumber: 2.6 Consensus size: 28
67022 AAAAATAAAA
* *
67032 ATTTACCAAAATACTA-CAAGTTTTTTTT
1 ATTTACCAAAATA-TATAAACTTTTTTTT
67060 ATTTACCAAAATATATAAACTTTTTTTT
1 ATTTACCAAAATATATAAACTTTTTTTT
67088 ATTTACCAAAATATAT
1 ATTTACCAAAATATAT
67104 CAAAAAAACC
Statistics
Matches: 41, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
27 2 0.05
28 39 0.95
ACGTcount: A:0.40, C:0.12, G:0.01, T:0.46
Consensus pattern (28 bp):
ATTTACCAAAATATATAAACTTTTTTTT
Found at i:80151 original size:14 final size:14
Alignment explanation
Indices: 80134--80161 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
80124 TAGCATGCTT
80134 TACTACAGTTTGTC
1 TACTACAGTTTGTC
80148 TACTACAGTTTGTC
1 TACTACAGTTTGTC
80162 GCTTCAATTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.21, C:0.21, G:0.14, T:0.43
Consensus pattern (14 bp):
TACTACAGTTTGTC
Found at i:81592 original size:88 final size:88
Alignment explanation
Indices: 81443--81616 Score: 330
Period size: 88 Copynumber: 2.0 Consensus size: 88
81433 AGGTATCTTT
*
81443 CCTTGTTTTTGGGGGTTTATTTCTGGAGCATTCTAATAATTTCCAAATTAGCTGGAAAATCTCAC
1 CCTTGTTTTTGGGGGTTTATTTCAGGAGCATTCTAATAATTTCCAAATTAGCTGGAAAATCTCAC
*
81508 AATTTGAGTCTAATGGGGTTTTC
66 AATTTGAGTCTAACGGGGTTTTC
81531 CCTTGTTTTTGGGGGTTTATTTCAGGAGCATTCTAATAATTTCCAAATTAGCTGGAAAATCTCAC
1 CCTTGTTTTTGGGGGTTTATTTCAGGAGCATTCTAATAATTTCCAAATTAGCTGGAAAATCTCAC
81596 AATTTGAGTCTAACGGGGTTT
66 AATTTGAGTCTAACGGGGTTT
81617 CTTCTAGGGT
Statistics
Matches: 84, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
88 84 1.00
ACGTcount: A:0.25, C:0.15, G:0.21, T:0.40
Consensus pattern (88 bp):
CCTTGTTTTTGGGGGTTTATTTCAGGAGCATTCTAATAATTTCCAAATTAGCTGGAAAATCTCAC
AATTTGAGTCTAACGGGGTTTTC
Found at i:84869 original size:29 final size:29
Alignment explanation
Indices: 84815--84872 Score: 75
Period size: 29 Copynumber: 2.0 Consensus size: 29
84805 TGAAATGTAA
*
84815 TCTCTCTACTTTTATTTCCAAGAATTTAG
1 TCTCTATACTTTTATTTCCAAGAATTTAG
84844 TCTCTATACTTTCATATTT-CAA-AATTTAG
1 TCTCTATACTTT--TATTTCCAAGAATTTAG
84873 GTCCAATTGT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
29 18 0.69
30 3 0.12
31 5 0.19
ACGTcount: A:0.28, C:0.19, G:0.05, T:0.48
Consensus pattern (29 bp):
TCTCTATACTTTTATTTCCAAGAATTTAG
Found at i:86477 original size:26 final size:24
Alignment explanation
Indices: 86422--86477 Score: 60
Period size: 25 Copynumber: 2.3 Consensus size: 24
86412 TTCAGTTGGT
* *
86422 TTATTAATGATATGTATTAATATG
1 TTATTAATGATATATATTAAAATG
*
86446 AT-TTAATGATTATATATTTAAAATG
1 TTATTAATGA-TATATA-TTAAAATG
86471 TTATTAA
1 TTATTAA
86478 CAGGGCTCTA
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
23 7 0.28
24 6 0.24
25 8 0.32
26 4 0.16
ACGTcount: A:0.41, C:0.00, G:0.09, T:0.50
Consensus pattern (24 bp):
TTATTAATGATATATATTAAAATG
Found at i:91513 original size:78 final size:78
Alignment explanation
Indices: 91384--91618 Score: 452
Period size: 78 Copynumber: 3.0 Consensus size: 78
91374 CGAGCACACG
*
91384 ACATAGGCTAGTAACTGAATCTAACCAAACTAATTTAATTACTACTATTTGGGTTAGAACTAAAT
1 ACATAGACTAGTAACTGAATCTAACCAAACTAATTTAATTACTACTATTTGGGTTAGAACTAAAT
91449 TTCAAAATTTGAA
66 TTCAAAATTTGAA
91462 ACATAGACTAGTAACTGAATCTAACCAAACTAATTTAATTACTACTATTTGGGTTAGAACTAAAT
1 ACATAGACTAGTAACTGAATCTAACCAAACTAATTTAATTACTACTATTTGGGTTAGAACTAAAT
91527 TTCAAAATTTGAA
66 TTCAAAATTTGAA
*
91540 ACATAGACTAGTAACTGAATCTAACCAAACTAATTTAATTACTACTATTTGGATTAGAACTAAAT
1 ACATAGACTAGTAACTGAATCTAACCAAACTAATTTAATTACTACTATTTGGGTTAGAACTAAAT
91605 TTCAAAATTTGAA
66 TTCAAAATTTGAA
91618 A
1 A
91619 AATAAAAGGA
Statistics
Matches: 155, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
78 155 1.00
ACGTcount: A:0.43, C:0.14, G:0.10, T:0.33
Consensus pattern (78 bp):
ACATAGACTAGTAACTGAATCTAACCAAACTAATTTAATTACTACTATTTGGGTTAGAACTAAAT
TTCAAAATTTGAA
Found at i:95954 original size:5 final size:5
Alignment explanation
Indices: 95929--96006 Score: 56
Period size: 5 Copynumber: 15.6 Consensus size: 5
95919 ACTTAAAATA
* * * *
95929 TATAT TATAA TATTAT AATAT TATAT CT-TAA T-TAT TA-AG TATA- TATAT
1 TATAT TATAT TA-TAT TATAT TATAT -TATAT TATAT TATAT TATAT TATAT
95977 TATAT TATAT TATAT TATAAT TATAAT TAT
1 TATAT TATAT TATAT TAT-AT TAT-AT TAT
96007 GAAATAAAGA
Statistics
Matches: 60, Mismatches: 7, Indels: 11
0.77 0.09 0.14
Matches are distributed among these distances:
4 11 0.18
5 34 0.57
6 15 0.25
ACGTcount: A:0.44, C:0.01, G:0.01, T:0.54
Consensus pattern (5 bp):
TATAT
Found at i:96005 original size:12 final size:11
Alignment explanation
Indices: 95927--96006 Score: 51
Period size: 11 Copynumber: 7.3 Consensus size: 11
95917 AAACTTAAAA
*
95927 TATATATTATAA
1 TATA-ATTATAT
* *
95939 TATTATAATAT
1 TATAATTATAT
*
95950 TATATCTTA-AT
1 TATA-ATTATAT
*
95961 TATTAAGTATA-
1 TA-TAATTATAT
95972 TAT-ATTATAT
1 TATAATTATAT
95982 TAT-ATTATAT
1 TATAATTATAT
95992 TATAATTATAAT
1 TATAATTAT-AT
96004 TAT
1 TAT
96007 GAAATAAAGA
Statistics
Matches: 53, Mismatches: 9, Indels: 12
0.72 0.12 0.16
Matches are distributed among these distances:
9 5 0.09
10 14 0.26
11 21 0.40
12 13 0.25
ACGTcount: A:0.44, C:0.01, G:0.01, T:0.54
Consensus pattern (11 bp):
TATAATTATAT
Found at i:96027 original size:17 final size:16
Alignment explanation
Indices: 96007--96104 Score: 54
Period size: 17 Copynumber: 5.8 Consensus size: 16
95997 TTATAATTAT
*
96007 GAAATAAAGAATAAATA
1 GAAAGAAAGAA-AAATA
*
96024 GAAAGAAAGAAAGATA
1 GAAAGAAAGAAAAATA
* * *
96040 GAAACGAAACAGAAAGA
1 GAAA-GAAAGAAAAATA
*
96057 AAAAGAAAGAAATAA-A
1 GAAAGAAAGAAA-AATA
*
96073 TGAAACAGAAAGAAAAAGA
1 -G-AA-AGAAAGAAAAATA
*
96092 AAAAGGAAAGAAA
1 GAAA-GAAAGAAA
96105 GGAAGGAGAA
Statistics
Matches: 63, Mismatches: 11, Indels: 14
0.72 0.12 0.16
Matches are distributed among these distances:
16 16 0.25
17 33 0.52
18 4 0.06
19 10 0.16
ACGTcount: A:0.71, C:0.03, G:0.19, T:0.06
Consensus pattern (16 bp):
GAAAGAAAGAAAAATA
Found at i:96030 original size:4 final size:4
Alignment explanation
Indices: 96023--96105 Score: 50
Period size: 4 Copynumber: 20.5 Consensus size: 4
96013 AAGAATAAAT
* *
96023 AGAA AGAA AGAA AGAT AGAA ACGAAA CAGAA AG-A A-AA AGAA AGAA ATAA
1 AGAA AGAA AGAA AGAA AGAA A-G-AA -AGAA AGAA AGAA AGAA AGAA AGAA
*
96072 ATGAAA CAGAA AG-A A-AA AGAA A-AA GGAA AGAA AG
1 A-G-AA -AGAA AGAA AGAA AGAA AGAA AGAA AGAA AG
96106 GAAGGAGAAA
Statistics
Matches: 62, Mismatches: 6, Indels: 22
0.69 0.07 0.24
Matches are distributed among these distances:
3 10 0.16
4 39 0.63
5 5 0.08
6 6 0.10
7 2 0.03
ACGTcount: A:0.71, C:0.04, G:0.22, T:0.04
Consensus pattern (4 bp):
AGAA
Found at i:96066 original size:29 final size:29
Alignment explanation
Indices: 96029--96093 Score: 103
Period size: 29 Copynumber: 2.2 Consensus size: 29
96019 AAATAGAAAG
*
96029 AAAGAAAGATAGAAACGAAACAGAAAGAA
1 AAAGAAAGAAAGAAACGAAACAGAAAGAA
* *
96058 AAAGAAAGAAATAAATGAAACAGAAAGAA
1 AAAGAAAGAAAGAAACGAAACAGAAAGAA
96087 AAAGAAA
1 AAAGAAA
96094 AAGGAAAGAA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
29 33 1.00
ACGTcount: A:0.72, C:0.05, G:0.18, T:0.05
Consensus pattern (29 bp):
AAAGAAAGAAAGAAACGAAACAGAAAGAA
Found at i:97041 original size:41 final size:39
Alignment explanation
Indices: 96981--97115 Score: 134
Period size: 41 Copynumber: 3.5 Consensus size: 39
96971 CGACTTCGAG
* *
96981 TCGATGAGACGCTGGGTGTCAATTTACTACTTTGAATTAAT
1 TCGATGAGACACTGGGTGTCAA-TTA-TACTTCGAATTAAT
* * *
97022 TCGATGAGGCACTGAGTGTCAATT-TACTTCGATTTAA-
1 TCGATGAGACACTGGGTGTCAATTATACTTCGAATTAAT
*
97059 -CAATGAGACACTGGGTGTCAAATTATTACTTCGAATT-AT
1 TCGATGAGACACTGGGTGTC-AATTA-TACTTCGAATTAAT
* *
97098 CCGATGAGGCACTGGGTG
1 TCGATGAGACACTGGGTG
97116 CCAAACTGGT
Statistics
Matches: 78, Mismatches: 11, Indels: 11
0.78 0.11 0.11
Matches are distributed among these distances:
36 16 0.21
37 4 0.05
38 12 0.15
39 10 0.13
40 17 0.22
41 19 0.24
ACGTcount: A:0.27, C:0.16, G:0.24, T:0.33
Consensus pattern (39 bp):
TCGATGAGACACTGGGTGTCAATTATACTTCGAATTAAT
Found at i:97065 original size:36 final size:40
Alignment explanation
Indices: 96996--97120 Score: 105
Period size: 40 Copynumber: 3.2 Consensus size: 40
96986 GAGACGCTGG
* * * * *
96996 GTGTCAATTTACTACTTTGAATTAATTCGATGAGGCACTGA
1 GTGTCAAATTATTACTTCGAATT-ATACAATGAGGCACTGA
* * *
97037 GTGTC-AA-T-TTACTTCGATTTA-ACAATGAGACACTGG
1 GTGTCAAATTATTACTTCGAATTATACAATGAGGCACTGA
* * *
97073 GTGTCAAATTATTACTTCGAATTATCCGATGAGGCACTGG
1 GTGTCAAATTATTACTTCGAATTATACAATGAGGCACTGA
*
97113 GTGCCAAA
1 GTGTCAAA
97121 CTGGTGTGTT
Statistics
