Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006550.1 Hibiscus syriacus cultivar Beakdansim tig00016004_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: 1576944
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 6 of 8
Found at i:964354 original size:82 final size:84
Alignment explanation
Indices: 964217--964558 Score: 411
Period size: 94 Copynumber: 3.9 Consensus size: 84
964207 GATTGCTTAG
* * *
964217 AAATTTATTCGGTTGCTGCCAATACTGCTAAATTGTTTATTCTTTAACACTGTGAAGTTAGTA-T
1 AAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGTATT
964281 TTGTCTTTTGGTTG-AAGT
66 TTGTCTTTTGGTTGAAAGT
964299 AAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGTATT
1 AAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGTA--
964364 TGTCTTTGTTTTGTCTTTTGGTTGAAAGT
64 --------TTTTGTCTTTTGGTTGAAAGT
*
964393 AAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGTATT
1 AAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGTA--
964458 TGTCTTTGTTTTGTCTTTTGGTTGAAAGT
64 --------TTTTGTCTTTTGGTTGAAAGT
* * * *
964487 AAATTTGTTCGGTTGCTGCCAATTCTGCTAAATTGTGTATTCTTTAATACTCTGAAGTTAGTA-T
1 AAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGTATT
964551 TTGTCTTT
66 TTGTCTTT
964559 ATTTTGTCTT
Statistics
Matches: 241, Mismatches: 7, Indels: 23
0.89 0.03 0.08
Matches are distributed among these distances:
82 60 0.25
83 9 0.04
93 15 0.06
94 157 0.65
ACGTcount: A:0.22, C:0.13, G:0.19, T:0.46
Consensus pattern (84 bp):
AAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGTATT
TTGTCTTTTGGTTGAAAGT
Found at i:964440 original size:94 final size:93
Alignment explanation
Indices: 964280--964581 Score: 532
Period size: 94 Copynumber: 3.2 Consensus size: 93
964270 GAAGTTAGTA
*
964280 TTTGTCTTTTGGTTGAAGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTA
1 TTTGTCTTTTGGTTGAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTA
964345 ACACTGTGAAGTTAGTATTTGTCTTTGT
66 ACACTGTGAAGTTAGTATTTGTCTTTGT
964373 TTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTT
1 TTTGTCTTTTGGTTG-AAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTT
964438 AACACTGTGAAGTTAGTATTTGTCTTTGT
65 AACACTGTGAAGTTAGTATTTGTCTTTGT
*
964467 TTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAATTGTGTATTCTTT
1 TTTGTCTTTTGGTTG-AAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTT
* * *
964532 AATACTCTGAAGTTAGTATTTGTCTTTAT
65 AACACTGTGAAGTTAGTATTTGTCTTTGT
*
964561 TTTGTCTTTTAGTTGAAGTAA
1 TTTGTCTTTTGGTTGAAGTAA
964582 TGCAATCCAT
Statistics
Matches: 202, Mismatches: 6, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
93 21 0.10
94 181 0.90
ACGTcount: A:0.21, C:0.12, G:0.19, T:0.48
Consensus pattern (93 bp):
TTTGTCTTTTGGTTGAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTA
ACACTGTGAAGTTAGTATTTGTCTTTGT
Found at i:964942 original size:42 final size:42
Alignment explanation
Indices: 964866--964945 Score: 106
Period size: 42 Copynumber: 1.9 Consensus size: 42
964856 GACTCGCCTG
* * *
964866 TCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCCCCTA
1 TCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCCCCTA
* * *
964908 TCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCC
1 TCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCC
964946 ATTGTCATCG
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
42 32 1.00
ACGTcount: A:0.21, C:0.39, G:0.17, T:0.23
Consensus pattern (42 bp):
TCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCCCCTA
Found at i:966356 original size:14 final size:14
Alignment explanation
Indices: 966337--966372 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
966327 ATTGTTTAAT
966337 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
966351 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
966365 TGATTTGT
1 TGATTTGT
966373 TTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.22, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:966495 original size:19 final size:17
Alignment explanation
Indices: 966479--966562 Score: 72
Period size: 14 Copynumber: 5.1 Consensus size: 17
966469 AAAAATGACT
966479 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATG--A
*
966498 ATCGCAA--CGAGA-GA
1 ATCGCAATGCGAAATGA
966512 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATG--A
*
966531 ATCGCAA--CGAGA-GA
1 ATCGCAATGCGAAATGA
966545 ATCGCAATGCGAAATGA
1 ATCGCAATGCGAAATGA
966562 A
1 A
966563 AATCGCAACG
Statistics
Matches: 53, Mismatches: 4, Indels: 18
0.71 0.05 0.24
Matches are distributed among these distances:
14 16 0.30
16 10 0.19
17 12 0.23
19 15 0.28
ACGTcount: A:0.45, C:0.18, G:0.24, T:0.13
Consensus pattern (17 bp):
ATCGCAATGCGAAATGA
Found at i:966521 original size:33 final size:33
Alignment explanation
Indices: 966479--966591 Score: 199
Period size: 33 Copynumber: 3.4 Consensus size: 33
966469 AAAAATGACT
966479 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
966512 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
* *
966545 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
*
966578 ATCGCAACGCGAAA
1 ATCGCAATGCGAAA
966592 CTAAATTCGC
Statistics
Matches: 77, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 77 1.00
ACGTcount: A:0.46, C:0.20, G:0.22, T:0.12
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:966568 original size:19 final size:19
Alignment explanation
Indices: 966479--966570 Score: 96
Period size: 19 Copynumber: 5.4 Consensus size: 19
966469 AAAAATGACT
966479 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
966498 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
966512 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
966531 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
966545 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
966564 ATCGCAA
1 ATCGCAA
966571 CGACAAAATC
Statistics
Matches: 59, Mismatches: 4, Indels: 20
0.71 0.05 0.24
Matches are distributed among these distances:
14 20 0.34
15 2 0.03
16 4 0.07
17 4 0.07
18 2 0.03
19 27 0.46
ACGTcount: A:0.46, C:0.18, G:0.23, T:0.13
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:966690 original size:14 final size:14
Alignment explanation
Indices: 966673--966700 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
966663 GTAATTTCCG
966673 CGTTGCGATTTTCA
1 CGTTGCGATTTTCA
966687 CGTTGCGATTTTCA
1 CGTTGCGATTTTCA
966701 TTTCGCATTG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.14, C:0.21, G:0.21, T:0.43
Consensus pattern (14 bp):
CGTTGCGATTTTCA
Found at i:966695 original size:53 final size:52
Alignment explanation
Indices: 966614--966714 Score: 166
Period size: 53 Copynumber: 1.9 Consensus size: 52
966604 TGCGATTTTC
*
966614 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATAGTA
1 ATTTCGCATTGCGATTCTCACGTTGCGATTTTCATTTCGCATTGCGATAGTA
* *
966666 ATTTCCGCGTTGCGATTTTCACGTTGCGATTTTCATTTCGCATTGCGAT
1 ATTT-CGCATTGCGATTCTCACGTTGCGATTTTCATTTCGCATTGCGAT
966715 TCTCTCGTTG
Statistics
Matches: 45, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
52 4 0.09
53 41 0.91
ACGTcount: A:0.16, C:0.22, G:0.20, T:0.43
Consensus pattern (52 bp):
ATTTCGCATTGCGATTCTCACGTTGCGATTTTCATTTCGCATTGCGATAGTA
Found at i:966737 original size:33 final size:34
Alignment explanation
Indices: 966655--966748 Score: 127
Period size: 33 Copynumber: 2.8 Consensus size: 34
966645 TCATTTCGCA
*
966655 TTGCGATAGTAATTTCCGCGTTGCGATTTTCACG
1 TTGCGATAGTAATTTCCGCGTTGCGATTCTCACG
** * * *
966689 TTGCGATTTTCATTT-CGCATTGCGATTCTCTCG
1 TTGCGATAGTAATTTCCGCGTTGCGATTCTCACG
966722 TTGCGATAGTAATTTCCGCGTTGCGAT
1 TTGCGATAGTAATTTCCGCGTTGCGAT
966749 AGACATTAAG
Statistics
Matches: 49, Mismatches: 10, Indels: 2
0.80 0.16 0.03
Matches are distributed among these distances:
33 27 0.55
34 22 0.45
ACGTcount: A:0.16, C:0.21, G:0.22, T:0.40
Consensus pattern (34 bp):
TTGCGATAGTAATTTCCGCGTTGCGATTCTCACG
Found at i:970244 original size:21 final size:21
Alignment explanation
Indices: 970220--970265 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
970210 TAATCGCGTT
970220 GCGAATTAGGAAAATCGCAAC
1 GCGAATTAGGAAAATCGCAAC
* * *
970241 GCGAATTTGGGAAATCGCAAT
1 GCGAATTAGGAAAATCGCAAC
970262 GCGA
1 GCGA
970266 TAGTCAGAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.37, C:0.17, G:0.28, T:0.17
Consensus pattern (21 bp):
GCGAATTAGGAAAATCGCAAC
Found at i:977259 original size:46 final size:46
Alignment explanation
Indices: 977200--977769 Score: 935
Period size: 46 Copynumber: 12.4 Consensus size: 46
977190 TTAATATAGT
* * *
977200 GTTATGTATTTTCATTTGTGGCATCCTTTCATGCCGATTATGCACC
1 GTTATGCATTTTCATTTATGGCATCCTTTCATGCCGATAATGCACC
* * *
977246 GCTATGCATTTTCATTTATGGCATCATTTCATGCCGATAATGCATC
1 GTTATGCATTTTCATTTATGGCATCCTTTCATGCCGATAATGCACC
*
977292 GTTATGCATTTTCATTTATGGCATCCTTTCATGCCAATAATGCACC
1 GTTATGCATTTTCATTTATGGCATCCTTTCATGCCGATAATGCACC
* * *
977338 ATTATGCATTTTCATTTATGGCATCCTTTCATGTCGATAATCCACC
1 GTTATGCATTTTCATTTATGGCATCCTTTCATGCCGATAATGCACC
*
977384 ATTATGCATTTTCATTTATGGCATCCTTTCATGCCGATAATGCACC
1 GTTATGCATTTTCATTTATGGCATCCTTTCATGCCGATAATGCACC
*
977430 GTTATGCATTTTCATTTATGACATCCTTTCATGCCGATAATGCACC
1 GTTATGCATTTTCATTTATGGCATCCTTTCATGCCGATAATGCACC
*
977476 GTTATGCATTTTCATTTATGACATCCTTTCATGCCGATAATGCACC
1 GTTATGCATTTTCATTTATGGCATCCTTTCATGCCGATAATGCACC
*
977522 GTTATGTATTTTCATTTATGG-ATCCTTTCATGCCGATAATGCACC
1 GTTATGCATTTTCATTTATGGCATCCTTTCATGCCGATAATGCACC
*
977567 CTTATGCATTTTCATTTATGGCATCCTTTCATGCCGATAATGCACC
1 GTTATGCATTTTCATTTATGGCATCCTTTCATGCCGATAATGCACC
* *
977613 ATTATGCATTTTCATTTATGACATCCTTTCATGCCGATAATGCACC
1 GTTATGCATTTTCATTTATGGCATCCTTTCATGCCGATAATGCACC
* * *
977659 CTTATGCATTTTCATTTATGACATCCTTTCATGCTGATAATGCACC
1 GTTATGCATTTTCATTTATGGCATCCTTTCATGCCGATAATGCACC
* *
977705 GTTATGCATTTTCATTTATGGCATCCTTTCATGCCGATAATTCACT
1 GTTATGCATTTTCATTTATGGCATCCTTTCATGCCGATAATGCACC
977751 GTTATGCATTTTCATTTAT
1 GTTATGCATTTTCATTTAT
977770 TCATTCATTT
Statistics
Matches: 492, Mismatches: 31, Indels: 2
0.94 0.06 0.00
Matches are distributed among these distances:
45 43 0.09
46 449 0.91
ACGTcount: A:0.23, C:0.23, G:0.13, T:0.41
Consensus pattern (46 bp):
GTTATGCATTTTCATTTATGGCATCCTTTCATGCCGATAATGCACC
Found at i:983415 original size:46 final size:46
Alignment explanation
Indices: 983358--983882 Score: 735
Period size: 46 Copynumber: 11.4 Consensus size: 46
983348 TTAATATAAT
* * *
983358 GTTATGTATTTTCATTTATGGCATCCTTTCATGCCAATTATGCACC
1 GTTATGCATTTTCATTTATGGCATCCTTTCATGCCGATAATGCACC
*
983404 GTTATGCATTTTCATTTATGGCATCCTTTCATGCCGATAATGCATC
1 GTTATGCATTTTCATTTATGGCATCCTTTCATGCCGATAATGCACC
* *
983450 GTTATGCATTTTCATTTTTGGCATCCTTTCATGTCGATAATGCACC
1 GTTATGCATTTTCATTTATGGCATCCTTTCATGCCGATAATGCACC
* * * *
983496 ATTATGCATTTTCATTTATGACACCCTTTCATGCTGATAATGCACC
1 GTTATGCATTTTCATTTATGGCATCCTTTCATGCCGATAATGCACC
* * * * *
983542 ATTATGCATTTTCATTTATGACATCCTTTAATACCTATAATGCACC
1 GTTATGCATTTTCATTTATGGCATCCTTTCATGCCGATAATGCACC
*
983588 GTTATGCATTTTCATTTATGGCATCCTTTCATGCCGATAATGAACC
1 GTTATGCATTTTCATTTATGGCATCCTTTCATGCCGATAATGCACC
* * *
983634 ATTATGCATTTTCATTTATGGCATCCTTTCATGCTGATAATGCACT
1 GTTATGCATTTTCATTTATGGCATCCTTTCATGCCGATAATGCACC
* * ** * **
983680 ATTGTGCATTTTCATTTATGAAATCCTTTTATGTTGATAATGCACC
1 GTTATGCATTTTCATTTATGGCATCCTTTCATGCCGATAATGCACC
* *
983726 ATTATGCATTTTCATTTATGGCATCCTTTCATGCCGATAATTCACC
1 GTTATGCATTTTCATTTATGGCATCCTTTCATGCCGATAATGCACC
* *
983772 GTTATGCATTTTCAGTTATGCCATCCTTTCATGCCGATAATGCACC
1 GTTATGCATTTTCATTTATGGCATCCTTTCATGCCGATAATGCACC
* * * *
983818 GTTATACATTTTCATTTATGGCATCTTTTCATGCTGATAATGCACT
1 GTTATGCATTTTCATTTATGGCATCCTTTCATGCCGATAATGCACC
*
983864 GTTATACATTTTCATTTAT
1 GTTATGCATTTTCATTTAT
983883 TCCTTCATTT
Statistics
Matches: 428, Mismatches: 51, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
46 428 1.00
ACGTcount: A:0.24, C:0.21, G:0.13, T:0.42
Consensus pattern (46 bp):
