Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009264.1 Hibiscus syriacus cultivar Beakdansim tig00112918_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: 131041
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.33
Found at i:2187 original size:2 final size:2
Alignment explanation
Indices: 2180--2213 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
2170 TTTAAAATTT
2180 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
2214 AGATAAGGTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2583 original size:16 final size:18
Alignment explanation
Indices: 2557--2590 Score: 54
Period size: 16 Copynumber: 2.0 Consensus size: 18
2547 TAACCATATC
2557 AATACTAATATAA-AATT
1 AATACTAATATAATAATT
2574 AATA-TAATATAATAATT
1 AATACTAATATAATAATT
2591 TGTTGATAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 8 0.50
17 8 0.50
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (18 bp):
AATACTAATATAATAATT
Found at i:24653 original size:21 final size:20
Alignment explanation
Indices: 24629--24692 Score: 59
Period size: 21 Copynumber: 3.4 Consensus size: 20
24619 AACTTTGAAA
24629 AAATAGTTTTCAAAGTTTGGT
1 AAAT-GTTTTCAAAGTTTGGT
*
24650 AAATG-TTTC----TTT-GA
1 AAATGTTTTCAAAGTTTGGT
24664 AAATGGTTTTCAAAGTTTGGT
1 AAAT-GTTTTCAAAGTTTGGT
24685 AAATGTTT
1 AAATGTTT
24693 CTTTGAAAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 15
0.67 0.04 0.29
Matches are distributed among these distances:
14 5 0.15
15 4 0.12
16 4 0.12
19 4 0.12
20 8 0.24
21 9 0.26
ACGTcount: A:0.31, C:0.05, G:0.19, T:0.45
Consensus pattern (20 bp):
AAATGTTTTCAAAGTTTGGT
Found at i:24735 original size:36 final size:36
Alignment explanation
Indices: 24621--24739 Score: 170
Period size: 35 Copynumber: 3.3 Consensus size: 36
24611 TAGTAACCAA
24621 CTTTGAAAAAATAGTTTTCAAAGTTTGGTAAATGTTT
1 CTTTG-AAAAATAGTTTTCAAAGTTTGGTAAATGTTT
*
24658 CTTTG-AAAATGGTTTTCAAAGTTTGGTAAATGTTT
1 CTTTGAAAAATAGTTTTCAAAGTTTGGTAAATGTTT
* *
24693 CTTTGAAAAATAGTTTTTCAAAGTTTGGTAGATGCTT
1 CTTTGAAAAATAG-TTTTCAAAGTTTGGTAAATGTTT
*
24730 -GTTGAAAAAT
1 CTTTGAAAAAT
24740 GATAATGGGA
Statistics
Matches: 75, Mismatches: 5, Indels: 5
0.88 0.06 0.06
Matches are distributed among these distances:
35 34 0.45
36 15 0.20
37 26 0.35
ACGTcount: A:0.33, C:0.06, G:0.18, T:0.43
Consensus pattern (36 bp):
CTTTGAAAAATAGTTTTCAAAGTTTGGTAAATGTTT
Found at i:25156 original size:16 final size:17
Alignment explanation
Indices: 25135--25166 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
25125 TTACTATTAA
25135 CGTGAATAGT-AAATTT
1 CGTGAATAGTGAAATTT
25151 CGTGAATAGTGAAATT
1 CGTGAATAGTGAAATT
25167 CAGTCGGCGA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.38, C:0.06, G:0.22, T:0.34
Consensus pattern (17 bp):
CGTGAATAGTGAAATTT
Found at i:29232 original size:21 final size:21
Alignment explanation
Indices: 29208--29268 Score: 64
Period size: 21 Copynumber: 3.2 Consensus size: 21
29198 AACTTTGAAA
29208 AAATGGTTTTCAAAGTTTGGT
1 AAATGGTTTTCAAAGTTTGGT
*
29229 AAAT-G-TTTC----TTT-GA
1 AAATGGTTTTCAAAGTTTGGT
29243 AAATGGTTTTCAAAGTTTGGT
1 AAATGGTTTTCAAAGTTTGGT
29264 AAATG
1 AAATG
29269 TTTCTTTGAA
Statistics
Matches: 31, Mismatches: 2, Indels: 14
0.66 0.04 0.30
Matches are distributed among these distances:
14 5 0.16
15 4 0.13
16 4 0.13
19 4 0.13
20 4 0.13
21 10 0.32
ACGTcount: A:0.31, C:0.05, G:0.21, T:0.43
Consensus pattern (21 bp):
AAATGGTTTTCAAAGTTTGGT
Found at i:29299 original size:37 final size:37
Alignment explanation
Indices: 29200--29318 Score: 174
Period size: 35 Copynumber: 3.3 Consensus size: 37
29190 TGGTAACCAA
29200 CTTTGAAAAA-ATGGTTTTCAAAGTTTGGTAAATGTTT
1 CTTTGAAAAATA-GGTTTTCAAAGTTTGGTAAATGTTT
29237 CTTTG-AAAAT-GGTTTTCAAAGTTTGGTAAATGTTT
1 CTTTGAAAAATAGGTTTTCAAAGTTTGGTAAATGTTT
* *
29272 CTTTGAAAAATAGTTTTTCAAAGTTTGGTAGATGTTT
1 CTTTGAAAAATAGGTTTTCAAAGTTTGGTAAATGTTT
*
29309 -GTTGAAAAAT
1 CTTTGAAAAAT
29319 GATAATGAGA
Statistics
Matches: 76, Mismatches: 3, Indels: 7
0.88 0.03 0.08
Matches are distributed among these distances:
35 30 0.39
36 18 0.24
37 28 0.37
ACGTcount: A:0.32, C:0.05, G:0.19, T:0.44
Consensus pattern (37 bp):
CTTTGAAAAATAGGTTTTCAAAGTTTGGTAAATGTTT
Found at i:31541 original size:30 final size:31
Alignment explanation
Indices: 31507--31566 Score: 77
Period size: 31 Copynumber: 2.0 Consensus size: 31
31497 AATATAATTT
*
31507 TGGAAAAAAAAT-AAAGTTTAGGTACTAAAA
1 TGGAAAAAAAATGAAAGTTTAAGTACTAAAA
* * *
31537 TGGAACAAAAGTGATAGTTTAAGTACTAAA
1 TGGAAAAAAAATGAAAGTTTAAGTACTAAA
31567 CATATAATTT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
30 10 0.40
31 15 0.60
ACGTcount: A:0.52, C:0.05, G:0.18, T:0.25
Consensus pattern (31 bp):
TGGAAAAAAAATGAAAGTTTAAGTACTAAAA
Found at i:31626 original size:23 final size:22
Alignment explanation
Indices: 31599--31651 Score: 63
Period size: 23 Copynumber: 2.4 Consensus size: 22
31589 ATTACATTTT
*
31599 TTATTTAAATTTTTGT-TCTATA
1 TTATTTAAATTTTTATGT-TATA
*
31621 TATATTTATATTTTTATGTTATA
1 T-TATTTAAATTTTTATGTTATA
31644 TTATTTAA
1 TTATTTAA
31652 TCATTTTTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
22 7 0.27
