Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003169.1 Hibiscus syriacus cultivar Beakdansim tig00006665_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: 91976
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:4115 original size:95 final size:95
Alignment explanation
Indices: 3947--4128 Score: 285
Period size: 95 Copynumber: 1.9 Consensus size: 95
3937 TAATATTTTA
* * * *
3947 TATACAATAAAGCTTGAGTTGTCCCTCTAGAGCAATTGGTTAAACGCCCCGGCTTTATGGATAAT
1 TATACAATAAAGCTTGAGCTGTCCCTCTAGAGCAATTAGTTAAACGCCCCAGCTTTATGGATAAG
* *
4012 ATTCAGCTAGCCTGATAAAGGTGATTATAC
66 ATTAAGCTAACCTGATAAAGGTGATTATAC
*
4042 TATACAATAAAGCTTGAGCTGTCCCTCTA-AGGCAATTAGTTAAACGCCCTAGCTTTATGGATAA
1 TATACAATAAAGCTTGAGCTGTCCCTCTAGA-GCAATTAGTTAAACGCCCCAGCTTTATGGATAA
4106 GATTAAGCTAACCTGATAAAGGT
65 GATTAAGCTAACCTGATAAAGGT
4129 ATTTACATAT
Statistics
Matches: 79, Mismatches: 7, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
94 1 0.01
95 78 0.99
ACGTcount: A:0.32, C:0.19, G:0.19, T:0.30
Consensus pattern (95 bp):
TATACAATAAAGCTTGAGCTGTCCCTCTAGAGCAATTAGTTAAACGCCCCAGCTTTATGGATAAG
ATTAAGCTAACCTGATAAAGGTGATTATAC
Found at i:4676 original size:19 final size:18
Alignment explanation
Indices: 4654--4690 Score: 56
Period size: 19 Copynumber: 2.0 Consensus size: 18
4644 TAAAAGGAGA
4654 TATATTTTCCAAAACTTTT
1 TATATTTTCCAAAA-TTTT
*
4673 TATATTTTTCAAAATTTT
1 TATATTTTCCAAAATTTT
4691 AAAAATTCAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 4 0.24
19 13 0.76
ACGTcount: A:0.32, C:0.11, G:0.00, T:0.57
Consensus pattern (18 bp):
TATATTTTCCAAAATTTT
Found at i:5549 original size:101 final size:101
Alignment explanation
Indices: 5369--5693 Score: 542
Period size: 101 Copynumber: 3.2 Consensus size: 101
5359 ATTCAAGTCA
* * * * *
5369 AAGCTCAACTTCACAGTGAAGGGGCGACTGTCTGTCAACAAAAAACTTCTTCAGAGTCAATTTCG
1 AAGCTCAACTTCACAGCGAAGGGGCGGCTGACTGTCAACAAACAACTTCTTCAGAGTCAATTTCA
*
5434 ACTTCACAACGAAGGATATTAGACTCAAGACAACAC
66 ACTTCACAGCGAAGGATATTAGACTCAAGACAACAC
*
5470 AAGCTCAACTTCACAGCGAAGGGGCGGCTGACTGTCAACAAACAACTTTTTCAGAGTCAATTTCA
1 AAGCTCAACTTCACAGCGAAGGGGCGGCTGACTGTCAACAAACAACTTCTTCAGAGTCAATTTCA
* * *
5535 ACTTCACAGTGAAGGATGTTAGACTCAAGACAGCAC
66 ACTTCACAGCGAAGGATATTAGACTCAAGACAACAC
* *
5571 AAGCTCAACGTCACAGCGAAGGGGCGGCTGAATGTCAACAAACAACTTCTTCAGAGTCAATTTCA
1 AAGCTCAACTTCACAGCGAAGGGGCGGCTGACTGTCAACAAACAACTTCTTCAGAGTCAATTTCA
5636 ACTTCACAGCGAAGGATATTAGACTCAAGACAACAC
66 ACTTCACAGCGAAGGATATTAGACTCAAGACAACAC
5672 AAGCTCAACTTCACAGCGAAGG
1 AAGCTCAACTTCACAGCGAAGG
5694 ATATTAGACT
Statistics
Matches: 207, Mismatches: 17, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
101 207 1.00
ACGTcount: A:0.36, C:0.24, G:0.20, T:0.20
Consensus pattern (101 bp):
AAGCTCAACTTCACAGCGAAGGGGCGGCTGACTGTCAACAAACAACTTCTTCAGAGTCAATTTCA
ACTTCACAGCGAAGGATATTAGACTCAAGACAACAC
Found at i:5694 original size:43 final size:43
Alignment explanation
Indices: 5633--5736 Score: 190
Period size: 43 Copynumber: 2.4 Consensus size: 43
5623 AGAGTCAATT
5633 TCAACTTCACAGCGAAGGATATTAGACTCAAGACAACACAAGC
1 TCAACTTCACAGCGAAGGATATTAGACTCAAGACAACACAAGC
*
5676 TCAACTTCACAGCGAAGGATATTAGACTCAAGACAGCACAAGC
1 TCAACTTCACAGCGAAGGATATTAGACTCAAGACAACACAAGC
*
5719 TCAACTTCACAACGAAGG
1 TCAACTTCACAGCGAAGG
5737 GGCGGTGACT
Statistics
Matches: 59, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
43 59 1.00
ACGTcount: A:0.40, C:0.26, G:0.17, T:0.16
Consensus pattern (43 bp):
TCAACTTCACAGCGAAGGATATTAGACTCAAGACAACACAAGC
Found at i:6295 original size:71 final size:71
Alignment explanation
Indices: 6174--6326 Score: 263
Period size: 71 Copynumber: 2.2 Consensus size: 71
6164 ATTGACCCAA
*
6174 CTTGAAACAAATTTGTCTCTCTTGAGACATTTCCCTTGAAACAATTTTTTGTCTCTCTTGAGAAA
1 CTTGAAACAAATTTGTCTCTCTTGAGACATTTCCCTTGAAACAATATTTTGTCTCTCTTGAGAAA
6239 GTTTCC
66 GTTTCC
* *
6245 CTTGAAACAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAA-ATTTTGTCTCTCTTGAGAC
1 CTTGAAACAAATTTGTCTCTCTTGAGACA-TTTCCCTTGAAACAATATTTTGTCTCTCTTGAGAA
6309 AGTTTCC
65 AGTTTCC
6316 CTTGAAACAAA
1 CTTGAAACAAA
6327 ATCTTTATGT
Statistics
Matches: 77, Mismatches: 4, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
71 62 0.81
72 15 0.19
ACGTcount: A:0.27, C:0.22, G:0.13, T:0.39
Consensus pattern (71 bp):
CTTGAAACAAATTTGTCTCTCTTGAGACATTTCCCTTGAAACAATATTTTGTCTCTCTTGAGAAA
GTTTCC
Found at i:6326 original size:36 final size:36
Alignment explanation
Indices: 6174--6326 Score: 258
Period size: 36 Copynumber: 4.3 Consensus size: 36
6164 ATTGACCCAA
6174 CTTGAAACAAA-TTTGTCTCTCTTGAGACA-TTTCC
1 CTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCC
* *
6208 CTTGAAACAATTTTTTGTCTCTCTTGAGAAAGTTTCC
1 CTTGAAACAA-ATTTTGTCTCTCTTGAGACAGTTTCC
6245 CTTGAAAC-AATTTTGTCTCTCTTGAGACAGTTTCC
1 CTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCC
6280 CTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCC
1 CTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCC
6316 CTTGAAACAAA
1 CTTGAAACAAA
6327 ATCTTTATGT
Statistics
Matches: 111, Mismatches: 4, Indels: 6
0.92 0.03 0.05
Matches are distributed among these distances:
34 10 0.09
35 32 0.29
36 56 0.50
37 13 0.12
ACGTcount: A:0.27, C:0.22, G:0.13, T:0.39
Consensus pattern (36 bp):
CTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCC
Found at i:6443 original size:33 final size:33
Alignment explanation
Indices: 6405--6468 Score: 110
Period size: 33 Copynumber: 1.9 Consensus size: 33
6395 TTTAAACAAA
*
6405 TTTGTCTCTCTCGAGACAGTTTCTCTTGAAAAT
1 TTTGTCTCCCTCGAGACAGTTTCTCTTGAAAAT
*
6438 TTTGTCTCCCTTGAGACAGTTTCTCTTGAAA
1 TTTGTCTCCCTCGAGACAGTTTCTCTTGAAA
6469 CACAAAATCT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.20, C:0.22, G:0.16, T:0.42
Consensus pattern (33 bp):
TTTGTCTCCCTCGAGACAGTTTCTCTTGAAAAT
Found at i:7052 original size:18 final size:17
Alignment explanation
Indices: 7026--7064 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 17
7016 CTATATATAA
7026 ATATAATATGTAATTTAT
1 ATATAATATGTAATTT-T
* *
7044 ATATTATATGTTATTTT
1 ATATAATATGTAATTTT
7061 ATAT
1 ATAT
7065 GTTATTTACA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 5 0.26
18 14 0.74
ACGTcount: A:0.38, C:0.00, G:0.05, T:0.56
Consensus pattern (17 bp):
ATATAATATGTAATTTT