GTTATGCATTTTCATTTATGGCATCCTTTCATGCCGATAATGCACC
Found at i:985909 original size:2 final size:2
Alignment explanation
Indices: 985902--985939 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
985892 ATTTACGATG
985902 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
985940 TATGGGGTAT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:986817 original size:25 final size:27
Alignment explanation
Indices: 986756--986851 Score: 94
Period size: 25 Copynumber: 3.6 Consensus size: 27
986746 TTAATTTTTT
* *
986756 TATA-ATTTATTATTTTATAACT-TATGA
1 TATATATTTATTTTTTTA-AAATATAT-A
986783 TATATATTTAATTTTTTTAAAATA-ATA
1 TATATATTT-ATTTTTTTAAAATATATA
986810 TA-AT-TTTATTATTTTTAAAATATATA
1 TATATATTTATT-TTTTTAAAATATATA
986836 TATATATTTTATTTTT
1 TATATA-TTTATTTTT
986852 AGTATTTTTA
Statistics
Matches: 59, Mismatches: 2, Indels: 15
0.78 0.03 0.20
Matches are distributed among these distances:
24 3 0.05
25 14 0.24
26 7 0.12
27 9 0.15
28 12 0.20
29 14 0.24
ACGTcount: A:0.39, C:0.01, G:0.01, T:0.59
Consensus pattern (27 bp):
TATATATTTATTTTTTTAAAATATATA
Found at i:986833 original size:45 final size:44
Alignment explanation
Indices: 986738--986834 Score: 106
Period size: 45 Copynumber: 2.2 Consensus size: 44
986728 TATATATTTA
* * *
986738 AAAATAT-TTTAATTTTTTTATAATTTATTATTTTATAACTTAT
1 AAAATATATTTAATTTTTTTAAAATATATAATTTTATAACTTAT
* * * * *
986781 GATATATATTTAATTTTTTTAAAATAATATAATTTTATTATTTTT
1 AAAATATATTTAATTTTTTTAAAAT-ATATAATTTTATAACTTAT
986826 AAAATATAT
1 AAAATATAT
986835 ATATATATTT
Statistics
Matches: 42, Mismatches: 10, Indels: 2
0.78 0.19 0.04
Matches are distributed among these distances:
43 5 0.12
44 16 0.38
45 21 0.50
ACGTcount: A:0.40, C:0.01, G:0.01, T:0.58
Consensus pattern (44 bp):
AAAATATATTTAATTTTTTTAAAATATATAATTTTATAACTTAT
Found at i:986866 original size:22 final size:22
Alignment explanation
Indices: 986833--986896 Score: 65
Period size: 22 Copynumber: 2.9 Consensus size: 22
986823 TTTAAAATAT
* *
986833 ATATATATATTTTATTTTTAGT
1 ATATTTATATTTTATTTTTAGA
* * *
986855 ATTTTTATATTTAATTTTTTGA
1 ATATTTATATTTTATTTTTAGA
*
986877 ATATTTATTTTTTATATTTT
1 ATATTTATATTTTAT-TTTT
986897 TAATTTTAAA
Statistics
Matches: 33, Mismatches: 8, Indels: 1
0.79 0.19 0.02
Matches are distributed among these distances:
22 29 0.88
23 4 0.12
ACGTcount: A:0.28, C:0.00, G:0.03, T:0.69
Consensus pattern (22 bp):
ATATTTATATTTTATTTTTAGA
Found at i:986882 original size:16 final size:16
Alignment explanation
Indices: 986856--986903 Score: 57
Period size: 15 Copynumber: 3.1 Consensus size: 16
986846 ATTTTTAGTA
986856 TTTT-TATATTTAATT
1 TTTTATATATTTAATT
986871 TTTTGA-ATATTT-ATT
1 TTTT-ATATATTTAATT
*
986886 TTTTATATTTTTAATT
1 TTTTATATATTTAATT
986902 TT
1 TT
986904 AAATTTAAGA
Statistics
Matches: 28, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
14 1 0.04
15 16 0.57
16 11 0.39
ACGTcount: A:0.25, C:0.00, G:0.02, T:0.73
Consensus pattern (16 bp):
TTTTATATATTTAATT
Found at i:986927 original size:38 final size:37
Alignment explanation
Indices: 986842--986928 Score: 88
Period size: 37 Copynumber: 2.3 Consensus size: 37
986832 TATATATATA
* **
986842 TTTTATTTTTAGTATTTTTATATTTAATTTTTTGAAT
1 TTTTATTTTTAGTATTTTTATATTTAAATTTAAGAAT
*
986879 ATTTATTTTTTA-TATTTTTA-ATTTTAAATTTAAGATAAT
1 TTTTA-TTTTTAGTATTTTTATA-TTTAAATTTAAG--AAT
986918 TTTTATTTTTA
1 TTTTATTTTTA
986929 AAAATTATAT
Statistics
Matches: 41, Mismatches: 5, Indels: 7
0.77 0.09 0.13
Matches are distributed among these distances:
36 1 0.02
37 21 0.51
38 12 0.29
39 7 0.17
ACGTcount: A:0.29, C:0.00, G:0.03, T:0.68
Consensus pattern (37 bp):
TTTTATTTTTAGTATTTTTATATTTAAATTTAAGAAT
Found at i:987347 original size:20 final size:20
Alignment explanation
Indices: 987324--987372 Score: 53
Period size: 20 Copynumber: 2.5 Consensus size: 20
987314 TGGTTGGTAA
987324 TTGACAAAACCAGTTGAAAT
1 TTGACAAAACCAGTTGAAAT
* * * **
987344 TTGATAAAAGCGGTTTCAAT
1 TTGACAAAACCAGTTGAAAT
987364 TTGACAAAA
1 TTGACAAAA
987373 TAGGAAAAGA
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.43, C:0.12, G:0.16, T:0.29
Consensus pattern (20 bp):
TTGACAAAACCAGTTGAAAT
Found at i:987650 original size:22 final size:22
Alignment explanation
Indices: 987619--987662 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
987609 TTTTATAAGT
987619 ATGTCCAACACCCCAAACATCG
1 ATGTCCAACACCCCAAACATCG
*
987641 ATGTCTAACACCCCAAACATCG
1 ATGTCCAACACCCCAAACATCG
987663 GCCTAGTGAC
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:0.36, C:0.39, G:0.09, T:0.16
Consensus pattern (22 bp):
ATGTCCAACACCCCAAACATCG
Found at i:989186 original size:47 final size:47
Alignment explanation
Indices: 989113--989203 Score: 146
Period size: 47 Copynumber: 1.9 Consensus size: 47
989103 AGTCGAGAGT
*
989113 TCTACGCGGTCCTTCGGGACAATTCTATATGGTCCTTCGGGACAAAC
1 TCTACGCGGTCCTTCGGGACAATTCTACATGGTCCTTCGGGACAAAC
* * *
989160 TCTACGCGGTCCTTTGGGACATTTCTACGTGGTCCTTCGGGACA
1 TCTACGCGGTCCTTCGGGACAATTCTACATGGTCCTTCGGGACA
989204 TTTCTATGTG
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
47 40 1.00
ACGTcount: A:0.18, C:0.27, G:0.25, T:0.30
Consensus pattern (47 bp):
TCTACGCGGTCCTTCGGGACAATTCTACATGGTCCTTCGGGACAAAC
Found at i:989220 original size:23 final size:23
Alignment explanation
Indices: 989112--989214 Score: 116
Period size: 23 Copynumber: 4.4 Consensus size: 23
989102 GAGTCGAGAG
* *
989112 TTCTACGCGGTCCTTCGGGACAA
1 TTCTACGTGGTCCTTCGGGACAT
** *
989135 TTCTATATGGTCCTTCGGGACAAA
1 TTCTACGTGGTCCTTCGGGAC-AT
* * *
989159 CTCTACGCGGTCCTTTGGGACAT
1 TTCTACGTGGTCCTTCGGGACAT
989182 TTCTACGTGGTCCTTCGGGACAT
1 TTCTACGTGGTCCTTCGGGACAT
*
989205 TTCTATGTGG
1 TTCTACGTGG
989215 CACTTCAGTG
Statistics
Matches: 66, Mismatches: 13, Indels: 2
0.81 0.16 0.02
Matches are distributed among these distances:
23 48 0.73
24 18 0.27
ACGTcount: A:0.17, C:0.25, G:0.25, T:0.33
Consensus pattern (23 bp):
TTCTACGTGGTCCTTCGGGACAT
Found at i:989262 original size:23 final size:24
Alignment explanation
Indices: 989205--989263 Score: 68
Period size: 24 Copynumber: 2.5 Consensus size: 24
989195 TTCGGGACAT
989205 TTCTATGTGGCACTTCAGTGTATA
1 TTCTATGTGGCACTTCAGTGTATA
** *
989229 TTCTACATGGCACTTC-GATG-CTA
1 TTCTATGTGGCACTTCAG-TGTATA
989252 TTCTATGTGGCA
1 TTCTATGTGGCA
989264 GTTTCGACTA
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
23 13 0.45
24 16 0.55
ACGTcount: A:0.20, C:0.20, G:0.20, T:0.39
Consensus pattern (24 bp):
TTCTATGTGGCACTTCAGTGTATA
Found at i:989714 original size:24 final size:24
Alignment explanation
Indices: 989687--989734 Score: 87
Period size: 24 Copynumber: 2.0 Consensus size: 24
989677 GATCAGTTTT
*
989687 TGTAAATATACTTTATTGTATTTA
1 TGTAAACATACTTTATTGTATTTA
989711 TGTAAACATACTTTATTGTATTTA
1 TGTAAACATACTTTATTGTATTTA
989735 AGGGTTCCAT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.33, C:0.06, G:0.08, T:0.52
Consensus pattern (24 bp):
TGTAAACATACTTTATTGTATTTA
Found at i:992889 original size:24 final size:24
Alignment explanation
Indices: 992862--992911 Score: 82
Period size: 24 Copynumber: 2.1 Consensus size: 24
992852 GGCCTAACTA
*
992862 CTTATATGGTGAACGTTGCTACAT
1 CTTATATGGTGAACATTGCTACAT
*
992886 CTTATATGGTGAATATTGCTACAT
1 CTTATATGGTGAACATTGCTACAT
992910 CT
1 CT
992912 ACACAGATCA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.26, C:0.16, G:0.18, T:0.40
Consensus pattern (24 bp):
CTTATATGGTGAACATTGCTACAT
Found at i:996116 original size:24 final size:24
Alignment explanation
Indices: 996079--996140 Score: 63
Period size: 23 Copynumber: 2.6 Consensus size: 24
996069 CAATTCTATA
* *
996079 TGGTTCTTTAGGACAAACTCTACG
1 TGGTCCTTTGGGACAAACTCTACG
* **
996103 TGGTCTTTTGGGAC-ATTTCTACG
1 TGGTCCTTTGGGACAAACTCTACG
*
996126 TTGTCCTTTGGGACA
1 TGGTCCTTTGGGACA
996141 TTTCTATGTG
Statistics
Matches: 30, Mismatches: 7, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
23 19 0.63
24 11 0.37
ACGTcount: A:0.18, C:0.19, G:0.24, T:0.39
Consensus pattern (24 bp):
TGGTCCTTTGGGACAAACTCTACG
Found at i:996123 original size:23 final size:23
Alignment explanation
Indices: 996097--996173 Score: 86
Period size: 23 Copynumber: 3.3 Consensus size: 23
996087 TAGGACAAAC
*
996097 TCTACGTGGTCTTTTGGGACATT
1 TCTACGTGGTCCTTTGGGACATT
*
996120 TCTACGTTGTCCTTTGGGACATT
1 TCTACGTGGTCCTTTGGGACATT
*
996143 TCTATGTGG-CACTTTGGTG-CATAT
1 TCTACGTGGTC-CTTTGG-GACAT-T
996167 TCTACGT
1 TCTACGT
996174 AGTACTTCGG
Statistics
Matches: 46, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
22 1 0.02
23 37 0.80
24 8 0.17
ACGTcount: A:0.14, C:0.19, G:0.23, T:0.43
Consensus pattern (23 bp):
TCTACGTGGTCCTTTGGGACATT
Found at i:996180 original size:24 final size:24
Alignment explanation
Indices: 996119--996193 Score: 66
Period size: 23 Copynumber: 3.2 Consensus size: 24
996109 TTTGGGACAT
* *
996119 TTCTACGTTGTCCTTTGG-GACAT-
1 TTCTACGTAGTACTTTGGTG-CATA
* * *
996142 TTCTATGTGGCACTTTGGTGCATA
1 TTCTACGTAGTACTTTGGTGCATA
*
996166 TTCTACGTAGTACTTCGGTGCA-A
1 TTCTACGTAGTACTTTGGTGCATA
996189 TTCTA
1 TTCTA
996194 TGTGACAGTT
Statistics
Matches: 42, Mismatches: 8, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
23 23 0.55
24 19 0.45
ACGTcount: A:0.17, C:0.20, G:0.21, T:0.41
Consensus pattern (24 bp):
TTCTACGTAGTACTTTGGTGCATA
Found at i:997934 original size:18 final size:18
Alignment explanation
Indices: 997913--997957 Score: 81
Period size: 18 Copynumber: 2.5 Consensus size: 18
997903 ACCAAAACCT
*
997913 TCTTATCAACCAAGGTCA
1 TCTTCTCAACCAAGGTCA
997931 TCTTCTCAACCAAGGTCA
1 TCTTCTCAACCAAGGTCA
997949 TCTTCTCAA
1 TCTTCTCAA
997958 GTAAGATCTT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.29, C:0.31, G:0.09, T:0.31
Consensus pattern (18 bp):
TCTTCTCAACCAAGGTCA
Found at i:999280 original size:13 final size:13
Alignment explanation
Indices: 999262--999286 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
999252 TTAAATTTGT
999262 TTATTTCTATACA
1 TTATTTCTATACA
999275 TTATTTCTATAC
1 TTATTTCTATAC
999287 TGAGAACAGG
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:0.28, C:0.16, G:0.00, T:0.56
Consensus pattern (13 bp):
TTATTTCTATACA
Found at i:1000541 original size:18 final size:17
Alignment explanation
Indices: 1000487--1000535 Score: 53
Period size: 19 Copynumber: 2.7 Consensus size: 17
1000477 TTGGACCCTT
* *
1000487 AGTGCATCGGTGCACTAA
1 AGTGCATCGATGCA-TCA
1000505 GAGTGCATCGATGCATCA
1 -AGTGCATCGATGCATCA
1000523 AGTGCATTCGATG
1 AGTGCA-TCGATG
1000536 TTTCAAAATA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 6 0.22
18 8 0.30
19 13 0.48
ACGTcount: A:0.27, C:0.20, G:0.29, T:0.24
Consensus pattern (17 bp):
AGTGCATCGATGCATCA
Found at i:1000593 original size:64 final size:64
Alignment explanation
Indices: 1000508--1000696 Score: 215
Period size: 65 Copynumber: 2.9 Consensus size: 64
1000498 GCACTAAGAG
* *
1000508 TGCATCGATGCATCAAGTGCATTCGATGTTTCAAAATAGCCAGAGTGCATCGATGCATGGCT-AA
1 TGCATCGATGCATCAAATGCATTCGATGTTTCAAAATATCCAGAGTGCATCGATGCATGG-TGAA
** *
1000572 TGCATCGATGCATCAAATGCATTCGATGTTTTCATAAA-ATCCCTAGTGCATCGATGCATGGTGT
1 TGCATCGATGCATCAAATGCATTCGATG-TTTCA-AAATATCCAGAGTGCATCGATGCATGGTGA
*
1000636 G
64 A
* * **
1000637 TGCATCGATGCATGAAATACATTCGATG-TTCAATTTATTCCATG-GTGCATCGATGCATGG
1 TGCATCGATGCATCAAATGCATTCGATGTTTCAAAATA-TCCA-GAGTGCATCGATGCATGG
1000697 ATTGGTGCAT
Statistics
Matches: 107, Mismatches: 12, Indels: 12
0.82 0.09 0.09
Matches are distributed among these distances:
62 1 0.01
63 5 0.05
64 47 0.44
65 51 0.48
66 3 0.03
ACGTcount: A:0.28, C:0.20, G:0.22, T:0.31
Consensus pattern (64 bp):
TGCATCGATGCATCAAATGCATTCGATGTTTCAAAATATCCAGAGTGCATCGATGCATGGTGAA
Found at i:1002902 original size:13 final size:13
Alignment explanation
Indices: 1002886--1002910 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1002876 AACATAATAA
1002886 AAAAATTAAATTT
1 AAAAATTAAATTT
1002899 AAAAATTAAATT
1 AAAAATTAAATT
1002911 CATATTTTCA