23 18 0.69
24 1 0.04
ACGTcount: A:0.30, C:0.02, G:0.04, T:0.64
Consensus pattern (22 bp):
TTATTTAAATTTTTATGTTATA
Found at i:40860 original size:34 final size:35
Alignment explanation
Indices: 40822--40893 Score: 101
Period size: 34 Copynumber: 2.1 Consensus size: 35
40812 TTATCATTAC
40822 ATTTAAATTAACTTATTAAAAATTATAAAT-AAAA
1 ATTTAAATTAACTTATTAAAAATTATAAATGAAAA
** * *
40856 ATTTACTTTGACTTCTTAAAAATTATAAATGAAAA
1 ATTTAAATTAACTTATTAAAAATTATAAATGAAAA
40891 ATT
1 ATT
40894 ACTTTTAGGA
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
34 26 0.79
35 7 0.21
ACGTcount: A:0.51, C:0.06, G:0.03, T:0.40
Consensus pattern (35 bp):
ATTTAAATTAACTTATTAAAAATTATAAATGAAAA
Found at i:40896 original size:34 final size:34
Alignment explanation
Indices: 40832--40898 Score: 109
Period size: 34 Copynumber: 2.0 Consensus size: 34
40822 ATTTAAATTA
40832 ACTTATTAAAAATTATAAATAAAAATTTACTTTG
1 ACTTATTAAAAATTATAAATAAAAATTTACTTTG
*
40866 ACTTCTTAAAAATTATAAATGAAAAA-TTACTTT
1 ACTTATTAAAAATTATAAAT-AAAAATTTACTTT
40899 TAGGATATCC
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
34 26 0.84
35 5 0.16
ACGTcount: A:0.49, C:0.07, G:0.03, T:0.40
Consensus pattern (34 bp):
ACTTATTAAAAATTATAAATAAAAATTTACTTTG
Found at i:42842 original size:22 final size:22
Alignment explanation
Indices: 42814--42856 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
42804 GCTTCTGAAG
42814 CAGGCTGGTAACAATCAAGAAA
1 CAGGCTGGTAACAATCAAGAAA
*
42836 CAGGCTGGTAACTATCAAGAA
1 CAGGCTGGTAACAATCAAGAA
42857 GCAATGGCTA
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:0.42, C:0.19, G:0.23, T:0.16
Consensus pattern (22 bp):
CAGGCTGGTAACAATCAAGAAA
Found at i:49716 original size:48 final size:48
Alignment explanation
Indices: 49649--49741 Score: 141
Period size: 48 Copynumber: 1.9 Consensus size: 48
49639 TGTTGCTGTT
* * *
49649 GTTGTTGTTGTTGATGCTGATCACTGTACGAATTGGAATGCTGCAGCG
1 GTTGTTGCTGTTGACGCTGATCACTGTACGAATTGGAACGCTGCAGCG
* *
49697 GTTGTTGCTGTTGGCGCTGATCATTGTACGAATTGGAACGCTGCA
1 GTTGTTGCTGTTGACGCTGATCACTGTACGAATTGGAACGCTGCA
49742 AAAGCTGAAC
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
48 40 1.00
ACGTcount: A:0.18, C:0.16, G:0.31, T:0.34
Consensus pattern (48 bp):
GTTGTTGCTGTTGACGCTGATCACTGTACGAATTGGAACGCTGCAGCG
Found at i:55395 original size:20 final size:20
Alignment explanation
Indices: 55370--55417 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
55360 GTCAGAGTGT
*
55370 GGCGGCGGACGGCTGACGGC
1 GGCGGCGGACGGCGGACGGC
* *
55390 GGCGGCAGACGGCGGGCGGC
1 GGCGGCGGACGGCGGACGGC
*
55410 GGCAGCGG
1 GGCGGCGG
55418 CCAGCAGGCA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.10, C:0.29, G:0.58, T:0.02
Consensus pattern (20 bp):
GGCGGCGGACGGCGGACGGC
Found at i:55407 original size:17 final size:16
Alignment explanation
Indices: 55387--55418 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
55377 GACGGCTGAC
55387 GGCGGCGGCAGACGGCG
1 GGCGGCGGCAG-CGGCG
55404 GGCGGCGGCAGCGGC
1 GGCGGCGGCAGCGGC
55419 CAGCAGGCAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.09, C:0.31, G:0.59, T:0.00
Consensus pattern (16 bp):
GGCGGCGGCAGCGGCG
Found at i:57001 original size:8 final size:7
Alignment explanation
Indices: 56974--57000 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
56964 AATTACTACT
56974 TTTTTTC
1 TTTTTTC
56981 TTTTTTC
1 TTTTTTC
56988 TTTTTTC
1 TTTTTTC
56995 TTTTTT
1 TTTTTT
57001 TGTGTGTGTG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.00, C:0.11, G:0.00, T:0.89
Consensus pattern (7 bp):
TTTTTTC
Found at i:63191 original size:27 final size:27
Alignment explanation
Indices: 63153--63249 Score: 167
Period size: 27 Copynumber: 3.6 Consensus size: 27
63143 GTGTAGGAAT
*
63153 TATAGAGTTATGATTTGTTACCATTCC
1 TATAGAGATATGATTTGTTACCATTCC
*
63180 TATATAGATATGATTTGTTACCATTCC
1 TATAGAGATATGATTTGTTACCATTCC
*
63207 TATAGAGATATGATTTGTTATCATTCC
1 TATAGAGATATGATTTGTTACCATTCC
63234 TATAGAGATATGATTT
1 TATAGAGATATGATTT
63250 TGTAAATAGA
Statistics
Matches: 66, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 66 1.00
ACGTcount: A:0.30, C:0.11, G:0.14, T:0.44
Consensus pattern (27 bp):
TATAGAGATATGATTTGTTACCATTCC
Found at i:66947 original size:27 final size:27
Alignment explanation
Indices: 66907--67029 Score: 178
Period size: 27 Copynumber: 4.6 Consensus size: 27
66897 GTGTAGGAAT
66907 TATAGAG--ATGATTTGTTACCATTCC
1 TATAGAGATATGATTTGTTACCATTCC
*
66932 TATAGAGTTATGATTTGTTACCATTCC
1 TATAGAGATATGATTTGTTACCATTCC
*
66959 TATATAGATATGATTTGTTACCATTCC
1 TATAGAGATATGATTTGTTACCATTCC
* *
66986 TATAAAAGATATGATTTGTTATCATTCC
1 TAT-AGAGATATGATTTGTTACCATTCC
*
67014 TATAGAAATATGATTT
1 TATAGAGATATGATTT
67030 TATAAATAGA
Statistics
Matches: 89, Mismatches: 6, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
25 7 0.08
27 57 0.64
28 25 0.28
ACGTcount: A:0.32, C:0.12, G:0.13, T:0.43
Consensus pattern (27 bp):
TATAGAGATATGATTTGTTACCATTCC
Found at i:67025 original size:55 final size:54
Alignment explanation
Indices: 66914--67029 Score: 178
Period size: 55 Copynumber: 2.1 Consensus size: 54
66904 AATTATAGAG
* * * *
66914 ATGATTTGTTACCATTCCTATAGAGTTATGATTTGTTACCATTCCTATATAGAT
