Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008445.1 Hibiscus syriacus cultivar Beakdansim tig00111250_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: 899959
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 4 of 4
Found at i:680883 original size:117 final size:117
Alignment explanation
Indices: 680762--681023 Score: 407
Period size: 117 Copynumber: 2.2 Consensus size: 117
680752 TCATACTATT
** *
680762 AGTATGATTTTGTTACCATTTTAGCACATAATATGCCCTATCTGGAAATCCATATTTTCAATATG
1 AGTATGATTTCCTTACCATTTTAGCACATAATATGCCCTATCTGGAAATCCATAATTTCAATATG
* * ** *
680827 ATTTCCTTATCATTTAGCACCCTTAGTGCTTTATCTAGAAACCCATACACTC
66 ATTTCCTTATCATTTAGCACACTCAGTGCTCCATATAGAAACCCATACACTC
*
680879 AGTATGATTCCCTTACCATTTTAGCACATAATATGCCCTATCTGGAAATCCATAATTTCAATATG
1 AGTATGATTTCCTTACCATTTTAGCACATAATATGCCCTATCTGGAAATCCATAATTTCAATATG
* * *
680944 ATTTCCTTATCATTTAGCACACTCAGTGCTCCATATGGAAATCTATACACTC
66 ATTTCCTTATCATTTAGCACACTCAGTGCTCCATATAGAAACCCATACACTC
*
680996 AGTATGATTTCCTTAACATTTTAGCACA
1 AGTATGATTTCCTTACCATTTTAGCACA
681024 CAAAGTGCCA
Statistics
Matches: 131, Mismatches: 14, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
117 131 1.00
ACGTcount: A:0.30, C:0.23, G:0.10, T:0.37
Consensus pattern (117 bp):
AGTATGATTTCCTTACCATTTTAGCACATAATATGCCCTATCTGGAAATCCATAATTTCAATATG
ATTTCCTTATCATTTAGCACACTCAGTGCTCCATATAGAAACCCATACACTC
Found at i:681470 original size:17 final size:18
Alignment explanation
Indices: 681428--681475 Score: 62
Period size: 19 Copynumber: 2.6 Consensus size: 18
681418 ATCTTAAGGG
681428 AGTGCATCGATACACTACC
1 AGTGCATCGATACACTA-C
*
681447 TGTGCATCGATACACT-C
1 AGTGCATCGATACACTAC
681464 AGTGCATTCGAT
1 AGTGCA-TCGAT
681476 GTTTATTTAT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
17 6 0.23
18 5 0.19
19 15 0.58
ACGTcount: A:0.27, C:0.27, G:0.19, T:0.27
Consensus pattern (18 bp):
AGTGCATCGATACACTAC
Found at i:681603 original size:16 final size:17
Alignment explanation
Indices: 681582--681618 Score: 67
Period size: 16 Copynumber: 2.2 Consensus size: 17
681572 TTAAATGCTC
681582 CATATTTCAACCCC-TT
1 CATATTTCAACCCCTTT
681598 CATATTTCAACCCCTTT
1 CATATTTCAACCCCTTT
681615 CATA
1 CATA
681619 CTCTTAACTC
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 14 0.70
17 6 0.30
ACGTcount: A:0.27, C:0.35, G:0.00, T:0.38
Consensus pattern (17 bp):
CATATTTCAACCCCTTT
Found at i:689166 original size:29 final size:29
Alignment explanation
Indices: 689106--689176 Score: 81
Period size: 29 Copynumber: 2.4 Consensus size: 29
689096 GGGTACCAAT
* * *
689106 TTTTTTTATCTTTATAATTAAAGCCTTCA
1 TTTTTTAATCTTTATAATTAAAGCCCTAA
*
689135 TTTTTTAATCTTTATAATT-GAGTCCCTAA
1 TTTTTTAATCTTTATAATTAAAG-CCCTAA
689164 TTTTTTAAATCTT
1 TTTTTT-AATCTT
689177 ATCTTTTACC
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
28 2 0.06
29 28 0.78
30 6 0.17
ACGTcount: A:0.27, C:0.13, G:0.04, T:0.56
Consensus pattern (29 bp):
TTTTTTAATCTTTATAATTAAAGCCCTAA
Found at i:694318 original size:43 final size:45
Alignment explanation
Indices: 694244--694507 Score: 156
Period size: 44 Copynumber: 5.8 Consensus size: 45
694234 CAATATTGTT
* *
694244 TTTACCTTTATAATTGAGG-TCTCTAA-TTTTTTTAATCCCAC-CA
1 TTTACCTTTATAATTGAGGCCCT-TAAGTTTTTTCAATCCCACTCA
* *
694287 TTTAACTTTATAATTGAGGCCCTTAAGTTTTTTCAATCTCACTTTCTA
1 TTTACCTTTATAATTGAGGCCCTTAAGTTTTTTCAATCCCAC--TC-A
* * * * * *
694335 CTTTTTCTACCTTTACAACTGAGGCTCATAAGTTTTTTCAATCTCA--AA
1 ----TT-TACCTTTATAATTGAGGCCCTTAAGTTTTTTCAATCCCACTCA
* * **
694383 TTCTCCCTTTATAATTGA-GCCCTTAA-TTTTTT-AATCCCTCTTT
1 TT-TACCTTTATAATTGAGGCCCTTAAGTTTTTTCAATCCCACTCA
* **
694426 TTTAACTTTATAATT-AGGGCCCTTAAGTTTTTTCAATTTCACT--
1 TTTACCTTTATAATTGA-GGCCCTTAAGTTTTTTCAATCCCACTCA
* *
694469 TTCTACCTTTATAGTTGTGGCCAC-TAAGTTTTTTCAATC
1 TT-TACCTTTATAATTGAGGCC-CTTAAGTTTTTTCAATC
694508 TCAATTTCTA
Statistics
Matches: 173, Mismatches: 28, Indels: 39
0.72 0.12 0.16
Matches are distributed among these distances:
41 6 0.03
42 17 0.10
43 39 0.23
44 65 0.38
45 7 0.04
47 1 0.01
48 2 0.01
52 2 0.01
53 34 0.20
ACGTcount: A:0.24, C:0.21, G:0.08, T:0.47
Consensus pattern (45 bp):
TTTACCTTTATAATTGAGGCCCTTAAGTTTTTTCAATCCCACTCA
Found at i:694479 original size:44 final size:43
Alignment explanation
Indices: 694338--694613 Score: 190
Period size: 44 Copynumber: 6.4 Consensus size: 43
694328 CTTTCTACTT
* * * *
694338 TTTCTACCTTTACAACTGAGGCTCATAAGTTTTTTCAATCTCAA
1 TTTCTACCTTTATAATTG-GGCCCTTAAGTTTTTTCAATCTCAA
* * * *
694382 ATTCTCCCTTTATAATTGAGCCCTTAA-TTTTTT-AATCCCTC-T
1 TTTCTACCTTTATAATTGGGCCCTTAAGTTTTTTCAAT--CTCAA
* * * *
694424 TTTTTAACTTTATAATTAGGGCCCTTAAGTTTTTTCAATTTCAC
1 TTTCTACCTTTATAATT-GGGCCCTTAAGTTTTTTCAATCTCAA
*
694468 TTTCTACCTTTATAGTTGTGGCCAC-TAAGTTTTTTCAATCTCAA
1 TTTCTACCTTTATAATTG-GGCC-CTTAAGTTTTTTCAATCTCAA
* * * * **
694512 TTTCTACCTTTTTAAGTGAGACACC-CAAGTTTTCCCAATCTCAA
1 TTTCTACCTTTATAATTG-GGC-CCTTAAGTTTTTTCAATCTCAA
* * * **
694556 -TTATACATTTATAATTGAGGCTCTT-A-TTTTTTCAATCTTGA
1 TTTCTACCTTTATAATTG-GGCCCTTAAGTTTTTTCAATCTCAA
*
694597 TTTCTATCTTTATAATT
1 TTTCTACCTTTATAATT
694614 AAGGCTTCTA
Statistics
Matches: 179, Mismatches: 42, Indels: 24
0.73 0.17 0.10
Matches are distributed among these distances:
41 14 0.08
42 34 0.19
43 37 0.21
44 89 0.50
45 5 0.03
ACGTcount: A:0.25, C:0.20, G:0.08, T:0.46
Consensus pattern (43 bp):
TTTCTACCTTTATAATTGGGCCCTTAAGTTTTTTCAATCTCAA
Found at i:696350 original size:11 final size:11
Alignment explanation
Indices: 696334--696358 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
696324 TAATATATAG
696334 TTTTGAAAACA
1 TTTTGAAAACA
696345 TTTTGAAAACA
1 TTTTGAAAACA
696356 TTT
1 TTT
696359 ATATATTATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.40, C:0.08, G:0.08, T:0.44
Consensus pattern (11 bp):
TTTTGAAAACA
Found at i:696465 original size:37 final size:37
Alignment explanation
Indices: 696315--696554 Score: 234
Period size: 38 Copynumber: 6.6 Consensus size: 37
696305 ATGGTTTTAG
* *
696315 AAAATTTTATAATATATAGTTTTGAAAACA-TTTTGA
1 AAAATTATATAATATATAGTTTTAAAAACATTTTTGA
* * *
696351 AAACATTTATATATTATATAGTTTTTAAAAC-GTTTTGA
1 AAA-A-TTATATAATATATAGTTTTAAAAACATTTTTGA
* *
696389 AAACTTATATAATATATAGCTTTTTAAAAAATATTTTTGA
1 AAAATTATATAATATATAG--TTTT-AAAAACATTTTTGA
696429 AAAATTATATAATATATAGTTTTAAAAACATTTTTG-
1 AAAATTATATAATATATAGTTTTAAAAACATTTTTGA
* *
696465 AAAATTATAT-A-GT-T--TTTAAAAAACATTTTTGA
1 AAAATTATATAATATATAGTTTTAAAAACATTTTTGA
*
696497 AAATTTATATAATATAT-GTTTTTAAAAAACATTTTT--
1 AAAATTATATAATATATAG-TTTT-AAAAACATTTTTGA
*
696533 AAAATT-TATATTATATAGTTTT
1 AAAATTATATAATATATAGTTTT
696555 TAAATACTTT
Statistics
Matches: 172, Mismatches: 17, Indels: 31
0.78 0.08 0.14
Matches are distributed among these distances:
31 16 0.09
32 9 0.05
33 2 0.01
34 2 0.01
35 15 0.09
36 33 0.19
37 16 0.09
38 51 0.30
39 4 0.02
40 24 0.14
ACGTcount: A:0.44, C:0.03, G:0.06, T:0.47
Consensus pattern (37 bp):
AAAATTATATAATATATAGTTTTAAAAACATTTTTGA
Found at i:696497 original size:68 final size:70
Alignment explanation
Indices: 696401--696543 Score: 222
Period size: 68 Copynumber: 2.1 Consensus size: 70
696391 ACTTATATAA
*
696401 TATATAGCTTTTTAAAAAATATTTTTGAAAAATTATATAATATATAG-TTTT-AAAAACATTTTT
1 TATATAGCTTTTTAAAAAACATTTTTGAAAAATTATATAATATAT-GTTTTTAAAAAACATTTTT
696464 GAAAA-T
65 -AAAATT
*
696470 TATATAG-TTTTTAAAAAACATTTTTGAAAATTTATATAATATATGTTTTTAAAAAACATTTTTA
1 TATATAGCTTTTTAAAAAACATTTTTGAAAAATTATATAATATATGTTTTTAAAAAACATTTTTA
696534 AAATT
66 AAATT
696539 TATAT
1 TATAT
696544 TATATAGTTT
Statistics
Matches: 69, Mismatches: 2, Indels: 6
0.90 0.03 0.08
Matches are distributed among these distances:
67 1 0.01
68 43 0.62
69 25 0.36
ACGTcount: A:0.45, C:0.03, G:0.05, T:0.47
Consensus pattern (70 bp):
TATATAGCTTTTTAAAAAACATTTTTGAAAAATTATATAATATATGTTTTTAAAAAACATTTTTA
AAATT
Found at i:696569 original size:38 final size:36
Alignment explanation
Indices: 696315--696558 Score: 204
Period size: 37 Copynumber: 6.7 Consensus size: 36
696305 ATGGTTTTAG
* * *
696315 AAAATTTTATAATATATAG-TTTT-GAAAACATTTTGA
1 AAAA-TTTATATTATATAGTTTTTAAAAAACATTTT-T
* *
696351 AAACATTTATATATTATATAGTTTTT--AAAACGTTTTG
1 AAA-A-TT-TATATTATATAGTTTTTAAAAAACATTTTT
* *
696388 AAAACTTATATAATATATAGCTTTTTAAAAAATATTTTT
1 AAAA-TT-TATATTATATAG-TTTTTAAAAAACATTTTT
*
696427 GAAAAATTATATAATATATAG-TTTT-AAAAACATTTTT
1 --AAAATT-TATATTATATAGTTTTTAAAAAACATTTTT
*
696464 -GAA---A-ATTATATAGTTTTTAAAAAACATTTTT
1 AAAATTTATATTATATAGTTTTTAAAAAACATTTTT
*
696495 GAAAATTTATATAATATATGTTTTTAAAAAACATTTTT
1 -AAAATTTATATTATATA-GTTTTTAAAAAACATTTTT
696533 AAAATTTATATTATATAGTTTTTAAA
1 AAAATTTATATTATATAGTTTTTAAA
696559 TACTTTATTT
Statistics
Matches: 177, Mismatches: 14, Indels: 34
0.79 0.06 0.15
Matches are distributed among these distances:
29 8 0.05
30 5 0.03
31 12 0.07
33 2 0.01
34 2 0.01
36 28 0.16
37 46 0.26
38 43 0.24
39 12 0.07
40 15 0.08
41 4 0.02
ACGTcount: A:0.45, C:0.03, G:0.06, T:0.46
Consensus pattern (36 bp):
AAAATTTATATTATATAGTTTTTAAAAAACATTTTT
Found at i:696577 original size:37 final size:37
Alignment explanation
Indices: 696360--696582 Score: 124
Period size: 37 Copynumber: 6.2 Consensus size: 37
696350 AAAACATTTA
* **
696360 TATATTATATAGTTTTT--AAAACGT-TTTGAAAACTT
1 TATATTATATAGTTTTTAAAAAACTTATTTTTAAA-TT
*
696395 ATATAATATATAGCTTTTTAAAAAA--TATTTTTGAAAAATT
1 -TATATTATATAG-TTTTTAAAAAACTTATTTTT---AAATT
* *
696435 ATATAATATATAG-TTTT-AAAAAC--ATTTTTGAA--
1 -TATATTATATAGTTTTTAAAAAACTTATTTTTAAATT
696467 -A-ATTATATAGTTTTTAAAAAAC--ATTTTTGAAAATT
1 TATATTATATAGTTTTTAAAAAACTTATTTTT--AAATT
*
696502 TATATAATATATGTTTTTAAAAAAC--ATTTTTAAAATT
1 TATATTATATA-GTTTTTAAAAAACTTATTTTT-AAATT
* *
696539 TATATTATATAGTTTTT-AAATACTTTATTTTTATATT
1 TATATTATATAGTTTTTAAAAAAC-TTATTTTTAAATT
696576 TAT-TTAT
1 TATATTAT
696583 TATTATTATT
Statistics
Matches: 157, Mismatches: 10, Indels: 40
0.76 0.05 0.19
Matches are distributed among these distances:
29 8 0.05
30 5 0.03
31 12 0.08
33 2 0.01
34 2 0.01
35 5 0.03
36 22 0.14
37 47 0.30
38 32 0.20
39 4 0.03
40 15 0.10
41 3 0.02
ACGTcount: A:0.42, C:0.03, G:0.05, T:0.50
Consensus pattern (37 bp):
TATATTATATAGTTTTTAAAAAACTTATTTTTAAATT
Found at i:696581 original size:16 final size:17
Alignment explanation
Indices: 696562--696606 Score: 56
Period size: 20 Copynumber: 2.5 Consensus size: 17
696552 TTTTAAATAC
696562 TTTATTTTTA-TATTTA
1 TTTATTTTTATTATTTA
696578 TTTATTATTATTATTATTTA
1 TTTA-T-TT-TTATTATTTA
696598 TTTATTTTT
1 TTTATTTTT
696607 GTCCAGGTTC
Statistics
Matches: 25, Mismatches: 0, Indels: 7
