Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007883.1 Hibiscus syriacus cultivar Beakdansim tig00110263_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: 1590433
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 9
Found at i:307256 original size:19 final size:19
Alignment explanation
Indices: 307215--307278 Score: 69
Period size: 19 Copynumber: 3.3 Consensus size: 19
307205 GTCGGGTCAG
*
307215 ACCGGTCAAACCGATTC-A
1 ACCGGTCAAACCGGTTCGA
307233 GACCGGTCAAACCGGTTCGA
1 -ACCGGTCAAACCGGTTCGA
*
307253 ACCGGTTGAAACCGG-TCAGA
1 ACCGG-TCAAACCGGTTC-GA
307273 ACCGGT
1 ACCGGT
307279 TGAAAACCGG
Statistics
Matches: 40, Mismatches: 2, Indels: 6
0.83 0.04 0.12
Matches are distributed among these distances:
19 24 0.60
20 16 0.40
ACGTcount: A:0.28, C:0.30, G:0.27, T:0.16
Consensus pattern (19 bp):
ACCGGTCAAACCGGTTCGA
Found at i:307266 original size:20 final size:20
Alignment explanation
Indices: 307241--307299 Score: 84
Period size: 20 Copynumber: 2.9 Consensus size: 20
307231 CAGACCGGTC
307241 AAACCGGTTCGAACCGGTTG-
1 AAACCGG-TCGAACCGGTTGA
307261 AAACCGGTCAGAACCGGTTGA
1 AAACCGGTC-GAACCGGTTGA
*
307282 AAACCGGTCAAACCGGTT
1 AAACCGGTCGAACCGGTT
307300 TCCAGCAGCC
Statistics
Matches: 36, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
19 2 0.06
20 25 0.69
21 9 0.25
ACGTcount: A:0.31, C:0.25, G:0.27, T:0.17
Consensus pattern (20 bp):
AAACCGGTCGAACCGGTTGA
Found at i:310548 original size:23 final size:23
Alignment explanation
Indices: 310529--310612 Score: 123
Period size: 23 Copynumber: 3.7 Consensus size: 23
310519 TATGGCATTA
310529 CGGTGCATTTCTACGCGGCACTT
1 CGGTGCATTTCTACGCGGCACTT
* * *
310552 CGGTGCAATTCTACGTGGCACTA
1 CGGTGCATTTCTACGCGGCACTT
*
310575 CTGTGCATTTCTACGCGGCACTT
1 CGGTGCATTTCTACGCGGCACTT
*
310598 CGGTGCATTTATACG
1 CGGTGCATTTCTACG
310613 AGCTGTGGTG
Statistics
Matches: 52, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 52 1.00
ACGTcount: A:0.17, C:0.27, G:0.25, T:0.31
Consensus pattern (23 bp):
CGGTGCATTTCTACGCGGCACTT
Found at i:312172 original size:10 final size:10
Alignment explanation
Indices: 312153--312185 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
312143 AAATTAGACT
312153 AATAAAATGA
1 AATAAAATGA
*
312163 AATGAAATGA
1 AATAAAATGA
312173 AATAAAAT-A
1 AATAAAATGA
312182 AATA
1 AATA
312186 TTAATAATAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
9 5 0.24
10 16 0.76
ACGTcount: A:0.70, C:0.00, G:0.09, T:0.21
Consensus pattern (10 bp):
AATAAAATGA
Found at i:312194 original size:38 final size:38
Alignment explanation
Indices: 312115--312202 Score: 101
Period size: 39 Copynumber: 2.3 Consensus size: 38
312105 CCTTGACAAA
* *
312115 AATAAAATAAATGAAACTAAATTAAATTAAATTAGACT
1 AATAAAATAAATGAAACTAAATAAAATAAAATTAGACT
312153 AATAAAATGAAATGAAA-TGAAATAAAATAAATATTA-A-T
1 AATAAAAT-AAATGAAACT-AAATAAAATAAA-ATTAGACT
*
312191 AATAATATAAAT
1 AATAAAATAAAT
312203 TATATAATAT
Statistics
Matches: 44, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
37 4 0.09
38 17 0.39
39 19 0.43
40 4 0.09
ACGTcount: A:0.64, C:0.02, G:0.06, T:0.28
Consensus pattern (38 bp):
AATAAAATAAATGAAACTAAATAAAATAAAATTAGACT
Found at i:312350 original size:39 final size:40
Alignment explanation
Indices: 312307--312389 Score: 123
Period size: 40 Copynumber: 2.1 Consensus size: 40
312297 GATTTTAAAA
* * * *
312307 ATATAAGTTTTC-CAAAATGTTTTTTTAAAACTTTATATT
1 ATATAAATTTTCAAAAAATGTTTTTTAAAAACTATATATT
312346 ATATAAATTTTCAAAAAATGTTTTTTAAAAACTATATATT
1 ATATAAATTTTCAAAAAATGTTTTTTAAAAACTATATATT
312386 ATAT
1 ATAT
312390 TGTCAAAATG
Statistics
Matches: 39, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
39 11 0.28
40 28 0.72
ACGTcount: A:0.42, C:0.06, G:0.04, T:0.48
Consensus pattern (40 bp):
ATATAAATTTTCAAAAAATGTTTTTTAAAAACTATATATT
Found at i:312410 original size:32 final size:32
Alignment explanation
Indices: 312373--312452 Score: 99
Period size: 35 Copynumber: 2.4 Consensus size: 32
312363 ATGTTTTTTA
312373 AAAACTATATATTAT-ATTGTCAAAATGATTTC
1 AAAACTATATATTATAATTGTCAAAATG-TTTC
* *
312405 AAAACTATATACTATATAATTTTCAAAATGTTTT
1 AAAACTATATA-T-TATAATTGTCAAAATGTTTC
312439 AAAACTTATATATT
1 AAAAC-TATATATT
312453 GTATATAAGA
Statistics
Matches: 42, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
32 11 0.26
33 2 0.05
34 12 0.29
35 17 0.40
ACGTcount: A:0.45, C:0.09, G:0.04, T:0.42
Consensus pattern (32 bp):
AAAACTATATATTATAATTGTCAAAATGTTTC
Found at i:312449 original size:35 final size:34
Alignment explanation
Indices: 312307--312451 Score: 127
Period size: 34 Copynumber: 4.1 Consensus size: 34
312297 GATTTTAAAA
*
312307 ATATAAGTTTTCCAAAATGTTTTTTTAAAACTTTATATT
1 ATATAA-TTTT-CAAAATG--TTTTTAAAACTATATA-T
312346 ATATAAATTTTCAAAAAATGTTTTTTAAAAACTATATAT
1 ATAT-AATTTTC--AAAATG-TTTTT-AAAACTATATAT
* * *
312385 -TAT-ATTGTCAAAATGATTTCAAAACTATATACT
1 ATATAATTTTCAAAATGTTTTTAAAACTATATA-T
312418 ATATAATTTTCAAAATG-TTTTAAAACT-TATAT
1 ATATAATTTTCAAAATGTTTTTAAAACTATATAT
312450 AT
1 AT
312452 TGTATATAAG
Statistics
Matches: 93, Mismatches: 6, Indels: 21
0.77 0.05 0.17
Matches are distributed among these distances:
32 14 0.15
33 8 0.09
34 18 0.19
35 11 0.12
36 5 0.05
38 4 0.04
39 15 0.16
40 18 0.19
ACGTcount: A:0.43, C:0.08, G:0.04, T:0.46
Consensus pattern (34 bp):
ATATAATTTTCAAAATGTTTTTAAAACTATATAT
Found at i:316579 original size:23 final size:23
Alignment explanation
Indices: 316560--316643 Score: 123
Period size: 23 Copynumber: 3.7 Consensus size: 23
316550 TATGGCATTA
316560 CGGTGCATTTCTACGCGGCACTT
1 CGGTGCATTTCTACGCGGCACTT
* * *
316583 CGGTGCAATTCTACGTGGCACTA
1 CGGTGCATTTCTACGCGGCACTT
*
316606 CTGTGCATTTCTACGCGGCACTT
1 CGGTGCATTTCTACGCGGCACTT
*
316629 CGGTGCATTTATACG
1 CGGTGCATTTCTACG
316644 AGCTGTGGTG
Statistics
Matches: 52, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 52 1.00
ACGTcount: A:0.17, C:0.27, G:0.25, T:0.31
Consensus pattern (23 bp):
CGGTGCATTTCTACGCGGCACTT
Found at i:316750 original size:2 final size:2
Alignment explanation
Indices: 316743--316797 Score: 110
Period size: 2 Copynumber: 27.5 Consensus size: 2
316733 CATGAATACA
316743 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
316785 AT AT AT AT AT AT A
1 AT AT AT AT AT AT A
316798 ATGTATGTGC
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 53 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:317868 original size:31 final size:31
Alignment explanation
Indices: 317830--317954 Score: 198
Period size: 31 Copynumber: 4.0 Consensus size: 31
317820 CCCGAAGGAC
* * *
317830 CAGTCCATA-GATTCCGAAGAACCTAGGTAAT
1 CAGTCCATATG-TCCCGAAGAACATAGGTAAA
*
317861 CAGTCCATATGTCCCGAAGGACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
317892 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
317923 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
317954 C
1 C
317955 CCTCGACCCT
Statistics
Matches: 88, Mismatches: 5, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
31 87 0.99
32 1 0.01
ACGTcount: A:0.37, C:0.23, G:0.20, T:0.20
Consensus pattern (31 bp):
CAGTCCATATGTCCCGAAGAACATAGGTAAA
Found at i:318784 original size:21 final size:21
Alignment explanation
Indices: 318754--318798 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
318744 ATTCTGTCGT
* *
318754 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
318775 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
318796 TTG
1 TTG
318799 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:320687 original size:29 final size:30
Alignment explanation
Indices: 320635--320699 Score: 80
Period size: 28 Copynumber: 2.2 Consensus size: 30
320625 AACTATATAT
320635 TATATAGTTTTCAAAAATG-ATTTTAAAAA
1 TATATAGTTTTCAAAAATGTATTTTAAAAA
* * *
320664 TATA-AGTTTTCCAAAATGTTTTTTTAAAAC
1 TATATAGTTTTCAAAAATG-TATTTTAAAAA
320694 TATATA
1 TATATA
320700 TTATATAAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
28 13 0.43
29 4 0.13
30 12 0.40
31 1 0.03
ACGTcount: A:0.43, C:0.06, G:0.06, T:0.45
Consensus pattern (30 bp):
TATATAGTTTTCAAAAATGTATTTTAAAAA
Found at i:320720 original size:40 final size:39
Alignment explanation
Indices: 320663--320882 Score: 170
Period size: 35 Copynumber: 5.9 Consensus size: 39
320653 GATTTTAAAA
* * *
320663 ATATAAGTTTTCCAAAATGTTTTTTTAAAACTATATATT
1 ATATAAATTTTCAAAAATGTTTTTTAAAAACTATATATT
320702 ATATAAATTTTCAAAAAATGTTTTTTAAAAACTATATA-T
1 ATATAAATTTTC-AAAAATGTTTTTTAAAAACTATATATT
* * *
320741 -TAT--ATTTTC-AAAATG--ATTTCAAAACTATATACT
1 ATATAAATTTTCAAAAATGTTTTTTAAAAACTATATATT
320774 ATAT-AATTTTC-AAAATG--TTTT-AAAACTTATATATTGT
1 ATATAAATTTTCAAAAATGTTTTTTAAAAAC-TATATA-T-T
* *
320811 ATATAAGA-TTTCAAAAACG--TTTTAAAAACTACATA--
1 ATATAA-ATTTTCAAAAATGTTTTTTAAAAACTATATATT
* *
320846 ATATATA-TTTCAAAAAATATTTTTTAAAAACTATATA
1 ATATAAATTTTC-AAAAATGTTTTTTAAAAACTATATA
320883 CTACATTTTT
Statistics
Matches: 154, Mismatches: 13, Indels: 30
0.78 0.07 0.15
Matches are distributed among these distances:
32 14 0.09
33 1 0.01
34 19 0.12
35 31 0.20
36 6 0.04
37 20 0.13
38 8 0.05
39 27 0.18
40 28 0.18
ACGTcount: A:0.45, C:0.08, G:0.04, T:0.43
Consensus pattern (39 bp):
ATATAAATTTTCAAAAATGTTTTTTAAAAACTATATATT
Found at i:320790 original size:35 final size:33
Alignment explanation
Indices: 320689--320860 Score: 118
Period size: 34 Copynumber: 4.8 Consensus size: 33
320679 ATGTTTTTTT
320689 AAAACTATATATTATATAAATTTTCAAAAAATGTTTTTTA
1 AAAACTATATA-TATAT-AATTTTC--AAAATG---TTTA
*
320729 AAAACTATATAT-TAT-ATTTTCAAAATGATTTC
1 AAAACTATATATATATAATTTTCAAAATG-TTTA
*
320761 AAAACTATATACTATATAATTTTCAAAATGTTTT
1 AAAACTATATA-TATATAATTTTCAAAATGTTTA
* *
320795 AAAACTTATATATTGTATATAAGATTTCAAAAACGTTTTA
1 AAAAC-TATATA---TATATAA-TTTTC-AAAATG-TTTA
*
320835 AAAACTACATA-ATAT-ATATTTCAAAA
1 AAAACTATATATATATAAT-TTTCAAAA
320861 AATATTTTTT
Statistics
Matches: 113, Mismatches: 9, Indels: 27
0.76 0.06 0.18
Matches are distributed among these distances:
32 14 0.12
33 5 0.04
34 22 0.19
35 22 0.19
36 6 0.05
37 7 0.06
38 7 0.06
39 11 0.10
40 19 0.17
ACGTcount: A:0.47, C:0.08, G:0.03, T:0.41
Consensus pattern (33 bp):
AAAACTATATATATATAATTTTCAAAATGTTTA
Found at i:323675 original size:3 final size:3
Alignment explanation
Indices: 323667--323740 Score: 121
Period size: 3 Copynumber: 24.7 Consensus size: 3
323657 TTTTTATCCA
*
323667 TAT TAT TAT TAT TAA TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* *
