Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000426.1 Hibiscus syriacus cultivar Beakdansim tig00000778_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 3165331
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 7 of 15
Found at i:1393160 original size:19 final size:19
Alignment explanation
Indices: 1393079--1393162 Score: 70
Period size: 19 Copynumber: 4.7 Consensus size: 19
1393069 GAAATGAAAA
* *
1393079 TCGCAATGCGATTTTGGTT
1 TCGCATTGCGATTTTCGTT
* *
1393098 TCGCGTTGCGATTTTGGTT
1 TCGCATTGCGATTTTCGTT
* *
1393117 TCGCGTTGCGA--TTC-TG
1 TCGCATTGCGATTTTCGTT
*
1393133 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCGTT
1393150 TCGCATTGCGATT
1 TCGCATTGCGATT
1393163 CTCTCGTTGC
Statistics
Matches: 55, Mismatches: 5, Indels: 10
0.79 0.07 0.14
Matches are distributed among these distances:
14 6 0.11
16 7 0.13
17 6 0.11
19 36 0.65
ACGTcount: A:0.11, C:0.19, G:0.26, T:0.44
Consensus pattern (19 bp):
TCGCATTGCGATTTTCGTT
Found at i:1393451 original size:93 final size:93
Alignment explanation
Indices: 1393292--1393607 Score: 623
Period size: 93 Copynumber: 3.4 Consensus size: 93
1393282 TCAGGGTATT
1393292 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
1 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
1393357 TACTATTTCACAGTGTTAAAGAATACAC
66 TACTATTTCACAGTGTTAAAGAATACAC
1393385 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
1 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
1393450 TACTATTTCACAGTGTTAAAGAATACAC
66 TACTATTTCACAGTGTTAAAGAATACAC
1393478 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
1 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
1393543 TACTATTTCACAGTGTTAAAGAATACAC
66 TACTATTTCACAGTGTTAAAGAATACAC
*
1393571 AGTTTAGCAGAATTGGCAGCAACCGAATAAATTTACT
1 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACT
1393608 AAGCAATCTA
Statistics
Matches: 222, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
93 222 1.00
ACGTcount: A:0.45, C:0.19, G:0.14, T:0.22
Consensus pattern (93 bp):
AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
TACTATTTCACAGTGTTAAAGAATACAC
Found at i:1395325 original size:20 final size:20
Alignment explanation
Indices: 1395294--1395390 Score: 100
Period size: 20 Copynumber: 5.2 Consensus size: 20
1395284 TTTTGGTTGA
1395294 AATGAAAATCGCAACGAGAG
1 AATGAAAATCGCAACGAGAG
***
1395314 AATGACTGTCGCAACGAGAG
1 AATGAAAATCGCAACGAGAG
1395334 AAATGAAAATCGCAAC--GAG
1 -AATGAAAATCGCAACGAGAG
*
1395353 -A-G--AATCGCAACGCGA-
1 AATGAAAATCGCAACGAGAG
1395368 AATGAAAATCGCAACGAGAG
1 AATGAAAATCGCAACGAGAG
1395388 AAT
1 AAT
1395391 CGCAATGCGA
Statistics
Matches: 62, Mismatches: 7, Indels: 16
0.73 0.08 0.19
Matches are distributed among these distances:
14 9 0.15
16 4 0.06
17 2 0.03
19 15 0.24
20 20 0.32
21 12 0.19
ACGTcount: A:0.46, C:0.18, G:0.25, T:0.11
Consensus pattern (20 bp):
AATGAAAATCGCAACGAGAG
Found at i:1395346 original size:21 final size:21
Alignment explanation
Indices: 1395292--1395356 Score: 96
Period size: 21 Copynumber: 3.1 Consensus size: 21
1395282 TCTTTTGGTT
1395292 GAAATGAAAATCGCAACGAGA
1 GAAATGAAAATCGCAACGAGA
***
1395313 G-AATGACTGTCGCAACGAGA
1 GAAATGAAAATCGCAACGAGA
1395333 GAAATGAAAATCGCAACGAGA
1 GAAATGAAAATCGCAACGAGA
1395354 GAA
1 GAA
1395357 TCGCAACGCG
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
20 17 0.46
21 20 0.54
ACGTcount: A:0.48, C:0.15, G:0.26, T:0.11
Consensus pattern (21 bp):
GAAATGAAAATCGCAACGAGA
Found at i:1395360 original size:14 final size:14
Alignment explanation
Indices: 1395341--1395395 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
1395331 GAGAAATGAA
1395341 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
1395355 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
1395374 AATCGCAACGAGAG
1 AATCGCAACGAGAG
1395388 AATCGCAA
1 AATCGCAA
1395396 TGCGATTTTG
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
14 18 0.53
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.29
ACGTcount: A:0.45, C:0.22, G:0.24, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:1395373 original size:33 final size:33
Alignment explanation
Indices: 1395292--1395400 Score: 128
Period size: 33 Copynumber: 3.1 Consensus size: 33
1395282 TCTTTTGGTT
*
1395292 GAAATGAAAATCGCAACGAGAGAATGACTGTCGCAACGAGA
1 GAAATGAAAATCGCAACGAGAG-A--A---TCGCAAC--GC
1395333 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
*
1395366 GAAATGAAAATCGCAACGAGAGAATCGCAATGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1395399 GA
1 GA
1395401 TTTTGGTTTC
Statistics
Matches: 66, Mismatches: 2, Indels: 8
0.87 0.03 0.11
Matches are distributed among these distances:
33 35 0.53
35 7 0.11
38 1 0.02
40 1 0.02
41 22 0.33
ACGTcount: A:0.45, C:0.18, G:0.26, T:0.11
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:1395448 original size:21 final size:21
Alignment explanation
Indices: 1395423--1395496 Score: 96
Period size: 21 Copynumber: 3.5 Consensus size: 21
1395413 GTTGCGATTC
1395423 TCTCGTTGCGATTTTCATTTT
1 TCTCGTTGCGATTTTCATTTT
**
1395444 TCTCGTTGCAGATAGTCA-TTT
1 TCTCGTTGC-GATTTTCATTTT
* *
1395465 TCACGTTGCGATTTTCATTTA
1 TCTCGTTGCGATTTTCATTTT
1395486 TCTCGTTGCGA
1 TCTCGTTGCGA
1395497 CTCTTCTACA
Statistics
Matches: 44, Mismatches: 7, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
20 6 0.14
21 32 0.73
22 6 0.14
ACGTcount: A:0.15, C:0.20, G:0.18, T:0.47
Consensus pattern (21 bp):
TCTCGTTGCGATTTTCATTTT
Found at i:1395618 original size:33 final size:33
Alignment explanation
Indices: 1395576--1395646 Score: 124
Period size: 33 Copynumber: 2.2 Consensus size: 33
1395566 AATACTAACT
1395576 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
1 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
* *
1395609 TGAAAATCGCAACGAGAGAATTGTAACGCGAAA
1 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
1395642 TGAAA
1 TGAAA
1395647 TCTAAGTGAA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.48, C:0.15, G:0.24, T:0.13
Consensus pattern (33 bp):
TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
Found at i:1396051 original size:20 final size:20
Alignment explanation
Indices: 1396026--1396238 Score: 286
Period size: 20 Copynumber: 10.6 Consensus size: 20
1396016 CTTTAAAAAT
1396026 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
1396046 CGCGTTGCGATTTTACGTAT-
1 CGCGTTGCGA-TTTACGGATA
*
1396066 TGTCGTTGCGATTTACGGATA
1 CG-CGTTGCGATTTACGGATA
*
1396087 CGCGTTGCGATATACGGATA
1 CGCGTTGCGATTTACGGATA
*
1396107 CGCATTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
1396127 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
1396147 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
1396167 CACGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
1396187 CGCGTTGCGATTTATGTG-TT
1 CGCGTTGCGATTTACG-GATA
* ** *
1396207 CGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATA
1396227 CGCGTTGCGATT
1 CGCGTTGCGATT
1396239 CTGGAAAATC
Statistics
Matches: 172, Mismatches: 16, Indels: 10
0.87 0.08 0.05
Matches are distributed among these distances:
20 154 0.90
21 18 0.10
ACGTcount: A:0.19, C:0.19, G:0.28, T:0.34
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:1400365 original size:30 final size:29
Alignment explanation
Indices: 1400303--1400365 Score: 76
Period size: 30 Copynumber: 2.1 Consensus size: 29
1400293 CCCTAAATTA
*
1400303 AAAACCCTAGAAATTGGGAATTTTTCAGT
1 AAAACCCTAGAAATTGGGAATTTTACAGT
1400332 AAAACCCTA-AAATTTTGGGAATTTTGACA-T
1 AAAACCCTAGAAA--TTGGGAATTTT-ACAGT
1400362 AAAA
1 AAAA
1400366 TTTTAATTCG
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
28 3 0.10
29 9 0.30
30 16 0.53
31 2 0.07
ACGTcount: A:0.43, C:0.13, G:0.14, T:0.30
Consensus pattern (29 bp):
AAAACCCTAGAAATTGGGAATTTTACAGT
Found at i:1403369 original size:22 final size:22
Alignment explanation
Indices: 1403299--1403379 Score: 85
Period size: 23 Copynumber: 3.7 Consensus size: 22
1403289 CAGAACCCAT
*
1403299 GGGGGTATCGATT-CCC-TCAA
1 GGGGGAATCGATTCCCCTTCAA
* *
1403319 GGAGGGAATCGGTTCCCATTCAAA
1 GG-GGGAATCGATTCCCCTTC-AA
*
1403343 GGGGGAATCGGTTCCCCTTCAA
1 GGGGGAATCGATTCCCCTTCAA
*
1403365 GGGGGTATCGATTCC
1 GGGGGAATCGATTCC
1403380 ATCTGCACTA
Statistics
Matches: 51, Mismatches: 6, Indels: 6
0.81 0.10 0.10
Matches are distributed among these distances:
20 2 0.04
21 9 0.18
22 17 0.33
23 19 0.37
24 4 0.08
ACGTcount: A:0.21, C:0.23, G:0.32, T:0.23
Consensus pattern (22 bp):
GGGGGAATCGATTCCCCTTCAA
Found at i:1409000 original size:2 final size:2
Alignment explanation
Indices: 1408993--1409051 Score: 118
Period size: 2 Copynumber: 29.5 Consensus size: 2
1408983 AGTTGTCCAT
1408993 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1409035 TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA T
1409052 GTGTGTGTGT
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 57 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1409078 original size:12 final size:12
Alignment explanation
Indices: 1409045--1409087 Score: 59
Period size: 12 Copynumber: 3.6 Consensus size: 12
1409035 TATATATATA
1409045 TATATATGTGTG
1 TATATATGTGTG
* * *
1409057 TGTGTGTGTGTG
1 TATATATGTGTG
1409069 TATATATGTGTG
1 TATATATGTGTG
1409081 TATATAT
1 TATATAT
1409088 ATATATATAT
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.21, C:0.00, G:0.28, T:0.51
Consensus pattern (12 bp):
TATATATGTGTG
Found at i:1410553 original size:21 final size:20
Alignment explanation
Indices: 1410527--1410571 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
1410517 GTCATATCTC
1410527 CAAAATAAAAGTATTTTTACA
1 CAAAAT-AAAGTATTTTTACA
** *
1410548 CAAAATTGATTATTTTTACA
1 CAAAATAAAGTATTTTTACA
1410568 CAAA
1 CAAA
1410572 TATCTATAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
20 15 0.71
21 6 0.29
ACGTcount: A:0.49, C:0.11, G:0.04, T:0.36
Consensus pattern (20 bp):
CAAAATAAAGTATTTTTACA
Found at i:1421938 original size:46 final size:43
Alignment explanation
Indices: 1421885--1421989 Score: 122
Period size: 44 Copynumber: 2.4 Consensus size: 43
1421875 TCATTCAAAA
* * *
1421885 AATTATTAATTTACTAATAGATAATAAAAATAATAATAAATTACT
1 AATTATTATTTTACTAATAAATAAT-AAAA-AATAATAAATTAAT
* *
1421930 AATCTATTAGTTTTA-TAATAAATAATTAAAAATACTAAATTAAT
1 AAT-TATTA-TTTTACTAATAAATAATAAAAAATAATAAATTAAT
1421974 AATTATTATTTTACTA
1 AATTATTATTTTACTA
1421990 TCGTGGAAAG
Statistics
Matches: 52, Mismatches: 5, Indels: 8
0.80 0.08 0.12
Matches are distributed among these distances:
42 5 0.10
43 7 0.13
44 15 0.29
45 6 0.12
46 15 0.29
47 4 0.08
ACGTcount: A:0.51, C:0.05, G:0.02, T:0.42
Consensus pattern (43 bp):
AATTATTATTTTACTAATAAATAATAAAAAATAATAAATTAAT
Found at i:1430724 original size:21 final size:21