0.78 0.00 0.22
Matches are distributed among these distances:
16 4 0.16
17 3 0.12
18 4 0.16
19 4 0.16
20 10 0.40
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (17 bp):
TTTATTTTTATTATTTA
Found at i:696833 original size:16 final size:16
Alignment explanation
Indices: 696812--696864 Score: 54
Period size: 16 Copynumber: 3.4 Consensus size: 16
696802 TGGCCAGAGA
696812 GGCGGTCAACGGCGGG
1 GGCGGTCAACGGCGGG
*** * *
696828 GGCGGTGGCCGG-AGA
1 GGCGGTCAACGGCGGG
696843 GGCGGTCAACGGCGGG
1 GGCGGTCAACGGCGGG
696859 GGCGGT
1 GGCGGT
696865 GGCCAGTCAT
Statistics
Matches: 26, Mismatches: 10, Indels: 2
0.68 0.26 0.05
Matches are distributed among these distances:
15 10 0.38
16 16 0.62
ACGTcount: A:0.11, C:0.23, G:0.58, T:0.08
Consensus pattern (16 bp):
GGCGGTCAACGGCGGG
Found at i:696835 original size:31 final size:31
Alignment explanation
Indices: 696797--696870 Score: 139
Period size: 31 Copynumber: 2.4 Consensus size: 31
696787 GGCCACCGGA
696797 GGCGGTGGCCAGAGAGGCGGTCAACGGCGGG
1 GGCGGTGGCCAGAGAGGCGGTCAACGGCGGG
*
696828 GGCGGTGGCCGGAGAGGCGGTCAACGGCGGG
1 GGCGGTGGCCAGAGAGGCGGTCAACGGCGGG
696859 GGCGGTGGCCAG
1 GGCGGTGGCCAG
696871 TCATCCCATC
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
31 41 1.00
ACGTcount: A:0.14, C:0.23, G:0.57, T:0.07
Consensus pattern (31 bp):
GGCGGTGGCCAGAGAGGCGGTCAACGGCGGG
Found at i:697266 original size:29 final size:28
Alignment explanation
Indices: 697219--697276 Score: 73
Period size: 27 Copynumber: 2.0 Consensus size: 28
697209 TACTCTTGTA
*
697219 TATATATATATTATTTATTTCTT-TTTT
1 TATATATATATTATATATTTCTTATTTT
*
697246 TATATATATACTCTATATATTTTTTATTTT
1 TATATATATA-T-TATATATTTCTTATTTT
697276 T
1 T
697277 TATTACTATT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
27 10 0.38
28 1 0.04
29 10 0.38
30 5 0.19
ACGTcount: A:0.28, C:0.05, G:0.00, T:0.67
Consensus pattern (28 bp):
TATATATATATTATATATTTCTTATTTT
Found at i:701102 original size:94 final size:94
Alignment explanation
Indices: 700936--701115 Score: 258
Period size: 94 Copynumber: 1.9 Consensus size: 94
700926 ATATTATATA
* * *
700936 TATATAATAAAGCTTGAGTTGTCCCTTAGAGCAATTGGTTAAACACCCCGGCTTTATGGATAATA
1 TATACAATAAAGCTTGAGTTGTCCCTTAGAGCAATTGGTTAAACACCCCGACTTTATGGATAAGA
*
701001 TTCAGCTAGCCTGATAAAGGTAATTTTAC
66 TTCAGCTAACCTGATAAAGGTAATTTTAC
*
701030 TATACAATAAAGCTTGAGCTT-TCCCTCTA-AGGCATTTGGTTAAACA-CCCGACTTTATGGATA
1 TATACAATAAAGCTTGAG-TTGTCCCT-TAGA-GCAATTGGTTAAACACCCCGACTTTATGGATA
*
701092 AGATTCAGCTAATCTGATAAAGGT
63 AGATTCAGCTAACCTGATAAAGGT
701116 GTTTATATAT
Statistics
Matches: 77, Mismatches: 6, Indels: 6
0.87 0.07 0.07
Matches are distributed among these distances:
94 59 0.77
95 18 0.23
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Consensus pattern (94 bp):
TATACAATAAAGCTTGAGTTGTCCCTTAGAGCAATTGGTTAAACACCCCGACTTTATGGATAAGA
TTCAGCTAACCTGATAAAGGTAATTTTAC
Found at i:702464 original size:83 final size:83
Alignment explanation
Indices: 702281--703259 Score: 1037
Period size: 83 Copynumber: 11.9 Consensus size: 83
702271 GCTCAAGGAA
* * * *
702281 AGAAGGGCTATTTGCCAACAAAAGACCTTCGAGTTCGACTACGCTCAGCT-CAGAGGTACATCAT
1 AGAAGGGCTATCTGCC-ACCAAAGACCTTCGAGTTTGACTACGCTCAGCTCCA-AGGCACATCAT
* * **
702345 TTGTAGCATAACTTAAGTTA
64 TTGCAGCATAGCTTAAGTCG
* * *
702365 AGAAGGGCTATCTGCCACCAAAAGACCTTCGAGTTTGACTACGTTCA-CTCTAAGGCATATCATT
1 AGAAGGGCTATCTGCCACC-AAAGACCTTCGAGTTTGACTACGCTCAGCTCCAAGGCACATCATT
* *
702429 TGCAGCAAAACTTAAGTCG
65 TGCAGCATAGCTTAAGTCG
* * *
702448 AGAAGGGTTATATGCCAACCAAAGACCTTCGAG-TTGACTACACTCAGCTCCAAGGCACATCATT
1 AGAAGGGCTATCTGCC-ACCAAAGACCTTCGAGTTTGACTACGCTCAGCTCCAAGGCACATCATT
*
702512 TGCAACATAGCTTAAGTCG
65 TGCAGCATAGCTTAAGTCG
* * * * *
702531 AGAAGGGCTATCTG---CCAAAGACCTTCGAGTTTGATTACACTTAGCTTCGAGGACACATCATT
1 AGAAGGGCTATCTGCCACCAAAGACCTTCGAGTTTGACTACGCTCAGCTCCAAGG-CACATCATT
* * *
702593 TGCAGCATAACTCAAGTCT
65 TGCAGCATAGCTTAAGTCG
* * * *
702612 ACAAGGGTTATCTGCCACCAAAATACCTTCAAGTTTGACTACGCTCAGCTCCAAGGCACATCATT
1 AGAAGGGCTATCTGCCACC-AAAGACCTTCGAGTTTGACTACGCTCAGCTCCAAGGCACATCATT
*
702677 TTCAGCATAGCTTAAGTCG
65 TGCAGCATAGCTTAAGTCG
* * * *
702696 AGAAGGGGTATCTG---TCAAAGACCCTCGAGTTTGACTACGCTCAGCTCTAAGGCACATCATTT
1 AGAAGGGCTATCTGCCACCAAAGACCTTCGAGTTTGACTACGCTCAGCTCCAAGGCACATCATTT
702758 GCAGCATAGCTTAAGTCG
66 GCAGCATAGCTTAAGTCG
* * * * * * *
702776 AGAAGGGCTATCT---ACCAAAGACCTTCGAGTTCGATTGCACTCAGCTCAAAGGTACCAACATT
1 AGAAGGGCTATCTGCCACCAAAGACCTTCGAGTTTGACTACGCTCAGCTCCAAGGCA-CATCATT
*
702838 TGCAGCATAACTTAAGTCG
65 TGCAGCATAGCTTAAGTCG
* *
702857 AGAAGGGTTATCTGCCAACCAAAGACCTTCAAGTTTGACTACGCTCAGCTCCAAGGCA-ATCATT
1 AGAAGGGCTATCTGCC-ACCAAAGACCTTCGAGTTTGACTACGCTCAGCTCCAAGGCACATCATT
*
702921 TGCAACATAGCTTAAGTCG
65 TGCAGCATAGCTTAAGTCG
* * * * * * * *
702940 AG-AGGGCTATCTG---CCAAAGACCCTCCAGTTCGATTACACTCAGCTTCGAGGGTACATCATT
1 AGAAGGGCTATCTGCCACCAAAGACCTTCGAGTTTGACTACGCTCAGC-TCCAAGGCACATCATT
* * * *
703001 TACAGCATAACTCAAGGCG
65 TGCAGCATAGCTTAAGTCG
* * * * * * *
703020 AGAAGGGTTACCTGCCACCAAAAACCTTCGAGTTCGACTACGTTCAGCTCCAAGGCAAAACATTT
1 AGAAGGGCTATCTGCCACCAAAGACCTTCGAGTTTGACTACGCTCAGCTCCAAGGCACATCATTT
703085 GCAGCATAGCTTAAGTCG
66 GCAGCATAGCTTAAGTCG
* ** *
703103 AGAAGGGCTATCTG---CCAAAGACCTTCGAGTTTGATTATACTCAGCTCAAAGGCACCATCATT
1 AGAAGGGCTATCTGCCACCAAAGACCTTCGAGTTTGACTACGCTCAGCTCCAAGGCA-CATCATT
*
703165 TGCAGCATAGCTTAAGTTG
65 TGCAGCATAGCTTAAGTCG
* ** * *
703184 AGAAGGGCTATCT-TCTTCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCTAGGCACCATCATT
1 AGAAGGGCTATCTGCCACCAAAGACCTTCGAGTTTGACTACGCTCAGCTCCAAGGCA-CATCATT
*
703248 TGCAACATAGCT
65 TGCAGCATAGCT
703260 CAAAGAAAGA
Statistics
Matches: 745, Mismatches: 124, Indels: 53
0.81 0.13 0.06
Matches are distributed among these distances:
78 26 0.03
79 21 0.03
80 176 0.24
81 118 0.16
82 21 0.03
83 213 0.29
84 107 0.14
85 63 0.08
ACGTcount: A:0.30, C:0.25, G:0.20, T:0.25
Consensus pattern (83 bp):
AGAAGGGCTATCTGCCACCAAAGACCTTCGAGTTTGACTACGCTCAGCTCCAAGGCACATCATTT
GCAGCATAGCTTAAGTCG
Found at i:702924 original size:164 final size:163
Alignment explanation
Indices: 702301--703259 Score: 1049
Period size: 164 Copynumber: 5.9 Consensus size: 163
702291 TTTGCCAACA
* * * * **
702301 AAAGACCTTCGAGTTCGACTACGCTCAGCTCAGAGGTACATCATTTGTAGCATAACTTAAGTTAA
1 AAAGACCTTCGAGTTCGACTACACTCAGCTCAAAGGCACATCATTTGCAGCATAACTTAAGTCGA
* * *
702366 GAAGGGCTATCTGCCACCAAAAGACCTTCGAGTTTGACTACGTTCA-CTCTAAGGCATATCATTT
66 GAAGGGCTATCTGCCACC-AAAGACCTTCGAGTTTGACTACGCTCAGCTCCAAGGCACATCATTT
* * * *
702430 GCAGCAAAACTTAAGTCGAGAAGGGTTATATGCCAACC
130 GCAGCATAGCTTAAGTCGAGAAGGG--CTAT--CTACC
* * *
702468 AAAGACCTTCGAGTT-GACTACACTCAGCTCCAAGGCACATCATTTGCAACATAGCTTAAGTCGA
1 AAAGACCTTCGAGTTCGACTACACTCAGCTCAAAGGCACATCATTTGCAGCATAACTTAAGTCGA
* * * * *
702532 GAAGGGCTATCTG---CCAAAGACCTTCGAGTTTGATTACACTTAGCTTCGAGGACACATCATTT
66 GAAGGGCTATCTGCCACCAAAGACCTTCGAGTTTGACTACGCTCAGCTCCAAGG-CACATCATTT
* * * * *
702594 GCAGCATAACTCAAGTCTACAAGGGTTATCTGCCACC
130 GCAGCATAGCTTAAGTCGAGAAGGGCTATCT---ACC
* * * * * * *
702631 AAAATACCTTCAAGTTTGACTACGCTCAGCTCCAAGGCACATCATTTTCAGCATAGCTTAAGTCG
1 -AAAGACCTTCGAGTTCGACTACACTCAGCTCAAAGGCACATCATTTGCAGCATAACTTAAGTCG
* * * *
702696 AGAAGGGGTATCTG---TCAAAGACCCTCGAGTTTGACTACGCTCAGCTCTAAGGCACATCATTT
65 AGAAGGGCTATCTGCCACCAAAGACCTTCGAGTTTGACTACGCTCAGCTCCAAGGCACATCATTT
702758 GCAGCATAGCTTAAGTCGAGAAGGGCTATCTACC
130 GCAGCATAGCTTAAGTCGAGAAGGGCTATCTACC
* * * *
702792 AAAGACCTTCGAGTTCGATTGCACTCAGCTCAAAGGTACCAACATTTGCAGCATAACTTAAGTCG
1 AAAGACCTTCGAGTTCGACTACACTCAGCTCAAAGGCA-CATCATTTGCAGCATAACTTAAGTCG
* *
702857 AGAAGGGTTATCTGCCAACCAAAGACCTTCAAGTTTGACTACGCTCAGCTCCAAGGCA-ATCATT
65 AGAAGGGCTATCTGCC-ACCAAAGACCTTCGAGTTTGACTACGCTCAGCTCCAAGGCACATCATT
* *
702921 TGCAACATAGCTTAAGTCGAG-AGGGCTATCTGCC
129 TGCAGCATAGCTTAAGTCGAGAAGGGCTATCTACC
* * * * * * * * *
702955 AAAGACCCTCCAGTTCGATTACACTCAGCTTCGAGGGTACATCATTTACAGCATAACTCAAGGCG
1 AAAGACCTTCGAGTTCGACTACACTCAGC-TCAAAGGCACATCATTTGCAGCATAACTTAAGTCG
* * * * * * *
703020 AGAAGGGTTACCTGCCACCAAAAACCTTCGAGTTCGACTACGTTCAGCTCCAAGGCAAAACATTT
65 AGAAGGGCTATCTGCCACCAAAGACCTTCGAGTTTGACTACGCTCAGCTCCAAGGCACATCATTT
*
703085 GCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCC
130 GCAGCATAGCTTAAGTCGAGAAGGGCTATCTACC
* * * * *
703119 AAAGACCTTCGAGTTTGATTATACTCAGCTCAAAGGCACCATCATTTGCAGCATAGCTTAAGTTG
1 AAAGACCTTCGAGTTCGACTACACTCAGCTCAAAGGCA-CATCATTTGCAGCATAACTTAAGTCG
* ** * *
703184 AGAAGGGCTATCT-TCTTCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCTAGGCACCATCATT
65 AGAAGGGCTATCTGCCACCAAAGACCTTCGAGTTTGACTACGCTCAGCTCCAAGGCA-CATCATT
*
703248 TGCAACATAGCT
129 TGCAGCATAGCT
703260 CAAAGAAAGA
Statistics
Matches: 676, Mismatches: 99, Indels: 37
0.83 0.12 0.05
Matches are distributed among these distances:
160 31 0.05
161 39 0.06
162 63 0.09
163 153 0.23
164 198 0.29
165 124 0.18
166 53 0.08
167 15 0.02
ACGTcount: A:0.30, C:0.25, G:0.20, T:0.25
Consensus pattern (163 bp):
AAAGACCTTCGAGTTCGACTACACTCAGCTCAAAGGCACATCATTTGCAGCATAACTTAAGTCGA
GAAGGGCTATCTGCCACCAAAGACCTTCGAGTTTGACTACGCTCAGCTCCAAGGCACATCATTTG
CAGCATAGCTTAAGTCGAGAAGGGCTATCTACC
Found at i:703092 original size:327 final size:325
Alignment explanation
Indices: 702262--703262 Score: 1158
Period size: 327 Copynumber: 3.0 Consensus size: 325
702252 AAGAAAACAG
*** * * *
702262 TGCAACATAGCTCAAGGAAAGAAGGGCTATTTGCCAACAAAAGACCTTCGAGTTCGACTACGCTC
1 TGCAACATAGCTCAAGTCGACAAGGGCTATCTGCC--CAAAAGACCTTCAAGTTCGACTACGCTC
** **
702327 AGCTCAGAGGTACATCATTTGTAGCATAACTTAAGTTAAGAAGGGCTATCTGCCACCAAAAGACC
64 AGCTCAG-GGTACATCATTTACAGCATAACTTAAGTCGAGAAGGGCTATCTGCCACCAAAA-ACC
* * *
702392 TTCGAGTTTGACTACGTTCA-CTCTAAGGCATATCATTTGCAGCAAAACTTAAGTCGAGAAGGGT
127 TTCGAGTTTGACTACGTTCAGCTCTAAGGCAAATCATTTGCAGCATAGCTTAAGTCGAGAAGGG-
* * * * *
702456 TATATGCCAACCAAAGACCTTCGAGTTGACTACACTCAGCTCCAAGGCA-CATCATTTGCAACAT
191 -CTAT--CTACCAAAGACCTTCGAGTTGATTACACTCAGCTCAAAGGCACCATCATTTGCAGCAT
* * * * *
702520 AGCTTAAGTCGAGAAGGGCTATCTG-CCAAAGACCTTCGAGTTTGATTACACTTAGCTTCGAGGA
253 AGCTTAAGTCGAGAAGGGCTATCTGCCCAAAGACCTTCGAGTTTGACTACGCTCAGCTCCAAGG-
702584 CACATCATT
317 CACATCATT
* * * * * *
702593 TGCAGCATAACTCAAGTCTACAAGGGTTATCTGCCACCAAAATACCTTCAAGTTTGACTACGCTC
1 TGCAACATAGCTCAAGTCGACAAGGGCTATCTG-C-CCAAAAGACCTTCAAGTTCGACTACGCTC
* * * * * * * *
702658 AGCTCCAAGGCACATCATTTTCAGCATAGCTTAAGTCGAGAAGGGGTATCTG---TCAAAGACCC
64 AGCT-CAGGGTACATCATTTACAGCATAACTTAAGTCGAGAAGGGCTATCTGCCACCAAAAACCT
* *
702720 TCGAGTTTGACTACGCTCAGCTCTAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCT
