Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005551.1 Hibiscus syriacus cultivar Beakdansim tig00012867_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: 108685
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
Found at i:9266 original size:5 final size:5
Alignment explanation
Indices: 9256--9289 Score: 50
Period size: 5 Copynumber: 6.8 Consensus size: 5
9246 ACCACGACCA
* *
9256 CGAGC CGAGC CGAGC CGAGC CGAGA CGAGA CGAG
1 CGAGC CGAGC CGAGC CGAGC CGAGC CGAGC CGAG
9290 ACGGACGGAC
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
5 28 1.00
ACGTcount: A:0.26, C:0.32, G:0.41, T:0.00
Consensus pattern (5 bp):
CGAGC
Found at i:12283 original size:17 final size:16
Alignment explanation
Indices: 12252--12285 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
12242 CACGTGAGGA
12252 TTATTTTCTTCTTATT
1 TTATTTTCTTCTTATT
*
12268 TTATTTATCTTTTTATT
1 TTATTT-TCTTCTTATT
12285 T
1 T
12286 ACTGTTTTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.15, C:0.09, G:0.00, T:0.76
Consensus pattern (16 bp):
TTATTTTCTTCTTATT
Found at i:19189 original size:3 final size:3
Alignment explanation
Indices: 19181--19206 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
19171 AGAGATATTC
19181 TCT TCT TCT TCT TCT TCT TCT TCT TC
1 TCT TCT TCT TCT TCT TCT TCT TCT TC
19207 ATGTACGAGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.00, C:0.35, G:0.00, T:0.65
Consensus pattern (3 bp):
TCT
Found at i:20939 original size:31 final size:32
Alignment explanation
Indices: 20886--21003 Score: 152
Period size: 32 Copynumber: 3.8 Consensus size: 32
20876 GTTCTACGGA
20886 ACATATGGACAGAATTACCTATGTCTTTCGAG
1 ACATATGGACAGAATTACCTATGTCTTTCGAG
** * *
20918 ACATATGGACATTA-TACCTATGTTCTATGGA-
1 ACATATGGACAGAATTACCTATG-TCTTTCGAG
20949 ACATATGGACAGAATTACCTATGTCTTTCGAG
1 ACATATGGACAGAATTACCTATGTCTTTCGAG
* *
20981 ACATATGGATAGTA-TACCTATGT
1 ACATATGGACAGAATTACCTATGT
21004 TCTAAGGAAC
Statistics
Matches: 73, Mismatches: 10, Indels: 7
0.81 0.11 0.08
Matches are distributed among these distances:
31 35 0.48
32 38 0.52
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Consensus pattern (32 bp):
ACATATGGACAGAATTACCTATGTCTTTCGAG
Found at i:20966 original size:63 final size:63
Alignment explanation
Indices: 20866--21020 Score: 274
Period size: 63 Copynumber: 2.5 Consensus size: 63
20856 AGAGTCGAGG
*
20866 GTATACCTATGTTCTACGGAACATATGGACAGAATTACCTATGTCTTTCGAGACATATGGACA
1 GTATACCTATGTTCTAAGGAACATATGGACAGAATTACCTATGTCTTTCGAGACATATGGACA
* * *
20929 TTATACCTATGTTCTATGGAACATATGGACAGAATTACCTATGTCTTTCGAGACATATGGATA
1 GTATACCTATGTTCTAAGGAACATATGGACAGAATTACCTATGTCTTTCGAGACATATGGACA
20992 GTATACCTATGTTCTAAGGAACATATGGA
1 GTATACCTATGTTCTAAGGAACATATGGA
21021 TAGTTTACCT
Statistics
Matches: 87, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
63 87 1.00
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.32
Consensus pattern (63 bp):
GTATACCTATGTTCTAAGGAACATATGGACAGAATTACCTATGTCTTTCGAGACATATGGACA
Found at i:21016 original size:31 final size:31
Alignment explanation
Indices: 20866--21036 Score: 175
Period size: 31 Copynumber: 5.5 Consensus size: 31
20856 AGAGTCGAGG
*
20866 GTATACCTATGTTCTACGGAACATATGGACA
1 GTATACCTATGTTCTATGGAACATATGGACA
* * *
20897 GAATTACCTATG-TCTTTCGAGACATATGGACA
1 GTA-TACCTATGTTCTATGGA-ACATATGGACA
*
20929 TTATACCTATGTTCTATGGAACATATGGACA
1 GTATACCTATGTTCTATGGAACATATGGACA
* * * *
20960 GAATTACCTATG-TCTTTCGAGACATATGGATA
1 GTA-TACCTATGTTCTATGGA-ACATATGGACA
* *
20992 GTATACCTATGTTCTAAGGAACATATGGATA
1 GTATACCTATGTTCTATGGAACATATGGACA
* *
21023 GTTTACCTAGGTTC
1 GTATACCTATGTTC
21037 ACCGGAACCT
Statistics
Matches: 115, Mismatches: 19, Indels: 12
0.79 0.13 0.08
Matches are distributed among these distances:
31 64 0.56
32 51 0.44
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.33
Consensus pattern (31 bp):
GTATACCTATGTTCTATGGAACATATGGACA
Found at i:21687 original size:11 final size:11
Alignment explanation
Indices: 21667--21696 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
21657 GACTCGTATC
*
21667 CGGGTCGGATA
1 CGGGTTGGATA
21678 CGGGTTGGATA
1 CGGGTTGGATA
21689 CGGGTTGG
1 CGGGTTGG
21697 GGGTGTTACA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.13, C:0.13, G:0.50, T:0.23
Consensus pattern (11 bp):
CGGGTTGGATA
