Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002530.1 Hibiscus syriacus cultivar Beakdansim tig00005143_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: 72572
ACGTcount: A:0.32, C:0.18, G:0.16, T:0.35
Found at i:4495 original size:22 final size:22
Alignment explanation
Indices: 4467--4522 Score: 94
Period size: 22 Copynumber: 2.5 Consensus size: 22
4457 AGCTACCCCA
4467 TCAAACCTTTGAGCATCAAATG
1 TCAAACCTTTGAGCATCAAATG
*
4489 TCAAACCTTTAAGCATCAAATG
1 TCAAACCTTTGAGCATCAAATG
*
4511 CCAAACCTTTGA
1 TCAAACCTTTGA
4523 CTAAACACAA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.38, C:0.25, G:0.11, T:0.27
Consensus pattern (22 bp):
TCAAACCTTTGAGCATCAAATG
Found at i:5744 original size:105 final size:105
Alignment explanation
Indices: 5462--6700 Score: 1671
Period size: 105 Copynumber: 12.0 Consensus size: 105
5452 ATATCGTGTC
* * * **
5462 ACTCGAGACAACACAAGTTCAACTTCA-AACGAA-GGATGGCTGGTTGTCAAC--AAACTT-CCA
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAAAACTTCCCA
*
5522 A-TTCAGAGCCAATTTCAACTTCA-AGCG-AGGATATTGG
66 ATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* * * *
5559 ACTCCAGACAA--CAAG-TCAACTT--C-ACGAAGGGACTGCTAGTTGTCAACAACAACTTCTCA
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAAAACTTC-CC
5618 AATTTCAGAGCCAATTT-AACTTCACAACGAAGGATATTGG
65 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* * *
5658 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAATATTTCCCA
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAAAACTTCCCA
*
5723 ATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
66 ATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* * * *
5763 ACTCAAGACAACGCAAATTCAACTTCATGACG-AGGGACCGCTGGTTGTCAATAAACAACTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAA-AACTTCCC
*
5827 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
65 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* * * *
5868 ACT-CAGACAAAGCAAGTTCAACTT--C-ACGAAGGGATCGCTGGTTGTCAACAACAACTTCTCA
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAAAACTTCCCA
5929 ATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
66 ATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
*
5969 ACTCCAGATAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAA-AACTTCCC
* * **
6034 AATTTCAGAGCCAATTTGAATTTCACAACGAAAAATATTGG
65 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* * *
6075 ACTCGAGACAACGCAAGTTCAACTTCACGACG-AGGGACCGCTGGTTTTCAATAAACAACTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAA-AACTTCCC
* *
6139 AATTTCAGAGCCAATTTCAATTTCACAACGAA-AATATTGG
65 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* * *
6179 ACTCGAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAA-AACTTCCC
* *
6244 -ATTTCGGAGCCAATTTCAACTTCACAACGAATGATATTGG
65 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* * * * *
6284 ACTCCA-ACAACGCAAGTTCAACTTCACGACGAAGGGACTGTTGGTTGTCAATAAACATTTCCCA
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAAAACTTCCCA
* *
6348 ATTTC-GAGCCAATTTCAACTTCACAGCGAATGATATTGG
66 ATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
*
6387 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGA-CGCTGGTTGTCAACAAACAACTTCTC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAA-AACTTCCC
6451 AATTTCAGAGCCAATTTCAAC-TCACAACGAAGGATA-TGG
65 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* *
6490 ACTCCAGACAACGCAAGTTCAACTTCACGAAGAAGGAACCGCTGGTTGTCAACAAATAACTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAA-AACTTCCC
6555 -ATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
65 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* * * * *
6595 ACTCGAGACAACGCAAGTTCAACTTCACGACGAAGGGACTGCT-G--GTCACCAAACAATTTCTC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAA-AACTTCCC
* * *
6657 -ATTCCAGAGCCAATTTCAACTTCACGACGGAGGATATTGG
65 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
6697 ACTC
1 ACTC
6701 GAACAATGCT
Statistics
Matches: 1034, Mismatches: 76, Indels: 59
0.88 0.07 0.05
Matches are distributed among these distances:
92 5 0.00
93 15 0.01
94 7 0.01
95 9 0.01
97 20 0.02
98 17 0.02
99 21 0.02
101 57 0.06
102 101 0.10
103 119 0.12
104 277 0.27
105 312 0.30
106 74 0.07
ACGTcount: A:0.34, C:0.25, G:0.18, T:0.23