Matches: 67, Mismatches: 13, Indels: 9
0.75 0.15 0.10
Matches are distributed among these distances:
36 16 0.24
37 3 0.04
38 10 0.15
39 13 0.19
40 20 0.30
41 5 0.07
ACGTcount: A:0.30, C:0.17, G:0.21, T:0.33
Consensus pattern (40 bp):
GTGTCAAATTATTACTTCGAATTATACAATGAGGCACTGA
Found at i:98320 original size:26 final size:26
Alignment explanation
Indices: 98291--98446 Score: 96
Period size: 26 Copynumber: 6.2 Consensus size: 26
98281 CTATCCGGGG
*
98291 TTCCTGATTAAAGGCTCTTCGTGAGC
1 TTCCTGATTAAAGGCTCTTTGTGAGC
* * * *
98317 TTCCTAATTAAAAGTTCTTTGTGAAC
1 TTCCTGATTAAAGGCTCTTTGTGAGC
* * *
98343 TTCCTGATT-ATGACTC-TTATGAGC
1 TTCCTGATTAAAGGCTCTTTGTGAGC
** *
98367 TTCCT-ATTATATA-GC-C-CGGATAAGC
1 TTCCTGATTA-A-AGGCTCTTTG-TGAGC
98392 TTCCTGA-T-AA-GCTCTTTGTGAGC
1 TTCCTGATTAAAGGCTCTTTGTGAGC
* * *
98415 TTCCCGATTAATGGTTCTTTGTGAGC
1 TTCCTGATTAAAGGCTCTTTGTGAGC
98441 TTCCTG
1 TTCCTG
98447 TTATATGGCT
Statistics
Matches: 95, Mismatches: 25, Indels: 20
0.68 0.18 0.14
Matches are distributed among these distances:
22 3 0.03
23 15 0.16
24 14 0.15
25 16 0.17
26 47 0.49
ACGTcount: A:0.21, C:0.21, G:0.19, T:0.39
Consensus pattern (26 bp):
TTCCTGATTAAAGGCTCTTTGTGAGC
Found at i:102203 original size:2 final size:2
Alignment explanation
Indices: 102196--102221 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
102186 TGCATTTTCC
102196 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
102222 CCTATTAATA
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:102783 original size:22 final size:20
Alignment explanation
Indices: 102751--102790 Score: 53
Period size: 22 Copynumber: 1.9 Consensus size: 20
102741 TATTAAATAT
*
102751 ATATATATTTTATTTTTAAA
1 ATATATATTTTAGTTTTAAA
102771 ATATACTAGTTTTAGTTTTA
1 ATATA-TA-TTTTAGTTTTA
102791 TTTTAAGTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 5 0.29
21 2 0.12
22 10 0.59
ACGTcount: A:0.35, C:0.03, G:0.05, T:0.57
Consensus pattern (20 bp):
ATATATATTTTAGTTTTAAA
Found at i:102843 original size:16 final size:16
Alignment explanation
Indices: 102822--102891 Score: 69
Period size: 16 Copynumber: 4.7 Consensus size: 16
102812 ATTTTGTTAC
102822 AACAATTAATACAATT
1 AACAATTAATACAATT
*
102838 AACAATTAATA-ATTT
1 AACAATTAATACAATT
* * *
102853 GATAATT-TTAC---T
1 AACAATTAATACAATT
102865 AACAATTAATACAATT
1 AACAATTAATACAATT
102881 AACAATTAATA
1 AACAATTAATA
102892 ATTTTTTTTA
Statistics
Matches: 42, Mismatches: 7, Indels: 10
0.71 0.12 0.17
Matches are distributed among these distances:
12 6 0.14
13 3 0.07
14 2 0.05
15 8 0.19
16 23 0.55
ACGTcount: A:0.53, C:0.10, G:0.01, T:0.36
Consensus pattern (16 bp):
AACAATTAATACAATT
Found at i:104079 original size:22 final size:20
Alignment explanation
Indices: 104047--104086 Score: 53
Period size: 22 Copynumber: 1.9 Consensus size: 20
104037 TATTAAATAT
*
104047 ATATATATTTTATTTTTAAA
1 ATATATATTTTAGTTTTAAA
104067 ATATACTAGTTTTAGTTTTA
1 ATATA-TA-TTTTAGTTTTA
104087 TTTTAAGTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 5 0.29
21 2 0.12
22 10 0.59
ACGTcount: A:0.35, C:0.03, G:0.05, T:0.57
Consensus pattern (20 bp):
ATATATATTTTAGTTTTAAA
Found at i:104139 original size:16 final size:16
Alignment explanation
Indices: 104118--104187 Score: 69
Period size: 16 Copynumber: 4.7 Consensus size: 16
104108 ATTTTGTTAC
104118 AACAATTAATACAATT
1 AACAATTAATACAATT
*
104134 AACAATTAATA-ATTT
1 AACAATTAATACAATT
* * *
104149 GATAATT-TTAC---T
1 AACAATTAATACAATT
104161 AACAATTAATACAATT
1 AACAATTAATACAATT
104177 AACAATTAATA
1 AACAATTAATA
104188 ATTTGATAAT
Statistics
Matches: 42, Mismatches: 7, Indels: 10
0.71 0.12 0.17
Matches are distributed among these distances:
12 6 0.14
13 3 0.07
14 2 0.05
15 8 0.19
16 23 0.55
ACGTcount: A:0.53, C:0.10, G:0.01, T:0.36
Consensus pattern (16 bp):
AACAATTAATACAATT
Found at i:104215 original size:16 final size:16
Alignment explanation
Indices: 104194--104236 Score: 68
Period size: 16 Copynumber: 2.7 Consensus size: 16
104184 AATAATTTGA
*
104194 TAATTTTACTAACAAT
1 TAATTTTAATAACAAT
104210 TAATTTTAATAACAAT
1 TAATTTTAATAACAAT
*
104226 TAGTTTTAATA
1 TAATTTTAATA
104237 TAAAAATATA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 25 1.00
ACGTcount: A:0.44, C:0.07, G:0.02, T:0.47
Consensus pattern (16 bp):
TAATTTTAATAACAAT
Found at i:104227 original size:43 final size:43
Alignment explanation
Indices: 104114--104213 Score: 193
Period size: 43 Copynumber: 2.3 Consensus size: 43
104104 TTAGATTTTG
104114 TTAC-AACAATTAATACAATTAACAATTAATAATTTGATAATT
1 TTACTAACAATTAATACAATTAACAATTAATAATTTGATAATT
104156 TTACTAACAATTAATACAATTAACAATTAATAATTTGATAATT
1 TTACTAACAATTAATACAATTAACAATTAATAATTTGATAATT
104199 TTACTAACAATTAAT
1 TTACTAACAATTAAT
104214 TTTAATAACA
Statistics
Matches: 57, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
42 4 0.07
43 53 0.93
ACGTcount: A:0.49, C:0.10, G:0.02, T:0.39
Consensus pattern (43 bp):
TTACTAACAATTAATACAATTAACAATTAATAATTTGATAATT
Found at i:104959 original size:33 final size:33
Alignment explanation
Indices: 104917--104979 Score: 101
Period size: 33 Copynumber: 1.9 Consensus size: 33
104907 GGCCCATTTT
104917 TATTTTAAAAAT-TTTAAAAAATTAAAAAAAAAG
1 TATTTTAAAAATATTT-AAAAATTAAAAAAAAAG
*
104950 TATTTTAAAAATATTTTAAAATTAAAAAAA
1 TATTTTAAAAATATTTAAAAATTAAAAAAA
104980 TTAAAAAATA
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
33 25 0.89
34 3 0.11
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.37
Consensus pattern (33 bp):
TATTTTAAAAATATTTAAAAATTAAAAAAAAAG
Found at i:104985 original size:8 final size:9
Alignment explanation
Indices: 104967--105014 Score: 53
Period size: 9 Copynumber: 5.3 Consensus size: 9
104957 AAAATATTTT
104967 AAAATTAAA
1 AAAATTAAA
104976 AAAATTAAA
1 AAAATTAAA
**
104985 AAATATT-TT
1 AAA-ATTAAA
104994 AAAATTAAA
1 AAAATTAAA
*
105003 AAAATTTAA
1 AAAATTAAA
105012 AAA
1 AAA
105015 GTATGTANNN
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
8 3 0.09
9 26 0.81
10 3 0.09
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (9 bp):
AAAATTAAA
Found at i:104986 original size:27 final size:27
Alignment explanation
Indices: 104956--105014 Score: 109
Period size: 27 Copynumber: 2.2 Consensus size: 27
104946 AAAGTATTTT
104956 AAAAATATTTTAAAATTAAAAAAATTA
1 AAAAATATTTTAAAATTAAAAAAATTA
*
104983 AAAAATATTTTAAAATTAAAAAAATTT
1 AAAAATATTTTAAAATTAAAAAAATTA
105010 AAAAA
1 AAAAA
105015 GTATGTANNN
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 31 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (27 bp):
AAAAATATTTTAAAATTAAAAAAATTA
Found at i:107079 original size:76 final size:76
Alignment explanation
Indices: 106995--107147 Score: 297
Period size: 76 Copynumber: 2.0 Consensus size: 76
106985 GCCCAGCCCG
106995 AGAAAAAAATCATAAGCCCGGGCCCGGCCTATTTTTATTTTAAAAATTTTAAAAAATTTAAAAAA
1 AGAAAAAAATCATAAGCCCGGGCCCGGCCTATTTTTATTTTAAAAATTTTAAAAAATTTAAAAAA
107060 AGCATTTTAAA
66 AGCATTTTAAA
*
107071 AGAAAAAAATCATAAGCCTGGGCCCGGCCTATTTTTATTTTAAAAATTTTAAAAAATTTAAAAAA
1 AGAAAAAAATCATAAGCCCGGGCCCGGCCTATTTTTATTTTAAAAATTTTAAAAAATTTAAAAAA
107136 AGCATTTTAAA
66 AGCATTTTAAA
107147 A
1 A
107148 TATTTTAAAA
Statistics
Matches: 76, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
76 76 1.00
ACGTcount: A:0.46, C:0.12, G:0.10, T:0.31
Consensus pattern (76 bp):
AGAAAAAAATCATAAGCCCGGGCCCGGCCTATTTTTATTTTAAAAATTTTAAAAAATTTAAAAAA
AGCATTTTAAA
Found at i:107127 original size:10 final size:10
Alignment explanation
Indices: 107107--107168 Score: 63
Period size: 10 Copynumber: 5.9 Consensus size: 10
107097 GCCTATTTTT
107107 ATTTT-AAAA
1 ATTTTAAAAA
107116 ATTTTAAAAA
1 ATTTTAAAAA
*
107126 ATTTAAAAAAA
1 ATTT-TAAAAA
*
107137 GCATTTTAAAAT
1 --ATTTTAAAAA
107149 ATTTTAAAAA
1 ATTTTAAAAA
107159 TATTTTAAAA
1 -ATTTTAAAA
107169 TAAAAAAATA
Statistics
Matches: 44, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
9 5 0.11
10 17 0.39
11 14 0.32
12 4 0.09
13 4 0.09
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.40
Consensus pattern (10 bp):
ATTTTAAAAA
Found at i:107212 original size:39 final size:38
Alignment explanation
Indices: 107149--107223 Score: 132
Period size: 38 Copynumber: 1.9 Consensus size: 38
107139 ATTTTAAAAT
107149 ATTTTAAAAATATTTTAAAATAAAAAAATAAAAAAAGG
1 ATTTTAAAAATATTTTAAAATAAAAAAATAAAAAAAGG
*
107187 ATTTTAAAAATATTTTAAAATTAAAAAAATTAAAAAA
1 ATTTTAAAAATATTTTAAAA-TAAAAAAATAAAAAAA
107224 TAAATATATT
Statistics
Matches: 35, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
38 20 0.57