Found at i:24577 original size:17 final size:16
Alignment explanation
Indices: 24546--24579 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
24536 CACGTGAGGA
24546 TTATTTTCTTCTTATT
1 TTATTTTCTTCTTATT
*
24562 TTATTTATCTTTTTATT
1 TTATTT-TCTTCTTATT
24579 T
1 T
24580 ACTGTTTTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.15, C:0.09, G:0.00, T:0.76
Consensus pattern (16 bp):
TTATTTTCTTCTTATT
Found at i:26771 original size:3 final size:3
Alignment explanation
Indices: 26758--26852 Score: 50
Period size: 3 Copynumber: 32.3 Consensus size: 3
26748 AAACATAAAC
* * * ** ** *
26758 AAT ATT AAT AAT AAT ACT AAT AAT AAT TAT AAT TTT AAT TGT TAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* * * * * *
26806 AAT AAT GAT AAT AGT TAT AAT -AT ATT ATT AAT AAT TAT AAT -AT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
26852 A
1 A
26853 TTTATAACCC
Statistics
Matches: 66, Mismatches: 24, Indels: 4
0.70 0.26 0.04
Matches are distributed among these distances:
2 4 0.06
3 62 0.94
ACGTcount: A:0.52, C:0.01, G:0.03, T:0.44
Consensus pattern (3 bp):
AAT
Found at i:26843 original size:20 final size:20
Alignment explanation
Indices: 26765--26859 Score: 75
Period size: 21 Copynumber: 4.7 Consensus size: 20
26755 AACAATATTA
* * *
26765 ATAATAATACTAATAATAATT
1 ATAATATTAATAATTATAA-T
* **
26786 ATAATTTTAATTGTTATAAT
1 ATAATATTAATAATTATAAT
*
26806 AATAATGA-TAATAGTTATAAT
1 -ATAAT-ATTAATAATTATAAT
*
26827 ATATTATTAATAATTATAAT
1 ATAATATTAATAATTATAAT
*
26847 ATAATATTTATAA
1 ATAATATTAATAA
26860 CCCAGACAAA
Statistics
Matches: 59, Mismatches: 12, Indels: 7
0.76 0.15 0.09
Matches are distributed among these distances:
19 1 0.02
20 28 0.47
21 30 0.51
ACGTcount: A:0.51, C:0.01, G:0.03, T:0.45
Consensus pattern (20 bp):
ATAATATTAATAATTATAAT
Found at i:27092 original size:53 final size:53
Alignment explanation
Indices: 27008--27179 Score: 258
Period size: 53 Copynumber: 3.2 Consensus size: 53
26998 CATCTTCTTT
* * *
27008 GAACAATCTTC-GACTAGCGGATTCGTTCCCTCTTGCTTTAGGGAGTAGAACTC
1 GAACAATCTTCTGCCTA-CGGGTTCGCTCCCTCTTGCTTTAGGGAGTAGAACTC
*
27061 AAACAATCTTCTGCCTACGGGTTCGCTCCCTCTTG-TTTCAGGGAGTAGAACTC
1 GAACAATCTTCTGCCTACGGGTTCGCTCCCTCTTGCTTT-AGGGAGTAGAACTC
* *
27114 GAATAATCTTCTGCCTACGGGTTCGCTCCCTCTTGCTTTAAGGAGTAGAACTC
1 GAACAATCTTCTGCCTACGGGTTCGCTCCCTCTTGCTTTAGGGAGTAGAACTC
27167 GAACAATCTTCTG
1 GAACAATCTTCTG
27180 GTGTGATTCT
Statistics
Matches: 108, Mismatches: 8, Indels: 6
0.89 0.07 0.05
Matches are distributed among these distances:
52 3 0.03
53 98 0.91
54 7 0.06
ACGTcount: A:0.22, C:0.26, G:0.21, T:0.31
Consensus pattern (53 bp):
GAACAATCTTCTGCCTACGGGTTCGCTCCCTCTTGCTTTAGGGAGTAGAACTC
Found at i:27236 original size:36 final size:36
Alignment explanation
Indices: 27189--27258 Score: 113
Period size: 36 Copynumber: 1.9 Consensus size: 36
27179 GGTGTGATTC
* **
27189 TGCTTCACTACTCTTCTGTGAAGGTTTAAGATGGTT
1 TGCTTCACTACTCTTCCGTGAAGGCATAAGATGGTT
27225 TGCTTCACTACTCTTCCGTGAAGGCATAAGATGG
1 TGCTTCACTACTCTTCCGTGAAGGCATAAGATGG
27259 CCCGGGGGAC
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 31 1.00
ACGTcount: A:0.21, C:0.20, G:0.23, T:0.36
Consensus pattern (36 bp):
TGCTTCACTACTCTTCCGTGAAGGCATAAGATGGTT
Found at i:27460 original size:42 final size:41
Alignment explanation
Indices: 27398--27480 Score: 139
Period size: 42 Copynumber: 2.0 Consensus size: 41
27388 TGCTCTTCTG
27398 TGAAGGCTTAAGATGGCCCGAAGGACTTAATCATCATGCTC
1 TGAAGGCTTAAGATGGCCCGAAGGACTTAATCATCATGCTC
* *
27439 TGAAGGCTTACTGATGGCCCGAAGGACTTTATCATCATGCTC
1 TGAAGGCTTA-AGATGGCCCGAAGGACTTAATCATCATGCTC
27481 GAAAGACTTA
Statistics
Matches: 39, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
41 10 0.26
42 29 0.74
ACGTcount: A:0.27, C:0.23, G:0.24, T:0.27
Consensus pattern (41 bp):
TGAAGGCTTAAGATGGCCCGAAGGACTTAATCATCATGCTC
Found at i:27579 original size:22 final size:21
Alignment explanation
Indices: 27551--27620 Score: 72
Period size: 22 Copynumber: 3.3 Consensus size: 21
27541 ACAAATTACC
27551 CGAAAGATTTAATCATCATGCT
1 CGAAAGATTTAA-CATCATGCT
* * *
27573 CGAAAGACTT-AC-TGATGGT
1 CGAAAGATTTAACATCATGCT
*
27592 CGAAGGATTTAAGCATCATGCT
1 CGAAAGATTTAA-CATCATGCT
27614 CGAAAGA
1 CGAAAGA
27621 CTTATTGATG
Statistics
Matches: 37, Mismatches: 8, Indels: 6
0.73 0.16 0.12
