Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009199.1 Hibiscus syriacus cultivar Beakdansim tig00112782_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: 83958
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.32
Found at i:2988 original size:16 final size:16
Alignment explanation
Indices: 2963--3076 Score: 60
Period size: 16 Copynumber: 7.4 Consensus size: 16
2953 ATAGTTTAAA
* *
2963 CGAAATTAACTCGAAC
1 CGAAAGTAACCCGAAC
*
2979 CGAAAGTAACCCAAAC
1 CGAAAGTAACCCGAAC
* *
2995 TGAAAAATAA-CCGAAC
1 CG-AAAGTAACCCGAAC
*
3011 CGAAAGCAACCCGAA-
1 CGAAAGTAACCCGAAC
*
3026 CTAAA-TCAACCCGAA-
1 CGAAAGT-AACCCGAAC
* ** *
3041 C-AAA-AAAATCAAAC
1 CGAAAGTAACCCGAAC
*
3055 CGAAAATAACCCGAAC
1 CGAAAGTAACCCGAAC
3071 CGAAAG
1 CGAAAG
3077 CAACTCAAAT
Statistics
Matches: 72, Mismatches: 20, Indels: 12
0.69 0.19 0.12
Matches are distributed among these distances:
13 5 0.07
14 4 0.06
15 21 0.29
16 36 0.50
17 6 0.08
ACGTcount: A:0.52, C:0.27, G:0.12, T:0.09
Consensus pattern (16 bp):
CGAAAGTAACCCGAAC
Found at i:3174 original size:3 final size:3
Alignment explanation
Indices: 3166--3226 Score: 95
Period size: 3 Copynumber: 19.7 Consensus size: 3
3156 ACAAATAATT
*
3166 TTA TTA TTA TTA TTA TTA TTA TCA TTA TTA TTA TTTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA
3212 TTA TTA TTA TCTA TT
1 TTA TTA TTA T-TA TT
3227 TTAGTAATTA
Statistics
Matches: 54, Mismatches: 2, Indels: 4
0.90 0.03 0.07
Matches are distributed among these distances:
3 48 0.89
4 6 0.11
ACGTcount: A:0.31, C:0.03, G:0.00, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:3651 original size:43 final size:45
Alignment explanation
Indices: 3576--3682 Score: 121
Period size: 44 Copynumber: 2.4 Consensus size: 45
3566 CCTAAACAAA
* * *
3576 AACCCGAATT-AGCTCGAAAATCTAAAGGTTGATTTGAATC-AAAAC
1 AACCCGAATTGA-CCCG-AAATCTAAAGGTTGATTCGAACCGAAAAC
* *
3621 AACCCGAATTGATCCGAAATCTAAA-GTTGATTCGAACCGAAACC
1 AACCCGAATTGACCCGAAATCTAAAGGTTGATTCGAACCGAAAAC
*
3665 AACCAGAATTGACCCGAA
1 AACCCGAATTGACCCGAA
3683 CCGAAACCAA
Statistics
Matches: 53, Mismatches: 7, Indels: 5
0.82 0.11 0.08
Matches are distributed among these distances:
43 11 0.21
44 29 0.55
45 12 0.23
46 1 0.02
ACGTcount: A:0.41, C:0.22, G:0.16, T:0.21
Consensus pattern (45 bp):
AACCCGAATTGACCCGAAATCTAAAGGTTGATTCGAACCGAAAAC
Found at i:3721 original size:31 final size:31
Alignment explanation
Indices: 3672--3787 Score: 108
Period size: 31 Copynumber: 3.7 Consensus size: 31
3662 ACCAACCAGA
* * *
3672 ATTGACCCGAAC-CGAAACCAATTGATTTGAT
1 ATTGACCCG-ACTCAAAACCAACTGATCTGAT
* *
3703 ATTGACCTGACTCAAAACCAACTGATCTGAG
1 ATTGACCCGACTCAAAACCAACTGATCTGAT
* * * *
3734 ATTAACCCGACCCAAACAACAACCGATCTGAT
1 ATTGACCCGACTCAAA-ACCAACTGATCTGAT
*
3766 TTTGACCCGACTCGAAAACCAA
1 ATTGACCCGACTC-AAAACCAA
3788 TCGACCCGAT
Statistics
Matches: 67, Mismatches: 15, Indels: 5
0.77 0.17 0.06
Matches are distributed among these distances:
30 2 0.03
31 36 0.54
32 26 0.39
33 3 0.04
ACGTcount: A:0.37, C:0.28, G:0.14, T:0.21
Consensus pattern (31 bp):
ATTGACCCGACTCAAAACCAACTGATCTGAT
Found at i:4825 original size:23 final size:20
Alignment explanation
Indices: 4793--4837 Score: 54
Period size: 20 Copynumber: 2.1 Consensus size: 20
4783 TTAGCATATT
4793 ATTTAAATATATCATGTGTGTGA
1 ATTTAAATAT-T-AT-TGTGTGA
*
4816 ATTTATATATTATTGTGTGA
1 ATTTAAATATTATTGTGTGA
4836 AT
1 AT
4838 ATGTGATATA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
20 9 0.43
21 2 0.10
22 1 0.05
23 9 0.43
ACGTcount: A:0.33, C:0.02, G:0.16, T:0.49
Consensus pattern (20 bp):
ATTTAAATATTATTGTGTGA
Found at i:4834 original size:20 final size:21
Alignment explanation
Indices: 4799--4837 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
4789 TATTATTTAA
4799 ATATATCATGTGTGTGAATTT
1 ATATATCATGTGTGTGAATTT
*
4820 ATATATTAT-TGTGTGAAT
1 ATATATCATGTGTGTGAAT
4838 ATGTGATATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.31, C:0.03, G:0.18, T:0.49