Alignment explanation
Indices: 1430683--1430721 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
1430673 TTCATCAAAT
1430683 ATATATTATTTTATTATTTAA
1 ATATATTATTTTATTATTTAA
*
1430704 ATATATTA-TGTATTATTT
1 ATATATTATTTTATTATTT
1430722 TAATTTTAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.36, C:0.00, G:0.03, T:0.62
Consensus pattern (21 bp):
ATATATTATTTTATTATTTAA
Found at i:1430737 original size:28 final size:28
Alignment explanation
Indices: 1430686--1430739 Score: 74
Period size: 28 Copynumber: 1.9 Consensus size: 28
1430676 ATCAAATATA
*
1430686 TATTATTTTATTATTTAAATATATTATG
1 TATTATTTTAATATTTAAATATATTATG
*
1430714 TATTATTTTAAT-TTTAATTAATATTA
1 TATTATTTTAATATTTAAAT-ATATTA
1430740 AATTTTACAC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
27 6 0.26
28 17 0.74
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (28 bp):
TATTATTTTAATATTTAAATATATTATG
Found at i:1430796 original size:35 final size:31
Alignment explanation
Indices: 1430734--1430796 Score: 81
Period size: 32 Copynumber: 1.9 Consensus size: 31
1430724 ATTTTAATTA
*
1430734 ATATTAAATTTTACACAATTTATCTAAACAT
1 ATATTAAATTTTACACAATTTAACTAAACAT
1430765 ATATTAAAATTTTACATCAACATTTAACTAAA
1 ATATT-AAATTTTACA-C-A-ATTTAACTAAA
1430797 TAAGCATATG
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
31 5 0.19
32 10 0.37
33 1 0.04
34 1 0.04
35 10 0.37
ACGTcount: A:0.48, C:0.13, G:0.00, T:0.40
Consensus pattern (31 bp):
ATATTAAATTTTACACAATTTAACTAAACAT
Found at i:1430849 original size:21 final size:21
Alignment explanation
Indices: 1430823--1430862 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
1430813 GTAATAAATG
1430823 AACCATTTTACTCCTACCATA
1 AACCATTTTACTCCTACCATA
1430844 AACCATTTTACTCCTACCA
1 AACCATTTTACTCCTACCA
1430863 AAATGTACAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.33, C:0.35, G:0.00, T:0.33
Consensus pattern (21 bp):
AACCATTTTACTCCTACCATA
Found at i:1430926 original size:22 final size:20
Alignment explanation
Indices: 1430899--1430953 Score: 56
Period size: 22 Copynumber: 2.5 Consensus size: 20
1430889 TATTTTTAAT
1430899 TTATTAATTATAAAATATATTA
1 TTATTAATTATAAAAT-TA-TA
*
1430921 TTATTAGTATTAAAAAATTATA
1 TTATTA--ATTATAAAATTATA
*
1430943 TTTTTAATTAT
1 TTATTAATTAT
1430954 TAGTATTAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
20 4 0.14
22 13 0.46
23 2 0.07
24 9 0.32
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (20 bp):
TTATTAATTATAAAATTATA
Found at i:1431544 original size:21 final size:23
Alignment explanation
Indices: 1431500--1431544 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
1431490 CTAATTCAAT
*
1431500 AATGTGAACTAATTCAATCAACA
1 AATGTGAACTAATCCAATCAACA
1431523 AATGTGAA-TAATCCAA-CAACA
1 AATGTGAACTAATCCAATCAACA
1431544 A
1 A
1431545 GCAAAGGGAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 6 0.29
22 7 0.33
23 8 0.38
ACGTcount: A:0.51, C:0.18, G:0.09, T:0.22
Consensus pattern (23 bp):
AATGTGAACTAATCCAATCAACA
Found at i:1434341 original size:73 final size:73
Alignment explanation
Indices: 1434156--1434665 Score: 577
Period size: 74 Copynumber: 6.9 Consensus size: 73
1434146 TCGGAGGACT
* * * *
1434156 TAATCATCAAGAAACCTTTGAAGATAAAAATTGGCTTCTTTTAAGAAATTCATTTG-AAA-AT-A
1 TAATCTTCAAGAAACCTTTGAAAATCAAACTTGGCTTC-TTTAA-AAATTCATTTGAAAACATCA
*
1434218 TATCAGTCGAGG
64 TATCGGT-GA-G
* * * * * * *
1434230 TACTCATCAATAGACCTTTGAAAATTAAACTTGACTTCTTTAAAAATTCATTTGGAAACATCATA
1 TAATCTTCAAGAAACCTTTGAAAATCAAACTTGGCTTCTTTAAAAATTCATTTGAAAACATCATA
*
1434295 TCAGCTGAG
66 TC-GGTGAG
* * ** *
1434304 TATTCTTCATGAAACCTTAAAAAAT-AAACTTGGCTTCTTTAAAAATTAATTTGAAAACATCATA
1 TAATCTTCAAGAAACCTTTGAAAATCAAACTTGGCTTCTTTAAAAATTCATTTGAAAACATCATA
*
1434368 TCGGTTGGG
66 TCGG-TGAG
*
1434377 TAATCTTCAAGAAACCTTTGAAAATCAAATTTGGCTTCTTTAAAAATTCATTTGAAAACATCATA
1 TAATCTTCAAGAAACCTTTGAAAATCAAACTTGGCTTCTTTAAAAATTCATTTGAAAACATCATA
1434442 TCGGTTG-G
66 TCGG-TGAG
* *
1434450 ATAATCTTTAAG-AACCTTTGAAAATCAAACTTGACTTCTTTAAAAATTCATTTGAAAACATCAT
1 -TAATCTTCAAGAAACCTTTGAAAATCAAACTTGGCTTCTTTAAAAATTCATTTGAAAACATCAT
*
1434514 ATCTGTCG-G
65 ATCGGT-GAG
* * *
1434523 TAATCTTCAAGAAACCTTTTGAAAATCAAACTTGGATTCTTTAATAATTCATTTGAAAACATTAT
1 TAATCTTCAAGAAACC-TTTGAAAATCAAACTTGGCTTCTTTAAAAATTCATTTGAAAACATCAT
*
1434588 ATGGGTCCGA-
65 ATCGGT--GAG
* * * *
1434598 TACTCATCAAGAAACCTTTGAAAATCAAACTTGGCTTCTTAAAAAATTCATTTGAAAATATCATA
1 TAATCTTCAAGAAACCTTTGAAAATCAAACTTGGCTTCTTTAAAAATTCATTTGAAAACATCATA
1434663 TCG
66 TCG
1434666 ATTGGTAACA
Statistics
Matches: 378, Mismatches: 46, Indels: 24
0.84 0.10 0.05
Matches are distributed among these distances:
72 23 0.06
73 131 0.35
74 200 0.53
75 23 0.06
76 1 0.00
ACGTcount: A:0.39, C:0.15, G:0.12, T:0.35
Consensus pattern (73 bp):
TAATCTTCAAGAAACCTTTGAAAATCAAACTTGGCTTCTTTAAAAATTCATTTGAAAACATCATA
TCGGTGAG
Found at i:1434396 original size:147 final size:148
Alignment explanation
Indices: 1434156--1434670 Score: 598
Period size: 147 Copynumber: 3.5 Consensus size: 148
1434146 TCGGAGGACT
* * * *
1434156 TAATCATCAAGAAACCTTTGAAGATAAAAATTGGCTTCTTTTAAGAAATTCATTTG-AAA-AT-A
1 TAATCTTCAAGAAACCTTTGAAAATCAAACTTGGCTTC-TTTAA-AAATTCATTTGAAAACATCA
* * * * * * *
1434218 TATCAGTCGAGGTACTCATCAATAGACCTTTGAAAATTAAACTTGACTTCTTTAAAAATTCATTT
64 TATCGGTTG-GGTAATCTTCAAGAAACCTTTGAAAATCAAACTTGACTTCTTTAAAAATTCATTT
* *
1434283 GGAAACATCATATCAGCTGAG
128 GAAAACATCATATCGGCTGAG
* * ** *
1434304 TATTCTTCATGAAACCTTAAAAAAT-AAACTTGGCTTCTTTAAAAATTAATTTGAAAACATCATA
1 TAATCTTCAAGAAACCTTTGAAAATCAAACTTGGCTTCTTTAAAAATTCATTTGAAAACATCATA
* *
1434368 TCGGTTGGGTAATCTTCAAGAAACCTTTGAAAATCAAATTTGGCTTCTTTAAAAATTCATTTGAA
66 TCGGTTGGGTAATCTTCAAGAAACCTTTGAAAATCAAACTTGACTTCTTTAAAAATTCATTTGAA
*
1434433 AACATCATATCGGTTG-G
131 AACATCATATCGGCTGAG
* *
1434450 ATAATCTTTAAG-AACCTTTGAAAATCAAACTTGACTTCTTTAAAAATTCATTTGAAAACATCAT
1 -TAATCTTCAAGAAACCTTTGAAAATCAAACTTGGCTTCTTTAAAAATTCATTTGAAAACATCAT
* * *
1434514 ATCTG-TCGGTAATCTTCAAGAAACCTTTTGAAAATCAAACTTGGA-TTCTTTAATAATTCATTT
65 ATCGGTTGGGTAATCTTCAAGAAACC-TTTGAAAATCAAACTT-GACTTCTTTAAAAATTCATTT
* * *
1434577 GAAAACATTATATGGGTCCGA-
128 GAAAACATCATATCGG-CTGAG
* * * *
1434598 TACTCATCAAGAAACCTTTGAAAATCAAACTTGGCTTCTTAAAAAATTCATTTGAAAATATCATA
1 TAATCTTCAAGAAACCTTTGAAAATCAAACTTGGCTTCTTTAAAAATTCATTTGAAAACATCATA
*
1434663 TCGATTGG
66 TCGGTTGG
1434671 TAACATGCCC
Statistics
Matches: 311, Mismatches: 45, Indels: 21
0.82 0.12 0.06
Matches are distributed among these distances:
145 10 0.03
146 39 0.13
147 179 0.58
148 81 0.26
149 2 0.01
ACGTcount: A:0.38, C:0.15, G:0.12, T:0.35
Consensus pattern (148 bp):
TAATCTTCAAGAAACCTTTGAAAATCAAACTTGGCTTCTTTAAAAATTCATTTGAAAACATCATA
TCGGTTGGGTAATCTTCAAGAAACCTTTGAAAATCAAACTTGACTTCTTTAAAAATTCATTTGAA
AACATCATATCGGCTGAG
Found at i:1434581 original size:221 final size:220
Alignment explanation
Indices: 1434156--1434670 Score: 653
Period size: 221 Copynumber: 2.3 Consensus size: 220
1434146 TCGGAGGACT
* *
1434156 TAATCATCAAGAAACCTTTGAAGATAAAAATTGGCTTCTTTTAAGAAATTCATTTG-AAAAT-AT
1 TAATCATCAAGAAACCTTTGAAAATCAAAATTGGCTTC-TTTAA-AAATTCATTTGAAAAATCAT
* * * * * *
1434219 ATCAGTCGAGGTACTCATCAATAGACCTTTGAAAATTAAACTTGACTTCTTTAAAAATTCATTTG
64 ATCGGTTG-GATAATCATCAAGAGACCTTTGAAAATCAAACTTGACTTCTTTAAAAATTCATTTG
* * * *
1434284 GAAACATCATATCAGCTGAGTATTCTTCATGAAACCTTAAAAAATAAACTTGGCTTCTTTAAAAA
128 AAAACATCATATCAGCTGAGTAATCTTCAAGAAACCTTAAAAAATAAACTTGGATTCTTTAAAAA
** *
1434349 TTAATTTGAAAACATCATATCGGTTGGG
193 TTAATTTGAAAACATCATATCGGTCCGA
* *
1434377 TAATCTTCAAGAAACCTTTGAAAATCAAATTTGGCTTCTTTAAAAATTCATTTGAAAACATCATA
1 TAATCATCAAGAAACCTTTGAAAATCAAAATTGGCTTCTTTAAAAATTCATTTGAAAA-ATCATA
* *
1434442 TCGGTTGGATAATCTTTAAGA-ACCTTTGAAAATCAAACTTGACTTCTTTAAAAATTCATTTGAA
65 TCGGTTGGATAATCATCAAGAGACCTTTGAAAATCAAACTTGACTTCTTTAAAAATTCATTTGAA
* ** *
1434506 AACATCATATCTG-TCG-GTAATCTTCAAGAAACCTTTTGAAAATCAAACTTGGATTCTTTAATA
130 AACATCATATCAGCT-GAGTAATCTTCAAGAAACC-TTAAAAAAT-AAACTTGGATTCTTTAAAA
* * *
1434569 ATTCATTTGAAAACATTATATGGGTCCGA
192 ATTAATTTGAAAACATCATATCGGTCCGA
* * *
1434598 TACTCATCAAGAAACCTTTGAAAATCAAACTTGGCTTCTTAAAAAATTCATTTGAAAATATCATA
1 TAATCATCAAGAAACCTTTGAAAATCAAAATTGGCTTCTTTAAAAATTCATTTGAAAA-ATCATA
*
1434663 TCGATTGG
65 TCGGTTGG
1434671 TAACATGCCC
Statistics
Matches: 256, Mismatches: 32, Indels: 12
0.85 0.11 0.04
Matches are distributed among these distances:
219 27 0.11
220 69 0.27
221 152 0.59
222 8 0.03
ACGTcount: A:0.38, C:0.15, G:0.12, T:0.35
Consensus pattern (220 bp):
TAATCATCAAGAAACCTTTGAAAATCAAAATTGGCTTCTTTAAAAATTCATTTGAAAAATCATAT
CGGTTGGATAATCATCAAGAGACCTTTGAAAATCAAACTTGACTTCTTTAAAAATTCATTTGAAA
ACATCATATCAGCTGAGTAATCTTCAAGAAACCTTAAAAAATAAACTTGGATTCTTTAAAAATTA
ATTTGAAAACATCATATCGGTCCGA
Found at i:1435275 original size:18 final size:18
Alignment explanation
Indices: 1435252--1435294 Score: 77
Period size: 18 Copynumber: 2.4 Consensus size: 18
1435242 CCTCCGCCGC
1435252 CACCGCCTACTTCTGTTT
1 CACCGCCTACTTCTGTTT
1435270 CACCGCCTACTTCTGTTT
1 CACCGCCTACTTCTGTTT
*
1435288 CGCCGCC
1 CACCGCC
1435295 AAATGCTCCT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.09, C:0.44, G:0.14, T:0.33
Consensus pattern (18 bp):
CACCGCCTACTTCTGTTT
Found at i:1467706 original size:12 final size:12
Alignment explanation
Indices: 1467689--1467713 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1467679 GTTACAGTCG
1467689 GAGGAGATGAAC
1 GAGGAGATGAAC
1467701 GAGGAGATGAAC
1 GAGGAGATGAAC
1467713 G
1 G
1467714 GGGAAGAGAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.40, C:0.08, G:0.44, T:0.08
Consensus pattern (12 bp):
GAGGAGATGAAC
Found at i:1472461 original size:156 final size:159
Alignment explanation
Indices: 1472141--1472613 Score: 482
Period size: 156 Copynumber: 3.0 Consensus size: 159
1472131 AACTAAGTTA
* * * * *
1472141 ATTTGATGCCATTTTGTTGCATTTTTAAGGAGTAT-GTTATGTATCAAATTAGATGAATGGTTCA
1 ATTTGATGCC-CTTTGTTGCA-TTTTATGGAGTATGGTCATGTATCGAATTAGATGAATGGTTCG
* * * *
1472205 ACCTGTTCACGAAATTTTAGTTCATTGAATGTATTTATTGTCTGTTCTTGTCATGTG-GATAATC
64 ACGTGTTCAC-AAA-TTTAGTTCATTGAATGCATTTAGTGTCTGTTCTTGT--TGTGTCATAATC
* ** *
1472269 AC----CGATTGAATGATGGCGTTGCTAACTTGCT
125 ACATATCGATCGAACAATGGCGTTGATAACTTGCT
*
1472300 GTTTGATGCCCTTTGTTGCATTTTATGGAGTATGGTCATGTATCGAATTAGATGAATGGTTCGAC
1 ATTTGATGCCCTTTGTTGCATTTTATGGAGTATGGTCATGTATCGAATTAGATGAATGGTTCGAC
1472365 GTGTTCACAAATTTAGTTCATTGAATGCATTTAGTGTCTGTTCTTGTTGTGTCATAATCACATAT
66 GTGTTCACAAATTTAGTTCATTGAATGCATTTAGTGTCTGTTCTTGTTGTGTCATAATCACATAT
1472430 CGATCGAACAATGGCG-T-AT-ACTTGCT
131 CGATCGAACAATGGCGTTGATAACTTGCT
* * *
1472456 ATTTGATGCCCTTTCTTGCGTTTTTATGGAGT-TGGTCATGTATCG-ATTAGATAAATGGTTCGA
1 ATTTGATGCCCTTTGTTGC-ATTTTATGGAGTATGGTCATGTATCGAATTAGATGAATGGTTCGA