Matches are distributed among these distances:
19 13 0.35
20 2 0.05
21 2 0.05
22 20 0.54
ACGTcount: A:0.36, C:0.17, G:0.21, T:0.26
Consensus pattern (21 bp):
CGAAAGATTTAACATCATGCT
Found at i:27601 original size:41 final size:42
Alignment explanation
Indices: 27549--27640 Score: 141
Period size: 41 Copynumber: 2.2 Consensus size: 42
27539 TTACAAATTA
* *
27549 CCCGAAAGATTTAATCATCATGCTCGAAAGACTTACTGATGG
1 CCCGAAGGATTTAAGCATCATGCTCGAAAGACTTACTGATGG
* *
27591 -TCGAAGGATTTAAGCATCATGCTCGAAAGACTTATTGATGG
1 CCCGAAGGATTTAAGCATCATGCTCGAAAGACTTACTGATGG
27632 CCCGAAGGA
1 CCCGAAGGA
27641 CTTACTAAGT
Statistics
Matches: 44, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
41 37 0.84
42 7 0.16
ACGTcount: A:0.33, C:0.20, G:0.23, T:0.25
Consensus pattern (42 bp):
CCCGAAGGATTTAAGCATCATGCTCGAAAGACTTACTGATGG
Found at i:27619 original size:134 final size:134
Alignment explanation
Indices: 27379--27629 Score: 364
Period size: 134 Copynumber: 1.9 Consensus size: 134
27369 TTAAGATGGT
* * * * *
27379 TTGCTTCACTGCTCTTCTGTGAAGGCTTAAGATGGCCCGAAGGACTTAATCATCATGCTCTGAAG
1 TTGCTTCACTACTCTTCCGTGAAGGCTTAAAATGACCCGAAAGACTTAATCATCATGCTCTGAAG
* *
27444 GCTTACTGATGGCCCGAAGGACTTTATCATCATGCTCGAAAGACTTATTGATATCACTTACTGAT
66 ACTTACTGATGGCCCGAAGGACTTTAGCATCATGCTCGAAAGACTTATTGATATCACTTACTGAT
27509 GGGA
131 GGGA
* *
27513 TTGCTTCACTACTCTTCCGTGAAGGCTTACAAATTACCCGAAAGATTTAATCATCATGCTC-GAA
1 TTGCTTCACTACTCTTCCGTGAAGGCTTA-AAATGACCCGAAAGACTTAATCATCATGCTCTG-A
*
27577 AGACTTACTGATGG-TCGAAGGA-TTTAAGCATCATGCTCGAAAGACTTATTGAT
64 AGACTTACTGATGGCCCGAAGGACTTT-AGCATCATGCTCGAAAGACTTATTGAT
27630 GGCCCGAAGG
Statistics
Matches: 104, Mismatches: 10, Indels: 6
0.87 0.08 0.05
Matches are distributed among these distances:
133 3 0.03
134 61 0.59
135 40 0.38
ACGTcount: A:0.28, C:0.21, G:0.20, T:0.31
Consensus pattern (134 bp):
TTGCTTCACTACTCTTCCGTGAAGGCTTAAAATGACCCGAAAGACTTAATCATCATGCTCTGAAG
ACTTACTGATGGCCCGAAGGACTTTAGCATCATGCTCGAAAGACTTATTGATATCACTTACTGAT
GGGA
Found at i:27824 original size:42 final size:41
Alignment explanation
Indices: 27760--27860 Score: 121
Period size: 42 Copynumber: 2.4 Consensus size: 41
27750 ATGTCTTATG
* * * * *
27760 GATGACCCGAATGACTTATCATCTTGCTCTAAAGGCTTACA
1 GATGACTCGAAGGACTTATCATCATGCTCGAAAGACTTACA
* *
27801 GATGACTCGAAGGATTTCATCATCATGCTCGAAAGACTTACT
1 GATGACTCGAAGGACTT-ATCATCATGCTCGAAAGACTTACA
*
27843 GATGGCTCGAAGGACTTA
1 GATGACTCGAAGGACTTA
27861 AATTGTTTAC
Statistics
Matches: 50, Mismatches: 9, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
41 15 0.30
42 35 0.70
ACGTcount: A:0.30, C:0.22, G:0.21, T:0.28
Consensus pattern (41 bp):
GATGACTCGAAGGACTTATCATCATGCTCGAAAGACTTACA
Found at i:32173 original size:19 final size:19
Alignment explanation
Indices: 32149--32185 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
32139 ATGACCAACA
*
32149 AAATCGCAATGCGATCTCT
1 AAATCGCAACGCGATCTCT
32168 AAATCGCAACGCGATCTC
1 AAATCGCAACGCGATCTC
32186 CAGTATCGCA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.32, C:0.30, G:0.16, T:0.22
Consensus pattern (19 bp):
AAATCGCAACGCGATCTCT
Found at i:32337 original size:41 final size:41
Alignment explanation
Indices: 32292--32408 Score: 207
Period size: 41 Copynumber: 2.9 Consensus size: 41
32282 GAATATGTAA
*
32292 ATCGCAACGCGATAATACAAAATCGCAACGCGATTCTGACT
1 ATCGCAATGCGATAATACAAAATCGCAACGCGATTCTGACT
*
32333 ATCGCAATGCGATAATACATAATCGCAACGCGATTCTGACT
1 ATCGCAATGCGATAATACAAAATCGCAACGCGATTCTGACT
*
32374 ATCGCAATGCGATAATACAAAATCGCAATGCGATT
1 ATCGCAATGCGATAATACAAAATCGCAACGCGATT
32409 TTCCAAATTT
Statistics
Matches: 72, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 72 1.00
ACGTcount: A:0.37, C:0.24, G:0.17, T:0.22
Consensus pattern (41 bp):
ATCGCAATGCGATAATACAAAATCGCAACGCGATTCTGACT
Found at i:32338 original size:20 final size:20
Alignment explanation
Indices: 32313--32386 Score: 87
Period size: 20 Copynumber: 3.6 Consensus size: 20
32303 ATAATACAAA
32313 ATCGCAACGCGATTCTGACT
1 ATCGCAACGCGATTCTGACT
* **
32333 ATCGCAATGCGATAAT-ACAT
1 ATCGCAACGCGATTCTGAC-T
32353 AATCGCAACGCGATTCTGACT
1 -ATCGCAACGCGATTCTGACT
*
32374 ATCGCAATGCGAT
1 ATCGCAACGCGAT
32387 AATACAAAAT
Statistics
Matches: 44, Mismatches: 7, Indels: 6
0.77 0.12 0.11
Matches are distributed among these distances:
19 2 0.05
20 26 0.59
21 14 0.32