1 ATGATTTGTTACCATTCCTATAAAGATATGATTTGTTACCATTCCTATAGAAAT
*
66968 ATGATTTGTTACCATTCCTATAAAAGATATGATTTGTTATCATTCCTATAGAAAT
1 ATGATTTGTTACCATTCCTAT-AAAGATATGATTTGTTACCATTCCTATAGAAAT
67023 ATGATTT
1 ATGATTT
67030 TATAAATAGA
Statistics
Matches: 56, Mismatches: 5, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
54 21 0.38
55 35 0.62
ACGTcount: A:0.31, C:0.13, G:0.12, T:0.44
Consensus pattern (54 bp):
ATGATTTGTTACCATTCCTATAAAGATATGATTTGTTACCATTCCTATAGAAAT
Found at i:72528 original size:18 final size:19
Alignment explanation
Indices: 72505--72547 Score: 61
Period size: 20 Copynumber: 2.3 Consensus size: 19
72495 CAGTAATCCT
72505 ATTCC-CTGGTAATCTTAC
1 ATTCCACTGGTAATCTTAC
*
72523 ATTCCCACTGGTAATCTTAT
1 ATT-CCACTGGTAATCTTAC
72543 ATTCC
1 ATTCC
72548 GTGAACCAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
18 3 0.14
19 4 0.18
20 15 0.68
ACGTcount: A:0.23, C:0.28, G:0.09, T:0.40
Consensus pattern (19 bp):
ATTCCACTGGTAATCTTAC
Found at i:72535 original size:20 final size:20
Alignment explanation
Indices: 72510--72547 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
72500 ATCCTATTCC
72510 CTGGTAATCTTACATTCCCA
1 CTGGTAATCTTACATTCCCA
*
72530 CTGGTAATCTTATATTCC
1 CTGGTAATCTTACATTCC
72548 GTGAACCAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.24, C:0.26, G:0.11, T:0.39
Consensus pattern (20 bp):
CTGGTAATCTTACATTCCCA
Found at i:74642 original size:18 final size:18
Alignment explanation
Indices: 74615--74655 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
74605 TCATTGTCCG
* *
74615 TATTATTATTCTTATCAT
1 TATTAGTATTATTATCAT
*
74633 TATTAGTATTATTTTCAT
1 TATTAGTATTATTATCAT
74651 TATTA
1 TATTA
74656 TCTCTTAGTC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.29, C:0.07, G:0.02, T:0.61
Consensus pattern (18 bp):
TATTAGTATTATTATCAT
Found at i:74940 original size:23 final size:23
Alignment explanation
Indices: 74898--74941 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
74888 CATATGAATT
*
74898 TGTCCCGAAAGACCGCGTAGAGA
1 TGTCCCGAAAGACCACGTAGAGA
* *
74921 TGTCCCGAATGACCATGTAGA
1 TGTCCCGAAAGACCACGTAGA
74942 ACCCTCGACT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.30, C:0.25, G:0.27, T:0.18
Consensus pattern (23 bp):
TGTCCCGAAAGACCACGTAGAGA
Found at i:76861 original size:20 final size:20
Alignment explanation
Indices: 76833--76890 Score: 62
Period size: 20 Copynumber: 2.7 Consensus size: 20
76823 TTCCAATTGA
* *
76833 AGTGTATCGGTGCATTCTTC
1 AGTGCATCGATGCATTCTTC
76853 AGTGCATCGATGCATTCTTTAAC
1 AGTGCATCGATGCATTC-TT--C
76876 ATGTGCATCGATGCA
1 A-GTGCATCGATGCA
76891 CTACCATGCA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
20 15 0.47
21 2 0.06
23 2 0.06
24 13 0.41
ACGTcount: A:0.22, C:0.21, G:0.22, T:0.34
Consensus pattern (20 bp):
AGTGCATCGATGCATTCTTC
Found at i:80492 original size:11 final size:13
Alignment explanation
Indices: 80476--80507 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
80466 CACATATGAG
80476 TCATAT-TATTT-
1 TCATATATATTTA
80487 TCATATATATTTA
1 TCATATATATTTA
80500 TCATATAT
1 TCATATAT
80508 TCATGATCAC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
11 6 0.32
12 5 0.26
13 8 0.42
ACGTcount: A:0.34, C:0.09, G:0.00, T:0.56
Consensus pattern (13 bp):
TCATATATATTTA
Found at i:80926 original size:20 final size:20
Alignment explanation
Indices: 80901--80939 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
80891 TTCCCATTGA
**
80901 AGTGCATCGGTGCATTCTTC
1 AGTGCATCGACGCATTCTTC
80921 AGTGCATCGACGCATTCTT
1 AGTGCATCGACGCATTCTT
80940 TAACATGTGC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.18, C:0.26, G:0.23, T:0.33
Consensus pattern (20 bp):
AGTGCATCGACGCATTCTTC
Found at i:91609 original size:21 final size:21
Alignment explanation
Indices: 91552--91610 Score: 91
Period size: 21 Copynumber: 2.8 Consensus size: 21
91542 AACCCTGCAG
**
91552 CGGTGGCATCTGACCTGGCTA
1 CGGTGGCATCTGATATGGCTA
*
91573 CGGTGGCATCTTATATGGCTA
1 CGGTGGCATCTGATATGGCTA
91594 CGGTGGCATCTGATATG
1 CGGTGGCATCTGATATG
91611 AAAACGGTGG
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.17, C:0.22, G:0.32, T:0.29
Consensus pattern (21 bp):
CGGTGGCATCTGATATGGCTA
Found at i:91617 original size:21 final size:21
Alignment explanation
Indices: 91572--91621 Score: 64
Period size: 21 Copynumber: 2.4 Consensus size: 21
91562 TGACCTGGCT
* ***
91572 ACGGTGGCATCTTATATGGCT
1 ACGGTGGCATCTGATATGAAA
91593 ACGGTGGCATCTGATATGAAA
1 ACGGTGGCATCTGATATGAAA
91614 ACGGTGGC
1 ACGGTGGC
91622 GTCTAACTCG
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.24, C:0.18, G:0.32, T:0.26
Consensus pattern (21 bp):
ACGGTGGCATCTGATATGAAA
Found at i:93367 original size:24 final size:24
Alignment explanation
Indices: 93339--93386 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
93329 AATATTTTAC
93339 CTTCTTAATATAAAGATTGATAAT
1 CTTCTTAATATAAAGATTGATAAT
93363 CTTCTTAATATAAAGATTGATAAT
1 CTTCTTAATATAAAGATTGATAAT
93387 ATGAATAATA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.42, C:0.08, G:0.08, T:0.42
Consensus pattern (24 bp):
CTTCTTAATATAAAGATTGATAAT