39 15 0.43
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.32
Consensus pattern (38 bp):
ATTTTAAAAATATTTTAAAATAAAAAAATAAAAAAAGG
Found at i:112542 original size:28 final size:28
Alignment explanation
Indices: 112511--112565 Score: 76
Period size: 28 Copynumber: 2.0 Consensus size: 28
112501 CTCTCTCAAC
112511 AAAAAATTTAAAATAAATTT-AAAATTTT
1 AAAAAATTTAAAA-AAATTTCAAAATTTT
* *
112539 AAAATATTTATAAAAATTTCAAAATTT
1 AAAAAATTTAAAAAAATTTCAAAATTT
112566 ATATATTTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
27 6 0.25
28 18 0.75
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (28 bp):
AAAAAATTTAAAAAAATTTCAAAATTTT
Found at i:112552 original size:19 final size:19
Alignment explanation
Indices: 112512--112568 Score: 64
Period size: 19 Copynumber: 3.1 Consensus size: 19
112502 TCTCTCAACA
*
112512 AAAAATTTAAAATAAATT-T
1 AAAAATTTAAAAT-ATTTAT
*
112531 AAAATTTTAAAATATTTAT
1 AAAAATTTAAAATATTTAT
*
112550 AAAAATTTCAAA-ATTTAT
1 AAAAATTTAAAATATTTAT
112568 A
1 A
112569 TATTTTTTAG
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
18 10 0.30
19 23 0.70
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (19 bp):
AAAAATTTAAAATATTTAT
Found at i:122940 original size:29 final size:27
Alignment explanation
Indices: 122896--122949 Score: 72
Period size: 29 Copynumber: 1.9 Consensus size: 27
122886 AAATAATAAA
*
122896 AAATTAATTATGAAAATAGGATATATTAT
1 AAATTAATTAT-AAAA-ATGATATATTAT
*
122925 AAATTATTTATAAAAATGATATATT
1 AAATTAATTATAAAAATGATATATT
122950 TTTTAAGATA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
27 9 0.39
28 4 0.17
29 10 0.43
ACGTcount: A:0.52, C:0.00, G:0.07, T:0.41
Consensus pattern (27 bp):
AAATTAATTATAAAAATGATATATTAT
Found at i:135988 original size:15 final size:16
Alignment explanation
Indices: 135960--135992 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
135950 ATTTTTTTAG
135960 ATTATTTTTATTAAAA
1 ATTATTTTTATTAAAA
135976 ATTATTTTT-TTAAAA
1 ATTATTTTTATTAAAA
135991 AT
1 AT
135993 ATAATACATT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 8 0.47
16 9 0.53
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (16 bp):
ATTATTTTTATTAAAA
Found at i:136119 original size:39 final size:41
Alignment explanation
Indices: 136045--136133 Score: 121
Period size: 39 Copynumber: 2.2 Consensus size: 41
136035 TCAAATATAT
* * *
136045 TTATATT-AAAAACACTATCATAAATATAATGAATGTTTTG
1 TTATATTAAAAAACACTATAATAAATATAATAAATGTTTTA
136085 TTATATTAAAAAACAC-A-AATAAATATAATAAATGTTTTA
1 TTATATTAAAAAACACTATAATAAATATAATAAATGTTTTA
*
136124 TTATGTTAAA
1 TTATATTAAA
136134 TATAAATTTT
Statistics
Matches: 44, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
39 28 0.64
40 8 0.18
41 8 0.18
ACGTcount: A:0.49, C:0.06, G:0.06, T:0.39
Consensus pattern (41 bp):
TTATATTAAAAAACACTATAATAAATATAATAAATGTTTTA
Found at i:136732 original size:21 final size:20
Alignment explanation
Indices: 136708--136749 Score: 66
Period size: 20 Copynumber: 2.0 Consensus size: 20
136698 GGTTTTAAAA
*
136708 TTTTAAAAATATAAAATTTAT
1 TTTTAAAAAT-TAAAAATTAT
136729 TTTTAAAAATTAAAAATTAT
1 TTTTAAAAATTAAAAATTAT
136749 T
1 T
136750 AAAATTATTA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
20 10 0.50
21 10 0.50
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (20 bp):
TTTTAAAAATTAAAAATTAT
Found at i:136761 original size:19 final size:18
Alignment explanation
Indices: 136737--136775 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 18
136727 ATTTTTAAAA
*
136737 ATTAAAAATTATTAAAATT
1 ATTAAAAAGTA-TAAAATT
136756 ATTAAAAAGTATAAAATT
1 ATTAAAAAGTATAAAATT
136774 AT
1 AT
136776 AAGAAAAATA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 9 0.47
19 10 0.53
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (18 bp):
ATTAAAAAGTATAAAATT
Found at i:138364 original size:38 final size:38
Alignment explanation
Indices: 138306--138391 Score: 100
Period size: 38 Copynumber: 2.3 Consensus size: 38
138296 AATAAATATA
* * * * *
138306 TTTAATACAATAACATATTTATTATATTTATTTGTGTT
1 TTTAATATAATAAAACATTTATTATATTTAGTAGTGTT
* * *
138344 TTTAATATAATAAAACATTTATTTTTTTTGGTAGTGTT
1 TTTAATATAATAAAACATTTATTATATTTAGTAGTGTT
138382 TTTAATATAA
1 TTTAATATAA
138392 ATAATTTTAA
Statistics
Matches: 40, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
38 40 1.00
ACGTcount: A:0.35, C:0.03, G:0.07, T:0.55
Consensus pattern (38 bp):
TTTAATATAATAAAACATTTATTATATTTAGTAGTGTT
Found at i:141194 original size:683 final size:675
Alignment explanation
Indices: 139843--141200 Score: 2617
Period size: 683 Copynumber: 2.0 Consensus size: 675
139833 TTTAATAGTC
* *
139843 TATATCTTTATAATTTTTAAATGATTAAATCAAATTTTTATCATTTTCAAAGTGTAATTTTACCA
1 TATATATTTATAATTTTTAAATGATTAAATCAAAATTTTATCATTTTCAAAGTGTAATTTTACCA
139908 TTATTAATTTAAAAATTTATAAACTATAAAAAGTTTAAATGAATTTTTTTTATTTTACAGGAGAC
66 TTATTAATTTAAAAATTTATAAACTATAAAAAGTTTAAATGAATTTTTTTTATTTTACAGGAGAC
139973 CAGGGCCCCTGCCAACCTTCATTGGCTCCGCCATTGTATGAATGAATATATATAAAGGTTGGTTT
131 CAGGGCCCCTGCCAACCTTCATTGGCTCCGCCATTGTATGAATGAATATATATAAAGGTTGGTTT
140038 GGATATTTTAGAGATTTTTAAAATACATTGTTTCAAAATATCTGTATTTGTAACTATTTTTTTAA
196 GGATATTTTAGAGATTTTTAAAATACATTGTTTCAAAATATCTGTATTTGTAACTATTTTTTTAA
140103 AATTGATAAAAGAAGAATAATTATATTAAATAAAAATAATATAAAACATTATATATTAAAATTAA
261 AATTGATAAAAGAAGAATAATTATATTAAATAAAAATAATATAAAACATTATATATTAAAATTAA
140168 TTAAATATAATATTTTGTAGTTTTAGTTTTTATATAGTGCGATATTATTAACATATTAAAAATGT
326 TTAAATATAATATTTTGTAGTTTTAGTTTTTATATAGTGCGATATTATTAACATATTAAAAATGT
140233 TATATTTAAATAAATATTGTAATCTCGGGGATGTAGCTCATATGGTAGAGCGCTCGCTTCGCATG
391 TATATTTAAATAAATATTGTAATCTCGGGGATGTAGCTCATATGGTAGAGCGCTCGCTTCGCATG
140298 CGAGAGGCACGGGGTTCGATTCCCCGCATCTCCAACACTTAATTATTTTATGGGCTCTCAAACAA
456 CGAGAGGCACGGGGTTCGATTCCCCGCATCTCCAACACTTAATTATTTTATGGGCTCTCAAACAA
140363 GCCCTAACGAACTTGACTGAATTGTTTTTAGAGGTTCGGCCCAAATCAGCAATATAGTTTCGTCC
521 GCCCTAACGAACTTGACTGAATTGTTTTTAGAGGTTCGGCCCAAATCAGCAATATAGTTTCGTCC
140428 ATTAACTCACTTTTAAACGATTTAAGAAAAAAGAAAGCCCACTTCAATCTTTTGCTAATGAATAT
586 ATTAACTCACTTTTAAACGATTTAAGAAAAAAGAAAGCCCACTTCAATCTTTTGCTAATGAATAT
140493 AAAATGAAGACACTTAAATTTAATT
651 AAAATGAAGACACTTAAATTTAATT
*
140518 TATATATTTATAATTTTTAAATGATTAAATCAAAATTTTATTATTTTTGGAAAGTCAAAGTGTAA
1 TATATATTTATAATTTTTAAATGATTAAATCAAAATTTTATCA--TTT------TCAAAGTGTAA
140583 TTTTACCATTATTAATTTAAAAATTTATAAACTATAAAAAGTTTAAATGAATTTTTTTTATTTTA
58 TTTTACCATTATTAATTTAAAAATTTATAAACTATAAAAAGTTTAAATGAATTTTTTTTATTTTA
140648 CAGGAGACCAGGGCCCCTGCCAACCTTCATTGGCTCCGCCATTGTATGAATGAATATATATAAAG
123 CAGGAGACCAGGGCCCCTGCCAACCTTCATTGGCTCCGCCATTGTATGAATGAATATATATAAAG
140713 GTTGGTTTGGATATTTTAGAGATTTTTAAAATACATTGTTTCAAAATATCTGTATTTGTAACTAT
188 GTTGGTTTGGATATTTTAGAGATTTTTAAAATACATTGTTTCAAAATATCTGTATTTGTAACTAT
140778 TTTTTTAAAATTGATAAAAGAAGAATAATTATATTAAATAAAAATAATATAAAACATTATATATT
253 TTTTTTAAAATTGATAAAAGAAGAATAATTATATTAAATAAAAATAATATAAAACATTATATATT
140843 AAAATTAATTAAATATAATATTTTGTAGTTTTAGTTTTTATATAGTGCGATATTATTAACATATT
318 AAAATTAATTAAATATAATATTTTGTAGTTTTAGTTTTTATATAGTGCGATATTATTAACATATT
140908 AAAAATGTTATATTTAAATAAATATTGTAATCTCGGGGATGTAGCTCATATGGTAGAGCGCTCGC
383 AAAAATGTTATATTTAAATAAATATTGTAATCTCGGGGATGTAGCTCATATGGTAGAGCGCTCGC
140973 TTCGCATGCGAGAGGCACGGGGTTCGATTCCCCGCATCTCCAACACTTAATTATTTTATGGGCTC
448 TTCGCATGCGAGAGGCACGGGGTTCGATTCCCCGCATCTCCAACACTTAATTATTTTATGGGCTC
141038 TCAAACAAGCCCTAACGAACTTGACTGAATTGTTTTTAGAGGTTCGGCCCAAATCAGCAATATAG
513 TCAAACAAGCCCTAACGAACTTGACTGAATTGTTTTTAGAGGTTCGGCCCAAATCAGCAATATAG
141103 TTTCGTCCATTAACTCACTTTTAAACGATTTAAGAAAAAAGAAAGCCCACTTCAATCTTTTGCTA
578 TTTCGTCCATTAACTCACTTTTAAACGATTTAAGAAAAAAGAAAGCCCACTTCAATCTTTTGCTA
141168 ATGAATATAAAATGAAGACACTTAAATTTAATT
643 ATGAATATAAAATGAAGACACTTAAATTTAATT
141201 ATTTTTCATT
Statistics
Matches: 672, Mismatches: 3, Indels: 8
0.98 0.00 0.01
Matches are distributed among these distances:
675 40 0.06
677 3 0.00
683 629 0.94
ACGTcount: A:0.37, C:0.13, G:0.13, T:0.38
Consensus pattern (675 bp):
TATATATTTATAATTTTTAAATGATTAAATCAAAATTTTATCATTTTCAAAGTGTAATTTTACCA
TTATTAATTTAAAAATTTATAAACTATAAAAAGTTTAAATGAATTTTTTTTATTTTACAGGAGAC
CAGGGCCCCTGCCAACCTTCATTGGCTCCGCCATTGTATGAATGAATATATATAAAGGTTGGTTT
GGATATTTTAGAGATTTTTAAAATACATTGTTTCAAAATATCTGTATTTGTAACTATTTTTTTAA
AATTGATAAAAGAAGAATAATTATATTAAATAAAAATAATATAAAACATTATATATTAAAATTAA
TTAAATATAATATTTTGTAGTTTTAGTTTTTATATAGTGCGATATTATTAACATATTAAAAATGT
TATATTTAAATAAATATTGTAATCTCGGGGATGTAGCTCATATGGTAGAGCGCTCGCTTCGCATG
CGAGAGGCACGGGGTTCGATTCCCCGCATCTCCAACACTTAATTATTTTATGGGCTCTCAAACAA