22 2 0.05
ACGTcount: A:0.31, C:0.26, G:0.19, T:0.24
Consensus pattern (20 bp):
ATCGCAACGCGATTCTGACT
Found at i:32415 original size:21 final size:21
Alignment explanation
Indices: 32290--32407 Score: 100
Period size: 21 Copynumber: 5.7 Consensus size: 21
32280 GCGAATATGT
*
32290 AAATCGCAACGCGATAATACA
1 AAATCGCAATGCGATAATACA
* **
32311 AAATCGCAACGCGATTCTGAC-
1 AAATCGCAATGCGATAAT-ACA
*
32332 -TATCGCAATGCGATAATACA
1 AAATCGCAATGCGATAATACA
* * **
32352 TAATCGCAACGCGATTCTGAC-
1 AAATCGCAATGCGATAAT-ACA
*
32373 -TATCGCAATGCGATAATACA
1 AAATCGCAATGCGATAATACA
32393 AAATCGCAATGCGAT
1 AAATCGCAATGCGAT
32408 TTTCCAAATT
Statistics
Matches: 76, Mismatches: 15, Indels: 12
0.74 0.15 0.12
Matches are distributed among these distances:
19 4 0.05
20 26 0.34
21 42 0.55
22 4 0.05
ACGTcount: A:0.38, C:0.24, G:0.17, T:0.21
Consensus pattern (21 bp):
AAATCGCAATGCGATAATACA
Found at i:32478 original size:40 final size:40
Alignment explanation
Indices: 32434--32521 Score: 149
Period size: 40 Copynumber: 2.2 Consensus size: 40
32424 AGTCCAAATT
*
32434 CGTTGCGATTTTCCAAATTCGTTGCGATAGTCGAAGTTCG
1 CGTTGCGATTTTCCAAATTCGTTGCGATAGTCCAAGTTCG
* *
32474 CGTTGTGATTTTCCAAATTTGTTGCGATAGTCCAAGTTCG
1 CGTTGCGATTTTCCAAATTCGTTGCGATAGTCCAAGTTCG
32514 CGTTGCGA
1 CGTTGCGA
32522 CTAAAATCGC
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
40 44 1.00
ACGTcount: A:0.19, C:0.19, G:0.25, T:0.36
Consensus pattern (40 bp):
CGTTGCGATTTTCCAAATTCGTTGCGATAGTCCAAGTTCG
Found at i:32507 original size:19 final size:19
Alignment explanation
Indices: 32423--32513 Score: 83
Period size: 19 Copynumber: 4.7 Consensus size: 19
32413 AAATTTACTT
32423 TAGTCCAAATTCGTTGCGA
1 TAGTCCAAATTCGTTGCGA
**
32442 TTTTCCAAATTCGTTGCGA
1 TAGTCCAAATTCGTTGCGA
* * *
32461 TAGTCGAAGTTCGCGTTGTGA
1 TAGTCCAAATT--CGTTGCGA
** *
32482 TTTTCCAAATTTGTTGCGA
1 TAGTCCAAATTCGTTGCGA
*
32501 TAGTCCAAGTTCG
1 TAGTCCAAATTCG
32514 CGTTGCGACT
Statistics
Matches: 53, Mismatches: 17, Indels: 4
0.72 0.23 0.05
Matches are distributed among these distances:
19 39 0.74
21 14 0.26
ACGTcount: A:0.22, C:0.19, G:0.22, T:0.37
Consensus pattern (19 bp):
TAGTCCAAATTCGTTGCGA
Found at i:32519 original size:21 final size:21
Alignment explanation
Indices: 32453--32521 Score: 70
Period size: 21 Copynumber: 3.4 Consensus size: 21
32443 TTTCCAAATT
*
32453 CGTTGCGATAGTCGAAGTTCG
1 CGTTGCGATAGTCCAAGTTCG
* ** *
32474 CGTTGTGATTTTCCAAATT--
1 CGTTGCGATAGTCCAAGTTCG
*
32493 TGTTGCGATAGTCCAAGTTCG
1 CGTTGCGATAGTCCAAGTTCG
32514 CGTTGCGA
1 CGTTGCGA
32522 CTAAAATCGC
Statistics
Matches: 35, Mismatches: 11, Indels: 4
0.70 0.22 0.08
Matches are distributed among these distances:
19 14 0.40
21 21 0.60
ACGTcount: A:0.19, C:0.19, G:0.28, T:0.35
Consensus pattern (21 bp):
CGTTGCGATAGTCCAAGTTCG
Found at i:32977 original size:22 final size:21
Alignment explanation
Indices: 32952--33008 Score: 55
Period size: 19 Copynumber: 2.7 Consensus size: 21
32942 ACTATCGCAA
*
32952 CAACACGTTTTTCAAACTCTCG
1 CAACAC-TTTTTCAAACTATCG
*
32974 CAACACATTTT--AACTATCG
1 CAACACTTTTTCAAACTATCG
*
32993 CAACATATTTTTCAAA
1 CAACA-CTTTTTCAAA
33009 ATCGCGTTGC
Statistics
Matches: 28, Mismatches: 4, Indels: 6
0.74 0.11 0.16
Matches are distributed among these distances:
19 12 0.43
20 4 0.14
21 4 0.14
22 8 0.29
ACGTcount: A:0.35, C:0.26, G:0.05, T:0.33
Consensus pattern (21 bp):
CAACACTTTTTCAAACTATCG
Found at i:32993 original size:19 final size:19
Alignment explanation
Indices: 32966--33003 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
32956 ACGTTTTTCA
*
32966 AACTCTCGCAACACATTTT
1 AACTATCGCAACACATTTT
*
32985 AACTATCGCAACATATTTT
1 AACTATCGCAACACATTTT
33004 TCAAAATCGC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.34, C:0.26, G:0.05, T:0.34
Consensus pattern (19 bp):
AACTATCGCAACACATTTT
Found at i:35235 original size:22 final size:22
Alignment explanation
Indices: 35207--35299 Score: 95
Period size: 22 Copynumber: 4.4 Consensus size: 22
35197 AATTTGGAAA
35207 ATCGCAACGACAACTGTAGACT
1 ATCGCAACGACAACTGTAGACT
* *
35229 TTCGCAACAACAACTGTAGACT
1 ATCGCAACGACAACTGTAGACT
* * **
35251 ATCGCAACG--AA-TTTGGAAA
1 ATCGCAACGACAACTGTAGACT
*
35270 ATCGCAACGAC-ATTGTAGACT
1 ATCGCAACGACAACTGTAGACT
35291 ATCGCAACG
1 ATCGCAACG
35300 CGAAATGGAA
Statistics
Matches: 56, Mismatches: 12, Indels: 7
