Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2394
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: 32570
ACGTcount: A:0.29, C:0.21, G:0.18, T:0.32
Found at i:2535 original size:508 final size:508
Alignment explanation
Indices: 1--2534 Score: 4043
Period size: 505 Copynumber: 5.0 Consensus size: 508
* * *
1 TGAGGTGTCTATAGCTACCCCCTCTTTGGCCGTTTCTGAGTATCAAGAACAGGCC-AAGACAAAT
1 TGAGGTGTCTACAGCT-GCCCCTCTTTGGCCGTTTCTGAGTATCAGGAACAGGCCAAAGACAAAT
* *
65 AGACACCATTTTGTCCGCGACCGCATGTTATGACCTTTGGGTGATTAATGCTTCGCCGTGATGAA
65 AGACACCATTTTGTCCGCGGCCGCATGTTATGACCTCTGGGTGATTAATGCTTCGCCGTGATGAA
*
130 GAGCCTATTTGCGGCGATTCCGATGAAAAAAATGAGTTTGTAGGGTTTGTCCTCCCTACTAGGTT
130 GAGCCTATTGGCGGCGATTCCGATGAAAAAAATGAGTTTGTAGGGTTTGTCCTCCCTACTAGGTT
*
195 TTGG-ATTTTCTAAGGCTTGA-C-CGTTAGATAGGTGTAGATTGGTGTAGAGTTTGGAA-GGATT
195 TTGGAATTTTCTAAGGCTTGACCTCCTTAGATAGGTGTAGATTGGTGTAGAGTTTGGAAGGGATT
256 TTGGAAGATTA-GGTCATTGCAATGTGCCACTGTGCAGATTCAAGGCCCGCAACACTGGGACTTA
260 TTGGAAGATTATGGTCATTGCAATGTGCCACTGTGCAGATTCAAGGCCCGCAACACT-GGACTTA
320 AAGATGATGAGGATGAAGAGTG-TAAAAGGACCAATACGTTGATTCACGGCCAACGATATTGGGT
324 AAGATGATGAGGATGAAGAGTGATAAAAGGACCAATACGTTGATTCACGGCCAACGATATTGGGT
* * * *
384 TTAAACATGAG-AAAA--ATGTCAAT-TG-TGA-TTACGGTCACCATTTCATCCCCACATAGGTC
389 TTAAAGATGAGAAAAAGGATGTCAATGTGCTGATTTACGGTCACCAATTCGTCCCCACATACGTC
*
443 GAATCTTCCACCTACTAGCTAGGCCTCAAATTATC-AAAATTGGCCCGGACAAAA
454 GAATCTTCCACCTACTAGCTAGGCCTCAAATTGTCAAAAATTGGCCCGGACAAAA
*
497 TGAAGTGTCTACAGCTGCCCCTCTTTGGCCGTTTCTGAGTATCAGGAACAGGCC-AAGACAAATT
1 TGAGGTGTCTACAGCTGCCCCTCTTTGGCCGTTTCTGAGTATCAGGAACAGGCCAAAGACAAA-T
* * * * *
561 AGACACCATTTTGTCCGCGGCAGCATGTTATGACCTCTGTGTGACT-AGGCTTCACCGTGATGAA
65 AGACACCATTTTGTCCGCGGCCGCATGTTATGACCTCTGGGTGATTAATGCTTCGCCGTGATGAA
*
625 GAGCCTATTGGCGGCGATTCCGATGAAGAAAATGAGTTTGTAGGGTTT-TCTCATCCCTACTAGG
130 GAGCCTATTGGCGGCGATTCCGATGAAAAAAATGAGTTTGTAGGGTTTGTC-C-TCCCTACTAGG
*
689 TTTTGGAATTTTCTATGGCTTGACCTCCTTAGATAGGTGTAGATTGGTGT-GAGTTTGGAAGGGA
193 TTTTGGAATTTTCTAAGGCTTGACCTCCTTAGATAGGTGTAGATTGGTGTAGAGTTTGGAAGGGA
* * * *
753 TTTTCGAATATTATGGTCATTGCAATGTGCCACTGTGCAAATTCAAGGCCCGCAACAC-GAAACT
258 TTTTGGAAGATTATGGTCATTGCAATGTGCCACTGTGCAGATTCAAGGCCCGCAACACTG-GACT
*
817 TAAAGATGATGAGGATGAAGAGTGATAAAAGGGCCAATACGTTGATTCACGGCCAACGATATT-G
322 TAAAGATGATGAGGATGAAGAGTGATAAAAGGACCAATACGTTGATTCACGGCCAACGATATTGG
* *
881 GTTTAAAGATGAGAAAATGGATGTCAATGTGCCTGATTTACGGTCACCAATTCGTCCCCACATAT
387 GTTTAAAGATGAGAAAAAGGATGTCAATGTG-CTGATTTACGGTCACCAATTCGTCCCCACATAC
*
946 ATCGAATCTTCCACCTACTAGCTAGGCCTCAAATTGTCAAAAATTGGCCCGGACAAAA
451 GTCGAATCTTCCACCTACTAGCTAGGCCTCAAATTGTCAAAAATTGGCCCGGACAAAA
* *
1004 TGAGGTGTCTACACGCTGCCCCTCTTTGGCCGTTTCTGAGTATCAGGAACAAGCCAATGAC-AAT
1 TGAGGTGTCTACA-GCTGCCCCTCTTTGGCCGTTTCTGAGTATCAGGAACAGGCCAAAGACAAAT
* * *
1068 AGACACCA-TTTGTCTGCGGCCGCCTGTTATGACCTCTGGGTGATTAATGCTTCGCCGTCATGAA
65 AGACACCATTTTGTCCGCGGCCGCATGTTATGACCTCTGGGTGATTAATGCTTCGCCGTGATGAA
*
1132 GAGCCTATTGGCGGCGATT-CGATGATAAAAATGAGTTTGTAGGGTTTTGTCCTCCCTACTAGGT
130 GAGCCTATTGGCGGCGATTCCGATGAAAAAAATGAGTTTGTAGGG-TTTGTCCTCCCTACTAGGT
1196 TTTGGAATTTTCTAAGGC-TGACCTCCTTAGATAGGTGTAGATTGGTGTAGAG-TTGGAAGGGAT
194 TTTGGAATTTTCTAAGGCTTGACCTCCTTAGATAGGTGTAGATTGGTGTAGAGTTTGGAAGGGAT
* *
1259 TTTGGAAAGATTATGGTCATTGCAATGTGCCACTATGCAGATTCAAGG-CTGCAACACTGGACCT
259 TTTGG-AAGATTATGGTCATTGCAATGTGCCACTGTGCAGATTCAAGGCCCGCAACACTGGA-CT
* * *
1323 T-AAGACGATGAGGATGAAAAGTGATATAAAGGACCAACACGTTGATTCACGGCCAACGATATTG
322 TAAAGATGATGAGGATGAAGAGTGATA-AAAGGACCAATACGTTGATTCACGGCCAACGATATTG
* * * * *
1387 GGTTTAAACATAAG-AAAAGGATTTCAATGTGCTGAATTACGGTCACCATTTCGTCCCCACATAC
386 GGTTTAAAGATGAGAAAAAGGATGTCAATGTGCTGATTTACGGTCACCAATTCGTCCCCACATAC
*
1451 GTCGAATCTTCCACCTACTAGCTAGGCCTCAAATTATCGAAAAATTGGCCCGGACAAAA
451 GTCGAATCTTCCACCTACTAGCTAGGCCTCAAATTGTC-AAAAATTGGCCCGGACAAAA
* * *
1510 TGAGCTGACTACAGCTGCCCCTC-TTGGCTGTTTCTGAGTATCAGGAACAGGCCAAAGACAAATA
1 TGAGGTGTCTACAGCTGCCCCTCTTTGGCCGTTTCTGAGTATCAGGAACAGGCCAAAGACAAATA
* * * * * *
1574 AACA-CATTTTGTCTGCGGCAGCATGTTATGACCTCTGTGTGACTAAGGCTTCGCCGTGATGAAG