Consensus pattern (105 bp):
ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAAAACTTCCCA
ATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
Found at i:6205 original size:312 final size:312
Alignment explanation
Indices: 5462--6706 Score: 1750
Period size: 312 Copynumber: 4.0 Consensus size: 312
5452 ATATCGTGTC
* * * ** *
5462 ACTCGAGACAACACAAGTTCAACTTCA-AACGAAGGATGGCTGGTTGTC-A-ACA-AACTT-CCA
1 ACTCGAGACAACGCAAGTTCAACTTCACGACGAGGGACCGCTGGTTGTCAATAAACAACTTCCCA
*
5522 A-TTCAGAGCCAATTTCAACTTCA-AGCG-AGGATATTGGACTCCAGACAA--CAAG-TCAACTT
66 ATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTT
* *
5581 CACGAAGGGACTGCTAGTTGTCAACAACAACTTCTCAAATTTCAGAGCCAATTT-AACTTCACAA
131 CACGAAGGGACCGCTGGTTGTCAACAACAACTTC-C-AATTTCAGAGCCAATTTCAACTTCACAA
5645 CGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAA
194 CGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAA
* * *
5710 TAAA-TATTTCCCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
259 CAAACAATTTCCCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* * *
5763 ACTCAAGACAACGCAAATTCAACTTCATGACGAGGGACCGCTGGTTGTCAATAAACAACTTCCCA
1 ACTCGAGACAACGCAAGTTCAACTTCACGACGAGGGACCGCTGGTTGTCAATAAACAACTTCCCA
* *
5828 ATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACT-CAGACAAAGCAAGTTCAACTT
66 ATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTT
*
5892 CACGAAGGGATCGCTGGTTGTCAACAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAAC
131 CACGAAGGGACCGCTGGTTGTCAACAACAACTTC-CAATTTCAGAGCCAATTTCAACTTCACAAC
*
5957 GAAGGATATTGGACTCCAGATAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAAC
195 GAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAAC
* * * **
6022 AAACAACTTCCCAATTTCAGAGCCAATTTGAATTTCACAACGAAAAATATTGG
260 AAACAATTTCCCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
*
6075 ACTCGAGACAACGCAAGTTCAACTTCACGACGAGGGACCGCTGGTTTTCAATAAACAACTTCCCA
1 ACTCGAGACAACGCAAGTTCAACTTCACGACGAGGGACCGCTGGTTGTCAATAAACAACTTCCCA
* * *
6140 ATTTCAGAGCCAATTTCAATTTCACAACGAA-AATATTGGACTCGAGACAACGCAAGTTCAACTT
66 ATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTT
* * * *
6204 CACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCCATTTCGGAGCCAATTTCAACTTCAC
131 --C-ACGAAGGGACCGCTGGTTGTCAA-CAACAACTTCCAATTTCAGAGCCAATTTCAACTTCAC
* * *
6269 AACGAATGATATTGGACTCCA-ACAACGCAAGTTCAACTTCACGACGAAGGGACTGTTGGTTGTC
192 AACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTC
* * *
6333 AATAAAC-ATTTCCCAATTTC-GAGCCAATTTCAACTTCACAGCGAATGATATTGG
257 AACAAACAATTTCCCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* * *
6387 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGA-CGCTGGTTGTCAACAAACAACTTCTC
1 ACTCGAGACAACGCAAGTTCAACTTCACGACG-AGGGACCGCTGGTTGTCAATAAACAACTTCCC
6451 AATTTCAGAGCCAATTTCAAC-TCACAACGAAGGATA-TGGACTCCAGACAACGCAAGTTCAACT
65 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACT
* *
6514 TCACGAAGAAGGAACCGCTGGTTGTCAACAAATAACTTCCCATTTCAGAGCCAATTTCAACTTCA
130 TCACGAAG--GG-ACCGCTGGTTGTCAAC-AACAACTTCCAATTTCAGAGCCAATTTCAACTTCA
* *
6579 CAACGAAGGATATTGGACTCGAGACAACGCAAGTTCAACTTCACGACGAAGGGACTGCT-G--GT
191 CAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGT
* * * * *
6641 CACCAAACAATTTCTC-ATTCCAGAGCCAATTTCAACTTCACGACGGAGGATATTGG
256 CAACAAACAATTTCCCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
6697 ACTCGA-ACAA
1 ACTCGAGACAA
6707 TGCTACTTGG
Statistics
Matches: 849, Mismatches: 68, Indels: 46
0.88 0.07 0.05
Matches are distributed among these distances:
301 24 0.03
302 17 0.02
303 1 0.00
304 2 0.00
305 5 0.01
306 4 0.00
307 22 0.03
308 17 0.02
309 30 0.04
310 64 0.08
311 232 0.27
312 292 0.34
313 17 0.02
314 47 0.06
315 67 0.08
316 8 0.01
ACGTcount: A:0.34, C:0.25, G:0.18, T:0.23
Consensus pattern (312 bp):
ACTCGAGACAACGCAAGTTCAACTTCACGACGAGGGACCGCTGGTTGTCAATAAACAACTTCCCA
ATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTT
CACGAAGGGACCGCTGGTTGTCAACAACAACTTCCAATTTCAGAGCCAATTTCAACTTCACAACG
AAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACA
AACAATTTCCCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
Found at i:7520 original size:37 final size:37
Alignment explanation
Indices: 7430--7526 Score: 140
Period size: 37 Copynumber: 2.6 Consensus size: 37