GCCCTAACGAACTTGACTGAATTGTTTTTAGAGGTTCGGCCCAAATCAGCAATATAGTTTCGTCC
ATTAACTCACTTTTAAACGATTTAAGAAAAAAGAAAGCCCACTTCAATCTTTTGCTAATGAATAT
AAAATGAAGACACTTAAATTTAATT
Found at i:146648 original size:4 final size:4
Alignment explanation
Indices: 146639--146669 Score: 62
Period size: 4 Copynumber: 7.8 Consensus size: 4
146629 GAAAAAATTG
146639 TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAA
1 TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAA
146670 TGTTTTTATA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (4 bp):
TAAA
Found at i:153121 original size:15 final size:15
Alignment explanation
Indices: 153101--153131 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
153091 CTGTATCAGT
153101 AATGAATCAGAGCAC
1 AATGAATCAGAGCAC
153116 AATGAATCAGAGCAC
1 AATGAATCAGAGCAC
153131 A
1 A
153132 CGGAACCGTC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.48, C:0.19, G:0.19, T:0.13
Consensus pattern (15 bp):
AATGAATCAGAGCAC
Found at i:162486 original size:18 final size:19
Alignment explanation
Indices: 162451--162487 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
162441 AAGCCAAATT
*
162451 TTAAAAAATTATTTTTATA
1 TTAAAAAATTATTATTATA
162470 TTAAAAAATTA-TATTATA
1 TTAAAAAATTATTATTATA
162488 GACATGAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 6 0.35
19 11 0.65
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (19 bp):
TTAAAAAATTATTATTATA
Found at i:163105 original size:11 final size:11
Alignment explanation
Indices: 163089--163123 Score: 54
Period size: 11 Copynumber: 3.2 Consensus size: 11
163079 ATAAATTATT
163089 AAAAAAAT-AA
1 AAAAAAATAAA
163099 AAAAAAATAAA
1 AAAAAAATAAA
163110 AAAAAAATTAAA
1 AAAAAAA-TAAA
163122 AA
1 AA
163124 TTTAATTCAA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
10 8 0.35
11 9 0.39
12 6 0.26
ACGTcount: A:0.89, C:0.00, G:0.00, T:0.11
Consensus pattern (11 bp):
AAAAAAATAAA
Found at i:163123 original size:10 final size:10
Alignment explanation
Indices: 163089--163115 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
163079 ATAAATTATT
163089 AAAAAAATAA
1 AAAAAAATAA
163099 AAAAAAATAA
1 AAAAAAATAA
163109 AAAAAAA
1 AAAAAAA
163116 ATTAAAAATT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.93, C:0.00, G:0.00, T:0.07
Consensus pattern (10 bp):
AAAAAAATAA
Found at i:164836 original size:3 final size:3
Alignment explanation
Indices: 164828--164886 Score: 118
Period size: 3 Copynumber: 19.7 Consensus size: 3
164818 TATGTCAAAT
164828 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
164876 ATA ATA ATA AT
1 ATA ATA ATA AT
164887 TGTTATGAAT
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 56 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:169634 original size:51 final size:51
Alignment explanation
Indices: 169537--169635 Score: 144
Period size: 51 Copynumber: 1.9 Consensus size: 51
169527 TTATTCGAGA
* *
169537 TAGTGATGGTTTCGTTCTCGGTGGCAGTGCAGGCTACAAGGGGGATCAGAT
1 TAGTGATGGTTTCGTTCTCGGTGGCAGTGCAGGCTACAAAGAGGATCAGAT
* * * *
169588 TAGTGATGGTTTCGTTGTCGGTGGCAGTGCGGGTTACAAATAGGATCA
1 TAGTGATGGTTTCGTTCTCGGTGGCAGTGCAGGCTACAAAGAGGATCA
169636 CATGAGTATG
Statistics
Matches: 42, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
51 42 1.00
ACGTcount: A:0.20, C:0.14, G:0.36, T:0.29
Consensus pattern (51 bp):
TAGTGATGGTTTCGTTCTCGGTGGCAGTGCAGGCTACAAAGAGGATCAGAT
Found at i:171766 original size:2 final size:2
Alignment explanation
Indices: 171759--171795 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
171749 GTTATTTAAA
171759 AT AT AT AT 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 AT AT AT AT A
171796 AAAATCACTC
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:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:172962 original size:224 final size:224
Alignment explanation
Indices: 172572--173178 Score: 1178
Period size: 224 Copynumber: 2.7 Consensus size: 224
172562 NNNNNNNNNN
172572 TATATATATATATATATATAGGAATATACTACTAATGATGATTATTTTTAATGAGACATATCATT
1 TATATATATATATATATATAGGAATATACTACTAATGATGATTATTTTTAATGAGACATATCATT
172637 TATACAATGAACATCCAAAGGGGAGTGTTATGAATGCTATTAAGTGGATGTTCATTATAATCAAC
66 TATACAATGAACATCCAAAGGGGAGTGTTATGAATGCTATTAAGTGGATGTTCATTATAATCAAC
172702 CTTTAACCTTTCATCTTCATTAACTCTTCACCTTTCGTCTCCTTGTAACTCTTTTACTATTTATG
131 CTTTAACCTTTCATCTTCATTAACTCTTCACCTTTCGTCTCCTTGTAACTCTTTTACTATTTATG
172767 TATTAGAAAAATAAGGAGTCTAATCTCCC
196 TATTAGAAAAATAAGGAGTCTAATCTCCC
172796 TATATATATATATATATATAGGAATATACTACTAATGATGATTATTTTTAATGAGACATATCATT
1 TATATATATATATATATATAGGAATATACTACTAATGATGATTATTTTTAATGAGACATATCATT
172861 TATACAATGAACATCCAAAGGGGAGTGTTATGAATGCTATTAAGTGGATGTTCATTATAATCAAC
66 TATACAATGAACATCCAAAGGGGAGTGTTATGAATGCTATTAAGTGGATGTTCATTATAATCAAC
172926 CTTTAACCTTTCATCTTCATTAACTCTTCACCTTTCGTCTCCTTGTAACTCTTTTACTATTTATG
131 CTTTAACCTTTCATCTTCATTAACTCTTCACCTTTCGTCTCCTTGTAACTCTTTTACTATTTATG
172991 TATTAGAAAAATAAGGAGTCTAATCTCCC
196 TATTAGAAAAATAAGGAGTCTAATCTCCC
173020 TATATATATATATATATATAGGAATATACTACTAATGATGATTATTTTTAATGAGACATATCATT
1 TATATATATATATATATATAGGAATATACTACTAATGATGATTATTTTTAATGAGACATATCATT
*
173085 TATACAATGAACATCCAAAGGGGAGTGTTATGAATGCTATTAAGTGTATGTTCATTATAATCAAC
66 TATACAATGAACATCCAAAGGGGAGTGTTATGAATGCTATTAAGTGGATGTTCATTATAATCAAC
* *
173150 CTTTCACCTTTCATCTTCTTGTAACTCTT
131 CTTTAACCTTTCATCTTCAT-TAACTCTT
173179 TTACTATTTA
Statistics
Matches: 379, Mismatches: 3, Indels: 1
0.99 0.01 0.00
Matches are distributed among these distances:
224 371 0.98
225 8 0.02
ACGTcount: A:0.34, C:0.15, G:0.12, T:0.40
Consensus pattern (224 bp):
TATATATATATATATATATAGGAATATACTACTAATGATGATTATTTTTAATGAGACATATCATT
TATACAATGAACATCCAAAGGGGAGTGTTATGAATGCTATTAAGTGGATGTTCATTATAATCAAC
CTTTAACCTTTCATCTTCATTAACTCTTCACCTTTCGTCTCCTTGTAACTCTTTTACTATTTATG
TATTAGAAAAATAAGGAGTCTAATCTCCC
Found at i:176251 original size:19 final size:18
Alignment explanation
Indices: 176227--176275 Score: 55
Period size: 19 Copynumber: 2.7 Consensus size: 18
176217 GTCTGATAAG
176227 TTTTATAATTTTTTACGAA
1 TTTTATAATTTTTTAC-AA
*
176246 TTTTAT-ATTTCTTTACAT
1 TTTTATAATTT-TTTACAA
*
176264 TTTTTTAATTTT
1 TTTTATAATTTT
176276 CTTATGACTT
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
18 11 0.42
19 15 0.58
ACGTcount: A:0.24, C:0.06, G:0.02, T:0.67
Consensus pattern (18 bp):
TTTTATAATTTTTTACAA
Found at i:176362 original size:40 final size:40
Alignment explanation
Indices: 176318--176395 Score: 113
Period size: 40 Copynumber: 1.9 Consensus size: 40
176308 TCTACATTTC
* *
176318 CAATTATTTTAT-ATTTTTTTACGATTTTTATAAAATTTTA
1 CAATT-TTTTATAATTTTTGTACGATTTTAATAAAATTTTA
*
176358 CAATTTTTTATAATTTTTGTACTATTTTAATAAAATTT
1 CAATTTTTTATAATTTTTGTACGATTTTAATAAAATTT
176396 ATATTTTTTA
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
39 6 0.18
40 28 0.82
ACGTcount: A:0.33, C:0.05, G:0.03, T:0.59
Consensus pattern (40 bp):
CAATTTTTTATAATTTTTGTACGATTTTAATAAAATTTTA
Found at i:176412 original size:27 final size:27
Alignment explanation
Indices: 176364--176433 Score: 79
Period size: 27 Copynumber: 2.5 Consensus size: 27
176354 TTTACAATTT
176364 TTTATAATTTTTGTACTATTTTAATAAAA
1 TTTAT-ATTTTT-TACTATTTTAATAAAA
*
176393 TTTATATTTTTTAC-ATTTTTATTAAAA
1 TTTATATTTTTTACTA-TTTTAATAAAA
*
176420 TTTAATAATTTTTA
1 TTT-ATATTTTTTA
176434 TTTATTTTTA
Statistics
Matches: 37, Mismatches: 2, Indels: 5
0.84 0.05 0.11
Matches are distributed among these distances:
26 1 0.03
27 16 0.43
28 15 0.41
29 5 0.14
ACGTcount: A:0.36, C:0.03, G:0.01, T:0.60
Consensus pattern (27 bp):
TTTATATTTTTTACTATTTTAATAAAA
Found at i:176861 original size:100 final size:101
Alignment explanation
Indices: 176731--176915 Score: 286
Period size: 100 Copynumber: 1.8 Consensus size: 101
176721 AAAAAAGGAG
* **
176731 CAGGGGTTTAATTGCATTTTTTGAAAAAGTTTGAGGGTCC-TTTTAATGCATTTTGGCAGTTCAA
1 CAGGGGCTTAATTGCATTTTTTGAAAAAGTTTGAGGG-CCTTTTTAATGCATTTTGAAAGTTCAA
176795 ATA-CTCAATTGAGTGCAAAAAGAAGAAGAAGAAGAAA
65 ATACCT-AATTGAGTGCAAAAAGAAGAAGAAGAAGAAA
* *
176832 CAGGGGCTTAATTGC-TTTTTTGAGAAAGTTTGAGGGCCTTTTTGATGCATTTTGAAAGTTCAAA
1 CAGGGGCTTAATTGCATTTTTTGAAAAAGTTTGAGGGCCTTTTTAATGCATTTTGAAAGTTCAAA
176896 TACCTAATTGAGTGCAAAAA
66 TACCTAATTGAGTGCAAAAA
176916 AAAGGGGGGG
Statistics
Matches: 77, Mismatches: 5, Indels: 5
0.89 0.06 0.06
Matches are distributed among these distances:
99 2 0.03
100 59 0.77
101 16 0.21
ACGTcount: A:0.34, C:0.11, G:0.23, T:0.33
Consensus pattern (101 bp):