323715 TAT TAT CAT CAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TA
323741 AATATATATT
Statistics
Matches: 67, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 67 1.00
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (3 bp):
TAT
Found at i:324237 original size:20 final size:19
Alignment explanation
Indices: 324209--324260 Score: 68
Period size: 20 Copynumber: 2.6 Consensus size: 19
324199 CCGAACTTGA
*
324209 AAAAAAAAAAAAGGGAGAC
1 AAAAAAAAAAAAGGAAGAC
*
324228 AAAAAGAAAAGAAGGAAGAC
1 AAAAA-AAAAAAAGGAAGAC
324248 AGAAAAAAAAAAA
1 A-AAAAAAAAAAA
324261 CAGAGAAAGA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
19 5 0.18
20 19 0.68
21 4 0.14
ACGTcount: A:0.77, C:0.04, G:0.19, T:0.00
Consensus pattern (19 bp):
AAAAAAAAAAAAGGAAGAC
Found at i:324340 original size:15 final size:15
Alignment explanation
Indices: 324320--324351 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
324310 AGCAACCAAG
324320 AAAAGAAAGAAAAGA
1 AAAAGAAAGAAAAGA
*
324335 AAAAGAAAGAAGAGA
1 AAAAGAAAGAAAAGA
324350 AA
1 AA
324352 CTTACTGTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (15 bp):
AAAAGAAAGAAAAGA
Found at i:325941 original size:28 final size:28
Alignment explanation
Indices: 325910--325968 Score: 68
Period size: 28 Copynumber: 2.1 Consensus size: 28
325900 TAATTCTTTC
*
325910 TTTTCA-AA-ATTTTTATATTTACTTATTA
1 TTTTCATAATATTTGTATATTTA-TT-TTA
*
325938 TTTTCATAATATTTGTATGTTTATTTTA
1 TTTTCATAATATTTGTATATTTATTTTA
325966 TTT
1 TTT
325969 GTAAGTATTT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
28 12 0.44
29 4 0.15
30 11 0.41
ACGTcount: A:0.27, C:0.05, G:0.03, T:0.64
Consensus pattern (28 bp):
TTTTCATAATATTTGTATATTTATTTTA
Found at i:333068 original size:18 final size:19
Alignment explanation
Indices: 333040--333076 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
333030 AGATGGCAAT
*
333040 CATTCTTTACATTTTTTTA
1 CATTCTTTACATTTATTTA
333059 CATT-TTTACATTTATTTA
1 CATTCTTTACATTTATTTA
333077 TTTCATAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 13 0.76
19 4 0.24
ACGTcount: A:0.24, C:0.14, G:0.00, T:0.62
Consensus pattern (19 bp):
CATTCTTTACATTTATTTA
Found at i:336614 original size:18 final size:18
Alignment explanation
Indices: 336591--336649 Score: 63
Period size: 18 Copynumber: 3.4 Consensus size: 18
336581 ATTATGCTTG
*
336591 AAGAAAAAATAAAAAAGA
1 AAGAAAAAAGAAAAAAGA
336609 AAG--AAAAGAAAAAA-A
1 AAGAAAAAAGAAAAAAGA
*
336624 TAGAAAAAAGAGAAAAAG-
1 AAGAAAAAAGA-AAAAAGA
336642 AAGAAAAA
1 AAGAAAAA
336650 GGGGGTCAAG
Statistics
Matches: 34, Mismatches: 3, Indels: 8
0.76 0.07 0.18
Matches are distributed among these distances:
15 3 0.09
16 10 0.29
17 6 0.18
18 15 0.44
ACGTcount: A:0.81, C:0.00, G:0.15, T:0.03
Consensus pattern (18 bp):
AAGAAAAAAGAAAAAAGA
Found at i:336615 original size:9 final size:8
Alignment explanation
Indices: 336601--336650 Score: 55
Period size: 9 Copynumber: 5.9 Consensus size: 8
336591 AAGAAAAAAT
336601 AAAAAAGA
1 AAAAAAGA
336609 AAGAAAAGA
1 AA-AAAAGA
*
336618 AAAAAATA
1 AAAAAAGA
336626 GAAAAAAGA
1 -AAAAAAGA
*
336635 GAAAAAGA
1 AAAAAAGA
336643 AGAAAAAG
1 A-AAAAAG
336651 GGGGTCAAGG
Statistics
Matches: 35, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
8 14 0.40
9 21 0.60
ACGTcount: A:0.80, C:0.00, G:0.18, T:0.02
Consensus pattern (8 bp):
AAAAAAGA
Found at i:336633 original size:17 final size:18
Alignment explanation
Indices: 336590--336649 Score: 65
Period size: 16 Copynumber: 3.5 Consensus size: 18
336580 TATTATGCTT
*
336590 GAAGAAAAAATA-AAAAA
1 GAAGAAAAAAGAGAAAAA
*
336607 GAA-AGAAAAGA-AAAAA
1 GAAGAAAAAAGAGAAAAA
336623 -ATAGAAAAAAGAGAAAAA
1 GA-AGAAAAAAGAGAAAAA
336641 GAAGAAAAA
1 GAAGAAAAA
336650 GGGGGTCAAG
Statistics
Matches: 36, Mismatches: 3, Indels: 7
0.78 0.07 0.15
Matches are distributed among these distances:
15 1 0.03
16 12 0.33
17 10 0.28
18 12 0.33
19 1 0.03
ACGTcount: A:0.80, C:0.00, G:0.17, T:0.03
Consensus pattern (18 bp):
GAAGAAAAAAGAGAAAAA
Found at i:336650 original size:17 final size:16
Alignment explanation
Indices: 336590--336650 Score: 54
Period size: 17 Copynumber: 3.6 Consensus size: 16
336580 TATTATGCTT
*
336590 GAAGAAAAAATAAAAAA
1 GAAG-AAAAAGAAAAAA
336607 GAA-AGAAAAGAAAAAA
1 GAAGA-AAAAGAAAAAA
336623 -ATAGAAAAAAGAGAAAAA
1 GA-AG-AAAAAGA-AAAAA
336641 GAAGAAAAAG
1 GAAGAAAAAG
336651 GGGGTCAAGG
Statistics
Matches: 37, Mismatches: 1, Indels: 12
0.74 0.02 0.24
Matches are distributed among these distances:
15 2 0.05
16 11 0.30
17 15 0.41
18 8 0.22
19 1 0.03
ACGTcount: A:0.79, C:0.00, G:0.18, T:0.03
Consensus pattern (16 bp):
GAAGAAAAAGAAAAAA
Found at i:336978 original size:16 final size:16
Alignment explanation
Indices: 336957--336996 Score: 55
Period size: 16 Copynumber: 2.5 Consensus size: 16
336947 ATACAATTCT
336957 ATTTATTTCA-AGTTCA
1 ATTTATTTCAGAG-TCA
*
336973 ATTTATTTGAGAGTCA
1 ATTTATTTCAGAGTCA
336989 ATTTATTT
1 ATTTATTT
336997 TTGGAAATTC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 20 0.91
17 2 0.09
ACGTcount: A:0.30, C:0.07, G:0.10, T:0.53
Consensus pattern (16 bp):
ATTTATTTCAGAGTCA
Found at i:338071 original size:82 final size:83
Alignment explanation
Indices: 337783--338329 Score: 838
Period size: 82 Copynumber: 6.6 Consensus size: 83
337773 AATAGAACAA
*
337783 ATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTGGACAGAATC
1 ATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAATC
* *
337848 AAGCATTGAATTTGGAAG
66 AATCATTGAATTTAGAAG
*
337866 ATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTGGACAGAATC
1 ATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAATC
*
337931 AAGCATTGAATTTAGAAG
66 AATCATTGAATTTAGAAG
337949 ATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAA-C
1 ATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAATC
*
338013 AATCATTGAGTTTAGAAG
66 AATCATTGAATTTAGAAG
*
338031 ATGAATTTGTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGG-CAGAA-
1 ATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGG-TTGGACAGAAT
*
338094 CAATCATTGAGTTTAGAAG
65 CAATCATTGAATTTAGAAG
* *
338113 ATGAATGTGTTC-ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAA-
1 ATGAATTTG-CCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAAT
* *
338176 CAATCAGTGAGTTTAGAAG
65 CAATCATTGAATTTAGAAG
*
338195 ATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGG-CAGAAC
1 ATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGG-TTGGACAGAAT
** *
338259 CAATCATTGAATTCGGAAC
65 CAATCATTGAATTTAGAAG
* * *
338278 ATGAATGTGTTC-ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATATGATCTG
1 ATGAATTTG-CCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTG
338330 ATTCAGTAGG
Statistics
Matches: 440, Mismatches: 17, Indels: 14
0.93 0.04 0.03
Matches are distributed among these distances:
81 5 0.01
82 219 0.50
83 215 0.49
84 1 0.00
ACGTcount: A:0.27, C:0.13, G:0.23, T:0.36
Consensus pattern (83 bp):
ATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAATC
AATCATTGAATTTAGAAG
Found at i:339473 original size:116 final size:114
Alignment explanation
Indices: 338980--339535 Score: 901
Period size: 115 Copynumber: 4.9 Consensus size: 114
338970 AAAGATCAGC
338980 TTTTCCAGAG-AAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAG
1 TTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAG
* ** * * *
339044 AAGAACTTGTTCAACC-TTTTACCTGAA-TCAATC-ATTTGATGGATCAGC
66 AAGAATTTGTTCAACCTTTTTTTCTGAATTC-ATCAAATTGATGGATTA-T
339092 TTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAG
1 TTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAG
*
339157 AAGAATTTGTTCAACC-TTTTTTCTGAAGTCATCAAATTGATGGATTAT
66 AAGAATTTGTTCAACCTTTTTTTCTGAATTCATCAAATTGATGGATTAT
* *
339205 CTTTTCCAGAGAAGGTTCATAATGAGAAGAACCCATCTGAAGAAGGAAGAAGAAGTTCATAATGA
1 -TTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGA
339270 GAAGAATTTGTTCAACCTTTTTTTCTGAATTCATCAAATTGATGGATTAT
65 GAAGAATTTGTTCAACCTTTTTTTCTGAATTCATCAAATTGATGGATTAT
339320 TTTTGCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGA
1 TTTT-CCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGA
*
339385 GAAGAATTTGTTCAACCTTTTTTTACCTGAATTCATC-ACTTGATGGATTAT
65 GAAGAATTTGTTCAACCTTTTTTT--CTGAATTCATCAAATTGATGGATTAT
339436 TTTTGCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGA
1 TTTT-CCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGA
*
339501 GAAGAATTTGTTCAACC-TTTTGTCTGAATTCATCA
65 GAAGAATTTGTTCAACCTTTTTTTCTGAATTCATCA
339536 TCTAAAGAAA
Statistics
Matches: 422, Mismatches: 13, Indels: 16
0.94 0.03 0.04
Matches are distributed among these distances:
112 10 0.02
113 92 0.22
114 96 0.23
115 118 0.28
116 95 0.23
117 11 0.03
ACGTcount: A:0.37, C:0.13, G:0.19, T:0.30
Consensus pattern (114 bp):
TTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAG
AAGAATTTGTTCAACCTTTTTTTCTGAATTCATCAAATTGATGGATTAT
Found at i:339832 original size:3 final size:3
Alignment explanation
Indices: 339824--339924 Score: 175
Period size: 3 Copynumber: 33.7 Consensus size: 3
339814 TTTTTATCCA
*
339824 TAT TAT TAT TAT TAA TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* *
339872 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT CAT CAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
339920 TAT TA
1 TAT TA
339925 AATATATATT
Statistics
Matches: 94, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 94 1.00
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:340524 original size:15 final size:15
Alignment explanation
Indices: 340504--340535 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
340494 AGCAACCAAG
340504 AAAAGAAAGAAAAGA
1 AAAAGAAAGAAAAGA
*
340519 AAAAGAAAGAAGAGA
1 AAAAGAAAGAAAAGA
340534 AA
1 AA
340536 CTTACTGTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (15 bp):
AAAAGAAAGAAAAGA
Found at i:342521 original size:14 final size:14
Alignment explanation
Indices: 342499--342555 Score: 59
Period size: 14 Copynumber: 4.4 Consensus size: 14
342489 CGTTCGTGAA
*
342499 CGTTCGGTTATGTT
1 CGTTTGGTTATGTT
342513 CGTTTGGTTATGTT
1 CGTTTGGTTATGTT
*
342527 C--AT--TTATGTT
1 CGTTTGGTTATGTT
*
342537 CGTTTGATTATGTT
1 CGTTTGGTTATGTT
342551 CGTTT
1 CGTTT
342556 ATGTTCATTC
Statistics
Matches: 36, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
10 8 0.22
12 2 0.06
14 26 0.72
ACGTcount: A:0.11, C:0.11, G:0.23, T:0.56
Consensus pattern (14 bp):
CGTTTGGTTATGTT
