Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001167.1 Hibiscus syriacus cultivar Beakdansim tig00002329_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: 153125
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.35
Found at i:325 original size:92 final size:88
Alignment explanation
Indices: 126--490 Score: 504
Period size: 92 Copynumber: 4.1 Consensus size: 88
116 TAGATTGCTT
* * *
126 AGTAAATTTATTCGGTTGCTGCCAATACTGC-AAACT-GTTTATTAACACTGTGAAGTTAGTATT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGGTATCTTAACACTGTGAAGTTAGTATT
*
189 GTGCTTTTGTTGTC-TTTGGTTGA
66 GT-CTTTTTTTGTCTTTTGGTTGA
212 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATCTTAACACTGTGAAGTTAGTAT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTG-GTATCTTAACACTGTGAAGTTAGTA-
277 TTGTCTTTGTTTTGTCTTTTGGTTGAA
64 TTGTCTTT-TTTTGTCTTTTGGTTG-A
* *
304 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGGTGTCTTTAACACTGTGAAGTTAGTAT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGGTATC-TTAACACTGTGAAGTTAGTA-
369 TTGTCTTTGTTTTGTCTTTTGGTTGAA
64 TTGTCTTT-TTTTGTCTTTTGGTTG-A
* * * *
396 AGTAAAATTTGTTC-GTTGCTGCCAATTCTGCTAAACTGGTATTCTTTATACTCTGAAGTTAGTA
1 AGT-AAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGGTA-TCTTAACACTGTGAAGTTAGTA
460 TTGTCTTTTGTTTGTCTTTTGGTTGA
64 TTGTCTTTT-TTTGTCTTTTGGTTGA
486 AGTAA
1 AGTAA
491 TGCAATCCAT
Statistics
Matches: 258, Mismatches: 10, Indels: 19
0.90 0.03 0.07
Matches are distributed among these distances:
86 30 0.12
87 5 0.02
89 29 0.11
90 15 0.06
91 35 0.14
92 132 0.51
93 12 0.05
ACGTcount: A:0.22, C:0.13, G:0.20, T:0.45
Consensus pattern (88 bp):
AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGGTATCTTAACACTGTGAAGTTAGTATT
GTCTTTTTTTGTCTTTTGGTTGA
Found at i:617 original size:19 final size:18
Alignment explanation
Indices: 595--664 Score: 67
Period size: 19 Copynumber: 4.0 Consensus size: 18
585 ATGAGAGAAT
595 GAAAATCGCAACGCGAAA
1 GAAAATCGCAACGCGAAA
613 CGAAAATCGCAA--CG--A
1 -GAAAATCGCAACGCGAAA
* * *
628 GAGAATTGCAACGCAAAA
1 GAAAATCGCAACGCGAAA
646 TGAAAATCGCAACGCGAAA
1 -GAAAATCGCAACGCGAAA
665 AATCCAACGC
Statistics
Matches: 40, Mismatches: 6, Indels: 10
0.71 0.11 0.18
Matches are distributed among these distances:
14 9 0.22
15 1 0.03
16 1 0.03
17 2 0.05
18 1 0.03
19 26 0.65
ACGTcount: A:0.49, C:0.21, G:0.21, T:0.09
Consensus pattern (18 bp):
GAAAATCGCAACGCGAAA
Found at i:668 original size:15 final size:14
Alignment explanation
Indices: 648--678 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 14
638 ACGCAAAATG
648 AAAATCGCAACGCGA
1 AAAATC-CAACGCGA
663 AAAATCCAACGCGA
1 AAAATCCAACGCGA
677 AA
1 AA
679 CTATATCGCG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 10 0.62
15 6 0.38
ACGTcount: A:0.52, C:0.26, G:0.16, T:0.06
Consensus pattern (14 bp):
AAAATCCAACGCGA
Found at i:673 original size:33 final size:33
Alignment explanation
Indices: 596--679 Score: 96
Period size: 33 Copynumber: 2.5 Consensus size: 33
586 TGAGAGAATG
*
596 AAAATCGCAACGCGAAACGAAAATCGCAACGAGA
1 AAAATC-CAACGCAAAACGAAAATCGCAACGAGA
* * * * *
630 GAATTGCAACGCAAAATGAAAATCGCAACGCGA
1 AAAATCCAACGCAAAACGAAAATCGCAACGAGA
*
663 AAAATCCAACGCGAAAC
1 AAAATCCAACGCAAAAC
680 TATATCGCGT
Statistics
Matches: 39, Mismatches: 11, Indels: 1
0.76 0.22 0.02
Matches are distributed among these distances:
33 36 0.92
34 3 0.08
ACGTcount: A:0.49, C:0.24, G:0.19, T:0.08
Consensus pattern (33 bp):
AAAATCCAACGCAAAACGAAAATCGCAACGAGA
Found at i:725 original size:27 final size:29
Alignment explanation
Indices: 687--754 Score: 95
Period size: 27 Copynumber: 2.3 Consensus size: 29
677 AACTATATCG
687 CGTTGCGATTCATTTCGCATT-ATT-TCT
1 CGTTGCGATTCATTTCGCATTGATTCTCT
*
714 CGTTGCGATTCATTTCGCGTTGCGATTCTCT
1 CGTTGCGATTCATTTCGCATT--GATTCTCT
745 CGTTGCGATT
1 CGTTGCGATT
755 TTCGTTTCGC
Statistics
Matches: 36, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
27 20 0.56
30 3 0.08
31 13 0.36
ACGTcount: A:0.12, C:0.24, G:0.21, T:0.44
Consensus pattern (29 bp):
CGTTGCGATTCATTTCGCATTGATTCTCT
Found at i:750 original size:14 final size:15
Alignment explanation
Indices: 710--786 Score: 61
Period size: 17 Copynumber: 4.9 Consensus size: 15
700 TTCGCATTAT
710 TTCTCGTTGCGATTC
1 TTCTCGTTGCGATTC
*
725 ATTTCGCGTTGCGATTC
1 --TTCTCGTTGCGATTC
742 -TCTCGTTGCGATTTTC
1 TTCTCGTTGCGA--TTC
*
758 GTTTCGCGTTGCGATT-
1 --TTCTCGTTGCGATTC
774 TTCTCG-TGCGATT
1 TTCTCGTTGCGATT
787 TTCATTTCGC
Statistics
Matches: 51, Mismatches: 4, Indels: 14
0.74 0.06 0.20
Matches are distributed among these distances:
13 7 0.14
14 15 0.29
16 3 0.06
17 16 0.31
19 10 0.20
ACGTcount: A:0.08, C:0.23, G:0.23, T:0.45
Consensus pattern (15 bp):
TTCTCGTTGCGATTC
Found at i:769 original size:19 final size:18
Alignment explanation
Indices: 709--804 Score: 70
Period size: 19 Copynumber: 5.8 Consensus size: 18
699 TTTCGCATTA
*
709 TTTCTCGTTGCGA--TTC
1 TTTCGCGTTGCGATTTTC
725 ATTTCGCGTTGCGA--TTC
1 -TTTCGCGTTGCGATTTTC
*
742 --TCTCGTTGCGATTTTC
1 TTTCGCGTTGCGATTTTC
758 GTTTCGCGTTGCGATTTTC
1 -TTTCGCGTTGCGATTTTC
777 --T--CG-TGCGATTTTC
1 TTTCGCGTTGCGATTTTC
790 ATTTCGCGTTGCGAT
1 -TTTCGCGTTGCGAT
805 AGTCATTTTT
Statistics
Matches: 65, Mismatches: 3, Indels: 20
0.74 0.03 0.23
Matches are distributed among these distances:
13 10 0.15
14 12 0.18
16 5 0.08
17 15 0.23
18 2 0.03
19 21 0.32
ACGTcount: A:0.08, C:0.23, G:0.23, T:0.46
Consensus pattern (18 bp):
TTTCGCGTTGCGATTTTC
Found at i:789 original size:32 final size:33
Alignment explanation
Indices: 709--804 Score: 153
Period size: 32 Copynumber: 3.0 Consensus size: 33
699 TTTCGCATTA
709 TTTCTCGTTGCGA--TTCATTTCGCGTTGCGAT
1 TTTCTCGTTGCGATTTTCATTTCGCGTTGCGAT
* *
740 TCTCTCGTTGCGATTTTCGTTTCGCGTTGCGAT
1 TTTCTCGTTGCGATTTTCATTTCGCGTTGCGAT
773 TTTCTCG-TGCGATTTTCATTTCGCGTTGCGAT
1 TTTCTCGTTGCGATTTTCATTTCGCGTTGCGAT
805 AGTCATTTTT
Statistics
Matches: 59, Mismatches: 4, Indels: 3
0.89 0.06 0.05
Matches are distributed among these distances:
31 12 0.20
32 24 0.41
33 23 0.39
ACGTcount: A:0.08, C:0.23, G:0.23, T:0.46
Consensus pattern (33 bp):
TTTCTCGTTGCGATTTTCATTTCGCGTTGCGAT
Found at i:1296 original size:21 final size:21
Alignment explanation
Indices: 1272--1338 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
1262 TCATTCCTCG
1272 AGAGTCCCCTCCCACCGTTCA
1 AGAGTCCCCTCCCACCGTTCA
* * ** * *
1293 AGAGGCCACTGTCATCGTTGA
1 AGAGTCCCCTCCCACCGTTCA
*
1314 AGAGGT-CCCTCCCACCATTCA
1 AGA-GTCCCCTCCCACCGTTCA
1335 AGAG
1 AGAG
1339 CCCGATTCAC
Statistics
Matches: 32, Mismatches: 13, Indels: 3
0.67 0.27 0.06
Matches are distributed among these distances:
20 1 0.03
21 30 0.94
22 1 0.03
ACGTcount: A:0.24, C:0.36, G:0.21, T:0.19
Consensus pattern (21 bp):
AGAGTCCCCTCCCACCGTTCA
Found at i:1298 original size:42 final size:42
Alignment explanation
Indices: 1250--1338 Score: 101
Period size: 42 Copynumber: 2.1 Consensus size: 42
1240 TCCTATGTTG
* *
1250 AAGAGGCCCCTATCATTCCTCG-AGA-GTCCCCTCCCACCGTTC
1 AAGAGGCCACTATCA-TCCTCGAAGAGGT-CCCTCCCACCATTC
* * *
1292 AAGAGGCCACTGTCATCGTTGAAGAGGTCCCTCCCACCATTC
1 AAGAGGCCACTATCATCCTCGAAGAGGTCCCTCCCACCATTC
1334 AAGAG
1 AAGAG
1339 CCCGATTCAC
Statistics
Matches: 40, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
41 4 0.10
42 34 0.85
43 2 0.05
ACGTcount: A:0.24, C:0.36, G:0.20, T:0.20
Consensus pattern (42 bp):
AAGAGGCCACTATCATCCTCGAAGAGGTCCCTCCCACCATTC
Found at i:2677 original size:14 final size:14
Alignment explanation
Indices: 2658--2690 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
2648 ATTGTTTAAT
2658 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
2672 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
2686 TGATT
1 TGATT
2691 GTTTTAATTG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.36, C:0.00, G:0.21, T:0.42
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:2842 original size:33 final size:33
Alignment explanation
Indices: 2805--2893 Score: 115
Period size: 33 Copynumber: 2.7 Consensus size: 33
2795 TGACTATCGT
* * * *
2805 AATGCAAAATGAAAATCGCAATGAGAGAATCAC
1 AATGCGAAATGAAAATCGCAACGACAAAATCAC
*
2838 AATGCGAAATGAAAATCGCAACGACAAAATCGC
1 AATGCGAAATGAAAATCGCAACGACAAAATCAC
* *
2871 AACGCGAAATTAAAATCGCAACG
1 AATGCGAAATGAAAATCGCAACG
2894 CGAAACTAAA
Statistics
Matches: 49, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 49 1.00
ACGTcount: A:0.49, C:0.19, G:0.18, T:0.13
Consensus pattern (33 bp):
AATGCGAAATGAAAATCGCAACGACAAAATCAC
Found at i:2887 original size:19 final size:19
Alignment explanation
Indices: 2863--2908 Score: 74
Period size: 19 Copynumber: 2.4 Consensus size: 19
2853 TCGCAACGAC
*
2863 AAAATCGCAACGCGAAATT
1 AAAATCGCAACGCGAAACT
2882 AAAATCGCAACGCGAAACT
1 AAAATCGCAACGCGAAACT
*
2901 AAATTCGC
1 AAAATCGC
2909 GTTGCGATTT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.46, C:0.24, G:0.15, T:0.15
Consensus pattern (19 bp):
AAAATCGCAACGCGAAACT
Found at i:2949 original size:32 final size:33
Alignment explanation
Indices: 2908--2999 Score: 127
Period size: 31 Copynumber: 2.8 Consensus size: 33
2898 ACTAAATTCG
*
2908 CGTTGCGATTTTCTTTTCGCTTTGCGATTC-CT
1 CGTTGCGATTTTCTTTTCGCATTGCGATTCTCT
*