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:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (13 bp):
AAAAATTAAATTT
Found at i:1003374 original size:23 final size:22
Alignment explanation
Indices: 1003344--1003423 Score: 90
Period size: 22 Copynumber: 3.6 Consensus size: 22
1003334 GCATGGCCTT
1003344 GTGCATCGATGCACATTCAAGG
1 GTGCATCGATGCACATTCAAGG
* * * *
1003366 CGTGCATCGGTACACCTTC-ATG
1 -GTGCATCGATGCACATTCAAGG
*
1003388 GTGTATCGATGCACATTCAAGG
1 GTGCATCGATGCACATTCAAGG
*
1003410 ATGCATCGATGCAC
1 GTGCATCGATGCAC
1003424 TGTTAGGTGT
Statistics
Matches: 45, Mismatches: 11, Indels: 3
0.76 0.19 0.05
Matches are distributed among these distances:
21 14 0.31
22 16 0.36
23 15 0.33
ACGTcount: A:0.25, C:0.25, G:0.25, T:0.25
Consensus pattern (22 bp):
GTGCATCGATGCACATTCAAGG
Found at i:1003398 original size:44 final size:42
Alignment explanation
Indices: 1003348--1003442 Score: 120
Period size: 44 Copynumber: 2.2 Consensus size: 42
1003338 GGCCTTGTGC
* *
1003348 ATCGATGCACATTCAAGGCGTGCATCGGTACACCT-TCATGGTGT
1 ATCGATGCACATTCAAGG-ATGCATCGATACA-CTGTCA-GGTGT
* *
1003392 ATCGATGCACATTCAAGGATGCATCGATGCACTGTTAGGTGT
1 ATCGATGCACATTCAAGGATGCATCGATACACTGTCAGGTGT
1003434 ATCGATGCA
1 ATCGATGCA
1003443 TTAAGCACAA
Statistics
Matches: 46, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
42 16 0.35
43 12 0.26
44 18 0.39
ACGTcount: A:0.25, C:0.22, G:0.25, T:0.27
Consensus pattern (42 bp):
ATCGATGCACATTCAAGGATGCATCGATACACTGTCAGGTGT
Found at i:1003439 original size:20 final size:21
Alignment explanation
Indices: 1003348--1003442 Score: 77
Period size: 21 Copynumber: 4.4 Consensus size: 21
1003338 GGCCTTGTGC
*
1003348 ATCGATGCACATTCAAGGCGTGC
1 ATCGATGCACATTCAA-G-GTGT
* * * *
1003371 ATCGGTACACCTTCATGGTGT
1 ATCGATGCACATTCAAGGTGT
*
1003392 ATCGATGCACATTCAAGGATGC
1 ATCGATGCACATTCAAGG-TGT
*
1003414 ATCGATGCAC-TGT-TAGGTGT
1 ATCGATGCACAT-TCAAGGTGT
1003434 ATCGATGCA
1 ATCGATGCA
1003443 TTAAGCACAA
Statistics
Matches: 58, Mismatches: 12, Indels: 7
0.75 0.16 0.09
Matches are distributed among these distances:
20 11 0.19
21 21 0.36
22 14 0.24
23 12 0.21
ACGTcount: A:0.25, C:0.22, G:0.25, T:0.27
Consensus pattern (21 bp):
ATCGATGCACATTCAAGGTGT
Found at i:1006912 original size:3 final size:3
Alignment explanation
Indices: 1006865--1006897 Score: 59
Period size: 3 Copynumber: 11.3 Consensus size: 3
1006855 TTATATTAAA
1006865 ATT A-T ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1006898 ATGTTACATA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.07
3 27 0.93
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:1020004 original size:18 final size:17
Alignment explanation
Indices: 1019983--1020021 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 17
1019973 AAAAAGGATT
*
1019983 AAAAAAGGAAAAAAAATG
1 AAAAAAAGAAAAAAAA-G
*
1020001 AAAAAAAGAAGAAAAAG
1 AAAAAAAGAAAAAAAAG
1020018 AAAA
1 AAAA
1020022 GGGAGGGTTC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 5 0.26
18 14 0.74
ACGTcount: A:0.82, C:0.00, G:0.15, T:0.03
Consensus pattern (17 bp):
AAAAAAAGAAAAAAAAG
Found at i:1021190 original size:54 final size:54
Alignment explanation
Indices: 1021108--1021296 Score: 265
Period size: 54 Copynumber: 3.5 Consensus size: 54
1021098 TAGTGAAGAA
1021108 GAAGAAGATGTTCGAGTTCTATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTT
1 GAAGAAGATGTTCGAGTTCTATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTT
* * *
1021162 GAAGAAGATGTCCGAGTTTTATACTCCCTAGAGAAAGAGGGAGCAAACCCGTTT
1 GAAGAAGATGTTCGAGTTCTATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTT
* * * **
1021216 GAAAAAGATATTCGAGTTCTATACTCTCT-GAAGAAAGAGGGAGCGAACCCGTAA
1 GAAGAAGATGTTCGAGTTCTATACTCCCTAG-AGAAAGAGGGAGCGAACCCGTTT
1021270 GAAGAAGATTGTTCGAG-TCTCATACTC
1 GAAGAAGA-TGTTCGAGTTCT-ATACTC
1021297 TCTGAAGGAA
Statistics
Matches: 119, Mismatches: 13, Indels: 5
0.87 0.09 0.04
Matches are distributed among these distances:
53 1 0.01
54 105 0.88
55 13 0.11
ACGTcount: A:0.34, C:0.18, G:0.25, T:0.23
Consensus pattern (54 bp):
GAAGAAGATGTTCGAGTTCTATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTT
Found at i:1021497 original size:55 final size:55
Alignment explanation
Indices: 1021110--1021515 Score: 242
Period size: 55 Copynumber: 7.4 Consensus size: 55
1021100 GTGAAGAAGA
* * * *
1021110 AGAAGA-TGTTCGAGTTCTATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTTGA
1 AGAAGATTGTTCGAGTTCTATACTCTCTAAAGAAAGAGGGAGCGAACCCATTTGT
* * * * * * *
1021164 AGAAGA-TGTCCGAGTTTTATACTCCCTAGAGAAAGAGGGAGCAAACCCGTTTGA
1 AGAAGATTGTTCGAGTTCTATACTCTCTAAAGAAAGAGGGAGCGAACCCATTTGT
* * * * ** *
1021218 AAAAGA-TATTCGAGTTCTATACTCTCTGAAGAAAGAGGGAGCGAACCCGTAAGA
1 AGAAGATTGTTCGAGTTCTATACTCTCTAAAGAAAGAGGGAGCGAACCCATTTGT
* * * *** *
1021272 AGAAGATTGTTCGAG-TCTCATACTCTCTGAAGGAATAGGGAGCAGAAATGA-TAGT
1 AGAAGATTGTTCGAGTTCT-ATACTCTCTAAAGAAAGAGGGAGC-GAACCCATTTGT
* * * **
1021327 TGAAGATTGTTCGAG-TCTTATACTCTCTAAAGGAATAGGGA--GAAGACATGATTGT
1 AGAAGATTGTTCGAGTTC-TATACTCTCTAAAGAAAGAGGGAGCGAACCCAT--TTGT
* * * * * * * *
1021382 TGAAGATTGTTCAAG-TCTTATACTCTCTTAAGGAATAGGGAAC-AGACACGA-GTGT
1 AGAAGATTGTTCGAGTTC-TATACTCTCTAAAGAAAGAGGGAGCGA-AC-CCATTTGT
* * * * *
1021437 TGAAGA-TGTTTGAGTTCTATACTCCCTGAAAGAAAGAGGGAACGAACCCATTGGT
1 AGAAGATTGTTCGAGTTCTATACTCTCT-AAAGAAAGAGGGAGCGAACCCATTTGT
* *
1021492 AGAAGACTGTTCGAGTTCCATACT
1 AGAAGATTGTTCGAGTTCTATACT
1021516 TCAGGAGCGA
Statistics
Matches: 289, Mismatches: 47, Indels: 30
0.79 0.13 0.08
Matches are distributed among these distances:
52 4 0.01
54 120 0.42
55 142 0.49
56 21 0.07
57 1 0.00
58 1 0.00
ACGTcount: A:0.33, C:0.16, G:0.25, T:0.25
Consensus pattern (55 bp):
AGAAGATTGTTCGAGTTCTATACTCTCTAAAGAAAGAGGGAGCGAACCCATTTGT
Found at i:1021497 original size:110 final size:108
Alignment explanation
Indices: 1021111--1021507 Score: 340
Period size: 110 Copynumber: 3.6 Consensus size: 108
1021101 TGAAGAAGAA
* * * *
1021111 GAAGATGTTCGAGTTCTATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTTGAAGAAGA-TGTCC
1 GAAGATGTTCGAGTTCTATACTCCCTAAAGAAAGAGGGAACGAACCCATTTGAAGAAGATTGTTC
* * * * * *
1021175 GAGTTTTATACTC-CCTAGAGAAAGAGGGAGCAAACCCG-T-TT
66 GAGTCTTATACTCTCTTA-AGGAATAGGGAGCAGACACGATGTT
* * * * * **
1021216 GAAAAAGATATTCGAGTTCTATACTCTCTGAAGAAAGAGGGAGCGAACCCGTAAGAAGAAGATTG
1 G---AAGATGTTCGAGTTCTATACTCCCTAAAGAAAGAGGGAACGAACCCATTTGAAGAAGATTG
* * * *
1021281 TTCGAGTCTCATACTCTCTGAAGGAATAGGGAGCAGAAATGATAGTT
63 TTCGAGTCTTATACTCTCTTAAGGAATAGGGAGCAGACACGAT-GTT
* * * ** **
1021328 GAAGATTGTTCGAG-TCTTATACTCTCTAAAGGAATAGGG-A-GAAGACATGATTGTTGAAGATT
1 GAAGA-TGTTCGAGTTC-TATACTCCCTAAAGAAAGAGGGAACGAACCCAT--TTGAAGAAGATT
* *
1021390 GTTCAAGTCTTATACTCTCTTAAGGAATAGGGAACAGACACGAGTGTT
62 GTTCGAGTCTTATACTCTCTTAAGGAATAGGGAGCAGACACGA-TGTT
* * * *
1021438 GAAGATGTTTGAGTTCTATACTCCCTGAAAGAAAGAGGGAACGAACCCATTGGTAGAAGACTGTT
1 GAAGATGTTCGAGTTCTATACTCCCT-AAAGAAAGAGGGAACGAACCCATTTGAAGAAGATTGTT
1021503 CGAGT
65 CGAGT
1021508 TCCATACTTC
Statistics
Matches: 230, Mismatches: 45, Indels: 29
0.76 0.15 0.10
Matches are distributed among these distances:
105 1 0.00
108 57 0.25
109 51 0.22
110 110 0.48
111 2 0.01
112 9 0.04
ACGTcount: A:0.34, C:0.15, G:0.26, T:0.25
Consensus pattern (108 bp):
GAAGATGTTCGAGTTCTATACTCCCTAAAGAAAGAGGGAACGAACCCATTTGAAGAAGATTGTTC
GAGTCTTATACTCTCTTAAGGAATAGGGAGCAGACACGATGTT
Found at i:1021817 original size:3 final size:3
Alignment explanation
Indices: 1021773--1021802 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
1021763 TTATATTAAA
1021773 ATT A-T ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1021803 ATGTTACATA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.08
3 24 0.92
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (3 bp):
ATT
Found at i:1026823 original size:65 final size:65
Alignment explanation
Indices: 1026689--1026848 Score: 200
Period size: 65 Copynumber: 2.5 Consensus size: 65
1026679 TGGACCCTTA
* *
1026689 GTGCATCGGTGCATCAAGTGCATTCGATG-TTTCAAAATAGCCAAAGTACATTGATGCATGGCTG
1 GTGCATCGATGCATCAAATGCATTCGATGTTTTCAAAATAGCCAAAGTACATTGATGCATGGCTG
* * * ** *
1026753 ATGCATCGATACATCAAATGCATTCGATGTTTTCATAAA-ATCCCCAGTGCATTGATGCATGG-T
1 GTGCATCGATGCATCAAATGCATTCGATGTTTTCA-AAATAGCCAAAGTACATTGATGCATGGCT
1026816 G
65 G
*
1026817 TGTGCATCGATGCATGAAATGCATTCGATGTT
1 -GTGCATCGATGCATCAAATGCATTCGATGTT
1026849 CAATTTATTC
Statistics
Matches: 82, Mismatches: 11, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
64 27 0.33
65 52 0.63
66 3 0.04
ACGTcount: A:0.28, C:0.19, G:0.23, T:0.31
Consensus pattern (65 bp):
GTGCATCGATGCATCAAATGCATTCGATGTTTTCAAAATAGCCAAAGTACATTGATGCATGGCTG
Found at i:1027851 original size:6 final size:6
Alignment explanation
Indices: 1027837--1027891 Score: 74
Period size: 6 Copynumber: 9.2 Consensus size: 6
1027827 AATTATGCAT
* * * *
1027837 ATTTGA ATTTTA ATTTTA ATTTTA ATTTCA ATTTCA ATTTCA ATTTCA
1 ATTTCA ATTTCA ATTTCA ATTTCA ATTTCA ATTTCA ATTTCA ATTTCA
1027885 ATTTCA A
1 ATTTCA A
1027892 CTTGAGCTCC
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 47 1.00
ACGTcount: A:0.35, C:0.09, G:0.02, T:0.55
Consensus pattern (6 bp):
ATTTCA
Found at i:1028858 original size:214 final size:214
Alignment explanation
Indices: 1028489--1029094 Score: 892
Period size: 214 Copynumber: 2.8 Consensus size: 214
1028479 GAAGGATATG
* ** *
1028489 CATGTATAAAGTATCGATACTTAGCTAAATTAACAATGTAAGCGGTAAAAGTCTACCAATATAAT
1 CATGTATAAAGTATCGATACTTAGCTAAATTAACAATGTAAACGGTAAAAGTCTACCGGTGTAAT
* * *
1028554 GAAAATAGGCATAAATAACAAGTATCGCTACTTGTTATTTACGACTATTTTCAATATACCGGAAC
66 GAAAATAGGCGTAAATAACAAGTATCGCTACTTGTTATTTACGGCTATTTTCATTATACCGGAAC
* * **
1028619 ACTTTTATCCGTTTACATTGTTAATTTACCTACTACTTTAAAGTAATAGGTTTTGAAATTCCAAG
131 ACTTTTATCTGTTTACATTGTTAATTTACCTATTACTTTAAAGTAATAGGTTTCAAAATTCCAAG
*
1028684 TATTGATACCTT-TTATTTA
196 TATCGATA-CTTGTTATTTA
* *
1028703 CATGTATAAAGTATTGATACTTAGCTAAATTAACAATGTAAACGGTAAGAGTCTACCGGTGTAAT
1 CATGTATAAAGTATCGATACTTAGCTAAATTAACAATGTAAACGGTAAAAGTCTACCGGTGTAAT
* * * **
1028768 GAAAATAGGCGTAAATAATAAGTATCGTTGCTTGTTATTTACGGCTATTTTCATTATACCATAAC
66 GAAAATAGGCGTAAATAACAAGTATCGCTACTTGTTATTTACGGCTATTTTCATTATACCGGAAC
* *
1028833 ATTTTTATCTATTTACATTGTTAATTTACCTATTACTTTAAAGTAATAGGTTTCAAAATTCCAAG
131 ACTTTTATCTGTTTACATTGTTAATTTACCTATTACTTTAAAGTAATAGGTTTCAAAATTCCAAG
1028898 TATCGATACTTGTTATTTA
196 TATCGATACTTGTTATTTA
* * * *
1028917 CATTTATAAAGTATCAATACTTAGGTAAATTAACAATGTAAATGGTAAAAGTCTACCGGTGTAAT
1 CATGTATAAAGTATCGATACTTAGCTAAATTAACAATGTAAACGGTAAAAGTCTACCGGTGTAAT
* * *
1028982 TAAAATTGGCGTAAATAACAAGTATTGCTACTTGTTATTTACGAG-TATTTTCATTATACCGGAA
66 GAAAATAGGCGTAAATAACAAGTATCGCTACTTGTTATTTACG-GCTATTTTCATTATACCGGAA
* * * *
1029046 AACTTTTATATGTTTACATTGTTAATTTACATATTAATTTAAAGTAATA
130 CACTTTTATCTGTTTACATTGTTAATTTACCTATTACTTTAAAGTAATA
1029095 AAGCACCTAT
Statistics
Matches: 349, Mismatches: 41, Indels: 4
0.89 0.10 0.01
Matches are distributed among these distances:
213 3 0.01
214 345 0.99
215 1 0.00
ACGTcount: A:0.36, C:0.13, G:0.13, T:0.38
Consensus pattern (214 bp):
CATGTATAAAGTATCGATACTTAGCTAAATTAACAATGTAAACGGTAAAAGTCTACCGGTGTAAT
GAAAATAGGCGTAAATAACAAGTATCGCTACTTGTTATTTACGGCTATTTTCATTATACCGGAAC
ACTTTTATCTGTTTACATTGTTAATTTACCTATTACTTTAAAGTAATAGGTTTCAAAATTCCAAG
TATCGATACTTGTTATTTA
Found at i:1029366 original size:74 final size:76
Alignment explanation
Indices: 1029284--1029447 Score: 235
Period size: 76 Copynumber: 2.2 Consensus size: 76
1029274 CTTAACTGAT
* * * *
1029284 TAAAATAAAATAGGCCCTACTTATTACG-T-TAATCACTTACCGGTTTGT-TTAAAGGTTACTAC
1 TAAAATAAAATAGGCCCTACCTATTACGTTATAAT-ACCTACCGGTTTGTATAAAAGGTTACTAA
* *
1029346 TAATGTAAATGG
65 TAATGGAAACGG
*
1029358 TAAAATAAAATAGGCGCTACCTATTACGTTATAATACCTACCGGTTTGTATAAAAGGTTACTAAT
1 TAAAATAAAATAGGCCCTACCTATTACGTTATAATACCTACCGGTTTGTATAAAAGGTTACTAAT
1029423 AATGGAAACGG
66 AATGGAAACGG