Found at i:342527 original size:24 final size:24
Alignment explanation
Indices: 342500--342561 Score: 97
Period size: 24 Copynumber: 2.6 Consensus size: 24
342490 GTTCGTGAAC
* *
342500 GTTCGGTTATGTTCGTTTGGTTAT
1 GTTCGTTTATGTTCGTTTGATTAT
*
342524 GTTCATTTATGTTCGTTTGATTAT
1 GTTCGTTTATGTTCGTTTGATTAT
342548 GTTCGTTTATGTTC
1 GTTCGTTTATGTTC
342562 ATTCATTTAT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 34 1.00
ACGTcount: A:0.11, C:0.10, G:0.23, T:0.56
Consensus pattern (24 bp):
GTTCGTTTATGTTCGTTTGATTAT
Found at i:342571 original size:24 final size:24
Alignment explanation
Indices: 342506--342574 Score: 68
Period size: 24 Copynumber: 2.9 Consensus size: 24
342496 GAACGTTCGG
* **
342506 TTATGTTCGTTTGGTTATGTTCAT
1 TTATGTTCGATTCATTATGTTCAT
* * *
342530 TTATGTTCGTTTGATTATGTTCGT
1 TTATGTTCGATTCATTATGTTCAT
342554 TTATGTTC-ATTCATTTATGTT
1 TTATGTTCGATTCA-TTATGTT
342575 TAACACAATC
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
23 3 0.08
24 37 0.93
ACGTcount: A:0.14, C:0.09, G:0.17, T:0.59
Consensus pattern (24 bp):
TTATGTTCGATTCATTATGTTCAT
Found at i:343313 original size:10 final size:10
Alignment explanation
Indices: 343298--343372 Score: 61
Period size: 10 Copynumber: 7.7 Consensus size: 10
343288 GGGTCTCCAA
343298 CGTTTATGTT
1 CGTTTATGTT
343308 CGTTTATGTT
1 CGTTTATGTT
343318 CGTGTTCAT-TT
1 CGT-TT-ATGTT
* **
343329 ATGTTCGTGTT
1 -CGTTTATGTT
343340 CGTTTATGTT
1 CGTTTATGTT
343350 CG----TGTT
1 CGTTTATGTT
343356 CGTTTATGTT
1 CGTTTATGTT
343366 CGTTTAT
1 CGTTTAT
343373 TTATTAAATG
Statistics
Matches: 51, Mismatches: 6, Indels: 16
0.70 0.08 0.22
Matches are distributed among these distances:
6 6 0.12
10 34 0.67
11 7 0.14
12 4 0.08
ACGTcount: A:0.09, C:0.12, G:0.21, T:0.57
Consensus pattern (10 bp):
CGTTTATGTT
Found at i:343329 original size:16 final size:16
Alignment explanation
Indices: 343304--343368 Score: 121
Period size: 16 Copynumber: 4.1 Consensus size: 16
343294 CCAACGTTTA
343304 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
*
343320 TGTTCATTTATGTTCG
1 TGTTCGTTTATGTTCG
343336 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
343352 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
343368 T
1 T
343369 TTATTTATTA
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 47 1.00
ACGTcount: A:0.08, C:0.12, G:0.23, T:0.57
Consensus pattern (16 bp):
TGTTCGTTTATGTTCG
Found at i:345260 original size:32 final size:32
Alignment explanation
Indices: 345222--345285 Score: 128
Period size: 32 Copynumber: 2.0 Consensus size: 32
345212 AATTAACTTA
345222 TAGATGAAAATTTAGCACGTCTCGTACCATTT
1 TAGATGAAAATTTAGCACGTCTCGTACCATTT
345254 TAGATGAAAATTTAGCACGTCTCGTACCATTT
1 TAGATGAAAATTTAGCACGTCTCGTACCATTT
345286 ATGCCGTATA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.31, C:0.19, G:0.16, T:0.34
Consensus pattern (32 bp):
TAGATGAAAATTTAGCACGTCTCGTACCATTT
Found at i:349310 original size:12 final size:12
Alignment explanation
Indices: 349293--349317 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
349283 AAGTCCTGAG
349293 ATTGATTGATTA
1 ATTGATTGATTA
349305 ATTGATTGATTA
1 ATTGATTGATTA
349317 A
1 A
349318 ATCATTGAAC
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:0.00, G:0.16, T:0.48
Consensus pattern (12 bp):
ATTGATTGATTA
Found at i:350642 original size:41 final size:41
Alignment explanation
Indices: 350591--350668 Score: 111
Period size: 41 Copynumber: 1.9 Consensus size: 41
350581 CCTTAGTAGG
* ** *
350591 AGATACAACATTTGAGATGATATGTGGAGTACCTTAGACGA
1 AGATACAACATTTGAAATGATATACGGAGGACCTTAGACGA
*
350632 AGATATAACATTTGAAATGATATACGGAGGACCTTAG
1 AGATACAACATTTGAAATGATATACGGAGGACCTTAG
350669 GTAGAGTTAC
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
41 32 1.00
ACGTcount: A:0.38, C:0.12, G:0.23, T:0.27
Consensus pattern (41 bp):
AGATACAACATTTGAAATGATATACGGAGGACCTTAGACGA
Found at i:359641 original size:44 final size:44
Alignment explanation
Indices: 359591--359676 Score: 129
Period size: 44 Copynumber: 2.0 Consensus size: 44
359581 CAACTCATAA
** *
359591 TTTGCACTGAAGTGCCACATAATTGTCCC-AAATGATCACATAGG
1 TTTGCACCAAAGTGCCACATAATTGTCCCGAAA-GACCACATAGG
359635 TTTGCACCAAAGTGCCACATAATTGTCCCGAAAGACCACATA
1 TTTGCACCAAAGTGCCACATAATTGTCCCGAAAGACCACATA
359677 AAACCCTCGA
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
44 35 0.92
45 3 0.08
ACGTcount: A:0.34, C:0.26, G:0.16, T:0.24
Consensus pattern (44 bp):
TTTGCACCAAAGTGCCACATAATTGTCCCGAAAGACCACATAGG
Found at i:363541 original size:16 final size:17
Alignment explanation
Indices: 363510--363543 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
363500 ATACATTAAT
*
363510 AAATATTTTATTTCAAC
1 AAATAATTTATTTCAAC
363527 AAATAATTT-TTTCAAC
1 AAATAATTTATTTCAAC
363543 A
1 A
363544 CTTTAAATGA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 8 0.50
17 8 0.50
ACGTcount: A:0.44, C:0.12, G:0.00, T:0.44
Consensus pattern (17 bp):
AAATAATTTATTTCAAC
Found at i:366926 original size:99 final size:97
Alignment explanation
Indices: 366777--366974 Score: 317
Period size: 99 Copynumber: 2.0 Consensus size: 97
366767 TTATGTTACC
*
366777 CATAATCTAATACTTATTGTTGGTATAGAAGAAGATTAATTGTAGTTCCGTTCTTCAAAAAATGG
1 CATAATCTAATACTTATTGTTCGTATAGAAGAAGATTAATTGTAGTTCCGTTCTTCAAAAAATGG
*
366842 GATAG-TTTTTTTTAATTAAATTTCTATTGGA
66 GAGAGTTTTTTTTTAATTAAATTTCTATTGGA
*
366873 CATAATCTAATACTTTTTGTTCGTATAGAAGAAGAAGATTAATTGTAGTTCCGTTCTTCAAAAAA
1 CATAATCTAATACTTATTGTTCGTAT---AGAAGAAGATTAATTGTAGTTCCGTTCTTCAAAAAA
366938 TGGGAGAGTTTTTTTTTTTAATTAAATTTCTATTGGA
63 TGGGAGAG--TTTTTTTTTAATTAAATTTCTATTGGA
366975 GAGAAGAAAA
Statistics
Matches: 93, Mismatches: 3, Indels: 6
0.91 0.03 0.06
Matches are distributed among these distances:
96 24 0.26
99 43 0.46
102 26 0.28
ACGTcount: A:0.33, C:0.09, G:0.16, T:0.43
Consensus pattern (97 bp):
CATAATCTAATACTTATTGTTCGTATAGAAGAAGATTAATTGTAGTTCCGTTCTTCAAAAAATGG
GAGAGTTTTTTTTTAATTAAATTTCTATTGGA
Found at i:379459 original size:18 final size:18
Alignment explanation
Indices: 379436--379470 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
379426 TTCGGTTTGC
379436 AAAAAACCGGATTTTAAA
1 AAAAAACCGGATTTTAAA
*
379454 AAAAAACCGGTTTTTAA
1 AAAAAACCGGATTTTAA
379471 TCCGGTAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.51, C:0.11, G:0.11, T:0.26
Consensus pattern (18 bp):
AAAAAACCGGATTTTAAA
Found at i:382074 original size:26 final size:26
Alignment explanation
Indices: 382022--382074 Score: 63
Period size: 26 Copynumber: 2.0 Consensus size: 26
382012 CATATACTCG
* *
382022 TATTTAAGAATGTAAGTATGATATTA
1 TATTTAAGAATATAAGTAAGATATTA
*
382048 TATTTAAGAATATATA-TAAGATTTTA
1 TATTTAAGAATATA-AGTAAGATATTA
382074 T
1 T
382075 GTTAAGGAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
26 22 0.96
27 1 0.04
ACGTcount: A:0.43, C:0.00, G:0.11, T:0.45
Consensus pattern (26 bp):
TATTTAAGAATATAAGTAAGATATTA
Found at i:383052 original size:83 final size:81
Alignment explanation
Indices: 382954--383232 Score: 290
Period size: 83 Copynumber: 3.4 Consensus size: 81
382944 ATACTTTAGC
* * * * * * *
382954 GGCGTTTTTTAAACAAACGCCGCAATTGAGTGGAAATTTCGCGGTGTTTATAGCTA-AAACACCG
1 GGCGTTTGTTCAACAAACGCCGCAATAGAGTGGTAATTTAGCGGCGTTTATA-C-ACAAACGCCG
383018 CAATAGATATGTTTATAGT
64 CAATAG-TATGTTTATAGT
* ** * * *
383037 GGCGTTTTTTCAACAAACGCCATAATAGAGTGGTAATTTAGCTGCGTTTTTACACAAACGCCGCG
1 GGCGTTTGTTCAACAAACGCCGCAATAGAGTGGTAATTTAGCGGCGTTTATACACAAACGCCGCA
*
383102 ATAGTGTTGTTTATAGT
66 ATAGT-ATGTTTATAGT
* * * ** *
383119 GGCGTTTGTTCAATAAACGACGCTATAGAGAAGTAATTTAGCGGCGTTTATCAAACAAACGCCGC
1 GGCGTTTGTTCAACAAACGCCGCAATAGAGTGGTAATTTAGCGGCGTTTAT-ACACAAACGCCGC
*
383184 AATATTATTGTTTATAGT
65 AATAGTA-TGTTTATAGT
* *
383202 GGCGTTTGTGCAAAAAACGCCGCAATAGAGT
1 GGCGTTTGTTCAACAAACGCCGCAATAGAGT
383233 AATAATATAG
Statistics
Matches: 161, Mismatches: 31, Indels: 8
0.81 0.16 0.04
Matches are distributed among these distances:
81 2 0.01
82 64 0.40
83 95 0.59
ACGTcount: A:0.30, C:0.16, G:0.22, T:0.31
Consensus pattern (81 bp):
GGCGTTTGTTCAACAAACGCCGCAATAGAGTGGTAATTTAGCGGCGTTTATACACAAACGCCGCA
ATAGTATGTTTATAGT
Found at i:383137 original size:41 final size:41
Alignment explanation
Indices: 383009--383229 Score: 132
Period size: 41 Copynumber: 5.4 Consensus size: 41
382999 GTTTATAGCT
* * *
383009 AAAACACCGCAATAGAT-ATGTTTATAGTGGCGTTTTTTCAA
1 AAAACGCCGCAATAG-TGTTGTTTATAGTGGCGTTTGTTCAA
* ** * *
383050 CAAACGCCATAATAGAGTGGTAATT-TAGCT-GCGTTT-TT-ACA
1 AAAACGCCGCAATAGTGTTGT--TTATAG-TGGCGTTTGTTCA-A
* *
383091 CAAACGCCGCGATAGTGTTGTTTATAGTGGCGTTTGTTCAA
1 AAAACGCCGCAATAGTGTTGTTTATAGTGGCGTTTGTTCAA
* * * * ** * *
383132 TAAACGACGCTATAGAGAAGTAATT-TAGCGGCGTTT-ATCAA
1 AAAACGCCGCAATAGTGTTGT--TTATAGTGGCGTTTGTTCAA
* * *
383173 ACAAACGCCGCAATATTATTGTTTATAGTGGCGTTTGTGCAA
1 A-AAACGCCGCAATAGTGTTGTTTATAGTGGCGTTTGTTCAA
383215 AAAACGCCGCAATAG
1 AAAACGCCGCAATAG
383230 AGTAATAATA
Statistics
Matches: 134, Mismatches: 32, Indels: 28
0.69 0.16 0.14
Matches are distributed among these distances:
39 3 0.02
40 12 0.09
41 77 0.57
42 37 0.28
43 5 0.04
ACGTcount: A:0.32, C:0.17, G:0.21, T:0.30
Consensus pattern (41 bp):
AAAACGCCGCAATAGTGTTGTTTATAGTGGCGTTTGTTCAA
Found at i:383260 original size:83 final size:81
Alignment explanation
Indices: 383010--383307 Score: 253
Period size: 83 Copynumber: 3.6 Consensus size: 81
383000 TTTATAGCTA
* * * * ** **
383010 AAACACCGCAATAGATATGTTTATAGTGGCGTTTTTTCAACAAACGCCATAATAGAGTGGTAATT
1 AAACGCCGCAATATAT-TGTTTATAGTGGCGTTTGTTCAAAAAACGCCGCAATAGAGTAATAATT
* * *
383075 TAGCTGCGTTTTTACAC
65 TAGCAGCGTTTATCCAC
* * * * *
383092 AAACGCCGCGATAGTGTTGTTTATAGTGGCGTTTGTTCAATAAACGACGCTATAGAG-AAGTAAT
1 AAACGCCGCAATA-TATTGTTTATAGTGGCGTTTGTTCAAAAAACGCCGCAATAGAGTAA-TAAT
* *
383156 TTAGCGGCGTTTATCAAAC
64 TTAGCAGCGTTTATC-CAC
* *
383175 AAACGCCGCAATATTATTGTTTATAGTGGCGTTTGTGCAAAAAACGCCGCAATAGAGTAATAATA
1 AAACGCCGCAATA-TATTGTTTATAGTGGCGTTTGTTCAAAAAACGCCGCAATAGAGTAATAATT
* * *
383240 TAGCAACATTTGTCCTAC
65 TAGCAGCGTTTATCC-AC
* * * *
383258 AAACGTCGTAATATGTTGTTTATCGTGGC-TTT-TAT-ATAAAAACGCCGCAA
1 AAACGCCGCAATATATTGTTTATAGTGGCGTTTGT-TCA-AAAAACGCCGCAA
383308 AAATATGCAC
Statistics
Matches: 175, Mismatches: 34, Indels: 15
0.78 0.15 0.07
Matches are distributed among these distances:
80 2 0.01
81 16 0.09
82 75 0.43
83 80 0.46
84 2 0.01
ACGTcount: A:0.32, C:0.17, G:0.20, T:0.31
Consensus pattern (81 bp):
