Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004549.1 Hibiscus syriacus cultivar Beakdansim tig00010100_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: 125670
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:6189 original size:16 final size:17
Alignment explanation
Indices: 6153--6242 Score: 139
Period size: 16 Copynumber: 5.2 Consensus size: 17
6143 AACGGTCAAC
6153 GTCAACGGTCGGGTCGGTCG
1 GTCAACGGTCGGGTC-G--G
6173 GTCAACGGTCGGGTCGG
1 GTCAACGGTCGGGTCGG
6190 GTCAAC-GTCGGGTCGG
1 GTCAACGGTCGGGTCGG
6206 GTCAAC-GTCGGGTCGG
1 GTCAACGGTCGGGTCGG
6222 GTCAACGGTCGGGTCGG
1 GTCAACGGTCGGGTCGG
6239 GTCA
1 GTCA
6243 GACCGGTCAA
Statistics
Matches: 69, Mismatches: 0, Indels: 5
0.93 0.00 0.07
Matches are distributed among these distances:
16 32 0.46
17 21 0.30
19 1 0.01
20 15 0.22
ACGTcount: A:0.12, C:0.24, G:0.44, T:0.19
Consensus pattern (17 bp):
GTCAACGGTCGGGTCGG
Found at i:6216 original size:32 final size:34
Alignment explanation
Indices: 6153--6242 Score: 139
Period size: 33 Copynumber: 2.6 Consensus size: 34
6143 AACGGTCAAC
6153 GTCAACGGTCGGGTCGGTCGGTCAACGGTCGGGTCGG
1 GTCAACGGTCGGGTC-G--GGTCAACGGTCGGGTCGG
6190 GTCAAC-GTCGGGTCGGGTCAAC-GTCGGGTCGG
1 GTCAACGGTCGGGTCGGGTCAACGGTCGGGTCGG
6222 GTCAACGGTCGGGTCGGGTCA
1 GTCAACGGTCGGGTCGGGTCA
6243 GACCGGTCAA
Statistics
Matches: 52, Mismatches: 0, Indels: 6
0.90 0.00 0.10
Matches are distributed among these distances:
32 16 0.31
33 21 0.40
35 1 0.02
36 8 0.15
37 6 0.12
ACGTcount: A:0.12, C:0.24, G:0.44, T:0.19
Consensus pattern (34 bp):
GTCAACGGTCGGGTCGGGTCAACGGTCGGGTCGG
Found at i:12709 original size:353 final size:355
Alignment explanation
Indices: 12059--12767 Score: 1331
Period size: 353 Copynumber: 2.0 Consensus size: 355
12049 TAATTACCTA
12059 ATTTTAGTTTTATTTTGAGCAGTCGTCATTAAAATCAACACAATAGTGATACGATATTTTTTAAC
1 ATTTTAGTTTTATTTTGAGCAGTCGTCATTAAAATCAACACAATAG-GATACGATATTTTTTAAC
12124 TGTGATATAATATTATCTTACGATAATACGTTAATTTTTACCATTAAGTTGAAGATTCCTAAAAA
65 TGTGATATAATATTATCTTACGATAATACGTTAATTTTTACCATTAAGTTGAAGATTCCTAAAAA
12189 AAATAGCTTTAAAATTATGCCCTTTGTAATATTAATTCAACTAAGAGGGTCTCGTTTATTTTAGT
130 AAATAGCTTTAAAATTATGCCCTTTGTAATATTAATTCAACTAAGAGGGTCTCGTTTATTTTAGT
12254 TATGAGGGATAAGTCCTCCGCATCAGCTACTCATAGATATCCAGGCACAGCTCCCTTCAATGCCC
195 TATGAGGGATAAGTCCTCCGCATCAGCTACTCATAGATATCCAGGCACAGCTCCCTTCAATGCCC
12319 GTAATTGTTATAGCTTCCGTAATGAGCACACCCCTTGCCATTGTTAACT-CTCTTAATTAAAGTG
260 GTAATTGTTATAGCTTCCGTAATGAGCACACCCCTTGCCATTGTTAACTCCTCTTAATTAAAGTG
12383 GTTAACTGTCA-TTTCATAGGAGTAAGCATC
325 GTTAACTGTCATTTTCATAGGAGTAAGCATC
12413 ATTTTAGTTTTATTTTGAGCAGTCGTCATTAGAAATCAACACAATA-GATACGATATTTTTTAAC
1 ATTTTAGTTTTATTTTGAGCAGTCGTCATTA-AAATCAACACAATAGGATACGATATTTTTTAAC
12477 TGTGATATAATATTATCTTACGATAATACGTTAATTTTTACCATTAAGTTGAAGATTCCTAAAAA
65 TGTGATATAATATTATCTTACGATAATACGTTAATTTTTACCATTAAGTTGAAGATTCCTAAAAA
12542 AAATAGCTTTAAAA-T-TGCCCTTTGTAATATTAATTCAACTAAGAGGGTCTCGTTTATTTTAGT
130 AAATAGCTTTAAAATTATGCCCTTTGTAATATTAATTCAACTAAGAGGGTCTCGTTTATTTTAGT
12605 TATGAGGGATAAGTCCTCCGCATCAGCTACTCATAGATATTCCATAGGCACAGCTCCCTTCAATG
195 TATGAGGGATAAGTCCTCCGCATCAGCTACTCATAGATA-TCC--AGGCACAGCTCCCTTCAATG
12670 CCCGTAATTGTTATAGCTTCCGTAATGAGCACA-CCCTTGCCATTGTTAACTCCTCTTAATTAAA
257 CCCGTAATTGTTATAGCTTCCGTAATGAGCACACCCCTTGCCATTGTTAACTCCTCTTAATTAAA
12734 GTGGTTAACTGTCATTTTCATAGGAGTAAGCATC
322 GTGGTTAACTGTCATTTTCATAGGAGTAAGCATC
12768 CAAAAACACT
Statistics
Matches: 349, Mismatches: 0, Indels: 11
0.97 0.00 0.03
Matches are distributed among these distances:
351 87 0.25
352 4 0.01
353 115 0.33
354 110 0.32
355 33 0.09
ACGTcount: A:0.31, C:0.18, G:0.15, T:0.36
Consensus pattern (355 bp):
ATTTTAGTTTTATTTTGAGCAGTCGTCATTAAAATCAACACAATAGGATACGATATTTTTTAACT
GTGATATAATATTATCTTACGATAATACGTTAATTTTTACCATTAAGTTGAAGATTCCTAAAAAA
AATAGCTTTAAAATTATGCCCTTTGTAATATTAATTCAACTAAGAGGGTCTCGTTTATTTTAGTT
ATGAGGGATAAGTCCTCCGCATCAGCTACTCATAGATATCCAGGCACAGCTCCCTTCAATGCCCG
TAATTGTTATAGCTTCCGTAATGAGCACACCCCTTGCCATTGTTAACTCCTCTTAATTAAAGTGG
TTAACTGTCATTTTCATAGGAGTAAGCATC
Found at i:14806 original size:5 final size:5
Alignment explanation
Indices: 14798--14851 Score: 81
Period size: 5 Copynumber: 10.8 Consensus size: 5
14788 CGTCTCGTCT
* * *
14798 CTCGG CTCGG CTCGG CTCGG CACGG CACGG CACGG CTCGG CTCGG CTCGG
1 CTCGG CTCGG CTCGG CTCGG CTCGG CTCGG CTCGG CTCGG CTCGG CTCGG
14848 CTCG
1 CTCG
14852 TGGTCGTGGT
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
5 47 1.00
ACGTcount: A:0.06, C:0.41, G:0.39, T:0.15
Consensus pattern (5 bp):
CTCGG
Found at i:14860 original size:6 final size:6
Alignment explanation
Indices: 14849--14939 Score: 182
Period size: 6 Copynumber: 15.2 Consensus size: 6
14839 TCGGCTCGGC
14849 TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG
1 TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG
14897 TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG T
1 TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG T