128 TCGAGTTTGACTACGTTCAGCTCTAAGGCAAATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCT
* * * *
702785 ATCTACCAAAGACCTTCGAGTTCGATTGCACTCAGCTCAAAGGTACCAACATTTGCAGCATAACT
193 ATCTACCAAAGACCTTCGAGTT-GATTACACTCAGCTCAAAGGCACCATCATTTGCAGCATAGCT
* *
702850 TAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCAAGTTTGACTACGCTCAGCTCCAAGGCA
257 TAAGTCGAGAAGGGCTATCTG-C--CCAAAGACCTTCGAGTTTGACTACGCTCAGCTCCAAGGCA
702915 -ATCATT
319 CATCATT
* * * * * *
702921 TGCAACATAGCTTAAGTCGA-GAGGGCTATCTG-CC-AAAGACCCTCCAGTTCGATTACACTCAG
1 TGCAACATAGCTCAAGTCGACAAGGGCTATCTGCCCAAAAGACCTTCAAGTTCGACTACGCTCAG
* * * *
702983 CTTCGAGGGTACATCATTTACAGCATAACTCAAGGCGAGAAGGGTTACCTGCCACCAAAAACCTT
66 C-TC-AGGGTACATCATTTACAGCATAACTTAAGTCGAGAAGGGCTATCTGCCACCAAAAACCTT
* * *
703048 CGAGTTCGACTACGTTCAGCTCCAAGGCAAAACATTTGCAGCATAGCTTAAGTCGAGAAGGGCTA
129 CGAGTTTGACTACGTTCAGCTCTAAGGCAAATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTA
* *
703113 TCTGCCAAAGACCTTCGAGTTTGATTATACTCAGCTCAAAGGCACCATCATTTGCAGCATAGCTT
194 TCTACCAAAGACCTTCGAG-TTGATTACACTCAGCTCAAAGGCACCATCATTTGCAGCATAGCTT
* * * * *
703178 AAGTTGAGAAGGGCTATCTTCTTCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCTAGGCACCA
258 AAGTCGAGAAGGGCTATCTGC-CCAAAGACCTTCGAGTTTGACTACGCTCAGCTCCAAGGCA-CA
703243 TCATT
321 TCATT
703248 TGCAACATAGCTCAA
1 TGCAACATAGCTCAA
703263 AGAAAGAGGG
Statistics
Matches: 567, Mismatches: 85, Indels: 40
0.82 0.12 0.06
Matches are distributed among these distances:
323 24 0.04
324 60 0.11
325 54 0.10
326 40 0.07
327 192 0.34
328 68 0.12
329 2 0.00
330 32 0.06
331 91 0.16
332 3 0.01
333 1 0.00
ACGTcount: A:0.31, C:0.25, G:0.20, T:0.25
Consensus pattern (325 bp):
TGCAACATAGCTCAAGTCGACAAGGGCTATCTGCCCAAAAGACCTTCAAGTTCGACTACGCTCAG
CTCAGGGTACATCATTTACAGCATAACTTAAGTCGAGAAGGGCTATCTGCCACCAAAAACCTTCG
AGTTTGACTACGTTCAGCTCTAAGGCAAATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATC
TACCAAAGACCTTCGAGTTGATTACACTCAGCTCAAAGGCACCATCATTTGCAGCATAGCTTAAG
TCGAGAAGGGCTATCTGCCCAAAGACCTTCGAGTTTGACTACGCTCAGCTCCAAGGCACATCATT
Found at i:703857 original size:2 final size:2
Alignment explanation
Indices: 703852--703890 Score: 53
Period size: 2 Copynumber: 20.0 Consensus size: 2
703842 TTTTTTTTTT
* *
703852 TA TA TA TA TA CA TA TA TA TA TC TA TA TA TA TA T- TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
703891 GTTTGCAAAT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.46, C:0.05, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:703943 original size:27 final size:27
Alignment explanation
Indices: 703913--703964 Score: 86
Period size: 27 Copynumber: 1.9 Consensus size: 27
703903 TTTTAGAAAA
703913 TTATATAATATATAGTTTTGAAAACAT
1 TTATATAATATATAGTTTTGAAAACAT
* *
703940 TTATATATTATATAGTTTTTAAAAC
1 TTATATAATATATAGTTTTGAAAAC
703965 GTTTTGAAAG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.42, C:0.04, G:0.06, T:0.48
Consensus pattern (27 bp):
TTATATAATATATAGTTTTGAAAACAT
Found at i:703949 original size:63 final size:63
Alignment explanation
Indices: 703878--703999 Score: 174
Period size: 63 Copynumber: 1.9 Consensus size: 63
703868 TATATCTATA
**
703878 TATATATTATATAGTTTGCAAATGGTTTTAGAAA-ATTATATAATATATAGTTTTGAAAACATT
1 TATATATTATATAGTTTGCAAAACGTTTT-GAAAGATTATATAATATATAGTTTTGAAAACATT
** * *
703941 TATATATTATATAGTTTTTAAAACGTTTTGAAAGCTTATATAATATATAGTTTTTAAAA
1 TATATATTATATAGTTTGCAAAACGTTTTGAAAGATTATATAATATATAGTTTTGAAAA
704000 AATATTTTTG
Statistics
Matches: 52, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
62 4 0.08
63 48 0.92
ACGTcount: A:0.41, C:0.03, G:0.10, T:0.46
Consensus pattern (63 bp):
TATATATTATATAGTTTGCAAAACGTTTTGAAAGATTATATAATATATAGTTTTGAAAACATT
Found at i:704013 original size:13 final size:13
Alignment explanation
Indices: 703991--704082 Score: 53
Period size: 13 Copynumber: 6.8 Consensus size: 13
703981 TAATATATAG
703991 TTTTTAAAAAATA
1 TTTTTAAAAAATA
*
704004 TTTTTGAAAAAT-
1 TTTTTAAAAAATA
* * * *
704016 TATATAATATATA
1 TTTTTAAAAAATA
*
704029 GTTTTAAAAACAT-
1 TTTTTAAAAA-ATA
*
704042 TTTTGAAAATTATATA
1 TTTTTAAAA--A-ATA
*
704058 GTTTTTAAAAAACA
1 -TTTTTAAAAAATA
704072 TTTTTAAAAAA
1 TTTTTAAAAAA
704083 ACTTATATAG
Statistics
Matches: 57, Mismatches: 16, Indels: 12
0.67 0.19 0.14
Matches are distributed among these distances:
12 7 0.12
13 34 0.60
14 4 0.07
15 4 0.07
17 8 0.14
ACGTcount: A:0.49, C:0.02, G:0.04, T:0.45
Consensus pattern (13 bp):
TTTTTAAAAAATA
Found at i:704090 original size:102 final size:100
Alignment explanation
Indices: 703909--704157 Score: 285
Period size: 102 Copynumber: 2.5 Consensus size: 100
703899 ATGGTTTTAG
* * * *
703909 AAAATTATATAATATATAGTTTTGAAAACATTTAT-ATATTATATAGTTTTTAAAACGTTTTGAA
1 AAAATTATATAATATATAGTTTTAAAAACATTTTTAAAATTATATAGTTTTTAAAACATTTTGAA
* *
703973 AGCTTATATAATATATAGTTTTTAAAAAATATTTTTGA
66 A---TATATAATATATAGTTTTTAAAAAACAGTTTTGA
704011 AAAATTATATAATATATAGTTTTAAAAACATTTTTGAAAATTATATAGTTTTTAAAAAACATTTT
1 AAAATTATATAATATATAGTTTTAAAAACATTTTT-AAAATTATATAGTTTTT--AAAACATTTT
*
704076 TAAA-A-A-AACTTATATAGTTTTTAAAAAACAGTTTTGA
63 GAAATATATAA--TATATAGTTTTTAAAAAACAGTTTTGA
* *
704113 AAATTTATATAATATGT--TTTTAAAAAACATTTTTAAAATTTATAT
1 AAAATTATATAATATATAGTTTT-AAAAACATTTTTAAAA-TTATAT
704158 TATATAGTTT
Statistics
Matches: 130, Mismatches: 9, Indels: 17
0.83 0.06 0.11
Matches are distributed among these distances:
100 10 0.08
101 19 0.15
102 74 0.57
104 15 0.12
106 12 0.09
ACGTcount: A:0.46, C:0.03, G:0.06, T:0.45
Consensus pattern (100 bp):
AAAATTATATAATATATAGTTTTAAAAACATTTTTAAAATTATATAGTTTTTAAAACATTTTGAA
ATATATAATATATAGTTTTTAAAAAACAGTTTTGA
Found at i:704139 original size:36 final size:36
Alignment explanation
Indices: 703926--704172 Score: 178
Period size: 36 Copynumber: 6.9 Consensus size: 36
703916 TATAATATAT
703926 AGTTTTGAAAACATTTATATATTATATAGTTTTT--AAAAC
1 AGTTTTG-AAA-ATTTATATA--ATAT-GTTTTTAAAAAAC
** *
703965 -GTTTTGAAAGCTTATATAATATATAGTTTTTAAAAAAT
1 AGTTTTGAAAATTTATAT-A-ATAT-GTTTTTAAAAAAC
* * *
704003 ATTTTTGAAAAATTATATAATATATAGTTTT-AAAAAC
1 AGTTTTGAAAATTTATATAATATGT--TTTTAAAAAAC
*
704040 ATTTTTGAAAA--T-TAT-ATA-GTTTTTAAAAAAC
1 AGTTTTGAAAATTTATATAATATGTTTTTAAAAAAC
* * **
704071 ATTTTTAAAAAAACT-TAT-ATA-GTTTTTAAAAAAC
1 AGTTTT-GAAAATTTATATAATATGTTTTTAAAAAAC
704105 AGTTTTGAAAATTTATATAATATGTTTTTAAAAAAC
1 AGTTTTGAAAATTTATATAATATGTTTTTAAAAAAC
* *
704141 A-TTTTTAAAATTTATATTATATAGTTTTTAAA
1 AGTTTTGAAAATTTATATAATAT-GTTTTTAAA
704173 TACTTTTTTA
Statistics
Matches: 178, Mismatches: 16, Indels: 31
0.79 0.07 0.14
Matches are distributed among these distances:
30 4 0.02
31 12 0.07
32 5 0.03
33 8 0.04
34 31 0.17
35 23 0.13
36 42 0.24
37 24 0.13
38 15 0.08
39 14 0.08
ACGTcount: A:0.45, C:0.03, G:0.06, T:0.46
Consensus pattern (36 bp):
AGTTTTGAAAATTTATATAATATGTTTTTAAAAAAC
Found at i:704191 original size:3 final size:3
Alignment explanation
Indices: 704183--704210 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
704173 TACTTTTTTA
704183 TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT T
704211 TATTTATTTA
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:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:706921 original size:28 final size:28
Alignment explanation
Indices: 706889--706943 Score: 76
Period size: 28 Copynumber: 2.0 Consensus size: 28
706879 TAAAGTATTC
706889 GCGACGTTTG-ATAAACAAACGCCGCTAA
1 GCGACGTTTGTATAAA-AAACGCCGCTAA
* *
706917 GCGACGTTTGTTTAAAAAACGTCGCTA
1 GCGACGTTTGTATAAAAAACGCCGCTA
706944 TAGATCTTGA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 20 0.83
29 4 0.17
ACGTcount: A:0.33, C:0.22, G:0.22, T:0.24
Consensus pattern (28 bp):
GCGACGTTTGTATAAAAAACGCCGCTAA
Found at i:706978 original size:43 final size:43
Alignment explanation
Indices: 706917--707005 Score: 124
Period size: 43 Copynumber: 2.1 Consensus size: 43
706907 ACGCCGCTAA
* * * *
706917 GCGACGTTTGTTTAAAAAACGTCGCTATAGATCTTGACCTTTT
1 GCGACATTTGTTTAAAAAACGCCGATATAGATCTTAACCTTTT
* *
706960 GCGACATTTGTTTCAAAAAGGCCGATATAGATCTTAACCTTTT
1 GCGACATTTGTTTAAAAAACGCCGATATAGATCTTAACCTTTT
707003 GCG
1 GCG
707006 CCGTTTTTTC
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
43 40 1.00
ACGTcount: A:0.27, C:0.19, G:0.19, T:0.35
Consensus pattern (43 bp):
GCGACATTTGTTTAAAAAACGCCGATATAGATCTTAACCTTTT
Found at i:711741 original size:46 final size:46
Alignment explanation
Indices: 711688--712208 Score: 777
Period size: 46 Copynumber: 11.5 Consensus size: 46
711678 GTATTAACAT
* *
711688 ATCCTTTCAGGCCTTTTAATTATGGCATCCTTTCATGCCTTAATGC
1 ATCCTTTCATGCATTTTAATTATGGCATCCTTTCATGCCTTAATGC
* * * *
711734 ATCCTTTCATGCATTTTAATTATGGAAACCTTTTATGCCTTAATAC
1 ATCCTTTCATGCATTTTAATTATGGCATCCTTTCATGCCTTAATGC
* * *
711780 ATCATTTCATGCATTTTAATTATGCCATCCTTTCATGACTTAATG-
1 ATCCTTTCATGCATTTTAATTATGGCATCCTTTCATGCCTTAATGC
* *
711825 ATCCTTTCATGCATTTTAATTATGACATCCTTTCATGCCTTAATGT
1 ATCCTTTCATGCATTTTAATTATGGCATCCTTTCATGCCTTAATGC
711871 ATCCTTTCATGCATTTTAATTATGGCATCCTTTCATGCCTTAATGC
1 ATCCTTTCATGCATTTTAATTATGGCATCCTTTCATGCCTTAATGC
* *
711917 ATCCTTTCATGCATTTTAATTATAGCATCATTTCATGCCTTAATGC
1 ATCCTTTCATGCATTTTAATTATGGCATCCTTTCATGCCTTAATGC
*
711963 ATCCTTTCATGCATTTTAATTATGGCATCCTTTTATGCCTTAATGC
1 ATCCTTTCATGCATTTTAATTATGGCATCCTTTCATGCCTTAATGC
* * *
712009 ATCCTATCATGC--CTT-A--AT-GCATCCTTTCATGCCTTATTGC
1 ATCCTTTCATGCATTTTAATTATGGCATCCTTTCATGCCTTAATGC
*
712049 ATCCTTTCATGCATTTTAATTATGACATCCTTTCATGCCTTAATGC
1 ATCCTTTCATGCATTTTAATTATGGCATCCTTTCATGCCTTAATGC
* *
712095 ATCCTTTCATACATTTTAATTATGACATCCTTTCATGCCTTAATGC
1 ATCCTTTCATGCATTTTAATTATGGCATCCTTTCATGCCTTAATGC
* * *
712141 ATCCCTTCATGCATTTTAATTATGACATCCTTTCATCCCTTAATGC
1 ATCCTTTCATGCATTTTAATTATGGCATCCTTTCATGCCTTAATGC
*
712187 ATCATTTCATGCATTTTAATTA
1 ATCCTTTCATGCATTTTAATTA
712209 CTCTAAAACT
Statistics
Matches: 431, Mismatches: 37, Indels: 14
0.89 0.08 0.03
Matches are distributed among these distances:
40 31 0.07
41 2 0.00
42 2 0.00
43 2 0.00
44 2 0.00
45 44 0.10
46 348 0.81
ACGTcount: A:0.24, C:0.23, G:0.09, T:0.44
Consensus pattern (46 bp):
ATCCTTTCATGCATTTTAATTATGGCATCCTTTCATGCCTTAATGC
Found at i:712000 original size:26 final size:25
Alignment explanation
Indices: 711688--712208 Score: 291
Period size: 20 Copynumber: 22.9 Consensus size: 25
711678 GTATTAACAT
* *
711688 ATCCTTTCAGGCCTTTTAATTATGGC
1 ATCCTTTCATGCATTTTAATTAT-GC
*
711714 ATCCTTTCATGC--CTT-A--ATGC
1 ATCCTTTCATGCATTTTAATTATGC
*
711734 ATCCTTTCATGCATTTTAATTATGGA
1 ATCCTTTCATGCATTTTAATTAT-GC
* * *
711760 AACCTTTTATGC--CTTAA-TA--C
