Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018825.1 Corchorus olitorius cultivar O-4 contig18858, 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: 50767
ACGTcount: A:0.33, C:0.19, G:0.15, T:0.32
Found at i:1719 original size:338 final size:330
Alignment explanation
Indices: 915--2561 Score: 1553
Period size: 329 Copynumber: 5.0 Consensus size: 330
905 TGTGGCTAAA
* * * * ** * *
915 AATTTTTGCAAAATTTTAACCGAAATC--GT-GAACCATCACTGTTTTTTTCCTAAAGACGTGTT
1 AATTGTTGCAAAATTTTAGCCGAAATCATGTCTAACCATCAC-GGTTTTTGGCTAAAAACGCGTT
* * *
977 CCGGAGCCTTAGGTCAGTTTTGCATGATTTTTTGTGGC-AAAACTCCTTGAAATATCTATATTCA
65 CCGGAGCCCTGGGTCAGTTTTGCATGATTTTTGGT-GCAAAAACTCCTTGAAATATCTATATTCA
* * * *
1041 TCTAACCAAATCTTAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATTTGAATCATGTTTC
129 TCTAACCAAATCTCAGCCACATTGGATTTAAGAATTTGTTTTTACAAGCATTTGAATCTTGTTTC
* * * * * * *
1106 GATTTAATTAAAAATTAATTTGGAAAAAGAGTAGGAAAAACGATATTAGAAGTGTGAGAAGCACT
194 GATTTAATTAGAAATTAATTCGGAAAAA-AAT-GGAAAAACAATATTAGAAGCGTGAAAAGCCCT
* * * * ** * * *
1171 TCAATCTTTTCGGCGTTGAATTATATATATTTTATGATTATTGTGGCTGAAAATTGAGAAAATA-
257 TCAATTTTTTTGGCGTTGAATTATATATTTTTTATGAGTATTGTGGCAAAAAATTAAAAAAAAAT
1235 TTTCGGGTC
322 TTTCGGGTC
* * * * * * *
1244 AATTTTTGCAAAACTTCAACCGAAATC--GTGT-ACCATCACAGTTTTTTGGCTAACAACGCGTT
1 AATTGTTGCAAAATTTTAGCCGAAATCATGTCTAACCATCAC-GGTTTTTGGCTAAAAACGCGTT
* * * * * * *
1306 CC-GAGCCCTCGACGT-AGTTTTGCATGGTTTTTGGCGTAAAGACTCCTTGAAATACCTATAATC
65 CCGGAGCCCT-G-GGTCAGTTTTGCATGATTTTTGGTGCAAAAACTCCTTGAAATATCTATATTC
* *
1369 ATCTAACCAAATCTCAGCCACATTGGATTTAAGAATTTGTTTTTACAAGTATTTGAATCTTGTAT
128 ATCTAACCAAATCTCAGCCACATTGGATTTAAGAATTTGTTTTTACAAGCATTTGAATCTTGTTT
* * * *
1434 CGAATTAATTAGAAATAAATTCGGGACAAAATGGAAAAACAATATTAGAAG-GTGAAAAGCCCTT
193 CGATTTAATTAGAAATTAATTCGGAAAAAAATGGAAAAACAATATTAGAAGCGTGAAAAGCCCTT
* *
1498 C-ATTTTTTTGGCGTTGAATTATAT-TTTTTTTTTAGTATTGTGGCAAAAAATTATAAAAAAAAA
258 CAATTTTTTTGGCGTTGAATTATATATTTTTTATGAGTATTGTGGCAAAAAA-T-T-----AAAA
*
1561 AAAATACTTTTCTGGTC
316 AAAA-A-TTTTCGGGTC
* * * * * *
1578 AGTTGTTGCAAAATTTTAAGTCGAAATCATATACTAACCATCACGGTTTTTGCCTGAAAATGCGT
1 AATTGTTGCAAAATTTT-AGCCGAAATCATGT-CTAACCATCACGGTTTTTGGCTAAAAACGCGT
* *
1643 TCCGGAGCCCTGGGTCAATTTTGCATGATTTTTGGTGCAAAAACTCCTTGAAATATCTTTATTCA
64 TCCGGAGCCCTGGGTCAGTTTTGCATGATTTTTGGTGCAAAAACTCCTTGAAATATCTATATTCA
* * * * *
1708 TCGAACCAAATCTCAGCCACATTGGATATAAGGATTTGTTTTTACAAGGATTTGAATTTTGTTTC
129 TCTAACCAAATCTCAGCCACATTGGATTTAAGAATTTGTTTTTACAAGCATTTGAATCTTGTTTC
* *
1773 GATTTAATTAGAAATTAATTTGGAAAAAAATGGAAAAACAATATTAGAAGCGTGAAAA-CCCGTC
194 GATTTAATTAGAAATTAATTCGGAAAAAAATGGAAAAACAATATTAGAAGCGTGAAAAGCCCTTC
* * * * *
1837 AATTTTTTTGGCATTCAATTATAT-TTTTTTCTGAGTATTGTGGCAAAAAAATTGAGAAAAAACT
259 AATTTTTTTGGCGTTGAATTATATATTTTTTATGAGTATTGTGGC-AAAAAATT-AAAAAAAAAT
1901 TTTCGGGT-
322 TTTCGGGTC
* * * ** * *
1909 --TAG-T------TTTTAGCCGAAATCGTGTACTTA--ATCACGGTTAATGGCTAAAAACACATT
1 AATTGTTGCAAAATTTTAGCCGAAATCATGT-CTAACCATCACGGTTTTTGGCTAAAAACGCGTT
* * * * * * * *
1963 TCGGGGCCCCGGGCTCAGTTTTGCGTGACTTTTGGTAG-AAAAAATCCTTGCAATATCGATATTC
65 CCGGAGCCCTGGG-TCAGTTTTGCATGATTTTTGGT-GCAAAAACTCCTTGAAATATCTATATTC
* * * *
2027 ATCTAACCAAATCTCAGCCACAATT-GATTTAAAAGATTTCTTTTTACGAGCATCTGAATCTTGT
128 ATCTAACCAAATCTCAGCCAC-ATTGGATTTAAGA-ATTTGTTTTTACAAGCATTTGAATCTTGT
* * * ** ** *
2091 TTCGATTTAATTAGAAATAAATTTGGAAAAAAATATGAAAAATGATATTAGATTCGTGAAAAGTC
191 TTCGATTTAATTAGAAATTAATTCGGAAAAAAAT-GGAAAAACAATATTAGAAGCGTGAAAAGCC
* ** *
2156 CTTCAATTTTTTTGGCGTTGAATTATATATTTTTTCTGAGTATTGTGGCAATGAATTGAAGAAAA
255 CTTCAATTTTTTTGGCGTTGAATTATATATTTTTTATGAGTATTGTGGCAAAAAATT-AAAAAAA
2221 AATTTTCGGGTC
319 AATTTTCGGGTC
* * ** *
2233 AATTTTTGCAAAATTTTAGCCGAAAT-A-GTTTAGTCATCACGATTTTTGGCTAAAAACGCGTTC
1 AATTGTTGCAAAATTTTAGCCGAAATCATGTCTAACCATCACGGTTTTTGGCTAAAAACGCGTTC
* * * * * * *
2296 TGGGGCCCTTGCTCAGTTTTGCATGATTTTTGGCGTAAATAA-TCCTTGAAATATCCATATTCAT
66 CGGAGCCCTGGGTCAGTTTTGCATGATTTTTGGTGCAAA-AACTCCTTGAAATATCTATATTCAT
* * ** *
2360 CGAACCAAATC-CTAGCCACATTCGATTTAACG-ATTTGTTTTTATGAGCATTCATCTAAATCTT
130 CTAACCAAATCTC-AGCCACATTGGATTTAA-GAATTTGTTTTTACAAGCA-T--T-TGAATCTT
* * *
2423 GTTTCGATTTAATTAGAAATTAATTCGGCAAAAAATGGAAAAACAATATTAGAAGCGTAAAAAAC
189 GTTTCGATTTAATTAGAAATTAATTCGGAAAAAAATGGAAAAACAATATTAGAAGCGTGAAAAGC
* * * * *