AAACGCCGCAATATATTGTTTATAGTGGCGTTTGTTCAAAAAACGCCGCAATAGAGTAATAATTT
AGCAGCGTTTATCCAC
Found at i:384728 original size:41 final size:41
Alignment explanation
Indices: 384682--384835 Score: 166
Period size: 42 Copynumber: 3.7 Consensus size: 41
384672 AAAGTAATTA
* * *
384682 GCGGCGTTTGTATCAAAAACGCCGCCATAGACCTAACTTTT
1 GCGGCGTTTGTATAAAAAACGCCACAATAGACCTAACTTTT
* * * *
384723 ACGGCGTTTGTATAAAAAAACGCCACTATAAACATAACTTTT
1 GCGGCGTTTGTAT-AAAAAACGCCACAATAGACCTAACTTTT
** * *
384765 GCGGCGTTTGTATAAAAAA-AACATTAATAGATCTAACTTTT
1 GCGGCGTTTGTATAAAAAACGCCA-CAATAGACCTAACTTTT
*
384806 GCGGCGTTTGTATCAAAAAACACCACAATA
1 GCGGCGTTTGTAT-AAAAAACGCCACAATA
384836 TGTTCATCCA
Statistics
Matches: 93, Mismatches: 16, Indels: 7
0.80 0.14 0.06
Matches are distributed among these distances:
40 2 0.02
41 43 0.46
42 45 0.48
43 3 0.03
ACGTcount: A:0.36, C:0.20, G:0.16, T:0.28
Consensus pattern (41 bp):
GCGGCGTTTGTATAAAAAACGCCACAATAGACCTAACTTTT
Found at i:384761 original size:42 final size:41
Alignment explanation
Indices: 384682--384831 Score: 153
Period size: 41 Copynumber: 3.6 Consensus size: 41
384672 AAAGTAATTA
* * * *
384682 GCGGCGTTTGTAT-CAAAAACGCCGCCATAGACCTAACTTTT
1 GCGGCGTTTGTATAAAAAAACGCCACTATA-AACTAACTTTT
*
384723 ACGGCGTTTGTATAAAAAAACGCCACTATAAACATAACTTTT
1 GCGGCGTTTGTATAAAAAAACGCCACTATAAAC-TAACTTTT
* * *
384765 GCGGCGTTTGTATAAAAAAA--ACATTAATAGATCTAACTTTT
1 GCGGCGTTTGTATAAAAAAACGCCACT-ATA-AACTAACTTTT
* *
384806 GCGGCGTTTGTATCAAAAAACACCAC
1 GCGGCGTTTGTATAAAAAAACGCCAC
384832 AATATGTTCA
Statistics
Matches: 91, Mismatches: 12, Indels: 10
0.81 0.11 0.09
Matches are distributed among these distances:
40 3 0.03
41 44 0.48
42 42 0.46
43 2 0.02
ACGTcount: A:0.35, C:0.21, G:0.16, T:0.28
Consensus pattern (41 bp):
GCGGCGTTTGTATAAAAAAACGCCACTATAAACTAACTTTT
Found at i:391014 original size:44 final size:44
Alignment explanation
Indices: 390938--391055 Score: 130
Period size: 44 Copynumber: 2.7 Consensus size: 44
390928 TACCAACTTT
* * * *
390938 TAGCGGCATTTGTATACTAAAAATGCCACTATAAACCAGGAATA
1 TAGCGGCGTTTGTATCCTAAAAACGTCACTATAAACCAGGAATA
* * ***
390982 TAGCGGCGTTTGTATCCTAAAAACGTCGCTATATACCAGTCCTA
1 TAGCGGCGTTTGTATCCTAAAAACGTCACTATAAACCAGGAATA
* *
391026 TCGCGACGTTT-TATCCTAAAAACGTCACTA
1 TAGCGGCGTTTGTATCCTAAAAACGTCACTA
391056 AATACCATAC
Statistics
Matches: 62, Mismatches: 12, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
43 18 0.29
44 44 0.71
ACGTcount: A:0.33, C:0.23, G:0.16, T:0.28
Consensus pattern (44 bp):
TAGCGGCGTTTGTATCCTAAAAACGTCACTATAAACCAGGAATA
Found at i:391150 original size:43 final size:43
Alignment explanation
Indices: 391091--391238 Score: 136
Period size: 43 Copynumber: 3.4 Consensus size: 43
391081 CATCTTCATA
* * * * * *
391091 AAAAATGCCGCGAAATATCAACACTTATTGTGGCGTTTGTGAT
1 AAAAACGCCGCTAAATATCAACACCTATTATGGCGTTTGTAAG
** *
391134 AAAAACGCCGCTAAATATTGACACCTATTATGGCGTTTTTAAG
1 AAAAACGCCGCTAAATATCAACACCTATTATGGCGTTTGTAAG
**** *
391177 AAAAACGCCGCTAAATATTGGTACCTATTACGGCGTTTGTTAA-
1 AAAAACGCCGCTAAATATCAACACCTATTATGGCGTTTG-TAAG
* *
391220 ACAAACGCCGCTATATATC
1 AAAAACGCCGCTAAATATC
391239 GTTACCTATT
Statistics
Matches: 88, Mismatches: 16, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
43 85 0.97
44 3 0.03
ACGTcount: A:0.34, C:0.20, G:0.18, T:0.29
Consensus pattern (43 bp):
AAAAACGCCGCTAAATATCAACACCTATTATGGCGTTTGTAAG
Found at i:391245 original size:43 final size:43
Alignment explanation
Indices: 391122--391275 Score: 161
Period size: 43 Copynumber: 3.5 Consensus size: 43
391112 CACTTATTGT
* * *
391122 GGCGTTTGTGATAA-AAACGCCGCTAAATATTGACACCTATTAT
1 GGCGTTTGTTA-AACAAACGCCGCTAAATATTGATACCTATTAC
* *
391165 GGCGTTT-TTAAGAAAAACGCCGCTAAATATTGGTACCTATTAC
1 GGCGTTTGTTAA-ACAAACGCCGCTAAATATTGATACCTATTAC
* * * *
391208 GGCGTTTGTTAAACAAACGCCGCTATATATCGTTACCTATTGC
1 GGCGTTTGTTAAACAAACGCCGCTAAATATTGATACCTATTAC
391251 GGCGTTTTTGGTT-AACAAACGCCGC
1 GGCG--TTT-GTTAAACAAACGCCGC
391276 GAACTTTAGC
Statistics
Matches: 96, Mismatches: 9, Indels: 10
0.83 0.08 0.09
Matches are distributed among these distances:
41 1 0.01
42 3 0.03
43 70 0.73
44 4 0.04
45 15 0.16
46 3 0.03
ACGTcount: A:0.29, C:0.21, G:0.20, T:0.31
Consensus pattern (43 bp):
GGCGTTTGTTAAACAAACGCCGCTAAATATTGATACCTATTAC
Found at i:391463 original size:12 final size:13
Alignment explanation
Indices: 391437--391469 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
391427 GAACACCAAA
391437 GAAGAAAAAAGAG
1 GAAGAAAAAAGAG
391450 GAAGAAAAAA-AG
1 GAAGAAAAAAGAG
391462 GAGAGAAA
1 GA-AGAAA
391470 TGAGTTAAGT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 4 0.21
13 15 0.79
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (13 bp):
GAAGAAAAAAGAG
Found at i:391518 original size:7 final size:7
Alignment explanation
Indices: 391506--391560 Score: 110
Period size: 7 Copynumber: 7.9 Consensus size: 7
391496 TCGACCCAGA
391506 AAAGGAG
1 AAAGGAG
391513 AAAGGAG
1 AAAGGAG
391520 AAAGGAG
1 AAAGGAG
391527 AAAGGAG
1 AAAGGAG
391534 AAAGGAG
1 AAAGGAG
391541 AAAGGAG
1 AAAGGAG
391548 AAAGGAG
1 AAAGGAG
391555 AAAGGA
1 AAAGGA
391561 ACTGAGACAA
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 48 1.00
ACGTcount: A:0.58, C:0.00, G:0.42, T:0.00
Consensus pattern (7 bp):
AAAGGAG
Found at i:394862 original size:32 final size:32
Alignment explanation
Indices: 394823--395031 Score: 222
Period size: 32 Copynumber: 6.5 Consensus size: 32
394813 ATTAGTAGTG
* **
394823 TGTTGCATTCAGATAATACACAGTAGTGTCAA
1 TGTTGCATTCAGATAATGCACAACAGTGTCAA
* *
394855 TGTTGCATTTAGATAATGCATAACAGTGTCAA
1 TGTTGCATTCAGATAATGCACAACAGTGTCAA
* ** * *
394887 TGTTGTATTCAGATAATGCACAGTAATGTCAT
1 TGTTGCATTCAGATAATGCACAACAGTGTCAA
* * * * * *
394919 TGTTGCATTTAGGTAATACACAATAGTGTTAT
1 TGTTGCATTCAGATAATGCACAACAGTGTCAA
* *
394951 TGTTGCATTTAGATAATGCACAACAGTGTCAG
1 TGTTGCATTCAGATAATGCACAACAGTGTCAA
*
394983 TGTTGCATTCAAATAATGCACAACAGTGTCAA
1 TGTTGCATTCAGATAATGCACAACAGTGTCAA
*
395015 GGTCT-CATTCAGATAAT
1 TGT-TGCATTCAGATAAT
395032 ACATAACTAT
Statistics
Matches: 147, Mismatches: 29, Indels: 2
0.83 0.16 0.01
Matches are distributed among these distances:
32 146 0.99
33 1 0.01
ACGTcount: A:0.33, C:0.14, G:0.19, T:0.34
Consensus pattern (32 bp):
TGTTGCATTCAGATAATGCACAACAGTGTCAA
Found at i:394924 original size:64 final size:64
Alignment explanation
Indices: 394823--395031 Score: 249
Period size: 64 Copynumber: 3.3 Consensus size: 64
394813 ATTAGTAGTG
* *
394823 TGTTGCATTCAGATAATACACAGTAGTGTCAATGTTGCATTTAGATAATGCATAACAGTGTCAA
1 TGTTGCATTCAGATAATGCACAGTAGTGTCAATGTTGCATTTAGATAATGCACAACAGTGTCAA
* * * * * * * *
394887 TGTTGTATTCAGATAATGCACAGTAATGTCATTGTTGCATTTAGGTAATACACAATAGTGTTAT
1 TGTTGCATTCAGATAATGCACAGTAGTGTCAATGTTGCATTTAGATAATGCACAACAGTGTCAA
* ** * * *
394951 TGTTGCATTTAGATAATGCACAACAGTGTCAGTGTTGCATTCAAATAATGCACAACAGTGTCAA
1 TGTTGCATTCAGATAATGCACAGTAGTGTCAATGTTGCATTTAGATAATGCACAACAGTGTCAA
*
395015 GGTCT-CATTCAGATAAT
1 TGT-TGCATTCAGATAAT
395032 ACATAACTAT
Statistics
Matches: 119, Mismatches: 25, Indels: 2
0.82 0.17 0.01
Matches are distributed among these distances:
64 118 0.99
65 1 0.01
ACGTcount: A:0.33, C:0.14, G:0.19, T:0.34
Consensus pattern (64 bp):
TGTTGCATTCAGATAATGCACAGTAGTGTCAATGTTGCATTTAGATAATGCACAACAGTGTCAA
Found at i:394987 original size:96 final size:96
Alignment explanation
Indices: 394823--395004 Score: 283
Period size: 96 Copynumber: 1.9 Consensus size: 96
394813 ATTAGTAGTG
* *
394823 TGTTGCATTCAGATAATACACAGTAGTGTCAATGTTGCATTTAGATAATGCATAACAGTGTCAAT
1 TGTTGCATTCAGATAATACACAATAGTGTCAATGTTGCATTTAGATAATGCACAACAGTGTCAAT
* *
394888 GTTGTATTCAGATAATGCACAGTAATGTCAT
66 GTTGCATTCAAATAATGCACAGTAATGTCAT
* * * * *
394919 TGTTGCATTTAGGTAATACACAATAGTGTTATTGTTGCATTTAGATAATGCACAACAGTGTCAGT
1 TGTTGCATTCAGATAATACACAATAGTGTCAATGTTGCATTTAGATAATGCACAACAGTGTCAAT
394984 GTTGCATTCAAATAATGCACA
66 GTTGCATTCAAATAATGCACA
395005 ACAGTGTCAA
Statistics
Matches: 77, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
96 77 1.00
ACGTcount: A:0.33, C:0.14, G:0.19, T:0.35
Consensus pattern (96 bp):
TGTTGCATTCAGATAATACACAATAGTGTCAATGTTGCATTTAGATAATGCACAACAGTGTCAAT
GTTGCATTCAAATAATGCACAGTAATGTCAT
Found at i:395013 original size:96 final size:96
Alignment explanation
Indices: 394823--395034 Score: 282
Period size: 96 Copynumber: 2.2 Consensus size: 96
394813 ATTAGTAGTG
* *
394823 TGTTGCATTCAGATAATACACAGTAGTGTCAATGTTGCATTTAGATAATGCATAACAGTGTCAAT
1 TGTTGCATTCAGATAATACACAATAGTGTCAATGTTGCATTTAGATAATGCACAACAGTGTCAAT
* * **
394888 GTTGTATTCAGATAATGCACAGTAATGTCAT
66 GTTGCATTCAAATAATGCACAACAATGTCAT
* * * * *
394919 TGTTGCATTTAGGTAATACACAATAGTGTTATTGTTGCATTTAGATAATGCACAACAGTGTCAGT
1 TGTTGCATTCAGATAATACACAATAGTGTCAATGTTGCATTTAGATAATGCACAACAGTGTCAAT
* *
394984 GTTGCATTCAAATAATGCACAACAGTGTCAA
66 GTTGCATTCAAATAATGCACAACAATGTCAT
*
395015 GGTCT-CATTCAGATAATACA
1 TGT-TGCATTCAGATAATACA
395035 TAACTATTAT
Statistics
Matches: 99, Mismatches: 16, Indels: 2
0.85 0.14 0.02
Matches are distributed among these distances:
96 98 0.99
97 1 0.01
ACGTcount: A:0.33, C:0.15, G:0.18, T:0.33
Consensus pattern (96 bp):
TGTTGCATTCAGATAATACACAATAGTGTCAATGTTGCATTTAGATAATGCACAACAGTGTCAAT
GTTGCATTCAAATAATGCACAACAATGTCAT
Found at i:397361 original size:27 final size:26
Alignment explanation
Indices: 397331--397381 Score: 75
Period size: 27 Copynumber: 1.9 Consensus size: 26
397321 TTTGTTGAGT
* *
397331 TGAAGGTCAACTTTAAGAAAATGTTTA
1 TGAAGATCAACTATAA-AAAATGTTTA
397358 TGAAGATCAACTATAAAAAATGTT
1 TGAAGATCAACTATAAAAAATGTT
397382 CAGCCACAGA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 8 0.36
27 14 0.64
ACGTcount: A:0.45, C:0.08, G:0.16, T:0.31
Consensus pattern (26 bp):
TGAAGATCAACTATAAAAAATGTTTA
Found at i:404238 original size:65 final size:64
Alignment explanation
Indices: 404105--404258 Score: 177
Period size: 65 Copynumber: 2.4 Consensus size: 64
404095 ACCCTGATTC
* * * * *
404105 GAATGCATTTTGTGTACCGATGCACATCCGTGCATCGATGCACTCCTGATTTTATTGAAACATC
1 GAATGCATTTTATGTACCGATGCACAACCATGCATCGATGCACTCCTGATCTTATTGAAACATA
* * *
404169 GAATGCATTTTATGTACCGATGCACAGACCATGCATCGATTCACTCCTGGCTCTT-TTGAAAGAT
1 GAATGCATTTTATGTACCGATGCACA-ACCATGCATCGATGCACTCCT-GATCTTATTGAAACAT
404233 A
64 A
* *
404234 GAATGTA-ATTAGTGTACCGATGCAC
1 GAATGCATTTTA-TGTACCGATGCAC
404259 TAAGTCATAT
Statistics
Matches: 77, Mismatches: 10, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