0.75 0.16 0.09
Matches are distributed among these distances:
19 13 0.23
20 3 0.05
21 13 0.23
22 27 0.48
ACGTcount: A:0.37, C:0.25, G:0.18, T:0.20
Consensus pattern (22 bp):
ATCGCAACGACAACTGTAGACT
Found at i:35528 original size:41 final size:41
Alignment explanation
Indices: 35248--35511 Score: 428
Period size: 41 Copynumber: 6.5 Consensus size: 41
35238 ACAACTGTAG
* *
35248 ACTATCGCAA--CGAATTTGGAAAATCGCAACGAC-ATTGT-A
1 ACTATCGCAACGCGAA-ATGGAAAATCGCAACG-CGATTTTCA
35287 GACTATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCA
1 -ACTATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCA
*
35329 ACTATCGCAACGCAAAATGGAAAATCGCAACGCGATTTTCA
1 ACTATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCA
35370 ACTATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCA
1 ACTATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCA
*
35411 ACTATAGCAACGCGAAATGGAAAATCGCAACGCGATTTTCA
1 ACTATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCA
*
35452 ACTATCGCAACGCGAAATGGAAAATCGCAACGCGATTTCCA
1 ACTATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCA
35493 ACTATCGCAACGCGAAATG
1 ACTATCGCAACGCGAAATG
35512 CAACGCGAAT
Statistics
Matches: 213, Mismatches: 7, Indels: 7
0.94 0.03 0.03
Matches are distributed among these distances:
40 11 0.05
41 197 0.92
42 5 0.02
ACGTcount: A:0.38, C:0.24, G:0.19, T:0.19
Consensus pattern (41 bp):
ACTATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCA
Found at i:52038 original size:31 final size:33
Alignment explanation
Indices: 52003--52063 Score: 99
Period size: 31 Copynumber: 1.9 Consensus size: 33
51993 ATTTTTTTTA
*
52003 AATTTAATTACT-TAACTTTC-AAATTATTCCT
1 AATTTAATCACTCTAACTTTCAAAATTATTCCT
52034 AATTTAATCACTCTAACTTTCAAAATTATT
1 AATTTAATCACTCTAACTTTCAAAATTATT
52064 TTTTCTCTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
31 11 0.41
32 8 0.30
33 8 0.30
ACGTcount: A:0.38, C:0.16, G:0.00, T:0.46
Consensus pattern (33 bp):
AATTTAATCACTCTAACTTTCAAAATTATTCCT
Found at i:53697 original size:19 final size:19
Alignment explanation
Indices: 53669--53794 Score: 126
Period size: 19 Copynumber: 6.3 Consensus size: 19
53659 TTATTTTGAA
*
53669 TTTTTTACTATCGCAACAC
1 TTTTTAACTATCGCAACAC
* *
53688 TTTTTCACTATAGCAACAACAC
1 TTTTTAACTAT--C-GCAACAC
53710 ATTTTTCAAACTATCGCAACAC
1 -TTTTT--AACTATCGCAACAC
*
53732 ATTTTAACTATCGCAACAC
1 TTTTTAACTATCGCAACAC
*
53751 ATTTTAACTATCGCAACAC
1 TTTTTAACTATCGCAACAC
* *
53770 ATTTTAACTATCACAACAC
1 TTTTTAACTATCGCAACAC
53789 ATTTTT
1 -TTTTT
53795 CAAAATCGCG
Statistics
Matches: 93, Mismatches: 7, Indels: 13
0.82 0.06 0.12
Matches are distributed among these distances:
19 61 0.66
20 4 0.04
21 5 0.05
22 12 0.13
23 6 0.06
25 5 0.05
ACGTcount: A:0.35, C:0.25, G:0.04, T:0.36
Consensus pattern (19 bp):
TTTTTAACTATCGCAACAC
Found at i:53766 original size:38 final size:38
Alignment explanation
Indices: 53670--53793 Score: 158
Period size: 38 Copynumber: 3.1 Consensus size: 38
53660 TATTTTGAAT
* * *
53670 TTTTTACTATCGCAACACTTTTTCACTATAGCAACAACACA
1 TTTTAACTATCGCAACACATTTTAACTAT--C-ACAACACA
*
53711 TTTTTCAAACTATCGCAACACATTTTAACTATCGCAACACA
1 -TTTT--AACTATCGCAACACATTTTAACTATCACAACACA
53752 TTTTAACTATCGCAACACATTTTAACTATCACAACACA
1 TTTTAACTATCGCAACACATTTTAACTATCACAACACA
53790 TTTT
1 TTTT
53794 TCAAAATCGC
Statistics
Matches: 75, Mismatches: 5, Indels: 8
0.85 0.06 0.09
Matches are distributed among these distances:
38 37 0.49
40 4 0.05
41 7 0.09
42 5 0.07
44 22 0.29
ACGTcount: A:0.35, C:0.26, G:0.04, T:0.35
Consensus pattern (38 bp):
TTTTAACTATCGCAACACATTTTAACTATCACAACACA
Found at i:57291 original size:3 final size:3
Alignment explanation
Indices: 57283--57362 Score: 115
Period size: 3 Copynumber: 26.7 Consensus size: 3
57273 TAATATAAAT
* *
57283 TAA TAA TAA TAA TAA TAA TAA TAA TAA TGA TAA TAA TAT TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
** *
57331 TAA GGA TAA TAA TAA TAT TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
57363 TGGATAAAAA
Statistics
Matches: 67, Mismatches: 10, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
3 67 1.00
ACGTcount: A:0.61, C:0.00, G:0.04, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:58267 original size:113 final size:112
Alignment explanation
Indices: 57617--58264 Score: 924