2940 CGTTGCGA-TTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCTTTTCGCATTGCGATTCTCT
*
2972 CGTTGCGATTTTCATTTT-GTATTGCGAT
1 CGTTGCGATTTTC-TTTTCGCATTGCGAT
3000 AGTCATTTCC
Statistics
Matches: 53, Mismatches: 4, Indels: 5
0.85 0.06 0.08
Matches are distributed among these distances:
31 19 0.36
32 18 0.34
33 13 0.25
34 3 0.06
ACGTcount: A:0.11, C:0.22, G:0.20, T:0.48
Consensus pattern (33 bp):
CGTTGCGATTTTCTTTTCGCATTGCGATTCTCT
Found at i:2979 original size:14 final size:14
Alignment explanation
Indices: 2929--2981 Score: 54
Period size: 14 Copynumber: 3.6 Consensus size: 14
2919 TCTTTTCGCT
2929 TTGCGATTC-CTCG
1 TTGCGATTCTCTCG
*
2942 TTGCGATTTCATTTCG
1 TTGCGA-TTC-TCTCG
2958 CATTGCGATTCTCTCG
1 --TTGCGATTCTCTCG
2974 TTGCGATT
1 TTGCGATT
2982 TTCATTTTGT
Statistics
Matches: 33, Mismatches: 2, Indels: 9
0.75 0.05 0.20
Matches are distributed among these distances:
13 6 0.18
14 11 0.33
16 7 0.21
17 3 0.09
18 6 0.18
ACGTcount: A:0.11, C:0.25, G:0.21, T:0.43
Consensus pattern (14 bp):
TTGCGATTCTCTCG
Found at i:5456 original size:23 final size:22
Alignment explanation
Indices: 5430--5480 Score: 75
Period size: 22 Copynumber: 2.3 Consensus size: 22
5420 CTGAAAAATC
5430 ATCAAAATCGAGTATTGACCAAG
1 ATCAAAAT-GAGTATTGACCAAG
* *
5453 ATCAAAGTGGGTATTGACCAAG
1 ATCAAAATGAGTATTGACCAAG
5475 ATCAAA
1 ATCAAA
5481 TTTCGAATAC
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
22 19 0.73
23 7 0.27
ACGTcount: A:0.43, C:0.16, G:0.20, T:0.22
Consensus pattern (22 bp):
ATCAAAATGAGTATTGACCAAG
Found at i:6361 original size:20 final size:21
Alignment explanation
Indices: 6337--6499 Score: 174
Period size: 20 Copynumber: 8.0 Consensus size: 21
6327 CAGAATCTCG
6337 TTGCGATTTAC-TAAATCGCA
1 TTGCGATTTACGTAAATCGCA
* *
6357 ATGCGA-TTACGTAAATCGAA
1 TTGCGATTTACGTAAATCGCA
* * * *
6377 ATGCGAATTAGGAAAATCGCA
1 TTGCGATTTACGTAAATCGCA
*
6398 ATGCGATTTACGT-AATCGCA
1 TTGCGATTTACGTAAATCGCA
* * *
6418 TTGCGATTTTCCTAATTCGCA
1 TTGCGATTTACGTAAATCGCA
6439 TTGCGATTTACGT-AATCGCA
1 TTGCGATTTACGTAAATCGCA
*
6459 TTGCGATTTACGT-ATTCGCA
1 TTGCGATTTACGTAAATCGCA
* *
6479 TTGCGATTTAGGAAAATCGCA
1 TTGCGATTTACGTAAATCGCA
6500 ACATGAATTT
Statistics
Matches: 120, Mismatches: 19, Indels: 7
0.82 0.13 0.05
Matches are distributed among these distances:
19 4 0.03
20 72 0.60
21 44 0.37
ACGTcount: A:0.30, C:0.18, G:0.20, T:0.32
Consensus pattern (21 bp):
TTGCGATTTACGTAAATCGCA
Found at i:6499 original size:41 final size:41
Alignment explanation
Indices: 6337--6488 Score: 166
Period size: 41 Copynumber: 3.8 Consensus size: 41
6327 CAGAATCTCG
* * *
6337 TTGCGATTTA-CTAAATCGCAATGCGA-TTACGTAAATCGAA
1 TTGCGATTTACCTAATTCGCATTGCGATTTACGT-AATCGCA
* * *** * *
6377 ATGCGAATTAGGAAAATCGCAATGCGATTTACGTAATCGCA
1 TTGCGATTTACCTAATTCGCATTGCGATTTACGTAATCGCA
*
6418 TTGCGATTTTCCTAATTCGCATTGCGATTTACGTAATCGCA
1 TTGCGATTTACCTAATTCGCATTGCGATTTACGTAATCGCA
*
6459 TTGCGATTTACGT-ATTCGCATTGCGATTTA
1 TTGCGATTTACCTAATTCGCATTGCGATTTA
6489 GGAAAATCGC
Statistics
Matches: 95, Mismatches: 15, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
40 25 0.26
41 64 0.67
42 6 0.06
ACGTcount: A:0.29, C:0.18, G:0.19, T:0.34
Consensus pattern (41 bp):
TTGCGATTTACCTAATTCGCATTGCGATTTACGTAATCGCA
Found at i:7302 original size:24 final size:24
Alignment explanation
Indices: 7275--7326 Score: 104
Period size: 24 Copynumber: 2.2 Consensus size: 24
7265 TTTATCACAT
7275 CTCAATCAATAGGTTAACATCCAG
1 CTCAATCAATAGGTTAACATCCAG
7299 CTCAATCAATAGGTTAACATCCAG
1 CTCAATCAATAGGTTAACATCCAG
7323 CTCA
1 CTCA
7327 GACAAATGTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.37, C:0.27, G:0.12, T:0.25
Consensus pattern (24 bp):
CTCAATCAATAGGTTAACATCCAG
Found at i:10464 original size:21 final size:22
Alignment explanation
Indices: 10439--10490 Score: 65
Period size: 20 Copynumber: 2.5 Consensus size: 22
10429 ACAAGGCGTT
*
10439 TCGATACTCTATCA-AAGGGTA
1 TCGATACTCTATCATAAGAGTA
*
10460 TCGATA--CTGTCATAAGAGTA
1 TCGATACTCTATCATAAGAGTA
10480 TCGATACTCTA
1 TCGATACTCTA
10491 GGGGGAGTAT
Statistics
Matches: 25, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
19 5 0.20
20 12 0.48
21 6 0.24
22 2 0.08
ACGTcount: A:0.33, C:0.19, G:0.17, T:0.31
Consensus pattern (22 bp):
TCGATACTCTATCATAAGAGTA
Found at i:15658 original size:21 final size:20
Alignment explanation
Indices: 15634--15689 Score: 60
Period size: 21 Copynumber: 2.7 Consensus size: 20
15624 TTTTTCGTCT
*
15634 ATAAAAAATTTAACATATAAA
1 ATAAAAAATTTAA-AGATAAA
*
15655 ATAAATAATTT-AAGATAAA
1 ATAAAAAATTTAAAGATAAA
15674 ATAACAAAAATTTAAA
1 AT-A-AAAAATTTAAA
15690 CAAATAATTT
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
19 8 0.28
20 2 0.07
21 17 0.59
22 2 0.07
ACGTcount: A:0.66, C:0.04, G:0.02, T:0.29
Consensus pattern (20 bp):
ATAAAAAATTTAAAGATAAA
Found at i:17933 original size:2 final size:2
Alignment explanation
Indices: 17926--17982 Score: 114
Period size: 2 Copynumber: 28.5 Consensus size: 2
17916 GGTTTTTAAC
17926 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
17968 TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA T
17983 CAATCTGCGT
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 55 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:25384 original size:2 final size:2
Alignment explanation
Indices: 25377--25412 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
25367 AAAAACACTA
25377 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
25413 GTCGAATAAC
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):
AT
Found at i:26148 original size:18 final size:16
Alignment explanation
Indices: 26125--26177 Score: 52
Period size: 18 Copynumber: 3.0 Consensus size: 16
26115 TAGTACTTTA
26125 ATTTTAGTCCTTTTATAT
1 ATTTTA-TCCTTTTA-AT
*
26143 ATTTTAATCATCTTTAAT
1 ATTTT-ATCCT-TTTAAT
26161 ATTTGTATCCTTTTAAT
1 ATTT-TATCCTTTTAAT
26178 TTAGTCCTTG
Statistics
Matches: 30, Mismatches: 2, Indels: 7
0.77 0.05 0.18
Matches are distributed among these distances:
17 6 0.20
18 18 0.60
19 6 0.20
ACGTcount: A:0.26, C:0.11, G:0.04, T:0.58
Consensus pattern (16 bp):
ATTTTATCCTTTTAAT
Found at i:27632 original size:29 final size:29
Alignment explanation
Indices: 27573--27633 Score: 68
Period size: 29 Copynumber: 2.1 Consensus size: 29
27563 ATTTTGTTTA
* * *
27573 TTTATTTCGATTTTGACATCCTATTGAAT
1 TTTATTTCAATTTGGACATCATATTGAAT
* * *
27602 TTTATTTCAATTTGGTCATCATTTTGGAT
1 TTTATTTCAATTTGGACATCATATTGAAT
27631 TTT
1 TTT
27634 GTTTATTTTG
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.21, C:0.11, G:0.11, T:0.56
Consensus pattern (29 bp):
TTTATTTCAATTTGGACATCATATTGAAT
Found at i:29893 original size:70 final size:70
Alignment explanation
Indices: 29780--29922 Score: 268
Period size: 70 Copynumber: 2.0 Consensus size: 70
29770 TTGATTTGAG
* *
29780 TTATTCGAGTTTCTATGCTAATTTTATTATAATTATTTATAGTATTATGATAAGGATTGGTTCCA
1 TTATTCGAGTTTCTATACTAATTTTATTATAATTATTTATAGTATTATGATAAGGATTGGTTCAA
29845 ATTTT
66 ATTTT
29850 TTATTCGAGTTTCTATACTAATTTTATTATAATTATTTATAGTATTATGATAAGGATTGGTTCAA
1 TTATTCGAGTTTCTATACTAATTTTATTATAATTATTTATAGTATTATGATAAGGATTGGTTCAA
29915 ATTTT
66 ATTTT
29920 TTA
1 TTA
29923 ACTTTCTCTA
Statistics
Matches: 71, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
70 71 1.00
ACGTcount: A:0.30, C:0.06, G:0.12, T:0.52
Consensus pattern (70 bp):
TTATTCGAGTTTCTATACTAATTTTATTATAATTATTTATAGTATTATGATAAGGATTGGTTCAA
ATTTT
Found at i:30057 original size:119 final size:118
Alignment explanation
Indices: 29859--30180 Score: 551
Period size: 116 Copynumber: 2.7 Consensus size: 118
29849 TTTATTCGAG
*
29859 TTTCTATA-CTAATTTTATTATAATTATTTATAGTATTATGATAAGGATTGGTTCAAATTTTTTA
1 TTTCTA-ACCTAATTTTATTATAATTATTTATAGTATTATGATAAGGATTGGTTCCAATTTTTTA
29923 ACTTTCTCTAACCATATAAGATATATATATATTTCATATTCTTTTTTATTATCAT
65 ACTTTCTCTAACCATATAAGATATATATATATTTCATATTC-TTTTTATTATCAT
29978 TTTCTAACCTAATTTTATTATAATTATTTATAGTATTATGATAAGGATTGGTTCCAATTTTTTAA
1 TTTCTAACCTAATTTTATTATAATTATTTATAGTATTATGATAAGGATTGGTTCCAATTTTTTAA
* *
30043 CCTTCTCTAACCATATAAG--ATATATATATTTCATATTCTTTTTATTGTCAT
66 CTTTCTCTAACCATATAAGATATATATATATTTCATATTCTTTTTATTATCAT
* * *
30094 TTTCTAACCTAATTTTATTATAATTATTTATAGTATTTTGATAAAGATTGGTTCCAAATTTTTAA
1 TTTCTAACCTAATTTTATTATAATTATTTATAGTATTATGATAAGGATTGGTTCCAATTTTTTAA
30159 CTTTCTCTAACCATATAAGATA
66 CTTTCTCTAACCATATAAGATA
30181 GAGAAAATCG
Statistics
Matches: 193, Mismatches: 7, Indels: 7
0.93 0.03 0.03
Matches are distributed among these distances:
116 92 0.48
117 19 0.10
118 2 0.01
119 80 0.41
ACGTcount: A:0.33, C:0.11, G:0.07, T:0.50
Consensus pattern (118 bp):
TTTCTAACCTAATTTTATTATAATTATTTATAGTATTATGATAAGGATTGGTTCCAATTTTTTAA
CTTTCTCTAACCATATAAGATATATATATATTTCATATTCTTTTTATTATCAT
Found at i:30131 original size:58 final size:56
Alignment explanation
Indices: 29948--30131 Score: 129
Period size: 58 Copynumber: 3.2 Consensus size: 56
29938 ATAAGATATA
29948 TATATATTTCATATTCTTTTTTATTATCATTTTCTAACCTAATTTTATTATAATTATT
1 TATATATTTCATATTC-TTTTTATT-TCATTTTCTAACCTAATTTTATTATAATTATT
* **** ** * * ** * * * * *
30006 TATAGTATTATGATA-AGGATTGGTTCCAATTTTTTAACCTTCTCTAACCATATAA-GATA