14940 AATACGTGTC
Statistics
Matches: 85, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 85 1.00
ACGTcount: A:0.00, C:0.16, G:0.49, T:0.34
Consensus pattern (6 bp):
TCGTGG
Found at i:15097 original size:40 final size:40
Alignment explanation
Indices: 15015--15090 Score: 152
Period size: 40 Copynumber: 1.9 Consensus size: 40
15005 TTTGAAAGAA
15015 ACAAATGGAAAATGTGAAAGATATCAACGTTTCAGCTGTT
1 ACAAATGGAAAATGTGAAAGATATCAACGTTTCAGCTGTT
15055 ACAAATGGAAAATGTGAAAGATATCAACGTTTCAGC
1 ACAAATGGAAAATGTGAAAGATATCAACGTTTCAGC
15091 GATTACACAC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 36 1.00
ACGTcount: A:0.42, C:0.13, G:0.20, T:0.25
Consensus pattern (40 bp):
ACAAATGGAAAATGTGAAAGATATCAACGTTTCAGCTGTT
Found at i:20291 original size:5 final size:5
Alignment explanation
Indices: 20281--20319 Score: 51
Period size: 5 Copynumber: 7.8 Consensus size: 5
20271 CGTCCGTCGT
* * *
20281 CTCGG CTCGG CTCGG CACGG CACGG CACGG CTCGG CTCG
1 CTCGG CTCGG CTCGG CTCGG CTCGG CTCGG CTCGG CTCG
20320 TGGTCGTGGT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
5 32 1.00
ACGTcount: A:0.08, C:0.41, G:0.38, T:0.13
Consensus pattern (5 bp):
CTCGG
Found at i:20328 original size:6 final size:6
Alignment explanation
Indices: 20317--20389 Score: 128
Period size: 6 Copynumber: 12.2 Consensus size: 6
20307 ACGGCTCGGC
* *
20317 TCGTGG TCGTGG TCGTGG TCGTGG TCGAGG TCGAGG TCGTGG TCGTGG
1 TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG
20365 TCGTGG TCGTGG TCGTGG TCGTGG T
1 TCGTGG TCGTGG TCGTGG TCGTGG T
20390 AATACGTGTC
Statistics
Matches: 65, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 65 1.00
ACGTcount: A:0.03, C:0.16, G:0.49, T:0.32
Consensus pattern (6 bp):
TCGTGG
Found at i:20689 original size:22 final size:22
Alignment explanation
Indices: 20664--20718 Score: 56
Period size: 22 Copynumber: 2.5 Consensus size: 22
20654 TCAGGAGTTA
* *
20664 CAGGAGTTATTTGATTTAATTC
1 CAGGAGTTATATGATATAATTC
* * *
20686 CAGGGGTTACATGATATAATTT
1 CAGGAGTTATATGATATAATTC
*
20708 CGGGAGTTATA
1 CAGGAGTTATA
20719 ACAGCTGAAT
Statistics
Matches: 25, Mismatches: 8, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.29, C:0.09, G:0.24, T:0.38
Consensus pattern (22 bp):
CAGGAGTTATATGATATAATTC
Found at i:22992 original size:15 final size:15
Alignment explanation
Indices: 22969--23016 Score: 69
Period size: 15 Copynumber: 3.2 Consensus size: 15
22959 TTAGCTGGGT
22969 GGGCGGATGTGGGGC
1 GGGCGGATGTGGGGC
* *
22984 GGGCAGATGTGGGGT
1 GGGCGGATGTGGGGC
*
22999 GGGCGGATGCGGGGC
1 GGGCGGATGTGGGGC
23014 GGG
1 GGG
23017 TAATGTCTCA
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
15 28 1.00
ACGTcount: A:0.08, C:0.12, G:0.67, T:0.12
Consensus pattern (15 bp):
GGGCGGATGTGGGGC
Found at i:40931 original size:26 final size:26
Alignment explanation
Indices: 40893--40947 Score: 83
Period size: 26 Copynumber: 2.1 Consensus size: 26
40883 CCTAAGATTG
40893 TTTCTTAAATTGAGTTCGAAACAAGT
1 TTTCTTAAATTGAGTTCGAAACAAGT
* * *
40919 TTTCTTAATTTGAGTTTGAAACAGGT
1 TTTCTTAAATTGAGTTCGAAACAAGT
40945 TTT
1 TTT
40948 GTAAAGGAGA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.29, C:0.09, G:0.16, T:0.45
Consensus pattern (26 bp):
TTTCTTAAATTGAGTTCGAAACAAGT
Found at i:44597 original size:34 final size:29
Alignment explanation
Indices: 44529--44588 Score: 84
Period size: 29 Copynumber: 2.0 Consensus size: 29
44519 AAATTTTGAA
* *
44529 TAAATTCAATTAAGTCCAAATATATTTTG
1 TAAATTCAATTAAGTCCAAAAACATTTTG
44558 TAAATTCAATTCAAGTCCAAAAACCATTTTG
1 TAAATTCAATT-AAGTCCAAAAA-CATTTTG
44589 CCTTAAATTG
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
29 11 0.41
30 10 0.37
31 6 0.22
ACGTcount: A:0.42, C:0.15, G:0.07, T:0.37
Consensus pattern (29 bp):
TAAATTCAATTAAGTCCAAAAACATTTTG
Found at i:44732 original size:15 final size:16
Alignment explanation
Indices: 44712--44745 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
44702 TCCATAAAAA
*
44712 TAAAATTTTAAATT-T
1 TAAAATTTAAAATTAT
44727 TAAAATTTAAAATTAT
1 TAAAATTTAAAATTAT
44743 TAA
1 TAA
44746 TAAATATATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 13 0.76
16 4 0.24
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (16 bp):
TAAAATTTAAAATTAT
Found at i:45018 original size:23 final size:24
Alignment explanation
Indices: 44963--45031 Score: 68
Period size: 23 Copynumber: 2.9 Consensus size: 24
44953 TTATAATAAT
* * *
44963 AATATTATTATATTATATTATTAAA
1 AATATTAATAAATAATATT-TTAAA
44988 AATATTAATAAATAA-ATTTTAAA
1 AATATTAATAAATAATATTTTAAA
* * *
45011 TATGTTAATAATTAATATTTT
1 AATATTAATAAATAATATTTT
45032 TATTAAAATG
Statistics
Matches: 37, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
23 17 0.46
24 8 0.22
25 12 0.32
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.49
Consensus pattern (24 bp):
AATATTAATAAATAATATTTTAAA
Found at i:58500 original size:3 final size:3
Alignment explanation
Indices: 58492--58538 Score: 85