Found at i:7064 original size:12 final size:12
Alignment explanation
Indices: 7047--7071 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
7037 AATTTATATA
7047 TTATATGTTATT
1 TTATATGTTATT
7059 TTATATGTTATT
1 TTATATGTTATT
7071 T
1 T
7072 ACATGTCCTG
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:0.24, C:0.00, G:0.08, T:0.68
Consensus pattern (12 bp):
TTATATGTTATT
Found at i:8337 original size:19 final size:19
Alignment explanation
Indices: 8313--8371 Score: 59
Period size: 19 Copynumber: 3.2 Consensus size: 19
8303 TACCTTCATG
8313 TATATTATATTTATTTATA
1 TATATTATATTTATTTATA
* *
8332 TATATTATTTTTTTTTAT-
1 TATATTATATTTATTTATA
* *
8350 TAT-TTCGTATTTATGTATA
1 TATATT-ATATTTATTTATA
8369 TAT
1 TAT
8372 TCCCATTTTT
Statistics
Matches: 32, Mismatches: 6, Indels: 4
0.76 0.14 0.10
Matches are distributed among these distances:
17 2 0.06
18 11 0.34
19 19 0.59
ACGTcount: A:0.29, C:0.02, G:0.03, T:0.66
Consensus pattern (19 bp):
TATATTATATTTATTTATA
Found at i:13059 original size:3 final size:3
Alignment explanation
Indices: 13051--13103 Score: 79
Period size: 3 Copynumber: 17.7 Consensus size: 3
13041 GTCGATCTCT
* * *
13051 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TAC TAC TAC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
13099 TTC TT
1 TTC TT
13104 TTCAGTCAAT
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 48 1.00
ACGTcount: A:0.06, C:0.32, G:0.00, T:0.62
Consensus pattern (3 bp):
TTC
Found at i:14092 original size:17 final size:17
Alignment explanation
Indices: 14070--14104 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
14060 TTGGTCGAGA
* *
14070 ATTTTATTTTCAGTAAT
1 ATTTTATTATCAATAAT
14087 ATTTTATTATCAATAAT
1 ATTTTATTATCAATAAT
14104 A
1 A
14105 GATGTTTTGG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.37, C:0.06, G:0.03, T:0.54
Consensus pattern (17 bp):
ATTTTATTATCAATAAT
Found at i:14472 original size:18 final size:18
Alignment explanation
Indices: 14428--14475 Score: 62
Period size: 18 Copynumber: 2.7 Consensus size: 18
14418 TTTTTAAAGA
*
14428 AAATATATAAATATTTTAC
1 AAATATAT-AATATTATAC
*
14447 -AATTTATAATATTATAC
1 AAATATATAATATTATAC
14464 AAATATATAATA
1 AAATATATAATA
14476 AGGACAATTT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
17 9 0.36
18 16 0.64
ACGTcount: A:0.54, C:0.04, G:0.00, T:0.42
Consensus pattern (18 bp):
AAATATATAATATTATAC
Found at i:16188 original size:3 final size:3
Alignment explanation
Indices: 16180--16204 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
16170 GAATAGGGTT
16180 TTG TTG TTG TTG TTG TTG TTG TTG T
1 TTG TTG TTG TTG TTG TTG TTG TTG T
16205 ACACATTAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.00, C:0.00, G:0.32, T:0.68
Consensus pattern (3 bp):
TTG
Found at i:16386 original size:2 final size:2
Alignment explanation
Indices: 16379--16412 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
16369 TTTATACTCG
16379 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
16413 TATCTTAACG
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):
AT
Found at i:16544 original size:3 final size:3
Alignment explanation
Indices: 16536--16570 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
16526 GCACTATTTT
16536 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
16571 GAGGAAAAAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:18017 original size:14 final size:14
Alignment explanation
Indices: 17998--18027 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
17988 CCTAAAAAAA
*
17998 TTTAAATTATTATT
1 TTTAAATAATTATT
18012 TTTAAATAATTATT
1 TTTAAATAATTATT
18026 TT
1 TT
18028 GAATTTTACA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (14 bp):
TTTAAATAATTATT
Found at i:27489 original size:14 final size:14
Alignment explanation
Indices: 27456--27492 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
27446 GAATGTAAAT
*
27456 GAACACAAACGAAC
1 GAACATAAACGAAC
*
27470 GAACATAAATGAAC
1 GAACATAAACGAAC
27484 GAACATAAA
1 GAACATAAA
27493 ATTAAATGGA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.59, C:0.19, G:0.14, T:0.08
Consensus pattern (14 bp):
GAACATAAACGAAC
Found at i:27694 original size:14 final size:14
Alignment explanation
Indices: 27675--27720 Score: 65
Period size: 14 Copynumber: 3.3 Consensus size: 14
27665 GGAGAACATA
*
27675 AACAAATATAAACG
1 AACAAACATAAACG
*
27689 AACAAACATAAACA
1 AACAAACATAAACG
*
27703 AACAAACATAAATG
1 AACAAACATAAACG
27717 AACA
1 AACA
27721 TATTATTGAA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 28 1.00
ACGTcount: A:0.67, C:0.17, G:0.04, T:0.11
Consensus pattern (14 bp):
AACAAACATAAACG
Found at i:28573 original size:15 final size:17
Alignment explanation
Indices: 28541--28596 Score: 66
Period size: 17 Copynumber: 3.4 Consensus size: 17
28531 TTAAATGTAT
28541 ATATAATAT-TATTAATA
1 ATATAATATATA-TAATA
28558 AT-TAA-ATATATAATA
1 ATATAATATATATAATA
28573 ATATAATATATAT-ATA
1 ATATAATATATATAATA
28589 TATATAAT
1 -ATATAAT
28597 CCATAACCGG
Statistics
Matches: 35, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
15 9 0.26
16 11 0.31
17 15 0.43
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (17 bp):
ATATAATATATATAATA
Found at i:28993 original size:2 final size:2
Alignment explanation
Indices: 28986--29038 Score: 56
Period size: 2 Copynumber: 27.5 Consensus size: 2
28976 TCGGGTCGAG
* * * *
28986 TA TA TA TA TA TT TA AA T- TA AA TA TA TA AA TA T- 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
29026 TA TA TA TA TA TA T
1 TA TA TA TA TA TA T
29039 TTAATTTAAA
Statistics
Matches: 41, Mismatches: 8, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
1 2 0.05
2 39 0.95
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:29195 original size:35 final size:35
Alignment explanation
Indices: 29149--29222 Score: 112
Period size: 35 Copynumber: 2.1 Consensus size: 35
29139 ACTAATCCCG
29149 TCCCCATCCCCGTTTAGCATAAACAGCTTTCCCCA
1 TCCCCATCCCCGTTTAGCATAAACAGCTTTCCCCA
* * * *
29184 TCCCCGTCCCCGTTTAGCATAAACGGTTTTCTCCA
1 TCCCCATCCCCGTTTAGCATAAACAGCTTTCCCCA
29219 TCCC
1 TCCC
29223 TGTTTAATTC
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.19, C:0.42, G:0.11, T:0.28
Consensus pattern (35 bp):
TCCCCATCCCCGTTTAGCATAAACAGCTTTCCCCA