7420 CCTTTTCGTC
7430 CTACTAGGATTCAAACTCCTAAAAATATGATAGAATT
1 CTACTAGGATTCAAACTCCTAAAAATATGATAGAATT
* * *
7467 TTGCTAGGATTCAAACTCCTAAAAATATGATAGAGTT
1 CTACTAGGATTCAAACTCCTAAAAATATGATAGAATT
** *
7504 CTACTATTATTTAAACTCCTAAA
1 CTACTAGGATTCAAACTCCTAAA
7527 GATAGGATCC
Statistics
Matches: 52, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
37 52 1.00
ACGTcount: A:0.40, C:0.16, G:0.10, T:0.33
Consensus pattern (37 bp):
CTACTAGGATTCAAACTCCTAAAAATATGATAGAATT
Found at i:8086 original size:100 final size:94
Alignment explanation
Indices: 7917--8108 Score: 242
Period size: 94 Copynumber: 2.0 Consensus size: 94
7907 ATTTAACTCT
* * *
7917 TATTATTTATATGTATATATATATATAATTATATTTTATTTATTTATTTATTATAATTTTTTTCA
1 TATTATTTATATATATATATATATATAATTATATTTTATTTATTTACTTATTATAATTTTTTACA
* *
7982 TTTTTCTTTACGTTATATATATTATTTTCC
66 TTTTTCCTAACGTTATATATA-TATTTTCC
* * *
8012 TATTA-TTATATATATATATATATATTATTATTTTTTATCTATGTTTACTTATTTACTATATTTT
1 TATTATTTATATATATATATATATATAATTATATTTTAT-T-TATTTACTTA-TTA-TA-ATTTT
8076 TTACTATTTTTCCTAACGTTATATATATATTTT
61 TTAC-ATTTTTCCTAACGTTATATATATATTTT
8109 ACTTCATTTT
Statistics
Matches: 83, Mismatches: 8, Indels: 8
0.84 0.08 0.08
Matches are distributed among these distances:
94 30 0.36
95 6 0.07
96 8 0.10
97 3 0.04
98 2 0.02
99 14 0.17
100 20 0.24
ACGTcount: A:0.30, C:0.06, G:0.02, T:0.62
Consensus pattern (94 bp):
TATTATTTATATATATATATATATATAATTATATTTTATTTATTTACTTATTATAATTTTTTACA
TTTTTCCTAACGTTATATATATATTTTCC
Found at i:8144 original size:100 final size:100
Alignment explanation
Indices: 7955--8148 Score: 234
Period size: 100 Copynumber: 1.9 Consensus size: 100
7945 TTATATTTTA
* * * * *
7955 TTTATTTATTTATTATAATTTTTTTCATTTTTCTTTACGTTATATATATTATTTTCCTATTATTA
1 TTTACTTATTTACTATAATTTTTTACATTTTTCCTAACGTTATATATATTATTTTCCTATTATTA
*
8020 TATATATATATATATATTATTATTTTTTATCTATG
66 TATATATATATATATATTACTATTTTTTATCTATG
*
8055 TTTACTTATTTACTAT-ATTTTTTACTATTTTTCCTAACGTTATATATA-TATTTTACTTCATT-
1 TTTACTTATTTACTATAATTTTTTAC-ATTTTTCCTAACGTTATATATATTATTTT-CCT-ATTA
* * *
8117 TTAT-TTTATATTTCTATGATTACTATTTTTTA
63 TTATATATATATATATAT-ATTACTATTTTTTA
8149 GTTAATATTA
Statistics
Matches: 80, Mismatches: 10, Indels: 8
0.82 0.10 0.08
Matches are distributed among these distances:
99 24 0.30
100 53 0.66
101 3 0.04
ACGTcount: A:0.27, C:0.08, G:0.02, T:0.63
Consensus pattern (100 bp):
TTTACTTATTTACTATAATTTTTTACATTTTTCCTAACGTTATATATATTATTTTCCTATTATTA
TATATATATATATATATTACTATTTTTTATCTATG
Found at i:8285 original size:26 final size:25
Alignment explanation
Indices: 8177--8286 Score: 83
Period size: 25 Copynumber: 4.5 Consensus size: 25
8167 TTTATTTTTC
8177 ATTTATTTATTATTTT-TACTATTT
1 ATTTATTTATTATTTTATACTATTT
* * **
8201 A-GTATTTTATTATATTATAC-ATAC
1 ATTTA-TTTATTATTTTATACTATTT
8225 A-TT-TTTA-TATTTTTATA-TATATT
1 ATTTATTTATTA-TTTTATACTAT-TT
8248 -TTTATTTTATTATTTTATACTATTT
1 ATTTA-TTTATTATTTTATACTATTT
8273 ATTTATTTCATTAT
1 ATTTATTT-ATTAT
8287 GTTTTAGTTT
Statistics
Matches: 66, Mismatches: 8, Indels: 22
0.69 0.08 0.23
Matches are distributed among these distances:
21 2 0.03
22 12 0.18
23 4 0.06
24 15 0.23
25 19 0.29
26 14 0.21
ACGTcount: A:0.29, C:0.05, G:0.01, T:0.65
Consensus pattern (25 bp):
ATTTATTTATTATTTTATACTATTT
Found at i:9567 original size:15 final size:16
Alignment explanation
Indices: 9538--9568 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
9528 TCTTCACTAC
9538 GTTTATTTCATTTTTT
1 GTTTATTTCATTTTTT
9554 GTTTATTT-ATTTTTT
1 GTTTATTTCATTTTTT
9569 AGAAAAAGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 7 0.47
16 8 0.53
ACGTcount: A:0.13, C:0.03, G:0.06, T:0.77
Consensus pattern (16 bp):
GTTTATTTCATTTTTT
Found at i:11702 original size:63 final size:62
Alignment explanation
Indices: 11586--11704 Score: 159
Period size: 63 Copynumber: 1.9 Consensus size: 62
11576 CCTCGACAAC
* * * *
11586 TGTCCATAGGTCTCAAAGAACCTAGGTAAACTGTCTATATGTTCCTTATAACATAGATATAA
1 TGTCCATAGGTCTCAAAGAACATAGGTAAACTGTCCATATGTTCCGTAGAACATAGATATAA
* *
11648 TGTCCATATGTCTCGAAAG-ACATAGGTAAAACTTTCCATATGTTCCGTAGAACATAG
1 TGTCCATAGGTCTC-AAAGAACATAGGT-AAACTGTCCATATGTTCCGTAGAACATAG
11705 GTAAACCCTC
Statistics
Matches: 49, Mismatches: 6, Indels: 3
0.84 0.10 0.05
Matches are distributed among these distances:
62 20 0.41
63 29 0.59
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.31
Consensus pattern (62 bp):
TGTCCATAGGTCTCAAAGAACATAGGTAAACTGTCCATATGTTCCGTAGAACATAGATATAA
Found at i:11703 original size:32 final size:32
Alignment explanation
Indices: 11602--11709 Score: 98
Period size: 31 Copynumber: 3.4 Consensus size: 32
11592 TAGGTCTCAA
* * *
11602 AGAACCTAGGT-AAACTGTCTATATGTTCCTT
1 AGAACATAGGTAAAACTGTCCATATGTTCCGT
* * *
11633 ATAACATAGATATAA-TGTCCATATG-TCTCG-
1 AGAACATAGGTAAAACTGTCCATATGTTC-CGT
* *
11663 AAAGACATAGGTAAAACTTTCCATATGTTCCGT
1 AGA-ACATAGGTAAAACTGTCCATATGTTCCGT
11696 AGAACATAGGTAAA
1 AGAACATAGGTAAA
11710 CCCTCGACTC
Statistics
Matches: 60, Mismatches: 11, Indels: 11
0.73 0.13 0.13
Matches are distributed among these distances:
30 4 0.07
31 28 0.47
32 24 0.40
33 4 0.07
ACGTcount: A:0.37, C:0.17, G:0.16, T:0.31
Consensus pattern (32 bp):
AGAACATAGGTAAAACTGTCCATATGTTCCGT
Found at i:13463 original size:22 final size:22
Alignment explanation
Indices: 13438--13556 Score: 184
Period size: 22 Copynumber: 5.4 Consensus size: 22
13428 TATTATGTCT
*
13438 CCGAAGGACCACTAGATACGTC
1 CCGAAGGACCACTGGATACGTC
* *
13460 CCGAATGACCATTGGATACGTC
1 CCGAAGGACCACTGGATACGTC
* *
13482 CCAAAAGACCACTGGATACGTC
1 CCGAAGGACCACTGGATACGTC
13504 CCGAAGGACCACTGGATACGTC
1 CCGAAGGACCACTGGATACGTC
13526 CCGAAGGACCACTGGATACGTC
1 CCGAAGGACCACTGGATACGTC
*
13548 TCGAAGGAC
1 CCGAAGGAC
13557 TAATATACCC
Statistics
Matches: 88, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 88 1.00
ACGTcount: A:0.30, C:0.30, G:0.24, T:0.15
Consensus pattern (22 bp):
CCGAAGGACCACTGGATACGTC
Found at i:14263 original size:2 final size:2
Alignment explanation
Indices: 14256--14293 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
14246 TACAAATTCC
14256 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
14294 CTCATGTAAT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:19529 original size:32 final size:31
Alignment explanation
Indices: 19428--19536 Score: 125
Period size: 31 Copynumber: 3.5 Consensus size: 31
19418 TAGGTCCCGA
* *
19428 AGAACCTAGGTAAACTGTTCATATGTTCCTT
1 AGAACATAGGTAAACTGTTCATATGTTCCGT
*
19459 AGAACATAGGTATACTGTTCATATG-TCTCG-
1 AGAACATAGGTAAACTGTTCATATGTTC-CGT
*
19489 AAAGACATAGGTAAAACT-TTCCATATGTTCCGT
1 AGA-ACATAGGT-AAACTGTT-CATATGTTCCGT
19522 AGAACATAGGTAAAC
1 AGAACATAGGTAAAC
19537 CCTTGACTCT
Statistics
Matches: 66, Mismatches: 6, Indels: 12
0.79 0.07 0.14
Matches are distributed among these distances:
30 4 0.06
31 38 0.58
32 20 0.30
33 4 0.06
ACGTcount: A:0.35, C:0.17, G:0.17, T:0.30
Consensus pattern (31 bp):
AGAACATAGGTAAACTGTTCATATGTTCCGT
Found at i:20487 original size:24 final size:20
Alignment explanation
Indices: 20430--20487 Score: 62
Period size: 20 Copynumber: 2.7 Consensus size: 20
20420 TTTCCCTTGA
*
20430 AGTGCATCGATACATTCTAC
1 AGTGCATCGATGCATTCTAC
*
20450 AGTGTATCGATGCATTCTTTAAC
1 AGTGCATCGATGCATTC--T-AC
20473 ATGTGCATCGATGCA
1 A-GTGCATCGATGCA
20488 CTACCCATGC
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
20 15 0.48
22 1 0.03
23 3 0.10
24 12 0.39
ACGTcount: A:0.28, C:0.21, G:0.19, T:0.33
Consensus pattern (20 bp):
AGTGCATCGATGCATTCTAC
Found at i:31904 original size:28 final size:28
Alignment explanation
Indices: 31867--31922 Score: 87
Period size: 28 Copynumber: 2.0 Consensus size: 28
31857 TTAATAGAGT
*
31867 ATAAAGTAAAATATA-TTTAATAAGTTAA
1 ATAAAATAAAATATATTTTAA-AAGTTAA
31895 ATAAAATAAAATATATTTTAAAAGTTAA
1 ATAAAATAAAATATATTTTAAAAGTTAA
31923 GATATAAAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
28 21 0.81
29 5 0.19
ACGTcount: A:0.59, C:0.00, G:0.05, T:0.36
Consensus pattern (28 bp):
ATAAAATAAAATATATTTTAAAAGTTAA
Found at i:31929 original size:26 final size:26
Alignment explanation
Indices: 31873--31940 Score: 77
Period size: 28 Copynumber: 2.5 Consensus size: 26
31863 GAGTATAAAG
31873 TAAAATATATTTAATAAGTTAAATAAAA
1 TAAAATATATTTAATAAGTTAAAT--AA
31901 TAAAATATATTTTAA-AAGTTAAGAT-A
1 TAAAATATA-TTTAATAAGTTAA-ATAA
31927 TAAAATATACTTTA
1 TAAAATATA-TTTA
31941 TTTTTTATTA
Statistics
Matches: 37, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
26 14 0.38
28 16 0.43
29 7 0.19
ACGTcount: A:0.56, C:0.01, G:0.04, T:0.38