Period size: 3 Copynumber: 15.7 Consensus size: 3
58482 CAAAGACCTT
*
58492 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTG TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
58539 TATCGAAAAC
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:63947 original size:49 final size:50
Alignment explanation
Indices: 63851--63948 Score: 128
Period size: 49 Copynumber: 2.0 Consensus size: 50
63841 GATAAAATTT
* * *
63851 AATAAAAAATATATTTTATTAAAACTCGTCACCTCAAGCTGACGAGTTTG
1 AATAAAAAATATATTTTATCAAAACTCGTCACATCAAGCTGAAGAGTTTG
* *
63901 AATAAAAAATAT-TTTTATCAGAACTCGTCACATCCA-CGTGAAGAGTTT
1 AATAAAAAATATATTTTATCAAAACTCGTCACATCAAGC-TGAAGAGTTT
63949 CATTACTATT
Statistics
Matches: 42, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
48 1 0.02
49 29 0.69
50 12 0.29
ACGTcount: A:0.40, C:0.16, G:0.12, T:0.32
Consensus pattern (50 bp):
AATAAAAAATATATTTTATCAAAACTCGTCACATCAAGCTGAAGAGTTTG
Found at i:65106 original size:12 final size:13
Alignment explanation
Indices: 65084--65112 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
65074 AAACACATTG
65084 TAATATAATTAAT
1 TAATATAATTAAT
65097 TAAT-TAATTAAT
1 TAATATAATTAAT
65109 TAAT
1 TAAT
65113 CTTCCAGATA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 12 0.75
13 4 0.25
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (13 bp):
TAATATAATTAAT
Found at i:66433 original size:2 final size:2
Alignment explanation
Indices: 66379--66414 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
66369 TAAATGCTCG
66379 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
66415 TTGTGAATAT
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:66970 original size:2 final size:2
Alignment explanation
Indices: 66963--66995 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
66953 TCAATCACAG
66963 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
66996 CACATACATA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:67353 original size:20 final size:19
Alignment explanation
Indices: 67314--67357 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 19
67304 TCCCTTTGGG
* *
67314 TGATTCGAATTCAGAAATT
1 TGATTCGAACTCAAAAATT
67333 TGATTCGAACTCGAAAAATT
1 TGATTCGAACTC-AAAAATT
67353 T-ATTC
1 TGATTC
67358 AGTCAAATTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 15 0.68
20 7 0.32
ACGTcount: A:0.36, C:0.14, G:0.14, T:0.36
Consensus pattern (19 bp):
TGATTCGAACTCAAAAATT
Found at i:77353 original size:13 final size:13
Alignment explanation
Indices: 77332--77386 Score: 58
Period size: 13 Copynumber: 4.2 Consensus size: 13
77322 AAGTTCGATA
*
77332 AATTCAAATACTT
1 AATTGAAATACTT
77345 AATTGAAATACTT
1 AATTGAAATACTT
* *
77358 AATT-AACTCAACAT
1 AATTGAAAT--ACTT
77372 AATTGAAATACTT
1 AATTGAAATACTT
77385 AA
1 AA
77387 ATACTTCCAA
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
12 3 0.09
13 21 0.62
14 7 0.21
15 3 0.09
ACGTcount: A:0.49, C:0.13, G:0.04, T:0.35
Consensus pattern (13 bp):
AATTGAAATACTT
Found at i:77468 original size:32 final size:33
Alignment explanation
Indices: 77372--77470 Score: 164
Period size: 33 Copynumber: 3.0 Consensus size: 33
77362 AACTCAACAT
* * *
77372 AATTGAAATACTTAAATACTTCCAAGTTTGATA
1 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
77405 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
1 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
77438 AATTCAAATACTTAAAAACTT-CAAGTTCGATA
1 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
77470 A
1 A
77471 TTGAAACAAA
Statistics
Matches: 63, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
32 12 0.19
33 51 0.81
ACGTcount: A:0.45, C:0.15, G:0.07, T:0.32
Consensus pattern (33 bp):
AATTCAAATACTTAAAAACTTCCAAGTTCGATA
Found at i:77489 original size:21 final size:21
Alignment explanation
Indices: 77465--77504 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
77455 ACTTCAAGTT
77465 CGATAATTGAAACAAAGTTTA
1 CGATAATTGAAACAAAGTTTA
*
77486 CGATAATTGAAATAAAGTT
1 CGATAATTGAAACAAAGTT
77505 ATAAAATAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.47, C:0.07, G:0.15, T:0.30
Consensus pattern (21 bp):
CGATAATTGAAACAAAGTTTA
Found at i:80692 original size:37 final size:39
Alignment explanation
Indices: 80607--80692 Score: 122
Period size: 39 Copynumber: 2.3 Consensus size: 39
80597 AATTATACTT
* *
80607 AAAAATTTATTTTTTATTTCATTTTAATACTCGCCATTA
1 AAAAATTTAATTTTTATATCATTTTAATACTCGCCATTA
* *
80646 AAAACTTTAATTTTTATATCATTTTAATAC-CG-TATTA
1 AAAAATTTAATTTTTATATCATTTTAATACTCGCCATTA
80683 AAAAATTTAA
1 AAAAATTTAA
80693 CATTAAATTT
Statistics
Matches: 42, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
37 13 0.31
38 2 0.05
39 27 0.64
ACGTcount: A:0.40, C:0.10, G:0.02, T:0.48
Consensus pattern (39 bp):
AAAAATTTAATTTTTATATCATTTTAATACTCGCCATTA
Found at i:86955 original size:20 final size:20
Alignment explanation
Indices: 86919--86956 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
86909 ATCATATTCT