66 GACACCATTTTGTCCGCGGCCGCATGTTATGACCTCTGGGTGATTAATGCTTCGCCGTGATGAAG
* * *
1638 AGCCTATTGGCGGCAATTCCGATG-AAAAGATGAGTTTGTAGGGTTTCTCCTCCCTACTAGGTTT
131 AGCCTATTGGCGGCGATTCCGATGAAAAAAATGAGTTTGTAGGGTTTGTCCTCCCTACTAGGTTT
1702 TGGAATTTTCTAAGGCTTGACCTCCTTAGATAGGTGTAGATTGGTGTAGAGTTTGGAAGGGATTT
196 TGGAATTTTCTAAGGCTTGACCTCCTTAGATAGGTGTAGATTGGTGTAGAGTTTGGAAGGGATTT
*
1767 TGGAAGATTATGGTCATTGCAATGTGCAACTGTGCAGATTCAAGGCCCGCAACACTGGACTT-AA
261 TGGAAGATTATGGTCATTGCAATGTGCCACTGTGCAGATTCAAGGCCCGCAACACTGGACTTAAA
*
1831 GATGATGAGGATGAAGAGTGATAAAAGGACCAATACGTTGATTCTCGGCCAACGATATTGGGTTT
326 GATGATGAGGATGAAGAGTGATAAAAGGACCAATACGTTGATTCACGGCCAACGATATTGGGTTT
* *
1896 AAAGATGAGAAAAAGGATGTCAATGTGCTGATTTATGGTCACCAATTTGTCCCCACATACGTCGA
391 AAAGATGAGAAAAAGGATGTCAATGTGCTGATTTACGGTCACCAATTCGTCCCCACATACGTCGA
*
1961 ATCTTCCACCTACTAGCTAGGCATCAAATTGTCAAAAATTGGCCCGGACAAAA
456 ATCTTCCACCTACTAGCTAGGCCTCAAATTGTCAAAAATTGGCCCGGACAAAA
*
2014 TGAGGTGTCTACAACTGCCCCTCTTTGGCCGTTTCTGAGTATCAGGAACAGGCCAAAGACAAATA
1 TGAGGTGTCTACAGCTGCCCCTCTTTGGCCGTTTCTGAGTATCAGGAACAGGCCAAAGACAAATA
* *
2079 GACACCATTTTGTCCGCGGCCGCATGTTATGACCTTTGGGTGATTCATGCTTCGCCGTGATGAAG
66 GACACCATTTTGTCCGCGGCCGCATGTTATGACCTCTGGGTGATTAATGCTTCGCCGTGATGAAG
*
2144 AGCCTATTGGCAGCGATTCCGATGAAAAAAATGAGTTTGTAGGGTTTGTCCTCCCTACTAGGTTT
131 AGCCTATTGGCGGCGATTCCGATGAAAAAAATGAGTTTGTAGGGTTTGTCCTCCCTACTAGGTTT
2209 TGGAATTTTCTAAGGCTTGACCTCCTTAGATAGGTGTAGATTGGTGTAGAGTTTGGAAGGGATTT
196 TGGAATTTTCTAAGGCTTGACCTCCTTAGATAGGTGTAGATTGGTGTAGAGTTTGGAAGGGATTT
* * *
2274 TGGAAGATTATGGTCATTGTAATGTGCCACTATGCAGATTCAAGGCCTGCAACACTGGACTTAAA
261 TGGAAGATTATGGTCATTGCAATGTGCCACTGTGCAGATTCAAGGCCCGCAACACTGGACTTAAA
* * *
2339 GACGATGAGGATGAAAAGTGATAAAAGGACCAACACGTTGATTCACGGCCAACGATATTGGGTTT
326 GATGATGAGGATGAAGAGTGATAAAAGGACCAATACGTTGATTCACGGCCAACGATATTGGGTTT
*
2404 AAAGATGAGAAAAAGGATGTCAATGTGCTGATTTACGGTCACCAATTCATCCCCACATACGTCGA
391 AAAGATGAGAAAAAGGATGTCAATGTGCTGATTTACGGTCACCAATTCGTCCCCACATACGTCGA
* * *
2469 ATCTTCCACCTACTAGCTAGGCCTTAAATTGTCGAAAATTAGCCCGGACAAAA
456 ATCTTCCACCTACTAGCTAGGCCTCAAATTGTCAAAAATTGGCCCGGACAAAA
2522 TGAGGTGTCTACA
1 TGAGGTGTCTACA
2535 ATTGCCATGT
Statistics
Matches: 1874, Mismatches: 123, Indels: 70
0.91 0.06 0.03
Matches are distributed among these distances:
494 2 0.00
495 107 0.06
496 73 0.04
497 15 0.01
498 12 0.01
499 77 0.04
500 83 0.04
502 8 0.00
503 2 0.00
504 158 0.08
505 472 0.25
506 379 0.20
507 251 0.13
508 231 0.12
509 4 0.00
ACGTcount: A:0.28, C:0.20, G:0.24, T:0.28
Consensus pattern (508 bp):
TGAGGTGTCTACAGCTGCCCCTCTTTGGCCGTTTCTGAGTATCAGGAACAGGCCAAAGACAAATA
GACACCATTTTGTCCGCGGCCGCATGTTATGACCTCTGGGTGATTAATGCTTCGCCGTGATGAAG
AGCCTATTGGCGGCGATTCCGATGAAAAAAATGAGTTTGTAGGGTTTGTCCTCCCTACTAGGTTT
TGGAATTTTCTAAGGCTTGACCTCCTTAGATAGGTGTAGATTGGTGTAGAGTTTGGAAGGGATTT
TGGAAGATTATGGTCATTGCAATGTGCCACTGTGCAGATTCAAGGCCCGCAACACTGGACTTAAA
GATGATGAGGATGAAGAGTGATAAAAGGACCAATACGTTGATTCACGGCCAACGATATTGGGTTT
AAAGATGAGAAAAAGGATGTCAATGTGCTGATTTACGGTCACCAATTCGTCCCCACATACGTCGA
ATCTTCCACCTACTAGCTAGGCCTCAAATTGTCAAAAATTGGCCCGGACAAAA
Found at i:3683 original size:27 final size:27
Alignment explanation
Indices: 3646--4081 Score: 498
Period size: 27 Copynumber: 15.9 Consensus size: 27
3636 TTTCTTTTCA
* *
3646 AAGTCCACAACTCCATGTCATCCTTTT
1 AAGTCCACAACTCCGTGGCATCCTTTT
*
3673 AAGTCCACAACTCCGTGGTATCCTTTT
1 AAGTCCACAACTCCGTGGCATCCTTTT
** *
3700 AAAGTCCACAACTCTATGGTATCCTTTT
1 -AAGTCCACAACTCCGTGGCATCCTTTT
* *
3728 AAAGTCTACAACTCCGTGG-ACCCTTTT
1 -AAGTCCACAACTCCGTGGCATCCTTTT
* *
3755 AAAGTCCATAACTCTGTGGCATCCTTTT
1 -AAGTCCACAACTCCGTGGCATCCTTTT
* *
3783 AAGTCCACAACTCCGTGGCACCCTTTA
1 AAGTCCACAACTCCGTGGCATCCTTTT
*
3810 AAGTCCACAACTCCGTGGCATCCTTTC
1 AAGTCCACAACTCCGTGGCATCCTTTT
* *
3837 AAGTCCACAACTTCGTGGCACCCTTTT
1 AAGTCCACAACTCCGTGGCATCCTTTT
* *
3864 AAGTCCACAACTCTGTGGCATCCGTTTC
1 AAGTCCACAACTCCGTGGCATCC-TTTT
*
3892 AAGTCCACAACTCCGTGGCATCCGTTTC
1 AAGTCCACAACTCCGTGGCATCC-TTTT
* * *
3920 AAGTCCACAACTCTGTGGCGTTCTTTT
1 AAGTCCACAACTCCGTGGCATCCTTTT
* *
3947 AAAGTCCACAACTCCATGGCACCCTTTT
1 -AAGTCCACAACTCCGTGGCATCCTTTT