Found at i:93395 original size:24 final size:24
Alignment explanation
Indices: 93344--93396 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
93334 TTTACCTTCT
* ***
93344 TAATATAAAGATTGATAATCTTCT
1 TAATATAAAGATTGATAATATGAA
93368 TAATATAAAGATTGATAATATGAA
1 TAATATAAAGATTGATAATATGAA
93392 TAATA
1 TAATA
93397 AGAGAATTTG
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.49, C:0.04, G:0.09, T:0.38
Consensus pattern (24 bp):
TAATATAAAGATTGATAATATGAA
Found at i:94775 original size:29 final size:31
Alignment explanation
Indices: 94742--94809 Score: 77
Period size: 34 Copynumber: 2.2 Consensus size: 31
94732 AAACTTTAAA
94742 TTTATT-TA-AAAATTAATTTACCTGTAATG
1 TTTATTATACAAAATTAATTTACCTGTAATG
**
94771 TTTATTGCATATCAACCTTAATTTACCTGTAATG
1 TTTATT--ATA-CAAAATTAATTTACCTGTAATG
94805 TTTAT
1 TTTAT
94810 GACATATCAA
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
29 6 0.19
32 2 0.06
34 24 0.75
ACGTcount: A:0.32, C:0.12, G:0.07, T:0.49
Consensus pattern (31 bp):
TTTATTATACAAAATTAATTTACCTGTAATG
Found at i:94797 original size:34 final size:34
Alignment explanation
Indices: 94754--94821 Score: 120
Period size: 34 Copynumber: 2.0 Consensus size: 34
94744 TATTTAAAAA
94754 TTAATTTACCTGTAATGTTTATTG-CATATCAACC
1 TTAATTTACCTGTAATGTTTA-TGACATATCAACC
94788 TTAATTTACCTGTAATGTTTATGACATATCAACC
1 TTAATTTACCTGTAATGTTTATGACATATCAACC
94822 AGCTTTTTTT
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
33 2 0.06
34 31 0.94
ACGTcount: A:0.31, C:0.18, G:0.09, T:0.43
Consensus pattern (34 bp):
TTAATTTACCTGTAATGTTTATGACATATCAACC
Found at i:95785 original size:16 final size:16
Alignment explanation
Indices: 95755--95785 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
95745 TAATATTAAA
*
95755 ACTTGAACTCAAAAAG
1 ACTTGAACTAAAAAAG
95771 ACTTGAACTAAAAAA
1 ACTTGAACTAAAAAA
95786 AAAATTTAGA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.55, C:0.16, G:0.10, T:0.19
Consensus pattern (16 bp):
ACTTGAACTAAAAAAG
Found at i:103098 original size:2 final size:2
Alignment explanation
Indices: 103091--103132 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
103081 GAGAAACTTC
103091 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
103133 ATCATTTTCA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:105303 original size:30 final size:30
Alignment explanation
Indices: 105258--105424 Score: 125
Period size: 30 Copynumber: 5.8 Consensus size: 30
105248 TTTGTGGTTT
* * *
105258 AGTCCCTTAAGTTTCTATTTTTTCTATTTA
1 AGTCCTTTAACTTTCTGTTTTTTCTATTTA
* *
105288 AGTCCTTTAACTTTCTGTTGTTGT-TATTTT
1 AGTCCTTTAACTTTCTGTT-TTTTCTATTTA
**
105318 AGTCCTTTAACTTTCTGTTTTAGCTATTTTA
1 AGTCCTTTAACTTTCTGTTTTTTCTA-TTTA
*
105349 A-TCCTTCAA---T-T-TTTTTTCTATTTA
1 AGTCCTTTAACTTTCTGTTTTTTCTATTTA
* * * * *
105373 AGTCCTTAAACTTTTTG-TTGTGCTATTTT
1 AGTCCTTTAACTTTCTGTTTTTTCTATTTA
* *
105402 GGGCCTTTAACTTTCTGTTTTTT
1 AGTCCTTTAACTTTCTGTTTTTT
105425 TTTTCAATTT
Statistics
Matches: 106, Mismatches: 21, Indels: 20
0.72 0.14 0.14
Matches are distributed among these distances:
24 5 0.05
25 14 0.13
26 1 0.01
27 1 0.01
28 1 0.01
29 25 0.24
30 52 0.49
31 7 0.07
ACGTcount: A:0.17, C:0.16, G:0.10, T:0.57
Consensus pattern (30 bp):
AGTCCTTTAACTTTCTGTTTTTTCTATTTA
Found at i:105805 original size:5 final size:5
Alignment explanation
Indices: 105795--105825 Score: 53
Period size: 5 Copynumber: 6.2 Consensus size: 5
105785 CGCTTATCAC
*
105795 TTTTA TTTTA TTTTG TTTTA TTTTA TTTTA T
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA T
105826 CTTTGCGAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.16, C:0.00, G:0.03, T:0.81
Consensus pattern (5 bp):
TTTTA
Found at i:108103 original size:40 final size:40
Alignment explanation
Indices: 108048--108128 Score: 153
Period size: 40 Copynumber: 2.0 Consensus size: 40
108038 CCAAACATTC
*
108048 AATCTCAGCTACTTCCATTGCAATGATGGATGCCATTACT
1 AATCTCAGCTACTTCCATTGCAATGATGAATGCCATTACT
108088 AATCTCAGCTACTTCCATTGCAATGATGAATGCCATTACT
1 AATCTCAGCTACTTCCATTGCAATGATGAATGCCATTACT
108128 A
1 A
108129 CGAGTGTCTT
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
40 40 1.00
ACGTcount: A:0.30, C:0.25, G:0.14, T:0.32
Consensus pattern (40 bp):
AATCTCAGCTACTTCCATTGCAATGATGAATGCCATTACT
Found at i:115476 original size:21 final size:20
Alignment explanation
Indices: 115452--115584 Score: 74
Period size: 20 Copynumber: 6.5 Consensus size: 20
115442 CGATCTCCAG
115452 AATCGCAACGCGATTATGAA
1 AATCGCAACGCGATTATGAA
*
115472 GAATCGCAATGCGA-TA-GTACA
1 -AATCGCAACGCGATTATG-A-A
* ** * * *
115493 AATTAGCATTGCGATTTTCCAG
1 AA-TCGCAACGCGATTAT-GAA
*
115515 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGATTATGAA
**
115535 AATCGCAACGCGAACAT-ATA
1 AATCGCAACGCGATTATGA-A
* *
115555 AATCGCAACGCGATTCTGAC
1 AATCGCAACGCGATTATGAA
*
115575 TATCGCAACG
1 AATCGCAACG
115585 AGTATCCGTA
Statistics
Matches: 85, Mismatches: 19, Indels: 17
0.70 0.16 0.14
Matches are distributed among these distances:
19 2 0.02
20 46 0.54
21 33 0.39
22 3 0.04
23 1 0.01
ACGTcount: A:0.37, C:0.23, G:0.20, T:0.21
Consensus pattern (20 bp):
AATCGCAACGCGATTATGAA