Consensus pattern (21 bp):
ATATATCATGTGTGTGAATTT
Found at i:16165 original size:51 final size:51
Alignment explanation
Indices: 16105--16217 Score: 124
Period size: 51 Copynumber: 2.2 Consensus size: 51
16095 GCTCTTTGTC
* * **
16105 CCGCGCTATATGTTGATTTAGCGT-CACGTGGGGTATAGCGCG-CCCTCTG-T
1 CCGCGCTATACGCTGACATAGCGTACACGT-GGGTATAGCGCGACCC-CTGAT
* *
16155 ACCGCGCTATACGCTGACATGGCTTACACGTGGGTATAGCGCGACCCCTGAT
1 -CCGCGCTATACGCTGACATAGCGTACACGTGGGTATAGCGCGACCCCTGAT
16207 CCGCGCTATAC
1 CCGCGCTATAC
16218 ACCACGTAGG
Statistics
Matches: 53, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
51 44 0.83
52 9 0.17
ACGTcount: A:0.18, C:0.30, G:0.27, T:0.25
Consensus pattern (51 bp):
CCGCGCTATACGCTGACATAGCGTACACGTGGGTATAGCGCGACCCCTGAT
Found at i:16529 original size:15 final size:16
Alignment explanation
Indices: 16509--16556 Score: 62
Period size: 16 Copynumber: 3.1 Consensus size: 16
16499 TCGTTATAAA
16509 TTTTATTATAATT-TT
1 TTTTATTATAATTATT
*
16524 TTTTATTATACTTATT
1 TTTTATTATAATTATT
* *
16540 GTTTATTATGATTATT
1 TTTTATTATAATTATT
16556 T
1 T
16557 GAAAAAAATA
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
15 12 0.44
16 15 0.56
ACGTcount: A:0.25, C:0.02, G:0.04, T:0.69
Consensus pattern (16 bp):
TTTTATTATAATTATT
Found at i:19173 original size:31 final size:31
Alignment explanation
Indices: 19135--19228 Score: 163
Period size: 31 Copynumber: 3.0 Consensus size: 31
19125 AGGGTCGAGG
19135 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
19166 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
*
19197 GTTTACCTAGGTTCTTCGGGATC-TATGGACT
1 GTTTACCTATGTTCTTCGGGA-CATATGGACT
19228 G
1 G
19229 GTCATTCGGG
Statistics
Matches: 61, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
31 60 0.98
32 1 0.02
ACGTcount: A:0.18, C:0.19, G:0.24, T:0.38
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGGGACATATGGACT
Found at i:20383 original size:18 final size:17
Alignment explanation
Indices: 20360--20413 Score: 81
Period size: 18 Copynumber: 3.1 Consensus size: 17
20350 TGTGTTGGAG
*
20360 GCATCATATATGGCTGC
1 GCATCATAAATGGCTGC
20377 AGCATCATAAATGGCTGC
1 -GCATCATAAATGGCTGC
20395 GACATCATAAATGGCTGC
1 G-CATCATAAATGGCTGC
20413 G
1 G
20414 GTGGCTGCTG
Statistics
Matches: 34, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
17 1 0.03
18 33 0.97
ACGTcount: A:0.30, C:0.22, G:0.24, T:0.24
Consensus pattern (17 bp):
GCATCATAAATGGCTGC
Found at i:22126 original size:18 final size:17
Alignment explanation
Indices: 22094--22139 Score: 56
Period size: 18 Copynumber: 2.6 Consensus size: 17
22084 AAATTATATT
22094 AGTAAAATATTAAATAA
1 AGTAAAATATTAAATAA
*
22111 AGTAAAATGCTTAAATAA
1 AGTAAAAT-ATTAAATAA
*
22129 ATTAAATATAT
1 AGTAAA-ATAT
22140 AATATTAAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
17 8 0.33
18 14 0.58
19 2 0.08
ACGTcount: A:0.59, C:0.02, G:0.07, T:0.33
Consensus pattern (17 bp):
AGTAAAATATTAAATAA
Found at i:22147 original size:23 final size:24
Alignment explanation
Indices: 22121--22173 Score: 58
Period size: 23 Copynumber: 2.3 Consensus size: 24
22111 AGTAAAATGC
*
22121 TTAAATAA-ATTA-AATATATAATA
1 TTAAATAATATTATAAAATAT-ATA
*
22144 TTAAA-AATATTATAAAATATATC
1 TTAAATAATATTATAAAATATATA
22167 TTAAATA
1 TTAAATA
22174 GAGAGAGTAT
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
22 2 0.08
23 16 0.64
24 7 0.28
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (24 bp):
TTAAATAATATTATAAAATATATA
Found at i:27867 original size:23 final size:23
Alignment explanation
Indices: 27841--27888 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 23
27831 ATAAAATACA
*
27841 ATAACATACTAGGTAGCGCTTAT
1 ATAACATAATAGGTAGCGCTTAT
**
27864 ATAATGTAATAGGTAGCGCTTAT
1 ATAACATAATAGGTAGCGCTTAT
27887 AT
1 AT
27889 TTACCTATTT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.35, C:0.12, G:0.19, T:0.33