**
86919 CTGGTAATCTTTTATTCCCA
1 CTGGTAATCTTACATTCCCA
86939 CTGGTAATCTTACATTCC
1 CTGGTAATCTTACATTCC
86957 GTGAACCAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.21, C:0.26, G:0.11, T:0.42
Consensus pattern (20 bp):
CTGGTAATCTTACATTCCCA
Found at i:87064 original size:30 final size:30
Alignment explanation
Indices: 87029--87103 Score: 141
Period size: 30 Copynumber: 2.5 Consensus size: 30
87019 AAATTACATG
87029 TTTAGTACTTAAATTATTAATTTTATCCAT
1 TTTAGTACTTAAATTATTAATTTTATCCAT
87059 TTTAGTACTTAAATTATTAATTTTATCCAT
1 TTTAGTACTTAAATTATTAATTTTATCCAT
*
87089 TTTGGTACTTAAATT
1 TTTAGTACTTAAATT
87104 TTTTTTCAAA
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
30 44 1.00
ACGTcount: A:0.32, C:0.09, G:0.05, T:0.53
Consensus pattern (30 bp):
TTTAGTACTTAAATTATTAATTTTATCCAT
Found at i:89079 original size:20 final size:20
Alignment explanation
Indices: 89056--89270 Score: 139
Period size: 20 Copynumber: 10.7 Consensus size: 20
89046 CGTTGCGATT
*
89056 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGAATACGAA
* *
89076 AATCGCAACGCGAACA-TATA
1 AATCGCAACGCGAATACGA-A
* * *
89096 AATCACAACGCG-ATTCTAA
1 AATCGCAACGCGAATACGAA
* * * *
89115 CTATCGCAACGAGTATCCGTAA
1 -AATCGCAACGCGAATACG-AA
* * *
89137 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGAATACGAA
89157 AATCGCAACGAC-AATACGTAA
1 AATCGCAACG-CGAATACG-AA
* * *
89178 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGAATACGAA
* *
89198 AATCGCAACGAGAATACGTA
1 AATCGCAACGCGAATACGAA
* ** *
89218 AATCGCAACGCGTATTTGTA
1 AATCGCAACGCGAATACGAA
* *
89238 AATCGCAACGAGAATACGTA
1 AATCGCAACGCGAATACGAA
*
89258 AATCGCAATGCGA
1 AATCGCAACGCGA
89271 TTTTGGTTTC
Statistics
Matches: 155, Mismatches: 32, Indels: 16
0.76 0.16 0.08
Matches are distributed among these distances:
19 3 0.02
20 115 0.74
21 35 0.23
22 2 0.01
ACGTcount: A:0.39, C:0.24, G:0.18, T:0.19
Consensus pattern (20 bp):
AATCGCAACGCGAATACGAA
Found at i:89148 original size:41 final size:40
Alignment explanation
Indices: 89056--89265 Score: 237
Period size: 40 Copynumber: 5.2 Consensus size: 40
89046 CGTTGCGATT
* * * * **
89056 AATCGCAACGCGAATAT-GAAAATCGCAACGCGAACATATA
1 AATCGCAACGCGTAT-TCGTAAATCGCAACGAGAATACGTA
* * *
89096 AATCACAACGCG-ATTC-TAACTATCGCAACGAGTATCCGTAA
1 AATCGCAACGCGTATTCGTAA--ATCGCAACGAGAATACGT-A
* *
89137 AATCGCAACGCGTATCCGTAAATCGCAACGACAATACGTAA
1 AATCGCAACGCGTATTCGTAAATCGCAACGAGAATACGT-A
*
89178 AATCGCAACGCGTATCCGTAAATCGCAACGAGAATACGTA
1 AATCGCAACGCGTATTCGTAAATCGCAACGAGAATACGTA
*
89218 AATCGCAACGCGTATTTGTAAATCGCAACGAGAATACGTA
1 AATCGCAACGCGTATTCGTAAATCGCAACGAGAATACGTA
89258 AATCGCAA
1 AATCGCAA
89266 TGCGATTTTG
Statistics
Matches: 148, Mismatches: 16, Indels: 12
0.84 0.09 0.07
Matches are distributed among these distances:
38 3 0.02
39 2 0.01
40 70 0.47
41 67 0.45
42 3 0.02
43 3 0.02
ACGTcount: A:0.40, C:0.24, G:0.18, T:0.19
Consensus pattern (40 bp):
AATCGCAACGCGTATTCGTAAATCGCAACGAGAATACGTA
Found at i:90197 original size:14 final size:14
Alignment explanation
Indices: 90178--90213 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
90168 AACTGTATAA
90178 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
90192 AATCGCAACGAGTG
1 AATCGCAACGAGAG
90206 AATCGCAA
1 AATCGCAA
90214 TGCGAAAATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.42, C:0.22, G:0.25, T:0.11
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:90270 original size:20 final size:19
Alignment explanation
Indices: 90245--90351 Score: 99
Period size: 20 Copynumber: 6.1 Consensus size: 19
90235 GCGAAATTAG
*
90245 TTTCGCGTTGCGATTTTCA
1 TTTCGCATTGCGATTTTCA
90264 TTTTCGCATTGCGA--TTCA
1 -TTTCGCATTGCGATTTTCA
*
90282 -CTCG--TTGCGATTTTCA
1 TTTCGCATTGCGATTTTCA
90298 TTTTCGCATTGCGA--TTCA
1 -TTTCGCATTGCGATTTTCA
*
90316 -CTCG--TTGCGATTTTCA
1 TTTCGCATTGCGATTTTCA
90332 TTTCGCATTGCGATTTTCA
1 TTTCGCATTGCGATTTTCA
90351 T
1 T
90352 GTTGGGATAG
Statistics
Matches: 71, Mismatches: 5, Indels: 23
0.72 0.05 0.23
Matches are distributed among these distances:
14 12 0.17
16 14 0.20
17 3 0.04
18 11 0.15
19 13 0.18
20 18 0.25
ACGTcount: A:0.14, C:0.22, G:0.18, T:0.46
Consensus pattern (19 bp):
TTTCGCATTGCGATTTTCA
Found at i:90293 original size:34 final size:34
Alignment explanation
Indices: 90250--90346 Score: 187
Period size: 34 Copynumber: 2.9 Consensus size: 34
90240 ATTAGTTTCG
90250 CGTTGCGATTTTCATTTTCGCATTGCGATTCACT
1 CGTTGCGATTTTCATTTTCGCATTGCGATTCACT
90284 CGTTGCGATTTTCATTTTCGCATTGCGATTCACT
1 CGTTGCGATTTTCATTTTCGCATTGCGATTCACT
90318 CGTTGCGATTTTCA-TTTCGCATTGCGATT
1 CGTTGCGATTTTCATTTTCGCATTGCGATT
90347 TTCATGTTGG
Statistics
Matches: 63, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
33 15 0.24
34 48 0.76
ACGTcount: A:0.14, C:0.23, G:0.19, T:0.44
Consensus pattern (34 bp):
CGTTGCGATTTTCATTTTCGCATTGCGATTCACT
Found at i:90366 original size:67 final size:68
Alignment explanation
Indices: 90250--90379 Score: 176
Period size: 67 Copynumber: 1.9 Consensus size: 68