2488 TCTTCAATCTTTTTGGCATTGAATTATATATTTTTTATGAGTATTGTGACAAAAAAAATTGAGAA
254 CCTTCAATTTTTTTGGCGTTGAATTATATATTTTTTATGAGTATTGTGGC--AAAAAATT-AAAA
2553 AAAAATTTT
316 AAAAATTTT
2562 TCGAGTAAGT
Statistics
Matches: 1082, Mismatches: 182, Indels: 102
0.79 0.13 0.07
Matches are distributed among these distances:
319 30 0.03
320 67 0.06
321 76 0.07
322 26 0.02
323 48 0.04
324 40 0.04
325 22 0.02
326 14 0.01
327 19 0.02
328 10 0.01
329 177 0.16
330 23 0.02
331 73 0.07
332 41 0.04
333 79 0.07
334 68 0.06
335 26 0.02
337 3 0.00
338 172 0.16
339 62 0.06
340 6 0.01
ACGTcount: A:0.33, C:0.14, G:0.17, T:0.36
Consensus pattern (330 bp):
AATTGTTGCAAAATTTTAGCCGAAATCATGTCTAACCATCACGGTTTTTGGCTAAAAACGCGTTC
CGGAGCCCTGGGTCAGTTTTGCATGATTTTTGGTGCAAAAACTCCTTGAAATATCTATATTCATC
TAACCAAATCTCAGCCACATTGGATTTAAGAATTTGTTTTTACAAGCATTTGAATCTTGTTTCGA
TTTAATTAGAAATTAATTCGGAAAAAAATGGAAAAACAATATTAGAAGCGTGAAAAGCCCTTCAA
TTTTTTTGGCGTTGAATTATATATTTTTTATGAGTATTGTGGCAAAAAATTAAAAAAAAATTTTC
GGGTC
Found at i:5073 original size:51 final size:51
Alignment explanation
Indices: 5012--5166 Score: 211
Period size: 51 Copynumber: 3.0 Consensus size: 51
5002 TGCATCTCCT
* * * * * *
5012 CCACCACCAAAGAAACCATATCATCCACCAGGCCACTACAAATCACCGCCA
1 CCACCACCAAAGCACCCACAACACCCACCAGGCCACTACAAATCACCACCA
*
5063 CCACCCCCAAAGCACCCACAACACCCACCAGGCCACTACAAATCACCACCA
1 CCACCACCAAAGCACCCACAACACCCACCAGGCCACTACAAATCACCACCA
* * * *
5114 CCACCACCAAAGCACCCGCACCACCCACCAGGCCATTACAAGTCACCACCA
1 CCACCACCAAAGCACCCACAACACCCACCAGGCCACTACAAATCACCACCA
5165 CC
1 CC
5167 TCTAAAGCAT
Statistics
Matches: 92, Mismatches: 12, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
51 92 1.00
ACGTcount: A:0.36, C:0.50, G:0.08, T:0.06
Consensus pattern (51 bp):
CCACCACCAAAGCACCCACAACACCCACCAGGCCACTACAAATCACCACCA
Found at i:5290 original size:48 final size:48
Alignment explanation
Indices: 5237--5754 Score: 685
Period size: 48 Copynumber: 11.1 Consensus size: 48
5227 TCCTCCCCCA
* * * *
5237 CCATATCACCCCAAGACACCATATGTTCCTCTTCCTAAGCTTTCTCCT
1 CCATCTCACCCCAAGACACCCTATGTTCCTCTTCCCAAGCTTCCTCCT
* * *
5285 CCATATCTCCCCAAGACACCCTATGTTCCTCTTCCCAAGCTTTCTCCT
1 CCATCTCACCCCAAGACACCCTATGTTCCTCTTCCCAAGCTTCCTCCT
* * *
5333 CCATATCTCCCCAAGACACCCTATGTTCCTCTTCCGAAGCTTCCTCCT
1 CCATCTCACCCCAAGACACCCTATGTTCCTCTTCCCAAGCTTCCTCCT
* * *
5381 CCATCTCTCCCCAAGACACCATATGTTCCTCTTCCGAAGCTTCCTCCT
1 CCATCTCACCCCAAGACACCCTATGTTCCTCTTCCCAAGCTTCCTCCT
* *
5429 CCATCTCTCCCCAAGACACCATATGTTCCTCTTCCCAAGCTTCCTCCT
1 CCATCTCACCCCAAGACACCCTATGTTCCTCTTCCCAAGCTTCCTCCT
*
5477 CCATCTCACCCCAAGTAAACCCTATGTTCCTCTTCCCAAGCTTCCTCCT
1 CCATCTCACCCCAAG-ACACCCTATGTTCCTCTTCCCAAGCTTCCTCCT
*
5526 CCATCTCACCCCAAGAAACCCTATGTTCCTCTTCCCAAGCTTCCTCCT
1 CCATCTCACCCCAAGACACCCTATGTTCCTCTTCCCAAGCTTCCTCCT
5574 CCATCTCA--CC--G-C-CCCTATGTTCCTCTTCCCAAGCTTCCTCCT
1 CCATCTCACCCCAAGACACCCTATGTTCCTCTTCCCAAGCTTCCTCCT
* *
5616 CCATCTCACCCCAAGAAACCCTATGTTCCTCTTCCTAAGCTTCCTCCT
1 CCATCTCACCCCAAGACACCCTATGTTCCTCTTCCCAAGCTTCCTCCT
*
5664 CCATCT------AAGAAACCCTATGTTCCTCTTCCCAAGCTTCCTCCT
1 CCATCTCACCCCAAGACACCCTATGTTCCTCTTCCCAAGCTTCCTCCT
* * * *
5706 CCATCT------AAGAAACCCTACGTCCCTCTTCCCAAGCTTCCTCCC
1 CCATCTCACCCCAAGACACCCTATGTTCCTCTTCCCAAGCTTCCTCCT
5748 CCATCTC
1 CCATCTC
5755 CATACCTTTA
Statistics
Matches: 444, Mismatches: 18, Indels: 21
0.92 0.04 0.04
Matches are distributed among these distances:
42 118 0.27
44 3 0.01
46 3 0.01
48 274 0.62
49 46 0.10
ACGTcount: A:0.19, C:0.45, G:0.07, T:0.29
Consensus pattern (48 bp):
CCATCTCACCCCAAGACACCCTATGTTCCTCTTCCCAAGCTTCCTCCT
Found at i:6182 original size:60 final size:60
Alignment explanation
Indices: 6113--6242 Score: 188
Period size: 60 Copynumber: 2.2 Consensus size: 60
6103 GCCAAAATGT
* * *
6113 TCAATTAAGGACTCAATCTTTTAATTTGGCCAAATAAGAGCCTAACGTTATCGAAAATAC
1 TCAAATAAGGACCCAATCTTTTAATTTAGCCAAATAAGAGCCTAACGTTATCGAAAATAC
** * * *
6173 TCAAATAAGGACCCGGTCTTTTAATTTAGCCAAATAAGGGTCTAACGTTATCGAAAATGC
1 TCAAATAAGGACCCAATCTTTTAATTTAGCCAAATAAGAGCCTAACGTTATCGAAAATAC
6233 TCAAATAAGG
1 TCAAATAAGG
6243 GCATGGCGTC
Statistics
Matches: 62, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
60 62 1.00
ACGTcount: A:0.38, C:0.18, G:0.16, T:0.28
Consensus pattern (60 bp):
TCAAATAAGGACCCAATCTTTTAATTTAGCCAAATAAGAGCCTAACGTTATCGAAAATAC
Found at i:6456 original size:60 final size:60
Alignment explanation