*
3975 AAGTCCACAACTTCGTGGCA-CTCTTTT
1 AAGTCCACAACTCCGTGGCATC-CTTTT
* *
4002 AAGTCCACAACTCCCTGGCATCTTTTT
1 AAGTCCACAACTCCGTGGCATCCTTTT
* *
4029 TAGTCCACAACTTCGTGGCATCCTTTTT
1 AAGTCCACAACTCCGTGGCATCC-TTTT
* * * *
4057 AAGCCCACAAGTCAGTGGCACCCTT
1 AAGTCCACAACTCCGTGGCATCCTT
4082 CCAAAGTCCA
Statistics
Matches: 351, Mismatches: 51, Indels: 14
0.84 0.12 0.03
Matches are distributed among these distances:
26 1 0.00
27 208 0.59
28 142 0.40
ACGTcount: A:0.24, C:0.32, G:0.14, T:0.30
Consensus pattern (27 bp):
AAGTCCACAACTCCGTGGCATCCTTTT
Found at i:4182 original size:32 final size:32
Alignment explanation
Indices: 4062--5405 Score: 1039
Period size: 32 Copynumber: 44.8 Consensus size: 32
4052 TTTTTAAGCC
* *
4062 CACAAGTCAGTGGC-ACCC-TTCCAAAG-TC-
1 CACAAGTCAGTGGCAACCCATTTCAAAGCCCA
* * **
4090 CATAAGTCAGTGGC-ACCCTTTTTTAAG-CC-
1 CACAAGTCAGTGGCAACCCATTTCAAAGCCCA
* **
4119 CACAAGTTAGTGGC-A-TTATTTCAAAGCCCA
1 CACAAGTCAGTGGCAACCCATTTCAAAGCCCA
* * *
4149 CACAAGTCGGTGGCAACTCATTTGAAAGCCCA
1 CACAAGTCAGTGGCAACCCATTTCAAAGCCCA
* *
4181 CACAAGTCGGTGGCAACCCATTTCAAAGGCCA
1 CACAAGTCAGTGGCAACCCATTTCAAAGCCCA
* *
4213 CACAAGTCAGTGGCAACCCATTTGAAAGCCAA
1 CACAAGTCAGTGGCAACCCATTTCAAAGCCCA
* *
4245 CACAAGTAAGTGGTAACCCATTTCAAAGCCCA
1 CACAAGTCAGTGGCAACCCATTTCAAAGCCCA
* *
4277 CACAAGTCGGTGGCAACCCATTTTAAAG-CC-
1 CACAAGTCAGTGGCAACCCATTTCAAAGCCCA
* *
4307 CACAAGTCAGTGGC-A-TCAGTTCAAAGCCCA
1 CACAAGTCAGTGGCAACCCATTTCAAAGCCCA
* * *
4337 CACAAGTCGGTGGTAACCCATTTCAACA-CTCA
1 CACAAGTCAGTGGCAACCCATTTCAA-AGCCCA
* *
4369 TACAAGTCGGTGGCAACCCATTTCAAAGCCCA
1 CACAAGTCAGTGGCAACCCATTTCAAAGCCCA
** *
4401 CACAAGTTGGTGGCAACCCATTTCATAG-CC-
1 CACAAGTCAGTGGCAACCCATTTCAAAGCCCA
* *
4431 CACAAGTCAGTGGC-A-TCAATTCAAAGCCCA
1 CACAAGTCAGTGGCAACCCATTTCAAAGCCCA
* *
4461 CACAAGTCAGTGGTAACCCATTTCAACA-CTCA
1 CACAAGTCAGTGGCAACCCATTTCAA-AGCCCA
** *
4493 TTCAAGTCGGTGGCAACCCATTTCAAAGCCCA
1 CACAAGTCAGTGGCAACCCATTTCAAAGCCCA
**
4525 CACAAGTTGGTGGCAACCCATTTCAAAGCCCA
1 CACAAGTCAGTGGCAACCCATTTCAAAGCCCA
* *
4557 CACAAGTC-GTGGCAACTCTTTTCAAAG-CC-
1 CACAAGTCAGTGGCAACCCATTTCAAAGCCCA
* * *
4586 CACAAGTCAGTGGCATCTC--TTCAAAAGACC-
1 CACAAGTCAGTGGCAACCCATTTC-AAAGCCCA
* *
4616 C-CAAGTTAGTGGC-ATCC-TTTCAAA--CCA
1 CACAAGTCAGTGGCAACCCATTTCAAAGCCCA
*
4643 CACAACTCAGTGGCATACCC-TTTCAAAG-CC-
1 CACAAGTCAGTGGCA-ACCCATTTCAAAGCCCA
*
4673 CACAAGTC-GATGGC-ACCC-TTCCAAAG-CC-
1 CACAAGTCAG-TGGCAACCCATTTCAAAGCCCA
*
4701 CACAAGTCAGTAGC-ACCC-TTTCAAAG-CC-
1 CACAAGTCAGTGGCAACCCATTTCAAAGCCCA
*
4729 CACAAGTCAGTGGC-ACCC-TTCCAAAG-CC-
1 CACAAGTCAGTGGCAACCCATTTCAAAGCCCA
*
4757 CACAAGTCAGTGGC-ACCC-TTCCAAAG-CC-
1 CACAAGTCAGTGGCAACCCATTTCAAAGCCCA
*
4785 CACAAGTCAGTGGAATACCC-TTTCAAAG-CC-
1 CACAAGTCAGTGGCA-ACCCATTTCAAAGCCCA
** * *
4815 CACAAGTTGGTGGC-ACCC-TTCCAAAG-TC-
1 CACAAGTCAGTGGCAACCCATTTCAAAGCCCA
* * **
4843 CACAAGTCAATGGC-ACCCCTTTTTAAG-CC-
1 CACAAGTCAGTGGCAACCCATTTCAAAGCCCA
* **
4872 CACAAGTCAATGGC-A-TTATTTCAAAG-CC-
1 CACAAGTCAGTGGCAACCCATTTCAAAGCCCA
**
4900 CACAAGTCAGTGGC-A-TTATTTCAAAGCCCA
1 CACAAGTCAGTGGCAACCCATTTCAAAGCCCA
* * *
4930 CACAAGTCGGTGGCAACTCATTTAAAAGCCCA
1 CACAAGTCAGTGGCAACCCATTTCAAAGCCCA
* *
4962 CACAAGTTATTGGCAACCCATTTCAAAGCCCA
1 CACAAGTCAGTGGCAACCCATTTCAAAGCCCA
*
4994 CACAAGTCGGTGGCAACCCATTTCAAAG-CC-
1 CACAAGTCAGTGGCAACCCATTTCAAAGCCCA
** * * *
5024 CACAAGTTGGTGGC-A-TCAGTTCAAAGTCCA
1 CACAAGTCAGTGGCAACCCATTTCAAAGCCCA
5054 CACAAGTCAGTGGCAACCCATTTCAAAGCCCA
1 CACAAGTCAGTGGCAACCCATTTCAAAGCCCA
* *
5086 CACAAGTCGGTGGTAACCCATTTCAAAGCCCA
1 CACAAGTCAGTGGCAACCCATTTCAAAGCCCA
* * * *
5118 CACAAGTCTGTGGTAACCCATTTCAAAACCTA
1 CACAAGTCAGTGGCAACCCATTTCAAAGCCCA
* * * *
5150 CACAAGTCGGTGGTAACCTATTTCAAAGCTCA
1 CACAAGTCAGTGGCAACCCATTTCAAAGCCCA
5182 CA-AA-TCAGTGGC-ACCC-TTTCAAAG-CC-
1 CACAAGTCAGTGGCAACCCATTTCAAAGCCCA
*
5208 CACAAGTCAGTGGC-ACCC-TTTCAAAG-TC-
1 CACAAGTCAGTGGCAACCCATTTCAAAGCCCA
* * *
5236 CACAAGTCGGTGGC-ATCCTTTTCAAAG-CC-
1 CACAAGTCAGTGGCAACCCATTTCAAAGCCCA
* * *
5265 CACAAGTCTGTGGC-A-TCTTTTCAAAGCCCA
1 CACAAGTCAGTGGCAACCCATTTCAAAGCCCA
5295 CA-AA-TCAGTGGC-ACCC-TTTCAAAG-CC-
1 CACAAGTCAGTGGCAACCCATTTCAAAGCCCA