1 TATA-TATT-TCATATTCTTTTTATTTC-ATTTTCTAACCTAATTTTA--TTATAATTATT
30065 TATATATTTCATATTCTTTTTATTGTCATTTTCTAACCTAATTTTATTATAATTATT
1 TATATATTTCATATTCTTTTTATT-TCATTTTCTAACCTAATTTTATTATAATTATT
30122 TATAGTATTT
1 TATA-TATTT
30132 TGATAAAGAT
Statistics
Matches: 85, Mismatches: 32, Indels: 18
0.63 0.24 0.13
Matches are distributed among these distances:
56 5 0.06
57 11 0.13
58 49 0.58
59 11 0.13
60 9 0.11
ACGTcount: A:0.30, C:0.11, G:0.05, T:0.54
Consensus pattern (56 bp):
TATATATTTCATATTCTTTTTATTTCATTTTCTAACCTAATTTTATTATAATTATT
Found at i:30310 original size:20 final size:20
Alignment explanation
Indices: 30263--30692 Score: 335
Period size: 20 Copynumber: 21.2 Consensus size: 20
30253 AATGACCAAC
30263 AAAATCGCAACGCGATATC--
1 AAAATCGCAACGCGAT-TCAG
* *
30282 AAAACCGCAACGCGATTTAG
1 AAAATCGCAACGCGATTCAG
* * **
30302 AAAAGCGCAACGTTGA-AAAG
1 AAAATCGCAACG-CGATTCAG
* *
30322 AAGATCGCAACACGATCTTCCA-
1 AAAATCGCAACGCGA--TT-CAG
* * *
30344 AGAATCGCAATGCGATTCAT
1 AAAATCGCAACGCGATTCAG
30364 AAAATCGCAACGCGATCTTCCA-
1 AAAATCGCAACGCGA--TT-CAG
*
30386 AGAATCGCAACGCGATTCAG
1 AAAATCGCAACGCGATTCAG
*
30406 AAAATCGCAACGCGGTTCAG
1 AAAATCGCAACGCGATTCAG
*
30426 AAAATCGCAACGCGGTTCAG
1 AAAATCGCAACGCGATTCAG
*
30446 AAAATCGCAACGCGATTAAG
1 AAAATCGCAACGCGATTCAG
30466 AAAATCGCAACGCGATTCCA-
1 AAAATCGCAACGCGATT-CAG
*
30486 AGAATCGCAACGCGATTCAG
1 AAAATCGCAACGCGATTCAG
30506 AAAATCGCAACGCGATTCCA-
1 AAAATCGCAACGCGATT-CAG
*
30526 AGAATCGCAACGCGATTCCA-
1 AAAATCGCAACGCGATT-CAG
* ***
30546 AGAATCGCAACGCGATTTTC
1 AAAATCGCAACGCGATTCAG
** ***
30566 TTAATCGCGTTGCGATTCCA-
1 AAAATCGCAACGCGATT-CAG
*
30586 AGAATCGCAACGCGATTCCA-
1 AAAATCGCAACGCGATT-CAG
*
30606 AGAATCGCAACGCGATTCCA-
1 AAAATCGCAACGCGATT-CAG
* *
30626 AGAATCGCAACGCGATTAAG
1 AAAATCGCAACGCGATTCAG
30646 AAAATCGCAACGCGATCTTCCA-
1 AAAATCGCAACGCGA--TT-CAG
* *
30668 AGAATCGCAACGCGATTAAG
1 AAAATCGCAACGCGATTCAG
30688 AAAAT
1 AAAAT
30693 GAGTAAATTC
Statistics
Matches: 342, Mismatches: 47, Indels: 43
0.79 0.11 0.10
Matches are distributed among these distances:
18 1 0.00
19 25 0.07
20 264 0.77
21 5 0.01
22 43 0.13
23 4 0.01
ACGTcount: A:0.37, C:0.26, G:0.20, T:0.17
Consensus pattern (20 bp):
AAAATCGCAACGCGATTCAG
Found at i:30689 original size:60 final size:59
Alignment explanation
Indices: 30346--30689 Score: 371
Period size: 60 Copynumber: 5.7 Consensus size: 59
30336 ATCTTCCAAG
* * *
30346 AATCGCAATGCGATT-CATAAAATCGCAACGCGATCTTCCAAGAATCGCAACGCGATTCAGAA
1 AATCGCAACGCGATTCCA-AGAATCGCAACGCGA--TT-CAAGAATCGCAACGCGATTAAGAA
* * * *
30408 AATCGCAACGCGGTT-CAGAAAATCGCAACGCGGTTCAGAAAATCGCAACGCGATTAAGAA
1 AATCGCAACGCGATTCCA-AGAATCGCAACGCGATTCA-AGAATCGCAACGCGATTAAGAA
*
30468 AATCGCAACGCGATTCCAAGAATCGCAACGCGATTCAGAAAATCGCAACGCGATTCCAAG--
1 AATCGCAACGCGATTCCAAGAATCGCAACGCGATTCA-AGAATCGCAACGCGATT--AAGAA
** ***
30528 AATCGCAACGCGATTCCAAGAATCGCAACGCGATTTTC-TTAATCGCGTTGCGATTCCAAG--
1 AATCGCAACGCGATTCCAAGAATCGCAACGCGA--TTCAAGAATCGCAACGCGATT--AAGAA
30588 AATCGCAACGCGATTCCAAGAATCGCAACGCGATTCCAAGAATCGCAACGCGATTAAGAA
1 AATCGCAACGCGATTCCAAGAATCGCAACGCGATT-CAAGAATCGCAACGCGATTAAGAA
30648 AATCGCAACGCGATCTTCCAAGAATCGCAACGCGATT-AAGAA
1 AATCGCAACGCGA--TTCCAAGAATCGCAACGCGATTCAAGAA
30690 AATGAGTAAA
Statistics
Matches: 251, Mismatches: 19, Indels: 26
0.85 0.06 0.09
Matches are distributed among these distances:
58 5 0.02
59 3 0.01
60 184 0.73
61 2 0.01
62 57 0.23
ACGTcount: A:0.36, C:0.26, G:0.20, T:0.18
Consensus pattern (59 bp):
AATCGCAACGCGATTCCAAGAATCGCAACGCGATTCAAGAATCGCAACGCGATTAAGAA
Found at i:30799 original size:6 final size:6
Alignment explanation
Indices: 30788--30843 Score: 105
Period size: 6 Copynumber: 9.5 Consensus size: 6
30778 GACACGTATT
30788 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
30836 ACC-CG ACC
1 ACCACG ACC
30844 CGAGACGAGA
Statistics
Matches: 50, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
5 5 0.10
6 45 0.90
ACGTcount: A:0.32, C:0.52, G:0.16, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:31356 original size:6 final size:6
Alignment explanation
Indices: 31340--31414 Score: 143
Period size: 6 Copynumber: 12.7 Consensus size: 6
31330 TCTCGTCTCG
31340 GGTCG- GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
31387 GGTCGT GGTCGT GGTCGT GGTCGT GGTC
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTC
31415 ATACGTGTCT
Statistics
Matches: 69, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
5 5 0.07
6 64 0.93
ACGTcount: A:0.00, C:0.17, G:0.51, T:0.32
Consensus pattern (6 bp):
GGTCGT
Found at i:31565 original size:20 final size:20
Alignment explanation
Indices: 31509--31942 Score: 445
Period size: 20 Copynumber: 21.2 Consensus size: 20
31499 GAATTTACTC
31509 ATTTTCTGAATCGCGTTGCG
1 ATTTTCTGAATCGCGTTGCG
**
31529 ATTCTTGGGAGATCGCGTTGCG
1 ATT-TTCTGA-ATCGCGTTGCG
* *
31551 AATTACTGAATCGCGTTGCG
1 ATTTTCTGAATCGCGTTGCG
*
31571 ATTTTCTTAATCGCGTTGCG
1 ATTTTCTGAATCGCGTTGCG
*
31591 ATTCTT-GGAAGATCGCGTTGCG
1 ATT-TTCTG-A-ATCGCGTTGCG
*
31613 ATTTTCTTAATCGCGTTGCG
1 ATTTTCTGAATCGCGTTGCG
*
31633 ATTCTT-GGAATCGCGTTGCG
1 ATT-TTCTGAATCGCGTTGCG
31653 ATTTTCTGAATCGCGTTGCG
1 ATTTTCTGAATCGCGTTGCG
*
31673 ATTCTT-GGAATCGCGTTGCG
1 ATT-TTCTGAATCGCGTTGCG
*
31693 ATTTTCTTAATCGCGTTGCG
1 ATTTTCTGAATCGCGTTGCG
*
31713 ATTCTT-GGAAGATCGCGTTGCG
1 ATT-TTCTG-A-ATCGCGTTGCG
31735 ATTTTCTGAATCGCGTTGCG
1 ATTTTCTGAATCGCGTTGCG
31755 ATTTTCTGAATCGCGTTGCG
1 ATTTTCTGAATCGCGTTGCG
31775 ATTTTCTGAATCGCGTTGCG
1 ATTTTCTGAATCGCGTTGCG
31795 ATTTTCTGAATCGCGTTGCG
1 ATTTTCTGAATCGCGTTGCG
*
31815 ATTCTT-GGAAGATCGCGTTGCG
1 ATT-TTCTG-A-ATCGCGTTGCG
* *
31837 ATTTTATGAATCGCATTGCG
1 ATTTTCTGAATCGCGTTGCG
*
31857 ATTCTT-GGAAGATCGCGTTGCG
1 ATT-TTCTG-A-ATCGCGTTGCG
* ** *
31879 ATCTTCT-TTTCAACGTTGCG
1 ATTTTCTGAATC-GCGTTGCG
* *
31899 CTTTTCTAAATCGCGTTGCG
1 ATTTTCTGAATCGCGTTGCG
*
31919 -GTTT-TGATATCGCGTTGCG
1 ATTTTCTGA-ATCGCGTTGCG
31938 ATTTT
1 ATTTT
31943 GTTGGTCATT
Statistics
Matches: 348, Mismatches: 40, Indels: 52
0.79 0.09 0.12
Matches are distributed among these distances:
18 2 0.01
19 20 0.06
20 221 0.64
21 36 0.10
22 69 0.20
ACGTcount: A:0.16, C:0.19, G:0.26, T:0.38
Consensus pattern (20 bp):
ATTTTCTGAATCGCGTTGCG
Found at i:31687 original size:102 final size:100
Alignment explanation
Indices: 31518--31859 Score: 422
Period size: 102 Copynumber: 3.3 Consensus size: 100
31508 CATTTTCTGA
* * *
31518 ATCGCGTTGCGATTCTTGGGAGATCGCGTTGCGAATTACTGAATCGCGTTGCGATTTTCTT-AAT
1 ATCGCGTTGCGATT-TTAGGA-ATCGCGTTGCGATTTTCTGAATCGCGTTGCGA--TTCTTGAAT
* **
31582 CGCGTTGCGATTCTTGGAAGATCGCGTTGCGATT-TTCTTA-
62 CGCGTTGCGATT-TTCG-A-ATCGCGTTGCGATTCTTCGAAG
31622 ATCGCGTTGCGATTCTT-GGAATCGCGTTGCGATTTTCTGAATCGCGTTGCGATTCTTGGAATCG
1 ATCGCGTTGCGATT-TTAGGAATCGCGTTGCGATTTTCTGAATCGCGTTGCGATTCTT-GAATCG
* *
31686 CGTTGCGATTTTCTTAATCGCGTTGCGATTCTTGGAAG
64 CGTTGCGATTTTC-GAATCGCGTTGCGATTCTTCGAAG
** *
31724 ATCGCGTTGCGATTTTCTGAATCGCGTTGCGATTTTCTGAATCGCGTTGCGATTTTCTGAATCGC
1 ATCGCGTTGCGATTTTAGGAATCGCGTTGCGATTTTCTGAATCGCGTTGCGATTCT-TGAATCGC
*
31789 GTTGCGATTTTCTGAATCGCGTTGCGATTCTTGGAAG
65 GTTGCGATTTTC-GAATCGCGTTGCGATTCTTCGAAG
* *
31826 ATCGCGTTGCGATTTTATGAATCGCATTGCGATT
1 ATCGCGTTGCGATTTTAGGAATCGCGTTGCGATT
31860 CTTGGAAGAT
Statistics
Matches: 219, Mismatches: 12, Indels: 16
0.89 0.05 0.06
Matches are distributed among these distances:
100 19 0.09
101 8 0.04
102 171 0.78
103 4 0.02
104 17 0.08
ACGTcount: A:0.17, C:0.19, G:0.27, T:0.37
Consensus pattern (100 bp):
ATCGCGTTGCGATTTTAGGAATCGCGTTGCGATTTTCTGAATCGCGTTGCGATTCTTGAATCGCG
TTGCGATTTTCGAATCGCGTTGCGATTCTTCGAAG
Found at i:31898 original size:42 final size:40
Alignment explanation
Indices: 31744--31880 Score: 136
Period size: 42 Copynumber: 3.3 Consensus size: 40
31734 GATTTTCTGA
* * *
31744 ATCGCGTTGCGATTTTCTGAATCGCGTTGCGATT-TTCTG-A-
1 ATCGCGTTGCGATTTTATCAAT--CGTTGCGATTCTT-GGAAG
* *
31784 ATCGCGTTGCGATTTTCTGAATCGCGTTGCGATTCTTGGAAG
1 ATCGCGTTGCGATTTTATCAAT--CGTTGCGATTCTTGGAAG
*
31826 ATCGCGTTGCGATTTTATGAATCGCATTGCGATTCTTGGAAG
1 ATCGCGTTGCGATTTTATCAATCG--TTGCGATTCTTGGAAG
31868 ATCGCGTTGCGAT
1 ATCGCGTTGCGAT
31881 CTTCTTTTCA
Statistics
Matches: 90, Mismatches: 2, Indels: 8
0.90 0.02 0.08
Matches are distributed among these distances:
40 37 0.41
41 3 0.03
42 50 0.56
ACGTcount: A:0.18, C:0.19, G:0.27, T:0.36
Consensus pattern (40 bp):
ATCGCGTTGCGATTTTATCAATCGTTGCGATTCTTGGAAG
Found at i:33209 original size:29 final size:29
Alignment explanation
Indices: 33167--33255 Score: 169
Period size: 29 Copynumber: 3.1 Consensus size: 29
33157 GCATATGTTC
33167 AACAAATATAATGAGGGAAGACATTTAAA
1 AACAAATATAATGAGGGAAGACATTTAAA
33196 AACAAATATAATGAGGGAAGACATTTAAA
1 AACAAATATAATGAGGGAAGACATTTAAA
*
33225 AACAAATATAATGAGGGAAGATATTTAAA
1 AACAAATATAATGAGGGAAGACATTTAAA
33254 AA
1 AA
33256 TAAAATTTAA
Statistics
Matches: 59, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
29 59 1.00
ACGTcount: A:0.56, C:0.06, G:0.17, T:0.21
Consensus pattern (29 bp):
AACAAATATAATGAGGGAAGACATTTAAA
Found at i:36611 original size:34 final size:32
Alignment explanation
Indices: 36542--36612 Score: 79
Period size: 34 Copynumber: 2.2 Consensus size: 32
36532 ACCTTACAAA