Indices: 6289--6448 Score: 212
Period size: 60 Copynumber: 2.6 Consensus size: 60
6279 ACGCCAAGCC
* * *
6289 CTTATTTGAGCATTTTGGCAAACATTAGGCCTTTATTTGGCCAAATTAAAAGATCGGGCC
1 CTTATTTGAGCATTTTGGCAAACATTAGGCCCTTATTTGGCCAAATTAAAAGATCAGGCA
* * * * * *
6349 CCTATTTGAACATTTTGGTAAACATTAGGTCCTTATTTGGCCAAATTAAAATATCATGCA
1 CTTATTTGAGCATTTTGGCAAACATTAGGCCCTTATTTGGCCAAATTAAAAGATCAGGCA
* *
6409 TTTATTTGAGCATTTTGACAAACATTTAGGCCCTTATTTG
1 CTTATTTGAGCATTTTGGCAAACA-TTAGGCCCTTATTTG
6449 AACAATTAGC
Statistics
Matches: 84, Mismatches: 15, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
60 70 0.83
61 14 0.17
ACGTcount: A:0.29, C:0.17, G:0.16, T:0.38
Consensus pattern (60 bp):
CTTATTTGAGCATTTTGGCAAACATTAGGCCCTTATTTGGCCAAATTAAAAGATCAGGCA
Found at i:7884 original size:54 final size:54
Alignment explanation
Indices: 7820--7938 Score: 166
Period size: 54 Copynumber: 2.2 Consensus size: 54
7810 TGCATCTCCT
* * *
7820 CCACCACCAAAGCAACCGTATCATCCACCAGGCCACTACAAATCACCACCACCA
1 CCACCACCAAAGCAACCGCACCACCCACCAGGCCACTACAAATCACCACCACCA
* * * *
7874 CCACCCCCAAAGCACCCGCACCACCCACCAGGCCATTACAAGTCACCACCACCA
1 CCACCACCAAAGCAACCGCACCACCCACCAGGCCACTACAAATCACCACCACCA
*
7928 CCACCTCCAAA
1 CCACCACCAAA
7939 ACGTCTTCCT
Statistics
Matches: 57, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
54 57 1.00
ACGTcount: A:0.34, C:0.50, G:0.08, T:0.08
Consensus pattern (54 bp):
CCACCACCAAAGCAACCGCACCACCCACCAGGCCACTACAAATCACCACCACCA
Found at i:8278 original size:42 final size:42
Alignment explanation
Indices: 8222--8357 Score: 155
Period size: 42 Copynumber: 3.1 Consensus size: 42
8212 CCCCAAGACA
*
8222 CCCTATGTTCCTCTTCCTAAGCTTCCTCCTCCATCTCACCAC
1 CCCTATGTTCCTCTTCCCAAGCTTCCTCCTCCATCTCACCAC
*
8264 CCCTATGTTCCTCTTCCCAAGCTTCCTCCTCCATCTCACCGC
1 CCCTATGTTCCTCTTCCCAAGCTTCCTCCTCCATCTCACCAC
* * * * *
8306 CCTTATGCCCCTCCACTTCTCCCCAAGCTTCCTCCTCCATCTCGCCTC
1 CCCTATG----TTC-C-TCTTCCCAAGCTTCCTCCTCCATCTCACCAC
8354 CCCT
1 CCCT
8358 CAACAATCCG
Statistics
Matches: 80, Mismatches: 8, Indels: 6
0.85 0.09 0.06
Matches are distributed among these distances:
42 46 0.57
46 2 0.03
47 1 0.01
48 31 0.39
ACGTcount: A:0.12, C:0.51, G:0.06, T:0.31
Consensus pattern (42 bp):
CCCTATGTTCCTCTTCCCAAGCTTCCTCCTCCATCTCACCAC
Found at i:14559 original size:18 final size:19
Alignment explanation
Indices: 14531--14569 Score: 71
Period size: 18 Copynumber: 2.1 Consensus size: 19
14521 GAGCCGGGGG
14531 GGGGGGATACATTTGAGGT
1 GGGGGGATACATTTGAGGT
14550 GGGGGG-TACATTTGAGGT
1 GGGGGGATACATTTGAGGT
14568 GG
1 GG
14570 CGGATAAACT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 14 0.70
19 6 0.30
ACGTcount: A:0.18, C:0.05, G:0.51, T:0.26
Consensus pattern (19 bp):
GGGGGGATACATTTGAGGT
Found at i:22809 original size:48 final size:48
Alignment explanation
Indices: 22752--23569 Score: 306
Period size: 48 Copynumber: 17.2 Consensus size: 48
22742 ACCTCCCACC
* * * *
22752 TACTACTATAAGTCTCCGCCACCGCCTTCTCCATCACCTCCTCCTCCC
1 TACTACTATAAGTCTCCCCCACCACCATCTCCATCACCTCCTCCTCCA
* * * *
22800 TACGT-CTATAAGTC-CCCTCCACCACCATCCCCATCTCCACCTCCACCA
1 TAC-TACTATAAGTCTCCC-CCACCACCATCTCCATCACCTCCTCCTCCA
* * * *
22848 TACTATTATAAGTCTCCCCCACCACCGTCTCCTTCACCTCCTCCTCCT
1 TACTACTATAAGTCTCCCCCACCACCATCTCCATCACCTCCTCCTCCA
** * * * * * * * * *
22896 TA-TGTGTACAAATCTCCTCCACCTCCATCGCCATCTCCCCCTCCACCT
1 TACT-ACTATAAGTCTCCCCCACCACCATCTCCATCACCTCCTCCTCCA
* * * * * * * * *
22944 TACTATTACAAGTCACCCCCACCTCCTTCCCCTTCTCCTCCTCCTCCT
1 TACTACTATAAGTCTCCCCCACCACCATCTCCATCACCTCCTCCTCCA
* * * * * * * *
22992 TACTACTACAAGTCACCACCTCCACCATCTCCTAGC-CCACCACCACCA
1 TACTACTATAAGTCTCCCCCACCACCATCTCC-ATCACCTCCTCCTCCA
* * * * * *
23040 TATTACTACAAGTCACCACC-CCACCATCTCCTAGTCCACCACCACCT---
1 TACTACTATAAGTCTCCCCCACCACCATCTCC-A-T-CACCTCCTCCTCCA
* * * * * * * *
23087 TACCACTACAAGTCACCACCTCCACCATCTCC-T-AGTCCACCACCACCA
1 TACTACTATAAGTCTCCCCCACCACCATCTCCATCA--CCTCCTCCTCCA
* * * *** * * *
23135 TACTACTACAAGTCTCCACCTCCACCATCTCCAAGTCCACCACCACCA
1 TACTACTATAAGTCTCCCCCACCACCATCTCCATCACCTCCTCCTCCA
* * * * *
23183 TACTACTATAAGTCACCACC-CCACCCTCTCCATCACCACCTCCTCCT
1 TACTACTATAAGTCTCCCCCACCACCATCTCCATCACCTCCTCCTCCA
* * * * * *
23230 TACTACTACAAGTCACCACCTCCACCATCTCC-T-AGTCC-CCACCACCA
1 TACTACTATAAGTCTCCCCCACCACCATCTCCATCA--CCTCCTCCTCCA
* * * * * *
23277 TACTACTACAAGTCACCACCC-CCACCATCTCCCTCACCACCACCTCCT