64 28 0.36
65 45 0.58
66 4 0.05
ACGTcount: A:0.27, C:0.22, G:0.19, T:0.31
Consensus pattern (64 bp):
GAATGCATTTTATGTACCGATGCACAACCATGCATCGATGCACTCCTGATCTTATTGAAACATA
Found at i:410067 original size:23 final size:23
Alignment explanation
Indices: 410041--410109 Score: 70
Period size: 23 Copynumber: 3.1 Consensus size: 23
410031 ATGAAAGTGT
410041 ATCGATGCATTACTTGAATATGC
1 ATCGATGCATTACTTGAATATGC
* *
410064 ATCGATGCACTA--TGAAGATGC
1 ATCGATGCATTACTTGAATATGC
* ** *
410085 ACCGATGCATGCCTTGAATGTGC
1 ATCGATGCATTACTTGAATATGC
410108 AT
1 AT
410110 AGATACACTA
Statistics
Matches: 35, Mismatches: 9, Indels: 4
0.73 0.19 0.08
Matches are distributed among these distances:
21 16 0.46
23 19 0.54
ACGTcount: A:0.29, C:0.20, G:0.22, T:0.29
Consensus pattern (23 bp):
ATCGATGCATTACTTGAATATGC
Found at i:410084 original size:21 final size:22
Alignment explanation
Indices: 410041--410093 Score: 63
Period size: 21 Copynumber: 2.4 Consensus size: 22
410031 ATGAAAGTGT
* *
410041 ATCGATGCATTACTTGAATATGC
1 ATCGATGCACTAC-TGAAGATGC
410064 ATCGATGCACTA-TGAAGATGC
1 ATCGATGCACTACTGAAGATGC
*
410085 ACCGATGCA
1 ATCGATGCA
410094 TGCCTTGAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
21 16 0.59
23 11 0.41
ACGTcount: A:0.32, C:0.21, G:0.21, T:0.26
Consensus pattern (22 bp):
ATCGATGCACTACTGAAGATGC
Found at i:410575 original size:18 final size:19
Alignment explanation
Indices: 410549--410590 Score: 50
Period size: 18 Copynumber: 2.2 Consensus size: 19
410539 AAAAATTTGC
*
410549 TTTTAATTTTATTA-ATGT
1 TTTTAATTTAATTAGATGT
*
410567 TTTTGATTTAATTATGATGT
1 TTTTAATTTAATTA-GATGT
410587 TTTT
1 TTTT
410591 TTCTCATGAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
18 12 0.60
20 8 0.40
ACGTcount: A:0.24, C:0.00, G:0.10, T:0.67
Consensus pattern (19 bp):
TTTTAATTTAATTAGATGT
Found at i:412885 original size:64 final size:65
Alignment explanation
Indices: 412810--412965 Score: 192
Period size: 65 Copynumber: 2.4 Consensus size: 65
412800 ACACCCTGAT
* * * *
412810 TCGAATACATTTTATGTACCGATGCACA-TCCATGCATCGATGCACTTCT-GATTTTATTGAAAC
1 TCGAATGCATTTTATGTACCGATGCACAGACCATGCATCGATGCACTCCTAGATCTT-TTGAAAC
412873 A
65 A
* * *
412874 TCGAATGCATTTTATATATCGATGCACAGACCATGCATCGATGCACTCCTAGCTCTTTTGAAACA
1 TCGAATGCATTTTATGTACCGATGCACAGACCATGCATCGATGCACTCCTAGATCTTTTGAAACA
* *
412939 TCGAATGTA-ATTAGTGTACCGATGCAC
1 TCGAATGCATTTTA-TGTACCGATGCAC
412966 CCCAAAGTGT
Statistics
Matches: 78, Mismatches: 11, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
64 28 0.36
65 46 0.59
66 4 0.05
ACGTcount: A:0.29, C:0.22, G:0.16, T:0.32
Consensus pattern (65 bp):
TCGAATGCATTTTATGTACCGATGCACAGACCATGCATCGATGCACTCCTAGATCTTTTGAAACA
Found at i:414370 original size:19 final size:19
Alignment explanation
Indices: 414323--414370 Score: 53
Period size: 19 Copynumber: 2.5 Consensus size: 19
414313 AAAGTTTAAA
414323 TTAGGATTTATCTTTGTTTT
1 TTAGGA-TTATCTTTGTTTT
* *
414343 TAAGAATTATCTTT-TATTT
1 TTAGGATTATCTTTGT-TTT
414362 TTAGGATTA
1 TTAGGATTA
414371 AGTTTGAATG
Statistics
Matches: 23, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
18 1 0.04
19 18 0.78
20 4 0.17
ACGTcount: A:0.25, C:0.04, G:0.12, T:0.58
Consensus pattern (19 bp):
TTAGGATTATCTTTGTTTT
Found at i:415540 original size:17 final size:18
Alignment explanation
Indices: 415520--415554 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
415510 ACGAATCCAC
415520 GAACAAACACC-AAGAAT
1 GAACAAACACCGAAGAAT
*
415537 GAACAAATACCGAAGAAT
1 GAACAAACACCGAAGAAT
415555 CGATTGACAC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 10 0.62
18 6 0.38
ACGTcount: A:0.57, C:0.20, G:0.14, T:0.09
Consensus pattern (18 bp):
GAACAAACACCGAAGAAT
Found at i:417901 original size:29 final size:29
Alignment explanation
Indices: 417833--417903 Score: 106
Period size: 29 Copynumber: 2.4 Consensus size: 29
417823 TCGGTTAATT
*
417833 GAACCAAAATTTATTTGAAAATTATTAACC
1 GAACC-AAATTAATTTGAAAATTATTAACC
*
417863 GAACCGAATTAATTTGAAAATTATTAACC
1 GAACCAAATTAATTTGAAAATTATTAACC
*
417892 GAACTAAATTAA
1 GAACCAAATTAA
417904 CTGGATTTTT
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
29 32 0.86
30 5 0.14
ACGTcount: A:0.48, C:0.13, G:0.08, T:0.31
Consensus pattern (29 bp):
GAACCAAATTAATTTGAAAATTATTAACC
Found at i:417963 original size:126 final size:124
Alignment explanation
Indices: 417822--418218 Score: 499
Period size: 136 Copynumber: 3.1 Consensus size: 124
417812 GTTAATTTGG
*
417822 TTCGGTTAATTGAACCAAAATTTATTTGAAAATTATTAACCGAACCGAATTAATTTGAAAATTAT
1 TTCGGTTAATCGAACCAAAATTTATTTGAAAATTATTAACCGAACCGAATTAATTTGAAAATTAT
* *
417887 TAACCGAACTAAATTAACTGGATTTTTTTTAAATTATTAACTGAATTAATCGAAGAAAAAA
66 TAACCGAACCAAATTAA-T-GATTTTTTTTAAATTATTAACCGAATTAATCGAAGAAAAAA
**
417948 TTCGGTTAATCGAACCAAAATTTATTTGAAAATTATTAATTGAACCGAATTAATTTGAAAATTAT
1 TTCGGTTAATCGAACCAAAATTTATTTGAAAATTATTAACCGAACCGAATTAATTTGAAAATTAT
* * * *
418013 TAATCGAACCAAATTAATCA-TTTCTTTAAATTATTAACCAAATTAATCGAAGCAAAATTTGATT
66 TAACCGAACCAAATTAATGATTTTTTTTAAATTATTAACCGAATTAATCGAAG--AAA----A--
418077 AA
123 AA
*
418079 TTCGGTTCGGTTAATCGAACCAAAATTTATTTGAAAATTATTAACCGAACCGAATTTATTTGAAA
1 -----TTCGGTTAATCGAACCAAAATTTATTTGAAAATTATTAACCGAACCGAATTAATTTGAAA
* * ** *
418144 ATTATTAACCAAACCGAATTAATCGATTTTTTTTAAATTATTAACCGAATTAATTTAAGCAAAAA
61 ATTATTAACCGAACCAAATTAAT-GATTTTTTTTAAATTATTAACCGAATTAATCGAAGAAAAAA
*
418209 TTTGGTTAAT
1 TTCGGTTAAT
418219 TCGGTTCGGT
Statistics
Matches: 234, Mismatches: 22, Indels: 31
0.82 0.08 0.11
Matches are distributed among these distances:
123 29 0.12
124 1 0.00
125 13 0.06
126 77 0.33
129 1 0.00
130 2 0.01
131 2 0.01
132 1 0.00
136 79 0.34
137 1 0.00
138 28 0.12
ACGTcount: A:0.42, C:0.11, G:0.10, T:0.37
Consensus pattern (124 bp):
TTCGGTTAATCGAACCAAAATTTATTTGAAAATTATTAACCGAACCGAATTAATTTGAAAATTAT
TAACCGAACCAAATTAATGATTTTTTTTAAATTATTAACCGAATTAATCGAAGAAAAAA
Found at i:418005 original size:29 final size:29
Alignment explanation
Indices: 417953--418030 Score: 120
Period size: 29 Copynumber: 2.7 Consensus size: 29
417943 AAAAATTCGG
*
417953 TTAATCGAACCAAAATTTATTTGAAAATTA
1 TTAATCGAACC-AAATTAATTTGAAAATTA
* *
417983 TTAATTGAACCGAATTAATTTGAAAATTA
1 TTAATCGAACCAAATTAATTTGAAAATTA
418012 TTAATCGAACCAAATTAAT
1 TTAATCGAACCAAATTAAT
418031 CATTTCTTTA
Statistics
Matches: 43, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
29 33 0.77
30 10 0.23
ACGTcount: A:0.46, C:0.10, G:0.08, T:0.36
Consensus pattern (29 bp):
TTAATCGAACCAAATTAATTTGAAAATTA
Found at i:418107 original size:136 final size:139
Alignment explanation
Indices: 417948--418291 Score: 523
Period size: 139 Copynumber: 2.5 Consensus size: 139
417938 GAAGAAAAAA
**
417948 TTCGGTTAATCGAACCAAAATTTATTTGAAAATTATTAATTGAACCGAATTAATTTGAAAATTAT
1 TTCGGTTAATCGAACCAAAATTTATTTGAAAATTATTAACCGAACCGAATTAATTTGAAAATTAT
* *
418013 TAATCGAACCAAATTAATC-A-TTTCTTTAAATTATTAACCAAATTAATCGAAGC-AAAATTTGA
66 TAACCAAACCAAATTAATCGATTTTCTTTAAATTATTAACCAAATTAATCGAAGCAAAAATTTGA
418075 TTAATTCGG
131 TTAATTCGG
*
418084 TTCGGTTAATCGAACCAAAATTTATTTGAAAATTATTAACCGAACCGAATTTATTTGAAAATTAT
1 TTCGGTTAATCGAACCAAAATTTATTTGAAAATTATTAACCGAACCGAATTAATTTGAAAATTAT
* * * ** *
418149 TAACCAAACCGAATTAATCGATTTTTTTTAAATTATTAACCGAATTAATTTAAGCAAAAATTTGG
66 TAACCAAACCAAATTAATCGATTTTCTTTAAATTATTAACCAAATTAATCGAAGCAAAAATTTGA
418214 TTAATTCGG
131 TTAATTCGG
* * * * *
418223 TTCGGTTAATTGAACCAAAGTTTTTTTGAAAATTATTAACCAAACCAAATTAATTTGAAAATTAT
1 TTCGGTTAATCGAACCAAAATTTATTTGAAAATTATTAACCGAACCGAATTAATTTGAAAATTAT
418288 TAAC
66 TAAC
418292 TGAGCTGAAT
Statistics
Matches: 188, Mismatches: 17, Indels: 3
0.90 0.08 0.01
Matches are distributed among these distances:
136 78 0.41
137 1 0.01
138 29 0.15
139 80 0.43
ACGTcount: A:0.41, C:0.12, G:0.10, T:0.37
Consensus pattern (139 bp):
TTCGGTTAATCGAACCAAAATTTATTTGAAAATTATTAACCGAACCGAATTAATTTGAAAATTAT
TAACCAAACCAAATTAATCGATTTTCTTTAAATTATTAACCAAATTAATCGAAGCAAAAATTTGA
TTAATTCGG
Found at i:418137 original size:29 final size:29
Alignment explanation
Indices: 418102--418163 Score: 115
Period size: 29 Copynumber: 2.1 Consensus size: 29
418092 ATCGAACCAA
*
418102 AATTTATTTGAAAATTATTAACCGAACCG
1 AATTTATTTGAAAATTATTAACCAAACCG
418131 AATTTATTTGAAAATTATTAACCAAACCG
1 AATTTATTTGAAAATTATTAACCAAACCG
418160 AATT
1 AATT
418164 AATCGATTTT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 32 1.00
ACGTcount: A:0.44, C:0.13, G:0.08, T:0.35
Consensus pattern (29 bp):
AATTTATTTGAAAATTATTAACCAAACCG
Found at i:418336 original size:129 final size:133
Alignment explanation
Indices: 417804--418362 Score: 490
Period size: 139 Copynumber: 4.2 Consensus size: 133
417794 GTTAAATAAT
* * * * *
417804 AAAATTCGGTTAATTTGGTTCGGTTAATTGAACCAAAATTTATTTGAAAATTATTAACCGAACCG
1 AAAATTTGATTAATTCGGTTCGGTTAATTGAACCAAAATTTATTTGAAAATTATTAACCAAACCA
* ** * * *
417869 AATTAATTTGAAAATTATTAACCGAACTAAATTAACTGGATTTTTTTTAAATTATTAACTGAATT
66 AATTAATTTGAAAATTATTAACCAAACCGAATTAA-TCGATATTTTTTAAA-TATTAA-TTAATT
*
417934 -AATCGA
128 GAAGC-A
* ***
417940 AGAAA----A--AA-----TTCGGTTAATCGAACCAAAATTTATTTGAAAATTATTAATTGAACC
1 A-AAATTTGATTAATTCGGTTCGGTTAATTGAACCAAAATTTATTTGAAAATTATTAACCAAACC
* * * * *
417994 GAATTAATTTGAAAATTATTAATCGAACCAAATTAATC-AT-TTCTTTAAATTATTAACCAAATT
65 AAATTAATTTGAAAATTATTAACCAAACCGAATTAATCGATATTTTTTAAA-TATT-----AATT
*
418057 AATCGAAGC-
124 AATTGAAGCA
* * *
418066 AAAATTTGATTAATTCGGTTCGGTTAATCGAACCAAAATTTATTTGAAAATTATTAACCGAACCG
1 AAAATTTGATTAATTCGGTTCGGTTAATTGAACCAAAATTTATTTGAAAATTATTAACCAAACCA
* *
418131 AATTTATTTGAAAATTATTAACCAAACCGAATTAATCGATTTTTTTTAAATTATTAACCGAATTA
66 AATTAATTTGAAAATTATTAACCAAACCGAATTAATCGATATTTTTTAAA-TATT-----AATTA
*
418196 ATTTAAGCA
125 ATTGAAGCA
* * *
418205 AAAATTTGGTTAATTCGGTTCGGTTAATTGAACCAAAGTTTTTTTGAAAATTATTAACCAAACCA
1 AAAATTTGATTAATTCGGTTCGGTTAATTGAACCAAAATTTATTTGAAAATTATTAACCAAACCA
** * * * *
418270 AATTAATTTGAAAATTATTAACTGAGCTGAATTGA-C-CTATTTTTTAAA-ATT-ATTAATTGAA
66 AATTAATTTGAAAATTATTAACCAAACCGAATTAATCGATATTTTTTAAATATTAATTAATTGAA
418331 GCA
131 GCA
*
418334 AAAATTCGATTAATTCGGTTCGGTTAATT
1 AAAATTTGATTAATTCGGTTCGGTTAATT
418363 TATTTGAAAA
Statistics
Matches: 364, Mismatches: 38, Indels: 49
0.81 0.08 0.11
Matches are distributed among these distances:
123 13 0.04
124 2 0.01
125 4 0.01
126 78 0.21
127 4 0.01
128 5 0.01
129 40 0.11
131 4 0.01
135 3 0.01
136 79 0.22
137 15 0.04
138 29 0.08
139 88 0.24