* * *
36542 TTCCCTAGTTTTTCCGGGATAAACTAGTACCT
1 TTCCCTAGTTTTACCGGGATAAACTAGAACAT
* *
36574 TTCCCTAGCTTTTACACGGGATTAGCTAGAACAT
1 TTCCCTAG-TTTTAC-CGGGATAAACTAGAACAT
36608 TTCCC
1 TTCCC
36613 CTTTACAAAA
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
32 8 0.25
33 5 0.16
34 19 0.59
ACGTcount: A:0.23, C:0.27, G:0.15, T:0.35
Consensus pattern (32 bp):
TTCCCTAGTTTTACCGGGATAAACTAGAACAT
Found at i:36921 original size:21 final size:21
Alignment explanation
Indices: 36895--36936 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
36885 CCAGAATGGG
*
36895 GGGAATCGGTACCCCTTCATA
1 GGGAATCGATACCCCTTCATA
36916 GGGAATCGATACCCCTTCATA
1 GGGAATCGATACCCCTTCATA
36937 ATATTCAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.26, C:0.29, G:0.21, T:0.24
Consensus pattern (21 bp):
GGGAATCGATACCCCTTCATA
Found at i:37092 original size:19 final size:19
Alignment explanation
Indices: 37046--37093 Score: 69
Period size: 19 Copynumber: 2.5 Consensus size: 19
37036 CTCTGGTTAA
* * *
37046 TGTTCAAACAGTGATTTAC
1 TGTTCAAATAGTAATGTAC
37065 TGTTCAAATAGTAATGTAC
1 TGTTCAAATAGTAATGTAC
37084 TGTTCAAATA
1 TGTTCAAATA
37094 ATAAATTACT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.35, C:0.12, G:0.15, T:0.38
Consensus pattern (19 bp):
TGTTCAAATAGTAATGTAC
Found at i:37103 original size:19 final size:18
Alignment explanation
Indices: 37061--37108 Score: 60
Period size: 19 Copynumber: 2.6 Consensus size: 18
37051 AAACAGTGAT
*
37061 TTACTGTTCAAATAGTAA
1 TTACTGTTCAAATAATAA
37079 TGTACTGTTCAAATAATAAA
1 T-TACTGTTCAAATAAT-AA
*
37099 TTACTATTCA
1 TTACTGTTCA
37109 TAAAAACATT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
18 1 0.04
19 22 0.85
20 3 0.12
ACGTcount: A:0.40, C:0.12, G:0.08, T:0.40
Consensus pattern (18 bp):
TTACTGTTCAAATAATAA
Found at i:37205 original size:29 final size:31
Alignment explanation
Indices: 37173--37232 Score: 97
Period size: 29 Copynumber: 2.0 Consensus size: 31
37163 AAATTTTGAA
*
37173 TAAATTCAATT-AAGTCCAAATA-CATTTTG
1 TAAATTCAATTCAAGTCCAAAAACCATTTTG
37202 TAAATTCAATTCAAGTCCAAAAACCATTTTG
1 TAAATTCAATTCAAGTCCAAAAACCATTTTG
37233 CCTTAAATTG
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
29 11 0.39
30 10 0.36
31 7 0.25
ACGTcount: A:0.42, C:0.17, G:0.07, T:0.35
Consensus pattern (31 bp):
TAAATTCAATTCAAGTCCAAAAACCATTTTG
Found at i:41225 original size:187 final size:185
Alignment explanation
Indices: 40966--41345 Score: 643
Period size: 187 Copynumber: 2.0 Consensus size: 185
40956 ATAAAAACTA
* *
40966 AATATTTTTTAATTAAAAATATAGTTTATAATTAATTTAAATAATATATAATTATAAAATAAAAA
1 AATATTTTTTAATTAAAAAAATAGTTTACAATTAATTTAAATAATATATAATTATAAAATAAAAA
** *
41031 ATTTATATAATTTTTTTAATTAATTAATATTGATTTAGGTTTAAAAGTTATTGGATCTTAAATTA
66 ATTTATATAAAATTTTTAATCAATTAATATTGATTTAGGTTTAAAAGTTATTGGATCTTAAATTA
* *
41096 TTAATTGGGTTTTAAATGGTTTGGGCTGAGCCCATATGTTATATATAATATATTT
131 TTAATTGAGTTTTAAATGGTTTGAGCTGAGCCCATATGTTATATATAATATATTT
41151 AATATTTTTTAATTCAAAAAAAATAGTTTACAATTAATTTAAATAATATATAATTATAAAATAAA
1 AATATTTTTTAATT--AAAAAAATAGTTTACAATTAATTTAAATAATATATAATTATAAAATAAA
*
41216 AATTTTATATAAAATTTTTAATCAATTAATATTGATTTAGGTTTAAAAGTTATTGGATCTTAAAT
64 AAATTTATATAAAATTTTTAATCAATTAATATTGATTTAGGTTTAAAAGTTATTGGATCTTAAAT
* *
41281 TATTAATTGAGTTTTAAATGGTTTGAGTTGAGCTCATATGTTATATATAATATATTT
129 TATTAATTGAGTTTTAAATGGTTTGAGCTGAGCCCATATGTTATATATAATATATTT
*
41338 AAAATTTT
1 AATATTTT
41346 AAATTTAATT
Statistics
Matches: 182, Mismatches: 11, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
185 14 0.08
187 168 0.92
ACGTcount: A:0.42, C:0.03, G:0.09, T:0.46
Consensus pattern (185 bp):
AATATTTTTTAATTAAAAAAATAGTTTACAATTAATTTAAATAATATATAATTATAAAATAAAAA
ATTTATATAAAATTTTTAATCAATTAATATTGATTTAGGTTTAAAAGTTATTGGATCTTAAATTA
TTAATTGAGTTTTAAATGGTTTGAGCTGAGCCCATATGTTATATATAATATATTT
Found at i:41770 original size:20 final size:20
Alignment explanation
Indices: 41745--41783 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
41735 AATCATCTTA
*
41745 GTTCATCTAGTATTGATACC
1 GTTCATCTAGTATCGATACC
41765 GTTCATCTAGTATCGATAC
1 GTTCATCTAGTATCGATAC
41784 ACAAACTCAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.26, C:0.21, G:0.15, T:0.38
Consensus pattern (20 bp):
GTTCATCTAGTATCGATACC
Found at i:42614 original size:22 final size:22
Alignment explanation
Indices: 42586--42628 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
42576 TACTAACGTG
*
42586 GAATTTATGGTGTTACATACAA
1 GAATTTAGGGTGTTACATACAA
42608 GAATTTAGGGTGTTACATACA
1 GAATTTAGGGTGTTACATACA
42629 GGATGCTAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.35, C:0.09, G:0.21, T:0.35
Consensus pattern (22 bp):
GAATTTAGGGTGTTACATACAA
Found at i:43939 original size:29 final size:29
Alignment explanation
Indices: 43896--43952 Score: 96
Period size: 29 Copynumber: 2.0 Consensus size: 29
43886 TCGTCCCTTT
*
43896 AAGTTTATTTTTTTAAAATAAAATTTTGC
1 AAGTTTATTTCTTTAAAATAAAATTTTGC
*
43925 AAGTTTATTTCTTTAAAATTAAATTTTG
1 AAGTTTATTTCTTTAAAATAAAATTTTG
43953 GGTACGTCAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.37, C:0.04, G:0.07, T:0.53
Consensus pattern (29 bp):
AAGTTTATTTCTTTAAAATAAAATTTTGC
Found at i:46463 original size:21 final size:21
Alignment explanation
Indices: 46424--46464 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
46414 TAAAAAAAAT
* *
46424 TACCTAAAACATTATTATTTC
1 TACCTAAAACATCAATATTTC
*
46445 TACCTAAAATATCAATATTT
1 TACCTAAAACATCAATATTT
46465 TTTAAATTTC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.41, C:0.17, G:0.00, T:0.41
Consensus pattern (21 bp):
TACCTAAAACATCAATATTTC
Found at i:46819 original size:2 final size:2
Alignment explanation
Indices: 46812--46850 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
46802 ATTCATGCAT
46812 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
46851 TATTAATCTA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:50221 original size:16 final size:15
Alignment explanation
Indices: 50200--50229 Score: 51
Period size: 15 Copynumber: 1.9 Consensus size: 15
50190 TATCTATAAT
50200 ATTATAATATTTAAAA
1 ATTATAA-ATTTAAAA
50216 ATTATAAATTTAAA
1 ATTATAAATTTAAA
50230 TGCGTTTGAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (15 bp):
ATTATAAATTTAAAA
Found at i:62253 original size:27 final size:25
Alignment explanation
Indices: 62223--62272 Score: 64
Period size: 27 Copynumber: 1.9 Consensus size: 25
62213 TATAAAAAAT
62223 ATTTAAATAATATAAATTATAATCTAG
1 ATTTAAATAATAT-AA-TATAATCTAG
* *
62250 ATTTTAATTATATAATATAATCT
1 ATTTAAATAATATAATATAATCT
62273 GTCCATTATA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 8 0.38
26 2 0.10
27 11 0.52
ACGTcount: A:0.48, C:0.04, G:0.02, T:0.46
Consensus pattern (25 bp):
ATTTAAATAATATAATATAATCTAG
Found at i:63580 original size:22 final size:22
Alignment explanation
Indices: 63546--63587 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
63536 TTTAAGTATG
* *
63546 TTTTTATAATTTTATAATTTAA
1 TTTTAATAATTTTAAAATTTAA
*
63568 TTTTAATATTTTTAAAATTT
1 TTTTAATAATTTTAAAATTT
63588 TATACTACAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (22 bp):
TTTTAATAATTTTAAAATTTAA
Found at i:63667 original size:3 final size:3
Alignment explanation
Indices: 63659--63696 Score: 67
Period size: 3 Copynumber: 12.7 Consensus size: 3
63649 GTGTATATAG
*
63659 TAT TAT TAT TAT TAT TAT TGT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
63697 AAATAAAAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.32, C:0.00, G:0.03, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:65094 original size:18 final size:18
Alignment explanation
Indices: 65071--65134 Score: 94
Period size: 18 Copynumber: 3.6 Consensus size: 18
65061 TGTCCCAAAC
*
65071 GATAATCGTGCTTCCAAT
1 GATAATCGTGCTTCCTAT
*
65089 GATAATCGTGCTTCCTAC
1 GATAATCGTGCTTCCTAT
65107 GATAATCAG-GCTTCCTAT
1 GATAATC-GTGCTTCCTAT
65125 GATAATCGTG
1 GATAATCGTG
65135 TTTCTTATAG
Statistics
Matches: 41, Mismatches: 3, Indels: 4
0.85 0.06 0.08
Matches are distributed among these distances:
17 1 0.02
18 39 0.95
19 1 0.02
ACGTcount: A:0.27, C:0.22, G:0.19, T:0.33
Consensus pattern (18 bp):
GATAATCGTGCTTCCTAT
Found at i:77910 original size:17 final size:17
Alignment explanation
Indices: 77888--77920 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
77878 ATAAAAAATA
77888 TTTTTAATTA-ATTATTG
1 TTTTT-ATTATATTATTG
77905 TTTTTATTATATTATT
1 TTTTTATTATATTATT
77921 TAACAATCAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.27, C:0.00, G:0.03, T:0.70
Consensus pattern (17 bp):
TTTTTATTATATTATTG
Found at i:86407 original size:20 final size:20
Alignment explanation
Indices: 86374--86430 Score: 66
Period size: 17 Copynumber: 3.0 Consensus size: 20
86364 TTTAATTAAA
* *
86374 AAATAATTTACAATTAATTT
1 AAATAATATCCAATTAATTT
86394 AAATAATATCCAATT-A--T
1 AAATAATATCCAATTAATTT
*
86411 AAATAATATCTAATTAATTT
1 AAATAATATCCAATTAATTT
86431 GATTCAAACA
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
17 15 0.48
18 1 0.03
19 1 0.03
20 14 0.45
ACGTcount: A:0.51, C:0.07, G:0.00, T:0.42
Consensus pattern (20 bp):
AAATAATATCCAATTAATTT
Found at i:92803 original size:54 final size:54