Consensus pattern (26 bp):
TAAAATATATTTAATAAGTTAAATAA
Found at i:32923 original size:15 final size:16
Alignment explanation
Indices: 32902--32939 Score: 53
Period size: 15 Copynumber: 2.5 Consensus size: 16
32892 TCACCCACTG
32902 AATATTTTTTAT-TAA
1 AATATTTTTTATATAA
*
32917 TATA-TTTTTATATAA
1 AATATTTTTTATATAA
32932 AATATTTT
1 AATATTTT
32940 CAATTATATC
Statistics
Matches: 19, Mismatches: 2, Indels: 3
0.79 0.08 0.12
Matches are distributed among these distances:
14 7 0.37
15 9 0.47
16 3 0.16
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (16 bp):
AATATTTTTTATATAA
Found at i:39544 original size:17 final size:17
Alignment explanation
Indices: 39522--39559 Score: 76
Period size: 17 Copynumber: 2.2 Consensus size: 17
39512 ATTTTGATCA
39522 CTTATCACCGCTAATTT
1 CTTATCACCGCTAATTT
39539 CTTATCACCGCTAATTT
1 CTTATCACCGCTAATTT
39556 CTTA
1 CTTA
39560 AAGAAGAGAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.24, C:0.29, G:0.05, T:0.42
Consensus pattern (17 bp):
CTTATCACCGCTAATTT
Found at i:47533 original size:12 final size:12
Alignment explanation
Indices: 47516--47550 Score: 54
Period size: 12 Copynumber: 2.9 Consensus size: 12
47506 TATTTATTAT
47516 ATATTT-ATAAAA
1 ATATTTAAT-AAA
47528 ATATTTAATAAA
1 ATATTTAATAAA
47540 ATATTTAATAA
1 ATATTTAATAA
47551 TAAAAATACA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
12 20 0.91
13 2 0.09
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (12 bp):
ATATTTAATAAA
Found at i:49019 original size:3 final size:3
Alignment explanation
Indices: 49011--49150 Score: 172
Period size: 3 Copynumber: 46.7 Consensus size: 3
49001 TAATATAAAT
* * *
49011 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TGA TAA TAA TGA TAT TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
** * **
49059 TAA TAA TAA GGA TAA TAA TAA TAT TAA TAA TAA TAA GGA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* ** *
49107 TAT TAA TAA TAA TAA GGA TAA TAA TAA TAT TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
49151 TGGATAAAAA
Statistics
Matches: 113, Mismatches: 24, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
3 113 1.00
ACGTcount: A:0.60, C:0.00, G:0.06, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:49157 original size:27 final size:27
Alignment explanation
Indices: 49016--49148 Score: 239
Period size: 27 Copynumber: 4.9 Consensus size: 27
49006 TAAATTAATA
* *
49016 ATAATAATAATAATAATAATAATAATG
1 ATAATAATAATATTAATAATAATAAGG
*
49043 ATAATAATGATATTAATAATAATAAGG
1 ATAATAATAATATTAATAATAATAAGG
49070 ATAATAATAATATTAATAATAATAAGG
1 ATAATAATAATATTAATAATAATAAGG
49097 ATAATAATAATATTAATAATAATAAGG
1 ATAATAATAATATTAATAATAATAAGG
49124 ATAATAATAATATTAATAATAATAA
1 ATAATAATAATATTAATAATAATAA
49149 TATGGATAAA
Statistics
Matches: 102, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 102 1.00
ACGTcount: A:0.60, C:0.00, G:0.06, T:0.34
Consensus pattern (27 bp):
ATAATAATAATATTAATAATAATAAGG
Found at i:49599 original size:113 final size:113
Alignment explanation
Indices: 49401--49946 Score: 821
Period size: 113 Copynumber: 4.8 Consensus size: 113
49391 TCTTGATGAG
49401 TTCTTCTCATTATGAACTT-TCTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTAC-C
1 TTCTTCTCATTATGAACTTCT-TCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTT-CTC
* * * *
49464 TGGCAATGTTGATCCATCAAATGATGAATTCAAGCAAAAGGTTGAACAAA
64 TGGAAAAGCTGATCCATCAAATGATGGATTCAAGCAAAAGGTTGAACAAA
49514 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
* * * * *
49579 GAAAAGATGATTCACCAAATGATGGATTCAGGTAAAAGGTTGAACAAA
66 GAAAAGCTGATCCATCAAATGATGGATTCAAGCAAAAGGTTGAACAAA
* *
49627 TTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTCTCTG
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
* * * * * * * *
49692 GCAATGTTGATCCATCAAATGATGAATTTAAACAAAAAGTTGAACAAG
66 GAAAAGCTGATCCATCAAATGATGGATTCAAGCAAAAGGTTGAACAAA
*
49740 TTCTTCTCATTATGAACTTCTTCTTCTTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
* *
49805 GAAAAGCTGATCCATCAAATGACGGATTCAAG-TAAAGGTTGAACAAA
66 GAAAAGCTGATCCATCAAATGATGGATTCAAGCAAAAGGTTGAACAAA
* *
49852 TTCTTCTTATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATG-ACCTTCTCTG
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
*