1 ATCCTTTCATGCATTTTAATTATGC
*
711780 ATCATTTCATGCATTTTAATTATGCC
1 ATCCTTTCATGCATTTTAATTATG-C
*
711806 ATCCTTTCATG-A-CTT-A--ATG-
1 ATCCTTTCATGCATTTTAATTATGC
711825 ATCCTTTCATGCATTTTAATTATGAC
1 ATCCTTTCATGCATTTTAATTATG-C
* *
711851 ATCCTTTCATGC--CTT-A--ATGT
1 ATCCTTTCATGCATTTTAATTATGC
711871 ATCCTTTCATGCATTTTAATTATGGC
1 ATCCTTTCATGCATTTTAATTAT-GC
*
711897 ATCCTTTCATGC--CTT-A--ATGC
1 ATCCTTTCATGCATTTTAATTATGC
711917 ATCCTTTCATGCATTTTAATTATAGC
1 ATCCTTTCATGCATTTTAATTAT-GC
* *
711943 ATCATTTCATGC--CTT-A--ATGC
1 ATCCTTTCATGCATTTTAATTATGC
711963 ATCCTTTCATGCATTTTAATTATGGC
1 ATCCTTTCATGCATTTTAATTAT-GC
* *
711989 ATCCTTTTATGC--CTT-A--ATGC
1 ATCCTTTCATGCATTTTAATTATGC
* *
712009 ATCCTATCATGC--CTT-A--ATGC
1 ATCCTTTCATGCATTTTAATTATGC
*
712029 ATCCTTTCATGC--CTT-A-T-TGC
1 ATCCTTTCATGCATTTTAATTATGC
712049 ATCCTTTCATGCATTTTAATTATGAC
1 ATCCTTTCATGCATTTTAATTATG-C
*
712075 ATCCTTTCATGC--CTT-A--ATGC
1 ATCCTTTCATGCATTTTAATTATGC
*
712095 ATCCTTTCATACATTTTAATTATGAC
1 ATCCTTTCATGCATTTTAATTATG-C
*
712121 ATCCTTTCATGC--CTT-A--ATGC
1 ATCCTTTCATGCATTTTAATTATGC
*
712141 ATCCCTTCATGCATTTTAATTATGAC
1 ATCCTTTCATGCATTTTAATTATG-C
**
712167 ATCCTTTCAT-C-CCTT-A--ATGC
1 ATCCTTTCATGCATTTTAATTATGC
*
712187 ATCATTTCATGCATTTTAATTA
1 ATCCTTTCATGCATTTTAATTA
712209 CTCTAAAACT
Statistics
Matches: 390, Mismatches: 44, Indels: 123
0.70 0.08 0.22
Matches are distributed among these distances:
19 11 0.03
20 147 0.38
21 26 0.07
22 21 0.05
23 21 0.05
24 26 0.07
25 19 0.05
26 119 0.31
ACGTcount: A:0.24, C:0.23, G:0.09, T:0.44
Consensus pattern (25 bp):
ATCCTTTCATGCATTTTAATTATGC
Found at i:712127 original size:224 final size:226
Alignment explanation
Indices: 711688--712208 Score: 807
Period size: 224 Copynumber: 2.3 Consensus size: 226
711678 GTATTAACAT
* *
711688 ATCCTTTCAGGCCTTTTAATTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGCATTTTAA
1 ATCCTTTCATGCATTTTAATTAT-GCATCCTTTCATGCCTTAATGCATCCTTTCATGCATTTTAA
* *
711753 TTATGGAAACCTTTTATGCCTTAATACATCATTTCATGCATTTTAATTATGCCATCCTTTCATGA
65 TTATGGAAACCTTTTATGCCTTAATACATCATATCATGCA-CTTAA-TATGCCATCCTTTCATGA
* *
711818 CTTAATGATCCTTTCATGCATTTTAATTATGACATCCTTTCATGCCTTAATGTATCCTTTCATGC
128 CTTAATGATCCTTTCATGCATTTTAATTATGACATCCTTTCATGCCTTAATGCATCCTTTCATAC
*
711883 ATTTTAATTATGGCATCCTTTCATGCCTTAATGC
193 ATTTTAATTATGACATCCTTTCATGCCTTAATGC
*
711917 ATCCTTTCATGCATTTTAATTATAGCATCATTTCATGCCTTAATGCATCCTTTCATGCATTTTAA
1 ATCCTTTCATGCATTTTAATTAT-GCATCCTTTCATGCCTTAATGCATCCTTTCATGCATTTTAA
* * * * *
711982 TTATGGCATCCTTTTATGCCTTAATGCATCCTATCATGC-CTT-A-ATG-CATCCTTTCATGCCT
65 TTATGGAAACCTTTTATGCCTTAATACATCATATCATGCACTTAATATGCCATCCTTTCATGACT
*
712043 TATTGCATCCTTTCATGCATTTTAATTATGACATCCTTTCATGCCTTAATGCATCCTTTCATACA
130 TAATG-ATCCTTTCATGCATTTTAATTATGACATCCTTTCATGCCTTAATGCATCCTTTCATACA
712108 TTTTAATTATGACATCCTTTCATGCCTTAATGC
194 TTTTAATTATGACATCCTTTCATGCCTTAATGC
* * *
712141 ATCCCTTCATGCATTTTAATTATGACATCCTTTCATCCCTTAATGCATCATTTCATGCATTTTAA
1 ATCCTTTCATGCATTTTAATTATG-CATCCTTTCATGCCTTAATGCATCCTTTCATGCATTTTAA
712206 TTA
65 TTA
712209 CTCTAAAACT
Statistics
Matches: 271, Mismatches: 19, Indels: 9
0.91 0.06 0.03
Matches are distributed among these distances:
223 19 0.07
224 154 0.57
226 1 0.00
227 2 0.01
229 95 0.35
ACGTcount: A:0.24, C:0.23, G:0.09, T:0.44
Consensus pattern (226 bp):
ATCCTTTCATGCATTTTAATTATGCATCCTTTCATGCCTTAATGCATCCTTTCATGCATTTTAAT
TATGGAAACCTTTTATGCCTTAATACATCATATCATGCACTTAATATGCCATCCTTTCATGACTT
AATGATCCTTTCATGCATTTTAATTATGACATCCTTTCATGCCTTAATGCATCCTTTCATACATT
TTAATTATGACATCCTTTCATGCCTTAATGC
Found at i:712131 original size:178 final size:182
Alignment explanation
Indices: 711688--712199 Score: 759
Period size: 178 Copynumber: 2.8 Consensus size: 182
711678 GTATTAACAT
* *
711688 ATCCTTTCAGGCCTTTTAATTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGCATTTTAA
1 ATCCTTTCATGCATTTTAATTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGCATTTTAA
* * * * *
711753 TTATGGA-AACCTTTTATGCCTTAATACATCATTTCATGCATTTTAATTATGCCATCCTTTCATG
66 TTAT-GACATCCTTTCATGCCTTAATGCATCCTTTCATGCATTTTAATTATGACATCCTTTCATG
* * *
711817 ACTTAATG-ATCCTTTCATGCATTTTAATTATGACATCCTTTCATGCCTTAATGT
130 CCTTAATGCATCCTTTCATGCA-CTTAA-TATGACATCCTTTCATGCCTTAATGC
711871 ATCCTTTCATGCATTTTAATTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGCATTTTAA
1 ATCCTTTCATGCATTTTAATTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGCATTTTAA
* * *
711936 TTAT-AGCATCATTTCATGCCTTAATGCATCCTTTCATGCATTTTAATTATGGCATCCTTTTATG
66 TTATGA-CATCCTTTCATGCCTTAATGCATCCTTTCATGCATTTTAATTATGACATCCTTTCATG
* *
712000 CCTTAATGCATCCTATCATGC-CTT-A-ATG-CATCCTTTCATGCCTTATTGC
130 CCTTAATGCATCCTTTCATGCACTTAATATGACATCCTTTCATGCCTTAATGC
* *
712049 ATCCTTTCATGCATTTTAATTATGACATCCTTTCATGCCTTAATGCATCCTTTCATACATTTTAA
1 ATCCTTTCATGCATTTTAATTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGCATTTTAA
* *
712114 TTATGACATCCTTTCATGCCTTAATGCATCCCTTCATGCATTTTAATTATGACATCCTTTCATCC
66 TTATGACATCCTTTCATGCCTTAATGCATCCTTTCATGCATTTTAATTATGACATCCTTTCATGC
*
712179 CTTAATGCATCATTTCATGCA
131 CTTAATGCATCCTTTCATGCA
712200 TTTTAATTAC
Statistics
Matches: 301, Mismatches: 23, Indels: 14
0.89 0.07 0.04
Matches are distributed among these distances:
178 158 0.52
179 4 0.01
181 2 0.01
182 2 0.01
183 124 0.41
184 11 0.04
ACGTcount: A:0.24, C:0.24, G:0.09, T:0.43
Consensus pattern (182 bp):
ATCCTTTCATGCATTTTAATTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGCATTTTAA
TTATGACATCCTTTCATGCCTTAATGCATCCTTTCATGCATTTTAATTATGACATCCTTTCATGC
CTTAATGCATCCTTTCATGCACTTAATATGACATCCTTTCATGCCTTAATGC
Found at i:712761 original size:95 final size:93
Alignment explanation
Indices: 712578--712791 Score: 287
Period size: 95 Copynumber: 2.3 Consensus size: 93
712568 ATATAGTATG
* *
712578 ATCGATA--CTTACCCTGGTA-CGATACT--TCTACTATGTACCGATACCCCTTTCGGTATTGAT
1 ATCGATACCCTTACCATGGTATCGATACTACTCTACTATGTACCAATACCCCTTTCGGTATTGAT
* * * *
712638 ATCAATTTTAACTTCTACGTTTCCTGGT
66 ACCAATTCTAACTTCGACGTTGCCTGGT
712666 ATCGATACCCTTACCATGGTATCGATACTACTCTACTATGGTACCAATACCCCTTTACGGTATTG
1 ATCGATACCCTTACCATGGTATCGATACTACTCTACTAT-GTACCAATACCCCTTT-CGGTATTG
* *
712731 ATACCGATTCTAGA-TTCGATGTTGCCTGGT
64 ATACCAATTCTA-ACTTCGACGTTGCCTGGT
712761 ATCGATACCCTTACCATGGTATCGATACTAC
1 ATCGATACCCTTACCATGGTATCGATACTAC
712792 CTCGTAGGTA
Statistics
Matches: 110, Mismatches: 8, Indels: 9
0.87 0.06 0.07
Matches are distributed among these distances:
88 7 0.06
90 11 0.10
91 7 0.06
93 8 0.07
94 15 0.14
95 61 0.55
96 1 0.01
ACGTcount: A:0.24, C:0.26, G:0.15, T:0.35
Consensus pattern (93 bp):
ATCGATACCCTTACCATGGTATCGATACTACTCTACTATGTACCAATACCCCTTTCGGTATTGAT
ACCAATTCTAACTTCGACGTTGCCTGGT
Found at i:718964 original size:20 final size:20
Alignment explanation
Indices: 718941--718979 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
718931 TTTTCACGTA
*
718941 TTAACATATCCTTTCATGCC
1 TTAACACATCCTTTCATGCC
**
718961 TTAATGCATCCTTTCATGC
1 TTAACACATCCTTTCATGC
718980 ATTTTAATTA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.23, C:0.28, G:0.08, T:0.41
Consensus pattern (20 bp):
TTAACACATCCTTTCATGCC
Found at i:719002 original size:26 final size:26
Alignment explanation
Indices: 718966--719168 Score: 165
Period size: 26 Copynumber: 8.5 Consensus size: 26
718956 ATGCCTTAAT
718966 GCATCCTTTCATGCATTTTAATTATG
1 GCATCCTTTCATGCATTTTAATTATG
*
718992 GCATCCTTTCATGC--CTT-A--AT-
1 GCATCCTTTCATGCATTTTAATTATG
*
719012 GCAT-CATTCATGCATTTTAATTATG
1 GCATCCTTTCATGCATTTTAATTATG
* **
719037 GTATCCTTTCATATATTTTAATTATG
1 GCATCCTTTCATGCATTTTAATTATG
* * *
719063 ACATCCTATCATGC--CTT-A--AT-
1 GCATCCTTTCATGCATTTTAATTATG
719083 GCATCCTTTCATGCATTTTAATTATG
1 GCATCCTTTCATGCATTTTAATTATG
* *
719109 GAATCCTTTCATGC--CTT-A--AT-
1 GCATCCTTTCATGCATTTTAATTATG
* *
719129 GCATCATTTCGTGCATTTTAATTATG
1 GCATCCTTTCATGCATTTTAATTATG
719155 GCATCCTTTCATGC
1 GCATCCTTTCATGC
719169 GCTAATGCAT
Statistics
Matches: 134, Mismatches: 24, Indels: 38
0.68 0.12 0.19
Matches are distributed among these distances:
19 8 0.06
20 27 0.20
21 8 0.06
22 5 0.04
23 5 0.04
24 8 0.06
25 7 0.05
26 66 0.49
ACGTcount: A:0.24, C:0.21, G:0.11, T:0.44
Consensus pattern (26 bp):
GCATCCTTTCATGCATTTTAATTATG
Found at i:719037 original size:45 final size:46
Alignment explanation
Indices: 718948--719048 Score: 177
Period size: 45 Copynumber: 2.2 Consensus size: 46
718938 GTATTAACAT
*
718948 ATCCTTTCATGCCTTAATGCATCCTTTCATGCATTTTAATTATGGC
1 ATCCTTTCATGCCTTAATGCATCCATTCATGCATTTTAATTATGGC
*
718994 ATCCTTTCATGCCTTAATGCAT-CATTCATGCATTTTAATTATGGT
1 ATCCTTTCATGCCTTAATGCATCCATTCATGCATTTTAATTATGGC
719039 ATCCTTTCAT
1 ATCCTTTCAT
719049 ATATTTTAAT
Statistics
Matches: 53, Mismatches: 2, Indels: 1
0.95 0.04 0.02
Matches are distributed among these distances:
45 31 0.58
46 22 0.42
ACGTcount: A:0.23, C:0.23, G:0.10, T:0.45
Consensus pattern (46 bp):
ATCCTTTCATGCCTTAATGCATCCATTCATGCATTTTAATTATGGC
Found at i:719045 original size:71 final size:72
Alignment explanation
Indices: 718968--719122 Score: 249
Period size: 71 Copynumber: 2.2 Consensus size: 72
718958 GCCTTAATGC
* *
718968 ATCCTTTCATGCATTTTAATTATGGCATCCTTTCATGCCTTAATGCAT-CATTCATGCATTTTAA
1 ATCCTTTCATGCATTTTAATTATGACATCCTATCATGCCTTAATGCATCCATTCATGCATTTTAA
*
719032 TTATGGT
66 TTATGGA
** *
719039 ATCCTTTCATATATTTTAATTATGACATCCTATCATGCCTTAATGCATCCTTTCATGCATTTTAA
1 ATCCTTTCATGCATTTTAATTATGACATCCTATCATGCCTTAATGCATCCATTCATGCATTTTAA
719104 TTATGGA
66 TTATGGA
719111 ATCCTTTCATGC
1 ATCCTTTCATGC
719123 CTTAATGCAT
Statistics
Matches: 75, Mismatches: 8, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
71 44 0.59
72 31 0.41
ACGTcount: A:0.25, C:0.21, G:0.10, T:0.45
Consensus pattern (72 bp):
ATCCTTTCATGCATTTTAATTATGACATCCTATCATGCCTTAATGCATCCATTCATGCATTTTAA
TTATGGA
Found at i:719180 original size:46 final size:46
Alignment explanation
Indices: 719051--719183 Score: 205
Period size: 46 Copynumber: 2.9 Consensus size: 46
719041 CCTTTCATAT
* * *
719051 ATTTTAATTATGACATCCTATCATGCCTTAATGCATCCTTTCATGC
1 ATTTTAATTATGGCATCCTTTCATGCCTTAATGCATCATTTCATGC
* *
719097 ATTTTAATTATGGAATCCTTTCATGCCTTAATGCATCATTTCGTGC
1 ATTTTAATTATGGCATCCTTTCATGCCTTAATGCATCATTTCATGC
719143 ATTTTAATTATGGCATCCTTTCATGCGC-TAATGCATCATTT
1 ATTTTAATTATGGCATCCTTTCATGC-CTTAATGCATCATTT
719184 ACTCTAAAAC
Statistics
Matches: 80, Mismatches: 6, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
46 79 0.99
47 1 0.01
ACGTcount: A:0.25, C:0.21, G:0.11, T:0.43
Consensus pattern (46 bp):
ATTTTAATTATGGCATCCTTTCATGCCTTAATGCATCATTTCATGC