Alignment explanation
Indices: 92721--92885 Score: 330
Period size: 54 Copynumber: 3.1 Consensus size: 54
92711 AAAGTTAAAC
92721 TTACATCTTAAACACTAAATTATAACTCATAACCCATAAATTATAAGCCTTAAG
1 TTACATCTTAAACACTAAATTATAACTCATAACCCATAAATTATAAGCCTTAAG
92775 TTACATCTTAAACACTAAATTATAACTCATAACCCATAAATTATAAGCCTTAAG
1 TTACATCTTAAACACTAAATTATAACTCATAACCCATAAATTATAAGCCTTAAG
92829 TTACATCTTAAACACTAAATTATAACTCATAACCCATAAATTATAAGCCTTAAG
1 TTACATCTTAAACACTAAATTATAACTCATAACCCATAAATTATAAGCCTTAAG
92883 TTA
1 TTA
92886 TAAAATCATA
Statistics
Matches: 111, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
54 111 1.00
ACGTcount: A:0.44, C:0.20, G:0.04, T:0.32
Consensus pattern (54 bp):
TTACATCTTAAACACTAAATTATAACTCATAACCCATAAATTATAAGCCTTAAG
Found at i:92942 original size:19 final size:21
Alignment explanation
Indices: 92902--92962 Score: 65
Period size: 20 Copynumber: 3.0 Consensus size: 21
92892 CATATCTCTT
*
92902 AAATAAA-ATAAATTGTATTA
1 AAATAAATATAAATTATATTA
92922 AAATAAATA-AAATTATA-TA
1 AAATAAATATAAATTATATTA
*
92941 AACTAAATATCAAATTTATATT
1 AAATAAATAT-AAA-TTATATT
92963 TGATTATTTG
Statistics
Matches: 34, Mismatches: 2, Indels: 7
0.79 0.05 0.16
Matches are distributed among these distances:
19 10 0.29
20 14 0.41
21 4 0.12
22 5 0.15
23 1 0.03
ACGTcount: A:0.59, C:0.03, G:0.02, T:0.36
Consensus pattern (21 bp):
AAATAAATATAAATTATATTA
Found at i:92990 original size:46 final size:46
Alignment explanation
Indices: 92933--93022 Score: 153
Period size: 46 Copynumber: 2.0 Consensus size: 46
92923 AATAAATAAA
* *
92933 ATTATATAAACTAAATATCAAATTTATATTTGATTATTTGTTTGAT
1 ATTATAAAAACTAAATATCAAAGTTATATTTGATTATTTGTTTGAT
*
92979 ATTATAAAAACTAAATTTCAAAGTTATATTTGATTATTTGTTTG
1 ATTATAAAAACTAAATATCAAAGTTATATTTGATTATTTGTTTG
93023 GTTTCATCAT
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
46 41 1.00
ACGTcount: A:0.39, C:0.04, G:0.08, T:0.49
Consensus pattern (46 bp):
ATTATAAAAACTAAATATCAAAGTTATATTTGATTATTTGTTTGAT
Found at i:93492 original size:60 final size:60
Alignment explanation
Indices: 93347--93503 Score: 172
Period size: 60 Copynumber: 2.6 Consensus size: 60
93337 AGAGTCTTTC
* * * * *
93347 TTTGTTGAGTCTCCTGACTATTAAAAATTATGAAATAATCCTTTGACTATGGGATATTAT
1 TTTGTTGAGTCTCTTGACTATTAAAAGTTATAAAATAATCCTTTGACTATAGGACATTAT
* * * ** * *
93407 TTTGTTGAGTCTCTTAATTACTAAAAGTTATAAAATGGTCTTTTGACTATATGACATTAT
1 TTTGTTGAGTCTCTTGACTATTAAAAGTTATAAAATAATCCTTTGACTATAGGACATTAT
* *
93467 TTTGTTGAGTC-CATTGACAATTAAAAGTTACAAAATA
1 TTTGTTGAGTCTC-TTGACTATTAAAAGTTATAAAATA
93504 GGCACTTGAT
Statistics
Matches: 78, Mismatches: 18, Indels: 2
0.80 0.18 0.02
Matches are distributed among these distances:
59 1 0.01
60 77 0.99
ACGTcount: A:0.34, C:0.11, G:0.14, T:0.41
Consensus pattern (60 bp):
TTTGTTGAGTCTCTTGACTATTAAAAGTTATAAAATAATCCTTTGACTATAGGACATTAT
Found at i:94760 original size:20 final size:22
Alignment explanation
Indices: 94735--94784 Score: 61
Period size: 20 Copynumber: 2.4 Consensus size: 22
94725 GTTTAGGTAT
94735 GATTTAAG-GGTTAAGATT-AA
1 GATTTAAGAGGTTAAGATTCAA
* *
94755 GATTT-AGAGTTTAAGGTTCAA
1 GATTTAAGAGGTTAAGATTCAA
94776 GATTTAAGA
1 GATTTAAGA
94785 TTTACATTTA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
19 2 0.08
20 13 0.52
21 7 0.28
22 3 0.12
ACGTcount: A:0.38, C:0.02, G:0.24, T:0.36
Consensus pattern (22 bp):
GATTTAAGAGGTTAAGATTCAA
Found at i:94794 original size:27 final size:26
Alignment explanation
Indices: 94736--94795 Score: 77
Period size: 27 Copynumber: 2.2 Consensus size: 26
94726 TTTAGGTATG
*
94736 ATTTAAGGGTTAAGATTAAGATTTAG
1 ATTTAAGGGTTAAGATTAAGATTTAC
94762 AGTTTAA-GGTTCAAGATTTAAGATTTAC
1 A-TTTAAGGGTT-AAGA-TTAAGATTTAC
94790 ATTTAA
1 ATTTAA
94796 TTTTGATTAT
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
26 5 0.17
27 14 0.47
28 11 0.37
ACGTcount: A:0.38, C:0.03, G:0.18, T:0.40
Consensus pattern (26 bp):
ATTTAAGGGTTAAGATTAAGATTTAC
Found at i:96525 original size:19 final size:17
Alignment explanation
Indices: 96497--96550 Score: 51
Period size: 19 Copynumber: 3.2 Consensus size: 17
96487 TAAATATAAA
96497 TAAT-ATTAATTAAATT
1 TAATAATTAATTAAATT
* *
96513 TAAGTACATTAATAAAATA
1 TAA-TA-ATTAATTAAATT
96532 TAATAATT--TTAAATT
1 TAATAATTAATTAAATT
96547 TAAT
1 TAAT
96551 TAATATTGAA
Statistics
Matches: 31, Mismatches: 4, Indels: 7
0.74 0.10 0.17
Matches are distributed among these distances:
15 9 0.29
16 3 0.10
17 4 0.13
18 2 0.06
19 13 0.42
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.44
Consensus pattern (17 bp):
TAATAATTAATTAAATT
Found at i:99572 original size:14 final size:14
Alignment explanation
Indices: 99551--99594 Score: 54
Period size: 14 Copynumber: 3.1 Consensus size: 14
99541 ATATTCCTCT
99551 TTAT-TTATTTATA
1 TTATATTATTTATA
*
99564 TTATATTATTTTTA
1 TTATATTATTTATA
99578 TTATATATATCTTATA
1 TTATAT-TAT-TTATA
99594 T
1 T
99595 CATTATATAT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
13 4 0.15
14 14 0.54
15 3 0.12
16 5 0.19
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.66
Consensus pattern (14 bp):
TTATATTATTTATA
Found at i:99592 original size:25 final size:26
Alignment explanation
Indices: 99550--99613 Score: 71
Period size: 25 Copynumber: 2.6 Consensus size: 26
99540 TATATTCCTC
* *
99550 TTTATT-TATTTATATTATATTATT-
1 TTTATTATATATATATTATATCATTA
*
99574 TTTATTATATATATCTTATATCATTA
1 TTTATTATATATATATTATATCATTA
*
99600 TATA-TATATATATA
1 TTTATTATATATATA
99614 GATATATTAA
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
24 6 0.18
25 24 0.73
26 3 0.09
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.61
Consensus pattern (26 bp):
TTTATTATATATATATTATATCATTA
Found at i:99741 original size:18 final size:18
Alignment explanation
Indices: 99715--99752 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
99705 TTTATATATA
99715 TTATATTTTTACT-TTATT
1 TTATATTTTT-CTATTATT
*
99733 TTATTTTTTTCTATTATT
1 TTATATTTTTCTATTATT
99751 TT
1 TT
99753 TTCCCTTAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 2 0.11
18 16 0.89
ACGTcount: A:0.18, C:0.05, G:0.00, T:0.76
Consensus pattern (18 bp):
TTATATTTTTCTATTATT
Found at i:99968 original size:18 final size:16
Alignment explanation
Indices: 99947--99986 Score: 53
Period size: 19 Copynumber: 2.3 Consensus size: 16
99937 TTTTTTTAAC
99947 ATTTTATTCATTTTGTTT
1 ATTTTATT-ATTTT-TTT
99965 ATTTTTATTATTTTTTT
1 A-TTTTATTATTTTTTT
99982 ATTTT
1 ATTTT
99987 TTACGTGTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
16 4 0.19
17 4 0.19
18 6 0.29
19 7 0.33
ACGTcount: A:0.17, C:0.03, G:0.03, T:0.78
Consensus pattern (16 bp):
ATTTTATTATTTTTTT
Found at i:99989 original size:18 final size:19
Alignment explanation
Indices: 99948--99987 Score: 66
Period size: 17 Copynumber: 2.2 Consensus size: 19
99938 TTTTTTAACA
99948 TTTTATTCATTTTGTTTAT
1 TTTTATTCATTTTGTTTAT
99967 TTTTATT-ATTTT-TTTAT
1 TTTTATTCATTTTGTTTAT
99984 TTTT
1 TTTT
99988 TACGTGTTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
17 9 0.43
18 5 0.24
19 7 0.33
ACGTcount: A:0.15, C:0.03, G:0.03, T:0.80
Consensus pattern (19 bp):
TTTTATTCATTTTGTTTAT
Found at i:100029 original size:26 final size:26
Alignment explanation
Indices: 99967--100025 Score: 75
Period size: 26 Copynumber: 2.3 Consensus size: 26
99957 TTTTGTTTAT
*
99967 TTTTATTATTTTTTTATTTTTTACGTG
1 TTTTATTA-TTTTTCATTTTTTACGTG
* *
99994 TTTTGTTATTTTTCATTTTTT-CTTG
1 TTTTATTATTTTTCATTTTTTACGTG
100019 TTTTATT
1 TTTTATT
100026 TATTATTCTC
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
25 9 0.32
26 12 0.43
27 7 0.25
ACGTcount: A:0.12, C:0.05, G:0.07, T:0.76
Consensus pattern (26 bp):
TTTTATTATTTTTCATTTTTTACGTG
Found at i:103079 original size:23 final size:24
Alignment explanation
Indices: 103053--103097 Score: 83
Period size: 24 Copynumber: 1.9 Consensus size: 24
103043 TCAAAACAAA
103053 AAAGAG-AAAAAAAGAGAAAAAGT
1 AAAGAGAAAAAAAAGAGAAAAAGT
103076 AAAGAGAAAAAAAAGAGAAAAA
1 AAAGAGAAAAAAAAGAGAAAAA
103098 AAAACAAAGG
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
23 6 0.29
24 15 0.71
ACGTcount: A:0.78, C:0.00, G:0.20, T:0.02
Consensus pattern (24 bp):
AAAGAGAAAAAAAAGAGAAAAAGT
Found at i:103081 original size:13 final size:11
Alignment explanation
Indices: 103050--103100 Score: 77
Period size: 11 Copynumber: 4.5 Consensus size: 11
103040 CAATCAAAAC
103050 AAAAAAGAG-A
1 AAAAAAGAGAA
103060 AAAAAAGAGAA
1 AAAAAAGAGAA
103071 AAAGTAAAGAGAA
1 AAA--AAAGAGAA
103084 AAAAAAGAGAA
1 AAAAAAGAGAA
103095 AAAAAA
1 AAAAAA
103101 ACAAAGGAAA
Statistics
Matches: 38, Mismatches: 0, Indels: 5
0.88 0.00 0.12
Matches are distributed among these distances:
10 9 0.24
11 18 0.47
13 11 0.29
ACGTcount: A:0.80, C:0.00, G:0.18, T:0.02
Consensus pattern (11 bp):
AAAAAAGAGAA
Found at i:103101 original size:13 final size:13
Alignment explanation
Indices: 103059--103101 Score: 54
Period size: 13 Copynumber: 3.5 Consensus size: 13
103049 CAAAAAAGAG
103059 AAAAAAAGAGAAA
1 AAAAAAAGAGAAA
**
103072 AAGTAAAGAG--A
1 AAAAAAAGAGAAA
103083 AAAAAAAGAGAAA
1 AAAAAAAGAGAAA
103096 AAAAAA
1 AAAAAA
103102 CAAAGGAAAT
Statistics
Matches: 24, Mismatches: 4, Indels: 4
0.75 0.12 0.12