ACGTcount: A:0.40, C:0.11, G:0.11, T:0.37
Consensus pattern (133 bp):
AAAATTTGATTAATTCGGTTCGGTTAATTGAACCAAAATTTATTTGAAAATTATTAACCAAACCA
AATTAATTTGAAAATTATTAACCAAACCGAATTAATCGATATTTTTTAAATATTAATTAATTGAA
GCA
Found at i:418576 original size:20 final size:20
Alignment explanation
Indices: 418551--418591 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
418541 ATTAGTCGTG
418551 AATAATTTAATTAATTTTTT
1 AATAATTTAATTAATTTTTT
**
418571 AATAATTTGTTTAATTTTTT
1 AATAATTTAATTAATTTTTT
418591 A
1 A
418592 TCATTAACAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (20 bp):
AATAATTTAATTAATTTTTT
Found at i:420595 original size:11 final size:11
Alignment explanation
Indices: 420579--420609 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
420569 GAATAAGCGC
420579 AGAAAAAAGAG
1 AGAAAAAAGAG
420590 AGAAAAAAGAG
1 AGAAAAAAGAG
*
420601 AGAGAAAAG
1 AGAAAAAAG
420610 GGGTGTTCGA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.71, C:0.00, G:0.29, T:0.00
Consensus pattern (11 bp):
AGAAAAAAGAG
Found at i:420636 original size:13 final size:14
Alignment explanation
Indices: 420618--420646 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
420608 AGGGGTGTTC
420618 GAAAAG-AGAAAAA
1 GAAAAGAAGAAAAA
420631 GAAAAGAAGAAAAA
1 GAAAAGAAGAAAAA
420645 GA
1 GA
420647 TTAATAGAGT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 6 0.40
14 9 0.60
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (14 bp):
GAAAAGAAGAAAAA
Found at i:422766 original size:2 final size:2
Alignment explanation
Indices: 422759--422805 Score: 85
Period size: 2 Copynumber: 23.5 Consensus size: 2
422749 TAAATACCTT
*
422759 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TG 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
422801 TA TA T
1 TA TA T
422806 TCAAGATTGA
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (2 bp):
TA
Found at i:422969 original size:2 final size:2
Alignment explanation
Indices: 422964--423012 Score: 80
Period size: 2 Copynumber: 24.0 Consensus size: 2
422954 TCCTACATAC
*
422964 TA TA TA TA GCA 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
423007 TA TA TA
1 TA TA TA
423013 AACACTTAAA
Statistics
Matches: 44, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
2 43 0.98
3 1 0.02
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (2 bp):
TA
Found at i:424766 original size:112 final size:111
Alignment explanation
Indices: 424540--424904 Score: 479
Period size: 112 Copynumber: 3.3 Consensus size: 111
424530 TGTTACTTAT
424540 GGAATATCAAATCTT-GACAGAGAGGGATATGTTCTGCTTCTTCT--AAGGGAATATCAGATATG
1 GGAATATCAAATCTTGGA-AGAGAGGGATATGTTCTGCTTCTT-TGAAAGGGAATATCAGATAT-
* *
424602 GGAAAGTTGATATATTGAATC-AGAGTAGACTTGTTCCT-CTGTCACTCAG
63 GGAAAATTGATACATTGAATCGAG-GTAGACTTGTT-CTGCTGTCACTCAG
*
424651 GGAATATCAAATCTTGGAAGAGAGAGATATGTTCTGCTTCTTTGAAAGGGAATATCAGATATGTG
1 GGAATATCAAATCTTGGAAGAGAGGGATATGTTCTGCTTCTTTGAAAGGGAATATCAGATATG-G
* * * * *
424716 AAAATTAATCCATTTAATCGAGGTAGACTTGTTTTGCTGTTACTCAG
65 AAAATTGATACATTGAATCGAGGTAGACTTGTTCTGCTGTCACTCAG
* ** *
424763 GGAATATCAAATCTTGGAAGAGAGGGATCTGTTCCACTTCTTTGAAAGGGAATATCAGATCTGGA
1 GGAATATCAAATCTTGGAAGAGAGGGATATGTTCTGCTTCTTTGAAAGGGAATATCAGATATGG-
* * * *
424828 AAAATCGATTCATTGAATCGAGGTAGACTTGTTCCGCTGTCACTCAA
65 AAAATTGATACATTGAATCGAGGTAGACTTGTTCTGCTGTCACTCAG
424875 GGAATATCAAATCTTGGAAGAGAGGTGATA
1 GGAATATCAAATCTTGGAAGAGAGG-GATA
424905 ACTCCGTAAA
Statistics
Matches: 224, Mismatches: 22, Indels: 14
0.86 0.08 0.05
Matches are distributed among these distances:
110 1 0.00
111 41 0.18
112 177 0.79
113 5 0.02
ACGTcount: A:0.32, C:0.14, G:0.24, T:0.31
Consensus pattern (111 bp):
GGAATATCAAATCTTGGAAGAGAGGGATATGTTCTGCTTCTTTGAAAGGGAATATCAGATATGGA
AAATTGATACATTGAATCGAGGTAGACTTGTTCTGCTGTCACTCAG
Found at i:425907 original size:52 final size:52
Alignment explanation
Indices: 425829--425959 Score: 253
Period size: 52 Copynumber: 2.5 Consensus size: 52
425819 TTTGCCTTAA
425829 CATTGTAAGAGCATCGAGAGATCGCCTGGGGTTTTGGTGAAACATGTTTGGG
1 CATTGTAAGAGCATCGAGAGATCGCCTGGGGTTTTGGTGAAACATGTTTGGG
425881 CATTGTAAGAGCATCGAGAGATCGCCTGGGGTTTTGGTGAAACATGTTTGGG
1 CATTGTAAGAGCATCGAGAGATCGCCTGGGGTTTTGGTGAAACATGTTTGGG
*
425933 CATTGTAAGAGCATCGAGAGATAGCCT
1 CATTGTAAGAGCATCGAGAGATCGCCT
425960 TTTGTCTAGA
Statistics
Matches: 78, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
52 78 1.00
ACGTcount: A:0.25, C:0.15, G:0.33, T:0.27
Consensus pattern (52 bp):
CATTGTAAGAGCATCGAGAGATCGCCTGGGGTTTTGGTGAAACATGTTTGGG
Found at i:428042 original size:20 final size:20
Alignment explanation
Indices: 428002--428040 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
427992 CATTGCAGGA
*
428002 ATTTATGGCTTCGACAAAAG
1 ATTTATGGCTTCCACAAAAG
428022 ATTTCATGGCTTCCACAAA
1 ATTT-ATGGCTTCCACAAA
428041 GACCTTGATG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.33, C:0.21, G:0.15, T:0.31
Consensus pattern (20 bp):
ATTTATGGCTTCCACAAAAG
Found at i:438007 original size:11 final size:11
Alignment explanation
Indices: 437988--438082 Score: 66
Period size: 11 Copynumber: 8.4 Consensus size: 11
437978 TGAACCCTCC
*
437988 TTTTATTTTTT
1 TTTTCTTTTTT
437999 TTTTCTTTTCTT
1 TTTTCTTTT-TT
**
438011 TTTTCTCATTT
1 TTTTCTTTTTT
*
438022 TTTTC-TTTCT
1 TTTTCTTTTTT
*
438032 TTTTCTTTTCT
1 TTTTCTTTTTT
*
438043 TTTTCATTTTT
1 TTTTCTTTTTT
** *
438054 TAGTCTTTTTCA
1 TTTTCTTTTT-T
438066 TTTTCATTTTCTT
1 TTTTC-TTTT-TT
438079 TTTT
1 TTTT
438083 AGGTGAAATA
Statistics
Matches: 64, Mismatches: 15, Indels: 8
0.74 0.17 0.09
Matches are distributed among these distances:
10 7 0.11
11 36 0.56
12 12 0.19
13 8 0.12
14 1 0.02
ACGTcount: A:0.06, C:0.14, G:0.01, T:0.79
Consensus pattern (11 bp):
TTTTCTTTTTT
Found at i:438047 original size:6 final size:6
Alignment explanation
Indices: 437988--438081 Score: 61
Period size: 6 Copynumber: 15.7 Consensus size: 6
437978 TGAACCCTCC
* *
437988 TTTTAT TTTT-T TTTTC- TTTTCTT TTTTCT CATTTTTT TCTTTCT TTTTC-
1 TTTTCT TTTTCT TTTTCT TTTTC-T TTTTCT --TTTTCT T-TTTCT TTTTCT
* ** * *
438037 TTTTCT TTTTCA TTTT-T TAGTCT TTTTCA TTTTCA TTTTCT TTTT
1 TTTTCT TTTTCT TTTTCT TTTTCT TTTTCT TTTTCT TTTTCT TTTT
438082 TAGGTGAAAT
Statistics
Matches: 70, Mismatches: 10, Indels: 16
0.73 0.10 0.17
Matches are distributed among these distances:
5 17 0.24
6 38 0.54
7 10 0.14
8 5 0.07
ACGTcount: A:0.06, C:0.14, G:0.01, T:0.79
Consensus pattern (6 bp):
TTTTCT
Found at i:438060 original size:28 final size:28
Alignment explanation
Indices: 438029--438084 Score: 87
Period size: 28 Copynumber: 2.0 Consensus size: 28
438019 TTTTTTTCTT
*
438029 TCTTTTTC-TTTTCTTTTTCATTTTTTAG
1 TCTTTTTCATTTTCATTTTC-TTTTTTAG
438057 TCTTTTTCATTTTCATTTTCTTTTTTAG
1 TCTTTTTCATTTTCATTTTCTTTTTTAG
438085 GTGAAATACT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
28 16 0.62
29 10 0.38
ACGTcount: A:0.09, C:0.14, G:0.04, T:0.73
Consensus pattern (28 bp):
TCTTTTTCATTTTCATTTTCTTTTTTAG
Found at i:438080 original size:17 final size:17
Alignment explanation
Indices: 437988--438081 Score: 69
Period size: 17 Copynumber: 5.9 Consensus size: 17
437978 TGAACCCTCC
* *
437988 TTTTATTTTTTTTTTC-
1 TTTTCTTTTCTTTTTCA
*
438004 TTTTC-TTT-TTTCTCA
1 TTTTCTTTTCTTTTTCA
*
438019 -TTT-TTTTC--TTTCT
1 TTTTCTTTTCTTTTTCA
438032 TTTTCTTTTCTTTTTCA
1 TTTTCTTTTCTTTTTCA
*
438049 TTTT-TTAGTCTTTTTCA
1 TTTTCTT-TTCTTTTTCA
438066 TTTTCATTTTCTTTTT
1 TTTTC-TTTTCTTTTT
438082 TAGGTGAAAT
Statistics
Matches: 61, Mismatches: 7, Indels: 18
0.71 0.08 0.21
Matches are distributed among these distances:
13 3 0.05
14 14 0.23
15 8 0.13
16 6 0.10
17 21 0.34
18 7 0.11
19 2 0.03
ACGTcount: A:0.06, C:0.14, G:0.01, T:0.79
Consensus pattern (17 bp):
TTTTCTTTTCTTTTTCA
Found at i:443658 original size:21 final size:21
Alignment explanation
Indices: 443634--443675 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
443624 TTCTTCAGAG
* *
443634 GTAATACCAATAGTTGGAGCT
1 GTAACACCAATAGTTGAAGCT
443655 GTAACACCAATAGTTGAAGCT
1 GTAACACCAATAGTTGAAGCT
443676 TTTCCACGAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.36, C:0.17, G:0.21, T:0.26
Consensus pattern (21 bp):
GTAACACCAATAGTTGAAGCT
Found at i:447612 original size:25 final size:25
Alignment explanation
Indices: 447557--447614 Score: 73
Period size: 25 Copynumber: 2.3 Consensus size: 25
447547 ATAAGTCTAG
*
447557 ATTCAATATTTTGATACATGATTGCA
1 ATTC-ATATTATGATACATGATTGCA
*
447583 TTTCATATTATGATACATGATATG-A
1 ATTCATATTATGATACATGAT-TGCA
447608 ATTCATA
1 ATTCATA
447615 CCATATGCAT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
25 23 0.82
26 5 0.18
ACGTcount: A:0.36, C:0.10, G:0.10, T:0.43
Consensus pattern (25 bp):
ATTCATATTATGATACATGATTGCA
Found at i:447696 original size:30 final size:30
Alignment explanation
Indices: 447662--447730 Score: 102
Period size: 30 Copynumber: 2.3 Consensus size: 30
447652 TTATATGAGT
* *
447662 TATGTGATAAAGGTATGGAAATGATATGTC
1 TATGTGATAAAGGTATGAAAATAATATGTC
*
447692 TATGTGATAAAGGTATGAAAATAATGTGTC
1 TATGTGATAAAGGTATGAAAATAATATGTC
*
447722 TACGTGATA
1 TATGTGATA
447731 CAAATTATGT
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 35 1.00
ACGTcount: A:0.38, C:0.04, G:0.25, T:0.33
Consensus pattern (30 bp):
TATGTGATAAAGGTATGAAAATAATATGTC
Found at i:447975 original size:23 final size:23
Alignment explanation
Indices: 447941--448008 Score: 77
Period size: 23 Copynumber: 3.0 Consensus size: 23
447931 ATTATTATAG
447941 GGCACTAC-GGTGCAATTCTACGC
1 GGCACT-CTGGTGCAATTCTACGC
*
447964 GGCACTCTGGTGCAATTCTACGT
1 GGCACTCTGGTGCAATTCTACGC
* *
447987 GGCA-TTTCGGTGCAATTATACG
1 GGCACTCT-GGTGCAATTCTACG
448009 AGCTGTGGTG
Statistics
Matches: 40, Mismatches: 3, Indels: 4
0.85 0.06 0.09
Matches are distributed among these distances:
22 3 0.08
23 37 0.93
ACGTcount: A:0.21, C:0.25, G:0.26, T:0.28
Consensus pattern (23 bp):
GGCACTCTGGTGCAATTCTACGC
Found at i:454627 original size:29 final size:30
Alignment explanation
Indices: 454595--454662 Score: 93
Period size: 30 Copynumber: 2.3 Consensus size: 30
454585 TTATATGAGT
* *
454595 TATGTGATAAAGG-ATGGAAATGATATGTC
1 TATGTGATAAAGGTATGAAAATAATATGTC
*
454624 TATGTGATAAAGGTATGAAAATAATGTGTC
1 TATGTGATAAAGGTATGAAAATAATATGTC
*
454654 TACGTGATA
1 TATGTGATA
454663 CAAATTATGT
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
29 13 0.38
30 21 0.62
ACGTcount: A:0.38, C:0.04, G:0.25, T:0.32
Consensus pattern (30 bp):