90240 ATTAGTTTCG
** *
90250 CGTTGCGATTTTCATTTTCGCATTGCGATTCACTCGTTGCGATTTTCATTTTCGCATTGCGATTC
1 CGTTGCGATTTTCATTTTCGCATTGCGATTCACTCGTTGCGATAGTCATTTCCGCATTGCGATTC
90315 ACT
66 ACT
* *
90318 CGTTGCGATTTTCA-TTTCGCATTGCGATTTTCA-T-GTTGGGATAGTCATTTCCGCGTTGCGAT
1 CGTTGCGATTTTCATTTTCGCATTGCGA--TTCACTCGTTGCGATAGTCATTTCCGCATTGCGAT
90380 AGTCTGTTTT
Statistics
Matches: 55, Mismatches: 5, Indels: 5
0.85 0.08 0.08
Matches are distributed among these distances:
67 36 0.65
68 15 0.27
69 4 0.07
ACGTcount: A:0.15, C:0.22, G:0.21, T:0.43
Consensus pattern (68 bp):
CGTTGCGATTTTCATTTTCGCATTGCGATTCACTCGTTGCGATAGTCATTTCCGCATTGCGATTC
ACT
Found at i:90500 original size:14 final size:14
Alignment explanation
Indices: 90481--90517 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
90471 CATCAATTAA
90481 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
90495 ACAAATCATCTTTT
1 ACAAATCAACATTT
90509 ACAAATCAA
1 ACAAATCAA
90518 TTAAACAATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACATTT
Found at i:91968 original size:42 final size:42
Alignment explanation
Indices: 91889--91981 Score: 107
Period size: 42 Copynumber: 2.2 Consensus size: 42
91879 CCTCTTCAAC
* * *
91889 GATGACAGTGGCCTCTTGAACGGTGGGAGGGGACTCTTGAGG
1 GATGACAGGGGCCTCTTGAACGATGGGAGAGGACTCTTGAGG
* * **
91931 GATGATAGGGGCCTCTTGAACGATAGGG-GAGGCCTCTTGAAC
1 GATGACAGGGGCCTCTTGAACGAT-GGGAGAGGACTCTTGAGG
91973 GATGACAGG
1 GATGACAGG
91982 TGAGTCGGCC
Statistics
Matches: 42, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
42 39 0.93
43 3 0.07
ACGTcount: A:0.23, C:0.17, G:0.40, T:0.20
Consensus pattern (42 bp):
GATGACAGGGGCCTCTTGAACGATGGGAGAGGACTCTTGAGG
Found at i:92485 original size:20 final size:20
Alignment explanation
Indices: 92461--92527 Score: 80
Period size: 20 Copynumber: 3.4 Consensus size: 20
92451 GAAACTTAAA
*
92461 ATCGCAACGCGAAAATGACT
1 ATCGCAATGCGAAAATGACT
* *
92481 TTCGCAATGTGAAAATGACT
1 ATCGCAATGCGAAAATGACT
** *
92501 ATCGCAATGCGAATTTTACT
1 ATCGCAATGCGAAAATGACT
92521 ATCGCAA
1 ATCGCAA
92528 CGAGAGAATC
Statistics
Matches: 39, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 39 1.00
ACGTcount: A:0.36, C:0.21, G:0.18, T:0.25
Consensus pattern (20 bp):
ATCGCAATGCGAAAATGACT
Found at i:92586 original size:19 final size:19
Alignment explanation
Indices: 92563--92605 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 19
92553 AATCGCAACA
92563 CGATTACAGTTTCGCGTTG
1 CGATTACAGTTTCGCGTTG
* ***
92582 TGATTTTGGTTTCGCGTTG
1 CGATTACAGTTTCGCGTTG
92601 CGATT
1 CGATT
92606 TTGGTTTCGC
Statistics
Matches: 19, Mismatches: 5, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.12, C:0.16, G:0.28, T:0.44
Consensus pattern (19 bp):
CGATTACAGTTTCGCGTTG
Found at i:92606 original size:19 final size:19
Alignment explanation
Indices: 92571--92623 Score: 88
Period size: 19 Copynumber: 2.8 Consensus size: 19
92561 CACGATTACA
*
92571 GTTTCGCGTTGTGATTTTG
1 GTTTCGCGTTGCGATTTTG
92590 GTTTCGCGTTGCGATTTTG
1 GTTTCGCGTTGCGATTTTG
*
92609 GTTTCGCGTTTCGAT
1 GTTTCGCGTTGCGAT
92624 AGTCATTTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 32 1.00
ACGTcount: A:0.06, C:0.15, G:0.30, T:0.49
Consensus pattern (19 bp):
GTTTCGCGTTGCGATTTTG
Found at i:92857 original size:94 final size:94
Alignment explanation
Indices: 92711--93090 Score: 611
Period size: 94 Copynumber: 4.1 Consensus size: 94
92701 ATGGATTGCA
* *
92711 TTAC-TTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCAGAGTATTAAAGAATACACAGT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
* *
92775 TTAACAGAATTGGCAGTAACTGAACAAAT
66 TTAACAGAATTGGCAGCAACCGAACAAAT
92804 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
* *
92869 TTAGCATAATTGGCAGCAACCGAACAAAT
66 TTAACAGAATTGGCAGCAACCGAACAAAT
92898 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
* * *
92963 TTAACATAATTGGCAGCAACCAAATAAAT
66 TTAACAGAATTGGCAGCAACCGAACAAAT
* *
92992 TTAC-TTCAACCAAAAGACAAAACAAAAGACAAATACTAATTTCACAGTGTTAAAGAATAAACAG
1 TTACTTTCAACCAAAAGACAAAAC-AAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAG
* * *
93056 TTTAGCAGTATTGGCAGCAACCGAATAAAT
65 TTTAACAGAATTGGCAGCAACCGAACAAAT
93086 TTACT
1 TTACT
93091 AAGCAATCTA
Statistics
Matches: 269, Mismatches: 15, Indels: 4
0.93 0.05 0.01
Matches are distributed among these distances:
93 23 0.09
94 246 0.91
ACGTcount: A:0.48, C:0.18, G:0.11, T:0.22
Consensus pattern (94 bp):
TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
TTAACAGAATTGGCAGCAACCGAACAAAT
Found at i:93848 original size:31 final size:31
Alignment explanation
Indices: 93810--93872 Score: 126
Period size: 31 Copynumber: 2.0 Consensus size: 31
93800 AGGAATATCA
93810 TTTGAAGTTTTTAATGCATATGTCTGCATGC
1 TTTGAAGTTTTTAATGCATATGTCTGCATGC
93841 TTTGAAGTTTTTAATGCATATGTCTGCATGC
1 TTTGAAGTTTTTAATGCATATGTCTGCATGC
93872 T
1 T
93873 GGGGAAAGCC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.22, C:0.13, G:0.19, T:0.46