Matches are distributed among these distances:
11 9 0.38
13 15 0.62
ACGTcount: A:0.81, C:0.00, G:0.16, T:0.02
Consensus pattern (13 bp):
AAAAAAAGAGAAA
Found at i:104301 original size:32 final size:32
Alignment explanation
Indices: 104229--104340 Score: 138
Period size: 31 Copynumber: 3.5 Consensus size: 32
104219 TGAGGGCATC
*
104229 TTTGAAGATTCAACATCAAATGTTGGGCCATTT
1 TTTG-AGATTCAACATCAAATGTTGGGGCATTT
*
104262 TTT-AGATTTAACATCAAATGTTGGGGCATTT
1 TTTGAGATTCAACATCAAATGTTGGGGCATTT
* * *
104293 TTTGAGATTCAACATCGAATATTGGGGCA-TC
1 TTTGAGATTCAACATCAAATGTTGGGGCATTT
*
104324 TTTGGGAATTCAACATC
1 TTTGAG-ATTCAACATC
104341 CTGATGCAAA
Statistics
Matches: 70, Mismatches: 7, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
31 35 0.50
32 32 0.46
33 3 0.04
ACGTcount: A:0.29, C:0.14, G:0.20, T:0.37
Consensus pattern (32 bp):
TTTGAGATTCAACATCAAATGTTGGGGCATTT
Found at i:105301 original size:36 final size:36
Alignment explanation
Indices: 105214--105332 Score: 130
Period size: 36 Copynumber: 3.3 Consensus size: 36
105204 TATGTTTTAT
* ** * * *
105214 TTGAAAAAAATTTCATCTCCCTTGAGACATTTTCTT
1 TTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCTC
* * *
105250 TTGGAACTAAGTTTTGTCTCTCTTGGGACAGTTTCTC
1 TTGAAAC-AAATTTTGTCTCTCTTGAGACAGTTTCTC
* *
105287 TTGAAACAAATTTTGTCTCTCTTGAGATAGTTTCCC
1 TTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCTC
105323 TTGAAACAAA
1 TTGAAACAAA
105333 ATCTTTGAAT
Statistics
Matches: 68, Mismatches: 14, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
36 40 0.59
37 28 0.41
ACGTcount: A:0.27, C:0.18, G:0.14, T:0.40
Consensus pattern (36 bp):
TTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCTC
Found at i:105394 original size:65 final size:65
Alignment explanation
Indices: 105290--105463 Score: 215
Period size: 65 Copynumber: 2.6 Consensus size: 65
105280 GTTTCTCTTG
* * * **
105290 AAACAAATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATCTTTGAATTTATTTCCCCTA
1 AAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACAAAATCTTCAAATTTATTTCCCCTA
*
105355 AAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACACAAAATCTTCAAATTTATTTCCCT
1 AAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTG-AA-ACAAAATCTTCAAATTTATTTCCCC
105420 TA
64 TA
* * * * *
105422 AAACAAAATTGTATTTCCCTTGAGACCGTTT-TCATGAAACAA
1 AAAC-AAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACAA
105464 CAGATATCTT
Statistics
Matches: 95, Mismatches: 11, Indels: 6
0.85 0.10 0.05
Matches are distributed among these distances:
65 37 0.39
66 4 0.04
67 32 0.34
68 22 0.23
ACGTcount: A:0.33, C:0.21, G:0.09, T:0.37
Consensus pattern (65 bp):
AAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACAAAATCTTCAAATTTATTTCCCCTA
Found at i:105460 original size:67 final size:67
Alignment explanation
Indices: 105290--105462 Score: 190
Period size: 67 Copynumber: 2.6 Consensus size: 67
105280 GTTTCTCTTG
* * * * * * **
105290 AAACAAATTTTGTCTCTCTTGAGATAGTTTCCCTTG-AA-ACAAAATCTTTGAATTTATTTCCCC
1 AAACAAATTGTATCTCCCTTGAGACAGTTTCTCATGAAACACAAAATCTTCAAATTTATTTCCCC
105353 TA
66 TA
* * * *
105355 AAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACACAAAATCTTCAAATTTATTTCCCT
1 AAACAAATTGTATCTCCCTTGAGACAGTTTCTCATGAAACACAAAATCTTCAAATTTATTTCCCC
105420 TA
66 TA
* *
105422 AAACAAAATTGTATTTCCCTTGAGACCGTTT-TCATGAAACA
1 AAAC-AAATTGTATCTCCCTTGAGACAGTTTCTCATGAAACA
105463 ACAGATATCT
Statistics
Matches: 94, Mismatches: 11, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
65 33 0.35
66 2 0.02
67 37 0.39
68 22 0.23
ACGTcount: A:0.33, C:0.21, G:0.09, T:0.37
Consensus pattern (67 bp):
AAACAAATTGTATCTCCCTTGAGACAGTTTCTCATGAAACACAAAATCTTCAAATTTATTTCCCC
TA
Found at i:106427 original size:103 final size:106
Alignment explanation
Indices: 106172--106435 Score: 297
Period size: 110 Copynumber: 2.5 Consensus size: 106
106162 TCGAAGGGGC
* * * *
106172 TTCCCAGTTTCATAGCCAATTTCAACTTCACA-GCGAGGGATATTGGACTCAAGACAAAACAAGC
1 TTCCCAGTTCCAGAGCCAATTTTAACTTCACACG-GA-GGATATTGGACTCGAGACAAAACAAGC
*
106236 TCAACTTCACAACGAAGGGGCGACTGATTGTCAACAAACAACT
64 TCAACTTCACAACGAAGGGGCGACTGACTGTCAACAAACAACT
* * * * *
106279 TT-TCAGTTTCATTCAGAGTCAATTTTAACTTCACAGCGAAGGATATTGAACTCGAGACAACACA
1 TTCCCAG-TTC---CAGAGCCAATTTTAACTTCACA-CGGAGGATATTGGACTCGAGACAAAACA
* * *
106343 AGCTCAACTTCAC-A-G-CGGGGCGGCTGGCTGTCAACAAACAA-T
61 AGCTCAACTTCACAACGAAGGGGCGACTGACTGTCAACAAACAACT
106385 TTCCCAGTTCCAGAGCCAATTTTAACTTCACGACGGAGGATATTGGACTCG
1 TTCCCAGTTCCAGAGCCAATTTTAACTTCAC-ACGGAGGATATTGGACTCG
106436 GAACAATACT
Statistics
Matches: 132, Mismatches: 17, Indels: 20
0.78 0.10 0.12
Matches are distributed among these distances:
103 36 0.27
104 1 0.01
106 9 0.07
107 29 0.22
108 1 0.01
109 1 0.01
110 53 0.40
111 1 0.01
112 1 0.01
ACGTcount: A:0.32, C:0.25, G:0.19, T:0.24
Consensus pattern (106 bp):
TTCCCAGTTCCAGAGCCAATTTTAACTTCACACGGAGGATATTGGACTCGAGACAAAACAAGCTC
AACTTCACAACGAAGGGGCGACTGACTGTCAACAAACAACT
Found at i:107618 original size:15 final size:16
Alignment explanation
Indices: 107591--107624 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
107581 TCGTCCCCTA
107591 TATATATATTTTTAAT
1 TATATATATTTTTAAT
*
107607 TATATA-ATTTTTATT
1 TATATATATTTTTAAT
107622 TAT
1 TAT
107625 TTACTATATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 11 0.65
16 6 0.35
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (16 bp):
TATATATATTTTTAAT
Found at i:107662 original size:14 final size:14
Alignment explanation
Indices: 107643--107682 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 14
107633 TTCCTCTTTT
107643 TTATTTATATTATA
1 TTATTTATATTATA
*
107657 TTATTTTTATTATA
1 TTATTTATATTATA
107671 TATATCTTATAT
1 T-TAT-TTATAT
107683 CATTATATAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
14 14 0.64
15 3 0.14
16 5 0.23
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.65
Consensus pattern (14 bp):
TTATTTATATTATA
Found at i:107845 original size:16 final size:17
Alignment explanation
Indices: 107809--107859 Score: 54
Period size: 16 Copynumber: 3.2 Consensus size: 17
107799 TTTGTTTTTA
*
107809 TTTATTTATA-TA-TAT
1 TTTATTTTTACTATTAT
*
107824 TATATTTTTACT-TTAT
1 TTTATTTTTACTATTAT
*
107840 TTTATTTTTTCTATTAT
1 TTTATTTTTACTATTAT
107857 TTT
1 TTT
107860 TTTCCTTAAT
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
15 8 0.28
16 14 0.48
17 7 0.24
ACGTcount: A:0.24, C:0.04, G:0.00, T:0.73
Consensus pattern (17 bp):
TTTATTTTTACTATTAT
Found at i:107848 original size:17 final size:17
Alignment explanation
Indices: 107804--107859 Score: 53
Period size: 17 Copynumber: 3.2 Consensus size: 17
107794 CTATTTTTGT
*
107804 TTTTATTTATTTA-TATA
1 TTTTATTT-TTTACTTTA
*
107821 TATTATATTTTTACTTTA
1 TTTTAT-TTTTTACTTTA
107839 TTTTATTTTTT-CTATTA
1 TTTTATTTTTTACT-TTA
107856 TTTT
1 TTTT
107860 TTTCCTTAAT
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
16 2 0.06
17 21 0.64
18 10 0.30
ACGTcount: A:0.23, C:0.04, G:0.00, T:0.73
Consensus pattern (17 bp):
TTTTATTTTTTACTTTA
Found at i:108074 original size:18 final size:17
Alignment explanation
Indices: 108053--108088 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
108043 TTTTTTAACA
*
108053 TTTTATTCATTTTTTTAT
1 TTTTATT-AGTTTTTTAT
108071 TTTTATTAGTTTTTTAT
1 TTTTATTAGTTTTTTAT
108088 T
1 T
108089 ATTTTTTTAC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 10 0.59
18 7 0.41
ACGTcount: A:0.17, C:0.03, G:0.03, T:0.78
Consensus pattern (17 bp):
TTTTATTAGTTTTTTAT
Found at i:108085 original size:20 final size:20
Alignment explanation
Indices: 108062--108113 Score: 61
Period size: 20 Copynumber: 2.6 Consensus size: 20
108052 ATTTTATTCA
* *
108062 TTTTTTTATTTTTATTA-GTT
1 TTTTATTATTTTT-TTACGTG
108082 TTTTATTATTTTTTTACGTG
1 TTTTATTATTTTTTTACGTG
*
108102 TTTTGTTATTTT
1 TTTTATTATTTT
108114 CCATTTTTTC
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
19 3 0.11
20 25 0.89
ACGTcount: A:0.13, C:0.02, G:0.08, T:0.77
Consensus pattern (20 bp):
TTTTATTATTTTTTTACGTG
Found at i:109612 original size:21 final size:21
Alignment explanation
Indices: 109586--109650 Score: 112
Period size: 21 Copynumber: 3.1 Consensus size: 21
109576 AATCAGATTG
109586 CCCAGGGGGTACAGATTCCCC
1 CCCAGGGGGTACAGATTCCCC
109607 CCCAGGGGGTACAGATTCCCC
1 CCCAGGGGGTACAGATTCCCC
* *
109628 CTCAGGGGGTACCGATTCCCC
1 CCCAGGGGGTACAGATTCCCC
109649 CC
1 CC
109651 TGTCTAACGG
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 41 1.00
ACGTcount: A:0.17, C:0.40, G:0.28, T:0.15
Consensus pattern (21 bp):
CCCAGGGGGTACAGATTCCCC
Found at i:110037 original size:34 final size:32
Alignment explanation
Indices: 109998--110067 Score: 104
Period size: 34 Copynumber: 2.1 Consensus size: 32
109988 TTTTGTAAAG
*
109998 GGGAAAGGTTCTAGCTTAGCCCGTGTAAAAGCTA
1 GGGAAAGGTTCTAGCTTAGCCCG-G-AAAAACTA
*
110032 GGGAAAGGTTCTAGTTTAGCCCGGAAAAACTA
1 GGGAAAGGTTCTAGCTTAGCCCGGAAAAACTA
110064 GGGA
1 GGGA
110068 GTTTGTAAGG
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
32 11 0.32
33 1 0.03
34 22 0.65
ACGTcount: A:0.31, C:0.16, G:0.31, T:0.21
Consensus pattern (32 bp):
GGGAAAGGTTCTAGCTTAGCCCGGAAAAACTA
Found at i:110825 original size:23 final size:24