* * * * *
1472519 TGTGCTCAC--A---AGTGCATT-AAGTGCATTTAGTGTCTGTTCTTTTTATGTCGATAAT-ACA
65 CGTGTTCACAAATTTAGTTCATTGAA-TGCATTTAGTGTCTGTTCTTGTTGTGTC-ATAATCACA
* * *
1472577 TATCGATTGAA-AGATGACGTT-ACTAACTCGCT
128 TATCGATCGAACA-ATGGCGTTGA-TAACTTGCT
1472609 ATTTG
1 ATTTG
1472614 TAATCAATAT
Statistics
Matches: 275, Mismatches: 26, Indels: 32
0.83 0.08 0.10
Matches are distributed among these distances:
149 3 0.01
150 51 0.19
151 7 0.03
152 1 0.00
153 12 0.04
154 4 0.01
155 32 0.12
156 71 0.26
157 27 0.10
158 45 0.16
159 22 0.08
ACGTcount: A:0.24, C:0.14, G:0.21, T:0.41
Consensus pattern (159 bp):
ATTTGATGCCCTTTGTTGCATTTTATGGAGTATGGTCATGTATCGAATTAGATGAATGGTTCGAC
GTGTTCACAAATTTAGTTCATTGAATGCATTTAGTGTCTGTTCTTGTTGTGTCATAATCACATAT
CGATCGAACAATGGCGTTGATAACTTGCT
Found at i:1487911 original size:18 final size:17
Alignment explanation
Indices: 1487874--1487912 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
1487864 TATGGAATTG
* *
1487874 GATTTTAATTCCTGACA
1 GATTTCAATTCCTCACA
1487891 GATTTCAATTCCTTCACA
1 GATTTCAATTCC-TCACA
1487909 GATT
1 GATT
1487913 CTAATCCCCT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 11 0.58
18 8 0.42
ACGTcount: A:0.28, C:0.21, G:0.10, T:0.41
Consensus pattern (17 bp):
GATTTCAATTCCTCACA
Found at i:1490597 original size:10 final size:10
Alignment explanation
Indices: 1490584--1490620 Score: 58
Period size: 10 Copynumber: 3.7 Consensus size: 10
1490574 ACACGCTGGG
1490584 CATCCGAGGC
1 CATCCGAGGC
1490594 CATCCGAGAG-
1 CATCCGAG-GC
1490604 CATCCGAGGC
1 CATCCGAGGC
1490614 CATCCGA
1 CATCCGA
1490621 ATGAGCTATG
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
9 1 0.04
10 23 0.92
11 1 0.04
ACGTcount: A:0.24, C:0.38, G:0.27, T:0.11
Consensus pattern (10 bp):
CATCCGAGGC
Found at i:1490608 original size:20 final size:20
Alignment explanation
Indices: 1490583--1490620 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
1490573 AACACGCTGG
1490583 GCATCCGAGGCCATCCGAGA
1 GCATCCGAGGCCATCCGAGA
1490603 GCATCCGAGGCCATCCGA
1 GCATCCGAGGCCATCCGA
1490621 ATGAGCTATG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.24, C:0.37, G:0.29, T:0.11
Consensus pattern (20 bp):
GCATCCGAGGCCATCCGAGA
Found at i:1490713 original size:10 final size:10
Alignment explanation
Indices: 1490694--1490781 Score: 59
Period size: 10 Copynumber: 8.5 Consensus size: 10
1490684 GCATAGCTCG
*
1490694 CTCGGTTGCC
1 CTCGGATGCC
1490704 CTCGGATGCC
1 CTCGGATGCC
**
1490714 CTCTCATAGCTC
1 CTCGGAT-GC-C
* *
1490726 GTTCGGATGGC
1 -CTCGGATGCC
*
1490737 CTCGGATGCT
1 CTCGGATGCC
*
1490747 CTCGGATGGC
1 CTCGGATGCC
*
1490757 CTCGGATGCT
1 CTCGGATGCC
* *
1490767 TTCGGATGGC
1 CTCGGATGCC
1490777 CTCGG
1 CTCGG
1490782 TCGGATGGCC
Statistics
Matches: 57, Mismatches: 18, Indels: 6
0.70 0.22 0.07
Matches are distributed among these distances:
10 48 0.84
11 3 0.05
12 2 0.04
13 4 0.07
ACGTcount: A:0.09, C:0.32, G:0.32, T:0.27
Consensus pattern (10 bp):
CTCGGATGCC
Found at i:1490722 original size:33 final size:33
Alignment explanation
Indices: 1490679--1490750 Score: 99
Period size: 33 Copynumber: 2.2 Consensus size: 33
1490669 GGGCGACCTA
*
1490679 CCCTCGCATAGCTCGCTCGGTTGCCCTCGGATG
1 CCCTCGCATAGCTCGCTCGGATGCCCTCGGATG
* * *
1490712 CCCTCTCATAGCTCGTTCGGATGGCCTCGGATG
1 CCCTCGCATAGCTCGCTCGGATGCCCTCGGATG
*
1490745 CTCTCG
1 CCCTCG
1490751 GATGGCCTCG
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.10, C:0.38, G:0.26, T:0.26
Consensus pattern (33 bp):
CCCTCGCATAGCTCGCTCGGATGCCCTCGGATG
Found at i:1490753 original size:20 final size:20
Alignment explanation
Indices: 1490728--1490781 Score: 99
Period size: 20 Copynumber: 2.7 Consensus size: 20
1490718 CATAGCTCGT
1490728 TCGGATGGCCTCGGATGCTC
1 TCGGATGGCCTCGGATGCTC
*
1490748 TCGGATGGCCTCGGATGCTT
1 TCGGATGGCCTCGGATGCTC
1490768 TCGGATGGCCTCGG
1 TCGGATGGCCTCGG
1490782 TCGGATGGCC
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.09, C:0.28, G:0.37, T:0.26
Consensus pattern (20 bp):
TCGGATGGCCTCGGATGCTC
Found at i:1492438 original size:16 final size:16
Alignment explanation
Indices: 1492417--1492465 Score: 53
Period size: 16 Copynumber: 3.1 Consensus size: 16
1492407 TATTATAGTG
1492417 ATAAAATAATTATTTT
1 ATAAAATAATTATTTT
* * *
1492433 ATAAAAAAATTAATTA
1 ATAAAATAATTATTTT
**
1492449 ATTTAATAATTATTTT
1 ATAAAATAATTATTTT
1492465 A
1 A
1492466 AAATTTTAAA
Statistics
Matches: 25, Mismatches: 8, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
16 25 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (16 bp):
ATAAAATAATTATTTT
Found at i:1492446 original size:20 final size:20
Alignment explanation
Indices: 1492387--1492453 Score: 55
Period size: 20 Copynumber: 3.2 Consensus size: 20
1492377 TATCATTAAA
1492387 TTTATCAAAAAAATTATAATTAT
1 TTTAT-AAAAAAA-T-TAATTAT
* * *
1492410 TATAGTGATAAAA-TAATTAT
1 TTTA-TAAAAAAATTAATTAT
*
1492430 TTTATAAAAAAATTAATTAA
1 TTTATAAAAAAATTAATTAT
1492450 TTTA
1 TTTA
1492454 ATAATTATTT
Statistics
Matches: 35, Mismatches: 7, Indels: 7
0.71 0.14 0.14
Matches are distributed among these distances:
19 6 0.17
20 20 0.57
23 8 0.23
24 1 0.03
ACGTcount: A:0.52, C:0.01, G:0.03, T:0.43
Consensus pattern (20 bp):
TTTATAAAAAAATTAATTAT
Found at i:1495156 original size:14 final size:14
Alignment explanation
Indices: 1495124--1495157 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
1495114 TGTTTCACTG
*
1495124 AAAACGTTTTTCGA
1 AAAATGTTTTTCGA
*
1495138 AAAATGTTTTTCGT
1 AAAATGTTTTTCGA
1495152 AAAATG
1 AAAATG
1495158 AATTACATTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.38, C:0.09, G:0.15, T:0.38
Consensus pattern (14 bp):
AAAATGTTTTTCGA
Found at i:1495327 original size:22 final size:23
Alignment explanation
Indices: 1495288--1495338 Score: 61
Period size: 22 Copynumber: 2.3 Consensus size: 23
1495278 TATAATAAAC
1495288 AATATTATTTATCATAAAACA-T
1 AATATTATTTATCATAAAACATT
* *
1495310 AATATTA-TTATTCTTAAAATATT
1 AATATTATTTA-TCATAAAACATT
1495333 AATATT
1 AATATT
1495339 GGTATATTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
21 3 0.12
22 15 0.60
23 7 0.28
ACGTcount: A:0.47, C:0.06, G:0.00, T:0.47
Consensus pattern (23 bp):
AATATTATTTATCATAAAACATT
Found at i:1495514 original size:19 final size:19
Alignment explanation
Indices: 1495446--1495526 Score: 64
Period size: 19 Copynumber: 4.3 Consensus size: 19
1495436 TTAAATATCT
1495446 TTATTAA-AATATTATTAGA
1 TTATTAATAATATTATTA-A
1495465 TTATTATATTAATATTA--AA
1 TTATTA-A-TAATATTATTAA
* *
1495484 TATATAAATAATATTATTCA
1 T-TATTAATAATATTATTAA
*
1495504 TTATTAATAAT-TTAATAA
1 TTATTAATAATATTATTAA
1495522 -TATTA
1 TTATTA
1495527 TTTCTATGAA
Statistics
Matches: 51, Mismatches: 5, Indels: 14
0.73 0.07 0.20
Matches are distributed among these distances:
17 5 0.10
18 13 0.25
19 18 0.35
20 8 0.16
22 7 0.14
ACGTcount: A:0.48, C:0.01, G:0.01, T:0.49
Consensus pattern (19 bp):
TTATTAATAATATTATTAA
Found at i:1495687 original size:22 final size:23
Alignment explanation
Indices: 1495659--1495705 Score: 69
Period size: 22 Copynumber: 2.1 Consensus size: 23
1495649 TTGATTATTT
1495659 TATTATAATATTAAAAATA-TAA
1 TATTATAATATTAAAAATATTAA
* *
1495681 TATTATATTATTAGAAATATTAA
1 TATTATAATATTAAAAATATTAA
1495704 TA
1 TA
1495706 AATATATTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 17 0.77
23 5 0.23
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (23 bp):
TATTATAATATTAAAAATATTAA
Found at i:1495710 original size:22 final size:21
Alignment explanation
Indices: 1495666--1495728 Score: 56
Period size: 22 Copynumber: 2.9 Consensus size: 21
1495656 TTTTATTATA
*
1495666 ATATTAAAAATA-TAATATTAT
1 ATATTAAAAATATTAATA-AAT
*
1495687 ATTATTAGAAATATTAATAAAT
1 A-TATTAAAAATATTAATAAAT
**
1495709 ATATTTTAAATATTTAATAA
1 ATATTAAAAATA-TTAATAA
1495729 TTAATATTTT
Statistics
Matches: 35, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
21 10 0.29
22 20 0.57
23 5 0.14
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (21 bp):
ATATTAAAAATATTAATAAAT
Found at i:1495719 original size:21 final size:23
Alignment explanation
Indices: 1495695--1495740 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 23
1495685 ATATTATTAG
1495695 AAATA-TTAATAAAT-ATATTTT
1 AAATATTTAATAAATAATATTTT
*
1495716 AAATATTTAATAATTAATATTTT
1 AAATATTTAATAAATAATATTTT
1495739 AA
1 AA
1495741 TTAAAATGAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 5 0.23
22 8 0.36
23 9 0.41
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (23 bp):
AAATATTTAATAAATAATATTTT
Found at i:1497065 original size:31 final size:29
Alignment explanation
Indices: 1497030--1497088 Score: 75
Period size: 29 Copynumber: 2.0 Consensus size: 29
1497020 CTTGATTCAT
1497030 AAATCACTC-AATTATCAATAAAATTATAAAC
1 AAATCA-TCGAATT-TCAA-AAAATTATAAAC
*
1497061 AAATCATCGAATTTCAAAACATTATAAA
1 AAATCATCGAATTTCAAAAAATTATAAA
1497089 TGAGCCACTC
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
29 10 0.38
30 6 0.23
31 10 0.38
ACGTcount: A:0.54, C:0.15, G:0.02, T:0.29
Consensus pattern (29 bp):
AAATCATCGAATTTCAAAAAATTATAAAC
Found at i:1497660 original size:16 final size:18
Alignment explanation
Indices: 1497618--1497662 Score: 58
Period size: 20 Copynumber: 2.5 Consensus size: 18
1497608 TAATTGAATG
1497618 TAAGATTACCAGTAGAAA
1 TAAGATTACCAGTAGAAA
1497636 TAAAAGATTACCAGT-G-AA
1 T--AAGATTACCAGTAGAAA
1497654 TAAGATTAC
1 TAAGATTAC
1497663 TGTGAATGTT
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
16 8 0.32
18 4 0.16
19 1 0.04
20 12 0.48
ACGTcount: A:0.49, C:0.11, G:0.16, T:0.24
Consensus pattern (18 bp):
TAAGATTACCAGTAGAAA
Found at i:1499801 original size:18 final size:18
Alignment explanation
Indices: 1499778--1499827 Score: 64
Period size: 18 Copynumber: 2.8 Consensus size: 18
1499768 TTTCGATTCT
*
1499778 TTCGACCGATTAAACCGG
1 TTCGACCGATTAAACCGA
* *
1499796 TTCGACCAATTAGACCGA
1 TTCGACCGATTAAACCGA
*
1499814 TTCAACCGATTAAA
1 TTCGACCGATTAAA
1499828 TCAATAAATC
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.34, C:0.26, G:0.16, T:0.24
Consensus pattern (18 bp):
TTCGACCGATTAAACCGA
Found at i:1501118 original size:14 final size:14
Alignment explanation
Indices: 1501101--1501127 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
1501091 AAACACAGAT
1501101 TGCAAAGTACAACA
1 TGCAAAGTACAACA
1501115 TGCAAAGTACAAC
1 TGCAAAGTACAAC
1501128 CTACAAAGGC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.48, C:0.22, G:0.15, T:0.15
Consensus pattern (14 bp):
TGCAAAGTACAACA
Found at i:1506661 original size:29 final size:30
Alignment explanation
Indices: 1506619--1506716 Score: 103
Period size: 29 Copynumber: 3.3 Consensus size: 30
1506609 ACCCGACCCA
* *
1506619 GTGACACTTTGGGAATTATTTTG-AAAAAT