1 TACTACTATAAGTCTCC-CCCACCACCATCTCCATCACCTCCTCCTCCA
* * * * *** * *
23325 TACTACTACAAGTCTCCACCACCACCTTCACCAAGTCCTCCGCCACCA
1 TACTACTATAAGTCTCCCCCACCACCATCTCCATCACCTCCTCCTCCA
* * * *
23373 TACTAC---AAGTCACCACCC-CCACCATCTCCATCACCACCACCCCCA
1 TACTACTATAAGTCTCC-CCCACCACCATCTCCATCACCTCCTCCTCCA
* * * * * * * * * *
23418 TACTACTACAAATCTCCTCCTCCACCATCTCCTTCTCCACCACCACCT
1 TACTACTATAAGTCTCCCCCACCACCATCTCCATCACCTCCTCCTCCA
* * * * * * * * *
23466 TACTACTACAAATCTCCACCACCTCCTTCTCCATCACCACCACCACCT
1 TACTACTATAAGTCTCCCCCACCACCATCTCCATCACCTCCTCCTCCA
* * * * * * * *
23514 TACTATTATAAGTCACCCCCTCCACCATCTCCCTCTCCACCACCTCCC
1 TACTACTATAAGTCTCCCCCACCACCATCTCCATCACCTCCTCCTCCA
23562 TACTACTA
1 TACTACTA
23570 CAAATCACCT
Statistics
Matches: 614, Mismatches: 125, Indels: 62
0.77 0.16 0.08
Matches are distributed among these distances:
43 1 0.00
45 41 0.07
46 3 0.00
47 115 0.19
48 438 0.71
49 8 0.01
50 8 0.01
ACGTcount: A:0.24, C:0.50, G:0.03, T:0.22
Consensus pattern (48 bp):
TACTACTATAAGTCTCCCCCACCACCATCTCCATCACCTCCTCCTCCA
Found at i:23038 original size:96 final size:96
Alignment explanation
Indices: 22738--23578 Score: 662
Period size: 96 Copynumber: 8.8 Consensus size: 96
22728 CACAAGTCTC
* * * * * * * * * * *
22738 CACCACCTCCCACC-TACTACTATAAGTCTCCGCCACCGCCTTCTCCATCACCTCCTCCTCCCTA
1 CACCACC-ACCACCATACTACTACAAGTCTCCACCACCACCATCTCCTTCTCCACCACCACCTTA
* * * *
22802 CGT-CTATAAGTCCCCTCCACCACCATCCCCAT
65 C-TACTACAAGTCACCACCACCACCATCTCCAT
* * * * * * * * * *
22834 CTCCACCTCCACCATACTATTATAAGTCTCCCCCACCACCGTCTCCTTCACCTCCTCCTCCTTA-
1 CACCACCACCACCATACTACTACAAGTCTCCACCACCACCATCTCCTTCTCCACCACCACCTTAC
** * * * * *
22898 TGTGTACAAATCTCCTCCACCTCCATCGCCAT
66 T-ACTACAAGTCACCACCACCACCATCTCCAT
* * * * * * * * * * * * *
22930 CTCCCCCTCCACCTTACTATTACAAGTCACCCCCACCTCCTTCCCCTTCTCCTCCTCCTCCTTAC
1 CACCACCACCACCATACTACTACAAGTCTCCACCACCACCATCTCCTTCTCCACCACCACCTTAC
* *
22995 TACTACAAGTCACCACCTCCACCATCTCCTAG
66 TACTACAAGTCACCACCACCACCATCTCC-AT
* * **
23027 C-CCACCACCACCATATTACTACAAGTCACCACC-CCACCATCTCCTAGTCCACCACCACCTTAC
1 CACCACCACCACCATACTACTACAAGTCTCCACCACCACCATCTCCTTCTCCACCACCACCTTAC
* *
23090 CACTACAAGTCACCACCTCCACCATCTCC-T
66 TACTACAAGTCACCACCACCACCATCTCCAT
* *** *
23120 -AGTCCACCACCACCATACTACTACAAGTCTCCACCTCCACCATCTCCAAGTCCACCACCACCAT
1 CA--CCACCACCACCATACTACTACAAGTCTCCACCACCACCATCTCCTTCTCCACCACCACCTT
* *
23184 ACTACTATAAGTCACCACC-CCACCCTCTCCAT
64 ACTACTACAAGTCACCACCACCACCATCTCCAT
* * * * * ** *
23216 CACCACCTCCTCCTTACTACTACAAGTCACCACCTCCACCATCTCCTAGTCC-CCACCACCATAC
1 CACCACCACCACCATACTACTACAAGTCTCCACCACCACCATCTCCTTCTCCACCACCACCTTAC
* *
23280 TACTACAAGTCACCACCCCCACCATCTCCCT
66 TACTACAAGTCACCACCACCACCATCTCCAT
* * * * *** * *
23311 CACCACCACCTCCTTACTACTACAAGTCTCCACCACCACCTTCACCAAGTCCTCCGCCACC--A-
1 CACCACCACCACCATACTACTACAAGTCTCCACCACCACCATCTCCTTCTCCACCACCACCTTAC
*
23373 TACTACAAGTCACCACCCCCACCATCTCCAT
66 TACTACAAGTCACCACCACCACCATCTCCAT
* * * *
23404 CACCACCACCCCCATACTACTACAAATCTCCTCCTCCACCATCTCCTTCTCCACCACCACCTTAC
1 CACCACCACCACCATACTACTACAAGTCTCCACCACCACCATCTCCTTCTCCACCACCACCTTAC
* * * *
23469 TACTACAAATCTCCACCACCTCCTTCTCCAT
66 TACTACAAGTCACCACCACCACCATCTCCAT
* * * * * * * * *
23500 CACCACCACCACCTTACTATTATAAGTCACCCCCTCCACCATCTCCCTCTCCACCACCTCCCTAC
1 CACCACCACCACCATACTACTACAAGTCTCCACCACCACCATCTCCTTCTCCACCACCACCTTAC
*
23565 TACTACAAATCACC
66 TACTACAAGTCACC
23579 TCCTCCTCCA
Statistics
Matches: 631, Mismatches: 98, Indels: 32
0.83 0.13 0.04
Matches are distributed among these distances:
93 79 0.13
94 30 0.05
95 198 0.31
96 320 0.51
97 4 0.01
ACGTcount: A:0.24, C:0.50, G:0.03, T:0.22
Consensus pattern (96 bp):
CACCACCACCACCATACTACTACAAGTCTCCACCACCACCATCTCCTTCTCCACCACCACCTTAC
TACTACAAGTCACCACCACCACCATCTCCAT
Found at i:23108 original size:95 final size:96
Alignment explanation
Indices: 22989--23584 Score: 690
Period size: 95 Copynumber: 6.3 Consensus size: 96
22979 TCCTCCTCCT
* *
22989 CCTTACTACTACAAGTCACCACCTCCACCATCTCCTAGC-CCACCACCACCATATTACTACAAGT
1 CCTTACTACTACAAGTCACCACCTCCACCATCTCC-ATCACCACCACCACCATACTACTACAAGT
23053 CACCACC-CCACCATCTCCTAGTCCACCACCA
65 CACCACCTCCACCATCTCCTAGTCCACCACCA
*
23084 CCTTACCACTACAAGTCACCACCTCCACCATCTCC-T-AGTCCACCACCACCATACTACTACAAG
1 CCTTACTACTACAAGTCACCACCTCCACCATCTCCATCA--CCACCACCACCATACTACTACAAG
* *
23147 TCTCCACCTCCACCATCTCCAAGTCCACCACCA