** *
5321 CACAAGTCAGTGGC-ATTC-TTTCAAAG-TC-
1 CACAAGTCAGTGGCAACCCATTTCAAAGCCCA
* *
5349 CACAAGTCAATGAC-ACCC-TTTCAAAGCCCA
1 CACAAGTCAGTGGCAACCCATTTCAAAGCCCA
* *
5379 CGCAAGTC-GATGGCAACCCTTTTCAAA
1 CACAAGTCAG-TGGCAACCCATTTCAAA
5406 TCACCATTTT
Statistics
Matches: 1112, Mismatches: 152, Indels: 100
0.82 0.11 0.07
Matches are distributed among these distances:
26 6 0.01
27 8 0.01
28 341 0.31
29 113 0.10
30 177 0.16
31 38 0.03
32 427 0.38
33 2 0.00
ACGTcount: A:0.31, C:0.31, G:0.17, T:0.21
Consensus pattern (32 bp):
CACAAGTCAGTGGCAACCCATTTCAAAGCCCA
Found at i:4394 original size:124 final size:123
Alignment explanation
Indices: 4057--5335 Score: 1169
Period size: 124 Copynumber: 10.7 Consensus size: 123
4047 CATCCTTTTT
* * * * * * **
4057 AAGCCCACAAGTCAGTGGCACCCTTCCAAAG-TC-CATAAGTCAGTGGC-ACCCTTTTTTAAGCC
1 AAGCCCACAAGTCAGTGGCATCATTTCAAAGCCCACACAAGTCAGTGGCAACCCATTTCAAAGCC
* ** * *
4119 -CACAAGTTAGTGGC-A-TTATTTCAAAGCCCACACAAGTCGGTGGCAACTCATTTGA
66 ACACAAGTCAGTGGCAACCCATTTCAAAGCCCACACAAGTCGGTGGCAACCCATTTCA
* * * *
4174 AAGCCCACACAAGTCGGTGGCAACCCATTTCAAAGGCCACACAAGTCAGTGGCAACCCATTTGAA
1 AAG-CC-CACAAGTCAGTGGC-A-TCATTTCAAAGCCCACACAAGTCAGTGGCAACCCATTTCAA
* * *
4239 AGCCAACACAAGTAAGTGGTAACCCATTTCAAAGCCCACACAAGTCGGTGGCAACCCATTTTA
62 AGCC-ACACAAGTCAGTGGCAACCCATTTCAAAGCCCACACAAGTCGGTGGCAACCCATTTCA
* * *
4302 AAGCCCACAAGTCAGTGGCATCAGTTCAAAGCCCACACAAGTCGGTGGTAACCCATTTCAACA-C
1 AAGCCCACAAGTCAGTGGCATCATTTCAAAGCCCACACAAGTCAGTGGCAACCCATTTCAA-AGC
* * *
4366 TCATACAAGTCGGTGGCAACCCATTTCAAAGCCCACACAAGTTGGTGGCAACCCATTTCA
65 -CACACAAGTCAGTGGCAACCCATTTCAAAGCCCACACAAGTCGGTGGCAACCCATTTCA
* * *
4426 TAGCCCACAAGTCAGTGGCATCAATTCAAAGCCCACACAAGTCAGTGGTAACCCATTTCAACA-C
1 AAGCCCACAAGTCAGTGGCATCATTTCAAAGCCCACACAAGTCAGTGGCAACCCATTTCAA-AGC
** * *
4490 TCATTCAAGTCGGTGGCAACCCATTTCAAAGCCCACACAAGTTGGTGGCAACCCATTTCA
65 -CACACAAGTCAGTGGCAACCCATTTCAAAGCCCACACAAGTCGGTGGCAACCCATTTCA
* * *
4550 AAGCCCACACAAGTC-GTGGCAACTCTTTTCAAAG-CC-CACAAGTCAGTGGCATCTC--TTCAA
1 AAG-CC-CACAAGTCAGTGGC-A-TCATTTCAAAGCCCACACAAGTCAGTGGCAACCCATTTC-A
* * * *
4610 AAGACC-C-CAAGTTAGTGGC-ATCC-TTTCAAA--CCACACAACTCAGTGGCATACCC-TTTCA
61 AAG-CCACACAAGTCAGTGGCAACCCATTTCAAAGCCCACACAAGTCGGTGGCA-ACCCATTTCA
* * * *
4668 AAGCCCACAAGTC-GATGGCACCCTTCCAAAG-CC-CACAAGTCAGTAGC-ACCC-TTTCAAAGC
1 AAGCCCACAAGTCAG-TGGCATCATTTCAAAGCCCACACAAGTCAGTGGCAACCCATTTCAAAGC
* * *
4728 C-CACAAGTCAGTGGC-ACCC-TTCCAAAG-CC-CACAAGTCAGTGGC-ACCC-TTCCA
65 CACACAAGTCAGTGGCAACCCATTTCAAAGCCCACACAAGTCGGTGGCAACCCATTTCA
* * ** *
4780 AAGCCCACAAGTCAGTGGAATACCCTTTCAAAG-CC-CACAAGTTGGTGGC-ACCC-TTCCAAAG
1 AAGCCCACAAGTCAGTGGCAT--CATTTCAAAGCCCACACAAGTCAGTGGCAACCCATTTCAAAG
* * * ** ** **
4841 TC-CACAAGTCAATGGC-ACCCCTTTTTAAG-CC-CACAAGTCAATGGC-A-TTATTTCA
64 CCACACAAGTCAGTGGCAACCCATTTCAAAGCCCACACAAGTCGGTGGCAACCCATTTCA
* * * *
4895 AAGCCCACAAGTCAGTGGCATTATTTCAAAGCCCACACAAGTCGGTGGCAACTCATTTAAAAGCC
1 AAGCCCACAAGTCAGTGGCATCATTTCAAAGCCCACACAAGTCAGTGGCAACCCATTTCAAAG-C
* *
4960 CACACAAGTTATTGGCAACCCATTTCAAAGCCCACACAAGTCGGTGGCAACCCATTTCA
65 CACACAAGTCAGTGGCAACCCATTTCAAAGCCCACACAAGTCGGTGGCAACCCATTTCA
** * *
5019 AAGCCCACAAGTTGGTGGCATCAGTTCAAAGTCCACACAAGTCAGTGGCAACCCATTTCAAAGCC
1 AAGCCCACAAGTCAGTGGCATCATTTCAAAGCCCACACAAGTCAGTGGCAACCCATTTCAAAG-C
* * * *
5084 CACACAAGTCGGTGGTAACCCATTTCAAAGCCCACACAAGTCTGTGGTAACCCATTTCA
65 CACACAAGTCAGTGGCAACCCATTTCAAAGCCCACACAAGTCGGTGGCAACCCATTTCA
* * * * *
5143 AAACCTACACAAGTCGGTGGTAACCTATTTCAAAGCTCACA-AA-TCAGTGGC-ACCC-TTTCAA
1 AAGCC--CACAAGTCAGTGG-CATC-ATTTCAAAGCCCACACAAGTCAGTGGCAACCCATTTCAA
* * *
5204 AGCC-CACAAGTCAGTGGC-ACCC-TTTCAAAG-TC-CACAAGTCGGTGGC-ATCCTTTTCA
62 AGCCACACAAGTCAGTGGCAACCCATTTCAAAGCCCACACAAGTCGGTGGCAACCCATTTCA
* *
5260 AAGCCCACAAGTCTGTGGCATCTTTTCAAAGCCCACA-AA-TCAGTGGC-ACCC-TTTCAAAGCC
1 AAGCCCACAAGTCAGTGGCATCATTTCAAAGCCCACACAAGTCAGTGGCAACCCATTTCAAAGCC
5321 -CACAAGTCAGTGGCA
66 ACACAAGTCAGTGGCA
5336 TTCTTTCAAA
Statistics
Matches: 994, Mismatches: 122, Indels: 95
0.82 0.10 0.08
Matches are distributed among these distances:
112 25 0.03
113 63 0.06
114 94 0.09
115 98 0.10