CAGGGGCTTAATTGCATTTTTTGAAAAAGTTTGAGGGCCTTTTTAATGCATTTTGAAAGTTCAAA
TACCTAATTGAGTGCAAAAAGAAGAAGAAGAAGAAA
Found at i:177626 original size:19 final size:21
Alignment explanation
Indices: 177588--177629 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 21
177578 CTCAACACCT
177588 TTTTTAATTTCATAATATATTA
1 TTTTTAATTT-ATAATATATTA
177610 TTTTTAATTT-T-ATATATTA
1 TTTTTAATTTATAATATATTA
177629 T
1 T
177630 CTAATTTAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
19 9 0.45
20 1 0.05
22 10 0.50
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.64
Consensus pattern (21 bp):
TTTTTAATTTATAATATATTA
Found at i:179300 original size:51 final size:51
Alignment explanation
Indices: 179179--179870 Score: 485
Period size: 49 Copynumber: 13.6 Consensus size: 51
179169 ACAAAAAAAA
* * * * * *
179179 TTTGGGTGCTAGCCTGTCAATAGCTGACACCAGCAGTACAAAAAATTTTTTT
1 TTTGGGTGCTGGCCTGTCAATGGCCGGCACCACCAGTAC-GAAAATTTTTTT
* * * **
179231 TTTGGGTGCTGACCTGTCAATGACCAGCACCAGTAGTACGAAAATTTTTTT
1 TTTGGGTGCTGGCCTGTCAATGGCCGGCACCACCAGTACGAAAATTTTTTT
* *
179282 TTTGGGTGCTGGCTTGTCAATGGTCGGCACCACCAGTACGAAAA-TTTTTT
1 TTTGGGTGCTGGCCTGTCAATGGCCGGCACCACCAGTACGAAAATTTTTTT
** * * * *
179332 TTTGGGTAATGGCCTATCAATGGTCGGCATCACCAATACG-AAA-TTTTTT
1 TTTGGGTGCTGGCCTGTCAATGGCCGGCACCACCAGTACGAAAATTTTTTT
* * * ** **
179381 TTGGGGTTCTGGCCTGTCAATGGCCGGTACCATTA-TACGAAAAAAAAGTTTTT
1 TTTGGGTGCTGGCCTGTCAATGGCCGGCACCACCAGTACG---AAAATTTTTTT
* * * * *
179434 TTTGGGTGTTGGCCTGTTAATGGCCTGCACCAGCAGTATGAAAATTTTTTT
1 TTTGGGTGCTGGCCTGTCAATGGCCGGCACCACCAGTACGAAAATTTTTTT
* * ** *
179485 TTT--GTGCTGGCCTGTCAATGGTCAGCACCAGTA-TACGAAAA-ATTTTT
1 TTTGGGTGCTGGCCTGTCAATGGCCGGCACCACCAGTACGAAAATTTTTTT
* * ** * * * * **
179532 TTTGGGTGTTGGCCTGTGAACCGCTGACACGAGCAGTACGAAAAAAAAATAATTTT
1 TTTGGGTGCTGGCCTGTCAATGGCCGGCACCACCAGTACG-----AAAATTTTTTT
* * * *
179588 TTTGGGTGCTGGCCTGTCAATGGTCGGTAACTCCAGTAC-AAAATTTTTTT
1 TTTGGGTGCTGGCCTGTCAATGGCCGGCACCACCAGTACGAAAATTTTTTT
* * * * * ** * ** *
179638 TTTTGGAGCTAGCCTATTAATGGCTAGCACCACCAGTAGGAAAAAAAATATTT
1 TTTGGGTGCTGGCCTGTCAATGGCCGGCACCACCAGTACG--AAAATTTTTTT
* * *
179691 TTTGGGTGCTGGCTTGTCAATGGCTGACACCACCAGTAC---AATTTTTTT
1 TTTGGGTGCTGGCCTGTCAATGGCCGGCACCACCAGTACGAAAATTTTTTT
* * * * * * * *
179739 TTTTGGTGTTGGCTTGTCAATGACTGGCACAACCGGTATGAAAATTTTTTT
1 TTTGGGTGCTGGCCTGTCAATGGCCGGCACCACCAGTACGAAAATTTTTTT
* * *
179790 TTTGGGTGCTGGCTTGTCAATGGCTGGCACCACCTGTACG--AATTTTTTT
1 TTTGGGTGCTGGCCTGTCAATGGCCGGCACCACCAGTACGAAAATTTTTTT
* * *
179839 TTTTGGTGTTGGCCTGCCAATGGCCGGCACCA
1 TTTGGGTGCTGGCCTGTCAATGGCCGGCACCA
179871 GTGCACGGAA
Statistics
Matches: 499, Mismatches: 120, Indels: 45
0.75 0.18 0.07
Matches are distributed among these distances:
47 8 0.02
48 49 0.10
49 116 0.23
50 80 0.16
51 103 0.21
52 34 0.07
53 70 0.14
54 3 0.01
55 4 0.01
56 32 0.06
ACGTcount: A:0.24, C:0.18, G:0.23, T:0.34
Consensus pattern (51 bp):
TTTGGGTGCTGGCCTGTCAATGGCCGGCACCACCAGTACGAAAATTTTTTT
Found at i:179377 original size:49 final size:50
Alignment explanation
Indices: 179220--179870 Score: 254
Period size: 50 Copynumber: 12.8 Consensus size: 50
179210 AGCAGTACAA
* * ** * ** *
179220 AAAATTTTTTTTTTGGGTGCTGACCTGTCAATGACCAGCACCAGTAGTACG
1 AAAA-TTTTTTTTTGGGTACTGGCCTGTCAATGGTCGGCACCACCAATACG
* * *
179271 AAAATTTTTTTTTTGGGTGCTGGCTTGTCAATGGTCGGCACCACCAGTACG
1 AAAA-TTTTTTTTTGGGTACTGGCCTGTCAATGGTCGGCACCACCAATACG
* * *
179322 AAAATTTTTTTTTGGGTAATGGCCTATCAATGGTCGGCATCACCAATACG
1 AAAATTTTTTTTTGGGTACTGGCCTGTCAATGGTCGGCACCACCAATACG
* * * * **
179372 -AAATTTTTTTTGGGGTTCTGGCCTGTCAATGGCCGGTACCA-TTATACG
1 AAAATTTTTTTTTGGGTACTGGCCTGTCAATGGTCGGCACCACCAATACG
* ** * * * * * *
179420 AAAAAAAAGTTTTTTTTGGGTGTTGGCCTGTTAATGGCCTGCACCAGCAGTATG
1 ----AAAATTTTTTTTTGGGTACTGGCCTGTCAATGGTCGGCACCACCAATACG
* * * **
179474 AAAATTTTTTTTT-TGTGCTGGCCTGTCAATGGTCAGCACCA-GTATACG
1 AAAATTTTTTTTTGGGTACTGGCCTGTCAATGGTCGGCACCACCAATACG
* ** * ** * * * *
179522 AAAAATTTTTTTTGGGTGTTGGCCTGTGAACCG-CTGACACGAGCAGTACG
1 AAAATTTTTTTTTGGGTACTGGCCTGTCAATGGTC-GGCACCACCAATACG
* * * * * *
179572 AAAAAAAAATAATTTTTTTGGGTGCTGGCCTGTCAATGGTCGGTAACTCCAGTAC-
1 -----AAAAT-TTTTTTTTGGGTACTGGCCTGTCAATGGTCGGCACCACCAATACG
* * * * * * *
179627 AAAATTTTTTTTTTTGG-AGCTAGCCTATTAATGG-CTAGCACCACCAGTAGG
1 AAAA-TTTTTTTTTGGGTA-CTGGCCTGTCAATGGTC-GGCACCACCAATACG
* * * * * *
179678 AAAAAAAATATTTTTTGGGTGCTGGCTTGTCAATGG-CTGACACCACCAGTAC-
1 ---AAAATTTTTTTTTGGGTACTGGCCTGTCAATGGTC-GGCACCACCAATACG
** * * * ** *
179730 AATTTTTTTTTTTGGTGT--TGGCTTGTCAAT-GACTGGCACAACCGGTATG
1 AAAATTTTTTTTTGG-GTACTGGCCTGTCAATGGTC-GGCACCACCAATACG
* * **
179779 AAAATTTTTTTTTTGGGTGCTGGCTTGTCAATGG-CTGGCACCACCTGTACG
1 AAAA-TTTTTTTTTGGGTACTGGCCTGTCAATGGTC-GGCACCACCAATACG
** * *
179830 AATTTTTTTTTTTGGTGT--TGGCCTGCCAATGGCCGGCACCA
1 AAAATTTTTTTTTGG-GTACTGGCCTGTCAATGGTCGGCACCA
179871 GTGCACGGAA
Statistics
Matches: 461, Mismatches: 106, Indels: 68
0.73 0.17 0.11
Matches are distributed among these distances:
47 1 0.00
48 45 0.10
49 110 0.24
50 115 0.25
51 79 0.17
52 1 0.00
53 67 0.15
54 7 0.02
55 4 0.01
56 31 0.07
57 1 0.00
ACGTcount: A:0.24, C:0.18, G:0.23, T:0.35
Consensus pattern (50 bp):
AAAATTTTTTTTTGGGTACTGGCCTGTCAATGGTCGGCACCACCAATACG
Found at i:179456 original size:102 final size:98
Alignment explanation
Indices: 179179--179870 Score: 306
Period size: 103 Copynumber: 6.8 Consensus size: 98
179169 ACAAAAAAAA
* * * * * * *
179179 TTTGGGTGCTAGCCTGTCAATAG-CTGACACCAGCAGTACAAAAAATTTTTTTTTTGGGTGCTGA
1 TTTGGGTGCTGGCCTGTCAATGGCCAG-CACCAGTA-TACGAAAAA--TTTTTTTTGGGTGTTGG
* * ** *
179243 CCTGTCAATGACCAGCACCAGTAGTACGAAAATTTTTTT
62 CCTGTCAATGGCCGGCACCACCAATACGAAAA--TTTTT
* * * ** * **
179282 TTTGGGTGCTGGCTTGTCAATGGTCGGCACCACCAGTACGAAAATTTTTTTTTGGGTAATGGCCT
1 TTTGGGTGCTGGCCTGTCAATGGCCAGCACCAGTA-TACGAAAAATTTTTTTTGGGTGTTGGCCT
* * *
179347 ATCAATGGTCGGCATCACCAATACG-AAATTTTT
65 GTCAATGGCCGGCACCACCAATACGAAAATTTTT
* * * *
179380 TTTGGGGTTCTGGCCTGTCAATGGCCGGTACCATTATACGAAAAAAAAGTTTTTTTTGGGTGTTG
1 TTT-GGGTGCTGGCCTGTCAATGGCCAGCACCAGTATACG---AAAAA-TTTTTTTTGGGTGTTG
* * * * *
179445 GCCTGTTAATGGCCTGCACCAGCAGTATGAAAATTTTT
61 GCCTGTCAATGGCCGGCACCACCAATACGAAAATTTTT
** *
179483 TTTTTGTGCTGGCCTGTCAATGGTCAGCACCAGTATACGAAAAATTTTTTTTGGGTGTTGGCCTG
1 TTTGGGTGCTGGCCTGTCAATGGCCAGCACCAGTATACGAAAAATTTTTTTTGGGTGTTGGCCTG
* ** * * * * *
179548 TGAACCGCTGACACGAGCAGTACGAAAAAAAAATAATTTT
66 TCAATGGCCGGCACCACCAATACG-----AAAAT--TTTT
* * * * * * * *
179588 TTTGGGTGCTGGCCTGTCAATGGTCGGTAACTCCAG--TAC-AAAATTTTTTTTTTTGGAGCTAG
1 TTTGGGTGCTGGCCTGTCAATGG-C--CAGCACCAGTATACGAAAA-ATTTTTTTTGGGTGTTGG
* * ** * * *
179650 CCTATTAATGGCTAGCACCACCAGTAGGAAAAAAAATATTT
62 CCTGTCAATGGCCGGCACCACCAATACG----AAAATTTTT
* * ** *
179691 TTTGGGTGCTGGCTTGTCAATGGCTGACACCACCAG--TAC--AATTTTTTTTTTTGGTGTTGGC
1 TTTGGGTGCTGGCCTGTCAATGGC---CAGCACCAGTATACGAAAAATTTTTTTTGGGTGTTGGC
* * * * ** *
179752 TTGTCAATGACTGGCACAACCGGTATGAAAATTTTTTT
63 CTGTCAATGGCCGGCACCACCAATACGAAAA--TTTTT
* ** * * ** *
179790 TTTGGGTGCTGGCTTGTCAATGGCTGGCACCACCTGTACG-AATTTTTTTTTTTGGTGTTGGCCT
1 TTTGGGTGCTGGCCTGTCAATGGCCAGCACCA-GTATACGAAAAATTTTTTTTGGGTGTTGGCCT
*
179854 GCCAATGGCCGGCACCA
65 GTCAATGGCCGGCACCA
179871 GTGCACGGAA
Statistics
Matches: 466, Mismatches: 98, Indels: 53
0.76 0.16 0.09
Matches are distributed among these distances:
96 5 0.01
97 4 0.01
98 49 0.11
99 62 0.13
100 39 0.08
101 73 0.16
102 67 0.14
103 86 0.18
104 2 0.00
105 38 0.08
106 35 0.08
108 6 0.01
ACGTcount: A:0.24, C:0.18, G:0.23, T:0.34
Consensus pattern (98 bp):
TTTGGGTGCTGGCCTGTCAATGGCCAGCACCAGTATACGAAAAATTTTTTTTGGGTGTTGGCCTG
TCAATGGCCGGCACCACCAATACGAAAATTTTT
Found at i:179636 original size:152 final size:150
Alignment explanation
Indices: 179277--179639 Score: 372
Period size: 152 Copynumber: 2.4 Consensus size: 150
179267 TACGAAAATT
*
179277 TTTTTTTTGGGTGCTGGCTTGTCAATGGTCGGCACCACCAGTACGAAAATTTTTTTTTGGGTAAT
1 TTTTTTTTGGGTGCTGGCCTGTCAATGGTCGGCACCACCAGTAC-AAAATTTTTTTTT-GGTAAT
* * **
179342 GGCCTATCAATGGTCGGCATCACCAATACGAAATTTTTTTTGGGGTTCTGGCCTGTCAATGGCCG
64 GGCCTATCAATGGTCAGCACCACCAATACGAAATTTTTTTTGGGGTTCTGGCCTGTCAACCGCCG
** ** *
179407 GTACCATTATACGAAAAAAAAG
129 ACACCAGCATACGAAAAAAAAA
* * * * * * * **
179429 TTTTTTTTGGGTGTTGGCCTGTTAATGGCCTGCACCAGCAGTATGAAAATTTTTTTTTTGTGCTG
1 TTTTTTTTGGGTGCTGGCCTGTCAATGGTCGGCACCACCAGTA-CAAAATTTTTTTTTGGTAATG
* ** *
179494 GCCTGTCAATGGTCAGCACCA-GTATACGAAAAATTTTTTTT-GGGTGT-TGGCCTGTGAACCGC
65 GCCTATCAATGGTCAGCACCACCAATACG--AAATTTTTTTTGGGGT-TCTGGCCTGTCAACCGC