1 GTGACATTTTGGGAATTATTTTGTAAAAAG
*
1506648 GTGACATTTTGGGAATTA-TTTGTAAAACG
1 GTGACATTTTGGGAATTATTTTGTAAAAAG
* *
1506677 GTGATATTTTGGTAATTATTTT-TAATAAAG
1 GTGACATTTTGGGAATTATTTTGTAA-AAAG
* *
1506707 ATGATATTTT
1 GTGACATTTT
1506717 TGTAATTTTT
Statistics
Matches: 59, Mismatches: 7, Indels: 5
0.83 0.10 0.07
Matches are distributed among these distances:
28 4 0.07
29 40 0.68
30 15 0.25
ACGTcount: A:0.33, C:0.04, G:0.19, T:0.44
Consensus pattern (30 bp):
GTGACATTTTGGGAATTATTTTGTAAAAAG
Found at i:1506722 original size:30 final size:29
Alignment explanation
Indices: 1506626--1506727 Score: 93
Period size: 29 Copynumber: 3.5 Consensus size: 29
1506616 CCAGTGACAC
* *
1506626 TTTGGGAATTATTT-TGAAAAATG-TGACAT
1 TTTGGTAATTATTTGT-AAAAA-GATGATAT
* * *
1506655 TTTGGGAATTATTTGTAAAACGGTGATAT
1 TTTGGTAATTATTTGTAAAAAGATGATAT
*
1506684 TTTGGTAATTATTTTTAATAAAGATGATAT
1 TTTGGTAATTATTTGTAA-AAAGATGATAT
*
1506714 TTTTGTAATT-TTTG
1 TTTGGTAATTATTTG
1506728 AATGTGGACT
Statistics
Matches: 62, Mismatches: 8, Indels: 6
0.82 0.11 0.08
Matches are distributed among these distances:
28 1 0.02
29 42 0.68
30 19 0.31
ACGTcount: A:0.31, C:0.02, G:0.19, T:0.48
Consensus pattern (29 bp):
TTTGGTAATTATTTGTAAAAAGATGATAT
Found at i:1510183 original size:3 final size:3
Alignment explanation
Indices: 1510175--1510233 Score: 109
Period size: 3 Copynumber: 19.3 Consensus size: 3
1510165 ATTATGTTTA
1510175 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATAT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT AT-T ATT ATT ATT ATT ATT
1510221 ATT ATT ATT ATT A
1 ATT ATT ATT ATT A
1510234 AATAAATTAA
Statistics
Matches: 55, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
3 52 0.95
4 3 0.05
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:1510197 original size:28 final size:30
Alignment explanation
Indices: 1510175--1510233 Score: 100
Period size: 31 Copynumber: 1.9 Consensus size: 30
1510165 ATTATGTTTA
1510175 ATTATTATTATTATTATTATTATTATTATAT
1 ATTATTATTATTATTATTATTA-TATTATAT
1510206 ATTATTATTATTATTATTATTATTATTA
1 ATTATTATTATTATTATTATTA-TATTA
1510234 AATAAATTAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (30 bp):
ATTATTATTATTATTATTATTATATTATAT
Found at i:1511792 original size:12 final size:12
Alignment explanation
Indices: 1511712--1511794 Score: 71
Period size: 12 Copynumber: 6.8 Consensus size: 12
1511702 TTAATTTTAT
1511712 TTATTTATTCATTA
1 TTATTT-TT-ATTA
* *
1511726 TTTATTTGTAATA
1 -TTATTTTTATTA
1511739 TTA-TTTTATTA
1 TTATTTTTATTA
* *
1511750 TTACTTTAATTA
1 TTATTTTTATTA
* *
1511762 TTACTTTAATTA
1 TTATTTTTATTA
1511774 TTA-TTTTATTA
1 TTATTTTTATTA
1511785 TTATTTTTAT
1 TTATTTTTAT
1511795 CTTAGTCTTA
Statistics
Matches: 60, Mismatches: 6, Indels: 7
0.82 0.08 0.10
Matches are distributed among these distances:
11 19 0.32
12 31 0.52
13 3 0.05
14 1 0.02
15 6 0.10
ACGTcount: A:0.29, C:0.04, G:0.01, T:0.66
Consensus pattern (12 bp):
TTATTTTTATTA
Found at i:1513119 original size:6 final size:6
Alignment explanation
Indices: 1511817--1513117 Score: 2249
Period size: 6 Copynumber: 221.8 Consensus size: 6
1511807 AATATATATA
1511817 TGTATG TGTATG TGTATG TGTATG TGTATG TGTATGTG TGTATG TGTATG
1 TGTATG TGTATG TGTATG TGTATG TGTATG TGTA--TG TGTATG TGTATG
* * *
1511867 TGTATG TTTATG TGTATG TGTATG TGTATG TGTGATG TGTGTA TGTATG
1 TGTATG TGTATG TGTATG TGTATG TGTATG TGT-ATG TGTATG TGTATG
1511916 TGTATG TGTATG TGTATG TGTATG TGTATG TGTATG TGTATG TGTATG
1 TGTATG TGTATG TGTATG TGTATG TGTATG TGTATG TGTATG TGTATG
1511964 -GTATG TGTATG TGTATG TGTATG TG--TG TGTATG TGTATG TGTATG
1 TGTATG TGTATG TGTATG TGTATG TGTATG TGTATG TGTATG TGTATG
1512009 TGTATG TGTATG TGTATG TGTATG TGTATG TGTATG TGTATG TGTATG
1 TGTATG TGTATG TGTATG TGTATG TGTATG TGTATG TGTATG TGTATG
1512057 TGTATG TGTATG TGTATG TGTATG TGTATG TGTATG TGTATG TGTATG
1 TGTATG TGTATG TGTATG TGTATG TGTATG TGTATG TGTATG TGTATG
*
1512105 TGTATG TGTATG TG--TG TATATG TGTATG TGTATG TGTATG TGTATG
1 TGTATG TGTATG TGTATG TGTATG TGTATG TGTATG TGTATG TGTATG
1512151 TGTATG TGTATG TGTATG TGTATG TGTATG TGTATG TGTATG TGTATG
1 TGTATG TGTATG TGTATG TGTATG TGTATG TGTATG TGTATG TGTATG
1512199 TGTATG TGTATG TGTATG TGTATG TGTATG TGTATG TGTATG TGTATG
1 TGTATG TGTATG TGTATG TGTATG TGTATG TGTATG TGTATG TGTATG
1512247 TGTA-- TGTATG TGTATG TGTATG TGTA-G TGTATG TGTATG TGTATG
1 TGTATG TGTATG TGTATG TGTATG TGTATG TGTATG TGTATG TGTATG
1512292 TGTATG TGTATG TGTATG TGTATG TGTATG TGTATG TGTATG TGTATG
1 TGTATG TGTATG TGTATG TGTATG TGTATG TGTATG TGTATG TGTATG
1512340 TGTA-- TGTATG TGTATG TGTATG TGTATG TGTA-- TGTATG TGTATG
1 TGTATG TGTATG TGTATG TGTATG TGTATG TGTATG TGTATG TGTATG
1512384 TGTATG TGTATG TGTATG TGTATG TGTATG TGTATG TGTA-- TGTATG
1 TGTATG TGTATG TGTATG TGTATG TGTATG TGTATG TGTATG TGTATG
1512430 TGTATG TGTATG TG--TG TGTATG TGTATG TGTATG TGTATG TGTATG
1 TGTATG TGTATG TGTATG TGTATG TGTATG TGTATG TGTATG TGTATG
1512476 TGTATG TGTATG TGTATG TGTATG TGTA-- TGTATG TGTATG TGTATG
1 TGTATG TGTATG TGTATG TGTATG TGTATG TGTATG TGTATG TGTATG
1512522 TGTATG TGTATG TGTATG TG--TG TGTATG TGTATG TGTATG TGTATG
1 TGTATG TGTATG TGTATG TGTATG TGTATG TGTATG TGTATG TGTATG
*
1512568 TGTATG TGTATG TGTATG TGTATG TGTATG TGTATG TGTATG -GGATG
1 TGTATG TGTATG TGTATG TGTATG TGTATG TGTATG TGTATG TGTATG
1512615 TGTATG TGTA-- TGTATG TGTATG TGTATG TGTATG TGTATG TGTATG
1 TGTATG TGTATG TGTATG TGTATG TGTATG TGTATG TGTATG TGTATG
1512661 TGTATG TGTATG T-TATG TGTA-G TGTATG TGTATG TGTATG TGTATG
1 TGTATG TGTATG TGTATG TGTATG TGTATG TGTATG TGTATG TGTATG
1512707 TGTATG TGTATG TGTATG TG--T- TGTATG TGTATG TGTATG TGTATG
1 TGTATG TGTATG TGTATG TGTATG TGTATG TGTATG TGTATG TGTATG
1512752 TGTATG TGTATG TGTATG -GTATG TGTA-- TGTATG TGTATG TGTATG
1 TGTATG TGTATG TGTATG TGTATG TGTATG TGTATG TGTATG TGTATG
1512797 TGTATG TGTATG TGTATG TGTATG TGTATG TGTATG TGTATG TGTATG
1 TGTATG TGTATG TGTATG TGTATG TGTATG TGTATG TGTATG TGTATG
1512845 TGTATG TGTATG TGTATG TGTATG TGTA-- TGTATG TGTATG TGTATG
1 TGTATG TGTATG TGTATG TGTATG TGTATG TGTATG TGTATG TGTATG
1512891 TGTATG TGTATG TGTATG TGTATG TGTA-- TGTATG TGTATGTG TGTATG
1 TGTATG TGTATG TGTATG TGTATG TGTATG TGTATG TGTA--TG TGTATG
1512939 TGTATG TGTATG TGTATG TGTATG TGTATG TGTATG TGTATG TGTATG
1 TGTATG TGTATG TGTATG TGTATG TGTATG TGTATG TGTATG TGTATG
1512987 TGTATG TGTATG TGTATG TGTATG TGTATG TGTATG TGTATG TGTATG
1 TGTATG TGTATG TGTATG TGTATG TGTATG TGTATG TGTATG TGTATG
1513035 TGTATG TGTATG TGTATG TGTATG TGTATG TGTATG TGTATG TGTATG
1 TGTATG TGTATG TGTATG TGTATG TGTATG TGTATG TGTATG TGTATG
* *
1513083 TGTATG TGTATG TGTATG TGTATA TGTATA TGTAT
1 TGTATG TGTATG TGTATG TGTATG TGTATG TGTAT
1513118 ATATATATTT
Statistics
Matches: 1244, Mismatches: 11, Indels: 80
0.93 0.01 0.06
Matches are distributed among these distances:
3 2 0.00
4 52 0.04
5 30 0.02
6 1142 0.92
7 6 0.00
8 12 0.01
ACGTcount: A:0.17, C:0.00, G:0.33, T:0.50
Consensus pattern (6 bp):
TGTATG
Found at i:1513376 original size:21 final size:19
Alignment explanation
Indices: 1513351--1513398 Score: 55
Period size: 18 Copynumber: 2.5 Consensus size: 19
1513341 ATATTCTTAA
1513351 ATAAATAAATATCATATTTTT
1 ATAAATAAATATC-TA-TTTT
*
1513372 ATAAAT-TATATCTATTTT
1 ATAAATAAATATCTATTTT
1513390 -TAAATAAAT
1 ATAAATAAAT
1513399 GTTTTAATAT
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
17 5 0.21
18 6 0.25
19 2 0.08
20 5 0.21
21 6 0.25
ACGTcount: A:0.48, C:0.04, G:0.00, T:0.48
Consensus pattern (19 bp):
ATAAATAAATATCTATTTT
Found at i:1514414 original size:27 final size:25
Alignment explanation
Indices: 1514343--1514416 Score: 71
Period size: 28 Copynumber: 2.9 Consensus size: 25
1514333 CATAAGATGG
*
1514343 AAATAAAT-AAATAAATAGAAATTC
1 AAATAAATAAAATAAATAAAAATTC
*
1514367 AAGTAAATAAAA-AATATTAAATAATTC
1 AAATAAATAAAATAA-A-TAAA-AATTC
*
1514394 AAAATAAATAAAATAAGTAAAAA
1 -AAATAAATAAAATAAATAAAAA
1514417 ATGACTAAAT
Statistics
Matches: 40, Mismatches: 4, Indels: 10
0.74 0.07 0.19
Matches are distributed among these distances:
24 9 0.22
25 4 0.10
26 5 0.12
27 9 0.22
28 11 0.28
29 2 0.05
ACGTcount: A:0.69, C:0.03, G:0.04, T:0.24
Consensus pattern (25 bp):
AAATAAATAAAATAAATAAAAATTC
Found at i:1514416 original size:19 final size:20
Alignment explanation
Indices: 1514351--1514416 Score: 53
Period size: 19 Copynumber: 3.1 Consensus size: 20
1514341 GGAAATAAAT
*
1514351 AAATAAATAGAAATTCAAGTAA
1 AAATAAATATAAA-T-AAGTAA
* * *
1514373 ATAAAAAATATTAAATAATTCA
1 A-AATAAATA-TAAATAAGTAA
1514395 AAATAAATA-AAATAAGTAA
1 AAATAAATATAAATAAGTAA
1514414 AAA
1 AAA
1514417 ATGACTAAAT
Statistics
Matches: 35, Mismatches: 7, Indels: 7
0.71 0.14 0.14
Matches are distributed among these distances:
19 11 0.31
21 7 0.20
22 6 0.17
23 8 0.23
24 3 0.09
ACGTcount: A:0.68, C:0.03, G:0.05, T:0.24
Consensus pattern (20 bp):
AAATAAATATAAATAAGTAA
Found at i:1514447 original size:14 final size:15
Alignment explanation
Indices: 1514413--1514446 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
1514403 AAAATAAGTA
*
1514413 AAAAATGACTAAATT
1 AAAAATGACTAAACT
*
1514428 AAAAATGATTAAACT
1 AAAAATGACTAAACT
1514443 AAAA
1 AAAA
1514447 TAACATAGAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.65, C:0.06, G:0.06, T:0.24
Consensus pattern (15 bp):
AAAAATGACTAAACT
Found at i:1516022 original size:60 final size:60
Alignment explanation
Indices: 1515947--1516060 Score: 158
Period size: 60 Copynumber: 1.9 Consensus size: 60
1515937 AAATGATCCC
* *
1515947 TTAACTATATGATATTATTTTATTAAATCCTTTAACTATTAAAAGTTACAAAATAGTCTT
1 TTAACTATATGATATTATTTTATTAAATCCATCAACTATTAAAAGTTACAAAATAGTCTT
* * * *
1516007 TTAACTATA-GAATATTATTTTGTTGAGTCCATCAATTATTAAAAGTTACAAAAT
1 TTAACTATATG-ATATTATTTTATTAAATCCATCAACTATTAAAAGTTACAAAAT
1516061 GGTCACTCGA
Statistics
Matches: 47, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
59 1 0.02
60 46 0.98
ACGTcount: A:0.40, C:0.10, G:0.07, T:0.43
Consensus pattern (60 bp):
TTAACTATATGATATTATTTTATTAAATCCATCAACTATTAAAAGTTACAAAATAGTCTT
Found at i:1523216 original size:24 final size:24
Alignment explanation
Indices: 1523196--1523303 Score: 164
Period size: 24 Copynumber: 4.5 Consensus size: 24
1523186 TTATGATCTA
1523196 ATACTTGACATGGATTCTGATATG
1 ATACTTGACATGGATTCTGATATG
*
1523220 ATA-TCTGACATAGATTCTGATATG
1 ATACT-TGACATGGATTCTGATATG
*
1523244 ATACTTGACTTGGATTCTGATATG
1 ATACTTGACATGGATTCTGATATG
* *
1523268 ATACTTGACCTGGATTTTGATATG
1 ATACTTGACATGGATTCTGATATG
1523292 ATACTTGACATG
1 ATACTTGACATG
1523304 AATTATGTTT
Statistics
Matches: 76, Mismatches: 6, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
23 1 0.01
24 74 0.97
25 1 0.01
ACGTcount: A:0.29, C:0.13, G:0.19, T:0.39