TATGTGATAAAGGTATGAAAATAATATGTC
Found at i:454906 original size:23 final size:23
Alignment explanation
Indices: 454873--454940 Score: 91
Period size: 23 Copynumber: 3.0 Consensus size: 23
454863 ATTATTATAT
454873 GGCACTACGGTGTAATTCTACGC
1 GGCACTACGGTGTAATTCTACGC
* *
454896 GGCACTCCGGTGTAATTCTACGT
1 GGCACTACGGTGTAATTCTACGC
* * *
454919 GGCACTTCGGTGCAATTATACG
1 GGCACTACGGTGTAATTCTACG
454941 AGCTGTGGTG
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 40 1.00
ACGTcount: A:0.21, C:0.25, G:0.26, T:0.28
Consensus pattern (23 bp):
GGCACTACGGTGTAATTCTACGC
Found at i:458238 original size:73 final size:73
Alignment explanation
Indices: 458119--458265 Score: 285
Period size: 73 Copynumber: 2.0 Consensus size: 73
458109 GTTACCTTCG
458119 TACCTACAAAACTATGAGTTGCATATGAGGGAGTTGAGTTGCCTTCACCTCATCTTATGATTATG
1 TACCTACAAAACTATGAGTTGCATATGAGGGAGTTGAGTTGCCTTCACCTCATCTTATGATTATG
458184 GATTTACT
66 GATTTACT
*
458192 TACCTACAAAACTATGAGTTGCATATGAGGGAGTTGGGTTGCCTTCACCTCATCTTATGATTATG
1 TACCTACAAAACTATGAGTTGCATATGAGGGAGTTGAGTTGCCTTCACCTCATCTTATGATTATG
458257 GATTTACT
66 GATTTACT
458265 T
1 T
458266 GAGAGGTTGA
Statistics
Matches: 73, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
73 73 1.00
ACGTcount: A:0.27, C:0.18, G:0.20, T:0.36
Consensus pattern (73 bp):
TACCTACAAAACTATGAGTTGCATATGAGGGAGTTGAGTTGCCTTCACCTCATCTTATGATTATG
GATTTACT
Found at i:463528 original size:21 final size:21
Alignment explanation
Indices: 463504--463581 Score: 120
Period size: 21 Copynumber: 3.7 Consensus size: 21
463494 TGAATATGTC
*
463504 AAAAGTGTATAGAAAACTGAA
1 AAAAGTGAATAGAAAACTGAA
*
463525 AAAAGTGAATAGGAAACTGAA
1 AAAAGTGAATAGAAAACTGAA
*
463546 AAAAGTGAATAGGAAACTGAA
1 AAAAGTGAATAGAAAACTGAA
*
463567 AAAAGTTAATAGAAA
1 AAAAGTGAATAGAAA
463582 GCCCTAAACA
Statistics
Matches: 53, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 53 1.00
ACGTcount: A:0.59, C:0.04, G:0.21, T:0.17
Consensus pattern (21 bp):
AAAAGTGAATAGAAAACTGAA
Found at i:463856 original size:50 final size:51
Alignment explanation
Indices: 463761--463856 Score: 133
Period size: 50 Copynumber: 1.9 Consensus size: 51
463751 TTTACTTTAC
* *
463761 ATAGTTAATGCTTGTGACCTCCATATGTAATGTTATTTAGTTGTATTGTAT
1 ATAGTCAATGCTTGTGACCTCCACATGTAATGTTATTTAGTTGTATTGTAT
* *
463812 ATAGTCAATGCTTGTG-CTTCCACATGTTATGTTATTTTA-TTGTAT
1 ATAGTCAATGCTTGTGACCTCCACATGTAATGTTA-TTTAGTTGTAT
463857 ATAGTCAATT
Statistics
Matches: 40, Mismatches: 4, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
50 21 0.52
51 19 0.47
ACGTcount: A:0.24, C:0.11, G:0.17, T:0.48
Consensus pattern (51 bp):
ATAGTCAATGCTTGTGACCTCCACATGTAATGTTATTTAGTTGTATTGTAT
Found at i:464125 original size:15 final size:17
Alignment explanation
Indices: 464104--464141 Score: 53
Period size: 15 Copynumber: 2.4 Consensus size: 17
464094 ATCAATTGAT
*
464104 TATGTTGAT-AATTATG
1 TATGTTGATGAAATATG
464120 -ATGTTGATGAAATATG
1 TATGTTGATGAAATATG
464136 TATGTT
1 TATGTT
464142 TATTTTTGTT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
15 8 0.42
16 6 0.32
17 5 0.26
ACGTcount: A:0.32, C:0.00, G:0.21, T:0.47
Consensus pattern (17 bp):
TATGTTGATGAAATATG
Found at i:467849 original size:26 final size:26
Alignment explanation
Indices: 467820--467878 Score: 73
Period size: 26 Copynumber: 2.3 Consensus size: 26
467810 CTTCTATTCT
* * * *
467820 TCTTCTTCTTTCTTCGCTATCGTTCC
1 TCTTCTTCTTCCTTCACAATAGTTCC
*
467846 TCTTCTTCTTCCTTCACAATAGTTTC
1 TCTTCTTCTTCCTTCACAATAGTTCC
467872 TCTTCTT
1 TCTTCTT
467879 TTTTAGTAGC
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.08, C:0.32, G:0.05, T:0.54
Consensus pattern (26 bp):
TCTTCTTCTTCCTTCACAATAGTTCC
Found at i:480685 original size:48 final size:48
Alignment explanation
Indices: 480605--480707 Score: 143
Period size: 48 Copynumber: 2.1 Consensus size: 48
480595 TTACTCTGTC
* * * *
480605 GAAGAACTACCACTACCATTAGACCGAGCAGATTGTTGCTGTTCTGCT
1 GAAGCACTACCAATACCATTAGACCGAACAGATTGTTACTGTTCTGCT
* * *
480653 GAAGCACTACCAATATCATTAGACCTAACAGATTGTTATTGTTCTGCT
1 GAAGCACTACCAATACCATTAGACCGAACAGATTGTTACTGTTCTGCT
480701 GAAGCAC
1 GAAGCAC
480708 CAAAACTTGG
Statistics
Matches: 48, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
48 48 1.00
ACGTcount: A:0.30, C:0.23, G:0.18, T:0.28
Consensus pattern (48 bp):
GAAGCACTACCAATACCATTAGACCGAACAGATTGTTACTGTTCTGCT
Found at i:481915 original size:70 final size:70
Alignment explanation
Indices: 481829--481970 Score: 284
Period size: 70 Copynumber: 2.0 Consensus size: 70
481819 AGAAACATTA
481829 CAAACACCAAGAACAGTAAAACCACAAAATAGATTGTCACCATTAGACTCACTCAAATTATGACC
1 CAAACACCAAGAACAGTAAAACCACAAAATAGATTGTCACCATTAGACTCACTCAAATTATGACC
481894 AGATT
66 AGATT
481899 CAAACACCAAGAACAGTAAAACCACAAAATAGATTGTCACCATTAGACTCACTCAAATTATGACC
1 CAAACACCAAGAACAGTAAAACCACAAAATAGATTGTCACCATTAGACTCACTCAAATTATGACC
481964 AGATT
66 AGATT
481969 CA
1 CA
481971 GAAACAACAC
Statistics
Matches: 72, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
70 72 1.00
ACGTcount: A:0.46, C:0.25, G:0.10, T:0.20
Consensus pattern (70 bp):
CAAACACCAAGAACAGTAAAACCACAAAATAGATTGTCACCATTAGACTCACTCAAATTATGACC
AGATT
Found at i:490667 original size:60 final size:60
Alignment explanation
Indices: 490594--490714 Score: 233
Period size: 60 Copynumber: 2.0 Consensus size: 60
490584 AGGGGCTAAA
490594 ATGTTCTAAGCTAACTTCATTACCCACAATTAAAGGTATTTAATGAGTTAAGCAGCTCGT
1 ATGTTCTAAGCTAACTTCATTACCCACAATTAAAGGTATTTAATGAGTTAAGCAGCTCGT
*
490654 ATGTTCTAAGCTAACTTCATTACCCACAATTAAGGGTATTTAATGAGTTAAGCAGCTCGT
1 ATGTTCTAAGCTAACTTCATTACCCACAATTAAAGGTATTTAATGAGTTAAGCAGCTCGT
490714 A
1 A
490715 AGTTATTCAA
Statistics
Matches: 60, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
60 60 1.00
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33
Consensus pattern (60 bp):
ATGTTCTAAGCTAACTTCATTACCCACAATTAAAGGTATTTAATGAGTTAAGCAGCTCGT
Found at i:491783 original size:59 final size:59
Alignment explanation
Indices: 491688--491800 Score: 158
Period size: 59 Copynumber: 1.9 Consensus size: 59
491678 CAAATGATCC
* *
491688 CCAACTATAAGTGTTGCTTTATTGAGTCTTCCGACTATTAAAGGTTATAAAATGTTTCT
1 CCAACTATAAGTGTTGCTTTATTGAGTCTTCCGACTATTAAAAGTTACAAAATGTTTCT
* *
491747 CCAACTATAAGTTGTTGCTTT-TTTAGTCATT-TGACTATTAAAAGTTACAAAATG
1 CCAACTATAAG-TGTTGCTTTATTGAGTC-TTCCGACTATTAAAAGTTACAAAATG
491801 GTCACTCAAC
Statistics
Matches: 48, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
59 37 0.77
60 11 0.23
ACGTcount: A:0.31, C:0.14, G:0.14, T:0.41
Consensus pattern (59 bp):
CCAACTATAAGTGTTGCTTTATTGAGTCTTCCGACTATTAAAAGTTACAAAATGTTTCT
Found at i:491811 original size:59 final size:59
Alignment explanation
Indices: 491688--491813 Score: 150
Period size: 59 Copynumber: 2.1 Consensus size: 59
491678 CAAATGATCC
* * **
491688 CCAACTATAAGTGTTGCTTTATTGAGTCTTCCGACTATTAAAGGTTATAAAATGTTTCT
1 CCAACTATAAGTGTTGCTTTATTGAGTCTTCCGACTATTAAAAGTTACAAAATGTCACT
* *
491747 CCAACTATAAGTTGTTGCTTT-TTTAGTCATT-TGACTATTAAAAGTTACAAAATGGTCACT
1 CCAACTATAAG-TGTTGCTTTATTGAGTC-TTCCGACTATTAAAAGTTACAAAAT-GTCACT
491807 -CAACTAT
1 CCAACTAT
491814 TCATATGTTT
Statistics
Matches: 58, Mismatches: 6, Indels: 6
0.83 0.09 0.09
Matches are distributed among these distances:
59 43 0.74
60 15 0.26
ACGTcount: A:0.31, C:0.16, G:0.13, T:0.40
Consensus pattern (59 bp):
CCAACTATAAGTGTTGCTTTATTGAGTCTTCCGACTATTAAAAGTTACAAAATGTCACT
Found at i:501626 original size:23 final size:23
Alignment explanation
Indices: 501600--501647 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
501590 ATAAACATCA
* *
501600 AATACAATGAATAAT-ATTATTTT
1 AATAAAAT-AATAATAATAATTTT
501623 AATAAAATAATAATAATAATTTT
1 AATAAAATAATAATAATAATTTT
501646 AA
1 AA
501648 ATATTAGAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
22 6 0.27
23 16 0.73
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.40
Consensus pattern (23 bp):
AATAAAATAATAATAATAATTTT
Found at i:501792 original size:19 final size:17
Alignment explanation
Indices: 501739--501843 Score: 63
Period size: 18 Copynumber: 5.7 Consensus size: 17
501729 TACTATTATT
*
501739 ATATTTAATTAAAATAAA
1 ATATTT-ATTAAAATATA
501757 AT-TATTA-TAAACTATATCA
1 ATAT-TTATTAAA--ATAT-A
501776 ACTATTTATTAAAATATA
1 A-TATTTATTAAAATATA
* *
501794 ATATATTACTAATTATATTA
1 ATAT-TTATTAA-AATA-TA
501814 ATTATTTATTAAAATAATA
1 A-TATTTATTAAAAT-ATA
501833 ATA-TTATTAAA
1 ATATTTATTAAA
501844 TTATTAAAAA
Statistics
Matches: 70, Mismatches: 5, Indels: 25
0.70 0.05 0.25
Matches are distributed among these distances:
16 4 0.06
17 13 0.19
18 17 0.24
19 14 0.20
20 14 0.20
21 8 0.11
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.45
Consensus pattern (17 bp):
ATATTTATTAAAATATA
Found at i:501846 original size:38 final size:38
Alignment explanation
Indices: 501740--501847 Score: 125
Period size: 38 Copynumber: 2.8 Consensus size: 38
501730 ACTATTATTA
*
501740 TATTTAATTAAAATAA-AATTATTA-TAAACTATATCAAC
1 TATTT-ATTAAAATAATAA-TATTATTAAATTATATCAAC
* *
501778 TATTTATTAAAAT-ATAATA-TATTACTAATTATATTAAT
1 TATTTATTAAAATAATAATATTATTA--AATTATATCAAC
501816 TATTTATTAAAATAATAATATTATTAAATTAT
1 TATTTATTAAAATAATAATATTATTAAATTAT
501848 TAAAAATTAT
Statistics
Matches: 61, Mismatches: 3, Indels: 12
0.80 0.04 0.16
Matches are distributed among these distances:
35 2 0.03
36 5 0.08
37 10 0.16
38 33 0.54
39 6 0.10
40 5 0.08
ACGTcount: A:0.50, C:0.04, G:0.00, T:0.46
Consensus pattern (38 bp):
TATTTATTAAAATAATAATATTATTAAATTATATCAAC
Found at i:502020 original size:29 final size:29
Alignment explanation
Indices: 501973--502029 Score: 71
Period size: 29 Copynumber: 2.0 Consensus size: 29
501963 TTAATATTCT
* *
501973 ATTATATATTATTAAAATAAAAGTATAAC
1 ATTATACATTATTAAAATAAAACTATAAC
*
502002 ATTATACATTA-TAATAATATAACTATAA
1 ATTATACATTATTAA-AATAAAACTATAA
502030 TAATAAAATA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
28 3 0.12
29 21 0.88
ACGTcount: A:0.54, C:0.05, G:0.02, T:0.39
Consensus pattern (29 bp):
ATTATACATTATTAAAATAAAACTATAAC
Found at i:502030 original size:14 final size:13
Alignment explanation
Indices: 502011--502044 Score: 50
Period size: 14 Copynumber: 2.5 Consensus size: 13
502001 CATTATACAT
*
502011 TATAATAATATAAC
1 TATAATAATA-AAA
502025 TATAATAATAAAA
1 TATAATAATAAAA
502038 TATAATA
1 TATAATA
502045 TTGTATTATT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 9 0.47
14 10 0.53
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.35