116 13 0.01
117 27 0.03
118 38 0.04
119 30 0.03
120 26 0.03
121 18 0.02
122 35 0.04
123 20 0.02
124 353 0.36
125 31 0.03
126 56 0.06
127 16 0.02
128 51 0.05
ACGTcount: A:0.31, C:0.31, G:0.18, T:0.20
Consensus pattern (123 bp):
AAGCCCACAAGTCAGTGGCATCATTTCAAAGCCCACACAAGTCAGTGGCAACCCATTTCAAAGCC
ACACAAGTCAGTGGCAACCCATTTCAAAGCCCACACAAGTCGGTGGCAACCCATTTCA
Found at i:5536 original size:48 final size:48
Alignment explanation
Indices: 5471--5649 Score: 286
Period size: 48 Copynumber: 3.7 Consensus size: 48
5461 GCACCATTTC
*
5471 TAGCTCAATGTCACTGGCCTTGAATCAGCACATTGTCCACTTTTCCCT
1 TAGCTCAATGTCGCTGGCCTTGAATCAGCACATTGTCCACTTTTCCCT
5519 TAGCTCAATGTCGCTGGCCTTGAATCAGCACATTGTCCACTTTTCCCT
1 TAGCTCAATGTCGCTGGCCTTGAATCAGCACATTGTCCACTTTTCCCT
* *
5567 TAGCTCAATGTCGCTGGCCTTGAATCAGCATATTGTCCACTTTTCCCA
1 TAGCTCAATGTCGCTGGCCTTGAATCAGCACATTGTCCACTTTTCCCT
* * * **
5615 TAGCTCGATGTTGTTGGCCTTGAATTGGCACATTG
1 TAGCTCAATGTCGCTGGCCTTGAATCAGCACATTG
5650 GCACTCCTCT
Statistics
Matches: 122, Mismatches: 9, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
48 122 1.00
ACGTcount: A:0.20, C:0.28, G:0.18, T:0.34
Consensus pattern (48 bp):
TAGCTCAATGTCGCTGGCCTTGAATCAGCACATTGTCCACTTTTCCCT
Found at i:7326 original size:19 final size:19
Alignment explanation
Indices: 7292--7330 Score: 53
Period size: 20 Copynumber: 2.1 Consensus size: 19
7282 CCATGCATTT
*
7292 TTTTTATTATGTTTCATGCA
1 TTTTTAATATGTTTCA-GCA
7312 TTTTTAATATG-TTCAGCA
1 TTTTTAATATGTTTCAGCA
7330 T
1 T
7331 CTCATTGAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 4 0.22
19 4 0.22
20 10 0.56
ACGTcount: A:0.23, C:0.10, G:0.10, T:0.56
Consensus pattern (19 bp):
TTTTTAATATGTTTCAGCA
Found at i:8625 original size:32 final size:34
Alignment explanation
Indices: 8584--8670 Score: 108
Period size: 36 Copynumber: 2.6 Consensus size: 34
8574 ACTATCTTTC
8584 AAGGCTAAGATAGAAACCTC-C-CTATCTTTT-CA
1 AAGGCTAAGATAG-AACCTCTCTCTATCTTTTACA
**
8616 TGGGCTAAGATAGAACCTTTCTCTCTATCTTTTACA
1 AAGGCTAAGATAGAACC--TCTCTCTATCTTTTACA
8652 AAGGCTAAGATAGAACCTC
1 AAGGCTAAGATAGAACCTC
8671 ACAATCACTT
Statistics
Matches: 46, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
31 4 0.09
32 11 0.24
33 2 0.04
34 3 0.07
35 9 0.20
36 17 0.37
ACGTcount: A:0.32, C:0.23, G:0.15, T:0.30
Consensus pattern (34 bp):
AAGGCTAAGATAGAACCTCTCTCTATCTTTTACA
Found at i:11118 original size:40 final size:40
Alignment explanation
Indices: 10993--11139 Score: 136
Period size: 41 Copynumber: 3.6 Consensus size: 40
10983 CGTTAACTTG
* *
10993 TATGGTTTCATCTTGGTCAATTCTTCTAACTCATTGACTCA
1 TATGGTTTCATCTTGGTCAACT-TTCTAACTCTTTGACTCA
**** ** *
11034 TATGGTTTCATCCCAATCAAACCCTCTAACT-TGGTGACTCA
1 TATGGTTTCATCTTGGTC-AACTTTCTAACTCT-TTGACTCA
* *
11075 TATGGTTTCATCTTGGTTAACTTTCTAACTCTTTGACTTA
1 TATGGTTTCATCTTGGTCAACTTTCTAACTCTTTGACTCA
* *
11115 TATGGTTTTATTTTGGTCAA-TTTCT
1 TATGGTTTCATCTTGGTCAACTTTCT
11140 TAAACTATAG
Statistics
Matches: 82, Mismatches: 21, Indels: 8
0.74 0.19 0.07
Matches are distributed among these distances:
39 5 0.06
40 33 0.40
41 42 0.51
42 2 0.02
ACGTcount: A:0.22, C:0.20, G:0.13, T:0.45
Consensus pattern (40 bp):
TATGGTTTCATCTTGGTCAACTTTCTAACTCTTTGACTCA
Found at i:11312 original size:41 final size:41
Alignment explanation
Indices: 11257--11355 Score: 137
Period size: 41 Copynumber: 2.4 Consensus size: 41
11247 TTGGTCATCA
* * *
11257 CCTTTAACTCGTTGACTCATATGGTTTTAT-CTCAGTCAACC
1 CCTTTAACTTGTTGACTCATATGGTTTCATCCT-AGCCAACC
*
11298 CCTTAAACTTGTTGACTCATATGGTTTCATCCTAGCCAACC
1 CCTTTAACTTGTTGACTCATATGGTTTCATCCTAGCCAACC
*
11339 CGTTTAACTTGTTGACT
1 CCTTTAACTTGTTGACT
11356 TGTTAGTTTA
Statistics
Matches: 51, Mismatches: 6, Indels: 2
0.86 0.10 0.03
Matches are distributed among these distances:
41 49 0.96
42 2 0.04
ACGTcount: A:0.22, C:0.26, G:0.13, T:0.38
Consensus pattern (41 bp):
CCTTTAACTTGTTGACTCATATGGTTTCATCCTAGCCAACC
Found at i:11466 original size:40 final size:40
Alignment explanation
Indices: 11422--11588 Score: 137
Period size: 40 Copynumber: 4.2 Consensus size: 40
11412 TCAACTCTTC
*
11422 TCATCTTGTTCAACCCCTTAAACTTGCTGACTTGTTAGTT