Found at i:115522 original size:63 final size:59
Alignment explanation
Indices: 115411--115568 Score: 190
Period size: 62 Copynumber: 2.6 Consensus size: 59
115401 AATGACCAAC
*
115411 AAAATCGCAATGCGAAATAAAAATAGCAACGCGATCTCCAGAATCGCAACGCGATTATG
1 AAAATCGCAATGCGAAATAAAAATAGCAACGCGATCTCCAGAATCGCAACGCGAATATG
* * ** *
115470 AAGAATCGCAATGCGATAGTACAAATTAGCATTGCGATTTTCCAGAATCGCAACGCGAATATG
1 AA-AATCGCAATGCGA-AATA-AAAATAGCAACGCGA-TCTCCAGAATCGCAACGCGAATATG
* * *
115533 AAAATCGCAACGCGAACATATAAATCGCAACGCGAT
1 AAAATCGCAATGCGAA-ATAAAAATAGCAACGCGAT
115569 TCTGACTATC
Statistics
Matches: 81, Mismatches: 13, Indels: 9
0.79 0.13 0.09
Matches are distributed among these distances:
59 2 0.02
60 14 0.17
61 14 0.17
62 26 0.32
63 25 0.31
ACGTcount: A:0.41, C:0.22, G:0.19, T:0.19
Consensus pattern (59 bp):
AAAATCGCAATGCGAAATAAAAATAGCAACGCGATCTCCAGAATCGCAACGCGAATATG
Found at i:115540 original size:20 final size:20
Alignment explanation
Indices: 115515--115770 Score: 162
Period size: 20 Copynumber: 12.7 Consensus size: 20
115505 GATTTTCCAG
*
115515 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGAATACGAA
* *
115535 AATCGCAACGCGAACA-TATA
1 AATCGCAACGCGAATACGA-A
* *
115555 AATCGCAACGCG-ATTCTGAC
1 AATCGCAACGCGAATAC-GAA
* * * *
115575 TATCGCAACGAGTATCCGTAA
1 AATCGCAACGCGAATACG-AA
* * *
115596 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGAATACGAA
115616 AATCGCAACGAC-AATACGTAA
1 AATCGCAACG-CGAATACG-AA
* *
115637 AATCGCAACGAGAATACGTA
1 AATCGCAACGCGAATACGAA
* *
115657 AATCGCAACGCGTAT-CTGTA
1 AATCGCAACGCGAATAC-GAA
* * *
115677 AATCACAACGAGAATACGTA
1 AATCGCAACGCGAATACGAA
* * * * *
115697 AATCGCAATGTGTATCCGTA
1 AATCGCAACGCGAATACGAA
115717 AATCGCAACGAC-AATACGTAA
1 AATCGCAACG-CGAATACG-AA
* * *
115738 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGAATACGAA
115758 AATCGCAACGCGA
1 AATCGCAACGCGA
115771 TTTTTAAAGC
Statistics
Matches: 186, Mismatches: 37, Indels: 26
0.75 0.15 0.10
Matches are distributed among these distances:
19 3 0.02
20 128 0.69
21 55 0.30
ACGTcount: A:0.39, C:0.25, G:0.18, T:0.18
Consensus pattern (20 bp):
AATCGCAACGCGAATACGAA
Found at i:115618 original size:61 final size:61
Alignment explanation
Indices: 115576--115726 Score: 205
Period size: 61 Copynumber: 2.5 Consensus size: 61
115566 GATTCTGACT
* *
115576 ATCGCAACGAGTATCCGTAAAATCGCAACGCGTATCCGTAAATCGCAACGACAATACGTAAA
1 ATCGCAACGAGAATACGT-AAATCGCAACGCGTATCCGTAAATCGCAACGACAATACGTAAA
* * *
115638 ATCGCAACGAGAATACGTAAATCGCAACGCGTATCTGTAAATCACAACGAGAATACGT-AA
1 ATCGCAACGAGAATACGTAAATCGCAACGCGTATCCGTAAATCGCAACGACAATACGTAAA
* * * *
115698 ATCGCAATGTGTATCCGTAAATCGCAACG
1 ATCGCAACGAGAATACGTAAATCGCAACG
115727 ACAATACGTA
Statistics
Matches: 80, Mismatches: 9, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
60 27 0.34
61 37 0.46
62 16 0.20
ACGTcount: A:0.38, C:0.24, G:0.19, T:0.19
Consensus pattern (61 bp):
ATCGCAACGAGAATACGTAAATCGCAACGCGTATCCGTAAATCGCAACGACAATACGTAAA
Found at i:115678 original size:41 final size:40
Alignment explanation
Indices: 115576--115767 Score: 242
Period size: 41 Copynumber: 4.7 Consensus size: 40
115566 GATTCTGACT
* * * *
115576 ATCGCAACGAGTATCCGTAAAATCGCAACGCGTATCCGTAA
1 ATCGCAACGCGTATCCGT-AAATCGCAACGAGAATACGTAA
* *
115617 ATCGCAACGAC-AATACGTAAAATCGCAACGAGAATACGTAA
1 ATCGCAACG-CGTATCCGT-AAATCGCAACGAGAATACGTAA
* *
115658 ATCGCAACGCGTATCTGTAAATCACAACGAGAATACGTAA
1 ATCGCAACGCGTATCCGTAAATCGCAACGAGAATACGTAA
* * *
115698 ATCGCAATGTGTATCCGTAAATCGCAACGACAATACGTAAA
1 ATCGCAACGCGTATCCGTAAATCGCAACGAGAATACGT-AA
115739 ATCGCAACGCGTATCCGTAAATCGCAACG
1 ATCGCAACGCGTATCCGTAAATCGCAACG
115768 CGATTTTTAA
Statistics
Matches: 131, Mismatches: 17, Indels: 6
0.85 0.11 0.04
Matches are distributed among these distances:
40 55 0.42
41 76 0.58
ACGTcount: A:0.39, C:0.24, G:0.18, T:0.19
Consensus pattern (40 bp):
ATCGCAACGCGTATCCGTAAATCGCAACGAGAATACGTAA
Found at i:116352 original size:20 final size:20
Alignment explanation
Indices: 116327--116377 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
116317 TTCTAAACTT
* *
116327 AAAATCGCAACATGAAAATG
1 AAAATCACAACACGAAAATG
116347 AAAATCACAACACGAAAATG
1 AAAATCACAACACGAAAATG
**
116367 ACTATCACAAC
1 AAAATCACAAC
116378 GAGAGAATCG
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.55, C:0.22, G:0.10, T:0.14
Consensus pattern (20 bp):
AAAATCACAACACGAAAATG
Found at i:116411 original size:33 final size:33
Alignment explanation
Indices: 116374--116441 Score: 100
Period size: 33 Copynumber: 2.1 Consensus size: 33
116364 ATGACTATCA
* **
116374 CAACGAGAGAATCGTAACGCGAAATGAAAATCG
1 CAACGAGAGAATCGCAACGCGAAACCAAAATCG
*
116407 CAACGAGATAATCGCAACGCGAAACCAAAATCG
1 CAACGAGAGAATCGCAACGCGAAACCAAAATCG
116440 CA
1 CA
116442 TTGCGATTTT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.46, C:0.24, G:0.21, T:0.10
Consensus pattern (33 bp):
CAACGAGAGAATCGCAACGCGAAACCAAAATCG
Found at i:116459 original size:19 final size:19
Alignment explanation
Indices: 116437--116487 Score: 75
Period size: 19 Copynumber: 2.7 Consensus size: 19
116427 GAAACCAAAA
* **
116437 TCGCATTGCGATTTTCGTT
1 TCGCGTTGCGATTTTAATT