Consensus pattern (31 bp):
TTTGAAGTTTTTAATGCATATGTCTGCATGC
Found at i:94905 original size:19 final size:19
Alignment explanation
Indices: 94881--95002 Score: 83
Period size: 20 Copynumber: 6.5 Consensus size: 19
94871 AGAATCACAA
**
94881 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTCATTTCGCGT
94900 TGCGATTTTCATTTCGCGT
1 TGCGATTTTCATTTCGCGT
* *
94919 TACGA--TTC---TCTCGT
1 TGCGATTTTCATTTCGCGT
94933 TGCGATTTTCATTTCGCTCGT
1 TGCGATTTTCATTTCG--CGT
** *
94954 TGCGATAGTCATTTTCGTGT
1 TGCGATTTTCA-TTTCGCGT
* **
94974 TGCGGTTTTCATTTTCATGT
1 TGCGATTTTCA-TTTCGCGT
94994 TGCGATTTT
1 TGCGATTTT
95003 AAGTTTAGAA
Statistics
Matches: 81, Mismatches: 14, Indels: 15
0.74 0.13 0.14
Matches are distributed among these distances:
14 9 0.11
16 3 0.04
17 3 0.04
19 23 0.28
20 26 0.32
21 12 0.15
22 5 0.06
ACGTcount: A:0.11, C:0.19, G:0.22, T:0.48
Consensus pattern (19 bp):
TGCGATTTTCATTTCGCGT
Found at i:94954 original size:21 final size:21
Alignment explanation
Indices: 94928--94987 Score: 70
Period size: 21 Copynumber: 2.9 Consensus size: 21
94918 TTACGATTCT
94928 CTCGTTGCGATTTTCATTTCG
1 CTCGTTGCGATTTTCATTTCG
**
94949 CTCGTTGCGATAGTCATTTTCG
1 CTCGTTGCGATTTTCA-TTTCG
*
94971 -T-GTTGCGGTTTTCATTT
1 CTCGTTGCGATTTTCATTT
94988 TCATGTTGCG
Statistics
Matches: 33, Mismatches: 5, Indels: 4
0.79 0.12 0.10
Matches are distributed among these distances:
19 3 0.09
20 10 0.30
21 15 0.45
22 5 0.15
ACGTcount: A:0.10, C:0.20, G:0.22, T:0.48
Consensus pattern (21 bp):
CTCGTTGCGATTTTCATTTCG
Found at i:95593 original size:20 final size:20
Alignment explanation
Indices: 95565--95774 Score: 226
Period size: 20 Copynumber: 10.3 Consensus size: 20
95555 AAAAATCGCA
95565 TTGCGATTTACGGATACGCG
1 TTGCGATTTACGGATACGCG
* * * *
95585 TTACGATTTTATGTAT-TGTCG
1 TTGCGA-TTTACGGATACG-CG
*
95606 TTGCGATTTACGGATACGCA
1 TTGCGATTTACGGATACGCG
* * *
95626 TTGCGATTTACGTATTCTCG
1 TTGCGATTTACGGATACGCG
*
95646 TTGCGATTTACAGATACGCG
1 TTGCGATTTACGGATACGCG
* * *
95666 TTGCGATTTACGTATTCTCG
1 TTGCGATTTACGGATACGCG
95686 TTGCGATTTACGGATACGCG
1 TTGCGATTTACGGATACGCG
* *
95706 TTGCGATTTTACGTAT-TGTCG
1 TTGCGA-TTTACGGATACG-CG
95727 TTGCGATTTACGGATACGCG
1 TTGCGATTTACGGATACGCG
*
95747 TTGCGATTTTACGGATACTCG
1 TTGCGA-TTTACGGATACGCG
95768 TTGCGAT
1 TTGCGAT
95775 AGTTAGAATC
Statistics
Matches: 154, Mismatches: 29, Indels: 14
0.78 0.15 0.07
Matches are distributed among these distances:
20 103 0.67
21 51 0.33
ACGTcount: A:0.19, C:0.18, G:0.25, T:0.38
Consensus pattern (20 bp):
TTGCGATTTACGGATACGCG
Found at i:95717 original size:81 final size:82
Alignment explanation
Indices: 95565--95835 Score: 329
Period size: 81 Copynumber: 3.3 Consensus size: 82
95555 AAAAATCGCA
* * * * *
95565 TTGCGATTTACGGATACGCGTTACGATTTTATGTATTGTCGTTGCGATTTACGGATACGCATTGC
1 TTGCGATTTACAGATACGCGTTGCGATTTTACGTATTCTCGTTGCGATTTACGGATACGCGTTGC
95630 GA-TTTACGTATTCTCG
66 GATTTTACGTATTCTCG
95646 TTGCGATTTACAGATACGCGTTGCGA-TTTACGTATTCTCGTTGCGATTTACGGATACGCGTTGC
1 TTGCGATTTACAGATACGCGTTGCGATTTTACGTATTCTCGTTGCGATTTACGGATACGCGTTGC
*
95710 GATTTTACGTATTGTCG
66 GATTTTACGTATTCTCG
* * * * *
95727 TTGCGATTTACGGATACGCGTTGCGATTTTACGGATACTCGTTGCGATAGTTA-GAAT-CGTGTT
1 TTGCGATTTACAGATACGCGTTGCGATTTTACGTATTCTCGTTGCGAT--TTACGGATACGCGTT
* *
95790 GCGATTTATA--TGTTCGCG
64 GCGATTT-TACGTATTCTCG
* * *
95808 TTGCGATTTTCATATTCGCGTTGCGATT
1 TTGCGATTTACAGATACGCGTTGCGATT
95836 CTGGAAAATC
Statistics
Matches: 167, Mismatches: 18, Indels: 10
0.86 0.09 0.05
Matches are distributed among these distances:
80 37 0.22
81 91 0.54
82 31 0.19
83 5 0.03
84 3 0.02
ACGTcount: A:0.19, C:0.17, G:0.25, T:0.39
Consensus pattern (82 bp):
TTGCGATTTACAGATACGCGTTGCGATTTTACGTATTCTCGTTGCGATTTACGGATACGCGTTGC
GATTTTACGTATTCTCG
Found at i:95758 original size:41 final size:41
Alignment explanation
Indices: 95565--95774 Score: 334
Period size: 41 Copynumber: 5.2 Consensus size: 41
95555 AAAAATCGCA
* * *
95565 TTGCGATTTACGGATACGCGTTACGATTTTATGTATTGTCG
1 TTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCTCG
*
95606 TTGCGATTTACGGATACGCATTGCGA-TTTACGTATTCTCG
1 TTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCTCG
*
95646 TTGCGATTTACAGATACGCGTTGCGA-TTTACGTATTCTCG
1 TTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCTCG
*
95686 TTGCGATTTACGGATACGCGTTGCGATTTTACGTATTGTCG
1 TTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCTCG
* *
95727 TTGCGATTTACGGATACGCGTTGCGATTTTACGGATACTCG
1 TTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCTCG
95768 TTGCGAT
1 TTGCGAT
95775 AGTTAGAATC
Statistics
Matches: 157, Mismatches: 11, Indels: 2
0.92 0.06 0.01
Matches are distributed among these distances:
40 75 0.48
41 82 0.52
ACGTcount: A:0.19, C:0.18, G:0.25, T:0.38
Consensus pattern (41 bp):
TTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCTCG
Found at i:95791 original size:41 final size:41
Alignment explanation
Indices: 95565--95835 Score: 297