Found at i:726381 original size:53 final size:53
Alignment explanation
Indices: 726318--726481 Score: 258
Period size: 53 Copynumber: 3.1 Consensus size: 53
726308 ACTAAGGTCA
*
726318 CGAAATGGTAATTCACAAACTTATTATGAATACCAT-GAGTGCACACATAGTGC
1 CGAAATGGTAATTCACAAACTCATTATGAATACCATGGA-TGCACACATAGTGC
*
726371 CGAAATGGTAATTCACAAACTCATTATGAATACCATGGATGCACACATAGTGT
1 CGAAATGGTAATTCACAAACTCATTATGAATACCATGGATGCACACATAGTGC
* * *
726424 CGAAATGGTAATTCAAAAACTCATTATGAATACCATGGATGCATACACAGTGC
1 CGAAATGGTAATTCACAAACTCATTATGAATACCATGGATGCACACATAGTGC
*
726477 TGAAA
1 CGAAA
726482 GTACACAAAG
Statistics
Matches: 103, Mismatches: 7, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
53 101 0.98
54 2 0.02
ACGTcount: A:0.39, C:0.18, G:0.17, T:0.26
Consensus pattern (53 bp):
CGAAATGGTAATTCACAAACTCATTATGAATACCATGGATGCACACATAGTGC
Found at i:732763 original size:2 final size:2
Alignment explanation
Indices: 732756--732784 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
732746 AAATACATAC
732756 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
732785 AATACATCTA
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:734172 original size:90 final size:89
Alignment explanation
Indices: 734062--734233 Score: 308
Period size: 90 Copynumber: 1.9 Consensus size: 89
734052 CCGACTATTT
* *
734062 AATTTCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAATCCCTAATTTGATTAGGA
1 AATTCCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAA-CCCTAATATGATTAGGA
734127 TAACTTGGATATAAAAGGATTAATA
65 TAACTTGGATATAAAAGGATTAATA
734152 AATTCCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAACCCTAATATGATTAGGAT
1 AATTCCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAACCCTAATATGATTAGGAT
*
734217 AACTTGGCTATAAAAGG
66 AACTTGGATATAAAAGG
734234 GTGTGTTAGG
Statistics
Matches: 79, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
89 33 0.42
90 46 0.58
ACGTcount: A:0.47, C:0.07, G:0.10, T:0.36
Consensus pattern (89 bp):
AATTCCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAACCCTAATATGATTAGGAT
AACTTGGATATAAAAGGATTAATA
Found at i:746131 original size:20 final size:20
Alignment explanation
Indices: 746106--746157 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
746096 CCAAGGTTCC
*
746106 AGTATCGATACTCGCATATG
1 AGTATCAATACTCGCATATG
746126 AGTATCAATACTCGCATATG
1 AGTATCAATACTCGCATATG
746146 AGTATCAATACT
1 AGTATCAATACT
746158 TCCCATAACC
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.35, C:0.19, G:0.15, T:0.31
Consensus pattern (20 bp):
AGTATCAATACTCGCATATG
Found at i:746429 original size:12 final size:13
Alignment explanation
Indices: 746407--746437 Score: 55
Period size: 12 Copynumber: 2.5 Consensus size: 13
746397 ATTTCCCACT
746407 TATTTTCTCTTCA
1 TATTTTCTCTTCA
746420 TATTTT-TCTTCA
1 TATTTTCTCTTCA
746432 TATTTT
1 TATTTT
746438 ATTCCTTAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 12 0.67
13 6 0.33
ACGTcount: A:0.16, C:0.16, G:0.00, T:0.68
Consensus pattern (13 bp):
TATTTTCTCTTCA
Found at i:750707 original size:173 final size:174
Alignment explanation
Indices: 750418--750761 Score: 647
Period size: 173 Copynumber: 2.0 Consensus size: 174
750408 GCTAAACCTA
750418 AAAGAAGAATAACAACACCAAAGGGGAAAAAACATGATATACGGTTGCACAAGTGCTTGAGGAAG
1 AAAGAAGAATAACAACACCAAAGGGGAAAAAACATGATATACGGTTGCACAAGTGCTTGAGGAAG
750483 ACCAACAGGAGAGGGGAAAAAAGAAAAAGTTTGGGTTTGATTAATCATTTGATGTGATCATCC-A
66 ACCAACAGGAGAGGGGAAAAAAGAAAAAGTTTGGGTTTGATTAATCATTTGATGTGATCATCCAA
750547 AAAAAACGATACAATATTCAAAGTTCCTTTTTTATTGTCTTCTG
131 AAAAAACGATACAATATTCAAAGTTCCTTTTTTATTGTCTTCTG
*
750591 AAAGAAGAATAACAACACCAAAGGGG-GAAAACATGATATACGGTTGCACAAGTGCTTGAGGAAG
1 AAAGAAGAATAACAACACCAAAGGGGAAAAAACATGATATACGGTTGCACAAGTGCTTGAGGAAG
*
750655 ACCAACAGGAGAGGGGGAAAAAAGAAGAAGTTTGGGTTTGATTAATCATTTGATGTGATCATCCA
66 ACCAACAGGAGA-GGGGAAAAAAGAAAAAGTTTGGGTTTGATTAATCATTTGATGTGATCATCCA
750720 AAAAAAACGATACAATATTCAAAGTTCCTTTTTTATTGTCTT
130 AAAAAAACGATACAATATTCAAAGTTCCTTTTTTATTGTCTT
750762 TTACCCTTTT
Statistics
Matches: 167, Mismatches: 2, Indels: 3
0.97 0.01 0.02
Matches are distributed among these distances:
172 49 0.29
173 76 0.46
174 42 0.25
ACGTcount: A:0.41, C:0.13, G:0.22, T:0.25
Consensus pattern (174 bp):
AAAGAAGAATAACAACACCAAAGGGGAAAAAACATGATATACGGTTGCACAAGTGCTTGAGGAAG
ACCAACAGGAGAGGGGAAAAAAGAAAAAGTTTGGGTTTGATTAATCATTTGATGTGATCATCCAA
AAAAAACGATACAATATTCAAAGTTCCTTTTTTATTGTCTTCTG
Found at i:753281 original size:3 final size:3
Alignment explanation
Indices: 753267--753348 Score: 76
Period size: 3 Copynumber: 27.0 Consensus size: 3
753257 ATTGGGCTTG
* *
753267 TAA TATA TAA TAA TAA TATA TAT TAA TAA TAA TAA AAA T-A TAA TAA
1 TAA TA-A TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA TAA
* * * * *
753313 TTA TAA TAA TTA TAA TAA AAA TAA AAA TAA AAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
753349 AACGGTAAAA
Statistics
Matches: 62, Mismatches: 14, Indels: 6
0.76 0.17 0.07
Matches are distributed among these distances:
2 2 0.03
3 54 0.87
4 6 0.10
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:754021 original size:22 final size:22
Alignment explanation
Indices: 753955--754044 Score: 102
Period size: 22 Copynumber: 4.3 Consensus size: 22
753945 CATTATGAAC
*
753955 TTCTTTTTCCTCTTCAGATAGG
1 TTCTTCTTCCTCTTCAGATAGG
* *
753977 TTCTTC-T-C-ATT-ATGA-A-C
1 TTCTTCTTCCTCTTCA-GATAGG
753994 TTCTTCTTCCTCTTCAGATAGG
1 TTCTTCTTCCTCTTCAGATAGG
754016 TTCTTCTTCCTCTTCAGATAGG
1 TTCTTCTTCCTCTTCAGATAGG
754038 TTCTTCT
1 TTCTTCT
754045 CATTATGAAC
Statistics
Matches: 56, Mismatches: 5, Indels: 14
0.75 0.07 0.19
Matches are distributed among these distances:
17 6 0.11
18 3 0.05
19 5 0.09
20 5 0.09
21 3 0.05
22 34 0.61
ACGTcount: A:0.14, C:0.26, G:0.11, T:0.49
Consensus pattern (22 bp):
TTCTTCTTCCTCTTCAGATAGG
Found at i:754024 original size:42 final size:39
Alignment explanation
Indices: 753937--754022 Score: 163
Period size: 39 Copynumber: 2.2 Consensus size: 39
753927 GGTTGATCAA
*
753937 GTTCTTCTCATTATGAACTTCTTTTTCCTCTTCAGATAG
1 GTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATAG
753976 GTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATAG
1 GTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATAG
754015 GTTCTTCT
1 GTTCTTCT
754023 TCCTCTTCAG
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
39 46 1.00
ACGTcount: A:0.16, C:0.24, G:0.10, T:0.49
Consensus pattern (39 bp):
GTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATAG
Found at i:763018 original size:15 final size:15
Alignment explanation
Indices: 762998--763029 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
762988 TAATGCAATG
762998 AATGAATGTATGCAA
1 AATGAATGTATGCAA
763013 AATGAATGTATGCAA
1 AATGAATGTATGCAA
763028 AA
1 AA
763030 GGTATTGATC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.50, C:0.06, G:0.19, T:0.25
Consensus pattern (15 bp):
AATGAATGTATGCAA
Found at i:766990 original size:21 final size:21
Alignment explanation
Indices: 766949--766989 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
766939 AAAAAAATAT
766949 TAATAAAACATTTATCTAAAA
1 TAATAAAACATTTATCTAAAA
* *
766970 TAATTAAATATTTAT-TAAAA
1 TAATAAAACATTTATCTAAAA
766990 AATGTCAGAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.56, C:0.05, G:0.00, T:0.39
Consensus pattern (21 bp):
TAATAAAACATTTATCTAAAA
Found at i:767297 original size:27 final size:28
Alignment explanation
Indices: 767267--767321 Score: 69
Period size: 27 Copynumber: 2.0 Consensus size: 28
767257 TATAAAGCAA
*
767267 TAAAGATAT-TAAAAATAAT-GCCTAAAT
1 TAAA-ATATATAAAAATAAATGCCTAAAT
*
767294 TAAAATATATTAAAATAAATGCCTAAAT
1 TAAAATATATAAAAATAAATGCCTAAAT
767322 CATAAATTAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
26 4 0.17
27 12 0.50
28 8 0.33
ACGTcount: A:0.56, C:0.07, G:0.05, T:0.31
Consensus pattern (28 bp):
TAAAATATATAAAAATAAATGCCTAAAT
Found at i:768597 original size:3 final size:3
Alignment explanation
Indices: 768589--768675 Score: 70
Period size: 3 Copynumber: 29.0 Consensus size: 3
768579 CTGTAATATG
* * * *
768589 TAA TAA TAA TATT TAT TAA TAA TAA TAA AAA T-A TAA TAA TAA TTA
1 TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* * * *
768634 TAAA TTA TAA CAA TTA TAA TAA TTA TAA TAA TAA TAA -AA TAA
1 T-AA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
768676 ACGGACAAAA
Statistics
Matches: 66, Mismatches: 14, Indels: 8
0.75 0.16 0.09
Matches are distributed among these distances:
2 4 0.06
3 58 0.88
4 4 0.06
ACGTcount: A:0.61, C:0.01, G:0.00, T:0.38
Consensus pattern (3 bp):
TAA
Found at i:771475 original size:17 final size:17
Alignment explanation
Indices: 771453--771485 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
771443 CTAGTCTGAC
771453 CCGACCCGACCGTTGAA
1 CCGACCCGACCGTTGAA
*
771470 CCGACCCGGCCGTTGA
1 CCGACCCGACCGTTGA
771486 CCGTTGACCG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.18, C:0.42, G:0.27, T:0.12
Consensus pattern (17 bp):
CCGACCCGACCGTTGAA
Found at i:771501 original size:6 final size:7
Alignment explanation
Indices: 771479--771507 Score: 51
Period size: 7 Copynumber: 4.3 Consensus size: 7
771469 ACCGACCCGG
771479 CCGTTGA
1 CCGTTGA
771486 CCGTTGA
1 CCGTTGA
771493 CCG-TGA
1 CCGTTGA
771499 CCGTTGA
1 CCGTTGA
771506 CC
1 CC
771508 TCCTTTGACC
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
6 6 0.29
7 15 0.71
ACGTcount: A:0.14, C:0.34, G:0.28, T:0.24
Consensus pattern (7 bp):
CCGTTGA
Found at i:771501 original size:13 final size:13
Alignment explanation
Indices: 771483--771507 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
771473 ACCCGGCCGT
771483 TGACCGTTGACCG
1 TGACCGTTGACCG
771496 TGACCGTTGACC
1 TGACCGTTGACC
771508 TCCTTTGACC
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:0.16, C:0.32, G:0.28, T:0.24
Consensus pattern (13 bp):
TGACCGTTGACCG
Found at i:778248 original size:17 final size:17
Alignment explanation
Indices: 778226--778264 Score: 69
Period size: 17 Copynumber: 2.3 Consensus size: 17
778216 CGAACCGATC
*
778226 TGACCCGACCCGACTGT
1 TGACCCGACCCGACCGT
778243 TGACCCGACCCGACCGT
1 TGACCCGACCCGACCGT
778260 TGACC
1 TGACC
778265 GTTGACCGTT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.18, C:0.44, G:0.23, T:0.15
Consensus pattern (17 bp):
TGACCCGACCCGACCGT
Found at i:778266 original size:7 final size:7
Alignment explanation
Indices: 778254--778285 Score: 55
Period size: 7 Copynumber: 4.6 Consensus size: 7
778244 GACCCGACCC
778254 GACCGTT