Consensus pattern (23 bp):
ATAACATAATAGGTAGCGCTTAT
Found at i:28249 original size:20 final size:20
Alignment explanation
Indices: 28224--28262 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
28214 TCCACAGTGA
* *
28224 AAAAAGTATGGACACTTTAT
1 AAAAAGGATAGACACTTTAT
28244 AAAAAGGATAGACACTTTA
1 AAAAAGGATAGACACTTTA
28263 CAATATAACC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.49, C:0.10, G:0.15, T:0.26
Consensus pattern (20 bp):
AAAAAGGATAGACACTTTAT
Found at i:28290 original size:21 final size:20
Alignment explanation
Indices: 28260--28311 Score: 68
Period size: 21 Copynumber: 2.5 Consensus size: 20
28250 GATAGACACT
*
28260 TTACAATATAACCACTACCTA
1 TTACATTATAACCA-TACCTA
*
28281 TTACATTATAAACGATACCTA
1 TTACATTAT-AACCATACCTA
28302 TTACATTATA
1 TTACATTATA
28312 TAAGGGCTAC
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
20 1 0.04
21 23 0.82
22 4 0.14
ACGTcount: A:0.42, C:0.21, G:0.02, T:0.35
Consensus pattern (20 bp):
TTACATTATAACCATACCTA
Found at i:28322 original size:23 final size:22
Alignment explanation
Indices: 28265--28335 Score: 81
Period size: 23 Copynumber: 3.2 Consensus size: 22
28255 ACACTTTACA
*
28265 ATATAACCACTACCTATTACATT
1 ATATAA-CGCTACCTATTACATT
*
28288 ATA-AACGATACCTATTACATT
1 ATATAACGCTACCTATTACATT
* *
28309 ATATAAGGGCTACCTATTACATC
1 ATATAA-CGCTACCTATTACATT
28332 ATAT
1 ATAT
28336 GTTTACCTAT
Statistics
Matches: 41, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
21 17 0.41
22 4 0.10
23 20 0.49
ACGTcount: A:0.39, C:0.21, G:0.06, T:0.34
Consensus pattern (22 bp):
ATATAACGCTACCTATTACATT
Found at i:28790 original size:39 final size:39
Alignment explanation
Indices: 28736--28822 Score: 156
Period size: 39 Copynumber: 2.2 Consensus size: 39
28726 TCAAGTTGTA
*
28736 GATTTTGATTTCCTTTTGCTTGGCATCATATGAGATTTG
1 GATTTTGATTTCCTTTTGCTTGGCACCATATGAGATTTG
*
28775 GATTTTGATTTCCTTTTGCTTGGCACCATATGAGCTTTG
1 GATTTTGATTTCCTTTTGCTTGGCACCATATGAGATTTG
28814 GATTTTGAT
1 GATTTTGAT
28823 GAGCATCGGA
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
39 46 1.00
ACGTcount: A:0.17, C:0.14, G:0.21, T:0.48
Consensus pattern (39 bp):
GATTTTGATTTCCTTTTGCTTGGCACCATATGAGATTTG
Found at i:29672 original size:183 final size:184
Alignment explanation
Indices: 29127--29837 Score: 1307
Period size: 184 Copynumber: 3.9 Consensus size: 184
29117 TTCAAATTAC
* * *
29127 CGACACTTTTTTAAATGGTATCGACACATTTTTATTCCAATCTGGACATAAAGTACCGACACAAT
1 CGACACTTTTTTAAATCGTATCGACACATTTTTCTTCCAATATGGACATAAAGTACCGACACAAT
* * *
29192 ATTATAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGGTATATTTATACCGGTT
66 ATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAGACCGGTATATTTATACCGGTT
* * *
29257 ATATTACAAAATTATCTATTACATTATAATTATGGGTTCCGATGTGTAAAATGT
131 ATATTGCAAATTTACCTATTACATTATAATTATGGGTTCCGATGTGTAAAATGT
*
29311 CGACACTTTTTTAAATCGTATCGACACATTTTTCTTCCAATATGGACATAAAGTACCGATACAAT
1 CGACACTTTTTTAAATCGTATCGACACATTTTTCTTCCAATATGGACATAAAGTACCGACACAAT
29376 ATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAGACCGGTATATTTATACCGGTT
66 ATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAGACCGGTATATTTATACCGGTT
29441 ATATTGCAAATTTACCTATTACATTATAATTATGGGTTCCGATGTGTAAAATGT
131 ATATTGCAAATTTACCTATTACATTATAATTATGGGTTCCGATGTGTAAAATGT
29495 CGACACTTTTTTAAATCGTATCGACACATTTTTCTTCCAATATGGACATAAAGTACCGACACAAT
1 CGACACTTTTTTAAATCGTATCGACACATTTTTCTTCCAATATGGACATAAAGTACCGACACAAT
29560 ATT-AAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAGACCGGTATATTTATACCGGTT
66 ATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAGACCGGTATATTTATACCGGTT
29624 ATATTGCAAATTTACCTATTACATTATAATTATGGGTTCCGATGTGTAAAATGT
131 ATATTGCAAATTTACCTATTACATTATAATTATGGGTTCCGATGTGTAAAATGT
29678 CGACACTTTTTTAAATCGTATCGACACATTTTTCTTCCAATATGGACATAAAGTACCGACACAAT
1 CGACACTTTTTTAAATCGTATCGACACATTTTTCTTCCAATATGGACATAAAGTACCGACACAAT
29743 ATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAGACCGGTATATTTATACCGGTT
66 ATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAGACCGGTATATTTATACCGGTT
**
29808 ATATTGCAAATTTACCTATTTTATTATAAT
131 ATATTGCAAATTTACCTATTACATTATAAT
29838 ATGTTGAAAG
Statistics
Matches: 513, Mismatches: 13, Indels: 2
0.97 0.02 0.00
Matches are distributed among these distances:
183 183 0.36
184 330 0.64
ACGTcount: A:0.33, C:0.17, G:0.15, T:0.35
Consensus pattern (184 bp):
CGACACTTTTTTAAATCGTATCGACACATTTTTCTTCCAATATGGACATAAAGTACCGACACAAT
ATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAGACCGGTATATTTATACCGGTT
ATATTGCAAATTTACCTATTACATTATAATTATGGGTTCCGATGTGTAAAATGT
Found at i:29801 original size:367 final size:368
Alignment explanation
Indices: 29127--29837 Score: 1316
Period size: 367 Copynumber: 1.9 Consensus size: 368
29117 TTCAAATTAC
* *
29127 CGACACTTTTTTAAATGGTATCGACACATTTTTATTCCAATCTGGACATAAAGTACCGACACAAT
1 CGACACTTTTTTAAATCGTATCGACACATTTTTATTCCAATATGGACATAAAGTACCGACACAAT
*
29192 ATTATAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGGTATATTTATACCGGTT
66 ATTATAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAAACCGGTATATTTATACCGGTT
*
29257 ATATTACAAAATTATCTATTACATTATAATTATGGGTTCCGATGTGTAAAATGTCGACACTTTTT
131 ATATTACAAAATTACCTATTACATTATAATTATGGGTTCCGATGTGTAAAATGTCGACACTTTTT
*
29322 TAAATCGTATCGACACATTTTTCTTCCAATATGGACATAAAGTACCGATACAATATTAAAAAGTG
196 TAAATCGTATCGACACATTTTTCTTCCAATATGGACATAAAGTACCGACACAATATTAAAAAGTG
29387 TCGATATAGGTTGTAGACCTATTCGCGCATAAGACCGGTATATTTATACCGGTTATATTGCAAAT
261 TCGATATAGGTTGTAGACCTATTCGCGCATAAGACCGGTATATTTATACCGGTTATATTGCAAAT
29452 TTACCTATTACATTATAATTATGGGTTCCGATGTGTAAAATGT
326 TTACCTATTACATTATAATTATGGGTTCCGATGTGTAAAATGT
*
29495 CGACACTTTTTTAAATCGTATCGACACATTTTTCTTCCAATATGGACATAAAGTACCGACACAAT
1 CGACACTTTTTTAAATCGTATCGACACATTTTTATTCCAATATGGACATAAAGTACCGACACAAT
*
29560 ATTA-AAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAGACCGGTATATTTATACCGGTT
66 ATTATAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAAACCGGTATATTTATACCGGTT
* *
29624 ATATTGCAAATTTACCTATTACATTATAATTATGGGTTCCGATGTGTAAAATGTCGACACTTTTT
131 ATATTACAAAATTACCTATTACATTATAATTATGGGTTCCGATGTGTAAAATGTCGACACTTTTT
29689 TAAATCGTATCGACACATTTTTCTTCCAATATGGACATAAAGTACCGACACAATATTAAAAAGTG
196 TAAATCGTATCGACACATTTTTCTTCCAATATGGACATAAAGTACCGACACAATATTAAAAAGTG
29754 TCGATATAGGTTGTAGACCTATTCGCGCATAAGACCGGTATATTTATACCGGTTATATTGCAAAT
261 TCGATATAGGTTGTAGACCTATTCGCGCATAAGACCGGTATATTTATACCGGTTATATTGCAAAT
**
29819 TTACCTATTTTATTATAAT
326 TTACCTATTACATTATAAT
29838 ATGTTGAAAG
Statistics
Matches: 332, Mismatches: 11, Indels: 1
0.97 0.03 0.00
Matches are distributed among these distances:
367 266 0.80
368 66 0.20
ACGTcount: A:0.33, C:0.17, G:0.15, T:0.35
Consensus pattern (368 bp):
CGACACTTTTTTAAATCGTATCGACACATTTTTATTCCAATATGGACATAAAGTACCGACACAAT
ATTATAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAAACCGGTATATTTATACCGGTT
ATATTACAAAATTACCTATTACATTATAATTATGGGTTCCGATGTGTAAAATGTCGACACTTTTT
TAAATCGTATCGACACATTTTTCTTCCAATATGGACATAAAGTACCGACACAATATTAAAAAGTG
TCGATATAGGTTGTAGACCTATTCGCGCATAAGACCGGTATATTTATACCGGTTATATTGCAAAT
TTACCTATTACATTATAATTATGGGTTCCGATGTGTAAAATGT
Found at i:31293 original size:3 final size:3
Alignment explanation
Indices: 31285--31371 Score: 84
Period size: 3 Copynumber: 29.0 Consensus size: 3
31275 ACTTGTTTGG
* * * **
31285 ATC ATC ATC TTC ATC ATC ATC ATC ATC ATC GTC ATC ATC TTC ATC GCC
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC
* * * * *
31333 AGC TTC ATC GTC ATC ATC ATC ATC ATC GTC ATC TTC ATC
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC
31372 GTCAGCTTCA
Statistics
Matches: 65, Mismatches: 19, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
3 65 1.00
ACGTcount: A:0.24, C:0.34, G:0.06, T:0.36
Consensus pattern (3 bp):
ATC
Found at i:31308 original size:18 final size:18
Alignment explanation
Indices: 31285--31386 Score: 87