64 TCACCACCTCCACCATCTCCTAGTCCACCACCA
* * * * * *
23180 CCATACTACTATAAGTCACCACC-CCACCCTCTCCATCACCACCTCCTCCTTACTACTACAAGTC
1 CCTTACTACTACAAGTCACCACCTCCACCATCTCCATCACCACCACCACCATACTACTACAAGTC
23244 ACCACCTCCACCATCTCCTAGTCC-CCACCA
66 ACCACCTCCACCATCTCCTAGTCCACCACCA
* * * * *
23274 CCATACTACTACAAGTCACCACCCCCACCATCTCCCTCACCACCACCTCCTTACTACTACAAGTC
1 CCTTACTACTACAAGTCACCACCTCCACCATCTCCATCACCACCACCACCATACTACTACAAGTC
* * * * * * *
23339 TCCACCACCACCTTCACCAAGTCCTCCGCCA
66 ACCACCTCCACCATCTCCTAGTCCACCACCA
* * *
23370 CC--A-TACTACAAGTCACCACCCCCACCATCTCCATCACCACCACCCCCATACTACTACAAATC
1 CCTTACTACTACAAGTCACCACCTCCACCATCTCCATCACCACCACCACCATACTACTACAAGTC
* * **
23432 TCCTCCTCCACCATCTCCTTCTCCACCACCA
66 ACCACCTCCACCATCTCCTAGTCCACCACCA
* * * * * * * *
23463 CCTTACTACTACAAATCTCCACCACCTCCTTCTCCATCACCACCACCACCTTACTATTATAAGTC
1 CCTTACTACTACAAGTCACCACCTCCACCATCTCCATCACCACCACCACCATACTACTACAAGTC
* * *
23528 ACCCCCTCCACCATCTCCCT-CTCCACCACCT
66 ACCACCTCCACCATCT-CCTAGTCCACCACCA
* * *
23559 CCCTACTACTACAAATCACCTCCTCC
1 CCTTACTACTACAAGTCACCACCTCC
23585 TCCAATGAAG
Statistics
Matches: 435, Mismatches: 54, Indels: 23
0.85 0.11 0.04
Matches are distributed among these distances:
93 79 0.18
94 29 0.07
95 177 0.41
96 146 0.34
97 4 0.01
ACGTcount: A:0.27, C:0.50, G:0.03, T:0.20
Consensus pattern (96 bp):
CCTTACTACTACAAGTCACCACCTCCACCATCTCCATCACCACCACCACCATACTACTACAAGTC
ACCACCTCCACCATCTCCTAGTCCACCACCA
Found at i:23449 original size:15 final size:15
Alignment explanation
Indices: 23429--23459 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
23419 ACTACTACAA
23429 ATCTCCTCCTCCACC
1 ATCTCCTCCTCCACC
*
23444 ATCTCCTTCTCCACC
1 ATCTCCTCCTCCACC
23459 A
1 A
23460 CCACCTTACT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.16, C:0.55, G:0.00, T:0.29
Consensus pattern (15 bp):
ATCTCCTCCTCCACC
Found at i:23553 original size:15 final size:15
Alignment explanation
Indices: 23533--23562 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
23523 AAGTCACCCC
*
23533 CTCCACCATCTCCCT
1 CTCCACCACCTCCCT
23548 CTCCACCACCTCCCT
1 CTCCACCACCTCCCT
23563 ACTACTACAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.13, C:0.63, G:0.00, T:0.23
Consensus pattern (15 bp):
CTCCACCACCTCCCT
Found at i:23578 original size:48 final size:48
Alignment explanation
Indices: 22920--23584 Score: 598
Period size: 48 Copynumber: 14.0 Consensus size: 48
22910 TCCTCCACCT
* * * * * * * *
22920 CCATCGCCATCTCCCCCTCCACCTTACTATTACAAGTCACCCCCACCT
1 CCATCTCCCTCTCCACCACCACCTTACTACTACAAGTCACCACCTCCA
* * * *
22968 CCTTC-CCCTTCTCCTCCTCCTCCTTACTACTACAAGTCACCACCTCCA
1 CCATCTCCC-TCTCCACCACCACCTTACTACTACAAGTCACCACCTCCA
* *
23016 CCATCT-CCTAGC-CCACCACCACCATATTACTACAAGTCACCACC-CCA
1 CCATCTCCCT--CTCCACCACCACCTTACTACTACAAGTCACCACCTCCA
* *
23063 CCATCT-CCTAGTCCACCACCACCTTACCACTACAAGTCACCACCTCCA
1 CCATCTCCCT-CTCCACCACCACCTTACTACTACAAGTCACCACCTCCA
* * *
23111 CCATCT-CCTAGTCCACCACCACCATACTACTACAAGTCTCCACCTCCA
1 CCATCTCCCT-CTCCACCACCACCTTACTACTACAAGTCACCACCTCCA
*** * *
23159 CCATCTCCAAGTCCACCACCACCATACTACTATAAGTCACCACC-CCA
1 CCATCTCCCTCTCCACCACCACCTTACTACTACAAGTCACCACCTCCA
* * * * *
23206 CCCTCTCCATCACCACCTCCTCCTTACTACTACAAGTCACCACCTCCA
1 CCATCTCCCTCTCCACCACCACCTTACTACTACAAGTCACCACCTCCA
* * *
23254 CCATCT-CCTAGTCC-CCACCACCATACTACTACAAGTCACCACCCCCA
1 CCATCTCCCT-CTCCACCACCACCTTACTACTACAAGTCACCACCTCCA
* * * *
23301 CCATCTCCCTCACCACCACCTCCTTACTACTACAAGTCTCCACCACCA
1 CCATCTCCCTCTCCACCACCACCTTACTACTACAAGTCACCACCTCCA
* * *** * * *
23349 CCTTCACCAAGTCCTCCGCCACC--A-TACTACAAGTCACCACCCCCA
1 CCATCTCCCTCTCCACCACCACCTTACTACTACAAGTCACCACCTCCA
* * * * * * *
23394 CCATCTCCATCACCACCACCCCCATACTACTACAAATCTCCTCCTCCA
1 CCATCTCCCTCTCCACCACCACCTTACTACTACAAGTCACCACCTCCA
* * * * *
23442 CCATCTCCTTCTCCACCACCACCTTACTACTACAAATCTCCACCACCT
1 CCATCTCCCTCTCCACCACCACCTTACTACTACAAGTCACCACCTCCA
* * * * * *
23490 CCTTCTCCATCACCACCACCACCTTACTATTATAAGTCACCCCCTCCA
1 CCATCTCCCTCTCCACCACCACCTTACTACTACAAGTCACCACCTCCA
* * * *
23538 CCATCTCCCTCTCCACCACCTCCCTACTACTACAAATCACCTCCTCC
1 CCATCTCCCTCTCCACCACCACCTTACTACTACAAGTCACCACCTCC
23585 TCCAATGAAG
Statistics
Matches: 506, Mismatches: 97, Indels: 28
0.80 0.15 0.04
Matches are distributed among these distances:
45 34 0.07
46 1 0.00
47 123 0.24
48 346 0.68
49 2 0.00
ACGTcount: A:0.25, C:0.51, G:0.03, T:0.21