1 TCATCTTGTTCAACCCCTTAAACTTGCTGACTTGTCAGTT
* *
11462 TCATCTTGATT-AA-CCCTT---CTTGTCTATCAACTTGTTAGTT
1 TCATCTTG-TTCAACCCCTTAAACTTG-C--T-GACTTGTCAGTT
* * * *
11502 TCATCTTGATCAACCTCTTAAACTTGTTGATTTGTCAGTT
1 TCATCTTGTTCAACCCCTTAAACTTGCTGACTTGTCAGTT
* * * * * *
11542 TTATCTTGGTCAACCCTTTAAACTTGTTGACTTCTCAATT
1 TCATCTTGTTCAACCCCTTAAACTTGCTGACTTGTCAGTT
11582 TCATCTT
1 TCATCTT
11589 TGTCAAGCCT
Statistics
Matches: 102, Mismatches: 15, Indels: 20
0.74 0.11 0.15
Matches are distributed among these distances:
36 4 0.04
37 1 0.01
39 7 0.07
40 79 0.77
41 7 0.07
44 4 0.04
ACGTcount: A:0.21, C:0.23, G:0.11, T:0.46
Consensus pattern (40 bp):
TCATCTTGTTCAACCCCTTAAACTTGCTGACTTGTCAGTT
Found at i:11594 original size:40 final size:40
Alignment explanation
Indices: 11491--11680 Score: 134
Period size: 40 Copynumber: 4.8 Consensus size: 40
11481 TTGTCTATCA
* *
11491 ACTTGTTAGTTTCATC-TTGATCAA-CCTCTTAAACTTGTTG
1 ACTTGTCAATTTCATCTTTG-TCAACCCT-TTAAACTTGTTG
* * * *
11531 ATTTGTCAGTTTTATCTTGGTCAACCCTTTAAACTTGTTG
1 ACTTGTCAATTTCATCTTTGTCAACCCTTTAAACTTGTTG
* * * * * *
11571 ACTTCTCAATTTCATCTTTGTCAAGCCTTCTCATC-TGCTA
1 ACTTGTCAATTTCATCTTTGTCAACCCTT-TAAACTTGTTG
* *** *
11611 ACTTGTCGATTTCATCCCAGTCAACCTTTTAAACTTGTTG
1 ACTTGTCAATTTCATCTTTGTCAACCCTTTAAACTTGTTG
* ** * *
11651 ACTTGTCGATTTTGTCTTGGTTAACCCTTT
1 ACTTGTCAATTTCATCTTTGTCAACCCTTT
11681 TGACCTATTG
Statistics
Matches: 114, Mismatches: 32, Indels: 8
0.74 0.21 0.05
Matches are distributed among these distances:
39 3 0.03
40 103 0.90
41 8 0.07
ACGTcount: A:0.20, C:0.23, G:0.13, T:0.45
Consensus pattern (40 bp):
ACTTGTCAATTTCATCTTTGTCAACCCTTTAAACTTGTTG
Found at i:11600 original size:120 final size:120
Alignment explanation
Indices: 11424--11680 Score: 272
Period size: 120 Copynumber: 2.1 Consensus size: 120
11414 AACTCTTCTC
* * * * * * ** *
11424 ATCTTGTTCAACCCCTTAAACTTGCTGACTTGTTAGTTTCATCTTGATTAACCCTTCTTGTCT-A
1 ATCTTGGTCAACCCTTTAAACTTGCTGACTTCTCAATTTCATCTTGATCAACCCTTCTCATCTGC
** *
11488 TCAACTTGTTAG-TTTCAT-CTTGATCAACCTCTTAAACTTGTTGATTTGTC-AGTTTT
66 T-AACTTG-TAGATTTCATCCCAG-TCAACCTCTTAAACTTGTTGACTTGTCGA-TTTT
* *
11544 ATCTTGGTCAACCCTTTAAACTTGTTGACTTCTCAATTTCATCTTTG-TCAAGCCTTCTCATCTG
1 ATCTTGGTCAACCCTTTAAACTTGCTGACTTCTCAATTTCATC-TTGATCAACCCTTCTCATCTG
* *
11608 CTAACTTGTCGATTTCATCCCAGTCAACCTTTTAAACTTGTTGACTTGTCGATTTT
65 CTAACTTGTAGATTTCATCCCAGTCAACCTCTTAAACTTGTTGACTTGTCGATTTT
* *
11664 GTCTTGGTTAACCCTTT
1 ATCTTGGTCAACCCTTT
11681 TGACCTATTG
Statistics
Matches: 114, Mismatches: 18, Indels: 10
0.80 0.13 0.07
Matches are distributed among these distances:
119 2 0.02
120 105 0.92
121 7 0.06
ACGTcount: A:0.20, C:0.23, G:0.12, T:0.44
Consensus pattern (120 bp):
ATCTTGGTCAACCCTTTAAACTTGCTGACTTCTCAATTTCATCTTGATCAACCCTTCTCATCTGC
TAACTTGTAGATTTCATCCCAGTCAACCTCTTAAACTTGTTGACTTGTCGATTTT
Found at i:11984 original size:92 final size:90
Alignment explanation
Indices: 11829--12008 Score: 315
Period size: 92 Copynumber: 2.0 Consensus size: 90
11819 TCAAGACTTT
* *
11829 ATGGCCCAAATGAAATTGTCTATTTGGTCTTTGTCTTGTTCCTAATTCTGAACAATAGACAAAGA
1 ATGGCCCAAACGAAATTGTCTATTTGGTCTTTGTCTTGTTCCTAATTCTCAACAATAGACAAAGA
11894 GATGTAGTTATTAACACCTAATTCC
66 GATGTAGTTATTAACACCTAATTCC
11919 ATGGCCCAAACGAAATTATGTCTATTTGGTCTTTGTCTTGTTCCTAATTCTCAACAATAGACAAA
1 ATGGCCCAAACGAAA-T-TGTCTATTTGGTCTTTGTCTTGTTCCTAATTCTCAACAATAGACAAA
*
11984 GAGATGTAGTTATTGACACCTAATT
64 GAGATGTAGTTATTAACACCTAATT
12009 TCGTCTAAGC
Statistics
Matches: 85, Mismatches: 3, Indels: 2
0.94 0.03 0.02
Matches are distributed among these distances:
90 14 0.16
91 1 0.01
92 70 0.82
ACGTcount: A:0.31, C:0.18, G:0.16, T:0.36
Consensus pattern (90 bp):
ATGGCCCAAACGAAATTGTCTATTTGGTCTTTGTCTTGTTCCTAATTCTCAACAATAGACAAAGA
GATGTAGTTATTAACACCTAATTCC
Found at i:15378 original size:20 final size:20
Alignment explanation
Indices: 15353--15489 Score: 74
Period size: 20 Copynumber: 6.8 Consensus size: 20
15343 TTTTTACAAT
15353 TTGTATCGATACATTGTTCA
1 TTGTATCGATACATTGTTCA
15373 TTGTATCGATACATTCTGGGTTTACCCA
1 TTGTATCGATACA-T-T--G-TT---CA