1 GACCGTT
778261 GACCGTT
1 GACCGTT
778268 GACCGTT
1 GACCGTT
*
778275 AACCGTT
1 GACCGTT
778282 GACC
1 GACC
778286 TCCTTTAACC
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:0.19, C:0.31, G:0.25, T:0.25
Consensus pattern (7 bp):
GACCGTT
Found at i:780927 original size:15 final size:16
Alignment explanation
Indices: 780907--780939 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
780897 ATATTTTTTT
*
780907 ATTAATTTTAA-AATA
1 ATTAATATTAATAATA
780922 ATTAATATTAATAATA
1 ATTAATATTAATAATA
780938 AT
1 AT
780940 ATTTATTATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 10 0.62
16 6 0.38
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (16 bp):
ATTAATATTAATAATA
Found at i:780986 original size:19 final size:20
Alignment explanation
Indices: 780915--780999 Score: 66
Period size: 22 Copynumber: 4.1 Consensus size: 20
780905 TTATTAATTT
* *
780915 TAAAATAATTAATATTAATAA
1 TAAATTAATT-ATTTTAATAA
* *
780936 TAATATTTATTATTTTCATAA
1 TAA-ATTAATTATTTTAATAA
780957 TATAATATAATTATTTTAATAA
1 TA-AAT-TAATTATTTTAATAA
*
780979 -AAATTAATATAATTT-ATAA
1 TAAATTAAT-TATTTTAATAA
780998 TA
1 TA
781000 TTTTATTTTA
Statistics
Matches: 52, Mismatches: 7, Indels: 11
0.74 0.10 0.16
Matches are distributed among these distances:
19 8 0.15
20 9 0.17
21 16 0.31
22 19 0.37
ACGTcount: A:0.52, C:0.01, G:0.00, T:0.47
Consensus pattern (20 bp):
TAAATTAATTATTTTAATAA
Found at i:781069 original size:28 final size:29
Alignment explanation
Indices: 781025--781088 Score: 85
Period size: 28 Copynumber: 2.2 Consensus size: 29
781015 ATCATAGTCT
* * *
781025 TAATATTTTATTTATAAAA-TTATATAAA
1 TAATATTTTAATAATAAAACTGATATAAA
*
781053 TAATATTTTAATAATAAAACTGATGTAAA
1 TAATATTTTAATAATAAAACTGATATAAA
781082 TAATATT
1 TAATATT
781089 AAATAAATTA
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
28 17 0.55
29 14 0.45
ACGTcount: A:0.50, C:0.02, G:0.03, T:0.45
Consensus pattern (29 bp):
TAATATTTTAATAATAAAACTGATATAAA
Found at i:783355 original size:17 final size:17
Alignment explanation
Indices: 783315--783357 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
783305 TAGTTAATTA
*
783315 ATTAAACTATTTCATTG
1 ATTAAACTACTTCATTG
* * *
783332 ATCAAACTACTTCCTTT
1 ATTAAACTACTTCATTG
783349 ATTAAACTA
1 ATTAAACTA
783358 ACTCTCAATT
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.37, C:0.19, G:0.02, T:0.42
Consensus pattern (17 bp):
ATTAAACTACTTCATTG
Found at i:793776 original size:16 final size:18
Alignment explanation
Indices: 793744--793781 Score: 62
Period size: 17 Copynumber: 2.2 Consensus size: 18
793734 ACTTCATTTG
793744 TTTTTTTTGGTGTTGG-A
1 TTTTTTTTGGTGTTGGAA
793761 TTTTTTTTGGTG-TGGAA
1 TTTTTTTTGGTGTTGGAA
793778 TTTT
1 TTTT
793782 CATCATCAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
16 3 0.15
17 17 0.85
ACGTcount: A:0.08, C:0.00, G:0.26, T:0.66
Consensus pattern (18 bp):
TTTTTTTTGGTGTTGGAA
Found at i:798924 original size:18 final size:19
Alignment explanation
Indices: 798893--798936 Score: 72
Period size: 18 Copynumber: 2.4 Consensus size: 19
798883 CCACATTTAT
798893 TTATTTTCAGATTCACAAC
1 TTATTTTCAGATTCACAAC
798912 TTATTTT-AGATTCACAAC
1 TTATTTTCAGATTCACAAC
*
798930 TCATTTT
1 TTATTTT
798937 TAGACTCATA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
18 17 0.71
19 7 0.29
ACGTcount: A:0.30, C:0.18, G:0.05, T:0.48
Consensus pattern (19 bp):
TTATTTTCAGATTCACAAC
Found at i:799004 original size:20 final size:20
Alignment explanation
Indices: 798948--799007 Score: 84
Period size: 20 Copynumber: 3.0 Consensus size: 20
798938 AGACTCATAT
* *
798948 TTCATCTTTCATATTCATAG
1 TTCATCTTTCAAATTCGTAG
*
798968 TTCATCTTTCAGATTCGTAG
1 TTCATCTTTCAAATTCGTAG
*
798988 TTTATCTTTCAAATTCGTAG
1 TTCATCTTTCAAATTCGTAG
799008 CCCAATACAT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 36 1.00
ACGTcount: A:0.23, C:0.18, G:0.10, T:0.48
Consensus pattern (20 bp):
TTCATCTTTCAAATTCGTAG
Found at i:806828 original size:15 final size:12
Alignment explanation
Indices: 806791--806827 Score: 65
Period size: 12 Copynumber: 3.1 Consensus size: 12
806781 AACTGTCAAT
*
806791 CAAACCCTCCTC
1 CAAATCCTCCTC
806803 CAAATCCTCCTC
1 CAAATCCTCCTC
806815 CAAATCCTCCTC
1 CAAATCCTCCTC
806827 C
1 C
806828 TATCCCACCA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.24, C:0.54, G:0.00, T:0.22
Consensus pattern (12 bp):
CAAATCCTCCTC
Found at i:816448 original size:12 final size:12
Alignment explanation
Indices: 816423--816462 Score: 55
Period size: 12 Copynumber: 3.3 Consensus size: 12
816413 GATGTAGGAG
*
816423 TTTTTT-TTTCT
1 TTTTTTCTTTTT
816434 TTTTTTCTTTTT
1 TTTTTTCTTTTT
816446 TTTTTTCTTTTT
1 TTTTTTCTTTTT
816458 ATTTT
1 -TTTT
816463 GTTGCAGTAC
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
11 6 0.23
12 16 0.62
13 4 0.15
ACGTcount: A:0.03, C:0.07, G:0.00, T:0.90
Consensus pattern (12 bp):
TTTTTTCTTTTT
Found at i:822305 original size:217 final size:214
Alignment explanation
Indices: 821935--822353 Score: 605
Period size: 217 Copynumber: 1.9 Consensus size: 214
821925 AGCCGAGTCA
* * * * *
821935 AAAAAATTTTGAGTTGTTTGAGTTGACGAGTCGTATTTTACAATTCGAACTTAACTTGAAATTTT
1 AAAAAATTTCGAGTTATTGGAGTTGACAAGTCGTATTTTACAACTCGAACTTAACTTGAAATTTT
822000 TTCGAGTCGAGTTTAAGGAATTAGAGTCAAGTTATTCGAGTTTCTATACTAATTTTATTATAATT
66 TTCGAGTCGAGTTTAAGGAATTAGAGTCAAGTTATTCGAGTTTCTATACTAATTTTATTATAATT
* *
822065 ATTTATAGTATTATGGCAATGATTTTTTCTAA-TTTTTTGAATTTATCTAA-CCATATA-ATAAA
131 ATTTATAGTATTATGGCAATGATTTGTTCCAACTTTTTT-AATTTATCTAACCCATATATATAAA
822127 TATATATGTCAAGTTGAGTT
195 TATATATGTCAAGTTGAGTT
*
822147 AAAAAATTTCGAGTTATTGGAGTTGACAAGTTGTATTTTACAACTCGAACTTAACTTGAAATTGT
1 AAAAAATTTCGAGTTATTGGAGTTGACAAGTCGTATTTTACAACTCGAACTTAACTTGAAATT-T
* *
822212 TTCGAGTCGAGTCGAGTTTAAGGAATTAGAGTTGAA-TTATTCGAGTTTCTATATTAA-TTTATT
65 TT----TCGAGTCGAGTTTAAGGAATTAGAG-TCAAGTTATTCGAGTTTCTATACTAATTTTATT
* *
822275 ATAAATTATTTTTAGTATTATGGCAATGATTTGTTCCAACTTTTTTACTTTATCTAACCCCATAT
125 AT-AATTATTTATAGTATTATGGCAATGATTTGTTCCAACTTTTTTAATTTATCTAA-CCCATAT
*
822340 ATATATATATATAT
188 ATATAAATATATAT
822354 ATATTCTTTC
Statistics
Matches: 183, Mismatches: 13, Indels: 14
0.87 0.06 0.07
Matches are distributed among these distances:
212 57 0.31
213 3 0.02
216 8 0.04
217 88 0.48
218 9 0.05
219 7 0.04
220 11 0.06
ACGTcount: A:0.32, C:0.10, G:0.14, T:0.44
Consensus pattern (214 bp):
AAAAAATTTCGAGTTATTGGAGTTGACAAGTCGTATTTTACAACTCGAACTTAACTTGAAATTTT
TTCGAGTCGAGTTTAAGGAATTAGAGTCAAGTTATTCGAGTTTCTATACTAATTTTATTATAATT
ATTTATAGTATTATGGCAATGATTTGTTCCAACTTTTTTAATTTATCTAACCCATATATATAAAT
ATATATGTCAAGTTGAGTT
Found at i:822974 original size:159 final size:158
Alignment explanation
Indices: 822798--823087 Score: 476
Period size: 159 Copynumber: 1.8 Consensus size: 158
822788 TCAAATTTGG
822798 TAAAATAAATGAAGAATTGAAGAAATAAAGAGATTATGAAAAATT-AAAGGACTAAATTGAAAAA
1 TAAAATAAATGAAGAATTGAAGAAATAAAGAGATTATGAAAAATTGAAA-GACTAAATTGAAAAA
* *
822862 TAAAAAATTTGTTATC-AAAAAGAGAAATTGAAAGTACACATGTATTCTACTATGGTTTAGGAGC
65 T-AAAAATTTATTATCAAAAAAGAG-AATTGAAAGTACACATGTATTCTACTATGATTTAGGAGC
822926 ATGTGACTCAAATATGGTAAAAAAATTGACT
128 ATGTGACTCAAATATGGTAAAAAAATTGACT
* * *
822957 TAAAATAAATGACGAATTGAAGAAATAAGGAGATTATGAAAAATTGAAAGACTAGATTGAAAAAT
1 TAAAATAAATGAAGAATTGAAGAAATAAAGAGATTATGAAAAATTGAAAGACTAAATTGAAAAAT
*
823022 AAAAATTTATTATCAAAAAAGATGAATTGAAAGTATACATGTATTCTACTATGATTTAGGAGCAT
66 AAAAATTTATTATCAAAAAAGA-GAATTGAAAGTACACATGTATTCTACTATGATTTAGGAGCAT
823087 G
130 G
823088 CAGTTTAAAT
Statistics
Matches: 122, Mismatches: 6, Indels: 6
0.91 0.04 0.04
Matches are distributed among these distances:
158 13 0.11
159 105 0.86
160 4 0.03
ACGTcount: A:0.50, C:0.06, G:0.17, T:0.28
Consensus pattern (158 bp):
TAAAATAAATGAAGAATTGAAGAAATAAAGAGATTATGAAAAATTGAAAGACTAAATTGAAAAAT
AAAAATTTATTATCAAAAAAGAGAATTGAAAGTACACATGTATTCTACTATGATTTAGGAGCATG
TGACTCAAATATGGTAAAAAAATTGACT
Found at i:823108 original size:159 final size:158
Alignment explanation
Indices: 822798--823143 Score: 466
Period size: 159 Copynumber: 2.2 Consensus size: 158
822788 TCAAATTTGG
822798 TAAAATAAATGAAGAATTGAAGAAATAAAGAGATTATGAAAAATTAAAGGACTAAATTGAAAAAT
1 TAAAATAAATG-AGAATTGAAGAAATAAAGAGATTATGAAAAATTAAAGGACTAAATTGAAAAAT
* *
822863 AAAAAATTTGTTATCAAAAAGAGAAATTGAAAGTACACATGTATTCTACTATGGTTTAGGAGCAT
65 AAAAAATTTATTATCAAAAAGAGAAATTGAAAGTACACATGTATTCTACTATGATTTAGGAGCAT
* * *
822928 GTGACTCAAATATGGTAAAAAAATTGACT
130 GAGACTCAAATATGATAAAAAAATAGACT
* *
822957 TAAAATAAATGACGAATTGAAGAAATAAGGAGATTATGAAAAATTGAAA-GACTAGATTGAAAAA
1 TAAAATAAATGA-GAATTGAAGAAATAAAGAGATTATGAAAAATT-AAAGGACTAAATTGAAAAA
*
823021 T-AAAAATTTATTATCAAAAA-AGATGAATTGAAAGTATACATGTATTCTACTATGATTTAGGAG
64 TAAAAAATTTATTATCAAAAAGAGA--AATTGAAAGTACACATGTATTCTACTATGATTTAGGAG
* * * *
823084 CATGCAG-TTTAAATTTGATTAAAAAATAGACT
127 CATG-AGACTCAAATATGATAAAAAAATAGACT
* * *
823116 TAAAATGAAGGAGAAAATGAAGAAATAA
1 TAAAATAAATGAG-AATTGAAGAAATAA
823144 TGAAATTAGG
Statistics
Matches: 166, Mismatches: 15, Indels: 12
0.86 0.08 0.06
Matches are distributed among these distances:
157 3 0.02
158 20 0.12
159 139 0.84
160 4 0.02
ACGTcount: A:0.51, C:0.05, G:0.16, T:0.27
Consensus pattern (158 bp):
TAAAATAAATGAGAATTGAAGAAATAAAGAGATTATGAAAAATTAAAGGACTAAATTGAAAAATA
AAAAATTTATTATCAAAAAGAGAAATTGAAAGTACACATGTATTCTACTATGATTTAGGAGCATG
AGACTCAAATATGATAAAAAAATAGACT
Found at i:830763 original size:2 final size:2
Alignment explanation
Indices: 830752--830794 Score: 79
Period size: 2 Copynumber: 22.0 Consensus size: 2
830742 GCATGTTTTA
830752 AT AT -T 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
830793 AT
1 AT
830795 GTCAATCATA
Statistics
Matches: 40, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 39 0.98
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:831634 original size:112 final size:112
Alignment explanation
Indices: 831426--831649 Score: 351
Period size: 112 Copynumber: 2.0 Consensus size: 112
831416 GTGATCGATT
* * *
831426 GGGAGGTAGTGTACCTGTAGAATTTTCAACTACATATGGGAATAGTGGCATGGCTCTAATTCTTG
1 GGGAGGTAGTGTACCTGTAGAATTTTCAACTACATATGGGAATAGTAGCACGACTCTAATTCTTG
*
831491 TGGGTGAATTCATGTTACCCAACTCACCTTCAAGGAATGACACTCTC
66 TGGGTGAATTCATGTTACCCAACACACCTTCAAGGAATGACACTCTC
* *
831538 GGGAGGTAGTGTACCTGTAGAATTTTCAACTACATATAGGG-ATATTATCACGACTCTAATTCTT
1 GGGAGGTAGTGTACCTGTAGAATTTTCAACTACATAT-GGGAATAGTAGCACGACTCTAATTCTT
** *
831602 GTGGGTGAATTCATGTTATTCAACACATCTTCAAGGAATGACACTCTC
65 GTGGGTGAATTCATGTTACCCAACACACCTTCAAGGAATGACACTCTC
831650 ATTCAACAAG
Statistics