Consensus pattern (48 bp):
CCATCTCCCTCTCCACCACCACCTTACTACTACAAGTCACCACCTCCA
Found at i:23587 original size:96 final size:96
Alignment explanation
Indices: 22920--23584 Score: 643
Period size: 95 Copynumber: 7.0 Consensus size: 96
22910 TCCTCCACCT
* * * * * * * * * * *
22920 CCATCGCCATCTCCCCCTCCACCTTACTATTACAAGTCACCCCCACCTCCTTC-CCCTTCTCCTC
1 CCATCTCCATCACCACCACCACCATACTACTACAAGTCACCACCTCCACCATCTCCC-TCTCCAC
* *
22984 CTCCTCCTTACTACTACAAGTCACCACCTCCA
65 CACCACCTTACTACTACAAGTCACCACCTCCA
* * *
23016 CCATCTCCTAGC-CCACCACCACCATATTACTACAAGTCACCACC-CCACCATCT-CCTAGTCCA
1 CCATCTCC-ATCACCACCACCACCATACTACTACAAGTCACCACCTCCACCATCTCCCT-CTCCA
*
23078 CCACCACCTTACCACTACAAGTCACCACCTCCA
64 CCACCACCTTACTACTACAAGTCACCACCTCCA
* ***
23111 CCATCTCC-T-AGTCCACCACCACCATACTACTACAAGTCTCCACCTCCACCATCTCCAAGTCCA
1 CCATCTCCATCA--CCACCACCACCATACTACTACAAGTCACCACCTCCACCATCTCCCTCTCCA
* *
23174 CCACCACCATACTACTATAAGTCACCACC-CCA
64 CCACCACCTTACTACTACAAGTCACCACCTCCA
* * * * *
23206 CCCTCTCCATCACCACCTCCTCCTTACTACTACAAGTCACCACCTCCACCATCT-CCTAGTCC-C
1 CCATCTCCATCACCACCACCACCATACTACTACAAGTCACCACCTCCACCATCTCCCT-CTCCAC
* *
23269 CACCACCATACTACTACAAGTCACCACCCCCA
65 CACCACCTTACTACTACAAGTCACCACCTCCA
* * * * * * * *** *
23301 CCATCTCCCTCACCACCACCTCCTTACTACTACAAGTCTCCACCACCACCTTCACCAAGTCCTCC
1 CCATCTCCATCACCACCACCACCATACTACTACAAGTCACCACCTCCACCATCTCCCTCTCCACC
* *
23366 GCCACC--A-TACTACAAGTCACCACCCCCA
66 ACCACCTTACTACTACAAGTCACCACCTCCA
* * * * *
23394 CCATCTCCATCACCACCACCCCCATACTACTACAAATCTCCTCCTCCACCATCTCCTTCTCCACC
1 CCATCTCCATCACCACCACCACCATACTACTACAAGTCACCACCTCCACCATCTCCCTCTCCACC
* * * *
23459 ACCACCTTACTACTACAAATCTCCACCACCT
66 ACCACCTTACTACTACAAGTCACCACCTCCA
* * * * *
23490 CCTTCTCCATCACCACCACCACCTTACTATTATAAGTCACCCCCTCCACCATCTCCCTCTCCACC
1 CCATCTCCATCACCACCACCACCATACTACTACAAGTCACCACCTCCACCATCTCCCTCTCCACC
* * * *
23555 ACCTCCCTACTACTACAAATCACCTCCTCC
66 ACCACCTTACTACTACAAGTCACCACCTCC
23585 TCCAATGAAG
Statistics
Matches: 480, Mismatches: 72, Indels: 34
0.82 0.12 0.06
Matches are distributed among these distances:
93 79 0.16
94 31 0.06
95 186 0.39
96 180 0.38
97 4 0.01
ACGTcount: A:0.25, C:0.51, G:0.03, T:0.21
Consensus pattern (96 bp):
CCATCTCCATCACCACCACCACCATACTACTACAAGTCACCACCTCCACCATCTCCCTCTCCACC
ACCACCTTACTACTACAAGTCACCACCTCCA
Found at i:27282 original size:48 final size:48
Alignment explanation
Indices: 26387--27261 Score: 820
Period size: 48 Copynumber: 18.1 Consensus size: 48
26377 CTTCTACAAG
* * * * * * * *
26387 TCACCACCTCCACCTCCTTCATAT-TCTTACAAATCTCCGCCACCTCCG
1 TCACCATCTCCACCTCCTCCTTATGTC-TACAAGTCTCCACCTCCACCA
* * * * * * *
26435 TCTCCATCACCACCTCCTCCATATGTGTACAAGTCTCCTCCACCCCCA
1 TCACCATCTCCACCTCCTCCTTATGTCTACAAGTCTCCACCTCCACCA
* * * * *
26483 TCACCCTCCCCACCTCCTCCATATGTTTATAAGTCTCCACCTCCACCA
1 TCACCATCTCCACCTCCTCCTTATGTCTACAAGTCTCCACCTCCACCA
*
26531 TCACCATCTCCACCTCCTCCTTATGTGTACAAGTCTCCACCTCCACCA
1 TCACCATCTCCACCTCCTCCTTATGTCTACAAGTCTCCACCTCCACCA
* * *
26579 TCACCATCACCCTCCCCACCTCCTCCATATGTTTATAAGTCTCCACCTCCACCA
1 TCACCAT----CT--CCACCTCCTCCTTATGTCTACAAGTCTCCACCTCCACCA
26633 TCACCATCTCCACCTCCTCCTTATGTCTACAAGTCTCCACCTCCACCA
1 TCACCATCTCCACCTCCTCCTTATGTCTACAAGTCTCCACCTCCACCA
*
26681 TCACCATCTCCACCTCCTCCTTATGTGTACAAGTCTCCACCTCCACCA
1 TCACCATCTCCACCTCCTCCTTATGTCTACAAGTCTCCACCTCCACCA
* * * * *
26729 TCACCCTCCCCACCTCCTCCATATGTTTATAAGTCTCCACCTCCACCA
1 TCACCATCTCCACCTCCTCCTTATGTCTACAAGTCTCCACCTCCACCA
26777 TCACCATCTCCACCTCCTCCTTATGTCTACAAGTCTCCACCTCCACCA
1 TCACCATCTCCACCTCCTCCTTATGTCTACAAGTCTCCACCTCCACCA
*
26825 TCACCATCTCCACCTCCTCCTTATGTGTACAAGTCTCCACCTCCACCA
1 TCACCATCTCCACCTCCTCCTTATGTCTACAAGTCTCCACCTCCACCA
* * * * * *
26873 TCGCCGTCACCACCTCCTCCTTATATCTACAAATCTCCACCTCCGCCA
1 TCACCATCTCCACCTCCTCCTTATGTCTACAAGTCTCCACCTCCACCA
* * * * *
26921 TCACCATCACCACCTCCTCCTTATGTCTACAAGTCCCCACCACCTCCT
1 TCACCATCTCCACCTCCTCCTTATGTCTACAAGTCTCCACCTCCACCA
* * * * * * * * * *
26969 TCTCCTTCTCCACCCCCACCATATGTCTATAAATCCCCACCACCACCT
1 TCACCATCTCCACCTCCTCCTTATGTCTACAAGTCTCCACCTCCACCA
* * * ** * *
27017 TCTCCATCACCACCCCCTCCTTACATCTATAAGTCTCCACCACCACCA
1 TCACCATCTCCACCTCCTCCTTATGTCTACAAGTCTCCACCTCCACCA
* * ** * * * *
27065 TCACCATCGCCACCTCCTCCATACATTTACAAGTCCCCTCCTCCCCCA
1 TCACCATCTCCACCTCCTCCTTATGTCTACAAGTCTCCACCTCCACCA
* * * * * * * * *
27113 TCTCCCTCACCTCCCCCTCCTTATGTCTATAAATCCCCACCACCACCA