Period size: 113 Copynumber: 5.7 Consensus size: 112
57607 TCTTGATGAG
*
57617 TTCTTCTCATTATGAACTT-TCTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTACCT
1 TTCTTCTCATTATGAACTTCT-TCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAAC-TTATCT
* *
57681 GGCAATGTTGATCCATCAAATGATGAATTCAAGCAAAAGGTTGAACAAA
64 GGAAATGTTGATCCATCAAATGATGAATTTAAGCAAAAGGTTGAACAAA
* * *
57730 TTCTTCTCATTATGAACTTATTTTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTACCTG
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAAC-TTATCTG
* * *
57795 GCAATGTTGATCCATCAAATGATGAATTTAGGTAAAAGGTTGAACAAA
65 GAAATGTTGATCCATCAAATGATGAATTTAAGCAAAAGGTTGAACAAA
* * *
57843 TTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAATTCTTCTCATTATGAACCTTCTCTG
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAA-CTTATCTG
* *
57908 GAAATGTTGATCCATCAAATGATGAATTTAGGTAAAAGGTTGAACAAA
65 GAAATGTTGATCCATCAAATGATGAATTTAAGCAAAAGGTTGAACAAA
* * *
57956 TTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAATTCTTCTCATTATGAACCTTCTCTG
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAA-CTTATCTG
* *
58021 GAAATGTTGATCCATCAAATGATGAATTTAAACAACAA-GTTGAACAAG
65 GAAATGTTGATCCATCAAATGATGAATTTAAGCAA-AAGGTTGAACAAA
* *
58069 TTCTTCTTATTATGAACTTCTTCTTCTTTCTTCAGATGAGTTCTTCTCATTATGAACTTATCTGG
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTATCTGG
* * * * * *
58134 TAATGAATGATCCATCAAGTGACGAATTTAAACAACAA-GTTGAACAAG
66 AAATG-TTGATCCATCAAATGATGAATTTAAGCAA-AAGGTTGAACAAA
*
58182 TTCTTCTCATTATGAACTTCTTCTTCTTTCTTCAGATGAGTTCTTCTCATTATGAACTTATCTGG
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTATCTGG
* *
58247 TAATGAATGATCCATCAA
66 AAATG-TTGATCCATCAA
58265 GTGGATTTGA
Statistics
Matches: 506, Mismatches: 25, Indels: 8
0.94 0.05 0.01
Matches are distributed among these distances:
112 12 0.02
113 490 0.97
114 4 0.01
ACGTcount: A:0.29, C:0.19, G:0.13, T:0.40
Consensus pattern (112 bp):
TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTATCTGG
AAATGTTGATCCATCAAATGATGAATTTAAGCAAAAGGTTGAACAAA
Found at i:58902 original size:50 final size:50
Alignment explanation
Indices: 58827--59068 Score: 448
Period size: 50 Copynumber: 4.8 Consensus size: 50
58817 ATACACTTCT
* *
58827 TCAGATCAAATAACTCAAAGAACACTTCCAGAAGATGTTATTCTGTCTAA
1 TCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTCTGTCTAA
*
58877 TCAGATCAGATAACTCAAAGAACACTTCTAGAAGATGCTATTCTGTCTAA
1 TCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTCTGTCTAA
58927 TCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTCTGTCTAA
1 TCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTCTGTCTAA
*
58977 TCAGATCAGATAACTCAAAGAACACTTCCAGAAGATACTATTCTGTCTAA
1 TCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTCTGTCTAA
59027 TCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATT
1 TCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATT
59069 GGTAAATTCA
Statistics
Matches: 186, Mismatches: 6, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
50 186 1.00
ACGTcount: A:0.39, C:0.21, G:0.13, T:0.26
Consensus pattern (50 bp):
TCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTCTGTCTAA
Found at i:59201 original size:131 final size:131
Alignment explanation
Indices: 58978--59220 Score: 477
Period size: 131 Copynumber: 1.9 Consensus size: 131
58968 TCTGTCTAAT
58978 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATACTATTCTGTCTAATCAGATCAGATAACTC
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATACTATTCTGTCTAATCAGATCAGATAACTC
59043 AAAGAACACTTCCAGAAGATGCTATTGGTAAATTCATCTTTCATTTACTGATTGGTTCTGTTCAA
66 AAAGAACACTTCCAGAAGATGCTATTGGTAAATTCATCTTTCATTTACTGATTGGTTCTGTTCAA
59108 C
131 C
*
59109 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTCTGTCTAATCAGATCAGATAACTC
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATACTATTCTGTCTAATCAGATCAGATAACTC
59174 AAAGAACACTTCCAGAAGATGCTATTGGTAAATTCATCTTTCATTTA
66 AAAGAACACTTCCAGAAGATGCTATTGGTAAATTCATCTTTCATTTA
59221 ATGTTTGGAC
Statistics
Matches: 111, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
131 111 1.00
ACGTcount: A:0.36, C:0.21, G:0.14, T:0.30
Consensus pattern (131 bp):
CAGATCAGATAACTCAAAGAACACTTCCAGAAGATACTATTCTGTCTAATCAGATCAGATAACTC
AAAGAACACTTCCAGAAGATGCTATTGGTAAATTCATCTTTCATTTACTGATTGGTTCTGTTCAA
C