Consensus pattern (24 bp):
ATACTTGACATGGATTCTGATATG
Found at i:1523317 original size:24 final size:24
Alignment explanation
Indices: 1523185--1523310 Score: 146
Period size: 24 Copynumber: 5.2 Consensus size: 24
1523175 TTCGATTTGA
* *
1523185 ATTATGATCTAATACTTGACATGG
1 ATTATGATATGATACTTGACATGG
* *
1523209 ATTCTGATATGATA-TCTGACATAG
1 ATTATGATATGATACT-TGACATGG
* *
1523233 ATTCTGATATGATACTTGACTTGG
1 ATTATGATATGATACTTGACATGG
* *
1523257 ATTCTGATATGATACTTGACCTGG
1 ATTATGATATGATACTTGACATGG
* *
1523281 ATTTTGATATGATACTTGACATGA
1 ATTATGATATGATACTTGACATGG
1523305 ATTATG
1 ATTATG
1523311 TTTTGATTTA
Statistics
Matches: 89, Mismatches: 11, Indels: 4
0.86 0.11 0.04
Matches are distributed among these distances:
23 1 0.01
24 87 0.98
25 1 0.01
ACGTcount: A:0.30, C:0.12, G:0.18, T:0.40
Consensus pattern (24 bp):
ATTATGATATGATACTTGACATGG
Found at i:1523481 original size:43 final size:43
Alignment explanation
Indices: 1523419--1523513 Score: 147
Period size: 43 Copynumber: 2.2 Consensus size: 43
1523409 GGGCTTTACT
* *
1523419 TGGTGTGTTGGTGGATGTATGGTTCTGGGGAA-CCTACACATTA
1 TGGTGTGTTGGTGGATGTATGGTTAT-AGGAAGCCTACACATTA
*
1523462 TGGTGTGTTGGTGGGTGTATGGTTATAGGAAGCCTACACATTA
1 TGGTGTGTTGGTGGATGTATGGTTATAGGAAGCCTACACATTA
1523505 TGGTGTGTT
1 TGGTGTGTT
1523514 CGGTTGGAGG
Statistics
Matches: 48, Mismatches: 3, Indels: 2
0.91 0.06 0.04
Matches are distributed among these distances:
42 4 0.08
43 44 0.92
ACGTcount: A:0.18, C:0.09, G:0.36, T:0.37
Consensus pattern (43 bp):
TGGTGTGTTGGTGGATGTATGGTTATAGGAAGCCTACACATTA
Found at i:1528396 original size:48 final size:48
Alignment explanation
Indices: 1528327--1528441 Score: 169
Period size: 48 Copynumber: 2.4 Consensus size: 48
1528317 ATTTGAATTA
*
1528327 TGATCTGATACTTGACATGGATTCTGATATGATA-TCTGACATAGATTC
1 TGATATGATACTTGACATGGATTCTGATATGATACT-TGACATAGATTC
* * * *
1528375 TGATATGATACTTGACTTGGATTCTGATATGATACTTGACCTGGATTT
1 TGATATGATACTTGACATGGATTCTGATATGATACTTGACATAGATTC
1528423 TGATATGATACTTGACATG
1 TGATATGATACTTGACATG
1528442 AATTATGTTT
Statistics
Matches: 60, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
48 59 0.98
49 1 0.02
ACGTcount: A:0.28, C:0.13, G:0.20, T:0.39
Consensus pattern (48 bp):
TGATATGATACTTGACATGGATTCTGATATGATACTTGACATAGATTC
Found at i:1528455 original size:24 final size:24
Alignment explanation
Indices: 1528320--1528445 Score: 148
Period size: 24 Copynumber: 5.2 Consensus size: 24
1528310 ATTTTTGATT
* *
1528320 TGAATTATGATCTGATACTTGACA
1 TGAATTCTGATATGATACTTGACA
*
1528344 TGGATTCTGATATGATA-TCTGACA
1 TGAATTCTGATATGATACT-TGACA
*
1528368 T-AGATTCTGATATGATACTTGACT
1 TGA-ATTCTGATATGATACTTGACA
* *
1528392 TGGATTCTGATATGATACTTGACC
1 TGAATTCTGATATGATACTTGACA
* *
1528416 TGGATTTTGATATGATACTTGACA
1 TGAATTCTGATATGATACTTGACA
1528440 TGAATT
1 TGAATT
1528446 ATGTTTTGAT
Statistics
Matches: 88, Mismatches: 10, Indels: 8
0.83 0.09 0.08
Matches are distributed among these distances:
23 1 0.01
24 86 0.98
25 1 0.01
ACGTcount: A:0.29, C:0.12, G:0.19, T:0.40
Consensus pattern (24 bp):
TGAATTCTGATATGATACTTGACA
Found at i:1528619 original size:43 final size:43
Alignment explanation
Indices: 1528557--1528651 Score: 156
Period size: 43 Copynumber: 2.2 Consensus size: 43
1528547 GGGCTTTACT
*
1528557 TGGTGTGTTGGTGGATGTATGGTTCTGGGGAA-CCTACACATTA
1 TGGTGTGTTGGTGGATGTATGGTTAT-GGGAAGCCTACACATTA
*
1528600 TGGTGTGTTGGTGGGTGTATGGTTATGGGAAGCCTACACATTA
1 TGGTGTGTTGGTGGATGTATGGTTATGGGAAGCCTACACATTA
1528643 TGGTGTGTT
1 TGGTGTGTT
1528652 CGGTTGGAGG
Statistics
Matches: 49, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
42 5 0.10
43 44 0.90
ACGTcount: A:0.17, C:0.09, G:0.37, T:0.37
Consensus pattern (43 bp):
TGGTGTGTTGGTGGATGTATGGTTATGGGAAGCCTACACATTA
Found at i:1534099 original size:37 final size:37
Alignment explanation
Indices: 1534057--1534130 Score: 103
Period size: 37 Copynumber: 2.0 Consensus size: 37
1534047 AGAGGACGGA
* *
1534057 GAAAAACCGTTTATGTTAAACGGGGACGGGGACGGGG
1 GAAAAACCGTTTATGCTAAACGGAGACGGGGACGGGG
* * *
1534094 GAAAAATCGTTTATGCTAAATGGAGACGGGGATGGGG
1 GAAAAACCGTTTATGCTAAACGGAGACGGGGACGGGG
1534131 ACGAGTTTGG
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
37 32 1.00
ACGTcount: A:0.31, C:0.11, G:0.39, T:0.19
Consensus pattern (37 bp):
GAAAAACCGTTTATGCTAAACGGAGACGGGGACGGGG
Found at i:1534242 original size:2 final size:2
Alignment explanation
Indices: 1534235--1534289 Score: 60
Period size: 2 Copynumber: 28.5 Consensus size: 2
1534225 ATTTAATTTA
* *
1534235 AT AT AT AT AT AT AT AT AT AT AT A- AT AT TT AT AT AT TT A- AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* *
1534275 TT AA AT AT AT AT AT A
1 AT AT AT AT AT AT AT A
1534290 CCCGACCCGA
Statistics
Matches: 43, Mismatches: 8, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
1 2 0.05
2 41 0.95
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:1534287 original size:48 final size:48
Alignment explanation
Indices: 1534196--1534289 Score: 147
Period size: 48 Copynumber: 2.0 Consensus size: 48
1534186 TAATAATTAT
*
1534196 TATATATATATATAATATTAATAAATTTAATTTAATTTAATATATATA
1 TATATATATATATAATATTAATAAATTTAATTTAATATAATATATATA
* *
1534244 TATATATATATATAATATTTATATATTTAATTTAA-AT-ATATATATA
1 TATATATATATATAATATTAATAAATTTAATTTAATATAATATATATA
1534290 CCCGACCCGA
Statistics
Matches: 43, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
46 9 0.21
47 1 0.02
48 33 0.77
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (48 bp):
TATATATATATATAATATTAATAAATTTAATTTAATATAATATATATA
Found at i:1537153 original size:21 final size:21
Alignment explanation
Indices: 1537129--1537195 Score: 73
Period size: 21 Copynumber: 3.2 Consensus size: 21
1537119 AGATTTAAGC
* *
1537129 TTTAGGGTTTATAGATTAGGA
1 TTTAGGGTTTAGAGATTATGA
**
1537150 TTTAATGTTTAGAGATTATGA
1 TTTAGGGTTTAGAGATTATGA
*
1537171 TTT-GGGATTTAGAGTTTATGA
1 TTTAGGG-TTTAGAGATTATGA
1537192 TTTA
1 TTTA
1537196 AAATTTAGGG
Statistics
Matches: 37, Mismatches: 7, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
20 1 0.03
21 36 0.97
ACGTcount: A:0.28, C:0.00, G:0.24, T:0.48
Consensus pattern (21 bp):
TTTAGGGTTTAGAGATTATGA
Found at i:1537168 original size:28 final size:28
Alignment explanation
Indices: 1537113--1537181 Score: 70
Period size: 28 Copynumber: 2.5 Consensus size: 28
1537103 TATAGTTTGG
* * *
1537113 GATTTAAGATTTAAGCTTTAGGGTTTAT
1 GATTTAGGATTTAAGCTTTAGAGATTAT
1537141 AGA-TTAGGATTTAATG-TTTAGAGATTAT
1 -GATTTAGGATTTAA-GCTTTAGAGATTAT
*
1537169 GATTTGGGATTTA
1 GATTTAGGATTTA
1537182 GAGTTTATGA
Statistics
Matches: 34, Mismatches: 4, Indels: 5
0.79 0.09 0.12
Matches are distributed among these distances:
27 2 0.06
28 29 0.85
29 3 0.09
ACGTcount: A:0.30, C:0.01, G:0.23, T:0.45
Consensus pattern (28 bp):
GATTTAGGATTTAAGCTTTAGAGATTAT
Found at i:1537201 original size:21 final size:21
Alignment explanation
Indices: 1537148--1537208 Score: 59
Period size: 21 Copynumber: 2.9 Consensus size: 21
1537138 TATAGATTAG
** *
1537148 GATTTAATGTTTAGAGATTAT
1 GATTTAAAATTTAGAGTTTAT
***
1537169 GATTTGGGATTTAGAGTTTAT
1 GATTTAAAATTTAGAGTTTAT
*
1537190 GATTTAAAATTTAGGGTTT
1 GATTTAAAATTTAGAGTTT
1537209 GATATTTGGG
Statistics
Matches: 31, Mismatches: 9, Indels: 0
0.77 0.22 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.30, C:0.00, G:0.23, T:0.48
Consensus pattern (21 bp):
GATTTAAAATTTAGAGTTTAT
Found at i:1538304 original size:13 final size:13
Alignment explanation
Indices: 1538286--1538310 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1538276 AATGAATTTT
1538286 AAGATTTTCTAAA
1 AAGATTTTCTAAA
1538299 AAGATTTTCTAA
1 AAGATTTTCTAA
1538311 GTATATTCGA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.44, C:0.08, G:0.08, T:0.40
Consensus pattern (13 bp):
AAGATTTTCTAAA
Found at i:1544265 original size:20 final size:20
Alignment explanation
Indices: 1544229--1544309 Score: 60
Period size: 20 Copynumber: 3.9 Consensus size: 20
1544219 TTTTGGTACA
*
1544229 GAGGGAATCGATACCCCC-AT
1 GAGGGAA-CGATTCCCCCTAT
*
1544249 GAGGGAACAGATTCCCCCTTT
1 GAGGGAAC-GATTCCCCCTAT
1544270 GAAGGGGAACTGATTCCCCCTA-
1 G-A-GGGAAC-GATTCCCCCTAT
*
1544292 G-GGGAATCGATACCCCCT
1 GAGGGAA-CGATTCCCCCT
1544310 GGGGTTCTGG
Statistics
Matches: 51, Mismatches: 5, Indels: 11
0.76 0.07 0.16
Matches are distributed among these distances:
19 15 0.29
20 16 0.31
21 2 0.04
22 2 0.04
23 16 0.31
ACGTcount: A:0.26, C:0.30, G:0.26, T:0.19
Consensus pattern (20 bp):
GAGGGAACGATTCCCCCTAT
Found at i:1544307 original size:19 final size:19
Alignment explanation
Indices: 1544272--1544313 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
1544262 CCCCCTTTGA
*
1544272 AGGGGAACTGATTCCCCCT
1 AGGGGAACTGATACCCCCT
1544291 AGGGGAA-TCGATACCCCCT
1 AGGGGAACT-GATACCCCCT
1544310 -GGGG
1 AGGGG
1544314 TTCTGGATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
18 5 0.24
19 16 0.76
ACGTcount: A:0.21, C:0.29, G:0.33, T:0.17
Consensus pattern (19 bp):
AGGGGAACTGATACCCCCT
Found at i:1547900 original size:34 final size:33
Alignment explanation
Indices: 1547862--1547941 Score: 83
Period size: 34 Copynumber: 2.4 Consensus size: 33
1547852 TTTTATATTT
1547862 AATATTAATATAATA-ATCTAA-TAATATTTTAATA
1 AATA-TAATATAATATAT-TAATTAATATTTTAA-A
* * *
1547896 AATATATTTAAAATATATTAATTAATATTTTTAA
1 AATATA-ATATAATATATTAATTAATATTTTAAA
1547930 AATATAATATAA
1 AATATAATATAA
1547942 CACTATTACT
Statistics
Matches: 38, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
33 6 0.16
34 20 0.53
35 12 0.32
ACGTcount: A:0.54, C:0.01, G:0.00, T:0.45
Consensus pattern (33 bp):
AATATAATATAATATATTAATTAATATTTTAAA
Found at i:1547910 original size:23 final size:23
Alignment explanation
Indices: 1547863--1547935 Score: 85
Period size: 23 Copynumber: 3.1 Consensus size: 23
1547853 TTTATATTTA
*
1547863 ATATTAATATAATA-ATCTAATAAT
1 ATATTAATA-AATATATTTAA-AAT
*
1547887 ATTTTAATAAATATATTTAAAAT
1 ATATTAATAAATATATTTAAAAT
* *
1547910 ATATTAATTAATATTTTTAAAAT
1 ATATTAATAAATATATTTAAAAT
1547933 ATA
1 ATA
1547936 ATATAACACT
Statistics
Matches: 43, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
23 30 0.70
24 13 0.30
ACGTcount: A:0.52, C:0.01, G:0.00, T:0.47
Consensus pattern (23 bp):
ATATTAATAAATATATTTAAAAT
Found at i:1548069 original size:27 final size:25
Alignment explanation
Indices: 1548039--1548089 Score: 68
Period size: 25 Copynumber: 2.0 Consensus size: 25
1548029 AATATAAAAA
1548039 TAATATTTAATAATAAATAA-ATTATTT
1 TAATATTT--TAA-AAATAATATTATTT
1548066 TAATATTTTAAAAATAATATTATT
1 TAATATTTTAAAAATAATATTATT
1548090 AACTTTTATG
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
24 6 0.26
25 9 0.39
27 8 0.35
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (25 bp):