49916 GAAAAGCTGTTCCATCAAATGATGGATTCAA
66 GAAAAGCTGATCCATCAAATGATGGATTCAA
49947 TCTTTGCTAA
Statistics
Matches: 391, Mismatches: 40, Indels: 6
0.89 0.09 0.01
Matches are distributed among these distances:
111 38 0.10
112 65 0.17
113 287 0.73
114 1 0.00
ACGTcount: A:0.28, C:0.20, G:0.14, T:0.38
Consensus pattern (113 bp):
TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
GAAAAGCTGATCCATCAAATGATGGATTCAAGCAAAAGGTTGAACAAA
Found at i:50807 original size:82 final size:82
Alignment explanation
Indices: 50559--50986 Score: 655
Period size: 82 Copynumber: 5.2 Consensus size: 82
50549 TTTACTATGA
* *
50559 GCAAATTCATCTTCCAAATTCAATGATTGTTCTG-TCCAACCAGATCAGATAACTTAAAGAACAC
1 GCAAATTCATCTTCCAAATTCAATGATTGTTCTGAT-AAACCAGATCAGATAACTCAAAGAACAC
50623 TTCCAGAAGATGCTATTG
65 TTCCAGAAGATGCTATTG
* * *
50641 GCAAATTCATCTTCCAAATTCAATGCTTGGTTCT-ATATAATCAGATCAAATAACTCAAAGAACA
1 GCAAATTCATCTTCCAAATTCAATGATT-GTTCTGATA-AACCAGATCAGATAACTCAAAGAACA
50705 CTTCCAGAAGATGCTATTG
64 CTTCCAGAAGATGCTATTG
* * *
50724 GCAAATTCATCTTCTAAATTCAATGATTGTTCTGCTAAACCAGGTCAGATAACTCAAAGAACACT
1 GCAAATTCATCTTCCAAATTCAATGATTGTTCTGATAAACCAGATCAGATAACTCAAAGAACACT
50789 TCCAGAAGATGCTATTG
66 TCCAGAAGATGCTATTG
* * *
50806 GCAAATTCATCTTCCAAATTCAATGCTTGGTTCT-ATATAATCAGATCAAATAACTCAAAGAACA
1 GCAAATTCATCTTCCAAATTCAATGATT-GTTCTGATA-AACCAGATCAGATAACTCAAAGAACA
50870 CTTCCAGAAGATGCTATTG
64 CTTCCAGAAGATGCTATTG
* * *
50889 GCAAATTCATCTTCTAAATTCAATGATTGTTCTGCTAAACCAGGTCAGATAACTCAAAGAACACT
1 GCAAATTCATCTTCCAAATTCAATGATTGTTCTGATAAACCAGATCAGATAACTCAAAGAACACT
50954 TCCAGAAGATGCTATTG
66 TCCAGAAGATGCTATTG
*
50971 GTAAATTCATCTTCCA
1 GCAAATTCATCTTCCA
50987 TTTAATGTTT
Statistics
Matches: 314, Mismatches: 25, Indels: 14
0.89 0.07 0.04
Matches are distributed among these distances:
82 163 0.52
83 151 0.48
ACGTcount: A:0.36, C:0.21, G:0.13, T:0.30
Consensus pattern (82 bp):
GCAAATTCATCTTCCAAATTCAATGATTGTTCTGATAAACCAGATCAGATAACTCAAAGAACACT
TCCAGAAGATGCTATTG
Found at i:50831 original size:165 final size:165
Alignment explanation
Indices: 50559--50986 Score: 795
Period size: 165 Copynumber: 2.6 Consensus size: 165
50549 TTTACTATGA
* * * *
50559 GCAAATTCATCTTCCAAATTCAATGATTGTTCTG-TCCAACCAGATCAGATAACTTAAAGAACAC
1 GCAAATTCATCTTCTAAATTCAATGATTGTTCTGCT-AAACCAGGTCAGATAACTCAAAGAACAC
50623 TTCCAGAAGATGCTATTGGCAAATTCATCTTCCAAATTCAATGCTTGGTTCTATATAATCAGATC
65 TTCCAGAAGATGCTATTGGCAAATTCATCTTCCAAATTCAATGCTTGGTTCTATATAATCAGATC
50688 AAATAACTCAAAGAACACTTCCAGAAGATGCTATTG
130 AAATAACTCAAAGAACACTTCCAGAAGATGCTATTG
50724 GCAAATTCATCTTCTAAATTCAATGATTGTTCTGCTAAACCAGGTCAGATAACTCAAAGAACACT
1 GCAAATTCATCTTCTAAATTCAATGATTGTTCTGCTAAACCAGGTCAGATAACTCAAAGAACACT
50789 TCCAGAAGATGCTATTGGCAAATTCATCTTCCAAATTCAATGCTTGGTTCTATATAATCAGATCA
66 TCCAGAAGATGCTATTGGCAAATTCATCTTCCAAATTCAATGCTTGGTTCTATATAATCAGATCA
50854 AATAACTCAAAGAACACTTCCAGAAGATGCTATTG
131 AATAACTCAAAGAACACTTCCAGAAGATGCTATTG
50889 GCAAATTCATCTTCTAAATTCAATGATTGTTCTGCTAAACCAGGTCAGATAACTCAAAGAACACT
1 GCAAATTCATCTTCTAAATTCAATGATTGTTCTGCTAAACCAGGTCAGATAACTCAAAGAACACT
*
50954 TCCAGAAGATGCTATTGGTAAATTCATCTTCCA
66 TCCAGAAGATGCTATTGGCAAATTCATCTTCCA
50987 TTTAATGTTT
Statistics
Matches: 257, Mismatches: 5, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
165 256 1.00
166 1 0.00
ACGTcount: A:0.36, C:0.21, G:0.13, T:0.30
Consensus pattern (165 bp):
GCAAATTCATCTTCTAAATTCAATGATTGTTCTGCTAAACCAGGTCAGATAACTCAAAGAACACT
TCCAGAAGATGCTATTGGCAAATTCATCTTCCAAATTCAATGCTTGGTTCTATATAATCAGATCA
AATAACTCAAAGAACACTTCCAGAAGATGCTATTG
Found at i:52127 original size:11 final size:11
Alignment explanation
Indices: 52111--52196 Score: 54
Period size: 11 Copynumber: 8.0 Consensus size: 11
52101 TGACCCCCTT
52111 TCTTTTTCTTC
1 TCTTTTTCTTC
*
52122 TCTTTTT-TTT
1 TCTTTTTCTTC
* *
52132 TCATTTTC-TA
1 TCTTTTTCTTC
52142 T-TTTTT-TTC
1 TCTTTTTCTTC
* *
52151 TATTTTTTTTC
1 TCTTTTTCTTC
* *
52162 TTTTCTTTCTTT
1 TCTT-TTTCTTC
*
52174 TCTTTTTCTTT
1 TCTTTTTCTTC
52185 TCTTTTTTCTTC
1 TC-TTTTTCTTC
52197 AAGCATTATA
Statistics
Matches: 59, Mismatches: 10, Indels: 11
0.74 0.12 0.14
Matches are distributed among these distances:
9 6 0.10
10 15 0.25
11 22 0.37
12 16 0.27
ACGTcount: A:0.03, C:0.17, G:0.00, T:0.79
Consensus pattern (11 bp):