Period size: 40 Copynumber: 6.7 Consensus size: 41
95555 AAAAATCGCA
* * * *
95565 TTGCGATTTACGGATACGCGTTACGATTTTATGTATTGTCG
1 TTGCGATTTACGAATACGCGTTGCGATTTTACGTATTCTCG
* *
95606 TTGCGATTTACGGATACGCATTGCGA-TTTACGTATTCTCG
1 TTGCGATTTACGAATACGCGTTGCGATTTTACGTATTCTCG
95646 TTGCGATTTAC-AGATACGCGTTGCGA-TTTACGTATTCTCG
1 TTGCGATTTACGA-ATACGCGTTGCGATTTTACGTATTCTCG
* *
95686 TTGCGATTTACGGATACGCGTTGCGATTTTACGTATTGTCG
1 TTGCGATTTACGAATACGCGTTGCGATTTTACGTATTCTCG
* * *
95727 TTGCGATTTACGGATACGCGTTGCGATTTTACGGATACTCG
1 TTGCGATTTACGAATACGCGTTGCGATTTTACGTATTCTCG
* * *
95768 TTGCGATAGTTA-GAAT-CGTGTTGCGATTTATA--TGTTCGCG
1 TTGCGAT--TTACGAATACGCGTTGCGATTT-TACGTATTCTCG
* *
95808 TTGCGATTTTC-ATATTCGCGTTGCGATT
1 TTGCGATTTACGA-ATACGCGTTGCGATT
95836 CTGGAAAATC
Statistics
Matches: 202, Mismatches: 19, Indels: 19
0.84 0.08 0.08
Matches are distributed among these distances:
38 3 0.01
39 2 0.01
40 95 0.47
41 94 0.47
42 5 0.02
43 3 0.01
ACGTcount: A:0.19, C:0.17, G:0.25, T:0.39
Consensus pattern (41 bp):
TTGCGATTTACGAATACGCGTTGCGATTTTACGTATTCTCG
Found at i:95810 original size:20 final size:20
Alignment explanation
Indices: 95787--95835 Score: 73
Period size: 20 Copynumber: 2.5 Consensus size: 20
95777 TTAGAATCGT
*
95787 GTTGCGATTTAT-ATGTTCGC
1 GTTGCGATTT-TCATATTCGC
95807 GTTGCGATTTTCATATTCGC
1 GTTGCGATTTTCATATTCGC
95827 GTTGCGATT
1 GTTGCGATT
95836 CTGGAAAATC
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
19 1 0.04
20 26 0.96
ACGTcount: A:0.14, C:0.16, G:0.24, T:0.45
Consensus pattern (20 bp):
GTTGCGATTTTCATATTCGC
Found at i:95934 original size:20 final size:19
Alignment explanation
Indices: 95864--95938 Score: 60
Period size: 20 Copynumber: 3.7 Consensus size: 19
95854 AATTTATACT
* *
95864 ATCGCATTGCGATTCTTCATG
1 ATCGCGTTGCGATTC-TGA-G
*
95885 ATCGCGTTGCGATTCTGGG
1 ATCGCGTTGCGATTCTGAG
* **
95904 AACTGATTTGCGATTCTAGAG
1 ATC-GCGTTGCGATTCT-GAG
95925 ATCGCGTTGCGATT
1 ATCGCGTTGCGATT
95939 TTTATTTCGC
Statistics
Matches: 42, Mismatches: 10, Indels: 5
0.74 0.18 0.09
Matches are distributed among these distances:
19 3 0.07
20 21 0.50
21 18 0.43
ACGTcount: A:0.19, C:0.20, G:0.27, T:0.35
Consensus pattern (19 bp):
ATCGCGTTGCGATTCTGAG
Found at i:97098 original size:2 final size:2
Alignment explanation
Indices: 97091--97136 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
97081 TTTCGATTTC
97091 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
97133 AT AT
1 AT AT
97137 TCACGAGAAT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:97659 original size:22 final size:22
Alignment explanation
Indices: 97631--97684 Score: 108
Period size: 22 Copynumber: 2.5 Consensus size: 22
97621 ACTAAATCCC
97631 TATTTTTATTGAATAAAAATAA
1 TATTTTTATTGAATAAAAATAA
97653 TATTTTTATTGAATAAAAATAA
1 TATTTTTATTGAATAAAAATAA
97675 TATTTTTATT
1 TATTTTTATT
97685 ATTATTTCGG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.44, C:0.00, G:0.04, T:0.52
Consensus pattern (22 bp):
TATTTTTATTGAATAAAAATAA
Found at i:103118 original size:21 final size:21
Alignment explanation
Indices: 103079--103137 Score: 57
Period size: 21 Copynumber: 2.8 Consensus size: 21
103069 ATTATCCAAT
*
103079 AAACTTGACAT-CTATAACAAC
1 AAACTTGAAATAC-ATAACAAC
* * * *
103100 AAATTTTAAATCCATAACAAG
1 AAACTTGAAATACATAACAAC
103121 AAACTTGAAATACATAA
1 AAACTTGAAATACATAA
103138 TAATAAATCA
Statistics
Matches: 30, Mismatches: 7, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
21 29 0.97
22 1 0.03
ACGTcount: A:0.53, C:0.17, G:0.05, T:0.25
Consensus pattern (21 bp):
AAACTTGAAATACATAACAAC
Found at i:106832 original size:41 final size:40
Alignment explanation
Indices: 106781--107015 Score: 204
Period size: 41 Copynumber: 5.7 Consensus size: 40
106771 TGAAAAAAAC
* * * *
106781 AAACACCACTACAGTTCGAATCTTTAGCGACGTTTGTATAA
1 AAACGCCACTAAAGTACGAATCTTTAGCG-CATTTGTATAA
*
106822 AAACGCCACTAAAGTACGAATCTTTAGCGGTATTTGTATAA
1 AAACGCCACTAAAGTACGAATCTTTAGC-GCATTTGTATAA
* * * * * *
106863 AAATGCTACTAAAATATGAGTCTTTAGCTGCATTTGTAAACA
1 AAACGCCACTAAAGTACGAATCTTTAGC-GCATTTGTATA-A
** * *
106905 TAAACGCCACTAAAGTACGTGTCTTTAGCGGCATTAGTATAC
1 -AAACGCCACTAAAGTACGAATCTTTAGC-GCATTTGTATAA
* *
106947 AAACGCCA-TGAAAGTAC-AAGTCTTTAGCCGCGTTTGTATAC
1 AAACGCCACT-AAAGTACGAA-TCTTTAG-CGCATTTGTATAA
* *
106988 AAACGCCACTAAAGTATGATTCTTTAGC
1 AAACGCCACTAAAGTACGAATCTTTAGC
107016 AGTGTTTTTG
Statistics
Matches: 158, Mismatches: 28, Indels: 17
0.78 0.14 0.08
Matches are distributed among these distances:
40 2 0.01
41 119 0.75
42 5 0.03
43 32 0.20
ACGTcount: A:0.34, C:0.20, G:0.17, T:0.29
Consensus pattern (40 bp):
AAACGCCACTAAAGTACGAATCTTTAGCGCATTTGTATAA
Found at i:106919 original size:84 final size:82
Alignment explanation
Indices: 106813--107015 Score: 221
Period size: 84 Copynumber: 2.5 Consensus size: 82
106803 TTTAGCGACG
* * * *
106813 TTTGTATAA-AAACGCCACTAAAGTACGAATCTTTAGCGGTATTTGTATAAAAATGCTACT-AAA
1 TTTGTA-AACAAACGCCACTAAAGTACGAATCTTTAGCGGCATTAGTATAAAAACGCCA-TGAAA