Consensus pattern (13 bp):
TATAATAATAAAA
Found at i:502911 original size:16 final size:15
Alignment explanation
Indices: 502890--502932 Score: 61
Period size: 16 Copynumber: 2.8 Consensus size: 15
502880 TGTGCAAATC
502890 CGGGTACCCGGATTTT
1 CGGGTACCCGGA-TTT
502906 CGGGTACCC-GATTT
1 CGGGTACCCGGATTT
502920 CTGGGTACCCGGA
1 C-GGGTACCCGGA
502933 ACTTCCGGGT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
14 4 0.16
15 10 0.40
16 11 0.44
ACGTcount: A:0.14, C:0.28, G:0.33, T:0.26
Consensus pattern (15 bp):
CGGGTACCCGGATTT
Found at i:502925 original size:15 final size:15
Alignment explanation
Indices: 502890--502930 Score: 57
Period size: 15 Copynumber: 2.7 Consensus size: 15
502880 TGTGCAAATC
502890 CGGGTACCCGGATTTT
1 CGGGTACCC-GATTTT
502906 CGGGTACCCGA-TTT
1 CGGGTACCCGATTTT
502920 CTGGGTACCCG
1 C-GGGTACCCG
502931 GAACTTCCGG
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
14 4 0.17
15 11 0.46
16 9 0.38
ACGTcount: A:0.12, C:0.29, G:0.32, T:0.27
Consensus pattern (15 bp):
CGGGTACCCGATTTT
Found at i:503017 original size:17 final size:16
Alignment explanation
Indices: 502968--503035 Score: 70
Period size: 17 Copynumber: 4.3 Consensus size: 16
502958 CCGTGTCCCG
*
502968 ACCCGGATGTTACGGGT
1 ACCCGGATATT-CGGGT
*
502985 ACCC-GATAATCGGGT
1 ACCCGGATATTCGGGT
*
503000 ACCCGGATTTTGCGGGT
1 ACCCGGATATT-CGGGT
503017 ACCCGGA-A-TCGGGT
1 ACCCGGATATTCGGGT
503031 ACCCG
1 ACCCG
503036 ATACCCGGTT
Statistics
Matches: 44, Mismatches: 5, Indels: 7
0.79 0.09 0.12
Matches are distributed among these distances:
14 10 0.23
15 10 0.23
16 8 0.18
17 16 0.36
ACGTcount: A:0.19, C:0.28, G:0.32, T:0.21
Consensus pattern (16 bp):
ACCCGGATATTCGGGT
Found at i:503030 original size:31 final size:32
Alignment explanation
Indices: 502968--503035 Score: 102
Period size: 32 Copynumber: 2.2 Consensus size: 32
502958 CCGTGTCCCG
*
502968 ACCCGGATGTTACGGGTACCCGATAATCGGGT
1 ACCCGGATGTTACGGGTACCCGAGAATCGGGT
* *
503000 ACCCGGATTTTGCGGGTACCCG-GAATCGGGT
1 ACCCGGATGTTACGGGTACCCGAGAATCGGGT
503031 ACCCG
1 ACCCG
503036 ATACCCGGTT
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
31 13 0.39
32 20 0.61
ACGTcount: A:0.19, C:0.28, G:0.32, T:0.21
Consensus pattern (32 bp):
ACCCGGATGTTACGGGTACCCGAGAATCGGGT
Found at i:505297 original size:2 final size:2
Alignment explanation
Indices: 505290--505314 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
505280 AACATAAATA
505290 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 A
505315 CTATTCATTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:505564 original size:2 final size:2
Alignment explanation
Indices: 505557--505585 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
505547 AAAAACATAA
505557 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
505586 CTATTCATTC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:505709 original size:268 final size:269
Alignment explanation
Indices: 505230--505766 Score: 1026
Period size: 268 Copynumber: 2.0 Consensus size: 269
505220 TTGTTTCATA
505230 AACTATTTAAAACCTTCCTAAATACTGCTTAATTAGAAAACCATTTTAAAAACATAAATAATATA
1 AACTATTTAAAACCTTCCTAAATACTGCTTAATTAGAAAACCATTTTAAAAACATAAATAATATA
505295 TATATATATATATATATATACTATTCATTCTTAAATATGGATATATTTATACTAACAACAAATAA
66 TATATATATATATATATATACTATTCATTCTTAAATATGGATATATTTATACTAACAACAAATAA
505360 ATGGTCATAGTTTACTATTACAGATAAGACAAACCCGATAAGCAACATACAAATATAATATACAT
131 A-GGTCATAGTTTACTATTACAGATAAGACAAACCCGATAAGCAACATACAAATATAATATACAT
505425 GCCACTAATAGATCAAAGATAGGATGTATTACTGATATTGTTATTAGACATGATTTTTCTGGAAA
195 GCCACTAATAGATCAAAGATAGGATGTATTACTGATATTGTTATTAGACATGATTTTTCTGGAAA
505490 GATGCTCAAT
260 GATGCTCAAT
505500 AACTATTTAAAACCTTCCTAAATACTGCTTTAATTAGAAAACCA-TTTAAAAACATAAATATATA
1 AACTATTTAAAACCTTCCTAAATACTGC-TTAATTAGAAAACCATTTTAAAAACATAAATA-ATA
505564 TATATATATATATATATATATACTATTCATTCTT-AATATGGATATATTTATACTAACAACAAAT
64 TATATATATATATATATATATACTATTCATTCTTAAATATGGATATATTTATACTAACAACAAAT
505628 AAA-GTCATAGTTTACTATTACAGATAAGACAAACCCGATAAGCAACATACAAATATAATATACA
129 AAAGGTCATAGTTTACTATTACAGATAAGACAAACCCGATAAGCAACATACAAATATAATATACA
505692 TGCCACTAATAGATCAAAGATAGGATGTATTACTGATATTGTTATTAGACATGATTTTTCTGGAA
194 TGCCACTAATAGATCAAAGATAGGATGTATTACTGATATTGTTATTAGACATGATTTTTCTGGAA
505757 AGATGCTCAA
259 AGATGCTCAA
505767 GAGGCTCCTC
Statistics
Matches: 265, Mismatches: 0, Indels: 6
0.98 0.00 0.02
Matches are distributed among these distances:
268 136 0.51
270 77 0.29
271 52 0.20
ACGTcount: A:0.44, C:0.13, G:0.09, T:0.34
Consensus pattern (269 bp):
AACTATTTAAAACCTTCCTAAATACTGCTTAATTAGAAAACCATTTTAAAAACATAAATAATATA
TATATATATATATATATATACTATTCATTCTTAAATATGGATATATTTATACTAACAACAAATAA
AGGTCATAGTTTACTATTACAGATAAGACAAACCCGATAAGCAACATACAAATATAATATACATG
CCACTAATAGATCAAAGATAGGATGTATTACTGATATTGTTATTAGACATGATTTTTCTGGAAAG
ATGCTCAAT
Found at i:507859 original size:32 final size:32
Alignment explanation
Indices: 507821--507893 Score: 137
Period size: 32 Copynumber: 2.3 Consensus size: 32
507811 GAAATTCATG
507821 CAATTTCAATCATCATAACATCAAATTAAATC
1 CAATTTCAATCATCATAACATCAAATTAAATC
*
507853 CAATTTCAATCATCATAACATCCAATTAAATC
1 CAATTTCAATCATCATAACATCAAATTAAATC
507885 CAATTTCAA
1 CAATTTCAA
507894 CCAATTTCCA
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
32 40 1.00
ACGTcount: A:0.45, C:0.23, G:0.00, T:0.32
Consensus pattern (32 bp):
CAATTTCAATCATCATAACATCAAATTAAATC
Found at i:515979 original size:18 final size:18
Alignment explanation
Indices: 515956--515997 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
515946 ATCTTAATCC
515956 TTTAAATTTTCAAAACTT
1 TTTAAATTTTCAAAACTT
*
515974 TTTAAATTTTCCAAACTT
1 TTTAAATTTTCAAAACTT
*
515992 TGTAAA
1 TTTAAA
515998 ATGTCTCTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.38, C:0.12, G:0.02, T:0.48
Consensus pattern (18 bp):
TTTAAATTTTCAAAACTT
Found at i:516982 original size:24 final size:24
Alignment explanation
Indices: 516937--516986 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 24
516927 TGGTGGTTGG
516937 TTTAATGGATGTTTAAACTTTATT
1 TTTAATGGATGTTTAAACTTTATT
*
516961 TTTAATGGTATGTTT-AAGTTTATT
1 TTTAATGG-ATGTTTAAACTTTATT
516985 TT
1 TT
516987 GGTTCTTTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
24 18 0.75
25 6 0.25
ACGTcount: A:0.26, C:0.02, G:0.14, T:0.58
Consensus pattern (24 bp):
TTTAATGGATGTTTAAACTTTATT
Found at i:522604 original size:24 final size:24
Alignment explanation
Indices: 522559--522608 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 24
522549 TGGTGGTTGG
522559 TTTAATGGATGTTTAAACTTTATT
1 TTTAATGGATGTTTAAACTTTATT
*
522583 TTTAATGGTATGTTT-AAGTTTATT
1 TTTAATGG-ATGTTTAAACTTTATT
522607 TT
1 TT
522609 GGTTCTTTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
24 18 0.75
25 6 0.25
ACGTcount: A:0.26, C:0.02, G:0.14, T:0.58
Consensus pattern (24 bp):
TTTAATGGATGTTTAAACTTTATT
Found at i:524504 original size:30 final size:31
Alignment explanation
Indices: 524440--524511 Score: 83
Period size: 30 Copynumber: 2.4 Consensus size: 31
524430 ACAAAAATAT
* * *
524440 AACTTTTAAAAATTTACAATTTTAGTTCCTA
1 AACTTTTAAAAATTTACAACTTTAGTCCCCA
* *
524471 AACTTTTACAACTTTAC-ACTTTAGTCCCCA
1 AACTTTTAAAAATTTACAACTTTAGTCCCCA
*
524501 AACTTCTAAAA
1 AACTTTTAAAA
524512 TTTTCATTTC
Statistics
Matches: 34, Mismatches: 7, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
30 19 0.56
31 15 0.44
ACGTcount: A:0.38, C:0.21, G:0.03, T:0.39
Consensus pattern (31 bp):
AACTTTTAAAAATTTACAACTTTAGTCCCCA
Found at i:526476 original size:10 final size:10
Alignment explanation
Indices: 526463--526504 Score: 52
Period size: 9 Copynumber: 4.3 Consensus size: 10
526453 CAAAACACGT
526463 AAAAATAATA
1 AAAAATAATA
526473 AAAAATAAT-
1 AAAAATAATA
526482 AAAAATAA-A
1 AAAAATAATA
*
526491 CAAAATGAATA
1 AAAAAT-AATA
526502 AAA
1 AAA
526505 TGTTAAAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
9 13 0.48
10 11 0.41
11 3 0.11
ACGTcount: A:0.79, C:0.02, G:0.02, T:0.17
Consensus pattern (10 bp):
AAAAATAATA
Found at i:526484 original size:19 final size:19
Alignment explanation
Indices: 526462--526504 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
526452 ACAAAACACG
526462 TAAAAATAATAAAAAAT-AA
1 TAAAAATAA-AAAAAATGAA
*
526481 TAAAAATAAACAAAATGAA
1 TAAAAATAAAAAAAATGAA
526500 TAAAA
1 TAAAA
526505 TGTTAAAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 6 0.27
19 16 0.73
ACGTcount: A:0.77, C:0.02, G:0.02, T:0.19
Consensus pattern (19 bp):
TAAAAATAAAAAAAATGAA
Found at i:526711 original size:14 final size:14
Alignment explanation
Indices: 526692--526736 Score: 54
Period size: 14 Copynumber: 3.1 Consensus size: 14
526682 TATGATATTA
526692 AGAAAAAATATAAT
1 AGAAAAAATATAAT
*
526706 AGAAAAAATAAAAT
1 AGAAAAAATATAAT
*
526720 AAAGTAAAAATATAAT
1 --AGAAAAAATATAAT
526736 A
1 A
526737 TATATAAATA
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
14 14 0.54
16 12 0.46
ACGTcount: A:0.73, C:0.00, G:0.07, T:0.20
Consensus pattern (14 bp):
AGAAAAAATATAAT
Found at i:526760 original size:31 final size:30
Alignment explanation
Indices: 526695--526768 Score: 78
Period size: 31 Copynumber: 2.4 Consensus size: 30
526685 GATATTAAGA
* **
526695 AAAAATATAATAGAAAAAATAAAATAAAGT
1 AAAAATATAATATAAAAAATAAAATAAAAC
*
526725 AAAAATATAATATATATAAAT-AAATAAAAAC
1 AAAAATATAATATA-AAAAATAAAAT-AAAAC
*
526756 AAAAATAGAATAT
1 AAAAATATAATAT
526769 TAAGACTATA
Statistics
Matches: 37, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
30 17 0.46
31 20 0.54
ACGTcount: A:0.72, C:0.01, G:0.04, T:0.23
Consensus pattern (30 bp):
AAAAATATAATATAAAAAATAAAATAAAAC
Found at i:526817 original size:35 final size:34
Alignment explanation
Indices: 526706--526817 Score: 99
Period size: 35 Copynumber: 3.4 Consensus size: 34
526696 AAAATATAAT
*
526706 AGAAAAAATA-AAATAAAGTAAAAATATAATA-TA
1 AGAAAAAATATAAA-AACGTAAAAATATAATATTA
* * *
526739 TATAAATAA-ATAAAAAC--AAAAATAGAATATTA
1 -AGAAAAAATATAAAAACGTAAAAATATAATATTA
** *
526771 AGACTATATATAAAAACGTATAAAATATAATATTA
1 AGAAAAAATATAAAAACGTA-AAAATATAATATTA
526806 AGAAAAAATATA
1 AGAAAAAATATA
526818 TGCATAGTAA
Statistics
Matches: 59, Mismatches: 13, Indels: 11
0.71 0.16 0.13
Matches are distributed among these distances:
31 14 0.24
32 10 0.17
33 3 0.05
34 10 0.17
35 22 0.37
ACGTcount: A:0.67, C:0.03, G:0.05, T:0.25
Consensus pattern (34 bp):
AGAAAAAATATAAAAACGTAAAAATATAATATTA
Done.