* *
179556 TGACACGAGCAGTACGAAAAAAAAA
127 CGACACCAGCA-TACGAAAAAAAAA
* * *
179581 TAATTTTTTTGGGTGCTGGCCTGTCAATGGTCGGTAACTCCAGTACAAAATTTTTTTTT
1 T--TTTTTTTGGGTGCTGGCCTGTCAATGGTCGGCACCACCAGTACAAAATTTTTTTTT
179640 TTGGAGCTAG
Statistics
Matches: 170, Mismatches: 34, Indels: 13
0.78 0.16 0.06
Matches are distributed among these distances:
150 5 0.03
151 43 0.25
152 75 0.44
153 13 0.08
154 34 0.20
ACGTcount: A:0.24, C:0.17, G:0.23, T:0.35
Consensus pattern (150 bp):
TTTTTTTTGGGTGCTGGCCTGTCAATGGTCGGCACCACCAGTACAAAATTTTTTTTTGGTAATGG
CCTATCAATGGTCAGCACCACCAATACGAAATTTTTTTTGGGGTTCTGGCCTGTCAACCGCCGAC
ACCAGCATACGAAAAAAAAA
Found at i:179759 original size:48 final size:48
Alignment explanation
Indices: 179688--179870 Score: 213
Period size: 51 Copynumber: 3.7 Consensus size: 48
179678 AAAAAAAATA
*
179688 TTTTTTGGGTGCTGGCTTGTCAATGGCTGACACCACCAGTACAATTTT
1 TTTTTTGGGTGCTGGCTTGTCAATGGCTGGCACCACCAGTACAATTTT
* * * * * *
179736 TTTTTTTGGTGTTGGCTTGTCAATGACTGGCACAACCGGTATGAAAATTTT
1 TTTTTTGGGTGCTGGCTTGTCAATGGCTGGCACCACCAG--T-ACAATTTT
*
179787 TTTTTTGGGTGCTGGCTTGTCAATGGCTGGCACCACCTGTACGAATTTT
1 TTTTTTGGGTGCTGGCTTGTCAATGGCTGGCACCACCAGTAC-AATTTT
* * * * *
179836 TTTTTTTGGTGTTGGCCTGCCAATGGCCGGCACCA
1 TTTTTTGGGTGCTGGCTTGTCAATGGCTGGCACCA
179871 GTGCACGGAA
Statistics
Matches: 113, Mismatches: 18, Indels: 7
0.82 0.13 0.05
Matches are distributed among these distances:
48 34 0.30
49 37 0.33
50 1 0.01
51 41 0.36
ACGTcount: A:0.17, C:0.20, G:0.25, T:0.38
Consensus pattern (48 bp):
TTTTTTGGGTGCTGGCTTGTCAATGGCTGGCACCACCAGTACAATTTT
Found at i:185321 original size:48 final size:48
Alignment explanation
Indices: 185162--185596 Score: 291
Period size: 48 Copynumber: 9.0 Consensus size: 48
185152 TTTGATAAAT
* * *
185162 TTGGTGTCAGCCATTGACACGCCAGCA-CCAAATTTTTTTTT-GTACTG
1 TTGGTGACGGCCATTGACAGGCCAGCACCCAAATTTTTTTTTCGTA-TG
* * * * *
185209 TTGGTG-CTAGCCATTGACAGGTTC-GCACCTAATTTTTTTTTTCGTATC
1 TTGGTGAC-GGCCATTGACAGG-CCAGCACCCAAATTTTTTTTTCGTATG
* * * ** * *
185257 CTAGTGCCAACTATTGACAGGCCAGCACCCAAATTTTTTTTTCGTATA
1 TTGGTGACGGCCATTGACAGGCCAGCACCCAAATTTTTTTTTCGTATG
* *
185305 TTGGTGACGGCCATTGATAGGCCGGCACCCAAA-TTTTTTTT-GTACTG
1 TTGGTGACGGCCATTGACAGGCCAGCACCCAAATTTTTTTTTCGTA-TG
* * * *
185352 GTGATGCCAGCCATTGACAGGCCAGCACCC-AATTTTTTTTTCGTAT-
1 TTGGTGACGGCCATTGACAGGCCAGCACCCAAATTTTTTTTTCGTATG
* *
185398 TAGTGGTGCCGGCCATTAACAGGCCAGCACCCAAATTTTTTTTT--TCATG
1 T--TGGTGACGGCCATTGACAGGCCAGCACCCAAATTTTTTTTTCGT-ATG
* * * * *
185447 CTGGTGGTACGGGTCATTAACAAGCCAGCACCCAATTTTTTATTTTCGTATTG
1 TTGGT-G-AC-GGCCATTGACAGGCCAGCACCCAAATTTTT-TTTTCGTA-TG
* * * * * *
185500 CTGGTGTCGGTCATTGACAAGCTAGCACCCCCAATTTTTTTTT-GTACTG
1 TTGGTGACGGCCATTGACAGGCCAGCA-CCCAAATTTTTTTTTCGTA-TG
* ** * *
185549 CTGGT-ACAGGTTATTGACAGGCCAGCACCTAAAAGTTTTTTTTCGTAT
1 TTGGTGAC-GGCCATTGACAGGCCAGCACC-CAAATTTTTTTTTCGTAT
185597 TGCTGGTGCA
Statistics
Matches: 313, Mismatches: 50, Indels: 48
0.76 0.12 0.12
Matches are distributed among these distances:
46 6 0.02
47 69 0.22
48 110 0.35
49 53 0.17
50 51 0.16
51 14 0.04
52 2 0.01
53 8 0.03
ACGTcount: A:0.22, C:0.23, G:0.20, T:0.36
Consensus pattern (48 bp):
TTGGTGACGGCCATTGACAGGCCAGCACCCAAATTTTTTTTTCGTATG
Found at i:185344 original size:143 final size:143
Alignment explanation
Indices: 185162--185441 Score: 359
Period size: 143 Copynumber: 2.0 Consensus size: 143
185152 TTTGATAAAT
* * * *
185162 TTGGTGTCAGCCATTGACACGCCAGCACCAAATTTTTTTTTGTACTGTTGGTGCTAGCCATTGAC
1 TTGGTGACAGCCATTGACACGCCAGCACCAAATTTTTTTTTGTACTGGTGATGCCAGCCATTGAC
* * * * *
185227 AGGTTC-GCACCTAATTTTTTTTTTCGTA-TCCTAGTGCCAACTATTGACAGGCCAGCACCCAAA
66 AGG-CCAGCACCCAA-TTTTTTTTTCGTATTACTAGTGCCAACCATTAACAGGCCAGCACCCAAA
185290 TTTTTTTTTCGTATA
129 TTTTTTTTTCGTATA
* * * *
185305 TTGGTGACGGCCATTGATAGGCCGGCACCCAAA-TTTTTTTTGTACTGGTGATGCCAGCCATTGA
1 TTGGTGACAGCCATTGACACGCCAGCA-CCAAATTTTTTTTTGTACTGGTGATGCCAGCCATTGA
* * **
185369 CAGGCCAGCACCCAATTTTTTTTTCGTATTAGTGGTGCCGGCCATTAACAGGCCAGCACCCAAAT
65 CAGGCCAGCACCCAATTTTTTTTTCGTATTACTAGTGCCAACCATTAACAGGCCAGCACCCAAAT
185434 TTTTTTTT
130 TTTTTTTT
185442 TCATGCTGGT
Statistics
Matches: 117, Mismatches: 17, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
142 14 0.12
143 98 0.84
144 5 0.04
ACGTcount: A:0.21, C:0.24, G:0.20, T:0.35
Consensus pattern (143 bp):
TTGGTGACAGCCATTGACACGCCAGCACCAAATTTTTTTTTGTACTGGTGATGCCAGCCATTGAC
AGGCCAGCACCCAATTTTTTTTTCGTATTACTAGTGCCAACCATTAACAGGCCAGCACCCAAATT
TTTTTTTCGTATA
Found at i:185360 original size:95 final size:95
Alignment explanation
Indices: 185261--185548 Score: 283
Period size: 95 Copynumber: 3.0 Consensus size: 95
185251 CGTATCCTAG
* * * *
185261 TGCCAACTATTGACAGGCCAGCACCCAAATTTTTTTTTCGTA-TATTGGTGACGGCCATTGATAG
1 TGCCAACCATTGACAGGCCAGCACCC-AATTTTTTTTTCGTATTAGTGGTGACGGCCATTAACAG
*
185325 GCCGGCACCCAAATTTTTTTTGTACTGGTGA
65 GCCAGCACCCAAATTTTTTTTGTACTGGTGA
* *
185356 TGCCAGCCATTGACAGGCCAGCACCCAATTTTTTTTTCGTATTAGTGGTGCCGGCCATTAACAGG
1 TGCCAACCATTGACAGGCCAGCACCCAATTTTTTTTTCGTATTAGTGGTGACGGCCATTAACAGG
* *
185421 CCAGCACCCAAATTTTTTTTTTCATGCTGGTGG
66 CCAGCACCCAAATTTTTTTTGT-A--CTGGTGA
* **** * * * * *
185454 TACGGGTCATTAACAAGCCAGCACCCAATTTTTTATTTTCGTATT-GCTGGTGTCGGTCATTGAC
1 TGCCAACCATTGACAGGCCAGCACCCAA-TTTTT-TTTTCGTATTAG-TGGTGACGGCCATTAAC
* * *
185518 AAGCTAGCACCCCCAATTTTTTTTTGTACTG
63 AGGCCAGCA--CCCAAATTTTTTTTGTACTG
185549 CTGGTACAGG
Statistics
Matches: 162, Mismatches: 22, Indels: 14
0.82 0.11 0.07
Matches are distributed among these distances:
94 15 0.09
95 63 0.39
96 1 0.01
98 28 0.17
99 9 0.06
100 31 0.19
101 1 0.01
102 14 0.09
ACGTcount: A:0.22, C:0.24, G:0.20, T:0.34
Consensus pattern (95 bp):
TGCCAACCATTGACAGGCCAGCACCCAATTTTTTTTTCGTATTAGTGGTGACGGCCATTAACAGG
CCAGCACCCAAATTTTTTTTGTACTGGTGA
Found at i:185486 original size:143 final size:141
Alignment explanation
Indices: 185171--185487 Score: 343
Period size: 143 Copynumber: 2.2 Consensus size: 141
185161 TTTGGTGTCA
* * * * * *
185171 GCCATTGACACGCCAGCACCAAATTTTTTTTTGTACTGTTGGTGCTAGCCATTGACAGGTTCGCA
1 GCCATTGACAAGCCAGCACCCAA-TTTTTTTTGTACTGGTGATGCCAGCCATTGACAGGTCCGCA
* * * *
185236 CCTAATTTTTTTTTTCGTATCCTAGTGCCAACTATTGACAGGCCAGCACCCAAATTTTTTTTTCG
65 CCCAATTTTTTTTTTCGTATACTAGTGCCAACCATTAACAGGCCAGCACCCAAATTTTTTTTTCG
*
185301 TATATTGGTGACG
130 -ATACTGGTGACG
* * *
185314 GCCATTGATAGGCCGGCACCCAAATTTTTTTTGTACTGGTGATGCCAGCCATTGACAGG-CCAGC
1 GCCATTGACAAGCCAGCACCC-AATTTTTTTTGTACTGGTGATGCCAGCCATTGACAGGTCC-GC
* * **
185378 ACCCAA-TTTTTTTTTCGTATTAGTGGTGCCGGCCATTAACAGGCCAGCACCCAAATTTTTTTTT
64 ACCCAATTTTTTTTTTCGTA-TACTAGTGCCAACCATTAACAGGCCAGCACCCAAA-TTTTTTTT
*
185442 TC-ATGCTGGTGGTACGG
127 TCGATACTGGT-G-AC-G
* *
185459 GTCATTAACAAGCCAGCACCCAATTTTTT
1 GCCATTGACAAGCCAGCACCCAATTTTTT
185488 ATTTTCGTAT
Statistics
Matches: 144, Mismatches: 23, Indels: 13
0.80 0.13 0.07
Matches are distributed among these distances:
142 20 0.14
143 85 0.59
144 22 0.15
145 17 0.12
ACGTcount: A:0.22, C:0.24, G:0.20, T:0.34
Consensus pattern (141 bp):
GCCATTGACAAGCCAGCACCCAATTTTTTTTGTACTGGTGATGCCAGCCATTGACAGGTCCGCAC
CCAATTTTTTTTTTCGTATACTAGTGCCAACCATTAACAGGCCAGCACCCAAATTTTTTTTTCGA
TACTGGTGACG
Found at i:185566 original size:49 final size:51
Alignment explanation
Indices: 185363--185577 Score: 157
Period size: 50 Copynumber: 4.4 Consensus size: 51
185353 TGATGCCAGC
* * * *
185363 CATTGACAGGCCAGCA--CCCAA-TTTTT-TTTTCGTATTAG-TGGTGCCGGC
1 CATTGACAAGCCAGCACCCCCAATTTTTTATTTTCGTACT-GCTGGT-ACGGT
* * * * * *
185411 CATTAACAGGCCAGCA-CCCAAATTTTTT-TTTTCATGCTGGTGGTACGGGT
1 CATTGACAAGCCAGCACCCCCAATTTTTTATTTTCGTACTGCTGGTAC-GGT
* * *
185461 CATTAACAAGCCAGCA--CCCAATTTTTTATTTTCGTATTGCTGGTGTCGGT
1 CATTGACAAGCCAGCACCCCCAATTTTTTATTTTCGTACTGCTGGT-ACGGT
*
185511 CATTGACAAGCTAGCACCCCCAA-TTTTT-TTTT-GTACTGCTGGTACAGGT
1 CATTGACAAGCCAGCACCCCCAATTTTTTATTTTCGTACTGCTGGTAC-GGT
* *
185560 TATTGACAGGCCAGCACC
1 CATTGACAAGCCAGCACC
185578 TAAAAGTTTT
Statistics
Matches: 137, Mismatches: 21, Indels: 17
0.78 0.12 0.10
Matches are distributed among these distances:
48 16 0.12
49 44 0.32
50 66 0.48
51 6 0.04
52 5 0.04
ACGTcount: A:0.22, C:0.24, G:0.20, T:0.33
Consensus pattern (51 bp):
CATTGACAAGCCAGCACCCCCAATTTTTTATTTTCGTACTGCTGGTACGGT
Found at i:186461 original size:19 final size:21
Alignment explanation
Indices: 186359--186455 Score: 153
Period size: 21 Copynumber: 4.7 Consensus size: 21
186349 ATTTTCGAGG
186359 ATATACAATCTTAGATATG--
1 ATATACAATCTTAGATATGAT
186378 ATATACAATCTTAGATATGAT