116456 TCGCGTTGCGATTTTAATT
1 TCGCGTTGCGATTTTAATT
116475 TCGCGTTGCGATT
1 TCGCGTTGCGATT
116488 CTCTCGTTGC
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.12, C:0.20, G:0.24, T:0.45
Consensus pattern (19 bp):
TCGCGTTGCGATTTTAATT
Found at i:116547 original size:20 final size:20
Alignment explanation
Indices: 116485--116540 Score: 87
Period size: 20 Copynumber: 2.8 Consensus size: 20
116475 TCGCGTTGCG
116485 ATTCTCTCGTTGCGATAGTC
1 ATTCTCTCGTTGCGATAGTC
*
116505 ATT-TCCGCGTTGCGATAGTC
1 ATTCT-CTCGTTGCGATAGTC
116525 ATTCTCTCGTTGCGAT
1 ATTCTCTCGTTGCGAT
116541 TTTCATTTCA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
19 1 0.03
20 30 0.94
21 1 0.03
ACGTcount: A:0.14, C:0.25, G:0.21, T:0.39
Consensus pattern (20 bp):
ATTCTCTCGTTGCGATAGTC
Found at i:118406 original size:95 final size:94
Alignment explanation
Indices: 118243--118623 Score: 622
Period size: 94 Copynumber: 4.1 Consensus size: 94
118233 TAGATTGCTT
* * *
118243 AGTAAATTTATTCGGTTGCTGCCAATACTGCTAAACTGTTTATTCTTTAACACTGTGAAATTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
118308 ATTTGTCTTTTTGTTTTGTCTTTTGGTTG-A
66 ATTTGTC--TTTGTTTTGTCTTTTGGTTGAA
118338 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
118403 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
* * *
118432 AGTAAATTTGTTCAGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACATTGTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
* *
118497 ATTTGTCTTTGTTTTGCCTTTCGGTTGAA
66 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
* * * *
118526 AGTAAATTTGTTCGGTTGCTGCCAATTCTACTAAACTGTGTATTCTTTAATACTCTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
118591 ATTTGTCTTTGTTTTGTCTTTTGGTTG-A
66 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
118619 AGTAA
1 AGTAA
118624 TGCAATCCAT
Statistics
Matches: 270, Mismatches: 15, Indels: 4
0.93 0.05 0.01
Matches are distributed among these distances:
93 26 0.10
94 175 0.65
95 69 0.26
ACGTcount: A:0.22, C:0.13, G:0.18, T:0.47
Consensus pattern (94 bp):
AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:118727 original size:19 final size:19
Alignment explanation
Indices: 118671--118795 Score: 89
Period size: 19 Copynumber: 6.7 Consensus size: 19
118661 TAGTTTACTT
* *
118671 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAA-TGAAAA
* **
118691 TCGCAACGTGAAAAATGACTA
1 TCGCAACGCG--AAATGAAAA
118712 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
118731 TCGCAA--CG--A-GAGAA
1 TCGCAACGCGAAATGAAAA
118745 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
* ***
118764 TCGCAATGCGAAACCTAAA
1 TCGCAACGCGAAATGAAAA
*
118783 TCGCAACGTGAAA
1 TCGCAACGCGAAA
118796 CTATAATCGC
Statistics
Matches: 82, Mismatches: 16, Indels: 15
0.73 0.14 0.13
Matches are distributed among these distances:
14 10 0.12
15 1 0.01
16 2 0.02
17 2 0.02
18 1 0.01
19 43 0.52
20 8 0.10
21 12 0.15
22 3 0.04
ACGTcount: A:0.45, C:0.22, G:0.19, T:0.14
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:118796 original size:19 final size:18
Alignment explanation
Indices: 118743--118805 Score: 65
Period size: 19 Copynumber: 3.3 Consensus size: 18
118733 GCAACGAGAG
118743 AATCGCAACGCGAAA-TGAA
1 AATCGCAACGCGAAACT--A
*
118762 AATCGCAATGCGAAACCTA
1 AATCGCAACGCGAAA-CTA
*
118781 AATCGCAACGTGAAACTA
1 AATCGCAACGCGAAACTA
118799 TAATCGC
1 -AATCGC
118806 GTTGCGATTT
Statistics
Matches: 38, Mismatches: 3, Indels: 6
0.81 0.06 0.13
Matches are distributed among these distances:
18 3 0.08
19 34 0.89
21 1 0.03
ACGTcount: A:0.43, C:0.24, G:0.17, T:0.16
Consensus pattern (18 bp):
AATCGCAACGCGAAACTA
Found at i:118824 original size:19 final size:19
Alignment explanation
Indices: 118802--118866 Score: 59
Period size: 19 Copynumber: 3.7 Consensus size: 19
118792 GAAACTATAA
118802 TCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
118821 TCGCATTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* * *
118835 TCTCTTTGCGATTTCCATT
1 TCGCGTTGCGATTTTCATT
118854 TCGCGTTGCGATT
1 TCGCGTTGCGATT
118867 CTCTCGTTGC
Statistics
Matches: 35, Mismatches: 6, Indels: 10
0.69 0.12 0.20
Matches are distributed among these distances:
14 9 0.26
16 2 0.06
17 3 0.09
19 21 0.60
ACGTcount: A:0.11, C:0.25, G:0.20, T:0.45
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:118854 original size:33 final size:33
Alignment explanation
Indices: 118805--118879 Score: 123
Period size: 33 Copynumber: 2.3 Consensus size: 33
118795 ACTATAATCG
*
118805 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTCCATTTCGCATTGCGATTCTCT
* *
118838 CTTTGCGATTTCCATTTCGCGTTGCGATTCTCT
1 CGTTGCGATTTCCATTTCGCATTGCGATTCTCT
118871 CGTTGCGAT
1 CGTTGCGAT
118880 AGTCATTTTT
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 38 1.00
ACGTcount: A:0.11, C:0.25, G:0.20, T:0.44
Consensus pattern (33 bp):
CGTTGCGATTTCCATTTCGCATTGCGATTCTCT
Found at i:120986 original size:33 final size:33
Alignment explanation
Indices: 120944--121089 Score: 157
Period size: 33 Copynumber: 4.2 Consensus size: 33
120934 ACTAAATTCG
*
120944 CGTTGCGATTTTCATTTCGCTTTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