Period size: 18 Copynumber: 5.7 Consensus size: 18
31275 ACTTGTTTGG
31285 ATCATCATCTTCATCATC
1 ATCATCATCTTCATCATC
* *
31303 ATCATCATCATCGTCATC
1 ATCATCATCTTCATCATC
* ** * *
31321 ATCTTCATCGCCAGCTTC
1 ATCATCATCTTCATCATC
* *
31339 ATCGTCATCATCATCATC
1 ATCATCATCTTCATCATC
* *
31357 ATCGTCATCTTCATCGTC
1 ATCATCATCTTCATCATC
* *
31375 AGCTTCATCTTC
1 ATCATCATCTTC
31387 TGCGACCGCT
Statistics
Matches: 67, Mismatches: 17, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
18 67 1.00
ACGTcount: A:0.23, C:0.34, G:0.07, T:0.36
Consensus pattern (18 bp):
ATCATCATCTTCATCATC
Found at i:31352 original size:42 final size:42
Alignment explanation
Indices: 31293--31383 Score: 146
Period size: 42 Copynumber: 2.2 Consensus size: 42
31283 GGATCATCAT
*
31293 CTTCATCATCATCATCATCATCGTCATCATCTTCATCGCCAG
1 CTTCATCATCATCATCATCATCATCATCATCTTCATCGCCAG
* * *
31335 CTTCATCGTCATCATCATCATCATCGTCATCTTCATCGTCAG
1 CTTCATCATCATCATCATCATCATCATCATCTTCATCGCCAG
31377 CTTCATC
1 CTTCATC
31384 TTCTGCGACC
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 45 1.00
ACGTcount: A:0.22, C:0.35, G:0.08, T:0.35
Consensus pattern (42 bp):
CTTCATCATCATCATCATCATCATCATCATCTTCATCGCCAG
Found at i:33741 original size:197 final size:199
Alignment explanation
Indices: 32842--34845 Score: 3616
Period size: 197 Copynumber: 10.1 Consensus size: 199
32832 TTTAAATTAG
32842 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
32907 ATTGTACCGGTTAGATTG-AAAATTACATATTACATTATACTTTTGGGTTCGATGA-TTTGGGAT
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
* *
32970 CGACACTTTTTATATATGGATCGACACTTTATTGGTGCACCTTGTTTTTAATTCATTATGG-AAA
131 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTGGAAAA
33034 AAAA
196 AAAA
*
33038 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
* *
33103 ATTGTAACGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
*
33168 CGACACTTTTTTATATATGGATCTACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTGGAAA
131 CGACAC-TTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTGGAAA
33233 AAAAA
195 AAAAA
33238 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCAT-AAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
33302 ATTGTA-CGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
* *
33366 CGACACTTTTTATATATGGATCGACACTTTATTGGTGCACCTTGTTTTTAATTCATTCT-G-TAA
131 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTGGAAAA
33429 AAAA
196 AAAA
* *
33433 -ATCGACACAAACTATATTAGTGTTGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
33497 ATTGTACCGGTTAGATT-AAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
*
33561 CGACACTTTTTTATATATGGATCGACACTTTATGGGTGCACCTTG-TTTTAATTCATTCTGG-GA
131 CGACAC-TTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTGGAAA
33624 AAAAA
195 AAAAA
33629 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
*
33694 CTTGTACCGGTTAGATTGAAAAATTACATATTACATTATAC-TTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
33758 CGACAC-TTTT-TATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTGGAAAA
131 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTGG-AAA
33821 AAAAA
195 AAAAA
* *
33826 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAATCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
*
33891 ATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
33956 CGACACTTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTGGAAA
131 CGACAC-TTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTGGAAA
34021 AAAAA
195 AAAAA
34026 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
*
34091 CTTGTACCGGTTAGATTGAAAAATTACATATTACATTATAC-TTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
*
34155 CGACACTTTTTATATATGGATCGACACTTTATTGGTGCACCTTGTTTTTAATTCATTCTGGAAAA
131 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTGGAAAA
34220 AAAA
196 AAAA
*
34224 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