Found at i:30956 original size:21 final size:22
Alignment explanation
Indices: 30907--30959 Score: 74
Period size: 21 Copynumber: 2.5 Consensus size: 22
30897 TCGGGCAGTG
30907 TCGATACCATAAGAGAGTGGTA
1 TCGATACCATAAGAGAGTGGTA
30929 TCGATACCATAAG-G-GTGAGTA
1 TCGATACCATAAGAGAGTG-GTA
*
30950 TCTATACCAT
1 TCGATACCAT
30960 CATGAATAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
20 3 0.10
21 13 0.45
22 13 0.45
ACGTcount: A:0.34, C:0.17, G:0.23, T:0.26
Consensus pattern (22 bp):
TCGATACCATAAGAGAGTGGTA
Found at i:32144 original size:30 final size:33
Alignment explanation
Indices: 32085--32163 Score: 92
Period size: 32 Copynumber: 2.4 Consensus size: 33
32075 ATATTTAAAA
* *
32085 TATATTTATTAATAGTTCTAATAATATAAT-AT
1 TATATTTATTAATAGTTATAATAAAATAATAAT
32117 TATATTT-TTAATA-TTATAATAAAATAATAAAT
1 TATATTTATTAATAGTTATAATAAAATAAT-AAT
*
32149 TATATTATAATAATA
1 TATATT-TATTAATA
32164 TAAGATATTA
Statistics
Matches: 40, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
30 13 0.32
31 6 0.15
32 15 0.38
33 1 0.03
34 5 0.12
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.48
Consensus pattern (33 bp):
TATATTTATTAATAGTTATAATAAAATAATAAT
Found at i:32152 original size:18 final size:18
Alignment explanation
Indices: 32129--32163 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
32119 TATTTTTAAT
32129 ATTATAATAAAATAATAA
1 ATTATAATAAAATAATAA
* *
32147 ATTATATTATAATAATA
1 ATTATAATAAAATAATA
32164 TAAGATATTA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (18 bp):
ATTATAATAAAATAATAA
Found at i:32156 original size:23 final size:23
Alignment explanation
Indices: 32127--32179 Score: 79
Period size: 23 Copynumber: 2.3 Consensus size: 23
32117 TATATTTTTA
*
32127 ATATTATAATAAAATAATAAATT
1 ATATTATAATAAAATAAGAAATT
* *
32150 ATATTATAATAATATAAGATATT
1 ATATTATAATAAAATAAGAAATT
32173 ATATTAT
1 ATATTAT
32180 TATTTTAAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (23 bp):
ATATTATAATAAAATAAGAAATT
Found at i:32259 original size:8 final size:8
Alignment explanation
Indices: 32246--32277 Score: 64
Period size: 8 Copynumber: 4.0 Consensus size: 8
32236 TAGAAATAAT
32246 ATTATTAA
1 ATTATTAA
32254 ATTATTAA
1 ATTATTAA
32262 ATTATTAA
1 ATTATTAA
32270 ATTATTAA
1 ATTATTAA
32278 TAATAAATAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (8 bp):
ATTATTAA
Found at i:32292 original size:19 final size:19
Alignment explanation
Indices: 32270--32338 Score: 61
Period size: 19 Copynumber: 3.6 Consensus size: 19
32260 AAATTATTAA
32270 ATTATTAATAATAAATAAT
1 ATTATTAATAATAAATAAT
* **
32289 ATTATTTAT-ATATTTAAT
1 ATTATTAATAATAAATAAT
*
32307 ATTAATATAATAATCTAATAAT
1 ATT-AT-TAATAAT-AAATAAT
32329 ATT-TTAATAA
1 ATTATTAATAA
32339 AGATATTTAA
Statistics
Matches: 39, Mismatches: 7, Indels: 8
0.72 0.13 0.15
Matches are distributed among these distances:
18 10 0.26
19 16 0.41
20 4 0.10
21 2 0.05
22 7 0.18
ACGTcount: A:0.51, C:0.01, G:0.00, T:0.48
Consensus pattern (19 bp):
ATTATTAATAATAAATAAT
Found at i:32359 original size:23 final size:23
Alignment explanation
Indices: 32333--32377 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
32323 AATAATATTT
32333 TAATAAAGATATTTAAAATATAC
1 TAATAAAGATATTTAAAATATAC
* * *
32356 TAATTAATATTTTTAAAATATA
1 TAATAAAGATATTTAAAATATA
32378 TTATAACACT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.42
Consensus pattern (23 bp):
TAATAAAGATATTTAAAATATAC
Found at i:32443 original size:31 final size:29
Alignment explanation
Indices: 32418--32497 Score: 74
Period size: 28 Copynumber: 2.7 Consensus size: 29
32408 ATATAATTTA
32418 TAATATTTTTATTTCAATAAAATATACCAATAT
1 TAATATTTTTA-TT-AATAAAATATA--AATAT
**
32451 TAATATTTTTATTAATAAAATTATAAGCA-
1 TAATATTTTTATTAATAAAA-TATAAATAT
*
32480 TAATA-TTTTAATAATAAA
1 TAATATTTTTATTAATAAA
32498 TAAATTATTT
Statistics
Matches: 43, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
28 12 0.28
29 5 0.12
30 2 0.05
31 7 0.16
32 6 0.14
33 11 0.26
ACGTcount: A:0.49, C:0.05, G:0.01, T:0.45
Consensus pattern (29 bp):
TAATATTTTTATTAATAAAATATAAATAT
Found at i:34181 original size:12 final size:11
Alignment explanation
Indices: 34135--34301 Score: 55
Period size: 12 Copynumber: 14.5 Consensus size: 11
34125 AATATATGTA
34135 TATTTTTATTT
1 TATTTTTATTT
*
34146 GTTTTTTTAATTAT
1 -TATTTTT-ATT-T
**
34160 TATTAGTATTAT
1 TATTTTTATT-T
34172 TATTTTTATTT
1 TATTTTTATTT
34183 TATTTTATCTCATTT
1 TA-TTT-T-T-ATTT
*
34198 TATTTCTTAGATT
1 TATTT-TTA-TTT
34211 TATTTTTA-TT
1 TATTTTTATTT
34221 TA--TTTATTT
1 TATTTTTATTT
34230 T-TTTCTCTATTT
1 TATTT-T-TATTT
*
34242 T-TTTCTATTT
1 TATTTTTATTT
*
34252 T-TTCTTCTCTTT
1 TATT-TT-TATTT
34264 TGA-TTTT-TTT
1 T-ATTTTTATTT
*
34274 GATTTATT-TTAT
1 TATTT-TTATT-T
34286 TATTTTTATTT
1 TATTTTTATTT
34297 TATTT
1 TATTT
34302 CCATATTTTT
Statistics
Matches: 122, Mismatches: 13, Indels: 41
0.69 0.07 0.23
Matches are distributed among these distances:
8 4 0.03
9 4 0.03
10 18 0.15
11 18 0.15
12 49 0.40
13 17 0.14
14 6 0.05
15 6 0.05
ACGTcount: A:0.18, C:0.05, G:0.03, T:0.74
Consensus pattern (11 bp):
TATTTTTATTT
Found at i:34190 original size:10 final size:10
Alignment explanation
Indices: 34175--34301 Score: 50
Period size: 10 Copynumber: 12.3 Consensus size: 10
34165 GTATTATTAT
34175 TTTTATTTTA
1 TTTTATTTTA
* *
34185 TTTTATCTCA
1 TTTTATTTTA
34195 TTTTATTTCTTA
1 TTTTA-TT-TTA
*
34207 GATTTATTTT-
1 -TTTTATTTTA
34217 TATTTA-TTTA
1 T-TTTATTTTA
*
34227 TTTTTTTCTCTA
1 TTTTATT-T-TA
34239 TTTT-TTTCTA
1 TTTTATTT-TA
* *
34249 TTTTTTCTTCTC
1 TTTTAT-TT-TA
34261 TTTTGATTTT-
1 TTTT-ATTTTA
*
34271 TTTGA-TTTA
1 TTTTATTTTA
*
34280 TTTTATTAT-
1 TTTTATTTTA
34289 TTTTATTTTA
1 TTTTATTTTA
34299 TTT
1 TTT
34302 CCATATTTTT
Statistics
Matches: 90, Mismatches: 13, Indels: 28
0.69 0.10 0.21
Matches are distributed among these distances:
8 3 0.03
9 19 0.21
10 35 0.39
11 8 0.09
12 20 0.22
13 5 0.06
ACGTcount: A:0.16, C:0.07, G:0.02, T:0.75
Consensus pattern (10 bp):
TTTTATTTTA
Found at i:35795 original size:26 final size:27
Alignment explanation
Indices: 35742--35807 Score: 89
Period size: 27 Copynumber: 2.4 Consensus size: 27
35732 ACCTGATCTA
*
35742 ATCCGAAAAATATATAACATCCATCCG
1 ATCCGAAAAATATATAACATCCACCCG
*
35769 ATCCGAAAAATATATAAC-TCGACCCG