** *
106876 ATATGAGTCTTTAGCTGCA
64 ATACAAGTCTTTAGCCGCA
** *
106895 TTTGTAAACATAAACGCCACTAAAGTACGTGTCTTTAGCGGCATTAGTATACAAACGCCATGAAA
1 TTTGTAAAC--AAACGCCACTAAAGTACGAATCTTTAGCGGCATTAGTATAAAAACGCCATGAAA
* *
106960 GTACAAGTCTTTAGCCGCG
64 ATACAAGTCTTTAGCCGCA
* * *
106979 TTTGTATACAAACGCCACTAAAGTATGATTCTTTAGC
1 TTTGTAAACAAACGCCACTAAAGTACGAATCTTTAGC
107016 AGTGTTTTTG
Statistics
Matches: 101, Mismatches: 16, Indels: 8
0.81 0.13 0.06
Matches are distributed among these distances:
81 2 0.02
82 31 0.31
83 1 0.01
84 67 0.66
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.31
Consensus pattern (82 bp):
TTTGTAAACAAACGCCACTAAAGTACGAATCTTTAGCGGCATTAGTATAAAAACGCCATGAAAAT
ACAAGTCTTTAGCCGCA
Found at i:107897 original size:14 final size:14
Alignment explanation
Indices: 107863--107900 Score: 60
Period size: 13 Copynumber: 2.8 Consensus size: 14
107853 TTTTAAGAAT
*
107863 TTTAAGAATCTTTC
1 TTTAAGAATTTTTC
107877 TTT-AGAATTTTTC
1 TTTAAGAATTTTTC
107890 TTTAAGAATTT
1 TTTAAGAATTT
107901 CACACGAAAG
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 12 0.55
14 10 0.45
ACGTcount: A:0.29, C:0.08, G:0.08, T:0.55
Consensus pattern (14 bp):
TTTAAGAATTTTTC
Found at i:110944 original size:2 final size:2
Alignment explanation
Indices: 110937--110963 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
110927 CATTATAGTT
110937 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 T
110964 GTATCTTATA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:111011 original size:2 final size:2
Alignment explanation
Indices: 111004--111042 Score: 53
Period size: 2 Copynumber: 20.0 Consensus size: 2
110994 TTGATTTTAA
* *
111004 AT AT AT AT AA AT AT AA AT AT AT AT AT AT AT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
111043 TTTCTAATTA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (2 bp):
AT
Found at i:111112 original size:14 final size:14
Alignment explanation
Indices: 111095--111121 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
111085 ATATATTTTC
111095 ATTTAATTATTAAT
1 ATTTAATTATTAAT
111109 ATTTAATTATTAA
1 ATTTAATTATTAA
111122 CTTTTCGATC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (14 bp):
ATTTAATTATTAAT
Found at i:113259 original size:19 final size:19
Alignment explanation
Indices: 113212--113267 Score: 66
Period size: 19 Copynumber: 3.1 Consensus size: 19
113202 GTCATTGATT
113212 ATAACAAAAACT-AT-AT-A
1 ATAACAAAAA-TAATAATAA
113229 ATAA-AAATAATAATAATAA
1 ATAACAAA-AATAATAATAA
113248 ATAACAAAAATAATAATAA
1 ATAACAAAAATAATAATAA
113267 A
1 A
113268 GGATGAAATG
Statistics
Matches: 34, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
16 4 0.12
17 8 0.24
18 2 0.06
19 17 0.50
20 3 0.09
ACGTcount: A:0.71, C:0.05, G:0.00, T:0.23
Consensus pattern (19 bp):
ATAACAAAAATAATAATAA
Found at i:115014 original size:23 final size:23
Alignment explanation
Indices: 114986--115031 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
114976 TTGGGATTTA
114986 TATTTAATGTTA-TAATGATATAT
1 TATTT-ATGTTATTAATGATATAT
* *
115009 TATTTATTTTATTGATGATATAT
1 TATTTATGTTATTAATGATATAT
115032 AAAAGTATAC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 5 0.25
23 15 0.75
ACGTcount: A:0.35, C:0.00, G:0.09, T:0.57
Consensus pattern (23 bp):
TATTTATGTTATTAATGATATAT
Found at i:116152 original size:4 final size:4
Alignment explanation
Indices: 116143--116265 Score: 246
Period size: 4 Copynumber: 30.8 Consensus size: 4
116133 TAGGTTTATT
116143 ATGA ATGA ATGA ATGA ATGA ATGA ATGA ATGA ATGA ATGA ATGA ATGA
1 ATGA ATGA ATGA ATGA ATGA ATGA ATGA ATGA ATGA ATGA ATGA ATGA
116191 ATGA ATGA ATGA ATGA ATGA ATGA ATGA ATGA ATGA ATGA ATGA ATGA
1 ATGA ATGA ATGA ATGA ATGA ATGA ATGA ATGA ATGA ATGA ATGA ATGA
116239 ATGA ATGA ATGA ATGA ATGA ATGA ATG
1 ATGA ATGA ATGA ATGA ATGA ATGA ATG
116266 GGGAATTTTG
Statistics
Matches: 119, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 119 1.00
ACGTcount: A:0.50, C:0.00, G:0.25, T:0.25
Consensus pattern (4 bp):
ATGA
Found at i:118003 original size:23 final size:23
Alignment explanation
Indices: 117976--118019 Score: 88
Period size: 23 Copynumber: 1.9 Consensus size: 23
117966 AAAATGGCTA
117976 ATGTATGTGTGCAATCAAGTATG
1 ATGTATGTGTGCAATCAAGTATG
117999 ATGTATGTGTGCAATCAAGTA
1 ATGTATGTGTGCAATCAAGTA
118020 CGACTGGCGT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.32, C:0.09, G:0.25, T:0.34
Consensus pattern (23 bp):
ATGTATGTGTGCAATCAAGTATG
Found at i:124935 original size:20 final size:21
Alignment explanation
Indices: 124905--124946 Score: 77
Period size: 20 Copynumber: 2.0 Consensus size: 21
124895 CACCCTTTTT
124905 ATATATTTAAAACTAATAATC
1 ATATATTTAAAACTAATAATC
124926 ATAT-TTTAAAACTAATAATC
1 ATATATTTAAAACTAATAATC
124946 A
1 A
124947 CCGTCCTATC
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 17 0.81
21 4 0.19
ACGTcount: A:0.52, C:0.10, G:0.00, T:0.38
Consensus pattern (21 bp):
ATATATTTAAAACTAATAATC
Done.