1 TCACCATCTCCACCTCCTCCTTATGTCTACAAGTCTCCACCTCCACCA
* * *** * * * *
27161 TCACCAAGC-CCACCACCTCCTTACCACTACAAGTCACCACCACCTCCT
1 TCACC-ATCTCCACCTCCTCCTTATGTCTACAAGTCTCCACCTCCACCA
* * * * * * *
27209 TCACCATCACCTCCCCCTCCATACTAT-TACAAGTCTCCTCCACCACCA
1 TCACCATCTCCACCTCCTCCTTA-TGTCTACAAGTCTCCACCTCCACCA
27257 TCACC
1 TCACC
27262 CTCCCCTCCA
Statistics
Matches: 696, Mismatches: 121, Indels: 20
0.83 0.14 0.02
Matches are distributed among these distances:
47 2 0.00
48 645 0.93
49 2 0.00
50 2 0.00
52 2 0.00
54 43 0.06
ACGTcount: A:0.22, C:0.49, G:0.04, T:0.25
Consensus pattern (48 bp):
TCACCATCTCCACCTCCTCCTTATGTCTACAAGTCTCCACCTCCACCA
Found at i:27297 original size:48 final size:48
Alignment explanation
Indices: 26995--27358 Score: 184
Period size: 48 Copynumber: 7.6 Consensus size: 48
26985 CACCATATGT
* * * * * * *
26995 CTATAAATCCCCACCACCACCTTCTCCATCACCACCCCCTCCTTAC-A
1 CTATAAATCACCTCCACCACCATCACCATCACCTCCACCTCCATACTA
* * * * * *
27042 TCTATAAGTCTCCACCACCACCATCACCATCGCCACCTCCTCCATAC-A
1 -CTATAAATCACCTCCACCACCATCACCATCACCTCCACCTCCATACTA
* * * * * * * * *
27090 -TTTACAAGTCCCCTCCTCCCCCATCTCCCTCACCTCCCCCTCCTTA-TGT
1 CTATA-AA-TCACCTCCACCACCATCACCATCACCTCCACCTCCATACT-A
* * * * * *
27139 CTATAAATCCCCACCACCACCATCACCAAGC-CCACCACCTCCTTACCA
1 CTATAAATCACCTCCACCACCATCACC-ATCACCTCCACCTCCATACTA
* * * * * *
27187 CTACAAGTCACCACCACCTCCTTCACCATCACCTCCCCCTCCATACTA
1 CTATAAATCACCTCCACCACCATCACCATCACCTCCACCTCCATACTA
* * * * * *
27235 TTACAAGTCTCCTCCACCACCATCACCCTCCCCTCCACCTCCATACTA
1 CTATAAATCACCTCCACCACCATCACCATCACCTCCACCTCCATACTA
* ** * * *
27283 CTATAAATCACCTCCTCCACCCA-CAAAATTACCACCAACTCCATACTA
1 CTATAAATCACCTCCACCA-CCATCACCATCACCTCCACCTCCATACTA
* *
27331 -TCATAAATCACCACCACAACCATCACCA
1 CT-ATAAATCACCTCCACCACCATCACCA
27359 GTACTTCCCC
Statistics
Matches: 239, Mismatches: 66, Indels: 22
0.73 0.20 0.07
Matches are distributed among these distances:
46 3 0.01
47 7 0.03
48 220 0.92
49 6 0.03
50 3 0.01
ACGTcount: A:0.27, C:0.50, G:0.02, T:0.21
Consensus pattern (48 bp):
CTATAAATCACCTCCACCACCATCACCATCACCTCCACCTCCATACTA
Found at i:27318 original size:144 final size:144
Alignment explanation
Indices: 26759--27358 Score: 377
Period size: 144 Copynumber: 4.2 Consensus size: 144
26749 ATATGTTTAT
* * * * * ** * * * *
26759 AAGTCTCCACCTCCACCATCACCATCTCCACCTCCTCCTTATGTCTACAAGTCTCCACCTCCACC
1 AAGTCACCACCACCACCATCACCATCACCACCCCCTCCATACATTTACAAGTCCCCTCCACCACC
* * * * * ** * * * * * **** *
26824 ATCACCATCTCCACCTCCTCCTTATGTGTACAAGTCTCCACCTCCACCATCGCCGTCACCACCTC
66 ATCACCCTCACCTCCACCTCCATATGACTATAAATCACCACCACCACCATCACAAAGACCACCAC
*
26889 CTCCTTATATCTAC
131 CTCCTTACATCTAC
* * * * * * ** * * *
26903 AAATCTCCACCTCCGCCATCACCATCACCACCTCCTCCTTATGTCTACAAGTCCCCACCACCTCC
1 AAGTCACCACCACCACCATCACCATCACCACCCCCTCCATACATTTACAAGTCCCCTCCACCACC
* * * * * * * * * * * * ** *
26968 TTCTCCTTCTCCACCCCCACCATATGTCTATAAATCCCCACCACCACCTTCTCCATCACCACCCC
66 ATCACCCTCACCTCCACCTCCATATGACTATAAATCACCACCACCACCATCACAAAGACCACCAC
*
27033 CTCCTTACATCTAT
131 CTCCTTACATCTAC
* * * * *
27047 AAGTCTCCACCACCACCATCACCATCGCCACCTCCTCCATACATTTACAAGTCCCCTCCTCCCCC
1 AAGTCACCACCACCACCATCACCATCACCACCCCCTCCATACATTTACAAGTCCCCTCCACCACC
* * * * * * *
27112 ATCTCCCTCACCTCCCCCTCCTTATGTCTATAAATCCCCACCACCACCATCACCAAGCCCACCAC
66 ATCACCCTCACCTCCACCTCCATATGACTATAAATCACCACCACCACCATCACAAAGACCACCAC
27177 CTCCTTACCA-CTAC
131 CTCCTTA-CATCTAC
* * * *
27191 AAGTCACCACCACCTCCTTCACCATCACCTCCCCCTCCATAC-TATTACAAGTCTCCTCCACCAC
1 AAGTCACCACCACCACCATCACCATCACCACCCCCTCCATACAT-TTACAAGTCCCCTCCACCAC
* * * *
27255 CATCACCCTCCCCTCCACCTCCATACT-ACTATAAATCACCTCCTCCACC--CACAAAATTACCA
65 CATCACCCTCACCTCCACCTCCATA-TGACTATAAATCACCACCACCACCATCAC-AAA-GACCA
* *
27317 CCAACTCCATACTATCATA-
127 CCACCTCCTTAC-ATC-TAC
*
27336 AA-TCACCACCACAACCATCACCA
1 AAGTCACCACCACCACCATCACCA
27359 GTACTTCCCC
Statistics
Matches: 376, Mismatches: 72, Indels: 16
0.81 0.16 0.03
Matches are distributed among these distances:
142 3 0.01
143 4 0.01
144 361 0.96
145 6 0.02
146 2 0.01
ACGTcount: A:0.25, C:0.49, G:0.03, T:0.23
Consensus pattern (144 bp):
AAGTCACCACCACCACCATCACCATCACCACCCCCTCCATACATTTACAAGTCCCCTCCACCACC
ATCACCCTCACCTCCACCTCCATATGACTATAAATCACCACCACCACCATCACAAAGACCACCAC
CTCCTTACATCTAC
Found at i:36617 original size:6 final size:6
Alignment explanation