TCTTTTTCTTC
Found at i:52149 original size:20 final size:21
Alignment explanation
Indices: 52114--52197 Score: 73
Period size: 20 Copynumber: 4.0 Consensus size: 21
52104 CCCCCTTTCT
* *
52114 TTTTCTTCTCTTTTTTTTTCA
1 TTTTCTTTTCTTTTTTATTCA
**
52135 TTTTCTATTT-TTTTTCTATTTT
1 TTTTCT-TTTCTTTTT-TATTCA
* *
52157 TTTTCTTTTCTTTCTT-TTCT
1 TTTTCTTTTCTTTTTTATTCA
*
52177 TTTTCTTTTCTTTTTTCTTCA
1 TTTTCTTTTCTTTTTTATTCA
52198 AGCATTATAT
Statistics
Matches: 51, Mismatches: 8, Indels: 8
0.76 0.12 0.12
Matches are distributed among these distances:
20 18 0.35
21 18 0.35
22 15 0.29
ACGTcount: A:0.05, C:0.17, G:0.00, T:0.79
Consensus pattern (21 bp):
TTTTCTTTTCTTTTTTATTCA
Found at i:52160 original size:43 final size:43
Alignment explanation
Indices: 52113--52194 Score: 112
Period size: 43 Copynumber: 1.9 Consensus size: 43
52103 ACCCCCTTTC
*
52113 TTTTTCTTCTCTTTTTTTTTCATTTTCTATT-TTTTTTCTATTT
1 TTTTTCTTCTC-TTTCTTTTCATTTTCTATTCTTTTTTCTATTT
* * *
52156 TTTTTCTTTTCTTTCTTTTCTTTTTCTTTTCTTTTTTCT
1 TTTTTCTTCTCTTTCTTTTCATTTTCTATTCTTTTTTCT
52195 TCAAGCATTA
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
42 16 0.47
43 18 0.53
ACGTcount: A:0.04, C:0.16, G:0.00, T:0.80
Consensus pattern (43 bp):
TTTTTCTTCTCTTTCTTTTCATTTTCTATTCTTTTTTCTATTT
Found at i:52192 original size:27 final size:26
Alignment explanation
Indices: 52115--52195 Score: 85
Period size: 25 Copynumber: 3.1 Consensus size: 26
52105 CCCCTTTCTT
* * *
52115 TTTCTTCTCTTTTTTTTTCATTTTCTA
1 TTTCTTTTCTTTTTTTTTC-TTTTTTC
*
52142 TTTTTTTTCTATTTTTTTTC--TTTTC
1 TTTCTTTTCT-TTTTTTTTCTTTTTTC
52167 TTTCTTTTCTTTTTCTTTTCTTTTTTC
1 TTTCTTTTCTTTTT-TTTTCTTTTTTC
52194 TT
1 TT
52196 CAAGCATTAT
Statistics
Matches: 45, Mismatches: 5, Indels: 8
0.78 0.09 0.14
Matches are distributed among these distances:
24 4 0.09
25 17 0.38
27 15 0.33
28 9 0.20
ACGTcount: A:0.04, C:0.16, G:0.00, T:0.80
Consensus pattern (26 bp):
TTTCTTTTCTTTTTTTTTCTTTTTTC
Found at i:57116 original size:70 final size:70
Alignment explanation
Indices: 57003--57142 Score: 280
Period size: 70 Copynumber: 2.0 Consensus size: 70
56993 TTTGATTGAG
57003 GATTTTCATCAAAGCATTCCTATGCGCTTCTGAATTCATCAAAAGATCAAGAATAGAAATTCTCG
1 GATTTTCATCAAAGCATTCCTATGCGCTTCTGAATTCATCAAAAGATCAAGAATAGAAATTCTCG
57068 CCTGT
66 CCTGT
57073 GATTTTCATCAAAGCATTCCTATGCGCTTCTGAATTCATCAAAAGATCAAGAATAGAAATTCTCG
1 GATTTTCATCAAAGCATTCCTATGCGCTTCTGAATTCATCAAAAGATCAAGAATAGAAATTCTCG
57138 CCTGT
66 CCTGT
57143 TGTTTGTGTA
Statistics
Matches: 70, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
70 70 1.00
ACGTcount: A:0.33, C:0.21, G:0.14, T:0.31
Consensus pattern (70 bp):
GATTTTCATCAAAGCATTCCTATGCGCTTCTGAATTCATCAAAAGATCAAGAATAGAAATTCTCG
CCTGT
Found at i:62919 original size:17 final size:17
Alignment explanation
Indices: 62879--62920 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 17
62869 ATACTTACAA
*
62879 ATAAAACATATAAATATT
1 ATAAAA-ATATAAATATC
62897 ATAAAAATAATAAATA-C
1 ATAAAAAT-ATAAATATC
62914 ATAAAAA
1 ATAAAAA
62921 ATTTGAAAAG
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
17 9 0.41
18 13 0.59
ACGTcount: A:0.69, C:0.05, G:0.00, T:0.26
Consensus pattern (17 bp):
ATAAAAATATAAATATC
Found at i:64592 original size:20 final size:20
Alignment explanation
Indices: 64569--64613 Score: 65
Period size: 20 Copynumber: 2.2 Consensus size: 20
64559 CGGTTCTGTC
*
64569 TCTCTTTTTTTTCTCTCGG-T
1 TCTCTGTTTTTTCTCT-GGTT
64589 TCTCTGTTTTTTCTCTGGTT
1 TCTCTGTTTTTTCTCTGGTT
64609 TCTCT
1 TCTCT
64614 CCTTTCTTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 2 0.09
20 21 0.91
ACGTcount: A:0.00, C:0.24, G:0.11, T:0.64
Consensus pattern (20 bp):
TCTCTGTTTTTTCTCTGGTT
Found at i:65085 original size:3 final size:3
Alignment explanation
Indices: 65079--65199 Score: 172
Period size: 3 Copynumber: 40.7 Consensus size: 3
65069 ATAATATATT
*
65079 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TGA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
** * **
65127 TAA TAA TAA TAA TAA TAA GGA T-A TAA TAA TAT TAA TAA TAA TAA GGA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
65174 TAA TAA TAA TAT TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TA
65200 TGGATAAAAA
Statistics