Found at i:59996 original size:16 final size:17
Alignment explanation
Indices: 59958--60002 Score: 65
Period size: 18 Copynumber: 2.6 Consensus size: 17
59948 AATATAAAAG
*
59958 AATAAATTGAATTTCAAA
1 AATAAATTGAATCTC-AA
59976 AATAAATTGAATCTC-A
1 AATAAATTGAATCTCAA
59992 AATAAATTGAA
1 AATAAATTGAA
60003 CTTGAAATAG
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
16 12 0.46
18 14 0.54
ACGTcount: A:0.56, C:0.07, G:0.07, T:0.31
Consensus pattern (17 bp):
AATAAATTGAATCTCAA
Found at i:60347 original size:11 final size:11
Alignment explanation
Indices: 60331--60367 Score: 74
Period size: 11 Copynumber: 3.4 Consensus size: 11
60321 CTTGACCCCC
60331 CTTTTTTTTTT
1 CTTTTTTTTTT
60342 CTTTTTTTTTT
1 CTTTTTTTTTT
60353 CTTTTTTTTTT
1 CTTTTTTTTTT
60364 CTTT
1 CTTT
60368 AAGCATAATA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 26 1.00
ACGTcount: A:0.00, C:0.11, G:0.00, T:0.89
Consensus pattern (11 bp):
CTTTTTTTTTT
Found at i:70954 original size:13 final size:15
Alignment explanation
Indices: 70936--70969 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
70926 TTGACATAAA
70936 AAAATAC-TG-AAAT
1 AAAATACTTGCAAAT
70949 AAAATACTTGCAAAT
1 AAAATACTTGCAAAT
70964 AAAATA
1 AAAATA
70970 AAACATATAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 7 0.37
14 2 0.11
15 10 0.53
ACGTcount: A:0.62, C:0.09, G:0.06, T:0.24
Consensus pattern (15 bp):
AAAATACTTGCAAAT
Found at i:73082 original size:3 final size:3
Alignment explanation
Indices: 73074--73149 Score: 79
Period size: 3 Copynumber: 26.7 Consensus size: 3
73064 TAATATAAAT
* *
73074 TAA TAA TAA TAA TAA TAA TAA TAA TAA T-G TAA TAA TAT TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
** *
73121 TAA GGA T-A TAA T-A TAT TAA T-A TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
73150 TGGATAATAT
Statistics
Matches: 60, Mismatches: 9, Indels: 8
0.78 0.12 0.10
Matches are distributed among these distances:
2 7 0.12
3 53 0.88
ACGTcount: A:0.59, C:0.00, G:0.04, T:0.37
Consensus pattern (3 bp):
TAA
Found at i:73106 original size:23 final size:23
Alignment explanation
Indices: 73080--73148 Score: 79
Period size: 23 Copynumber: 3.0 Consensus size: 23
73070 AAATTAATAA
73080 TAATAATAATAATAATAATAATG
1 TAATAATAATAATAATAATAATG
*
73103 TAATAATATTAATAATAATAA-G
1 TAATAATAATAATAATAATAATG
*
73125 GATATAATATATTAAT-ATAATAAT
1 TA-ATAATA-A-TAATAATAATAAT
73149 ATGGATAATA
Statistics
Matches: 39, Mismatches: 3, Indels: 6
0.81 0.06 0.12
Matches are distributed among these distances:
22 2 0.05
23 26 0.67
24 7 0.18
25 4 0.10
ACGTcount: A:0.58, C:0.00, G:0.04, T:0.38
Consensus pattern (23 bp):
TAATAATAATAATAATAATAATG
Found at i:79381 original size:16 final size:17
Alignment explanation
Indices: 79360--79392 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
79350 TAAAAACTCT
*
79360 ACAAAA-ATTTAAAATG
1 ACAAAATATTGAAAATG
79376 ACAAAATATTGAAAATG
1 ACAAAATATTGAAAATG
79393 TAAAAACATA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.61, C:0.06, G:0.09, T:0.24
Consensus pattern (17 bp):
ACAAAATATTGAAAATG
Found at i:81552 original size:24 final size:25
Alignment explanation
Indices: 81517--81565 Score: 73
Period size: 24 Copynumber: 2.0 Consensus size: 25
81507 GAGAGGTTAC
*
81517 TATCATATTATATCT-AAATAAATT
1 TATCATAATATATCTCAAATAAATT
*
81541 TATCATAATATATCTCAACTAAATT
1 TATCATAATATATCTCAAATAAATT
81566 CATACATGAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 14 0.64
25 8 0.36
ACGTcount: A:0.45, C:0.12, G:0.00, T:0.43
Consensus pattern (25 bp):
TATCATAATATATCTCAAATAAATT
Found at i:82469 original size:40 final size:41
Alignment explanation
Indices: 82424--82520 Score: 160
Period size: 41 Copynumber: 2.4 Consensus size: 41
82414 TCTTCACCAC
82424 GGGATAGGGATGGGAGAAG-TTTATCCCCAAAGCTCAAATG
1 GGGATAGGGATGGGAGAAGTTTTATCCCCAAAGCTCAAATG
*
82464 GGGATAGGGATGGGGGAAGTTTTATCCCCAAAGCTCAAATG
1 GGGATAGGGATGGGAGAAGTTTTATCCCCAAAGCTCAAATG
*
82505 GGGATAAGGATAGGGA
1 GGGATAGGGAT-GGGA
82521 TTGTTATATC
Statistics
Matches: 52, Mismatches: 3, Indels: 2
0.91 0.05 0.04
Matches are distributed among these distances:
40 18 0.35
41 31 0.60
42 3 0.06
ACGTcount: A:0.32, C:0.12, G:0.36, T:0.20
Consensus pattern (41 bp):
GGGATAGGGATGGGAGAAGTTTTATCCCCAAAGCTCAAATG
Found at i:82531 original size:41 final size:41
Alignment explanation