1 ATCCGAAAAATATATAACATCCACCCG
*
35795 ACCCGAAATAATA
1 ATCCGAAA-AATA
35808 GAAAATAATA
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
26 13 0.37
27 22 0.63
ACGTcount: A:0.45, C:0.26, G:0.09, T:0.20
Consensus pattern (27 bp):
ATCCGAAAAATATATAACATCCACCCG
Found at i:36315 original size:17 final size:17
Alignment explanation
Indices: 36281--36322 Score: 59
Period size: 17 Copynumber: 2.5 Consensus size: 17
36271 CCGAAAAGAA
*
36281 TATATTTATATATTTAT
1 TATATATATATATTTAT
36298 TATATATAT-TATTATAT
1 TATATATATATATT-TAT
36315 TATATATA
1 TATATATA
36323 AGATAAACTA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 4 0.17
17 19 0.83
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (17 bp):
TATATATATATATTTAT
Found at i:37126 original size:19 final size:19
Alignment explanation
Indices: 37102--37167 Score: 105
Period size: 19 Copynumber: 3.5 Consensus size: 19
37092 AAAATATTAG
37102 TTAAAATAATATAAAGTAA
1 TTAAAATAATATAAAGTAA
* *
37121 TTAAAATAACATAAACTAA
1 TTAAAATAATATAAAGTAA
*
37140 TTAAAAGAATATAAAGTAA
1 TTAAAATAATATAAAGTAA
37159 TTAAAATAA
1 TTAAAATAA
37168 AAAAAACTTG
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 41 1.00
ACGTcount: A:0.64, C:0.03, G:0.05, T:0.29
Consensus pattern (19 bp):
TTAAAATAATATAAAGTAA
Found at i:37175 original size:38 final size:40
Alignment explanation
Indices: 37083--37175 Score: 129
Period size: 38 Copynumber: 2.4 Consensus size: 40
37073 AAAGATGAGA
*
37083 AAAATAAAAAAAA-TATTAGTTAAAATAATATAAAGTAATT
1 AAAATAAAAAAAACTA-TAGTTAAAAGAATATAAAGTAATT
* *
37123 AAAATAACATAAACTA-A-TTAAAAGAATATAAAGTAATT
1 AAAATAAAAAAAACTATAGTTAAAAGAATATAAAGTAATT
37161 AAAATAAAAAAAACT
1 AAAATAAAAAAAACT
37176 TGTCGTAACC
Statistics
Matches: 47, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
38 33 0.70
39 1 0.02
40 11 0.23
41 2 0.04
ACGTcount: A:0.67, C:0.03, G:0.04, T:0.26
Consensus pattern (40 bp):
AAAATAAAAAAAACTATAGTTAAAAGAATATAAAGTAATT
Found at i:39183 original size:3 final size:3
Alignment explanation
Indices: 39175--39236 Score: 97
Period size: 3 Copynumber: 20.3 Consensus size: 3
39165 ATATTTATTA
* *
39175 AAT AAT AAT AATT AAT AAT AAT AAT AAT TAG AAT AAT AAT AAT AAT
1 AAT AAT AAT AA-T AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
39221 AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT A
39237 TAAATAACAT
Statistics
Matches: 54, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
3 51 0.94
4 3 0.06
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.34
Consensus pattern (3 bp):
AAT
Found at i:39590 original size:120 final size:123
Alignment explanation
Indices: 39378--39666 Score: 342
Period size: 120 Copynumber: 2.4 Consensus size: 123
39368 TTGAATAAAT
* * * * ** * * * *
39378 TCTTC-TCTTTCTTCAGATGAGTTCTTCTTATTATGAACTTTCCACTGG---GGATGATGCTAAT
1 TCTTCTTCTTTCTTCAAATGAGTTATTCTCATTATGAACTCTCTTCTGGAAATGCTGATGATGAT
*
39439 ATATCTCCTTCTGTGATAGAATTATGCAAAAGG-CTGAACAAACTCTTCTCATTATGAA
66 ATATCTCCTTCTGTGATAGAATCATGCAAAAGGTC-GAACAAACTCTTCTCATTATGAA
39497 -CTTCTTC-TTCTTCAAATGAGTTATTCTCATTATGAACTC-CTTCTGGAAATGCTGATGATGAT
1 TCTTCTTCTTTCTTCAAATGAGTTATTCTCATTATGAACTCTCTTCTGGAAATGCTGATGATGAT
* * * *
39559 ATATCTCTTTCTGTGATAGAGTCCTGCAAAAGGTCGAACAAGCTCTTCTCATTATGAA
66 ATATCTCCTTCTGTGATAGAATCATGCAAAAGGTCGAACAAACTCTTCTCATTATGAA
* *
39617 CTTCTTCTTCTTTCTTCAGATGAGTTCTTCTCATTATGAACTCTCTTCTG
1 --TCTTCTTCTTTCTTCAAATGAGTTATTCTCATTATGAACTCTCTTCTG
39667 AAAAGTTGAT
Statistics
Matches: 143, Mismatches: 17, Indels: 14
0.82 0.10 0.08
Matches are distributed among these distances:
117 5 0.03
118 32 0.22
119 2 0.01
120 60 0.42
121 1 0.01
123 7 0.05
124 30 0.21
125 6 0.04
ACGTcount: A:0.25, C:0.21, G:0.15, T:0.40
Consensus pattern (123 bp):
TCTTCTTCTTTCTTCAAATGAGTTATTCTCATTATGAACTCTCTTCTGGAAATGCTGATGATGAT
ATATCTCCTTCTGTGATAGAATCATGCAAAAGGTCGAACAAACTCTTCTCATTATGAA
Found at i:39731 original size:113 final size:113
Alignment explanation
Indices: 39584--40132 Score: 823
Period size: 113 Copynumber: 4.9 Consensus size: 113
39574 ATAGAGTCCT
* ** *
39584 GCAAAAGGTCGAACAAGCTCTTCTCATTATGAACTTCTTCTTCTTTCTTCAGATGAGTTCTTCTC
1 GCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
*** * * *
39649 ATTATGAACTCTCTTCT-GAAAAGTTGATCTATCGAGTGATGAATTCGA
66 ATTATGAACTC-GAACTGGAAAAGTTGATCCATCAAGTGATGAATTTGA
* * * *
39697 GCGAAAA-GTTGAACAAGTTCTTCTTATTATGAACTTCTTCTTCCTTCTTCAGATAAATTCTTCT
1 GC-AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCT
*** * *
39761 CATTATGAACTCTTTCTGGAAAAGTTAATCCATCAAATGATGAATTTGA
65 CATTATGAACTCGAACTGGAAAAGTTGATCCATCAAGTGATGAATTTGA
*
39810 GCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTT
1 GCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
*
39875 ATTATGAACTCGAACTGGAAAAGTTGATCCATCAAGTGATGGATTTGA
66 ATTATGAACTCGAACTGGAAAAGTTGATCCATCAAGTGATGAATTTGA
*
39923 GCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTTTTCAGATGAGTTCTTCTC
1 GCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
* *
39988 ATTATGAACTCGAACTGGAAAAGTTGATCTATCAAGTGATGGATTTGA
66 ATTATGAACTCGAACTGGAAAAGTTGATCCATCAAGTGATGAATTTGA
40036 GCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
1 GCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
* **
40101 ATTATGAACTCGAACTGGCACTGTTGATCCAT
66 ATTATGAACTCGAACTGGAAAAGTTGATCCAT
40133 TGAATGATGG
Statistics
Matches: 402, Mismatches: 31, Indels: 6
0.92 0.07 0.01
Matches are distributed among these distances:
112 8 0.02
113 390 0.97
114 4 0.01
ACGTcount: A:0.28, C:0.19, G:0.15, T:0.37
Consensus pattern (113 bp):
GCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
ATTATGAACTCGAACTGGAAAAGTTGATCCATCAAGTGATGAATTTGA
Found at i:41102 original size:83 final size:83
Alignment explanation
Indices: 40963--41351 Score: 679
Period size: 83 Copynumber: 4.7 Consensus size: 83
40953 CTGTGGTTCA
*
40963 TACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTTC
1 TACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTCC
*
41028 AAATTCAATGATTGGTTT
66 AAATTCAATAATTGGTTT
*
41046 TACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTTC
1 TACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTCC
*
41111 AAATTCAATGATTGGTTT
66 AAATTCAATAATTGGTTT
* * *
41129 TACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTAGTACATTCCTCTTCC
1 TACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTCC
41194 AAATTCAATAATTGGTTT
66 AAATTCAATAATTGGTTT
*
41212 TACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCCTCTTCC
1 TACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTCC
41277 AAATTCAATAATTGGTTT
66 AAATTCAATAATTGGTTT
* * *
41295 TACCAAACCAGATCAGTTAACTCTAAGAACACTTCCAGAAGATGCTATGAGTACATT
1 TACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATT
41352 GCATTTGTTC
Statistics
Matches: 296, Mismatches: 10, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
83 296 1.00
ACGTcount: A:0.38, C:0.23, G:0.13, T:0.27
Consensus pattern (83 bp):
TACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTCC
AAATTCAATAATTGGTTT
Found at i:41200 original size:166 final size:166
Alignment explanation
Indices: 40865--41351 Score: 740
Period size: 166 Copynumber: 2.9 Consensus size: 166
40855 ATTGGTTCTG
* * * *
40865 GGTTTATATCAAACCAAATCAGAGAACTCAAAGAACACTTCCAGAAGATGCTATTAGCACATTCC
1 GGTTT-TACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCC
* *
40930 TCTTCCAAATTCAATAACTGGTTCTGTGGTTCATACCAAACCAGATCAGATAACTCAAAGAACAC
65 TCTTCCAAATTC---AA-T-G--AT-TGGTT-TTACCAAACCAGATCAGATAACTCAAAGAACAC
* * *
40995 TTCCAGAAGATGCTATGAGCACATTCATCTTTCAAATTCAATGATT
121 TTCCAGAAGATGCTATGAGTACATTCATCTTCCAAATTCAATAATT
*
41041 GGTTTTACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCAT
1 GGTTTTACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCCT
*
41106 CTTTCAAATTCAATGATTGGTTTTACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGA
66 CTTCCAAATTCAATGATTGGTTTTACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGA
* *
41171 TGCTATTAGTACATTCCTCTTCCAAATTCAATAATT
131 TGCTATGAGTACATTCATCTTCCAAATTCAATAATT
41207 GGTTTTACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCCT
1 GGTTTTACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCCT
* * *
41272 CTTCCAAATTCAATAATTGGTTTTACCAAACCAGATCAGTTAACTCTAAGAACACTTCCAGAAGA
66 CTTCCAAATTCAATGATTGGTTTTACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGA
41337 TGCTATGAGTACATT
131 TGCTATGAGTACATT
41352 GCATTTGTTC
Statistics
Matches: 292, Mismatches: 19, Indels: 10
0.91 0.06 0.03
Matches are distributed among these distances:
166 212 0.73
167 5 0.02
168 1 0.00
170 1 0.00
171 1 0.00
172 2 0.01
175 65 0.22
176 5 0.02
ACGTcount: A:0.37, C:0.23, G:0.13, T:0.28
Consensus pattern (166 bp):
GGTTTTACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCCT
CTTCCAAATTCAATGATTGGTTTTACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGA
TGCTATGAGTACATTCATCTTCCAAATTCAATAATT
Found at i:41325 original size:249 final size:253
Alignment explanation
Indices: 40865--41351 Score: 793
Period size: 249 Copynumber: 1.9 Consensus size: 253
40855 ATTGGTTCTG
*
40865 GGTTTATATCAAACCAAATCAGAGAACTCAAAGAACACTTCCAGAAGATGCTATTAGCACATTCC
1 GGTTTATACCAAACCAAATCAGAGAACTCAAAGAACACTTCCAGAAGATGCTATTAGCACATTCC
40930 TCTTCCAAATTCAATAACTGGTTCTGTGGTTCATACCAAACCAGATCAGATAACTCAAAGAACAC
66 TCTTCCAAATTCAATAA-----T-TGTGGTTCATACCAAACCAGATCAGATAACTCAAAGAACAC
* *
40995 TTCCAGAAGATGCTATGAGCACATTCATCTTTCAAATTCAATGATTGGTTTTACCAAACCAGATC
125 TTCCAGAAGATGCTATGAGCACATTCATCTTCCAAATTCAATAATTGGTTTTACCAAACCAGATC
41060 AGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTTCAAATTCAATGATT
190 AGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTTCAAATTCAATGATT
* * *
41124 GGTTT-TACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTAGTACATTCC
1 GGTTTATACCAAACCAAATCAGAGAACTCAAAGAACACTTCCAGAAGATGCTATTAGCACATTCC
*
41188 TCTTCCAAATTCAATAA-T-TGGTT-TTACCAAACCAGATCAGATAACTCAAAGAACACTTCCAG
66 TCTTCCAAATTCAATAATTGTGGTTCATACCAAACCAGATCAGATAACTCAAAGAACACTTCCAG
* *
41250 AAGATGCTATGAGCACATTCCTCTTCCAAATTCAATAATTGGTTTTACCAAACCAGATCAGTTAA
131 AAGATGCTATGAGCACATTCATCTTCCAAATTCAATAATTGGTTTTACCAAACCAGATCAGATAA
* *
41315 CTCTAAGAACACTTCCAGAAGATGCTATGAGTACATT
196 CTCAAAGAACACTTCCAGAAGATGCTATGAGCACATT
41352 GCATTTGTTC
Statistics
Matches: 217, Mismatches: 11, Indels: 10
0.91 0.05 0.04
Matches are distributed among these distances:
249 134 0.62
250 5 0.02
251 1 0.00
258 72 0.33
259 5 0.02
ACGTcount: A:0.37, C:0.23, G:0.13, T:0.28
Consensus pattern (253 bp):
GGTTTATACCAAACCAAATCAGAGAACTCAAAGAACACTTCCAGAAGATGCTATTAGCACATTCC
TCTTCCAAATTCAATAATTGTGGTTCATACCAAACCAGATCAGATAACTCAAAGAACACTTCCAG
AAGATGCTATGAGCACATTCATCTTCCAAATTCAATAATTGGTTTTACCAAACCAGATCAGATAA
CTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTTCAAATTCAATGATT
Found at i:42516 original size:17 final size:17
Alignment explanation
Indices: 42496--42557 Score: 74
Period size: 17 Copynumber: 3.6 Consensus size: 17
42486 CTTGACCCCT
42496 TTTTTTCTTTTTCTTTC
1 TTTTTTCTTTTTCTTTC
42513 TTTTTTC-TTTTCTTTTC
1 TTTTTTCTTTTTC-TTTC
*
42530 TTTTTT-TCTTTTCTTTT
1 TTTTTTCT-TTTTCTTTC
42547 TTTCTTTCTTT
1 TTT-TTTCTTT
42558 GTTTTTCTCT
Statistics
Matches: 39, Mismatches: 1, Indels: 9
0.80 0.02 0.18
Matches are distributed among these distances:
16 5 0.13
17 23 0.59
18 10 0.26
19 1 0.03
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (17 bp):
TTTTTTCTTTTTCTTTC
Found at i:42523 original size:5 final size:5
Alignment explanation
Indices: 42498--42557 Score: 58
Period size: 5 Copynumber: 12.6 Consensus size: 5
42488 TGACCCCTTT
*
42498 TTTTC TTTTTC TTTCTT TTTTC TTTTC TTTTC -TTT- TTTTC TTTTC -TTT-
1 TTTTC -TTTTC TTT-TC TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC
42546 TTTTC -TTTC TTT
1 TTTTC TTTTC TTT
42558 GTTTTTCTCT
Statistics
Matches: 46, Mismatches: 2, Indels: 13
0.75 0.03 0.21
Matches are distributed among these distances:
4 16 0.35
5 21 0.46
6 9 0.20
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (5 bp):
TTTTC
Found at i:42533 original size:35 final size:35
Alignment explanation
Indices: 42494--42565 Score: 103
Period size: 35 Copynumber: 2.1 Consensus size: 35
42484 ACCTTGACCC
42494 CTTTTTTTCTTTTTCTTTCTTT-TTTCTTT-TCTTTT
1 CTTTTTTTC-TTTTCTTTCTTTCTTTCTTTGT-TTTT
*
42529 CTTTTTTTCTTTTCTTTTTTTCTTTCTTTGTTTTT
1 CTTTTTTTCTTTTCTTTCTTTCTTTCTTTGTTTTT
42564 CT
1 CT
42566 CTTCAAGCAT
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
34 11 0.32
35 22 0.65
36 1 0.03
ACGTcount: A:0.00, C:0.17, G:0.01, T:0.82
Consensus pattern (35 bp):