34289 ATTGTACCGGTTAGATT-AAAAATTACATATTACATTATAC-TTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
34352 CGACACTTTTTTATATATGGATCGACACTTTAT-GGTGCACCTTGTTTTTAATTCATTCTGGAAA
131 CGACAC-TTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTGGAAA
34416 AAAAA
195 AAAAA
34421 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
* *
34486 CTTGTACCGGTTAGATTGAACAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
*
34551 CGACACTTTTTATATATGGATCGACACTTTATTGGTGCACCTTGTTTTTAATTCATTCTGGAAAA
131 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTGGAAAA
34616 AAAA
196 AAAA
34620 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGAC-TATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
*
34684 ATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
34749 CGACACTTTTT-TATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTGGAAAA
131 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTGGAAAA
34813 AAAA
196 AAAA
*
34817 TATCGACACAAACTATATTAGTATCGACA
1 TATCGACACAAACTATATTAGTGTCGACA
34846 TGACCCTTAA
Statistics
Matches: 1749, Mismatches: 38, Indels: 41
0.96 0.02 0.02
Matches are distributed among these distances:
194 82 0.05
195 110 0.06
196 135 0.08
197 555 0.32
198 441 0.25
199 204 0.12
200 173 0.10
201 49 0.03
ACGTcount: A:0.32, C:0.15, G:0.15, T:0.38
Consensus pattern (199 bp):
TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTGGAAAA
AAAA
Found at i:34606 original size:396 final size:399
Alignment explanation
Indices: 32842--34845 Score: 3744
Period size: 396 Copynumber: 5.1 Consensus size: 399
32832 TTTAAATTAG
32842 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
*
32907 ATTGTACCGGTTAGATTG-AAAATTACATATTACATTATACTTTTGGGTTCGATGA-TTTGGGAT
66 CTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
*
32970 CGACACTTTTTATATATGGATCGACACTTTATTGGTGCACCTTGTTTTTAATTCATTATGG-AAA
131 CGACACTTTTTATATATGGATCGACACTTTATTGGTGCACCTTGTTTTTAATTCATTCTGGAAAA
33034 AAAATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGG
196 AAAATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGG
*
33099 TATAATTGTAACGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTG
261 TATAATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTG
*
33164 GGATCGACACTTTTTTATATATGGATCTACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTG
326 GGATCGACACTTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTG
33229 GAAAAAAAA
391 GAAAAAAAA
33238 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCAT-AAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
*
33302 ATTGTA-CGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 CTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
*
33366 CGACACTTTTTATATATGGATCGACACTTTATTGGTGCACCTTGTTTTTAATTCATTCT-G-TAA
131 CGACACTTTTTATATATGGATCGACACTTTATTGGTGCACCTTGTTTTTAATTCATTCTGGAAAA
*
33429 AAAA-ATCGACACAAACTATATTAGTGTTGACACATTATTTAGACTTATTCTCTCATAAAACCGG
196 AAAATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGG
33493 TATAATTGTACCGGTTAGATT-AAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTG
261 TATAATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTG
33557 GGATCGACACTTTTTTATATATGGATCGACACTTTATGGGTGCACCTTG-TTTTAATTCATTCTG
326 GGATCGACACTTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTG
*
33621 G-GAAAAAA
391 GAAAAAAAA
33629 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
33694 CTTGTACCGGTTAGATTGAAAAATTACATATTACATTATAC-TTTGGGTTCGATGATTTTGGGAT
66 CTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
*
33758 CGACAC-TTTT-TATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTGGAAAA
131 CGACACTTTTTATATATGGATCGACACTTTATTGGTGCACCTTGTTTTTAATTCATTCTGG-AAA
*
33821 AAAAATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAATCG
195 AAAAATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCG
33886 GTATAATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTT
260 GTATAATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTT
33951 GGGATCGACACTTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCT
325 GGGATCGACACTTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCT
34016 GGAAAAAAAA
390 GGAAAAAAAA
34026 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
34091 CTTGTACCGGTTAGATTGAAAAATTACATATTACATTATAC-TTTGGGTTCGATGATTTTGGGAT
66 CTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
34155 CGACACTTTTTATATATGGATCGACACTTTATTGGTGCACCTTGTTTTTAATTCATTCTGGAAAA
131 CGACACTTTTTATATATGGATCGACACTTTATTGGTGCACCTTGTTTTTAATTCATTCTGGAAAA
34220 AAAATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGG
196 AAAATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGG
34285 TATAATTGTACCGGTTAGATT-AAAAATTACATATTACATTATAC-TTTGGGTTCGATGATTTTG
261 TATAATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTG
34348 GGATCGACACTTTTTTATATATGGATCGACACTTTAT-GGTGCACCTTGTTTTTAATTCATTCTG
326 GGATCGACACTTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTG
34412 GAAAAAAAA
391 GAAAAAAAA
34421 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
*
34486 CTTGTACCGGTTAGATTGAACAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 CTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
34551 CGACACTTTTTATATATGGATCGACACTTTATTGGTGCACCTTGTTTTTAATTCATTCTGGAAAA
131 CGACACTTTTTATATATGGATCGACACTTTATTGGTGCACCTTGTTTTTAATTCATTCTGGAAAA
34616 AAAATATCGACACAAACTATATTAGTGTCGACACATTATTTAGAC-TATTCTCTCATAAAACCGG
196 AAAATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGG
34680 TATAATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTG
261 TATAATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTG
34745 GGATCGACAC-TTTTT-TATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTG
326 GGATCGACACTTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTG
34808 GAAAAAAAA
391 GAAAAAAAA
*
34817 TATCGACACAAACTATATTAGTATCGACA
1 TATCGACACAAACTATATTAGTGTCGACA
34846 TGACCCTTAA
Statistics
Matches: 1575, Mismatches: 16, Indels: 34
0.97 0.01 0.02
Matches are distributed among these distances:
390 46 0.03
391 64 0.04
392 61 0.04
393 131 0.08
394 169 0.11
395 354 0.22
396 416 0.26
397 193 0.12
398 93 0.06
399 48 0.03
ACGTcount: A:0.32, C:0.15, G:0.15, T:0.38
Consensus pattern (399 bp):
TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
CTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
CGACACTTTTTATATATGGATCGACACTTTATTGGTGCACCTTGTTTTTAATTCATTCTGGAAAA
AAAATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGG
TATAATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTG
GGATCGACACTTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTG
GAAAAAAAA
Found at i:34969 original size:19 final size:19
Alignment explanation
Indices: 34923--34971 Score: 80
Period size: 19 Copynumber: 2.6 Consensus size: 19
34913 TTATATTCAC
*
34923 ATACAAAAATATAAATCGT
1 ATACAAAATTATAAATCGT
*
34942 ATACAAAATTATAAATCTT
1 ATACAAAATTATAAATCGT
34961 ATACAAAATTA
1 ATACAAAATTA
34972 ACTCGACATT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.57, C:0.10, G:0.02, T:0.31
Consensus pattern (19 bp):
ATACAAAATTATAAATCGT
Found at i:36792 original size:33 final size:33
Alignment explanation
Indices: 36755--36820 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 33
36745 CATCTTAATA
*
36755 TCACCCCTTAACACCGAAACTTCTTTCACCACT
1 TCACCCCTCAACACCGAAACTTCTTTCACCACT
***
36788 TCACCCCTCAACACCTCTACTTCTTTCACCACT
1 TCACCCCTCAACACCGAAACTTCTTTCACCACT
36821 CCATCTATTT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.24, C:0.45, G:0.02, T:0.29
Consensus pattern (33 bp):
TCACCCCTCAACACCGAAACTTCTTTCACCACT
Found at i:39175 original size:20 final size:19
Alignment explanation
Indices: 39129--39175 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 19
39119 TCCGGTATCA
*
39129 TTTTACCGTTTTTATCATT
1 TTTTACCGGTTTTATCATT
*
39148 TTGATACCGGTTTTATCATAT
1 TT-TTACCGGTTTTATCAT-T
39169 TTTTACC
1 TTTTACC