Indices: 82424--82531 Score: 132
Period size: 41 Copynumber: 2.7 Consensus size: 41
82414 TCTTCACCAC
*
82424 GGGATAGGGATG-GGAGAAGTT-TATCCCCAAAGCTCAAATG
1 GGGATAAGGATGAGG-GAAGTTATATCCCCAAAGCTCAAATG
* * *
82464 GGGATAGGGATGGGGGAAGTTTTATCCCCAAAGCTCAAATG
1 GGGATAAGGATGAGGGAAGTTATATCCCCAAAGCTCAAATG
*
82505 GGGATAAGGAT-AGGGATTGTTATATCC
1 GGGATAAGGATGAGGGA-AGTTATATCC
82532 GAACCATGGA
Statistics
Matches: 61, Mismatches: 4, Indels: 5
0.87 0.06 0.07
Matches are distributed among these distances:
40 22 0.36
41 39 0.64
ACGTcount: A:0.31, C:0.13, G:0.33, T:0.23
Consensus pattern (41 bp):
GGGATAAGGATGAGGGAAGTTATATCCCCAAAGCTCAAATG
Found at i:84945 original size:33 final size:33
Alignment explanation
Indices: 84903--85022 Score: 213
Period size: 33 Copynumber: 3.6 Consensus size: 33
84893 TATATAATTC
84903 AACATGTCATTAATTATATTTCTTTTATGTAAA
1 AACATGTCATTAATTATATTTCTTTTATGTAAA
84936 AACATGTCATTAATTATATTTCTTTTATGTAAA
1 AACATGTCATTAATTATATTTCTTTTATGTAAA
84969 AACATGTCATTAATTATATTTCTTTTATGTAAA
1 AACATGTCATTAATTATATTTCTTTTATGTAAA
* * *
85002 AACATGCCATTAGTTTTATTT
1 AACATGTCATTAATTATATTT
85023 AATAATTAAA
Statistics
Matches: 84, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 84 1.00
ACGTcount: A:0.35, C:0.10, G:0.07, T:0.48
Consensus pattern (33 bp):
AACATGTCATTAATTATATTTCTTTTATGTAAA
Found at i:85776 original size:14 final size:14
Alignment explanation
Indices: 85757--85784 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
85747 CAATGCTAAT
85757 ACATGAGATAATTA
1 ACATGAGATAATTA
85771 ACATGAGATAATTA
1 ACATGAGATAATTA
85785 GAGACAAACA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.50, C:0.07, G:0.14, T:0.29
Consensus pattern (14 bp):
ACATGAGATAATTA
Found at i:86504 original size:33 final size:35
Alignment explanation
Indices: 86466--86556 Score: 132
Period size: 35 Copynumber: 2.7 Consensus size: 35
86456 TCTAACTTTG
*
86466 AATTACATTCTAAACCCCAAATTC-CAAA-ACTTC
1 AATTACATTCTAAACCCCAAATTCAAAAATACTTC
* *
86499 AATTACATTCTAAACCCCAAATTCAAAAATATTTT
1 AATTACATTCTAAACCCCAAATTCAAAAATACTTC
*
86534 AATTACATTCTAAACCCTAAATT
1 AATTACATTCTAAACCCCAAATT
86557 GAAGTATTTT
Statistics
Matches: 52, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
33 24 0.46
34 3 0.06
35 25 0.48
ACGTcount: A:0.44, C:0.24, G:0.00, T:0.32
Consensus pattern (35 bp):
AATTACATTCTAAACCCCAAATTCAAAAATACTTC
Found at i:86521 original size:19 final size:19
Alignment explanation
Indices: 86466--86521 Score: 50
Period size: 19 Copynumber: 3.2 Consensus size: 19
86456 TCTAACTTTG
86466 AATTACATTCTAAACCCCA
1 AATTACATTCTAAACCCCA
* **
86485 AATT-C---CAAAACTTC-
1 AATTACATTCTAAACCCCA
86499 AATTACATTCTAAACCCCA
1 AATTACATTCTAAACCCCA
86518 AATT
1 AATT
86522 CAAAAATATT
Statistics
Matches: 26, Mismatches: 6, Indels: 10
0.62 0.14 0.24
Matches are distributed among these distances:
14 4 0.15
15 7 0.27
18 7 0.27
19 8 0.31
ACGTcount: A:0.43, C:0.29, G:0.00, T:0.29
Consensus pattern (19 bp):
AATTACATTCTAAACCCCA
Found at i:86627 original size:35 final size:34
Alignment explanation
Indices: 86551--86628 Score: 86
Period size: 35 Copynumber: 2.2 Consensus size: 34
86541 TTCTAAACCC
* *
86551 TAAATTGAAGTATTTTTAAATTTAGGGTTTAAAA
1 TAAATTGAAGTATTTTGAAATTTAGAGTTTAAAA
* *
86585 TATAATTGAATTATTTTGAAATTT-GTAGTTTAGAA
1 TA-AATTGAAGTATTTTGAAATTTAG-AGTTTAAAA
86620 TGAAATTGA
1 T-AAATTGA
86629 GGATTATGTT
Statistics
Matches: 37, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
34 3 0.08
35 33 0.89
36 1 0.03
ACGTcount: A:0.40, C:0.00, G:0.15, T:0.45
Consensus pattern (34 bp):
TAAATTGAAGTATTTTGAAATTTAGAGTTTAAAA
Found at i:93139 original size:2 final size:2
Alignment explanation
Indices: 93132--93165 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
93122 ATGAATTTTA
93132 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
93166 TGTAATCTGT
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:97880 original size:14 final size:14
Alignment explanation
Indices: 97861--97890 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
97851 CAAACATTTA
97861 ATTTTAAGACAAAT
1 ATTTTAAGACAAAT
*
97875 ATTTTAAGACACAT
1 ATTTTAAGACAAAT
97889 AT
1 AT
97891 GAATACTTTT
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:0.47, C:0.10, G:0.07, T:0.37
Consensus pattern (14 bp):
ATTTTAAGACAAAT
Done.