1029434 TAAAATAAAATAGG
1 TAAAATAAAATAGG
1029448 TGTAAATGTC
Statistics
Matches: 80, Mismatches: 7, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
74 26 0.32
75 14 0.17
76 40 0.50
ACGTcount: A:0.40, C:0.13, G:0.16, T:0.31
Consensus pattern (76 bp):
TAAAATAAAATAGGCCCTACCTATTACGTTATAATACCTACCGGTTTGTATAAAAGGTTACTAAT
AATGGAAACGG
Found at i:1029941 original size:200 final size:198
Alignment explanation
Indices: 1029488--1030258 Score: 839
Period size: 200 Copynumber: 3.9 Consensus size: 198
1029478 GCCCATACCA
* * * * *
1029488 ATACTCTTATTCCATTATGCTTCTCAAACAATTTGCCCGTAACAAAGA-ATCGATAGC-CATATA
1 ATACTTTTATTCCAGTATGCTTCACAAACAATTTGCACGCAA-AAA-ATATCGATA-CACATATA
* * *
1029551 TTAAGTATCGATACTGGGAATTTTGAAACCTATTACTTTAAAGTAATAGGTAAATTTACAATGAA
63 TAAAGTATCGATACTTGGAATTTTCAAACCTATTACTTTAAAGTAATAGGTAAATTTACAATGAA
* * * *
1029616 AACAGTAAAAGTCTATCGGTATAATGATAATAGGCGTAAACATCAAGTATCTATACTTTGTTTCT
128 AACAGTAAAAGTCTACCGGTATAATGATAATAGGCGTAAACATAAAGTAT-TATACTTT-TATAT
*
1029681 CGGTATTG
191 CGGTATCG
* * ** * * *
1029689 ATACTTTTATTCTAGTATG-TTTATCAAACAATTTAAACACAAAAAGTATCGATACACTTATATA
1 ATACTTTTATTCCAGTATGCTTCA-CAAACAATTTGCACGCAAAAAATATCGATACACATATATA
* *
1029753 AAGTACCAATACTTGGAA-TTTCAAAGCCTATTACTTTAAAGTAATAGGTAAATTTACAAT-ATA
65 AAGTATCGATACTTGGAATTTTCAAA-CCTATTACTTTAAAGTAATAGGTAAATTTACAATGA-A
*
1029816 AACGGTAAAAGTCTACCGGTATAATGATAATAGGCGTAAACATAAAGTATATATACTTTTATATC
128 AACAGTAAAAGTCTACCGGTATAATGATAATAGGCGTAAACATAAAGTAT-TATACTTTTATATC
1029881 GGTATCG
192 GGTATCG
* * *
1029888 ATACTTTTATTCCAATATGCTTCACAAACAATTTGTACGCAACAAAATATCGATACTCATATATA
1 ATACTTTTATTCCAGTATGCTTCACAAACAATTTGCACGCAA-AAAATATCGATACACATATATA
* * * * * *
1029953 AAGTATCGATAC-TGGTAATTTTGAAAACTTTTGCTTTAAAGTAATAGGTAAATTTATAATGTAA
65 AAGTATCGATACTTGG-AATTTTCAAACCTATTACTTTAAAGTAATAGGTAAATTTACAATGAAA
* * * * * * * *
1030017 GCGGTAAAAGTCTACCGATATAATGATAATAGGCTTAAA-TTATAAGT-TT-TA---ATATGTTG
129 ACAGTAAAAGTCTACCGGTATAATGATAATAGGCGTAAACATA-AAGTATTATACTTTTATATCG
*
1030076 ATATCG
193 GTATCG
* * * * * *
1030082 ATACATTTATTCTAGTATGCTTCTCAAACAATTTGCACGCAAAACATATCGATGCACATATATGA
1 ATACTTTTATTCCAGTATGCTTCACAAACAATTTGCACGCAAAAAATATCGATACACATATATAA
* ** *
1030147 ATTATCGATACTTATAA-TTTCGAAACCTATTACTTTAAAGTAATAGGTTAATTTACAATGAAAA
66 AGTATCGATACTTGGAATTTTC-AAACCTATTACTTTAAAGTAATAGGTAAATTTACAATGAAAA
* * * *
1030211 TAGTAAAAGTATATCGGTATAATGATAATAGGCGTAAACATCAAGTAT
130 CAGTAAAAGTCTACCGGTATAATGATAATAGGCGTAAACATAAAGTAT
1030259 CGGTACACAT
Statistics
Matches: 478, Mismatches: 77, Indels: 37
0.81 0.13 0.06
Matches are distributed among these distances:
192 3 0.01
193 102 0.21
194 50 0.10
197 2 0.00
198 1 0.00
199 56 0.12
200 229 0.48
201 35 0.07
ACGTcount: A:0.39, C:0.13, G:0.13, T:0.34
Consensus pattern (198 bp):
ATACTTTTATTCCAGTATGCTTCACAAACAATTTGCACGCAAAAAATATCGATACACATATATAA
AGTATCGATACTTGGAATTTTCAAACCTATTACTTTAAAGTAATAGGTAAATTTACAATGAAAAC
AGTAAAAGTCTACCGGTATAATGATAATAGGCGTAAACATAAAGTATTATACTTTTATATCGGTA
TCG
Found at i:1031035 original size:226 final size:223
Alignment explanation
Indices: 1030366--1031066 Score: 869
Period size: 226 Copynumber: 3.1 Consensus size: 223
1030356 GGTATAATGA
* *
1030366 AAATAAACGCTACTTGTTATGTTAATATGGTTGATAATGTTTCCAGTAATTAACTTATTTTGTTA
1 AAATAAGCGCTACTTGTTATGTTATTATGGTTGATAATGTTTCCAGTAATTAACTTATTTTGTTA
* * *
1030431 TCGTCGGATTTCTAAGACTCTATCAGCTTAAACTTTGGTAACATTTTAGGCACTTTCTAATATAT
66 TCGTCGGATTTCTAATACTCCATCAGCTTAAACTTTGGTAACATTTTAGGCAC--TCTAATATGT
*
1030496 TGATAATATTGATAACAAATAAAGTAATTAACCTATTTTGTTATCGTCGGATTTCTAAGACCCCA
129 TGATAATATTGATAACAAATAAAGTAATTAACCTATTTTGTTATCGTCGGATTTCTAAG-GCCCA
* *
1030561 TCAGCTTTAAACA-GTCGCTACCTATTACATT
193 TCAACTTTAAACATG-CGCTATCTATTACATT
* * * *
1030592 AAATAAGCGTTACTTGTTATGTTATTATGGTTGACAATGTTTCCAGTAATTAACTTGTTTTATTA
1 AAATAAGCGCTACTTGTTATGTTATTATGGTTGATAATGTTTCCAGTAATTAACTTATTTTGTTA
* * * * *
1030657 TCTTCGGATTTATAAGGATGGCTCCATTAGCTTAAAATTTGGTAACATTTTAGG-----T-ATAT
66 TCGTCGGATTTCT-A--AT-ACTCCATCAGCTTAAACTTTGGTAACATTTTAGGCACTCTAATAT
* * *
1030716 GTTGATAAAATTGATAACAAATTAAGTAATTAACCTATTTTGTTATCATCGGATTTCTAAGGCTC
127 GTTGATAATATTGATAACAAATAAAGTAATTAACCTATTTTGTTATCGTCGGATTTCTAAGGC-C
1030781 CATCAGA-TTTAAACATGCGCTATCTATTACATT
191 CATCA-ACTTTAAACATGCGCTATCTATTACATT
* * *
1030814 AAATAAGCGCTACTTGTTATGTTATTATGGTTGATAATGTTTTCGGTAATTAACCTATTTTGTTA
1 AAATAAGCGCTACTTGTTATGTTATTATGGTTGATAATGTTTCCAGTAATTAACTTATTTTGTTA
** *
1030879 TCGTCTAATTTCTAATACTCCATCAACTTAAACTTTGGTAACATTTTAGGCACTACCTAATATGT
66 TCGTCGGATTTCTAATACTCCATCAGCTTAAACTTTGGTAACATTTTAGGCACT--CTAATATGT
* * * * * *
1030944 TGATAATATTAATAACAAATCAAGCAATTAACTTAATTTGTTATCGTCAGATTTCTAAGGCCACA
129 TGATAATATTGATAACAAATAAAGTAATTAACCTATTTTGTTATCGTCGGATTTCTAAGGCC-CA
* * * *
1031009 CCAACTTTAAAAATGCTCTATCTATTACGTT
193 TCAACTTTAAACATGCGCTATCTATTACATT
* * * *
1031040 ATATAAGTGATACCTGTTATGTTATTA
1 AAATAAGCGCTACTTGTTATGTTATTA
1031067 ATGTTTCAAG
Statistics
Matches: 407, Mismatches: 51, Indels: 34
0.83 0.10 0.07
Matches are distributed among these distances:
218 30 0.07
219 2 0.00
221 2 0.00
222 157 0.39
223 2 0.00
225 3 0.01
226 179 0.44
227 1 0.00
229 1 0.00
230 30 0.07
ACGTcount: A:0.32, C:0.15, G:0.13, T:0.40
Consensus pattern (223 bp):
AAATAAGCGCTACTTGTTATGTTATTATGGTTGATAATGTTTCCAGTAATTAACTTATTTTGTTA
TCGTCGGATTTCTAATACTCCATCAGCTTAAACTTTGGTAACATTTTAGGCACTCTAATATGTTG
ATAATATTGATAACAAATAAAGTAATTAACCTATTTTGTTATCGTCGGATTTCTAAGGCCCATCA
ACTTTAAACATGCGCTATCTATTACATT
Found at i:1034827 original size:16 final size:16
Alignment explanation
Indices: 1034773--1034828 Score: 51
Period size: 16 Copynumber: 3.3 Consensus size: 16
1034763 AGGAATAAGT
1034773 TCTTCTCATTATGAAC
1 TCTTCTCATTATGAAC
* *
1034789 T-TTCTCTTTTATGATGAGT
1 TCTTCTC-ATTATGA--A-C
1034808 TCTTCTCATTATGAAC
1 TCTTCTCATTATGAAC
1034824 TCTTC
1 TCTTC
1034829 ATTGGAAATG
Statistics
Matches: 31, Mismatches: 4, Indels: 10
0.69 0.09 0.22
Matches are distributed among these distances:
15 5 0.16
16 12 0.39
17 1 0.03
18 1 0.03
19 7 0.23
20 5 0.16
ACGTcount: A:0.20, C:0.21, G:0.09, T:0.50
Consensus pattern (16 bp):
TCTTCTCATTATGAAC
Found at i:1035070 original size:91 final size:92
Alignment explanation
Indices: 1034904--1035070 Score: 275
Period size: 91 Copynumber: 1.8 Consensus size: 92
1034894 TCAAAAAAAC
1034904 TCTTCTCATTATGAACTTCTTCTCCCTCTATCGGATGAGTTCTTTTCATTATGAACTCTCCATTG
1 TCTTCTCATTATGAACTTCTTCTCCCTCTATCGGATGAGTTCTTTTCATTATGAACTCTCCATTG
1034969 AAAATATTGATGCGAAGTTGAACAAGT
66 AAAATATTGATGCGAAGTTGAACAAGT
* *
1034996 TCTTCTCATTATGAACTTCTTCTCTCTC-ATTGGATGAGTTCTTCTT-ATTATGAACTCTCCATT
1 TCTTCTCATTATGAACTTCTTCTCCCTCTATCGGATGAGTTCTT-TTCATTATGAACTCTCCATT
* *
1035059 GGAAATGTTGAT
65 GAAAATATTGAT
1035071 CCATCTCTTT
Statistics
Matches: 70, Mismatches: 4, Indels: 3
0.91 0.05 0.04
Matches are distributed among these distances:
91 41 0.59
92 29 0.41
ACGTcount: A:0.24, C:0.20, G:0.14, T:0.42
Consensus pattern (92 bp):
TCTTCTCATTATGAACTTCTTCTCCCTCTATCGGATGAGTTCTTTTCATTATGAACTCTCCATTG
AAAATATTGATGCGAAGTTGAACAAGT
Found at i:1035305 original size:332 final size:332
Alignment explanation
Indices: 1034699--1035668 Score: 1165
Period size: 332 Copynumber: 2.8 Consensus size: 332
1034689 CCTTTAGGAC
* * * ** * *
1034699 GAGTTCTTCTCATTATGAACTCTTCA-GGAAATGTTGGTTCACCTCCATCTGTGGTGAATTTGAA
1 GAGTTCTTCTCATTATGAACTCTTCATGGAAATGTTGATCCATCTCTTTCTGTGATGAACTTGAA
* * *
1034763 AGGAATAAGTTCTTCTCATTATGAACTTTCTCTTTTATGATGAGTTCTTCTCATTATGAACTCTT
66 AGGAACAAGTTCTTCTCATTATGAACTTTCTCCTTTAGGATGAGTTCTTCTCATTATGAACTCTT
* * ** * *
1034828 CATTGGAAATGTCGATCCCTCAAGCGAGGCATCATTGATTCGAAATGTCGTGAATCAAGTGATAG
131 CA-TGGAAATATCGATCCCTCAAGCAAGGTGTCACTGATTCGAAATGTCGTGAATCGAGTGATAG
* * * *
1034893 GTCAAAAAAACTCTTCTCATTATGAACTTCTTCTCCCTCTATCGGATGAGTTCTTTTCATTATGA
195 GTCGAACAAGCTCTTCTCATTATGAACTTCTTCTCCCTCTATCGGATGAGTTCTTCTCATTATGA
1034958 ACTCTCCATTGAAAATATTGATGCGAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTC-TCTC
260 ACTCTCCATTGAAAATATTGATGCGAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTC-C
1035022 TCATTGGAT
324 TCATTGGAT
* * *
1035031 GAGTTCTTCTTATTATGAACTCTCCATTGGAAATGTTGATCCATCTCTTTCTGTGATGGACTTGA
1 GAGTTCTTCTCATTATGAACTCTTCA-TGGAAATGTTGATCCATCTCTTTCTGTGATGAACTTGA
1035096 AAGGAACAAGTTCTTCTCATTATGAACTTTCTCCTTTAGGATGAGTTCTTCTCATTATGAACTCT
65 AAGGAACAAGTTCTTCTCATTATGAACTTTCTCCTTTAGGATGAGTTCTTCTCATTATGAACTCT
* * * * *
1035161 TC-TGAAAATATCAATCCCTCAAGCTAGGTGTCACTAATTCGAAATGTCATGAATCGAGTGATAG
130 TCATGGAAATATCGATCCCTCAAGCAAGGTGTCACTGATTCGAAATGTCGTGAATCGAGTGATAG
* *
1035225 GTCGAACAAGCTCTTCTCATTATGAACTTCTTCTCCCTCTTTCGGACGAGTTCTTCTCATTATGA
195 GTCGAACAAGCTCTTCTCATTATGAACTTCTTCTCCCTCTATCGGATGAGTTCTTCTCATTATGA
* * *
1035290 GCCCTCCATTGAAAATGTTGATGCGAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCT
260 ACTCTCCATTGAAAATATTGATGCGAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCT
* *
1035355 CGTTTGAT
325 CATTGGAT
* *
1035363 GAGTTCTTCTCATTATGAACTCTTTACTGGAAATGTTGATCCCTCAAGCGAGGTGTCACTGATTC
1 GAGTTCTTCTCATTATGAACTCTTCA-TGGAAATGTTGA----TC---C-A----TCTCT--TTC
* * * *
1035428 GAAATGTTATGAATCGAGTGATAGGTCGAACAAGCTCTTCTCATTATGAACTTCTTCTCCCTCTG
51 ----TGTGATGAA-C--TTGA-AAG--GAACAAGTTCTTCTCATTATGAAC-T-TTCT-CCT-T-
* * *
1035493 TCGGATGAGTTCTTCTCATTATGAACTCTCCATTGGAAATA-CTGATCCTTCAAGCAAGGTGTCA
101 TAGGATGAGTTCTTCTCATTATGAACTCTTCA-TGGAAATATC-GATCCCTCAAGCAAGGTGTCA
*
1035557 CTGATTCAAAATGTCGTGAATCGAGTGATAGGTCGAACAAGCTCTTCTCATTATGAACTTCTTCT
164 CTGATTCGAAATGTCGTGAATCGAGTGATAGGTCGAACAAGCTCTTCTCATTATGAACTTCTTCT
* * *
1035622 CCCTCTGTCGGATGAGTTCTTCTTATTATGAACTCTCCATTGGAAAT
229 CCCTCTATCGGATGAGTTCTTCTCATTATGAACTCTCCATTGAAAAT
1035669 GCTGGTTCAC
Statistics
Matches: 544, Mismatches: 59, Indels: 39
0.85 0.09 0.06
Matches are distributed among these distances:
332 235 0.43
333 2 0.00
334 93 0.17
336 2 0.00
339 1 0.00
340 1 0.00
344 4 0.01
346 3 0.01
350 7 0.01
351 1 0.00
353 3 0.01
354 2 0.00
356 23 0.04
357 1 0.00
358 4 0.01
359 3 0.01
360 1 0.00
361 29 0.05
362 1 0.00
363 128 0.24
ACGTcount: A:0.26, C:0.21, G:0.17, T:0.37
Consensus pattern (332 bp):
GAGTTCTTCTCATTATGAACTCTTCATGGAAATGTTGATCCATCTCTTTCTGTGATGAACTTGAA
AGGAACAAGTTCTTCTCATTATGAACTTTCTCCTTTAGGATGAGTTCTTCTCATTATGAACTCTT
CATGGAAATATCGATCCCTCAAGCAAGGTGTCACTGATTCGAAATGTCGTGAATCGAGTGATAGG
TCGAACAAGCTCTTCTCATTATGAACTTCTTCTCCCTCTATCGGATGAGTTCTTCTCATTATGAA
CTCTCCATTGAAAATATTGATGCGAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTC
ATTGGAT
Found at i:1035488 original size:227 final size:221
Alignment explanation
Indices: 1035099--1035532 Score: 681
Period size: 227 Copynumber: 1.9 Consensus size: 221
1035089 GACTTGAAAG
1035099 GAACAAGTTCTTCTCATTATGAACTTTCTCCTTTAGGATGAGTTCTTCTCATTATGAACTCTTCT
1 GAACAAGTTCTTCTCATTATGAACTTTCTCCTTTAGGATGAGTTCTTCTCATTATGAACTCTTCT
*
1035164 GAAAATATCAATCCCTCAAGCTAGGTGTCACTAATTCGAAATGTCATGAATCGAGTGATAGGTCG
66 GAAAATATCAATCCCTCAAGCGAGGTGTCACTAATTCGAAATGTCATGAATCGAGTGATAGGTCG
* *
1035229 AACAAGCTCTTCTCATTATGAACTTCTTCTCCCTCTTTCGGACGAGTTCTTCTCATTATGAGCCC
131 AACAAGCTCTTCTCATTATGAACTTCTTCTCCCTCTGTCGGACGAGTTCTTCTCATTATGAACCC
1035294 TCCATTGAAAATGTTGATGCGAAGTT
196 TCCATTGAAAATGTTGATGCGAAGTT
*
1035320 GAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCGTT-TGATGAGTTCTTCTCATTATGAACT
1 GAACAAGTTCTTCTCATTATGAAC-T-TTC-TCCT--TTAGGATGAGTTCTTCTCATTATGAACT
* * ** * *
1035384 CTTTACTGGAAATGTTGATCCCTCAAGCGAGGTGTCACTGATTCGAAATGTTATGAATCGAGTGA
61 C-TT-CTGAAAATATCAATCCCTCAAGCGAGGTGTCACTAATTCGAAATGTCATGAATCGAGTGA
*
1035449 TAGGTCGAACAAGCTCTTCTCATTATGAACTTCTTCTCCCTCTGTCGGATGAGTTCTTCTCATTA
124 TAGGTCGAACAAGCTCTTCTCATTATGAACTTCTTCTCCCTCTGTCGGACGAGTTCTTCTCATTA
* *
1035514 TGAACTCTCCATTGGAAAT
189 TGAACCCTCCATTGAAAAT
1035533 ACTGATCCTT
Statistics
Matches: 193, Mismatches: 13, Indels: 8
0.90 0.06 0.04
Matches are distributed among these distances:
221 24 0.12
222 1 0.01
223 3 0.02
224 4 0.02
225 25 0.13
226 4 0.02
227 132 0.68
ACGTcount: A:0.25, C:0.22, G:0.17, T:0.36
Consensus pattern (221 bp):
GAACAAGTTCTTCTCATTATGAACTTTCTCCTTTAGGATGAGTTCTTCTCATTATGAACTCTTCT
GAAAATATCAATCCCTCAAGCGAGGTGTCACTAATTCGAAATGTCATGAATCGAGTGATAGGTCG
AACAAGCTCTTCTCATTATGAACTTCTTCTCCCTCTGTCGGACGAGTTCTTCTCATTATGAACCC
TCCATTGAAAATGTTGATGCGAAGTT
Found at i:1035563 original size:136 final size:136
Alignment explanation
Indices: 1035320--1035668 Score: 556
Period size: 136 Copynumber: 2.6 Consensus size: 136
1035310 ATGCGAAGTT
* * **
1035320 GAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTC-GTTTGATGAGTTCTTCTCATTATGAACT
1 GAACAAGCTCTTCTCATTATGAACTTCTTCTCCCTCTGTCGGATGAGTTCTTCTCATTATGAACT
** * ** * * *
1035384 CTTTACTGGAAATGTTGATCCCTCAAGCGAGGTGTCACTGATTCGAAATGTTATGAATCGAGTGA
66 CTCCATTGGAAATACTGATCCCTCAAGCAAGGTGTCACTGATTCAAAATGTCATGAATCGAGTGA
1035449 TAGGTC
131 TAGGTC
1035455 GAACAAGCTCTTCTCATTATGAACTTCTTCTCCCTCTGTCGGATGAGTTCTTCTCATTATGAACT
1 GAACAAGCTCTTCTCATTATGAACTTCTTCTCCCTCTGTCGGATGAGTTCTTCTCATTATGAACT
* *
1035520 CTCCATTGGAAATACTGATCCTTCAAGCAAGGTGTCACTGATTCAAAATGTCGTGAATCGAGTGA
66 CTCCATTGGAAATACTGATCCCTCAAGCAAGGTGTCACTGATTCAAAATGTCATGAATCGAGTGA
1035585 TAGGTC
131 TAGGTC
*
1035591 GAACAAGCTCTTCTCATTATGAACTTCTTCTCCCTCTGTCGGATGAGTTCTTCTTATTATGAACT
1 GAACAAGCTCTTCTCATTATGAACTTCTTCTCCCTCTGTCGGATGAGTTCTTCTCATTATGAACT
1035656 CTCCATTGGAAAT
66 CTCCATTGGAAAT
1035669 GCTGGTTCAC
Statistics
Matches: 198, Mismatches: 15, Indels: 1
0.93 0.07 0.00
Matches are distributed among these distances:
135 34 0.17
136 164 0.83
ACGTcount: A:0.25, C:0.22, G:0.18, T:0.36
Consensus pattern (136 bp):
GAACAAGCTCTTCTCATTATGAACTTCTTCTCCCTCTGTCGGATGAGTTCTTCTCATTATGAACT
CTCCATTGGAAATACTGATCCCTCAAGCAAGGTGTCACTGATTCAAAATGTCATGAATCGAGTGA
TAGGTC
Found at i:1036556 original size:25 final size:25
Alignment explanation
Indices: 1036528--1036597 Score: 74
Period size: 25 Copynumber: 2.8 Consensus size: 25
1036518 AAACCCTCCT
1036528 TTTTCTCTTTTT-ATTTTTTCATTT-C
1 TTTTCTCTTTTTCATTTTTT--TTTCC
*
1036553 TTTTTTCATTTTTCATTTTTTTTTCC
1 TTTTCTC-TTTTTCATTTTTTTTTCC
1036579 TTTTCAT-TTTTTCATTTTT
1 TTTTC-TCTTTTTCATTTTT
1036598 CATCTTTTTA
Statistics
Matches: 39, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
25 21 0.54
26 10 0.26
27 8 0.21
ACGTcount: A:0.09, C:0.14, G:0.00, T:0.77
Consensus pattern (25 bp):
TTTTCTCTTTTTCATTTTTTTTTCC
Found at i:1036564 original size:19 final size:19
Alignment explanation
Indices: 1036529--1036587 Score: 70
Period size: 19 Copynumber: 3.2 Consensus size: 19
1036519 AACCCTCCTT
1036529 TTTCTCTTTTT-ATTTTTTCA
1 TTTCT-TTTTTCA-TTTTTCA
1036549 TTTCTTTTTTCATTTTTCA
1 TTTCTTTTTTCATTTTTCA
*
1036568 TTT-TTTTTTC-CTTTTCA
1 TTTCTTTTTTCATTTTTCA
1036585 TTT
1 TTT
1036588 TTTCATTTTT
Statistics
Matches: 37, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
17 9 0.24
18 7 0.19
19 15 0.41
20 6 0.16
ACGTcount: A:0.08, C:0.15, G:0.00, T:0.76
Consensus pattern (19 bp):
TTTCTTTTTTCATTTTTCA
Found at i:1036590 original size:19 final size:19
Alignment explanation
Indices: 1036543--1036590 Score: 64
Period size: 18 Copynumber: 2.6 Consensus size: 19
1036533 TCTTTTTATT
* *
1036543 TTTTCATTTCTTTTTTCAT
1 TTTTCATTTTTTTTTTCAC
1036562 TTTTCA-TTTTTTTTTC-C
1 TTTTCATTTTTTTTTTCAC
1036579 TTTTCATTTTTT
1 TTTTCATTTTTT
1036591 CATTTTTCAT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
17 6 0.23
18 14 0.54
19 6 0.23
ACGTcount: A:0.08, C:0.15, G:0.00, T:0.77
Consensus pattern (19 bp):
TTTTCATTTTTTTTTTCAC
Found at i:1036594 original size:32 final size:30
Alignment explanation
Indices: 1036541--1036606 Score: 96
Period size: 32 Copynumber: 2.1 Consensus size: 30
1036531 TCTCTTTTTA
*
1036541 TTTTTTCATTTCTTTTTTCATTTTTCATTT
1 TTTTTTCATTTCTTTTTTCATTTTTCATCT
*
1036571 TTTTTTCCTTTTCATTTTTTCATTTTTCATCT
1 TTTTTT-CATTTC-TTTTTTCATTTTTCATCT
1036603 TTTT
1 TTTT
1036607 ATTTGTTCCC
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
30 6 0.19
31 5 0.16
32 21 0.66
ACGTcount: A:0.09, C:0.15, G:0.00, T:0.76
Consensus pattern (30 bp):
TTTTTTCATTTCTTTTTTCATTTTTCATCT
Found at i:1036606 original size:24 final size:25
Alignment explanation
Indices: 1036533--1036610 Score: 66
Period size: 24 Copynumber: 3.5 Consensus size: 25
1036523 CTCCTTTTTC
1036533 TCTTTTT-ATTTTTTCA---TTTC-
1 TCTTTTTCATTTTTTCATTTTTTCA
**
1036553 T-TTTTTCA-TTTTTCATTTTTTTT
1 TCTTTTTCATTTTTTCATTTTTTCA
*
1036576 TCCTTTTCATTTTTTCA-TTTTTCA
1 TCTTTTTCATTTTTTCATTTTTTCA
1036600 TCTTTTT-ATTT
1 TCTTTTTCATTT
1036611 GTTCCCTTTT
Statistics
Matches: 46, Mismatches: 5, Indels: 11
0.74 0.08 0.18
Matches are distributed among these distances:
19 12 0.26
20 2 0.04
22 3 0.07
23 5 0.11
24 17 0.37
25 7 0.15
ACGTcount: A:0.10, C:0.14, G:0.00, T:0.76
Consensus pattern (25 bp):
TCTTTTTCATTTTTTCATTTTTTCA
Found at i:1036621 original size:32 final size:31
Alignment explanation
Indices: 1036552--1036622 Score: 81
Period size: 32 Copynumber: 2.2 Consensus size: 31
1036542 TTTTTCATTT
* *
1036552 CTTTTTTCATTTTTCATTTTTTTTTCCTTTTC
1 CTTTTTTCATTTTTCATTTTTTTTT-CGTTCC
*
1036584 ATTTTTTCATTTTTCATCTTTTTATTT-GTTCC
1 CTTTTTTCATTTTTCAT-TTTTT-TTTCGTTCC
1036616 CTTTTTT
1 CTTTTTT
1036623 TTCTTCAAGC
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
32 25 0.76
33 5 0.15
34 3 0.09
ACGTcount: A:0.08, C:0.17, G:0.01, T:0.73
Consensus pattern (31 bp):
CTTTTTTCATTTTTCATTTTTTTTTCGTTCC
Found at i:1036627 original size:24 final size:23
Alignment explanation
Indices: 1036555--1036627 Score: 67
Period size: 24 Copynumber: 3.1 Consensus size: 23
1036545 TTCATTTCTT
1036555 TTTTCATTTTT-CATTTTTTTTTCC
1 TTTTCATTTTTCCA-TTTTTTTT-C
* **
1036579 TTTTCATTTTTTCATTTTTCATC
1 TTTTCATTTTTCCATTTTTTTTC
* *
1036602 TTTTTATTTGTTCCCTTTTTTTTC
1 TTTTCATTT-TTCCATTTTTTTTC
1036626 TT
1 TT
1036628 CAAGCATAGT
Statistics
Matches: 40, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
23 9 0.22
24 29 0.73
25 2 0.05
ACGTcount: A:0.08, C:0.16, G:0.01, T:0.74
Consensus pattern (23 bp):
TTTTCATTTTTCCATTTTTTTTC
Found at i:1052958 original size:34 final size:34
Alignment explanation
Indices: 1052920--1053002 Score: 166
Period size: 34 Copynumber: 2.4 Consensus size: 34
1052910 CTCTATTAAG
1052920 AAAATGAAATTATTTTTTTAAAAAGACAAAAAGA
1 AAAATGAAATTATTTTTTTAAAAAGACAAAAAGA
1052954 AAAATGAAATTATTTTTTTAAAAAGACAAAAAGA
1 AAAATGAAATTATTTTTTTAAAAAGACAAAAAGA
1052988 AAAATGAAATTATTT
1 AAAATGAAATTATTT
1053003 CCCAATCCCT
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 49 1.00
ACGTcount: A:0.58, C:0.02, G:0.08, T:0.31
Consensus pattern (34 bp):
AAAATGAAATTATTTTTTTAAAAAGACAAAAAGA
Found at i:1053815 original size:109 final size:109
Alignment explanation
Indices: 1053516--1053817 Score: 276
Period size: 108 Copynumber: 2.8 Consensus size: 109
1053506 TTTCAGATTA
* * * *
1053516 CAACCGAAACTGTTACCACAACTTATAAGATTTTCCACTCCCAA-TCTAATTTGTTACCATCGAT
1 CAACC-AAATTGTTACCACAA-ATATAACATTTTCCGCTCCCAACT-TAATTTGTTACCATCGAT
** * * * * *
1053580 ATTTTGAT-AGACCCAATTT-TCGTTACACGGTAATATTTTTCGGGTG
63 ATTAAGTTGA-ACCCAATTTATCGCTACAAGGTAACATTTTTCAGGTG
* * * * * * *
1053626 CAATCGAATCTGTTACCACAAA-ATAACAATTTT-CGCTTCTAACCTAATTTGTTACCTTCTATA
1 CAACCAAAT-TGTTACCACAAATATAAC-ATTTTCCGCTCCCAACTTAATTTGTTACCATCGATA
* * * *
1053689 TTAATTTGGATCAAATTTAT-GCTACAAGGTAACATTTTT-AGGTG
64 TTAAGTTGAACCCAATTTATCGCTACAAGGTAACATTTTTCAGGTG
*
1053733 CAACCAAAATTGTTACCATAAAGTATAACATTTTCCGCTCCCAACTTAATTTGTTACCATCGATA
1 CAACC-AAATTGTTACCACAAA-TATAACATTTTCCGCTCCCAACTTAATTTGTTACCATCGATA
1053798 TTAAGTTGAACCCAATTTAT
64 TTAAGTTGAACCCAATTTAT
1053818 TAACTCGAAT
Statistics
Matches: 149, Mismatches: 34, Indels: 19
0.74 0.17 0.09
Matches are distributed among these distances:
107 19 0.13
108 61 0.41
109 54 0.36
110 15 0.10
ACGTcount: A:0.32, C:0.21, G:0.11, T:0.36
Consensus pattern (109 bp):
CAACCAAATTGTTACCACAAATATAACATTTTCCGCTCCCAACTTAATTTGTTACCATCGATATT
AAGTTGAACCCAATTTATCGCTACAAGGTAACATTTTTCAGGTG
Found at i:1055618 original size:18 final size:19
Alignment explanation
Indices: 1055584--1055619 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
1055574 TAAATGGTGC
*
1055584 CTGGACATTTGAAACAAAA
1 CTGGAAATTTGAAACAAAA
1055603 CTGGAAATTT-AAACAAA
1 CTGGAAATTTGAAACAAA
1055620 TAAGGAACCG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.50, C:0.14, G:0.14, T:0.22
Consensus pattern (19 bp):
CTGGAAATTTGAAACAAAA
Found at i:1056890 original size:44 final size:44
Alignment explanation
Indices: 1056827--1057063 Score: 181
Period size: 44 Copynumber: 5.3 Consensus size: 44
1056817 TAAAAATGTC
*
1056827 GATCCACCTCCTTCTGTGATGGAATCGAACGATATGTCGATGCT
1 GATCCACCTCCTTCTGTGATGGAATCGAACGAAATGTCGATGCT
* * * * * *
1056871 GATCTACCTCCTTCTGTGATAGAATCGAGCAAAAAGTTGACT-CT
1 GATCCACCTCCTTCTGTGATGGAATCGAACGAAATGTCGA-TGCT
* * * * * ****
1056915 GATCCAACTCCTTCTGCGATGGATTTGAGCGAAAATAAAAATG-T
1 GATCCACCTCCTTCTGTGATGGAATCGAACG-AAATGTCGATGCT
* *
1056959 CGATCCACCTCCTTTTGTGATGGAAATCGAACGATATGTCGATGCT
1 -GATCCACCTCCTTCTGTGATGG-AATCGAACGAAATGTCGATGCT
* * * * * * * *
1057005 AATCTACCTCCTTCTGTGATAGAATCGAGCAAAAAGTTGACGCT
1 GATCCACCTCCTTCTGTGATGGAATCGAACGAAATGTCGATGCT
*
1057049 GATCCAACTCCTTCT
1 GATCCACCTCCTTCT
1057064 CCTTCCGTGA
Statistics
Matches: 144, Mismatches: 43, Indels: 12
0.72 0.22 0.06
Matches are distributed among these distances:
44 89 0.62
45 48 0.33
46 7 0.05
ACGTcount: A:0.28, C:0.24, G:0.19, T:0.29
Consensus pattern (44 bp):
GATCCACCTCCTTCTGTGATGGAATCGAACGAAATGTCGATGCT
Found at i:1056953 original size:133 final size:134
Alignment explanation
Indices: 1056745--1057063 Score: 543
Period size: 133 Copynumber: 2.4 Consensus size: 134
1056735 CCAACTCCTT
* * * *
1056745 CTCCTTCTGTGATGGAATCGAGCTAAAAGTTGGA-ACTGATCCAAATCCTTCTGTGATGGATTTG
1 CTCCTTCTGTGATAGAATCGAGCAAAAAGTT-GACACTGATCCAACTCCTTCTGCGATGGATTTG
*
1056809 AGCGAAAATAAAAATGTCGATCCACCTCCTTCTGTGATGG-AATCGAACGATATGTCGATGCTGA
65 AGCGAAAATAAAAATGTCGATCCACCTCCTTCTGTGATGGAAATCGAACGATATGTCGATGCTAA
1056873 TCTAC
130 TCTAC
*
1056878 CTCCTTCTGTGATAGAATCGAGCAAAAAGTTGACTCTGATCCAACTCCTTCTGCGATGGATTTGA
1 CTCCTTCTGTGATAGAATCGAGCAAAAAGTTGACACTGATCCAACTCCTTCTGCGATGGATTTGA
*
1056943 GCGAAAATAAAAATGTCGATCCACCTCCTTTTGTGATGGAAATCGAACGATATGTCGATGCTAAT
66 GCGAAAATAAAAATGTCGATCCACCTCCTTCTGTGATGGAAATCGAACGATATGTCGATGCTAAT
1057008 CTAC
131 CTAC
*
1057012 CTCCTTCTGTGATAGAATCGAGCAAAAAGTTGACGCTGATCCAACTCCTTCT
1 CTCCTTCTGTGATAGAATCGAGCAAAAAGTTGACACTGATCCAACTCCTTCT
1057064 CCTTCCGTGA
Statistics
Matches: 176, Mismatches: 8, Indels: 3
0.94 0.04 0.02
Matches are distributed among these distances:
132 2 0.01
133 95 0.54
134 79 0.45
ACGTcount: A:0.29, C:0.22, G:0.20, T:0.29
Consensus pattern (134 bp):
CTCCTTCTGTGATAGAATCGAGCAAAAAGTTGACACTGATCCAACTCCTTCTGCGATGGATTTGA
GCGAAAATAAAAATGTCGATCCACCTCCTTCTGTGATGGAAATCGAACGATATGTCGATGCTAAT
CTAC
Found at i:1057496 original size:39 final size:39
Alignment explanation
Indices: 1057452--1057942 Score: 802
Period size: 39 Copynumber: 12.6 Consensus size: 39
1057442 AAGAAAAATG
* *
1057452 TCTCAAGTGAGACAAAATTTTCTGTTTCGAGGGAAACTA
1 TCTCAAGCGAGACAAAATCTTCTGTTTCGAGGGAAACTA
* * *
1057491 TCTCAAGTGACACAAAATCTTCTGTTTTGAGGGAAACTA
1 TCTCAAGCGAGACAAAATCTTCTGTTTCGAGGGAAACTA
*
1057530 TCTCAAGCGAGATAAAATCTTCTGTTTCGAGGGAAACTA
1 TCTCAAGCGAGACAAAATCTTCTGTTTCGAGGGAAACTA
*
1057569 TCTCAAGCGAGATAAAATCTTCTGTTTCGAGGGAAACTA
1 TCTCAAGCGAGACAAAATCTTCTGTTTCGAGGGAAACTA
*
1057608 TCTCAAGTGAGACAAAATCTTCTGTTTCGAGGGAAACTA
1 TCTCAAGCGAGACAAAATCTTCTGTTTCGAGGGAAACTA
*
1057647 TCTCAAGCAAGACAAAATCTTCTGTTTCGAGGGAAACTA
1 TCTCAAGCGAGACAAAATCTTCTGTTTCGAGGGAAACTA
* *
1057686 TCTCAAGCGAGACAAAAACTTCTGTTTCGAGGGAAACAA
1 TCTCAAGCGAGACAAAATCTTCTGTTTCGAGGGAAACTA
* *
1057725 TCTCAAGCGAGATAAAATCTTCTGTTTCGAGGGAAATTA
1 TCTCAAGCGAGACAAAATCTTCTGTTTCGAGGGAAACTA