* *
15401 GATGTATCGATACATT-TTGAA
1 -TTGTATCGATACATTGTT-CA
* *
15422 TTGTATTGATACACTGTTCA
1 TTGTATCGATACATTGTTCA
*
15442 TTGTATCGATACA----ACA
1 TTGTATCGATACATTGTTCA
*
15458 ---TATCGATACATTGCTCA
1 TTGTATCGATACATTGTTCA
15475 TTGTATCGATACATT
1 TTGTATCGATACATT
15490 CTGGATTTAC
Statistics
Matches: 90, Mismatches: 10, Indels: 34
0.67 0.07 0.25
Matches are distributed among these distances:
13 10 0.11
16 2 0.02
17 2 0.02
20 50 0.56
21 4 0.04
22 1 0.01
23 2 0.02
24 1 0.01
25 2 0.02
27 1 0.01
28 3 0.03
29 12 0.13
ACGTcount: A:0.28, C:0.17, G:0.15, T:0.40
Consensus pattern (20 bp):
TTGTATCGATACATTGTTCA
Found at i:18105 original size:79 final size:79
Alignment explanation
Indices: 17887--18263 Score: 476
Period size: 79 Copynumber: 4.8 Consensus size: 79
17877 TTCACAATCA
* *
17887 GGGATACTCCAACTCCGATTTTATTTTCAAAACACCAA-TTTCTCACAATCGGGGATACTCCAAC
1 GGGATACTCCAACCCCGATTTTATTTTCAAAACACCAATTTTCT-ATAATCGGGGATACTCCAAC
17951 CCTGTTATTTTC-AG
65 CCTGTTATTTTCGAG
* *** * * * *
17965 GGGATACTCCAACCCTGGCCTTA-TTTCTAAAGCATCAAGTTTTC-ACAATTGGGGATACTCCAA
1 GGGATACTCCAACCCCGATTTTATTTTC-AAAACACCAA-TTTTCTATAATCGGGGATACTCCAA
18028 CCCTGTTATTTTCGAG
64 CCCTGTTATTTTCGAG
** * *
18044 GGGATACTCTGATCCCGATTTTATTTTCAAAACACCAATTTTCTATAATCAGGGATACTCCAACC
1 GGGATACTCCAACCCCGATTTTATTTTCAAAACACCAATTTTCTATAATCGGGGATACTCCAACC
*
18109 CTGTTATTTCCGAG
66 CTGTTATTTTCGAG
* * * * **
18123 GGGATACTCCAACCCCAATTTTATATTT-AAAATACCGATTTTTTATAATCAAGGATACTCCAAC
1 GGGATACTCCAACCCCGATTTTAT-TTTCAAAACACCAATTTTCTATAATCGGGGATACTCCAAC
18187 CCTGTTATTTTCGAG
65 CCTGTTATTTTCGAG
* *
18202 GGGATACTCCAACCCCGATTTTACTTTCAAAACACCGATTTTCTATAATCGGGGATACTCCA
1 GGGATACTCCAACCCCGATTTTATTTTCAAAACACCAATTTTCTATAATCGGGGATACTCCA
18264 GCCCCGTGGT
Statistics
Matches: 255, Mismatches: 36, Indels: 15
0.83 0.12 0.05
Matches are distributed among these distances:
77 4 0.02
78 65 0.25
79 175 0.69
80 11 0.04
ACGTcount: A:0.28, C:0.25, G:0.14, T:0.33
Consensus pattern (79 bp):
GGGATACTCCAACCCCGATTTTATTTTCAAAACACCAATTTTCTATAATCGGGGATACTCCAACC
CTGTTATTTTCGAG
Found at i:22703 original size:20 final size:20
Alignment explanation
Indices: 22678--22731 Score: 108
Period size: 20 Copynumber: 2.7 Consensus size: 20
22668 GCCAAGGAAA
22678 TGTATCGATACATTTTTCTG
1 TGTATCGATACATTTTTCTG
22698 TGTATCGATACATTTTTCTG
1 TGTATCGATACATTTTTCTG
22718 TGTATCGATACATT
1 TGTATCGATACATT
22732 GTATCGACAC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.22, C:0.15, G:0.15, T:0.48
Consensus pattern (20 bp):
TGTATCGATACATTTTTCTG
Found at i:25115 original size:51 final size:53
Alignment explanation
Indices: 25051--25392 Score: 182
Period size: 52 Copynumber: 6.5 Consensus size: 53
25041 AGTTTCTCAG
* * * *
25051 TTCTCCACAATCGGGGATATTCCAACTCCGATTTTATTTTC-AAAACACTAA-
1 TTCTTCACAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAAACACCAAT
* *
25102 TT-TTCTATAATCGGGGATACTCTAACTCCGATTTTATTTCCAAAAAACACCAAT
1 TTCTTC-ACAATCGGGGATACTCCAACTCCGATTTTATTTCC-AAAAACACCAAT
* * * * * *
25156 TTCTTCACAATCGGGGATACTCCAACCCCG--TTAATCATCGGGGATACTCCAAC-CCCAT
1 TTCTTCACAATCGGGGATACTCCAACTCCGATTTTAT-TTC---CA-A---AAACACCAAT
* * * *
25214 TAT-TTC-CGA--GGGGATACTCCAAC-CTCGGTTTTA--TCGCTAAAACACTAAT
1 T-TCTTCACAATCGGGGATACTCCAACTC-CGATTTTATTTC-CAAAAACACCAAT
* * *
25263 TT-TTCCACAATCGGGGATACTCCAA-TCCCGGTTTTATTTTC-AAAACGCCAATT
1 TTCTT-CACAATCGGGGATACTCCAACT-CCGATTTTATTTCCAAAAACACCAA-T
* * * *
25316 TTCCTT--TAATCGGGGATACTCCAATTTCGATTTTATTTCCAAAAATACCAAT
1 TT-CTTCACAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAAACACCAAT
*
25368 TT-TTCACAATCGAGGATACTCCAAC
1 TTCTTCACAATCGGGGATACTCCAAC
25393 CTCGTTATTT
Statistics
Matches: 224, Mismatches: 34, Indels: 65
0.69 0.11 0.20
Matches are distributed among these distances:
48 6 0.03
49 5 0.02
50 6 0.03
51 34 0.15
52 81 0.36
53 25 0.11
54 27 0.12
55 22 0.10
56 1 0.00
57 5 0.02
58 8 0.04
59 4 0.02
ACGTcount: A:0.30, C:0.26, G:0.12, T:0.32
Consensus pattern (53 bp):
TTCTTCACAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAAACACCAAT
Found at i:25235 original size:28 final size:27