39176 TGTTATATCG
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
19 2 0.09
20 18 0.78
21 3 0.13
ACGTcount: A:0.19, C:0.17, G:0.09, T:0.55
Consensus pattern (19 bp):
TTTTACCGGTTTTATCATT
Found at i:39322 original size:20 final size:20
Alignment explanation
Indices: 39296--39341 Score: 76
Period size: 20 Copynumber: 2.3 Consensus size: 20
39286 CACTTTTAAA
39296 TTTACCGGTTTTATCAT-TT
1 TTTACCGGTTTTATCATATT
39315 TGTTACCGGTTTTATCATATT
1 T-TTACCGGTTTTATCATATT
39336 TTTACC
1 TTTACC
39342 TGGTATATCG
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
19 1 0.04
20 21 0.84
21 3 0.12
ACGTcount: A:0.17, C:0.17, G:0.11, T:0.54
Consensus pattern (20 bp):
TTTACCGGTTTTATCATATT
Found at i:42645 original size:20 final size:22
Alignment explanation
Indices: 42596--42647 Score: 63
Period size: 20 Copynumber: 2.4 Consensus size: 22
42586 ACATATAATT
42596 ATAAATTATTTAAAAATTTAAAG
1 ATAAATTATTTAAAAA-TTAAAG
* *
42619 GTGAATTATTT-AAAA-TAAAG
1 ATAAATTATTTAAAAATTAAAG
42639 ATAAATTAT
1 ATAAATTAT
42648 ACCAATGACA
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
20 12 0.48
22 4 0.16
23 9 0.36
ACGTcount: A:0.54, C:0.00, G:0.08, T:0.38
Consensus pattern (22 bp):
ATAAATTATTTAAAAATTAAAG
Found at i:51128 original size:37 final size:39
Alignment explanation
Indices: 51050--51129 Score: 94
Period size: 37 Copynumber: 2.1 Consensus size: 39
51040 TTAGCTTTGC
* **
51050 TTCATTTTAGTACCCACCATTAAAAACTTTAGTTTTTGT
1 TTCATTTTAGTACCCACCATTAAAAACTTTAATTTAAGT
*
51089 TTCATTTTAGTA-CC-CCATTCAAAA-TTTAATGTTAAGT
1 TTCATTTTAGTACCCACCATTAAAAACTTTAAT-TTAAGT
51126 TTCA
1 TTCA
51130 AAAAATCGAA
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
36 5 0.14
37 17 0.47
38 2 0.06
39 12 0.33
ACGTcount: A:0.30, C:0.17, G:0.07, T:0.45
Consensus pattern (39 bp):
TTCATTTTAGTACCCACCATTAAAAACTTTAATTTAAGT
Found at i:59880 original size:24 final size:24
Alignment explanation
Indices: 59848--59895 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
59838 ACACACACAT
59848 ATATATAATTTTGTAATCACTTTA
1 ATATATAATTTTGTAATCACTTTA
59872 ATATATAATTTTGTAATCACTTTA
1 ATATATAATTTTGTAATCACTTTA
59896 GATTAATAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.38, C:0.08, G:0.04, T:0.50
Consensus pattern (24 bp):
ATATATAATTTTGTAATCACTTTA
Found at i:77446 original size:3 final size:3
Alignment explanation
Indices: 77438--77471 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
77428 TGGATGGTAT
77438 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
77472 GACGTTTATA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:78446 original size:9 final size:9
Alignment explanation
Indices: 78432--78465 Score: 52
Period size: 9 Copynumber: 3.9 Consensus size: 9
78422 TATGTAAAAT
78432 ATTAAATAA
1 ATTAAATAA
78441 ATTAAAT-A
1 ATTAAATAA
*
78449 CTTAAATAA
1 ATTAAATAA
78458 ATTAAATA
1 ATTAAATA
78466 CAAAATATTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
8 7 0.32
9 15 0.68
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.35
Consensus pattern (9 bp):
ATTAAATAA
Found at i:78464 original size:17 final size:17
Alignment explanation
Indices: 78428--78466 Score: 71
Period size: 17 Copynumber: 2.4 Consensus size: 17
78418 TATTTATGTA
78428 AAATA-TTAAATAAATT
1 AAATACTTAAATAAATT
78444 AAATACTTAAATAAATT
1 AAATACTTAAATAAATT
78461 AAATAC
1 AAATAC
78467 AAAATATTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
16 5 0.23
17 17 0.77
ACGTcount: A:0.62, C:0.05, G:0.00, T:0.33
Consensus pattern (17 bp):
AAATACTTAAATAAATT
Found at i:80554 original size:12 final size:12
Alignment explanation
Indices: 80537--80562 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
80527 CCCCCCCCCC
80537 CTAATTTAGAAT
1 CTAATTTAGAAT
80549 CTAATTTAGAAT
1 CTAATTTAGAAT
80561 CT
1 CT
80563 TCTTATTAAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.38, C:0.12, G:0.08, T:0.42
Consensus pattern (12 bp):
CTAATTTAGAAT
Done.