*
120977 CGTTGCGATTTTCATTTCGCATTGCGATAGTCATTTCCG
1 CGTTGCGATTTTCATTTCGCATTGCGAT--TC---T-CT
* * * *
121016 CGTTGCGATATTCATATTCGCGTTGCGATTTTCA
1 CGTTGCGATTTTCAT-TTCGCATTGCGATTCTCT
* *
121050 CGTTGCGATTTTCATTTCGCATTACAATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
121083 CGTTGCG
1 CGTTGCG
121090 GTAGTAATTT
Statistics
Matches: 94, Mismatches: 12, Indels: 14
0.78 0.10 0.12
Matches are distributed among these distances:
33 47 0.50
34 15 0.16
35 3 0.03
38 2 0.02
39 15 0.16
40 12 0.13
ACGTcount: A:0.14, C:0.23, G:0.19, T:0.43
Consensus pattern (33 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
Found at i:121023 original size:20 final size:19
Alignment explanation
Indices: 120940--121049 Score: 104
Period size: 20 Copynumber: 5.9 Consensus size: 19
120930 CGAAACTAAA
*
120940 TTCGCGTTGCGATTTTCAT
1 TTCGCGTTGCGATATTCAT
*
120959 TTCGCTTTGCG--ATTC--
1 TTCGCGTTGCGATATTCAT
* *
120974 -TCTCGTTGCGATTTTCAT
1 TTCGCGTTGCGATATTCAT
* *
120992 TTCGCATTGCGATAGTCAT
1 TTCGCGTTGCGATATTCAT
121011 TTCCGCGTTGCGATATTCAT
1 TT-CGCGTTGCGATATTCAT
*
121031 ATTCGCGTTGCGATTTTCA
1 -TTCGCGTTGCGATATTCA
121050 CGTTGCGATT
Statistics
Matches: 72, Mismatches: 12, Indels: 13
0.74 0.12 0.13
Matches are distributed among these distances:
14 8 0.11
16 3 0.04
17 3 0.04
19 26 0.36
20 30 0.42
21 2 0.03
ACGTcount: A:0.14, C:0.23, G:0.20, T:0.44
Consensus pattern (19 bp):
TTCGCGTTGCGATATTCAT
Found at i:121055 original size:14 final size:14
Alignment explanation
Indices: 121036--121063 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
121026 TTCATATTCG
121036 CGTTGCGATTTTCA
1 CGTTGCGATTTTCA
121050 CGTTGCGATTTTCA
1 CGTTGCGATTTTCA
121064 TTTCGCATTA
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:124536 original size:21 final size:21
Alignment explanation
Indices: 124510--124555 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
124500 TATTCACATT
124510 GCGAATTAGGAAAATCGCAAC
1 GCGAATTAGGAAAATCGCAAC
* * *
124531 GCGAATTTGGGAAATCGCAAT
1 GCGAATTAGGAAAATCGCAAC
124552 GCGA
1 GCGA
124556 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:125067 original size:71 final size:70
Alignment explanation
Indices: 124888--125104 Score: 291
Period size: 71 Copynumber: 3.1 Consensus size: 70
124878 GATAAGATCG
* * * * *
124888 ATACTTTTCCACAAGTATTGATATTTTCAAATTTAAAAAAAATAGAAAATGGGAAGGTTGTAAAG
1 ATACTTTTCCACAAATATCGATATTTTCGAATTTAAAAAAAATAGAAAATGAGAAGGTTGCAAAG
124953 TATCA
66 TATCA
124958 ATACTTTT-CAC-AATATCGATATTTTCGAATTTAAAAAAAATTAGAAAATGAGAAGGTTGCAAA
1 ATACTTTTCCACAAATATCGATATTTTCGAATTTAAAAAAAA-TAGAAAATGAGAAGGTTGCAAA
*
125021 GTTTCA
65 GTATCA
* *
125027 ATACTTTTCCACAAATATCAATACTTTT-GAATTTAAAAAAACATATAAAATGAGAA-GTCTGCA
1 ATACTTTTCCACAAATATCGATA-TTTTCGAATTTAAAAAAA-ATAGAAAATGAGAAGGT-TGCA
125090 AAGTATCA
63 AAGTATCA
125098 ATA-TTTT
1 ATACTTTT
125105 GAATTTTTAT
Statistics
Matches: 132, Mismatches: 9, Indels: 12
0.86 0.06 0.08
Matches are distributed among these distances:
68 26 0.20
69 36 0.27
70 17 0.13
71 48 0.36
72 5 0.04
ACGTcount: A:0.44, C:0.11, G:0.12, T:0.34
Consensus pattern (70 bp):
ATACTTTTCCACAAATATCGATATTTTCGAATTTAAAAAAAATAGAAAATGAGAAGGTTGCAAAG
TATCA
Found at i:125256 original size:20 final size:19
Alignment explanation
Indices: 125189--125257 Score: 84
Period size: 19 Copynumber: 3.6 Consensus size: 19
125179 TTGTTATTTT
*
125189 TAACAAGTTTTGATCCTCG
1 TAACAAGTTTCGATCCTCG
* *
125208 TAAAAAGTTTTGATCCTCG
1 TAACAAGTTTCGATCCTCG
* *
125227 TAACAAGTTTCGATTCTCA
1 TAACAAGTTTCGATCCTCG
125246 TAACAAAGTTTC
1 TAAC-AAGTTTC
125258 AATACTTTGT
Statistics
Matches: 44, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
19 37 0.84
20 7 0.16
ACGTcount: A:0.32, C:0.19, G:0.13, T:0.36
Consensus pattern (19 bp):
TAACAAGTTTCGATCCTCG
Found at i:125508 original size:53 final size:54
Alignment explanation
Indices: 125370--125781 Score: 352
Period size: 54 Copynumber: 7.8 Consensus size: 54
125360 TAAAACTGGG
* * *
125370 TTACCTTATAAGTAGGACTAACGTT-ATGGTTGT-CTCTT-TT-TTTTTAACTAGCA
1 TTACCTTATAAGTAGGAGTAACGTTAACGGTTGTGC-CTTGTTATTTTTAA-TCG-A
* * * *
125423 --ACCTTATATAAATAAGAGTAACTTTAACGGTTGTTCCTTGTTATTTTTAA-CAGA
1 TTACC-T-TATAAGTAGGAGTAACGTTAACGGTTGTGCCTTGTTATTTTTAATC-GA
* * * * *
125477 TTACC-TATAAGTAGGACTAATGTTTATGGTTGTGCC-T-TT-TTTTTAATCGG
1 TTACCTTATAAGTAGGAGTAACGTTAACGGTTGTGCCTTGTTATTTTTAATCGA
* ** * * **
125527 TAACCTTATAAGTAAAAGTAACTTTAATGGTTGCACCTTG-T-TTTTTAATC-A
1 TTACCTTATAAGTAGGAGTAACGTTAACGGTTGTGCCTTGTTATTTTTAATCGA
* * * *
125578 TTAACCTTATAAGTAGGAGTAACTTTAACGGTTGCGTCTTGTTATTTTTAACCGA
1 TT-ACCTTATAAGTAGGAGTAACGTTAACGGTTGTGCCTTGTTATTTTTAATCGA
* * * *
125633 TTACCTTATAAGTAGGATTAACGTTAACAG-TGACGCCTTG-TATTTTTAATCGG
1 TTACCTTATAAGTAGGAGTAACGTTAACGGTTG-TGCCTTGTTATTTTTAATCGA
* *
125686 TTACCTTATAAGTAGGAGTAACGTTAACGTTTATGCCTTGTTATTTTTAATCGA
1 TTACCTTATAAGTAGGAGTAACGTTAACGGTTGTGCCTTGTTATTTTTAATCGA
* * *
125740 TTACCTTATAAGTAGGAGTAACGTTTACGATTGCGCCTTGTT
1 TTACCTTATAAGTAGGAGTAACGTTAACGGTTGTGCCTTGTT
125782 TTCTTTTTCC
Statistics
Matches: 291, Mismatches: 48, Indels: 39
0.77 0.13 0.10
Matches are distributed among these distances:
50 12 0.04
51 30 0.10
52 46 0.16
53 85 0.29
54 101 0.35
55 7 0.02
56 10 0.03
ACGTcount: A:0.28, C:0.14, G:0.17, T:0.42
Consensus pattern (54 bp):
TTACCTTATAAGTAGGAGTAACGTTAACGGTTGTGCCTTGTTATTTTTAATCGA
Found at i:125568 original size:104 final size:106
Alignment explanation
Indices: 125370--125600 Score: 264
Period size: 106 Copynumber: 2.2 Consensus size: 106
125360 TAAAACTGGG
125370 TTACCTTATAAGTAGGACTAACGTTATGGTTGTCTCTTTTTTTTTAACTAGCAACCTTATATAAA
1 TTACCTTATAAGTAGGACTAACGTTATGGTTGTCTCTTTTTTTTTAACTAGCAACCTTATATAAA
* **
125435 TAAGAGTAACTTTAACGGTTGTTCCTTGTTATTTTTAACAGA
66 TAAAAGTAACTTTAACGGTTGCACCTTGTT-TTTTTAACAGA
* * *
125477 TTACC-TATAAGTAGGACTAATGTTTATGGTTGTGC-C-TTTTTTTTAA-TCGGTAACC-T-TAT
1 TTACCTTATAAGTAGGACTAACG-TTATGGTTGT-CTCTTTTTTTTTAACT-AGCAACCTTATAT
* *
125536 AAGTAAAAGTAACTTTAATGGTTGCACCTTG-TTTTTTAATC--A
63 AAATAAAAGTAACTTTAACGGTTGCACCTTGTTTTTTTAA-CAGA
*
125578 TTAACCTTATAAGTAGGAGTAAC
1 TT-ACCTTATAAGTAGGACTAAC
125601 TTTAACGGTT
Statistics
Matches: 108, Mismatches: 10, Indels: 16
0.81 0.07 0.12
Matches are distributed among these distances:
101 3 0.03
102 10 0.09
103 16 0.15
104 29 0.27
105 2 0.02
106 31 0.29
107 16 0.15
108 1 0.01
ACGTcount: A:0.29, C:0.13, G:0.15, T:0.42
Consensus pattern (106 bp):
TTACCTTATAAGTAGGACTAACGTTATGGTTGTCTCTTTTTTTTTAACTAGCAACCTTATATAAA
TAAAAGTAACTTTAACGGTTGCACCTTGTTTTTTTAACAGA
Found at i:125660 original size:54 final size:54
Alignment explanation
Indices: 125429--125781 Score: 357
Period size: 54 Copynumber: 6.7 Consensus size: 54
125419 AGCAACCTTA
* * * **
125429 TATAAATAAGAGTAACTTTAACGGTTGTTCCTTGTTATTTTTAA-CAGATTACC-
1 TATAAGTAGGAGTAACGTTAACGGTTGCGCCTTGTTATTTTTAATC-GATTACCT
* * * * * * *
125482 TATAAGTAGGACTAATGTTTATGGTTGTGCC-T-TT-TTTTTAATCGGTAACCT
1 TATAAGTAGGAGTAACGTTAACGGTTGCGCCTTGTTATTTTTAATCGATTACCT
** * * *
125533 TATAAGTAAAAGTAACTTTAATGGTTGCACCTTG-T-TTTTTAATC-ATTAACCT
1 TATAAGTAGGAGTAACGTTAACGGTTGCGCCTTGTTATTTTTAATCGATT-ACCT
* * *
125585 TATAAGTAGGAGTAACTTTAACGGTTGCGTCTTGTTATTTTTAACCGATTACCT
1 TATAAGTAGGAGTAACGTTAACGGTTGCGCCTTGTTATTTTTAATCGATTACCT
* * *
125639 TATAAGTAGGATTAACGTTAACAG-TGACGCCTTG-TATTTTTAATCGGTTACCT
1 TATAAGTAGGAGTAACGTTAACGGTTG-CGCCTTGTTATTTTTAATCGATTACCT
* **
125692 TATAAGTAGGAGTAACGTTAACGTTTATGCCTTGTTATTTTTAATCGATTACCT
1 TATAAGTAGGAGTAACGTTAACGGTTGCGCCTTGTTATTTTTAATCGATTACCT
* *
125746 TATAAGTAGGAGTAACGTTTACGATTGCGCCTTGTT
1 TATAAGTAGGAGTAACGTTAACGGTTGCGCCTTGTT
125782 TTCTTTTTCC
Statistics
Matches: 247, Mismatches: 42, Indels: 21
0.80 0.14 0.07
Matches are distributed among these distances:
50 12 0.05
51 27 0.11
52 45 0.18
53 70 0.28
54 90 0.36
55 3 0.01
ACGTcount: A:0.28, C:0.14, G:0.17, T:0.41
Consensus pattern (54 bp):
TATAAGTAGGAGTAACGTTAACGGTTGCGCCTTGTTATTTTTAATCGATTACCT
Found at i:125701 original size:107 final size:106
Alignment explanation
Indices: 125562--125783 Score: 313
Period size: 107 Copynumber: 2.1 Consensus size: 106
125552 AATGGTTGCA
* * *
125562 CCTTGTTTTTTAATCATTAACCTTATAAGTAGGAGTAACTTTAACGGTTGCGTCTTGTTATTTTT
1 CCTTGTTTTTTAATCATTAACCTTATAAGTAGGAGTAACGTTAACGGTTACGCCTTGTTATTTTT
*
125627 AACCGATTACCTTATAAGTAGGATTAACGTTAACAGTGACG
66 AACCGATTACCTTATAAGTAGGAGTAACGTTAACAGTGACG
* * *
125668 CCTTGTATTTTTAATCGGTT-ACCTTATAAGTAGGAGTAACGTTAACGTTTATGCCTTGTTATTT
1 CCTTGT-TTTTTAATC-ATTAACCTTATAAGTAGGAGTAACGTTAACGGTTACGCCTTGTTATTT
* * *
125732 TTAATCGATTACCTTATAAGTAGGAGTAACGTTTACGATTG-CG
64 TTAACCGATTACCTTATAAGTAGGAGTAACGTTAAC-AGTGACG
125775 CCTTGTTTT
1 CCTTGTTTT
125784 CTTTTTCCGG
Statistics
Matches: 103, Mismatches: 10, Indels: 6
0.87 0.08 0.05
Matches are distributed among these distances:
106 9 0.09
107 89 0.86
108 5 0.05
ACGTcount: A:0.26, C:0.15, G:0.18, T:0.41
Consensus pattern (106 bp):
CCTTGTTTTTTAATCATTAACCTTATAAGTAGGAGTAACGTTAACGGTTACGCCTTGTTATTTTT
AACCGATTACCTTATAAGTAGGAGTAACGTTAACAGTGACG
Found at i:126519 original size:105 final size:106
Alignment explanation
Indices: 126274--126534 Score: 286
Period size: 105 Copynumber: 2.5 Consensus size: 106
126264 CATTTTAGGT
* *
126274 GCAACCTAATATGTTAATAATATTTATAATAAAATAAGTAA-T---CTATTTTGTTTTCGTGAGA
1 GCAACCTAATATGTTAATAATATTTATAAAAAAATAAGTAATTAACCTATTTTATTTTCGTGAGA
** * * * **
126335 TTTTAAGTATTCATCGGCTTAAATTTTGGTAATATTTTAAAC
66 TTTTAAGTACCCATCAGCTTAAACTCTCATAATA-TTTAAAC
* * * *
126377 GCAACCAAATATGTTAATAGTATTTATAACAACATAAGTAATTAACCTATTTTATTATT-GTG-G
1 GCAACCTAATATGTTAATAATATTTATAAAAAAATAAGTAATTAACCTATTTTATT-TTCGTGAG
126440 ATTTCTAAG-ACCCTATCAGCTTAAACTCTCATAATA-TTAAAC
65 ATTT-TAAGTACCC-ATCAGCTTAAACTCTCATAATATTTAAAC
* * *
126482 GCAACCTAATATGTTGATAATATTAATAAAAAAATAAGTAATTAACTTATTTT
1 GCAACCTAATATGTTAATAATATTTATAAAAAAATAAGTAATTAACCTATTTT
126535 CTTACCTTAC
Statistics
Matches: 132, Mismatches: 19, Indels: 12
0.81 0.12 0.07
Matches are distributed among these distances:
103 37 0.28
104 1 0.01
105 52 0.39
106 7 0.05
107 33 0.25
108 2 0.02
ACGTcount: A:0.39, C:0.11, G:0.10, T:0.39
Consensus pattern (106 bp):
GCAACCTAATATGTTAATAATATTTATAAAAAAATAAGTAATTAACCTATTTTATTTTCGTGAGA
TTTTAAGTACCCATCAGCTTAAACTCTCATAATATTTAAAC
Done.