Alignment explanation
Indices: 25168--25237 Score: 86
Period size: 27 Copynumber: 2.6 Consensus size: 27
25158 CTTCACAATC
* **
25168 GGGGATACTCCAACCCCGTTAATCATC
1 GGGGATACTCCAACCCCATTAATCAGA
* *
25195 GGGGATACTCCAACCCCATTATTTCCGA
1 GGGGATACTCCAACCCCATTA-ATCAGA
25223 GGGGATACTCCAACC
1 GGGGATACTCCAACC
25238 TCGGTTTTAT
Statistics
Matches: 37, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
27 20 0.54
28 17 0.46
ACGTcount: A:0.26, C:0.33, G:0.20, T:0.21
Consensus pattern (27 bp):
GGGGATACTCCAACCCCATTAATCAGA
Found at i:25376 original size:104 final size:103
Alignment explanation
Indices: 25056--25393 Score: 292
Period size: 104 Copynumber: 3.2 Consensus size: 103
25046 CTCAGTTCTC
* * * *
25056 CACAATCGGGGATATTCCAACTCCGATTTTATTTTCAAAACACTAATTTT-CTATAATCGGGGAT
1 CACAATCGGGGATACTCCAAC-CCGGTTTTATTTTCAAAACACCAATTTTCCTTTAATCGGGGAT
* *
25120 ACTCTAACTCCGATTTTATTTCCAAAAAACACCAATTTCTT
65 ACTCCAACTTCGATTTTATTTCC-AAAAACACCAATTT-TT
* * ** * * * ** * *
25161 CACAATCGGGGATACTCCAACCCCG-TTAATCATCGGGGATACTCCAA--CCCCATTATTTCCGA
1 CACAATCGGGGATACTCCAACCCGGTTTTATTTTC---AAAACACCAATTTTCCTTTA-AT-C--
* * * *
25223 GGGGATACTCCAACCTCGGTTTTA--TCGCTAAAACACTAATTTTT
59 GGGGATACTCCAACTTCGATTTTATTTC-CAAAAACACCAATTTTT
*
25267 CCACAATCGGGGATACTCCAATCCCGGTTTTATTTTCAAAACGCCAATTTTCCTTTAATCGGGGA
1 -CACAATCGGGGATACTCCAA-CCCGGTTTTATTTTCAAAACACCAATTTTCCTTTAATCGGGGA
* *
25332 TACTCCAATTTCGATTTTATTTCCAAAAATACCAATTTTT
64 TACTCCAACTTCGATTTTATTTCCAAAAACACCAATTTTT
*
25372 CACAATCGAGGATACTCCAACC
1 CACAATCGGGGATACTCCAACC
25394 TCGTTATTTC
Statistics
Matches: 178, Mismatches: 39, Indels: 34
0.71 0.16 0.14
Matches are distributed among these distances:
103 8 0.04
104 42 0.24
105 37 0.21
106 19 0.11
107 36 0.20
108 10 0.06
109 26 0.15
ACGTcount: A:0.30, C:0.26, G:0.12, T:0.32
Consensus pattern (103 bp):
CACAATCGGGGATACTCCAACCCGGTTTTATTTTCAAAACACCAATTTTCCTTTAATCGGGGATA
CTCCAACTTCGATTTTATTTCCAAAAACACCAATTTTT
Found at i:25412 original size:28 final size:28
Alignment explanation
Indices: 25376--25447 Score: 90
Period size: 28 Copynumber: 2.6 Consensus size: 28
25366 ATTTTTCACA
* * *
25376 ATCGAGGATACTCCAACCTCGTTATTTC
1 ATCGGGGATACTCCAACCCCGTTACTTC
25404 ATCGGGGATACTCCAACCCCGTTACTTC
1 ATCGGGGATACTCCAACCCCGTTACTTC
***
25432 CGAGGGGATACTCCAA
1 ATCGGGGATACTCCAA
25448 TCCTGATTTT
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 38 1.00
ACGTcount: A:0.25, C:0.31, G:0.19, T:0.25
Consensus pattern (28 bp):
ATCGGGGATACTCCAACCCCGTTACTTC
Found at i:25421 original size:212 final size:212
Alignment explanation
Indices: 25054--25447 Score: 614
Period size: 212 Copynumber: 1.9 Consensus size: 212
25044 TTCTCAGTTC
* *
25054 TCCACAATCGGGGATATTCCAACTCCGATTTTATTTTCAAAACACTAATTTTCTATAATCGGGGA
1 TCCACAATCGGGGATACTCCAACTCCGATTTTATTTTCAAAACACCAATTTTCTATAATCGGGGA
* *
25119 TACTCTAACTCCGATTTTATTTCCAAAAAACACCAATTTCTTCACAATCGGGGATACTCCAACCC
66 TACTCCAACTCCGATTTTATTTCCAAAAAACACCAATTTCTTCACAATCGAGGATACTCCAACCC
*
25184 CGTTAATCATCGGGGATACTCCAACCCCATTATTTCCGAGGGGATACTCCAACCTCGGTTTTATC
131 CGTTAATCATCGGGGATACTCCAACCCCATTACTTCCGAGGGGATACTCCAACCTCGGTTTTATC
25249 GCTAAAACACTAATTTT
196 GCTAAAACACTAATTTT
* * *
25266 TCCACAATCGGGGATACTCCAA-TCCCGGTTTTATTTTCAAAACGCCAATTTTCCTTTAATCGGG
1 TCCACAATCGGGGATACTCCAACT-CCGATTTTATTTTCAAAACACCAATTTT-CTATAATCGGG
* * *
25330 GATACTCCAATTTCGATTTTATTTCC-AAAAATACCAATTT-TTCACAATCGAGGATACTCCAAC
64 GATACTCCAACTCCGATTTTATTTCCAAAAAACACCAATTTCTTCACAATCGAGGATACTCCAAC
* * *
25393 CTCGTTATTTCATCGGGGATACTCCAACCCCGTTACTTCCGAGGGGATACTCCAA
129 CCCGTTA-ATCATCGGGGATACTCCAACCCCATTACTTCCGAGGGGATACTCCAA
25448 TCCTGATTTT
Statistics
Matches: 165, Mismatches: 14, Indels: 6
0.89 0.08 0.03
Matches are distributed among these distances:
211 29 0.18
212 103 0.62
213 33 0.20
ACGTcount: A:0.29, C:0.27, G:0.13, T:0.31
Consensus pattern (212 bp):
TCCACAATCGGGGATACTCCAACTCCGATTTTATTTTCAAAACACCAATTTTCTATAATCGGGGA
TACTCCAACTCCGATTTTATTTCCAAAAAACACCAATTTCTTCACAATCGAGGATACTCCAACCC
CGTTAATCATCGGGGATACTCCAACCCCATTACTTCCGAGGGGATACTCCAACCTCGGTTTTATC
GCTAAAACACTAATTTT
Done.