1057764 TCTCAAGCGAGACAAAATCTTCTGTTTCGAGGGAAACTA
1 TCTCAAGCGAGACAAAATCTTCTGTTTCGAGGGAAACTA
* *
1057803 TCTCAAGCGAGATAAAATCTTCTGTTTCGAGGAAAACTA
1 TCTCAAGCGAGACAAAATCTTCTGTTTCGAGGGAAACTA
*
1057842 TCTCAAGCGAGATAAAATCTTCTGTTTCGAGGGAAACTA
1 TCTCAAGCGAGACAAAATCTTCTGTTTCGAGGGAAACTA
* * *
1057881 TCTCAAGTGAGACAAAATCTTATGTTTCAAGGGAAACTA
1 TCTCAAGCGAGACAAAATCTTCTGTTTCGAGGGAAACTA
*
1057920 TCTCAAGCGAGATAAAATCTTCT
1 TCTCAAGCGAGACAAAATCTTCT
1057943 TTAAAAAAAT
Statistics
Matches: 422, Mismatches: 30, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
39 422 1.00
ACGTcount: A:0.35, C:0.18, G:0.19, T:0.28
Consensus pattern (39 bp):
TCTCAAGCGAGACAAAATCTTCTGTTTCGAGGGAAACTA
Found at i:1057872 original size:20 final size:20
Alignment explanation
Indices: 1057810--1057872 Score: 58
Period size: 20 Copynumber: 3.2 Consensus size: 20
1057800 CTATCTCAAG
1057810 CGAGATAAAATCTTCTGTTT
1 CGAGATAAAATCTTCTGTTT
* ****
1057830 CGAG-GAAAA-CTATCTCAAG
1 CGAGATAAAATCT-TCTGTTT
1057849 CGAGATAAAATCTTCTGTTT
1 CGAGATAAAATCTTCTGTTT
1057869 CGAG
1 CGAG
1057873 GGAAACTATC
Statistics
Matches: 30, Mismatches: 10, Indels: 6
0.65 0.22 0.13
Matches are distributed among these distances:
18 2 0.07
19 11 0.37
20 15 0.50
21 2 0.07
ACGTcount: A:0.33, C:0.17, G:0.19, T:0.30
Consensus pattern (20 bp):
CGAGATAAAATCTTCTGTTT
Found at i:1062767 original size:18 final size:18
Alignment explanation
Indices: 1062725--1062767 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
1062715 AAAAACTGGG
*
1062725 TGATTTTAATAAAATATT
1 TGATTTTAATAAAATATC
*
1062743 TTATTTTAATAAAATA-C
1 TGATTTTAATAAAATATC
1062760 TGAGTTTT
1 TGA-TTTT
1062768 GGGGTCTACG
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
17 2 0.10
18 19 0.90
ACGTcount: A:0.40, C:0.02, G:0.07, T:0.51
Consensus pattern (18 bp):
TGATTTTAATAAAATATC
Found at i:1065134 original size:44 final size:44
Alignment explanation
Indices: 1064821--1065588 Score: 140
Period size: 44 Copynumber: 17.3 Consensus size: 44
1064811 GCACGGAAGG
* * * * *
1064821 AGAAGGAGTTGGATCAGTGTCAACTTT-TAGCTTGATTCTACCAC
1 AGAAGGAGGTGGATCAGCGTCAA-TTTATTGCTCGATTCTATCAC
* * * * ** * * *
1064865 AGAAGGAGGTAGATCATCATCGACATATCGTTCGATTTTATCAC
1 AGAAGGAGGTGGATCAGCGTCAATTTATTGCTCGATTCTATCAC
* * * * * *
1064909 AGAAGGAGGTGGAT---CGACATTTTTATCTTCGCTCAAATCCATCGC
1 AGAAGGAGGTGGATCAGCGTCA-ATTTA--TT-GCTCGATTCTATCAC
* * * *
1064954 AGAAAGAGTTGGATCAGCGTCAACTTT-TTACTTGATTCTATCAC
1 AGAAGGAGGTGGATCAGCGTCAA-TTTATTGCTCGATTCTATCAC
* * * ** * * *
1064998 AGAAGGAGGTTGATCAGCATCGACATATCGTTCGATTTCCATCAC
1 AGAAGGAGGTGGATCAGCGTCAATTTATTGCTCGA-TTCTATCAC
* * * * * * *
1065043 AGAAGGTGGTGGAT---CGACATTTTTATTTCGCTCAAATCCATCGC
1 AGAAGGAGGTGGATCAGCGTCA-ATTTA-TT-GCTCGATTCTATCAC
*
1065087 AGAAGGAGTTGGATCAGCGTCAATTTATTGCTCGATTCTATCAC
1 AGAAGGAGGTGGATCAGCGTCAATTTATTGCTCGATTCTATCAC
* * * * ** * * * * *
1065131 AGAATGAGGTAGATCAGCATCGACATCTCGTTCGATTCCATCAA
1 AGAAGGAGGTGGATCAGCGTCAATTTATTGCTCGATTCTATCAC
* * * * ** * *
1065175 AAAAGAAGGTGGATC-G-AT-ATTTTTATTTCGCTC-AAGCCATCGC
1 AGAAGGAGGTGGATCAGCGTCA-ATTTA-TT-GCTCGATTCTATCAC
* * ** * *
1065218 GGAAAGATTTGAATCAGCGTCAATTTTTTGCTCGATTCTATCAC
1 AGAAGGAGGTGGATCAGCGTCAATTTATTGCTCGATTCTATCAC
* * * ** * * * *
1065262 AGAAGGAGGTAGATCAGCATCGACATCTCGTTCGATTTCCATCAC
1 AGAAGGAGGTGGATCAGCGTCAATTTATTGCTCGA-TTCTATCAC
* * ** * * *
1065307 AGAAGGAGGTGGAT---CGACATTTTTATTTTAGCTTAAATCCATCGC
1 AGAAGGAGGTGGATCAGCGTCA-ATTTA--TT-GCTCGATTCTATCAC
* * * *
1065352 AGAAGGAGTTGGATTAGCGTTAACTTT-TTGCTCGTTTCTATCAC
1 AGAAGGAGGTGGATCAGCGTCAA-TTTATTGCTCGATTCTATCAC
* * * ** * ** *
1065396 AGAATGAGGTAGATCAACACCAACATT-TCACTCGATTCCATCAC
1 AGAAGGAGGTGGATCAGCGTCAA-TTTATTGCTCGATTCTATCAC
* ** * * * *
1065440 AGAAGGAGGTGGATC-GACTTTTTTATTTTTTGCTCAAATCCATCAC
1 AGAAGGAGGTGGATCAG-C--GTCAATTTATTGCTCGATTCTATCAC
* * *
1065486 AGAAGGAGTTGGATCAGCATCAACTTT-TTGCTC-ATTTCTATGAC
1 AGAAGGAGGTGGATCAGCGTCAA-TTTATTGCTCGA-TTCTATCAC
* * * ** * *
1065530 AAAAGGAGATAGATCAGCACCAACATT-TCGCTCGATT-TCATCAC
1 AGAAGGAGGTGGATCAGCGTCAA-TTTATTGCTCGATTCT-ATCAC
1065574 AGAAGGAGGTGGATC
1 AGAAGGAGGTGGATC
1065589 GACATTTTTA
Statistics
Matches: 491, Mismatches: 191, Indels: 84
0.64 0.25 0.11
Matches are distributed among these distances:
41 2 0.00
42 9 0.02
43 27 0.05
44 295 0.60
45 103 0.21
46 37 0.08
47 5 0.01
48 13 0.03
ACGTcount: A:0.29, C:0.20, G:0.21, T:0.30
Consensus pattern (44 bp):
AGAAGGAGGTGGATCAGCGTCAATTTATTGCTCGATTCTATCAC
Found at i:1065396 original size:134 final size:134
Alignment explanation
Indices: 1064821--1065662 Score: 1112
Period size: 133 Copynumber: 6.3 Consensus size: 134
1064811 GCACGGAAGG
* * * * *
1064821 AGAAGGAGTTGGATCAGTGTCAACTTTTAGCTTGATTCTACCACAGAAGGAGGTAGATCATCATC
1 AGAAGGAGTTGGATCAGCGTCAACTTTTTGCTCGATTCTATCACAGAAGGAGGTAGATCAGCATC
* *
1064886 GACATATCGTTCGATTT-TATCACAGAAGGAGGTGGATCGACATTTTTATCTTCGCTCAAATCCA
66 GACATATCGTTCGATTTCCATCACAGAAGGAGGTGGATCGACATTTTTATTTTCGCTCAAATCCA
1064950 TCGC
131 TCGC
* * * *
1064954 AGAAAGAGTTGGATCAGCGTCAACTTTTTACTTGATTCTATCACAGAAGGAGGTTGATCAGCATC
1 AGAAGGAGTTGGATCAGCGTCAACTTTTTGCTCGATTCTATCACAGAAGGAGGTAGATCAGCATC
*
1065019 GACATATCGTTCGATTTCCATCACAGAAGGTGGTGGATCGACATTTTTA-TTTCGCTCAAATCCA
66 GACATATCGTTCGATTTCCATCACAGAAGGAGGTGGATCGACATTTTTATTTTCGCTCAAATCCA
1065083 TCGC
131 TCGC
*
1065087 AGAAGGAGTTGGATCAGCGTCAA-TTTATTGCTCGATTCTATCACAGAATGAGGTAGATCAGCAT
1 AGAAGGAGTTGGATCAGCGTCAACTTT-TTGCTCGATTCTATCACAGAAGGAGGTAGATCAGCAT
* * * * * *
1065151 CGACATCTCGTTCGA-TTCCATCAAAAAAGAAGGTGGATCGATATTTTTA-TTTCGCTC-AAGCC
65 CGACATATCGTTCGATTTCCATCACAGAAGGAGGTGGATCGACATTTTTATTTTCGCTCAAATCC
1065213 ATCGC
130 ATCGC
* * * * *
1065218 GGAAAGATTTGAATCAGCGTCAATTTTTTGCTCGATTCTATCACAGAAGGAGGTAGATCAGCATC
1 AGAAGGAGTTGGATCAGCGTCAACTTTTTGCTCGATTCTATCACAGAAGGAGGTAGATCAGCATC
* * *
1065283 GACATCTCGTTCGATTTCCATCACAGAAGGAGGTGGATCGACATTTTTATTTTAGCTTAAATCCA
66 GACATATCGTTCGATTTCCATCACAGAAGGAGGTGGATCGACATTTTTATTTTCGCTCAAATCCA
1065348 TCGC
131 TCGC
* * * * * *
1065352 AGAAGGAGTTGGATTAGCGTTAACTTTTTGCTCGTTTCTATCACAGAATGAGGTAGATCAACACC
1 AGAAGGAGTTGGATCAGCGTCAACTTTTTGCTCGATTCTATCACAGAAGGAGGTAGATCAGCATC
* * ** * *
1065417 AACATTTCACTCGA-TTCCATCACAGAAGGAGGTGGATCGACTTTTTTATTTTTTGCTCAAATCC
66 GACATATCGTTCGATTTCCATCACAGAAGGAGGTGGATCGACATTTTTA-TTTTCGCTCAAATCC
*
1065481 ATCAC
130 ATCGC
* * * * *
1065486 AGAAGGAGTTGGATCAGCATCAACTTTTTGCTC-ATTTCTATGACAAAAGGAGATAGATCAGCAC
1 AGAAGGAGTTGGATCAGCGTCAACTTTTTGCTCGA-TTCTATCACAGAAGGAGGTAGATCAGCAT
* * * * *
1065550 CAACATTTCGCTCGATTT-CATCACAGAAGGAGGTGGATCGACATTTTTATTTTCACTTAAATCC
65 CGACATATCGTTCGATTTCCATCACAGAAGGAGGTGGATCGACATTTTTATTTTCGCTCAAATCC
1065614 ATCGC
130 ATCGC
*
1065619 AGAAGGAGTTGGATCAGCGTC-ATTTTCTTGCTCGATTC-ATCACA
1 AGAAGGAGTTGGATCAGCGTCAACTTT-TTGCTCGATTCTATCACA
1065663 TATGGAGTTG
Statistics
Matches: 627, Mismatches: 71, Indels: 23
0.87 0.10 0.03
Matches are distributed among these distances:
131 79 0.13
132 82 0.13
133 246 0.39
134 218 0.35
135 2 0.00
ACGTcount: A:0.29, C:0.20, G:0.21, T:0.31
Consensus pattern (134 bp):
AGAAGGAGTTGGATCAGCGTCAACTTTTTGCTCGATTCTATCACAGAAGGAGGTAGATCAGCATC
GACATATCGTTCGATTTCCATCACAGAAGGAGGTGGATCGACATTTTTATTTTCGCTCAAATCCA
TCGC
Found at i:1067315 original size:150 final size:155
Alignment explanation
Indices: 1067135--1067447 Score: 591
Period size: 150 Copynumber: 2.1 Consensus size: 155
1067125 ATTATTTTTG
1067135 TAGTTAAAGAACTAAATTTCTATTTATTATTATTTAGCCCTTTTAGTAAGAATGATCAGTTTTTT
1 TAGTTAAAGAACTAAATTTCTATTTATTATTATTTAGCCCTTTTAGTAAGAATGATCAGTTTTTT
1067200 TTAAATTTG-ACATTGAAATCTCGTGTTTA-GTTTTTAGTTAAA-TTTATTATTATTTTTAATAC
66 TTAAATTTGTACATTGAAATCTCGTGTTTATGTTTTTAGTTAAATTTTATTATTATTTTTAATAC
1067262 GCATG-ATATATAATTTGTT-ATAT
131 GCATGTATATATAATTTGTTAATAT
1067285 TAGTTAAAGAACTAAATTTCTATTTATTATTATTTAGCCCTTTTAGTAAGAATGATCAGTTTTTT
1 TAGTTAAAGAACTAAATTTCTATTTATTATTATTTAGCCCTTTTAGTAAGAATGATCAGTTTTTT
1067350 TTAAATTTGTACATTGAAATCTCGTGTTTATGTTTTTAGTTAAATTTTATTATTATTTTTAATAC
66 TTAAATTTGTACATTGAAATCTCGTGTTTATGTTTTTAGTTAAATTTTATTATTATTTTTAATAC
1067415 GCATGTATATATAATTTGTTAATAT
131 GCATGTATATATAATTTGTTAATAT
1067440 TAGTTAAA
1 TAGTTAAA
1067448 CTATATTTAT
Statistics
Matches: 158, Mismatches: 0, Indels: 5
0.97 0.00 0.03
Matches are distributed among these distances:
150 74 0.47
151 20 0.13
152 13 0.08
153 25 0.16
154 14 0.09
155 12 0.08
ACGTcount: A:0.32, C:0.07, G:0.11, T:0.50
Consensus pattern (155 bp):
TAGTTAAAGAACTAAATTTCTATTTATTATTATTTAGCCCTTTTAGTAAGAATGATCAGTTTTTT
TTAAATTTGTACATTGAAATCTCGTGTTTATGTTTTTAGTTAAATTTTATTATTATTTTTAATAC
GCATGTATATATAATTTGTTAATAT
Found at i:1068850 original size:17 final size:18
Alignment explanation
Indices: 1068818--1068851 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
1068808 AAAACTGAAA
1068818 GTTTAGATACCAAAACAC
1 GTTTAGATACCAAAACAC
*
1068836 GTTTAG-TACCTAAACA
1 GTTTAGATACCAAAACA
1068852 TACTTAAGTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.41, C:0.21, G:0.12, T:0.26
Consensus pattern (18 bp):
GTTTAGATACCAAAACAC
Found at i:1074666 original size:2 final size:2
Alignment explanation
Indices: 1074661--1074711 Score: 88
Period size: 2 Copynumber: 26.5 Consensus size: 2
1074651 TGTGTGTTTT
1074661 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1074702 TA TA TA -A TA T
1 TA TA TA TA TA T
1074712 CATGCTTTCA
Statistics
Matches: 47, Mismatches: 0, Indels: 4
0.92 0.00 0.08
Matches are distributed among these distances:
1 2 0.04
2 45 0.96
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1078014 original size:6 final size:7
Alignment explanation
Indices: 1077992--1078021 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
1077982 GTCAAAGGAA
1077992 GTCAACG
1 GTCAACG
1077999 GTCAACG
1 GTCAACG
1078006 GTC-ACG
1 GTCAACG
1078012 GTCAACG
1 GTCAACG
1078019 GTC
1 GTC
1078022 GGGTCGGGTC
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
6 6 0.27
7 16 0.73
ACGTcount: A:0.23, C:0.30, G:0.30, T:0.17
Consensus pattern (7 bp):
GTCAACG
Found at i:1078014 original size:13 final size:13
Alignment explanation
Indices: 1077996--1078021 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1077986 AAGGAAGTCA
1077996 ACGGTCAACGGTC
1 ACGGTCAACGGTC
1078009 ACGGTCAACGGTC
1 ACGGTCAACGGTC
1078022 GGGTCGGGTC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.23, C:0.31, G:0.31, T:0.15
Consensus pattern (13 bp):
ACGGTCAACGGTC
Found at i:1078109 original size:9 final size:9
Alignment explanation
Indices: 1078042--1078111 Score: 59
Period size: 9 Copynumber: 7.3 Consensus size: 9
1078032 GGTCGGGTTG
*
1078042 GGTCAGACC
1 GGTCAAACC
*
1078051 GGTCAAATC
1 GGTCAAACC
*
1078060 GGTCAAAACT
1 GGTC-AAACC
1078070 GGTCAAACC
1 GGTCAAACC
*
1078079 GGTTAGAACC
1 GGTCA-AACC
*
1078089 GGTTGAAAACC
1 GG-T-CAAACC
1078100 GGTCAAACC
1 GGTCAAACC
1078109 GGT
1 GGT
1078112 TTCCATCCCT
Statistics
Matches: 49, Mismatches: 8, Indels: 8
0.75 0.12 0.12
Matches are distributed among these distances:
9 27 0.55
10 14 0.29
11 7 0.14
12 1 0.02
ACGTcount: A:0.31, C:0.24, G:0.27, T:0.17
Consensus pattern (9 bp):
GGTCAAACC
Found at i:1078110 original size:20 final size:21
Alignment explanation
Indices: 1078074--1078112 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
1078064 AAAACTGGTC
*
1078074 AAACCGGTTAGAACCGGTTGA
1 AAACCGGTCAGAACCGGTTGA
1078095 AAACCGGTCA-AACCGGTT
1 AAACCGGTCAGAACCGGTT
1078113 TCCATCCCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.33, C:0.23, G:0.26, T:0.18
Consensus pattern (21 bp):
AAACCGGTCAGAACCGGTTGA
Found at i:1083681 original size:7 final size:7
Alignment explanation
Indices: 1083669--1083705 Score: 58
Period size: 7 Copynumber: 5.4 Consensus size: 7
1083659 GTCAAAGGTA
1083669 GTCAACG
1 GTCAACG
1083676 GTCAACG
1 GTCAACG
1083683 GTC-ACG
1 GTCAACG
1083689 GTCAACG
1 GTCAACG
*
1083696 GTCAATG
1 GTCAACG
1083703 GTC
1 GTC
1083706 GGGTCGGGTC