TAATATTTTAAAAATAATATTATTT
Found at i:1551465 original size:29 final size:28
Alignment explanation
Indices: 1551428--1551483 Score: 67
Period size: 28 Copynumber: 2.0 Consensus size: 28
1551418 TTGCTCTTGA
* * *
1551428 TTCATTTATATTACTGAATTTTTAGTTTT
1 TTCAATTATAGTA-TGAAATTTTAGTTTT
*
1551457 TTCAATTATAGTATTAAATTTTAGTTT
1 TTCAATTATAGTATGAAATTTTAGTTT
1551484 AACATTCAAT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
28 12 0.52
29 11 0.48
ACGTcount: A:0.29, C:0.05, G:0.07, T:0.59
Consensus pattern (28 bp):
TTCAATTATAGTATGAAATTTTAGTTTT
Found at i:1552966 original size:14 final size:11
Alignment explanation
Indices: 1552934--1552959 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
1552924 AACCAAAATT
1552934 TATAAATAAGA
1 TATAAATAAGA
1552945 TATAAATAAGA
1 TATAAATAAGA
1552956 TATA
1 TATA
1552960 TTAAATATTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.62, C:0.00, G:0.08, T:0.31
Consensus pattern (11 bp):
TATAAATAAGA
Found at i:1555293 original size:29 final size:29
Alignment explanation
Indices: 1555238--1555295 Score: 71
Period size: 29 Copynumber: 2.0 Consensus size: 29
1555228 AAGAACAATT
* * * **
1555238 TTTAAAATTCAATGAATAAATTTAAAAAA
1 TTTAAAATACAATAAAAAAATAAAAAAAA
1555267 TTTAAAATACAATAAAAAAATAAAAAAAA
1 TTTAAAATACAATAAAAAAATAAAAAAAA
1555296 ACAATAACTT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
29 24 1.00
ACGTcount: A:0.67, C:0.03, G:0.02, T:0.28
Consensus pattern (29 bp):
TTTAAAATACAATAAAAAAATAAAAAAAA
Found at i:1561177 original size:7 final size:7
Alignment explanation
Indices: 1561162--1561193 Score: 55
Period size: 7 Copynumber: 4.6 Consensus size: 7
1561152 ATAAATGTAA
1561162 TGGGTAG
1 TGGGTAG
*
1561169 TGGGCAG
1 TGGGTAG
1561176 TGGGTAG
1 TGGGTAG
1561183 TGGGTAG
1 TGGGTAG
1561190 TGGG
1 TGGG
1561194 CACCCGTCCT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.12, C:0.03, G:0.59, T:0.25
Consensus pattern (7 bp):
TGGGTAG
Found at i:1563179 original size:27 final size:26
Alignment explanation
Indices: 1563139--1563204 Score: 69
Period size: 27 Copynumber: 2.4 Consensus size: 26
1563129 CTAAATCATC
* * *
1563139 CAACACTTGTGTTTCGTCGCCAAAGTT
1 CAACA-TTGAGTTTCCTCACCAAAGTT
*
1563166 CAACATTTGAGTTTCCTCACCAAGGTT
1 CAACA-TTGAGTTTCCTCACCAAAGTT
1563193 CAGACATTGAGT
1 CA-ACATTGAGT
1563205 CTCGAACTCA
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
27 30 0.91
28 3 0.09
ACGTcount: A:0.26, C:0.24, G:0.18, T:0.32
Consensus pattern (26 bp):
CAACATTGAGTTTCCTCACCAAAGTT
Found at i:1568482 original size:2 final size:2
Alignment explanation
Indices: 1568477--1568503 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1568467 TATCAATAAA
1568477 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 A
1568504 CACGTATTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1571156 original size:3 final size:3
Alignment explanation
Indices: 1571148--1571175 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
1571138 ATAACAAACT
1571148 TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1571176 GTACAAAGAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:1580898 original size:19 final size:20
Alignment explanation
Indices: 1580811--1580899 Score: 101
Period size: 19 Copynumber: 4.3 Consensus size: 20
1580801 CGCGATTTTA
1580811 AAAAATGTGTTGCGATAGT-
1 AAAAATGTGTTGCGATAGTG
* *
1580830 TAAAATGTGTTGCGAGAGTTTG
1 AAAAATGTGTTGCGATAG--TG
1580852 AAAAACGTGTTGTTGCGATAGTG
1 AAAAA--TG-TGTTGCGATAGTG
1580875 AAAAA-GTGTTGCGATAGTG
1 AAAAATGTGTTGCGATAGTG
1580894 AAAAAT
1 AAAAAT
1580900 CCAAAATAAG
Statistics
Matches: 59, Mismatches: 4, Indels: 13
0.78 0.05 0.17
Matches are distributed among these distances:
19 34 0.58
20 1 0.02
21 1 0.02
22 4 0.07
23 7 0.12
24 2 0.03
25 10 0.17
ACGTcount: A:0.36, C:0.06, G:0.28, T:0.30
Consensus pattern (20 bp):
AAAAATGTGTTGCGATAGTG
Found at i:1581944 original size:20 final size:20
Alignment explanation
Indices: 1581921--1581964 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
1581911 GGTTTGGTCA
* *
1581921 ATATTATTCAAGTTTTAAAT
1 ATATTATTAAAATTTTAAAT
*
1581941 ATATTCTTAAAATTTTAAAT
1 ATATTATTAAAATTTTAAAT
1581961 ATAT
1 ATAT
1581965 ATTTGAAAGA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.43, C:0.05, G:0.02, T:0.50
Consensus pattern (20 bp):
ATATTATTAAAATTTTAAAT
Found at i:1581968 original size:13 final size:13
Alignment explanation
Indices: 1581952--1581994 Score: 50
Period size: 13 Copynumber: 3.3 Consensus size: 13
1581942 TATTCTTAAA
1581952 ATTTTAAATATAT
1 ATTTTAAATATAT
* *
1581965 ATTTGAAAGATAT
1 ATTTTAAATATAT
* *
1581978 ATTTTATATTTAT
1 ATTTTAAATATAT
1581991 ATTT
1 ATTT
1581995 ATATTTATGT
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.40, C:0.00, G:0.05, T:0.56
Consensus pattern (13 bp):
ATTTTAAATATAT
Found at i:1585653 original size:289 final size:288
Alignment explanation
Indices: 1585017--1585882 Score: 1375
Period size: 289 Copynumber: 3.0 Consensus size: 288
1585007 ATTCAACTCA
* * * *
1585017 AAAATTTTACAT--TTCACCCGACTCGACCAGACCCGAAGAATATATACTCTCCACCCGACCTAA
1 AAAATTTTACATCCTTCACCCGACTTGACCAGACCCAAAGAATATATACTCTCCACCTGACCCAA
** * *
1585080 ACCCGACATGACTTTTTGAGATAAAATTCAAACTCTATCCGACCCATCCCGAAACAATAAAAATA
66 ACCCGACCCGACTTTTTGAGATAAAATTCAAACCCGATCCGACCCATCCCGAAACAATAAAAATA
* *
1585145 TTATTTTTATTTAATAAAAACAGTAATTTAATT-AAAAAATAATATATAGAGGGATATTATTGTA
131 TTATTTTTATTCAAT-AAAACAGTAATTTAATTAAAAAAATAATATATAGAGGG-TATTATTATA
* * * *
1585209 ATTATTCATAAATATATAAAGTAAAATTATATATTTTTTTGGGTCGGGCCGGTTGTGTATTTTTC
194 ATTATTCCTAAATATATAAGGT-AAA--ATATATTTTTTTGGGTCGGTCGGGTTGTGTATTTTTC
1585274 ATCCTAAACCCGAATCCGACCCGACCTGACCCG
256 ATCCTAAACCCGAATCCGACCCGACCTGACCCG
1585307 AAAATTTTACATCCTTCA-CCGACTTGACCAGACCCAAAGAATATATACTCTCCACCTGACCCAA
1 AAAATTTTACATCCTTCACCCGACTTGACCAGACCCAAAGAATATATACTCTCCACCTGACCCAA
*
1585371 ACCCGACCCGACTTTTTGAGATAAAATTCAAACCCGATCTGACCCATCCCGAAACAATAAAAATA
66 ACCCGACCCGACTTTTTGAGATAAAATTCAAACCCGATCCGACCCATCCCGAAACAATAAAAATA
1585436 TTATTTTTATTCAATAAAACAGTAATTTAATTGAAAAAAATAATATATAGAGGAGTATTATTATA
131 TTATTTTTATTCAATAAAACAGTAATTTAATT-AAAAAAATAATATATAGAGG-GTATTATTATA
1585501 ATTATTCCTAAATATATAAGGTAAAATATA-TTTTTTGGGTCTGGTCGGGTTGTGTATTTTTCAT
194 ATTATTCCTAAATATATAAGGTAAAATATATTTTTTTGGGTC-GGTCGGGTTGTGTATTTTTCAT
1585565 CCTAAA-CCGAATCCGACCCGACCTGACCCG
258 CCTAAACCCGAATCCGACCCGACCTGACCCG
1585595 AAAATTTTACATCCTTCACCCGACTTGACCAGACCCAAAGAATATATACTCTCCACCTGACCCAA
1 AAAATTTTACATCCTTCACCCGACTTGACCAGACCCAAAGAATATATACTCTCCACCTGACCCAA
*
1585660 ACCCGACCCGACTTTTTGAAATAAAATTCAAACCCGATCCGACCCATCCCGAAACAATAAAAATA
66 ACCCGACCCGACTTTTTGAGATAAAATTCAAACCCGATCCGACCCATCCCGAAACAATAAAAATA
*
1585725 TTATTTTTATTCAATAAAACAGTAATTTAATTTTAAAAAAAAAATATATAGAGGGGTATTATTAT
131 TTATTTTTATTCAATAAAACAGTAATTTAA--TTAAAAAAATAATATATAGA-GGGTATTATTAT
* *
1585790 AATTATTCCTAAATATAGAAGGTAAAATTATATTTTTTTTTGGGTCGGGTCGGGTTGGGTATTTT
193 AATTATTCCTAAATATATAAGGTAAAA-TATA--TTTTTTTGGGTC-GGTCGGGTTGTGTATTTT
*
1585855 TCATCATAAACCCGAATCCGACCCGACC
254 TCATCCTAAACCCGAATCCGACCCGACC
1585883 CGAATATCAC
Statistics
Matches: 539, Mismatches: 22, Indels: 25
0.92 0.04 0.04
Matches are distributed among these distances:
288 53 0.10
289 170 0.32
290 82 0.15
291 127 0.24
292 52 0.10
293 1 0.00
294 37 0.07
295 17 0.03
ACGTcount: A:0.37, C:0.21, G:0.12, T:0.30
Consensus pattern (288 bp):
AAAATTTTACATCCTTCACCCGACTTGACCAGACCCAAAGAATATATACTCTCCACCTGACCCAA
ACCCGACCCGACTTTTTGAGATAAAATTCAAACCCGATCCGACCCATCCCGAAACAATAAAAATA
TTATTTTTATTCAATAAAACAGTAATTTAATTAAAAAAATAATATATAGAGGGTATTATTATAAT
TATTCCTAAATATATAAGGTAAAATATATTTTTTTGGGTCGGTCGGGTTGTGTATTTTTCATCCT
AAACCCGAATCCGACCCGACCTGACCCG
Found at i:1588586 original size:43 final size:44
Alignment explanation
Indices: 1588468--1588627 Score: 163
Period size: 43 Copynumber: 3.7 Consensus size: 44
1588458 CGGGCAATTT
* *
1588468 TTTTTACCTTTATAATTGATG-C-CGTTAATTTTTGTAATCTCA-
1 TTTTTACCTTTATAATTGAGGACTC-TTAATTTTTTTAATCTCAC
* * *
1588510 TTTTCTACCTTTATAATTGA-AACCCTTACTTTTTTTAATCTCAC
1 TTTT-TACCTTTATAATTGAGGACTCTTAATTTTTTTAATCTCAC
*
1588554 TTTTTACCTTTATAATTGAGGACTC-TAATTTTTTCAATC-CAAC
1 TTTTTACCTTTATAATTGAGGACTCTTAATTTTTTTAATCTC-AC
* * *
1588597 CTTTTACTTTTATAATTTAGG-CTCTTAATTT
1 TTTTTACCTTTATAATTGAGGACTCTTAATTT
1588628 AATCATTTTT
Statistics
Matches: 101, Mismatches: 10, Indels: 13
0.81 0.08 0.10
Matches are distributed among these distances:
42 8 0.08
43 85 0.84
44 8 0.08
ACGTcount: A:0.25, C:0.17, G:0.06, T:0.51
Consensus pattern (44 bp):
TTTTTACCTTTATAATTGAGGACTCTTAATTTTTTTAATCTCAC
Found at i:1589629 original size:41 final size:41
Alignment explanation
Indices: 1589561--1589638 Score: 93
Period size: 41 Copynumber: 1.9 Consensus size: 41
1589551 ACTATGTTTG
* *
1589561 TGTTTGTTTGTTTAATATTGAAGGTGTTCATGTTCGGGTCA
1 TGTTTATTTGTTTAATATTGAACGTGTTCATGTTCGGGTCA
* * * **
1589602 TGTTTATTTGTTTATTTTTTAACGTGTTTGTGTTCGG
1 TGTTTATTTGTTTAATATTGAACGTGTTCATGTTCGG
1589639 TTCGTCTAGC
Statistics
Matches: 30, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
41 30 1.00
ACGTcount: A:0.14, C:0.06, G:0.24, T:0.55
Consensus pattern (41 bp):
TGTTTATTTGTTTAATATTGAACGTGTTCATGTTCGGGTCA
Found at i:1595319 original size:19 final size:19
Alignment explanation
Indices: 1595292--1595330 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
1595282 ATTAGATAGC
* *
1595292 AAAATTAATATTTTTGATA
1 AAAAATAATATTTTAGATA
1595311 AAAAATAATATTTTAGATA
1 AAAAATAATATTTTAGATA
1595330 A
1 A
1595331 CGTTTTATTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.54, C:0.00, G:0.05, T:0.41
Consensus pattern (19 bp):
AAAAATAATATTTTAGATA
Found at i:1604406 original size:23 final size:26
Alignment explanation
Indices: 1604374--1604448 Score: 88
Period size: 25 Copynumber: 3.0 Consensus size: 26
1604364 ATTTGATTTT
*
1604374 AATTTTAATATTAATTTTTAA-A-TA
1 AATTATAATATTAATTTTTAATATTA
1604398 AATTA-AATATTAATTTTTAATATTA
1 AATTATAATATTAATTTTTAATATTA
*
1604423 TATTATAGATATTAA--TTTAATATTA
1 AATTATA-ATATTAATTTTTAATATTA
1604448 A
1 A
1604449 TTTTTAAATA
Statistics
Matches: 44, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
23 15 0.34
24 5 0.11
25 16 0.36
26 1 0.02
27 7 0.16
ACGTcount: A:0.47, C:0.00, G:0.01, T:0.52
Consensus pattern (26 bp):
AATTATAATATTAATTTTTAATATTA
Found at i:1604435 original size:27 final size:27
Alignment explanation
Indices: 1604381--1604503 Score: 92
Period size: 23 Copynumber: 4.4 Consensus size: 27
1604371 TTTAATTTTA
1604381 ATATTAATTTTTAA-A-TAAATTA-A-
1 ATATTAATTTTTAATATTAAATTATAG
*
1604404 ATATTAATTTTTAATATTATATTATAG
1 ATATTAATTTTTAATATTAAATTATAG
* * *
1604431 ATATTAATTTAATATTAATTTTTAAATAAATTAA
1 ATATTAA-TT--T-TTAA-TATTAAAT-TA-TAG