Matches: 102, Mismatches: 9, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
112 99 0.97
113 3 0.03
ACGTcount: A:0.28, C:0.19, G:0.21, T:0.32
Consensus pattern (112 bp):
GGGAGGTAGTGTACCTGTAGAATTTTCAACTACATATGGGAATAGTAGCACGACTCTAATTCTTG
TGGGTGAATTCATGTTACCCAACACACCTTCAAGGAATGACACTCTC
Found at i:835311 original size:22 final size:23
Alignment explanation
Indices: 835263--835322 Score: 86
Period size: 22 Copynumber: 2.7 Consensus size: 23
835253 GACAAACTGT
*
835263 TAATATCAGGAGTTACATTGATT
1 TAATATCAGGAGTTACATTGATA
* *
835286 TAATTTTAGGAGTTACA-TGATA
1 TAATATCAGGAGTTACATTGATA
835308 TAATATCAGGAGTTA
1 TAATATCAGGAGTTA
835323 TAACAGCTGA
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
22 17 0.53
23 15 0.47
ACGTcount: A:0.37, C:0.07, G:0.18, T:0.38
Consensus pattern (23 bp):
TAATATCAGGAGTTACATTGATA
Found at i:843157 original size:15 final size:15
Alignment explanation
Indices: 843137--843166 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
843127 ATCTAAACAT
843137 GAAATGACCCGACCC
1 GAAATGACCCGACCC
843152 GAAATGACCCGACCC
1 GAAATGACCCGACCC
843167 AAACCCGATC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.33, C:0.40, G:0.20, T:0.07
Consensus pattern (15 bp):
GAAATGACCCGACCC
Found at i:846216 original size:3 final size:3
Alignment explanation
Indices: 846210--846238 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
846200 ATATAAAAAT
846210 ATA ATA ATA ATA ATA ATA ATA ATA A-A ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
846239 TTATGTTAGT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.08
3 23 0.92
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
ATA
Found at i:847637 original size:9 final size:9
Alignment explanation
Indices: 847623--847659 Score: 53
Period size: 9 Copynumber: 4.4 Consensus size: 9
847613 TAACCGCTAA
847623 ATTTTATTT
1 ATTTTATTT
847632 ATTTTATTT
1 ATTTTATTT
847641 A-TTTA--T
1 ATTTTATTT
847647 ATTTTATTT
1 ATTTTATTT
847656 ATTT
1 ATTT
847660 GCAACCCCCT
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
6 2 0.08
7 4 0.16
8 4 0.16
9 15 0.60
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (9 bp):
ATTTTATTT
Found at i:847651 original size:15 final size:15
Alignment explanation
Indices: 847631--847659 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
847621 AAATTTTATT
847631 TATTTTATTTATTTA
1 TATTTTATTTATTTA
847646 TATTTTATTTATTT
1 TATTTTATTTATTT
847660 GCAACCCCCT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (15 bp):
TATTTTATTTATTTA
Found at i:852739 original size:21 final size:21
Alignment explanation
Indices: 852713--852777 Score: 85
Period size: 21 Copynumber: 3.0 Consensus size: 21
852703 GTCGAGGGTT
852713 TCATAGGTCCTTCGGGACAAC
1 TCATAGGTCCTTCGGGACAAC
*
852734 TCATAGGTCCTTCGGGACATATAT
1 TCATAGGTCCTTCGGGAC--A-AC
*
852758 TCACAGGTCCTTCGGGACAA
1 TCATAGGTCCTTCGGGACAA
852778 ATCTCATATG
Statistics
Matches: 39, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
21 19 0.49
22 1 0.03
23 1 0.03
24 18 0.46
ACGTcount: A:0.25, C:0.26, G:0.23, T:0.26
Consensus pattern (21 bp):
TCATAGGTCCTTCGGGACAAC
Found at i:852770 original size:24 final size:22
Alignment explanation
Indices: 852712--852785 Score: 96
Period size: 24 Copynumber: 3.3 Consensus size: 22
852702 AGTCGAGGGT
852712 TTCATAGGTCCTTCGGGAC-AA
1 TTCATAGGTCCTTCGGGACAAA
*
852733 CTCATAGGTCCTTCGGGACATATA
1 TTCATAGGTCCTTCGGGACA-A-A
*
852757 TTCACAGGTCCTTCGGGACAAA
1 TTCATAGGTCCTTCGGGACAAA
852779 TCTCATA
1 T-TCATA
852786 TGCCACTCAG
Statistics
Matches: 45, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
21 18 0.40
22 2 0.04
23 6 0.13
24 19 0.42
ACGTcount: A:0.26, C:0.26, G:0.20, T:0.28
Consensus pattern (22 bp):
TTCATAGGTCCTTCGGGACAAA
Found at i:856144 original size:8 final size:8
Alignment explanation
Indices: 856133--856159 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
856123 ATTAAAGGCT
856133 TTTTAAAA
1 TTTTAAAA
856141 TTTTAAAA
1 TTTTAAAA
856149 TTTTAAAA
1 TTTTAAAA
856157 TTT
1 TTT
856160 ATATAAAAAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (8 bp):
TTTTAAAA
Found at i:856470 original size:21 final size:21
Alignment explanation
Indices: 856446--856486 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
856436 ATATATATTA
*
856446 ATATAAAAATATAAAATATAT
1 ATATAAAAATAAAAAATATAT
**
856467 ATATAATTATAAAAAATATA
1 ATATAAAAATAAAAAATATA
856487 AAATATTATA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (21 bp):
ATATAAAAATAAAAAATATAT
Found at i:856506 original size:29 final size:31
Alignment explanation
Indices: 856426--856511 Score: 124
Period size: 28 Copynumber: 2.8 Consensus size: 31
856416 CCCGAACCCG
*
856426 AAAATATTTTATATATATTAATATAAAAATAT
1 AAAATATTATATATATATT-ATATAAAAATAT
856458 AAAATA-TATATATA-ATTATA-AAAAATAT
1 AAAATATTATATATATATTATATAAAAATAT
856486 AAAATATTATATATATATATATATAA
1 AAAATATTATATATATAT-TATATAA
856512 TCGGGACGGG
Statistics
Matches: 49, Mismatches: 1, Indels: 8
0.84 0.02 0.14
Matches are distributed among these distances:
28 14 0.29
29 11 0.22
30 5 0.10
31 11 0.22
32 8 0.16
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (31 bp):
AAAATATTATATATATATTATATAAAAATAT
Found at i:857139 original size:21 final size:21
Alignment explanation
Indices: 857085--857149 Score: 55
Period size: 21 Copynumber: 3.0 Consensus size: 21
857075 CTTGAAACTT
*
857085 TTAATATATTTT-TTAAT-AAA
1 TTAA-ATATTTTATTTATAAAA
*
857105 TTAAAT-TTAATATTTATAAAA
1 TTAAATATT-TTATTTATAAAA
857126 TTAAATATTTTATTATATTAAAA
1 TTAAATATTTTATT-TA-TAAAA
857149 T
1 T
857150 ATATAATTTT
Statistics
Matches: 36, Mismatches: 3, Indels: 9
0.75 0.06 0.19
Matches are distributed among these distances:
18 2 0.06
19 3 0.08
20 8 0.22
21 13 0.36
22 4 0.11
23 6 0.17
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (21 bp):
TTAAATATTTTATTTATAAAA
Found at i:857762 original size:25 final size:26
Alignment explanation
Indices: 857729--857784 Score: 69
Period size: 27 Copynumber: 2.2 Consensus size: 26
857719 ATACTTTTAA
* * *
857729 AAATTAAAAT-AAATTATATATTTTT
1 AAATGAAAATAAAATGAAATATTTTT
857754 AAATGAAAATAAAAATGAAATATTTTT
1 AAATGAAAAT-AAAATGAAATATTTTT
857781 AAAT
1 AAAT
857785 TAAGTTAATA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
25 9 0.35
27 17 0.65
ACGTcount: A:0.57, C:0.00, G:0.04, T:0.39
Consensus pattern (26 bp):
AAATGAAAATAAAATGAAATATTTTT
Found at i:857801 original size:27 final size:25
Alignment explanation
Indices: 857771--857831 Score: 70
Period size: 25 Copynumber: 2.4 Consensus size: 25
857761 AATAAAAATG
*
857771 AAATATTTTTAAATTAAGTTAATAGT-A
1 AAATATTTTT-AA-TAAGTTAACA-TAA
*
857798 AAATATATTTAATAAGTTAACATAA
1 AAATATTTTTAATAAGTTAACATAA
857823 AAATATTTT
1 AAATATTTT
857832 AAGTTAAAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
24 1 0.03
25 18 0.60
26 2 0.07
27 9 0.30
ACGTcount: A:0.51, C:0.02, G:0.05, T:0.43
Consensus pattern (25 bp):
AAATATTTTTAATAAGTTAACATAA
Found at i:857825 original size:25 final size:25
Alignment explanation
Indices: 857771--857838 Score: 68
Period size: 25 Copynumber: 2.6 Consensus size: 25
857761 AATAAAAATG
*
857771 AAATATTTTTAAATTAAGTTAATAGTA
1 AAATA-TTTT-AATTAAGTTAACAGTA
857798 AAATATATTTAA-TAAGTTAACA-TAA
1 AAATAT-TTTAATTAAGTTAACAGT-A
857823 AAATATTTTAAGTTAA
1 AAATATTTTAA-TTAA
857839 AATATATATT
Statistics
Matches: 36, Mismatches: 1, Indels: 9
0.78 0.02 0.20
Matches are distributed among these distances:
24 6 0.17
25 16 0.44
26 6 0.17
27 8 0.22
ACGTcount: A:0.51, C:0.01, G:0.06, T:0.41
Consensus pattern (25 bp):
AAATATTTTAATTAAGTTAACAGTA
Found at i:857946 original size:2 final size:2
Alignment explanation
Indices: 857910--857935 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
857900 TTCTTTAAAT
857910 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
857936 AAAGTTATAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:858420 original size:22 final size:23
Alignment explanation
Indices: 858372--858421 Score: 57
Period size: 22 Copynumber: 2.2 Consensus size: 23
858362 AAAATCATTT
* *
858372 TTTTTAATTACAAATACATGATC
1 TTTTTAATTACAAATACACGATA
* *
858395 TTTTT-ATTATAAATACCCGATA
1 TTTTTAATTACAAATACACGATA
858417 TTTTT
1 TTTTT
858422 TAACTGGGTC
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
22 18 0.78
23 5 0.22
ACGTcount: A:0.34, C:0.12, G:0.04, T:0.50
Consensus pattern (23 bp):
TTTTTAATTACAAATACACGATA
Found at i:858666 original size:31 final size:31
Alignment explanation
Indices: 858631--858691 Score: 104
Period size: 31 Copynumber: 2.0 Consensus size: 31
858621 CACAAATTAT
*
858631 TTAAATAAAAACGAAAGTGACCATATCTTAA
1 TTAAATAAAAACAAAAGTGACCATATCTTAA
*
858662 TTAAATAAAAACAAAAGTGATCATATCTTA
1 TTAAATAAAAACAAAAGTGACCATATCTTA
858692 TGTTTTTTAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.52, C:0.11, G:0.08, T:0.28
Consensus pattern (31 bp):
TTAAATAAAAACAAAAGTGACCATATCTTAA
Found at i:859735 original size:31 final size:31
Alignment explanation
Indices: 859699--859757 Score: 109
Period size: 31 Copynumber: 1.9 Consensus size: 31
859689 AACTTAAAAG
*
859699 AGTTTTGCAATACTGAAATTTAAATAATTTT
1 AGTTTTACAATACTGAAATTTAAATAATTTT
859730 AGTTTTACAATACTGAAATTTAAATAAT
1 AGTTTTACAATACTGAAATTTAAATAAT
859758 CCATACAACT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.42, C:0.07, G:0.08, T:0.42
Consensus pattern (31 bp):
AGTTTTACAATACTGAAATTTAAATAATTTT
Found at i:859806 original size:22 final size:22
Alignment explanation
Indices: 859781--859824 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
859771 ATAATTAATT
859781 TTTTAAAATAAATCAATCTATA
1 TTTTAAAATAAATCAATCTATA
*
859803 TTTTAAAATAAATCAATTTATA
1 TTTTAAAATAAATCAATCTATA
859825 CTAATAAATT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.50, C:0.07, G:0.00, T:0.43
Consensus pattern (22 bp):
TTTTAAAATAAATCAATCTATA
Found at i:859833 original size:22 final size:22
Alignment explanation
Indices: 859784--859832 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
859774 ATTAATTTTT
**
859784 TAAAATAAATCAATCTATATTT
1 TAAAATAAATCAATCTATATAA
*
859806 TAAAATAAATCAATTTATACTAA
1 TAAAATAAATCAATCTATA-TAA
859829 TAAA
1 TAAA
859833 TTATTTAATA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
22 18 0.78
23 5 0.22
ACGTcount: A:0.55, C:0.08, G:0.00, T:0.37
Consensus pattern (22 bp):
TAAAATAAATCAATCTATATAA
Found at i:859964 original size:31 final size:31
Alignment explanation
Indices: 859922--859980 Score: 109
Period size: 31 Copynumber: 1.9 Consensus size: 31
859912 AATTTAAAAG
*
859922 AGTTTTGCAATACTGAAATTTAAATAATTTT