Alignment explanation
Indices: 110790--110835 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
110780 TGATTTCAAA
110790 TTTTAAAATCAAAAA-AGATTTTC
1 TTTTAAAATCAAAAATAGATTTTC
110813 TTTTGAAAA-CAAAAATAGATTTT
1 TTTT-AAAATCAAAAATAGATTTT
110836 GAAAGCCAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
23 10 0.48
24 11 0.52
ACGTcount: A:0.48, C:0.07, G:0.07, T:0.39
Consensus pattern (24 bp):
TTTTAAAATCAAAAATAGATTTTC
Found at i:110837 original size:19 final size:20
Alignment explanation
Indices: 110813--110860 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 20
110803 AAAGATTTTC
*
110813 TTTTGAAAACAAAAAT-AGA
1 TTTTGAAAACAAAAATGAAA
* *
110832 TTTTGAAAGCCAAAATGAAA
1 TTTTGAAAACAAAAATGAAA
110852 TTTTGAAAA
1 TTTTGAAAA
110861 ATGATTTAGA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 14 0.58
20 10 0.42
ACGTcount: A:0.52, C:0.06, G:0.12, T:0.29
Consensus pattern (20 bp):
TTTTGAAAACAAAAATGAAA
Found at i:112181 original size:23 final size:23
Alignment explanation
Indices: 112134--112199 Score: 75
Period size: 23 Copynumber: 3.0 Consensus size: 23
112124 AATCAGATTG
* *
112134 CCCAGTGGGTACAGATT--CCCC
1 CCCAGGGGGAACAGATTCCCCCC
112155 CCCAGGGGGAACAGATTCCCCCC
1 CCCAGGGGGAACAGATTCCCCCC
*
112178 CCCAGGGGGTACCA-ATTCCCCC
1 CCCAGGGGG-AACAGATTCCCCC
112200 TGTCTAAAGG
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
21 15 0.38
23 21 0.54
24 3 0.08
ACGTcount: A:0.20, C:0.42, G:0.24, T:0.14
Consensus pattern (23 bp):
CCCAGGGGGAACAGATTCCCCCC
Found at i:112198 original size:21 final size:21
Alignment explanation
Indices: 112134--112199 Score: 80
Period size: 21 Copynumber: 3.0 Consensus size: 21
112124 AATCAGATTG
*
112134 CCCAGTGGGTACAGATTCCCC
1 CCCAGGGGGTACAGATTCCCC
*
112155 CCCAGGGGGAACAGATTCCCCCC
1 CCCAGGGGGTACAGATT--CCCC
112178 CCCAGGGGGTACCA-ATTCCCC
1 CCCAGGGGGTA-CAGATTCCCC
112199 C
1 C
112200 TGTCTAAAGG
Statistics
Matches: 39, Mismatches: 3, Indels: 6
0.81 0.06 0.12
Matches are distributed among these distances:
21 20 0.51
23 17 0.44
24 2 0.05
ACGTcount: A:0.20, C:0.42, G:0.24, T:0.14
Consensus pattern (21 bp):
CCCAGGGGGTACAGATTCCCC
Found at i:113333 original size:16 final size:16
Alignment explanation
Indices: 113311--113351 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
113301 AATAATAACT
113311 CAGTAACAACTAA-AAA
1 CAGTAACAAC-AAGAAA
*
113327 TAGTAACAACAAGAAA
1 CAGTAACAACAAGAAA
113343 CAGTAACAA
1 CAGTAACAA
113352 TTATGATGTC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
15 2 0.09
16 20 0.91
ACGTcount: A:0.61, C:0.17, G:0.10, T:0.12
Consensus pattern (16 bp):
CAGTAACAACAAGAAA
Found at i:113771 original size:32 final size:32
Alignment explanation
Indices: 113735--113880 Score: 138
Period size: 32 Copynumber: 4.6 Consensus size: 32
113725 AGTAGTATCA
*
113735 GTGTTGCATTCAAATAATGCATAGTAGAGTCT
1 GTGTTGCATTCAAATAATGCACAGTAGAGTCT
* * * *
113767 GTGTTACATTCAGATAATGCACAGTGGAGTCA
1 GTGTTGCATTCAAATAATGCACAGTAGAGTCT
*
113799 GTGTTGCATTCAAACAATGCACA-TCAGAGT-T
1 GTGTTGCATTCAAATAATGCACAGT-AGAGTCT
* * *
113830 AGTATTGCAGTCAAACAATGCACA-TCAGAGT-T
1 -GTGTTGCATTCAAATAATGCACAGT-AGAGTCT
*
113862 AGTATTGCATTCAAATAAT
1 -GTGTTGCATTCAAATAAT
113881 TCATATGAGT
Statistics
Matches: 98, Mismatches: 14, Indels: 4
0.84 0.12 0.03
Matches are distributed among these distances:
31 1 0.01
32 97 0.99
ACGTcount: A:0.34, C:0.16, G:0.20, T:0.30
Consensus pattern (32 bp):
GTGTTGCATTCAAATAATGCACAGTAGAGTCT
Found at i:113850 original size:64 final size:64
Alignment explanation
Indices: 113732--113876 Score: 152
Period size: 64 Copynumber: 2.3 Consensus size: 64
113722 CATAGTAGTA
* * * * * * *
113732 TCAGTGTTGCATTCAAATAATGCATAGTAGAGTCTGTGTTACATTCAGATAATGCACAGT-GGAG
1 TCAGTGTTGCATTCAAACAATGCACAGTAGAGTCTGTATTACAGTCAAACAATGCACA-TCAGAG
*
113796 TCAGTGTTGCATTCAAACAATGCACA-TCAGAGT-TAGTATTGCAGTCAAACAATGCACATCAGA
1 TCAGTGTTGCATTCAAACAATGCACAGT-AGAGTCT-GTATTACAGTCAAACAATGCACATCAGA
113859 G
64 G
* *
113860 TTAGTATTGCATTCAAA
1 TCAGTGTTGCATTCAAA
113877 TAATTCATAT
Statistics
Matches: 68, Mismatches: 10, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
63 3 0.04
64 65 0.96
ACGTcount: A:0.34, C:0.17, G:0.20, T:0.30
Consensus pattern (64 bp):
TCAGTGTTGCATTCAAACAATGCACAGTAGAGTCTGTATTACAGTCAAACAATGCACATCAGAG
Found at i:116409 original size:16 final size:16
Alignment explanation
Indices: 116388--116419 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
116378 ATAAATAAAC
116388 GAACATAAACGAACAA
1 GAACATAAACGAACAA
116404 GAACATAAACGAACAA
1 GAACATAAACGAACAA
116420 AAATCTTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.62, C:0.19, G:0.12, T:0.06
Consensus pattern (16 bp):
GAACATAAACGAACAA
Found at i:116499 original size:10 final size:10
Alignment explanation
Indices: 116484--116557 Score: 59
Period size: 10 Copynumber: 7.6 Consensus size: 10
116474 CATTTAATAA
116484 ATAAACGAAC
1 ATAAACGAAC
116494 ATAAACGAAC
1 ATAAACGAAC
116504 ----ACGAAC
1 ATAAACGAAC
116510 ATAAACGAAC
1 ATAAACGAAC
** *
116520 ACGAAC-ATAA
1 ATAAACGA-AC
116530 ATGAACACGAAC
1 AT-AA-ACGAAC
116542 ATAAACGAAC
1 ATAAACGAAC
116552 ATAAAC
1 ATAAAC
116558 CTTGGAGACC
Statistics
Matches: 50, Mismatches: 6, Indels: 16
0.69 0.08 0.22
Matches are distributed among these distances:
6 6 0.12
9 1 0.02
10 34 0.68
11 3 0.06
12 5 0.10
13 1 0.02
ACGTcount: A:0.58, C:0.22, G:0.11, T:0.09
Consensus pattern (10 bp):
ATAAACGAAC
Found at i:116509 original size:16 final size:16
Alignment explanation
Indices: 116488--116552 Score: 121
Period size: 16 Copynumber: 4.1 Consensus size: 16
116478 TAATAAATAA
116488 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
116504 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
*
116520 ACGAACATAAATGAAC
1 ACGAACATAAACGAAC
116536 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
116552 A
1 A
116553 TAAACCTTGG
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 47 1.00
ACGTcount: A:0.57, C:0.23, G:0.12, T:0.08
Consensus pattern (16 bp):
ACGAACATAAACGAAC
Found at i:117603 original size:24 final size:24
Alignment explanation
Indices: 117576--117637 Score: 88
Period size: 24 Copynumber: 2.6 Consensus size: 24
117566 TATTGGGTTA
* *
117576 AACATAAATGAATGAACATAAACG
1 AACATAAACGAACGAACATAAACG
*
117600 AACATAACCGAACGAACATAAACG
1 AACATAAACGAACGAACATAAACG
*
117624 AACATAACCGAACG
1 AACATAAACGAACG
117638 TTCACGAACG
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 35 1.00
ACGTcount: A:0.55, C:0.21, G:0.13, T:0.11
Consensus pattern (24 bp):
AACATAAACGAACGAACATAAACG
Found at i:117604 original size:10 final size:10
Alignment explanation
Indices: 117589--117636 Score: 51
Period size: 10 Copynumber: 4.4 Consensus size: 10
117579 ATAAATGAAT
117589 GAACATAAAC
1 GAACATAAAC
117599 GAACATAACCGAAC
1 GAACAT-A---AAC
117613 GAACATAAAC
1 GAACATAAAC
*
117623 GAACATAACC
1 GAACATAAAC
117633 GAAC
1 GAAC
117637 GTTCACGAAC
Statistics
Matches: 33, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
10 22 0.67
11 1 0.03
13 1 0.03
14 9 0.27
ACGTcount: A:0.54, C:0.25, G:0.12, T:0.08
Consensus pattern (10 bp):
GAACATAAAC
Found at i:117613 original size:14 final size:14
Alignment explanation
Indices: 117596--117637 Score: 56
Period size: 14 Copynumber: 3.3 Consensus size: 14
117586 AATGAACATA
117596 AACGAACATAACCG
1 AACGAACATAACCG
117610 AACGAACAT-A---
1 AACGAACATAACCG
117620 AACGAACATAACCG
1 AACGAACATAACCG
117634 AACG
1 AACG
117638 TTCACGAACG
Statistics
Matches: 24, Mismatches: 0, Indels: 8
0.75 0.00 0.25
Matches are distributed among these distances:
10 9 0.38
11 1 0.04
13 1 0.04
14 13 0.54
ACGTcount: A:0.52, C:0.26, G:0.14, T:0.07
Consensus pattern (14 bp):
AACGAACATAACCG
Found at i:118433 original size:32 final size:32
Alignment explanation
Indices: 118397--118472 Score: 125
Period size: 32 Copynumber: 2.4 Consensus size: 32
118387 ACAAAGTTTA
*
118397 CGATAATTGAAATACTTAAATACTTCCAAGTT
1 CGATAATTGAAATACTTAAAAACTTCCAAGTT
*
118429 CGATAATTCAAATACTTAAAAACTTCCAAGTT
1 CGATAATTGAAATACTTAAAAACTTCCAAGTT
*
118461 TGATAATTGAAA
1 CGATAATTGAAA
118473 CAAAGTTTAA
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
32 40 1.00
ACGTcount: A:0.43, C:0.14, G:0.09, T:0.33
Consensus pattern (32 bp):
CGATAATTGAAATACTTAAAAACTTCCAAGTT
Found at i:123971 original size:49 final size:49
Alignment explanation
Indices: 123915--124013 Score: 189
Period size: 49 Copynumber: 2.0 Consensus size: 49
123905 TATTATGGTA
*
123915 AGGATTGGTTCCAATTTTTTGACTTTCTATATATATATATTCTTTTCAC
1 AGGATTGGTTCCAATTATTTGACTTTCTATATATATATATTCTTTTCAC
123964 AGGATTGGTTCCAATTATTTGACTTTCTATATATATATATTCTTTTCAC
1 AGGATTGGTTCCAATTATTTGACTTTCTATATATATATATTCTTTTCAC
124013 A
1 A
124014 TTATAATGCT
Statistics
Matches: 49, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
49 49 1.00
ACGTcount: A:0.26, C:0.14, G:0.10, T:0.49
Consensus pattern (49 bp):
AGGATTGGTTCCAATTATTTGACTTTCTATATATATATATTCTTTTCAC
Found at i:126207 original size:13 final size:14
Alignment explanation
Indices: 126183--126211 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
126173 TTCAGCCATC
126183 TACATCAGATTAAT
1 TACATCAGATTAAT