CTTTTTTTCTTTTCTTTCTTTCTTTCTTTGTTTTT
Found at i:42538 original size:13 final size:13
Alignment explanation
Indices: 42498--42562 Score: 80
Period size: 13 Copynumber: 4.9 Consensus size: 13
42488 TGACCCCTTT
42498 TTTTCTTTTTCTTTC
1 TTTTC-TTTT-TTTC
*
42513 TTTT-TTCTTTTC
1 TTTTCTTTTTTTC
42525 TTTTCTTTTTTTC
1 TTTTCTTTTTTTC
42538 TTTTCTTTTTTTC
1 TTTTCTTTTTTTC
42551 -TTTCTTTGTTTT
1 TTTTCTTT-TTTT
42563 TCTCTTCAAG
Statistics
Matches: 46, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
12 15 0.33
13 27 0.59
15 4 0.09
ACGTcount: A:0.00, C:0.15, G:0.02, T:0.83
Consensus pattern (13 bp):
TTTTCTTTTTTTC
Found at i:42543 original size:30 final size:30
Alignment explanation
Indices: 42494--42557 Score: 87
Period size: 30 Copynumber: 2.1 Consensus size: 30
42484 ACCTTGACCC
*
42494 CTTTTTTTCTTTTTCTTTC-TTTTTTCTTTT
1 CTTTTCTTCTTTTTCTTTCTTTTTTTC-TTT
42524 CTTTTCTT-TTTTTCTTTTCTTTTTTTCTTT
1 CTTTTCTTCTTTTTC-TTTCTTTTTTTCTTT
42554 CTTT
1 CTTT
42558 GTTTTTCTCT
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
29 6 0.19
30 18 0.58
31 7 0.23
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (30 bp):
CTTTTCTTCTTTTTCTTTCTTTTTTTCTTT
Found at i:42563 original size:17 final size:15
Alignment explanation
Indices: 42495--42563 Score: 66
Period size: 17 Copynumber: 4.1 Consensus size: 15
42485 CCTTGACCCC
42495 TTTTTTTCTTTTTCTT
1 TTTTTTTCTTTTT-TT
42511 TCTTTTTTCTTTTCTTTT
1 T-TTTTTTC-TTT-TTTT
42529 CTTTTTTTCTTTTCTTT
1 -TTTTTTTCTTTT-TTT
42546 TTTTCTTTCTTTGTTTT
1 TTTT-TTTCTTT-TTTT
42563 T
1 T
42564 CTCTTCAAGC
Statistics
Matches: 46, Mismatches: 0, Indels: 13
0.78 0.00 0.22
Matches are distributed among these distances:
16 6 0.13
17 24 0.52
18 13 0.28
19 3 0.07
ACGTcount: A:0.00, C:0.14, G:0.01, T:0.84
Consensus pattern (15 bp):
TTTTTTTCTTTTTTT
Found at i:42568 original size:12 final size:10
Alignment explanation
Indices: 42498--42553 Score: 60
Period size: 11 Copynumber: 5.3 Consensus size: 10
42488 TGACCCCTTT
42498 TTTTCTTTTTC
1 TTTT-TTTTTC
42509 TTTCTTTTTTC
1 TTT-TTTTTTC
*
42520 TTTTCTTTTC
1 TTTTTTTTTC
42530 TTTTTTTCTT-
1 TTTTTTT-TTC
42540 TTCTTTTTTTC
1 TT-TTTTTTTC
42551 TTT
1 TTT
42554 CTTTGTTTTT
Statistics
Matches: 39, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
10 17 0.44
11 21 0.54
12 1 0.03
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (10 bp):
TTTTTTTTTC
Found at i:49897 original size:15 final size:15
Alignment explanation
Indices: 49874--49905 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
49864 TGAAATGAAT
49874 AATGAATGTATGCAA
1 AATGAATGTATGCAA
*
49889 AATGCATGTATGCAA
1 AATGAATGTATGCAA
49904 AA
1 AA
49906 AGGTATTGAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.47, C:0.09, G:0.19, T:0.25
Consensus pattern (15 bp):
AATGAATGTATGCAA
Found at i:55346 original size:3 final size:3
Alignment explanation
Indices: 55338--55424 Score: 129
Period size: 3 Copynumber: 28.3 Consensus size: 3
55328 ATATTTATTA
* * *
55338 AAT AAT AAT AATT AAT AAT AAT AAT AAT AAT TAG AAT TAT AAT AAT
1 AAT AAT AAT AA-T AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
55384 AAT AAT AAAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT -AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
55425 TAAATAACAT
Statistics
Matches: 76, Mismatches: 6, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
3 70 0.92
4 6 0.08
ACGTcount: A:0.64, C:0.00, G:0.01, T:0.34
Consensus pattern (3 bp):
AAT
Found at i:55388 original size:40 final size:40
Alignment explanation
Indices: 55334--55424 Score: 139
Period size: 40 Copynumber: 2.3 Consensus size: 40
55324 TGTAATATTT
* *
55334 ATTA-AATAATAATAATTAATAATAATAATAATAATTAGA
1 ATTATAATAATAATAATAAATAATAATAATAATAATAAGA
*
55373 ATTATAATAATAATAATAAATAATAATAATAATAATAATA
1 ATTATAATAATAATAATAAATAATAATAATAATAATAAGA
*
55413 ATAATAATAATA
1 ATTATAATAATA
55425 TAAATAACAT
Statistics
Matches: 47, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
39 4 0.09
40 43 0.91
ACGTcount: A:0.64, C:0.00, G:0.01, T:0.35
Consensus pattern (40 bp):
ATTATAATAATAATAATAAATAATAATAATAATAATAAGA
Found at i:55431 original size:40 final size:39
Alignment explanation
Indices: 55338--55427 Score: 125
Period size: 37 Copynumber: 2.4 Consensus size: 39
55328 ATATTTATTA
*
55338 AATAATAATAAT-TAAT-AATAATAATAATAATTAGAAT
1 AATAATAATAATATAATAAATAATAATAATAATAAGAAT
* *
55375 TATAATAAT-A-ATAATAAATAATAATAATAATAATAAT
1 AATAATAATAATATAATAAATAATAATAATAATAAGAAT
55412 AATAATAATAATATAA
1 AATAATAATAATATAA
55428 ATAACATTTA
Statistics
Matches: 45, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
36 5 0.11
37 35 0.78
38 1 0.02
39 4 0.09
ACGTcount: A:0.64, C:0.00, G:0.01, T:0.34
Consensus pattern (39 bp):
AATAATAATAATATAATAAATAATAATAATAATAAGAAT
Found at i:55831 original size:51 final size:50
Alignment explanation
Indices: 55755--55882 Score: 159
Period size: 51 Copynumber: 2.5 Consensus size: 50
55745 TTAGCTGTAA
**
55755 AGCGCGCCCCCTGCACCGCGCTATACGATGATTTGGCGTCACGAG-GGGTAT
1 AGCGCGCCCCCTGCACCGCGCTATACGATGAGCTGGCGTCA--AGTGGGTAT
** *
55806 AGCGCGCCCTTTGCACCGCGCTATACGGTGAGCTGGCGTCAAGTGGGTAT
1 AGCGCGCCCCCTGCACCGCGCTATACGATGAGCTGGCGTCAAGTGGGTAT
* * *
55856 AGCGCGACCCCTGCAGCGCACTATACG
1 AGCGCGCCCCCTGCACCGCGCTATACG
55883 TCACGTAGGG
Statistics
Matches: 66, Mismatches: 10, Indels: 3
0.84 0.13 0.04
Matches are distributed among these distances:
49 2 0.03
50 28 0.42
51 36 0.55
ACGTcount: A:0.18, C:0.32, G:0.31, T:0.19
Consensus pattern (50 bp):
AGCGCGCCCCCTGCACCGCGCTATACGATGAGCTGGCGTCAAGTGGGTAT
Found at i:57040 original size:18 final size:18
Alignment explanation
Indices: 57014--57048 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
57004 CAGCAGCCAC
*
57014 CGCAGCCATATATGATAT
1 CGCAACCATATATGATAT
57032 CGCAACCATATATGATA
1 CGCAACCATATATGATA
57049 CCGCCATCAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.37, C:0.23, G:0.14, T:0.26
Consensus pattern (18 bp):
CGCAACCATATATGATAT
Found at i:61241 original size:49 final size:51
Alignment explanation
Indices: 61130--61254 Score: 166
Period size: 49 Copynumber: 2.5 Consensus size: 51
61120 AGTTATATAA
*
61130 AACGCGGTACCTGCCCCGCGCTATATAAAATTATGTCAGGAGTAAAGGTAT
1 AACGCGGTACCTACCCCGCGCTATATAAAATTATGTCAGGAGTAAAGGTAT