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
6 6 0.21
7 22 0.79
ACGTcount: A:0.24, C:0.27, G:0.30, T:0.19
Consensus pattern (7 bp):
GTCAACG
Found at i:1083691 original size:13 final size:13
Alignment explanation
Indices: 1083673--1083699 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1083663 AAGGTAGTCA
1083673 ACGGTCAACGGTC
1 ACGGTCAACGGTC
1083686 ACGGTCAACGGTC
1 ACGGTCAACGGTC
1083699 A
1 A
1083700 ATGGTCGGGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.26, C:0.30, G:0.30, T:0.15
Consensus pattern (13 bp):
ACGGTCAACGGTC
Found at i:1083735 original size:9 final size:9
Alignment explanation
Indices: 1083717--1083756 Score: 53
Period size: 9 Copynumber: 4.3 Consensus size: 9
1083707 GGTCGGGTCG
*
1083717 GGTCAGACC
1 GGTCAAACC
1083726 GGTCAAACC
1 GGTCAAACC
*
1083735 GGTTCAGACC
1 GG-TCAAACC
1083745 GGTCAAACC
1 GGTCAAACC
1083754 GGT
1 GGT
1083757 TTCCAGTCCT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
9 19 0.70
10 8 0.30
ACGTcount: A:0.25, C:0.30, G:0.30, T:0.15
Consensus pattern (9 bp):
GGTCAAACC
Found at i:1083741 original size:19 final size:19
Alignment explanation
Indices: 1083719--1083757 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
1083709 TCGGGTCGGG
1083719 TCAGACCGGTCAAACCGGT
1 TCAGACCGGTCAAACCGGT
1083738 TCAGACCGGTCAAACCGGT
1 TCAGACCGGTCAAACCGGT
1083757 T
1 T
1083758 TCCAGTCCTC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.26, C:0.31, G:0.26, T:0.18
Consensus pattern (19 bp):
TCAGACCGGTCAAACCGGT
Found at i:1087390 original size:17 final size:17
Alignment explanation
Indices: 1087368--1087409 Score: 59
Period size: 17 Copynumber: 2.5 Consensus size: 17
1087358 GAAACCTAGG
1087368 GGGTCGGGTC-AGATCC
1 GGGTCGGGTCTAGATCC
*
1087384 TGGGTCGGGTCTGGATCC
1 -GGGTCGGGTCTAGATCC
1087402 GGGTCGGG
1 GGGTCGGG
1087410 CTTGAATCAG
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 18 0.78
18 5 0.22
ACGTcount: A:0.07, C:0.21, G:0.50, T:0.21
Consensus pattern (17 bp):
GGGTCGGGTCTAGATCC
Found at i:1087571 original size:3 final size:3
Alignment explanation
Indices: 1087557--1087616 Score: 75
Period size: 3 Copynumber: 19.3 Consensus size: 3
1087547 GTGTAAACAG
* *
1087557 AAT AATT AAT AAT AAT AAT AAT AAC AAT TAT AAT AAT AAT AATT AAT
1 AAT AA-T AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA-T AAT
*
1087604 AAT AAT ATT AAT A
1 AAT AAT AAT AAT A
1087617 TATTTGTAGA
Statistics
Matches: 49, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
3 43 0.88
4 6 0.12
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.37
Consensus pattern (3 bp):
AAT
Found at i:1088125 original size:24 final size:25
Alignment explanation
Indices: 1088080--1088132 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 25
1088070 GTTTAAAGAG
*
1088080 TTTTCGTTAAAAATAAGTGTCTAA-
1 TTTTCGTTAAAAATAAGCGTCTAAC
* *
1088104 TTTTCGTTAAAATTATGCGTCTAAC
1 TTTTCGTTAAAAATAAGCGTCTAAC
1088129 TTTT
1 TTTT
1088133 TCTCTTTTAT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
24 21 0.84
25 4 0.16
ACGTcount: A:0.30, C:0.11, G:0.11, T:0.47
Consensus pattern (25 bp):
TTTTCGTTAAAAATAAGCGTCTAAC
Found at i:1089160 original size:15 final size:15
Alignment explanation
Indices: 1089142--1089187 Score: 56
Period size: 15 Copynumber: 3.0 Consensus size: 15
1089132 GGATTCTTTA
1089142 ATAATTTTTAATTTT
1 ATAATTTTTAATTTT
*
1089157 ATAATTTTTAATATTG
1 ATAATTTTTAAT-TTT
* *
1089173 CTAATTTTTTATTTT
1 ATAATTTTTAATTTT
1089188 TTATTTGAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
15 14 0.54
16 12 0.46
ACGTcount: A:0.30, C:0.02, G:0.02, T:0.65
Consensus pattern (15 bp):
ATAATTTTTAATTTT
Found at i:1089215 original size:2 final size:2
Alignment explanation
Indices: 1089210--1089238 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1089200 AATAATAGGT
1089210 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1089239 TACCAACAAC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1092657 original size:24 final size:24
Alignment explanation
Indices: 1092627--1092711 Score: 116
Period size: 24 Copynumber: 3.5 Consensus size: 24
1092617 TTGAATTCTT
1092627 TATGATACTTGACATGGATTCTGA
1 TATGATACTTGACATGGATTCTGA
* * *
1092651 TTTGATACTTGACTTGGATTCTGG
1 TATGATACTTGACATGGATTCTGA
* *
1092675 TCTGATACTTGACATGGATTTTGA
1 TATGATACTTGACATGGATTCTGA
*
1092699 CATGATACTTGAC
1 TATGATACTTGAC
1092712 CTGAATTATG
Statistics
Matches: 52, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 52 1.00
ACGTcount: A:0.25, C:0.14, G:0.21, T:0.40
Consensus pattern (24 bp):
TATGATACTTGACATGGATTCTGA
Found at i:1094934 original size:148 final size:152
Alignment explanation
Indices: 1094662--1095019 Score: 435
Period size: 148 Copynumber: 2.4 Consensus size: 152
1094652 TATGATTTAC
* * * * * *
1094662 TTTA-TATTTATTATGTTTATTTAATTAATATTTGAAATTATTTATTAATAATTCT-ATTTTGCT
1 TTTATTATTTATTATATTTATTTCATTAATATTTGAAATGATTTATTAATGATTCTGTTTTTACT
* * * * * *
1094725 TTTATAGGGTATCTTTACAACAAGCATATTTAAAATGGTTTGTGAAAGACTTTGTTTTGATTCTT
66 TTTATAAGGCATCTTTACAACAAGCATATTTAAAAAGGTTGGTGAAAGACTCTATTTTGATTCTT
** *
1094790 CCCGTTAAATGTAAA-AA-A-T
131 CAAGTTAAAAGTAAATAATATT
1094809 TTTATTATTT-TTATATTTATTTCATTAATATTTGAAATGATTTATTAATGATTCTGTTTTTACT
1 TTTATTATTTATTATATTTATTTCATTAATATTTGAAATGATTTATTAATGATTCTGTTTTTACT
* *
1094873 TTTGTAAGGCATCTTTACAATAAGCATATTTAAAAAGGTTGGT-AAATGACTCTATTTTGATTCT
66 TTTATAAGGCATCTTTACAACAAGCATATTTAAAAAGGTTGGTGAAA-GACTCTATTTTGATTCT
*
1094937 TCAATTTAAAAGTAAATAATATT
130 TCAAGTTAAAAGTAAATAATATT
* * * *
1094960 TTTTTATATTTATTATATTTATTTCAATAATATTTAAAAATGATTTA-TAATGATTATGTT
1 TTTAT-TATTTATTATATTTATTTCATTAATATTT-GAAATGATTTATTAATGATTCTGTT
1095020 ATCGCTTTTG
Statistics
Matches: 180, Mismatches: 22, Indels: 12
0.84 0.10 0.06
Matches are distributed among these distances:
147 48 0.27
148 75 0.42
149 2 0.01
150 1 0.01
151 5 0.03
152 5 0.03
153 34 0.19
154 10 0.06
ACGTcount: A:0.34, C:0.06, G:0.09, T:0.50
Consensus pattern (152 bp):
TTTATTATTTATTATATTTATTTCATTAATATTTGAAATGATTTATTAATGATTCTGTTTTTACT
TTTATAAGGCATCTTTACAACAAGCATATTTAAAAAGGTTGGTGAAAGACTCTATTTTGATTCTT
CAAGTTAAAAGTAAATAATATT
Found at i:1100356 original size:2 final size:2
Alignment explanation
Indices: 1100349--1100384 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
1100339 AAATTACAAT
1100349 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1100385 ATAAACTTAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1100416 original size:18 final size:18
Alignment explanation
Indices: 1100393--1100435 Score: 86
Period size: 18 Copynumber: 2.4 Consensus size: 18
1100383 TAATAAACTT
1100393 ATTAATCTAATTATTATA
1 ATTAATCTAATTATTATA
1100411 ATTAATCTAATTATTATA
1 ATTAATCTAATTATTATA
1100429 ATTAATC
1 ATTAATC
1100436 GTGCACTTTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.44, C:0.07, G:0.00, T:0.49
Consensus pattern (18 bp):
ATTAATCTAATTATTATA
Found at i:1101261 original size:15 final size:15
Alignment explanation
Indices: 1101241--1101282 Score: 57
Period size: 15 Copynumber: 2.8 Consensus size: 15
1101231 AGCGCTTCCC
1101241 AAATTTCCCATGCTT
1 AAATTTCCCATGCTT
*
1101256 AAATTTCCCATGTTT
1 AAATTTCCCATGCTT
* *
1101271 GAATTTTCCATG
1 AAATTTCCCATG
1101283 ACCATGGCCG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.26, C:0.21, G:0.10, T:0.43
Consensus pattern (15 bp):
AAATTTCCCATGCTT
Found at i:1101704 original size:18 final size:18
Alignment explanation
Indices: 1101670--1101707 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
1101660 TCCTCCTAGA
*
1101670 GGAGGATATCCCCCTGGT
1 GGAGGATATCCACCTGGT
*
1101688 GGAGGATATCCAGCTGGT
1 GGAGGATATCCACCTGGT
1101706 GG
1 GG
1101708 GTATCCCTGA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.18, C:0.21, G:0.39, T:0.21
Consensus pattern (18 bp):
GGAGGATATCCACCTGGT
Found at i:1101763 original size:15 final size:15
Alignment explanation
Indices: 1101718--1101794 Score: 73
Period size: 15 Copynumber: 4.9 Consensus size: 15
1101708 GTATCCCTGA
1101718 GGAGGGTAGCCTTGT
1 GGAGGGTAGCCTTGT
* * * *
1101733 GGTGGATATCCATGT
1 GGAGGGTAGCCTTGT
1101748 GGAGGGTAGCCTTGT
1 GGAGGGTAGCCTTGT
* *
1101763 GGTGGTGGATATCCTTGT
1 GG-AG-GG-TAGCCTTGT
1101781 GGAGGGTAGCCTTG
1 GGAGGGTAGCCTTG
1101795 CGGTGGATAT
Statistics
Matches: 47, Mismatches: 12, Indels: 6
0.72 0.18 0.09
Matches are distributed among these distances:
15 31 0.66
16 3 0.06
17 3 0.06
18 10 0.21
ACGTcount: A:0.14, C:0.13, G:0.43, T:0.30
Consensus pattern (15 bp):
GGAGGGTAGCCTTGT
Found at i:1101773 original size:33 final size:30
Alignment explanation
Indices: 1101702--1101811 Score: 148
Period size: 30 Copynumber: 3.6 Consensus size: 30
1101692 GATATCCAGC
* * *
1101702 TGGTGGGTATCCCTGAGGAGGGTAGCCTTG
1 TGGTGGATATCCATGTGGAGGGTAGCCTTG
1101732 TGGTGGATATCCATGTGGAGGGTAGCCTTGTGG
1 TGGTGGATATCCATGTGGAGGGTAGCC-T-T-G
*
1101765 TGGTGGATATCCTTGTGGAGGGTAGCCTTG
1 TGGTGGATATCCATGTGGAGGGTAGCCTTG
*
1101795 CGGTGGATATCCATGTG
1 TGGTGGATATCCATGTG
1101812 TAGGATAATG
Statistics
Matches: 71, Mismatches: 6, Indels: 6
0.86 0.07 0.07
Matches are distributed among these distances:
30 40 0.56
31 2 0.03
32 2 0.03
33 27 0.38
ACGTcount: A:0.15, C:0.15, G:0.41, T:0.30
Consensus pattern (30 bp):
TGGTGGATATCCATGTGGAGGGTAGCCTTG
Found at i:1101778 original size:18 final size:18
Alignment explanation
Indices: 1101731--1101782 Score: 56
Period size: 18 Copynumber: 3.1 Consensus size: 18
1101721 GGGTAGCCTT
*
1101731 GTGGTGGATATCCATGTG
1 GTGGTGGATATCCTTGTG
* *
1101749 G-AG-GG-TAGCCTTGTG
1 GTGGTGGATATCCTTGTG
1101764 GTGGTGGATATCCTTGTG
1 GTGGTGGATATCCTTGTG
1101782 G
1 G
1101783 AGGGTAGCCT
Statistics
Matches: 26, Mismatches: 5, Indels: 6
0.70 0.14 0.16
Matches are distributed among these distances:
15 9 0.35
16 3 0.12
17 3 0.12
18 11 0.42
ACGTcount: A:0.13, C:0.12, G:0.42, T:0.33
Consensus pattern (18 bp):
GTGGTGGATATCCTTGTG
Found at i:1101800 original size:18 final size:17
Alignment explanation
Indices: 1101746--1101801 Score: 53
Period size: 18 Copynumber: 3.3 Consensus size: 17
1101736 GGATATCCAT
1101746 GTGGAGGGTAGCCTTGTG
1 GTGGAGGGTAGCCTTG-G
* * *
1101764 GTGGTGGATATCCTT--
1 GTGGAGGGTAGCCTTGG
1101779 GTGGAGGGTAGCCTTGCG
1 GTGGAGGGTAGCCTTG-G
1101797 GTGGA
1 GTGGA
1101802 TATCCATGTG
Statistics
Matches: 29, Mismatches: 6, Indels: 6
0.71 0.15 0.15
Matches are distributed among these distances:
15 12 0.41
18 17 0.59
ACGTcount: A:0.12, C:0.12, G:0.46, T:0.29
Consensus pattern (17 bp):
GTGGAGGGTAGCCTTGG
Found at i:1103758 original size:19 final size:19
Alignment explanation
Indices: 1103734--1103770 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
1103724 ATGACCAACA
* *
1103734 AAATCGTAATGCGATCTCT
1 AAATCGCAACGCGATCTCT
1103753 AAATCGCAACGCGATCTC
1 AAATCGCAACGCGATCTC
1103771 CAGTATCGCA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.32, C:0.27, G:0.16, T:0.24
Consensus pattern (19 bp):
AAATCGCAACGCGATCTCT
Found at i:1103819 original size:20 final size:20
Alignment explanation
Indices: 1103796--1103861 Score: 62
Period size: 20 Copynumber: 3.3 Consensus size: 20
1103786 GTTTCCAGAT
*
1103796 TCGCAAAGCGATTTTGACTA
1 TCGCAAAGCGATTATGACTA
* * *
1103816 TCGCAATGCGAATATGTA-AA
1 TCGCAAAGCGATTATG-ACTA
* *
1103836 TCGCAACGCGATTCTGACTA
1 TCGCAAAGCGATTATGACTA
1103856 TCGCAA
1 TCGCAA
1103862 TGTGATTTTC
Statistics
Matches: 36, Mismatches: 8, Indels: 4
0.75 0.17 0.08
Matches are distributed among these distances:
19 1 0.03
20 34 0.94
21 1 0.03
ACGTcount: A:0.32, C:0.23, G:0.20, T:0.26
Consensus pattern (20 bp):
TCGCAAAGCGATTATGACTA
Found at i:1104044 original size:22 final size:22
Alignment explanation
Indices: 1104018--1104063 Score: 74
Period size: 22 Copynumber: 2.1 Consensus size: 22
1104008 GCGACATTCG
*
1104018 TCCCCATCTCTGACGAAATCCA
1 TCCCCATCTCCGACGAAATCCA
*
1104040 TCCCCATCTCCGGCGAAATCCA
1 TCCCCATCTCCGACGAAATCCA
1104062 TC
1 TC