126197 TACATCA-ATTAAT
1 TACATCAGATTAAT
126210 TA
1 TA
126212 GTTGTTAATT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 8 0.53
14 7 0.47
ACGTcount: A:0.45, C:0.14, G:0.03, T:0.38
Consensus pattern (14 bp):
TACATCAGATTAAT
Found at i:127719 original size:40 final size:40
Alignment explanation
Indices: 127664--127747 Score: 168
Period size: 40 Copynumber: 2.1 Consensus size: 40
127654 TATACTTTAG
127664 TACCAAATCTAACTTTAACTTCTATATATGTTTGATCTCA
1 TACCAAATCTAACTTTAACTTCTATATATGTTTGATCTCA
127704 TACCAAATCTAACTTTAACTTCTATATATGTTTGATCTCA
1 TACCAAATCTAACTTTAACTTCTATATATGTTTGATCTCA
127744 TACC
1 TACC
127748 TAGTAGATAG
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 44 1.00
ACGTcount: A:0.32, C:0.21, G:0.05, T:0.42
Consensus pattern (40 bp):
TACCAAATCTAACTTTAACTTCTATATATGTTTGATCTCA
Found at i:135247 original size:53 final size:52
Alignment explanation
Indices: 135177--135290 Score: 192
Period size: 53 Copynumber: 2.2 Consensus size: 52
135167 ACTCATTTCC
* *
135177 ATCCTTTTTTAAACTTAAATTAGACTCTCATACCACGTAATTGCTCATTCTTT
1 ATCC-TTTTTAAACTTAAATTAGACTCTCATACCACGTAATTGCTCATACTTG
135230 ATCCATTTTTAAACTTAAATTAGACTCTCATACCACGTAATTGCTCATACTTG
1 ATCC-TTTTTAAACTTAAATTAGACTCTCATACCACGTAATTGCTCATACTTG
135283 ATCCTTTT
1 ATCCTTTT
135291 GATAATAGTA
Statistics
Matches: 58, Mismatches: 3, Indels: 1
0.94 0.05 0.02
Matches are distributed among these distances:
52 4 0.07
53 54 0.93
ACGTcount: A:0.29, C:0.23, G:0.06, T:0.42
Consensus pattern (52 bp):
ATCCTTTTTAAACTTAAATTAGACTCTCATACCACGTAATTGCTCATACTTG
Found at i:138221 original size:30 final size:32
Alignment explanation
Indices: 138169--138229 Score: 81
Period size: 30 Copynumber: 2.0 Consensus size: 32
138159 TTTAAAGGTC
* *
138169 ATTTTATAATAATTTGATAAAATTTAATGATT
1 ATTTTATAATAATTTGAAAAAATTCAATGATT
*
138201 ATTTTAT-A-AATTTTAAAAAATTCAATGAT
1 ATTTTATAATAATTTGAAAAAATTCAATGAT
138230 CAAAAACTCA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
30 18 0.69
31 1 0.04
32 7 0.27
ACGTcount: A:0.46, C:0.02, G:0.05, T:0.48
Consensus pattern (32 bp):
ATTTTATAATAATTTGAAAAAATTCAATGATT
Found at i:138807 original size:7 final size:7
Alignment explanation
Indices: 138795--138862 Score: 50
Period size: 7 Copynumber: 9.3 Consensus size: 7
138785 ATATTTTATT
138795 ATATTTA
1 ATATTTA
138802 ATATTTA
1 ATATTTA
*
138809 ATATTTT
1 ATATTTA
*
138816 ATTTTTA
1 ATATTTA
138823 ATTTATTTA
1 A--TATTTA
138832 AGTATTTAA
1 A-TATTT-A
*
138841 ATTTTTTA
1 A-TATTTA
138849 ATATTT-
1 ATATTTA
138855 -TATTTA
1 ATATTTA
138861 AT
1 AT
138863 TAATTTTTTT
Statistics
Matches: 48, Mismatches: 8, Indels: 10
0.73 0.12 0.15
Matches are distributed among these distances:
5 5 0.10
7 24 0.50
8 7 0.15
9 12 0.25
ACGTcount: A:0.35, C:0.00, G:0.01, T:0.63
Consensus pattern (7 bp):
ATATTTA
Found at i:138855 original size:8 final size:8
Alignment explanation
Indices: 138785--138856 Score: 60
Period size: 8 Copynumber: 9.0 Consensus size: 8
138775 TGTTTAAGGT
138785 ATATTTTA
1 ATATTTTA
*
138793 TTATATTTA
1 ATAT-TTTA
138802 ATA-TTTA
1 ATATTTTA
138809 ATATTTT-
1 ATATTTTA
138816 AT-TTTTA
1 ATATTTTA
*
138823 ATTTATTTA
1 ATAT-TTTA
*
138832 AGTATTTAA
1 A-TATTTTA
*
138841 ATTTTTTA
1 ATATTTTA
138849 ATATTTTA
1 ATATTTTA
138857 TTTAATTAAT
Statistics
Matches: 51, Mismatches: 7, Indels: 12
0.73 0.10 0.17
Matches are distributed among these distances:
6 4 0.08
7 11 0.22
8 19 0.37
9 15 0.29
10 2 0.04
ACGTcount: A:0.35, C:0.00, G:0.01, T:0.64
Consensus pattern (8 bp):
ATATTTTA
Found at i:143558 original size:15 final size:12
Alignment explanation
Indices: 143522--143546 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
143512 AATATTTGGA
143522 TGATAAAATACG
1 TGATAAAATACG
143534 TGATAAAATACG
1 TGATAAAATACG
143546 T
1 T
143547 ATGAATAAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.48, C:0.08, G:0.16, T:0.28
Consensus pattern (12 bp):
TGATAAAATACG
Found at i:143937 original size:37 final size:40
Alignment explanation
Indices: 143896--143992 Score: 105
Period size: 42 Copynumber: 2.5 Consensus size: 40
143886 ACTATTATAT
*
143896 TTTATTAAAATAAATA-TAT-TTA-AAATTCTATTAATTA
1 TTTATTAAAATAAATATTATATTATAAATTATATTAATTA
* *
143933 TTTATAAAAATATAAATATTATATTATCAATTATATTAATTA
1 TTTAT-TAAA-ATAAATATTATATTATAAATTATATTAATTA
*
143975 CTTATT-AAA-AAATATTAT
1 TTTATTAAAATAAATATTAT
143993 TATAATATCA
Statistics
Matches: 50, Mismatches: 5, Indels: 9
0.78 0.08 0.14
Matches are distributed among these distances:
37 5 0.10
38 12 0.24
39 8 0.16
40 5 0.10
41 3 0.06
42 17 0.34
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.47
Consensus pattern (40 bp):
TTTATTAAAATAAATATTATATTATAAATTATATTAATTA
Found at i:143970 original size:42 final size:41
Alignment explanation
Indices: 143919--144003 Score: 109
Period size: 42 Copynumber: 2.0 Consensus size: 41
143909 ATATATTTAA
* * *
143919 AATTCTATTAATTATTTA-TAAAAATATAAATATTATATTATC
1 AATTATATTAATTACTTATTAAAAA-AT-AATATTATAATATC
*
143961 AATTATATTAATTACTTATTAAAAAATATTATTATAATATC
1 AATTATATTAATTACTTATTAAAAAATAATATTATAATATC
144002 AA
1 AA
144004 AATAAATATT
Statistics
Matches: 38, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
41 14 0.37
42 18 0.47
43 6 0.16
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.46
Consensus pattern (41 bp):
AATTATATTAATTACTTATTAAAAAATAATATTATAATATC
Found at i:145791 original size:22 final size:22
Alignment explanation
Indices: 145742--145798 Score: 62
Period size: 22 Copynumber: 2.6 Consensus size: 22
145732 TCGTTGACAA
* *
145742 TATGATTGTTGACTTTGATCGG
1 TATGACTGTTGACTTTAATCGG
*
145764 TCTGACTGTTGACTTTAA-CTGG
1 TATGACTGTTGACTTTAATC-GG
*
145786 TATGACCGTTGAC
1 TATGACTGTTGAC
145799 CGTTAACTTT
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
21 1 0.03
22 28 0.97
ACGTcount: A:0.19, C:0.16, G:0.25, T:0.40
Consensus pattern (22 bp):
TATGACTGTTGACTTTAATCGG
Found at i:149529 original size:2 final size:2
Alignment explanation
Indices: 149522--149560 Score: 69
Period size: 2 Copynumber: 19.0 Consensus size: 2
149512 ATTAATCTAT
149522 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA GTA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA
149561 ATTTATAAAT
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 34 0.94
3 2 0.06
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (2 bp):
TA
Found at i:150906 original size:2 final size:2
Alignment explanation
Indices: 150899--150982 Score: 113
Period size: 2 Copynumber: 44.0 Consensus size: 2
150889 CTAAAAGAGT
*
150899 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA GA TA -A TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* *
150940 AA TA TA TA -A TA -A GA TA TA TA -A TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
150979 TA TA
1 TA TA
150983 AATAATGAGG
Statistics
Matches: 73, Mismatches: 5, Indels: 8
0.85 0.06 0.09
Matches are distributed among these distances:
1 4 0.05
2 69 0.95
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (2 bp):
TA
Found at i:151216 original size:2 final size:2
Alignment explanation
Indices: 151209--151248 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
151199 TAACTAACTA
151209 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
151249 GGCTACGATC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:151444 original size:2 final size:2
Alignment explanation
Indices: 151437--151468 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
151427 AGTTTTACAG
151437 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
151469 GGAAATCCAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:151844 original size:196 final size:197
Alignment explanation
Indices: 151491--151855 Score: 436
Period size: 197 Copynumber: 1.9 Consensus size: 197
151481 ACACTACGTG
* * * * * *
151491 AAACTCTTTTAGTTTTACATCTTTTTAGGACCATTGGATTAGCGAAATTAAATGTTGAGTTTACA
1 AAACTCTTTTAGTTTTACAACTTTTTAAGACCATTAGATGAGAGAAATTAAATGTTGAGTTAACA
* * * * * *
151556 GTAGAAAATAAGAAGATAACACTGAAAAACAAGGATTTAATCTCATCATTTTGATTTTCCTCAAT
66 ATAGAAAATAAGAAGATAACACTAAAAAACAAGGAATTAATCTCAACACTTTAATTTTCCTCAAT
** **
151621 CCGTGGTCCTAAAAAGGTGTAAAACT-AAAGTTT-TACACGGTAAGTGTATCTTAACCCATAATA
131 CAATAATCCTAAAAAGGTGTAAAACTAAAAGTTTATACACGGTAAGTGTATCTTAACCCATAATA
151684 TA
196 TA
151686 AAACTCTTTTAGTTTTACACACTTTTTAAGACCATTAGATGAGAGAAATTAAATGTTGAGATTAA
1 AAACTCTTTTAGTTTTACA-ACTTTTTAAGACCATTAGATGAGAGAAATTAAATGTTGAG-TTAA
* * * * *
151751 CAATAGAAAATGAGATG-T-TCATTAAAAAAAACAAGGAATTAATCTCAAC-CTTTAATTTTTCT
64 CAATAGAAAATAAGAAGATAACACT--AAAAAACAAGGAATTAATCTCAACACTTTAATTTTCCT
* *
151813 CAATTCAATAATCTTAAAAATGTGT-AAACTAAAAGTTTATACA
127 CAA-TCAATAATCCTAAAAAGGTGTAAAACTAAAAGTTTATACA
151856 AGTGGATCTT
Statistics
Matches: 140, Mismatches: 23, Indels: 11
0.80 0.13 0.06
Matches are distributed among these distances:
195 22 0.16
196 54 0.39
197 60 0.43
198 4 0.03
ACGTcount: A:0.40, C:0.13, G:0.13, T:0.34
Consensus pattern (197 bp):
AAACTCTTTTAGTTTTACAACTTTTTAAGACCATTAGATGAGAGAAATTAAATGTTGAGTTAACA
ATAGAAAATAAGAAGATAACACTAAAAAACAAGGAATTAATCTCAACACTTTAATTTTCCTCAAT
CAATAATCCTAAAAAGGTGTAAAACTAAAAGTTTATACACGGTAAGTGTATCTTAACCCATAATA
TA
Done.