Matches: 104, Mismatches: 13, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
2 2 0.02
3 102 0.98
ACGTcount: A:0.62, C:0.00, G:0.04, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:69237 original size:3 final size:3
Alignment explanation
Indices: 69223--69285 Score: 65
Period size: 3 Copynumber: 21.0 Consensus size: 3
69213 TCATATCATT
* ** *
69223 TTA TTT TTA TTA TTA TTA TTA TTA AAA TTA GTA TTA TTA TTA TTA -TA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
*
69270 TATA TTA TTA TAA TTA
1 T-TA TTA TTA TTA TTA
69286 AATAAAAAAT
Statistics
Matches: 48, Mismatches: 10, Indels: 4
0.77 0.16 0.06
Matches are distributed among these distances:
2 2 0.04
3 43 0.90
4 3 0.06
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (3 bp):
TTA
Found at i:69375 original size:3 final size:3
Alignment explanation
Indices: 69355--69423 Score: 68
Period size: 3 Copynumber: 22.7 Consensus size: 3
69345 AATTTTTTCA
* * * * *
69355 TAT TAT TTT TAT TTT TAT TAT TAT TAT TAT TAT TAA AAT TAG TAT TA-
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
69402 TAT ATAT ATAT TAT TAT TAT TA
1 TAT -TAT -TAT TAT TAT TAT TA
69424 AATAAAAAAT
Statistics
Matches: 54, Mismatches: 10, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
2 2 0.04
3 45 0.83
4 7 0.13
ACGTcount: A:0.36, C:0.00, G:0.01, T:0.62
Consensus pattern (3 bp):
TAT
Found at i:69444 original size:138 final size:138
Alignment explanation
Indices: 69179--69592 Score: 670
Period size: 138 Copynumber: 3.0 Consensus size: 138
69169 CAACCAGCAG
*
69179 CATTTTTTATTGCCTTCTGTAAACACTAATTTTTTCATATCA-TTTTATTTTTATTATTATTATT
1 CATTTTTTATTGCCTTCTGTAAACACTAATTTTTTCATATTATTTTTATTTTTATTATTATTATT
** * *
69243 ATTAAAATTAGTATTATTATTAT-TATATATATTATTATAATTAAATAAAAAATACAAGGCCCAA
66 ATT---ATTAAAATTAGTATTATATATATATATTATTATTATTAAATAAAAAATACAAGGCCCAA
69307 AATCGCGGCAA
128 AATCGCGGCAA
69318 CATTTTTTATTGCCTTCTGTAAACACTAATTTTTTCATATTATTTTTATTTTTATTATTATTATT
1 CATTTTTTATTGCCTTCTGTAAACACTAATTTTTTCATATTATTTTTATTTTTATTATTATTATT
69383 ATTATTAAAATTAGTATTATATATATATATTATTATTATTAAATAAAAAATACAAGGCCCAAAAT
66 ATTATTAAAATTAGTATTATATATATATATTATTATTATTAAATAAAAAATACAAGGCCCAAAAT
* *
69448 CGGGGCAG
131 CGCGGCAA
*
69456 CATTTTTTATTGCCTTCTGTAAACACTAATTTTTTCATATTATTTTTATTTTTATTTTTATTATT
1 CATTTTTTATTGCCTTCTGTAAACACTAATTTTTTCATATTATTTTTATTTTTATTATTATTATT
69521 ATTATTAAAATTAGTATTATTATATATATATATATTATTATTATTAAATAAAAAATACAAGGCCC
66 ATTATTAAAATTAG---TA-T-TATATATATATATTATTATTATTAAATAAAAAATACAAGGCCC
69586 AAAATCG
126 AAAATCG
69593 GGGCCTGATT
Statistics
Matches: 260, Mismatches: 8, Indels: 10
0.94 0.03 0.04
Matches are distributed among these distances:
137 14 0.05
138 127 0.49
139 41 0.16
140 25 0.10
141 2 0.01
142 1 0.00
143 50 0.19
ACGTcount: A:0.37, C:0.10, G:0.06, T:0.48
Consensus pattern (138 bp):
CATTTTTTATTGCCTTCTGTAAACACTAATTTTTTCATATTATTTTTATTTTTATTATTATTATT
ATTATTAAAATTAGTATTATATATATATATTATTATTATTAAATAAAAAATACAAGGCCCAAAAT
CGCGGCAA
Found at i:69521 original size:3 final size:3
Alignment explanation
Indices: 69493--69566 Score: 67
Period size: 3 Copynumber: 23.7 Consensus size: 3
69483 AATTTTTTCA
* * * * * *
69493 TAT TAT TTT TAT TTT TAT TTT TAT TAT TAT TAT TAA AAT TAG TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
69541 TAT ATAT ATAT ATAT TAT TAT TAT TA
1 TAT -TAT -TAT -TAT TAT TAT TAT TA
69567 AATAAAAAAT
Statistics
Matches: 58, Mismatches: 12, Indels: 2
0.81 0.17 0.03
Matches are distributed among these distances:
3 47 0.81
4 11 0.19
ACGTcount: A:0.35, C:0.00, G:0.01, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:70880 original size:16 final size:17
Alignment explanation
Indices: 70837--70910 Score: 55
Period size: 17 Copynumber: 4.1 Consensus size: 17
70827 CACTACTTTC
70837 ATTTATTTTTACAAGTTTT
1 ATTTATTTTT-CAA-TTTT
70856 A-TTACTTTTT-AATTTT
1 ATTTA-TTTTTCAATTTT
*
70872 ATTTATTTTAGTCATTGTTT
1 ATTTATTTT--TCAAT-TTT
70892 ATTTATATTTT-AATTTT
1 ATTTAT-TTTTCAATTTT
70909 AT
1 AT
70911 ATGATTATAT
Statistics
Matches: 46, Mismatches: 2, Indels: 16
0.72 0.03 0.25
Matches are distributed among these distances:
16 9 0.20
17 10 0.22
18 6 0.13
19 9 0.20
20 9 0.20
21 3 0.07
ACGTcount: A:0.26, C:0.04, G:0.04, T:0.66
Consensus pattern (17 bp):
ATTTATTTTTCAATTTT
Done.