1 ATATACAATCTTAGATATGAT
**
186399 ATATGTAATCTTAGATATGAT
1 ATATACAATCTTAGATATGAT
*
186420 ATATGCAATCTTAGATATGAT
1 ATATACAATCTTAGATATGAT
186441 ATATACAATCTTAGA
1 ATATACAATCTTAGA
186456 AGATATGATT
Statistics
Matches: 72, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
19 19 0.26
21 53 0.74
ACGTcount: A:0.41, C:0.09, G:0.11, T:0.38
Consensus pattern (21 bp):
ATATACAATCTTAGATATGAT
Found at i:186605 original size:13 final size:13
Alignment explanation
Indices: 186584--186616 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
186574 TTCATTGTCG
186584 AAAAAAAAAGAA-
1 AAAAAAAAAGAAT
186596 AAAAAGAAAAGAAT
1 AAAAA-AAAAGAAT
186610 AAAAAAA
1 AAAAAAA
186617 GGGAGAACGA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
12 5 0.26
13 9 0.47
14 5 0.26
ACGTcount: A:0.88, C:0.00, G:0.09, T:0.03
Consensus pattern (13 bp):
AAAAAAAAAGAAT
Found at i:186693 original size:52 final size:53
Alignment explanation
Indices: 186586--186689 Score: 185
Period size: 51 Copynumber: 2.0 Consensus size: 53
186576 CATTGTCGAA
186586 AAAAAAAGAAAAAAAGAAAAGAATAAAAAAAGGGAGAACGATTGGCAGTTTTT
1 AAAAAAAGAAAAAAAGAAAAGAATAAAAAAAGGGAGAACGATTGGCAGTTTTT
*
186639 AAAAAAA-AAGAAAAG-AAAGAATAAAAAAAGGGAGAACGATTGGCAGTTTTT
1 AAAAAAAGAAAAAAAGAAAAGAATAAAAAAAGGGAGAACGATTGGCAGTTTTT
186690 TAAAGGTGGN
Statistics
Matches: 50, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
51 36 0.72
52 7 0.14
53 7 0.14
ACGTcount: A:0.60, C:0.04, G:0.21, T:0.15
Consensus pattern (53 bp):
AAAAAAAGAAAAAAAGAAAAGAATAAAAAAAGGGAGAACGATTGGCAGTTTTT
Found at i:191663 original size:190 final size:190
Alignment explanation
Indices: 191308--191688 Score: 566
Period size: 190 Copynumber: 2.0 Consensus size: 190
191298 AAACTAAGGT
191308 CATAAGAAATCATTACGGTATTTCTTTAGTGTATGAGATTAGTGGAAATTAGGCATATGTTTTCA
1 CATAAGAAATCATTACGGTATTTCTTTAGTGTATGAGATTAGTGGAAATTAGGCATATGTTTTCA
* * *
191373 AGTTGTTCTTACATGTAATTGAATTAATTATGAATGCAGAATAAAATTAAATAGGTTCTTGTAGC
66 AGTTGTTCTGACATGTAACTGAATTAATTATGAATGCAGAATAAAATTAAACAGGTTCTTGTAGC
* ** * * *
191438 ATCCAGTACTCTGACTCAGGGATAGAGTTGGGTATGGGGTGTTACAATTCCGCTTAGTAA
131 ATCCAGTACTCTGACCCAACGATAGAGTCGGGTATGGGGCGTTACAATTCCACTTAGTAA
* * *
191498 CATAAGAAATCATTACGGTCTTTCTTTAGTGTATGAGATTAGTGGCAATTAGGCCTATGTTTTCA
1 CATAAGAAATCATTACGGTATTTCTTTAGTGTATGAGATTAGTGGAAATTAGGCATATGTTTTCA
* * * *
191563 AGTTGTTCTGACATGTAACTGAATTAATTATGAATGTATAGTAAAATTAAACGGGTTCTTGTAGC
66 AGTTGTTCTGACATGTAACTGAATTAATTATGAATGCAGAATAAAATTAAACAGGTTCTTGTAGC
* * * *
191628 ATTCGGTAC-CTAGACCCAACGATTGGGTCGGGTATGGGGCGTTACAATTCCACTTAGTAA
131 ATCCAGTACTCT-GACCCAACGATAGAGTCGGGTATGGGGCGTTACAATTCCACTTAGTAA
191688 C
1 C
191689 CACAATATAA
Statistics
Matches: 170, Mismatches: 20, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
189 2 0.01
190 168 0.99
ACGTcount: A:0.30, C:0.13, G:0.22, T:0.35
Consensus pattern (190 bp):
CATAAGAAATCATTACGGTATTTCTTTAGTGTATGAGATTAGTGGAAATTAGGCATATGTTTTCA
AGTTGTTCTGACATGTAACTGAATTAATTATGAATGCAGAATAAAATTAAACAGGTTCTTGTAGC
ATCCAGTACTCTGACCCAACGATAGAGTCGGGTATGGGGCGTTACAATTCCACTTAGTAA
Found at i:194755 original size:3 final size:3
Alignment explanation
Indices: 194747--194771 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
194737 TGAAGTGAAA
194747 AAG AAG AAG AAG AAG AAG AAG AAG A
1 AAG AAG AAG AAG AAG AAG AAG AAG A
194772 GAAAACAACT
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:0.32, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:195276 original size:31 final size:30
Alignment explanation
Indices: 195241--195305 Score: 85
Period size: 30 Copynumber: 2.1 Consensus size: 30
195231 AACATCCAAA
*
195241 TGACTCAAACAAAAACTTTTAAATAGTTTAG
1 TGACTCAAA-AAAAACTTTTAAATAGTTCAG
* * *
195272 TGACTTAAAAACAACTTTTGAATAGTTCAG
1 TGACTCAAAAAAAACTTTTAAATAGTTCAG
195302 TGAC
1 TGAC
195306 CTTTTTGTAA
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
30 22 0.73
31 8 0.27
ACGTcount: A:0.42, C:0.14, G:0.12, T:0.32
Consensus pattern (30 bp):
TGACTCAAAAAAAACTTTTAAATAGTTCAG
Found at i:199340 original size:14 final size:15
Alignment explanation
Indices: 199300--199340 Score: 50
Period size: 14 Copynumber: 2.9 Consensus size: 15
199290 ACAAAACTAC
199300 TTCTC-TTTCTTTAT
1 TTCTCTTTTCTTTAT
* *
199314 TTTTCTATTCTTT-T
1 TTCTCTTTTCTTTAT
199328 TTCTCTTTTCTTT
1 TTCTCTTTTCTTT
199341 GTCAAATTAC
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
14 16 0.73
15 6 0.27
ACGTcount: A:0.05, C:0.20, G:0.00, T:0.76
Consensus pattern (15 bp):
TTCTCTTTTCTTTAT
Found at i:199939 original size:29 final size:31
Alignment explanation
Indices: 199862--199941 Score: 87
Period size: 29 Copynumber: 2.6 Consensus size: 31
199852 TTAAATATAA
199862 ATTGGTACTTGAACTTTTTCATTTCTCCTAG
1 ATTGGTACTTGAACTTTTTCATTTCTCCTAG
* * *
199893 ATTGGTA-TTTAAGGTTTTT--TTTGT-CTCAG
1 ATTGGTACTTGAA-CTTTTTCATTTCTCCT-AG
199922 ATTGGTACTTGAACTTTTTC
1 ATTGGTACTTGAACTTTTTC
199942 TCCGTCAACT
Statistics
Matches: 40, Mismatches: 5, Indels: 9
0.74 0.09 0.17
Matches are distributed among these distances:
28 2 0.05
29 18 0.45
30 8 0.20
31 12 0.30
ACGTcount: A:0.19, C:0.14, G:0.16, T:0.51
Consensus pattern (31 bp):
ATTGGTACTTGAACTTTTTCATTTCTCCTAG
Found at i:200581 original size:18 final size:18
Alignment explanation
Indices: 200558--200600 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
200548 CAAGGACACG
*
200558 ATCAATAGCGTCACTAGC
1 ATCAATAGCGTCACAAGC
* *
200576 ATCAATATCGTCACAATC
1 ATCAATAGCGTCACAAGC
200594 ATCAATA
1 ATCAATA
200601 CCGATATCAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.40, C:0.26, G:0.09, T:0.26
Consensus pattern (18 bp):
ATCAATAGCGTCACAAGC
Found at i:201162 original size:11 final size:11
Alignment explanation
Indices: 201132--201195 Score: 65
Period size: 11 Copynumber: 5.7 Consensus size: 11
201122 AAACTAATCC
201132 TCTCTCAATTAT
1 TCTCTCAATT-T
*
201144 TTTCTCAATTT
1 TCTCTCAATTT
*
201155 TCTCTCAAATT
1 TCTCTCAATTT
*
201166 GCTCTCAATTT
1 TCTCTCAATTT
* * *
201177 CCTTTCAAATT
1 TCTCTCAATTT
201188 TCTCTCAA
1 TCTCTCAA
201196 ATCCATATTT
Statistics
Matches: 42, Mismatches: 10, Indels: 1
0.79 0.19 0.02
Matches are distributed among these distances:
11 33 0.79
12 9 0.21
ACGTcount: A:0.23, C:0.27, G:0.02, T:0.48
Consensus pattern (11 bp):
TCTCTCAATTT
Found at i:201174 original size:22 final size:22
Alignment explanation
Indices: 201146--201195 Score: 73
Period size: 22 Copynumber: 2.3 Consensus size: 22
201136 TCAATTATTT
*
201146 TCTCAATTTTCTCTCAAATTGC
1 TCTCAATTTCCTCTCAAATTGC
* *
201168 TCTCAATTTCCTTTCAAATTTC
1 TCTCAATTTCCTCTCAAATTGC
201190 TCTCAA
1 TCTCAA
201196 ATCCATATTT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.24, C:0.28, G:0.02, T:0.46
Consensus pattern (22 bp):
TCTCAATTTCCTCTCAAATTGC
Found at i:203076 original size:17 final size:19
Alignment explanation
Indices: 203044--203086 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 19
203034 TGCCAGGTGC
*
203044 GTATCCTAGCCCCTTA-AT
1 GTATCCTAGACCCTTATAT
203062 GTATCCTA-ACCCTTATAT
1 GTATCCTAGACCCTTATAT
*
203080 GTTTCCT
1 GTATCCT
203087 TTTTCGAGTC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
17 6 0.27
18 16 0.73
ACGTcount: A:0.21, C:0.30, G:0.09, T:0.40
Consensus pattern (19 bp):
GTATCCTAGACCCTTATAT
Found at i:203640 original size:22 final size:22
Alignment explanation
Indices: 203612--203676 Score: 123
Period size: 21 Copynumber: 3.0 Consensus size: 22
203602 NNNNNNNNNN
203612 CCTTAACTTAAAAACCCTAAAC
1 CCTTAACTTAAAAACCCTAAAC
203634 CCTTAACTTAAAAACCCT-AAC
1 CCTTAACTTAAAAACCCTAAAC
203655 CCTTAACTTAAAAACCCTAAAC
1 CCTTAACTTAAAAACCCTAAAC
203677 TAATTTATTA
Statistics
Matches: 42, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
21 21 0.50
22 21 0.50
ACGTcount: A:0.45, C:0.32, G:0.00, T:0.23
Consensus pattern (22 bp):
CCTTAACTTAAAAACCCTAAAC
Found at i:204857 original size:123 final size:124
Alignment explanation
Indices: 204640--205070 Score: 664
Period size: 123 Copynumber: 3.5 Consensus size: 124
204630 CAAACATGCT
* * * * *
204640 ACTGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTCATAAATTCTTCTGATAAAGCATCCTACTT
1 ACTGTAGCAAAAACGCGTCCACGTGGGAGCGATTTCAGAAATTCTTCTGATAAAGCATCCTGCTT
*
204705 GAAGCTTTTTTATACTATTCGCTCAGAAACGTCAACTCGAAATTA-TTTTTCAGGACCT
66 GAAGCTTTTTTATACTATTCGCTCAGAAACGTCAACTCGAAATTATTTTTTCAGGACCA
*
204763 ACTGTAGCAAAAACCCGTCCACGTGGGAGCGATTTCAGAAATTCTTCTGATAAAGCATCCTGCTT
1 ACTGTAGCAAAAACGCGTCCACGTGGGAGCGATTTCAGAAATTCTTCTGATAAAGCATCCTGCTT
*