1 AGTTTTACAATACTGAAATTTAAATAATTTT
859953 AGTTTTACAATACTGAAATTTAAATAAT
1 AGTTTTACAATACTGAAATTTAAATAAT
859981 CCATACAACT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.42, C:0.07, G:0.08, T:0.42
Consensus pattern (31 bp):
AGTTTTACAATACTGAAATTTAAATAATTTT
Found at i:864227 original size:2 final size:2
Alignment explanation
Indices: 864220--864250 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
864210 CCCGATTTAT
864220 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
864251 TGTTTTTTTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:864348 original size:39 final size:39
Alignment explanation
Indices: 864283--864399 Score: 125
Period size: 39 Copynumber: 3.0 Consensus size: 39
864273 TTTTTATTTA
* * *
864283 TAATT-CTCAAATTATATCAC-TCTAACATTCTAAATTCT
1 TAATTCCTTAAATTATTTCACAT-TAACATTCTAAATTAT
* *
864321 TAATTTCTTAAA-TATTGTCACCA-TAACATTCCAAATTAT
1 TAATTCCTTAAATTATT-TCA-CATTAACATTCTAAATTAT
*
864360 TAATTCCTTAAATTATTTCACATTAACACTCTAAATTAT
1 TAATTCCTTAAATTATTTCACATTAACATTCTAAATTAT
864399 T
1 T
864400 TTTTAGAATA
Statistics
Matches: 66, Mismatches: 7, Indels: 11
0.79 0.08 0.13
Matches are distributed among these distances:
38 10 0.15
39 51 0.77
40 5 0.08
ACGTcount: A:0.38, C:0.19, G:0.01, T:0.43
Consensus pattern (39 bp):
TAATTCCTTAAATTATTTCACATTAACATTCTAAATTAT
Found at i:865159 original size:31 final size:32
Alignment explanation
Indices: 865124--865214 Score: 96
Period size: 31 Copynumber: 2.8 Consensus size: 32
865114 AATAGTTTAT
865124 TTATAATTTAATATTCAAATTAT-TATATATA
1 TTATAATTTAATATTCAAATTATATATATATA
**
865155 TTATATTATAATTAATGATAAAAATTATATATATATA
1 TTATA--AT--TTAAT-ATTCAAATTATATATATATA
*
865192 TTAT-AGTTAATATTCAAATTATA
1 TTATAATTTAATATTCAAATTATA
865215 ATCATAAGAT
Statistics
Matches: 49, Mismatches: 5, Indels: 12
0.74 0.08 0.18
Matches are distributed among these distances:
31 15 0.31
32 5 0.10
33 2 0.04
34 1 0.02
35 5 0.10
36 9 0.18
37 12 0.24
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.48
Consensus pattern (32 bp):
TTATAATTTAATATTCAAATTATATATATATA
Found at i:867129 original size:22 final size:22
Alignment explanation
Indices: 867101--867153 Score: 70
Period size: 22 Copynumber: 2.4 Consensus size: 22
867091 ACTTTTGGTA
867101 GCCTTAAGGGGGCATAAAAGAG
1 GCCTTAAGGGGGCATAAAAGAG
* *
867123 GCCTTAAGGGGGCTTAAGAGAG
1 GCCTTAAGGGGGCATAAAAGAG
* *
867145 ACTTTAAGG
1 GCCTTAAGG
867154 AGCCATCTTC
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.32, C:0.13, G:0.36, T:0.19
Consensus pattern (22 bp):
GCCTTAAGGGGGCATAAAAGAG
Found at i:870295 original size:12 final size:12
Alignment explanation
Indices: 870274--870317 Score: 52
Period size: 12 Copynumber: 3.7 Consensus size: 12
870264 ATAGTATTGA
*
870274 TTCATATTGCAT
1 TTCATGTTGCAT
870286 TTCATGTTGCAT
1 TTCATGTTGCAT
* *
870298 TTCATGATCCAT
1 TTCATGTTGCAT
*
870310 TTAATGTT
1 TTCATGTT
870318 AAATAGTTAA
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
12 27 1.00
ACGTcount: A:0.23, C:0.16, G:0.11, T:0.50
Consensus pattern (12 bp):
TTCATGTTGCAT
Found at i:872364 original size:34 final size:32
Alignment explanation
Indices: 872298--872367 Score: 86
Period size: 34 Copynumber: 2.1 Consensus size: 32
872288 ACCTTACAAC
* * *
872298 TCCCTAGTTTTTCAGGGCTAAACTAGAACCTT
1 TCCCTAGTTTTACAGGGATAAACTAAAACCTT
*
872330 TCCCTAGCTTTTACACGGGATAAGCTAAAACCTT
1 TCCCTAG-TTTTACA-GGGATAAACTAAAACCTT
872364 TCCC
1 TCCC
872368 CATTACAAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
32 7 0.22
33 6 0.19
34 19 0.59
ACGTcount: A:0.26, C:0.29, G:0.14, T:0.31
Consensus pattern (32 bp):
TCCCTAGTTTTACAGGGATAAACTAAAACCTT
Found at i:872607 original size:20 final size:22
Alignment explanation
Indices: 872582--872621 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
872572 TGTTTTATAT
872582 AGCCG-TTGGGGATG-TTTTGG
1 AGCCGTTTGGGGATGATTTTGG
872602 AGCCGTTTGGGGATGATTTT
1 AGCCGTTTGGGGATGATTTT
872622 TCTACTCAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 5 0.28
21 9 0.50
22 4 0.22
ACGTcount: A:0.12, C:0.10, G:0.40, T:0.38
Consensus pattern (22 bp):
AGCCGTTTGGGGATGATTTTGG
Found at i:872763 original size:20 final size:20
Alignment explanation
Indices: 872734--872807 Score: 85
Period size: 20 Copynumber: 3.6 Consensus size: 20
872724 GTAGCCTTTG
*
872734 TGCATGGATGCACAGCAGGA
1 TGCATCGATGCACAGCAGGA
* **
872754 TGCATCGATGCACAACCTTGA
1 TGCATCGATGCAC-AGCAGGA
* *
872775 TGCATCGATGCACAGAAGTA
1 TGCATCGATGCACAGCAGGA
872795 TGCATCGATGCAC
1 TGCATCGATGCAC
872808 TAATTGCATT
Statistics
Matches: 44, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 27 0.61
21 17 0.39
ACGTcount: A:0.30, C:0.24, G:0.26, T:0.20
Consensus pattern (20 bp):
TGCATCGATGCACAGCAGGA
Found at i:872984 original size:29 final size:30
Alignment explanation
Indices: 872952--873015 Score: 94
Period size: 29 Copynumber: 2.2 Consensus size: 30
872942 GAAACCTTTT
872952 AAAACATTGAATAAATTCAATT-AAGTCCA
1 AAAACATTGAATAAATTCAATTCAAGTCCA
***
872981 AAAACATTTTGTAAATTCAATTCAAGTCCA
1 AAAACATTGAATAAATTCAATTCAAGTCCA
873011 AAAAC
1 AAAAC
873016 CATTTTGCCT
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
29 19 0.61
30 12 0.39
ACGTcount: A:0.50, C:0.16, G:0.06, T:0.28
Consensus pattern (30 bp):
AAAACATTGAATAAATTCAATTCAAGTCCA
Found at i:873010 original size:30 final size:30
Alignment explanation
Indices: 872963--873022 Score: 104
Period size: 29 Copynumber: 2.0 Consensus size: 30
872953 AAACATTGAA
872963 TAAATTCAATTAAGTCCAAAAA-CATTTTG
1 TAAATTCAATTAAGTCCAAAAACCATTTTG
872992 TAAATTCAATTCAAGTCCAAAAACCATTTTG
1 TAAATTCAATT-AAGTCCAAAAACCATTTTG
873023 CCTTAAATTT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
29 11 0.38
30 11 0.38
31 7 0.24
ACGTcount: A:0.43, C:0.17, G:0.07, T:0.33
Consensus pattern (30 bp):
TAAATTCAATTAAGTCCAAAAACCATTTTG
Found at i:877399 original size:21 final size:21
Alignment explanation
Indices: 877375--877417 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
877365 CTCTGAACGC
877375 AAACCAAATCCTATCTTTTTA
1 AAACCAAATCCTATCTTTTTA
877396 AAACCAAATCCTATCTTTTTA
1 AAACCAAATCCTATCTTTTTA
877417 A
1 A
877418 TTTTTTTATT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.40, C:0.23, G:0.00, T:0.37
Consensus pattern (21 bp):
AAACCAAATCCTATCTTTTTA
Found at i:877519 original size:15 final size:14
Alignment explanation
Indices: 877499--877530 Score: 55
Period size: 15 Copynumber: 2.2 Consensus size: 14
877489 ATTTCAAATC
877499 TTTTCTAAAATTTGA
1 TTTTCTAAAATTT-A
877514 TTTTCTAAAATTTA
1 TTTTCTAAAATTTA
877528 TTT
1 TTT
877531 CGATTTTTGC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 4 0.24
15 13 0.76
ACGTcount: A:0.31, C:0.06, G:0.03, T:0.59
Consensus pattern (14 bp):
TTTTCTAAAATTTA
Found at i:881680 original size:23 final size:23
Alignment explanation
Indices: 881650--881696 Score: 85
Period size: 23 Copynumber: 2.0 Consensus size: 23
881640 TTTGAGACAC
*
881650 AGTGAGTATAGTATAGTGGAGCA
1 AGTGAGTACAGTATAGTGGAGCA
881673 AGTGAGTACAGTATAGTGGAGCA
1 AGTGAGTACAGTATAGTGGAGCA
881696 A
1 A
881697 CTACACAAAC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.36, C:0.06, G:0.34, T:0.23
Consensus pattern (23 bp):
AGTGAGTACAGTATAGTGGAGCA
Found at i:886368 original size:5 final size:5
Alignment explanation
Indices: 886358--886453 Score: 81
Period size: 5 Copynumber: 18.2 Consensus size: 5
886348 TATTATGCTT
886358 GAAAA GAAAA GAAAAA GAAAA GAAAA -AGAAA GAAAA GAAAAA GAAAAA
1 GAAAA GAAAA G-AAAA GAAAA GAAAA GA-AAA GAAAA G-AAAA G-AAAA
* *
886406 GAAAA GAAAAA GAAAA TTAAAAA GAAAA -AAAA G-GAA GAAAAA GAAAA
1 GAAAA G-AAAA GAAAA --GAAAA GAAAA GAAAA GAAAA G-AAAA GAAAA
886453 G
1 G
886454 GAGGGTTCAG
Statistics
Matches: 77, Mismatches: 4, Indels: 20
0.76 0.04 0.20
Matches are distributed among these distances:
4 8 0.10
5 40 0.52
6 25 0.32
7 4 0.05
ACGTcount: A:0.79, C:0.00, G:0.19, T:0.02
Consensus pattern (5 bp):
GAAAA
Found at i:886375 original size:6 final size:6
Alignment explanation
Indices: 886359--886452 Score: 103
Period size: 6 Copynumber: 16.5 Consensus size: 6
886349 ATTATGCTTG
886359 AAAAG- AAAAGA AAAAG- AAAAGA AAAAG- -AAAG- AAAAGA AAAAGA
1 AAAAGA AAAAGA AAAAGA AAAAGA AAAAGA AAAAGA AAAAGA AAAAGA
**
886402 AAAAG- AAAAGA AAAAGA AAATTA AAAAGA AAAA-A AAGGAAGA AAAAGA
1 AAAAGA AAAAGA AAAAGA AAAAGA AAAAGA AAAAGA AA--AAGA AAAAGA
886450 AAA
1 AAA
886453 GGAGGGTTCA
Statistics
Matches: 77, Mismatches: 4, Indels: 15
0.80 0.04 0.16
Matches are distributed among these distances:
4 4 0.05
5 22 0.29
6 46 0.60
7 2 0.03
8 3 0.04
ACGTcount: A:0.81, C:0.00, G:0.17, T:0.02
Consensus pattern (6 bp):
AAAAGA
Found at i:886375 original size:11 final size:11
Alignment explanation
Indices: 886359--886453 Score: 119
Period size: 11 Copynumber: 8.9 Consensus size: 11
886349 ATTATGCTTG
886359 AAAAGAAAAGA
1 AAAAGAAAAGA
886370 AAAAGAAAAGA
1 AAAAGAAAAGA
886381 AAAAG-AAAG-
1 AAAAGAAAAGA
886390 AAAAGAAAAAGA
1 AAAAG-AAAAGA
886402 AAAAGAAAAGA
1 AAAAGAAAAGA
*
886413 AAAAGAAAATTA
1 AAAAGAAAA-GA
886425 AAAAG-AAA-A
1 AAAAGAAAAGA
*
886434 AAAAG-GAAGA
1 AAAAGAAAAGA
886444 AAAAGAAAAG
1 AAAAGAAAAG
886454 GAGGGTTCAG
Statistics
Matches: 75, Mismatches: 3, Indels: 12
0.83 0.03 0.13
Matches are distributed among these distances:
9 13 0.17
10 10 0.13
11 41 0.55
12 11 0.15
ACGTcount: A:0.80, C:0.00, G:0.18, T:0.02
Consensus pattern (11 bp):
AAAAGAAAAGA
Found at i:889522 original size:19 final size:21
Alignment explanation
Indices: 889494--889541 Score: 55
Period size: 19 Copynumber: 2.3 Consensus size: 21
889484 TAACTTAAAG
889494 TAAAACATTA-A-AAAATATA
1 TAAAACATTATAGAAAATATA
*
889513 TAAAATATTATAGAAAATATCA
1 TAAAACATTATAGAAAATAT-A
*
889535 TATAACA
1 TAAAACA
889542 ACATATTAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
19 9 0.39
20 1 0.04
21 7 0.30
22 6 0.26
ACGTcount: A:0.62, C:0.06, G:0.02, T:0.29
Consensus pattern (21 bp):
TAAAACATTATAGAAAATATA
Found at i:891881 original size:19 final size:19
Alignment explanation
Indices: 891813--891881 Score: 77
Period size: 19 Copynumber: 3.6 Consensus size: 19
891803 ACCATATCGA
*
891813 TAGATTCATA-CTATACTTT
1 TAGATTCATAGCTTTAC-TT
* *
891832 TAGATTCACAACTTTACTT
1 TAGATTCATAGCTTTACTT
*
891851 TAGATTCGTAGCTTTACTT
1 TAGATTCATAGCTTTACTT
*
891870 TATATTCATAGC
1 TAGATTCATAGC
891882 CCAATGTATA
Statistics
Matches: 42, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
19 37 0.88
20 5 0.12
ACGTcount: A:0.29, C:0.17, G:0.09, T:0.45
Consensus pattern (19 bp):
TAGATTCATAGCTTTACTT
Done.