* *
1604465 ATATTCATTTTTAATATTATATTATAG
1 ATATTAATTTTTAATATTAAATTATAG
1604492 ATATTTAATTTT
1 ATA-TTAATTTT
1604504 ATATCATAAA
Statistics
Matches: 77, Mismatches: 11, Indels: 19
0.72 0.10 0.18
Matches are distributed among these distances:
23 14 0.18
24 1 0.01
25 6 0.08
26 1 0.01
27 12 0.16
28 10 0.13
29 6 0.08
30 5 0.06
31 5 0.06
32 6 0.08
33 3 0.04
34 8 0.10
ACGTcount: A:0.44, C:0.01, G:0.02, T:0.54
Consensus pattern (27 bp):
ATATTAATTTTTAATATTAAATTATAG
Found at i:1604447 original size:11 final size:11
Alignment explanation
Indices: 1604357--1604451 Score: 66
Period size: 12 Copynumber: 7.9 Consensus size: 11
1604347 ATTTTTTATT
*
1604357 ATATTATATTTG
1 ATATTA-ATTTA
*
1604369 ATTTTAATTTTA
1 ATATTAA-TTTA
1604381 ATATTAATTTTTA
1 ATATTAA--TTTA
* *
1604394 A-ATAAATTAA
1 ATATTAATTTA
1604404 ATATTAATTTTTA
1 ATATTAA--TTTA
1604417 ATATTATATTATA
1 ATATTA-ATT-TA
1604430 GATATTAATTTA
1 -ATATTAATTTA
1604442 ATATTAATTT
1 ATATTAATTT
1604452 TTAAATAAAT
Statistics
Matches: 68, Mismatches: 7, Indels: 17
0.74 0.08 0.18
Matches are distributed among these distances:
10 4 0.06
11 15 0.22
12 22 0.32
13 20 0.29
14 7 0.10
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (11 bp):
ATATTAATTTA
Found at i:1604450 original size:61 final size:61
Alignment explanation
Indices: 1604357--1604507 Score: 243
Period size: 61 Copynumber: 2.5 Consensus size: 61
1604347 ATTTTTTATT
*
1604357 ATATTATATT-T-GATTTTAATTTTAATATTAATTTTTAAATAAATTAAATATTAATTTTTA
1 ATATTATATTATAGATATTAA-TTTAATATTAATTTTTAAATAAATTAAATATTAATTTTTA
*
1604417 ATATTATATTATAGATATTAATTTAATATTAATTTTTAAATAAATTAAATATTCATTTTTA
1 ATATTATATTATAGATATTAATTTAATATTAATTTTTAAATAAATTAAATATTAATTTTTA
*
1604478 ATATTATATTATAGATATTTAATTTTATAT
1 ATATTATATTATAGATA-TTAATTTAATAT
1604508 CATAAATTAT
Statistics
Matches: 85, Mismatches: 3, Indels: 4
0.92 0.03 0.04
Matches are distributed among these distances:
60 10 0.12
61 57 0.67
62 18 0.21
ACGTcount: A:0.42, C:0.01, G:0.02, T:0.55
Consensus pattern (61 bp):
ATATTATATTATAGATATTAATTTAATATTAATTTTTAAATAAATTAAATATTAATTTTTA
Found at i:1604451 original size:38 final size:37
Alignment explanation
Indices: 1604351--1604455 Score: 108
Period size: 38 Copynumber: 2.8 Consensus size: 37
1604341 TATTTAATTT
* * *
1604351 TTTATTATATTATATTTGATTTTAA-TTTTAATATTAA
1 TTTATAATATTA-ATTTAATATTAATTTTTAATATTAA
* * *
1604388 TTTTTAA-ATAAATTAAATATTAATTTTTAATATT-A
1 TTTATAATATTAATTTAATATTAATTTTTAATATTAA
1604423 TATTATAGATATTAATTTAATATTAATTTTTAA
1 T-TTATA-ATATTAATTTAATATTAATTTTTAA
1604456 ATAAATTAAA
Statistics
Matches: 55, Mismatches: 9, Indels: 7
0.77 0.13 0.10
Matches are distributed among these distances:
35 11 0.20
36 17 0.31
37 6 0.11
38 21 0.38
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (37 bp):
TTTATAATATTAATTTAATATTAATTTTTAATATTAA
Found at i:1604500 original size:21 final size:22
Alignment explanation
Indices: 1604474--1604528 Score: 67
Period size: 21 Copynumber: 2.5 Consensus size: 22
1604464 AATATTCATT
* *
1604474 TTTAATATTATATTATAGA-TA
1 TTTAATATTATATCATAAATTA
*
1604495 TTTAATTTTATATCATAAATTA
1 TTTAATATTATATCATAAATTA
1604517 TTTATATATTAT
1 TTTA-ATATTAT
1604529 TAAAATTTTA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
21 16 0.57
22 6 0.21
23 6 0.21
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.56
Consensus pattern (22 bp):
TTTAATATTATATCATAAATTA
Found at i:1604549 original size:18 final size:18
Alignment explanation
Indices: 1604517--1604562 Score: 51
Period size: 18 Copynumber: 2.6 Consensus size: 18
1604507 TCATAAATTA
1604517 TTTATATATTATTAA-AAT
1 TTTATAT-TTATTAATAAT
*
1604535 TTTATATTTATTTAATTAT
1 TTTATATTTA-TTAATAAT
1604554 TTTA-ATTTA
1 TTTATATTTA
1604563 AGTTTAAATA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
17 3 0.12
18 16 0.64
19 6 0.24
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (18 bp):
TTTATATTTATTAATAAT
Found at i:1608503 original size:3 final size:3
Alignment explanation
Indices: 1608495--1608525 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
1608485 TCCCTTTTTA
1608495 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1608526 GGGTTTAGGG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:1611466 original size:36 final size:37
Alignment explanation
Indices: 1611425--1611506 Score: 139
Period size: 36 Copynumber: 2.2 Consensus size: 37
1611415 AATTGAAGTT
*
1611425 AAATATGTAAGATTGTTAAGATCGATGACTAAATTA-
1 AAATATGTAAGATTGTTAAGATCAATGACTAAATTAC
1611461 AAATATGTAAGATTGTTAAGATCAATGACTAAATTAC
1 AAATATGTAAGATTGTTAAGATCAATGACTAAATTAC
*
1611498 AAATTTGTA
1 AAATATGTA
1611507 TAAGTTATGG
Statistics
Matches: 43, Mismatches: 2, Indels: 1
0.93 0.04 0.02
Matches are distributed among these distances:
36 35 0.81
37 8 0.19
ACGTcount: A:0.45, C:0.06, G:0.15, T:0.34
Consensus pattern (37 bp):
AAATATGTAAGATTGTTAAGATCAATGACTAAATTAC
Found at i:1613236 original size:17 final size:17
Alignment explanation
Indices: 1613197--1613267 Score: 54
Period size: 17 Copynumber: 4.2 Consensus size: 17
1613187 AATACAGTAT
* *
1613197 AGTAAGAGAAATAATAT
1 AGTAAAAGAAATAATAC
* *
1613214 AATAAAAGAAATTATAC
1 AGTAAAAGAAATAATAC
*
1613231 AGT-AAAGAAATCATCAC
1 AGTAAAAGAAATAAT-AC
* * *
1613248 AGAAAAAGGAACAATAC
1 AGTAAAAGAAATAATAC
1613265 AGT
1 AGT
1613268 GGAAGGAACG
Statistics
Matches: 41, Mismatches: 11, Indels: 4
0.73 0.20 0.07
Matches are distributed among these distances:
16 10 0.24
17 23 0.56
18 8 0.20
ACGTcount: A:0.59, C:0.08, G:0.14, T:0.18
Consensus pattern (17 bp):
AGTAAAAGAAATAATAC
Found at i:1613299 original size:17 final size:17
Alignment explanation
Indices: 1613279--1613323 Score: 65
Period size: 17 Copynumber: 2.6 Consensus size: 17
1613269 GAAGGAACGA
1613279 TACAGGAAAAAGAATAG
1 TACAGGAAAAAGAATAG
*
1613296 TACAGTG-AAAGGAATAG
1 TACAG-GAAAAAGAATAG
1613313 TACAGGAAAAA
1 TACAGGAAAAA
1613324 AAGAGTGAGT
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
16 1 0.04
17 22 0.92
18 1 0.04
ACGTcount: A:0.56, C:0.07, G:0.24, T:0.13
Consensus pattern (17 bp):
TACAGGAAAAAGAATAG
Found at i:1614872 original size:14 final size:14
Alignment explanation
Indices: 1614854--1614899 Score: 83
Period size: 14 Copynumber: 3.3 Consensus size: 14
1614844 GCTGGGCATC
*
1614854 CGAGGCCATCCGAC
1 CGAGGCCATCCGAA
1614868 CGAGGCCATCCGAA
1 CGAGGCCATCCGAA
1614882 CGAGGCCATCCGAA
1 CGAGGCCATCCGAA
1614896 CGAG
1 CGAG
1614900 CTATGCGAGG
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
14 31 1.00
ACGTcount: A:0.26, C:0.37, G:0.30, T:0.07
Consensus pattern (14 bp):
CGAGGCCATCCGAA
Found at i:1614985 original size:20 final size:20
Alignment explanation
Indices: 1614960--1615030 Score: 106
Period size: 20 Copynumber: 3.5 Consensus size: 20
1614950 ATGGCGACCT
*
1614960 GATGGCCTTGGATGCTCTCG
1 GATGGCCTCGGATGCTCTCG
1614980 GATGGCCTCGGATGCTCTCG
1 GATGGCCTCGGATGCTCTCG
* * *
1615000 GATGGCCTCAGATACTTTCG
1 GATGGCCTCGGATGCTCTCG
1615020 GATGGCCTCGG
1 GATGGCCTCGG
1615031 TCGGATGGCC
Statistics
Matches: 46, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 46 1.00
ACGTcount: A:0.13, C:0.27, G:0.34, T:0.27
Consensus pattern (20 bp):
GATGGCCTCGGATGCTCTCG
Found at i:1615036 original size:14 final size:14
Alignment explanation
Indices: 1615017--1615044 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
1615007 TCAGATACTT
1615017 TCGGATGGCCTCGG
1 TCGGATGGCCTCGG
1615031 TCGGATGGCCTCGG
1 TCGGATGGCCTCGG
1615045 ATGCCCAGCG
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:0.07, C:0.29, G:0.43, T:0.21
Consensus pattern (14 bp):
TCGGATGGCCTCGG
Found at i:1615047 original size:10 final size:10
Alignment explanation
Indices: 1614960--1615030 Score: 58
Period size: 10 Copynumber: 7.1 Consensus size: 10
1614950 ATGGCGACCT
*
1614960 GATGGCCTTG
1 GATGGCCTCG
1614970 GAT-GCTCTCG
1 GATGGC-CTCG
1614980 GATGGCCTCG
1 GATGGCCTCG
1614990 GAT-GCTCTCG
1 GATGGC-CTCG
*
1615000 GATGGCCTCA
1 GATGGCCTCG
* *
1615010 GAT-ACTTTCG
1 GATGGC-CTCG
1615020 GATGGCCTCG
1 GATGGCCTCG
1615030 G
1 G
1615031 TCGGATGGCC
Statistics
Matches: 48, Mismatches: 7, Indels: 12
0.72 0.10 0.18
Matches are distributed among these distances:
9 5 0.10
10 38 0.79
11 5 0.10
ACGTcount: A:0.13, C:0.27, G:0.34, T:0.27
Consensus pattern (10 bp):
GATGGCCTCG
Found at i:1615976 original size:24 final size:25
Alignment explanation
Indices: 1615936--1616000 Score: 71
Period size: 24 Copynumber: 2.6 Consensus size: 25
1615926 TAAACAAAAA
* *
1615936 TATAAACGAATATGTTCGA-GAACAT
1 TATAAACGAACACGTTC-ACGAACAT
1615961 T-TAAACGAACACGTTCACGAACAT
1 TATAAACGAACACGTTCACGAACAT
1615985 TAAATAAACGAACACG
1 T--ATAAACGAACACG
1616001 AACACCTTCA
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
23 1 0.03
24 20 0.59
25 1 0.03
27 12 0.35
ACGTcount: A:0.46, C:0.18, G:0.14, T:0.22
Consensus pattern (25 bp):
TATAAACGAACACGTTCACGAACAT
Found at i:1616002 original size:33 final size:29
Alignment explanation
Indices: 1615965--1616035 Score: 88
Period size: 29 Copynumber: 2.3 Consensus size: 29
1615955 GAACATTTAA
1615965 ACGAACACGTTCACGAACATTAAATAAACGAAC
1 ACGAACACGTTCA--AA-A-TAAATAAACGAAC
* *
1615998 ACGAACACCTTCAAAATAAATAAACGGAC
1 ACGAACACGTTCAAAATAAATAAACGAAC
1616027 ACGAACACG
1 ACGAACACG
1616036 ATATTAAAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
29 20 0.57
30 1 0.03
31 2 0.06
33 12 0.34
ACGTcount: A:0.49, C:0.25, G:0.13, T:0.13
Consensus pattern (29 bp):
ACGAACACGTTCAAAATAAATAAACGAAC
Found at i:1616769 original size:14 final size:14
Alignment explanation
Indices: 1616750--1616786 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
1616740 TGGACAAAAT
1616750 ATAAATGAACTAAC
1 ATAAATGAACTAAC
*
1616764 ATAAATAAACTAAC
1 ATAAATGAACTAAC
1616778 ATAAATGAA
1 ATAAATGAA
1616787 TGGATTATCG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.62, C:0.11, G:0.05, T:0.22
Consensus pattern (14 bp):
ATAAATGAACTAAC
Found at i:1617457 original size:29 final size:29
Alignment explanation
Indices: 1617403--1617475 Score: 83
Period size: 29 Copynumber: 2.5 Consensus size: 29
1617393 AACCCAACCA
* * **
1617403 TAGGTCGCCATGCACTCCCAGTGACCTCC
1 TAGGTCGCCATGCACGCCCAGCGACCAAC
* *
1617432 TAGGTCGCCATGCACGCCCGGCGACCAAG
1 TAGGTCGCCATGCACGCCCAGCGACCAAC
*
1617461 GAGGTCGCCATGCAC
1 TAGGTCGCCATGCAC
1617476 TCGGGGCGAC
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
29 37 1.00
ACGTcount: A:0.19, C:0.38, G:0.27, T:0.15
Consensus pattern (29 bp):
TAGGTCGCCATGCACGCCCAGCGACCAAC
Found at i:1617483 original size:29 final size:29
Alignment explanation
Indices: 1617433--1617491 Score: 91
Period size: 29 Copynumber: 2.0 Consensus size: 29
1617423 GTGACCTCCT
1617433 AGGTCGCCATGCACGCCCGGCGACCAAGG