** * *
61181 GTCTCGATACCTACCCCGCGCTATATAAAATTAT-T-AGGAGTAAAGGTAT
1 AACGCGGTACCTACCCCGCGCTATATAAAATTATGTCAGGAGTAAAGGTAT
*
61230 AACGCGGTACCTGA-TCCGCGCTATA
1 AACGCGGTACCT-ACCCCGCGCTATA
61255 CCCCTACGTG
Statistics
Matches: 63, Mismatches: 10, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
49 32 0.51
50 2 0.03
51 29 0.46
ACGTcount: A:0.30, C:0.23, G:0.22, T:0.25
Consensus pattern (51 bp):
AACGCGGTACCTACCCCGCGCTATATAAAATTATGTCAGGAGTAAAGGTAT
Found at i:61341 original size:50 final size:51
Alignment explanation
Indices: 61266--61393 Score: 150
Period size: 51 Copynumber: 2.5 Consensus size: 51
61256 CCCTACGTGG
* * * * **
61266 CGTATAGCGTGCTGCAGGGGCCGCGCTATA-CCCATGTGGCGCCAGCTCAC
1 CGTATAGCGCGGTGCAGGGGGCGCGCTATATCCCACGTGGCGCCAAATCAC
* *
61316 CGTATAGCGCGGTGCAGGGGGCGCGCTATATCCCACGTGGTGCCAAATCAT
1 CGTATAGCGCGGTGCAGGGGGCGCGCTATATCCCACGTGGCGCCAAATCAC
* * *
61367 CGTATAGCACGGTACAGGGGGCACGCT
1 CGTATAGCGCGGTGCAGGGGGCGCGCT
61394 TTACTGCTAA
Statistics
Matches: 66, Mismatches: 11, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
50 27 0.41
51 39 0.59
ACGTcount: A:0.19, C:0.30, G:0.34, T:0.18
Consensus pattern (51 bp):
CGTATAGCGCGGTGCAGGGGGCGCGCTATATCCCACGTGGCGCCAAATCAC
Found at i:62626 original size:29 final size:29
Alignment explanation
Indices: 62584--62643 Score: 120
Period size: 29 Copynumber: 2.1 Consensus size: 29
62574 CTCAGCTTCT
62584 CAGTTCCCTCTTTGGCACATATATTTACA
1 CAGTTCCCTCTTTGGCACATATATTTACA
62613 CAGTTCCCTCTTTGGCACATATATTTACA
1 CAGTTCCCTCTTTGGCACATATATTTACA
62642 CA
1 CA
62644 AGGCCATATC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.25, C:0.28, G:0.10, T:0.37
Consensus pattern (29 bp):
CAGTTCCCTCTTTGGCACATATATTTACA
Found at i:66649 original size:22 final size:22
Alignment explanation
Indices: 66621--66665 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
66611 AAATATGTAT
66621 TCTATGATGGTTTAAGAGCATA
1 TCTATGATGGTTTAAGAGCATA
66643 TCTATGATGGTTTAAGAGCATA
1 TCTATGATGGTTTAAGAGCATA
66665 T
1 T
66666 GATTCAATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.31, C:0.09, G:0.22, T:0.38
Consensus pattern (22 bp):
TCTATGATGGTTTAAGAGCATA
Found at i:67368 original size:21 final size:21
Alignment explanation
Indices: 67342--67384 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
67332 TACCCACTTG
67342 CCCAGTAACTGAATGATGAGA
1 CCCAGTAACTGAATGATGAGA
67363 CCCAGTAACTGAATGATGAGA
1 CCCAGTAACTGAATGATGAGA
67384 C
1 C
67385 TGTATCCACC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.37, C:0.21, G:0.23, T:0.19
Consensus pattern (21 bp):
CCCAGTAACTGAATGATGAGA
Found at i:69916 original size:2 final size:2
Alignment explanation
Indices: 69909--69934 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
69899 ACCTGGTTAA
69909 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
69935 TTAATTTATA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:70151 original size:16 final size:16
Alignment explanation
Indices: 70130--70173 Score: 79
Period size: 16 Copynumber: 2.8 Consensus size: 16
70120 TTATGAACTT
70130 TTATGTATTATTTATA
1 TTATGTATTATTTATA
70146 TTATGTATTATTTATA
1 TTATGTATTATTTATA
*
70162 TTATGGATTATT
1 TTATGTATTATT
70174 AGATTTTGTA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 27 1.00
ACGTcount: A:0.30, C:0.00, G:0.09, T:0.61
Consensus pattern (16 bp):
TTATGTATTATTTATA
Found at i:71986 original size:21 final size:21
Alignment explanation
Indices: 71944--71986 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
71934 TTTCTGGGTT
* * *
71944 AGGGGAATCGGTACCCATTCA
1 AGGGGAACCGATACCCACTCA
*
71965 AGGGGAACCGATACCCCCTCA
1 AGGGGAACCGATACCCACTCA
71986 A
1 A
71987 CGAAATGAAT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.30, C:0.30, G:0.26, T:0.14
Consensus pattern (21 bp):
AGGGGAACCGATACCCACTCA
Found at i:75550 original size:21 final size:21
Alignment explanation
Indices: 75508--75550 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
75498 TTTCTGGGTT
* * *
75508 AGGGGAATCGGTACCCATTCA
1 AGGGGAACCGATACCCACTCA
*
75529 AGGGGAACCGATACCCCCTCA
1 AGGGGAACCGATACCCACTCA
75550 A
1 A
75551 CGAAATGAAT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.30, C:0.30, G:0.26, T:0.14
Consensus pattern (21 bp):
AGGGGAACCGATACCCACTCA
Found at i:75616 original size:68 final size:69
Alignment explanation
Indices: 75530--75683 Score: 220
Period size: 69 Copynumber: 2.2 Consensus size: 69
75520 ACCCATTCAA
* *
75530 GGGGAACCGATACCCCCTCAACG-AAATGAATTTCCAGAATGCTAGAGGGGAATCGGTACCCCCA
1 GGGGAACCGATACCCCCTCAACGTAAATGAAATTCCAGAATGCTAGAGGGGAATCGATACCCCCA
*
75594 GGGG
66 AGGG
* * * * *
75598 GGGGAACCGATACCCCCTCATCGTATATGAAATTCCAGATTGCTTGAGGGGAATCGATACCCCTA
1 GGGGAACCGATACCCCCTCAACGTAAATGAAATTCCAGAATGCTAGAGGGGAATCGATACCCCCA
75663 AGGG
66 AGGG
*
75667 GGGGAACCGATTCCCCC
1 GGGGAACCGATACCCCC
75684 ATGAGAAAAA
Statistics
Matches: 76, Mismatches: 9, Indels: 1
0.88 0.10 0.01
Matches are distributed among these distances:
68 22 0.29
69 54 0.71
ACGTcount: A:0.27, C:0.27, G:0.28, T:0.18
Consensus pattern (69 bp):
GGGGAACCGATACCCCCTCAACGTAAATGAAATTCCAGAATGCTAGAGGGGAATCGATACCCCCA
AGGG
Found at i:76082 original size:34 final size:29
Alignment explanation
Indices: 75986--76085 Score: 175
Period size: 29 Copynumber: 3.5 Consensus size: 29
75976 CATATTATGA
* *
75986 TACATGACATGAATT-GTATTAAATGTAT
1 TACATGACATGAATTCATATTATATGTAT
76014 TACATGACATGAATTCATATTATATGTAT
1 TACATGACATGAATTCATATTATATGTAT
76043 TACATGACATGAATTCATATTATATGTAT
1 TACATGACATGAATTCATATTATATGTAT
76072 TACATGACATGAAT
1 TACATGACATGAAT
76086 GTGCAGAAAA
Statistics
Matches: 69, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
28 15 0.22
29 54 0.78
ACGTcount: A:0.39, C:0.10, G:0.12, T:0.39
Consensus pattern (29 bp):
TACATGACATGAATTCATATTATATGTAT
Found at i:76142 original size:30 final size:31
Alignment explanation
Indices: 76100--76159 Score: 95
Period size: 30 Copynumber: 2.0 Consensus size: 31
76090 AGAAAAAGTT
*
76100 ATATGCACTATGTGATAAAGGTATGTAAATG
1 ATATGCACTATGTGATAAAGGTATGGAAATG
*
76131 ATATGC-CTATGTGTTAAAGGTATGGAAAT
1 ATATGCACTATGTGATAAAGGTATGGAAAT
76160 ACTATGTCTA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
30 21 0.78
31 6 0.22
ACGTcount: A:0.37, C:0.07, G:0.23, T:0.33