Indices: 36597--36628 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
36587 TTGTACACCA
36597 TTTACT TTT--T TTTACT TTTACT TTTACT TTTA
1 TTTACT TTTACT TTTACT TTTACT TTTACT TTTA
36629 ACCATACATT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
4 4 0.17
6 20 0.83
ACGTcount: A:0.16, C:0.12, G:0.00, T:0.72
Consensus pattern (6 bp):
TTTACT
Found at i:37283 original size:131 final size:133
Alignment explanation
Indices: 37010--37272 Score: 440
Period size: 131 Copynumber: 2.0 Consensus size: 133
37000 TGTTCTAAAT
37010 ATTATTTATAAATATATATAATAAATATATATTAGTTTCCCTAACCAATCAATCTTGGACAAATA
1 ATTATTTATAAATATATATAATAAATATATATTAGTTTCCCTAACCAATCAATCTTGGACAAATA
* * * * *
37075 TCAACATGAGAGAAGCCAAATACTGAGTATACAGAGGTTTTGCGATAACTTTAATAGTAAAGGTA
66 TCAACATGAGAGAAGCCAAATACTAAGCATACAGAGGTTTGGAGATAACTTTAATAATAAAGGTA
37140 TAA
131 TAA
* * *
37143 ATTATTTATAAATATATATAAT-AATATGTATTAGTTT-CCTAACCAATCAATCTTGGATAAATG
1 ATTATTTATAAATATATATAATAAATATATATTAGTTTCCCTAACCAATCAATCTTGGACAAATA
37206 TCAACATGAGAGAAGCCAAATACTAAGCATACAGAGGTTTGGAGATAACTTTAATAATAAAGGTA
66 TCAACATGAGAGAAGCCAAATACTAAGCATACAGAGGTTTGGAGATAACTTTAATAATAAAGGTA
37271 TA
131 TA
37273 GATATATTAT
Statistics
Matches: 122, Mismatches: 8, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
131 86 0.70
132 14 0.11
133 22 0.18
ACGTcount: A:0.43, C:0.11, G:0.13, T:0.32
Consensus pattern (133 bp):
ATTATTTATAAATATATATAATAAATATATATTAGTTTCCCTAACCAATCAATCTTGGACAAATA
TCAACATGAGAGAAGCCAAATACTAAGCATACAGAGGTTTGGAGATAACTTTAATAATAAAGGTA
TAA
Found at i:38054 original size:6 final size:6
Alignment explanation
Indices: 38043--38074 Score: 64
Period size: 6 Copynumber: 5.3 Consensus size: 6
38033 TTTAGCTCTC
38043 TCTTTT TCTTTT TCTTTT TCTTTT TCTTTT TC
1 TCTTTT TCTTTT TCTTTT TCTTTT TCTTTT TC
38075 ATCTCTGATT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (6 bp):
TCTTTT
Found at i:41102 original size:21 final size:20
Alignment explanation
Indices: 41060--41098 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
41050 TTAGTATTTT
*
41060 TTTTAAAGTTTTGATAAATA
1 TTTTAAAGTTTTCATAAATA
41080 TTTTAAAGTTTTCATAAAT
1 TTTTAAAGTTTTCATAAAT
41099 TATTAAAGGG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.38, C:0.03, G:0.08, T:0.51
Consensus pattern (20 bp):
TTTTAAAGTTTTCATAAATA
Found at i:41106 original size:19 final size:20
Alignment explanation
Indices: 41062--41106 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
41052 AGTATTTTTT
* *
41062 TTAAAGTTTTGATAAATATT
1 TTAAAGTTTTCATAAATATA
41082 TTAAAGTTTTCATAAAT-TA
1 TTAAAGTTTTCATAAATATA
41101 TTAAAG
1 TTAAAG
41107 GGCTTATTGC
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 7 0.30
20 16 0.70
ACGTcount: A:0.42, C:0.02, G:0.09, T:0.47
Consensus pattern (20 bp):
TTAAAGTTTTCATAAATATA
Found at i:41340 original size:20 final size:20
Alignment explanation
Indices: 41315--41352 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
41305 GAATACATAC
41315 TTAATAGGGTTTGATTTTGA
1 TTAATAGGGTTTGATTTTGA
41335 TTAATAGGGTTTGATTTT
1 TTAATAGGGTTTGATTTT
41353 TAATTAACAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.24, C:0.00, G:0.24, T:0.53
Consensus pattern (20 bp):
TTAATAGGGTTTGATTTTGA
Found at i:41358 original size:21 final size:20
Alignment explanation
Indices: 41315--41359 Score: 72
Period size: 20 Copynumber: 2.2 Consensus size: 20
41305 GAATACATAC
*
41315 TTAATAGGGTTTGATTTTGA
1 TTAATAGGGTTTGATTTTAA
41335 TTAATAGGGTTTGATTTTTAA
1 TTAATAGGGTTTGA-TTTTAA
41356 TTAA
1 TTAA
41360 CATGATAATA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
20 14 0.61
21 9 0.39
ACGTcount: A:0.29, C:0.00, G:0.20, T:0.51
Consensus pattern (20 bp):
TTAATAGGGTTTGATTTTAA
Found at i:50644 original size:10 final size:10
Alignment explanation
Indices: 50631--50691 Score: 51
Period size: 10 Copynumber: 6.5 Consensus size: 10
50621 TTTTTATTTT
50631 TTAATTATTA
1 TTAATTATTA
50641 TT-A--ATTA
1 TTAATTATTA
50648 TTAATTATTA
1 TTAATTATTA
*
50658 TTAATT-TAAA
1 TTAATTAT-TA
*
50668 TT-GTTATTA
1 TTAATTATTA
*
50677 TTAATTATAA
1 TTAATTATTA
50687 TTAAT
1 TTAAT
50692 GAATAATAAT
Statistics
Matches: 40, Mismatches: 5, Indels: 12
0.70 0.09 0.21
Matches are distributed among these distances:
7 6 0.15
8 1 0.03
9 7 0.17
10 26 0.65
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (10 bp):
TTAATTATTA
Done.