1 AGGTCGCCATGCACGCCCGGCGACCAAGG
* **
1617462 AGGTCGCCATGCACTCGGGGCGACCAAGG
1 AGGTCGCCATGCACGCCCGGCGACCAAGG
1617491 A
1 A
1617492 TTCATGCATG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.22, C:0.34, G:0.36, T:0.08
Consensus pattern (29 bp):
AGGTCGCCATGCACGCCCGGCGACCAAGG
Found at i:1617739 original size:29 final size:29
Alignment explanation
Indices: 1617706--1617790 Score: 107
Period size: 29 Copynumber: 2.9 Consensus size: 29
1617696 AACAGGGGAT
* * **
1617706 GTCGCCGCGAGTGCATGGCGACCTCCTTG
1 GTCGCCGGGAGTGCATGGCGACCTACGAG
* *
1617735 GTCGCCGGGCGTGCATGGCGACCTAGGAG
1 GTCGCCGGGAGTGCATGGCGACCTACGAG
*
1617764 GTCGCTGGGAGTGCATGGCGACCTACG
1 GTCGCCGGGAGTGCATGGCGACCTACG
1617791 GCCACTGTTG
Statistics
Matches: 47, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
29 47 1.00
ACGTcount: A:0.13, C:0.29, G:0.40, T:0.18
Consensus pattern (29 bp):
GTCGCCGGGAGTGCATGGCGACCTACGAG
Found at i:1619478 original size:184 final size:184
Alignment explanation
Indices: 1619167--1620645 Score: 2831
Period size: 184 Copynumber: 8.1 Consensus size: 184
1619157 AGGAGGAGGA
* *
1619167 GGAGGAGAAGTGGCG-A--AGGAGTATGTGAAGAAGAAGAAAGTTTGCCCTAGTGTAGTTTCCTG
1 GGAGAAGAAGTGGCGAAGGAGGAGTATGTGAAGAAGAAGAAAGTTTGCCCTAGTGTAGTTTGCTG
* *
1619229 TGCTGATATGTTGACCACTGCTT-CTGGTGACTGTTAAAAATGTAAAACTCCTAGGTTAAAGGTG
66 TGCTGATATGTTGGCCGCTG-TTGCTGGTGACTGTTAAAAATGTAAAACTCCTAGGTTAAAGGTG
1619293 TTAAACAACTTGAACTGGAAGGACTTTGGCCTGAAGGCTCTGGGAAGGTGAAGGC
130 TTAAACAACTTGAACTGGAAGGACTTTGGCCTGAAGGCTCTGGGAAGGTGAAGGC
1619348 GGAGAAGAAGTGGCGAAGGAGGAGTATGTGAAGAAGAAGAAAGTTTGCCCTAGTGTAGTTTGCTG
1 GGAGAAGAAGTGGCGAAGGAGGAGTATGTGAAGAAGAAGAAAGTTTGCCCTAGTGTAGTTTGCTG
1619413 TGCTGATATGTTGGCCGCTGTTGCTGGTGACTGTTAAAAATGTAAAACTCCTAGGTTAAAGGTGT
66 TGCTGATATGTTGGCCGCTGTTGCTGGTGACTGTTAAAAATGTAAAACTCCTAGGTTAAAGGTGT
1619478 TAAACAACTTGAACTGGAAGGACTTTGGCCTGAAGGCTCTGGGAAGGTGAAGGC
131 TAAACAACTTGAACTGGAAGGACTTTGGCCTGAAGGCTCTGGGAAGGTGAAGGC
1619532 GGAGAAGAAGTGGCGAAGGAGGAGTATGTGAAGAAGAAGAAAGTTTGCCCTAGTGTAGTTTGCTG
1 GGAGAAGAAGTGGCGAAGGAGGAGTATGTGAAGAAGAAGAAAGTTTGCCCTAGTGTAGTTTGCTG
*
1619597 TGCTGATATGTTGGCCGCTGTTGCTGGTGACTGTTAAAAATGTAAAACTCCTAGGTTAAAGTTGT
66 TGCTGATATGTTGGCCGCTGTTGCTGGTGACTGTTAAAAATGTAAAACTCCTAGGTTAAAGGTGT
1619662 TAAACAACTTGAACTGGAAGGACTTTGGCCTGAAGGCTCTGGGAAGGTGAAGGC
131 TAAACAACTTGAACTGGAAGGACTTTGGCCTGAAGGCTCTGGGAAGGTGAAGGC
1619716 GGAGAAGAAGTGGCGAAGGAGGAGTATGTGAAGAAGAAGAAAGTTTGCCCTAGTGTAGTTTGCTG
1 GGAGAAGAAGTGGCGAAGGAGGAGTATGTGAAGAAGAAGAAAGTTTGCCCTAGTGTAGTTTGCTG
1619781 TGCTGATATGTTGGCCGCTGTTGCTGGTGACTGTTAAAAATGTAAAACTCCTAGGTTAAAGGTGT
66 TGCTGATATGTTGGCCGCTGTTGCTGGTGACTGTTAAAAATGTAAAACTCCTAGGTTAAAGGTGT
1619846 TAAACAACTTGAACTGGAAGGACTTTGGCCTGAAGGCTCTGGGAAGGTGAAGGC
131 TAAACAACTTGAACTGGAAGGACTTTGGCCTGAAGGCTCTGGGAAGGTGAAGGC
1619900 GGAGAAGAAGTGGCGAAGGAGGAGTATGTGAAGAAGAAGAAAGTTTGCCCTAGTGTAGTTTGCTG
1 GGAGAAGAAGTGGCGAAGGAGGAGTATGTGAAGAAGAAGAAAGTTTGCCCTAGTGTAGTTTGCTG
*
1619965 TGCTGATATGTTGGCCGCTGTTGCTGGTGACTGTTAAAAATGAAAAACTCCTAGGTTAAAGGTGT
66 TGCTGATATGTTGGCCGCTGTTGCTGGTGACTGTTAAAAATGTAAAACTCCTAGGTTAAAGGTGT
1620030 TAAACAACTTGAACTGGAAGGACTTTGGCCTGAAGGCTCTGGGAAGGTGAAGGC
131 TAAACAACTTGAACTGGAAGGACTTTGGCCTGAAGGCTCTGGGAAGGTGAAGGC
*
1620084 GGAGAAGAAGTGGCGAAGGAAGAGTATGTGAAGAAGAAGAAAGTTTGCCCTAGTGTAGTTTGCTG
1 GGAGAAGAAGTGGCGAAGGAGGAGTATGTGAAGAAGAAGAAAGTTTGCCCTAGTGTAGTTTGCTG
*
1620149 TGCTGATATGTTGGCCGCTGTTGCTGGTGACTGTTAAAAATGTAAAACTCCTAGGTTAAAGTTGT
66 TGCTGATATGTTGGCCGCTGTTGCTGGTGACTGTTAAAAATGTAAAACTCCTAGGTTAAAGGTGT
1620214 TAAACAACTTGAACTGGAAGGACTTTGGCCTGAAGGCTCTGGGAAGGTGAAGGC
131 TAAACAACTTGAACTGGAAGGACTTTGGCCTGAAGGCTCTGGGAAGGTGAAGGC
1620268 GGAGAAGAAGTGGCGAAGGAGGAGTATGTGAAGAAGAAGAAAGTTTGCCCTAGTGTAGTTTGCTG
1 GGAGAAGAAGTGGCGAAGGAGGAGTATGTGAAGAAGAAGAAAGTTTGCCCTAGTGTAGTTTGCTG
1620333 TGCTGATATGTTGGCCGCTGTTGCTGGTGACTGTTAAAAATGTAAAACTCCTAGGTTAAAGGTGT
66 TGCTGATATGTTGGCCGCTGTTGCTGGTGACTGTTAAAAATGTAAAACTCCTAGGTTAAAGGTGT
1620398 TAAACAACTTGAACTGGAAGGACTTTGGCCTGAAGGCTCTGGGAAGGTGAAGGC
131 TAAACAACTTGAACTGGAAGGACTTTGGCCTGAAGGCTCTGGGAAGGTGAAGGC
1620452 GGAGAAGAAGTGGCGAAGGAGGAGTATGTGAAGAAGAAGAAAGTTTGCCCTAGTGTAGTTTGCTG
1 GGAGAAGAAGTGGCGAAGGAGGAGTATGTGAAGAAGAAGAAAGTTTGCCCTAGTGTAGTTTGCTG
*
1620517 TGCTGATATGTTGGCCGCTGTTGCTGGTGACTGTTAAAAATGAAAAACTCCTAGGTTAAAGGTGT
66 TGCTGATATGTTGGCCGCTGTTGCTGGTGACTGTTAAAAATGTAAAACTCCTAGGTTAAAGGTGT
*
1620582 TAAACAACTTGAACTGGAAGGACTTTGGTCTGAAGGCTCTGGGAAGGTGAAGGC
131 TAAACAACTTGAACTGGAAGGACTTTGGCCTGAAGGCTCTGGGAAGGTGAAGGC
1620636 GGAGAAGAAG
1 GGAGAAGAAG
1620646 AAAATTTAGC
Statistics
Matches: 1280, Mismatches: 14, Indels: 5
0.99 0.01 0.00
Matches are distributed among these distances:
181 14 0.01
182 1 0.00
183 2 0.00
184 1263 0.99
ACGTcount: A:0.29, C:0.13, G:0.33, T:0.25
Consensus pattern (184 bp):
GGAGAAGAAGTGGCGAAGGAGGAGTATGTGAAGAAGAAGAAAGTTTGCCCTAGTGTAGTTTGCTG
TGCTGATATGTTGGCCGCTGTTGCTGGTGACTGTTAAAAATGTAAAACTCCTAGGTTAAAGGTGT
TAAACAACTTGAACTGGAAGGACTTTGGCCTGAAGGCTCTGGGAAGGTGAAGGC
Found at i:1621501 original size:18 final size:18
Alignment explanation
Indices: 1621472--1621508 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
1621462 GTTCATGTAA
1621472 AAATTAAATAATAATATTT
1 AAATTAAATAATAA-ATTT
1621491 AAATT-AATAATAAATTT
1 AAATTAAATAATAAATTT
1621508 A
1 A
1621509 TATGTTAGAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 5 0.28
18 8 0.44
19 5 0.28
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (18 bp):
AAATTAAATAATAAATTT
Found at i:1629900 original size:17 final size:17
Alignment explanation
Indices: 1629880--1629919 Score: 62
Period size: 17 Copynumber: 2.4 Consensus size: 17
1629870 GTTTATTTAT
*
1629880 TTTTTATTAAAAATATA
1 TTTTTATTAAAAAAATA
*
1629897 TTTTTTTTAAAAAAATA
1 TTTTTATTAAAAAAATA
1629914 TTTTTA
1 TTTTTA
1629920 CATTCCTTAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.57
Consensus pattern (17 bp):
TTTTTATTAAAAAAATA
Found at i:1638780 original size:19 final size:21
Alignment explanation
Indices: 1638744--1638783 Score: 66
Period size: 19 Copynumber: 2.0 Consensus size: 21
1638734 TAAAAATAAT
1638744 TAAAAATATTTGTTTAAAATA
1 TAAAAATATTTGTTTAAAATA
1638765 TAAAAATA-TT-TTTAAAATA
1 TAAAAATATTTGTTTAAAATA
1638784 ATTTTTAGAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 9 0.47
20 2 0.11
21 8 0.42
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (21 bp):
TAAAAATATTTGTTTAAAATA
Found at i:1642447 original size:51 final size:51
Alignment explanation
Indices: 1642287--1642447 Score: 121
Period size: 51 Copynumber: 3.1 Consensus size: 51
1642277 TGTACTTCAA
1642287 TCTGGTCTATATGTTAGTTTTAATTTACATTTTCAAAACTCTCTATGTTAT
1 TCTGGTCTATATGTTAGTTTTAATTTACATTTTCAAAACTCTCTATGTTAT
* ** * * *** * * ** * * *
1642338 TCTGGTAGTA-ATGTGGGATTTTATTTCTTAAAGGATGAGAA-GATGTACT-TCAA
1 TCTGGT-CTATATGTTAG-TTTTA-AT-TTACATTTTCAAAACTCTCTA-TGTTAT
1642391 TCTGGTCTATATGTTAGTTTTAATTTACATTTTCAAAACTCTCTATGTTAT
1 TCTGGTCTATATGTTAGTTTTAATTTACATTTTCAAAACTCTCTATGTTAT
1642442 TCTGGT
1 TCTGGT
1642448 AGTAATGTGG
Statistics
Matches: 72, Mismatches: 30, Indels: 16
0.61 0.25 0.14
Matches are distributed among these distances:
50 9 0.12
51 23 0.32
52 14 0.19
53 17 0.24
54 9 0.12
ACGTcount: A:0.26, C:0.12, G:0.16, T:0.47
Consensus pattern (51 bp):
TCTGGTCTATATGTTAGTTTTAATTTACATTTTCAAAACTCTCTATGTTAT
Found at i:1642454 original size:104 final size:104
Alignment explanation
Indices: 1642274--1642485 Score: 424
Period size: 104 Copynumber: 2.0 Consensus size: 104
1642264 TGCCTTATAT
1642274 AGATGTACTTCAATCTGGTCTATATGTTAGTTTTAATTTACATTTTCAAAACTCTCTATGTTATT
1 AGATGTACTTCAATCTGGTCTATATGTTAGTTTTAATTTACATTTTCAAAACTCTCTATGTTATT
1642339 CTGGTAGTAATGTGGGATTTTATTTCTTAAAGGATGAGA
66 CTGGTAGTAATGTGGGATTTTATTTCTTAAAGGATGAGA
1642378 AGATGTACTTCAATCTGGTCTATATGTTAGTTTTAATTTACATTTTCAAAACTCTCTATGTTATT
1 AGATGTACTTCAATCTGGTCTATATGTTAGTTTTAATTTACATTTTCAAAACTCTCTATGTTATT
1642443 CTGGTAGTAATGTGGGATTTTATTTCTTAAAGGATGAGA
66 CTGGTAGTAATGTGGGATTTTATTTCTTAAAGGATGAGA
1642482 AGAT
1 AGAT
1642486 TAAAAACGTT
Statistics
Matches: 108, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
104 108 1.00
ACGTcount: A:0.28, C:0.10, G:0.17, T:0.44
Consensus pattern (104 bp):
AGATGTACTTCAATCTGGTCTATATGTTAGTTTTAATTTACATTTTCAAAACTCTCTATGTTATT
CTGGTAGTAATGTGGGATTTTATTTCTTAAAGGATGAGA
Found at i:1650364 original size:40 final size:40
Alignment explanation
Indices: 1650304--1650384 Score: 135
Period size: 40 Copynumber: 2.0 Consensus size: 40
1650294 CGTCAAATAT
*
1650304 AGTGATCGTATGATAGAAGAGATCAAAATTTTACAGGGAA
1 AGTGATCGTATGATAAAAGAGATCAAAATTTTACAGGGAA
* *
1650344 AGTGATCGTATGATAAAAGAGATCAAAGTTTTACATGGAA
1 AGTGATCGTATGATAAAAGAGATCAAAATTTTACAGGGAA
1650384 A
1 A
1650385 ATCCTTGACG
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
40 38 1.00
ACGTcount: A:0.43, C:0.07, G:0.23, T:0.26
Consensus pattern (40 bp):
AGTGATCGTATGATAAAAGAGATCAAAATTTTACAGGGAA
Found at i:1651087 original size:21 final size:21
Alignment explanation
Indices: 1651045--1651087 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
1651035 AAGAGTTTTA
* *
1651045 ATATACATCAAATTTTGGGAT
1 ATATACATCAAATTATGAGAT
*
1651066 ATATATATCAAATTATGAGAT
1 ATATACATCAAATTATGAGAT
1651087 A
1 A
1651088 CAAGAAAATT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.44, C:0.07, G:0.12, T:0.37
Consensus pattern (21 bp):
ATATACATCAAATTATGAGAT
Found at i:1657253 original size:21 final size:21
Alignment explanation
Indices: 1657219--1657266 Score: 69
Period size: 21 Copynumber: 2.3 Consensus size: 21
1657209 TAATTTTCAA
* *
1657219 ACATTATTGCACCTAATTTTT
1 ACATTGTTGCACCTAATTTTG
*
1657240 ACATTGTTGTACCTAATTTTG
1 ACATTGTTGCACCTAATTTTG
1657261 ACATTG
1 ACATTG
1657267 CAATATTAGG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.27, C:0.17, G:0.10, T:0.46
Consensus pattern (21 bp):
ACATTGTTGCACCTAATTTTG
Found at i:1661917 original size:21 final size:21
Alignment explanation
Indices: 1661884--1661931 Score: 69
Period size: 21 Copynumber: 2.3 Consensus size: 21
1661874 TAATTTTCAA
* *
1661884 ACATTATTGCACCTAATTTTG
1 ACATTGTTACACCTAATTTTG
1661905 ACATTGTTACACCTAATTTTG
1 ACATTGTTACACCTAATTTTG
*
1661926 ATATTG
1 ACATTG
1661932 CAATATTAGG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.29, C:0.17, G:0.10, T:0.44
Consensus pattern (21 bp):
ACATTGTTACACCTAATTTTG
Found at i:1662633 original size:4 final size:4
Alignment explanation
Indices: 1662624--1662651 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
1662614 AGCCCATGAT
1662624 ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1662652 CACCATATAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.50, C:0.25, G:0.00, T:0.25
Consensus pattern (4 bp):
ATAC
Done.