204828 GAAGCGTTTTTATACTATTCGCTCAGAAACGTCAACTCGAAATTATTTTTTCAGGACCA
66 GAAGCTTTTTTATACTATTCGCTCAGAAACGTCAACTCGAAATTATTTTTTCAGGACCA
* *
204887 ACTGTAGCAAAAGCGCGTCCACGT-AG-GCG----C-GAAATTCTTCTGATAAAGCATCCTGCTT
1 ACTGTAGCAAAAACGCGTCCACGTGGGAGCGATTTCAGAAATTCTTCTGATAAAGCATCCTGCTT
204945 GAAGCATTTTTTATACTATTCGCTCAGAAACGTCAACTCGAAATTATTTTTTTCAGGACCA
66 GAAGC-TTTTTTATACTATTCGCTCAGAAACGTCAACTCGAAATTA-TTTTTTCAGGACCA
* *
205006 ACTATAGCAAAAACGCGTCCACGTGGGCA-CGATTTCAGAAATTCTTTTGATAAAGCATCCTGCT
1 ACTGTAGCAAAAACGCGTCCACGTGGG-AGCGATTTCAGAAATTCTTCTGATAAAGCATCCTGCT
205070 T
65 T
205071 TGATTTTATC
Statistics
Matches: 281, Mismatches: 16, Indels: 19
0.89 0.05 0.06
Matches are distributed among these distances:
117 33 0.12
118 40 0.14
119 36 0.13
120 1 0.00
121 2 0.01
122 3 0.01
123 104 0.37
124 34 0.12
125 1 0.00
126 27 0.10
ACGTcount: A:0.30, C:0.23, G:0.18, T:0.30
Consensus pattern (124 bp):
ACTGTAGCAAAAACGCGTCCACGTGGGAGCGATTTCAGAAATTCTTCTGATAAAGCATCCTGCTT
GAAGCTTTTTTATACTATTCGCTCAGAAACGTCAACTCGAAATTATTTTTTCAGGACCA
Found at i:205491 original size:28 final size:28
Alignment explanation
Indices: 205427--205491 Score: 69
Period size: 29 Copynumber: 2.3 Consensus size: 28
205417 ATTTTCAGGT
205427 AAAAGGGCCCATTCCGGTAAATAATAAA
1 AAAAGGGCCCATTCCGGTAAATAATAAA
** * *
205455 ATACCGGGCCCATTTCGGTAAAT-TTAAA
1 A-AAAGGGCCCATTCCGGTAAATAATAAA
205483 AAAATGGGC
1 AAAA-GGGC
205492 TTTTTTTGGT
Statistics
Matches: 29, Mismatches: 6, Indels: 4
0.74 0.15 0.10
Matches are distributed among these distances:
27 1 0.03
28 10 0.34
29 18 0.62
ACGTcount: A:0.40, C:0.18, G:0.20, T:0.22
Consensus pattern (28 bp):
AAAAGGGCCCATTCCGGTAAATAATAAA
Found at i:206828 original size:11 final size:11
Alignment explanation
Indices: 206812--206846 Score: 70
Period size: 11 Copynumber: 3.2 Consensus size: 11
206802 ATCTGAAAAG
206812 AAAATATCTAA
1 AAAATATCTAA
206823 AAAATATCTAA
1 AAAATATCTAA
206834 AAAATATCTAA
1 AAAATATCTAA
206845 AA
1 AA
206847 TTTTAAAATG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 24 1.00
ACGTcount: A:0.66, C:0.09, G:0.00, T:0.26
Consensus pattern (11 bp):
AAAATATCTAA
Found at i:206903 original size:8 final size:8
Alignment explanation
Indices: 206892--206934 Score: 50
Period size: 8 Copynumber: 5.1 Consensus size: 8
206882 TATATGTAAC
206892 TAAAAAAA
1 TAAAAAAA
206900 TAAAAAAA
1 TAAAAAAA
*
206908 TATTACAAAA
1 TA--AAAAAA
*
206918 TAAAAATA
1 TAAAAAAA
206926 TAAAAAAA
1 TAAAAAAA
206934 T
1 T
206935 TCAAGTTAGA
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
8 22 0.76
10 7 0.24
ACGTcount: A:0.77, C:0.02, G:0.00, T:0.21
Consensus pattern (8 bp):
TAAAAAAA
Found at i:207459 original size:6 final size:6
Alignment explanation
Indices: 207448--207474 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
207438 TTTTGAGTAA
207448 AAAATG AAAATG AAAATG AAAATG AAA
1 AAAATG AAAATG AAAATG AAAATG AAA
207475 TTGTATTTAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.70, C:0.00, G:0.15, T:0.15
Consensus pattern (6 bp):
AAAATG
Found at i:209093 original size:15 final size:14
Alignment explanation
Indices: 209072--209107 Score: 54
Period size: 15 Copynumber: 2.5 Consensus size: 14
209062 ATAATCTTTA
*
209072 ATAATTATCTTAAT
1 ATAATTATCCTAAT
209086 ATTAATTATCCTAAT
1 A-TAATTATCCTAAT
209101 ATAATTA
1 ATAATTA
209108 AAATAGAGTC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
14 7 0.35
15 13 0.65
ACGTcount: A:0.44, C:0.08, G:0.00, T:0.47
Consensus pattern (14 bp):
ATAATTATCCTAAT
Found at i:209669 original size:8 final size:8
Alignment explanation
Indices: 209656--209698 Score: 54
Period size: 8 Copynumber: 5.5 Consensus size: 8
209646 AGTCCCCAAA
209656 TTATTTTT
1 TTATTTTT
209664 TTA--TTT
1 TTATTTTT
209670 TTATTTTT
1 TTATTTTT
209678 TTATTATTT
1 TTATT-TTT
*
209687 ATATTTTT
1 TTATTTTT
209695 TTAT
1 TTAT
209699 CCTTTAGGAA
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
6 6 0.20
8 17 0.57
9 7 0.23
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (8 bp):
TTATTTTT
Found at i:209675 original size:14 final size:15
Alignment explanation
Indices: 209656--209695 Score: 64
Period size: 14 Copynumber: 2.7 Consensus size: 15
209646 AGTCCCCAAA
209656 TTATTTTTTTATT-T
1 TTATTTTTTTATTAT
209670 TTATTTTTTTATTAT
1 TTATTTTTTTATTAT
209685 TTATATTTTTT
1 TTAT-TTTTTT
209696 TATCCTTTAG
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
14 13 0.54
15 5 0.21
16 6 0.25
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.82
Consensus pattern (15 bp):
TTATTTTTTTATTAT
Found at i:209684 original size:17 final size:17
Alignment explanation
Indices: 209659--209698 Score: 64
Period size: 17 Copynumber: 2.4 Consensus size: 17
209649 CCCCAAATTA
*
209659 TTTTT-TTATTTTTATT
1 TTTTTATTATTTATATT
209675 TTTTTATTATTTATATT
1 TTTTTATTATTTATATT
209692 TTTTTAT
1 TTTTTAT
209699 CCTTTAGGAA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
16 5 0.23
17 17 0.77
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.82
Consensus pattern (17 bp):
TTTTTATTATTTATATT
Found at i:210735 original size:12 final size:12
Alignment explanation
Indices: 210710--210786 Score: 61
Period size: 12 Copynumber: 6.2 Consensus size: 12
210700 ATTAATATCC
*
210710 AAATAAGTAAT-
1 AAATAAATAATA
*
210721 AAATAATAAAATA
1 AAATAA-ATAATA
210734 AAATAAAGTAAT-
1 AAATAAA-TAATA
*
210746 AAATAAAGTAAAGA
1 AAATAAA-T-AATA
210760 AAATAAATAA-A
1 AAATAAATAATA
210771 TAAATAAATAATA
1 -AAATAAATAATA
210784 AAA
1 AAA
210787 ATTGGGTTGC
Statistics
Matches: 55, Mismatches: 4, Indels: 13
0.76 0.06 0.18
Matches are distributed among these distances:
11 7 0.13
12 28 0.51
13 13 0.24
14 7 0.13
ACGTcount: A:0.73, C:0.00, G:0.05, T:0.22
Consensus pattern (12 bp):
AAATAAATAATA
Found at i:210752 original size:4 final size:4
Alignment explanation
Indices: 210718--210785 Score: 61
Period size: 4 Copynumber: 16.5 Consensus size: 4
210708 CCAAATAAGT
*
210718 AATA AAT- AATAA AATAA AATA AAGT- AATA AATA AAGTA AAGAA AATA
1 AATA AATA AAT-A AAT-A AATA AA-TA AATA AATA AA-TA AA-TA AATA
210765 AATA AATA AATA AAT- AATA AA
1 AATA AATA AATA AATA AATA AA
210786 AATTGGGTTG
Statistics
Matches: 56, Mismatches: 2, Indels: 12
0.80 0.03 0.17
Matches are distributed among these distances:
3 7 0.12
4 32 0.57
5 17 0.30
ACGTcount: A:0.74, C:0.00, G:0.04, T:0.22
Consensus pattern (4 bp):
AATA
Found at i:210757 original size:22 final size:21
Alignment explanation
Indices: 210719--210778 Score: 63
Period size: 22 Copynumber: 2.8 Consensus size: 21
210709 CAAATAAGTA
210719 ATAAAT-AATAAAATAAA-ATAA
1 ATAAATAAAT-AAATAAAGA-AA
210740 AGT-AATAAATAAAGTAAAGAAA
1 A-TAAATAAATAAA-TAAAGAAA
210762 ATAAATAAATAAATAAA
1 ATAAATAAATAAATAAA
210779 TAATAAAAAT
Statistics
Matches: 34, Mismatches: 0, Indels: 10
0.77 0.00 0.23
Matches are distributed among these distances:
21 12 0.35
22 21 0.62
23 1 0.03
ACGTcount: A:0.73, C:0.00, G:0.05, T:0.22
Consensus pattern (21 bp):
ATAAATAAATAAATAAAGAAA
Found at i:211911 original size:121 final size:121
Alignment explanation
Indices: 211697--211938 Score: 396
Period size: 121 Copynumber: 2.0 Consensus size: 121
211687 CACATAGCCC
211697 TCTTAATTCCCAGATGGCCTATTTTGCATGGTATTGCAAACATGCCCTTATCCTTGCATTTTGCC
1 TCTTAATTCCCAGATGGCCTATTTTGCATGGTATTGCAAACATGCCCTTATCCTTGCATTTTGCC
**
211762 AACATTTTCCGCTGTAACACTGCAGATACATTCTCACCAACATTCACCCTTTCATT
66 AACATTTTCCGCAATAACACTGCAGATACATTCTCACCAACATTCACCCTTTCATT
* *
211818 TCTTAATTGCCAGATGGCCTATTTTGCATGGTATTGCAAACATGCTCC-TATCCTTTCATTTTGC
1 TCTTAATTCCCAGATGGCCTATTTTGCATGGTATTGCAAACATGC-CCTTATCCTTGCATTTTGC
*** *
211882 TGGCATTTTCCGCAATAACACTGCGGATACATTCTCACCAACATTCACCCTTTCATT
65 CAACATTTTCCGCAATAACACTGCAGATACATTCTCACCAACATTCACCCTTTCATT
211939 ATCTGTTAAT
Statistics
Matches: 112, Mismatches: 8, Indels: 2
0.92 0.07 0.02
Matches are distributed among these distances:
121 110 0.98
122 2 0.02
ACGTcount: A:0.24, C:0.28, G:0.12, T:0.36
Consensus pattern (121 bp):
TCTTAATTCCCAGATGGCCTATTTTGCATGGTATTGCAAACATGCCCTTATCCTTGCATTTTGCC
AACATTTTCCGCAATAACACTGCAGATACATTCTCACCAACATTCACCCTTTCATT
Found at i:216145 original size:12 final size:12
Alignment explanation
Indices: 216113--216137 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
216103 TTATTTGACT
216113 ATTATTATTATC
1 ATTATTATTATC
216125 ATTATTATTATC
1 ATTATTATTATC
216137 A
1 A
216138 GTTTTATTTT
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:0.36, C:0.08, G:0.00, T:0.56
Consensus pattern (12 bp):
ATTATTATTATC
Done.