Consensus pattern (31 bp):
ATATGCACTATGTGATAAAGGTATGGAAATG
Found at i:76453 original size:22 final size:22
Alignment explanation
Indices: 76379--76445 Score: 134
Period size: 22 Copynumber: 3.0 Consensus size: 22
76369 TTATGGACAT
76379 AATTCTACGGGCACTTCGGTGC
1 AATTCTACGGGCACTTCGGTGC
76401 AATTCTACGGGCACTTCGGTGC
1 AATTCTACGGGCACTTCGGTGC
76423 AATTCTACGGGCACTTCGGTGC
1 AATTCTACGGGCACTTCGGTGC
76445 A
1 A
76446 TTTATACGAG
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 45 1.00
ACGTcount: A:0.19, C:0.27, G:0.27, T:0.27
Consensus pattern (22 bp):
AATTCTACGGGCACTTCGGTGC
Found at i:82541 original size:67 final size:68
Alignment explanation
Indices: 82455--82606 Score: 216
Period size: 68 Copynumber: 2.2 Consensus size: 68
82445 ACCCATTCAA
* *
82455 GGGGAACCGATACCCCCTCAACG-AAATGAATTTCCAGAATGCTAGAGGGGAATCGGTACCCCCA
1 GGGGAACCGATACCCCCTCAACGTAAATGAAATTCCAGAATGCTAGAGGGGAATCGATACCCCCA
*
82519 GGG
66 AGG
* * * * *
82522 GGGGAACCGATACCCCCTCATCGTATATGAAATTCCAGATTGCTTGAGGGGAATCGATACCCCTA
1 GGGGAACCGATACCCCCTCAACGTAAATGAAATTCCAGAATGCTAGAGGGGAATCGATACCCCCA
82587 AGG
66 AGG
*
82590 GGGGAACCGATTCCCCC
1 GGGGAACCGATACCCCC
82607 ATGAGAAAAG
Statistics
Matches: 75, Mismatches: 9, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
67 22 0.29
68 53 0.71
ACGTcount: A:0.28, C:0.28, G:0.27, T:0.18
Consensus pattern (68 bp):
GGGGAACCGATACCCCCTCAACGTAAATGAAATTCCAGAATGCTAGAGGGGAATCGATACCCCCA
AGG
Found at i:83003 original size:34 final size:29
Alignment explanation
Indices: 82907--83006 Score: 175
Period size: 29 Copynumber: 3.5 Consensus size: 29
82897 CATATTATGA
* *
82907 TACATGACATGAATT-GTATTAAATGTAT
1 TACATGACATGAATTCATATTATATGTAT
82935 TACATGACATGAATTCATATTATATGTAT
1 TACATGACATGAATTCATATTATATGTAT
82964 TACATGACATGAATTCATATTATATGTAT
1 TACATGACATGAATTCATATTATATGTAT
82993 TACATGACATGAAT
1 TACATGACATGAAT
83007 GTGCAGAAAA
Statistics
Matches: 69, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
28 15 0.22
29 54 0.78
ACGTcount: A:0.39, C:0.10, G:0.12, T:0.39
Consensus pattern (29 bp):
TACATGACATGAATTCATATTATATGTAT
Found at i:83063 original size:30 final size:31
Alignment explanation
Indices: 83021--83080 Score: 95
Period size: 30 Copynumber: 2.0 Consensus size: 31
83011 AGAAAAAGTT
*
83021 ATATGCACTATGTGATAAAGGTATGTAAATG
1 ATATGCACTATGTGATAAAGGTATGGAAATG
*
83052 ATATGC-CTATGTGTTAAAGGTATGGAAAT
1 ATATGCACTATGTGATAAAGGTATGGAAAT
83081 ACTATGTCTA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
30 21 0.78
31 6 0.22
ACGTcount: A:0.37, C:0.07, G:0.23, T:0.33
Consensus pattern (31 bp):
ATATGCACTATGTGATAAAGGTATGGAAATG
Found at i:83374 original size:22 final size:22
Alignment explanation
Indices: 83300--83366 Score: 134
Period size: 22 Copynumber: 3.0 Consensus size: 22
83290 TTATGGACAT
83300 AATTCTACGGGCACTTCGGTGC
1 AATTCTACGGGCACTTCGGTGC
83322 AATTCTACGGGCACTTCGGTGC
1 AATTCTACGGGCACTTCGGTGC
83344 AATTCTACGGGCACTTCGGTGC
1 AATTCTACGGGCACTTCGGTGC
83366 A
1 A
83367 TTTATACGAG
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 45 1.00
ACGTcount: A:0.19, C:0.27, G:0.27, T:0.27
Consensus pattern (22 bp):
AATTCTACGGGCACTTCGGTGC
Found at i:85931 original size:33 final size:35
Alignment explanation
Indices: 85885--85952 Score: 95
Period size: 33 Copynumber: 2.0 Consensus size: 35
85875 ACCAATTCCA
85885 AAATTCTATTAAAAATGATTTATTATAAAATTATT
1 AAATTCTATTAAAAATGATTTATTATAAAATTATT
* * *
85920 AAATT-TA-TAAAATTTATTTATTATAAACTTATT
1 AAATTCTATTAAAAATGATTTATTATAAAATTATT
85953 TCATCATAAG
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
33 23 0.77
34 2 0.07
35 5 0.17
ACGTcount: A:0.47, C:0.03, G:0.01, T:0.49
Consensus pattern (35 bp):
AAATTCTATTAAAAATGATTTATTATAAAATTATT
Found at i:85953 original size:15 final size:15
Alignment explanation
Indices: 85891--85953 Score: 65
Period size: 15 Copynumber: 4.1 Consensus size: 15
85881 TCCAAAATTC
*
85891 TATTA-AAAATGATT
1 TATTATAAAATTATT
85905 TATTATAAAATTATT
1 TATTATAAAATTATT
*
85920 AAATTTATAAAATTTATT
1 -TA-TTATAAAA-TTATT
*
85938 TATTATAAACTTATT
1 TATTATAAAATTATT
85953 T
1 T
85954 CATCATAAGA
Statistics
Matches: 41, Mismatches: 4, Indels: 7
0.79 0.08 0.13
Matches are distributed among these distances:
14 5 0.12
15 14 0.34
16 8 0.20
17 9 0.22
18 5 0.12
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.51
Consensus pattern (15 bp):
TATTATAAAATTATT
Found at i:86281 original size:26 final size:26
Alignment explanation
Indices: 86232--86281 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 26
86222 TTAAAAATTT
* **
86232 TATTTAAAATAAAAAATTTAAAATCA
1 TATTAAAAATAAAAAAAATAAAATCA
*
86258 TATTAAAAATAAAAAAAATCAAAT
1 TATTAAAAATAAAAAAAATAAAAT
86282 TTGAAAATAT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
26 20 1.00
ACGTcount: A:0.66, C:0.04, G:0.00, T:0.30
Consensus pattern (26 bp):
TATTAAAAATAAAAAAAATAAAATCA
Found at i:87153 original size:20 final size:20
Alignment explanation
Indices: 87106--87158 Score: 81
Period size: 19 Copynumber: 2.7 Consensus size: 20
87096 AATTTTTGAA
87106 GGTGCATCGATGCAATAAGG
1 GGTGCATCGATGCAATAAGG
* *
87126 GG-GCATCGATGTAGTAAGG
1 GGTGCATCGATGCAATAAGG
87145 GGTGCATCGATGCA
1 GGTGCATCGATGCA
87159 TGGGAATTTC
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
19 17 0.59
20 12 0.41
ACGTcount: A:0.26, C:0.15, G:0.38, T:0.21
Consensus pattern (20 bp):
GGTGCATCGATGCAATAAGG
Found at i:88466 original size:22 final size:22
Alignment explanation
Indices: 88434--88483 Score: 64
Period size: 22 Copynumber: 2.3 Consensus size: 22
88424 ACTGTAGCAC
* *
88434 TGTTCATTACTGTTCACGATAT
1 TGTTCAATACTATTCACGATAT
* *
88456 TTTTCAATACTATTCACGGTAT
1 TGTTCAATACTATTCACGATAT
88478 TGTTCA
1 TGTTCA
88484 TACCGTATTT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.24, C:0.18, G:0.12, T:0.46
Consensus pattern (22 bp):
TGTTCAATACTATTCACGATAT
Found at i:89343 original size:7 final size:7
Alignment explanation
Indices: 89331--89357 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
89321 AACTACAATT
89331 TCTTCCA
1 TCTTCCA
89338 TCTTCCA
1 TCTTCCA
89345 TCTTCCA
1 TCTTCCA
89352 TCTTCC
1 TCTTCC
89358 TTCCACCTTC
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:0.11, C:0.44, G:0.00, T:0.44
Consensus pattern (7 bp):
TCTTCCA
Done.