1104064 TATCTCCATC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.24, C:0.43, G:0.11, T:0.22
Consensus pattern (22 bp):
TCCCCATCTCCGACGAAATCCA
Found at i:1104520 original size:20 final size:20
Alignment explanation
Indices: 1104474--1104520 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
1104464 TCGCGTTGCG
* *
1104474 ATTTTCTCGTTGCGATAGTC
1 ATTTTCGCGTTACGATAGTC
**
1104494 AAATTCGCGTTACGATAGTC
1 ATTTTCGCGTTACGATAGTC
1104514 ATTTTCG
1 ATTTTCG
1104521 TGTTGCGAAT
Statistics
Matches: 21, Mismatches: 6, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.21, C:0.19, G:0.19, T:0.40
Consensus pattern (20 bp):
ATTTTCGCGTTACGATAGTC
Found at i:1104559 original size:20 final size:20
Alignment explanation
Indices: 1104516--1104559 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
1104506 CGATAGTCAT
* *
1104516 TTTCGTGTTGCGAATTTCAT
1 TTTCGTGTTGCGAATTTAAG
*
1104536 TTTCGTGTTGCGATTTTAAG
1 TTTCGTGTTGCGAATTTAAG
1104556 TTTC
1 TTTC
1104560 ATAAACTATT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.14, C:0.14, G:0.20, T:0.52
Consensus pattern (20 bp):
TTTCGTGTTGCGAATTTAAG
Found at i:1106476 original size:20 final size:20
Alignment explanation
Indices: 1106453--1106521 Score: 93
Period size: 20 Copynumber: 3.5 Consensus size: 20
1106443 GAAACTTAAA
1106453 ATCGCAACGCGAAAATGACT
1 ATCGCAACGCGAAAATGACT
* *
1106473 ATCGCAACGTGGAAATGACT
1 ATCGCAACGCGAAAATGACT
* **
1106493 ATTGCAACGCGAATTTGACT
1 ATCGCAACGCGAAAATGACT
1106513 ATCGCAACG
1 ATCGCAACG
1106522 GGATAATCGC
Statistics
Matches: 41, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 41 1.00
ACGTcount: A:0.35, C:0.23, G:0.22, T:0.20
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGACT
Found at i:1106554 original size:33 final size:34
Alignment explanation
Indices: 1106517--1106582 Score: 107
Period size: 33 Copynumber: 2.0 Consensus size: 34
1106507 TTGACTATCG
*
1106517 CAACGGGATAATCGCAATGCG-AAATAAAAATCA
1 CAACGGGAAAATCGCAATGCGAAAATAAAAATCA
*
1106550 CAACGTGAAAATCGCAATGCGAAAATAAAAATC
1 CAACGGGAAAATCGCAATGCGAAAATAAAAATC
1106583 GCAATGCAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
33 19 0.63
34 11 0.37
ACGTcount: A:0.50, C:0.18, G:0.17, T:0.15
Consensus pattern (34 bp):
CAACGGGAAAATCGCAATGCGAAAATAAAAATCA
Found at i:1106620 original size:19 final size:20
Alignment explanation
Indices: 1106593--1106631 Score: 62
Period size: 19 Copynumber: 2.0 Consensus size: 20
1106583 GCAATGCAAA
*
1106593 TTTAGTTTCGCGTTGCGATT
1 TTTAGTTTCGCATTGCGATT
1106613 TTTA-TTTCGCATTGCGATT
1 TTTAGTTTCGCATTGCGATT
1106632 ATCTTGTTGC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 14 0.78
20 4 0.22
ACGTcount: A:0.13, C:0.15, G:0.21, T:0.51
Consensus pattern (20 bp):
TTTAGTTTCGCATTGCGATT
Found at i:1106700 original size:20 final size:20
Alignment explanation
Indices: 1106677--1106715 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
1106667 TCATTTCTGC
1106677 GTTGCGATTTTAAGTTTCAT
1 GTTGCGATTTTAAGTTTCAT
1106697 GTTGCGATTTTAAGTTTCA
1 GTTGCGATTTTAAGTTTCA
1106716 GAAACTGTTC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.21, C:0.10, G:0.21, T:0.49
Consensus pattern (20 bp):
GTTGCGATTTTAAGTTTCAT
Found at i:1107265 original size:42 final size:42
Alignment explanation
Indices: 1107219--1107311 Score: 125
Period size: 42 Copynumber: 2.2 Consensus size: 42
1107209 CTCTCCTATT
1107219 GTTCAAGAGGCCTCTATCATCCCTCAAGA-GTCCCCTCCCACC
1 GTTCAAGAGGCCTCTATCATCCCTCAAGAGGT-CCCTCCCACC
* ** *
1107261 GTTCAAGAGGCCTCTGTCATCGTTGAAGAGGTCCCTCCCACC
1 GTTCAAGAGGCCTCTATCATCCCTCAAGAGGTCCCTCCCACC
*
1107303 ATTCAAGAG
1 GTTCAAGAG
1107312 CCCGATTCAC
Statistics
Matches: 45, Mismatches: 5, Indels: 2
0.87 0.10 0.04
Matches are distributed among these distances:
42 43 0.96
43 2 0.04
ACGTcount: A:0.23, C:0.35, G:0.19, T:0.23
Consensus pattern (42 bp):
GTTCAAGAGGCCTCTATCATCCCTCAAGAGGTCCCTCCCACC
Found at i:1107266 original size:21 final size:21
Alignment explanation
Indices: 1107242--1107311 Score: 61
Period size: 21 Copynumber: 3.3 Consensus size: 21
1107232 CTATCATCCC
1107242 TCAAGAGTCCCCTCCCACCGT
1 TCAAGAGTCCCCTCCCACCGT
* * ** *
1107263 TCAAGAGGCCTCTGTCATCGT
1 TCAAGAGTCCCCTCCCACCGT
* *
1107284 TGAAGAGGT-CCCTCCCACCAT
1 TCAAGA-GTCCCCTCCCACCGT
1107305 TCAAGAG
1 TCAAGAG
1107312 CCCGATTCAC
Statistics
Matches: 35, Mismatches: 13, Indels: 3
0.69 0.25 0.06
Matches are distributed among these distances:
20 1 0.03
21 33 0.94
22 1 0.03
ACGTcount: A:0.23, C:0.36, G:0.20, T:0.21
Consensus pattern (21 bp):
TCAAGAGTCCCCTCCCACCGT
Found at i:1108843 original size:40 final size:40
Alignment explanation
Indices: 1108799--1108896 Score: 117
Period size: 40 Copynumber: 2.5 Consensus size: 40
1108789 AGGTACACTT
* * *
1108799 TCGCAACGCTAAACTCAAAATCGTAATACGAAAGTCAAAA
1 TCGCAACGCAAAACTCAAAATCGCAATACGAAAGCCAAAA
* * *
1108839 TCGCAATGCGAAAGC-CAAAATCGCAATGCGAAAGCCAAAA
1 TCGCAACGC-AAAACTCAAAATCGCAATACGAAAGCCAAAA
*
1108879 TCGCAACGCAAAAGTCAA
1 TCGCAACGCAAAACTCAA
1108897 TTCGCGTTGC
Statistics
Matches: 47, Mismatches: 9, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
39 3 0.06
40 41 0.87
41 3 0.06
ACGTcount: A:0.46, C:0.24, G:0.16, T:0.13
Consensus pattern (40 bp):
TCGCAACGCAAAACTCAAAATCGCAATACGAAAGCCAAAA
Found at i:1108892 original size:20 final size:20
Alignment explanation
Indices: 1108814--1108884 Score: 115
Period size: 20 Copynumber: 3.5 Consensus size: 20
1108804 ACGCTAAACT
* * *
1108814 CAAAATCGTAATACGAAAGT
1 CAAAATCGCAATGCGAAAGC
1108834 CAAAATCGCAATGCGAAAGC
1 CAAAATCGCAATGCGAAAGC
1108854 CAAAATCGCAATGCGAAAGC
1 CAAAATCGCAATGCGAAAGC
1108874 CAAAATCGCAA
1 CAAAATCGCAA
1108885 CGCAAAAGTC
Statistics
Matches: 48, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 48 1.00
ACGTcount: A:0.48, C:0.23, G:0.17, T:0.13
Consensus pattern (20 bp):
CAAAATCGCAATGCGAAAGC
Found at i:1108960 original size:20 final size:20
Alignment explanation
Indices: 1108935--1109031 Score: 149
Period size: 20 Copynumber: 4.8 Consensus size: 20
1108925 GTGATTTTCT
* *
1108935 CGTTGCGATAGTTAAATTCC
1 CGTTGCGATAGTCAAATTCG
* *
1108955 CGTTGCGATAATCAAATTCA
1 CGTTGCGATAGTCAAATTCG
1108975 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCG
1108995 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCG
*
1109015 CGTTGCGATATTCAAAT
1 CGTTGCGATAGTCAAAT
1109032 AAACGTGTAA
Statistics
Matches: 71, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 71 1.00
ACGTcount: A:0.28, C:0.20, G:0.21, T:0.32
Consensus pattern (20 bp):
CGTTGCGATAGTCAAATTCG
Found at i:1109457 original size:17 final size:17
Alignment explanation
Indices: 1109431--1109466 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
1109421 GATGGGGAAT
*
1109431 GATGTTGTTGGATATAG
1 GATGTCGTTGGATATAG
1109448 GATGTCGTTGGATATAG
1 GATGTCGTTGGATATAG
1109465 GA
1 GA
1109467 ACGGATGTCG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.25, C:0.03, G:0.36, T:0.36
Consensus pattern (17 bp):
GATGTCGTTGGATATAG
Found at i:1109636 original size:20 final size:20
Alignment explanation
Indices: 1109611--1109681 Score: 81
Period size: 20 Copynumber: 3.5 Consensus size: 20
1109601 TTGAAATTCA
1109611 GCGTTGCGATAGTCAGAATC
1 GCGTTGCGATAGTCAGAATC
* **
1109631 GCGTTGCGATTTTGT-ATTATC
1 GCGTTGCGA--TAGTCAGAATC
1109652 GCGTTGCGATAGTCAGAATC
1 GCGTTGCGATAGTCAGAATC
*
1109672 GCATTGCGAT
1 GCGTTGCGAT
1109682 TTACATATTC
Statistics
Matches: 41, Mismatches: 7, Indels: 6
0.76 0.13 0.11
Matches are distributed among these distances:
19 3 0.07
20 22 0.54
21 13 0.32
22 3 0.07
ACGTcount: A:0.21, C:0.18, G:0.28, T:0.32
Consensus pattern (20 bp):
GCGTTGCGATAGTCAGAATC
Found at i:1109812 original size:19 final size:19
Alignment explanation
Indices: 1109788--1109824 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
1109778 TGCGATACTG
* *
1109788 GAGATCGCGTTGCGATTTA
1 GAGATCGCATTACGATTTA
1109807 GAGATCGCATTACGATTT
1 GAGATCGCATTACGATTT
1109825 TGTTGGTCAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.24, C:0.16, G:0.27, T:0.32
Consensus pattern (19 bp):
GAGATCGCATTACGATTTA
Found at i:1114186 original size:24 final size:24
Alignment explanation
Indices: 1114158--1114239 Score: 85
Period size: 24 Copynumber: 3.4 Consensus size: 24
1114148 CAAACTAACG
*
1114158 CGTAGAATTTGCACCGAAGTGCCA
1 CGTAGAATTTGCATCGAAGTGCCA
* * *
1114182 CGTAGAATATGCATCAAAGTTCCA
1 CGTAGAATTTGCATCGAAGTGCCA
* * *
1114206 CATAGAATTTGTATAGAAG-GACCA
1 CGTAGAATTTGCATCGAAGTG-CCA
1114230 CGTAGAATTT
1 CGTAGAATTT
1114240 TTCCCAAAGG
Statistics
Matches: 46, Mismatches: 11, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
24 46 1.00
ACGTcount: A:0.35, C:0.18, G:0.21, T:0.26
Consensus pattern (24 bp):
CGTAGAATTTGCATCGAAGTGCCA
Found at i:1114268 original size:23 final size:24
Alignment explanation
Indices: 1114222--1114283 Score: 99
Period size: 23 Copynumber: 2.6 Consensus size: 24
1114212 ATTTGTATAG
1114222 AAGGACCACGTAGAATTTTTCCCA
1 AAGGACCACGTAGAATTTTTCCCA
*
1114246 AAGGACCACATAGAA-TTTTCCCA
1 AAGGACCACGTAGAATTTTTCCCA
*
1114269 AAGGATCACGTAGAA
1 AAGGACCACGTAGAA
1114284 CCCTCGACTC
Statistics
Matches: 35, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
23 21 0.60
24 14 0.40
ACGTcount: A:0.39, C:0.23, G:0.18, T:0.21
Consensus pattern (24 bp):
AAGGACCACGTAGAATTTTTCCCA
Found at i:1115062 original size:72 final size:73
Alignment explanation
Indices: 1114977--1115121 Score: 256
Period size: 73 Copynumber: 2.0 Consensus size: 73
1114967 TATCGATATT
* *
1114977 GTTCATTTGATTCATACA-TTTTCCTTCAATTTAACCTTGTAGTATCGATATTGTTCTTCCAGTA
1 GTTCATCTGATTCATACATTTTTCCTTCAATTTAACCTTATAGTATCGATATTGTTCTTCCAGTA
1115041 CCGATACC
66 CCGATACC
*
1115049 GTTCATCTGATTCATACATTTTTCCTTCAATTTAACCTTATAGTATCGGTATTGTTCTTCCAGTA
1 GTTCATCTGATTCATACATTTTTCCTTCAATTTAACCTTATAGTATCGATATTGTTCTTCCAGTA
1115114 CCGATACC
66 CCGATACC
1115122 CTTACCCATA
Statistics
Matches: 69, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
72 17 0.25
73 52 0.75
ACGTcount: A:0.23, C:0.23, G:0.11, T:0.43
Consensus pattern (73 bp):
GTTCATCTGATTCATACATTTTTCCTTCAATTTAACCTTATAGTATCGATATTGTTCTTCCAGTA
CCGATACC
Found at i:1121167 original size:24 final size:24
Alignment explanation
Indices: 1121135--1121197 Score: 81
Period size: 24 Copynumber: 2.6 Consensus size: 24
1121125 CAGTCGAAAC
* *
1121135 TGCCGCGTAGAATTTGCACCAAAG
1 TGCCACGTAGAATTTCCACCAAAG
* *
1121159 TGCCACGTAGAATATCCACCGAAG
1 TGCCACGTAGAATTTCCACCAAAG
*
1121183 TGCCACATAGAATTT
1 TGCCACGTAGAATTT
1121198 TTCCCGAAGG
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 33 1.00
ACGTcount: A:0.32, C:0.25, G:0.21, T:0.22
Consensus pattern (24 bp):
TGCCACGTAGAATTTCCACCAAAG
Found at i:1121204 original size:24 final size:24
Alignment explanation
Indices: 1121177--1121265 Score: 101
Period size: 24 Copynumber: 3.8 Consensus size: 24
1121167 AGAATATCCA
1121177 CCGAAGTG-CCACATAGAATTTTTC
1 CCGAAG-GACCACATAGAATTTTTC
* * * *
1121201 CCGAAGGATCGCGTAGAATTTGTC
1 CCGAAGGACCACATAGAATTTTTC
1121225 CCGAAGGACCACATAGAA-TTTTC
1 CCGAAGGACCACATAGAATTTTTC
* *
1121248 CCGAATGACCACGTAGAA
1 CCGAAGGACCACATAGAA
1121266 CCCTCGACTC
Statistics
Matches: 54, Mismatches: 10, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
23 21 0.39
24 33 0.61
ACGTcount: A:0.31, C:0.25, G:0.21, T:0.22
Consensus pattern (24 bp):
CCGAAGGACCACATAGAATTTTTC
Found at i:1121395 original size:15 final size:15
Alignment explanation
Indices: 1121375--1121422 Score: 60
Period size: 15 Copynumber: 3.1 Consensus size: 15
1121365 CTTATCCACG
*
1121375 TAGAACACTTTCTCA
1 TAGAACACTTTCACA
*
1121390 TAGAACATTTTTCACA
1 TAGAACA-CTTTCACA
*
1121406 TAGAACACATTCACA
1 TAGAACACTTTCACA
1121421 TA
1 TA
1121423 CACAAAAAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
15 15 0.54
16 13 0.46
ACGTcount: A:0.40, C:0.23, G:0.06, T:0.31
Consensus pattern (15 bp):
TAGAACACTTTCACA
Done.